Multiple sequence alignment - TraesCS1D01G097800

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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 TraesCS1D01G097800 chr1D 100.000 4247 0 0 1 4247 84721947 84726193 0.000000e+00 7843.0
1 TraesCS1D01G097800 chr1D 90.840 1048 75 14 2663 3708 84569413 84570441 0.000000e+00 1384.0
2 TraesCS1D01G097800 chr1D 88.295 1085 89 17 2709 3761 84612120 84613198 0.000000e+00 1266.0
3 TraesCS1D01G097800 chr1D 87.061 541 28 17 1586 2101 84611570 84612093 1.320000e-159 573.0
4 TraesCS1D01G097800 chr1D 82.935 627 52 30 937 1523 84565671 84566282 8.140000e-142 514.0
5 TraesCS1D01G097800 chr1D 82.343 572 43 21 979 1510 84610750 84611303 1.080000e-120 444.0
6 TraesCS1D01G097800 chr1D 86.294 394 30 10 1586 1955 84566392 84566785 1.420000e-109 407.0
7 TraesCS1D01G097800 chr1D 86.689 293 28 7 3965 4247 84613343 84613634 8.860000e-82 315.0
8 TraesCS1D01G097800 chr1D 83.278 299 47 3 2102 2399 431819991 431820287 5.410000e-69 272.0
9 TraesCS1D01G097800 chr1D 84.536 291 18 8 3694 3957 84570467 84570757 3.260000e-66 263.0
10 TraesCS1D01G097800 chr1D 87.075 147 14 3 4046 4187 84570972 84571118 1.220000e-35 161.0
11 TraesCS1D01G097800 chr1A 93.397 3574 118 33 707 4247 78953094 78956582 0.000000e+00 5184.0
12 TraesCS1D01G097800 chr1A 92.628 1058 64 7 2709 3758 78547294 78548345 0.000000e+00 1509.0
13 TraesCS1D01G097800 chr1A 90.860 919 68 10 2709 3625 78338531 78339435 0.000000e+00 1218.0
14 TraesCS1D01G097800 chr1A 87.732 538 29 14 1586 2101 78546744 78547266 1.020000e-165 593.0
15 TraesCS1D01G097800 chr1A 86.967 422 30 9 1586 1983 78338004 78338424 6.480000e-123 451.0
16 TraesCS1D01G097800 chr1A 84.950 299 43 2 2102 2399 539736448 539736151 6.900000e-78 302.0
17 TraesCS1D01G097800 chr1A 93.204 206 4 8 937 1141 78335358 78335554 1.150000e-75 294.0
18 TraesCS1D01G097800 chr1A 91.241 137 11 1 4110 4246 78339431 78339566 7.250000e-43 185.0
19 TraesCS1D01G097800 chr1A 85.465 172 17 6 2490 2654 115367925 115367755 5.650000e-39 172.0
20 TraesCS1D01G097800 chr1A 97.802 91 1 1 1133 1223 78335884 78335973 5.690000e-34 156.0
21 TraesCS1D01G097800 chr1A 82.550 149 19 5 1378 1519 78336025 78336173 1.600000e-24 124.0
22 TraesCS1D01G097800 chr1A 90.588 85 8 0 2017 2101 78338419 78338503 3.470000e-21 113.0
23 TraesCS1D01G097800 chr1A 97.222 36 1 0 3761 3796 221699758 221699793 1.280000e-05 62.1
24 TraesCS1D01G097800 chr1B 94.338 2190 93 13 1578 3758 137177893 137180060 0.000000e+00 3328.0
25 TraesCS1D01G097800 chr1B 94.774 2143 83 10 1585 3724 137445959 137448075 0.000000e+00 3310.0
26 TraesCS1D01G097800 chr1B 92.010 1577 58 14 1 1531 137444302 137445856 0.000000e+00 2152.0
27 TraesCS1D01G097800 chr1B 88.189 1397 90 28 2664 4026 137153075 137154430 0.000000e+00 1596.0
28 TraesCS1D01G097800 chr1B 88.909 1082 82 19 2709 3758 137174670 137175745 0.000000e+00 1299.0
29 TraesCS1D01G097800 chr1B 91.887 604 32 3 941 1543 137177327 137177914 0.000000e+00 828.0
30 TraesCS1D01G097800 chr1B 88.202 534 30 11 1586 2100 137174123 137174642 1.310000e-169 606.0
31 TraesCS1D01G097800 chr1B 89.827 462 34 5 3792 4247 137448144 137448598 7.920000e-162 580.0
32 TraesCS1D01G097800 chr1B 88.197 466 31 8 1586 2028 137152505 137152969 6.250000e-148 534.0
33 TraesCS1D01G097800 chr1B 91.259 286 7 4 938 1221 137151774 137152043 1.440000e-99 374.0
34 TraesCS1D01G097800 chr1B 84.333 300 43 4 2102 2399 59471831 59472128 1.490000e-74 291.0
35 TraesCS1D01G097800 chr1B 92.857 196 12 2 4046 4239 137154526 137154721 2.500000e-72 283.0
36 TraesCS1D01G097800 chr1B 83.893 149 17 5 1378 1519 137152097 137152245 7.410000e-28 135.0
37 TraesCS1D01G097800 chr1B 97.222 36 1 0 3761 3796 263552321 263552356 1.280000e-05 62.1
38 TraesCS1D01G097800 chr3B 84.615 299 44 2 2102 2399 757924530 757924233 3.210000e-76 296.0
39 TraesCS1D01G097800 chr3B 84.281 299 46 1 2102 2399 606574024 606573726 1.490000e-74 291.0
40 TraesCS1D01G097800 chr3B 89.600 125 10 2 2536 2657 383708258 383708134 5.690000e-34 156.0
41 TraesCS1D01G097800 chr4B 83.278 299 49 1 2102 2399 608260504 608260206 1.500000e-69 274.0
42 TraesCS1D01G097800 chr3A 92.623 122 7 2 2538 2657 383695621 383695500 1.570000e-39 174.0
43 TraesCS1D01G097800 chr3A 97.436 39 0 1 3760 3797 13151546 13151584 9.860000e-07 65.8
44 TraesCS1D01G097800 chr3D 89.344 122 9 3 2536 2653 290859721 290859600 2.650000e-32 150.0
45 TraesCS1D01G097800 chr7B 88.119 101 8 4 2519 2615 245610767 245610867 2.680000e-22 117.0
46 TraesCS1D01G097800 chr7A 80.851 94 7 5 3763 3845 573432798 573432705 3.550000e-06 63.9
47 TraesCS1D01G097800 chr7A 90.909 44 2 2 3753 3796 279180083 279180124 1.650000e-04 58.4
48 TraesCS1D01G097800 chr7D 90.909 44 2 2 3753 3796 258222758 258222799 1.650000e-04 58.4
49 TraesCS1D01G097800 chr2B 92.308 39 3 0 3758 3796 588070417 588070379 5.930000e-04 56.5


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 TraesCS1D01G097800 chr1D 84721947 84726193 4246 False 7843.00 7843 100.000000 1 4247 1 chr1D.!!$F1 4246
1 TraesCS1D01G097800 chr1D 84610750 84613634 2884 False 649.50 1266 86.097000 979 4247 4 chr1D.!!$F4 3268
2 TraesCS1D01G097800 chr1D 84565671 84571118 5447 False 545.80 1384 86.336000 937 4187 5 chr1D.!!$F3 3250
3 TraesCS1D01G097800 chr1A 78953094 78956582 3488 False 5184.00 5184 93.397000 707 4247 1 chr1A.!!$F1 3540
4 TraesCS1D01G097800 chr1A 78546744 78548345 1601 False 1051.00 1509 90.180000 1586 3758 2 chr1A.!!$F4 2172
5 TraesCS1D01G097800 chr1A 78335358 78339566 4208 False 363.00 1218 90.458857 937 4246 7 chr1A.!!$F3 3309
6 TraesCS1D01G097800 chr1B 137444302 137448598 4296 False 2014.00 3310 92.203667 1 4247 3 chr1B.!!$F5 4246
7 TraesCS1D01G097800 chr1B 137174123 137180060 5937 False 1515.25 3328 90.834000 941 3758 4 chr1B.!!$F4 2817
8 TraesCS1D01G097800 chr1B 137151774 137154721 2947 False 584.40 1596 88.879000 938 4239 5 chr1B.!!$F3 3301

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
38 39 0.179062 GATCCTCGTCCAGCTGCAAT 60.179 55.000 8.66 0.0 0.00 3.56 F
785 812 0.729116 CCAACACGATGATGAGTGGC 59.271 55.000 0.00 0.0 42.25 5.01 F
805 832 1.202806 CCGAATGGATGCCCACTATGT 60.203 52.381 0.00 0.0 46.98 2.29 F
2332 9522 0.118547 ACCAGCAACCCTAGTACCCT 59.881 55.000 0.00 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1295 3989 3.333381 TGAAGGGGATTTGAGTGGATTGA 59.667 43.478 0.00 0.00 0.0 2.57 R
2286 9476 0.984230 TTACTGGGTTGAGAGGGCTG 59.016 55.000 0.00 0.00 0.0 4.85 R
2440 9631 2.284995 GTGAGGAGGAGGGGCAGT 60.285 66.667 0.00 0.00 0.0 4.40 R
3441 10639 0.740737 AAACTGAACAGTGCAGGCAC 59.259 50.000 16.29 16.29 46.5 5.01 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
38 39 0.179062 GATCCTCGTCCAGCTGCAAT 60.179 55.000 8.66 0.00 0.00 3.56
50 51 0.810648 GCTGCAATTGGAATGTCGGA 59.189 50.000 7.72 0.00 0.00 4.55
127 128 7.786178 TCAATCGGTAGAAGATACCAATTTG 57.214 36.000 5.02 5.08 37.44 2.32
143 144 5.047802 ACCAATTTGTGTTGATGAGATGGTC 60.048 40.000 0.00 0.00 32.23 4.02
144 145 5.047872 CCAATTTGTGTTGATGAGATGGTCA 60.048 40.000 0.00 0.00 40.38 4.02
182 183 8.565896 TCCCATCATCATGTAAAAGTATATGC 57.434 34.615 0.00 0.00 30.87 3.14
188 189 9.223099 TCATCATGTAAAAGTATATGCAGGATG 57.777 33.333 10.72 10.72 45.47 3.51
259 260 7.041721 GCTGTATATCGTCCCAATCAATCATA 58.958 38.462 0.00 0.00 0.00 2.15
260 261 7.712639 GCTGTATATCGTCCCAATCAATCATAT 59.287 37.037 0.00 0.00 0.00 1.78
357 368 2.916527 AATCCAATCCCAGCCAGCCG 62.917 60.000 0.00 0.00 0.00 5.52
366 377 1.518572 CAGCCAGCCGTACTAACCG 60.519 63.158 0.00 0.00 0.00 4.44
416 427 2.009774 CGGACCATGAACTGATTCCAC 58.990 52.381 0.00 0.00 33.49 4.02
420 431 2.094675 CCATGAACTGATTCCACACCC 58.905 52.381 0.00 0.00 33.49 4.61
466 481 6.379988 GTGATTAAGGCCCAGGATTAAGAAAA 59.620 38.462 0.00 0.00 0.00 2.29
785 812 0.729116 CCAACACGATGATGAGTGGC 59.271 55.000 0.00 0.00 42.25 5.01
804 831 1.527034 CCGAATGGATGCCCACTATG 58.473 55.000 0.00 0.00 46.98 2.23
805 832 1.202806 CCGAATGGATGCCCACTATGT 60.203 52.381 0.00 0.00 46.98 2.29
807 834 2.746142 CGAATGGATGCCCACTATGTGT 60.746 50.000 0.00 0.00 46.98 3.72
808 835 2.645838 ATGGATGCCCACTATGTGTC 57.354 50.000 0.00 0.00 46.98 3.67
936 963 3.919216 ACTCGTCCATCTTTCTCAACTG 58.081 45.455 0.00 0.00 0.00 3.16
937 964 3.574396 ACTCGTCCATCTTTCTCAACTGA 59.426 43.478 0.00 0.00 0.00 3.41
988 3274 5.090139 CCCTAGAGAGAGAGAGAGAGAGAT 58.910 50.000 0.00 0.00 0.00 2.75
1223 3887 3.500343 CATCCAATCCAATCCCCCTTAC 58.500 50.000 0.00 0.00 0.00 2.34
1295 3989 7.982252 TGATTCATAGCAGATTTAATCCTCCT 58.018 34.615 0.78 0.00 0.00 3.69
1404 4161 5.518812 TCATTTCAATTCAAACACCAGTCG 58.481 37.500 0.00 0.00 0.00 4.18
1523 4292 4.250464 CTCAATTAGGCTCGGTTTACACA 58.750 43.478 0.00 0.00 0.00 3.72
1767 6338 2.363680 CTCTGACTATGGCTACCCACTG 59.636 54.545 0.00 0.00 45.77 3.66
1979 9129 4.201861 GCTGATTTCCTGACGGAGAAATTC 60.202 45.833 10.31 0.00 41.56 2.17
2132 9322 1.630369 AGATACTTGAGCCAACCAGCA 59.370 47.619 0.00 0.00 34.23 4.41
2184 9374 3.303928 GCCTCCGATACTCCCCCG 61.304 72.222 0.00 0.00 0.00 5.73
2248 9438 3.795688 TTACGATACTCCCCCGATACT 57.204 47.619 0.00 0.00 0.00 2.12
2332 9522 0.118547 ACCAGCAACCCTAGTACCCT 59.881 55.000 0.00 0.00 0.00 4.34
2417 9608 2.917227 TCACTCAGTGCCAGCGGA 60.917 61.111 0.00 0.00 32.98 5.54
2534 9725 7.859325 TGAAAGTAATATGCTGTTCCTAACC 57.141 36.000 0.00 0.00 0.00 2.85
2686 9879 9.253832 AGGTTCCATATGATGTTGATTTTAACA 57.746 29.630 3.65 0.00 43.93 2.41
2823 10019 3.439857 AAACATGGGCACAGATGTAGT 57.560 42.857 0.00 0.00 32.76 2.73
2885 10082 6.093495 TCAGAACATAGCTAAAAATGAACCCG 59.907 38.462 0.00 0.00 0.00 5.28
3056 10254 0.549950 AAGGATGTGCATGGGAGGAG 59.450 55.000 0.00 0.00 0.00 3.69
3061 10259 1.126948 TGTGCATGGGAGGAGTGTCA 61.127 55.000 0.00 0.00 0.00 3.58
3127 10325 1.668419 CAGGCTGGAATTTAGTCCCG 58.332 55.000 6.61 0.00 36.80 5.14
3128 10326 1.209504 CAGGCTGGAATTTAGTCCCGA 59.790 52.381 6.61 0.00 36.80 5.14
3141 10339 3.543680 AGTCCCGAATATGTGGTTGAG 57.456 47.619 0.00 0.00 0.00 3.02
3222 10420 1.380302 GGTGGAGGGCACTGTTGAT 59.620 57.895 0.00 0.00 0.00 2.57
3235 10433 5.008415 GGCACTGTTGATATCAAGATCCTTG 59.992 44.000 18.47 12.15 36.39 3.61
3274 10472 2.636830 CATGGGAAGATTGTCGCTTCT 58.363 47.619 0.00 0.00 41.11 2.85
3441 10639 3.492383 GCTGTCGGTGATGATGAGTTATG 59.508 47.826 0.00 0.00 0.00 1.90
3505 10703 1.957177 GATGAGAGTATCACCTGCGGA 59.043 52.381 0.00 0.00 41.91 5.54
3662 10887 5.353400 AGTCATGATACATGCTCAAACAGTG 59.647 40.000 0.00 0.00 0.00 3.66
3877 11185 6.953101 TGCCATCCTAAAAGTAATGTCTACA 58.047 36.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.230134 AGGATCCTGAGACTATGAGCAC 58.770 50.000 15.29 0.00 0.00 4.40
11 12 0.626382 TGGACGAGGATCCTGAGACT 59.374 55.000 22.02 0.00 39.75 3.24
38 39 2.612972 GCAGAACTCTCCGACATTCCAA 60.613 50.000 0.00 0.00 0.00 3.53
84 85 4.458256 TGATTGCATGGTTGGATCCTAT 57.542 40.909 14.23 0.00 0.00 2.57
127 128 3.119708 GCCTTTGACCATCTCATCAACAC 60.120 47.826 0.00 0.00 34.61 3.32
143 144 2.222027 GATGGGATCTTACGGCCTTTG 58.778 52.381 0.00 0.00 0.00 2.77
144 145 1.843851 TGATGGGATCTTACGGCCTTT 59.156 47.619 0.00 0.00 0.00 3.11
357 368 1.153568 GGGGGCGTTCGGTTAGTAC 60.154 63.158 0.00 0.00 0.00 2.73
366 377 0.463833 CCATCAAGTAGGGGGCGTTC 60.464 60.000 0.00 0.00 0.00 3.95
416 427 2.806503 TAATTGCGGTCCGTGGGGTG 62.807 60.000 13.94 0.00 33.83 4.61
420 431 3.375922 ACTTTATTAATTGCGGTCCGTGG 59.624 43.478 13.94 0.00 0.00 4.94
466 481 1.528309 CCTCGGCACAAAACCCACT 60.528 57.895 0.00 0.00 0.00 4.00
515 537 1.971695 CTTTTCAGGTGCCGACCCC 60.972 63.158 0.00 0.00 44.40 4.95
519 541 0.035439 GGATCCTTTTCAGGTGCCGA 60.035 55.000 3.84 0.00 41.69 5.54
528 552 1.037030 TGGCGGCATGGATCCTTTTC 61.037 55.000 14.23 0.89 0.00 2.29
669 693 0.937304 CTTCCCTCAACACACACACG 59.063 55.000 0.00 0.00 0.00 4.49
785 812 1.202806 ACATAGTGGGCATCCATTCGG 60.203 52.381 0.00 0.00 46.09 4.30
807 834 0.671796 ATTCACTGTGTGTCGTCCGA 59.328 50.000 7.79 0.00 34.79 4.55
808 835 0.784178 CATTCACTGTGTGTCGTCCG 59.216 55.000 7.79 0.00 34.79 4.79
857 884 2.175931 TCACAACTTGGGCCCTTTTAGA 59.824 45.455 25.70 9.52 0.00 2.10
988 3274 1.048724 CCGGCCATGGAAGAGGACTA 61.049 60.000 18.40 0.00 0.00 2.59
1223 3887 4.299155 ACCGAACATAACGAGATGCATAG 58.701 43.478 0.00 0.00 0.00 2.23
1295 3989 3.333381 TGAAGGGGATTTGAGTGGATTGA 59.667 43.478 0.00 0.00 0.00 2.57
1404 4161 9.674824 GAATTTGATGAATGAATGATACTGACC 57.325 33.333 0.00 0.00 0.00 4.02
1450 4211 6.037172 TGCTTCCGAATAAATCTAGCAGAAAC 59.963 38.462 0.00 0.00 32.92 2.78
1767 6338 5.392811 GGCTATGATGGTACCGTAGACATAC 60.393 48.000 6.60 6.12 32.66 2.39
2184 9374 3.786635 GGATACTCCATGGATACGCATC 58.213 50.000 16.63 9.35 36.28 3.91
2232 9422 2.289506 GGCAAAGTATCGGGGGAGTATC 60.290 54.545 0.00 0.00 0.00 2.24
2286 9476 0.984230 TTACTGGGTTGAGAGGGCTG 59.016 55.000 0.00 0.00 0.00 4.85
2440 9631 2.284995 GTGAGGAGGAGGGGCAGT 60.285 66.667 0.00 0.00 0.00 4.40
2885 10082 5.705609 TTGATTGAACTACCCTTGCTTTC 57.294 39.130 0.00 0.00 0.00 2.62
2898 10095 4.925646 GCTTGTTTCTGGGATTGATTGAAC 59.074 41.667 0.00 0.00 0.00 3.18
3056 10254 4.987832 ACTGAGTCTATCGTCATTGACAC 58.012 43.478 16.61 6.83 37.26 3.67
3061 10259 6.603997 AGTCCTTTACTGAGTCTATCGTCATT 59.396 38.462 0.00 0.00 36.93 2.57
3127 10325 4.693566 TGTTTCCGTCTCAACCACATATTC 59.306 41.667 0.00 0.00 0.00 1.75
3128 10326 4.454504 GTGTTTCCGTCTCAACCACATATT 59.545 41.667 0.00 0.00 0.00 1.28
3141 10339 1.295792 TGCTGACAAGTGTTTCCGTC 58.704 50.000 0.00 0.00 0.00 4.79
3222 10420 3.051032 AGGTCCCTCCAAGGATCTTGATA 60.051 47.826 9.01 0.00 45.61 2.15
3235 10433 1.846439 TGGAATTCATCAGGTCCCTCC 59.154 52.381 7.93 0.00 0.00 4.30
3379 10577 1.761784 AGCATCTCATCCACAGAGACC 59.238 52.381 0.00 0.00 44.23 3.85
3441 10639 0.740737 AAACTGAACAGTGCAGGCAC 59.259 50.000 16.29 16.29 46.50 5.01
3505 10703 4.530161 ACCTTCAGAAGCATCTTGTAGTCT 59.470 41.667 4.41 0.00 32.03 3.24
3630 10855 4.080695 AGCATGTATCATGACTGGTTCACT 60.081 41.667 12.98 0.00 36.92 3.41
3662 10887 5.983720 AGATACAATACACGCTGGAACATAC 59.016 40.000 0.00 0.00 38.20 2.39
3838 11144 5.468658 AGGATGGCAGTAAATACTACTCCT 58.531 41.667 0.00 0.00 34.13 3.69
3877 11185 5.447144 GCAATTCAACAAGGCGAAAAACTTT 60.447 36.000 0.00 0.00 0.00 2.66
4100 11563 8.846943 TGAAAGAATTGAATGCTACTACTGAA 57.153 30.769 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.