Multiple sequence alignment - TraesCS2A01G302300

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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 TraesCS2A01G302300 chr2A 100.000 5089 0 0 1 5089 517915972 517910884 0.000000e+00 9398
1 TraesCS2A01G302300 chr2A 85.714 224 25 6 4629 4847 517817447 517817226 3.960000e-56 230
2 TraesCS2A01G302300 chr2B 92.167 3562 173 48 1 3513 453819222 453815718 0.000000e+00 4935
3 TraesCS2A01G302300 chr2B 87.513 937 73 14 3505 4402 453815650 453814719 0.000000e+00 1042
4 TraesCS2A01G302300 chr2B 83.206 524 50 17 138 658 453827536 453827048 3.610000e-121 446
5 TraesCS2A01G302300 chr2D 92.854 2561 132 27 953 3489 383301925 383299392 0.000000e+00 3668
6 TraesCS2A01G302300 chr2D 92.642 897 51 4 3512 4394 383299298 383298403 0.000000e+00 1277
7 TraesCS2A01G302300 chr2D 87.304 575 59 4 4448 5015 383298307 383297740 0.000000e+00 645
8 TraesCS2A01G302300 chr2D 86.402 478 28 5 474 921 383302394 383301924 5.920000e-134 488
9 TraesCS2A01G302300 chr2D 80.303 330 32 8 1 299 383303087 383302760 8.580000e-53 219
10 TraesCS2A01G302300 chr3B 79.081 631 102 21 996 1620 373723 373117 1.710000e-109 407
11 TraesCS2A01G302300 chr3B 88.364 275 32 0 1346 1620 16462863 16462589 1.060000e-86 331
12 TraesCS2A01G302300 chr3D 86.182 275 38 0 1346 1620 3631983 3631709 1.070000e-76 298


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 TraesCS2A01G302300 chr2A 517910884 517915972 5088 True 9398.0 9398 100.000 1 5089 1 chr2A.!!$R2 5088
1 TraesCS2A01G302300 chr2B 453814719 453819222 4503 True 2988.5 4935 89.840 1 4402 2 chr2B.!!$R2 4401
2 TraesCS2A01G302300 chr2D 383297740 383303087 5347 True 1259.4 3668 87.901 1 5015 5 chr2D.!!$R1 5014
3 TraesCS2A01G302300 chr3B 373117 373723 606 True 407.0 407 79.081 996 1620 1 chr3B.!!$R1 624

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
582 893 0.108615 GTGATGTCGTCAGGGTCAGG 60.109 60.000 0.00 0.00 37.56 3.86 F
658 969 0.466372 TCCACACGCCATGGTTTTGA 60.466 50.000 14.67 0.18 38.47 2.69 F
704 1020 1.079543 CCGAGGACCAAGTGAGCAG 60.080 63.158 0.00 0.00 0.00 4.24 F
2089 2487 0.678048 AGAAAAGCCCCAGACATCGC 60.678 55.000 0.00 0.00 0.00 4.58 F
3325 3750 0.745845 CCTCGGCACCATCTTCAAGG 60.746 60.000 0.00 0.00 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 1968 0.036765 GCCCTCACACCAACGTCATA 60.037 55.0 0.00 0.00 0.00 2.15 R
1849 2239 0.179161 CGATGAACTCGGCGAACTCT 60.179 55.0 12.13 0.78 43.82 3.24 R
2259 2659 0.307760 CCTTGTCTGCACCACGAAAC 59.692 55.0 0.00 0.00 0.00 2.78 R
3966 4510 0.537143 ACGAATGGCCAGAAGCACAA 60.537 50.0 13.05 0.00 46.50 3.33 R
4916 5540 0.394899 GCCAGCTATGAGGGCTTTGT 60.395 55.0 4.80 0.00 44.32 2.83 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
29 30 3.117794 TGTGCTACGTGTTGTTCTACAC 58.882 45.455 0.00 7.29 43.86 2.90
60 61 6.695188 GTGTTCTTTCACTTCCGGAACGTAA 61.695 44.000 14.35 6.76 41.94 3.18
80 82 6.787515 ACGTAAGATATATACACGTTTCGACG 59.212 38.462 11.17 0.00 42.69 5.12
83 85 5.683859 AGATATATACACGTTTCGACGGAC 58.316 41.667 3.90 0.00 37.45 4.79
103 105 6.183360 ACGGACGACCCATCATATATATGAAG 60.183 42.308 25.37 21.17 44.96 3.02
151 171 1.067142 TGCGAAGGTTGTATCGAAGCT 60.067 47.619 0.00 0.00 41.43 3.74
154 174 2.416836 CGAAGGTTGTATCGAAGCTGGA 60.417 50.000 0.00 0.00 41.43 3.86
178 198 5.063180 TCTTAGAAAAATACGAGCACCGA 57.937 39.130 5.53 0.00 41.76 4.69
190 210 3.247442 CGAGCACCGATGTTAAGTGTAA 58.753 45.455 0.00 0.00 41.76 2.41
212 233 6.780457 AATACTTGATTCTGATGGGTTTGG 57.220 37.500 0.00 0.00 0.00 3.28
235 256 4.382685 GGATATCACTGTCCTTCGAACCAA 60.383 45.833 4.83 0.00 30.28 3.67
236 257 2.992124 TCACTGTCCTTCGAACCAAA 57.008 45.000 0.00 0.00 0.00 3.28
244 265 7.495934 CACTGTCCTTCGAACCAAATATAGATT 59.504 37.037 0.00 0.00 0.00 2.40
245 266 8.701895 ACTGTCCTTCGAACCAAATATAGATTA 58.298 33.333 0.00 0.00 0.00 1.75
281 314 4.022935 TGCCTTTGCTGTATGAAACTCTTG 60.023 41.667 0.00 0.00 38.71 3.02
285 318 1.202076 GCTGTATGAAACTCTTGCGGC 60.202 52.381 0.00 0.00 33.14 6.53
286 319 1.398390 CTGTATGAAACTCTTGCGGCC 59.602 52.381 0.00 0.00 0.00 6.13
340 648 2.736144 TCGCTGGTCGACTTGTTAAT 57.264 45.000 16.46 0.00 43.16 1.40
341 649 2.602878 TCGCTGGTCGACTTGTTAATC 58.397 47.619 16.46 0.00 43.16 1.75
342 650 2.230508 TCGCTGGTCGACTTGTTAATCT 59.769 45.455 16.46 0.00 43.16 2.40
344 652 2.599082 GCTGGTCGACTTGTTAATCTCG 59.401 50.000 16.46 0.00 0.00 4.04
345 653 3.179830 CTGGTCGACTTGTTAATCTCGG 58.820 50.000 16.46 0.00 0.00 4.63
346 654 2.821378 TGGTCGACTTGTTAATCTCGGA 59.179 45.455 16.46 0.00 0.00 4.55
347 655 3.256383 TGGTCGACTTGTTAATCTCGGAA 59.744 43.478 16.46 0.00 0.00 4.30
348 656 3.858238 GGTCGACTTGTTAATCTCGGAAG 59.142 47.826 16.46 0.00 0.00 3.46
349 657 3.858238 GTCGACTTGTTAATCTCGGAAGG 59.142 47.826 8.70 0.00 0.00 3.46
350 658 3.760151 TCGACTTGTTAATCTCGGAAGGA 59.240 43.478 0.00 0.00 0.00 3.36
351 659 4.106197 CGACTTGTTAATCTCGGAAGGAG 58.894 47.826 0.00 0.00 44.58 3.69
352 660 3.863041 ACTTGTTAATCTCGGAAGGAGC 58.137 45.455 0.00 0.00 42.82 4.70
353 661 2.981859 TGTTAATCTCGGAAGGAGCC 57.018 50.000 0.00 0.00 42.82 4.70
368 676 0.598680 GAGCCGTGAATCGATCCCAG 60.599 60.000 0.00 0.00 42.86 4.45
370 678 1.595382 CCGTGAATCGATCCCAGCC 60.595 63.158 0.00 0.00 42.86 4.85
374 682 0.673985 TGAATCGATCCCAGCCGTAG 59.326 55.000 0.00 0.00 0.00 3.51
394 702 6.228995 CGTAGGTACATCTATCACTGGACTA 58.771 44.000 0.00 0.00 0.00 2.59
411 719 1.202268 ACTAGACGGCTCACATAACGC 60.202 52.381 0.00 0.00 0.00 4.84
434 742 7.260570 GCTGTACCGAGCATTTGTGTAACAA 62.261 44.000 0.49 0.00 46.50 2.83
435 743 8.481079 GCTGTACCGAGCATTTGTGTAACAAT 62.481 42.308 0.49 0.00 46.95 2.71
547 858 1.199097 CCGGCCGCCATACAATAATTC 59.801 52.381 22.85 0.00 0.00 2.17
578 889 0.603569 GTGAGTGATGTCGTCAGGGT 59.396 55.000 0.00 0.00 37.56 4.34
579 890 0.888619 TGAGTGATGTCGTCAGGGTC 59.111 55.000 0.00 0.00 37.56 4.46
580 891 0.888619 GAGTGATGTCGTCAGGGTCA 59.111 55.000 0.00 0.00 37.56 4.02
581 892 0.891373 AGTGATGTCGTCAGGGTCAG 59.109 55.000 0.00 0.00 37.56 3.51
582 893 0.108615 GTGATGTCGTCAGGGTCAGG 60.109 60.000 0.00 0.00 37.56 3.86
583 894 1.257750 TGATGTCGTCAGGGTCAGGG 61.258 60.000 0.00 0.00 31.80 4.45
658 969 0.466372 TCCACACGCCATGGTTTTGA 60.466 50.000 14.67 0.18 38.47 2.69
704 1020 1.079543 CCGAGGACCAAGTGAGCAG 60.080 63.158 0.00 0.00 0.00 4.24
839 1191 2.441375 TCTCCCAGACCACATCACAAAA 59.559 45.455 0.00 0.00 0.00 2.44
940 1292 1.727467 GCACTCGTTTGCTTGTGGT 59.273 52.632 4.08 0.00 39.59 4.16
961 1313 2.032681 GGGTGGAGCTGTGGTGTC 59.967 66.667 0.00 0.00 0.00 3.67
1353 1743 3.691118 TGTCTGTGATGATTTTGCTAGGC 59.309 43.478 0.00 0.00 0.00 3.93
1645 2035 3.053896 GGTTGGCACCGGTACAGC 61.054 66.667 6.87 11.87 31.60 4.40
1688 2078 1.281867 TGGGCACTCATGAAGGTTAGG 59.718 52.381 0.00 0.00 0.00 2.69
1700 2090 2.112815 GGTTAGGCGCCATGGTGAC 61.113 63.158 31.54 27.09 0.00 3.67
1704 2094 1.920734 TAGGCGCCATGGTGACCATT 61.921 55.000 31.54 12.18 42.23 3.16
1714 2104 2.226330 TGGTGACCATTTCAGTTTCCG 58.774 47.619 0.00 0.00 33.71 4.30
1734 2124 2.028763 CGTAATGTTTGGTCGTCCATCG 59.971 50.000 1.21 0.00 43.91 3.84
1779 2169 2.466571 CGTGTACGTGTGACTTTCAGAC 59.533 50.000 0.00 0.00 37.31 3.51
1909 2299 1.537562 CCTACCATCGTTAAGGTCGCC 60.538 57.143 0.00 0.00 39.31 5.54
1939 2337 3.520569 CATGTCCATGTACATCGTGTCA 58.479 45.455 5.07 2.55 38.01 3.58
1950 2348 2.499520 CGTGTCATGCCAAACGCG 60.500 61.111 3.53 3.53 42.12 6.01
1993 2391 2.074547 ATCGTCACGGTTAACCTGTG 57.925 50.000 28.63 28.63 39.85 3.66
2089 2487 0.678048 AGAAAAGCCCCAGACATCGC 60.678 55.000 0.00 0.00 0.00 4.58
2137 2535 2.224137 TGTTCTGGTGAGCACTCTCTTG 60.224 50.000 0.16 0.00 40.03 3.02
2141 2539 2.297315 CTGGTGAGCACTCTCTTGTACA 59.703 50.000 0.00 0.00 40.03 2.90
2152 2552 5.351465 CACTCTCTTGTACACAACAGTGTTT 59.649 40.000 5.57 0.00 43.66 2.83
2185 2585 1.528129 TGTGTCACACAAACAGCACA 58.472 45.000 8.60 0.00 41.69 4.57
2187 2587 2.491298 TGTGTCACACAAACAGCACAAT 59.509 40.909 8.60 0.00 41.69 2.71
2211 2611 2.682856 GTGGCAGTTGAAAGTTCAGACA 59.317 45.455 0.00 0.00 38.61 3.41
2212 2612 3.316308 GTGGCAGTTGAAAGTTCAGACAT 59.684 43.478 0.00 0.00 38.61 3.06
2213 2613 3.316029 TGGCAGTTGAAAGTTCAGACATG 59.684 43.478 0.00 0.00 38.61 3.21
2216 2616 4.201950 GCAGTTGAAAGTTCAGACATGTGT 60.202 41.667 1.15 0.00 38.61 3.72
2219 2619 6.037062 CAGTTGAAAGTTCAGACATGTGTACA 59.963 38.462 1.15 0.00 38.61 2.90
2221 2621 7.283127 AGTTGAAAGTTCAGACATGTGTACAAT 59.717 33.333 1.15 0.00 38.61 2.71
2222 2622 6.958255 TGAAAGTTCAGACATGTGTACAATG 58.042 36.000 1.15 6.80 32.50 2.82
2224 2624 3.433274 AGTTCAGACATGTGTACAATGCG 59.567 43.478 1.15 6.95 0.00 4.73
2225 2625 1.731709 TCAGACATGTGTACAATGCGC 59.268 47.619 1.15 0.00 0.00 6.09
2232 2632 4.394610 ACATGTGTACAATGCGCTTGATAA 59.605 37.500 21.19 7.77 38.29 1.75
2233 2633 5.066375 ACATGTGTACAATGCGCTTGATAAT 59.934 36.000 21.19 0.00 38.29 1.28
2234 2634 5.559427 TGTGTACAATGCGCTTGATAATT 57.441 34.783 21.19 4.79 38.29 1.40
2235 2635 5.948588 TGTGTACAATGCGCTTGATAATTT 58.051 33.333 21.19 5.41 38.29 1.82
2236 2636 5.799435 TGTGTACAATGCGCTTGATAATTTG 59.201 36.000 21.19 6.90 38.29 2.32
2237 2637 4.797868 TGTACAATGCGCTTGATAATTTGC 59.202 37.500 21.19 6.66 38.29 3.68
2238 2638 3.847542 ACAATGCGCTTGATAATTTGCA 58.152 36.364 21.19 0.00 38.29 4.08
2239 2639 4.244066 ACAATGCGCTTGATAATTTGCAA 58.756 34.783 21.19 0.00 38.29 4.08
2240 2640 4.327898 ACAATGCGCTTGATAATTTGCAAG 59.672 37.500 21.19 12.92 43.26 4.01
2259 2659 4.205792 GCAAGCAAATAATTAAGCTGAGCG 59.794 41.667 0.00 3.44 37.41 5.03
2305 2705 1.374125 CGTGATGACCAACGCTCCA 60.374 57.895 0.00 0.00 0.00 3.86
2713 3131 3.606687 AGAGGTAATAAAACTGGGCACG 58.393 45.455 0.00 0.00 0.00 5.34
2716 3134 2.414957 GGTAATAAAACTGGGCACGCAC 60.415 50.000 0.00 0.00 0.00 5.34
2743 3161 5.257082 TGAGATCATCCGACGTAAATTGA 57.743 39.130 0.00 0.00 0.00 2.57
2890 3309 4.837298 TCATCTAGGAACATCATCTCAGGG 59.163 45.833 0.00 0.00 0.00 4.45
2929 3348 4.391216 CCAACCGTAGATATATCGAGTCGT 59.609 45.833 13.12 2.64 0.00 4.34
3053 3473 1.203994 ACAGTACGGCCACATCTACAC 59.796 52.381 2.24 0.00 0.00 2.90
3091 3512 9.658799 TTTCTCTCTATTACAGTTTCTTCCATG 57.341 33.333 0.00 0.00 0.00 3.66
3147 3572 1.420138 ACAGAGGACATTTTGACCGGT 59.580 47.619 6.92 6.92 37.28 5.28
3323 3748 0.911769 ATCCTCGGCACCATCTTCAA 59.088 50.000 0.00 0.00 0.00 2.69
3325 3750 0.745845 CCTCGGCACCATCTTCAAGG 60.746 60.000 0.00 0.00 0.00 3.61
3408 3833 2.584065 CGAGCTGTGCTATGCGCTC 61.584 63.158 9.73 6.32 43.99 5.03
3438 3863 2.727123 TCTGCCTTCTCACAAACCAA 57.273 45.000 0.00 0.00 0.00 3.67
3447 3872 6.003950 CCTTCTCACAAACCAATCCTTCTTA 58.996 40.000 0.00 0.00 0.00 2.10
3506 3931 8.059798 ACTACATTGCTCATAGCTGAAATTTT 57.940 30.769 0.00 0.00 42.97 1.82
3518 4062 4.692155 AGCTGAAATTTTAGTGCATTTGCC 59.308 37.500 11.22 0.00 41.18 4.52
3547 4091 3.760151 CAGGCATCAGATGAAGGTTTTCA 59.240 43.478 15.12 0.00 46.67 2.69
3566 4110 0.839946 ACATCCCAGCGGCTCTATTT 59.160 50.000 0.00 0.00 0.00 1.40
3576 4120 4.391830 CAGCGGCTCTATTTTTGACTTACA 59.608 41.667 0.00 0.00 0.00 2.41
3761 4305 1.005748 CAAGGAGAGCAGCACGTCA 60.006 57.895 0.00 0.00 0.00 4.35
3801 4345 2.764128 ACGATGCCGATCCTGGGT 60.764 61.111 0.00 0.00 39.50 4.51
3812 4356 2.814097 CGATCCTGGGTTGTTCACCTTT 60.814 50.000 0.00 0.00 46.38 3.11
3836 4380 3.059386 GCGCCCGTTTTCATCCCA 61.059 61.111 0.00 0.00 0.00 4.37
3852 4396 2.505777 CAGTGACGGCGCTCTCAG 60.506 66.667 0.00 0.00 31.06 3.35
3855 4399 3.295273 TGACGGCGCTCTCAGTGT 61.295 61.111 6.90 0.00 0.00 3.55
3873 4417 1.234821 GTTGAACATTGTCGCCCTCA 58.765 50.000 0.00 0.00 0.00 3.86
3966 4510 2.034687 GCTGTGGCTGGATGGTGT 59.965 61.111 0.00 0.00 35.22 4.16
3980 4524 1.827789 GGTGTTGTGCTTCTGGCCA 60.828 57.895 4.71 4.71 40.92 5.36
4001 4545 0.827925 TCGTGAGAGGGCTTGTCAGT 60.828 55.000 0.00 0.00 34.84 3.41
4115 4659 1.963515 GGGCTGGCCATCGAAATATTT 59.036 47.619 16.34 0.00 37.98 1.40
4128 4672 8.682016 CCATCGAAATATTTGAAGCGTAATTTC 58.318 33.333 5.17 0.00 0.00 2.17
4137 4681 3.806316 AAGCGTAATTTCGGTTCTGTG 57.194 42.857 14.91 0.00 46.00 3.66
4233 4803 7.257722 ACACAACAAATGACTAAACTGAAAGG 58.742 34.615 0.00 0.00 39.30 3.11
4316 4886 1.070615 ATTTGGTTTTGTGCGGGGC 59.929 52.632 0.00 0.00 0.00 5.80
4326 4896 4.015406 TGCGGGGCTTCGTGTGAT 62.015 61.111 3.24 0.00 0.00 3.06
4331 4901 1.401018 CGGGGCTTCGTGTGATTTTTC 60.401 52.381 0.00 0.00 0.00 2.29
4332 4902 1.067846 GGGGCTTCGTGTGATTTTTCC 60.068 52.381 0.00 0.00 0.00 3.13
4419 5001 8.458843 TCTTTCTTTACACTTTCTTTTCACCTG 58.541 33.333 0.00 0.00 0.00 4.00
4422 5004 7.535139 TCTTTACACTTTCTTTTCACCTGTTG 58.465 34.615 0.00 0.00 0.00 3.33
4423 5005 4.718940 ACACTTTCTTTTCACCTGTTGG 57.281 40.909 0.00 0.00 39.83 3.77
4425 5007 4.526650 ACACTTTCTTTTCACCTGTTGGTT 59.473 37.500 0.00 0.00 46.05 3.67
4426 5008 4.864247 CACTTTCTTTTCACCTGTTGGTTG 59.136 41.667 0.00 0.00 46.05 3.77
4427 5009 4.526650 ACTTTCTTTTCACCTGTTGGTTGT 59.473 37.500 0.00 0.00 46.05 3.32
4445 5031 0.240945 GTGTGCAACTACATGCCCAC 59.759 55.000 0.00 0.00 45.00 4.61
4446 5032 0.110295 TGTGCAACTACATGCCCACT 59.890 50.000 0.00 0.00 45.83 4.00
4457 5081 0.538057 ATGCCCACTGGTCACTTGTG 60.538 55.000 0.00 0.00 0.00 3.33
4477 5101 0.721718 GTTGCATGTCCACTAGTCGC 59.278 55.000 0.00 0.00 0.00 5.19
4478 5102 0.735978 TTGCATGTCCACTAGTCGCG 60.736 55.000 0.00 0.00 0.00 5.87
4480 5104 1.413767 GCATGTCCACTAGTCGCGTG 61.414 60.000 5.77 0.00 0.00 5.34
4485 5109 2.380410 CCACTAGTCGCGTGCAACC 61.380 63.158 5.77 0.00 0.00 3.77
4486 5110 1.663388 CACTAGTCGCGTGCAACCA 60.663 57.895 5.77 0.00 0.00 3.67
4502 5126 0.968405 ACCACATGTCCAATGGTTGC 59.032 50.000 0.00 0.00 44.51 4.17
4503 5127 0.967662 CCACATGTCCAATGGTTGCA 59.032 50.000 0.00 0.00 0.00 4.08
4504 5128 1.337074 CCACATGTCCAATGGTTGCAC 60.337 52.381 0.00 0.00 0.00 4.57
4509 5133 3.834489 TGTCCAATGGTTGCACAAAAT 57.166 38.095 0.00 0.00 0.00 1.82
4521 5145 5.861787 GGTTGCACAAAATTACATGTCTACC 59.138 40.000 0.00 0.00 0.00 3.18
4547 5171 2.110352 CGCAGCAGCATGTCCATCA 61.110 57.895 0.82 0.00 42.27 3.07
4548 5172 1.728069 GCAGCAGCATGTCCATCAG 59.272 57.895 0.00 0.00 41.58 2.90
4552 5176 1.171308 GCAGCATGTCCATCAGTTGT 58.829 50.000 0.00 0.00 39.31 3.32
4553 5177 1.135489 GCAGCATGTCCATCAGTTGTG 60.135 52.381 0.00 0.00 39.31 3.33
4555 5179 0.883153 GCATGTCCATCAGTTGTGCA 59.117 50.000 0.00 0.00 31.17 4.57
4558 5182 1.308047 TGTCCATCAGTTGTGCACAC 58.692 50.000 21.56 14.79 0.00 3.82
4606 5230 1.308069 ACAACTGCATGTCCATCGCC 61.308 55.000 0.00 0.00 0.00 5.54
4607 5231 1.750399 AACTGCATGTCCATCGCCC 60.750 57.895 0.00 0.00 0.00 6.13
4608 5232 2.124612 CTGCATGTCCATCGCCCA 60.125 61.111 0.00 0.00 0.00 5.36
4645 5269 2.039418 ACACCTACTGACTGAGTGCAA 58.961 47.619 0.00 0.00 35.96 4.08
4651 5275 7.147655 ACACCTACTGACTGAGTGCAATTATAT 60.148 37.037 0.00 0.00 35.96 0.86
4655 5279 9.926751 CTACTGACTGAGTGCAATTATATTTTG 57.073 33.333 0.00 0.00 35.96 2.44
4773 5397 3.651803 ATGGTGACGATTAGAGCTAGC 57.348 47.619 6.62 6.62 0.00 3.42
4800 5424 6.928492 ACACCCAAAATTTGTTACATGATGTC 59.072 34.615 0.00 0.00 0.00 3.06
4801 5425 6.368516 CACCCAAAATTTGTTACATGATGTCC 59.631 38.462 0.00 0.00 0.00 4.02
4816 5440 4.008539 GATGTCCGCATCTTTTTCTGTC 57.991 45.455 0.80 0.00 45.97 3.51
4903 5527 0.107456 CTCTAGCCCATCGTGCCAAT 59.893 55.000 0.00 0.00 0.00 3.16
4908 5532 1.419762 AGCCCATCGTGCCAATATACA 59.580 47.619 0.00 0.00 0.00 2.29
4916 5540 0.833949 TGCCAATATACACCGCCAGA 59.166 50.000 0.00 0.00 0.00 3.86
4929 5559 0.107703 CGCCAGACAAAGCCCTCATA 60.108 55.000 0.00 0.00 0.00 2.15
4934 5564 1.211457 AGACAAAGCCCTCATAGCTGG 59.789 52.381 0.00 0.00 40.49 4.85
4939 5569 3.865383 CCCTCATAGCTGGCGGCA 61.865 66.667 22.28 12.58 44.79 5.69
4941 5571 1.228063 CCTCATAGCTGGCGGCAAT 60.228 57.895 22.28 7.40 44.79 3.56
4984 5615 2.358247 AGGGGCAACGTTAGTGCG 60.358 61.111 0.00 0.00 37.94 5.34
4997 5628 2.266376 TAGTGCGGTAGCTGCAGTCG 62.266 60.000 16.64 14.74 45.03 4.18
5001 5632 2.496817 GGTAGCTGCAGTCGAGGG 59.503 66.667 16.64 0.00 0.00 4.30
5004 5635 2.060383 TAGCTGCAGTCGAGGGCAT 61.060 57.895 16.64 1.23 39.65 4.40
5018 5649 3.096495 GCATGTGGGGCCTAGGGA 61.096 66.667 11.72 0.00 0.00 4.20
5019 5650 3.125376 GCATGTGGGGCCTAGGGAG 62.125 68.421 11.72 0.00 0.00 4.30
5020 5651 2.039405 ATGTGGGGCCTAGGGAGG 60.039 66.667 11.72 0.00 46.93 4.30
5021 5652 2.973553 ATGTGGGGCCTAGGGAGGT 61.974 63.158 11.72 0.00 45.78 3.85
5028 5659 1.634960 GGCCTAGGGAGGTCTATCAC 58.365 60.000 11.72 0.00 44.89 3.06
5029 5660 1.634960 GCCTAGGGAGGTCTATCACC 58.365 60.000 11.72 0.00 45.78 4.02
5042 5673 6.424176 GGTCTATCACCTTAAGTTTCTTGC 57.576 41.667 0.97 0.00 42.84 4.01
5043 5674 5.354513 GGTCTATCACCTTAAGTTTCTTGCC 59.645 44.000 0.97 0.00 42.84 4.52
5044 5675 6.174049 GTCTATCACCTTAAGTTTCTTGCCT 58.826 40.000 0.97 0.00 0.00 4.75
5045 5676 6.314152 GTCTATCACCTTAAGTTTCTTGCCTC 59.686 42.308 0.97 0.00 0.00 4.70
5046 5677 4.706842 TCACCTTAAGTTTCTTGCCTCT 57.293 40.909 0.97 0.00 0.00 3.69
5047 5678 5.818678 TCACCTTAAGTTTCTTGCCTCTA 57.181 39.130 0.97 0.00 0.00 2.43
5048 5679 6.182507 TCACCTTAAGTTTCTTGCCTCTAA 57.817 37.500 0.97 0.00 0.00 2.10
5049 5680 5.995897 TCACCTTAAGTTTCTTGCCTCTAAC 59.004 40.000 0.97 0.00 0.00 2.34
5050 5681 5.998363 CACCTTAAGTTTCTTGCCTCTAACT 59.002 40.000 0.97 0.00 32.52 2.24
5051 5682 6.147985 CACCTTAAGTTTCTTGCCTCTAACTC 59.852 42.308 0.97 0.00 30.92 3.01
5052 5683 6.183361 ACCTTAAGTTTCTTGCCTCTAACTCA 60.183 38.462 0.97 0.00 30.92 3.41
5053 5684 6.881602 CCTTAAGTTTCTTGCCTCTAACTCAT 59.118 38.462 0.97 0.00 30.92 2.90
5054 5685 8.041323 CCTTAAGTTTCTTGCCTCTAACTCATA 58.959 37.037 0.97 0.00 30.92 2.15
5055 5686 9.436957 CTTAAGTTTCTTGCCTCTAACTCATAA 57.563 33.333 0.00 0.00 30.92 1.90
5056 5687 9.787435 TTAAGTTTCTTGCCTCTAACTCATAAA 57.213 29.630 0.00 0.00 30.92 1.40
5057 5688 8.870075 AAGTTTCTTGCCTCTAACTCATAAAT 57.130 30.769 0.00 0.00 30.92 1.40
5058 5689 9.959721 AAGTTTCTTGCCTCTAACTCATAAATA 57.040 29.630 0.00 0.00 30.92 1.40
5061 5692 9.561069 TTTCTTGCCTCTAACTCATAAATATCC 57.439 33.333 0.00 0.00 0.00 2.59
5062 5693 7.680730 TCTTGCCTCTAACTCATAAATATCCC 58.319 38.462 0.00 0.00 0.00 3.85
5063 5694 6.374417 TGCCTCTAACTCATAAATATCCCC 57.626 41.667 0.00 0.00 0.00 4.81
5064 5695 5.046591 TGCCTCTAACTCATAAATATCCCCG 60.047 44.000 0.00 0.00 0.00 5.73
5065 5696 5.187186 GCCTCTAACTCATAAATATCCCCGA 59.813 44.000 0.00 0.00 0.00 5.14
5066 5697 6.295688 GCCTCTAACTCATAAATATCCCCGAA 60.296 42.308 0.00 0.00 0.00 4.30
5067 5698 7.676947 CCTCTAACTCATAAATATCCCCGAAA 58.323 38.462 0.00 0.00 0.00 3.46
5068 5699 7.603024 CCTCTAACTCATAAATATCCCCGAAAC 59.397 40.741 0.00 0.00 0.00 2.78
5069 5700 7.447594 TCTAACTCATAAATATCCCCGAAACC 58.552 38.462 0.00 0.00 0.00 3.27
5070 5701 4.981812 ACTCATAAATATCCCCGAAACCC 58.018 43.478 0.00 0.00 0.00 4.11
5071 5702 4.663592 ACTCATAAATATCCCCGAAACCCT 59.336 41.667 0.00 0.00 0.00 4.34
5072 5703 5.133830 ACTCATAAATATCCCCGAAACCCTT 59.866 40.000 0.00 0.00 0.00 3.95
5073 5704 5.627135 TCATAAATATCCCCGAAACCCTTC 58.373 41.667 0.00 0.00 0.00 3.46
5074 5705 5.371472 TCATAAATATCCCCGAAACCCTTCT 59.629 40.000 0.00 0.00 0.00 2.85
5075 5706 4.603094 AAATATCCCCGAAACCCTTCTT 57.397 40.909 0.00 0.00 0.00 2.52
5076 5707 3.859061 ATATCCCCGAAACCCTTCTTC 57.141 47.619 0.00 0.00 0.00 2.87
5077 5708 1.368374 ATCCCCGAAACCCTTCTTCA 58.632 50.000 0.00 0.00 0.00 3.02
5078 5709 0.690762 TCCCCGAAACCCTTCTTCAG 59.309 55.000 0.00 0.00 0.00 3.02
5079 5710 0.690762 CCCCGAAACCCTTCTTCAGA 59.309 55.000 0.00 0.00 0.00 3.27
5080 5711 1.282157 CCCCGAAACCCTTCTTCAGAT 59.718 52.381 0.00 0.00 0.00 2.90
5081 5712 2.290960 CCCCGAAACCCTTCTTCAGATT 60.291 50.000 0.00 0.00 0.00 2.40
5082 5713 3.054655 CCCCGAAACCCTTCTTCAGATTA 60.055 47.826 0.00 0.00 0.00 1.75
5083 5714 3.939592 CCCGAAACCCTTCTTCAGATTAC 59.060 47.826 0.00 0.00 0.00 1.89
5084 5715 3.939592 CCGAAACCCTTCTTCAGATTACC 59.060 47.826 0.00 0.00 0.00 2.85
5085 5716 4.564821 CCGAAACCCTTCTTCAGATTACCA 60.565 45.833 0.00 0.00 0.00 3.25
5086 5717 5.186198 CGAAACCCTTCTTCAGATTACCAT 58.814 41.667 0.00 0.00 0.00 3.55
5087 5718 5.065218 CGAAACCCTTCTTCAGATTACCATG 59.935 44.000 0.00 0.00 0.00 3.66
5088 5719 5.779241 AACCCTTCTTCAGATTACCATGA 57.221 39.130 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.017440 TCCGGAAGTGAAAGAACACAATTAAG 60.017 38.462 0.00 0.00 42.45 1.85
49 50 5.700832 ACGTGTATATATCTTACGTTCCGGA 59.299 40.000 0.00 0.00 44.48 5.14
78 80 5.198207 TCATATATATGATGGGTCGTCCGT 58.802 41.667 19.44 0.00 37.76 4.69
80 82 6.516718 CCTTCATATATATGATGGGTCGTCC 58.483 44.000 31.91 0.00 46.33 4.79
103 105 3.096092 TCTTTGCCAAATCATACCCACC 58.904 45.455 0.00 0.00 0.00 4.61
134 136 2.930682 GTCCAGCTTCGATACAACCTTC 59.069 50.000 0.00 0.00 0.00 3.46
151 171 5.867716 GTGCTCGTATTTTTCTAAGAGTCCA 59.132 40.000 0.00 0.00 32.06 4.02
154 174 4.863131 CGGTGCTCGTATTTTTCTAAGAGT 59.137 41.667 0.00 0.00 32.06 3.24
190 210 5.044179 TCCCAAACCCATCAGAATCAAGTAT 60.044 40.000 0.00 0.00 0.00 2.12
198 218 4.478317 AGTGATATCCCAAACCCATCAGAA 59.522 41.667 0.00 0.00 0.00 3.02
199 219 4.047166 AGTGATATCCCAAACCCATCAGA 58.953 43.478 0.00 0.00 0.00 3.27
212 233 3.132289 TGGTTCGAAGGACAGTGATATCC 59.868 47.826 0.00 0.00 0.00 2.59
235 256 6.620733 GCAAATGGCGCGAACTAATCTATATT 60.621 38.462 12.10 0.00 0.00 1.28
236 257 5.163854 GCAAATGGCGCGAACTAATCTATAT 60.164 40.000 12.10 0.00 0.00 0.86
244 265 0.958382 AAGGCAAATGGCGCGAACTA 60.958 50.000 12.10 0.00 46.16 2.24
245 266 1.805428 AAAGGCAAATGGCGCGAACT 61.805 50.000 12.10 0.00 46.16 3.01
281 314 2.041686 TTGAATTGGTACCGGCCGC 61.042 57.895 22.85 6.58 0.00 6.53
285 318 1.662122 GCTACGTTGAATTGGTACCGG 59.338 52.381 7.57 0.00 0.00 5.28
286 319 1.662122 GGCTACGTTGAATTGGTACCG 59.338 52.381 7.57 0.00 0.00 4.02
328 636 3.760151 TCCTTCCGAGATTAACAAGTCGA 59.240 43.478 0.00 0.00 34.28 4.20
329 637 4.106029 TCCTTCCGAGATTAACAAGTCG 57.894 45.455 0.00 0.00 0.00 4.18
330 638 3.866327 GCTCCTTCCGAGATTAACAAGTC 59.134 47.826 0.00 0.00 41.63 3.01
333 641 3.261981 GGCTCCTTCCGAGATTAACAA 57.738 47.619 0.00 0.00 41.63 2.83
334 642 2.981859 GGCTCCTTCCGAGATTAACA 57.018 50.000 0.00 0.00 41.63 2.41
344 652 0.105039 ATCGATTCACGGCTCCTTCC 59.895 55.000 0.00 0.00 42.82 3.46
345 653 1.492720 GATCGATTCACGGCTCCTTC 58.507 55.000 0.00 0.00 42.82 3.46
346 654 0.105039 GGATCGATTCACGGCTCCTT 59.895 55.000 0.00 0.00 42.82 3.36
347 655 1.742768 GGATCGATTCACGGCTCCT 59.257 57.895 0.00 0.00 42.82 3.69
348 656 1.301009 GGGATCGATTCACGGCTCC 60.301 63.158 5.94 0.00 42.82 4.70
349 657 0.598680 CTGGGATCGATTCACGGCTC 60.599 60.000 5.94 0.00 42.82 4.70
350 658 1.443407 CTGGGATCGATTCACGGCT 59.557 57.895 5.94 0.00 42.82 5.52
351 659 4.033894 CTGGGATCGATTCACGGC 57.966 61.111 5.94 0.00 42.82 5.68
352 660 1.595382 GGCTGGGATCGATTCACGG 60.595 63.158 5.94 3.96 42.82 4.94
353 661 1.951130 CGGCTGGGATCGATTCACG 60.951 63.158 5.94 0.62 44.09 4.35
354 662 0.387929 TACGGCTGGGATCGATTCAC 59.612 55.000 5.94 0.00 0.00 3.18
355 663 0.673985 CTACGGCTGGGATCGATTCA 59.326 55.000 5.94 4.24 0.00 2.57
356 664 0.038159 CCTACGGCTGGGATCGATTC 60.038 60.000 0.00 0.00 0.00 2.52
357 665 0.759436 ACCTACGGCTGGGATCGATT 60.759 55.000 0.00 0.00 0.00 3.34
368 676 3.057456 CCAGTGATAGATGTACCTACGGC 60.057 52.174 0.00 0.00 0.00 5.68
370 678 5.064558 AGTCCAGTGATAGATGTACCTACG 58.935 45.833 0.00 0.00 0.00 3.51
374 682 5.179742 CGTCTAGTCCAGTGATAGATGTACC 59.820 48.000 0.00 0.00 31.00 3.34
382 690 2.092592 TGAGCCGTCTAGTCCAGTGATA 60.093 50.000 0.00 0.00 0.00 2.15
394 702 0.458543 CAGCGTTATGTGAGCCGTCT 60.459 55.000 0.00 0.00 0.00 4.18
411 719 3.743911 TGTTACACAAATGCTCGGTACAG 59.256 43.478 0.00 0.00 0.00 2.74
578 889 1.403647 CGAGCACGTTGTTATCCCTGA 60.404 52.381 0.00 0.00 34.56 3.86
579 890 0.999406 CGAGCACGTTGTTATCCCTG 59.001 55.000 0.00 0.00 34.56 4.45
580 891 3.436001 CGAGCACGTTGTTATCCCT 57.564 52.632 0.00 0.00 34.56 4.20
658 969 1.229359 CAGCCCAGCCAGATCCAAT 59.771 57.895 0.00 0.00 0.00 3.16
687 1003 1.739562 GCTGCTCACTTGGTCCTCG 60.740 63.158 0.00 0.00 0.00 4.63
704 1020 1.007038 TACGGAGGTGTGTGTTCGC 60.007 57.895 0.00 0.00 0.00 4.70
839 1191 7.829706 GGGACAAAAGGAAAACTACTCTATGAT 59.170 37.037 0.00 0.00 0.00 2.45
925 1277 1.533756 CCACAACCACAAGCAAACGAG 60.534 52.381 0.00 0.00 0.00 4.18
927 1279 0.527385 CCCACAACCACAAGCAAACG 60.527 55.000 0.00 0.00 0.00 3.60
929 1281 0.534412 CACCCACAACCACAAGCAAA 59.466 50.000 0.00 0.00 0.00 3.68
940 1292 2.382770 ACCACAGCTCCACCCACAA 61.383 57.895 0.00 0.00 0.00 3.33
1560 1950 3.782523 TCATACCTCTTGCAGAAGGGAAT 59.217 43.478 17.85 9.84 30.10 3.01
1578 1968 0.036765 GCCCTCACACCAACGTCATA 60.037 55.000 0.00 0.00 0.00 2.15
1580 1970 2.110213 GCCCTCACACCAACGTCA 59.890 61.111 0.00 0.00 0.00 4.35
1645 2035 2.261671 CCAGGAACTCGTGGTCGG 59.738 66.667 9.79 0.00 44.48 4.79
1688 2078 1.139520 GAAATGGTCACCATGGCGC 59.860 57.895 11.08 0.00 44.40 6.53
1700 2090 5.633182 CCAAACATTACGGAAACTGAAATGG 59.367 40.000 0.00 0.00 32.97 3.16
1704 2094 4.024725 CGACCAAACATTACGGAAACTGAA 60.025 41.667 0.00 0.00 0.00 3.02
1734 2124 0.816825 AGATGCATGGTCATGGCGAC 60.817 55.000 2.46 0.00 44.57 5.19
1779 2169 1.202687 TGGCCAGCTTCTCATATTCGG 60.203 52.381 0.00 0.00 0.00 4.30
1849 2239 0.179161 CGATGAACTCGGCGAACTCT 60.179 55.000 12.13 0.78 43.82 3.24
1909 2299 0.674581 ACATGGACATGGTCAGTGCG 60.675 55.000 15.94 0.00 42.91 5.34
1939 2337 0.525761 ATTTGCTACGCGTTTGGCAT 59.474 45.000 25.89 14.87 43.84 4.40
1950 2348 0.645868 GCACGAGACGGATTTGCTAC 59.354 55.000 0.00 0.00 0.00 3.58
1993 2391 1.971357 TCCCAGAGAACCTGAACTCAC 59.029 52.381 0.00 0.00 45.78 3.51
2089 2487 1.528309 ACCGGCCTTGAAGTTGTGG 60.528 57.895 0.00 0.00 0.00 4.17
2184 2584 5.830912 TGAACTTTCAACTGCCACTTATTG 58.169 37.500 0.00 0.00 33.55 1.90
2185 2585 5.827797 TCTGAACTTTCAACTGCCACTTATT 59.172 36.000 0.00 0.00 36.64 1.40
2187 2587 4.574828 GTCTGAACTTTCAACTGCCACTTA 59.425 41.667 0.00 0.00 36.64 2.24
2197 2597 6.993786 TTGTACACATGTCTGAACTTTCAA 57.006 33.333 0.00 0.00 36.64 2.69
2199 2599 5.853282 GCATTGTACACATGTCTGAACTTTC 59.147 40.000 15.05 0.00 0.00 2.62
2211 2611 5.756195 ATTATCAAGCGCATTGTACACAT 57.244 34.783 11.47 3.46 40.05 3.21
2212 2612 5.559427 AATTATCAAGCGCATTGTACACA 57.441 34.783 11.47 0.00 40.05 3.72
2213 2613 5.275881 GCAAATTATCAAGCGCATTGTACAC 60.276 40.000 11.47 0.00 40.05 2.90
2216 2616 4.991472 TGCAAATTATCAAGCGCATTGTA 58.009 34.783 11.47 4.38 40.05 2.41
2232 2632 7.201582 GCTCAGCTTAATTATTTGCTTGCAAAT 60.202 33.333 28.66 28.66 38.25 2.32
2233 2633 6.091169 GCTCAGCTTAATTATTTGCTTGCAAA 59.909 34.615 20.74 20.74 34.71 3.68
2234 2634 5.577945 GCTCAGCTTAATTATTTGCTTGCAA 59.422 36.000 3.70 3.70 34.71 4.08
2235 2635 5.104374 GCTCAGCTTAATTATTTGCTTGCA 58.896 37.500 16.21 0.00 34.71 4.08
2236 2636 4.205792 CGCTCAGCTTAATTATTTGCTTGC 59.794 41.667 0.00 10.46 33.03 4.01
2237 2637 5.335127 ACGCTCAGCTTAATTATTTGCTTG 58.665 37.500 0.00 4.38 33.03 4.01
2238 2638 5.567138 ACGCTCAGCTTAATTATTTGCTT 57.433 34.783 0.00 0.00 33.03 3.91
2239 2639 5.567138 AACGCTCAGCTTAATTATTTGCT 57.433 34.783 0.00 3.31 36.04 3.91
2240 2640 5.053025 CGAAACGCTCAGCTTAATTATTTGC 60.053 40.000 0.00 0.00 0.00 3.68
2241 2641 6.021596 ACGAAACGCTCAGCTTAATTATTTG 58.978 36.000 0.00 0.00 0.00 2.32
2242 2642 6.021596 CACGAAACGCTCAGCTTAATTATTT 58.978 36.000 0.00 0.00 0.00 1.40
2243 2643 5.447279 CCACGAAACGCTCAGCTTAATTATT 60.447 40.000 0.00 0.00 0.00 1.40
2244 2644 4.034048 CCACGAAACGCTCAGCTTAATTAT 59.966 41.667 0.00 0.00 0.00 1.28
2259 2659 0.307760 CCTTGTCTGCACCACGAAAC 59.692 55.000 0.00 0.00 0.00 2.78
2733 3151 7.581476 CACTGACCAAATACTTCAATTTACGT 58.419 34.615 0.00 0.00 0.00 3.57
2743 3161 5.536161 ACTGAAATGCACTGACCAAATACTT 59.464 36.000 0.00 0.00 0.00 2.24
2890 3309 2.052690 TGGTCTAGCGAGCAGGTCC 61.053 63.158 0.00 0.00 42.30 4.46
2929 3348 3.791973 ACTTGTTTTGCCATTTCGACA 57.208 38.095 0.00 0.00 0.00 4.35
3053 3473 3.399440 AGAGAGAAACTGCAGAAGGTG 57.601 47.619 23.35 0.00 0.00 4.00
3091 3512 3.260632 ACCCACCCAATCTGCAAAAATAC 59.739 43.478 0.00 0.00 0.00 1.89
3147 3572 4.467084 GCCGCCTGGATCCGTTGA 62.467 66.667 7.39 0.00 37.49 3.18
3234 3659 1.073897 GAACTGGGTCAAGCTGGCT 59.926 57.895 0.00 0.00 0.00 4.75
3350 3775 1.194997 ACGCGTCTACGATGAGATAGC 59.805 52.381 5.58 0.00 43.02 2.97
3408 3833 1.074566 AGAAGGCAGAAAGGTCCCAAG 59.925 52.381 0.00 0.00 0.00 3.61
3438 3863 3.579586 TGTGTACCGTTGGTAAGAAGGAT 59.420 43.478 0.00 0.00 40.12 3.24
3447 3872 3.735514 GCAAAAATGTGTGTACCGTTGGT 60.736 43.478 0.00 0.00 40.16 3.67
3506 3931 1.067669 TGCAAAACGGCAAATGCACTA 59.932 42.857 7.80 0.00 43.32 2.74
3518 4062 1.469703 TCATCTGATGCCTGCAAAACG 59.530 47.619 12.78 0.00 0.00 3.60
3533 4077 4.338879 CTGGGATGTGAAAACCTTCATCT 58.661 43.478 0.00 0.00 43.39 2.90
3547 4091 0.839946 AAATAGAGCCGCTGGGATGT 59.160 50.000 0.00 0.00 34.06 3.06
3566 4110 7.681679 TCAGGTGGTATATGTTGTAAGTCAAA 58.318 34.615 0.00 0.00 37.81 2.69
3788 4332 1.002624 GAACAACCCAGGATCGGCA 60.003 57.895 0.00 0.00 0.00 5.69
3801 4345 1.305201 GCCGAGTCAAAGGTGAACAA 58.695 50.000 0.00 0.00 34.87 2.83
3836 4380 2.986413 ACTGAGAGCGCCGTCACT 60.986 61.111 2.29 0.00 0.00 3.41
3852 4396 0.951558 AGGGCGACAATGTTCAACAC 59.048 50.000 0.00 0.00 0.00 3.32
3855 4399 1.234821 GTGAGGGCGACAATGTTCAA 58.765 50.000 0.00 0.00 0.00 2.69
3966 4510 0.537143 ACGAATGGCCAGAAGCACAA 60.537 50.000 13.05 0.00 46.50 3.33
3980 4524 0.976641 TGACAAGCCCTCTCACGAAT 59.023 50.000 0.00 0.00 0.00 3.34
4001 4545 2.969950 CGGGATCCCATACTTTCCACTA 59.030 50.000 30.42 0.00 35.37 2.74
4106 4650 6.685403 ACCGAAATTACGCTTCAAATATTTCG 59.315 34.615 16.44 16.44 46.63 3.46
4115 4659 3.185594 CACAGAACCGAAATTACGCTTCA 59.814 43.478 0.00 0.00 32.50 3.02
4136 4680 2.884320 TGTGGTAGGAGTAGTTCTGCA 58.116 47.619 0.00 0.00 36.95 4.41
4137 4681 4.473477 AATGTGGTAGGAGTAGTTCTGC 57.527 45.455 0.00 0.00 34.62 4.26
4233 4803 9.520204 AAATCACGATCAACAAATCCATATTTC 57.480 29.630 0.00 0.00 32.87 2.17
4316 4886 4.568152 AACTGGGAAAAATCACACGAAG 57.432 40.909 0.00 0.00 0.00 3.79
4326 4896 9.898152 ATCAACTAAATGAAAAACTGGGAAAAA 57.102 25.926 0.00 0.00 32.06 1.94
4394 4976 8.244113 ACAGGTGAAAAGAAAGTGTAAAGAAAG 58.756 33.333 0.00 0.00 0.00 2.62
4402 4984 4.086457 ACCAACAGGTGAAAAGAAAGTGT 58.914 39.130 0.00 0.00 33.38 3.55
4403 4985 4.718940 ACCAACAGGTGAAAAGAAAGTG 57.281 40.909 0.00 0.00 33.38 3.16
4404 4986 4.526650 ACAACCAACAGGTGAAAAGAAAGT 59.473 37.500 0.00 0.00 35.32 2.66
4406 4988 4.282195 ACACAACCAACAGGTGAAAAGAAA 59.718 37.500 0.00 0.00 35.32 2.52
4409 4991 3.510719 CACACAACCAACAGGTGAAAAG 58.489 45.455 0.00 0.00 35.32 2.27
4410 4992 2.353208 GCACACAACCAACAGGTGAAAA 60.353 45.455 0.00 0.00 35.32 2.29
4411 4993 1.203523 GCACACAACCAACAGGTGAAA 59.796 47.619 0.00 0.00 35.32 2.69
4414 4996 0.529833 TTGCACACAACCAACAGGTG 59.470 50.000 0.00 0.00 35.32 4.00
4415 4997 2.968737 TTGCACACAACCAACAGGT 58.031 47.368 0.00 0.00 37.19 4.00
4424 5006 0.958091 GGGCATGTAGTTGCACACAA 59.042 50.000 0.00 0.00 45.57 3.33
4425 5007 2.639970 GGGCATGTAGTTGCACACA 58.360 52.632 0.00 0.00 45.57 3.72
4439 5025 1.152984 CACAAGTGACCAGTGGGCA 60.153 57.895 15.83 15.83 39.14 5.36
4440 5026 1.898574 CCACAAGTGACCAGTGGGC 60.899 63.158 15.21 12.18 46.98 5.36
4441 5027 4.481195 CCACAAGTGACCAGTGGG 57.519 61.111 15.21 0.00 46.98 4.61
4445 5031 1.001048 CATGCAACCACAAGTGACCAG 60.001 52.381 0.94 0.00 0.00 4.00
4446 5032 1.031235 CATGCAACCACAAGTGACCA 58.969 50.000 0.94 0.00 0.00 4.02
4457 5081 1.359848 CGACTAGTGGACATGCAACC 58.640 55.000 0.00 0.00 0.00 3.77
4473 5097 2.127270 CATGTGGTTGCACGCGAC 60.127 61.111 15.93 4.74 0.00 5.19
4477 5101 0.597568 ATTGGACATGTGGTTGCACG 59.402 50.000 1.15 0.00 0.00 5.34
4478 5102 1.337074 CCATTGGACATGTGGTTGCAC 60.337 52.381 1.15 0.00 0.00 4.57
4480 5104 0.968405 ACCATTGGACATGTGGTTGC 59.032 50.000 10.37 0.00 43.44 4.17
4500 5124 4.155099 CCGGTAGACATGTAATTTTGTGCA 59.845 41.667 0.00 0.00 0.00 4.57
4502 5126 5.873179 ACCGGTAGACATGTAATTTTGTG 57.127 39.130 4.49 0.00 0.00 3.33
4503 5127 6.072342 GGAAACCGGTAGACATGTAATTTTGT 60.072 38.462 8.00 0.00 0.00 2.83
4504 5128 6.319399 GGAAACCGGTAGACATGTAATTTTG 58.681 40.000 8.00 0.00 0.00 2.44
4509 5133 3.615224 GGGAAACCGGTAGACATGTAA 57.385 47.619 8.00 0.00 43.64 2.41
4530 5154 1.030488 ACTGATGGACATGCTGCTGC 61.030 55.000 8.89 8.89 40.20 5.25
4531 5155 1.132453 CAACTGATGGACATGCTGCTG 59.868 52.381 0.00 0.00 0.00 4.41
4532 5156 1.271762 ACAACTGATGGACATGCTGCT 60.272 47.619 0.00 0.00 0.00 4.24
4533 5157 1.135489 CACAACTGATGGACATGCTGC 60.135 52.381 0.00 0.00 0.00 5.25
4534 5158 1.135489 GCACAACTGATGGACATGCTG 60.135 52.381 0.00 0.00 0.00 4.41
4535 5159 1.171308 GCACAACTGATGGACATGCT 58.829 50.000 0.00 0.00 0.00 3.79
4563 5187 1.745087 CATGTACACAGGGATGCAACC 59.255 52.381 4.00 4.00 0.00 3.77
4606 5230 1.330521 GTGCACTGTAGTTGTGTGTGG 59.669 52.381 10.32 0.00 37.70 4.17
4607 5231 2.006169 TGTGCACTGTAGTTGTGTGTG 58.994 47.619 19.41 0.00 37.70 3.82
4608 5232 2.006888 GTGTGCACTGTAGTTGTGTGT 58.993 47.619 19.41 0.00 37.70 3.72
4703 5327 9.639601 CTTTCAGTTCTACTTTGTTTTCCTTTT 57.360 29.630 0.00 0.00 0.00 2.27
4745 5369 7.952671 AGCTCTAATCGTCACCATAGAATTTA 58.047 34.615 0.00 0.00 0.00 1.40
4760 5384 1.269831 GGGTGTGGCTAGCTCTAATCG 60.270 57.143 15.72 0.00 0.00 3.34
4773 5397 5.605534 TCATGTAACAAATTTTGGGTGTGG 58.394 37.500 13.42 0.12 34.12 4.17
4800 5424 2.069273 ACTCGACAGAAAAAGATGCGG 58.931 47.619 0.00 0.00 0.00 5.69
4801 5425 2.092838 GGACTCGACAGAAAAAGATGCG 59.907 50.000 0.00 0.00 0.00 4.73
4864 5488 4.776322 CGATCTTGCCACCGCCCA 62.776 66.667 0.00 0.00 0.00 5.36
4903 5527 1.406341 GGCTTTGTCTGGCGGTGTATA 60.406 52.381 0.00 0.00 0.00 1.47
4908 5532 3.553095 GAGGGCTTTGTCTGGCGGT 62.553 63.158 0.00 0.00 0.00 5.68
4916 5540 0.394899 GCCAGCTATGAGGGCTTTGT 60.395 55.000 4.80 0.00 44.32 2.83
4929 5559 0.816825 CTACATCATTGCCGCCAGCT 60.817 55.000 0.00 0.00 44.23 4.24
4934 5564 3.741344 CCTACTAACTACATCATTGCCGC 59.259 47.826 0.00 0.00 0.00 6.53
4984 5615 2.496817 CCCTCGACTGCAGCTACC 59.503 66.667 15.27 0.00 0.00 3.18
5001 5632 3.096495 TCCCTAGGCCCCACATGC 61.096 66.667 2.05 0.00 0.00 4.06
5019 5650 5.354513 GGCAAGAAACTTAAGGTGATAGACC 59.645 44.000 7.53 0.00 46.58 3.85
5020 5651 6.174049 AGGCAAGAAACTTAAGGTGATAGAC 58.826 40.000 7.53 0.00 0.00 2.59
5021 5652 6.213600 AGAGGCAAGAAACTTAAGGTGATAGA 59.786 38.462 7.53 0.00 0.00 1.98
5022 5653 6.410540 AGAGGCAAGAAACTTAAGGTGATAG 58.589 40.000 7.53 0.00 0.00 2.08
5023 5654 6.374417 AGAGGCAAGAAACTTAAGGTGATA 57.626 37.500 7.53 0.00 0.00 2.15
5024 5655 5.248380 AGAGGCAAGAAACTTAAGGTGAT 57.752 39.130 7.53 0.00 0.00 3.06
5025 5656 4.706842 AGAGGCAAGAAACTTAAGGTGA 57.293 40.909 7.53 0.00 0.00 4.02
5026 5657 5.998363 AGTTAGAGGCAAGAAACTTAAGGTG 59.002 40.000 7.53 0.00 0.00 4.00
5027 5658 6.183361 TGAGTTAGAGGCAAGAAACTTAAGGT 60.183 38.462 7.53 0.00 32.51 3.50
5028 5659 6.231211 TGAGTTAGAGGCAAGAAACTTAAGG 58.769 40.000 7.53 0.00 32.51 2.69
5029 5660 7.913674 ATGAGTTAGAGGCAAGAAACTTAAG 57.086 36.000 0.00 0.00 32.51 1.85
5030 5661 9.787435 TTTATGAGTTAGAGGCAAGAAACTTAA 57.213 29.630 0.00 0.00 32.51 1.85
5031 5662 9.959721 ATTTATGAGTTAGAGGCAAGAAACTTA 57.040 29.630 0.00 0.00 32.51 2.24
5032 5663 8.870075 ATTTATGAGTTAGAGGCAAGAAACTT 57.130 30.769 0.00 0.00 32.51 2.66
5035 5666 9.561069 GGATATTTATGAGTTAGAGGCAAGAAA 57.439 33.333 0.00 0.00 0.00 2.52
5036 5667 8.157476 GGGATATTTATGAGTTAGAGGCAAGAA 58.843 37.037 0.00 0.00 0.00 2.52
5037 5668 7.256691 GGGGATATTTATGAGTTAGAGGCAAGA 60.257 40.741 0.00 0.00 0.00 3.02
5038 5669 6.881602 GGGGATATTTATGAGTTAGAGGCAAG 59.118 42.308 0.00 0.00 0.00 4.01
5039 5670 6.520061 CGGGGATATTTATGAGTTAGAGGCAA 60.520 42.308 0.00 0.00 0.00 4.52
5040 5671 5.046591 CGGGGATATTTATGAGTTAGAGGCA 60.047 44.000 0.00 0.00 0.00 4.75
5041 5672 5.187186 TCGGGGATATTTATGAGTTAGAGGC 59.813 44.000 0.00 0.00 0.00 4.70
5042 5673 6.852420 TCGGGGATATTTATGAGTTAGAGG 57.148 41.667 0.00 0.00 0.00 3.69
5043 5674 7.603024 GGTTTCGGGGATATTTATGAGTTAGAG 59.397 40.741 0.00 0.00 0.00 2.43
5044 5675 7.447594 GGTTTCGGGGATATTTATGAGTTAGA 58.552 38.462 0.00 0.00 0.00 2.10
5045 5676 6.653740 GGGTTTCGGGGATATTTATGAGTTAG 59.346 42.308 0.00 0.00 0.00 2.34
5046 5677 6.330778 AGGGTTTCGGGGATATTTATGAGTTA 59.669 38.462 0.00 0.00 0.00 2.24
5047 5678 5.133830 AGGGTTTCGGGGATATTTATGAGTT 59.866 40.000 0.00 0.00 0.00 3.01
5048 5679 4.663592 AGGGTTTCGGGGATATTTATGAGT 59.336 41.667 0.00 0.00 0.00 3.41
5049 5680 5.242795 AGGGTTTCGGGGATATTTATGAG 57.757 43.478 0.00 0.00 0.00 2.90
5050 5681 5.371472 AGAAGGGTTTCGGGGATATTTATGA 59.629 40.000 0.00 0.00 38.38 2.15
5051 5682 5.631119 AGAAGGGTTTCGGGGATATTTATG 58.369 41.667 0.00 0.00 38.38 1.90
5052 5683 5.924769 AGAAGGGTTTCGGGGATATTTAT 57.075 39.130 0.00 0.00 38.38 1.40
5053 5684 5.192121 TGAAGAAGGGTTTCGGGGATATTTA 59.808 40.000 0.00 0.00 38.38 1.40
5054 5685 4.017867 TGAAGAAGGGTTTCGGGGATATTT 60.018 41.667 0.00 0.00 38.38 1.40
5055 5686 3.526019 TGAAGAAGGGTTTCGGGGATATT 59.474 43.478 0.00 0.00 38.38 1.28
5056 5687 3.120108 TGAAGAAGGGTTTCGGGGATAT 58.880 45.455 0.00 0.00 38.38 1.63
5057 5688 2.504175 CTGAAGAAGGGTTTCGGGGATA 59.496 50.000 0.00 0.00 38.38 2.59
5058 5689 1.282157 CTGAAGAAGGGTTTCGGGGAT 59.718 52.381 0.00 0.00 38.38 3.85
5059 5690 0.690762 CTGAAGAAGGGTTTCGGGGA 59.309 55.000 0.00 0.00 38.38 4.81
5060 5691 0.690762 TCTGAAGAAGGGTTTCGGGG 59.309 55.000 0.00 0.00 38.38 5.73
5061 5692 2.789409 ATCTGAAGAAGGGTTTCGGG 57.211 50.000 0.00 0.00 38.38 5.14
5062 5693 3.939592 GGTAATCTGAAGAAGGGTTTCGG 59.060 47.826 0.00 0.00 38.38 4.30
5063 5694 4.575885 TGGTAATCTGAAGAAGGGTTTCG 58.424 43.478 0.00 0.00 38.38 3.46
5064 5695 6.180472 TCATGGTAATCTGAAGAAGGGTTTC 58.820 40.000 0.00 0.00 0.00 2.78
5065 5696 6.139679 TCATGGTAATCTGAAGAAGGGTTT 57.860 37.500 0.00 0.00 0.00 3.27
5066 5697 5.779241 TCATGGTAATCTGAAGAAGGGTT 57.221 39.130 0.00 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.