Multiple sequence alignment - TraesCS5D01G183000

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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 TraesCS5D01G183000 chr5D 100.000 7415 0 0 1 7415 284892588 284900002 0.000000e+00 13694.0
1 TraesCS5D01G183000 chr5D 90.476 63 3 3 1933 1994 262034645 262034585 6.170000e-11 80.5
2 TraesCS5D01G183000 chr5D 87.097 62 7 1 1933 1994 422454414 422454474 1.330000e-07 69.4
3 TraesCS5D01G183000 chr5B 95.735 5182 141 26 825 5999 322199928 322205036 0.000000e+00 8272.0
4 TraesCS5D01G183000 chr5B 92.237 1198 44 12 6018 7200 322205159 322206322 0.000000e+00 1652.0
5 TraesCS5D01G183000 chr5B 92.888 703 31 8 8 706 322198807 322199494 0.000000e+00 1003.0
6 TraesCS5D01G183000 chr5B 94.268 157 5 4 2353 2509 666223880 666224032 3.460000e-58 237.0
7 TraesCS5D01G183000 chr5B 90.566 106 10 0 4963 5068 422699572 422699467 2.790000e-29 141.0
8 TraesCS5D01G183000 chr5B 88.034 117 13 1 646 761 322199489 322199605 3.610000e-28 137.0
9 TraesCS5D01G183000 chr5A 92.289 2918 153 25 3084 5975 376466599 376469470 0.000000e+00 4076.0
10 TraesCS5D01G183000 chr5A 89.619 2283 122 33 105 2356 376463451 376465649 0.000000e+00 2796.0
11 TraesCS5D01G183000 chr5A 91.357 1076 49 19 6005 7061 376469558 376470608 0.000000e+00 1432.0
12 TraesCS5D01G183000 chr5A 83.282 323 31 7 2696 3014 376465965 376466268 7.330000e-70 276.0
13 TraesCS5D01G183000 chr5A 96.703 91 3 0 18 108 376463200 376463290 1.290000e-32 152.0
14 TraesCS5D01G183000 chr5A 96.552 58 2 0 7057 7114 376470757 376470814 6.120000e-16 97.1
15 TraesCS5D01G183000 chr6D 98.571 140 2 0 2353 2492 267532942 267532803 1.600000e-61 248.0
16 TraesCS5D01G183000 chr6D 88.119 101 12 0 1080 1180 115772136 115772236 3.630000e-23 121.0
17 TraesCS5D01G183000 chr3D 90.811 185 17 0 7230 7414 507760606 507760790 1.600000e-61 248.0
18 TraesCS5D01G183000 chr3D 92.233 103 8 0 4968 5070 204235125 204235023 6.000000e-31 147.0
19 TraesCS5D01G183000 chr2D 96.599 147 5 0 2353 2499 152869495 152869641 2.070000e-60 244.0
20 TraesCS5D01G183000 chr2D 92.453 106 8 0 4963 5068 159383560 159383455 1.290000e-32 152.0
21 TraesCS5D01G183000 chr7A 97.857 140 3 0 2353 2492 552975400 552975539 7.430000e-60 243.0
22 TraesCS5D01G183000 chr7A 89.623 106 11 0 4963 5068 143261666 143261771 1.300000e-27 135.0
23 TraesCS5D01G183000 chr3B 87.560 209 26 0 7207 7415 771385161 771384953 7.430000e-60 243.0
24 TraesCS5D01G183000 chr3B 91.176 102 9 0 4963 5064 158404808 158404707 1.000000e-28 139.0
25 TraesCS5D01G183000 chr3B 88.136 59 6 1 1933 1991 107795226 107795283 1.330000e-07 69.4
26 TraesCS5D01G183000 chr1B 94.872 156 6 2 2356 2509 531001717 531001562 7.430000e-60 243.0
27 TraesCS5D01G183000 chr1B 79.371 286 52 4 4799 5084 299121002 299121280 2.110000e-45 195.0
28 TraesCS5D01G183000 chr2A 95.364 151 5 2 2353 2503 53594671 53594819 9.620000e-59 239.0
29 TraesCS5D01G183000 chr2A 89.623 106 11 0 4963 5068 522231166 522231271 1.300000e-27 135.0
30 TraesCS5D01G183000 chr3A 92.683 164 9 3 2353 2514 375018127 375018289 4.470000e-57 233.0
31 TraesCS5D01G183000 chr6A 92.547 161 12 0 2356 2516 75877903 75877743 1.610000e-56 231.0
32 TraesCS5D01G183000 chr6A 88.119 101 12 0 1080 1180 144247530 144247630 3.630000e-23 121.0
33 TraesCS5D01G183000 chr6B 86.339 183 24 1 7233 7415 31121912 31121731 1.630000e-46 198.0
34 TraesCS5D01G183000 chr6B 85.106 188 27 1 7228 7415 31194765 31194579 2.730000e-44 191.0
35 TraesCS5D01G183000 chr6B 85.106 188 27 1 7228 7415 31205236 31205050 2.730000e-44 191.0
36 TraesCS5D01G183000 chr6B 84.574 188 28 1 7228 7415 31077751 31077565 1.270000e-42 185.0
37 TraesCS5D01G183000 chr6B 84.574 188 28 1 7228 7415 31184284 31184098 1.270000e-42 185.0
38 TraesCS5D01G183000 chr6B 84.043 188 29 1 7228 7415 31085826 31085640 5.910000e-41 180.0
39 TraesCS5D01G183000 chr6B 84.043 188 29 1 7228 7415 31111578 31111392 5.910000e-41 180.0
40 TraesCS5D01G183000 chr6B 88.119 101 12 0 1080 1180 205234742 205234842 3.630000e-23 121.0
41 TraesCS5D01G183000 chr1D 82.857 105 9 8 1922 2019 203067500 203067602 1.330000e-12 86.1
42 TraesCS5D01G183000 chr4B 87.097 62 7 1 1933 1994 436606734 436606794 1.330000e-07 69.4
43 TraesCS5D01G183000 chr4B 80.645 93 9 6 1933 2018 135541010 135540920 6.210000e-06 63.9
44 TraesCS5D01G183000 chr4B 80.645 93 9 6 1933 2018 436534908 436534998 6.210000e-06 63.9


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 TraesCS5D01G183000 chr5D 284892588 284900002 7414 False 13694.000000 13694 100.000000 1 7415 1 chr5D.!!$F1 7414
1 TraesCS5D01G183000 chr5B 322198807 322206322 7515 False 2766.000000 8272 92.223500 8 7200 4 chr5B.!!$F2 7192
2 TraesCS5D01G183000 chr5A 376463200 376470814 7614 False 1471.516667 4076 91.633667 18 7114 6 chr5A.!!$F1 7096

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
946 1426 0.040499 AGGTCTCTGTCCCTCTCCAC 59.960 60.000 0.00 0.0 0.00 4.02 F
1484 1965 0.110486 ATGTTGGACAAGGAGCGGTT 59.890 50.000 0.00 0.0 0.00 4.44 F
1757 2239 0.972883 AGGAAAGAAGTCTCTGCGCT 59.027 50.000 9.73 0.0 30.03 5.92 F
1906 2388 1.135746 GTTGCTTGCATCAGCTCAGAC 60.136 52.381 11.51 2.5 40.79 3.51 F
2792 3381 1.039856 GGCATTGGAAGTTGTGTGGT 58.960 50.000 0.00 0.0 0.00 4.16 F
3743 4608 1.539827 AGCGTATGTTGCAAAGAACCC 59.460 47.619 0.00 0.0 33.85 4.11 F
4303 5168 6.148811 TGGTTAGCAATAGCAACTTTAGTGTC 59.851 38.462 0.00 0.0 45.49 3.67 F
5270 6148 1.130373 CTGTCAGTCTCTCAGCTCGTC 59.870 57.143 0.00 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 2239 1.064463 CCAATAAGCAAGCCCCTGAGA 60.064 52.381 0.00 0.0 0.00 3.27 R
2379 2881 1.312815 GGTTCTGGCACATGGATAGC 58.687 55.000 0.00 0.0 38.20 2.97 R
2703 3205 2.547211 GTGCATCATGACTAGCCATCAC 59.453 50.000 12.45 0.0 0.00 3.06 R
3616 4469 2.949644 CGTCTCCTTCCCAGTTTGTTTT 59.050 45.455 0.00 0.0 0.00 2.43 R
4537 5402 3.899734 TGCACATTCTCCAAAAACATCG 58.100 40.909 0.00 0.0 0.00 3.84 R
4846 5718 1.633432 CCCCCTTCTTACCATCACACA 59.367 52.381 0.00 0.0 0.00 3.72 R
5957 6839 0.250038 GCAGCACACAGGAGACAAGA 60.250 55.000 0.00 0.0 0.00 3.02 R
6460 7456 0.249120 TTGGCCGAGATTCGACATGT 59.751 50.000 0.00 0.0 43.74 3.21 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
50 51 1.583495 GCGTTGGAGTTGCCCTTACC 61.583 60.000 0.00 0.00 34.97 2.85
73 74 3.744660 TCCTTTCTCTTGCCTTGAAGAC 58.255 45.455 0.00 0.00 0.00 3.01
100 101 6.266786 CCCCAAATTTAGTCAACCAAGTAAGT 59.733 38.462 0.00 0.00 0.00 2.24
108 109 6.229936 AGTCAACCAAGTAAGTACACTCAA 57.770 37.500 0.00 0.00 0.00 3.02
115 279 5.482908 CAAGTAAGTACACTCAAGATGCCT 58.517 41.667 0.00 0.00 0.00 4.75
116 280 5.746990 AGTAAGTACACTCAAGATGCCTT 57.253 39.130 0.00 0.00 0.00 4.35
152 316 3.754323 TCTTCCCAAACGCGTTAATCAAT 59.246 39.130 26.87 5.16 0.00 2.57
153 317 3.750639 TCCCAAACGCGTTAATCAATC 57.249 42.857 26.87 0.00 0.00 2.67
154 318 3.075148 TCCCAAACGCGTTAATCAATCA 58.925 40.909 26.87 1.10 0.00 2.57
155 319 3.502595 TCCCAAACGCGTTAATCAATCAA 59.497 39.130 26.87 1.37 0.00 2.57
293 457 1.844771 GCAGACACGAGCATGTGCAA 61.845 55.000 7.83 0.00 43.74 4.08
437 602 8.669243 CATCCACTAGCTTTTACTTTAAGGAAG 58.331 37.037 0.00 0.00 41.32 3.46
440 605 6.367969 CACTAGCTTTTACTTTAAGGAAGCGA 59.632 38.462 17.47 13.90 45.40 4.93
477 643 0.108396 AACCCAGTTGCCAATTTGCC 59.892 50.000 0.00 0.00 0.00 4.52
616 785 2.837591 TCCTGGCAGTAAATGAGCAGTA 59.162 45.455 14.43 0.00 0.00 2.74
706 926 2.265589 AACACCGGAAGTAAGTTGGG 57.734 50.000 9.46 0.00 0.00 4.12
789 1010 1.707427 AGGAGGGCTTCACAAATCACT 59.293 47.619 0.00 0.00 0.00 3.41
944 1424 1.006639 AGAAGGTCTCTGTCCCTCTCC 59.993 57.143 0.00 0.00 31.12 3.71
945 1425 0.787084 AAGGTCTCTGTCCCTCTCCA 59.213 55.000 0.00 0.00 0.00 3.86
946 1426 0.040499 AGGTCTCTGTCCCTCTCCAC 59.960 60.000 0.00 0.00 0.00 4.02
947 1427 0.973496 GGTCTCTGTCCCTCTCCACC 60.973 65.000 0.00 0.00 0.00 4.61
948 1428 0.973496 GTCTCTGTCCCTCTCCACCC 60.973 65.000 0.00 0.00 0.00 4.61
949 1429 1.687493 CTCTGTCCCTCTCCACCCC 60.687 68.421 0.00 0.00 0.00 4.95
950 1430 2.689034 CTGTCCCTCTCCACCCCC 60.689 72.222 0.00 0.00 0.00 5.40
951 1431 3.537506 TGTCCCTCTCCACCCCCA 61.538 66.667 0.00 0.00 0.00 4.96
952 1432 3.009714 GTCCCTCTCCACCCCCAC 61.010 72.222 0.00 0.00 0.00 4.61
953 1433 4.348495 TCCCTCTCCACCCCCACC 62.348 72.222 0.00 0.00 0.00 4.61
954 1434 4.354943 CCCTCTCCACCCCCACCT 62.355 72.222 0.00 0.00 0.00 4.00
955 1435 2.689034 CCTCTCCACCCCCACCTC 60.689 72.222 0.00 0.00 0.00 3.85
1327 1807 2.028925 TGCGCTTTCACTCGAGCA 59.971 55.556 13.61 0.00 38.81 4.26
1474 1955 0.167908 GAAATGCGCGATGTTGGACA 59.832 50.000 12.10 0.00 0.00 4.02
1484 1965 0.110486 ATGTTGGACAAGGAGCGGTT 59.890 50.000 0.00 0.00 0.00 4.44
1548 2029 4.019411 TGGTCTACTCATGGCAGATTTTGA 60.019 41.667 0.00 0.00 0.00 2.69
1573 2054 2.015587 CTTTGAGCTGGGAAGAGATGC 58.984 52.381 0.00 0.00 0.00 3.91
1635 2116 3.365472 ACAGTTTGAGGCTTTTGGTTCT 58.635 40.909 0.00 0.00 0.00 3.01
1665 2146 4.990526 AGGTCATTTTGTCTGATCTTGGT 58.009 39.130 0.00 0.00 29.74 3.67
1690 2171 2.031163 ACGCTGCAGGAACCAGAC 59.969 61.111 17.12 0.00 32.03 3.51
1749 2231 8.511604 TGATCCATTGAATAAGGAAAGAAGTC 57.488 34.615 0.00 0.00 34.62 3.01
1757 2239 0.972883 AGGAAAGAAGTCTCTGCGCT 59.027 50.000 9.73 0.00 30.03 5.92
1837 2319 5.060506 TGCTTTTCTTTAACGATGTCTGGA 58.939 37.500 0.00 0.00 0.00 3.86
1906 2388 1.135746 GTTGCTTGCATCAGCTCAGAC 60.136 52.381 11.51 2.50 40.79 3.51
1910 2392 3.005554 GCTTGCATCAGCTCAGACTTTA 58.994 45.455 3.04 0.00 42.74 1.85
1913 2395 5.563475 GCTTGCATCAGCTCAGACTTTAAAA 60.563 40.000 3.04 0.00 42.74 1.52
1966 2448 7.597288 AATATCGGATATCGGGTTCATATCA 57.403 36.000 10.77 0.00 35.64 2.15
2067 2550 9.897744 ACATCTGTTGAGTTATTTGTGTTTATG 57.102 29.630 0.00 0.00 0.00 1.90
2093 2576 5.290493 TGCCACTCCCACATAAATAGTAG 57.710 43.478 0.00 0.00 0.00 2.57
2271 2755 9.817809 AATCTGATGAAGTTGTACGTGTATATT 57.182 29.630 0.00 0.00 0.00 1.28
2300 2802 4.454161 TGGATAAAAATGACCTGTCACGTG 59.546 41.667 9.94 9.94 43.11 4.49
2379 2881 1.997874 AGGGGTGCCTGGAAGCTAG 60.998 63.158 3.45 0.00 0.00 3.42
2470 2972 3.637769 TGTTTGGGACTAAAGGCTTTGT 58.362 40.909 22.32 16.86 0.00 2.83
2471 2973 4.027437 TGTTTGGGACTAAAGGCTTTGTT 58.973 39.130 22.32 8.73 0.00 2.83
2472 2974 4.142049 TGTTTGGGACTAAAGGCTTTGTTG 60.142 41.667 22.32 13.85 0.00 3.33
2676 3178 3.243873 GGCAGAGTAACGATCATGGATGA 60.244 47.826 0.00 0.00 41.70 2.92
2703 3205 6.599244 AGTCATGGTGGTAAATTGTAGTCATG 59.401 38.462 0.00 0.00 0.00 3.07
2728 3314 2.705127 TGGCTAGTCATGATGCACCATA 59.295 45.455 16.31 0.00 0.00 2.74
2758 3347 5.053811 TGATAATGTTCGTTGTCAGTGTGT 58.946 37.500 1.20 0.00 0.00 3.72
2780 3369 2.050168 GCGTGTGTGTGGCATTGG 60.050 61.111 0.00 0.00 0.00 3.16
2792 3381 1.039856 GGCATTGGAAGTTGTGTGGT 58.960 50.000 0.00 0.00 0.00 4.16
2836 3425 4.024809 CGAAGTGGGTCTTTTTCTTCACTC 60.025 45.833 0.00 0.00 36.40 3.51
2909 3498 7.438160 GCTTTAAACCATTATAGTCAATTGCCC 59.562 37.037 0.00 0.00 0.00 5.36
2961 3550 8.057742 GTGATTGTTAATGTTGCTTTTTCTGTG 58.942 33.333 0.00 0.00 0.00 3.66
3071 3719 9.818796 GATTTCTGTGACTATTTTTCTCAAGTC 57.181 33.333 0.00 0.00 39.04 3.01
3267 4118 2.583593 GGGCACGACGATCTCTGC 60.584 66.667 0.00 0.00 0.00 4.26
3532 4385 5.939764 TCTTCAGGTACTTCTGCATACAT 57.060 39.130 0.00 0.00 34.60 2.29
3616 4469 3.517901 ACGACCAGAAATACAGAATGGGA 59.482 43.478 0.00 0.00 43.62 4.37
3677 4533 9.780186 AAGATGGTAAGTAATATAAAGCAGTCC 57.220 33.333 0.00 0.00 0.00 3.85
3743 4608 1.539827 AGCGTATGTTGCAAAGAACCC 59.460 47.619 0.00 0.00 33.85 4.11
4303 5168 6.148811 TGGTTAGCAATAGCAACTTTAGTGTC 59.851 38.462 0.00 0.00 45.49 3.67
4846 5718 4.811024 CACATACGGCTGTTCATGTCTATT 59.189 41.667 10.54 0.00 27.29 1.73
5270 6148 1.130373 CTGTCAGTCTCTCAGCTCGTC 59.870 57.143 0.00 0.00 0.00 4.20
5363 6241 4.454161 ACGCACTGATTAATGCAGTTTGTA 59.546 37.500 14.21 0.00 43.67 2.41
5576 6454 8.940397 TCTGATAGAAAACCTCTGGAAAATTT 57.060 30.769 0.00 0.00 35.41 1.82
5650 6528 1.474330 CCCAATTTGCAGGGTCCTAC 58.526 55.000 0.44 0.00 40.34 3.18
5939 6821 4.686839 GGTAACTTTGACTGCTTCATCC 57.313 45.455 0.00 0.00 32.84 3.51
5940 6822 4.072131 GGTAACTTTGACTGCTTCATCCA 58.928 43.478 0.00 0.00 32.84 3.41
5953 6835 7.743749 ACTGCTTCATCCATCATATTCTTAGT 58.256 34.615 0.00 0.00 0.00 2.24
5954 6836 8.216423 ACTGCTTCATCCATCATATTCTTAGTT 58.784 33.333 0.00 0.00 0.00 2.24
5955 6837 8.985315 TGCTTCATCCATCATATTCTTAGTTT 57.015 30.769 0.00 0.00 0.00 2.66
5956 6838 9.412460 TGCTTCATCCATCATATTCTTAGTTTT 57.588 29.630 0.00 0.00 0.00 2.43
5999 6881 5.350633 CCAGACAAGAAGAATTTGTTTGCA 58.649 37.500 3.85 0.00 38.56 4.08
6001 6883 6.480981 CCAGACAAGAAGAATTTGTTTGCAAT 59.519 34.615 0.00 0.00 38.56 3.56
6002 6884 7.342194 CAGACAAGAAGAATTTGTTTGCAATG 58.658 34.615 0.00 0.00 38.78 2.82
6003 6885 6.018507 AGACAAGAAGAATTTGTTTGCAATGC 60.019 34.615 0.00 0.00 38.78 3.56
6018 7014 4.009675 TGCAATGCTTAAGGTTGGAGTAG 58.990 43.478 6.82 0.00 0.00 2.57
6022 7018 6.177610 CAATGCTTAAGGTTGGAGTAGGTTA 58.822 40.000 4.29 0.00 0.00 2.85
6026 7022 3.329929 AAGGTTGGAGTAGGTTAAGCG 57.670 47.619 0.00 0.00 0.00 4.68
6035 7031 5.100943 GGAGTAGGTTAAGCGTTGAAGTAG 58.899 45.833 0.00 0.00 0.00 2.57
6051 7047 6.566079 TGAAGTAGGAATGAGATGTCCATT 57.434 37.500 0.00 0.00 36.28 3.16
6074 7070 1.566018 CGACACCTGACCGCCTTTTC 61.566 60.000 0.00 0.00 0.00 2.29
6075 7071 1.566018 GACACCTGACCGCCTTTTCG 61.566 60.000 0.00 0.00 0.00 3.46
6091 7087 5.105675 GCCTTTTCGGTTTCCACCATAAATA 60.106 40.000 0.00 0.00 44.53 1.40
6180 7176 1.219124 GGCCTGCAAGATCGTCTCA 59.781 57.895 0.00 0.00 34.07 3.27
6330 7326 1.307355 CGATCAACATGCACAGCCCA 61.307 55.000 0.00 0.00 0.00 5.36
6416 7412 0.390866 CGCAAGTCATCCTGCTGAGT 60.391 55.000 0.00 0.00 0.00 3.41
6417 7413 1.367659 GCAAGTCATCCTGCTGAGTC 58.632 55.000 0.00 0.00 0.00 3.36
6419 7415 1.277273 CAAGTCATCCTGCTGAGTCCA 59.723 52.381 0.00 0.00 0.00 4.02
6423 7419 3.149196 GTCATCCTGCTGAGTCCAAAAA 58.851 45.455 0.00 0.00 0.00 1.94
6460 7456 5.357314 AGTTAGCTTAATCGTCTGCTGTAGA 59.643 40.000 0.00 0.00 37.02 2.59
6486 7482 2.429250 TCGAATCTCGGCCAATCTGTAA 59.571 45.455 2.24 0.00 40.88 2.41
6487 7483 3.118920 TCGAATCTCGGCCAATCTGTAAA 60.119 43.478 2.24 0.00 40.88 2.01
6488 7484 3.001330 CGAATCTCGGCCAATCTGTAAAC 59.999 47.826 2.24 0.00 36.00 2.01
6489 7485 3.914426 ATCTCGGCCAATCTGTAAACT 57.086 42.857 2.24 0.00 0.00 2.66
6490 7486 2.972625 TCTCGGCCAATCTGTAAACTG 58.027 47.619 2.24 0.00 0.00 3.16
6491 7487 2.565391 TCTCGGCCAATCTGTAAACTGA 59.435 45.455 2.24 0.00 0.00 3.41
6492 7488 2.673368 CTCGGCCAATCTGTAAACTGAC 59.327 50.000 2.24 0.00 0.00 3.51
6493 7489 1.393539 CGGCCAATCTGTAAACTGACG 59.606 52.381 2.24 0.00 0.00 4.35
6494 7490 1.130561 GGCCAATCTGTAAACTGACGC 59.869 52.381 0.00 0.00 0.00 5.19
6495 7491 1.130561 GCCAATCTGTAAACTGACGCC 59.869 52.381 0.00 0.00 0.00 5.68
6496 7492 2.422597 CCAATCTGTAAACTGACGCCA 58.577 47.619 0.00 0.00 0.00 5.69
6497 7493 2.811431 CCAATCTGTAAACTGACGCCAA 59.189 45.455 0.00 0.00 0.00 4.52
6498 7494 3.440173 CCAATCTGTAAACTGACGCCAAT 59.560 43.478 0.00 0.00 0.00 3.16
6499 7495 4.437390 CCAATCTGTAAACTGACGCCAATC 60.437 45.833 0.00 0.00 0.00 2.67
6500 7496 3.678056 TCTGTAAACTGACGCCAATCT 57.322 42.857 0.00 0.00 0.00 2.40
6501 7497 3.325870 TCTGTAAACTGACGCCAATCTG 58.674 45.455 0.00 0.00 0.00 2.90
6502 7498 3.067106 CTGTAAACTGACGCCAATCTGT 58.933 45.455 0.00 0.00 32.66 3.41
6503 7499 4.021807 TCTGTAAACTGACGCCAATCTGTA 60.022 41.667 0.00 0.00 31.24 2.74
6752 7748 0.742281 CCTGCGCATGTAAGCACTCT 60.742 55.000 12.24 0.00 38.59 3.24
6763 7759 0.536006 AAGCACTCTGGTGTTCCTGC 60.536 55.000 0.00 0.00 44.65 4.85
6790 7786 4.362279 TCATTTGCTTCAGTTTTGAGTGC 58.638 39.130 0.00 0.00 36.10 4.40
6868 7865 9.004231 ACTACTCCCTCTATTCCAAAATGTAAT 57.996 33.333 0.00 0.00 0.00 1.89
7061 8225 6.682746 TCACACTCTCAGAAAACAGATACTC 58.317 40.000 0.00 0.00 0.00 2.59
7126 8290 0.529833 ACGAGAGTCAGCATCACCTG 59.470 55.000 0.00 0.00 44.19 4.00
7132 8296 2.429971 GAGTCAGCATCACCTGATCTGA 59.570 50.000 0.38 10.75 43.19 3.27
7133 8297 2.836372 AGTCAGCATCACCTGATCTGAA 59.164 45.455 14.08 0.00 43.19 3.02
7135 8299 3.808726 GTCAGCATCACCTGATCTGAATC 59.191 47.826 14.08 5.24 43.19 2.52
7144 8308 3.007940 ACCTGATCTGAATCGACAACCAA 59.992 43.478 0.38 0.00 34.39 3.67
7192 8356 5.782738 GAGAGAGCTCACAGCATTCAGCA 62.783 52.174 17.77 0.00 45.56 4.41
7200 8364 2.882876 GCATTCAGCAGGTGCAGG 59.117 61.111 4.48 0.00 45.16 4.85
7201 8365 1.975407 GCATTCAGCAGGTGCAGGT 60.975 57.895 4.48 0.00 45.16 4.00
7202 8366 1.530013 GCATTCAGCAGGTGCAGGTT 61.530 55.000 4.48 0.00 45.16 3.50
7203 8367 0.524862 CATTCAGCAGGTGCAGGTTC 59.475 55.000 4.48 0.00 45.16 3.62
7204 8368 0.111061 ATTCAGCAGGTGCAGGTTCA 59.889 50.000 4.48 0.00 45.16 3.18
7205 8369 0.535780 TTCAGCAGGTGCAGGTTCAG 60.536 55.000 4.48 0.00 45.16 3.02
7206 8370 1.970114 CAGCAGGTGCAGGTTCAGG 60.970 63.158 4.48 0.00 45.16 3.86
7207 8371 2.113986 GCAGGTGCAGGTTCAGGT 59.886 61.111 0.00 0.00 41.59 4.00
7208 8372 1.529244 GCAGGTGCAGGTTCAGGTT 60.529 57.895 0.00 0.00 41.59 3.50
7209 8373 1.518903 GCAGGTGCAGGTTCAGGTTC 61.519 60.000 0.00 0.00 41.59 3.62
7210 8374 0.890996 CAGGTGCAGGTTCAGGTTCC 60.891 60.000 0.00 0.00 0.00 3.62
7211 8375 1.150536 GGTGCAGGTTCAGGTTCCA 59.849 57.895 0.00 0.00 0.00 3.53
7212 8376 0.251341 GGTGCAGGTTCAGGTTCCAT 60.251 55.000 0.00 0.00 0.00 3.41
7213 8377 1.168714 GTGCAGGTTCAGGTTCCATC 58.831 55.000 0.00 0.00 0.00 3.51
7214 8378 0.038166 TGCAGGTTCAGGTTCCATCC 59.962 55.000 0.00 0.00 0.00 3.51
7215 8379 0.681243 GCAGGTTCAGGTTCCATCCC 60.681 60.000 0.00 0.00 0.00 3.85
7216 8380 0.034089 CAGGTTCAGGTTCCATCCCC 60.034 60.000 0.00 0.00 0.00 4.81
7217 8381 0.477597 AGGTTCAGGTTCCATCCCCA 60.478 55.000 0.00 0.00 0.00 4.96
7218 8382 0.407918 GGTTCAGGTTCCATCCCCAA 59.592 55.000 0.00 0.00 0.00 4.12
7219 8383 1.545841 GTTCAGGTTCCATCCCCAAC 58.454 55.000 0.00 0.00 0.00 3.77
7220 8384 0.407918 TTCAGGTTCCATCCCCAACC 59.592 55.000 0.00 0.00 42.26 3.77
7221 8385 1.378514 CAGGTTCCATCCCCAACCG 60.379 63.158 0.00 0.00 45.92 4.44
7222 8386 2.754254 GGTTCCATCCCCAACCGC 60.754 66.667 0.00 0.00 33.01 5.68
7223 8387 2.754254 GTTCCATCCCCAACCGCC 60.754 66.667 0.00 0.00 0.00 6.13
7224 8388 4.418328 TTCCATCCCCAACCGCCG 62.418 66.667 0.00 0.00 0.00 6.46
7274 8438 4.559063 CCCAGCGCTGATCCAGGG 62.559 72.222 38.06 25.37 45.35 4.45
7299 8463 3.499737 GCGTCACGGCATCCCTTG 61.500 66.667 0.00 0.00 0.00 3.61
7300 8464 2.047274 CGTCACGGCATCCCTTGT 60.047 61.111 0.00 0.00 32.48 3.16
7301 8465 2.390599 CGTCACGGCATCCCTTGTG 61.391 63.158 0.00 0.00 32.48 3.33
7302 8466 1.003839 GTCACGGCATCCCTTGTGA 60.004 57.895 0.00 0.00 38.91 3.58
7303 8467 1.021390 GTCACGGCATCCCTTGTGAG 61.021 60.000 0.00 0.00 41.59 3.51
7304 8468 1.746615 CACGGCATCCCTTGTGAGG 60.747 63.158 0.00 0.00 43.15 3.86
7305 8469 2.825836 CGGCATCCCTTGTGAGGC 60.826 66.667 0.00 0.00 42.09 4.70
7306 8470 2.825836 GGCATCCCTTGTGAGGCG 60.826 66.667 0.00 0.00 42.69 5.52
7307 8471 2.825836 GCATCCCTTGTGAGGCGG 60.826 66.667 0.00 0.00 42.09 6.13
7308 8472 2.989639 CATCCCTTGTGAGGCGGA 59.010 61.111 0.00 0.00 42.09 5.54
7309 8473 1.153289 CATCCCTTGTGAGGCGGAG 60.153 63.158 0.00 0.00 42.09 4.63
7310 8474 2.370445 ATCCCTTGTGAGGCGGAGG 61.370 63.158 0.00 0.00 42.09 4.30
7311 8475 2.822643 ATCCCTTGTGAGGCGGAGGA 62.823 60.000 0.00 0.00 42.09 3.71
7312 8476 2.581354 CCTTGTGAGGCGGAGGAG 59.419 66.667 0.00 0.00 35.94 3.69
7313 8477 2.581354 CTTGTGAGGCGGAGGAGG 59.419 66.667 0.00 0.00 0.00 4.30
7314 8478 2.203788 TTGTGAGGCGGAGGAGGT 60.204 61.111 0.00 0.00 0.00 3.85
7315 8479 2.513026 CTTGTGAGGCGGAGGAGGTG 62.513 65.000 0.00 0.00 0.00 4.00
7316 8480 2.997897 GTGAGGCGGAGGAGGTGT 60.998 66.667 0.00 0.00 0.00 4.16
7317 8481 2.203788 TGAGGCGGAGGAGGTGTT 60.204 61.111 0.00 0.00 0.00 3.32
7318 8482 1.841556 TGAGGCGGAGGAGGTGTTT 60.842 57.895 0.00 0.00 0.00 2.83
7319 8483 1.079057 GAGGCGGAGGAGGTGTTTC 60.079 63.158 0.00 0.00 0.00 2.78
7320 8484 1.827399 GAGGCGGAGGAGGTGTTTCA 61.827 60.000 0.00 0.00 0.00 2.69
7321 8485 1.201429 AGGCGGAGGAGGTGTTTCAT 61.201 55.000 0.00 0.00 0.00 2.57
7322 8486 1.026718 GGCGGAGGAGGTGTTTCATG 61.027 60.000 0.00 0.00 0.00 3.07
7323 8487 1.648467 GCGGAGGAGGTGTTTCATGC 61.648 60.000 0.00 0.00 0.00 4.06
7324 8488 1.361668 CGGAGGAGGTGTTTCATGCG 61.362 60.000 0.00 0.00 36.47 4.73
7325 8489 1.026718 GGAGGAGGTGTTTCATGCGG 61.027 60.000 0.00 0.00 0.00 5.69
7326 8490 1.002134 AGGAGGTGTTTCATGCGGG 60.002 57.895 0.00 0.00 0.00 6.13
7327 8491 2.046285 GGAGGTGTTTCATGCGGGG 61.046 63.158 0.00 0.00 0.00 5.73
7328 8492 1.002624 GAGGTGTTTCATGCGGGGA 60.003 57.895 0.00 0.00 0.00 4.81
7329 8493 1.002134 AGGTGTTTCATGCGGGGAG 60.002 57.895 0.00 0.00 0.00 4.30
7330 8494 2.046285 GGTGTTTCATGCGGGGAGG 61.046 63.158 0.00 0.00 0.00 4.30
7331 8495 2.361104 TGTTTCATGCGGGGAGGC 60.361 61.111 0.00 0.00 0.00 4.70
7332 8496 3.140814 GTTTCATGCGGGGAGGCC 61.141 66.667 0.00 0.00 0.00 5.19
7333 8497 4.794648 TTTCATGCGGGGAGGCCG 62.795 66.667 0.00 0.00 0.00 6.13
7348 8512 4.157120 CCGGGGGCGGTAGTCAAG 62.157 72.222 0.00 0.00 0.00 3.02
7349 8513 4.157120 CGGGGGCGGTAGTCAAGG 62.157 72.222 0.00 0.00 0.00 3.61
7350 8514 4.484872 GGGGGCGGTAGTCAAGGC 62.485 72.222 0.00 0.00 0.00 4.35
7351 8515 4.832608 GGGGCGGTAGTCAAGGCG 62.833 72.222 0.00 0.00 0.00 5.52
7352 8516 4.832608 GGGCGGTAGTCAAGGCGG 62.833 72.222 0.00 0.00 0.00 6.13
7353 8517 4.078516 GGCGGTAGTCAAGGCGGT 62.079 66.667 0.00 0.00 0.00 5.68
7354 8518 2.813908 GCGGTAGTCAAGGCGGTG 60.814 66.667 0.00 0.00 0.00 4.94
7355 8519 2.813908 CGGTAGTCAAGGCGGTGC 60.814 66.667 0.00 0.00 0.00 5.01
7383 8547 4.554363 CGGCGGCGATCGAAGTCT 62.554 66.667 29.19 0.00 42.43 3.24
7384 8548 2.655685 GGCGGCGATCGAAGTCTC 60.656 66.667 21.57 0.00 42.43 3.36
7385 8549 2.655685 GCGGCGATCGAAGTCTCC 60.656 66.667 21.57 8.28 42.43 3.71
7386 8550 2.798689 CGGCGATCGAAGTCTCCA 59.201 61.111 21.57 0.00 42.43 3.86
7387 8551 1.360551 CGGCGATCGAAGTCTCCAT 59.639 57.895 21.57 0.00 42.43 3.41
7388 8552 0.936764 CGGCGATCGAAGTCTCCATG 60.937 60.000 21.57 0.00 42.43 3.66
7389 8553 0.598680 GGCGATCGAAGTCTCCATGG 60.599 60.000 21.57 4.97 0.00 3.66
7390 8554 1.218230 GCGATCGAAGTCTCCATGGC 61.218 60.000 21.57 0.00 0.00 4.40
7391 8555 0.598680 CGATCGAAGTCTCCATGGCC 60.599 60.000 10.26 0.00 0.00 5.36
7392 8556 0.598680 GATCGAAGTCTCCATGGCCG 60.599 60.000 6.96 0.01 0.00 6.13
7393 8557 2.032860 ATCGAAGTCTCCATGGCCGG 62.033 60.000 6.96 0.00 0.00 6.13
7394 8558 2.514824 GAAGTCTCCATGGCCGGC 60.515 66.667 21.18 21.18 0.00 6.13
7395 8559 4.473520 AAGTCTCCATGGCCGGCG 62.474 66.667 22.54 6.52 0.00 6.46
7407 8571 3.461773 CCGGCGGTGACCTGAGAT 61.462 66.667 19.97 0.00 0.00 2.75
7408 8572 2.579201 CGGCGGTGACCTGAGATT 59.421 61.111 0.00 0.00 0.00 2.40
7409 8573 1.811266 CGGCGGTGACCTGAGATTG 60.811 63.158 0.00 0.00 0.00 2.67
7410 8574 1.450312 GGCGGTGACCTGAGATTGG 60.450 63.158 0.00 0.00 0.00 3.16
7411 8575 1.450312 GCGGTGACCTGAGATTGGG 60.450 63.158 0.00 0.00 0.00 4.12
7412 8576 1.983224 CGGTGACCTGAGATTGGGT 59.017 57.895 0.00 0.00 38.70 4.51
7413 8577 0.391661 CGGTGACCTGAGATTGGGTG 60.392 60.000 0.00 0.00 35.77 4.61
7414 8578 0.035056 GGTGACCTGAGATTGGGTGG 60.035 60.000 0.00 0.00 35.77 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.536498 CTGTTCGTTTGGGCGGCAC 62.536 63.158 12.47 0.00 0.00 5.01
3 4 3.283684 CTGTTCGTTTGGGCGGCA 61.284 61.111 12.47 0.00 0.00 5.69
4 5 2.975799 TCTGTTCGTTTGGGCGGC 60.976 61.111 0.00 0.00 0.00 6.53
5 6 1.234615 ATGTCTGTTCGTTTGGGCGG 61.235 55.000 0.00 0.00 0.00 6.13
6 7 0.110238 CATGTCTGTTCGTTTGGGCG 60.110 55.000 0.00 0.00 0.00 6.13
50 51 2.867109 TCAAGGCAAGAGAAAGGAGG 57.133 50.000 0.00 0.00 0.00 4.30
73 74 4.343814 ACTTGGTTGACTAAATTTGGGGTG 59.656 41.667 6.50 0.00 0.00 4.61
100 101 5.769662 ACATGAAAAAGGCATCTTGAGTGTA 59.230 36.000 0.00 0.00 32.75 2.90
108 109 7.059202 AGAGAAAAACATGAAAAAGGCATCT 57.941 32.000 0.00 0.00 0.00 2.90
115 279 7.064016 CGTTTGGGAAGAGAAAAACATGAAAAA 59.936 33.333 0.00 0.00 33.16 1.94
116 280 6.533367 CGTTTGGGAAGAGAAAAACATGAAAA 59.467 34.615 0.00 0.00 33.16 2.29
437 602 5.911280 GGTTTAGTTTACTCTGGTTTTTCGC 59.089 40.000 0.00 0.00 0.00 4.70
440 605 6.893554 ACTGGGTTTAGTTTACTCTGGTTTTT 59.106 34.615 0.00 0.00 0.00 1.94
477 643 0.029300 CTGTGCGTGTTTGGTGAAGG 59.971 55.000 0.00 0.00 0.00 3.46
510 676 4.486503 CAGCAGCTCCCTCTGGCC 62.487 72.222 0.00 0.00 34.74 5.36
564 733 3.292481 ATGAGCCCCTGGTTGCTGG 62.292 63.158 12.12 0.00 38.11 4.85
616 785 6.179906 TCCAGAGAGAAATGAAGAACTTGT 57.820 37.500 0.00 0.00 0.00 3.16
737 958 3.198409 TGGTGATTAGCGCAGATCAAT 57.802 42.857 22.10 8.62 34.34 2.57
789 1010 1.152860 CCTCTCTCTAGCTCGCCCA 60.153 63.158 0.00 0.00 0.00 5.36
812 1039 2.265904 GGTGGTTTGTTCCCCTCGC 61.266 63.158 0.00 0.00 0.00 5.03
944 1424 3.330720 GAGGTGGAGGTGGGGGTG 61.331 72.222 0.00 0.00 0.00 4.61
945 1425 4.677151 GGAGGTGGAGGTGGGGGT 62.677 72.222 0.00 0.00 0.00 4.95
950 1430 3.775654 GAGGCGGAGGTGGAGGTG 61.776 72.222 0.00 0.00 0.00 4.00
953 1433 4.787280 AGGGAGGCGGAGGTGGAG 62.787 72.222 0.00 0.00 0.00 3.86
954 1434 4.332543 AAGGGAGGCGGAGGTGGA 62.333 66.667 0.00 0.00 0.00 4.02
955 1435 3.787001 GAAGGGAGGCGGAGGTGG 61.787 72.222 0.00 0.00 0.00 4.61
1378 1858 1.299541 AAACTTGAGCACAGACACCG 58.700 50.000 0.00 0.00 0.00 4.94
1474 1955 1.875963 CGCAAATGAACCGCTCCTT 59.124 52.632 0.00 0.00 0.00 3.36
1484 1965 2.355756 GCTGAATCCTAAGCGCAAATGA 59.644 45.455 11.47 0.34 0.00 2.57
1548 2029 1.076024 TCTTCCCAGCTCAAAGGCAAT 59.924 47.619 0.00 0.00 34.17 3.56
1553 2034 2.015587 GCATCTCTTCCCAGCTCAAAG 58.984 52.381 0.00 0.00 0.00 2.77
1635 2116 6.957920 TCAGACAAAATGACCTTTTCATCA 57.042 33.333 0.00 0.00 44.86 3.07
1654 2135 2.783135 GTGCTGGAAACCAAGATCAGA 58.217 47.619 0.00 0.00 30.80 3.27
1749 2231 4.527583 GCCCCTGAGAGCGCAGAG 62.528 72.222 11.47 0.00 38.14 3.35
1757 2239 1.064463 CCAATAAGCAAGCCCCTGAGA 60.064 52.381 0.00 0.00 0.00 3.27
1770 2252 2.816087 CGATCCTTGCATCCCCAATAAG 59.184 50.000 0.00 0.00 0.00 1.73
1913 2395 4.098501 GCTTGTCCATAGCTGCCTATTTTT 59.901 41.667 0.00 0.00 35.74 1.94
1917 2399 2.053244 AGCTTGTCCATAGCTGCCTAT 58.947 47.619 0.00 0.00 46.71 2.57
1940 2422 7.926018 TGATATGAACCCGATATCCGATATTTG 59.074 37.037 2.36 0.00 41.76 2.32
1966 2448 2.550978 CGATATTGCCAAGGTCGAACT 58.449 47.619 0.00 0.00 34.46 3.01
2001 2483 2.626266 ACGCCTACACATCATCCGATAA 59.374 45.455 0.00 0.00 0.00 1.75
2067 2550 2.418368 TTATGTGGGAGTGGCATGAC 57.582 50.000 0.00 0.00 0.00 3.06
2271 2755 8.141268 GTGACAGGTCATTTTTATCCAGAAAAA 58.859 33.333 5.29 0.00 42.18 1.94
2379 2881 1.312815 GGTTCTGGCACATGGATAGC 58.687 55.000 0.00 0.00 38.20 2.97
2463 2965 3.496507 ACAACAACAACAACAACAAAGCC 59.503 39.130 0.00 0.00 0.00 4.35
2470 2972 8.082852 ACTATACAACAACAACAACAACAACAA 58.917 29.630 0.00 0.00 0.00 2.83
2471 2973 7.594714 ACTATACAACAACAACAACAACAACA 58.405 30.769 0.00 0.00 0.00 3.33
2472 2974 8.369588 CAACTATACAACAACAACAACAACAAC 58.630 33.333 0.00 0.00 0.00 3.32
2650 3152 3.525537 CATGATCGTTACTCTGCCAAGT 58.474 45.455 0.00 0.00 0.00 3.16
2676 3178 7.857456 TGACTACAATTTACCACCATGACTAT 58.143 34.615 0.00 0.00 0.00 2.12
2703 3205 2.547211 GTGCATCATGACTAGCCATCAC 59.453 50.000 12.45 0.00 0.00 3.06
2711 3297 6.423776 TCAAGATATGGTGCATCATGACTA 57.576 37.500 22.92 2.26 28.17 2.59
2728 3314 7.550551 ACTGACAACGAACATTATCATCAAGAT 59.449 33.333 0.00 0.00 40.86 2.40
2780 3369 6.348540 CCTTTCTGCTATTACCACACAACTTC 60.349 42.308 0.00 0.00 0.00 3.01
2792 3381 6.040209 TCGTAAACCACCTTTCTGCTATTA 57.960 37.500 0.00 0.00 0.00 0.98
2860 3449 8.845413 AGCAATTGAAACCAAATAAAATAGCA 57.155 26.923 10.34 0.00 0.00 3.49
3229 4080 3.640967 CCCAGGAACCAAGATTCAAAACA 59.359 43.478 0.00 0.00 0.00 2.83
3267 4118 6.510879 ACAAGCATATGGATATCATGCAAG 57.489 37.500 21.84 16.89 45.95 4.01
3616 4469 2.949644 CGTCTCCTTCCCAGTTTGTTTT 59.050 45.455 0.00 0.00 0.00 2.43
3743 4608 5.067805 ACCTTTCAAGAAGTTTGCACTAAGG 59.932 40.000 0.00 0.00 30.68 2.69
4537 5402 3.899734 TGCACATTCTCCAAAAACATCG 58.100 40.909 0.00 0.00 0.00 3.84
4846 5718 1.633432 CCCCCTTCTTACCATCACACA 59.367 52.381 0.00 0.00 0.00 3.72
4876 5754 6.323996 GTCCCTAAAATAAAAGCAATAGCCCT 59.676 38.462 0.00 0.00 43.56 5.19
4999 5877 3.868757 TCTACCGTTGATTGGACTCAG 57.131 47.619 0.00 0.00 0.00 3.35
5270 6148 2.653890 CAAGGACACAACAAATGAGCG 58.346 47.619 0.00 0.00 0.00 5.03
5363 6241 7.884877 TGGTGATTGACAAGAAGAAATCATACT 59.115 33.333 0.00 0.00 40.20 2.12
5535 6413 7.141758 TCTATCAGAAATGGCAAGACCTAAT 57.858 36.000 0.00 0.00 40.22 1.73
5576 6454 7.453393 AGTCAGAAATGACATGACCTAAAAGA 58.547 34.615 10.72 0.00 43.47 2.52
5756 6634 8.471609 TCGTAAATGTAGTCATATTCTTCCACA 58.528 33.333 0.00 0.00 33.49 4.17
5757 6635 8.867112 TCGTAAATGTAGTCATATTCTTCCAC 57.133 34.615 0.00 0.00 33.49 4.02
5786 6664 9.979578 CTCTTTCAGATAGCACTATCAAAGTAT 57.020 33.333 17.62 0.00 43.27 2.12
5852 6734 4.398319 TCAGGGCTTCTTTAACTTCTTGG 58.602 43.478 0.00 0.00 0.00 3.61
5953 6835 3.378112 CAGCACACAGGAGACAAGAAAAA 59.622 43.478 0.00 0.00 0.00 1.94
5954 6836 2.945008 CAGCACACAGGAGACAAGAAAA 59.055 45.455 0.00 0.00 0.00 2.29
5955 6837 2.564771 CAGCACACAGGAGACAAGAAA 58.435 47.619 0.00 0.00 0.00 2.52
5956 6838 1.811558 GCAGCACACAGGAGACAAGAA 60.812 52.381 0.00 0.00 0.00 2.52
5957 6839 0.250038 GCAGCACACAGGAGACAAGA 60.250 55.000 0.00 0.00 0.00 3.02
5958 6840 1.233285 GGCAGCACACAGGAGACAAG 61.233 60.000 0.00 0.00 0.00 3.16
5999 6881 4.929146 ACCTACTCCAACCTTAAGCATT 57.071 40.909 0.00 0.00 0.00 3.56
6001 6883 5.801380 CTTAACCTACTCCAACCTTAAGCA 58.199 41.667 0.00 0.00 0.00 3.91
6002 6884 4.634883 GCTTAACCTACTCCAACCTTAAGC 59.365 45.833 0.00 0.00 39.01 3.09
6003 6885 4.868734 CGCTTAACCTACTCCAACCTTAAG 59.131 45.833 0.00 0.00 0.00 1.85
6018 7014 4.933400 TCATTCCTACTTCAACGCTTAACC 59.067 41.667 0.00 0.00 0.00 2.85
6022 7018 4.537135 TCTCATTCCTACTTCAACGCTT 57.463 40.909 0.00 0.00 0.00 4.68
6026 7022 5.734720 TGGACATCTCATTCCTACTTCAAC 58.265 41.667 0.00 0.00 32.55 3.18
6035 7031 4.508124 GTCGTGTAATGGACATCTCATTCC 59.492 45.833 0.00 0.00 41.14 3.01
6051 7047 2.646719 GCGGTCAGGTGTCGTGTA 59.353 61.111 0.00 0.00 0.00 2.90
6074 7070 5.592688 ACCTGATTATTTATGGTGGAAACCG 59.407 40.000 0.00 0.00 0.00 4.44
6075 7071 7.123547 TGAACCTGATTATTTATGGTGGAAACC 59.876 37.037 0.00 0.00 0.00 3.27
6091 7087 3.087031 CCACATGCTTCTGAACCTGATT 58.913 45.455 0.00 0.00 0.00 2.57
6180 7176 2.881389 CTCGAGGCGAACTGCTCT 59.119 61.111 3.91 0.00 45.43 4.09
6330 7326 3.342477 GGAGAAGGCTTGCCCCCT 61.342 66.667 3.46 5.60 0.00 4.79
6416 7412 4.294347 ACTTTTCCACCCAGATTTTTGGA 58.706 39.130 0.00 0.00 40.87 3.53
6417 7413 4.687901 ACTTTTCCACCCAGATTTTTGG 57.312 40.909 0.00 0.00 38.00 3.28
6419 7415 5.602561 AGCTAACTTTTCCACCCAGATTTTT 59.397 36.000 0.00 0.00 0.00 1.94
6423 7419 4.388577 AAGCTAACTTTTCCACCCAGAT 57.611 40.909 0.00 0.00 29.41 2.90
6460 7456 0.249120 TTGGCCGAGATTCGACATGT 59.751 50.000 0.00 0.00 43.74 3.21
6486 7482 3.498397 CAGTTTACAGATTGGCGTCAGTT 59.502 43.478 0.00 0.00 0.00 3.16
6487 7483 3.067106 CAGTTTACAGATTGGCGTCAGT 58.933 45.455 0.00 0.00 0.00 3.41
6488 7484 3.123621 GTCAGTTTACAGATTGGCGTCAG 59.876 47.826 0.00 0.00 0.00 3.51
6489 7485 3.064207 GTCAGTTTACAGATTGGCGTCA 58.936 45.455 0.00 0.00 0.00 4.35
6490 7486 3.326747 AGTCAGTTTACAGATTGGCGTC 58.673 45.455 0.00 0.00 0.00 5.19
6491 7487 3.006967 AGAGTCAGTTTACAGATTGGCGT 59.993 43.478 0.00 0.00 0.00 5.68
6492 7488 3.589988 AGAGTCAGTTTACAGATTGGCG 58.410 45.455 0.00 0.00 0.00 5.69
6493 7489 4.757149 ACAAGAGTCAGTTTACAGATTGGC 59.243 41.667 0.00 0.00 0.00 4.52
6494 7490 6.867662 AACAAGAGTCAGTTTACAGATTGG 57.132 37.500 0.00 0.00 0.00 3.16
6495 7491 8.147642 AGAAACAAGAGTCAGTTTACAGATTG 57.852 34.615 12.06 0.00 38.01 2.67
6496 7492 8.207545 AGAGAAACAAGAGTCAGTTTACAGATT 58.792 33.333 12.06 0.00 38.01 2.40
6497 7493 7.731054 AGAGAAACAAGAGTCAGTTTACAGAT 58.269 34.615 12.06 0.43 38.01 2.90
6498 7494 7.113658 AGAGAAACAAGAGTCAGTTTACAGA 57.886 36.000 12.06 0.00 38.01 3.41
6499 7495 7.625553 CAAGAGAAACAAGAGTCAGTTTACAG 58.374 38.462 12.06 5.51 38.01 2.74
6500 7496 6.037172 GCAAGAGAAACAAGAGTCAGTTTACA 59.963 38.462 12.06 0.00 38.01 2.41
6501 7497 6.423042 GCAAGAGAAACAAGAGTCAGTTTAC 58.577 40.000 12.06 9.99 38.01 2.01
6502 7498 5.527582 GGCAAGAGAAACAAGAGTCAGTTTA 59.472 40.000 12.06 0.00 38.01 2.01
6503 7499 4.336713 GGCAAGAGAAACAAGAGTCAGTTT 59.663 41.667 11.96 11.96 40.38 2.66
6678 7674 8.522830 GGAAATGTGGTAAATGGATATATGTGG 58.477 37.037 0.00 0.00 0.00 4.17
6752 7748 2.359850 GATGCGGCAGGAACACCA 60.360 61.111 9.25 0.00 0.00 4.17
6824 7820 1.067212 AGTAGATTAGCCCGCAAGTCG 59.933 52.381 0.00 0.00 38.08 4.18
7114 8278 3.492137 CGATTCAGATCAGGTGATGCTGA 60.492 47.826 13.58 13.58 37.16 4.26
7121 8285 2.932614 GGTTGTCGATTCAGATCAGGTG 59.067 50.000 0.00 0.00 32.33 4.00
7126 8290 3.242870 GGCATTGGTTGTCGATTCAGATC 60.243 47.826 0.00 0.00 0.00 2.75
7132 8296 1.933115 GCGGGCATTGGTTGTCGATT 61.933 55.000 0.00 0.00 0.00 3.34
7133 8297 2.406616 GCGGGCATTGGTTGTCGAT 61.407 57.895 0.00 0.00 0.00 3.59
7135 8299 2.801113 CTTGCGGGCATTGGTTGTCG 62.801 60.000 0.00 0.00 0.00 4.35
7192 8356 1.352622 TGGAACCTGAACCTGCACCT 61.353 55.000 0.00 0.00 0.00 4.00
7196 8360 0.681243 GGGATGGAACCTGAACCTGC 60.681 60.000 0.00 0.00 0.00 4.85
7200 8364 1.545841 GTTGGGGATGGAACCTGAAC 58.454 55.000 0.00 0.00 0.00 3.18
7201 8365 0.407918 GGTTGGGGATGGAACCTGAA 59.592 55.000 0.00 0.00 38.91 3.02
7202 8366 1.847798 CGGTTGGGGATGGAACCTGA 61.848 60.000 0.00 0.00 39.69 3.86
7203 8367 1.378514 CGGTTGGGGATGGAACCTG 60.379 63.158 0.00 0.00 39.69 4.00
7204 8368 3.087065 CGGTTGGGGATGGAACCT 58.913 61.111 0.00 0.00 39.69 3.50
7205 8369 2.754254 GCGGTTGGGGATGGAACC 60.754 66.667 0.00 0.00 38.65 3.62
7206 8370 2.754254 GGCGGTTGGGGATGGAAC 60.754 66.667 0.00 0.00 0.00 3.62
7207 8371 4.418328 CGGCGGTTGGGGATGGAA 62.418 66.667 0.00 0.00 0.00 3.53
7257 8421 4.559063 CCCTGGATCAGCGCTGGG 62.559 72.222 35.36 26.68 0.00 4.45
7281 8445 4.778143 AAGGGATGCCGTGACGCC 62.778 66.667 0.00 0.00 0.00 5.68
7282 8446 3.499737 CAAGGGATGCCGTGACGC 61.500 66.667 13.94 0.00 0.00 5.19
7283 8447 2.047274 ACAAGGGATGCCGTGACG 60.047 61.111 25.03 0.00 0.00 4.35
7284 8448 1.003839 TCACAAGGGATGCCGTGAC 60.004 57.895 25.03 0.00 33.61 3.67
7285 8449 1.296392 CTCACAAGGGATGCCGTGA 59.704 57.895 25.03 18.07 36.92 4.35
7286 8450 1.746615 CCTCACAAGGGATGCCGTG 60.747 63.158 17.32 17.32 39.21 4.94
7287 8451 2.671070 CCTCACAAGGGATGCCGT 59.329 61.111 0.00 0.00 39.21 5.68
7288 8452 2.825836 GCCTCACAAGGGATGCCG 60.826 66.667 0.00 0.00 43.58 5.69
7289 8453 2.825836 CGCCTCACAAGGGATGCC 60.826 66.667 0.00 0.00 43.58 4.40
7290 8454 2.825836 CCGCCTCACAAGGGATGC 60.826 66.667 0.00 0.00 43.58 3.91
7291 8455 1.153289 CTCCGCCTCACAAGGGATG 60.153 63.158 0.00 0.00 43.58 3.51
7292 8456 2.370445 CCTCCGCCTCACAAGGGAT 61.370 63.158 0.00 0.00 43.58 3.85
7293 8457 3.003173 CCTCCGCCTCACAAGGGA 61.003 66.667 0.00 0.00 43.58 4.20
7294 8458 3.003173 TCCTCCGCCTCACAAGGG 61.003 66.667 0.00 0.00 43.58 3.95
7295 8459 2.581354 CTCCTCCGCCTCACAAGG 59.419 66.667 0.00 0.00 46.44 3.61
7296 8460 2.286523 ACCTCCTCCGCCTCACAAG 61.287 63.158 0.00 0.00 0.00 3.16
7297 8461 2.203788 ACCTCCTCCGCCTCACAA 60.204 61.111 0.00 0.00 0.00 3.33
7298 8462 2.997315 CACCTCCTCCGCCTCACA 60.997 66.667 0.00 0.00 0.00 3.58
7299 8463 2.113243 AAACACCTCCTCCGCCTCAC 62.113 60.000 0.00 0.00 0.00 3.51
7300 8464 1.827399 GAAACACCTCCTCCGCCTCA 61.827 60.000 0.00 0.00 0.00 3.86
7301 8465 1.079057 GAAACACCTCCTCCGCCTC 60.079 63.158 0.00 0.00 0.00 4.70
7302 8466 1.201429 ATGAAACACCTCCTCCGCCT 61.201 55.000 0.00 0.00 0.00 5.52
7303 8467 1.026718 CATGAAACACCTCCTCCGCC 61.027 60.000 0.00 0.00 0.00 6.13
7304 8468 1.648467 GCATGAAACACCTCCTCCGC 61.648 60.000 0.00 0.00 0.00 5.54
7305 8469 1.361668 CGCATGAAACACCTCCTCCG 61.362 60.000 0.00 0.00 0.00 4.63
7306 8470 1.026718 CCGCATGAAACACCTCCTCC 61.027 60.000 0.00 0.00 0.00 4.30
7307 8471 1.026718 CCCGCATGAAACACCTCCTC 61.027 60.000 0.00 0.00 0.00 3.71
7308 8472 1.002134 CCCGCATGAAACACCTCCT 60.002 57.895 0.00 0.00 0.00 3.69
7309 8473 2.046285 CCCCGCATGAAACACCTCC 61.046 63.158 0.00 0.00 0.00 4.30
7310 8474 1.002624 TCCCCGCATGAAACACCTC 60.003 57.895 0.00 0.00 0.00 3.85
7311 8475 1.002134 CTCCCCGCATGAAACACCT 60.002 57.895 0.00 0.00 0.00 4.00
7312 8476 2.046285 CCTCCCCGCATGAAACACC 61.046 63.158 0.00 0.00 0.00 4.16
7313 8477 2.700773 GCCTCCCCGCATGAAACAC 61.701 63.158 0.00 0.00 0.00 3.32
7314 8478 2.361104 GCCTCCCCGCATGAAACA 60.361 61.111 0.00 0.00 0.00 2.83
7315 8479 3.140814 GGCCTCCCCGCATGAAAC 61.141 66.667 0.00 0.00 0.00 2.78
7332 8496 4.157120 CCTTGACTACCGCCCCCG 62.157 72.222 0.00 0.00 0.00 5.73
7333 8497 4.484872 GCCTTGACTACCGCCCCC 62.485 72.222 0.00 0.00 0.00 5.40
7334 8498 4.832608 CGCCTTGACTACCGCCCC 62.833 72.222 0.00 0.00 0.00 5.80
7335 8499 4.832608 CCGCCTTGACTACCGCCC 62.833 72.222 0.00 0.00 0.00 6.13
7336 8500 4.078516 ACCGCCTTGACTACCGCC 62.079 66.667 0.00 0.00 0.00 6.13
7337 8501 2.813908 CACCGCCTTGACTACCGC 60.814 66.667 0.00 0.00 0.00 5.68
7338 8502 2.813908 GCACCGCCTTGACTACCG 60.814 66.667 0.00 0.00 0.00 4.02
7339 8503 2.436115 GGCACCGCCTTGACTACC 60.436 66.667 0.00 0.00 46.69 3.18
7366 8530 4.554363 AGACTTCGATCGCCGCCG 62.554 66.667 11.09 0.00 38.37 6.46
7367 8531 2.655685 GAGACTTCGATCGCCGCC 60.656 66.667 11.09 0.00 38.37 6.13
7368 8532 2.655685 GGAGACTTCGATCGCCGC 60.656 66.667 11.09 0.00 38.37 6.53
7369 8533 0.936764 CATGGAGACTTCGATCGCCG 60.937 60.000 11.09 6.07 41.18 6.46
7370 8534 0.598680 CCATGGAGACTTCGATCGCC 60.599 60.000 11.09 5.17 38.92 5.54
7371 8535 1.218230 GCCATGGAGACTTCGATCGC 61.218 60.000 18.40 0.00 0.00 4.58
7372 8536 0.598680 GGCCATGGAGACTTCGATCG 60.599 60.000 18.40 9.36 0.00 3.69
7373 8537 0.598680 CGGCCATGGAGACTTCGATC 60.599 60.000 18.40 0.00 0.00 3.69
7374 8538 1.443407 CGGCCATGGAGACTTCGAT 59.557 57.895 18.40 0.00 0.00 3.59
7375 8539 2.721167 CCGGCCATGGAGACTTCGA 61.721 63.158 18.40 0.00 0.00 3.71
7376 8540 2.202932 CCGGCCATGGAGACTTCG 60.203 66.667 18.40 8.34 0.00 3.79
7377 8541 2.514824 GCCGGCCATGGAGACTTC 60.515 66.667 18.11 0.00 0.00 3.01
7378 8542 4.473520 CGCCGGCCATGGAGACTT 62.474 66.667 23.46 0.00 0.00 3.01
7390 8554 3.019003 AATCTCAGGTCACCGCCGG 62.019 63.158 0.00 0.00 0.00 6.13
7391 8555 1.811266 CAATCTCAGGTCACCGCCG 60.811 63.158 0.00 0.00 0.00 6.46
7392 8556 1.450312 CCAATCTCAGGTCACCGCC 60.450 63.158 0.00 0.00 0.00 6.13
7393 8557 1.450312 CCCAATCTCAGGTCACCGC 60.450 63.158 0.00 0.00 0.00 5.68
7394 8558 0.391661 CACCCAATCTCAGGTCACCG 60.392 60.000 0.00 0.00 32.72 4.94
7395 8559 0.035056 CCACCCAATCTCAGGTCACC 60.035 60.000 0.00 0.00 32.72 4.02
7396 8560 3.558674 CCACCCAATCTCAGGTCAC 57.441 57.895 0.00 0.00 32.72 3.67


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

AutoCloner maintained by Alex Coulton.