Multiple sequence alignment - TraesCS6A01G096200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G096200 chr6A 100.000 4472 0 0 1 4472 63584665 63589136 0.000000e+00 8259.0
1 TraesCS6A01G096200 chr6B 92.670 3165 126 39 525 3613 119819871 119823005 0.000000e+00 4462.0
2 TraesCS6A01G096200 chr6B 86.220 508 36 17 1 503 119819008 119819486 1.840000e-143 520.0
3 TraesCS6A01G096200 chr6B 89.372 207 12 2 3594 3799 119827550 119827747 7.430000e-63 252.0
4 TraesCS6A01G096200 chr6B 92.424 132 9 1 3797 3928 119827859 119827989 2.120000e-43 187.0
5 TraesCS6A01G096200 chr6D 89.440 2216 122 42 222 2388 52694492 52696644 0.000000e+00 2693.0
6 TraesCS6A01G096200 chr6D 88.646 1735 114 23 2453 4144 52696751 52698445 0.000000e+00 2036.0
7 TraesCS6A01G096200 chr6D 94.059 202 11 1 1 202 52694300 52694500 5.620000e-79 305.0
8 TraesCS6A01G096200 chr6D 84.588 279 13 9 4195 4470 52699132 52699383 2.670000e-62 250.0
9 TraesCS6A01G096200 chr6D 79.775 89 17 1 2379 2466 12086452 12086364 3.730000e-06 63.9
10 TraesCS6A01G096200 chr3A 88.421 95 9 2 2378 2471 161458276 161458369 3.660000e-21 113.0
11 TraesCS6A01G096200 chr3A 85.227 88 11 2 2378 2464 303756790 303756876 6.160000e-14 89.8
12 TraesCS6A01G096200 chr2A 86.022 93 9 4 2377 2467 690329423 690329333 3.680000e-16 97.1
13 TraesCS6A01G096200 chr4A 85.057 87 13 0 2378 2464 575026756 575026670 6.160000e-14 89.8
14 TraesCS6A01G096200 chr2B 84.444 90 12 2 2376 2464 18809699 18809611 2.220000e-13 87.9
15 TraesCS6A01G096200 chr1B 88.889 72 5 3 2376 2447 591112870 591112938 7.970000e-13 86.1
16 TraesCS6A01G096200 chr4B 82.796 93 13 1 2372 2464 496466945 496467034 3.710000e-11 80.5


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 TraesCS6A01G096200 chr6A 63584665 63589136 4471 False 8259 8259 100.00000 1 4472 1 chr6A.!!$F1 4471
1 TraesCS6A01G096200 chr6B 119819008 119823005 3997 False 2491 4462 89.44500 1 3613 2 chr6B.!!$F1 3612
2 TraesCS6A01G096200 chr6D 52694300 52699383 5083 False 1321 2693 89.18325 1 4470 4 chr6D.!!$F1 4469

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
270 273 0.623723 TGGTGGTGATTAGGGAAGGC 59.376 55.000 0.00 0.0 0.00 4.35 F
334 337 0.749454 GCTGCTGGGATTGGATTCGT 60.749 55.000 0.00 0.0 0.00 3.85 F
409 413 1.585006 CGTCAGCCCTTGTAGTCGT 59.415 57.895 0.00 0.0 0.00 4.34 F
1093 1489 1.691196 CCTTTGTGACCAGGAAGCAA 58.309 50.000 0.00 0.0 30.81 3.91 F
1213 1609 3.064682 TGAAAACCACAATATCGATGCGG 59.935 43.478 8.54 0.0 0.00 5.69 F
1813 2226 3.146066 TGGTAAGATGTTCACACCTTGC 58.854 45.455 0.00 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1515 0.955428 TTCCTGCGGTGTCAGATTGC 60.955 55.000 0.0 0.0 36.19 3.56 R
1532 1945 1.270252 TGATTGAGCACTTGAGCGTCA 60.270 47.619 0.0 0.0 40.15 4.35 R
1571 1984 2.289631 TGAGTGTTAGCATGTCAGGTGG 60.290 50.000 0.0 0.0 0.00 4.61 R
2770 3251 0.671781 GCTTCAGACACGGCACAGAT 60.672 55.000 0.0 0.0 0.00 2.90 R
2771 3252 1.300931 GCTTCAGACACGGCACAGA 60.301 57.895 0.0 0.0 0.00 3.41 R
3753 4272 0.250234 CAGAGCACAGGATTTCCGGA 59.750 55.000 0.0 0.0 42.08 5.14 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
101 104 1.133915 CCTGCATATTTACACCCCCGT 60.134 52.381 0.00 0.00 0.00 5.28
103 106 0.666374 GCATATTTACACCCCCGTGC 59.334 55.000 0.00 0.00 44.40 5.34
110 113 1.312371 TACACCCCCGTGCTACGTAC 61.312 60.000 0.00 0.00 44.40 3.67
113 116 1.227147 CCCCCGTGCTACGTACATG 60.227 63.158 0.00 1.01 40.58 3.21
249 252 1.052287 CGTCGTTTACCGTGTACCAC 58.948 55.000 0.00 0.00 37.94 4.16
270 273 0.623723 TGGTGGTGATTAGGGAAGGC 59.376 55.000 0.00 0.00 0.00 4.35
334 337 0.749454 GCTGCTGGGATTGGATTCGT 60.749 55.000 0.00 0.00 0.00 3.85
386 389 4.715130 TGGGTCACTCGGAGGGGG 62.715 72.222 7.54 0.00 0.00 5.40
409 413 1.585006 CGTCAGCCCTTGTAGTCGT 59.415 57.895 0.00 0.00 0.00 4.34
457 461 7.013529 GCTTGTTTTGAATTCTCAATTGATGC 58.986 34.615 8.96 0.00 41.22 3.91
468 472 3.091545 TCAATTGATGCTCCCAGGTTTC 58.908 45.455 3.38 0.00 0.00 2.78
551 920 4.142381 GGGACCATAACTGATTTTGCACTC 60.142 45.833 0.00 0.00 0.00 3.51
560 929 7.559590 AACTGATTTTGCACTCTATATGGTC 57.440 36.000 0.00 0.00 0.00 4.02
633 1002 6.627243 ACATCAATCATTCCATGTTTCAGTG 58.373 36.000 0.00 0.00 0.00 3.66
659 1028 7.738437 ACAGGATTCCATTATGAACCAATTT 57.262 32.000 5.29 0.00 0.00 1.82
675 1044 8.675504 TGAACCAATTTCTAGTTCGTGTAAAAA 58.324 29.630 0.00 0.00 42.22 1.94
746 1115 4.516698 GTGGTCTGATAACATGCCCAATAG 59.483 45.833 0.00 0.00 0.00 1.73
783 1167 3.146847 CAACCAAAGAGGAGGTTACCAC 58.853 50.000 3.51 0.00 45.93 4.16
784 1168 2.702748 ACCAAAGAGGAGGTTACCACT 58.297 47.619 3.51 0.58 41.22 4.00
785 1169 3.053826 ACCAAAGAGGAGGTTACCACTT 58.946 45.455 3.51 0.00 41.23 3.16
786 1170 4.237018 ACCAAAGAGGAGGTTACCACTTA 58.763 43.478 3.51 0.00 39.25 2.24
787 1171 4.041321 ACCAAAGAGGAGGTTACCACTTAC 59.959 45.833 3.51 0.00 39.25 2.34
788 1172 4.565028 CCAAAGAGGAGGTTACCACTTACC 60.565 50.000 3.51 0.00 39.25 2.85
789 1173 3.555117 AGAGGAGGTTACCACTTACCA 57.445 47.619 3.51 0.00 36.87 3.25
836 1232 5.788014 TGGAATTTACCCTAAATGGCCTTTT 59.212 36.000 19.44 19.44 38.32 2.27
844 1240 6.292923 ACCCTAAATGGCCTTTTGTTTTTAC 58.707 36.000 23.25 0.00 0.00 2.01
847 1243 5.977171 AAATGGCCTTTTGTTTTTACGTC 57.023 34.783 15.39 0.00 0.00 4.34
1093 1489 1.691196 CCTTTGTGACCAGGAAGCAA 58.309 50.000 0.00 0.00 30.81 3.91
1119 1515 4.984785 TCAGATTCGCAGGAGATATTTTCG 59.015 41.667 0.00 0.00 0.00 3.46
1197 1593 5.349543 GCCATTGATTGTTGAGGATGAAAAC 59.650 40.000 0.00 0.00 0.00 2.43
1213 1609 3.064682 TGAAAACCACAATATCGATGCGG 59.935 43.478 8.54 0.00 0.00 5.69
1281 1677 4.314522 TTGCCTTGATAATGAAGGTCCA 57.685 40.909 4.37 0.00 41.93 4.02
1322 1718 9.853177 CTATGACCTGAAATACCCTTTTCTTAT 57.147 33.333 0.00 0.00 36.71 1.73
1500 1913 7.624360 AAGGTATTGATTCACGAGCATTTTA 57.376 32.000 0.00 0.00 0.00 1.52
1571 1984 3.430453 TCATCCTGAAATCCACCCAAAC 58.570 45.455 0.00 0.00 0.00 2.93
1813 2226 3.146066 TGGTAAGATGTTCACACCTTGC 58.854 45.455 0.00 0.00 0.00 4.01
1845 2258 7.759489 AGTGCCATGAACTAATTTTCTTACA 57.241 32.000 0.00 0.00 0.00 2.41
1846 2259 7.593825 AGTGCCATGAACTAATTTTCTTACAC 58.406 34.615 0.00 0.00 0.00 2.90
2056 2469 8.584157 TCCTTGCACATGTTACAAAATATCTTT 58.416 29.630 11.21 0.00 0.00 2.52
2129 2542 7.867909 CGAATGAGAACTAGATAACTTATGCCA 59.132 37.037 0.00 0.00 0.00 4.92
2164 2577 5.431765 TGGATTTCTTCCTATTCAGTGCTC 58.568 41.667 0.00 0.00 45.68 4.26
2184 2600 4.884164 GCTCTCAATATGGTTTGGCTACTT 59.116 41.667 0.00 0.00 0.00 2.24
2217 2633 5.511234 AGCCACTCATTATTTGCATCTTC 57.489 39.130 0.00 0.00 0.00 2.87
2397 2822 7.793948 ACATAGTACTCCCTCTGTAAACTTT 57.206 36.000 0.00 0.00 0.00 2.66
2445 2870 9.631452 AAACTAGTGACCTAAAACGTCTTATAC 57.369 33.333 0.00 0.00 0.00 1.47
2447 2872 8.796475 ACTAGTGACCTAAAACGTCTTATACAA 58.204 33.333 0.00 0.00 0.00 2.41
2448 2873 9.630098 CTAGTGACCTAAAACGTCTTATACAAA 57.370 33.333 0.00 0.00 0.00 2.83
2497 2962 4.006319 GGATGAGGCATGGTTATCTAAGC 58.994 47.826 0.00 0.00 0.00 3.09
2507 2972 5.149973 TGGTTATCTAAGCGTGGTTTGTA 57.850 39.130 0.00 0.00 36.53 2.41
2659 3136 7.814107 ACAATAACTCATGCTTGTAAATTGGTG 59.186 33.333 16.13 5.65 30.43 4.17
2770 3251 8.785329 TTGTGATTGTACAAGTATTAGCATCA 57.215 30.769 14.65 6.55 35.75 3.07
2771 3252 8.962884 TGTGATTGTACAAGTATTAGCATCAT 57.037 30.769 14.65 0.00 0.00 2.45
2778 3259 4.818546 ACAAGTATTAGCATCATCTGTGCC 59.181 41.667 0.00 0.00 43.50 5.01
2783 3264 0.742281 AGCATCATCTGTGCCGTGTC 60.742 55.000 0.00 0.00 43.50 3.67
2957 3438 5.660460 CAAAGCAAGAGTTAACCAAGGTTT 58.340 37.500 10.13 5.76 39.31 3.27
2960 3441 4.709886 AGCAAGAGTTAACCAAGGTTTGTT 59.290 37.500 10.13 0.00 39.31 2.83
3088 3569 2.299013 TGTGCCACCAAGTACTCTAGTG 59.701 50.000 11.16 11.16 0.00 2.74
3099 3580 4.988029 AGTACTCTAGTGACCAACAGTCT 58.012 43.478 0.00 0.00 46.46 3.24
3100 3581 4.762765 AGTACTCTAGTGACCAACAGTCTG 59.237 45.833 0.00 0.00 46.46 3.51
3283 3802 3.347216 TCCTGGCAAACAATAGCTTCTC 58.653 45.455 0.00 0.00 0.00 2.87
3286 3805 3.754965 TGGCAAACAATAGCTTCTCAGT 58.245 40.909 0.00 0.00 0.00 3.41
3288 3807 5.500234 TGGCAAACAATAGCTTCTCAGTAT 58.500 37.500 0.00 0.00 0.00 2.12
3323 3842 6.809630 AATTTGTAGCACCTTCTCTTTCTC 57.190 37.500 0.00 0.00 0.00 2.87
3325 3844 4.258702 TGTAGCACCTTCTCTTTCTCAC 57.741 45.455 0.00 0.00 0.00 3.51
3462 3981 3.071206 GAGCTGAGGACGCTGGGA 61.071 66.667 0.00 0.00 37.96 4.37
3537 4056 8.621532 TGTTGATTTACAGCATTCTCTTAGTT 57.378 30.769 0.00 0.00 34.95 2.24
3559 4078 3.838317 TGTTATGGGTGCACTCTCTACTT 59.162 43.478 19.48 0.00 0.00 2.24
3576 4095 8.500753 TCTCTACTTGTCTAGAAATCACTCTC 57.499 38.462 0.00 0.00 0.00 3.20
3577 4096 8.325787 TCTCTACTTGTCTAGAAATCACTCTCT 58.674 37.037 0.00 0.00 0.00 3.10
3578 4097 9.607988 CTCTACTTGTCTAGAAATCACTCTCTA 57.392 37.037 0.00 0.00 0.00 2.43
3615 4134 7.035004 AGTATATGTAACGGCTCGTACAAAAA 58.965 34.615 0.62 0.00 39.99 1.94
3676 4195 0.598065 GGCCATTCCATTATCACGCC 59.402 55.000 0.00 0.00 34.01 5.68
3684 4203 3.779759 TCCATTATCACGCCAAAAATGC 58.220 40.909 0.00 0.00 0.00 3.56
3694 4213 1.073763 GCCAAAAATGCCCCCTTTTCT 59.926 47.619 0.00 0.00 0.00 2.52
3766 4285 0.698818 AAGGCTTCCGGAAATCCTGT 59.301 50.000 28.48 19.01 0.00 4.00
3774 4293 0.036010 CGGAAATCCTGTGCTCTGGT 60.036 55.000 10.96 0.00 34.80 4.00
3777 4296 0.674895 AAATCCTGTGCTCTGGTCGC 60.675 55.000 10.96 0.00 34.80 5.19
3780 4299 2.644212 CCTGTGCTCTGGTCGCTCT 61.644 63.158 3.69 0.00 0.00 4.09
3787 4306 3.117171 CTGGTCGCTCTGTGCTGC 61.117 66.667 0.00 0.00 40.11 5.25
3804 4323 1.717113 CTGCGTCGTCGTGTAATTTCA 59.283 47.619 3.66 0.00 39.49 2.69
3823 4342 1.792757 ATTTGGGCTGAGCTGGGTGA 61.793 55.000 3.72 0.00 0.00 4.02
3862 4381 0.761187 ACGCCACTCTATGCATGGAT 59.239 50.000 13.66 4.68 35.33 3.41
3915 4434 2.969262 CCCTAAGGTTCTGATCCCTCTC 59.031 54.545 1.13 0.00 0.00 3.20
3916 4435 3.374762 CCCTAAGGTTCTGATCCCTCTCT 60.375 52.174 1.13 0.00 0.00 3.10
3917 4436 3.895041 CCTAAGGTTCTGATCCCTCTCTC 59.105 52.174 1.13 0.00 0.00 3.20
3918 4437 3.774842 AAGGTTCTGATCCCTCTCTCT 57.225 47.619 1.13 0.00 0.00 3.10
3919 4438 4.890499 AAGGTTCTGATCCCTCTCTCTA 57.110 45.455 1.13 0.00 0.00 2.43
3929 4448 6.306199 TGATCCCTCTCTCTAGATCTTTCTG 58.694 44.000 0.00 0.00 36.82 3.02
3945 4464 2.852714 TCTGGTATCCCCTCGGTTTA 57.147 50.000 0.00 0.00 0.00 2.01
3951 4470 3.007723 GGTATCCCCTCGGTTTATTCCTC 59.992 52.174 0.00 0.00 0.00 3.71
3962 4481 2.380084 TTATTCCTCGCGCTCACTTT 57.620 45.000 5.56 0.00 0.00 2.66
3963 4482 2.380084 TATTCCTCGCGCTCACTTTT 57.620 45.000 5.56 0.00 0.00 2.27
3964 4483 1.523758 ATTCCTCGCGCTCACTTTTT 58.476 45.000 5.56 0.00 0.00 1.94
3965 4484 0.865769 TTCCTCGCGCTCACTTTTTC 59.134 50.000 5.56 0.00 0.00 2.29
3966 4485 1.130613 CCTCGCGCTCACTTTTTCG 59.869 57.895 5.56 0.00 0.00 3.46
3967 4486 1.282248 CCTCGCGCTCACTTTTTCGA 61.282 55.000 5.56 0.00 0.00 3.71
3968 4487 0.716108 CTCGCGCTCACTTTTTCGAT 59.284 50.000 5.56 0.00 0.00 3.59
3997 4521 0.467290 TCATCGCCCCTATTTTGCCC 60.467 55.000 0.00 0.00 0.00 5.36
4003 4527 3.899700 CCTATTTTGCCCGGCCGC 61.900 66.667 22.85 7.85 0.00 6.53
4004 4528 2.828549 CTATTTTGCCCGGCCGCT 60.829 61.111 22.85 0.00 0.00 5.52
4005 4529 3.124798 CTATTTTGCCCGGCCGCTG 62.125 63.158 22.85 14.59 0.00 5.18
4016 4540 4.773117 GCCGCTGCTGCAAAGCTC 62.773 66.667 16.29 6.87 38.57 4.09
4017 4541 4.112341 CCGCTGCTGCAAAGCTCC 62.112 66.667 16.29 0.32 38.57 4.70
4018 4542 3.359523 CGCTGCTGCAAAGCTCCA 61.360 61.111 16.29 0.00 38.57 3.86
4019 4543 2.697761 CGCTGCTGCAAAGCTCCAT 61.698 57.895 16.29 0.00 38.57 3.41
4020 4544 1.153823 GCTGCTGCAAAGCTCCATG 60.154 57.895 11.11 0.00 37.69 3.66
4042 4566 1.068333 GCGAAGGAAAATTCTGCTGCA 60.068 47.619 0.88 0.88 0.00 4.41
4097 4621 1.016130 CACAGGCGAGACATGTCACC 61.016 60.000 27.02 22.80 0.00 4.02
4106 4630 2.184322 CATGTCACCGTCTCCCCG 59.816 66.667 0.00 0.00 0.00 5.73
4119 4643 4.060667 CCCCGGCCCACCATTTCT 62.061 66.667 0.00 0.00 34.57 2.52
4122 4646 1.304052 CCGGCCCACCATTTCTTCA 60.304 57.895 0.00 0.00 34.57 3.02
4144 4668 7.311092 TCAATTTAGAAGAAGGGTCAGTACA 57.689 36.000 0.00 0.00 0.00 2.90
4145 4669 7.918076 TCAATTTAGAAGAAGGGTCAGTACAT 58.082 34.615 0.00 0.00 0.00 2.29
4147 4671 3.618690 AGAAGAAGGGTCAGTACATGC 57.381 47.619 0.00 0.00 0.00 4.06
4148 4672 3.177228 AGAAGAAGGGTCAGTACATGCT 58.823 45.455 0.00 0.00 0.00 3.79
4150 4674 4.042187 AGAAGAAGGGTCAGTACATGCTTT 59.958 41.667 0.00 0.00 0.00 3.51
4151 4675 5.248477 AGAAGAAGGGTCAGTACATGCTTTA 59.752 40.000 0.00 0.00 0.00 1.85
4152 4676 5.499004 AGAAGGGTCAGTACATGCTTTAA 57.501 39.130 0.00 0.00 0.00 1.52
4153 4677 5.491982 AGAAGGGTCAGTACATGCTTTAAG 58.508 41.667 0.00 0.00 0.00 1.85
4154 4678 4.910458 AGGGTCAGTACATGCTTTAAGT 57.090 40.909 0.00 0.00 0.00 2.24
4156 4680 4.286032 AGGGTCAGTACATGCTTTAAGTGA 59.714 41.667 0.00 0.00 0.00 3.41
4157 4681 5.045578 AGGGTCAGTACATGCTTTAAGTGAT 60.046 40.000 0.00 0.00 0.00 3.06
4158 4682 5.294552 GGGTCAGTACATGCTTTAAGTGATC 59.705 44.000 0.00 0.00 0.00 2.92
4160 4684 6.540189 GGTCAGTACATGCTTTAAGTGATCAT 59.460 38.462 0.00 0.00 0.00 2.45
4161 4685 7.404985 GTCAGTACATGCTTTAAGTGATCATG 58.595 38.462 0.00 8.16 40.07 3.07
4162 4686 7.065085 GTCAGTACATGCTTTAAGTGATCATGT 59.935 37.037 16.04 16.04 46.34 3.21
4163 4687 7.607607 TCAGTACATGCTTTAAGTGATCATGTT 59.392 33.333 16.67 0.00 43.40 2.71
4164 4688 7.907045 CAGTACATGCTTTAAGTGATCATGTTC 59.093 37.037 16.67 13.13 43.40 3.18
4165 4689 6.822667 ACATGCTTTAAGTGATCATGTTCA 57.177 33.333 0.00 2.22 43.40 3.18
4167 4691 5.885230 TGCTTTAAGTGATCATGTTCAGG 57.115 39.130 6.72 0.00 0.00 3.86
4168 4692 5.316167 TGCTTTAAGTGATCATGTTCAGGT 58.684 37.500 6.72 1.28 0.00 4.00
4170 4694 5.446473 GCTTTAAGTGATCATGTTCAGGTCG 60.446 44.000 6.72 0.00 0.00 4.79
4171 4695 2.680312 AGTGATCATGTTCAGGTCGG 57.320 50.000 6.72 0.00 0.00 4.79
4172 4696 1.902508 AGTGATCATGTTCAGGTCGGT 59.097 47.619 6.72 0.00 0.00 4.69
4173 4697 2.303022 AGTGATCATGTTCAGGTCGGTT 59.697 45.455 6.72 0.00 0.00 4.44
4174 4698 2.673368 GTGATCATGTTCAGGTCGGTTC 59.327 50.000 6.72 0.00 0.00 3.62
4175 4699 2.567169 TGATCATGTTCAGGTCGGTTCT 59.433 45.455 2.22 0.00 0.00 3.01
4176 4700 3.767131 TGATCATGTTCAGGTCGGTTCTA 59.233 43.478 2.22 0.00 0.00 2.10
4177 4701 4.221924 TGATCATGTTCAGGTCGGTTCTAA 59.778 41.667 2.22 0.00 0.00 2.10
4178 4702 4.610605 TCATGTTCAGGTCGGTTCTAAA 57.389 40.909 0.00 0.00 0.00 1.85
4179 4703 4.566004 TCATGTTCAGGTCGGTTCTAAAG 58.434 43.478 0.00 0.00 0.00 1.85
4180 4704 4.039973 TCATGTTCAGGTCGGTTCTAAAGT 59.960 41.667 0.00 0.00 0.00 2.66
4181 4705 3.724374 TGTTCAGGTCGGTTCTAAAGTG 58.276 45.455 0.00 0.00 0.00 3.16
4182 4706 3.385433 TGTTCAGGTCGGTTCTAAAGTGA 59.615 43.478 0.00 0.00 0.00 3.41
4183 4707 4.039973 TGTTCAGGTCGGTTCTAAAGTGAT 59.960 41.667 0.00 0.00 0.00 3.06
4186 4710 5.258841 TCAGGTCGGTTCTAAAGTGATCTA 58.741 41.667 0.00 0.00 0.00 1.98
4187 4711 5.892119 TCAGGTCGGTTCTAAAGTGATCTAT 59.108 40.000 0.00 0.00 0.00 1.98
4188 4712 6.380274 TCAGGTCGGTTCTAAAGTGATCTATT 59.620 38.462 0.00 0.00 0.00 1.73
4189 4713 6.477033 CAGGTCGGTTCTAAAGTGATCTATTG 59.523 42.308 0.00 0.00 0.00 1.90
4192 4716 4.209288 CGGTTCTAAAGTGATCTATTGCCG 59.791 45.833 0.00 0.00 0.00 5.69
4193 4717 5.116882 GGTTCTAAAGTGATCTATTGCCGT 58.883 41.667 0.00 0.00 0.00 5.68
4194 4718 5.234543 GGTTCTAAAGTGATCTATTGCCGTC 59.765 44.000 0.00 0.00 0.00 4.79
4195 4719 5.592104 TCTAAAGTGATCTATTGCCGTCA 57.408 39.130 0.00 0.00 0.00 4.35
4196 4720 5.348986 TCTAAAGTGATCTATTGCCGTCAC 58.651 41.667 0.00 0.00 40.87 3.67
4197 4721 2.209838 AGTGATCTATTGCCGTCACG 57.790 50.000 0.00 0.00 44.20 4.35
4198 4722 0.577269 GTGATCTATTGCCGTCACGC 59.423 55.000 0.00 0.00 32.64 5.34
4240 5403 3.000815 GGTCTTTCGTGCTTGACCA 57.999 52.632 6.18 0.00 45.87 4.02
4251 5414 3.262420 GTGCTTGACCAACGAGTGATAT 58.738 45.455 0.00 0.00 32.82 1.63
4252 5415 3.307242 GTGCTTGACCAACGAGTGATATC 59.693 47.826 0.00 0.00 32.82 1.63
4276 5439 7.981142 TCTAAGGTTTTCACTGTTTTGTACTG 58.019 34.615 0.00 0.00 0.00 2.74
4306 5469 2.638354 TTTTGCCCAGCTGCATCGG 61.638 57.895 8.66 5.15 41.70 4.18
4350 5513 0.035343 GCAAAGACCACTCCTACCCC 60.035 60.000 0.00 0.00 0.00 4.95
4351 5514 0.618981 CAAAGACCACTCCTACCCCC 59.381 60.000 0.00 0.00 0.00 5.40
4385 5548 1.822990 TGGTTTGAGCGGTACTCCTAG 59.177 52.381 0.00 0.00 45.61 3.02
4386 5549 1.471153 GGTTTGAGCGGTACTCCTAGC 60.471 57.143 0.00 0.00 45.61 3.42
4387 5550 1.477295 GTTTGAGCGGTACTCCTAGCT 59.523 52.381 0.00 0.00 45.61 3.32
4388 5551 1.103803 TTGAGCGGTACTCCTAGCTG 58.896 55.000 0.00 0.00 45.61 4.24
4389 5552 0.034380 TGAGCGGTACTCCTAGCTGT 60.034 55.000 0.00 0.00 45.61 4.40
4390 5553 1.211212 TGAGCGGTACTCCTAGCTGTA 59.789 52.381 0.00 0.00 45.61 2.74
4391 5554 1.603326 GAGCGGTACTCCTAGCTGTAC 59.397 57.143 0.00 12.33 40.39 2.90
4397 5560 4.308899 GTACTCCTAGCTGTACCATGTG 57.691 50.000 0.00 0.00 34.59 3.21
4398 5561 1.482593 ACTCCTAGCTGTACCATGTGC 59.517 52.381 0.00 0.00 0.00 4.57
4399 5562 1.759445 CTCCTAGCTGTACCATGTGCT 59.241 52.381 0.00 0.00 39.30 4.40
4400 5563 1.482182 TCCTAGCTGTACCATGTGCTG 59.518 52.381 0.00 0.00 37.02 4.41
4401 5564 1.208052 CCTAGCTGTACCATGTGCTGT 59.792 52.381 0.00 0.00 37.02 4.40
4402 5565 2.274437 CTAGCTGTACCATGTGCTGTG 58.726 52.381 0.00 0.00 37.02 3.66
4403 5566 0.397941 AGCTGTACCATGTGCTGTGT 59.602 50.000 0.00 0.00 34.19 3.72
4404 5567 1.623311 AGCTGTACCATGTGCTGTGTA 59.377 47.619 0.00 0.00 34.19 2.90
4405 5568 1.732259 GCTGTACCATGTGCTGTGTAC 59.268 52.381 0.00 0.00 34.61 2.90
4415 5578 1.191489 TGCTGTGTACTAGCCAGGCA 61.191 55.000 15.80 0.00 40.42 4.75
4444 5607 9.667989 ATTTTTGTGTCCGTATTACAACTAAAC 57.332 29.630 0.00 0.00 34.38 2.01
4446 5609 7.642071 TTGTGTCCGTATTACAACTAAACTC 57.358 36.000 0.00 0.00 30.06 3.01
4451 5614 4.266976 CCGTATTACAACTAAACTCGGCTG 59.733 45.833 0.00 0.00 0.00 4.85
4453 5616 5.747197 CGTATTACAACTAAACTCGGCTGAT 59.253 40.000 0.00 0.00 0.00 2.90
4470 5633 1.281867 TGATGACAAAGGGCCCAGTAG 59.718 52.381 27.56 13.43 0.00 2.57
4471 5634 0.034089 ATGACAAAGGGCCCAGTAGC 60.034 55.000 27.56 10.94 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 104 1.961394 GATCCTCCCATGTACGTAGCA 59.039 52.381 0.00 0.00 0.00 3.49
103 106 1.068472 GCGATCCTCCCATGTACGTAG 60.068 57.143 0.00 0.00 0.00 3.51
110 113 0.671781 GAATCCGCGATCCTCCCATG 60.672 60.000 8.23 0.00 0.00 3.66
113 116 2.049063 CGAATCCGCGATCCTCCC 60.049 66.667 8.23 0.00 0.00 4.30
167 170 3.499737 CATTCGGTGCCGCTGACC 61.500 66.667 5.64 0.00 39.59 4.02
249 252 2.945890 GCCTTCCCTAATCACCACCAAG 60.946 54.545 0.00 0.00 0.00 3.61
265 268 1.884926 CAGCGATTCTCGGGCCTTC 60.885 63.158 0.84 0.00 40.84 3.46
270 273 1.227089 CTCCACAGCGATTCTCGGG 60.227 63.158 0.00 0.00 40.84 5.14
310 313 3.869272 CAATCCCAGCAGCGCGTC 61.869 66.667 8.43 0.00 0.00 5.19
313 316 2.068277 GAATCCAATCCCAGCAGCGC 62.068 60.000 0.00 0.00 0.00 5.92
314 317 1.779025 CGAATCCAATCCCAGCAGCG 61.779 60.000 0.00 0.00 0.00 5.18
315 318 0.749454 ACGAATCCAATCCCAGCAGC 60.749 55.000 0.00 0.00 0.00 5.25
316 319 1.755179 AACGAATCCAATCCCAGCAG 58.245 50.000 0.00 0.00 0.00 4.24
317 320 2.091541 GAAACGAATCCAATCCCAGCA 58.908 47.619 0.00 0.00 0.00 4.41
318 321 1.405463 GGAAACGAATCCAATCCCAGC 59.595 52.381 6.41 0.00 39.42 4.85
319 322 2.684881 CAGGAAACGAATCCAATCCCAG 59.315 50.000 12.54 0.00 42.27 4.45
320 323 2.722094 CAGGAAACGAATCCAATCCCA 58.278 47.619 12.54 0.00 42.27 4.37
321 324 1.405463 GCAGGAAACGAATCCAATCCC 59.595 52.381 12.54 0.00 42.27 3.85
334 337 0.673437 CGAAGCCAAAAGGCAGGAAA 59.327 50.000 9.42 0.00 37.35 3.13
349 352 4.537015 CCAGTAAAAAGCAAGGAACGAAG 58.463 43.478 0.00 0.00 0.00 3.79
350 353 3.316868 CCCAGTAAAAAGCAAGGAACGAA 59.683 43.478 0.00 0.00 0.00 3.85
356 359 3.222603 AGTGACCCAGTAAAAAGCAAGG 58.777 45.455 0.00 0.00 0.00 3.61
386 389 1.298859 CTACAAGGGCTGACGCAACC 61.299 60.000 0.00 0.00 38.10 3.77
409 413 0.537143 AGCCGGCAACTGTGAATCAA 60.537 50.000 31.54 0.00 0.00 2.57
457 461 3.423154 GCGCACGAAACCTGGGAG 61.423 66.667 0.30 0.00 0.00 4.30
468 472 1.442520 CCAACAAATCCAGCGCACG 60.443 57.895 11.47 0.00 0.00 5.34
551 920 9.334947 CCATTAGCATCCTTAATGACCATATAG 57.665 37.037 6.57 0.00 37.59 1.31
560 929 6.016777 GGACTGTTCCATTAGCATCCTTAATG 60.017 42.308 0.00 0.00 42.30 1.90
633 1002 7.823745 ATTGGTTCATAATGGAATCCTGTAC 57.176 36.000 0.00 0.00 0.00 2.90
659 1028 9.316730 ACAGTTTACATTTTTACACGAACTAGA 57.683 29.630 0.00 0.00 0.00 2.43
746 1115 4.241590 TGGTTGACAATGAAGAACATGC 57.758 40.909 0.00 0.00 39.39 4.06
785 1169 9.967451 TGAAATTTTGAAGTATGGATACTGGTA 57.033 29.630 0.00 0.00 42.47 3.25
786 1170 8.877864 TGAAATTTTGAAGTATGGATACTGGT 57.122 30.769 0.00 0.00 42.47 4.00
787 1171 9.740239 CATGAAATTTTGAAGTATGGATACTGG 57.260 33.333 0.00 0.00 42.47 4.00
788 1172 9.740239 CCATGAAATTTTGAAGTATGGATACTG 57.260 33.333 0.00 0.00 42.47 2.74
789 1173 9.699410 TCCATGAAATTTTGAAGTATGGATACT 57.301 29.630 0.00 0.00 45.04 2.12
836 1232 7.462109 AACATAGTAACACGACGTAAAAACA 57.538 32.000 0.00 0.00 0.00 2.83
869 1265 8.113462 AGAAAGGGTGGAACAAATTAATAGCTA 58.887 33.333 0.00 0.00 44.16 3.32
871 1267 7.170393 AGAAAGGGTGGAACAAATTAATAGC 57.830 36.000 0.00 0.00 44.16 2.97
917 1313 9.656323 AGGATAATGAAGTACCAGTCAACTATA 57.344 33.333 0.00 0.00 0.00 1.31
928 1324 4.689612 TCCTGCAGGATAATGAAGTACC 57.310 45.455 32.00 0.00 39.78 3.34
1093 1489 1.107114 ATCTCCTGCGAATCTGACGT 58.893 50.000 0.00 0.00 0.00 4.34
1119 1515 0.955428 TTCCTGCGGTGTCAGATTGC 60.955 55.000 0.00 0.00 36.19 3.56
1197 1593 2.687370 TCATCCGCATCGATATTGTGG 58.313 47.619 10.26 10.26 44.43 4.17
1281 1677 3.510360 GGTCATAGTGTAGTGTGGACTGT 59.490 47.826 0.00 0.00 33.21 3.55
1356 1769 3.052455 TGCGACATGGTAAACAGTGAT 57.948 42.857 0.00 0.00 0.00 3.06
1358 1771 3.829886 AATGCGACATGGTAAACAGTG 57.170 42.857 0.00 0.00 0.00 3.66
1359 1772 4.072131 AGAAATGCGACATGGTAAACAGT 58.928 39.130 0.00 0.00 0.00 3.55
1500 1913 7.928307 ACTCTACAAGTGCAATGTAAATGAT 57.072 32.000 12.98 0.00 36.65 2.45
1532 1945 1.270252 TGATTGAGCACTTGAGCGTCA 60.270 47.619 0.00 0.00 40.15 4.35
1571 1984 2.289631 TGAGTGTTAGCATGTCAGGTGG 60.290 50.000 0.00 0.00 0.00 4.61
1813 2226 8.668510 AAATTAGTTCATGGCACTAGACTATG 57.331 34.615 0.00 2.13 0.00 2.23
1948 2361 5.010922 TGCTGTTCATAGCCAAACATTTCTT 59.989 36.000 0.00 0.00 43.02 2.52
2164 2577 7.396540 AAAGAAGTAGCCAAACCATATTGAG 57.603 36.000 0.00 0.00 31.84 3.02
2217 2633 7.920160 ATACTGGCCACAAAATTAAAAATGG 57.080 32.000 0.00 0.00 0.00 3.16
2318 2739 4.308526 TGCTGGGACCATAAATTACACA 57.691 40.909 0.00 0.00 0.00 3.72
2422 2847 9.630098 TTTGTATAAGACGTTTTAGGTCACTAG 57.370 33.333 4.75 0.00 35.60 2.57
2444 2869 7.942341 TGAAATGTACTCCCTCTGTAAATTTGT 59.058 33.333 0.00 0.00 37.71 2.83
2445 2870 8.335532 TGAAATGTACTCCCTCTGTAAATTTG 57.664 34.615 0.00 0.00 37.71 2.32
2497 2962 1.025812 TGCCCAAAGTACAAACCACG 58.974 50.000 0.00 0.00 0.00 4.94
2507 2972 1.422531 TTTCCATGCTTGCCCAAAGT 58.577 45.000 0.00 0.00 38.25 2.66
2592 3060 9.278978 GTGTAGACTTATCTCTATCAGACATGA 57.721 37.037 0.00 0.00 36.74 3.07
2608 3077 3.093814 TCCCATTGAGCGTGTAGACTTA 58.906 45.455 0.00 0.00 0.00 2.24
2684 3164 7.287696 TGTCATTACATTCTCATCTAGCCTGTA 59.712 37.037 0.00 0.00 0.00 2.74
2769 3250 1.073964 CTTCAGACACGGCACAGATG 58.926 55.000 0.00 0.00 0.00 2.90
2770 3251 0.671781 GCTTCAGACACGGCACAGAT 60.672 55.000 0.00 0.00 0.00 2.90
2771 3252 1.300931 GCTTCAGACACGGCACAGA 60.301 57.895 0.00 0.00 0.00 3.41
2957 3438 9.567848 GATGTTTCTGTTTTTCTTTCTGTAACA 57.432 29.630 0.00 0.00 0.00 2.41
2960 3441 9.787532 CTTGATGTTTCTGTTTTTCTTTCTGTA 57.212 29.630 0.00 0.00 0.00 2.74
3099 3580 6.183360 GGCATTCAGATTTTCCCAACATATCA 60.183 38.462 0.00 0.00 0.00 2.15
3100 3581 6.183360 TGGCATTCAGATTTTCCCAACATATC 60.183 38.462 0.00 0.00 0.00 1.63
3109 3590 5.138125 TGAAACTGGCATTCAGATTTTCC 57.862 39.130 0.00 0.00 46.18 3.13
3255 3774 4.644685 GCTATTGTTTGCCAGGATAAGGAA 59.355 41.667 0.00 0.00 0.00 3.36
3256 3775 4.079787 AGCTATTGTTTGCCAGGATAAGGA 60.080 41.667 0.00 0.00 0.00 3.36
3257 3776 4.210331 AGCTATTGTTTGCCAGGATAAGG 58.790 43.478 0.00 0.00 0.00 2.69
3258 3777 5.591877 AGAAGCTATTGTTTGCCAGGATAAG 59.408 40.000 0.00 0.00 0.00 1.73
3259 3778 5.509498 AGAAGCTATTGTTTGCCAGGATAA 58.491 37.500 0.00 0.00 0.00 1.75
3260 3779 5.116084 AGAAGCTATTGTTTGCCAGGATA 57.884 39.130 0.00 0.00 0.00 2.59
3261 3780 3.950395 GAGAAGCTATTGTTTGCCAGGAT 59.050 43.478 0.00 0.00 0.00 3.24
3262 3781 3.244875 TGAGAAGCTATTGTTTGCCAGGA 60.245 43.478 0.00 0.00 0.00 3.86
3263 3782 3.084039 TGAGAAGCTATTGTTTGCCAGG 58.916 45.455 0.00 0.00 0.00 4.45
3264 3783 3.755378 ACTGAGAAGCTATTGTTTGCCAG 59.245 43.478 0.00 0.00 0.00 4.85
3265 3784 3.754965 ACTGAGAAGCTATTGTTTGCCA 58.245 40.909 0.00 0.00 0.00 4.92
3299 3818 6.772716 TGAGAAAGAGAAGGTGCTACAAATTT 59.227 34.615 0.00 0.00 0.00 1.82
3302 3821 5.057149 GTGAGAAAGAGAAGGTGCTACAAA 58.943 41.667 0.00 0.00 0.00 2.83
3325 3844 9.722056 AGCAAATCTTTTAGCATAAGTTTATCG 57.278 29.630 0.00 0.00 0.00 2.92
3462 3981 1.688735 TGCGGCTATGCTCAATAGAGT 59.311 47.619 0.00 0.00 44.00 3.24
3537 4056 3.441101 AGTAGAGAGTGCACCCATAACA 58.559 45.455 14.63 0.00 0.00 2.41
3559 4078 6.184068 AGCTGTAGAGAGTGATTTCTAGACA 58.816 40.000 0.00 0.00 0.00 3.41
3577 4096 8.347771 CCGTTACATATACTTCTACAAGCTGTA 58.652 37.037 0.00 0.00 32.09 2.74
3578 4097 7.201145 CCGTTACATATACTTCTACAAGCTGT 58.799 38.462 0.00 0.00 32.09 4.40
3615 4134 2.683211 AGGGGATGTTTCTTGCAGTT 57.317 45.000 0.00 0.00 0.00 3.16
3616 4135 2.519013 GAAGGGGATGTTTCTTGCAGT 58.481 47.619 0.00 0.00 0.00 4.40
3620 4139 1.812571 CGTGGAAGGGGATGTTTCTTG 59.187 52.381 0.00 0.00 0.00 3.02
3623 4142 2.868253 CCGTGGAAGGGGATGTTTC 58.132 57.895 0.00 0.00 38.48 2.78
3674 4193 1.073763 AGAAAAGGGGGCATTTTTGGC 59.926 47.619 0.00 0.00 27.44 4.52
3676 4195 5.187576 TGATAGAGAAAAGGGGGCATTTTTG 59.812 40.000 0.00 0.00 27.44 2.44
3684 4203 4.781934 ACGAAATGATAGAGAAAAGGGGG 58.218 43.478 0.00 0.00 0.00 5.40
3694 4213 6.392625 ACTAGCTGCTTACGAAATGATAGA 57.607 37.500 7.79 0.00 0.00 1.98
3752 4271 0.984230 AGAGCACAGGATTTCCGGAA 59.016 50.000 14.35 14.35 42.08 4.30
3753 4272 0.250234 CAGAGCACAGGATTTCCGGA 59.750 55.000 0.00 0.00 42.08 5.14
3756 4275 1.743996 GACCAGAGCACAGGATTTCC 58.256 55.000 0.00 0.00 0.00 3.13
3766 4285 2.653115 CACAGAGCGACCAGAGCA 59.347 61.111 0.00 0.00 37.01 4.26
3777 4296 3.168604 CGACGACGCAGCACAGAG 61.169 66.667 0.00 0.00 0.00 3.35
3780 4299 2.665172 TTACACGACGACGCAGCACA 62.665 55.000 7.30 0.00 43.96 4.57
3787 4306 4.079028 CCAAATGAAATTACACGACGACG 58.921 43.478 5.58 5.58 39.94 5.12
3792 4311 4.075682 TCAGCCCAAATGAAATTACACGA 58.924 39.130 0.00 0.00 33.67 4.35
3804 4323 1.304713 CACCCAGCTCAGCCCAAAT 60.305 57.895 0.00 0.00 0.00 2.32
3823 4342 3.119029 CGTTGCCATTTGATTGGAGGAAT 60.119 43.478 0.00 0.00 39.25 3.01
3862 4381 1.511299 AGGAGAGATGGATGGATGGGA 59.489 52.381 0.00 0.00 0.00 4.37
3929 4448 2.977580 AGGAATAAACCGAGGGGATACC 59.022 50.000 0.00 0.00 46.11 2.73
3945 4464 1.464997 GAAAAAGTGAGCGCGAGGAAT 59.535 47.619 12.10 0.00 0.00 3.01
3951 4470 1.241744 CAATCGAAAAAGTGAGCGCG 58.758 50.000 0.00 0.00 0.00 6.86
3962 4481 0.676466 ATGACAGGCGCCAATCGAAA 60.676 50.000 31.54 9.99 41.67 3.46
3963 4482 1.078497 ATGACAGGCGCCAATCGAA 60.078 52.632 31.54 10.74 41.67 3.71
3964 4483 1.521457 GATGACAGGCGCCAATCGA 60.521 57.895 31.54 15.45 41.67 3.59
3965 4484 2.874694 CGATGACAGGCGCCAATCG 61.875 63.158 31.54 28.99 42.12 3.34
3966 4485 3.017323 CGATGACAGGCGCCAATC 58.983 61.111 31.54 24.95 0.00 2.67
3967 4486 3.204827 GCGATGACAGGCGCCAAT 61.205 61.111 31.54 16.86 46.93 3.16
4006 4530 2.890371 GCCCATGGAGCTTTGCAG 59.110 61.111 15.22 0.00 0.00 4.41
4007 4531 3.063704 CGCCCATGGAGCTTTGCA 61.064 61.111 15.22 0.00 0.00 4.08
4008 4532 2.275547 CTTCGCCCATGGAGCTTTGC 62.276 60.000 15.22 5.76 0.00 3.68
4009 4533 1.660560 CCTTCGCCCATGGAGCTTTG 61.661 60.000 15.22 7.16 0.00 2.77
4010 4534 1.379044 CCTTCGCCCATGGAGCTTT 60.379 57.895 15.22 0.00 0.00 3.51
4011 4535 1.852157 TTCCTTCGCCCATGGAGCTT 61.852 55.000 15.22 0.00 30.03 3.74
4012 4536 1.852157 TTTCCTTCGCCCATGGAGCT 61.852 55.000 15.22 0.00 30.03 4.09
4013 4537 0.965363 TTTTCCTTCGCCCATGGAGC 60.965 55.000 15.22 14.17 30.03 4.70
4014 4538 1.767759 ATTTTCCTTCGCCCATGGAG 58.232 50.000 15.22 7.12 30.03 3.86
4015 4539 2.099405 GAATTTTCCTTCGCCCATGGA 58.901 47.619 15.22 0.00 0.00 3.41
4016 4540 2.102578 AGAATTTTCCTTCGCCCATGG 58.897 47.619 4.14 4.14 0.00 3.66
4017 4541 2.736400 GCAGAATTTTCCTTCGCCCATG 60.736 50.000 0.00 0.00 0.00 3.66
4018 4542 1.478105 GCAGAATTTTCCTTCGCCCAT 59.522 47.619 0.00 0.00 0.00 4.00
4019 4543 0.887933 GCAGAATTTTCCTTCGCCCA 59.112 50.000 0.00 0.00 0.00 5.36
4020 4544 1.135286 CAGCAGAATTTTCCTTCGCCC 60.135 52.381 0.00 0.00 0.00 6.13
4042 4566 1.303888 CCTCCAGCACAGCAATGGT 60.304 57.895 0.00 0.00 35.51 3.55
4065 4589 2.044555 CCTGTGATGGCTGTGCTGG 61.045 63.158 0.00 0.00 0.00 4.85
4089 4613 2.184322 CGGGGAGACGGTGACATG 59.816 66.667 0.00 0.00 0.00 3.21
4106 4630 3.701205 AAATTGAAGAAATGGTGGGCC 57.299 42.857 0.00 0.00 0.00 5.80
4119 4643 7.741785 TGTACTGACCCTTCTTCTAAATTGAA 58.258 34.615 0.00 0.00 0.00 2.69
4122 4646 6.599638 GCATGTACTGACCCTTCTTCTAAATT 59.400 38.462 0.00 0.00 0.00 1.82
4136 4660 6.968131 TGATCACTTAAAGCATGTACTGAC 57.032 37.500 0.00 0.00 0.00 3.51
4144 4668 5.948162 ACCTGAACATGATCACTTAAAGCAT 59.052 36.000 0.83 0.00 0.00 3.79
4145 4669 5.316167 ACCTGAACATGATCACTTAAAGCA 58.684 37.500 0.83 0.00 0.00 3.91
4147 4671 5.063944 CCGACCTGAACATGATCACTTAAAG 59.936 44.000 0.83 0.00 0.00 1.85
4148 4672 4.935205 CCGACCTGAACATGATCACTTAAA 59.065 41.667 0.83 0.00 0.00 1.52
4150 4674 3.513912 ACCGACCTGAACATGATCACTTA 59.486 43.478 0.83 0.00 0.00 2.24
4151 4675 2.303022 ACCGACCTGAACATGATCACTT 59.697 45.455 0.83 0.00 0.00 3.16
4152 4676 1.902508 ACCGACCTGAACATGATCACT 59.097 47.619 0.83 0.00 0.00 3.41
4153 4677 2.386661 ACCGACCTGAACATGATCAC 57.613 50.000 0.83 0.00 0.00 3.06
4154 4678 2.567169 AGAACCGACCTGAACATGATCA 59.433 45.455 5.47 5.47 0.00 2.92
4156 4680 4.819105 TTAGAACCGACCTGAACATGAT 57.181 40.909 0.00 0.00 0.00 2.45
4157 4681 4.039973 ACTTTAGAACCGACCTGAACATGA 59.960 41.667 0.00 0.00 0.00 3.07
4158 4682 4.152402 CACTTTAGAACCGACCTGAACATG 59.848 45.833 0.00 0.00 0.00 3.21
4160 4684 3.385433 TCACTTTAGAACCGACCTGAACA 59.615 43.478 0.00 0.00 0.00 3.18
4161 4685 3.986277 TCACTTTAGAACCGACCTGAAC 58.014 45.455 0.00 0.00 0.00 3.18
4162 4686 4.527038 AGATCACTTTAGAACCGACCTGAA 59.473 41.667 0.00 0.00 0.00 3.02
4163 4687 4.087182 AGATCACTTTAGAACCGACCTGA 58.913 43.478 0.00 0.00 0.00 3.86
4164 4688 4.457834 AGATCACTTTAGAACCGACCTG 57.542 45.455 0.00 0.00 0.00 4.00
4165 4689 6.574350 CAATAGATCACTTTAGAACCGACCT 58.426 40.000 0.00 0.00 0.00 3.85
4167 4691 5.234543 GGCAATAGATCACTTTAGAACCGAC 59.765 44.000 0.00 0.00 0.00 4.79
4168 4692 5.357257 GGCAATAGATCACTTTAGAACCGA 58.643 41.667 0.00 0.00 0.00 4.69
4170 4694 5.116882 ACGGCAATAGATCACTTTAGAACC 58.883 41.667 0.00 0.00 0.00 3.62
4171 4695 5.810587 TGACGGCAATAGATCACTTTAGAAC 59.189 40.000 0.00 0.00 0.00 3.01
4172 4696 5.810587 GTGACGGCAATAGATCACTTTAGAA 59.189 40.000 0.00 0.00 38.72 2.10
4173 4697 5.348986 GTGACGGCAATAGATCACTTTAGA 58.651 41.667 0.00 0.00 38.72 2.10
4174 4698 4.207224 CGTGACGGCAATAGATCACTTTAG 59.793 45.833 0.00 0.00 39.45 1.85
4175 4699 4.109766 CGTGACGGCAATAGATCACTTTA 58.890 43.478 0.00 0.00 39.45 1.85
4176 4700 2.930040 CGTGACGGCAATAGATCACTTT 59.070 45.455 0.00 0.00 39.45 2.66
4177 4701 2.540515 CGTGACGGCAATAGATCACTT 58.459 47.619 0.00 0.00 39.45 3.16
4178 4702 1.802880 GCGTGACGGCAATAGATCACT 60.803 52.381 7.25 0.00 39.45 3.41
4179 4703 0.577269 GCGTGACGGCAATAGATCAC 59.423 55.000 7.25 0.00 38.46 3.06
4180 4704 0.869880 CGCGTGACGGCAATAGATCA 60.870 55.000 7.25 0.00 38.44 2.92
4181 4705 1.846648 CGCGTGACGGCAATAGATC 59.153 57.895 7.25 0.00 38.44 2.75
4182 4706 4.012554 CGCGTGACGGCAATAGAT 57.987 55.556 7.25 0.00 38.44 1.98
4192 4716 2.742372 AGAATGCCCACGCGTGAC 60.742 61.111 39.10 29.01 38.08 3.67
4193 4717 2.741985 CAGAATGCCCACGCGTGA 60.742 61.111 39.10 21.17 38.08 4.35
4194 4718 2.616330 AACAGAATGCCCACGCGTG 61.616 57.895 31.77 31.77 42.53 5.34
4195 4719 2.281484 AACAGAATGCCCACGCGT 60.281 55.556 5.58 5.58 42.53 6.01
4196 4720 2.128853 AACAACAGAATGCCCACGCG 62.129 55.000 3.53 3.53 42.53 6.01
4197 4721 0.387239 GAACAACAGAATGCCCACGC 60.387 55.000 0.00 0.00 42.53 5.34
4198 4722 1.238439 AGAACAACAGAATGCCCACG 58.762 50.000 0.00 0.00 42.53 4.94
4240 5403 7.545965 CAGTGAAAACCTTAGATATCACTCGTT 59.454 37.037 5.32 0.00 44.00 3.85
4251 5414 7.414762 GCAGTACAAAACAGTGAAAACCTTAGA 60.415 37.037 0.00 0.00 0.00 2.10
4252 5415 6.691388 GCAGTACAAAACAGTGAAAACCTTAG 59.309 38.462 0.00 0.00 0.00 2.18
4306 5469 1.064654 GCATCTCATTTCTTGGACGCC 59.935 52.381 0.00 0.00 0.00 5.68
4366 5529 1.471153 GCTAGGAGTACCGCTCAAACC 60.471 57.143 0.00 0.00 45.88 3.27
4367 5530 1.477295 AGCTAGGAGTACCGCTCAAAC 59.523 52.381 0.00 0.00 45.88 2.93
4369 5532 1.103803 CAGCTAGGAGTACCGCTCAA 58.896 55.000 0.00 0.00 45.88 3.02
4386 5549 5.205386 GCTAGTACACAGCACATGGTACAG 61.205 50.000 13.04 1.41 39.72 2.74
4387 5550 3.368013 GCTAGTACACAGCACATGGTACA 60.368 47.826 13.04 0.00 40.36 2.90
4388 5551 3.187700 GCTAGTACACAGCACATGGTAC 58.812 50.000 13.04 0.00 38.93 3.34
4389 5552 2.167693 GGCTAGTACACAGCACATGGTA 59.832 50.000 17.99 0.00 40.95 3.25
4390 5553 1.066143 GGCTAGTACACAGCACATGGT 60.066 52.381 17.99 0.00 40.95 3.55
4391 5554 1.066215 TGGCTAGTACACAGCACATGG 60.066 52.381 17.99 0.00 40.95 3.66
4392 5555 2.274437 CTGGCTAGTACACAGCACATG 58.726 52.381 17.99 0.00 40.95 3.21
4393 5556 1.208052 CCTGGCTAGTACACAGCACAT 59.792 52.381 17.99 0.00 40.95 3.21
4394 5557 0.608130 CCTGGCTAGTACACAGCACA 59.392 55.000 17.99 13.03 40.95 4.57
4395 5558 0.741221 GCCTGGCTAGTACACAGCAC 60.741 60.000 12.43 10.00 40.95 4.40
4396 5559 1.191489 TGCCTGGCTAGTACACAGCA 61.191 55.000 21.03 9.47 40.95 4.41
4397 5560 0.179000 ATGCCTGGCTAGTACACAGC 59.821 55.000 21.03 10.23 38.35 4.40
4398 5561 2.698855 AATGCCTGGCTAGTACACAG 57.301 50.000 21.03 0.00 0.00 3.66
4399 5562 4.771114 AATAATGCCTGGCTAGTACACA 57.229 40.909 21.03 0.00 0.00 3.72
4400 5563 6.127730 ACAAAAATAATGCCTGGCTAGTACAC 60.128 38.462 21.03 0.00 0.00 2.90
4401 5564 5.949354 ACAAAAATAATGCCTGGCTAGTACA 59.051 36.000 21.03 0.00 0.00 2.90
4402 5565 6.127730 ACACAAAAATAATGCCTGGCTAGTAC 60.128 38.462 21.03 0.00 0.00 2.73
4403 5566 5.949354 ACACAAAAATAATGCCTGGCTAGTA 59.051 36.000 21.03 10.16 0.00 1.82
4404 5567 4.772100 ACACAAAAATAATGCCTGGCTAGT 59.228 37.500 21.03 8.19 0.00 2.57
4405 5568 5.329035 ACACAAAAATAATGCCTGGCTAG 57.671 39.130 21.03 0.00 0.00 3.42
4444 5607 1.372087 GCCCTTTGTCATCAGCCGAG 61.372 60.000 0.00 0.00 0.00 4.63
4446 5609 2.409870 GGCCCTTTGTCATCAGCCG 61.410 63.158 0.00 0.00 0.00 5.52
4451 5614 2.019156 GCTACTGGGCCCTTTGTCATC 61.019 57.143 25.70 8.10 0.00 2.92
4453 5616 1.378762 GCTACTGGGCCCTTTGTCA 59.621 57.895 25.70 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.