Multiple sequence alignment - TraesCS1B01G410100

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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 TraesCS1B01G410100 chr1B 100.000 3614 0 0 699 4312 637286597 637282984 0.000000e+00 6674
1 TraesCS1B01G410100 chr1B 94.124 1004 37 7 2643 3645 651731558 651730576 0.000000e+00 1507
2 TraesCS1B01G410100 chr1B 93.234 1005 43 9 2643 3646 656439966 656440946 0.000000e+00 1456
3 TraesCS1B01G410100 chr1B 100.000 491 0 0 1 491 637287295 637286805 0.000000e+00 907
4 TraesCS1B01G410100 chr1B 88.932 515 50 5 987 1498 658914870 658914360 2.830000e-176 628
5 TraesCS1B01G410100 chr1B 90.071 282 26 2 1535 1815 658914353 658914073 8.810000e-97 364
6 TraesCS1B01G410100 chr4B 97.395 3378 82 4 935 4312 11349907 11346536 0.000000e+00 5746
7 TraesCS1B01G410100 chr4B 97.556 491 11 1 1 491 11350763 11350274 0.000000e+00 839
8 TraesCS1B01G410100 chr4B 97.571 247 6 0 702 948 11350264 11350018 1.430000e-114 424
9 TraesCS1B01G410100 chr4B 100.000 40 0 0 2164 2203 82373118 82373157 1.660000e-09 75
10 TraesCS1B01G410100 chr6B 94.328 1005 34 8 2643 3646 399208057 399207075 0.000000e+00 1519
11 TraesCS1B01G410100 chr6B 93.731 1005 41 7 2643 3646 617029027 617030010 0.000000e+00 1487
12 TraesCS1B01G410100 chr6B 94.880 664 31 3 3650 4312 423139116 423138455 0.000000e+00 1035
13 TraesCS1B01G410100 chr6B 95.260 654 28 3 3650 4302 101192181 101192832 0.000000e+00 1033
14 TraesCS1B01G410100 chr6B 92.153 548 38 5 3767 4312 399206899 399206355 0.000000e+00 769
15 TraesCS1B01G410100 chr6B 81.053 285 30 5 2211 2495 715680738 715680478 5.650000e-49 206
16 TraesCS1B01G410100 chr6B 92.222 90 7 0 2515 2604 76448946 76448857 1.260000e-25 128
17 TraesCS1B01G410100 chr5A 94.229 1005 36 7 2643 3646 692979665 692980648 0.000000e+00 1515
18 TraesCS1B01G410100 chr5A 95.789 665 23 5 3650 4312 629867100 629867761 0.000000e+00 1068
19 TraesCS1B01G410100 chr5A 89.866 671 54 11 3650 4312 516607387 516608051 0.000000e+00 850
20 TraesCS1B01G410100 chr5A 91.971 548 37 5 3767 4312 692980843 692981385 0.000000e+00 761
21 TraesCS1B01G410100 chr5A 91.078 269 17 1 1935 2203 4427206 4427467 1.470000e-94 357
22 TraesCS1B01G410100 chr5A 90.706 269 18 1 1935 2203 630723840 630724101 6.860000e-93 351
23 TraesCS1B01G410100 chr2B 94.030 1005 37 8 2643 3646 435352860 435351878 0.000000e+00 1502
24 TraesCS1B01G410100 chr2B 91.708 1013 69 7 2640 3647 622030317 622029315 0.000000e+00 1391
25 TraesCS1B01G410100 chr2B 93.976 664 38 2 3650 4312 760346446 760345784 0.000000e+00 1003
26 TraesCS1B01G410100 chr2B 92.602 392 17 3 1817 2203 502652182 502652566 1.750000e-153 553
27 TraesCS1B01G410100 chr2B 90.323 403 38 1 2202 2604 5923050 5922649 1.060000e-145 527
28 TraesCS1B01G410100 chr2B 85.876 177 20 4 3651 3823 72800306 72800481 2.650000e-42 183
29 TraesCS1B01G410100 chr2B 96.809 94 3 0 3650 3743 435351773 435351680 1.610000e-34 158
30 TraesCS1B01G410100 chr7B 93.930 1005 38 8 2643 3646 709654505 709655487 0.000000e+00 1496
31 TraesCS1B01G410100 chr7B 94.106 492 27 2 1 491 511940335 511939845 0.000000e+00 747
32 TraesCS1B01G410100 chr7B 91.200 250 22 0 699 948 511939838 511939589 1.490000e-89 340
33 TraesCS1B01G410100 chr4A 93.930 1005 37 8 2643 3646 602464694 602463713 0.000000e+00 1496
34 TraesCS1B01G410100 chr4A 93.293 999 56 6 2643 3637 574767029 574766038 0.000000e+00 1463
35 TraesCS1B01G410100 chr4A 81.757 148 10 1 2515 2645 690648288 690648141 1.640000e-19 108
36 TraesCS1B01G410100 chr6A 93.594 999 56 5 2643 3637 394643003 394643997 0.000000e+00 1483
37 TraesCS1B01G410100 chr6A 79.720 286 27 8 2211 2495 614589105 614588850 1.230000e-40 178
38 TraesCS1B01G410100 chr3A 93.293 999 55 6 2643 3637 224968721 224969711 0.000000e+00 1463
39 TraesCS1B01G410100 chr3A 93.791 306 19 0 2340 2645 346427859 346427554 1.090000e-125 460
40 TraesCS1B01G410100 chr3A 80.000 295 50 7 2199 2493 103682997 103683282 4.370000e-50 209
41 TraesCS1B01G410100 chr2D 95.616 844 30 3 1808 2645 29139373 29140215 0.000000e+00 1347
42 TraesCS1B01G410100 chr2D 94.715 492 21 2 1 491 29132699 29133186 0.000000e+00 760
43 TraesCS1B01G410100 chr2D 94.309 492 23 2 1 491 63383070 63382583 0.000000e+00 749
44 TraesCS1B01G410100 chr2D 91.045 402 23 5 1808 2203 432582511 432582905 8.210000e-147 531
45 TraesCS1B01G410100 chr2D 90.796 402 24 4 1808 2203 537412116 537412510 3.820000e-145 525
46 TraesCS1B01G410100 chr2D 90.571 403 24 8 1808 2203 432539207 432539602 4.940000e-144 521
47 TraesCS1B01G410100 chr2D 94.037 218 13 0 731 948 29133216 29133433 8.940000e-87 331
48 TraesCS1B01G410100 chr2D 100.000 40 0 0 2164 2203 431064847 431064886 1.660000e-09 75
49 TraesCS1B01G410100 chr6D 95.379 844 33 2 1808 2645 60795249 60796092 0.000000e+00 1338
50 TraesCS1B01G410100 chr6D 91.045 402 23 6 1808 2203 460928359 460928753 8.210000e-147 531
51 TraesCS1B01G410100 chr6D 93.578 218 14 0 731 948 60794471 60794688 4.160000e-85 326
52 TraesCS1B01G410100 chr6D 86.869 198 20 2 2211 2402 469537826 469537629 2.610000e-52 217
53 TraesCS1B01G410100 chr5D 94.905 844 37 2 1808 2645 471426519 471425676 0.000000e+00 1315
54 TraesCS1B01G410100 chr5D 92.202 218 17 0 731 948 546416930 546417147 4.190000e-80 309
55 TraesCS1B01G410100 chr7A 93.563 668 36 5 3650 4312 14527191 14526526 0.000000e+00 989
56 TraesCS1B01G410100 chr1A 86.982 845 85 15 981 1815 568108306 568107477 0.000000e+00 928
57 TraesCS1B01G410100 chr7D 95.325 492 21 2 1 491 490749008 490748518 0.000000e+00 780
58 TraesCS1B01G410100 chr7D 94.512 492 26 1 1 491 67749226 67748735 0.000000e+00 758
59 TraesCS1B01G410100 chr7D 95.056 445 20 2 1 444 157757142 157757585 0.000000e+00 699
60 TraesCS1B01G410100 chr7D 92.558 215 16 0 734 948 490748485 490748271 4.190000e-80 309
61 TraesCS1B01G410100 chr7D 100.000 40 0 0 2164 2203 192977996 192977957 1.660000e-09 75
62 TraesCS1B01G410100 chr5B 95.445 483 21 1 9 491 500555397 500554916 0.000000e+00 769
63 TraesCS1B01G410100 chr5B 93.600 250 16 0 699 948 500554909 500554660 1.460000e-99 374
64 TraesCS1B01G410100 chr5B 92.000 250 20 0 699 948 510439857 510440106 6.860000e-93 351
65 TraesCS1B01G410100 chr5B 98.276 58 1 0 2337 2394 613492612 613492555 7.630000e-18 102
66 TraesCS1B01G410100 chr3B 94.512 492 24 3 1 491 740148815 740149304 0.000000e+00 756
67 TraesCS1B01G410100 chr3B 93.200 250 17 0 699 948 740149311 740149560 6.810000e-98 368
68 TraesCS1B01G410100 chr3B 86.765 136 13 2 2515 2645 221508698 221508563 3.470000e-31 147
69 TraesCS1B01G410100 chr3B 90.426 94 8 1 2515 2608 215398971 215398879 5.860000e-24 122
70 TraesCS1B01G410100 chr1D 87.968 374 35 6 960 1327 473862449 473862080 2.380000e-117 433
71 TraesCS1B01G410100 chr2A 81.757 148 10 1 2515 2645 576664468 576664615 1.640000e-19 108


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 TraesCS1B01G410100 chr1B 637282984 637287295 4311 True 3790.500000 6674 100.000000 1 4312 2 chr1B.!!$R2 4311
1 TraesCS1B01G410100 chr1B 651730576 651731558 982 True 1507.000000 1507 94.124000 2643 3645 1 chr1B.!!$R1 1002
2 TraesCS1B01G410100 chr1B 656439966 656440946 980 False 1456.000000 1456 93.234000 2643 3646 1 chr1B.!!$F1 1003
3 TraesCS1B01G410100 chr1B 658914073 658914870 797 True 496.000000 628 89.501500 987 1815 2 chr1B.!!$R3 828
4 TraesCS1B01G410100 chr4B 11346536 11350763 4227 True 2336.333333 5746 97.507333 1 4312 3 chr4B.!!$R1 4311
5 TraesCS1B01G410100 chr6B 617029027 617030010 983 False 1487.000000 1487 93.731000 2643 3646 1 chr6B.!!$F2 1003
6 TraesCS1B01G410100 chr6B 399206355 399208057 1702 True 1144.000000 1519 93.240500 2643 4312 2 chr6B.!!$R4 1669
7 TraesCS1B01G410100 chr6B 423138455 423139116 661 True 1035.000000 1035 94.880000 3650 4312 1 chr6B.!!$R2 662
8 TraesCS1B01G410100 chr6B 101192181 101192832 651 False 1033.000000 1033 95.260000 3650 4302 1 chr6B.!!$F1 652
9 TraesCS1B01G410100 chr5A 692979665 692981385 1720 False 1138.000000 1515 93.100000 2643 4312 2 chr5A.!!$F5 1669
10 TraesCS1B01G410100 chr5A 629867100 629867761 661 False 1068.000000 1068 95.789000 3650 4312 1 chr5A.!!$F3 662
11 TraesCS1B01G410100 chr5A 516607387 516608051 664 False 850.000000 850 89.866000 3650 4312 1 chr5A.!!$F2 662
12 TraesCS1B01G410100 chr2B 622029315 622030317 1002 True 1391.000000 1391 91.708000 2640 3647 1 chr2B.!!$R2 1007
13 TraesCS1B01G410100 chr2B 760345784 760346446 662 True 1003.000000 1003 93.976000 3650 4312 1 chr2B.!!$R3 662
14 TraesCS1B01G410100 chr2B 435351680 435352860 1180 True 830.000000 1502 95.419500 2643 3743 2 chr2B.!!$R4 1100
15 TraesCS1B01G410100 chr7B 709654505 709655487 982 False 1496.000000 1496 93.930000 2643 3646 1 chr7B.!!$F1 1003
16 TraesCS1B01G410100 chr7B 511939589 511940335 746 True 543.500000 747 92.653000 1 948 2 chr7B.!!$R1 947
17 TraesCS1B01G410100 chr4A 602463713 602464694 981 True 1496.000000 1496 93.930000 2643 3646 1 chr4A.!!$R2 1003
18 TraesCS1B01G410100 chr4A 574766038 574767029 991 True 1463.000000 1463 93.293000 2643 3637 1 chr4A.!!$R1 994
19 TraesCS1B01G410100 chr6A 394643003 394643997 994 False 1483.000000 1483 93.594000 2643 3637 1 chr6A.!!$F1 994
20 TraesCS1B01G410100 chr3A 224968721 224969711 990 False 1463.000000 1463 93.293000 2643 3637 1 chr3A.!!$F2 994
21 TraesCS1B01G410100 chr2D 29139373 29140215 842 False 1347.000000 1347 95.616000 1808 2645 1 chr2D.!!$F1 837
22 TraesCS1B01G410100 chr2D 29132699 29133433 734 False 545.500000 760 94.376000 1 948 2 chr2D.!!$F6 947
23 TraesCS1B01G410100 chr6D 60794471 60796092 1621 False 832.000000 1338 94.478500 731 2645 2 chr6D.!!$F2 1914
24 TraesCS1B01G410100 chr5D 471425676 471426519 843 True 1315.000000 1315 94.905000 1808 2645 1 chr5D.!!$R1 837
25 TraesCS1B01G410100 chr7A 14526526 14527191 665 True 989.000000 989 93.563000 3650 4312 1 chr7A.!!$R1 662
26 TraesCS1B01G410100 chr1A 568107477 568108306 829 True 928.000000 928 86.982000 981 1815 1 chr1A.!!$R1 834
27 TraesCS1B01G410100 chr7D 490748271 490749008 737 True 544.500000 780 93.941500 1 948 2 chr7D.!!$R3 947
28 TraesCS1B01G410100 chr5B 500554660 500555397 737 True 571.500000 769 94.522500 9 948 2 chr5B.!!$R2 939
29 TraesCS1B01G410100 chr3B 740148815 740149560 745 False 562.000000 756 93.856000 1 948 2 chr3B.!!$F1 947

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
975 1128 0.839946 ATAGCCACATTTCCGCCTCT 59.16 50.000 0.00 0.00 0.0 3.69 F
1956 2292 1.059835 CTTCGTTAGCAAGCGAGCTTC 59.94 52.381 11.13 3.62 43.7 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2800 3136 0.041839 CGTTTCAGGAGCGCATATGC 60.042 55.000 18.08 18.08 37.78 3.14 R
3495 3840 2.971413 CTGCAGCCCTAGCATCGC 60.971 66.667 0.00 0.00 41.82 4.58 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
118 121 5.885912 AGTCTAGTGAAAATTTGTGTGGTGT 59.114 36.000 0.00 0.00 0.00 4.16
329 332 7.437713 AAAGAAAAGAAAAAGATCCCAACCT 57.562 32.000 0.00 0.00 0.00 3.50
331 334 5.899547 AGAAAAGAAAAAGATCCCAACCTGT 59.100 36.000 0.00 0.00 0.00 4.00
332 335 5.535753 AAAGAAAAAGATCCCAACCTGTG 57.464 39.130 0.00 0.00 0.00 3.66
389 392 2.844839 CCCTCGTCCCCATCTCCC 60.845 72.222 0.00 0.00 0.00 4.30
948 951 1.211457 GATCCATGGTGCACTCCTTCT 59.789 52.381 17.98 0.00 0.00 2.85
949 952 1.951209 TCCATGGTGCACTCCTTCTA 58.049 50.000 17.98 0.00 0.00 2.10
950 953 1.833630 TCCATGGTGCACTCCTTCTAG 59.166 52.381 17.98 0.00 0.00 2.43
964 1117 3.052869 TCCTTCTAGTCTCCATAGCCACA 60.053 47.826 0.00 0.00 0.00 4.17
968 1121 5.537300 TCTAGTCTCCATAGCCACATTTC 57.463 43.478 0.00 0.00 0.00 2.17
969 1122 3.567478 AGTCTCCATAGCCACATTTCC 57.433 47.619 0.00 0.00 0.00 3.13
975 1128 0.839946 ATAGCCACATTTCCGCCTCT 59.160 50.000 0.00 0.00 0.00 3.69
1017 1170 1.395045 CGATGGAGCTAGGCCTCACA 61.395 60.000 9.68 2.41 33.47 3.58
1032 1185 2.997315 ACACTCCAGCTAGCCGCA 60.997 61.111 12.13 0.00 42.61 5.69
1074 1233 1.508632 GGTATATTGCATCGCCGTGT 58.491 50.000 0.00 0.00 0.00 4.49
1095 1254 1.381928 CGCCAGTAAGGAGCGGAGTA 61.382 60.000 0.00 0.00 45.88 2.59
1482 1806 6.906157 AAATTCAGGAATCTGTCATTGTGT 57.094 33.333 0.00 0.00 41.59 3.72
1503 1827 6.765989 TGTGTAGCAGAAGTAAATGACAGTTT 59.234 34.615 0.00 0.00 0.00 2.66
1721 2049 3.441222 TCGTTGGTCAGTAGCTTTCGATA 59.559 43.478 0.00 0.00 0.00 2.92
1825 2153 2.642311 TCCAAAGCACCAGGTTGATCTA 59.358 45.455 0.00 0.00 35.26 1.98
1955 2291 1.071605 CTTCGTTAGCAAGCGAGCTT 58.928 50.000 11.13 4.26 43.70 3.74
1956 2292 1.059835 CTTCGTTAGCAAGCGAGCTTC 59.940 52.381 11.13 3.62 43.70 3.86
2016 2352 4.925054 CACGCCTCATTTGAATTTGTGATT 59.075 37.500 0.00 0.00 0.00 2.57
2117 2453 8.635765 AAGTAGTAAAATTGAGAATGGCAAGA 57.364 30.769 0.00 0.00 0.00 3.02
2160 2496 5.240623 TGCTCTTTCATTGTACCACGAAATT 59.759 36.000 0.00 0.00 0.00 1.82
2677 3013 6.543465 TGATTATTTGTCTAGTGATTGCCTGG 59.457 38.462 0.00 0.00 0.00 4.45
3027 3363 2.938451 GCTTGCCTGCTTCAAAGTTTTT 59.062 40.909 0.00 0.00 0.00 1.94
3204 3546 2.697715 TGGAACAAGGGGTACCAGAAGA 60.698 50.000 15.35 0.00 46.76 2.87
3355 3700 4.940046 ACTTTGGATGCTCATGTACAAGAG 59.060 41.667 21.05 21.05 35.01 2.85
3495 3840 0.879765 CTGCAAAGAGTTGAGGCCAG 59.120 55.000 5.01 0.00 36.83 4.85
3789 4260 1.340502 TGGTTGACTGCCAAACTGTGA 60.341 47.619 0.00 0.00 42.87 3.58
3794 4265 2.223782 TGACTGCCAAACTGTGAAATGC 60.224 45.455 0.00 0.00 0.00 3.56
3797 4268 3.054878 CTGCCAAACTGTGAAATGCTTC 58.945 45.455 0.00 0.00 0.00 3.86
4148 4629 2.750814 TCAGCCACATCAGATCCTACA 58.249 47.619 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 9.453572 TTTGTATGCATTTCTGATCTTTCTAGT 57.546 29.630 3.54 0.00 0.00 2.57
118 121 9.723601 AGCTATCAAAAATATTTTGCAAAAGGA 57.276 25.926 27.08 18.62 0.00 3.36
325 328 1.365105 TAGGGTTTGGGCCACAGGTT 61.365 55.000 5.23 0.00 0.00 3.50
329 332 2.137177 GAGCTAGGGTTTGGGCCACA 62.137 60.000 5.23 0.00 0.00 4.17
331 334 1.850289 TGAGCTAGGGTTTGGGCCA 60.850 57.895 0.00 0.00 0.00 5.36
332 335 1.077429 CTGAGCTAGGGTTTGGGCC 60.077 63.158 0.00 0.00 0.00 5.80
792 795 3.311110 GACGGTGAGGGTGGAGCA 61.311 66.667 0.00 0.00 0.00 4.26
948 951 3.069586 CGGAAATGTGGCTATGGAGACTA 59.930 47.826 0.00 0.00 0.00 2.59
949 952 2.158900 CGGAAATGTGGCTATGGAGACT 60.159 50.000 0.00 0.00 0.00 3.24
950 953 2.213499 CGGAAATGTGGCTATGGAGAC 58.787 52.381 0.00 0.00 0.00 3.36
1074 1233 4.451150 CCGCTCCTTACTGGCGCA 62.451 66.667 10.83 0.00 46.35 6.09
1482 1806 8.035394 CCTCTAAACTGTCATTTACTTCTGCTA 58.965 37.037 0.00 0.00 0.00 3.49
1521 1848 8.216453 CCAGAATCTTGTAAAAATTCTTTTGCG 58.784 33.333 0.00 0.00 39.28 4.85
1615 1943 3.493350 GGAGACACACAACACAGACTCAT 60.493 47.826 0.00 0.00 0.00 2.90
1721 2049 4.516321 GTGGTTTGTGGTTTATCGGTTACT 59.484 41.667 0.00 0.00 0.00 2.24
1825 2153 1.210538 TCTCCCATGCTCAGCAATCT 58.789 50.000 1.73 0.00 43.62 2.40
2117 2453 7.992754 AGAGCAGTTCAGTTGAAGAATTTAT 57.007 32.000 0.00 0.00 34.27 1.40
2160 2496 7.759489 ACATAGCAAAACTTCAGTATTTCCA 57.241 32.000 0.00 0.00 0.00 3.53
2250 2586 1.153745 GAGCGCGAAGGACACATCT 60.154 57.895 12.10 0.00 0.00 2.90
2285 2621 5.566429 GCTCACCATCTGATGAAGTCGATAT 60.566 44.000 18.92 0.00 0.00 1.63
2677 3013 4.928615 CGAAAGATGGGAAGATAGATGCTC 59.071 45.833 0.00 0.00 0.00 4.26
2800 3136 0.041839 CGTTTCAGGAGCGCATATGC 60.042 55.000 18.08 18.08 37.78 3.14
3204 3546 4.021719 CAGCAACATTCTTTGGTTCTCCAT 60.022 41.667 0.00 0.00 43.91 3.41
3355 3700 5.725362 TCCTTCTCAAGCTTTTACTCTAGC 58.275 41.667 0.00 0.00 37.66 3.42
3495 3840 2.971413 CTGCAGCCCTAGCATCGC 60.971 66.667 0.00 0.00 41.82 4.58
3765 4236 4.022068 CACAGTTTGGCAGTCAACCAATAT 60.022 41.667 0.00 0.00 46.25 1.28
4148 4629 4.846367 TCATTACTAATGAGCCTAGGCCAT 59.154 41.667 30.42 26.70 42.69 4.40


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

AutoCloner maintained by Alex Coulton.