Multiple sequence alignment - TraesCS4B01G216500

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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 TraesCS4B01G216500 chr4B 100.000 2861 0 0 275 3135 456381923 456379063 0.000000e+00 5284.0
1 TraesCS4B01G216500 chr4B 94.455 2020 75 18 275 2267 456361312 456363321 0.000000e+00 3075.0
2 TraesCS4B01G216500 chr4B 86.033 2019 127 51 311 2204 599589883 599587895 0.000000e+00 2023.0
3 TraesCS4B01G216500 chr4B 85.895 1503 101 31 826 2271 668363776 668365224 0.000000e+00 1498.0
4 TraesCS4B01G216500 chr4B 85.405 1247 85 31 1119 2302 669472215 669473427 0.000000e+00 1205.0
5 TraesCS4B01G216500 chr4B 85.117 1243 83 29 1119 2302 668588194 668589393 0.000000e+00 1177.0
6 TraesCS4B01G216500 chr4B 85.084 1247 80 30 1119 2302 668513550 668514753 0.000000e+00 1175.0
7 TraesCS4B01G216500 chr4B 86.563 1094 91 14 1145 2204 599464344 599463273 0.000000e+00 1155.0
8 TraesCS4B01G216500 chr4B 84.418 1245 103 29 1119 2302 668973487 668974701 0.000000e+00 1140.0
9 TraesCS4B01G216500 chr4B 83.347 1255 110 38 1119 2302 669341928 669340702 0.000000e+00 1068.0
10 TraesCS4B01G216500 chr4B 83.037 1238 100 33 1119 2302 668446233 668447414 0.000000e+00 1022.0
11 TraesCS4B01G216500 chr4B 85.827 889 77 12 1462 2302 668216606 668217493 0.000000e+00 898.0
12 TraesCS4B01G216500 chr4B 82.348 1116 95 37 1241 2275 673297428 673296334 0.000000e+00 876.0
13 TraesCS4B01G216500 chr4B 84.036 996 28 37 275 1149 599466379 599465394 0.000000e+00 837.0
14 TraesCS4B01G216500 chr4B 83.948 841 91 17 1496 2302 669161644 669160814 0.000000e+00 765.0
15 TraesCS4B01G216500 chr4B 83.694 601 38 33 316 872 668649338 668649922 2.160000e-141 512.0
16 TraesCS4B01G216500 chr4B 83.694 601 38 33 316 872 669471385 669471969 2.160000e-141 512.0
17 TraesCS4B01G216500 chr4B 83.752 597 39 31 316 872 669558024 669558602 2.160000e-141 512.0
18 TraesCS4B01G216500 chr4B 83.636 605 35 35 316 872 668972653 668973241 7.760000e-141 510.0
19 TraesCS4B01G216500 chr4B 83.636 605 35 35 316 872 669342762 669342174 7.760000e-141 510.0
20 TraesCS4B01G216500 chr4B 93.195 338 9 3 1131 1463 668216197 668216525 4.700000e-133 484.0
21 TraesCS4B01G216500 chr4B 82.523 555 23 20 275 763 668891325 668891871 1.340000e-113 420.0
22 TraesCS4B01G216500 chr4B 90.159 315 18 2 2455 2756 668404881 668405195 6.300000e-107 398.0
23 TraesCS4B01G216500 chr4B 88.146 329 20 4 2441 2756 668652190 668652512 1.060000e-99 374.0
24 TraesCS4B01G216500 chr4B 83.188 345 16 16 277 587 668445552 668445888 8.560000e-71 278.0
25 TraesCS4B01G216500 chr4B 83.122 237 9 10 2305 2536 668217583 668217793 1.480000e-43 187.0
26 TraesCS4B01G216500 chr4B 83.122 237 9 8 2305 2536 668589644 668589854 1.480000e-43 187.0
27 TraesCS4B01G216500 chr4B 82.700 237 10 11 2305 2536 669160725 669160515 6.910000e-42 182.0
28 TraesCS4B01G216500 chr4B 82.700 237 10 10 2305 2536 669340612 669340402 6.910000e-42 182.0
29 TraesCS4B01G216500 chr4B 82.278 237 11 8 2305 2536 668365328 668365538 3.210000e-40 176.0
30 TraesCS4B01G216500 chr4B 95.349 86 0 1 3019 3100 673296320 673296235 1.960000e-27 134.0
31 TraesCS4B01G216500 chr4B 100.000 67 0 0 1 67 456382197 456382131 1.180000e-24 124.0
32 TraesCS4B01G216500 chr4B 92.982 57 0 1 582 638 668216149 668216201 2.590000e-11 80.5
33 TraesCS4B01G216500 chr4B 92.982 57 0 1 582 638 668402915 668402967 2.590000e-11 80.5
34 TraesCS4B01G216500 chr4B 100.000 32 0 0 275 306 668214407 668214438 3.380000e-05 60.2
35 TraesCS4B01G216500 chr4B 100.000 32 0 0 275 306 668401157 668401188 3.380000e-05 60.2
36 TraesCS4B01G216500 chrUn 89.043 1661 92 29 1477 3081 28897766 28899392 0.000000e+00 1977.0
37 TraesCS4B01G216500 chrUn 84.280 2112 116 66 276 2205 79802909 79804986 0.000000e+00 1862.0
38 TraesCS4B01G216500 chrUn 85.058 1372 96 35 897 2204 30531054 30529728 0.000000e+00 1297.0
39 TraesCS4B01G216500 chrUn 83.971 1385 114 33 897 2204 134396295 134394942 0.000000e+00 1229.0
40 TraesCS4B01G216500 chrUn 84.116 1001 89 37 1235 2204 99741975 99741014 0.000000e+00 904.0
41 TraesCS4B01G216500 chrUn 84.116 1001 89 37 1235 2204 100353319 100352358 0.000000e+00 904.0
42 TraesCS4B01G216500 chrUn 88.329 754 57 13 1477 2204 29602423 29601675 0.000000e+00 876.0
43 TraesCS4B01G216500 chrUn 85.891 808 80 14 1478 2252 99649764 99650570 0.000000e+00 830.0
44 TraesCS4B01G216500 chrUn 91.322 484 15 5 2639 3100 79806220 79806698 1.230000e-178 636.0
45 TraesCS4B01G216500 chrUn 83.752 597 39 31 316 872 346448454 346449032 2.160000e-141 512.0
46 TraesCS4B01G216500 chrUn 83.694 601 38 33 316 872 348077484 348076900 2.160000e-141 512.0
47 TraesCS4B01G216500 chrUn 93.962 265 15 1 2455 2718 29363329 29363065 1.750000e-107 399.0
48 TraesCS4B01G216500 chrUn 82.377 488 18 17 452 872 30531601 30531115 2.300000e-96 363.0
49 TraesCS4B01G216500 chrUn 91.304 230 8 4 1235 1455 28897549 28897775 1.410000e-78 303.0
50 TraesCS4B01G216500 chrUn 91.304 230 8 4 1235 1455 29365090 29364864 1.410000e-78 303.0
51 TraesCS4B01G216500 chrUn 85.953 299 12 14 2353 2641 29601401 29601123 3.060000e-75 292.0
52 TraesCS4B01G216500 chrUn 94.149 188 2 5 2124 2302 29364164 29363977 8.560000e-71 278.0
53 TraesCS4B01G216500 chrUn 90.184 163 6 6 2485 2637 100351876 100351714 1.470000e-48 204.0
54 TraesCS4B01G216500 chrUn 96.364 110 4 0 901 1010 99649532 99649641 6.910000e-42 182.0
55 TraesCS4B01G216500 chrUn 98.077 104 2 0 2480 2583 100351980 100351877 6.910000e-42 182.0
56 TraesCS4B01G216500 chrUn 91.200 125 6 2 897 1016 346449100 346449224 6.960000e-37 165.0
57 TraesCS4B01G216500 chrUn 91.200 125 6 2 897 1016 348076832 348076708 6.960000e-37 165.0
58 TraesCS4B01G216500 chrUn 89.333 75 5 2 2685 2756 134394337 134394263 1.200000e-14 91.6
59 TraesCS4B01G216500 chrUn 97.500 40 1 0 2717 2756 100351436 100351397 5.610000e-08 69.4
60 TraesCS4B01G216500 chrUn 97.500 40 1 0 2717 2756 100351586 100351547 5.610000e-08 69.4
61 TraesCS4B01G216500 chrUn 83.333 84 2 1 2685 2756 134394101 134394018 2.020000e-07 67.6
62 TraesCS4B01G216500 chrUn 100.000 34 0 0 2685 2718 30528949 30528916 2.610000e-06 63.9
63 TraesCS4B01G216500 chrUn 100.000 32 0 0 275 306 29604653 29604622 3.380000e-05 60.2
64 TraesCS4B01G216500 chr6D 83.627 2217 128 73 275 2302 1068986 1071156 0.000000e+00 1866.0
65 TraesCS4B01G216500 chr6D 91.304 483 17 4 2639 3100 1071942 1072420 1.230000e-178 636.0
66 TraesCS4B01G216500 chr6D 83.704 270 15 13 2305 2569 1071270 1071515 8.750000e-56 228.0
67 TraesCS4B01G216500 chr6D 93.478 46 3 0 2711 2756 1071687 1071732 5.610000e-08 69.4
68 TraesCS4B01G216500 chr5A 84.610 1462 92 55 1235 2600 707578379 707579803 0.000000e+00 1330.0
69 TraesCS4B01G216500 chr5A 85.737 1248 94 27 1119 2304 707848866 707850091 0.000000e+00 1242.0
70 TraesCS4B01G216500 chr5A 82.701 1370 138 32 896 2204 709530294 709531625 0.000000e+00 1125.0
71 TraesCS4B01G216500 chr5A 84.965 1144 84 27 1119 2204 707983761 707984874 0.000000e+00 1079.0
72 TraesCS4B01G216500 chr5A 90.683 483 20 4 2639 3100 709532493 709532971 1.240000e-173 619.0
73 TraesCS4B01G216500 chr5A 81.602 674 30 30 275 872 707982860 707983515 3.660000e-129 472.0
74 TraesCS4B01G216500 chr5A 80.123 649 21 28 275 872 707848029 707848620 4.900000e-103 385.0
75 TraesCS4B01G216500 chr5A 84.058 414 22 13 2363 2756 707985090 707985479 2.970000e-95 359.0
76 TraesCS4B01G216500 chr5A 79.386 456 30 28 275 675 684312158 684312604 2.400000e-66 263.0
77 TraesCS4B01G216500 chr5A 92.000 125 5 2 897 1016 707848688 707848812 1.500000e-38 171.0
78 TraesCS4B01G216500 chr5A 92.000 125 5 2 897 1016 707983583 707983707 1.500000e-38 171.0
79 TraesCS4B01G216500 chr5A 84.127 189 9 10 582 764 709530115 709530288 2.500000e-36 163.0
80 TraesCS4B01G216500 chr5A 91.129 124 3 2 2983 3098 707580023 707580146 9.000000e-36 161.0
81 TraesCS4B01G216500 chr5A 94.545 55 3 0 2711 2765 707579937 707579991 5.570000e-13 86.1
82 TraesCS4B01G216500 chr5A 92.593 54 3 1 3083 3135 478013870 478013817 3.350000e-10 76.8
83 TraesCS4B01G216500 chr5A 94.000 50 2 1 3087 3135 528581269 528581318 1.210000e-09 75.0
84 TraesCS4B01G216500 chr5A 93.750 48 1 2 3088 3135 257556931 257556886 1.560000e-08 71.3
85 TraesCS4B01G216500 chr2D 79.213 178 16 9 2293 2470 27834907 27835063 1.540000e-18 104.0
86 TraesCS4B01G216500 chr4A 96.721 61 2 0 1 61 92740503 92740563 5.530000e-18 102.0
87 TraesCS4B01G216500 chr4D 96.667 60 2 0 8 67 371136349 371136290 1.990000e-17 100.0
88 TraesCS4B01G216500 chr6A 97.674 43 1 0 3089 3131 547739157 547739199 1.210000e-09 75.0
89 TraesCS4B01G216500 chr3A 92.157 51 3 1 3086 3135 481974806 481974756 1.560000e-08 71.3
90 TraesCS4B01G216500 chr3A 90.566 53 3 2 3084 3135 264024114 264024063 5.610000e-08 69.4
91 TraesCS4B01G216500 chr2A 93.750 48 1 2 3088 3135 471775599 471775554 1.560000e-08 71.3
92 TraesCS4B01G216500 chr7A 90.385 52 5 0 3084 3135 408044902 408044851 5.610000e-08 69.4
93 TraesCS4B01G216500 chr2B 90.385 52 5 0 3084 3135 52470881 52470932 5.610000e-08 69.4


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 TraesCS4B01G216500 chr4B 456379063 456382197 3134 True 2704.000000 5284 100.000000 1 3135 2 chr4B.!!$R2 3134
1 TraesCS4B01G216500 chr4B 456361312 456363321 2009 False 3075.000000 3075 94.455000 275 2267 1 chr4B.!!$F1 1992
2 TraesCS4B01G216500 chr4B 599587895 599589883 1988 True 2023.000000 2023 86.033000 311 2204 1 chr4B.!!$R1 1893
3 TraesCS4B01G216500 chr4B 668513550 668514753 1203 False 1175.000000 1175 85.084000 1119 2302 1 chr4B.!!$F2 1183
4 TraesCS4B01G216500 chr4B 599463273 599466379 3106 True 996.000000 1155 85.299500 275 2204 2 chr4B.!!$R3 1929
5 TraesCS4B01G216500 chr4B 669471385 669473427 2042 False 858.500000 1205 84.549500 316 2302 2 chr4B.!!$F12 1986
6 TraesCS4B01G216500 chr4B 668363776 668365538 1762 False 837.000000 1498 84.086500 826 2536 2 chr4B.!!$F6 1710
7 TraesCS4B01G216500 chr4B 668972653 668974701 2048 False 825.000000 1140 84.027000 316 2302 2 chr4B.!!$F11 1986
8 TraesCS4B01G216500 chr4B 668588194 668589854 1660 False 682.000000 1177 84.119500 1119 2536 2 chr4B.!!$F9 1417
9 TraesCS4B01G216500 chr4B 668445552 668447414 1862 False 650.000000 1022 83.112500 277 2302 2 chr4B.!!$F8 2025
10 TraesCS4B01G216500 chr4B 669340402 669342762 2360 True 586.666667 1068 83.227667 316 2536 3 chr4B.!!$R5 2220
11 TraesCS4B01G216500 chr4B 669558024 669558602 578 False 512.000000 512 83.752000 316 872 1 chr4B.!!$F4 556
12 TraesCS4B01G216500 chr4B 673296235 673297428 1193 True 505.000000 876 88.848500 1241 3100 2 chr4B.!!$R6 1859
13 TraesCS4B01G216500 chr4B 669160515 669161644 1129 True 473.500000 765 83.324000 1496 2536 2 chr4B.!!$R4 1040
14 TraesCS4B01G216500 chr4B 668649338 668652512 3174 False 443.000000 512 85.920000 316 2756 2 chr4B.!!$F10 2440
15 TraesCS4B01G216500 chr4B 668891325 668891871 546 False 420.000000 420 82.523000 275 763 1 chr4B.!!$F3 488
16 TraesCS4B01G216500 chr4B 668214407 668217793 3386 False 341.940000 898 91.025200 275 2536 5 chr4B.!!$F5 2261
17 TraesCS4B01G216500 chrUn 79802909 79806698 3789 False 1249.000000 1862 87.801000 276 3100 2 chrUn.!!$F2 2824
18 TraesCS4B01G216500 chrUn 28897549 28899392 1843 False 1140.000000 1977 90.173500 1235 3081 2 chrUn.!!$F1 1846
19 TraesCS4B01G216500 chrUn 99741014 99741975 961 True 904.000000 904 84.116000 1235 2204 1 chrUn.!!$R1 969
20 TraesCS4B01G216500 chrUn 30528916 30531601 2685 True 574.633333 1297 89.145000 452 2718 3 chrUn.!!$R4 2266
21 TraesCS4B01G216500 chrUn 99649532 99650570 1038 False 506.000000 830 91.127500 901 2252 2 chrUn.!!$F3 1351
22 TraesCS4B01G216500 chrUn 134394018 134396295 2277 True 462.733333 1229 85.545667 897 2756 3 chrUn.!!$R6 1859
23 TraesCS4B01G216500 chrUn 29601123 29604653 3530 True 409.400000 876 91.427333 275 2641 3 chrUn.!!$R3 2366
24 TraesCS4B01G216500 chrUn 346448454 346449224 770 False 338.500000 512 87.476000 316 1016 2 chrUn.!!$F4 700
25 TraesCS4B01G216500 chrUn 348076708 348077484 776 True 338.500000 512 87.447000 316 1016 2 chrUn.!!$R7 700
26 TraesCS4B01G216500 chrUn 29363065 29365090 2025 True 326.666667 399 93.138333 1235 2718 3 chrUn.!!$R2 1483
27 TraesCS4B01G216500 chrUn 100351397 100353319 1922 True 285.760000 904 93.475400 1235 2756 5 chrUn.!!$R5 1521
28 TraesCS4B01G216500 chr6D 1068986 1072420 3434 False 699.850000 1866 88.028250 275 3100 4 chr6D.!!$F1 2825
29 TraesCS4B01G216500 chr5A 709530115 709532971 2856 False 635.666667 1125 85.837000 582 3100 3 chr5A.!!$F6 2518
30 TraesCS4B01G216500 chr5A 707848029 707850091 2062 False 599.333333 1242 85.953333 275 2304 3 chr5A.!!$F4 2029
31 TraesCS4B01G216500 chr5A 707578379 707580146 1767 False 525.700000 1330 90.094667 1235 3098 3 chr5A.!!$F3 1863
32 TraesCS4B01G216500 chr5A 707982860 707985479 2619 False 520.250000 1079 85.656250 275 2756 4 chr5A.!!$F5 2481

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
59 60 0.171903 GCGCTACGGTAAGGACAGAA 59.828 55.000 0.00 0.0 0.0 3.02 F
60 61 1.202382 GCGCTACGGTAAGGACAGAAT 60.202 52.381 0.00 0.0 0.0 2.40 F
65 66 1.274167 ACGGTAAGGACAGAATTGCGA 59.726 47.619 0.00 0.0 0.0 5.10 F
2046 5467 1.813178 TGAAAATAATTGCGGCGGTGA 59.187 42.857 9.78 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 5359 0.102663 GACCGGATCCTCCTCGAAAC 59.897 60.000 9.46 0.0 33.30 2.78 R
2030 5451 0.732571 CAGTCACCGCCGCAATTATT 59.267 50.000 0.00 0.0 0.00 1.40 R
2053 5474 4.388499 ATCGGGACACGCGGCTTT 62.388 61.111 12.47 0.0 43.86 3.51 R
3104 9137 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.0 0.00 4.44 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
22 23 3.756783 CGAGGGGAGGGAGGAGGT 61.757 72.222 0.00 0.00 0.00 3.85
23 24 2.788589 GAGGGGAGGGAGGAGGTT 59.211 66.667 0.00 0.00 0.00 3.50
24 25 1.690985 GAGGGGAGGGAGGAGGTTG 60.691 68.421 0.00 0.00 0.00 3.77
25 26 2.692741 GGGGAGGGAGGAGGTTGG 60.693 72.222 0.00 0.00 0.00 3.77
26 27 3.412408 GGGAGGGAGGAGGTTGGC 61.412 72.222 0.00 0.00 0.00 4.52
27 28 3.787001 GGAGGGAGGAGGTTGGCG 61.787 72.222 0.00 0.00 0.00 5.69
28 29 4.475135 GAGGGAGGAGGTTGGCGC 62.475 72.222 0.00 0.00 0.00 6.53
50 51 4.485834 CACTGCGGCGCTACGGTA 62.486 66.667 33.26 10.57 0.00 4.02
51 52 3.751246 ACTGCGGCGCTACGGTAA 61.751 61.111 33.26 9.75 0.00 2.85
52 53 2.954868 CTGCGGCGCTACGGTAAG 60.955 66.667 33.26 16.08 0.00 2.34
53 54 4.501714 TGCGGCGCTACGGTAAGG 62.502 66.667 33.26 0.00 0.00 2.69
54 55 4.197498 GCGGCGCTACGGTAAGGA 62.197 66.667 26.86 0.00 0.00 3.36
55 56 2.278401 CGGCGCTACGGTAAGGAC 60.278 66.667 7.64 0.00 0.00 3.85
56 57 2.887360 GGCGCTACGGTAAGGACA 59.113 61.111 7.64 0.00 0.00 4.02
57 58 1.226888 GGCGCTACGGTAAGGACAG 60.227 63.158 7.64 0.00 0.00 3.51
58 59 1.660560 GGCGCTACGGTAAGGACAGA 61.661 60.000 7.64 0.00 0.00 3.41
59 60 0.171903 GCGCTACGGTAAGGACAGAA 59.828 55.000 0.00 0.00 0.00 3.02
60 61 1.202382 GCGCTACGGTAAGGACAGAAT 60.202 52.381 0.00 0.00 0.00 2.40
61 62 2.737679 GCGCTACGGTAAGGACAGAATT 60.738 50.000 0.00 0.00 0.00 2.17
62 63 2.858344 CGCTACGGTAAGGACAGAATTG 59.142 50.000 0.00 0.00 0.00 2.32
63 64 2.608090 GCTACGGTAAGGACAGAATTGC 59.392 50.000 0.00 0.00 0.00 3.56
64 65 1.722011 ACGGTAAGGACAGAATTGCG 58.278 50.000 0.00 0.00 0.00 4.85
65 66 1.274167 ACGGTAAGGACAGAATTGCGA 59.726 47.619 0.00 0.00 0.00 5.10
66 67 1.927174 CGGTAAGGACAGAATTGCGAG 59.073 52.381 0.00 0.00 0.00 5.03
1516 4833 6.644347 TCTTCCTGACATTAAATCCTCTGTC 58.356 40.000 0.00 0.00 38.74 3.51
1729 5129 2.108566 CTCCTCTGCCCGCTGATG 59.891 66.667 0.00 0.00 0.00 3.07
1917 5326 7.105588 TCAGCAATTAAGCTCTTACATCTGAA 58.894 34.615 0.00 0.00 44.54 3.02
1978 5396 3.199880 GAGGATCCGGTCACAAATCAT 57.800 47.619 5.98 0.00 0.00 2.45
1984 5402 2.093711 TCCGGTCACAAATCATGTCGAT 60.094 45.455 0.00 0.00 41.46 3.59
1997 5415 3.257624 TCATGTCGATCTGCTGAGCATAT 59.742 43.478 7.94 6.25 38.13 1.78
2030 5451 3.569194 TGGCTGTTCCTGTACTTGAAA 57.431 42.857 0.00 0.00 35.26 2.69
2046 5467 1.813178 TGAAAATAATTGCGGCGGTGA 59.187 42.857 9.78 0.00 0.00 4.02
2224 5774 8.480133 ACCAACCCTTTATGTTTGTATGTAAA 57.520 30.769 0.00 0.00 0.00 2.01
2360 6434 7.969690 AGACTACATATAGGGAGGATGAATG 57.030 40.000 0.97 0.00 32.08 2.67
2368 6442 4.970860 AGGGAGGATGAATGTAGACATG 57.029 45.455 0.00 0.00 36.56 3.21
2408 6566 4.271049 CACTCATTTTGCTCCGTATGTAGG 59.729 45.833 0.00 0.00 0.00 3.18
2409 6567 4.161565 ACTCATTTTGCTCCGTATGTAGGA 59.838 41.667 0.00 0.00 36.20 2.94
2410 6568 5.092554 TCATTTTGCTCCGTATGTAGGAA 57.907 39.130 0.00 0.00 37.32 3.36
2637 7733 4.100189 CCTATCTCCATTTCCTCTTGTCGT 59.900 45.833 0.00 0.00 0.00 4.34
2653 8242 3.590574 GTGCCCACCTCCCCCTTT 61.591 66.667 0.00 0.00 0.00 3.11
2663 8252 0.771127 CTCCCCCTTTTCCTGACACA 59.229 55.000 0.00 0.00 0.00 3.72
2677 8426 3.570125 CCTGACACACACTCTAGTTGAGA 59.430 47.826 8.66 0.00 45.39 3.27
2682 8431 4.402793 ACACACACTCTAGTTGAGAACTGT 59.597 41.667 8.66 0.00 45.39 3.55
2913 8919 4.326227 TAGGCGTCCCCACACCCT 62.326 66.667 0.00 0.00 35.39 4.34
2972 8985 2.588464 TCCTCTCCTCTGACTCGTTT 57.412 50.000 0.00 0.00 0.00 3.60
2973 8986 2.877866 TCCTCTCCTCTGACTCGTTTT 58.122 47.619 0.00 0.00 0.00 2.43
3100 9133 8.079809 GGCAAGTGATTTCTCTAGTATCTACTC 58.920 40.741 0.00 0.00 37.73 2.59
3101 9134 8.079809 GCAAGTGATTTCTCTAGTATCTACTCC 58.920 40.741 0.00 0.00 37.73 3.85
3102 9135 8.573035 CAAGTGATTTCTCTAGTATCTACTCCC 58.427 40.741 0.00 0.00 37.73 4.30
3103 9136 8.052621 AGTGATTTCTCTAGTATCTACTCCCT 57.947 38.462 0.00 0.00 37.73 4.20
3104 9137 8.161425 AGTGATTTCTCTAGTATCTACTCCCTC 58.839 40.741 0.00 0.00 37.73 4.30
3105 9138 7.392393 GTGATTTCTCTAGTATCTACTCCCTCC 59.608 44.444 0.00 0.00 37.73 4.30
3106 9139 5.486735 TTCTCTAGTATCTACTCCCTCCG 57.513 47.826 0.00 0.00 37.73 4.63
3107 9140 4.491675 TCTCTAGTATCTACTCCCTCCGT 58.508 47.826 0.00 0.00 37.73 4.69
3108 9141 4.906664 TCTCTAGTATCTACTCCCTCCGTT 59.093 45.833 0.00 0.00 37.73 4.44
3109 9142 5.011943 TCTCTAGTATCTACTCCCTCCGTTC 59.988 48.000 0.00 0.00 37.73 3.95
3110 9143 3.226682 AGTATCTACTCCCTCCGTTCC 57.773 52.381 0.00 0.00 0.00 3.62
3111 9144 2.512896 AGTATCTACTCCCTCCGTTCCA 59.487 50.000 0.00 0.00 0.00 3.53
3112 9145 2.544844 ATCTACTCCCTCCGTTCCAA 57.455 50.000 0.00 0.00 0.00 3.53
3113 9146 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
3114 9147 2.829023 TCTACTCCCTCCGTTCCAAAT 58.171 47.619 0.00 0.00 0.00 2.32
3115 9148 3.178865 TCTACTCCCTCCGTTCCAAATT 58.821 45.455 0.00 0.00 0.00 1.82
3116 9149 4.355549 TCTACTCCCTCCGTTCCAAATTA 58.644 43.478 0.00 0.00 0.00 1.40
3117 9150 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
3118 9151 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
3119 9152 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
3120 9153 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
3121 9154 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
3122 9155 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
3123 9156 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
3124 9157 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
3125 9158 1.722464 CGTTCCAAATTACTCGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
3126 9159 2.156117 CGTTCCAAATTACTCGTCGCAA 59.844 45.455 0.00 0.00 0.00 4.85
3127 9160 3.363182 CGTTCCAAATTACTCGTCGCAAA 60.363 43.478 0.00 0.00 0.00 3.68
3128 9161 4.529446 GTTCCAAATTACTCGTCGCAAAA 58.471 39.130 0.00 0.00 0.00 2.44
3129 9162 4.815040 TCCAAATTACTCGTCGCAAAAA 57.185 36.364 0.00 0.00 0.00 1.94
3130 9163 5.365403 TCCAAATTACTCGTCGCAAAAAT 57.635 34.783 0.00 0.00 0.00 1.82
3131 9164 6.483385 TCCAAATTACTCGTCGCAAAAATA 57.517 33.333 0.00 0.00 0.00 1.40
3132 9165 6.539324 TCCAAATTACTCGTCGCAAAAATAG 58.461 36.000 0.00 0.00 0.00 1.73
3133 9166 6.369340 TCCAAATTACTCGTCGCAAAAATAGA 59.631 34.615 0.00 0.00 0.00 1.98
3134 9167 7.065324 TCCAAATTACTCGTCGCAAAAATAGAT 59.935 33.333 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.318922 AACCTCCTCCCTCCCCTCG 62.319 68.421 0.00 0.00 0.00 4.63
6 7 1.690985 CAACCTCCTCCCTCCCCTC 60.691 68.421 0.00 0.00 0.00 4.30
7 8 2.456840 CAACCTCCTCCCTCCCCT 59.543 66.667 0.00 0.00 0.00 4.79
8 9 2.692741 CCAACCTCCTCCCTCCCC 60.693 72.222 0.00 0.00 0.00 4.81
9 10 3.412408 GCCAACCTCCTCCCTCCC 61.412 72.222 0.00 0.00 0.00 4.30
10 11 3.787001 CGCCAACCTCCTCCCTCC 61.787 72.222 0.00 0.00 0.00 4.30
11 12 4.475135 GCGCCAACCTCCTCCCTC 62.475 72.222 0.00 0.00 0.00 4.30
33 34 3.975083 TTACCGTAGCGCCGCAGTG 62.975 63.158 13.36 0.00 0.00 3.66
34 35 3.695022 CTTACCGTAGCGCCGCAGT 62.695 63.158 13.36 5.54 0.00 4.40
35 36 2.954868 CTTACCGTAGCGCCGCAG 60.955 66.667 13.36 1.49 0.00 5.18
36 37 4.501714 CCTTACCGTAGCGCCGCA 62.502 66.667 13.36 0.00 0.00 5.69
37 38 4.197498 TCCTTACCGTAGCGCCGC 62.197 66.667 2.29 0.00 0.00 6.53
38 39 2.278401 GTCCTTACCGTAGCGCCG 60.278 66.667 2.29 0.10 0.00 6.46
39 40 1.226888 CTGTCCTTACCGTAGCGCC 60.227 63.158 2.29 0.00 0.00 6.53
40 41 0.171903 TTCTGTCCTTACCGTAGCGC 59.828 55.000 0.00 0.00 0.00 5.92
41 42 2.858344 CAATTCTGTCCTTACCGTAGCG 59.142 50.000 0.00 0.00 0.00 4.26
42 43 2.608090 GCAATTCTGTCCTTACCGTAGC 59.392 50.000 0.00 0.00 0.00 3.58
43 44 2.858344 CGCAATTCTGTCCTTACCGTAG 59.142 50.000 0.00 0.00 0.00 3.51
44 45 2.492881 TCGCAATTCTGTCCTTACCGTA 59.507 45.455 0.00 0.00 0.00 4.02
45 46 1.274167 TCGCAATTCTGTCCTTACCGT 59.726 47.619 0.00 0.00 0.00 4.83
46 47 1.927174 CTCGCAATTCTGTCCTTACCG 59.073 52.381 0.00 0.00 0.00 4.02
1729 5129 2.555199 CATTTCCAGGACGACTCCATC 58.445 52.381 0.00 0.00 39.39 3.51
1883 5292 5.411053 AGAGCTTAATTGCTGAGTTCTTCAC 59.589 40.000 0.00 0.00 44.17 3.18
1948 5357 1.381928 CCGGATCCTCCTCGAAACGA 61.382 60.000 10.75 0.00 33.30 3.85
1950 5359 0.102663 GACCGGATCCTCCTCGAAAC 59.897 60.000 9.46 0.00 33.30 2.78
1953 5362 1.453379 GTGACCGGATCCTCCTCGA 60.453 63.158 9.46 0.00 33.30 4.04
1965 5374 3.000623 CAGATCGACATGATTTGTGACCG 59.999 47.826 0.00 0.00 39.18 4.79
1973 5391 2.159000 TGCTCAGCAGATCGACATGATT 60.159 45.455 0.00 0.00 32.89 2.57
1975 5393 0.819582 TGCTCAGCAGATCGACATGA 59.180 50.000 0.00 0.00 33.32 3.07
1978 5396 3.387397 CAATATGCTCAGCAGATCGACA 58.613 45.455 7.36 0.00 39.68 4.35
1997 5415 4.079787 AGGAACAGCCATATCCTTTAGCAA 60.080 41.667 0.00 0.00 40.70 3.91
2011 5429 6.569179 TTATTTTCAAGTACAGGAACAGCC 57.431 37.500 0.00 0.00 0.00 4.85
2030 5451 0.732571 CAGTCACCGCCGCAATTATT 59.267 50.000 0.00 0.00 0.00 1.40
2053 5474 4.388499 ATCGGGACACGCGGCTTT 62.388 61.111 12.47 0.00 43.86 3.51
2346 6197 4.284490 GCATGTCTACATTCATCCTCCCTA 59.716 45.833 0.00 0.00 33.61 3.53
2349 6204 4.348863 AGCATGTCTACATTCATCCTCC 57.651 45.455 0.00 0.00 33.61 4.30
2351 6206 7.129457 TCTAAAGCATGTCTACATTCATCCT 57.871 36.000 0.00 0.00 33.61 3.24
2360 6434 4.491676 TCCACGTTCTAAAGCATGTCTAC 58.508 43.478 0.00 0.00 0.00 2.59
2637 7733 2.785389 AAAAGGGGGAGGTGGGCA 60.785 61.111 0.00 0.00 0.00 5.36
2653 8242 3.958147 TCAACTAGAGTGTGTGTCAGGAA 59.042 43.478 0.00 0.00 0.00 3.36
2663 8252 3.243907 GCCACAGTTCTCAACTAGAGTGT 60.244 47.826 0.00 0.00 44.98 3.55
2677 8426 2.704572 GCAACTAGATCTGCCACAGTT 58.295 47.619 5.18 3.63 32.61 3.16
2682 8431 1.153369 GGCGCAACTAGATCTGCCA 60.153 57.895 10.83 0.00 42.03 4.92
2913 8919 1.229951 ATGGGGGAGAGCAGTGGAA 60.230 57.895 0.00 0.00 0.00 3.53
2972 8985 5.663456 AGAAATCACTGCTGCAAAAAGAAA 58.337 33.333 3.02 0.00 0.00 2.52
2973 8986 5.163530 TGAGAAATCACTGCTGCAAAAAGAA 60.164 36.000 3.02 0.00 0.00 2.52
3100 9133 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3101 9134 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3102 9135 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
3103 9136 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
3104 9137 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
3105 9138 1.722464 TGCGACGAGTAATTTGGAACG 59.278 47.619 0.00 0.00 0.00 3.95
3106 9139 3.799137 TTGCGACGAGTAATTTGGAAC 57.201 42.857 0.00 0.00 0.00 3.62
3107 9140 4.815040 TTTTGCGACGAGTAATTTGGAA 57.185 36.364 0.00 0.00 0.00 3.53
3108 9141 4.815040 TTTTTGCGACGAGTAATTTGGA 57.185 36.364 0.00 0.00 0.00 3.53
3109 9142 6.539324 TCTATTTTTGCGACGAGTAATTTGG 58.461 36.000 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.