Multiple sequence alignment - TraesCS7A01G064400

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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 TraesCS7A01G064400 chr7A 100.000 4807 0 0 1 4807 32038784 32033978 0.000000e+00 8877
1 TraesCS7A01G064400 chr7A 96.422 3466 87 16 66 3518 32297023 32293582 0.000000e+00 5679
2 TraesCS7A01G064400 chr7A 90.975 1241 93 10 257 1488 32063362 32062132 0.000000e+00 1653
3 TraesCS7A01G064400 chr7A 83.990 1243 112 45 3521 4739 32293453 32292274 0.000000e+00 1112
4 TraesCS7A01G064400 chr7A 86.455 694 53 19 1789 2456 32129255 32128577 0.000000e+00 723
5 TraesCS7A01G064400 chr7A 84.929 637 51 30 3508 4126 32197298 32196689 1.910000e-168 603
6 TraesCS7A01G064400 chr7A 86.940 536 47 6 4112 4644 32196360 32195845 8.970000e-162 580
7 TraesCS7A01G064400 chr7A 77.778 945 145 36 3007 3903 32027142 32026215 5.510000e-144 521
8 TraesCS7A01G064400 chr7A 83.607 427 50 12 1664 2086 32009436 32009846 2.710000e-102 383
9 TraesCS7A01G064400 chr7A 87.611 113 9 4 18 128 32069081 32068972 5.050000e-25 126
10 TraesCS7A01G064400 chr7A 89.320 103 8 2 4314 4413 32291793 32291691 5.050000e-25 126
11 TraesCS7A01G064400 chr7D 90.975 4798 267 77 66 4807 31962276 31957589 0.000000e+00 6309
12 TraesCS7A01G064400 chr7D 93.058 1066 41 11 1499 2560 32004569 32003533 0.000000e+00 1528
13 TraesCS7A01G064400 chr7D 82.809 477 70 10 3560 4034 32002924 32002458 2.680000e-112 416
14 TraesCS7A01G064400 chr7D 84.742 426 51 10 1664 2086 31943093 31943507 9.630000e-112 414
15 TraesCS7A01G064400 chr7D 90.741 216 19 1 3007 3221 31950226 31950011 2.190000e-73 287
16 TraesCS7A01G064400 chr7D 76.613 248 47 11 14 258 32050114 32049875 5.050000e-25 126
17 TraesCS7A01G064400 chr7D 88.350 103 9 2 4314 4413 31957608 31957506 2.350000e-23 121
18 TraesCS7A01G064400 chrUn 89.874 3012 214 46 1487 4443 298011982 298009007 0.000000e+00 3788
19 TraesCS7A01G064400 chrUn 89.594 1624 124 20 1505 3104 238523559 238521957 0.000000e+00 2021
20 TraesCS7A01G064400 chrUn 89.594 1624 124 20 1505 3104 238537668 238536066 0.000000e+00 2021
21 TraesCS7A01G064400 chrUn 89.594 1624 124 20 1505 3104 271022440 271020838 0.000000e+00 2021
22 TraesCS7A01G064400 chrUn 89.551 1627 125 20 1502 3104 278812437 278814042 0.000000e+00 2021
23 TraesCS7A01G064400 chrUn 89.534 1567 119 18 1566 3105 176753955 176755503 0.000000e+00 1943
24 TraesCS7A01G064400 chrUn 83.861 979 120 21 531 1488 238524688 238523727 0.000000e+00 898
25 TraesCS7A01G064400 chrUn 83.861 979 120 21 531 1488 238538797 238537836 0.000000e+00 898
26 TraesCS7A01G064400 chrUn 83.861 979 120 21 531 1488 271023569 271022608 0.000000e+00 898
27 TraesCS7A01G064400 chrUn 83.861 979 120 21 531 1488 278811311 278812272 0.000000e+00 898
28 TraesCS7A01G064400 chrUn 83.436 978 125 20 531 1488 176718583 176719543 0.000000e+00 874
29 TraesCS7A01G064400 chr3B 90.045 1567 111 16 1566 3105 713873994 713872446 0.000000e+00 1988
30 TraesCS7A01G064400 chr3B 83.742 978 122 19 531 1488 713771907 713770947 0.000000e+00 891
31 TraesCS7A01G064400 chr3B 83.742 978 122 19 531 1488 713807090 713806130 0.000000e+00 891
32 TraesCS7A01G064400 chr4A 95.647 781 28 5 4029 4804 695993768 695994547 0.000000e+00 1249
33 TraesCS7A01G064400 chr4A 89.655 667 58 8 3329 3991 695993009 695993668 0.000000e+00 839
34 TraesCS7A01G064400 chr4A 77.471 941 147 36 3007 3898 696003990 696004914 2.000000e-138 503
35 TraesCS7A01G064400 chr4A 83.765 425 56 10 1666 2086 696010992 696010577 1.620000e-104 390
36 TraesCS7A01G064400 chr2D 81.863 408 45 17 62 458 91446580 91446969 2.790000e-82 316


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 TraesCS7A01G064400 chr7A 32033978 32038784 4806 True 8877.000000 8877 100.000000 1 4807 1 chr7A.!!$R2 4806
1 TraesCS7A01G064400 chr7A 32291691 32297023 5332 True 2305.666667 5679 89.910667 66 4739 3 chr7A.!!$R7 4673
2 TraesCS7A01G064400 chr7A 32062132 32063362 1230 True 1653.000000 1653 90.975000 257 1488 1 chr7A.!!$R3 1231
3 TraesCS7A01G064400 chr7A 32128577 32129255 678 True 723.000000 723 86.455000 1789 2456 1 chr7A.!!$R5 667
4 TraesCS7A01G064400 chr7A 32195845 32197298 1453 True 591.500000 603 85.934500 3508 4644 2 chr7A.!!$R6 1136
5 TraesCS7A01G064400 chr7A 32026215 32027142 927 True 521.000000 521 77.778000 3007 3903 1 chr7A.!!$R1 896
6 TraesCS7A01G064400 chr7D 31957506 31962276 4770 True 3215.000000 6309 89.662500 66 4807 2 chr7D.!!$R3 4741
7 TraesCS7A01G064400 chr7D 32002458 32004569 2111 True 972.000000 1528 87.933500 1499 4034 2 chr7D.!!$R4 2535
8 TraesCS7A01G064400 chrUn 298009007 298011982 2975 True 3788.000000 3788 89.874000 1487 4443 1 chrUn.!!$R1 2956
9 TraesCS7A01G064400 chrUn 176753955 176755503 1548 False 1943.000000 1943 89.534000 1566 3105 1 chrUn.!!$F2 1539
10 TraesCS7A01G064400 chrUn 238521957 238524688 2731 True 1459.500000 2021 86.727500 531 3104 2 chrUn.!!$R2 2573
11 TraesCS7A01G064400 chrUn 238536066 238538797 2731 True 1459.500000 2021 86.727500 531 3104 2 chrUn.!!$R3 2573
12 TraesCS7A01G064400 chrUn 271020838 271023569 2731 True 1459.500000 2021 86.727500 531 3104 2 chrUn.!!$R4 2573
13 TraesCS7A01G064400 chrUn 278811311 278814042 2731 False 1459.500000 2021 86.706000 531 3104 2 chrUn.!!$F3 2573
14 TraesCS7A01G064400 chrUn 176718583 176719543 960 False 874.000000 874 83.436000 531 1488 1 chrUn.!!$F1 957
15 TraesCS7A01G064400 chr3B 713872446 713873994 1548 True 1988.000000 1988 90.045000 1566 3105 1 chr3B.!!$R3 1539
16 TraesCS7A01G064400 chr3B 713770947 713771907 960 True 891.000000 891 83.742000 531 1488 1 chr3B.!!$R1 957
17 TraesCS7A01G064400 chr3B 713806130 713807090 960 True 891.000000 891 83.742000 531 1488 1 chr3B.!!$R2 957
18 TraesCS7A01G064400 chr4A 695993009 695994547 1538 False 1044.000000 1249 92.651000 3329 4804 2 chr4A.!!$F2 1475
19 TraesCS7A01G064400 chr4A 696003990 696004914 924 False 503.000000 503 77.471000 3007 3898 1 chr4A.!!$F1 891

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
93 94 0.250989 TGGAGGCGGGAAAACGAAAT 60.251 50.0 0.0 0.0 35.47 2.17 F
387 393 0.321564 TGAACTCATGCCCACGGAAG 60.322 55.0 0.0 0.0 0.00 3.46 F
410 416 0.755686 CTATGTCACTGCCTCCCCTC 59.244 60.0 0.0 0.0 0.00 4.30 F
943 964 1.171308 GTGGCAGCACAGATCACATT 58.829 50.0 0.0 0.0 0.00 2.71 F
3196 3446 1.885049 TCCAGCAAGAGAGCCCTTAT 58.115 50.0 0.0 0.0 34.23 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1771 1961 2.692557 GCTGCAGATGAGGTCTTCTCTA 59.307 50.000 20.43 0.0 42.86 2.43 R
2935 3169 5.038033 GTCGAAGCTATCTGGACTTGTTAG 58.962 45.833 0.00 0.0 0.00 2.34 R
2960 3195 8.196771 TGTGTATGCCAGATCCAAATTAAATTC 58.803 33.333 0.00 0.0 0.00 2.17 R
3478 3757 0.110192 GCTTGCTGTTAGTTGCCGTC 60.110 55.000 0.00 0.0 0.00 4.79 R
4008 4503 0.110486 GGGGTTGACATCACACCAGT 59.890 55.000 12.36 0.0 32.43 4.00 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
20 21 3.156288 GGCTAAACTCCAAAGGGAACT 57.844 47.619 0.00 0.00 44.38 3.01
21 22 3.082548 GGCTAAACTCCAAAGGGAACTC 58.917 50.000 0.00 0.00 44.38 3.01
22 23 3.497942 GGCTAAACTCCAAAGGGAACTCA 60.498 47.826 0.00 0.00 44.38 3.41
23 24 4.142038 GCTAAACTCCAAAGGGAACTCAA 58.858 43.478 0.00 0.00 44.38 3.02
24 25 4.216472 GCTAAACTCCAAAGGGAACTCAAG 59.784 45.833 0.00 0.00 44.38 3.02
25 26 2.278332 ACTCCAAAGGGAACTCAAGC 57.722 50.000 0.00 0.00 44.38 4.01
26 27 1.777272 ACTCCAAAGGGAACTCAAGCT 59.223 47.619 0.00 0.00 44.38 3.74
27 28 2.157738 CTCCAAAGGGAACTCAAGCTG 58.842 52.381 0.00 0.00 44.38 4.24
28 29 1.774254 TCCAAAGGGAACTCAAGCTGA 59.226 47.619 0.00 0.00 42.68 4.26
29 30 2.174639 TCCAAAGGGAACTCAAGCTGAA 59.825 45.455 0.00 0.00 42.68 3.02
30 31 3.160269 CCAAAGGGAACTCAAGCTGAAT 58.840 45.455 0.00 0.00 42.68 2.57
31 32 3.192212 CCAAAGGGAACTCAAGCTGAATC 59.808 47.826 0.00 0.00 42.68 2.52
32 33 3.795688 AAGGGAACTCAAGCTGAATCA 57.204 42.857 0.00 0.00 42.68 2.57
33 34 3.795688 AGGGAACTCAAGCTGAATCAA 57.204 42.857 0.00 0.00 32.90 2.57
34 35 3.683802 AGGGAACTCAAGCTGAATCAAG 58.316 45.455 0.00 0.00 32.90 3.02
35 36 3.073650 AGGGAACTCAAGCTGAATCAAGT 59.926 43.478 0.00 0.00 32.90 3.16
36 37 3.438434 GGGAACTCAAGCTGAATCAAGTC 59.562 47.826 0.00 0.00 0.00 3.01
37 38 4.067896 GGAACTCAAGCTGAATCAAGTCA 58.932 43.478 0.00 0.00 0.00 3.41
38 39 4.083590 GGAACTCAAGCTGAATCAAGTCAC 60.084 45.833 0.00 0.00 0.00 3.67
39 40 4.348863 ACTCAAGCTGAATCAAGTCACT 57.651 40.909 0.00 0.00 0.00 3.41
40 41 5.474578 ACTCAAGCTGAATCAAGTCACTA 57.525 39.130 0.00 0.00 0.00 2.74
41 42 5.477510 ACTCAAGCTGAATCAAGTCACTAG 58.522 41.667 0.00 0.00 0.00 2.57
42 43 5.011533 ACTCAAGCTGAATCAAGTCACTAGT 59.988 40.000 0.00 0.00 0.00 2.57
43 44 5.233225 TCAAGCTGAATCAAGTCACTAGTG 58.767 41.667 17.17 17.17 0.00 2.74
44 45 3.594134 AGCTGAATCAAGTCACTAGTGC 58.406 45.455 18.45 12.92 0.00 4.40
45 46 2.675348 GCTGAATCAAGTCACTAGTGCC 59.325 50.000 18.45 6.95 0.00 5.01
46 47 3.265791 CTGAATCAAGTCACTAGTGCCC 58.734 50.000 18.45 10.77 0.00 5.36
47 48 2.637382 TGAATCAAGTCACTAGTGCCCA 59.363 45.455 18.45 0.00 0.00 5.36
48 49 3.072330 TGAATCAAGTCACTAGTGCCCAA 59.928 43.478 18.45 0.00 0.00 4.12
49 50 3.788227 ATCAAGTCACTAGTGCCCAAA 57.212 42.857 18.45 3.94 0.00 3.28
50 51 3.569194 TCAAGTCACTAGTGCCCAAAA 57.431 42.857 18.45 0.00 0.00 2.44
51 52 3.211045 TCAAGTCACTAGTGCCCAAAAC 58.789 45.455 18.45 9.80 0.00 2.43
52 53 3.118038 TCAAGTCACTAGTGCCCAAAACT 60.118 43.478 18.45 11.95 0.00 2.66
53 54 4.101898 TCAAGTCACTAGTGCCCAAAACTA 59.898 41.667 18.45 0.00 0.00 2.24
58 59 3.831715 CTAGTGCCCAAAACTAGTTGC 57.168 47.619 9.34 8.75 41.41 4.17
59 60 1.328279 AGTGCCCAAAACTAGTTGCC 58.672 50.000 9.34 2.99 0.00 4.52
60 61 0.317160 GTGCCCAAAACTAGTTGCCC 59.683 55.000 9.34 0.00 0.00 5.36
61 62 0.830023 TGCCCAAAACTAGTTGCCCC 60.830 55.000 9.34 0.00 0.00 5.80
62 63 0.830023 GCCCAAAACTAGTTGCCCCA 60.830 55.000 9.34 0.00 0.00 4.96
63 64 1.710816 CCCAAAACTAGTTGCCCCAA 58.289 50.000 9.34 0.00 0.00 4.12
64 65 1.618343 CCCAAAACTAGTTGCCCCAAG 59.382 52.381 9.34 0.00 0.00 3.61
84 85 2.528127 TGAAAGGTGGAGGCGGGA 60.528 61.111 0.00 0.00 0.00 5.14
92 93 1.148723 TGGAGGCGGGAAAACGAAA 59.851 52.632 0.00 0.00 35.47 3.46
93 94 0.250989 TGGAGGCGGGAAAACGAAAT 60.251 50.000 0.00 0.00 35.47 2.17
115 116 1.170290 AGGGTTCAAACGGCGGAAAG 61.170 55.000 13.24 0.00 0.00 2.62
133 134 4.509600 GGAAAGCGGAGAGAGAATGTTATG 59.490 45.833 0.00 0.00 0.00 1.90
134 135 3.742433 AGCGGAGAGAGAATGTTATGG 57.258 47.619 0.00 0.00 0.00 2.74
151 157 3.064324 GTGGCCCAGCGCATCTTT 61.064 61.111 11.47 0.00 40.31 2.52
159 165 1.672363 CCAGCGCATCTTTTAGCATCA 59.328 47.619 11.47 0.00 0.00 3.07
191 197 4.201901 TGCACCATACAACATTCTTATGCG 60.202 41.667 0.00 0.00 35.03 4.73
219 225 2.918934 TCAACTCCCATCCTCCAATGAA 59.081 45.455 0.00 0.00 0.00 2.57
234 240 3.269178 CAATGAAGTGAGCTCTTCCTCC 58.731 50.000 16.19 0.00 41.96 4.30
235 241 2.317371 TGAAGTGAGCTCTTCCTCCT 57.683 50.000 16.19 0.00 41.96 3.69
236 242 1.898472 TGAAGTGAGCTCTTCCTCCTG 59.102 52.381 16.19 0.00 41.96 3.86
242 248 0.972883 AGCTCTTCCTCCTGTCACAC 59.027 55.000 0.00 0.00 0.00 3.82
271 277 3.947196 CTGGCCTAGCACATGAATACAAA 59.053 43.478 3.32 0.00 0.00 2.83
295 301 4.681942 CAGATAAATCCAGCTGCTACGTAC 59.318 45.833 8.66 0.00 0.00 3.67
356 362 6.757010 TCCAGTTAATGAGAGCGAAACTAATC 59.243 38.462 0.00 0.00 0.00 1.75
387 393 0.321564 TGAACTCATGCCCACGGAAG 60.322 55.000 0.00 0.00 0.00 3.46
410 416 0.755686 CTATGTCACTGCCTCCCCTC 59.244 60.000 0.00 0.00 0.00 4.30
943 964 1.171308 GTGGCAGCACAGATCACATT 58.829 50.000 0.00 0.00 0.00 2.71
1117 1140 2.045045 CAGCCGGATCCTTTGCCA 60.045 61.111 5.05 0.00 0.00 4.92
1421 1459 8.811017 CAGTAATATGATGGTAGATGGAGTCTT 58.189 37.037 0.00 0.00 38.42 3.01
1771 1961 5.769662 TCAGAATGAATGCTGTAAAACTGGT 59.230 36.000 0.00 0.00 45.97 4.00
2493 2726 4.034742 AGCAAAACTGTACGGTAGTTTGTG 59.965 41.667 23.46 16.82 44.98 3.33
2651 2884 3.515502 TGACATAGTCCTCAGTTTCCTGG 59.484 47.826 0.00 0.00 39.31 4.45
2910 3143 5.880332 TGGTACAAATGATTCCTCTTGCTAC 59.120 40.000 0.00 0.00 31.92 3.58
2960 3195 3.119316 ACAAGTCCAGATAGCTTCGACAG 60.119 47.826 0.00 3.08 0.00 3.51
3196 3446 1.885049 TCCAGCAAGAGAGCCCTTAT 58.115 50.000 0.00 0.00 34.23 1.73
3292 3557 9.871238 GTGAACAGGTCTAATTAACAGATTAGA 57.129 33.333 3.83 3.83 43.05 2.10
3382 3656 5.724854 AGTGGTATTTAAGTCTGGCCTTCTA 59.275 40.000 3.32 0.00 0.00 2.10
3433 3712 2.969821 TGCATTCCAACAAGTAGGGT 57.030 45.000 0.00 0.00 0.00 4.34
3434 3713 2.790433 TGCATTCCAACAAGTAGGGTC 58.210 47.619 0.00 0.00 0.00 4.46
3478 3757 9.429359 ACTAATCACTTGTACTTTCAGAAGATG 57.571 33.333 0.00 0.00 36.69 2.90
3530 3935 5.348451 GCACCCTAATACAAAAAGTTGCATG 59.652 40.000 0.00 0.00 38.39 4.06
3602 4029 6.702716 AAGTAACCCTTTTCATTTGACGAA 57.297 33.333 0.00 0.00 0.00 3.85
3711 4138 7.912056 CTGATACAATTCTTCAGGTTCAGAA 57.088 36.000 0.00 0.00 34.55 3.02
3835 4262 6.833933 TGAACATCAGAACAGGCTACTAGATA 59.166 38.462 0.00 0.00 0.00 1.98
3909 4339 8.880878 AGTTGTAAAAATAAATGTCACCAACC 57.119 30.769 0.00 0.00 31.31 3.77
3912 4342 7.887381 TGTAAAAATAAATGTCACCAACCGAT 58.113 30.769 0.00 0.00 0.00 4.18
3975 4406 9.672673 ACTATAACTTTGCATGAAACAGAGTAT 57.327 29.630 0.00 0.84 31.81 2.12
3992 4423 9.778741 AACAGAGTATATTGAACTGTCAGAAAA 57.221 29.630 6.91 0.00 40.23 2.29
4007 4502 6.871844 TGTCAGAAAACAGAGAGATATCCAG 58.128 40.000 0.00 0.00 0.00 3.86
4008 4503 6.665248 TGTCAGAAAACAGAGAGATATCCAGA 59.335 38.462 0.00 0.00 0.00 3.86
4010 4505 6.894654 TCAGAAAACAGAGAGATATCCAGACT 59.105 38.462 0.00 0.00 0.00 3.24
4011 4506 6.979817 CAGAAAACAGAGAGATATCCAGACTG 59.020 42.308 0.00 7.10 0.00 3.51
4012 4507 5.867903 AAACAGAGAGATATCCAGACTGG 57.132 43.478 15.99 15.99 39.43 4.00
4013 4508 4.534647 ACAGAGAGATATCCAGACTGGT 57.465 45.455 21.06 11.03 39.03 4.00
4014 4509 4.214310 ACAGAGAGATATCCAGACTGGTG 58.786 47.826 21.06 10.88 39.03 4.17
4016 4511 4.037803 CAGAGAGATATCCAGACTGGTGTG 59.962 50.000 21.06 5.18 39.03 3.82
4017 4512 4.079500 AGAGAGATATCCAGACTGGTGTGA 60.080 45.833 21.06 1.95 39.03 3.58
4019 4514 4.588106 AGAGATATCCAGACTGGTGTGATG 59.412 45.833 21.06 0.00 39.03 3.07
4021 4516 4.343526 AGATATCCAGACTGGTGTGATGTC 59.656 45.833 21.06 13.92 39.03 3.06
4022 4517 1.715785 TCCAGACTGGTGTGATGTCA 58.284 50.000 21.06 0.00 39.03 3.58
4024 4519 2.146342 CCAGACTGGTGTGATGTCAAC 58.854 52.381 13.84 0.00 33.56 3.18
4025 4520 2.146342 CAGACTGGTGTGATGTCAACC 58.854 52.381 0.00 7.15 33.56 3.77
4026 4521 1.072331 AGACTGGTGTGATGTCAACCC 59.928 52.381 10.02 3.32 33.56 4.11
4027 4522 0.110486 ACTGGTGTGATGTCAACCCC 59.890 55.000 10.02 1.41 0.00 4.95
4168 5021 5.985175 TTGTCCCCCAGATAAATGTCATA 57.015 39.130 0.00 0.00 0.00 2.15
4212 5065 4.785511 TCTAAGTCTAACTGCTGTGTCC 57.214 45.455 0.00 0.00 0.00 4.02
4301 5154 5.185249 GTCTCACCACTATCCAGTAAAGTGA 59.815 44.000 3.37 0.00 42.59 3.41
4723 5584 1.285280 CCAGATGTCCCCAGGTTACA 58.715 55.000 0.00 0.00 0.00 2.41
4747 6044 1.203262 ACTGGGACTAAGTAGCCCACA 60.203 52.381 13.41 1.36 41.50 4.17
4804 6101 5.363939 CCTAGAGATCAATTCCAACACTCC 58.636 45.833 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.082548 GAGTTCCCTTTGGAGTTTAGCC 58.917 50.000 0.00 0.00 43.07 3.93
1 2 3.751518 TGAGTTCCCTTTGGAGTTTAGC 58.248 45.455 0.00 0.00 43.07 3.09
2 3 4.216472 GCTTGAGTTCCCTTTGGAGTTTAG 59.784 45.833 0.00 0.00 43.07 1.85
3 4 4.141251 AGCTTGAGTTCCCTTTGGAGTTTA 60.141 41.667 0.00 0.00 43.07 2.01
4 5 2.959030 GCTTGAGTTCCCTTTGGAGTTT 59.041 45.455 0.00 0.00 43.07 2.66
5 6 2.175715 AGCTTGAGTTCCCTTTGGAGTT 59.824 45.455 0.00 0.00 43.07 3.01
6 7 1.777272 AGCTTGAGTTCCCTTTGGAGT 59.223 47.619 0.00 0.00 43.07 3.85
7 8 2.157738 CAGCTTGAGTTCCCTTTGGAG 58.842 52.381 0.00 0.00 43.07 3.86
8 9 1.774254 TCAGCTTGAGTTCCCTTTGGA 59.226 47.619 0.00 0.00 39.54 3.53
9 10 2.276732 TCAGCTTGAGTTCCCTTTGG 57.723 50.000 0.00 0.00 0.00 3.28
10 11 3.822735 TGATTCAGCTTGAGTTCCCTTTG 59.177 43.478 0.00 0.00 0.00 2.77
11 12 4.104383 TGATTCAGCTTGAGTTCCCTTT 57.896 40.909 0.00 0.00 0.00 3.11
12 13 3.795688 TGATTCAGCTTGAGTTCCCTT 57.204 42.857 0.00 0.00 0.00 3.95
13 14 3.073650 ACTTGATTCAGCTTGAGTTCCCT 59.926 43.478 0.00 0.00 0.00 4.20
14 15 3.416156 ACTTGATTCAGCTTGAGTTCCC 58.584 45.455 0.00 0.00 0.00 3.97
15 16 4.067896 TGACTTGATTCAGCTTGAGTTCC 58.932 43.478 0.00 0.00 0.00 3.62
16 17 4.754114 AGTGACTTGATTCAGCTTGAGTTC 59.246 41.667 0.00 0.00 0.00 3.01
17 18 4.712476 AGTGACTTGATTCAGCTTGAGTT 58.288 39.130 0.00 0.00 0.00 3.01
18 19 4.348863 AGTGACTTGATTCAGCTTGAGT 57.651 40.909 0.00 0.00 0.00 3.41
19 20 5.348179 CACTAGTGACTTGATTCAGCTTGAG 59.652 44.000 18.45 0.00 0.00 3.02
20 21 5.233225 CACTAGTGACTTGATTCAGCTTGA 58.767 41.667 18.45 0.00 0.00 3.02
21 22 4.142945 GCACTAGTGACTTGATTCAGCTTG 60.143 45.833 27.08 0.00 0.00 4.01
22 23 3.999663 GCACTAGTGACTTGATTCAGCTT 59.000 43.478 27.08 0.00 0.00 3.74
23 24 3.594134 GCACTAGTGACTTGATTCAGCT 58.406 45.455 27.08 0.00 0.00 4.24
24 25 2.675348 GGCACTAGTGACTTGATTCAGC 59.325 50.000 27.08 5.97 35.21 4.26
25 26 3.265791 GGGCACTAGTGACTTGATTCAG 58.734 50.000 27.55 0.00 39.02 3.02
26 27 2.637382 TGGGCACTAGTGACTTGATTCA 59.363 45.455 27.55 13.40 39.02 2.57
27 28 3.334583 TGGGCACTAGTGACTTGATTC 57.665 47.619 27.55 10.84 39.02 2.52
28 29 3.788227 TTGGGCACTAGTGACTTGATT 57.212 42.857 27.55 0.00 39.02 2.57
29 30 3.788227 TTTGGGCACTAGTGACTTGAT 57.212 42.857 27.55 0.00 39.02 2.57
30 31 3.118038 AGTTTTGGGCACTAGTGACTTGA 60.118 43.478 27.55 11.43 39.02 3.02
31 32 3.214328 AGTTTTGGGCACTAGTGACTTG 58.786 45.455 27.55 0.37 39.02 3.16
32 33 3.577805 AGTTTTGGGCACTAGTGACTT 57.422 42.857 27.55 4.83 39.02 3.01
33 34 4.273148 CTAGTTTTGGGCACTAGTGACT 57.727 45.455 27.55 20.31 39.24 3.41
38 39 2.488153 GGCAACTAGTTTTGGGCACTAG 59.512 50.000 15.22 7.88 46.42 2.57
39 40 2.510613 GGCAACTAGTTTTGGGCACTA 58.489 47.619 15.22 0.00 0.00 2.74
40 41 1.328279 GGCAACTAGTTTTGGGCACT 58.672 50.000 15.22 0.00 0.00 4.40
41 42 0.317160 GGGCAACTAGTTTTGGGCAC 59.683 55.000 16.54 10.36 0.00 5.01
42 43 0.830023 GGGGCAACTAGTTTTGGGCA 60.830 55.000 16.54 0.00 0.00 5.36
43 44 0.830023 TGGGGCAACTAGTTTTGGGC 60.830 55.000 5.07 7.40 0.00 5.36
44 45 1.618343 CTTGGGGCAACTAGTTTTGGG 59.382 52.381 5.07 0.00 0.00 4.12
45 46 2.296190 GTCTTGGGGCAACTAGTTTTGG 59.704 50.000 5.07 0.00 0.00 3.28
46 47 3.004734 CAGTCTTGGGGCAACTAGTTTTG 59.995 47.826 5.07 0.00 0.00 2.44
47 48 3.117663 TCAGTCTTGGGGCAACTAGTTTT 60.118 43.478 5.07 0.00 0.00 2.43
48 49 2.441750 TCAGTCTTGGGGCAACTAGTTT 59.558 45.455 5.07 0.00 0.00 2.66
49 50 2.054799 TCAGTCTTGGGGCAACTAGTT 58.945 47.619 1.12 1.12 0.00 2.24
50 51 1.729586 TCAGTCTTGGGGCAACTAGT 58.270 50.000 0.00 0.00 0.00 2.57
51 52 2.859165 TTCAGTCTTGGGGCAACTAG 57.141 50.000 0.00 0.00 0.00 2.57
52 53 2.224769 CCTTTCAGTCTTGGGGCAACTA 60.225 50.000 0.00 0.00 0.00 2.24
53 54 1.479389 CCTTTCAGTCTTGGGGCAACT 60.479 52.381 0.00 0.00 0.00 3.16
54 55 0.961753 CCTTTCAGTCTTGGGGCAAC 59.038 55.000 0.00 0.00 0.00 4.17
55 56 0.555769 ACCTTTCAGTCTTGGGGCAA 59.444 50.000 0.00 0.00 0.00 4.52
56 57 0.178992 CACCTTTCAGTCTTGGGGCA 60.179 55.000 0.00 0.00 0.00 5.36
57 58 0.895559 CCACCTTTCAGTCTTGGGGC 60.896 60.000 0.00 0.00 0.00 5.80
58 59 0.771127 TCCACCTTTCAGTCTTGGGG 59.229 55.000 0.00 0.00 0.00 4.96
59 60 1.271597 CCTCCACCTTTCAGTCTTGGG 60.272 57.143 0.00 0.00 0.00 4.12
60 61 1.884067 GCCTCCACCTTTCAGTCTTGG 60.884 57.143 0.00 0.00 0.00 3.61
61 62 1.528129 GCCTCCACCTTTCAGTCTTG 58.472 55.000 0.00 0.00 0.00 3.02
62 63 0.035458 CGCCTCCACCTTTCAGTCTT 59.965 55.000 0.00 0.00 0.00 3.01
63 64 1.674057 CGCCTCCACCTTTCAGTCT 59.326 57.895 0.00 0.00 0.00 3.24
64 65 1.376037 CCGCCTCCACCTTTCAGTC 60.376 63.158 0.00 0.00 0.00 3.51
84 85 6.614160 CCGTTTGAACCCTATATTTCGTTTT 58.386 36.000 0.00 0.00 0.00 2.43
92 93 1.764134 TCCGCCGTTTGAACCCTATAT 59.236 47.619 0.00 0.00 0.00 0.86
93 94 1.193323 TCCGCCGTTTGAACCCTATA 58.807 50.000 0.00 0.00 0.00 1.31
115 116 3.126831 CACCATAACATTCTCTCTCCGC 58.873 50.000 0.00 0.00 0.00 5.54
134 135 1.312371 TAAAAGATGCGCTGGGCCAC 61.312 55.000 14.44 8.03 42.61 5.01
151 157 4.136796 GGTGCACCAGATTATGATGCTAA 58.863 43.478 31.23 0.00 37.20 3.09
175 181 2.092646 AGGGCCGCATAAGAATGTTGTA 60.093 45.455 0.00 0.00 35.38 2.41
191 197 1.077429 GATGGGAGTTGACAGGGCC 60.077 63.158 0.00 0.00 0.00 5.80
219 225 1.203112 TGACAGGAGGAAGAGCTCACT 60.203 52.381 17.77 10.92 0.00 3.41
234 240 0.031178 GCCAGCCTTTTGTGTGACAG 59.969 55.000 0.00 0.00 0.00 3.51
235 241 1.391157 GGCCAGCCTTTTGTGTGACA 61.391 55.000 0.00 0.00 0.00 3.58
236 242 1.109323 AGGCCAGCCTTTTGTGTGAC 61.109 55.000 5.04 0.00 45.70 3.67
271 277 3.133003 ACGTAGCAGCTGGATTTATCTGT 59.867 43.478 17.12 0.00 0.00 3.41
295 301 2.357034 AGCAACACCTACACGGCG 60.357 61.111 4.80 4.80 35.61 6.46
410 416 1.937108 GCAAACAGAGGAGAGGACGTG 60.937 57.143 0.00 0.00 0.00 4.49
811 831 4.676723 CGTGGAAAATGACAACCTGTGTTT 60.677 41.667 0.00 0.00 41.96 2.83
1117 1140 4.699257 GGTGAACTCTCTGATGCAGAAAAT 59.301 41.667 0.00 0.00 40.18 1.82
1421 1459 6.070021 AGGATCCAGTTTAACATCTGACATGA 60.070 38.462 15.82 0.00 34.02 3.07
1560 1749 4.038763 TGTCAAATTGTAGTCAGACTCGGT 59.961 41.667 6.27 0.00 0.00 4.69
1561 1750 4.556233 TGTCAAATTGTAGTCAGACTCGG 58.444 43.478 6.27 0.00 0.00 4.63
1562 1751 6.366061 TCATTGTCAAATTGTAGTCAGACTCG 59.634 38.462 6.27 0.00 0.00 4.18
1771 1961 2.692557 GCTGCAGATGAGGTCTTCTCTA 59.307 50.000 20.43 0.00 42.86 2.43
2930 3164 7.544566 CGAAGCTATCTGGACTTGTTAGTTTTA 59.455 37.037 0.00 0.00 33.84 1.52
2935 3169 5.038033 GTCGAAGCTATCTGGACTTGTTAG 58.962 45.833 0.00 0.00 0.00 2.34
2960 3195 8.196771 TGTGTATGCCAGATCCAAATTAAATTC 58.803 33.333 0.00 0.00 0.00 2.17
3221 3471 7.228507 GCTCTCTAATCATGTCTTCTCTGTAGA 59.771 40.741 0.00 0.00 0.00 2.59
3303 3569 4.777366 TCTTGGTGATGATCTAGGTTGTGA 59.223 41.667 0.00 0.00 0.00 3.58
3370 3643 3.313803 GCTTTAGCAATAGAAGGCCAGAC 59.686 47.826 5.01 0.00 41.59 3.51
3420 3697 0.768622 TGGTGGACCCTACTTGTTGG 59.231 55.000 0.00 0.00 34.29 3.77
3433 3712 7.343574 TGATTAGTAGTTAAGTAGCATGGTGGA 59.656 37.037 7.89 0.00 0.00 4.02
3434 3713 7.438459 GTGATTAGTAGTTAAGTAGCATGGTGG 59.562 40.741 7.89 0.00 0.00 4.61
3465 3744 2.808543 GTTGCCGTCATCTTCTGAAAGT 59.191 45.455 0.00 0.00 35.07 2.66
3477 3756 1.225855 CTTGCTGTTAGTTGCCGTCA 58.774 50.000 0.00 0.00 0.00 4.35
3478 3757 0.110192 GCTTGCTGTTAGTTGCCGTC 60.110 55.000 0.00 0.00 0.00 4.79
3501 3780 6.024552 ACTTTTTGTATTAGGGTGCATGTG 57.975 37.500 0.00 0.00 0.00 3.21
3505 3784 4.342378 TGCAACTTTTTGTATTAGGGTGCA 59.658 37.500 0.00 0.00 34.90 4.57
3506 3785 4.877282 TGCAACTTTTTGTATTAGGGTGC 58.123 39.130 0.00 0.00 34.90 5.01
3530 3935 6.635030 AACTTGAGAACTGATGTTAAACCC 57.365 37.500 0.00 0.00 36.39 4.11
3581 4004 6.909909 AGATTCGTCAAATGAAAAGGGTTAC 58.090 36.000 0.00 0.00 0.00 2.50
3597 4024 5.236047 CCTGATCATTGGAAGAAGATTCGTC 59.764 44.000 0.00 0.51 35.38 4.20
3602 4029 3.474600 CGCCTGATCATTGGAAGAAGAT 58.525 45.455 5.19 0.00 0.00 2.40
3659 4086 4.156556 GCAGCCACAATTTTCATCTGTCTA 59.843 41.667 0.00 0.00 0.00 2.59
3711 4138 3.117360 GGACCCTTGGATTCATCTTCCAT 60.117 47.826 0.00 0.00 42.69 3.41
3835 4262 2.991250 AGTTCAGTGCAACAACAGAGT 58.009 42.857 0.00 0.00 41.43 3.24
3907 4337 1.909700 AACCTGAATGCAACATCGGT 58.090 45.000 0.00 0.00 0.00 4.69
3908 4338 3.009723 ACTAACCTGAATGCAACATCGG 58.990 45.455 0.00 0.00 0.00 4.18
3909 4339 3.684305 TGACTAACCTGAATGCAACATCG 59.316 43.478 0.00 0.00 0.00 3.84
3912 4342 4.350368 TCTGACTAACCTGAATGCAACA 57.650 40.909 0.00 0.00 0.00 3.33
3916 4346 7.792374 TGAATAATCTGACTAACCTGAATGC 57.208 36.000 0.00 0.00 0.00 3.56
3947 4378 9.672673 ACTCTGTTTCATGCAAAGTTATAGTAT 57.327 29.630 0.00 0.00 0.00 2.12
3949 4380 7.986085 ACTCTGTTTCATGCAAAGTTATAGT 57.014 32.000 0.00 0.00 0.00 2.12
3975 4406 7.726216 TCTCTCTGTTTTCTGACAGTTCAATA 58.274 34.615 1.59 0.00 45.64 1.90
3979 4410 7.491048 GGATATCTCTCTGTTTTCTGACAGTTC 59.509 40.741 1.59 0.00 45.64 3.01
3992 4423 4.214310 CACCAGTCTGGATATCTCTCTGT 58.786 47.826 26.18 0.00 40.96 3.41
4005 4500 2.146342 GGTTGACATCACACCAGTCTG 58.854 52.381 0.00 0.00 33.56 3.51
4007 4502 1.523758 GGGTTGACATCACACCAGTC 58.476 55.000 12.36 0.00 32.43 3.51
4008 4503 0.110486 GGGGTTGACATCACACCAGT 59.890 55.000 12.36 0.00 32.43 4.00
4010 4505 0.553333 TTGGGGTTGACATCACACCA 59.447 50.000 0.00 0.00 32.43 4.17
4011 4506 1.698506 TTTGGGGTTGACATCACACC 58.301 50.000 0.00 0.00 0.00 4.16
4012 4507 4.306600 GAAATTTGGGGTTGACATCACAC 58.693 43.478 0.00 0.00 0.00 3.82
4013 4508 3.323403 GGAAATTTGGGGTTGACATCACA 59.677 43.478 0.00 0.00 0.00 3.58
4014 4509 3.323403 TGGAAATTTGGGGTTGACATCAC 59.677 43.478 0.00 0.00 0.00 3.06
4016 4511 4.824479 ATGGAAATTTGGGGTTGACATC 57.176 40.909 0.00 0.00 0.00 3.06
4017 4512 5.581350 AAATGGAAATTTGGGGTTGACAT 57.419 34.783 0.00 0.00 0.00 3.06
4019 4514 5.859495 TGTAAATGGAAATTTGGGGTTGAC 58.141 37.500 0.00 0.00 0.00 3.18
4021 4516 6.471146 TCATGTAAATGGAAATTTGGGGTTG 58.529 36.000 0.00 0.00 0.00 3.77
4022 4517 6.694445 TCATGTAAATGGAAATTTGGGGTT 57.306 33.333 0.00 0.00 0.00 4.11
4024 4519 8.578448 AATTTCATGTAAATGGAAATTTGGGG 57.422 30.769 0.00 0.00 44.46 4.96
4168 5021 8.083828 AGATCCATCTGTTTGTACTTCTATGT 57.916 34.615 0.00 0.00 35.42 2.29
4212 5065 5.767269 ACTTGACAGCGACATCTATATGAG 58.233 41.667 0.00 0.00 36.54 2.90
4433 5292 5.700402 AGAGGCACCAAAGACACTTATAT 57.300 39.130 0.00 0.00 0.00 0.86
4575 5434 5.762711 TCGTTGCTGGTATATGCACAAATAT 59.237 36.000 0.00 0.00 39.05 1.28
4597 5456 0.390603 TATTGAGGGTGTTGGCGTCG 60.391 55.000 0.00 0.00 0.00 5.12
4723 5584 2.838813 GGGCTACTTAGTCCCAGTTTCT 59.161 50.000 4.45 0.00 42.26 2.52
4761 6058 0.249398 CTAACCTCCTGACAACCCGG 59.751 60.000 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.