Multiple sequence alignment - TraesCS6A01G248400

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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 TraesCS6A01G248400 chr6A 100.000 4027 0 0 1 4027 461144380 461148406 0.000000e+00 7437.0
1 TraesCS6A01G248400 chr6A 87.981 624 61 5 3316 3937 175338133 175338744 0.000000e+00 725.0
2 TraesCS6A01G248400 chr6A 95.798 119 5 0 847 965 4929203 4929085 4.110000e-45 193.0
3 TraesCS6A01G248400 chr6A 88.136 59 7 0 3316 3374 352749200 352749142 2.010000e-08 71.3
4 TraesCS6A01G248400 chr6D 93.065 3259 146 29 51 3266 323712731 323715952 0.000000e+00 4693.0
5 TraesCS6A01G248400 chr6D 98.113 53 1 0 1 53 323712661 323712713 4.290000e-15 93.5
6 TraesCS6A01G248400 chr6B 91.858 3218 161 43 51 3199 500213107 500209922 0.000000e+00 4397.0
7 TraesCS6A01G248400 chr6B 98.113 53 1 0 1 53 500213177 500213125 4.290000e-15 93.5
8 TraesCS6A01G248400 chr2A 93.118 712 47 2 3316 4025 209230704 209231415 0.000000e+00 1042.0
9 TraesCS6A01G248400 chr2A 93.496 123 8 0 848 970 774084097 774083975 2.470000e-42 183.0
10 TraesCS6A01G248400 chr2A 93.243 74 4 1 1298 1371 774083901 774083829 1.530000e-19 108.0
11 TraesCS6A01G248400 chr4D 95.122 123 6 0 848 970 493213131 493213253 1.140000e-45 195.0
12 TraesCS6A01G248400 chr4D 93.151 73 4 1 1299 1371 493213328 493213399 5.500000e-19 106.0
13 TraesCS6A01G248400 chr4D 90.541 74 6 1 1298 1371 251093164 251093092 3.310000e-16 97.1
14 TraesCS6A01G248400 chr4D 95.455 44 2 0 1245 1288 493213254 493213297 2.010000e-08 71.3
15 TraesCS6A01G248400 chr7D 93.548 124 7 1 848 970 139228840 139228717 2.470000e-42 183.0
16 TraesCS6A01G248400 chr7D 93.243 74 4 1 1298 1371 139228643 139228571 1.530000e-19 108.0
17 TraesCS6A01G248400 chr7D 95.455 44 2 0 1245 1288 139228716 139228673 2.010000e-08 71.3
18 TraesCS6A01G248400 chr7B 93.496 123 8 0 843 965 616912392 616912514 2.470000e-42 183.0
19 TraesCS6A01G248400 chr7B 89.855 69 6 1 1303 1371 114039359 114039426 1.990000e-13 87.9
20 TraesCS6A01G248400 chr7B 89.655 58 3 3 3316 3373 235845591 235845537 2.010000e-08 71.3
21 TraesCS6A01G248400 chr3D 93.496 123 8 0 848 970 77840481 77840603 2.470000e-42 183.0
22 TraesCS6A01G248400 chr3D 92.754 69 4 1 1303 1371 77840682 77840749 9.210000e-17 99.0
23 TraesCS6A01G248400 chr4B 92.683 123 9 0 843 965 548863072 548862950 1.150000e-40 178.0
24 TraesCS6A01G248400 chr4B 85.714 77 7 4 3309 3384 151905310 151905383 1.200000e-10 78.7
25 TraesCS6A01G248400 chr5A 80.263 152 30 0 2546 2697 394181729 394181578 9.150000e-22 115.0
26 TraesCS6A01G248400 chr5D 79.605 152 31 0 2546 2697 303759498 303759347 4.260000e-20 110.0
27 TraesCS6A01G248400 chr5B 79.605 152 31 0 2546 2697 348448641 348448490 4.260000e-20 110.0
28 TraesCS6A01G248400 chr5B 78.767 146 12 11 1245 1371 484772059 484771914 3.340000e-11 80.5
29 TraesCS6A01G248400 chr3B 91.892 74 5 1 1298 1371 210688239 210688311 7.120000e-18 102.0
30 TraesCS6A01G248400 chr2B 91.304 69 5 1 1303 1371 24042162 24042095 4.290000e-15 93.5
31 TraesCS6A01G248400 chr2B 89.855 69 6 1 1303 1371 24003188 24003255 1.990000e-13 87.9
32 TraesCS6A01G248400 chr2B 83.951 81 9 3 3316 3392 412057638 412057558 1.550000e-09 75.0
33 TraesCS6A01G248400 chr7A 97.826 46 1 0 3339 3384 593430540 593430495 3.340000e-11 80.5
34 TraesCS6A01G248400 chr1A 92.453 53 3 1 3339 3390 148861135 148861083 1.550000e-09 75.0
35 TraesCS6A01G248400 chr1D 83.784 74 6 5 3321 3392 248221060 248221129 9.340000e-07 65.8
36 TraesCS6A01G248400 chr2D 84.848 66 7 3 3316 3381 56064498 56064436 3.360000e-06 63.9


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G248400 chr6A 461144380 461148406 4026 False 7437.00 7437 100.0000 1 4027 1 chr6A.!!$F2 4026
1 TraesCS6A01G248400 chr6A 175338133 175338744 611 False 725.00 725 87.9810 3316 3937 1 chr6A.!!$F1 621
2 TraesCS6A01G248400 chr6D 323712661 323715952 3291 False 2393.25 4693 95.5890 1 3266 2 chr6D.!!$F1 3265
3 TraesCS6A01G248400 chr6B 500209922 500213177 3255 True 2245.25 4397 94.9855 1 3199 2 chr6B.!!$R1 3198
4 TraesCS6A01G248400 chr2A 209230704 209231415 711 False 1042.00 1042 93.1180 3316 4025 1 chr2A.!!$F1 709

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
824 849 0.663153 GCCCTTTGCCTAACGCTATG 59.337 55.0 0.00 0.00 38.78 2.23 F
2107 2180 0.319383 ATGATCGATGAGGTGCGCTC 60.319 55.0 9.73 4.47 0.00 5.03 F
2460 2558 0.465460 TTCGCCTGACAGTTTTGCCT 60.465 50.0 0.93 0.00 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2652 2750 0.030369 GGTCGTCGCCGATGTAGATT 59.970 55.0 6.17 0.00 46.30 2.40 R
2954 3052 0.093026 GCACGAGAACCAAACGATCG 59.907 55.0 14.88 14.88 39.22 3.69 R
3271 3371 0.106769 TTGGCCTTGCTGTTGAGTCA 60.107 50.0 3.32 0.00 0.00 3.41 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
65 86 1.202188 GCTTGGTTCTTATGCTTCGGC 60.202 52.381 0.00 0.00 42.19 5.54
126 149 1.063912 TCTGGCAATTTAATCGCGCTG 59.936 47.619 5.56 0.00 0.00 5.18
142 165 2.579013 GCTGAACTTGCGTACAGAAC 57.421 50.000 0.00 0.00 32.90 3.01
182 205 5.388408 ACCTACCGTTCTTAAGTTCAGAG 57.612 43.478 1.63 0.00 0.00 3.35
371 396 9.599866 GTTTACCGTACCTTAACCATAGTTAAT 57.400 33.333 0.00 0.00 45.16 1.40
386 411 4.788925 AGTTAATGCCAACCCAGCTATA 57.211 40.909 0.00 0.00 0.00 1.31
407 432 9.065871 GCTATATGCAAGTTTTTACTTTGACAG 57.934 33.333 0.00 0.00 42.31 3.51
422 447 5.105351 ACTTTGACAGTTTCCCTTTTCCTTG 60.105 40.000 0.00 0.00 27.32 3.61
430 455 4.400529 TTCCCTTTTCCTTGTGCTTTTC 57.599 40.909 0.00 0.00 0.00 2.29
519 544 2.656007 TGGTTGTCGACGTCGTGC 60.656 61.111 34.40 27.15 40.80 5.34
542 567 7.117812 GTGCAAGTAACTAGTCTGCTATTTGAA 59.882 37.037 15.82 3.53 0.00 2.69
575 600 4.503714 ACTGAAAAGGTCCTCTTGTTGA 57.496 40.909 0.00 0.00 35.55 3.18
605 630 2.288666 GCAGTGACACCTTCTGAACAA 58.711 47.619 0.84 0.00 0.00 2.83
633 658 5.297029 AGTTTTCTCGAAAAGGAGGTTGAAG 59.703 40.000 5.15 0.00 40.53 3.02
637 662 0.881796 GAAAAGGAGGTTGAAGCCCG 59.118 55.000 0.00 0.00 0.00 6.13
667 692 5.499313 TGCATCATTCTGAACATTGGAGTA 58.501 37.500 0.00 0.00 0.00 2.59
711 736 3.429410 GCTTTTCCTATGTGCCAATCCAC 60.429 47.826 0.00 0.00 36.28 4.02
716 741 3.118261 TCCTATGTGCCAATCCACTCTTC 60.118 47.826 0.00 0.00 36.68 2.87
757 782 3.194329 TCTCTCAGCATGACAAGGTACTG 59.806 47.826 0.00 0.00 42.56 2.74
758 783 2.899900 TCTCAGCATGACAAGGTACTGT 59.100 45.455 0.00 0.00 42.56 3.55
759 784 4.086457 TCTCAGCATGACAAGGTACTGTA 58.914 43.478 0.00 0.00 42.56 2.74
760 785 4.082190 TCTCAGCATGACAAGGTACTGTAC 60.082 45.833 9.46 9.46 42.56 2.90
761 786 3.832490 TCAGCATGACAAGGTACTGTACT 59.168 43.478 16.79 0.00 42.56 2.73
824 849 0.663153 GCCCTTTGCCTAACGCTATG 59.337 55.000 0.00 0.00 38.78 2.23
827 852 1.331756 CCTTTGCCTAACGCTATGCTG 59.668 52.381 0.00 0.00 38.78 4.41
940 965 2.672478 CGACAAGACAGTGGGCTAAGAG 60.672 54.545 0.00 0.00 0.00 2.85
980 1005 2.047274 CCGCCGTTCTGACCACAT 60.047 61.111 0.00 0.00 0.00 3.21
1209 1234 1.490693 CCATGAAATCCTCGTCGCCG 61.491 60.000 0.00 0.00 0.00 6.46
1251 1276 2.997315 GGCCAGGAAAACCTGCCC 60.997 66.667 10.37 5.69 36.57 5.36
1254 1279 1.675641 CCAGGAAAACCTGCCCGAG 60.676 63.158 10.37 0.00 36.57 4.63
1299 1324 7.041508 GCATGGATGGTAAGAAGATTGACTTAG 60.042 40.741 0.00 0.00 39.13 2.18
1305 1330 6.014584 TGGTAAGAAGATTGACTTAGTGAGCA 60.015 38.462 0.00 0.00 39.13 4.26
1319 1344 7.396418 ACTTAGTGAGCAGTAGTCTAGTTACT 58.604 38.462 0.00 0.00 0.00 2.24
1370 1408 3.730761 CGTCTTGTGCTGCAGGCC 61.731 66.667 17.12 0.00 40.92 5.19
1436 1474 1.271656 GCACAAGGCAAGAAGATTGCT 59.728 47.619 11.90 0.00 44.36 3.91
1439 1477 2.295349 ACAAGGCAAGAAGATTGCTGTG 59.705 45.455 11.90 11.80 44.36 3.66
1443 1481 2.352127 GGCAAGAAGATTGCTGTGTTCC 60.352 50.000 11.90 0.00 44.36 3.62
1512 1550 0.830648 CGTCATGTCCCCTGTGGTAT 59.169 55.000 0.00 0.00 34.77 2.73
1513 1551 1.473257 CGTCATGTCCCCTGTGGTATG 60.473 57.143 0.00 0.00 33.73 2.39
1520 1558 2.304761 GTCCCCTGTGGTATGTCAGAAA 59.695 50.000 0.00 0.00 34.02 2.52
1524 1562 4.398319 CCCTGTGGTATGTCAGAAAAACT 58.602 43.478 0.00 0.00 34.02 2.66
1542 1583 9.999009 AGAAAAACTTGCTTAAACTAGTAACAC 57.001 29.630 0.00 0.00 0.00 3.32
1552 1593 8.068380 GCTTAAACTAGTAACACTTCTTGGTTG 58.932 37.037 0.00 0.00 0.00 3.77
1591 1632 5.242838 CCTGCTTATAGTTGTCCCAAAAACA 59.757 40.000 0.00 0.00 0.00 2.83
1760 1811 6.183360 CCAGTGATATGCAATTATATGCCTGG 60.183 42.308 0.00 0.00 45.83 4.45
1815 1866 9.458727 AGAATCCTAGTGATATGCAATTAATGG 57.541 33.333 0.00 0.00 31.83 3.16
1982 2033 4.589216 TTTCCTGCTCATTTGTTTCAGG 57.411 40.909 0.00 0.00 44.18 3.86
1994 2045 9.525409 CTCATTTGTTTCAGGGATGATAAAATC 57.475 33.333 0.00 0.00 0.00 2.17
2009 2082 3.764885 AAAATCCACTGTCTTATGCGC 57.235 42.857 0.00 0.00 0.00 6.09
2018 2091 1.858458 TGTCTTATGCGCGCAATACTC 59.142 47.619 39.68 26.23 0.00 2.59
2021 2094 1.592543 CTTATGCGCGCAATACTCACA 59.407 47.619 39.68 11.83 0.00 3.58
2022 2095 1.646189 TATGCGCGCAATACTCACAA 58.354 45.000 39.68 10.93 0.00 3.33
2025 2098 1.198867 TGCGCGCAATACTCACAATTT 59.801 42.857 34.66 0.00 0.00 1.82
2107 2180 0.319383 ATGATCGATGAGGTGCGCTC 60.319 55.000 9.73 4.47 0.00 5.03
2206 2285 2.433239 AGGGATTCCATTCATGCAAAGC 59.567 45.455 4.80 0.00 34.83 3.51
2228 2307 4.376413 GCTCAGTGATTCTTGTGTTGTACG 60.376 45.833 0.00 0.00 0.00 3.67
2229 2308 4.689071 TCAGTGATTCTTGTGTTGTACGT 58.311 39.130 0.00 0.00 0.00 3.57
2230 2309 5.834169 TCAGTGATTCTTGTGTTGTACGTA 58.166 37.500 0.00 0.00 0.00 3.57
2231 2310 5.688621 TCAGTGATTCTTGTGTTGTACGTAC 59.311 40.000 18.90 18.90 0.00 3.67
2287 2366 1.257743 CCCTCTTGGAAGTCACGAGA 58.742 55.000 0.00 0.00 42.38 4.04
2383 2462 2.788191 AAAAGAGACCCTGCGCCTCG 62.788 60.000 4.18 0.00 32.52 4.63
2426 2509 2.561569 CTCTTCTCTCGGTCTCTCCTC 58.438 57.143 0.00 0.00 0.00 3.71
2460 2558 0.465460 TTCGCCTGACAGTTTTGCCT 60.465 50.000 0.93 0.00 0.00 4.75
2469 2567 1.068585 AGTTTTGCCTGCTTGCTGC 59.931 52.632 0.00 0.00 43.25 5.25
2520 2618 1.207329 GTAAACGAGGTGCTGGAGGAT 59.793 52.381 0.00 0.00 0.00 3.24
2527 2625 1.691219 GTGCTGGAGGATTTCCCCA 59.309 57.895 6.63 6.63 46.19 4.96
2625 2723 3.184683 CTGCTTCAGTCGCTCGGC 61.185 66.667 0.00 0.00 0.00 5.54
2652 2750 2.355986 CCCCGAGAACGTGATCCCA 61.356 63.158 0.00 0.00 37.88 4.37
2799 2897 1.168714 GTTGGTTCCATCAGGTGCTC 58.831 55.000 0.00 0.00 35.89 4.26
2817 2915 4.148825 CGGGAGAGGAACTGCGGG 62.149 72.222 0.00 0.00 41.55 6.13
2907 3005 9.262358 TCTGAAGTAAAGCTCTTTCTAGTTTTC 57.738 33.333 0.00 0.00 32.88 2.29
2951 3049 4.002982 TCTGTTCAACGAATGGATTCCTG 58.997 43.478 3.95 0.00 33.28 3.86
2952 3050 4.002982 CTGTTCAACGAATGGATTCCTGA 58.997 43.478 3.95 0.00 33.28 3.86
2953 3051 4.588899 TGTTCAACGAATGGATTCCTGAT 58.411 39.130 3.95 0.00 33.28 2.90
2954 3052 4.635765 TGTTCAACGAATGGATTCCTGATC 59.364 41.667 3.95 0.00 33.28 2.92
3033 3131 2.145053 GCACTCGCTATGAACAAACG 57.855 50.000 0.00 0.00 34.30 3.60
3043 3141 3.703001 ATGAACAAACGGGAGATGACT 57.297 42.857 0.00 0.00 0.00 3.41
3044 3142 2.766313 TGAACAAACGGGAGATGACTG 58.234 47.619 0.00 0.00 0.00 3.51
3103 3203 3.609644 CGTAGCTAGGGTCGAATGATGTC 60.610 52.174 5.50 0.00 0.00 3.06
3192 3292 1.474077 AGAAATTTGATCGGTGGCTGC 59.526 47.619 0.00 0.00 0.00 5.25
3213 3313 3.496884 GCGTTGGTCTCTTGACATTGTAA 59.503 43.478 0.00 0.00 44.61 2.41
3225 3325 5.058149 TGACATTGTAATTCGCAAGCAAT 57.942 34.783 0.00 0.00 37.18 3.56
3226 3326 6.188400 TGACATTGTAATTCGCAAGCAATA 57.812 33.333 0.00 0.00 37.18 1.90
3227 3327 6.794374 TGACATTGTAATTCGCAAGCAATAT 58.206 32.000 0.00 0.00 37.18 1.28
3246 3346 0.391597 TATAGGCCTTTTCCCTCGCG 59.608 55.000 12.58 0.00 33.88 5.87
3266 3366 6.547283 TCGCGTTCAATGCTGATAAATAAAA 58.453 32.000 5.77 0.00 0.00 1.52
3267 3367 7.024171 TCGCGTTCAATGCTGATAAATAAAAA 58.976 30.769 5.77 0.00 0.00 1.94
3286 3386 3.996150 AAACATGACTCAACAGCAAGG 57.004 42.857 0.00 0.00 0.00 3.61
3287 3387 1.242076 ACATGACTCAACAGCAAGGC 58.758 50.000 0.00 0.00 0.00 4.35
3288 3388 0.524862 CATGACTCAACAGCAAGGCC 59.475 55.000 0.00 0.00 0.00 5.19
3289 3389 0.111061 ATGACTCAACAGCAAGGCCA 59.889 50.000 5.01 0.00 0.00 5.36
3290 3390 0.106769 TGACTCAACAGCAAGGCCAA 60.107 50.000 5.01 0.00 0.00 4.52
3291 3391 1.032014 GACTCAACAGCAAGGCCAAA 58.968 50.000 5.01 0.00 0.00 3.28
3292 3392 1.408702 GACTCAACAGCAAGGCCAAAA 59.591 47.619 5.01 0.00 0.00 2.44
3293 3393 1.136891 ACTCAACAGCAAGGCCAAAAC 59.863 47.619 5.01 0.00 0.00 2.43
3294 3394 1.410153 CTCAACAGCAAGGCCAAAACT 59.590 47.619 5.01 0.00 0.00 2.66
3295 3395 1.408702 TCAACAGCAAGGCCAAAACTC 59.591 47.619 5.01 0.00 0.00 3.01
3296 3396 0.752658 AACAGCAAGGCCAAAACTCC 59.247 50.000 5.01 0.00 0.00 3.85
3297 3397 0.396974 ACAGCAAGGCCAAAACTCCA 60.397 50.000 5.01 0.00 0.00 3.86
3298 3398 0.316204 CAGCAAGGCCAAAACTCCAG 59.684 55.000 5.01 0.00 0.00 3.86
3299 3399 1.005748 GCAAGGCCAAAACTCCAGC 60.006 57.895 5.01 0.00 0.00 4.85
3300 3400 1.286880 CAAGGCCAAAACTCCAGCG 59.713 57.895 5.01 0.00 0.00 5.18
3301 3401 1.150536 AAGGCCAAAACTCCAGCGA 59.849 52.632 5.01 0.00 0.00 4.93
3302 3402 0.467290 AAGGCCAAAACTCCAGCGAA 60.467 50.000 5.01 0.00 0.00 4.70
3303 3403 0.251341 AGGCCAAAACTCCAGCGAAT 60.251 50.000 5.01 0.00 0.00 3.34
3304 3404 1.004277 AGGCCAAAACTCCAGCGAATA 59.996 47.619 5.01 0.00 0.00 1.75
3305 3405 1.132453 GGCCAAAACTCCAGCGAATAC 59.868 52.381 0.00 0.00 0.00 1.89
3306 3406 2.084546 GCCAAAACTCCAGCGAATACT 58.915 47.619 0.00 0.00 0.00 2.12
3307 3407 2.488153 GCCAAAACTCCAGCGAATACTT 59.512 45.455 0.00 0.00 0.00 2.24
3308 3408 3.670627 GCCAAAACTCCAGCGAATACTTG 60.671 47.826 0.00 0.00 0.00 3.16
3309 3409 3.492313 CAAAACTCCAGCGAATACTTGC 58.508 45.455 0.00 0.00 0.00 4.01
3310 3410 1.739067 AACTCCAGCGAATACTTGCC 58.261 50.000 0.00 0.00 0.00 4.52
3311 3411 0.613260 ACTCCAGCGAATACTTGCCA 59.387 50.000 0.00 0.00 0.00 4.92
3312 3412 1.210478 ACTCCAGCGAATACTTGCCAT 59.790 47.619 0.00 0.00 0.00 4.40
3313 3413 1.869767 CTCCAGCGAATACTTGCCATC 59.130 52.381 0.00 0.00 0.00 3.51
3314 3414 0.583438 CCAGCGAATACTTGCCATCG 59.417 55.000 0.00 0.00 38.28 3.84
3440 3541 2.603776 ACCTTTCCTCGGGAGCGT 60.604 61.111 0.00 0.00 31.21 5.07
3458 3559 0.460987 GTCCGATTGTCTCTGGGCTG 60.461 60.000 0.00 0.00 0.00 4.85
3464 3565 3.791586 GTCTCTGGGCTGGGGCTC 61.792 72.222 0.00 0.00 39.89 4.70
3653 3754 1.751162 CTCCTCGCCCTCGTCTTCT 60.751 63.158 0.00 0.00 36.96 2.85
3665 3766 2.125912 TCTTCTTCTCTGCGCCGC 60.126 61.111 4.18 0.00 0.00 6.53
3749 3850 1.525995 CTGCACCAACGACCCTGTT 60.526 57.895 0.00 0.00 0.00 3.16
3758 3859 1.154225 CGACCCTGTTTGCATTCGC 60.154 57.895 0.00 0.00 39.24 4.70
3855 3957 2.002586 CTGTGATTGCTAAGGTGTCCG 58.997 52.381 0.00 0.00 0.00 4.79
3924 4026 4.385405 AGCCTGGACAGAGTGCGC 62.385 66.667 0.00 0.00 0.00 6.09
3962 4064 3.140814 GTTGCGCCCAATCTCCCC 61.141 66.667 4.18 0.00 32.75 4.81
3973 4075 1.700042 AATCTCCCCCTCGTGATGGC 61.700 60.000 0.00 0.00 0.00 4.40
4025 4127 0.104855 TCTGTGTTCTGCAACGCTCT 59.895 50.000 3.91 0.00 42.61 4.09
4026 4128 0.510359 CTGTGTTCTGCAACGCTCTC 59.490 55.000 3.91 0.00 42.61 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.965643 ACGTCAGGTTACAGCAGGTTA 59.034 47.619 0.00 0.00 0.00 2.85
65 86 0.955428 ATTGCGCCGCTATACCATGG 60.955 55.000 11.67 11.19 0.00 3.66
182 205 2.033424 GGTGAGTGTTTCTGTTTCTGCC 59.967 50.000 0.00 0.00 0.00 4.85
339 364 5.772672 TGGTTAAGGTACGGTAAACTACTCA 59.227 40.000 4.44 0.00 0.00 3.41
340 365 6.267496 TGGTTAAGGTACGGTAAACTACTC 57.733 41.667 4.44 0.00 0.00 2.59
341 366 6.857437 ATGGTTAAGGTACGGTAAACTACT 57.143 37.500 4.44 0.00 0.00 2.57
342 367 7.772166 ACTATGGTTAAGGTACGGTAAACTAC 58.228 38.462 4.44 0.00 0.00 2.73
371 396 0.550432 TGCATATAGCTGGGTTGGCA 59.450 50.000 0.00 0.00 45.94 4.92
386 411 7.277760 GGAAACTGTCAAAGTAAAAACTTGCAT 59.722 33.333 0.00 0.00 38.56 3.96
407 432 3.819564 AAGCACAAGGAAAAGGGAAAC 57.180 42.857 0.00 0.00 0.00 2.78
422 447 3.733443 AACAACATCCAGGAAAAGCAC 57.267 42.857 0.00 0.00 0.00 4.40
430 455 4.401925 AGAGGAAGAAAACAACATCCAGG 58.598 43.478 0.00 0.00 32.47 4.45
519 544 8.764524 AGTTCAAATAGCAGACTAGTTACTTG 57.235 34.615 0.00 0.00 34.57 3.16
542 567 3.117776 ACCTTTTCAGTTACCCGGAAAGT 60.118 43.478 0.73 0.00 38.27 2.66
563 588 5.106712 TGCACGAATTAATCAACAAGAGGAC 60.107 40.000 0.00 0.00 0.00 3.85
575 600 3.674997 AGGTGTCACTGCACGAATTAAT 58.325 40.909 2.35 0.00 40.08 1.40
605 630 3.391049 CTCCTTTTCGAGAAAACTCCGT 58.609 45.455 6.89 0.00 35.57 4.69
615 640 1.807142 GGCTTCAACCTCCTTTTCGAG 59.193 52.381 0.00 0.00 0.00 4.04
637 662 0.182061 TCAGAATGATGCAGAGGCCC 59.818 55.000 0.00 0.00 42.56 5.80
667 692 1.363807 GCAAAGCCAGCTCCGTTTT 59.636 52.632 0.00 0.00 0.00 2.43
711 736 9.234827 AGAGATGACACATCTATATCAGAAGAG 57.765 37.037 13.15 0.00 36.67 2.85
716 741 8.564509 TGAGAGAGATGACACATCTATATCAG 57.435 38.462 21.39 0.00 34.12 2.90
757 782 7.215085 AGGTAATTCGGGATGATTTGTAGTAC 58.785 38.462 0.00 0.00 0.00 2.73
758 783 7.369551 AGGTAATTCGGGATGATTTGTAGTA 57.630 36.000 0.00 0.00 0.00 1.82
759 784 6.248569 AGGTAATTCGGGATGATTTGTAGT 57.751 37.500 0.00 0.00 0.00 2.73
760 785 6.992715 AGAAGGTAATTCGGGATGATTTGTAG 59.007 38.462 0.00 0.00 43.16 2.74
761 786 6.895782 AGAAGGTAATTCGGGATGATTTGTA 58.104 36.000 0.00 0.00 43.16 2.41
824 849 0.612744 AACTGAGGAGAGAAGGCAGC 59.387 55.000 0.00 0.00 0.00 5.25
827 852 1.620819 TGTGAACTGAGGAGAGAAGGC 59.379 52.381 0.00 0.00 0.00 4.35
940 965 3.119316 TCGTCTCTCTTTCAGCTGGATTC 60.119 47.826 15.13 0.00 0.00 2.52
994 1019 1.133025 GTTGCTCAAATCCATCGGGTG 59.867 52.381 0.00 0.00 34.93 4.61
1209 1234 0.110823 CCACGTTGTGCTTCTTACGC 60.111 55.000 0.00 0.00 37.51 4.42
1251 1276 1.339610 CTGTAGGCAGGATCTTCCTCG 59.660 57.143 4.62 0.00 45.66 4.63
1254 1279 1.474143 GCACTGTAGGCAGGATCTTCC 60.474 57.143 0.00 0.00 46.62 3.46
1299 1324 6.913673 GCATAAGTAACTAGACTACTGCTCAC 59.086 42.308 0.00 0.00 35.58 3.51
1305 1330 8.276477 AGAAGAGGCATAAGTAACTAGACTACT 58.724 37.037 0.00 0.00 0.00 2.57
1319 1344 6.365970 AGTCTTTCTTCAGAAGAGGCATAA 57.634 37.500 12.74 3.85 39.03 1.90
1370 1408 1.035932 CCAGAGCAGAGGGGCATTTG 61.036 60.000 0.00 0.00 35.83 2.32
1436 1474 1.548719 CCATCGTAGTCCAGGAACACA 59.451 52.381 0.00 0.00 0.00 3.72
1439 1477 0.535335 TGCCATCGTAGTCCAGGAAC 59.465 55.000 0.00 0.00 0.00 3.62
1443 1481 1.144057 GGGTGCCATCGTAGTCCAG 59.856 63.158 0.00 0.00 0.00 3.86
1512 1550 8.276252 ACTAGTTTAAGCAAGTTTTTCTGACA 57.724 30.769 0.00 0.00 0.00 3.58
1520 1558 9.392259 AGAAGTGTTACTAGTTTAAGCAAGTTT 57.608 29.630 0.00 0.00 0.00 2.66
1524 1562 7.771826 ACCAAGAAGTGTTACTAGTTTAAGCAA 59.228 33.333 0.00 0.00 0.00 3.91
1542 1583 4.741676 GCTCATTTGTTGACAACCAAGAAG 59.258 41.667 15.59 12.26 38.91 2.85
1552 1593 2.056094 GCAGGTGCTCATTTGTTGAC 57.944 50.000 0.00 0.00 38.21 3.18
1591 1632 5.130809 AGCAGCTCTCATCTAAGGAGAAAAT 59.869 40.000 0.00 0.00 40.64 1.82
1657 1700 1.198759 CCTTCTTCCGGGACCTTCCA 61.199 60.000 0.00 0.00 38.64 3.53
1835 1886 7.953005 TCAAGAACCTGCATAAATTGGAATA 57.047 32.000 0.00 0.00 0.00 1.75
1982 2033 7.571983 CGCATAAGACAGTGGATTTTATCATCC 60.572 40.741 0.00 0.00 43.03 3.51
1994 2045 1.634757 TTGCGCGCATAAGACAGTGG 61.635 55.000 36.83 0.00 0.00 4.00
2009 2082 7.743104 AGAGTTAAGAAATTGTGAGTATTGCG 58.257 34.615 0.00 0.00 0.00 4.85
2018 2091 8.936864 CCCTACAAGTAGAGTTAAGAAATTGTG 58.063 37.037 8.76 0.00 35.21 3.33
2021 2094 7.686434 TGCCCTACAAGTAGAGTTAAGAAATT 58.314 34.615 8.76 0.00 35.21 1.82
2022 2095 7.253905 TGCCCTACAAGTAGAGTTAAGAAAT 57.746 36.000 8.76 0.00 35.21 2.17
2025 2098 6.495872 TCTTTGCCCTACAAGTAGAGTTAAGA 59.504 38.462 8.76 8.91 40.06 2.10
2107 2180 8.610896 CAGCTTCATCAGAGTTAAATAAGAAGG 58.389 37.037 0.00 0.00 32.73 3.46
2179 2258 3.255149 GCATGAATGGAATCCCTGTCATC 59.745 47.826 0.00 0.00 0.00 2.92
2206 2285 4.745125 ACGTACAACACAAGAATCACTGAG 59.255 41.667 0.00 0.00 0.00 3.35
2228 2307 7.629130 TGCGAAAAATACCCATTAATACGTAC 58.371 34.615 0.00 0.00 0.00 3.67
2229 2308 7.783090 TGCGAAAAATACCCATTAATACGTA 57.217 32.000 0.00 0.00 0.00 3.57
2230 2309 6.680874 TGCGAAAAATACCCATTAATACGT 57.319 33.333 0.00 0.00 0.00 3.57
2231 2310 6.967767 TGTTGCGAAAAATACCCATTAATACG 59.032 34.615 0.00 0.00 0.00 3.06
2287 2366 2.105128 CTCGCGCCTTCGATTCCT 59.895 61.111 0.00 0.00 37.87 3.36
2314 2393 3.173668 ACAGACACGCAGAACTTGTTA 57.826 42.857 0.00 0.00 29.43 2.41
2367 2446 4.742649 TCGAGGCGCAGGGTCTCT 62.743 66.667 16.43 0.00 45.46 3.10
2426 2509 1.889105 CGAATCTGCCGTCCATGGG 60.889 63.158 13.02 0.00 0.00 4.00
2469 2567 3.073735 AGCTCCCAGTCCTGCGAG 61.074 66.667 4.89 4.89 38.25 5.03
2527 2625 1.202651 CCCGTTGGTCACTTTGAGAGT 60.203 52.381 0.00 0.00 39.89 3.24
2625 2723 3.068691 TTCTCGGGGTCGCTCAGG 61.069 66.667 0.00 0.00 36.13 3.86
2635 2733 0.178068 ATTGGGATCACGTTCTCGGG 59.822 55.000 0.00 0.00 42.43 5.14
2652 2750 0.030369 GGTCGTCGCCGATGTAGATT 59.970 55.000 6.17 0.00 46.30 2.40
2799 2897 4.148825 CCGCAGTTCCTCTCCCGG 62.149 72.222 0.00 0.00 33.77 5.73
2817 2915 0.310232 GCGAGACCAGTATCCCGTAC 59.690 60.000 0.00 0.00 0.00 3.67
2907 3005 1.003597 AGCAGGAGCAGAGCACAAG 60.004 57.895 0.00 0.00 45.49 3.16
2951 3049 2.279136 CACGAGAACCAAACGATCGATC 59.721 50.000 24.34 15.68 37.16 3.69
2952 3050 2.259618 CACGAGAACCAAACGATCGAT 58.740 47.619 24.34 7.21 37.16 3.59
2953 3051 1.693467 CACGAGAACCAAACGATCGA 58.307 50.000 24.34 0.00 37.16 3.59
2954 3052 0.093026 GCACGAGAACCAAACGATCG 59.907 55.000 14.88 14.88 39.22 3.69
3033 3131 2.758979 TCGGAAACTACAGTCATCTCCC 59.241 50.000 0.00 0.00 0.00 4.30
3043 3141 0.242825 CTGTCGCCTCGGAAACTACA 59.757 55.000 0.00 0.00 0.00 2.74
3044 3142 0.243095 ACTGTCGCCTCGGAAACTAC 59.757 55.000 0.00 0.00 0.00 2.73
3103 3203 1.426041 CGAATTAACAGGGGACGGCG 61.426 60.000 4.80 4.80 0.00 6.46
3192 3292 5.862924 ATTACAATGTCAAGAGACCAACG 57.137 39.130 0.00 0.00 44.33 4.10
3213 3313 4.848357 AGGCCTATATATTGCTTGCGAAT 58.152 39.130 1.29 0.00 0.00 3.34
3225 3325 2.232941 CGCGAGGGAAAAGGCCTATATA 59.767 50.000 5.16 0.00 0.00 0.86
3226 3326 1.002087 CGCGAGGGAAAAGGCCTATAT 59.998 52.381 5.16 0.00 0.00 0.86
3227 3327 0.391597 CGCGAGGGAAAAGGCCTATA 59.608 55.000 5.16 0.00 0.00 1.31
3266 3366 2.035066 GCCTTGCTGTTGAGTCATGTTT 59.965 45.455 0.00 0.00 0.00 2.83
3267 3367 1.610522 GCCTTGCTGTTGAGTCATGTT 59.389 47.619 0.00 0.00 0.00 2.71
3268 3368 1.242076 GCCTTGCTGTTGAGTCATGT 58.758 50.000 0.00 0.00 0.00 3.21
3269 3369 0.524862 GGCCTTGCTGTTGAGTCATG 59.475 55.000 0.00 0.00 0.00 3.07
3270 3370 0.111061 TGGCCTTGCTGTTGAGTCAT 59.889 50.000 3.32 0.00 0.00 3.06
3271 3371 0.106769 TTGGCCTTGCTGTTGAGTCA 60.107 50.000 3.32 0.00 0.00 3.41
3272 3372 1.032014 TTTGGCCTTGCTGTTGAGTC 58.968 50.000 3.32 0.00 0.00 3.36
3273 3373 1.136891 GTTTTGGCCTTGCTGTTGAGT 59.863 47.619 3.32 0.00 0.00 3.41
3274 3374 1.410153 AGTTTTGGCCTTGCTGTTGAG 59.590 47.619 3.32 0.00 0.00 3.02
3275 3375 1.408702 GAGTTTTGGCCTTGCTGTTGA 59.591 47.619 3.32 0.00 0.00 3.18
3276 3376 1.538849 GGAGTTTTGGCCTTGCTGTTG 60.539 52.381 3.32 0.00 0.00 3.33
3277 3377 0.752658 GGAGTTTTGGCCTTGCTGTT 59.247 50.000 3.32 0.00 0.00 3.16
3278 3378 0.396974 TGGAGTTTTGGCCTTGCTGT 60.397 50.000 3.32 0.00 0.00 4.40
3279 3379 0.316204 CTGGAGTTTTGGCCTTGCTG 59.684 55.000 3.32 0.00 0.00 4.41
3280 3380 1.466851 GCTGGAGTTTTGGCCTTGCT 61.467 55.000 3.32 0.00 0.00 3.91
3281 3381 1.005748 GCTGGAGTTTTGGCCTTGC 60.006 57.895 3.32 0.00 0.00 4.01
3282 3382 1.172180 TCGCTGGAGTTTTGGCCTTG 61.172 55.000 3.32 0.00 0.00 3.61
3283 3383 0.467290 TTCGCTGGAGTTTTGGCCTT 60.467 50.000 3.32 0.00 0.00 4.35
3284 3384 0.251341 ATTCGCTGGAGTTTTGGCCT 60.251 50.000 3.32 0.00 0.00 5.19
3285 3385 1.132453 GTATTCGCTGGAGTTTTGGCC 59.868 52.381 0.00 0.00 0.00 5.36
3286 3386 2.084546 AGTATTCGCTGGAGTTTTGGC 58.915 47.619 0.00 0.00 0.00 4.52
3287 3387 3.670627 GCAAGTATTCGCTGGAGTTTTGG 60.671 47.826 0.00 0.00 0.00 3.28
3288 3388 3.492313 GCAAGTATTCGCTGGAGTTTTG 58.508 45.455 0.00 0.00 0.00 2.44
3289 3389 2.488153 GGCAAGTATTCGCTGGAGTTTT 59.512 45.455 0.00 0.00 0.00 2.43
3290 3390 2.084546 GGCAAGTATTCGCTGGAGTTT 58.915 47.619 0.00 0.00 0.00 2.66
3291 3391 1.003118 TGGCAAGTATTCGCTGGAGTT 59.997 47.619 0.00 0.00 0.00 3.01
3292 3392 0.613260 TGGCAAGTATTCGCTGGAGT 59.387 50.000 0.00 0.00 0.00 3.85
3293 3393 1.869767 GATGGCAAGTATTCGCTGGAG 59.130 52.381 0.00 0.00 0.00 3.86
3294 3394 1.806247 CGATGGCAAGTATTCGCTGGA 60.806 52.381 0.00 0.00 0.00 3.86
3295 3395 0.583438 CGATGGCAAGTATTCGCTGG 59.417 55.000 0.00 0.00 0.00 4.85
3296 3396 1.258982 GACGATGGCAAGTATTCGCTG 59.741 52.381 7.31 0.00 35.08 5.18
3297 3397 1.571919 GACGATGGCAAGTATTCGCT 58.428 50.000 7.31 0.00 35.08 4.93
3298 3398 0.582005 GGACGATGGCAAGTATTCGC 59.418 55.000 7.31 1.38 35.08 4.70
3299 3399 0.852777 CGGACGATGGCAAGTATTCG 59.147 55.000 5.94 5.94 37.60 3.34
3300 3400 1.217882 CCGGACGATGGCAAGTATTC 58.782 55.000 0.00 0.00 0.00 1.75
3301 3401 3.379650 CCGGACGATGGCAAGTATT 57.620 52.632 0.00 0.00 0.00 1.89
3413 3514 0.246910 GAGGAAAGGTCGAGGACACC 59.753 60.000 0.00 0.00 33.68 4.16
3440 3541 1.617018 CCAGCCCAGAGACAATCGGA 61.617 60.000 0.00 0.00 0.00 4.55
3487 3588 4.899239 CACCCGCCGATGAGGAGC 62.899 72.222 0.00 0.00 45.00 4.70
3563 3664 2.438434 CACATGGCCTTCCGGGAC 60.438 66.667 3.32 0.00 45.52 4.46
3636 3737 1.304217 AAGAAGACGAGGGCGAGGA 60.304 57.895 0.00 0.00 41.64 3.71
3653 3754 3.356639 AATCTCGCGGCGCAGAGAA 62.357 57.895 38.43 28.29 39.78 2.87
3665 3766 4.554292 CATACATGTCCTGAGGAATCTCG 58.446 47.826 0.96 0.00 42.79 4.04
3894 3996 2.110967 CAGGCTCCTGCAATGTCCG 61.111 63.158 2.59 0.00 41.91 4.79
3924 4026 3.545481 CAGAGCTAACGCACGCGG 61.545 66.667 16.70 0.00 44.69 6.46
4001 4103 0.953727 GTTGCAGAACACAGATGCCA 59.046 50.000 0.00 0.00 39.22 4.92


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

AutoCloner maintained by Alex Coulton.