Multiple sequence alignment - TraesCS2B01G032900

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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 TraesCS2B01G032900 chr2B 100.000 5063 0 0 1 5063 15804716 15809778 0.000000e+00 9350.0
1 TraesCS2B01G032900 chr2B 99.269 5064 35 2 1 5063 15680694 15685756 0.000000e+00 9145.0
2 TraesCS2B01G032900 chr2B 98.776 5065 60 2 1 5063 15742945 15748009 0.000000e+00 9009.0
3 TraesCS2B01G032900 chr2B 99.829 4099 7 0 1 4099 15903056 15907154 0.000000e+00 7531.0
4 TraesCS2B01G032900 chr2B 92.713 1482 101 4 2923 4399 15699165 15700644 0.000000e+00 2132.0
5 TraesCS2B01G032900 chr2B 92.713 1482 101 4 2923 4399 15822473 15823952 0.000000e+00 2132.0
6 TraesCS2B01G032900 chr2B 90.008 1331 110 15 550 1870 15820720 15822037 0.000000e+00 1700.0
7 TraesCS2B01G032900 chr2B 89.932 1331 111 15 550 1870 15759536 15760853 0.000000e+00 1694.0
8 TraesCS2B01G032900 chr2B 89.782 1331 112 16 550 1870 15697413 15698729 0.000000e+00 1683.0
9 TraesCS2B01G032900 chr2B 90.231 1167 98 10 711 1870 15762432 15763589 0.000000e+00 1509.0
10 TraesCS2B01G032900 chr2B 86.650 412 39 8 2520 2918 15698721 15699129 4.650000e-120 442.0
11 TraesCS2B01G032900 chr2B 86.408 412 40 8 2520 2918 15760845 15761253 2.160000e-118 436.0
12 TraesCS2B01G032900 chr2B 86.408 412 40 8 2520 2918 15822029 15822437 2.160000e-118 436.0
13 TraesCS2B01G032900 chr2B 86.386 404 37 11 2520 2909 15763581 15763980 4.690000e-115 425.0
14 TraesCS2B01G032900 chr2B 88.473 347 34 6 4716 5060 15873196 15873538 1.010000e-111 414.0
15 TraesCS2B01G032900 chr2B 88.473 347 34 6 4716 5060 15973128 15973470 1.010000e-111 414.0
16 TraesCS2B01G032900 chr2B 88.525 305 31 4 4716 5019 15771056 15771357 2.880000e-97 366.0
17 TraesCS2B01G032900 chr2B 97.462 197 4 1 1898 2094 577237727 577237532 8.120000e-88 335.0
18 TraesCS2B01G032900 chr2B 85.106 329 36 6 2202 2518 789132703 789132376 1.760000e-84 324.0
19 TraesCS2B01G032900 chr2B 89.655 174 17 1 139 312 15805515 15805687 2.370000e-53 220.0
20 TraesCS2B01G032900 chr2B 89.655 174 17 1 139 312 15903855 15904027 2.370000e-53 220.0
21 TraesCS2B01G032900 chr2B 89.535 172 18 0 139 310 15681493 15681664 8.530000e-53 219.0
22 TraesCS2B01G032900 chr2B 90.798 163 15 0 150 312 15697668 15697830 8.530000e-53 219.0
23 TraesCS2B01G032900 chr2B 90.798 163 15 0 150 312 15759791 15759953 8.530000e-53 219.0
24 TraesCS2B01G032900 chrUn 99.704 2368 7 0 1732 4099 255038573 255036206 0.000000e+00 4335.0
25 TraesCS2B01G032900 chrUn 100.000 2085 0 0 348 2432 354974127 354972043 0.000000e+00 3851.0
26 TraesCS2B01G032900 chrUn 99.674 1535 5 0 3433 4967 391312988 391314522 0.000000e+00 2808.0
27 TraesCS2B01G032900 chrUn 78.684 1140 229 10 2930 4059 38680061 38678926 0.000000e+00 747.0
28 TraesCS2B01G032900 chrUn 88.473 347 34 6 4716 5060 250795712 250796054 1.010000e-111 414.0
29 TraesCS2B01G032900 chrUn 88.286 350 35 6 4716 5063 258356444 258356099 1.010000e-111 414.0
30 TraesCS2B01G032900 chrUn 88.473 347 34 6 4716 5060 363334329 363334671 1.010000e-111 414.0
31 TraesCS2B01G032900 chrUn 87.692 325 35 4 2195 2518 71298374 71298054 1.720000e-99 374.0
32 TraesCS2B01G032900 chrUn 86.207 348 42 3 4056 4399 439973634 439973979 6.190000e-99 372.0
33 TraesCS2B01G032900 chrUn 89.655 174 17 1 139 312 354973675 354973503 2.370000e-53 220.0
34 TraesCS2B01G032900 chrUn 96.154 78 3 0 2096 2173 67495602 67495679 1.480000e-25 128.0
35 TraesCS2B01G032900 chrUn 96.154 78 3 0 2096 2173 199880231 199880154 1.480000e-25 128.0
36 TraesCS2B01G032900 chrUn 96.154 78 3 0 2096 2173 229313522 229313599 1.480000e-25 128.0
37 TraesCS2B01G032900 chr2A 91.118 1914 122 25 2520 4394 11216160 11218064 0.000000e+00 2549.0
38 TraesCS2B01G032900 chr2A 93.225 1476 92 6 2921 4394 11189170 11190639 0.000000e+00 2165.0
39 TraesCS2B01G032900 chr2A 91.532 1488 105 11 392 1870 11140293 11141768 0.000000e+00 2030.0
40 TraesCS2B01G032900 chr2A 93.678 522 24 6 319 840 11214685 11215197 0.000000e+00 773.0
41 TraesCS2B01G032900 chr2A 92.903 310 21 1 2606 2914 11188824 11189133 2.780000e-122 449.0
42 TraesCS2B01G032900 chr2A 97.970 197 2 2 1909 2105 527913702 527913508 1.750000e-89 340.0
43 TraesCS2B01G032900 chr7D 93.243 296 19 1 4426 4720 29971647 29971352 7.780000e-118 435.0
44 TraesCS2B01G032900 chr1D 88.301 359 30 7 2171 2518 11137512 11137869 2.180000e-113 420.0
45 TraesCS2B01G032900 chr1D 87.730 326 32 6 2195 2515 493379005 493379327 1.720000e-99 374.0
46 TraesCS2B01G032900 chr7B 87.963 324 31 5 2195 2518 744931927 744931612 4.790000e-100 375.0
47 TraesCS2B01G032900 chr4D 91.667 252 19 2 4470 4720 120448155 120448405 1.040000e-91 348.0
48 TraesCS2B01G032900 chr4A 97.073 205 5 1 1907 2110 531079322 531079118 1.350000e-90 344.0
49 TraesCS2B01G032900 chr4A 96.954 197 5 1 1898 2094 67310552 67310747 3.780000e-86 329.0
50 TraesCS2B01G032900 chr1A 100.000 186 0 0 1911 2096 162803344 162803529 1.350000e-90 344.0
51 TraesCS2B01G032900 chr1A 96.970 33 1 0 4403 4435 90687859 90687891 7.080000e-04 56.5
52 TraesCS2B01G032900 chr6B 97.970 197 2 2 1911 2107 62703775 62703969 1.750000e-89 340.0
53 TraesCS2B01G032900 chr6B 95.000 40 2 0 4396 4435 311402398 311402437 4.230000e-06 63.9
54 TraesCS2B01G032900 chr6B 73.575 193 36 12 1161 1344 31016299 31016113 5.470000e-05 60.2
55 TraesCS2B01G032900 chr1B 90.533 169 9 3 1899 2062 375421894 375422060 3.070000e-52 217.0
56 TraesCS2B01G032900 chr1B 98.718 78 1 0 2096 2173 80808577 80808654 6.840000e-29 139.0
57 TraesCS2B01G032900 chr3A 96.000 100 3 1 1899 1998 494040175 494040077 1.460000e-35 161.0
58 TraesCS2B01G032900 chr5A 80.282 142 24 1 471 612 468881052 468881189 2.490000e-18 104.0
59 TraesCS2B01G032900 chr7A 100.000 33 0 0 4404 4436 21751394 21751426 1.520000e-05 62.1
60 TraesCS2B01G032900 chr7A 100.000 33 0 0 4403 4435 479703639 479703607 1.520000e-05 62.1
61 TraesCS2B01G032900 chr7A 100.000 32 0 0 4404 4435 77316289 77316258 5.470000e-05 60.2
62 TraesCS2B01G032900 chr3D 94.444 36 2 0 4394 4429 358840314 358840349 7.080000e-04 56.5


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 TraesCS2B01G032900 chr2B 15804716 15809778 5062 False 9350.000000 9350 100.000000 1 5063 1 chr2B.!!$F5 5062
1 TraesCS2B01G032900 chr2B 15680694 15685756 5062 False 9145.000000 9145 99.269000 1 5063 1 chr2B.!!$F1 5062
2 TraesCS2B01G032900 chr2B 15742945 15748009 5064 False 9009.000000 9009 98.776000 1 5063 1 chr2B.!!$F3 5062
3 TraesCS2B01G032900 chr2B 15903056 15907154 4098 False 3875.500000 7531 94.742000 1 4099 2 chr2B.!!$F12 4098
4 TraesCS2B01G032900 chr2B 15820720 15823952 3232 False 1422.666667 2132 89.709667 550 4399 3 chr2B.!!$F11 3849
5 TraesCS2B01G032900 chr2B 15697413 15700644 3231 False 1119.000000 2132 89.985750 150 4399 4 chr2B.!!$F9 4249
6 TraesCS2B01G032900 chr2B 15759536 15763980 4444 False 856.600000 1694 88.751000 150 2918 5 chr2B.!!$F10 2768
7 TraesCS2B01G032900 chrUn 255036206 255038573 2367 True 4335.000000 4335 99.704000 1732 4099 1 chrUn.!!$R4 2367
8 TraesCS2B01G032900 chrUn 391312988 391314522 1534 False 2808.000000 2808 99.674000 3433 4967 1 chrUn.!!$F5 1534
9 TraesCS2B01G032900 chrUn 354972043 354974127 2084 True 2035.500000 3851 94.827500 139 2432 2 chrUn.!!$R6 2293
10 TraesCS2B01G032900 chrUn 38678926 38680061 1135 True 747.000000 747 78.684000 2930 4059 1 chrUn.!!$R1 1129
11 TraesCS2B01G032900 chr2A 11140293 11141768 1475 False 2030.000000 2030 91.532000 392 1870 1 chr2A.!!$F1 1478
12 TraesCS2B01G032900 chr2A 11214685 11218064 3379 False 1661.000000 2549 92.398000 319 4394 2 chr2A.!!$F3 4075
13 TraesCS2B01G032900 chr2A 11188824 11190639 1815 False 1307.000000 2165 93.064000 2606 4394 2 chr2A.!!$F2 1788

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
2434 3109 2.275134 TGACCAGCTTTGATTCTGCA 57.725 45.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4121 4855 6.963322 ACTCCTTTGATGGCTAGAATTAACT 58.037 36.0 0.0 0.0 0.0 2.24 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
2432 3107 4.843220 AGTTTGACCAGCTTTGATTCTG 57.157 40.909 0.00 0.00 0.00 3.02
2433 3108 3.005155 AGTTTGACCAGCTTTGATTCTGC 59.995 43.478 0.00 0.00 0.00 4.26
2434 3109 2.275134 TGACCAGCTTTGATTCTGCA 57.725 45.000 0.00 0.00 0.00 4.41
2435 3110 2.585330 TGACCAGCTTTGATTCTGCAA 58.415 42.857 0.00 0.00 0.00 4.08
2436 3111 2.957680 TGACCAGCTTTGATTCTGCAAA 59.042 40.909 0.00 0.00 36.43 3.68
2486 3161 7.333528 TGATTTTAATGTTCATAGAGGGTGC 57.666 36.000 0.00 0.00 0.00 5.01
2487 3162 6.321181 TGATTTTAATGTTCATAGAGGGTGCC 59.679 38.462 0.00 0.00 0.00 5.01
2488 3163 5.450818 TTTAATGTTCATAGAGGGTGCCT 57.549 39.130 0.00 0.00 36.03 4.75
2489 3164 6.569127 TTTAATGTTCATAGAGGGTGCCTA 57.431 37.500 0.00 0.00 31.76 3.93
2490 3165 4.696479 AATGTTCATAGAGGGTGCCTAG 57.304 45.455 0.00 0.00 31.76 3.02
2491 3166 2.398588 TGTTCATAGAGGGTGCCTAGG 58.601 52.381 3.67 3.67 31.76 3.02
2492 3167 1.070914 GTTCATAGAGGGTGCCTAGGC 59.929 57.143 27.71 27.71 42.35 3.93
2504 3179 3.854669 CTAGGCACCCGGGAGCTG 61.855 72.222 36.82 24.42 32.43 4.24
2508 3183 4.344865 GCACCCGGGAGCTGGAAA 62.345 66.667 32.83 0.00 29.82 3.13
2509 3184 2.434331 CACCCGGGAGCTGGAAAA 59.566 61.111 32.02 0.00 29.82 2.29
2510 3185 1.971695 CACCCGGGAGCTGGAAAAC 60.972 63.158 32.02 0.00 29.82 2.43
2511 3186 2.361230 CCCGGGAGCTGGAAAACC 60.361 66.667 18.48 0.00 29.82 3.27
2512 3187 2.434331 CCGGGAGCTGGAAAACCA 59.566 61.111 0.00 0.00 29.82 3.67
2513 3188 1.971695 CCGGGAGCTGGAAAACCAC 60.972 63.158 0.00 0.00 29.82 4.16
2514 3189 1.073199 CGGGAGCTGGAAAACCACT 59.927 57.895 0.00 0.00 0.00 4.00
2515 3190 0.955919 CGGGAGCTGGAAAACCACTC 60.956 60.000 0.00 0.00 0.00 3.51
2516 3191 0.402121 GGGAGCTGGAAAACCACTCT 59.598 55.000 0.00 0.00 0.00 3.24
2517 3192 1.611936 GGGAGCTGGAAAACCACTCTC 60.612 57.143 0.00 0.00 0.00 3.20
2518 3193 1.433534 GAGCTGGAAAACCACTCTCG 58.566 55.000 0.00 0.00 0.00 4.04
2519 3194 0.759346 AGCTGGAAAACCACTCTCGT 59.241 50.000 0.00 0.00 0.00 4.18
2520 3195 1.149148 GCTGGAAAACCACTCTCGTC 58.851 55.000 0.00 0.00 0.00 4.20
2521 3196 1.270358 GCTGGAAAACCACTCTCGTCT 60.270 52.381 0.00 0.00 0.00 4.18
2522 3197 2.678324 CTGGAAAACCACTCTCGTCTC 58.322 52.381 0.00 0.00 0.00 3.36
2523 3198 1.000607 TGGAAAACCACTCTCGTCTCG 60.001 52.381 0.00 0.00 0.00 4.04
2524 3199 1.268899 GGAAAACCACTCTCGTCTCGA 59.731 52.381 0.00 0.00 0.00 4.04
2525 3200 2.288030 GGAAAACCACTCTCGTCTCGAA 60.288 50.000 0.00 0.00 34.74 3.71
2526 3201 3.378339 GAAAACCACTCTCGTCTCGAAA 58.622 45.455 0.00 0.00 34.74 3.46
2527 3202 2.418983 AACCACTCTCGTCTCGAAAC 57.581 50.000 0.00 0.00 34.74 2.78
4121 4855 9.275398 CCGGTATGTAGCCACTATAAAATAAAA 57.725 33.333 0.00 0.00 0.00 1.52
4231 5205 5.662211 TGTACTTTTCGTTTGAGCTTACC 57.338 39.130 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2460 3135 8.250332 GCACCCTCTATGAACATTAAAATCAAA 58.750 33.333 0.00 0.00 0.00 2.69
2461 3136 7.147915 GGCACCCTCTATGAACATTAAAATCAA 60.148 37.037 0.00 0.00 0.00 2.57
2462 3137 6.321181 GGCACCCTCTATGAACATTAAAATCA 59.679 38.462 0.00 0.00 0.00 2.57
2463 3138 6.547510 AGGCACCCTCTATGAACATTAAAATC 59.452 38.462 0.00 0.00 0.00 2.17
2464 3139 6.435164 AGGCACCCTCTATGAACATTAAAAT 58.565 36.000 0.00 0.00 0.00 1.82
2465 3140 5.826643 AGGCACCCTCTATGAACATTAAAA 58.173 37.500 0.00 0.00 0.00 1.52
2466 3141 5.450818 AGGCACCCTCTATGAACATTAAA 57.549 39.130 0.00 0.00 0.00 1.52
2467 3142 5.071788 CCTAGGCACCCTCTATGAACATTAA 59.928 44.000 0.00 0.00 34.61 1.40
2468 3143 4.593206 CCTAGGCACCCTCTATGAACATTA 59.407 45.833 0.00 0.00 34.61 1.90
2469 3144 3.392616 CCTAGGCACCCTCTATGAACATT 59.607 47.826 0.00 0.00 34.61 2.71
2470 3145 2.975489 CCTAGGCACCCTCTATGAACAT 59.025 50.000 0.00 0.00 34.61 2.71
2471 3146 2.398588 CCTAGGCACCCTCTATGAACA 58.601 52.381 0.00 0.00 34.61 3.18
2472 3147 1.070914 GCCTAGGCACCCTCTATGAAC 59.929 57.143 29.33 0.00 41.49 3.18
2473 3148 1.424638 GCCTAGGCACCCTCTATGAA 58.575 55.000 29.33 0.00 41.49 2.57
2474 3149 3.149436 GCCTAGGCACCCTCTATGA 57.851 57.895 29.33 0.00 41.49 2.15
2487 3162 3.854669 CAGCTCCCGGGTGCCTAG 61.855 72.222 37.33 25.70 36.61 3.02
2491 3166 3.860930 TTTTCCAGCTCCCGGGTGC 62.861 63.158 35.10 35.10 41.62 5.01
2492 3167 1.971695 GTTTTCCAGCTCCCGGGTG 60.972 63.158 22.86 20.53 42.50 4.61
2493 3168 2.434774 GTTTTCCAGCTCCCGGGT 59.565 61.111 22.86 0.00 0.00 5.28
2494 3169 2.361230 GGTTTTCCAGCTCCCGGG 60.361 66.667 16.85 16.85 40.31 5.73
2495 3170 2.434331 TGGTTTTCCAGCTCCCGG 59.566 61.111 0.00 0.00 46.22 5.73
2513 3188 2.031069 TGAGTTGGTTTCGAGACGAGAG 60.031 50.000 0.00 0.00 37.14 3.20
2514 3189 1.951602 TGAGTTGGTTTCGAGACGAGA 59.048 47.619 0.00 0.00 37.14 4.04
2515 3190 2.417339 TGAGTTGGTTTCGAGACGAG 57.583 50.000 0.00 0.00 37.14 4.18
2516 3191 2.875087 TTGAGTTGGTTTCGAGACGA 57.125 45.000 0.00 0.00 0.00 4.20
2517 3192 2.412089 GGATTGAGTTGGTTTCGAGACG 59.588 50.000 0.00 0.00 0.00 4.18
2518 3193 3.399330 TGGATTGAGTTGGTTTCGAGAC 58.601 45.455 0.00 0.00 0.00 3.36
2519 3194 3.762407 TGGATTGAGTTGGTTTCGAGA 57.238 42.857 0.00 0.00 0.00 4.04
2520 3195 5.156355 CAATTGGATTGAGTTGGTTTCGAG 58.844 41.667 0.00 0.00 42.83 4.04
2521 3196 4.022416 CCAATTGGATTGAGTTGGTTTCGA 60.022 41.667 20.50 0.00 42.83 3.71
2522 3197 4.236935 CCAATTGGATTGAGTTGGTTTCG 58.763 43.478 20.50 0.00 42.83 3.46
2523 3198 3.996363 GCCAATTGGATTGAGTTGGTTTC 59.004 43.478 29.02 0.79 42.83 2.78
2524 3199 3.390639 TGCCAATTGGATTGAGTTGGTTT 59.609 39.130 29.02 0.00 42.83 3.27
2525 3200 2.971330 TGCCAATTGGATTGAGTTGGTT 59.029 40.909 29.02 0.00 42.83 3.67
2526 3201 2.299867 GTGCCAATTGGATTGAGTTGGT 59.700 45.455 29.02 0.00 42.83 3.67
2527 3202 2.299582 TGTGCCAATTGGATTGAGTTGG 59.700 45.455 29.02 0.00 42.83 3.77
3431 4165 7.611213 AAACCGAAAAATACATCCTGTAGAG 57.389 36.000 0.00 0.00 36.14 2.43
4121 4855 6.963322 ACTCCTTTGATGGCTAGAATTAACT 58.037 36.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.