Multiple sequence alignment - TraesCS7A01G214200

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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 TraesCS7A01G214200 chr7A 100.000 7912 0 0 1 7912 178288469 178296380 0.000000e+00 14611.0
1 TraesCS7A01G214200 chr7D 95.609 3803 132 10 3357 7126 176170937 176167137 0.000000e+00 6065.0
2 TraesCS7A01G214200 chr7D 94.881 1094 50 5 1531 2622 176172886 176171797 0.000000e+00 1705.0
3 TraesCS7A01G214200 chr7D 92.705 987 49 12 569 1540 176173941 176172963 0.000000e+00 1402.0
4 TraesCS7A01G214200 chr7D 96.561 756 16 4 7164 7912 176167135 176166383 0.000000e+00 1243.0
5 TraesCS7A01G214200 chr7D 96.986 730 21 1 2617 3345 176171719 176170990 0.000000e+00 1225.0
6 TraesCS7A01G214200 chr7D 87.207 469 37 7 4 464 176174398 176173945 5.480000e-141 512.0
7 TraesCS7A01G214200 chr7B 95.613 3693 127 18 3357 7022 141853075 141856759 0.000000e+00 5890.0
8 TraesCS7A01G214200 chr7B 90.491 2282 134 41 362 2622 141849996 141852215 0.000000e+00 2935.0
9 TraesCS7A01G214200 chr7B 95.879 728 27 3 2617 3342 141852293 141853019 0.000000e+00 1175.0
10 TraesCS7A01G214200 chr7B 97.472 633 15 1 7280 7912 141864318 141864949 0.000000e+00 1079.0
11 TraesCS7A01G214200 chr7B 92.388 289 13 4 7005 7284 141863770 141864058 3.440000e-108 403.0
12 TraesCS7A01G214200 chr7B 79.963 539 57 29 185 710 141849849 141850349 4.540000e-92 350.0
13 TraesCS7A01G214200 chr1A 79.837 491 69 16 5022 5489 549048813 549048330 1.650000e-86 331.0
14 TraesCS7A01G214200 chr1A 95.918 49 1 1 2565 2613 94566719 94566766 2.370000e-10 78.7
15 TraesCS7A01G214200 chr2B 76.984 504 84 24 7418 7910 491711749 491712231 7.880000e-65 259.0
16 TraesCS7A01G214200 chr1D 84.234 222 25 7 4971 5186 455114995 455114778 2.890000e-49 207.0
17 TraesCS7A01G214200 chr1D 95.833 48 2 0 2566 2613 212459130 212459083 2.370000e-10 78.7
18 TraesCS7A01G214200 chrUn 95.833 48 2 0 2566 2613 170994741 170994788 2.370000e-10 78.7
19 TraesCS7A01G214200 chrUn 95.833 48 2 0 2566 2613 448324880 448324833 2.370000e-10 78.7
20 TraesCS7A01G214200 chr4D 95.833 48 2 0 2566 2613 123545627 123545674 2.370000e-10 78.7
21 TraesCS7A01G214200 chr4B 95.833 48 2 0 2566 2613 623333798 623333845 2.370000e-10 78.7
22 TraesCS7A01G214200 chr3D 95.833 48 2 0 2566 2613 602873323 602873276 2.370000e-10 78.7


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 TraesCS7A01G214200 chr7A 178288469 178296380 7911 False 14611.000000 14611 100.0000 1 7912 1 chr7A.!!$F1 7911
1 TraesCS7A01G214200 chr7D 176166383 176174398 8015 True 2025.333333 6065 93.9915 4 7912 6 chr7D.!!$R1 7908
2 TraesCS7A01G214200 chr7B 141849849 141856759 6910 False 2587.500000 5890 90.4865 185 7022 4 chr7B.!!$F1 6837
3 TraesCS7A01G214200 chr7B 141863770 141864949 1179 False 741.000000 1079 94.9300 7005 7912 2 chr7B.!!$F2 907

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
866 885 0.321653 GAAACTCACTCGGCCACCAT 60.322 55.000 2.24 0.00 0.00 3.55 F
1314 1338 0.313987 AGTAAAAGGCGCCAACTTGC 59.686 50.000 31.54 20.52 0.00 4.01 F
1945 2064 0.741221 GCATGTCTCTCCGGTGGAAC 60.741 60.000 0.00 1.71 0.00 3.62 F
2974 3187 0.391793 GGCACTGCTGAAGAGGTACC 60.392 60.000 2.73 2.73 0.00 3.34 F
3930 4188 1.081892 CCAAGCAACGAGGTGATCTG 58.918 55.000 0.00 0.00 0.00 2.90 F
4062 4320 1.299541 CATTCACATCCAGTACCGCC 58.700 55.000 0.00 0.00 0.00 6.13 F
5652 5938 1.371558 GACGGAGGGTCTGCAAGTT 59.628 57.895 0.00 0.00 42.62 2.66 F
6437 6724 1.412079 TTTGGTGAATTGGCAGTGCT 58.588 45.000 16.11 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1880 0.897401 TGCGTTTGATCCCCAATGCA 60.897 50.000 10.65 10.65 41.28 3.96 R
2185 2305 1.004628 TCAGCACACATTGTAGGCCAT 59.995 47.619 5.01 0.00 0.00 4.40 R
3905 4163 1.066143 CACCTCGTTGCTTGGTCCTAT 60.066 52.381 0.00 0.00 30.72 2.57 R
4647 4905 0.035317 ACAGCGCTCCAAGTCATTCA 59.965 50.000 7.13 0.00 0.00 2.57 R
5843 6129 0.243636 GGGGTTCGAGTTGCCATTTG 59.756 55.000 0.00 0.00 0.00 2.32 R
5897 6183 5.365021 AGCTAGTGATGCTCATTACCTTT 57.635 39.130 1.78 0.00 35.67 3.11 R
6824 7112 1.133216 TCGAAGCTCTGATCTTCCACG 59.867 52.381 13.83 5.40 37.29 4.94 R
7817 8385 0.669318 TCAAGGCGTCCAACATCGTC 60.669 55.000 0.00 0.00 0.00 4.20 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
19 20 2.819595 GCTCCCGCGCATTCTTCA 60.820 61.111 8.75 0.00 0.00 3.02
79 80 1.238439 CTCAACCGAGCACAACCAAT 58.762 50.000 0.00 0.00 31.00 3.16
102 104 3.719144 GTACCACAACACGGCGCC 61.719 66.667 19.07 19.07 0.00 6.53
123 125 3.906649 CTGCGTGCTCGTCGATGC 61.907 66.667 10.18 2.52 39.49 3.91
157 166 2.477375 TGTTAGGTGTTCGACGAAATGC 59.523 45.455 12.67 5.39 0.00 3.56
158 167 2.735134 GTTAGGTGTTCGACGAAATGCT 59.265 45.455 12.67 0.00 0.00 3.79
166 175 3.953874 TCGACGAAATGCTGAAAACAA 57.046 38.095 0.00 0.00 0.00 2.83
175 184 6.364165 CGAAATGCTGAAAACAAACATCTCAT 59.636 34.615 0.00 0.00 0.00 2.90
192 201 2.291365 TCATCAAATGAGGCATCACCG 58.709 47.619 1.71 0.00 46.52 4.94
212 221 2.045340 GGGTGCACTGCCCGTATT 60.045 61.111 17.98 0.00 36.30 1.89
214 223 2.112815 GGTGCACTGCCCGTATTCC 61.113 63.158 17.98 0.00 0.00 3.01
296 305 1.165270 CCGTTTGGAGTTGGCCTAAG 58.835 55.000 3.32 0.00 37.49 2.18
336 345 0.460459 TTGACACTCGGTGCGTCAAA 60.460 50.000 10.24 0.00 42.54 2.69
339 348 1.282248 ACACTCGGTGCGTCAAATCG 61.282 55.000 4.23 0.00 36.98 3.34
347 356 1.128507 GTGCGTCAAATCGAGCAATCA 59.871 47.619 0.00 0.00 41.56 2.57
351 360 3.239026 GCGTCAAATCGAGCAATCAAATG 59.761 43.478 0.00 0.00 0.00 2.32
355 364 4.458642 TCAAATCGAGCAATCAAATGTGGA 59.541 37.500 0.00 0.00 0.00 4.02
418 427 4.090642 GTGAGTGAGTGAGCGATTTGTAAG 59.909 45.833 0.00 0.00 0.00 2.34
431 440 6.204882 AGCGATTTGTAAGAAAACTAGCAACT 59.795 34.615 0.00 0.00 0.00 3.16
496 507 2.166664 AGCCGGCTTTAAAACACACAAA 59.833 40.909 27.08 0.00 0.00 2.83
497 508 2.930682 GCCGGCTTTAAAACACACAAAA 59.069 40.909 22.15 0.00 0.00 2.44
498 509 3.371285 GCCGGCTTTAAAACACACAAAAA 59.629 39.130 22.15 0.00 0.00 1.94
536 547 8.940952 AGTGAACATTTATTGAAGCTCTAGAAC 58.059 33.333 0.00 0.00 0.00 3.01
548 559 9.520204 TTGAAGCTCTAGAACATTTTTGAAAAG 57.480 29.630 0.00 0.00 0.00 2.27
552 563 8.131731 AGCTCTAGAACATTTTTGAAAAGACAC 58.868 33.333 0.00 0.00 0.00 3.67
554 565 9.443283 CTCTAGAACATTTTTGAAAAGACACAG 57.557 33.333 0.00 0.00 0.00 3.66
559 570 8.776376 AACATTTTTGAAAAGACACAGATGTT 57.224 26.923 8.14 8.14 39.95 2.71
707 725 2.955609 TTTTTGAGGGATCACCGCC 58.044 52.632 0.00 0.00 46.96 6.13
739 758 1.450312 GAACAGGGATCACCGGCTG 60.450 63.158 0.00 1.42 46.96 4.85
820 839 2.374342 CACTCCCCCTCCCAGGAT 59.626 66.667 0.00 0.00 37.67 3.24
866 885 0.321653 GAAACTCACTCGGCCACCAT 60.322 55.000 2.24 0.00 0.00 3.55
879 898 3.771160 ACCATCACCTCCGGTCGC 61.771 66.667 0.00 0.00 31.02 5.19
986 1005 4.321675 GCCGAGAAGAAGAAGAAGAAGACT 60.322 45.833 0.00 0.00 0.00 3.24
1163 1187 2.352960 CGCTGAAGCTATTGTTCTTCCC 59.647 50.000 0.10 0.00 38.26 3.97
1195 1219 2.203788 TGGAGCGGAGGAGGTTGT 60.204 61.111 0.00 0.00 0.00 3.32
1289 1313 2.929903 GCAAATGCCGGTTGCTGGA 61.930 57.895 18.29 0.00 46.31 3.86
1314 1338 0.313987 AGTAAAAGGCGCCAACTTGC 59.686 50.000 31.54 20.52 0.00 4.01
1337 1361 4.997395 CGTGTTATGATTCCAGGGGATTAG 59.003 45.833 0.00 0.00 0.00 1.73
1356 1380 1.152546 GGGGGAGGCTGTTTGTGTT 60.153 57.895 0.00 0.00 0.00 3.32
1360 1384 2.554344 GGGGAGGCTGTTTGTGTTGATA 60.554 50.000 0.00 0.00 0.00 2.15
1391 1415 4.946784 AGCGATGTTCTAATGTGTTTCC 57.053 40.909 0.00 0.00 0.00 3.13
1402 1432 9.827411 GTTCTAATGTGTTTCCTTACAAGATTC 57.173 33.333 0.00 0.00 0.00 2.52
1405 1435 7.454260 AATGTGTTTCCTTACAAGATTCTCC 57.546 36.000 0.00 0.00 0.00 3.71
1406 1436 6.187727 TGTGTTTCCTTACAAGATTCTCCT 57.812 37.500 0.00 0.00 0.00 3.69
1407 1437 6.601332 TGTGTTTCCTTACAAGATTCTCCTT 58.399 36.000 0.00 0.00 0.00 3.36
1469 1499 6.924060 CCTTCTCCCGTATTAAGATAGTTGTG 59.076 42.308 0.00 0.00 0.00 3.33
1470 1500 7.414222 TTCTCCCGTATTAAGATAGTTGTGT 57.586 36.000 0.00 0.00 0.00 3.72
1473 1503 8.627403 TCTCCCGTATTAAGATAGTTGTGTAAG 58.373 37.037 0.00 0.00 0.00 2.34
1481 1511 8.922058 TTAAGATAGTTGTGTAAGATTCCGAC 57.078 34.615 0.00 0.00 0.00 4.79
1561 1678 1.479730 TGTTGCAGTTTTGGCATGACA 59.520 42.857 0.00 0.00 41.58 3.58
1573 1690 4.443913 TGGCATGACACATGAAATTGAG 57.556 40.909 14.65 0.00 0.00 3.02
1574 1691 4.080687 TGGCATGACACATGAAATTGAGA 58.919 39.130 14.65 0.00 0.00 3.27
1579 1696 7.412563 GGCATGACACATGAAATTGAGAAATTG 60.413 37.037 14.65 0.00 0.00 2.32
1581 1698 7.933728 TGACACATGAAATTGAGAAATTGTG 57.066 32.000 0.00 0.00 0.00 3.33
1596 1713 7.867403 TGAGAAATTGTGGCAATTCTAAGTTTC 59.133 33.333 7.44 1.96 32.54 2.78
1597 1714 7.955918 AGAAATTGTGGCAATTCTAAGTTTCT 58.044 30.769 7.44 3.88 30.69 2.52
1601 1718 6.801539 TGTGGCAATTCTAAGTTTCTAGTG 57.198 37.500 0.00 0.00 0.00 2.74
1671 1790 7.909485 TTCTTATCGTAGGAGGGAAATAAGT 57.091 36.000 0.00 0.00 31.67 2.24
1683 1802 6.296836 GGAGGGAAATAAGTCTTAGGGTCAAA 60.297 42.308 0.00 0.00 0.00 2.69
1732 1851 5.859205 ATTCCTTGATGGGATTTGCTTAC 57.141 39.130 0.00 0.00 35.07 2.34
1761 1880 4.043310 TCACTTCAGGTGGAATTGGAATCT 59.957 41.667 0.00 0.00 45.38 2.40
1785 1904 3.760580 TTGGGGATCAAACGCAAAAAT 57.239 38.095 0.00 0.00 37.75 1.82
1850 1969 2.046892 CAGCGTGGGGAGTTCTGG 60.047 66.667 0.00 0.00 0.00 3.86
1945 2064 0.741221 GCATGTCTCTCCGGTGGAAC 60.741 60.000 0.00 1.71 0.00 3.62
2080 2200 2.386661 ACATTTCACGAGCGGAGAAT 57.613 45.000 0.00 0.00 0.00 2.40
2122 2242 0.802494 CCTCCACGTGCACATAAACC 59.198 55.000 18.64 0.00 0.00 3.27
2169 2289 7.390440 TGTTACCACTTTATCCTGTGAAATGAG 59.610 37.037 0.00 0.00 36.38 2.90
2177 2297 8.684386 TTTATCCTGTGAAATGAGTTTGTGTA 57.316 30.769 0.00 0.00 0.00 2.90
2185 2305 7.713073 TGTGAAATGAGTTTGTGTATGTGACTA 59.287 33.333 0.00 0.00 0.00 2.59
2276 2402 1.032014 GCAGCCTGGTCACAAGAAAA 58.968 50.000 0.00 0.00 0.00 2.29
2312 2438 2.290367 CTGTGAAAACGGCATCAGTTCA 59.710 45.455 0.00 0.00 0.00 3.18
2601 2731 2.637382 TGCTAATGTTGGTGACTGGAGA 59.363 45.455 0.00 0.00 0.00 3.71
2614 2744 5.129485 GGTGACTGGAGATATCTTTCTTCCA 59.871 44.000 6.70 8.44 0.00 3.53
2626 2839 8.794335 ATATCTTTCTTCCAAAGTACTGAACC 57.206 34.615 0.00 0.00 0.00 3.62
2719 2932 2.783135 CAGCACTTACTGTGGAATGGT 58.217 47.619 0.00 0.00 46.27 3.55
2830 3043 8.811017 ACATGAAACAATAATTCCCACATGTTA 58.189 29.630 0.00 0.00 41.48 2.41
2883 3096 3.394674 TGCAGTTCCATCGTACTTTCA 57.605 42.857 0.00 0.00 0.00 2.69
2974 3187 0.391793 GGCACTGCTGAAGAGGTACC 60.392 60.000 2.73 2.73 0.00 3.34
2991 3204 3.251972 GGTACCGTATCGTCTCCCTTAAG 59.748 52.174 0.00 0.00 0.00 1.85
3011 3224 7.095899 CCTTAAGATTTTGCTTGCTGAAGAAAC 60.096 37.037 3.36 0.00 0.00 2.78
3077 3291 9.249457 CCTTGAAGTTTTTCAGATTTAAGAACC 57.751 33.333 0.00 0.00 43.76 3.62
3181 3396 7.312657 TCTTCTGAAGCAGCATATTGTAAAG 57.687 36.000 12.54 0.00 0.00 1.85
3262 3477 4.238514 CACTCAACTTGACAGCTAGGTAC 58.761 47.826 0.00 0.00 0.00 3.34
3304 3519 2.553602 TGTGTGCTTGAGTTTAGGCATG 59.446 45.455 0.00 0.00 37.05 4.06
3314 3529 4.167892 TGAGTTTAGGCATGTCCCCATATT 59.832 41.667 0.00 0.00 34.51 1.28
3342 3557 8.687292 AACATCTTGCATCAGTAATCATACAT 57.313 30.769 0.00 0.00 34.29 2.29
3345 3560 8.780249 CATCTTGCATCAGTAATCATACATGAA 58.220 33.333 0.00 0.00 40.69 2.57
3346 3561 8.913487 TCTTGCATCAGTAATCATACATGAAT 57.087 30.769 0.00 0.00 40.69 2.57
3595 3851 9.877178 TTTCAGTTCTGAAGTTAATCCTCTATC 57.123 33.333 13.69 0.00 0.00 2.08
3599 3855 8.474025 AGTTCTGAAGTTAATCCTCTATCAGTG 58.526 37.037 0.00 0.00 35.50 3.66
3807 4065 3.861840 TCAAGATGGAACTAGGCTTTCG 58.138 45.455 0.00 0.00 0.00 3.46
3905 4163 8.038944 AGAAGTTAATACGGAACATAGCTTCAA 58.961 33.333 13.61 0.00 33.29 2.69
3912 4170 4.058817 CGGAACATAGCTTCAATAGGACC 58.941 47.826 0.00 0.00 0.00 4.46
3930 4188 1.081892 CCAAGCAACGAGGTGATCTG 58.918 55.000 0.00 0.00 0.00 2.90
3933 4191 1.450312 GCAACGAGGTGATCTGGGG 60.450 63.158 0.00 0.00 0.00 4.96
4036 4294 4.334759 CGAAAGATGAATCATCCAGCAGTT 59.665 41.667 18.69 3.74 41.36 3.16
4042 4300 5.571784 TGAATCATCCAGCAGTTCAAATC 57.428 39.130 0.00 0.00 0.00 2.17
4058 4316 6.375455 AGTTCAAATCCATTCACATCCAGTAC 59.625 38.462 0.00 0.00 0.00 2.73
4059 4317 5.192927 TCAAATCCATTCACATCCAGTACC 58.807 41.667 0.00 0.00 0.00 3.34
4062 4320 1.299541 CATTCACATCCAGTACCGCC 58.700 55.000 0.00 0.00 0.00 6.13
4086 4344 5.566032 CGAAATACCAAAAAGGAAAGGGGAC 60.566 44.000 0.00 0.00 41.22 4.46
4200 4458 3.958798 GCACCCTACTAGATTCTACACCA 59.041 47.826 0.00 0.00 0.00 4.17
4414 4672 4.755411 CAGGAAGCCTTTGAGATACGTTA 58.245 43.478 0.00 0.00 0.00 3.18
4501 4759 9.284968 ACAAGTTTTTCTATGTGCTGTTATAGT 57.715 29.630 0.00 0.00 0.00 2.12
4647 4905 7.831193 ACCTATAATGCAAATTCAGTCTGAACT 59.169 33.333 17.49 3.79 39.45 3.01
4662 4920 2.414481 CTGAACTGAATGACTTGGAGCG 59.586 50.000 0.00 0.00 0.00 5.03
4670 4928 3.819564 ATGACTTGGAGCGCTGTATTA 57.180 42.857 18.48 0.00 0.00 0.98
4682 4940 6.062434 AGCGCTGTATTACTAGTAAGTCTG 57.938 41.667 19.58 17.17 37.15 3.51
4703 4961 8.299570 AGTCTGAAACTTGGCAAAATATTAGTG 58.700 33.333 0.00 0.00 33.03 2.74
4722 4980 5.779806 AGTGATTCTACGATTTTCCAACG 57.220 39.130 0.00 0.00 0.00 4.10
4723 4981 4.092968 AGTGATTCTACGATTTTCCAACGC 59.907 41.667 0.00 0.00 0.00 4.84
4762 5022 2.327325 TAAGGTTCAGGGACAGAGCT 57.673 50.000 0.00 0.00 0.00 4.09
4777 5037 9.381038 AGGGACAGAGCTAGAAATATATGTTTA 57.619 33.333 0.00 0.00 0.00 2.01
4794 5054 5.376756 TGTTTAAGGTGACCAAGGTAGTT 57.623 39.130 3.63 0.00 0.00 2.24
4919 5179 1.909986 GTAGGGTTTTGGAGAGAGGCT 59.090 52.381 0.00 0.00 0.00 4.58
5088 5349 3.953712 GCTAAGGCCCAAAGCTAAAAA 57.046 42.857 13.00 0.00 43.05 1.94
5145 5406 8.115384 TAAATGAGATTTTGAGGATCCTTTCCA 58.885 33.333 17.42 6.63 39.09 3.53
5508 5794 3.580458 ACAGAGACCATCACCTATATGCC 59.420 47.826 0.00 0.00 0.00 4.40
5652 5938 1.371558 GACGGAGGGTCTGCAAGTT 59.628 57.895 0.00 0.00 42.62 2.66
5758 6044 9.283768 TGTTTTCTGTTGTATGTAGATTGTCAT 57.716 29.630 0.00 0.00 0.00 3.06
5843 6129 2.030274 GGCAACCACGGAATTATATGGC 60.030 50.000 0.00 0.00 35.49 4.40
6168 6455 3.407698 TGACGGAATTGTTGTATGTGCT 58.592 40.909 0.00 0.00 0.00 4.40
6233 6520 6.491745 TGCATTTGGTTTACTTTCCATGACTA 59.508 34.615 0.00 0.00 33.50 2.59
6375 6662 7.008901 CAGCATAAATTGTGTAGCATGTTTCAG 59.991 37.037 0.00 0.00 0.00 3.02
6401 6688 5.416862 TGTATTGGCATACAAATGTAGCG 57.583 39.130 7.14 0.00 42.01 4.26
6427 6714 9.574516 GGTATGAAGGATAGTATTTTGGTGAAT 57.425 33.333 0.00 0.00 0.00 2.57
6437 6724 1.412079 TTTGGTGAATTGGCAGTGCT 58.588 45.000 16.11 0.00 0.00 4.40
6687 6975 2.202851 CGCTTGCGCCAGAGAGAT 60.203 61.111 13.50 0.00 0.00 2.75
6728 7016 2.421424 CCAGAAAAGCACCAGTGATAGC 59.579 50.000 0.99 0.00 0.00 2.97
6730 7018 2.040278 AGAAAAGCACCAGTGATAGCCA 59.960 45.455 0.99 0.00 0.00 4.75
6824 7112 2.019984 GACCATGAGCATGAGTTTCCC 58.980 52.381 11.84 0.00 41.20 3.97
6826 7114 1.679944 CCATGAGCATGAGTTTCCCGT 60.680 52.381 11.84 0.00 41.20 5.28
6833 7121 2.941415 GCATGAGTTTCCCGTGGAAGAT 60.941 50.000 0.00 0.13 43.06 2.40
6854 7142 1.197949 CAGAGCTTCGACGAAGAGACA 59.802 52.381 35.39 3.05 41.71 3.41
6866 7154 2.143122 GAAGAGACATTTGTGCGGACA 58.857 47.619 5.33 5.33 0.00 4.02
6890 7178 2.010582 GCTGCCCGTGTGGTTTTTCA 62.011 55.000 0.00 0.00 36.04 2.69
6964 7252 0.042731 TGCCTAGTGTAGGGAGCCTT 59.957 55.000 2.19 0.00 46.32 4.35
7027 7315 7.914346 GCATTTATTTCATCCACTGAGAAAGAG 59.086 37.037 0.00 0.00 35.05 2.85
7122 7414 5.531634 AGTAGCATCAACAACAACAAATGG 58.468 37.500 0.00 0.00 0.00 3.16
7147 7439 7.872483 GGCAAATATAAACTTGTGATTATGGGG 59.128 37.037 0.00 0.00 0.00 4.96
7424 7992 4.554036 GCCTCCACCTCGGCCATC 62.554 72.222 2.24 0.00 40.43 3.51
7661 8229 3.170672 AGCTCCAGCACCACCACA 61.171 61.111 0.48 0.00 45.16 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.464459 GGTGAAGAATGCGCGGGAG 61.464 63.158 8.83 0.00 0.00 4.30
4 5 2.435938 GGTGAAGAATGCGCGGGA 60.436 61.111 8.83 0.00 0.00 5.14
5 6 3.864686 CGGTGAAGAATGCGCGGG 61.865 66.667 8.83 0.00 0.00 6.13
7 8 2.697425 CTCGGTGAAGAATGCGCG 59.303 61.111 0.00 0.00 0.00 6.86
8 9 1.709147 ATGCTCGGTGAAGAATGCGC 61.709 55.000 0.00 0.00 0.00 6.09
10 11 0.302890 CGATGCTCGGTGAAGAATGC 59.697 55.000 0.00 0.00 36.00 3.56
11 12 1.857217 CTCGATGCTCGGTGAAGAATG 59.143 52.381 5.87 0.00 40.88 2.67
12 13 1.751351 TCTCGATGCTCGGTGAAGAAT 59.249 47.619 5.87 0.00 40.88 2.40
19 20 2.122167 GGGTCTCTCGATGCTCGGT 61.122 63.158 5.87 0.00 40.88 4.69
33 34 0.252284 TGGAGAGGAGGAAGTGGGTC 60.252 60.000 0.00 0.00 0.00 4.46
38 39 2.406559 CATGGATGGAGAGGAGGAAGT 58.593 52.381 0.00 0.00 0.00 3.01
72 73 3.755810 TGGTACCCCACATTGGTTG 57.244 52.632 10.07 0.00 37.31 3.77
124 126 4.160635 CTAACAAAGGCGGCCGCG 62.161 66.667 41.05 29.93 43.06 6.46
135 144 3.059461 GCATTTCGTCGAACACCTAACAA 60.059 43.478 7.29 0.00 0.00 2.83
147 156 3.788694 TGTTTGTTTTCAGCATTTCGTCG 59.211 39.130 0.00 0.00 0.00 5.12
157 166 8.806177 TCATTTGATGAGATGTTTGTTTTCAG 57.194 30.769 0.00 0.00 33.59 3.02
175 184 1.811965 CAACGGTGATGCCTCATTTGA 59.188 47.619 0.00 0.00 32.98 2.69
205 214 1.619807 AACGGACAGGGGAATACGGG 61.620 60.000 0.00 0.00 0.00 5.28
206 215 0.251073 AAACGGACAGGGGAATACGG 59.749 55.000 0.00 0.00 0.00 4.02
212 221 1.152204 TCTCCAAACGGACAGGGGA 60.152 57.895 0.00 0.00 0.00 4.81
214 223 0.037232 GAGTCTCCAAACGGACAGGG 60.037 60.000 0.00 0.00 35.18 4.45
248 257 5.412286 CCCAAACCAACATGAAATTTGATCC 59.588 40.000 0.00 0.00 33.08 3.36
326 335 0.447801 ATTGCTCGATTTGACGCACC 59.552 50.000 0.00 0.00 32.77 5.01
336 345 2.352651 CGTCCACATTTGATTGCTCGAT 59.647 45.455 0.00 0.00 0.00 3.59
339 348 2.483877 TGTCGTCCACATTTGATTGCTC 59.516 45.455 0.00 0.00 0.00 4.26
347 356 2.337583 CACTCGATGTCGTCCACATTT 58.662 47.619 2.04 0.00 46.53 2.32
351 360 1.153823 CCCACTCGATGTCGTCCAC 60.154 63.158 2.04 0.00 40.80 4.02
355 364 2.573869 CAGCCCACTCGATGTCGT 59.426 61.111 2.04 0.00 40.80 4.34
396 405 2.820059 ACAAATCGCTCACTCACTCA 57.180 45.000 0.00 0.00 0.00 3.41
418 427 6.207614 AGGGAAGAAATCAGTTGCTAGTTTTC 59.792 38.462 0.00 0.00 0.00 2.29
431 440 7.006509 AGAAATCAGAACAAGGGAAGAAATCA 58.993 34.615 0.00 0.00 0.00 2.57
512 523 8.846943 TGTTCTAGAGCTTCAATAAATGTTCA 57.153 30.769 8.15 0.00 0.00 3.18
528 539 9.443283 CTGTGTCTTTTCAAAAATGTTCTAGAG 57.557 33.333 0.00 0.00 0.00 2.43
530 541 9.956720 ATCTGTGTCTTTTCAAAAATGTTCTAG 57.043 29.630 0.00 0.00 0.00 2.43
534 545 8.776376 AACATCTGTGTCTTTTCAAAAATGTT 57.224 26.923 2.36 2.36 37.67 2.71
567 578 5.732185 CGCATTTTTCAAAAAGTCACAAACC 59.268 36.000 1.08 0.00 0.00 3.27
572 583 6.088719 TGTTCGCATTTTTCAAAAAGTCAC 57.911 33.333 1.08 0.00 0.00 3.67
717 735 0.613260 CCGGTGATCCCTGTTCTCAA 59.387 55.000 0.00 0.00 0.00 3.02
718 736 1.899437 GCCGGTGATCCCTGTTCTCA 61.899 60.000 1.90 0.00 0.00 3.27
719 737 1.153349 GCCGGTGATCCCTGTTCTC 60.153 63.158 1.90 0.00 0.00 2.87
721 739 1.450312 CAGCCGGTGATCCCTGTTC 60.450 63.158 1.90 0.00 0.00 3.18
739 758 2.919494 CGGGCTTTCAGCAACACCC 61.919 63.158 0.00 0.00 44.75 4.61
820 839 3.998672 GAGGCGTCGTGGGACCAA 61.999 66.667 0.00 0.00 40.17 3.67
929 948 2.253403 GAGGGGTTAGTGGAAGCGGG 62.253 65.000 0.00 0.00 36.33 6.13
938 957 1.062044 GGGAGGAGATGAGGGGTTAGT 60.062 57.143 0.00 0.00 0.00 2.24
966 985 7.628580 GCCTCTAGTCTTCTTCTTCTTCTTCTC 60.629 44.444 0.00 0.00 0.00 2.87
967 986 6.152831 GCCTCTAGTCTTCTTCTTCTTCTTCT 59.847 42.308 0.00 0.00 0.00 2.85
968 987 6.152831 AGCCTCTAGTCTTCTTCTTCTTCTTC 59.847 42.308 0.00 0.00 0.00 2.87
986 1005 1.237954 CCGCATCGCTAGAGCCTCTA 61.238 60.000 0.70 0.70 37.91 2.43
1231 1255 2.046700 ATTTCCCTTTCGCGGCGA 60.047 55.556 22.69 22.69 0.00 5.54
1289 1313 0.688487 TGGCGCCTTTTACTACCTGT 59.312 50.000 29.70 0.00 0.00 4.00
1314 1338 3.492102 ATCCCCTGGAATCATAACACG 57.508 47.619 0.00 0.00 34.34 4.49
1356 1380 4.607293 ACATCGCTAGCTCCATTTATCA 57.393 40.909 13.93 0.00 0.00 2.15
1360 1384 3.550437 AGAACATCGCTAGCTCCATTT 57.450 42.857 13.93 0.00 0.00 2.32
1425 1455 9.091220 GGAGAAGGAATACAGGTGTATAAGTAT 57.909 37.037 3.06 0.00 40.10 2.12
1437 1467 7.286215 TCTTAATACGGGAGAAGGAATACAG 57.714 40.000 0.00 0.00 0.00 2.74
1469 1499 6.273825 TCAGCTCATTTAGTCGGAATCTTAC 58.726 40.000 0.00 0.00 0.00 2.34
1470 1500 6.465439 TCAGCTCATTTAGTCGGAATCTTA 57.535 37.500 0.00 0.00 0.00 2.10
1473 1503 5.582665 AGTTTCAGCTCATTTAGTCGGAATC 59.417 40.000 0.00 0.00 0.00 2.52
1478 1508 7.582435 TCTAAAGTTTCAGCTCATTTAGTCG 57.418 36.000 0.00 0.00 35.76 4.18
1481 1511 7.369803 TGCTCTAAAGTTTCAGCTCATTTAG 57.630 36.000 16.53 0.00 35.66 1.85
1529 1560 6.460123 CCAAAACTGCAACACTTTCAGTAGAT 60.460 38.462 0.00 0.00 39.86 1.98
1545 1662 2.063266 CATGTGTCATGCCAAAACTGC 58.937 47.619 0.00 0.00 0.00 4.40
1553 1670 4.707030 TCTCAATTTCATGTGTCATGCC 57.293 40.909 5.03 0.00 0.00 4.40
1561 1678 5.856156 TGCCACAATTTCTCAATTTCATGT 58.144 33.333 0.00 0.00 29.41 3.21
1573 1690 9.346725 CTAGAAACTTAGAATTGCCACAATTTC 57.653 33.333 6.97 0.86 0.00 2.17
1574 1691 8.860088 ACTAGAAACTTAGAATTGCCACAATTT 58.140 29.630 6.97 1.45 0.00 1.82
1579 1696 7.435068 TTCACTAGAAACTTAGAATTGCCAC 57.565 36.000 0.00 0.00 0.00 5.01
1621 1740 6.787085 AGGAACTATTTTCAGAACTCAACG 57.213 37.500 0.00 0.00 36.02 4.10
1650 1769 7.909485 AAGACTTATTTCCCTCCTACGATAA 57.091 36.000 0.00 0.00 0.00 1.75
1651 1770 7.668886 CCTAAGACTTATTTCCCTCCTACGATA 59.331 40.741 0.00 0.00 0.00 2.92
1669 1788 8.832735 TCCATAACTAAATTTGACCCTAAGACT 58.167 33.333 0.00 0.00 0.00 3.24
1671 1790 9.681062 CTTCCATAACTAAATTTGACCCTAAGA 57.319 33.333 0.00 0.00 0.00 2.10
1683 1802 9.255029 ACATAAGTTTGCCTTCCATAACTAAAT 57.745 29.630 0.00 0.00 34.46 1.40
1690 1809 7.582719 AGGAATACATAAGTTTGCCTTCCATA 58.417 34.615 14.46 0.00 34.93 2.74
1761 1880 0.897401 TGCGTTTGATCCCCAATGCA 60.897 50.000 10.65 10.65 41.28 3.96
1785 1904 3.257873 TCCGTTCGGTATTGACTTTACCA 59.742 43.478 11.04 0.00 39.29 3.25
2122 2242 6.259550 ACAGGTTAGAAGCTAAATGCAAAG 57.740 37.500 0.00 0.00 45.94 2.77
2169 2289 4.261801 AGGCCATAGTCACATACACAAAC 58.738 43.478 5.01 0.00 0.00 2.93
2177 2297 4.080356 ACACATTGTAGGCCATAGTCACAT 60.080 41.667 5.01 0.00 0.00 3.21
2185 2305 1.004628 TCAGCACACATTGTAGGCCAT 59.995 47.619 5.01 0.00 0.00 4.40
2601 2731 7.549488 CGGTTCAGTACTTTGGAAGAAAGATAT 59.451 37.037 0.00 0.00 0.00 1.63
2614 2744 2.567615 AGATGCCTCGGTTCAGTACTTT 59.432 45.455 0.00 0.00 0.00 2.66
2626 2839 3.181506 GGTTTAGCTTGAAAGATGCCTCG 60.182 47.826 0.00 0.00 0.00 4.63
2671 2884 5.489792 AAACAGATAGAACTGAAGCCTGA 57.510 39.130 0.00 0.00 40.63 3.86
2719 2932 3.004419 CGTCCAGTTTCAGAGTGTCTACA 59.996 47.826 0.00 0.00 0.00 2.74
2848 3061 5.184671 TGGAACTGCATGCACAATAAATGTA 59.815 36.000 18.46 0.00 41.46 2.29
2974 3187 5.050972 GCAAAATCTTAAGGGAGACGATACG 60.051 44.000 1.85 0.00 0.00 3.06
2991 3204 6.361748 CACTAGTTTCTTCAGCAAGCAAAATC 59.638 38.462 0.00 0.00 0.00 2.17
3181 3396 1.873486 GCAAACCATTTGTGGGTCAGC 60.873 52.381 3.44 0.00 42.56 4.26
3262 3477 4.035558 ACAATTAGTTGCATGGTGCTATCG 59.964 41.667 3.41 0.00 45.31 2.92
3272 3487 4.279169 ACTCAAGCACACAATTAGTTGCAT 59.721 37.500 0.00 0.00 38.96 3.96
3304 3519 6.463995 TGCAAGATGTTAAAATATGGGGAC 57.536 37.500 0.00 0.00 0.00 4.46
3401 3657 8.131100 ACATAAAATTCAGTTCTCAACACTGTG 58.869 33.333 6.19 6.19 42.12 3.66
3595 3851 5.728351 TGGAGAACTTACGAAAAACACTG 57.272 39.130 0.00 0.00 0.00 3.66
3599 3855 4.577693 AGGGTTGGAGAACTTACGAAAAAC 59.422 41.667 0.00 0.00 32.15 2.43
3687 3945 2.659428 AGGTATGGCTCAAAAGATGGC 58.341 47.619 0.00 0.00 0.00 4.40
3772 4030 2.286365 TCTTGATTTGGTGTCCCCAC 57.714 50.000 0.00 0.00 45.19 4.61
3807 4065 2.236395 ACTACATGGTAGTGCCCTTGTC 59.764 50.000 8.16 0.00 40.79 3.18
3905 4163 1.066143 CACCTCGTTGCTTGGTCCTAT 60.066 52.381 0.00 0.00 30.72 2.57
3912 4170 1.081892 CCAGATCACCTCGTTGCTTG 58.918 55.000 0.00 0.00 0.00 4.01
3930 4188 4.931601 GCTGATGTTCTTTTCAAATTCCCC 59.068 41.667 0.00 0.00 0.00 4.81
3933 4191 6.201425 TGCAAGCTGATGTTCTTTTCAAATTC 59.799 34.615 0.00 0.00 0.00 2.17
4036 4294 5.192927 GGTACTGGATGTGAATGGATTTGA 58.807 41.667 0.00 0.00 0.00 2.69
4042 4300 1.299541 GCGGTACTGGATGTGAATGG 58.700 55.000 3.34 0.00 0.00 3.16
4058 4316 1.813786 TCCTTTTTGGTATTTCGGCGG 59.186 47.619 7.21 0.00 37.07 6.13
4059 4317 3.562567 TTCCTTTTTGGTATTTCGGCG 57.437 42.857 0.00 0.00 37.07 6.46
4062 4320 4.525100 TCCCCTTTCCTTTTTGGTATTTCG 59.475 41.667 0.00 0.00 37.07 3.46
4086 4344 3.044986 CAGTTGCAACTCAAATTCCACG 58.955 45.455 28.97 10.25 37.08 4.94
4200 4458 9.906660 TCTGCATTTTTACGTAATTTCTTCAAT 57.093 25.926 9.18 0.00 0.00 2.57
4319 4577 2.231964 ACAACATCAACATGCACCCATC 59.768 45.455 0.00 0.00 32.57 3.51
4414 4672 0.901580 CCACCTCCAGCAAAGGCAAT 60.902 55.000 0.00 0.00 44.61 3.56
4647 4905 0.035317 ACAGCGCTCCAAGTCATTCA 59.965 50.000 7.13 0.00 0.00 2.57
4662 4920 9.857957 AAGTTTCAGACTTACTAGTAATACAGC 57.142 33.333 15.57 4.48 46.61 4.40
4670 4928 5.546621 TGCCAAGTTTCAGACTTACTAGT 57.453 39.130 0.00 0.00 46.75 2.57
4682 4940 9.860898 AGAATCACTAATATTTTGCCAAGTTTC 57.139 29.630 0.00 0.00 0.00 2.78
4699 4957 5.290158 GCGTTGGAAAATCGTAGAATCACTA 59.710 40.000 0.00 0.00 43.58 2.74
4703 4961 4.593597 TGCGTTGGAAAATCGTAGAATC 57.406 40.909 0.00 0.00 43.58 2.52
4717 4975 3.604314 GCACAAATTGAATGTTGCGTTGG 60.604 43.478 0.00 0.00 0.00 3.77
4719 4977 3.456280 AGCACAAATTGAATGTTGCGTT 58.544 36.364 0.00 0.00 33.23 4.84
4721 4979 5.766702 AATAGCACAAATTGAATGTTGCG 57.233 34.783 0.00 0.00 33.23 4.85
4722 4980 7.331687 ACCTTAATAGCACAAATTGAATGTTGC 59.668 33.333 0.00 0.00 0.00 4.17
4723 4981 8.761575 ACCTTAATAGCACAAATTGAATGTTG 57.238 30.769 0.00 0.00 0.00 3.33
4777 5037 7.610305 CACAAATATAACTACCTTGGTCACCTT 59.390 37.037 0.00 0.00 0.00 3.50
4794 5054 5.650266 CCTGTTTGGTAGGTGCACAAATATA 59.350 40.000 20.43 0.03 36.60 0.86
5145 5406 2.807676 CCCAAAGGAGCACCAAGTTAT 58.192 47.619 2.07 0.00 38.94 1.89
5508 5794 0.535780 TGTGCAGCCACTTCTCAAGG 60.536 55.000 0.00 0.00 42.54 3.61
5652 5938 1.402456 GCAGGCGACTCGTTTTCTCTA 60.402 52.381 0.00 0.00 40.21 2.43
5758 6044 5.617252 AGTTGAAAATCCTCTTTGGTCGTA 58.383 37.500 0.00 0.00 37.07 3.43
5843 6129 0.243636 GGGGTTCGAGTTGCCATTTG 59.756 55.000 0.00 0.00 0.00 2.32
5897 6183 5.365021 AGCTAGTGATGCTCATTACCTTT 57.635 39.130 1.78 0.00 35.67 3.11
6168 6455 7.723172 ACCTCCAAAATGGCATTTTTAAATTCA 59.277 29.630 30.19 11.70 40.27 2.57
6264 6551 7.778083 ACATTACTAGGTTGTATCAACGATCA 58.222 34.615 6.55 0.00 0.00 2.92
6346 6633 5.885352 ACATGCTACACAATTTATGCTGGTA 59.115 36.000 0.00 0.00 0.00 3.25
6375 6662 7.301054 GCTACATTTGTATGCCAATACATCTC 58.699 38.462 0.00 0.00 46.23 2.75
6401 6688 8.974060 TTCACCAAAATACTATCCTTCATACC 57.026 34.615 0.00 0.00 0.00 2.73
6427 6714 0.179059 TGACGAAAGAGCACTGCCAA 60.179 50.000 0.00 0.00 0.00 4.52
6437 6724 5.366829 TTTCTCACTACGATGACGAAAGA 57.633 39.130 0.00 0.00 42.66 2.52
6478 6765 5.470098 ACAAACATGTCACATCACCTTAGTC 59.530 40.000 0.00 0.00 0.00 2.59
6687 6975 5.428457 TCTGGGGATTATCAACTTTAGCTGA 59.572 40.000 0.00 0.00 0.00 4.26
6750 7038 1.418342 GCGCGTGTACGATGATTGGT 61.418 55.000 8.43 0.00 43.02 3.67
6824 7112 1.133216 TCGAAGCTCTGATCTTCCACG 59.867 52.381 13.83 5.40 37.29 4.94
6826 7114 1.133216 CGTCGAAGCTCTGATCTTCCA 59.867 52.381 13.83 0.71 37.29 3.53
6833 7121 1.465387 GTCTCTTCGTCGAAGCTCTGA 59.535 52.381 26.65 18.41 39.29 3.27
6866 7154 3.591835 CCACACGGGCAGCGTTTT 61.592 61.111 0.00 0.00 0.00 2.43
6890 7178 4.202461 TGCTACAATTCCTCAACTTGGAGT 60.202 41.667 0.00 0.00 34.05 3.85
6998 7286 6.182627 TCTCAGTGGATGAAATAAATGCAGT 58.817 36.000 0.00 0.00 37.52 4.40
7027 7315 4.421948 CCTTGCTGAGCATTCAAATTCTC 58.578 43.478 8.44 0.00 38.76 2.87
7122 7414 7.872483 CCCCCATAATCACAAGTTTATATTTGC 59.128 37.037 0.00 0.00 0.00 3.68
7195 7489 5.634896 CGCTTTCATTTGACTCATAAGCTT 58.365 37.500 3.48 3.48 33.22 3.74
7661 8229 1.081641 CGACGTGTACAGCTTCGGT 60.082 57.895 11.21 0.00 0.00 4.69
7817 8385 0.669318 TCAAGGCGTCCAACATCGTC 60.669 55.000 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.