Multiple sequence alignment - TraesCS6A01G072400

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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 TraesCS6A01G072400 chr6A 100.000 3882 0 0 1 3882 39495942 39492061 0.000000e+00 7169
1 TraesCS6A01G072400 chr6A 79.339 484 57 20 3407 3882 565689951 565690399 2.270000e-77 300
2 TraesCS6A01G072400 chr6D 92.932 2561 107 25 1 2524 35624954 35622431 0.000000e+00 3659
3 TraesCS6A01G072400 chr6D 89.427 785 47 16 2643 3408 35622246 35621479 0.000000e+00 957
4 TraesCS6A01G072400 chr6B 91.044 1686 107 19 898 2556 73902799 73901131 0.000000e+00 2237
5 TraesCS6A01G072400 chr6B 91.029 1360 60 23 1787 3125 75027580 75026262 0.000000e+00 1779
6 TraesCS6A01G072400 chr6B 91.146 881 71 7 921 1799 75028477 75027602 0.000000e+00 1188
7 TraesCS6A01G072400 chr6B 93.829 551 30 4 1 549 75029480 75028932 0.000000e+00 826
8 TraesCS6A01G072400 chr6B 94.505 364 14 4 597 956 75028839 75028478 1.220000e-154 556
9 TraesCS6A01G072400 chr6B 91.315 403 32 3 14 415 73947782 73947382 7.330000e-152 547
10 TraesCS6A01G072400 chr6B 91.463 328 23 5 14 339 73903352 73903028 2.750000e-121 446
11 TraesCS6A01G072400 chr6B 86.269 386 51 1 898 1283 73947385 73947002 6.000000e-113 418
12 TraesCS6A01G072400 chr6B 84.892 417 51 9 3395 3807 283705255 283705663 1.000000e-110 411
13 TraesCS6A01G072400 chr6B 91.781 292 22 2 2591 2882 73901028 73900739 4.670000e-109 405
14 TraesCS6A01G072400 chr6B 84.487 419 49 15 3397 3807 42161045 42161455 2.170000e-107 399
15 TraesCS6A01G072400 chr6B 93.304 224 12 3 3064 3286 73900567 73900346 1.040000e-85 327
16 TraesCS6A01G072400 chr6B 92.929 99 7 0 317 415 73902894 73902796 1.120000e-30 145
17 TraesCS6A01G072400 chr6B 96.970 66 1 1 3817 3882 519422866 519422802 4.100000e-20 110
18 TraesCS6A01G072400 chr3B 87.561 410 42 9 3403 3807 815525815 815525410 2.110000e-127 466
19 TraesCS6A01G072400 chr3B 87.317 410 43 9 3403 3807 815606175 815605770 9.830000e-126 460
20 TraesCS6A01G072400 chr3B 87.317 410 43 9 3403 3807 815654886 815654481 9.830000e-126 460
21 TraesCS6A01G072400 chr3B 93.939 66 4 0 3817 3882 294284726 294284661 2.470000e-17 100
22 TraesCS6A01G072400 chr2B 87.469 407 42 9 3407 3807 161406033 161405630 9.830000e-126 460
23 TraesCS6A01G072400 chr2B 87.073 410 41 11 3404 3807 597884785 597885188 1.640000e-123 453
24 TraesCS6A01G072400 chr3D 86.893 412 48 6 3400 3806 606343628 606344038 1.270000e-124 457
25 TraesCS6A01G072400 chr3D 84.235 425 55 12 3387 3806 108435818 108436235 1.680000e-108 403
26 TraesCS6A01G072400 chr2D 87.192 406 42 10 3408 3807 522908854 522908453 1.640000e-123 453
27 TraesCS6A01G072400 chr2D 85.748 421 47 10 3395 3807 339656208 339656623 2.140000e-117 433
28 TraesCS6A01G072400 chr7A 86.634 404 46 7 3408 3807 734469922 734470321 1.280000e-119 440
29 TraesCS6A01G072400 chr1D 84.977 426 54 10 3395 3814 500540 500119 1.290000e-114 424
30 TraesCS6A01G072400 chr1D 81.395 473 52 21 3416 3882 270605956 270606398 1.720000e-93 353
31 TraesCS6A01G072400 chr1D 93.939 66 3 1 3817 3882 137069502 137069566 8.880000e-17 99
32 TraesCS6A01G072400 chr4A 84.096 415 57 9 3392 3800 744492506 744492095 3.640000e-105 392
33 TraesCS6A01G072400 chr4A 82.974 417 62 7 3394 3805 224250096 224249684 6.130000e-98 368
34 TraesCS6A01G072400 chr7D 83.933 417 54 13 3397 3807 37418886 37419295 1.690000e-103 387
35 TraesCS6A01G072400 chr7D 77.650 349 60 11 3416 3749 636375191 636374846 3.060000e-46 196
36 TraesCS6A01G072400 chr7B 83.493 418 55 14 3397 3807 674649816 674649406 1.020000e-100 377
37 TraesCS6A01G072400 chr7B 93.939 66 4 0 3817 3882 14187737 14187802 2.470000e-17 100
38 TraesCS6A01G072400 chrUn 93.939 66 4 0 3817 3882 229617992 229618057 2.470000e-17 100
39 TraesCS6A01G072400 chr1B 93.939 66 3 1 3817 3882 683441650 683441586 8.880000e-17 99


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 TraesCS6A01G072400 chr6A 39492061 39495942 3881 True 7169.00 7169 100.00000 1 3882 1 chr6A.!!$R1 3881
1 TraesCS6A01G072400 chr6D 35621479 35624954 3475 True 2308.00 3659 91.17950 1 3408 2 chr6D.!!$R1 3407
2 TraesCS6A01G072400 chr6B 75026262 75029480 3218 True 1087.25 1779 92.62725 1 3125 4 chr6B.!!$R4 3124
3 TraesCS6A01G072400 chr6B 73900346 73903352 3006 True 712.00 2237 92.10420 14 3286 5 chr6B.!!$R2 3272
4 TraesCS6A01G072400 chr6B 73947002 73947782 780 True 482.50 547 88.79200 14 1283 2 chr6B.!!$R3 1269

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
174 175 1.985473 AACATGCCTGCTTGTCTTCA 58.015 45.0 10.59 0.0 33.97 3.02 F
1137 1384 0.387929 TCTTTGTGTTCGGCGACTCT 59.612 50.0 10.16 0.0 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1266 1513 0.106268 TGGCTTGCTCACCCAAGAAA 60.106 50.0 6.12 0.0 43.79 2.52 R
2963 3385 0.593128 CCACGAAAGGCAAAGACCAG 59.407 55.0 0.00 0.0 0.00 4.00 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
70 71 5.939296 TGCATCAATTGTTCTGACTGACATA 59.061 36.000 5.13 0.00 0.00 2.29
131 132 7.310664 CGTAACTCTGACTTAGTTGGTAATCA 58.689 38.462 0.00 0.00 37.71 2.57
174 175 1.985473 AACATGCCTGCTTGTCTTCA 58.015 45.000 10.59 0.00 33.97 3.02
190 191 7.684317 TTGTCTTCATTATAGGGGTGATGTA 57.316 36.000 0.00 0.00 0.00 2.29
346 505 2.101249 TGCTCAGCAAAAACTTTCTGGG 59.899 45.455 0.00 0.00 34.76 4.45
444 603 8.447787 AGTGTTGTTTATGCATTTTATTCGTC 57.552 30.769 3.54 0.00 0.00 4.20
478 640 4.342427 TGCCTCCATGCATGTTCC 57.658 55.556 24.58 10.72 36.04 3.62
557 742 4.635699 AACAATCGGTTTTACTCCCTCT 57.364 40.909 0.00 0.00 35.82 3.69
604 812 2.268796 TCCCATGTTGAGATGGAGGA 57.731 50.000 8.62 0.00 45.24 3.71
661 871 6.749139 TGATTGTGCTCTGTATATACCACTC 58.251 40.000 10.38 6.42 0.00 3.51
794 1006 4.327680 AGAACCTAGACAATTGTGGCTTC 58.672 43.478 17.58 15.30 42.06 3.86
943 1187 7.765695 TCTTCCATCAGAATATAAATTGGCC 57.234 36.000 0.00 0.00 32.82 5.36
1075 1319 2.240612 GATCCGGTTGCTGTTCGTGC 62.241 60.000 0.00 0.00 0.00 5.34
1103 1347 4.457496 CAGCACCGTCGCCTCCAT 62.457 66.667 0.00 0.00 0.00 3.41
1137 1384 0.387929 TCTTTGTGTTCGGCGACTCT 59.612 50.000 10.16 0.00 0.00 3.24
1143 1390 1.241990 TGTTCGGCGACTCTACTGCT 61.242 55.000 10.16 0.00 0.00 4.24
1194 1441 2.036256 AGCGCCAGGGCTGATTTT 59.964 55.556 8.58 0.00 42.86 1.82
1266 1513 3.211963 GGCTTCATTGGCGCCGAT 61.212 61.111 24.20 24.20 33.64 4.18
1307 1554 6.674519 GCCAATTGATCACATGCTTTTGAATG 60.675 38.462 7.12 0.00 41.33 2.67
1321 1568 1.819632 GAATGAATGGCGGCTCGGT 60.820 57.895 11.43 0.00 0.00 4.69
1338 1585 2.628178 TCGGTTGTCTGTCTGATCAGTT 59.372 45.455 21.92 0.00 36.85 3.16
1344 1591 5.022282 TGTCTGTCTGATCAGTTGTGAAA 57.978 39.130 21.92 9.04 35.88 2.69
1399 1646 1.451567 CCGCCGTACCTCTCTCTCA 60.452 63.158 0.00 0.00 0.00 3.27
1449 1696 1.503542 GACGACGAAGAAGCCGGTA 59.496 57.895 1.90 0.00 0.00 4.02
1533 1780 2.466867 GGTACGTCCAAGCCACATG 58.533 57.895 0.00 0.00 35.97 3.21
1540 1787 0.399833 TCCAAGCCACATGTGCTGTA 59.600 50.000 20.81 7.60 39.48 2.74
1565 1812 6.773976 ACATTTCTGACTCTGTTTTTCCAA 57.226 33.333 0.00 0.00 0.00 3.53
1649 1912 8.788806 ACATAAATTTCGACTGAATTGGTTACA 58.211 29.630 0.00 0.00 33.20 2.41
1866 2179 9.979578 TTAAAAATCAGCAAGTACAATTGACAT 57.020 25.926 13.59 0.00 31.55 3.06
2005 2318 2.526873 AGACTGGGTGCCTTCGGT 60.527 61.111 0.00 0.00 0.00 4.69
2182 2495 3.382278 AGACCTGACCAGTGATGATCAT 58.618 45.455 8.25 8.25 0.00 2.45
2183 2496 3.779183 AGACCTGACCAGTGATGATCATT 59.221 43.478 10.14 0.00 0.00 2.57
2184 2497 4.226846 AGACCTGACCAGTGATGATCATTT 59.773 41.667 10.14 0.00 0.00 2.32
2185 2498 4.521146 ACCTGACCAGTGATGATCATTTC 58.479 43.478 10.14 6.33 0.00 2.17
2186 2499 3.881688 CCTGACCAGTGATGATCATTTCC 59.118 47.826 10.14 0.00 0.00 3.13
2187 2500 4.520179 CTGACCAGTGATGATCATTTCCA 58.480 43.478 10.14 0.14 0.00 3.53
2227 2544 5.221641 ACTCAGCCAAACTCACTGTGTTATA 60.222 40.000 7.79 0.00 35.29 0.98
2544 2861 7.459394 AAAAATAAATCGCAGCATTCTGATG 57.541 32.000 0.00 0.00 42.95 3.07
2556 2873 4.815308 AGCATTCTGATGTCAAGCTGATAC 59.185 41.667 0.00 0.00 35.63 2.24
2557 2874 4.573607 GCATTCTGATGTCAAGCTGATACA 59.426 41.667 0.00 0.00 35.63 2.29
2558 2875 5.238868 GCATTCTGATGTCAAGCTGATACAT 59.761 40.000 8.20 8.20 36.57 2.29
2561 2878 6.966534 TCTGATGTCAAGCTGATACATCTA 57.033 37.500 24.99 16.18 46.22 1.98
2593 2984 1.759445 ACATCTAGAGTCTGCGGCATT 59.241 47.619 1.75 0.00 0.00 3.56
2618 3009 2.293677 TCGTACATCGCTCATGCTTT 57.706 45.000 0.00 0.00 39.67 3.51
2680 3071 2.734591 ACGGAGTTGAAGAGCGCA 59.265 55.556 11.47 0.00 37.78 6.09
2716 3107 3.920196 AGGTTCAACGCCGACGGT 61.920 61.111 16.73 0.00 46.04 4.83
2835 3226 4.060038 GTTCTTCGACGGGCCGGA 62.060 66.667 31.78 16.28 0.00 5.14
2917 3339 3.763897 TCATTCCACGACATGAGAGAGAA 59.236 43.478 0.00 0.00 0.00 2.87
2936 3358 6.877236 AGAGAATCAAATGTGGTTTTGTGTT 58.123 32.000 0.00 0.00 37.73 3.32
2963 3385 0.526211 GCCGGTCCAAGTCAAAATCC 59.474 55.000 1.90 0.00 0.00 3.01
3036 3458 6.268617 TGTCCAAATTGGGTGTTGATTAATGA 59.731 34.615 12.67 0.00 38.32 2.57
3037 3459 7.038445 TGTCCAAATTGGGTGTTGATTAATGAT 60.038 33.333 12.67 0.00 38.32 2.45
3038 3460 7.823799 GTCCAAATTGGGTGTTGATTAATGATT 59.176 33.333 12.67 0.00 38.32 2.57
3039 3461 9.040259 TCCAAATTGGGTGTTGATTAATGATTA 57.960 29.630 12.67 0.00 38.32 1.75
3040 3462 9.664332 CCAAATTGGGTGTTGATTAATGATTAA 57.336 29.630 3.60 0.00 32.67 1.40
3044 3466 9.820725 ATTGGGTGTTGATTAATGATTAATGTG 57.179 29.630 14.63 0.00 36.04 3.21
3045 3467 7.264221 TGGGTGTTGATTAATGATTAATGTGC 58.736 34.615 14.63 2.29 36.04 4.57
3046 3468 7.123997 TGGGTGTTGATTAATGATTAATGTGCT 59.876 33.333 14.63 0.00 36.04 4.40
3047 3469 8.629158 GGGTGTTGATTAATGATTAATGTGCTA 58.371 33.333 14.63 0.00 36.04 3.49
3080 3502 1.064003 TTGGGGCAGACACACACTAT 58.936 50.000 0.00 0.00 0.00 2.12
3087 3509 3.612860 GGCAGACACACACTATTTACTCG 59.387 47.826 0.00 0.00 0.00 4.18
3095 3517 4.330894 ACACACTATTTACTCGTCGATCGA 59.669 41.667 15.15 15.15 46.83 3.59
3120 3543 0.037326 CGTGCACACTGACCTGGTAT 60.037 55.000 18.64 0.00 0.00 2.73
3174 3597 6.753913 TCAATTTATGAGCTGAGGGAGTAT 57.246 37.500 0.00 0.00 33.04 2.12
3305 3728 8.243426 GTGATTCTTATGTTTATGTTCCAAGCA 58.757 33.333 0.00 0.00 0.00 3.91
3322 3763 0.244721 GCATTGTTCTGGCTGGTTCC 59.755 55.000 0.00 0.00 0.00 3.62
3338 3779 6.288294 GCTGGTTCCCTAAAAGTTTCATTTT 58.712 36.000 0.00 0.00 36.40 1.82
3352 3793 9.768662 AAAGTTTCATTTTGAATATCAGCAAGT 57.231 25.926 0.00 0.00 36.11 3.16
3353 3794 8.976986 AGTTTCATTTTGAATATCAGCAAGTC 57.023 30.769 0.00 0.00 36.11 3.01
3357 3798 8.114331 TCATTTTGAATATCAGCAAGTCTGTT 57.886 30.769 0.00 0.00 43.32 3.16
3358 3799 8.024865 TCATTTTGAATATCAGCAAGTCTGTTG 58.975 33.333 0.00 0.00 43.32 3.33
3371 3812 4.149019 TGTTGCAGCCCCAACCCA 62.149 61.111 12.80 0.00 43.36 4.51
3375 3816 1.694133 TTGCAGCCCCAACCCAAAAG 61.694 55.000 0.00 0.00 0.00 2.27
3376 3817 2.140138 GCAGCCCCAACCCAAAAGT 61.140 57.895 0.00 0.00 0.00 2.66
3389 3830 6.548251 CCAACCCAAAAGTCTAGTTCCTTTTA 59.452 38.462 13.34 0.00 38.48 1.52
3426 3867 2.814280 ACTAGTACATATGCCCGTGC 57.186 50.000 1.58 0.00 38.26 5.34
3427 3868 1.000607 ACTAGTACATATGCCCGTGCG 60.001 52.381 1.58 0.00 41.78 5.34
3428 3869 1.000607 CTAGTACATATGCCCGTGCGT 60.001 52.381 1.58 0.00 41.78 5.24
3429 3870 0.177141 AGTACATATGCCCGTGCGTT 59.823 50.000 1.58 0.00 41.78 4.84
3430 3871 0.303493 GTACATATGCCCGTGCGTTG 59.697 55.000 1.58 0.00 41.78 4.10
3431 3872 1.433053 TACATATGCCCGTGCGTTGC 61.433 55.000 1.58 0.00 41.78 4.17
3432 3873 2.437537 ATATGCCCGTGCGTTGCA 60.438 55.556 8.11 8.11 41.78 4.08
3433 3874 2.043405 ATATGCCCGTGCGTTGCAA 61.043 52.632 0.00 0.00 41.47 4.08
3434 3875 2.265073 ATATGCCCGTGCGTTGCAAC 62.265 55.000 19.89 19.89 41.47 4.17
3486 3927 9.573133 AAGTTAGTGAAAATTATATGTGCAAGC 57.427 29.630 0.00 0.00 0.00 4.01
3487 3928 8.739039 AGTTAGTGAAAATTATATGTGCAAGCA 58.261 29.630 0.00 0.00 0.00 3.91
3488 3929 9.352784 GTTAGTGAAAATTATATGTGCAAGCAA 57.647 29.630 0.00 0.00 0.00 3.91
3489 3930 9.920133 TTAGTGAAAATTATATGTGCAAGCAAA 57.080 25.926 0.00 0.00 0.00 3.68
3490 3931 8.830201 AGTGAAAATTATATGTGCAAGCAAAA 57.170 26.923 0.00 0.00 0.00 2.44
3491 3932 8.711457 AGTGAAAATTATATGTGCAAGCAAAAC 58.289 29.630 0.00 0.00 0.00 2.43
3492 3933 7.956943 GTGAAAATTATATGTGCAAGCAAAACC 59.043 33.333 0.00 0.00 0.00 3.27
3493 3934 6.983474 AAATTATATGTGCAAGCAAAACCC 57.017 33.333 0.00 0.00 0.00 4.11
3494 3935 4.464069 TTATATGTGCAAGCAAAACCCC 57.536 40.909 0.00 0.00 0.00 4.95
3495 3936 0.600557 TATGTGCAAGCAAAACCCCG 59.399 50.000 0.00 0.00 0.00 5.73
3496 3937 1.398958 ATGTGCAAGCAAAACCCCGT 61.399 50.000 0.00 0.00 0.00 5.28
3497 3938 1.591327 GTGCAAGCAAAACCCCGTG 60.591 57.895 0.00 0.00 0.00 4.94
3498 3939 2.055042 TGCAAGCAAAACCCCGTGT 61.055 52.632 0.00 0.00 0.00 4.49
3499 3940 1.591327 GCAAGCAAAACCCCGTGTG 60.591 57.895 0.00 0.00 0.00 3.82
3500 3941 1.591327 CAAGCAAAACCCCGTGTGC 60.591 57.895 0.00 0.00 37.26 4.57
3501 3942 2.055042 AAGCAAAACCCCGTGTGCA 61.055 52.632 0.00 0.00 39.50 4.57
3502 3943 1.398958 AAGCAAAACCCCGTGTGCAT 61.399 50.000 0.00 0.00 39.50 3.96
3503 3944 1.664333 GCAAAACCCCGTGTGCATG 60.664 57.895 0.00 0.00 36.97 4.06
3504 3945 1.739049 CAAAACCCCGTGTGCATGT 59.261 52.632 0.00 0.00 0.00 3.21
3505 3946 0.597118 CAAAACCCCGTGTGCATGTG 60.597 55.000 0.00 0.00 0.00 3.21
3506 3947 0.753479 AAAACCCCGTGTGCATGTGA 60.753 50.000 0.00 0.00 0.00 3.58
3507 3948 0.753479 AAACCCCGTGTGCATGTGAA 60.753 50.000 0.00 0.00 0.00 3.18
3508 3949 0.753479 AACCCCGTGTGCATGTGAAA 60.753 50.000 0.00 0.00 0.00 2.69
3509 3950 0.753479 ACCCCGTGTGCATGTGAAAA 60.753 50.000 0.00 0.00 0.00 2.29
3510 3951 0.387202 CCCCGTGTGCATGTGAAAAA 59.613 50.000 0.00 0.00 0.00 1.94
3511 3952 1.602668 CCCCGTGTGCATGTGAAAAAG 60.603 52.381 0.00 0.00 0.00 2.27
3512 3953 1.602668 CCCGTGTGCATGTGAAAAAGG 60.603 52.381 0.00 0.00 0.00 3.11
3513 3954 1.336440 CCGTGTGCATGTGAAAAAGGA 59.664 47.619 0.00 0.00 0.00 3.36
3514 3955 2.223688 CCGTGTGCATGTGAAAAAGGAA 60.224 45.455 0.00 0.00 0.00 3.36
3515 3956 2.788786 CGTGTGCATGTGAAAAAGGAAC 59.211 45.455 0.00 0.00 0.00 3.62
3516 3957 3.733380 CGTGTGCATGTGAAAAAGGAACA 60.733 43.478 0.00 0.00 0.00 3.18
3517 3958 4.370917 GTGTGCATGTGAAAAAGGAACAT 58.629 39.130 0.00 0.00 0.00 2.71
3518 3959 4.810491 GTGTGCATGTGAAAAAGGAACATT 59.190 37.500 0.00 0.00 0.00 2.71
3519 3960 5.294060 GTGTGCATGTGAAAAAGGAACATTT 59.706 36.000 0.00 0.00 0.00 2.32
3520 3961 6.478344 GTGTGCATGTGAAAAAGGAACATTTA 59.522 34.615 0.00 0.00 0.00 1.40
3521 3962 6.700960 TGTGCATGTGAAAAAGGAACATTTAG 59.299 34.615 0.00 0.00 0.00 1.85
3522 3963 5.695816 TGCATGTGAAAAAGGAACATTTAGC 59.304 36.000 0.00 0.00 0.00 3.09
3523 3964 5.928264 GCATGTGAAAAAGGAACATTTAGCT 59.072 36.000 0.00 0.00 0.00 3.32
3524 3965 6.424812 GCATGTGAAAAAGGAACATTTAGCTT 59.575 34.615 0.00 0.00 0.00 3.74
3525 3966 7.359514 GCATGTGAAAAAGGAACATTTAGCTTC 60.360 37.037 0.00 0.00 0.00 3.86
3526 3967 7.346751 TGTGAAAAAGGAACATTTAGCTTCT 57.653 32.000 0.00 0.00 0.00 2.85
3527 3968 7.425606 TGTGAAAAAGGAACATTTAGCTTCTC 58.574 34.615 0.00 0.00 0.00 2.87
3528 3969 6.578919 GTGAAAAAGGAACATTTAGCTTCTCG 59.421 38.462 0.00 0.00 0.00 4.04
3529 3970 5.629079 AAAAGGAACATTTAGCTTCTCGG 57.371 39.130 0.00 0.00 0.00 4.63
3530 3971 3.983044 AGGAACATTTAGCTTCTCGGT 57.017 42.857 0.00 0.00 0.00 4.69
3531 3972 4.287766 AGGAACATTTAGCTTCTCGGTT 57.712 40.909 0.00 0.00 0.00 4.44
3532 3973 4.652822 AGGAACATTTAGCTTCTCGGTTT 58.347 39.130 0.00 0.00 0.00 3.27
3533 3974 5.070685 AGGAACATTTAGCTTCTCGGTTTT 58.929 37.500 0.00 0.00 0.00 2.43
3534 3975 5.048713 AGGAACATTTAGCTTCTCGGTTTTG 60.049 40.000 0.00 0.00 0.00 2.44
3535 3976 4.160736 ACATTTAGCTTCTCGGTTTTGC 57.839 40.909 0.00 0.00 0.00 3.68
3536 3977 3.057526 ACATTTAGCTTCTCGGTTTTGCC 60.058 43.478 0.00 0.00 0.00 4.52
3545 3986 3.527641 GGTTTTGCCGGGTGTGAA 58.472 55.556 2.18 0.00 0.00 3.18
3546 3987 1.362355 GGTTTTGCCGGGTGTGAAG 59.638 57.895 2.18 0.00 0.00 3.02
3547 3988 1.388837 GGTTTTGCCGGGTGTGAAGT 61.389 55.000 2.18 0.00 0.00 3.01
3548 3989 1.310904 GTTTTGCCGGGTGTGAAGTA 58.689 50.000 2.18 0.00 0.00 2.24
3549 3990 1.677052 GTTTTGCCGGGTGTGAAGTAA 59.323 47.619 2.18 0.00 0.00 2.24
3550 3991 2.279935 TTTGCCGGGTGTGAAGTAAT 57.720 45.000 2.18 0.00 0.00 1.89
3551 3992 1.816074 TTGCCGGGTGTGAAGTAATC 58.184 50.000 2.18 0.00 0.00 1.75
3552 3993 0.687920 TGCCGGGTGTGAAGTAATCA 59.312 50.000 2.18 0.00 35.05 2.57
3553 3994 1.072489 TGCCGGGTGTGAAGTAATCAA 59.928 47.619 2.18 0.00 40.50 2.57
3554 3995 2.290641 TGCCGGGTGTGAAGTAATCAAT 60.291 45.455 2.18 0.00 40.50 2.57
3555 3996 2.354821 GCCGGGTGTGAAGTAATCAATC 59.645 50.000 2.18 0.00 40.50 2.67
3556 3997 2.943033 CCGGGTGTGAAGTAATCAATCC 59.057 50.000 0.00 0.00 40.50 3.01
3557 3998 2.607635 CGGGTGTGAAGTAATCAATCCG 59.392 50.000 0.00 0.00 40.50 4.18
3558 3999 3.606687 GGGTGTGAAGTAATCAATCCGT 58.393 45.455 0.00 0.00 40.50 4.69
3559 4000 4.007659 GGGTGTGAAGTAATCAATCCGTT 58.992 43.478 0.00 0.00 40.50 4.44
3560 4001 5.180271 GGGTGTGAAGTAATCAATCCGTTA 58.820 41.667 0.00 0.00 40.50 3.18
3561 4002 5.820947 GGGTGTGAAGTAATCAATCCGTTAT 59.179 40.000 0.00 0.00 40.50 1.89
3562 4003 6.317893 GGGTGTGAAGTAATCAATCCGTTATT 59.682 38.462 0.00 0.00 40.50 1.40
3563 4004 7.148137 GGGTGTGAAGTAATCAATCCGTTATTT 60.148 37.037 0.00 0.00 40.50 1.40
3564 4005 8.241367 GGTGTGAAGTAATCAATCCGTTATTTT 58.759 33.333 0.00 0.00 40.50 1.82
3565 4006 9.620660 GTGTGAAGTAATCAATCCGTTATTTTT 57.379 29.630 0.00 0.00 40.50 1.94
3603 4044 9.630098 TCGAGAATATTTAAGAGTTTTGTACGT 57.370 29.630 0.00 0.00 0.00 3.57
3613 4054 6.144577 AGAGTTTTGTACGTTATTGTACGC 57.855 37.500 0.00 0.00 46.08 4.42
3614 4055 5.119125 AGAGTTTTGTACGTTATTGTACGCC 59.881 40.000 0.00 0.00 46.08 5.68
3615 4056 4.749099 AGTTTTGTACGTTATTGTACGCCA 59.251 37.500 0.00 0.00 46.08 5.69
3616 4057 5.409214 AGTTTTGTACGTTATTGTACGCCAT 59.591 36.000 0.00 0.00 46.08 4.40
3617 4058 6.589523 AGTTTTGTACGTTATTGTACGCCATA 59.410 34.615 0.00 0.00 46.08 2.74
3618 4059 6.572153 TTTGTACGTTATTGTACGCCATAG 57.428 37.500 0.00 0.00 46.08 2.23
3619 4060 5.497635 TGTACGTTATTGTACGCCATAGA 57.502 39.130 0.00 0.00 46.08 1.98
3620 4061 5.889219 TGTACGTTATTGTACGCCATAGAA 58.111 37.500 0.00 0.00 46.08 2.10
3621 4062 5.972973 TGTACGTTATTGTACGCCATAGAAG 59.027 40.000 0.00 0.00 46.08 2.85
3622 4063 4.365723 ACGTTATTGTACGCCATAGAAGG 58.634 43.478 0.00 0.00 45.06 3.46
3661 4102 8.721478 TCAATCTACTTTTTCTTTCAATCGAGG 58.279 33.333 0.00 0.00 0.00 4.63
3662 4103 8.721478 CAATCTACTTTTTCTTTCAATCGAGGA 58.279 33.333 0.00 0.00 0.00 3.71
3663 4104 7.891183 TCTACTTTTTCTTTCAATCGAGGAG 57.109 36.000 0.00 0.00 0.00 3.69
3664 4105 7.667557 TCTACTTTTTCTTTCAATCGAGGAGA 58.332 34.615 0.00 0.00 0.00 3.71
3665 4106 6.546972 ACTTTTTCTTTCAATCGAGGAGAC 57.453 37.500 0.00 0.00 0.00 3.36
3667 4108 6.768381 ACTTTTTCTTTCAATCGAGGAGACTT 59.232 34.615 0.00 0.00 44.43 3.01
3668 4109 7.283354 ACTTTTTCTTTCAATCGAGGAGACTTT 59.717 33.333 0.00 0.00 44.43 2.66
3669 4110 7.568199 TTTTCTTTCAATCGAGGAGACTTTT 57.432 32.000 0.00 0.00 44.43 2.27
3670 4111 8.671384 TTTTCTTTCAATCGAGGAGACTTTTA 57.329 30.769 0.00 0.00 44.43 1.52
3671 4112 8.671384 TTTCTTTCAATCGAGGAGACTTTTAA 57.329 30.769 0.00 0.00 44.43 1.52
3672 4113 7.891183 TCTTTCAATCGAGGAGACTTTTAAG 57.109 36.000 0.00 0.00 44.43 1.85
3673 4114 6.874134 TCTTTCAATCGAGGAGACTTTTAAGG 59.126 38.462 0.00 0.00 44.43 2.69
3674 4115 5.740290 TCAATCGAGGAGACTTTTAAGGT 57.260 39.130 0.00 0.00 44.43 3.50
3675 4116 6.845758 TCAATCGAGGAGACTTTTAAGGTA 57.154 37.500 0.00 0.00 44.43 3.08
3676 4117 7.419711 TCAATCGAGGAGACTTTTAAGGTAT 57.580 36.000 0.00 0.00 44.43 2.73
3677 4118 7.265673 TCAATCGAGGAGACTTTTAAGGTATG 58.734 38.462 0.00 0.00 44.43 2.39
3678 4119 7.123697 TCAATCGAGGAGACTTTTAAGGTATGA 59.876 37.037 0.00 0.00 44.43 2.15
3679 4120 6.845758 TCGAGGAGACTTTTAAGGTATGAA 57.154 37.500 0.00 0.00 44.43 2.57
3680 4121 6.864342 TCGAGGAGACTTTTAAGGTATGAAG 58.136 40.000 0.00 0.00 44.43 3.02
3681 4122 6.436532 TCGAGGAGACTTTTAAGGTATGAAGT 59.563 38.462 0.00 0.00 44.43 3.01
3682 4123 7.039223 TCGAGGAGACTTTTAAGGTATGAAGTT 60.039 37.037 0.00 0.00 44.43 2.66
3683 4124 7.603024 CGAGGAGACTTTTAAGGTATGAAGTTT 59.397 37.037 0.00 0.00 44.43 2.66
3684 4125 8.850007 AGGAGACTTTTAAGGTATGAAGTTTC 57.150 34.615 0.00 0.00 37.44 2.78
3685 4126 8.661345 AGGAGACTTTTAAGGTATGAAGTTTCT 58.339 33.333 0.00 0.00 37.44 2.52
3686 4127 8.722394 GGAGACTTTTAAGGTATGAAGTTTCTG 58.278 37.037 0.00 0.00 35.08 3.02
3687 4128 9.490379 GAGACTTTTAAGGTATGAAGTTTCTGA 57.510 33.333 0.00 0.00 33.16 3.27
3688 4129 9.847224 AGACTTTTAAGGTATGAAGTTTCTGAA 57.153 29.630 0.00 0.00 32.85 3.02
3697 4138 9.838339 AGGTATGAAGTTTCTGAATATTGTAGG 57.162 33.333 0.00 0.00 0.00 3.18
3698 4139 9.832445 GGTATGAAGTTTCTGAATATTGTAGGA 57.168 33.333 0.00 0.00 0.00 2.94
3702 4143 9.567776 TGAAGTTTCTGAATATTGTAGGAAACA 57.432 29.630 21.01 9.55 42.49 2.83
3705 4146 9.739276 AGTTTCTGAATATTGTAGGAAACATGA 57.261 29.630 21.01 2.44 42.49 3.07
3708 4149 8.506168 TCTGAATATTGTAGGAAACATGAACC 57.494 34.615 0.00 0.00 38.10 3.62
3709 4150 8.106462 TCTGAATATTGTAGGAAACATGAACCA 58.894 33.333 0.00 0.00 38.10 3.67
3710 4151 8.821686 TGAATATTGTAGGAAACATGAACCAT 57.178 30.769 0.00 0.00 38.10 3.55
3711 4152 9.253832 TGAATATTGTAGGAAACATGAACCATT 57.746 29.630 0.00 0.00 38.10 3.16
3720 4161 8.846943 AGGAAACATGAACCATTTTTAAATCC 57.153 30.769 0.00 0.00 0.00 3.01
3721 4162 8.659527 AGGAAACATGAACCATTTTTAAATCCT 58.340 29.630 0.00 0.00 0.00 3.24
3722 4163 9.936759 GGAAACATGAACCATTTTTAAATCCTA 57.063 29.630 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 175 6.928348 TGATTCGTACATCACCCCTATAAT 57.072 37.500 0.00 0.00 0.00 1.28
190 191 6.872628 ATGACAGATGCAAATATGATTCGT 57.127 33.333 0.00 0.00 0.00 3.85
346 505 1.134907 CCAATCAGCACAGCATTTCCC 60.135 52.381 0.00 0.00 0.00 3.97
478 640 2.135933 GGTATCCGCCTCTGAAAATCG 58.864 52.381 0.00 0.00 0.00 3.34
604 812 4.973168 TGTCAGCCAAATCAGAACTACTT 58.027 39.130 0.00 0.00 0.00 2.24
661 871 3.639561 TCAGCATGGGAATTCATTGATGG 59.360 43.478 7.93 0.00 36.16 3.51
794 1006 3.217626 ACCACAAGGCTGAAGAGAAAAG 58.782 45.455 0.00 0.00 39.06 2.27
1016 1260 4.065110 GGAGTGCCGTTGAAGCTT 57.935 55.556 0.00 0.00 0.00 3.74
1103 1347 2.119484 AAAGATCGCCGGAACCACCA 62.119 55.000 5.05 0.00 38.90 4.17
1137 1384 1.357137 TGTTCCCCACATCAGCAGTA 58.643 50.000 0.00 0.00 0.00 2.74
1143 1390 2.746279 AGTTGTTGTTCCCCACATCA 57.254 45.000 0.00 0.00 34.43 3.07
1191 1438 0.871722 CGACGCCATTGTGAGGAAAA 59.128 50.000 0.00 0.00 0.00 2.29
1194 1441 1.080093 GTCGACGCCATTGTGAGGA 60.080 57.895 0.00 0.00 0.00 3.71
1266 1513 0.106268 TGGCTTGCTCACCCAAGAAA 60.106 50.000 6.12 0.00 43.79 2.52
1287 1534 6.592220 CCATTCATTCAAAAGCATGTGATCAA 59.408 34.615 0.00 0.00 0.00 2.57
1307 1554 2.746277 ACAACCGAGCCGCCATTC 60.746 61.111 0.00 0.00 0.00 2.67
1321 1568 4.670896 TCACAACTGATCAGACAGACAA 57.329 40.909 29.27 5.43 40.63 3.18
1338 1585 2.030371 TGGACAGCTGCAAATTTCACA 58.970 42.857 15.27 0.63 0.00 3.58
1344 1591 0.892755 CCATGTGGACAGCTGCAAAT 59.107 50.000 15.27 2.04 37.39 2.32
1380 1627 1.451747 GAGAGAGAGGTACGGCGGT 60.452 63.158 13.24 1.39 0.00 5.68
1449 1696 3.406200 ATGGAGGCAGAAGCGGCT 61.406 61.111 0.00 0.00 45.92 5.52
1533 1780 5.237344 ACAGAGTCAGAAATGTTTACAGCAC 59.763 40.000 0.00 0.00 0.00 4.40
1540 1787 7.169158 TGGAAAAACAGAGTCAGAAATGTTT 57.831 32.000 2.50 2.50 45.21 2.83
1619 1879 4.593597 TTCAGTCGAAATTTATGTCCGC 57.406 40.909 0.00 0.00 0.00 5.54
1621 1881 6.852664 ACCAATTCAGTCGAAATTTATGTCC 58.147 36.000 0.00 0.00 34.01 4.02
1649 1912 7.831690 ACAAAATTTCAAATGTACTTGGGGTTT 59.168 29.630 0.00 0.00 0.00 3.27
1687 1950 5.182001 CCACCTAAATTCTTCCAGTGAACAG 59.818 44.000 0.00 0.00 0.00 3.16
1866 2179 1.194121 TTGCTGGCACTAGCTGAGGA 61.194 55.000 7.54 0.00 44.01 3.71
2005 2318 4.373116 GACAGGAAGGCCGACGCA 62.373 66.667 0.00 0.00 39.96 5.24
2182 2495 3.454719 TGAAGCCTGATGGAATGGAAA 57.545 42.857 0.00 0.00 34.57 3.13
2183 2496 3.091545 GTTGAAGCCTGATGGAATGGAA 58.908 45.455 0.00 0.00 34.57 3.53
2184 2497 2.309755 AGTTGAAGCCTGATGGAATGGA 59.690 45.455 0.00 0.00 34.57 3.41
2185 2498 2.686915 GAGTTGAAGCCTGATGGAATGG 59.313 50.000 0.00 0.00 34.57 3.16
2186 2499 3.349927 TGAGTTGAAGCCTGATGGAATG 58.650 45.455 0.00 0.00 34.57 2.67
2187 2500 3.618351 CTGAGTTGAAGCCTGATGGAAT 58.382 45.455 0.00 0.00 34.57 3.01
2544 2861 5.665459 ACTTGGTAGATGTATCAGCTTGAC 58.335 41.667 0.00 0.00 30.76 3.18
2556 2873 8.678593 TCTAGATGTACTGTACTTGGTAGATG 57.321 38.462 17.98 1.90 0.00 2.90
2557 2874 8.496088 ACTCTAGATGTACTGTACTTGGTAGAT 58.504 37.037 17.98 2.40 0.00 1.98
2558 2875 7.859540 ACTCTAGATGTACTGTACTTGGTAGA 58.140 38.462 17.98 16.12 0.00 2.59
2561 2878 6.600032 CAGACTCTAGATGTACTGTACTTGGT 59.400 42.308 17.98 7.85 0.00 3.67
2593 2984 3.489416 GCATGAGCGATGTACGAATTACA 59.511 43.478 0.00 0.00 45.03 2.41
2618 3009 1.876799 CCACGTTACATTCTTGGTGCA 59.123 47.619 0.00 0.00 0.00 4.57
2757 3148 1.279558 GGAAGTCCCAGAAGAGGAACC 59.720 57.143 0.00 0.00 34.43 3.62
2839 3230 2.106332 GTGATCGGGCCGACGAAT 59.894 61.111 33.71 16.39 46.92 3.34
2936 3358 1.834822 CTTGGACCGGCCCCAAAAA 60.835 57.895 23.89 4.02 42.51 1.94
2948 3370 3.756117 AGACCAGGATTTTGACTTGGAC 58.244 45.455 0.00 0.00 37.81 4.02
2963 3385 0.593128 CCACGAAAGGCAAAGACCAG 59.407 55.000 0.00 0.00 0.00 4.00
3041 3463 8.647796 GCCCCAATAGTATGTATATATAGCACA 58.352 37.037 0.00 3.22 0.00 4.57
3042 3464 8.647796 TGCCCCAATAGTATGTATATATAGCAC 58.352 37.037 0.00 0.00 0.00 4.40
3043 3465 8.791298 TGCCCCAATAGTATGTATATATAGCA 57.209 34.615 0.00 0.00 0.00 3.49
3044 3466 9.090103 TCTGCCCCAATAGTATGTATATATAGC 57.910 37.037 0.00 0.00 0.00 2.97
3046 3468 9.945633 TGTCTGCCCCAATAGTATGTATATATA 57.054 33.333 0.00 0.00 0.00 0.86
3047 3469 8.705594 GTGTCTGCCCCAATAGTATGTATATAT 58.294 37.037 0.00 0.00 0.00 0.86
3048 3470 7.676468 TGTGTCTGCCCCAATAGTATGTATATA 59.324 37.037 0.00 0.00 0.00 0.86
3049 3471 6.500400 TGTGTCTGCCCCAATAGTATGTATAT 59.500 38.462 0.00 0.00 0.00 0.86
3050 3472 5.841783 TGTGTCTGCCCCAATAGTATGTATA 59.158 40.000 0.00 0.00 0.00 1.47
3051 3473 4.658435 TGTGTCTGCCCCAATAGTATGTAT 59.342 41.667 0.00 0.00 0.00 2.29
3059 3481 1.064003 AGTGTGTGTCTGCCCCAATA 58.936 50.000 0.00 0.00 0.00 1.90
3095 3517 1.070758 AGGTCAGTGTGCACGAGAATT 59.929 47.619 13.13 0.00 36.20 2.17
3120 3543 9.713684 ATTTTGGATAATTTAGATGGTCTCCAA 57.286 29.630 0.00 0.00 39.18 3.53
3174 3597 5.550232 TGTTGAGCGTCGTCTACTTATAA 57.450 39.130 0.00 0.00 0.00 0.98
3297 3720 1.614903 CAGCCAGAACAATGCTTGGAA 59.385 47.619 2.97 0.00 31.77 3.53
3303 3726 0.244721 GGAACCAGCCAGAACAATGC 59.755 55.000 0.00 0.00 0.00 3.56
3350 3791 1.529244 GTTGGGGCTGCAACAGACT 60.529 57.895 0.50 0.00 39.87 3.24
3351 3792 2.564721 GGTTGGGGCTGCAACAGAC 61.565 63.158 0.50 0.00 39.10 3.51
3352 3793 2.203480 GGTTGGGGCTGCAACAGA 60.203 61.111 0.50 0.00 32.44 3.41
3353 3794 3.305516 GGGTTGGGGCTGCAACAG 61.306 66.667 0.50 0.00 33.31 3.16
3357 3798 2.041508 TTTTGGGTTGGGGCTGCA 60.042 55.556 0.50 0.00 0.00 4.41
3358 3799 2.099652 GACTTTTGGGTTGGGGCTGC 62.100 60.000 0.00 0.00 0.00 5.25
3362 3803 2.971901 ACTAGACTTTTGGGTTGGGG 57.028 50.000 0.00 0.00 0.00 4.96
3408 3849 1.000607 ACGCACGGGCATATGTACTAG 60.001 52.381 11.77 0.00 41.24 2.57
3409 3850 1.034356 ACGCACGGGCATATGTACTA 58.966 50.000 11.77 0.00 41.24 1.82
3410 3851 0.177141 AACGCACGGGCATATGTACT 59.823 50.000 11.77 0.00 41.24 2.73
3411 3852 0.303493 CAACGCACGGGCATATGTAC 59.697 55.000 11.77 0.00 41.24 2.90
3412 3853 1.433053 GCAACGCACGGGCATATGTA 61.433 55.000 11.77 0.00 41.24 2.29
3413 3854 2.760159 GCAACGCACGGGCATATGT 61.760 57.895 11.77 0.00 41.24 2.29
3414 3855 2.024588 GCAACGCACGGGCATATG 59.975 61.111 11.77 6.17 41.24 1.78
3415 3856 2.043405 TTGCAACGCACGGGCATAT 61.043 52.632 11.77 0.00 38.71 1.78
3416 3857 2.669910 TTGCAACGCACGGGCATA 60.670 55.556 11.77 0.00 38.71 3.14
3417 3858 4.341502 GTTGCAACGCACGGGCAT 62.342 61.111 14.90 0.00 38.71 4.40
3460 3901 9.573133 GCTTGCACATATAATTTTCACTAACTT 57.427 29.630 0.00 0.00 0.00 2.66
3461 3902 8.739039 TGCTTGCACATATAATTTTCACTAACT 58.261 29.630 0.00 0.00 0.00 2.24
3462 3903 8.909708 TGCTTGCACATATAATTTTCACTAAC 57.090 30.769 0.00 0.00 0.00 2.34
3463 3904 9.920133 TTTGCTTGCACATATAATTTTCACTAA 57.080 25.926 0.00 0.00 0.00 2.24
3464 3905 9.920133 TTTTGCTTGCACATATAATTTTCACTA 57.080 25.926 0.00 0.00 0.00 2.74
3465 3906 8.711457 GTTTTGCTTGCACATATAATTTTCACT 58.289 29.630 0.00 0.00 0.00 3.41
3466 3907 7.956943 GGTTTTGCTTGCACATATAATTTTCAC 59.043 33.333 0.00 0.00 0.00 3.18
3467 3908 7.118971 GGGTTTTGCTTGCACATATAATTTTCA 59.881 33.333 0.00 0.00 0.00 2.69
3468 3909 7.413988 GGGGTTTTGCTTGCACATATAATTTTC 60.414 37.037 0.00 0.00 0.00 2.29
3469 3910 6.374053 GGGGTTTTGCTTGCACATATAATTTT 59.626 34.615 0.00 0.00 0.00 1.82
3470 3911 5.879777 GGGGTTTTGCTTGCACATATAATTT 59.120 36.000 0.00 0.00 0.00 1.82
3471 3912 5.427378 GGGGTTTTGCTTGCACATATAATT 58.573 37.500 0.00 0.00 0.00 1.40
3472 3913 4.441356 CGGGGTTTTGCTTGCACATATAAT 60.441 41.667 0.00 0.00 0.00 1.28
3473 3914 3.119316 CGGGGTTTTGCTTGCACATATAA 60.119 43.478 0.00 0.00 0.00 0.98
3474 3915 2.425312 CGGGGTTTTGCTTGCACATATA 59.575 45.455 0.00 0.00 0.00 0.86
3475 3916 1.204467 CGGGGTTTTGCTTGCACATAT 59.796 47.619 0.00 0.00 0.00 1.78
3476 3917 0.600557 CGGGGTTTTGCTTGCACATA 59.399 50.000 0.00 0.00 0.00 2.29
3477 3918 1.367102 CGGGGTTTTGCTTGCACAT 59.633 52.632 0.00 0.00 0.00 3.21
3478 3919 2.055042 ACGGGGTTTTGCTTGCACA 61.055 52.632 0.00 0.00 0.00 4.57
3479 3920 1.591327 CACGGGGTTTTGCTTGCAC 60.591 57.895 0.00 0.00 0.00 4.57
3480 3921 2.055042 ACACGGGGTTTTGCTTGCA 61.055 52.632 0.00 0.00 0.00 4.08
3481 3922 1.591327 CACACGGGGTTTTGCTTGC 60.591 57.895 0.00 0.00 0.00 4.01
3482 3923 1.591327 GCACACGGGGTTTTGCTTG 60.591 57.895 0.00 0.00 32.00 4.01
3483 3924 1.398958 ATGCACACGGGGTTTTGCTT 61.399 50.000 0.00 0.00 35.91 3.91
3484 3925 1.832167 ATGCACACGGGGTTTTGCT 60.832 52.632 0.00 0.00 35.91 3.91
3485 3926 1.664333 CATGCACACGGGGTTTTGC 60.664 57.895 0.00 0.00 35.45 3.68
3486 3927 0.597118 CACATGCACACGGGGTTTTG 60.597 55.000 0.00 0.00 0.00 2.44
3487 3928 0.753479 TCACATGCACACGGGGTTTT 60.753 50.000 0.00 0.00 0.00 2.43
3488 3929 0.753479 TTCACATGCACACGGGGTTT 60.753 50.000 0.00 0.00 0.00 3.27
3489 3930 0.753479 TTTCACATGCACACGGGGTT 60.753 50.000 0.00 0.00 0.00 4.11
3490 3931 0.753479 TTTTCACATGCACACGGGGT 60.753 50.000 0.00 0.00 0.00 4.95
3491 3932 0.387202 TTTTTCACATGCACACGGGG 59.613 50.000 0.00 0.00 0.00 5.73
3492 3933 1.602668 CCTTTTTCACATGCACACGGG 60.603 52.381 0.00 0.00 0.00 5.28
3493 3934 1.336440 TCCTTTTTCACATGCACACGG 59.664 47.619 0.00 0.00 0.00 4.94
3494 3935 2.772568 TCCTTTTTCACATGCACACG 57.227 45.000 0.00 0.00 0.00 4.49
3495 3936 3.779759 TGTTCCTTTTTCACATGCACAC 58.220 40.909 0.00 0.00 0.00 3.82
3496 3937 4.669206 ATGTTCCTTTTTCACATGCACA 57.331 36.364 0.00 0.00 29.74 4.57
3497 3938 5.989551 AAATGTTCCTTTTTCACATGCAC 57.010 34.783 0.00 0.00 31.37 4.57
3498 3939 5.695816 GCTAAATGTTCCTTTTTCACATGCA 59.304 36.000 0.00 0.00 31.37 3.96
3499 3940 5.928264 AGCTAAATGTTCCTTTTTCACATGC 59.072 36.000 0.00 0.00 31.37 4.06
3500 3941 7.869429 AGAAGCTAAATGTTCCTTTTTCACATG 59.131 33.333 0.00 0.00 31.37 3.21
3501 3942 7.955918 AGAAGCTAAATGTTCCTTTTTCACAT 58.044 30.769 0.00 0.00 32.31 3.21
3502 3943 7.346751 AGAAGCTAAATGTTCCTTTTTCACA 57.653 32.000 0.00 0.00 0.00 3.58
3503 3944 6.578919 CGAGAAGCTAAATGTTCCTTTTTCAC 59.421 38.462 0.00 0.00 0.00 3.18
3504 3945 6.293955 CCGAGAAGCTAAATGTTCCTTTTTCA 60.294 38.462 0.00 0.00 0.00 2.69
3505 3946 6.086871 CCGAGAAGCTAAATGTTCCTTTTTC 58.913 40.000 0.00 0.00 0.00 2.29
3506 3947 5.535030 ACCGAGAAGCTAAATGTTCCTTTTT 59.465 36.000 0.00 0.00 0.00 1.94
3507 3948 5.070685 ACCGAGAAGCTAAATGTTCCTTTT 58.929 37.500 0.00 0.00 0.00 2.27
3508 3949 4.652822 ACCGAGAAGCTAAATGTTCCTTT 58.347 39.130 0.00 0.00 0.00 3.11
3509 3950 4.287766 ACCGAGAAGCTAAATGTTCCTT 57.712 40.909 0.00 0.00 0.00 3.36
3510 3951 3.983044 ACCGAGAAGCTAAATGTTCCT 57.017 42.857 0.00 0.00 0.00 3.36
3511 3952 5.154222 CAAAACCGAGAAGCTAAATGTTCC 58.846 41.667 0.00 0.00 0.00 3.62
3512 3953 4.617223 GCAAAACCGAGAAGCTAAATGTTC 59.383 41.667 0.00 0.00 0.00 3.18
3513 3954 4.546570 GCAAAACCGAGAAGCTAAATGTT 58.453 39.130 0.00 0.00 0.00 2.71
3514 3955 3.057526 GGCAAAACCGAGAAGCTAAATGT 60.058 43.478 0.00 0.00 0.00 2.71
3515 3956 3.501950 GGCAAAACCGAGAAGCTAAATG 58.498 45.455 0.00 0.00 0.00 2.32
3516 3957 3.850122 GGCAAAACCGAGAAGCTAAAT 57.150 42.857 0.00 0.00 0.00 1.40
3528 3969 1.362355 CTTCACACCCGGCAAAACC 59.638 57.895 0.00 0.00 0.00 3.27
3529 3970 1.310904 TACTTCACACCCGGCAAAAC 58.689 50.000 0.00 0.00 0.00 2.43
3530 3971 2.054232 TTACTTCACACCCGGCAAAA 57.946 45.000 0.00 0.00 0.00 2.44
3531 3972 2.156098 GATTACTTCACACCCGGCAAA 58.844 47.619 0.00 0.00 0.00 3.68
3532 3973 1.072489 TGATTACTTCACACCCGGCAA 59.928 47.619 0.00 0.00 0.00 4.52
3533 3974 0.687920 TGATTACTTCACACCCGGCA 59.312 50.000 0.00 0.00 0.00 5.69
3534 3975 1.816074 TTGATTACTTCACACCCGGC 58.184 50.000 0.00 0.00 32.84 6.13
3535 3976 2.943033 GGATTGATTACTTCACACCCGG 59.057 50.000 0.00 0.00 32.84 5.73
3536 3977 2.607635 CGGATTGATTACTTCACACCCG 59.392 50.000 0.00 0.00 35.72 5.28
3537 3978 3.606687 ACGGATTGATTACTTCACACCC 58.393 45.455 0.00 0.00 32.84 4.61
3538 3979 6.920569 ATAACGGATTGATTACTTCACACC 57.079 37.500 0.00 0.00 32.84 4.16
3539 3980 9.620660 AAAAATAACGGATTGATTACTTCACAC 57.379 29.630 0.00 0.00 32.84 3.82
3577 4018 9.630098 ACGTACAAAACTCTTAAATATTCTCGA 57.370 29.630 0.00 0.00 0.00 4.04
3587 4028 8.213812 GCGTACAATAACGTACAAAACTCTTAA 58.786 33.333 0.00 0.00 44.64 1.85
3588 4029 7.148820 GGCGTACAATAACGTACAAAACTCTTA 60.149 37.037 0.00 0.00 44.64 2.10
3589 4030 6.346838 GGCGTACAATAACGTACAAAACTCTT 60.347 38.462 0.00 0.00 44.64 2.85
3590 4031 5.119125 GGCGTACAATAACGTACAAAACTCT 59.881 40.000 0.00 0.00 44.64 3.24
3591 4032 5.107530 TGGCGTACAATAACGTACAAAACTC 60.108 40.000 0.00 0.00 44.64 3.01
3592 4033 4.749099 TGGCGTACAATAACGTACAAAACT 59.251 37.500 0.00 0.00 44.64 2.66
3593 4034 5.016275 TGGCGTACAATAACGTACAAAAC 57.984 39.130 0.00 0.00 44.64 2.43
3594 4035 5.859521 ATGGCGTACAATAACGTACAAAA 57.140 34.783 0.00 0.00 44.64 2.44
3595 4036 6.328714 TCTATGGCGTACAATAACGTACAAA 58.671 36.000 0.00 0.00 44.64 2.83
3596 4037 5.889219 TCTATGGCGTACAATAACGTACAA 58.111 37.500 0.00 0.00 44.64 2.41
3597 4038 5.497635 TCTATGGCGTACAATAACGTACA 57.502 39.130 0.00 0.00 44.64 2.90
3598 4039 5.400485 CCTTCTATGGCGTACAATAACGTAC 59.600 44.000 0.00 0.00 44.64 3.67
3599 4040 5.522456 CCTTCTATGGCGTACAATAACGTA 58.478 41.667 0.00 0.00 44.64 3.57
3600 4041 4.365723 CCTTCTATGGCGTACAATAACGT 58.634 43.478 0.00 0.00 44.64 3.99
3601 4042 3.183775 GCCTTCTATGGCGTACAATAACG 59.816 47.826 0.00 0.00 43.74 3.18
3602 4043 4.727235 GCCTTCTATGGCGTACAATAAC 57.273 45.455 0.00 0.00 43.74 1.89
3635 4076 8.721478 CCTCGATTGAAAGAAAAAGTAGATTGA 58.279 33.333 0.00 0.00 0.00 2.57
3636 4077 8.721478 TCCTCGATTGAAAGAAAAAGTAGATTG 58.279 33.333 0.00 0.00 0.00 2.67
3637 4078 8.848474 TCCTCGATTGAAAGAAAAAGTAGATT 57.152 30.769 0.00 0.00 0.00 2.40
3638 4079 8.314751 TCTCCTCGATTGAAAGAAAAAGTAGAT 58.685 33.333 0.00 0.00 0.00 1.98
3639 4080 7.599245 GTCTCCTCGATTGAAAGAAAAAGTAGA 59.401 37.037 0.00 0.00 0.00 2.59
3640 4081 7.600752 AGTCTCCTCGATTGAAAGAAAAAGTAG 59.399 37.037 0.00 0.00 0.00 2.57
3641 4082 7.442656 AGTCTCCTCGATTGAAAGAAAAAGTA 58.557 34.615 0.00 0.00 0.00 2.24
3642 4083 6.292150 AGTCTCCTCGATTGAAAGAAAAAGT 58.708 36.000 0.00 0.00 0.00 2.66
3643 4084 6.793492 AGTCTCCTCGATTGAAAGAAAAAG 57.207 37.500 0.00 0.00 0.00 2.27
3644 4085 7.568199 AAAGTCTCCTCGATTGAAAGAAAAA 57.432 32.000 0.00 0.00 0.00 1.94
3645 4086 7.568199 AAAAGTCTCCTCGATTGAAAGAAAA 57.432 32.000 0.00 0.00 0.00 2.29
3646 4087 8.671384 TTAAAAGTCTCCTCGATTGAAAGAAA 57.329 30.769 0.00 0.00 0.00 2.52
3647 4088 7.387948 CCTTAAAAGTCTCCTCGATTGAAAGAA 59.612 37.037 0.00 0.00 0.00 2.52
3648 4089 6.874134 CCTTAAAAGTCTCCTCGATTGAAAGA 59.126 38.462 0.00 0.00 0.00 2.52
3649 4090 6.651225 ACCTTAAAAGTCTCCTCGATTGAAAG 59.349 38.462 0.00 0.00 0.00 2.62
3650 4091 6.531021 ACCTTAAAAGTCTCCTCGATTGAAA 58.469 36.000 0.00 0.00 0.00 2.69
3651 4092 6.110411 ACCTTAAAAGTCTCCTCGATTGAA 57.890 37.500 0.00 0.00 0.00 2.69
3652 4093 5.740290 ACCTTAAAAGTCTCCTCGATTGA 57.260 39.130 0.00 0.00 0.00 2.57
3653 4094 7.265673 TCATACCTTAAAAGTCTCCTCGATTG 58.734 38.462 0.00 0.00 0.00 2.67
3654 4095 7.419711 TCATACCTTAAAAGTCTCCTCGATT 57.580 36.000 0.00 0.00 0.00 3.34
3655 4096 7.124448 ACTTCATACCTTAAAAGTCTCCTCGAT 59.876 37.037 0.00 0.00 0.00 3.59
3656 4097 6.436532 ACTTCATACCTTAAAAGTCTCCTCGA 59.563 38.462 0.00 0.00 0.00 4.04
3657 4098 6.631962 ACTTCATACCTTAAAAGTCTCCTCG 58.368 40.000 0.00 0.00 0.00 4.63
3658 4099 8.850007 AAACTTCATACCTTAAAAGTCTCCTC 57.150 34.615 0.00 0.00 30.99 3.71
3659 4100 8.661345 AGAAACTTCATACCTTAAAAGTCTCCT 58.339 33.333 0.00 0.00 30.99 3.69
3660 4101 8.722394 CAGAAACTTCATACCTTAAAAGTCTCC 58.278 37.037 0.00 0.00 30.99 3.71
3661 4102 9.490379 TCAGAAACTTCATACCTTAAAAGTCTC 57.510 33.333 0.00 0.00 30.99 3.36
3662 4103 9.847224 TTCAGAAACTTCATACCTTAAAAGTCT 57.153 29.630 0.00 0.00 30.99 3.24
3671 4112 9.838339 CCTACAATATTCAGAAACTTCATACCT 57.162 33.333 0.00 0.00 0.00 3.08
3672 4113 9.832445 TCCTACAATATTCAGAAACTTCATACC 57.168 33.333 0.00 0.00 0.00 2.73
3676 4117 9.567776 TGTTTCCTACAATATTCAGAAACTTCA 57.432 29.630 19.52 6.96 42.12 3.02
3679 4120 9.739276 TCATGTTTCCTACAATATTCAGAAACT 57.261 29.630 19.52 10.04 42.12 2.66
3682 4123 8.956426 GGTTCATGTTTCCTACAATATTCAGAA 58.044 33.333 0.00 0.00 40.89 3.02
3683 4124 8.106462 TGGTTCATGTTTCCTACAATATTCAGA 58.894 33.333 0.00 0.00 40.89 3.27
3684 4125 8.279970 TGGTTCATGTTTCCTACAATATTCAG 57.720 34.615 0.00 0.00 40.89 3.02
3685 4126 8.821686 ATGGTTCATGTTTCCTACAATATTCA 57.178 30.769 0.00 0.00 40.89 2.57
3694 4135 9.936759 GGATTTAAAAATGGTTCATGTTTCCTA 57.063 29.630 0.00 0.00 33.82 2.94
3695 4136 8.659527 AGGATTTAAAAATGGTTCATGTTTCCT 58.340 29.630 0.00 0.00 33.82 3.36
3696 4137 8.846943 AGGATTTAAAAATGGTTCATGTTTCC 57.153 30.769 0.00 0.00 33.82 3.13
3756 4197 9.393512 TGTTTCCATTTCAAATTTTGTTCTCAT 57.606 25.926 8.89 0.00 0.00 2.90
3757 4198 8.783833 TGTTTCCATTTCAAATTTTGTTCTCA 57.216 26.923 8.89 0.00 0.00 3.27
3758 4199 9.868389 GATGTTTCCATTTCAAATTTTGTTCTC 57.132 29.630 8.89 0.00 0.00 2.87
3759 4200 9.617523 AGATGTTTCCATTTCAAATTTTGTTCT 57.382 25.926 8.89 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.