Multiple sequence alignment - TraesCS3D01G382000

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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 TraesCS3D01G382000 chr3D 100.000 3424 0 0 1 3424 497866597 497870020 0.000000e+00 6324.0
1 TraesCS3D01G382000 chr3D 83.897 621 89 8 946 1559 567848347 567848963 1.770000e-162 582.0
2 TraesCS3D01G382000 chr3D 80.444 721 109 27 1829 2524 570079287 570078574 3.920000e-144 521.0
3 TraesCS3D01G382000 chr3D 74.645 1057 211 45 992 2007 520319253 520318213 6.840000e-112 414.0
4 TraesCS3D01G382000 chr3D 74.850 1002 191 36 1253 2203 520322352 520321361 6.880000e-107 398.0
5 TraesCS3D01G382000 chr3D 88.492 252 23 4 2930 3176 498096200 498096450 2.000000e-77 300.0
6 TraesCS3D01G382000 chr3D 83.264 239 25 12 2931 3163 497958906 497959135 4.480000e-49 206.0
7 TraesCS3D01G382000 chr3D 86.842 190 18 4 3237 3424 498096565 498096749 4.480000e-49 206.0
8 TraesCS3D01G382000 chr3D 86.387 191 16 5 3237 3423 497905876 497906060 2.080000e-47 200.0
9 TraesCS3D01G382000 chr3D 78.571 294 53 6 2060 2352 570145519 570145235 5.840000e-43 185.0
10 TraesCS3D01G382000 chr3D 81.675 191 15 9 3239 3424 520219224 520219399 1.280000e-29 141.0
11 TraesCS3D01G382000 chr3D 81.967 183 14 9 3237 3418 497959267 497959431 1.660000e-28 137.0
12 TraesCS3D01G382000 chr3D 100.000 28 0 0 3220 3247 497959233 497959260 6.000000e-03 52.8
13 TraesCS3D01G382000 chr3B 92.605 2015 132 10 730 2730 658489665 658491676 0.000000e+00 2880.0
14 TraesCS3D01G382000 chr3B 83.869 1649 211 28 824 2431 756687003 756685369 0.000000e+00 1520.0
15 TraesCS3D01G382000 chr3B 89.953 637 52 6 1307 1942 684765206 684765831 0.000000e+00 811.0
16 TraesCS3D01G382000 chr3B 91.913 507 32 5 1 505 658488282 658488781 0.000000e+00 701.0
17 TraesCS3D01G382000 chr3B 85.231 562 64 13 659 1205 684764608 684765165 8.300000e-156 560.0
18 TraesCS3D01G382000 chr3B 83.210 542 66 6 2101 2641 684765831 684766348 1.110000e-129 473.0
19 TraesCS3D01G382000 chr3B 84.146 410 50 8 2770 3176 658492232 658492629 1.930000e-102 383.0
20 TraesCS3D01G382000 chr3B 73.733 967 218 25 984 1937 756824184 756823241 2.530000e-91 346.0
21 TraesCS3D01G382000 chr3B 82.222 405 53 13 2767 3163 659067855 659068248 7.080000e-87 331.0
22 TraesCS3D01G382000 chr3B 93.665 221 11 2 512 732 658489334 658489551 9.160000e-86 327.0
23 TraesCS3D01G382000 chr3B 89.474 228 23 1 1 227 684763976 684764203 1.550000e-73 287.0
24 TraesCS3D01G382000 chr3B 85.532 235 21 7 2935 3163 659000888 659001115 2.050000e-57 233.0
25 TraesCS3D01G382000 chr3B 85.581 215 14 5 3220 3424 658604087 658604294 3.460000e-50 209.0
26 TraesCS3D01G382000 chr3B 86.772 189 19 6 2939 3122 658935163 658935350 4.480000e-49 206.0
27 TraesCS3D01G382000 chr3B 78.723 282 51 5 2071 2352 756707950 756707678 2.710000e-41 180.0
28 TraesCS3D01G382000 chr3B 78.723 282 51 5 2071 2352 756743470 756743198 2.710000e-41 180.0
29 TraesCS3D01G382000 chr3B 82.635 167 24 2 3237 3403 658492750 658492911 3.560000e-30 143.0
30 TraesCS3D01G382000 chr3B 81.481 189 16 8 3239 3424 685061745 685061917 1.660000e-28 137.0
31 TraesCS3D01G382000 chr3B 82.812 128 10 5 2770 2885 658501336 658501463 1.680000e-18 104.0
32 TraesCS3D01G382000 chr3B 100.000 28 0 0 3220 3247 658492716 658492743 6.000000e-03 52.8
33 TraesCS3D01G382000 chr3A 91.584 1509 103 12 534 2027 636539106 636537607 0.000000e+00 2061.0
34 TraesCS3D01G382000 chr3A 82.442 1720 246 37 747 2441 702953056 702951368 0.000000e+00 1452.0
35 TraesCS3D01G382000 chr3A 84.848 858 118 8 1179 2026 702589758 702588903 0.000000e+00 854.0
36 TraesCS3D01G382000 chr3A 92.870 547 38 1 2017 2563 636537518 636536973 0.000000e+00 793.0
37 TraesCS3D01G382000 chr3A 88.088 638 52 12 1307 1942 655894626 655894011 0.000000e+00 736.0
38 TraesCS3D01G382000 chr3A 83.828 606 70 18 659 1248 655895219 655894626 4.990000e-153 551.0
39 TraesCS3D01G382000 chr3A 88.112 429 37 6 1 428 636540147 636539732 6.600000e-137 497.0
40 TraesCS3D01G382000 chr3A 88.251 366 36 5 2781 3143 636536457 636536096 6.790000e-117 431.0
41 TraesCS3D01G382000 chr3A 82.057 457 77 5 2070 2525 702587542 702587090 5.360000e-103 385.0
42 TraesCS3D01G382000 chr3A 88.055 293 27 6 2877 3168 636400971 636400686 1.180000e-89 340.0
43 TraesCS3D01G382000 chr3A 82.564 390 58 5 1 388 655630073 655630454 5.480000e-88 335.0
44 TraesCS3D01G382000 chr3A 85.337 341 28 3 2101 2441 655894011 655893693 1.970000e-87 333.0
45 TraesCS3D01G382000 chr3A 86.192 239 21 7 2931 3163 636159050 636158818 7.340000e-62 248.0
46 TraesCS3D01G382000 chr3A 86.458 192 16 7 3237 3424 636158691 636158506 5.790000e-48 202.0
47 TraesCS3D01G382000 chr3A 85.106 188 23 2 3237 3424 636393427 636393245 1.620000e-43 187.0
48 TraesCS3D01G382000 chr3A 83.598 189 16 4 3237 3424 636400566 636400392 2.730000e-36 163.0
49 TraesCS3D01G382000 chr3A 85.294 136 20 0 2068 2203 655629860 655629995 1.280000e-29 141.0
50 TraesCS3D01G382000 chr3A 81.481 189 18 6 3239 3424 655647033 655647207 4.610000e-29 139.0
51 TraesCS3D01G382000 chr3A 87.368 95 12 0 990 1084 655886621 655886527 3.610000e-20 110.0
52 TraesCS3D01G382000 chr3A 85.263 95 14 0 1089 1183 702594477 702594383 7.820000e-17 99.0
53 TraesCS3D01G382000 chr3A 97.143 35 1 0 2578 2612 636536955 636536989 3.690000e-05 60.2
54 TraesCS3D01G382000 chr3A 100.000 28 0 0 3220 3247 636393461 636393434 6.000000e-03 52.8
55 TraesCS3D01G382000 chr5D 73.146 1497 325 53 979 2424 297736863 297738333 1.860000e-127 466.0
56 TraesCS3D01G382000 chr5D 84.091 264 34 6 569 825 297750649 297750911 7.340000e-62 248.0
57 TraesCS3D01G382000 chr5D 85.417 144 17 4 862 1003 297751139 297751280 2.750000e-31 147.0
58 TraesCS3D01G382000 chr5D 91.525 59 3 2 3160 3218 481806202 481806146 2.830000e-11 80.5
59 TraesCS3D01G382000 chr5A 74.307 1082 232 31 870 1917 401317780 401316711 1.900000e-112 416.0
60 TraesCS3D01G382000 chr5A 82.222 450 61 15 569 1003 401314260 401313815 1.500000e-98 370.0
61 TraesCS3D01G382000 chr5B 82.183 449 62 13 569 1003 338484812 338485256 1.500000e-98 370.0
62 TraesCS3D01G382000 chr5B 74.319 697 155 18 862 1542 338481131 338481819 1.210000e-69 274.0
63 TraesCS3D01G382000 chr1B 96.154 52 2 0 3167 3218 154165056 154165107 6.090000e-13 86.1
64 TraesCS3D01G382000 chr4B 94.444 54 3 0 3166 3219 526954612 526954559 2.190000e-12 84.2
65 TraesCS3D01G382000 chr2D 97.917 48 1 0 3167 3214 594457001 594457048 2.190000e-12 84.2
66 TraesCS3D01G382000 chr2D 94.444 54 3 0 3165 3218 633850168 633850221 2.190000e-12 84.2
67 TraesCS3D01G382000 chr2B 96.000 50 2 0 3165 3214 765569349 765569300 7.880000e-12 82.4
68 TraesCS3D01G382000 chr4D 94.231 52 3 0 3167 3218 252173795 252173744 2.830000e-11 80.5
69 TraesCS3D01G382000 chr4D 94.340 53 2 1 3162 3214 320593724 320593775 2.830000e-11 80.5
70 TraesCS3D01G382000 chr7A 90.164 61 3 3 3159 3218 88945425 88945483 3.660000e-10 76.8


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 TraesCS3D01G382000 chr3D 497866597 497870020 3423 False 6324.00 6324 100.000000 1 3424 1 chr3D.!!$F1 3423
1 TraesCS3D01G382000 chr3D 567848347 567848963 616 False 582.00 582 83.897000 946 1559 1 chr3D.!!$F4 613
2 TraesCS3D01G382000 chr3D 570078574 570079287 713 True 521.00 521 80.444000 1829 2524 1 chr3D.!!$R1 695
3 TraesCS3D01G382000 chr3D 520318213 520322352 4139 True 406.00 414 74.747500 992 2203 2 chr3D.!!$R3 1211
4 TraesCS3D01G382000 chr3D 498096200 498096749 549 False 253.00 300 87.667000 2930 3424 2 chr3D.!!$F6 494
5 TraesCS3D01G382000 chr3B 756685369 756687003 1634 True 1520.00 1520 83.869000 824 2431 1 chr3B.!!$R1 1607
6 TraesCS3D01G382000 chr3B 658488282 658492911 4629 False 747.80 2880 90.827333 1 3403 6 chr3B.!!$F7 3402
7 TraesCS3D01G382000 chr3B 684763976 684766348 2372 False 532.75 811 86.967000 1 2641 4 chr3B.!!$F8 2640
8 TraesCS3D01G382000 chr3B 756823241 756824184 943 True 346.00 346 73.733000 984 1937 1 chr3B.!!$R4 953
9 TraesCS3D01G382000 chr3A 702951368 702953056 1688 True 1452.00 1452 82.442000 747 2441 1 chr3A.!!$R3 1694
10 TraesCS3D01G382000 chr3A 636536096 636540147 4051 True 945.50 2061 90.204250 1 3143 4 chr3A.!!$R7 3142
11 TraesCS3D01G382000 chr3A 702587090 702589758 2668 True 619.50 854 83.452500 1179 2525 2 chr3A.!!$R9 1346
12 TraesCS3D01G382000 chr3A 655893693 655895219 1526 True 540.00 736 85.751000 659 2441 3 chr3A.!!$R8 1782
13 TraesCS3D01G382000 chr3A 636400392 636400971 579 True 251.50 340 85.826500 2877 3424 2 chr3A.!!$R6 547
14 TraesCS3D01G382000 chr3A 655629860 655630454 594 False 238.00 335 83.929000 1 2203 2 chr3A.!!$F3 2202
15 TraesCS3D01G382000 chr3A 636158506 636159050 544 True 225.00 248 86.325000 2931 3424 2 chr3A.!!$R4 493
16 TraesCS3D01G382000 chr5D 297736863 297738333 1470 False 466.00 466 73.146000 979 2424 1 chr5D.!!$F1 1445
17 TraesCS3D01G382000 chr5A 401313815 401317780 3965 True 393.00 416 78.264500 569 1917 2 chr5A.!!$R1 1348
18 TraesCS3D01G382000 chr5B 338481131 338485256 4125 False 322.00 370 78.251000 569 1542 2 chr5B.!!$F1 973

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
654 1297 0.035630 AGCAGCCAGAACAGTCATCC 60.036 55.0 0.00 0.0 0.0 3.51 F
656 1299 0.617413 CAGCCAGAACAGTCATCCCT 59.383 55.0 0.00 0.0 0.0 4.20 F
896 1704 0.622665 GCCATCCCCAGCTAGCATAT 59.377 55.0 18.83 0.0 0.0 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 3851 0.969149 TGCTACTGGAGTGGTGTCAG 59.031 55.0 0.0 0.0 34.91 3.51 R
2222 5842 1.133809 TCCTGTTTGGGGTGAGGAGG 61.134 60.0 0.0 0.0 36.20 4.30 R
2687 6464 0.250770 GTCCAGGGGAGAACAACACC 60.251 60.0 0.0 0.0 29.39 4.16 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
33 34 4.857679 TGGTGATGTCATGGATGAATTCA 58.142 39.130 11.26 11.26 38.75 2.57
47 48 0.251916 AATTCATGAGGACCGCGGAA 59.748 50.000 35.90 13.77 0.00 4.30
98 99 2.134287 GGAGCGGGCTAGATGTCCA 61.134 63.158 0.00 0.00 41.50 4.02
124 125 1.496060 ATGCTGGTTGTATCCCTCGA 58.504 50.000 0.00 0.00 0.00 4.04
185 188 3.332034 TGATGACAGTGAACAGATGCTG 58.668 45.455 0.00 0.00 37.52 4.41
258 261 3.058224 GCGTGCTTTGAAGGTAATCAACT 60.058 43.478 0.00 0.00 38.95 3.16
391 396 1.135315 AGTTTGCAAGCTGTGTGTGTG 60.135 47.619 15.61 0.00 0.00 3.82
393 398 2.352686 GCAAGCTGTGTGTGTGCG 60.353 61.111 0.00 0.00 0.00 5.34
394 399 3.101209 CAAGCTGTGTGTGTGCGT 58.899 55.556 0.00 0.00 0.00 5.24
395 400 1.297819 CAAGCTGTGTGTGTGCGTG 60.298 57.895 0.00 0.00 0.00 5.34
396 401 3.112126 AAGCTGTGTGTGTGCGTGC 62.112 57.895 0.00 0.00 0.00 5.34
397 402 4.612536 GCTGTGTGTGTGCGTGCC 62.613 66.667 0.00 0.00 0.00 5.01
398 403 4.297891 CTGTGTGTGTGCGTGCCG 62.298 66.667 0.00 0.00 0.00 5.69
432 437 4.759693 AGTGATGCTGGTTTTATCGTTCAA 59.240 37.500 0.00 0.00 0.00 2.69
449 484 0.110688 CAACAAGGCATGACACGACG 60.111 55.000 0.00 0.00 0.00 5.12
455 490 2.730672 GCATGACACGACGACTGGC 61.731 63.158 0.00 0.00 0.00 4.85
456 491 2.094659 CATGACACGACGACTGGCC 61.095 63.158 0.00 0.00 0.00 5.36
506 541 4.098349 ACCATGGCATGACATGTTTGTATC 59.902 41.667 34.09 0.00 45.21 2.24
507 542 4.340097 CCATGGCATGACATGTTTGTATCT 59.660 41.667 34.09 0.00 45.21 1.98
508 543 4.968812 TGGCATGACATGTTTGTATCTG 57.031 40.909 16.62 0.00 35.79 2.90
510 1129 4.766373 TGGCATGACATGTTTGTATCTGTT 59.234 37.500 16.62 0.00 35.79 3.16
652 1295 3.641434 ATAAGCAGCCAGAACAGTCAT 57.359 42.857 0.00 0.00 0.00 3.06
654 1297 0.035630 AGCAGCCAGAACAGTCATCC 60.036 55.000 0.00 0.00 0.00 3.51
656 1299 0.617413 CAGCCAGAACAGTCATCCCT 59.383 55.000 0.00 0.00 0.00 4.20
806 1601 6.885952 TTGACCGAATCTTTCATTAAACCA 57.114 33.333 0.00 0.00 0.00 3.67
828 1623 0.682292 GTATGAGCTGGCCCTAGGAC 59.318 60.000 11.48 0.00 0.00 3.85
896 1704 0.622665 GCCATCCCCAGCTAGCATAT 59.377 55.000 18.83 0.00 0.00 1.78
898 1706 2.239654 GCCATCCCCAGCTAGCATATAA 59.760 50.000 18.83 0.00 0.00 0.98
965 1781 3.891422 ATCTTGCTCTCTCAGGTTCAG 57.109 47.619 0.00 0.00 0.00 3.02
1273 3422 6.750148 AGATTTCTGAAGAAGTACAAGTCGT 58.250 36.000 0.00 0.00 35.21 4.34
1304 3461 2.630158 CTGAGCAGAACAGGATGAAGG 58.370 52.381 0.00 0.00 39.69 3.46
1396 3553 2.125350 GACTTGGGCTGCTCCTCG 60.125 66.667 0.00 0.00 34.39 4.63
1677 3843 6.966534 CCTTCATTGGCTATCAAAGGTATT 57.033 37.500 9.89 0.00 39.05 1.89
1678 3844 6.742109 CCTTCATTGGCTATCAAAGGTATTG 58.258 40.000 9.89 0.00 39.05 1.90
1682 3851 6.767902 TCATTGGCTATCAAAGGTATTGAGTC 59.232 38.462 0.00 0.00 39.05 3.36
1761 3946 5.530543 GGCTCCTGAAGATTTAAGGATGAAG 59.469 44.000 0.00 0.00 39.36 3.02
1791 3976 3.804325 CGGTGTATGACATGGATGAGAAC 59.196 47.826 0.00 0.00 0.00 3.01
1844 4029 3.126858 GGAGCTTATGCACGACAATTCAA 59.873 43.478 3.16 0.00 42.74 2.69
1899 4086 3.766545 CAAAGAATTGGTCCCAGAAGGA 58.233 45.455 0.00 0.00 36.07 3.36
2007 4194 2.124403 GCCATGGCCTCAGAGGTG 60.124 66.667 27.24 8.37 37.80 4.00
2015 4202 2.435805 TGGCCTCAGAGGTGAATACATC 59.564 50.000 18.37 0.00 37.80 3.06
2026 4312 9.014297 CAGAGGTGAATACATCCTTTACTTTTT 57.986 33.333 0.00 0.00 38.33 1.94
2034 4321 9.869757 AATACATCCTTTACTTTTTAACCATGC 57.130 29.630 0.00 0.00 0.00 4.06
2038 4325 7.354751 TCCTTTACTTTTTAACCATGCTGTT 57.645 32.000 0.00 0.00 0.00 3.16
2302 5950 0.526954 CAGCATTTTGGATCGCCAGC 60.527 55.000 0.00 0.00 46.91 4.85
2324 5972 5.531659 AGCAGAGATCATGGATGAATTTGTC 59.468 40.000 0.00 0.00 40.69 3.18
2431 6102 1.471287 CACCAAGGCATGACATGACAG 59.529 52.381 23.23 14.39 42.15 3.51
2462 6133 1.410517 GCTGCTGCTAGTCTGTATCCA 59.589 52.381 8.53 0.00 36.03 3.41
2493 6164 9.467258 CAATTTGTGACATGTCTGTAAAATTCT 57.533 29.630 25.55 9.75 34.27 2.40
2494 6165 9.467258 AATTTGTGACATGTCTGTAAAATTCTG 57.533 29.630 25.55 0.00 35.14 3.02
2526 6197 0.530744 TCGGATTTGTGAGAGACGGG 59.469 55.000 0.00 0.00 0.00 5.28
2533 6204 1.446272 GTGAGAGACGGGAAAGGCG 60.446 63.158 0.00 0.00 0.00 5.52
2539 6210 3.228453 AGAGACGGGAAAGGCGAATATA 58.772 45.455 0.00 0.00 0.00 0.86
2563 6234 4.202131 TGCTGAAATTGCATTGTGAGACAA 60.202 37.500 0.00 0.00 42.95 3.18
2570 6241 2.033675 TGCATTGTGAGACAAGCACTTG 59.966 45.455 8.82 8.82 41.94 3.16
2687 6464 6.644248 TCCATGGCAATCTCATAAGAATTG 57.356 37.500 6.96 0.00 34.49 2.32
2700 6477 5.710099 TCATAAGAATTGGTGTTGTTCTCCC 59.290 40.000 0.00 0.00 31.37 4.30
2719 6496 0.326048 CCTGGACCCATCTCTCCTGT 60.326 60.000 0.00 0.00 0.00 4.00
2738 6515 5.709631 TCCTGTCTCTCATCTATGCTATCAC 59.290 44.000 0.00 0.00 0.00 3.06
2746 6697 4.220163 TCATCTATGCTATCACTGAGGCAG 59.780 45.833 12.84 0.00 38.11 4.85
2754 6705 3.817508 ACTGAGGCAGTGAGGCAT 58.182 55.556 0.00 0.00 43.63 4.40
2755 6706 1.298993 ACTGAGGCAGTGAGGCATG 59.701 57.895 0.00 0.00 43.63 4.06
2756 6707 2.194388 ACTGAGGCAGTGAGGCATGG 62.194 60.000 0.00 0.00 43.63 3.66
2758 6709 3.336568 AGGCAGTGAGGCATGGCT 61.337 61.111 23.58 23.58 46.43 4.75
2760 6711 2.707849 GGCAGTGAGGCATGGCTTG 61.708 63.158 24.18 18.24 43.51 4.01
2761 6712 1.676635 GCAGTGAGGCATGGCTTGA 60.677 57.895 24.18 10.51 0.00 3.02
2762 6713 1.654954 GCAGTGAGGCATGGCTTGAG 61.655 60.000 24.18 14.26 0.00 3.02
2763 6714 0.035725 CAGTGAGGCATGGCTTGAGA 60.036 55.000 24.18 5.22 0.00 3.27
2764 6715 0.917533 AGTGAGGCATGGCTTGAGAT 59.082 50.000 24.18 5.47 0.00 2.75
2765 6716 1.134159 AGTGAGGCATGGCTTGAGATC 60.134 52.381 24.18 10.05 0.00 2.75
2767 6718 1.282738 TGAGGCATGGCTTGAGATCAA 59.717 47.619 24.18 0.00 0.00 2.57
2768 6719 2.291089 TGAGGCATGGCTTGAGATCAAA 60.291 45.455 24.18 0.00 35.15 2.69
2787 7099 4.051922 CAAAGAACTACTCGAACACAGCT 58.948 43.478 0.00 0.00 0.00 4.24
2789 7101 3.903360 AGAACTACTCGAACACAGCTTC 58.097 45.455 0.00 0.00 0.00 3.86
2819 7131 3.305335 GGCAAGTCCCTGTGTACAAATTG 60.305 47.826 0.00 0.00 0.00 2.32
2823 7135 3.957497 AGTCCCTGTGTACAAATTGCAAA 59.043 39.130 1.71 0.00 0.00 3.68
2850 7162 3.435327 TGCTGTAAATAAACTGGAGCGTG 59.565 43.478 0.00 0.00 0.00 5.34
2852 7164 4.435651 GCTGTAAATAAACTGGAGCGTGTC 60.436 45.833 0.00 0.00 0.00 3.67
2914 7227 3.965379 TGCATGCAAATTGATTCCTGT 57.035 38.095 20.30 0.00 0.00 4.00
3029 7343 1.923227 GCTAGACGGGCTGTTTTGGC 61.923 60.000 0.00 2.35 0.00 4.52
3063 7378 6.875726 TGATTTCTCACTAACTCTTCCATGTG 59.124 38.462 0.00 0.00 0.00 3.21
3182 7537 9.756571 TCTTTATCTCTATATTGTACTCCCTCC 57.243 37.037 0.00 0.00 0.00 4.30
3183 7538 8.577048 TTTATCTCTATATTGTACTCCCTCCG 57.423 38.462 0.00 0.00 0.00 4.63
3185 7540 6.692849 TCTCTATATTGTACTCCCTCCGTA 57.307 41.667 0.00 0.00 0.00 4.02
3186 7541 7.083062 TCTCTATATTGTACTCCCTCCGTAA 57.917 40.000 0.00 0.00 0.00 3.18
3189 7544 7.520798 TCTATATTGTACTCCCTCCGTAAAGA 58.479 38.462 0.00 0.00 0.00 2.52
3190 7545 8.000709 TCTATATTGTACTCCCTCCGTAAAGAA 58.999 37.037 0.00 0.00 0.00 2.52
3191 7546 5.750352 ATTGTACTCCCTCCGTAAAGAAA 57.250 39.130 0.00 0.00 0.00 2.52
3196 7551 8.537728 TGTACTCCCTCCGTAAAGAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
3199 7554 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
3200 7555 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
3201 7556 6.325545 TCCCTCCGTAAAGAAATATAAGAGCA 59.674 38.462 0.00 0.00 0.00 4.26
3202 7557 7.016268 TCCCTCCGTAAAGAAATATAAGAGCAT 59.984 37.037 0.00 0.00 0.00 3.79
3204 7559 9.057089 CCTCCGTAAAGAAATATAAGAGCATTT 57.943 33.333 0.00 0.00 0.00 2.32
3274 7681 1.786579 GCATTCAGAAACAACAACGGC 59.213 47.619 0.00 0.00 0.00 5.68
3291 7709 1.594518 CGGCACAGTTCAAGTTTGACG 60.595 52.381 0.00 0.00 36.83 4.35
3293 7711 2.538939 GGCACAGTTCAAGTTTGACGAC 60.539 50.000 0.00 0.00 36.83 4.34
3312 7730 7.684670 TGACGACATCTACAAAATCAATAAGC 58.315 34.615 0.00 0.00 0.00 3.09
3328 9185 7.936496 TCAATAAGCTGACAATAATGGACAA 57.064 32.000 0.00 0.00 0.00 3.18
3363 9396 0.179029 AGGTGCACGGCTACAACTTT 60.179 50.000 11.45 0.00 26.08 2.66
3365 9398 1.066454 GGTGCACGGCTACAACTTTTT 59.934 47.619 11.45 0.00 0.00 1.94
3418 9656 5.163893 CCTCAACAATCAGCATTTTTCATGC 60.164 40.000 0.00 0.00 44.85 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.768164 CCTCATGAATTCATCCATGACATCA 59.232 40.000 18.16 6.12 42.76 3.07
47 48 0.896019 CCTCTAGGATCCATCGCCGT 60.896 60.000 15.82 0.00 37.39 5.68
53 54 2.978278 CAAGCTTCCCTCTAGGATCCAT 59.022 50.000 15.82 1.47 46.94 3.41
98 99 4.537688 AGGGATACAACCAGCATAGCATAT 59.462 41.667 0.00 0.00 39.74 1.78
124 125 4.078980 AGGGACCTGATAATCATGCCTTTT 60.079 41.667 0.00 0.00 24.64 2.27
170 172 3.811497 TCAAAGACAGCATCTGTTCACTG 59.189 43.478 0.66 0.00 45.44 3.66
185 188 2.863704 GCACACATTTGGCCTCAAAGAC 60.864 50.000 3.32 0.00 44.87 3.01
258 261 9.247861 ACATGTGCATATACTATACATCAGAGA 57.752 33.333 0.00 0.00 30.15 3.10
335 340 2.158667 AGTTCTTCTTTTCGGCCCTTGA 60.159 45.455 0.00 0.00 0.00 3.02
336 341 2.030805 CAGTTCTTCTTTTCGGCCCTTG 60.031 50.000 0.00 0.00 0.00 3.61
393 398 0.310854 CACTCTTGGGTTTTCGGCAC 59.689 55.000 0.00 0.00 0.00 5.01
394 399 0.181587 TCACTCTTGGGTTTTCGGCA 59.818 50.000 0.00 0.00 0.00 5.69
395 400 1.200020 CATCACTCTTGGGTTTTCGGC 59.800 52.381 0.00 0.00 0.00 5.54
396 401 1.200020 GCATCACTCTTGGGTTTTCGG 59.800 52.381 0.00 0.00 0.00 4.30
397 402 2.095567 CAGCATCACTCTTGGGTTTTCG 60.096 50.000 0.00 0.00 0.00 3.46
398 403 2.229784 CCAGCATCACTCTTGGGTTTTC 59.770 50.000 0.00 0.00 0.00 2.29
432 437 0.944311 GTCGTCGTGTCATGCCTTGT 60.944 55.000 0.00 0.00 0.00 3.16
449 484 2.933056 GCTAAGAACTCACAGGCCAGTC 60.933 54.545 5.01 0.00 0.00 3.51
455 490 5.971763 AGATACAAGCTAAGAACTCACAGG 58.028 41.667 0.00 0.00 0.00 4.00
456 491 6.862209 AGAGATACAAGCTAAGAACTCACAG 58.138 40.000 10.95 0.00 0.00 3.66
531 1150 5.825593 AAGTGTCAAACTGGGATAAGAGA 57.174 39.130 0.00 0.00 39.81 3.10
606 1249 4.160252 GGGGCAATGAAATAGTCAATGTGT 59.840 41.667 0.00 0.00 39.09 3.72
652 1295 4.151121 TCATTTTCAATGCTCAACAGGGA 58.849 39.130 0.00 0.00 0.00 4.20
654 1297 6.847956 TTTTCATTTTCAATGCTCAACAGG 57.152 33.333 0.00 0.00 0.00 4.00
656 1299 8.890718 TCAATTTTTCATTTTCAATGCTCAACA 58.109 25.926 0.00 0.00 0.00 3.33
806 1601 1.418334 CTAGGGCCAGCTCATACACT 58.582 55.000 6.18 0.00 0.00 3.55
828 1623 2.093306 TGGGTCAACGTGCTTATCAG 57.907 50.000 0.00 0.00 0.00 2.90
898 1706 3.066760 CCGGAAGTTCAGCTCTTGTTTTT 59.933 43.478 0.00 0.00 0.00 1.94
965 1781 3.228017 GGCTAGCCTCCGGAGACC 61.228 72.222 33.39 21.79 0.00 3.85
1244 3391 9.699703 ACTTGTACTTCTTCAGAAATCTAGTTC 57.300 33.333 0.00 0.00 33.07 3.01
1304 3461 1.596477 CCGCTGCTTCTATCAGGGC 60.596 63.158 0.00 0.00 41.43 5.19
1561 3723 2.092646 ACCAGTTACAACAACAGGCTCA 60.093 45.455 0.00 0.00 30.87 4.26
1666 3831 5.013079 TGGTGTCAGACTCAATACCTTTGAT 59.987 40.000 1.31 0.00 0.00 2.57
1677 3843 1.332195 CTGGAGTGGTGTCAGACTCA 58.668 55.000 12.10 0.00 40.43 3.41
1678 3844 1.333177 ACTGGAGTGGTGTCAGACTC 58.667 55.000 1.31 0.00 38.32 3.36
1682 3851 0.969149 TGCTACTGGAGTGGTGTCAG 59.031 55.000 0.00 0.00 34.91 3.51
1761 3946 1.745232 TGTCATACACCGGGATTTGC 58.255 50.000 6.32 0.00 0.00 3.68
1844 4029 5.360714 TGCAGGAAAAGTGTGAAATCTTTCT 59.639 36.000 4.46 0.00 38.02 2.52
1899 4086 3.644861 GAGGGAAACAACCATCCGT 57.355 52.632 0.00 0.00 36.54 4.69
1952 4139 1.761784 CAGTTCCCCAGATGAGAGAGG 59.238 57.143 0.00 0.00 0.00 3.69
2015 4202 9.705290 AATAACAGCATGGTTAAAAAGTAAAGG 57.295 29.630 0.00 0.00 43.62 3.11
2026 4312 7.637631 TCATTAGCAAATAACAGCATGGTTA 57.362 32.000 0.00 0.00 43.62 2.85
2222 5842 1.133809 TCCTGTTTGGGGTGAGGAGG 61.134 60.000 0.00 0.00 36.20 4.30
2302 5950 6.017026 CCTGACAAATTCATCCATGATCTCTG 60.017 42.308 0.00 0.00 36.56 3.35
2324 5972 4.069232 TGCTTCTCGCCGGTCCTG 62.069 66.667 1.90 0.00 38.05 3.86
2390 6041 2.544267 GAGCGATACAACCAGCATAACC 59.456 50.000 0.00 0.00 0.00 2.85
2431 6102 2.546321 CAGCAGCGACACGTCAAC 59.454 61.111 0.00 0.00 0.00 3.18
2441 6112 4.157457 TGGATACAGACTAGCAGCAGCG 62.157 54.545 0.00 0.00 46.17 5.18
2462 6133 3.084039 AGACATGTCACAAATTGGCGAT 58.916 40.909 27.02 0.00 29.36 4.58
2493 6164 6.072230 TCACAAATCCGATTAAGTTTGATGCA 60.072 34.615 0.00 0.00 35.93 3.96
2494 6165 6.321717 TCACAAATCCGATTAAGTTTGATGC 58.678 36.000 3.96 0.00 35.93 3.91
2526 6197 6.088616 GCAATTTCAGCATATATTCGCCTTTC 59.911 38.462 0.00 0.00 0.00 2.62
2563 6234 4.986659 GCTGAAATGAAAATGACAAGTGCT 59.013 37.500 0.00 0.00 0.00 4.40
2576 6247 8.668353 GTGAGACATATACTTTGCTGAAATGAA 58.332 33.333 0.00 0.00 0.00 2.57
2578 6249 7.977904 TGTGAGACATATACTTTGCTGAAATG 58.022 34.615 0.00 0.00 0.00 2.32
2579 6250 8.565896 TTGTGAGACATATACTTTGCTGAAAT 57.434 30.769 0.00 0.00 0.00 2.17
2687 6464 0.250770 GTCCAGGGGAGAACAACACC 60.251 60.000 0.00 0.00 29.39 4.16
2700 6477 0.326048 ACAGGAGAGATGGGTCCAGG 60.326 60.000 0.00 0.00 35.02 4.45
2719 6496 5.945191 CCTCAGTGATAGCATAGATGAGAGA 59.055 44.000 13.62 0.00 35.78 3.10
2738 6515 1.451567 CCATGCCTCACTGCCTCAG 60.452 63.158 0.00 0.00 37.52 3.35
2746 6697 1.307097 GATCTCAAGCCATGCCTCAC 58.693 55.000 0.00 0.00 0.00 3.51
2748 6699 2.048444 TTGATCTCAAGCCATGCCTC 57.952 50.000 0.00 0.00 0.00 4.70
2749 6700 2.025605 TCTTTGATCTCAAGCCATGCCT 60.026 45.455 0.00 0.00 37.15 4.75
2750 6701 2.372264 TCTTTGATCTCAAGCCATGCC 58.628 47.619 0.00 0.00 37.15 4.40
2751 6702 3.442977 AGTTCTTTGATCTCAAGCCATGC 59.557 43.478 0.00 0.00 37.15 4.06
2752 6703 5.879223 AGTAGTTCTTTGATCTCAAGCCATG 59.121 40.000 0.00 0.00 37.15 3.66
2754 6705 5.482908 GAGTAGTTCTTTGATCTCAAGCCA 58.517 41.667 0.00 0.00 37.15 4.75
2755 6706 4.564769 CGAGTAGTTCTTTGATCTCAAGCC 59.435 45.833 0.00 0.00 37.15 4.35
2756 6707 5.403246 TCGAGTAGTTCTTTGATCTCAAGC 58.597 41.667 0.00 0.00 37.15 4.01
2757 6708 6.863645 TGTTCGAGTAGTTCTTTGATCTCAAG 59.136 38.462 0.00 0.00 37.15 3.02
2758 6709 6.641314 GTGTTCGAGTAGTTCTTTGATCTCAA 59.359 38.462 0.00 0.00 0.00 3.02
2760 6711 6.150318 TGTGTTCGAGTAGTTCTTTGATCTC 58.850 40.000 0.00 0.00 0.00 2.75
2761 6712 6.085555 TGTGTTCGAGTAGTTCTTTGATCT 57.914 37.500 0.00 0.00 0.00 2.75
2762 6713 5.164041 GCTGTGTTCGAGTAGTTCTTTGATC 60.164 44.000 0.00 0.00 0.00 2.92
2763 6714 4.686554 GCTGTGTTCGAGTAGTTCTTTGAT 59.313 41.667 0.00 0.00 0.00 2.57
2764 6715 4.049186 GCTGTGTTCGAGTAGTTCTTTGA 58.951 43.478 0.00 0.00 0.00 2.69
2765 6716 4.051922 AGCTGTGTTCGAGTAGTTCTTTG 58.948 43.478 0.00 0.00 0.00 2.77
2767 6718 4.202121 TGAAGCTGTGTTCGAGTAGTTCTT 60.202 41.667 0.00 0.00 0.00 2.52
2768 6719 3.318275 TGAAGCTGTGTTCGAGTAGTTCT 59.682 43.478 0.00 0.00 0.00 3.01
2787 7099 1.039856 GGGACTTGCCTTTTGCTGAA 58.960 50.000 0.00 0.00 42.00 3.02
2789 7101 0.316204 CAGGGACTTGCCTTTTGCTG 59.684 55.000 0.00 0.00 37.50 4.41
2804 7116 4.050553 CAGTTTGCAATTTGTACACAGGG 58.949 43.478 0.00 0.00 0.00 4.45
2819 7131 6.308766 CCAGTTTATTTACAGCATCAGTTTGC 59.691 38.462 0.00 0.00 43.09 3.68
2823 7135 5.355350 GCTCCAGTTTATTTACAGCATCAGT 59.645 40.000 0.00 0.00 0.00 3.41
2850 7162 2.476051 CACTGCATTGCGACGGAC 59.524 61.111 3.84 0.00 0.00 4.79
2852 7164 4.465512 GCCACTGCATTGCGACGG 62.466 66.667 3.84 5.00 37.47 4.79
2853 7165 4.465512 GGCCACTGCATTGCGACG 62.466 66.667 0.00 0.00 40.13 5.12
2856 7168 2.103538 GATGGCCACTGCATTGCG 59.896 61.111 8.16 1.69 40.13 4.85
2857 7169 2.352821 TGGATGGCCACTGCATTGC 61.353 57.895 8.16 0.46 39.92 3.56
2858 7170 4.021559 TGGATGGCCACTGCATTG 57.978 55.556 8.16 0.00 39.92 2.82
3063 7378 4.320641 GGACTGATACCTTCTATGCGTCTC 60.321 50.000 0.00 0.00 0.00 3.36
3210 7565 0.692476 TTGGTGGCATGCACTCTAGT 59.308 50.000 21.36 0.00 0.00 2.57
3211 7566 1.825090 TTTGGTGGCATGCACTCTAG 58.175 50.000 21.36 0.00 0.00 2.43
3213 7568 0.963962 CTTTTGGTGGCATGCACTCT 59.036 50.000 21.36 0.00 0.00 3.24
3214 7569 0.668401 GCTTTTGGTGGCATGCACTC 60.668 55.000 21.36 9.60 0.00 3.51
3215 7570 1.368579 GCTTTTGGTGGCATGCACT 59.631 52.632 21.36 0.00 0.00 4.40
3218 7573 2.383368 TTATGCTTTTGGTGGCATGC 57.617 45.000 9.90 9.90 46.75 4.06
3274 7681 4.271049 AGATGTCGTCAAACTTGAACTGTG 59.729 41.667 0.00 0.00 39.21 3.66
3291 7709 8.668353 TGTCAGCTTATTGATTTTGTAGATGTC 58.332 33.333 0.00 0.00 0.00 3.06
3328 9185 5.236478 CGTGCACCTCGGATTAATTAATTCT 59.764 40.000 12.15 0.00 0.00 2.40
3342 9375 2.048597 TTGTAGCCGTGCACCTCG 60.049 61.111 12.15 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.