Multiple sequence alignment - TraesCS5B01G019500

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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 TraesCS5B01G019500 chr5B 100.000 2957 0 0 959 3915 19010545 19013501 0.000000e+00 5461
1 TraesCS5B01G019500 chr5B 100.000 584 0 0 1 584 19009587 19010170 0.000000e+00 1079
2 TraesCS5B01G019500 chr5B 86.892 946 81 24 1575 2516 536048467 536049373 0.000000e+00 1020
3 TraesCS5B01G019500 chr5B 94.463 596 19 6 1 584 515119004 515118411 0.000000e+00 905
4 TraesCS5B01G019500 chr5B 90.909 220 20 0 2550 2769 536046543 536046762 2.960000e-76 296
5 TraesCS5B01G019500 chr5B 86.294 197 23 3 1577 1773 536047841 536048033 1.100000e-50 211
6 TraesCS5B01G019500 chr7B 96.756 2343 69 5 1575 3915 688959783 688962120 0.000000e+00 3899
7 TraesCS5B01G019500 chr7B 96.625 2341 78 1 1575 3915 675573450 675575789 0.000000e+00 3884
8 TraesCS5B01G019500 chr7B 96.750 1077 31 2 2843 3915 428479230 428480306 0.000000e+00 1792
9 TraesCS5B01G019500 chr7B 94.020 1087 48 5 2842 3911 236935587 236934501 0.000000e+00 1631
10 TraesCS5B01G019500 chr7B 94.309 615 35 0 959 1573 675572537 675573151 0.000000e+00 942
11 TraesCS5B01G019500 chr7B 95.205 584 25 2 4 584 627292233 627291650 0.000000e+00 920
12 TraesCS5B01G019500 chr7B 96.183 262 9 1 1312 1573 688959224 688959484 1.010000e-115 427
13 TraesCS5B01G019500 chr7B 94.924 197 10 0 2584 2780 675573180 675573376 3.800000e-80 309
14 TraesCS5B01G019500 chr7B 94.472 199 11 0 995 1193 688959026 688959224 1.370000e-79 307
15 TraesCS5B01G019500 chr7B 92.481 133 10 0 2514 2646 605713710 605713578 1.440000e-44 191
16 TraesCS5B01G019500 chr2B 96.541 2342 55 12 1575 3915 761955612 761957928 0.000000e+00 3853
17 TraesCS5B01G019500 chr2B 95.447 615 28 0 959 1573 761954700 761955314 0.000000e+00 981
18 TraesCS5B01G019500 chr2B 94.007 584 33 2 1 584 779216961 779217542 0.000000e+00 883
19 TraesCS5B01G019500 chr2B 92.182 550 28 6 959 1499 773160248 773159705 0.000000e+00 763
20 TraesCS5B01G019500 chr4A 96.546 1274 41 2 1575 2848 647886290 647887560 0.000000e+00 2106
21 TraesCS5B01G019500 chr4A 96.840 1076 32 1 2842 3915 647888427 647889502 0.000000e+00 1797
22 TraesCS5B01G019500 chr4A 95.034 584 28 1 1 584 664673650 664674232 0.000000e+00 917
23 TraesCS5B01G019500 chr7A 94.851 1107 37 10 2825 3915 707175157 707176259 0.000000e+00 1711
24 TraesCS5B01G019500 chr7A 93.756 1121 36 10 2825 3915 271152223 271151107 0.000000e+00 1652
25 TraesCS5B01G019500 chr7A 95.778 900 29 2 3025 3915 648151658 648150759 0.000000e+00 1443
26 TraesCS5B01G019500 chr7A 95.122 328 16 0 2521 2848 21535159 21535486 5.800000e-143 518
27 TraesCS5B01G019500 chr5A 94.842 1105 39 8 2825 3915 155930018 155931118 0.000000e+00 1709
28 TraesCS5B01G019500 chr5A 93.381 1118 43 14 2825 3915 557963281 557964394 0.000000e+00 1626
29 TraesCS5B01G019500 chr5A 93.220 1121 42 9 2825 3915 685309112 685310228 0.000000e+00 1618
30 TraesCS5B01G019500 chr5A 92.789 943 60 6 1575 2516 556681025 556681960 0.000000e+00 1358
31 TraesCS5B01G019500 chr5A 94.627 335 18 0 2514 2848 557962108 557962442 1.610000e-143 520
32 TraesCS5B01G019500 chr5A 85.928 334 28 6 1024 1357 435002776 435002462 4.850000e-89 339
33 TraesCS5B01G019500 chr5A 91.441 222 19 0 2548 2769 556679787 556680008 4.910000e-79 305
34 TraesCS5B01G019500 chr1B 94.112 1104 47 8 2825 3915 562637049 562635951 0.000000e+00 1663
35 TraesCS5B01G019500 chr1B 94.463 596 20 5 1 584 163908988 163908394 0.000000e+00 905
36 TraesCS5B01G019500 chr1B 94.237 590 26 4 1 584 144275810 144275223 0.000000e+00 894
37 TraesCS5B01G019500 chr1B 82.779 331 36 9 1024 1354 36923372 36923681 3.850000e-70 276
38 TraesCS5B01G019500 chr1B 84.127 315 17 15 2525 2836 615797668 615797384 1.390000e-69 274
39 TraesCS5B01G019500 chr1B 82.063 223 18 10 2621 2836 543850284 543850077 1.870000e-38 171
40 TraesCS5B01G019500 chr1B 87.179 156 13 1 2621 2769 641575388 641575233 1.870000e-38 171
41 TraesCS5B01G019500 chr5D 95.970 943 36 2 1575 2516 440644134 440645075 0.000000e+00 1530
42 TraesCS5B01G019500 chr5D 92.476 319 24 0 2518 2836 440642919 440643237 1.280000e-124 457
43 TraesCS5B01G019500 chr5D 83.333 342 30 9 1024 1357 297793507 297793185 1.380000e-74 291
44 TraesCS5B01G019500 chr5D 83.481 339 29 9 1024 1354 384072994 384073313 1.380000e-74 291
45 TraesCS5B01G019500 chrUn 95.556 585 22 2 1 581 88593652 88594236 0.000000e+00 933
46 TraesCS5B01G019500 chr3B 95.051 586 25 4 1 584 714327753 714328336 0.000000e+00 918
47 TraesCS5B01G019500 chr3B 94.463 596 20 5 1 584 706297911 706297317 0.000000e+00 905
48 TraesCS5B01G019500 chr2D 93.578 545 27 4 959 1501 630407515 630406977 0.000000e+00 806
49 TraesCS5B01G019500 chr2A 92.572 552 25 7 959 1500 760584228 760583683 0.000000e+00 778
50 TraesCS5B01G019500 chr6B 91.892 333 25 1 2518 2848 241094105 241094437 7.660000e-127 464
51 TraesCS5B01G019500 chr6B 91.395 337 25 3 2514 2848 242426747 242426413 3.560000e-125 459
52 TraesCS5B01G019500 chr4B 92.532 308 21 1 2518 2823 129046146 129045839 1.290000e-119 440
53 TraesCS5B01G019500 chr4B 90.879 307 23 3 1024 1330 81207764 81207463 1.310000e-109 407
54 TraesCS5B01G019500 chr7D 83.776 339 28 7 1024 1354 37275106 37275425 2.960000e-76 296
55 TraesCS5B01G019500 chr7D 83.626 342 29 9 1024 1357 219843285 219842963 2.960000e-76 296
56 TraesCS5B01G019500 chr7D 90.355 197 14 1 2640 2836 70220699 70220890 1.810000e-63 254
57 TraesCS5B01G019500 chr3D 83.776 339 28 7 1024 1354 70728903 70729222 2.960000e-76 296
58 TraesCS5B01G019500 chr3D 83.776 339 28 9 1024 1354 443944865 443945184 2.960000e-76 296


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 TraesCS5B01G019500 chr5B 19009587 19013501 3914 False 3270.000000 5461 100.000000 1 3915 2 chr5B.!!$F1 3914
1 TraesCS5B01G019500 chr5B 515118411 515119004 593 True 905.000000 905 94.463000 1 584 1 chr5B.!!$R1 583
2 TraesCS5B01G019500 chr5B 536046543 536049373 2830 False 509.000000 1020 88.031667 1575 2769 3 chr5B.!!$F2 1194
3 TraesCS5B01G019500 chr7B 428479230 428480306 1076 False 1792.000000 1792 96.750000 2843 3915 1 chr7B.!!$F1 1072
4 TraesCS5B01G019500 chr7B 675572537 675575789 3252 False 1711.666667 3884 95.286000 959 3915 3 chr7B.!!$F2 2956
5 TraesCS5B01G019500 chr7B 236934501 236935587 1086 True 1631.000000 1631 94.020000 2842 3911 1 chr7B.!!$R1 1069
6 TraesCS5B01G019500 chr7B 688959026 688962120 3094 False 1544.333333 3899 95.803667 995 3915 3 chr7B.!!$F3 2920
7 TraesCS5B01G019500 chr7B 627291650 627292233 583 True 920.000000 920 95.205000 4 584 1 chr7B.!!$R3 580
8 TraesCS5B01G019500 chr2B 761954700 761957928 3228 False 2417.000000 3853 95.994000 959 3915 2 chr2B.!!$F2 2956
9 TraesCS5B01G019500 chr2B 779216961 779217542 581 False 883.000000 883 94.007000 1 584 1 chr2B.!!$F1 583
10 TraesCS5B01G019500 chr2B 773159705 773160248 543 True 763.000000 763 92.182000 959 1499 1 chr2B.!!$R1 540
11 TraesCS5B01G019500 chr4A 647886290 647889502 3212 False 1951.500000 2106 96.693000 1575 3915 2 chr4A.!!$F2 2340
12 TraesCS5B01G019500 chr4A 664673650 664674232 582 False 917.000000 917 95.034000 1 584 1 chr4A.!!$F1 583
13 TraesCS5B01G019500 chr7A 707175157 707176259 1102 False 1711.000000 1711 94.851000 2825 3915 1 chr7A.!!$F2 1090
14 TraesCS5B01G019500 chr7A 271151107 271152223 1116 True 1652.000000 1652 93.756000 2825 3915 1 chr7A.!!$R1 1090
15 TraesCS5B01G019500 chr7A 648150759 648151658 899 True 1443.000000 1443 95.778000 3025 3915 1 chr7A.!!$R2 890
16 TraesCS5B01G019500 chr5A 155930018 155931118 1100 False 1709.000000 1709 94.842000 2825 3915 1 chr5A.!!$F1 1090
17 TraesCS5B01G019500 chr5A 685309112 685310228 1116 False 1618.000000 1618 93.220000 2825 3915 1 chr5A.!!$F2 1090
18 TraesCS5B01G019500 chr5A 557962108 557964394 2286 False 1073.000000 1626 94.004000 2514 3915 2 chr5A.!!$F4 1401
19 TraesCS5B01G019500 chr5A 556679787 556681960 2173 False 831.500000 1358 92.115000 1575 2769 2 chr5A.!!$F3 1194
20 TraesCS5B01G019500 chr1B 562635951 562637049 1098 True 1663.000000 1663 94.112000 2825 3915 1 chr1B.!!$R4 1090
21 TraesCS5B01G019500 chr1B 163908394 163908988 594 True 905.000000 905 94.463000 1 584 1 chr1B.!!$R2 583
22 TraesCS5B01G019500 chr1B 144275223 144275810 587 True 894.000000 894 94.237000 1 584 1 chr1B.!!$R1 583
23 TraesCS5B01G019500 chr5D 440642919 440645075 2156 False 993.500000 1530 94.223000 1575 2836 2 chr5D.!!$F2 1261
24 TraesCS5B01G019500 chrUn 88593652 88594236 584 False 933.000000 933 95.556000 1 581 1 chrUn.!!$F1 580
25 TraesCS5B01G019500 chr3B 714327753 714328336 583 False 918.000000 918 95.051000 1 584 1 chr3B.!!$F1 583
26 TraesCS5B01G019500 chr3B 706297317 706297911 594 True 905.000000 905 94.463000 1 584 1 chr3B.!!$R1 583
27 TraesCS5B01G019500 chr2D 630406977 630407515 538 True 806.000000 806 93.578000 959 1501 1 chr2D.!!$R1 542
28 TraesCS5B01G019500 chr2A 760583683 760584228 545 True 778.000000 778 92.572000 959 1500 1 chr2A.!!$R1 541

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
407 441 0.326143 TCCCGATCCAATCTCACCCA 60.326 55.000 0.0 0.0 0.0 4.51 F
1060 1101 0.694771 AATGCTGCTGGAGGACTTCA 59.305 50.000 0.0 0.0 0.0 3.02 F
1309 1350 1.519719 GACTTCGCCAGCATCTCCT 59.480 57.895 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 4144 1.971481 ACTGCATCAAGTCAGTGCAA 58.029 45.0 0.0 0.0 46.9 4.08 R
2558 4587 0.817654 TTCATGGCGTCGAGATCTGT 59.182 50.0 0.0 0.0 0.0 3.41 R
3092 5996 1.140312 GGGCTGGACTGGATTGGATA 58.860 55.0 0.0 0.0 0.0 2.59 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
26 28 1.408969 AAACGTCATTTGGGGCACTT 58.591 45.000 0.00 0.00 0.00 3.16
34 36 4.452114 GTCATTTGGGGCACTTGAAAAATC 59.548 41.667 0.00 0.00 0.00 2.17
242 247 0.603707 CCATTCCCACGGATCGATGG 60.604 60.000 0.54 0.00 33.15 3.51
306 339 1.618143 ATCCGTCCATCCACCCCAA 60.618 57.895 0.00 0.00 0.00 4.12
363 397 3.090532 ATCGCACCCTTCTCCCCC 61.091 66.667 0.00 0.00 0.00 5.40
407 441 0.326143 TCCCGATCCAATCTCACCCA 60.326 55.000 0.00 0.00 0.00 4.51
1060 1101 0.694771 AATGCTGCTGGAGGACTTCA 59.305 50.000 0.00 0.00 0.00 3.02
1309 1350 1.519719 GACTTCGCCAGCATCTCCT 59.480 57.895 0.00 0.00 0.00 3.69
1411 1466 2.754658 CTCAGTAGTCGCCCCCGT 60.755 66.667 0.00 0.00 35.54 5.28
1453 1508 4.644685 GCCAATTACAATCTAAGCTTCCCA 59.355 41.667 0.00 0.00 0.00 4.37
1569 1630 5.006386 ACCAATATGCTTAGCAAGATAGGC 58.994 41.667 12.08 0.00 43.62 3.93
1573 1634 3.912496 TGCTTAGCAAGATAGGCTCAA 57.088 42.857 3.67 0.00 42.62 3.02
1818 3843 4.201657 TGCTGAATATGACCATCCACTTG 58.798 43.478 0.00 0.00 0.00 3.16
1890 3915 6.384224 CGTTGTGGTAGACTATGTACAGAAA 58.616 40.000 0.33 0.00 0.00 2.52
2021 4046 6.549736 TCAGCAGGTAATAACATAGCTCACTA 59.450 38.462 0.00 0.00 31.52 2.74
2101 4126 9.255304 GTGATTCAGATTGAGGTATTCTTAGTC 57.745 37.037 0.00 0.00 0.00 2.59
2135 4160 1.875514 TCTGTTGCACTGACTTGATGC 59.124 47.619 0.00 0.00 39.88 3.91
2353 4380 9.109393 GCATAATGACCTCTGTTTTGTAGATTA 57.891 33.333 0.00 0.00 0.00 1.75
2495 4524 8.724229 CAATTAACTGACACATGATTCTCTCAA 58.276 33.333 0.00 0.00 37.44 3.02
2558 4587 0.531090 GTTGGGTCGTGTGTGTGCTA 60.531 55.000 0.00 0.00 0.00 3.49
2619 4648 0.601311 GTGCTCAAGCTCAACGGAGT 60.601 55.000 3.32 0.00 43.37 3.85
2638 4667 4.033776 CTCGGCACCACCATGGGT 62.034 66.667 18.09 1.61 43.37 4.51
2685 4714 0.995024 CCCACCCATCCTCTTCACTT 59.005 55.000 0.00 0.00 0.00 3.16
2687 4716 1.065126 CCACCCATCCTCTTCACTTCC 60.065 57.143 0.00 0.00 0.00 3.46
2754 4783 4.819105 TCAGTTAGATTCGTCCCAACAT 57.181 40.909 0.00 0.00 0.00 2.71
2854 5756 2.494073 GTCTCTGCCTGCTTAGTGTAGT 59.506 50.000 0.00 0.00 0.00 2.73
3092 5996 3.544684 TGTTGTCACTTTGTCAGCATCT 58.455 40.909 0.00 0.00 0.00 2.90
3207 6129 4.022849 GGCTGTTTGGCATCCTATGTATTC 60.023 45.833 0.00 0.00 41.37 1.75
3219 6141 6.731292 TCCTATGTATTCTTTGCTGCTAGA 57.269 37.500 0.00 0.89 0.00 2.43
3474 6437 6.215845 AGTTTATGTGATTTGAACCTGCAAC 58.784 36.000 0.00 0.00 0.00 4.17
3675 6657 5.636123 TGTAAATAAAAGAGGACTTGGCCA 58.364 37.500 0.00 0.00 36.39 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
242 247 2.338381 GGATGGATGAGTGCCATGC 58.662 57.895 0.00 0.00 45.81 4.06
306 339 1.966451 GCTAGGGTTTGTGCTGCGT 60.966 57.895 0.00 0.00 0.00 5.24
981 1015 4.825679 GGGAGGGGGCTGGCTAGT 62.826 72.222 0.00 0.00 0.00 2.57
1041 1082 0.694771 TGAAGTCCTCCAGCAGCATT 59.305 50.000 0.00 0.00 0.00 3.56
1309 1350 3.057548 CTTGCTGCCACCGATGCA 61.058 61.111 0.00 0.00 37.17 3.96
1453 1508 4.941873 GGTTCAATTCCGATTCCAGTAGTT 59.058 41.667 0.00 0.00 0.00 2.24
1569 1630 9.979270 GAGTAATAAAGATGTCACAACATTGAG 57.021 33.333 0.00 0.00 46.20 3.02
1680 3075 9.471702 AACATTGATCAGAGAACCAGATTAATT 57.528 29.630 0.00 0.00 29.04 1.40
1818 3843 2.737252 CGGCCAACAGAGTCTAGAAAAC 59.263 50.000 2.24 0.00 0.00 2.43
2021 4046 2.865119 TCAATGACAGACCTGCATGT 57.135 45.000 0.00 0.00 31.32 3.21
2101 4126 7.547019 TCAGTGCAACAGAAAATATCAGTAGAG 59.453 37.037 0.00 0.00 41.43 2.43
2119 4144 1.971481 ACTGCATCAAGTCAGTGCAA 58.029 45.000 0.00 0.00 46.90 4.08
2135 4160 4.574421 TCAGACACAAACCATTACACACTG 59.426 41.667 0.00 0.00 0.00 3.66
2353 4380 2.373169 TGGAGTTGGAGCACTTCTCAAT 59.627 45.455 0.00 0.00 43.70 2.57
2363 4390 4.525912 ATTTCAATGTTGGAGTTGGAGC 57.474 40.909 0.00 0.00 0.00 4.70
2486 4515 4.684485 CGAGGGTATTGGCTTTGAGAGAAT 60.684 45.833 0.00 0.00 0.00 2.40
2495 4524 1.340991 ACAATGCGAGGGTATTGGCTT 60.341 47.619 9.18 0.00 46.63 4.35
2544 4573 1.986378 GATCTGTAGCACACACACGAC 59.014 52.381 0.00 0.00 32.33 4.34
2558 4587 0.817654 TTCATGGCGTCGAGATCTGT 59.182 50.000 0.00 0.00 0.00 3.41
2619 4648 3.716195 CCATGGTGGTGCCGAGGA 61.716 66.667 2.57 0.00 41.21 3.71
2638 4667 2.594303 CACTTGAGGCCGGTGCAA 60.594 61.111 1.90 4.42 40.13 4.08
2649 4678 2.829384 GGGTGGGGTGCTCACTTGA 61.829 63.158 0.00 0.00 35.61 3.02
2685 4714 3.528905 AGGTGAATCAATTGATCTGGGGA 59.471 43.478 20.95 0.00 32.75 4.81
2687 4716 4.441079 GCAAGGTGAATCAATTGATCTGGG 60.441 45.833 20.95 10.64 32.75 4.45
2754 4783 2.827604 GCAAGCTGCGAGACTACAA 58.172 52.632 0.00 0.00 31.71 2.41
2854 5756 8.851145 GGACATCTCATAGTGAGTCTAATACAA 58.149 37.037 6.83 0.00 44.58 2.41
3092 5996 1.140312 GGGCTGGACTGGATTGGATA 58.860 55.000 0.00 0.00 0.00 2.59
3207 6129 6.974932 TTATTTCTGAGTCTAGCAGCAAAG 57.025 37.500 0.00 0.00 33.45 2.77
3219 6141 5.361571 TGCCATTCATGCATTATTTCTGAGT 59.638 36.000 0.00 0.00 32.85 3.41
3675 6657 6.022958 AGGGCCTTTTTACAATCCAATAGTT 58.977 36.000 0.00 0.00 0.00 2.24
3796 6778 4.488770 TGGGCCTCAACCTTTTTAGAATT 58.511 39.130 4.53 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.