Multiple sequence alignment - TraesCS5D01G028300

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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 TraesCS5D01G028300 chr5D 100.000 3924 0 0 1 3924 26927855 26923932 0.000000e+00 7247.0
1 TraesCS5D01G028300 chr5D 85.668 1235 158 10 1298 2530 27053322 27054539 0.000000e+00 1282.0
2 TraesCS5D01G028300 chr5D 85.691 1202 158 7 1330 2530 27261750 27260562 0.000000e+00 1254.0
3 TraesCS5D01G028300 chr5D 93.008 472 23 2 2213 2684 26936854 26936393 0.000000e+00 680.0
4 TraesCS5D01G028300 chr5D 77.030 1219 238 28 1302 2505 27260500 27259309 0.000000e+00 662.0
5 TraesCS5D01G028300 chr5D 82.420 529 70 10 1078 1598 26968879 26968366 1.290000e-119 440.0
6 TraesCS5D01G028300 chr5D 95.238 84 3 1 2679 2762 26932554 26932472 8.850000e-27 132.0
7 TraesCS5D01G028300 chr5D 90.323 62 3 2 3856 3914 352696605 352696544 1.170000e-10 78.7
8 TraesCS5D01G028300 chr5D 97.368 38 1 0 3848 3885 95236351 95236388 9.100000e-07 65.8
9 TraesCS5D01G028300 chr5B 91.342 3881 243 27 1 3826 19458214 19454372 0.000000e+00 5219.0
10 TraesCS5D01G028300 chr5B 85.167 2009 202 33 1078 3041 19460421 19458464 0.000000e+00 1971.0
11 TraesCS5D01G028300 chr5B 88.406 69 7 1 3855 3922 122434236 122434168 9.040000e-12 82.4
12 TraesCS5D01G028300 chr5A 89.409 2691 218 39 1078 3722 18663763 18661094 0.000000e+00 3328.0
13 TraesCS5D01G028300 chr5A 85.691 1237 161 9 1298 2532 18679123 18680345 0.000000e+00 1290.0
14 TraesCS5D01G028300 chr5A 82.908 1451 178 39 1590 3011 62978360 62976951 0.000000e+00 1242.0
15 TraesCS5D01G028300 chr5A 88.710 62 4 2 3856 3914 193612383 193612322 5.440000e-09 73.1
16 TraesCS5D01G028300 chr7B 85.450 2000 217 34 1292 3252 595531024 595532988 0.000000e+00 2013.0
17 TraesCS5D01G028300 chr1B 85.358 1243 157 15 1298 2532 630923543 630922318 0.000000e+00 1264.0
18 TraesCS5D01G028300 chr1B 88.235 68 7 1 3856 3922 561254696 561254629 3.250000e-11 80.5
19 TraesCS5D01G028300 chr3A 90.323 62 3 2 3856 3914 286444509 286444570 1.170000e-10 78.7
20 TraesCS5D01G028300 chr2A 90.000 60 5 1 3854 3912 628585147 628585088 4.200000e-10 76.8
21 TraesCS5D01G028300 chr4B 87.500 64 6 2 3856 3918 364681452 364681514 5.440000e-09 73.1
22 TraesCS5D01G028300 chrUn 97.297 37 1 0 3849 3885 79069209 79069245 3.270000e-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 TraesCS5D01G028300 chr5D 26923932 26927855 3923 True 7247 7247 100.0000 1 3924 1 chr5D.!!$R1 3923
1 TraesCS5D01G028300 chr5D 27053322 27054539 1217 False 1282 1282 85.6680 1298 2530 1 chr5D.!!$F1 1232
2 TraesCS5D01G028300 chr5D 27259309 27261750 2441 True 958 1254 81.3605 1302 2530 2 chr5D.!!$R5 1228
3 TraesCS5D01G028300 chr5D 26968366 26968879 513 True 440 440 82.4200 1078 1598 1 chr5D.!!$R2 520
4 TraesCS5D01G028300 chr5D 26932472 26936854 4382 True 406 680 94.1230 2213 2762 2 chr5D.!!$R4 549
5 TraesCS5D01G028300 chr5B 19454372 19460421 6049 True 3595 5219 88.2545 1 3826 2 chr5B.!!$R2 3825
6 TraesCS5D01G028300 chr5A 18661094 18663763 2669 True 3328 3328 89.4090 1078 3722 1 chr5A.!!$R1 2644
7 TraesCS5D01G028300 chr5A 18679123 18680345 1222 False 1290 1290 85.6910 1298 2532 1 chr5A.!!$F1 1234
8 TraesCS5D01G028300 chr5A 62976951 62978360 1409 True 1242 1242 82.9080 1590 3011 1 chr5A.!!$R2 1421
9 TraesCS5D01G028300 chr7B 595531024 595532988 1964 False 2013 2013 85.4500 1292 3252 1 chr7B.!!$F1 1960
10 TraesCS5D01G028300 chr1B 630922318 630923543 1225 True 1264 1264 85.3580 1298 2532 1 chr1B.!!$R2 1234

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
115 2323 0.109365 CTCCATATGCGCTCCTCGAG 60.109 60.0 9.73 5.13 41.67 4.04 F
1832 4071 0.112025 TGTTCCATGATGCACCCACA 59.888 50.0 0.00 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 4158 0.381801 CACAGTGTGGTTCCAGCAAC 59.618 55.0 15.86 0.0 0.00 4.17 R
3656 10019 0.108396 CATGTCACCTGTGGTCACCA 59.892 55.0 0.00 0.0 31.02 4.17 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
106 2314 0.605589 GGTCCTCTCCTCCATATGCG 59.394 60.000 0.00 0.00 0.00 4.73
108 2316 0.178950 TCCTCTCCTCCATATGCGCT 60.179 55.000 9.73 0.00 0.00 5.92
109 2317 0.246086 CCTCTCCTCCATATGCGCTC 59.754 60.000 9.73 0.00 0.00 5.03
110 2318 0.246086 CTCTCCTCCATATGCGCTCC 59.754 60.000 9.73 0.00 0.00 4.70
111 2319 0.178950 TCTCCTCCATATGCGCTCCT 60.179 55.000 9.73 0.00 0.00 3.69
112 2320 0.246086 CTCCTCCATATGCGCTCCTC 59.754 60.000 9.73 0.00 0.00 3.71
113 2321 1.080230 CCTCCATATGCGCTCCTCG 60.080 63.158 9.73 0.00 42.12 4.63
114 2322 1.527433 CCTCCATATGCGCTCCTCGA 61.527 60.000 9.73 0.00 41.67 4.04
115 2323 0.109365 CTCCATATGCGCTCCTCGAG 60.109 60.000 9.73 5.13 41.67 4.04
116 2324 1.080230 CCATATGCGCTCCTCGAGG 60.080 63.158 26.32 26.32 41.67 4.63
169 2377 7.336427 GCGGGACTATAGTTAGCTCTCTTATAA 59.664 40.741 6.88 0.00 0.00 0.98
245 2454 7.449704 GCCATGTGGATTAAGAATAAGATTCCT 59.550 37.037 2.55 0.00 37.39 3.36
284 2493 2.119611 TGGCGAAGAGGAGGTGGA 59.880 61.111 0.00 0.00 0.00 4.02
305 2514 3.755112 TGGTCGTTTGGTCATTAGTCA 57.245 42.857 0.00 0.00 0.00 3.41
314 2523 7.555195 TCGTTTGGTCATTAGTCATCTAGAGTA 59.445 37.037 0.00 0.00 0.00 2.59
335 2544 2.705658 AGTGGATCTGGTTCTGTGTTCA 59.294 45.455 0.00 0.00 0.00 3.18
345 2554 4.464244 TGGTTCTGTGTTCATGTTTTTGGA 59.536 37.500 0.00 0.00 0.00 3.53
373 2582 2.143925 CTTTGGAAGGTCCGTCAAGAC 58.856 52.381 7.15 0.00 40.17 3.01
375 2584 1.124780 TGGAAGGTCCGTCAAGACAA 58.875 50.000 7.15 0.00 40.17 3.18
382 2591 1.300620 CCGTCAAGACAACGCCTCA 60.301 57.895 0.72 0.00 38.77 3.86
415 2624 4.092675 CCTTCAGCTTCTTCTTCGATTGAC 59.907 45.833 0.00 0.00 0.00 3.18
452 2678 7.440523 ACTGTGTTCATGTTAGATCTTTTCC 57.559 36.000 0.00 0.00 0.00 3.13
473 2699 3.065371 CCGATTTAGGCTCATTGTCAACC 59.935 47.826 0.00 0.00 0.00 3.77
474 2700 3.941483 CGATTTAGGCTCATTGTCAACCT 59.059 43.478 0.00 0.00 34.42 3.50
541 2767 5.362143 TCTCTAGGATGGTGATCTGTTTCTG 59.638 44.000 0.00 0.00 0.00 3.02
543 2769 4.484537 AGGATGGTGATCTGTTTCTGAG 57.515 45.455 0.00 0.00 0.00 3.35
555 2781 6.516739 TCTGTTTCTGAGATCGTTATCACT 57.483 37.500 0.00 0.00 34.28 3.41
556 2782 6.325596 TCTGTTTCTGAGATCGTTATCACTG 58.674 40.000 0.00 0.00 34.28 3.66
596 2822 4.404098 ATTTCCCGCCCGCTTCGT 62.404 61.111 0.00 0.00 0.00 3.85
603 2829 1.636340 CGCCCGCTTCGTCAAATAG 59.364 57.895 0.00 0.00 0.00 1.73
616 2842 4.161565 TCGTCAAATAGTGTTGCCCTATCT 59.838 41.667 0.00 0.00 0.00 1.98
630 2856 2.470821 CCTATCTTCGGCGGTGTTTAG 58.529 52.381 7.21 2.64 0.00 1.85
653 2879 1.310904 GTCTAGAGGCGGAATCGAGT 58.689 55.000 0.00 0.00 39.00 4.18
659 2885 1.818363 GGCGGAATCGAGTTTCCCC 60.818 63.158 11.35 9.83 41.87 4.81
663 2889 0.743345 GGAATCGAGTTTCCCCCACG 60.743 60.000 6.54 0.00 39.46 4.94
684 2910 3.764049 GCGTCGCCGTTGAGTGTC 61.764 66.667 5.75 0.00 36.15 3.67
709 2935 2.747989 GGAAGACTTCGTCAATTTCCCC 59.252 50.000 9.08 0.00 32.05 4.81
820 3046 6.252967 TCAGTTTTATTGCATCGACACAAT 57.747 33.333 16.39 16.39 39.69 2.71
877 3103 3.181463 ACCCGCCGCTGTATAATAAAAGA 60.181 43.478 0.00 0.00 0.00 2.52
1026 3252 2.188994 GGCTGAGCCTGAGCGAAT 59.811 61.111 17.96 0.00 46.69 3.34
1174 3400 0.823769 TCCGCTCGCATCTACATCCT 60.824 55.000 0.00 0.00 0.00 3.24
1275 3508 3.062466 CTGTCTCTCCACCGGCGA 61.062 66.667 9.30 0.00 0.00 5.54
1284 3517 4.803426 CACCGGCGACTGAGGCTC 62.803 72.222 9.30 7.79 34.19 4.70
1363 3596 1.475392 CGAGATCCCTGACCTCGTACT 60.475 57.143 0.00 0.00 43.20 2.73
1380 3613 3.602513 CTTGCCGGCTCTGTCTGCT 62.603 63.158 29.70 0.00 0.00 4.24
1381 3614 3.182590 TTGCCGGCTCTGTCTGCTT 62.183 57.895 29.70 0.00 0.00 3.91
1383 3616 2.125350 CCGGCTCTGTCTGCTTCC 60.125 66.667 0.00 0.00 0.00 3.46
1474 3707 0.681887 TACACCTCTGAATCCGCCGA 60.682 55.000 0.00 0.00 0.00 5.54
1522 3755 2.168496 CGTGGAGAAGAGGGTCTACAA 58.832 52.381 0.00 0.00 40.24 2.41
1538 3771 3.249189 AAGCTGACCCTGCCGGAA 61.249 61.111 5.05 0.00 34.64 4.30
1743 3976 1.701847 ACCCAAGTCACTCTGCAAGAT 59.298 47.619 3.37 0.00 45.62 2.40
1761 3994 1.806542 GATGAGCTTTCTTCACGCCAA 59.193 47.619 0.00 0.00 0.00 4.52
1832 4071 0.112025 TGTTCCATGATGCACCCACA 59.888 50.000 0.00 0.00 0.00 4.17
1833 4072 0.813184 GTTCCATGATGCACCCACAG 59.187 55.000 0.00 0.00 0.00 3.66
1834 4073 0.697658 TTCCATGATGCACCCACAGA 59.302 50.000 0.00 0.00 0.00 3.41
1835 4074 0.921166 TCCATGATGCACCCACAGAT 59.079 50.000 0.00 0.00 0.00 2.90
1836 4075 1.029681 CCATGATGCACCCACAGATG 58.970 55.000 0.00 0.00 0.00 2.90
1837 4076 1.409101 CCATGATGCACCCACAGATGA 60.409 52.381 0.00 0.00 0.00 2.92
1890 4129 3.307762 GCCATACACTCACCTCTCCTTTT 60.308 47.826 0.00 0.00 0.00 2.27
1916 4158 0.036164 TTGGGGATGACAAGTGGACG 59.964 55.000 0.00 0.00 0.00 4.79
2059 4301 0.765510 ATTATCAAGGGGAGGGACGC 59.234 55.000 0.00 0.00 0.00 5.19
2119 4361 3.368571 GGGTGGTCTGCTGCTTGC 61.369 66.667 0.00 0.00 43.25 4.01
2158 4400 3.103447 TGATGATCCTGATGAAGACGC 57.897 47.619 0.00 0.00 0.00 5.19
2254 4496 1.067354 GGAAGTTGATTGCTTGCCTGG 60.067 52.381 0.00 0.00 0.00 4.45
2349 4591 6.650427 ATCATGCCTACTTTACTGACGATA 57.350 37.500 0.00 0.00 0.00 2.92
2396 4638 4.639310 AGTAGTCGTCGTGATATTGGAGTT 59.361 41.667 0.00 0.00 0.00 3.01
2477 4719 1.153349 GCCTTCTCCCGTGTGGATC 60.153 63.158 0.00 0.00 44.07 3.36
3234 6684 9.678260 GATGGATACTTGGCTGATATATTCTTT 57.322 33.333 0.00 0.00 37.61 2.52
3537 9797 1.226802 CTGATCTCGTGTCTGGCCG 60.227 63.158 0.00 0.00 0.00 6.13
3540 9800 3.649277 ATCTCGTGTCTGGCCGCAC 62.649 63.158 13.01 13.01 0.00 5.34
3584 9844 3.127533 GGTGTCATGGCGAGGTGC 61.128 66.667 0.00 0.00 45.38 5.01
3656 10019 3.289834 CCTGCTGCCGTGCAAAGT 61.290 61.111 0.00 0.00 42.83 2.66
3685 10048 2.634453 ACAGGTGACATGTCATGACTGA 59.366 45.455 37.30 16.65 42.18 3.41
3697 10061 0.837691 ATGACTGAGGGTGGTGCTCA 60.838 55.000 0.00 0.00 0.00 4.26
3723 10087 5.065704 TCCTCTTCATTCTCAGTTTCTCG 57.934 43.478 0.00 0.00 0.00 4.04
3734 10098 5.001874 TCTCAGTTTCTCGCTTGAGTAGTA 58.998 41.667 0.88 0.00 40.76 1.82
3736 10100 6.151312 TCTCAGTTTCTCGCTTGAGTAGTAAT 59.849 38.462 0.88 0.00 40.76 1.89
3738 10102 7.152645 TCAGTTTCTCGCTTGAGTAGTAATTT 58.847 34.615 0.00 0.00 40.76 1.82
3739 10103 7.656137 TCAGTTTCTCGCTTGAGTAGTAATTTT 59.344 33.333 0.00 0.00 40.76 1.82
3768 10132 2.202295 TTGTTCTTTTGCGTGAAGGC 57.798 45.000 0.00 0.00 0.00 4.35
3813 10178 0.250467 AGCATTTGCCTCACTGACGT 60.250 50.000 0.00 0.00 43.38 4.34
3816 10181 2.146342 CATTTGCCTCACTGACGTCTT 58.854 47.619 17.92 0.17 0.00 3.01
3821 10186 1.728971 GCCTCACTGACGTCTTCATTG 59.271 52.381 17.92 6.61 36.45 2.82
3823 10188 2.289072 CCTCACTGACGTCTTCATTGGT 60.289 50.000 17.92 1.75 35.93 3.67
3825 10190 2.364002 TCACTGACGTCTTCATTGGTGA 59.636 45.455 17.92 14.61 35.58 4.02
3826 10191 3.130633 CACTGACGTCTTCATTGGTGAA 58.869 45.455 17.92 0.00 41.89 3.18
3827 10192 3.748048 CACTGACGTCTTCATTGGTGAAT 59.252 43.478 17.92 0.00 43.08 2.57
3828 10193 3.748048 ACTGACGTCTTCATTGGTGAATG 59.252 43.478 17.92 0.00 43.08 2.67
3829 10194 2.483877 TGACGTCTTCATTGGTGAATGC 59.516 45.455 17.92 0.00 43.08 3.56
3830 10195 1.464608 ACGTCTTCATTGGTGAATGCG 59.535 47.619 10.61 10.61 43.08 4.73
3831 10196 1.731709 CGTCTTCATTGGTGAATGCGA 59.268 47.619 0.00 0.00 43.08 5.10
3832 10197 2.222886 CGTCTTCATTGGTGAATGCGAG 60.223 50.000 0.00 0.00 43.08 5.03
3833 10198 2.096496 GTCTTCATTGGTGAATGCGAGG 59.904 50.000 0.00 0.00 43.08 4.63
3834 10199 2.086869 CTTCATTGGTGAATGCGAGGT 58.913 47.619 0.00 0.00 43.08 3.85
3835 10200 2.198827 TCATTGGTGAATGCGAGGTT 57.801 45.000 0.00 0.00 39.16 3.50
3836 10201 2.083774 TCATTGGTGAATGCGAGGTTC 58.916 47.619 0.00 0.00 39.16 3.62
3837 10202 1.133025 CATTGGTGAATGCGAGGTTCC 59.867 52.381 0.00 0.00 32.83 3.62
3838 10203 0.608035 TTGGTGAATGCGAGGTTCCC 60.608 55.000 0.00 0.00 0.00 3.97
3839 10204 1.299976 GGTGAATGCGAGGTTCCCT 59.700 57.895 0.00 0.00 36.03 4.20
3840 10205 0.744771 GGTGAATGCGAGGTTCCCTC 60.745 60.000 0.00 0.00 46.44 4.30
3855 10220 6.605471 GGTTCCCTCAAACCATTATTTTCT 57.395 37.500 1.00 0.00 46.62 2.52
3856 10221 7.712204 GGTTCCCTCAAACCATTATTTTCTA 57.288 36.000 1.00 0.00 46.62 2.10
3857 10222 7.544622 GGTTCCCTCAAACCATTATTTTCTAC 58.455 38.462 1.00 0.00 46.62 2.59
3858 10223 7.363530 GGTTCCCTCAAACCATTATTTTCTACC 60.364 40.741 1.00 0.00 46.62 3.18
3859 10224 6.192044 TCCCTCAAACCATTATTTTCTACCC 58.808 40.000 0.00 0.00 0.00 3.69
3860 10225 5.362717 CCCTCAAACCATTATTTTCTACCCC 59.637 44.000 0.00 0.00 0.00 4.95
3861 10226 5.362717 CCTCAAACCATTATTTTCTACCCCC 59.637 44.000 0.00 0.00 0.00 5.40
3862 10227 6.160483 TCAAACCATTATTTTCTACCCCCT 57.840 37.500 0.00 0.00 0.00 4.79
3863 10228 6.192044 TCAAACCATTATTTTCTACCCCCTC 58.808 40.000 0.00 0.00 0.00 4.30
3864 10229 4.808767 ACCATTATTTTCTACCCCCTCC 57.191 45.455 0.00 0.00 0.00 4.30
3865 10230 3.137728 ACCATTATTTTCTACCCCCTCCG 59.862 47.826 0.00 0.00 0.00 4.63
3866 10231 3.137728 CCATTATTTTCTACCCCCTCCGT 59.862 47.826 0.00 0.00 0.00 4.69
3867 10232 4.385977 CCATTATTTTCTACCCCCTCCGTT 60.386 45.833 0.00 0.00 0.00 4.44
3868 10233 4.492494 TTATTTTCTACCCCCTCCGTTC 57.508 45.455 0.00 0.00 0.00 3.95
3869 10234 0.986527 TTTTCTACCCCCTCCGTTCC 59.013 55.000 0.00 0.00 0.00 3.62
3870 10235 0.117742 TTTCTACCCCCTCCGTTCCT 59.882 55.000 0.00 0.00 0.00 3.36
3871 10236 1.009997 TTCTACCCCCTCCGTTCCTA 58.990 55.000 0.00 0.00 0.00 2.94
3872 10237 1.009997 TCTACCCCCTCCGTTCCTAA 58.990 55.000 0.00 0.00 0.00 2.69
3873 10238 1.362237 TCTACCCCCTCCGTTCCTAAA 59.638 52.381 0.00 0.00 0.00 1.85
3874 10239 2.022722 TCTACCCCCTCCGTTCCTAAAT 60.023 50.000 0.00 0.00 0.00 1.40
3875 10240 2.574074 ACCCCCTCCGTTCCTAAATA 57.426 50.000 0.00 0.00 0.00 1.40
3876 10241 2.121948 ACCCCCTCCGTTCCTAAATAC 58.878 52.381 0.00 0.00 0.00 1.89
3877 10242 2.121129 CCCCCTCCGTTCCTAAATACA 58.879 52.381 0.00 0.00 0.00 2.29
3878 10243 2.506644 CCCCCTCCGTTCCTAAATACAA 59.493 50.000 0.00 0.00 0.00 2.41
3879 10244 3.433173 CCCCCTCCGTTCCTAAATACAAG 60.433 52.174 0.00 0.00 0.00 3.16
3880 10245 3.199289 CCCCTCCGTTCCTAAATACAAGT 59.801 47.826 0.00 0.00 0.00 3.16
3881 10246 4.439968 CCCTCCGTTCCTAAATACAAGTC 58.560 47.826 0.00 0.00 0.00 3.01
3882 10247 4.161754 CCCTCCGTTCCTAAATACAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
3883 10248 5.338137 CCCTCCGTTCCTAAATACAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
3884 10249 6.171213 CCTCCGTTCCTAAATACAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
3885 10250 7.325694 CCTCCGTTCCTAAATACAAGTCTTTA 58.674 38.462 0.00 0.00 0.00 1.85
3886 10251 7.985752 CCTCCGTTCCTAAATACAAGTCTTTAT 59.014 37.037 0.00 0.00 0.00 1.40
3887 10252 8.712285 TCCGTTCCTAAATACAAGTCTTTATG 57.288 34.615 0.00 0.00 0.00 1.90
3888 10253 8.533657 TCCGTTCCTAAATACAAGTCTTTATGA 58.466 33.333 0.00 0.00 0.00 2.15
3889 10254 8.818057 CCGTTCCTAAATACAAGTCTTTATGAG 58.182 37.037 0.00 0.00 0.00 2.90
3890 10255 9.582431 CGTTCCTAAATACAAGTCTTTATGAGA 57.418 33.333 0.00 0.00 0.00 3.27
3897 10262 9.965902 AAATACAAGTCTTTATGAGATTCCACT 57.034 29.630 0.00 0.00 36.61 4.00
3900 10265 8.954950 ACAAGTCTTTATGAGATTCCACTATG 57.045 34.615 0.00 0.00 36.61 2.23
3901 10266 8.762645 ACAAGTCTTTATGAGATTCCACTATGA 58.237 33.333 0.00 0.00 36.61 2.15
3902 10267 9.605275 CAAGTCTTTATGAGATTCCACTATGAA 57.395 33.333 0.00 0.00 36.61 2.57
3903 10268 9.829507 AAGTCTTTATGAGATTCCACTATGAAG 57.170 33.333 0.00 0.00 36.61 3.02
3904 10269 8.986991 AGTCTTTATGAGATTCCACTATGAAGT 58.013 33.333 0.00 0.00 36.61 3.01
3911 10276 7.649057 TGAGATTCCACTATGAAGTACATACG 58.351 38.462 0.00 0.00 40.07 3.06
3912 10277 6.982852 AGATTCCACTATGAAGTACATACGG 58.017 40.000 0.00 0.00 40.07 4.02
3913 10278 6.776116 AGATTCCACTATGAAGTACATACGGA 59.224 38.462 0.00 0.00 40.07 4.69
3914 10279 6.971726 TTCCACTATGAAGTACATACGGAT 57.028 37.500 0.00 0.00 37.58 4.18
3915 10280 6.327279 TCCACTATGAAGTACATACGGATG 57.673 41.667 5.94 5.94 40.07 3.51
3916 10281 4.923871 CCACTATGAAGTACATACGGATGC 59.076 45.833 7.78 0.00 40.07 3.91
3917 10282 5.508994 CCACTATGAAGTACATACGGATGCA 60.509 44.000 7.78 0.00 40.07 3.96
3918 10283 6.159293 CACTATGAAGTACATACGGATGCAT 58.841 40.000 7.78 0.00 40.07 3.96
3919 10284 6.309009 CACTATGAAGTACATACGGATGCATC 59.691 42.308 18.81 18.81 40.07 3.91
3920 10285 4.937201 TGAAGTACATACGGATGCATCT 57.063 40.909 25.28 10.06 36.43 2.90
3921 10286 6.590234 ATGAAGTACATACGGATGCATCTA 57.410 37.500 25.28 12.00 37.46 1.98
3922 10287 6.590234 TGAAGTACATACGGATGCATCTAT 57.410 37.500 25.28 16.00 36.43 1.98
3923 10288 7.696992 TGAAGTACATACGGATGCATCTATA 57.303 36.000 25.28 17.53 36.43 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 2272 1.076549 GGCTCACCAATGGGGAACA 59.923 57.895 5.44 0.00 33.19 3.18
66 2274 2.770130 GGGCTCACCAATGGGGAA 59.230 61.111 5.44 0.00 33.19 3.97
110 2318 4.089757 TTCCCCCTCCCCCTCGAG 62.090 72.222 5.13 5.13 0.00 4.04
111 2319 4.410033 GTTCCCCCTCCCCCTCGA 62.410 72.222 0.00 0.00 0.00 4.04
126 2334 2.113139 CAACACAGAGCCCGGGTT 59.887 61.111 24.63 18.47 0.00 4.11
169 2377 1.227383 CCGGGAGCAAAGCCCTAAT 59.773 57.895 0.00 0.00 43.72 1.73
195 2404 5.004630 CACTGCATTAATTATTGCCACAACG 59.995 40.000 22.94 11.05 38.08 4.10
205 2414 4.894705 TCCACATGGCACTGCATTAATTAT 59.105 37.500 2.82 0.00 34.44 1.28
245 2454 1.731709 CGACAATGTGGCAAGAATCGA 59.268 47.619 0.00 0.00 0.00 3.59
284 2493 4.280436 TGACTAATGACCAAACGACCAT 57.720 40.909 0.00 0.00 0.00 3.55
305 2514 6.068010 CAGAACCAGATCCACTACTCTAGAT 58.932 44.000 0.00 0.00 0.00 1.98
314 2523 2.705658 TGAACACAGAACCAGATCCACT 59.294 45.455 0.00 0.00 0.00 4.00
335 2544 9.492973 CTTCCAAAGAATACATTCCAAAAACAT 57.507 29.630 0.00 0.00 37.51 2.71
345 2554 4.918588 ACGGACCTTCCAAAGAATACATT 58.081 39.130 0.00 0.00 35.91 2.71
373 2582 4.060038 AGGACTAATACATGAGGCGTTG 57.940 45.455 0.00 0.00 0.00 4.10
375 2584 3.704566 TGAAGGACTAATACATGAGGCGT 59.295 43.478 0.00 0.00 0.00 5.68
382 2591 7.430760 AGAAGAAGCTGAAGGACTAATACAT 57.569 36.000 0.00 0.00 0.00 2.29
431 2640 6.721571 TCGGAAAAGATCTAACATGAACAC 57.278 37.500 0.00 0.00 0.00 3.32
434 2643 9.109393 CCTAAATCGGAAAAGATCTAACATGAA 57.891 33.333 0.00 0.00 0.00 2.57
435 2644 7.226720 GCCTAAATCGGAAAAGATCTAACATGA 59.773 37.037 0.00 0.00 0.00 3.07
436 2645 7.227512 AGCCTAAATCGGAAAAGATCTAACATG 59.772 37.037 0.00 0.00 0.00 3.21
452 2678 3.941483 AGGTTGACAATGAGCCTAAATCG 59.059 43.478 0.00 0.00 0.00 3.34
482 2708 8.842280 ACGAAAAAGGTTGACAATATTTCTGTA 58.158 29.630 0.00 0.00 0.00 2.74
533 2759 6.252441 GTCAGTGATAACGATCTCAGAAACAG 59.748 42.308 0.00 0.00 32.79 3.16
541 2767 3.312973 AGGACGTCAGTGATAACGATCTC 59.687 47.826 18.91 0.00 32.79 2.75
543 2769 3.312973 AGAGGACGTCAGTGATAACGATC 59.687 47.826 18.91 5.11 0.00 3.69
555 2781 2.791347 AGAAGAGCTAGAGGACGTCA 57.209 50.000 18.91 0.00 0.00 4.35
556 2782 3.562557 CCTTAGAAGAGCTAGAGGACGTC 59.437 52.174 7.13 7.13 33.11 4.34
596 2822 5.116180 CGAAGATAGGGCAACACTATTTGA 58.884 41.667 0.00 0.00 39.74 2.69
616 2842 0.968405 ACCTACTAAACACCGCCGAA 59.032 50.000 0.00 0.00 0.00 4.30
630 2856 1.536331 CGATTCCGCCTCTAGACCTAC 59.464 57.143 0.00 0.00 0.00 3.18
797 3023 5.681337 TTGTGTCGATGCAATAAAACTGA 57.319 34.783 0.00 0.00 0.00 3.41
848 3074 0.754217 TACAGCGGCGGGTCTATTCT 60.754 55.000 9.78 0.00 0.00 2.40
925 3151 4.918201 GGAGGCCGGAATCAGCGG 62.918 72.222 5.05 0.00 0.00 5.52
926 3152 4.918201 GGGAGGCCGGAATCAGCG 62.918 72.222 5.05 0.00 0.00 5.18
927 3153 4.918201 CGGGAGGCCGGAATCAGC 62.918 72.222 5.05 0.00 0.00 4.26
928 3154 4.918201 GCGGGAGGCCGGAATCAG 62.918 72.222 5.05 1.07 34.80 2.90
997 3223 4.087892 TCAGCCTTCCTCTGCGGC 62.088 66.667 0.00 0.00 44.09 6.53
1026 3252 1.744320 CGTACCGCTGGATCCATGGA 61.744 60.000 30.32 18.88 0.00 3.41
1275 3508 3.386237 GGACGCCTGAGCCTCAGT 61.386 66.667 19.89 2.78 42.80 3.41
1340 3573 2.037871 GAGGTCAGGGATCTCGAGC 58.962 63.158 7.81 8.09 29.79 5.03
1363 3596 3.182590 AAGCAGACAGAGCCGGCAA 62.183 57.895 31.54 0.00 0.00 4.52
1432 3665 4.814294 GGCACGGCGTCTGGGTAG 62.814 72.222 10.85 0.00 0.00 3.18
1474 3707 3.136123 GGCACGCCACATGCTCAT 61.136 61.111 2.36 0.00 42.93 2.90
1522 3755 4.021925 GTTCCGGCAGGGTCAGCT 62.022 66.667 2.05 0.00 38.33 4.24
1538 3771 3.699894 CTGCTGCGGAGAGGTGGT 61.700 66.667 8.65 0.00 0.00 4.16
1721 3954 2.300152 TCTTGCAGAGTGACTTGGGTAG 59.700 50.000 0.00 0.00 0.00 3.18
1743 3976 0.944386 GTTGGCGTGAAGAAAGCTCA 59.056 50.000 0.00 0.00 33.25 4.26
1832 4071 2.363680 CACGATGTAGCTTCCCTCATCT 59.636 50.000 0.00 0.00 35.82 2.90
1833 4072 2.546795 CCACGATGTAGCTTCCCTCATC 60.547 54.545 0.00 0.00 34.98 2.92
1834 4073 1.414181 CCACGATGTAGCTTCCCTCAT 59.586 52.381 0.00 0.00 0.00 2.90
1835 4074 0.824109 CCACGATGTAGCTTCCCTCA 59.176 55.000 0.00 0.00 0.00 3.86
1836 4075 0.824759 ACCACGATGTAGCTTCCCTC 59.175 55.000 0.00 0.00 0.00 4.30
1837 4076 0.537188 CACCACGATGTAGCTTCCCT 59.463 55.000 0.00 0.00 0.00 4.20
1890 4129 2.711009 ACTTGTCATCCCCAACTCTTGA 59.289 45.455 0.00 0.00 0.00 3.02
1916 4158 0.381801 CACAGTGTGGTTCCAGCAAC 59.618 55.000 15.86 0.00 0.00 4.17
2059 4301 2.546494 GCATCCGGATCAAAGCCCG 61.546 63.158 15.88 1.38 44.94 6.13
2072 4314 3.127548 CCTGAACAATGTGTACAGCATCC 59.872 47.826 0.00 0.00 0.00 3.51
2158 4400 3.538591 GGAACAGGTATTTTAGGGTCGG 58.461 50.000 0.00 0.00 0.00 4.79
2216 4458 2.740055 ACAAGCTTCTCTGCGCCG 60.740 61.111 4.18 0.00 38.13 6.46
2254 4496 1.444895 CCAAGAAACAGCGCATGGC 60.445 57.895 11.47 0.00 44.05 4.40
2349 4591 6.163476 TCTTACGTGCTTGATTGTACTGATT 58.837 36.000 0.00 0.00 0.00 2.57
2396 4638 6.605194 TGCTATTATAATTGCCCAAGTCAACA 59.395 34.615 23.28 4.01 36.52 3.33
2627 5986 4.279659 CGACCTACTTTTTCAAACACTGC 58.720 43.478 0.00 0.00 0.00 4.40
2756 6177 4.885325 ATGATAACTTCACAGCATCATGCA 59.115 37.500 13.38 0.00 41.04 3.96
2854 6292 1.610363 AACACAACCACACACACACA 58.390 45.000 0.00 0.00 0.00 3.72
3185 6635 5.008217 TCAACGTAACTAAAAACAGCAGCAT 59.992 36.000 0.00 0.00 0.00 3.79
3234 6684 8.526978 TGTGAGCATGGCTTATAAAATACAAAA 58.473 29.630 0.00 0.00 39.88 2.44
3369 9629 6.314896 CCAACAAGTATGCCTTTCAACAAAAA 59.685 34.615 0.00 0.00 0.00 1.94
3479 9739 9.588096 TTCTGTCATATGAATAAGCTAGGACTA 57.412 33.333 7.07 0.00 29.93 2.59
3553 9813 3.818787 CACCATCTGCAAGCGCCC 61.819 66.667 2.29 0.00 37.32 6.13
3656 10019 0.108396 CATGTCACCTGTGGTCACCA 59.892 55.000 0.00 0.00 31.02 4.17
3672 10035 1.280133 ACCACCCTCAGTCATGACATG 59.720 52.381 27.02 20.27 0.00 3.21
3697 10061 5.250313 AGAAACTGAGAATGAAGAGGATGGT 59.750 40.000 0.00 0.00 0.00 3.55
3709 10073 4.264460 ACTCAAGCGAGAAACTGAGAAT 57.736 40.909 5.01 0.00 42.34 2.40
3739 10103 4.998033 ACGCAAAAGAACAAAAGGGAAAAA 59.002 33.333 0.00 0.00 0.00 1.94
3744 10108 3.157932 TCACGCAAAAGAACAAAAGGG 57.842 42.857 0.00 0.00 0.00 3.95
3749 10113 1.474478 TGCCTTCACGCAAAAGAACAA 59.526 42.857 0.00 0.00 35.32 2.83
3768 10132 1.272490 TGTCGACAAGAGGCCTAAGTG 59.728 52.381 17.62 6.77 0.00 3.16
3816 10181 2.083774 GAACCTCGCATTCACCAATGA 58.916 47.619 0.00 0.00 41.97 2.57
3833 10198 7.363530 GGGTAGAAAATAATGGTTTGAGGGAAC 60.364 40.741 0.00 0.00 0.00 3.62
3834 10199 6.666113 GGGTAGAAAATAATGGTTTGAGGGAA 59.334 38.462 0.00 0.00 0.00 3.97
3835 10200 6.192044 GGGTAGAAAATAATGGTTTGAGGGA 58.808 40.000 0.00 0.00 0.00 4.20
3836 10201 5.362717 GGGGTAGAAAATAATGGTTTGAGGG 59.637 44.000 0.00 0.00 0.00 4.30
3837 10202 5.362717 GGGGGTAGAAAATAATGGTTTGAGG 59.637 44.000 0.00 0.00 0.00 3.86
3838 10203 6.194967 AGGGGGTAGAAAATAATGGTTTGAG 58.805 40.000 0.00 0.00 0.00 3.02
3839 10204 6.160483 AGGGGGTAGAAAATAATGGTTTGA 57.840 37.500 0.00 0.00 0.00 2.69
3840 10205 5.362717 GGAGGGGGTAGAAAATAATGGTTTG 59.637 44.000 0.00 0.00 0.00 2.93
3841 10206 5.525484 GGAGGGGGTAGAAAATAATGGTTT 58.475 41.667 0.00 0.00 0.00 3.27
3842 10207 4.385977 CGGAGGGGGTAGAAAATAATGGTT 60.386 45.833 0.00 0.00 0.00 3.67
3843 10208 3.137728 CGGAGGGGGTAGAAAATAATGGT 59.862 47.826 0.00 0.00 0.00 3.55
3844 10209 3.137728 ACGGAGGGGGTAGAAAATAATGG 59.862 47.826 0.00 0.00 0.00 3.16
3845 10210 4.432980 ACGGAGGGGGTAGAAAATAATG 57.567 45.455 0.00 0.00 0.00 1.90
3846 10211 4.141321 GGAACGGAGGGGGTAGAAAATAAT 60.141 45.833 0.00 0.00 0.00 1.28
3847 10212 3.200605 GGAACGGAGGGGGTAGAAAATAA 59.799 47.826 0.00 0.00 0.00 1.40
3848 10213 2.773661 GGAACGGAGGGGGTAGAAAATA 59.226 50.000 0.00 0.00 0.00 1.40
3849 10214 1.562942 GGAACGGAGGGGGTAGAAAAT 59.437 52.381 0.00 0.00 0.00 1.82
3850 10215 0.986527 GGAACGGAGGGGGTAGAAAA 59.013 55.000 0.00 0.00 0.00 2.29
3851 10216 0.117742 AGGAACGGAGGGGGTAGAAA 59.882 55.000 0.00 0.00 0.00 2.52
3852 10217 1.009997 TAGGAACGGAGGGGGTAGAA 58.990 55.000 0.00 0.00 0.00 2.10
3853 10218 1.009997 TTAGGAACGGAGGGGGTAGA 58.990 55.000 0.00 0.00 0.00 2.59
3854 10219 1.870064 TTTAGGAACGGAGGGGGTAG 58.130 55.000 0.00 0.00 0.00 3.18
3855 10220 2.574074 ATTTAGGAACGGAGGGGGTA 57.426 50.000 0.00 0.00 0.00 3.69
3856 10221 2.121948 GTATTTAGGAACGGAGGGGGT 58.878 52.381 0.00 0.00 0.00 4.95
3857 10222 2.121129 TGTATTTAGGAACGGAGGGGG 58.879 52.381 0.00 0.00 0.00 5.40
3858 10223 3.199289 ACTTGTATTTAGGAACGGAGGGG 59.801 47.826 0.00 0.00 0.00 4.79
3859 10224 4.161754 AGACTTGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
3860 10225 5.340439 AGACTTGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
3861 10226 8.818057 CATAAAGACTTGTATTTAGGAACGGAG 58.182 37.037 6.68 0.00 0.00 4.63
3862 10227 8.533657 TCATAAAGACTTGTATTTAGGAACGGA 58.466 33.333 11.18 0.04 31.07 4.69
3863 10228 8.712285 TCATAAAGACTTGTATTTAGGAACGG 57.288 34.615 11.18 0.00 31.07 4.44
3864 10229 9.582431 TCTCATAAAGACTTGTATTTAGGAACG 57.418 33.333 13.52 6.25 33.00 3.95
3871 10236 9.965902 AGTGGAATCTCATAAAGACTTGTATTT 57.034 29.630 0.00 0.00 36.65 1.40
3875 10240 8.762645 TCATAGTGGAATCTCATAAAGACTTGT 58.237 33.333 0.00 0.00 36.65 3.16
3876 10241 9.605275 TTCATAGTGGAATCTCATAAAGACTTG 57.395 33.333 0.00 0.00 36.65 3.16
3877 10242 9.829507 CTTCATAGTGGAATCTCATAAAGACTT 57.170 33.333 0.00 0.00 36.65 3.01
3878 10243 8.986991 ACTTCATAGTGGAATCTCATAAAGACT 58.013 33.333 0.00 0.00 32.58 3.24
3885 10250 8.300286 CGTATGTACTTCATAGTGGAATCTCAT 58.700 37.037 0.00 0.00 39.36 2.90
3886 10251 7.255486 CCGTATGTACTTCATAGTGGAATCTCA 60.255 40.741 0.00 0.00 39.36 3.27
3887 10252 7.040617 TCCGTATGTACTTCATAGTGGAATCTC 60.041 40.741 0.00 0.00 39.60 2.75
3888 10253 6.776116 TCCGTATGTACTTCATAGTGGAATCT 59.224 38.462 0.00 0.00 39.60 2.40
3889 10254 6.978338 TCCGTATGTACTTCATAGTGGAATC 58.022 40.000 0.00 0.00 39.60 2.52
3890 10255 6.971726 TCCGTATGTACTTCATAGTGGAAT 57.028 37.500 0.00 0.00 39.60 3.01
3891 10256 6.737622 GCATCCGTATGTACTTCATAGTGGAA 60.738 42.308 10.59 0.00 42.65 3.53
3892 10257 5.278808 GCATCCGTATGTACTTCATAGTGGA 60.279 44.000 0.00 9.57 43.10 4.02
3893 10258 4.923871 GCATCCGTATGTACTTCATAGTGG 59.076 45.833 0.00 0.00 39.36 4.00
3894 10259 5.528870 TGCATCCGTATGTACTTCATAGTG 58.471 41.667 0.00 0.00 39.36 2.74
3895 10260 5.784578 TGCATCCGTATGTACTTCATAGT 57.215 39.130 0.00 0.00 39.36 2.12
3896 10261 6.625362 AGATGCATCCGTATGTACTTCATAG 58.375 40.000 23.06 0.00 39.36 2.23
3897 10262 6.590234 AGATGCATCCGTATGTACTTCATA 57.410 37.500 23.06 0.00 37.91 2.15
3898 10263 5.474578 AGATGCATCCGTATGTACTTCAT 57.525 39.130 23.06 0.00 40.25 2.57
3899 10264 4.937201 AGATGCATCCGTATGTACTTCA 57.063 40.909 23.06 0.00 35.38 3.02


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

AutoCloner maintained by Alex Coulton.