Multiple sequence alignment - TraesCS1D01G014200

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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 TraesCS1D01G014200 chr1D 100.000 4091 0 0 1 4091 7016922 7021012 0.000000e+00 7555.0
1 TraesCS1D01G014200 chr1D 100.000 1967 0 0 4467 6433 7021388 7023354 0.000000e+00 3633.0
2 TraesCS1D01G014200 chr1D 79.945 733 122 20 2703 3416 20948563 20947837 3.440000e-142 516.0
3 TraesCS1D01G014200 chr1D 95.473 243 2 9 3849 4091 440870671 440870438 4.710000e-101 379.0
4 TraesCS1D01G014200 chr1D 90.000 290 28 1 5147 5436 7345055 7345343 2.190000e-99 374.0
5 TraesCS1D01G014200 chr1D 78.881 554 99 14 4892 5436 30082148 30081604 6.130000e-95 359.0
6 TraesCS1D01G014200 chr1D 84.097 371 47 12 2057 2423 20949554 20949192 1.330000e-91 348.0
7 TraesCS1D01G014200 chr1D 81.022 411 67 8 921 1321 20950561 20950152 3.740000e-82 316.0
8 TraesCS1D01G014200 chr1D 77.223 461 85 8 60 500 66267266 66266806 1.070000e-62 252.0
9 TraesCS1D01G014200 chr1D 81.126 302 35 7 5534 5834 7345417 7345697 8.390000e-54 222.0
10 TraesCS1D01G014200 chr5D 83.482 896 96 28 2690 3564 8050919 8050055 0.000000e+00 787.0
11 TraesCS1D01G014200 chr5D 83.233 662 94 12 4777 5435 8049003 8048356 5.550000e-165 592.0
12 TraesCS1D01G014200 chr5D 99.167 240 1 1 3853 4091 481337801 481338040 1.280000e-116 431.0
13 TraesCS1D01G014200 chr5D 83.982 437 59 8 2022 2453 8052079 8051649 6.000000e-110 409.0
14 TraesCS1D01G014200 chr5D 98.701 231 1 2 3862 4091 464548020 464547791 6.000000e-110 409.0
15 TraesCS1D01G014200 chr5D 96.653 239 3 5 3854 4091 364374447 364374681 6.050000e-105 392.0
16 TraesCS1D01G014200 chr5D 78.159 641 81 40 3194 3792 8410384 8411007 2.850000e-93 353.0
17 TraesCS1D01G014200 chr5D 81.176 425 58 11 921 1328 8052957 8052538 8.050000e-84 322.0
18 TraesCS1D01G014200 chr5D 78.058 515 86 11 11 500 505372193 505371681 3.770000e-77 300.0
19 TraesCS1D01G014200 chr5D 84.912 285 37 4 4467 4748 8049273 8048992 3.800000e-72 283.0
20 TraesCS1D01G014200 chr5D 79.790 381 46 17 2693 3060 8409970 8410332 1.390000e-61 248.0
21 TraesCS1D01G014200 chr5D 82.109 313 27 19 1477 1775 8052499 8052202 2.320000e-59 241.0
22 TraesCS1D01G014200 chr5D 84.348 230 21 9 2480 2703 8051174 8050954 1.820000e-50 211.0
23 TraesCS1D01G014200 chr5D 81.855 248 40 2 258 500 462041141 462041388 3.040000e-48 204.0
24 TraesCS1D01G014200 chr5D 74.286 385 79 13 17 392 51454664 51455037 1.870000e-30 145.0
25 TraesCS1D01G014200 chr5D 85.401 137 16 2 921 1053 8407345 8407481 8.700000e-29 139.0
26 TraesCS1D01G014200 chr5D 78.824 170 24 9 2496 2660 8260202 8260364 3.170000e-18 104.0
27 TraesCS1D01G014200 chr5D 92.857 56 4 0 1538 1593 8418370 8418315 1.490000e-11 82.4
28 TraesCS1D01G014200 chr5A 82.195 893 108 33 2690 3562 6434548 6433687 0.000000e+00 721.0
29 TraesCS1D01G014200 chr5A 82.265 874 99 30 2690 3539 6440743 6439902 0.000000e+00 704.0
30 TraesCS1D01G014200 chr5A 82.265 874 98 30 2690 3539 6446953 6446113 0.000000e+00 702.0
31 TraesCS1D01G014200 chr5A 78.698 1075 164 42 4777 5813 6439576 6438529 0.000000e+00 656.0
32 TraesCS1D01G014200 chr5A 78.605 1075 165 42 4777 5813 6445787 6444740 0.000000e+00 651.0
33 TraesCS1D01G014200 chr5A 83.958 480 55 16 4777 5254 6433235 6432776 2.130000e-119 440.0
34 TraesCS1D01G014200 chr5A 83.599 439 60 9 2022 2454 6448126 6447694 1.000000e-107 401.0
35 TraesCS1D01G014200 chr5A 78.404 639 82 40 3194 3792 6618572 6619194 1.320000e-96 364.0
36 TraesCS1D01G014200 chr5A 82.630 403 63 6 2022 2422 6435861 6435464 3.690000e-92 350.0
37 TraesCS1D01G014200 chr5A 82.382 403 64 6 2022 2422 6442059 6441662 1.720000e-90 344.0
38 TraesCS1D01G014200 chr5A 80.094 427 63 12 921 1330 6449005 6448584 1.360000e-76 298.0
39 TraesCS1D01G014200 chr5A 83.451 284 42 3 4467 4748 6439845 6439565 6.400000e-65 259.0
40 TraesCS1D01G014200 chr5A 82.746 284 44 3 4467 4748 6446056 6445776 1.390000e-61 248.0
41 TraesCS1D01G014200 chr5A 79.265 381 49 18 2693 3060 6618157 6618520 8.340000e-59 239.0
42 TraesCS1D01G014200 chr5A 83.843 229 22 9 2480 2703 6447206 6446988 3.040000e-48 204.0
43 TraesCS1D01G014200 chr5A 83.099 213 24 7 2481 2687 6434805 6434599 3.960000e-42 183.0
44 TraesCS1D01G014200 chr5A 82.727 220 22 10 2480 2693 6523682 6523891 1.420000e-41 182.0
45 TraesCS1D01G014200 chr5A 78.065 155 21 8 2496 2646 6485093 6484948 1.150000e-12 86.1
46 TraesCS1D01G014200 chr5A 89.831 59 6 0 1535 1593 6625739 6625681 6.920000e-10 76.8
47 TraesCS1D01G014200 chr5B 83.535 662 92 11 4777 5435 8375383 8374736 2.570000e-168 603.0
48 TraesCS1D01G014200 chr5B 83.524 613 74 16 2949 3539 8376316 8375709 1.220000e-151 547.0
49 TraesCS1D01G014200 chr5B 83.045 578 77 13 2995 3555 652935024 652935597 7.440000e-139 505.0
50 TraesCS1D01G014200 chr5B 81.475 556 75 16 2690 3234 22094467 22095005 1.280000e-116 431.0
51 TraesCS1D01G014200 chr5B 83.827 439 59 9 2022 2454 8377766 8377334 2.160000e-109 407.0
52 TraesCS1D01G014200 chr5B 83.562 438 62 7 2022 2454 652933516 652933948 1.000000e-107 401.0
53 TraesCS1D01G014200 chr5B 80.336 417 60 11 921 1320 8378790 8378379 4.880000e-76 296.0
54 TraesCS1D01G014200 chr5B 86.245 269 29 5 2690 2954 8376604 8376340 1.060000e-72 285.0
55 TraesCS1D01G014200 chr5B 85.821 268 33 3 2690 2954 652934678 652934943 4.910000e-71 279.0
56 TraesCS1D01G014200 chr5B 78.118 425 65 18 921 1328 652932688 652933101 1.790000e-60 244.0
57 TraesCS1D01G014200 chr5B 76.048 501 100 10 15 500 82441319 82440824 6.440000e-60 243.0
58 TraesCS1D01G014200 chr5B 82.192 292 32 10 2693 2979 8527871 8528147 3.880000e-57 233.0
59 TraesCS1D01G014200 chr5B 82.648 219 22 12 2480 2693 652934428 652934635 5.120000e-41 180.0
60 TraesCS1D01G014200 chr5B 80.800 250 26 14 1534 1775 8378124 8377889 6.630000e-40 176.0
61 TraesCS1D01G014200 chr5B 81.818 220 25 12 2480 2693 22094214 22094424 3.080000e-38 171.0
62 TraesCS1D01G014200 chr5B 80.786 229 27 12 2480 2703 8376855 8376639 5.160000e-36 163.0
63 TraesCS1D01G014200 chr5B 86.131 137 15 2 921 1053 8524498 8524634 1.870000e-30 145.0
64 TraesCS1D01G014200 chr5B 73.791 393 87 13 921 1303 653010216 653009830 2.420000e-29 141.0
65 TraesCS1D01G014200 chr5B 77.731 238 31 17 3628 3859 653006684 653006463 6.770000e-25 126.0
66 TraesCS1D01G014200 chr5B 85.833 120 9 6 1477 1589 652933140 652933258 3.150000e-23 121.0
67 TraesCS1D01G014200 chr5B 83.871 124 16 2 921 1040 655303810 655303933 1.470000e-21 115.0
68 TraesCS1D01G014200 chr5B 92.593 54 4 0 1540 1593 8542802 8542749 1.920000e-10 78.7
69 TraesCS1D01G014200 chr5B 90.741 54 2 2 1540 1592 33116892 33116841 1.160000e-07 69.4
70 TraesCS1D01G014200 chr3D 99.587 242 0 1 3851 4091 266539641 266539882 2.130000e-119 440.0
71 TraesCS1D01G014200 chr3D 99.184 245 1 1 3848 4091 579171320 579171076 2.130000e-119 440.0
72 TraesCS1D01G014200 chr3D 98.776 245 2 1 3848 4091 612673761 612673517 9.910000e-118 435.0
73 TraesCS1D01G014200 chr4D 99.134 231 1 1 3862 4091 25165448 25165678 1.290000e-111 414.0
74 TraesCS1D01G014200 chr4D 99.537 216 0 1 3876 4091 178673414 178673200 6.050000e-105 392.0
75 TraesCS1D01G014200 chr4D 84.367 371 45 12 2057 2423 73365566 73365205 1.030000e-92 351.0
76 TraesCS1D01G014200 chr4D 81.022 411 67 8 921 1321 73366573 73366164 3.740000e-82 316.0
77 TraesCS1D01G014200 chr1B 85.095 369 46 8 2057 2423 34254553 34254192 1.020000e-97 368.0
78 TraesCS1D01G014200 chr1B 81.457 453 71 11 4991 5440 34252166 34251724 6.130000e-95 359.0
79 TraesCS1D01G014200 chr1B 79.720 429 65 18 4892 5310 47632338 47631922 2.270000e-74 291.0
80 TraesCS1D01G014200 chr1B 76.400 500 90 13 23 500 587021640 587022133 1.790000e-60 244.0
81 TraesCS1D01G014200 chr1B 84.848 66 10 0 6161 6226 9694809 9694874 4.160000e-07 67.6
82 TraesCS1D01G014200 chr7D 78.016 514 85 13 11 500 595869703 595869194 1.360000e-76 298.0
83 TraesCS1D01G014200 chr7D 83.843 229 25 7 921 1141 123360540 123360316 2.350000e-49 207.0
84 TraesCS1D01G014200 chr2D 75.932 590 94 24 23 568 6180936 6181521 6.400000e-65 259.0
85 TraesCS1D01G014200 chr2D 81.651 218 26 9 921 1127 612720953 612721167 1.110000e-37 169.0
86 TraesCS1D01G014200 chr6B 76.844 488 93 9 33 500 113443846 113443359 2.300000e-64 257.0
87 TraesCS1D01G014200 chr4B 76.218 513 94 13 9 500 66802092 66802597 4.980000e-61 246.0
88 TraesCS1D01G014200 chr4B 75.514 486 99 9 34 500 63761140 63760656 3.020000e-53 220.0
89 TraesCS1D01G014200 chr4A 75.591 508 91 21 11 500 583973033 583972541 3.020000e-53 220.0
90 TraesCS1D01G014200 chr4A 81.513 119 14 4 389 499 597170367 597170485 2.470000e-14 91.6
91 TraesCS1D01G014200 chr4A 90.323 62 6 0 514 575 582503284 582503223 1.490000e-11 82.4
92 TraesCS1D01G014200 chr4A 74.405 168 37 3 65 227 607264304 607264470 4.160000e-07 67.6
93 TraesCS1D01G014200 chr2B 83.621 232 29 7 274 500 752824816 752824589 6.540000e-50 209.0
94 TraesCS1D01G014200 chr2B 76.050 238 43 8 258 484 541205426 541205192 1.900000e-20 111.0
95 TraesCS1D01G014200 chr6A 77.011 174 40 0 62 235 470410760 470410933 4.100000e-17 100.0


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 TraesCS1D01G014200 chr1D 7016922 7023354 6432 False 5594.000000 7555 100.000000 1 6433 2 chr1D.!!$F1 6432
1 TraesCS1D01G014200 chr1D 20947837 20950561 2724 True 393.333333 516 81.688000 921 3416 3 chr1D.!!$R4 2495
2 TraesCS1D01G014200 chr1D 30081604 30082148 544 True 359.000000 359 78.881000 4892 5436 1 chr1D.!!$R1 544
3 TraesCS1D01G014200 chr1D 7345055 7345697 642 False 298.000000 374 85.563000 5147 5834 2 chr1D.!!$F2 687
4 TraesCS1D01G014200 chr5D 8048356 8052957 4601 True 406.428571 787 83.320286 921 5435 7 chr5D.!!$R4 4514
5 TraesCS1D01G014200 chr5D 505371681 505372193 512 True 300.000000 300 78.058000 11 500 1 chr5D.!!$R3 489
6 TraesCS1D01G014200 chr5D 8407345 8411007 3662 False 246.666667 353 81.116667 921 3792 3 chr5D.!!$F6 2871
7 TraesCS1D01G014200 chr5A 6432776 6449005 16229 True 440.071429 721 82.130714 921 5813 14 chr5A.!!$R3 4892
8 TraesCS1D01G014200 chr5A 6618157 6619194 1037 False 301.500000 364 78.834500 2693 3792 2 chr5A.!!$F2 1099
9 TraesCS1D01G014200 chr5B 8374736 8378790 4054 True 353.857143 603 82.721857 921 5435 7 chr5B.!!$R4 4514
10 TraesCS1D01G014200 chr5B 22094214 22095005 791 False 301.000000 431 81.646500 2480 3234 2 chr5B.!!$F3 754
11 TraesCS1D01G014200 chr5B 652932688 652935597 2909 False 288.333333 505 83.171167 921 3555 6 chr5B.!!$F4 2634
12 TraesCS1D01G014200 chr4D 73365205 73366573 1368 True 333.500000 351 82.694500 921 2423 2 chr4D.!!$R2 1502
13 TraesCS1D01G014200 chr1B 34251724 34254553 2829 True 363.500000 368 83.276000 2057 5440 2 chr1B.!!$R2 3383
14 TraesCS1D01G014200 chr7D 595869194 595869703 509 True 298.000000 298 78.016000 11 500 1 chr7D.!!$R2 489
15 TraesCS1D01G014200 chr2D 6180936 6181521 585 False 259.000000 259 75.932000 23 568 1 chr2D.!!$F1 545
16 TraesCS1D01G014200 chr4B 66802092 66802597 505 False 246.000000 246 76.218000 9 500 1 chr4B.!!$F1 491

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
288 304 0.032515 TCTCCGGTGGATCTGCCTTA 60.033 55.0 0.00 0.0 37.63 2.69 F
705 750 0.033894 TTCCCGCCCTTTGTATTCCC 60.034 55.0 0.00 0.0 0.00 3.97 F
760 805 0.035725 TCTGCCTTGCTCCATCACAG 60.036 55.0 0.00 0.0 0.00 3.66 F
846 891 0.036105 TGCTGACAATCAGTGGCGAT 60.036 50.0 7.62 0.0 45.94 4.58 F
1480 2041 0.110104 GGAGGGAGAGGAATGCCATG 59.890 60.0 0.00 0.0 36.29 3.66 F
1988 2906 0.111253 CTATTGCCCCACATCCTCCC 59.889 60.0 0.00 0.0 0.00 4.30 F
2554 4016 0.530431 CAGCCCAACAACAACAAGGC 60.530 55.0 0.00 0.0 40.79 4.35 F
3364 17370 0.877071 AAGCAACTTGAGGTGCATCG 59.123 50.0 21.84 0.0 0.00 3.84 F
3798 18475 0.039798 CTTACCATCATGCATGCCGC 60.040 55.0 22.25 0.0 42.89 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 2006 0.034380 TCTCCCTCCGACCTACACTG 60.034 60.0 0.00 0.00 0.00 3.66 R
1969 2887 0.111253 GGGAGGATGTGGGGCAATAG 59.889 60.0 0.00 0.00 0.00 1.73 R
1978 2896 0.394216 TTTGGATGCGGGAGGATGTG 60.394 55.0 0.00 0.00 42.67 3.21 R
1979 2897 0.552848 ATTTGGATGCGGGAGGATGT 59.447 50.0 0.00 0.00 42.67 3.06 R
3073 17063 0.595567 TCGTCGTAGTGTTGGTGTGC 60.596 55.0 0.00 0.00 0.00 4.57 R
3493 17521 0.030638 AGAAAACACATGCGCACACC 59.969 50.0 14.90 0.00 0.00 4.16 R
3706 18379 0.391263 CCCCGTTCTCACTTGCTACC 60.391 60.0 0.00 0.00 0.00 3.18 R
4773 19461 0.804364 GACAAGATGCGCATCCACAA 59.196 50.0 39.38 5.13 38.58 3.33 R
5455 20191 0.179089 ACCTAGAATCTGCAGCTGCG 60.179 55.0 32.11 25.46 45.83 5.18 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)


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

AutoCloner maintained by Alex Coulton.