Multiple sequence alignment - TraesCS3B01G222500

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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 TraesCS3B01G222500 chr3B 100.000 2810 0 0 1 2810 283636773 283639582 0.000000e+00 5190
1 TraesCS3B01G222500 chr3B 97.468 158 4 0 1 158 81070733 81070576 1.280000e-68 270
2 TraesCS3B01G222500 chr6B 90.936 2681 156 50 157 2810 708219042 708221662 0.000000e+00 3524
3 TraesCS3B01G222500 chr6B 91.053 1710 120 18 157 1857 118023805 118025490 0.000000e+00 2279
4 TraesCS3B01G222500 chr6B 88.194 1728 130 39 148 1857 671127437 671129108 0.000000e+00 1993
5 TraesCS3B01G222500 chr6B 96.429 952 32 1 1858 2809 118026034 118026983 0.000000e+00 1568
6 TraesCS3B01G222500 chr2D 96.176 1700 57 5 159 1857 518213804 518215496 0.000000e+00 2772
7 TraesCS3B01G222500 chr2D 96.347 958 30 4 1857 2810 518249875 518250831 0.000000e+00 1570
8 TraesCS3B01G222500 chr5A 95.535 1702 65 7 158 1857 676351313 676353005 0.000000e+00 2712
9 TraesCS3B01G222500 chr5A 96.440 955 30 3 1857 2810 676353551 676354502 0.000000e+00 1572
10 TraesCS3B01G222500 chr5A 84.284 649 58 17 331 961 656943154 656942532 6.700000e-166 593
11 TraesCS3B01G222500 chr5A 90.881 329 21 5 241 566 326658472 326658794 1.550000e-117 433
12 TraesCS3B01G222500 chr7A 89.854 1715 108 29 159 1857 674512073 674510409 0.000000e+00 2143
13 TraesCS3B01G222500 chr7A 96.653 956 30 2 1857 2810 674509863 674508908 0.000000e+00 1587
14 TraesCS3B01G222500 chrUn 87.907 1720 141 43 159 1857 50575488 50577161 0.000000e+00 1962
15 TraesCS3B01G222500 chr4A 87.819 1724 135 39 157 1857 690354429 690356100 0.000000e+00 1951
16 TraesCS3B01G222500 chr4A 97.708 960 18 4 1854 2810 690356644 690357602 0.000000e+00 1648
17 TraesCS3B01G222500 chr5B 93.624 1239 77 2 159 1396 382497942 382499179 0.000000e+00 1849
18 TraesCS3B01G222500 chr5B 96.859 955 28 2 1857 2810 382535183 382536136 0.000000e+00 1596
19 TraesCS3B01G222500 chr5B 90.722 1067 90 6 158 1221 680392900 680391840 0.000000e+00 1413
20 TraesCS3B01G222500 chr5B 82.504 663 67 25 326 962 665814378 665813739 1.150000e-148 536
21 TraesCS3B01G222500 chr5B 96.855 159 5 0 1 159 605966278 605966436 1.660000e-67 267
22 TraesCS3B01G222500 chr1B 86.853 1719 142 47 159 1857 638558162 638556508 0.000000e+00 1845
23 TraesCS3B01G222500 chr7D 94.583 960 43 7 1858 2810 58620565 58621522 0.000000e+00 1476
24 TraesCS3B01G222500 chr7D 90.814 958 80 4 1858 2810 118903364 118902410 0.000000e+00 1275
25 TraesCS3B01G222500 chr7D 82.631 783 96 20 203 962 58508597 58509362 0.000000e+00 656
26 TraesCS3B01G222500 chr7B 97.468 158 4 0 1 158 79295801 79295644 1.280000e-68 270
27 TraesCS3B01G222500 chr7B 96.855 159 5 0 1 159 586455225 586455067 1.660000e-67 267
28 TraesCS3B01G222500 chr2B 97.468 158 4 0 1 158 761034134 761034291 1.280000e-68 270
29 TraesCS3B01G222500 chr4B 97.436 156 4 0 1 156 387072999 387073154 1.660000e-67 267
30 TraesCS3B01G222500 chr6A 96.835 158 5 0 1 158 440929858 440930015 5.970000e-67 265
31 TraesCS3B01G222500 chr4D 96.855 159 4 1 1 158 25151855 25152013 5.970000e-67 265
32 TraesCS3B01G222500 chr1D 96.835 158 5 0 1 158 210285246 210285089 5.970000e-67 265


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 TraesCS3B01G222500 chr3B 283636773 283639582 2809 False 5190.0 5190 100.0000 1 2810 1 chr3B.!!$F1 2809
1 TraesCS3B01G222500 chr6B 708219042 708221662 2620 False 3524.0 3524 90.9360 157 2810 1 chr6B.!!$F2 2653
2 TraesCS3B01G222500 chr6B 671127437 671129108 1671 False 1993.0 1993 88.1940 148 1857 1 chr6B.!!$F1 1709
3 TraesCS3B01G222500 chr6B 118023805 118026983 3178 False 1923.5 2279 93.7410 157 2809 2 chr6B.!!$F3 2652
4 TraesCS3B01G222500 chr2D 518213804 518215496 1692 False 2772.0 2772 96.1760 159 1857 1 chr2D.!!$F1 1698
5 TraesCS3B01G222500 chr2D 518249875 518250831 956 False 1570.0 1570 96.3470 1857 2810 1 chr2D.!!$F2 953
6 TraesCS3B01G222500 chr5A 676351313 676354502 3189 False 2142.0 2712 95.9875 158 2810 2 chr5A.!!$F2 2652
7 TraesCS3B01G222500 chr5A 656942532 656943154 622 True 593.0 593 84.2840 331 961 1 chr5A.!!$R1 630
8 TraesCS3B01G222500 chr7A 674508908 674512073 3165 True 1865.0 2143 93.2535 159 2810 2 chr7A.!!$R1 2651
9 TraesCS3B01G222500 chrUn 50575488 50577161 1673 False 1962.0 1962 87.9070 159 1857 1 chrUn.!!$F1 1698
10 TraesCS3B01G222500 chr4A 690354429 690357602 3173 False 1799.5 1951 92.7635 157 2810 2 chr4A.!!$F1 2653
11 TraesCS3B01G222500 chr5B 382497942 382499179 1237 False 1849.0 1849 93.6240 159 1396 1 chr5B.!!$F1 1237
12 TraesCS3B01G222500 chr5B 382535183 382536136 953 False 1596.0 1596 96.8590 1857 2810 1 chr5B.!!$F2 953
13 TraesCS3B01G222500 chr5B 680391840 680392900 1060 True 1413.0 1413 90.7220 158 1221 1 chr5B.!!$R2 1063
14 TraesCS3B01G222500 chr5B 665813739 665814378 639 True 536.0 536 82.5040 326 962 1 chr5B.!!$R1 636
15 TraesCS3B01G222500 chr1B 638556508 638558162 1654 True 1845.0 1845 86.8530 159 1857 1 chr1B.!!$R1 1698
16 TraesCS3B01G222500 chr7D 58620565 58621522 957 False 1476.0 1476 94.5830 1858 2810 1 chr7D.!!$F2 952
17 TraesCS3B01G222500 chr7D 118902410 118903364 954 True 1275.0 1275 90.8140 1858 2810 1 chr7D.!!$R1 952
18 TraesCS3B01G222500 chr7D 58508597 58509362 765 False 656.0 656 82.6310 203 962 1 chr7D.!!$F1 759

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
539 573 0.687757 TCCGTCCCCTCATCCTCTTG 60.688 60.0 0.0 0.0 0.0 3.02 F
1504 1590 1.023719 TCCTTCTATCACCCCTCCCA 58.976 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 1764 0.613777 GATGACGAACCCTCCCAACT 59.386 55.000 0.0 0.0 0.00 3.16 R
2562 3754 1.062886 TCCTATCCTAGCACCTGCACT 60.063 52.381 0.0 0.0 45.16 4.40 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 1.733385 ACCGTACTGTTAAAGGGGGT 58.267 50.000 0.00 0.00 0.00 4.95
20 21 1.625315 ACCGTACTGTTAAAGGGGGTC 59.375 52.381 0.00 0.00 0.00 4.46
21 22 1.404583 CCGTACTGTTAAAGGGGGTCG 60.405 57.143 0.00 0.00 0.00 4.79
22 23 1.545582 CGTACTGTTAAAGGGGGTCGA 59.454 52.381 0.00 0.00 0.00 4.20
23 24 2.416431 CGTACTGTTAAAGGGGGTCGAG 60.416 54.545 0.00 0.00 0.00 4.04
24 25 0.981943 ACTGTTAAAGGGGGTCGAGG 59.018 55.000 0.00 0.00 0.00 4.63
25 26 0.981943 CTGTTAAAGGGGGTCGAGGT 59.018 55.000 0.00 0.00 0.00 3.85
26 27 2.181975 CTGTTAAAGGGGGTCGAGGTA 58.818 52.381 0.00 0.00 0.00 3.08
27 28 2.568509 CTGTTAAAGGGGGTCGAGGTAA 59.431 50.000 0.00 0.00 0.00 2.85
28 29 3.183801 TGTTAAAGGGGGTCGAGGTAAT 58.816 45.455 0.00 0.00 0.00 1.89
29 30 4.360889 TGTTAAAGGGGGTCGAGGTAATA 58.639 43.478 0.00 0.00 0.00 0.98
30 31 4.162131 TGTTAAAGGGGGTCGAGGTAATAC 59.838 45.833 0.00 0.00 0.00 1.89
31 32 2.862850 AAGGGGGTCGAGGTAATACT 57.137 50.000 0.00 0.00 0.00 2.12
32 33 3.979501 AAGGGGGTCGAGGTAATACTA 57.020 47.619 0.00 0.00 0.00 1.82
33 34 3.979501 AGGGGGTCGAGGTAATACTAA 57.020 47.619 0.00 0.00 0.00 2.24
34 35 3.842206 AGGGGGTCGAGGTAATACTAAG 58.158 50.000 0.00 0.00 0.00 2.18
35 36 2.896044 GGGGGTCGAGGTAATACTAAGG 59.104 54.545 0.00 0.00 0.00 2.69
36 37 3.437052 GGGGGTCGAGGTAATACTAAGGA 60.437 52.174 0.00 0.00 0.00 3.36
37 38 4.218312 GGGGTCGAGGTAATACTAAGGAA 58.782 47.826 0.00 0.00 0.00 3.36
38 39 4.651045 GGGGTCGAGGTAATACTAAGGAAA 59.349 45.833 0.00 0.00 0.00 3.13
39 40 5.452496 GGGGTCGAGGTAATACTAAGGAAAC 60.452 48.000 0.00 0.00 0.00 2.78
41 42 6.271566 GGTCGAGGTAATACTAAGGAAACTG 58.728 44.000 0.00 0.00 42.68 3.16
42 43 6.096001 GGTCGAGGTAATACTAAGGAAACTGA 59.904 42.308 0.00 0.00 42.68 3.41
43 44 7.201893 GGTCGAGGTAATACTAAGGAAACTGAT 60.202 40.741 0.00 0.00 42.68 2.90
44 45 8.196103 GTCGAGGTAATACTAAGGAAACTGATT 58.804 37.037 0.00 0.00 42.68 2.57
45 46 8.755977 TCGAGGTAATACTAAGGAAACTGATTT 58.244 33.333 0.00 0.00 42.68 2.17
46 47 9.032420 CGAGGTAATACTAAGGAAACTGATTTC 57.968 37.037 0.00 0.00 42.68 2.17
57 58 5.382618 GAAACTGATTTCCAAGTGATGCT 57.617 39.130 0.00 0.00 38.67 3.79
58 59 5.382618 AAACTGATTTCCAAGTGATGCTC 57.617 39.130 0.00 0.00 0.00 4.26
59 60 4.025040 ACTGATTTCCAAGTGATGCTCA 57.975 40.909 0.00 0.00 0.00 4.26
60 61 4.597004 ACTGATTTCCAAGTGATGCTCAT 58.403 39.130 0.00 0.00 0.00 2.90
61 62 4.639310 ACTGATTTCCAAGTGATGCTCATC 59.361 41.667 3.03 3.03 38.29 2.92
62 63 4.851843 TGATTTCCAAGTGATGCTCATCT 58.148 39.130 10.76 0.00 38.60 2.90
63 64 4.880120 TGATTTCCAAGTGATGCTCATCTC 59.120 41.667 10.76 7.46 38.60 2.75
64 65 3.986996 TTCCAAGTGATGCTCATCTCA 57.013 42.857 10.76 0.00 38.60 3.27
65 66 3.986996 TCCAAGTGATGCTCATCTCAA 57.013 42.857 10.76 0.00 38.60 3.02
66 67 4.290711 TCCAAGTGATGCTCATCTCAAA 57.709 40.909 10.76 0.00 38.60 2.69
67 68 4.654915 TCCAAGTGATGCTCATCTCAAAA 58.345 39.130 10.76 0.00 38.60 2.44
68 69 5.258841 TCCAAGTGATGCTCATCTCAAAAT 58.741 37.500 10.76 0.00 38.60 1.82
69 70 5.713389 TCCAAGTGATGCTCATCTCAAAATT 59.287 36.000 10.76 0.00 38.60 1.82
70 71 6.034591 CCAAGTGATGCTCATCTCAAAATTC 58.965 40.000 10.76 0.00 38.60 2.17
71 72 6.127703 CCAAGTGATGCTCATCTCAAAATTCT 60.128 38.462 10.76 0.00 38.60 2.40
72 73 7.066645 CCAAGTGATGCTCATCTCAAAATTCTA 59.933 37.037 10.76 0.00 38.60 2.10
73 74 7.551035 AGTGATGCTCATCTCAAAATTCTAC 57.449 36.000 10.76 0.00 38.60 2.59
74 75 7.108194 AGTGATGCTCATCTCAAAATTCTACA 58.892 34.615 10.76 0.00 38.60 2.74
75 76 7.065563 AGTGATGCTCATCTCAAAATTCTACAC 59.934 37.037 10.76 0.00 38.60 2.90
76 77 6.317140 TGATGCTCATCTCAAAATTCTACACC 59.683 38.462 10.76 0.00 38.60 4.16
77 78 5.809001 TGCTCATCTCAAAATTCTACACCT 58.191 37.500 0.00 0.00 0.00 4.00
78 79 6.946340 TGCTCATCTCAAAATTCTACACCTA 58.054 36.000 0.00 0.00 0.00 3.08
79 80 6.818644 TGCTCATCTCAAAATTCTACACCTAC 59.181 38.462 0.00 0.00 0.00 3.18
80 81 6.258947 GCTCATCTCAAAATTCTACACCTACC 59.741 42.308 0.00 0.00 0.00 3.18
81 82 6.650120 TCATCTCAAAATTCTACACCTACCC 58.350 40.000 0.00 0.00 0.00 3.69
82 83 6.214615 TCATCTCAAAATTCTACACCTACCCA 59.785 38.462 0.00 0.00 0.00 4.51
83 84 6.442541 TCTCAAAATTCTACACCTACCCAA 57.557 37.500 0.00 0.00 0.00 4.12
84 85 7.027874 TCTCAAAATTCTACACCTACCCAAT 57.972 36.000 0.00 0.00 0.00 3.16
85 86 7.110155 TCTCAAAATTCTACACCTACCCAATC 58.890 38.462 0.00 0.00 0.00 2.67
86 87 6.184789 TCAAAATTCTACACCTACCCAATCC 58.815 40.000 0.00 0.00 0.00 3.01
87 88 6.011981 TCAAAATTCTACACCTACCCAATCCT 60.012 38.462 0.00 0.00 0.00 3.24
88 89 6.402981 AAATTCTACACCTACCCAATCCTT 57.597 37.500 0.00 0.00 0.00 3.36
89 90 5.632034 ATTCTACACCTACCCAATCCTTC 57.368 43.478 0.00 0.00 0.00 3.46
90 91 3.028850 TCTACACCTACCCAATCCTTCG 58.971 50.000 0.00 0.00 0.00 3.79
91 92 1.946984 ACACCTACCCAATCCTTCGA 58.053 50.000 0.00 0.00 0.00 3.71
92 93 1.831736 ACACCTACCCAATCCTTCGAG 59.168 52.381 0.00 0.00 0.00 4.04
93 94 1.831736 CACCTACCCAATCCTTCGAGT 59.168 52.381 0.00 0.00 0.00 4.18
94 95 1.831736 ACCTACCCAATCCTTCGAGTG 59.168 52.381 0.00 0.00 33.82 3.51
95 96 2.108168 CCTACCCAATCCTTCGAGTGA 58.892 52.381 0.00 0.00 36.14 3.41
96 97 2.500098 CCTACCCAATCCTTCGAGTGAA 59.500 50.000 0.00 0.00 36.14 3.18
105 106 2.099141 CTTCGAGTGAAGCCATTGGA 57.901 50.000 6.95 0.00 44.70 3.53
106 107 2.426522 CTTCGAGTGAAGCCATTGGAA 58.573 47.619 6.95 0.00 44.70 3.53
107 108 2.559698 TCGAGTGAAGCCATTGGAAA 57.440 45.000 6.95 0.00 0.00 3.13
108 109 3.071874 TCGAGTGAAGCCATTGGAAAT 57.928 42.857 6.95 0.00 0.00 2.17
109 110 3.009723 TCGAGTGAAGCCATTGGAAATC 58.990 45.455 6.95 1.46 0.00 2.17
110 111 3.012518 CGAGTGAAGCCATTGGAAATCT 58.987 45.455 6.95 0.00 0.00 2.40
111 112 3.064545 CGAGTGAAGCCATTGGAAATCTC 59.935 47.826 6.95 6.15 0.00 2.75
112 113 4.012374 GAGTGAAGCCATTGGAAATCTCA 58.988 43.478 6.95 0.00 0.00 3.27
113 114 4.607239 AGTGAAGCCATTGGAAATCTCAT 58.393 39.130 6.95 0.00 0.00 2.90
114 115 5.759059 AGTGAAGCCATTGGAAATCTCATA 58.241 37.500 6.95 0.00 0.00 2.15
115 116 6.371278 AGTGAAGCCATTGGAAATCTCATAT 58.629 36.000 6.95 0.00 0.00 1.78
116 117 6.489361 AGTGAAGCCATTGGAAATCTCATATC 59.511 38.462 6.95 0.00 0.00 1.63
117 118 6.263842 GTGAAGCCATTGGAAATCTCATATCA 59.736 38.462 6.95 0.00 0.00 2.15
118 119 6.489022 TGAAGCCATTGGAAATCTCATATCAG 59.511 38.462 6.95 0.00 0.00 2.90
119 120 5.950023 AGCCATTGGAAATCTCATATCAGT 58.050 37.500 6.95 0.00 0.00 3.41
120 121 6.371278 AGCCATTGGAAATCTCATATCAGTT 58.629 36.000 6.95 0.00 0.00 3.16
121 122 6.489361 AGCCATTGGAAATCTCATATCAGTTC 59.511 38.462 6.95 0.00 0.00 3.01
122 123 6.263842 GCCATTGGAAATCTCATATCAGTTCA 59.736 38.462 6.95 0.00 0.00 3.18
123 124 7.201848 GCCATTGGAAATCTCATATCAGTTCAA 60.202 37.037 6.95 0.00 0.00 2.69
124 125 8.857098 CCATTGGAAATCTCATATCAGTTCAAT 58.143 33.333 0.00 0.00 0.00 2.57
125 126 9.894783 CATTGGAAATCTCATATCAGTTCAATC 57.105 33.333 0.00 0.00 0.00 2.67
126 127 9.636789 ATTGGAAATCTCATATCAGTTCAATCA 57.363 29.630 0.00 0.00 0.00 2.57
127 128 9.465199 TTGGAAATCTCATATCAGTTCAATCAA 57.535 29.630 0.00 0.00 0.00 2.57
128 129 9.636789 TGGAAATCTCATATCAGTTCAATCAAT 57.363 29.630 0.00 0.00 0.00 2.57
139 140 7.806409 TCAGTTCAATCAATTTCTTCAGTGA 57.194 32.000 0.00 0.00 0.00 3.41
140 141 8.224389 TCAGTTCAATCAATTTCTTCAGTGAA 57.776 30.769 5.25 5.25 0.00 3.18
141 142 8.685427 TCAGTTCAATCAATTTCTTCAGTGAAA 58.315 29.630 7.06 0.00 39.79 2.69
142 143 8.965172 CAGTTCAATCAATTTCTTCAGTGAAAG 58.035 33.333 7.06 1.83 39.01 2.62
143 144 8.906867 AGTTCAATCAATTTCTTCAGTGAAAGA 58.093 29.630 7.06 4.19 39.01 2.52
144 145 9.178427 GTTCAATCAATTTCTTCAGTGAAAGAG 57.822 33.333 7.06 0.00 39.01 2.85
145 146 8.681486 TCAATCAATTTCTTCAGTGAAAGAGA 57.319 30.769 7.06 0.00 39.01 3.10
146 147 8.562892 TCAATCAATTTCTTCAGTGAAAGAGAC 58.437 33.333 7.06 0.00 39.01 3.36
147 148 6.530913 TCAATTTCTTCAGTGAAAGAGACG 57.469 37.500 7.06 0.00 39.01 4.18
148 149 6.280643 TCAATTTCTTCAGTGAAAGAGACGA 58.719 36.000 7.06 0.00 39.01 4.20
149 150 6.761242 TCAATTTCTTCAGTGAAAGAGACGAA 59.239 34.615 7.06 3.17 39.01 3.85
150 151 7.442364 TCAATTTCTTCAGTGAAAGAGACGAAT 59.558 33.333 7.06 0.00 39.01 3.34
151 152 8.712363 CAATTTCTTCAGTGAAAGAGACGAATA 58.288 33.333 7.06 0.00 39.01 1.75
152 153 9.442047 AATTTCTTCAGTGAAAGAGACGAATAT 57.558 29.630 7.06 1.21 39.01 1.28
153 154 8.467402 TTTCTTCAGTGAAAGAGACGAATATC 57.533 34.615 7.06 0.00 36.66 1.63
154 155 7.397892 TCTTCAGTGAAAGAGACGAATATCT 57.602 36.000 7.06 0.00 31.71 1.98
155 156 7.831753 TCTTCAGTGAAAGAGACGAATATCTT 58.168 34.615 7.06 0.00 38.03 2.40
224 225 3.837146 TGGAATTGCCAAGCCAAATTCTA 59.163 39.130 10.40 4.29 45.87 2.10
248 249 3.892588 TGTTTGGGGTGGTACAAGATTTC 59.107 43.478 0.00 0.00 44.16 2.17
340 341 1.807573 GACGAGCTCGGAAAGGCTG 60.808 63.158 36.93 9.41 44.95 4.85
433 440 1.227664 CTCGCTCCTGACTCCCCTA 59.772 63.158 0.00 0.00 0.00 3.53
487 515 3.834056 CCGGCCCTCCTCTCCCTA 61.834 72.222 0.00 0.00 0.00 3.53
539 573 0.687757 TCCGTCCCCTCATCCTCTTG 60.688 60.000 0.00 0.00 0.00 3.02
548 583 3.492309 CCCTCATCCTCTTGATCTGTTCG 60.492 52.174 0.00 0.00 0.00 3.95
698 748 6.127479 TGTGAAGCTCTAATTTTTGTGGTGTT 60.127 34.615 0.00 0.00 0.00 3.32
703 753 7.593825 AGCTCTAATTTTTGTGGTGTTCATAC 58.406 34.615 0.00 0.00 0.00 2.39
747 826 4.772624 TGTTCACTGTAGCTCCTTAGATGT 59.227 41.667 0.00 0.00 0.00 3.06
788 867 4.900635 AAGAGCTCGATTTTGTGTGTTT 57.099 36.364 8.37 0.00 0.00 2.83
792 871 5.934625 AGAGCTCGATTTTGTGTGTTTCTAT 59.065 36.000 8.37 0.00 0.00 1.98
828 907 1.668826 ACTATGCAGGTTTCCAGGGA 58.331 50.000 0.00 0.00 0.00 4.20
848 929 7.119387 CAGGGAATTTAGGAGGTCAAATTACT 58.881 38.462 0.00 0.00 35.93 2.24
862 943 2.675658 ATTACTGTGGTGCCAAGGTT 57.324 45.000 0.00 0.00 0.00 3.50
1087 1173 9.906660 GGATATTGTTGACAAAACAGTATTTCA 57.093 29.630 0.10 0.00 39.55 2.69
1364 1450 5.883115 TGTTCTTACAAGTTGTTGGACATGA 59.117 36.000 14.90 0.71 38.07 3.07
1504 1590 1.023719 TCCTTCTATCACCCCTCCCA 58.976 55.000 0.00 0.00 0.00 4.37
1566 1652 4.804261 GCACTAGATGGGTGTCATATTCCC 60.804 50.000 0.00 0.00 41.41 3.97
2174 3361 1.536766 AGCATCACAACAATGGTGACG 59.463 47.619 4.82 0.00 46.99 4.35
2258 3445 5.931724 ACATGTGATGTTGACATTACGAAGA 59.068 36.000 12.49 0.00 43.32 2.87
2562 3754 7.661027 TCATATATTCAAAAGATCATGCGACCA 59.339 33.333 0.00 0.00 0.00 4.02
2639 3831 3.239449 TGTTGAAGAAGCTCCTGAGGTA 58.761 45.455 0.00 0.00 38.35 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.625315 GACCCCCTTTAACAGTACGGT 59.375 52.381 0.00 0.00 0.00 4.83
1 2 1.404583 CGACCCCCTTTAACAGTACGG 60.405 57.143 0.00 0.00 0.00 4.02
2 3 1.545582 TCGACCCCCTTTAACAGTACG 59.454 52.381 0.00 0.00 0.00 3.67
3 4 2.093816 CCTCGACCCCCTTTAACAGTAC 60.094 54.545 0.00 0.00 0.00 2.73
4 5 2.181975 CCTCGACCCCCTTTAACAGTA 58.818 52.381 0.00 0.00 0.00 2.74
6 7 0.981943 ACCTCGACCCCCTTTAACAG 59.018 55.000 0.00 0.00 0.00 3.16
8 9 3.920231 ATTACCTCGACCCCCTTTAAC 57.080 47.619 0.00 0.00 0.00 2.01
9 10 4.623863 AGTATTACCTCGACCCCCTTTAA 58.376 43.478 0.00 0.00 0.00 1.52
10 11 4.270317 AGTATTACCTCGACCCCCTTTA 57.730 45.455 0.00 0.00 0.00 1.85
11 12 3.126323 AGTATTACCTCGACCCCCTTT 57.874 47.619 0.00 0.00 0.00 3.11
12 13 2.862850 AGTATTACCTCGACCCCCTT 57.137 50.000 0.00 0.00 0.00 3.95
13 14 3.437637 CCTTAGTATTACCTCGACCCCCT 60.438 52.174 0.00 0.00 0.00 4.79
14 15 2.896044 CCTTAGTATTACCTCGACCCCC 59.104 54.545 0.00 0.00 0.00 5.40
15 16 3.837355 TCCTTAGTATTACCTCGACCCC 58.163 50.000 0.00 0.00 0.00 4.95
16 17 5.362143 AGTTTCCTTAGTATTACCTCGACCC 59.638 44.000 0.00 0.00 0.00 4.46
17 18 6.096001 TCAGTTTCCTTAGTATTACCTCGACC 59.904 42.308 0.00 0.00 0.00 4.79
18 19 7.093322 TCAGTTTCCTTAGTATTACCTCGAC 57.907 40.000 0.00 0.00 0.00 4.20
19 20 7.893124 ATCAGTTTCCTTAGTATTACCTCGA 57.107 36.000 0.00 0.00 0.00 4.04
20 21 8.943909 AAATCAGTTTCCTTAGTATTACCTCG 57.056 34.615 0.00 0.00 0.00 4.63
35 36 5.048504 TGAGCATCACTTGGAAATCAGTTTC 60.049 40.000 0.00 0.00 42.56 2.78
36 37 4.828939 TGAGCATCACTTGGAAATCAGTTT 59.171 37.500 0.00 0.00 42.56 2.66
37 38 4.401022 TGAGCATCACTTGGAAATCAGTT 58.599 39.130 0.00 0.00 42.56 3.16
38 39 4.025040 TGAGCATCACTTGGAAATCAGT 57.975 40.909 0.00 0.00 42.56 3.41
52 53 6.541641 AGGTGTAGAATTTTGAGATGAGCATC 59.458 38.462 2.27 2.27 38.09 3.91
53 54 6.421485 AGGTGTAGAATTTTGAGATGAGCAT 58.579 36.000 0.00 0.00 0.00 3.79
54 55 5.809001 AGGTGTAGAATTTTGAGATGAGCA 58.191 37.500 0.00 0.00 0.00 4.26
55 56 6.258947 GGTAGGTGTAGAATTTTGAGATGAGC 59.741 42.308 0.00 0.00 0.00 4.26
56 57 6.763610 GGGTAGGTGTAGAATTTTGAGATGAG 59.236 42.308 0.00 0.00 0.00 2.90
57 58 6.214615 TGGGTAGGTGTAGAATTTTGAGATGA 59.785 38.462 0.00 0.00 0.00 2.92
58 59 6.414732 TGGGTAGGTGTAGAATTTTGAGATG 58.585 40.000 0.00 0.00 0.00 2.90
59 60 6.636454 TGGGTAGGTGTAGAATTTTGAGAT 57.364 37.500 0.00 0.00 0.00 2.75
60 61 6.442541 TTGGGTAGGTGTAGAATTTTGAGA 57.557 37.500 0.00 0.00 0.00 3.27
61 62 6.318900 GGATTGGGTAGGTGTAGAATTTTGAG 59.681 42.308 0.00 0.00 0.00 3.02
62 63 6.011981 AGGATTGGGTAGGTGTAGAATTTTGA 60.012 38.462 0.00 0.00 0.00 2.69
63 64 6.187682 AGGATTGGGTAGGTGTAGAATTTTG 58.812 40.000 0.00 0.00 0.00 2.44
64 65 6.402981 AGGATTGGGTAGGTGTAGAATTTT 57.597 37.500 0.00 0.00 0.00 1.82
65 66 6.402981 AAGGATTGGGTAGGTGTAGAATTT 57.597 37.500 0.00 0.00 0.00 1.82
66 67 5.396436 CGAAGGATTGGGTAGGTGTAGAATT 60.396 44.000 0.00 0.00 0.00 2.17
67 68 4.101119 CGAAGGATTGGGTAGGTGTAGAAT 59.899 45.833 0.00 0.00 0.00 2.40
68 69 3.449737 CGAAGGATTGGGTAGGTGTAGAA 59.550 47.826 0.00 0.00 0.00 2.10
69 70 3.028850 CGAAGGATTGGGTAGGTGTAGA 58.971 50.000 0.00 0.00 0.00 2.59
70 71 3.028850 TCGAAGGATTGGGTAGGTGTAG 58.971 50.000 0.00 0.00 0.00 2.74
71 72 3.028850 CTCGAAGGATTGGGTAGGTGTA 58.971 50.000 0.00 0.00 0.00 2.90
72 73 1.831736 CTCGAAGGATTGGGTAGGTGT 59.168 52.381 0.00 0.00 0.00 4.16
73 74 1.831736 ACTCGAAGGATTGGGTAGGTG 59.168 52.381 0.00 0.00 0.00 4.00
74 75 1.831736 CACTCGAAGGATTGGGTAGGT 59.168 52.381 0.00 0.00 0.00 3.08
75 76 2.108168 TCACTCGAAGGATTGGGTAGG 58.892 52.381 0.00 0.00 0.00 3.18
76 77 3.786635 CTTCACTCGAAGGATTGGGTAG 58.213 50.000 0.00 0.00 44.25 3.18
77 78 3.887621 CTTCACTCGAAGGATTGGGTA 57.112 47.619 0.00 0.00 44.25 3.69
78 79 2.770164 CTTCACTCGAAGGATTGGGT 57.230 50.000 0.00 0.00 44.25 4.51
87 88 2.559698 TTCCAATGGCTTCACTCGAA 57.440 45.000 0.00 0.00 0.00 3.71
88 89 2.559698 TTTCCAATGGCTTCACTCGA 57.440 45.000 0.00 0.00 0.00 4.04
89 90 3.012518 AGATTTCCAATGGCTTCACTCG 58.987 45.455 0.00 0.00 0.00 4.18
90 91 4.012374 TGAGATTTCCAATGGCTTCACTC 58.988 43.478 0.00 0.79 0.00 3.51
91 92 4.038271 TGAGATTTCCAATGGCTTCACT 57.962 40.909 0.00 0.00 0.00 3.41
92 93 4.996788 ATGAGATTTCCAATGGCTTCAC 57.003 40.909 0.00 0.00 0.00 3.18
93 94 6.367161 TGATATGAGATTTCCAATGGCTTCA 58.633 36.000 0.00 0.00 0.00 3.02
94 95 6.489361 ACTGATATGAGATTTCCAATGGCTTC 59.511 38.462 0.00 0.00 0.00 3.86
95 96 6.371278 ACTGATATGAGATTTCCAATGGCTT 58.629 36.000 0.00 0.00 0.00 4.35
96 97 5.950023 ACTGATATGAGATTTCCAATGGCT 58.050 37.500 0.00 0.00 0.00 4.75
97 98 6.263842 TGAACTGATATGAGATTTCCAATGGC 59.736 38.462 0.00 0.00 0.00 4.40
98 99 7.812690 TGAACTGATATGAGATTTCCAATGG 57.187 36.000 0.00 0.00 0.00 3.16
99 100 9.894783 GATTGAACTGATATGAGATTTCCAATG 57.105 33.333 0.00 0.00 0.00 2.82
100 101 9.636789 TGATTGAACTGATATGAGATTTCCAAT 57.363 29.630 0.00 0.00 0.00 3.16
101 102 9.465199 TTGATTGAACTGATATGAGATTTCCAA 57.535 29.630 0.00 0.00 0.00 3.53
102 103 9.636789 ATTGATTGAACTGATATGAGATTTCCA 57.363 29.630 0.00 0.00 0.00 3.53
113 114 9.506018 TCACTGAAGAAATTGATTGAACTGATA 57.494 29.630 0.00 0.00 0.00 2.15
114 115 8.400184 TCACTGAAGAAATTGATTGAACTGAT 57.600 30.769 0.00 0.00 0.00 2.90
115 116 7.806409 TCACTGAAGAAATTGATTGAACTGA 57.194 32.000 0.00 0.00 0.00 3.41
116 117 8.861033 TTTCACTGAAGAAATTGATTGAACTG 57.139 30.769 0.00 0.00 32.88 3.16
117 118 8.906867 TCTTTCACTGAAGAAATTGATTGAACT 58.093 29.630 0.00 0.00 36.94 3.01
118 119 9.178427 CTCTTTCACTGAAGAAATTGATTGAAC 57.822 33.333 0.00 0.00 36.94 3.18
119 120 9.123902 TCTCTTTCACTGAAGAAATTGATTGAA 57.876 29.630 0.00 0.00 36.94 2.69
120 121 8.562892 GTCTCTTTCACTGAAGAAATTGATTGA 58.437 33.333 0.00 0.00 36.94 2.57
121 122 7.533222 CGTCTCTTTCACTGAAGAAATTGATTG 59.467 37.037 0.00 0.00 36.94 2.67
122 123 7.442364 TCGTCTCTTTCACTGAAGAAATTGATT 59.558 33.333 0.00 0.00 36.94 2.57
123 124 6.931281 TCGTCTCTTTCACTGAAGAAATTGAT 59.069 34.615 0.00 0.00 36.94 2.57
124 125 6.280643 TCGTCTCTTTCACTGAAGAAATTGA 58.719 36.000 0.00 0.00 36.94 2.57
125 126 6.530913 TCGTCTCTTTCACTGAAGAAATTG 57.469 37.500 0.00 0.00 36.94 2.32
126 127 7.736447 ATTCGTCTCTTTCACTGAAGAAATT 57.264 32.000 0.00 0.00 36.94 1.82
127 128 9.092876 GATATTCGTCTCTTTCACTGAAGAAAT 57.907 33.333 0.00 0.00 36.94 2.17
128 129 8.307483 AGATATTCGTCTCTTTCACTGAAGAAA 58.693 33.333 0.00 0.00 35.38 2.52
129 130 7.831753 AGATATTCGTCTCTTTCACTGAAGAA 58.168 34.615 0.00 0.00 35.38 2.52
130 131 7.397892 AGATATTCGTCTCTTTCACTGAAGA 57.602 36.000 0.00 0.00 34.63 2.87
131 132 7.973388 AGAAGATATTCGTCTCTTTCACTGAAG 59.027 37.037 0.00 0.00 29.23 3.02
132 133 7.831753 AGAAGATATTCGTCTCTTTCACTGAA 58.168 34.615 0.00 0.00 29.23 3.02
133 134 7.397892 AGAAGATATTCGTCTCTTTCACTGA 57.602 36.000 0.00 0.00 29.23 3.41
134 135 8.184848 TGTAGAAGATATTCGTCTCTTTCACTG 58.815 37.037 0.00 0.00 36.62 3.66
135 136 8.185505 GTGTAGAAGATATTCGTCTCTTTCACT 58.814 37.037 0.00 0.00 36.62 3.41
136 137 7.432838 GGTGTAGAAGATATTCGTCTCTTTCAC 59.567 40.741 0.00 3.97 36.62 3.18
137 138 7.416438 GGGTGTAGAAGATATTCGTCTCTTTCA 60.416 40.741 0.00 0.00 36.62 2.69
138 139 6.919115 GGGTGTAGAAGATATTCGTCTCTTTC 59.081 42.308 0.00 0.00 36.62 2.62
139 140 6.608002 AGGGTGTAGAAGATATTCGTCTCTTT 59.392 38.462 0.00 0.00 36.62 2.52
140 141 6.039941 CAGGGTGTAGAAGATATTCGTCTCTT 59.960 42.308 0.00 0.00 36.62 2.85
141 142 5.533154 CAGGGTGTAGAAGATATTCGTCTCT 59.467 44.000 0.00 0.00 36.62 3.10
142 143 5.299782 ACAGGGTGTAGAAGATATTCGTCTC 59.700 44.000 0.00 0.00 36.62 3.36
143 144 5.202004 ACAGGGTGTAGAAGATATTCGTCT 58.798 41.667 0.00 0.00 38.67 4.18
144 145 5.517322 ACAGGGTGTAGAAGATATTCGTC 57.483 43.478 0.00 0.00 0.00 4.20
145 146 5.934402 AACAGGGTGTAGAAGATATTCGT 57.066 39.130 0.00 0.00 0.00 3.85
146 147 5.523916 CCAAACAGGGTGTAGAAGATATTCG 59.476 44.000 0.00 0.00 0.00 3.34
147 148 6.650120 TCCAAACAGGGTGTAGAAGATATTC 58.350 40.000 0.00 0.00 38.24 1.75
148 149 6.636454 TCCAAACAGGGTGTAGAAGATATT 57.364 37.500 0.00 0.00 38.24 1.28
149 150 6.595682 CATCCAAACAGGGTGTAGAAGATAT 58.404 40.000 0.00 0.00 43.99 1.63
150 151 5.989477 CATCCAAACAGGGTGTAGAAGATA 58.011 41.667 0.00 0.00 43.99 1.98
151 152 4.848357 CATCCAAACAGGGTGTAGAAGAT 58.152 43.478 0.00 0.00 43.99 2.40
152 153 4.286297 CATCCAAACAGGGTGTAGAAGA 57.714 45.455 0.00 0.00 43.99 2.87
224 225 3.603965 TCTTGTACCACCCCAAACAAT 57.396 42.857 0.00 0.00 31.88 2.71
248 249 1.006220 GGCCAAGTTTTCCAAGCCG 60.006 57.895 0.00 0.00 0.00 5.52
433 440 3.660111 GCTGTCGCCGGTTGCTTT 61.660 61.111 1.90 0.00 38.05 3.51
460 488 1.375326 GAGGGCCGGAGAACAAACT 59.625 57.895 5.05 0.00 0.00 2.66
487 515 2.691252 GGAAGGGACGGATGGGGT 60.691 66.667 0.00 0.00 0.00 4.95
539 573 2.537560 CCATGGCCGCGAACAGATC 61.538 63.158 8.23 0.00 0.00 2.75
548 583 4.778143 AGGTCGTTCCATGGCCGC 62.778 66.667 6.96 7.98 39.02 6.53
660 709 1.537889 TTCACACGGAGGGGATGGT 60.538 57.895 0.00 0.00 0.00 3.55
698 748 7.876068 ACCACAAAAATTCTAGTTCTCGTATGA 59.124 33.333 0.00 0.00 0.00 2.15
703 753 6.300354 ACACCACAAAAATTCTAGTTCTCG 57.700 37.500 0.00 0.00 0.00 4.04
747 826 6.627508 GCTCTTAAATTCGAGGAACTGGACTA 60.628 42.308 0.00 0.00 44.43 2.59
792 871 8.892723 CCTGCATAGTTCAAACAAATCATACTA 58.107 33.333 0.00 0.00 0.00 1.82
828 907 7.176690 CACCACAGTAATTTGACCTCCTAAATT 59.823 37.037 0.00 0.00 39.21 1.82
848 929 4.929479 AGATAATAAACCTTGGCACCACA 58.071 39.130 0.00 0.00 0.00 4.17
1077 1163 8.454106 GCTAGACATGACATTTTGAAATACTGT 58.546 33.333 0.00 0.00 0.00 3.55
1087 1173 5.097529 CGCAAATGCTAGACATGACATTTT 58.902 37.500 0.00 0.00 39.92 1.82
1364 1450 5.245977 CCACCCAACATCCTCATTTTAAGTT 59.754 40.000 0.00 0.00 0.00 2.66
1504 1590 6.976934 AAACCACTTCCACTTGTAATCATT 57.023 33.333 0.00 0.00 0.00 2.57
1566 1652 2.973224 GTCAGCAGCATTAACAAACACG 59.027 45.455 0.00 0.00 0.00 4.49
1678 1764 0.613777 GATGACGAACCCTCCCAACT 59.386 55.000 0.00 0.00 0.00 3.16
2115 3302 1.627864 TGTCGTGTCCATCTCAGGAA 58.372 50.000 0.00 0.00 39.92 3.36
2174 3361 3.256558 GCTTCCAACCATTTTGAGCATC 58.743 45.455 0.00 0.00 0.00 3.91
2258 3445 9.883142 TGTTTTGATTCTTCCTGTTATGTTTTT 57.117 25.926 0.00 0.00 0.00 1.94
2562 3754 1.062886 TCCTATCCTAGCACCTGCACT 60.063 52.381 0.00 0.00 45.16 4.40


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

AutoCloner maintained by Alex Coulton.