Multiple sequence alignment - TraesCS7D01G124700

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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 TraesCS7D01G124700 chr7D 100.000 3205 0 0 733 3937 78189670 78192874 0.000000e+00 5919.0
1 TraesCS7D01G124700 chr7D 100.000 363 0 0 1 363 78188938 78189300 0.000000e+00 671.0
2 TraesCS7D01G124700 chr7A 88.712 3269 191 76 733 3937 81632223 81635377 0.000000e+00 3829.0
3 TraesCS7D01G124700 chr7A 86.410 493 46 8 1669 2161 658724319 658724790 1.620000e-143 520.0
4 TraesCS7D01G124700 chr7A 87.124 466 36 13 1669 2130 728374749 728374304 1.260000e-139 507.0
5 TraesCS7D01G124700 chr7A 85.513 497 44 9 1665 2161 576381986 576381518 9.830000e-136 494.0
6 TraesCS7D01G124700 chr7A 84.746 295 25 8 73 356 81631913 81632198 1.080000e-70 278.0
7 TraesCS7D01G124700 chr7A 79.447 253 34 13 1325 1560 728375000 728374749 3.150000e-36 163.0
8 TraesCS7D01G124700 chr7A 84.211 171 11 10 1382 1548 658724149 658724307 6.810000e-33 152.0
9 TraesCS7D01G124700 chr7B 90.373 2223 124 45 995 3193 25587504 25589660 0.000000e+00 2837.0
10 TraesCS7D01G124700 chr7B 91.368 753 32 13 3205 3926 25589716 25590466 0.000000e+00 1000.0
11 TraesCS7D01G124700 chr7B 84.953 319 16 15 1 313 25586937 25587229 1.070000e-75 294.0
12 TraesCS7D01G124700 chr7B 91.071 112 1 5 733 842 25587286 25587390 4.100000e-30 143.0
13 TraesCS7D01G124700 chr7B 83.824 136 17 4 2012 2147 630365266 630365396 1.490000e-24 124.0
14 TraesCS7D01G124700 chr6A 80.231 865 85 50 1243 2076 254936332 254937141 4.410000e-159 571.0
15 TraesCS7D01G124700 chr6A 88.525 61 6 1 1316 1375 596750224 596750164 5.460000e-09 73.1
16 TraesCS7D01G124700 chr4A 80.277 867 81 51 1243 2076 651217722 651218531 4.410000e-159 571.0
17 TraesCS7D01G124700 chr3A 86.410 493 45 7 1669 2161 604999784 604999314 1.620000e-143 520.0
18 TraesCS7D01G124700 chr3A 82.377 244 21 13 1325 1560 605000013 604999784 4.010000e-45 193.0
19 TraesCS7D01G124700 chr4B 86.503 489 43 12 1669 2156 228742526 228742992 2.100000e-142 516.0
20 TraesCS7D01G124700 chr4B 78.582 677 64 45 1243 1888 344472038 344472664 4.800000e-99 372.0
21 TraesCS7D01G124700 chr4B 80.592 304 26 22 1389 1691 53487048 53486777 1.850000e-48 204.0
22 TraesCS7D01G124700 chr5B 85.400 500 52 7 1662 2161 56020324 56020802 2.110000e-137 499.0
23 TraesCS7D01G124700 chr5B 77.650 868 94 52 1243 2076 167760528 167759727 1.680000e-118 436.0
24 TraesCS7D01G124700 chr5D 83.217 143 12 8 1084 1226 147722917 147722787 1.920000e-23 121.0
25 TraesCS7D01G124700 chr6D 88.525 61 6 1 1316 1375 451111151 451111091 5.460000e-09 73.1
26 TraesCS7D01G124700 chr6B 88.525 61 6 1 1316 1375 685201642 685201582 5.460000e-09 73.1


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 TraesCS7D01G124700 chr7D 78188938 78192874 3936 False 3295.0 5919 100.00000 1 3937 2 chr7D.!!$F1 3936
1 TraesCS7D01G124700 chr7A 81631913 81635377 3464 False 2053.5 3829 86.72900 73 3937 2 chr7A.!!$F1 3864
2 TraesCS7D01G124700 chr7A 658724149 658724790 641 False 336.0 520 85.31050 1382 2161 2 chr7A.!!$F2 779
3 TraesCS7D01G124700 chr7A 728374304 728375000 696 True 335.0 507 83.28550 1325 2130 2 chr7A.!!$R2 805
4 TraesCS7D01G124700 chr7B 25586937 25590466 3529 False 1068.5 2837 89.44125 1 3926 4 chr7B.!!$F2 3925
5 TraesCS7D01G124700 chr6A 254936332 254937141 809 False 571.0 571 80.23100 1243 2076 1 chr6A.!!$F1 833
6 TraesCS7D01G124700 chr4A 651217722 651218531 809 False 571.0 571 80.27700 1243 2076 1 chr4A.!!$F1 833
7 TraesCS7D01G124700 chr3A 604999314 605000013 699 True 356.5 520 84.39350 1325 2161 2 chr3A.!!$R1 836
8 TraesCS7D01G124700 chr4B 344472038 344472664 626 False 372.0 372 78.58200 1243 1888 1 chr4B.!!$F2 645
9 TraesCS7D01G124700 chr5B 167759727 167760528 801 True 436.0 436 77.65000 1243 2076 1 chr5B.!!$R1 833

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
992 1021 0.035343 GTAGAAGGTGGAAGGTGGCC 60.035 60.0 0.0 0.0 0.00 5.36 F
1565 1644 0.249155 CAGCAGCACACCAAAACCAG 60.249 55.0 0.0 0.0 0.00 4.00 F
1943 2066 0.250640 AGTGGCCACTTTCTGCTCTG 60.251 55.0 33.2 0.0 38.83 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2552 2675 0.307760 CACTGGTCGGTTTTGTGCTC 59.692 55.0 0.0 0.0 0.00 4.26 R
2556 2679 0.395173 AAGGCACTGGTCGGTTTTGT 60.395 50.0 0.0 0.0 40.86 2.83 R
3798 4002 0.248012 TTGCCGGTTAGATCGCTGAA 59.752 50.0 1.9 0.0 0.00 3.02 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
25 28 2.620242 TGAAAAATACCGGGAGTACGC 58.380 47.619 6.32 0.00 32.46 4.42
35 38 1.602311 GGGAGTACGCGAGAGGATTA 58.398 55.000 15.93 0.00 0.00 1.75
36 39 1.266446 GGGAGTACGCGAGAGGATTAC 59.734 57.143 15.93 2.32 0.00 1.89
37 40 2.220313 GGAGTACGCGAGAGGATTACT 58.780 52.381 15.93 8.24 0.00 2.24
38 41 3.397482 GGAGTACGCGAGAGGATTACTA 58.603 50.000 15.93 0.00 0.00 1.82
62 65 4.994201 TCGACGCAGACACCACGC 62.994 66.667 0.00 0.00 0.00 5.34
91 97 2.882876 CCGTACCACAGAGACCCG 59.117 66.667 0.00 0.00 0.00 5.28
92 98 2.181021 CGTACCACAGAGACCCGC 59.819 66.667 0.00 0.00 0.00 6.13
199 214 2.691409 TAAATGCAACCCTCTCCTCG 57.309 50.000 0.00 0.00 0.00 4.63
213 228 2.745100 CTCGGCAGCACAGCACAT 60.745 61.111 0.00 0.00 35.83 3.21
214 229 2.743538 TCGGCAGCACAGCACATC 60.744 61.111 0.00 0.00 35.83 3.06
215 230 4.156622 CGGCAGCACAGCACATCG 62.157 66.667 0.00 0.00 35.83 3.84
216 231 4.471726 GGCAGCACAGCACATCGC 62.472 66.667 0.00 0.00 42.91 4.58
217 232 3.729698 GCAGCACAGCACATCGCA 61.730 61.111 0.00 0.00 46.13 5.10
218 233 2.479198 CAGCACAGCACATCGCAG 59.521 61.111 0.00 0.00 46.13 5.18
219 234 3.429141 AGCACAGCACATCGCAGC 61.429 61.111 0.00 0.00 46.13 5.25
220 235 3.729698 GCACAGCACATCGCAGCA 61.730 61.111 0.00 0.00 46.13 4.41
221 236 2.175078 CACAGCACATCGCAGCAC 59.825 61.111 0.00 0.00 46.13 4.40
222 237 2.281002 ACAGCACATCGCAGCACA 60.281 55.556 0.00 0.00 46.13 4.57
270 292 2.962421 GGAAAACCAAACAGTCCATCCA 59.038 45.455 0.00 0.00 0.00 3.41
324 350 2.837291 CCCGAGCAGAGGAGAGGG 60.837 72.222 0.00 0.00 0.00 4.30
326 352 2.837291 CGAGCAGAGGAGAGGGGG 60.837 72.222 0.00 0.00 0.00 5.40
327 353 2.366570 GAGCAGAGGAGAGGGGGT 59.633 66.667 0.00 0.00 0.00 4.95
335 361 3.330998 CAGAGGAGAGGGGGTAAAAGTTT 59.669 47.826 0.00 0.00 0.00 2.66
337 363 2.168496 GGAGAGGGGGTAAAAGTTTGC 58.832 52.381 0.00 0.00 0.00 3.68
341 367 2.963101 GAGGGGGTAAAAGTTTGCTTGT 59.037 45.455 0.00 0.00 34.71 3.16
342 368 2.963101 AGGGGGTAAAAGTTTGCTTGTC 59.037 45.455 0.00 0.00 34.71 3.18
343 369 2.963101 GGGGGTAAAAGTTTGCTTGTCT 59.037 45.455 0.00 0.00 34.71 3.41
919 948 0.261696 GAGCCCTTCTCTCTCCTCCT 59.738 60.000 0.00 0.00 38.78 3.69
926 955 2.441164 TCTCTCCTCCTGCTCCGC 60.441 66.667 0.00 0.00 0.00 5.54
971 1000 3.838271 TCTCGGCGTGATCTGGCC 61.838 66.667 15.17 15.17 45.95 5.36
976 1005 2.279517 GCGTGATCTGGCCGGTAG 60.280 66.667 12.43 1.88 0.00 3.18
977 1006 2.782222 GCGTGATCTGGCCGGTAGA 61.782 63.158 12.43 12.04 0.00 2.59
978 1007 1.813859 CGTGATCTGGCCGGTAGAA 59.186 57.895 12.43 0.00 0.00 2.10
992 1021 0.035343 GTAGAAGGTGGAAGGTGGCC 60.035 60.000 0.00 0.00 0.00 5.36
1017 1048 2.447379 ATGGAGGAGCGGCAGGAT 60.447 61.111 1.45 0.00 0.00 3.24
1020 1051 3.157252 GAGGAGCGGCAGGATGGA 61.157 66.667 1.45 0.00 35.86 3.41
1030 1061 0.394899 GCAGGATGGAGGGTTTGGAG 60.395 60.000 0.00 0.00 35.86 3.86
1031 1062 0.257039 CAGGATGGAGGGTTTGGAGG 59.743 60.000 0.00 0.00 0.00 4.30
1032 1063 0.921256 AGGATGGAGGGTTTGGAGGG 60.921 60.000 0.00 0.00 0.00 4.30
1033 1064 1.615262 GATGGAGGGTTTGGAGGGG 59.385 63.158 0.00 0.00 0.00 4.79
1034 1065 1.935931 ATGGAGGGTTTGGAGGGGG 60.936 63.158 0.00 0.00 0.00 5.40
1035 1066 4.062032 GGAGGGTTTGGAGGGGGC 62.062 72.222 0.00 0.00 0.00 5.80
1197 1228 4.039357 CAGCAGCAGCACCAGCAC 62.039 66.667 3.17 0.00 45.49 4.40
1414 1485 2.636893 TCTGCCTTTTCTGCTCTTCTCT 59.363 45.455 0.00 0.00 0.00 3.10
1465 1540 2.344441 CGCTTGCTTGCTTGATTGATTG 59.656 45.455 0.00 0.00 0.00 2.67
1548 1623 1.068333 CAATTCCAACAAGGTCCGCAG 60.068 52.381 0.00 0.00 39.02 5.18
1556 1635 4.996434 AGGTCCGCAGCAGCACAC 62.996 66.667 0.82 0.00 42.27 3.82
1565 1644 0.249155 CAGCAGCACACCAAAACCAG 60.249 55.000 0.00 0.00 0.00 4.00
1613 1695 1.678635 CCTGAATTTCGGGGCTGCA 60.679 57.895 15.47 0.00 39.28 4.41
1659 1741 0.893727 GTGTGTTCATGGGGTGGGTC 60.894 60.000 0.00 0.00 0.00 4.46
1751 1846 3.873952 GGTCAGTAAATGCATCTCTGGAC 59.126 47.826 18.73 14.87 0.00 4.02
1787 1888 4.641094 TCTGAGTAGAGGCTAACTTGCTAC 59.359 45.833 3.72 2.63 33.43 3.58
1831 1932 2.788786 CCAAACTGCAAACATTGACGTC 59.211 45.455 9.11 9.11 0.00 4.34
1837 1938 1.136336 GCAAACATTGACGTCGGAGTC 60.136 52.381 11.62 4.59 41.30 3.36
1879 1981 8.122952 GTGTTGTCCTTATTGATTCTTTATCCG 58.877 37.037 0.00 0.00 31.87 4.18
1899 2006 4.519350 TCCGATCGATAGTGAAGTAATGCT 59.481 41.667 18.66 0.00 37.40 3.79
1901 2008 5.452777 CGATCGATAGTGAAGTAATGCTGA 58.547 41.667 10.26 0.00 37.40 4.26
1943 2066 0.250640 AGTGGCCACTTTCTGCTCTG 60.251 55.000 33.20 0.00 38.83 3.35
1959 2082 3.568430 TGCTCTGTCGAGTGTTTTCTAGA 59.432 43.478 0.00 0.00 39.53 2.43
2022 2145 5.217393 CAATGGGATTTGTAATGCTGATCG 58.783 41.667 0.00 0.00 0.00 3.69
2062 2185 2.803492 GCTAGTTTCCTAGTGCGGATGG 60.803 54.545 0.00 0.00 42.35 3.51
2147 2270 7.612244 TGGTAGGTGCTAATAATTAAACTGCAA 59.388 33.333 7.16 0.00 0.00 4.08
2192 2315 9.013490 CAGTTCAAATGCAAGTATTAATACAGC 57.987 33.333 24.05 24.39 37.20 4.40
2198 2321 8.614994 AATGCAAGTATTAATACAGCGTTTTC 57.385 30.769 27.43 12.54 40.01 2.29
2335 2458 5.072600 ACTTGGTGTTAGTGGGAGAAATGTA 59.927 40.000 0.00 0.00 0.00 2.29
2391 2514 1.884235 AACCAAAGTTCAGGAGCTCG 58.116 50.000 7.83 0.00 0.00 5.03
2398 2521 1.135257 AGTTCAGGAGCTCGTCATTCG 60.135 52.381 5.82 0.00 41.41 3.34
2406 2529 1.402259 AGCTCGTCATTCGTTCGATCT 59.598 47.619 0.00 0.00 40.80 2.75
2498 2621 1.578206 GCCTCCGTTTCACTTGGAGC 61.578 60.000 1.95 0.00 46.42 4.70
2555 2678 3.449018 TGAATCCTCAGAGGTAACAGAGC 59.551 47.826 16.65 0.13 36.53 4.09
2556 2679 2.604912 TCCTCAGAGGTAACAGAGCA 57.395 50.000 16.65 0.00 36.53 4.26
2557 2680 2.171840 TCCTCAGAGGTAACAGAGCAC 58.828 52.381 16.65 0.00 36.53 4.40
2558 2681 1.895798 CCTCAGAGGTAACAGAGCACA 59.104 52.381 8.54 0.00 41.41 4.57
2559 2682 2.300152 CCTCAGAGGTAACAGAGCACAA 59.700 50.000 8.54 0.00 41.41 3.33
2560 2683 3.244215 CCTCAGAGGTAACAGAGCACAAA 60.244 47.826 8.54 0.00 41.41 2.83
2561 2684 4.380531 CTCAGAGGTAACAGAGCACAAAA 58.619 43.478 0.00 0.00 41.41 2.44
2562 2685 4.127171 TCAGAGGTAACAGAGCACAAAAC 58.873 43.478 0.00 0.00 41.41 2.43
2563 2686 3.251004 CAGAGGTAACAGAGCACAAAACC 59.749 47.826 0.00 0.00 41.41 3.27
2564 2687 2.218603 AGGTAACAGAGCACAAAACCG 58.781 47.619 0.00 0.00 41.41 4.44
2565 2688 2.158871 AGGTAACAGAGCACAAAACCGA 60.159 45.455 0.00 0.00 41.41 4.69
2567 2690 1.021968 AACAGAGCACAAAACCGACC 58.978 50.000 0.00 0.00 0.00 4.79
2568 2691 0.107410 ACAGAGCACAAAACCGACCA 60.107 50.000 0.00 0.00 0.00 4.02
2571 2694 0.307760 GAGCACAAAACCGACCAGTG 59.692 55.000 0.00 0.00 0.00 3.66
2577 2700 1.265905 CAAAACCGACCAGTGCCTTAC 59.734 52.381 0.00 0.00 0.00 2.34
2581 2704 1.142262 ACCGACCAGTGCCTTACTTTT 59.858 47.619 0.00 0.00 37.60 2.27
2584 2707 3.074412 CGACCAGTGCCTTACTTTTGAT 58.926 45.455 0.00 0.00 37.60 2.57
2585 2708 3.120199 CGACCAGTGCCTTACTTTTGATG 60.120 47.826 0.00 0.00 37.60 3.07
2586 2709 2.558359 ACCAGTGCCTTACTTTTGATGC 59.442 45.455 0.00 0.00 37.60 3.91
2591 2714 5.975344 CAGTGCCTTACTTTTGATGCATATG 59.025 40.000 0.00 0.00 37.60 1.78
2594 2717 5.163530 TGCCTTACTTTTGATGCATATGGTG 60.164 40.000 0.00 0.00 0.00 4.17
2595 2718 5.163519 GCCTTACTTTTGATGCATATGGTGT 60.164 40.000 0.00 0.00 0.00 4.16
2606 2729 4.343231 TGCATATGGTGTTGAGGTTTCAT 58.657 39.130 4.56 0.00 32.27 2.57
2628 2751 7.944061 TCATGAAGATTTTTCTCACAACATGT 58.056 30.769 0.00 0.00 34.84 3.21
2642 2765 9.554395 TCTCACAACATGTATTCTTCTGTTTTA 57.446 29.630 0.00 0.00 29.74 1.52
2663 2786 0.467384 AGATGATGTTGCGAGGGGAG 59.533 55.000 0.00 0.00 0.00 4.30
2664 2787 0.179000 GATGATGTTGCGAGGGGAGT 59.821 55.000 0.00 0.00 0.00 3.85
2666 2789 0.321564 TGATGTTGCGAGGGGAGTTG 60.322 55.000 0.00 0.00 0.00 3.16
2712 2835 1.136695 CTCAGGACAGAGCTGATCCAC 59.863 57.143 16.14 0.00 35.02 4.02
2771 2897 3.567530 CAGCATTTTCATTTGTCTCGCA 58.432 40.909 0.00 0.00 0.00 5.10
2772 2898 3.362831 CAGCATTTTCATTTGTCTCGCAC 59.637 43.478 0.00 0.00 0.00 5.34
2790 2916 2.159114 GCACACACCACACCTTTTCATT 60.159 45.455 0.00 0.00 0.00 2.57
2791 2917 3.705604 CACACACCACACCTTTTCATTC 58.294 45.455 0.00 0.00 0.00 2.67
2801 2930 6.096705 CCACACCTTTTCATTCTAATGCCATA 59.903 38.462 0.00 0.00 36.36 2.74
2882 3014 4.087907 TGAACCATTTTGATGGATGCTCA 58.912 39.130 12.12 6.38 44.39 4.26
2915 3047 3.059884 GCAGTCACATGATATGGTACCG 58.940 50.000 7.57 0.00 33.60 4.02
2987 3119 7.013083 AGAGCCAATCAGTCAAGCATATAAAAG 59.987 37.037 0.00 0.00 0.00 2.27
3099 3231 3.935828 CTCCTTTTAGACTAAGGCTGCAC 59.064 47.826 0.50 0.00 41.59 4.57
3101 3233 3.686726 CCTTTTAGACTAAGGCTGCACTG 59.313 47.826 0.50 0.00 36.08 3.66
3126 3258 7.928167 TGGGCATCGTGATAGATTATGATAATC 59.072 37.037 15.59 15.59 0.00 1.75
3141 3273 3.936453 TGATAATCCAACTTTTCCGACCG 59.064 43.478 0.00 0.00 0.00 4.79
3156 3288 3.936453 TCCGACCGGATTTTGTCTATTTG 59.064 43.478 9.46 0.00 39.76 2.32
3221 3397 8.126700 CGGTAGATTGTAAAAACAAAGTTCAGT 58.873 33.333 0.00 0.00 32.94 3.41
3355 3539 2.488153 GTCTAGGATGTGCCCAAAACAC 59.512 50.000 0.00 0.00 37.37 3.32
3449 3633 5.003804 CAGCCAGTAATGAAACAGGTAAGT 58.996 41.667 0.00 0.00 0.00 2.24
3488 3672 4.390264 AGTTGACTAAGAAGACTTTGGCC 58.610 43.478 0.00 0.00 36.36 5.36
3492 3677 6.182507 TGACTAAGAAGACTTTGGCCTAAA 57.817 37.500 3.32 2.03 36.36 1.85
3619 3805 6.157994 TGTTTTCTCCCCATGCTACTTACTAT 59.842 38.462 0.00 0.00 0.00 2.12
3674 3865 5.596361 ACAATTATTTATCCCGTGCATTCCA 59.404 36.000 0.00 0.00 0.00 3.53
3761 3952 4.764172 ACAGCAGCTTAGGAAGTGATTAG 58.236 43.478 0.00 0.00 0.00 1.73
3771 3962 5.746990 AGGAAGTGATTAGCAGTAACACT 57.253 39.130 0.00 0.00 42.40 3.55
3852 4067 2.901839 AGCTTTGCCAATCATTGACCTT 59.098 40.909 0.00 0.00 0.00 3.50
3865 4080 0.037975 TGACCTTTCCGTTACCGCTC 60.038 55.000 0.00 0.00 0.00 5.03
3870 4085 3.893813 ACCTTTCCGTTACCGCTCTATAT 59.106 43.478 0.00 0.00 0.00 0.86
3871 4086 5.072741 ACCTTTCCGTTACCGCTCTATATA 58.927 41.667 0.00 0.00 0.00 0.86
3872 4087 5.182760 ACCTTTCCGTTACCGCTCTATATAG 59.817 44.000 3.10 3.10 0.00 1.31
3873 4088 5.182760 CCTTTCCGTTACCGCTCTATATAGT 59.817 44.000 9.58 0.00 0.00 2.12
3875 4090 5.618056 TCCGTTACCGCTCTATATAGTTG 57.382 43.478 9.58 5.59 0.00 3.16
3876 4091 5.065914 TCCGTTACCGCTCTATATAGTTGT 58.934 41.667 9.58 5.77 0.00 3.32
3877 4092 6.230472 TCCGTTACCGCTCTATATAGTTGTA 58.770 40.000 9.58 4.95 0.00 2.41
3878 4093 6.147821 TCCGTTACCGCTCTATATAGTTGTAC 59.852 42.308 9.58 0.00 0.00 2.90
3912 4130 1.746615 GGCCTGAGCGCTTCATCAA 60.747 57.895 13.26 0.00 41.24 2.57
3914 4132 0.307146 GCCTGAGCGCTTCATCAATC 59.693 55.000 13.26 0.00 34.68 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 18 1.445716 AATCCTCTCGCGTACTCCCG 61.446 60.000 5.77 0.00 0.00 5.14
16 19 1.266446 GTAATCCTCTCGCGTACTCCC 59.734 57.143 5.77 0.00 0.00 4.30
25 28 4.750598 TCGAGTGATGTAGTAATCCTCTCG 59.249 45.833 15.84 15.84 43.38 4.04
35 38 1.130749 GTCTGCGTCGAGTGATGTAGT 59.869 52.381 0.00 0.00 42.49 2.73
36 39 1.130561 TGTCTGCGTCGAGTGATGTAG 59.869 52.381 0.00 0.00 43.04 2.74
37 40 1.135774 GTGTCTGCGTCGAGTGATGTA 60.136 52.381 0.00 0.00 33.44 2.29
38 41 0.387367 GTGTCTGCGTCGAGTGATGT 60.387 55.000 0.00 0.00 33.44 3.06
91 97 2.357034 TCTGGGTTTCTGCGTCGC 60.357 61.111 11.10 11.10 0.00 5.19
92 98 1.738099 CCTCTGGGTTTCTGCGTCG 60.738 63.158 0.00 0.00 0.00 5.12
192 198 4.074526 GCTGTGCTGCCGAGGAGA 62.075 66.667 0.00 0.00 0.00 3.71
199 214 4.471726 GCGATGTGCTGTGCTGCC 62.472 66.667 0.00 0.00 41.73 4.85
213 228 2.917227 TGGGAGTCTGTGCTGCGA 60.917 61.111 0.00 0.00 0.00 5.10
214 229 2.433838 CTGGGAGTCTGTGCTGCG 60.434 66.667 0.00 0.00 0.00 5.18
215 230 1.079266 CTCTGGGAGTCTGTGCTGC 60.079 63.158 0.00 0.00 0.00 5.25
216 231 1.595882 CCTCTGGGAGTCTGTGCTG 59.404 63.158 0.00 0.00 33.58 4.41
217 232 2.289532 GCCTCTGGGAGTCTGTGCT 61.290 63.158 0.00 0.00 33.58 4.40
218 233 2.267324 GCCTCTGGGAGTCTGTGC 59.733 66.667 0.00 0.00 33.58 4.57
219 234 1.595882 CTGCCTCTGGGAGTCTGTG 59.404 63.158 0.00 0.00 36.37 3.66
220 235 2.289532 GCTGCCTCTGGGAGTCTGT 61.290 63.158 6.96 0.00 43.30 3.41
221 236 2.241479 CTGCTGCCTCTGGGAGTCTG 62.241 65.000 6.96 0.99 43.30 3.51
222 237 1.988956 CTGCTGCCTCTGGGAGTCT 60.989 63.158 6.96 0.00 43.30 3.24
270 292 4.135153 CGTGTCAGCTAGCGGGCT 62.135 66.667 20.09 0.00 44.10 5.19
314 340 3.293215 AACTTTTACCCCCTCTCCTCT 57.707 47.619 0.00 0.00 0.00 3.69
319 345 3.230976 CAAGCAAACTTTTACCCCCTCT 58.769 45.455 0.00 0.00 32.29 3.69
324 350 4.911514 TGAGACAAGCAAACTTTTACCC 57.088 40.909 0.00 0.00 32.29 3.69
863 892 1.152546 GGAGGAGAGAGAGGGGCTC 60.153 68.421 0.00 0.00 44.29 4.70
864 893 2.710826 GGGAGGAGAGAGAGGGGCT 61.711 68.421 0.00 0.00 0.00 5.19
865 894 2.123033 GGGAGGAGAGAGAGGGGC 60.123 72.222 0.00 0.00 0.00 5.80
866 895 2.612251 GGGGAGGAGAGAGAGGGG 59.388 72.222 0.00 0.00 0.00 4.79
867 896 2.612251 GGGGGAGGAGAGAGAGGG 59.388 72.222 0.00 0.00 0.00 4.30
868 897 2.197324 CGGGGGAGGAGAGAGAGG 59.803 72.222 0.00 0.00 0.00 3.69
869 898 2.520741 GCGGGGGAGGAGAGAGAG 60.521 72.222 0.00 0.00 0.00 3.20
870 899 3.024356 AGCGGGGGAGGAGAGAGA 61.024 66.667 0.00 0.00 0.00 3.10
871 900 2.520741 GAGCGGGGGAGGAGAGAG 60.521 72.222 0.00 0.00 0.00 3.20
872 901 4.144727 GGAGCGGGGGAGGAGAGA 62.145 72.222 0.00 0.00 0.00 3.10
900 929 0.261696 AGGAGGAGAGAGAAGGGCTC 59.738 60.000 0.00 0.00 44.29 4.70
901 930 0.032217 CAGGAGGAGAGAGAAGGGCT 60.032 60.000 0.00 0.00 0.00 5.19
902 931 1.685355 GCAGGAGGAGAGAGAAGGGC 61.685 65.000 0.00 0.00 0.00 5.19
903 932 0.032217 AGCAGGAGGAGAGAGAAGGG 60.032 60.000 0.00 0.00 0.00 3.95
904 933 1.402787 GAGCAGGAGGAGAGAGAAGG 58.597 60.000 0.00 0.00 0.00 3.46
905 934 1.402787 GGAGCAGGAGGAGAGAGAAG 58.597 60.000 0.00 0.00 0.00 2.85
906 935 0.395036 CGGAGCAGGAGGAGAGAGAA 60.395 60.000 0.00 0.00 0.00 2.87
907 936 1.225983 CGGAGCAGGAGGAGAGAGA 59.774 63.158 0.00 0.00 0.00 3.10
971 1000 0.249398 CCACCTTCCACCTTCTACCG 59.751 60.000 0.00 0.00 0.00 4.02
973 1002 0.035343 GGCCACCTTCCACCTTCTAC 60.035 60.000 0.00 0.00 0.00 2.59
974 1003 1.550130 CGGCCACCTTCCACCTTCTA 61.550 60.000 2.24 0.00 0.00 2.10
976 1005 2.359975 CGGCCACCTTCCACCTTC 60.360 66.667 2.24 0.00 0.00 3.46
977 1006 3.966543 CCGGCCACCTTCCACCTT 61.967 66.667 2.24 0.00 0.00 3.50
1013 1044 0.921256 CCCTCCAAACCCTCCATCCT 60.921 60.000 0.00 0.00 0.00 3.24
1017 1048 2.534272 CCCCCTCCAAACCCTCCA 60.534 66.667 0.00 0.00 0.00 3.86
1414 1485 1.593265 GCCGGAAAACGTAGAGGGA 59.407 57.895 5.05 0.00 42.24 4.20
1548 1623 1.592400 GCTGGTTTTGGTGTGCTGC 60.592 57.895 0.00 0.00 0.00 5.25
1556 1635 2.989253 GGGGACGGCTGGTTTTGG 60.989 66.667 0.00 0.00 0.00 3.28
1565 1644 1.171308 GAAAAGTAAAGGGGGACGGC 58.829 55.000 0.00 0.00 0.00 5.68
1613 1695 7.066766 GCATTCAGATTCAGGAACAGTAATTCT 59.933 37.037 0.00 0.00 0.00 2.40
1751 1846 0.036952 ACTCAGACATCAACCAGCCG 60.037 55.000 0.00 0.00 0.00 5.52
1787 1888 7.546358 TGGACCATCAGTTAAAATAAATGCAG 58.454 34.615 0.00 0.00 0.00 4.41
1831 1932 2.325761 CACGGTAAAACTCTGACTCCG 58.674 52.381 0.00 0.00 41.77 4.63
1837 1938 2.249844 ACACCCACGGTAAAACTCTG 57.750 50.000 0.00 0.00 32.11 3.35
1879 1981 6.673106 TCTCAGCATTACTTCACTATCGATC 58.327 40.000 0.00 0.00 0.00 3.69
1899 2006 5.335897 GCTGTGCTATGTGGAAATTTTCTCA 60.336 40.000 8.93 3.78 0.00 3.27
1901 2008 4.523943 TGCTGTGCTATGTGGAAATTTTCT 59.476 37.500 8.93 0.00 0.00 2.52
1943 2066 5.462405 AGATGTGTCTAGAAAACACTCGAC 58.538 41.667 10.81 0.00 45.73 4.20
1968 2091 8.717717 TCCATGGAAATCAACAGTTCTATCTAT 58.282 33.333 13.46 0.00 26.35 1.98
1969 2092 8.089625 TCCATGGAAATCAACAGTTCTATCTA 57.910 34.615 13.46 0.00 26.35 1.98
1970 2093 6.962182 TCCATGGAAATCAACAGTTCTATCT 58.038 36.000 13.46 0.00 26.35 1.98
1971 2094 7.814264 ATCCATGGAAATCAACAGTTCTATC 57.186 36.000 20.67 0.00 26.35 2.08
1990 2113 7.502696 CATTACAAATCCCATTGTGAATCCAT 58.497 34.615 3.10 0.00 43.13 3.41
2022 2145 8.451908 AACTAGCCCTAACATATCAACATTTC 57.548 34.615 0.00 0.00 0.00 2.17
2192 2315 2.540157 GGAAAATATCGGGGCGAAAACG 60.540 50.000 0.00 0.00 39.99 3.60
2198 2321 1.602605 GGGGGAAAATATCGGGGCG 60.603 63.158 0.00 0.00 0.00 6.13
2208 2331 1.992557 ACAGCATCTGTAGGGGGAAAA 59.007 47.619 0.00 0.00 43.46 2.29
2362 2485 3.951680 CTGAACTTTGGTTTACAGGTGGT 59.048 43.478 0.00 0.00 35.58 4.16
2391 2514 5.896922 ATTCATCAGATCGAACGAATGAC 57.103 39.130 14.31 3.13 31.80 3.06
2398 2521 5.595885 TGAGGAGAATTCATCAGATCGAAC 58.404 41.667 8.44 0.00 39.05 3.95
2406 2529 7.764141 TGATTTTGTTGAGGAGAATTCATCA 57.236 32.000 8.44 6.11 41.94 3.07
2498 2621 1.004918 GAAGGTGGGACTGTGACGG 60.005 63.158 0.00 0.00 0.00 4.79
2552 2675 0.307760 CACTGGTCGGTTTTGTGCTC 59.692 55.000 0.00 0.00 0.00 4.26
2555 2678 1.101049 AGGCACTGGTCGGTTTTGTG 61.101 55.000 0.00 0.00 37.18 3.33
2556 2679 0.395173 AAGGCACTGGTCGGTTTTGT 60.395 50.000 0.00 0.00 40.86 2.83
2557 2680 1.265905 GTAAGGCACTGGTCGGTTTTG 59.734 52.381 0.00 0.00 40.86 2.44
2558 2681 1.142262 AGTAAGGCACTGGTCGGTTTT 59.858 47.619 0.00 0.00 40.86 2.43
2559 2682 0.763035 AGTAAGGCACTGGTCGGTTT 59.237 50.000 0.00 0.00 40.86 3.27
2560 2683 0.763035 AAGTAAGGCACTGGTCGGTT 59.237 50.000 0.00 0.00 40.86 4.44
2561 2684 0.763035 AAAGTAAGGCACTGGTCGGT 59.237 50.000 0.00 0.00 40.86 4.69
2562 2685 1.535462 CAAAAGTAAGGCACTGGTCGG 59.465 52.381 0.00 0.00 40.86 4.79
2563 2686 2.489971 TCAAAAGTAAGGCACTGGTCG 58.510 47.619 0.00 0.00 40.86 4.79
2564 2687 3.366374 GCATCAAAAGTAAGGCACTGGTC 60.366 47.826 0.00 0.00 40.86 4.02
2565 2688 2.558359 GCATCAAAAGTAAGGCACTGGT 59.442 45.455 0.00 0.00 40.86 4.00
2567 2690 3.921119 TGCATCAAAAGTAAGGCACTG 57.079 42.857 0.00 0.00 40.86 3.66
2571 2694 5.163519 ACACCATATGCATCAAAAGTAAGGC 60.164 40.000 0.19 0.00 0.00 4.35
2577 2700 5.105635 ACCTCAACACCATATGCATCAAAAG 60.106 40.000 0.19 0.00 0.00 2.27
2581 2704 3.650281 ACCTCAACACCATATGCATCA 57.350 42.857 0.19 0.00 0.00 3.07
2584 2707 3.760738 TGAAACCTCAACACCATATGCA 58.239 40.909 0.00 0.00 0.00 3.96
2585 2708 4.398988 TCATGAAACCTCAACACCATATGC 59.601 41.667 0.00 0.00 34.49 3.14
2586 2709 6.375174 TCTTCATGAAACCTCAACACCATATG 59.625 38.462 9.88 0.00 34.49 1.78
2591 2714 5.712152 AATCTTCATGAAACCTCAACACC 57.288 39.130 9.88 0.00 34.49 4.16
2594 2717 8.137437 TGAGAAAAATCTTCATGAAACCTCAAC 58.863 33.333 9.88 0.34 34.49 3.18
2595 2718 8.137437 GTGAGAAAAATCTTCATGAAACCTCAA 58.863 33.333 9.88 0.00 34.49 3.02
2606 2729 9.897744 GAATACATGTTGTGAGAAAAATCTTCA 57.102 29.630 2.30 0.00 0.00 3.02
2642 2765 1.281867 TCCCCTCGCAACATCATCTTT 59.718 47.619 0.00 0.00 0.00 2.52
2771 2897 3.631250 AGAATGAAAAGGTGTGGTGTGT 58.369 40.909 0.00 0.00 0.00 3.72
2772 2898 5.766150 TTAGAATGAAAAGGTGTGGTGTG 57.234 39.130 0.00 0.00 0.00 3.82
2790 2916 2.441750 GGTGAAGGGGTATGGCATTAGA 59.558 50.000 4.78 0.00 0.00 2.10
2791 2917 2.489073 GGGTGAAGGGGTATGGCATTAG 60.489 54.545 4.78 0.00 0.00 1.73
2801 2930 1.388217 TTCAAGGGGGTGAAGGGGT 60.388 57.895 0.00 0.00 32.56 4.95
2882 3014 1.068588 TGTGACTGCTCTTTGCTACGT 59.931 47.619 0.00 0.00 43.37 3.57
2915 3047 3.327464 CACATGCCGTGTATTTGCC 57.673 52.632 0.00 0.00 39.62 4.52
3022 3154 8.454106 GTGATCACACTTAAAGCATGTTTATCT 58.546 33.333 21.07 0.00 42.99 1.98
3099 3231 5.077134 TCATAATCTATCACGATGCCCAG 57.923 43.478 0.00 0.00 0.00 4.45
3101 3233 7.386299 GGATTATCATAATCTATCACGATGCCC 59.614 40.741 15.63 0.00 0.00 5.36
3126 3258 4.783667 TCCGGTCGGAAAAGTTGG 57.216 55.556 9.90 0.00 42.05 3.77
3137 3269 4.142469 CCACCAAATAGACAAAATCCGGTC 60.142 45.833 0.00 0.00 0.00 4.79
3141 3273 5.399013 CGAACCACCAAATAGACAAAATCC 58.601 41.667 0.00 0.00 0.00 3.01
3156 3288 1.447314 CCTCGTTAGCCGAACCACC 60.447 63.158 0.00 0.00 46.75 4.61
3180 3312 4.680237 CCGAGGCCACGAAGCACA 62.680 66.667 24.92 0.00 35.09 4.57
3221 3397 3.320256 TGTGGTTGCTGAATTATGTTGCA 59.680 39.130 0.00 0.00 0.00 4.08
3376 3560 5.104900 AGGGTAAAGCTTGAAGTATCGACAT 60.105 40.000 0.00 0.00 0.00 3.06
3449 3633 4.449743 GTCAACTACCGCATGTCTAAACAA 59.550 41.667 0.00 0.00 39.30 2.83
3488 3672 9.708222 CTGAAGTCATTGAACCGATTAATTTAG 57.292 33.333 0.00 0.00 0.00 1.85
3492 3677 6.878923 TCACTGAAGTCATTGAACCGATTAAT 59.121 34.615 0.00 0.00 33.46 1.40
3619 3805 3.194755 TCCAACTTAGCAATCGTAGCAGA 59.805 43.478 0.00 0.00 0.00 4.26
3674 3865 6.504398 TCTGTCGATGCTTCGTTAAGATATT 58.496 36.000 19.92 0.00 45.65 1.28
3798 4002 0.248012 TTGCCGGTTAGATCGCTGAA 59.752 50.000 1.90 0.00 0.00 3.02
3829 4040 3.056322 AGGTCAATGATTGGCAAAGCTTC 60.056 43.478 12.25 0.00 36.88 3.86
3870 4085 6.089820 CCGCTTCAAGAATTAACGTACAACTA 59.910 38.462 0.00 0.00 0.00 2.24
3871 4086 5.107220 CCGCTTCAAGAATTAACGTACAACT 60.107 40.000 0.00 0.00 0.00 3.16
3872 4087 5.077424 CCGCTTCAAGAATTAACGTACAAC 58.923 41.667 0.00 0.00 0.00 3.32
3873 4088 4.377635 GCCGCTTCAAGAATTAACGTACAA 60.378 41.667 0.00 0.00 0.00 2.41
3875 4090 3.484721 GGCCGCTTCAAGAATTAACGTAC 60.485 47.826 0.00 0.00 0.00 3.67
3876 4091 2.674357 GGCCGCTTCAAGAATTAACGTA 59.326 45.455 0.00 0.00 0.00 3.57
3877 4092 1.467342 GGCCGCTTCAAGAATTAACGT 59.533 47.619 0.00 0.00 0.00 3.99
3878 4093 1.737793 AGGCCGCTTCAAGAATTAACG 59.262 47.619 0.00 0.00 0.00 3.18
3912 4130 7.161773 CTCTCTAGCTACTACTACTACCGAT 57.838 44.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.