Multiple sequence alignment - TraesCS2D01G258700

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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 TraesCS2D01G258700 chr2D 100.000 5166 0 0 2555 7720 314493899 314499064 0.000000e+00 9540.0
1 TraesCS2D01G258700 chr2D 100.000 2074 0 0 1 2074 314491345 314493418 0.000000e+00 3831.0
2 TraesCS2D01G258700 chr2D 87.143 140 15 3 7583 7719 314050875 314050736 1.040000e-33 156.0
3 TraesCS2D01G258700 chr2D 84.956 113 14 1 7542 7651 314796135 314796247 2.280000e-20 111.0
4 TraesCS2D01G258700 chr2A 96.518 4107 104 12 2555 6644 421067857 421063773 0.000000e+00 6756.0
5 TraesCS2D01G258700 chr2A 94.270 1082 40 4 6642 7720 421063712 421062650 0.000000e+00 1635.0
6 TraesCS2D01G258700 chr2A 91.816 1173 60 6 6058 7221 422127682 422128827 0.000000e+00 1602.0
7 TraesCS2D01G258700 chr2A 96.193 683 20 3 5235 5914 422111211 422111890 0.000000e+00 1112.0
8 TraesCS2D01G258700 chr2A 95.043 585 26 1 1087 1668 421077294 421076710 0.000000e+00 917.0
9 TraesCS2D01G258700 chr2A 92.807 431 12 9 1663 2074 421068530 421068100 2.380000e-169 606.0
10 TraesCS2D01G258700 chr2A 97.987 149 3 0 5096 5244 422110649 422110797 7.690000e-65 259.0
11 TraesCS2D01G258700 chr2A 94.340 159 7 2 5906 6063 422113768 422113925 7.740000e-60 243.0
12 TraesCS2D01G258700 chr2A 89.266 177 17 2 7542 7716 422222876 422223052 3.630000e-53 220.0
13 TraesCS2D01G258700 chr2A 89.080 174 17 2 7542 7713 421059402 421059229 1.690000e-51 215.0
14 TraesCS2D01G258700 chr2A 95.902 122 2 1 4983 5101 422104348 422104469 2.200000e-45 195.0
15 TraesCS2D01G258700 chr2B 94.227 2910 87 24 4828 7720 382595509 382598354 0.000000e+00 4368.0
16 TraesCS2D01G258700 chr2B 96.455 2285 74 5 2555 4836 382590902 382593182 0.000000e+00 3764.0
17 TraesCS2D01G258700 chr2B 94.048 1008 36 10 1087 2074 382589822 382590825 0.000000e+00 1507.0
18 TraesCS2D01G258700 chr2B 86.749 483 46 10 6407 6881 733898096 733898568 8.880000e-144 521.0
19 TraesCS2D01G258700 chr2B 91.818 110 8 1 7600 7708 382733962 382734071 1.340000e-32 152.0
20 TraesCS2D01G258700 chrUn 88.561 1967 176 24 4928 6881 2105294 2103364 0.000000e+00 2340.0
21 TraesCS2D01G258700 chrUn 88.717 1099 94 26 1 1083 132202558 132203642 0.000000e+00 1315.0
22 TraesCS2D01G258700 chr4A 86.913 1918 204 25 4925 6831 722099186 722101067 0.000000e+00 2108.0
23 TraesCS2D01G258700 chr4A 86.861 1918 205 25 4925 6831 722081800 722083681 0.000000e+00 2102.0
24 TraesCS2D01G258700 chr7D 89.715 1089 93 9 1 1083 411325341 411326416 0.000000e+00 1373.0
25 TraesCS2D01G258700 chr7D 91.704 904 63 11 1 897 587997891 587998789 0.000000e+00 1243.0
26 TraesCS2D01G258700 chr7D 84.671 972 123 22 1 959 173032739 173033697 0.000000e+00 946.0
27 TraesCS2D01G258700 chr5D 88.597 1105 95 16 1 1081 15224368 15225465 0.000000e+00 1314.0
28 TraesCS2D01G258700 chr5D 87.967 1097 102 19 1 1083 46686765 46687845 0.000000e+00 1267.0
29 TraesCS2D01G258700 chr1D 88.353 1099 100 22 1 1085 226940842 226941926 0.000000e+00 1295.0
30 TraesCS2D01G258700 chr4D 88.151 1114 92 28 1 1086 458941688 458940587 0.000000e+00 1290.0
31 TraesCS2D01G258700 chr4D 87.228 1104 90 31 1 1090 422953802 422954868 0.000000e+00 1210.0
32 TraesCS2D01G258700 chr4D 74.182 275 51 14 6996 7259 177015429 177015164 6.380000e-16 97.1
33 TraesCS2D01G258700 chr3D 88.332 1097 96 18 1 1083 12150261 12151339 0.000000e+00 1288.0
34 TraesCS2D01G258700 chr5A 86.804 1114 113 25 1 1087 602716096 602714990 0.000000e+00 1212.0
35 TraesCS2D01G258700 chr5B 90.948 707 54 7 1 703 539170552 539171252 0.000000e+00 942.0
36 TraesCS2D01G258700 chr7B 85.675 363 36 10 6521 6876 482950195 482950548 1.220000e-97 368.0
37 TraesCS2D01G258700 chr1B 90.052 191 14 3 4925 5115 84365697 84365882 7.740000e-60 243.0
38 TraesCS2D01G258700 chr3A 75.000 340 71 12 6929 7260 708916162 708916495 2.250000e-30 145.0
39 TraesCS2D01G258700 chr7A 77.578 223 37 9 7046 7260 500165023 500165240 1.050000e-23 122.0


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 TraesCS2D01G258700 chr2D 314491345 314499064 7719 False 6685.5 9540 100.000000 1 7720 2 chr2D.!!$F2 7719
1 TraesCS2D01G258700 chr2A 421059229 421068530 9301 True 2303.0 6756 93.168750 1663 7720 4 chr2A.!!$R2 6057
2 TraesCS2D01G258700 chr2A 422127682 422128827 1145 False 1602.0 1602 91.816000 6058 7221 1 chr2A.!!$F2 1163
3 TraesCS2D01G258700 chr2A 421076710 421077294 584 True 917.0 917 95.043000 1087 1668 1 chr2A.!!$R1 581
4 TraesCS2D01G258700 chr2A 422110649 422113925 3276 False 538.0 1112 96.173333 5096 6063 3 chr2A.!!$F4 967
5 TraesCS2D01G258700 chr2B 382589822 382598354 8532 False 3213.0 4368 94.910000 1087 7720 3 chr2B.!!$F3 6633
6 TraesCS2D01G258700 chrUn 2103364 2105294 1930 True 2340.0 2340 88.561000 4928 6881 1 chrUn.!!$R1 1953
7 TraesCS2D01G258700 chrUn 132202558 132203642 1084 False 1315.0 1315 88.717000 1 1083 1 chrUn.!!$F1 1082
8 TraesCS2D01G258700 chr4A 722099186 722101067 1881 False 2108.0 2108 86.913000 4925 6831 1 chr4A.!!$F2 1906
9 TraesCS2D01G258700 chr4A 722081800 722083681 1881 False 2102.0 2102 86.861000 4925 6831 1 chr4A.!!$F1 1906
10 TraesCS2D01G258700 chr7D 411325341 411326416 1075 False 1373.0 1373 89.715000 1 1083 1 chr7D.!!$F2 1082
11 TraesCS2D01G258700 chr7D 587997891 587998789 898 False 1243.0 1243 91.704000 1 897 1 chr7D.!!$F3 896
12 TraesCS2D01G258700 chr7D 173032739 173033697 958 False 946.0 946 84.671000 1 959 1 chr7D.!!$F1 958
13 TraesCS2D01G258700 chr5D 15224368 15225465 1097 False 1314.0 1314 88.597000 1 1081 1 chr5D.!!$F1 1080
14 TraesCS2D01G258700 chr5D 46686765 46687845 1080 False 1267.0 1267 87.967000 1 1083 1 chr5D.!!$F2 1082
15 TraesCS2D01G258700 chr1D 226940842 226941926 1084 False 1295.0 1295 88.353000 1 1085 1 chr1D.!!$F1 1084
16 TraesCS2D01G258700 chr4D 458940587 458941688 1101 True 1290.0 1290 88.151000 1 1086 1 chr4D.!!$R2 1085
17 TraesCS2D01G258700 chr4D 422953802 422954868 1066 False 1210.0 1210 87.228000 1 1090 1 chr4D.!!$F1 1089
18 TraesCS2D01G258700 chr3D 12150261 12151339 1078 False 1288.0 1288 88.332000 1 1083 1 chr3D.!!$F1 1082
19 TraesCS2D01G258700 chr5A 602714990 602716096 1106 True 1212.0 1212 86.804000 1 1087 1 chr5A.!!$R1 1086
20 TraesCS2D01G258700 chr5B 539170552 539171252 700 False 942.0 942 90.948000 1 703 1 chr5B.!!$F1 702

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
725 786 0.464554 GGATCTAGTGGGTGCTTGGC 60.465 60.000 0.00 0.0 0.00 4.52 F
988 1063 0.482887 TCTATCATCAGGGCCTCCGA 59.517 55.000 0.95 0.0 38.33 4.55 F
2029 2127 1.181098 GCTGTTTGCCACCTGACCAT 61.181 55.000 0.00 0.0 35.15 3.55 F
2832 2930 4.579454 TCCTATCTTATCGTTTGGTCCG 57.421 45.455 0.00 0.0 0.00 4.79 F
3628 3728 0.961019 TTGGTTGTTCATCTGCTGCC 59.039 50.000 0.00 0.0 0.00 4.85 F
4470 4570 0.250640 AGTCTTGGCTTGCAGTGGAG 60.251 55.000 0.00 0.0 0.00 3.86 F
5561 8421 0.961019 TGCTGTCATGGTTTCTTGGC 59.039 50.000 0.00 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1820 1.167851 CTGTCGGTTGCATGATTGGT 58.832 50.000 0.00 0.0 0.00 3.67 R
2832 2930 0.712222 GACACGCCAACGCTACTTAC 59.288 55.000 0.00 0.0 45.53 2.34 R
3491 3591 1.740025 GGCTTCCTATGAACACAGCAC 59.260 52.381 0.00 0.0 0.00 4.40 R
4374 4474 1.302832 CCTGAAGCTCGCCCAAACT 60.303 57.895 0.00 0.0 0.00 2.66 R
4836 4937 1.161843 ACCCGCAAAAGGTGATAACG 58.838 50.000 0.00 0.0 35.85 3.18 R
6455 11214 2.659428 AGCACTCAGGAAAAGCTGTTT 58.341 42.857 0.00 0.0 33.67 2.83 R
7343 12175 0.178767 TGCAGCGCAGGATCTACAAT 59.821 50.000 11.47 0.0 33.32 2.71 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
51 52 7.365117 CCCTCAACTTTCTCCTTATACACATCT 60.365 40.741 0.00 0.00 0.00 2.90
91 92 6.724893 TGATGGACATACTCTTTAATCGGA 57.275 37.500 0.00 0.00 0.00 4.55
122 123 0.691078 ACTCCCACATCATACCGCCT 60.691 55.000 0.00 0.00 0.00 5.52
170 171 5.236695 GGTTAATCTAATTGAGGACGCTTCC 59.763 44.000 0.00 0.00 43.22 3.46
197 198 6.986231 ACTTTCACGACAATATCATCATAGCA 59.014 34.615 0.00 0.00 0.00 3.49
300 302 8.432013 TGCACATTCACTAGTTTATCCATCTAT 58.568 33.333 0.00 0.00 0.00 1.98
425 433 2.419159 GCACTAACCCTAACCCTAACCG 60.419 54.545 0.00 0.00 0.00 4.44
440 466 4.141937 CCCTAACCGTAACCCTAACCTAAC 60.142 50.000 0.00 0.00 0.00 2.34
441 467 3.981071 AACCGTAACCCTAACCTAACC 57.019 47.619 0.00 0.00 0.00 2.85
442 468 3.190383 ACCGTAACCCTAACCTAACCT 57.810 47.619 0.00 0.00 0.00 3.50
443 469 4.331159 ACCGTAACCCTAACCTAACCTA 57.669 45.455 0.00 0.00 0.00 3.08
444 470 4.683643 ACCGTAACCCTAACCTAACCTAA 58.316 43.478 0.00 0.00 0.00 2.69
453 496 5.488561 CCCTAACCTAACCTAACTAAACCCA 59.511 44.000 0.00 0.00 0.00 4.51
479 522 6.183810 ACCCTAACACTTAAGCTAGTTTGT 57.816 37.500 12.06 1.93 0.00 2.83
538 592 5.336372 CCATAAATACACCATAAATGCCCCG 60.336 44.000 0.00 0.00 0.00 5.73
725 786 0.464554 GGATCTAGTGGGTGCTTGGC 60.465 60.000 0.00 0.00 0.00 4.52
772 837 1.482593 GAGCTCGGGGAAGAAGATGAA 59.517 52.381 0.00 0.00 0.00 2.57
792 857 2.457323 GGAGTGGGTGGGTGGTGAA 61.457 63.158 0.00 0.00 0.00 3.18
800 865 3.672503 GGGTGGTGAATGGGCCCT 61.673 66.667 25.70 2.15 36.49 5.19
815 883 2.243994 GGGCCCTACAAACCTTATCCTT 59.756 50.000 17.04 0.00 0.00 3.36
855 927 2.364579 TCGGCGGTAGGGTTGGAT 60.365 61.111 7.21 0.00 0.00 3.41
886 961 1.452833 GTAGACGGCGGTAGGTCCT 60.453 63.158 13.24 0.00 33.66 3.85
900 975 0.818040 GGTCCTTTTGCCACGTCAGT 60.818 55.000 0.00 0.00 0.00 3.41
918 993 0.676782 GTGCCCGTTAACAGCCAGAT 60.677 55.000 13.43 0.00 0.00 2.90
930 1005 4.961637 CCAGATGGCCGTCAATGA 57.038 55.556 26.70 0.00 0.00 2.57
944 1019 1.626321 TCAATGAAACCTACCGCCAGA 59.374 47.619 0.00 0.00 0.00 3.86
945 1020 2.238646 TCAATGAAACCTACCGCCAGAT 59.761 45.455 0.00 0.00 0.00 2.90
946 1021 2.332063 ATGAAACCTACCGCCAGATG 57.668 50.000 0.00 0.00 0.00 2.90
959 1034 4.853142 AGATGGGGCGGCGGTAGA 62.853 66.667 9.78 0.00 0.00 2.59
973 1048 4.581868 GGCGGTAGACTGTAGATCTCTAT 58.418 47.826 0.00 0.00 0.00 1.98
975 1050 5.239351 GCGGTAGACTGTAGATCTCTATCA 58.761 45.833 0.00 0.00 34.28 2.15
988 1063 0.482887 TCTATCATCAGGGCCTCCGA 59.517 55.000 0.95 0.00 38.33 4.55
1001 1076 1.202498 GCCTCCGACGGTAGCTAAAAT 60.202 52.381 14.79 0.00 0.00 1.82
1045 1120 6.770286 AATTATACATGGGTCAGATCCTGT 57.230 37.500 0.07 5.74 32.61 4.00
1056 1131 3.864003 GTCAGATCCTGTTAAACTACGCC 59.136 47.826 0.00 0.00 32.61 5.68
1060 1136 5.180492 CAGATCCTGTTAAACTACGCCAAAA 59.820 40.000 0.00 0.00 0.00 2.44
1077 1153 4.026062 GCCAAAAGGTCAAAACACGAAATC 60.026 41.667 0.00 0.00 0.00 2.17
1267 1346 1.333636 CGTCCTCCCTCTGCAGGAAT 61.334 60.000 15.13 0.00 43.65 3.01
1357 1436 2.047830 CCCGGGTAATCCTCTAGCTTT 58.952 52.381 14.18 0.00 0.00 3.51
1359 1438 2.224305 CCGGGTAATCCTCTAGCTTTGG 60.224 54.545 0.00 0.00 0.00 3.28
1395 1474 5.744666 TTTACTGCTGCTTTACGTTTTCT 57.255 34.783 0.00 0.00 0.00 2.52
1423 1502 4.236935 CGTTCTTCCCATGATTGTTTTGG 58.763 43.478 0.00 0.00 0.00 3.28
1433 1512 5.183522 CCATGATTGTTTTGGGGATTTTTGG 59.816 40.000 0.00 0.00 0.00 3.28
1512 1591 3.197790 CAAGGGTGCGCATCGGAG 61.198 66.667 15.91 1.14 0.00 4.63
1545 1624 5.333721 GCTTCAGACTTCAGTTGCTTAGTTC 60.334 44.000 0.00 0.00 0.00 3.01
1550 1629 3.565902 ACTTCAGTTGCTTAGTTCTTGGC 59.434 43.478 0.00 0.00 0.00 4.52
1649 1728 5.516984 TGTTTGGTTTTAGGGTTTACTGGA 58.483 37.500 0.00 0.00 0.00 3.86
1650 1729 6.137559 TGTTTGGTTTTAGGGTTTACTGGAT 58.862 36.000 0.00 0.00 0.00 3.41
1651 1730 6.612049 TGTTTGGTTTTAGGGTTTACTGGATT 59.388 34.615 0.00 0.00 0.00 3.01
1741 1820 1.883732 GTGGAGCAGCTCGAGTGTA 59.116 57.895 16.47 0.00 0.00 2.90
1776 1855 3.046390 CGACAGAGTGAGTTTCAGTCAC 58.954 50.000 14.41 3.86 46.56 3.67
1807 1887 7.615403 AGAATAGAAAACTGAGCTACACATGA 58.385 34.615 0.00 0.00 0.00 3.07
2029 2127 1.181098 GCTGTTTGCCACCTGACCAT 61.181 55.000 0.00 0.00 35.15 3.55
2611 2709 8.435187 AGAAGCATCATACTTTATCCATCAAGA 58.565 33.333 0.00 0.00 0.00 3.02
2669 2767 8.862325 TTTTCTATCAGGCATCAGAAACTAAA 57.138 30.769 0.00 0.00 36.89 1.85
2676 2774 6.321181 TCAGGCATCAGAAACTAAAAACACTT 59.679 34.615 0.00 0.00 0.00 3.16
2679 2777 9.515226 AGGCATCAGAAACTAAAAACACTTATA 57.485 29.630 0.00 0.00 0.00 0.98
2777 2875 7.693969 AATTACTTTTGACATGAGGAGAAGG 57.306 36.000 0.00 0.00 0.00 3.46
2814 2912 6.989169 GCTCACAGTTTCAGAATATGTATCCT 59.011 38.462 1.46 0.00 0.00 3.24
2832 2930 4.579454 TCCTATCTTATCGTTTGGTCCG 57.421 45.455 0.00 0.00 0.00 4.79
3201 3301 6.479972 TTCATCGTTCTTATACACCATCCT 57.520 37.500 0.00 0.00 0.00 3.24
3442 3542 4.697352 GCTCATGCTCTTCTCCTTGTTTTA 59.303 41.667 0.00 0.00 36.03 1.52
3577 3677 3.362986 CGGTATCAACATGCGCTCATAAC 60.363 47.826 9.73 0.00 0.00 1.89
3603 3703 7.363705 CCATTCTACAATTAATGCCACCAAAGA 60.364 37.037 0.00 0.00 32.79 2.52
3628 3728 0.961019 TTGGTTGTTCATCTGCTGCC 59.039 50.000 0.00 0.00 0.00 4.85
3788 3888 6.017605 GCTTCTGAAACTCAATGACTCTGAAA 60.018 38.462 0.00 0.00 0.00 2.69
3917 4017 6.811665 TGACCGACATAGTTTGAGTAAAGATG 59.188 38.462 0.00 0.00 0.00 2.90
3943 4043 2.958355 ACAGTTTGGAATTGTGTCAGGG 59.042 45.455 0.00 0.00 0.00 4.45
3971 4071 3.134442 CCTCCAGCTCTTCTGCTCTTTAT 59.866 47.826 0.00 0.00 41.98 1.40
4032 4132 8.133627 AGATATATTTGTGAAACTTGCAGATGC 58.866 33.333 0.00 0.00 38.04 3.91
4157 4257 7.322222 CAGCAATCTTTTCTTACGAAGTTGAAG 59.678 37.037 0.00 0.00 37.78 3.02
4278 4378 6.690957 TGTTTGTTTGCTGAAATTACTTCGAG 59.309 34.615 0.00 0.00 36.78 4.04
4374 4474 5.897824 TCCCCATTTTTGTTAAGTGGTGTAA 59.102 36.000 0.00 0.00 0.00 2.41
4470 4570 0.250640 AGTCTTGGCTTGCAGTGGAG 60.251 55.000 0.00 0.00 0.00 3.86
4747 4847 2.565841 GAGCTTCTGTGTGAGTTGGTT 58.434 47.619 0.00 0.00 0.00 3.67
4826 4927 5.045872 GCATTTCTGCTTCTGTTTGTCTTT 58.954 37.500 0.00 0.00 45.32 2.52
4836 4937 8.721478 TGCTTCTGTTTGTCTTTATAAGTGATC 58.279 33.333 0.00 0.00 0.00 2.92
4840 7276 9.917129 TCTGTTTGTCTTTATAAGTGATCGTTA 57.083 29.630 0.00 0.00 0.00 3.18
5054 7490 6.151144 GTCCAATGTAAATTGTACTTCAGGCT 59.849 38.462 4.91 0.00 0.00 4.58
5245 8104 5.120830 GGCAATGTAAGCAGAAGATATACCG 59.879 44.000 0.00 0.00 0.00 4.02
5561 8421 0.961019 TGCTGTCATGGTTTCTTGGC 59.039 50.000 0.00 0.00 0.00 4.52
5898 8765 2.095853 GCGTTGCAGTGCACATAAGTAT 59.904 45.455 19.58 0.00 38.71 2.12
5965 10719 4.318903 CGGCAATTTGTAACGACACTTACA 60.319 41.667 0.00 0.00 34.48 2.41
6006 10761 1.210155 GCGTTTGCTGACCCATGAC 59.790 57.895 0.00 0.00 38.39 3.06
6181 10936 5.530915 GTGCATTGTGCCCAGTATCTATTAA 59.469 40.000 0.00 0.00 44.23 1.40
6408 11167 1.619654 TTCACTGGCAGTTCAATGGG 58.380 50.000 19.43 4.87 0.00 4.00
6455 11214 7.950512 TCATGACAAGGAAAATAAGAGCAAAA 58.049 30.769 0.00 0.00 0.00 2.44
6919 11751 2.828933 GTCTTGGACGCTTCTCCAC 58.171 57.895 0.00 0.00 40.24 4.02
6971 11803 1.379916 CCCTCATTGCCTGGTCACA 59.620 57.895 0.00 0.00 0.00 3.58
7143 11975 2.203181 GCTGAGCATCCCCTCTGC 60.203 66.667 0.00 5.51 45.25 4.26
7197 12029 1.138247 GTGTACGTGGCTAGGTCGG 59.862 63.158 0.00 0.00 0.00 4.79
7200 12032 0.244721 GTACGTGGCTAGGTCGGTTT 59.755 55.000 0.00 0.00 0.00 3.27
7235 12067 6.503217 TCTCCCCTCTATCAATGCAAAGATAT 59.497 38.462 10.71 0.00 0.00 1.63
7271 12103 8.263950 CGTATTCGCGAAAAAGTTTATGATCTA 58.736 33.333 27.23 5.27 0.00 1.98
7314 12146 7.225734 GGCTGAATCTTACAGATAAGGAAGTTC 59.774 40.741 0.00 0.00 38.72 3.01
7338 12170 0.671472 CGTCAGGCTGCAGACAATCA 60.671 55.000 24.55 0.00 34.48 2.57
7339 12171 1.747709 GTCAGGCTGCAGACAATCAT 58.252 50.000 24.55 0.00 34.93 2.45
7340 12172 1.400846 GTCAGGCTGCAGACAATCATG 59.599 52.381 24.55 11.20 34.93 3.07
7341 12173 1.279846 TCAGGCTGCAGACAATCATGA 59.720 47.619 24.55 13.70 0.00 3.07
7342 12174 1.400846 CAGGCTGCAGACAATCATGAC 59.599 52.381 24.55 0.00 0.00 3.06
7343 12175 1.003928 AGGCTGCAGACAATCATGACA 59.996 47.619 24.55 0.00 0.00 3.58
7344 12176 2.022195 GGCTGCAGACAATCATGACAT 58.978 47.619 20.43 0.00 0.00 3.06
7345 12177 2.426024 GGCTGCAGACAATCATGACATT 59.574 45.455 20.43 0.00 0.00 2.71
7346 12178 3.435566 GCTGCAGACAATCATGACATTG 58.564 45.455 20.43 2.06 39.35 2.82
7407 12249 7.762615 TGATATTTTGTAGGTACCTTCTTCACG 59.237 37.037 22.11 0.00 0.00 4.35
7410 12252 5.376854 TTGTAGGTACCTTCTTCACGTAC 57.623 43.478 22.11 9.25 35.28 3.67
7603 12445 4.558095 GCACAAATGATTCAGTCAGCAACT 60.558 41.667 0.00 0.00 40.92 3.16
7604 12446 5.335113 GCACAAATGATTCAGTCAGCAACTA 60.335 40.000 0.00 0.00 40.92 2.24
7605 12447 6.671190 CACAAATGATTCAGTCAGCAACTAA 58.329 36.000 0.00 0.00 40.92 2.24
7606 12448 6.800408 CACAAATGATTCAGTCAGCAACTAAG 59.200 38.462 0.00 0.00 40.92 2.18
7607 12449 6.072286 ACAAATGATTCAGTCAGCAACTAAGG 60.072 38.462 0.00 0.00 40.92 2.69
7608 12450 3.942829 TGATTCAGTCAGCAACTAAGGG 58.057 45.455 0.00 0.00 36.07 3.95
7609 12451 3.582647 TGATTCAGTCAGCAACTAAGGGA 59.417 43.478 0.00 0.00 36.07 4.20
7610 12452 3.402628 TTCAGTCAGCAACTAAGGGAC 57.597 47.619 0.00 0.00 36.07 4.46
7611 12453 1.623811 TCAGTCAGCAACTAAGGGACC 59.376 52.381 0.00 0.00 36.07 4.46
7612 12454 1.625818 CAGTCAGCAACTAAGGGACCT 59.374 52.381 0.00 0.00 36.07 3.85
7613 12455 2.039084 CAGTCAGCAACTAAGGGACCTT 59.961 50.000 8.86 8.86 36.07 3.50
7614 12456 2.303311 AGTCAGCAACTAAGGGACCTTC 59.697 50.000 6.92 0.00 36.07 3.46
7615 12457 2.038557 GTCAGCAACTAAGGGACCTTCA 59.961 50.000 6.92 0.00 37.47 3.02
7616 12458 2.708861 TCAGCAACTAAGGGACCTTCAA 59.291 45.455 6.92 0.00 37.47 2.69
7617 12459 3.137544 TCAGCAACTAAGGGACCTTCAAA 59.862 43.478 6.92 0.00 37.47 2.69
7618 12460 3.253432 CAGCAACTAAGGGACCTTCAAAC 59.747 47.826 6.92 0.00 37.47 2.93
7619 12461 3.117663 AGCAACTAAGGGACCTTCAAACA 60.118 43.478 6.92 0.00 37.47 2.83
7686 15956 3.697045 TGGAAATTTAGGTTGGCATACGG 59.303 43.478 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 5.011586 TCCATCAACTCTCAATTGCATTGA 58.988 37.500 0.00 8.04 46.30 2.57
67 68 7.119709 TCCGATTAAAGAGTATGTCCATCAA 57.880 36.000 0.00 0.00 0.00 2.57
91 92 4.044065 TGATGTGGGAGTGGGAGTAAAATT 59.956 41.667 0.00 0.00 0.00 1.82
122 123 5.647658 CCAAGTGATGGTGTGAAGCTTATTA 59.352 40.000 0.00 0.00 44.85 0.98
154 155 1.906574 AGTGGGAAGCGTCCTCAATTA 59.093 47.619 18.54 0.00 44.28 1.40
170 171 6.609237 ATGATGATATTGTCGTGAAAGTGG 57.391 37.500 0.00 0.00 0.00 4.00
197 198 0.458260 GGTTTTTGACACAAGCCCGT 59.542 50.000 0.00 0.00 0.00 5.28
399 405 3.046374 AGGGTTAGGGTTAGTGCTATGG 58.954 50.000 0.00 0.00 0.00 2.74
425 433 8.041323 GGTTTAGTTAGGTTAGGTTAGGGTTAC 58.959 40.741 0.00 0.00 0.00 2.50
440 466 6.825213 GTGTTAGGGTTATGGGTTTAGTTAGG 59.175 42.308 0.00 0.00 0.00 2.69
441 467 7.627311 AGTGTTAGGGTTATGGGTTTAGTTAG 58.373 38.462 0.00 0.00 0.00 2.34
442 468 7.572546 AGTGTTAGGGTTATGGGTTTAGTTA 57.427 36.000 0.00 0.00 0.00 2.24
443 469 6.458630 AGTGTTAGGGTTATGGGTTTAGTT 57.541 37.500 0.00 0.00 0.00 2.24
444 470 6.458630 AAGTGTTAGGGTTATGGGTTTAGT 57.541 37.500 0.00 0.00 0.00 2.24
453 496 8.380867 ACAAACTAGCTTAAGTGTTAGGGTTAT 58.619 33.333 4.02 0.00 0.00 1.89
479 522 8.465999 AGTAATTTGTGTCAATTCTTGTTGTGA 58.534 29.630 0.00 0.00 0.00 3.58
725 786 2.367512 CCCCCTCTTCTCCCCCAG 60.368 72.222 0.00 0.00 0.00 4.45
772 837 2.121506 ACCACCCACCCACTCCAT 60.122 61.111 0.00 0.00 0.00 3.41
792 857 2.177016 GGATAAGGTTTGTAGGGCCCAT 59.823 50.000 27.56 12.06 0.00 4.00
815 883 2.363795 CTGGCGGTAGGGTCCTGA 60.364 66.667 0.00 0.00 0.00 3.86
870 945 1.190178 AAAAGGACCTACCGCCGTCT 61.190 55.000 0.00 0.00 44.74 4.18
872 947 1.004200 CAAAAGGACCTACCGCCGT 60.004 57.895 0.00 0.00 44.74 5.68
918 993 1.612199 GGTAGGTTTCATTGACGGCCA 60.612 52.381 2.24 0.00 0.00 5.36
930 1005 1.607612 CCCATCTGGCGGTAGGTTT 59.392 57.895 0.00 0.00 0.00 3.27
959 1034 5.016173 GCCCTGATGATAGAGATCTACAGT 58.984 45.833 0.00 0.00 35.84 3.55
973 1048 3.147595 CGTCGGAGGCCCTGATGA 61.148 66.667 14.07 0.00 0.00 2.92
975 1050 3.369410 TACCGTCGGAGGCCCTGAT 62.369 63.158 20.51 0.00 33.69 2.90
988 1063 5.497474 AGATTTGACCATTTTAGCTACCGT 58.503 37.500 0.00 0.00 0.00 4.83
1019 1094 7.721399 ACAGGATCTGACCCATGTATAATTTTC 59.279 37.037 1.59 0.00 35.18 2.29
1025 1100 7.347222 AGTTTAACAGGATCTGACCCATGTATA 59.653 37.037 1.59 0.00 35.18 1.47
1030 1105 5.395324 CGTAGTTTAACAGGATCTGACCCAT 60.395 44.000 1.59 0.00 35.18 4.00
1031 1106 4.081862 CGTAGTTTAACAGGATCTGACCCA 60.082 45.833 1.59 0.00 35.18 4.51
1045 1120 5.831702 TTTGACCTTTTGGCGTAGTTTAA 57.168 34.783 0.00 0.00 45.59 1.52
1056 1131 6.695245 CAAGATTTCGTGTTTTGACCTTTTG 58.305 36.000 0.00 0.00 0.00 2.44
1060 1136 3.243401 GGCAAGATTTCGTGTTTTGACCT 60.243 43.478 0.00 0.00 0.00 3.85
1357 1436 5.647658 AGCAGTAAATCAAATCATCGAACCA 59.352 36.000 0.00 0.00 0.00 3.67
1359 1438 5.453587 GCAGCAGTAAATCAAATCATCGAAC 59.546 40.000 0.00 0.00 0.00 3.95
1395 1474 1.198094 TCATGGGAAGAACGGGAGCA 61.198 55.000 0.00 0.00 0.00 4.26
1423 1502 9.426837 GTTTACCTAATAACAACCAAAAATCCC 57.573 33.333 0.00 0.00 0.00 3.85
1433 1512 9.135843 GAATTGCCTTGTTTACCTAATAACAAC 57.864 33.333 0.00 0.00 38.82 3.32
1545 1624 1.413118 AACAGTCAAAAGGGGCCAAG 58.587 50.000 4.39 0.00 0.00 3.61
1550 1629 5.810095 AGAGAGATAAACAGTCAAAAGGGG 58.190 41.667 0.00 0.00 0.00 4.79
1651 1730 9.217278 TGCAAGTTTGGTACGTTAATTCTAATA 57.783 29.630 0.00 0.00 0.00 0.98
1701 1780 4.201990 ACGAGACATCTTACAATACGGACC 60.202 45.833 0.00 0.00 0.00 4.46
1741 1820 1.167851 CTGTCGGTTGCATGATTGGT 58.832 50.000 0.00 0.00 0.00 3.67
1940 2038 7.878495 AGGGGATGAAACAGGTAAATATGTAA 58.122 34.615 0.00 0.00 0.00 2.41
2029 2127 5.394443 GCAGCTAAACCCATCATCAAAATGA 60.394 40.000 0.00 0.00 45.73 2.57
2562 2660 3.260100 AGGGCAGGTTGGTCCAGG 61.260 66.667 0.00 0.00 39.02 4.45
2564 2662 1.852157 ATGAGGGCAGGTTGGTCCA 60.852 57.895 0.00 0.00 39.02 4.02
2565 2663 1.379044 CATGAGGGCAGGTTGGTCC 60.379 63.158 0.00 0.00 0.00 4.46
2586 2684 8.613060 TCTTGATGGATAAAGTATGATGCTTC 57.387 34.615 0.00 0.00 0.00 3.86
2710 2808 6.813152 CAGGAGGTTGCAAAATAAAATGTAGG 59.187 38.462 0.00 0.00 0.00 3.18
2777 2875 1.228245 TGTGAGCTTCACCCTTGCC 60.228 57.895 11.99 0.00 46.40 4.52
2814 2912 6.455360 ACTTACGGACCAAACGATAAGATA 57.545 37.500 0.00 0.00 33.45 1.98
2832 2930 0.712222 GACACGCCAACGCTACTTAC 59.288 55.000 0.00 0.00 45.53 2.34
3491 3591 1.740025 GGCTTCCTATGAACACAGCAC 59.260 52.381 0.00 0.00 0.00 4.40
3577 3677 5.850557 TGGTGGCATTAATTGTAGAATGG 57.149 39.130 0.00 0.00 34.29 3.16
3603 3703 4.022589 CAGCAGATGAACAACCAACAGAAT 60.023 41.667 0.00 0.00 0.00 2.40
3628 3728 2.987149 AGTGTCGTGACTTATGCTTTCG 59.013 45.455 1.23 0.00 0.00 3.46
3643 3743 2.660236 GGTGCTTTTAGTCGTAGTGTCG 59.340 50.000 0.00 0.00 0.00 4.35
3788 3888 5.479375 ACAGGCAAATGAAGTCATCTTTCAT 59.521 36.000 0.00 0.00 35.10 2.57
3917 4017 2.129607 CACAATTCCAAACTGTGCAGC 58.870 47.619 0.00 0.00 34.55 5.25
3971 4071 4.094887 GTCTTCTGTGTCACTTTGCTCAAA 59.905 41.667 4.27 0.00 0.00 2.69
4032 4132 7.872113 AAGAAAGTTGCTAATCTAGGAATGG 57.128 36.000 0.00 0.00 38.40 3.16
4157 4257 5.874810 TGATGAGTACTTGGTTACAGATTGC 59.125 40.000 0.00 0.00 0.00 3.56
4374 4474 1.302832 CCTGAAGCTCGCCCAAACT 60.303 57.895 0.00 0.00 0.00 2.66
4470 4570 9.539825 ACATGAACATTTCAGTCTACTATCATC 57.460 33.333 0.00 0.00 43.98 2.92
4747 4847 8.308931 AGTACCTACAAGACATAACGAAAATCA 58.691 33.333 0.00 0.00 0.00 2.57
4836 4937 1.161843 ACCCGCAAAAGGTGATAACG 58.838 50.000 0.00 0.00 35.85 3.18
4840 7276 2.556622 CAAACTACCCGCAAAAGGTGAT 59.443 45.455 0.00 0.00 38.36 3.06
5262 8121 4.228824 ACCTACAGTCTGGGTAACTTTCA 58.771 43.478 4.53 0.00 0.00 2.69
5271 8130 9.310449 ACTATATAAACATACCTACAGTCTGGG 57.690 37.037 4.53 0.00 0.00 4.45
5561 8421 6.563398 TGCTACATCTTTAATAACACGTCG 57.437 37.500 0.00 0.00 0.00 5.12
5709 8574 7.976734 CACTTATCCGGACCTATTATCTTGATC 59.023 40.741 6.12 0.00 0.00 2.92
5965 10719 7.773690 ACGCAGGAGTCCTAAATAACATATTTT 59.226 33.333 12.53 0.00 29.64 1.82
5970 10724 4.755266 ACGCAGGAGTCCTAAATAACAT 57.245 40.909 12.53 0.00 29.64 2.71
6181 10936 7.439108 AAATATGGAAGCTACTAACTGACCT 57.561 36.000 0.00 0.00 0.00 3.85
6400 11159 3.806949 AACTTAGTGCCTCCCATTGAA 57.193 42.857 0.00 0.00 0.00 2.69
6408 11167 3.770388 AGAGGAACCTAACTTAGTGCCTC 59.230 47.826 8.86 8.86 40.66 4.70
6455 11214 2.659428 AGCACTCAGGAAAAGCTGTTT 58.341 42.857 0.00 0.00 33.67 2.83
7071 11903 2.224992 TGCATTAACTCCTTTGGCTCCA 60.225 45.455 0.00 0.00 0.00 3.86
7197 12029 5.230323 AGAGGGGAGAAAGTACAGAAAAC 57.770 43.478 0.00 0.00 0.00 2.43
7200 12032 5.838955 TGATAGAGGGGAGAAAGTACAGAA 58.161 41.667 0.00 0.00 0.00 3.02
7338 12170 2.103771 AGCGCAGGATCTACAATGTCAT 59.896 45.455 11.47 0.00 0.00 3.06
7339 12171 1.482182 AGCGCAGGATCTACAATGTCA 59.518 47.619 11.47 0.00 0.00 3.58
7340 12172 1.863454 CAGCGCAGGATCTACAATGTC 59.137 52.381 11.47 0.00 0.00 3.06
7341 12173 1.945387 CAGCGCAGGATCTACAATGT 58.055 50.000 11.47 0.00 0.00 2.71
7342 12174 0.585357 GCAGCGCAGGATCTACAATG 59.415 55.000 11.47 0.00 0.00 2.82
7343 12175 0.178767 TGCAGCGCAGGATCTACAAT 59.821 50.000 11.47 0.00 33.32 2.71
7344 12176 0.740868 GTGCAGCGCAGGATCTACAA 60.741 55.000 11.47 0.00 40.08 2.41
7345 12177 1.153568 GTGCAGCGCAGGATCTACA 60.154 57.895 11.47 0.00 40.08 2.74
7346 12178 1.884926 GGTGCAGCGCAGGATCTAC 60.885 63.158 11.47 0.00 40.08 2.59
7347 12179 1.898330 TTGGTGCAGCGCAGGATCTA 61.898 55.000 11.47 0.00 40.08 1.98
7377 12219 9.802039 AAGAAGGTACCTACAAAATATCAACAA 57.198 29.630 16.67 0.00 0.00 2.83
7410 12252 5.243207 CCACTAAACCAGTACCACTTAAGG 58.757 45.833 7.53 0.00 34.98 2.69
7501 12343 4.095946 TGCCCAATGGAAGCTCTTAATTT 58.904 39.130 0.00 0.00 0.00 1.82
7503 12345 3.386932 TGCCCAATGGAAGCTCTTAAT 57.613 42.857 0.00 0.00 0.00 1.40
7603 12445 4.862371 AGTGTTTGTTTGAAGGTCCCTTA 58.138 39.130 0.00 0.00 36.26 2.69
7604 12446 3.708451 AGTGTTTGTTTGAAGGTCCCTT 58.292 40.909 0.00 0.00 39.23 3.95
7605 12447 3.382083 AGTGTTTGTTTGAAGGTCCCT 57.618 42.857 0.00 0.00 0.00 4.20
7606 12448 3.445805 TCAAGTGTTTGTTTGAAGGTCCC 59.554 43.478 0.00 0.00 35.73 4.46
7607 12449 4.712122 TCAAGTGTTTGTTTGAAGGTCC 57.288 40.909 0.00 0.00 35.73 4.46
7608 12450 7.117667 ACAAATTCAAGTGTTTGTTTGAAGGTC 59.882 33.333 5.95 0.00 43.80 3.85
7609 12451 6.934083 ACAAATTCAAGTGTTTGTTTGAAGGT 59.066 30.769 5.95 2.37 43.80 3.50
7610 12452 7.235777 CACAAATTCAAGTGTTTGTTTGAAGG 58.764 34.615 5.95 1.89 43.80 3.46
7611 12453 6.737750 GCACAAATTCAAGTGTTTGTTTGAAG 59.262 34.615 5.95 0.00 43.80 3.02
7612 12454 6.203530 TGCACAAATTCAAGTGTTTGTTTGAA 59.796 30.769 1.12 2.58 43.80 2.69
7613 12455 5.698089 TGCACAAATTCAAGTGTTTGTTTGA 59.302 32.000 1.12 0.00 43.80 2.69
7614 12456 5.924786 TGCACAAATTCAAGTGTTTGTTTG 58.075 33.333 1.12 0.00 43.80 2.93
7615 12457 6.740411 ATGCACAAATTCAAGTGTTTGTTT 57.260 29.167 0.00 0.00 43.80 2.83
7616 12458 6.815641 TGTATGCACAAATTCAAGTGTTTGTT 59.184 30.769 0.00 0.00 43.80 2.83
7617 12459 6.255453 GTGTATGCACAAATTCAAGTGTTTGT 59.745 34.615 9.26 0.00 46.29 2.83
7618 12460 6.639212 GTGTATGCACAAATTCAAGTGTTTG 58.361 36.000 9.26 0.00 44.64 2.93
7619 12461 6.826893 GTGTATGCACAAATTCAAGTGTTT 57.173 33.333 9.26 0.36 44.64 2.83


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

AutoCloner maintained by Alex Coulton.