Multiple sequence alignment - TraesCS4B01G117100

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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 TraesCS4B01G117100 chr4B 100.000 3027 0 0 1 3027 135210405 135213431 0.000000e+00 5590.0
1 TraesCS4B01G117100 chr4B 95.882 170 5 1 504 671 211593425 211593256 1.070000e-69 274.0
2 TraesCS4B01G117100 chr4B 95.882 170 5 1 504 671 286753629 286753460 1.070000e-69 274.0
3 TraesCS4B01G117100 chr4A 96.036 2775 75 12 285 3027 483952130 483949359 0.000000e+00 4482.0
4 TraesCS4B01G117100 chr4A 98.616 289 4 0 1 289 483952456 483952168 2.080000e-141 512.0
5 TraesCS4B01G117100 chr4A 92.793 222 13 1 859 1077 373804806 373805027 4.870000e-83 318.0
6 TraesCS4B01G117100 chr4A 92.793 222 13 1 859 1077 606355196 606355417 4.870000e-83 318.0
7 TraesCS4B01G117100 chr4A 97.619 168 4 0 504 671 624286536 624286703 3.820000e-74 289.0
8 TraesCS4B01G117100 chr4D 94.946 2770 73 18 288 3027 95780388 95783120 0.000000e+00 4277.0
9 TraesCS4B01G117100 chr4D 97.938 291 1 3 1 289 95780051 95780338 1.620000e-137 499.0
10 TraesCS4B01G117100 chr5A 83.502 594 68 21 853 1428 282588085 282587504 7.430000e-146 527.0
11 TraesCS4B01G117100 chr5A 92.793 222 13 1 859 1077 598933355 598933576 4.870000e-83 318.0
12 TraesCS4B01G117100 chr2A 79.630 810 99 45 854 1637 706995025 706995794 3.460000e-144 521.0
13 TraesCS4B01G117100 chr2A 78.529 340 65 7 1093 1428 645311418 645311753 1.830000e-52 217.0
14 TraesCS4B01G117100 chr5D 79.872 780 101 37 680 1428 214919998 214919244 1.240000e-143 520.0
15 TraesCS4B01G117100 chr5B 83.025 595 70 22 853 1428 230248676 230248094 7.490000e-141 510.0
16 TraesCS4B01G117100 chr5B 95.882 170 5 1 504 671 36727182 36727351 1.070000e-69 274.0
17 TraesCS4B01G117100 chr5B 100.000 33 0 0 504 536 573176983 573176951 9.060000e-06 62.1
18 TraesCS4B01G117100 chr2D 82.333 600 73 23 854 1428 567477118 567477709 9.750000e-135 490.0
19 TraesCS4B01G117100 chr2B 86.897 435 46 7 1001 1428 680193945 680194375 7.590000e-131 477.0
20 TraesCS4B01G117100 chr2B 91.860 86 5 2 764 849 141003017 141003100 5.300000e-23 119.0
21 TraesCS4B01G117100 chr1D 95.909 220 8 1 537 756 12646754 12646536 3.710000e-94 355.0
22 TraesCS4B01G117100 chr1D 90.698 86 6 2 764 849 185107795 185107878 2.470000e-21 113.0
23 TraesCS4B01G117100 chr6B 94.170 223 9 2 859 1077 60485158 60484936 1.340000e-88 337.0
24 TraesCS4B01G117100 chr7D 93.722 223 11 1 859 1078 548559393 548559615 6.260000e-87 331.0
25 TraesCS4B01G117100 chr1B 92.793 222 13 1 859 1077 258836430 258836651 4.870000e-83 318.0
26 TraesCS4B01G117100 chr7A 96.471 170 4 1 504 671 169392764 169392933 2.300000e-71 279.0
27 TraesCS4B01G117100 chr3B 96.471 170 4 1 504 671 327795860 327795691 2.300000e-71 279.0


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 TraesCS4B01G117100 chr4B 135210405 135213431 3026 False 5590 5590 100.000 1 3027 1 chr4B.!!$F1 3026
1 TraesCS4B01G117100 chr4A 483949359 483952456 3097 True 2497 4482 97.326 1 3027 2 chr4A.!!$R1 3026
2 TraesCS4B01G117100 chr4D 95780051 95783120 3069 False 2388 4277 96.442 1 3027 2 chr4D.!!$F1 3026
3 TraesCS4B01G117100 chr5A 282587504 282588085 581 True 527 527 83.502 853 1428 1 chr5A.!!$R1 575
4 TraesCS4B01G117100 chr2A 706995025 706995794 769 False 521 521 79.630 854 1637 1 chr2A.!!$F2 783
5 TraesCS4B01G117100 chr5D 214919244 214919998 754 True 520 520 79.872 680 1428 1 chr5D.!!$R1 748
6 TraesCS4B01G117100 chr5B 230248094 230248676 582 True 510 510 83.025 853 1428 1 chr5B.!!$R1 575
7 TraesCS4B01G117100 chr2D 567477118 567477709 591 False 490 490 82.333 854 1428 1 chr2D.!!$F1 574

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
193 194 0.249120 AAATGTCACATCCGGCGAGA 59.751 50.0 9.3 4.16 0.0 4.04 F
1617 1730 0.108945 CAGCAGAGCACGATCACAGA 60.109 55.0 0.0 0.00 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 2120 0.606401 CGAACTGCCCCTGTCATGTT 60.606 55.0 0.0 0.0 0.0 2.71 R
2591 2726 0.324943 TCCTTGCACCTCTAGTTGGC 59.675 55.0 0.0 0.0 0.0 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
193 194 0.249120 AAATGTCACATCCGGCGAGA 59.751 50.000 9.30 4.16 0.00 4.04
260 261 1.122632 TTCCAAGCGGACCACAGGTA 61.123 55.000 0.00 0.00 42.67 3.08
302 354 6.984474 TCTGCCAAATTACTACTACTACATGC 59.016 38.462 0.00 0.00 0.00 4.06
330 382 6.521162 TCAGTTGAAAGTGCACAGTAGAATA 58.479 36.000 21.04 0.00 0.00 1.75
348 400 8.371699 AGTAGAATAGACTCTTATTGGCAATCC 58.628 37.037 17.41 0.79 0.00 3.01
624 676 5.451242 GCAGCTAGCTAGACACTGAAACTAT 60.451 44.000 25.15 0.00 41.15 2.12
818 870 6.205658 GCCCTCATGTACCAGAGAAAATATTC 59.794 42.308 11.93 0.00 33.74 1.75
969 1065 1.455402 TTGCCACAGCCAGCAAGAA 60.455 52.632 0.00 0.00 43.74 2.52
1233 1343 2.759795 GGCCTGCTCCTGTCCTTT 59.240 61.111 0.00 0.00 0.00 3.11
1508 1621 2.686835 GAGTCCCAGGGAGCAGCT 60.687 66.667 9.15 1.31 29.39 4.24
1513 1626 4.031129 CCAGGGAGCAGCTGCAGT 62.031 66.667 38.24 21.10 45.16 4.40
1533 1646 4.435970 CAGCAGCCATGGAGCCCA 62.436 66.667 18.40 0.00 38.19 5.36
1557 1670 1.150567 GCTACAGCACATCCAGCTCG 61.151 60.000 0.00 0.00 41.14 5.03
1617 1730 0.108945 CAGCAGAGCACGATCACAGA 60.109 55.000 0.00 0.00 0.00 3.41
1673 1786 5.818136 TGAACTGAGGAACAAAACAAGAG 57.182 39.130 0.00 0.00 0.00 2.85
1912 2025 1.752198 CCGTGTCTCCAGTTCCCAA 59.248 57.895 0.00 0.00 0.00 4.12
1913 2026 0.324943 CCGTGTCTCCAGTTCCCAAT 59.675 55.000 0.00 0.00 0.00 3.16
1937 2050 5.489792 ACTGGTCAGTACTGAAACATCAT 57.510 39.130 26.74 13.61 41.85 2.45
1958 2074 3.163630 TGAGTTGAATCATCGATCGCA 57.836 42.857 11.09 0.00 0.00 5.10
2023 2141 0.606401 AACATGACAGGGGCAGTTCG 60.606 55.000 0.00 0.00 0.00 3.95
2025 2143 0.249120 CATGACAGGGGCAGTTCGTA 59.751 55.000 0.00 0.00 0.00 3.43
2052 2170 0.665298 TGACGAGGAGATCTGATGCG 59.335 55.000 0.00 0.88 0.00 4.73
2143 2261 2.290260 ACTACTGCTGCTATGCACCAAA 60.290 45.455 0.00 0.00 38.12 3.28
2350 2476 2.262266 AAAAGAGAGGGGGAGAGAGG 57.738 55.000 0.00 0.00 0.00 3.69
2360 2486 0.260523 GGGAGAGAGGGCTAGACAGT 59.739 60.000 0.00 0.00 0.00 3.55
2564 2699 5.066764 GGTGGTGTAACTGCTTTCACTTTTA 59.933 40.000 0.00 0.00 36.74 1.52
2591 2726 4.397103 TCAATAGGCTCAATGCTTTCACTG 59.603 41.667 0.00 0.00 42.39 3.66
2614 2749 4.687219 GCCAACTAGAGGTGCAAGGATTAT 60.687 45.833 0.00 0.00 0.00 1.28
2617 2752 5.283457 ACTAGAGGTGCAAGGATTATGTC 57.717 43.478 0.00 0.00 0.00 3.06
2765 2903 6.374333 TGGAAACATAGCCACTCTAACAATTC 59.626 38.462 0.00 0.00 33.40 2.17
2797 2935 5.240403 GGAAAATTTAGCAAATGCCCAACAA 59.760 36.000 0.94 0.00 43.38 2.83
2799 2937 6.897706 AAATTTAGCAAATGCCCAACAATT 57.102 29.167 0.94 0.00 43.38 2.32
2941 3079 0.106769 TGCAAGTGGGCTCAGTTTCA 60.107 50.000 3.16 2.54 34.53 2.69
2990 3128 3.263170 TGGCTAAGCTGATGGTCTAACAA 59.737 43.478 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
193 194 1.671742 CGTCTTGGTACTGCCTGGT 59.328 57.895 0.00 0.00 38.35 4.00
297 349 4.520111 TGCACTTTCAACTGAATAGCATGT 59.480 37.500 8.83 0.00 33.62 3.21
302 354 5.679734 ACTGTGCACTTTCAACTGAATAG 57.320 39.130 19.41 4.41 33.54 1.73
357 409 1.894978 GCCTCCCATTTTTACCTGGCA 60.895 52.381 0.00 0.00 38.99 4.92
424 476 5.196695 GTCATTAGCTTCCCATTTCCTCTT 58.803 41.667 0.00 0.00 0.00 2.85
624 676 6.670695 TGCTGATGCTGAGGTTAGAATATA 57.329 37.500 0.00 0.00 40.48 0.86
749 801 3.845781 TTGATCTTGGAGGGAGCATAC 57.154 47.619 0.00 0.00 0.00 2.39
818 870 0.748450 GGGTGCCCATGTGATGAATG 59.252 55.000 1.66 0.00 35.81 2.67
960 1052 1.878953 ACGTGTTAGGTTCTTGCTGG 58.121 50.000 0.00 0.00 0.00 4.85
969 1065 1.212441 TGGGTGGAAAACGTGTTAGGT 59.788 47.619 0.00 0.00 0.00 3.08
1107 1211 0.678048 GCGTCAGGGCCTTCTCAAAT 60.678 55.000 1.32 0.00 0.00 2.32
1513 1626 2.591753 GCTCCATGGCTGCTGGTA 59.408 61.111 18.35 0.00 35.19 3.25
1557 1670 2.205843 GGCCGGGCTAGTAGGGTAC 61.206 68.421 22.87 0.00 0.00 3.34
1673 1786 6.197842 CGTTAGAGGTATGAAATGGTAACGTC 59.802 42.308 0.00 0.00 37.68 4.34
1912 2025 7.004555 TGATGTTTCAGTACTGACCAGTTAT 57.995 36.000 25.13 13.08 42.54 1.89
1913 2026 6.413783 TGATGTTTCAGTACTGACCAGTTA 57.586 37.500 25.13 6.83 42.54 2.24
1937 2050 3.520569 TGCGATCGATGATTCAACTCAA 58.479 40.909 21.57 0.00 0.00 3.02
1958 2074 9.461312 TTTCAGAATTATATGTGGCTACTTGTT 57.539 29.630 0.64 0.00 0.00 2.83
2004 2120 0.606401 CGAACTGCCCCTGTCATGTT 60.606 55.000 0.00 0.00 0.00 2.71
2023 2141 6.038825 TCAGATCTCCTCGTCATCTTCTTTAC 59.961 42.308 0.00 0.00 0.00 2.01
2025 2143 4.952957 TCAGATCTCCTCGTCATCTTCTTT 59.047 41.667 0.00 0.00 0.00 2.52
2143 2261 2.819608 CGGGTCAATTCAAACCTGTCAT 59.180 45.455 2.96 0.00 37.19 3.06
2350 2476 2.442413 AGTCTGTCTCACTGTCTAGCC 58.558 52.381 0.00 0.00 0.00 3.93
2360 2486 8.190784 CACATATACATACACAAGTCTGTCTCA 58.809 37.037 0.00 0.00 36.58 3.27
2382 2508 3.244318 TGAAGCACTCAGACATGACACAT 60.244 43.478 0.00 0.00 0.00 3.21
2383 2509 2.102925 TGAAGCACTCAGACATGACACA 59.897 45.455 0.00 0.00 0.00 3.72
2591 2726 0.324943 TCCTTGCACCTCTAGTTGGC 59.675 55.000 0.00 0.00 0.00 4.52
2614 2749 6.795098 AAAGTAACAGAATACATTGCGACA 57.205 33.333 0.00 0.00 0.00 4.35
2617 2752 9.988350 AGATTTAAAGTAACAGAATACATTGCG 57.012 29.630 0.00 0.00 0.00 4.85
2765 2903 7.245604 GCATTTGCTAAATTTTCCTTTCATGG 58.754 34.615 0.00 0.00 38.21 3.66
2941 3079 7.556635 GCCTTTTGTTTCAGTATCCTATTAGGT 59.443 37.037 9.57 0.59 36.53 3.08
2990 3128 0.546122 TTGTGTCTGGACTTGGTGCT 59.454 50.000 2.38 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.