Multiple sequence alignment - TraesCS7B01G485100

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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 TraesCS7B01G485100 chr7B 100.000 1738 0 0 977 2714 741762314 741764051 0.000000e+00 3210
1 TraesCS7B01G485100 chr7B 100.000 734 0 0 1 734 741749856 741750589 0.000000e+00 1356
2 TraesCS7B01G485100 chr7B 100.000 734 0 0 1 734 741761338 741762071 0.000000e+00 1356
3 TraesCS7B01G485100 chr7B 88.082 923 106 4 1104 2023 741935314 741936235 0.000000e+00 1092
4 TraesCS7B01G485100 chr7B 88.904 712 44 17 1 709 438390477 438391156 0.000000e+00 845
5 TraesCS7B01G485100 chr7B 81.515 779 122 12 1340 2107 741773988 741774755 2.970000e-174 621
6 TraesCS7B01G485100 chr7B 81.009 674 101 11 1489 2162 741807133 741807779 6.700000e-141 510
7 TraesCS7B01G485100 chr7B 81.413 651 94 11 1512 2162 741834583 741835206 8.670000e-140 507
8 TraesCS7B01G485100 chr7B 81.413 651 94 11 1512 2162 741839396 741840019 8.670000e-140 507
9 TraesCS7B01G485100 chr7B 88.424 406 45 1 977 1382 741896804 741897207 3.140000e-134 488
10 TraesCS7B01G485100 chr7B 81.658 567 88 8 999 1562 741806617 741807170 8.860000e-125 457
11 TraesCS7B01G485100 chr7B 82.320 543 80 8 999 1538 741838857 741839386 8.860000e-125 457
12 TraesCS7B01G485100 chr7B 94.737 228 10 1 2431 2658 742803292 742803067 1.200000e-93 353
13 TraesCS7B01G485100 chr7B 94.444 216 10 1 2431 2646 742763947 742763734 5.600000e-87 331
14 TraesCS7B01G485100 chr7B 94.444 216 10 1 2431 2646 742798518 742798305 5.600000e-87 331
15 TraesCS7B01G485100 chr7B 84.014 294 39 4 984 1276 741929006 741929292 2.660000e-70 276
16 TraesCS7B01G485100 chr7B 83.673 294 39 5 984 1276 741875662 741875947 4.450000e-68 268
17 TraesCS7B01G485100 chr7B 84.120 233 36 1 1792 2023 741936457 741936689 9.780000e-55 224
18 TraesCS7B01G485100 chr7B 94.444 144 8 0 2477 2620 741898127 741898270 3.520000e-54 222
19 TraesCS7B01G485100 chr7B 88.235 187 13 4 2435 2620 741941452 741941630 5.890000e-52 215
20 TraesCS7B01G485100 chr7B 77.451 306 55 10 1443 1744 741940348 741940643 1.290000e-38 171
21 TraesCS7B01G485100 chr7B 93.258 89 4 2 2267 2354 741809254 741809341 2.190000e-26 130
22 TraesCS7B01G485100 chr7B 93.258 89 4 2 2267 2354 741836707 741836794 2.190000e-26 130
23 TraesCS7B01G485100 chr7B 93.258 89 4 2 2267 2354 741842056 741842143 2.190000e-26 130
24 TraesCS7B01G485100 chr7D 90.941 1435 115 7 982 2415 634391310 634389890 0.000000e+00 1916
25 TraesCS7B01G485100 chr7D 97.042 710 19 2 1 710 159004208 159004915 0.000000e+00 1194
26 TraesCS7B01G485100 chr7D 82.068 1093 150 24 1104 2158 634364114 634363030 0.000000e+00 891
27 TraesCS7B01G485100 chr7D 80.650 708 107 12 1403 2101 634401879 634401193 3.100000e-144 521
28 TraesCS7B01G485100 chr7D 96.842 190 6 0 2431 2620 634389907 634389718 4.360000e-83 318
29 TraesCS7B01G485100 chr7D 94.737 190 10 0 2431 2620 634272326 634272137 2.040000e-76 296
30 TraesCS7B01G485100 chr7D 94.211 190 11 0 2431 2620 634204884 634204695 9.510000e-75 291
31 TraesCS7B01G485100 chr7D 83.280 311 48 4 1713 2020 634362264 634361955 1.590000e-72 283
32 TraesCS7B01G485100 chr7D 88.235 187 21 1 2435 2620 634400992 634400806 3.520000e-54 222
33 TraesCS7B01G485100 chr7D 86.667 165 15 3 1701 1863 634274202 634274043 2.780000e-40 176
34 TraesCS7B01G485100 chr7D 88.983 118 12 1 2299 2415 634204984 634204867 7.830000e-31 145
35 TraesCS7B01G485100 chr7D 86.466 133 13 3 2288 2415 634401111 634400979 1.010000e-29 141
36 TraesCS7B01G485100 chr7D 88.034 117 13 1 2300 2415 634272425 634272309 1.310000e-28 137
37 TraesCS7B01G485100 chr6D 92.827 711 35 7 1 709 262411245 262411941 0.000000e+00 1016
38 TraesCS7B01G485100 chr4A 92.372 721 41 8 1 719 236538025 236538733 0.000000e+00 1014
39 TraesCS7B01G485100 chr4A 86.813 91 10 2 631 721 437914879 437914967 1.720000e-17 100
40 TraesCS7B01G485100 chr1A 91.472 727 48 8 1 724 548722681 548721966 0.000000e+00 987
41 TraesCS7B01G485100 chr7A 84.350 754 111 4 1407 2156 732003579 732004329 0.000000e+00 732
42 TraesCS7B01G485100 chr7A 81.125 853 138 12 1260 2101 731981242 731982082 0.000000e+00 662
43 TraesCS7B01G485100 chr7A 82.403 591 76 16 984 1562 731980937 731981511 8.730000e-135 490
44 TraesCS7B01G485100 chr7A 81.575 597 87 7 984 1562 732003110 732003701 3.160000e-129 472
45 TraesCS7B01G485100 chr7A 92.593 297 13 3 415 710 643766149 643766437 4.180000e-113 418
46 TraesCS7B01G485100 chr7A 84.848 264 19 7 2158 2415 732034097 732034345 2.090000e-61 246
47 TraesCS7B01G485100 chr7A 91.667 132 7 3 981 1112 731180280 731180407 2.150000e-41 180
48 TraesCS7B01G485100 chr7A 86.364 132 12 4 2288 2415 731982164 731982293 3.640000e-29 139
49 TraesCS7B01G485100 chr3A 93.289 298 11 3 415 711 555424148 555423859 5.370000e-117 431
50 TraesCS7B01G485100 chr2A 91.216 296 18 1 415 710 746745135 746745422 1.960000e-106 396
51 TraesCS7B01G485100 chr2B 90.541 296 15 6 415 710 415415065 415414783 1.970000e-101 379
52 TraesCS7B01G485100 chrUn 91.176 136 7 4 981 1115 376792006 376792137 2.150000e-41 180
53 TraesCS7B01G485100 chrUn 91.667 132 7 3 981 1112 380379393 380379266 2.150000e-41 180
54 TraesCS7B01G485100 chr3B 87.097 93 11 1 631 723 820423827 820423918 1.330000e-18 104


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 TraesCS7B01G485100 chr7B 741761338 741764051 2713 False 2283.000000 3210 100.000000 1 2714 2 chr7B.!!$F6 2713
1 TraesCS7B01G485100 chr7B 741749856 741750589 733 False 1356.000000 1356 100.000000 1 734 1 chr7B.!!$F2 733
2 TraesCS7B01G485100 chr7B 438390477 438391156 679 False 845.000000 845 88.904000 1 709 1 chr7B.!!$F1 708
3 TraesCS7B01G485100 chr7B 741773988 741774755 767 False 621.000000 621 81.515000 1340 2107 1 chr7B.!!$F3 767
4 TraesCS7B01G485100 chr7B 741935314 741941630 6316 False 425.500000 1092 84.472000 1104 2620 4 chr7B.!!$F10 1516
5 TraesCS7B01G485100 chr7B 741806617 741809341 2724 False 365.666667 510 85.308333 999 2354 3 chr7B.!!$F7 1355
6 TraesCS7B01G485100 chr7B 741896804 741898270 1466 False 355.000000 488 91.434000 977 2620 2 chr7B.!!$F9 1643
7 TraesCS7B01G485100 chr7B 741834583 741842143 7560 False 346.200000 507 86.332400 999 2354 5 chr7B.!!$F8 1355
8 TraesCS7B01G485100 chr7D 159004208 159004915 707 False 1194.000000 1194 97.042000 1 710 1 chr7D.!!$F1 709
9 TraesCS7B01G485100 chr7D 634389718 634391310 1592 True 1117.000000 1916 93.891500 982 2620 2 chr7D.!!$R4 1638
10 TraesCS7B01G485100 chr7D 634361955 634364114 2159 True 587.000000 891 82.674000 1104 2158 2 chr7D.!!$R3 1054
11 TraesCS7B01G485100 chr7D 634400806 634401879 1073 True 294.666667 521 85.117000 1403 2620 3 chr7D.!!$R5 1217
12 TraesCS7B01G485100 chr7D 634272137 634274202 2065 True 203.000000 296 89.812667 1701 2620 3 chr7D.!!$R2 919
13 TraesCS7B01G485100 chr6D 262411245 262411941 696 False 1016.000000 1016 92.827000 1 709 1 chr6D.!!$F1 708
14 TraesCS7B01G485100 chr4A 236538025 236538733 708 False 1014.000000 1014 92.372000 1 719 1 chr4A.!!$F1 718
15 TraesCS7B01G485100 chr1A 548721966 548722681 715 True 987.000000 987 91.472000 1 724 1 chr1A.!!$R1 723
16 TraesCS7B01G485100 chr7A 732003110 732004329 1219 False 602.000000 732 82.962500 984 2156 2 chr7A.!!$F5 1172
17 TraesCS7B01G485100 chr7A 731980937 731982293 1356 False 430.333333 662 83.297333 984 2415 3 chr7A.!!$F4 1431

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
996 1023 1.671845 GGTTAAGCACGTCAACAACCA 59.328 47.619 11.76 0.0 36.32 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 12283 1.156736 CGCAAGAAACTGGGACGAAT 58.843 50.0 0.0 0.0 43.02 3.34 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
996 1023 1.671845 GGTTAAGCACGTCAACAACCA 59.328 47.619 11.76 0.0 36.32 3.67
1040 4317 1.153107 CCATCGATGCAGGCTTCCA 60.153 57.895 20.25 0.0 0.00 3.53
1152 4437 6.335471 TCGTGTCATGTTTCTAGGAAAGTA 57.665 37.500 0.00 0.0 0.00 2.24
1155 4440 6.811665 CGTGTCATGTTTCTAGGAAAGTATCA 59.188 38.462 0.00 0.0 0.00 2.15
1178 4463 2.569404 GGTCAGAAGAAGGTGAGGTCAT 59.431 50.000 0.00 0.0 0.00 3.06
1186 4471 0.544357 AGGTGAGGTCATTGACGGGA 60.544 55.000 10.56 0.0 32.65 5.14
1235 4520 0.108756 GGTGAGTACCTCAAGACCGC 60.109 60.000 0.00 0.0 42.46 5.68
1329 4614 1.228675 CAGCAAGGGTGGCTTCCTT 60.229 57.895 6.20 6.2 44.76 3.36
1338 4623 1.074775 TGGCTTCCTTCACCGCATT 59.925 52.632 0.00 0.0 0.00 3.56
1382 4668 1.887707 CCCGCGGGCTCAAGAATAC 60.888 63.158 34.96 0.0 0.00 1.89
1393 4679 3.065925 GCTCAAGAATACCAGCAACATCC 59.934 47.826 0.00 0.0 0.00 3.51
1395 4681 3.009723 CAAGAATACCAGCAACATCCGT 58.990 45.455 0.00 0.0 0.00 4.69
1405 4691 1.969589 AACATCCGTTCAACCCGCC 60.970 57.895 0.00 0.0 0.00 6.13
1493 4869 2.483876 ACGTGACCTCAATGACAACAG 58.516 47.619 0.00 0.0 0.00 3.16
1504 4880 6.349528 CCTCAATGACAACAGCATCAAATACA 60.350 38.462 0.00 0.0 0.00 2.29
1558 4934 7.095229 GCAAATATATATGCGACCTCAAGAACA 60.095 37.037 0.00 0.0 32.17 3.18
1615 4991 3.817084 CCTCAAGAATGTCAACAAGAGCA 59.183 43.478 0.00 0.0 0.00 4.26
1795 5174 3.188786 GCTTCTAGCACACGCCGG 61.189 66.667 0.00 0.0 41.89 6.13
1809 5188 1.227674 GCCGGTGATCTCCATCCAC 60.228 63.158 13.99 0.0 0.00 4.02
1958 11381 6.540083 TGATGAATAGATGGTCTACGGACTA 58.460 40.000 0.00 0.0 41.82 2.59
2108 11557 3.617263 GGTGTTATCGAGTCATGTTGTCC 59.383 47.826 0.00 0.0 0.00 4.02
2123 11572 5.621197 TGTTGTCCGATGACCAAATAAAG 57.379 39.130 0.00 0.0 41.01 1.85
2180 12283 4.039852 TGAACTACATCTGGCTTGTGTGTA 59.960 41.667 0.00 0.0 0.00 2.90
2414 14553 9.433153 AGTGGTATTAACTTACTTAACTTGCTC 57.567 33.333 0.00 0.0 0.00 4.26
2415 14554 9.433153 GTGGTATTAACTTACTTAACTTGCTCT 57.567 33.333 0.00 0.0 0.00 4.09
2421 14560 9.688592 TTAACTTACTTAACTTGCTCTACTGTC 57.311 33.333 0.00 0.0 0.00 3.51
2422 14561 7.286215 ACTTACTTAACTTGCTCTACTGTCA 57.714 36.000 0.00 0.0 0.00 3.58
2423 14562 7.723324 ACTTACTTAACTTGCTCTACTGTCAA 58.277 34.615 0.00 0.0 0.00 3.18
2424 14563 8.202137 ACTTACTTAACTTGCTCTACTGTCAAA 58.798 33.333 0.00 0.0 0.00 2.69
2425 14564 8.951787 TTACTTAACTTGCTCTACTGTCAAAA 57.048 30.769 0.00 0.0 0.00 2.44
2426 14565 7.859325 ACTTAACTTGCTCTACTGTCAAAAA 57.141 32.000 0.00 0.0 0.00 1.94
2547 14686 1.789751 CTTGTGCGTGCGATGTGAT 59.210 52.632 0.00 0.0 0.00 3.06
2594 14734 4.401022 TGAACCTTGACATGATCTTTGCT 58.599 39.130 0.00 0.0 0.00 3.91
2597 14737 6.660521 TGAACCTTGACATGATCTTTGCTTAT 59.339 34.615 0.00 0.0 0.00 1.73
2620 14761 6.579666 TTGGCCAGCTGATGAAATATAATC 57.420 37.500 17.39 0.0 0.00 1.75
2624 14765 7.772292 TGGCCAGCTGATGAAATATAATCTATC 59.228 37.037 17.39 0.0 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
979 1006 5.694816 CATAATTGGTTGTTGACGTGCTTA 58.305 37.500 0.00 0.00 0.00 3.09
1040 4317 1.076632 TTTGCTCCGGTTGGGTTGT 60.077 52.632 0.00 0.00 37.00 3.32
1152 4437 2.232452 CTCACCTTCTTCTGACCGTGAT 59.768 50.000 0.00 0.00 33.03 3.06
1155 4440 0.969894 CCTCACCTTCTTCTGACCGT 59.030 55.000 0.00 0.00 0.00 4.83
1186 4471 4.596585 CTTGGGGTTGTGGGCGGT 62.597 66.667 0.00 0.00 0.00 5.68
1221 4506 0.535335 TGATGGCGGTCTTGAGGTAC 59.465 55.000 0.00 0.00 0.00 3.34
1235 4520 0.883833 GGAGCCACTGTTGTTGATGG 59.116 55.000 0.00 0.00 35.17 3.51
1329 4614 2.333926 CTGACGTTCTTAATGCGGTGA 58.666 47.619 0.00 0.00 0.00 4.02
1338 4623 2.076100 CTGCCATTGCTGACGTTCTTA 58.924 47.619 0.00 0.00 38.61 2.10
1382 4668 0.240945 GGTTGAACGGATGTTGCTGG 59.759 55.000 0.00 0.00 38.78 4.85
1393 4679 3.047877 GAGGTGGCGGGTTGAACG 61.048 66.667 0.00 0.00 0.00 3.95
1395 4681 1.228124 CTTGAGGTGGCGGGTTGAA 60.228 57.895 0.00 0.00 0.00 2.69
1405 4691 2.675844 TGTTGTTGTCGTTCTTGAGGTG 59.324 45.455 0.00 0.00 0.00 4.00
1476 4777 2.636647 TGCTGTTGTCATTGAGGTCA 57.363 45.000 0.00 0.00 0.00 4.02
1493 4869 2.355756 AGGTCGCATGTGTATTTGATGC 59.644 45.455 6.09 0.00 39.31 3.91
1504 4880 1.291877 GCGTTCTTGAGGTCGCATGT 61.292 55.000 12.76 0.00 46.40 3.21
1523 4899 4.851014 CGCATATATATTTGCCGTTGTTGG 59.149 41.667 18.75 2.88 35.41 3.77
1558 4934 1.881709 CGTCGCTGATGCTGCTGAT 60.882 57.895 0.00 0.00 36.97 2.90
1660 5039 1.299316 TGTCGTCGACCGGTTTGAC 60.299 57.895 23.73 23.73 37.11 3.18
1740 5119 0.039798 GGCACGACTACGACTTGTCA 60.040 55.000 0.00 0.00 42.66 3.58
1795 5174 1.269102 CCGTACGTGGATGGAGATCAC 60.269 57.143 15.21 0.00 0.00 3.06
1809 5188 3.577462 ATCGAAGATGGACGCCGTACG 62.577 57.143 8.69 8.69 46.50 3.67
2108 11557 8.190122 TGATTCATTTCCTTTATTTGGTCATCG 58.810 33.333 0.00 0.00 0.00 3.84
2180 12283 1.156736 CGCAAGAAACTGGGACGAAT 58.843 50.000 0.00 0.00 43.02 3.34
2433 14572 9.391006 CCACTAATATTGGAGCAAGTTAAGTAA 57.609 33.333 5.74 0.00 36.02 2.24
2434 14573 8.545472 ACCACTAATATTGGAGCAAGTTAAGTA 58.455 33.333 5.74 0.00 37.58 2.24
2435 14574 7.402862 ACCACTAATATTGGAGCAAGTTAAGT 58.597 34.615 5.74 0.00 37.58 2.24
2436 14575 7.865706 ACCACTAATATTGGAGCAAGTTAAG 57.134 36.000 5.74 0.00 37.58 1.85
2437 14576 9.742144 TTAACCACTAATATTGGAGCAAGTTAA 57.258 29.630 5.74 8.48 37.58 2.01
2438 14577 9.169592 GTTAACCACTAATATTGGAGCAAGTTA 57.830 33.333 5.74 3.64 37.58 2.24
2439 14578 7.148306 CGTTAACCACTAATATTGGAGCAAGTT 60.148 37.037 5.74 4.45 37.58 2.66
2440 14579 6.315393 CGTTAACCACTAATATTGGAGCAAGT 59.685 38.462 5.74 0.00 37.58 3.16
2441 14580 6.537301 TCGTTAACCACTAATATTGGAGCAAG 59.463 38.462 5.74 0.00 37.58 4.01
2442 14581 6.408035 TCGTTAACCACTAATATTGGAGCAA 58.592 36.000 5.74 0.00 37.58 3.91
2443 14582 5.979993 TCGTTAACCACTAATATTGGAGCA 58.020 37.500 5.74 0.00 37.58 4.26
2444 14583 6.278363 TCTCGTTAACCACTAATATTGGAGC 58.722 40.000 5.74 0.00 37.58 4.70
2547 14686 4.853142 ATAGGAGTCGGCCGGCCA 62.853 66.667 42.78 27.76 35.37 5.36
2594 14734 8.654485 ATTATATTTCATCAGCTGGCCAATAA 57.346 30.769 15.13 3.64 0.00 1.40
2597 14737 6.309357 AGATTATATTTCATCAGCTGGCCAA 58.691 36.000 15.13 2.44 0.00 4.52


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

AutoCloner maintained by Alex Coulton.