Multiple sequence alignment - TraesCS4B01G303400

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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 TraesCS4B01G303400 chr4B 100.000 2480 0 0 1 2480 591235039 591232560 0.000000e+00 4580.0
1 TraesCS4B01G303400 chr4B 89.506 991 78 13 1501 2473 139202187 139201205 0.000000e+00 1230.0
2 TraesCS4B01G303400 chr4A 94.478 1503 82 1 1 1502 486299631 486298129 0.000000e+00 2314.0
3 TraesCS4B01G303400 chr6D 94.212 1503 80 5 1 1502 128082526 128084022 0.000000e+00 2287.0
4 TraesCS4B01G303400 chr6D 89.831 59 6 0 1323 1381 359233158 359233216 2.640000e-10 76.8
5 TraesCS4B01G303400 chr2D 91.012 1502 135 0 1 1502 531631182 531629681 0.000000e+00 2026.0
6 TraesCS4B01G303400 chr6A 91.012 1502 133 2 1 1502 180929561 180928062 0.000000e+00 2025.0
7 TraesCS4B01G303400 chr5A 90.479 1502 142 1 1 1502 122126473 122127973 0.000000e+00 1980.0
8 TraesCS4B01G303400 chr5A 86.436 1504 200 4 1 1503 584030327 584031827 0.000000e+00 1644.0
9 TraesCS4B01G303400 chr6B 90.466 1353 126 2 1 1351 546087718 546086367 0.000000e+00 1781.0
10 TraesCS4B01G303400 chr6B 89.178 961 91 9 1501 2452 313934831 313933875 0.000000e+00 1186.0
11 TraesCS4B01G303400 chr6B 88.218 993 94 12 1501 2479 570737462 570738445 0.000000e+00 1164.0
12 TraesCS4B01G303400 chr6B 77.230 1502 299 31 24 1505 452147791 452146313 0.000000e+00 839.0
13 TraesCS4B01G303400 chr5D 94.920 1122 53 4 1 1122 511890220 511889103 0.000000e+00 1753.0
14 TraesCS4B01G303400 chr1D 94.278 1101 62 1 345 1445 74292546 74293645 0.000000e+00 1683.0
15 TraesCS4B01G303400 chr2B 85.960 1510 187 11 1 1507 183306953 183308440 0.000000e+00 1591.0
16 TraesCS4B01G303400 chr2B 84.289 1012 109 32 1499 2480 696264333 696263342 0.000000e+00 942.0
17 TraesCS4B01G303400 chr2B 84.600 974 114 27 1511 2460 98096853 98095892 0.000000e+00 935.0
18 TraesCS4B01G303400 chr2B 81.883 977 143 24 1501 2452 231924093 231925060 0.000000e+00 793.0
19 TraesCS4B01G303400 chr2B 83.582 469 53 13 2030 2480 161869384 161869846 3.810000e-113 418.0
20 TraesCS4B01G303400 chr2B 89.177 231 22 3 1502 1731 50072644 50072872 4.040000e-73 285.0
21 TraesCS4B01G303400 chr2B 82.143 308 41 9 1503 1802 270181346 270181045 4.090000e-63 252.0
22 TraesCS4B01G303400 chr7B 89.126 984 81 18 1504 2472 184700433 184699461 0.000000e+00 1201.0
23 TraesCS4B01G303400 chr7B 86.939 980 103 17 1501 2460 402082657 402083631 0.000000e+00 1077.0
24 TraesCS4B01G303400 chr3B 88.810 992 92 10 1501 2479 494256172 494257157 0.000000e+00 1199.0
25 TraesCS4B01G303400 chr1B 89.215 955 88 12 1516 2460 599074622 599075571 0.000000e+00 1179.0
26 TraesCS4B01G303400 chr1B 88.634 959 92 10 1511 2460 599065316 599066266 0.000000e+00 1151.0
27 TraesCS4B01G303400 chr1B 94.346 566 30 2 941 1506 685662331 685662894 0.000000e+00 867.0
28 TraesCS4B01G303400 chr5B 89.858 562 48 5 1 555 254507848 254508407 0.000000e+00 713.0
29 TraesCS4B01G303400 chr4D 77.974 622 117 16 885 1502 336832659 336832054 3.010000e-99 372.0


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 TraesCS4B01G303400 chr4B 591232560 591235039 2479 True 4580 4580 100.000 1 2480 1 chr4B.!!$R2 2479
1 TraesCS4B01G303400 chr4B 139201205 139202187 982 True 1230 1230 89.506 1501 2473 1 chr4B.!!$R1 972
2 TraesCS4B01G303400 chr4A 486298129 486299631 1502 True 2314 2314 94.478 1 1502 1 chr4A.!!$R1 1501
3 TraesCS4B01G303400 chr6D 128082526 128084022 1496 False 2287 2287 94.212 1 1502 1 chr6D.!!$F1 1501
4 TraesCS4B01G303400 chr2D 531629681 531631182 1501 True 2026 2026 91.012 1 1502 1 chr2D.!!$R1 1501
5 TraesCS4B01G303400 chr6A 180928062 180929561 1499 True 2025 2025 91.012 1 1502 1 chr6A.!!$R1 1501
6 TraesCS4B01G303400 chr5A 122126473 122127973 1500 False 1980 1980 90.479 1 1502 1 chr5A.!!$F1 1501
7 TraesCS4B01G303400 chr5A 584030327 584031827 1500 False 1644 1644 86.436 1 1503 1 chr5A.!!$F2 1502
8 TraesCS4B01G303400 chr6B 546086367 546087718 1351 True 1781 1781 90.466 1 1351 1 chr6B.!!$R3 1350
9 TraesCS4B01G303400 chr6B 313933875 313934831 956 True 1186 1186 89.178 1501 2452 1 chr6B.!!$R1 951
10 TraesCS4B01G303400 chr6B 570737462 570738445 983 False 1164 1164 88.218 1501 2479 1 chr6B.!!$F1 978
11 TraesCS4B01G303400 chr6B 452146313 452147791 1478 True 839 839 77.230 24 1505 1 chr6B.!!$R2 1481
12 TraesCS4B01G303400 chr5D 511889103 511890220 1117 True 1753 1753 94.920 1 1122 1 chr5D.!!$R1 1121
13 TraesCS4B01G303400 chr1D 74292546 74293645 1099 False 1683 1683 94.278 345 1445 1 chr1D.!!$F1 1100
14 TraesCS4B01G303400 chr2B 183306953 183308440 1487 False 1591 1591 85.960 1 1507 1 chr2B.!!$F3 1506
15 TraesCS4B01G303400 chr2B 696263342 696264333 991 True 942 942 84.289 1499 2480 1 chr2B.!!$R3 981
16 TraesCS4B01G303400 chr2B 98095892 98096853 961 True 935 935 84.600 1511 2460 1 chr2B.!!$R1 949
17 TraesCS4B01G303400 chr2B 231924093 231925060 967 False 793 793 81.883 1501 2452 1 chr2B.!!$F4 951
18 TraesCS4B01G303400 chr7B 184699461 184700433 972 True 1201 1201 89.126 1504 2472 1 chr7B.!!$R1 968
19 TraesCS4B01G303400 chr7B 402082657 402083631 974 False 1077 1077 86.939 1501 2460 1 chr7B.!!$F1 959
20 TraesCS4B01G303400 chr3B 494256172 494257157 985 False 1199 1199 88.810 1501 2479 1 chr3B.!!$F1 978
21 TraesCS4B01G303400 chr1B 599074622 599075571 949 False 1179 1179 89.215 1516 2460 1 chr1B.!!$F2 944
22 TraesCS4B01G303400 chr1B 599065316 599066266 950 False 1151 1151 88.634 1511 2460 1 chr1B.!!$F1 949
23 TraesCS4B01G303400 chr1B 685662331 685662894 563 False 867 867 94.346 941 1506 1 chr1B.!!$F3 565
24 TraesCS4B01G303400 chr5B 254507848 254508407 559 False 713 713 89.858 1 555 1 chr5B.!!$F1 554
25 TraesCS4B01G303400 chr4D 336832054 336832659 605 True 372 372 77.974 885 1502 1 chr4D.!!$R1 617

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
117 120 0.606604 TGGCGGGACTAAACTCACTC 59.393 55.000 0.0 0.0 0.0 3.51 F
962 993 1.338674 TGTTAATGCACACTCCCCTCG 60.339 52.381 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1174 1205 0.316204 CCTGCCTTTTGTGCAAGGAG 59.684 55.0 6.34 1.46 45.79 3.69 R
2288 2373 0.035598 TTCCGGCGAATCTTTCCACA 59.964 50.0 9.30 0.00 0.00 4.17 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
106 108 1.607148 GGCAAAGTATTATGGCGGGAC 59.393 52.381 0.00 0.00 32.19 4.46
117 120 0.606604 TGGCGGGACTAAACTCACTC 59.393 55.000 0.00 0.00 0.00 3.51
303 307 6.205784 TGAAGATTTGGTGAATCAAACGTTC 58.794 36.000 0.00 0.00 45.42 3.95
349 358 1.531748 GCAATTCCCCTCCCGATGA 59.468 57.895 0.00 0.00 0.00 2.92
538 552 2.882137 TCTTGTCCGGCAAAGGTTAAAG 59.118 45.455 13.91 1.34 36.53 1.85
539 553 1.611519 TGTCCGGCAAAGGTTAAAGG 58.388 50.000 0.00 0.00 0.00 3.11
641 668 1.699054 CCATCATGCTCGAAGGGGGA 61.699 60.000 0.00 0.00 0.00 4.81
650 677 2.635427 GCTCGAAGGGGGAAGAAGATAT 59.365 50.000 0.00 0.00 0.00 1.63
655 682 7.202972 TCGAAGGGGGAAGAAGATATAAAAA 57.797 36.000 0.00 0.00 0.00 1.94
879 907 3.864003 GGGATAGACGCAAACTAGTTCAC 59.136 47.826 8.95 3.19 0.00 3.18
880 908 4.381718 GGGATAGACGCAAACTAGTTCACT 60.382 45.833 8.95 6.85 0.00 3.41
962 993 1.338674 TGTTAATGCACACTCCCCTCG 60.339 52.381 0.00 0.00 0.00 4.63
1009 1040 4.508584 GGACAAGACCTCCTATGGGTTTTT 60.509 45.833 0.00 0.00 37.17 1.94
1174 1205 3.560636 TGGCTCTTAGATTTGGCCTAC 57.439 47.619 3.32 0.00 42.84 3.18
1191 1222 2.229792 CTACTCCTTGCACAAAAGGCA 58.770 47.619 0.00 0.00 45.49 4.75
1227 1258 9.016623 CGTCTTGTCGTTAATTCTGATAATACA 57.983 33.333 0.00 0.00 0.00 2.29
1440 1472 2.488153 GCCTTTGAGGGACATTGTACAC 59.512 50.000 0.57 0.00 35.37 2.90
1450 1482 9.038072 TGAGGGACATTGTACACTTACTTATTA 57.962 33.333 0.57 0.00 0.00 0.98
1694 1738 5.185056 ACTTAGCCAACAGTTGTTCAAGTTT 59.815 36.000 12.42 0.00 35.83 2.66
1705 1749 8.962679 ACAGTTGTTCAAGTTTAATTAAGTCCA 58.037 29.630 0.00 0.00 0.00 4.02
1786 1832 4.517832 GCATGAGCATGGATCAACATAAGA 59.482 41.667 12.00 0.00 41.58 2.10
1788 1834 6.669278 CATGAGCATGGATCAACATAAGAAG 58.331 40.000 2.54 0.00 35.24 2.85
1792 1838 4.889409 GCATGGATCAACATAAGAAGGGAA 59.111 41.667 0.00 0.00 0.00 3.97
1880 1938 5.408299 GCATGAACATCACAAGTACACTACA 59.592 40.000 0.00 0.00 0.00 2.74
1892 1950 9.856488 CACAAGTACACTACATAGAAACATAGT 57.144 33.333 0.00 0.00 0.00 2.12
1973 2031 5.105797 TGCAAGCATTTAACCAACTAGATGG 60.106 40.000 17.02 17.02 46.38 3.51
2048 2106 2.159198 GGCCATCACCAACATCAACATC 60.159 50.000 0.00 0.00 0.00 3.06
2099 2179 9.933723 GAAAGGAAATACTAACAGGTAGTACAA 57.066 33.333 7.56 0.00 45.93 2.41
2100 2180 9.939802 AAAGGAAATACTAACAGGTAGTACAAG 57.060 33.333 7.56 0.00 45.93 3.16
2101 2181 8.661752 AGGAAATACTAACAGGTAGTACAAGT 57.338 34.615 7.56 0.00 45.93 3.16
2145 2228 1.656652 CAACTCTAAGCATCACCGGG 58.343 55.000 6.32 0.00 0.00 5.73
2283 2368 4.452733 CCGGGGAGAAGTGCGGAC 62.453 72.222 0.00 0.00 0.00 4.79
2284 2369 4.796231 CGGGGAGAAGTGCGGACG 62.796 72.222 0.00 0.00 0.00 4.79
2288 2373 1.218316 GGAGAAGTGCGGACGGATT 59.782 57.895 0.00 0.00 0.00 3.01
2342 2428 1.677633 GGGGGCTGTTTACGTGCAT 60.678 57.895 0.00 0.00 0.00 3.96
2383 2471 6.734137 TCAGAATGTTAACACATGGTGAAAC 58.266 36.000 11.22 7.65 43.34 2.78
2428 2516 2.030946 CGAGATGAAGAAATGGGCGTTC 59.969 50.000 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 79 6.809196 CGCCATAATACTTTGCCAAGTAAAAA 59.191 34.615 13.80 4.02 46.45 1.94
117 120 4.340950 ACCCGCCAGATATAACCATTTTTG 59.659 41.667 0.00 0.00 0.00 2.44
175 179 1.676916 CGCACAGTTCAGGATCCATGT 60.677 52.381 15.82 7.57 0.00 3.21
349 358 9.976511 CCAAGCAATGAAATCTGACATATTATT 57.023 29.630 0.00 0.00 0.00 1.40
436 449 5.731599 TGTTGCAATTTTGTTCCATGTTC 57.268 34.783 0.59 0.00 0.00 3.18
538 552 1.737793 CAAGGTACGCCAGATGAAACC 59.262 52.381 0.00 0.00 37.19 3.27
539 553 1.130561 GCAAGGTACGCCAGATGAAAC 59.869 52.381 0.00 0.00 37.19 2.78
655 682 7.714377 TGCCTTTTGACACATGAATAAAATGTT 59.286 29.630 0.00 0.00 36.10 2.71
759 786 7.769044 TCTGGCATAAGTAGTAAGAATTCCAAC 59.231 37.037 0.65 0.58 0.00 3.77
843 871 4.261909 CGTCTATCCCACCATAAGTACCAC 60.262 50.000 0.00 0.00 0.00 4.16
879 907 6.642540 GGTTTGCATCTTGAAACTTTCCTTAG 59.357 38.462 0.00 0.00 33.41 2.18
880 908 6.097554 TGGTTTGCATCTTGAAACTTTCCTTA 59.902 34.615 0.00 0.00 33.41 2.69
962 993 3.454812 TCCTCCTGATTTAGTAGTTGCCC 59.545 47.826 0.00 0.00 0.00 5.36
1009 1040 5.509498 AGAGGCATCACCATTAAGCTTAAA 58.491 37.500 22.13 6.51 43.14 1.52
1022 1053 4.077300 TCATGGTCATAAGAGGCATCAC 57.923 45.455 0.00 0.00 0.00 3.06
1174 1205 0.316204 CCTGCCTTTTGTGCAAGGAG 59.684 55.000 6.34 1.46 45.79 3.69
1191 1222 1.148310 CGACAAGACGATTGCAACCT 58.852 50.000 0.00 0.00 35.09 3.50
1227 1258 9.452287 CCATTTTCCATTATTTCAATCACCTTT 57.548 29.630 0.00 0.00 0.00 3.11
1310 1341 6.611381 TCAAATCTAACAAGCGGAAAATCAG 58.389 36.000 0.00 0.00 0.00 2.90
1392 1423 7.453752 TCCTCAAACCAGTCAGTAGTAACTAAT 59.546 37.037 0.00 0.00 33.48 1.73
1601 1633 0.910338 GGAAGGTCCTAACTGGGTCC 59.090 60.000 0.00 0.00 36.20 4.46
1673 1717 6.761099 TTAAACTTGAACAACTGTTGGCTA 57.239 33.333 23.15 11.30 38.56 3.93
1705 1749 7.885297 TCAGCTTATTGCATTCAAGTTTAACT 58.115 30.769 0.00 0.00 45.94 2.24
1774 1819 4.943705 TGCACTTCCCTTCTTATGTTGATC 59.056 41.667 0.00 0.00 0.00 2.92
1786 1832 4.892934 TGTTAAGAATGTTGCACTTCCCTT 59.107 37.500 0.00 0.00 0.00 3.95
1788 1834 4.846779 TGTTAAGAATGTTGCACTTCCC 57.153 40.909 0.00 0.00 0.00 3.97
1792 1838 6.016360 TGTTGCTATGTTAAGAATGTTGCACT 60.016 34.615 0.00 0.00 0.00 4.40
1880 1938 8.693120 TGCTAGTAGTGCTACTATGTTTCTAT 57.307 34.615 16.60 0.00 44.76 1.98
1892 1950 4.944619 ATTGCTGATGCTAGTAGTGCTA 57.055 40.909 0.00 0.00 40.48 3.49
1895 1953 9.428097 TGATATTTATTGCTGATGCTAGTAGTG 57.572 33.333 0.00 0.00 40.48 2.74
1973 2031 4.104776 CCGTTGTTATGCATGTTCCATTC 58.895 43.478 10.16 0.00 0.00 2.67
2016 2074 0.463654 GTGATGGCCTTCGGTGCATA 60.464 55.000 13.54 0.00 0.00 3.14
2048 2106 9.914131 TCATATGTTTATGCTTGCTAGTAGTAG 57.086 33.333 1.90 0.00 36.03 2.57
2087 2145 7.095270 GTGCTATGTTTACTTGTACTACCTGT 58.905 38.462 0.00 0.00 0.00 4.00
2099 2179 7.197071 TGTTCATTTTCGTGCTATGTTTACT 57.803 32.000 0.00 0.00 0.00 2.24
2100 2180 7.461416 GCATGTTCATTTTCGTGCTATGTTTAC 60.461 37.037 0.00 0.00 41.56 2.01
2101 2181 6.526325 GCATGTTCATTTTCGTGCTATGTTTA 59.474 34.615 0.00 0.00 41.56 2.01
2145 2228 8.958175 TTGTTGAAAATATGGTTATCGTTGTC 57.042 30.769 0.00 0.00 0.00 3.18
2233 2316 0.611618 CCCAGGCAAGCCACAATACA 60.612 55.000 14.40 0.00 38.92 2.29
2283 2368 1.064060 GGCGAATCTTTCCACAATCCG 59.936 52.381 0.00 0.00 0.00 4.18
2284 2369 1.064060 CGGCGAATCTTTCCACAATCC 59.936 52.381 0.00 0.00 0.00 3.01
2288 2373 0.035598 TTCCGGCGAATCTTTCCACA 59.964 50.000 9.30 0.00 0.00 4.17
2383 2471 1.066143 AGCCCGTTCTATTGGTCACAG 60.066 52.381 0.00 0.00 0.00 3.66
2406 2494 1.207089 ACGCCCATTTCTTCATCTCGA 59.793 47.619 0.00 0.00 0.00 4.04
2428 2516 4.032900 CGTAACTCCAAATGAGGTGAATCG 59.967 45.833 0.00 0.00 42.46 3.34


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

AutoCloner maintained by Alex Coulton.