Multiple sequence alignment - TraesCS2A01G405700

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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 TraesCS2A01G405700 chr2A 100.000 6259 0 0 1 6259 661457026 661450768 0.000000e+00 11559
1 TraesCS2A01G405700 chr2A 89.024 164 14 2 1 161 718128116 718127954 3.830000e-47 200
2 TraesCS2A01G405700 chr2A 80.769 208 12 14 6054 6259 661406369 661406188 3.040000e-28 137
3 TraesCS2A01G405700 chr2D 90.394 2946 169 56 177 3045 517096932 517094024 0.000000e+00 3768
4 TraesCS2A01G405700 chr2D 88.946 1556 123 13 4115 5639 517091582 517090045 0.000000e+00 1875
5 TraesCS2A01G405700 chr2D 91.932 942 49 7 3211 4135 517094032 517093101 0.000000e+00 1293
6 TraesCS2A01G405700 chr2D 84.828 580 50 15 5409 5982 517083949 517083402 3.300000e-152 549
7 TraesCS2A01G405700 chr2D 89.474 323 19 7 5940 6259 517089991 517089681 1.640000e-105 394
8 TraesCS2A01G405700 chr2D 89.754 244 23 1 5168 5411 517084343 517084102 1.690000e-80 311
9 TraesCS2A01G405700 chr2D 85.827 254 14 11 6009 6259 517056863 517056629 3.750000e-62 250
10 TraesCS2A01G405700 chr2B 89.380 2985 151 60 182 3045 608946891 608943952 0.000000e+00 3603
11 TraesCS2A01G405700 chr2B 90.472 2120 144 26 3211 5300 608943960 608941869 0.000000e+00 2743
12 TraesCS2A01G405700 chr2B 87.086 604 56 13 5353 5950 608941870 608941283 0.000000e+00 664
13 TraesCS2A01G405700 chr2B 89.720 214 8 2 5954 6167 608940669 608940470 1.730000e-65 261
14 TraesCS2A01G405700 chr5A 98.810 168 2 0 3043 3210 437036979 437037146 3.670000e-77 300
15 TraesCS2A01G405700 chr5A 97.576 165 4 0 3046 3210 535156933 535156769 3.690000e-72 283
16 TraesCS2A01G405700 chr5A 91.925 161 13 0 1 161 613684786 613684626 6.310000e-55 226
17 TraesCS2A01G405700 chr1A 99.394 165 1 0 3046 3210 501034129 501034293 3.670000e-77 300
18 TraesCS2A01G405700 chr1A 99.394 165 1 0 3046 3210 501034719 501034883 3.670000e-77 300
19 TraesCS2A01G405700 chr1A 96.407 167 6 0 3046 3212 53691642 53691476 6.180000e-70 276
20 TraesCS2A01G405700 chr1A 90.683 161 15 0 1 161 130742321 130742481 1.370000e-51 215
21 TraesCS2A01G405700 chr3A 96.407 167 6 0 3045 3211 491454118 491454284 6.180000e-70 276
22 TraesCS2A01G405700 chr6A 94.798 173 8 1 3045 3217 613273429 613273258 1.030000e-67 268
23 TraesCS2A01G405700 chr6A 95.758 165 7 0 3046 3210 610234314 610234150 3.720000e-67 267
24 TraesCS2A01G405700 chr7A 91.257 183 16 0 3038 3220 40718595 40718777 3.750000e-62 250
25 TraesCS2A01G405700 chr7A 90.566 159 15 0 1 159 182371312 182371154 1.770000e-50 211
26 TraesCS2A01G405700 chr4B 89.506 162 16 1 1 161 82605057 82604896 2.960000e-48 204
27 TraesCS2A01G405700 chr4A 89.308 159 17 0 3 161 134542607 134542765 3.830000e-47 200
28 TraesCS2A01G405700 chrUn 88.820 161 18 0 1 161 79228813 79228973 1.380000e-46 198
29 TraesCS2A01G405700 chr6B 89.172 157 17 0 5 161 552763550 552763706 4.950000e-46 196
30 TraesCS2A01G405700 chr4D 88.608 158 15 3 3 158 326479338 326479494 8.280000e-44 189


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 TraesCS2A01G405700 chr2A 661450768 661457026 6258 True 11559.00 11559 100.0000 1 6259 1 chr2A.!!$R2 6258
1 TraesCS2A01G405700 chr2D 517089681 517096932 7251 True 1832.50 3768 90.1865 177 6259 4 chr2D.!!$R3 6082
2 TraesCS2A01G405700 chr2D 517083402 517084343 941 True 430.00 549 87.2910 5168 5982 2 chr2D.!!$R2 814
3 TraesCS2A01G405700 chr2B 608940470 608946891 6421 True 1817.75 3603 89.1645 182 6167 4 chr2B.!!$R1 5985
4 TraesCS2A01G405700 chr1A 501034129 501034883 754 False 300.00 300 99.3940 3046 3210 2 chr1A.!!$F2 164

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
179 180 0.035176 TGTTAAAGGACCCGGTTCCG 59.965 55.0 13.03 4.08 41.04 4.30 F
510 562 0.252057 GTATGCCCCCAAACCCAAGT 60.252 55.0 0.00 0.00 0.00 3.16 F
1627 1757 0.248215 GGATTTCGATGCGGCAACTG 60.248 55.0 6.82 0.00 0.00 3.16 F
2703 2860 0.179081 GTCCTCCGGCATGTTACCTC 60.179 60.0 0.00 0.00 0.00 3.85 F
4158 5936 1.323791 GTGAAAACATGTTACGCGCC 58.676 50.0 12.39 0.00 0.00 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1028 1148 0.250513 AAAAAGGAGCTCGAGCCGAT 59.749 50.0 32.94 16.02 43.38 4.18 R
1950 2086 0.456312 CAACCGTGGAGTACTCGCTC 60.456 60.0 16.56 9.42 34.89 5.03 R
3057 3219 0.105349 CGGGGGTAAGAGGGACCATA 60.105 60.0 0.00 0.00 38.86 2.74 R
4363 6142 0.184933 TGCTAAACCAGGGCTGTTGT 59.815 50.0 0.00 0.00 0.00 3.32 R
5372 7181 0.036875 GCCTCCAGTTTACAGTGCCT 59.963 55.0 0.00 0.00 0.00 4.75 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
64 65 6.573664 TTCACCATCAACTTAATTGTCTGG 57.426 37.500 13.55 13.55 42.78 3.86
65 66 5.875224 TCACCATCAACTTAATTGTCTGGA 58.125 37.500 17.65 0.00 41.15 3.86
66 67 6.303054 TCACCATCAACTTAATTGTCTGGAA 58.697 36.000 17.65 9.85 41.15 3.53
67 68 6.947733 TCACCATCAACTTAATTGTCTGGAAT 59.052 34.615 17.65 0.00 41.15 3.01
68 69 7.451255 TCACCATCAACTTAATTGTCTGGAATT 59.549 33.333 17.65 0.00 41.15 2.17
69 70 8.739039 CACCATCAACTTAATTGTCTGGAATTA 58.261 33.333 17.65 0.00 41.15 1.40
70 71 8.739972 ACCATCAACTTAATTGTCTGGAATTAC 58.260 33.333 17.65 0.00 41.15 1.89
71 72 8.960591 CCATCAACTTAATTGTCTGGAATTACT 58.039 33.333 0.00 0.00 41.15 2.24
161 162 9.284968 TGAATAGAAAGAAGAAAAGTTAGGGTG 57.715 33.333 0.00 0.00 0.00 4.61
162 163 9.286170 GAATAGAAAGAAGAAAAGTTAGGGTGT 57.714 33.333 0.00 0.00 0.00 4.16
163 164 9.642343 AATAGAAAGAAGAAAAGTTAGGGTGTT 57.358 29.630 0.00 0.00 0.00 3.32
166 167 9.470399 AGAAAGAAGAAAAGTTAGGGTGTTAAA 57.530 29.630 0.00 0.00 0.00 1.52
167 168 9.731819 GAAAGAAGAAAAGTTAGGGTGTTAAAG 57.268 33.333 0.00 0.00 0.00 1.85
168 169 7.818997 AGAAGAAAAGTTAGGGTGTTAAAGG 57.181 36.000 0.00 0.00 0.00 3.11
169 170 7.580007 AGAAGAAAAGTTAGGGTGTTAAAGGA 58.420 34.615 0.00 0.00 0.00 3.36
170 171 7.501559 AGAAGAAAAGTTAGGGTGTTAAAGGAC 59.498 37.037 0.00 0.00 0.00 3.85
171 172 6.066690 AGAAAAGTTAGGGTGTTAAAGGACC 58.933 40.000 0.00 0.00 0.00 4.46
174 175 4.728409 GGGTGTTAAAGGACCCGG 57.272 61.111 0.00 0.00 42.61 5.73
175 176 1.763120 GGGTGTTAAAGGACCCGGT 59.237 57.895 0.00 0.00 42.61 5.28
176 177 0.111061 GGGTGTTAAAGGACCCGGTT 59.889 55.000 0.00 0.00 42.61 4.44
177 178 1.527034 GGTGTTAAAGGACCCGGTTC 58.473 55.000 0.00 0.00 0.00 3.62
178 179 1.527034 GTGTTAAAGGACCCGGTTCC 58.473 55.000 10.70 10.70 35.66 3.62
179 180 0.035176 TGTTAAAGGACCCGGTTCCG 59.965 55.000 13.03 4.08 41.04 4.30
251 255 0.521735 GTGCCTCAAAGCTTAACCGG 59.478 55.000 0.00 0.00 0.00 5.28
265 269 2.604046 AACCGGTCACAGATCATAGC 57.396 50.000 8.04 0.00 0.00 2.97
289 295 1.953686 TGCTTCCTGCCAAAACTGTAC 59.046 47.619 0.00 0.00 42.00 2.90
305 311 1.542472 TGTACTACGTAGCAGCAGCAA 59.458 47.619 22.40 0.00 45.49 3.91
339 345 2.983030 TGTTTGCAAGCGCCGGAT 60.983 55.556 5.05 0.00 37.32 4.18
365 371 2.814341 CACAGAGCAGAGCAGCGG 60.814 66.667 0.00 0.00 40.15 5.52
429 469 1.656441 CAGCAAACCTCACACCTGC 59.344 57.895 0.00 0.00 0.00 4.85
442 482 2.025155 ACACCTGCTAGTAGATCCACG 58.975 52.381 9.72 0.00 0.00 4.94
443 483 1.338337 CACCTGCTAGTAGATCCACGG 59.662 57.143 9.72 0.00 0.00 4.94
459 507 2.586792 GGAGGCCAGGCAGTACAG 59.413 66.667 15.19 0.00 0.00 2.74
495 547 1.062873 CGCGCCAACAAAACCGTATG 61.063 55.000 0.00 0.00 0.00 2.39
510 562 0.252057 GTATGCCCCCAAACCCAAGT 60.252 55.000 0.00 0.00 0.00 3.16
519 574 2.103432 CCCAAACCCAAGTTAACCCAAC 59.897 50.000 0.88 0.00 34.19 3.77
546 601 0.900647 AGATTAGGGATCCGAGGCCG 60.901 60.000 5.45 0.00 35.21 6.13
571 626 2.282958 TCCGTCACTCGCTCCCTT 60.283 61.111 0.00 0.00 38.35 3.95
573 628 2.811317 CGTCACTCGCTCCCTTGC 60.811 66.667 0.00 0.00 0.00 4.01
654 710 1.523711 CCGGTCCGTCCATCCAATG 60.524 63.158 11.06 0.00 35.57 2.82
756 836 1.503818 CCACGGGACAAACGACAAGG 61.504 60.000 0.00 0.00 34.93 3.61
810 890 2.117865 AGATCCTTCTCTTCCCTGCTG 58.882 52.381 0.00 0.00 0.00 4.41
811 891 0.545646 ATCCTTCTCTTCCCTGCTGC 59.454 55.000 0.00 0.00 0.00 5.25
812 892 1.077858 CCTTCTCTTCCCTGCTGCC 60.078 63.158 0.00 0.00 0.00 4.85
813 893 1.077858 CTTCTCTTCCCTGCTGCCC 60.078 63.158 0.00 0.00 0.00 5.36
863 951 2.612115 CCAACCCCCTCTCTGCCT 60.612 66.667 0.00 0.00 0.00 4.75
868 956 2.366167 CCCCTCTCTGCCTCCTCA 59.634 66.667 0.00 0.00 0.00 3.86
869 957 1.761667 CCCCTCTCTGCCTCCTCAG 60.762 68.421 0.00 0.00 35.46 3.35
880 968 3.429080 CTCCTCAGCCGAGCTCAGC 62.429 68.421 14.30 14.30 36.40 4.26
881 969 3.459965 CCTCAGCCGAGCTCAGCT 61.460 66.667 18.90 18.90 43.88 4.24
890 978 4.098722 AGCTCAGCTCAGCCCAGC 62.099 66.667 5.75 9.12 40.65 4.85
892 980 4.486503 CTCAGCTCAGCCCAGCCC 62.487 72.222 0.00 0.00 40.65 5.19
894 982 4.798344 CAGCTCAGCCCAGCCCAG 62.798 72.222 0.00 0.00 40.65 4.45
897 985 4.486503 CTCAGCCCAGCCCAGCTC 62.487 72.222 0.00 0.00 36.40 4.09
902 990 4.823732 CCCAGCCCAGCTCCCCTA 62.824 72.222 0.00 0.00 36.40 3.53
909 997 1.333636 CCCAGCTCCCCTACTCACTG 61.334 65.000 0.00 0.00 0.00 3.66
1016 1136 4.514577 CGGGGCGAGCAGTAGGTG 62.515 72.222 0.00 0.00 0.00 4.00
1028 1148 2.715046 CAGTAGGTGGGTACACTACGA 58.285 52.381 0.00 0.00 46.85 3.43
1624 1754 2.118404 GGGGATTTCGATGCGGCAA 61.118 57.895 6.82 0.00 0.00 4.52
1626 1756 1.376609 GGGATTTCGATGCGGCAACT 61.377 55.000 6.82 0.00 0.00 3.16
1627 1757 0.248215 GGATTTCGATGCGGCAACTG 60.248 55.000 6.82 0.00 0.00 3.16
1628 1758 0.863119 GATTTCGATGCGGCAACTGC 60.863 55.000 6.82 0.00 41.14 4.40
1773 1909 2.165845 CTCGTCGTGGGACTTCCTAAAT 59.834 50.000 0.00 0.00 41.16 1.40
1926 2062 1.378250 GGAGGAGGACGACGAGGAA 60.378 63.158 0.00 0.00 0.00 3.36
1929 2065 0.538977 AGGAGGACGACGAGGAAACA 60.539 55.000 0.00 0.00 0.00 2.83
1950 2086 1.519455 GGTCGTGAAGGAGATGGCG 60.519 63.158 0.00 0.00 0.00 5.69
2002 2138 4.849329 ATCGCGGCTCGTTCGGTC 62.849 66.667 6.13 0.00 39.67 4.79
2157 2299 3.929095 CGTTAAGACGCAGCTTGTC 57.071 52.632 7.62 7.62 43.03 3.18
2473 2615 4.459685 TCCTTGACACTAGAGAAGCTGTAC 59.540 45.833 0.00 0.00 0.00 2.90
2476 2618 6.406692 TTGACACTAGAGAAGCTGTACTTT 57.593 37.500 0.00 0.00 39.29 2.66
2532 2674 5.813080 AACTCATATTTCCGTTAAGCACC 57.187 39.130 0.00 0.00 0.00 5.01
2538 2680 7.332557 TCATATTTCCGTTAAGCACCTTTCTA 58.667 34.615 0.00 0.00 0.00 2.10
2568 2710 0.820226 TGGTCTCCGATCTTGAGCTG 59.180 55.000 0.00 0.00 0.00 4.24
2581 2723 6.312426 CGATCTTGAGCTGTGATTTTAGTTCT 59.688 38.462 0.00 0.00 0.00 3.01
2600 2747 3.765381 TCTTCATGAAATGTGCAAGGGA 58.235 40.909 9.88 0.00 46.80 4.20
2607 2754 4.885413 TGAAATGTGCAAGGGAATTTGAG 58.115 39.130 0.00 0.00 0.00 3.02
2623 2770 7.370383 GGAATTTGAGTAAGAATGCTTGTGAA 58.630 34.615 0.00 0.00 35.56 3.18
2650 2797 4.040755 ACAGAAGGTAATCTATGCCAGGT 58.959 43.478 0.00 0.00 35.99 4.00
2652 2799 5.665812 ACAGAAGGTAATCTATGCCAGGTTA 59.334 40.000 0.00 0.00 35.99 2.85
2665 2812 2.699954 CCAGGTTACAATTCTGTCGCT 58.300 47.619 0.00 0.00 36.96 4.93
2690 2847 0.539051 CAGTGTCATCTGGGTCCTCC 59.461 60.000 0.00 0.00 0.00 4.30
2699 2856 1.613928 TGGGTCCTCCGGCATGTTA 60.614 57.895 0.00 0.00 38.76 2.41
2700 2857 1.153229 GGGTCCTCCGGCATGTTAC 60.153 63.158 0.00 0.00 33.83 2.50
2703 2860 0.179081 GTCCTCCGGCATGTTACCTC 60.179 60.000 0.00 0.00 0.00 3.85
2718 2875 7.254932 GCATGTTACCTCACCTTAATCTGAATC 60.255 40.741 0.00 0.00 0.00 2.52
2721 2878 7.606456 TGTTACCTCACCTTAATCTGAATCAAC 59.394 37.037 0.00 0.00 0.00 3.18
2722 2879 5.501156 ACCTCACCTTAATCTGAATCAACC 58.499 41.667 0.00 0.00 0.00 3.77
2726 2883 7.148171 CCTCACCTTAATCTGAATCAACCTTTC 60.148 40.741 0.00 0.00 0.00 2.62
2757 2914 4.406003 TGGTCTTCTGGATCTTTAGGTAGC 59.594 45.833 0.00 0.00 0.00 3.58
2758 2915 4.651962 GGTCTTCTGGATCTTTAGGTAGCT 59.348 45.833 0.00 0.00 0.00 3.32
2759 2916 5.129650 GGTCTTCTGGATCTTTAGGTAGCTT 59.870 44.000 0.00 0.00 0.00 3.74
2763 2920 8.822805 TCTTCTGGATCTTTAGGTAGCTTTTTA 58.177 33.333 0.00 0.00 0.00 1.52
2792 2949 4.821260 GTCCAATGGCCTTTTTGTTTGAAT 59.179 37.500 3.32 0.00 0.00 2.57
2800 2958 6.545298 TGGCCTTTTTGTTTGAATAAAAGCAT 59.455 30.769 3.32 0.00 37.48 3.79
2870 3029 6.887002 ACTTAATCTTTTCTGTGGGGAGATTC 59.113 38.462 0.00 0.00 37.94 2.52
2886 3045 5.397326 GGAGATTCATGTCAAGCAAAAGTC 58.603 41.667 0.00 0.00 0.00 3.01
2911 3070 4.040217 TGCAATTTTTCAGCACCCACTAAT 59.960 37.500 0.00 0.00 32.55 1.73
3016 3178 2.543777 TGTGTGCACTTTAGGAGTCC 57.456 50.000 19.41 0.00 36.10 3.85
3030 3192 1.768684 GAGTCCAGGTGGTCTTGGCA 61.769 60.000 0.00 0.00 40.13 4.92
3036 3198 2.357050 CCAGGTGGTCTTGGCATGATAA 60.357 50.000 6.35 0.00 34.17 1.75
3037 3199 3.559069 CAGGTGGTCTTGGCATGATAAT 58.441 45.455 6.35 0.00 0.00 1.28
3038 3200 4.446167 CCAGGTGGTCTTGGCATGATAATA 60.446 45.833 6.35 0.00 34.17 0.98
3039 3201 5.132502 CAGGTGGTCTTGGCATGATAATAA 58.867 41.667 6.35 0.00 0.00 1.40
3040 3202 5.593909 CAGGTGGTCTTGGCATGATAATAAA 59.406 40.000 6.35 0.00 0.00 1.40
3041 3203 6.266103 CAGGTGGTCTTGGCATGATAATAAAT 59.734 38.462 6.35 0.00 0.00 1.40
3042 3204 6.491403 AGGTGGTCTTGGCATGATAATAAATC 59.509 38.462 6.35 0.00 0.00 2.17
3043 3205 6.265196 GGTGGTCTTGGCATGATAATAAATCA 59.735 38.462 6.35 0.00 0.00 2.57
3044 3206 7.201902 GGTGGTCTTGGCATGATAATAAATCAA 60.202 37.037 6.35 0.00 0.00 2.57
3387 3558 3.475566 TTAGGTATGCTAAGCTGGCTG 57.524 47.619 12.19 0.00 0.00 4.85
3394 3565 3.634397 TGCTAAGCTGGCTGTTCTTAT 57.366 42.857 12.19 0.00 0.00 1.73
3474 3648 8.233868 TGTTAACAAGGTCATCGTATCAAAATG 58.766 33.333 5.64 0.00 0.00 2.32
3476 3650 6.422776 ACAAGGTCATCGTATCAAAATGAC 57.577 37.500 6.23 6.23 45.45 3.06
3597 3772 6.136857 AGTGTCCCATATGCTTCTAACTAGA 58.863 40.000 0.00 0.00 0.00 2.43
3604 3779 8.085296 CCCATATGCTTCTAACTAGAACTACTG 58.915 40.741 0.00 0.00 37.40 2.74
3772 3961 3.325870 CTCATAAGGTTGACGCAACTCA 58.674 45.455 17.89 7.74 43.14 3.41
3806 3995 5.006386 AGGAAGCTGTCAACAAAGATAAGG 58.994 41.667 0.00 0.00 0.00 2.69
3884 4073 4.386711 AGGAACTAGTGCCACAAGTTAAC 58.613 43.478 22.67 0.00 36.02 2.01
3919 4108 4.346127 AGGGTACGTCTCCTTTTAAACTGT 59.654 41.667 0.00 0.00 0.00 3.55
4036 4225 6.564709 TTTCATCTTATGCACTGCCATATC 57.435 37.500 0.00 0.00 0.00 1.63
4069 4258 5.065218 GGAGCACACATTTGAATCTAACGAT 59.935 40.000 0.00 0.00 0.00 3.73
4076 4265 8.729756 ACACATTTGAATCTAACGATGAAATCA 58.270 29.630 0.00 0.00 45.97 2.57
4113 4302 3.008485 GGATTGTTCCAGGAGTCTGTCTT 59.992 47.826 0.00 0.00 42.12 3.01
4134 5912 9.890629 TGTCTTACTCTTGCATAATCTGTATTT 57.109 29.630 0.00 0.00 0.00 1.40
4155 5933 6.503616 TTTCATTGTGAAAACATGTTACGC 57.496 33.333 12.39 15.29 42.72 4.42
4158 5936 1.323791 GTGAAAACATGTTACGCGCC 58.676 50.000 12.39 0.00 0.00 6.53
4169 5947 2.735663 TGTTACGCGCCGAAGATAAAAA 59.264 40.909 5.73 0.00 0.00 1.94
4186 5965 7.701445 AGATAAAAATTCCGATTGCTCTTCTG 58.299 34.615 0.00 0.00 0.00 3.02
4206 5985 4.098055 TGACATACGTTCTCTCTGAAGC 57.902 45.455 0.00 0.00 35.01 3.86
4261 6040 8.697507 ATTCTAACAAACTGATCACCTCTTTT 57.302 30.769 0.00 0.00 0.00 2.27
4301 6080 3.118592 GGCAAGACAAGCTACACTCCTAT 60.119 47.826 0.00 0.00 0.00 2.57
4310 6089 6.155221 ACAAGCTACACTCCTATCAGATTCAA 59.845 38.462 0.00 0.00 0.00 2.69
4311 6090 6.155475 AGCTACACTCCTATCAGATTCAAC 57.845 41.667 0.00 0.00 0.00 3.18
4313 6092 6.382570 AGCTACACTCCTATCAGATTCAACTT 59.617 38.462 0.00 0.00 0.00 2.66
4331 6110 5.877012 TCAACTTCAAGTGATATCAGAAGCC 59.123 40.000 23.28 7.41 39.33 4.35
4375 6154 2.041153 GTGGAAACAACAGCCCTGG 58.959 57.895 0.00 0.00 46.06 4.45
4379 6158 2.312390 GGAAACAACAGCCCTGGTTTA 58.688 47.619 0.00 0.00 33.92 2.01
4457 6236 1.731613 CGCGCACAGGAACTTCGTA 60.732 57.895 8.75 0.00 34.60 3.43
4466 6245 4.444720 CACAGGAACTTCGTAAAGTCACTC 59.555 45.833 0.00 0.00 45.07 3.51
4544 6323 3.686045 GGGAGGATAGGCGCTCCG 61.686 72.222 7.64 0.00 37.88 4.63
4595 6374 0.467384 AAGCCATGGACAGGATCTCG 59.533 55.000 18.40 0.00 0.00 4.04
4649 6428 4.435436 TCGAGCGTGCGCCATCTT 62.435 61.111 13.21 0.00 43.17 2.40
4667 6446 0.752054 TTTGGGAGCAGCAAAACCTG 59.248 50.000 0.00 0.00 35.93 4.00
4706 6485 2.490685 GCGGTTCGAGAGAGGGAC 59.509 66.667 0.00 0.00 43.69 4.46
4729 6508 4.916041 AGTGGATGAAGATGTTGGAGAA 57.084 40.909 0.00 0.00 0.00 2.87
4756 6535 2.363683 GCTGGAGATCAACAAGGAAGG 58.636 52.381 0.00 0.00 0.00 3.46
4757 6536 2.290577 GCTGGAGATCAACAAGGAAGGT 60.291 50.000 0.00 0.00 0.00 3.50
4845 6624 2.156446 CGAACGTACGAGGCGCATT 61.156 57.895 24.41 3.12 35.09 3.56
4853 6632 0.870307 ACGAGGCGCATTGTATCGAC 60.870 55.000 14.35 0.00 37.16 4.20
4855 6634 1.548973 GAGGCGCATTGTATCGACGG 61.549 60.000 10.83 0.00 39.03 4.79
4856 6635 1.881252 GGCGCATTGTATCGACGGT 60.881 57.895 10.83 0.00 0.00 4.83
4875 6654 4.666532 GCAGCGTGCACGTGAACC 62.667 66.667 36.80 21.63 44.26 3.62
4884 6663 2.031163 ACGTGAACCTGAGGCTGC 59.969 61.111 0.00 0.00 0.00 5.25
4886 6665 2.031516 CGTGAACCTGAGGCTGCTG 61.032 63.158 0.00 0.00 0.00 4.41
4887 6666 2.033141 TGAACCTGAGGCTGCTGC 59.967 61.111 7.10 7.10 38.76 5.25
4902 6681 1.897225 GCTGCTTCAGGCTCTGGAGA 61.897 60.000 13.08 0.65 39.34 3.71
4903 6682 0.176219 CTGCTTCAGGCTCTGGAGAG 59.824 60.000 13.08 0.00 39.34 3.20
4922 6701 0.609131 GCTTTGCTGCCAGTTCCCTA 60.609 55.000 0.00 0.00 0.00 3.53
4959 6738 6.428083 AGATACCGAGACTAGATGAAGAGA 57.572 41.667 0.00 0.00 0.00 3.10
4961 6740 3.199677 ACCGAGACTAGATGAAGAGACG 58.800 50.000 0.00 0.00 0.00 4.18
5002 6781 4.699522 GAGGGTGCCACGGTGACC 62.700 72.222 10.28 10.02 0.00 4.02
5013 6818 0.034896 ACGGTGACCTGCTTGTAAGG 59.965 55.000 0.00 0.00 40.93 2.69
5068 6874 5.751028 GGATGAGTAGTCTGTAGTTTCATGC 59.249 44.000 0.00 0.00 0.00 4.06
5076 6882 5.105187 AGTCTGTAGTTTCATGCTGATGCTA 60.105 40.000 0.00 0.00 40.48 3.49
5165 6974 0.798776 CTGAAGCGTTTGTGGGCTAG 59.201 55.000 0.00 0.00 38.88 3.42
5241 7050 1.564348 TCTAATGGGAAGGCTGGAACC 59.436 52.381 0.00 0.00 0.00 3.62
5325 7134 2.224378 TGGAAAGCAGAGACCAACTGAG 60.224 50.000 0.00 0.00 37.54 3.35
5327 7136 1.428869 AAGCAGAGACCAACTGAGGT 58.571 50.000 0.00 0.00 46.82 3.85
5372 7181 0.611618 CAGCATGGTGCCCTTGGTTA 60.612 55.000 12.67 0.00 46.52 2.85
5431 7395 7.255836 GGGTAACTAATTTATGGATGGGCTTTC 60.256 40.741 0.00 0.00 0.00 2.62
5442 7406 0.884704 TGGGCTTTCGTGCAGAAGAC 60.885 55.000 8.22 5.39 40.40 3.01
5587 7551 5.519927 CGTTGCATATATCTGACAAGTGACA 59.480 40.000 0.00 0.00 0.00 3.58
5592 7556 6.201806 GCATATATCTGACAAGTGACAAGTCC 59.798 42.308 5.24 0.00 0.00 3.85
5615 7579 1.302033 CTCTGCAGGGTCGTTGCTT 60.302 57.895 15.13 0.00 42.02 3.91
5616 7580 1.572085 CTCTGCAGGGTCGTTGCTTG 61.572 60.000 15.13 0.00 42.02 4.01
5617 7581 3.259425 CTGCAGGGTCGTTGCTTGC 62.259 63.158 5.57 0.00 42.02 4.01
5618 7582 4.043200 GCAGGGTCGTTGCTTGCC 62.043 66.667 0.00 0.00 38.51 4.52
5647 7611 0.658829 TCGTTTTCAATTGCCGCACG 60.659 50.000 0.00 6.74 0.00 5.34
5653 7617 4.418401 AATTGCCGCACGCGCATT 62.418 55.556 5.73 1.17 42.08 3.56
5659 7625 2.276244 CGCACGCGCATTTGAGAG 60.276 61.111 5.73 0.00 38.40 3.20
5664 7630 0.110056 ACGCGCATTTGAGAGCTTTG 60.110 50.000 5.73 0.00 0.00 2.77
5672 7638 4.393062 GCATTTGAGAGCTTTGCTGTACTA 59.607 41.667 0.00 0.00 39.88 1.82
5673 7639 5.672321 GCATTTGAGAGCTTTGCTGTACTAC 60.672 44.000 0.00 0.00 39.88 2.73
5679 7645 2.105821 AGCTTTGCTGTACTACCCACAA 59.894 45.455 0.00 0.00 37.57 3.33
5705 7675 4.430137 AGCACAGCATGATTTAGTGTTG 57.570 40.909 0.00 0.00 39.69 3.33
5713 7683 4.154737 GCATGATTTAGTGTTGTCAGAGCA 59.845 41.667 0.00 0.00 0.00 4.26
5743 7713 1.733399 GTGCTCCGTCGTCAGGTTC 60.733 63.158 0.00 0.00 0.00 3.62
5748 7718 1.154263 CCGTCGTCAGGTTCGAGTC 60.154 63.158 0.00 0.00 37.99 3.36
5749 7719 1.154263 CGTCGTCAGGTTCGAGTCC 60.154 63.158 1.17 1.17 37.99 3.85
5750 7720 1.848932 CGTCGTCAGGTTCGAGTCCA 61.849 60.000 10.54 0.00 37.99 4.02
5768 7738 5.134661 AGTCCATTTAACAAGGGAACGAAA 58.865 37.500 0.00 0.00 44.48 3.46
5771 7741 5.009210 TCCATTTAACAAGGGAACGAAACTG 59.991 40.000 0.00 0.00 39.98 3.16
5773 7743 6.460399 CCATTTAACAAGGGAACGAAACTGAA 60.460 38.462 0.00 0.00 35.72 3.02
5774 7744 5.744666 TTAACAAGGGAACGAAACTGAAG 57.255 39.130 0.00 0.00 0.00 3.02
5776 7746 3.617284 ACAAGGGAACGAAACTGAAGTT 58.383 40.909 0.00 0.00 40.50 2.66
5777 7747 3.626217 ACAAGGGAACGAAACTGAAGTTC 59.374 43.478 0.00 0.00 42.36 3.01
5778 7748 3.553828 AGGGAACGAAACTGAAGTTCA 57.446 42.857 5.25 5.25 44.20 3.18
5792 7762 6.106648 CTGAAGTTCAGGCTGATATATCCA 57.893 41.667 22.95 10.63 40.71 3.41
5820 7790 6.791887 TGCAGATCTAAAGTTCTGAACAAG 57.208 37.500 21.50 14.94 41.86 3.16
5830 7800 2.489722 GTTCTGAACAAGCCCTTCATCC 59.510 50.000 15.34 0.00 0.00 3.51
5882 7852 2.813908 GGACGTGTGGATCGTGGC 60.814 66.667 0.00 0.00 41.64 5.01
5915 7885 5.642063 TGTGCATCGATGTAGAGATACGATA 59.358 40.000 25.47 0.00 40.77 2.92
5922 7892 8.549338 TCGATGTAGAGATACGATATGTTCTT 57.451 34.615 0.00 0.00 0.00 2.52
5923 7893 9.000486 TCGATGTAGAGATACGATATGTTCTTT 58.000 33.333 0.00 0.00 0.00 2.52
5924 7894 9.613957 CGATGTAGAGATACGATATGTTCTTTT 57.386 33.333 0.00 0.00 0.00 2.27
5990 8570 2.564062 AGTTTCATGGGCATGGAAGTTG 59.436 45.455 0.00 0.00 36.76 3.16
6000 8580 2.616510 GCATGGAAGTTGCCTAGACAGT 60.617 50.000 0.00 0.00 33.95 3.55
6001 8581 2.839486 TGGAAGTTGCCTAGACAGTG 57.161 50.000 0.00 0.00 0.00 3.66
6002 8582 2.325484 TGGAAGTTGCCTAGACAGTGA 58.675 47.619 0.00 0.00 0.00 3.41
6003 8583 2.906389 TGGAAGTTGCCTAGACAGTGAT 59.094 45.455 0.00 0.00 0.00 3.06
6004 8584 4.093743 TGGAAGTTGCCTAGACAGTGATA 58.906 43.478 0.00 0.00 0.00 2.15
6005 8585 4.160439 TGGAAGTTGCCTAGACAGTGATAG 59.840 45.833 0.00 0.00 0.00 2.08
6006 8586 4.160626 GGAAGTTGCCTAGACAGTGATAGT 59.839 45.833 0.00 0.00 0.00 2.12
6007 8587 4.993029 AGTTGCCTAGACAGTGATAGTC 57.007 45.455 0.00 0.00 36.26 2.59
6062 8642 2.100631 CCCAGAAAGTACTGCCGCG 61.101 63.158 0.00 0.00 36.67 6.46
6137 8717 1.963338 GTGCTGTGACCTGAGTGCC 60.963 63.158 0.00 0.00 0.00 5.01
6148 8728 2.279517 GAGTGCCGGCGGATACAG 60.280 66.667 33.44 1.21 0.00 2.74
6155 8735 1.529948 CGGCGGATACAGGGGACTA 60.530 63.158 0.00 0.00 40.21 2.59
6160 8740 3.518303 GGCGGATACAGGGGACTAATATT 59.482 47.826 0.00 0.00 40.21 1.28
6161 8741 4.504858 GCGGATACAGGGGACTAATATTG 58.495 47.826 0.00 0.00 40.21 1.90
6162 8742 4.020485 GCGGATACAGGGGACTAATATTGT 60.020 45.833 0.00 0.00 40.21 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 8.739039 CCAGACAATTAAGTTGATGGTGAAATA 58.261 33.333 0.00 0.00 40.33 1.40
39 40 7.451255 TCCAGACAATTAAGTTGATGGTGAAAT 59.549 33.333 16.28 0.00 43.02 2.17
40 41 6.775142 TCCAGACAATTAAGTTGATGGTGAAA 59.225 34.615 16.28 0.00 43.02 2.69
41 42 6.303054 TCCAGACAATTAAGTTGATGGTGAA 58.697 36.000 16.28 5.51 43.02 3.18
42 43 5.875224 TCCAGACAATTAAGTTGATGGTGA 58.125 37.500 16.28 0.00 43.02 4.02
43 44 6.573664 TTCCAGACAATTAAGTTGATGGTG 57.426 37.500 16.28 0.00 43.02 4.17
44 45 7.781324 AATTCCAGACAATTAAGTTGATGGT 57.219 32.000 16.28 0.00 43.02 3.55
45 46 8.960591 AGTAATTCCAGACAATTAAGTTGATGG 58.039 33.333 13.63 13.63 43.43 3.51
135 136 9.284968 CACCCTAACTTTTCTTCTTTCTATTCA 57.715 33.333 0.00 0.00 0.00 2.57
136 137 9.286170 ACACCCTAACTTTTCTTCTTTCTATTC 57.714 33.333 0.00 0.00 0.00 1.75
137 138 9.642343 AACACCCTAACTTTTCTTCTTTCTATT 57.358 29.630 0.00 0.00 0.00 1.73
140 141 9.470399 TTTAACACCCTAACTTTTCTTCTTTCT 57.530 29.630 0.00 0.00 0.00 2.52
141 142 9.731819 CTTTAACACCCTAACTTTTCTTCTTTC 57.268 33.333 0.00 0.00 0.00 2.62
142 143 8.692710 CCTTTAACACCCTAACTTTTCTTCTTT 58.307 33.333 0.00 0.00 0.00 2.52
143 144 8.057011 TCCTTTAACACCCTAACTTTTCTTCTT 58.943 33.333 0.00 0.00 0.00 2.52
144 145 7.501559 GTCCTTTAACACCCTAACTTTTCTTCT 59.498 37.037 0.00 0.00 0.00 2.85
145 146 7.255381 GGTCCTTTAACACCCTAACTTTTCTTC 60.255 40.741 0.00 0.00 0.00 2.87
146 147 6.548622 GGTCCTTTAACACCCTAACTTTTCTT 59.451 38.462 0.00 0.00 0.00 2.52
147 148 6.066690 GGTCCTTTAACACCCTAACTTTTCT 58.933 40.000 0.00 0.00 0.00 2.52
148 149 6.323203 GGTCCTTTAACACCCTAACTTTTC 57.677 41.667 0.00 0.00 0.00 2.29
158 159 1.527034 GAACCGGGTCCTTTAACACC 58.473 55.000 8.85 0.00 0.00 4.16
159 160 1.527034 GGAACCGGGTCCTTTAACAC 58.473 55.000 32.24 1.10 34.56 3.32
160 161 0.035176 CGGAACCGGGTCCTTTAACA 59.965 55.000 35.15 0.00 35.31 2.41
161 162 2.845019 CGGAACCGGGTCCTTTAAC 58.155 57.895 35.15 9.13 35.31 2.01
172 173 1.443872 CTCGTCTCAACCGGAACCG 60.444 63.158 9.46 6.25 39.44 4.44
173 174 1.737008 GCTCGTCTCAACCGGAACC 60.737 63.158 9.46 0.00 0.00 3.62
174 175 2.087009 CGCTCGTCTCAACCGGAAC 61.087 63.158 9.46 0.00 0.00 3.62
175 176 1.236616 TACGCTCGTCTCAACCGGAA 61.237 55.000 9.46 0.00 0.00 4.30
176 177 1.028330 ATACGCTCGTCTCAACCGGA 61.028 55.000 9.46 0.00 0.00 5.14
177 178 0.591741 GATACGCTCGTCTCAACCGG 60.592 60.000 0.00 0.00 0.00 5.28
178 179 0.591741 GGATACGCTCGTCTCAACCG 60.592 60.000 9.42 0.00 0.00 4.44
179 180 0.454600 TGGATACGCTCGTCTCAACC 59.545 55.000 9.42 4.12 42.51 3.77
180 181 2.186076 CTTGGATACGCTCGTCTCAAC 58.814 52.381 9.42 0.00 42.51 3.18
184 185 0.101399 CAGCTTGGATACGCTCGTCT 59.899 55.000 0.00 0.00 42.51 4.18
251 255 1.194098 GCATGCGCTATGATCTGTGAC 59.806 52.381 19.56 0.89 39.21 3.67
289 295 0.389817 TGGTTGCTGCTGCTACGTAG 60.390 55.000 18.47 18.47 43.88 3.51
339 345 3.243816 TGCTCTGTGCTGCCTCCA 61.244 61.111 0.00 0.00 43.37 3.86
363 369 2.510238 GCTGTAGACTGCCTGCCG 60.510 66.667 0.35 0.00 35.17 5.69
365 371 2.510238 CCGCTGTAGACTGCCTGC 60.510 66.667 6.02 0.00 37.50 4.85
429 469 1.249407 GGCCTCCGTGGATCTACTAG 58.751 60.000 7.68 4.78 38.35 2.57
442 482 2.586792 CTGTACTGCCTGGCCTCC 59.413 66.667 17.53 1.94 0.00 4.30
443 483 2.586792 CCTGTACTGCCTGGCCTC 59.413 66.667 17.53 4.48 0.00 4.70
455 503 1.447140 GCATTGACGGACGCCTGTA 60.447 57.895 0.00 0.00 30.59 2.74
459 507 3.799755 GGTGCATTGACGGACGCC 61.800 66.667 0.00 0.00 0.00 5.68
495 547 0.682852 GTTAACTTGGGTTTGGGGGC 59.317 55.000 0.00 0.00 36.92 5.80
519 574 0.037232 GATCCCTAATCTTCCCGGCG 60.037 60.000 0.00 0.00 0.00 6.46
607 663 3.551407 GCGAGGGATGGGAGGGAC 61.551 72.222 0.00 0.00 0.00 4.46
654 710 0.541863 AATGTGAGGATCCGGTGACC 59.458 55.000 5.98 3.62 0.00 4.02
657 713 0.179045 GGGAATGTGAGGATCCGGTG 60.179 60.000 5.98 0.00 33.90 4.94
695 753 0.758123 GGAATCAGCAGAGGGGAGAG 59.242 60.000 0.00 0.00 0.00 3.20
704 762 3.540211 ACGGAAGTGGAATCAGCAG 57.460 52.632 0.00 0.00 46.97 4.24
756 836 2.785713 TACACTTTTCTTTTGCGGGC 57.214 45.000 0.00 0.00 0.00 6.13
812 892 3.839432 GAAGGTCTCCGCGGAGGG 61.839 72.222 45.31 28.75 42.20 4.30
813 893 3.839432 GGAAGGTCTCCGCGGAGG 61.839 72.222 45.31 30.46 42.20 4.30
855 943 2.757508 CGGCTGAGGAGGCAGAGA 60.758 66.667 0.00 0.00 45.23 3.10
863 951 3.456365 GCTGAGCTCGGCTGAGGA 61.456 66.667 35.32 3.00 40.13 3.71
880 968 4.486503 GAGCTGGGCTGGGCTGAG 62.487 72.222 0.00 0.00 39.88 3.35
885 973 4.823732 TAGGGGAGCTGGGCTGGG 62.824 72.222 0.00 0.00 39.88 4.45
886 974 3.483869 GTAGGGGAGCTGGGCTGG 61.484 72.222 0.00 0.00 39.88 4.85
887 975 2.366167 AGTAGGGGAGCTGGGCTG 60.366 66.667 0.00 0.00 39.88 4.85
888 976 2.041405 GAGTAGGGGAGCTGGGCT 60.041 66.667 0.00 0.00 43.88 5.19
889 977 2.365635 TGAGTAGGGGAGCTGGGC 60.366 66.667 0.00 0.00 0.00 5.36
890 978 1.002274 AGTGAGTAGGGGAGCTGGG 59.998 63.158 0.00 0.00 0.00 4.45
891 979 1.965754 GCAGTGAGTAGGGGAGCTGG 61.966 65.000 0.00 0.00 0.00 4.85
892 980 1.519719 GCAGTGAGTAGGGGAGCTG 59.480 63.158 0.00 0.00 0.00 4.24
893 981 1.687493 GGCAGTGAGTAGGGGAGCT 60.687 63.158 0.00 0.00 0.00 4.09
894 982 2.736826 GGGCAGTGAGTAGGGGAGC 61.737 68.421 0.00 0.00 0.00 4.70
895 983 0.618968 AAGGGCAGTGAGTAGGGGAG 60.619 60.000 0.00 0.00 0.00 4.30
896 984 0.617820 GAAGGGCAGTGAGTAGGGGA 60.618 60.000 0.00 0.00 0.00 4.81
897 985 0.618968 AGAAGGGCAGTGAGTAGGGG 60.619 60.000 0.00 0.00 0.00 4.79
898 986 0.539051 CAGAAGGGCAGTGAGTAGGG 59.461 60.000 0.00 0.00 0.00 3.53
899 987 0.107945 GCAGAAGGGCAGTGAGTAGG 60.108 60.000 0.00 0.00 0.00 3.18
900 988 0.901124 AGCAGAAGGGCAGTGAGTAG 59.099 55.000 0.00 0.00 35.83 2.57
901 989 1.002430 CAAGCAGAAGGGCAGTGAGTA 59.998 52.381 0.00 0.00 35.83 2.59
902 990 0.250640 CAAGCAGAAGGGCAGTGAGT 60.251 55.000 0.00 0.00 35.83 3.41
909 997 2.361737 GGGGACAAGCAGAAGGGC 60.362 66.667 0.00 0.00 0.00 5.19
1016 1136 0.310232 GAGCCGATCGTAGTGTACCC 59.690 60.000 15.09 0.00 0.00 3.69
1028 1148 0.250513 AAAAAGGAGCTCGAGCCGAT 59.749 50.000 32.94 16.02 43.38 4.18
1242 1363 2.363018 CGGAGGAGGAGGTGCAGA 60.363 66.667 0.00 0.00 0.00 4.26
1324 1454 4.603946 GTCCGGGAGCGGCATACC 62.604 72.222 0.00 2.41 0.00 2.73
1325 1455 4.603946 GGTCCGGGAGCGGCATAC 62.604 72.222 10.92 0.00 0.00 2.39
1460 1590 1.586303 GGCGCGTACCCGTAGTAAC 60.586 63.158 8.43 0.00 36.15 2.50
1610 1740 1.137404 GCAGTTGCCGCATCGAAAT 59.863 52.632 0.00 0.00 34.31 2.17
1773 1909 1.866601 TCGTCGTAGTTCTCGAACACA 59.133 47.619 11.90 0.00 43.47 3.72
1926 2062 1.410004 TCTCCTTCACGACCACTGTT 58.590 50.000 0.00 0.00 0.00 3.16
1929 2065 0.898320 CCATCTCCTTCACGACCACT 59.102 55.000 0.00 0.00 0.00 4.00
1950 2086 0.456312 CAACCGTGGAGTACTCGCTC 60.456 60.000 16.56 9.42 34.89 5.03
1985 2121 4.849329 GACCGAACGAGCCGCGAT 62.849 66.667 8.23 0.00 44.57 4.58
2002 2138 1.070758 CTCCGGGATGGTATTGACAGG 59.929 57.143 0.00 0.00 39.52 4.00
2049 2191 2.586079 CGGTATGCTGGTCGCCTG 60.586 66.667 0.00 0.00 38.05 4.85
2294 2436 7.435305 ACAGTGAGTCAGATCATTCAGATATG 58.565 38.462 0.00 0.00 45.23 1.78
2411 2553 0.786435 ACCTTGCCTTCTTCCCCAAT 59.214 50.000 0.00 0.00 0.00 3.16
2473 2615 2.575805 ACAGCTTCCTCTCCCAAAAG 57.424 50.000 0.00 0.00 0.00 2.27
2476 2618 1.839994 CCATACAGCTTCCTCTCCCAA 59.160 52.381 0.00 0.00 0.00 4.12
2538 2680 5.144100 AGATCGGAGACCATTTCTACTCAT 58.856 41.667 0.00 0.00 42.51 2.90
2568 2710 8.642020 GCACATTTCATGAAGAACTAAAATCAC 58.358 33.333 8.41 0.00 35.56 3.06
2581 2723 5.486735 AATTCCCTTGCACATTTCATGAA 57.513 34.783 3.38 3.38 0.00 2.57
2623 2770 8.543774 CCTGGCATAGATTACCTTCTGTTATAT 58.456 37.037 0.00 0.00 0.00 0.86
2627 2774 4.475016 ACCTGGCATAGATTACCTTCTGTT 59.525 41.667 0.00 0.00 0.00 3.16
2631 2778 5.925509 TGTAACCTGGCATAGATTACCTTC 58.074 41.667 0.00 0.00 0.00 3.46
2643 2790 2.422597 CGACAGAATTGTAACCTGGCA 58.577 47.619 0.00 0.00 37.76 4.92
2645 2792 2.416547 CAGCGACAGAATTGTAACCTGG 59.583 50.000 0.00 0.00 37.76 4.45
2650 2797 5.743026 TGTTTTCAGCGACAGAATTGTAA 57.257 34.783 0.00 0.00 37.76 2.41
2652 2799 4.214980 CTGTTTTCAGCGACAGAATTGT 57.785 40.909 0.00 0.00 44.65 2.71
2665 2812 3.476552 GACCCAGATGACACTGTTTTCA 58.523 45.455 0.00 0.00 36.30 2.69
2690 2847 2.684001 TAAGGTGAGGTAACATGCCG 57.316 50.000 0.00 0.00 41.41 5.69
2699 2856 5.251700 AGGTTGATTCAGATTAAGGTGAGGT 59.748 40.000 0.00 0.00 0.00 3.85
2700 2857 5.749462 AGGTTGATTCAGATTAAGGTGAGG 58.251 41.667 0.00 0.00 0.00 3.86
2703 2860 6.660949 AGGAAAGGTTGATTCAGATTAAGGTG 59.339 38.462 0.00 0.00 0.00 4.00
2722 2879 3.307059 CCAGAAGACCACACCTAGGAAAG 60.307 52.174 17.98 7.44 0.00 2.62
2726 2883 1.938585 TCCAGAAGACCACACCTAGG 58.061 55.000 7.41 7.41 0.00 3.02
2731 2888 4.020128 ACCTAAAGATCCAGAAGACCACAC 60.020 45.833 0.00 0.00 0.00 3.82
2757 2914 8.846943 AAAGGCCATTGGACTAAATTAAAAAG 57.153 30.769 12.63 0.00 42.44 2.27
2758 2915 9.634021 AAAAAGGCCATTGGACTAAATTAAAAA 57.366 25.926 12.63 0.00 42.44 1.94
2759 2916 9.061435 CAAAAAGGCCATTGGACTAAATTAAAA 57.939 29.630 12.63 0.00 42.44 1.52
2763 2920 6.186420 ACAAAAAGGCCATTGGACTAAATT 57.814 33.333 12.63 4.91 42.44 1.82
2792 2949 7.557358 TCCATTATTCAGCTCAAGATGCTTTTA 59.443 33.333 0.00 0.00 38.92 1.52
2800 2958 4.384537 CCCACTCCATTATTCAGCTCAAGA 60.385 45.833 0.00 0.00 0.00 3.02
2849 3007 5.261040 TGAATCTCCCCACAGAAAAGATT 57.739 39.130 0.00 0.00 38.91 2.40
2870 3029 3.708890 TGCAAGACTTTTGCTTGACATG 58.291 40.909 12.45 0.00 44.16 3.21
2886 3045 2.545106 GTGGGTGCTGAAAAATTGCAAG 59.455 45.455 4.94 0.00 38.50 4.01
2899 3058 3.449746 TGCCTTTAATTAGTGGGTGCT 57.550 42.857 7.60 0.00 0.00 4.40
2935 3095 7.754924 CCAACCAGTTATAAATAGCAACAAGTG 59.245 37.037 0.00 0.00 0.00 3.16
2947 3107 5.536916 CCAGAACCAACCAACCAGTTATAAA 59.463 40.000 0.00 0.00 0.00 1.40
2951 3111 2.242708 ACCAGAACCAACCAACCAGTTA 59.757 45.455 0.00 0.00 0.00 2.24
2953 3113 0.629058 ACCAGAACCAACCAACCAGT 59.371 50.000 0.00 0.00 0.00 4.00
2954 3114 2.158667 AGTACCAGAACCAACCAACCAG 60.159 50.000 0.00 0.00 0.00 4.00
2955 3115 1.847737 AGTACCAGAACCAACCAACCA 59.152 47.619 0.00 0.00 0.00 3.67
3016 3178 2.715749 TATCATGCCAAGACCACCTG 57.284 50.000 0.00 0.00 0.00 4.00
3038 3200 8.470002 GGACCATATTAAAACTGCTCTTGATTT 58.530 33.333 0.00 0.00 0.00 2.17
3039 3201 7.068716 GGGACCATATTAAAACTGCTCTTGATT 59.931 37.037 0.00 0.00 0.00 2.57
3040 3202 6.547510 GGGACCATATTAAAACTGCTCTTGAT 59.452 38.462 0.00 0.00 0.00 2.57
3041 3203 5.885912 GGGACCATATTAAAACTGCTCTTGA 59.114 40.000 0.00 0.00 0.00 3.02
3042 3204 5.888161 AGGGACCATATTAAAACTGCTCTTG 59.112 40.000 0.00 0.00 0.00 3.02
3043 3205 6.069381 AGAGGGACCATATTAAAACTGCTCTT 60.069 38.462 0.00 0.00 0.00 2.85
3044 3206 5.430089 AGAGGGACCATATTAAAACTGCTCT 59.570 40.000 0.00 0.00 0.00 4.09
3057 3219 0.105349 CGGGGGTAAGAGGGACCATA 60.105 60.000 0.00 0.00 38.86 2.74
3247 3418 8.286191 CCATTAGGCTTTGAGAAAGATACTTT 57.714 34.615 0.00 0.00 41.02 2.66
3432 3606 8.237267 CCTTGTTAACAAAGTTGGAAGCTATAG 58.763 37.037 20.89 4.45 35.15 1.31
3597 3772 8.083828 AGACATGATCTATTGAACCAGTAGTT 57.916 34.615 0.00 0.00 37.36 2.24
3626 3801 7.839705 AGGAGAAATACTGTCAAGTAGGATACA 59.160 37.037 0.00 0.00 46.26 2.29
3638 3827 4.083271 GCCACACAAAGGAGAAATACTGTC 60.083 45.833 0.00 0.00 0.00 3.51
3806 3995 2.030946 GGCAATGACACGAACAGCTATC 59.969 50.000 0.00 0.00 0.00 2.08
4036 4225 6.139048 TCAAATGTGTGCTCCATTCATATG 57.861 37.500 0.00 0.00 31.49 1.78
4076 4265 9.784531 CTGGAACAATCCTAGATGTAAATGTAT 57.215 33.333 0.00 0.00 46.70 2.29
4134 5912 4.215201 CGCGTAACATGTTTTCACAATGA 58.785 39.130 17.78 0.00 36.16 2.57
4153 5931 2.372350 GGAATTTTTATCTTCGGCGCG 58.628 47.619 0.00 0.00 0.00 6.86
4155 5933 3.936902 TCGGAATTTTTATCTTCGGCG 57.063 42.857 0.00 0.00 0.00 6.46
4158 5936 6.719365 AGAGCAATCGGAATTTTTATCTTCG 58.281 36.000 0.00 0.00 0.00 3.79
4169 5947 3.616956 TGTCAGAAGAGCAATCGGAAT 57.383 42.857 0.00 0.00 0.00 3.01
4186 5965 4.101942 CAGCTTCAGAGAGAACGTATGTC 58.898 47.826 0.00 0.00 31.61 3.06
4206 5985 8.893219 TTGCACCTAATGAGAAATAGATACAG 57.107 34.615 0.00 0.00 0.00 2.74
4261 6040 2.093288 TGCCACATTTTTGCAAACCTGA 60.093 40.909 21.12 2.59 30.85 3.86
4301 6080 8.534496 TCTGATATCACTTGAAGTTGAATCTGA 58.466 33.333 0.00 5.73 0.00 3.27
4310 6089 5.426689 TGGCTTCTGATATCACTTGAAGT 57.573 39.130 23.61 0.00 37.17 3.01
4311 6090 6.748333 TTTGGCTTCTGATATCACTTGAAG 57.252 37.500 20.83 20.83 37.69 3.02
4313 6092 6.071952 GGTTTTTGGCTTCTGATATCACTTGA 60.072 38.462 0.00 0.00 0.00 3.02
4331 6110 1.028905 TGACCGAAGCCAGGTTTTTG 58.971 50.000 0.00 0.00 43.01 2.44
4363 6142 0.184933 TGCTAAACCAGGGCTGTTGT 59.815 50.000 0.00 0.00 0.00 3.32
4368 6147 0.704076 TCCATTGCTAAACCAGGGCT 59.296 50.000 0.00 0.00 0.00 5.19
4372 6151 3.420893 TCCAGTTCCATTGCTAAACCAG 58.579 45.455 0.00 0.00 0.00 4.00
4375 6154 3.084786 AGCTCCAGTTCCATTGCTAAAC 58.915 45.455 0.00 0.00 0.00 2.01
4379 6158 2.191400 TCTAGCTCCAGTTCCATTGCT 58.809 47.619 0.00 0.00 34.92 3.91
4457 6236 3.446442 AGCCATCCATTGAGTGACTTT 57.554 42.857 0.00 0.00 0.00 2.66
4466 6245 2.219458 CAGAGTGCTAGCCATCCATTG 58.781 52.381 13.29 1.35 0.00 2.82
4544 6323 3.058293 TGTTGCAGATGACGAAAATCACC 60.058 43.478 0.00 0.00 0.00 4.02
4595 6374 1.726853 CGTTGACCACATCCTTCTCC 58.273 55.000 0.00 0.00 0.00 3.71
4649 6428 1.114722 CCAGGTTTTGCTGCTCCCAA 61.115 55.000 0.00 0.00 0.00 4.12
4706 6485 4.582869 TCTCCAACATCTTCATCCACTTG 58.417 43.478 0.00 0.00 0.00 3.16
4729 6508 0.107945 GTTGATCTCCAGCGCCTTCT 60.108 55.000 2.29 0.00 0.00 2.85
4756 6535 1.527311 GCTTCCTGTTCAACTCGTCAC 59.473 52.381 0.00 0.00 0.00 3.67
4757 6536 1.412710 AGCTTCCTGTTCAACTCGTCA 59.587 47.619 0.00 0.00 0.00 4.35
4817 6596 0.651610 CGTACGTTCGTATCGTCGGG 60.652 60.000 7.22 0.00 41.72 5.14
4845 6624 1.354155 CGCTGCTACCGTCGATACA 59.646 57.895 0.00 0.00 0.00 2.29
4855 6634 2.307309 TTCACGTGCACGCTGCTAC 61.307 57.895 37.35 0.00 45.31 3.58
4856 6635 2.028337 TTCACGTGCACGCTGCTA 59.972 55.556 37.35 20.76 45.31 3.49
4874 6653 2.350134 TGAAGCAGCAGCCTCAGG 59.650 61.111 0.00 0.00 43.56 3.86
4902 6681 1.905354 GGGAACTGGCAGCAAAGCT 60.905 57.895 15.89 0.00 40.77 3.74
4903 6682 0.609131 TAGGGAACTGGCAGCAAAGC 60.609 55.000 15.89 0.00 43.88 3.51
4910 6689 1.362224 AAGCTTCTAGGGAACTGGCA 58.638 50.000 0.00 0.00 43.88 4.92
4911 6690 2.360844 GAAAGCTTCTAGGGAACTGGC 58.639 52.381 0.00 0.00 43.88 4.85
4922 6701 2.432510 CGGTATCTCCTGGAAAGCTTCT 59.567 50.000 0.00 0.00 0.00 2.85
4961 6740 0.959372 TCCCTCTCGACGACCTTGTC 60.959 60.000 0.00 0.00 35.49 3.18
4973 6752 1.950973 GCACCCTCGAACTCCCTCTC 61.951 65.000 0.00 0.00 0.00 3.20
5002 6781 3.882888 TCTGGAAAACACCTTACAAGCAG 59.117 43.478 0.00 0.00 0.00 4.24
5003 6782 3.892284 TCTGGAAAACACCTTACAAGCA 58.108 40.909 0.00 0.00 0.00 3.91
5013 6818 4.741676 CAGATTGCAAGTTCTGGAAAACAC 59.258 41.667 18.45 0.00 39.03 3.32
5018 6823 2.886523 CCACAGATTGCAAGTTCTGGAA 59.113 45.455 26.08 0.00 42.93 3.53
5019 6824 2.106338 TCCACAGATTGCAAGTTCTGGA 59.894 45.455 26.08 19.46 42.93 3.86
5068 6874 4.872357 CCACCAGGCTAGCATCAG 57.128 61.111 18.24 5.68 0.00 2.90
5165 6974 5.116882 CCATAGCCTTACCTTACACAAGAC 58.883 45.833 0.00 0.00 33.20 3.01
5241 7050 2.230940 GCACGATCACGATCACCCG 61.231 63.158 7.75 0.00 42.66 5.28
5325 7134 8.671921 CACCTCTGCATATCATATAATTTCACC 58.328 37.037 0.00 0.00 0.00 4.02
5327 7136 7.337689 GCCACCTCTGCATATCATATAATTTCA 59.662 37.037 0.00 0.00 0.00 2.69
5372 7181 0.036875 GCCTCCAGTTTACAGTGCCT 59.963 55.000 0.00 0.00 0.00 4.75
5407 7216 7.012989 ACGAAAGCCCATCCATAAATTAGTTAC 59.987 37.037 0.00 0.00 0.00 2.50
5411 7375 5.762045 CACGAAAGCCCATCCATAAATTAG 58.238 41.667 0.00 0.00 0.00 1.73
5414 7378 2.362077 GCACGAAAGCCCATCCATAAAT 59.638 45.455 0.00 0.00 0.00 1.40
5431 7395 0.735632 GCTCTCTGGTCTTCTGCACG 60.736 60.000 0.00 0.00 0.00 5.34
5442 7406 2.581354 CCCGTCCAAGCTCTCTGG 59.419 66.667 0.00 0.00 0.00 3.86
5587 7551 1.374190 CCTGCAGAGCACTGGACTT 59.626 57.895 17.39 0.00 43.62 3.01
5592 7556 2.433838 CGACCCTGCAGAGCACTG 60.434 66.667 17.39 6.80 45.91 3.66
5615 7579 3.271729 TGAAAACGACTAACACAAGGCA 58.728 40.909 0.00 0.00 0.00 4.75
5616 7580 3.955771 TGAAAACGACTAACACAAGGC 57.044 42.857 0.00 0.00 0.00 4.35
5617 7581 5.173131 GCAATTGAAAACGACTAACACAAGG 59.827 40.000 10.34 0.00 0.00 3.61
5618 7582 5.173131 GGCAATTGAAAACGACTAACACAAG 59.827 40.000 10.34 0.00 0.00 3.16
5647 7611 0.109412 AGCAAAGCTCTCAAATGCGC 60.109 50.000 0.00 0.00 41.72 6.09
5653 7617 3.306780 GGGTAGTACAGCAAAGCTCTCAA 60.307 47.826 2.06 0.00 36.40 3.02
5655 7619 2.233922 TGGGTAGTACAGCAAAGCTCTC 59.766 50.000 2.06 0.00 36.40 3.20
5656 7620 2.028020 GTGGGTAGTACAGCAAAGCTCT 60.028 50.000 2.06 0.00 36.40 4.09
5659 7625 2.178912 TGTGGGTAGTACAGCAAAGC 57.821 50.000 2.06 0.00 0.00 3.51
5664 7630 2.833631 ACTGTTGTGGGTAGTACAGC 57.166 50.000 2.06 0.00 41.22 4.40
5672 7638 0.535102 GCTGTGCTACTGTTGTGGGT 60.535 55.000 0.00 0.00 0.00 4.51
5673 7639 0.534877 TGCTGTGCTACTGTTGTGGG 60.535 55.000 0.00 0.00 0.00 4.61
5679 7645 4.633126 CACTAAATCATGCTGTGCTACTGT 59.367 41.667 0.00 0.00 0.00 3.55
5705 7675 0.952984 AGCGGCTCTTTTGCTCTGAC 60.953 55.000 0.00 0.00 32.44 3.51
5743 7713 3.124636 CGTTCCCTTGTTAAATGGACTCG 59.875 47.826 0.00 0.00 30.62 4.18
5748 7718 5.009210 TCAGTTTCGTTCCCTTGTTAAATGG 59.991 40.000 0.00 0.00 0.00 3.16
5749 7719 6.067263 TCAGTTTCGTTCCCTTGTTAAATG 57.933 37.500 0.00 0.00 0.00 2.32
5750 7720 6.320418 ACTTCAGTTTCGTTCCCTTGTTAAAT 59.680 34.615 0.00 0.00 0.00 1.40
5768 7738 5.604231 TGGATATATCAGCCTGAACTTCAGT 59.396 40.000 16.10 1.86 42.80 3.41
5771 7741 6.471146 ACATGGATATATCAGCCTGAACTTC 58.529 40.000 14.60 0.00 32.17 3.01
5773 7743 6.445451 AACATGGATATATCAGCCTGAACT 57.555 37.500 14.60 0.00 32.17 3.01
5774 7744 6.569226 GCAAACATGGATATATCAGCCTGAAC 60.569 42.308 14.60 0.00 32.17 3.18
5776 7746 5.005740 GCAAACATGGATATATCAGCCTGA 58.994 41.667 14.60 0.00 32.17 3.86
5777 7747 4.763279 TGCAAACATGGATATATCAGCCTG 59.237 41.667 14.60 7.95 32.17 4.85
5778 7748 4.989277 TGCAAACATGGATATATCAGCCT 58.011 39.130 14.60 0.00 32.17 4.58
5779 7749 5.005740 TCTGCAAACATGGATATATCAGCC 58.994 41.667 14.60 0.00 0.00 4.85
5781 7751 9.662947 TTAGATCTGCAAACATGGATATATCAG 57.337 33.333 14.60 6.33 0.00 2.90
5786 7756 8.757982 AACTTTAGATCTGCAAACATGGATAT 57.242 30.769 5.18 0.00 0.00 1.63
5788 7758 6.888632 AGAACTTTAGATCTGCAAACATGGAT 59.111 34.615 5.18 0.00 0.00 3.41
5789 7759 6.149973 CAGAACTTTAGATCTGCAAACATGGA 59.850 38.462 5.18 0.00 37.96 3.41
5790 7760 6.149973 TCAGAACTTTAGATCTGCAAACATGG 59.850 38.462 5.18 0.00 42.48 3.66
5792 7762 7.229306 TGTTCAGAACTTTAGATCTGCAAACAT 59.771 33.333 14.51 0.00 42.48 2.71
5820 7790 2.622064 ACTCGTAATGGATGAAGGGC 57.378 50.000 0.00 0.00 0.00 5.19
5830 7800 5.639506 AGATCACCAACTGAAACTCGTAATG 59.360 40.000 0.00 0.00 30.60 1.90
5936 7906 3.954258 CTCCCCAATTAATGACAGAACCC 59.046 47.826 0.00 0.00 0.00 4.11
5937 7907 4.855340 TCTCCCCAATTAATGACAGAACC 58.145 43.478 0.00 0.00 0.00 3.62
5938 7908 6.834168 TTTCTCCCCAATTAATGACAGAAC 57.166 37.500 0.00 0.00 0.00 3.01
5990 8570 6.234920 TCTATCAGACTATCACTGTCTAGGC 58.765 44.000 0.00 0.00 42.21 3.93
6000 8580 4.393371 CGAAGGCGATCTATCAGACTATCA 59.607 45.833 0.00 0.00 40.82 2.15
6001 8581 4.632251 TCGAAGGCGATCTATCAGACTATC 59.368 45.833 0.00 0.00 42.51 2.08
6002 8582 4.580868 TCGAAGGCGATCTATCAGACTAT 58.419 43.478 0.00 0.00 42.51 2.12
6003 8583 4.004196 TCGAAGGCGATCTATCAGACTA 57.996 45.455 0.00 0.00 42.51 2.59
6004 8584 2.852449 TCGAAGGCGATCTATCAGACT 58.148 47.619 0.00 0.00 42.51 3.24
6024 8604 1.002134 ATTGCACTTGGCTAGCCGT 60.002 52.632 28.28 18.25 45.15 5.68
6062 8642 3.119137 AGTTGACCTGCAAAGTGAAAACC 60.119 43.478 0.00 0.00 38.44 3.27
6137 8717 1.111116 TTAGTCCCCTGTATCCGCCG 61.111 60.000 0.00 0.00 0.00 6.46
6170 8750 8.183571 ACATACTAGTCCCCTGTATATATGGA 57.816 38.462 0.00 0.00 0.00 3.41
6174 8754 7.935755 GCGATACATACTAGTCCCCTGTATATA 59.064 40.741 0.00 0.00 34.17 0.86
6175 8755 6.771749 GCGATACATACTAGTCCCCTGTATAT 59.228 42.308 0.00 0.00 34.17 0.86
6176 8756 6.118170 GCGATACATACTAGTCCCCTGTATA 58.882 44.000 0.00 0.00 34.17 1.47


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

AutoCloner maintained by Alex Coulton.