Multiple sequence alignment - TraesCS7B01G178600

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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 TraesCS7B01G178600 chr7B 100.000 3994 0 0 1 3994 259606482 259610475 0.000000e+00 7376.0
1 TraesCS7B01G178600 chr7B 95.613 1550 64 2 2446 3994 400833704 400832158 0.000000e+00 2483.0
2 TraesCS7B01G178600 chr7B 96.587 586 20 0 2496 3081 195421630 195422215 0.000000e+00 972.0
3 TraesCS7B01G178600 chr7B 95.726 585 25 0 2497 3081 305430721 305431305 0.000000e+00 942.0
4 TraesCS7B01G178600 chr7B 85.165 910 101 17 3089 3994 482843723 482844602 0.000000e+00 902.0
5 TraesCS7B01G178600 chr7B 92.780 277 19 1 2171 2446 400834044 400833768 2.240000e-107 399.0
6 TraesCS7B01G178600 chr7B 93.860 228 12 1 1946 2171 732518900 732519127 3.820000e-90 342.0
7 TraesCS7B01G178600 chr7B 93.805 226 12 1 1946 2169 423441264 423441039 4.940000e-89 339.0
8 TraesCS7B01G178600 chr7B 85.024 207 26 3 2215 2416 238176618 238176824 5.230000e-49 206.0
9 TraesCS7B01G178600 chr7B 86.905 168 16 5 2215 2377 415183558 415183724 2.450000e-42 183.0
10 TraesCS7B01G178600 chr7B 89.583 96 9 1 1085 1179 665241859 665241764 1.950000e-23 121.0
11 TraesCS7B01G178600 chr1B 98.174 3997 69 3 1 3994 203691642 203695637 0.000000e+00 6974.0
12 TraesCS7B01G178600 chr1B 84.364 857 89 20 618 1443 453028526 453027684 0.000000e+00 798.0
13 TraesCS7B01G178600 chr1B 92.118 203 16 0 1 203 200039252 200039050 1.820000e-73 287.0
14 TraesCS7B01G178600 chr1B 80.874 366 44 13 816 1180 282277309 282277649 8.510000e-67 265.0
15 TraesCS7B01G178600 chr1B 96.364 55 2 0 1389 1443 203693080 203693134 1.530000e-14 91.6
16 TraesCS7B01G178600 chr6B 96.968 1550 46 1 2446 3994 369661749 369660200 0.000000e+00 2601.0
17 TraesCS7B01G178600 chr6B 92.644 503 28 3 1946 2446 369662308 369661813 0.000000e+00 715.0
18 TraesCS7B01G178600 chr6B 100.000 28 0 0 2172 2199 41365382 41365409 7.000000e-03 52.8
19 TraesCS7B01G178600 chr6B 100.000 28 0 0 2172 2199 288803197 288803170 7.000000e-03 52.8
20 TraesCS7B01G178600 chr3B 96.065 1550 47 5 2446 3994 279520584 279519048 0.000000e+00 2512.0
21 TraesCS7B01G178600 chr3B 93.439 503 27 3 1946 2446 279521146 279520648 0.000000e+00 741.0
22 TraesCS7B01G178600 chr3B 90.667 225 17 3 1 225 514505189 514505409 3.020000e-76 296.0
23 TraesCS7B01G178600 chr3B 88.776 98 10 1 1083 1179 823387498 823387595 7.010000e-23 119.0
24 TraesCS7B01G178600 chr2D 87.313 1537 140 24 2491 3994 234347908 234346394 0.000000e+00 1707.0
25 TraesCS7B01G178600 chr2B 97.156 633 16 2 2775 3406 341066114 341066745 0.000000e+00 1068.0
26 TraesCS7B01G178600 chr2B 85.181 911 111 10 3089 3994 492591211 492590320 0.000000e+00 913.0
27 TraesCS7B01G178600 chr2B 93.833 227 12 1 1946 2170 300324058 300324284 1.370000e-89 340.0
28 TraesCS7B01G178600 chr2B 91.133 203 18 0 1 203 324795285 324795083 3.930000e-70 276.0
29 TraesCS7B01G178600 chr2B 91.045 201 18 0 1 201 485689260 485689060 5.090000e-69 272.0
30 TraesCS7B01G178600 chr2B 94.152 171 10 0 2497 2667 341065946 341066116 1.100000e-65 261.0
31 TraesCS7B01G178600 chr4D 84.740 924 102 20 3089 3994 143392045 143392947 0.000000e+00 889.0
32 TraesCS7B01G178600 chr4D 82.550 149 17 9 1478 1621 259036077 259035933 5.420000e-24 122.0
33 TraesCS7B01G178600 chr5D 90.604 596 55 1 3400 3994 489088124 489088719 0.000000e+00 789.0
34 TraesCS7B01G178600 chr5D 81.102 254 33 8 1569 1820 98742563 98742323 5.270000e-44 189.0
35 TraesCS7B01G178600 chr4B 82.690 855 110 15 618 1443 287382030 287381185 0.000000e+00 725.0
36 TraesCS7B01G178600 chr4B 94.771 306 13 3 1623 1927 178353228 178353531 1.300000e-129 473.0
37 TraesCS7B01G178600 chr4B 84.337 415 55 5 618 1028 287401924 287401516 8.040000e-107 398.0
38 TraesCS7B01G178600 chr4B 87.043 301 36 2 1437 1737 287381241 287380944 1.780000e-88 337.0
39 TraesCS7B01G178600 chr4B 92.118 203 16 0 1 203 456147836 456148038 1.820000e-73 287.0
40 TraesCS7B01G178600 chr4B 90.640 203 19 0 1 203 378469251 378469049 1.830000e-68 270.0
41 TraesCS7B01G178600 chr4B 84.360 211 28 2 2215 2420 598538256 598538466 6.770000e-48 202.0
42 TraesCS7B01G178600 chr4B 100.000 28 0 0 2172 2199 12552287 12552260 7.000000e-03 52.8
43 TraesCS7B01G178600 chr4B 100.000 28 0 0 2172 2199 148375176 148375149 7.000000e-03 52.8
44 TraesCS7B01G178600 chr1D 85.308 633 74 11 2675 3293 20044650 20045277 1.570000e-178 636.0
45 TraesCS7B01G178600 chr5B 78.045 665 93 23 2676 3318 479622391 479621758 1.750000e-98 370.0
46 TraesCS7B01G178600 chr5B 93.035 201 12 1 1 201 22036677 22036479 3.900000e-75 292.0
47 TraesCS7B01G178600 chr5B 91.045 201 18 0 1 201 463406333 463406133 5.090000e-69 272.0
48 TraesCS7B01G178600 chr5B 90.722 97 9 0 1083 1179 627462038 627461942 3.240000e-26 130.0
49 TraesCS7B01G178600 chr4A 94.714 227 10 1 1946 2170 284252872 284252646 6.350000e-93 351.0
50 TraesCS7B01G178600 chr2A 94.298 228 11 1 1946 2171 300219238 300219011 8.220000e-92 348.0
51 TraesCS7B01G178600 chr2A 94.298 228 11 1 1946 2171 361484784 361485011 8.220000e-92 348.0
52 TraesCS7B01G178600 chr5A 77.064 654 96 26 2684 3318 504860127 504859509 1.070000e-85 327.0
53 TraesCS7B01G178600 chr6D 86.809 235 28 3 2213 2446 347254035 347253803 3.960000e-65 259.0
54 TraesCS7B01G178600 chrUn 100.000 28 0 0 2172 2199 85443863 85443890 7.000000e-03 52.8


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 TraesCS7B01G178600 chr7B 259606482 259610475 3993 False 7376.0 7376 100.0000 1 3994 1 chr7B.!!$F3 3993
1 TraesCS7B01G178600 chr7B 400832158 400834044 1886 True 1441.0 2483 94.1965 2171 3994 2 chr7B.!!$R3 1823
2 TraesCS7B01G178600 chr7B 195421630 195422215 585 False 972.0 972 96.5870 2496 3081 1 chr7B.!!$F1 585
3 TraesCS7B01G178600 chr7B 305430721 305431305 584 False 942.0 942 95.7260 2497 3081 1 chr7B.!!$F4 584
4 TraesCS7B01G178600 chr7B 482843723 482844602 879 False 902.0 902 85.1650 3089 3994 1 chr7B.!!$F6 905
5 TraesCS7B01G178600 chr1B 203691642 203695637 3995 False 3532.8 6974 97.2690 1 3994 2 chr1B.!!$F2 3993
6 TraesCS7B01G178600 chr1B 453027684 453028526 842 True 798.0 798 84.3640 618 1443 1 chr1B.!!$R2 825
7 TraesCS7B01G178600 chr6B 369660200 369662308 2108 True 1658.0 2601 94.8060 1946 3994 2 chr6B.!!$R2 2048
8 TraesCS7B01G178600 chr3B 279519048 279521146 2098 True 1626.5 2512 94.7520 1946 3994 2 chr3B.!!$R1 2048
9 TraesCS7B01G178600 chr2D 234346394 234347908 1514 True 1707.0 1707 87.3130 2491 3994 1 chr2D.!!$R1 1503
10 TraesCS7B01G178600 chr2B 492590320 492591211 891 True 913.0 913 85.1810 3089 3994 1 chr2B.!!$R3 905
11 TraesCS7B01G178600 chr2B 341065946 341066745 799 False 664.5 1068 95.6540 2497 3406 2 chr2B.!!$F2 909
12 TraesCS7B01G178600 chr4D 143392045 143392947 902 False 889.0 889 84.7400 3089 3994 1 chr4D.!!$F1 905
13 TraesCS7B01G178600 chr5D 489088124 489088719 595 False 789.0 789 90.6040 3400 3994 1 chr5D.!!$F1 594
14 TraesCS7B01G178600 chr4B 287380944 287382030 1086 True 531.0 725 84.8665 618 1737 2 chr4B.!!$R5 1119
15 TraesCS7B01G178600 chr1D 20044650 20045277 627 False 636.0 636 85.3080 2675 3293 1 chr1D.!!$F1 618
16 TraesCS7B01G178600 chr5B 479621758 479622391 633 True 370.0 370 78.0450 2676 3318 1 chr5B.!!$R3 642
17 TraesCS7B01G178600 chr5A 504859509 504860127 618 True 327.0 327 77.0640 2684 3318 1 chr5A.!!$R1 634

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
336 337 0.170561 CTCTCCGTCCTACAACCACG 59.829 60.000 0.0 0.0 0.0 4.94 F
569 570 0.395862 GGAGGAGACGAGGACCATCA 60.396 60.000 0.0 0.0 0.0 3.07 F
1062 1067 1.530283 CCCCCTCCCCAAACGATAC 59.470 63.158 0.0 0.0 0.0 2.24 F
1976 2005 3.056250 TCTGTTGCATCTCTGTTCTCCTC 60.056 47.826 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 1981 4.019501 AGGAGAACAGAGATGCAACAGATT 60.020 41.667 0.0 0.0 0.00 2.40 R
1976 2005 5.234543 GGAAATAGAGCAGCTAACCTTAACG 59.765 44.000 0.0 0.0 31.66 3.18 R
2009 2038 6.247229 AGCACCCACATAAGATAATACACA 57.753 37.500 0.0 0.0 0.00 3.72 R
3334 3516 3.093814 TGCATGAATGGTGCAGAAAGAT 58.906 40.909 0.0 0.0 46.76 2.40 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
25 26 0.459237 CTTCGCTGGCTGTTCGATCT 60.459 55.000 0.00 0.00 31.96 2.75
73 74 2.202440 CCGTTCGATCGTCGCTGT 60.202 61.111 22.16 0.00 40.21 4.40
98 99 1.463056 CTGCGCACTCATTTTTACCGA 59.537 47.619 5.66 0.00 0.00 4.69
172 173 2.441164 AAACGGCTGGGTGTTGCA 60.441 55.556 0.00 0.00 0.00 4.08
228 229 3.849953 CGCGCGACAAACCCTAGC 61.850 66.667 28.94 0.00 0.00 3.42
271 272 3.844090 GCCGCACTCCTCCTCCTC 61.844 72.222 0.00 0.00 0.00 3.71
286 287 2.774351 CTCCCCCATCCCACCCTC 60.774 72.222 0.00 0.00 0.00 4.30
306 307 3.032667 TTAGCCGCCGCCACCATTA 62.033 57.895 0.00 0.00 34.57 1.90
322 323 1.627834 CATTATGCCTCCCTCCTCTCC 59.372 57.143 0.00 0.00 0.00 3.71
336 337 0.170561 CTCTCCGTCCTACAACCACG 59.829 60.000 0.00 0.00 0.00 4.94
403 404 1.826921 CGCGTAAGAGGCTAGGGGA 60.827 63.158 0.00 0.00 43.02 4.81
569 570 0.395862 GGAGGAGACGAGGACCATCA 60.396 60.000 0.00 0.00 0.00 3.07
610 611 2.107953 GGACCATCGAGGAGCAGC 59.892 66.667 0.00 0.00 41.22 5.25
694 697 2.096248 CTCGCTTCTCCACTCCTACTT 58.904 52.381 0.00 0.00 0.00 2.24
785 788 7.094248 TGGACATTGTCAGAATGGTCAATTTAG 60.094 37.037 18.09 0.00 38.31 1.85
847 850 6.405176 GCCTCCAAGGTAATTCTCAAGAATTG 60.405 42.308 22.36 10.70 43.59 2.32
899 902 3.354948 AGTGCATATGCTCCAGTTTGA 57.645 42.857 27.13 1.78 42.66 2.69
900 903 3.012518 AGTGCATATGCTCCAGTTTGAC 58.987 45.455 27.13 13.97 42.66 3.18
1012 1016 4.393371 GGAAGTTAGGAATGTCAACTCTGC 59.607 45.833 0.00 0.00 31.43 4.26
1062 1067 1.530283 CCCCCTCCCCAAACGATAC 59.470 63.158 0.00 0.00 0.00 2.24
1485 1514 4.327982 TTCTGTACATATCAGGAGCTGC 57.672 45.455 0.00 0.00 34.15 5.25
1629 1658 6.197168 TGGAGCAATTTCCATCCTCTATTTT 58.803 36.000 0.00 0.00 42.24 1.82
1750 1779 5.046159 TGGTTTACATGGGTAGTACCTGAAG 60.046 44.000 18.85 9.18 38.64 3.02
1908 1937 8.408043 TTTTTCTGATAAGTGAATGTGGACAT 57.592 30.769 0.00 0.00 38.41 3.06
1914 1943 9.716531 CTGATAAGTGAATGTGGACATATACAT 57.283 33.333 0.00 0.00 39.08 2.29
1921 1950 9.758651 GTGAATGTGGACATATACATACAGTAA 57.241 33.333 0.00 0.00 36.56 2.24
1952 1981 3.257375 AGATACGCCAACACTGTTCTACA 59.743 43.478 0.00 0.00 0.00 2.74
1976 2005 3.056250 TCTGTTGCATCTCTGTTCTCCTC 60.056 47.826 0.00 0.00 0.00 3.71
2009 2038 5.151454 AGCTGCTCTATTTCCTAGGTACAT 58.849 41.667 9.08 2.14 0.00 2.29
2384 2416 2.336945 TCCTCTCCGCTACGTATTCA 57.663 50.000 0.00 0.00 0.00 2.57
2544 2704 9.489084 TTTTCTGTATATATGTCTTCCATTCCG 57.511 33.333 0.00 0.00 34.86 4.30
3393 3581 9.495754 GAATTCTTTCATTATTGGAGTCTTTCG 57.504 33.333 0.00 0.00 0.00 3.46
3732 3922 7.179160 GGGGATAAATCATTATGGAAGGGAAAG 59.821 40.741 0.00 0.00 31.83 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.153765 CAGATCGAACAGCCAGCGA 60.154 57.895 0.00 0.00 38.51 4.93
16 17 0.032815 TGGTCAACGCAGATCGAACA 59.967 50.000 0.00 0.00 41.67 3.18
25 26 1.757682 AAAAAGACCTGGTCAACGCA 58.242 45.000 27.48 0.00 34.60 5.24
55 56 2.908088 TACAGCGACGATCGAACGGC 62.908 60.000 28.09 15.78 43.74 5.68
57 58 1.463805 ATTACAGCGACGATCGAACG 58.536 50.000 24.34 24.88 43.74 3.95
73 74 5.636837 GGTAAAAATGAGTGCGCAGAATTA 58.363 37.500 12.22 0.00 0.00 1.40
98 99 1.226974 CTCGCCACGATTCACCGAT 60.227 57.895 0.00 0.00 34.61 4.18
172 173 4.759205 GCCCCCGCACCAGGAAAT 62.759 66.667 0.00 0.00 34.03 2.17
208 209 3.943479 TAGGGTTTGTCGCGCGCAT 62.943 57.895 32.61 10.35 0.00 4.73
306 307 2.123077 CGGAGAGGAGGGAGGCAT 60.123 66.667 0.00 0.00 0.00 4.40
322 323 2.025418 GTGGCGTGGTTGTAGGACG 61.025 63.158 0.00 0.00 36.18 4.79
353 354 1.590525 GATATGGCGCCACGAACGA 60.591 57.895 35.50 13.41 0.00 3.85
511 512 4.131088 GCCTCCTCCCACGACGAC 62.131 72.222 0.00 0.00 0.00 4.34
569 570 0.031616 CTCCTCCCCTGCTACTCCTT 60.032 60.000 0.00 0.00 0.00 3.36
610 611 4.452733 GAGTTCGGCGGTCCCCTG 62.453 72.222 7.21 0.00 0.00 4.45
694 697 0.620556 GCATGGGAGGGAGAGTGAAA 59.379 55.000 0.00 0.00 0.00 2.69
785 788 8.534333 TGATATCTGAAAATAATACGCCAGAC 57.466 34.615 3.98 0.00 34.08 3.51
900 903 8.306038 TCATATTCAAAAGACCATCAAAAGTGG 58.694 33.333 0.00 0.00 42.55 4.00
1012 1016 2.025969 CGCTGAGCCTGACACACAG 61.026 63.158 0.00 0.00 45.36 3.66
1062 1067 1.891060 GCGTGAACTGAAGCAGACCG 61.891 60.000 0.82 0.00 35.18 4.79
1485 1514 4.386867 TTGATCTAGTGGAGCCTAAACG 57.613 45.455 0.00 0.00 0.00 3.60
1629 1658 5.794687 CATCCACGTATGCTCAGTAAAAA 57.205 39.130 0.00 0.00 0.00 1.94
1750 1779 9.959721 TCCATAGGAGTGGAAATATAAATAAGC 57.040 33.333 0.00 0.00 45.03 3.09
1952 1981 4.019501 AGGAGAACAGAGATGCAACAGATT 60.020 41.667 0.00 0.00 0.00 2.40
1976 2005 5.234543 GGAAATAGAGCAGCTAACCTTAACG 59.765 44.000 0.00 0.00 31.66 3.18
2009 2038 6.247229 AGCACCCACATAAGATAATACACA 57.753 37.500 0.00 0.00 0.00 3.72
2544 2704 7.937394 ACTTTATATAAGCACCCAAGGATACAC 59.063 37.037 0.00 0.00 41.41 2.90
3091 3264 6.607004 TTCTCAGTTTAGAAACCCTAGAGG 57.393 41.667 1.52 0.00 39.71 3.69
3207 3381 4.000988 CCCAAGTACACGCTTACAATCTT 58.999 43.478 0.00 0.00 0.00 2.40
3334 3516 3.093814 TGCATGAATGGTGCAGAAAGAT 58.906 40.909 0.00 0.00 46.76 2.40


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

AutoCloner maintained by Alex Coulton.