Multiple sequence alignment - TraesCS4D01G345900

Loading Multiple Alignment...

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 TraesCS4D01G345900 chr4D 100.000 2456 0 0 1 2456 500287006 500284551 0.000000e+00 4536.0
1 TraesCS4D01G345900 chr4D 81.070 766 64 43 483 1217 500292818 500292103 9.990000e-149 536.0
2 TraesCS4D01G345900 chr4D 80.597 536 53 29 650 1176 500271575 500271082 1.390000e-97 366.0
3 TraesCS4D01G345900 chr4D 97.917 144 3 0 1 144 490601115 490601258 1.460000e-62 250.0
4 TraesCS4D01G345900 chr4D 85.632 174 15 5 299 470 500297150 500296985 9.030000e-40 174.0
5 TraesCS4D01G345900 chr4D 84.404 109 13 3 1152 1259 500276050 500275945 1.200000e-18 104.0
6 TraesCS4D01G345900 chr4D 87.692 65 3 3 1177 1239 500299160 500299099 1.220000e-08 71.3
7 TraesCS4D01G345900 chrUn 81.994 1555 168 50 145 1644 60373615 60375112 0.000000e+00 1218.0
8 TraesCS4D01G345900 chrUn 83.014 783 93 26 1709 2456 60463850 60464627 0.000000e+00 673.0
9 TraesCS4D01G345900 chrUn 80.301 863 98 34 670 1497 60456673 60457498 9.790000e-164 586.0
10 TraesCS4D01G345900 chrUn 83.759 548 45 26 1589 2106 307771361 307770828 1.710000e-131 479.0
11 TraesCS4D01G345900 chrUn 84.634 410 35 17 1725 2106 285030219 285029810 1.380000e-102 383.0
12 TraesCS4D01G345900 chrUn 84.504 413 36 17 1722 2106 293564476 293564888 1.380000e-102 383.0
13 TraesCS4D01G345900 chrUn 84.504 413 36 17 1722 2106 315390710 315391122 1.380000e-102 383.0
14 TraesCS4D01G345900 chrUn 84.634 410 35 17 1725 2106 345623030 345622621 1.380000e-102 383.0
15 TraesCS4D01G345900 chrUn 77.904 353 50 13 871 1217 307772043 307771713 6.930000e-46 195.0
16 TraesCS4D01G345900 chr4B 81.643 1558 174 50 145 1647 643492943 643491443 0.000000e+00 1190.0
17 TraesCS4D01G345900 chr4B 81.806 753 93 30 1709 2423 643491441 643490695 2.100000e-165 592.0
18 TraesCS4D01G345900 chr4B 80.664 512 41 26 299 804 643625475 643625016 6.500000e-91 344.0
19 TraesCS4D01G345900 chr4B 97.143 35 1 0 1172 1206 643627297 643627263 2.640000e-05 60.2
20 TraesCS4D01G345900 chr5A 89.586 941 74 12 1010 1945 680887632 680886711 0.000000e+00 1173.0
21 TraesCS4D01G345900 chr5A 81.497 1443 173 45 1068 2449 680976386 680974977 0.000000e+00 1099.0
22 TraesCS4D01G345900 chr5A 92.387 486 37 0 1372 1857 680885984 680885499 0.000000e+00 693.0
23 TraesCS4D01G345900 chr5A 83.502 297 28 9 586 874 680976800 680976517 8.710000e-65 257.0
24 TraesCS4D01G345900 chr5A 95.000 120 5 1 2006 2124 680886682 680886563 1.160000e-43 187.0
25 TraesCS4D01G345900 chr5A 87.261 157 15 4 299 451 680976984 680976829 9.030000e-40 174.0
26 TraesCS4D01G345900 chr5A 93.939 66 4 0 854 919 680887716 680887651 1.550000e-17 100.0
27 TraesCS4D01G345900 chr5A 89.062 64 2 3 1178 1239 680979383 680979323 9.420000e-10 75.0
28 TraesCS4D01G345900 chr5A 84.000 75 12 0 993 1067 680910489 680910415 3.390000e-09 73.1
29 TraesCS4D01G345900 chr6D 97.931 145 3 0 1 145 1935579 1935723 4.050000e-63 252.0
30 TraesCS4D01G345900 chr6D 97.931 145 3 0 1 145 448333527 448333671 4.050000e-63 252.0
31 TraesCS4D01G345900 chr6D 97.917 144 3 0 1 144 4731969 4731826 1.460000e-62 250.0
32 TraesCS4D01G345900 chr6D 97.917 144 3 0 1 144 375494117 375494260 1.460000e-62 250.0
33 TraesCS4D01G345900 chr6D 97.279 147 4 0 1 147 464257166 464257312 1.460000e-62 250.0
34 TraesCS4D01G345900 chr6D 97.917 144 3 0 1 144 472835235 472835378 1.460000e-62 250.0
35 TraesCS4D01G345900 chr2D 97.931 145 3 0 1 145 586334668 586334812 4.050000e-63 252.0
36 TraesCS4D01G345900 chr1D 97.917 144 3 0 1 144 24631226 24631083 1.460000e-62 250.0


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 TraesCS4D01G345900 chr4D 500284551 500287006 2455 True 4536.00 4536 100.0000 1 2456 1 chr4D.!!$R3 2455
1 TraesCS4D01G345900 chr4D 500292103 500292818 715 True 536.00 536 81.0700 483 1217 1 chr4D.!!$R4 734
2 TraesCS4D01G345900 chrUn 60373615 60375112 1497 False 1218.00 1218 81.9940 145 1644 1 chrUn.!!$F1 1499
3 TraesCS4D01G345900 chrUn 60463850 60464627 777 False 673.00 673 83.0140 1709 2456 1 chrUn.!!$F3 747
4 TraesCS4D01G345900 chrUn 60456673 60457498 825 False 586.00 586 80.3010 670 1497 1 chrUn.!!$F2 827
5 TraesCS4D01G345900 chrUn 307770828 307772043 1215 True 337.00 479 80.8315 871 2106 2 chrUn.!!$R3 1235
6 TraesCS4D01G345900 chr4B 643490695 643492943 2248 True 891.00 1190 81.7245 145 2423 2 chr4B.!!$R1 2278
7 TraesCS4D01G345900 chr4B 643625016 643627297 2281 True 202.10 344 88.9035 299 1206 2 chr4B.!!$R2 907
8 TraesCS4D01G345900 chr5A 680885499 680887716 2217 True 538.25 1173 92.7280 854 2124 4 chr5A.!!$R2 1270
9 TraesCS4D01G345900 chr5A 680974977 680979383 4406 True 401.25 1099 85.3305 299 2449 4 chr5A.!!$R3 2150

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
20 21 0.038343 GTGGCACGAACCGGTACTAA 60.038 55.0 8.0 0.0 0.0 2.24 F
643 3056 0.178987 TGGTATCTCTCCGGCTCTCC 60.179 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1308 3856 0.539669 GTTTGGGACTTGGGAGGTGG 60.540 60.000 0.0 0.0 0.00 4.61 R
2188 6114 1.202177 GCAGAATACCCATGCAACACG 60.202 52.381 0.0 0.0 39.75 4.49 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
18 19 2.341176 GTGGCACGAACCGGTACT 59.659 61.111 8.00 0.00 0.00 2.73
19 20 1.586028 GTGGCACGAACCGGTACTA 59.414 57.895 8.00 0.00 0.00 1.82
20 21 0.038343 GTGGCACGAACCGGTACTAA 60.038 55.000 8.00 0.00 0.00 2.24
21 22 0.678395 TGGCACGAACCGGTACTAAA 59.322 50.000 8.00 0.00 0.00 1.85
22 23 1.275856 TGGCACGAACCGGTACTAAAT 59.724 47.619 8.00 0.00 0.00 1.40
23 24 1.662122 GGCACGAACCGGTACTAAATG 59.338 52.381 8.00 1.92 0.00 2.32
24 25 2.340337 GCACGAACCGGTACTAAATGT 58.660 47.619 8.00 0.00 0.00 2.71
25 26 2.738314 GCACGAACCGGTACTAAATGTT 59.262 45.455 8.00 0.00 0.00 2.71
26 27 3.181527 GCACGAACCGGTACTAAATGTTC 60.182 47.826 8.00 0.00 33.66 3.18
27 28 3.989167 CACGAACCGGTACTAAATGTTCA 59.011 43.478 8.00 0.00 36.07 3.18
28 29 4.448395 CACGAACCGGTACTAAATGTTCAA 59.552 41.667 8.00 0.00 36.07 2.69
29 30 4.448732 ACGAACCGGTACTAAATGTTCAAC 59.551 41.667 8.00 0.00 36.07 3.18
31 32 5.613142 CGAACCGGTACTAAATGTTCAACAC 60.613 44.000 8.00 0.00 36.07 3.32
33 34 3.989167 CCGGTACTAAATGTTCAACACGA 59.011 43.478 0.00 0.00 0.00 4.35
42 43 2.709170 TTCAACACGAACCGGCATT 58.291 47.368 0.00 0.00 0.00 3.56
46 47 2.160615 TCAACACGAACCGGCATTAATG 59.839 45.455 11.27 11.27 0.00 1.90
47 48 1.091537 ACACGAACCGGCATTAATGG 58.908 50.000 17.02 3.25 0.00 3.16
48 49 1.339247 ACACGAACCGGCATTAATGGA 60.339 47.619 17.02 0.00 0.00 3.41
49 50 1.946768 CACGAACCGGCATTAATGGAT 59.053 47.619 17.02 0.00 0.00 3.41
50 51 3.135225 CACGAACCGGCATTAATGGATA 58.865 45.455 17.02 0.00 0.00 2.59
51 52 3.186409 CACGAACCGGCATTAATGGATAG 59.814 47.826 17.02 0.00 0.00 2.08
53 54 2.200373 ACCGGCATTAATGGATAGCC 57.800 50.000 17.02 10.23 41.86 3.93
57 58 3.831715 GGCATTAATGGATAGCCGTTC 57.168 47.619 17.02 0.00 42.42 3.95
59 60 3.064207 GCATTAATGGATAGCCGTTCGA 58.936 45.455 17.02 0.00 42.42 3.71
61 62 4.610680 GCATTAATGGATAGCCGTTCGAAC 60.611 45.833 18.47 18.47 42.42 3.95
62 63 1.949465 AATGGATAGCCGTTCGAACC 58.051 50.000 22.07 9.45 39.17 3.62
63 64 0.249322 ATGGATAGCCGTTCGAACCG 60.249 55.000 22.07 16.66 36.79 4.44
70 71 1.373246 CCGTTCGAACCGGCACTAA 60.373 57.895 22.07 0.00 38.85 2.24
72 73 0.368907 CGTTCGAACCGGCACTAATG 59.631 55.000 22.07 0.54 0.00 1.90
73 74 0.725117 GTTCGAACCGGCACTAATGG 59.275 55.000 17.68 0.00 0.00 3.16
75 76 1.184431 TCGAACCGGCACTAATGGTA 58.816 50.000 0.00 0.00 34.11 3.25
76 77 1.135024 TCGAACCGGCACTAATGGTAC 60.135 52.381 0.00 0.00 34.11 3.34
78 79 0.985760 AACCGGCACTAATGGTACCA 59.014 50.000 18.99 18.99 34.11 3.25
79 80 1.209621 ACCGGCACTAATGGTACCAT 58.790 50.000 22.23 22.23 38.46 3.55
81 82 2.773087 ACCGGCACTAATGGTACCATTA 59.227 45.455 34.62 34.62 43.92 1.90
92 93 1.972795 GGTACCATTAGTATCGGGCCA 59.027 52.381 7.15 0.00 32.28 5.36
93 94 2.369532 GGTACCATTAGTATCGGGCCAA 59.630 50.000 7.15 0.00 32.28 4.52
94 95 3.181452 GGTACCATTAGTATCGGGCCAAA 60.181 47.826 7.15 0.00 32.28 3.28
96 97 4.178956 ACCATTAGTATCGGGCCAAAAT 57.821 40.909 4.39 0.00 0.00 1.82
98 99 4.141287 CCATTAGTATCGGGCCAAAATCA 58.859 43.478 4.39 0.00 0.00 2.57
99 100 4.582656 CCATTAGTATCGGGCCAAAATCAA 59.417 41.667 4.39 0.00 0.00 2.57
100 101 5.068460 CCATTAGTATCGGGCCAAAATCAAA 59.932 40.000 4.39 0.00 0.00 2.69
101 102 5.570234 TTAGTATCGGGCCAAAATCAAAC 57.430 39.130 4.39 0.00 0.00 2.93
102 103 2.758423 AGTATCGGGCCAAAATCAAACC 59.242 45.455 4.39 0.00 0.00 3.27
103 104 0.530288 ATCGGGCCAAAATCAAACCG 59.470 50.000 4.39 0.00 42.45 4.44
104 105 1.080161 CGGGCCAAAATCAAACCGG 60.080 57.895 4.39 0.00 37.80 5.28
105 106 1.295101 GGGCCAAAATCAAACCGGG 59.705 57.895 6.32 0.00 0.00 5.73
109 110 2.164338 GCCAAAATCAAACCGGGACTA 58.836 47.619 6.32 0.00 0.00 2.59
110 111 2.559231 GCCAAAATCAAACCGGGACTAA 59.441 45.455 6.32 0.00 0.00 2.24
111 112 3.194755 GCCAAAATCAAACCGGGACTAAT 59.805 43.478 6.32 0.00 0.00 1.73
112 113 4.743493 CCAAAATCAAACCGGGACTAATG 58.257 43.478 6.32 0.00 0.00 1.90
113 114 4.219725 CCAAAATCAAACCGGGACTAATGT 59.780 41.667 6.32 0.00 0.00 2.71
115 116 3.713826 ATCAAACCGGGACTAATGTGT 57.286 42.857 6.32 0.00 0.00 3.72
116 117 3.048337 TCAAACCGGGACTAATGTGTC 57.952 47.619 6.32 0.00 36.31 3.67
118 119 3.000727 CAAACCGGGACTAATGTGTCTC 58.999 50.000 6.32 0.00 37.16 3.36
119 120 1.933021 ACCGGGACTAATGTGTCTCA 58.067 50.000 6.32 0.00 37.29 3.27
132 133 4.974645 TGTGTCTCACATTAGGTCCTTT 57.025 40.909 0.00 0.00 39.62 3.11
134 135 5.690865 TGTGTCTCACATTAGGTCCTTTTT 58.309 37.500 0.00 0.00 39.62 1.94
137 138 7.159372 GTGTCTCACATTAGGTCCTTTTTCTA 58.841 38.462 0.00 0.00 34.08 2.10
138 139 7.117956 GTGTCTCACATTAGGTCCTTTTTCTAC 59.882 40.741 0.00 0.00 34.08 2.59
139 140 7.016268 TGTCTCACATTAGGTCCTTTTTCTACT 59.984 37.037 0.00 0.00 0.00 2.57
140 141 8.529476 GTCTCACATTAGGTCCTTTTTCTACTA 58.471 37.037 0.00 0.00 0.00 1.82
141 142 8.750298 TCTCACATTAGGTCCTTTTTCTACTAG 58.250 37.037 0.00 0.00 0.00 2.57
142 143 8.431910 TCACATTAGGTCCTTTTTCTACTAGT 57.568 34.615 0.00 0.00 0.00 2.57
143 144 8.311836 TCACATTAGGTCCTTTTTCTACTAGTG 58.688 37.037 5.39 0.00 0.00 2.74
168 169 3.256631 ACATCACCATCCTTGAAACTTGC 59.743 43.478 0.00 0.00 0.00 4.01
173 174 3.181423 ACCATCCTTGAAACTTGCCCTTA 60.181 43.478 0.00 0.00 0.00 2.69
179 180 2.238521 TGAAACTTGCCCTTAGCCAAG 58.761 47.619 8.58 8.58 42.71 3.61
364 2755 5.738619 ACCATGAGTTAAACCCCATTTTC 57.261 39.130 0.00 0.00 0.00 2.29
422 2826 4.669965 CGTCGTATGAACTTAACCACTCGA 60.670 45.833 0.00 0.00 0.00 4.04
435 2839 0.314302 CACTCGAACGAGGTCCACTT 59.686 55.000 24.33 2.86 45.88 3.16
453 2857 0.388134 TTTTTCTCCTCCGCGTCTCG 60.388 55.000 4.92 0.00 38.08 4.04
494 2898 5.916969 TGCAGTTTTTGTTTTGTTTTACCG 58.083 33.333 0.00 0.00 0.00 4.02
540 2949 1.538419 CGGTAGGTTAAGCTAGCTGGC 60.538 57.143 30.39 15.23 0.00 4.85
566 2976 5.844396 CGACCGAGACTTTGAAAAATGTTAC 59.156 40.000 0.00 0.00 0.00 2.50
614 3025 3.121019 CGAGATCCGTCCCACTCC 58.879 66.667 0.00 0.00 0.00 3.85
615 3026 2.491022 CGAGATCCGTCCCACTCCC 61.491 68.421 0.00 0.00 0.00 4.30
616 3027 2.442272 AGATCCGTCCCACTCCCG 60.442 66.667 0.00 0.00 0.00 5.14
617 3028 2.441532 GATCCGTCCCACTCCCGA 60.442 66.667 0.00 0.00 0.00 5.14
618 3029 1.833049 GATCCGTCCCACTCCCGAT 60.833 63.158 0.00 0.00 0.00 4.18
619 3030 1.807495 GATCCGTCCCACTCCCGATC 61.807 65.000 0.00 0.00 0.00 3.69
637 3050 2.251409 TCTACGTGGTATCTCTCCGG 57.749 55.000 0.00 0.00 0.00 5.14
639 3052 0.182061 TACGTGGTATCTCTCCGGCT 59.818 55.000 0.00 0.00 0.00 5.52
640 3053 1.102222 ACGTGGTATCTCTCCGGCTC 61.102 60.000 0.00 0.00 0.00 4.70
641 3054 0.820074 CGTGGTATCTCTCCGGCTCT 60.820 60.000 0.00 0.00 0.00 4.09
642 3055 0.955905 GTGGTATCTCTCCGGCTCTC 59.044 60.000 0.00 0.00 0.00 3.20
643 3056 0.178987 TGGTATCTCTCCGGCTCTCC 60.179 60.000 0.00 0.00 0.00 3.71
677 3090 8.028938 GCCACAATTTTTGTCTGAAGTACATAT 58.971 33.333 0.00 0.00 43.23 1.78
688 3101 7.872483 TGTCTGAAGTACATATATACGGTCGTA 59.128 37.037 5.67 5.67 34.87 3.43
704 3121 6.834876 ACGGTCGTATTTTTATTCTTTGACC 58.165 36.000 0.00 0.00 39.89 4.02
775 3210 1.341531 CCGCGTATTCCTCTCCTTCAT 59.658 52.381 4.92 0.00 0.00 2.57
790 3225 7.333174 CCTCTCCTTCATTTCTCTGTCTTAAAC 59.667 40.741 0.00 0.00 0.00 2.01
830 3268 6.302313 GTCATTTTCACTCGACAATTAAACGG 59.698 38.462 0.00 0.00 0.00 4.44
834 3276 2.727798 CACTCGACAATTAAACGGACGT 59.272 45.455 0.00 0.00 0.00 4.34
880 3322 7.773690 ACATTATAAGTATCCACACAAGAACCC 59.226 37.037 0.00 0.00 0.00 4.11
948 3400 3.542875 CCACGTACGTACACTACTGATCG 60.543 52.174 22.34 9.59 0.00 3.69
1069 3527 1.170919 GCGACCGTGGAGCTATCCTA 61.171 60.000 0.00 0.00 46.80 2.94
1260 3804 4.039004 TGCATTACACACATCTTTTTGCCT 59.961 37.500 0.00 0.00 0.00 4.75
1263 3807 1.963515 ACACACATCTTTTTGCCTCCC 59.036 47.619 0.00 0.00 0.00 4.30
1308 3856 3.803555 CGTTGCAGTTTCAGATCTTGAC 58.196 45.455 0.00 0.00 34.94 3.18
1323 3871 1.423794 TTGACCACCTCCCAAGTCCC 61.424 60.000 0.00 0.00 0.00 4.46
1406 5244 1.374252 CCACCAGTTTCCCTCGACG 60.374 63.158 0.00 0.00 0.00 5.12
1426 5267 5.447144 CGACGCAAAATTTATGATCCTGTCA 60.447 40.000 0.00 0.00 42.06 3.58
1443 5284 4.946157 CCTGTCAGCAATTACTCCTTTCAT 59.054 41.667 0.00 0.00 0.00 2.57
1553 5402 2.667473 CGTAGGGTTTCTTCGGACAT 57.333 50.000 0.00 0.00 33.48 3.06
1567 5446 6.472887 TCTTCGGACATCACCTTTAGATTTT 58.527 36.000 0.00 0.00 0.00 1.82
1601 5480 3.217626 CCTATTGTTTCTCCAGCATCCC 58.782 50.000 0.00 0.00 0.00 3.85
1605 5486 2.601702 TTTCTCCAGCATCCCGCCA 61.602 57.895 0.00 0.00 44.04 5.69
1620 5501 1.678101 CCGCCAAAGGAGGAATTCATC 59.322 52.381 11.64 11.64 45.77 2.92
1697 5578 1.916181 ACCTCCTGGACTATGGGTTTG 59.084 52.381 4.88 0.00 37.04 2.93
1732 5613 9.801873 GATAGATATGTAGAGATCTCCTTTTGC 57.198 37.037 19.30 5.05 32.30 3.68
1815 5700 7.169140 GGTTTTTGTAGTGGATGTTTTGTCATC 59.831 37.037 0.00 0.00 42.20 2.92
1893 5784 6.533819 TTTGACTGTACGATTAGTTTGTGG 57.466 37.500 0.00 0.00 0.00 4.17
1909 5800 6.118170 AGTTTGTGGATGTCTATTGGATCTG 58.882 40.000 0.00 0.00 0.00 2.90
1914 5805 2.229675 TGTCTATTGGATCTGCGCTG 57.770 50.000 9.73 8.88 0.00 5.18
1933 5824 6.208797 TGCGCTGTACTAGTCTAATTATGGAT 59.791 38.462 9.73 0.00 0.00 3.41
1957 5848 4.781934 AGTTGCAGTGAGGGGATAATAAC 58.218 43.478 0.00 0.00 0.00 1.89
1965 5856 5.602978 AGTGAGGGGATAATAACGAGAACAT 59.397 40.000 0.00 0.00 0.00 2.71
1966 5857 6.781014 AGTGAGGGGATAATAACGAGAACATA 59.219 38.462 0.00 0.00 0.00 2.29
1976 5867 6.715344 ATAACGAGAACATAGTTTTCGCAA 57.285 33.333 18.66 10.12 34.84 4.85
1977 5868 4.647291 ACGAGAACATAGTTTTCGCAAG 57.353 40.909 18.66 0.00 34.84 4.01
2018 5942 5.116084 ACAATGTGTATTAGCCTGGTGAT 57.884 39.130 0.00 0.00 0.00 3.06
2044 5968 7.974504 AGAGAAGATTAAAGAACTTGTACCCA 58.025 34.615 0.00 0.00 0.00 4.51
2147 6072 9.911788 AGATTTACTCTCAACAATATGTCCAAT 57.088 29.630 0.00 0.00 0.00 3.16
2240 6167 6.541278 GTGGAGTATTACCCAAGTGATTTACC 59.459 42.308 5.83 0.00 33.69 2.85
2250 6177 3.478857 AGTGATTTACCGTGTGTTGGA 57.521 42.857 0.00 0.00 0.00 3.53
2265 6192 7.148323 CCGTGTGTTGGAATTTTAGATGTATGA 60.148 37.037 0.00 0.00 0.00 2.15
2270 6197 8.519526 TGTTGGAATTTTAGATGTATGAACACC 58.480 33.333 0.00 0.00 38.78 4.16
2280 6208 9.631257 TTAGATGTATGAACACCATGAATTGAT 57.369 29.630 0.00 0.00 38.78 2.57
2323 6252 7.770433 TGACTAAGTATCATTGGGTTGATCAAG 59.230 37.037 8.80 0.00 37.51 3.02
2407 6336 6.713762 AGATTTGGTTCTTGAACACATGAA 57.286 33.333 14.38 0.00 0.00 2.57
2414 6343 4.163441 TCTTGAACACATGAAGGTTCCA 57.837 40.909 19.33 12.09 42.04 3.53
2423 6352 4.099266 CACATGAAGGTTCCACTCCAAAAA 59.901 41.667 0.00 0.00 0.00 1.94
2424 6353 4.901250 ACATGAAGGTTCCACTCCAAAAAT 59.099 37.500 0.00 0.00 0.00 1.82
2442 6371 6.491403 CCAAAAATATCTCCCATAAGACAGGG 59.509 42.308 0.00 0.00 46.90 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.038343 TTAGTACCGGTTCGTGCCAC 60.038 55.000 15.04 1.99 0.00 5.01
3 4 1.662122 CATTTAGTACCGGTTCGTGCC 59.338 52.381 15.04 0.00 0.00 5.01
5 6 3.989167 TGAACATTTAGTACCGGTTCGTG 59.011 43.478 15.04 9.70 40.42 4.35
6 7 4.255833 TGAACATTTAGTACCGGTTCGT 57.744 40.909 15.04 0.00 40.42 3.85
7 8 4.448395 TGTTGAACATTTAGTACCGGTTCG 59.552 41.667 15.04 0.00 40.42 3.95
9 10 4.211794 CGTGTTGAACATTTAGTACCGGTT 59.788 41.667 15.04 0.00 0.00 4.44
10 11 3.742369 CGTGTTGAACATTTAGTACCGGT 59.258 43.478 13.98 13.98 0.00 5.28
11 12 3.989167 TCGTGTTGAACATTTAGTACCGG 59.011 43.478 0.00 0.00 0.00 5.28
24 25 1.880271 TAATGCCGGTTCGTGTTGAA 58.120 45.000 1.90 0.00 0.00 2.69
25 26 1.880271 TTAATGCCGGTTCGTGTTGA 58.120 45.000 1.90 0.00 0.00 3.18
26 27 2.514902 CATTAATGCCGGTTCGTGTTG 58.485 47.619 1.90 0.00 0.00 3.33
27 28 1.470890 CCATTAATGCCGGTTCGTGTT 59.529 47.619 10.11 0.00 0.00 3.32
28 29 1.091537 CCATTAATGCCGGTTCGTGT 58.908 50.000 10.11 0.00 0.00 4.49
29 30 1.374560 TCCATTAATGCCGGTTCGTG 58.625 50.000 10.11 0.00 0.00 4.35
31 32 2.159627 GCTATCCATTAATGCCGGTTCG 59.840 50.000 10.11 0.00 0.00 3.95
33 34 2.514803 GGCTATCCATTAATGCCGGTT 58.485 47.619 10.11 0.00 33.96 4.44
38 39 3.064207 TCGAACGGCTATCCATTAATGC 58.936 45.455 10.11 0.00 0.00 3.56
39 40 4.084013 GGTTCGAACGGCTATCCATTAATG 60.084 45.833 21.34 8.58 0.00 1.90
40 41 4.062991 GGTTCGAACGGCTATCCATTAAT 58.937 43.478 21.34 0.00 0.00 1.40
42 43 2.544277 CGGTTCGAACGGCTATCCATTA 60.544 50.000 21.34 0.00 0.00 1.90
46 47 1.590792 CCGGTTCGAACGGCTATCC 60.591 63.158 25.58 9.16 45.34 2.59
47 48 4.008035 CCGGTTCGAACGGCTATC 57.992 61.111 25.58 9.62 45.34 2.08
53 54 0.368907 CATTAGTGCCGGTTCGAACG 59.631 55.000 21.34 15.88 0.00 3.95
54 55 0.725117 CCATTAGTGCCGGTTCGAAC 59.275 55.000 20.14 20.14 0.00 3.95
56 57 1.135024 GTACCATTAGTGCCGGTTCGA 60.135 52.381 1.90 0.00 34.12 3.71
57 58 1.283736 GTACCATTAGTGCCGGTTCG 58.716 55.000 1.90 0.00 34.12 3.95
59 60 3.867549 GGTACCATTAGTGCCGGTT 57.132 52.632 7.15 0.00 41.78 4.44
70 71 2.570302 GGCCCGATACTAATGGTACCAT 59.430 50.000 22.23 22.23 38.46 3.55
72 73 1.972795 TGGCCCGATACTAATGGTACC 59.027 52.381 4.43 4.43 32.72 3.34
73 74 3.756933 TTGGCCCGATACTAATGGTAC 57.243 47.619 0.00 0.00 32.72 3.34
75 76 3.655615 TTTTGGCCCGATACTAATGGT 57.344 42.857 0.00 0.00 0.00 3.55
76 77 4.141287 TGATTTTGGCCCGATACTAATGG 58.859 43.478 0.00 0.00 0.00 3.16
78 79 5.068591 GGTTTGATTTTGGCCCGATACTAAT 59.931 40.000 0.00 0.00 0.00 1.73
79 80 4.399934 GGTTTGATTTTGGCCCGATACTAA 59.600 41.667 0.00 0.00 0.00 2.24
81 82 2.758423 GGTTTGATTTTGGCCCGATACT 59.242 45.455 0.00 0.00 0.00 2.12
83 84 1.746220 CGGTTTGATTTTGGCCCGATA 59.254 47.619 0.00 0.00 37.66 2.92
84 85 0.530288 CGGTTTGATTTTGGCCCGAT 59.470 50.000 0.00 0.00 37.66 4.18
85 86 1.528292 CCGGTTTGATTTTGGCCCGA 61.528 55.000 0.00 0.00 37.66 5.14
86 87 1.080161 CCGGTTTGATTTTGGCCCG 60.080 57.895 0.00 0.00 35.32 6.13
87 88 1.188871 TCCCGGTTTGATTTTGGCCC 61.189 55.000 0.00 0.00 0.00 5.80
88 89 0.037697 GTCCCGGTTTGATTTTGGCC 60.038 55.000 0.00 0.00 0.00 5.36
89 90 0.966179 AGTCCCGGTTTGATTTTGGC 59.034 50.000 0.00 0.00 0.00 4.52
92 93 4.830600 ACACATTAGTCCCGGTTTGATTTT 59.169 37.500 0.00 0.00 0.00 1.82
93 94 4.403734 ACACATTAGTCCCGGTTTGATTT 58.596 39.130 0.00 0.00 0.00 2.17
94 95 4.007659 GACACATTAGTCCCGGTTTGATT 58.992 43.478 0.00 0.00 32.36 2.57
96 97 2.635915 AGACACATTAGTCCCGGTTTGA 59.364 45.455 0.00 0.00 39.34 2.69
98 99 2.635915 TGAGACACATTAGTCCCGGTTT 59.364 45.455 0.00 0.00 39.34 3.27
99 100 2.028385 GTGAGACACATTAGTCCCGGTT 60.028 50.000 0.00 0.00 39.34 4.44
100 101 1.549170 GTGAGACACATTAGTCCCGGT 59.451 52.381 0.00 0.00 39.34 5.28
101 102 1.548719 TGTGAGACACATTAGTCCCGG 59.451 52.381 0.00 0.00 39.62 5.73
112 113 5.998363 AGAAAAAGGACCTAATGTGAGACAC 59.002 40.000 0.00 0.00 34.56 3.67
113 114 6.187727 AGAAAAAGGACCTAATGTGAGACA 57.812 37.500 0.00 0.00 0.00 3.41
115 116 7.554959 AGTAGAAAAAGGACCTAATGTGAGA 57.445 36.000 0.00 0.00 0.00 3.27
116 117 8.532819 ACTAGTAGAAAAAGGACCTAATGTGAG 58.467 37.037 3.59 0.00 0.00 3.51
118 119 8.311836 TCACTAGTAGAAAAAGGACCTAATGTG 58.688 37.037 3.59 0.00 0.00 3.21
119 120 8.312564 GTCACTAGTAGAAAAAGGACCTAATGT 58.687 37.037 3.59 0.00 0.00 2.71
122 123 7.288389 TGTGTCACTAGTAGAAAAAGGACCTAA 59.712 37.037 3.59 0.00 0.00 2.69
124 125 5.601313 TGTGTCACTAGTAGAAAAAGGACCT 59.399 40.000 3.59 0.00 0.00 3.85
125 126 5.850614 TGTGTCACTAGTAGAAAAAGGACC 58.149 41.667 3.59 0.00 0.00 4.46
126 127 7.152645 TGATGTGTCACTAGTAGAAAAAGGAC 58.847 38.462 3.59 0.00 0.00 3.85
127 128 7.297936 TGATGTGTCACTAGTAGAAAAAGGA 57.702 36.000 3.59 0.00 0.00 3.36
142 143 3.786368 TTCAAGGATGGTGATGTGTCA 57.214 42.857 0.00 0.00 0.00 3.58
143 144 4.074970 AGTTTCAAGGATGGTGATGTGTC 58.925 43.478 0.00 0.00 0.00 3.67
168 169 2.425143 TTCTGCATCTTGGCTAAGGG 57.575 50.000 10.21 4.16 34.59 3.95
173 174 2.243221 AGGGTAATTCTGCATCTTGGCT 59.757 45.455 0.00 0.00 34.04 4.75
179 180 2.609459 CACACGAGGGTAATTCTGCATC 59.391 50.000 0.00 0.00 0.00 3.91
403 2796 5.156355 TCGTTCGAGTGGTTAAGTTCATAC 58.844 41.667 0.00 0.00 0.00 2.39
422 2826 2.438392 AGGAGAAAAAGTGGACCTCGTT 59.562 45.455 0.00 0.00 0.00 3.85
435 2839 1.211969 CGAGACGCGGAGGAGAAAA 59.788 57.895 12.47 0.00 36.03 2.29
453 2857 1.464997 GCAATGACGAGTTCAGGAACC 59.535 52.381 8.47 0.53 42.06 3.62
540 2949 3.936902 TTTTTCAAAGTCTCGGTCGTG 57.063 42.857 0.00 0.00 0.00 4.35
614 3025 2.743126 GGAGAGATACCACGTAGATCGG 59.257 54.545 0.00 0.00 44.69 4.18
615 3026 2.412429 CGGAGAGATACCACGTAGATCG 59.588 54.545 0.00 0.00 46.00 3.69
616 3027 2.743126 CCGGAGAGATACCACGTAGATC 59.257 54.545 0.00 0.00 0.00 2.75
617 3028 2.780714 CCGGAGAGATACCACGTAGAT 58.219 52.381 0.00 0.00 0.00 1.98
618 3029 1.813092 GCCGGAGAGATACCACGTAGA 60.813 57.143 5.05 0.00 0.00 2.59
619 3030 0.592148 GCCGGAGAGATACCACGTAG 59.408 60.000 5.05 0.00 0.00 3.51
645 3058 0.033366 ACAAAAATTGTGGCCCGAGC 59.967 50.000 0.00 0.00 43.48 5.03
646 3059 1.613437 AGACAAAAATTGTGGCCCGAG 59.387 47.619 0.00 0.00 45.52 4.63
647 3060 1.339610 CAGACAAAAATTGTGGCCCGA 59.660 47.619 0.00 0.00 45.52 5.14
688 3101 5.778862 CCACACCGGTCAAAGAATAAAAAT 58.221 37.500 2.59 0.00 0.00 1.82
704 3121 1.341531 ACTCTTCTTCAGACCACACCG 59.658 52.381 0.00 0.00 0.00 4.94
719 3149 3.797256 CGTGTGAGAAAACGAAGACTCTT 59.203 43.478 0.00 0.00 42.32 2.85
830 3268 2.075338 ACTCTCACCGAGAACTACGTC 58.925 52.381 0.00 0.00 42.62 4.34
834 3276 2.818432 GTCCAACTCTCACCGAGAACTA 59.182 50.000 0.00 0.00 42.62 2.24
838 3280 1.924731 ATGTCCAACTCTCACCGAGA 58.075 50.000 0.00 0.00 42.62 4.04
849 3291 8.500753 TTGTGTGGATACTTATAATGTCCAAC 57.499 34.615 12.54 12.63 40.38 3.77
880 3322 0.957395 ATGACTGCCTCCAAACTGCG 60.957 55.000 0.00 0.00 0.00 5.18
948 3400 3.625313 GGCAAAGAGGAGCTTGATTAGTC 59.375 47.826 0.00 0.00 36.80 2.59
983 3435 3.243101 CGCCATTAGTTCTCTTCTCGCTA 60.243 47.826 0.00 0.00 0.00 4.26
984 3436 2.480416 CGCCATTAGTTCTCTTCTCGCT 60.480 50.000 0.00 0.00 0.00 4.93
985 3437 1.855360 CGCCATTAGTTCTCTTCTCGC 59.145 52.381 0.00 0.00 0.00 5.03
986 3438 2.464865 CCGCCATTAGTTCTCTTCTCG 58.535 52.381 0.00 0.00 0.00 4.04
987 3439 2.205911 GCCGCCATTAGTTCTCTTCTC 58.794 52.381 0.00 0.00 0.00 2.87
988 3440 1.555075 TGCCGCCATTAGTTCTCTTCT 59.445 47.619 0.00 0.00 0.00 2.85
989 3441 2.024176 TGCCGCCATTAGTTCTCTTC 57.976 50.000 0.00 0.00 0.00 2.87
990 3442 2.171448 AGATGCCGCCATTAGTTCTCTT 59.829 45.455 0.00 0.00 0.00 2.85
991 3443 1.765314 AGATGCCGCCATTAGTTCTCT 59.235 47.619 0.00 0.00 0.00 3.10
1069 3527 8.471609 GGTACTGCTAAGAGAAGAGTTAAGAAT 58.528 37.037 0.00 0.00 0.00 2.40
1136 3603 1.230324 GGCTTTATCGGCTGGATGAC 58.770 55.000 0.00 0.00 36.55 3.06
1260 3804 7.154656 CACAGATTATTATCACGAGATTGGGA 58.845 38.462 0.00 0.00 35.67 4.37
1263 3807 6.400409 CGCCACAGATTATTATCACGAGATTG 60.400 42.308 0.00 0.00 35.67 2.67
1308 3856 0.539669 GTTTGGGACTTGGGAGGTGG 60.540 60.000 0.00 0.00 0.00 4.61
1323 3871 3.125146 CACCATCGTGTCCTATGTGTTTG 59.875 47.826 0.00 0.00 35.10 2.93
1406 5244 5.653507 TGCTGACAGGATCATAAATTTTGC 58.346 37.500 4.26 0.00 36.48 3.68
1426 5267 7.613022 TGATTCTTCATGAAAGGAGTAATTGCT 59.387 33.333 9.88 0.00 38.29 3.91
1443 5284 2.018644 GCCGGCCTTCATGATTCTTCA 61.019 52.381 18.11 0.00 36.00 3.02
1574 5453 6.313519 TGCTGGAGAAACAATAGGTATTCT 57.686 37.500 0.00 0.00 32.92 2.40
1578 5457 4.141482 GGGATGCTGGAGAAACAATAGGTA 60.141 45.833 0.00 0.00 0.00 3.08
1581 5460 2.874701 CGGGATGCTGGAGAAACAATAG 59.125 50.000 0.00 0.00 0.00 1.73
1601 5480 1.331756 CGATGAATTCCTCCTTTGGCG 59.668 52.381 2.27 0.00 0.00 5.69
1605 5486 2.806945 TGGCGATGAATTCCTCCTTT 57.193 45.000 2.27 0.00 0.00 3.11
1620 5501 5.286082 GTGATGTTATTGCTAAAGTTTGGCG 59.714 40.000 17.76 0.00 40.39 5.69
1786 5670 6.071051 ACAAAACATCCACTACAAAAACCACT 60.071 34.615 0.00 0.00 0.00 4.00
1798 5683 5.132502 TCAACTGATGACAAAACATCCACT 58.867 37.500 0.00 0.00 43.96 4.00
1880 5771 6.761242 TCCAATAGACATCCACAAACTAATCG 59.239 38.462 0.00 0.00 0.00 3.34
1893 5784 2.735663 CAGCGCAGATCCAATAGACATC 59.264 50.000 11.47 0.00 0.00 3.06
1909 5800 6.010294 TCCATAATTAGACTAGTACAGCGC 57.990 41.667 0.00 0.00 0.00 5.92
1933 5824 6.354130 GTTATTATCCCCTCACTGCAACTTA 58.646 40.000 0.00 0.00 0.00 2.24
1939 5830 3.321111 TCTCGTTATTATCCCCTCACTGC 59.679 47.826 0.00 0.00 0.00 4.40
1957 5848 4.903638 TCTTGCGAAAACTATGTTCTCG 57.096 40.909 2.30 2.30 0.00 4.04
2018 5942 9.096823 TGGGTACAAGTTCTTTAATCTTCTCTA 57.903 33.333 0.00 0.00 0.00 2.43
2044 5968 6.708285 AGACGAACCAAGAAAGTATACCAAT 58.292 36.000 0.00 0.00 0.00 3.16
2150 6076 4.202245 AGCTACCGAGAACTGCAATAAA 57.798 40.909 0.00 0.00 0.00 1.40
2184 6110 3.823873 AGAATACCCATGCAACACGAAAA 59.176 39.130 0.00 0.00 0.00 2.29
2187 6113 2.355197 CAGAATACCCATGCAACACGA 58.645 47.619 0.00 0.00 0.00 4.35
2188 6114 1.202177 GCAGAATACCCATGCAACACG 60.202 52.381 0.00 0.00 39.75 4.49
2194 6120 2.300433 TGTGATGCAGAATACCCATGC 58.700 47.619 0.00 0.00 40.40 4.06
2240 6167 7.747888 TCATACATCTAAAATTCCAACACACG 58.252 34.615 0.00 0.00 0.00 4.49
2294 6222 9.950496 GATCAACCCAATGATACTTAGTCATAT 57.050 33.333 0.00 0.00 40.08 1.78
2295 6223 8.933653 TGATCAACCCAATGATACTTAGTCATA 58.066 33.333 0.00 0.00 40.08 2.15
2296 6224 7.805163 TGATCAACCCAATGATACTTAGTCAT 58.195 34.615 0.00 0.00 40.08 3.06
2297 6225 7.194112 TGATCAACCCAATGATACTTAGTCA 57.806 36.000 0.00 0.00 40.08 3.41
2298 6226 7.770897 ACTTGATCAACCCAATGATACTTAGTC 59.229 37.037 3.38 0.00 40.08 2.59
2299 6227 7.633789 ACTTGATCAACCCAATGATACTTAGT 58.366 34.615 3.38 0.00 40.08 2.24
2300 6228 9.784531 ATACTTGATCAACCCAATGATACTTAG 57.215 33.333 3.38 0.00 40.08 2.18
2301 6229 9.778741 GATACTTGATCAACCCAATGATACTTA 57.221 33.333 3.38 0.00 40.08 2.24
2302 6230 8.274322 TGATACTTGATCAACCCAATGATACTT 58.726 33.333 3.38 0.00 41.80 2.24
2303 6231 7.805163 TGATACTTGATCAACCCAATGATACT 58.195 34.615 3.38 0.00 41.80 2.12
2323 6252 9.173939 GCAAGACAATAAGCATAAACATGATAC 57.826 33.333 0.00 0.00 0.00 2.24
2345 6274 1.376424 ACTCTCATGGTGGCGCAAG 60.376 57.895 10.83 0.00 43.44 4.01
2388 6317 4.277476 ACCTTCATGTGTTCAAGAACCAA 58.723 39.130 10.19 0.00 40.46 3.67
2400 6329 2.566833 TGGAGTGGAACCTTCATGTG 57.433 50.000 0.00 0.00 37.80 3.21
2401 6330 3.593442 TTTGGAGTGGAACCTTCATGT 57.407 42.857 0.00 0.00 37.80 3.21
2407 6336 5.510430 GGAGATATTTTTGGAGTGGAACCT 58.490 41.667 0.00 0.00 37.80 3.50
2414 6343 7.872138 TGTCTTATGGGAGATATTTTTGGAGT 58.128 34.615 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.