Multiple sequence alignment - TraesCS7D01G525900

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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 TraesCS7D01G525900 chr7D 100.000 5147 0 0 1 5147 621315222 621310076 0.000000e+00 9505.0
1 TraesCS7D01G525900 chr7D 89.751 361 28 7 293 649 621310720 621310365 2.190000e-123 453.0
2 TraesCS7D01G525900 chr7D 80.402 398 58 16 1855 2241 606108884 606109272 8.440000e-73 285.0
3 TraesCS7D01G525900 chr7D 89.385 179 16 1 1 176 622089140 622089318 6.710000e-54 222.0
4 TraesCS7D01G525900 chr7D 73.984 492 112 13 3676 4160 606703780 606704262 8.800000e-43 185.0
5 TraesCS7D01G525900 chr7D 79.878 164 18 9 1658 1814 606303218 606303373 7.050000e-19 106.0
6 TraesCS7D01G525900 chr7A 95.492 5036 181 25 1 5024 716502532 716507533 0.000000e+00 8000.0
7 TraesCS7D01G525900 chr7A 94.784 4640 176 31 406 5024 716608823 716604229 0.000000e+00 7167.0
8 TraesCS7D01G525900 chr7A 89.106 358 31 6 296 649 716604749 716604396 6.120000e-119 438.0
9 TraesCS7D01G525900 chr7A 88.827 358 32 6 296 649 716507013 716507366 2.850000e-117 433.0
10 TraesCS7D01G525900 chr7A 79.385 553 88 16 939 1470 699019023 699019570 2.930000e-97 366.0
11 TraesCS7D01G525900 chr7A 78.455 492 83 18 2150 2637 716374348 716373876 3.010000e-77 300.0
12 TraesCS7D01G525900 chr7A 80.151 398 59 17 1855 2241 697825528 697825916 3.920000e-71 279.0
13 TraesCS7D01G525900 chr7A 95.556 45 2 0 1 45 716608858 716608814 7.150000e-09 73.1
14 TraesCS7D01G525900 chr7B 95.340 5043 178 20 1 5024 718572558 718577562 0.000000e+00 7958.0
15 TraesCS7D01G525900 chr7B 95.160 3120 102 13 1 3102 718596048 718599136 0.000000e+00 4879.0
16 TraesCS7D01G525900 chr7B 96.283 2287 79 3 2739 5024 718508683 718510964 0.000000e+00 3747.0
17 TraesCS7D01G525900 chr7B 91.620 358 25 4 4503 4858 718572853 718573207 1.670000e-134 490.0
18 TraesCS7D01G525900 chr7B 91.620 358 25 4 4503 4858 718596343 718596697 1.670000e-134 490.0
19 TraesCS7D01G525900 chr7B 80.631 444 63 18 1810 2239 690032349 690032783 6.430000e-84 322.0
20 TraesCS7D01G525900 chr7B 75.676 481 109 7 3686 4163 690919074 690919549 3.100000e-57 233.0
21 TraesCS7D01G525900 chr7B 86.034 179 19 4 1 176 719869073 719869248 2.450000e-43 187.0
22 TraesCS7D01G525900 chrUn 96.283 2287 79 3 2739 5024 293895833 293898114 0.000000e+00 3747.0
23 TraesCS7D01G525900 chrUn 94.158 2191 83 20 1 2176 329802165 329800005 0.000000e+00 3295.0
24 TraesCS7D01G525900 chrUn 96.953 1411 43 0 2739 4149 270666414 270667824 0.000000e+00 2368.0
25 TraesCS7D01G525900 chrUn 96.359 1181 32 5 1006 2176 429197404 429198583 0.000000e+00 1932.0
26 TraesCS7D01G525900 chrUn 92.169 996 45 4 1 992 384893740 384892774 0.000000e+00 1376.0
27 TraesCS7D01G525900 chrUn 74.858 1412 280 48 2012 3402 33121126 33122483 5.780000e-159 571.0
28 TraesCS7D01G525900 chrUn 92.179 358 23 4 4503 4858 329801870 329801516 7.690000e-138 501.0
29 TraesCS7D01G525900 chrUn 92.179 358 23 4 4503 4858 384893445 384893091 7.690000e-138 501.0
30 TraesCS7D01G525900 chr3A 74.663 1409 289 38 2012 3402 704579253 704580611 3.480000e-156 562.0
31 TraesCS7D01G525900 chr3A 74.593 1413 286 47 2012 3402 704778819 704777458 2.090000e-153 553.0
32 TraesCS7D01G525900 chr3A 78.444 617 95 24 877 1470 704695785 704695184 8.140000e-98 368.0
33 TraesCS7D01G525900 chr3A 78.010 623 99 23 871 1470 704571196 704571803 1.760000e-94 357.0
34 TraesCS7D01G525900 chr3A 75.154 487 99 16 3686 4162 704777276 704776802 5.220000e-50 209.0
35 TraesCS7D01G525900 chr5D 87.371 483 48 8 681 1157 459578439 459578914 4.530000e-150 542.0
36 TraesCS7D01G525900 chr5D 94.340 53 3 0 123 175 459578308 459578360 1.190000e-11 82.4
37 TraesCS7D01G525900 chr5B 85.361 485 54 10 681 1159 563716746 563717219 2.150000e-133 486.0
38 TraesCS7D01G525900 chr5B 85.155 485 55 10 681 1159 563736820 563737293 1.000000e-131 481.0
39 TraesCS7D01G525900 chr5B 94.340 53 3 0 123 175 563865215 563865267 1.190000e-11 82.4


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 TraesCS7D01G525900 chr7D 621310076 621315222 5146 True 9505.0 9505 100.0000 1 5147 1 chr7D.!!$R1 5146
1 TraesCS7D01G525900 chr7A 716604229 716608823 4594 True 7167.0 7167 94.7840 406 5024 1 chr7A.!!$R2 4618
2 TraesCS7D01G525900 chr7A 716502532 716507533 5001 False 4216.5 8000 92.1595 1 5024 2 chr7A.!!$F3 5023
3 TraesCS7D01G525900 chr7A 699019023 699019570 547 False 366.0 366 79.3850 939 1470 1 chr7A.!!$F2 531
4 TraesCS7D01G525900 chr7B 718572558 718577562 5004 False 7958.0 7958 95.3400 1 5024 1 chr7B.!!$F4 5023
5 TraesCS7D01G525900 chr7B 718508683 718510964 2281 False 3747.0 3747 96.2830 2739 5024 1 chr7B.!!$F3 2285
6 TraesCS7D01G525900 chr7B 718596048 718599136 3088 False 2684.5 4879 93.3900 1 4858 2 chr7B.!!$F7 4857
7 TraesCS7D01G525900 chrUn 293895833 293898114 2281 False 3747.0 3747 96.2830 2739 5024 1 chrUn.!!$F3 2285
8 TraesCS7D01G525900 chrUn 270666414 270667824 1410 False 2368.0 2368 96.9530 2739 4149 1 chrUn.!!$F2 1410
9 TraesCS7D01G525900 chrUn 429197404 429198583 1179 False 1932.0 1932 96.3590 1006 2176 1 chrUn.!!$F4 1170
10 TraesCS7D01G525900 chrUn 329800005 329802165 2160 True 1898.0 3295 93.1685 1 4858 2 chrUn.!!$R1 4857
11 TraesCS7D01G525900 chrUn 384892774 384893740 966 True 938.5 1376 92.1740 1 4858 2 chrUn.!!$R2 4857
12 TraesCS7D01G525900 chrUn 33121126 33122483 1357 False 571.0 571 74.8580 2012 3402 1 chrUn.!!$F1 1390
13 TraesCS7D01G525900 chr3A 704579253 704580611 1358 False 562.0 562 74.6630 2012 3402 1 chr3A.!!$F2 1390
14 TraesCS7D01G525900 chr3A 704776802 704778819 2017 True 381.0 553 74.8735 2012 4162 2 chr3A.!!$R2 2150
15 TraesCS7D01G525900 chr3A 704695184 704695785 601 True 368.0 368 78.4440 877 1470 1 chr3A.!!$R1 593
16 TraesCS7D01G525900 chr3A 704571196 704571803 607 False 357.0 357 78.0100 871 1470 1 chr3A.!!$F1 599
17 TraesCS7D01G525900 chr5D 459578308 459578914 606 False 312.2 542 90.8555 123 1157 2 chr5D.!!$F1 1034

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
857 872 0.178068 GCGAGGAAGCCATTGTAGGA 59.822 55.000 0.00 0.0 0.00 2.94 F
933 953 1.411930 GGGTTTGTGTTGGTTACCCCT 60.412 52.381 0.00 0.0 42.13 4.79 F
2104 2154 2.026915 TGCAGTGCTATCTGTGGATTGT 60.027 45.455 17.60 0.0 37.70 2.71 F
2409 2460 1.834188 CCAAGGGTGGTATGGACAAC 58.166 55.000 0.00 0.0 40.42 3.32 F
3257 3361 0.953960 AAACTGTCGGATGCGGGAAC 60.954 55.000 6.82 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2140 2190 0.037697 TCACCAAATAGTCGCACGCT 60.038 50.000 0.00 0.0 0.00 5.07 R
2264 2315 3.685272 GGCTGCACTCTATCATCATCATG 59.315 47.826 0.50 0.0 0.00 3.07 R
3257 3361 0.379669 GTCAATGGAGCCAGCGAATG 59.620 55.000 0.00 0.0 0.00 2.67 R
3867 4020 0.877071 CGCCATCAAGCTTGTCAGTT 59.123 50.000 25.19 4.8 0.00 3.16 R
4972 5130 0.171455 GGCAGACAGAGAGTGTACGG 59.829 60.000 0.00 0.0 40.56 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
53 54 5.652891 AGTAAAAAGACGCTCTCTCCATCTA 59.347 40.000 0.00 0.00 0.00 1.98
120 124 4.464069 TGGTGGGAAAACAACAAAAGAG 57.536 40.909 0.00 0.00 34.60 2.85
145 149 6.636454 AGATATAAAACAGGAACAGACCCA 57.364 37.500 0.00 0.00 0.00 4.51
205 209 6.660949 CACCTCTTTCAAAGAAATATCTGGGT 59.339 38.462 0.48 0.00 37.02 4.51
378 382 1.686052 GGTGAGAATCGAGATGAGGCT 59.314 52.381 0.00 0.00 38.61 4.58
388 392 3.321111 TCGAGATGAGGCTGGGTATTAAC 59.679 47.826 0.00 0.00 0.00 2.01
427 433 5.648092 CCAAGACCCTCTTTTGTAATACAGG 59.352 44.000 0.00 0.00 33.78 4.00
468 474 3.379372 CAGCATCGGGAGAAAACATCAAT 59.621 43.478 0.00 0.00 45.37 2.57
530 536 5.782893 TTTGACAATGGACGGAAAGAAAT 57.217 34.783 0.00 0.00 0.00 2.17
857 872 0.178068 GCGAGGAAGCCATTGTAGGA 59.822 55.000 0.00 0.00 0.00 2.94
873 892 7.614192 CCATTGTAGGAGGTAAAACAATAAGGT 59.386 37.037 0.00 0.00 39.80 3.50
908 928 1.619654 TGGGTTGTGCTCTTGATTGG 58.380 50.000 0.00 0.00 0.00 3.16
933 953 1.411930 GGGTTTGTGTTGGTTACCCCT 60.412 52.381 0.00 0.00 42.13 4.79
993 1014 3.534357 TTGCCAGGTGGGAAGAATTTA 57.466 42.857 0.00 0.00 40.75 1.40
1098 1120 2.955402 GCTGTGGACGACGACTCT 59.045 61.111 0.00 0.00 0.00 3.24
1560 1609 8.687824 AATTTTGGAGAAAGTATACAATTGCG 57.312 30.769 5.05 0.00 0.00 4.85
1836 1885 7.605410 TGTGCTATAGTTACTTTTTAGCCAC 57.395 36.000 14.56 13.06 35.52 5.01
1964 2013 2.634982 TTTGCTTCACCGATTGCATC 57.365 45.000 0.00 0.00 35.27 3.91
2104 2154 2.026915 TGCAGTGCTATCTGTGGATTGT 60.027 45.455 17.60 0.00 37.70 2.71
2140 2190 3.053768 TGATGAAGGGCATAACACATGGA 60.054 43.478 0.00 0.00 37.34 3.41
2264 2315 6.645700 ACAACAACAACAACAACAATGATC 57.354 33.333 0.00 0.00 0.00 2.92
2409 2460 1.834188 CCAAGGGTGGTATGGACAAC 58.166 55.000 0.00 0.00 40.42 3.32
2643 2695 8.573035 GTCATCTACAGGTTTATTTTTGACCAA 58.427 33.333 0.00 0.00 35.89 3.67
2749 2803 6.152661 TGGGGAAACTATCAATGTAAGCTTTG 59.847 38.462 3.20 0.00 0.00 2.77
2774 2828 6.765989 GGTAATGCACCTAACATGAAGATGTA 59.234 38.462 0.00 0.00 42.15 2.29
3098 3193 5.125257 TCATGCGTAACCATGAACATGAAAT 59.875 36.000 15.21 4.77 46.18 2.17
3257 3361 0.953960 AAACTGTCGGATGCGGGAAC 60.954 55.000 6.82 0.00 0.00 3.62
3364 3468 1.072159 GGCGATTCCTATGCTGGCT 59.928 57.895 0.00 0.00 0.00 4.75
3495 3599 6.009908 TCTCCCATCTCATCAAATGTGAAT 57.990 37.500 0.00 0.00 37.30 2.57
3806 3959 6.226052 TCTCAATGACACATACAGATATGGC 58.774 40.000 0.00 0.00 42.32 4.40
3858 4011 5.139727 TCCAACCATCAGACAGAAAATGTT 58.860 37.500 0.00 0.00 44.17 2.71
3861 4014 6.016360 CCAACCATCAGACAGAAAATGTTGTA 60.016 38.462 0.00 0.00 44.17 2.41
3867 4020 7.977789 TCAGACAGAAAATGTTGTAGCAATA 57.022 32.000 0.00 0.00 44.17 1.90
3985 4138 4.102210 TCAAGGACTTCTCATGGGATGATC 59.898 45.833 15.03 8.50 38.85 2.92
4046 4200 4.096382 CGTTGGCTTTTATCTAGGCATTGT 59.904 41.667 0.00 0.00 45.97 2.71
4165 4322 8.268878 AGAATAGTTCTGTCTATTAGCCCAAT 57.731 34.615 0.00 0.00 39.69 3.16
4175 4332 3.492102 ATTAGCCCAATCTATGCACGT 57.508 42.857 0.00 0.00 0.00 4.49
4219 4376 6.494893 TGGCAACTTGTACACTAATCATTC 57.505 37.500 0.00 0.00 37.61 2.67
4233 4390 5.700832 ACTAATCATTCGTCTGTTCTTGCAA 59.299 36.000 0.00 0.00 0.00 4.08
4288 4445 1.915141 AGTTGGAAGCATGGTCTTGG 58.085 50.000 0.00 0.00 0.00 3.61
4315 4472 8.902806 TGGGTAATCTATTTTACATGAGCTTTG 58.097 33.333 0.00 0.00 34.42 2.77
4491 4648 0.815615 GCCTTAGGACCCATGCTTCG 60.816 60.000 0.69 0.00 0.00 3.79
4595 4752 3.260884 TGAGATGAGGCCGGGTATTAATC 59.739 47.826 2.18 0.00 0.00 1.75
4637 4794 8.375493 AGACCCTCTTTTGTAATACACAGATA 57.625 34.615 0.00 0.00 38.72 1.98
4736 4893 6.705381 TGACATTTGACAATGGAATGAAAACC 59.295 34.615 11.32 0.00 43.82 3.27
4927 5085 2.552315 AGGGCACTACATTTTCACGTTG 59.448 45.455 0.00 0.00 0.00 4.10
4934 5092 0.709467 CATTTTCACGTTGCCATGCG 59.291 50.000 0.00 0.00 0.00 4.73
4947 5105 1.120530 CCATGCGAGTAGGTAGGGTT 58.879 55.000 0.00 0.00 0.00 4.11
4972 5130 0.524392 CTGACCGCTGAGACGATGAC 60.524 60.000 0.00 0.00 34.06 3.06
4985 5143 2.460243 CGATGACCGTACACTCTCTG 57.540 55.000 0.00 0.00 0.00 3.35
4987 5145 2.223066 CGATGACCGTACACTCTCTGTC 60.223 54.545 0.00 0.00 33.91 3.51
4992 5150 0.171455 CGTACACTCTCTGTCTGCCC 59.829 60.000 0.00 0.00 33.91 5.36
5017 5175 5.707764 GGTCAAAGGAAGTAAGAAGCAAGAT 59.292 40.000 0.00 0.00 0.00 2.40
5020 5178 4.495690 AGGAAGTAAGAAGCAAGATCCC 57.504 45.455 0.00 0.00 0.00 3.85
5021 5179 4.107820 AGGAAGTAAGAAGCAAGATCCCT 58.892 43.478 0.00 0.00 0.00 4.20
5024 5182 3.730269 AGTAAGAAGCAAGATCCCTCCT 58.270 45.455 0.00 0.00 0.00 3.69
5025 5183 3.709141 AGTAAGAAGCAAGATCCCTCCTC 59.291 47.826 0.00 0.00 0.00 3.71
5026 5184 2.566708 AGAAGCAAGATCCCTCCTCT 57.433 50.000 0.00 0.00 0.00 3.69
5027 5185 2.844369 AGAAGCAAGATCCCTCCTCTT 58.156 47.619 0.00 0.00 33.25 2.85
5028 5186 2.771372 AGAAGCAAGATCCCTCCTCTTC 59.229 50.000 0.00 0.00 30.60 2.87
5029 5187 1.118838 AGCAAGATCCCTCCTCTTCG 58.881 55.000 0.00 0.00 30.60 3.79
5030 5188 0.531753 GCAAGATCCCTCCTCTTCGC 60.532 60.000 0.00 0.00 30.60 4.70
5031 5189 0.105778 CAAGATCCCTCCTCTTCGCC 59.894 60.000 0.00 0.00 30.60 5.54
5032 5190 0.325671 AAGATCCCTCCTCTTCGCCA 60.326 55.000 0.00 0.00 0.00 5.69
5033 5191 0.105246 AGATCCCTCCTCTTCGCCAT 60.105 55.000 0.00 0.00 0.00 4.40
5034 5192 1.148027 AGATCCCTCCTCTTCGCCATA 59.852 52.381 0.00 0.00 0.00 2.74
5035 5193 1.548269 GATCCCTCCTCTTCGCCATAG 59.452 57.143 0.00 0.00 0.00 2.23
5036 5194 0.261991 TCCCTCCTCTTCGCCATAGT 59.738 55.000 0.00 0.00 0.00 2.12
5037 5195 0.676736 CCCTCCTCTTCGCCATAGTC 59.323 60.000 0.00 0.00 0.00 2.59
5038 5196 0.676736 CCTCCTCTTCGCCATAGTCC 59.323 60.000 0.00 0.00 0.00 3.85
5039 5197 1.403814 CTCCTCTTCGCCATAGTCCA 58.596 55.000 0.00 0.00 0.00 4.02
5040 5198 1.967066 CTCCTCTTCGCCATAGTCCAT 59.033 52.381 0.00 0.00 0.00 3.41
5041 5199 2.366916 CTCCTCTTCGCCATAGTCCATT 59.633 50.000 0.00 0.00 0.00 3.16
5042 5200 3.572642 TCCTCTTCGCCATAGTCCATTA 58.427 45.455 0.00 0.00 0.00 1.90
5043 5201 3.321111 TCCTCTTCGCCATAGTCCATTAC 59.679 47.826 0.00 0.00 0.00 1.89
5044 5202 3.069586 CCTCTTCGCCATAGTCCATTACA 59.930 47.826 0.00 0.00 0.00 2.41
5045 5203 4.442893 CCTCTTCGCCATAGTCCATTACAA 60.443 45.833 0.00 0.00 0.00 2.41
5046 5204 5.092554 TCTTCGCCATAGTCCATTACAAA 57.907 39.130 0.00 0.00 0.00 2.83
5047 5205 5.680619 TCTTCGCCATAGTCCATTACAAAT 58.319 37.500 0.00 0.00 0.00 2.32
5048 5206 6.119536 TCTTCGCCATAGTCCATTACAAATT 58.880 36.000 0.00 0.00 0.00 1.82
5049 5207 6.601613 TCTTCGCCATAGTCCATTACAAATTT 59.398 34.615 0.00 0.00 0.00 1.82
5050 5208 7.771361 TCTTCGCCATAGTCCATTACAAATTTA 59.229 33.333 0.00 0.00 0.00 1.40
5051 5209 7.254227 TCGCCATAGTCCATTACAAATTTAC 57.746 36.000 0.00 0.00 0.00 2.01
5052 5210 6.824196 TCGCCATAGTCCATTACAAATTTACA 59.176 34.615 0.00 0.00 0.00 2.41
5053 5211 7.337184 TCGCCATAGTCCATTACAAATTTACAA 59.663 33.333 0.00 0.00 0.00 2.41
5054 5212 8.134895 CGCCATAGTCCATTACAAATTTACAAT 58.865 33.333 0.00 0.00 0.00 2.71
5055 5213 9.463443 GCCATAGTCCATTACAAATTTACAATC 57.537 33.333 0.00 0.00 0.00 2.67
5056 5214 9.663904 CCATAGTCCATTACAAATTTACAATCG 57.336 33.333 0.00 0.00 0.00 3.34
5059 5217 7.461107 AGTCCATTACAAATTTACAATCGTCG 58.539 34.615 0.00 0.00 0.00 5.12
5060 5218 6.193959 GTCCATTACAAATTTACAATCGTCGC 59.806 38.462 0.00 0.00 0.00 5.19
5061 5219 5.454232 CCATTACAAATTTACAATCGTCGCC 59.546 40.000 0.00 0.00 0.00 5.54
5062 5220 5.608676 TTACAAATTTACAATCGTCGCCA 57.391 34.783 0.00 0.00 0.00 5.69
5063 5221 4.695217 ACAAATTTACAATCGTCGCCAT 57.305 36.364 0.00 0.00 0.00 4.40
5064 5222 4.411327 ACAAATTTACAATCGTCGCCATG 58.589 39.130 0.00 0.00 0.00 3.66
5065 5223 4.083003 ACAAATTTACAATCGTCGCCATGT 60.083 37.500 0.00 0.00 0.00 3.21
5066 5224 3.673746 ATTTACAATCGTCGCCATGTG 57.326 42.857 7.39 0.00 0.00 3.21
5067 5225 2.371910 TTACAATCGTCGCCATGTGA 57.628 45.000 7.39 0.00 0.00 3.58
5068 5226 2.595124 TACAATCGTCGCCATGTGAT 57.405 45.000 7.39 0.00 0.00 3.06
5069 5227 1.290203 ACAATCGTCGCCATGTGATC 58.710 50.000 0.00 0.00 0.00 2.92
5070 5228 0.583438 CAATCGTCGCCATGTGATCC 59.417 55.000 0.00 0.00 0.00 3.36
5071 5229 0.465705 AATCGTCGCCATGTGATCCT 59.534 50.000 0.00 0.00 0.00 3.24
5072 5230 0.465705 ATCGTCGCCATGTGATCCTT 59.534 50.000 0.00 0.00 0.00 3.36
5073 5231 0.249120 TCGTCGCCATGTGATCCTTT 59.751 50.000 0.00 0.00 0.00 3.11
5074 5232 1.086696 CGTCGCCATGTGATCCTTTT 58.913 50.000 0.00 0.00 0.00 2.27
5075 5233 1.468520 CGTCGCCATGTGATCCTTTTT 59.531 47.619 0.00 0.00 0.00 1.94
5091 5249 2.248280 TTTTTCTCTGCTGCGGTACA 57.752 45.000 8.55 0.00 0.00 2.90
5100 5258 2.731721 TGCGGTACAGCAACGACG 60.732 61.111 18.65 0.00 45.06 5.12
5101 5259 3.475774 GCGGTACAGCAACGACGG 61.476 66.667 13.42 0.00 37.05 4.79
5102 5260 2.049802 CGGTACAGCAACGACGGT 60.050 61.111 0.00 0.00 0.00 4.83
5103 5261 2.369629 CGGTACAGCAACGACGGTG 61.370 63.158 8.96 8.96 40.25 4.94
5104 5262 1.007038 GGTACAGCAACGACGGTGA 60.007 57.895 18.96 0.00 37.81 4.02
5105 5263 0.389426 GGTACAGCAACGACGGTGAT 60.389 55.000 18.96 7.72 37.81 3.06
5106 5264 0.713883 GTACAGCAACGACGGTGATG 59.286 55.000 28.05 28.05 37.81 3.07
5107 5265 0.389296 TACAGCAACGACGGTGATGG 60.389 55.000 31.88 15.94 37.81 3.51
5108 5266 1.374125 CAGCAACGACGGTGATGGA 60.374 57.895 22.89 0.00 36.48 3.41
5109 5267 0.740868 CAGCAACGACGGTGATGGAT 60.741 55.000 22.89 0.00 36.48 3.41
5110 5268 0.740868 AGCAACGACGGTGATGGATG 60.741 55.000 18.96 0.00 0.00 3.51
5111 5269 1.705337 GCAACGACGGTGATGGATGG 61.705 60.000 18.96 0.00 0.00 3.51
5112 5270 1.089481 CAACGACGGTGATGGATGGG 61.089 60.000 7.21 0.00 0.00 4.00
5113 5271 1.261938 AACGACGGTGATGGATGGGA 61.262 55.000 0.00 0.00 0.00 4.37
5114 5272 1.261938 ACGACGGTGATGGATGGGAA 61.262 55.000 0.00 0.00 0.00 3.97
5115 5273 0.530650 CGACGGTGATGGATGGGAAG 60.531 60.000 0.00 0.00 0.00 3.46
5116 5274 0.830648 GACGGTGATGGATGGGAAGA 59.169 55.000 0.00 0.00 0.00 2.87
5117 5275 0.541863 ACGGTGATGGATGGGAAGAC 59.458 55.000 0.00 0.00 0.00 3.01
5118 5276 0.541392 CGGTGATGGATGGGAAGACA 59.459 55.000 0.00 0.00 0.00 3.41
5119 5277 1.473965 CGGTGATGGATGGGAAGACAG 60.474 57.143 0.00 0.00 0.00 3.51
5120 5278 1.673168 GTGATGGATGGGAAGACAGC 58.327 55.000 0.00 0.00 0.00 4.40
5121 5279 1.065199 GTGATGGATGGGAAGACAGCA 60.065 52.381 0.00 0.00 0.00 4.41
5122 5280 1.848388 TGATGGATGGGAAGACAGCAT 59.152 47.619 0.00 0.00 0.00 3.79
5123 5281 2.158711 TGATGGATGGGAAGACAGCATC 60.159 50.000 0.00 0.00 0.00 3.91
5124 5282 0.178767 TGGATGGGAAGACAGCATCG 59.821 55.000 0.00 0.00 0.00 3.84
5125 5283 0.465705 GGATGGGAAGACAGCATCGA 59.534 55.000 0.00 0.00 0.00 3.59
5126 5284 1.134401 GGATGGGAAGACAGCATCGAA 60.134 52.381 0.00 0.00 0.00 3.71
5127 5285 2.208431 GATGGGAAGACAGCATCGAAG 58.792 52.381 0.00 0.00 0.00 3.79
5128 5286 1.266178 TGGGAAGACAGCATCGAAGA 58.734 50.000 0.00 0.00 45.75 2.87
5129 5287 1.833630 TGGGAAGACAGCATCGAAGAT 59.166 47.619 0.00 0.00 45.12 2.40
5130 5288 2.208431 GGGAAGACAGCATCGAAGATG 58.792 52.381 4.08 4.08 45.12 2.90
5131 5289 1.596727 GGAAGACAGCATCGAAGATGC 59.403 52.381 22.99 22.99 45.12 3.91
5137 5295 2.614581 GCATCGAAGATGCTCAGGG 58.385 57.895 23.11 0.00 45.12 4.45
5138 5296 0.179062 GCATCGAAGATGCTCAGGGT 60.179 55.000 23.11 0.00 45.12 4.34
5139 5297 1.579698 CATCGAAGATGCTCAGGGTG 58.420 55.000 0.00 0.00 45.12 4.61
5140 5298 0.467384 ATCGAAGATGCTCAGGGTGG 59.533 55.000 0.00 0.00 45.12 4.61
5141 5299 1.153289 CGAAGATGCTCAGGGTGGG 60.153 63.158 0.00 0.00 0.00 4.61
5142 5300 1.225704 GAAGATGCTCAGGGTGGGG 59.774 63.158 0.00 0.00 0.00 4.96
5143 5301 1.229951 AAGATGCTCAGGGTGGGGA 60.230 57.895 0.00 0.00 0.00 4.81
5144 5302 0.846427 AAGATGCTCAGGGTGGGGAA 60.846 55.000 0.00 0.00 0.00 3.97
5145 5303 1.225704 GATGCTCAGGGTGGGGAAG 59.774 63.158 0.00 0.00 0.00 3.46
5146 5304 2.276309 GATGCTCAGGGTGGGGAAGG 62.276 65.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 2.667470 TGCTAATAGCGAAGGAGAGGT 58.333 47.619 7.84 0.00 46.26 3.85
120 124 7.110155 TGGGTCTGTTCCTGTTTTATATCTTC 58.890 38.462 0.00 0.00 0.00 2.87
145 149 3.618351 CATGAGAGGAGAGCAAAACCAT 58.382 45.455 0.00 0.00 0.00 3.55
205 209 3.384348 GGACGGGCCTAGTGTGAA 58.616 61.111 0.84 0.00 0.00 3.18
367 371 3.322254 AGTTAATACCCAGCCTCATCTCG 59.678 47.826 0.00 0.00 0.00 4.04
427 433 6.462552 TGCTGGAGCTATAGATGATATCAC 57.537 41.667 7.78 2.47 42.66 3.06
468 474 1.543871 GGGCCAGTCTTGGTTTTCGTA 60.544 52.381 4.39 0.00 46.80 3.43
530 536 3.036091 CCCTTCCACGAACCTTCCTATA 58.964 50.000 0.00 0.00 0.00 1.31
873 892 6.826741 GCACAACCCAAAACCTCTATTAGATA 59.173 38.462 0.00 0.00 0.00 1.98
908 928 1.950973 AACCAACACAAACCCCGCAC 61.951 55.000 0.00 0.00 0.00 5.34
933 953 6.925165 AGAAACCACTAATTAGAAAACGACGA 59.075 34.615 19.38 0.00 0.00 4.20
993 1014 1.149174 CATAGCCGCCATGTTCCCT 59.851 57.895 0.00 0.00 0.00 4.20
1098 1120 0.976641 CCAGTACCTTGAGGCAGACA 59.023 55.000 0.00 0.00 39.32 3.41
1287 1329 1.714794 GTGATCACCAGGTCGAACTG 58.285 55.000 23.91 23.91 38.21 3.16
1418 1465 4.116961 CAGCTCATGGCATGTTAAAATGG 58.883 43.478 25.62 8.98 44.79 3.16
1484 1533 6.770746 ATTCAGGAGTAAAAGTACGCTCTA 57.229 37.500 0.00 0.00 35.20 2.43
1660 1709 8.138928 TCAAGGAGATTGAAGAAGAGTAATCA 57.861 34.615 0.00 0.00 45.00 2.57
1964 2013 6.991485 AGTTAAATGTTCTTCAAATGTGCG 57.009 33.333 0.00 0.00 0.00 5.34
1996 2046 6.179906 TGATGTTTTCCCCAATGCTTAAAA 57.820 33.333 0.00 0.00 0.00 1.52
2104 2154 3.405831 CTTCATCACAGCCTTCTTGTCA 58.594 45.455 0.00 0.00 0.00 3.58
2140 2190 0.037697 TCACCAAATAGTCGCACGCT 60.038 50.000 0.00 0.00 0.00 5.07
2264 2315 3.685272 GGCTGCACTCTATCATCATCATG 59.315 47.826 0.50 0.00 0.00 3.07
2409 2460 7.664082 TCTAGAAATTTGTTCTGAAGCTCAG 57.336 36.000 0.00 6.79 45.59 3.35
2749 2803 5.590259 ACATCTTCATGTTAGGTGCATTACC 59.410 40.000 9.72 0.00 44.56 2.85
2799 2854 7.431249 TCCACGGTATAACAAGACTCATTATC 58.569 38.462 0.00 0.00 0.00 1.75
2812 2867 4.037684 AGTGTAGAGCATCCACGGTATAAC 59.962 45.833 0.00 0.00 33.32 1.89
3098 3193 4.265856 AGACCAGAGGACATACACCATA 57.734 45.455 0.00 0.00 0.00 2.74
3257 3361 0.379669 GTCAATGGAGCCAGCGAATG 59.620 55.000 0.00 0.00 0.00 2.67
3364 3468 2.039974 CCAGCTTACCACGCATGCA 61.040 57.895 19.57 0.00 0.00 3.96
3495 3599 4.321899 GCCATTTCATTTTGCACCTCTACA 60.322 41.667 0.00 0.00 0.00 2.74
3858 4011 5.304778 TCAAGCTTGTCAGTTATTGCTACA 58.695 37.500 25.19 0.00 0.00 2.74
3861 4014 4.157289 CCATCAAGCTTGTCAGTTATTGCT 59.843 41.667 25.19 0.00 0.00 3.91
3867 4020 0.877071 CGCCATCAAGCTTGTCAGTT 59.123 50.000 25.19 4.80 0.00 3.16
3966 4119 4.703379 AAGATCATCCCATGAGAAGTCC 57.297 45.455 0.00 0.00 43.53 3.85
3985 4138 1.604604 TCCAGCGGGTTGAGAAAAAG 58.395 50.000 1.81 0.00 34.93 2.27
4046 4200 8.676401 CACATGTCCAACTCAACAATTCATATA 58.324 33.333 0.00 0.00 0.00 0.86
4165 4322 3.125146 GCAGAAAACATCACGTGCATAGA 59.875 43.478 11.67 0.00 0.00 1.98
4175 4332 1.608109 ACGCACATGCAGAAAACATCA 59.392 42.857 4.49 0.00 42.21 3.07
4200 4357 7.152645 ACAGACGAATGATTAGTGTACAAGTT 58.847 34.615 0.00 0.00 0.00 2.66
4219 4376 5.688823 TGATACAATTTGCAAGAACAGACG 58.311 37.500 0.00 0.00 0.00 4.18
4233 4390 8.801299 TGGTACACACAATTTCATGATACAATT 58.199 29.630 0.00 0.00 0.00 2.32
4288 4445 8.451908 AAGCTCATGTAAAATAGATTACCCAC 57.548 34.615 0.00 0.00 35.38 4.61
4315 4472 9.535878 TCAAAATACAACACCAACTTAAAATCC 57.464 29.630 0.00 0.00 0.00 3.01
4491 4648 1.069500 CATTTTCGTTCGGGTGTGTCC 60.069 52.381 0.00 0.00 0.00 4.02
4537 4694 4.573900 TGTTTTGGTGCATTGAAACAGTT 58.426 34.783 15.83 0.00 37.15 3.16
4637 4794 6.239261 CCGATGCTGGAGCTATAGATGATATT 60.239 42.308 3.21 0.00 42.66 1.28
4736 4893 3.689649 CCTCCACGAACCTTCCTATTTTG 59.310 47.826 0.00 0.00 0.00 2.44
4927 5085 1.367840 CCCTACCTACTCGCATGGC 59.632 63.158 0.00 0.00 0.00 4.40
4934 5092 2.966516 CAGATCCCAACCCTACCTACTC 59.033 54.545 0.00 0.00 0.00 2.59
4947 5105 1.000359 TCTCAGCGGTCAGATCCCA 60.000 57.895 0.00 0.00 0.00 4.37
4972 5130 0.171455 GGCAGACAGAGAGTGTACGG 59.829 60.000 0.00 0.00 40.56 4.02
4985 5143 0.955919 CTTCCTTTGACCGGGCAGAC 60.956 60.000 11.51 0.00 0.00 3.51
4987 5145 0.323629 TACTTCCTTTGACCGGGCAG 59.676 55.000 11.51 0.00 0.00 4.85
4992 5150 3.399330 TGCTTCTTACTTCCTTTGACCG 58.601 45.455 0.00 0.00 0.00 4.79
5017 5175 0.261991 ACTATGGCGAAGAGGAGGGA 59.738 55.000 0.00 0.00 0.00 4.20
5020 5178 1.403814 TGGACTATGGCGAAGAGGAG 58.596 55.000 0.00 0.00 0.00 3.69
5021 5179 2.088104 ATGGACTATGGCGAAGAGGA 57.912 50.000 0.00 0.00 0.00 3.71
5024 5182 4.746535 TTGTAATGGACTATGGCGAAGA 57.253 40.909 0.00 0.00 0.00 2.87
5025 5183 6.377327 AATTTGTAATGGACTATGGCGAAG 57.623 37.500 0.00 0.00 0.00 3.79
5026 5184 6.767524 AAATTTGTAATGGACTATGGCGAA 57.232 33.333 0.00 0.00 0.00 4.70
5027 5185 6.824196 TGTAAATTTGTAATGGACTATGGCGA 59.176 34.615 0.00 0.00 0.00 5.54
5028 5186 7.022055 TGTAAATTTGTAATGGACTATGGCG 57.978 36.000 0.00 0.00 0.00 5.69
5029 5187 9.463443 GATTGTAAATTTGTAATGGACTATGGC 57.537 33.333 0.00 0.00 0.00 4.40
5030 5188 9.663904 CGATTGTAAATTTGTAATGGACTATGG 57.336 33.333 0.00 0.00 0.00 2.74
5033 5191 8.597227 CGACGATTGTAAATTTGTAATGGACTA 58.403 33.333 13.92 0.00 0.00 2.59
5034 5192 7.461107 CGACGATTGTAAATTTGTAATGGACT 58.539 34.615 13.92 0.00 0.00 3.85
5035 5193 6.193959 GCGACGATTGTAAATTTGTAATGGAC 59.806 38.462 0.00 9.25 0.00 4.02
5036 5194 6.252281 GCGACGATTGTAAATTTGTAATGGA 58.748 36.000 0.00 0.00 0.00 3.41
5037 5195 5.454232 GGCGACGATTGTAAATTTGTAATGG 59.546 40.000 0.00 5.51 0.00 3.16
5038 5196 6.024664 TGGCGACGATTGTAAATTTGTAATG 58.975 36.000 0.00 0.68 0.00 1.90
5039 5197 6.184580 TGGCGACGATTGTAAATTTGTAAT 57.815 33.333 0.00 1.35 0.00 1.89
5040 5198 5.608676 TGGCGACGATTGTAAATTTGTAA 57.391 34.783 0.00 0.00 0.00 2.41
5041 5199 5.122554 ACATGGCGACGATTGTAAATTTGTA 59.877 36.000 0.00 0.00 0.00 2.41
5042 5200 4.083003 ACATGGCGACGATTGTAAATTTGT 60.083 37.500 0.00 0.00 0.00 2.83
5043 5201 4.262743 CACATGGCGACGATTGTAAATTTG 59.737 41.667 0.00 0.00 0.00 2.32
5044 5202 4.155099 TCACATGGCGACGATTGTAAATTT 59.845 37.500 0.00 0.00 0.00 1.82
5045 5203 3.687212 TCACATGGCGACGATTGTAAATT 59.313 39.130 0.00 0.00 0.00 1.82
5046 5204 3.266636 TCACATGGCGACGATTGTAAAT 58.733 40.909 0.00 0.00 0.00 1.40
5047 5205 2.689646 TCACATGGCGACGATTGTAAA 58.310 42.857 0.00 0.00 0.00 2.01
5048 5206 2.371910 TCACATGGCGACGATTGTAA 57.628 45.000 0.00 0.00 0.00 2.41
5049 5207 2.469826 GATCACATGGCGACGATTGTA 58.530 47.619 0.00 0.00 0.00 2.41
5050 5208 1.290203 GATCACATGGCGACGATTGT 58.710 50.000 0.00 0.00 0.00 2.71
5051 5209 0.583438 GGATCACATGGCGACGATTG 59.417 55.000 0.00 0.00 0.00 2.67
5052 5210 0.465705 AGGATCACATGGCGACGATT 59.534 50.000 0.00 0.00 0.00 3.34
5053 5211 0.465705 AAGGATCACATGGCGACGAT 59.534 50.000 0.00 0.00 0.00 3.73
5054 5212 0.249120 AAAGGATCACATGGCGACGA 59.751 50.000 0.00 0.00 0.00 4.20
5055 5213 1.086696 AAAAGGATCACATGGCGACG 58.913 50.000 0.00 0.00 0.00 5.12
5072 5230 2.143122 CTGTACCGCAGCAGAGAAAAA 58.857 47.619 0.00 0.00 38.52 1.94
5073 5231 1.795768 CTGTACCGCAGCAGAGAAAA 58.204 50.000 0.00 0.00 38.52 2.29
5074 5232 3.514777 CTGTACCGCAGCAGAGAAA 57.485 52.632 0.00 0.00 38.52 2.52
5083 5241 2.731721 CGTCGTTGCTGTACCGCA 60.732 61.111 7.99 7.99 38.31 5.69
5084 5242 3.475774 CCGTCGTTGCTGTACCGC 61.476 66.667 1.80 1.80 0.00 5.68
5085 5243 2.049802 ACCGTCGTTGCTGTACCG 60.050 61.111 0.00 0.00 0.00 4.02
5086 5244 0.389426 ATCACCGTCGTTGCTGTACC 60.389 55.000 0.00 0.00 0.00 3.34
5087 5245 0.713883 CATCACCGTCGTTGCTGTAC 59.286 55.000 0.00 0.00 0.00 2.90
5088 5246 0.389296 CCATCACCGTCGTTGCTGTA 60.389 55.000 0.00 0.00 0.00 2.74
5089 5247 1.667830 CCATCACCGTCGTTGCTGT 60.668 57.895 0.00 0.00 0.00 4.40
5090 5248 0.740868 ATCCATCACCGTCGTTGCTG 60.741 55.000 0.00 0.00 0.00 4.41
5091 5249 0.740868 CATCCATCACCGTCGTTGCT 60.741 55.000 0.00 0.00 0.00 3.91
5092 5250 1.705337 CCATCCATCACCGTCGTTGC 61.705 60.000 0.00 0.00 0.00 4.17
5093 5251 1.089481 CCCATCCATCACCGTCGTTG 61.089 60.000 0.00 0.00 0.00 4.10
5094 5252 1.220749 CCCATCCATCACCGTCGTT 59.779 57.895 0.00 0.00 0.00 3.85
5095 5253 1.261938 TTCCCATCCATCACCGTCGT 61.262 55.000 0.00 0.00 0.00 4.34
5096 5254 0.530650 CTTCCCATCCATCACCGTCG 60.531 60.000 0.00 0.00 0.00 5.12
5097 5255 0.830648 TCTTCCCATCCATCACCGTC 59.169 55.000 0.00 0.00 0.00 4.79
5098 5256 0.541863 GTCTTCCCATCCATCACCGT 59.458 55.000 0.00 0.00 0.00 4.83
5099 5257 0.541392 TGTCTTCCCATCCATCACCG 59.459 55.000 0.00 0.00 0.00 4.94
5100 5258 1.748591 GCTGTCTTCCCATCCATCACC 60.749 57.143 0.00 0.00 0.00 4.02
5101 5259 1.065199 TGCTGTCTTCCCATCCATCAC 60.065 52.381 0.00 0.00 0.00 3.06
5102 5260 1.288188 TGCTGTCTTCCCATCCATCA 58.712 50.000 0.00 0.00 0.00 3.07
5103 5261 2.502295 GATGCTGTCTTCCCATCCATC 58.498 52.381 0.00 0.00 31.47 3.51
5104 5262 1.202734 CGATGCTGTCTTCCCATCCAT 60.203 52.381 0.00 0.00 33.53 3.41
5105 5263 0.178767 CGATGCTGTCTTCCCATCCA 59.821 55.000 0.00 0.00 33.53 3.41
5106 5264 0.465705 TCGATGCTGTCTTCCCATCC 59.534 55.000 0.00 0.00 33.53 3.51
5107 5265 2.159043 TCTTCGATGCTGTCTTCCCATC 60.159 50.000 0.00 0.00 33.71 3.51
5108 5266 1.833630 TCTTCGATGCTGTCTTCCCAT 59.166 47.619 0.00 0.00 0.00 4.00
5109 5267 1.266178 TCTTCGATGCTGTCTTCCCA 58.734 50.000 0.00 0.00 0.00 4.37
5110 5268 2.208431 CATCTTCGATGCTGTCTTCCC 58.792 52.381 0.00 0.00 0.00 3.97
5111 5269 1.596727 GCATCTTCGATGCTGTCTTCC 59.403 52.381 18.68 0.00 41.52 3.46
5119 5277 0.179062 ACCCTGAGCATCTTCGATGC 60.179 55.000 18.39 18.39 44.85 3.91
5120 5278 1.579698 CACCCTGAGCATCTTCGATG 58.420 55.000 0.00 0.00 34.92 3.84
5121 5279 0.467384 CCACCCTGAGCATCTTCGAT 59.533 55.000 0.00 0.00 34.92 3.59
5122 5280 1.617018 CCCACCCTGAGCATCTTCGA 61.617 60.000 0.00 0.00 34.92 3.71
5123 5281 1.153289 CCCACCCTGAGCATCTTCG 60.153 63.158 0.00 0.00 34.92 3.79
5124 5282 1.225704 CCCCACCCTGAGCATCTTC 59.774 63.158 0.00 0.00 34.92 2.87
5125 5283 0.846427 TTCCCCACCCTGAGCATCTT 60.846 55.000 0.00 0.00 34.92 2.40
5126 5284 1.229951 TTCCCCACCCTGAGCATCT 60.230 57.895 0.00 0.00 34.92 2.90
5127 5285 1.225704 CTTCCCCACCCTGAGCATC 59.774 63.158 0.00 0.00 0.00 3.91
5128 5286 2.311854 CCTTCCCCACCCTGAGCAT 61.312 63.158 0.00 0.00 0.00 3.79
5129 5287 2.935481 CCTTCCCCACCCTGAGCA 60.935 66.667 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.