Multiple sequence alignment - TraesCS2B01G183100

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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 TraesCS2B01G183100 chr2B 100.000 3035 0 0 1 3035 158145363 158148397 0.000000e+00 5605.0
1 TraesCS2B01G183100 chr2B 82.609 138 22 2 1223 1359 489849194 489849330 1.480000e-23 121.0
2 TraesCS2B01G183100 chr2B 89.855 69 5 2 186 253 158145615 158145548 1.500000e-13 87.9
3 TraesCS2B01G183100 chr2D 93.622 2336 61 33 252 2530 108312325 108314629 0.000000e+00 3408.0
4 TraesCS2B01G183100 chr2D 87.619 420 41 6 2572 2986 108314613 108315026 7.610000e-131 477.0
5 TraesCS2B01G183100 chr2D 82.517 143 23 2 1218 1359 417625365 417625506 1.140000e-24 124.0
6 TraesCS2B01G183100 chr2D 88.608 79 9 0 1354 1432 417626499 417626577 2.490000e-16 97.1
7 TraesCS2B01G183100 chr2D 97.143 35 1 0 197 231 108312294 108312328 3.270000e-05 60.2
8 TraesCS2B01G183100 chr2A 92.412 2280 81 37 254 2478 104449642 104451884 0.000000e+00 3168.0
9 TraesCS2B01G183100 chr2A 84.161 423 53 7 2572 2986 104451905 104452321 6.100000e-107 398.0
10 TraesCS2B01G183100 chr2A 82.394 142 23 2 1218 1358 572487557 572487417 4.110000e-24 122.0
11 TraesCS2B01G183100 chr2A 88.608 79 9 0 1354 1432 572486441 572486363 2.490000e-16 97.1
12 TraesCS2B01G183100 chr2A 91.525 59 3 2 2946 3004 103732556 103732500 2.510000e-11 80.5
13 TraesCS2B01G183100 chr5B 94.203 138 8 0 1222 1359 402751419 402751282 8.530000e-51 211.0
14 TraesCS2B01G183100 chr5B 90.000 80 4 4 1355 1432 266501783 266501860 1.930000e-17 100.0
15 TraesCS2B01G183100 chr5A 94.203 138 8 0 1222 1359 443742557 443742420 8.530000e-51 211.0
16 TraesCS2B01G183100 chr5A 85.507 138 20 0 997 1134 316085017 316085154 8.770000e-31 145.0
17 TraesCS2B01G183100 chr5A 88.608 79 9 0 1354 1432 316085399 316085477 2.490000e-16 97.1
18 TraesCS2B01G183100 chr5D 93.478 138 9 0 1222 1359 342712890 342712753 3.970000e-49 206.0
19 TraesCS2B01G183100 chr5D 85.926 135 19 0 1000 1134 238557792 238557658 8.770000e-31 145.0
20 TraesCS2B01G183100 chr5D 90.909 77 3 4 1358 1432 238557411 238557337 1.930000e-17 100.0
21 TraesCS2B01G183100 chr5D 90.164 61 4 2 2944 3004 526559562 526559620 9.020000e-11 78.7
22 TraesCS2B01G183100 chr5D 89.231 65 4 2 2941 3004 532592453 532592515 9.020000e-11 78.7
23 TraesCS2B01G183100 chr4D 91.150 113 10 0 1001 1113 107710734 107710622 1.460000e-33 154.0
24 TraesCS2B01G183100 chr4D 86.667 90 7 5 1358 1445 107710356 107710270 8.960000e-16 95.3
25 TraesCS2B01G183100 chr4D 93.103 58 2 1 2947 3004 456274875 456274820 1.940000e-12 84.2
26 TraesCS2B01G183100 chr4D 90.323 62 3 3 2943 3004 34710679 34710621 9.020000e-11 78.7
27 TraesCS2B01G183100 chr4B 91.150 113 10 0 1001 1113 168984879 168984991 1.460000e-33 154.0
28 TraesCS2B01G183100 chr4B 86.022 93 8 5 1355 1445 168985244 168985333 8.960000e-16 95.3
29 TraesCS2B01G183100 chr4A 91.150 113 10 0 1001 1113 468603250 468603362 1.460000e-33 154.0
30 TraesCS2B01G183100 chr7D 90.164 61 4 2 2944 3004 518683974 518684032 9.020000e-11 78.7
31 TraesCS2B01G183100 chr1D 91.379 58 3 2 2947 3004 462985146 462985091 9.020000e-11 78.7


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 TraesCS2B01G183100 chr2B 158145363 158148397 3034 False 5605.000000 5605 100.000000 1 3035 1 chr2B.!!$F1 3034
1 TraesCS2B01G183100 chr2D 108312294 108315026 2732 False 1315.066667 3408 92.794667 197 2986 3 chr2D.!!$F1 2789
2 TraesCS2B01G183100 chr2A 104449642 104452321 2679 False 1783.000000 3168 88.286500 254 2986 2 chr2A.!!$F1 2732

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
79 80 0.032678 CCTGACGCCGCTAAGATGAT 59.967 55.0 0.0 0.0 0.0 2.45 F
813 833 0.040351 CCTCTCCTCACCTCACTCCA 59.960 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1176 1230 0.881118 AACAACCATGCGATCCACAC 59.119 50.0 0.0 0.0 0.0 3.82 R
2542 2629 0.387565 TTTTGGAAAAGGGACGCAGC 59.612 50.0 0.0 0.0 0.0 5.25 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
17 18 3.503749 AGGTTTGCGTTGCGACAA 58.496 50.000 4.64 0.00 0.00 3.18
18 19 1.355210 AGGTTTGCGTTGCGACAAG 59.645 52.632 4.64 0.00 0.00 3.16
30 31 3.593247 CGACAAGCATGCTTAGCAC 57.407 52.632 31.48 20.03 43.04 4.40
31 32 0.798159 CGACAAGCATGCTTAGCACA 59.202 50.000 31.48 0.00 43.04 4.57
32 33 1.464687 CGACAAGCATGCTTAGCACAC 60.465 52.381 31.48 16.96 43.04 3.82
33 34 0.518636 ACAAGCATGCTTAGCACACG 59.481 50.000 31.48 19.49 43.04 4.49
34 35 0.795735 CAAGCATGCTTAGCACACGC 60.796 55.000 31.48 12.87 43.04 5.34
35 36 2.244436 AAGCATGCTTAGCACACGCG 62.244 55.000 31.09 3.53 43.04 6.01
36 37 2.276868 CATGCTTAGCACACGCGC 60.277 61.111 9.82 0.00 43.04 6.86
37 38 3.499737 ATGCTTAGCACACGCGCC 61.500 61.111 9.82 0.00 43.04 6.53
40 41 3.545481 CTTAGCACACGCGCCGAG 61.545 66.667 5.73 0.00 45.49 4.63
41 42 4.351938 TTAGCACACGCGCCGAGT 62.352 61.111 5.73 0.00 45.49 4.18
42 43 4.771356 TAGCACACGCGCCGAGTC 62.771 66.667 5.73 0.00 45.49 3.36
60 61 3.056328 GGACTTTGGCCGTGGCTC 61.056 66.667 11.25 0.00 41.60 4.70
61 62 3.056328 GACTTTGGCCGTGGCTCC 61.056 66.667 11.25 0.00 41.60 4.70
62 63 3.553095 GACTTTGGCCGTGGCTCCT 62.553 63.158 11.25 0.00 41.60 3.69
63 64 3.058160 CTTTGGCCGTGGCTCCTG 61.058 66.667 11.25 0.00 41.60 3.86
64 65 3.551496 CTTTGGCCGTGGCTCCTGA 62.551 63.158 11.25 0.00 41.60 3.86
65 66 3.842925 TTTGGCCGTGGCTCCTGAC 62.843 63.158 11.25 0.00 41.60 3.51
73 74 4.143333 GGCTCCTGACGCCGCTAA 62.143 66.667 0.00 0.00 37.87 3.09
74 75 2.583593 GCTCCTGACGCCGCTAAG 60.584 66.667 0.00 0.00 0.00 2.18
75 76 3.064987 GCTCCTGACGCCGCTAAGA 62.065 63.158 0.00 0.00 0.00 2.10
76 77 1.736586 CTCCTGACGCCGCTAAGAT 59.263 57.895 0.00 0.00 0.00 2.40
77 78 0.596083 CTCCTGACGCCGCTAAGATG 60.596 60.000 0.00 0.00 0.00 2.90
78 79 1.035385 TCCTGACGCCGCTAAGATGA 61.035 55.000 0.00 0.00 0.00 2.92
79 80 0.032678 CCTGACGCCGCTAAGATGAT 59.967 55.000 0.00 0.00 0.00 2.45
80 81 1.413382 CTGACGCCGCTAAGATGATC 58.587 55.000 0.00 0.00 0.00 2.92
81 82 0.744281 TGACGCCGCTAAGATGATCA 59.256 50.000 0.00 0.00 0.00 2.92
82 83 1.269257 TGACGCCGCTAAGATGATCAG 60.269 52.381 0.09 0.00 0.00 2.90
83 84 1.001268 GACGCCGCTAAGATGATCAGA 60.001 52.381 0.09 0.00 0.00 3.27
84 85 1.615883 ACGCCGCTAAGATGATCAGAT 59.384 47.619 0.09 0.00 0.00 2.90
85 86 2.257894 CGCCGCTAAGATGATCAGATC 58.742 52.381 0.09 3.11 0.00 2.75
86 87 2.352127 CGCCGCTAAGATGATCAGATCA 60.352 50.000 15.69 15.69 44.55 2.92
95 96 3.766068 ATGATCAGATCATCTGCGGTT 57.234 42.857 18.86 0.00 46.62 4.44
96 97 4.879197 ATGATCAGATCATCTGCGGTTA 57.121 40.909 18.86 0.00 46.62 2.85
97 98 3.982475 TGATCAGATCATCTGCGGTTAC 58.018 45.455 10.10 0.00 43.95 2.50
98 99 3.384467 TGATCAGATCATCTGCGGTTACA 59.616 43.478 10.10 1.31 43.95 2.41
99 100 3.885724 TCAGATCATCTGCGGTTACAA 57.114 42.857 10.10 0.00 43.95 2.41
100 101 3.521560 TCAGATCATCTGCGGTTACAAC 58.478 45.455 10.10 0.00 43.95 3.32
101 102 3.195610 TCAGATCATCTGCGGTTACAACT 59.804 43.478 10.10 0.00 43.95 3.16
102 103 3.935203 CAGATCATCTGCGGTTACAACTT 59.065 43.478 0.47 0.00 37.72 2.66
103 104 5.105513 TCAGATCATCTGCGGTTACAACTTA 60.106 40.000 10.10 0.00 43.95 2.24
104 105 5.005779 CAGATCATCTGCGGTTACAACTTAC 59.994 44.000 0.47 0.00 37.72 2.34
105 106 4.530710 TCATCTGCGGTTACAACTTACT 57.469 40.909 0.00 0.00 0.00 2.24
106 107 5.648178 TCATCTGCGGTTACAACTTACTA 57.352 39.130 0.00 0.00 0.00 1.82
107 108 5.647589 TCATCTGCGGTTACAACTTACTAG 58.352 41.667 0.00 0.00 0.00 2.57
108 109 5.184479 TCATCTGCGGTTACAACTTACTAGT 59.816 40.000 0.00 0.00 35.68 2.57
109 110 6.375174 TCATCTGCGGTTACAACTTACTAGTA 59.625 38.462 0.00 0.00 33.17 1.82
110 111 5.942872 TCTGCGGTTACAACTTACTAGTAC 58.057 41.667 0.91 0.00 33.17 2.73
111 112 5.473162 TCTGCGGTTACAACTTACTAGTACA 59.527 40.000 0.91 0.00 33.17 2.90
112 113 6.016360 TCTGCGGTTACAACTTACTAGTACAA 60.016 38.462 0.91 0.00 33.17 2.41
113 114 6.151691 TGCGGTTACAACTTACTAGTACAAG 58.848 40.000 0.91 2.84 33.17 3.16
114 115 6.152379 GCGGTTACAACTTACTAGTACAAGT 58.848 40.000 0.91 3.54 36.56 3.16
115 116 7.040755 TGCGGTTACAACTTACTAGTACAAGTA 60.041 37.037 10.71 5.77 33.92 2.24
116 117 7.807907 GCGGTTACAACTTACTAGTACAAGTAA 59.192 37.037 10.71 10.41 39.14 2.24
117 118 9.118236 CGGTTACAACTTACTAGTACAAGTAAC 57.882 37.037 22.92 22.92 37.10 2.50
118 119 9.965824 GGTTACAACTTACTAGTACAAGTAACA 57.034 33.333 27.05 11.76 38.52 2.41
166 167 1.818674 CCATTTCCTTTTGGGAGACGG 59.181 52.381 0.00 0.00 46.01 4.79
167 168 1.202348 CATTTCCTTTTGGGAGACGGC 59.798 52.381 0.00 0.00 46.01 5.68
168 169 0.183971 TTTCCTTTTGGGAGACGGCA 59.816 50.000 0.00 0.00 46.01 5.69
169 170 0.250727 TTCCTTTTGGGAGACGGCAG 60.251 55.000 0.00 0.00 46.01 4.85
170 171 2.335712 CCTTTTGGGAGACGGCAGC 61.336 63.158 0.00 0.00 37.23 5.25
171 172 2.282180 TTTTGGGAGACGGCAGCC 60.282 61.111 0.00 0.00 0.00 4.85
231 232 2.562912 CAGGTCGCAACATGCCAC 59.437 61.111 0.00 0.00 41.12 5.01
232 233 3.049674 AGGTCGCAACATGCCACG 61.050 61.111 0.00 0.00 41.12 4.94
233 234 4.759096 GGTCGCAACATGCCACGC 62.759 66.667 0.00 0.00 41.12 5.34
234 235 4.759096 GTCGCAACATGCCACGCC 62.759 66.667 0.00 0.00 41.12 5.68
236 237 4.118995 CGCAACATGCCACGCCAT 62.119 61.111 0.00 0.00 41.12 4.40
237 238 2.507547 GCAACATGCCACGCCATG 60.508 61.111 9.06 9.06 46.19 3.66
238 239 2.507547 CAACATGCCACGCCATGC 60.508 61.111 10.19 0.00 44.98 4.06
239 240 3.762247 AACATGCCACGCCATGCC 61.762 61.111 10.19 0.00 44.98 4.40
250 251 4.195334 CCATGCCCCCGGGAGAAG 62.195 72.222 26.32 8.91 37.50 2.85
251 252 4.195334 CATGCCCCCGGGAGAAGG 62.195 72.222 26.32 16.53 37.50 3.46
435 445 0.613012 CTGGCCCCTTTCCCTTTCTG 60.613 60.000 0.00 0.00 0.00 3.02
456 466 2.807045 GTCTCTGCACGCACCTCG 60.807 66.667 0.00 0.00 45.38 4.63
466 476 3.844090 GCACCTCGCCTCCCTCTC 61.844 72.222 0.00 0.00 32.94 3.20
483 493 3.071602 CCTCTCTCTCCCTCTCTCTACAG 59.928 56.522 0.00 0.00 0.00 2.74
529 539 0.526524 GCTCGCAGGCTACAGTAGTG 60.527 60.000 9.42 1.96 0.00 2.74
630 644 1.662446 CTGTGCTTTGCTTTGGGCG 60.662 57.895 0.00 0.00 45.43 6.13
631 645 2.356194 GTGCTTTGCTTTGGGCGG 60.356 61.111 0.00 0.00 45.43 6.13
632 646 3.614698 TGCTTTGCTTTGGGCGGG 61.615 61.111 0.00 0.00 45.43 6.13
734 748 0.116342 TGCTTGTCCTCACCCTCCTA 59.884 55.000 0.00 0.00 0.00 2.94
735 749 0.537653 GCTTGTCCTCACCCTCCTAC 59.462 60.000 0.00 0.00 0.00 3.18
736 750 1.897647 GCTTGTCCTCACCCTCCTACT 60.898 57.143 0.00 0.00 0.00 2.57
737 751 2.623502 GCTTGTCCTCACCCTCCTACTA 60.624 54.545 0.00 0.00 0.00 1.82
813 833 0.040351 CCTCTCCTCACCTCACTCCA 59.960 60.000 0.00 0.00 0.00 3.86
1176 1230 1.599419 CCGGTTCTTGCCTTCGTTTTG 60.599 52.381 0.00 0.00 0.00 2.44
1199 1253 1.539388 TGGATCGCATGGTTGTTTGTC 59.461 47.619 0.00 0.00 0.00 3.18
1227 1281 1.439228 CCTCGATCGATGTGCAGGT 59.561 57.895 19.78 0.00 0.00 4.00
1281 1335 3.971109 GACCAACTACCTGCGCCCC 62.971 68.421 4.18 0.00 0.00 5.80
2042 2099 3.962063 GGTTACCCTTTCTAGCTAGCTCT 59.038 47.826 23.26 0.00 0.00 4.09
2058 2115 2.236395 AGCTCTACCGTGCCAAGTTATT 59.764 45.455 0.00 0.00 0.00 1.40
2072 2129 5.585047 GCCAAGTTATTAAGGTCGATGTTCT 59.415 40.000 0.00 0.00 0.00 3.01
2133 2192 3.048337 TGCCCACCTAACGAAAACTAG 57.952 47.619 0.00 0.00 0.00 2.57
2190 2252 0.979665 CAGCTTCCTTGGTCTCCTGA 59.020 55.000 0.00 0.00 0.00 3.86
2230 2293 9.705290 GCATAGTTTTCATTTAGGGAAAAGAAA 57.295 29.630 0.00 0.00 42.87 2.52
2294 2363 6.926826 TGTAACTGTGACTTGGTACTATGTTG 59.073 38.462 0.00 0.00 0.00 3.33
2400 2470 9.973450 ATTAGTACATGTCATGTCTTCTATCAC 57.027 33.333 21.65 11.67 43.67 3.06
2401 2471 7.652524 AGTACATGTCATGTCTTCTATCACT 57.347 36.000 21.65 13.63 43.67 3.41
2402 2472 8.753497 AGTACATGTCATGTCTTCTATCACTA 57.247 34.615 21.65 0.00 43.67 2.74
2421 2491 6.509656 TCACTACTAATTAACCAGTATGCCG 58.490 40.000 0.00 0.00 31.97 5.69
2425 2495 8.208903 ACTACTAATTAACCAGTATGCCGAATT 58.791 33.333 0.00 0.00 31.97 2.17
2480 2567 8.499403 AGTTAGTTGATTAATCTTTGGAGCTC 57.501 34.615 16.24 4.71 0.00 4.09
2503 2590 7.381766 TCTTTCATGGTCAGTATGTCAATTG 57.618 36.000 0.00 0.00 37.40 2.32
2530 2617 6.044287 TGCCTGTCATATATTTCCACCACTAT 59.956 38.462 0.00 0.00 0.00 2.12
2531 2618 6.372659 GCCTGTCATATATTTCCACCACTATG 59.627 42.308 0.00 0.00 0.00 2.23
2532 2619 6.372659 CCTGTCATATATTTCCACCACTATGC 59.627 42.308 0.00 0.00 0.00 3.14
2533 2620 6.836242 TGTCATATATTTCCACCACTATGCA 58.164 36.000 0.00 0.00 0.00 3.96
2534 2621 6.936335 TGTCATATATTTCCACCACTATGCAG 59.064 38.462 0.00 0.00 0.00 4.41
2535 2622 7.161404 GTCATATATTTCCACCACTATGCAGA 58.839 38.462 0.00 0.00 0.00 4.26
2536 2623 7.332926 GTCATATATTTCCACCACTATGCAGAG 59.667 40.741 6.84 6.84 0.00 3.35
2537 2624 2.787473 TTTCCACCACTATGCAGAGG 57.213 50.000 13.85 4.14 38.41 3.69
2538 2625 0.253044 TTCCACCACTATGCAGAGGC 59.747 55.000 13.85 0.00 36.05 4.70
2539 2626 1.153086 CCACCACTATGCAGAGGCC 60.153 63.158 13.85 0.00 40.13 5.19
2540 2627 1.522355 CACCACTATGCAGAGGCCG 60.522 63.158 13.85 1.70 40.13 6.13
2541 2628 2.109799 CCACTATGCAGAGGCCGG 59.890 66.667 13.85 6.32 40.13 6.13
2542 2629 2.109799 CACTATGCAGAGGCCGGG 59.890 66.667 13.85 0.00 40.13 5.73
2543 2630 3.866582 ACTATGCAGAGGCCGGGC 61.867 66.667 22.67 22.67 40.13 6.13
2544 2631 3.554342 CTATGCAGAGGCCGGGCT 61.554 66.667 33.40 33.40 40.13 5.19
2545 2632 3.821636 CTATGCAGAGGCCGGGCTG 62.822 68.421 38.01 24.09 40.13 4.85
2556 2643 3.431725 CGGGCTGCGTCCCTTTTC 61.432 66.667 10.86 0.00 44.30 2.29
2557 2644 3.062466 GGGCTGCGTCCCTTTTCC 61.062 66.667 5.88 0.00 43.13 3.13
2558 2645 2.282180 GGCTGCGTCCCTTTTCCA 60.282 61.111 0.00 0.00 0.00 3.53
2559 2646 1.901464 GGCTGCGTCCCTTTTCCAA 60.901 57.895 0.00 0.00 0.00 3.53
2560 2647 1.460273 GGCTGCGTCCCTTTTCCAAA 61.460 55.000 0.00 0.00 0.00 3.28
2561 2648 0.387565 GCTGCGTCCCTTTTCCAAAA 59.612 50.000 0.00 0.00 0.00 2.44
2562 2649 1.000843 GCTGCGTCCCTTTTCCAAAAT 59.999 47.619 0.00 0.00 0.00 1.82
2563 2650 2.230266 GCTGCGTCCCTTTTCCAAAATA 59.770 45.455 0.00 0.00 0.00 1.40
2564 2651 3.119137 GCTGCGTCCCTTTTCCAAAATAT 60.119 43.478 0.00 0.00 0.00 1.28
2565 2652 4.097286 GCTGCGTCCCTTTTCCAAAATATA 59.903 41.667 0.00 0.00 0.00 0.86
2566 2653 5.221244 GCTGCGTCCCTTTTCCAAAATATAT 60.221 40.000 0.00 0.00 0.00 0.86
2567 2654 6.016610 GCTGCGTCCCTTTTCCAAAATATATA 60.017 38.462 0.00 0.00 0.00 0.86
2568 2655 7.309194 GCTGCGTCCCTTTTCCAAAATATATAT 60.309 37.037 0.00 0.00 0.00 0.86
2569 2656 9.226606 CTGCGTCCCTTTTCCAAAATATATATA 57.773 33.333 0.00 0.00 0.00 0.86
2570 2657 9.747898 TGCGTCCCTTTTCCAAAATATATATAT 57.252 29.630 0.00 0.00 0.00 0.86
2619 2706 4.771114 ATGCCAAATACTAGTACCTGCA 57.229 40.909 16.05 16.05 0.00 4.41
2620 2707 3.869065 TGCCAAATACTAGTACCTGCAC 58.131 45.455 4.31 1.94 0.00 4.57
2757 2852 5.172934 GGTCCACTACATGACAACGATTTA 58.827 41.667 0.00 0.00 33.09 1.40
2774 2869 4.219944 CGATTTATCCCTCGGGTGATTAGA 59.780 45.833 1.18 0.00 36.47 2.10
2799 2894 6.725834 AGGAGTTGGTACCAATTGATCAAATT 59.274 34.615 29.40 1.15 39.13 1.82
2801 2896 7.331687 GGAGTTGGTACCAATTGATCAAATTTG 59.668 37.037 29.40 12.15 36.28 2.32
2818 2913 8.498054 TCAAATTTGAAATTAAACTTGGTGCA 57.502 26.923 18.45 0.00 33.55 4.57
2837 2932 7.665690 TGGTGCATGTATTTTTCTACAATTGT 58.334 30.769 16.68 16.68 35.37 2.71
2844 2939 7.653647 TGTATTTTTCTACAATTGTTTCGGCT 58.346 30.769 17.78 0.00 0.00 5.52
2851 2946 7.681939 TCTACAATTGTTTCGGCTTCTAAAT 57.318 32.000 17.78 0.00 0.00 1.40
2893 2988 6.598753 TTCTAAAAAGTCTGAGAACAACCG 57.401 37.500 0.00 0.00 0.00 4.44
2894 2989 5.054477 TCTAAAAAGTCTGAGAACAACCGG 58.946 41.667 0.00 0.00 0.00 5.28
2910 3005 6.413783 ACAACCGGTATTTTTCCTTTTCAT 57.586 33.333 8.00 0.00 0.00 2.57
2914 3009 3.303229 CGGTATTTTTCCTTTTCATGCGC 59.697 43.478 0.00 0.00 0.00 6.09
2921 3016 2.083774 TCCTTTTCATGCGCGAGAATT 58.916 42.857 12.10 0.00 0.00 2.17
2925 3020 4.402583 CTTTTCATGCGCGAGAATTAACA 58.597 39.130 12.10 0.00 0.00 2.41
2927 3022 1.323235 TCATGCGCGAGAATTAACACG 59.677 47.619 12.10 0.00 0.00 4.49
2928 3023 0.650512 ATGCGCGAGAATTAACACGG 59.349 50.000 12.10 0.00 0.00 4.94
2939 3034 6.254281 AGAATTAACACGGGATGAACAAAG 57.746 37.500 0.00 0.00 0.00 2.77
2953 3048 7.365295 GGGATGAACAAAGTATTACTACTCCCA 60.365 40.741 0.00 0.00 37.20 4.37
2955 3050 6.704310 TGAACAAAGTATTACTACTCCCACC 58.296 40.000 0.00 0.00 37.20 4.61
2956 3051 5.334724 ACAAAGTATTACTACTCCCACCG 57.665 43.478 0.00 0.00 37.20 4.94
3017 3112 9.613428 TTAATGATCTAAAGGGAGTACAACATG 57.387 33.333 0.00 0.00 0.00 3.21
3018 3113 5.989477 TGATCTAAAGGGAGTACAACATGG 58.011 41.667 0.00 0.00 0.00 3.66
3019 3114 5.487488 TGATCTAAAGGGAGTACAACATGGT 59.513 40.000 0.00 0.00 0.00 3.55
3020 3115 5.160607 TCTAAAGGGAGTACAACATGGTG 57.839 43.478 9.83 9.83 0.00 4.17
3021 3116 4.841813 TCTAAAGGGAGTACAACATGGTGA 59.158 41.667 19.90 0.00 0.00 4.02
3022 3117 3.703001 AAGGGAGTACAACATGGTGAG 57.297 47.619 19.90 0.00 0.00 3.51
3023 3118 1.279271 AGGGAGTACAACATGGTGAGC 59.721 52.381 19.90 9.46 0.00 4.26
3024 3119 1.359848 GGAGTACAACATGGTGAGCG 58.640 55.000 19.90 0.00 0.00 5.03
3025 3120 1.337823 GGAGTACAACATGGTGAGCGT 60.338 52.381 19.90 0.00 0.00 5.07
3026 3121 2.094390 GGAGTACAACATGGTGAGCGTA 60.094 50.000 19.90 0.00 0.00 4.42
3027 3122 3.430374 GGAGTACAACATGGTGAGCGTAT 60.430 47.826 19.90 0.00 0.00 3.06
3028 3123 3.782046 AGTACAACATGGTGAGCGTATC 58.218 45.455 19.90 0.00 0.00 2.24
3029 3124 3.447586 AGTACAACATGGTGAGCGTATCT 59.552 43.478 19.90 0.00 0.00 1.98
3030 3125 4.643334 AGTACAACATGGTGAGCGTATCTA 59.357 41.667 19.90 0.00 0.00 1.98
3031 3126 4.046938 ACAACATGGTGAGCGTATCTAG 57.953 45.455 19.90 0.00 0.00 2.43
3032 3127 3.699538 ACAACATGGTGAGCGTATCTAGA 59.300 43.478 19.90 0.00 0.00 2.43
3033 3128 4.342378 ACAACATGGTGAGCGTATCTAGAT 59.658 41.667 19.90 10.73 0.00 1.98
3034 3129 4.775058 ACATGGTGAGCGTATCTAGATC 57.225 45.455 8.95 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.355210 CTTGTCGCAACGCAAACCT 59.645 52.632 0.00 0.00 0.00 3.50
1 2 2.292916 GCTTGTCGCAACGCAAACC 61.293 57.895 0.00 0.00 38.92 3.27
2 3 3.211604 GCTTGTCGCAACGCAAAC 58.788 55.556 0.00 0.00 38.92 2.93
11 12 0.522076 GTGCTAAGCATGCTTGTCGC 60.522 55.000 37.21 32.40 41.91 5.19
12 13 0.798159 TGTGCTAAGCATGCTTGTCG 59.202 50.000 37.21 26.04 41.91 4.35
13 14 1.464687 CGTGTGCTAAGCATGCTTGTC 60.465 52.381 37.21 27.85 41.91 3.18
14 15 0.518636 CGTGTGCTAAGCATGCTTGT 59.481 50.000 37.21 19.31 41.91 3.16
15 16 0.795735 GCGTGTGCTAAGCATGCTTG 60.796 55.000 37.21 27.35 43.37 4.01
16 17 1.503542 GCGTGTGCTAAGCATGCTT 59.496 52.632 33.70 33.70 43.37 3.91
17 18 2.743752 CGCGTGTGCTAAGCATGCT 61.744 57.895 16.30 16.30 44.22 3.79
18 19 2.276868 CGCGTGTGCTAAGCATGC 60.277 61.111 10.51 10.51 41.91 4.06
19 20 2.276868 GCGCGTGTGCTAAGCATG 60.277 61.111 8.43 0.00 41.91 4.06
20 21 3.499737 GGCGCGTGTGCTAAGCAT 61.500 61.111 8.43 0.00 41.91 3.79
23 24 3.545481 CTCGGCGCGTGTGCTAAG 61.545 66.667 8.43 0.00 39.65 2.18
24 25 4.351938 ACTCGGCGCGTGTGCTAA 62.352 61.111 8.43 0.00 39.65 3.09
25 26 4.771356 GACTCGGCGCGTGTGCTA 62.771 66.667 7.48 0.00 39.65 3.49
43 44 3.056328 GAGCCACGGCCAAAGTCC 61.056 66.667 2.24 0.00 43.17 3.85
44 45 3.056328 GGAGCCACGGCCAAAGTC 61.056 66.667 2.24 0.00 43.17 3.01
45 46 3.570212 AGGAGCCACGGCCAAAGT 61.570 61.111 2.24 0.00 43.17 2.66
46 47 3.058160 CAGGAGCCACGGCCAAAG 61.058 66.667 2.24 0.00 43.17 2.77
47 48 3.565214 TCAGGAGCCACGGCCAAA 61.565 61.111 2.24 0.00 43.17 3.28
48 49 4.329545 GTCAGGAGCCACGGCCAA 62.330 66.667 2.24 0.00 43.17 4.52
57 58 2.356818 ATCTTAGCGGCGTCAGGAGC 62.357 60.000 9.37 0.00 0.00 4.70
58 59 0.596083 CATCTTAGCGGCGTCAGGAG 60.596 60.000 9.37 0.09 0.00 3.69
59 60 1.035385 TCATCTTAGCGGCGTCAGGA 61.035 55.000 9.37 2.74 0.00 3.86
60 61 0.032678 ATCATCTTAGCGGCGTCAGG 59.967 55.000 9.37 0.00 0.00 3.86
61 62 1.269257 TGATCATCTTAGCGGCGTCAG 60.269 52.381 9.37 1.98 0.00 3.51
62 63 0.744281 TGATCATCTTAGCGGCGTCA 59.256 50.000 9.37 0.00 0.00 4.35
63 64 1.001268 TCTGATCATCTTAGCGGCGTC 60.001 52.381 9.37 0.13 0.00 5.19
64 65 1.032794 TCTGATCATCTTAGCGGCGT 58.967 50.000 9.37 0.00 0.00 5.68
65 66 2.257894 GATCTGATCATCTTAGCGGCG 58.742 52.381 12.66 0.51 0.00 6.46
66 67 3.309961 TGATCTGATCATCTTAGCGGC 57.690 47.619 16.06 0.00 33.59 6.53
80 81 3.525537 AGTTGTAACCGCAGATGATCTG 58.474 45.455 17.83 17.83 46.90 2.90
81 82 3.895232 AGTTGTAACCGCAGATGATCT 57.105 42.857 0.00 0.00 0.00 2.75
82 83 5.109903 AGTAAGTTGTAACCGCAGATGATC 58.890 41.667 0.00 0.00 0.00 2.92
83 84 5.086104 AGTAAGTTGTAACCGCAGATGAT 57.914 39.130 0.00 0.00 0.00 2.45
84 85 4.530710 AGTAAGTTGTAACCGCAGATGA 57.469 40.909 0.00 0.00 0.00 2.92
85 86 5.408356 ACTAGTAAGTTGTAACCGCAGATG 58.592 41.667 0.00 0.00 29.00 2.90
86 87 5.656213 ACTAGTAAGTTGTAACCGCAGAT 57.344 39.130 0.00 0.00 29.00 2.90
87 88 5.473162 TGTACTAGTAAGTTGTAACCGCAGA 59.527 40.000 3.61 0.00 37.15 4.26
88 89 5.702865 TGTACTAGTAAGTTGTAACCGCAG 58.297 41.667 3.61 0.00 37.15 5.18
89 90 5.703978 TGTACTAGTAAGTTGTAACCGCA 57.296 39.130 3.61 0.00 37.15 5.69
90 91 6.152379 ACTTGTACTAGTAAGTTGTAACCGC 58.848 40.000 8.27 0.00 37.15 5.68
91 92 9.118236 GTTACTTGTACTAGTAAGTTGTAACCG 57.882 37.037 24.24 5.99 40.31 4.44
92 93 9.965824 TGTTACTTGTACTAGTAAGTTGTAACC 57.034 33.333 24.24 13.61 40.31 2.85
146 147 1.818674 CCGTCTCCCAAAAGGAAATGG 59.181 52.381 0.00 0.00 46.94 3.16
147 148 1.202348 GCCGTCTCCCAAAAGGAAATG 59.798 52.381 0.00 0.00 46.94 2.32
148 149 1.203001 TGCCGTCTCCCAAAAGGAAAT 60.203 47.619 0.00 0.00 46.94 2.17
149 150 0.183971 TGCCGTCTCCCAAAAGGAAA 59.816 50.000 0.00 0.00 46.94 3.13
150 151 0.250727 CTGCCGTCTCCCAAAAGGAA 60.251 55.000 0.00 0.00 46.94 3.36
151 152 1.374947 CTGCCGTCTCCCAAAAGGA 59.625 57.895 0.00 0.00 44.91 3.36
152 153 2.335712 GCTGCCGTCTCCCAAAAGG 61.336 63.158 0.00 0.00 0.00 3.11
153 154 2.335712 GGCTGCCGTCTCCCAAAAG 61.336 63.158 1.35 0.00 0.00 2.27
154 155 2.282180 GGCTGCCGTCTCCCAAAA 60.282 61.111 1.35 0.00 0.00 2.44
155 156 4.697756 CGGCTGCCGTCTCCCAAA 62.698 66.667 31.72 0.00 42.73 3.28
186 187 4.195334 CATGCCCCCGGGAGAAGG 62.195 72.222 26.32 16.53 37.50 3.46
187 188 4.195334 CCATGCCCCCGGGAGAAG 62.195 72.222 26.32 8.91 37.50 2.85
233 234 4.195334 CTTCTCCCGGGGGCATGG 62.195 72.222 23.50 3.80 34.68 3.66
234 235 4.195334 CCTTCTCCCGGGGGCATG 62.195 72.222 23.50 10.48 34.68 4.06
239 240 1.847968 ATATGGCCTTCTCCCGGGG 60.848 63.158 23.50 12.05 0.00 5.73
240 241 1.376466 CATATGGCCTTCTCCCGGG 59.624 63.158 16.85 16.85 0.00 5.73
241 242 1.376466 CCATATGGCCTTCTCCCGG 59.624 63.158 9.29 0.00 0.00 5.73
242 243 0.250467 CACCATATGGCCTTCTCCCG 60.250 60.000 22.18 0.00 39.32 5.14
243 244 0.538287 GCACCATATGGCCTTCTCCC 60.538 60.000 22.18 0.00 39.32 4.30
244 245 3.027419 GCACCATATGGCCTTCTCC 57.973 57.895 22.18 0.00 39.32 3.71
252 253 2.124362 TGGCGTGGCACCATATGG 60.124 61.111 20.68 20.68 42.17 2.74
456 466 1.152546 GAGGGAGAGAGAGGGAGGC 60.153 68.421 0.00 0.00 0.00 4.70
466 476 4.398044 GTCAAACTGTAGAGAGAGGGAGAG 59.602 50.000 0.00 0.00 0.00 3.20
483 493 3.771577 TCCTTCCTTGAGGAGTCAAAC 57.228 47.619 0.00 0.00 46.36 2.93
734 748 2.363925 GGAGCGGGGTGAGGTAGT 60.364 66.667 0.00 0.00 0.00 2.73
735 749 3.155167 GGGAGCGGGGTGAGGTAG 61.155 72.222 0.00 0.00 0.00 3.18
736 750 3.674050 GAGGGAGCGGGGTGAGGTA 62.674 68.421 0.00 0.00 0.00 3.08
768 783 1.079750 GGTGAGGTGGAGACGAAGC 60.080 63.158 0.00 0.00 0.00 3.86
813 833 1.429148 GCCGCTGCTACGCTACAAAT 61.429 55.000 0.00 0.00 33.53 2.32
1176 1230 0.881118 AACAACCATGCGATCCACAC 59.119 50.000 0.00 0.00 0.00 3.82
1199 1253 3.058155 ACATCGATCGAGGGATTTAGTCG 60.058 47.826 30.54 6.20 31.51 4.18
1227 1281 0.894835 TCTTGCTACACCGCATCAGA 59.105 50.000 0.00 0.00 40.04 3.27
1722 1776 2.047274 ATGTTCGCGGTGGTGAGG 60.047 61.111 6.13 0.00 33.51 3.86
1958 2012 1.452145 GCCATGGTGGTCGTTGTTGT 61.452 55.000 14.67 0.00 40.46 3.32
2042 2099 4.506758 GACCTTAATAACTTGGCACGGTA 58.493 43.478 0.00 0.00 0.00 4.02
2058 2115 3.884091 GAGCTAGGAGAACATCGACCTTA 59.116 47.826 0.00 0.00 32.46 2.69
2072 2129 1.333931 CATCAGTAACGCGAGCTAGGA 59.666 52.381 15.93 3.07 0.00 2.94
2133 2192 6.155049 ACCGAGGTACTACTAGAGGATCTATC 59.845 46.154 0.00 0.00 43.20 2.08
2230 2293 1.078989 ACTAGCTACCACAACCTCCCT 59.921 52.381 0.00 0.00 0.00 4.20
2294 2363 4.948341 AGTACAAAACCCAAAACCCATC 57.052 40.909 0.00 0.00 0.00 3.51
2400 2470 8.603242 AATTCGGCATACTGGTTAATTAGTAG 57.397 34.615 7.54 0.00 33.32 2.57
2401 2471 8.426489 AGAATTCGGCATACTGGTTAATTAGTA 58.574 33.333 0.00 4.80 34.23 1.82
2402 2472 7.226720 CAGAATTCGGCATACTGGTTAATTAGT 59.773 37.037 0.00 1.07 0.00 2.24
2480 2567 6.032094 GCAATTGACATACTGACCATGAAAG 58.968 40.000 10.34 0.00 0.00 2.62
2503 2590 3.503748 GGTGGAAATATATGACAGGCAGC 59.496 47.826 0.00 0.00 0.00 5.25
2541 2628 1.460273 TTTGGAAAAGGGACGCAGCC 61.460 55.000 0.00 0.00 0.00 4.85
2542 2629 0.387565 TTTTGGAAAAGGGACGCAGC 59.612 50.000 0.00 0.00 0.00 5.25
2543 2630 4.718940 ATATTTTGGAAAAGGGACGCAG 57.281 40.909 0.00 0.00 0.00 5.18
2544 2631 9.747898 ATATATATATTTTGGAAAAGGGACGCA 57.252 29.630 0.00 0.00 0.00 5.24
2597 2684 4.881850 GTGCAGGTACTAGTATTTGGCATT 59.118 41.667 18.19 0.00 36.02 3.56
2717 2812 0.693049 ACCACTCCGAGGAAGCAAAT 59.307 50.000 0.00 0.00 0.00 2.32
2757 2852 1.503784 TCCTCTAATCACCCGAGGGAT 59.496 52.381 16.26 0.00 43.54 3.85
2774 2869 4.927267 TGATCAATTGGTACCAACTCCT 57.073 40.909 29.35 14.54 38.88 3.69
2799 2894 9.553064 AAATACATGCACCAAGTTTAATTTCAA 57.447 25.926 0.00 0.00 0.00 2.69
2807 2902 7.721402 TGTAGAAAAATACATGCACCAAGTTT 58.279 30.769 0.00 0.00 30.76 2.66
2808 2903 7.283625 TGTAGAAAAATACATGCACCAAGTT 57.716 32.000 0.00 0.00 30.76 2.66
2818 2913 8.303876 AGCCGAAACAATTGTAGAAAAATACAT 58.696 29.630 12.39 0.00 35.65 2.29
2837 2932 5.995282 TCTTGAACAGATTTAGAAGCCGAAA 59.005 36.000 0.00 0.00 0.00 3.46
2869 2964 6.037830 CCGGTTGTTCTCAGACTTTTTAGAAA 59.962 38.462 0.00 0.00 30.24 2.52
2872 2967 4.814771 ACCGGTTGTTCTCAGACTTTTTAG 59.185 41.667 0.00 0.00 0.00 1.85
2875 2970 3.277142 ACCGGTTGTTCTCAGACTTTT 57.723 42.857 0.00 0.00 0.00 2.27
2879 2974 5.334646 GGAAAAATACCGGTTGTTCTCAGAC 60.335 44.000 15.04 0.00 0.00 3.51
2891 2986 3.857093 CGCATGAAAAGGAAAAATACCGG 59.143 43.478 0.00 0.00 0.00 5.28
2893 2988 3.303229 CGCGCATGAAAAGGAAAAATACC 59.697 43.478 8.75 0.00 0.00 2.73
2894 2989 4.162812 TCGCGCATGAAAAGGAAAAATAC 58.837 39.130 8.75 0.00 0.00 1.89
2910 3005 1.355796 CCCGTGTTAATTCTCGCGCA 61.356 55.000 8.75 0.00 36.45 6.09
2914 3009 3.930229 TGTTCATCCCGTGTTAATTCTCG 59.070 43.478 0.00 0.00 0.00 4.04
2921 3016 7.388437 AGTAATACTTTGTTCATCCCGTGTTA 58.612 34.615 0.00 0.00 0.00 2.41
2925 3020 7.179076 AGTAGTAATACTTTGTTCATCCCGT 57.821 36.000 0.00 0.00 0.00 5.28
2927 3022 6.990939 GGGAGTAGTAATACTTTGTTCATCCC 59.009 42.308 4.06 4.50 0.00 3.85
2928 3023 7.494952 GTGGGAGTAGTAATACTTTGTTCATCC 59.505 40.741 4.06 0.00 0.00 3.51
2939 3034 5.835113 TTACACGGTGGGAGTAGTAATAC 57.165 43.478 13.48 0.00 0.00 1.89
2953 3048 7.859325 ATGCTCTTATATTTGTTTACACGGT 57.141 32.000 0.00 0.00 0.00 4.83
2991 3086 9.613428 CATGTTGTACTCCCTTTAGATCATTAA 57.387 33.333 0.00 0.00 0.00 1.40
2992 3087 8.210946 CCATGTTGTACTCCCTTTAGATCATTA 58.789 37.037 0.00 0.00 0.00 1.90
2993 3088 7.056635 CCATGTTGTACTCCCTTTAGATCATT 58.943 38.462 0.00 0.00 0.00 2.57
2994 3089 6.158695 ACCATGTTGTACTCCCTTTAGATCAT 59.841 38.462 0.00 0.00 0.00 2.45
2995 3090 5.487488 ACCATGTTGTACTCCCTTTAGATCA 59.513 40.000 0.00 0.00 0.00 2.92
2996 3091 5.817816 CACCATGTTGTACTCCCTTTAGATC 59.182 44.000 0.00 0.00 0.00 2.75
2997 3092 5.487488 TCACCATGTTGTACTCCCTTTAGAT 59.513 40.000 0.00 0.00 0.00 1.98
2998 3093 4.841813 TCACCATGTTGTACTCCCTTTAGA 59.158 41.667 0.00 0.00 0.00 2.10
2999 3094 5.160607 TCACCATGTTGTACTCCCTTTAG 57.839 43.478 0.00 0.00 0.00 1.85
3000 3095 4.564821 GCTCACCATGTTGTACTCCCTTTA 60.565 45.833 0.00 0.00 0.00 1.85
3001 3096 3.810743 GCTCACCATGTTGTACTCCCTTT 60.811 47.826 0.00 0.00 0.00 3.11
3002 3097 2.290323 GCTCACCATGTTGTACTCCCTT 60.290 50.000 0.00 0.00 0.00 3.95
3003 3098 1.279271 GCTCACCATGTTGTACTCCCT 59.721 52.381 0.00 0.00 0.00 4.20
3004 3099 1.739067 GCTCACCATGTTGTACTCCC 58.261 55.000 0.00 0.00 0.00 4.30
3005 3100 1.337823 ACGCTCACCATGTTGTACTCC 60.338 52.381 0.00 0.00 0.00 3.85
3006 3101 2.080286 ACGCTCACCATGTTGTACTC 57.920 50.000 0.00 0.00 0.00 2.59
3007 3102 3.447586 AGATACGCTCACCATGTTGTACT 59.552 43.478 0.00 0.00 0.00 2.73
3008 3103 3.782046 AGATACGCTCACCATGTTGTAC 58.218 45.455 0.00 0.00 0.00 2.90
3009 3104 4.885325 TCTAGATACGCTCACCATGTTGTA 59.115 41.667 0.00 0.00 0.00 2.41
3010 3105 3.699538 TCTAGATACGCTCACCATGTTGT 59.300 43.478 0.00 0.00 0.00 3.32
3011 3106 4.307443 TCTAGATACGCTCACCATGTTG 57.693 45.455 0.00 0.00 0.00 3.33
3012 3107 5.127693 GATCTAGATACGCTCACCATGTT 57.872 43.478 4.89 0.00 0.00 2.71
3013 3108 4.775058 GATCTAGATACGCTCACCATGT 57.225 45.455 4.89 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.