Multiple sequence alignment - TraesCS6D01G057300

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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 TraesCS6D01G057300 chr6D 100.000 3685 0 0 1 3685 27314826 27311142 0.000000e+00 6806.0
1 TraesCS6D01G057300 chr6D 99.257 942 6 1 2745 3685 119989869 119988928 0.000000e+00 1700.0
2 TraesCS6D01G057300 chr6D 81.992 1516 214 37 869 2344 27329245 27327749 0.000000e+00 1232.0
3 TraesCS6D01G057300 chr6D 82.211 1411 184 39 978 2343 27126964 27125576 0.000000e+00 1153.0
4 TraesCS6D01G057300 chr6D 82.133 1388 183 42 999 2343 27209671 27208306 0.000000e+00 1129.0
5 TraesCS6D01G057300 chr6D 84.504 413 41 9 2348 2750 27208084 27207685 1.610000e-103 387.0
6 TraesCS6D01G057300 chr6D 86.294 197 20 6 173 363 445739875 445739680 1.340000e-49 207.0
7 TraesCS6D01G057300 chr6D 78.201 289 32 19 2467 2744 27326970 27326702 4.930000e-34 156.0
8 TraesCS6D01G057300 chr6D 84.783 92 14 0 2575 2666 27511522 27511431 3.920000e-15 93.5
9 TraesCS6D01G057300 chrUn 92.202 1885 85 24 914 2750 76831372 76833242 0.000000e+00 2610.0
10 TraesCS6D01G057300 chrUn 92.202 1885 85 24 914 2750 241635449 241637319 0.000000e+00 2610.0
11 TraesCS6D01G057300 chrUn 99.468 939 4 1 2748 3685 268486110 268487048 0.000000e+00 1705.0
12 TraesCS6D01G057300 chrUn 83.929 560 63 14 952 1487 76751875 76751319 9.130000e-141 510.0
13 TraesCS6D01G057300 chr7D 99.361 939 5 1 2748 3685 9080602 9079664 0.000000e+00 1700.0
14 TraesCS6D01G057300 chr7D 99.153 945 6 2 2743 3685 16497199 16496255 0.000000e+00 1700.0
15 TraesCS6D01G057300 chr7D 99.153 944 6 2 2744 3685 40522461 40523404 0.000000e+00 1698.0
16 TraesCS6D01G057300 chr7D 99.255 940 6 1 2747 3685 18905002 18905941 0.000000e+00 1696.0
17 TraesCS6D01G057300 chr7D 81.987 594 68 26 173 748 214107524 214106952 5.570000e-128 468.0
18 TraesCS6D01G057300 chr7D 81.026 585 69 26 173 743 37974192 37973636 9.460000e-116 427.0
19 TraesCS6D01G057300 chr2D 99.361 939 5 1 2748 3685 8402529 8403467 0.000000e+00 1700.0
20 TraesCS6D01G057300 chr1D 99.255 940 6 1 2747 3685 489565052 489565991 0.000000e+00 1696.0
21 TraesCS6D01G057300 chr1D 98.135 965 13 4 2725 3685 41696507 41697470 0.000000e+00 1677.0
22 TraesCS6D01G057300 chr1D 81.834 589 68 26 173 743 329673437 329674004 3.350000e-125 459.0
23 TraesCS6D01G057300 chr1D 78.974 585 74 26 173 743 492483705 492483156 1.630000e-93 353.0
24 TraesCS6D01G057300 chr1D 87.838 148 13 2 1 143 398248846 398248993 6.330000e-38 169.0
25 TraesCS6D01G057300 chr6A 82.558 1376 174 37 987 2318 31159870 31161223 0.000000e+00 1151.0
26 TraesCS6D01G057300 chr6A 81.030 1476 205 36 913 2344 31044008 31045452 0.000000e+00 1105.0
27 TraesCS6D01G057300 chr6A 96.291 674 13 3 1594 2256 31108176 31108848 0.000000e+00 1096.0
28 TraesCS6D01G057300 chr6A 93.023 645 32 3 967 1599 31092489 31093132 0.000000e+00 929.0
29 TraesCS6D01G057300 chr6A 91.984 499 27 7 2257 2750 31109055 31109545 0.000000e+00 688.0
30 TraesCS6D01G057300 chr6A 80.000 585 67 23 173 743 606621980 606622528 1.610000e-103 387.0
31 TraesCS6D01G057300 chr6A 83.688 282 31 10 2467 2739 31046238 31046513 6.110000e-63 252.0
32 TraesCS6D01G057300 chr6A 96.774 31 1 0 938 968 31060178 31060208 7.000000e-03 52.8
33 TraesCS6D01G057300 chr6B 79.625 1227 181 52 1160 2343 49701288 49700088 0.000000e+00 817.0
34 TraesCS6D01G057300 chr6B 82.850 414 47 9 2349 2750 49699871 49699470 2.110000e-92 350.0
35 TraesCS6D01G057300 chr6B 87.234 94 12 0 2575 2668 60088513 60088420 1.400000e-19 108.0
36 TraesCS6D01G057300 chr6B 78.378 148 30 2 1784 1930 75267628 75267482 1.090000e-15 95.3
37 TraesCS6D01G057300 chr6B 84.783 92 14 0 2575 2666 51138276 51138185 3.920000e-15 93.5
38 TraesCS6D01G057300 chr5D 80.143 559 74 22 173 725 540082756 540082229 2.080000e-102 383.0
39 TraesCS6D01G057300 chr5D 87.586 145 13 2 4 143 550983295 550983439 2.940000e-36 163.0
40 TraesCS6D01G057300 chr5D 87.075 147 14 2 2 143 520643252 520643106 1.060000e-35 161.0
41 TraesCS6D01G057300 chr5B 78.694 582 81 19 173 743 528933552 528933003 7.570000e-92 348.0
42 TraesCS6D01G057300 chr5B 77.654 358 44 22 173 507 406607829 406608173 6.280000e-43 185.0
43 TraesCS6D01G057300 chr5B 88.028 142 12 2 7 143 507687774 507687633 2.940000e-36 163.0
44 TraesCS6D01G057300 chr7A 78.425 584 86 30 173 741 39663691 39663133 9.800000e-91 344.0
45 TraesCS6D01G057300 chr7A 86.897 145 13 5 3 141 634322350 634322206 1.370000e-34 158.0
46 TraesCS6D01G057300 chr7B 82.289 367 51 11 372 728 585878867 585878505 4.620000e-79 305.0
47 TraesCS6D01G057300 chr7B 87.919 149 12 2 1 143 113517339 113517487 1.760000e-38 171.0
48 TraesCS6D01G057300 chr7B 88.732 142 11 2 7 143 74586413 74586272 6.330000e-38 169.0
49 TraesCS6D01G057300 chr2A 82.745 255 40 4 1052 1304 762930803 762930551 1.330000e-54 224.0
50 TraesCS6D01G057300 chr3D 87.912 182 12 6 173 347 72255060 72254882 4.820000e-49 206.0
51 TraesCS6D01G057300 chr3D 88.811 143 10 2 7 143 481517783 481517641 1.760000e-38 171.0
52 TraesCS6D01G057300 chr3A 85.354 198 21 4 173 363 741512773 741512969 8.070000e-47 198.0
53 TraesCS6D01G057300 chr3A 85.000 200 20 4 173 363 741476540 741476738 1.040000e-45 195.0
54 TraesCS6D01G057300 chr3A 84.925 199 21 4 173 363 741388327 741388524 3.760000e-45 193.0
55 TraesCS6D01G057300 chr3A 84.925 199 21 4 173 363 741426554 741426751 3.760000e-45 193.0
56 TraesCS6D01G057300 chr3A 84.925 199 21 4 173 363 741589785 741589982 3.760000e-45 193.0
57 TraesCS6D01G057300 chr4B 87.671 146 15 2 1 143 642425152 642425297 2.280000e-37 167.0
58 TraesCS6D01G057300 chr5A 78.723 235 33 13 308 532 447144145 447144372 1.380000e-29 141.0


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 TraesCS6D01G057300 chr6D 27311142 27314826 3684 True 6806.0 6806 100.0000 1 3685 1 chr6D.!!$R2 3684
1 TraesCS6D01G057300 chr6D 119988928 119989869 941 True 1700.0 1700 99.2570 2745 3685 1 chr6D.!!$R4 940
2 TraesCS6D01G057300 chr6D 27125576 27126964 1388 True 1153.0 1153 82.2110 978 2343 1 chr6D.!!$R1 1365
3 TraesCS6D01G057300 chr6D 27207685 27209671 1986 True 758.0 1129 83.3185 999 2750 2 chr6D.!!$R6 1751
4 TraesCS6D01G057300 chr6D 27326702 27329245 2543 True 694.0 1232 80.0965 869 2744 2 chr6D.!!$R7 1875
5 TraesCS6D01G057300 chrUn 76831372 76833242 1870 False 2610.0 2610 92.2020 914 2750 1 chrUn.!!$F1 1836
6 TraesCS6D01G057300 chrUn 241635449 241637319 1870 False 2610.0 2610 92.2020 914 2750 1 chrUn.!!$F2 1836
7 TraesCS6D01G057300 chrUn 268486110 268487048 938 False 1705.0 1705 99.4680 2748 3685 1 chrUn.!!$F3 937
8 TraesCS6D01G057300 chrUn 76751319 76751875 556 True 510.0 510 83.9290 952 1487 1 chrUn.!!$R1 535
9 TraesCS6D01G057300 chr7D 9079664 9080602 938 True 1700.0 1700 99.3610 2748 3685 1 chr7D.!!$R1 937
10 TraesCS6D01G057300 chr7D 16496255 16497199 944 True 1700.0 1700 99.1530 2743 3685 1 chr7D.!!$R2 942
11 TraesCS6D01G057300 chr7D 40522461 40523404 943 False 1698.0 1698 99.1530 2744 3685 1 chr7D.!!$F2 941
12 TraesCS6D01G057300 chr7D 18905002 18905941 939 False 1696.0 1696 99.2550 2747 3685 1 chr7D.!!$F1 938
13 TraesCS6D01G057300 chr7D 214106952 214107524 572 True 468.0 468 81.9870 173 748 1 chr7D.!!$R4 575
14 TraesCS6D01G057300 chr7D 37973636 37974192 556 True 427.0 427 81.0260 173 743 1 chr7D.!!$R3 570
15 TraesCS6D01G057300 chr2D 8402529 8403467 938 False 1700.0 1700 99.3610 2748 3685 1 chr2D.!!$F1 937
16 TraesCS6D01G057300 chr1D 489565052 489565991 939 False 1696.0 1696 99.2550 2747 3685 1 chr1D.!!$F4 938
17 TraesCS6D01G057300 chr1D 41696507 41697470 963 False 1677.0 1677 98.1350 2725 3685 1 chr1D.!!$F1 960
18 TraesCS6D01G057300 chr1D 329673437 329674004 567 False 459.0 459 81.8340 173 743 1 chr1D.!!$F2 570
19 TraesCS6D01G057300 chr1D 492483156 492483705 549 True 353.0 353 78.9740 173 743 1 chr1D.!!$R1 570
20 TraesCS6D01G057300 chr6A 31159870 31161223 1353 False 1151.0 1151 82.5580 987 2318 1 chr6A.!!$F3 1331
21 TraesCS6D01G057300 chr6A 31092489 31093132 643 False 929.0 929 93.0230 967 1599 1 chr6A.!!$F2 632
22 TraesCS6D01G057300 chr6A 31108176 31109545 1369 False 892.0 1096 94.1375 1594 2750 2 chr6A.!!$F6 1156
23 TraesCS6D01G057300 chr6A 31044008 31046513 2505 False 678.5 1105 82.3590 913 2739 2 chr6A.!!$F5 1826
24 TraesCS6D01G057300 chr6A 606621980 606622528 548 False 387.0 387 80.0000 173 743 1 chr6A.!!$F4 570
25 TraesCS6D01G057300 chr6B 49699470 49701288 1818 True 583.5 817 81.2375 1160 2750 2 chr6B.!!$R4 1590
26 TraesCS6D01G057300 chr5D 540082229 540082756 527 True 383.0 383 80.1430 173 725 1 chr5D.!!$R2 552
27 TraesCS6D01G057300 chr5B 528933003 528933552 549 True 348.0 348 78.6940 173 743 1 chr5B.!!$R2 570
28 TraesCS6D01G057300 chr7A 39663133 39663691 558 True 344.0 344 78.4250 173 741 1 chr7A.!!$R1 568

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
69 70 0.822811 AACCTGCACACAACATTGCA 59.177 45.000 0.00 0.0 46.43 4.08 F
73 74 1.101331 TGCACACAACATTGCAGTGA 58.899 45.000 16.98 0.0 43.79 3.41 F
780 840 1.144708 TGTGATGTTTTGGCTCTGGGA 59.855 47.619 0.00 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 1897 1.923204 CTCTGCTCGCATAACTGTCAC 59.077 52.381 0.0 0.0 0.00 3.67 R
2166 2292 5.796350 ATCTTAACACAAGAACGGCATAC 57.204 39.130 0.0 0.0 0.00 2.39 R
2687 3753 0.954452 GGTTTCCTGCTCAACCAGTG 59.046 55.000 0.0 0.0 41.97 3.66 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
68 69 1.938625 AAACCTGCACACAACATTGC 58.061 45.000 0.00 0.00 39.33 3.56
69 70 0.822811 AACCTGCACACAACATTGCA 59.177 45.000 0.00 0.00 46.43 4.08
72 73 3.644774 TGCACACAACATTGCAGTG 57.355 47.368 7.79 7.79 43.79 3.66
73 74 1.101331 TGCACACAACATTGCAGTGA 58.899 45.000 16.98 0.00 43.79 3.41
74 75 1.475682 TGCACACAACATTGCAGTGAA 59.524 42.857 16.98 7.80 43.79 3.18
75 76 2.094338 TGCACACAACATTGCAGTGAAA 60.094 40.909 16.98 0.00 43.79 2.69
76 77 3.125316 GCACACAACATTGCAGTGAAAT 58.875 40.909 16.98 0.00 38.81 2.17
77 78 3.556775 GCACACAACATTGCAGTGAAATT 59.443 39.130 16.98 0.00 38.81 1.82
78 79 4.551217 GCACACAACATTGCAGTGAAATTG 60.551 41.667 16.98 12.18 38.81 2.32
129 130 8.509690 ACACATATAATAATGCAGCTTTAGCAG 58.490 33.333 4.33 0.00 46.36 4.24
130 131 8.509690 CACATATAATAATGCAGCTTTAGCAGT 58.490 33.333 4.33 3.19 46.36 4.40
131 132 8.725148 ACATATAATAATGCAGCTTTAGCAGTC 58.275 33.333 0.36 0.00 46.36 3.51
132 133 8.944029 CATATAATAATGCAGCTTTAGCAGTCT 58.056 33.333 0.36 0.00 46.36 3.24
134 135 6.857777 AATAATGCAGCTTTAGCAGTCTAG 57.142 37.500 0.36 0.00 46.36 2.43
135 136 3.902881 ATGCAGCTTTAGCAGTCTAGT 57.097 42.857 4.33 0.00 46.36 2.57
136 137 3.238108 TGCAGCTTTAGCAGTCTAGTC 57.762 47.619 4.33 0.00 45.16 2.59
137 138 2.828520 TGCAGCTTTAGCAGTCTAGTCT 59.171 45.455 4.33 0.00 45.16 3.24
138 139 4.017126 TGCAGCTTTAGCAGTCTAGTCTA 58.983 43.478 4.33 0.00 45.16 2.59
139 140 4.462834 TGCAGCTTTAGCAGTCTAGTCTAA 59.537 41.667 4.33 0.00 45.16 2.10
140 141 5.127845 TGCAGCTTTAGCAGTCTAGTCTAAT 59.872 40.000 4.33 0.00 45.16 1.73
141 142 6.045955 GCAGCTTTAGCAGTCTAGTCTAATT 58.954 40.000 4.33 0.00 45.16 1.40
142 143 6.536941 GCAGCTTTAGCAGTCTAGTCTAATTT 59.463 38.462 4.33 0.00 45.16 1.82
143 144 7.065204 GCAGCTTTAGCAGTCTAGTCTAATTTT 59.935 37.037 4.33 0.00 45.16 1.82
144 145 8.940952 CAGCTTTAGCAGTCTAGTCTAATTTTT 58.059 33.333 4.33 0.00 45.16 1.94
145 146 8.940952 AGCTTTAGCAGTCTAGTCTAATTTTTG 58.059 33.333 4.33 0.00 45.16 2.44
146 147 8.722394 GCTTTAGCAGTCTAGTCTAATTTTTGT 58.278 33.333 0.00 0.00 41.59 2.83
148 149 9.555727 TTTAGCAGTCTAGTCTAATTTTTGTGT 57.444 29.630 0.00 0.00 0.00 3.72
151 152 9.726438 AGCAGTCTAGTCTAATTTTTGTGTAAT 57.274 29.630 0.00 0.00 0.00 1.89
445 463 5.771602 TGCACGTATACATTTACACACAG 57.228 39.130 3.32 0.00 0.00 3.66
543 589 3.807553 ACAAAAGCAACCCATGAAAAGG 58.192 40.909 0.00 0.00 0.00 3.11
544 590 2.549064 AAAGCAACCCATGAAAAGGC 57.451 45.000 0.00 0.00 0.00 4.35
568 614 4.990426 GCATAAACACACCAAAATTCAGCT 59.010 37.500 0.00 0.00 0.00 4.24
621 668 1.402968 CAATCGGATCCAAACAGCCTG 59.597 52.381 13.41 0.00 0.00 4.85
659 719 7.787725 ACGTGACAGAGAAAAGAAAAACTAT 57.212 32.000 0.00 0.00 0.00 2.12
660 720 7.852516 ACGTGACAGAGAAAAGAAAAACTATC 58.147 34.615 0.00 0.00 0.00 2.08
667 727 9.631452 CAGAGAAAAGAAAAACTATCCAAATCC 57.369 33.333 0.00 0.00 0.00 3.01
677 737 7.396540 AAACTATCCAAATCCTAAAGCACAG 57.603 36.000 0.00 0.00 0.00 3.66
710 770 5.278463 CCAGAAAATCGACTGACCACAAAAT 60.278 40.000 2.52 0.00 36.38 1.82
712 772 6.360681 CAGAAAATCGACTGACCACAAAATTC 59.639 38.462 0.00 0.00 36.38 2.17
728 788 7.254522 CCACAAAATTCAAATTCAGTTGACTGG 60.255 37.037 10.97 0.00 43.91 4.00
743 803 7.396339 TCAGTTGACTGGAATCTAGCTAAAGTA 59.604 37.037 10.97 0.00 43.91 2.24
744 804 7.489757 CAGTTGACTGGAATCTAGCTAAAGTAC 59.510 40.741 3.19 0.00 40.20 2.73
746 806 7.476540 TGACTGGAATCTAGCTAAAGTACAA 57.523 36.000 0.00 0.00 0.00 2.41
748 808 8.540388 TGACTGGAATCTAGCTAAAGTACAAAT 58.460 33.333 0.00 0.00 0.00 2.32
760 820 9.749340 AGCTAAAGTACAAATATAACAAAGGGT 57.251 29.630 0.00 0.00 0.00 4.34
761 821 9.783256 GCTAAAGTACAAATATAACAAAGGGTG 57.217 33.333 0.00 0.00 0.00 4.61
764 824 8.927675 AAGTACAAATATAACAAAGGGTGTGA 57.072 30.769 0.00 0.00 40.60 3.58
765 825 9.528489 AAGTACAAATATAACAAAGGGTGTGAT 57.472 29.630 0.00 0.00 40.60 3.06
766 826 8.956426 AGTACAAATATAACAAAGGGTGTGATG 58.044 33.333 0.00 0.00 40.60 3.07
767 827 7.775053 ACAAATATAACAAAGGGTGTGATGT 57.225 32.000 0.00 0.00 40.60 3.06
768 828 8.189119 ACAAATATAACAAAGGGTGTGATGTT 57.811 30.769 0.00 0.00 40.60 2.71
769 829 8.646900 ACAAATATAACAAAGGGTGTGATGTTT 58.353 29.630 0.00 0.00 41.02 2.83
770 830 9.487790 CAAATATAACAAAGGGTGTGATGTTTT 57.512 29.630 0.00 0.00 38.58 2.43
771 831 9.487790 AAATATAACAAAGGGTGTGATGTTTTG 57.512 29.630 0.00 0.00 38.58 2.44
772 832 3.817709 ACAAAGGGTGTGATGTTTTGG 57.182 42.857 0.00 0.00 39.72 3.28
773 833 2.158971 ACAAAGGGTGTGATGTTTTGGC 60.159 45.455 0.00 0.00 39.72 4.52
774 834 2.086610 AAGGGTGTGATGTTTTGGCT 57.913 45.000 0.00 0.00 0.00 4.75
775 835 1.620822 AGGGTGTGATGTTTTGGCTC 58.379 50.000 0.00 0.00 0.00 4.70
776 836 1.145738 AGGGTGTGATGTTTTGGCTCT 59.854 47.619 0.00 0.00 0.00 4.09
777 837 1.270550 GGGTGTGATGTTTTGGCTCTG 59.729 52.381 0.00 0.00 0.00 3.35
778 838 1.270550 GGTGTGATGTTTTGGCTCTGG 59.729 52.381 0.00 0.00 0.00 3.86
779 839 1.270550 GTGTGATGTTTTGGCTCTGGG 59.729 52.381 0.00 0.00 0.00 4.45
780 840 1.144708 TGTGATGTTTTGGCTCTGGGA 59.855 47.619 0.00 0.00 0.00 4.37
781 841 2.225091 TGTGATGTTTTGGCTCTGGGAT 60.225 45.455 0.00 0.00 0.00 3.85
782 842 2.827921 GTGATGTTTTGGCTCTGGGATT 59.172 45.455 0.00 0.00 0.00 3.01
783 843 2.827322 TGATGTTTTGGCTCTGGGATTG 59.173 45.455 0.00 0.00 0.00 2.67
784 844 2.380064 TGTTTTGGCTCTGGGATTGT 57.620 45.000 0.00 0.00 0.00 2.71
785 845 3.517296 TGTTTTGGCTCTGGGATTGTA 57.483 42.857 0.00 0.00 0.00 2.41
786 846 3.838565 TGTTTTGGCTCTGGGATTGTAA 58.161 40.909 0.00 0.00 0.00 2.41
787 847 4.415596 TGTTTTGGCTCTGGGATTGTAAT 58.584 39.130 0.00 0.00 0.00 1.89
788 848 4.462483 TGTTTTGGCTCTGGGATTGTAATC 59.538 41.667 0.00 0.00 34.66 1.75
789 849 4.314522 TTTGGCTCTGGGATTGTAATCA 57.685 40.909 6.90 0.00 37.15 2.57
790 850 4.524802 TTGGCTCTGGGATTGTAATCAT 57.475 40.909 6.90 0.00 37.15 2.45
791 851 5.645056 TTGGCTCTGGGATTGTAATCATA 57.355 39.130 6.90 0.00 37.15 2.15
792 852 5.645056 TGGCTCTGGGATTGTAATCATAA 57.355 39.130 6.90 0.00 37.15 1.90
793 853 6.204852 TGGCTCTGGGATTGTAATCATAAT 57.795 37.500 6.90 0.00 37.15 1.28
794 854 6.005823 TGGCTCTGGGATTGTAATCATAATG 58.994 40.000 6.90 0.00 37.15 1.90
795 855 5.416952 GGCTCTGGGATTGTAATCATAATGG 59.583 44.000 6.90 0.00 37.15 3.16
796 856 6.240894 GCTCTGGGATTGTAATCATAATGGA 58.759 40.000 6.90 0.00 37.15 3.41
797 857 6.716628 GCTCTGGGATTGTAATCATAATGGAA 59.283 38.462 6.90 0.00 37.15 3.53
798 858 7.231317 GCTCTGGGATTGTAATCATAATGGAAA 59.769 37.037 6.90 0.00 37.15 3.13
799 859 9.305555 CTCTGGGATTGTAATCATAATGGAAAT 57.694 33.333 6.90 0.00 37.15 2.17
936 999 3.126879 TGGGCTTCAATCGCGCAG 61.127 61.111 8.75 0.00 43.98 5.18
937 1000 3.880846 GGGCTTCAATCGCGCAGG 61.881 66.667 8.75 0.00 39.76 4.85
938 1001 4.543084 GGCTTCAATCGCGCAGGC 62.543 66.667 8.75 4.31 0.00 4.85
939 1002 4.543084 GCTTCAATCGCGCAGGCC 62.543 66.667 8.75 0.00 35.02 5.19
1095 1192 3.443479 ATCCTCCTCCGCCTCCCT 61.443 66.667 0.00 0.00 0.00 4.20
1777 1897 5.940470 GCCTATGGTCATTATAGGGACTTTG 59.060 44.000 11.75 0.00 44.77 2.77
2249 2404 2.079925 GCCTGATGACCTCTTCAACAC 58.920 52.381 0.00 0.00 37.92 3.32
2276 2637 3.181516 CGAATTAGTTCTGCAGTGCTTCC 60.182 47.826 17.60 1.65 32.00 3.46
2302 2671 1.200020 GATGCTTGCGTGGTAGCTTTT 59.800 47.619 0.00 0.00 38.22 2.27
2303 2672 1.028905 TGCTTGCGTGGTAGCTTTTT 58.971 45.000 0.00 0.00 38.22 1.94
2304 2673 1.268999 TGCTTGCGTGGTAGCTTTTTG 60.269 47.619 0.00 0.00 38.22 2.44
2325 2694 4.588899 TGTTTGATGGTTATGGTCTGGAG 58.411 43.478 0.00 0.00 0.00 3.86
2337 2706 2.037641 TGGTCTGGAGTCACATCTGTTG 59.962 50.000 0.00 0.00 0.00 3.33
2427 3024 5.482526 TGGTAGTGTTAGTGATGTGGTACAT 59.517 40.000 0.00 0.00 44.52 2.29
2432 3029 6.426937 AGTGTTAGTGATGTGGTACATGTTTC 59.573 38.462 2.30 0.00 44.52 2.78
2687 3753 7.042590 GCTGATCAAGATATGCTAGTATGATGC 60.043 40.741 3.24 0.00 0.00 3.91
2705 3772 0.312102 GCACTGGTTGAGCAGGAAAC 59.688 55.000 14.01 0.00 32.44 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 2.677337 GCAATGTTGTGTGCAGGTTTTT 59.323 40.909 0.00 0.00 40.58 1.94
48 49 2.278854 GCAATGTTGTGTGCAGGTTTT 58.721 42.857 0.00 0.00 40.58 2.43
49 50 1.206610 TGCAATGTTGTGTGCAGGTTT 59.793 42.857 0.00 0.00 45.52 3.27
50 51 0.822811 TGCAATGTTGTGTGCAGGTT 59.177 45.000 0.00 0.00 45.52 3.50
51 52 2.502633 TGCAATGTTGTGTGCAGGT 58.497 47.368 0.00 0.00 45.52 4.00
55 56 2.206815 TTCACTGCAATGTTGTGTGC 57.793 45.000 0.00 0.00 41.29 4.57
56 57 4.551217 GCAATTTCACTGCAATGTTGTGTG 60.551 41.667 0.00 11.76 39.69 3.82
57 58 3.556775 GCAATTTCACTGCAATGTTGTGT 59.443 39.130 0.00 0.00 39.69 3.72
58 59 3.556365 TGCAATTTCACTGCAATGTTGTG 59.444 39.130 0.00 0.00 46.47 3.33
59 60 3.794717 TGCAATTTCACTGCAATGTTGT 58.205 36.364 0.00 0.00 46.47 3.32
66 67 8.830201 ATTATAAAAAGTGCAATTTCACTGCA 57.170 26.923 13.16 0.00 45.77 4.41
93 94 9.506018 TGCATTATTATATGTGTATTCACTGCT 57.494 29.630 4.01 0.00 44.14 4.24
94 95 9.764870 CTGCATTATTATATGTGTATTCACTGC 57.235 33.333 4.01 2.92 44.14 4.40
95 96 9.764870 GCTGCATTATTATATGTGTATTCACTG 57.235 33.333 4.01 0.00 44.14 3.66
96 97 9.730705 AGCTGCATTATTATATGTGTATTCACT 57.269 29.630 1.02 0.00 44.14 3.41
102 103 9.500785 TGCTAAAGCTGCATTATTATATGTGTA 57.499 29.630 1.02 0.00 42.66 2.90
103 104 8.394971 TGCTAAAGCTGCATTATTATATGTGT 57.605 30.769 1.02 0.00 42.66 3.72
104 105 8.509690 ACTGCTAAAGCTGCATTATTATATGTG 58.490 33.333 1.02 0.00 42.72 3.21
105 106 8.627208 ACTGCTAAAGCTGCATTATTATATGT 57.373 30.769 1.02 0.00 42.72 2.29
106 107 8.944029 AGACTGCTAAAGCTGCATTATTATATG 58.056 33.333 1.02 0.00 42.72 1.78
108 109 9.645059 CTAGACTGCTAAAGCTGCATTATTATA 57.355 33.333 1.02 0.00 42.72 0.98
109 110 8.153550 ACTAGACTGCTAAAGCTGCATTATTAT 58.846 33.333 1.02 0.00 42.72 1.28
110 111 7.500992 ACTAGACTGCTAAAGCTGCATTATTA 58.499 34.615 1.02 0.00 42.72 0.98
111 112 6.352516 ACTAGACTGCTAAAGCTGCATTATT 58.647 36.000 1.02 0.00 42.72 1.40
112 113 5.923204 ACTAGACTGCTAAAGCTGCATTAT 58.077 37.500 1.02 0.00 42.72 1.28
113 114 5.127845 AGACTAGACTGCTAAAGCTGCATTA 59.872 40.000 1.02 0.00 42.72 1.90
114 115 4.081198 AGACTAGACTGCTAAAGCTGCATT 60.081 41.667 1.02 0.00 42.72 3.56
115 116 3.450457 AGACTAGACTGCTAAAGCTGCAT 59.550 43.478 1.02 0.00 42.72 3.96
116 117 2.828520 AGACTAGACTGCTAAAGCTGCA 59.171 45.455 1.02 0.00 42.72 4.41
117 118 3.518634 AGACTAGACTGCTAAAGCTGC 57.481 47.619 8.57 0.00 42.72 5.25
118 119 8.485976 AAAATTAGACTAGACTGCTAAAGCTG 57.514 34.615 4.90 7.24 44.21 4.24
119 120 8.940952 CAAAAATTAGACTAGACTGCTAAAGCT 58.059 33.333 4.90 0.00 42.66 3.74
120 121 8.722394 ACAAAAATTAGACTAGACTGCTAAAGC 58.278 33.333 4.90 0.00 42.50 3.51
122 123 9.555727 ACACAAAAATTAGACTAGACTGCTAAA 57.444 29.630 4.90 0.00 0.00 1.85
125 126 9.726438 ATTACACAAAAATTAGACTAGACTGCT 57.274 29.630 4.90 0.00 0.00 4.24
241 244 9.762933 TGCTAATTGTTTTCTGCTAATTTCTTT 57.237 25.926 0.00 0.00 0.00 2.52
244 247 9.962759 CAATGCTAATTGTTTTCTGCTAATTTC 57.037 29.630 0.00 0.00 38.72 2.17
283 287 9.431887 GGAAAATTAGTTTGTTTCCTTATTCCC 57.568 33.333 7.07 0.00 44.57 3.97
284 288 9.990360 TGGAAAATTAGTTTGTTTCCTTATTCC 57.010 29.630 13.82 0.00 46.95 3.01
291 295 7.835634 TTGTGTGGAAAATTAGTTTGTTTCC 57.164 32.000 7.33 7.33 46.99 3.13
296 300 8.487176 GTGCTAATTGTGTGGAAAATTAGTTTG 58.513 33.333 13.69 0.00 0.00 2.93
297 301 8.200792 TGTGCTAATTGTGTGGAAAATTAGTTT 58.799 29.630 13.69 0.00 0.00 2.66
300 304 8.586570 TTTGTGCTAATTGTGTGGAAAATTAG 57.413 30.769 9.69 9.69 0.00 1.73
301 305 8.948631 TTTTGTGCTAATTGTGTGGAAAATTA 57.051 26.923 0.00 0.00 0.00 1.40
409 426 8.791355 TGTATACGTGCAAGTAATACATGTAG 57.209 34.615 16.44 0.00 38.72 2.74
506 549 9.855021 GTTGCTTTTGTTTCCTATATGTGTATT 57.145 29.630 0.00 0.00 0.00 1.89
515 558 4.837860 TCATGGGTTGCTTTTGTTTCCTAT 59.162 37.500 0.00 0.00 0.00 2.57
516 559 4.219115 TCATGGGTTGCTTTTGTTTCCTA 58.781 39.130 0.00 0.00 0.00 2.94
519 562 5.220835 CCTTTTCATGGGTTGCTTTTGTTTC 60.221 40.000 0.00 0.00 0.00 2.78
543 589 3.738282 TGAATTTTGGTGTGTTTATGCGC 59.262 39.130 0.00 0.00 0.00 6.09
544 590 4.143347 GCTGAATTTTGGTGTGTTTATGCG 60.143 41.667 0.00 0.00 0.00 4.73
568 614 3.306780 GGGTCAGTCGATTTCCTTCTTGA 60.307 47.826 0.00 0.00 0.00 3.02
607 654 2.084546 GTGTACCAGGCTGTTTGGATC 58.915 52.381 14.43 0.00 39.08 3.36
621 668 1.003223 GTCACGTTTTGCTGGTGTACC 60.003 52.381 0.00 0.00 33.51 3.34
659 719 3.073798 TGGACTGTGCTTTAGGATTTGGA 59.926 43.478 0.00 0.00 0.00 3.53
660 720 3.420893 TGGACTGTGCTTTAGGATTTGG 58.579 45.455 0.00 0.00 0.00 3.28
667 727 1.474077 GGCCATTGGACTGTGCTTTAG 59.526 52.381 6.95 0.00 0.00 1.85
677 737 2.091541 TCGATTTTCTGGCCATTGGAC 58.908 47.619 5.51 3.54 0.00 4.02
710 770 7.094634 GCTAGATTCCAGTCAACTGAATTTGAA 60.095 37.037 11.70 6.50 46.59 2.69
712 772 6.373774 AGCTAGATTCCAGTCAACTGAATTTG 59.626 38.462 11.70 0.00 46.59 2.32
743 803 7.775053 ACATCACACCCTTTGTTATATTTGT 57.225 32.000 0.00 0.00 35.67 2.83
744 804 9.487790 AAAACATCACACCCTTTGTTATATTTG 57.512 29.630 0.00 0.00 35.67 2.32
746 806 8.093927 CCAAAACATCACACCCTTTGTTATATT 58.906 33.333 0.00 0.00 35.67 1.28
748 808 6.517529 GCCAAAACATCACACCCTTTGTTATA 60.518 38.462 0.00 0.00 35.67 0.98
750 810 4.442192 GCCAAAACATCACACCCTTTGTTA 60.442 41.667 0.00 0.00 35.67 2.41
751 811 3.681313 GCCAAAACATCACACCCTTTGTT 60.681 43.478 0.00 0.00 35.67 2.83
752 812 2.158971 GCCAAAACATCACACCCTTTGT 60.159 45.455 0.00 0.00 39.97 2.83
753 813 2.102925 AGCCAAAACATCACACCCTTTG 59.897 45.455 0.00 0.00 0.00 2.77
754 814 2.365293 GAGCCAAAACATCACACCCTTT 59.635 45.455 0.00 0.00 0.00 3.11
755 815 1.963515 GAGCCAAAACATCACACCCTT 59.036 47.619 0.00 0.00 0.00 3.95
756 816 1.145738 AGAGCCAAAACATCACACCCT 59.854 47.619 0.00 0.00 0.00 4.34
757 817 1.270550 CAGAGCCAAAACATCACACCC 59.729 52.381 0.00 0.00 0.00 4.61
758 818 1.270550 CCAGAGCCAAAACATCACACC 59.729 52.381 0.00 0.00 0.00 4.16
759 819 1.270550 CCCAGAGCCAAAACATCACAC 59.729 52.381 0.00 0.00 0.00 3.82
760 820 1.144708 TCCCAGAGCCAAAACATCACA 59.855 47.619 0.00 0.00 0.00 3.58
761 821 1.909700 TCCCAGAGCCAAAACATCAC 58.090 50.000 0.00 0.00 0.00 3.06
762 822 2.827322 CAATCCCAGAGCCAAAACATCA 59.173 45.455 0.00 0.00 0.00 3.07
763 823 2.827921 ACAATCCCAGAGCCAAAACATC 59.172 45.455 0.00 0.00 0.00 3.06
764 824 2.893424 ACAATCCCAGAGCCAAAACAT 58.107 42.857 0.00 0.00 0.00 2.71
765 825 2.380064 ACAATCCCAGAGCCAAAACA 57.620 45.000 0.00 0.00 0.00 2.83
766 826 4.462483 TGATTACAATCCCAGAGCCAAAAC 59.538 41.667 0.00 0.00 34.50 2.43
767 827 4.671831 TGATTACAATCCCAGAGCCAAAA 58.328 39.130 0.00 0.00 34.50 2.44
768 828 4.314522 TGATTACAATCCCAGAGCCAAA 57.685 40.909 0.00 0.00 34.50 3.28
769 829 4.524802 ATGATTACAATCCCAGAGCCAA 57.475 40.909 0.00 0.00 34.50 4.52
770 830 5.645056 TTATGATTACAATCCCAGAGCCA 57.355 39.130 0.00 0.00 34.50 4.75
771 831 5.416952 CCATTATGATTACAATCCCAGAGCC 59.583 44.000 0.00 0.00 34.50 4.70
772 832 6.240894 TCCATTATGATTACAATCCCAGAGC 58.759 40.000 0.00 0.00 34.50 4.09
773 833 8.696043 TTTCCATTATGATTACAATCCCAGAG 57.304 34.615 0.00 0.00 34.50 3.35
855 915 7.434013 GTGCGATTGAAGTTTTTCCTTTAGAAA 59.566 33.333 0.00 0.00 42.82 2.52
856 916 6.915843 GTGCGATTGAAGTTTTTCCTTTAGAA 59.084 34.615 0.00 0.00 32.09 2.10
857 917 6.262273 AGTGCGATTGAAGTTTTTCCTTTAGA 59.738 34.615 0.00 0.00 32.09 2.10
858 918 6.360681 CAGTGCGATTGAAGTTTTTCCTTTAG 59.639 38.462 0.00 0.00 32.09 1.85
859 919 6.205784 CAGTGCGATTGAAGTTTTTCCTTTA 58.794 36.000 0.00 0.00 32.09 1.85
860 920 5.043248 CAGTGCGATTGAAGTTTTTCCTTT 58.957 37.500 0.00 0.00 32.09 3.11
861 921 4.610945 CAGTGCGATTGAAGTTTTTCCTT 58.389 39.130 0.00 0.00 32.09 3.36
862 922 3.550842 GCAGTGCGATTGAAGTTTTTCCT 60.551 43.478 0.00 0.00 32.09 3.36
863 923 2.726241 GCAGTGCGATTGAAGTTTTTCC 59.274 45.455 0.00 0.00 32.09 3.13
864 924 3.371168 TGCAGTGCGATTGAAGTTTTTC 58.629 40.909 11.20 0.00 0.00 2.29
865 925 3.374745 CTGCAGTGCGATTGAAGTTTTT 58.625 40.909 11.20 0.00 0.00 1.94
866 926 2.859806 GCTGCAGTGCGATTGAAGTTTT 60.860 45.455 16.64 0.00 0.00 2.43
867 927 1.335324 GCTGCAGTGCGATTGAAGTTT 60.335 47.619 16.64 0.00 0.00 2.66
868 928 0.239347 GCTGCAGTGCGATTGAAGTT 59.761 50.000 16.64 0.00 0.00 2.66
869 929 0.604780 AGCTGCAGTGCGATTGAAGT 60.605 50.000 16.64 0.00 38.13 3.01
870 930 0.520404 AAGCTGCAGTGCGATTGAAG 59.480 50.000 16.64 1.81 38.13 3.02
871 931 0.518636 GAAGCTGCAGTGCGATTGAA 59.481 50.000 16.64 0.00 38.13 2.69
872 932 0.603439 TGAAGCTGCAGTGCGATTGA 60.603 50.000 16.64 1.83 38.13 2.57
873 933 0.450583 ATGAAGCTGCAGTGCGATTG 59.549 50.000 16.64 1.81 38.13 2.67
902 962 2.492088 GCCCAAAACTATCCTTCCACAC 59.508 50.000 0.00 0.00 0.00 3.82
904 964 3.087370 AGCCCAAAACTATCCTTCCAC 57.913 47.619 0.00 0.00 0.00 4.02
906 966 3.697166 TGAAGCCCAAAACTATCCTTCC 58.303 45.455 0.00 0.00 0.00 3.46
907 967 5.449177 CGATTGAAGCCCAAAACTATCCTTC 60.449 44.000 0.00 0.00 38.43 3.46
910 970 3.489229 GCGATTGAAGCCCAAAACTATCC 60.489 47.826 0.00 0.00 38.43 2.59
911 971 3.695816 GCGATTGAAGCCCAAAACTATC 58.304 45.455 0.00 0.00 38.43 2.08
912 972 2.097466 CGCGATTGAAGCCCAAAACTAT 59.903 45.455 0.00 0.00 38.43 2.12
936 999 1.268079 GAAAGTGAAAGTGCAGAGGCC 59.732 52.381 0.00 0.00 40.13 5.19
937 1000 1.268079 GGAAAGTGAAAGTGCAGAGGC 59.732 52.381 0.00 0.00 41.68 4.70
938 1001 1.882623 GGGAAAGTGAAAGTGCAGAGG 59.117 52.381 0.00 0.00 0.00 3.69
939 1002 1.882623 GGGGAAAGTGAAAGTGCAGAG 59.117 52.381 0.00 0.00 0.00 3.35
1777 1897 1.923204 CTCTGCTCGCATAACTGTCAC 59.077 52.381 0.00 0.00 0.00 3.67
2166 2292 5.796350 ATCTTAACACAAGAACGGCATAC 57.204 39.130 0.00 0.00 0.00 2.39
2249 2404 4.551603 GCACTGCAGAACTAATTCGCTATG 60.552 45.833 23.35 3.62 40.04 2.23
2276 2637 1.440850 CCACGCAAGCATCACAACG 60.441 57.895 0.00 0.00 45.62 4.10
2302 2671 4.991776 TCCAGACCATAACCATCAAACAA 58.008 39.130 0.00 0.00 0.00 2.83
2303 2672 4.042809 ACTCCAGACCATAACCATCAAACA 59.957 41.667 0.00 0.00 0.00 2.83
2304 2673 4.589908 ACTCCAGACCATAACCATCAAAC 58.410 43.478 0.00 0.00 0.00 2.93
2325 2694 3.753272 ACATAACCAGCAACAGATGTGAC 59.247 43.478 0.00 0.00 0.00 3.67
2337 2706 9.855021 ATTTAGTTCAATTGTTACATAACCAGC 57.145 29.630 5.13 0.00 35.37 4.85
2417 3008 5.885230 CATGACAGAAACATGTACCACAT 57.115 39.130 0.00 0.00 39.91 3.21
2588 3645 9.357652 CAAACAACCAATAACATTCTAATGGAG 57.642 33.333 7.56 0.00 40.70 3.86
2629 3686 2.890311 CCACCACCAATGCTTGTTTCTA 59.110 45.455 0.00 0.00 0.00 2.10
2687 3753 0.954452 GGTTTCCTGCTCAACCAGTG 59.046 55.000 0.00 0.00 41.97 3.66
2705 3772 8.373981 ACCTCATCATACATTCAGAAGATAAGG 58.626 37.037 0.00 0.00 0.00 2.69
3109 4179 3.842984 CGTAGTTTCGGTCTTAGTTCGTC 59.157 47.826 0.00 0.00 0.00 4.20
3232 4302 2.486548 CCCTCCCACGAAAAGAGTTTCA 60.487 50.000 0.00 0.00 42.90 2.69


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

AutoCloner maintained by Alex Coulton.