Multiple sequence alignment - TraesCS1A01G248100

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 TraesCS1A01G248100 chr1A 100.000 3815 0 0 1 3815 440075606 440071792 0.000000e+00 7046.0
1 TraesCS1A01G248100 chr1A 79.695 197 32 4 520 709 514199483 514199288 6.650000e-28 135.0
2 TraesCS1A01G248100 chr1D 95.119 2991 103 18 729 3708 340525524 340522566 0.000000e+00 4674.0
3 TraesCS1A01G248100 chr1D 87.989 716 69 13 28 730 340526289 340525578 0.000000e+00 830.0
4 TraesCS1A01G248100 chr1D 78.102 137 21 6 574 701 488099612 488099748 1.140000e-10 78.7
5 TraesCS1A01G248100 chr1B 94.477 2897 109 19 747 3631 455986196 455983339 0.000000e+00 4416.0
6 TraesCS1A01G248100 chr1B 84.272 515 54 11 28 518 455986692 455986181 9.590000e-131 477.0
7 TraesCS1A01G248100 chr1B 85.366 82 5 7 622 699 11171527 11171605 1.140000e-10 78.7
8 TraesCS1A01G248100 chr4B 83.000 200 26 5 517 709 599915132 599914934 1.410000e-39 174.0
9 TraesCS1A01G248100 chr4B 87.879 132 9 3 3552 3676 667029417 667029286 8.540000e-32 148.0
10 TraesCS1A01G248100 chr4B 89.773 88 8 1 520 606 37342288 37342375 1.120000e-20 111.0
11 TraesCS1A01G248100 chr7D 82.474 194 25 6 528 714 605118316 605118507 1.100000e-35 161.0
12 TraesCS1A01G248100 chr2B 82.143 196 25 7 520 709 98301470 98301279 3.940000e-35 159.0
13 TraesCS1A01G248100 chr2B 87.313 134 10 2 3550 3676 589349188 589349055 3.070000e-31 147.0
14 TraesCS1A01G248100 chr2B 87.121 132 10 4 3552 3676 9325413 9325282 3.970000e-30 143.0
15 TraesCS1A01G248100 chr2B 85.821 134 12 3 3550 3676 39647027 39646894 6.650000e-28 135.0
16 TraesCS1A01G248100 chr7B 90.323 124 7 2 3550 3668 700753233 700753356 1.420000e-34 158.0
17 TraesCS1A01G248100 chr5B 81.281 203 29 6 514 709 551228897 551229097 5.100000e-34 156.0
18 TraesCS1A01G248100 chr5B 78.173 197 32 8 520 709 477468408 477468600 8.660000e-22 115.0
19 TraesCS1A01G248100 chr5B 86.139 101 11 3 511 609 43160666 43160765 5.210000e-19 106.0
20 TraesCS1A01G248100 chr3A 80.612 196 32 3 520 709 574008659 574008854 3.070000e-31 147.0
21 TraesCS1A01G248100 chr3D 80.526 190 30 4 515 698 488391439 488391251 5.140000e-29 139.0
22 TraesCS1A01G248100 chr4A 79.688 192 32 4 520 704 503637032 503636841 8.600000e-27 132.0
23 TraesCS1A01G248100 chr6B 85.075 134 13 3 3550 3676 628251762 628251629 3.090000e-26 130.0
24 TraesCS1A01G248100 chr3B 78.010 191 31 9 522 703 390217471 390217659 4.030000e-20 110.0
25 TraesCS1A01G248100 chr5D 91.228 57 3 2 378 433 324101086 324101031 4.090000e-10 76.8
26 TraesCS1A01G248100 chr7A 100.000 28 0 0 391 418 474290325 474290298 7.000000e-03 52.8


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 TraesCS1A01G248100 chr1A 440071792 440075606 3814 True 7046.0 7046 100.0000 1 3815 1 chr1A.!!$R1 3814
1 TraesCS1A01G248100 chr1D 340522566 340526289 3723 True 2752.0 4674 91.5540 28 3708 2 chr1D.!!$R1 3680
2 TraesCS1A01G248100 chr1B 455983339 455986692 3353 True 2446.5 4416 89.3745 28 3631 2 chr1B.!!$R1 3603

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
902 1002 0.107606 AAAACCAAAACCAACCCGGC 60.108 50.000 0.0 0.0 39.03 6.13 F
1767 1867 1.219393 CCTCAAGTTCTCCTCCGCC 59.781 63.158 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 2254 0.179234 TGTCCTCAACGCCAAGAACA 59.821 50.0 0.0 0.0 0.0 3.18 R
3740 3854 0.042731 CCCTACTCTGACCTCCCCAA 59.957 60.0 0.0 0.0 0.0 4.12 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
18 19 3.173540 CAAAGGTCGATGATGCCCA 57.826 52.632 0.00 0.00 0.00 5.36
19 20 0.734889 CAAAGGTCGATGATGCCCAC 59.265 55.000 0.00 0.00 0.00 4.61
20 21 0.394352 AAAGGTCGATGATGCCCACC 60.394 55.000 0.00 0.00 0.00 4.61
21 22 1.561769 AAGGTCGATGATGCCCACCA 61.562 55.000 0.00 0.00 0.00 4.17
22 23 1.819632 GGTCGATGATGCCCACCAC 60.820 63.158 0.00 0.00 0.00 4.16
23 24 1.819632 GTCGATGATGCCCACCACC 60.820 63.158 0.00 0.00 0.00 4.61
24 25 1.995066 TCGATGATGCCCACCACCT 60.995 57.895 0.00 0.00 0.00 4.00
25 26 1.820906 CGATGATGCCCACCACCTG 60.821 63.158 0.00 0.00 0.00 4.00
26 27 1.609239 GATGATGCCCACCACCTGA 59.391 57.895 0.00 0.00 0.00 3.86
51 52 1.335964 TGTTCGGAGCGAAGAAGACAG 60.336 52.381 0.00 0.00 46.54 3.51
84 85 2.314246 TGTGGCATCAATTGGTTGTGA 58.686 42.857 5.42 0.00 36.69 3.58
104 105 7.575414 TGTGACTAACAATACCACAACAAAT 57.425 32.000 0.00 0.00 35.24 2.32
106 107 8.470805 TGTGACTAACAATACCACAACAAATTT 58.529 29.630 0.00 0.00 35.24 1.82
107 108 8.964150 GTGACTAACAATACCACAACAAATTTC 58.036 33.333 0.00 0.00 0.00 2.17
130 131 8.728337 TTCTGAGAAATCTTGGATATCACAAG 57.272 34.615 19.78 19.78 45.08 3.16
192 193 9.438228 TGTGACATAATTCCTACGTATCAAAAA 57.562 29.630 0.00 0.00 0.00 1.94
253 273 4.938575 ATACCCACCTAACCAAACATGA 57.061 40.909 0.00 0.00 0.00 3.07
267 287 4.215399 CCAAACATGACAAGTCACGGTTAT 59.785 41.667 17.17 8.98 43.11 1.89
269 289 3.334691 ACATGACAAGTCACGGTTATGG 58.665 45.455 4.84 0.00 43.11 2.74
316 336 6.963049 ATTTAGACGTGTCATTCTAACCAC 57.037 37.500 0.00 0.00 34.70 4.16
344 364 1.325338 ACGTGCGTAAACAAGTCACAC 59.675 47.619 0.00 0.00 0.00 3.82
348 368 0.931702 CGTAAACAAGTCACACGGCA 59.068 50.000 0.00 0.00 0.00 5.69
353 374 2.831685 ACAAGTCACACGGCATTCTA 57.168 45.000 0.00 0.00 0.00 2.10
438 462 6.032956 ACGCATATATTTTGATACGGAGGA 57.967 37.500 0.00 0.00 0.00 3.71
460 484 9.202273 GAGGAAGTATAACATTCTGCATAGAAG 57.798 37.037 0.00 0.00 45.53 2.85
482 509 8.386264 AGAAGAAAGAAAAATCTCAGTCCCATA 58.614 33.333 0.00 0.00 0.00 2.74
484 511 9.539194 AAGAAAGAAAAATCTCAGTCCCATATT 57.461 29.630 0.00 0.00 0.00 1.28
509 537 2.081462 CGACGGCTCCAAATAAAACCT 58.919 47.619 0.00 0.00 0.00 3.50
511 539 3.078837 GACGGCTCCAAATAAAACCTCA 58.921 45.455 0.00 0.00 0.00 3.86
526 554 2.316108 ACCTCAAAAAGCGGAACCAAT 58.684 42.857 0.00 0.00 0.00 3.16
547 575 2.571653 TCTGTGGTTGGATGGTTAGGAG 59.428 50.000 0.00 0.00 0.00 3.69
548 576 1.633432 TGTGGTTGGATGGTTAGGAGG 59.367 52.381 0.00 0.00 0.00 4.30
562 590 4.039366 GGTTAGGAGGACAGTGATATCCAC 59.961 50.000 0.00 0.00 46.03 4.02
583 611 0.539669 CCCCACCAAGGTTCAAGTCC 60.540 60.000 0.00 0.00 34.66 3.85
584 612 0.478507 CCCACCAAGGTTCAAGTCCT 59.521 55.000 0.00 0.00 36.81 3.85
586 614 1.142870 CCACCAAGGTTCAAGTCCTGA 59.857 52.381 0.00 0.00 35.27 3.86
601 629 3.887716 AGTCCTGATGCTTGCATTTATCC 59.112 43.478 9.59 0.00 0.00 2.59
603 631 3.887110 TCCTGATGCTTGCATTTATCCTG 59.113 43.478 9.59 1.31 0.00 3.86
605 633 4.523173 CCTGATGCTTGCATTTATCCTGAT 59.477 41.667 9.59 0.00 0.00 2.90
608 636 7.255695 CCTGATGCTTGCATTTATCCTGATTTA 60.256 37.037 9.59 0.00 0.00 1.40
651 684 2.317040 TCAGTGGAAGGAGACGTTTCT 58.683 47.619 6.02 0.00 33.37 2.52
652 685 2.035961 TCAGTGGAAGGAGACGTTTCTG 59.964 50.000 6.02 0.00 29.47 3.02
673 706 2.463553 CGACTACGAGGCGTTTATGA 57.536 50.000 0.00 0.00 42.99 2.15
688 723 7.042658 AGGCGTTTATGATCTTCGTAAAATCTC 60.043 37.037 4.04 0.00 38.94 2.75
691 726 9.625009 CGTTTATGATCTTCGTAAAATCTCAAG 57.375 33.333 4.04 0.00 38.94 3.02
701 736 7.338440 TCGTAAAATCTCAAGATGATATGCG 57.662 36.000 0.00 0.00 34.49 4.73
706 741 2.028658 TCTCAAGATGATATGCGGGCTC 60.029 50.000 0.00 0.00 0.00 4.70
707 742 1.693606 TCAAGATGATATGCGGGCTCA 59.306 47.619 0.00 0.00 0.00 4.26
721 756 1.474143 GGGCTCAGAGGTGCTCATAAC 60.474 57.143 0.00 0.00 34.18 1.89
725 760 2.688446 CTCAGAGGTGCTCATAACGGTA 59.312 50.000 0.00 0.00 32.06 4.02
736 826 4.575645 GCTCATAACGGTAGAGTCTGTACT 59.424 45.833 1.86 0.00 39.21 2.73
742 832 3.244491 ACGGTAGAGTCTGTACTGTGTCT 60.244 47.826 18.34 3.51 38.35 3.41
744 834 4.934001 CGGTAGAGTCTGTACTGTGTCTAA 59.066 45.833 1.86 0.86 35.56 2.10
745 835 5.063691 CGGTAGAGTCTGTACTGTGTCTAAG 59.936 48.000 1.86 8.25 35.56 2.18
833 929 2.434359 GTCGCCTCCGTCCCAAAG 60.434 66.667 0.00 0.00 35.54 2.77
847 943 3.088532 TCCCAAAGAACCCAATCAATCG 58.911 45.455 0.00 0.00 0.00 3.34
894 994 2.105134 CCCCCTAACCAAAACCAAAACC 59.895 50.000 0.00 0.00 0.00 3.27
895 995 2.772515 CCCCTAACCAAAACCAAAACCA 59.227 45.455 0.00 0.00 0.00 3.67
896 996 3.200165 CCCCTAACCAAAACCAAAACCAA 59.800 43.478 0.00 0.00 0.00 3.67
897 997 4.193090 CCCTAACCAAAACCAAAACCAAC 58.807 43.478 0.00 0.00 0.00 3.77
900 1000 1.066071 ACCAAAACCAAAACCAACCCG 60.066 47.619 0.00 0.00 0.00 5.28
901 1001 1.657822 CAAAACCAAAACCAACCCGG 58.342 50.000 0.00 0.00 42.50 5.73
902 1002 0.107606 AAAACCAAAACCAACCCGGC 60.108 50.000 0.00 0.00 39.03 6.13
903 1003 2.299503 AAACCAAAACCAACCCGGCG 62.300 55.000 0.00 0.00 39.03 6.46
904 1004 3.984749 CCAAAACCAACCCGGCGG 61.985 66.667 21.46 21.46 39.03 6.13
905 1005 4.656117 CAAAACCAACCCGGCGGC 62.656 66.667 23.20 0.00 39.03 6.53
924 1024 2.358247 TTTTCCCCTCGCGAGCAC 60.358 61.111 30.49 0.00 0.00 4.40
925 1025 3.894547 TTTTCCCCTCGCGAGCACC 62.895 63.158 30.49 0.00 0.00 5.01
1068 1168 2.126965 AAGAAGACCGACGTCGCG 60.127 61.111 31.73 25.16 44.28 5.87
1172 1272 4.856607 CTCCTTCCTCGGCGTCGC 62.857 72.222 9.22 9.22 36.13 5.19
1767 1867 1.219393 CCTCAAGTTCTCCTCCGCC 59.781 63.158 0.00 0.00 0.00 6.13
1809 1909 2.409651 CGCCGCACTCCTCTACTC 59.590 66.667 0.00 0.00 0.00 2.59
1937 2037 2.102357 CGAGGATGTGGACGACGG 59.898 66.667 0.00 0.00 0.00 4.79
2070 2170 4.421479 CTCTTCACCGCCGACGCT 62.421 66.667 0.00 0.00 38.22 5.07
2139 2239 1.521457 CCATGTCGACACCATCCGG 60.521 63.158 22.71 10.64 38.77 5.14
2154 2254 0.473117 TCCGGAACCTCCTGACCTTT 60.473 55.000 0.00 0.00 33.30 3.11
2211 2311 2.654912 CTTCGACGCCGTGTTCACC 61.655 63.158 0.00 0.00 37.05 4.02
2265 2365 0.813184 CAAGCATCTTCAACGGCCAT 59.187 50.000 2.24 0.00 0.00 4.40
2345 2445 1.130561 GCTTGTCCGGTCATACTTTGC 59.869 52.381 1.21 0.00 0.00 3.68
2974 3076 5.180271 TGAACCGTTTTATATGGTGAGACC 58.820 41.667 0.00 0.00 45.73 3.85
3022 3124 1.663074 GATCTTGCTCTAGCCGGCG 60.663 63.158 23.20 8.11 41.18 6.46
3034 3136 4.194720 CCGGCGAGGAAGGTCGAG 62.195 72.222 9.30 0.00 45.00 4.04
3060 3166 2.846652 CGGAGCTAGCTACGGGTGG 61.847 68.421 36.82 12.71 45.89 4.61
3148 3254 1.067635 GGGTCATGTTGTGTCCAATGC 60.068 52.381 0.00 0.00 37.71 3.56
3149 3255 1.612950 GGTCATGTTGTGTCCAATGCA 59.387 47.619 0.00 0.00 36.23 3.96
3150 3256 2.035704 GGTCATGTTGTGTCCAATGCAA 59.964 45.455 0.00 0.00 36.23 4.08
3151 3257 3.306225 GGTCATGTTGTGTCCAATGCAAT 60.306 43.478 0.00 0.00 36.23 3.56
3152 3258 3.676172 GTCATGTTGTGTCCAATGCAATG 59.324 43.478 0.00 0.00 32.11 2.82
3153 3259 3.321396 TCATGTTGTGTCCAATGCAATGT 59.679 39.130 0.21 0.00 32.11 2.71
3154 3260 3.815856 TGTTGTGTCCAATGCAATGTT 57.184 38.095 0.21 0.00 32.11 2.71
3155 3261 4.134379 TGTTGTGTCCAATGCAATGTTT 57.866 36.364 0.21 0.00 32.11 2.83
3156 3262 3.869832 TGTTGTGTCCAATGCAATGTTTG 59.130 39.130 0.21 0.00 32.11 2.93
3157 3263 4.118410 GTTGTGTCCAATGCAATGTTTGA 58.882 39.130 0.21 0.00 32.11 2.69
3158 3264 4.603989 TGTGTCCAATGCAATGTTTGAT 57.396 36.364 0.21 0.00 0.00 2.57
3169 3275 5.214417 TGCAATGTTTGATTTCTTCAGTCG 58.786 37.500 0.00 0.00 35.27 4.18
3173 3279 5.418310 TGTTTGATTTCTTCAGTCGGTTC 57.582 39.130 0.00 0.00 35.27 3.62
3180 3286 5.479716 TTTCTTCAGTCGGTTCTTGTTTC 57.520 39.130 0.00 0.00 0.00 2.78
3199 3305 0.603707 CTGTGGTCTGTGAACGGCAT 60.604 55.000 0.00 0.00 0.00 4.40
3200 3306 0.602638 TGTGGTCTGTGAACGGCATC 60.603 55.000 0.00 0.00 0.00 3.91
3201 3307 0.602638 GTGGTCTGTGAACGGCATCA 60.603 55.000 0.00 0.00 0.00 3.07
3208 3314 0.521242 GTGAACGGCATCATGCGAAC 60.521 55.000 2.82 0.00 46.21 3.95
3214 3320 1.451927 GCATCATGCGAACCCTGGA 60.452 57.895 0.00 0.00 31.71 3.86
3218 3324 0.109532 TCATGCGAACCCTGGAACAA 59.890 50.000 0.00 0.00 38.70 2.83
3220 3326 2.026729 TCATGCGAACCCTGGAACAATA 60.027 45.455 0.00 0.00 38.70 1.90
3233 3339 5.241403 TGGAACAATAGATGGTTGAGTGT 57.759 39.130 0.00 0.00 31.92 3.55
3283 3389 3.988379 TGATGTGTTTTGAGTGAAGCC 57.012 42.857 0.00 0.00 0.00 4.35
3285 3391 3.890756 TGATGTGTTTTGAGTGAAGCCAT 59.109 39.130 0.00 0.00 0.00 4.40
3407 3513 3.576078 AATGTCACTGTCCTTGACCAA 57.424 42.857 0.25 0.00 42.40 3.67
3431 3537 9.341899 CAATTCCTAATTTTGTTGTAGCACTAC 57.658 33.333 0.70 0.70 36.63 2.73
3556 3664 4.110482 CAGATTGTACCGTAGCCAGTAAC 58.890 47.826 0.00 0.00 0.00 2.50
3572 3680 5.122396 GCCAGTAACCTTACTCTGTTCATTG 59.878 44.000 0.00 0.00 41.82 2.82
3575 3683 7.876068 CCAGTAACCTTACTCTGTTCATTGTTA 59.124 37.037 0.00 0.00 41.82 2.41
3639 3753 1.067425 CCAACATGGCTCATGGTTGTG 60.067 52.381 16.39 9.94 38.83 3.33
3640 3754 1.614903 CAACATGGCTCATGGTTGTGT 59.385 47.619 16.39 0.00 38.83 3.72
3667 3781 2.958818 AGGTGAACCTACAGAGACACA 58.041 47.619 0.00 0.00 46.48 3.72
3668 3782 3.305720 AGGTGAACCTACAGAGACACAA 58.694 45.455 0.00 0.00 46.48 3.33
3669 3783 3.904339 AGGTGAACCTACAGAGACACAAT 59.096 43.478 0.00 0.00 46.48 2.71
3672 3786 3.260884 TGAACCTACAGAGACACAATCCC 59.739 47.826 0.00 0.00 0.00 3.85
3685 3799 2.165030 CACAATCCCATTGAGTGAAGCC 59.835 50.000 3.24 0.00 41.56 4.35
3694 3808 5.396772 CCCATTGAGTGAAGCCATAGTTAGA 60.397 44.000 0.00 0.00 0.00 2.10
3703 3817 5.127845 TGAAGCCATAGTTAGAGACCAGAAG 59.872 44.000 0.00 0.00 0.00 2.85
3707 3821 6.213600 AGCCATAGTTAGAGACCAGAAGAAAA 59.786 38.462 0.00 0.00 0.00 2.29
3708 3822 6.536941 GCCATAGTTAGAGACCAGAAGAAAAG 59.463 42.308 0.00 0.00 0.00 2.27
3709 3823 7.579723 GCCATAGTTAGAGACCAGAAGAAAAGA 60.580 40.741 0.00 0.00 0.00 2.52
3710 3824 8.314751 CCATAGTTAGAGACCAGAAGAAAAGAA 58.685 37.037 0.00 0.00 0.00 2.52
3711 3825 9.883142 CATAGTTAGAGACCAGAAGAAAAGAAT 57.117 33.333 0.00 0.00 0.00 2.40
3713 3827 8.840833 AGTTAGAGACCAGAAGAAAAGAATTC 57.159 34.615 0.00 0.00 0.00 2.17
3714 3828 7.880713 AGTTAGAGACCAGAAGAAAAGAATTCC 59.119 37.037 0.65 0.00 0.00 3.01
3715 3829 5.565509 AGAGACCAGAAGAAAAGAATTCCC 58.434 41.667 0.65 0.00 0.00 3.97
3716 3830 4.327680 AGACCAGAAGAAAAGAATTCCCG 58.672 43.478 0.65 0.00 0.00 5.14
3717 3831 2.820197 ACCAGAAGAAAAGAATTCCCGC 59.180 45.455 0.65 0.00 0.00 6.13
3718 3832 3.084786 CCAGAAGAAAAGAATTCCCGCT 58.915 45.455 0.65 0.00 0.00 5.52
3719 3833 3.507622 CCAGAAGAAAAGAATTCCCGCTT 59.492 43.478 0.65 1.19 0.00 4.68
3720 3834 4.700213 CCAGAAGAAAAGAATTCCCGCTTA 59.300 41.667 0.65 0.00 0.00 3.09
3721 3835 5.163713 CCAGAAGAAAAGAATTCCCGCTTAG 60.164 44.000 0.65 0.00 0.00 2.18
3722 3836 4.396478 AGAAGAAAAGAATTCCCGCTTAGC 59.604 41.667 0.65 0.00 0.00 3.09
3723 3837 3.956744 AGAAAAGAATTCCCGCTTAGCT 58.043 40.909 1.76 0.00 0.00 3.32
3724 3838 3.691609 AGAAAAGAATTCCCGCTTAGCTG 59.308 43.478 1.76 0.00 0.00 4.24
3725 3839 3.350219 AAAGAATTCCCGCTTAGCTGA 57.650 42.857 1.76 0.00 0.00 4.26
3726 3840 3.567478 AAGAATTCCCGCTTAGCTGAT 57.433 42.857 1.76 0.00 0.00 2.90
3727 3841 3.118905 AGAATTCCCGCTTAGCTGATC 57.881 47.619 1.76 0.00 0.00 2.92
3728 3842 2.703007 AGAATTCCCGCTTAGCTGATCT 59.297 45.455 1.76 0.00 0.00 2.75
3729 3843 3.135530 AGAATTCCCGCTTAGCTGATCTT 59.864 43.478 1.76 0.00 0.00 2.40
3730 3844 3.567478 ATTCCCGCTTAGCTGATCTTT 57.433 42.857 1.76 0.00 0.00 2.52
3731 3845 3.350219 TTCCCGCTTAGCTGATCTTTT 57.650 42.857 1.76 0.00 0.00 2.27
3732 3846 3.350219 TCCCGCTTAGCTGATCTTTTT 57.650 42.857 1.76 0.00 0.00 1.94
3733 3847 3.270877 TCCCGCTTAGCTGATCTTTTTC 58.729 45.455 1.76 0.00 0.00 2.29
3734 3848 3.009723 CCCGCTTAGCTGATCTTTTTCA 58.990 45.455 1.76 0.00 0.00 2.69
3735 3849 3.629398 CCCGCTTAGCTGATCTTTTTCAT 59.371 43.478 1.76 0.00 0.00 2.57
3736 3850 4.096984 CCCGCTTAGCTGATCTTTTTCATT 59.903 41.667 1.76 0.00 0.00 2.57
3737 3851 5.269313 CCGCTTAGCTGATCTTTTTCATTC 58.731 41.667 1.76 0.00 0.00 2.67
3738 3852 5.065731 CCGCTTAGCTGATCTTTTTCATTCT 59.934 40.000 1.76 0.00 0.00 2.40
3739 3853 6.190962 CGCTTAGCTGATCTTTTTCATTCTC 58.809 40.000 1.76 0.00 0.00 2.87
3740 3854 6.036953 CGCTTAGCTGATCTTTTTCATTCTCT 59.963 38.462 1.76 0.00 0.00 3.10
3741 3855 7.413877 CGCTTAGCTGATCTTTTTCATTCTCTT 60.414 37.037 1.76 0.00 0.00 2.85
3742 3856 7.697291 GCTTAGCTGATCTTTTTCATTCTCTTG 59.303 37.037 0.00 0.00 0.00 3.02
3743 3857 6.512342 AGCTGATCTTTTTCATTCTCTTGG 57.488 37.500 0.00 0.00 0.00 3.61
3744 3858 5.418209 AGCTGATCTTTTTCATTCTCTTGGG 59.582 40.000 0.00 0.00 0.00 4.12
3745 3859 5.393896 GCTGATCTTTTTCATTCTCTTGGGG 60.394 44.000 0.00 0.00 0.00 4.96
3746 3860 5.891198 TGATCTTTTTCATTCTCTTGGGGA 58.109 37.500 0.00 0.00 0.00 4.81
3747 3861 5.948162 TGATCTTTTTCATTCTCTTGGGGAG 59.052 40.000 0.00 0.00 43.12 4.30
3748 3862 4.666512 TCTTTTTCATTCTCTTGGGGAGG 58.333 43.478 0.00 0.00 42.10 4.30
3749 3863 4.106341 TCTTTTTCATTCTCTTGGGGAGGT 59.894 41.667 0.00 0.00 42.10 3.85
3750 3864 3.721087 TTTCATTCTCTTGGGGAGGTC 57.279 47.619 0.00 0.00 42.10 3.85
3751 3865 2.342406 TCATTCTCTTGGGGAGGTCA 57.658 50.000 0.00 0.00 42.10 4.02
3752 3866 2.191400 TCATTCTCTTGGGGAGGTCAG 58.809 52.381 0.00 0.00 42.10 3.51
3753 3867 2.191400 CATTCTCTTGGGGAGGTCAGA 58.809 52.381 0.00 0.00 42.10 3.27
3754 3868 1.944177 TTCTCTTGGGGAGGTCAGAG 58.056 55.000 0.00 0.00 42.10 3.35
3755 3869 0.787084 TCTCTTGGGGAGGTCAGAGT 59.213 55.000 0.00 0.00 42.10 3.24
3756 3870 2.000803 TCTCTTGGGGAGGTCAGAGTA 58.999 52.381 0.00 0.00 42.10 2.59
3757 3871 2.024846 TCTCTTGGGGAGGTCAGAGTAG 60.025 54.545 0.00 0.00 42.10 2.57
3758 3872 1.007238 TCTTGGGGAGGTCAGAGTAGG 59.993 57.143 0.00 0.00 0.00 3.18
3759 3873 0.042731 TTGGGGAGGTCAGAGTAGGG 59.957 60.000 0.00 0.00 0.00 3.53
3760 3874 1.075151 GGGGAGGTCAGAGTAGGGG 60.075 68.421 0.00 0.00 0.00 4.79
3761 3875 1.704704 GGGAGGTCAGAGTAGGGGT 59.295 63.158 0.00 0.00 0.00 4.95
3762 3876 0.932211 GGGAGGTCAGAGTAGGGGTA 59.068 60.000 0.00 0.00 0.00 3.69
3763 3877 1.133419 GGGAGGTCAGAGTAGGGGTAG 60.133 61.905 0.00 0.00 0.00 3.18
3764 3878 1.694844 GAGGTCAGAGTAGGGGTAGC 58.305 60.000 0.00 0.00 0.00 3.58
3765 3879 1.008403 AGGTCAGAGTAGGGGTAGCA 58.992 55.000 0.00 0.00 0.00 3.49
3766 3880 1.063567 AGGTCAGAGTAGGGGTAGCAG 60.064 57.143 0.00 0.00 0.00 4.24
3767 3881 1.063867 GGTCAGAGTAGGGGTAGCAGA 60.064 57.143 0.00 0.00 0.00 4.26
3768 3882 2.025898 GTCAGAGTAGGGGTAGCAGAC 58.974 57.143 0.00 0.00 0.00 3.51
3769 3883 1.639108 TCAGAGTAGGGGTAGCAGACA 59.361 52.381 0.00 0.00 0.00 3.41
3770 3884 1.751924 CAGAGTAGGGGTAGCAGACAC 59.248 57.143 0.00 0.00 0.00 3.67
3777 3891 0.466124 GGGTAGCAGACACCAGATCC 59.534 60.000 0.00 0.00 37.84 3.36
3778 3892 0.103208 GGTAGCAGACACCAGATCCG 59.897 60.000 0.00 0.00 36.01 4.18
3779 3893 0.103208 GTAGCAGACACCAGATCCGG 59.897 60.000 0.00 0.00 0.00 5.14
3780 3894 1.676678 TAGCAGACACCAGATCCGGC 61.677 60.000 0.00 0.00 0.00 6.13
3781 3895 2.187946 CAGACACCAGATCCGGCC 59.812 66.667 0.00 0.00 0.00 6.13
3782 3896 2.039624 AGACACCAGATCCGGCCT 59.960 61.111 0.00 0.00 0.00 5.19
3783 3897 2.187946 GACACCAGATCCGGCCTG 59.812 66.667 14.43 14.43 0.00 4.85
3784 3898 2.607750 ACACCAGATCCGGCCTGT 60.608 61.111 18.26 0.00 0.00 4.00
3785 3899 2.124983 CACCAGATCCGGCCTGTG 60.125 66.667 18.26 13.60 0.00 3.66
3786 3900 4.101448 ACCAGATCCGGCCTGTGC 62.101 66.667 18.26 0.00 0.00 4.57
3796 3910 4.373116 GCCTGTGCCGTTCGAGGA 62.373 66.667 0.00 0.00 0.00 3.71
3797 3911 2.125912 CCTGTGCCGTTCGAGGAG 60.126 66.667 0.00 0.00 0.00 3.69
3798 3912 2.636412 CCTGTGCCGTTCGAGGAGA 61.636 63.158 0.00 0.00 0.00 3.71
3799 3913 1.153939 CTGTGCCGTTCGAGGAGAG 60.154 63.158 0.00 0.00 0.00 3.20
3800 3914 2.507324 GTGCCGTTCGAGGAGAGC 60.507 66.667 0.00 0.00 0.00 4.09
3801 3915 2.989253 TGCCGTTCGAGGAGAGCA 60.989 61.111 0.00 0.00 0.00 4.26
3802 3916 2.351244 TGCCGTTCGAGGAGAGCAT 61.351 57.895 0.00 0.00 0.00 3.79
3803 3917 1.153549 GCCGTTCGAGGAGAGCATT 60.154 57.895 0.00 0.00 0.00 3.56
3804 3918 1.424493 GCCGTTCGAGGAGAGCATTG 61.424 60.000 0.00 0.00 0.00 2.82
3805 3919 0.173481 CCGTTCGAGGAGAGCATTGA 59.827 55.000 0.00 0.00 0.00 2.57
3806 3920 1.202463 CCGTTCGAGGAGAGCATTGAT 60.202 52.381 0.00 0.00 0.00 2.57
3807 3921 2.123342 CGTTCGAGGAGAGCATTGATC 58.877 52.381 0.00 0.00 0.00 2.92
3808 3922 2.223688 CGTTCGAGGAGAGCATTGATCT 60.224 50.000 3.65 3.65 0.00 2.75
3809 3923 3.122297 GTTCGAGGAGAGCATTGATCTG 58.878 50.000 9.56 0.00 0.00 2.90
3810 3924 2.659428 TCGAGGAGAGCATTGATCTGA 58.341 47.619 9.56 0.00 0.00 3.27
3811 3925 3.026694 TCGAGGAGAGCATTGATCTGAA 58.973 45.455 9.56 0.00 0.00 3.02
3812 3926 3.448660 TCGAGGAGAGCATTGATCTGAAA 59.551 43.478 9.56 0.00 0.00 2.69
3813 3927 4.100653 TCGAGGAGAGCATTGATCTGAAAT 59.899 41.667 9.56 0.00 0.00 2.17
3814 3928 4.815308 CGAGGAGAGCATTGATCTGAAATT 59.185 41.667 9.56 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.734889 GTGGGCATCATCGACCTTTG 59.265 55.000 0.00 0.00 0.00 2.77
1 2 0.394352 GGTGGGCATCATCGACCTTT 60.394 55.000 0.00 0.00 31.52 3.11
2 3 1.224592 GGTGGGCATCATCGACCTT 59.775 57.895 0.00 0.00 31.52 3.50
3 4 1.995066 TGGTGGGCATCATCGACCT 60.995 57.895 0.00 0.00 34.66 3.85
4 5 1.819632 GTGGTGGGCATCATCGACC 60.820 63.158 0.00 0.00 34.24 4.79
5 6 1.819632 GGTGGTGGGCATCATCGAC 60.820 63.158 0.00 0.00 0.00 4.20
6 7 1.995066 AGGTGGTGGGCATCATCGA 60.995 57.895 0.00 0.00 0.00 3.59
7 8 1.820906 CAGGTGGTGGGCATCATCG 60.821 63.158 0.00 0.00 0.00 3.84
8 9 0.034186 TTCAGGTGGTGGGCATCATC 60.034 55.000 0.00 0.00 0.00 2.92
9 10 0.632835 ATTCAGGTGGTGGGCATCAT 59.367 50.000 0.00 0.00 0.00 2.45
10 11 0.323633 CATTCAGGTGGTGGGCATCA 60.324 55.000 0.00 0.00 0.00 3.07
11 12 1.039233 CCATTCAGGTGGTGGGCATC 61.039 60.000 0.00 0.00 34.46 3.91
12 13 1.000739 CCATTCAGGTGGTGGGCAT 59.999 57.895 0.00 0.00 34.46 4.40
13 14 2.440147 CCATTCAGGTGGTGGGCA 59.560 61.111 0.00 0.00 34.46 5.36
22 23 1.361668 CGCTCCGAACACCATTCAGG 61.362 60.000 0.00 0.00 45.67 3.86
23 24 0.389817 TCGCTCCGAACACCATTCAG 60.390 55.000 0.00 0.00 31.06 3.02
24 25 0.034198 TTCGCTCCGAACACCATTCA 59.966 50.000 0.00 0.00 41.05 2.57
25 26 0.721718 CTTCGCTCCGAACACCATTC 59.278 55.000 0.00 0.00 41.05 2.67
26 27 0.320374 TCTTCGCTCCGAACACCATT 59.680 50.000 0.00 0.00 41.05 3.16
35 36 0.039074 ACACTGTCTTCTTCGCTCCG 60.039 55.000 0.00 0.00 0.00 4.63
51 52 3.503363 TGATGCCACAATCTTTCTCACAC 59.497 43.478 0.00 0.00 0.00 3.82
84 85 8.908903 TCAGAAATTTGTTGTGGTATTGTTAGT 58.091 29.630 0.00 0.00 0.00 2.24
94 95 7.170320 CCAAGATTTCTCAGAAATTTGTTGTGG 59.830 37.037 14.02 8.95 0.00 4.17
104 105 9.170734 CTTGTGATATCCAAGATTTCTCAGAAA 57.829 33.333 20.61 1.30 41.44 2.52
106 107 8.082672 TCTTGTGATATCCAAGATTTCTCAGA 57.917 34.615 22.45 7.15 42.43 3.27
149 150 6.584185 TGTCACACACTTAGTATGCTCTTA 57.416 37.500 0.00 0.00 0.00 2.10
164 165 7.102847 TGATACGTAGGAATTATGTCACACA 57.897 36.000 0.08 0.00 33.56 3.72
194 195 8.949177 TCCCTTCGTATCAAAATACTAAAAACC 58.051 33.333 0.00 0.00 36.40 3.27
195 196 9.983804 CTCCCTTCGTATCAAAATACTAAAAAC 57.016 33.333 0.00 0.00 36.40 2.43
196 197 9.729281 ACTCCCTTCGTATCAAAATACTAAAAA 57.271 29.630 0.00 0.00 36.40 1.94
215 235 7.575129 AGGTGGGTATATGTTAAATACTCCCTT 59.425 37.037 0.00 0.00 31.92 3.95
253 273 2.264005 TTGCCATAACCGTGACTTGT 57.736 45.000 0.00 0.00 0.00 3.16
267 287 0.820871 GTGTGTTTGTCCCTTTGCCA 59.179 50.000 0.00 0.00 0.00 4.92
269 289 2.094234 AGTTGTGTGTTTGTCCCTTTGC 60.094 45.455 0.00 0.00 0.00 3.68
316 336 1.255859 TGTTTACGCACGTTCAGTTCG 59.744 47.619 0.00 0.00 44.77 3.95
344 364 5.120830 GGTAGTATTTGCAGATAGAATGCCG 59.879 44.000 0.00 0.00 43.18 5.69
411 433 8.073768 CCTCCGTATCAAAATATATGCGTTTTT 58.926 33.333 0.00 0.00 30.49 1.94
460 484 8.960591 TGAATATGGGACTGAGATTTTTCTTTC 58.039 33.333 0.00 0.00 0.00 2.62
482 509 0.251916 TTTGGAGCCGTCGGATGAAT 59.748 50.000 17.49 0.00 0.00 2.57
484 511 1.116308 TATTTGGAGCCGTCGGATGA 58.884 50.000 17.49 0.00 0.00 2.92
509 537 2.955660 ACAGATTGGTTCCGCTTTTTGA 59.044 40.909 0.00 0.00 0.00 2.69
511 539 2.035832 CCACAGATTGGTTCCGCTTTTT 59.964 45.455 0.00 0.00 41.10 1.94
526 554 2.571653 CTCCTAACCATCCAACCACAGA 59.428 50.000 0.00 0.00 0.00 3.41
532 560 2.572104 ACTGTCCTCCTAACCATCCAAC 59.428 50.000 0.00 0.00 0.00 3.77
540 568 4.649674 TGTGGATATCACTGTCCTCCTAAC 59.350 45.833 4.83 0.00 46.20 2.34
547 575 1.141053 GGGGTGTGGATATCACTGTCC 59.859 57.143 4.83 0.50 46.20 4.02
548 576 1.837439 TGGGGTGTGGATATCACTGTC 59.163 52.381 4.83 0.00 46.20 3.51
562 590 0.106217 ACTTGAACCTTGGTGGGGTG 60.106 55.000 0.00 0.00 41.11 4.61
564 592 0.539669 GGACTTGAACCTTGGTGGGG 60.540 60.000 0.00 0.00 41.11 4.96
583 611 5.707242 ATCAGGATAAATGCAAGCATCAG 57.293 39.130 8.14 0.00 35.31 2.90
584 612 6.474140 AAATCAGGATAAATGCAAGCATCA 57.526 33.333 8.14 0.00 35.31 3.07
586 614 9.669887 TTTTTAAATCAGGATAAATGCAAGCAT 57.330 25.926 0.86 0.86 38.46 3.79
637 670 2.030981 AGTCGACAGAAACGTCTCCTTC 60.031 50.000 19.50 0.00 33.54 3.46
651 684 1.155889 TAAACGCCTCGTAGTCGACA 58.844 50.000 19.50 0.48 39.99 4.35
652 685 2.107178 CATAAACGCCTCGTAGTCGAC 58.893 52.381 7.70 7.70 39.99 4.20
665 698 9.625009 CTTGAGATTTTACGAAGATCATAAACG 57.375 33.333 0.00 0.00 0.00 3.60
688 723 2.074576 CTGAGCCCGCATATCATCTTG 58.925 52.381 0.00 0.00 0.00 3.02
691 726 1.405256 CCTCTGAGCCCGCATATCATC 60.405 57.143 0.00 0.00 0.00 2.92
699 734 4.828925 GAGCACCTCTGAGCCCGC 62.829 72.222 0.00 1.25 0.00 6.13
701 736 0.833287 TTATGAGCACCTCTGAGCCC 59.167 55.000 0.00 0.00 0.00 5.19
706 741 2.688446 TCTACCGTTATGAGCACCTCTG 59.312 50.000 0.00 0.00 0.00 3.35
707 742 2.952978 CTCTACCGTTATGAGCACCTCT 59.047 50.000 0.00 0.00 0.00 3.69
721 756 3.336468 AGACACAGTACAGACTCTACCG 58.664 50.000 0.00 0.00 31.73 4.02
725 760 7.584122 TTTTCTTAGACACAGTACAGACTCT 57.416 36.000 0.00 0.00 31.73 3.24
751 841 7.330262 CCACAAAATGCATATCCTTTTAGGTT 58.670 34.615 0.00 0.00 36.53 3.50
752 842 6.630188 GCCACAAAATGCATATCCTTTTAGGT 60.630 38.462 0.00 0.00 36.53 3.08
755 845 5.347342 CGCCACAAAATGCATATCCTTTTA 58.653 37.500 0.00 0.00 0.00 1.52
833 929 0.377203 GCGGACGATTGATTGGGTTC 59.623 55.000 0.00 0.00 0.00 3.62
888 988 4.656117 GCCGCCGGGTTGGTTTTG 62.656 66.667 4.77 0.00 41.21 2.44
894 994 4.050934 GAAAAGGCCGCCGGGTTG 62.051 66.667 4.77 0.00 34.97 3.77
903 1003 4.404098 TCGCGAGGGGAAAAGGCC 62.404 66.667 3.71 0.00 0.00 5.19
904 1004 2.820037 CTCGCGAGGGGAAAAGGC 60.820 66.667 28.40 0.00 0.00 4.35
905 1005 2.820037 GCTCGCGAGGGGAAAAGG 60.820 66.667 35.10 10.05 0.00 3.11
906 1006 2.047274 TGCTCGCGAGGGGAAAAG 60.047 61.111 35.10 10.82 0.00 2.27
1172 1272 2.202623 CGACGGCGAAGAGGAAGG 60.203 66.667 16.62 0.00 40.82 3.46
1767 1867 1.342082 CGACGCGGTACTTGAACCTG 61.342 60.000 12.47 0.00 37.39 4.00
1799 1899 1.448922 CGGCCGGAAGAGTAGAGGAG 61.449 65.000 20.10 0.00 0.00 3.69
2139 2239 3.493767 AGAACAAAGGTCAGGAGGTTC 57.506 47.619 0.00 0.00 35.95 3.62
2154 2254 0.179234 TGTCCTCAACGCCAAGAACA 59.821 50.000 0.00 0.00 0.00 3.18
2265 2365 5.748402 AGATAGTTCATGCTCATGTTCCAA 58.252 37.500 9.41 0.00 39.72 3.53
2345 2445 2.658593 GGACACGATCATCGCCCG 60.659 66.667 7.05 0.00 45.12 6.13
2887 2989 1.967319 TTTCACCTCAGCAACCTCAC 58.033 50.000 0.00 0.00 0.00 3.51
2974 3076 4.089208 GCGACATAGCTAAATGATCAGACG 59.911 45.833 0.09 0.00 0.00 4.18
3022 3124 2.564471 TCGAACCTCGACCTTCCTC 58.436 57.895 0.00 0.00 44.82 3.71
3034 3136 1.069091 GTAGCTAGCTCCGATCGAACC 60.069 57.143 23.26 3.64 0.00 3.62
3148 3254 5.762045 ACCGACTGAAGAAATCAAACATTG 58.238 37.500 0.00 0.00 37.67 2.82
3149 3255 6.263168 AGAACCGACTGAAGAAATCAAACATT 59.737 34.615 0.00 0.00 37.67 2.71
3150 3256 5.765182 AGAACCGACTGAAGAAATCAAACAT 59.235 36.000 0.00 0.00 37.67 2.71
3151 3257 5.123227 AGAACCGACTGAAGAAATCAAACA 58.877 37.500 0.00 0.00 37.67 2.83
3152 3258 5.674933 AGAACCGACTGAAGAAATCAAAC 57.325 39.130 0.00 0.00 37.67 2.93
3153 3259 5.588648 ACAAGAACCGACTGAAGAAATCAAA 59.411 36.000 0.00 0.00 37.67 2.69
3154 3260 5.123227 ACAAGAACCGACTGAAGAAATCAA 58.877 37.500 0.00 0.00 37.67 2.57
3155 3261 4.703897 ACAAGAACCGACTGAAGAAATCA 58.296 39.130 0.00 0.00 36.38 2.57
3156 3262 5.674933 AACAAGAACCGACTGAAGAAATC 57.325 39.130 0.00 0.00 0.00 2.17
3157 3263 5.823045 AGAAACAAGAACCGACTGAAGAAAT 59.177 36.000 0.00 0.00 0.00 2.17
3158 3264 5.064707 CAGAAACAAGAACCGACTGAAGAAA 59.935 40.000 0.00 0.00 0.00 2.52
3169 3275 3.065371 CACAGACCACAGAAACAAGAACC 59.935 47.826 0.00 0.00 0.00 3.62
3173 3279 3.242413 CGTTCACAGACCACAGAAACAAG 60.242 47.826 0.00 0.00 0.00 3.16
3180 3286 0.603707 ATGCCGTTCACAGACCACAG 60.604 55.000 0.00 0.00 0.00 3.66
3199 3305 0.109532 TTGTTCCAGGGTTCGCATGA 59.890 50.000 0.00 0.00 0.00 3.07
3200 3306 1.176527 ATTGTTCCAGGGTTCGCATG 58.823 50.000 0.00 0.00 0.00 4.06
3201 3307 2.238646 TCTATTGTTCCAGGGTTCGCAT 59.761 45.455 0.00 0.00 0.00 4.73
3208 3314 4.202441 CTCAACCATCTATTGTTCCAGGG 58.798 47.826 0.00 0.00 0.00 4.45
3214 3320 6.533730 TGAAGACACTCAACCATCTATTGTT 58.466 36.000 0.00 0.00 0.00 2.83
3218 3324 4.780021 ACCTGAAGACACTCAACCATCTAT 59.220 41.667 0.00 0.00 0.00 1.98
3220 3326 2.975489 ACCTGAAGACACTCAACCATCT 59.025 45.455 0.00 0.00 0.00 2.90
3283 3389 3.538591 TCAAATCAGGCAGCTCACTATG 58.461 45.455 0.00 0.00 0.00 2.23
3285 3391 3.008375 AGTTCAAATCAGGCAGCTCACTA 59.992 43.478 0.00 0.00 0.00 2.74
3407 3513 7.888546 AGGTAGTGCTACAACAAAATTAGGAAT 59.111 33.333 10.98 0.00 37.78 3.01
3431 3537 6.587990 CCGCATAATTAGATCACTAAGACAGG 59.412 42.308 0.00 0.00 41.12 4.00
3507 3615 9.930158 ACATAGTCCTAAACTTTCTCTCTCTAT 57.070 33.333 0.00 0.00 39.55 1.98
3508 3616 9.398538 GACATAGTCCTAAACTTTCTCTCTCTA 57.601 37.037 0.00 0.00 39.55 2.43
3509 3617 7.891183 TGACATAGTCCTAAACTTTCTCTCTCT 59.109 37.037 0.00 0.00 39.55 3.10
3510 3618 8.057536 TGACATAGTCCTAAACTTTCTCTCTC 57.942 38.462 0.00 0.00 39.55 3.20
3511 3619 7.891183 TCTGACATAGTCCTAAACTTTCTCTCT 59.109 37.037 0.00 0.00 39.55 3.10
3512 3620 8.057536 TCTGACATAGTCCTAAACTTTCTCTC 57.942 38.462 0.00 0.00 39.55 3.20
3513 3621 8.602472 ATCTGACATAGTCCTAAACTTTCTCT 57.398 34.615 0.00 0.00 39.55 3.10
3514 3622 9.092876 CAATCTGACATAGTCCTAAACTTTCTC 57.907 37.037 0.00 0.00 39.55 2.87
3526 3634 5.213675 GCTACGGTACAATCTGACATAGTC 58.786 45.833 0.00 0.00 0.00 2.59
3556 3664 8.446273 CACTGAATAACAATGAACAGAGTAAGG 58.554 37.037 0.00 0.00 0.00 2.69
3572 3680 4.379499 GCCTTACAAGCCACACTGAATAAC 60.379 45.833 0.00 0.00 0.00 1.89
3575 3683 2.162681 GCCTTACAAGCCACACTGAAT 58.837 47.619 0.00 0.00 0.00 2.57
3628 3742 1.538512 CTCAAGGCACACAACCATGAG 59.461 52.381 0.00 1.14 44.05 2.90
3639 3753 1.071699 TGTAGGTTCACCTCAAGGCAC 59.928 52.381 0.39 0.00 44.77 5.01
3640 3754 1.347707 CTGTAGGTTCACCTCAAGGCA 59.652 52.381 0.39 0.00 44.77 4.75
3656 3770 4.532126 ACTCAATGGGATTGTGTCTCTGTA 59.468 41.667 0.00 0.00 41.54 2.74
3657 3771 3.328931 ACTCAATGGGATTGTGTCTCTGT 59.671 43.478 0.00 0.00 41.54 3.41
3658 3772 3.688185 CACTCAATGGGATTGTGTCTCTG 59.312 47.826 0.00 0.00 42.92 3.35
3659 3773 3.584406 TCACTCAATGGGATTGTGTCTCT 59.416 43.478 0.00 0.00 42.92 3.10
3660 3774 3.942829 TCACTCAATGGGATTGTGTCTC 58.057 45.455 0.00 0.00 42.92 3.36
3661 3775 4.330250 CTTCACTCAATGGGATTGTGTCT 58.670 43.478 0.00 0.00 42.92 3.41
3662 3776 3.119708 GCTTCACTCAATGGGATTGTGTC 60.120 47.826 0.00 0.00 42.92 3.67
3663 3777 2.821969 GCTTCACTCAATGGGATTGTGT 59.178 45.455 0.00 0.00 44.88 3.72
3664 3778 2.165030 GGCTTCACTCAATGGGATTGTG 59.835 50.000 0.00 0.00 41.02 3.33
3666 3780 2.449464 TGGCTTCACTCAATGGGATTG 58.551 47.619 0.00 0.00 41.57 2.67
3667 3781 2.905415 TGGCTTCACTCAATGGGATT 57.095 45.000 0.00 0.00 0.00 3.01
3668 3782 3.461085 ACTATGGCTTCACTCAATGGGAT 59.539 43.478 0.00 0.00 0.00 3.85
3669 3783 2.846206 ACTATGGCTTCACTCAATGGGA 59.154 45.455 0.00 0.00 0.00 4.37
3672 3786 6.478344 GTCTCTAACTATGGCTTCACTCAATG 59.522 42.308 0.00 0.00 0.00 2.82
3685 3799 9.883142 ATTCTTTTCTTCTGGTCTCTAACTATG 57.117 33.333 0.00 0.00 0.00 2.23
3694 3808 4.327680 CGGGAATTCTTTTCTTCTGGTCT 58.672 43.478 5.23 0.00 0.00 3.85
3703 3817 3.689649 TCAGCTAAGCGGGAATTCTTTTC 59.310 43.478 5.23 0.00 0.00 2.29
3707 3821 2.703007 AGATCAGCTAAGCGGGAATTCT 59.297 45.455 5.23 0.00 0.00 2.40
3708 3822 3.118905 AGATCAGCTAAGCGGGAATTC 57.881 47.619 0.00 0.00 0.00 2.17
3709 3823 3.567478 AAGATCAGCTAAGCGGGAATT 57.433 42.857 0.00 0.00 0.00 2.17
3710 3824 3.567478 AAAGATCAGCTAAGCGGGAAT 57.433 42.857 0.00 0.00 0.00 3.01
3711 3825 3.350219 AAAAGATCAGCTAAGCGGGAA 57.650 42.857 0.00 0.00 0.00 3.97
3712 3826 3.270877 GAAAAAGATCAGCTAAGCGGGA 58.729 45.455 0.00 0.00 0.00 5.14
3713 3827 3.009723 TGAAAAAGATCAGCTAAGCGGG 58.990 45.455 0.00 0.00 0.00 6.13
3714 3828 4.889832 ATGAAAAAGATCAGCTAAGCGG 57.110 40.909 0.00 0.00 31.76 5.52
3715 3829 6.036953 AGAGAATGAAAAAGATCAGCTAAGCG 59.963 38.462 0.00 0.00 31.76 4.68
3716 3830 7.319142 AGAGAATGAAAAAGATCAGCTAAGC 57.681 36.000 0.00 0.00 31.76 3.09
3717 3831 8.182881 CCAAGAGAATGAAAAAGATCAGCTAAG 58.817 37.037 0.00 0.00 31.76 2.18
3718 3832 7.121759 CCCAAGAGAATGAAAAAGATCAGCTAA 59.878 37.037 0.00 0.00 31.76 3.09
3719 3833 6.600822 CCCAAGAGAATGAAAAAGATCAGCTA 59.399 38.462 0.00 0.00 31.76 3.32
3720 3834 5.418209 CCCAAGAGAATGAAAAAGATCAGCT 59.582 40.000 0.00 0.00 31.76 4.24
3721 3835 5.393896 CCCCAAGAGAATGAAAAAGATCAGC 60.394 44.000 0.00 0.00 31.76 4.26
3722 3836 5.948162 TCCCCAAGAGAATGAAAAAGATCAG 59.052 40.000 0.00 0.00 31.76 2.90
3723 3837 5.891198 TCCCCAAGAGAATGAAAAAGATCA 58.109 37.500 0.00 0.00 0.00 2.92
3724 3838 5.359292 CCTCCCCAAGAGAATGAAAAAGATC 59.641 44.000 0.00 0.00 46.50 2.75
3725 3839 5.222421 ACCTCCCCAAGAGAATGAAAAAGAT 60.222 40.000 0.00 0.00 46.50 2.40
3726 3840 4.106341 ACCTCCCCAAGAGAATGAAAAAGA 59.894 41.667 0.00 0.00 46.50 2.52
3727 3841 4.411013 ACCTCCCCAAGAGAATGAAAAAG 58.589 43.478 0.00 0.00 46.50 2.27
3728 3842 4.141041 TGACCTCCCCAAGAGAATGAAAAA 60.141 41.667 0.00 0.00 46.50 1.94
3729 3843 3.397618 TGACCTCCCCAAGAGAATGAAAA 59.602 43.478 0.00 0.00 46.50 2.29
3730 3844 2.986019 TGACCTCCCCAAGAGAATGAAA 59.014 45.455 0.00 0.00 46.50 2.69
3731 3845 2.573462 CTGACCTCCCCAAGAGAATGAA 59.427 50.000 0.00 0.00 46.50 2.57
3732 3846 2.191400 CTGACCTCCCCAAGAGAATGA 58.809 52.381 0.00 0.00 46.50 2.57
3733 3847 2.170187 CTCTGACCTCCCCAAGAGAATG 59.830 54.545 0.00 0.00 46.50 2.67
3734 3848 2.225753 ACTCTGACCTCCCCAAGAGAAT 60.226 50.000 5.59 0.00 46.50 2.40
3735 3849 1.150135 ACTCTGACCTCCCCAAGAGAA 59.850 52.381 5.59 0.00 46.50 2.87
3736 3850 0.787084 ACTCTGACCTCCCCAAGAGA 59.213 55.000 5.59 0.00 46.50 3.10
3737 3851 2.383855 CTACTCTGACCTCCCCAAGAG 58.616 57.143 0.00 0.00 42.83 2.85
3738 3852 1.007238 CCTACTCTGACCTCCCCAAGA 59.993 57.143 0.00 0.00 0.00 3.02
3739 3853 1.490574 CCTACTCTGACCTCCCCAAG 58.509 60.000 0.00 0.00 0.00 3.61
3740 3854 0.042731 CCCTACTCTGACCTCCCCAA 59.957 60.000 0.00 0.00 0.00 4.12
3741 3855 1.704082 CCCTACTCTGACCTCCCCA 59.296 63.158 0.00 0.00 0.00 4.96
3742 3856 1.075151 CCCCTACTCTGACCTCCCC 60.075 68.421 0.00 0.00 0.00 4.81
3743 3857 0.932211 TACCCCTACTCTGACCTCCC 59.068 60.000 0.00 0.00 0.00 4.30
3744 3858 1.754910 GCTACCCCTACTCTGACCTCC 60.755 61.905 0.00 0.00 0.00 4.30
3745 3859 1.063867 TGCTACCCCTACTCTGACCTC 60.064 57.143 0.00 0.00 0.00 3.85
3746 3860 1.008403 TGCTACCCCTACTCTGACCT 58.992 55.000 0.00 0.00 0.00 3.85
3747 3861 1.063867 TCTGCTACCCCTACTCTGACC 60.064 57.143 0.00 0.00 0.00 4.02
3748 3862 2.025898 GTCTGCTACCCCTACTCTGAC 58.974 57.143 0.00 0.00 0.00 3.51
3749 3863 1.639108 TGTCTGCTACCCCTACTCTGA 59.361 52.381 0.00 0.00 0.00 3.27
3750 3864 1.751924 GTGTCTGCTACCCCTACTCTG 59.248 57.143 0.00 0.00 0.00 3.35
3751 3865 1.342175 GGTGTCTGCTACCCCTACTCT 60.342 57.143 0.00 0.00 31.89 3.24
3752 3866 1.112950 GGTGTCTGCTACCCCTACTC 58.887 60.000 0.00 0.00 31.89 2.59
3753 3867 0.412244 TGGTGTCTGCTACCCCTACT 59.588 55.000 0.00 0.00 37.40 2.57
3754 3868 0.824759 CTGGTGTCTGCTACCCCTAC 59.175 60.000 0.00 0.00 37.40 3.18
3755 3869 0.708209 TCTGGTGTCTGCTACCCCTA 59.292 55.000 0.00 0.00 37.40 3.53
3756 3870 0.043334 ATCTGGTGTCTGCTACCCCT 59.957 55.000 0.00 0.00 37.40 4.79
3757 3871 0.466124 GATCTGGTGTCTGCTACCCC 59.534 60.000 0.00 0.00 37.40 4.95
3758 3872 0.466124 GGATCTGGTGTCTGCTACCC 59.534 60.000 0.00 0.00 37.40 3.69
3759 3873 0.103208 CGGATCTGGTGTCTGCTACC 59.897 60.000 0.00 0.00 38.71 3.18
3760 3874 0.103208 CCGGATCTGGTGTCTGCTAC 59.897 60.000 12.93 0.00 0.00 3.58
3761 3875 1.676678 GCCGGATCTGGTGTCTGCTA 61.677 60.000 21.88 0.00 0.00 3.49
3762 3876 3.023949 GCCGGATCTGGTGTCTGCT 62.024 63.158 21.88 0.00 0.00 4.24
3763 3877 2.512515 GCCGGATCTGGTGTCTGC 60.513 66.667 21.88 2.41 0.00 4.26
3764 3878 2.187946 GGCCGGATCTGGTGTCTG 59.812 66.667 21.88 0.00 0.00 3.51
3765 3879 2.039624 AGGCCGGATCTGGTGTCT 59.960 61.111 21.88 13.65 0.00 3.41
3766 3880 2.187946 CAGGCCGGATCTGGTGTC 59.812 66.667 21.88 11.71 0.00 3.67
3767 3881 2.607750 ACAGGCCGGATCTGGTGT 60.608 61.111 21.88 15.78 36.62 4.16
3768 3882 2.124983 CACAGGCCGGATCTGGTG 60.125 66.667 21.88 15.13 36.62 4.17
3769 3883 4.101448 GCACAGGCCGGATCTGGT 62.101 66.667 21.88 0.00 36.62 4.00
3779 3893 4.373116 TCCTCGAACGGCACAGGC 62.373 66.667 0.00 0.00 40.13 4.85
3780 3894 2.125912 CTCCTCGAACGGCACAGG 60.126 66.667 0.00 0.00 0.00 4.00
3781 3895 1.153939 CTCTCCTCGAACGGCACAG 60.154 63.158 0.00 0.00 0.00 3.66
3782 3896 2.962569 CTCTCCTCGAACGGCACA 59.037 61.111 0.00 0.00 0.00 4.57
3783 3897 2.507324 GCTCTCCTCGAACGGCAC 60.507 66.667 0.00 0.00 0.00 5.01
3784 3898 1.888436 AATGCTCTCCTCGAACGGCA 61.888 55.000 0.00 0.00 0.00 5.69
3785 3899 1.153549 AATGCTCTCCTCGAACGGC 60.154 57.895 0.00 0.00 0.00 5.68
3786 3900 0.173481 TCAATGCTCTCCTCGAACGG 59.827 55.000 0.00 0.00 0.00 4.44
3787 3901 2.123342 GATCAATGCTCTCCTCGAACG 58.877 52.381 0.00 0.00 0.00 3.95
3788 3902 3.122297 CAGATCAATGCTCTCCTCGAAC 58.878 50.000 0.00 0.00 0.00 3.95
3789 3903 3.026694 TCAGATCAATGCTCTCCTCGAA 58.973 45.455 0.00 0.00 0.00 3.71
3790 3904 2.659428 TCAGATCAATGCTCTCCTCGA 58.341 47.619 0.00 0.00 0.00 4.04
3791 3905 3.449528 TTCAGATCAATGCTCTCCTCG 57.550 47.619 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.