Multiple sequence alignment - TraesCS4B01G335000

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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 TraesCS4B01G335000 chr4B 100.000 2706 0 0 698 3403 625983626 625986331 0.000000e+00 4998.0
1 TraesCS4B01G335000 chr4B 100.000 344 0 0 1 344 625982929 625983272 1.330000e-178 636.0
2 TraesCS4B01G335000 chr3D 94.784 2454 103 9 701 3135 564303848 564301401 0.000000e+00 3799.0
3 TraesCS4B01G335000 chr3D 94.544 2456 109 13 701 3135 301439100 301436649 0.000000e+00 3770.0
4 TraesCS4B01G335000 chr3D 93.858 2426 119 15 717 3135 31719074 31721476 0.000000e+00 3627.0
5 TraesCS4B01G335000 chr3D 93.353 331 20 1 12 342 41141429 41141101 3.950000e-134 488.0
6 TraesCS4B01G335000 chr3D 93.750 320 20 0 12 331 25538709 25538390 6.600000e-132 481.0
7 TraesCS4B01G335000 chr3D 92.332 313 24 0 12 324 301439894 301439582 2.410000e-121 446.0
8 TraesCS4B01G335000 chr2D 94.608 2448 114 10 698 3135 36681844 36684283 0.000000e+00 3773.0
9 TraesCS4B01G335000 chr2D 94.209 2452 103 16 701 3135 5707768 5705339 0.000000e+00 3705.0
10 TraesCS4B01G335000 chr6D 94.519 2463 100 16 701 3135 24841055 24838600 0.000000e+00 3768.0
11 TraesCS4B01G335000 chr6D 92.145 331 18 1 12 342 450673602 450673280 8.600000e-126 460.0
12 TraesCS4B01G335000 chr6D 92.652 313 20 3 12 324 38577389 38577698 6.700000e-122 448.0
13 TraesCS4B01G335000 chr6D 89.489 352 17 2 11 342 24841454 24841103 8.730000e-116 427.0
14 TraesCS4B01G335000 chr6D 95.131 267 12 1 12 277 90888544 90888278 1.460000e-113 420.0
15 TraesCS4B01G335000 chr6D 95.652 92 4 0 12 103 38582524 38582615 7.610000e-32 148.0
16 TraesCS4B01G335000 chr6D 94.737 95 5 0 12 106 90883731 90883637 7.610000e-32 148.0
17 TraesCS4B01G335000 chr7D 95.105 2390 101 9 752 3135 496104921 496102542 0.000000e+00 3751.0
18 TraesCS4B01G335000 chr7D 95.004 2302 102 7 840 3135 23676160 23678454 0.000000e+00 3602.0
19 TraesCS4B01G335000 chr7D 94.062 320 18 1 12 331 23675449 23675767 5.110000e-133 484.0
20 TraesCS4B01G335000 chr7D 93.272 327 22 0 12 338 496105656 496105330 1.840000e-132 483.0
21 TraesCS4B01G335000 chrUn 94.142 2458 112 20 701 3135 101051987 101049539 0.000000e+00 3712.0
22 TraesCS4B01G335000 chrUn 100.000 269 0 0 3135 3403 339466317 339466585 6.560000e-137 497.0
23 TraesCS4B01G335000 chrUn 100.000 267 0 0 3137 3403 356965696 356965430 8.480000e-136 494.0
24 TraesCS4B01G335000 chrUn 93.072 332 21 2 11 342 96240642 96240313 5.110000e-133 484.0
25 TraesCS4B01G335000 chrUn 89.625 347 16 2 12 338 101052843 101052497 1.130000e-114 424.0
26 TraesCS4B01G335000 chrUn 84.615 156 15 9 30 183 88588667 88588519 2.740000e-31 147.0
27 TraesCS4B01G335000 chrUn 94.737 95 3 1 12 106 96235416 96235324 2.740000e-31 147.0
28 TraesCS4B01G335000 chr1D 94.120 2449 108 16 698 3135 226462746 226465169 0.000000e+00 3692.0
29 TraesCS4B01G335000 chr1D 95.255 2318 99 5 824 3135 452230120 452232432 0.000000e+00 3661.0
30 TraesCS4B01G335000 chr1D 93.656 331 21 0 12 342 456923922 456923592 2.360000e-136 496.0
31 TraesCS4B01G335000 chr1D 93.656 331 21 0 12 342 470880757 470880427 2.360000e-136 496.0
32 TraesCS4B01G335000 chr1D 97.308 260 7 0 12 271 452229529 452229788 3.120000e-120 442.0
33 TraesCS4B01G335000 chr1D 89.318 337 15 3 12 328 495121262 495120927 1.470000e-108 403.0
34 TraesCS4B01G335000 chr1D 93.333 45 3 0 294 338 452229784 452229828 2.190000e-07 67.6
35 TraesCS4B01G335000 chr3A 93.261 2404 138 11 748 3135 514267293 514264898 0.000000e+00 3520.0
36 TraesCS4B01G335000 chr3A 99.635 274 1 0 3130 3403 253651502 253651775 5.070000e-138 501.0
37 TraesCS4B01G335000 chr7A 100.000 270 0 0 3134 3403 353732824 353732555 1.820000e-137 499.0
38 TraesCS4B01G335000 chr1B 100.000 269 0 0 3135 3403 510281099 510281367 6.560000e-137 497.0
39 TraesCS4B01G335000 chr1A 100.000 269 0 0 3135 3403 426332183 426332451 6.560000e-137 497.0
40 TraesCS4B01G335000 chr4A 97.887 284 5 1 3121 3403 348259201 348259484 1.100000e-134 490.0
41 TraesCS4B01G335000 chr4A 98.561 278 3 1 3126 3403 494561212 494561488 1.100000e-134 490.0
42 TraesCS4B01G335000 chr5B 99.625 267 1 0 3137 3403 98460473 98460207 3.950000e-134 488.0
43 TraesCS4B01G335000 chr4D 91.803 305 16 6 30 329 502875940 502876240 1.890000e-112 416.0
44 TraesCS4B01G335000 chr5D 92.150 293 18 5 38 329 297757756 297758044 3.160000e-110 409.0


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 TraesCS4B01G335000 chr4B 625982929 625986331 3402 False 2817.0 4998 100.000000 1 3403 2 chr4B.!!$F1 3402
1 TraesCS4B01G335000 chr3D 564301401 564303848 2447 True 3799.0 3799 94.784000 701 3135 1 chr3D.!!$R3 2434
2 TraesCS4B01G335000 chr3D 31719074 31721476 2402 False 3627.0 3627 93.858000 717 3135 1 chr3D.!!$F1 2418
3 TraesCS4B01G335000 chr3D 301436649 301439894 3245 True 2108.0 3770 93.438000 12 3135 2 chr3D.!!$R4 3123
4 TraesCS4B01G335000 chr2D 36681844 36684283 2439 False 3773.0 3773 94.608000 698 3135 1 chr2D.!!$F1 2437
5 TraesCS4B01G335000 chr2D 5705339 5707768 2429 True 3705.0 3705 94.209000 701 3135 1 chr2D.!!$R1 2434
6 TraesCS4B01G335000 chr6D 24838600 24841454 2854 True 2097.5 3768 92.004000 11 3135 2 chr6D.!!$R4 3124
7 TraesCS4B01G335000 chr7D 496102542 496105656 3114 True 2117.0 3751 94.188500 12 3135 2 chr7D.!!$R1 3123
8 TraesCS4B01G335000 chr7D 23675449 23678454 3005 False 2043.0 3602 94.533000 12 3135 2 chr7D.!!$F1 3123
9 TraesCS4B01G335000 chrUn 101049539 101052843 3304 True 2068.0 3712 91.883500 12 3135 2 chrUn.!!$R5 3123
10 TraesCS4B01G335000 chr1D 226462746 226465169 2423 False 3692.0 3692 94.120000 698 3135 1 chr1D.!!$F1 2437
11 TraesCS4B01G335000 chr1D 452229529 452232432 2903 False 1390.2 3661 95.298667 12 3135 3 chr1D.!!$F2 3123
12 TraesCS4B01G335000 chr3A 514264898 514267293 2395 True 3520.0 3520 93.261000 748 3135 1 chr3A.!!$R1 2387

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
872 1205 1.476007 CCCGATCTGGATCAGGGTCC 61.476 65.0 21.24 0.0 41.95 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2510 2873 0.745845 GTGACCAAGGCGATGATGCT 60.746 55.0 0.0 0.0 34.52 3.79 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
43 44 9.672673 ATGTGTATAGTCTTTCTTGCACTTTAT 57.327 29.630 0.00 0.00 0.00 1.40
342 363 4.477975 CGGCCGAGGTCTGTCGTC 62.478 72.222 24.07 0.00 38.32 4.20
835 1040 4.320456 CCATCGGGGCTGGATCGG 62.320 72.222 0.00 0.00 35.70 4.18
872 1205 1.476007 CCCGATCTGGATCAGGGTCC 61.476 65.000 21.24 0.00 41.95 4.46
942 1286 1.822990 TCTTCTTCGGGCTATGTCGTT 59.177 47.619 0.00 0.00 0.00 3.85
949 1293 1.674817 CGGGCTATGTCGTTGTTCCTT 60.675 52.381 0.00 0.00 0.00 3.36
967 1311 2.289882 CCTTGGTGCTCAGTGATCTTCA 60.290 50.000 0.00 0.00 0.00 3.02
1004 1348 1.523154 GAGTTTGCGGGGTTCATGCA 61.523 55.000 0.00 0.00 36.72 3.96
1011 1355 1.887956 GCGGGGTTCATGCATATCCAT 60.888 52.381 0.00 0.00 0.00 3.41
1068 1422 3.637273 GTCCCCTGTCCGCCTTGT 61.637 66.667 0.00 0.00 0.00 3.16
1070 1424 3.636231 CCCCTGTCCGCCTTGTCA 61.636 66.667 0.00 0.00 0.00 3.58
1075 1429 1.338674 CCTGTCCGCCTTGTCATGTTA 60.339 52.381 0.00 0.00 0.00 2.41
1134 1488 1.077930 TGCTGATGCTTCTCAGGCC 60.078 57.895 0.00 0.00 42.42 5.19
1169 1523 2.363680 CCAAGGCTCTCGATGATACTGT 59.636 50.000 0.00 0.00 0.00 3.55
1328 1682 1.254975 TTCGCCTCGGAGTTCATGGA 61.255 55.000 4.02 0.00 0.00 3.41
1410 1764 4.790718 TGCTCTCTACCTATCTGTGGTA 57.209 45.455 0.00 0.00 38.88 3.25
1548 1902 1.334689 CGTTGCTGTCAGACTACACGA 60.335 52.381 3.32 0.00 0.00 4.35
1688 2042 1.671742 TTCGTGCTGAAGAGACCCC 59.328 57.895 0.00 0.00 31.44 4.95
1714 2074 2.938838 CTGGGTTACTTGTGGTTCCAA 58.061 47.619 0.00 0.00 0.00 3.53
1717 2077 3.227614 GGGTTACTTGTGGTTCCAACAT 58.772 45.455 0.00 0.00 0.00 2.71
1758 2118 4.007644 CCACCTGCTCGCCTCACA 62.008 66.667 0.00 0.00 0.00 3.58
1860 2222 0.037734 TCTGTGGGTACTGCTCTCGA 59.962 55.000 0.00 0.00 0.00 4.04
1899 2261 0.320771 ATTGCCGTGAGAAGAAGCGT 60.321 50.000 0.00 0.00 0.00 5.07
1938 2300 0.618680 CCAGTGGGACTCCTGGATCA 60.619 60.000 0.00 0.00 46.22 2.92
2140 2502 4.543590 ATGTCTTCTGATTCTTCCGTGT 57.456 40.909 0.00 0.00 0.00 4.49
2157 2519 0.596577 TGTTGTCTTCTCTCCGACCG 59.403 55.000 0.00 0.00 0.00 4.79
2183 2545 7.624360 TTGATTCGCCTGTTAATGTTCTTAT 57.376 32.000 0.00 0.00 0.00 1.73
2231 2593 0.693049 AGCCGTGGTCTTCTTTCCAT 59.307 50.000 0.00 0.00 36.09 3.41
2248 2611 8.021898 TCTTTCCATTCCATCTTTTTCTGTTT 57.978 30.769 0.00 0.00 0.00 2.83
2283 2646 0.036388 TTCCTCGCCTCACCATGAAC 60.036 55.000 0.00 0.00 0.00 3.18
2320 2683 4.827284 CCCAACTTACTGATTCTGGTTGTT 59.173 41.667 0.00 0.00 34.22 2.83
2345 2708 5.869888 GTGTCATTCTTGATACCGACTCTTT 59.130 40.000 0.00 0.00 37.86 2.52
2389 2752 2.501602 GCTTTGGTTGGTGCTGGCT 61.502 57.895 0.00 0.00 0.00 4.75
2456 2819 2.905996 TTCCTTCCGCTGCCACCAT 61.906 57.895 0.00 0.00 0.00 3.55
2505 2868 0.319555 CTTCGTCTGCGTCCTTCCAA 60.320 55.000 0.00 0.00 39.49 3.53
2510 2873 1.000506 GTCTGCGTCCTTCCAACAGTA 59.999 52.381 0.00 0.00 0.00 2.74
2530 2893 1.718757 GCATCATCGCCTTGGTCACC 61.719 60.000 0.00 0.00 0.00 4.02
2536 2899 1.855295 TCGCCTTGGTCACCTATGTA 58.145 50.000 0.00 0.00 0.00 2.29
2571 2934 2.811410 TCTTTAGTTCGTCAGGGCCTA 58.189 47.619 5.28 0.00 0.00 3.93
2670 3033 4.950475 CCTACCAGTGAGTCAGTATCTCAA 59.050 45.833 0.00 0.00 42.42 3.02
2693 3056 7.711772 TCAACGTCCTTTTGACTTAGTTCATTA 59.288 33.333 0.00 0.00 42.13 1.90
2790 3153 2.163815 TCGCTACACTTGGCTCTACTTC 59.836 50.000 0.00 0.00 0.00 3.01
2856 3219 1.247567 CCATGGTTCACACCCAGTTC 58.752 55.000 2.57 0.00 43.49 3.01
2871 3234 2.435938 TTCTCCACGCCCATTCGC 60.436 61.111 0.00 0.00 0.00 4.70
2882 3245 0.591170 CCCATTCGCACTTTTCGTGT 59.409 50.000 0.00 0.00 45.57 4.49
2956 3319 1.741770 GGTACTCTTGCCCAGTGCG 60.742 63.158 0.00 0.00 45.60 5.34
3018 3381 5.636121 ACGTAAGCATCGTCATTTACTTGAA 59.364 36.000 0.00 0.00 45.62 2.69
3026 3389 3.185594 CGTCATTTACTTGAAACGGCTCA 59.814 43.478 0.00 0.00 0.00 4.26
3053 3416 0.543277 ATGATTGCCGCTTCTCTCCA 59.457 50.000 0.00 0.00 0.00 3.86
3060 3424 1.376037 CGCTTCTCTCCAACCCCAC 60.376 63.158 0.00 0.00 0.00 4.61
3135 3499 3.315544 TGCTCTGCAGGGTGGTATA 57.684 52.632 16.66 0.00 33.32 1.47
3136 3500 1.806496 TGCTCTGCAGGGTGGTATAT 58.194 50.000 16.66 0.00 33.32 0.86
3137 3501 2.970987 TGCTCTGCAGGGTGGTATATA 58.029 47.619 16.66 0.00 33.32 0.86
3138 3502 3.313791 TGCTCTGCAGGGTGGTATATAA 58.686 45.455 16.66 0.00 33.32 0.98
3139 3503 3.071023 TGCTCTGCAGGGTGGTATATAAC 59.929 47.826 16.66 0.00 33.32 1.89
3140 3504 3.861131 GCTCTGCAGGGTGGTATATAACG 60.861 52.174 16.66 0.00 0.00 3.18
3141 3505 2.036733 TCTGCAGGGTGGTATATAACGC 59.963 50.000 15.13 2.52 0.00 4.84
3142 3506 1.071071 TGCAGGGTGGTATATAACGCC 59.929 52.381 20.33 20.33 0.00 5.68
3143 3507 1.609841 GCAGGGTGGTATATAACGCCC 60.610 57.143 33.81 33.81 41.66 6.13
3144 3508 2.410790 AGGGTGGTATATAACGCCCT 57.589 50.000 36.63 36.63 44.67 5.19
3145 3509 2.028385 CAGGGTGGTATATAACGCCCTC 60.028 54.545 38.52 20.24 45.71 4.30
3146 3510 1.067354 GGGTGGTATATAACGCCCTCG 60.067 57.143 33.59 0.00 39.54 4.63
3147 3511 1.888512 GGTGGTATATAACGCCCTCGA 59.111 52.381 18.19 0.00 39.41 4.04
3148 3512 2.494870 GGTGGTATATAACGCCCTCGAT 59.505 50.000 18.19 0.00 39.41 3.59
3149 3513 3.508762 GTGGTATATAACGCCCTCGATG 58.491 50.000 0.00 0.00 39.41 3.84
3150 3514 2.094390 TGGTATATAACGCCCTCGATGC 60.094 50.000 0.00 0.00 39.41 3.91
3157 3521 2.970639 GCCCTCGATGCGGCTATA 59.029 61.111 10.26 0.00 42.21 1.31
3158 3522 1.517832 GCCCTCGATGCGGCTATAT 59.482 57.895 10.26 0.00 42.21 0.86
3159 3523 0.528684 GCCCTCGATGCGGCTATATC 60.529 60.000 10.26 0.00 42.21 1.63
3160 3524 1.107114 CCCTCGATGCGGCTATATCT 58.893 55.000 0.00 0.00 0.00 1.98
3161 3525 1.066303 CCCTCGATGCGGCTATATCTC 59.934 57.143 0.00 0.00 0.00 2.75
3162 3526 1.066303 CCTCGATGCGGCTATATCTCC 59.934 57.143 0.00 0.00 0.00 3.71
3163 3527 1.066303 CTCGATGCGGCTATATCTCCC 59.934 57.143 0.00 0.00 0.00 4.30
3164 3528 0.817654 CGATGCGGCTATATCTCCCA 59.182 55.000 0.00 0.00 0.00 4.37
3165 3529 1.469940 CGATGCGGCTATATCTCCCAC 60.470 57.143 0.00 0.00 0.00 4.61
3166 3530 0.532573 ATGCGGCTATATCTCCCACG 59.467 55.000 0.00 0.00 0.00 4.94
3167 3531 0.826256 TGCGGCTATATCTCCCACGT 60.826 55.000 0.00 0.00 0.00 4.49
3168 3532 0.388649 GCGGCTATATCTCCCACGTG 60.389 60.000 9.08 9.08 0.00 4.49
3169 3533 0.959553 CGGCTATATCTCCCACGTGT 59.040 55.000 15.65 0.00 0.00 4.49
3170 3534 1.068472 CGGCTATATCTCCCACGTGTC 60.068 57.143 15.65 0.00 0.00 3.67
3171 3535 1.068472 GGCTATATCTCCCACGTGTCG 60.068 57.143 15.65 4.04 0.00 4.35
3172 3536 1.878088 GCTATATCTCCCACGTGTCGA 59.122 52.381 15.65 8.55 0.00 4.20
3173 3537 2.292569 GCTATATCTCCCACGTGTCGAA 59.707 50.000 15.65 0.00 0.00 3.71
3174 3538 3.609644 GCTATATCTCCCACGTGTCGAAG 60.610 52.174 15.65 6.13 0.00 3.79
3175 3539 0.454600 TATCTCCCACGTGTCGAAGC 59.545 55.000 15.65 0.00 0.00 3.86
3176 3540 1.532604 ATCTCCCACGTGTCGAAGCA 61.533 55.000 15.65 0.00 0.00 3.91
3177 3541 2.022129 CTCCCACGTGTCGAAGCAC 61.022 63.158 15.65 0.00 36.12 4.40
3188 3552 0.170561 TCGAAGCACGACTTAGAGGC 59.829 55.000 2.09 0.00 46.45 4.70
3189 3553 0.109272 CGAAGCACGACTTAGAGGCA 60.109 55.000 0.00 0.00 45.77 4.75
3190 3554 1.469940 CGAAGCACGACTTAGAGGCAT 60.470 52.381 0.00 0.00 45.77 4.40
3191 3555 2.223502 CGAAGCACGACTTAGAGGCATA 60.224 50.000 0.00 0.00 45.77 3.14
3192 3556 3.733988 CGAAGCACGACTTAGAGGCATAA 60.734 47.826 0.00 0.00 45.77 1.90
3193 3557 3.166489 AGCACGACTTAGAGGCATAAC 57.834 47.619 0.00 0.00 0.00 1.89
3194 3558 2.159085 AGCACGACTTAGAGGCATAACC 60.159 50.000 0.00 0.00 39.61 2.85
3195 3559 2.460918 CACGACTTAGAGGCATAACCG 58.539 52.381 0.00 0.00 46.52 4.44
3196 3560 1.202382 ACGACTTAGAGGCATAACCGC 60.202 52.381 0.00 0.00 46.52 5.68
3197 3561 1.202371 CGACTTAGAGGCATAACCGCA 60.202 52.381 0.00 0.00 46.52 5.69
3198 3562 2.545952 CGACTTAGAGGCATAACCGCAT 60.546 50.000 0.00 0.00 46.52 4.73
3199 3563 3.467803 GACTTAGAGGCATAACCGCATT 58.532 45.455 0.00 0.00 46.52 3.56
3200 3564 3.206150 ACTTAGAGGCATAACCGCATTG 58.794 45.455 0.00 0.00 46.52 2.82
3201 3565 3.118408 ACTTAGAGGCATAACCGCATTGA 60.118 43.478 0.00 0.00 46.52 2.57
3202 3566 2.418368 AGAGGCATAACCGCATTGAA 57.582 45.000 0.00 0.00 46.52 2.69
3203 3567 2.722094 AGAGGCATAACCGCATTGAAA 58.278 42.857 0.00 0.00 46.52 2.69
3204 3568 2.684881 AGAGGCATAACCGCATTGAAAG 59.315 45.455 0.00 0.00 46.52 2.62
3205 3569 1.134946 AGGCATAACCGCATTGAAAGC 59.865 47.619 0.00 0.00 46.52 3.51
3206 3570 1.135141 GGCATAACCGCATTGAAAGCA 60.135 47.619 0.00 0.00 0.00 3.91
3207 3571 2.605030 GCATAACCGCATTGAAAGCAA 58.395 42.857 0.00 0.00 38.60 3.91
3208 3572 3.189285 GCATAACCGCATTGAAAGCAAT 58.811 40.909 0.00 0.00 45.33 3.56
3217 3581 3.648339 ATTGAAAGCAATGTCGCAAGT 57.352 38.095 0.00 0.00 42.91 3.16
3218 3582 2.404265 TGAAAGCAATGTCGCAAGTG 57.596 45.000 0.00 0.00 39.48 3.16
3219 3583 1.946081 TGAAAGCAATGTCGCAAGTGA 59.054 42.857 0.00 0.00 39.48 3.41
3220 3584 2.031769 TGAAAGCAATGTCGCAAGTGAG 60.032 45.455 0.00 0.00 39.48 3.51
3221 3585 0.877071 AAGCAATGTCGCAAGTGAGG 59.123 50.000 0.00 0.00 39.48 3.86
3222 3586 0.250467 AGCAATGTCGCAAGTGAGGT 60.250 50.000 0.00 0.00 39.48 3.85
3223 3587 1.001974 AGCAATGTCGCAAGTGAGGTA 59.998 47.619 0.00 0.00 39.48 3.08
3224 3588 1.804151 GCAATGTCGCAAGTGAGGTAA 59.196 47.619 0.00 0.00 39.48 2.85
3225 3589 2.420022 GCAATGTCGCAAGTGAGGTAAT 59.580 45.455 0.00 0.00 39.48 1.89
3226 3590 3.485877 GCAATGTCGCAAGTGAGGTAATC 60.486 47.826 0.00 0.00 39.48 1.75
3227 3591 3.895232 ATGTCGCAAGTGAGGTAATCT 57.105 42.857 0.00 0.00 39.48 2.40
3228 3592 3.678056 TGTCGCAAGTGAGGTAATCTT 57.322 42.857 0.00 0.00 39.48 2.40
3229 3593 3.585862 TGTCGCAAGTGAGGTAATCTTC 58.414 45.455 0.00 0.00 39.48 2.87
3230 3594 3.006430 TGTCGCAAGTGAGGTAATCTTCA 59.994 43.478 0.00 0.00 39.48 3.02
3231 3595 3.368236 GTCGCAAGTGAGGTAATCTTCAC 59.632 47.826 2.97 2.97 46.51 3.18
3238 3602 3.751698 GTGAGGTAATCTTCACACAACCC 59.248 47.826 5.78 0.00 45.79 4.11
3239 3603 3.392947 TGAGGTAATCTTCACACAACCCA 59.607 43.478 0.00 0.00 0.00 4.51
3240 3604 4.042809 TGAGGTAATCTTCACACAACCCAT 59.957 41.667 0.00 0.00 0.00 4.00
3241 3605 4.335416 AGGTAATCTTCACACAACCCATG 58.665 43.478 0.00 0.00 0.00 3.66
3242 3606 4.079253 GGTAATCTTCACACAACCCATGT 58.921 43.478 0.00 0.00 45.34 3.21
3243 3607 5.013704 AGGTAATCTTCACACAACCCATGTA 59.986 40.000 0.00 0.00 41.46 2.29
3244 3608 5.708230 GGTAATCTTCACACAACCCATGTAA 59.292 40.000 0.00 0.00 41.46 2.41
3245 3609 6.377146 GGTAATCTTCACACAACCCATGTAAT 59.623 38.462 0.00 0.00 41.46 1.89
3246 3610 7.554835 GGTAATCTTCACACAACCCATGTAATA 59.445 37.037 0.00 0.00 41.46 0.98
3247 3611 7.391148 AATCTTCACACAACCCATGTAATAC 57.609 36.000 0.00 0.00 41.46 1.89
3248 3612 5.870706 TCTTCACACAACCCATGTAATACA 58.129 37.500 0.00 0.00 41.46 2.29
3249 3613 6.480763 TCTTCACACAACCCATGTAATACAT 58.519 36.000 0.00 0.00 41.46 2.29
3250 3614 7.625469 TCTTCACACAACCCATGTAATACATA 58.375 34.615 5.49 0.00 41.46 2.29
3251 3615 8.103935 TCTTCACACAACCCATGTAATACATAA 58.896 33.333 5.49 0.00 41.46 1.90
3252 3616 7.857734 TCACACAACCCATGTAATACATAAG 57.142 36.000 5.49 3.25 41.46 1.73
3253 3617 6.826231 TCACACAACCCATGTAATACATAAGG 59.174 38.462 15.94 15.94 41.46 2.69
3254 3618 6.039270 CACACAACCCATGTAATACATAAGGG 59.961 42.308 20.91 20.91 43.69 3.95
3255 3619 6.069323 ACACAACCCATGTAATACATAAGGGA 60.069 38.462 26.38 0.00 41.79 4.20
3256 3620 6.831353 CACAACCCATGTAATACATAAGGGAA 59.169 38.462 26.38 0.00 41.79 3.97
3257 3621 7.340743 CACAACCCATGTAATACATAAGGGAAA 59.659 37.037 26.38 0.00 41.79 3.13
3258 3622 7.559897 ACAACCCATGTAATACATAAGGGAAAG 59.440 37.037 26.38 18.92 41.79 2.62
3259 3623 7.460214 ACCCATGTAATACATAAGGGAAAGA 57.540 36.000 26.38 0.00 41.79 2.52
3260 3624 7.518188 ACCCATGTAATACATAAGGGAAAGAG 58.482 38.462 26.38 7.48 41.79 2.85
3261 3625 7.349859 ACCCATGTAATACATAAGGGAAAGAGA 59.650 37.037 26.38 0.00 41.79 3.10
3262 3626 8.386264 CCCATGTAATACATAAGGGAAAGAGAT 58.614 37.037 18.88 0.00 41.79 2.75
3272 3636 8.432805 ACATAAGGGAAAGAGATACATAGTTGG 58.567 37.037 0.00 0.00 0.00 3.77
3273 3637 5.297569 AGGGAAAGAGATACATAGTTGGC 57.702 43.478 0.00 0.00 0.00 4.52
3274 3638 4.971924 AGGGAAAGAGATACATAGTTGGCT 59.028 41.667 0.00 0.00 0.00 4.75
3275 3639 5.430089 AGGGAAAGAGATACATAGTTGGCTT 59.570 40.000 0.00 0.00 0.00 4.35
3276 3640 6.615726 AGGGAAAGAGATACATAGTTGGCTTA 59.384 38.462 0.00 0.00 0.00 3.09
3277 3641 6.706716 GGGAAAGAGATACATAGTTGGCTTAC 59.293 42.308 0.00 0.00 0.00 2.34
3278 3642 7.272978 GGAAAGAGATACATAGTTGGCTTACA 58.727 38.462 0.00 0.00 0.00 2.41
3279 3643 7.769044 GGAAAGAGATACATAGTTGGCTTACAA 59.231 37.037 0.00 0.00 36.54 2.41
3280 3644 9.331282 GAAAGAGATACATAGTTGGCTTACAAT 57.669 33.333 0.00 0.00 41.95 2.71
3281 3645 8.894768 AAGAGATACATAGTTGGCTTACAATC 57.105 34.615 0.00 0.00 41.95 2.67
3282 3646 7.148641 AGAGATACATAGTTGGCTTACAATCG 58.851 38.462 0.00 0.00 41.95 3.34
3283 3647 5.696724 AGATACATAGTTGGCTTACAATCGC 59.303 40.000 0.00 0.00 41.95 4.58
3284 3648 2.943033 ACATAGTTGGCTTACAATCGCC 59.057 45.455 0.00 0.00 46.46 5.54
3290 3654 1.448985 GGCTTACAATCGCCACTTCA 58.551 50.000 0.00 0.00 45.59 3.02
3291 3655 1.130561 GGCTTACAATCGCCACTTCAC 59.869 52.381 0.00 0.00 45.59 3.18
3292 3656 1.804151 GCTTACAATCGCCACTTCACA 59.196 47.619 0.00 0.00 0.00 3.58
3293 3657 2.412847 GCTTACAATCGCCACTTCACAC 60.413 50.000 0.00 0.00 0.00 3.82
3294 3658 2.535012 TACAATCGCCACTTCACACA 57.465 45.000 0.00 0.00 0.00 3.72
3295 3659 1.674359 ACAATCGCCACTTCACACAA 58.326 45.000 0.00 0.00 0.00 3.33
3296 3660 2.229792 ACAATCGCCACTTCACACAAT 58.770 42.857 0.00 0.00 0.00 2.71
3297 3661 2.622942 ACAATCGCCACTTCACACAATT 59.377 40.909 0.00 0.00 0.00 2.32
3298 3662 3.818210 ACAATCGCCACTTCACACAATTA 59.182 39.130 0.00 0.00 0.00 1.40
3299 3663 4.158384 CAATCGCCACTTCACACAATTAC 58.842 43.478 0.00 0.00 0.00 1.89
3300 3664 2.839975 TCGCCACTTCACACAATTACA 58.160 42.857 0.00 0.00 0.00 2.41
3301 3665 3.407698 TCGCCACTTCACACAATTACAT 58.592 40.909 0.00 0.00 0.00 2.29
3302 3666 3.188254 TCGCCACTTCACACAATTACATG 59.812 43.478 0.00 0.00 0.00 3.21
3303 3667 3.188254 CGCCACTTCACACAATTACATGA 59.812 43.478 0.00 0.00 0.00 3.07
3304 3668 4.320129 CGCCACTTCACACAATTACATGAA 60.320 41.667 0.00 0.00 0.00 2.57
3305 3669 5.619757 CGCCACTTCACACAATTACATGAAT 60.620 40.000 0.00 0.00 31.00 2.57
3306 3670 6.403092 CGCCACTTCACACAATTACATGAATA 60.403 38.462 0.00 0.00 31.00 1.75
3307 3671 7.312154 GCCACTTCACACAATTACATGAATAA 58.688 34.615 0.00 0.00 31.00 1.40
3308 3672 7.812191 GCCACTTCACACAATTACATGAATAAA 59.188 33.333 0.00 0.00 31.00 1.40
3309 3673 9.345517 CCACTTCACACAATTACATGAATAAAG 57.654 33.333 0.00 0.00 31.00 1.85
3310 3674 8.853345 CACTTCACACAATTACATGAATAAAGC 58.147 33.333 0.00 0.00 31.00 3.51
3311 3675 8.575589 ACTTCACACAATTACATGAATAAAGCA 58.424 29.630 0.00 0.00 31.00 3.91
3312 3676 9.577110 CTTCACACAATTACATGAATAAAGCAT 57.423 29.630 0.00 0.00 31.00 3.79
3313 3677 9.926158 TTCACACAATTACATGAATAAAGCATT 57.074 25.926 0.00 0.00 0.00 3.56
3323 3687 8.467963 ACATGAATAAAGCATTACATCATCCA 57.532 30.769 0.00 0.00 32.62 3.41
3324 3688 8.573885 ACATGAATAAAGCATTACATCATCCAG 58.426 33.333 0.00 3.07 32.62 3.86
3325 3689 8.789762 CATGAATAAAGCATTACATCATCCAGA 58.210 33.333 8.19 0.00 32.62 3.86
3326 3690 8.929260 TGAATAAAGCATTACATCATCCAGAT 57.071 30.769 0.00 0.00 37.48 2.90
3329 3693 9.797642 AATAAAGCATTACATCATCCAGATACA 57.202 29.630 0.00 0.00 34.43 2.29
3330 3694 9.797642 ATAAAGCATTACATCATCCAGATACAA 57.202 29.630 0.00 0.00 34.43 2.41
3331 3695 8.701908 AAAGCATTACATCATCCAGATACAAT 57.298 30.769 0.00 0.00 34.43 2.71
3332 3696 7.918536 AGCATTACATCATCCAGATACAATC 57.081 36.000 0.00 0.00 34.43 2.67
3333 3697 7.455891 AGCATTACATCATCCAGATACAATCA 58.544 34.615 0.00 0.00 34.43 2.57
3334 3698 7.940688 AGCATTACATCATCCAGATACAATCAA 59.059 33.333 0.00 0.00 34.43 2.57
3335 3699 8.235226 GCATTACATCATCCAGATACAATCAAG 58.765 37.037 0.00 0.00 34.43 3.02
3336 3700 8.727910 CATTACATCATCCAGATACAATCAAGG 58.272 37.037 0.00 0.00 34.43 3.61
3337 3701 6.257994 ACATCATCCAGATACAATCAAGGT 57.742 37.500 0.00 0.00 34.43 3.50
3338 3702 6.294473 ACATCATCCAGATACAATCAAGGTC 58.706 40.000 0.00 0.00 34.43 3.85
3339 3703 5.296151 TCATCCAGATACAATCAAGGTCC 57.704 43.478 0.00 0.00 0.00 4.46
3340 3704 3.819564 TCCAGATACAATCAAGGTCCG 57.180 47.619 0.00 0.00 0.00 4.79
3341 3705 3.371034 TCCAGATACAATCAAGGTCCGA 58.629 45.455 0.00 0.00 0.00 4.55
3342 3706 3.132289 TCCAGATACAATCAAGGTCCGAC 59.868 47.826 0.00 0.00 0.00 4.79
3343 3707 3.133003 CCAGATACAATCAAGGTCCGACT 59.867 47.826 0.00 0.00 0.00 4.18
3344 3708 4.341235 CCAGATACAATCAAGGTCCGACTA 59.659 45.833 0.00 0.00 0.00 2.59
3345 3709 5.282510 CAGATACAATCAAGGTCCGACTAC 58.717 45.833 0.00 0.00 0.00 2.73
3346 3710 2.649331 ACAATCAAGGTCCGACTACG 57.351 50.000 0.00 0.00 39.43 3.51
3362 3726 6.470557 CGACTACGGAACCAAAATAAAAGA 57.529 37.500 0.00 0.00 35.72 2.52
3363 3727 6.890558 CGACTACGGAACCAAAATAAAAGAA 58.109 36.000 0.00 0.00 35.72 2.52
3364 3728 7.013529 CGACTACGGAACCAAAATAAAAGAAG 58.986 38.462 0.00 0.00 35.72 2.85
3365 3729 7.095523 CGACTACGGAACCAAAATAAAAGAAGA 60.096 37.037 0.00 0.00 35.72 2.87
3366 3730 8.454570 ACTACGGAACCAAAATAAAAGAAGAA 57.545 30.769 0.00 0.00 0.00 2.52
3367 3731 8.347771 ACTACGGAACCAAAATAAAAGAAGAAC 58.652 33.333 0.00 0.00 0.00 3.01
3368 3732 6.509656 ACGGAACCAAAATAAAAGAAGAACC 58.490 36.000 0.00 0.00 0.00 3.62
3369 3733 5.924254 CGGAACCAAAATAAAAGAAGAACCC 59.076 40.000 0.00 0.00 0.00 4.11
3370 3734 6.228258 GGAACCAAAATAAAAGAAGAACCCC 58.772 40.000 0.00 0.00 0.00 4.95
3371 3735 6.183361 GGAACCAAAATAAAAGAAGAACCCCA 60.183 38.462 0.00 0.00 0.00 4.96
3372 3736 6.816616 ACCAAAATAAAAGAAGAACCCCAA 57.183 33.333 0.00 0.00 0.00 4.12
3373 3737 7.201702 ACCAAAATAAAAGAAGAACCCCAAA 57.798 32.000 0.00 0.00 0.00 3.28
3374 3738 7.811282 ACCAAAATAAAAGAAGAACCCCAAAT 58.189 30.769 0.00 0.00 0.00 2.32
3375 3739 7.719193 ACCAAAATAAAAGAAGAACCCCAAATG 59.281 33.333 0.00 0.00 0.00 2.32
3376 3740 7.308529 CCAAAATAAAAGAAGAACCCCAAATGC 60.309 37.037 0.00 0.00 0.00 3.56
3377 3741 3.385193 AAAAGAAGAACCCCAAATGCG 57.615 42.857 0.00 0.00 0.00 4.73
3378 3742 2.286365 AAGAAGAACCCCAAATGCGA 57.714 45.000 0.00 0.00 0.00 5.10
3379 3743 1.534729 AGAAGAACCCCAAATGCGAC 58.465 50.000 0.00 0.00 0.00 5.19
3380 3744 1.202879 AGAAGAACCCCAAATGCGACA 60.203 47.619 0.00 0.00 0.00 4.35
3381 3745 1.611491 GAAGAACCCCAAATGCGACAA 59.389 47.619 0.00 0.00 0.00 3.18
3382 3746 1.698506 AGAACCCCAAATGCGACAAA 58.301 45.000 0.00 0.00 0.00 2.83
3383 3747 1.613437 AGAACCCCAAATGCGACAAAG 59.387 47.619 0.00 0.00 0.00 2.77
3384 3748 0.678950 AACCCCAAATGCGACAAAGG 59.321 50.000 0.00 0.00 0.00 3.11
3385 3749 0.469144 ACCCCAAATGCGACAAAGGT 60.469 50.000 0.00 0.00 0.00 3.50
3386 3750 0.243636 CCCCAAATGCGACAAAGGTC 59.756 55.000 0.00 0.00 40.77 3.85
3387 3751 0.243636 CCCAAATGCGACAAAGGTCC 59.756 55.000 0.00 0.00 41.13 4.46
3388 3752 0.243636 CCAAATGCGACAAAGGTCCC 59.756 55.000 0.00 0.00 41.13 4.46
3389 3753 0.243636 CAAATGCGACAAAGGTCCCC 59.756 55.000 0.00 0.00 41.13 4.81
3390 3754 1.241315 AAATGCGACAAAGGTCCCCG 61.241 55.000 0.00 0.00 41.13 5.73
3391 3755 2.119484 AATGCGACAAAGGTCCCCGA 62.119 55.000 0.00 0.00 41.13 5.14
3392 3756 1.910580 ATGCGACAAAGGTCCCCGAT 61.911 55.000 0.00 0.00 41.13 4.18
3393 3757 1.814169 GCGACAAAGGTCCCCGATC 60.814 63.158 0.00 0.00 41.13 3.69
3394 3758 1.518572 CGACAAAGGTCCCCGATCG 60.519 63.158 8.51 8.51 41.13 3.69
3395 3759 1.895238 GACAAAGGTCCCCGATCGA 59.105 57.895 18.66 0.00 38.12 3.59
3396 3760 0.459759 GACAAAGGTCCCCGATCGAC 60.460 60.000 18.66 6.80 38.12 4.20
3401 3765 3.078836 GTCCCCGATCGACCCCAA 61.079 66.667 18.66 0.00 0.00 4.12
3402 3766 3.078836 TCCCCGATCGACCCCAAC 61.079 66.667 18.66 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.469807 CTATACACATCTAACATCTTTCAGACC 57.530 37.037 0.00 0.00 0.00 3.85
30 31 7.686438 ACATGTGTATGATAAAGTGCAAGAA 57.314 32.000 0.00 0.00 37.73 2.52
43 44 6.295632 GGGCCAGTACATATACATGTGTATGA 60.296 42.308 35.45 22.04 45.17 2.15
175 196 2.601868 GAGGTAGAGGGAGGCCGA 59.398 66.667 0.00 0.00 0.00 5.54
220 241 4.779733 GGGAGAGAGACGGGGGCA 62.780 72.222 0.00 0.00 0.00 5.36
228 249 4.144727 GGCGGGGAGGGAGAGAGA 62.145 72.222 0.00 0.00 0.00 3.10
733 922 4.335647 CAGGCGCAGGGAGGTTGT 62.336 66.667 10.83 0.00 0.00 3.32
804 1008 1.762460 GATGGAGGAAGCGAGGGGA 60.762 63.158 0.00 0.00 0.00 4.81
809 1013 3.154473 CCCCGATGGAGGAAGCGA 61.154 66.667 0.00 0.00 35.39 4.93
835 1040 1.371145 GATCAGACTCGCGCTAGCC 60.371 63.158 9.66 0.00 41.18 3.93
838 1170 2.543802 CGGGATCAGACTCGCGCTA 61.544 63.158 5.56 0.00 43.20 4.26
909 1253 2.416701 CGAAGAAGACAAGAGGAGCTCC 60.417 54.545 26.22 26.22 0.00 4.70
919 1263 2.416836 CGACATAGCCCGAAGAAGACAA 60.417 50.000 0.00 0.00 0.00 3.18
942 1286 0.836606 TCACTGAGCACCAAGGAACA 59.163 50.000 0.00 0.00 0.00 3.18
949 1293 3.340928 CATTGAAGATCACTGAGCACCA 58.659 45.455 0.00 0.00 29.66 4.17
1004 1348 1.137086 GGAGACCGCGCATATGGATAT 59.863 52.381 8.75 0.00 0.00 1.63
1011 1355 1.320344 ACAGAAGGAGACCGCGCATA 61.320 55.000 8.75 0.00 0.00 3.14
1068 1422 1.555075 GGAGCCACAGGAGTAACATGA 59.445 52.381 0.00 0.00 34.19 3.07
1070 1424 1.958288 AGGAGCCACAGGAGTAACAT 58.042 50.000 0.00 0.00 0.00 2.71
1075 1429 1.306226 GGGTAGGAGCCACAGGAGT 60.306 63.158 0.00 0.00 35.40 3.85
1169 1523 4.590222 TCTGCTGATCATAGGCATCAACTA 59.410 41.667 8.40 0.00 35.37 2.24
1293 1647 1.270358 GCGAACTGAGGAAGGACACTT 60.270 52.381 0.00 0.00 40.34 3.16
1410 1764 1.079543 GAGTGCATGCTCCTGACGT 60.080 57.895 20.33 0.00 0.00 4.34
1447 1801 7.392673 AGAGCACTGTGAATAAAACTCATCAAT 59.607 33.333 12.86 0.00 0.00 2.57
1495 1849 1.297456 ACGACGGTCCGAAGAGAGTC 61.297 60.000 20.51 1.61 0.00 3.36
1496 1850 0.888285 AACGACGGTCCGAAGAGAGT 60.888 55.000 20.51 5.33 0.00 3.24
1497 1851 0.240411 AAACGACGGTCCGAAGAGAG 59.760 55.000 20.51 4.70 0.00 3.20
1548 1902 2.009774 CGCTGAAACTCCAAATCGGAT 58.990 47.619 0.00 0.00 45.19 4.18
1688 2042 1.611673 CCACAAGTAACCCAGCAGAGG 60.612 57.143 0.00 0.00 0.00 3.69
1714 2074 4.652131 TCGGGCGGCCAACAATGT 62.652 61.111 29.19 0.00 0.00 2.71
1790 2150 1.553248 CATAAGAAGGACGACCCACCA 59.447 52.381 0.00 0.00 37.41 4.17
1830 2192 1.416243 ACCCACAGAAGGTGTTACGA 58.584 50.000 0.00 0.00 46.44 3.43
1834 2196 1.202770 GCAGTACCCACAGAAGGTGTT 60.203 52.381 0.00 0.00 46.44 3.32
1938 2300 1.753463 GAGTGACGGGGTCGAGGAT 60.753 63.158 0.00 0.00 40.11 3.24
2140 2502 0.894184 AGCGGTCGGAGAGAAGACAA 60.894 55.000 0.00 0.00 36.95 3.18
2157 2519 3.764885 ACATTAACAGGCGAATCAAGC 57.235 42.857 0.00 0.00 0.00 4.01
2231 2593 8.519799 AACACTAGAAACAGAAAAAGATGGAA 57.480 30.769 0.00 0.00 0.00 3.53
2320 2683 4.462834 AGAGTCGGTATCAAGAATGACACA 59.537 41.667 0.00 0.00 34.57 3.72
2456 2819 1.679977 GCATGGGAGCTGGCTGAAA 60.680 57.895 0.00 0.00 0.00 2.69
2505 2868 1.473965 CCAAGGCGATGATGCTACTGT 60.474 52.381 0.00 0.00 34.52 3.55
2510 2873 0.745845 GTGACCAAGGCGATGATGCT 60.746 55.000 0.00 0.00 34.52 3.79
2571 2934 5.721225 ACATCTCCAGATACAGACCCTAAT 58.279 41.667 0.00 0.00 32.63 1.73
2693 3056 1.701847 GAGCAGGACCCCATACATCAT 59.298 52.381 0.00 0.00 0.00 2.45
2856 3219 3.499737 GTGCGAATGGGCGTGGAG 61.500 66.667 0.00 0.00 35.06 3.86
2882 3245 0.468226 AAACTCACCAGCGGAGTCAA 59.532 50.000 1.50 0.00 44.50 3.18
2954 3317 4.107051 GTGCACCAGGACATGCGC 62.107 66.667 5.22 0.00 45.13 6.09
3018 3381 0.538584 TCATCAGAGCATGAGCCGTT 59.461 50.000 0.00 0.00 42.53 4.44
3026 3389 0.179026 AGCGGCAATCATCAGAGCAT 60.179 50.000 1.45 0.00 0.00 3.79
3060 3424 3.129988 CAGAAATAGCCTCAGCCCAAAAG 59.870 47.826 0.00 0.00 41.25 2.27
3141 3505 1.066303 GAGATATAGCCGCATCGAGGG 59.934 57.143 0.00 0.00 0.00 4.30
3142 3506 1.066303 GGAGATATAGCCGCATCGAGG 59.934 57.143 0.00 0.00 0.00 4.63
3143 3507 1.066303 GGGAGATATAGCCGCATCGAG 59.934 57.143 0.00 0.00 0.00 4.04
3144 3508 1.103803 GGGAGATATAGCCGCATCGA 58.896 55.000 0.00 0.00 0.00 3.59
3145 3509 0.817654 TGGGAGATATAGCCGCATCG 59.182 55.000 0.00 0.00 0.00 3.84
3146 3510 1.469940 CGTGGGAGATATAGCCGCATC 60.470 57.143 0.00 0.00 0.00 3.91
3147 3511 0.532573 CGTGGGAGATATAGCCGCAT 59.467 55.000 0.00 0.00 0.00 4.73
3148 3512 0.826256 ACGTGGGAGATATAGCCGCA 60.826 55.000 0.00 0.00 0.00 5.69
3149 3513 0.388649 CACGTGGGAGATATAGCCGC 60.389 60.000 7.95 0.00 0.00 6.53
3150 3514 0.959553 ACACGTGGGAGATATAGCCG 59.040 55.000 21.57 0.00 0.00 5.52
3151 3515 1.068472 CGACACGTGGGAGATATAGCC 60.068 57.143 21.57 0.00 0.00 3.93
3152 3516 1.878088 TCGACACGTGGGAGATATAGC 59.122 52.381 21.57 0.00 0.00 2.97
3153 3517 3.609644 GCTTCGACACGTGGGAGATATAG 60.610 52.174 21.57 11.01 0.00 1.31
3154 3518 2.292569 GCTTCGACACGTGGGAGATATA 59.707 50.000 21.57 0.63 0.00 0.86
3155 3519 1.067212 GCTTCGACACGTGGGAGATAT 59.933 52.381 21.57 0.00 0.00 1.63
3156 3520 0.454600 GCTTCGACACGTGGGAGATA 59.545 55.000 21.57 1.34 0.00 1.98
3157 3521 1.215647 GCTTCGACACGTGGGAGAT 59.784 57.895 21.57 0.00 0.00 2.75
3158 3522 2.197605 TGCTTCGACACGTGGGAGA 61.198 57.895 21.57 12.82 0.00 3.71
3159 3523 2.022129 GTGCTTCGACACGTGGGAG 61.022 63.158 21.57 8.15 0.00 4.30
3160 3524 2.028484 GTGCTTCGACACGTGGGA 59.972 61.111 21.57 13.88 0.00 4.37
3169 3533 0.170561 GCCTCTAAGTCGTGCTTCGA 59.829 55.000 0.92 0.92 46.83 3.71
3170 3534 0.109272 TGCCTCTAAGTCGTGCTTCG 60.109 55.000 0.00 0.00 38.57 3.79
3171 3535 2.301577 ATGCCTCTAAGTCGTGCTTC 57.698 50.000 0.00 0.00 38.57 3.86
3172 3536 3.522553 GTTATGCCTCTAAGTCGTGCTT 58.477 45.455 0.00 1.30 41.05 3.91
3173 3537 2.159085 GGTTATGCCTCTAAGTCGTGCT 60.159 50.000 0.00 0.00 0.00 4.40
3174 3538 2.202566 GGTTATGCCTCTAAGTCGTGC 58.797 52.381 0.00 0.00 0.00 5.34
3175 3539 2.460918 CGGTTATGCCTCTAAGTCGTG 58.539 52.381 0.00 0.00 34.25 4.35
3176 3540 1.202382 GCGGTTATGCCTCTAAGTCGT 60.202 52.381 0.00 0.00 34.25 4.34
3177 3541 1.202371 TGCGGTTATGCCTCTAAGTCG 60.202 52.381 0.00 0.00 34.25 4.18
3178 3542 2.596904 TGCGGTTATGCCTCTAAGTC 57.403 50.000 0.00 0.00 34.25 3.01
3179 3543 3.118408 TCAATGCGGTTATGCCTCTAAGT 60.118 43.478 0.00 0.00 34.25 2.24
3180 3544 3.466836 TCAATGCGGTTATGCCTCTAAG 58.533 45.455 0.00 0.00 34.25 2.18
3181 3545 3.552132 TCAATGCGGTTATGCCTCTAA 57.448 42.857 0.00 0.00 34.25 2.10
3182 3546 3.552132 TTCAATGCGGTTATGCCTCTA 57.448 42.857 0.00 0.00 34.25 2.43
3183 3547 2.418368 TTCAATGCGGTTATGCCTCT 57.582 45.000 0.00 0.00 34.25 3.69
3184 3548 2.796032 GCTTTCAATGCGGTTATGCCTC 60.796 50.000 0.00 0.00 34.25 4.70
3185 3549 1.134946 GCTTTCAATGCGGTTATGCCT 59.865 47.619 0.00 0.00 34.25 4.75
3186 3550 1.135141 TGCTTTCAATGCGGTTATGCC 60.135 47.619 0.00 0.00 0.00 4.40
3187 3551 2.276472 TGCTTTCAATGCGGTTATGC 57.724 45.000 0.00 0.00 0.00 3.14
3197 3561 3.004629 TCACTTGCGACATTGCTTTCAAT 59.995 39.130 0.00 0.00 43.31 2.57
3198 3562 2.357323 TCACTTGCGACATTGCTTTCAA 59.643 40.909 0.00 0.00 36.51 2.69
3199 3563 1.946081 TCACTTGCGACATTGCTTTCA 59.054 42.857 0.00 0.00 35.36 2.69
3200 3564 2.578495 CTCACTTGCGACATTGCTTTC 58.422 47.619 0.00 0.00 35.36 2.62
3201 3565 1.267806 CCTCACTTGCGACATTGCTTT 59.732 47.619 0.00 0.00 35.36 3.51
3202 3566 0.877071 CCTCACTTGCGACATTGCTT 59.123 50.000 0.00 0.00 35.36 3.91
3203 3567 0.250467 ACCTCACTTGCGACATTGCT 60.250 50.000 0.00 0.00 35.36 3.91
3204 3568 1.438651 TACCTCACTTGCGACATTGC 58.561 50.000 0.00 0.00 0.00 3.56
3205 3569 3.935203 AGATTACCTCACTTGCGACATTG 59.065 43.478 0.00 0.00 0.00 2.82
3206 3570 4.207891 AGATTACCTCACTTGCGACATT 57.792 40.909 0.00 0.00 0.00 2.71
3207 3571 3.895232 AGATTACCTCACTTGCGACAT 57.105 42.857 0.00 0.00 0.00 3.06
3208 3572 3.006430 TGAAGATTACCTCACTTGCGACA 59.994 43.478 0.00 0.00 0.00 4.35
3209 3573 3.368236 GTGAAGATTACCTCACTTGCGAC 59.632 47.826 0.00 0.00 0.00 5.19
3210 3574 3.006430 TGTGAAGATTACCTCACTTGCGA 59.994 43.478 4.07 0.00 34.51 5.10
3211 3575 3.123621 GTGTGAAGATTACCTCACTTGCG 59.876 47.826 4.07 0.00 34.51 4.85
3212 3576 4.065088 TGTGTGAAGATTACCTCACTTGC 58.935 43.478 4.07 0.00 34.51 4.01
3213 3577 5.049405 GGTTGTGTGAAGATTACCTCACTTG 60.049 44.000 4.07 0.00 34.51 3.16
3214 3578 5.063880 GGTTGTGTGAAGATTACCTCACTT 58.936 41.667 4.07 0.00 34.51 3.16
3215 3579 4.505039 GGGTTGTGTGAAGATTACCTCACT 60.505 45.833 4.07 0.00 34.51 3.41
3216 3580 3.751698 GGGTTGTGTGAAGATTACCTCAC 59.248 47.826 0.00 0.00 0.00 3.51
3217 3581 3.392947 TGGGTTGTGTGAAGATTACCTCA 59.607 43.478 0.00 0.00 0.00 3.86
3218 3582 4.015872 TGGGTTGTGTGAAGATTACCTC 57.984 45.455 0.00 0.00 0.00 3.85
3219 3583 4.202567 ACATGGGTTGTGTGAAGATTACCT 60.203 41.667 0.00 0.00 37.11 3.08
3220 3584 4.079253 ACATGGGTTGTGTGAAGATTACC 58.921 43.478 0.00 0.00 37.11 2.85
3221 3585 6.811253 TTACATGGGTTGTGTGAAGATTAC 57.189 37.500 0.00 0.00 39.48 1.89
3222 3586 8.103935 TGTATTACATGGGTTGTGTGAAGATTA 58.896 33.333 0.00 0.00 39.48 1.75
3223 3587 6.945435 TGTATTACATGGGTTGTGTGAAGATT 59.055 34.615 0.00 0.00 39.48 2.40
3224 3588 6.480763 TGTATTACATGGGTTGTGTGAAGAT 58.519 36.000 0.00 0.00 39.48 2.40
3225 3589 5.870706 TGTATTACATGGGTTGTGTGAAGA 58.129 37.500 0.00 0.00 39.48 2.87
3226 3590 6.757897 ATGTATTACATGGGTTGTGTGAAG 57.242 37.500 8.51 0.00 37.45 3.02
3227 3591 7.338196 CCTTATGTATTACATGGGTTGTGTGAA 59.662 37.037 17.68 1.51 39.53 3.18
3228 3592 6.826231 CCTTATGTATTACATGGGTTGTGTGA 59.174 38.462 17.68 0.00 39.53 3.58
3229 3593 6.039270 CCCTTATGTATTACATGGGTTGTGTG 59.961 42.308 17.68 4.59 39.53 3.82
3230 3594 6.069323 TCCCTTATGTATTACATGGGTTGTGT 60.069 38.462 22.47 0.74 40.71 3.72
3231 3595 6.361433 TCCCTTATGTATTACATGGGTTGTG 58.639 40.000 22.47 11.74 40.71 3.33
3232 3596 6.584471 TCCCTTATGTATTACATGGGTTGT 57.416 37.500 22.47 1.91 40.71 3.32
3233 3597 7.777910 TCTTTCCCTTATGTATTACATGGGTTG 59.222 37.037 22.47 16.30 40.71 3.77
3234 3598 7.878495 TCTTTCCCTTATGTATTACATGGGTT 58.122 34.615 22.47 3.08 40.71 4.11
3235 3599 7.349859 TCTCTTTCCCTTATGTATTACATGGGT 59.650 37.037 22.47 3.38 40.71 4.51
3236 3600 7.745717 TCTCTTTCCCTTATGTATTACATGGG 58.254 38.462 19.48 19.48 41.04 4.00
3246 3610 8.432805 CCAACTATGTATCTCTTTCCCTTATGT 58.567 37.037 0.00 0.00 0.00 2.29
3247 3611 7.389053 GCCAACTATGTATCTCTTTCCCTTATG 59.611 40.741 0.00 0.00 0.00 1.90
3248 3612 7.293535 AGCCAACTATGTATCTCTTTCCCTTAT 59.706 37.037 0.00 0.00 0.00 1.73
3249 3613 6.615726 AGCCAACTATGTATCTCTTTCCCTTA 59.384 38.462 0.00 0.00 0.00 2.69
3250 3614 5.430089 AGCCAACTATGTATCTCTTTCCCTT 59.570 40.000 0.00 0.00 0.00 3.95
3251 3615 4.971924 AGCCAACTATGTATCTCTTTCCCT 59.028 41.667 0.00 0.00 0.00 4.20
3252 3616 5.297569 AGCCAACTATGTATCTCTTTCCC 57.702 43.478 0.00 0.00 0.00 3.97
3253 3617 7.272978 TGTAAGCCAACTATGTATCTCTTTCC 58.727 38.462 0.00 0.00 0.00 3.13
3254 3618 8.718102 TTGTAAGCCAACTATGTATCTCTTTC 57.282 34.615 0.00 0.00 0.00 2.62
3255 3619 9.331282 GATTGTAAGCCAACTATGTATCTCTTT 57.669 33.333 0.00 0.00 35.44 2.52
3256 3620 7.653713 CGATTGTAAGCCAACTATGTATCTCTT 59.346 37.037 0.00 0.00 35.44 2.85
3257 3621 7.148641 CGATTGTAAGCCAACTATGTATCTCT 58.851 38.462 0.00 0.00 35.44 3.10
3258 3622 6.128795 GCGATTGTAAGCCAACTATGTATCTC 60.129 42.308 0.00 0.00 35.44 2.75
3259 3623 5.696724 GCGATTGTAAGCCAACTATGTATCT 59.303 40.000 0.00 0.00 35.44 1.98
3260 3624 5.916969 GCGATTGTAAGCCAACTATGTATC 58.083 41.667 0.00 0.00 35.44 2.24
3261 3625 5.924475 GCGATTGTAAGCCAACTATGTAT 57.076 39.130 0.00 0.00 35.44 2.29
3272 3636 1.804151 TGTGAAGTGGCGATTGTAAGC 59.196 47.619 0.00 0.00 0.00 3.09
3273 3637 2.805671 TGTGTGAAGTGGCGATTGTAAG 59.194 45.455 0.00 0.00 0.00 2.34
3274 3638 2.839975 TGTGTGAAGTGGCGATTGTAA 58.160 42.857 0.00 0.00 0.00 2.41
3275 3639 2.535012 TGTGTGAAGTGGCGATTGTA 57.465 45.000 0.00 0.00 0.00 2.41
3276 3640 1.674359 TTGTGTGAAGTGGCGATTGT 58.326 45.000 0.00 0.00 0.00 2.71
3277 3641 2.995466 ATTGTGTGAAGTGGCGATTG 57.005 45.000 0.00 0.00 0.00 2.67
3278 3642 3.818210 TGTAATTGTGTGAAGTGGCGATT 59.182 39.130 0.00 0.00 0.00 3.34
3279 3643 3.407698 TGTAATTGTGTGAAGTGGCGAT 58.592 40.909 0.00 0.00 0.00 4.58
3280 3644 2.839975 TGTAATTGTGTGAAGTGGCGA 58.160 42.857 0.00 0.00 0.00 5.54
3281 3645 3.188254 TCATGTAATTGTGTGAAGTGGCG 59.812 43.478 0.00 0.00 0.00 5.69
3282 3646 4.764679 TCATGTAATTGTGTGAAGTGGC 57.235 40.909 0.00 0.00 0.00 5.01
3283 3647 9.345517 CTTTATTCATGTAATTGTGTGAAGTGG 57.654 33.333 0.00 0.00 34.45 4.00
3284 3648 8.853345 GCTTTATTCATGTAATTGTGTGAAGTG 58.147 33.333 0.00 0.00 34.45 3.16
3285 3649 8.575589 TGCTTTATTCATGTAATTGTGTGAAGT 58.424 29.630 0.00 0.00 34.45 3.01
3286 3650 8.969121 TGCTTTATTCATGTAATTGTGTGAAG 57.031 30.769 0.00 0.00 34.45 3.02
3287 3651 9.926158 AATGCTTTATTCATGTAATTGTGTGAA 57.074 25.926 0.00 0.00 35.33 3.18
3297 3661 9.571816 TGGATGATGTAATGCTTTATTCATGTA 57.428 29.630 17.80 9.21 29.90 2.29
3298 3662 8.467963 TGGATGATGTAATGCTTTATTCATGT 57.532 30.769 17.80 4.48 29.90 3.21
3299 3663 8.789762 TCTGGATGATGTAATGCTTTATTCATG 58.210 33.333 17.80 9.46 29.90 3.07
3300 3664 8.929260 TCTGGATGATGTAATGCTTTATTCAT 57.071 30.769 14.98 14.98 31.23 2.57
3301 3665 8.929260 ATCTGGATGATGTAATGCTTTATTCA 57.071 30.769 9.10 9.10 33.43 2.57
3303 3667 9.797642 TGTATCTGGATGATGTAATGCTTTATT 57.202 29.630 0.00 0.00 36.65 1.40
3304 3668 9.797642 TTGTATCTGGATGATGTAATGCTTTAT 57.202 29.630 0.00 0.00 36.65 1.40
3305 3669 9.797642 ATTGTATCTGGATGATGTAATGCTTTA 57.202 29.630 0.00 0.00 36.65 1.85
3306 3670 8.701908 ATTGTATCTGGATGATGTAATGCTTT 57.298 30.769 0.00 0.00 36.65 3.51
3307 3671 7.940688 TGATTGTATCTGGATGATGTAATGCTT 59.059 33.333 0.00 0.00 36.65 3.91
3308 3672 7.455891 TGATTGTATCTGGATGATGTAATGCT 58.544 34.615 0.00 0.00 36.65 3.79
3309 3673 7.677454 TGATTGTATCTGGATGATGTAATGC 57.323 36.000 0.00 0.00 36.65 3.56
3310 3674 8.727910 CCTTGATTGTATCTGGATGATGTAATG 58.272 37.037 0.00 0.00 36.65 1.90
3311 3675 8.443176 ACCTTGATTGTATCTGGATGATGTAAT 58.557 33.333 0.00 0.00 36.65 1.89
3312 3676 7.805163 ACCTTGATTGTATCTGGATGATGTAA 58.195 34.615 0.00 0.00 36.65 2.41
3313 3677 7.379059 ACCTTGATTGTATCTGGATGATGTA 57.621 36.000 0.00 0.00 36.65 2.29
3314 3678 6.257994 ACCTTGATTGTATCTGGATGATGT 57.742 37.500 0.00 0.00 36.65 3.06
3315 3679 5.704515 GGACCTTGATTGTATCTGGATGATG 59.295 44.000 0.00 0.00 36.65 3.07
3316 3680 5.512060 CGGACCTTGATTGTATCTGGATGAT 60.512 44.000 0.00 0.00 39.11 2.45
3317 3681 4.202253 CGGACCTTGATTGTATCTGGATGA 60.202 45.833 0.00 0.00 0.00 2.92
3318 3682 4.060900 CGGACCTTGATTGTATCTGGATG 58.939 47.826 0.00 0.00 0.00 3.51
3319 3683 3.967326 TCGGACCTTGATTGTATCTGGAT 59.033 43.478 0.00 0.00 0.00 3.41
3320 3684 3.132289 GTCGGACCTTGATTGTATCTGGA 59.868 47.826 0.00 0.00 0.00 3.86
3321 3685 3.133003 AGTCGGACCTTGATTGTATCTGG 59.867 47.826 4.14 0.00 0.00 3.86
3322 3686 4.392921 AGTCGGACCTTGATTGTATCTG 57.607 45.455 4.14 0.00 0.00 2.90
3323 3687 4.036498 CGTAGTCGGACCTTGATTGTATCT 59.964 45.833 4.14 0.00 0.00 1.98
3324 3688 4.288531 CGTAGTCGGACCTTGATTGTATC 58.711 47.826 4.14 0.00 0.00 2.24
3325 3689 4.303086 CGTAGTCGGACCTTGATTGTAT 57.697 45.455 4.14 0.00 0.00 2.29
3326 3690 3.770263 CGTAGTCGGACCTTGATTGTA 57.230 47.619 4.14 0.00 0.00 2.41
3327 3691 2.649331 CGTAGTCGGACCTTGATTGT 57.351 50.000 4.14 0.00 0.00 2.71
3339 3703 6.470557 TCTTTTATTTTGGTTCCGTAGTCG 57.529 37.500 0.00 0.00 0.00 4.18
3340 3704 8.091385 TCTTCTTTTATTTTGGTTCCGTAGTC 57.909 34.615 0.00 0.00 0.00 2.59
3341 3705 8.347771 GTTCTTCTTTTATTTTGGTTCCGTAGT 58.652 33.333 0.00 0.00 0.00 2.73
3342 3706 7.806487 GGTTCTTCTTTTATTTTGGTTCCGTAG 59.194 37.037 0.00 0.00 0.00 3.51
3343 3707 7.255555 GGGTTCTTCTTTTATTTTGGTTCCGTA 60.256 37.037 0.00 0.00 0.00 4.02
3344 3708 6.461927 GGGTTCTTCTTTTATTTTGGTTCCGT 60.462 38.462 0.00 0.00 0.00 4.69
3345 3709 5.924254 GGGTTCTTCTTTTATTTTGGTTCCG 59.076 40.000 0.00 0.00 0.00 4.30
3346 3710 6.183361 TGGGGTTCTTCTTTTATTTTGGTTCC 60.183 38.462 0.00 0.00 0.00 3.62
3347 3711 6.822442 TGGGGTTCTTCTTTTATTTTGGTTC 58.178 36.000 0.00 0.00 0.00 3.62
3348 3712 6.816616 TGGGGTTCTTCTTTTATTTTGGTT 57.183 33.333 0.00 0.00 0.00 3.67
3349 3713 6.816616 TTGGGGTTCTTCTTTTATTTTGGT 57.183 33.333 0.00 0.00 0.00 3.67
3350 3714 7.308529 GCATTTGGGGTTCTTCTTTTATTTTGG 60.309 37.037 0.00 0.00 0.00 3.28
3351 3715 7.571059 CGCATTTGGGGTTCTTCTTTTATTTTG 60.571 37.037 0.00 0.00 0.00 2.44
3352 3716 6.426633 CGCATTTGGGGTTCTTCTTTTATTTT 59.573 34.615 0.00 0.00 0.00 1.82
3353 3717 5.931724 CGCATTTGGGGTTCTTCTTTTATTT 59.068 36.000 0.00 0.00 0.00 1.40
3354 3718 5.245075 TCGCATTTGGGGTTCTTCTTTTATT 59.755 36.000 0.00 0.00 0.00 1.40
3355 3719 4.770010 TCGCATTTGGGGTTCTTCTTTTAT 59.230 37.500 0.00 0.00 0.00 1.40
3356 3720 4.022676 GTCGCATTTGGGGTTCTTCTTTTA 60.023 41.667 0.00 0.00 0.00 1.52
3357 3721 2.962421 TCGCATTTGGGGTTCTTCTTTT 59.038 40.909 0.00 0.00 0.00 2.27
3358 3722 2.296190 GTCGCATTTGGGGTTCTTCTTT 59.704 45.455 0.00 0.00 0.00 2.52
3359 3723 1.886542 GTCGCATTTGGGGTTCTTCTT 59.113 47.619 0.00 0.00 0.00 2.52
3360 3724 1.202879 TGTCGCATTTGGGGTTCTTCT 60.203 47.619 0.00 0.00 0.00 2.85
3361 3725 1.243902 TGTCGCATTTGGGGTTCTTC 58.756 50.000 0.00 0.00 0.00 2.87
3362 3726 1.698506 TTGTCGCATTTGGGGTTCTT 58.301 45.000 0.00 0.00 0.00 2.52
3363 3727 1.613437 CTTTGTCGCATTTGGGGTTCT 59.387 47.619 0.00 0.00 0.00 3.01
3364 3728 1.336795 CCTTTGTCGCATTTGGGGTTC 60.337 52.381 0.00 0.00 0.00 3.62
3365 3729 0.678950 CCTTTGTCGCATTTGGGGTT 59.321 50.000 0.00 0.00 0.00 4.11
3366 3730 0.469144 ACCTTTGTCGCATTTGGGGT 60.469 50.000 0.00 0.00 0.00 4.95
3367 3731 0.243636 GACCTTTGTCGCATTTGGGG 59.756 55.000 0.00 0.00 0.00 4.96
3368 3732 0.243636 GGACCTTTGTCGCATTTGGG 59.756 55.000 0.00 0.00 42.73 4.12
3369 3733 3.792716 GGACCTTTGTCGCATTTGG 57.207 52.632 0.00 0.00 42.73 3.28
3384 3748 3.078836 TTGGGGTCGATCGGGGAC 61.079 66.667 16.41 6.05 0.00 4.46
3385 3749 3.078836 GTTGGGGTCGATCGGGGA 61.079 66.667 16.41 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.