Multiple sequence alignment - TraesCS3A01G075600

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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 TraesCS3A01G075600 chr3A 100.000 3900 0 0 1 3900 46992512 46996411 0.000000e+00 7203
1 TraesCS3A01G075600 chr3D 93.598 3296 157 34 1 3264 36580260 36583533 0.000000e+00 4868
2 TraesCS3A01G075600 chr3D 88.716 514 31 6 3206 3695 36583675 36584185 1.550000e-168 603
3 TraesCS3A01G075600 chr3B 94.745 2721 117 16 2 2718 59184827 59187525 0.000000e+00 4209
4 TraesCS3A01G075600 chr3B 88.273 469 36 11 2780 3235 59187533 59187995 9.530000e-151 544
5 TraesCS3A01G075600 chr3B 83.236 513 50 16 3206 3698 59188169 59188665 4.630000e-119 438
6 TraesCS3A01G075600 chr7A 97.436 117 3 0 3697 3813 277729309 277729193 2.380000e-47 200
7 TraesCS3A01G075600 chr7A 99.083 109 1 0 3696 3804 694064016 694063908 3.070000e-46 196
8 TraesCS3A01G075600 chr7A 97.248 109 3 0 3696 3804 726489959 726490067 6.650000e-43 185
9 TraesCS3A01G075600 chr7B 99.074 108 1 0 3697 3804 735980191 735980084 1.110000e-45 195
10 TraesCS3A01G075600 chr7B 96.522 115 4 0 3694 3808 750444580 750444694 1.430000e-44 191
11 TraesCS3A01G075600 chr6A 99.074 108 1 0 3697 3804 499656178 499656071 1.110000e-45 195
12 TraesCS3A01G075600 chr6A 91.538 130 7 4 3681 3808 542194256 542194383 4.000000e-40 176
13 TraesCS3A01G075600 chr5A 98.214 112 1 1 3697 3808 585213314 585213424 1.110000e-45 195
14 TraesCS3A01G075600 chr4D 96.364 110 4 0 3696 3805 419491530 419491639 8.610000e-42 182


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 TraesCS3A01G075600 chr3A 46992512 46996411 3899 False 7203.000000 7203 100.000000 1 3900 1 chr3A.!!$F1 3899
1 TraesCS3A01G075600 chr3D 36580260 36584185 3925 False 2735.500000 4868 91.157000 1 3695 2 chr3D.!!$F1 3694
2 TraesCS3A01G075600 chr3B 59184827 59188665 3838 False 1730.333333 4209 88.751333 2 3698 3 chr3B.!!$F1 3696

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
478 489 0.103937 GATCAGAGCAAGGTCTCCGG 59.896 60.0 0.0 0.0 33.66 5.14 F
978 989 0.470341 GGATAGGCAGGACCAAGGAC 59.530 60.0 0.0 0.0 43.14 3.85 F
2568 2585 0.034670 GGCCAGAGGAGCATGAAGTT 60.035 55.0 0.0 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 2159 0.032952 GCTCACCGGTGTGTACTTCA 59.967 55.0 32.74 11.25 43.26 3.02 R
2744 2762 0.370273 GCGACTAATGTTCAGTGCCG 59.630 55.0 0.00 0.00 0.00 5.69 R
3804 4072 0.035881 AGAGCGATCCGGGTCGTATA 59.964 55.0 35.59 0.00 43.27 1.47 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
41 42 6.632834 GGTAATGTCGACACAAATATCAATGC 59.367 38.462 22.71 1.08 35.64 3.56
147 149 8.669946 TTCAATCGAGTTTATATTACATGCCA 57.330 30.769 0.00 0.00 0.00 4.92
185 193 2.729491 GAAAACGCGGTTGCAGGC 60.729 61.111 11.66 0.00 42.97 4.85
312 321 0.933700 CCTCTCTCTTCCCCTCCTCT 59.066 60.000 0.00 0.00 0.00 3.69
321 330 1.162951 TCCCCTCCTCTTCCCCTCTT 61.163 60.000 0.00 0.00 0.00 2.85
387 396 4.699522 GACCCGCGCACCTTCCTT 62.700 66.667 8.75 0.00 0.00 3.36
442 453 2.370633 GGAGCTCCCTTCTCCCCT 59.629 66.667 23.19 0.00 43.32 4.79
472 483 4.323104 GGTTAGAACAGATCAGAGCAAGGT 60.323 45.833 0.00 0.00 0.00 3.50
474 485 3.172339 AGAACAGATCAGAGCAAGGTCT 58.828 45.455 0.00 0.00 0.00 3.85
477 488 1.110442 AGATCAGAGCAAGGTCTCCG 58.890 55.000 0.00 0.00 33.66 4.63
478 489 0.103937 GATCAGAGCAAGGTCTCCGG 59.896 60.000 0.00 0.00 33.66 5.14
480 491 2.284258 AGAGCAAGGTCTCCGGCT 60.284 61.111 0.00 7.48 40.56 5.52
482 493 2.604686 AGCAAGGTCTCCGGCTCA 60.605 61.111 0.00 0.00 34.89 4.26
483 494 1.965754 GAGCAAGGTCTCCGGCTCAT 61.966 60.000 21.27 0.00 46.88 2.90
485 496 1.965754 GCAAGGTCTCCGGCTCATCT 61.966 60.000 0.00 0.00 0.00 2.90
494 505 3.941483 TCTCCGGCTCATCTTTTTCATTC 59.059 43.478 0.00 0.00 0.00 2.67
530 541 1.523938 GGTGCTAGTGGGATTCGCC 60.524 63.158 0.00 0.00 0.00 5.54
540 551 1.353022 TGGGATTCGCCAGGTTTACTT 59.647 47.619 0.00 0.00 38.95 2.24
585 596 2.626266 GTTCCTCCGGGTGAAATTTTGT 59.374 45.455 0.00 0.00 0.00 2.83
587 598 2.625790 TCCTCCGGGTGAAATTTTGTTG 59.374 45.455 0.00 0.00 0.00 3.33
589 600 3.068873 CCTCCGGGTGAAATTTTGTTGAA 59.931 43.478 0.00 0.00 0.00 2.69
676 687 2.497107 ATTCGCATGCTGTTAATGGC 57.503 45.000 17.13 0.00 0.00 4.40
722 733 3.564053 AGTAACTTTTGTTCCCCGTCA 57.436 42.857 0.00 0.00 42.45 4.35
726 737 2.938838 ACTTTTGTTCCCCGTCAATCA 58.061 42.857 0.00 0.00 0.00 2.57
828 839 2.101415 TCGCAAATCTCGATCTGTGGAT 59.899 45.455 0.00 0.00 34.45 3.41
874 885 4.344865 GGGCAGCCCCGTGAGAAA 62.345 66.667 21.62 0.00 42.67 2.52
927 938 1.617947 GGCAGTGGTAGGAGGAGGTG 61.618 65.000 0.00 0.00 0.00 4.00
978 989 0.470341 GGATAGGCAGGACCAAGGAC 59.530 60.000 0.00 0.00 43.14 3.85
1080 1091 2.136878 CCTCCTCTCCATGGACCCG 61.137 68.421 11.44 0.99 0.00 5.28
1161 1178 2.431683 GCCAGTGCTGACAGGGAA 59.568 61.111 4.26 0.00 33.53 3.97
1182 1199 1.089481 TCTTCATCATTCCGCGGCAC 61.089 55.000 23.51 0.00 0.00 5.01
1329 1346 2.029844 GTCTGAGGTTGCGCTGACC 61.030 63.158 21.19 21.19 37.44 4.02
1350 1367 0.605319 TTCCAAAGTCGAGCGGCAAT 60.605 50.000 1.45 0.00 0.00 3.56
1452 1469 0.610687 ACTACTTCAGGCCTGCACTC 59.389 55.000 28.91 0.00 0.00 3.51
1527 1544 1.254026 TTGACAAGTCCGATCTCCGT 58.746 50.000 0.00 0.00 36.31 4.69
1564 1581 0.737219 GCAGCATGACATGGAGAACC 59.263 55.000 17.03 0.00 39.69 3.62
1587 1604 5.048294 CCTGTACATGTGGGTTTTTAAGGAC 60.048 44.000 9.11 0.00 0.00 3.85
1668 1685 1.819632 CGGGGAGCCATCTTTTCCG 60.820 63.158 0.00 0.00 31.59 4.30
1698 1715 0.472471 ACAAGGGCTTTTCGAGGTCA 59.528 50.000 0.00 0.00 0.00 4.02
1836 1853 1.134551 GCTGAGCTTACAGGAAGGGAG 60.135 57.143 0.00 0.00 38.22 4.30
1849 1866 4.880696 CAGGAAGGGAGCTTAATTTCTCAG 59.119 45.833 0.00 0.00 0.00 3.35
1854 1871 4.783227 AGGGAGCTTAATTTCTCAGTACCA 59.217 41.667 0.00 0.00 0.00 3.25
1855 1872 5.430089 AGGGAGCTTAATTTCTCAGTACCAT 59.570 40.000 0.00 0.00 0.00 3.55
1940 1957 2.558313 GCCAGCAGCGTCAAAGAC 59.442 61.111 0.00 0.00 0.00 3.01
1945 1962 2.668280 GCAGCGTCAAAGACCGTCC 61.668 63.158 0.00 0.00 0.00 4.79
2013 2030 5.766590 TCAGGTCTGAATCTATCTACACCA 58.233 41.667 0.00 0.00 36.53 4.17
2103 2120 1.405526 GGCGTAGAAGAGGATTGTGCA 60.406 52.381 0.00 0.00 0.00 4.57
2142 2159 2.281830 CGAGAGGGAGCAAGAGGTT 58.718 57.895 0.00 0.00 0.00 3.50
2148 2165 2.567615 GAGGGAGCAAGAGGTTGAAGTA 59.432 50.000 0.00 0.00 35.46 2.24
2425 2442 2.600729 CCTTCCCCTGAGCACTGCT 61.601 63.158 2.22 2.22 43.88 4.24
2439 2456 3.302347 CTGCTCTCCCGGCGAGTTT 62.302 63.158 9.30 0.00 39.84 2.66
2511 2528 0.655626 CGTATTACGACGAGACCGGC 60.656 60.000 10.70 0.00 46.05 6.13
2535 2552 1.341531 GGACTGGAGATCATGGTACCG 59.658 57.143 7.57 0.00 0.00 4.02
2568 2585 0.034670 GGCCAGAGGAGCATGAAGTT 60.035 55.000 0.00 0.00 0.00 2.66
2682 2700 1.820906 CCGGTGTCATGCCATGAGG 60.821 63.158 7.83 1.76 40.53 3.86
2717 2735 2.621526 CAGCAAAGCTATCATCATGCCA 59.378 45.455 0.00 0.00 36.40 4.92
2729 2747 5.880164 TCATCATGCCATGGATCAAAAAT 57.120 34.783 18.40 0.00 0.00 1.82
2744 2762 8.987890 TGGATCAAAAATCGGAAATTTTCTTTC 58.012 29.630 8.93 0.00 31.53 2.62
2748 2766 4.513198 AATCGGAAATTTTCTTTCGGCA 57.487 36.364 8.93 0.00 0.00 5.69
2950 2971 4.448720 TCTGTCCCTGTATATTCCGAGA 57.551 45.455 0.00 0.00 0.00 4.04
2953 2974 5.839063 TCTGTCCCTGTATATTCCGAGAATT 59.161 40.000 4.76 0.00 0.00 2.17
3051 3072 5.994054 AGGCATCTTAGCATACTTGTATGTG 59.006 40.000 18.39 10.77 35.83 3.21
3060 3081 6.493116 AGCATACTTGTATGTGTCGTACTAC 58.507 40.000 18.39 0.00 0.00 2.73
3100 3121 2.746472 GCTCTCGGCATAAATGGGAACT 60.746 50.000 0.00 0.00 41.35 3.01
3112 3133 8.470002 GCATAAATGGGAACTTAAGATTCTGTT 58.530 33.333 10.09 0.00 0.00 3.16
3113 3134 9.793252 CATAAATGGGAACTTAAGATTCTGTTG 57.207 33.333 10.09 0.53 0.00 3.33
3125 3147 4.352600 GATTCTGTTGCCTGAATCTGTG 57.647 45.455 12.31 0.00 45.42 3.66
3127 3149 0.524862 CTGTTGCCTGAATCTGTGCC 59.475 55.000 0.00 0.00 0.00 5.01
3131 3153 2.046023 CCTGAATCTGTGCCCGCA 60.046 61.111 0.00 0.00 0.00 5.69
3135 3157 1.675641 GAATCTGTGCCCGCACCTT 60.676 57.895 16.77 8.00 45.63 3.50
3136 3158 1.926511 GAATCTGTGCCCGCACCTTG 61.927 60.000 16.77 7.62 45.63 3.61
3137 3159 3.925630 ATCTGTGCCCGCACCTTGG 62.926 63.158 16.77 5.36 45.63 3.61
3144 3166 1.663379 GCCCGCACCTTGGTTATTCC 61.663 60.000 0.00 0.00 0.00 3.01
3146 3168 1.094785 CCGCACCTTGGTTATTCCTG 58.905 55.000 0.00 0.00 37.07 3.86
3147 3169 0.451783 CGCACCTTGGTTATTCCTGC 59.548 55.000 0.00 0.00 37.07 4.85
3150 3172 2.879756 GCACCTTGGTTATTCCTGCTGA 60.880 50.000 0.00 0.00 37.07 4.26
3154 3176 3.629398 CCTTGGTTATTCCTGCTGATGAC 59.371 47.826 0.00 0.00 37.07 3.06
3161 3194 2.677289 CCTGCTGATGACCAGGGCT 61.677 63.158 0.00 0.00 43.87 5.19
3162 3195 1.153208 CTGCTGATGACCAGGGCTC 60.153 63.158 0.00 0.00 43.13 4.70
3170 3203 2.032071 ACCAGGGCTCGGTTTTCG 59.968 61.111 0.00 0.00 40.90 3.46
3171 3204 2.746277 CCAGGGCTCGGTTTTCGG 60.746 66.667 0.00 0.00 39.77 4.30
3179 3212 2.739287 CGGTTTTCGGCAGCGGTA 60.739 61.111 0.00 0.00 34.75 4.02
3182 3215 1.371595 GGTTTTCGGCAGCGGTAATA 58.628 50.000 0.00 0.00 0.00 0.98
3196 3229 2.726760 CGGTAATACTGAATCTCGCTGC 59.273 50.000 0.00 0.00 0.00 5.25
3198 3231 3.984633 GGTAATACTGAATCTCGCTGCTC 59.015 47.826 0.00 0.00 0.00 4.26
3220 3455 2.103042 GCTCGCTCCAGCACGAAAT 61.103 57.895 0.00 0.00 42.21 2.17
3225 3460 1.442769 GCTCCAGCACGAAATTCTCA 58.557 50.000 0.00 0.00 41.59 3.27
3235 3470 4.641954 CACGAAATTCTCAGTTTCATCCG 58.358 43.478 0.00 0.00 35.77 4.18
3277 3512 9.107177 CTGTGTGAGCAAATAAGAAGATATTCT 57.893 33.333 0.00 0.00 0.00 2.40
3308 3543 9.509956 TGTTTACAGTACAAAGGTATATTTGCT 57.490 29.630 0.00 0.00 42.68 3.91
3317 3552 7.168219 ACAAAGGTATATTTGCTGAGACTTGA 58.832 34.615 0.00 0.00 42.68 3.02
3378 3613 4.757594 AGTGATGATCAGAGCTCAGTTTC 58.242 43.478 17.77 10.20 0.00 2.78
3385 3620 0.320247 AGAGCTCAGTTTCCACAGCG 60.320 55.000 17.77 0.00 36.95 5.18
3401 3636 2.094762 AGCGGTAACAAAATCTCGCT 57.905 45.000 0.00 0.00 46.89 4.93
3433 3668 2.027285 TCAACTCGGGATGCATTTCTCA 60.027 45.455 0.00 0.00 0.00 3.27
3446 3681 4.943705 TGCATTTCTCAGTTTATCCTGACC 59.056 41.667 0.00 0.00 36.57 4.02
3477 3720 2.234661 TCTCTGGGTTGATGCTGTGTAG 59.765 50.000 0.00 0.00 0.00 2.74
3504 3764 5.391950 CCACATTTGCAGTACAAGGATACAC 60.392 44.000 0.00 0.00 40.06 2.90
3507 3767 6.094048 ACATTTGCAGTACAAGGATACACATC 59.906 38.462 0.00 0.00 40.06 3.06
3537 3800 9.403110 CTTGACTATTCCTTTCTTTGAAACATG 57.597 33.333 0.00 0.00 0.00 3.21
3646 3909 4.024809 TCTGTCGATATCTCGCTGTTGTAG 60.025 45.833 0.34 0.00 44.65 2.74
3698 3966 6.550843 TGTATGTATTGTGCATTTGTGCTAC 58.449 36.000 0.00 0.09 35.49 3.58
3699 3967 5.902613 ATGTATTGTGCATTTGTGCTACT 57.097 34.783 0.00 0.00 35.49 2.57
3700 3968 5.295431 TGTATTGTGCATTTGTGCTACTC 57.705 39.130 0.00 0.00 35.49 2.59
3701 3969 3.855689 ATTGTGCATTTGTGCTACTCC 57.144 42.857 0.00 0.00 35.49 3.85
3702 3970 1.533625 TGTGCATTTGTGCTACTCCC 58.466 50.000 0.00 0.00 35.49 4.30
3703 3971 1.073763 TGTGCATTTGTGCTACTCCCT 59.926 47.619 0.00 0.00 35.49 4.20
3704 3972 1.740025 GTGCATTTGTGCTACTCCCTC 59.260 52.381 0.00 0.00 35.49 4.30
3705 3973 1.630369 TGCATTTGTGCTACTCCCTCT 59.370 47.619 1.86 0.00 35.49 3.69
3706 3974 2.012673 GCATTTGTGCTACTCCCTCTG 58.987 52.381 0.00 0.00 0.00 3.35
3707 3975 2.616510 GCATTTGTGCTACTCCCTCTGT 60.617 50.000 0.00 0.00 0.00 3.41
3708 3976 3.679389 CATTTGTGCTACTCCCTCTGTT 58.321 45.455 0.00 0.00 0.00 3.16
3709 3977 3.857157 TTTGTGCTACTCCCTCTGTTT 57.143 42.857 0.00 0.00 0.00 2.83
3710 3978 4.967084 TTTGTGCTACTCCCTCTGTTTA 57.033 40.909 0.00 0.00 0.00 2.01
3711 3979 3.955650 TGTGCTACTCCCTCTGTTTAC 57.044 47.619 0.00 0.00 0.00 2.01
3712 3980 3.507411 TGTGCTACTCCCTCTGTTTACT 58.493 45.455 0.00 0.00 0.00 2.24
3713 3981 3.901844 TGTGCTACTCCCTCTGTTTACTT 59.098 43.478 0.00 0.00 0.00 2.24
3714 3982 4.347000 TGTGCTACTCCCTCTGTTTACTTT 59.653 41.667 0.00 0.00 0.00 2.66
3715 3983 5.163237 TGTGCTACTCCCTCTGTTTACTTTT 60.163 40.000 0.00 0.00 0.00 2.27
3716 3984 6.042322 TGTGCTACTCCCTCTGTTTACTTTTA 59.958 38.462 0.00 0.00 0.00 1.52
3717 3985 7.104290 GTGCTACTCCCTCTGTTTACTTTTAT 58.896 38.462 0.00 0.00 0.00 1.40
3718 3986 8.255905 GTGCTACTCCCTCTGTTTACTTTTATA 58.744 37.037 0.00 0.00 0.00 0.98
3719 3987 8.818860 TGCTACTCCCTCTGTTTACTTTTATAA 58.181 33.333 0.00 0.00 0.00 0.98
3720 3988 9.315525 GCTACTCCCTCTGTTTACTTTTATAAG 57.684 37.037 0.00 0.00 37.40 1.73
3723 3991 8.319881 ACTCCCTCTGTTTACTTTTATAAGACC 58.680 37.037 0.00 0.00 35.30 3.85
3724 3992 8.445361 TCCCTCTGTTTACTTTTATAAGACCT 57.555 34.615 0.00 0.00 35.30 3.85
3725 3993 8.887393 TCCCTCTGTTTACTTTTATAAGACCTT 58.113 33.333 0.00 0.00 35.30 3.50
3726 3994 9.163899 CCCTCTGTTTACTTTTATAAGACCTTC 57.836 37.037 0.00 0.00 35.30 3.46
3727 3995 9.720769 CCTCTGTTTACTTTTATAAGACCTTCA 57.279 33.333 0.00 0.00 35.30 3.02
3744 4012 8.503458 AGACCTTCAAGATATTTCAGACAATG 57.497 34.615 0.00 0.00 0.00 2.82
3745 4013 8.105829 AGACCTTCAAGATATTTCAGACAATGT 58.894 33.333 0.00 0.00 0.00 2.71
3746 4014 9.383519 GACCTTCAAGATATTTCAGACAATGTA 57.616 33.333 0.00 0.00 0.00 2.29
3747 4015 9.167311 ACCTTCAAGATATTTCAGACAATGTAC 57.833 33.333 0.00 0.00 0.00 2.90
3748 4016 9.166173 CCTTCAAGATATTTCAGACAATGTACA 57.834 33.333 0.00 0.00 0.00 2.90
3755 4023 8.970691 ATATTTCAGACAATGTACAAAACAGC 57.029 30.769 0.00 0.00 42.70 4.40
3756 4024 4.829064 TCAGACAATGTACAAAACAGCC 57.171 40.909 0.00 0.00 42.70 4.85
3757 4025 3.568007 TCAGACAATGTACAAAACAGCCC 59.432 43.478 0.00 0.00 42.70 5.19
3758 4026 3.317711 CAGACAATGTACAAAACAGCCCA 59.682 43.478 0.00 0.00 42.70 5.36
3759 4027 4.022068 CAGACAATGTACAAAACAGCCCAT 60.022 41.667 0.00 0.00 42.70 4.00
3760 4028 4.588528 AGACAATGTACAAAACAGCCCATT 59.411 37.500 0.00 0.00 42.70 3.16
3761 4029 5.070313 AGACAATGTACAAAACAGCCCATTT 59.930 36.000 0.00 0.00 42.70 2.32
3762 4030 5.679601 ACAATGTACAAAACAGCCCATTTT 58.320 33.333 0.00 0.00 42.70 1.82
3764 4032 5.543507 ATGTACAAAACAGCCCATTTTGA 57.456 34.783 19.09 3.50 45.75 2.69
3765 4033 4.942852 TGTACAAAACAGCCCATTTTGAG 58.057 39.130 19.09 1.00 45.75 3.02
3766 4034 2.837498 ACAAAACAGCCCATTTTGAGC 58.163 42.857 19.09 0.00 45.75 4.26
3767 4035 2.435437 ACAAAACAGCCCATTTTGAGCT 59.565 40.909 19.09 0.00 45.75 4.09
3772 4040 1.542492 AGCCCATTTTGAGCTGTCTG 58.458 50.000 0.00 0.00 34.99 3.51
3773 4041 1.074405 AGCCCATTTTGAGCTGTCTGA 59.926 47.619 0.00 0.00 34.99 3.27
3774 4042 1.888512 GCCCATTTTGAGCTGTCTGAA 59.111 47.619 0.00 0.00 0.00 3.02
3775 4043 2.297033 GCCCATTTTGAGCTGTCTGAAA 59.703 45.455 0.00 0.00 0.00 2.69
3776 4044 3.056322 GCCCATTTTGAGCTGTCTGAAAT 60.056 43.478 0.00 0.00 0.00 2.17
3777 4045 4.491676 CCCATTTTGAGCTGTCTGAAATG 58.508 43.478 0.00 0.57 37.04 2.32
3778 4046 4.219070 CCCATTTTGAGCTGTCTGAAATGA 59.781 41.667 13.84 0.00 38.18 2.57
3779 4047 5.159209 CCATTTTGAGCTGTCTGAAATGAC 58.841 41.667 13.84 0.00 38.18 3.06
3780 4048 5.048224 CCATTTTGAGCTGTCTGAAATGACT 60.048 40.000 13.84 0.00 38.18 3.41
3781 4049 6.444633 CATTTTGAGCTGTCTGAAATGACTT 58.555 36.000 0.00 0.00 38.18 3.01
3782 4050 7.308770 CCATTTTGAGCTGTCTGAAATGACTTA 60.309 37.037 13.84 0.00 38.18 2.24
3783 4051 6.545504 TTTGAGCTGTCTGAAATGACTTAC 57.454 37.500 0.00 0.00 37.79 2.34
3784 4052 5.213891 TGAGCTGTCTGAAATGACTTACA 57.786 39.130 0.00 0.00 37.79 2.41
3785 4053 5.610398 TGAGCTGTCTGAAATGACTTACAA 58.390 37.500 0.00 0.00 37.79 2.41
3786 4054 6.054941 TGAGCTGTCTGAAATGACTTACAAA 58.945 36.000 0.00 0.00 37.79 2.83
3787 4055 6.542005 TGAGCTGTCTGAAATGACTTACAAAA 59.458 34.615 0.00 0.00 37.79 2.44
3788 4056 6.963796 AGCTGTCTGAAATGACTTACAAAAG 58.036 36.000 0.00 0.00 37.79 2.27
3790 4058 6.634436 GCTGTCTGAAATGACTTACAAAAGTG 59.366 38.462 0.00 0.00 46.09 3.16
3791 4059 7.467267 GCTGTCTGAAATGACTTACAAAAGTGA 60.467 37.037 0.00 0.00 46.09 3.41
3792 4060 8.275015 TGTCTGAAATGACTTACAAAAGTGAA 57.725 30.769 0.00 0.00 46.09 3.18
3793 4061 8.181573 TGTCTGAAATGACTTACAAAAGTGAAC 58.818 33.333 0.00 0.00 46.09 3.18
3794 4062 7.373441 GTCTGAAATGACTTACAAAAGTGAACG 59.627 37.037 0.00 0.00 46.09 3.95
3795 4063 6.491394 TGAAATGACTTACAAAAGTGAACGG 58.509 36.000 0.00 0.00 46.09 4.44
3796 4064 6.316640 TGAAATGACTTACAAAAGTGAACGGA 59.683 34.615 0.00 0.00 46.09 4.69
3797 4065 5.924475 ATGACTTACAAAAGTGAACGGAG 57.076 39.130 0.00 0.00 46.09 4.63
3798 4066 4.124238 TGACTTACAAAAGTGAACGGAGG 58.876 43.478 0.00 0.00 46.09 4.30
3799 4067 3.473625 ACTTACAAAAGTGAACGGAGGG 58.526 45.455 0.00 0.00 44.40 4.30
3800 4068 3.135167 ACTTACAAAAGTGAACGGAGGGA 59.865 43.478 0.00 0.00 44.40 4.20
3801 4069 2.256117 ACAAAAGTGAACGGAGGGAG 57.744 50.000 0.00 0.00 0.00 4.30
3802 4070 1.489230 ACAAAAGTGAACGGAGGGAGT 59.511 47.619 0.00 0.00 0.00 3.85
3803 4071 2.701951 ACAAAAGTGAACGGAGGGAGTA 59.298 45.455 0.00 0.00 0.00 2.59
3804 4072 3.326880 ACAAAAGTGAACGGAGGGAGTAT 59.673 43.478 0.00 0.00 0.00 2.12
3805 4073 4.529377 ACAAAAGTGAACGGAGGGAGTATA 59.471 41.667 0.00 0.00 0.00 1.47
3806 4074 5.189145 ACAAAAGTGAACGGAGGGAGTATAT 59.811 40.000 0.00 0.00 0.00 0.86
3807 4075 6.381994 ACAAAAGTGAACGGAGGGAGTATATA 59.618 38.462 0.00 0.00 0.00 0.86
3808 4076 6.402456 AAAGTGAACGGAGGGAGTATATAC 57.598 41.667 4.60 4.60 0.00 1.47
3809 4077 4.070716 AGTGAACGGAGGGAGTATATACG 58.929 47.826 7.23 0.00 0.00 3.06
3810 4078 4.067896 GTGAACGGAGGGAGTATATACGA 58.932 47.826 7.23 0.00 0.00 3.43
3811 4079 4.067896 TGAACGGAGGGAGTATATACGAC 58.932 47.826 7.23 6.01 0.00 4.34
3812 4080 3.064900 ACGGAGGGAGTATATACGACC 57.935 52.381 16.58 16.58 0.00 4.79
3813 4081 2.290577 ACGGAGGGAGTATATACGACCC 60.291 54.545 28.23 28.23 43.05 4.46
3814 4082 2.363683 GGAGGGAGTATATACGACCCG 58.636 57.143 28.54 0.00 45.31 5.28
3815 4083 2.363683 GAGGGAGTATATACGACCCGG 58.636 57.143 28.54 0.00 45.31 5.73
3816 4084 1.988107 AGGGAGTATATACGACCCGGA 59.012 52.381 28.54 0.00 45.31 5.14
3817 4085 2.579860 AGGGAGTATATACGACCCGGAT 59.420 50.000 28.54 17.93 45.31 4.18
3818 4086 2.948315 GGGAGTATATACGACCCGGATC 59.052 54.545 24.60 0.00 37.69 3.36
3819 4087 6.727587 AGGGAGTATATACGACCCGGATCG 62.728 54.167 28.54 19.09 45.31 3.69
3820 4088 2.012673 AGTATATACGACCCGGATCGC 58.987 52.381 20.89 0.00 46.22 4.58
3821 4089 2.012673 GTATATACGACCCGGATCGCT 58.987 52.381 20.89 8.86 46.22 4.93
3822 4090 1.093159 ATATACGACCCGGATCGCTC 58.907 55.000 20.89 0.00 46.22 5.03
3823 4091 0.035881 TATACGACCCGGATCGCTCT 59.964 55.000 20.89 5.46 46.22 4.09
3824 4092 1.235948 ATACGACCCGGATCGCTCTC 61.236 60.000 20.89 0.00 46.22 3.20
3825 4093 4.315122 CGACCCGGATCGCTCTCG 62.315 72.222 4.60 0.00 34.90 4.04
3826 4094 3.967335 GACCCGGATCGCTCTCGG 61.967 72.222 0.73 8.60 43.05 4.63
3829 4097 3.983494 CCGGATCGCTCTCGGCAT 61.983 66.667 0.00 0.00 41.91 4.40
3830 4098 2.626780 CCGGATCGCTCTCGGCATA 61.627 63.158 0.00 0.00 41.91 3.14
3831 4099 1.285950 CGGATCGCTCTCGGCATAA 59.714 57.895 0.00 0.00 41.91 1.90
3832 4100 0.318699 CGGATCGCTCTCGGCATAAA 60.319 55.000 0.00 0.00 41.91 1.40
3833 4101 1.670087 CGGATCGCTCTCGGCATAAAT 60.670 52.381 0.00 0.00 41.91 1.40
3834 4102 1.728971 GGATCGCTCTCGGCATAAATG 59.271 52.381 0.00 0.00 41.91 2.32
3835 4103 1.728971 GATCGCTCTCGGCATAAATGG 59.271 52.381 0.00 0.00 41.91 3.16
3836 4104 0.249868 TCGCTCTCGGCATAAATGGG 60.250 55.000 0.00 0.00 41.91 4.00
3837 4105 1.230635 CGCTCTCGGCATAAATGGGG 61.231 60.000 0.00 0.00 41.91 4.96
3838 4106 0.108585 GCTCTCGGCATAAATGGGGA 59.891 55.000 0.00 0.00 41.35 4.81
3839 4107 1.884235 CTCTCGGCATAAATGGGGAC 58.116 55.000 0.00 0.00 0.00 4.46
3855 4123 1.414550 GGGACCTAAGATCCTGTCTGC 59.585 57.143 0.00 0.00 37.23 4.26
3856 4124 1.414550 GGACCTAAGATCCTGTCTGCC 59.585 57.143 0.00 0.00 37.23 4.85
3857 4125 1.414550 GACCTAAGATCCTGTCTGCCC 59.585 57.143 0.00 0.00 37.23 5.36
3858 4126 0.390860 CCTAAGATCCTGTCTGCCCG 59.609 60.000 0.00 0.00 37.23 6.13
3859 4127 1.403814 CTAAGATCCTGTCTGCCCGA 58.596 55.000 0.00 0.00 37.23 5.14
3860 4128 1.339610 CTAAGATCCTGTCTGCCCGAG 59.660 57.143 0.00 0.00 37.23 4.63
3861 4129 0.616111 AAGATCCTGTCTGCCCGAGT 60.616 55.000 0.00 0.00 37.23 4.18
3862 4130 1.040339 AGATCCTGTCTGCCCGAGTC 61.040 60.000 0.00 0.00 35.31 3.36
3863 4131 1.000993 ATCCTGTCTGCCCGAGTCT 59.999 57.895 0.00 0.00 0.00 3.24
3864 4132 1.326213 ATCCTGTCTGCCCGAGTCTG 61.326 60.000 0.00 0.00 0.00 3.51
3865 4133 2.279069 CCTGTCTGCCCGAGTCTGT 61.279 63.158 0.00 0.00 0.00 3.41
3866 4134 1.668294 CTGTCTGCCCGAGTCTGTT 59.332 57.895 0.00 0.00 0.00 3.16
3867 4135 0.389166 CTGTCTGCCCGAGTCTGTTC 60.389 60.000 0.00 0.00 0.00 3.18
3868 4136 0.827925 TGTCTGCCCGAGTCTGTTCT 60.828 55.000 0.00 0.00 0.00 3.01
3869 4137 0.389166 GTCTGCCCGAGTCTGTTCTG 60.389 60.000 0.00 0.00 0.00 3.02
3870 4138 1.079543 CTGCCCGAGTCTGTTCTGG 60.080 63.158 0.00 0.00 0.00 3.86
3871 4139 2.435059 GCCCGAGTCTGTTCTGGC 60.435 66.667 0.00 0.00 39.70 4.85
3872 4140 2.125912 CCCGAGTCTGTTCTGGCG 60.126 66.667 0.00 0.00 0.00 5.69
3873 4141 2.811317 CCGAGTCTGTTCTGGCGC 60.811 66.667 0.00 0.00 0.00 6.53
3874 4142 2.811317 CGAGTCTGTTCTGGCGCC 60.811 66.667 22.73 22.73 0.00 6.53
3875 4143 2.659610 GAGTCTGTTCTGGCGCCT 59.340 61.111 29.70 2.62 0.00 5.52
3876 4144 1.004440 GAGTCTGTTCTGGCGCCTT 60.004 57.895 29.70 1.30 0.00 4.35
3877 4145 1.294659 GAGTCTGTTCTGGCGCCTTG 61.295 60.000 29.70 20.24 0.00 3.61
3878 4146 2.032528 TCTGTTCTGGCGCCTTGG 59.967 61.111 29.70 17.48 0.00 3.61
3879 4147 3.741476 CTGTTCTGGCGCCTTGGC 61.741 66.667 29.70 15.70 45.12 4.52
3887 4155 2.751436 GCGCCTTGGCCATTCAGA 60.751 61.111 6.09 0.00 0.00 3.27
3888 4156 2.123428 GCGCCTTGGCCATTCAGAT 61.123 57.895 6.09 0.00 0.00 2.90
3889 4157 2.028130 CGCCTTGGCCATTCAGATC 58.972 57.895 6.09 0.00 0.00 2.75
3890 4158 0.465097 CGCCTTGGCCATTCAGATCT 60.465 55.000 6.09 0.00 0.00 2.75
3891 4159 1.316651 GCCTTGGCCATTCAGATCTC 58.683 55.000 6.09 0.00 0.00 2.75
3892 4160 1.409241 GCCTTGGCCATTCAGATCTCA 60.409 52.381 6.09 0.00 0.00 3.27
3893 4161 2.573369 CCTTGGCCATTCAGATCTCAG 58.427 52.381 6.09 0.00 0.00 3.35
3894 4162 2.092538 CCTTGGCCATTCAGATCTCAGT 60.093 50.000 6.09 0.00 0.00 3.41
3895 4163 3.618351 CTTGGCCATTCAGATCTCAGTT 58.382 45.455 6.09 0.00 0.00 3.16
3896 4164 3.726557 TGGCCATTCAGATCTCAGTTT 57.273 42.857 0.00 0.00 0.00 2.66
3897 4165 4.038271 TGGCCATTCAGATCTCAGTTTT 57.962 40.909 0.00 0.00 0.00 2.43
3898 4166 4.012374 TGGCCATTCAGATCTCAGTTTTC 58.988 43.478 0.00 0.00 0.00 2.29
3899 4167 3.064545 GGCCATTCAGATCTCAGTTTTCG 59.935 47.826 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.607988 ATTGATATTTGTGTCGACATTACCTTA 57.392 29.630 23.12 9.55 30.13 2.69
20 21 5.816449 TGCATTGATATTTGTGTCGACAT 57.184 34.783 23.12 8.17 30.13 3.06
32 33 8.250332 ACCGTGTAAAATTTCTTGCATTGATAT 58.750 29.630 0.00 0.00 0.00 1.63
41 42 9.113876 GTGATTTCTACCGTGTAAAATTTCTTG 57.886 33.333 0.00 0.00 0.00 3.02
51 52 4.283978 TCTTTGGGTGATTTCTACCGTGTA 59.716 41.667 0.00 0.00 39.14 2.90
284 292 1.850345 GGAAGAGAGAGGAGAGGGAGA 59.150 57.143 0.00 0.00 0.00 3.71
312 321 4.667935 TGGGGCGGAAGAGGGGAA 62.668 66.667 0.00 0.00 0.00 3.97
389 398 4.200283 GTGGAGGAGGCGCTCTCG 62.200 72.222 7.64 0.00 43.34 4.04
442 453 3.519510 CTGATCTGTTCTAACCTTGGGGA 59.480 47.826 0.00 0.00 36.25 4.81
472 483 3.634397 ATGAAAAAGATGAGCCGGAGA 57.366 42.857 5.05 0.00 0.00 3.71
474 485 3.941483 GAGAATGAAAAAGATGAGCCGGA 59.059 43.478 5.05 0.00 0.00 5.14
477 488 3.488216 GCCGAGAATGAAAAAGATGAGCC 60.488 47.826 0.00 0.00 0.00 4.70
478 489 3.689346 GCCGAGAATGAAAAAGATGAGC 58.311 45.455 0.00 0.00 0.00 4.26
480 491 2.677836 CCGCCGAGAATGAAAAAGATGA 59.322 45.455 0.00 0.00 0.00 2.92
482 493 1.401905 GCCGCCGAGAATGAAAAAGAT 59.598 47.619 0.00 0.00 0.00 2.40
483 494 0.802494 GCCGCCGAGAATGAAAAAGA 59.198 50.000 0.00 0.00 0.00 2.52
485 496 0.951525 TCGCCGCCGAGAATGAAAAA 60.952 50.000 0.00 0.00 38.82 1.94
530 541 3.242413 CGAATCATGCCGAAGTAAACCTG 60.242 47.826 0.00 0.00 0.00 4.00
540 551 0.249197 CTGCTCTCGAATCATGCCGA 60.249 55.000 4.99 4.99 0.00 5.54
676 687 3.593632 CACAATCGTCAAATGAACGAACG 59.406 43.478 2.24 0.00 39.38 3.95
790 801 0.389948 CGACGAGGGTTCCTTCCTTG 60.390 60.000 0.00 0.00 40.73 3.61
799 810 0.736325 CGAGATTTGCGACGAGGGTT 60.736 55.000 0.00 0.00 0.00 4.11
800 811 1.153823 CGAGATTTGCGACGAGGGT 60.154 57.895 0.00 0.00 0.00 4.34
828 839 0.250295 CGAGTCTTTCTGCCCACCAA 60.250 55.000 0.00 0.00 0.00 3.67
874 885 2.044053 CCCAATCATGGCACGGGT 60.044 61.111 0.00 0.00 46.09 5.28
927 938 2.475371 TTTCTCCTGCCTCCTGCTGC 62.475 60.000 0.00 0.00 42.00 5.25
946 957 1.409381 GCCTATCCTTGCCTGCTCTTT 60.409 52.381 0.00 0.00 0.00 2.52
978 989 0.032217 AGAGCTCCCTCCTCTCCTTG 60.032 60.000 10.93 0.00 38.96 3.61
1161 1178 0.811616 GCCGCGGAATGATGAAGAGT 60.812 55.000 33.48 0.00 0.00 3.24
1182 1199 2.375766 GCCTTGACGCACAGACTCG 61.376 63.158 0.00 0.00 0.00 4.18
1305 1322 1.364626 GCGCAACCTCAGACTCATGG 61.365 60.000 0.30 0.00 0.00 3.66
1329 1346 2.391389 GCCGCTCGACTTTGGAAGG 61.391 63.158 0.00 0.00 0.00 3.46
1452 1469 0.321671 TCTCCTTTGCCTTCTCCACG 59.678 55.000 0.00 0.00 0.00 4.94
1527 1544 1.699083 TGCACCAGGAAGACATCAAGA 59.301 47.619 0.00 0.00 0.00 3.02
1564 1581 5.048294 GGTCCTTAAAAACCCACATGTACAG 60.048 44.000 0.00 0.00 0.00 2.74
1668 1685 2.617274 GCCCTTGTCCGCACTGAAC 61.617 63.158 0.00 0.00 0.00 3.18
1836 1853 7.466590 GCTTCAGATGGTACTGAGAAATTAAGC 60.467 40.741 0.00 0.00 45.63 3.09
1849 1866 2.164624 AGTCACTCGCTTCAGATGGTAC 59.835 50.000 0.00 0.00 0.00 3.34
1854 1871 3.006323 ACTCAAAGTCACTCGCTTCAGAT 59.994 43.478 0.00 0.00 0.00 2.90
1855 1872 2.362397 ACTCAAAGTCACTCGCTTCAGA 59.638 45.455 0.00 0.00 0.00 3.27
1940 1957 1.414158 ATGAGAGGTATGTGGGACGG 58.586 55.000 0.00 0.00 0.00 4.79
2001 2018 3.883489 CTGATGACGGTGGTGTAGATAGA 59.117 47.826 0.00 0.00 0.00 1.98
2103 2120 3.384467 CGGAACAGGAATTATTGGCCATT 59.616 43.478 6.09 5.63 0.00 3.16
2130 2147 3.067833 GTGTACTTCAACCTCTTGCTCC 58.932 50.000 0.00 0.00 0.00 4.70
2142 2159 0.032952 GCTCACCGGTGTGTACTTCA 59.967 55.000 32.74 11.25 43.26 3.02
2425 2442 2.154798 CTCACAAACTCGCCGGGAGA 62.155 60.000 22.16 0.00 46.23 3.71
2430 2447 1.738099 CTCCCTCACAAACTCGCCG 60.738 63.158 0.00 0.00 0.00 6.46
2511 2528 1.836166 ACCATGATCTCCAGTCCAGTG 59.164 52.381 0.00 0.00 0.00 3.66
2553 2570 2.264455 ACCTGAACTTCATGCTCCTCT 58.736 47.619 0.00 0.00 0.00 3.69
2568 2585 1.304381 GGGCCTCATGCAAACCTGA 60.304 57.895 0.84 0.00 43.89 3.86
2682 2700 3.275338 GCTGCTATGCTCCGGTGC 61.275 66.667 21.41 21.41 0.00 5.01
2717 2735 9.506018 AAAGAAAATTTCCGATTTTTGATCCAT 57.494 25.926 1.57 0.00 32.03 3.41
2729 2747 2.882137 AGTGCCGAAAGAAAATTTCCGA 59.118 40.909 1.57 0.00 0.00 4.55
2744 2762 0.370273 GCGACTAATGTTCAGTGCCG 59.630 55.000 0.00 0.00 0.00 5.69
2748 2766 5.807520 CAGATAAGTGCGACTAATGTTCAGT 59.192 40.000 0.00 0.00 0.00 3.41
2950 2971 7.417797 GCTGTCCACATTATTATGAACCCAATT 60.418 37.037 0.00 0.00 35.65 2.32
2953 2974 4.887071 GCTGTCCACATTATTATGAACCCA 59.113 41.667 0.00 0.00 35.65 4.51
3051 3072 4.431661 GGCCATACCTATGTAGTACGAC 57.568 50.000 0.00 0.00 34.51 4.34
3112 3133 2.046023 CGGGCACAGATTCAGGCA 60.046 61.111 0.00 0.00 0.00 4.75
3113 3134 3.512516 GCGGGCACAGATTCAGGC 61.513 66.667 0.00 0.00 0.00 4.85
3125 3147 1.663379 GGAATAACCAAGGTGCGGGC 61.663 60.000 0.00 0.00 38.79 6.13
3127 3149 1.094785 CAGGAATAACCAAGGTGCGG 58.905 55.000 0.00 0.00 42.04 5.69
3131 3153 3.266772 TCATCAGCAGGAATAACCAAGGT 59.733 43.478 0.00 0.00 42.04 3.50
3135 3157 2.575735 TGGTCATCAGCAGGAATAACCA 59.424 45.455 0.00 0.00 42.04 3.67
3136 3158 3.209410 CTGGTCATCAGCAGGAATAACC 58.791 50.000 0.00 0.00 43.38 2.85
3144 3166 1.153208 GAGCCCTGGTCATCAGCAG 60.153 63.158 0.00 0.00 46.18 4.24
3146 3168 2.202987 CGAGCCCTGGTCATCAGC 60.203 66.667 0.00 0.00 42.05 4.26
3147 3169 1.903877 AACCGAGCCCTGGTCATCAG 61.904 60.000 0.00 0.00 39.29 2.90
3150 3172 0.322546 GAAAACCGAGCCCTGGTCAT 60.323 55.000 0.00 0.00 39.29 3.06
3154 3176 2.746277 CCGAAAACCGAGCCCTGG 60.746 66.667 0.00 0.00 41.76 4.45
3161 3194 2.712325 TTACCGCTGCCGAAAACCGA 62.712 55.000 0.00 0.00 41.76 4.69
3162 3195 1.641123 ATTACCGCTGCCGAAAACCG 61.641 55.000 0.00 0.00 36.29 4.44
3170 3203 3.060602 GAGATTCAGTATTACCGCTGCC 58.939 50.000 0.00 0.00 33.09 4.85
3171 3204 2.726760 CGAGATTCAGTATTACCGCTGC 59.273 50.000 0.00 0.00 33.09 5.25
3179 3212 2.697751 AGGAGCAGCGAGATTCAGTATT 59.302 45.455 0.00 0.00 0.00 1.89
3182 3215 0.175302 CAGGAGCAGCGAGATTCAGT 59.825 55.000 0.00 0.00 0.00 3.41
3216 3451 6.969828 AGTACGGATGAAACTGAGAATTTC 57.030 37.500 0.00 0.00 36.73 2.17
3220 3455 4.988540 CACAAGTACGGATGAAACTGAGAA 59.011 41.667 3.80 0.00 0.00 2.87
3225 3460 2.370849 ACCCACAAGTACGGATGAAACT 59.629 45.455 3.80 0.00 0.00 2.66
3235 3470 1.806542 CACAGCATCACCCACAAGTAC 59.193 52.381 0.00 0.00 0.00 2.73
3287 3522 7.549488 GTCTCAGCAAATATACCTTTGTACTGT 59.451 37.037 0.00 0.00 38.19 3.55
3308 3543 7.617329 TCAAGAAAGATCCTCTATCAAGTCTCA 59.383 37.037 0.00 0.00 37.03 3.27
3317 3552 7.125507 ACATGTCAGTCAAGAAAGATCCTCTAT 59.874 37.037 0.00 0.00 0.00 1.98
3378 3613 2.159707 CGAGATTTTGTTACCGCTGTGG 60.160 50.000 5.54 5.54 46.41 4.17
3385 3620 5.806089 CAAAACAGCGAGATTTTGTTACC 57.194 39.130 9.16 0.00 39.75 2.85
3401 3636 1.021202 CCGAGTTGAGCCACAAAACA 58.979 50.000 0.00 0.00 40.36 2.83
3433 3668 2.305927 CACCCACAGGTCAGGATAAACT 59.694 50.000 0.00 0.00 46.45 2.66
3446 3681 0.987294 AACCCAGAGATCACCCACAG 59.013 55.000 0.00 0.00 0.00 3.66
3477 3720 0.965439 TTGTACTGCAAATGTGGGGC 59.035 50.000 0.00 0.00 33.53 5.80
3504 3764 4.166919 AGAAAGGAATAGTCAAGGGGGATG 59.833 45.833 0.00 0.00 0.00 3.51
3507 3767 4.592997 AAGAAAGGAATAGTCAAGGGGG 57.407 45.455 0.00 0.00 0.00 5.40
3560 3823 5.188434 CCAATCCTCGGAATATATGCACAT 58.812 41.667 0.00 0.00 0.00 3.21
3665 3933 4.815846 TGCACAATACATACAGGTATGCTG 59.184 41.667 17.10 14.12 45.06 4.41
3698 3966 8.541234 AGGTCTTATAAAAGTAAACAGAGGGAG 58.459 37.037 0.00 0.00 34.13 4.30
3699 3967 8.445361 AGGTCTTATAAAAGTAAACAGAGGGA 57.555 34.615 0.00 0.00 34.13 4.20
3700 3968 9.163899 GAAGGTCTTATAAAAGTAAACAGAGGG 57.836 37.037 0.00 0.00 34.13 4.30
3701 3969 9.720769 TGAAGGTCTTATAAAAGTAAACAGAGG 57.279 33.333 0.00 0.00 34.13 3.69
3718 3986 8.954350 CATTGTCTGAAATATCTTGAAGGTCTT 58.046 33.333 0.00 0.00 0.00 3.01
3719 3987 8.105829 ACATTGTCTGAAATATCTTGAAGGTCT 58.894 33.333 0.00 0.00 0.00 3.85
3720 3988 8.273780 ACATTGTCTGAAATATCTTGAAGGTC 57.726 34.615 0.00 0.00 0.00 3.85
3721 3989 9.167311 GTACATTGTCTGAAATATCTTGAAGGT 57.833 33.333 0.00 0.00 0.00 3.50
3722 3990 9.166173 TGTACATTGTCTGAAATATCTTGAAGG 57.834 33.333 0.00 0.00 0.00 3.46
3729 3997 9.065871 GCTGTTTTGTACATTGTCTGAAATATC 57.934 33.333 0.00 0.00 35.85 1.63
3730 3998 8.028938 GGCTGTTTTGTACATTGTCTGAAATAT 58.971 33.333 0.00 0.00 35.85 1.28
3731 3999 7.367285 GGCTGTTTTGTACATTGTCTGAAATA 58.633 34.615 0.00 0.00 35.85 1.40
3732 4000 6.215845 GGCTGTTTTGTACATTGTCTGAAAT 58.784 36.000 0.00 0.00 35.85 2.17
3733 4001 5.451242 GGGCTGTTTTGTACATTGTCTGAAA 60.451 40.000 0.00 0.00 35.85 2.69
3734 4002 4.037446 GGGCTGTTTTGTACATTGTCTGAA 59.963 41.667 0.00 0.00 35.85 3.02
3735 4003 3.568007 GGGCTGTTTTGTACATTGTCTGA 59.432 43.478 0.00 0.00 35.85 3.27
3736 4004 3.317711 TGGGCTGTTTTGTACATTGTCTG 59.682 43.478 0.00 0.00 35.85 3.51
3737 4005 3.561143 TGGGCTGTTTTGTACATTGTCT 58.439 40.909 0.00 0.00 35.85 3.41
3738 4006 4.519540 ATGGGCTGTTTTGTACATTGTC 57.480 40.909 0.00 0.00 35.85 3.18
3739 4007 4.953940 AATGGGCTGTTTTGTACATTGT 57.046 36.364 0.00 0.00 35.85 2.71
3740 4008 5.757320 TCAAAATGGGCTGTTTTGTACATTG 59.243 36.000 19.52 0.00 43.52 2.82
3741 4009 5.923204 TCAAAATGGGCTGTTTTGTACATT 58.077 33.333 19.52 0.00 43.52 2.71
3742 4010 5.540911 CTCAAAATGGGCTGTTTTGTACAT 58.459 37.500 19.52 0.00 43.52 2.29
3743 4011 4.739137 GCTCAAAATGGGCTGTTTTGTACA 60.739 41.667 19.52 0.00 41.63 2.90
3744 4012 3.740832 GCTCAAAATGGGCTGTTTTGTAC 59.259 43.478 19.52 12.95 41.63 2.90
3745 4013 3.988819 GCTCAAAATGGGCTGTTTTGTA 58.011 40.909 19.52 10.81 41.63 2.41
3746 4014 2.837498 GCTCAAAATGGGCTGTTTTGT 58.163 42.857 19.52 0.00 41.63 2.83
3754 4022 1.538047 TCAGACAGCTCAAAATGGGC 58.462 50.000 0.00 0.00 46.33 5.36
3755 4023 4.219070 TCATTTCAGACAGCTCAAAATGGG 59.781 41.667 12.29 0.00 36.21 4.00
3756 4024 5.048224 AGTCATTTCAGACAGCTCAAAATGG 60.048 40.000 12.29 0.00 40.98 3.16
3757 4025 6.010294 AGTCATTTCAGACAGCTCAAAATG 57.990 37.500 0.00 0.00 40.98 2.32
3758 4026 6.645790 AAGTCATTTCAGACAGCTCAAAAT 57.354 33.333 0.00 0.00 40.98 1.82
3759 4027 6.542005 TGTAAGTCATTTCAGACAGCTCAAAA 59.458 34.615 0.00 0.00 40.98 2.44
3760 4028 6.054941 TGTAAGTCATTTCAGACAGCTCAAA 58.945 36.000 0.00 0.00 40.98 2.69
3761 4029 5.610398 TGTAAGTCATTTCAGACAGCTCAA 58.390 37.500 0.00 0.00 40.98 3.02
3762 4030 5.213891 TGTAAGTCATTTCAGACAGCTCA 57.786 39.130 0.00 0.00 40.98 4.26
3763 4031 6.545504 TTTGTAAGTCATTTCAGACAGCTC 57.454 37.500 0.00 0.00 40.98 4.09
3764 4032 6.543831 ACTTTTGTAAGTCATTTCAGACAGCT 59.456 34.615 0.00 0.00 40.60 4.24
3765 4033 6.634436 CACTTTTGTAAGTCATTTCAGACAGC 59.366 38.462 0.00 0.00 42.67 4.40
3766 4034 7.919690 TCACTTTTGTAAGTCATTTCAGACAG 58.080 34.615 0.00 0.00 42.67 3.51
3767 4035 7.857734 TCACTTTTGTAAGTCATTTCAGACA 57.142 32.000 0.00 0.00 42.67 3.41
3768 4036 7.373441 CGTTCACTTTTGTAAGTCATTTCAGAC 59.627 37.037 0.00 0.00 42.67 3.51
3769 4037 7.406553 CGTTCACTTTTGTAAGTCATTTCAGA 58.593 34.615 0.00 0.00 42.67 3.27
3770 4038 6.632834 CCGTTCACTTTTGTAAGTCATTTCAG 59.367 38.462 0.00 0.00 42.67 3.02
3771 4039 6.316640 TCCGTTCACTTTTGTAAGTCATTTCA 59.683 34.615 0.00 0.00 42.67 2.69
3772 4040 6.721321 TCCGTTCACTTTTGTAAGTCATTTC 58.279 36.000 0.00 0.00 42.67 2.17
3773 4041 6.238648 CCTCCGTTCACTTTTGTAAGTCATTT 60.239 38.462 0.00 0.00 42.67 2.32
3774 4042 5.238650 CCTCCGTTCACTTTTGTAAGTCATT 59.761 40.000 0.00 0.00 42.67 2.57
3775 4043 4.755123 CCTCCGTTCACTTTTGTAAGTCAT 59.245 41.667 0.00 0.00 42.67 3.06
3776 4044 4.124238 CCTCCGTTCACTTTTGTAAGTCA 58.876 43.478 0.00 0.00 42.67 3.41
3777 4045 3.497262 CCCTCCGTTCACTTTTGTAAGTC 59.503 47.826 0.00 0.00 42.67 3.01
3778 4046 3.135167 TCCCTCCGTTCACTTTTGTAAGT 59.865 43.478 0.00 0.00 45.40 2.24
3779 4047 3.735591 TCCCTCCGTTCACTTTTGTAAG 58.264 45.455 0.00 0.00 37.40 2.34
3780 4048 3.135167 ACTCCCTCCGTTCACTTTTGTAA 59.865 43.478 0.00 0.00 0.00 2.41
3781 4049 2.701951 ACTCCCTCCGTTCACTTTTGTA 59.298 45.455 0.00 0.00 0.00 2.41
3782 4050 1.489230 ACTCCCTCCGTTCACTTTTGT 59.511 47.619 0.00 0.00 0.00 2.83
3783 4051 2.256117 ACTCCCTCCGTTCACTTTTG 57.744 50.000 0.00 0.00 0.00 2.44
3784 4052 5.952347 ATATACTCCCTCCGTTCACTTTT 57.048 39.130 0.00 0.00 0.00 2.27
3785 4053 5.009410 CGTATATACTCCCTCCGTTCACTTT 59.991 44.000 11.05 0.00 0.00 2.66
3786 4054 4.518211 CGTATATACTCCCTCCGTTCACTT 59.482 45.833 11.05 0.00 0.00 3.16
3787 4055 4.070716 CGTATATACTCCCTCCGTTCACT 58.929 47.826 11.05 0.00 0.00 3.41
3788 4056 4.067896 TCGTATATACTCCCTCCGTTCAC 58.932 47.826 11.05 0.00 0.00 3.18
3789 4057 4.067896 GTCGTATATACTCCCTCCGTTCA 58.932 47.826 11.05 0.00 0.00 3.18
3790 4058 3.438434 GGTCGTATATACTCCCTCCGTTC 59.562 52.174 11.05 0.00 0.00 3.95
3791 4059 3.416156 GGTCGTATATACTCCCTCCGTT 58.584 50.000 11.05 0.00 0.00 4.44
3792 4060 2.290577 GGGTCGTATATACTCCCTCCGT 60.291 54.545 23.99 0.00 36.11 4.69
3793 4061 2.363683 GGGTCGTATATACTCCCTCCG 58.636 57.143 23.99 7.67 36.11 4.63
3794 4062 2.363683 CGGGTCGTATATACTCCCTCC 58.636 57.143 26.20 15.20 36.53 4.30
3795 4063 2.026822 TCCGGGTCGTATATACTCCCTC 60.027 54.545 26.20 13.71 36.53 4.30
3796 4064 1.988107 TCCGGGTCGTATATACTCCCT 59.012 52.381 26.20 0.00 36.53 4.20
3797 4065 2.496899 TCCGGGTCGTATATACTCCC 57.503 55.000 22.56 22.56 35.86 4.30
3798 4066 2.611292 CGATCCGGGTCGTATATACTCC 59.389 54.545 28.99 11.96 36.88 3.85
3799 4067 2.031437 GCGATCCGGGTCGTATATACTC 59.969 54.545 35.59 14.69 43.27 2.59
3800 4068 2.012673 GCGATCCGGGTCGTATATACT 58.987 52.381 35.59 0.00 43.27 2.12
3801 4069 2.012673 AGCGATCCGGGTCGTATATAC 58.987 52.381 35.59 19.31 43.27 1.47
3802 4070 2.093288 AGAGCGATCCGGGTCGTATATA 60.093 50.000 35.59 0.00 43.27 0.86
3803 4071 1.093159 GAGCGATCCGGGTCGTATAT 58.907 55.000 35.59 20.50 43.27 0.86
3804 4072 0.035881 AGAGCGATCCGGGTCGTATA 59.964 55.000 35.59 0.00 43.27 1.47
3805 4073 1.228184 AGAGCGATCCGGGTCGTAT 60.228 57.895 35.59 25.50 43.27 3.06
3806 4074 1.890979 GAGAGCGATCCGGGTCGTA 60.891 63.158 35.59 0.00 43.27 3.43
3807 4075 3.210528 GAGAGCGATCCGGGTCGT 61.211 66.667 35.59 23.25 43.27 4.34
3808 4076 4.315122 CGAGAGCGATCCGGGTCG 62.315 72.222 32.59 32.59 44.14 4.79
3809 4077 3.967335 CCGAGAGCGATCCGGGTC 61.967 72.222 18.87 4.00 40.82 4.46
3819 4087 0.108585 TCCCCATTTATGCCGAGAGC 59.891 55.000 0.00 0.00 44.14 4.09
3820 4088 1.543429 GGTCCCCATTTATGCCGAGAG 60.543 57.143 0.00 0.00 0.00 3.20
3821 4089 0.472471 GGTCCCCATTTATGCCGAGA 59.528 55.000 0.00 0.00 0.00 4.04
3822 4090 0.474184 AGGTCCCCATTTATGCCGAG 59.526 55.000 0.00 0.00 0.00 4.63
3823 4091 1.809133 TAGGTCCCCATTTATGCCGA 58.191 50.000 0.00 0.00 0.00 5.54
3824 4092 2.105821 TCTTAGGTCCCCATTTATGCCG 59.894 50.000 0.00 0.00 0.00 5.69
3825 4093 3.876309 TCTTAGGTCCCCATTTATGCC 57.124 47.619 0.00 0.00 0.00 4.40
3826 4094 4.043435 AGGATCTTAGGTCCCCATTTATGC 59.957 45.833 8.09 0.00 36.36 3.14
3827 4095 5.073691 ACAGGATCTTAGGTCCCCATTTATG 59.926 44.000 8.09 0.53 36.36 1.90
3828 4096 5.235534 ACAGGATCTTAGGTCCCCATTTAT 58.764 41.667 8.09 0.00 36.36 1.40
3829 4097 4.641868 ACAGGATCTTAGGTCCCCATTTA 58.358 43.478 8.09 0.00 36.36 1.40
3830 4098 3.459969 GACAGGATCTTAGGTCCCCATTT 59.540 47.826 8.09 0.00 36.36 2.32
3831 4099 3.049344 GACAGGATCTTAGGTCCCCATT 58.951 50.000 8.09 0.00 36.36 3.16
3832 4100 2.251338 AGACAGGATCTTAGGTCCCCAT 59.749 50.000 8.09 0.00 36.36 4.00
3833 4101 1.651770 AGACAGGATCTTAGGTCCCCA 59.348 52.381 8.09 0.00 36.36 4.96
3834 4102 2.043227 CAGACAGGATCTTAGGTCCCC 58.957 57.143 8.09 0.00 34.41 4.81
3835 4103 1.414550 GCAGACAGGATCTTAGGTCCC 59.585 57.143 8.09 0.00 34.41 4.46
3836 4104 1.414550 GGCAGACAGGATCTTAGGTCC 59.585 57.143 2.71 2.71 34.41 4.46
3837 4105 1.414550 GGGCAGACAGGATCTTAGGTC 59.585 57.143 0.00 0.00 34.41 3.85
3838 4106 1.501582 GGGCAGACAGGATCTTAGGT 58.498 55.000 0.00 0.00 34.41 3.08
3839 4107 0.390860 CGGGCAGACAGGATCTTAGG 59.609 60.000 0.00 0.00 34.41 2.69
3840 4108 1.339610 CTCGGGCAGACAGGATCTTAG 59.660 57.143 0.00 0.00 34.41 2.18
3841 4109 1.342076 ACTCGGGCAGACAGGATCTTA 60.342 52.381 0.00 0.00 34.41 2.10
3842 4110 0.616111 ACTCGGGCAGACAGGATCTT 60.616 55.000 0.00 0.00 34.41 2.40
3843 4111 1.000993 ACTCGGGCAGACAGGATCT 59.999 57.895 0.00 0.00 38.66 2.75
3844 4112 1.040339 AGACTCGGGCAGACAGGATC 61.040 60.000 0.00 0.00 0.00 3.36
3845 4113 1.000993 AGACTCGGGCAGACAGGAT 59.999 57.895 0.00 0.00 0.00 3.24
3846 4114 1.979155 CAGACTCGGGCAGACAGGA 60.979 63.158 0.00 0.00 0.00 3.86
3847 4115 1.821061 AACAGACTCGGGCAGACAGG 61.821 60.000 0.00 0.00 0.00 4.00
3848 4116 0.389166 GAACAGACTCGGGCAGACAG 60.389 60.000 0.00 0.00 0.00 3.51
3849 4117 0.827925 AGAACAGACTCGGGCAGACA 60.828 55.000 0.00 0.00 0.00 3.41
3850 4118 0.389166 CAGAACAGACTCGGGCAGAC 60.389 60.000 0.00 0.00 0.00 3.51
3851 4119 1.536073 CCAGAACAGACTCGGGCAGA 61.536 60.000 0.00 0.00 0.00 4.26
3852 4120 1.079543 CCAGAACAGACTCGGGCAG 60.080 63.158 0.00 0.00 0.00 4.85
3853 4121 3.059982 CCAGAACAGACTCGGGCA 58.940 61.111 0.00 0.00 0.00 5.36
3855 4123 2.125912 CGCCAGAACAGACTCGGG 60.126 66.667 0.00 0.00 34.13 5.14
3856 4124 2.811317 GCGCCAGAACAGACTCGG 60.811 66.667 0.00 0.00 0.00 4.63
3857 4125 2.771763 AAGGCGCCAGAACAGACTCG 62.772 60.000 31.54 0.00 0.00 4.18
3858 4126 1.004440 AAGGCGCCAGAACAGACTC 60.004 57.895 31.54 0.00 0.00 3.36
3859 4127 1.302033 CAAGGCGCCAGAACAGACT 60.302 57.895 31.54 0.00 0.00 3.24
3860 4128 2.328099 CCAAGGCGCCAGAACAGAC 61.328 63.158 31.54 0.00 0.00 3.51
3861 4129 2.032528 CCAAGGCGCCAGAACAGA 59.967 61.111 31.54 0.00 0.00 3.41
3862 4130 3.741476 GCCAAGGCGCCAGAACAG 61.741 66.667 31.54 11.85 0.00 3.16
3870 4138 2.068277 GATCTGAATGGCCAAGGCGC 62.068 60.000 10.96 0.00 43.06 6.53
3871 4139 0.465097 AGATCTGAATGGCCAAGGCG 60.465 55.000 10.96 0.00 43.06 5.52
3872 4140 1.316651 GAGATCTGAATGGCCAAGGC 58.683 55.000 10.96 1.52 41.06 4.35
3873 4141 2.092538 ACTGAGATCTGAATGGCCAAGG 60.093 50.000 10.96 0.00 0.00 3.61
3874 4142 3.278668 ACTGAGATCTGAATGGCCAAG 57.721 47.619 10.96 2.10 0.00 3.61
3875 4143 3.726557 AACTGAGATCTGAATGGCCAA 57.273 42.857 10.96 0.00 0.00 4.52
3876 4144 3.726557 AAACTGAGATCTGAATGGCCA 57.273 42.857 8.56 8.56 0.00 5.36
3877 4145 3.064545 CGAAAACTGAGATCTGAATGGCC 59.935 47.826 0.00 0.00 0.00 5.36
3878 4146 4.270178 CGAAAACTGAGATCTGAATGGC 57.730 45.455 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.