Multiple sequence alignment - TraesCS7D01G192100

Loading Multiple Alignment...

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 TraesCS7D01G192100 chr7D 100.000 4127 0 0 1 4127 147692670 147688544 0.000000e+00 7622.0
1 TraesCS7D01G192100 chr7B 91.173 3750 123 75 458 4127 110701996 110698375 0.000000e+00 4900.0
2 TraesCS7D01G192100 chr7B 87.162 148 9 7 230 368 110702144 110701998 4.270000e-35 159.0
3 TraesCS7D01G192100 chr7B 87.629 97 11 1 372 467 674647116 674647020 1.210000e-20 111.0
4 TraesCS7D01G192100 chr7A 89.167 3794 152 107 458 4127 148988792 148985134 0.000000e+00 4490.0
5 TraesCS7D01G192100 chr7A 90.588 85 8 0 375 459 712701250 712701166 3.370000e-21 113.0
6 TraesCS7D01G192100 chr6B 85.455 220 30 2 6 224 705759786 705760004 1.150000e-55 228.0
7 TraesCS7D01G192100 chr6B 81.579 152 20 6 6 156 706640532 706640676 7.250000e-23 119.0
8 TraesCS7D01G192100 chr4B 85.782 211 27 3 21 229 514608519 514608310 1.930000e-53 220.0
9 TraesCS7D01G192100 chr4B 78.750 240 29 3 7 224 585726114 585726353 1.550000e-29 141.0
10 TraesCS7D01G192100 chr3A 90.526 95 8 1 368 461 158688612 158688706 1.560000e-24 124.0
11 TraesCS7D01G192100 chr3D 76.923 234 34 9 6 220 4860660 4860892 9.370000e-22 115.0
12 TraesCS7D01G192100 chr2A 89.888 89 9 0 373 461 577214409 577214321 9.370000e-22 115.0
13 TraesCS7D01G192100 chr2A 76.623 231 37 14 6 220 623101099 623101328 1.210000e-20 111.0
14 TraesCS7D01G192100 chr4A 90.588 85 7 1 374 457 423375185 423375269 1.210000e-20 111.0
15 TraesCS7D01G192100 chr4A 88.764 89 10 0 373 461 577975140 577975052 4.360000e-20 110.0
16 TraesCS7D01G192100 chr5A 88.764 89 10 0 373 461 429112115 429112027 4.360000e-20 110.0
17 TraesCS7D01G192100 chr3B 83.621 116 19 0 105 220 66627890 66628005 4.360000e-20 110.0
18 TraesCS7D01G192100 chr3B 94.286 35 0 2 202 234 212156623 212156589 7.000000e-03 52.8
19 TraesCS7D01G192100 chrUn 84.071 113 17 1 5 116 79889028 79889140 1.570000e-19 108.0
20 TraesCS7D01G192100 chr6A 87.640 89 10 1 373 461 559261624 559261711 7.300000e-18 102.0
21 TraesCS7D01G192100 chr1A 86.517 89 12 0 373 461 583816698 583816786 9.440000e-17 99.0


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 TraesCS7D01G192100 chr7D 147688544 147692670 4126 True 7622.0 7622 100.0000 1 4127 1 chr7D.!!$R1 4126
1 TraesCS7D01G192100 chr7B 110698375 110702144 3769 True 2529.5 4900 89.1675 230 4127 2 chr7B.!!$R2 3897
2 TraesCS7D01G192100 chr7A 148985134 148988792 3658 True 4490.0 4490 89.1670 458 4127 1 chr7A.!!$R1 3669

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
757 793 0.034960 TCAGTCAGGTCCCTCTCGAG 60.035 60.0 5.93 5.93 0.0 4.04 F
872 908 0.035343 CGGGAAAGAAAGGGAGTCCC 60.035 60.0 21.81 21.81 45.9 4.46 F
2378 2493 0.249489 GGTGCGCTCATACCCTACTG 60.249 60.0 9.73 0.00 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2552 2667 0.107897 ACAACCACTCACTCGTGCAA 60.108 50.0 0.00 0.0 33.6 4.08 R
2594 2712 0.609131 ATCAAACCAGCAAGTCCCGG 60.609 55.0 0.00 0.0 0.0 5.73 R
3307 3459 0.321919 ACACTACGTACGGCCAGAGA 60.322 55.0 21.06 0.0 0.0 3.10 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
17 18 2.267006 ACAGTGAGCGCATCCAGG 59.733 61.111 11.47 2.57 0.00 4.45
18 19 2.285773 ACAGTGAGCGCATCCAGGA 61.286 57.895 11.47 0.00 0.00 3.86
19 20 1.078918 CAGTGAGCGCATCCAGGAA 60.079 57.895 11.47 0.00 0.00 3.36
20 21 1.078848 AGTGAGCGCATCCAGGAAC 60.079 57.895 11.47 0.00 0.00 3.62
21 22 2.125552 TGAGCGCATCCAGGAACG 60.126 61.111 11.47 10.27 0.00 3.95
52 53 4.042251 GGAGGAGGTCCAGGTGAG 57.958 66.667 0.00 0.00 46.10 3.51
53 54 1.687493 GGAGGAGGTCCAGGTGAGG 60.687 68.421 0.00 0.00 46.10 3.86
54 55 1.687493 GAGGAGGTCCAGGTGAGGG 60.687 68.421 0.00 0.00 38.89 4.30
55 56 2.689034 GGAGGTCCAGGTGAGGGG 60.689 72.222 0.00 0.00 35.64 4.79
56 57 2.450243 GAGGTCCAGGTGAGGGGA 59.550 66.667 0.00 0.00 0.00 4.81
57 58 1.003573 GAGGTCCAGGTGAGGGGAT 59.996 63.158 0.00 0.00 35.25 3.85
58 59 1.307343 AGGTCCAGGTGAGGGGATG 60.307 63.158 0.00 0.00 35.25 3.51
59 60 2.378634 GGTCCAGGTGAGGGGATGG 61.379 68.421 0.00 0.00 35.25 3.51
60 61 1.616628 GTCCAGGTGAGGGGATGGT 60.617 63.158 0.00 0.00 35.25 3.55
61 62 1.616327 TCCAGGTGAGGGGATGGTG 60.616 63.158 0.00 0.00 34.32 4.17
62 63 2.683465 CCAGGTGAGGGGATGGTGG 61.683 68.421 0.00 0.00 0.00 4.61
63 64 3.017581 AGGTGAGGGGATGGTGGC 61.018 66.667 0.00 0.00 0.00 5.01
64 65 4.129148 GGTGAGGGGATGGTGGCC 62.129 72.222 0.00 0.00 0.00 5.36
65 66 4.489771 GTGAGGGGATGGTGGCCG 62.490 72.222 0.00 0.00 0.00 6.13
94 95 4.503314 GACGTCTAACGGCCGGGG 62.503 72.222 31.76 18.43 45.60 5.73
112 113 2.884685 CTGCGCGCTGAGAGGAAG 60.885 66.667 33.29 14.75 0.00 3.46
113 114 3.348055 CTGCGCGCTGAGAGGAAGA 62.348 63.158 33.29 6.44 0.00 2.87
114 115 2.125912 GCGCGCTGAGAGGAAGAA 60.126 61.111 26.67 0.00 0.00 2.52
115 116 2.164026 GCGCGCTGAGAGGAAGAAG 61.164 63.158 26.67 0.00 0.00 2.85
116 117 1.518133 CGCGCTGAGAGGAAGAAGG 60.518 63.158 5.56 0.00 0.00 3.46
117 118 1.893786 GCGCTGAGAGGAAGAAGGA 59.106 57.895 0.00 0.00 0.00 3.36
118 119 0.179113 GCGCTGAGAGGAAGAAGGAG 60.179 60.000 0.00 0.00 0.00 3.69
119 120 1.468985 CGCTGAGAGGAAGAAGGAGA 58.531 55.000 0.00 0.00 0.00 3.71
120 121 2.031120 CGCTGAGAGGAAGAAGGAGAT 58.969 52.381 0.00 0.00 0.00 2.75
121 122 2.223782 CGCTGAGAGGAAGAAGGAGATG 60.224 54.545 0.00 0.00 0.00 2.90
122 123 3.030291 GCTGAGAGGAAGAAGGAGATGA 58.970 50.000 0.00 0.00 0.00 2.92
123 124 3.068590 GCTGAGAGGAAGAAGGAGATGAG 59.931 52.174 0.00 0.00 0.00 2.90
124 125 3.638160 CTGAGAGGAAGAAGGAGATGAGG 59.362 52.174 0.00 0.00 0.00 3.86
125 126 3.270696 TGAGAGGAAGAAGGAGATGAGGA 59.729 47.826 0.00 0.00 0.00 3.71
126 127 4.264577 TGAGAGGAAGAAGGAGATGAGGAA 60.265 45.833 0.00 0.00 0.00 3.36
127 128 4.693420 AGAGGAAGAAGGAGATGAGGAAA 58.307 43.478 0.00 0.00 0.00 3.13
128 129 4.716287 AGAGGAAGAAGGAGATGAGGAAAG 59.284 45.833 0.00 0.00 0.00 2.62
129 130 4.434195 AGGAAGAAGGAGATGAGGAAAGT 58.566 43.478 0.00 0.00 0.00 2.66
130 131 4.469586 AGGAAGAAGGAGATGAGGAAAGTC 59.530 45.833 0.00 0.00 0.00 3.01
131 132 4.223923 GGAAGAAGGAGATGAGGAAAGTCA 59.776 45.833 0.00 0.00 0.00 3.41
132 133 5.280215 GGAAGAAGGAGATGAGGAAAGTCAA 60.280 44.000 0.00 0.00 0.00 3.18
133 134 5.159273 AGAAGGAGATGAGGAAAGTCAAC 57.841 43.478 0.00 0.00 0.00 3.18
134 135 3.601443 AGGAGATGAGGAAAGTCAACG 57.399 47.619 0.00 0.00 0.00 4.10
135 136 2.003301 GGAGATGAGGAAAGTCAACGC 58.997 52.381 0.00 0.00 0.00 4.84
136 137 1.656095 GAGATGAGGAAAGTCAACGCG 59.344 52.381 3.53 3.53 0.00 6.01
137 138 0.095417 GATGAGGAAAGTCAACGCGC 59.905 55.000 5.73 0.00 0.00 6.86
138 139 1.626654 ATGAGGAAAGTCAACGCGCG 61.627 55.000 30.96 30.96 0.00 6.86
139 140 2.279918 AGGAAAGTCAACGCGCGT 60.280 55.556 32.73 32.73 0.00 6.01
140 141 1.005294 GAGGAAAGTCAACGCGCGTA 61.005 55.000 37.93 20.05 0.00 4.42
141 142 1.007336 AGGAAAGTCAACGCGCGTAG 61.007 55.000 37.93 7.73 0.00 3.51
142 143 1.005294 GGAAAGTCAACGCGCGTAGA 61.005 55.000 37.93 16.12 0.00 2.59
143 144 0.989890 GAAAGTCAACGCGCGTAGAT 59.010 50.000 37.93 19.16 0.00 1.98
144 145 0.989890 AAAGTCAACGCGCGTAGATC 59.010 50.000 37.93 24.58 0.00 2.75
145 146 1.132199 AAGTCAACGCGCGTAGATCG 61.132 55.000 37.93 21.22 43.12 3.69
146 147 1.581912 GTCAACGCGCGTAGATCGA 60.582 57.895 37.93 23.12 42.86 3.59
147 148 1.129879 GTCAACGCGCGTAGATCGAA 61.130 55.000 37.93 13.41 42.86 3.71
148 149 1.129879 TCAACGCGCGTAGATCGAAC 61.130 55.000 37.93 0.00 42.86 3.95
149 150 1.154169 AACGCGCGTAGATCGAACA 60.154 52.632 37.93 0.00 42.86 3.18
150 151 1.132199 AACGCGCGTAGATCGAACAG 61.132 55.000 37.93 1.48 42.86 3.16
151 152 1.582937 CGCGCGTAGATCGAACAGT 60.583 57.895 24.19 0.00 42.86 3.55
152 153 1.132199 CGCGCGTAGATCGAACAGTT 61.132 55.000 24.19 0.00 42.86 3.16
153 154 0.294887 GCGCGTAGATCGAACAGTTG 59.705 55.000 8.43 0.00 42.86 3.16
154 155 0.914551 CGCGTAGATCGAACAGTTGG 59.085 55.000 0.00 0.00 42.86 3.77
155 156 1.278238 GCGTAGATCGAACAGTTGGG 58.722 55.000 0.00 0.00 42.86 4.12
156 157 1.922570 CGTAGATCGAACAGTTGGGG 58.077 55.000 0.00 0.00 42.86 4.96
157 158 1.653151 GTAGATCGAACAGTTGGGGC 58.347 55.000 0.00 0.00 0.00 5.80
158 159 1.207329 GTAGATCGAACAGTTGGGGCT 59.793 52.381 0.00 0.00 0.00 5.19
159 160 0.250513 AGATCGAACAGTTGGGGCTC 59.749 55.000 0.00 0.00 0.00 4.70
160 161 1.079127 ATCGAACAGTTGGGGCTCG 60.079 57.895 0.00 0.00 0.00 5.03
161 162 1.827399 ATCGAACAGTTGGGGCTCGT 61.827 55.000 0.00 0.00 0.00 4.18
162 163 1.597027 CGAACAGTTGGGGCTCGTT 60.597 57.895 0.00 0.00 0.00 3.85
163 164 1.841663 CGAACAGTTGGGGCTCGTTG 61.842 60.000 0.00 0.00 0.00 4.10
164 165 2.130073 GAACAGTTGGGGCTCGTTGC 62.130 60.000 0.00 0.00 41.94 4.17
165 166 2.594303 CAGTTGGGGCTCGTTGCA 60.594 61.111 5.65 0.00 45.15 4.08
166 167 1.973281 CAGTTGGGGCTCGTTGCAT 60.973 57.895 0.00 0.00 45.15 3.96
167 168 1.675641 AGTTGGGGCTCGTTGCATC 60.676 57.895 0.00 0.00 45.15 3.91
168 169 2.745884 TTGGGGCTCGTTGCATCG 60.746 61.111 10.93 10.93 45.15 3.84
169 170 4.776322 TGGGGCTCGTTGCATCGG 62.776 66.667 16.60 8.90 45.15 4.18
197 198 4.657824 CGCGACCGACCCAACTGT 62.658 66.667 0.00 0.00 36.29 3.55
198 199 2.280592 GCGACCGACCCAACTGTT 60.281 61.111 0.00 0.00 0.00 3.16
199 200 2.604174 GCGACCGACCCAACTGTTG 61.604 63.158 13.50 13.50 0.00 3.33
278 279 0.732880 CGTGACACTTGCTCTACGGG 60.733 60.000 3.68 0.00 0.00 5.28
288 289 7.280356 ACACTTGCTCTACGGGAAAAATATAT 58.720 34.615 0.00 0.00 0.00 0.86
290 291 8.070171 CACTTGCTCTACGGGAAAAATATATTG 58.930 37.037 0.00 0.00 0.00 1.90
291 292 7.990886 ACTTGCTCTACGGGAAAAATATATTGA 59.009 33.333 0.00 0.00 0.00 2.57
329 339 2.920076 AAAGGCAACCAGGGAACGCA 62.920 55.000 0.00 0.00 37.17 5.24
337 347 1.314534 CCAGGGAACGCAATGCATGA 61.315 55.000 5.91 0.00 0.00 3.07
350 360 0.179092 TGCATGAGCGAGTCAGGATG 60.179 55.000 0.00 0.00 46.23 3.51
357 367 2.107953 GAGTCAGGATGGAGCGCC 59.892 66.667 2.29 0.00 36.16 6.53
368 378 2.585247 GAGCGCCGCGGAGTATTT 60.585 61.111 33.48 13.28 0.00 1.40
369 379 1.299620 GAGCGCCGCGGAGTATTTA 60.300 57.895 33.48 0.00 0.00 1.40
370 380 0.872881 GAGCGCCGCGGAGTATTTAA 60.873 55.000 33.48 0.00 0.00 1.52
371 381 0.249741 AGCGCCGCGGAGTATTTAAT 60.250 50.000 33.48 4.25 0.00 1.40
372 382 0.110823 GCGCCGCGGAGTATTTAATG 60.111 55.000 33.48 5.20 0.00 1.90
373 383 0.511221 CGCCGCGGAGTATTTAATGG 59.489 55.000 33.48 0.00 0.00 3.16
374 384 1.870580 CGCCGCGGAGTATTTAATGGA 60.871 52.381 33.48 0.00 0.00 3.41
375 385 2.215196 GCCGCGGAGTATTTAATGGAA 58.785 47.619 33.48 0.00 0.00 3.53
376 386 2.614983 GCCGCGGAGTATTTAATGGAAA 59.385 45.455 33.48 0.00 0.00 3.13
377 387 3.065648 GCCGCGGAGTATTTAATGGAAAA 59.934 43.478 33.48 0.00 0.00 2.29
378 388 4.788521 GCCGCGGAGTATTTAATGGAAAAG 60.789 45.833 33.48 0.00 0.00 2.27
379 389 4.573201 CCGCGGAGTATTTAATGGAAAAGA 59.427 41.667 24.07 0.00 0.00 2.52
380 390 5.065474 CCGCGGAGTATTTAATGGAAAAGAA 59.935 40.000 24.07 0.00 0.00 2.52
381 391 6.238648 CCGCGGAGTATTTAATGGAAAAGAAT 60.239 38.462 24.07 0.00 0.00 2.40
382 392 7.193595 CGCGGAGTATTTAATGGAAAAGAATT 58.806 34.615 0.00 0.00 0.00 2.17
383 393 8.339714 CGCGGAGTATTTAATGGAAAAGAATTA 58.660 33.333 0.00 0.00 0.00 1.40
408 418 2.367486 AGACTAGGTCTCACGGTTAGC 58.633 52.381 0.00 0.00 38.71 3.09
409 419 2.089980 GACTAGGTCTCACGGTTAGCA 58.910 52.381 0.00 0.00 0.00 3.49
410 420 2.688958 GACTAGGTCTCACGGTTAGCAT 59.311 50.000 0.00 0.00 0.00 3.79
411 421 2.427453 ACTAGGTCTCACGGTTAGCATG 59.573 50.000 0.00 0.00 0.00 4.06
412 422 1.267121 AGGTCTCACGGTTAGCATGT 58.733 50.000 0.00 0.00 0.00 3.21
413 423 1.066858 AGGTCTCACGGTTAGCATGTG 60.067 52.381 0.00 0.00 34.96 3.21
414 424 1.067142 GGTCTCACGGTTAGCATGTGA 60.067 52.381 0.00 4.33 40.12 3.58
417 427 2.363788 TCACGGTTAGCATGTGAGAC 57.636 50.000 0.00 0.00 37.69 3.36
418 428 1.067142 TCACGGTTAGCATGTGAGACC 60.067 52.381 0.00 0.00 37.69 3.85
419 429 0.249398 ACGGTTAGCATGTGAGACCC 59.751 55.000 0.00 0.00 0.00 4.46
420 430 0.249120 CGGTTAGCATGTGAGACCCA 59.751 55.000 0.00 0.00 0.00 4.51
421 431 1.739067 GGTTAGCATGTGAGACCCAC 58.261 55.000 0.00 0.00 45.88 4.61
422 432 1.679032 GGTTAGCATGTGAGACCCACC 60.679 57.143 0.00 0.00 45.09 4.61
423 433 1.279271 GTTAGCATGTGAGACCCACCT 59.721 52.381 0.00 0.00 45.09 4.00
424 434 1.656587 TAGCATGTGAGACCCACCTT 58.343 50.000 0.00 0.00 45.09 3.50
425 435 1.656587 AGCATGTGAGACCCACCTTA 58.343 50.000 0.00 0.00 45.09 2.69
426 436 1.985159 AGCATGTGAGACCCACCTTAA 59.015 47.619 0.00 0.00 45.09 1.85
427 437 2.578021 AGCATGTGAGACCCACCTTAAT 59.422 45.455 0.00 0.00 45.09 1.40
428 438 3.780294 AGCATGTGAGACCCACCTTAATA 59.220 43.478 0.00 0.00 45.09 0.98
429 439 4.227300 AGCATGTGAGACCCACCTTAATAA 59.773 41.667 0.00 0.00 45.09 1.40
430 440 4.947388 GCATGTGAGACCCACCTTAATAAA 59.053 41.667 0.00 0.00 45.09 1.40
431 441 5.594317 GCATGTGAGACCCACCTTAATAAAT 59.406 40.000 0.00 0.00 45.09 1.40
432 442 6.460123 GCATGTGAGACCCACCTTAATAAATG 60.460 42.308 0.00 0.00 45.09 2.32
433 443 6.381498 TGTGAGACCCACCTTAATAAATGA 57.619 37.500 0.00 0.00 45.09 2.57
434 444 6.177610 TGTGAGACCCACCTTAATAAATGAC 58.822 40.000 0.00 0.00 45.09 3.06
435 445 6.177610 GTGAGACCCACCTTAATAAATGACA 58.822 40.000 0.00 0.00 39.86 3.58
436 446 6.093633 GTGAGACCCACCTTAATAAATGACAC 59.906 42.308 0.00 0.00 39.86 3.67
437 447 5.183228 AGACCCACCTTAATAAATGACACG 58.817 41.667 0.00 0.00 0.00 4.49
438 448 4.913784 ACCCACCTTAATAAATGACACGT 58.086 39.130 0.00 0.00 0.00 4.49
439 449 4.698304 ACCCACCTTAATAAATGACACGTG 59.302 41.667 15.48 15.48 0.00 4.49
440 450 4.938832 CCCACCTTAATAAATGACACGTGA 59.061 41.667 25.01 0.00 0.00 4.35
441 451 5.163794 CCCACCTTAATAAATGACACGTGAC 60.164 44.000 25.01 17.68 0.00 3.67
442 452 5.410132 CCACCTTAATAAATGACACGTGACA 59.590 40.000 25.01 23.44 0.00 3.58
443 453 6.093495 CCACCTTAATAAATGACACGTGACAT 59.907 38.462 24.49 24.49 32.16 3.06
444 454 7.361713 CCACCTTAATAAATGACACGTGACATT 60.362 37.037 31.25 31.25 40.91 2.71
445 455 8.020819 CACCTTAATAAATGACACGTGACATTT 58.979 33.333 39.80 39.80 46.33 2.32
447 457 9.485591 CCTTAATAAATGACACGTGACATTTAC 57.514 33.333 41.21 19.91 46.62 2.01
451 461 9.906660 AATAAATGACACGTGACATTTACAAAT 57.093 25.926 41.21 31.94 46.62 2.32
452 462 9.906660 ATAAATGACACGTGACATTTACAAATT 57.093 25.926 41.21 31.03 46.62 1.82
454 464 8.722342 AATGACACGTGACATTTACAAATTAC 57.278 30.769 31.25 0.20 37.17 1.89
455 465 7.247929 TGACACGTGACATTTACAAATTACA 57.752 32.000 25.01 0.00 0.00 2.41
456 466 7.694886 TGACACGTGACATTTACAAATTACAA 58.305 30.769 25.01 0.00 0.00 2.41
460 470 7.166638 CACGTGACATTTACAAATTACAAAGCA 59.833 33.333 10.90 0.00 0.00 3.91
471 481 5.357742 AATTACAAAGCAATTCCCATCCC 57.642 39.130 0.00 0.00 0.00 3.85
494 504 2.735126 GCACCGCAATTAATCCACAAGG 60.735 50.000 0.00 0.00 0.00 3.61
503 513 2.967397 TCCACAAGGAGCCGTACG 59.033 61.111 8.69 8.69 39.61 3.67
507 517 1.080025 ACAAGGAGCCGTACGAAGC 60.080 57.895 18.76 12.85 0.00 3.86
523 533 2.096819 CGAAGCACAGTCCTCTCTCTAC 59.903 54.545 0.00 0.00 0.00 2.59
541 551 0.613012 ACATTTTGAGGAGCCCTGCC 60.613 55.000 0.00 0.00 31.76 4.85
543 553 2.520657 ATTTTGAGGAGCCCTGCCCC 62.521 60.000 0.00 0.00 31.76 5.80
544 554 4.682714 TTGAGGAGCCCTGCCCCT 62.683 66.667 0.00 0.00 31.76 4.79
630 644 6.585322 CACAAGCAGAATTTTCTCATTCTTCC 59.415 38.462 0.00 0.00 40.86 3.46
631 645 5.911378 AGCAGAATTTTCTCATTCTTCCC 57.089 39.130 0.00 0.00 40.86 3.97
632 646 5.578073 AGCAGAATTTTCTCATTCTTCCCT 58.422 37.500 0.00 0.00 40.86 4.20
633 647 5.651576 AGCAGAATTTTCTCATTCTTCCCTC 59.348 40.000 0.00 0.00 40.86 4.30
636 650 3.350219 TTTTCTCATTCTTCCCTCCCG 57.650 47.619 0.00 0.00 0.00 5.14
682 696 3.698820 CCCTGGGCAAAAGCCAGC 61.699 66.667 8.94 0.00 0.00 4.85
744 780 1.839994 GTCCCCCATCATCTTCAGTCA 59.160 52.381 0.00 0.00 0.00 3.41
745 781 2.121948 TCCCCCATCATCTTCAGTCAG 58.878 52.381 0.00 0.00 0.00 3.51
746 782 1.142465 CCCCCATCATCTTCAGTCAGG 59.858 57.143 0.00 0.00 0.00 3.86
747 783 1.842562 CCCCATCATCTTCAGTCAGGT 59.157 52.381 0.00 0.00 0.00 4.00
748 784 2.158842 CCCCATCATCTTCAGTCAGGTC 60.159 54.545 0.00 0.00 0.00 3.85
750 786 2.158842 CCATCATCTTCAGTCAGGTCCC 60.159 54.545 0.00 0.00 0.00 4.46
751 787 2.630889 TCATCTTCAGTCAGGTCCCT 57.369 50.000 0.00 0.00 0.00 4.20
752 788 2.461695 TCATCTTCAGTCAGGTCCCTC 58.538 52.381 0.00 0.00 0.00 4.30
753 789 2.043664 TCATCTTCAGTCAGGTCCCTCT 59.956 50.000 0.00 0.00 0.00 3.69
754 790 2.223803 TCTTCAGTCAGGTCCCTCTC 57.776 55.000 0.00 0.00 0.00 3.20
755 791 0.814457 CTTCAGTCAGGTCCCTCTCG 59.186 60.000 0.00 0.00 0.00 4.04
756 792 0.404426 TTCAGTCAGGTCCCTCTCGA 59.596 55.000 0.00 0.00 0.00 4.04
757 793 0.034960 TCAGTCAGGTCCCTCTCGAG 60.035 60.000 5.93 5.93 0.00 4.04
758 794 0.034960 CAGTCAGGTCCCTCTCGAGA 60.035 60.000 15.70 15.70 0.00 4.04
759 795 0.254747 AGTCAGGTCCCTCTCGAGAG 59.745 60.000 31.55 31.55 41.71 3.20
760 796 0.253610 GTCAGGTCCCTCTCGAGAGA 59.746 60.000 38.04 20.62 44.74 3.10
872 908 0.035343 CGGGAAAGAAAGGGAGTCCC 60.035 60.000 21.81 21.81 45.90 4.46
923 959 2.167861 GCTTAGCGCCAGTTCTCCG 61.168 63.158 2.29 0.00 0.00 4.63
1170 1215 2.255770 TCTCCTCCCCTTCCTTTCTC 57.744 55.000 0.00 0.00 0.00 2.87
1171 1216 0.827368 CTCCTCCCCTTCCTTTCTCG 59.173 60.000 0.00 0.00 0.00 4.04
1190 1236 3.660865 TCGCATCCATCATCTTCATCAG 58.339 45.455 0.00 0.00 0.00 2.90
1233 1279 1.139520 GCCACCGCCATCAATCAAC 59.860 57.895 0.00 0.00 0.00 3.18
1234 1280 1.809207 CCACCGCCATCAATCAACC 59.191 57.895 0.00 0.00 0.00 3.77
1235 1281 0.964860 CCACCGCCATCAATCAACCA 60.965 55.000 0.00 0.00 0.00 3.67
1236 1282 0.887247 CACCGCCATCAATCAACCAA 59.113 50.000 0.00 0.00 0.00 3.67
1251 1297 2.741985 CAACGTCCTGATGCCGCA 60.742 61.111 0.00 0.00 0.00 5.69
1253 1299 4.760047 ACGTCCTGATGCCGCACC 62.760 66.667 0.00 0.00 0.00 5.01
1297 1345 1.347817 CTTTGCTCGCTCTGTCCGTC 61.348 60.000 0.00 0.00 0.00 4.79
1373 1421 1.421410 GAGGAACTGGTACGCGCATG 61.421 60.000 5.73 0.00 41.55 4.06
1382 1431 0.581529 GTACGCGCATGCATACACAT 59.418 50.000 19.57 0.00 39.48 3.21
1384 1433 1.369568 CGCGCATGCATACACATGG 60.370 57.895 19.57 0.00 46.14 3.66
1388 1437 1.529865 CGCATGCATACACATGGAGAG 59.470 52.381 19.57 0.00 46.14 3.20
1389 1438 2.804212 CGCATGCATACACATGGAGAGA 60.804 50.000 19.57 0.00 46.14 3.10
1390 1439 2.806818 GCATGCATACACATGGAGAGAG 59.193 50.000 14.21 0.00 46.14 3.20
1391 1440 3.743584 GCATGCATACACATGGAGAGAGT 60.744 47.826 14.21 0.00 46.14 3.24
1442 1491 1.961394 TCGCCTGAGACTTACTGTGTT 59.039 47.619 0.00 0.00 0.00 3.32
1792 1873 1.650528 ACTAACCAGGCTGCTTCTCT 58.349 50.000 9.56 0.00 0.00 3.10
1793 1874 1.277557 ACTAACCAGGCTGCTTCTCTG 59.722 52.381 9.56 0.00 0.00 3.35
1794 1875 1.277557 CTAACCAGGCTGCTTCTCTGT 59.722 52.381 9.56 0.00 0.00 3.41
1795 1876 0.475906 AACCAGGCTGCTTCTCTGTT 59.524 50.000 9.56 2.99 0.00 3.16
2268 2377 5.926542 GCATTACTGGTTTCTTTCTTTTCCC 59.073 40.000 0.00 0.00 0.00 3.97
2366 2481 0.883833 CTCCATGAAAAAGGTGCGCT 59.116 50.000 9.73 0.00 0.00 5.92
2368 2483 0.597568 CCATGAAAAAGGTGCGCTCA 59.402 50.000 9.73 1.60 0.00 4.26
2369 2484 1.203052 CCATGAAAAAGGTGCGCTCAT 59.797 47.619 9.73 4.39 0.00 2.90
2370 2485 2.423185 CCATGAAAAAGGTGCGCTCATA 59.577 45.455 9.73 0.00 0.00 2.15
2371 2486 3.429085 CATGAAAAAGGTGCGCTCATAC 58.571 45.455 9.73 0.00 0.00 2.39
2372 2487 1.810151 TGAAAAAGGTGCGCTCATACC 59.190 47.619 9.73 7.90 37.23 2.73
2373 2488 1.132453 GAAAAAGGTGCGCTCATACCC 59.868 52.381 9.73 0.00 37.70 3.69
2374 2489 0.328258 AAAAGGTGCGCTCATACCCT 59.672 50.000 9.73 1.06 37.70 4.34
2375 2490 1.200519 AAAGGTGCGCTCATACCCTA 58.799 50.000 9.73 0.00 37.70 3.53
2378 2493 0.249489 GGTGCGCTCATACCCTACTG 60.249 60.000 9.73 0.00 0.00 2.74
2450 2565 2.721425 TTCTACCGGGCTTTAATGGG 57.279 50.000 6.32 0.00 0.00 4.00
2451 2566 1.587066 TCTACCGGGCTTTAATGGGT 58.413 50.000 6.32 0.00 34.81 4.51
2456 2571 1.014352 CGGGCTTTAATGGGTTCTCG 58.986 55.000 0.00 0.00 0.00 4.04
2525 2640 3.371097 TACTAGTGGCAGCGGCAGC 62.371 63.158 11.88 9.05 43.71 5.25
2549 2664 7.068226 AGCGGCTTTAATTGATAGTGGTATTTT 59.932 33.333 0.00 0.00 0.00 1.82
2551 2666 7.647715 CGGCTTTAATTGATAGTGGTATTTTGG 59.352 37.037 0.00 0.00 0.00 3.28
2552 2667 8.474831 GGCTTTAATTGATAGTGGTATTTTGGT 58.525 33.333 0.00 0.00 0.00 3.67
2553 2668 9.869757 GCTTTAATTGATAGTGGTATTTTGGTT 57.130 29.630 0.00 0.00 0.00 3.67
2555 2670 9.646427 TTTAATTGATAGTGGTATTTTGGTTGC 57.354 29.630 0.00 0.00 0.00 4.17
2556 2671 6.849085 ATTGATAGTGGTATTTTGGTTGCA 57.151 33.333 0.00 0.00 0.00 4.08
2557 2672 5.637006 TGATAGTGGTATTTTGGTTGCAC 57.363 39.130 0.00 0.00 0.00 4.57
2594 2712 4.514066 TGTAATGATGATGTGATGCTGCTC 59.486 41.667 0.00 0.00 0.00 4.26
2595 2713 1.963172 TGATGATGTGATGCTGCTCC 58.037 50.000 0.00 0.00 0.00 4.70
2596 2714 0.866427 GATGATGTGATGCTGCTCCG 59.134 55.000 0.00 0.00 0.00 4.63
2597 2715 0.534427 ATGATGTGATGCTGCTCCGG 60.534 55.000 0.00 0.00 0.00 5.14
2598 2716 1.890979 GATGTGATGCTGCTCCGGG 60.891 63.158 0.00 0.00 0.00 5.73
2599 2717 2.315781 GATGTGATGCTGCTCCGGGA 62.316 60.000 0.00 0.00 0.00 5.14
3215 3362 5.186992 TCGATCATATTATTCCCACGACCAT 59.813 40.000 0.00 0.00 0.00 3.55
3289 3436 6.078479 CAGTGTCTGATTATATCGTCGTACC 58.922 44.000 0.00 0.00 32.44 3.34
3303 3455 1.213799 GTACCAGTTCCGTCGGACC 59.786 63.158 15.07 7.20 0.00 4.46
3307 3459 1.605058 CCAGTTCCGTCGGACCTGAT 61.605 60.000 33.29 8.47 43.60 2.90
3308 3460 0.179134 CAGTTCCGTCGGACCTGATC 60.179 60.000 29.35 9.62 43.60 2.92
3344 3501 3.924686 AGTGTACAATGTAACAGCTACGC 59.075 43.478 0.00 0.00 32.65 4.42
3408 3565 4.226427 ACACATGCCTGTTATGAGATGT 57.774 40.909 0.00 0.00 31.62 3.06
3596 3753 3.446161 TCCGATACGACCAATCTCAACTT 59.554 43.478 0.00 0.00 0.00 2.66
3613 3772 4.576873 TCAACTTCTCGATCAGCTAGGTAG 59.423 45.833 0.00 0.00 0.00 3.18
3616 3775 5.871834 ACTTCTCGATCAGCTAGGTAGTAT 58.128 41.667 0.00 0.00 0.00 2.12
3656 3819 7.258441 TCGAGTACTATCTTTGATTCTTGTGG 58.742 38.462 0.00 0.00 0.00 4.17
3659 3822 7.907389 AGTACTATCTTTGATTCTTGTGGTCA 58.093 34.615 0.00 0.00 0.00 4.02
3660 3823 8.375506 AGTACTATCTTTGATTCTTGTGGTCAA 58.624 33.333 0.00 0.00 0.00 3.18
3679 3842 5.048013 GGTCAAGATCGGGTGAAATTTTTCT 60.048 40.000 4.80 0.00 38.02 2.52
3755 3919 2.292845 GGAGCTTTATGCATGAAGGAGC 59.707 50.000 26.93 16.89 45.94 4.70
3756 3920 3.212685 GAGCTTTATGCATGAAGGAGCT 58.787 45.455 26.93 20.73 45.94 4.09
3945 4113 1.811558 CGGGAGCGATGGAATGATTGT 60.812 52.381 0.00 0.00 0.00 2.71
3946 4114 2.301346 GGGAGCGATGGAATGATTGTT 58.699 47.619 0.00 0.00 0.00 2.83
3947 4115 2.033801 GGGAGCGATGGAATGATTGTTG 59.966 50.000 0.00 0.00 0.00 3.33
3948 4116 2.684881 GGAGCGATGGAATGATTGTTGT 59.315 45.455 0.00 0.00 0.00 3.32
3949 4117 3.488047 GGAGCGATGGAATGATTGTTGTG 60.488 47.826 0.00 0.00 0.00 3.33
3950 4118 2.159338 AGCGATGGAATGATTGTTGTGC 60.159 45.455 0.00 0.00 0.00 4.57
3954 4122 4.616604 CGATGGAATGATTGTTGTGCTTGT 60.617 41.667 0.00 0.00 0.00 3.16
3980 4148 1.717937 CCTTGAGCGAGGAAATGCG 59.282 57.895 0.00 0.00 39.25 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.830587 TTCCTGGATGCGCTCACTGT 61.831 55.000 9.73 0.00 0.00 3.55
1 2 1.078918 TTCCTGGATGCGCTCACTG 60.079 57.895 9.73 2.34 0.00 3.66
2 3 1.078848 GTTCCTGGATGCGCTCACT 60.079 57.895 9.73 0.00 0.00 3.41
3 4 2.456119 CGTTCCTGGATGCGCTCAC 61.456 63.158 9.73 0.00 0.00 3.51
4 5 2.125552 CGTTCCTGGATGCGCTCA 60.126 61.111 9.73 3.59 0.00 4.26
5 6 3.567797 GCGTTCCTGGATGCGCTC 61.568 66.667 27.45 3.37 45.48 5.03
29 30 4.779733 TGGACCTCCTCCCTCCGC 62.780 72.222 0.00 0.00 38.49 5.54
30 31 2.443016 CTGGACCTCCTCCCTCCG 60.443 72.222 0.00 0.00 38.49 4.63
31 32 2.041405 CCTGGACCTCCTCCCTCC 60.041 72.222 0.00 0.00 38.49 4.30
32 33 1.687493 CACCTGGACCTCCTCCCTC 60.687 68.421 0.00 0.00 38.49 4.30
33 34 2.174876 CTCACCTGGACCTCCTCCCT 62.175 65.000 0.00 0.00 38.49 4.20
34 35 1.687493 CTCACCTGGACCTCCTCCC 60.687 68.421 0.00 0.00 38.49 4.30
35 36 1.687493 CCTCACCTGGACCTCCTCC 60.687 68.421 0.00 0.00 39.97 4.30
36 37 1.687493 CCCTCACCTGGACCTCCTC 60.687 68.421 0.00 0.00 36.82 3.71
37 38 2.452114 CCCTCACCTGGACCTCCT 59.548 66.667 0.00 0.00 36.82 3.69
38 39 2.553438 ATCCCCTCACCTGGACCTCC 62.553 65.000 0.00 0.00 32.36 4.30
39 40 1.003573 ATCCCCTCACCTGGACCTC 59.996 63.158 0.00 0.00 32.36 3.85
40 41 1.307343 CATCCCCTCACCTGGACCT 60.307 63.158 0.00 0.00 32.36 3.85
41 42 2.378634 CCATCCCCTCACCTGGACC 61.379 68.421 0.00 0.00 32.36 4.46
42 43 1.616628 ACCATCCCCTCACCTGGAC 60.617 63.158 0.00 0.00 32.36 4.02
43 44 1.616327 CACCATCCCCTCACCTGGA 60.616 63.158 0.00 0.00 34.54 3.86
44 45 2.683465 CCACCATCCCCTCACCTGG 61.683 68.421 0.00 0.00 34.84 4.45
45 46 3.001514 CCACCATCCCCTCACCTG 58.998 66.667 0.00 0.00 0.00 4.00
46 47 3.017581 GCCACCATCCCCTCACCT 61.018 66.667 0.00 0.00 0.00 4.00
47 48 4.129148 GGCCACCATCCCCTCACC 62.129 72.222 0.00 0.00 0.00 4.02
48 49 4.489771 CGGCCACCATCCCCTCAC 62.490 72.222 2.24 0.00 0.00 3.51
67 68 2.110967 TTAGACGTCCTCTCGGCCG 61.111 63.158 22.12 22.12 40.00 6.13
68 69 1.432657 GTTAGACGTCCTCTCGGCC 59.567 63.158 13.01 0.00 40.00 6.13
69 70 1.062206 CGTTAGACGTCCTCTCGGC 59.938 63.158 13.01 0.00 36.74 5.54
70 71 1.720301 CCGTTAGACGTCCTCTCGG 59.280 63.158 13.01 16.80 40.58 4.63
71 72 1.062206 GCCGTTAGACGTCCTCTCG 59.938 63.158 13.01 11.89 40.58 4.04
72 73 1.432657 GGCCGTTAGACGTCCTCTC 59.567 63.158 13.01 0.00 36.59 3.20
73 74 2.404995 CGGCCGTTAGACGTCCTCT 61.405 63.158 19.50 0.00 37.51 3.69
74 75 2.101770 CGGCCGTTAGACGTCCTC 59.898 66.667 19.50 1.98 37.51 3.71
75 76 3.446570 CCGGCCGTTAGACGTCCT 61.447 66.667 26.12 2.17 37.51 3.85
76 77 4.503314 CCCGGCCGTTAGACGTCC 62.503 72.222 26.12 0.00 40.58 4.79
77 78 4.503314 CCCCGGCCGTTAGACGTC 62.503 72.222 26.12 7.70 40.58 4.34
80 81 4.832608 CAGCCCCGGCCGTTAGAC 62.833 72.222 26.12 8.62 43.17 2.59
95 96 2.825726 TTCTTCCTCTCAGCGCGCAG 62.826 60.000 35.10 26.96 0.00 5.18
96 97 2.825726 CTTCTTCCTCTCAGCGCGCA 62.826 60.000 35.10 13.17 0.00 6.09
97 98 2.125912 TTCTTCCTCTCAGCGCGC 60.126 61.111 26.66 26.66 0.00 6.86
98 99 1.518133 CCTTCTTCCTCTCAGCGCG 60.518 63.158 0.00 0.00 0.00 6.86
99 100 0.179113 CTCCTTCTTCCTCTCAGCGC 60.179 60.000 0.00 0.00 0.00 5.92
100 101 1.468985 TCTCCTTCTTCCTCTCAGCG 58.531 55.000 0.00 0.00 0.00 5.18
101 102 3.030291 TCATCTCCTTCTTCCTCTCAGC 58.970 50.000 0.00 0.00 0.00 4.26
102 103 3.638160 CCTCATCTCCTTCTTCCTCTCAG 59.362 52.174 0.00 0.00 0.00 3.35
103 104 3.270696 TCCTCATCTCCTTCTTCCTCTCA 59.729 47.826 0.00 0.00 0.00 3.27
104 105 3.909732 TCCTCATCTCCTTCTTCCTCTC 58.090 50.000 0.00 0.00 0.00 3.20
105 106 4.344938 TTCCTCATCTCCTTCTTCCTCT 57.655 45.455 0.00 0.00 0.00 3.69
106 107 4.469586 ACTTTCCTCATCTCCTTCTTCCTC 59.530 45.833 0.00 0.00 0.00 3.71
107 108 4.434195 ACTTTCCTCATCTCCTTCTTCCT 58.566 43.478 0.00 0.00 0.00 3.36
108 109 4.223923 TGACTTTCCTCATCTCCTTCTTCC 59.776 45.833 0.00 0.00 0.00 3.46
109 110 5.413309 TGACTTTCCTCATCTCCTTCTTC 57.587 43.478 0.00 0.00 0.00 2.87
110 111 5.555966 GTTGACTTTCCTCATCTCCTTCTT 58.444 41.667 0.00 0.00 0.00 2.52
111 112 4.322349 CGTTGACTTTCCTCATCTCCTTCT 60.322 45.833 0.00 0.00 0.00 2.85
112 113 3.929610 CGTTGACTTTCCTCATCTCCTTC 59.070 47.826 0.00 0.00 0.00 3.46
113 114 3.866449 GCGTTGACTTTCCTCATCTCCTT 60.866 47.826 0.00 0.00 0.00 3.36
114 115 2.354203 GCGTTGACTTTCCTCATCTCCT 60.354 50.000 0.00 0.00 0.00 3.69
115 116 2.003301 GCGTTGACTTTCCTCATCTCC 58.997 52.381 0.00 0.00 0.00 3.71
116 117 1.656095 CGCGTTGACTTTCCTCATCTC 59.344 52.381 0.00 0.00 0.00 2.75
117 118 1.714794 CGCGTTGACTTTCCTCATCT 58.285 50.000 0.00 0.00 0.00 2.90
118 119 0.095417 GCGCGTTGACTTTCCTCATC 59.905 55.000 8.43 0.00 0.00 2.92
119 120 1.626654 CGCGCGTTGACTTTCCTCAT 61.627 55.000 24.19 0.00 0.00 2.90
120 121 2.307309 CGCGCGTTGACTTTCCTCA 61.307 57.895 24.19 0.00 0.00 3.86
121 122 1.005294 TACGCGCGTTGACTTTCCTC 61.005 55.000 42.10 0.00 0.00 3.71
122 123 1.007038 TACGCGCGTTGACTTTCCT 60.007 52.632 42.10 14.58 0.00 3.36
123 124 1.005294 TCTACGCGCGTTGACTTTCC 61.005 55.000 42.10 0.00 0.00 3.13
124 125 0.989890 ATCTACGCGCGTTGACTTTC 59.010 50.000 40.46 0.00 33.27 2.62
125 126 0.989890 GATCTACGCGCGTTGACTTT 59.010 50.000 40.46 28.73 33.27 2.66
126 127 1.132199 CGATCTACGCGCGTTGACTT 61.132 55.000 40.46 29.39 33.27 3.01
127 128 1.582937 CGATCTACGCGCGTTGACT 60.583 57.895 40.46 29.94 33.27 3.41
128 129 1.129879 TTCGATCTACGCGCGTTGAC 61.130 55.000 40.46 31.33 42.26 3.18
129 130 1.129879 GTTCGATCTACGCGCGTTGA 61.130 55.000 39.86 39.86 42.26 3.18
130 131 1.266089 GTTCGATCTACGCGCGTTG 59.734 57.895 42.10 37.17 42.26 4.10
131 132 1.132199 CTGTTCGATCTACGCGCGTT 61.132 55.000 42.10 24.57 42.26 4.84
132 133 1.582937 CTGTTCGATCTACGCGCGT 60.583 57.895 39.05 39.05 42.26 6.01
133 134 1.132199 AACTGTTCGATCTACGCGCG 61.132 55.000 30.96 30.96 42.26 6.86
134 135 0.294887 CAACTGTTCGATCTACGCGC 59.705 55.000 5.73 0.00 42.26 6.86
135 136 0.914551 CCAACTGTTCGATCTACGCG 59.085 55.000 3.53 3.53 42.26 6.01
136 137 1.278238 CCCAACTGTTCGATCTACGC 58.722 55.000 0.00 0.00 42.26 4.42
137 138 1.922570 CCCCAACTGTTCGATCTACG 58.077 55.000 0.00 0.00 44.09 3.51
138 139 1.207329 AGCCCCAACTGTTCGATCTAC 59.793 52.381 0.00 0.00 0.00 2.59
139 140 1.480954 GAGCCCCAACTGTTCGATCTA 59.519 52.381 0.00 0.00 0.00 1.98
140 141 0.250513 GAGCCCCAACTGTTCGATCT 59.749 55.000 0.00 0.00 0.00 2.75
141 142 1.084370 CGAGCCCCAACTGTTCGATC 61.084 60.000 0.00 0.00 33.38 3.69
142 143 1.079127 CGAGCCCCAACTGTTCGAT 60.079 57.895 0.00 0.00 33.38 3.59
143 144 2.035237 AACGAGCCCCAACTGTTCGA 62.035 55.000 4.53 0.00 35.42 3.71
144 145 1.597027 AACGAGCCCCAACTGTTCG 60.597 57.895 0.00 0.00 37.31 3.95
145 146 1.949257 CAACGAGCCCCAACTGTTC 59.051 57.895 0.00 0.00 0.00 3.18
146 147 2.193536 GCAACGAGCCCCAACTGTT 61.194 57.895 0.00 0.00 37.23 3.16
147 148 2.594592 GCAACGAGCCCCAACTGT 60.595 61.111 0.00 0.00 37.23 3.55
148 149 1.926511 GATGCAACGAGCCCCAACTG 61.927 60.000 0.00 0.00 44.83 3.16
149 150 1.675641 GATGCAACGAGCCCCAACT 60.676 57.895 0.00 0.00 44.83 3.16
150 151 2.877691 GATGCAACGAGCCCCAAC 59.122 61.111 0.00 0.00 44.83 3.77
151 152 2.745884 CGATGCAACGAGCCCCAA 60.746 61.111 11.36 0.00 44.83 4.12
152 153 4.776322 CCGATGCAACGAGCCCCA 62.776 66.667 18.77 0.00 44.83 4.96
180 181 4.657824 ACAGTTGGGTCGGTCGCG 62.658 66.667 0.00 0.00 0.00 5.87
181 182 2.280592 AACAGTTGGGTCGGTCGC 60.281 61.111 0.00 0.00 0.00 5.19
182 183 3.637714 CAACAGTTGGGTCGGTCG 58.362 61.111 5.25 0.00 0.00 4.79
214 215 1.812686 TAATAGGCGGGTGCTAGGCG 61.813 60.000 0.00 0.00 42.25 5.52
215 216 0.037232 CTAATAGGCGGGTGCTAGGC 60.037 60.000 0.00 0.00 42.25 3.93
216 217 1.339097 ACTAATAGGCGGGTGCTAGG 58.661 55.000 0.00 0.00 42.25 3.02
217 218 4.495422 CATAACTAATAGGCGGGTGCTAG 58.505 47.826 0.00 0.00 42.25 3.42
218 219 3.306502 GCATAACTAATAGGCGGGTGCTA 60.307 47.826 0.00 0.00 42.25 3.49
219 220 2.550208 GCATAACTAATAGGCGGGTGCT 60.550 50.000 0.00 0.00 42.25 4.40
220 221 1.804748 GCATAACTAATAGGCGGGTGC 59.195 52.381 0.00 0.00 41.71 5.01
221 222 3.244078 TGAGCATAACTAATAGGCGGGTG 60.244 47.826 0.00 0.00 45.74 4.61
222 223 2.969950 TGAGCATAACTAATAGGCGGGT 59.030 45.455 0.00 0.00 45.74 5.28
223 224 3.678056 TGAGCATAACTAATAGGCGGG 57.322 47.619 0.00 0.00 45.74 6.13
224 225 5.057149 ACTTTGAGCATAACTAATAGGCGG 58.943 41.667 0.00 0.00 45.74 6.13
225 226 6.604735 AACTTTGAGCATAACTAATAGGCG 57.395 37.500 0.00 0.00 45.74 5.52
226 227 7.067008 TCCAAACTTTGAGCATAACTAATAGGC 59.933 37.037 2.87 0.00 41.57 3.93
227 228 8.506168 TCCAAACTTTGAGCATAACTAATAGG 57.494 34.615 2.87 0.00 0.00 2.57
228 229 9.383519 TCTCCAAACTTTGAGCATAACTAATAG 57.616 33.333 2.87 0.00 0.00 1.73
290 291 9.162764 TGCCTTTTCTTGTATACTTGTTCTATC 57.837 33.333 4.17 0.00 0.00 2.08
291 292 9.515226 TTGCCTTTTCTTGTATACTTGTTCTAT 57.485 29.630 4.17 0.00 0.00 1.98
305 313 1.703411 TCCCTGGTTGCCTTTTCTTG 58.297 50.000 0.00 0.00 0.00 3.02
307 315 1.704641 GTTCCCTGGTTGCCTTTTCT 58.295 50.000 0.00 0.00 0.00 2.52
308 316 0.313987 CGTTCCCTGGTTGCCTTTTC 59.686 55.000 0.00 0.00 0.00 2.29
314 324 1.080569 CATTGCGTTCCCTGGTTGC 60.081 57.895 0.00 0.00 0.00 4.17
329 339 0.538584 TCCTGACTCGCTCATGCATT 59.461 50.000 0.00 0.00 39.64 3.56
337 347 2.780094 CGCTCCATCCTGACTCGCT 61.780 63.158 0.00 0.00 0.00 4.93
350 360 2.688526 TAAATACTCCGCGGCGCTCC 62.689 60.000 30.54 0.85 0.00 4.70
357 367 5.728351 TCTTTTCCATTAAATACTCCGCG 57.272 39.130 0.00 0.00 0.00 6.46
388 398 2.290768 TGCTAACCGTGAGACCTAGTCT 60.291 50.000 0.00 0.00 46.42 3.24
389 399 2.089980 TGCTAACCGTGAGACCTAGTC 58.910 52.381 0.00 0.00 0.00 2.59
390 400 2.211250 TGCTAACCGTGAGACCTAGT 57.789 50.000 0.00 0.00 0.00 2.57
391 401 2.427453 ACATGCTAACCGTGAGACCTAG 59.573 50.000 0.00 0.00 34.47 3.02
392 402 2.165641 CACATGCTAACCGTGAGACCTA 59.834 50.000 0.00 0.00 34.47 3.08
393 403 1.066858 CACATGCTAACCGTGAGACCT 60.067 52.381 0.00 0.00 34.47 3.85
394 404 1.067142 TCACATGCTAACCGTGAGACC 60.067 52.381 0.00 0.00 34.83 3.85
395 405 2.363788 TCACATGCTAACCGTGAGAC 57.636 50.000 0.00 0.00 34.83 3.36
398 408 1.067142 GGTCTCACATGCTAACCGTGA 60.067 52.381 0.00 0.00 37.33 4.35
399 409 1.359848 GGTCTCACATGCTAACCGTG 58.640 55.000 0.00 0.00 36.50 4.94
400 410 0.249398 GGGTCTCACATGCTAACCGT 59.751 55.000 0.00 0.00 0.00 4.83
401 411 0.249120 TGGGTCTCACATGCTAACCG 59.751 55.000 0.00 0.00 0.00 4.44
402 412 1.739067 GTGGGTCTCACATGCTAACC 58.261 55.000 0.00 0.00 45.39 2.85
411 421 6.093633 GTGTCATTTATTAAGGTGGGTCTCAC 59.906 42.308 0.00 0.00 45.34 3.51
412 422 6.177610 GTGTCATTTATTAAGGTGGGTCTCA 58.822 40.000 0.00 0.00 0.00 3.27
413 423 5.293569 CGTGTCATTTATTAAGGTGGGTCTC 59.706 44.000 0.00 0.00 0.00 3.36
414 424 5.183228 CGTGTCATTTATTAAGGTGGGTCT 58.817 41.667 0.00 0.00 0.00 3.85
415 425 4.939439 ACGTGTCATTTATTAAGGTGGGTC 59.061 41.667 0.00 0.00 0.00 4.46
416 426 4.698304 CACGTGTCATTTATTAAGGTGGGT 59.302 41.667 7.58 0.00 0.00 4.51
417 427 4.938832 TCACGTGTCATTTATTAAGGTGGG 59.061 41.667 16.51 0.00 0.00 4.61
418 428 5.410132 TGTCACGTGTCATTTATTAAGGTGG 59.590 40.000 16.51 0.00 0.00 4.61
419 429 6.474819 TGTCACGTGTCATTTATTAAGGTG 57.525 37.500 16.51 0.00 0.00 4.00
420 430 7.681939 AATGTCACGTGTCATTTATTAAGGT 57.318 32.000 27.81 9.40 31.57 3.50
421 431 9.485591 GTAAATGTCACGTGTCATTTATTAAGG 57.514 33.333 38.49 8.41 42.89 2.69
425 435 9.906660 ATTTGTAAATGTCACGTGTCATTTATT 57.093 25.926 38.49 27.92 42.89 1.40
426 436 9.906660 AATTTGTAAATGTCACGTGTCATTTAT 57.093 25.926 38.49 29.28 42.89 1.40
428 438 9.176181 GTAATTTGTAAATGTCACGTGTCATTT 57.824 29.630 37.21 37.21 42.91 2.32
429 439 8.346300 TGTAATTTGTAAATGTCACGTGTCATT 58.654 29.630 27.81 27.81 35.81 2.57
430 440 7.866729 TGTAATTTGTAAATGTCACGTGTCAT 58.133 30.769 20.34 20.34 0.00 3.06
431 441 7.247929 TGTAATTTGTAAATGTCACGTGTCA 57.752 32.000 17.50 17.50 0.00 3.58
432 442 8.549777 TTTGTAATTTGTAAATGTCACGTGTC 57.450 30.769 16.51 10.98 0.00 3.67
433 443 7.166804 GCTTTGTAATTTGTAAATGTCACGTGT 59.833 33.333 16.51 0.00 0.00 4.49
434 444 7.166638 TGCTTTGTAATTTGTAAATGTCACGTG 59.833 33.333 9.94 9.94 0.00 4.49
435 445 7.197017 TGCTTTGTAATTTGTAAATGTCACGT 58.803 30.769 0.00 0.00 0.00 4.49
436 446 7.616103 TGCTTTGTAATTTGTAAATGTCACG 57.384 32.000 0.00 0.00 0.00 4.35
440 450 8.998377 GGGAATTGCTTTGTAATTTGTAAATGT 58.002 29.630 0.00 0.00 28.76 2.71
441 451 8.997323 TGGGAATTGCTTTGTAATTTGTAAATG 58.003 29.630 0.00 0.00 28.76 2.32
442 452 9.737844 ATGGGAATTGCTTTGTAATTTGTAAAT 57.262 25.926 0.00 0.00 28.76 1.40
443 453 9.213799 GATGGGAATTGCTTTGTAATTTGTAAA 57.786 29.630 0.00 0.00 28.76 2.01
444 454 7.821846 GGATGGGAATTGCTTTGTAATTTGTAA 59.178 33.333 0.00 0.00 28.76 2.41
445 455 7.327214 GGATGGGAATTGCTTTGTAATTTGTA 58.673 34.615 0.00 0.00 28.76 2.41
446 456 6.172630 GGATGGGAATTGCTTTGTAATTTGT 58.827 36.000 0.00 0.00 28.76 2.83
447 457 5.585844 GGGATGGGAATTGCTTTGTAATTTG 59.414 40.000 0.00 0.00 28.76 2.32
448 458 5.250313 TGGGATGGGAATTGCTTTGTAATTT 59.750 36.000 0.00 0.00 28.76 1.82
449 459 4.782156 TGGGATGGGAATTGCTTTGTAATT 59.218 37.500 0.00 0.00 31.08 1.40
450 460 4.360889 TGGGATGGGAATTGCTTTGTAAT 58.639 39.130 0.00 0.00 0.00 1.89
451 461 3.768757 CTGGGATGGGAATTGCTTTGTAA 59.231 43.478 0.00 0.00 0.00 2.41
452 462 3.364549 CTGGGATGGGAATTGCTTTGTA 58.635 45.455 0.00 0.00 0.00 2.41
453 463 2.181975 CTGGGATGGGAATTGCTTTGT 58.818 47.619 0.00 0.00 0.00 2.83
454 464 1.134610 GCTGGGATGGGAATTGCTTTG 60.135 52.381 0.00 0.00 0.00 2.77
455 465 1.197812 GCTGGGATGGGAATTGCTTT 58.802 50.000 0.00 0.00 0.00 3.51
456 466 0.041535 TGCTGGGATGGGAATTGCTT 59.958 50.000 0.00 0.00 0.00 3.91
460 470 1.076777 CGGTGCTGGGATGGGAATT 60.077 57.895 0.00 0.00 0.00 2.17
471 481 1.472082 TGTGGATTAATTGCGGTGCTG 59.528 47.619 0.00 0.00 0.00 4.41
494 504 1.071567 GACTGTGCTTCGTACGGCTC 61.072 60.000 16.52 12.85 0.00 4.70
503 513 3.085533 TGTAGAGAGAGGACTGTGCTTC 58.914 50.000 2.58 3.64 0.00 3.86
507 517 6.030548 TCAAAATGTAGAGAGAGGACTGTG 57.969 41.667 0.00 0.00 0.00 3.66
523 533 1.325476 GGGCAGGGCTCCTCAAAATG 61.325 60.000 0.00 0.00 0.00 2.32
547 557 4.088762 CATGCCCACACACGCGAC 62.089 66.667 15.93 0.00 0.00 5.19
549 559 3.313007 CTTCATGCCCACACACGCG 62.313 63.158 3.53 3.53 0.00 6.01
630 644 5.469084 GGTTCTTATTATTAGTTGCGGGAGG 59.531 44.000 0.00 0.00 0.00 4.30
631 645 6.053005 TGGTTCTTATTATTAGTTGCGGGAG 58.947 40.000 0.00 0.00 0.00 4.30
632 646 5.991861 TGGTTCTTATTATTAGTTGCGGGA 58.008 37.500 0.00 0.00 0.00 5.14
633 647 6.687081 TTGGTTCTTATTATTAGTTGCGGG 57.313 37.500 0.00 0.00 0.00 6.13
672 686 1.602323 TGTACCCGGCTGGCTTTTG 60.602 57.895 5.85 0.00 37.83 2.44
751 787 1.128200 CCCCTCTCTCTCTCTCGAGA 58.872 60.000 15.70 15.70 43.82 4.04
752 788 1.070758 CTCCCCTCTCTCTCTCTCGAG 59.929 61.905 5.93 5.93 38.67 4.04
753 789 1.128200 CTCCCCTCTCTCTCTCTCGA 58.872 60.000 0.00 0.00 0.00 4.04
754 790 0.108585 CCTCCCCTCTCTCTCTCTCG 59.891 65.000 0.00 0.00 0.00 4.04
755 791 0.478507 CCCTCCCCTCTCTCTCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
756 792 0.998945 CCCCTCCCCTCTCTCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
757 793 1.541672 CCCCTCCCCTCTCTCTCTC 59.458 68.421 0.00 0.00 0.00 3.20
758 794 2.018086 CCCCCTCCCCTCTCTCTCT 61.018 68.421 0.00 0.00 0.00 3.10
759 795 1.000041 TACCCCCTCCCCTCTCTCTC 61.000 65.000 0.00 0.00 0.00 3.20
760 796 0.331036 ATACCCCCTCCCCTCTCTCT 60.331 60.000 0.00 0.00 0.00 3.10
761 797 1.469082 TATACCCCCTCCCCTCTCTC 58.531 60.000 0.00 0.00 0.00 3.20
762 798 1.951618 TTATACCCCCTCCCCTCTCT 58.048 55.000 0.00 0.00 0.00 3.10
872 908 2.093288 TGCTTAGCTTGATCCTGGACTG 60.093 50.000 5.60 0.00 0.00 3.51
923 959 1.159098 AGACGCCGATCGAGAGTACC 61.159 60.000 18.66 4.17 41.67 3.34
1135 1172 0.676151 GAGAAGGCAGGGCTCACTTG 60.676 60.000 0.00 0.00 0.00 3.16
1170 1215 2.742589 CCTGATGAAGATGATGGATGCG 59.257 50.000 0.00 0.00 0.00 4.73
1171 1216 2.488545 GCCTGATGAAGATGATGGATGC 59.511 50.000 0.00 0.00 0.00 3.91
1190 1236 1.287815 GGTTTGGTTTACAGGCGCC 59.712 57.895 21.89 21.89 0.00 6.53
1256 1302 1.193426 GATTAGCAATCGCCGAAGAGC 59.807 52.381 0.00 0.00 39.83 4.09
1262 1310 2.600792 GCAAAGAGATTAGCAATCGCCG 60.601 50.000 8.28 0.00 42.75 6.46
1297 1345 3.204526 GAGATCCCATCTGCTCAAACAG 58.795 50.000 0.00 0.00 40.38 3.16
1373 1421 2.697751 AGGACTCTCTCCATGTGTATGC 59.302 50.000 0.00 0.00 42.46 3.14
1382 1431 0.407528 AGTGCAGAGGACTCTCTCCA 59.592 55.000 0.00 0.00 46.79 3.86
1384 1433 1.892474 ACAAGTGCAGAGGACTCTCTC 59.108 52.381 0.00 0.00 46.79 3.20
1388 1437 0.681733 TGGACAAGTGCAGAGGACTC 59.318 55.000 0.00 0.00 0.00 3.36
1389 1438 1.071385 CTTGGACAAGTGCAGAGGACT 59.929 52.381 3.93 0.00 33.87 3.85
1390 1439 1.517242 CTTGGACAAGTGCAGAGGAC 58.483 55.000 3.93 0.00 33.87 3.85
1425 1474 2.289694 CCCCAACACAGTAAGTCTCAGG 60.290 54.545 0.00 0.00 0.00 3.86
1429 1478 3.945640 AAACCCCAACACAGTAAGTCT 57.054 42.857 0.00 0.00 0.00 3.24
1442 1491 1.208293 GTGCAAGAAACCAAAACCCCA 59.792 47.619 0.00 0.00 0.00 4.96
1792 1873 1.403679 CCAAGCGACCAAGAACAAACA 59.596 47.619 0.00 0.00 0.00 2.83
1793 1874 1.864029 GCCAAGCGACCAAGAACAAAC 60.864 52.381 0.00 0.00 0.00 2.93
1794 1875 0.383949 GCCAAGCGACCAAGAACAAA 59.616 50.000 0.00 0.00 0.00 2.83
1795 1876 0.465460 AGCCAAGCGACCAAGAACAA 60.465 50.000 0.00 0.00 0.00 2.83
1946 2028 2.258286 GCTGGCGGCGAATGTTTT 59.742 55.556 12.98 0.00 0.00 2.43
1990 2075 6.324770 GGTCAATAATTTCATGGAGGATGGTT 59.675 38.462 0.00 0.00 32.26 3.67
2268 2377 7.082602 CCACACAAGAATGAGAGAAAGAAATG 58.917 38.462 0.00 0.00 0.00 2.32
2366 2481 2.177016 TCCAGCTAGCAGTAGGGTATGA 59.823 50.000 18.83 0.00 0.00 2.15
2368 2483 3.551635 ATCCAGCTAGCAGTAGGGTAT 57.448 47.619 18.83 1.23 0.00 2.73
2369 2484 3.330126 AATCCAGCTAGCAGTAGGGTA 57.670 47.619 18.83 0.00 0.00 3.69
2370 2485 2.182516 AATCCAGCTAGCAGTAGGGT 57.817 50.000 18.83 6.48 0.00 4.34
2371 2486 3.951775 CTAATCCAGCTAGCAGTAGGG 57.048 52.381 18.83 10.01 0.00 3.53
2394 2509 2.432444 GCAGTGGGCTATAAACACACA 58.568 47.619 9.75 0.00 40.25 3.72
2525 2640 7.647715 CCAAAATACCACTATCAATTAAAGCCG 59.352 37.037 0.00 0.00 0.00 5.52
2549 2664 1.227527 CCACTCACTCGTGCAACCA 60.228 57.895 0.00 0.00 33.60 3.67
2551 2666 0.304705 CAACCACTCACTCGTGCAAC 59.695 55.000 0.00 0.00 33.60 4.17
2552 2667 0.107897 ACAACCACTCACTCGTGCAA 60.108 50.000 0.00 0.00 33.60 4.08
2553 2668 0.809636 CACAACCACTCACTCGTGCA 60.810 55.000 0.00 0.00 33.60 4.57
2554 2669 0.810031 ACACAACCACTCACTCGTGC 60.810 55.000 0.00 0.00 33.60 5.34
2555 2670 2.502213 TACACAACCACTCACTCGTG 57.498 50.000 0.00 0.00 34.71 4.35
2556 2671 3.069016 TCATTACACAACCACTCACTCGT 59.931 43.478 0.00 0.00 0.00 4.18
2557 2672 3.649073 TCATTACACAACCACTCACTCG 58.351 45.455 0.00 0.00 0.00 4.18
2594 2712 0.609131 ATCAAACCAGCAAGTCCCGG 60.609 55.000 0.00 0.00 0.00 5.73
2595 2713 0.804989 GATCAAACCAGCAAGTCCCG 59.195 55.000 0.00 0.00 0.00 5.14
2596 2714 0.804989 CGATCAAACCAGCAAGTCCC 59.195 55.000 0.00 0.00 0.00 4.46
2597 2715 1.808411 TCGATCAAACCAGCAAGTCC 58.192 50.000 0.00 0.00 0.00 3.85
2598 2716 2.096496 CCATCGATCAAACCAGCAAGTC 59.904 50.000 0.00 0.00 0.00 3.01
2599 2717 2.086869 CCATCGATCAAACCAGCAAGT 58.913 47.619 0.00 0.00 0.00 3.16
2629 2751 4.101448 GTCCTCCGCCACCTGCAT 62.101 66.667 0.00 0.00 41.33 3.96
2797 2919 2.170738 CGTAGGGGTCGACGTACAA 58.829 57.895 9.92 0.00 37.26 2.41
3064 3189 0.686441 TAGGACGACATGGGAGTGGG 60.686 60.000 0.00 0.00 0.00 4.61
3148 3285 2.231745 TAGAGCAACGACGACGACGG 62.232 60.000 22.36 7.97 44.46 4.79
3215 3362 2.359354 CGTTTGGCGTGGGATGGA 60.359 61.111 0.00 0.00 35.54 3.41
3237 3384 4.210724 TGATTTGGGGTTAACTAGTCCG 57.789 45.455 5.42 0.00 0.00 4.79
3303 3455 1.264557 CTACGTACGGCCAGAGATCAG 59.735 57.143 21.06 0.00 0.00 2.90
3307 3459 0.321919 ACACTACGTACGGCCAGAGA 60.322 55.000 21.06 0.00 0.00 3.10
3308 3460 1.063174 GTACACTACGTACGGCCAGAG 59.937 57.143 21.06 13.67 41.13 3.35
3344 3501 1.371337 ATGCATGCACACCGCTACTG 61.371 55.000 25.37 0.00 43.06 2.74
3408 3565 1.208776 CCTCAGGTGTCATGCATCTCA 59.791 52.381 0.00 0.00 36.14 3.27
3596 3753 5.230323 ACATACTACCTAGCTGATCGAGA 57.770 43.478 0.00 0.00 0.00 4.04
3613 3772 2.555325 TCGATCCATGGTCCGTACATAC 59.445 50.000 21.36 0.00 0.00 2.39
3616 3775 1.029681 CTCGATCCATGGTCCGTACA 58.970 55.000 21.36 7.82 0.00 2.90
3656 3819 5.858581 CAGAAAAATTTCACCCGATCTTGAC 59.141 40.000 8.47 0.00 39.61 3.18
3659 3822 6.490040 TCTTCAGAAAAATTTCACCCGATCTT 59.510 34.615 8.47 0.00 39.61 2.40
3660 3823 6.003950 TCTTCAGAAAAATTTCACCCGATCT 58.996 36.000 8.47 0.00 39.61 2.75
3679 3842 3.694072 CGCCTCCACCATTAAAATCTTCA 59.306 43.478 0.00 0.00 0.00 3.02
3755 3919 4.380550 GGCCCCGAAATTTTTCTTACAGAG 60.381 45.833 0.00 0.00 35.07 3.35
3756 3920 3.508402 GGCCCCGAAATTTTTCTTACAGA 59.492 43.478 0.00 0.00 35.07 3.41
3799 3963 3.610911 CAGGAACCCACAATAGTTCTCC 58.389 50.000 3.22 0.00 41.69 3.71
3949 4117 4.347453 CAAGGCCGGTGCACAAGC 62.347 66.667 20.43 19.65 40.13 4.01
3950 4118 2.594303 TCAAGGCCGGTGCACAAG 60.594 61.111 20.43 11.86 40.13 3.16
3980 4148 4.395583 GCTGTTGCTCGCCTGCAC 62.396 66.667 0.00 0.00 43.20 4.57


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

AutoCloner maintained by Alex Coulton.