Multiple sequence alignment - TraesCS7D01G508300

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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 TraesCS7D01G508300 chr7D 100.000 4187 0 0 1 4187 611858188 611854002 0.000000e+00 7733.0
1 TraesCS7D01G508300 chr7D 93.339 3678 163 23 527 4186 612286605 612290218 0.000000e+00 5360.0
2 TraesCS7D01G508300 chr7D 88.329 2956 235 62 1012 3923 611871167 611868278 0.000000e+00 3446.0
3 TraesCS7D01G508300 chr7D 84.274 1895 212 49 520 2351 612325653 612327524 0.000000e+00 1770.0
4 TraesCS7D01G508300 chr7D 81.986 1571 161 66 2403 3923 612327527 612329025 0.000000e+00 1221.0
5 TraesCS7D01G508300 chr7D 79.841 1766 276 41 601 2307 612403627 612405371 0.000000e+00 1216.0
6 TraesCS7D01G508300 chr7D 80.712 1602 219 42 662 2219 595346729 595348284 0.000000e+00 1164.0
7 TraesCS7D01G508300 chr7D 91.636 538 45 0 1 538 612284669 612285206 0.000000e+00 745.0
8 TraesCS7D01G508300 chr7D 81.868 921 132 21 1371 2281 595348304 595349199 0.000000e+00 743.0
9 TraesCS7D01G508300 chr7D 82.480 371 46 11 3242 3604 612430075 612430434 1.460000e-79 307.0
10 TraesCS7D01G508300 chr7D 83.417 199 20 6 3542 3735 595350072 595350262 5.570000e-39 172.0
11 TraesCS7D01G508300 chr7D 91.489 94 6 2 3945 4037 595350540 595350632 1.220000e-25 128.0
12 TraesCS7D01G508300 chr7A 95.743 3195 110 11 1010 4186 702237701 702240887 0.000000e+00 5123.0
13 TraesCS7D01G508300 chr7A 82.793 3516 387 126 520 3922 702407298 702410708 0.000000e+00 2940.0
14 TraesCS7D01G508300 chr7A 81.850 1697 227 34 662 2305 688345399 688347067 0.000000e+00 1352.0
15 TraesCS7D01G508300 chr7A 90.798 652 56 4 1 651 702237053 702237701 0.000000e+00 869.0
16 TraesCS7D01G508300 chr7A 85.776 464 60 5 3165 3625 702620622 702621082 1.750000e-133 486.0
17 TraesCS7D01G508300 chr7A 82.571 459 54 16 3285 3735 688347698 688348138 8.490000e-102 381.0
18 TraesCS7D01G508300 chr7A 79.891 184 14 7 3874 4038 702410895 702411074 3.420000e-21 113.0
19 TraesCS7D01G508300 chr7A 71.067 553 107 39 3122 3646 701602870 701602343 7.460000e-13 86.1
20 TraesCS7D01G508300 chr7A 96.970 33 1 0 2354 2386 57700891 57700923 5.850000e-04 56.5
21 TraesCS7D01G508300 chr7B 93.706 2399 124 14 371 2762 701457251 701459629 0.000000e+00 3568.0
22 TraesCS7D01G508300 chr7B 94.903 1236 35 4 2956 4186 701459809 701461021 0.000000e+00 1908.0
23 TraesCS7D01G508300 chr7B 83.240 2136 234 61 1646 3735 701647729 701649786 0.000000e+00 1847.0
24 TraesCS7D01G508300 chr7B 81.477 745 99 21 947 1654 701645934 701646676 3.630000e-160 575.0
25 TraesCS7D01G508300 chr7B 86.311 431 44 9 535 954 701644545 701644971 4.930000e-124 455.0
26 TraesCS7D01G508300 chr7B 77.764 823 95 34 3285 4036 672772390 672773195 3.870000e-115 425.0
27 TraesCS7D01G508300 chr7B 86.149 296 11 4 3747 4038 701650301 701650570 4.090000e-75 292.0
28 TraesCS7D01G508300 chr7B 78.326 466 80 15 774 1233 702316485 702316935 8.860000e-72 281.0
29 TraesCS7D01G508300 chr7B 91.710 193 12 2 3874 4066 701650114 701650302 8.930000e-67 265.0
30 TraesCS7D01G508300 chr7B 79.762 336 48 9 734 1068 701153848 701153532 4.210000e-55 226.0
31 TraesCS7D01G508300 chr7B 93.421 152 8 2 2821 2972 701459638 701459787 1.510000e-54 224.0
32 TraesCS7D01G508300 chr7B 79.545 220 32 5 2723 2929 702171897 702172116 1.210000e-30 145.0
33 TraesCS7D01G508300 chrUn 96.647 835 25 2 2956 3788 368811826 368812659 0.000000e+00 1384.0
34 TraesCS7D01G508300 chrUn 92.177 882 53 9 371 1251 87707442 87708308 0.000000e+00 1232.0
35 TraesCS7D01G508300 chrUn 94.415 752 40 2 1674 2425 368810826 368811575 0.000000e+00 1155.0
36 TraesCS7D01G508300 chrUn 90.022 892 59 13 371 1248 324358807 324357932 0.000000e+00 1127.0
37 TraesCS7D01G508300 chrUn 89.933 894 59 13 371 1248 324305195 324304317 0.000000e+00 1123.0
38 TraesCS7D01G508300 chrUn 92.157 510 28 2 745 1248 445548116 445547613 0.000000e+00 710.0
39 TraesCS7D01G508300 chrUn 95.581 430 19 0 1244 1673 388947914 388948343 0.000000e+00 689.0
40 TraesCS7D01G508300 chrUn 89.973 369 27 8 371 738 375666430 375666789 6.340000e-128 468.0
41 TraesCS7D01G508300 chrUn 88.265 392 10 5 3795 4186 465862390 465862035 1.790000e-118 436.0
42 TraesCS7D01G508300 chrUn 88.761 347 36 3 3 347 324305529 324305184 5.000000e-114 422.0
43 TraesCS7D01G508300 chrUn 88.761 347 36 3 3 347 324359141 324358796 5.000000e-114 422.0
44 TraesCS7D01G508300 chrUn 93.421 152 9 1 2821 2972 368811654 368811804 1.510000e-54 224.0
45 TraesCS7D01G508300 chr2B 91.489 47 3 1 3062 3107 252978027 252977981 3.490000e-06 63.9
46 TraesCS7D01G508300 chr1D 80.723 83 11 5 2306 2386 208149958 208150037 4.520000e-05 60.2


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 TraesCS7D01G508300 chr7D 611854002 611858188 4186 True 7733.00 7733 100.000000 1 4187 1 chr7D.!!$R1 4186
1 TraesCS7D01G508300 chr7D 611868278 611871167 2889 True 3446.00 3446 88.329000 1012 3923 1 chr7D.!!$R2 2911
2 TraesCS7D01G508300 chr7D 612284669 612290218 5549 False 3052.50 5360 92.487500 1 4186 2 chr7D.!!$F4 4185
3 TraesCS7D01G508300 chr7D 612325653 612329025 3372 False 1495.50 1770 83.130000 520 3923 2 chr7D.!!$F5 3403
4 TraesCS7D01G508300 chr7D 612403627 612405371 1744 False 1216.00 1216 79.841000 601 2307 1 chr7D.!!$F1 1706
5 TraesCS7D01G508300 chr7D 595346729 595350632 3903 False 551.75 1164 84.371500 662 4037 4 chr7D.!!$F3 3375
6 TraesCS7D01G508300 chr7A 702237053 702240887 3834 False 2996.00 5123 93.270500 1 4186 2 chr7A.!!$F4 4185
7 TraesCS7D01G508300 chr7A 702407298 702411074 3776 False 1526.50 2940 81.342000 520 4038 2 chr7A.!!$F5 3518
8 TraesCS7D01G508300 chr7A 688345399 688348138 2739 False 866.50 1352 82.210500 662 3735 2 chr7A.!!$F3 3073
9 TraesCS7D01G508300 chr7B 701457251 701461021 3770 False 1900.00 3568 94.010000 371 4186 3 chr7B.!!$F4 3815
10 TraesCS7D01G508300 chr7B 701644545 701650570 6025 False 686.80 1847 85.777400 535 4066 5 chr7B.!!$F5 3531
11 TraesCS7D01G508300 chr7B 672772390 672773195 805 False 425.00 425 77.764000 3285 4036 1 chr7B.!!$F1 751
12 TraesCS7D01G508300 chrUn 87707442 87708308 866 False 1232.00 1232 92.177000 371 1251 1 chrUn.!!$F1 880
13 TraesCS7D01G508300 chrUn 368810826 368812659 1833 False 921.00 1384 94.827667 1674 3788 3 chrUn.!!$F4 2114
14 TraesCS7D01G508300 chrUn 324357932 324359141 1209 True 774.50 1127 89.391500 3 1248 2 chrUn.!!$R4 1245
15 TraesCS7D01G508300 chrUn 324304317 324305529 1212 True 772.50 1123 89.347000 3 1248 2 chrUn.!!$R3 1245
16 TraesCS7D01G508300 chrUn 445547613 445548116 503 True 710.00 710 92.157000 745 1248 1 chrUn.!!$R1 503

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
166 169 0.308993 GTCTTAGGATGCAATGCCGC 59.691 55.0 1.53 0.0 33.77 6.53 F
1110 3551 0.471211 TCCCCTCCGGCTTAATCGAT 60.471 55.0 0.00 0.0 0.00 3.59 F
2655 7122 0.746923 TGTGCTCAGATGCTCATGGC 60.747 55.0 0.00 0.0 42.22 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 3899 0.460109 CACCGCCGTCAATGAGATGA 60.460 55.0 0.0 0.0 35.12 2.92 R
2831 7312 0.558712 TTGTACCAAACCCCAAGGCT 59.441 50.0 0.0 0.0 36.11 4.58 R
3535 8418 0.251916 CGGTAAGGGGAGCATTCACA 59.748 55.0 0.0 0.0 0.00 3.58 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
49 50 9.364989 GAGATTGAGATAATGATAGTTAGGTGC 57.635 37.037 0.00 0.00 0.00 5.01
64 65 0.541764 GGTGCCAACCCAAAGGATCA 60.542 55.000 0.00 0.00 41.04 2.92
84 85 5.309323 TCACCATTCGATTTTGATCCAAC 57.691 39.130 0.00 0.00 0.00 3.77
86 87 4.006989 ACCATTCGATTTTGATCCAACGA 58.993 39.130 0.00 0.00 0.00 3.85
89 90 5.391950 CCATTCGATTTTGATCCAACGACTT 60.392 40.000 0.00 0.00 0.00 3.01
125 126 2.465860 ATTTTAAAAAGGGCGCCACC 57.534 45.000 30.85 12.35 37.93 4.61
166 169 0.308993 GTCTTAGGATGCAATGCCGC 59.691 55.000 1.53 0.00 33.77 6.53
181 184 4.531912 CGCGCGGCTCTTCGTCTA 62.532 66.667 24.84 0.00 0.00 2.59
192 195 1.554160 TCTTCGTCTACCTCCGACTCT 59.446 52.381 0.00 0.00 31.95 3.24
209 212 1.002544 CTCTTTGACGCTTCCTCCCTT 59.997 52.381 0.00 0.00 0.00 3.95
274 277 1.264557 AGATTCATCGCCGTCTAGTCG 59.735 52.381 2.16 2.16 0.00 4.18
288 291 4.260702 CGTCTAGTCGAGATAAGGTGTTCC 60.261 50.000 3.09 0.00 36.29 3.62
303 306 2.622942 GTGTTCCTTTGATGCTGTTGGA 59.377 45.455 0.00 0.00 0.00 3.53
305 308 3.896888 TGTTCCTTTGATGCTGTTGGAAT 59.103 39.130 0.00 0.00 36.23 3.01
315 318 8.523915 TTGATGCTGTTGGAATACTCATTAAT 57.476 30.769 0.00 0.00 0.00 1.40
335 338 3.678056 TCGTCTAGCACCTGTGAAATT 57.322 42.857 0.51 0.00 0.00 1.82
401 404 1.815421 CGTTCGCCCCCTCATCTTG 60.815 63.158 0.00 0.00 0.00 3.02
422 425 0.826256 TCCTAGCACACACCAGACGT 60.826 55.000 0.00 0.00 0.00 4.34
590 2010 2.045131 GGTCGTCCGCCAGTCTACT 61.045 63.158 0.00 0.00 0.00 2.57
641 2071 5.562890 GCACAATTCTAGGGTTTTGTCACTC 60.563 44.000 0.00 0.00 30.23 3.51
642 2072 5.048713 CACAATTCTAGGGTTTTGTCACTCC 60.049 44.000 0.00 0.00 30.23 3.85
643 2073 3.396260 TTCTAGGGTTTTGTCACTCCG 57.604 47.619 0.00 0.00 0.00 4.63
644 2074 2.322658 TCTAGGGTTTTGTCACTCCGT 58.677 47.619 0.00 0.00 0.00 4.69
645 2075 2.298163 TCTAGGGTTTTGTCACTCCGTC 59.702 50.000 0.00 0.00 0.00 4.79
972 3380 2.278857 CTCAAGATCCGCGTCCCG 60.279 66.667 4.92 0.00 0.00 5.14
1078 3519 2.187493 CGGCTCGATCCGGAGAAGA 61.187 63.158 19.71 8.22 45.38 2.87
1110 3551 0.471211 TCCCCTCCGGCTTAATCGAT 60.471 55.000 0.00 0.00 0.00 3.59
1319 3800 3.560278 CACGGCCCGCGACATTAC 61.560 66.667 8.23 0.00 0.00 1.89
1369 3853 0.881796 CGTCTGCTGTGAGACCAGTA 59.118 55.000 0.00 0.00 39.47 2.74
1415 3899 2.325082 CCGCGCTTAAGCAGTTGGT 61.325 57.895 26.29 0.00 42.21 3.67
1518 4008 1.799916 GCCGCGTATTGTGTTTGGC 60.800 57.895 4.92 0.00 0.00 4.52
2003 6442 2.834631 TATGCCCGCCATACTGTCT 58.165 52.632 0.00 0.00 35.34 3.41
2074 6516 5.246981 AGAAGTGGAGTTCAATGGATTCA 57.753 39.130 0.00 0.00 0.00 2.57
2075 6517 5.251764 AGAAGTGGAGTTCAATGGATTCAG 58.748 41.667 0.00 0.00 0.00 3.02
2604 7071 6.854381 GGTTGTGCACGTATAATTTATTAGCC 59.146 38.462 13.13 0.00 0.00 3.93
2654 7121 1.015109 GTGTGCTCAGATGCTCATGG 58.985 55.000 0.00 0.00 38.44 3.66
2655 7122 0.746923 TGTGCTCAGATGCTCATGGC 60.747 55.000 0.00 0.00 42.22 4.40
2748 7224 8.900983 TTACCTAAATTGCTCTTTTGCATTTT 57.099 26.923 11.96 11.96 43.89 1.82
2831 7312 6.520021 AGGTTATCCCATCTGAATTCATCA 57.480 37.500 8.96 0.00 33.96 3.07
2851 7332 1.149077 AGCCTTGGGGTTTGGTACAAT 59.851 47.619 0.00 0.00 38.21 2.71
2923 7404 1.654105 CTGTCAGCGTGTATTCCGTTC 59.346 52.381 0.00 0.00 0.00 3.95
2949 7449 4.944962 TCTGGTTTTGCATCTGTATTCG 57.055 40.909 0.00 0.00 0.00 3.34
3044 7620 7.416022 GTTTCTTTCTGCTCTCATCATATTGG 58.584 38.462 0.00 0.00 0.00 3.16
3108 7685 5.316987 TCCCCTCTGTTCTCATTCTTTTTC 58.683 41.667 0.00 0.00 0.00 2.29
3513 8396 3.495001 TGACGACGACATTGCATGTTTTA 59.505 39.130 0.00 0.00 45.03 1.52
3535 8418 8.726870 TTTAAGCGGTAGTAAAATTATCTGCT 57.273 30.769 0.00 0.00 38.85 4.24
3814 8846 3.636153 ATCTGGGCTCTTGTTAGTTCC 57.364 47.619 0.00 0.00 0.00 3.62
3958 9225 4.636249 CAGTCTAGTTGTGCCTCTCTTTT 58.364 43.478 0.00 0.00 0.00 2.27
3961 9228 4.816925 GTCTAGTTGTGCCTCTCTTTTTGT 59.183 41.667 0.00 0.00 0.00 2.83
4011 9593 2.434336 TCAGATCCTTTGTGTATCCCCG 59.566 50.000 0.00 0.00 0.00 5.73
4076 9663 7.147976 GGTTTATCTAATGAATGGTTGGATGC 58.852 38.462 0.00 0.00 30.73 3.91
4186 9774 7.443575 CCTTATCCTGTAACTCCTCAAATGATG 59.556 40.741 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.236489 ATGGTGATCCTTTGGGTTGG 57.764 50.000 0.00 0.0 34.23 3.77
64 65 4.006989 TCGTTGGATCAAAATCGAATGGT 58.993 39.130 0.00 0.0 37.28 3.55
84 85 4.141855 ACGCAACCATTTTTCTAAGTCG 57.858 40.909 0.00 0.0 0.00 4.18
86 87 9.968870 TTAAAATACGCAACCATTTTTCTAAGT 57.031 25.926 0.00 0.0 36.18 2.24
125 126 1.068472 AGAGTTTGTCGTCGCACTAGG 60.068 52.381 0.00 0.0 0.00 3.02
127 128 2.810274 ACTAGAGTTTGTCGTCGCACTA 59.190 45.455 0.00 0.0 0.00 2.74
132 135 4.391216 TCCTAAGACTAGAGTTTGTCGTCG 59.609 45.833 0.00 0.0 38.16 5.12
166 169 2.278013 GGTAGACGAAGAGCCGCG 60.278 66.667 0.00 0.0 0.00 6.46
181 184 1.179814 AGCGTCAAAGAGTCGGAGGT 61.180 55.000 0.00 0.0 0.00 3.85
192 195 1.002087 GAGAAGGGAGGAAGCGTCAAA 59.998 52.381 1.14 0.0 0.00 2.69
209 212 2.507058 CAAAGGAGGTCATGGGATGAGA 59.493 50.000 0.00 0.0 40.53 3.27
274 277 5.065731 CAGCATCAAAGGAACACCTTATCTC 59.934 44.000 0.00 0.0 42.43 2.75
288 291 5.885230 TGAGTATTCCAACAGCATCAAAG 57.115 39.130 0.00 0.0 0.00 2.77
290 293 7.936496 TTAATGAGTATTCCAACAGCATCAA 57.064 32.000 0.00 0.0 0.00 2.57
292 295 7.041780 ACGATTAATGAGTATTCCAACAGCATC 60.042 37.037 0.00 0.0 0.00 3.91
303 306 7.148641 CAGGTGCTAGACGATTAATGAGTATT 58.851 38.462 0.00 0.0 0.00 1.89
305 308 5.593095 ACAGGTGCTAGACGATTAATGAGTA 59.407 40.000 0.00 0.0 0.00 2.59
315 318 3.678056 AATTTCACAGGTGCTAGACGA 57.322 42.857 0.00 0.0 0.00 4.20
401 404 1.797025 GTCTGGTGTGTGCTAGGAAC 58.203 55.000 0.00 0.0 0.00 3.62
422 425 1.139734 GCTCGCCATCTTGACTCGA 59.860 57.895 0.00 0.0 0.00 4.04
433 436 0.460811 CTGCTGTATGAAGCTCGCCA 60.461 55.000 0.00 0.0 43.90 5.69
542 1960 1.692519 AGCAAGTACGAGGGTTCAACT 59.307 47.619 0.00 0.0 0.00 3.16
590 2010 0.770499 TGGGGACTGAAACTGATGCA 59.230 50.000 0.00 0.0 0.00 3.96
663 2095 2.203365 ATCGACGCCCGGATCTCT 60.203 61.111 0.73 0.0 39.14 3.10
972 3380 1.742880 TCCACGCTGCTGCTTGATC 60.743 57.895 21.25 0.0 40.37 2.92
1078 3519 3.155167 GGGGAGGCGGAAGTCGAT 61.155 66.667 0.00 0.0 43.49 3.59
1110 3551 2.670592 TCGACAGCGAGGGAACGA 60.671 61.111 0.00 0.0 42.51 3.85
1415 3899 0.460109 CACCGCCGTCAATGAGATGA 60.460 55.000 0.00 0.0 35.12 2.92
1518 4008 0.593128 CCTTGTTGAGGCTCCAAACG 59.407 55.000 12.86 0.0 39.09 3.60
2003 6442 1.760613 ACCTCCAGTTCGACTCACAAA 59.239 47.619 0.00 0.0 0.00 2.83
2074 6516 1.680522 AACTCATGATCCGCTCCGCT 61.681 55.000 0.00 0.0 0.00 5.52
2075 6517 0.811616 AAACTCATGATCCGCTCCGC 60.812 55.000 0.00 0.0 0.00 5.54
2497 6955 5.733620 ACGATTAACAGTTACTTCCTCCA 57.266 39.130 0.00 0.0 0.00 3.86
2748 7224 5.824624 GGCAAGATCAATGAAGAGGATTGTA 59.175 40.000 0.00 0.0 33.33 2.41
2831 7312 0.558712 TTGTACCAAACCCCAAGGCT 59.441 50.000 0.00 0.0 36.11 4.58
2923 7404 7.641411 CGAATACAGATGCAAAACCAGAAATAG 59.359 37.037 0.00 0.0 0.00 1.73
2949 7449 5.007682 TCTGGGAACTGTATTTTTGCTACC 58.992 41.667 0.00 0.0 0.00 3.18
3065 7641 3.583526 GGAGACTCCCCCTGTATTATTCC 59.416 52.174 10.74 0.0 0.00 3.01
3108 7685 4.926238 AGAAACAAGCTCAAGTCAGTATCG 59.074 41.667 0.00 0.0 0.00 2.92
3513 8396 6.037172 CACAGCAGATAATTTTACTACCGCTT 59.963 38.462 0.00 0.0 0.00 4.68
3535 8418 0.251916 CGGTAAGGGGAGCATTCACA 59.748 55.000 0.00 0.0 0.00 3.58
3814 8846 4.739046 AATCAGAGCTTCACAAAGTTCG 57.261 40.909 0.00 0.0 44.75 3.95
3958 9225 5.904984 AAGCCATACATGTATCCCTACAA 57.095 39.130 15.60 0.0 41.09 2.41
3961 9228 4.020573 CCGAAAGCCATACATGTATCCCTA 60.021 45.833 15.60 0.0 0.00 3.53


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

AutoCloner maintained by Alex Coulton.