Multiple sequence alignment - TraesCS4D01G115800

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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 TraesCS4D01G115800 chr4D 100.000 3311 0 0 1 3311 96891462 96894772 0.000000e+00 6115.0
1 TraesCS4D01G115800 chr4D 91.392 2428 146 22 176 2565 96711285 96713687 0.000000e+00 3267.0
2 TraesCS4D01G115800 chr4A 96.018 2813 78 9 233 3032 481065533 481062742 0.000000e+00 4543.0
3 TraesCS4D01G115800 chr4A 92.212 2337 153 13 250 2565 479625496 479623168 0.000000e+00 3280.0
4 TraesCS4D01G115800 chr4A 91.185 2303 153 24 230 2507 479904303 479902026 0.000000e+00 3083.0
5 TraesCS4D01G115800 chr4A 91.582 1972 128 16 614 2565 480558132 480556179 0.000000e+00 2687.0
6 TraesCS4D01G115800 chr4A 91.028 1917 135 13 614 2511 479431440 479429542 0.000000e+00 2553.0
7 TraesCS4D01G115800 chr4A 91.489 705 40 10 230 933 479647838 479647153 0.000000e+00 952.0
8 TraesCS4D01G115800 chr4A 88.827 537 49 7 2033 2564 479620970 479620440 0.000000e+00 649.0
9 TraesCS4D01G115800 chr4A 94.085 355 18 3 230 583 479431787 479431435 1.350000e-148 536.0
10 TraesCS4D01G115800 chr4A 93.803 355 19 3 230 583 480558479 480558127 6.290000e-147 531.0
11 TraesCS4D01G115800 chr4A 97.458 236 5 1 3076 3311 481062242 481062008 5.150000e-108 401.0
12 TraesCS4D01G115800 chr4A 90.213 235 17 2 3077 3311 479428792 479428564 5.370000e-78 302.0
13 TraesCS4D01G115800 chr4A 87.288 236 13 2 3076 3311 479614529 479614311 1.520000e-63 254.0
14 TraesCS4D01G115800 chr4A 89.944 179 11 2 3076 3254 479900658 479900487 1.200000e-54 224.0
15 TraesCS4D01G115800 chr4A 89.444 180 13 3 3075 3254 480555162 480554989 4.300000e-54 222.0
16 TraesCS4D01G115800 chr4A 96.875 64 2 0 378 441 479647156 479647093 1.260000e-19 108.0
17 TraesCS4D01G115800 chr4A 100.000 30 0 0 3280 3309 480554989 480554960 4.620000e-04 56.5
18 TraesCS4D01G115800 chr4B 88.648 2308 179 30 224 2507 137701669 137703917 0.000000e+00 2734.0
19 TraesCS4D01G115800 chr4B 90.473 1480 118 8 1051 2511 138276147 138277622 0.000000e+00 1930.0
20 TraesCS4D01G115800 chr4B 90.930 430 22 10 627 1055 138275810 138276223 2.230000e-156 562.0
21 TraesCS4D01G115800 chr4B 91.949 236 14 2 3076 3311 137705193 137705423 3.190000e-85 326.0
22 TraesCS4D01G115800 chr4B 90.123 162 10 2 3079 3240 138278172 138278327 4.330000e-49 206.0
23 TraesCS4D01G115800 chr4B 90.566 106 10 0 3169 3274 137705836 137705941 1.240000e-29 141.0
24 TraesCS4D01G115800 chr4B 91.250 80 7 0 3161 3240 138278791 138278870 3.490000e-20 110.0
25 TraesCS4D01G115800 chr4B 97.727 44 1 0 3268 3311 138278335 138278378 3.540000e-10 76.8
26 TraesCS4D01G115800 chr7A 86.304 1285 148 16 1051 2315 79335044 79333768 0.000000e+00 1373.0


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 TraesCS4D01G115800 chr4D 96891462 96894772 3310 False 6115.000000 6115 100.000000 1 3311 1 chr4D.!!$F2 3310
1 TraesCS4D01G115800 chr4D 96711285 96713687 2402 False 3267.000000 3267 91.392000 176 2565 1 chr4D.!!$F1 2389
2 TraesCS4D01G115800 chr4A 481062008 481065533 3525 True 2472.000000 4543 96.738000 233 3311 2 chr4A.!!$R7 3078
3 TraesCS4D01G115800 chr4A 479620440 479625496 5056 True 1964.500000 3280 90.519500 250 2565 2 chr4A.!!$R3 2315
4 TraesCS4D01G115800 chr4A 479900487 479904303 3816 True 1653.500000 3083 90.564500 230 3254 2 chr4A.!!$R5 3024
5 TraesCS4D01G115800 chr4A 479428564 479431787 3223 True 1130.333333 2553 91.775333 230 3311 3 chr4A.!!$R2 3081
6 TraesCS4D01G115800 chr4A 480554960 480558479 3519 True 874.125000 2687 93.707250 230 3309 4 chr4A.!!$R6 3079
7 TraesCS4D01G115800 chr4A 479647093 479647838 745 True 530.000000 952 94.182000 230 933 2 chr4A.!!$R4 703
8 TraesCS4D01G115800 chr4B 137701669 137705941 4272 False 1067.000000 2734 90.387667 224 3311 3 chr4B.!!$F1 3087
9 TraesCS4D01G115800 chr4B 138275810 138278870 3060 False 576.960000 1930 92.100600 627 3311 5 chr4B.!!$F2 2684
10 TraesCS4D01G115800 chr7A 79333768 79335044 1276 True 1373.000000 1373 86.304000 1051 2315 1 chr7A.!!$R1 1264

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
443 461 0.178861 AATCTCACCACCCCTCCTGT 60.179 55.000 0.00 0.0 0.0 4.00 F
459 477 1.142060 CCTGTATCCCATTTACCGCCA 59.858 52.381 0.00 0.0 0.0 5.69 F
461 479 1.223187 GTATCCCATTTACCGCCACG 58.777 55.000 0.00 0.0 0.0 4.94 F
1554 1576 0.815734 ACCAACTGTACGATCCGGAG 59.184 55.000 11.34 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 1420 0.108424 GCTCAGACTTGTCATCCGCT 60.108 55.000 3.49 0.0 0.00 5.52 R
1554 1576 3.870274 ACTTAACATTTCGGGCTCTACC 58.130 45.455 0.00 0.0 37.93 3.18 R
2213 2253 5.308237 AGCGGAGATACAATTTCTTCCCTAT 59.692 40.000 0.00 0.0 0.00 2.57 R
3039 3786 0.260816 AGCAAGATGGATGGCATGGT 59.739 50.000 3.81 0.0 0.00 3.55 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
35 36 4.830765 GCCACCGGCGCATAGACA 62.831 66.667 10.83 0.00 39.62 3.41
36 37 2.586079 CCACCGGCGCATAGACAG 60.586 66.667 10.83 0.00 0.00 3.51
37 38 2.586079 CACCGGCGCATAGACAGG 60.586 66.667 10.83 2.75 0.00 4.00
38 39 4.530857 ACCGGCGCATAGACAGGC 62.531 66.667 10.83 0.00 0.00 4.85
39 40 4.529219 CCGGCGCATAGACAGGCA 62.529 66.667 10.83 0.00 0.00 4.75
40 41 3.264897 CGGCGCATAGACAGGCAC 61.265 66.667 10.83 0.00 0.00 5.01
41 42 2.125147 GGCGCATAGACAGGCACA 60.125 61.111 10.83 0.00 0.00 4.57
42 43 2.464459 GGCGCATAGACAGGCACAC 61.464 63.158 10.83 0.00 0.00 3.82
43 44 2.802667 GCGCATAGACAGGCACACG 61.803 63.158 0.30 0.00 0.00 4.49
44 45 2.802667 CGCATAGACAGGCACACGC 61.803 63.158 0.00 0.00 37.44 5.34
59 60 4.803908 CGCCCTGCCCTTCCCTTC 62.804 72.222 0.00 0.00 0.00 3.46
60 61 4.448976 GCCCTGCCCTTCCCTTCC 62.449 72.222 0.00 0.00 0.00 3.46
61 62 3.744155 CCCTGCCCTTCCCTTCCC 61.744 72.222 0.00 0.00 0.00 3.97
62 63 2.615288 CCTGCCCTTCCCTTCCCT 60.615 66.667 0.00 0.00 0.00 4.20
63 64 2.241659 CCTGCCCTTCCCTTCCCTT 61.242 63.158 0.00 0.00 0.00 3.95
64 65 1.304617 CTGCCCTTCCCTTCCCTTC 59.695 63.158 0.00 0.00 0.00 3.46
65 66 2.216782 CTGCCCTTCCCTTCCCTTCC 62.217 65.000 0.00 0.00 0.00 3.46
66 67 1.931180 GCCCTTCCCTTCCCTTCCT 60.931 63.158 0.00 0.00 0.00 3.36
67 68 2.002625 CCCTTCCCTTCCCTTCCTG 58.997 63.158 0.00 0.00 0.00 3.86
68 69 0.846870 CCCTTCCCTTCCCTTCCTGT 60.847 60.000 0.00 0.00 0.00 4.00
69 70 0.621082 CCTTCCCTTCCCTTCCTGTC 59.379 60.000 0.00 0.00 0.00 3.51
70 71 1.362224 CTTCCCTTCCCTTCCTGTCA 58.638 55.000 0.00 0.00 0.00 3.58
71 72 1.003696 CTTCCCTTCCCTTCCTGTCAC 59.996 57.143 0.00 0.00 0.00 3.67
72 73 0.193574 TCCCTTCCCTTCCTGTCACT 59.806 55.000 0.00 0.00 0.00 3.41
73 74 0.326264 CCCTTCCCTTCCTGTCACTG 59.674 60.000 0.00 0.00 0.00 3.66
74 75 1.352083 CCTTCCCTTCCTGTCACTGA 58.648 55.000 0.00 0.00 0.00 3.41
75 76 1.002544 CCTTCCCTTCCTGTCACTGAC 59.997 57.143 1.86 1.86 0.00 3.51
76 77 1.694150 CTTCCCTTCCTGTCACTGACA 59.306 52.381 11.44 11.44 40.50 3.58
84 85 2.048127 GTCACTGACAGCGGGTCC 60.048 66.667 1.25 0.00 46.38 4.46
85 86 2.203640 TCACTGACAGCGGGTCCT 60.204 61.111 1.25 0.00 46.38 3.85
86 87 1.076014 TCACTGACAGCGGGTCCTA 59.924 57.895 1.25 0.00 46.38 2.94
87 88 1.215647 CACTGACAGCGGGTCCTAC 59.784 63.158 1.25 0.00 46.38 3.18
88 89 2.341101 ACTGACAGCGGGTCCTACG 61.341 63.158 1.25 0.00 46.38 3.51
95 96 2.660802 CGGGTCCTACGCCAAACT 59.339 61.111 0.00 0.00 0.00 2.66
96 97 1.740296 CGGGTCCTACGCCAAACTG 60.740 63.158 0.00 0.00 0.00 3.16
97 98 1.675219 GGGTCCTACGCCAAACTGA 59.325 57.895 0.00 0.00 0.00 3.41
98 99 0.672711 GGGTCCTACGCCAAACTGAC 60.673 60.000 0.00 0.00 0.00 3.51
99 100 1.012486 GGTCCTACGCCAAACTGACG 61.012 60.000 0.00 0.00 0.00 4.35
100 101 0.319297 GTCCTACGCCAAACTGACGT 60.319 55.000 0.00 0.00 43.45 4.34
101 102 0.319211 TCCTACGCCAAACTGACGTG 60.319 55.000 0.00 0.00 40.78 4.49
102 103 0.319211 CCTACGCCAAACTGACGTGA 60.319 55.000 0.00 0.00 40.78 4.35
103 104 0.782384 CTACGCCAAACTGACGTGAC 59.218 55.000 0.00 0.00 40.78 3.67
104 105 0.386476 TACGCCAAACTGACGTGACT 59.614 50.000 0.00 0.00 40.78 3.41
105 106 0.461339 ACGCCAAACTGACGTGACTT 60.461 50.000 0.00 0.00 38.85 3.01
106 107 1.202440 ACGCCAAACTGACGTGACTTA 60.202 47.619 0.00 0.00 38.85 2.24
107 108 1.455786 CGCCAAACTGACGTGACTTAG 59.544 52.381 0.00 0.00 0.00 2.18
108 109 1.798813 GCCAAACTGACGTGACTTAGG 59.201 52.381 0.00 0.00 0.00 2.69
109 110 2.805657 GCCAAACTGACGTGACTTAGGT 60.806 50.000 0.00 0.00 0.00 3.08
110 111 2.800544 CCAAACTGACGTGACTTAGGTG 59.199 50.000 0.00 0.00 0.00 4.00
111 112 3.454375 CAAACTGACGTGACTTAGGTGT 58.546 45.455 0.00 0.00 0.00 4.16
112 113 2.795175 ACTGACGTGACTTAGGTGTG 57.205 50.000 0.00 0.00 0.00 3.82
113 114 2.029623 ACTGACGTGACTTAGGTGTGT 58.970 47.619 0.00 0.00 0.00 3.72
114 115 3.216800 ACTGACGTGACTTAGGTGTGTA 58.783 45.455 0.00 0.00 0.00 2.90
115 116 3.004106 ACTGACGTGACTTAGGTGTGTAC 59.996 47.826 0.00 0.00 0.00 2.90
116 117 2.950975 TGACGTGACTTAGGTGTGTACA 59.049 45.455 0.00 0.00 0.00 2.90
117 118 3.380954 TGACGTGACTTAGGTGTGTACAA 59.619 43.478 0.00 0.00 0.00 2.41
118 119 3.709987 ACGTGACTTAGGTGTGTACAAC 58.290 45.455 0.00 0.00 0.00 3.32
119 120 3.130869 ACGTGACTTAGGTGTGTACAACA 59.869 43.478 0.00 0.00 35.62 3.33
120 121 4.202182 ACGTGACTTAGGTGTGTACAACAT 60.202 41.667 0.00 0.00 41.97 2.71
121 122 4.384846 CGTGACTTAGGTGTGTACAACATC 59.615 45.833 0.00 0.00 41.97 3.06
122 123 4.384846 GTGACTTAGGTGTGTACAACATCG 59.615 45.833 0.00 0.00 45.29 3.84
123 124 4.038282 TGACTTAGGTGTGTACAACATCGT 59.962 41.667 0.00 0.00 45.29 3.73
124 125 5.241285 TGACTTAGGTGTGTACAACATCGTA 59.759 40.000 0.00 0.00 45.29 3.43
125 126 6.071784 TGACTTAGGTGTGTACAACATCGTAT 60.072 38.462 0.00 0.00 45.29 3.06
126 127 6.694447 ACTTAGGTGTGTACAACATCGTATT 58.306 36.000 0.00 0.00 45.29 1.89
127 128 7.156673 ACTTAGGTGTGTACAACATCGTATTT 58.843 34.615 0.00 0.00 45.29 1.40
128 129 8.306038 ACTTAGGTGTGTACAACATCGTATTTA 58.694 33.333 0.00 0.00 45.29 1.40
129 130 6.956299 AGGTGTGTACAACATCGTATTTAC 57.044 37.500 0.00 0.00 45.29 2.01
130 131 6.457355 AGGTGTGTACAACATCGTATTTACA 58.543 36.000 0.00 0.00 45.29 2.41
131 132 6.366877 AGGTGTGTACAACATCGTATTTACAC 59.633 38.462 0.00 0.00 45.29 2.90
132 133 6.366877 GGTGTGTACAACATCGTATTTACACT 59.633 38.462 0.00 0.00 41.97 3.55
133 134 7.224710 GTGTGTACAACATCGTATTTACACTG 58.775 38.462 0.00 0.00 41.97 3.66
134 135 6.924612 TGTGTACAACATCGTATTTACACTGT 59.075 34.615 0.00 0.00 39.89 3.55
135 136 7.438757 TGTGTACAACATCGTATTTACACTGTT 59.561 33.333 0.00 0.00 39.89 3.16
136 137 8.914654 GTGTACAACATCGTATTTACACTGTTA 58.085 33.333 0.00 0.00 37.43 2.41
137 138 9.473640 TGTACAACATCGTATTTACACTGTTAA 57.526 29.630 0.00 0.00 32.56 2.01
140 141 8.284693 ACAACATCGTATTTACACTGTTAAACC 58.715 33.333 0.00 0.00 32.56 3.27
141 142 7.966246 ACATCGTATTTACACTGTTAAACCA 57.034 32.000 0.00 0.00 0.00 3.67
142 143 8.380743 ACATCGTATTTACACTGTTAAACCAA 57.619 30.769 0.00 0.00 0.00 3.67
143 144 8.500773 ACATCGTATTTACACTGTTAAACCAAG 58.499 33.333 0.00 0.00 0.00 3.61
144 145 8.500773 CATCGTATTTACACTGTTAAACCAAGT 58.499 33.333 0.00 0.00 0.00 3.16
145 146 8.436046 TCGTATTTACACTGTTAAACCAAGTT 57.564 30.769 0.00 0.00 0.00 2.66
146 147 8.550376 TCGTATTTACACTGTTAAACCAAGTTC 58.450 33.333 0.00 0.00 0.00 3.01
147 148 8.553696 CGTATTTACACTGTTAAACCAAGTTCT 58.446 33.333 0.00 0.00 0.00 3.01
153 154 7.541162 ACACTGTTAAACCAAGTTCTTAAACC 58.459 34.615 0.00 0.00 35.92 3.27
154 155 7.177041 ACACTGTTAAACCAAGTTCTTAAACCA 59.823 33.333 0.00 0.00 35.92 3.67
155 156 8.194769 CACTGTTAAACCAAGTTCTTAAACCAT 58.805 33.333 0.00 0.00 35.92 3.55
156 157 8.755028 ACTGTTAAACCAAGTTCTTAAACCATT 58.245 29.630 0.00 0.00 35.92 3.16
157 158 9.594478 CTGTTAAACCAAGTTCTTAAACCATTT 57.406 29.630 0.00 0.00 35.92 2.32
216 217 6.874134 ACTGTTATGCCAAGTTCTAACACTAG 59.126 38.462 0.00 0.00 32.35 2.57
217 218 6.765403 TGTTATGCCAAGTTCTAACACTAGT 58.235 36.000 0.00 0.00 31.14 2.57
257 271 4.193380 GCGCGAAAGTTTTCAAATCAAAC 58.807 39.130 12.10 0.00 37.01 2.93
324 341 1.153628 GGTCGCATAACTGACGCCT 60.154 57.895 0.00 0.00 35.95 5.52
443 461 0.178861 AATCTCACCACCCCTCCTGT 60.179 55.000 0.00 0.00 0.00 4.00
459 477 1.142060 CCTGTATCCCATTTACCGCCA 59.858 52.381 0.00 0.00 0.00 5.69
461 479 1.223187 GTATCCCATTTACCGCCACG 58.777 55.000 0.00 0.00 0.00 4.94
562 580 1.743394 CGGGCAATTAGTTGGTTCTCC 59.257 52.381 0.00 0.00 35.83 3.71
798 820 5.669477 GGTGTGCTTCTTCTCAGATTAGAT 58.331 41.667 0.00 0.00 0.00 1.98
799 821 6.460261 CGGTGTGCTTCTTCTCAGATTAGATA 60.460 42.308 0.00 0.00 0.00 1.98
800 822 6.699642 GGTGTGCTTCTTCTCAGATTAGATAC 59.300 42.308 0.00 0.00 0.00 2.24
801 823 7.417342 GGTGTGCTTCTTCTCAGATTAGATACT 60.417 40.741 0.00 0.00 0.00 2.12
802 824 8.625651 GTGTGCTTCTTCTCAGATTAGATACTA 58.374 37.037 0.00 0.00 0.00 1.82
803 825 8.625651 TGTGCTTCTTCTCAGATTAGATACTAC 58.374 37.037 0.00 0.00 0.00 2.73
804 826 8.846211 GTGCTTCTTCTCAGATTAGATACTACT 58.154 37.037 0.00 0.00 0.00 2.57
805 827 9.062524 TGCTTCTTCTCAGATTAGATACTACTC 57.937 37.037 0.00 0.00 0.00 2.59
806 828 8.512138 GCTTCTTCTCAGATTAGATACTACTCC 58.488 40.741 0.00 0.00 0.00 3.85
1065 1087 6.472715 GCAGGATGTATTGAGAAAGGTCTCG 61.473 48.000 0.00 0.00 46.06 4.04
1398 1420 4.019771 TCATCACATGGTTGGCTAGTTACA 60.020 41.667 0.00 0.00 0.00 2.41
1554 1576 0.815734 ACCAACTGTACGATCCGGAG 59.184 55.000 11.34 0.00 0.00 4.63
1575 1612 3.518303 AGGTAGAGCCCGAAATGTTAAGT 59.482 43.478 0.00 0.00 38.26 2.24
1918 1955 3.099170 AGGCTCCATGGGGCGATT 61.099 61.111 30.12 15.48 0.00 3.34
2213 2253 5.763204 GTGTTCTTAACCTGGAAGATGACAA 59.237 40.000 0.00 0.00 34.07 3.18
2348 2388 1.917568 TGTACCTTGGTTATGGGGTCC 59.082 52.381 0.00 0.00 33.74 4.46
2581 2683 9.548631 TTGTTTGATATTTTCCCCCTTATAACA 57.451 29.630 0.00 0.00 0.00 2.41
2747 3051 2.421073 AGCCATTGAACGTGACATCATG 59.579 45.455 0.00 0.00 38.76 3.07
2802 3537 3.433598 GCAGTTGCTAATCCCTGTCCATA 60.434 47.826 0.00 0.00 38.21 2.74
2949 3696 9.915629 TCTCACTAGAAACAGTTTAGAATCTTC 57.084 33.333 0.00 0.00 0.00 2.87
2957 3704 9.617975 GAAACAGTTTAGAATCTTCAATTCAGG 57.382 33.333 0.00 0.00 0.00 3.86
3024 3771 2.287129 ACATGTAACGGTGGCGTTTTTC 60.287 45.455 0.00 0.00 33.80 2.29
3028 3775 1.449726 AACGGTGGCGTTTTTCCCTC 61.450 55.000 0.00 0.00 0.00 4.30
3029 3776 1.894756 CGGTGGCGTTTTTCCCTCA 60.895 57.895 0.00 0.00 0.00 3.86
3030 3777 1.241315 CGGTGGCGTTTTTCCCTCAT 61.241 55.000 0.00 0.00 0.00 2.90
3032 3779 1.336795 GGTGGCGTTTTTCCCTCATTG 60.337 52.381 0.00 0.00 0.00 2.82
3035 3782 2.035321 TGGCGTTTTTCCCTCATTGAAC 59.965 45.455 0.00 0.00 0.00 3.18
3037 3784 3.243737 GGCGTTTTTCCCTCATTGAACTT 60.244 43.478 0.00 0.00 0.00 2.66
3038 3785 4.368315 GCGTTTTTCCCTCATTGAACTTT 58.632 39.130 0.00 0.00 0.00 2.66
3039 3786 5.508320 GGCGTTTTTCCCTCATTGAACTTTA 60.508 40.000 0.00 0.00 0.00 1.85
3040 3787 5.401376 GCGTTTTTCCCTCATTGAACTTTAC 59.599 40.000 0.00 0.00 0.00 2.01
3041 3788 5.918576 CGTTTTTCCCTCATTGAACTTTACC 59.081 40.000 0.00 0.00 0.00 2.85
3042 3789 6.460399 CGTTTTTCCCTCATTGAACTTTACCA 60.460 38.462 0.00 0.00 0.00 3.25
3043 3790 7.441836 GTTTTTCCCTCATTGAACTTTACCAT 58.558 34.615 0.00 0.00 0.00 3.55
3044 3791 6.588719 TTTCCCTCATTGAACTTTACCATG 57.411 37.500 0.00 0.00 0.00 3.66
3045 3792 4.016444 TCCCTCATTGAACTTTACCATGC 58.984 43.478 0.00 0.00 0.00 4.06
3046 3793 3.131046 CCCTCATTGAACTTTACCATGCC 59.869 47.826 0.00 0.00 0.00 4.40
3047 3794 3.763360 CCTCATTGAACTTTACCATGCCA 59.237 43.478 0.00 0.00 0.00 4.92
3048 3795 4.403432 CCTCATTGAACTTTACCATGCCAT 59.597 41.667 0.00 0.00 0.00 4.40
3049 3796 5.450965 CCTCATTGAACTTTACCATGCCATC 60.451 44.000 0.00 0.00 0.00 3.51
3050 3797 4.402155 TCATTGAACTTTACCATGCCATCC 59.598 41.667 0.00 0.00 0.00 3.51
3051 3798 3.448093 TGAACTTTACCATGCCATCCA 57.552 42.857 0.00 0.00 0.00 3.41
3052 3799 3.979911 TGAACTTTACCATGCCATCCAT 58.020 40.909 0.00 0.00 33.39 3.41
3054 3801 3.959495 ACTTTACCATGCCATCCATCT 57.041 42.857 0.00 0.00 29.71 2.90
3055 3802 4.255510 ACTTTACCATGCCATCCATCTT 57.744 40.909 0.00 0.00 29.71 2.40
3056 3803 3.956199 ACTTTACCATGCCATCCATCTTG 59.044 43.478 0.00 0.00 29.71 3.02
3057 3804 1.985473 TACCATGCCATCCATCTTGC 58.015 50.000 0.00 0.00 29.71 4.01
3059 3806 1.496001 ACCATGCCATCCATCTTGCTA 59.504 47.619 0.00 0.00 29.71 3.49
3061 3808 2.578786 CATGCCATCCATCTTGCTACA 58.421 47.619 0.00 0.00 29.71 2.74
3065 3812 4.582869 TGCCATCCATCTTGCTACATATC 58.417 43.478 0.00 0.00 0.00 1.63
3066 3813 4.287845 TGCCATCCATCTTGCTACATATCT 59.712 41.667 0.00 0.00 0.00 1.98
3068 3815 4.634883 CCATCCATCTTGCTACATATCTGC 59.365 45.833 0.00 0.00 0.00 4.26
3069 3816 4.277515 TCCATCTTGCTACATATCTGCC 57.722 45.455 0.00 0.00 0.00 4.85
3070 3817 3.647590 TCCATCTTGCTACATATCTGCCA 59.352 43.478 0.00 0.00 0.00 4.92
3071 3818 4.287845 TCCATCTTGCTACATATCTGCCAT 59.712 41.667 0.00 0.00 0.00 4.40
3073 3820 4.961438 TCTTGCTACATATCTGCCATGA 57.039 40.909 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.830765 TGTCTATGCGCCGGTGGC 62.831 66.667 18.41 14.87 46.75 5.01
19 20 2.586079 CTGTCTATGCGCCGGTGG 60.586 66.667 18.41 3.39 0.00 4.61
20 21 2.586079 CCTGTCTATGCGCCGGTG 60.586 66.667 11.67 11.67 0.00 4.94
21 22 4.530857 GCCTGTCTATGCGCCGGT 62.531 66.667 4.18 0.00 0.00 5.28
22 23 4.529219 TGCCTGTCTATGCGCCGG 62.529 66.667 4.18 0.00 0.00 6.13
23 24 3.264897 GTGCCTGTCTATGCGCCG 61.265 66.667 4.18 0.00 31.95 6.46
24 25 2.125147 TGTGCCTGTCTATGCGCC 60.125 61.111 4.18 0.00 37.19 6.53
25 26 2.802667 CGTGTGCCTGTCTATGCGC 61.803 63.158 0.00 0.00 38.44 6.09
26 27 2.802667 GCGTGTGCCTGTCTATGCG 61.803 63.158 0.00 0.00 33.98 4.73
27 28 3.093278 GCGTGTGCCTGTCTATGC 58.907 61.111 0.00 0.00 33.98 3.14
42 43 4.803908 GAAGGGAAGGGCAGGGCG 62.804 72.222 0.00 0.00 0.00 6.13
43 44 4.448976 GGAAGGGAAGGGCAGGGC 62.449 72.222 0.00 0.00 0.00 5.19
44 45 3.744155 GGGAAGGGAAGGGCAGGG 61.744 72.222 0.00 0.00 0.00 4.45
45 46 2.216782 GAAGGGAAGGGAAGGGCAGG 62.217 65.000 0.00 0.00 0.00 4.85
46 47 1.304617 GAAGGGAAGGGAAGGGCAG 59.695 63.158 0.00 0.00 0.00 4.85
47 48 2.238701 GGAAGGGAAGGGAAGGGCA 61.239 63.158 0.00 0.00 0.00 5.36
48 49 1.931180 AGGAAGGGAAGGGAAGGGC 60.931 63.158 0.00 0.00 0.00 5.19
49 50 0.846870 ACAGGAAGGGAAGGGAAGGG 60.847 60.000 0.00 0.00 0.00 3.95
50 51 0.621082 GACAGGAAGGGAAGGGAAGG 59.379 60.000 0.00 0.00 0.00 3.46
51 52 1.003696 GTGACAGGAAGGGAAGGGAAG 59.996 57.143 0.00 0.00 0.00 3.46
52 53 1.064825 GTGACAGGAAGGGAAGGGAA 58.935 55.000 0.00 0.00 0.00 3.97
53 54 0.193574 AGTGACAGGAAGGGAAGGGA 59.806 55.000 0.00 0.00 0.00 4.20
54 55 0.326264 CAGTGACAGGAAGGGAAGGG 59.674 60.000 0.00 0.00 0.00 3.95
55 56 1.002544 GTCAGTGACAGGAAGGGAAGG 59.997 57.143 18.54 0.00 32.09 3.46
56 57 1.694150 TGTCAGTGACAGGAAGGGAAG 59.306 52.381 22.06 0.00 37.67 3.46
57 58 1.801242 TGTCAGTGACAGGAAGGGAA 58.199 50.000 22.06 0.00 37.67 3.97
58 59 3.550692 TGTCAGTGACAGGAAGGGA 57.449 52.632 22.06 0.00 37.67 4.20
66 67 2.734591 GACCCGCTGTCAGTGACA 59.265 61.111 24.09 24.09 43.85 3.58
67 68 1.248785 TAGGACCCGCTGTCAGTGAC 61.249 60.000 16.68 16.68 46.38 3.67
68 69 1.076014 TAGGACCCGCTGTCAGTGA 59.924 57.895 15.13 0.00 46.38 3.41
69 70 1.215647 GTAGGACCCGCTGTCAGTG 59.784 63.158 6.41 6.41 46.38 3.66
70 71 2.341101 CGTAGGACCCGCTGTCAGT 61.341 63.158 0.93 0.00 46.38 3.41
71 72 2.490217 CGTAGGACCCGCTGTCAG 59.510 66.667 0.00 0.00 46.38 3.51
72 73 3.755628 GCGTAGGACCCGCTGTCA 61.756 66.667 7.77 0.00 46.38 3.58
78 79 1.740296 CAGTTTGGCGTAGGACCCG 60.740 63.158 0.00 0.00 0.00 5.28
79 80 0.672711 GTCAGTTTGGCGTAGGACCC 60.673 60.000 0.00 0.00 0.00 4.46
80 81 1.012486 CGTCAGTTTGGCGTAGGACC 61.012 60.000 0.00 0.00 41.12 4.46
81 82 2.442084 CGTCAGTTTGGCGTAGGAC 58.558 57.895 0.00 0.00 41.12 3.85
82 83 4.979204 CGTCAGTTTGGCGTAGGA 57.021 55.556 0.00 0.00 41.12 2.94
88 89 1.798813 CCTAAGTCACGTCAGTTTGGC 59.201 52.381 0.00 0.00 0.00 4.52
89 90 2.800544 CACCTAAGTCACGTCAGTTTGG 59.199 50.000 5.98 5.98 0.00 3.28
90 91 3.245284 CACACCTAAGTCACGTCAGTTTG 59.755 47.826 0.00 0.00 0.00 2.93
91 92 3.118884 ACACACCTAAGTCACGTCAGTTT 60.119 43.478 0.00 0.00 0.00 2.66
92 93 2.429610 ACACACCTAAGTCACGTCAGTT 59.570 45.455 0.00 0.00 0.00 3.16
93 94 2.029623 ACACACCTAAGTCACGTCAGT 58.970 47.619 0.00 0.00 0.00 3.41
94 95 2.795175 ACACACCTAAGTCACGTCAG 57.205 50.000 0.00 0.00 0.00 3.51
95 96 2.950975 TGTACACACCTAAGTCACGTCA 59.049 45.455 0.00 0.00 0.00 4.35
96 97 3.631145 TGTACACACCTAAGTCACGTC 57.369 47.619 0.00 0.00 0.00 4.34
97 98 3.130869 TGTTGTACACACCTAAGTCACGT 59.869 43.478 0.00 0.00 0.00 4.49
98 99 3.708890 TGTTGTACACACCTAAGTCACG 58.291 45.455 0.00 0.00 0.00 4.35
99 100 4.384846 CGATGTTGTACACACCTAAGTCAC 59.615 45.833 0.00 0.00 38.61 3.67
100 101 4.038282 ACGATGTTGTACACACCTAAGTCA 59.962 41.667 0.00 0.00 38.61 3.41
101 102 4.553323 ACGATGTTGTACACACCTAAGTC 58.447 43.478 0.00 0.00 38.61 3.01
102 103 4.595762 ACGATGTTGTACACACCTAAGT 57.404 40.909 0.00 0.00 38.61 2.24
103 104 7.591006 AAATACGATGTTGTACACACCTAAG 57.409 36.000 0.00 0.00 38.61 2.18
104 105 8.087136 TGTAAATACGATGTTGTACACACCTAA 58.913 33.333 0.00 0.00 38.61 2.69
105 106 7.541783 GTGTAAATACGATGTTGTACACACCTA 59.458 37.037 0.00 0.00 40.51 3.08
106 107 6.366877 GTGTAAATACGATGTTGTACACACCT 59.633 38.462 0.00 0.00 40.51 4.00
107 108 6.366877 AGTGTAAATACGATGTTGTACACACC 59.633 38.462 12.70 0.00 42.30 4.16
108 109 7.095940 ACAGTGTAAATACGATGTTGTACACAC 60.096 37.037 12.70 0.00 42.30 3.82
109 110 6.924612 ACAGTGTAAATACGATGTTGTACACA 59.075 34.615 12.70 0.00 42.30 3.72
110 111 7.342318 ACAGTGTAAATACGATGTTGTACAC 57.658 36.000 0.00 0.00 40.90 2.90
111 112 7.949903 AACAGTGTAAATACGATGTTGTACA 57.050 32.000 0.00 0.00 36.64 2.90
114 115 8.284693 GGTTTAACAGTGTAAATACGATGTTGT 58.715 33.333 16.92 3.11 37.73 3.32
115 116 8.283992 TGGTTTAACAGTGTAAATACGATGTTG 58.716 33.333 16.92 2.66 37.73 3.33
116 117 8.380743 TGGTTTAACAGTGTAAATACGATGTT 57.619 30.769 13.99 13.99 39.34 2.71
117 118 7.966246 TGGTTTAACAGTGTAAATACGATGT 57.034 32.000 0.00 0.00 0.00 3.06
118 119 8.500773 ACTTGGTTTAACAGTGTAAATACGATG 58.499 33.333 0.00 0.00 0.00 3.84
119 120 8.611654 ACTTGGTTTAACAGTGTAAATACGAT 57.388 30.769 0.00 0.00 0.00 3.73
120 121 8.436046 AACTTGGTTTAACAGTGTAAATACGA 57.564 30.769 0.00 0.00 0.00 3.43
121 122 8.553696 AGAACTTGGTTTAACAGTGTAAATACG 58.446 33.333 0.00 0.00 0.00 3.06
127 128 8.676401 GGTTTAAGAACTTGGTTTAACAGTGTA 58.324 33.333 0.00 0.00 36.03 2.90
128 129 7.177041 TGGTTTAAGAACTTGGTTTAACAGTGT 59.823 33.333 0.00 0.00 36.03 3.55
129 130 7.540299 TGGTTTAAGAACTTGGTTTAACAGTG 58.460 34.615 0.00 0.00 36.03 3.66
130 131 7.706100 TGGTTTAAGAACTTGGTTTAACAGT 57.294 32.000 0.00 0.00 36.03 3.55
131 132 9.594478 AAATGGTTTAAGAACTTGGTTTAACAG 57.406 29.630 0.00 0.00 36.03 3.16
174 175 9.405587 GCATAACAGTTCATTTTAGTGCTAAAA 57.594 29.630 16.42 16.42 45.56 1.52
192 193 6.874134 ACTAGTGTTAGAACTTGGCATAACAG 59.126 38.462 10.10 0.00 38.44 3.16
194 195 6.092259 CCACTAGTGTTAGAACTTGGCATAAC 59.908 42.308 21.18 0.00 0.00 1.89
216 217 1.004927 GCGAGCGATCAATTACACCAC 60.005 52.381 0.00 0.00 0.00 4.16
217 218 1.286501 GCGAGCGATCAATTACACCA 58.713 50.000 0.00 0.00 0.00 4.17
257 271 7.493313 CGAACGATTCCTTTTTCATTTTCTTG 58.507 34.615 0.00 0.00 0.00 3.02
324 341 1.471829 TTGCAGAGGTGAGCGGAGAA 61.472 55.000 0.00 0.00 0.00 2.87
443 461 0.107081 CCGTGGCGGTAAATGGGATA 59.893 55.000 0.00 0.00 42.73 2.59
481 499 2.125512 AAGGCAGAAGGTAGCGCG 60.126 61.111 0.00 0.00 0.00 6.86
798 820 4.021916 GGACTTGGCTTGTAGGAGTAGTA 58.978 47.826 0.00 0.00 0.00 1.82
799 821 2.832733 GGACTTGGCTTGTAGGAGTAGT 59.167 50.000 0.00 0.00 0.00 2.73
800 822 2.832129 TGGACTTGGCTTGTAGGAGTAG 59.168 50.000 0.00 0.00 0.00 2.57
801 823 2.897350 TGGACTTGGCTTGTAGGAGTA 58.103 47.619 0.00 0.00 0.00 2.59
802 824 1.729586 TGGACTTGGCTTGTAGGAGT 58.270 50.000 0.00 0.00 0.00 3.85
803 825 2.859165 TTGGACTTGGCTTGTAGGAG 57.141 50.000 0.00 0.00 0.00 3.69
804 826 3.420893 CAATTGGACTTGGCTTGTAGGA 58.579 45.455 0.00 0.00 0.00 2.94
805 827 2.493278 CCAATTGGACTTGGCTTGTAGG 59.507 50.000 20.50 0.00 39.32 3.18
806 828 3.855689 CCAATTGGACTTGGCTTGTAG 57.144 47.619 20.50 0.00 39.32 2.74
1038 1060 3.535561 CTTTCTCAATACATCCTGCGGT 58.464 45.455 0.00 0.00 0.00 5.68
1065 1087 0.392336 TTTCAGTTTGCATGGGTGGC 59.608 50.000 0.00 0.00 0.00 5.01
1174 1196 2.583520 CCAGGAGGAGCTGACAGC 59.416 66.667 20.12 20.12 42.84 4.40
1398 1420 0.108424 GCTCAGACTTGTCATCCGCT 60.108 55.000 3.49 0.00 0.00 5.52
1554 1576 3.870274 ACTTAACATTTCGGGCTCTACC 58.130 45.455 0.00 0.00 37.93 3.18
1555 1577 6.511282 GCATAACTTAACATTTCGGGCTCTAC 60.511 42.308 0.00 0.00 0.00 2.59
2213 2253 5.308237 AGCGGAGATACAATTTCTTCCCTAT 59.692 40.000 0.00 0.00 0.00 2.57
2498 2546 7.122650 AGGAAAGAAATGTGAGAACAGAAAACA 59.877 33.333 0.00 0.00 0.00 2.83
2581 2683 5.067023 GGTTACTACGTGGCTTGTACTATCT 59.933 44.000 0.00 0.00 0.00 1.98
2747 3051 9.520204 AACATTTGCTGATAATATTTAGTGCAC 57.480 29.630 9.40 9.40 0.00 4.57
2949 3696 2.086869 AGTGACATTCGGCCTGAATTG 58.913 47.619 16.81 14.59 45.06 2.32
2957 3704 1.131126 CCAATCACAGTGACATTCGGC 59.869 52.381 5.05 0.00 0.00 5.54
3024 3771 3.131046 GGCATGGTAAAGTTCAATGAGGG 59.869 47.826 0.00 0.00 0.00 4.30
3028 3775 4.160065 TGGATGGCATGGTAAAGTTCAATG 59.840 41.667 3.81 0.00 0.00 2.82
3029 3776 4.352009 TGGATGGCATGGTAAAGTTCAAT 58.648 39.130 3.81 0.00 0.00 2.57
3030 3777 3.772387 TGGATGGCATGGTAAAGTTCAA 58.228 40.909 3.81 0.00 0.00 2.69
3032 3779 4.210331 AGATGGATGGCATGGTAAAGTTC 58.790 43.478 3.81 0.00 0.00 3.01
3035 3782 3.243636 GCAAGATGGATGGCATGGTAAAG 60.244 47.826 3.81 0.00 0.00 1.85
3037 3784 2.091720 AGCAAGATGGATGGCATGGTAA 60.092 45.455 3.81 0.00 0.00 2.85
3038 3785 1.496001 AGCAAGATGGATGGCATGGTA 59.504 47.619 3.81 0.00 0.00 3.25
3039 3786 0.260816 AGCAAGATGGATGGCATGGT 59.739 50.000 3.81 0.00 0.00 3.55
3040 3787 1.884579 GTAGCAAGATGGATGGCATGG 59.115 52.381 3.81 0.00 0.00 3.66
3041 3788 2.578786 TGTAGCAAGATGGATGGCATG 58.421 47.619 3.81 0.00 0.00 4.06
3042 3789 3.520691 ATGTAGCAAGATGGATGGCAT 57.479 42.857 0.00 0.00 0.00 4.40
3043 3790 4.287845 AGATATGTAGCAAGATGGATGGCA 59.712 41.667 0.00 0.00 0.00 4.92
3044 3791 4.634883 CAGATATGTAGCAAGATGGATGGC 59.365 45.833 0.00 0.00 0.00 4.40
3045 3792 4.634883 GCAGATATGTAGCAAGATGGATGG 59.365 45.833 0.00 0.00 0.00 3.51
3046 3793 4.634883 GGCAGATATGTAGCAAGATGGATG 59.365 45.833 0.00 0.00 0.00 3.51
3047 3794 4.287845 TGGCAGATATGTAGCAAGATGGAT 59.712 41.667 0.00 0.00 0.00 3.41
3048 3795 3.647590 TGGCAGATATGTAGCAAGATGGA 59.352 43.478 0.00 0.00 0.00 3.41
3049 3796 4.011966 TGGCAGATATGTAGCAAGATGG 57.988 45.455 0.00 0.00 0.00 3.51
3050 3797 5.243207 TCATGGCAGATATGTAGCAAGATG 58.757 41.667 0.00 0.00 0.00 2.90
3051 3798 5.494390 TCATGGCAGATATGTAGCAAGAT 57.506 39.130 0.00 0.00 0.00 2.40
3052 3799 4.961438 TCATGGCAGATATGTAGCAAGA 57.039 40.909 0.00 0.00 0.00 3.02
3054 3801 5.231702 TGATCATGGCAGATATGTAGCAA 57.768 39.130 0.00 0.00 0.00 3.91
3055 3802 4.895668 TGATCATGGCAGATATGTAGCA 57.104 40.909 0.00 0.00 0.00 3.49
3056 3803 5.425630 TGATGATCATGGCAGATATGTAGC 58.574 41.667 14.30 0.00 0.00 3.58
3057 3804 6.037281 GCTTGATGATCATGGCAGATATGTAG 59.963 42.308 14.30 0.00 0.00 2.74
3059 3806 4.700692 GCTTGATGATCATGGCAGATATGT 59.299 41.667 14.30 0.00 0.00 2.29
3061 3808 4.263771 TGGCTTGATGATCATGGCAGATAT 60.264 41.667 26.31 0.00 46.73 1.63
3065 3812 1.687563 TGGCTTGATGATCATGGCAG 58.312 50.000 26.31 9.89 46.73 4.85
3068 3815 3.751518 TGAGATGGCTTGATGATCATGG 58.248 45.455 14.30 4.33 0.00 3.66
3069 3816 4.379918 GCATGAGATGGCTTGATGATCATG 60.380 45.833 14.30 0.00 43.31 3.07
3070 3817 3.759086 GCATGAGATGGCTTGATGATCAT 59.241 43.478 8.25 8.25 0.00 2.45
3071 3818 3.146847 GCATGAGATGGCTTGATGATCA 58.853 45.455 0.00 0.00 0.00 2.92
3073 3820 3.181443 TGAGCATGAGATGGCTTGATGAT 60.181 43.478 0.00 0.00 41.22 2.45


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

AutoCloner maintained by Alex Coulton.