Multiple sequence alignment - TraesCS7B01G363100

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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 TraesCS7B01G363100 chr7B 100.000 7032 0 0 1 7032 625302664 625295633 0.000000e+00 12986.0
1 TraesCS7B01G363100 chr7B 92.432 185 11 3 2279 2463 592343227 592343408 1.950000e-65 261.0
2 TraesCS7B01G363100 chr7B 94.118 51 2 1 2207 2256 592343187 592343237 7.560000e-10 76.8
3 TraesCS7B01G363100 chr7A 90.631 4504 233 78 2283 6677 657720222 657715799 0.000000e+00 5805.0
4 TraesCS7B01G363100 chr7A 88.106 2270 117 57 72 2258 657722496 657720297 0.000000e+00 2555.0
5 TraesCS7B01G363100 chr7A 90.811 185 10 2 2279 2463 632546288 632546465 2.530000e-59 241.0
6 TraesCS7B01G363100 chr7A 80.836 287 27 13 6716 6990 657715795 657715525 4.300000e-47 200.0
7 TraesCS7B01G363100 chr7D 93.610 2817 113 35 3772 6559 568951725 568948947 0.000000e+00 4143.0
8 TraesCS7B01G363100 chr7D 90.143 2313 110 43 5 2253 568955530 568953272 0.000000e+00 2900.0
9 TraesCS7B01G363100 chr7D 91.039 1473 86 26 2279 3729 568953278 568951830 0.000000e+00 1947.0
10 TraesCS7B01G363100 chr7D 89.074 421 36 4 2279 2690 548771500 548771919 1.350000e-141 514.0
11 TraesCS7B01G363100 chr7D 80.399 301 26 14 6561 6848 568948898 568948618 1.550000e-46 198.0
12 TraesCS7B01G363100 chr7D 92.157 51 3 1 2207 2256 548771460 548771510 3.520000e-08 71.3
13 TraesCS7B01G363100 chr7D 92.308 52 0 3 6985 7032 568948479 568948428 3.520000e-08 71.3
14 TraesCS7B01G363100 chr4A 95.108 1022 45 2 3504 4525 639045657 639046673 0.000000e+00 1605.0
15 TraesCS7B01G363100 chr4A 95.652 46 2 0 4398 4443 639046724 639046679 2.720000e-09 75.0
16 TraesCS7B01G363100 chr6D 79.521 376 67 8 3069 3442 91519119 91519486 7.000000e-65 259.0
17 TraesCS7B01G363100 chr6D 78.571 392 66 16 2336 2715 91518359 91518744 7.050000e-60 243.0
18 TraesCS7B01G363100 chr6B 79.521 376 67 8 3069 3442 175340079 175340446 7.000000e-65 259.0
19 TraesCS7B01G363100 chr6B 78.061 392 68 16 2336 2715 175339319 175339704 1.530000e-56 231.0
20 TraesCS7B01G363100 chr6B 97.143 35 1 0 282 316 175337544 175337578 7.620000e-05 60.2
21 TraesCS7B01G363100 chr6A 79.474 380 60 13 3069 3442 109985281 109985648 3.260000e-63 254.0
22 TraesCS7B01G363100 chr6A 97.143 35 1 0 282 316 109982741 109982775 7.620000e-05 60.2
23 TraesCS7B01G363100 chr5B 79.899 199 40 0 5532 5730 44781737 44781935 5.680000e-31 147.0
24 TraesCS7B01G363100 chr5A 79.899 199 40 0 5532 5730 35632169 35632367 5.680000e-31 147.0
25 TraesCS7B01G363100 chr5D 79.397 199 41 0 5532 5730 44912591 44912789 2.640000e-29 141.0
26 TraesCS7B01G363100 chr2B 84.466 103 14 2 1735 1836 766557988 766558089 4.490000e-17 100.0
27 TraesCS7B01G363100 chr2B 83.333 108 16 2 5623 5729 766566843 766566949 1.610000e-16 99.0
28 TraesCS7B01G363100 chr2B 82.000 100 14 3 1739 1836 714128224 714128321 1.630000e-11 82.4
29 TraesCS7B01G363100 chr2A 84.466 103 14 2 1735 1836 755769246 755769347 4.490000e-17 100.0
30 TraesCS7B01G363100 chr2A 84.848 99 13 2 5632 5729 755774288 755774385 1.610000e-16 99.0
31 TraesCS7B01G363100 chr2A 81.000 100 15 3 1739 1836 724297755 724297852 7.560000e-10 76.8
32 TraesCS7B01G363100 chr2D 83.333 108 16 2 5623 5729 624367319 624367425 1.610000e-16 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 TraesCS7B01G363100 chr7B 625295633 625302664 7031 True 12986.000000 12986 100.000000 1 7032 1 chr7B.!!$R1 7031
1 TraesCS7B01G363100 chr7A 657715525 657722496 6971 True 2853.333333 5805 86.524333 72 6990 3 chr7A.!!$R1 6918
2 TraesCS7B01G363100 chr7D 568948428 568955530 7102 True 1851.860000 4143 89.499800 5 7032 5 chr7D.!!$R1 7027
3 TraesCS7B01G363100 chr4A 639045657 639046673 1016 False 1605.000000 1605 95.108000 3504 4525 1 chr4A.!!$F1 1021
4 TraesCS7B01G363100 chr6D 91518359 91519486 1127 False 251.000000 259 79.046000 2336 3442 2 chr6D.!!$F1 1106

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
231 273 0.313672 AACGAAAGGGCGTACGTACA 59.686 50.000 24.50 0.0 44.86 2.90 F
449 491 0.459237 CTGTAACCGCAGCTCCTGAG 60.459 60.000 0.00 0.0 32.44 3.35 F
870 980 1.333931 GTTTATTAGGGAAGGCGCTGC 59.666 52.381 7.64 0.0 37.89 5.25 F
2544 2735 1.276421 GCTCCTCTACACTTTCCAGCA 59.724 52.381 0.00 0.0 0.00 4.41 F
3938 4239 0.315251 CACTCAGACTGAAGCGACCA 59.685 55.000 6.61 0.0 0.00 4.02 F
5436 5767 1.002366 GAGCATTGACCGCACACTAG 58.998 55.000 0.00 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1844 1.134580 GCTCCTCAGCAGCTGTAATGA 60.135 52.381 22.10 15.53 46.06 2.57 R
2037 2177 1.891722 GCTGTGGAGGCAAATTGGGG 61.892 60.000 0.00 0.00 0.00 4.96 R
2784 2982 1.283905 ACCTTCACCCGGGGAAAATAG 59.716 52.381 27.92 12.61 0.00 1.73 R
4351 4652 1.696063 ACTGAGGTTGCATTTGCTGT 58.304 45.000 3.94 0.00 42.66 4.40 R
5709 6041 0.320374 CTTACTGCCAAGGGTCGTCA 59.680 55.000 0.00 0.00 0.00 4.35 R
6869 7299 0.038251 GGATGCGAGCGTGATGGATA 60.038 55.000 0.00 0.00 0.00 2.59 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 2.490165 GAGTAGCCGCACTCCACTA 58.510 57.895 10.25 0.00 39.26 2.74
45 46 3.944422 AAACGTTCACATCACTCACAC 57.056 42.857 0.00 0.00 0.00 3.82
57 66 0.319900 ACTCACACAGGCACATCGTC 60.320 55.000 0.00 0.00 0.00 4.20
60 69 0.674581 CACACAGGCACATCGTCCAT 60.675 55.000 0.00 0.00 0.00 3.41
62 71 1.746615 ACAGGCACATCGTCCATGC 60.747 57.895 0.00 0.00 35.65 4.06
64 73 1.002257 AGGCACATCGTCCATGCAA 60.002 52.632 0.00 0.00 41.27 4.08
65 74 1.137404 GGCACATCGTCCATGCAAC 59.863 57.895 0.00 0.00 41.27 4.17
66 75 1.226101 GCACATCGTCCATGCAACG 60.226 57.895 11.38 11.38 39.23 4.10
67 76 1.226101 CACATCGTCCATGCAACGC 60.226 57.895 12.46 0.00 39.90 4.84
68 77 1.375908 ACATCGTCCATGCAACGCT 60.376 52.632 12.46 2.44 39.90 5.07
69 78 1.349627 CATCGTCCATGCAACGCTC 59.650 57.895 12.46 0.00 39.90 5.03
70 79 1.079197 ATCGTCCATGCAACGCTCA 60.079 52.632 12.46 0.00 39.90 4.26
71 80 1.361668 ATCGTCCATGCAACGCTCAC 61.362 55.000 12.46 0.00 39.90 3.51
72 81 2.029288 CGTCCATGCAACGCTCACT 61.029 57.895 6.01 0.00 32.84 3.41
73 82 1.790387 GTCCATGCAACGCTCACTC 59.210 57.895 0.00 0.00 0.00 3.51
114 130 2.615227 ATTCCGGGGAGCATGAGCAC 62.615 60.000 0.00 0.00 45.49 4.40
174 212 6.090898 CCTGCACAACTGTACAAGTATACTTC 59.909 42.308 15.35 5.58 38.56 3.01
175 213 6.755206 TGCACAACTGTACAAGTATACTTCT 58.245 36.000 15.35 6.89 38.56 2.85
176 214 6.645003 TGCACAACTGTACAAGTATACTTCTG 59.355 38.462 15.35 8.95 38.56 3.02
177 215 6.401153 GCACAACTGTACAAGTATACTTCTGC 60.401 42.308 15.35 8.45 38.56 4.26
178 216 6.868864 CACAACTGTACAAGTATACTTCTGCT 59.131 38.462 15.35 1.67 38.56 4.24
179 217 8.027189 CACAACTGTACAAGTATACTTCTGCTA 58.973 37.037 15.35 0.78 38.56 3.49
180 218 8.027771 ACAACTGTACAAGTATACTTCTGCTAC 58.972 37.037 15.35 11.98 38.56 3.58
181 219 7.941431 ACTGTACAAGTATACTTCTGCTACT 57.059 36.000 15.35 0.00 37.36 2.57
182 220 9.458727 AACTGTACAAGTATACTTCTGCTACTA 57.541 33.333 15.35 4.26 38.56 1.82
183 221 8.891720 ACTGTACAAGTATACTTCTGCTACTAC 58.108 37.037 15.35 5.83 37.36 2.73
184 222 9.111613 CTGTACAAGTATACTTCTGCTACTACT 57.888 37.037 15.35 0.00 33.11 2.57
185 223 9.107177 TGTACAAGTATACTTCTGCTACTACTC 57.893 37.037 15.35 0.00 33.11 2.59
186 224 9.328845 GTACAAGTATACTTCTGCTACTACTCT 57.671 37.037 15.35 0.00 33.11 3.24
188 226 9.328845 ACAAGTATACTTCTGCTACTACTCTAC 57.671 37.037 15.35 0.00 33.11 2.59
189 227 9.550406 CAAGTATACTTCTGCTACTACTCTACT 57.450 37.037 15.35 0.00 33.11 2.57
191 229 9.768662 AGTATACTTCTGCTACTACTCTACTTC 57.231 37.037 0.00 0.00 0.00 3.01
216 258 3.888934 AGTCGCTTAGTAAAACGAACGA 58.111 40.909 8.73 0.00 35.18 3.85
217 259 4.290155 AGTCGCTTAGTAAAACGAACGAA 58.710 39.130 8.73 0.00 35.18 3.85
218 260 4.739716 AGTCGCTTAGTAAAACGAACGAAA 59.260 37.500 8.73 0.00 35.18 3.46
219 261 5.062432 GTCGCTTAGTAAAACGAACGAAAG 58.938 41.667 8.73 0.00 35.18 2.62
231 273 0.313672 AACGAAAGGGCGTACGTACA 59.686 50.000 24.50 0.00 44.86 2.90
249 291 6.314784 ACGTACAGTACACGATTTTACTACC 58.685 40.000 11.37 0.00 41.91 3.18
250 292 6.072728 ACGTACAGTACACGATTTTACTACCA 60.073 38.462 11.37 0.00 41.91 3.25
251 293 6.467047 CGTACAGTACACGATTTTACTACCAG 59.533 42.308 11.37 0.00 41.91 4.00
372 414 0.546267 AAGCAGCCAGAGGAGGAAGA 60.546 55.000 0.00 0.00 0.00 2.87
408 450 0.673437 CCAAGAAAAGCAAAGCCGGA 59.327 50.000 5.05 0.00 0.00 5.14
447 489 4.192000 CTGTAACCGCAGCTCCTG 57.808 61.111 0.00 0.00 34.12 3.86
448 490 1.591703 CTGTAACCGCAGCTCCTGA 59.408 57.895 0.00 0.00 32.44 3.86
449 491 0.459237 CTGTAACCGCAGCTCCTGAG 60.459 60.000 0.00 0.00 32.44 3.35
597 686 3.967335 CGGCTCCTCGGATCGACC 61.967 72.222 0.00 0.00 0.00 4.79
711 801 2.597510 GGCAACTTGGGCGGAACT 60.598 61.111 0.00 0.00 0.00 3.01
724 814 2.106683 GGAACTCCCGCGGTGATTG 61.107 63.158 26.12 8.39 0.00 2.67
826 936 2.185608 GAGTTGGCGAGGAGGAGC 59.814 66.667 0.00 0.00 0.00 4.70
870 980 1.333931 GTTTATTAGGGAAGGCGCTGC 59.666 52.381 7.64 0.00 37.89 5.25
916 1026 2.042435 CTCCGCTCTCCCCTTCCT 60.042 66.667 0.00 0.00 0.00 3.36
918 1028 1.681486 CTCCGCTCTCCCCTTCCTTC 61.681 65.000 0.00 0.00 0.00 3.46
921 1031 2.379459 GCTCTCCCCTTCCTTCCCC 61.379 68.421 0.00 0.00 0.00 4.81
922 1032 2.040606 TCTCCCCTTCCTTCCCCG 59.959 66.667 0.00 0.00 0.00 5.73
1240 1367 4.219507 GCTCTCTCCTCGGATTGATTATGA 59.780 45.833 0.00 0.00 0.00 2.15
1256 1383 2.509336 GACCGTGTGATCAGGCCG 60.509 66.667 0.00 0.00 0.00 6.13
1315 1442 7.806680 AATATTTGGATTTGTTAGGGGTTGT 57.193 32.000 0.00 0.00 0.00 3.32
1322 1449 4.762289 TTTGTTAGGGGTTGTTGCAATT 57.238 36.364 0.59 0.00 0.00 2.32
1379 1506 4.798387 GGTACTTTTATGCCTGCGAAATTG 59.202 41.667 0.00 0.00 0.00 2.32
1394 1521 5.080068 GCGAAATTGCAGTTCAGTACTAAC 58.920 41.667 11.46 1.25 34.56 2.34
1407 1539 7.230712 AGTTCAGTACTAACTTTTTGGAATGGG 59.769 37.037 0.00 0.00 33.39 4.00
1456 1588 1.407979 CCATCCAATTTCCTGCTCTGC 59.592 52.381 0.00 0.00 0.00 4.26
1466 1598 3.603158 TCCTGCTCTGCGTGTTAATTA 57.397 42.857 0.00 0.00 0.00 1.40
1608 1740 5.332743 TGCCCACCTTCTTGAATAATCTTT 58.667 37.500 0.00 0.00 0.00 2.52
1612 1744 7.416777 GCCCACCTTCTTGAATAATCTTTAAGG 60.417 40.741 0.00 0.00 35.79 2.69
1669 1807 8.997323 CCTAGAGCCATCATTATCTGTTAAAAG 58.003 37.037 0.00 0.00 0.00 2.27
1674 1812 9.064706 AGCCATCATTATCTGTTAAAAGATCAG 57.935 33.333 11.58 3.91 37.98 2.90
1685 1823 5.822519 TGTTAAAAGATCAGCACTGACAAGT 59.177 36.000 1.71 0.00 43.11 3.16
1689 1827 4.348863 AGATCAGCACTGACAAGTCTTT 57.651 40.909 1.71 0.00 43.11 2.52
1703 1841 8.791327 TGACAAGTCTTTTGCTCATATGATTA 57.209 30.769 5.72 0.00 0.00 1.75
1706 1844 9.182214 ACAAGTCTTTTGCTCATATGATTATGT 57.818 29.630 5.72 0.00 37.16 2.29
1758 1896 2.996168 ATTCGGAGCTATGGCACGCC 62.996 60.000 12.16 0.00 41.70 5.68
1843 1981 3.730761 GCGAGCAGGTTGGTGCAG 61.731 66.667 0.00 0.00 46.60 4.41
1907 2046 3.744719 CCTCCGTCGCCGAACAGA 61.745 66.667 0.00 0.00 35.63 3.41
2037 2177 2.359531 CGAGTCTCAGATCCCCAACTAC 59.640 54.545 0.00 0.00 0.00 2.73
2142 2282 4.962155 ACCAGCTAAGTAATATCACTGCC 58.038 43.478 0.00 0.00 0.00 4.85
2252 2392 6.256643 ACCACTTAACCCGGTAATTCATAT 57.743 37.500 0.00 0.00 0.00 1.78
2253 2393 6.293698 ACCACTTAACCCGGTAATTCATATC 58.706 40.000 0.00 0.00 0.00 1.63
2254 2394 6.126710 ACCACTTAACCCGGTAATTCATATCA 60.127 38.462 0.00 0.00 0.00 2.15
2256 2396 6.990349 CACTTAACCCGGTAATTCATATCACT 59.010 38.462 0.00 0.00 0.00 3.41
2257 2397 7.170998 CACTTAACCCGGTAATTCATATCACTC 59.829 40.741 0.00 0.00 0.00 3.51
2258 2398 5.888982 AACCCGGTAATTCATATCACTCT 57.111 39.130 0.00 0.00 0.00 3.24
2259 2399 5.888982 ACCCGGTAATTCATATCACTCTT 57.111 39.130 0.00 0.00 0.00 2.85
2260 2400 6.248569 ACCCGGTAATTCATATCACTCTTT 57.751 37.500 0.00 0.00 0.00 2.52
2263 2403 7.067008 ACCCGGTAATTCATATCACTCTTTTTG 59.933 37.037 0.00 0.00 0.00 2.44
2264 2404 7.067008 CCCGGTAATTCATATCACTCTTTTTGT 59.933 37.037 0.00 0.00 0.00 2.83
2265 2405 7.910162 CCGGTAATTCATATCACTCTTTTTGTG 59.090 37.037 0.00 0.00 36.82 3.33
2266 2406 8.450964 CGGTAATTCATATCACTCTTTTTGTGT 58.549 33.333 0.00 0.00 36.83 3.72
2267 2407 9.559958 GGTAATTCATATCACTCTTTTTGTGTG 57.440 33.333 0.00 0.00 40.41 3.82
2271 2411 7.800155 TCATATCACTCTTTTTGTGTGTGAA 57.200 32.000 0.00 0.00 40.37 3.18
2274 2414 9.467258 CATATCACTCTTTTTGTGTGTGAAATT 57.533 29.630 0.00 0.00 40.37 1.82
2276 2416 8.776376 ATCACTCTTTTTGTGTGTGAAATTTT 57.224 26.923 0.00 0.00 40.37 1.82
2277 2417 8.600449 TCACTCTTTTTGTGTGTGAAATTTTT 57.400 26.923 0.00 0.00 40.09 1.94
2527 2718 3.117171 CGCTGGTCTGTGCTGCTC 61.117 66.667 0.00 0.00 0.00 4.26
2544 2735 1.276421 GCTCCTCTACACTTTCCAGCA 59.724 52.381 0.00 0.00 0.00 4.41
2548 2739 3.582647 TCCTCTACACTTTCCAGCATGAA 59.417 43.478 0.00 0.00 39.69 2.57
2555 2746 5.535333 ACACTTTCCAGCATGAATTTTGAG 58.465 37.500 0.00 0.00 39.69 3.02
2564 2756 6.366877 CCAGCATGAATTTTGAGTTTACTTGG 59.633 38.462 0.00 0.00 39.69 3.61
2581 2773 3.287222 CTTGGTTTCTTGGAGTGAACCA 58.713 45.455 2.88 2.88 38.24 3.67
2582 2774 2.930950 TGGTTTCTTGGAGTGAACCAG 58.069 47.619 2.88 0.00 41.19 4.00
2584 2776 2.879026 GGTTTCTTGGAGTGAACCAGAC 59.121 50.000 0.00 0.00 41.19 3.51
2632 2829 7.368059 CCTGTAACTTTTTGTAGGATTTCACC 58.632 38.462 0.00 0.00 0.00 4.02
2731 2929 4.780275 TGAGTGTTCTCAGTCTCTGATG 57.220 45.455 0.00 0.00 44.58 3.07
2776 2974 4.082081 GGAACAATGTCAAGCATGATTCCA 60.082 41.667 13.68 0.00 44.19 3.53
2784 2982 5.106038 TGTCAAGCATGATTCCATCTGTTTC 60.106 40.000 0.00 0.00 38.01 2.78
2785 2983 5.125097 GTCAAGCATGATTCCATCTGTTTCT 59.875 40.000 0.00 0.00 38.01 2.52
2795 2996 4.523083 TCCATCTGTTTCTATTTTCCCCG 58.477 43.478 0.00 0.00 0.00 5.73
2809 3010 1.374572 TCCCCGGGTGAAGGTTTATT 58.625 50.000 21.85 0.00 0.00 1.40
2816 3017 5.106038 CCCGGGTGAAGGTTTATTTTAAGAC 60.106 44.000 14.18 0.00 0.00 3.01
2826 3037 9.726232 AAGGTTTATTTTAAGACAACGAAGAAC 57.274 29.630 0.00 0.00 0.00 3.01
2827 3038 9.117183 AGGTTTATTTTAAGACAACGAAGAACT 57.883 29.630 0.00 0.00 0.00 3.01
2833 3044 6.823678 TTAAGACAACGAAGAACTTCACTC 57.176 37.500 13.72 3.57 39.46 3.51
2844 3055 6.690957 CGAAGAACTTCACTCATAAGCTCTAG 59.309 42.308 13.72 0.00 39.46 2.43
2967 3199 5.163854 GGTATGTTCATTCTTCCAACACTCG 60.164 44.000 0.00 0.00 32.96 4.18
2968 3200 4.066646 TGTTCATTCTTCCAACACTCGA 57.933 40.909 0.00 0.00 0.00 4.04
2969 3201 4.058124 TGTTCATTCTTCCAACACTCGAG 58.942 43.478 11.84 11.84 0.00 4.04
2970 3202 4.202212 TGTTCATTCTTCCAACACTCGAGA 60.202 41.667 21.68 0.00 0.00 4.04
2972 3204 4.498241 TCATTCTTCCAACACTCGAGATG 58.502 43.478 21.68 15.67 0.00 2.90
2973 3205 4.220602 TCATTCTTCCAACACTCGAGATGA 59.779 41.667 21.68 10.53 0.00 2.92
2976 3208 6.471233 TTCTTCCAACACTCGAGATGATAT 57.529 37.500 21.68 0.00 0.00 1.63
2980 3212 6.961360 TCCAACACTCGAGATGATATAACT 57.039 37.500 21.68 0.00 0.00 2.24
2985 3217 4.920340 CACTCGAGATGATATAACTGGCAC 59.080 45.833 21.68 0.00 0.00 5.01
3000 3232 2.419739 GCACCCCTCTCTCCTCGAC 61.420 68.421 0.00 0.00 0.00 4.20
3006 3238 1.071071 CCCTCTCTCCTCGACGTCTAT 59.929 57.143 14.70 0.00 0.00 1.98
3009 3241 3.459145 CTCTCTCCTCGACGTCTATTCA 58.541 50.000 14.70 0.00 0.00 2.57
3011 3243 4.259356 TCTCTCCTCGACGTCTATTCAAA 58.741 43.478 14.70 0.00 0.00 2.69
3014 3246 5.579718 TCTCCTCGACGTCTATTCAAATTC 58.420 41.667 14.70 0.00 0.00 2.17
3015 3247 5.357314 TCTCCTCGACGTCTATTCAAATTCT 59.643 40.000 14.70 0.00 0.00 2.40
3016 3248 5.340803 TCCTCGACGTCTATTCAAATTCTG 58.659 41.667 14.70 0.00 0.00 3.02
3017 3249 4.504461 CCTCGACGTCTATTCAAATTCTGG 59.496 45.833 14.70 0.00 0.00 3.86
3018 3250 5.068234 TCGACGTCTATTCAAATTCTGGT 57.932 39.130 14.70 0.00 0.00 4.00
3020 3252 6.802608 TCGACGTCTATTCAAATTCTGGTAT 58.197 36.000 14.70 0.00 0.00 2.73
3021 3253 6.695713 TCGACGTCTATTCAAATTCTGGTATG 59.304 38.462 14.70 0.00 0.00 2.39
3038 3270 3.003068 GGTATGTGCATGCAGATTCTCAC 59.997 47.826 32.26 23.51 32.10 3.51
3051 3283 5.159209 CAGATTCTCACTGGTCAAATTTGC 58.841 41.667 13.54 8.47 0.00 3.68
3053 3285 1.266718 TCTCACTGGTCAAATTTGCGC 59.733 47.619 13.54 0.00 0.00 6.09
3057 3289 1.888512 ACTGGTCAAATTTGCGCATCT 59.111 42.857 12.75 0.00 0.00 2.90
3141 3373 2.821969 ACAAACTGTCATGCCATCTTCC 59.178 45.455 0.00 0.00 0.00 3.46
3150 3382 1.788229 TGCCATCTTCCGTCCTATCA 58.212 50.000 0.00 0.00 0.00 2.15
3266 3499 5.493133 AAGTGTATGCTTTCGTTTGTTCA 57.507 34.783 0.00 0.00 0.00 3.18
3295 3529 9.744468 GTTTTTCCTTCTGAATGCTTTAAGTTA 57.256 29.630 0.00 0.00 31.67 2.24
3298 3532 9.744468 TTTCCTTCTGAATGCTTTAAGTTAAAC 57.256 29.630 3.88 3.20 31.67 2.01
3432 3668 6.851222 TTGAGACAGAAGAATCAAGTGTTC 57.149 37.500 0.00 0.00 0.00 3.18
3443 3679 1.899814 TCAAGTGTTCGGAGGTATGCT 59.100 47.619 0.00 0.00 0.00 3.79
3452 3688 7.773690 AGTGTTCGGAGGTATGCTAAATTAAAT 59.226 33.333 0.00 0.00 0.00 1.40
3477 3713 8.801715 TTTTGATGTGCTTTTCATCTTTACTC 57.198 30.769 7.30 0.00 41.30 2.59
3478 3714 7.750229 TTGATGTGCTTTTCATCTTTACTCT 57.250 32.000 7.30 0.00 41.30 3.24
3479 3715 8.846943 TTGATGTGCTTTTCATCTTTACTCTA 57.153 30.769 7.30 0.00 41.30 2.43
3481 3717 9.283768 TGATGTGCTTTTCATCTTTACTCTAAA 57.716 29.630 7.30 0.00 41.30 1.85
3497 3733 5.846203 ACTCTAAAAACATGTTGCAGCAAT 58.154 33.333 12.82 0.00 0.00 3.56
3500 3736 7.925483 ACTCTAAAAACATGTTGCAGCAATAAA 59.075 29.630 12.82 0.60 0.00 1.40
3501 3737 8.830201 TCTAAAAACATGTTGCAGCAATAAAT 57.170 26.923 12.82 3.16 0.00 1.40
3502 3738 8.710551 TCTAAAAACATGTTGCAGCAATAAATG 58.289 29.630 12.82 16.79 0.00 2.32
3673 3913 7.287466 TGAAGGTATATTTACGGGCTAACACTA 59.713 37.037 0.00 0.00 0.00 2.74
3734 3974 6.740122 GCCTGTTGTTTACCCATGTATTGTTT 60.740 38.462 0.00 0.00 0.00 2.83
3768 4058 5.526506 AATTCCTATTGAGATTGCTTGGC 57.473 39.130 0.00 0.00 0.00 4.52
3795 4096 4.993584 ACTTCACAGTTTAGCATGACAGAG 59.006 41.667 0.00 0.00 0.00 3.35
3938 4239 0.315251 CACTCAGACTGAAGCGACCA 59.685 55.000 6.61 0.00 0.00 4.02
4131 4432 1.929836 GTGGCTTCGAGATAGTGCAAG 59.070 52.381 0.00 0.00 0.00 4.01
4351 4652 4.083324 CCGCTTCTGCAAAGTCAGATTTTA 60.083 41.667 9.40 0.00 42.12 1.52
4579 4880 3.119884 TGCAACAACAGAAGAATATGGCG 60.120 43.478 0.00 0.00 0.00 5.69
4870 5171 2.665000 CCTCAGTCCACCACGCAT 59.335 61.111 0.00 0.00 0.00 4.73
5041 5342 2.027745 TCTGATGCAAGGAGGTCTTCAC 60.028 50.000 0.00 0.00 32.41 3.18
5065 5366 2.347939 CGAGAATGATTCGACGGCAATG 60.348 50.000 15.66 0.00 40.36 2.82
5092 5393 6.660949 CCTATTCCACTTCCAATTTTCTGAGT 59.339 38.462 0.00 0.00 0.00 3.41
5256 5557 9.702494 TCTCTATATGACAAGCAATCATGTTAG 57.298 33.333 7.43 8.16 37.38 2.34
5263 5567 6.939730 TGACAAGCAATCATGTTAGTTCCTTA 59.060 34.615 0.00 0.00 0.00 2.69
5350 5677 3.342377 TGCCCATTTCGTGACTATCAA 57.658 42.857 0.00 0.00 0.00 2.57
5351 5678 3.884895 TGCCCATTTCGTGACTATCAAT 58.115 40.909 0.00 0.00 0.00 2.57
5352 5679 5.029807 TGCCCATTTCGTGACTATCAATA 57.970 39.130 0.00 0.00 0.00 1.90
5353 5680 5.620206 TGCCCATTTCGTGACTATCAATAT 58.380 37.500 0.00 0.00 0.00 1.28
5397 5728 4.558226 TGGTAGAAACACATCTGATGCT 57.442 40.909 17.24 8.47 0.00 3.79
5436 5767 1.002366 GAGCATTGACCGCACACTAG 58.998 55.000 0.00 0.00 0.00 2.57
5444 5775 2.486982 TGACCGCACACTAGAACTAGAC 59.513 50.000 14.64 0.00 36.97 2.59
5475 5807 3.185246 AGATGCTCGGATGTTTGGTAG 57.815 47.619 0.00 0.00 0.00 3.18
5476 5808 1.599542 GATGCTCGGATGTTTGGTAGC 59.400 52.381 0.00 0.00 0.00 3.58
5485 5817 3.572255 GGATGTTTGGTAGCTTGTTCCAA 59.428 43.478 0.00 0.00 39.12 3.53
5487 5819 4.582701 TGTTTGGTAGCTTGTTCCAATG 57.417 40.909 11.23 0.00 40.28 2.82
5490 5822 1.202989 TGGTAGCTTGTTCCAATGCCA 60.203 47.619 0.00 0.00 0.00 4.92
5493 5825 1.412079 AGCTTGTTCCAATGCCACAA 58.588 45.000 0.00 0.00 0.00 3.33
5494 5826 1.069049 AGCTTGTTCCAATGCCACAAC 59.931 47.619 0.00 0.00 0.00 3.32
5499 5831 2.964464 TGTTCCAATGCCACAACTGATT 59.036 40.909 0.00 0.00 0.00 2.57
5622 5954 1.526225 GGAACTGGGGCGCCTATTC 60.526 63.158 28.56 22.11 0.00 1.75
5709 6041 2.273912 GGACGTCCTTCTGGTCGGT 61.274 63.158 27.64 0.00 46.35 4.69
5773 6105 7.202016 TGATCTGTGTTACTTCATTTTCCAC 57.798 36.000 0.00 0.00 0.00 4.02
6022 6355 2.401766 GGTCGGCTCGGTCGAAGTA 61.402 63.158 2.21 0.00 42.59 2.24
6040 6373 3.361786 AGTAGAGTTCTGAAGAGAGGGC 58.638 50.000 0.00 0.00 0.00 5.19
6147 6489 1.269257 GGAACTGGAAAGCAAGCACAC 60.269 52.381 0.00 0.00 0.00 3.82
6223 6568 5.587844 GCCATGTGATCTCATGTTAAGAAGT 59.412 40.000 27.38 0.00 42.29 3.01
6233 6578 8.064336 TCTCATGTTAAGAAGTAGTAGGAACC 57.936 38.462 0.00 0.00 0.00 3.62
6304 6649 5.827756 TCTCTTCTGTGGAATACTCCTACA 58.172 41.667 0.00 0.00 42.94 2.74
6352 6697 5.344066 TCTAGTCATCAATTCTCTTGTCGC 58.656 41.667 0.00 0.00 0.00 5.19
6353 6698 3.930336 AGTCATCAATTCTCTTGTCGCA 58.070 40.909 0.00 0.00 0.00 5.10
6355 6700 3.928992 GTCATCAATTCTCTTGTCGCAGA 59.071 43.478 0.00 0.00 0.00 4.26
6356 6701 4.032672 GTCATCAATTCTCTTGTCGCAGAG 59.967 45.833 0.88 0.88 41.69 3.35
6357 6702 2.341257 TCAATTCTCTTGTCGCAGAGC 58.659 47.619 2.19 0.00 40.33 4.09
6368 6713 2.574736 GCAGAGCGTCGTCGACTC 60.575 66.667 22.18 15.20 39.01 3.36
6369 6714 2.276120 CAGAGCGTCGTCGACTCG 60.276 66.667 22.18 20.11 41.38 4.18
6370 6715 2.737757 AGAGCGTCGTCGACTCGT 60.738 61.111 22.18 7.21 41.38 4.18
6371 6716 2.275935 GAGCGTCGTCGACTCGTC 60.276 66.667 22.18 12.15 39.71 4.20
6381 6726 2.097918 GACTCGTCGTCGTCGCAT 59.902 61.111 7.01 0.00 38.33 4.73
6396 6741 3.308595 CGTCGCATTTGCCTATCTTGTTA 59.691 43.478 0.00 0.00 37.91 2.41
6408 6753 8.327941 TGCCTATCTTGTTAATATTCTGCATC 57.672 34.615 0.00 0.00 0.00 3.91
6493 6859 4.036498 GCATTGATCTTCACTTCCAGATGG 59.964 45.833 0.00 0.00 29.41 3.51
6555 6921 1.442526 GCCGATCAGAACTGGCATGG 61.443 60.000 6.15 1.55 46.76 3.66
6556 6922 0.107508 CCGATCAGAACTGGCATGGT 60.108 55.000 0.00 0.00 0.00 3.55
6558 6924 1.673168 GATCAGAACTGGCATGGTCC 58.327 55.000 0.00 0.00 0.00 4.46
6577 6989 2.499303 CTTCCATGGGTGGGGTGGAC 62.499 65.000 13.02 0.00 46.06 4.02
6604 7016 1.890552 AAGATGGATGGACAGAGGCT 58.109 50.000 0.00 0.00 0.00 4.58
6612 7024 0.984230 TGGACAGAGGCTACCTTTGG 59.016 55.000 8.81 0.00 39.68 3.28
6613 7025 0.984995 GGACAGAGGCTACCTTTGGT 59.015 55.000 8.81 0.00 39.68 3.67
6614 7026 1.351350 GGACAGAGGCTACCTTTGGTT 59.649 52.381 8.81 0.00 39.68 3.67
6615 7027 2.570302 GGACAGAGGCTACCTTTGGTTA 59.430 50.000 8.81 0.00 39.68 2.85
6707 7123 2.202623 CGTAGCGCTGGACCAGTC 60.203 66.667 22.90 14.39 33.43 3.51
6733 7155 2.361610 CACCCCACCATGTGAGGC 60.362 66.667 0.00 0.00 34.68 4.70
6736 7158 2.273449 CCCACCATGTGAGGCCTC 59.727 66.667 26.78 26.78 35.23 4.70
6738 7160 2.124983 CACCATGTGAGGCCTCCG 60.125 66.667 29.95 15.05 35.23 4.63
6743 7165 3.924013 ATGTGAGGCCTCCGGGTCA 62.924 63.158 29.95 19.30 40.27 4.02
6757 7179 3.065306 GTCACATCCGACCCACCA 58.935 61.111 0.00 0.00 0.00 4.17
6760 7182 0.695924 TCACATCCGACCCACCAATT 59.304 50.000 0.00 0.00 0.00 2.32
6761 7183 0.810648 CACATCCGACCCACCAATTG 59.189 55.000 0.00 0.00 0.00 2.32
6763 7185 0.964860 CATCCGACCCACCAATTGCA 60.965 55.000 0.00 0.00 0.00 4.08
6766 7188 0.173255 CCGACCCACCAATTGCATTC 59.827 55.000 0.00 0.00 0.00 2.67
6767 7189 0.173255 CGACCCACCAATTGCATTCC 59.827 55.000 0.00 0.00 0.00 3.01
6768 7190 1.265236 GACCCACCAATTGCATTCCA 58.735 50.000 0.00 0.00 0.00 3.53
6769 7191 1.832998 GACCCACCAATTGCATTCCAT 59.167 47.619 0.00 0.00 0.00 3.41
6770 7192 2.236893 GACCCACCAATTGCATTCCATT 59.763 45.455 0.00 0.00 0.00 3.16
6771 7193 2.027007 ACCCACCAATTGCATTCCATTG 60.027 45.455 0.00 2.42 0.00 2.82
6772 7194 2.011222 CCACCAATTGCATTCCATTGC 58.989 47.619 0.00 0.00 43.07 3.56
6818 7240 6.366061 CGAATTGGGGATTTCTCTTTTGAAAC 59.634 38.462 0.00 0.00 38.54 2.78
6820 7242 5.789643 TGGGGATTTCTCTTTTGAAACTG 57.210 39.130 0.00 0.00 38.54 3.16
6823 7245 4.021104 GGGATTTCTCTTTTGAAACTGGGG 60.021 45.833 0.00 0.00 38.54 4.96
6839 7261 1.078656 TGGGGGAAAAGGAAAGATGGG 59.921 52.381 0.00 0.00 0.00 4.00
6842 7272 2.492753 GGGGAAAAGGAAAGATGGGTGT 60.493 50.000 0.00 0.00 0.00 4.16
6854 7284 4.489771 GGGTGTGATGCCCCTCCG 62.490 72.222 0.00 0.00 40.26 4.63
6858 7288 3.399181 GTGATGCCCCTCCGTCCA 61.399 66.667 0.00 0.00 0.00 4.02
6861 7291 2.040464 ATGCCCCTCCGTCCATCT 60.040 61.111 0.00 0.00 0.00 2.90
6862 7292 2.388890 GATGCCCCTCCGTCCATCTG 62.389 65.000 0.00 0.00 33.18 2.90
6865 7295 1.381872 CCCCTCCGTCCATCTGTCT 60.382 63.158 0.00 0.00 0.00 3.41
6869 7299 2.489985 CCCTCCGTCCATCTGTCTATCT 60.490 54.545 0.00 0.00 0.00 1.98
6898 7332 1.600957 CGCTCGCATCCATTTCTTCAT 59.399 47.619 0.00 0.00 0.00 2.57
6903 7337 2.100252 CGCATCCATTTCTTCATGCCTT 59.900 45.455 0.00 0.00 38.77 4.35
6907 7341 5.694910 GCATCCATTTCTTCATGCCTTAATG 59.305 40.000 0.00 0.00 36.44 1.90
6909 7343 7.494211 CATCCATTTCTTCATGCCTTAATGAA 58.506 34.615 10.21 0.18 42.78 2.57
6910 7344 7.664552 TCCATTTCTTCATGCCTTAATGAAT 57.335 32.000 10.21 0.00 43.70 2.57
6911 7345 8.081517 TCCATTTCTTCATGCCTTAATGAATT 57.918 30.769 10.21 0.00 43.70 2.17
6912 7346 9.199645 TCCATTTCTTCATGCCTTAATGAATTA 57.800 29.630 10.21 0.00 43.70 1.40
6913 7347 9.820725 CCATTTCTTCATGCCTTAATGAATTAA 57.179 29.630 10.21 0.00 43.70 1.40
6915 7349 9.822185 ATTTCTTCATGCCTTAATGAATTAACC 57.178 29.630 0.44 0.00 43.70 2.85
6916 7350 7.026631 TCTTCATGCCTTAATGAATTAACCG 57.973 36.000 0.44 0.00 43.70 4.44
6938 7372 1.685224 GTGCTCCCAATCCAGTCCA 59.315 57.895 0.00 0.00 0.00 4.02
6953 7387 0.326238 GTCCAGTCCCCAGGTATCCA 60.326 60.000 0.00 0.00 0.00 3.41
6977 7411 4.140829 TCACTCCATCAGTCTATCCATCCT 60.141 45.833 0.00 0.00 30.26 3.24
6983 7417 5.723405 CCATCAGTCTATCCATCCTTCCATA 59.277 44.000 0.00 0.00 0.00 2.74
7015 7469 2.407616 CGTGCATCGTCGCCTCTA 59.592 61.111 0.00 0.00 34.52 2.43
7016 7470 1.655654 CGTGCATCGTCGCCTCTAG 60.656 63.158 0.00 0.00 34.52 2.43
7017 7471 1.433879 GTGCATCGTCGCCTCTAGT 59.566 57.895 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.382515 CTAGTGGAGTGCGGCTACTC 59.617 60.000 18.26 18.26 44.96 2.59
1 2 1.038130 CCTAGTGGAGTGCGGCTACT 61.038 60.000 0.00 3.03 34.57 2.57
2 3 1.437986 CCTAGTGGAGTGCGGCTAC 59.562 63.158 0.00 0.00 34.57 3.58
3 4 1.756950 CCCTAGTGGAGTGCGGCTA 60.757 63.158 0.00 0.00 35.39 3.93
18 19 3.139077 GTGATGTGAACGTTTTCTCCCT 58.861 45.455 0.46 0.00 32.36 4.20
24 25 3.687212 TGTGTGAGTGATGTGAACGTTTT 59.313 39.130 0.46 0.00 0.00 2.43
45 46 1.307355 TTGCATGGACGATGTGCCTG 61.307 55.000 0.00 0.00 38.06 4.85
57 66 1.364626 GAGGAGTGAGCGTTGCATGG 61.365 60.000 0.00 0.00 0.00 3.66
60 69 1.300931 GTGAGGAGTGAGCGTTGCA 60.301 57.895 0.00 0.00 0.00 4.08
62 71 1.287730 GCAGTGAGGAGTGAGCGTTG 61.288 60.000 0.00 0.00 0.00 4.10
64 73 2.203082 TGCAGTGAGGAGTGAGCGT 61.203 57.895 0.00 0.00 0.00 5.07
65 74 1.735920 GTGCAGTGAGGAGTGAGCG 60.736 63.158 0.00 0.00 0.00 5.03
66 75 0.036577 ATGTGCAGTGAGGAGTGAGC 60.037 55.000 0.00 0.00 0.00 4.26
67 76 1.723220 CATGTGCAGTGAGGAGTGAG 58.277 55.000 0.00 0.00 0.00 3.51
68 77 0.321034 GCATGTGCAGTGAGGAGTGA 60.321 55.000 0.00 0.00 41.59 3.41
69 78 1.303799 GGCATGTGCAGTGAGGAGTG 61.304 60.000 7.36 0.00 44.36 3.51
70 79 1.002868 GGCATGTGCAGTGAGGAGT 60.003 57.895 7.36 0.00 44.36 3.85
71 80 1.002990 TGGCATGTGCAGTGAGGAG 60.003 57.895 7.36 0.00 44.36 3.69
72 81 1.302752 GTGGCATGTGCAGTGAGGA 60.303 57.895 7.36 0.00 44.36 3.71
73 82 1.601477 TGTGGCATGTGCAGTGAGG 60.601 57.895 7.36 0.00 44.36 3.86
114 130 0.952497 AGCAGTGTTGATGAGGCGTG 60.952 55.000 0.00 0.00 0.00 5.34
174 212 4.951094 ACTTGGGAAGTAGAGTAGTAGCAG 59.049 45.833 0.00 0.00 40.69 4.24
175 213 4.931914 ACTTGGGAAGTAGAGTAGTAGCA 58.068 43.478 0.00 0.00 40.69 3.49
176 214 4.035441 CGACTTGGGAAGTAGAGTAGTAGC 59.965 50.000 0.00 0.00 43.03 3.58
177 215 4.035441 GCGACTTGGGAAGTAGAGTAGTAG 59.965 50.000 0.00 0.00 43.03 2.57
178 216 3.944015 GCGACTTGGGAAGTAGAGTAGTA 59.056 47.826 0.00 0.00 43.03 1.82
179 217 2.754002 GCGACTTGGGAAGTAGAGTAGT 59.246 50.000 0.00 0.00 43.03 2.73
180 218 3.018149 AGCGACTTGGGAAGTAGAGTAG 58.982 50.000 0.00 0.00 43.03 2.57
181 219 3.083122 AGCGACTTGGGAAGTAGAGTA 57.917 47.619 0.00 0.00 43.03 2.59
182 220 1.926108 AGCGACTTGGGAAGTAGAGT 58.074 50.000 0.00 0.00 43.03 3.24
183 221 3.444388 ACTAAGCGACTTGGGAAGTAGAG 59.556 47.826 7.59 0.00 43.03 2.43
184 222 3.428532 ACTAAGCGACTTGGGAAGTAGA 58.571 45.455 7.59 0.00 43.03 2.59
185 223 3.870633 ACTAAGCGACTTGGGAAGTAG 57.129 47.619 7.59 0.00 43.03 2.57
186 224 5.726980 TTTACTAAGCGACTTGGGAAGTA 57.273 39.130 7.59 3.23 43.03 2.24
187 225 4.612264 TTTACTAAGCGACTTGGGAAGT 57.388 40.909 7.59 0.00 46.38 3.01
188 226 4.143179 CGTTTTACTAAGCGACTTGGGAAG 60.143 45.833 7.59 0.00 39.94 3.46
189 227 3.742369 CGTTTTACTAAGCGACTTGGGAA 59.258 43.478 7.59 3.11 39.94 3.97
190 228 3.005684 TCGTTTTACTAAGCGACTTGGGA 59.994 43.478 7.59 0.00 41.17 4.37
191 229 3.319755 TCGTTTTACTAAGCGACTTGGG 58.680 45.455 7.59 2.17 41.17 4.12
216 258 2.636768 GTACTGTACGTACGCCCTTT 57.363 50.000 20.18 0.00 39.15 3.11
231 273 5.018809 TCCCTGGTAGTAAAATCGTGTACT 58.981 41.667 0.00 0.00 34.89 2.73
246 288 1.227249 CCCTCTCTCTCTCCCTGGTA 58.773 60.000 0.00 0.00 0.00 3.25
247 289 1.589399 CCCCTCTCTCTCTCCCTGGT 61.589 65.000 0.00 0.00 0.00 4.00
248 290 1.232792 CCCCTCTCTCTCTCCCTGG 59.767 68.421 0.00 0.00 0.00 4.45
249 291 1.232792 CCCCCTCTCTCTCTCCCTG 59.767 68.421 0.00 0.00 0.00 4.45
250 292 3.782918 CCCCCTCTCTCTCTCCCT 58.217 66.667 0.00 0.00 0.00 4.20
347 389 1.602888 CCTCTGGCTGCTTGCTTGT 60.603 57.895 0.00 0.00 42.39 3.16
372 414 3.368571 GGCTCGGCTTGCTTGCTT 61.369 61.111 1.96 0.00 0.00 3.91
408 450 2.203337 TTGCTTGCTTGCCTCGGT 60.203 55.556 0.00 0.00 0.00 4.69
450 492 1.811359 CCTTTCCTGCTTGCTTCAGAG 59.189 52.381 2.73 0.00 33.54 3.35
451 493 1.421268 TCCTTTCCTGCTTGCTTCAGA 59.579 47.619 2.73 0.00 33.54 3.27
452 494 1.811359 CTCCTTTCCTGCTTGCTTCAG 59.189 52.381 0.00 0.00 0.00 3.02
453 495 1.546323 CCTCCTTTCCTGCTTGCTTCA 60.546 52.381 0.00 0.00 0.00 3.02
485 559 4.827087 AGACGGGCATGCTCGCTG 62.827 66.667 38.47 19.00 44.98 5.18
486 560 4.521062 GAGACGGGCATGCTCGCT 62.521 66.667 38.47 32.94 44.98 4.93
674 764 2.186384 CTCCGAGGGCAGCAGAAG 59.814 66.667 0.00 0.00 0.00 2.85
724 814 3.798511 CTTCCTTCCTCCCCGGGC 61.799 72.222 17.73 0.00 0.00 6.13
826 936 2.586792 CTTTCCCGGCTCCTCCTG 59.413 66.667 0.00 0.00 0.00 3.86
870 980 1.474077 CCTCCTTTTCAGGCCAAATCG 59.526 52.381 5.01 0.00 40.58 3.34
978 1100 4.528531 TTTTTGTTGCGATGAAAAAGGC 57.471 36.364 0.00 0.00 0.00 4.35
1226 1353 3.131400 TCACACGGTCATAATCAATCCGA 59.869 43.478 8.84 0.00 43.22 4.55
1240 1367 3.296709 GACGGCCTGATCACACGGT 62.297 63.158 0.00 8.07 0.00 4.83
1256 1383 2.514013 CGACGCATTGGGCTACGAC 61.514 63.158 0.00 0.00 41.67 4.34
1315 1442 7.908827 AGCATTTTCATGTAATCAATTGCAA 57.091 28.000 0.00 0.00 36.04 4.08
1322 1449 7.595875 CACACAAGAAGCATTTTCATGTAATCA 59.404 33.333 0.00 0.00 30.40 2.57
1379 1506 6.613755 TCCAAAAAGTTAGTACTGAACTGC 57.386 37.500 5.39 0.00 39.39 4.40
1394 1521 6.647895 CAGAACTGAAATCCCATTCCAAAAAG 59.352 38.462 0.00 0.00 0.00 2.27
1608 1740 5.308976 TCTGAATTCATATGCTGGCCTTA 57.691 39.130 8.96 0.00 0.00 2.69
1612 1744 3.058155 CAGCTCTGAATTCATATGCTGGC 60.058 47.826 29.70 16.37 38.46 4.85
1669 1807 4.781071 CAAAAGACTTGTCAGTGCTGATC 58.219 43.478 5.11 0.00 42.18 2.92
1674 1812 2.355756 TGAGCAAAAGACTTGTCAGTGC 59.644 45.455 12.32 12.32 31.22 4.40
1703 1841 2.502947 TCCTCAGCAGCTGTAATGACAT 59.497 45.455 22.10 0.00 34.24 3.06
1706 1844 1.134580 GCTCCTCAGCAGCTGTAATGA 60.135 52.381 22.10 15.53 46.06 2.57
1843 1981 3.650647 TGCACTGGAGGTGGAATTC 57.349 52.632 0.00 0.00 43.13 2.17
2037 2177 1.891722 GCTGTGGAGGCAAATTGGGG 61.892 60.000 0.00 0.00 0.00 4.96
2142 2282 9.480053 AACCAATGATCAAACAAAAAGATACTG 57.520 29.630 0.00 0.00 0.00 2.74
2171 2311 4.067896 CGCATCAGCCTGAAGGTAATAAT 58.932 43.478 0.00 0.00 37.52 1.28
2252 2392 8.600449 AAAAATTTCACACACAAAAAGAGTGA 57.400 26.923 0.00 0.00 40.74 3.41
2276 2416 8.629158 GCACATAGGACATGGTAAATATGAAAA 58.371 33.333 0.00 0.00 0.00 2.29
2277 2417 7.777440 TGCACATAGGACATGGTAAATATGAAA 59.223 33.333 0.00 0.00 0.00 2.69
2278 2418 7.286313 TGCACATAGGACATGGTAAATATGAA 58.714 34.615 0.00 0.00 0.00 2.57
2279 2419 6.836242 TGCACATAGGACATGGTAAATATGA 58.164 36.000 0.00 0.00 0.00 2.15
2280 2420 7.229306 ACTTGCACATAGGACATGGTAAATATG 59.771 37.037 0.00 1.35 0.00 1.78
2281 2421 7.290061 ACTTGCACATAGGACATGGTAAATAT 58.710 34.615 0.00 0.00 0.00 1.28
2313 2504 8.880991 AAGTTACTCTCTTGGATACTGAGTTA 57.119 34.615 0.00 0.00 38.67 2.24
2370 2561 3.510531 TCAGCAGGTAGATACGGATCT 57.489 47.619 15.99 15.99 44.90 2.75
2527 2718 3.616956 TCATGCTGGAAAGTGTAGAGG 57.383 47.619 0.00 0.00 0.00 3.69
2548 2739 8.073467 TCCAAGAAACCAAGTAAACTCAAAAT 57.927 30.769 0.00 0.00 0.00 1.82
2555 2746 6.263344 GTTCACTCCAAGAAACCAAGTAAAC 58.737 40.000 0.00 0.00 0.00 2.01
2564 2756 2.879026 GGTCTGGTTCACTCCAAGAAAC 59.121 50.000 0.00 0.00 37.01 2.78
2581 2773 6.926630 AGTTAGAAGAAGAGTTGATGGTCT 57.073 37.500 0.00 0.00 0.00 3.85
2582 2774 6.128418 GCAAGTTAGAAGAAGAGTTGATGGTC 60.128 42.308 0.00 0.00 0.00 4.02
2584 2776 5.123027 GGCAAGTTAGAAGAAGAGTTGATGG 59.877 44.000 0.00 0.00 0.00 3.51
2632 2829 2.360726 TGTGCTGGAGGCTGCATG 60.361 61.111 9.81 5.14 41.45 4.06
2776 2974 3.268595 ACCCGGGGAAAATAGAAACAGAT 59.731 43.478 27.92 0.00 0.00 2.90
2784 2982 1.283905 ACCTTCACCCGGGGAAAATAG 59.716 52.381 27.92 12.61 0.00 1.73
2785 2983 1.374572 ACCTTCACCCGGGGAAAATA 58.625 50.000 27.92 3.23 0.00 1.40
2795 2996 6.859508 CGTTGTCTTAAAATAAACCTTCACCC 59.140 38.462 0.00 0.00 0.00 4.61
2809 3010 6.814644 TGAGTGAAGTTCTTCGTTGTCTTAAA 59.185 34.615 4.17 0.00 0.00 1.52
2816 3017 5.406780 AGCTTATGAGTGAAGTTCTTCGTTG 59.593 40.000 4.17 2.75 0.00 4.10
2826 3037 6.369890 TGCAAAACTAGAGCTTATGAGTGAAG 59.630 38.462 0.00 0.00 0.00 3.02
2827 3038 6.230472 TGCAAAACTAGAGCTTATGAGTGAA 58.770 36.000 0.00 0.00 0.00 3.18
2833 3044 4.937620 TGACCTGCAAAACTAGAGCTTATG 59.062 41.667 0.00 0.00 0.00 1.90
2844 3055 1.856802 CTTTGGCTGACCTGCAAAAC 58.143 50.000 0.00 0.00 32.95 2.43
2914 3146 1.374758 GACAGAGTCCCCAGCAACG 60.375 63.158 0.00 0.00 0.00 4.10
2967 3199 3.584848 AGGGGTGCCAGTTATATCATCTC 59.415 47.826 0.00 0.00 0.00 2.75
2968 3200 3.584848 GAGGGGTGCCAGTTATATCATCT 59.415 47.826 0.00 0.00 0.00 2.90
2969 3201 3.584848 AGAGGGGTGCCAGTTATATCATC 59.415 47.826 0.00 0.00 0.00 2.92
2970 3202 3.584848 GAGAGGGGTGCCAGTTATATCAT 59.415 47.826 0.00 0.00 0.00 2.45
2972 3204 3.243724 AGAGAGGGGTGCCAGTTATATC 58.756 50.000 0.00 0.00 0.00 1.63
2973 3205 3.243724 GAGAGAGGGGTGCCAGTTATAT 58.756 50.000 0.00 0.00 0.00 0.86
2976 3208 0.617820 GGAGAGAGGGGTGCCAGTTA 60.618 60.000 0.00 0.00 0.00 2.24
2980 3212 2.039624 GAGGAGAGAGGGGTGCCA 59.960 66.667 0.00 0.00 0.00 4.92
2985 3217 1.820481 GACGTCGAGGAGAGAGGGG 60.820 68.421 12.85 0.00 0.00 4.79
3000 3232 6.037062 TGCACATACCAGAATTTGAATAGACG 59.963 38.462 0.00 0.00 0.00 4.18
3006 3238 4.220163 TGCATGCACATACCAGAATTTGAA 59.780 37.500 18.46 0.00 0.00 2.69
3009 3241 4.018490 TCTGCATGCACATACCAGAATTT 58.982 39.130 18.46 0.00 30.48 1.82
3011 3243 3.286329 TCTGCATGCACATACCAGAAT 57.714 42.857 18.46 0.00 30.48 2.40
3014 3246 3.211865 AGAATCTGCATGCACATACCAG 58.788 45.455 18.46 5.29 0.00 4.00
3015 3247 3.208594 GAGAATCTGCATGCACATACCA 58.791 45.455 18.46 0.00 0.00 3.25
3016 3248 3.003068 GTGAGAATCTGCATGCACATACC 59.997 47.826 18.46 8.12 34.92 2.73
3017 3249 3.875727 AGTGAGAATCTGCATGCACATAC 59.124 43.478 18.46 7.37 34.92 2.39
3018 3250 3.875134 CAGTGAGAATCTGCATGCACATA 59.125 43.478 18.46 5.63 34.92 2.29
3020 3252 2.081462 CAGTGAGAATCTGCATGCACA 58.919 47.619 18.46 7.34 34.92 4.57
3021 3253 1.400846 CCAGTGAGAATCTGCATGCAC 59.599 52.381 18.46 7.15 34.92 4.57
3038 3270 2.523015 GAGATGCGCAAATTTGACCAG 58.477 47.619 22.31 10.10 0.00 4.00
3051 3283 3.691118 TCCTGAAAATTCAAGGAGATGCG 59.309 43.478 9.06 0.00 36.64 4.73
3053 3285 7.094075 TGTCATTCCTGAAAATTCAAGGAGATG 60.094 37.037 11.51 14.71 36.54 2.90
3057 3289 6.323482 TGTTGTCATTCCTGAAAATTCAAGGA 59.677 34.615 9.06 9.06 36.64 3.36
3150 3382 3.359033 ACCAATGTGCATGCTATCACTT 58.641 40.909 20.33 3.85 34.49 3.16
3198 3430 5.365403 TTGTAAACCGGCTATTTGTTGAG 57.635 39.130 0.00 0.00 0.00 3.02
3246 3479 4.670621 CACTGAACAAACGAAAGCATACAC 59.329 41.667 0.00 0.00 0.00 2.90
3257 3490 5.286082 CAGAAGGAAAAACACTGAACAAACG 59.714 40.000 0.00 0.00 0.00 3.60
3266 3499 5.859205 AAGCATTCAGAAGGAAAAACACT 57.141 34.783 0.00 0.00 39.39 3.55
3317 3553 5.013287 TGGTATAACAAACTCACAAGGGCTA 59.987 40.000 0.00 0.00 0.00 3.93
3432 3668 9.965824 ATCAAAATTTAATTTAGCATACCTCCG 57.034 29.630 3.17 0.00 0.00 4.63
3452 3688 8.632679 AGAGTAAAGATGAAAAGCACATCAAAA 58.367 29.630 0.00 0.00 44.29 2.44
3474 3710 4.916983 TGCTGCAACATGTTTTTAGAGT 57.083 36.364 8.77 0.00 0.00 3.24
3475 3711 7.872163 TTATTGCTGCAACATGTTTTTAGAG 57.128 32.000 18.51 0.00 0.00 2.43
3477 3713 8.868744 CATTTATTGCTGCAACATGTTTTTAG 57.131 30.769 18.51 8.56 0.00 1.85
3500 3736 9.915629 GACTGCTAATAGTTAATACAGTAGCAT 57.084 33.333 13.07 7.01 38.42 3.79
3501 3737 9.132923 AGACTGCTAATAGTTAATACAGTAGCA 57.867 33.333 12.44 12.44 37.05 3.49
3502 3738 9.968870 AAGACTGCTAATAGTTAATACAGTAGC 57.031 33.333 0.00 6.49 37.05 3.58
3734 3974 7.284820 TCTCAATAGGAATTTGCATCTCATCA 58.715 34.615 0.00 0.00 0.00 3.07
3768 4058 7.118245 TCTGTCATGCTAAACTGTGAAGTTATG 59.882 37.037 0.00 0.00 0.00 1.90
3795 4096 5.232838 CCTGCATTTTTCACAGACAAAGTTC 59.767 40.000 0.00 0.00 33.10 3.01
3806 4107 2.137523 CAGCCAACCTGCATTTTTCAC 58.862 47.619 0.00 0.00 34.21 3.18
4201 4502 3.097614 AGGCTGTAGACCAAGTAACGAT 58.902 45.455 0.00 0.00 0.00 3.73
4351 4652 1.696063 ACTGAGGTTGCATTTGCTGT 58.304 45.000 3.94 0.00 42.66 4.40
4579 4880 5.907207 TGAGAATATGCTGACTGGTAGTTC 58.093 41.667 0.00 0.00 0.00 3.01
4870 5171 4.141711 GGTGTTGAGGATAGCTGTTCCATA 60.142 45.833 17.10 5.36 35.59 2.74
5041 5342 1.113253 CCGTCGAATCATTCTCGTCG 58.887 55.000 0.00 5.19 43.89 5.12
5065 5366 4.711846 AGAAAATTGGAAGTGGAATAGGGC 59.288 41.667 0.00 0.00 0.00 5.19
5092 5393 5.768980 AGGAGAAATCATGTTGAGAAGGA 57.231 39.130 0.00 0.00 0.00 3.36
5263 5567 8.650143 TTCAGGGAAATAAGCAAGATAGTTTT 57.350 30.769 0.00 0.00 0.00 2.43
5353 5680 9.474313 ACCAATTTTAAGGCATGTCTTTCTATA 57.526 29.630 19.32 0.00 0.00 1.31
5455 5786 2.743183 GCTACCAAACATCCGAGCATCT 60.743 50.000 0.00 0.00 0.00 2.90
5456 5787 1.599542 GCTACCAAACATCCGAGCATC 59.400 52.381 0.00 0.00 0.00 3.91
5459 5790 1.398390 CAAGCTACCAAACATCCGAGC 59.602 52.381 0.00 0.00 0.00 5.03
5463 5794 3.153919 TGGAACAAGCTACCAAACATCC 58.846 45.455 0.00 0.00 31.92 3.51
5476 5808 7.934578 CAAATCAGTTGTGGCATTGGAACAAG 61.935 42.308 0.00 0.00 36.44 3.16
5512 5844 4.214310 ACCTGTTTGATGTTCACATGGAA 58.786 39.130 0.00 0.00 36.57 3.53
5709 6041 0.320374 CTTACTGCCAAGGGTCGTCA 59.680 55.000 0.00 0.00 0.00 4.35
5789 6121 2.594303 TTGGAAGGTGCGGCACTG 60.594 61.111 29.92 0.00 34.40 3.66
6022 6355 1.181786 CGCCCTCTCTTCAGAACTCT 58.818 55.000 0.00 0.00 0.00 3.24
6102 6441 4.263435 GTCTCGAAAACTAGGGAGAGAGA 58.737 47.826 0.00 0.13 36.31 3.10
6105 6445 2.427812 GGGTCTCGAAAACTAGGGAGAG 59.572 54.545 0.00 0.00 36.31 3.20
6147 6489 5.606348 AAAGAGCTAGTAGGAATGGTCTG 57.394 43.478 0.00 0.00 37.35 3.51
6223 6568 3.719268 TCACGGTACAGGTTCCTACTA 57.281 47.619 0.00 0.00 0.00 1.82
6263 6608 1.144913 AGAGTTTTGGCAGGCTTACCA 59.855 47.619 1.84 1.84 39.06 3.25
6304 6649 6.784969 AGAGCCTACATTCACAGGATTAGTAT 59.215 38.462 0.00 0.00 33.42 2.12
6352 6697 2.276120 CGAGTCGACGACGCTCTG 60.276 66.667 25.57 9.87 39.00 3.35
6353 6698 2.728679 GACGAGTCGACGACGCTCT 61.729 63.158 27.75 13.02 39.00 4.09
6364 6709 1.063951 AAATGCGACGACGACGAGTC 61.064 55.000 22.94 9.86 46.16 3.36
6365 6710 1.081641 AAATGCGACGACGACGAGT 60.082 52.632 22.94 7.59 42.66 4.18
6366 6711 1.337150 CAAATGCGACGACGACGAG 59.663 57.895 22.94 8.60 42.66 4.18
6367 6712 2.712918 GCAAATGCGACGACGACGA 61.713 57.895 22.94 8.81 42.66 4.20
6368 6713 2.275202 GCAAATGCGACGACGACG 60.275 61.111 15.13 15.13 42.66 5.12
6369 6714 1.074319 TAGGCAAATGCGACGACGAC 61.074 55.000 12.29 3.11 43.26 4.34
6370 6715 0.179121 ATAGGCAAATGCGACGACGA 60.179 50.000 12.29 0.00 43.26 4.20
6371 6716 0.229753 GATAGGCAAATGCGACGACG 59.770 55.000 2.12 2.12 43.26 5.12
6372 6717 1.571919 AGATAGGCAAATGCGACGAC 58.428 50.000 0.00 0.00 43.26 4.34
6373 6718 1.933181 CAAGATAGGCAAATGCGACGA 59.067 47.619 0.00 0.00 43.26 4.20
6374 6719 1.665679 ACAAGATAGGCAAATGCGACG 59.334 47.619 0.00 0.00 43.26 5.12
6375 6720 3.764885 AACAAGATAGGCAAATGCGAC 57.235 42.857 0.00 0.00 43.26 5.19
6376 6721 7.744087 ATATTAACAAGATAGGCAAATGCGA 57.256 32.000 0.00 0.00 43.26 5.10
6377 6722 8.292448 AGAATATTAACAAGATAGGCAAATGCG 58.708 33.333 0.00 0.00 43.26 4.73
6378 6723 9.403110 CAGAATATTAACAAGATAGGCAAATGC 57.597 33.333 0.00 0.00 41.14 3.56
6379 6724 9.403110 GCAGAATATTAACAAGATAGGCAAATG 57.597 33.333 0.00 0.00 0.00 2.32
6380 6725 9.135189 TGCAGAATATTAACAAGATAGGCAAAT 57.865 29.630 0.00 0.00 0.00 2.32
6381 6726 8.518430 TGCAGAATATTAACAAGATAGGCAAA 57.482 30.769 0.00 0.00 0.00 3.68
6408 6753 4.373532 GTGGAACAAAAATGCAATGTCG 57.626 40.909 0.00 0.00 44.16 4.35
6539 6905 1.211457 AGGACCATGCCAGTTCTGATC 59.789 52.381 1.00 0.00 0.00 2.92
6577 6989 0.259647 TCCATCCATCTTTGGGCCTG 59.740 55.000 4.53 0.00 43.81 4.85
6604 7016 3.187112 CTCTTCCCCCTAACCAAAGGTA 58.813 50.000 0.00 0.00 33.12 3.08
6612 7024 4.412528 ACATACATTCCTCTTCCCCCTAAC 59.587 45.833 0.00 0.00 0.00 2.34
6613 7025 4.641868 ACATACATTCCTCTTCCCCCTAA 58.358 43.478 0.00 0.00 0.00 2.69
6614 7026 4.295905 ACATACATTCCTCTTCCCCCTA 57.704 45.455 0.00 0.00 0.00 3.53
6615 7027 3.151542 ACATACATTCCTCTTCCCCCT 57.848 47.619 0.00 0.00 0.00 4.79
6677 7093 4.147322 CTACGCGTGCAAAGCCGG 62.147 66.667 24.59 0.00 38.42 6.13
6678 7094 4.794241 GCTACGCGTGCAAAGCCG 62.794 66.667 24.59 0.00 38.42 5.52
6743 7165 0.965363 GCAATTGGTGGGTCGGATGT 60.965 55.000 7.72 0.00 0.00 3.06
6770 7192 1.138464 TGCCAAAGTCTTTGCAATGCA 59.862 42.857 18.30 17.97 39.31 3.96
6771 7193 1.868469 TGCCAAAGTCTTTGCAATGC 58.132 45.000 18.30 15.91 39.31 3.56
6772 7194 3.122278 CGATTGCCAAAGTCTTTGCAATG 59.878 43.478 30.90 23.61 42.13 2.82
6773 7195 3.005684 TCGATTGCCAAAGTCTTTGCAAT 59.994 39.130 28.60 28.60 43.37 3.56
6774 7196 2.360483 TCGATTGCCAAAGTCTTTGCAA 59.640 40.909 24.44 24.44 39.28 4.08
6775 7197 1.952990 TCGATTGCCAAAGTCTTTGCA 59.047 42.857 18.30 16.16 39.31 4.08
6776 7198 2.704725 TCGATTGCCAAAGTCTTTGC 57.295 45.000 18.30 14.10 39.31 3.68
6818 7240 2.460669 CCATCTTTCCTTTTCCCCCAG 58.539 52.381 0.00 0.00 0.00 4.45
6820 7242 1.078823 ACCCATCTTTCCTTTTCCCCC 59.921 52.381 0.00 0.00 0.00 5.40
6823 7245 3.496331 TCACACCCATCTTTCCTTTTCC 58.504 45.455 0.00 0.00 0.00 3.13
6839 7261 2.125106 GACGGAGGGGCATCACAC 60.125 66.667 0.00 0.00 0.00 3.82
6842 7272 2.366837 ATGGACGGAGGGGCATCA 60.367 61.111 0.00 0.00 0.00 3.07
6854 7284 6.404184 CGTGATGGATAGATAGACAGATGGAC 60.404 46.154 0.00 0.00 0.00 4.02
6858 7288 5.260424 AGCGTGATGGATAGATAGACAGAT 58.740 41.667 0.00 0.00 0.00 2.90
6861 7291 3.437049 CGAGCGTGATGGATAGATAGACA 59.563 47.826 0.00 0.00 0.00 3.41
6862 7292 3.729462 GCGAGCGTGATGGATAGATAGAC 60.729 52.174 0.00 0.00 0.00 2.59
6865 7295 2.159382 TGCGAGCGTGATGGATAGATA 58.841 47.619 0.00 0.00 0.00 1.98
6869 7299 0.038251 GGATGCGAGCGTGATGGATA 60.038 55.000 0.00 0.00 0.00 2.59
6898 7332 5.067153 CACCATCGGTTAATTCATTAAGGCA 59.933 40.000 0.00 0.00 33.31 4.75
6903 7337 4.819630 GGAGCACCATCGGTTAATTCATTA 59.180 41.667 0.00 0.00 31.02 1.90
6907 7341 1.947456 GGGAGCACCATCGGTTAATTC 59.053 52.381 1.58 0.00 39.85 2.17
6909 7343 0.916086 TGGGAGCACCATCGGTTAAT 59.084 50.000 1.58 0.00 46.80 1.40
6910 7344 2.378211 TGGGAGCACCATCGGTTAA 58.622 52.632 1.58 0.00 46.80 2.01
6911 7345 4.138665 TGGGAGCACCATCGGTTA 57.861 55.556 1.58 0.00 46.80 2.85
6938 7372 1.295292 AGTGATGGATACCTGGGGACT 59.705 52.381 0.00 0.00 0.00 3.85
6953 7387 4.776837 GGATGGATAGACTGATGGAGTGAT 59.223 45.833 0.00 0.00 33.83 3.06


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

AutoCloner maintained by Alex Coulton.