Multiple sequence alignment - TraesCS6A01G352500

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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 TraesCS6A01G352500 chr6A 100.000 2348 0 0 1 2348 584955989 584953642 0.000000e+00 4337
1 TraesCS6A01G352500 chr6A 82.770 296 40 7 37 323 577005100 577005393 1.080000e-63 254
2 TraesCS6A01G352500 chr6D 90.647 2010 140 20 155 2147 436763790 436761812 0.000000e+00 2627
3 TraesCS6A01G352500 chr6D 84.459 296 35 7 37 323 68688800 68688507 4.940000e-72 281
4 TraesCS6A01G352500 chr6B 91.766 1178 72 14 499 1663 660252810 660251645 0.000000e+00 1615
5 TraesCS6A01G352500 chr6B 90.873 252 23 0 1980 2231 660251644 660251393 2.890000e-89 339
6 TraesCS6A01G352500 chr6B 87.500 128 7 3 2222 2348 660251364 660251245 3.150000e-29 139
7 TraesCS6A01G352500 chr5D 85.196 331 38 6 1 323 534011001 534010674 1.740000e-86 329
8 TraesCS6A01G352500 chr5D 83.438 320 38 6 6 315 371873709 371873395 1.370000e-72 283
9 TraesCS6A01G352500 chr1B 85.455 330 33 10 4 323 579943137 579942813 1.740000e-86 329
10 TraesCS6A01G352500 chr4D 85.196 331 36 9 1 321 505165550 505165877 6.260000e-86 327
11 TraesCS6A01G352500 chr4B 85.196 331 35 5 1 323 479401717 479401393 6.260000e-86 327
12 TraesCS6A01G352500 chr4B 79.825 342 58 10 1 333 211982642 211982981 3.020000e-59 239
13 TraesCS6A01G352500 chr5B 86.897 290 34 4 35 323 572401411 572401697 2.910000e-84 322
14 TraesCS6A01G352500 chr5B 90.196 102 8 2 496 596 276159489 276159589 5.270000e-27 132
15 TraesCS6A01G352500 chr7D 86.129 310 27 8 1 299 509064693 509064997 1.050000e-83 320
16 TraesCS6A01G352500 chr2D 86.230 305 30 6 28 323 28866852 28866551 1.050000e-83 320
17 TraesCS6A01G352500 chr1A 83.234 334 40 11 1 323 61131067 61130739 2.280000e-75 292
18 TraesCS6A01G352500 chr3B 82.209 326 42 9 4 319 533855188 533854869 1.380000e-67 267
19 TraesCS6A01G352500 chr7A 82.175 331 38 9 1 323 62841476 62841159 4.980000e-67 265
20 TraesCS6A01G352500 chr2A 81.138 334 50 9 1 323 73938934 73938603 2.990000e-64 255
21 TraesCS6A01G352500 chr5A 82.042 284 45 5 1 280 62975716 62975435 1.080000e-58 237


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 TraesCS6A01G352500 chr6A 584953642 584955989 2347 True 4337.000000 4337 100.000000 1 2348 1 chr6A.!!$R1 2347
1 TraesCS6A01G352500 chr6D 436761812 436763790 1978 True 2627.000000 2627 90.647000 155 2147 1 chr6D.!!$R2 1992
2 TraesCS6A01G352500 chr6B 660251245 660252810 1565 True 697.666667 1615 90.046333 499 2348 3 chr6B.!!$R1 1849

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
772 785 0.103572 AAAGCTGCCTTGCTGTGTTG 59.896 50.0 0.0 0.0 43.24 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 1818 0.532573 GCTCTGTCGACAATCCAGGA 59.467 55.0 20.49 10.98 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
54 55 9.897744 AAATTATGTGGTAGATAATTTGATGCG 57.102 29.630 12.87 0.00 41.34 4.73
55 56 8.621532 ATTATGTGGTAGATAATTTGATGCGT 57.378 30.769 0.00 0.00 0.00 5.24
56 57 5.733226 TGTGGTAGATAATTTGATGCGTG 57.267 39.130 0.00 0.00 0.00 5.34
57 58 5.423886 TGTGGTAGATAATTTGATGCGTGA 58.576 37.500 0.00 0.00 0.00 4.35
58 59 5.523552 TGTGGTAGATAATTTGATGCGTGAG 59.476 40.000 0.00 0.00 0.00 3.51
59 60 5.050091 GTGGTAGATAATTTGATGCGTGAGG 60.050 44.000 0.00 0.00 0.00 3.86
60 61 5.057149 GGTAGATAATTTGATGCGTGAGGT 58.943 41.667 0.00 0.00 0.00 3.85
61 62 5.527582 GGTAGATAATTTGATGCGTGAGGTT 59.472 40.000 0.00 0.00 0.00 3.50
62 63 5.741388 AGATAATTTGATGCGTGAGGTTC 57.259 39.130 0.00 0.00 0.00 3.62
63 64 2.900122 AATTTGATGCGTGAGGTTCG 57.100 45.000 0.00 0.00 0.00 3.95
64 65 2.093306 ATTTGATGCGTGAGGTTCGA 57.907 45.000 0.00 0.00 0.00 3.71
65 66 2.093306 TTTGATGCGTGAGGTTCGAT 57.907 45.000 0.00 0.00 0.00 3.59
66 67 2.093306 TTGATGCGTGAGGTTCGATT 57.907 45.000 0.00 0.00 0.00 3.34
67 68 1.640428 TGATGCGTGAGGTTCGATTC 58.360 50.000 0.00 0.00 0.00 2.52
68 69 1.067213 TGATGCGTGAGGTTCGATTCA 60.067 47.619 0.00 0.00 0.00 2.57
69 70 1.999735 GATGCGTGAGGTTCGATTCAA 59.000 47.619 0.00 0.00 0.00 2.69
70 71 2.093306 TGCGTGAGGTTCGATTCAAT 57.907 45.000 0.00 0.00 0.00 2.57
71 72 2.422597 TGCGTGAGGTTCGATTCAATT 58.577 42.857 0.00 0.00 0.00 2.32
72 73 2.811431 TGCGTGAGGTTCGATTCAATTT 59.189 40.909 0.00 0.00 0.00 1.82
73 74 3.252215 TGCGTGAGGTTCGATTCAATTTT 59.748 39.130 0.00 0.00 0.00 1.82
74 75 4.226761 GCGTGAGGTTCGATTCAATTTTT 58.773 39.130 0.00 0.00 0.00 1.94
75 76 5.049336 TGCGTGAGGTTCGATTCAATTTTTA 60.049 36.000 0.00 0.00 0.00 1.52
76 77 5.508224 GCGTGAGGTTCGATTCAATTTTTAG 59.492 40.000 0.00 0.00 0.00 1.85
77 78 6.619874 GCGTGAGGTTCGATTCAATTTTTAGA 60.620 38.462 0.00 0.00 0.00 2.10
78 79 7.464358 CGTGAGGTTCGATTCAATTTTTAGAT 58.536 34.615 0.00 0.00 0.00 1.98
79 80 7.636359 CGTGAGGTTCGATTCAATTTTTAGATC 59.364 37.037 0.00 0.00 0.00 2.75
80 81 8.450964 GTGAGGTTCGATTCAATTTTTAGATCA 58.549 33.333 0.00 0.00 0.00 2.92
81 82 9.177608 TGAGGTTCGATTCAATTTTTAGATCAT 57.822 29.630 0.00 0.00 0.00 2.45
82 83 9.657121 GAGGTTCGATTCAATTTTTAGATCATC 57.343 33.333 0.00 0.00 0.00 2.92
83 84 9.401058 AGGTTCGATTCAATTTTTAGATCATCT 57.599 29.630 0.00 0.00 0.00 2.90
84 85 9.443283 GGTTCGATTCAATTTTTAGATCATCTG 57.557 33.333 0.00 0.00 0.00 2.90
85 86 9.443283 GTTCGATTCAATTTTTAGATCATCTGG 57.557 33.333 0.00 0.00 0.00 3.86
86 87 8.962884 TCGATTCAATTTTTAGATCATCTGGA 57.037 30.769 0.00 0.00 0.00 3.86
87 88 8.830580 TCGATTCAATTTTTAGATCATCTGGAC 58.169 33.333 0.00 0.00 0.00 4.02
88 89 8.615211 CGATTCAATTTTTAGATCATCTGGACA 58.385 33.333 0.00 0.00 0.00 4.02
91 92 9.690913 TTCAATTTTTAGATCATCTGGACATCT 57.309 29.630 0.00 0.00 0.00 2.90
92 93 9.117183 TCAATTTTTAGATCATCTGGACATCTG 57.883 33.333 0.00 0.00 0.00 2.90
93 94 9.117183 CAATTTTTAGATCATCTGGACATCTGA 57.883 33.333 0.00 0.00 0.00 3.27
94 95 8.905660 ATTTTTAGATCATCTGGACATCTGAG 57.094 34.615 0.00 0.00 0.00 3.35
95 96 5.465532 TTAGATCATCTGGACATCTGAGC 57.534 43.478 0.00 0.00 0.00 4.26
96 97 3.306613 AGATCATCTGGACATCTGAGCA 58.693 45.455 0.00 0.00 0.00 4.26
97 98 3.322541 AGATCATCTGGACATCTGAGCAG 59.677 47.826 0.00 0.00 0.00 4.24
98 99 1.138464 TCATCTGGACATCTGAGCAGC 59.862 52.381 0.00 0.00 0.00 5.25
99 100 1.139256 CATCTGGACATCTGAGCAGCT 59.861 52.381 0.00 0.00 0.00 4.24
100 101 0.822811 TCTGGACATCTGAGCAGCTC 59.177 55.000 16.21 16.21 0.00 4.09
101 102 0.825410 CTGGACATCTGAGCAGCTCT 59.175 55.000 23.15 2.04 0.00 4.09
102 103 0.822811 TGGACATCTGAGCAGCTCTC 59.177 55.000 23.15 11.57 42.23 3.20
132 133 7.823745 AAAATACAAATCAGGTCAGAACAGT 57.176 32.000 0.00 0.00 0.00 3.55
133 134 6.808008 AATACAAATCAGGTCAGAACAGTG 57.192 37.500 0.00 0.00 0.00 3.66
134 135 4.156455 ACAAATCAGGTCAGAACAGTGT 57.844 40.909 0.00 0.00 0.00 3.55
135 136 3.879295 ACAAATCAGGTCAGAACAGTGTG 59.121 43.478 0.00 0.00 0.00 3.82
136 137 3.845781 AATCAGGTCAGAACAGTGTGT 57.154 42.857 0.00 0.00 0.00 3.72
137 138 2.602257 TCAGGTCAGAACAGTGTGTG 57.398 50.000 0.00 0.00 0.00 3.82
138 139 2.107366 TCAGGTCAGAACAGTGTGTGA 58.893 47.619 0.00 0.00 0.00 3.58
139 140 2.499693 TCAGGTCAGAACAGTGTGTGAA 59.500 45.455 9.58 0.00 0.00 3.18
140 141 2.609459 CAGGTCAGAACAGTGTGTGAAC 59.391 50.000 13.71 13.71 0.00 3.18
141 142 2.236146 AGGTCAGAACAGTGTGTGAACA 59.764 45.455 20.59 0.00 0.00 3.18
142 143 2.609459 GGTCAGAACAGTGTGTGAACAG 59.391 50.000 15.81 0.00 0.00 3.16
143 144 3.262420 GTCAGAACAGTGTGTGAACAGT 58.738 45.455 9.58 0.00 0.00 3.55
144 145 4.430007 GTCAGAACAGTGTGTGAACAGTA 58.570 43.478 9.58 0.00 0.00 2.74
145 146 4.868171 GTCAGAACAGTGTGTGAACAGTAA 59.132 41.667 9.58 0.00 0.00 2.24
146 147 5.350365 GTCAGAACAGTGTGTGAACAGTAAA 59.650 40.000 9.58 0.00 0.00 2.01
147 148 5.935206 TCAGAACAGTGTGTGAACAGTAAAA 59.065 36.000 0.00 0.00 0.00 1.52
148 149 6.428465 TCAGAACAGTGTGTGAACAGTAAAAA 59.572 34.615 0.00 0.00 0.00 1.94
149 150 7.120579 TCAGAACAGTGTGTGAACAGTAAAAAT 59.879 33.333 0.00 0.00 0.00 1.82
150 151 7.218773 CAGAACAGTGTGTGAACAGTAAAAATG 59.781 37.037 0.00 0.00 0.00 2.32
151 152 5.339990 ACAGTGTGTGAACAGTAAAAATGC 58.660 37.500 0.00 0.00 0.00 3.56
152 153 5.125417 ACAGTGTGTGAACAGTAAAAATGCT 59.875 36.000 0.00 0.00 0.00 3.79
153 154 5.682862 CAGTGTGTGAACAGTAAAAATGCTC 59.317 40.000 0.00 0.00 0.00 4.26
183 184 2.247790 TTTTTGCCGAGAGCTGCTC 58.752 52.632 21.72 21.72 44.23 4.26
222 223 7.416964 TTTGGAAATTGAAGAGAACCTCAAA 57.583 32.000 0.00 0.00 32.06 2.69
224 225 5.890985 TGGAAATTGAAGAGAACCTCAAACA 59.109 36.000 0.00 0.00 32.06 2.83
225 226 6.550854 TGGAAATTGAAGAGAACCTCAAACAT 59.449 34.615 0.00 0.00 32.06 2.71
226 227 7.087007 GGAAATTGAAGAGAACCTCAAACATC 58.913 38.462 0.00 0.00 32.06 3.06
227 228 7.255590 GGAAATTGAAGAGAACCTCAAACATCA 60.256 37.037 0.00 0.00 32.06 3.07
228 229 7.587037 AATTGAAGAGAACCTCAAACATCAA 57.413 32.000 0.00 0.00 32.06 2.57
229 230 7.587037 ATTGAAGAGAACCTCAAACATCAAA 57.413 32.000 0.00 0.00 32.06 2.69
246 247 7.994425 ACATCAAAATATCTACCACACACAA 57.006 32.000 0.00 0.00 0.00 3.33
314 315 2.364973 TCGGGATGGGTGCAGCTA 60.365 61.111 16.65 10.72 0.00 3.32
352 361 8.958119 TTACCGAGAATTTCAGTGCTATATTT 57.042 30.769 0.00 0.00 0.00 1.40
353 362 7.251704 ACCGAGAATTTCAGTGCTATATTTG 57.748 36.000 0.00 0.00 0.00 2.32
390 399 4.808895 GTGACATCTGAACATACGCCAATA 59.191 41.667 0.00 0.00 0.00 1.90
436 445 4.607235 CGATAGAAAATAAATTGACGGCGC 59.393 41.667 6.90 0.00 39.76 6.53
452 461 0.169672 GCGCATGCATATGTCCATCC 59.830 55.000 19.57 0.00 42.15 3.51
472 481 2.254546 ACAGTTGTGAATCTTCGCCA 57.745 45.000 1.34 0.00 36.89 5.69
474 483 1.197721 CAGTTGTGAATCTTCGCCACC 59.802 52.381 4.61 0.00 34.85 4.61
475 484 1.202758 AGTTGTGAATCTTCGCCACCA 60.203 47.619 4.61 0.00 34.85 4.17
482 491 3.730761 CTTCGCCACCACTGCAGC 61.731 66.667 15.27 0.00 0.00 5.25
526 535 6.709397 CCTTTTGCAGATAGATTCATGAGCTA 59.291 38.462 9.09 9.09 0.00 3.32
527 536 7.307870 CCTTTTGCAGATAGATTCATGAGCTAC 60.308 40.741 8.91 5.08 0.00 3.58
528 537 5.796424 TGCAGATAGATTCATGAGCTACA 57.204 39.130 8.91 2.21 0.00 2.74
553 563 3.627577 CACACCTGTCCATAATAACCTGC 59.372 47.826 0.00 0.00 0.00 4.85
586 597 2.952978 AGAGTAGGCTATGTTGTCTCCG 59.047 50.000 0.00 0.00 0.00 4.63
605 616 2.264813 CGGAGTACCCATTAACGTGTG 58.735 52.381 0.00 0.00 34.14 3.82
615 626 3.064820 CCATTAACGTGTGCCAGATTACC 59.935 47.826 0.00 0.00 0.00 2.85
635 646 1.678728 CGATTACCTGGAGCAAGCCAA 60.679 52.381 0.00 0.00 37.52 4.52
679 692 4.617298 GCCATGCTTTACACAACCGTAATT 60.617 41.667 0.00 0.00 31.65 1.40
680 693 4.856487 CCATGCTTTACACAACCGTAATTG 59.144 41.667 0.00 0.00 31.65 2.32
681 694 5.457140 CATGCTTTACACAACCGTAATTGT 58.543 37.500 0.00 0.00 43.67 2.71
682 695 5.098218 TGCTTTACACAACCGTAATTGTC 57.902 39.130 0.00 0.00 40.89 3.18
683 696 4.575236 TGCTTTACACAACCGTAATTGTCA 59.425 37.500 0.00 0.00 40.89 3.58
684 697 5.239744 TGCTTTACACAACCGTAATTGTCAT 59.760 36.000 0.00 0.00 40.89 3.06
685 698 6.146898 GCTTTACACAACCGTAATTGTCATT 58.853 36.000 0.00 0.00 40.89 2.57
695 708 2.437200 AATTGTCATTTGCCACCGTG 57.563 45.000 0.00 0.00 0.00 4.94
748 761 3.243035 CGTGATCTTCAAACCAAAGCACA 60.243 43.478 0.00 0.00 0.00 4.57
768 781 1.406903 AAGAAAAGCTGCCTTGCTGT 58.593 45.000 0.00 0.00 43.24 4.40
772 785 0.103572 AAAGCTGCCTTGCTGTGTTG 59.896 50.000 0.00 0.00 43.24 3.33
785 798 3.988379 CTGTGTTGAGCAGCCTTAAAA 57.012 42.857 0.00 0.00 0.00 1.52
917 931 2.524306 CAAGAGAGTCAGACCAGAGGT 58.476 52.381 0.00 0.00 39.44 3.85
924 938 2.232452 AGTCAGACCAGAGGTGAAATCG 59.768 50.000 0.00 0.00 35.25 3.34
939 953 5.353123 GGTGAAATCGCAGTTAAGACCATAA 59.647 40.000 0.00 0.00 0.00 1.90
942 956 3.603158 TCGCAGTTAAGACCATAAGCA 57.397 42.857 0.00 0.00 0.00 3.91
964 980 0.109086 AATCACAGGAGAGTGCGACG 60.109 55.000 0.00 0.00 39.35 5.12
1086 1102 0.311165 CTATGAGGGTGTACTCCGCG 59.689 60.000 0.00 0.00 36.66 6.46
1376 1406 3.332485 AGGGGCAAACATTTACCTAGTGA 59.668 43.478 0.00 0.00 0.00 3.41
1431 1461 7.745155 GCTGTAAGGAATAACGACTTCTTTTTC 59.255 37.037 0.00 0.00 0.00 2.29
1432 1462 8.091385 TGTAAGGAATAACGACTTCTTTTTCC 57.909 34.615 0.00 0.00 33.04 3.13
1435 1465 4.157289 GGAATAACGACTTCTTTTTCCCCC 59.843 45.833 0.00 0.00 0.00 5.40
1444 1474 2.688477 TCTTTTTCCCCCTGTTGCATT 58.312 42.857 0.00 0.00 0.00 3.56
1482 1512 8.523915 ACATAGATCAATCCAATTTAGCACAA 57.476 30.769 0.00 0.00 0.00 3.33
1503 1533 7.032580 CACAAAGAAACAGGTAAAATGACACA 58.967 34.615 0.00 0.00 0.00 3.72
1529 1559 3.754323 GTCCGGTGAAAACAATGATACCA 59.246 43.478 0.00 0.00 0.00 3.25
1547 1577 6.323739 TGATACCACAGATACATAGAACAGCA 59.676 38.462 0.00 0.00 0.00 4.41
1548 1578 5.620738 ACCACAGATACATAGAACAGCAT 57.379 39.130 0.00 0.00 0.00 3.79
1676 1706 5.221501 ACAGAAATGTTAAGCACAGGCAATT 60.222 36.000 0.00 0.00 44.61 2.32
1677 1707 6.015519 ACAGAAATGTTAAGCACAGGCAATTA 60.016 34.615 0.00 0.00 44.61 1.40
1681 1711 6.588719 ATGTTAAGCACAGGCAATTAAGAA 57.411 33.333 0.00 0.00 44.61 2.52
1682 1712 6.398234 TGTTAAGCACAGGCAATTAAGAAA 57.602 33.333 0.00 0.00 44.61 2.52
1684 1714 3.559238 AGCACAGGCAATTAAGAAACG 57.441 42.857 0.00 0.00 44.61 3.60
1686 1716 2.030274 GCACAGGCAATTAAGAAACGGT 60.030 45.455 0.00 0.00 40.72 4.83
1690 1720 4.023193 ACAGGCAATTAAGAAACGGTTGAG 60.023 41.667 0.00 0.00 0.00 3.02
1694 1724 6.093633 AGGCAATTAAGAAACGGTTGAGATAC 59.906 38.462 0.00 0.00 0.00 2.24
1712 1742 6.656270 TGAGATACACAAACATTGCTCTTGAT 59.344 34.615 0.00 0.00 0.00 2.57
1746 1776 9.926158 AAATTATGTGCAGAAACATCATGTAAA 57.074 25.926 0.00 0.00 41.09 2.01
1788 1818 4.864704 AAACACGCCACCAATATCTTTT 57.135 36.364 0.00 0.00 0.00 2.27
1795 1825 4.218312 GCCACCAATATCTTTTCCTGGAT 58.782 43.478 0.00 0.00 0.00 3.41
1836 1866 6.929049 TGATGAAAACGAGAACTACATGTCTT 59.071 34.615 0.00 0.00 0.00 3.01
1837 1867 7.441157 TGATGAAAACGAGAACTACATGTCTTT 59.559 33.333 0.00 0.00 0.00 2.52
1843 1873 7.216973 ACGAGAACTACATGTCTTTAGTCTT 57.783 36.000 0.00 0.00 0.00 3.01
1907 1937 4.785511 TGGTAGACAGTAGAAGCTCAAC 57.214 45.455 0.00 0.00 0.00 3.18
1921 1951 1.077787 TCAACCCTTGCTATGGCCG 60.078 57.895 0.00 0.00 37.74 6.13
1933 1963 1.609635 TATGGCCGGCGAAGAAGTCA 61.610 55.000 22.54 10.56 0.00 3.41
1935 1965 1.964373 GGCCGGCGAAGAAGTCAAA 60.964 57.895 22.54 0.00 0.00 2.69
1938 1968 1.327764 GCCGGCGAAGAAGTCAAATAG 59.672 52.381 12.58 0.00 0.00 1.73
1941 1971 2.603560 CGGCGAAGAAGTCAAATAGTCC 59.396 50.000 0.00 0.00 0.00 3.85
1944 1974 4.246458 GCGAAGAAGTCAAATAGTCCACT 58.754 43.478 0.00 0.00 0.00 4.00
2002 2032 3.633525 TGATACATGATCCTGCAAAAGGC 59.366 43.478 0.00 0.00 46.92 4.35
2023 2053 4.213482 GGCCATACGTTTCCATTAGCTAAG 59.787 45.833 12.54 4.37 0.00 2.18
2055 2085 5.464057 TGAACAGTACTCGTTAACAATGTGG 59.536 40.000 6.39 0.00 0.00 4.17
2059 2089 0.179200 CTCGTTAACAATGTGGGCGC 60.179 55.000 6.39 0.00 0.00 6.53
2066 2096 1.372004 CAATGTGGGCGCAGTTGTG 60.372 57.895 10.83 0.00 0.00 3.33
2084 2114 6.037500 CAGTTGTGGTACATATCCATGAGTTG 59.962 42.308 0.00 0.00 44.52 3.16
2093 2123 9.722056 GTACATATCCATGAGTTGAACAATTTC 57.278 33.333 0.00 0.00 35.96 2.17
2109 2139 5.241662 ACAATTTCCTGAGAGTGAGCTAAC 58.758 41.667 0.00 0.00 0.00 2.34
2113 2143 3.767711 TCCTGAGAGTGAGCTAACTTGA 58.232 45.455 4.84 0.00 0.00 3.02
2158 2188 7.306013 AGTCCACATATTACTAAGGAGATCCA 58.694 38.462 0.92 0.00 38.89 3.41
2161 2191 8.998814 TCCACATATTACTAAGGAGATCCAAAA 58.001 33.333 0.92 0.00 38.89 2.44
2187 2217 4.018506 TCTGAAACAAGCTTATCCCCATGA 60.019 41.667 0.00 0.00 0.00 3.07
2200 2230 2.041485 TCCCCATGACAAAAGCATCAGA 59.959 45.455 0.00 0.00 0.00 3.27
2211 2241 5.175859 CAAAAGCATCAGAGCAAAATCCAT 58.824 37.500 0.00 0.00 36.85 3.41
2213 2243 6.534475 AAAGCATCAGAGCAAAATCCATTA 57.466 33.333 0.00 0.00 36.85 1.90
2217 2247 6.071221 AGCATCAGAGCAAAATCCATTAACAA 60.071 34.615 0.00 0.00 36.85 2.83
2224 2254 8.316214 AGAGCAAAATCCATTAACAACATCAAT 58.684 29.630 0.00 0.00 0.00 2.57
2231 2261 8.585471 ATCCATTAACAACATCAATCAGTTCT 57.415 30.769 0.00 0.00 0.00 3.01
2232 2262 9.685276 ATCCATTAACAACATCAATCAGTTCTA 57.315 29.630 0.00 0.00 0.00 2.10
2233 2263 9.513906 TCCATTAACAACATCAATCAGTTCTAA 57.486 29.630 0.00 0.00 0.00 2.10
2266 2335 9.979578 AAATGTATAATCAACAAAGCAACTTCA 57.020 25.926 0.00 0.00 0.00 3.02
2267 2336 9.979578 AATGTATAATCAACAAAGCAACTTCAA 57.020 25.926 0.00 0.00 0.00 2.69
2268 2337 9.979578 ATGTATAATCAACAAAGCAACTTCAAA 57.020 25.926 0.00 0.00 0.00 2.69
2312 2381 7.970061 ACATTACATTCAATTGAACAAGATCCG 59.030 33.333 22.71 10.09 36.80 4.18
2341 2410 0.825010 GATGTGGATGTGGATGGGGC 60.825 60.000 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 9.897744 CGCATCAAATTATCTACCACATAATTT 57.102 29.630 5.08 5.08 42.94 1.82
29 30 9.066892 ACGCATCAAATTATCTACCACATAATT 57.933 29.630 0.00 0.00 37.82 1.40
30 31 8.506437 CACGCATCAAATTATCTACCACATAAT 58.494 33.333 0.00 0.00 0.00 1.28
31 32 7.713073 TCACGCATCAAATTATCTACCACATAA 59.287 33.333 0.00 0.00 0.00 1.90
32 33 7.213678 TCACGCATCAAATTATCTACCACATA 58.786 34.615 0.00 0.00 0.00 2.29
33 34 6.054941 TCACGCATCAAATTATCTACCACAT 58.945 36.000 0.00 0.00 0.00 3.21
34 35 5.423886 TCACGCATCAAATTATCTACCACA 58.576 37.500 0.00 0.00 0.00 4.17
35 36 5.050091 CCTCACGCATCAAATTATCTACCAC 60.050 44.000 0.00 0.00 0.00 4.16
36 37 5.056480 CCTCACGCATCAAATTATCTACCA 58.944 41.667 0.00 0.00 0.00 3.25
37 38 5.057149 ACCTCACGCATCAAATTATCTACC 58.943 41.667 0.00 0.00 0.00 3.18
38 39 6.562270 CGAACCTCACGCATCAAATTATCTAC 60.562 42.308 0.00 0.00 0.00 2.59
39 40 5.462068 CGAACCTCACGCATCAAATTATCTA 59.538 40.000 0.00 0.00 0.00 1.98
40 41 4.271049 CGAACCTCACGCATCAAATTATCT 59.729 41.667 0.00 0.00 0.00 1.98
41 42 4.270084 TCGAACCTCACGCATCAAATTATC 59.730 41.667 0.00 0.00 0.00 1.75
42 43 4.188462 TCGAACCTCACGCATCAAATTAT 58.812 39.130 0.00 0.00 0.00 1.28
43 44 3.591023 TCGAACCTCACGCATCAAATTA 58.409 40.909 0.00 0.00 0.00 1.40
44 45 2.422597 TCGAACCTCACGCATCAAATT 58.577 42.857 0.00 0.00 0.00 1.82
45 46 2.093306 TCGAACCTCACGCATCAAAT 57.907 45.000 0.00 0.00 0.00 2.32
46 47 2.093306 ATCGAACCTCACGCATCAAA 57.907 45.000 0.00 0.00 0.00 2.69
47 48 1.999735 GAATCGAACCTCACGCATCAA 59.000 47.619 0.00 0.00 0.00 2.57
48 49 1.067213 TGAATCGAACCTCACGCATCA 60.067 47.619 0.00 0.00 0.00 3.07
49 50 1.640428 TGAATCGAACCTCACGCATC 58.360 50.000 0.00 0.00 0.00 3.91
50 51 2.093306 TTGAATCGAACCTCACGCAT 57.907 45.000 0.00 0.00 0.00 4.73
51 52 2.093306 ATTGAATCGAACCTCACGCA 57.907 45.000 0.00 0.00 0.00 5.24
52 53 3.471495 AAATTGAATCGAACCTCACGC 57.529 42.857 0.00 0.00 0.00 5.34
53 54 6.827641 TCTAAAAATTGAATCGAACCTCACG 58.172 36.000 0.00 0.00 0.00 4.35
54 55 8.450964 TGATCTAAAAATTGAATCGAACCTCAC 58.549 33.333 0.00 0.00 0.00 3.51
55 56 8.560355 TGATCTAAAAATTGAATCGAACCTCA 57.440 30.769 0.00 0.00 0.00 3.86
56 57 9.657121 GATGATCTAAAAATTGAATCGAACCTC 57.343 33.333 0.00 0.00 0.00 3.85
57 58 9.401058 AGATGATCTAAAAATTGAATCGAACCT 57.599 29.630 0.00 0.00 0.00 3.50
58 59 9.443283 CAGATGATCTAAAAATTGAATCGAACC 57.557 33.333 0.00 0.00 0.00 3.62
59 60 9.443283 CCAGATGATCTAAAAATTGAATCGAAC 57.557 33.333 0.00 0.00 0.00 3.95
60 61 9.394767 TCCAGATGATCTAAAAATTGAATCGAA 57.605 29.630 0.00 0.00 0.00 3.71
61 62 8.830580 GTCCAGATGATCTAAAAATTGAATCGA 58.169 33.333 0.00 0.00 0.00 3.59
62 63 8.615211 TGTCCAGATGATCTAAAAATTGAATCG 58.385 33.333 0.00 0.00 0.00 3.34
65 66 9.690913 AGATGTCCAGATGATCTAAAAATTGAA 57.309 29.630 0.00 0.00 0.00 2.69
66 67 9.117183 CAGATGTCCAGATGATCTAAAAATTGA 57.883 33.333 0.00 0.00 0.00 2.57
67 68 9.117183 TCAGATGTCCAGATGATCTAAAAATTG 57.883 33.333 0.00 0.00 0.00 2.32
68 69 9.339850 CTCAGATGTCCAGATGATCTAAAAATT 57.660 33.333 0.00 0.00 0.00 1.82
69 70 7.444792 GCTCAGATGTCCAGATGATCTAAAAAT 59.555 37.037 0.00 0.00 0.00 1.82
70 71 6.765036 GCTCAGATGTCCAGATGATCTAAAAA 59.235 38.462 0.00 0.00 0.00 1.94
71 72 6.126968 TGCTCAGATGTCCAGATGATCTAAAA 60.127 38.462 0.00 0.00 0.00 1.52
72 73 5.364735 TGCTCAGATGTCCAGATGATCTAAA 59.635 40.000 0.00 0.00 0.00 1.85
73 74 4.897670 TGCTCAGATGTCCAGATGATCTAA 59.102 41.667 0.00 0.00 0.00 2.10
74 75 4.477249 TGCTCAGATGTCCAGATGATCTA 58.523 43.478 0.00 0.00 0.00 1.98
75 76 3.306613 TGCTCAGATGTCCAGATGATCT 58.693 45.455 0.00 0.00 0.00 2.75
76 77 3.655486 CTGCTCAGATGTCCAGATGATC 58.345 50.000 0.00 0.00 0.00 2.92
77 78 2.224329 GCTGCTCAGATGTCCAGATGAT 60.224 50.000 0.29 0.00 0.00 2.45
78 79 1.138464 GCTGCTCAGATGTCCAGATGA 59.862 52.381 0.29 0.00 0.00 2.92
79 80 1.139256 AGCTGCTCAGATGTCCAGATG 59.861 52.381 0.00 0.00 0.00 2.90
80 81 1.413445 GAGCTGCTCAGATGTCCAGAT 59.587 52.381 24.02 1.39 0.00 2.90
81 82 0.822811 GAGCTGCTCAGATGTCCAGA 59.177 55.000 24.02 0.00 0.00 3.86
82 83 0.825410 AGAGCTGCTCAGATGTCCAG 59.175 55.000 29.49 0.00 32.06 3.86
83 84 0.822811 GAGAGCTGCTCAGATGTCCA 59.177 55.000 29.49 0.00 43.38 4.02
84 85 3.665544 GAGAGCTGCTCAGATGTCC 57.334 57.895 29.49 2.47 43.38 4.02
107 108 8.137437 CACTGTTCTGACCTGATTTGTATTTTT 58.863 33.333 0.00 0.00 0.00 1.94
108 109 7.285401 ACACTGTTCTGACCTGATTTGTATTTT 59.715 33.333 0.00 0.00 0.00 1.82
109 110 6.772716 ACACTGTTCTGACCTGATTTGTATTT 59.227 34.615 0.00 0.00 0.00 1.40
110 111 6.205464 CACACTGTTCTGACCTGATTTGTATT 59.795 38.462 0.00 0.00 0.00 1.89
111 112 5.702670 CACACTGTTCTGACCTGATTTGTAT 59.297 40.000 0.00 0.00 0.00 2.29
112 113 5.056480 CACACTGTTCTGACCTGATTTGTA 58.944 41.667 0.00 0.00 0.00 2.41
113 114 3.879295 CACACTGTTCTGACCTGATTTGT 59.121 43.478 0.00 0.00 0.00 2.83
114 115 3.879295 ACACACTGTTCTGACCTGATTTG 59.121 43.478 0.00 0.00 0.00 2.32
115 116 3.879295 CACACACTGTTCTGACCTGATTT 59.121 43.478 0.00 0.00 0.00 2.17
116 117 3.134623 TCACACACTGTTCTGACCTGATT 59.865 43.478 0.00 0.00 0.00 2.57
117 118 2.700371 TCACACACTGTTCTGACCTGAT 59.300 45.455 0.00 0.00 0.00 2.90
118 119 2.107366 TCACACACTGTTCTGACCTGA 58.893 47.619 0.00 0.00 0.00 3.86
119 120 2.602257 TCACACACTGTTCTGACCTG 57.398 50.000 0.00 0.00 0.00 4.00
120 121 2.236146 TGTTCACACACTGTTCTGACCT 59.764 45.455 0.00 0.00 0.00 3.85
121 122 2.609459 CTGTTCACACACTGTTCTGACC 59.391 50.000 0.00 0.00 0.00 4.02
122 123 3.262420 ACTGTTCACACACTGTTCTGAC 58.738 45.455 0.00 0.00 0.00 3.51
123 124 3.610040 ACTGTTCACACACTGTTCTGA 57.390 42.857 0.00 0.00 0.00 3.27
124 125 5.794687 TTTACTGTTCACACACTGTTCTG 57.205 39.130 0.00 0.00 31.81 3.02
125 126 6.811253 TTTTTACTGTTCACACACTGTTCT 57.189 33.333 0.00 0.00 31.81 3.01
126 127 6.020678 GCATTTTTACTGTTCACACACTGTTC 60.021 38.462 0.00 0.00 31.81 3.18
127 128 5.804979 GCATTTTTACTGTTCACACACTGTT 59.195 36.000 0.00 0.00 31.81 3.16
128 129 5.125417 AGCATTTTTACTGTTCACACACTGT 59.875 36.000 0.00 0.00 33.75 3.55
129 130 5.581605 AGCATTTTTACTGTTCACACACTG 58.418 37.500 0.00 0.00 0.00 3.66
130 131 5.221048 GGAGCATTTTTACTGTTCACACACT 60.221 40.000 0.00 0.00 0.00 3.55
131 132 4.976116 GGAGCATTTTTACTGTTCACACAC 59.024 41.667 0.00 0.00 0.00 3.82
132 133 4.260990 CGGAGCATTTTTACTGTTCACACA 60.261 41.667 0.00 0.00 0.00 3.72
133 134 4.219033 CGGAGCATTTTTACTGTTCACAC 58.781 43.478 0.00 0.00 0.00 3.82
134 135 3.252215 CCGGAGCATTTTTACTGTTCACA 59.748 43.478 0.00 0.00 0.00 3.58
135 136 3.500680 TCCGGAGCATTTTTACTGTTCAC 59.499 43.478 0.00 0.00 0.00 3.18
136 137 3.745799 TCCGGAGCATTTTTACTGTTCA 58.254 40.909 0.00 0.00 0.00 3.18
137 138 4.965119 ATCCGGAGCATTTTTACTGTTC 57.035 40.909 11.34 0.00 0.00 3.18
138 139 5.010617 ACAAATCCGGAGCATTTTTACTGTT 59.989 36.000 11.34 0.00 0.00 3.16
139 140 4.522789 ACAAATCCGGAGCATTTTTACTGT 59.477 37.500 11.34 0.00 0.00 3.55
140 141 5.059404 ACAAATCCGGAGCATTTTTACTG 57.941 39.130 11.34 0.00 0.00 2.74
141 142 5.010282 AGACAAATCCGGAGCATTTTTACT 58.990 37.500 11.34 5.56 0.00 2.24
142 143 5.310720 AGACAAATCCGGAGCATTTTTAC 57.689 39.130 11.34 3.40 0.00 2.01
143 144 5.975693 AAGACAAATCCGGAGCATTTTTA 57.024 34.783 11.34 0.00 0.00 1.52
144 145 4.871933 AAGACAAATCCGGAGCATTTTT 57.128 36.364 11.34 1.61 0.00 1.94
145 146 4.871933 AAAGACAAATCCGGAGCATTTT 57.128 36.364 11.34 2.05 0.00 1.82
146 147 4.871933 AAAAGACAAATCCGGAGCATTT 57.128 36.364 11.34 2.47 0.00 2.32
147 148 4.871933 AAAAAGACAAATCCGGAGCATT 57.128 36.364 11.34 1.75 0.00 3.56
178 179 5.340803 CAAATCATTTGGACATCTGAGCAG 58.659 41.667 1.73 0.00 37.01 4.24
202 203 7.651808 TGATGTTTGAGGTTCTCTTCAATTTC 58.348 34.615 0.00 0.00 38.94 2.17
209 210 9.525826 AGATATTTTGATGTTTGAGGTTCTCTT 57.474 29.630 0.00 0.00 0.00 2.85
212 213 9.178758 GGTAGATATTTTGATGTTTGAGGTTCT 57.821 33.333 0.00 0.00 0.00 3.01
222 223 7.994425 TTGTGTGTGGTAGATATTTTGATGT 57.006 32.000 0.00 0.00 0.00 3.06
314 315 3.004090 GGTAATCCACCCGGGCTT 58.996 61.111 24.08 11.94 42.07 4.35
339 348 6.662755 ACATTTCCCTCAAATATAGCACTGA 58.337 36.000 0.00 0.00 32.48 3.41
352 361 3.855255 TGTCACTCAACATTTCCCTCA 57.145 42.857 0.00 0.00 0.00 3.86
353 362 4.394300 CAGATGTCACTCAACATTTCCCTC 59.606 45.833 0.00 0.00 39.93 4.30
390 399 7.375834 TCGTGTCATAACTGTGAGACTAAAAT 58.624 34.615 2.99 0.00 39.49 1.82
436 445 3.483421 ACTGTGGATGGACATATGCATG 58.517 45.455 10.16 0.00 36.94 4.06
452 461 1.872952 TGGCGAAGATTCACAACTGTG 59.127 47.619 3.33 3.33 46.91 3.66
472 481 2.032223 CTGAGCAGCTGCAGTGGT 59.968 61.111 38.24 19.47 45.16 4.16
474 483 1.004799 AGACTGAGCAGCTGCAGTG 60.005 57.895 38.24 27.36 44.77 3.66
482 491 1.675415 GGAAGCAAGGAGACTGAGCAG 60.675 57.143 0.00 0.00 42.68 4.24
526 535 3.806949 ATTATGGACAGGTGTGGTTGT 57.193 42.857 0.00 0.00 0.00 3.32
527 536 4.398044 GGTTATTATGGACAGGTGTGGTTG 59.602 45.833 0.00 0.00 0.00 3.77
528 537 4.291249 AGGTTATTATGGACAGGTGTGGTT 59.709 41.667 0.00 0.00 0.00 3.67
553 563 6.719370 ACATAGCCTACTCTAGAGATTTCCAG 59.281 42.308 26.57 11.27 0.00 3.86
586 597 2.004733 GCACACGTTAATGGGTACTCC 58.995 52.381 1.33 0.00 0.00 3.85
605 616 2.367567 TCCAGGTAATCGGTAATCTGGC 59.632 50.000 0.00 0.00 40.93 4.85
615 626 0.107703 TGGCTTGCTCCAGGTAATCG 60.108 55.000 0.00 0.00 0.00 3.34
679 692 1.169661 GGTCACGGTGGCAAATGACA 61.170 55.000 21.54 0.00 42.66 3.58
680 693 1.579429 GGTCACGGTGGCAAATGAC 59.421 57.895 15.45 15.19 40.62 3.06
681 694 1.963855 CGGTCACGGTGGCAAATGA 60.964 57.895 15.45 0.00 36.18 2.57
682 695 2.560861 CGGTCACGGTGGCAAATG 59.439 61.111 15.45 0.00 36.18 2.32
683 696 3.361977 GCGGTCACGGTGGCAAAT 61.362 61.111 15.45 0.00 41.36 2.32
706 719 0.169009 GCGAGGAAAATGAGTGGCAC 59.831 55.000 10.29 10.29 0.00 5.01
748 761 1.758862 ACAGCAAGGCAGCTTTTCTTT 59.241 42.857 1.44 0.00 43.70 2.52
768 781 2.660572 TGGTTTTAAGGCTGCTCAACA 58.339 42.857 0.00 0.00 0.00 3.33
772 785 1.401539 CGCTTGGTTTTAAGGCTGCTC 60.402 52.381 0.00 0.00 0.00 4.26
785 798 0.248458 CGCAAAGTCAAACGCTTGGT 60.248 50.000 0.00 0.00 33.01 3.67
820 833 1.350684 TCTCCATGGTGTGCTTGCTAA 59.649 47.619 12.58 0.00 0.00 3.09
917 931 5.064707 GCTTATGGTCTTAACTGCGATTTCA 59.935 40.000 0.00 0.00 0.00 2.69
924 938 7.062255 GTGATTTTTGCTTATGGTCTTAACTGC 59.938 37.037 0.00 0.00 0.00 4.40
939 953 2.555757 GCACTCTCCTGTGATTTTTGCT 59.444 45.455 0.00 0.00 40.12 3.91
942 956 2.808543 GTCGCACTCTCCTGTGATTTTT 59.191 45.455 0.00 0.00 40.12 1.94
964 980 2.086054 TTCTTCTGCTTTCGCCTCTC 57.914 50.000 0.00 0.00 34.43 3.20
985 1001 1.095228 TCCATGGATTTCGCCTTCGC 61.095 55.000 11.44 0.00 35.26 4.70
1086 1102 2.045634 GGTACCTTCCCGGTTGCC 60.046 66.667 4.06 0.00 46.37 4.52
1089 1105 2.144952 AAACGGTACCTTCCCGGTT 58.855 52.632 10.90 2.44 46.72 4.44
1125 1141 3.342477 GGGCTCTTGGGCTTCCCT 61.342 66.667 3.27 0.00 45.70 4.20
1197 1213 4.424626 TGTCTTTATCATCAGTGAGTCGC 58.575 43.478 0.00 0.00 37.87 5.19
1251 1270 2.225117 CCCTTCAAACCCACCTTGATCT 60.225 50.000 0.00 0.00 32.98 2.75
1396 1426 7.707893 GTCGTTATTCCTTACAGCTGGTTAATA 59.292 37.037 19.93 11.08 0.00 0.98
1419 1449 2.271944 ACAGGGGGAAAAAGAAGTCG 57.728 50.000 0.00 0.00 0.00 4.18
1431 1461 1.784358 ATCATCAATGCAACAGGGGG 58.216 50.000 0.00 0.00 0.00 5.40
1432 1462 2.761767 TGAATCATCAATGCAACAGGGG 59.238 45.455 0.00 0.00 30.99 4.79
1435 1465 3.127376 TCGGTGAATCATCAATGCAACAG 59.873 43.478 0.00 0.00 37.30 3.16
1444 1474 5.789643 TGATCTATGTCGGTGAATCATCA 57.210 39.130 0.00 0.00 0.00 3.07
1482 1512 7.093945 ACAACTGTGTCATTTTACCTGTTTCTT 60.094 33.333 0.00 0.00 29.49 2.52
1503 1533 3.283751 TCATTGTTTTCACCGGACAACT 58.716 40.909 9.46 0.00 36.25 3.16
1511 1541 5.957842 TCTGTGGTATCATTGTTTTCACC 57.042 39.130 0.00 0.00 0.00 4.02
1512 1542 8.039603 TGTATCTGTGGTATCATTGTTTTCAC 57.960 34.615 0.00 0.00 0.00 3.18
1655 1685 7.090173 TCTTAATTGCCTGTGCTTAACATTTC 58.910 34.615 0.00 0.00 38.39 2.17
1664 1694 2.228822 CCGTTTCTTAATTGCCTGTGCT 59.771 45.455 0.00 0.00 38.71 4.40
1665 1695 2.030274 ACCGTTTCTTAATTGCCTGTGC 60.030 45.455 0.00 0.00 38.26 4.57
1666 1696 3.915437 ACCGTTTCTTAATTGCCTGTG 57.085 42.857 0.00 0.00 0.00 3.66
1667 1697 3.886505 TCAACCGTTTCTTAATTGCCTGT 59.113 39.130 0.00 0.00 0.00 4.00
1676 1706 6.762187 TGTTTGTGTATCTCAACCGTTTCTTA 59.238 34.615 0.00 0.00 0.00 2.10
1677 1707 5.587043 TGTTTGTGTATCTCAACCGTTTCTT 59.413 36.000 0.00 0.00 0.00 2.52
1681 1711 5.757886 CAATGTTTGTGTATCTCAACCGTT 58.242 37.500 0.00 0.00 0.00 4.44
1682 1712 4.320202 GCAATGTTTGTGTATCTCAACCGT 60.320 41.667 0.00 0.00 0.00 4.83
1684 1714 5.182001 AGAGCAATGTTTGTGTATCTCAACC 59.818 40.000 0.00 0.00 0.00 3.77
1686 1716 6.486320 TCAAGAGCAATGTTTGTGTATCTCAA 59.514 34.615 0.00 0.00 0.00 3.02
1690 1720 5.514204 GCATCAAGAGCAATGTTTGTGTATC 59.486 40.000 0.00 0.00 0.00 2.24
1694 1724 3.909430 AGCATCAAGAGCAATGTTTGTG 58.091 40.909 0.00 0.00 0.00 3.33
1712 1742 3.419943 TCTGCACATAATTTGGTGAGCA 58.580 40.909 11.94 10.29 39.11 4.26
1746 1776 8.888716 GTGTTTTTGGAAATGTGGTTTAGAAAT 58.111 29.630 0.00 0.00 0.00 2.17
1788 1818 0.532573 GCTCTGTCGACAATCCAGGA 59.467 55.000 20.49 10.98 0.00 3.86
1795 1825 3.663025 TCATCATTTGCTCTGTCGACAA 58.337 40.909 20.49 9.70 0.00 3.18
1836 1866 6.524101 ACTTTGCCAAACTTTGAAGACTAA 57.476 33.333 2.87 0.00 0.00 2.24
1837 1867 7.338449 AGTTACTTTGCCAAACTTTGAAGACTA 59.662 33.333 2.87 0.00 29.25 2.59
1843 1873 5.221165 GGCTAGTTACTTTGCCAAACTTTGA 60.221 40.000 19.02 0.00 44.34 2.69
1921 1951 3.371285 GTGGACTATTTGACTTCTTCGCC 59.629 47.826 0.00 0.00 0.00 5.54
1924 1954 4.997395 TGCAGTGGACTATTTGACTTCTTC 59.003 41.667 0.00 0.00 0.00 2.87
1956 1986 1.340248 CAGTATACCTCGTTGCCGGAT 59.660 52.381 5.05 0.00 33.95 4.18
1960 1990 2.240493 ATGCAGTATACCTCGTTGCC 57.760 50.000 10.51 0.00 33.98 4.52
2002 2032 4.814234 TGCTTAGCTAATGGAAACGTATGG 59.186 41.667 6.64 0.00 0.00 2.74
2023 2053 4.992381 ACGAGTACTGTTCATTTTCTGC 57.008 40.909 0.00 0.00 0.00 4.26
2055 2085 1.597663 GATATGTACCACAACTGCGCC 59.402 52.381 4.18 0.00 0.00 6.53
2059 2089 5.674525 ACTCATGGATATGTACCACAACTG 58.325 41.667 0.00 0.00 40.36 3.16
2066 2096 7.807977 ATTGTTCAACTCATGGATATGTACC 57.192 36.000 0.00 0.00 35.73 3.34
2084 2114 4.322567 AGCTCACTCTCAGGAAATTGTTC 58.677 43.478 0.00 0.00 0.00 3.18
2093 2123 4.493547 CTTCAAGTTAGCTCACTCTCAGG 58.506 47.826 0.00 0.00 0.00 3.86
2109 2139 9.167311 ACTATTTATTAGTTGCACTCCTTCAAG 57.833 33.333 0.00 0.00 37.96 3.02
2113 2143 7.553044 GTGGACTATTTATTAGTTGCACTCCTT 59.447 37.037 0.00 0.00 41.35 3.36
2161 2191 5.332743 TGGGGATAAGCTTGTTTCAGATTT 58.667 37.500 9.86 0.00 0.00 2.17
2187 2217 4.039488 TGGATTTTGCTCTGATGCTTTTGT 59.961 37.500 0.00 0.00 0.00 2.83
2200 2230 8.095792 TGATTGATGTTGTTAATGGATTTTGCT 58.904 29.630 0.00 0.00 0.00 3.91
2213 2243 8.862325 TGGTATTAGAACTGATTGATGTTGTT 57.138 30.769 0.00 0.00 0.00 2.83
2292 2361 5.959527 CGTACGGATCTTGTTCAATTGAATG 59.040 40.000 23.05 15.79 36.33 2.67
2298 2367 5.006153 TCATCGTACGGATCTTGTTCAAT 57.994 39.130 16.52 0.00 31.28 2.57
2303 2372 4.098044 ACATCTTCATCGTACGGATCTTGT 59.902 41.667 16.52 8.18 31.28 3.16
2304 2373 4.442403 CACATCTTCATCGTACGGATCTTG 59.558 45.833 16.52 7.57 31.28 3.02
2305 2374 4.499865 CCACATCTTCATCGTACGGATCTT 60.500 45.833 16.52 0.00 31.28 2.40
2306 2375 3.004839 CCACATCTTCATCGTACGGATCT 59.995 47.826 16.52 0.00 31.28 2.75
2312 2381 3.804325 CCACATCCACATCTTCATCGTAC 59.196 47.826 0.00 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.