Multiple sequence alignment - TraesCS2D01G388800

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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 TraesCS2D01G388800 chr2D 100.000 7000 0 0 1 7000 495093985 495100984 0.000000e+00 12927.0
1 TraesCS2D01G388800 chr2D 87.861 519 52 5 3253 3769 495096763 495097272 3.610000e-167 599.0
2 TraesCS2D01G388800 chr2D 87.861 519 52 5 2779 3288 495097237 495097753 3.610000e-167 599.0
3 TraesCS2D01G388800 chr2D 80.717 446 52 21 3331 3771 495096131 495096547 4.080000e-82 316.0
4 TraesCS2D01G388800 chr2D 80.717 446 52 21 2147 2563 495097315 495097755 4.080000e-82 316.0
5 TraesCS2D01G388800 chr2D 86.905 252 23 5 3083 3334 495096342 495096583 2.490000e-69 274.0
6 TraesCS2D01G388800 chr2D 86.905 252 23 5 2358 2599 495097067 495097318 2.490000e-69 274.0
7 TraesCS2D01G388800 chr2D 88.889 180 16 3 6123 6301 129947317 129947141 1.180000e-52 219.0
8 TraesCS2D01G388800 chr2D 90.385 156 12 2 2079 2231 495095975 495096130 1.190000e-47 202.0
9 TraesCS2D01G388800 chr2D 90.385 156 12 2 1991 2146 495096063 495096215 1.190000e-47 202.0
10 TraesCS2D01G388800 chr2D 76.904 394 63 24 2672 3041 495095937 495096326 1.540000e-46 198.0
11 TraesCS2D01G388800 chr2D 76.904 394 63 24 1953 2342 495096656 495097025 1.540000e-46 198.0
12 TraesCS2D01G388800 chr2D 92.632 95 7 0 3768 3862 165009322 165009228 3.410000e-28 137.0
13 TraesCS2D01G388800 chr2D 98.571 70 1 0 6051 6120 495100001 495100070 2.650000e-24 124.0
14 TraesCS2D01G388800 chr2D 98.571 70 1 0 6017 6086 495100035 495100104 2.650000e-24 124.0
15 TraesCS2D01G388800 chr2D 92.105 76 6 0 6923 6998 129946762 129946687 2.670000e-19 108.0
16 TraesCS2D01G388800 chr2D 97.436 39 0 1 6080 6117 495099995 495100033 1.630000e-06 65.8
17 TraesCS2D01G388800 chr2D 97.436 39 0 1 6011 6049 495100064 495100101 1.630000e-06 65.8
18 TraesCS2D01G388800 chr2B 97.181 2199 45 7 3855 6049 582805641 582807826 0.000000e+00 3701.0
19 TraesCS2D01G388800 chr2B 93.067 1630 79 11 2147 3769 582804036 582805638 0.000000e+00 2353.0
20 TraesCS2D01G388800 chr2B 91.055 1554 64 27 551 2064 582802467 582803985 0.000000e+00 2030.0
21 TraesCS2D01G388800 chr2B 95.346 924 37 4 6080 7000 582807788 582808708 0.000000e+00 1463.0
22 TraesCS2D01G388800 chr2B 88.694 513 47 5 3253 3763 582804657 582805160 3.590000e-172 616.0
23 TraesCS2D01G388800 chr2B 86.629 531 41 16 5 515 582801949 582802469 1.710000e-155 560.0
24 TraesCS2D01G388800 chr2B 85.660 523 59 7 2779 3294 582805131 582805644 2.870000e-148 536.0
25 TraesCS2D01G388800 chr2B 86.806 432 49 5 3856 4283 389409868 389410295 6.350000e-130 475.0
26 TraesCS2D01G388800 chr2B 89.474 247 18 3 3083 3329 582804245 582804483 8.820000e-79 305.0
27 TraesCS2D01G388800 chr2B 81.984 383 43 11 2665 3041 582803867 582804229 1.140000e-77 302.0
28 TraesCS2D01G388800 chr2B 79.355 465 55 11 2147 2583 582805209 582805660 8.880000e-74 289.0
29 TraesCS2D01G388800 chr2B 90.000 220 22 0 3550 3769 582804231 582804450 1.150000e-72 285.0
30 TraesCS2D01G388800 chr2B 78.535 396 53 22 1953 2342 582804550 582804919 1.520000e-56 231.0
31 TraesCS2D01G388800 chr2B 95.946 74 3 0 2079 2152 582803912 582803985 3.430000e-23 121.0
32 TraesCS2D01G388800 chr2B 100.000 36 0 0 6051 6086 582807794 582807829 4.530000e-07 67.6
33 TraesCS2D01G388800 chr2A 96.464 2206 50 12 3851 6052 638686523 638684342 0.000000e+00 3616.0
34 TraesCS2D01G388800 chr2A 94.899 1431 61 9 2350 3771 638687947 638686520 0.000000e+00 2228.0
35 TraesCS2D01G388800 chr2A 89.886 1582 69 37 514 2067 638689356 638687838 0.000000e+00 1951.0
36 TraesCS2D01G388800 chr2A 94.469 669 26 2 6332 7000 638683690 638683033 0.000000e+00 1020.0
37 TraesCS2D01G388800 chr2A 89.808 520 39 9 3253 3769 638687510 638687002 0.000000e+00 654.0
38 TraesCS2D01G388800 chr2A 89.066 503 17 14 5 475 638689854 638689358 2.170000e-164 590.0
39 TraesCS2D01G388800 chr2A 87.023 524 58 3 2779 3294 638687037 638686516 3.640000e-162 582.0
40 TraesCS2D01G388800 chr2A 94.510 255 9 4 6080 6333 638684383 638684133 8.510000e-104 388.0
41 TraesCS2D01G388800 chr2A 93.725 255 11 4 6080 6333 638684048 638683798 1.840000e-100 377.0
42 TraesCS2D01G388800 chr2A 77.551 686 91 40 1953 2599 638687617 638686956 8.640000e-94 355.0
43 TraesCS2D01G388800 chr2A 85.308 211 26 3 3564 3769 638687938 638687728 5.500000e-51 213.0
44 TraesCS2D01G388800 chr2A 86.243 189 23 1 2154 2342 638686954 638686769 1.190000e-47 202.0
45 TraesCS2D01G388800 chr2A 94.643 112 6 0 2669 2780 638687955 638687844 2.600000e-39 174.0
46 TraesCS2D01G388800 chr2A 94.231 52 3 0 6001 6052 638684058 638684007 5.820000e-11 80.5
47 TraesCS2D01G388800 chr2A 100.000 36 0 0 6051 6086 638684042 638684007 4.530000e-07 67.6
48 TraesCS2D01G388800 chr2A 100.000 36 0 0 6051 6086 638684377 638684342 4.530000e-07 67.6
49 TraesCS2D01G388800 chr1A 88.827 179 16 3 6123 6301 497217824 497217650 4.250000e-52 217.0
50 TraesCS2D01G388800 chr1A 88.953 172 14 4 6831 7000 403664226 403664058 2.560000e-49 207.0
51 TraesCS2D01G388800 chr5D 89.017 173 15 3 6123 6294 361591043 361590874 1.980000e-50 211.0
52 TraesCS2D01G388800 chr5D 85.455 110 16 0 1153 1262 494219428 494219319 1.600000e-21 115.0
53 TraesCS2D01G388800 chr5D 91.892 74 6 0 6925 6998 361590486 361590413 3.450000e-18 104.0
54 TraesCS2D01G388800 chr6B 93.548 93 6 0 3764 3856 679569261 679569169 9.470000e-29 139.0
55 TraesCS2D01G388800 chr4B 92.708 96 7 0 3766 3861 136939787 136939882 9.470000e-29 139.0
56 TraesCS2D01G388800 chr7B 93.478 92 6 0 3770 3861 388716424 388716515 3.410000e-28 137.0
57 TraesCS2D01G388800 chr5B 90.566 106 7 3 3753 3858 331307503 331307401 3.410000e-28 137.0
58 TraesCS2D01G388800 chr3D 91.919 99 7 1 3761 3859 554346109 554346206 3.410000e-28 137.0
59 TraesCS2D01G388800 chr7D 88.991 109 12 0 3752 3860 34845539 34845647 1.220000e-27 135.0
60 TraesCS2D01G388800 chr7D 91.000 100 7 2 3764 3863 535305051 535305148 4.400000e-27 134.0
61 TraesCS2D01G388800 chr7A 88.073 109 11 2 3754 3861 20732911 20733018 2.050000e-25 128.0
62 TraesCS2D01G388800 chr5A 85.455 110 16 0 1153 1262 617210538 617210429 1.600000e-21 115.0


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 TraesCS2D01G388800 chr2D 495093985 495100984 6999 False 12927.000000 12927 100.000000 1 7000 1 chr2D.!!$F1 6999
1 TraesCS2D01G388800 chr2D 495095937 495100104 4167 False 254.114286 599 88.397000 1953 6120 14 chr2D.!!$F2 4167
2 TraesCS2D01G388800 chr2B 582801949 582808708 6759 False 918.542857 3701 89.494714 5 7000 14 chr2B.!!$F2 6995
3 TraesCS2D01G388800 chr2A 638683033 638689854 6821 True 785.356250 3616 91.739125 5 7000 16 chr2A.!!$R1 6995

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
35 36 0.941463 CACTGACTGTCTGCACGGAC 60.941 60.0 13.73 2.53 36.81 4.79 F
1103 1195 0.393132 GCCGGGGGAGAAAAGAAGAG 60.393 60.0 2.18 0.00 0.00 2.85 F
1560 1663 0.323629 TTGCGATTTCTCCCGGAAGT 59.676 50.0 0.73 0.00 35.16 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1379 0.108585 CGAGGAGAGGAGAGGAGAGG 59.891 65.000 0.0 0.0 0.00 3.69 R
1905 2009 7.187824 AGATGAGCTTGTAATAACAGAGGAA 57.812 36.000 0.0 0.0 36.83 3.36 R
6029 6205 2.706350 TCCCAGGGCAGATAATTAGCT 58.294 47.619 0.0 0.0 0.00 3.32 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
35 36 0.941463 CACTGACTGTCTGCACGGAC 60.941 60.000 13.73 2.53 36.81 4.79
39 40 3.406361 CTGTCTGCACGGACACGC 61.406 66.667 8.22 0.00 46.04 5.34
255 260 3.467119 CCGTACTCGTGCGTGCAC 61.467 66.667 14.81 14.81 43.01 4.57
288 305 6.183360 GGCATTCTGTAAAAACAAAAACGTGT 60.183 34.615 0.00 0.00 0.00 4.49
289 306 7.230914 GCATTCTGTAAAAACAAAAACGTGTT 58.769 30.769 0.00 0.00 43.58 3.32
296 313 5.425577 AAAACAAAAACGTGTTGGCTTTT 57.574 30.435 14.68 10.61 40.86 2.27
324 341 3.375443 AGAGAATCCGGCCGGAGGA 62.375 63.158 45.98 28.83 46.99 3.71
482 535 2.032681 GACTGACAGGTGGGCCAC 59.967 66.667 28.69 28.69 37.19 5.01
526 579 2.173852 TGGGACCCACAGAGAGAGA 58.826 57.895 9.95 0.00 0.00 3.10
531 584 2.643551 GACCCACAGAGAGAGAGAGAG 58.356 57.143 0.00 0.00 0.00 3.20
651 713 2.049228 CCGCGATCGTGAGTAATTACC 58.951 52.381 29.21 4.78 0.00 2.85
687 749 1.524863 GCATGCTGCAGGATCCATCC 61.525 60.000 18.91 0.00 44.26 3.51
715 779 4.649088 TCTTCGTCTCAACTCAACTCAA 57.351 40.909 0.00 0.00 0.00 3.02
717 781 5.043903 TCTTCGTCTCAACTCAACTCAAAG 58.956 41.667 0.00 0.00 0.00 2.77
749 821 1.289380 GTCGTCTGGTCCCAGTCAC 59.711 63.158 12.88 4.41 43.96 3.67
1103 1195 0.393132 GCCGGGGGAGAAAAGAAGAG 60.393 60.000 2.18 0.00 0.00 2.85
1105 1197 1.276622 CGGGGGAGAAAAGAAGAGGA 58.723 55.000 0.00 0.00 0.00 3.71
1106 1198 1.628846 CGGGGGAGAAAAGAAGAGGAA 59.371 52.381 0.00 0.00 0.00 3.36
1107 1199 2.355209 CGGGGGAGAAAAGAAGAGGAAG 60.355 54.545 0.00 0.00 0.00 3.46
1109 1201 2.913617 GGGGAGAAAAGAAGAGGAAGGA 59.086 50.000 0.00 0.00 0.00 3.36
1110 1202 3.330998 GGGGAGAAAAGAAGAGGAAGGAA 59.669 47.826 0.00 0.00 0.00 3.36
1111 1203 4.566697 GGGGAGAAAAGAAGAGGAAGGAAG 60.567 50.000 0.00 0.00 0.00 3.46
1112 1204 4.042311 GGGAGAAAAGAAGAGGAAGGAAGT 59.958 45.833 0.00 0.00 0.00 3.01
1113 1205 5.456907 GGGAGAAAAGAAGAGGAAGGAAGTT 60.457 44.000 0.00 0.00 0.00 2.66
1114 1206 6.239915 GGGAGAAAAGAAGAGGAAGGAAGTTA 60.240 42.308 0.00 0.00 0.00 2.24
1115 1207 6.876789 GGAGAAAAGAAGAGGAAGGAAGTTAG 59.123 42.308 0.00 0.00 0.00 2.34
1116 1208 6.234920 AGAAAAGAAGAGGAAGGAAGTTAGC 58.765 40.000 0.00 0.00 0.00 3.09
1263 1358 0.867753 CTTCCGCGAGATCAAGGTCG 60.868 60.000 8.23 0.00 39.25 4.79
1284 1379 1.725066 CCGCGTTCTCTCCTCTCTC 59.275 63.158 4.92 0.00 0.00 3.20
1290 1385 2.745152 CGTTCTCTCCTCTCTCCTCTCC 60.745 59.091 0.00 0.00 0.00 3.71
1324 1421 2.182030 CCGACCGGAGCTTGACTC 59.818 66.667 9.46 0.00 45.45 3.36
1341 1438 8.260818 AGCTTGACTCTGTTTGCTTATTATCTA 58.739 33.333 0.00 0.00 0.00 1.98
1345 1442 9.973450 TGACTCTGTTTGCTTATTATCTATCTC 57.027 33.333 0.00 0.00 0.00 2.75
1346 1443 9.418045 GACTCTGTTTGCTTATTATCTATCTCC 57.582 37.037 0.00 0.00 0.00 3.71
1412 1509 4.070552 ACGCTGGCCTCCTTCGTC 62.071 66.667 3.32 0.00 29.81 4.20
1498 1595 2.035632 GGTGACGGGATCTCTTCTCAT 58.964 52.381 0.25 0.00 0.00 2.90
1499 1596 2.035321 GGTGACGGGATCTCTTCTCATC 59.965 54.545 0.25 0.00 0.00 2.92
1500 1597 2.955660 GTGACGGGATCTCTTCTCATCT 59.044 50.000 0.25 0.00 0.00 2.90
1501 1598 3.004315 GTGACGGGATCTCTTCTCATCTC 59.996 52.174 0.25 0.00 0.00 2.75
1502 1599 2.556622 GACGGGATCTCTTCTCATCTCC 59.443 54.545 0.00 0.00 0.00 3.71
1556 1659 1.378531 TTGATTGCGATTTCTCCCGG 58.621 50.000 0.00 0.00 0.00 5.73
1560 1663 0.323629 TTGCGATTTCTCCCGGAAGT 59.676 50.000 0.73 0.00 35.16 3.01
1581 1684 5.296813 GTCTAAAACAAGACGCATCCAAT 57.703 39.130 0.00 0.00 36.80 3.16
1774 1878 7.978975 GGCATTCTTAGGTTATTTTTGTATGCA 59.021 33.333 0.00 0.00 36.22 3.96
1803 1907 2.677199 CTCTGCTACTTGACTTTCGCA 58.323 47.619 0.00 0.00 0.00 5.10
1928 2032 6.019479 CGTTCCTCTGTTATTACAAGCTCATC 60.019 42.308 0.00 0.00 32.92 2.92
1943 2047 6.428159 ACAAGCTCATCTTTCTGTCGTTAAAT 59.572 34.615 0.00 0.00 31.27 1.40
1947 2051 7.041098 AGCTCATCTTTCTGTCGTTAAATTGTT 60.041 33.333 0.00 0.00 0.00 2.83
1949 2053 7.359595 TCATCTTTCTGTCGTTAAATTGTTGG 58.640 34.615 0.00 0.00 0.00 3.77
6029 6205 7.004086 AGATGATGGGTTTGTTCTTTCTGTTA 58.996 34.615 0.00 0.00 0.00 2.41
6030 6206 6.633500 TGATGGGTTTGTTCTTTCTGTTAG 57.367 37.500 0.00 0.00 0.00 2.34
6031 6207 4.911514 TGGGTTTGTTCTTTCTGTTAGC 57.088 40.909 0.00 0.00 0.00 3.09
6032 6208 4.532834 TGGGTTTGTTCTTTCTGTTAGCT 58.467 39.130 0.00 0.00 0.00 3.32
6033 6209 5.686753 TGGGTTTGTTCTTTCTGTTAGCTA 58.313 37.500 0.00 0.00 0.00 3.32
6034 6210 6.123651 TGGGTTTGTTCTTTCTGTTAGCTAA 58.876 36.000 0.86 0.86 0.00 3.09
6035 6211 6.775629 TGGGTTTGTTCTTTCTGTTAGCTAAT 59.224 34.615 9.88 0.00 0.00 1.73
6036 6212 7.286775 TGGGTTTGTTCTTTCTGTTAGCTAATT 59.713 33.333 9.88 0.00 0.00 1.40
6037 6213 8.789762 GGGTTTGTTCTTTCTGTTAGCTAATTA 58.210 33.333 9.88 1.43 0.00 1.40
6042 6218 8.883731 TGTTCTTTCTGTTAGCTAATTATCTGC 58.116 33.333 9.88 0.00 0.00 4.26
6043 6219 8.338986 GTTCTTTCTGTTAGCTAATTATCTGCC 58.661 37.037 9.88 0.00 0.00 4.85
6044 6220 6.992715 TCTTTCTGTTAGCTAATTATCTGCCC 59.007 38.462 9.88 0.00 0.00 5.36
6045 6221 6.500589 TTCTGTTAGCTAATTATCTGCCCT 57.499 37.500 9.88 0.00 0.00 5.19
6046 6222 5.858381 TCTGTTAGCTAATTATCTGCCCTG 58.142 41.667 9.88 0.00 0.00 4.45
6047 6223 4.973168 TGTTAGCTAATTATCTGCCCTGG 58.027 43.478 9.88 0.00 0.00 4.45
6048 6224 4.202461 TGTTAGCTAATTATCTGCCCTGGG 60.202 45.833 9.88 8.86 0.00 4.45
6049 6225 2.706350 AGCTAATTATCTGCCCTGGGA 58.294 47.619 19.27 0.28 0.00 4.37
6050 6226 3.263724 AGCTAATTATCTGCCCTGGGAT 58.736 45.455 19.27 3.46 0.00 3.85
6051 6227 3.009916 AGCTAATTATCTGCCCTGGGATG 59.990 47.826 19.27 8.06 0.00 3.51
6052 6228 3.245052 GCTAATTATCTGCCCTGGGATGT 60.245 47.826 19.27 0.97 0.00 3.06
6053 6229 3.979501 AATTATCTGCCCTGGGATGTT 57.020 42.857 19.27 5.61 0.00 2.71
6054 6230 3.515602 ATTATCTGCCCTGGGATGTTC 57.484 47.619 19.27 0.00 0.00 3.18
6055 6231 2.196742 TATCTGCCCTGGGATGTTCT 57.803 50.000 19.27 0.00 0.00 3.01
6056 6232 1.302907 ATCTGCCCTGGGATGTTCTT 58.697 50.000 19.27 0.00 0.00 2.52
6057 6233 1.075601 TCTGCCCTGGGATGTTCTTT 58.924 50.000 19.27 0.00 0.00 2.52
6058 6234 1.004745 TCTGCCCTGGGATGTTCTTTC 59.995 52.381 19.27 0.00 0.00 2.62
6059 6235 1.005215 CTGCCCTGGGATGTTCTTTCT 59.995 52.381 19.27 0.00 0.00 2.52
6060 6236 1.272092 TGCCCTGGGATGTTCTTTCTG 60.272 52.381 19.27 0.00 0.00 3.02
6061 6237 1.272147 GCCCTGGGATGTTCTTTCTGT 60.272 52.381 19.27 0.00 0.00 3.41
6062 6238 2.819348 GCCCTGGGATGTTCTTTCTGTT 60.819 50.000 19.27 0.00 0.00 3.16
6063 6239 3.561313 GCCCTGGGATGTTCTTTCTGTTA 60.561 47.826 19.27 0.00 0.00 2.41
6064 6240 4.265073 CCCTGGGATGTTCTTTCTGTTAG 58.735 47.826 7.01 0.00 0.00 2.34
6065 6241 3.691609 CCTGGGATGTTCTTTCTGTTAGC 59.308 47.826 0.00 0.00 0.00 3.09
6066 6242 4.566488 CCTGGGATGTTCTTTCTGTTAGCT 60.566 45.833 0.00 0.00 0.00 3.32
6067 6243 5.338381 CCTGGGATGTTCTTTCTGTTAGCTA 60.338 44.000 0.00 0.00 0.00 3.32
6068 6244 6.121776 TGGGATGTTCTTTCTGTTAGCTAA 57.878 37.500 0.86 0.86 0.00 3.09
6069 6245 6.721318 TGGGATGTTCTTTCTGTTAGCTAAT 58.279 36.000 9.88 0.00 0.00 1.73
6070 6246 7.175104 TGGGATGTTCTTTCTGTTAGCTAATT 58.825 34.615 9.88 0.00 0.00 1.40
6071 6247 8.325787 TGGGATGTTCTTTCTGTTAGCTAATTA 58.674 33.333 9.88 1.43 0.00 1.40
6072 6248 9.343539 GGGATGTTCTTTCTGTTAGCTAATTAT 57.656 33.333 9.88 0.00 0.00 1.28
6076 6252 8.883731 TGTTCTTTCTGTTAGCTAATTATCTGC 58.116 33.333 9.88 0.00 0.00 4.26
6077 6253 8.338986 GTTCTTTCTGTTAGCTAATTATCTGCC 58.661 37.037 9.88 0.00 0.00 4.85
6078 6254 6.992715 TCTTTCTGTTAGCTAATTATCTGCCC 59.007 38.462 9.88 0.00 0.00 5.36
6079 6255 6.500589 TTCTGTTAGCTAATTATCTGCCCT 57.499 37.500 9.88 0.00 0.00 5.19
6080 6256 5.858381 TCTGTTAGCTAATTATCTGCCCTG 58.142 41.667 9.88 0.00 0.00 4.45
6081 6257 4.973168 TGTTAGCTAATTATCTGCCCTGG 58.027 43.478 9.88 0.00 0.00 4.45
6082 6258 4.202461 TGTTAGCTAATTATCTGCCCTGGG 60.202 45.833 9.88 8.86 0.00 4.45
6083 6259 2.422746 AGCTAATTATCTGCCCTGGGT 58.577 47.619 15.56 0.00 0.00 4.51
6084 6260 2.785857 AGCTAATTATCTGCCCTGGGTT 59.214 45.455 15.56 0.90 0.00 4.11
6085 6261 2.887152 GCTAATTATCTGCCCTGGGTTG 59.113 50.000 15.56 7.67 0.00 3.77
6086 6262 3.688414 GCTAATTATCTGCCCTGGGTTGT 60.688 47.826 15.56 1.00 0.00 3.32
6087 6263 3.473113 AATTATCTGCCCTGGGTTGTT 57.527 42.857 15.56 5.39 0.00 2.83
6088 6264 2.507407 TTATCTGCCCTGGGTTGTTC 57.493 50.000 15.56 0.00 0.00 3.18
6089 6265 1.668826 TATCTGCCCTGGGTTGTTCT 58.331 50.000 15.56 0.00 0.00 3.01
6090 6266 0.779997 ATCTGCCCTGGGTTGTTCTT 59.220 50.000 15.56 0.00 0.00 2.52
6091 6267 0.555769 TCTGCCCTGGGTTGTTCTTT 59.444 50.000 15.56 0.00 0.00 2.52
6092 6268 0.961753 CTGCCCTGGGTTGTTCTTTC 59.038 55.000 15.56 0.00 0.00 2.62
6093 6269 0.555769 TGCCCTGGGTTGTTCTTTCT 59.444 50.000 15.56 0.00 0.00 2.52
6094 6270 0.961753 GCCCTGGGTTGTTCTTTCTG 59.038 55.000 15.56 0.00 0.00 3.02
6095 6271 1.754201 GCCCTGGGTTGTTCTTTCTGT 60.754 52.381 15.56 0.00 0.00 3.41
6096 6272 2.666317 CCCTGGGTTGTTCTTTCTGTT 58.334 47.619 3.97 0.00 0.00 3.16
6187 6363 8.307483 TCAGAGTTGTTGAATGTTTACCAAAAA 58.693 29.630 0.00 0.00 0.00 1.94
6369 6989 8.606602 AGAACAATTGCATCTGTTTTTCTTTTC 58.393 29.630 13.43 1.09 35.93 2.29
6404 7024 7.276438 TGACGAGATTCATACAAATTCAGTCTG 59.724 37.037 0.00 0.00 0.00 3.51
6538 7160 4.233789 TGCTGAAGTTCAACAACAACAAC 58.766 39.130 6.49 0.00 34.60 3.32
6642 7264 6.706055 TCTTTCAACTATGTGACGATGTTC 57.294 37.500 0.00 0.00 0.00 3.18
6722 7344 1.139058 AGTGCGAGGACACAGAACTTT 59.861 47.619 0.00 0.00 43.23 2.66
6824 7446 3.016736 AGCCTCATTGGGTGTAATTTCG 58.983 45.455 0.00 0.00 46.19 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.087892 CAGAGGCCGTGGAGTGGG 62.088 72.222 0.00 0.00 0.00 4.61
277 293 2.158645 GCAAAAGCCAACACGTTTTTGT 59.841 40.909 17.48 0.00 40.70 2.83
288 305 2.336088 GCGCTCTGCAAAAGCCAA 59.664 55.556 13.54 0.00 45.45 4.52
321 338 2.978156 TTTTGTTGGCATCTCCTCCT 57.022 45.000 0.00 0.00 35.26 3.69
323 340 4.488879 GTTGATTTTGTTGGCATCTCCTC 58.511 43.478 0.00 0.00 35.26 3.71
324 341 3.057315 CGTTGATTTTGTTGGCATCTCCT 60.057 43.478 0.00 0.00 35.26 3.69
326 343 3.244976 CCGTTGATTTTGTTGGCATCTC 58.755 45.455 0.00 0.00 0.00 2.75
333 375 4.048504 GTTTCCTCCCGTTGATTTTGTTG 58.951 43.478 0.00 0.00 0.00 3.33
482 535 1.671850 CGGTGTGCTGGTACTACTTGG 60.672 57.143 0.00 0.00 0.00 3.61
509 562 0.333312 TCTCTCTCTCTGTGGGTCCC 59.667 60.000 0.00 0.00 0.00 4.46
512 565 1.284785 CCTCTCTCTCTCTCTGTGGGT 59.715 57.143 0.00 0.00 0.00 4.51
526 579 2.282958 TGAACGACGGGCCTCTCT 60.283 61.111 0.84 0.00 0.00 3.10
547 600 1.973138 CTCGCTCGTTCCTTCGTTAA 58.027 50.000 0.00 0.00 0.00 2.01
651 713 1.114722 TGCCTTGGCAGTTTTGGAGG 61.115 55.000 10.65 0.00 0.00 4.30
687 749 6.642950 AGTTGAGTTGAGACGAAGATTAGTTG 59.357 38.462 0.00 0.00 0.00 3.16
726 798 0.179134 CTGGGACCAGACGACGATTC 60.179 60.000 13.06 0.00 46.30 2.52
790 862 3.394836 GCACCGGCCCTCTTCTCT 61.395 66.667 0.00 0.00 0.00 3.10
1091 1183 6.370442 GCTAACTTCCTTCCTCTTCTTTTCTC 59.630 42.308 0.00 0.00 0.00 2.87
1103 1195 1.451567 GCGGGGCTAACTTCCTTCC 60.452 63.158 0.00 0.00 0.00 3.46
1105 1197 2.675371 GGCGGGGCTAACTTCCTT 59.325 61.111 0.00 0.00 0.00 3.36
1106 1198 3.782443 CGGCGGGGCTAACTTCCT 61.782 66.667 0.00 0.00 0.00 3.36
1277 1372 1.421646 GAGGAGAGGAGAGGAGAGAGG 59.578 61.905 0.00 0.00 0.00 3.69
1284 1379 0.108585 CGAGGAGAGGAGAGGAGAGG 59.891 65.000 0.00 0.00 0.00 3.69
1290 1385 3.591835 GCGGCGAGGAGAGGAGAG 61.592 72.222 12.98 0.00 0.00 3.20
1324 1421 7.155328 ACCGGAGATAGATAATAAGCAAACAG 58.845 38.462 9.46 0.00 0.00 3.16
1341 1438 1.207329 CGAAGGAAAGGAACCGGAGAT 59.793 52.381 9.46 0.00 0.00 2.75
1343 1440 1.019805 GCGAAGGAAAGGAACCGGAG 61.020 60.000 9.46 0.00 0.00 4.63
1344 1441 1.004200 GCGAAGGAAAGGAACCGGA 60.004 57.895 9.46 0.00 0.00 5.14
1345 1442 1.298859 CTGCGAAGGAAAGGAACCGG 61.299 60.000 0.00 0.00 0.00 5.28
1346 1443 1.298859 CCTGCGAAGGAAAGGAACCG 61.299 60.000 1.89 0.00 32.43 4.44
1498 1595 3.836617 TCCCACGAGGAGAGGAGA 58.163 61.111 0.00 0.00 40.93 3.71
1556 1659 4.451096 TGGATGCGTCTTGTTTTAGACTTC 59.549 41.667 5.77 0.00 41.89 3.01
1560 1663 5.957842 AATTGGATGCGTCTTGTTTTAGA 57.042 34.783 5.77 0.00 0.00 2.10
1774 1878 1.274728 CAAGTAGCAGAGCTGGACACT 59.725 52.381 0.00 0.00 40.10 3.55
1887 1991 2.541762 GGAACGCTGTATGCTCTCATTC 59.458 50.000 0.00 0.00 40.11 2.67
1905 2009 7.187824 AGATGAGCTTGTAATAACAGAGGAA 57.812 36.000 0.00 0.00 36.83 3.36
1928 2032 7.979115 TTTCCAACAATTTAACGACAGAAAG 57.021 32.000 0.00 0.00 0.00 2.62
1943 2047 7.504924 ACGACTTTGAAGATATTTCCAACAA 57.495 32.000 0.00 0.00 0.00 2.83
6029 6205 2.706350 TCCCAGGGCAGATAATTAGCT 58.294 47.619 0.00 0.00 0.00 3.32
6030 6206 3.245052 ACATCCCAGGGCAGATAATTAGC 60.245 47.826 0.00 0.00 0.00 3.09
6031 6207 4.647564 ACATCCCAGGGCAGATAATTAG 57.352 45.455 0.00 0.00 0.00 1.73
6032 6208 4.665009 AGAACATCCCAGGGCAGATAATTA 59.335 41.667 0.00 0.00 0.00 1.40
6033 6209 3.464833 AGAACATCCCAGGGCAGATAATT 59.535 43.478 0.00 0.00 0.00 1.40
6034 6210 3.059097 AGAACATCCCAGGGCAGATAAT 58.941 45.455 0.00 0.00 0.00 1.28
6035 6211 2.492025 AGAACATCCCAGGGCAGATAA 58.508 47.619 0.00 0.00 0.00 1.75
6036 6212 2.196742 AGAACATCCCAGGGCAGATA 57.803 50.000 0.00 0.00 0.00 1.98
6037 6213 1.302907 AAGAACATCCCAGGGCAGAT 58.697 50.000 0.00 0.00 0.00 2.90
6038 6214 1.004745 GAAAGAACATCCCAGGGCAGA 59.995 52.381 0.00 0.00 0.00 4.26
6039 6215 1.005215 AGAAAGAACATCCCAGGGCAG 59.995 52.381 0.00 0.00 0.00 4.85
6040 6216 1.075601 AGAAAGAACATCCCAGGGCA 58.924 50.000 0.00 0.00 0.00 5.36
6041 6217 1.272147 ACAGAAAGAACATCCCAGGGC 60.272 52.381 0.00 0.00 0.00 5.19
6042 6218 2.887151 ACAGAAAGAACATCCCAGGG 57.113 50.000 0.00 0.00 0.00 4.45
6043 6219 3.691609 GCTAACAGAAAGAACATCCCAGG 59.308 47.826 0.00 0.00 0.00 4.45
6044 6220 4.583871 AGCTAACAGAAAGAACATCCCAG 58.416 43.478 0.00 0.00 0.00 4.45
6045 6221 4.640771 AGCTAACAGAAAGAACATCCCA 57.359 40.909 0.00 0.00 0.00 4.37
6046 6222 7.631717 AATTAGCTAACAGAAAGAACATCCC 57.368 36.000 8.70 0.00 0.00 3.85
6050 6226 8.883731 GCAGATAATTAGCTAACAGAAAGAACA 58.116 33.333 8.70 0.00 0.00 3.18
6051 6227 8.338986 GGCAGATAATTAGCTAACAGAAAGAAC 58.661 37.037 8.70 0.00 0.00 3.01
6052 6228 7.499232 GGGCAGATAATTAGCTAACAGAAAGAA 59.501 37.037 8.70 0.00 0.00 2.52
6053 6229 6.992715 GGGCAGATAATTAGCTAACAGAAAGA 59.007 38.462 8.70 0.00 0.00 2.52
6054 6230 6.995091 AGGGCAGATAATTAGCTAACAGAAAG 59.005 38.462 8.70 0.00 0.00 2.62
6055 6231 6.767902 CAGGGCAGATAATTAGCTAACAGAAA 59.232 38.462 8.70 0.00 0.00 2.52
6056 6232 6.291377 CAGGGCAGATAATTAGCTAACAGAA 58.709 40.000 8.70 0.00 0.00 3.02
6057 6233 5.221722 CCAGGGCAGATAATTAGCTAACAGA 60.222 44.000 8.70 0.00 0.00 3.41
6058 6234 4.999950 CCAGGGCAGATAATTAGCTAACAG 59.000 45.833 8.70 0.00 0.00 3.16
6059 6235 4.202461 CCCAGGGCAGATAATTAGCTAACA 60.202 45.833 8.70 0.00 0.00 2.41
6060 6236 4.202472 ACCCAGGGCAGATAATTAGCTAAC 60.202 45.833 8.70 0.00 0.00 2.34
6061 6237 3.980698 ACCCAGGGCAGATAATTAGCTAA 59.019 43.478 8.99 8.99 0.00 3.09
6062 6238 3.598264 ACCCAGGGCAGATAATTAGCTA 58.402 45.455 4.91 0.00 0.00 3.32
6063 6239 2.422746 ACCCAGGGCAGATAATTAGCT 58.577 47.619 4.91 0.00 0.00 3.32
6064 6240 2.887152 CAACCCAGGGCAGATAATTAGC 59.113 50.000 4.91 0.00 0.00 3.09
6065 6241 4.170468 ACAACCCAGGGCAGATAATTAG 57.830 45.455 4.91 0.00 0.00 1.73
6066 6242 4.229582 AGAACAACCCAGGGCAGATAATTA 59.770 41.667 4.91 0.00 0.00 1.40
6067 6243 3.011708 AGAACAACCCAGGGCAGATAATT 59.988 43.478 4.91 0.00 0.00 1.40
6068 6244 2.582636 AGAACAACCCAGGGCAGATAAT 59.417 45.455 4.91 0.00 0.00 1.28
6069 6245 1.992557 AGAACAACCCAGGGCAGATAA 59.007 47.619 4.91 0.00 0.00 1.75
6070 6246 1.668826 AGAACAACCCAGGGCAGATA 58.331 50.000 4.91 0.00 0.00 1.98
6071 6247 0.779997 AAGAACAACCCAGGGCAGAT 59.220 50.000 4.91 0.00 0.00 2.90
6072 6248 0.555769 AAAGAACAACCCAGGGCAGA 59.444 50.000 4.91 0.00 0.00 4.26
6073 6249 0.961753 GAAAGAACAACCCAGGGCAG 59.038 55.000 4.91 0.00 0.00 4.85
6074 6250 0.555769 AGAAAGAACAACCCAGGGCA 59.444 50.000 4.91 0.00 0.00 5.36
6075 6251 0.961753 CAGAAAGAACAACCCAGGGC 59.038 55.000 4.91 0.00 0.00 5.19
6076 6252 2.364972 ACAGAAAGAACAACCCAGGG 57.635 50.000 2.85 2.85 0.00 4.45
6077 6253 3.253432 GCTAACAGAAAGAACAACCCAGG 59.747 47.826 0.00 0.00 0.00 4.45
6078 6254 4.137543 AGCTAACAGAAAGAACAACCCAG 58.862 43.478 0.00 0.00 0.00 4.45
6079 6255 4.164843 AGCTAACAGAAAGAACAACCCA 57.835 40.909 0.00 0.00 0.00 4.51
6080 6256 6.819397 ATTAGCTAACAGAAAGAACAACCC 57.181 37.500 8.70 0.00 0.00 4.11
6081 6257 9.989869 GATAATTAGCTAACAGAAAGAACAACC 57.010 33.333 8.70 0.00 0.00 3.77
6084 6260 8.883731 GCAGATAATTAGCTAACAGAAAGAACA 58.116 33.333 8.70 0.00 0.00 3.18
6085 6261 8.338986 GGCAGATAATTAGCTAACAGAAAGAAC 58.661 37.037 8.70 0.00 0.00 3.01
6086 6262 7.499232 GGGCAGATAATTAGCTAACAGAAAGAA 59.501 37.037 8.70 0.00 0.00 2.52
6087 6263 6.992715 GGGCAGATAATTAGCTAACAGAAAGA 59.007 38.462 8.70 0.00 0.00 2.52
6088 6264 6.995091 AGGGCAGATAATTAGCTAACAGAAAG 59.005 38.462 8.70 0.00 0.00 2.62
6089 6265 6.767902 CAGGGCAGATAATTAGCTAACAGAAA 59.232 38.462 8.70 0.00 0.00 2.52
6090 6266 6.291377 CAGGGCAGATAATTAGCTAACAGAA 58.709 40.000 8.70 0.00 0.00 3.02
6091 6267 5.221722 CCAGGGCAGATAATTAGCTAACAGA 60.222 44.000 8.70 0.00 0.00 3.41
6092 6268 4.999950 CCAGGGCAGATAATTAGCTAACAG 59.000 45.833 8.70 0.00 0.00 3.16
6093 6269 4.202461 CCCAGGGCAGATAATTAGCTAACA 60.202 45.833 8.70 0.00 0.00 2.41
6094 6270 4.202472 ACCCAGGGCAGATAATTAGCTAAC 60.202 45.833 8.70 0.00 0.00 2.34
6095 6271 3.980698 ACCCAGGGCAGATAATTAGCTAA 59.019 43.478 8.99 8.99 0.00 3.09
6096 6272 3.598264 ACCCAGGGCAGATAATTAGCTA 58.402 45.455 4.91 0.00 0.00 3.32
6137 6313 7.441157 TGAAGGTTTACAATCACACAGAACTAG 59.559 37.037 0.00 0.00 0.00 2.57
6285 6461 7.278646 TGAAACTCTCGATTACATGAATCTTGG 59.721 37.037 0.00 0.00 41.72 3.61
6369 6989 2.262211 TGAATCTCGTCAGTTCATGCG 58.738 47.619 0.00 0.00 0.00 4.73
6404 7024 1.979155 GCCCTGAGGGTTTGCCTTC 60.979 63.158 20.64 0.00 46.51 3.46
6425 7045 1.281419 ATACCACCATCCGTCCAACA 58.719 50.000 0.00 0.00 0.00 3.33
6502 7122 3.117663 ACTTCAGCAGTTTTAGGGGTTGA 60.118 43.478 0.00 0.00 27.32 3.18
6642 7264 1.035385 TGAAGCATGGCAGCTCATGG 61.035 55.000 19.53 7.18 45.89 3.66
6722 7344 7.684317 TTATGATGAGGTACCAAATAGTCCA 57.316 36.000 15.94 1.93 0.00 4.02
6789 7411 0.038159 GAGGCTCGATCATTACCGGG 60.038 60.000 6.32 0.00 0.00 5.73
6792 7414 3.070018 CCAATGAGGCTCGATCATTACC 58.930 50.000 10.42 0.00 43.74 2.85
6795 7417 1.492176 ACCCAATGAGGCTCGATCATT 59.508 47.619 10.42 6.87 45.88 2.57
6796 7418 1.135094 ACCCAATGAGGCTCGATCAT 58.865 50.000 10.42 0.00 39.06 2.45


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

AutoCloner maintained by Alex Coulton.