Multiple sequence alignment - TraesCS7B01G153600

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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 TraesCS7B01G153600 chr7B 100.000 2987 0 0 1 2987 204063012 204060026 0.000000e+00 5517.0
1 TraesCS7B01G153600 chr7B 100.000 1166 0 0 3196 4361 204059817 204058652 0.000000e+00 2154.0
2 TraesCS7B01G153600 chr7B 93.290 462 29 2 1 462 598900385 598900844 0.000000e+00 680.0
3 TraesCS7B01G153600 chr7B 80.856 444 67 15 4 438 641179678 641179244 2.510000e-87 333.0
4 TraesCS7B01G153600 chr7B 97.647 85 1 1 463 546 598900878 598900962 1.260000e-30 145.0
5 TraesCS7B01G153600 chr7D 92.788 2468 98 30 562 2969 233018920 233016473 0.000000e+00 3498.0
6 TraesCS7B01G153600 chr7D 91.451 386 27 4 3249 3628 233015845 233015460 3.860000e-145 525.0
7 TraesCS7B01G153600 chr7D 86.154 455 41 15 12 462 419373175 419372739 5.110000e-129 472.0
8 TraesCS7B01G153600 chr7D 96.386 83 1 2 463 544 419372705 419372624 7.610000e-28 135.0
9 TraesCS7B01G153600 chr7D 98.148 54 1 0 4272 4325 232942893 232942840 1.290000e-15 95.3
10 TraesCS7B01G153600 chr7D 96.154 52 1 1 3610 3660 29876376 29876427 2.790000e-12 84.2
11 TraesCS7B01G153600 chr7D 96.078 51 2 0 3610 3660 311882125 311882075 2.790000e-12 84.2
12 TraesCS7B01G153600 chr7A 95.122 1804 72 10 817 2609 245931622 245933420 0.000000e+00 2830.0
13 TraesCS7B01G153600 chr7A 84.945 631 49 21 3200 3816 245935686 245936284 8.070000e-167 597.0
14 TraesCS7B01G153600 chr7A 86.053 380 15 18 2618 2969 245934141 245934510 1.480000e-99 374.0
15 TraesCS7B01G153600 chr7A 88.971 272 21 4 4091 4361 245936915 245937178 1.170000e-85 327.0
16 TraesCS7B01G153600 chr7A 92.742 124 6 1 562 685 245929423 245929543 4.480000e-40 176.0
17 TraesCS7B01G153600 chr7A 96.000 50 1 1 3613 3662 629047062 629047014 3.620000e-11 80.5
18 TraesCS7B01G153600 chrUn 100.000 1195 0 0 1 1195 391404070 391402876 0.000000e+00 2207.0
19 TraesCS7B01G153600 chrUn 99.833 1195 1 1 1 1195 391493907 391492714 0.000000e+00 2194.0
20 TraesCS7B01G153600 chrUn 100.000 812 0 0 3196 4007 217710166 217710977 0.000000e+00 1500.0
21 TraesCS7B01G153600 chrUn 100.000 557 0 0 639 1195 217707982 217708538 0.000000e+00 1029.0
22 TraesCS7B01G153600 chr4D 85.683 461 42 15 4 462 109916032 109915594 8.540000e-127 464.0
23 TraesCS7B01G153600 chr4D 97.647 85 1 1 463 546 109915560 109915476 1.260000e-30 145.0
24 TraesCS7B01G153600 chr4D 92.453 53 2 1 3610 3662 170225236 170225286 1.680000e-09 75.0
25 TraesCS7B01G153600 chr5D 81.250 464 68 19 12 465 515241774 515241320 1.490000e-94 357.0
26 TraesCS7B01G153600 chr4A 81.023 469 70 18 5 463 715077306 715076847 5.360000e-94 355.0
27 TraesCS7B01G153600 chr4A 87.356 87 8 3 463 547 39585763 39585678 3.590000e-16 97.1
28 TraesCS7B01G153600 chr3B 78.867 459 75 20 12 460 625623048 625623494 1.530000e-74 291.0
29 TraesCS7B01G153600 chr1A 93.023 86 5 1 463 547 318507176 318507091 1.650000e-24 124.0
30 TraesCS7B01G153600 chr6D 90.909 88 8 0 463 550 160478219 160478306 7.660000e-23 119.0
31 TraesCS7B01G153600 chr6D 80.851 94 15 2 3610 3703 245567841 245567931 2.180000e-08 71.3
32 TraesCS7B01G153600 chr4B 88.095 84 10 0 463 546 624515366 624515449 2.780000e-17 100.0
33 TraesCS7B01G153600 chr2B 94.118 51 2 1 3610 3660 794694470 794694519 4.680000e-10 76.8
34 TraesCS7B01G153600 chr2B 94.118 51 2 1 3610 3660 794803371 794803420 4.680000e-10 76.8
35 TraesCS7B01G153600 chr5B 80.851 94 14 3 3610 3702 17982606 17982696 2.180000e-08 71.3


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 TraesCS7B01G153600 chr7B 204058652 204063012 4360 True 3835.5 5517 100.0000 1 4361 2 chr7B.!!$R2 4360
1 TraesCS7B01G153600 chr7B 598900385 598900962 577 False 412.5 680 95.4685 1 546 2 chr7B.!!$F1 545
2 TraesCS7B01G153600 chr7D 233015460 233018920 3460 True 2011.5 3498 92.1195 562 3628 2 chr7D.!!$R3 3066
3 TraesCS7B01G153600 chr7D 419372624 419373175 551 True 303.5 472 91.2700 12 544 2 chr7D.!!$R4 532
4 TraesCS7B01G153600 chr7A 245929423 245937178 7755 False 860.8 2830 89.5666 562 4361 5 chr7A.!!$F1 3799
5 TraesCS7B01G153600 chrUn 391402876 391404070 1194 True 2207.0 2207 100.0000 1 1195 1 chrUn.!!$R1 1194
6 TraesCS7B01G153600 chrUn 391492714 391493907 1193 True 2194.0 2194 99.8330 1 1195 1 chrUn.!!$R2 1194
7 TraesCS7B01G153600 chrUn 217707982 217710977 2995 False 1264.5 1500 100.0000 639 4007 2 chrUn.!!$F1 3368
8 TraesCS7B01G153600 chr4D 109915476 109916032 556 True 304.5 464 91.6650 4 546 2 chr4D.!!$R1 542

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
1205 3291 5.944007 ACATGGTTAATTAGTTCCTGACCAC 59.056 40.000 5.31 0.00 38.39 4.16 F
1503 3595 0.462937 CGAGTGGGTGGACAACAACA 60.463 55.000 0.00 0.00 39.06 3.33 F
1781 3873 1.342672 ACTTCCTCAACCACACCCGT 61.343 55.000 0.00 0.00 0.00 5.28 F
1967 4059 1.388837 TAGCCGCGATGGACAAGCTA 61.389 55.000 8.23 6.51 42.00 3.32 F
2137 4229 2.351276 GAGGTCCAACATGCCGGT 59.649 61.111 1.90 0.00 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 4229 1.000233 GTACAGCGCGAAGACGAACA 61.000 55.000 12.1 0.0 42.66 3.18 R
2798 5605 4.033702 GGCGAGCCTAATGTACAAACTTAC 59.966 45.833 6.9 0.0 0.00 2.34 R
2835 5674 5.633182 TCTTTTTGCGAATAATTCACAAGCC 59.367 36.000 0.0 0.0 33.73 4.35 R
2867 5707 7.339212 TCGAGGTGAAATGAAAATACAATCCAT 59.661 33.333 0.0 0.0 0.00 3.41 R
4007 8617 0.242825 GGGTTTCGCTAGGTTTTGGC 59.757 55.000 0.0 0.0 0.00 4.52 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
1205 3291 5.944007 ACATGGTTAATTAGTTCCTGACCAC 59.056 40.000 5.31 0.00 38.39 4.16
1225 3311 1.480954 CTGACCACCGTGGCTAACTAT 59.519 52.381 17.99 0.00 42.67 2.12
1226 3312 1.903860 TGACCACCGTGGCTAACTATT 59.096 47.619 17.99 0.00 42.67 1.73
1503 3595 0.462937 CGAGTGGGTGGACAACAACA 60.463 55.000 0.00 0.00 39.06 3.33
1781 3873 1.342672 ACTTCCTCAACCACACCCGT 61.343 55.000 0.00 0.00 0.00 5.28
1892 3984 1.514443 GAGCAGCCACTACGTCGAC 60.514 63.158 5.18 5.18 0.00 4.20
1967 4059 1.388837 TAGCCGCGATGGACAAGCTA 61.389 55.000 8.23 6.51 42.00 3.32
2096 4188 3.499737 GCCCGTCGGATGCACAAG 61.500 66.667 14.39 0.00 0.00 3.16
2137 4229 2.351276 GAGGTCCAACATGCCGGT 59.649 61.111 1.90 0.00 0.00 5.28
2222 4314 3.721625 GTTCTACCCGAACGGTACC 57.278 57.895 12.23 0.16 45.97 3.34
2755 5560 9.373450 AGAAAATAGATTCTAGCTAGGTGATGA 57.627 33.333 20.58 3.11 37.88 2.92
2798 5605 8.487028 AGAAGGATGAGTTTAATACTAGTTGGG 58.513 37.037 0.00 0.00 37.17 4.12
2835 5674 3.005897 AGGCTCGCCATTGTACATACTAG 59.994 47.826 11.02 0.00 38.92 2.57
2904 5744 0.948623 TCACCTCGAAACATGTGCGG 60.949 55.000 17.84 5.52 0.00 5.69
2982 6982 3.159213 TCCATTTGGACTTGATGTGCT 57.841 42.857 0.00 0.00 39.78 4.40
2983 6983 3.499338 TCCATTTGGACTTGATGTGCTT 58.501 40.909 0.00 0.00 39.78 3.91
2984 6984 3.896888 TCCATTTGGACTTGATGTGCTTT 59.103 39.130 0.00 0.00 39.78 3.51
2985 6985 4.344679 TCCATTTGGACTTGATGTGCTTTT 59.655 37.500 0.00 0.00 39.78 2.27
2986 6986 5.058490 CCATTTGGACTTGATGTGCTTTTT 58.942 37.500 0.00 0.00 37.91 1.94
4025 8635 3.786809 GCCAAAACCTAGCGAAACC 57.213 52.632 0.00 0.00 0.00 3.27
4026 8636 0.242825 GCCAAAACCTAGCGAAACCC 59.757 55.000 0.00 0.00 0.00 4.11
4027 8637 0.519961 CCAAAACCTAGCGAAACCCG 59.480 55.000 0.00 0.00 42.21 5.28
4028 8638 1.515081 CAAAACCTAGCGAAACCCGA 58.485 50.000 0.00 0.00 41.76 5.14
4029 8639 1.196127 CAAAACCTAGCGAAACCCGAC 59.804 52.381 0.00 0.00 41.76 4.79
4030 8640 0.668401 AAACCTAGCGAAACCCGACG 60.668 55.000 0.00 0.00 41.76 5.12
4082 8692 5.606348 TGGTTCTTTTGGTGCAGTTTATT 57.394 34.783 0.00 0.00 0.00 1.40
4089 8699 9.738832 TTCTTTTGGTGCAGTTTATTAGTTTAC 57.261 29.630 0.00 0.00 0.00 2.01
4137 8830 7.131907 AGCCTTTTGTGTTTTATTAACCCTT 57.868 32.000 0.00 0.00 0.00 3.95
4138 8831 7.214381 AGCCTTTTGTGTTTTATTAACCCTTC 58.786 34.615 0.00 0.00 0.00 3.46
4208 8902 7.593825 AGTACATGAACACTTTTCTAATTGCC 58.406 34.615 0.00 0.00 0.00 4.52
4210 8904 4.497473 TGAACACTTTTCTAATTGCCCG 57.503 40.909 0.00 0.00 0.00 6.13
4230 8924 5.449862 GCCCGAGCATTTATAAAACACATGA 60.450 40.000 0.00 0.00 39.53 3.07
4269 8963 9.894783 TGCATGATCAATTTTTAAAAACATTGG 57.105 25.926 15.35 5.91 36.94 3.16
4270 8964 9.896263 GCATGATCAATTTTTAAAAACATTGGT 57.104 25.926 15.35 12.86 36.94 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1205 3291 0.892755 TAGTTAGCCACGGTGGTCAG 59.107 55.000 26.86 3.43 40.46 3.51
1325 3417 2.970639 CGGAGGAGCTTGACGGAA 59.029 61.111 0.00 0.00 0.00 4.30
1485 3577 1.880027 GATGTTGTTGTCCACCCACTC 59.120 52.381 0.00 0.00 0.00 3.51
1531 3623 2.566570 TTGCCGACGAGCAGGTACA 61.567 57.895 10.21 0.00 45.13 2.90
1607 3699 1.361668 CGTGGCGGAGGTTCTTCATG 61.362 60.000 0.00 0.00 0.00 3.07
1859 3951 2.398554 GCTCGCATTGCCCTCGAAA 61.399 57.895 2.41 0.00 0.00 3.46
2096 4188 4.090057 GCTGGCGTGCCGAGTTTC 62.090 66.667 6.37 0.00 39.42 2.78
2137 4229 1.000233 GTACAGCGCGAAGACGAACA 61.000 55.000 12.10 0.00 42.66 3.18
2235 4327 2.358737 CCTGCCGGTGAGGTCAAC 60.359 66.667 12.35 0.00 43.70 3.18
2740 5545 8.998277 ACTATTAAACTCATCACCTAGCTAGA 57.002 34.615 22.70 2.71 0.00 2.43
2790 5597 7.065443 GCCTAATGTACAAACTTACCCAACTAG 59.935 40.741 0.00 0.00 0.00 2.57
2791 5598 6.880529 GCCTAATGTACAAACTTACCCAACTA 59.119 38.462 0.00 0.00 0.00 2.24
2792 5599 5.708697 GCCTAATGTACAAACTTACCCAACT 59.291 40.000 0.00 0.00 0.00 3.16
2798 5605 4.033702 GGCGAGCCTAATGTACAAACTTAC 59.966 45.833 6.90 0.00 0.00 2.34
2835 5674 5.633182 TCTTTTTGCGAATAATTCACAAGCC 59.367 36.000 0.00 0.00 33.73 4.35
2867 5707 7.339212 TCGAGGTGAAATGAAAATACAATCCAT 59.661 33.333 0.00 0.00 0.00 3.41
2870 5710 8.964420 TTTCGAGGTGAAATGAAAATACAATC 57.036 30.769 0.00 0.00 41.59 2.67
4007 8617 0.242825 GGGTTTCGCTAGGTTTTGGC 59.757 55.000 0.00 0.00 0.00 4.52
4008 8618 0.519961 CGGGTTTCGCTAGGTTTTGG 59.480 55.000 0.00 0.00 0.00 3.28
4009 8619 1.196127 GTCGGGTTTCGCTAGGTTTTG 59.804 52.381 0.00 0.00 39.05 2.44
4010 8620 1.516161 GTCGGGTTTCGCTAGGTTTT 58.484 50.000 0.00 0.00 39.05 2.43
4011 8621 0.668401 CGTCGGGTTTCGCTAGGTTT 60.668 55.000 0.00 0.00 39.05 3.27
4012 8622 1.080298 CGTCGGGTTTCGCTAGGTT 60.080 57.895 0.00 0.00 39.05 3.50
4013 8623 2.205243 GACGTCGGGTTTCGCTAGGT 62.205 60.000 0.00 0.00 39.05 3.08
4014 8624 1.515736 GACGTCGGGTTTCGCTAGG 60.516 63.158 0.00 0.00 39.05 3.02
4015 8625 0.387622 TTGACGTCGGGTTTCGCTAG 60.388 55.000 11.62 0.00 39.05 3.42
4016 8626 0.664166 GTTGACGTCGGGTTTCGCTA 60.664 55.000 11.62 0.00 39.05 4.26
4017 8627 1.952635 GTTGACGTCGGGTTTCGCT 60.953 57.895 11.62 0.00 39.05 4.93
4018 8628 2.547798 GTTGACGTCGGGTTTCGC 59.452 61.111 11.62 0.00 39.05 4.70
4019 8629 2.651137 CCGTTGACGTCGGGTTTCG 61.651 63.158 11.62 8.63 43.68 3.46
4020 8630 2.946752 GCCGTTGACGTCGGGTTTC 61.947 63.158 15.06 0.00 46.90 2.78
4021 8631 2.968697 GCCGTTGACGTCGGGTTT 60.969 61.111 15.06 0.00 46.90 3.27
4022 8632 4.974989 GGCCGTTGACGTCGGGTT 62.975 66.667 15.06 0.00 46.90 4.11
4026 8636 3.695022 CTAGGGGCCGTTGACGTCG 62.695 68.421 11.62 0.00 37.74 5.12
4027 8637 2.183555 CTAGGGGCCGTTGACGTC 59.816 66.667 9.11 9.11 37.74 4.34
4028 8638 3.387947 CCTAGGGGCCGTTGACGT 61.388 66.667 3.09 0.00 37.74 4.34
4029 8639 4.157120 CCCTAGGGGCCGTTGACG 62.157 72.222 21.44 0.00 35.35 4.35
4055 8665 3.513515 ACTGCACCAAAAGAACCAAAAGA 59.486 39.130 0.00 0.00 0.00 2.52
4056 8666 3.860641 ACTGCACCAAAAGAACCAAAAG 58.139 40.909 0.00 0.00 0.00 2.27
4060 8670 5.606348 AATAAACTGCACCAAAAGAACCA 57.394 34.783 0.00 0.00 0.00 3.67
4062 8672 8.642908 AAACTAATAAACTGCACCAAAAGAAC 57.357 30.769 0.00 0.00 0.00 3.01
4082 8692 8.999905 AAACCTGGTTCCAAAATAGTAAACTA 57.000 30.769 13.36 0.00 0.00 2.24
4089 8699 9.366216 GCTAAATAAAACCTGGTTCCAAAATAG 57.634 33.333 13.36 11.85 0.00 1.73
4095 8705 5.005628 AGGCTAAATAAAACCTGGTTCCA 57.994 39.130 13.36 4.00 0.00 3.53
4096 8706 5.995565 AAGGCTAAATAAAACCTGGTTCC 57.004 39.130 13.36 7.04 31.32 3.62
4097 8707 7.170828 CACAAAAGGCTAAATAAAACCTGGTTC 59.829 37.037 13.36 0.00 31.32 3.62
4101 8794 8.432110 AAACACAAAAGGCTAAATAAAACCTG 57.568 30.769 0.00 0.00 31.32 4.00
4111 8804 8.252624 AGGGTTAATAAAACACAAAAGGCTAA 57.747 30.769 0.00 0.00 0.00 3.09
4184 8878 6.806739 GGGCAATTAGAAAAGTGTTCATGTAC 59.193 38.462 0.00 0.00 33.27 2.90
4186 8880 5.564651 CGGGCAATTAGAAAAGTGTTCATGT 60.565 40.000 0.00 0.00 33.27 3.21
4208 8902 6.468956 GTGTCATGTGTTTTATAAATGCTCGG 59.531 38.462 0.00 0.00 0.00 4.63
4210 8904 8.970691 AAGTGTCATGTGTTTTATAAATGCTC 57.029 30.769 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.