Multiple sequence alignment - TraesCS5B01G005300

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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 TraesCS5B01G005300 chr5B 100.000 5225 0 0 1 5225 6838707 6833483 0.000000e+00 9649.0
1 TraesCS5B01G005300 chr5B 97.789 3438 68 6 1792 5225 24629802 24626369 0.000000e+00 5921.0
2 TraesCS5B01G005300 chr5B 94.887 1506 60 10 3721 5223 30923090 30921599 0.000000e+00 2338.0
3 TraesCS5B01G005300 chr5B 94.705 1511 65 11 3721 5223 30997236 30995733 0.000000e+00 2333.0
4 TraesCS5B01G005300 chr5B 91.750 897 62 10 1959 2854 48417552 48418437 0.000000e+00 1236.0
5 TraesCS5B01G005300 chr5B 89.559 929 72 9 1948 2854 24675829 24674904 0.000000e+00 1155.0
6 TraesCS5B01G005300 chr5B 88.913 929 78 9 1948 2854 6856110 6855185 0.000000e+00 1122.0
7 TraesCS5B01G005300 chr5B 90.656 610 15 8 1227 1795 24640645 24640037 0.000000e+00 773.0
8 TraesCS5B01G005300 chr5B 92.407 540 35 4 3190 3725 30940812 30940275 0.000000e+00 765.0
9 TraesCS5B01G005300 chr5B 82.166 914 127 17 4026 4924 6853912 6853020 0.000000e+00 752.0
10 TraesCS5B01G005300 chr5B 81.897 928 123 26 4026 4924 48419632 48420543 0.000000e+00 741.0
11 TraesCS5B01G005300 chr5B 90.590 542 45 5 3190 3730 6668431 6668967 0.000000e+00 713.0
12 TraesCS5B01G005300 chr5B 84.605 760 56 22 1227 1946 6857014 6856276 0.000000e+00 699.0
13 TraesCS5B01G005300 chr5B 83.377 770 54 29 1227 1946 24676753 24676008 0.000000e+00 645.0
14 TraesCS5B01G005300 chr5B 85.762 597 56 20 1983 2574 48322314 48321742 5.790000e-169 604.0
15 TraesCS5B01G005300 chr5B 82.288 638 77 27 1968 2575 6668176 6668807 2.160000e-143 520.0
16 TraesCS5B01G005300 chr5B 79.106 761 100 48 1968 2697 30941067 30940335 2.200000e-128 470.0
17 TraesCS5B01G005300 chr5B 82.519 532 63 11 4404 4924 24666687 24666175 1.730000e-119 440.0
18 TraesCS5B01G005300 chr5B 83.878 490 36 20 1411 1886 48416995 48417455 1.340000e-115 427.0
19 TraesCS5B01G005300 chr5B 84.718 373 53 4 1968 2339 31016911 31016542 2.300000e-98 370.0
20 TraesCS5B01G005300 chr5B 81.473 421 37 9 1248 1628 6858810 6859229 1.830000e-79 307.0
21 TraesCS5B01G005300 chr5B 79.208 505 56 32 1452 1923 48322890 48322402 6.570000e-79 305.0
22 TraesCS5B01G005300 chr5B 85.473 296 23 10 4932 5225 24392806 24393083 1.840000e-74 291.0
23 TraesCS5B01G005300 chr5B 81.096 365 41 23 2238 2575 6835505 6835142 3.100000e-67 267.0
24 TraesCS5B01G005300 chr5B 80.108 372 46 23 2231 2575 24628400 24628030 8.690000e-63 252.0
25 TraesCS5B01G005300 chr5B 91.620 179 11 3 1227 1404 48416752 48416927 1.450000e-60 244.0
26 TraesCS5B01G005300 chr5B 87.437 199 17 8 351 545 11301586 11301780 6.810000e-54 222.0
27 TraesCS5B01G005300 chr5B 88.824 170 17 2 3027 3195 48418711 48418879 1.910000e-49 207.0
28 TraesCS5B01G005300 chr5B 88.095 168 14 6 4940 5103 24666094 24665929 1.480000e-45 195.0
29 TraesCS5B01G005300 chr5B 89.000 100 11 0 3096 3195 24674520 24674421 1.980000e-24 124.0
30 TraesCS5B01G005300 chr5B 93.443 61 4 0 600 660 11301780 11301840 2.000000e-14 91.6
31 TraesCS5B01G005300 chr5B 85.294 68 10 0 3 70 388073807 388073740 2.610000e-08 71.3
32 TraesCS5B01G005300 chr5A 88.711 1745 130 27 3190 4917 3799046 3800740 0.000000e+00 2069.0
33 TraesCS5B01G005300 chr5A 88.539 1745 132 28 3190 4917 3758932 3760625 0.000000e+00 2052.0
34 TraesCS5B01G005300 chr5A 88.481 1745 136 25 3190 4917 3726371 3728067 0.000000e+00 2049.0
35 TraesCS5B01G005300 chr5A 88.080 1745 141 27 3190 4917 3771538 3773232 0.000000e+00 2008.0
36 TraesCS5B01G005300 chr5A 90.753 1460 73 21 1409 2847 3983106 3981688 0.000000e+00 1892.0
37 TraesCS5B01G005300 chr5A 98.170 601 11 0 1 601 324958193 324958793 0.000000e+00 1050.0
38 TraesCS5B01G005300 chr5A 87.232 932 71 12 1948 2837 4044335 4045260 0.000000e+00 1018.0
39 TraesCS5B01G005300 chr5A 83.254 842 116 18 4026 4851 4047667 4048499 0.000000e+00 750.0
40 TraesCS5B01G005300 chr5A 82.004 928 122 30 4026 4924 3980319 3979408 0.000000e+00 747.0
41 TraesCS5B01G005300 chr5A 92.373 472 21 1 744 1215 324959917 324960373 0.000000e+00 658.0
42 TraesCS5B01G005300 chr5A 80.834 767 55 33 1227 1946 4043435 4044156 7.760000e-143 518.0
43 TraesCS5B01G005300 chr5A 83.014 418 33 11 1248 1628 4035727 4035311 1.390000e-90 344.0
44 TraesCS5B01G005300 chr5A 85.813 289 21 11 4940 5225 3800828 3801099 6.620000e-74 289.0
45 TraesCS5B01G005300 chr5A 93.651 189 12 0 3007 3195 3981664 3981476 3.080000e-72 283.0
46 TraesCS5B01G005300 chr5A 87.448 239 17 9 1411 1637 4007069 4007306 4.010000e-66 263.0
47 TraesCS5B01G005300 chr5A 90.576 191 3 1 1024 1214 324959742 324959917 6.760000e-59 239.0
48 TraesCS5B01G005300 chr5A 80.460 261 33 10 1662 1919 4007302 4007547 3.210000e-42 183.0
49 TraesCS5B01G005300 chr5A 82.727 220 17 7 2654 2854 4046120 4046337 5.380000e-40 176.0
50 TraesCS5B01G005300 chr5A 95.062 81 4 0 1320 1400 3998465 3998385 1.530000e-25 128.0
51 TraesCS5B01G005300 chr6A 86.495 1281 104 34 1 1229 61385815 61384552 0.000000e+00 1343.0
52 TraesCS5B01G005300 chr6A 97.882 661 14 0 1 661 607442660 607443320 0.000000e+00 1144.0
53 TraesCS5B01G005300 chr6A 92.657 572 17 7 651 1214 607443360 607443914 0.000000e+00 800.0
54 TraesCS5B01G005300 chr5D 90.881 987 70 10 3777 4751 5101131 5100153 0.000000e+00 1306.0
55 TraesCS5B01G005300 chr5D 92.203 513 36 3 3190 3701 5101668 5101159 0.000000e+00 723.0
56 TraesCS5B01G005300 chr5D 82.602 638 75 27 1968 2575 5101923 5101292 9.960000e-147 531.0
57 TraesCS5B01G005300 chr5D 82.923 609 76 18 1991 2573 3929812 3929206 1.670000e-144 523.0
58 TraesCS5B01G005300 chr5D 83.721 301 37 8 4932 5225 3927495 3927200 1.850000e-69 274.0
59 TraesCS5B01G005300 chr5D 92.593 54 3 1 3121 3174 4798658 4798606 5.610000e-10 76.8
60 TraesCS5B01G005300 chr3B 90.375 987 74 12 3777 4751 62670384 62671361 0.000000e+00 1277.0
61 TraesCS5B01G005300 chr3B 97.703 653 15 0 1 653 12037097 12037749 0.000000e+00 1123.0
62 TraesCS5B01G005300 chr3B 94.346 566 16 2 651 1216 12037797 12038346 0.000000e+00 854.0
63 TraesCS5B01G005300 chr3B 91.618 513 39 3 3190 3701 62669849 62670358 0.000000e+00 706.0
64 TraesCS5B01G005300 chr3B 90.775 271 21 4 351 618 375979907 375979638 4.970000e-95 359.0
65 TraesCS5B01G005300 chr3B 85.764 288 21 10 4940 5225 62671908 62672177 2.380000e-73 287.0
66 TraesCS5B01G005300 chr4A 92.531 897 56 9 1959 2854 17802221 17803107 0.000000e+00 1275.0
67 TraesCS5B01G005300 chr4A 88.242 927 81 12 1948 2854 17852011 17852929 0.000000e+00 1083.0
68 TraesCS5B01G005300 chr4A 82.131 929 120 31 4026 4924 17804066 17804978 0.000000e+00 754.0
69 TraesCS5B01G005300 chr4A 84.992 653 83 13 1951 2599 17847578 17846937 0.000000e+00 649.0
70 TraesCS5B01G005300 chr4A 84.751 682 43 27 1227 1886 17801482 17802124 1.240000e-175 627.0
71 TraesCS5B01G005300 chr4A 80.959 751 53 30 1241 1946 17851127 17851832 3.610000e-141 512.0
72 TraesCS5B01G005300 chr4A 82.775 418 34 14 1248 1628 17848396 17847980 6.480000e-89 339.0
73 TraesCS5B01G005300 chr4A 87.552 241 17 9 1409 1637 17760707 17760468 3.100000e-67 267.0
74 TraesCS5B01G005300 chr4A 87.647 170 19 2 3027 3195 17803222 17803390 4.130000e-46 196.0
75 TraesCS5B01G005300 chr4A 86.458 96 11 2 2707 2801 150228966 150228872 2.570000e-18 104.0
76 TraesCS5B01G005300 chr4A 85.714 98 9 4 1662 1759 17760472 17760380 1.200000e-16 99.0
77 TraesCS5B01G005300 chrUn 98.033 661 13 0 1 661 427113368 427112708 0.000000e+00 1149.0
78 TraesCS5B01G005300 chrUn 96.466 481 16 1 651 1131 427112668 427112189 0.000000e+00 793.0
79 TraesCS5B01G005300 chr1B 97.731 661 15 0 1 661 608365530 608366190 0.000000e+00 1138.0
80 TraesCS5B01G005300 chr1B 95.782 569 20 4 651 1218 608366230 608366795 0.000000e+00 915.0
81 TraesCS5B01G005300 chr1D 88.321 137 6 6 1080 1215 383657645 383657518 7.010000e-34 156.0
82 TraesCS5B01G005300 chr1D 87.591 137 11 5 1080 1214 475696722 475696854 2.520000e-33 154.0
83 TraesCS5B01G005300 chr6D 87.050 139 11 5 1080 1216 47792712 47792579 3.260000e-32 150.0
84 TraesCS5B01G005300 chr3D 86.620 142 11 7 1080 1218 535654475 535654339 3.260000e-32 150.0
85 TraesCS5B01G005300 chr4B 96.591 88 2 1 2855 2942 2744841 2744755 1.520000e-30 145.0
86 TraesCS5B01G005300 chr4B 83.200 125 19 1 373 495 11750469 11750593 4.280000e-21 113.0
87 TraesCS5B01G005300 chr4B 87.500 96 10 2 2707 2801 398558537 398558443 5.530000e-20 110.0
88 TraesCS5B01G005300 chr7D 82.857 140 16 4 2716 2854 633524144 633524012 9.190000e-23 119.0
89 TraesCS5B01G005300 chr6B 85.507 69 8 2 3 70 254016183 254016116 2.610000e-08 71.3
90 TraesCS5B01G005300 chr7A 83.824 68 9 2 4 70 712111711 712111777 4.370000e-06 63.9
91 TraesCS5B01G005300 chr4D 83.824 68 9 1 784 851 198594700 198594765 4.370000e-06 63.9


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 TraesCS5B01G005300 chr5B 6833483 6838707 5224 True 4958.000000 9649 90.548000 1 5225 2 chr5B.!!$R6 5224
1 TraesCS5B01G005300 chr5B 24626369 24629802 3433 True 3086.500000 5921 88.948500 1792 5225 2 chr5B.!!$R8 3433
2 TraesCS5B01G005300 chr5B 30921599 30923090 1491 True 2338.000000 2338 94.887000 3721 5223 1 chr5B.!!$R2 1502
3 TraesCS5B01G005300 chr5B 30995733 30997236 1503 True 2333.000000 2333 94.705000 3721 5223 1 chr5B.!!$R3 1502
4 TraesCS5B01G005300 chr5B 6853020 6857014 3994 True 857.666667 1122 85.228000 1227 4924 3 chr5B.!!$R7 3697
5 TraesCS5B01G005300 chr5B 24640037 24640645 608 True 773.000000 773 90.656000 1227 1795 1 chr5B.!!$R1 568
6 TraesCS5B01G005300 chr5B 24674421 24676753 2332 True 641.333333 1155 87.312000 1227 3195 3 chr5B.!!$R10 1968
7 TraesCS5B01G005300 chr5B 30940275 30941067 792 True 617.500000 765 85.756500 1968 3725 2 chr5B.!!$R11 1757
8 TraesCS5B01G005300 chr5B 6668176 6668967 791 False 616.500000 713 86.439000 1968 3730 2 chr5B.!!$F3 1762
9 TraesCS5B01G005300 chr5B 48416752 48420543 3791 False 571.000000 1236 87.593800 1227 4924 5 chr5B.!!$F5 3697
10 TraesCS5B01G005300 chr5B 48321742 48322890 1148 True 454.500000 604 82.485000 1452 2574 2 chr5B.!!$R12 1122
11 TraesCS5B01G005300 chr5B 24665929 24666687 758 True 317.500000 440 85.307000 4404 5103 2 chr5B.!!$R9 699
12 TraesCS5B01G005300 chr5A 3758932 3760625 1693 False 2052.000000 2052 88.539000 3190 4917 1 chr5A.!!$F2 1727
13 TraesCS5B01G005300 chr5A 3726371 3728067 1696 False 2049.000000 2049 88.481000 3190 4917 1 chr5A.!!$F1 1727
14 TraesCS5B01G005300 chr5A 3771538 3773232 1694 False 2008.000000 2008 88.080000 3190 4917 1 chr5A.!!$F3 1727
15 TraesCS5B01G005300 chr5A 3799046 3801099 2053 False 1179.000000 2069 87.262000 3190 5225 2 chr5A.!!$F4 2035
16 TraesCS5B01G005300 chr5A 3979408 3983106 3698 True 974.000000 1892 88.802667 1409 4924 3 chr5A.!!$R3 3515
17 TraesCS5B01G005300 chr5A 324958193 324960373 2180 False 649.000000 1050 93.706333 1 1215 3 chr5A.!!$F7 1214
18 TraesCS5B01G005300 chr5A 4043435 4048499 5064 False 615.500000 1018 83.511750 1227 4851 4 chr5A.!!$F6 3624
19 TraesCS5B01G005300 chr6A 61384552 61385815 1263 True 1343.000000 1343 86.495000 1 1229 1 chr6A.!!$R1 1228
20 TraesCS5B01G005300 chr6A 607442660 607443914 1254 False 972.000000 1144 95.269500 1 1214 2 chr6A.!!$F1 1213
21 TraesCS5B01G005300 chr5D 5100153 5101923 1770 True 853.333333 1306 88.562000 1968 4751 3 chr5D.!!$R3 2783
22 TraesCS5B01G005300 chr5D 3927200 3929812 2612 True 398.500000 523 83.322000 1991 5225 2 chr5D.!!$R2 3234
23 TraesCS5B01G005300 chr3B 12037097 12038346 1249 False 988.500000 1123 96.024500 1 1216 2 chr3B.!!$F1 1215
24 TraesCS5B01G005300 chr3B 62669849 62672177 2328 False 756.666667 1277 89.252333 3190 5225 3 chr3B.!!$F2 2035
25 TraesCS5B01G005300 chr4A 17851127 17852929 1802 False 797.500000 1083 84.600500 1241 2854 2 chr4A.!!$F2 1613
26 TraesCS5B01G005300 chr4A 17801482 17804978 3496 False 713.000000 1275 86.765000 1227 4924 4 chr4A.!!$F1 3697
27 TraesCS5B01G005300 chr4A 17846937 17848396 1459 True 494.000000 649 83.883500 1248 2599 2 chr4A.!!$R3 1351
28 TraesCS5B01G005300 chrUn 427112189 427113368 1179 True 971.000000 1149 97.249500 1 1131 2 chrUn.!!$R1 1130
29 TraesCS5B01G005300 chr1B 608365530 608366795 1265 False 1026.500000 1138 96.756500 1 1218 2 chr1B.!!$F1 1217

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
849 1856 1.003812 CCTGGGGTTGAATCCGTACAA 59.996 52.381 0.0 0.0 0.0 2.41 F
1274 2340 1.133792 CCCGCCTGTGAAAATCCCTAT 60.134 52.381 0.0 0.0 0.0 2.57 F
3134 4733 0.777446 TGGGAAAAGGGAGGGAACAG 59.223 55.000 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2546 4144 3.124297 CAGATCTGAGAGGAAAAACGCAC 59.876 47.826 18.34 0.0 0.00 5.34 R
3218 4817 0.178970 GCCATGGCCATCTGGAGAAT 60.179 55.000 26.61 0.0 37.39 2.40 R
4647 9877 0.798771 CAGCTCTACGGTGCTTCGTC 60.799 60.000 8.06 0.0 42.82 4.20 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
274 276 6.861065 TGAGAATCAGTTTCTGTTGTAACC 57.139 37.500 0.00 0.00 44.88 2.85
382 408 5.633182 TGCTTTCATCCTTTTATTCGTTTGC 59.367 36.000 0.00 0.00 0.00 3.68
443 469 6.919662 GGGTATGACGTTCGACAATATTTCTA 59.080 38.462 0.00 0.00 0.00 2.10
574 600 7.510343 TGAGAGTATCCTTCATGGTGAATATGA 59.490 37.037 0.00 0.00 35.59 2.15
721 797 4.959839 TGCCTGTCATGTATAGAGTAACCA 59.040 41.667 0.00 0.00 0.00 3.67
790 1797 8.414003 GTGGACAGTTGTATATGTTCTGATCTA 58.586 37.037 0.00 0.00 0.00 1.98
849 1856 1.003812 CCTGGGGTTGAATCCGTACAA 59.996 52.381 0.00 0.00 0.00 2.41
949 1956 4.394078 CGAGTGGTTCCGCGACGA 62.394 66.667 8.23 0.00 0.00 4.20
971 1978 2.313172 CGCTGTGGACTGTGCAGAC 61.313 63.158 0.98 0.00 32.39 3.51
1011 2025 3.750371 CGAGATCTAGATGGACTCAGGT 58.250 50.000 10.74 0.00 0.00 4.00
1053 2067 3.147595 CGAGATCTGGTGCGGGGA 61.148 66.667 0.00 0.00 0.00 4.81
1205 2269 4.610605 TTCAACCAACTCGTCCATTAGA 57.389 40.909 0.00 0.00 0.00 2.10
1274 2340 1.133792 CCCGCCTGTGAAAATCCCTAT 60.134 52.381 0.00 0.00 0.00 2.57
1278 2344 2.360165 GCCTGTGAAAATCCCTATGCTG 59.640 50.000 0.00 0.00 0.00 4.41
1310 2376 2.349755 CCCGACCCGGTTTCACAT 59.650 61.111 0.00 0.00 46.80 3.21
2081 3676 7.330946 CCCATTACGATATCGCTTTCTTGAATA 59.669 37.037 24.59 3.02 44.43 1.75
2127 3722 6.234177 AGTTACCATCTTTCTGTGAAGAAGG 58.766 40.000 12.66 12.66 45.46 3.46
2546 4144 6.882610 TTGGATTCATGGAAGAAATATCGG 57.117 37.500 0.00 0.00 0.00 4.18
2564 4162 1.872237 CGGTGCGTTTTTCCTCTCAGA 60.872 52.381 0.00 0.00 0.00 3.27
2576 4174 3.145286 TCCTCTCAGATCTGTGATAGCG 58.855 50.000 23.79 14.03 33.36 4.26
2592 4190 9.163903 CTGTGATAGCGTCTATATGATTATTCG 57.836 37.037 0.28 0.00 0.00 3.34
2594 4192 9.885934 GTGATAGCGTCTATATGATTATTCGAT 57.114 33.333 0.00 0.00 0.00 3.59
2626 4224 8.870075 AAGCTAATGTGTTCTCTCCTATTTTT 57.130 30.769 0.00 0.00 0.00 1.94
2692 4290 9.443283 GTATCTATTTGCTCACTTTTATGCAAG 57.557 33.333 0.00 0.00 44.52 4.01
2720 4318 8.574251 AACAATGTTCAGTAATTGGTAGCATA 57.426 30.769 0.00 0.00 37.96 3.14
2903 4501 4.763073 TGATCGATCCTTGATCATATGCC 58.237 43.478 22.31 0.00 45.37 4.40
2957 4555 4.717629 CCCGACGACGAAGCAGCA 62.718 66.667 9.28 0.00 42.66 4.41
2961 4559 2.280119 ACGACGAAGCAGCAGCAA 60.280 55.556 3.17 0.00 45.49 3.91
3134 4733 0.777446 TGGGAAAAGGGAGGGAACAG 59.223 55.000 0.00 0.00 0.00 3.16
3196 4795 5.186992 GCCCAACCTATAATTTGGTTTGAGT 59.813 40.000 9.96 0.00 43.27 3.41
3218 4817 3.009584 TGGCACCACAATGTATACTTCCA 59.990 43.478 4.17 0.00 0.00 3.53
3439 5041 3.117663 GGGGCCAGTTATTGACTTGGATA 60.118 47.826 4.39 0.00 36.10 2.59
3579 7675 8.085296 AGTGCTGTGATAGTATTAGACTAATGC 58.915 37.037 16.52 15.06 43.96 3.56
3807 8412 9.790389 TGTAAGAAAATCGAGAACTAGATCTTC 57.210 33.333 0.00 0.00 0.00 2.87
4147 9358 4.201608 ACATGTTATGGCGTACGTTTAACG 60.202 41.667 17.90 16.31 43.12 3.18
4329 9545 4.906618 TCAACGGAAAGCCTATTTCTTCT 58.093 39.130 0.86 0.00 0.00 2.85
4340 9557 8.512966 AAGCCTATTTCTTCTAAATTGAGGTC 57.487 34.615 0.00 0.00 0.00 3.85
4463 9683 8.889717 CCTACAATTATCAGTTGGAAAATACGT 58.110 33.333 0.00 0.00 33.32 3.57
4492 9712 3.243535 GCATATGCAAAGGCCCTTTAGAC 60.244 47.826 22.84 2.35 41.59 2.59
4647 9877 4.335082 TGTTTCACACACTCAAAGAACG 57.665 40.909 0.00 0.00 0.00 3.95
4794 10027 7.310664 TCTCAAGTACGTATAGTCCACTTTTG 58.689 38.462 0.00 0.00 31.27 2.44
5031 10702 3.759086 TGTTTGTGCTTGTAGGTTTGTCA 59.241 39.130 0.00 0.00 0.00 3.58
5038 10709 2.666272 TGTAGGTTTGTCAATGGGCA 57.334 45.000 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
237 239 8.682936 AACTGATTCTCAACTCAAATGTAGTT 57.317 30.769 0.00 0.00 37.67 2.24
443 469 5.047519 CCTCAAAGTCAGCATTGAAGGATTT 60.048 40.000 0.00 0.00 35.31 2.17
721 797 7.238710 ACTTGGGAGGAACATATACAACTTTT 58.761 34.615 0.00 0.00 0.00 2.27
790 1797 6.745450 GCTTTGTTTGTTATGCATACGTGTAT 59.255 34.615 5.74 0.00 34.84 2.29
949 1956 4.969196 CACAGTCCACAGCGCCGT 62.969 66.667 2.29 0.00 0.00 5.68
971 1978 4.227134 CGCCCGACTCCATCTGGG 62.227 72.222 0.00 0.00 41.50 4.45
997 2011 0.033503 TCGCCACCTGAGTCCATCTA 60.034 55.000 0.00 0.00 0.00 1.98
1053 2067 0.107654 GCCTGCCGTAGAACCTCATT 60.108 55.000 0.00 0.00 0.00 2.57
1274 2340 2.556559 GGGGGTTTGAAGTAATCCAGCA 60.557 50.000 0.00 0.00 30.99 4.41
1278 2344 2.362736 GTCGGGGGTTTGAAGTAATCC 58.637 52.381 0.00 0.00 0.00 3.01
1721 2931 9.944376 AACAAGAGAATTGCAACTAGTTAGATA 57.056 29.630 8.04 0.00 0.00 1.98
1843 3100 8.500753 AAAACAGTTGCGGAACAGATTATATA 57.499 30.769 22.29 0.00 34.17 0.86
1844 3101 7.391148 AAAACAGTTGCGGAACAGATTATAT 57.609 32.000 22.29 0.00 34.17 0.86
1845 3102 6.811253 AAAACAGTTGCGGAACAGATTATA 57.189 33.333 22.29 0.00 34.17 0.98
2081 3676 5.192522 ACTTGATAGGTTGATCCACCTCAAT 59.807 40.000 21.23 10.94 44.63 2.57
2127 3722 3.880610 ACGTCTTCGGCAAATTTTACAC 58.119 40.909 0.00 0.00 41.85 2.90
2546 4144 3.124297 CAGATCTGAGAGGAAAAACGCAC 59.876 47.826 18.34 0.00 0.00 5.34
2592 4190 6.705381 AGAGAACACATTAGCTTAGCATCATC 59.295 38.462 7.07 0.00 0.00 2.92
2594 4192 5.982356 AGAGAACACATTAGCTTAGCATCA 58.018 37.500 7.07 0.00 0.00 3.07
2626 4224 9.590451 TTGACTTCTAACGAAAAGTAAGAAGAA 57.410 29.630 15.25 3.00 43.73 2.52
2628 4226 9.634300 GTTTGACTTCTAACGAAAAGTAAGAAG 57.366 33.333 8.45 8.45 45.53 2.85
2692 4290 8.293867 TGCTACCAATTACTGAACATTGTTAAC 58.706 33.333 1.15 0.00 0.00 2.01
2720 4318 3.392616 CCCTACTCAGCAACCCAATCTAT 59.607 47.826 0.00 0.00 0.00 1.98
2903 4501 5.065602 CACATATCAGTGACACATCAAAGGG 59.934 44.000 8.59 0.00 42.05 3.95
2957 4555 1.377725 CACGCCTCCCATTCTTGCT 60.378 57.895 0.00 0.00 0.00 3.91
2961 4559 1.296715 GACACACGCCTCCCATTCT 59.703 57.895 0.00 0.00 0.00 2.40
3134 4733 6.171369 GGCAATTTTGGCCCAAATTTAGCC 62.171 45.833 27.00 27.00 46.85 3.93
3177 4776 5.185056 GTGCCACTCAAACCAAATTATAGGT 59.815 40.000 0.00 0.00 40.61 3.08
3196 4795 3.009584 TGGAAGTATACATTGTGGTGCCA 59.990 43.478 5.50 0.00 0.00 4.92
3218 4817 0.178970 GCCATGGCCATCTGGAGAAT 60.179 55.000 26.61 0.00 37.39 2.40
3439 5041 5.528870 GTTGACCATTCCGACAATTTTTCT 58.471 37.500 0.00 0.00 0.00 2.52
3579 7675 5.941948 AAAAGAACAATTAGGAGACACCG 57.058 39.130 0.00 0.00 44.74 4.94
3793 8398 3.305744 GCCCCATCGAAGATCTAGTTCTC 60.306 52.174 3.79 0.00 45.12 2.87
3807 8412 1.827969 CTTCCTATCTAGGCCCCATCG 59.172 57.143 0.00 0.00 43.31 3.84
3991 8974 2.222819 CCAGCTTCTATCAAACGCGTTC 60.223 50.000 26.77 9.24 0.00 3.95
4147 9358 8.044060 TCTTGAACAATAAGACCATCATCAAC 57.956 34.615 0.00 0.00 29.68 3.18
4463 9683 2.363038 GGCCTTTGCATATGCTCATCAA 59.637 45.455 27.13 10.98 42.66 2.57
4492 9712 7.295952 ACTTACAGAAATATGAACTTCAGCG 57.704 36.000 0.00 0.00 0.00 5.18
4647 9877 0.798771 CAGCTCTACGGTGCTTCGTC 60.799 60.000 8.06 0.00 42.82 4.20
4784 10017 9.744468 AACAATTTATCTACAACAAAAGTGGAC 57.256 29.630 0.00 0.00 32.76 4.02
5031 10702 2.821969 CAGCTCAAAGTTAGTGCCCATT 59.178 45.455 0.00 0.00 0.00 3.16
5038 10709 4.137116 TGTCACACAGCTCAAAGTTAGT 57.863 40.909 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.