Multiple sequence alignment - TraesCS5A01G225400

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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 TraesCS5A01G225400 chr5A 100.000 2273 0 0 1 2273 440976298 440974026 0.000000e+00 4198.0
1 TraesCS5A01G225400 chr4D 84.860 1037 150 7 268 1301 20529786 20530818 0.000000e+00 1038.0
2 TraesCS5A01G225400 chr3A 82.759 1044 169 10 268 1307 48445403 48446439 0.000000e+00 920.0
3 TraesCS5A01G225400 chr3A 82.426 1047 166 12 268 1305 48365967 48367004 0.000000e+00 898.0
4 TraesCS5A01G225400 chr6A 82.529 1036 173 6 268 1301 27563756 27562727 0.000000e+00 904.0
5 TraesCS5A01G225400 chr1B 82.359 1043 168 13 268 1308 668197898 668196870 0.000000e+00 893.0
6 TraesCS5A01G225400 chr5D 83.122 1025 98 28 1308 2273 339725813 339724805 0.000000e+00 865.0
7 TraesCS5A01G225400 chr2B 81.485 1037 181 10 268 1301 789542956 789541928 0.000000e+00 841.0
8 TraesCS5A01G225400 chr2B 71.822 472 125 8 271 738 797483624 797483157 6.590000e-26 128.0
9 TraesCS5A01G225400 chr2B 94.286 35 1 1 1938 1972 790759803 790759770 4.000000e-03 52.8
10 TraesCS5A01G225400 chr7B 81.118 1038 182 13 268 1301 713141736 713142763 0.000000e+00 819.0
11 TraesCS5A01G225400 chr2D 85.025 601 88 2 704 1304 632650972 632650374 5.370000e-171 610.0
12 TraesCS5A01G225400 chr5B 89.238 446 44 2 652 1097 393790921 393790480 2.550000e-154 555.0
13 TraesCS5A01G225400 chr5B 88.144 388 45 1 268 655 393823538 393823152 5.720000e-126 460.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G225400 chr5A 440974026 440976298 2272 True 4198 4198 100.000 1 2273 1 chr5A.!!$R1 2272
1 TraesCS5A01G225400 chr4D 20529786 20530818 1032 False 1038 1038 84.860 268 1301 1 chr4D.!!$F1 1033
2 TraesCS5A01G225400 chr3A 48445403 48446439 1036 False 920 920 82.759 268 1307 1 chr3A.!!$F2 1039
3 TraesCS5A01G225400 chr3A 48365967 48367004 1037 False 898 898 82.426 268 1305 1 chr3A.!!$F1 1037
4 TraesCS5A01G225400 chr6A 27562727 27563756 1029 True 904 904 82.529 268 1301 1 chr6A.!!$R1 1033
5 TraesCS5A01G225400 chr1B 668196870 668197898 1028 True 893 893 82.359 268 1308 1 chr1B.!!$R1 1040
6 TraesCS5A01G225400 chr5D 339724805 339725813 1008 True 865 865 83.122 1308 2273 1 chr5D.!!$R1 965
7 TraesCS5A01G225400 chr2B 789541928 789542956 1028 True 841 841 81.485 268 1301 1 chr2B.!!$R1 1033
8 TraesCS5A01G225400 chr7B 713141736 713142763 1027 False 819 819 81.118 268 1301 1 chr7B.!!$F1 1033
9 TraesCS5A01G225400 chr2D 632650374 632650972 598 True 610 610 85.025 704 1304 1 chr2D.!!$R1 600

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
394 396 0.033796 ACTCCGTTGGATACTCCCGA 60.034 55.0 0.0 0.0 35.03 5.14 F
821 823 0.102300 ATCACGATCAATGCCGACGA 59.898 50.0 0.0 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1249 0.973632 TCATGGTGTTACAGTCCGCT 59.026 50.0 0.0 0.0 0.00 5.52 R
2115 2175 2.545113 GCCGAATAGCGTGATTAGTGGA 60.545 50.0 0.0 0.0 38.67 4.02 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
56 57 9.465985 TTTTTACGGACTTCCAAACATTTATTC 57.534 29.630 0.00 0.00 35.14 1.75
57 58 5.638596 ACGGACTTCCAAACATTTATTCC 57.361 39.130 0.00 0.00 35.14 3.01
58 59 5.074115 ACGGACTTCCAAACATTTATTCCA 58.926 37.500 0.00 0.00 35.14 3.53
59 60 5.536916 ACGGACTTCCAAACATTTATTCCAA 59.463 36.000 0.00 0.00 35.14 3.53
60 61 6.041069 ACGGACTTCCAAACATTTATTCCAAA 59.959 34.615 0.00 0.00 35.14 3.28
61 62 6.586082 CGGACTTCCAAACATTTATTCCAAAG 59.414 38.462 0.00 0.00 35.14 2.77
62 63 7.441836 GGACTTCCAAACATTTATTCCAAAGT 58.558 34.615 0.00 0.00 35.64 2.66
63 64 7.598869 GGACTTCCAAACATTTATTCCAAAGTC 59.401 37.037 0.00 0.00 38.61 3.01
64 65 7.145323 ACTTCCAAACATTTATTCCAAAGTCG 58.855 34.615 0.00 0.00 0.00 4.18
65 66 6.642707 TCCAAACATTTATTCCAAAGTCGT 57.357 33.333 0.00 0.00 0.00 4.34
66 67 6.442952 TCCAAACATTTATTCCAAAGTCGTG 58.557 36.000 0.00 0.00 0.00 4.35
67 68 5.118510 CCAAACATTTATTCCAAAGTCGTGC 59.881 40.000 0.00 0.00 0.00 5.34
68 69 5.446143 AACATTTATTCCAAAGTCGTGCA 57.554 34.783 0.00 0.00 0.00 4.57
69 70 4.794169 ACATTTATTCCAAAGTCGTGCAC 58.206 39.130 6.82 6.82 0.00 4.57
70 71 4.277174 ACATTTATTCCAAAGTCGTGCACA 59.723 37.500 18.64 0.81 0.00 4.57
71 72 5.048083 ACATTTATTCCAAAGTCGTGCACAT 60.048 36.000 18.64 1.56 0.00 3.21
72 73 6.150307 ACATTTATTCCAAAGTCGTGCACATA 59.850 34.615 18.64 0.42 0.00 2.29
73 74 6.751514 TTTATTCCAAAGTCGTGCACATAT 57.248 33.333 18.64 0.00 0.00 1.78
74 75 6.751514 TTATTCCAAAGTCGTGCACATATT 57.248 33.333 18.64 4.58 0.00 1.28
75 76 5.643379 ATTCCAAAGTCGTGCACATATTT 57.357 34.783 18.64 10.69 0.00 1.40
76 77 6.751514 ATTCCAAAGTCGTGCACATATTTA 57.248 33.333 18.64 0.00 0.00 1.40
77 78 6.561737 TTCCAAAGTCGTGCACATATTTAA 57.438 33.333 18.64 3.66 0.00 1.52
78 79 6.561737 TCCAAAGTCGTGCACATATTTAAA 57.438 33.333 18.64 0.00 0.00 1.52
79 80 6.971602 TCCAAAGTCGTGCACATATTTAAAA 58.028 32.000 18.64 0.78 0.00 1.52
80 81 6.858993 TCCAAAGTCGTGCACATATTTAAAAC 59.141 34.615 18.64 0.51 0.00 2.43
81 82 6.861055 CCAAAGTCGTGCACATATTTAAAACT 59.139 34.615 18.64 2.77 0.00 2.66
82 83 7.060633 CCAAAGTCGTGCACATATTTAAAACTC 59.939 37.037 18.64 0.00 0.00 3.01
83 84 6.795098 AGTCGTGCACATATTTAAAACTCA 57.205 33.333 18.64 0.00 0.00 3.41
84 85 7.377766 AGTCGTGCACATATTTAAAACTCAT 57.622 32.000 18.64 0.00 0.00 2.90
85 86 7.243487 AGTCGTGCACATATTTAAAACTCATG 58.757 34.615 18.64 0.00 0.00 3.07
86 87 7.119116 AGTCGTGCACATATTTAAAACTCATGA 59.881 33.333 18.64 0.00 0.00 3.07
87 88 7.748683 GTCGTGCACATATTTAAAACTCATGAA 59.251 33.333 18.64 0.00 0.00 2.57
88 89 7.748683 TCGTGCACATATTTAAAACTCATGAAC 59.251 33.333 18.64 0.00 0.00 3.18
89 90 7.536964 CGTGCACATATTTAAAACTCATGAACA 59.463 33.333 18.64 0.00 0.00 3.18
90 91 9.357652 GTGCACATATTTAAAACTCATGAACAT 57.642 29.630 13.17 0.00 0.00 2.71
91 92 9.926158 TGCACATATTTAAAACTCATGAACATT 57.074 25.926 0.00 0.00 0.00 2.71
98 99 9.912634 ATTTAAAACTCATGAACATTGTTCGAT 57.087 25.926 21.27 14.09 0.00 3.59
102 103 9.559958 AAAACTCATGAACATTGTTCGATATTC 57.440 29.630 21.27 0.89 0.00 1.75
103 104 7.848223 ACTCATGAACATTGTTCGATATTCA 57.152 32.000 21.27 6.34 0.00 2.57
104 105 8.442632 ACTCATGAACATTGTTCGATATTCAT 57.557 30.769 21.27 8.22 37.28 2.57
109 110 9.673454 ATGAACATTGTTCGATATTCATGATTG 57.327 29.630 21.27 0.00 35.89 2.67
110 111 8.676401 TGAACATTGTTCGATATTCATGATTGT 58.324 29.630 21.27 0.00 0.00 2.71
111 112 9.507280 GAACATTGTTCGATATTCATGATTGTT 57.493 29.630 13.42 0.00 0.00 2.83
112 113 9.859427 AACATTGTTCGATATTCATGATTGTTT 57.141 25.926 0.00 0.00 0.00 2.83
113 114 9.859427 ACATTGTTCGATATTCATGATTGTTTT 57.141 25.926 0.00 0.00 0.00 2.43
116 117 9.905171 TTGTTCGATATTCATGATTGTTTTTCA 57.095 25.926 0.00 0.00 0.00 2.69
117 118 9.905171 TGTTCGATATTCATGATTGTTTTTCAA 57.095 25.926 0.00 0.00 40.53 2.69
192 193 7.524294 TTTTTGAGTGAGCAAACATTTTCTC 57.476 32.000 0.00 0.00 37.48 2.87
193 194 5.833406 TTGAGTGAGCAAACATTTTCTCA 57.167 34.783 3.03 3.03 37.94 3.27
194 195 5.833406 TGAGTGAGCAAACATTTTCTCAA 57.167 34.783 8.05 0.00 40.95 3.02
195 196 5.581605 TGAGTGAGCAAACATTTTCTCAAC 58.418 37.500 8.05 6.81 40.95 3.18
196 197 4.601019 AGTGAGCAAACATTTTCTCAACG 58.399 39.130 8.05 0.00 40.95 4.10
197 198 4.335315 AGTGAGCAAACATTTTCTCAACGA 59.665 37.500 8.05 0.00 40.95 3.85
198 199 5.034152 GTGAGCAAACATTTTCTCAACGAA 58.966 37.500 8.05 0.00 40.95 3.85
199 200 5.687285 GTGAGCAAACATTTTCTCAACGAAT 59.313 36.000 8.05 0.00 40.95 3.34
200 201 6.855914 GTGAGCAAACATTTTCTCAACGAATA 59.144 34.615 8.05 0.00 40.95 1.75
201 202 7.538678 GTGAGCAAACATTTTCTCAACGAATAT 59.461 33.333 8.05 0.00 40.95 1.28
202 203 8.081633 TGAGCAAACATTTTCTCAACGAATATT 58.918 29.630 4.51 0.00 37.47 1.28
203 204 8.816640 AGCAAACATTTTCTCAACGAATATTT 57.183 26.923 0.00 0.00 0.00 1.40
204 205 9.260002 AGCAAACATTTTCTCAACGAATATTTT 57.740 25.926 0.00 0.00 0.00 1.82
205 206 9.862585 GCAAACATTTTCTCAACGAATATTTTT 57.137 25.926 0.00 0.00 29.13 1.94
288 289 5.659525 TGATTTAGAGGAAGGGACGATTACA 59.340 40.000 0.00 0.00 0.00 2.41
296 297 3.914426 AGGGACGATTACAGAAGCATT 57.086 42.857 0.00 0.00 0.00 3.56
301 302 5.758296 GGGACGATTACAGAAGCATTATCAA 59.242 40.000 0.00 0.00 0.00 2.57
310 311 9.809096 TTACAGAAGCATTATCAACAAACAAAA 57.191 25.926 0.00 0.00 0.00 2.44
313 314 9.033481 CAGAAGCATTATCAACAAACAAAAAGA 57.967 29.630 0.00 0.00 0.00 2.52
327 328 1.915141 AAAAGATGTGGACAGCCCTG 58.085 50.000 0.00 0.00 35.38 4.45
335 336 1.603739 GGACAGCCCTGTGGAAACC 60.604 63.158 5.53 0.00 45.05 3.27
361 363 0.107654 CATCCCCAAGGTTCGAGTCC 60.108 60.000 1.17 1.17 0.00 3.85
372 374 2.125912 CGAGTCCTCTGTTGGCGG 60.126 66.667 0.00 0.00 0.00 6.13
393 395 1.336125 GTACTCCGTTGGATACTCCCG 59.664 57.143 0.00 0.00 35.03 5.14
394 396 0.033796 ACTCCGTTGGATACTCCCGA 60.034 55.000 0.00 0.00 35.03 5.14
429 431 2.030274 GCAATACCGCCATATCAAACCC 60.030 50.000 0.00 0.00 0.00 4.11
432 434 1.513858 ACCGCCATATCAAACCCCTA 58.486 50.000 0.00 0.00 0.00 3.53
447 449 1.000955 CCCCTAGGTATGTGCGACATC 59.999 57.143 8.29 0.00 39.88 3.06
523 525 0.832626 AAAGTTTTGGCTGGCAGCTT 59.167 45.000 35.73 20.07 41.99 3.74
528 530 0.251474 TTTGGCTGGCAGCTTGAGAT 60.251 50.000 35.73 0.00 41.99 2.75
534 536 2.807392 GCTGGCAGCTTGAGATAGATTC 59.193 50.000 31.37 0.00 38.45 2.52
567 569 2.268076 ACGGCTGCATCCAAACACC 61.268 57.895 7.47 0.00 0.00 4.16
569 571 0.676466 CGGCTGCATCCAAACACCTA 60.676 55.000 7.47 0.00 0.00 3.08
591 593 6.263842 CCTAGGCTCATGATATTTTGCTTGAA 59.736 38.462 0.00 0.00 0.00 2.69
597 599 7.330208 GCTCATGATATTTTGCTTGAACAACTT 59.670 33.333 0.00 0.00 0.00 2.66
608 610 4.142381 GCTTGAACAACTTTTCACAGAGGT 60.142 41.667 0.00 0.00 35.18 3.85
650 652 7.585579 TCACAATCATGCACAATATATGGTT 57.414 32.000 0.00 0.00 0.00 3.67
677 679 1.887854 CAATTGCTGGACACATGACCA 59.112 47.619 0.00 5.31 37.52 4.02
694 696 1.338107 CCATGACGGCTATGACCCTA 58.662 55.000 0.00 0.00 0.00 3.53
741 743 3.691609 AGACTTTGGCGATTTTGGAGATC 59.308 43.478 0.00 0.00 0.00 2.75
753 755 6.572119 CGATTTTGGAGATCCCATCAAAACAA 60.572 38.462 12.21 0.00 46.10 2.83
768 770 0.603065 AACAAAAGATTCAGCCGGCC 59.397 50.000 26.15 7.28 0.00 6.13
787 789 1.302511 GGACAGTGTTGGCGACCAT 60.303 57.895 1.61 0.00 31.53 3.55
790 792 1.374125 CAGTGTTGGCGACCATCGA 60.374 57.895 1.61 0.00 43.74 3.59
814 816 1.233019 GGGCTGGATCACGATCAATG 58.767 55.000 9.17 0.00 39.54 2.82
821 823 0.102300 ATCACGATCAATGCCGACGA 59.898 50.000 0.00 0.00 0.00 4.20
876 878 0.391661 GTGGTGTGGCTCGATCACAT 60.392 55.000 19.84 0.00 45.32 3.21
915 917 2.557869 TGGAGTAAGCCCTTACATGGT 58.442 47.619 17.63 0.33 45.79 3.55
920 922 3.523564 AGTAAGCCCTTACATGGTGTGAT 59.476 43.478 17.63 0.00 45.79 3.06
923 925 1.953559 CCCTTACATGGTGTGATCGG 58.046 55.000 0.00 0.00 0.00 4.18
927 929 0.828022 TACATGGTGTGATCGGTCCC 59.172 55.000 0.00 0.00 0.00 4.46
934 936 1.207089 GTGTGATCGGTCCCTTCATCA 59.793 52.381 0.00 0.00 0.00 3.07
937 939 2.103094 GTGATCGGTCCCTTCATCATGA 59.897 50.000 0.00 0.00 0.00 3.07
955 957 3.764237 TGAAACTTTTAGCTCTCCGGT 57.236 42.857 0.00 0.00 0.00 5.28
961 963 0.398098 TTTAGCTCTCCGGTAGGGGG 60.398 60.000 0.00 0.00 38.99 5.40
970 972 2.506644 CTCCGGTAGGGGGTGATTTTTA 59.493 50.000 0.00 0.00 38.33 1.52
974 976 3.538591 GGTAGGGGGTGATTTTTACTCG 58.461 50.000 0.00 0.00 0.00 4.18
986 988 4.534794 TTTTTACTCGGTTTCGTGGTTC 57.465 40.909 0.00 0.00 37.69 3.62
1013 1015 6.156083 TCACATGTGATAATGGAGGTTGACTA 59.844 38.462 24.56 0.00 34.14 2.59
1058 1060 2.243957 CGCGCGGCAATTCCAGATA 61.244 57.895 24.84 0.00 34.01 1.98
1119 1126 3.900703 GTGCTAGTTTCGCTTCTTTTTCG 59.099 43.478 0.00 0.00 0.00 3.46
1133 1140 4.462133 TCTTTTTCGGTTACCCATGTCAA 58.538 39.130 0.00 0.00 0.00 3.18
1143 1150 3.431411 ACCCATGTCAATAGGGAGGTA 57.569 47.619 13.61 0.00 45.80 3.08
1169 1176 2.916703 GGCCCACCAATGTGCACA 60.917 61.111 24.08 24.08 41.35 4.57
1242 1249 1.860641 TCCTTCATCCTTGCCTACGA 58.139 50.000 0.00 0.00 0.00 3.43
1248 1255 2.017559 ATCCTTGCCTACGAGCGGAC 62.018 60.000 0.00 0.00 34.65 4.79
1345 1352 8.334632 CAAACATTATTTCAAAACCAGGAACAC 58.665 33.333 0.00 0.00 0.00 3.32
1346 1353 7.360113 ACATTATTTCAAAACCAGGAACACT 57.640 32.000 0.00 0.00 0.00 3.55
1347 1354 7.791029 ACATTATTTCAAAACCAGGAACACTT 58.209 30.769 0.00 0.00 0.00 3.16
1348 1355 8.264347 ACATTATTTCAAAACCAGGAACACTTT 58.736 29.630 0.00 0.00 0.00 2.66
1349 1356 9.108284 CATTATTTCAAAACCAGGAACACTTTT 57.892 29.630 0.00 0.00 0.00 2.27
1359 1366 5.591067 ACCAGGAACACTTTTTGAATTCGTA 59.409 36.000 0.04 0.00 0.00 3.43
1361 1368 7.145323 CCAGGAACACTTTTTGAATTCGTAAT 58.855 34.615 0.04 0.00 0.00 1.89
1362 1369 7.651704 CCAGGAACACTTTTTGAATTCGTAATT 59.348 33.333 0.04 0.00 0.00 1.40
1363 1370 9.030301 CAGGAACACTTTTTGAATTCGTAATTT 57.970 29.630 0.04 0.00 0.00 1.82
1502 1509 4.634004 CCCGAAAAGAAAAAGCAAAACCTT 59.366 37.500 0.00 0.00 0.00 3.50
1505 1512 7.398746 CCGAAAAGAAAAAGCAAAACCTTAAG 58.601 34.615 0.00 0.00 0.00 1.85
1529 1536 5.922739 AACGAAATGAAATCTTTTTGGGC 57.077 34.783 11.53 0.00 32.00 5.36
1530 1537 3.987220 ACGAAATGAAATCTTTTTGGGCG 59.013 39.130 11.53 0.00 32.00 6.13
1540 1569 0.467290 TTTTTGGGCGGCAGAGAACT 60.467 50.000 12.47 0.00 0.00 3.01
1541 1570 1.172180 TTTTGGGCGGCAGAGAACTG 61.172 55.000 12.47 0.00 45.91 3.16
1544 1573 2.817396 GGCGGCAGAGAACTGAGC 60.817 66.667 3.07 0.00 46.03 4.26
1550 1579 1.633852 GCAGAGAACTGAGCGCTTGG 61.634 60.000 13.26 10.39 46.03 3.61
1594 1623 1.002868 ACCCAGTGAGCTGTGCATC 60.003 57.895 0.00 0.00 41.02 3.91
1626 1655 3.029735 GCGCCAAACTGTTTGCCG 61.030 61.111 26.28 26.28 43.46 5.69
1642 1671 4.902443 TTGCCGTGTTTTCAGTTGAATA 57.098 36.364 0.00 0.00 33.54 1.75
1643 1672 5.446143 TTGCCGTGTTTTCAGTTGAATAT 57.554 34.783 0.00 0.00 33.54 1.28
1651 1680 7.990499 CGTGTTTTCAGTTGAATATTTGAAACG 59.010 33.333 10.98 9.39 38.75 3.60
1652 1681 8.803799 GTGTTTTCAGTTGAATATTTGAAACGT 58.196 29.630 10.98 0.00 38.75 3.99
1796 1844 5.233476 CGTGCTTATCAGTAAAATAGCCGAA 59.767 40.000 0.00 0.00 0.00 4.30
2166 2226 1.961277 GAGGTGCCATATTCGCCCG 60.961 63.158 1.71 0.00 34.75 6.13
2171 2231 1.069090 GCCATATTCGCCCGACTCA 59.931 57.895 0.00 0.00 0.00 3.41
2173 2233 1.878102 GCCATATTCGCCCGACTCATT 60.878 52.381 0.00 0.00 0.00 2.57
2178 2238 0.676466 TTCGCCCGACTCATTTGCAT 60.676 50.000 0.00 0.00 0.00 3.96
2192 2253 1.630223 TTGCATGGCAAAGATGGTCA 58.370 45.000 0.41 0.00 45.96 4.02
2199 2260 6.600427 TGCATGGCAAAGATGGTCATATATAG 59.400 38.462 0.00 0.00 34.76 1.31
2200 2261 6.600822 GCATGGCAAAGATGGTCATATATAGT 59.399 38.462 0.00 0.00 0.00 2.12
2216 2280 9.154632 TCATATATAGTTAAAGACTGCTTCCCA 57.845 33.333 0.00 0.00 39.48 4.37
2235 2299 7.626876 GCTTCCCAATTTTTCATGCAATTTAGG 60.627 37.037 0.00 0.00 0.00 2.69
2236 2300 6.179040 TCCCAATTTTTCATGCAATTTAGGG 58.821 36.000 0.00 10.79 0.00 3.53
2265 2329 9.436957 AAATCCTATTTGGTGCTTATAGATACG 57.563 33.333 0.00 0.00 37.07 3.06
2268 2332 6.812160 CCTATTTGGTGCTTATAGATACGGAC 59.188 42.308 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.465985 GAATAAATGTTTGGAAGTCCGTAAAAA 57.534 29.630 0.00 0.00 39.43 1.94
31 32 8.083462 GGAATAAATGTTTGGAAGTCCGTAAAA 58.917 33.333 0.00 0.00 39.43 1.52
32 33 7.230913 TGGAATAAATGTTTGGAAGTCCGTAAA 59.769 33.333 0.00 0.00 39.43 2.01
33 34 6.715718 TGGAATAAATGTTTGGAAGTCCGTAA 59.284 34.615 0.00 0.00 39.43 3.18
34 35 6.239396 TGGAATAAATGTTTGGAAGTCCGTA 58.761 36.000 0.00 0.00 39.43 4.02
35 36 5.074115 TGGAATAAATGTTTGGAAGTCCGT 58.926 37.500 0.00 0.00 39.43 4.69
36 37 5.637006 TGGAATAAATGTTTGGAAGTCCG 57.363 39.130 0.00 0.00 39.43 4.79
37 38 7.441836 ACTTTGGAATAAATGTTTGGAAGTCC 58.558 34.615 0.00 0.00 0.00 3.85
38 39 7.326063 CGACTTTGGAATAAATGTTTGGAAGTC 59.674 37.037 0.00 0.00 37.17 3.01
39 40 7.145323 CGACTTTGGAATAAATGTTTGGAAGT 58.855 34.615 0.00 0.00 0.00 3.01
40 41 7.114811 CACGACTTTGGAATAAATGTTTGGAAG 59.885 37.037 0.00 0.00 0.00 3.46
41 42 6.920758 CACGACTTTGGAATAAATGTTTGGAA 59.079 34.615 0.00 0.00 0.00 3.53
42 43 6.442952 CACGACTTTGGAATAAATGTTTGGA 58.557 36.000 0.00 0.00 0.00 3.53
43 44 5.118510 GCACGACTTTGGAATAAATGTTTGG 59.881 40.000 0.00 0.00 0.00 3.28
44 45 5.689514 TGCACGACTTTGGAATAAATGTTTG 59.310 36.000 0.00 0.00 0.00 2.93
45 46 5.689961 GTGCACGACTTTGGAATAAATGTTT 59.310 36.000 0.00 0.00 0.00 2.83
46 47 5.219633 GTGCACGACTTTGGAATAAATGTT 58.780 37.500 0.00 0.00 0.00 2.71
47 48 4.277174 TGTGCACGACTTTGGAATAAATGT 59.723 37.500 13.13 0.00 0.00 2.71
48 49 4.793071 TGTGCACGACTTTGGAATAAATG 58.207 39.130 13.13 0.00 0.00 2.32
49 50 5.643379 ATGTGCACGACTTTGGAATAAAT 57.357 34.783 13.13 0.00 0.00 1.40
50 51 6.751514 ATATGTGCACGACTTTGGAATAAA 57.248 33.333 13.13 0.00 0.00 1.40
51 52 6.751514 AATATGTGCACGACTTTGGAATAA 57.248 33.333 13.13 0.00 0.00 1.40
52 53 6.751514 AAATATGTGCACGACTTTGGAATA 57.248 33.333 13.13 1.25 0.00 1.75
53 54 5.643379 AAATATGTGCACGACTTTGGAAT 57.357 34.783 13.13 0.00 0.00 3.01
54 55 6.561737 TTAAATATGTGCACGACTTTGGAA 57.438 33.333 13.13 1.43 0.00 3.53
55 56 6.561737 TTTAAATATGTGCACGACTTTGGA 57.438 33.333 13.13 2.79 0.00 3.53
56 57 6.861055 AGTTTTAAATATGTGCACGACTTTGG 59.139 34.615 13.13 0.00 0.00 3.28
57 58 7.589587 TGAGTTTTAAATATGTGCACGACTTTG 59.410 33.333 13.13 0.00 0.00 2.77
58 59 7.644490 TGAGTTTTAAATATGTGCACGACTTT 58.356 30.769 13.13 12.96 0.00 2.66
59 60 7.197071 TGAGTTTTAAATATGTGCACGACTT 57.803 32.000 13.13 5.50 0.00 3.01
60 61 6.795098 TGAGTTTTAAATATGTGCACGACT 57.205 33.333 13.13 1.80 0.00 4.18
61 62 7.240674 TCATGAGTTTTAAATATGTGCACGAC 58.759 34.615 13.13 0.00 0.00 4.34
62 63 7.371126 TCATGAGTTTTAAATATGTGCACGA 57.629 32.000 13.13 2.60 0.00 4.35
63 64 7.536964 TGTTCATGAGTTTTAAATATGTGCACG 59.463 33.333 13.13 0.00 0.00 5.34
64 65 8.741101 TGTTCATGAGTTTTAAATATGTGCAC 57.259 30.769 10.75 10.75 0.00 4.57
65 66 9.926158 AATGTTCATGAGTTTTAAATATGTGCA 57.074 25.926 0.00 0.00 0.00 4.57
72 73 9.912634 ATCGAACAATGTTCATGAGTTTTAAAT 57.087 25.926 23.72 0.00 0.00 1.40
76 77 9.559958 GAATATCGAACAATGTTCATGAGTTTT 57.440 29.630 23.72 8.97 29.87 2.43
77 78 8.729756 TGAATATCGAACAATGTTCATGAGTTT 58.270 29.630 23.72 11.90 33.48 2.66
78 79 8.267620 TGAATATCGAACAATGTTCATGAGTT 57.732 30.769 23.72 13.00 33.48 3.01
79 80 7.848223 TGAATATCGAACAATGTTCATGAGT 57.152 32.000 23.72 8.53 33.48 3.41
83 84 9.673454 CAATCATGAATATCGAACAATGTTCAT 57.327 29.630 23.72 17.60 43.84 2.57
84 85 8.676401 ACAATCATGAATATCGAACAATGTTCA 58.324 29.630 23.72 12.51 39.89 3.18
85 86 9.507280 AACAATCATGAATATCGAACAATGTTC 57.493 29.630 15.62 15.62 0.00 3.18
86 87 9.859427 AAACAATCATGAATATCGAACAATGTT 57.141 25.926 0.00 0.00 0.00 2.71
87 88 9.859427 AAAACAATCATGAATATCGAACAATGT 57.141 25.926 0.00 0.00 0.00 2.71
90 91 9.905171 TGAAAAACAATCATGAATATCGAACAA 57.095 25.926 0.00 0.00 0.00 2.83
91 92 9.905171 TTGAAAAACAATCATGAATATCGAACA 57.095 25.926 0.00 0.00 33.18 3.18
168 169 7.095910 TGAGAAAATGTTTGCTCACTCAAAAA 58.904 30.769 11.30 0.00 45.58 1.94
169 170 6.629128 TGAGAAAATGTTTGCTCACTCAAAA 58.371 32.000 11.30 0.00 45.58 2.44
170 171 6.206395 TGAGAAAATGTTTGCTCACTCAAA 57.794 33.333 11.30 0.00 45.58 2.69
171 172 5.833406 TGAGAAAATGTTTGCTCACTCAA 57.167 34.783 11.30 0.00 45.58 3.02
177 178 8.452989 AATATTCGTTGAGAAAATGTTTGCTC 57.547 30.769 6.54 6.54 42.91 4.26
178 179 8.816640 AAATATTCGTTGAGAAAATGTTTGCT 57.183 26.923 0.00 0.00 42.91 3.91
179 180 9.862585 AAAAATATTCGTTGAGAAAATGTTTGC 57.137 25.926 0.00 0.00 42.91 3.68
256 257 9.726438 CGTCCCTTCCTCTAAATCATAAAATAT 57.274 33.333 0.00 0.00 0.00 1.28
257 258 8.930527 TCGTCCCTTCCTCTAAATCATAAAATA 58.069 33.333 0.00 0.00 0.00 1.40
258 259 7.802117 TCGTCCCTTCCTCTAAATCATAAAAT 58.198 34.615 0.00 0.00 0.00 1.82
259 260 7.190335 TCGTCCCTTCCTCTAAATCATAAAA 57.810 36.000 0.00 0.00 0.00 1.52
260 261 6.801718 TCGTCCCTTCCTCTAAATCATAAA 57.198 37.500 0.00 0.00 0.00 1.40
261 262 6.996180 ATCGTCCCTTCCTCTAAATCATAA 57.004 37.500 0.00 0.00 0.00 1.90
262 263 6.996180 AATCGTCCCTTCCTCTAAATCATA 57.004 37.500 0.00 0.00 0.00 2.15
263 264 5.896073 AATCGTCCCTTCCTCTAAATCAT 57.104 39.130 0.00 0.00 0.00 2.45
264 265 5.659525 TGTAATCGTCCCTTCCTCTAAATCA 59.340 40.000 0.00 0.00 0.00 2.57
265 266 6.040616 TCTGTAATCGTCCCTTCCTCTAAATC 59.959 42.308 0.00 0.00 0.00 2.17
266 267 5.897824 TCTGTAATCGTCCCTTCCTCTAAAT 59.102 40.000 0.00 0.00 0.00 1.40
288 289 9.768662 ATCTTTTTGTTTGTTGATAATGCTTCT 57.231 25.926 0.00 0.00 0.00 2.85
296 297 7.776107 TGTCCACATCTTTTTGTTTGTTGATA 58.224 30.769 0.00 0.00 0.00 2.15
301 302 4.432712 GCTGTCCACATCTTTTTGTTTGT 58.567 39.130 0.00 0.00 0.00 2.83
310 311 0.037303 CACAGGGCTGTCCACATCTT 59.963 55.000 0.00 0.00 42.83 2.40
313 314 1.426251 TTCCACAGGGCTGTCCACAT 61.426 55.000 0.00 0.00 42.83 3.21
327 328 1.824852 GGGATGACATTGGGTTTCCAC 59.175 52.381 0.00 0.00 43.94 4.02
335 336 2.102578 GAACCTTGGGGATGACATTGG 58.897 52.381 0.00 0.00 36.25 3.16
361 363 1.218316 GGAGTACCCGCCAACAGAG 59.782 63.158 0.00 0.00 0.00 3.35
393 395 6.400621 GGCGGTATTGCAAGTTAACAAAATTC 60.401 38.462 8.61 0.64 36.28 2.17
394 396 5.407084 GGCGGTATTGCAAGTTAACAAAATT 59.593 36.000 8.61 0.00 36.28 1.82
429 431 2.864097 GCAGATGTCGCACATACCTAGG 60.864 54.545 7.41 7.41 39.27 3.02
432 434 0.536724 TGCAGATGTCGCACATACCT 59.463 50.000 2.37 0.00 39.27 3.08
447 449 0.661552 CCTCATTCATCGCCTTGCAG 59.338 55.000 0.00 0.00 0.00 4.41
504 506 0.832626 AAGCTGCCAGCCAAAACTTT 59.167 45.000 14.25 0.00 43.77 2.66
507 509 0.319297 CTCAAGCTGCCAGCCAAAAC 60.319 55.000 14.25 0.00 43.77 2.43
514 516 3.058450 CGAATCTATCTCAAGCTGCCAG 58.942 50.000 0.00 0.00 0.00 4.85
523 525 8.322091 TGGTAGATGTAGATCGAATCTATCTCA 58.678 37.037 18.44 13.57 43.25 3.27
528 530 5.642491 CCGTGGTAGATGTAGATCGAATCTA 59.358 44.000 9.61 9.61 40.76 1.98
534 536 1.880675 AGCCGTGGTAGATGTAGATCG 59.119 52.381 0.00 0.00 33.34 3.69
567 569 6.872628 TCAAGCAAAATATCATGAGCCTAG 57.127 37.500 0.09 0.00 0.00 3.02
569 571 5.419788 TGTTCAAGCAAAATATCATGAGCCT 59.580 36.000 0.09 0.00 0.00 4.58
591 593 3.279434 GTCCACCTCTGTGAAAAGTTGT 58.721 45.455 0.00 0.00 45.76 3.32
597 599 2.485479 GCTTCTGTCCACCTCTGTGAAA 60.485 50.000 0.00 0.00 45.76 2.69
608 610 3.008266 TGTGATGATCTTGCTTCTGTCCA 59.992 43.478 0.00 0.00 0.00 4.02
677 679 3.774734 TGTATAGGGTCATAGCCGTCAT 58.225 45.455 0.00 0.00 41.56 3.06
694 696 0.324943 ACCCACTTCAGCGCTTGTAT 59.675 50.000 7.50 0.00 0.00 2.29
741 743 4.692155 GGCTGAATCTTTTGTTTTGATGGG 59.308 41.667 0.00 0.00 0.00 4.00
753 755 2.438434 CCGGCCGGCTGAATCTTT 60.438 61.111 37.00 0.00 0.00 2.52
768 770 3.041940 GGTCGCCAACACTGTCCG 61.042 66.667 0.00 0.00 0.00 4.79
787 789 0.036388 GTGATCCAGCCCACTTTCGA 60.036 55.000 0.00 0.00 0.00 3.71
790 792 0.620556 ATCGTGATCCAGCCCACTTT 59.379 50.000 0.00 0.00 0.00 2.66
821 823 3.134574 TGTCCTCAACATTAACCGCTT 57.865 42.857 0.00 0.00 31.20 4.68
876 878 1.327690 AAGCTCCCAGGAACGCGATA 61.328 55.000 15.93 0.00 0.00 2.92
906 908 2.550978 GGACCGATCACACCATGTAAG 58.449 52.381 0.00 0.00 0.00 2.34
915 917 1.567357 TGATGAAGGGACCGATCACA 58.433 50.000 0.32 0.05 0.00 3.58
920 922 2.571653 AGTTTCATGATGAAGGGACCGA 59.428 45.455 8.01 0.00 37.70 4.69
923 925 6.151817 AGCTAAAAGTTTCATGATGAAGGGAC 59.848 38.462 8.01 4.33 37.70 4.46
927 929 7.470900 GGAGAGCTAAAAGTTTCATGATGAAG 58.529 38.462 8.01 0.00 37.70 3.02
934 936 4.287766 ACCGGAGAGCTAAAAGTTTCAT 57.712 40.909 9.46 0.00 0.00 2.57
937 939 3.055312 CCCTACCGGAGAGCTAAAAGTTT 60.055 47.826 9.46 0.00 0.00 2.66
955 957 3.183801 ACCGAGTAAAAATCACCCCCTA 58.816 45.455 0.00 0.00 0.00 3.53
961 963 4.024641 ACCACGAAACCGAGTAAAAATCAC 60.025 41.667 0.00 0.00 0.00 3.06
970 972 0.033090 GAGGAACCACGAAACCGAGT 59.967 55.000 0.00 0.00 0.00 4.18
974 976 1.535462 CATGTGAGGAACCACGAAACC 59.465 52.381 0.00 0.00 39.80 3.27
986 988 4.428294 ACCTCCATTATCACATGTGAGG 57.572 45.455 30.63 25.24 43.61 3.86
1013 1015 4.540099 TCCAGAGGTTAACCAAATCCTGAT 59.460 41.667 26.26 1.96 38.89 2.90
1058 1060 1.019673 CAAGATAGGCGCTGCAACAT 58.980 50.000 7.64 0.00 0.00 2.71
1133 1140 2.105993 GCCGGAACATTTACCTCCCTAT 59.894 50.000 5.05 0.00 0.00 2.57
1143 1150 0.544120 ATTGGTGGGCCGGAACATTT 60.544 50.000 5.05 0.00 37.67 2.32
1169 1176 2.102757 CACTCTGATGTGCAGGCTAGAT 59.897 50.000 0.00 0.00 44.98 1.98
1242 1249 0.973632 TCATGGTGTTACAGTCCGCT 59.026 50.000 0.00 0.00 0.00 5.52
1316 1323 8.243961 TCCTGGTTTTGAAATAATGTTTGAGA 57.756 30.769 0.00 0.00 0.00 3.27
1318 1325 8.260818 TGTTCCTGGTTTTGAAATAATGTTTGA 58.739 29.630 0.00 0.00 0.00 2.69
1322 1329 7.360113 AGTGTTCCTGGTTTTGAAATAATGT 57.640 32.000 0.00 0.00 0.00 2.71
1336 1343 4.932146 ACGAATTCAAAAAGTGTTCCTGG 58.068 39.130 6.22 0.00 0.00 4.45
1337 1344 8.574196 AATTACGAATTCAAAAAGTGTTCCTG 57.426 30.769 6.22 0.00 0.00 3.86
1456 1463 9.379791 CGGGTTTAGTTCTTTACTTCTTCATAT 57.620 33.333 0.00 0.00 38.33 1.78
1475 1482 6.092396 GGTTTTGCTTTTTCTTTTCGGGTTTA 59.908 34.615 0.00 0.00 0.00 2.01
1502 1509 9.255304 CCCAAAAAGATTTCATTTCGTTTCTTA 57.745 29.630 0.00 0.00 0.00 2.10
1505 1512 6.362686 GCCCAAAAAGATTTCATTTCGTTTC 58.637 36.000 0.00 0.00 0.00 2.78
1525 1532 2.922503 TCAGTTCTCTGCCGCCCA 60.923 61.111 0.00 0.00 41.10 5.36
1529 1536 3.184683 GCGCTCAGTTCTCTGCCG 61.185 66.667 0.00 0.00 41.10 5.69
1530 1537 1.375268 AAGCGCTCAGTTCTCTGCC 60.375 57.895 12.06 0.00 41.10 4.85
1563 1592 2.954753 CTGGGTGAGACGCAAACGC 61.955 63.158 0.00 0.00 45.53 4.84
1594 1623 1.162800 GGCGCAGGAGCTCCTATTTG 61.163 60.000 34.67 23.50 46.65 2.32
1626 1655 8.803799 ACGTTTCAAATATTCAACTGAAAACAC 58.196 29.630 12.42 3.88 38.97 3.32
2115 2175 2.545113 GCCGAATAGCGTGATTAGTGGA 60.545 50.000 0.00 0.00 38.67 4.02
2189 2250 9.425577 GGGAAGCAGTCTTTAACTATATATGAC 57.574 37.037 0.00 0.00 36.07 3.06
2199 2260 6.983890 TGAAAAATTGGGAAGCAGTCTTTAAC 59.016 34.615 0.00 0.00 31.48 2.01
2200 2261 7.118496 TGAAAAATTGGGAAGCAGTCTTTAA 57.882 32.000 0.00 0.00 31.48 1.52
2205 2269 3.681417 GCATGAAAAATTGGGAAGCAGTC 59.319 43.478 0.00 0.00 0.00 3.51
2208 2272 3.766068 TGCATGAAAAATTGGGAAGCA 57.234 38.095 0.00 0.00 0.00 3.91
2216 2280 8.688747 TTTCACCCTAAATTGCATGAAAAATT 57.311 26.923 0.00 0.00 34.16 1.82
2235 2299 6.715347 ATAAGCACCAAATAGGATTTCACC 57.285 37.500 0.00 0.00 41.22 4.02
2236 2300 8.677148 TCTATAAGCACCAAATAGGATTTCAC 57.323 34.615 0.00 0.00 41.22 3.18


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

AutoCloner maintained by Alex Coulton.