Multiple sequence alignment - TraesCS7D01G209600

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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 TraesCS7D01G209600 chr7D 100.000 2848 0 0 1 2848 167558793 167555946 0.000000e+00 5260.0
1 TraesCS7D01G209600 chr7D 84.228 298 30 13 4 288 91997200 91996907 1.010000e-69 274.0
2 TraesCS7D01G209600 chr7A 93.211 2180 84 17 288 2418 169305628 169303464 0.000000e+00 3147.0
3 TraesCS7D01G209600 chr7A 96.296 54 2 0 2795 2848 621793143 621793196 3.910000e-14 89.8
4 TraesCS7D01G209600 chr7B 92.785 2093 81 32 392 2430 132111147 132109071 0.000000e+00 2964.0
5 TraesCS7D01G209600 chr7B 80.089 447 59 22 2428 2848 334976028 334975586 3.560000e-79 305.0
6 TraesCS7D01G209600 chr7B 85.859 297 27 12 4 288 720342193 720341900 4.610000e-78 302.0
7 TraesCS7D01G209600 chr7B 90.654 107 9 1 288 393 132111515 132111409 1.060000e-29 141.0
8 TraesCS7D01G209600 chr7B 94.643 56 3 0 2793 2848 606394329 606394384 1.410000e-13 87.9
9 TraesCS7D01G209600 chr3A 90.000 380 17 8 2429 2788 505210535 505210913 3.320000e-129 472.0
10 TraesCS7D01G209600 chr3A 93.950 281 12 3 2428 2708 550215838 550215563 1.220000e-113 420.0
11 TraesCS7D01G209600 chr3A 87.671 292 35 1 2428 2719 494235340 494235630 3.510000e-89 339.0
12 TraesCS7D01G209600 chr3A 84.797 296 30 11 4 288 44229134 44228843 1.670000e-72 283.0
13 TraesCS7D01G209600 chr3A 98.485 66 1 0 2783 2848 505211052 505211117 1.790000e-22 117.0
14 TraesCS7D01G209600 chr5A 89.600 375 19 7 2428 2782 642718471 642718845 2.590000e-125 459.0
15 TraesCS7D01G209600 chr5A 94.718 284 14 1 2426 2708 472907399 472907116 9.370000e-120 440.0
16 TraesCS7D01G209600 chr5A 96.491 57 2 0 2783 2839 642718989 642719045 8.400000e-16 95.3
17 TraesCS7D01G209600 chr2A 93.841 276 17 0 2428 2703 189015352 189015627 1.580000e-112 416.0
18 TraesCS7D01G209600 chr2A 88.652 282 32 0 2429 2710 740044371 740044090 7.550000e-91 344.0
19 TraesCS7D01G209600 chr4A 93.214 280 18 1 2429 2708 26007652 26007374 7.340000e-111 411.0
20 TraesCS7D01G209600 chr4A 96.296 54 2 0 2795 2848 22735033 22734980 3.910000e-14 89.8
21 TraesCS7D01G209600 chr6A 91.786 280 22 1 2429 2708 12264740 12265018 3.440000e-104 388.0
22 TraesCS7D01G209600 chr6A 92.500 80 6 0 1619 1698 524364159 524364238 6.450000e-22 115.0
23 TraesCS7D01G209600 chr6D 88.776 294 22 9 4 290 396461835 396461546 1.620000e-92 350.0
24 TraesCS7D01G209600 chr6D 83.502 297 33 15 10 296 4427908 4427618 2.180000e-66 263.0
25 TraesCS7D01G209600 chr6D 92.405 79 6 0 1620 1698 382563463 382563541 2.320000e-21 113.0
26 TraesCS7D01G209600 chr1B 87.050 278 34 2 2428 2703 172266873 172267150 2.130000e-81 313.0
27 TraesCS7D01G209600 chr3D 85.859 297 31 10 4 294 535730402 535730111 3.560000e-79 305.0
28 TraesCS7D01G209600 chr1D 84.932 292 26 14 4 288 486887794 486887514 2.160000e-71 279.0
29 TraesCS7D01G209600 chr4D 82.566 304 33 15 5 292 394671987 394672286 1.690000e-62 250.0
30 TraesCS7D01G209600 chr1A 83.456 272 29 11 20 287 34156108 34156367 3.670000e-59 239.0
31 TraesCS7D01G209600 chr6B 92.405 79 6 0 1620 1698 572113107 572113185 2.320000e-21 113.0
32 TraesCS7D01G209600 chr3B 96.429 56 2 0 2793 2848 8638156 8638211 3.020000e-15 93.5
33 TraesCS7D01G209600 chr5B 96.296 54 2 0 2795 2848 489069667 489069614 3.910000e-14 89.8


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 TraesCS7D01G209600 chr7D 167555946 167558793 2847 True 5260.00 5260 100.0000 1 2848 1 chr7D.!!$R2 2847
1 TraesCS7D01G209600 chr7A 169303464 169305628 2164 True 3147.00 3147 93.2110 288 2418 1 chr7A.!!$R1 2130
2 TraesCS7D01G209600 chr7B 132109071 132111515 2444 True 1552.50 2964 91.7195 288 2430 2 chr7B.!!$R3 2142
3 TraesCS7D01G209600 chr3A 505210535 505211117 582 False 294.50 472 94.2425 2429 2848 2 chr3A.!!$F2 419
4 TraesCS7D01G209600 chr5A 642718471 642719045 574 False 277.15 459 93.0455 2428 2839 2 chr5A.!!$F1 411

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
49 50 0.037734 CTTCGCCCCTTAGTTGGGTT 59.962 55.0 0.00 0.0 45.70 4.11 F
119 120 0.038892 TCGAACTTTAGCCGAGCGTT 60.039 50.0 0.00 0.0 0.00 4.84 F
487 754 0.178068 CGGCTTTAGCAAGGGAGCTA 59.822 55.0 3.88 0.0 44.50 3.32 F
1378 1672 1.195115 ATGTGCCTATCGTCACCAGT 58.805 50.0 0.00 0.0 32.51 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1427 1721 0.741915 CGCTGTAGAGGAGGAAGGTC 59.258 60.000 0.0 0.0 0.00 3.85 R
1557 1853 3.054802 ACAGTTCAGAGCTTGGGGATTAG 60.055 47.826 0.0 0.0 0.00 1.73 R
1814 2136 3.190118 CGGCAATCTTCTTCTTCAAGCTT 59.810 43.478 0.0 0.0 0.00 3.74 R
2658 2984 2.960384 TGCATCATCCATTGAACATCCC 59.040 45.455 0.0 0.0 38.03 3.85 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
18 19 4.452733 GGCGGCGTACTTCCAGCT 62.453 66.667 9.37 0.00 0.00 4.24
19 20 2.886124 GCGGCGTACTTCCAGCTC 60.886 66.667 9.37 0.00 0.00 4.09
20 21 2.885861 CGGCGTACTTCCAGCTCT 59.114 61.111 0.00 0.00 0.00 4.09
21 22 1.226717 CGGCGTACTTCCAGCTCTC 60.227 63.158 0.00 0.00 0.00 3.20
22 23 1.890894 GGCGTACTTCCAGCTCTCA 59.109 57.895 0.00 0.00 0.00 3.27
23 24 0.246635 GGCGTACTTCCAGCTCTCAA 59.753 55.000 0.00 0.00 0.00 3.02
24 25 1.351153 GCGTACTTCCAGCTCTCAAC 58.649 55.000 0.00 0.00 0.00 3.18
25 26 1.618861 CGTACTTCCAGCTCTCAACG 58.381 55.000 0.00 0.00 0.00 4.10
26 27 1.199327 CGTACTTCCAGCTCTCAACGA 59.801 52.381 0.00 0.00 0.00 3.85
27 28 2.597520 GTACTTCCAGCTCTCAACGAC 58.402 52.381 0.00 0.00 0.00 4.34
28 29 1.333177 ACTTCCAGCTCTCAACGACT 58.667 50.000 0.00 0.00 0.00 4.18
29 30 1.689273 ACTTCCAGCTCTCAACGACTT 59.311 47.619 0.00 0.00 0.00 3.01
30 31 2.288518 ACTTCCAGCTCTCAACGACTTC 60.289 50.000 0.00 0.00 0.00 3.01
31 32 1.621992 TCCAGCTCTCAACGACTTCT 58.378 50.000 0.00 0.00 0.00 2.85
32 33 1.964223 TCCAGCTCTCAACGACTTCTT 59.036 47.619 0.00 0.00 0.00 2.52
33 34 2.029828 TCCAGCTCTCAACGACTTCTTC 60.030 50.000 0.00 0.00 0.00 2.87
42 43 3.347411 CGACTTCTTCGCCCCTTAG 57.653 57.895 0.00 0.00 41.87 2.18
43 44 0.531200 CGACTTCTTCGCCCCTTAGT 59.469 55.000 0.00 0.00 41.87 2.24
44 45 1.067071 CGACTTCTTCGCCCCTTAGTT 60.067 52.381 0.00 0.00 41.87 2.24
45 46 2.347731 GACTTCTTCGCCCCTTAGTTG 58.652 52.381 0.00 0.00 0.00 3.16
46 47 1.003233 ACTTCTTCGCCCCTTAGTTGG 59.997 52.381 0.00 0.00 0.00 3.77
47 48 0.326927 TTCTTCGCCCCTTAGTTGGG 59.673 55.000 0.00 0.00 46.56 4.12
48 49 0.838987 TCTTCGCCCCTTAGTTGGGT 60.839 55.000 0.00 0.00 45.70 4.51
49 50 0.037734 CTTCGCCCCTTAGTTGGGTT 59.962 55.000 0.00 0.00 45.70 4.11
50 51 0.479378 TTCGCCCCTTAGTTGGGTTT 59.521 50.000 0.00 0.00 45.70 3.27
51 52 0.479378 TCGCCCCTTAGTTGGGTTTT 59.521 50.000 0.00 0.00 45.70 2.43
52 53 1.133419 TCGCCCCTTAGTTGGGTTTTT 60.133 47.619 0.00 0.00 45.70 1.94
77 78 8.929827 TTAAATATCTTATGGAACGTCGAACA 57.070 30.769 0.00 0.00 0.00 3.18
78 79 9.537192 TTAAATATCTTATGGAACGTCGAACAT 57.463 29.630 0.00 2.87 0.00 2.71
79 80 7.408132 AATATCTTATGGAACGTCGAACATG 57.592 36.000 0.00 0.00 0.00 3.21
80 81 4.182693 TCTTATGGAACGTCGAACATGT 57.817 40.909 0.00 0.00 0.00 3.21
81 82 4.171005 TCTTATGGAACGTCGAACATGTC 58.829 43.478 0.00 0.00 0.00 3.06
99 100 9.425893 GAACATGTCGAATATATGTCAAGTTTG 57.574 33.333 0.00 0.00 38.83 2.93
100 101 8.492673 ACATGTCGAATATATGTCAAGTTTGT 57.507 30.769 0.00 0.00 35.16 2.83
101 102 8.604035 ACATGTCGAATATATGTCAAGTTTGTC 58.396 33.333 0.00 0.00 35.16 3.18
102 103 7.216920 TGTCGAATATATGTCAAGTTTGTCG 57.783 36.000 0.00 0.00 0.00 4.35
103 104 7.030768 TGTCGAATATATGTCAAGTTTGTCGA 58.969 34.615 0.00 0.00 0.00 4.20
104 105 7.542824 TGTCGAATATATGTCAAGTTTGTCGAA 59.457 33.333 0.00 0.00 35.78 3.71
105 106 7.839837 GTCGAATATATGTCAAGTTTGTCGAAC 59.160 37.037 0.00 0.00 35.78 3.95
114 115 3.102052 AGTTTGTCGAACTTTAGCCGA 57.898 42.857 0.00 0.00 46.34 5.54
115 116 3.057734 AGTTTGTCGAACTTTAGCCGAG 58.942 45.455 0.00 0.00 46.34 4.63
116 117 1.425412 TTGTCGAACTTTAGCCGAGC 58.575 50.000 0.00 0.00 32.65 5.03
117 118 0.731514 TGTCGAACTTTAGCCGAGCG 60.732 55.000 0.00 0.00 32.65 5.03
118 119 0.731855 GTCGAACTTTAGCCGAGCGT 60.732 55.000 0.00 0.00 32.65 5.07
119 120 0.038892 TCGAACTTTAGCCGAGCGTT 60.039 50.000 0.00 0.00 0.00 4.84
120 121 0.788391 CGAACTTTAGCCGAGCGTTT 59.212 50.000 0.00 0.00 0.00 3.60
121 122 1.193874 CGAACTTTAGCCGAGCGTTTT 59.806 47.619 0.00 0.00 0.00 2.43
122 123 2.409378 CGAACTTTAGCCGAGCGTTTTA 59.591 45.455 0.00 0.00 0.00 1.52
123 124 3.061697 CGAACTTTAGCCGAGCGTTTTAT 59.938 43.478 0.00 0.00 0.00 1.40
124 125 4.575718 GAACTTTAGCCGAGCGTTTTATC 58.424 43.478 0.00 0.00 0.00 1.75
125 126 2.934553 ACTTTAGCCGAGCGTTTTATCC 59.065 45.455 0.00 0.00 0.00 2.59
126 127 2.676632 TTAGCCGAGCGTTTTATCCA 57.323 45.000 0.00 0.00 0.00 3.41
127 128 2.676632 TAGCCGAGCGTTTTATCCAA 57.323 45.000 0.00 0.00 0.00 3.53
128 129 2.038387 AGCCGAGCGTTTTATCCAAT 57.962 45.000 0.00 0.00 0.00 3.16
129 130 2.365582 AGCCGAGCGTTTTATCCAATT 58.634 42.857 0.00 0.00 0.00 2.32
130 131 2.752903 AGCCGAGCGTTTTATCCAATTT 59.247 40.909 0.00 0.00 0.00 1.82
131 132 2.851824 GCCGAGCGTTTTATCCAATTTG 59.148 45.455 0.00 0.00 0.00 2.32
132 133 2.851824 CCGAGCGTTTTATCCAATTTGC 59.148 45.455 0.00 0.00 0.00 3.68
133 134 2.851824 CGAGCGTTTTATCCAATTTGCC 59.148 45.455 0.00 0.00 0.00 4.52
134 135 2.851824 GAGCGTTTTATCCAATTTGCCG 59.148 45.455 0.00 0.00 0.00 5.69
135 136 2.490115 AGCGTTTTATCCAATTTGCCGA 59.510 40.909 0.00 0.00 0.00 5.54
136 137 3.057174 AGCGTTTTATCCAATTTGCCGAA 60.057 39.130 0.00 0.00 0.00 4.30
137 138 3.862845 GCGTTTTATCCAATTTGCCGAAT 59.137 39.130 0.00 0.00 0.00 3.34
138 139 4.328712 GCGTTTTATCCAATTTGCCGAATT 59.671 37.500 0.00 0.00 38.49 2.17
139 140 5.500131 GCGTTTTATCCAATTTGCCGAATTC 60.500 40.000 0.00 0.00 35.79 2.17
140 141 5.005299 CGTTTTATCCAATTTGCCGAATTCC 59.995 40.000 0.00 0.00 35.79 3.01
141 142 2.869233 ATCCAATTTGCCGAATTCCG 57.131 45.000 0.00 0.00 35.79 4.30
142 143 1.540267 TCCAATTTGCCGAATTCCGT 58.460 45.000 0.00 0.00 35.79 4.69
143 144 1.889829 TCCAATTTGCCGAATTCCGTT 59.110 42.857 0.00 0.00 35.79 4.44
144 145 2.297597 TCCAATTTGCCGAATTCCGTTT 59.702 40.909 0.00 0.00 35.79 3.60
145 146 3.063485 CCAATTTGCCGAATTCCGTTTT 58.937 40.909 0.00 0.00 35.79 2.43
146 147 3.496507 CCAATTTGCCGAATTCCGTTTTT 59.503 39.130 0.00 0.00 35.79 1.94
147 148 4.376920 CCAATTTGCCGAATTCCGTTTTTC 60.377 41.667 0.00 0.00 35.79 2.29
148 149 3.719173 TTTGCCGAATTCCGTTTTTCT 57.281 38.095 0.00 0.00 36.31 2.52
149 150 3.719173 TTGCCGAATTCCGTTTTTCTT 57.281 38.095 0.00 0.00 36.31 2.52
150 151 4.832590 TTGCCGAATTCCGTTTTTCTTA 57.167 36.364 0.00 0.00 36.31 2.10
151 152 4.832590 TGCCGAATTCCGTTTTTCTTAA 57.167 36.364 0.00 0.00 36.31 1.85
152 153 5.184340 TGCCGAATTCCGTTTTTCTTAAA 57.816 34.783 0.00 0.00 36.31 1.52
153 154 5.589192 TGCCGAATTCCGTTTTTCTTAAAA 58.411 33.333 0.00 0.00 36.31 1.52
154 155 6.040878 TGCCGAATTCCGTTTTTCTTAAAAA 58.959 32.000 0.00 0.00 35.16 1.94
155 156 6.199342 TGCCGAATTCCGTTTTTCTTAAAAAG 59.801 34.615 0.00 0.00 40.71 2.27
156 157 6.418523 GCCGAATTCCGTTTTTCTTAAAAAGA 59.581 34.615 0.00 0.00 40.71 2.52
157 158 7.043258 GCCGAATTCCGTTTTTCTTAAAAAGAA 60.043 33.333 0.00 0.00 40.71 2.52
158 159 8.809478 CCGAATTCCGTTTTTCTTAAAAAGAAA 58.191 29.630 10.07 10.07 44.50 2.52
167 168 4.461992 TCTTAAAAAGAAACCGCGTCTG 57.538 40.909 4.92 0.00 33.83 3.51
168 169 3.249080 TCTTAAAAAGAAACCGCGTCTGG 59.751 43.478 4.92 0.00 33.83 3.86
169 170 0.666374 AAAAAGAAACCGCGTCTGGG 59.334 50.000 4.92 0.00 0.00 4.45
221 222 2.438795 GCCCCCACGCCGATTTTA 60.439 61.111 0.00 0.00 0.00 1.52
222 223 2.478033 GCCCCCACGCCGATTTTAG 61.478 63.158 0.00 0.00 0.00 1.85
223 224 2.478033 CCCCCACGCCGATTTTAGC 61.478 63.158 0.00 0.00 0.00 3.09
228 229 4.293626 CGCCGATTTTAGCGCCGG 62.294 66.667 15.00 15.00 46.50 6.13
250 251 2.282462 CTCCCAGGCAGCGGTTTT 60.282 61.111 0.00 0.00 0.00 2.43
251 252 1.002624 CTCCCAGGCAGCGGTTTTA 60.003 57.895 0.00 0.00 0.00 1.52
252 253 0.608035 CTCCCAGGCAGCGGTTTTAA 60.608 55.000 0.00 0.00 0.00 1.52
253 254 0.608035 TCCCAGGCAGCGGTTTTAAG 60.608 55.000 0.00 0.00 0.00 1.85
254 255 1.212751 CCAGGCAGCGGTTTTAAGC 59.787 57.895 0.00 0.00 0.00 3.09
261 262 2.360726 CGGTTTTAAGCGCCCCCT 60.361 61.111 2.29 0.00 43.20 4.79
262 263 2.696759 CGGTTTTAAGCGCCCCCTG 61.697 63.158 2.29 0.00 43.20 4.45
263 264 2.348104 GGTTTTAAGCGCCCCCTGG 61.348 63.158 2.29 0.00 0.00 4.45
286 287 3.805267 CAACGGCTGGAGATGCTC 58.195 61.111 0.00 0.00 0.00 4.26
290 291 1.195115 ACGGCTGGAGATGCTCTTAA 58.805 50.000 0.00 0.00 0.00 1.85
319 321 1.366319 AGACCAGTTCCAGCCAATCT 58.634 50.000 0.00 0.00 0.00 2.40
337 339 2.388735 TCTGGGCAGTCTGTACTATGG 58.611 52.381 0.93 0.00 33.48 2.74
380 383 5.532406 GGCACTATTATTTGAGGATCTTGCA 59.468 40.000 0.00 0.00 34.92 4.08
388 391 8.806429 TTATTTGAGGATCTTGCATTTAGACA 57.194 30.769 0.00 0.00 34.92 3.41
396 662 7.234371 AGGATCTTGCATTTAGACAGCTATAGA 59.766 37.037 3.21 0.00 0.00 1.98
416 682 9.186837 CTATAGAAGTAGGAGACTAACCAAACA 57.813 37.037 0.00 0.00 46.54 2.83
477 744 0.460459 GAGGTCAGACCGGCTTTAGC 60.460 60.000 14.32 0.41 44.90 3.09
479 746 0.321298 GGTCAGACCGGCTTTAGCAA 60.321 55.000 3.05 0.00 44.36 3.91
487 754 0.178068 CGGCTTTAGCAAGGGAGCTA 59.822 55.000 3.88 0.00 44.50 3.32
490 757 1.210722 GCTTTAGCAAGGGAGCTAGGT 59.789 52.381 0.00 0.00 46.77 3.08
876 1152 2.342279 CGAGGGACCAAAGACGCA 59.658 61.111 0.00 0.00 0.00 5.24
936 1212 2.232696 ACCGTTCCAGCTTTTGTTGTTT 59.767 40.909 0.00 0.00 0.00 2.83
940 1216 3.244033 TCCAGCTTTTGTTGTTTGGTG 57.756 42.857 0.00 0.00 0.00 4.17
942 1218 3.450457 TCCAGCTTTTGTTGTTTGGTGAT 59.550 39.130 0.00 0.00 0.00 3.06
943 1219 4.646945 TCCAGCTTTTGTTGTTTGGTGATA 59.353 37.500 0.00 0.00 0.00 2.15
944 1220 4.744631 CCAGCTTTTGTTGTTTGGTGATAC 59.255 41.667 0.00 0.00 0.00 2.24
945 1221 5.347342 CAGCTTTTGTTGTTTGGTGATACA 58.653 37.500 0.00 0.00 0.00 2.29
1376 1670 1.277842 ACAATGTGCCTATCGTCACCA 59.722 47.619 0.00 0.00 32.51 4.17
1378 1672 1.195115 ATGTGCCTATCGTCACCAGT 58.805 50.000 0.00 0.00 32.51 4.00
1396 1690 3.181461 CCAGTTTCTCTTCTCCTGTGTGT 60.181 47.826 0.00 0.00 0.00 3.72
1397 1691 3.806521 CAGTTTCTCTTCTCCTGTGTGTG 59.193 47.826 0.00 0.00 0.00 3.82
1398 1692 3.452627 AGTTTCTCTTCTCCTGTGTGTGT 59.547 43.478 0.00 0.00 0.00 3.72
1399 1693 3.459232 TTCTCTTCTCCTGTGTGTGTG 57.541 47.619 0.00 0.00 0.00 3.82
1400 1694 1.688735 TCTCTTCTCCTGTGTGTGTGG 59.311 52.381 0.00 0.00 0.00 4.17
1427 1721 2.464459 GGCGATTGAGGACAAGCCG 61.464 63.158 0.00 0.00 43.43 5.52
1557 1853 1.535462 TGCCTCTTCTTTTTACGCAGC 59.465 47.619 0.00 0.00 0.00 5.25
1701 1997 4.023021 CGCTACCTCCTCTTCAAGGTATAC 60.023 50.000 1.96 0.00 44.92 1.47
1732 2054 4.083431 TGAATTGAATTGGCCAATTTTGCG 60.083 37.500 37.54 0.00 42.35 4.85
1743 2065 6.402222 TGGCCAATTTTGCGTAAGATTATTT 58.598 32.000 0.61 0.00 43.02 1.40
1814 2136 1.669760 GTTGGCCACCGACATCGAA 60.670 57.895 3.88 0.00 43.02 3.71
1832 2154 6.429385 ACATCGAAAGCTTGAAGAAGAAGATT 59.571 34.615 0.00 0.00 30.44 2.40
1943 2265 0.604578 ACCATCCACTGCATTTGTGC 59.395 50.000 0.00 0.00 34.38 4.57
2042 2364 9.847224 AGTTTCTGGAAGTCTTCTATTGTTTTA 57.153 29.630 12.31 0.00 33.76 1.52
2076 2398 4.080582 TGTTCATATGGGAAACGTGATCCT 60.081 41.667 17.42 4.62 37.14 3.24
2096 2418 9.830975 TGATCCTTCGAATTGACTTTATATGAA 57.169 29.630 0.00 0.00 0.00 2.57
2148 2472 5.424895 AGAGGATAAGTGACTCAAAGCTGAT 59.575 40.000 0.00 0.00 33.76 2.90
2223 2548 8.824159 AGGTGTAAATCATGATCTCTTAATCG 57.176 34.615 9.06 0.00 0.00 3.34
2426 2752 5.232838 GCAATTGCCTGATATTTGTAGTTGC 59.767 40.000 20.06 0.00 34.31 4.17
2459 2785 7.619512 TTCCTTATTTGGCCCTTTCTTAAAA 57.380 32.000 0.00 0.00 0.00 1.52
2467 2793 5.689835 TGGCCCTTTCTTAAAATTTGCTTT 58.310 33.333 0.00 0.00 0.00 3.51
2579 2905 5.575606 CACTAACGGTGTTAAGTATGAGGTG 59.424 44.000 0.00 0.00 40.79 4.00
2658 2984 9.541143 AAAGTAATAAGTTCACCCATGTTTTTG 57.459 29.630 0.00 0.00 0.00 2.44
2680 3006 3.576982 GGGATGTTCAATGGATGATGCAT 59.423 43.478 0.00 0.00 38.03 3.96
2714 3040 9.920133 TGTATGCTTCAATATATTCTCTCACTC 57.080 33.333 0.00 0.00 0.00 3.51
2732 3076 6.704493 TCTCACTCGTAAAAGCTGTACAAAAT 59.296 34.615 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.452733 AGCTGGAAGTACGCCGCC 62.453 66.667 15.23 5.61 35.30 6.13
2 3 2.886124 GAGCTGGAAGTACGCCGC 60.886 66.667 0.00 12.78 35.30 6.53
3 4 1.226717 GAGAGCTGGAAGTACGCCG 60.227 63.158 0.00 0.00 35.30 6.46
4 5 0.246635 TTGAGAGCTGGAAGTACGCC 59.753 55.000 0.00 1.31 35.30 5.68
5 6 1.351153 GTTGAGAGCTGGAAGTACGC 58.649 55.000 0.00 0.00 35.30 4.42
6 7 1.199327 TCGTTGAGAGCTGGAAGTACG 59.801 52.381 0.00 0.00 35.30 3.67
7 8 2.229302 AGTCGTTGAGAGCTGGAAGTAC 59.771 50.000 0.00 0.00 35.30 2.73
8 9 2.515854 AGTCGTTGAGAGCTGGAAGTA 58.484 47.619 0.00 0.00 35.30 2.24
9 10 1.333177 AGTCGTTGAGAGCTGGAAGT 58.667 50.000 0.00 0.00 35.30 3.01
10 11 2.029470 AGAAGTCGTTGAGAGCTGGAAG 60.029 50.000 0.00 0.00 0.00 3.46
11 12 1.964223 AGAAGTCGTTGAGAGCTGGAA 59.036 47.619 0.00 0.00 0.00 3.53
12 13 1.621992 AGAAGTCGTTGAGAGCTGGA 58.378 50.000 0.00 0.00 0.00 3.86
13 14 2.333014 GAAGAAGTCGTTGAGAGCTGG 58.667 52.381 0.00 0.00 0.00 4.85
14 15 1.982223 CGAAGAAGTCGTTGAGAGCTG 59.018 52.381 0.00 0.00 45.09 4.24
15 16 2.339728 CGAAGAAGTCGTTGAGAGCT 57.660 50.000 0.00 0.00 45.09 4.09
25 26 2.347731 CAACTAAGGGGCGAAGAAGTC 58.652 52.381 0.00 0.00 0.00 3.01
26 27 1.003233 CCAACTAAGGGGCGAAGAAGT 59.997 52.381 0.00 0.00 0.00 3.01
27 28 1.679032 CCCAACTAAGGGGCGAAGAAG 60.679 57.143 0.00 0.00 45.60 2.85
28 29 0.326927 CCCAACTAAGGGGCGAAGAA 59.673 55.000 0.00 0.00 45.60 2.52
29 30 1.988015 CCCAACTAAGGGGCGAAGA 59.012 57.895 0.00 0.00 45.60 2.87
30 31 4.637771 CCCAACTAAGGGGCGAAG 57.362 61.111 0.00 0.00 45.60 3.79
51 52 9.368674 TGTTCGACGTTCCATAAGATATTTAAA 57.631 29.630 0.00 0.00 0.00 1.52
52 53 8.929827 TGTTCGACGTTCCATAAGATATTTAA 57.070 30.769 0.00 0.00 0.00 1.52
53 54 8.974408 CATGTTCGACGTTCCATAAGATATTTA 58.026 33.333 0.00 0.00 0.00 1.40
54 55 7.494625 ACATGTTCGACGTTCCATAAGATATTT 59.505 33.333 0.00 0.00 0.00 1.40
55 56 6.984474 ACATGTTCGACGTTCCATAAGATATT 59.016 34.615 0.00 0.00 0.00 1.28
56 57 6.513180 ACATGTTCGACGTTCCATAAGATAT 58.487 36.000 0.00 0.00 0.00 1.63
57 58 5.898174 ACATGTTCGACGTTCCATAAGATA 58.102 37.500 0.00 0.00 0.00 1.98
58 59 4.755411 ACATGTTCGACGTTCCATAAGAT 58.245 39.130 0.00 0.00 0.00 2.40
59 60 4.171005 GACATGTTCGACGTTCCATAAGA 58.829 43.478 0.00 0.00 0.00 2.10
60 61 4.500703 GACATGTTCGACGTTCCATAAG 57.499 45.455 0.00 0.00 0.00 1.73
73 74 9.425893 CAAACTTGACATATATTCGACATGTTC 57.574 33.333 0.00 0.00 33.16 3.18
74 75 8.946085 ACAAACTTGACATATATTCGACATGTT 58.054 29.630 0.00 0.00 33.16 2.71
75 76 8.492673 ACAAACTTGACATATATTCGACATGT 57.507 30.769 0.00 0.00 35.65 3.21
76 77 7.789302 CGACAAACTTGACATATATTCGACATG 59.211 37.037 0.00 0.00 0.00 3.21
77 78 7.704899 TCGACAAACTTGACATATATTCGACAT 59.295 33.333 0.00 0.00 0.00 3.06
78 79 7.030768 TCGACAAACTTGACATATATTCGACA 58.969 34.615 0.00 0.00 0.00 4.35
79 80 7.445900 TCGACAAACTTGACATATATTCGAC 57.554 36.000 0.00 0.00 0.00 4.20
80 81 7.758076 AGTTCGACAAACTTGACATATATTCGA 59.242 33.333 0.00 0.00 46.26 3.71
81 82 7.895870 AGTTCGACAAACTTGACATATATTCG 58.104 34.615 0.00 0.00 46.26 3.34
95 96 2.411160 GCTCGGCTAAAGTTCGACAAAC 60.411 50.000 0.00 0.00 38.21 2.93
96 97 1.796459 GCTCGGCTAAAGTTCGACAAA 59.204 47.619 0.00 0.00 0.00 2.83
97 98 1.425412 GCTCGGCTAAAGTTCGACAA 58.575 50.000 0.00 0.00 0.00 3.18
98 99 0.731514 CGCTCGGCTAAAGTTCGACA 60.732 55.000 0.00 0.00 0.00 4.35
99 100 0.731855 ACGCTCGGCTAAAGTTCGAC 60.732 55.000 0.00 0.00 0.00 4.20
100 101 0.038892 AACGCTCGGCTAAAGTTCGA 60.039 50.000 0.00 0.00 0.00 3.71
101 102 0.788391 AAACGCTCGGCTAAAGTTCG 59.212 50.000 0.00 0.00 0.00 3.95
102 103 2.963498 AAAACGCTCGGCTAAAGTTC 57.037 45.000 0.00 0.00 0.00 3.01
103 104 3.373130 GGATAAAACGCTCGGCTAAAGTT 59.627 43.478 0.00 0.00 0.00 2.66
104 105 2.934553 GGATAAAACGCTCGGCTAAAGT 59.065 45.455 0.00 0.00 0.00 2.66
105 106 2.933906 TGGATAAAACGCTCGGCTAAAG 59.066 45.455 0.00 0.00 0.00 1.85
106 107 2.975266 TGGATAAAACGCTCGGCTAAA 58.025 42.857 0.00 0.00 0.00 1.85
107 108 2.676632 TGGATAAAACGCTCGGCTAA 57.323 45.000 0.00 0.00 0.00 3.09
108 109 2.676632 TTGGATAAAACGCTCGGCTA 57.323 45.000 0.00 0.00 0.00 3.93
109 110 2.038387 ATTGGATAAAACGCTCGGCT 57.962 45.000 0.00 0.00 0.00 5.52
110 111 2.844122 AATTGGATAAAACGCTCGGC 57.156 45.000 0.00 0.00 0.00 5.54
111 112 2.851824 GCAAATTGGATAAAACGCTCGG 59.148 45.455 0.00 0.00 0.00 4.63
112 113 2.851824 GGCAAATTGGATAAAACGCTCG 59.148 45.455 0.00 0.00 0.00 5.03
113 114 2.851824 CGGCAAATTGGATAAAACGCTC 59.148 45.455 0.00 0.00 0.00 5.03
114 115 2.490115 TCGGCAAATTGGATAAAACGCT 59.510 40.909 0.00 0.00 0.00 5.07
115 116 2.869897 TCGGCAAATTGGATAAAACGC 58.130 42.857 0.00 0.00 0.00 4.84
116 117 5.005299 GGAATTCGGCAAATTGGATAAAACG 59.995 40.000 0.00 0.00 37.70 3.60
117 118 5.005299 CGGAATTCGGCAAATTGGATAAAAC 59.995 40.000 0.00 0.00 37.70 2.43
118 119 5.105752 CGGAATTCGGCAAATTGGATAAAA 58.894 37.500 0.00 0.00 37.70 1.52
119 120 4.158764 ACGGAATTCGGCAAATTGGATAAA 59.841 37.500 12.54 0.00 44.45 1.40
120 121 3.697045 ACGGAATTCGGCAAATTGGATAA 59.303 39.130 12.54 0.00 44.45 1.75
121 122 3.283751 ACGGAATTCGGCAAATTGGATA 58.716 40.909 12.54 0.00 44.45 2.59
122 123 2.099405 ACGGAATTCGGCAAATTGGAT 58.901 42.857 12.54 0.00 44.45 3.41
123 124 1.540267 ACGGAATTCGGCAAATTGGA 58.460 45.000 12.54 0.00 44.45 3.53
124 125 2.362169 AACGGAATTCGGCAAATTGG 57.638 45.000 12.54 0.00 44.45 3.16
125 126 4.447389 AGAAAAACGGAATTCGGCAAATTG 59.553 37.500 12.54 0.00 44.45 2.32
126 127 4.627058 AGAAAAACGGAATTCGGCAAATT 58.373 34.783 12.54 3.83 44.45 1.82
127 128 4.251543 AGAAAAACGGAATTCGGCAAAT 57.748 36.364 12.54 0.00 44.45 2.32
128 129 3.719173 AGAAAAACGGAATTCGGCAAA 57.281 38.095 12.54 0.00 44.45 3.68
129 130 3.719173 AAGAAAAACGGAATTCGGCAA 57.281 38.095 12.54 0.00 44.45 4.52
130 131 4.832590 TTAAGAAAAACGGAATTCGGCA 57.167 36.364 12.54 0.00 44.45 5.69
131 132 6.418523 TCTTTTTAAGAAAAACGGAATTCGGC 59.581 34.615 12.54 0.00 37.65 5.54
132 133 7.917720 TCTTTTTAAGAAAAACGGAATTCGG 57.082 32.000 11.17 11.17 37.65 4.30
145 146 4.260866 CCAGACGCGGTTTCTTTTTAAGAA 60.261 41.667 12.47 0.00 45.30 2.52
146 147 3.249080 CCAGACGCGGTTTCTTTTTAAGA 59.751 43.478 12.47 0.00 35.26 2.10
147 148 3.551551 CCAGACGCGGTTTCTTTTTAAG 58.448 45.455 12.47 0.00 0.00 1.85
148 149 2.291190 CCCAGACGCGGTTTCTTTTTAA 59.709 45.455 12.47 0.00 0.00 1.52
149 150 1.874872 CCCAGACGCGGTTTCTTTTTA 59.125 47.619 12.47 0.00 0.00 1.52
150 151 0.666374 CCCAGACGCGGTTTCTTTTT 59.334 50.000 12.47 0.00 0.00 1.94
151 152 1.170290 CCCCAGACGCGGTTTCTTTT 61.170 55.000 12.47 0.00 0.00 2.27
152 153 1.599797 CCCCAGACGCGGTTTCTTT 60.600 57.895 12.47 0.00 0.00 2.52
153 154 2.032071 CCCCAGACGCGGTTTCTT 59.968 61.111 12.47 0.00 0.00 2.52
154 155 4.016706 CCCCCAGACGCGGTTTCT 62.017 66.667 12.47 0.32 0.00 2.52
204 205 2.438795 TAAAATCGGCGTGGGGGC 60.439 61.111 6.85 0.00 37.98 5.80
205 206 2.478033 GCTAAAATCGGCGTGGGGG 61.478 63.158 6.85 0.00 0.00 5.40
206 207 2.819552 CGCTAAAATCGGCGTGGGG 61.820 63.158 6.85 0.00 45.34 4.96
207 208 2.707039 CGCTAAAATCGGCGTGGG 59.293 61.111 6.85 0.00 45.34 4.61
213 214 2.895372 AGCCGGCGCTAAAATCGG 60.895 61.111 23.20 15.00 46.08 4.18
233 234 0.608035 TTAAAACCGCTGCCTGGGAG 60.608 55.000 11.32 11.32 0.00 4.30
234 235 0.608035 CTTAAAACCGCTGCCTGGGA 60.608 55.000 0.00 0.00 0.00 4.37
235 236 1.883021 CTTAAAACCGCTGCCTGGG 59.117 57.895 0.00 0.00 0.00 4.45
236 237 1.212751 GCTTAAAACCGCTGCCTGG 59.787 57.895 0.00 0.00 0.00 4.45
237 238 1.154225 CGCTTAAAACCGCTGCCTG 60.154 57.895 0.00 0.00 0.00 4.85
238 239 2.978018 GCGCTTAAAACCGCTGCCT 61.978 57.895 0.00 0.00 46.14 4.75
239 240 2.504026 GCGCTTAAAACCGCTGCC 60.504 61.111 0.00 0.00 46.14 4.85
244 245 2.360726 AGGGGGCGCTTAAAACCG 60.361 61.111 7.64 0.00 0.00 4.44
245 246 2.348104 CCAGGGGGCGCTTAAAACC 61.348 63.158 7.64 0.00 0.00 3.27
246 247 2.348104 CCCAGGGGGCGCTTAAAAC 61.348 63.158 7.64 0.00 35.35 2.43
247 248 2.036572 CCCAGGGGGCGCTTAAAA 59.963 61.111 7.64 0.00 35.35 1.52
269 270 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
280 281 5.766150 TCTAGCTGAGACTTAAGAGCATC 57.234 43.478 10.09 0.00 33.67 3.91
319 321 1.496060 CCCATAGTACAGACTGCCCA 58.504 55.000 1.25 0.00 36.28 5.36
337 339 2.864968 CCAACGAGCGAGTATATAGCC 58.135 52.381 0.00 0.00 0.00 3.93
380 383 9.292195 GTCTCCTACTTCTATAGCTGTCTAAAT 57.708 37.037 0.00 0.00 0.00 1.40
388 391 7.151694 TGGTTAGTCTCCTACTTCTATAGCT 57.848 40.000 0.00 0.00 39.80 3.32
396 662 5.221843 TGCATGTTTGGTTAGTCTCCTACTT 60.222 40.000 0.00 0.00 39.80 2.24
443 710 1.820519 GACCTCATCAATGGCAGCAAA 59.179 47.619 0.00 0.00 0.00 3.68
450 717 1.473965 CCGGTCTGACCTCATCAATGG 60.474 57.143 23.49 11.37 36.69 3.16
454 721 0.904865 AAGCCGGTCTGACCTCATCA 60.905 55.000 23.49 0.00 35.66 3.07
477 744 1.517832 CCGACACCTAGCTCCCTTG 59.482 63.158 0.00 0.00 0.00 3.61
479 746 2.760385 GCCGACACCTAGCTCCCT 60.760 66.667 0.00 0.00 0.00 4.20
490 757 4.717629 CAGAACGAGCCGCCGACA 62.718 66.667 8.04 0.00 0.00 4.35
597 864 3.751175 TGAAAAAGACTTGGCCTCATACG 59.249 43.478 3.32 0.00 0.00 3.06
857 1125 2.264794 CGTCTTTGGTCCCTCGGG 59.735 66.667 0.00 0.00 0.00 5.14
936 1212 1.745653 CTCTCGCTCTGTGTATCACCA 59.254 52.381 0.00 0.00 32.73 4.17
940 1216 0.031449 GGCCTCTCGCTCTGTGTATC 59.969 60.000 0.00 0.00 37.74 2.24
942 1218 2.407428 CGGCCTCTCGCTCTGTGTA 61.407 63.158 0.00 0.00 37.74 2.90
943 1219 3.753434 CGGCCTCTCGCTCTGTGT 61.753 66.667 0.00 0.00 37.74 3.72
944 1220 3.408501 CTCGGCCTCTCGCTCTGTG 62.409 68.421 0.00 0.00 37.74 3.66
945 1221 3.137459 CTCGGCCTCTCGCTCTGT 61.137 66.667 0.00 0.00 37.74 3.41
1140 1426 7.905265 ACTCGGCTGATAGATACTAGTACTAA 58.095 38.462 4.31 0.00 0.00 2.24
1376 1670 3.452627 ACACACACAGGAGAAGAGAAACT 59.547 43.478 0.00 0.00 0.00 2.66
1378 1672 3.432186 CCACACACACAGGAGAAGAGAAA 60.432 47.826 0.00 0.00 0.00 2.52
1397 1691 3.628646 AATCGCCTCCCACTGCCAC 62.629 63.158 0.00 0.00 0.00 5.01
1398 1692 3.329889 AATCGCCTCCCACTGCCA 61.330 61.111 0.00 0.00 0.00 4.92
1399 1693 2.825836 CAATCGCCTCCCACTGCC 60.826 66.667 0.00 0.00 0.00 4.85
1400 1694 1.817099 CTCAATCGCCTCCCACTGC 60.817 63.158 0.00 0.00 0.00 4.40
1427 1721 0.741915 CGCTGTAGAGGAGGAAGGTC 59.258 60.000 0.00 0.00 0.00 3.85
1557 1853 3.054802 ACAGTTCAGAGCTTGGGGATTAG 60.055 47.826 0.00 0.00 0.00 1.73
1701 1997 4.760715 TGGCCAATTCAATTCAAACATTGG 59.239 37.500 0.61 5.07 44.64 3.16
1743 2065 6.849085 AACACCAAAGCATCCATGTAAATA 57.151 33.333 0.00 0.00 0.00 1.40
1814 2136 3.190118 CGGCAATCTTCTTCTTCAAGCTT 59.810 43.478 0.00 0.00 0.00 3.74
1832 2154 3.410631 TGAGTTTATTCTGTTCCGGCA 57.589 42.857 0.00 0.00 0.00 5.69
2223 2548 9.503427 GTTATTTGCATGTAAACCTCATAAGTC 57.497 33.333 11.35 0.00 0.00 3.01
2280 2605 7.939784 AAGATAACTCATTAGTTTCAACCCC 57.060 36.000 0.00 0.00 43.60 4.95
2369 2695 5.743872 GGTATAAACTGTTGCTGCTAAATGC 59.256 40.000 0.00 0.00 43.25 3.56
2426 2752 4.582240 GGGCCAAATAAGGAATTCTCTCTG 59.418 45.833 4.39 0.00 0.00 3.35
2459 2785 6.432403 TTTGGGTCAAATAGGAAAGCAAAT 57.568 33.333 0.00 0.00 0.00 2.32
2579 2905 3.832490 ACTAGGGGCAAAATGGTCTTTTC 59.168 43.478 0.00 0.00 0.00 2.29
2658 2984 2.960384 TGCATCATCCATTGAACATCCC 59.040 45.455 0.00 0.00 38.03 3.85
2703 3029 5.140747 ACAGCTTTTACGAGTGAGAGAAT 57.859 39.130 0.00 0.00 0.00 2.40
2708 3034 5.900339 TTTGTACAGCTTTTACGAGTGAG 57.100 39.130 0.00 0.00 0.00 3.51
2709 3035 6.854496 ATTTTGTACAGCTTTTACGAGTGA 57.146 33.333 0.00 0.00 0.00 3.41
2711 3037 7.201496 CGGATATTTTGTACAGCTTTTACGAGT 60.201 37.037 0.00 0.00 0.00 4.18
2712 3038 7.117454 CGGATATTTTGTACAGCTTTTACGAG 58.883 38.462 0.00 0.00 0.00 4.18
2713 3039 6.591062 ACGGATATTTTGTACAGCTTTTACGA 59.409 34.615 12.24 0.00 0.00 3.43
2714 3040 6.768078 ACGGATATTTTGTACAGCTTTTACG 58.232 36.000 0.00 1.05 0.00 3.18


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

AutoCloner maintained by Alex Coulton.