Multiple sequence alignment - TraesCS1A01G238700

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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 TraesCS1A01G238700 chr1A 100.000 7180 0 0 1 7180 425266283 425259104 0.000000e+00 13260.0
1 TraesCS1A01G238700 chr1A 94.315 2058 77 14 1586 3642 417401266 417399248 0.000000e+00 3116.0
2 TraesCS1A01G238700 chr1A 94.781 1303 49 7 3642 4930 534170632 534169335 0.000000e+00 2012.0
3 TraesCS1A01G238700 chr1A 95.033 765 24 8 818 1576 417410099 417409343 0.000000e+00 1190.0
4 TraesCS1A01G238700 chr1A 93.419 775 25 10 5495 6269 417398539 417397791 0.000000e+00 1125.0
5 TraesCS1A01G238700 chr1A 95.050 505 21 3 4939 5441 417399257 417398755 0.000000e+00 791.0
6 TraesCS1A01G238700 chr1A 92.420 343 23 1 6301 6640 417397788 417397446 3.010000e-133 486.0
7 TraesCS1A01G238700 chr1A 88.152 422 26 11 6751 7164 417397324 417396919 1.400000e-131 481.0
8 TraesCS1A01G238700 chr1A 89.035 228 17 4 6941 7163 406580948 406581172 7.100000e-70 276.0
9 TraesCS1A01G238700 chr1A 90.449 178 13 4 6987 7163 407519740 407519566 1.560000e-56 231.0
10 TraesCS1A01G238700 chr1A 90.449 178 14 3 6987 7163 421635171 421635346 1.560000e-56 231.0
11 TraesCS1A01G238700 chr1A 92.391 92 7 0 6623 6714 417397416 417397325 1.630000e-26 132.0
12 TraesCS1A01G238700 chr1A 91.667 72 6 0 746 817 417410782 417410711 4.580000e-17 100.0
13 TraesCS1A01G238700 chr1D 92.901 2127 96 25 4939 7028 328455807 328453699 0.000000e+00 3040.0
14 TraesCS1A01G238700 chr1D 94.961 1290 56 9 3630 4915 8479244 8477960 0.000000e+00 2013.0
15 TraesCS1A01G238700 chr1D 94.651 1290 60 9 3630 4915 8517117 8515833 0.000000e+00 1991.0
16 TraesCS1A01G238700 chr1D 90.659 1274 104 8 3643 4907 382258527 382259794 0.000000e+00 1679.0
17 TraesCS1A01G238700 chr1D 95.010 982 36 6 2273 3253 328457391 328456422 0.000000e+00 1530.0
18 TraesCS1A01G238700 chr1D 93.120 843 32 13 746 1567 328459029 328458192 0.000000e+00 1212.0
19 TraesCS1A01G238700 chr1D 93.459 688 17 8 1567 2249 328458152 328457488 0.000000e+00 996.0
20 TraesCS1A01G238700 chr1D 96.203 395 15 0 3249 3643 328456191 328455797 0.000000e+00 647.0
21 TraesCS1A01G238700 chr1D 91.480 223 16 3 6941 7163 322379357 322379576 3.250000e-78 303.0
22 TraesCS1A01G238700 chr1B 93.523 1374 76 7 2273 3643 442625415 442624052 0.000000e+00 2032.0
23 TraesCS1A01G238700 chr1B 88.950 1466 58 45 832 2249 442626918 442625509 0.000000e+00 1714.0
24 TraesCS1A01G238700 chr1B 89.895 1138 71 17 5110 6228 442623890 442622778 0.000000e+00 1424.0
25 TraesCS1A01G238700 chr1B 93.189 602 35 4 6303 6903 442622744 442622148 0.000000e+00 880.0
26 TraesCS1A01G238700 chr1B 90.667 225 14 6 6941 7163 435358933 435359152 7.050000e-75 292.0
27 TraesCS1A01G238700 chr1B 89.610 231 13 7 6941 7163 326929041 326928814 4.240000e-72 283.0
28 TraesCS1A01G238700 chr1B 96.552 58 2 0 749 806 442627064 442627007 5.930000e-16 97.1
29 TraesCS1A01G238700 chr7D 94.910 1277 42 9 3642 4916 64225112 64226367 0.000000e+00 1977.0
30 TraesCS1A01G238700 chr7D 89.264 1304 117 12 3641 4930 89717685 89718979 0.000000e+00 1611.0
31 TraesCS1A01G238700 chr7D 91.814 452 29 5 1567 2013 75655318 75654870 2.200000e-174 623.0
32 TraesCS1A01G238700 chr6D 91.919 1287 86 11 3643 4916 157039616 157038335 0.000000e+00 1784.0
33 TraesCS1A01G238700 chr6D 92.632 95 6 1 2170 2263 122992193 122992099 1.260000e-27 135.0
34 TraesCS1A01G238700 chr5B 91.210 1297 91 11 3646 4922 594138699 594139992 0.000000e+00 1742.0
35 TraesCS1A01G238700 chr5A 90.986 1298 88 11 3642 4925 436615804 436617086 0.000000e+00 1722.0
36 TraesCS1A01G238700 chr3B 90.465 1311 97 16 3638 4930 803061097 803062397 0.000000e+00 1703.0
37 TraesCS1A01G238700 chr3B 82.805 599 79 6 4318 4905 86070179 86069594 1.380000e-141 514.0
38 TraesCS1A01G238700 chr3B 94.253 87 5 0 2172 2258 487224399 487224485 4.520000e-27 134.0
39 TraesCS1A01G238700 chr3A 95.200 750 34 1 1 748 656462645 656463394 0.000000e+00 1184.0
40 TraesCS1A01G238700 chr7A 92.667 750 30 3 1 748 627149538 627150264 0.000000e+00 1057.0
41 TraesCS1A01G238700 chr6B 95.238 84 4 0 2170 2253 713700329 713700246 4.520000e-27 134.0
42 TraesCS1A01G238700 chr7B 93.258 89 5 1 2166 2253 533304597 533304509 5.850000e-26 130.0
43 TraesCS1A01G238700 chr4A 89.320 103 9 2 2163 2264 625404768 625404869 2.100000e-25 128.0
44 TraesCS1A01G238700 chr2B 92.222 90 7 0 2168 2257 394723040 394722951 2.100000e-25 128.0
45 TraesCS1A01G238700 chr5D 92.222 90 6 1 2168 2257 134916491 134916579 7.560000e-25 126.0
46 TraesCS1A01G238700 chr3D 90.426 94 9 0 2171 2264 75148045 75147952 2.720000e-24 124.0


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 TraesCS1A01G238700 chr1A 425259104 425266283 7179 True 13260.000000 13260 100.0000 1 7180 1 chr1A.!!$R2 7179
1 TraesCS1A01G238700 chr1A 534169335 534170632 1297 True 2012.000000 2012 94.7810 3642 4930 1 chr1A.!!$R3 1288
2 TraesCS1A01G238700 chr1A 417396919 417401266 4347 True 1021.833333 3116 92.6245 1586 7164 6 chr1A.!!$R4 5578
3 TraesCS1A01G238700 chr1A 417409343 417410782 1439 True 645.000000 1190 93.3500 746 1576 2 chr1A.!!$R5 830
4 TraesCS1A01G238700 chr1D 8477960 8479244 1284 True 2013.000000 2013 94.9610 3630 4915 1 chr1D.!!$R1 1285
5 TraesCS1A01G238700 chr1D 8515833 8517117 1284 True 1991.000000 1991 94.6510 3630 4915 1 chr1D.!!$R2 1285
6 TraesCS1A01G238700 chr1D 382258527 382259794 1267 False 1679.000000 1679 90.6590 3643 4907 1 chr1D.!!$F2 1264
7 TraesCS1A01G238700 chr1D 328453699 328459029 5330 True 1485.000000 3040 94.1386 746 7028 5 chr1D.!!$R3 6282
8 TraesCS1A01G238700 chr1B 442622148 442627064 4916 True 1229.420000 2032 92.4218 749 6903 5 chr1B.!!$R2 6154
9 TraesCS1A01G238700 chr7D 64225112 64226367 1255 False 1977.000000 1977 94.9100 3642 4916 1 chr7D.!!$F1 1274
10 TraesCS1A01G238700 chr7D 89717685 89718979 1294 False 1611.000000 1611 89.2640 3641 4930 1 chr7D.!!$F2 1289
11 TraesCS1A01G238700 chr6D 157038335 157039616 1281 True 1784.000000 1784 91.9190 3643 4916 1 chr6D.!!$R2 1273
12 TraesCS1A01G238700 chr5B 594138699 594139992 1293 False 1742.000000 1742 91.2100 3646 4922 1 chr5B.!!$F1 1276
13 TraesCS1A01G238700 chr5A 436615804 436617086 1282 False 1722.000000 1722 90.9860 3642 4925 1 chr5A.!!$F1 1283
14 TraesCS1A01G238700 chr3B 803061097 803062397 1300 False 1703.000000 1703 90.4650 3638 4930 1 chr3B.!!$F2 1292
15 TraesCS1A01G238700 chr3B 86069594 86070179 585 True 514.000000 514 82.8050 4318 4905 1 chr3B.!!$R1 587
16 TraesCS1A01G238700 chr3A 656462645 656463394 749 False 1184.000000 1184 95.2000 1 748 1 chr3A.!!$F1 747
17 TraesCS1A01G238700 chr7A 627149538 627150264 726 False 1057.000000 1057 92.6670 1 748 1 chr7A.!!$F1 747

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
667 668 0.035439 TTTTGGCGATGTCCCTCCTC 60.035 55.000 0.0 0.0 0.00 3.71 F
1322 1970 0.611200 CACGTGAGGGGGTTGATACA 59.389 55.000 10.9 0.0 0.00 2.29 F
2521 3290 0.477204 ACTGCTGGGATCATGGGATG 59.523 55.000 0.0 0.0 32.67 3.51 F
2522 3291 0.769247 CTGCTGGGATCATGGGATGA 59.231 55.000 0.0 0.0 44.55 2.92 F
2819 3590 1.002792 GGAATTATCGTTCAAGGCCGC 60.003 52.381 0.0 0.0 0.00 6.53 F
4296 5312 1.218875 GCACACCGACATCGTCAACA 61.219 55.000 0.0 0.0 37.74 3.33 F
4917 5968 1.074850 GAGGAGGGAGGAGGGGAAG 60.075 68.421 0.0 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 2703 0.746659 ATAAAAGCCCATTCCGCTGC 59.253 50.000 0.00 0.00 36.47 5.25 R
3306 4314 3.191162 TGAGAACCACAACATGCATAAGC 59.809 43.478 0.00 0.00 42.57 3.09 R
3845 4856 0.382515 GCTCCGACTCTTCGCTATGT 59.617 55.000 0.00 0.00 44.43 2.29 R
4513 5534 0.820891 CTTGTGCTCTGGTGTGGCTT 60.821 55.000 0.00 0.00 0.00 4.35 R
4574 5595 1.154221 GCTCGACCCCCTCCTCTAT 59.846 63.158 0.00 0.00 0.00 1.98 R
5847 7174 0.587768 CAATGACACGCTGTGCTTCA 59.412 50.000 8.31 6.55 36.98 3.02 R
6590 7928 0.034059 AGCACTTCCCGTCTGTTCAG 59.966 55.000 0.00 0.00 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
26 27 2.027192 TGATAGGAACTGAACCCACTGC 60.027 50.000 0.00 0.00 41.52 4.40
176 177 1.704628 TGAGGAATTGGAAGCAGACCA 59.295 47.619 0.00 0.00 35.47 4.02
190 191 0.036010 AGACCAATCAGCAAGGACGG 60.036 55.000 0.00 0.00 0.00 4.79
211 212 4.916983 GCAATGAAGCCCATACATACAA 57.083 40.909 0.00 0.00 34.45 2.41
225 226 6.543465 CCATACATACAAAGAGGAGCAAATGA 59.457 38.462 0.00 0.00 0.00 2.57
268 269 7.922278 GCATATGGAAATTAAACTCTGATGCAA 59.078 33.333 4.56 0.00 35.89 4.08
269 270 9.976511 CATATGGAAATTAAACTCTGATGCAAT 57.023 29.630 0.00 0.00 0.00 3.56
311 312 2.359850 TGTGGCTGGAACCATCGC 60.360 61.111 0.00 0.00 43.01 4.58
491 492 8.735692 TCAGTCATCATAATGCTGAATAACAA 57.264 30.769 1.76 0.00 40.19 2.83
529 530 2.505819 GCTCTTTTCCCCCTAGTCATGA 59.494 50.000 0.00 0.00 0.00 3.07
634 635 2.757868 GCTGCTCTAGGAAGAAGACAGA 59.242 50.000 0.00 0.00 30.35 3.41
667 668 0.035439 TTTTGGCGATGTCCCTCCTC 60.035 55.000 0.00 0.00 0.00 3.71
669 670 2.444895 GGCGATGTCCCTCCTCCT 60.445 66.667 0.00 0.00 0.00 3.69
726 727 7.502561 AGCTCTTCCATTGTTACTTAAGTTGTT 59.497 33.333 14.49 0.00 0.00 2.83
740 741 6.770785 ACTTAAGTTGTTGCTGGTTTGATCTA 59.229 34.615 1.12 0.00 0.00 1.98
857 1472 1.739750 CAGCCCTCCTTATCCATCCT 58.260 55.000 0.00 0.00 0.00 3.24
858 1473 1.627834 CAGCCCTCCTTATCCATCCTC 59.372 57.143 0.00 0.00 0.00 3.71
860 1475 1.270907 CCCTCCTTATCCATCCTCCG 58.729 60.000 0.00 0.00 0.00 4.63
1222 1867 4.723309 GGTACCTCGACTTTCCTATCCTA 58.277 47.826 4.06 0.00 0.00 2.94
1223 1868 4.518590 GGTACCTCGACTTTCCTATCCTAC 59.481 50.000 4.06 0.00 0.00 3.18
1224 1869 3.564264 ACCTCGACTTTCCTATCCTACC 58.436 50.000 0.00 0.00 0.00 3.18
1225 1870 2.892215 CCTCGACTTTCCTATCCTACCC 59.108 54.545 0.00 0.00 0.00 3.69
1226 1871 3.436761 CCTCGACTTTCCTATCCTACCCT 60.437 52.174 0.00 0.00 0.00 4.34
1250 1898 1.599071 TGCTATTTACATGCGCTCTGC 59.401 47.619 9.73 0.82 46.70 4.26
1322 1970 0.611200 CACGTGAGGGGGTTGATACA 59.389 55.000 10.90 0.00 0.00 2.29
1527 2175 5.172205 GTGAGAACCTTATCTGAAGGACAC 58.828 45.833 10.29 9.90 39.81 3.67
1542 2190 1.271163 GGACACTTCACCGGAATGGAA 60.271 52.381 9.46 5.43 42.00 3.53
1596 2287 1.595794 AGTTAACACTTGTGCCGTTCG 59.404 47.619 8.61 0.00 0.00 3.95
1634 2325 3.259064 GTCTGATTGCGTTTGCCTAGTA 58.741 45.455 0.00 0.00 41.78 1.82
1713 2405 5.087323 TGGACTCTTTCTTCCTACTCACAT 58.913 41.667 0.00 0.00 32.55 3.21
1745 2437 8.545472 ACTAATAGTGCCCAACTAATTAGACAA 58.455 33.333 19.38 0.00 44.57 3.18
1790 2482 4.736126 TGTTCTTGACAGTTGTGAGAGA 57.264 40.909 0.00 0.00 33.40 3.10
1791 2483 4.686972 TGTTCTTGACAGTTGTGAGAGAG 58.313 43.478 0.00 0.00 33.40 3.20
1802 2494 0.687354 GTGAGAGAGGGCAAAGTCCA 59.313 55.000 0.00 0.00 0.00 4.02
2009 2703 6.292811 GGTTTTGGTGCAAATGTAATGAACAG 60.293 38.462 0.00 0.00 42.70 3.16
2146 2841 2.294233 GTCTCTGCAGCAAACCATGAAA 59.706 45.455 9.47 0.00 0.00 2.69
2257 2952 9.303116 ACACTTATTATGGATCAGAGGTAGTAG 57.697 37.037 0.00 0.00 0.00 2.57
2299 3067 9.732130 ACAAAGAAATCAGAGCTTTCTACTATT 57.268 29.630 0.00 0.00 41.01 1.73
2404 3172 9.543018 GTACTGTTATGTCAAGTTTTAGAATGC 57.457 33.333 0.00 0.00 0.00 3.56
2519 3288 1.348008 GGACTGCTGGGATCATGGGA 61.348 60.000 0.00 0.00 0.00 4.37
2521 3290 0.477204 ACTGCTGGGATCATGGGATG 59.523 55.000 0.00 0.00 32.67 3.51
2522 3291 0.769247 CTGCTGGGATCATGGGATGA 59.231 55.000 0.00 0.00 44.55 2.92
2563 3332 6.299805 TGATGAACAACTAGGACTAGCATT 57.700 37.500 6.28 0.00 36.66 3.56
2655 3424 3.402628 GACCTGTAGTCAAGGCTTTGA 57.597 47.619 7.24 7.24 45.55 2.69
2712 3481 6.389830 TTGCACTTGTTCTGTTGATTATGT 57.610 33.333 0.00 0.00 0.00 2.29
2819 3590 1.002792 GGAATTATCGTTCAAGGCCGC 60.003 52.381 0.00 0.00 0.00 6.53
2850 3621 3.290710 GGGCATGTGATTGGTCAAGTAT 58.709 45.455 0.00 0.00 35.80 2.12
2856 3627 6.484643 GCATGTGATTGGTCAAGTATAGTCAT 59.515 38.462 0.00 0.00 35.80 3.06
2863 3634 9.378551 GATTGGTCAAGTATAGTCATTACACAA 57.621 33.333 0.00 0.00 0.00 3.33
2930 3703 3.341823 CAGTCTACCAAGAAGCAAGCAT 58.658 45.455 0.00 0.00 32.16 3.79
2961 3734 1.915489 AGAATCTACACCATGTGCCCA 59.085 47.619 0.00 0.00 36.98 5.36
3268 4276 6.013293 AGGAACTAGGTACTTGCTCAATCTTT 60.013 38.462 0.00 0.00 41.75 2.52
3325 4333 3.574284 TGCTTATGCATGTTGTGGTTC 57.426 42.857 10.16 0.00 45.31 3.62
3328 4336 3.191162 GCTTATGCATGTTGTGGTTCTCA 59.809 43.478 10.16 0.00 39.41 3.27
3433 4441 5.292765 AGATGAATTGCACGGACTATACAG 58.707 41.667 0.00 0.00 0.00 2.74
3629 4637 5.191727 TCCCCTCATTCTGCATTTAGAAA 57.808 39.130 0.00 0.00 39.87 2.52
3637 4645 8.761575 TCATTCTGCATTTAGAAATTGAAACC 57.238 30.769 0.00 0.00 39.87 3.27
3638 4646 8.366401 TCATTCTGCATTTAGAAATTGAAACCA 58.634 29.630 0.00 0.00 39.87 3.67
3639 4647 9.158233 CATTCTGCATTTAGAAATTGAAACCAT 57.842 29.630 0.00 0.00 39.87 3.55
3843 4854 2.970324 TGCCTCAACCGTGAACGC 60.970 61.111 0.00 0.00 38.18 4.84
3845 4856 2.539338 GCCTCAACCGTGAACGCAA 61.539 57.895 0.00 0.00 38.18 4.85
4083 5096 3.580319 ACCCGGCAAGCCCTCTTT 61.580 61.111 5.34 0.00 0.00 2.52
4095 5108 1.544825 CCCTCTTTGCCTCCGAGACA 61.545 60.000 0.00 0.00 0.00 3.41
4296 5312 1.218875 GCACACCGACATCGTCAACA 61.219 55.000 0.00 0.00 37.74 3.33
4513 5534 2.036098 CCATTCACCAGCCAGCCA 59.964 61.111 0.00 0.00 0.00 4.75
4597 5618 1.457831 GGAGGGGGTCGAGCATACT 60.458 63.158 17.59 10.62 0.00 2.12
4915 5966 3.036959 GGAGGAGGGAGGAGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
4916 5967 2.647949 GGAGGAGGGAGGAGGGGAA 61.648 68.421 0.00 0.00 0.00 3.97
4917 5968 1.074850 GAGGAGGGAGGAGGGGAAG 60.075 68.421 0.00 0.00 0.00 3.46
4918 5969 2.040359 GGAGGGAGGAGGGGAAGG 60.040 72.222 0.00 0.00 0.00 3.46
5023 6110 3.102204 CTCCTAAAAGTCTAACCCCGGA 58.898 50.000 0.73 0.00 0.00 5.14
5031 6118 4.417426 AGTCTAACCCCGGAACAATATG 57.583 45.455 0.73 0.00 0.00 1.78
5062 6149 6.986231 ACGATGATGAGTGAATGTGCTTTATA 59.014 34.615 0.00 0.00 0.00 0.98
5180 6269 6.658831 ACTGTTTGTCAATTTAGACATGTCG 58.341 36.000 19.85 5.07 46.90 4.35
5251 6352 1.754107 GCCAAACAAGCCCCACAAT 59.246 52.632 0.00 0.00 0.00 2.71
5422 6524 7.663043 TTTTAAATTAAACCTGGGTCTGTGT 57.337 32.000 0.00 0.00 0.00 3.72
5443 6545 6.601613 TGTGTTTCCTGGGCATATAAAGTTAG 59.398 38.462 0.00 0.00 0.00 2.34
5473 6578 7.764443 ACGACATGCACATATTTACTCTTAAGT 59.236 33.333 1.63 0.00 39.66 2.24
5477 6582 6.677781 GCACATATTTACTCTTAAGTGCCA 57.322 37.500 1.63 0.00 43.72 4.92
5480 6585 8.190784 GCACATATTTACTCTTAAGTGCCAAAT 58.809 33.333 15.96 15.96 43.72 2.32
5531 6858 8.678593 AGGTTGAAAAACTAAAGTTCTAGGAG 57.321 34.615 0.00 0.00 46.27 3.69
5532 6859 8.272889 AGGTTGAAAAACTAAAGTTCTAGGAGT 58.727 33.333 0.00 0.00 46.27 3.85
5533 6860 9.551734 GGTTGAAAAACTAAAGTTCTAGGAGTA 57.448 33.333 0.00 0.00 37.25 2.59
5535 6862 9.551734 TTGAAAAACTAAAGTTCTAGGAGTACC 57.448 33.333 0.00 0.00 37.25 3.34
5581 6908 9.565090 GATTAATCATGGCCATCTATTATGCTA 57.435 33.333 17.61 8.31 0.00 3.49
5713 7040 9.812347 TTTCATAATTCCAGCACAAGGATATAT 57.188 29.630 0.00 0.00 34.56 0.86
5714 7041 8.797350 TCATAATTCCAGCACAAGGATATATG 57.203 34.615 0.00 0.00 36.45 1.78
5715 7042 5.972107 AATTCCAGCACAAGGATATATGC 57.028 39.130 0.00 0.00 38.39 3.14
5805 7132 2.359900 CAGAGTGTTGGGCTAATCACC 58.640 52.381 10.83 5.37 0.00 4.02
5844 7171 3.591023 GGAAGTTGTCAAGAGGCTAGTC 58.409 50.000 0.00 0.00 0.00 2.59
5847 7174 1.067495 GTTGTCAAGAGGCTAGTCGCT 60.067 52.381 0.00 0.00 39.13 4.93
5959 7286 3.057734 GGTATCTAATGGTGTACGCTGC 58.942 50.000 6.35 0.00 0.00 5.25
6103 7431 6.486253 TTCAATACAATGAGACTGACAAGC 57.514 37.500 0.00 0.00 0.00 4.01
6142 7470 3.758554 AGCCACTTGTCAATTACACATCC 59.241 43.478 0.00 0.00 38.00 3.51
6419 7754 3.555966 AGAAGTTTTGGAGGTGGTGAAG 58.444 45.455 0.00 0.00 0.00 3.02
6464 7799 7.062605 GGCTGAAATGACACATTTATTGTCTTG 59.937 37.037 9.24 0.00 43.30 3.02
6469 7804 6.951062 TGACACATTTATTGTCTTGGTTCA 57.049 33.333 4.27 0.00 43.30 3.18
6471 7806 7.424803 TGACACATTTATTGTCTTGGTTCAAG 58.575 34.615 4.27 1.53 43.30 3.02
6485 7820 3.056107 TGGTTCAAGAGGTAGATGGTTCG 60.056 47.826 0.00 0.00 0.00 3.95
6488 7823 3.427573 TCAAGAGGTAGATGGTTCGACA 58.572 45.455 0.00 0.00 0.00 4.35
6578 7916 4.799564 TCACATGCCCAAAGGTTATTTC 57.200 40.909 0.00 0.00 34.57 2.17
6637 7975 6.202762 TGTGTCGGATAATATTCTCATTGCAC 59.797 38.462 3.54 6.63 0.00 4.57
6726 8111 3.402110 TCATAAAGCATATGTCCGGCTG 58.598 45.455 4.29 0.00 38.04 4.85
6762 8147 3.198635 TGAGGAGAATGATGGACTGAACC 59.801 47.826 0.00 0.00 0.00 3.62
6784 8175 1.133025 GGTTTGCTGACCGATGGATTG 59.867 52.381 0.00 0.00 0.00 2.67
6815 8208 4.341366 TGAATCGTGCCTCATCATATGT 57.659 40.909 1.90 0.00 0.00 2.29
6816 8209 4.707105 TGAATCGTGCCTCATCATATGTT 58.293 39.130 1.90 0.00 0.00 2.71
6881 8276 1.304962 TGAGAGGCTTACGGCAGGA 60.305 57.895 0.00 0.00 44.01 3.86
6899 8294 2.593026 GGATGACTCCTCCTTCTCGAT 58.407 52.381 0.00 0.00 38.65 3.59
6942 8349 2.324541 AGGCACTCTCAAGTCTCAAGT 58.675 47.619 0.00 0.00 31.71 3.16
6961 8368 4.706842 AGTACACAACTCCATCCACTTT 57.293 40.909 0.00 0.00 30.33 2.66
6962 8369 4.642429 AGTACACAACTCCATCCACTTTC 58.358 43.478 0.00 0.00 30.33 2.62
6969 8376 0.704076 TCCATCCACTTTCCCCCTTG 59.296 55.000 0.00 0.00 0.00 3.61
7030 8437 0.395686 CATGGATGGAGATGGCGACT 59.604 55.000 0.00 0.00 0.00 4.18
7149 8556 3.591254 AAGGTCGCGGCAGGAGTTC 62.591 63.158 14.93 0.00 0.00 3.01
7155 8562 4.421479 CGGCAGGAGTTCGTCGCT 62.421 66.667 0.00 0.00 0.00 4.93
7161 8568 2.507324 GAGTTCGTCGCTGAGGGC 60.507 66.667 0.00 0.00 37.64 5.19
7164 8571 2.361992 TTCGTCGCTGAGGGCCTA 60.362 61.111 5.73 0.00 37.74 3.93
7165 8572 1.980232 TTCGTCGCTGAGGGCCTAA 60.980 57.895 5.73 0.00 37.74 2.69
7166 8573 2.202756 CGTCGCTGAGGGCCTAAC 60.203 66.667 5.73 0.00 37.74 2.34
7167 8574 2.202756 GTCGCTGAGGGCCTAACG 60.203 66.667 5.73 11.30 37.74 3.18
7168 8575 3.458163 TCGCTGAGGGCCTAACGG 61.458 66.667 5.73 0.23 37.74 4.44
7178 8585 3.127533 CCTAACGGCAGGTGCAGC 61.128 66.667 8.11 8.11 44.36 5.25
7179 8586 3.490759 CTAACGGCAGGTGCAGCG 61.491 66.667 10.78 6.81 44.36 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.265904 TGACCGTCCACCTCGTCTG 61.266 63.158 0.00 0.00 0.00 3.51
55 56 2.262423 ACAGAGCCAGGTTTCTGAAC 57.738 50.000 22.77 0.00 42.67 3.18
176 177 0.813184 CATTGCCGTCCTTGCTGATT 59.187 50.000 0.00 0.00 0.00 2.57
190 191 4.916983 TTGTATGTATGGGCTTCATTGC 57.083 40.909 0.00 0.00 37.30 3.56
211 212 2.704572 CGGTTCTCATTTGCTCCTCTT 58.295 47.619 0.00 0.00 0.00 2.85
225 226 4.016706 CCTTCCGGTGGCGGTTCT 62.017 66.667 0.00 0.00 0.00 3.01
268 269 3.199071 TCGCCAGTATTGGTTAGGAACAT 59.801 43.478 6.10 0.00 46.80 2.71
269 270 2.568062 TCGCCAGTATTGGTTAGGAACA 59.432 45.455 6.10 0.00 46.80 3.18
311 312 4.481195 CACCCTGGTGTGTTCTGG 57.519 61.111 8.20 0.00 40.91 3.86
360 361 0.609957 CTTCTGGGTCCTTGCATGCA 60.610 55.000 18.46 18.46 0.00 3.96
476 477 9.787532 GATTACTTGCTTTGTTATTCAGCATTA 57.212 29.630 0.00 0.00 35.33 1.90
491 492 2.234908 AGAGCCGACAGATTACTTGCTT 59.765 45.455 0.00 0.00 0.00 3.91
529 530 8.031277 GAAAATATTCATGAAGTGCCTCACTTT 58.969 33.333 14.54 3.47 43.19 2.66
570 571 2.797792 GCTGGATCTTCTCACGCTACTG 60.798 54.545 0.00 0.00 0.00 2.74
634 635 4.906618 TCGCCAAAAATAAAGAGGTCTCT 58.093 39.130 0.00 0.00 42.75 3.10
761 762 6.208566 TCGAACTCGCTGACTAATGAGTCC 62.209 50.000 7.81 0.00 44.26 3.85
775 776 0.784778 CCACTTTGACTCGAACTCGC 59.215 55.000 0.00 0.00 39.60 5.03
857 1472 1.364901 GTCGTTTCCTCCACACGGA 59.635 57.895 0.00 0.00 39.79 4.69
858 1473 1.666872 GGTCGTTTCCTCCACACGG 60.667 63.158 0.00 0.00 34.61 4.94
860 1475 1.228657 GCTGGTCGTTTCCTCCACAC 61.229 60.000 0.00 0.00 0.00 3.82
1218 1863 6.591935 CATGTAAATAGCAAAGAGGGTAGGA 58.408 40.000 0.00 0.00 0.00 2.94
1222 1867 3.627577 CGCATGTAAATAGCAAAGAGGGT 59.372 43.478 0.00 0.00 0.00 4.34
1223 1868 3.548818 GCGCATGTAAATAGCAAAGAGGG 60.549 47.826 0.30 0.00 0.00 4.30
1224 1869 3.313526 AGCGCATGTAAATAGCAAAGAGG 59.686 43.478 11.47 0.00 0.00 3.69
1225 1870 4.272018 AGAGCGCATGTAAATAGCAAAGAG 59.728 41.667 11.47 0.00 0.00 2.85
1226 1871 4.034394 CAGAGCGCATGTAAATAGCAAAGA 59.966 41.667 11.47 0.00 0.00 2.52
1313 1961 2.432510 CTCCTGGTCCTCTGTATCAACC 59.567 54.545 0.00 0.00 0.00 3.77
1315 1963 2.111384 GCTCCTGGTCCTCTGTATCAA 58.889 52.381 0.00 0.00 0.00 2.57
1322 1970 1.305718 GTCAGGCTCCTGGTCCTCT 60.306 63.158 15.32 0.00 43.75 3.69
1527 2175 2.488153 GGTTTCTTCCATTCCGGTGAAG 59.512 50.000 0.00 10.07 37.44 3.02
1596 2287 7.626452 GCAATCAGACAAGGAAAGTGGTAATAC 60.626 40.741 0.00 0.00 0.00 1.89
1634 2325 6.988622 TTACGGAAATTGGAACGAACATAT 57.011 33.333 0.00 0.00 0.00 1.78
1713 2405 3.844211 AGTTGGGCACTATTAGTCAGGAA 59.156 43.478 0.00 0.00 31.97 3.36
1790 2482 2.116125 GCCACTGGACTTTGCCCT 59.884 61.111 0.00 0.00 0.00 5.19
1791 2483 2.991540 GGCCACTGGACTTTGCCC 60.992 66.667 0.00 0.00 36.07 5.36
1802 2494 3.006967 CCATATCTTAGCTAACGGCCACT 59.993 47.826 2.24 0.00 43.05 4.00
1877 2571 2.426738 CGCCCTCCAATGATTTAGCAAA 59.573 45.455 0.00 0.00 0.00 3.68
2009 2703 0.746659 ATAAAAGCCCATTCCGCTGC 59.253 50.000 0.00 0.00 36.47 5.25
2065 2759 9.605275 CTTAGTCCAAATATCATTGTGAGAGAA 57.395 33.333 0.00 0.00 0.00 2.87
2257 2952 7.603963 TTTCTTTGTTGGAAAGGCTAAAAAC 57.396 32.000 0.00 0.00 0.00 2.43
2262 2957 6.068010 TCTGATTTCTTTGTTGGAAAGGCTA 58.932 36.000 0.00 0.00 36.35 3.93
2343 3111 6.043854 ACTAGACCTCCAAAAGAAGCTTAG 57.956 41.667 0.00 0.00 0.00 2.18
2478 3247 7.037297 AGTCCTAGGAAATTGGAGAGAAATGAA 60.037 37.037 14.65 0.00 33.12 2.57
2524 3293 9.844790 GTTGTTCATCAATATCACAAATCTGAA 57.155 29.630 0.00 0.00 38.38 3.02
2525 3294 9.234827 AGTTGTTCATCAATATCACAAATCTGA 57.765 29.630 0.00 0.00 38.38 3.27
2930 3703 5.192176 TGGTGTAGATTCTTATTGCATGCA 58.808 37.500 18.46 18.46 0.00 3.96
3268 4276 7.936496 TTGCTTGACATAATCATACAAAGGA 57.064 32.000 0.00 0.00 37.11 3.36
3306 4314 3.191162 TGAGAACCACAACATGCATAAGC 59.809 43.478 0.00 0.00 42.57 3.09
3607 4615 4.860802 TTCTAAATGCAGAATGAGGGGA 57.139 40.909 0.00 0.00 39.69 4.81
3629 4637 6.687604 CCTTTTTCGGTAAGATGGTTTCAAT 58.312 36.000 0.00 0.00 0.00 2.57
3637 4645 4.403453 CGAAAGCCTTTTTCGGTAAGATG 58.597 43.478 12.72 0.00 45.17 2.90
3638 4646 4.680171 CGAAAGCCTTTTTCGGTAAGAT 57.320 40.909 12.72 0.00 45.17 2.40
3843 4854 2.455032 CTCCGACTCTTCGCTATGTTG 58.545 52.381 0.00 0.00 44.43 3.33
3845 4856 0.382515 GCTCCGACTCTTCGCTATGT 59.617 55.000 0.00 0.00 44.43 2.29
4083 5096 2.640302 GCACTCTGTCTCGGAGGCA 61.640 63.158 12.37 12.37 40.86 4.75
4296 5312 1.228675 CTTTGCTGCCCCTTCACCT 60.229 57.895 0.00 0.00 0.00 4.00
4513 5534 0.820891 CTTGTGCTCTGGTGTGGCTT 60.821 55.000 0.00 0.00 0.00 4.35
4574 5595 1.154221 GCTCGACCCCCTCCTCTAT 59.846 63.158 0.00 0.00 0.00 1.98
4930 5981 2.764637 AAAGATGGTTTCCGCCGCCT 62.765 55.000 0.00 0.00 0.00 5.52
4931 5982 2.340328 AAAGATGGTTTCCGCCGCC 61.340 57.895 0.00 0.00 0.00 6.13
4932 5983 1.154035 CAAAGATGGTTTCCGCCGC 60.154 57.895 0.00 0.00 0.00 6.53
4933 5984 1.506262 CCAAAGATGGTTTCCGCCG 59.494 57.895 0.00 0.00 42.18 6.46
4942 5993 7.253542 ACCAGAAAAGGTCATACCAAAGATGG 61.254 42.308 0.00 3.95 45.49 3.51
5015 6102 2.422377 GCCTACATATTGTTCCGGGGTT 60.422 50.000 0.00 0.00 0.00 4.11
5023 6110 5.610398 TCATCATCGTGCCTACATATTGTT 58.390 37.500 0.00 0.00 0.00 2.83
5031 6118 2.871182 TCACTCATCATCGTGCCTAC 57.129 50.000 0.00 0.00 0.00 3.18
5062 6149 5.010820 ACTGAAGTTAGCTAACGAAGTCCTT 59.989 40.000 26.66 15.77 45.00 3.36
5074 6161 2.634940 TGCCTGAGAACTGAAGTTAGCT 59.365 45.455 0.00 0.00 38.56 3.32
5180 6269 3.197983 TCCAAGAGCTCCTAAAGTTAGCC 59.802 47.826 10.93 0.00 36.92 3.93
5352 6454 8.905660 TCATGGTCATTTTGAAACATTTTGAT 57.094 26.923 0.00 0.00 27.95 2.57
5402 6504 5.069914 GGAAACACAGACCCAGGTTTAATTT 59.930 40.000 0.00 0.00 33.92 1.82
5421 6523 7.875327 TTCTAACTTTATATGCCCAGGAAAC 57.125 36.000 0.00 0.00 0.00 2.78
5422 6524 8.745590 GTTTTCTAACTTTATATGCCCAGGAAA 58.254 33.333 0.00 0.00 0.00 3.13
5443 6545 7.464358 AGAGTAAATATGTGCATGTCGTTTTC 58.536 34.615 0.00 0.00 0.00 2.29
5549 6876 5.202765 AGATGGCCATGATTAATCACAACA 58.797 37.500 26.56 15.95 40.03 3.33
5581 6908 5.171339 ACTGAGCTCCATCTTGTACAAAT 57.829 39.130 12.15 3.88 0.00 2.32
5713 7040 1.599518 CAGTACCAGCAAACCGGCA 60.600 57.895 0.00 0.00 35.83 5.69
5714 7041 1.170290 AACAGTACCAGCAAACCGGC 61.170 55.000 0.00 0.00 0.00 6.13
5715 7042 0.872388 GAACAGTACCAGCAAACCGG 59.128 55.000 0.00 0.00 0.00 5.28
5788 7115 0.981183 TCGGTGATTAGCCCAACACT 59.019 50.000 0.00 0.00 34.28 3.55
5805 7132 1.207089 TCCCTTGCTGGTACAATCTCG 59.793 52.381 0.00 0.00 38.70 4.04
5847 7174 0.587768 CAATGACACGCTGTGCTTCA 59.412 50.000 8.31 6.55 36.98 3.02
5859 7186 4.279169 CCAGAAAGCTTTTCTCCAATGACA 59.721 41.667 14.05 0.00 0.00 3.58
6103 7431 1.068753 CTCCAGCCTACATGCTCCG 59.931 63.158 0.00 0.00 40.32 4.63
6419 7754 0.179119 CCACCGACATTACTCCCGAC 60.179 60.000 0.00 0.00 0.00 4.79
6464 7799 3.194968 TCGAACCATCTACCTCTTGAACC 59.805 47.826 0.00 0.00 0.00 3.62
6469 7804 4.527038 TCTTTGTCGAACCATCTACCTCTT 59.473 41.667 0.00 0.00 0.00 2.85
6471 7806 4.451629 TCTTTGTCGAACCATCTACCTC 57.548 45.455 0.00 0.00 0.00 3.85
6485 7820 5.106515 GGGCTGAAACTGAGTATTCTTTGTC 60.107 44.000 8.29 2.75 0.00 3.18
6488 7823 4.985538 TGGGCTGAAACTGAGTATTCTTT 58.014 39.130 8.29 0.00 0.00 2.52
6578 7916 1.284982 CTGTTCAGTCACCTTCGGCG 61.285 60.000 0.00 0.00 0.00 6.46
6590 7928 0.034059 AGCACTTCCCGTCTGTTCAG 59.966 55.000 0.00 0.00 0.00 3.02
6637 7975 4.199840 TGATTCGATGAATGCATTCGTG 57.800 40.909 33.32 24.42 39.62 4.35
6726 8111 4.021102 TCTCCTCAGAAAACACCATTCC 57.979 45.455 0.00 0.00 0.00 3.01
6762 8147 2.398554 CCATCGGTCAGCAAACCCG 61.399 63.158 2.25 0.00 43.03 5.28
6784 8175 8.506437 TGATGAGGCACGATTCATTATTAATTC 58.494 33.333 0.00 0.00 34.33 2.17
6799 8190 5.523552 TCTTGTAAACATATGATGAGGCACG 59.476 40.000 10.38 0.00 0.00 5.34
6815 8208 7.925043 TCCGCATTAAACCTAATCTTGTAAA 57.075 32.000 0.00 0.00 0.00 2.01
6816 8209 7.825270 TCTTCCGCATTAAACCTAATCTTGTAA 59.175 33.333 0.00 0.00 0.00 2.41
6881 8276 3.025322 ACATCGAGAAGGAGGAGTCAT 57.975 47.619 0.00 0.00 0.00 3.06
6890 8285 6.137794 ACTAGAACATGTACATCGAGAAGG 57.862 41.667 5.07 0.00 0.00 3.46
6891 8286 7.542477 ACAAACTAGAACATGTACATCGAGAAG 59.458 37.037 5.07 4.15 0.00 2.85
6892 8287 7.328493 CACAAACTAGAACATGTACATCGAGAA 59.672 37.037 5.07 0.00 0.00 2.87
6899 8294 5.606505 TCAGCACAAACTAGAACATGTACA 58.393 37.500 0.00 0.00 0.00 2.90
6936 8343 3.997021 GTGGATGGAGTTGTGTACTTGAG 59.003 47.826 0.00 0.00 37.17 3.02
6937 8344 3.646162 AGTGGATGGAGTTGTGTACTTGA 59.354 43.478 0.00 0.00 37.17 3.02
6938 8345 4.008074 AGTGGATGGAGTTGTGTACTTG 57.992 45.455 0.00 0.00 37.17 3.16
6939 8346 4.706842 AAGTGGATGGAGTTGTGTACTT 57.293 40.909 0.00 0.00 37.17 2.24
6940 8347 4.505039 GGAAAGTGGATGGAGTTGTGTACT 60.505 45.833 0.00 0.00 40.71 2.73
6941 8348 3.751698 GGAAAGTGGATGGAGTTGTGTAC 59.248 47.826 0.00 0.00 0.00 2.90
6942 8349 3.244770 GGGAAAGTGGATGGAGTTGTGTA 60.245 47.826 0.00 0.00 0.00 2.90
6961 8368 0.845102 GGAGGGAGAAACAAGGGGGA 60.845 60.000 0.00 0.00 0.00 4.81
6962 8369 1.691823 GGAGGGAGAAACAAGGGGG 59.308 63.158 0.00 0.00 0.00 5.40
7149 8556 2.202756 GTTAGGCCCTCAGCGACG 60.203 66.667 0.00 0.00 45.17 5.12
7161 8568 3.127533 GCTGCACCTGCCGTTAGG 61.128 66.667 0.00 0.97 43.71 2.69


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

AutoCloner maintained by Alex Coulton.