Multiple sequence alignment - TraesCS7A01G524500

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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 TraesCS7A01G524500 chr7A 100.000 3254 0 0 1 3254 706898959 706902212 0.000000e+00 6010.0
1 TraesCS7A01G524500 chr7A 83.824 544 83 3 1717 2258 634477173 634477713 2.240000e-141 512.0
2 TraesCS7A01G524500 chr7A 83.640 544 84 3 1717 2258 634464243 634464783 1.040000e-139 507.0
3 TraesCS7A01G524500 chr7A 83.704 540 84 2 1717 2254 634605749 634606286 1.040000e-139 507.0
4 TraesCS7A01G524500 chr7A 85.714 140 17 1 986 1125 634605533 634605669 9.410000e-31 145.0
5 TraesCS7A01G524500 chr7A 84.173 139 19 1 986 1124 634464031 634464166 7.330000e-27 132.0
6 TraesCS7A01G524500 chr7A 84.173 139 19 1 986 1124 634476961 634477096 7.330000e-27 132.0
7 TraesCS7A01G524500 chr7A 93.478 46 3 0 3059 3104 622383650 622383605 5.830000e-08 69.4
8 TraesCS7A01G524500 chr7B 89.136 1574 100 22 1 1559 706850142 706851659 0.000000e+00 1893.0
9 TraesCS7A01G524500 chr7B 91.551 864 52 8 1551 2412 706853017 706853861 0.000000e+00 1171.0
10 TraesCS7A01G524500 chr7B 85.949 548 73 3 1717 2261 592534594 592534048 1.680000e-162 582.0
11 TraesCS7A01G524500 chr7B 84.502 542 79 3 1719 2258 592718723 592719261 6.180000e-147 531.0
12 TraesCS7A01G524500 chr7B 86.598 194 16 3 2587 2770 706854028 706854221 4.260000e-49 206.0
13 TraesCS7A01G524500 chr7B 85.612 139 17 1 986 1124 592807963 592808098 3.380000e-30 143.0
14 TraesCS7A01G524500 chr7B 85.612 139 17 1 986 1124 592867754 592867889 3.380000e-30 143.0
15 TraesCS7A01G524500 chr7D 92.098 1139 60 7 1701 2813 614535884 614537018 0.000000e+00 1578.0
16 TraesCS7A01G524500 chr7D 88.016 1235 72 20 1 1217 614534675 614535851 0.000000e+00 1391.0
17 TraesCS7A01G524500 chr7D 90.995 422 25 9 2846 3254 614537114 614537535 1.020000e-154 556.0
18 TraesCS7A01G524500 chr7D 84.375 544 80 3 1717 2258 549274575 549275115 2.220000e-146 529.0
19 TraesCS7A01G524500 chr7D 84.007 544 80 5 1718 2258 549135038 549135577 1.730000e-142 516.0
20 TraesCS7A01G524500 chr7D 82.447 188 24 3 943 1129 548916091 548915912 4.350000e-34 156.0
21 TraesCS7A01G524500 chr7D 84.892 139 18 1 986 1124 549134824 549134959 1.570000e-28 137.0
22 TraesCS7A01G524500 chr7D 86.567 67 8 1 3038 3104 540731354 540731289 4.500000e-09 73.1
23 TraesCS7A01G524500 chr4D 83.333 150 22 3 2865 3011 391035374 391035225 5.660000e-28 135.0
24 TraesCS7A01G524500 chr4D 90.000 70 7 0 3028 3097 5782351 5782282 1.240000e-14 91.6
25 TraesCS7A01G524500 chr5A 83.453 139 17 2 3035 3167 578063815 578063953 1.230000e-24 124.0
26 TraesCS7A01G524500 chr6B 85.333 75 9 2 3025 3097 607006735 607006809 3.480000e-10 76.8
27 TraesCS7A01G524500 chr6D 93.750 48 3 0 3050 3097 404601607 404601654 4.500000e-09 73.1
28 TraesCS7A01G524500 chr2A 77.692 130 22 5 3035 3158 411110280 411110408 4.500000e-09 73.1


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 TraesCS7A01G524500 chr7A 706898959 706902212 3253 False 6010.0 6010 100.000000 1 3254 1 chr7A.!!$F1 3253
1 TraesCS7A01G524500 chr7A 634605533 634606286 753 False 326.0 507 84.709000 986 2254 2 chr7A.!!$F4 1268
2 TraesCS7A01G524500 chr7A 634476961 634477713 752 False 322.0 512 83.998500 986 2258 2 chr7A.!!$F3 1272
3 TraesCS7A01G524500 chr7A 634464031 634464783 752 False 319.5 507 83.906500 986 2258 2 chr7A.!!$F2 1272
4 TraesCS7A01G524500 chr7B 706850142 706854221 4079 False 1090.0 1893 89.095000 1 2770 3 chr7B.!!$F4 2769
5 TraesCS7A01G524500 chr7B 592534048 592534594 546 True 582.0 582 85.949000 1717 2261 1 chr7B.!!$R1 544
6 TraesCS7A01G524500 chr7B 592718723 592719261 538 False 531.0 531 84.502000 1719 2258 1 chr7B.!!$F1 539
7 TraesCS7A01G524500 chr7D 614534675 614537535 2860 False 1175.0 1578 90.369667 1 3254 3 chr7D.!!$F3 3253
8 TraesCS7A01G524500 chr7D 549274575 549275115 540 False 529.0 529 84.375000 1717 2258 1 chr7D.!!$F1 541
9 TraesCS7A01G524500 chr7D 549134824 549135577 753 False 326.5 516 84.449500 986 2258 2 chr7D.!!$F2 1272

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
483 496 0.033504 TCAAAGCTGGTGAGACGTCC 59.966 55.0 13.01 4.42 0.00 4.79 F
1170 1204 0.178891 TTCTGGGTTCTGCTCCCTCT 60.179 55.0 2.65 0.00 44.84 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 3574 0.178950 CCAGGAGATCATCGGGGAGA 60.179 60.0 0.00 0.00 0.0 3.71 R
2423 3829 0.245266 TGATACTTGCGTTCGCCTCA 59.755 50.0 14.44 6.98 0.0 3.86 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 6.978343 ATGCCAACATTTTCTGATGAAATG 57.022 33.333 11.41 11.41 41.24 2.32
28 29 6.522946 TGCCAACATTTTCTGATGAAATGAA 58.477 32.000 17.33 0.00 41.24 2.57
29 30 6.424509 TGCCAACATTTTCTGATGAAATGAAC 59.575 34.615 17.33 7.48 41.24 3.18
49 50 4.601406 ACATTAAACCTATCAGGCCCAA 57.399 40.909 0.00 0.00 39.63 4.12
53 54 0.034089 AACCTATCAGGCCCAAGTGC 60.034 55.000 0.00 0.00 39.63 4.40
68 69 3.443976 CAAGTGCCTTGTTTGTTGGTAC 58.556 45.455 6.74 0.00 36.79 3.34
76 77 4.261994 CCTTGTTTGTTGGTACATCCTTGG 60.262 45.833 0.00 0.00 39.30 3.61
83 84 2.615391 TGGTACATCCTTGGTCACAGA 58.385 47.619 0.00 0.00 37.07 3.41
88 89 3.947868 ACATCCTTGGTCACAGAATCAG 58.052 45.455 0.00 0.00 0.00 2.90
140 141 1.055040 GAGGGATCCTGATGAGTGGG 58.945 60.000 12.58 0.00 31.76 4.61
244 246 2.686915 GCTTTCCCATCATGGTCAGAAG 59.313 50.000 2.07 2.46 35.17 2.85
262 264 1.067295 AGCTTCCACACCATCTTGGA 58.933 50.000 0.00 0.00 40.96 3.53
307 309 6.070309 AGGCCTAAATTATGATTTTGCACCAA 60.070 34.615 1.29 0.00 36.82 3.67
456 469 2.679450 CACACATTTCAACCATGCTGG 58.321 47.619 1.16 1.16 45.02 4.85
457 470 1.619827 ACACATTTCAACCATGCTGGG 59.380 47.619 7.06 0.29 43.37 4.45
483 496 0.033504 TCAAAGCTGGTGAGACGTCC 59.966 55.000 13.01 4.42 0.00 4.79
493 506 1.402613 GTGAGACGTCCTCTTAGCCTC 59.597 57.143 13.01 0.00 42.44 4.70
521 534 0.534873 AAAACGTGCCTGCCAACTTT 59.465 45.000 0.00 0.00 0.00 2.66
530 543 3.244044 TGCCTGCCAACTTTGATTAAACC 60.244 43.478 0.00 0.00 0.00 3.27
532 545 3.323403 CCTGCCAACTTTGATTAAACCCA 59.677 43.478 0.00 0.00 0.00 4.51
591 609 1.079543 CCTTCTCCACGCTCCTGTG 60.080 63.158 0.00 0.00 39.60 3.66
616 634 7.091993 TGTGAATCCCCTCCTATAAATTCAAGT 60.092 37.037 0.00 0.00 35.56 3.16
617 635 7.780271 GTGAATCCCCTCCTATAAATTCAAGTT 59.220 37.037 0.00 0.00 35.56 2.66
727 746 8.623310 TTGAAAACTTTCGTTAATTTCCAGAC 57.377 30.769 0.00 0.00 40.01 3.51
748 767 1.151899 AGTCCCCACACAAGGCCTA 60.152 57.895 5.16 0.00 0.00 3.93
749 768 1.002502 GTCCCCACACAAGGCCTAC 60.003 63.158 5.16 0.00 0.00 3.18
750 769 2.228480 TCCCCACACAAGGCCTACC 61.228 63.158 5.16 0.00 0.00 3.18
751 770 2.355115 CCCACACAAGGCCTACCC 59.645 66.667 5.16 0.00 36.11 3.69
771 790 0.788391 CGTCCGTGAAAGCTGGTTAC 59.212 55.000 0.00 0.00 0.00 2.50
795 814 4.842531 TTCTCCCTGCATGATTAGACAA 57.157 40.909 0.00 0.00 0.00 3.18
796 815 4.842531 TCTCCCTGCATGATTAGACAAA 57.157 40.909 0.00 0.00 0.00 2.83
797 816 4.774124 TCTCCCTGCATGATTAGACAAAG 58.226 43.478 0.00 0.00 0.00 2.77
798 817 3.282021 TCCCTGCATGATTAGACAAAGC 58.718 45.455 0.00 0.00 0.00 3.51
799 818 3.018856 CCCTGCATGATTAGACAAAGCA 58.981 45.455 0.00 0.00 37.99 3.91
800 819 3.444742 CCCTGCATGATTAGACAAAGCAA 59.555 43.478 0.00 0.00 36.98 3.91
801 820 4.098960 CCCTGCATGATTAGACAAAGCAAT 59.901 41.667 0.00 0.00 36.98 3.56
802 821 5.394883 CCCTGCATGATTAGACAAAGCAATT 60.395 40.000 0.00 0.00 36.98 2.32
803 822 6.103997 CCTGCATGATTAGACAAAGCAATTT 58.896 36.000 0.00 0.00 36.98 1.82
804 823 6.255020 CCTGCATGATTAGACAAAGCAATTTC 59.745 38.462 0.00 0.00 36.98 2.17
805 824 5.801444 TGCATGATTAGACAAAGCAATTTCG 59.199 36.000 0.00 0.00 36.98 3.46
815 834 6.017109 AGACAAAGCAATTTCGAAGCTTCTAA 60.017 34.615 23.50 16.49 46.95 2.10
829 848 3.515901 AGCTTCTAAACAGGACTACAGGG 59.484 47.826 0.00 0.00 0.00 4.45
843 862 4.016706 AGGGGCCTTCGTTGACCG 62.017 66.667 0.84 0.00 38.13 4.79
891 910 2.350498 GGAATTCCACCATGTACGTTCG 59.650 50.000 20.04 0.00 35.64 3.95
926 945 6.667848 TCCTCATTCATGGAAGTTCACTAGTA 59.332 38.462 5.01 0.00 0.00 1.82
937 956 9.790344 TGGAAGTTCACTAGTACTATATACTCC 57.210 37.037 2.33 0.37 0.00 3.85
967 986 0.512952 GCAGTCGTTTCTCGTTGCAT 59.487 50.000 0.00 0.00 44.01 3.96
977 996 7.414639 CGTTTCTCGTTGCATATGTGCTGAT 62.415 44.000 15.89 0.00 42.24 2.90
987 1006 4.869215 CATATGTGCTGATCGAGAACTCT 58.131 43.478 0.00 0.00 30.16 3.24
1108 1139 3.612371 GACTTCTGCGTCGCCGACT 62.612 63.158 16.07 1.09 35.63 4.18
1126 1157 2.036862 GACTCCACGTCCAAAGGTAAGT 59.963 50.000 0.00 0.00 36.62 2.24
1139 1173 2.528564 AGGTAAGTAACACTGGCCGTA 58.471 47.619 0.00 0.00 31.02 4.02
1140 1174 2.232208 AGGTAAGTAACACTGGCCGTAC 59.768 50.000 0.00 0.00 31.02 3.67
1141 1175 2.253603 GTAAGTAACACTGGCCGTACG 58.746 52.381 8.69 8.69 0.00 3.67
1142 1176 0.675633 AAGTAACACTGGCCGTACGT 59.324 50.000 15.21 0.00 0.00 3.57
1157 1191 2.572095 TACGTGCGCATCCTTCTGGG 62.572 60.000 15.91 0.00 0.00 4.45
1170 1204 0.178891 TTCTGGGTTCTGCTCCCTCT 60.179 55.000 2.65 0.00 44.84 3.69
1187 1221 3.621715 CCCTCTGTTCTAATTTACACGGC 59.378 47.826 0.00 0.00 0.00 5.68
1203 1237 1.226379 GGCGCCACACATTTCGATG 60.226 57.895 24.80 0.00 0.00 3.84
1218 1252 5.811399 TTTCGATGTTCAACTTTGACTGT 57.189 34.783 0.00 0.00 36.83 3.55
1228 1262 7.483375 TGTTCAACTTTGACTGTTAATTTGACG 59.517 33.333 8.47 0.00 36.83 4.35
1252 1287 9.522804 ACGAATAAAACTCAACTTATTTTTGCA 57.477 25.926 0.00 0.00 29.84 4.08
1278 1313 7.468141 AGAGAAATTACATCAAAAGTTCCCC 57.532 36.000 0.00 0.00 32.76 4.81
1288 1323 3.131933 TCAAAAGTTCCCCATTGTGTGTG 59.868 43.478 0.00 0.00 0.00 3.82
1289 1324 2.452600 AAGTTCCCCATTGTGTGTGT 57.547 45.000 0.00 0.00 0.00 3.72
1290 1325 1.691196 AGTTCCCCATTGTGTGTGTG 58.309 50.000 0.00 0.00 0.00 3.82
1356 1391 7.040686 TGCTTACTCCCTCTGTTTGAAATTAAC 60.041 37.037 0.00 0.00 0.00 2.01
1363 1398 9.581289 TCCCTCTGTTTGAAATTAACTGAATTA 57.419 29.630 0.00 0.00 36.71 1.40
1519 1554 7.011828 TGCAGACTTTAACACAAAGTTAGAC 57.988 36.000 4.06 0.00 43.20 2.59
1548 1583 8.864024 GTTTGCTCAAATTTAGAGAAATTAGGC 58.136 33.333 16.82 3.27 43.10 3.93
1549 1584 7.944729 TGCTCAAATTTAGAGAAATTAGGCT 57.055 32.000 16.82 0.00 43.10 4.58
1590 2992 6.681729 TCAACTAATTTAGAGTGGGAGTGT 57.318 37.500 10.39 0.00 0.00 3.55
1591 2993 6.464222 TCAACTAATTTAGAGTGGGAGTGTG 58.536 40.000 10.39 0.00 0.00 3.82
1592 2994 6.042781 TCAACTAATTTAGAGTGGGAGTGTGT 59.957 38.462 10.39 0.00 0.00 3.72
1596 2998 9.263446 ACTAATTTAGAGTGGGAGTGTGTATTA 57.737 33.333 10.39 0.00 0.00 0.98
1602 3004 6.173339 AGAGTGGGAGTGTGTATTATTGTTG 58.827 40.000 0.00 0.00 0.00 3.33
1631 3033 8.093307 ACTGATGATCAATACTCGCTAAATCAT 58.907 33.333 0.00 0.00 35.64 2.45
1634 3036 8.837788 ATGATCAATACTCGCTAAATCATGAA 57.162 30.769 0.00 0.00 32.66 2.57
1635 3037 8.661352 TGATCAATACTCGCTAAATCATGAAA 57.339 30.769 0.00 0.00 0.00 2.69
1636 3038 9.108284 TGATCAATACTCGCTAAATCATGAAAA 57.892 29.630 0.00 0.00 0.00 2.29
1637 3039 9.591404 GATCAATACTCGCTAAATCATGAAAAG 57.409 33.333 0.00 0.00 0.00 2.27
1638 3040 7.409697 TCAATACTCGCTAAATCATGAAAAGC 58.590 34.615 14.21 14.21 0.00 3.51
1643 3045 4.882671 GCTAAATCATGAAAAGCGAGGA 57.117 40.909 0.00 0.00 0.00 3.71
1644 3046 4.592179 GCTAAATCATGAAAAGCGAGGAC 58.408 43.478 0.00 0.00 0.00 3.85
1645 3047 3.747099 AAATCATGAAAAGCGAGGACG 57.253 42.857 0.00 0.00 42.93 4.79
1740 3142 0.391793 TGCGCGTGAATGGGTTATCA 60.392 50.000 8.43 0.00 0.00 2.15
1788 3190 1.080705 CGACTTCTTCTTCGCCGGT 60.081 57.895 1.90 0.00 0.00 5.28
1833 3238 2.466982 CGAGCGCTACGGGTACTCA 61.467 63.158 11.50 0.00 0.00 3.41
1854 3259 2.981302 CTGACCGTGCAGATCCCA 59.019 61.111 0.00 0.00 38.14 4.37
2026 3431 1.004560 CTCTTCGCCAAGGTGCTCA 60.005 57.895 0.00 0.00 0.00 4.26
2187 3592 1.255882 CTCTCCCCGATGATCTCCTG 58.744 60.000 0.00 0.00 0.00 3.86
2299 3705 4.556942 TTATCGCATTTTCTCAGGCATG 57.443 40.909 0.00 0.00 0.00 4.06
2308 3714 5.441718 TTTTCTCAGGCATGGTAATCTCT 57.558 39.130 0.00 0.00 0.00 3.10
2316 3722 5.468072 CAGGCATGGTAATCTCTATGTGTTC 59.532 44.000 0.00 0.00 0.00 3.18
2323 3729 8.862325 TGGTAATCTCTATGTGTTCATTTGTT 57.138 30.769 0.00 0.00 35.70 2.83
2401 3807 3.739167 CGACCTTTTCGGGTGCAA 58.261 55.556 0.00 0.00 44.60 4.08
2402 3808 1.574428 CGACCTTTTCGGGTGCAAG 59.426 57.895 0.00 0.00 44.60 4.01
2403 3809 0.882927 CGACCTTTTCGGGTGCAAGA 60.883 55.000 0.00 0.00 44.60 3.02
2404 3810 0.875059 GACCTTTTCGGGTGCAAGAG 59.125 55.000 0.00 0.00 40.06 2.85
2405 3811 1.172812 ACCTTTTCGGGTGCAAGAGC 61.173 55.000 0.00 0.00 38.30 4.09
2406 3812 3.808692 ACCTTTTCGGGTGCAAGAGCA 62.809 52.381 0.00 0.00 43.00 4.26
2417 3823 0.947244 GCAAGAGCATCATAACCGGG 59.053 55.000 6.32 0.00 41.58 5.73
2418 3824 1.475034 GCAAGAGCATCATAACCGGGA 60.475 52.381 6.32 0.00 41.58 5.14
2419 3825 2.213499 CAAGAGCATCATAACCGGGAC 58.787 52.381 6.32 0.00 37.82 4.46
2420 3826 1.794714 AGAGCATCATAACCGGGACT 58.205 50.000 6.32 0.00 37.82 3.85
2421 3827 2.958818 AGAGCATCATAACCGGGACTA 58.041 47.619 6.32 0.00 37.82 2.59
2422 3828 3.305720 AGAGCATCATAACCGGGACTAA 58.694 45.455 6.32 0.00 37.82 2.24
2423 3829 3.904339 AGAGCATCATAACCGGGACTAAT 59.096 43.478 6.32 0.00 37.82 1.73
2424 3830 3.997021 GAGCATCATAACCGGGACTAATG 59.003 47.826 6.32 5.19 33.17 1.90
2425 3831 3.646162 AGCATCATAACCGGGACTAATGA 59.354 43.478 6.32 7.63 0.00 2.57
2426 3832 3.997021 GCATCATAACCGGGACTAATGAG 59.003 47.826 6.32 3.38 30.65 2.90
2427 3833 4.569943 CATCATAACCGGGACTAATGAGG 58.430 47.826 6.32 5.28 30.65 3.86
2428 3834 2.367567 TCATAACCGGGACTAATGAGGC 59.632 50.000 6.32 0.00 0.00 4.70
2429 3835 0.748450 TAACCGGGACTAATGAGGCG 59.252 55.000 6.32 0.00 0.00 5.52
2430 3836 0.974010 AACCGGGACTAATGAGGCGA 60.974 55.000 6.32 0.00 0.00 5.54
2431 3837 0.974010 ACCGGGACTAATGAGGCGAA 60.974 55.000 6.32 0.00 0.00 4.70
2432 3838 0.529992 CCGGGACTAATGAGGCGAAC 60.530 60.000 0.00 0.00 0.00 3.95
2433 3839 0.870307 CGGGACTAATGAGGCGAACG 60.870 60.000 0.00 0.00 0.00 3.95
2522 3964 8.553459 TGAGGATGTTAGAGAATTTTTCTGAC 57.447 34.615 5.27 5.27 40.87 3.51
2551 4036 9.139174 CATACCCACAAATGAAAGACAAATTAC 57.861 33.333 0.00 0.00 0.00 1.89
2657 4151 7.098074 AGTAAGTTCTAGCACATGGTACTAC 57.902 40.000 0.00 0.00 0.00 2.73
2665 4159 2.418628 GCACATGGTACTACGCATTGTT 59.581 45.455 0.00 0.00 0.00 2.83
2700 4194 4.202050 GCCTTAAGATTTGCACACCCATAG 60.202 45.833 3.36 0.00 0.00 2.23
2706 4200 1.904287 TTGCACACCCATAGTTGGAC 58.096 50.000 0.00 0.00 46.92 4.02
2716 4234 6.780522 ACACCCATAGTTGGACAAAACTAATT 59.219 34.615 1.28 0.00 46.92 1.40
2824 4366 3.916989 GAGGATCCCTGTTATTATGGGGT 59.083 47.826 8.55 0.00 41.22 4.95
2832 4374 4.095782 CCTGTTATTATGGGGTCACGTTTG 59.904 45.833 0.00 0.00 0.00 2.93
2835 4377 2.188062 TTATGGGGTCACGTTTGGAC 57.812 50.000 0.00 0.00 34.52 4.02
2840 4382 1.005867 GGTCACGTTTGGACCGCTA 60.006 57.895 7.70 0.00 44.80 4.26
2860 4444 1.564348 ACCCTGTCTGTTTGGTCACTT 59.436 47.619 0.00 0.00 0.00 3.16
2861 4445 2.222027 CCCTGTCTGTTTGGTCACTTC 58.778 52.381 0.00 0.00 0.00 3.01
2862 4446 2.222027 CCTGTCTGTTTGGTCACTTCC 58.778 52.381 0.00 0.00 0.00 3.46
2866 4450 3.139077 GTCTGTTTGGTCACTTCCGATT 58.861 45.455 0.00 0.00 0.00 3.34
2907 4502 0.467804 GCACTCCCTCCTCTGATTCC 59.532 60.000 0.00 0.00 0.00 3.01
2939 4534 2.644992 GTGAAACCAAGGCAGGCG 59.355 61.111 0.00 0.00 0.00 5.52
2968 4563 1.007849 CAACTTTTTGGTCGGCCCG 60.008 57.895 2.12 0.00 35.15 6.13
2969 4564 2.852180 AACTTTTTGGTCGGCCCGC 61.852 57.895 2.12 0.00 35.15 6.13
2987 4582 1.523154 GCGATTTGGCAGGGTGAACA 61.523 55.000 0.00 0.00 0.00 3.18
2992 4587 2.017668 TTGGCAGGGTGAACATGGGT 62.018 55.000 0.00 0.00 0.00 4.51
3014 4609 2.244769 AGCAACCAAATAGCCCCTATGT 59.755 45.455 0.00 0.00 0.00 2.29
3018 4613 2.849943 ACCAAATAGCCCCTATGTGTCA 59.150 45.455 2.68 0.00 31.60 3.58
3054 4650 3.076785 AGGATCCTTCCCTCGATGAGTAT 59.923 47.826 9.02 0.00 43.76 2.12
3140 4736 1.027792 ACGGAAGAGAGACCTCGCTC 61.028 60.000 3.84 0.00 44.08 5.03
3144 4740 0.251386 AAGAGAGACCTCGCTCACCA 60.251 55.000 8.53 0.00 43.85 4.17
3188 4784 0.525668 GCTGATTGGACGACGACGAT 60.526 55.000 15.32 0.00 42.66 3.73
3228 4824 1.743958 CATCTCTACGAGGTCACCGTT 59.256 52.381 0.00 0.00 40.95 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.532834 TGGGCCTGATAGGTTTAATGTTC 58.467 43.478 4.53 0.00 37.80 3.18
28 29 4.017499 ACTTGGGCCTGATAGGTTTAATGT 60.017 41.667 4.53 0.00 37.80 2.71
29 30 4.339247 CACTTGGGCCTGATAGGTTTAATG 59.661 45.833 4.53 0.00 37.80 1.90
49 50 2.729194 TGTACCAACAAACAAGGCACT 58.271 42.857 0.00 0.00 33.11 4.40
53 54 4.261994 CCAAGGATGTACCAACAAACAAGG 60.262 45.833 0.00 0.00 39.58 3.61
68 69 3.947868 ACTGATTCTGTGACCAAGGATG 58.052 45.455 0.00 0.00 0.00 3.51
76 77 5.049129 CCAAAGAGGAAACTGATTCTGTGAC 60.049 44.000 0.00 0.00 44.43 3.67
83 84 7.010160 TCCATTTACCAAAGAGGAAACTGATT 58.990 34.615 0.00 0.00 44.43 2.57
88 89 5.538813 AGGTTCCATTTACCAAAGAGGAAAC 59.461 40.000 12.35 12.35 42.20 2.78
124 125 2.122768 ACTTCCCACTCATCAGGATCC 58.877 52.381 2.48 2.48 0.00 3.36
140 141 3.510360 TGCTCACCTACTTCACCTACTTC 59.490 47.826 0.00 0.00 0.00 3.01
244 246 1.271597 ACTCCAAGATGGTGTGGAAGC 60.272 52.381 3.48 0.00 42.10 3.86
262 264 5.166398 GCCTCGTGTATACAACTGTTAACT 58.834 41.667 7.25 0.00 0.00 2.24
307 309 1.119684 GCAACAAAAGACTTGGGGGT 58.880 50.000 0.00 0.00 0.00 4.95
456 469 2.761213 CCAGCTTTGATGGGCCCC 60.761 66.667 22.27 4.91 33.94 5.80
457 470 2.037847 ACCAGCTTTGATGGGCCC 59.962 61.111 17.59 17.59 42.48 5.80
521 534 2.298729 GGTTGCAAGCTGGGTTTAATCA 59.701 45.455 21.06 0.00 0.00 2.57
530 543 2.133742 CTTCCACGGTTGCAAGCTGG 62.134 60.000 27.29 27.29 0.00 4.85
532 545 2.555547 GCTTCCACGGTTGCAAGCT 61.556 57.895 24.83 10.44 38.58 3.74
565 583 4.080299 AGGAGCGTGGAGAAGGATTAAATT 60.080 41.667 0.00 0.00 0.00 1.82
569 587 1.757118 CAGGAGCGTGGAGAAGGATTA 59.243 52.381 0.00 0.00 0.00 1.75
591 609 7.290813 ACTTGAATTTATAGGAGGGGATTCAC 58.709 38.462 0.00 0.00 34.38 3.18
616 634 1.667467 GCGAATTTTTGGCGTGCCTAA 60.667 47.619 12.84 8.11 36.94 2.69
617 635 0.109504 GCGAATTTTTGGCGTGCCTA 60.110 50.000 12.84 0.89 36.94 3.93
725 744 1.004918 CTTGTGTGGGGACTCCGTC 60.005 63.158 0.00 0.00 38.76 4.79
727 746 2.347490 CCTTGTGTGGGGACTCCG 59.653 66.667 0.00 0.00 38.76 4.63
737 756 2.528378 ACGGGGTAGGCCTTGTGT 60.528 61.111 12.58 0.00 34.45 3.72
748 767 3.239253 AGCTTTCACGGACGGGGT 61.239 61.111 0.00 0.00 0.00 4.95
749 768 2.742372 CAGCTTTCACGGACGGGG 60.742 66.667 0.00 0.00 0.00 5.73
750 769 2.742372 CCAGCTTTCACGGACGGG 60.742 66.667 0.00 0.00 0.00 5.28
751 770 0.320073 TAACCAGCTTTCACGGACGG 60.320 55.000 0.00 0.00 0.00 4.79
771 790 5.188434 TGTCTAATCATGCAGGGAGAAAAG 58.812 41.667 0.00 0.00 0.00 2.27
796 815 5.335191 CCTGTTTAGAAGCTTCGAAATTGCT 60.335 40.000 29.45 11.04 34.99 3.91
797 816 4.853743 CCTGTTTAGAAGCTTCGAAATTGC 59.146 41.667 29.45 20.16 34.99 3.56
798 817 6.073003 AGTCCTGTTTAGAAGCTTCGAAATTG 60.073 38.462 29.45 24.02 34.99 2.32
799 818 5.998363 AGTCCTGTTTAGAAGCTTCGAAATT 59.002 36.000 29.45 13.00 34.99 1.82
800 819 5.552178 AGTCCTGTTTAGAAGCTTCGAAAT 58.448 37.500 29.45 15.11 34.99 2.17
801 820 4.957296 AGTCCTGTTTAGAAGCTTCGAAA 58.043 39.130 25.17 25.17 30.96 3.46
802 821 4.602340 AGTCCTGTTTAGAAGCTTCGAA 57.398 40.909 20.43 18.59 0.00 3.71
803 822 4.521639 TGTAGTCCTGTTTAGAAGCTTCGA 59.478 41.667 20.43 13.21 0.00 3.71
804 823 4.806330 TGTAGTCCTGTTTAGAAGCTTCG 58.194 43.478 20.43 5.36 0.00 3.79
805 824 5.172205 CCTGTAGTCCTGTTTAGAAGCTTC 58.828 45.833 19.11 19.11 0.00 3.86
815 834 0.475828 AAGGCCCCTGTAGTCCTGTT 60.476 55.000 0.00 0.00 0.00 3.16
891 910 2.045926 AATGAGGAGCCGTGGTGC 60.046 61.111 0.00 0.00 0.00 5.01
967 986 5.368989 TCTAGAGTTCTCGATCAGCACATA 58.631 41.667 0.00 0.00 0.00 2.29
977 996 2.630158 CGGGTCTTCTAGAGTTCTCGA 58.370 52.381 6.57 0.00 0.00 4.04
978 997 1.064357 GCGGGTCTTCTAGAGTTCTCG 59.936 57.143 7.65 7.65 0.00 4.04
979 998 1.406180 GGCGGGTCTTCTAGAGTTCTC 59.594 57.143 0.00 0.00 0.00 2.87
980 999 1.272536 TGGCGGGTCTTCTAGAGTTCT 60.273 52.381 0.00 0.00 0.00 3.01
981 1000 1.183549 TGGCGGGTCTTCTAGAGTTC 58.816 55.000 0.00 0.00 0.00 3.01
982 1001 1.482593 CATGGCGGGTCTTCTAGAGTT 59.517 52.381 0.00 0.00 0.00 3.01
983 1002 1.115467 CATGGCGGGTCTTCTAGAGT 58.885 55.000 0.00 0.00 0.00 3.24
984 1003 0.390860 CCATGGCGGGTCTTCTAGAG 59.609 60.000 0.00 0.00 0.00 2.43
987 1006 1.689233 AGCCATGGCGGGTCTTCTA 60.689 57.895 30.50 0.00 44.26 2.10
1108 1139 3.387374 TGTTACTTACCTTTGGACGTGGA 59.613 43.478 0.00 0.00 0.00 4.02
1126 1157 1.373246 GCACGTACGGCCAGTGTTA 60.373 57.895 21.06 0.00 38.10 2.41
1139 1173 2.434884 CCAGAAGGATGCGCACGT 60.435 61.111 14.90 5.73 36.89 4.49
1140 1174 3.197790 CCCAGAAGGATGCGCACG 61.198 66.667 14.90 0.00 38.24 5.34
1141 1175 1.648467 GAACCCAGAAGGATGCGCAC 61.648 60.000 14.90 6.86 39.89 5.34
1142 1176 1.377202 GAACCCAGAAGGATGCGCA 60.377 57.895 14.96 14.96 39.89 6.09
1157 1191 3.963428 TTAGAACAGAGGGAGCAGAAC 57.037 47.619 0.00 0.00 0.00 3.01
1170 1204 1.733360 GGCGCCGTGTAAATTAGAACA 59.267 47.619 12.58 0.00 0.00 3.18
1187 1221 1.196581 TGAACATCGAAATGTGTGGCG 59.803 47.619 0.00 0.00 45.48 5.69
1203 1237 7.694784 TCGTCAAATTAACAGTCAAAGTTGAAC 59.305 33.333 11.12 0.00 40.20 3.18
1252 1287 8.367911 GGGGAACTTTTGATGTAATTTCTCTTT 58.632 33.333 0.00 0.00 0.00 2.52
1319 1354 4.030913 AGGGAGTAAGCAGTGTAGCATAA 58.969 43.478 0.00 0.00 36.85 1.90
1409 1444 9.783256 GTGTTATAGATGTTGGTGTATTTTTCC 57.217 33.333 0.00 0.00 0.00 3.13
1472 1507 8.196103 TGCAGCATCAAATATATAAAGCACAAA 58.804 29.630 0.00 0.00 0.00 2.83
1473 1508 7.714703 TGCAGCATCAAATATATAAAGCACAA 58.285 30.769 0.00 0.00 0.00 3.33
1494 1529 7.126398 GTCTAACTTTGTGTTAAAGTCTGCAG 58.874 38.462 7.63 7.63 40.24 4.41
1545 1580 8.731605 GTTGAAGCTCTAAATTTACTTAAGCCT 58.268 33.333 1.29 2.63 0.00 4.58
1546 1581 8.731605 AGTTGAAGCTCTAAATTTACTTAAGCC 58.268 33.333 1.29 2.50 0.00 4.35
1564 2966 6.092807 CACTCCCACTCTAAATTAGTTGAAGC 59.907 42.308 0.00 0.00 0.00 3.86
1596 2998 8.820933 CGAGTATTGATCATCAGTTACAACAAT 58.179 33.333 0.00 0.00 0.00 2.71
1602 3004 8.575565 TTTAGCGAGTATTGATCATCAGTTAC 57.424 34.615 0.00 0.00 0.00 2.50
1638 3040 1.431488 CCATTCACATGGCGTCCTCG 61.431 60.000 0.00 0.00 43.95 4.63
1639 3041 2.397751 CCATTCACATGGCGTCCTC 58.602 57.895 0.00 0.00 43.95 3.71
1640 3042 4.643795 CCATTCACATGGCGTCCT 57.356 55.556 0.00 0.00 43.95 3.85
1647 3049 1.825191 CTCGGCCCCCATTCACATG 60.825 63.158 0.00 0.00 0.00 3.21
1705 3107 3.057806 ACGCGCACTGCATAGTACATATA 60.058 43.478 5.73 0.00 46.97 0.86
1706 3108 2.288213 ACGCGCACTGCATAGTACATAT 60.288 45.455 5.73 0.00 46.97 1.78
1833 3238 3.997064 GATCTGCACGGTCAGCGCT 62.997 63.158 2.64 2.64 34.19 5.92
1854 3259 2.351276 CCCTGCGTGTTAAGGCCT 59.649 61.111 0.00 0.00 36.33 5.19
2026 3431 2.665185 GAACACGTCGCCCTTGCT 60.665 61.111 0.00 0.00 34.43 3.91
2169 3574 0.178950 CCAGGAGATCATCGGGGAGA 60.179 60.000 0.00 0.00 0.00 3.71
2187 3592 1.226717 CGTGAGGAGCGTCTTAGCC 60.227 63.158 0.00 0.00 38.01 3.93
2283 3689 4.340381 AGATTACCATGCCTGAGAAAATGC 59.660 41.667 0.00 0.00 0.00 3.56
2358 3764 3.123050 CGTGATGGAATATCACTCGCAA 58.877 45.455 15.53 0.00 44.50 4.85
2399 3805 2.158900 AGTCCCGGTTATGATGCTCTTG 60.159 50.000 0.00 0.00 0.00 3.02
2400 3806 2.119495 AGTCCCGGTTATGATGCTCTT 58.881 47.619 0.00 0.00 0.00 2.85
2401 3807 1.794714 AGTCCCGGTTATGATGCTCT 58.205 50.000 0.00 0.00 0.00 4.09
2402 3808 3.746045 TTAGTCCCGGTTATGATGCTC 57.254 47.619 0.00 0.00 0.00 4.26
2403 3809 3.646162 TCATTAGTCCCGGTTATGATGCT 59.354 43.478 0.00 0.00 0.00 3.79
2404 3810 3.997021 CTCATTAGTCCCGGTTATGATGC 59.003 47.826 0.00 0.00 0.00 3.91
2405 3811 4.569943 CCTCATTAGTCCCGGTTATGATG 58.430 47.826 0.00 0.00 0.00 3.07
2406 3812 3.008049 GCCTCATTAGTCCCGGTTATGAT 59.992 47.826 0.00 0.00 0.00 2.45
2407 3813 2.367567 GCCTCATTAGTCCCGGTTATGA 59.632 50.000 0.00 1.08 0.00 2.15
2408 3814 2.767505 GCCTCATTAGTCCCGGTTATG 58.232 52.381 0.00 0.00 0.00 1.90
2409 3815 1.343465 CGCCTCATTAGTCCCGGTTAT 59.657 52.381 0.00 0.00 0.00 1.89
2410 3816 0.748450 CGCCTCATTAGTCCCGGTTA 59.252 55.000 0.00 0.00 0.00 2.85
2411 3817 0.974010 TCGCCTCATTAGTCCCGGTT 60.974 55.000 0.00 0.00 0.00 4.44
2412 3818 0.974010 TTCGCCTCATTAGTCCCGGT 60.974 55.000 0.00 0.00 0.00 5.28
2413 3819 0.529992 GTTCGCCTCATTAGTCCCGG 60.530 60.000 0.00 0.00 0.00 5.73
2414 3820 0.870307 CGTTCGCCTCATTAGTCCCG 60.870 60.000 0.00 0.00 0.00 5.14
2415 3821 1.152383 GCGTTCGCCTCATTAGTCCC 61.152 60.000 5.87 0.00 0.00 4.46
2416 3822 0.459585 TGCGTTCGCCTCATTAGTCC 60.460 55.000 14.44 0.00 0.00 3.85
2417 3823 1.324736 CTTGCGTTCGCCTCATTAGTC 59.675 52.381 14.44 0.00 0.00 2.59
2418 3824 1.337823 ACTTGCGTTCGCCTCATTAGT 60.338 47.619 14.44 5.77 0.00 2.24
2419 3825 1.359848 ACTTGCGTTCGCCTCATTAG 58.640 50.000 14.44 5.23 0.00 1.73
2420 3826 2.658373 TACTTGCGTTCGCCTCATTA 57.342 45.000 14.44 0.00 0.00 1.90
2421 3827 1.933853 GATACTTGCGTTCGCCTCATT 59.066 47.619 14.44 0.00 0.00 2.57
2422 3828 1.134818 TGATACTTGCGTTCGCCTCAT 60.135 47.619 14.44 3.06 0.00 2.90
2423 3829 0.245266 TGATACTTGCGTTCGCCTCA 59.755 50.000 14.44 6.98 0.00 3.86
2424 3830 1.571919 ATGATACTTGCGTTCGCCTC 58.428 50.000 14.44 4.75 0.00 4.70
2425 3831 2.864343 GTTATGATACTTGCGTTCGCCT 59.136 45.455 14.44 0.18 0.00 5.52
2426 3832 2.605818 TGTTATGATACTTGCGTTCGCC 59.394 45.455 14.44 0.00 0.00 5.54
2427 3833 3.306166 ACTGTTATGATACTTGCGTTCGC 59.694 43.478 10.34 10.34 0.00 4.70
2428 3834 6.416750 TGATACTGTTATGATACTTGCGTTCG 59.583 38.462 0.00 0.00 0.00 3.95
2429 3835 7.694388 TGATACTGTTATGATACTTGCGTTC 57.306 36.000 0.00 0.00 0.00 3.95
2430 3836 7.926018 TCATGATACTGTTATGATACTTGCGTT 59.074 33.333 0.00 0.00 28.77 4.84
2431 3837 7.433680 TCATGATACTGTTATGATACTTGCGT 58.566 34.615 0.00 0.00 28.77 5.24
2432 3838 7.873739 TCATGATACTGTTATGATACTTGCG 57.126 36.000 0.00 0.00 28.77 4.85
2433 3839 9.265901 ACTTCATGATACTGTTATGATACTTGC 57.734 33.333 0.00 0.00 33.40 4.01
2522 3964 6.513806 TGTCTTTCATTTGTGGGTATGATG 57.486 37.500 0.00 0.00 31.34 3.07
2551 4036 4.556135 GCGAATGACATGTCACTCAATTTG 59.444 41.667 30.31 23.23 43.11 2.32
2657 4151 1.670811 CCTTAGGCCACTAACAATGCG 59.329 52.381 5.01 0.00 35.42 4.73
2824 4366 1.005867 GGTAGCGGTCCAAACGTGA 60.006 57.895 0.00 0.00 0.00 4.35
2825 4367 2.030958 GGGTAGCGGTCCAAACGTG 61.031 63.158 0.00 0.00 0.00 4.49
2832 4374 1.542187 AACAGACAGGGTAGCGGTCC 61.542 60.000 10.59 0.00 31.99 4.46
2835 4377 0.673644 CCAAACAGACAGGGTAGCGG 60.674 60.000 0.00 0.00 0.00 5.52
2837 4379 1.071699 TGACCAAACAGACAGGGTAGC 59.928 52.381 0.00 0.00 32.77 3.58
2840 4382 1.213296 AGTGACCAAACAGACAGGGT 58.787 50.000 0.00 0.00 36.05 4.34
2866 4450 1.876497 GCGAGCTGGGCATCCAAAAA 61.876 55.000 0.00 0.00 43.51 1.94
2899 4493 2.513753 ACAATTTGGCGTGGAATCAGA 58.486 42.857 0.78 0.00 0.00 3.27
2900 4494 2.988493 CAACAATTTGGCGTGGAATCAG 59.012 45.455 0.78 0.00 0.00 2.90
2968 4563 1.212751 GTTCACCCTGCCAAATCGC 59.787 57.895 0.00 0.00 0.00 4.58
2969 4564 1.135315 CATGTTCACCCTGCCAAATCG 60.135 52.381 0.00 0.00 0.00 3.34
2976 4571 1.032114 GCTACCCATGTTCACCCTGC 61.032 60.000 0.00 0.00 0.00 4.85
2978 4573 1.072266 TTGCTACCCATGTTCACCCT 58.928 50.000 0.00 0.00 0.00 4.34
2982 4577 2.666272 TTGGTTGCTACCCATGTTCA 57.334 45.000 15.00 0.00 44.35 3.18
2987 4582 2.666317 GGCTATTTGGTTGCTACCCAT 58.334 47.619 15.00 9.26 44.35 4.00
2992 4587 3.461831 ACATAGGGGCTATTTGGTTGCTA 59.538 43.478 0.00 0.00 0.00 3.49
3003 4598 1.496060 CTGGTGACACATAGGGGCTA 58.504 55.000 8.08 0.00 35.60 3.93
3005 4600 1.452108 GCTGGTGACACATAGGGGC 60.452 63.158 8.08 0.00 35.60 5.80
3030 4625 0.972883 CATCGAGGGAAGGATCCTCC 59.027 60.000 16.52 17.12 46.01 4.30
3140 4736 1.835483 GCGCCGATATGAGCTTGGTG 61.835 60.000 0.00 0.00 0.00 4.17
3144 4740 2.031163 GGGCGCCGATATGAGCTT 59.969 61.111 22.54 0.00 0.00 3.74
3197 4793 1.344458 GTAGAGATGGCATCGCATCG 58.656 55.000 28.79 0.00 33.37 3.84
3228 4824 3.834231 ACTAAAACTAGGCGAGGTACCAA 59.166 43.478 15.94 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.