Multiple sequence alignment - TraesCS4B01G225100

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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 TraesCS4B01G225100 chr4B 100.000 3877 0 0 1 3877 471651432 471655308 0.000000e+00 7160.0
1 TraesCS4B01G225100 chr4B 75.000 184 33 11 1606 1784 42395475 42395650 5.370000e-09 73.1
2 TraesCS4B01G225100 chr4A 90.991 3330 170 54 1 3260 66337202 66340471 0.000000e+00 4368.0
3 TraesCS4B01G225100 chr4A 89.811 265 10 8 3534 3785 66342410 66342670 1.340000e-84 324.0
4 TraesCS4B01G225100 chr4A 76.571 175 28 11 1615 1784 573326969 573326803 2.480000e-12 84.2
5 TraesCS4B01G225100 chr4A 97.872 47 1 0 3803 3849 66342669 66342715 8.930000e-12 82.4
6 TraesCS4B01G225100 chr4D 94.323 2783 85 30 529 3260 384669596 384672356 0.000000e+00 4196.0
7 TraesCS4B01G225100 chr4D 86.947 452 34 13 3437 3874 384672366 384672806 5.820000e-133 484.0
8 TraesCS4B01G225100 chr4D 87.678 211 22 4 336 543 145579716 145579507 3.870000e-60 243.0
9 TraesCS4B01G225100 chr4D 84.337 166 22 4 3271 3433 418391611 418391775 4.010000e-35 159.0
10 TraesCS4B01G225100 chr4D 71.569 408 86 26 1386 1784 29828330 29828716 2.480000e-12 84.2
11 TraesCS4B01G225100 chr3A 85.782 211 26 4 336 543 7161384 7161175 1.810000e-53 220.0
12 TraesCS4B01G225100 chr3A 78.968 252 49 4 1838 2087 623777529 623777778 6.660000e-38 169.0
13 TraesCS4B01G225100 chr1A 84.834 211 28 4 336 543 464856190 464855981 3.930000e-50 209.0
14 TraesCS4B01G225100 chr5B 84.762 210 28 4 337 543 447183446 447183238 1.410000e-49 207.0
15 TraesCS4B01G225100 chr5B 84.663 163 22 2 3274 3433 696341281 696341443 4.010000e-35 159.0
16 TraesCS4B01G225100 chr5B 83.529 170 24 4 3271 3437 467139497 467139329 5.190000e-34 156.0
17 TraesCS4B01G225100 chr5A 84.834 211 26 6 337 543 7113982 7114190 1.410000e-49 207.0
18 TraesCS4B01G225100 chr5A 86.885 183 20 4 336 515 556237325 556237506 6.570000e-48 202.0
19 TraesCS4B01G225100 chr5A 84.080 201 27 5 346 543 571687938 571687740 5.110000e-44 189.0
20 TraesCS4B01G225100 chr7B 83.886 211 30 4 336 543 322488502 322488711 8.500000e-47 198.0
21 TraesCS4B01G225100 chr7B 84.431 167 22 3 3271 3433 23717499 23717333 1.110000e-35 161.0
22 TraesCS4B01G225100 chr3B 79.608 255 42 9 1838 2087 641805196 641805445 1.430000e-39 174.0
23 TraesCS4B01G225100 chr3B 84.337 166 23 3 3271 3433 666193418 666193583 4.010000e-35 159.0
24 TraesCS4B01G225100 chr1B 86.061 165 19 3 3271 3432 566716661 566716498 1.430000e-39 174.0
25 TraesCS4B01G225100 chr1B 84.118 170 23 3 3271 3437 32752768 32752600 1.110000e-35 161.0
26 TraesCS4B01G225100 chr5D 85.455 165 21 2 3272 3433 238673299 238673463 6.660000e-38 169.0
27 TraesCS4B01G225100 chr7A 84.337 166 23 1 3271 3433 680684386 680684221 4.010000e-35 159.0
28 TraesCS4B01G225100 chr3D 77.778 252 52 4 1838 2087 480969939 480970188 6.710000e-33 152.0


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 TraesCS4B01G225100 chr4B 471651432 471655308 3876 False 7160.000000 7160 100.000000 1 3877 1 chr4B.!!$F2 3876
1 TraesCS4B01G225100 chr4A 66337202 66342715 5513 False 1591.466667 4368 92.891333 1 3849 3 chr4A.!!$F1 3848
2 TraesCS4B01G225100 chr4D 384669596 384672806 3210 False 2340.000000 4196 90.635000 529 3874 2 chr4D.!!$F3 3345

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
103 104 0.037697 TGCGTCGACCAGTAGCATTT 60.038 50.000 10.58 0.0 32.43 2.32 F
189 190 0.388520 GAAAATTGACGGGCTGCACC 60.389 55.000 0.50 0.0 37.93 5.01 F
630 662 1.153349 TGTGTGCCACAGTACGCAA 60.153 52.632 0.00 0.0 44.61 4.85 F
2200 2288 1.133407 CCACGGTGAGCTCTACTCTTC 59.867 57.143 16.19 0.0 46.41 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 1996 0.102663 TCACGTTGCTGTTGTACCGA 59.897 50.000 0.00 0.0 0.00 4.69 R
2200 2288 4.063689 AGCATGAACAAGTGACAGAGAAG 58.936 43.478 0.00 0.0 0.00 2.85 R
2587 2704 0.534412 ATCTCTTGCTGGAGTCACCG 59.466 55.000 0.00 0.0 42.61 4.94 R
3049 3177 0.032117 ACCCAGATCCACATCTCGGA 60.032 55.000 2.97 0.0 39.26 4.55 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
81 82 0.537653 TTCACGTGTCAAGGGTGTGA 59.462 50.000 16.51 0.00 37.76 3.58
89 90 0.602638 TCAAGGGTGTGATGTGCGTC 60.603 55.000 0.00 0.00 0.00 5.19
90 91 1.667830 AAGGGTGTGATGTGCGTCG 60.668 57.895 0.00 0.00 0.00 5.12
91 92 2.048597 GGGTGTGATGTGCGTCGA 60.049 61.111 0.00 0.00 0.00 4.20
92 93 2.380410 GGGTGTGATGTGCGTCGAC 61.380 63.158 5.18 5.18 0.00 4.20
93 94 2.380410 GGTGTGATGTGCGTCGACC 61.380 63.158 10.58 3.43 0.00 4.79
94 95 1.663388 GTGTGATGTGCGTCGACCA 60.663 57.895 10.58 6.30 0.00 4.02
95 96 1.372872 TGTGATGTGCGTCGACCAG 60.373 57.895 10.58 0.00 0.00 4.00
96 97 1.372997 GTGATGTGCGTCGACCAGT 60.373 57.895 10.58 1.22 0.00 4.00
97 98 0.109458 GTGATGTGCGTCGACCAGTA 60.109 55.000 10.58 2.18 0.00 2.74
98 99 0.170339 TGATGTGCGTCGACCAGTAG 59.830 55.000 10.58 0.00 0.00 2.57
99 100 1.140407 GATGTGCGTCGACCAGTAGC 61.140 60.000 10.58 7.73 0.00 3.58
100 101 1.873270 ATGTGCGTCGACCAGTAGCA 61.873 55.000 10.58 10.51 35.27 3.49
101 102 1.153823 GTGCGTCGACCAGTAGCAT 60.154 57.895 16.30 0.00 40.11 3.79
102 103 0.736325 GTGCGTCGACCAGTAGCATT 60.736 55.000 16.30 0.00 40.11 3.56
103 104 0.037697 TGCGTCGACCAGTAGCATTT 60.038 50.000 10.58 0.00 32.43 2.32
104 105 1.076332 GCGTCGACCAGTAGCATTTT 58.924 50.000 10.58 0.00 0.00 1.82
105 106 1.463444 GCGTCGACCAGTAGCATTTTT 59.537 47.619 10.58 0.00 0.00 1.94
143 144 2.615227 ATCATTCTGGCGCTGACCCC 62.615 60.000 7.64 0.00 0.00 4.95
151 152 3.047877 CGCTGACCCCGGTTTCAC 61.048 66.667 0.00 0.00 0.00 3.18
159 160 1.740296 CCCGGTTTCACACTAGCCG 60.740 63.158 0.00 0.00 41.82 5.52
189 190 0.388520 GAAAATTGACGGGCTGCACC 60.389 55.000 0.50 0.00 37.93 5.01
216 217 4.741676 CAGCAGTTTGGCTAAAAAGAACAG 59.258 41.667 0.00 0.00 43.68 3.16
269 270 4.274421 CACTCTGTGCTGCATTATTGAG 57.726 45.455 5.27 11.32 0.00 3.02
270 271 3.064958 CACTCTGTGCTGCATTATTGAGG 59.935 47.826 5.27 1.35 0.00 3.86
274 275 3.419943 TGTGCTGCATTATTGAGGTTGA 58.580 40.909 5.27 0.00 0.00 3.18
333 334 6.095021 GCACTCCCTCCGTTTTTATTTATTCT 59.905 38.462 0.00 0.00 0.00 2.40
334 335 7.472543 CACTCCCTCCGTTTTTATTTATTCTG 58.527 38.462 0.00 0.00 0.00 3.02
519 545 7.715264 AACTTTAGACAAATTTAATACGCGC 57.285 32.000 5.73 0.00 0.00 6.86
533 559 8.770850 TTTAATACGCGCAGTAAATAAAATCC 57.229 30.769 5.73 0.00 39.04 3.01
552 584 2.301009 TCCGAGGGAGTAGTGGAAAAAC 59.699 50.000 0.00 0.00 0.00 2.43
627 659 1.590525 ACGTGTGTGCCACAGTACG 60.591 57.895 24.44 24.44 45.43 3.67
628 660 2.935955 GTGTGTGCCACAGTACGC 59.064 61.111 0.00 0.00 45.43 4.42
629 661 1.885388 GTGTGTGCCACAGTACGCA 60.885 57.895 0.00 0.00 45.43 5.24
630 662 1.153349 TGTGTGCCACAGTACGCAA 60.153 52.632 0.00 0.00 44.61 4.85
631 663 1.278637 GTGTGCCACAGTACGCAAC 59.721 57.895 0.00 0.00 38.77 4.17
859 919 3.125316 CCGTTTCAGTTCTGTCGGTAAA 58.875 45.455 17.26 3.89 34.38 2.01
860 920 3.556775 CCGTTTCAGTTCTGTCGGTAAAA 59.443 43.478 17.26 3.39 34.38 1.52
900 971 5.538877 TCTACTCCCCAAATCTTACTCCAT 58.461 41.667 0.00 0.00 0.00 3.41
958 1046 1.635663 CGTCCGTGCAAATCTCACCC 61.636 60.000 0.00 0.00 0.00 4.61
1158 1246 3.047877 CGCGTGGGGAACAACCTC 61.048 66.667 0.00 0.00 40.19 3.85
1650 1738 2.291043 CCTGGTGAACGCCTACCCT 61.291 63.158 5.99 0.00 36.10 4.34
2200 2288 1.133407 CCACGGTGAGCTCTACTCTTC 59.867 57.143 16.19 0.00 46.41 2.87
2211 2299 4.700213 AGCTCTACTCTTCTTCTCTGTCAC 59.300 45.833 0.00 0.00 0.00 3.67
2236 2324 6.403866 TGTTCATGCTTACATTGACCTTTT 57.596 33.333 0.00 0.00 32.87 2.27
2239 2327 4.832266 TCATGCTTACATTGACCTTTTGGT 59.168 37.500 0.00 0.00 45.85 3.67
2486 2589 3.265479 CCAGATTCTTCTTTCCTCCCTGT 59.735 47.826 0.00 0.00 0.00 4.00
2491 2594 4.127918 TCTTCTTTCCTCCCTGTGTAGA 57.872 45.455 0.00 0.00 0.00 2.59
2525 2628 5.652014 TCATTCTCAGGTTTCAAAACACTGT 59.348 36.000 16.60 3.51 40.63 3.55
2574 2691 9.969001 AAGGCTTCCAAACTAAATAAGTATACA 57.031 29.630 5.50 0.00 37.50 2.29
2575 2692 9.969001 AGGCTTCCAAACTAAATAAGTATACAA 57.031 29.630 5.50 0.00 37.50 2.41
2633 2750 0.969894 CTGGAGTTCTCACTTCCCGT 59.030 55.000 2.24 0.00 31.22 5.28
2636 2753 3.170717 TGGAGTTCTCACTTCCCGTTAT 58.829 45.455 2.24 0.00 31.22 1.89
2681 2798 2.217393 GCGTCTAGAATCGAATGCAGTG 59.783 50.000 6.92 0.00 0.00 3.66
2687 2804 0.036388 AATCGAATGCAGTGTCCGGT 60.036 50.000 0.00 0.00 0.00 5.28
2699 2816 3.006110 CAGTGTCCGGTAGGTGTTCTTTA 59.994 47.826 0.00 0.00 39.05 1.85
2704 2821 1.404583 CGGTAGGTGTTCTTTACGGGG 60.405 57.143 0.00 0.00 0.00 5.73
2713 2830 0.974010 TCTTTACGGGGCCGATCTGT 60.974 55.000 0.00 0.00 42.83 3.41
2770 2887 6.211184 TCATTTTATTGCTTTCCTCATGTGGT 59.789 34.615 13.34 0.00 0.00 4.16
2786 2903 3.827625 TGTGGTGTTTCTCGTTTGTTTG 58.172 40.909 0.00 0.00 0.00 2.93
2788 2905 4.231439 GTGGTGTTTCTCGTTTGTTTGTT 58.769 39.130 0.00 0.00 0.00 2.83
2898 3015 3.577848 AGGTACTGAGATCATCATGGAGC 59.422 47.826 0.00 0.00 37.18 4.70
2939 3061 2.679082 GCTGAGATTCAGGGGTAGGTA 58.321 52.381 8.06 0.00 44.43 3.08
2947 3069 5.378985 AGATTCAGGGGTAGGTAGATAGGAA 59.621 44.000 0.00 0.00 0.00 3.36
2948 3070 4.743705 TCAGGGGTAGGTAGATAGGAAG 57.256 50.000 0.00 0.00 0.00 3.46
2955 3077 6.298901 GGGGTAGGTAGATAGGAAGGGAATAT 60.299 46.154 0.00 0.00 0.00 1.28
3049 3177 1.957177 TGCTGAAGACGAAGACTGAGT 59.043 47.619 0.00 0.00 30.05 3.41
3074 3202 2.703007 AGATGTGGATCTGGGTAAGCTC 59.297 50.000 0.00 0.00 37.56 4.09
3102 3230 5.095691 ACGATTAATTTGATGGCATCGAC 57.904 39.130 21.65 6.82 37.53 4.20
3184 3312 5.064579 CCAAATCATTCGGTTTTAATTGCCC 59.935 40.000 0.00 0.00 0.00 5.36
3218 3346 4.485875 TGTTCTCTTGAGTAGTACCCCAA 58.514 43.478 0.00 1.48 0.00 4.12
3260 3388 2.346766 TGAGGTGCAAAAGCTGAAGA 57.653 45.000 0.00 0.00 36.52 2.87
3263 3391 0.040067 GGTGCAAAAGCTGAAGACCG 60.040 55.000 0.00 0.00 0.00 4.79
3264 3392 0.663153 GTGCAAAAGCTGAAGACCGT 59.337 50.000 0.00 0.00 0.00 4.83
3266 3394 1.748493 TGCAAAAGCTGAAGACCGTTT 59.252 42.857 0.00 0.00 0.00 3.60
3269 3397 3.372060 CAAAAGCTGAAGACCGTTTTCC 58.628 45.455 0.00 0.00 0.00 3.13
3270 3398 2.640316 AAGCTGAAGACCGTTTTCCT 57.360 45.000 0.00 0.00 0.00 3.36
3271 3399 3.764237 AAGCTGAAGACCGTTTTCCTA 57.236 42.857 0.00 0.00 0.00 2.94
3272 3400 3.983044 AGCTGAAGACCGTTTTCCTAT 57.017 42.857 0.00 0.00 0.00 2.57
3273 3401 3.863041 AGCTGAAGACCGTTTTCCTATC 58.137 45.455 0.00 0.00 0.00 2.08
3274 3402 3.260884 AGCTGAAGACCGTTTTCCTATCA 59.739 43.478 0.00 0.00 0.00 2.15
3275 3403 4.080863 AGCTGAAGACCGTTTTCCTATCAT 60.081 41.667 0.00 0.00 0.00 2.45
3276 3404 4.271291 GCTGAAGACCGTTTTCCTATCATC 59.729 45.833 0.00 0.00 0.00 2.92
3277 3405 5.665459 CTGAAGACCGTTTTCCTATCATCT 58.335 41.667 0.00 0.00 0.00 2.90
3278 3406 6.049955 TGAAGACCGTTTTCCTATCATCTT 57.950 37.500 0.00 0.00 0.00 2.40
3279 3407 5.874810 TGAAGACCGTTTTCCTATCATCTTG 59.125 40.000 0.00 0.00 0.00 3.02
3280 3408 5.677319 AGACCGTTTTCCTATCATCTTGA 57.323 39.130 0.00 0.00 0.00 3.02
3281 3409 5.665459 AGACCGTTTTCCTATCATCTTGAG 58.335 41.667 0.00 0.00 0.00 3.02
3282 3410 5.422331 AGACCGTTTTCCTATCATCTTGAGA 59.578 40.000 0.00 0.00 0.00 3.27
3283 3411 6.098982 AGACCGTTTTCCTATCATCTTGAGAT 59.901 38.462 0.00 0.00 34.56 2.75
3284 3412 6.653989 ACCGTTTTCCTATCATCTTGAGATT 58.346 36.000 0.00 0.00 31.21 2.40
3285 3413 7.112779 ACCGTTTTCCTATCATCTTGAGATTT 58.887 34.615 0.00 0.00 31.21 2.17
3286 3414 8.265055 ACCGTTTTCCTATCATCTTGAGATTTA 58.735 33.333 0.00 0.00 31.21 1.40
3287 3415 8.552034 CCGTTTTCCTATCATCTTGAGATTTAC 58.448 37.037 0.00 0.00 31.21 2.01
3288 3416 8.269424 CGTTTTCCTATCATCTTGAGATTTACG 58.731 37.037 0.00 0.00 31.21 3.18
3289 3417 9.314321 GTTTTCCTATCATCTTGAGATTTACGA 57.686 33.333 0.00 0.00 31.21 3.43
3290 3418 9.534565 TTTTCCTATCATCTTGAGATTTACGAG 57.465 33.333 0.00 0.00 31.21 4.18
3291 3419 7.220741 TCCTATCATCTTGAGATTTACGAGG 57.779 40.000 0.00 0.00 31.21 4.63
3292 3420 6.778069 TCCTATCATCTTGAGATTTACGAGGT 59.222 38.462 0.00 0.00 31.21 3.85
3293 3421 7.040340 TCCTATCATCTTGAGATTTACGAGGTC 60.040 40.741 0.00 0.00 31.21 3.85
3294 3422 5.914898 TCATCTTGAGATTTACGAGGTCA 57.085 39.130 0.00 0.00 31.21 4.02
3295 3423 6.471233 TCATCTTGAGATTTACGAGGTCAT 57.529 37.500 0.00 0.00 31.21 3.06
3296 3424 6.507900 TCATCTTGAGATTTACGAGGTCATC 58.492 40.000 0.00 0.00 31.21 2.92
3297 3425 5.400782 CATCTTGAGATTTACGAGGTCATCG 59.599 44.000 5.17 5.17 44.41 3.84
3304 3432 2.353607 CGAGGTCATCGTAGGCGC 60.354 66.667 0.00 0.00 46.62 6.53
3305 3433 2.027751 GAGGTCATCGTAGGCGCC 59.972 66.667 21.89 21.89 38.14 6.53
3306 3434 2.442272 AGGTCATCGTAGGCGCCT 60.442 61.111 34.85 34.85 38.14 5.52
3307 3435 2.017559 GAGGTCATCGTAGGCGCCTT 62.018 60.000 37.74 19.11 38.14 4.35
3308 3436 1.153429 GGTCATCGTAGGCGCCTTT 60.153 57.895 37.74 15.08 38.14 3.11
3309 3437 0.743345 GGTCATCGTAGGCGCCTTTT 60.743 55.000 37.74 14.17 38.14 2.27
3310 3438 0.651031 GTCATCGTAGGCGCCTTTTC 59.349 55.000 37.74 23.18 38.14 2.29
3311 3439 0.248012 TCATCGTAGGCGCCTTTTCA 59.752 50.000 37.74 14.74 38.14 2.69
3312 3440 1.134521 TCATCGTAGGCGCCTTTTCAT 60.135 47.619 37.74 18.56 38.14 2.57
3313 3441 1.003545 CATCGTAGGCGCCTTTTCATG 60.004 52.381 37.74 25.29 38.14 3.07
3314 3442 0.742990 TCGTAGGCGCCTTTTCATGG 60.743 55.000 37.74 15.65 38.14 3.66
3315 3443 0.742990 CGTAGGCGCCTTTTCATGGA 60.743 55.000 37.74 11.48 0.00 3.41
3316 3444 0.733150 GTAGGCGCCTTTTCATGGAC 59.267 55.000 37.74 20.50 0.00 4.02
3317 3445 0.326595 TAGGCGCCTTTTCATGGACA 59.673 50.000 37.74 9.65 0.00 4.02
3318 3446 0.962356 AGGCGCCTTTTCATGGACAG 60.962 55.000 27.08 0.00 0.00 3.51
3319 3447 1.508088 GCGCCTTTTCATGGACAGG 59.492 57.895 1.31 1.31 0.00 4.00
3320 3448 0.960364 GCGCCTTTTCATGGACAGGA 60.960 55.000 10.64 0.00 0.00 3.86
3321 3449 1.533625 CGCCTTTTCATGGACAGGAA 58.466 50.000 10.64 0.00 0.00 3.36
3322 3450 1.200020 CGCCTTTTCATGGACAGGAAC 59.800 52.381 10.64 0.00 30.22 3.62
3323 3451 1.200020 GCCTTTTCATGGACAGGAACG 59.800 52.381 10.64 0.00 30.22 3.95
3324 3452 2.504367 CCTTTTCATGGACAGGAACGT 58.496 47.619 0.00 0.00 30.22 3.99
3325 3453 2.884639 CCTTTTCATGGACAGGAACGTT 59.115 45.455 0.00 0.00 30.22 3.99
3326 3454 3.317993 CCTTTTCATGGACAGGAACGTTT 59.682 43.478 0.00 0.00 30.22 3.60
3327 3455 4.537015 CTTTTCATGGACAGGAACGTTTC 58.463 43.478 0.46 0.00 30.22 2.78
3337 3465 2.865119 GGAACGTTTCCTTCCCCTAA 57.135 50.000 0.46 0.00 46.57 2.69
3338 3466 3.144657 GGAACGTTTCCTTCCCCTAAA 57.855 47.619 0.46 0.00 46.57 1.85
3339 3467 3.489355 GGAACGTTTCCTTCCCCTAAAA 58.511 45.455 0.46 0.00 46.57 1.52
3340 3468 3.890756 GGAACGTTTCCTTCCCCTAAAAA 59.109 43.478 0.46 0.00 46.57 1.94
3341 3469 4.261741 GGAACGTTTCCTTCCCCTAAAAAC 60.262 45.833 0.46 0.00 46.57 2.43
3342 3470 3.900971 ACGTTTCCTTCCCCTAAAAACA 58.099 40.909 0.00 0.00 31.72 2.83
3343 3471 3.633525 ACGTTTCCTTCCCCTAAAAACAC 59.366 43.478 0.00 0.00 31.72 3.32
3344 3472 3.633065 CGTTTCCTTCCCCTAAAAACACA 59.367 43.478 0.00 0.00 31.72 3.72
3345 3473 4.279922 CGTTTCCTTCCCCTAAAAACACAT 59.720 41.667 0.00 0.00 31.72 3.21
3346 3474 5.564063 CGTTTCCTTCCCCTAAAAACACATC 60.564 44.000 0.00 0.00 31.72 3.06
3347 3475 3.681593 TCCTTCCCCTAAAAACACATCG 58.318 45.455 0.00 0.00 0.00 3.84
3348 3476 2.163613 CCTTCCCCTAAAAACACATCGC 59.836 50.000 0.00 0.00 0.00 4.58
3349 3477 1.828979 TCCCCTAAAAACACATCGCC 58.171 50.000 0.00 0.00 0.00 5.54
3350 3478 0.450184 CCCCTAAAAACACATCGCCG 59.550 55.000 0.00 0.00 0.00 6.46
3351 3479 1.444836 CCCTAAAAACACATCGCCGA 58.555 50.000 0.00 0.00 0.00 5.54
3352 3480 1.807742 CCCTAAAAACACATCGCCGAA 59.192 47.619 0.00 0.00 0.00 4.30
3353 3481 2.226912 CCCTAAAAACACATCGCCGAAA 59.773 45.455 0.00 0.00 0.00 3.46
3354 3482 3.304794 CCCTAAAAACACATCGCCGAAAA 60.305 43.478 0.00 0.00 0.00 2.29
3355 3483 4.481463 CCTAAAAACACATCGCCGAAAAT 58.519 39.130 0.00 0.00 0.00 1.82
3356 3484 4.557301 CCTAAAAACACATCGCCGAAAATC 59.443 41.667 0.00 0.00 0.00 2.17
3357 3485 2.629639 AAACACATCGCCGAAAATCC 57.370 45.000 0.00 0.00 0.00 3.01
3358 3486 1.821216 AACACATCGCCGAAAATCCT 58.179 45.000 0.00 0.00 0.00 3.24
3359 3487 1.086696 ACACATCGCCGAAAATCCTG 58.913 50.000 0.00 0.00 0.00 3.86
3360 3488 1.338674 ACACATCGCCGAAAATCCTGA 60.339 47.619 0.00 0.00 0.00 3.86
3361 3489 1.737236 CACATCGCCGAAAATCCTGAA 59.263 47.619 0.00 0.00 0.00 3.02
3362 3490 2.161410 CACATCGCCGAAAATCCTGAAA 59.839 45.455 0.00 0.00 0.00 2.69
3363 3491 3.016736 ACATCGCCGAAAATCCTGAAAT 58.983 40.909 0.00 0.00 0.00 2.17
3364 3492 4.035091 CACATCGCCGAAAATCCTGAAATA 59.965 41.667 0.00 0.00 0.00 1.40
3365 3493 4.638421 ACATCGCCGAAAATCCTGAAATAA 59.362 37.500 0.00 0.00 0.00 1.40
3366 3494 5.124776 ACATCGCCGAAAATCCTGAAATAAA 59.875 36.000 0.00 0.00 0.00 1.40
3367 3495 5.828299 TCGCCGAAAATCCTGAAATAAAT 57.172 34.783 0.00 0.00 0.00 1.40
3368 3496 6.202516 TCGCCGAAAATCCTGAAATAAATT 57.797 33.333 0.00 0.00 0.00 1.82
3369 3497 6.262601 TCGCCGAAAATCCTGAAATAAATTC 58.737 36.000 0.00 0.00 38.60 2.17
3370 3498 6.033341 CGCCGAAAATCCTGAAATAAATTCA 58.967 36.000 0.00 0.00 45.71 2.57
3387 3515 6.973229 AAATTCAGAAATAATGCAAGCACC 57.027 33.333 0.00 0.00 0.00 5.01
3388 3516 3.763097 TCAGAAATAATGCAAGCACCG 57.237 42.857 0.00 0.00 0.00 4.94
3389 3517 2.423185 TCAGAAATAATGCAAGCACCGG 59.577 45.455 0.00 0.00 0.00 5.28
3390 3518 1.750778 AGAAATAATGCAAGCACCGGG 59.249 47.619 6.32 0.00 0.00 5.73
3391 3519 1.748493 GAAATAATGCAAGCACCGGGA 59.252 47.619 6.32 0.00 0.00 5.14
3392 3520 1.102978 AATAATGCAAGCACCGGGAC 58.897 50.000 6.32 0.00 0.00 4.46
3393 3521 0.255890 ATAATGCAAGCACCGGGACT 59.744 50.000 6.32 0.00 0.00 3.85
3394 3522 0.037590 TAATGCAAGCACCGGGACTT 59.962 50.000 6.32 5.81 0.00 3.01
3395 3523 1.526575 AATGCAAGCACCGGGACTTG 61.527 55.000 26.09 26.09 44.88 3.16
3396 3524 2.281484 GCAAGCACCGGGACTTGA 60.281 61.111 31.51 0.00 44.89 3.02
3397 3525 1.896660 GCAAGCACCGGGACTTGAA 60.897 57.895 31.51 0.00 44.89 2.69
3398 3526 1.949257 CAAGCACCGGGACTTGAAC 59.051 57.895 26.23 0.00 44.89 3.18
3399 3527 0.535102 CAAGCACCGGGACTTGAACT 60.535 55.000 26.23 1.63 44.89 3.01
3400 3528 0.182775 AAGCACCGGGACTTGAACTT 59.817 50.000 6.32 0.00 0.00 2.66
3401 3529 0.182775 AGCACCGGGACTTGAACTTT 59.817 50.000 6.32 0.00 0.00 2.66
3402 3530 1.418637 AGCACCGGGACTTGAACTTTA 59.581 47.619 6.32 0.00 0.00 1.85
3403 3531 1.804748 GCACCGGGACTTGAACTTTAG 59.195 52.381 6.32 0.00 0.00 1.85
3404 3532 2.423577 CACCGGGACTTGAACTTTAGG 58.576 52.381 6.32 0.00 0.00 2.69
3405 3533 1.271217 ACCGGGACTTGAACTTTAGGC 60.271 52.381 6.32 0.00 0.00 3.93
3406 3534 1.003233 CCGGGACTTGAACTTTAGGCT 59.997 52.381 0.00 0.00 0.00 4.58
3407 3535 2.076863 CGGGACTTGAACTTTAGGCTG 58.923 52.381 0.00 0.00 0.00 4.85
3408 3536 2.437413 GGGACTTGAACTTTAGGCTGG 58.563 52.381 0.00 0.00 0.00 4.85
3409 3537 2.039879 GGGACTTGAACTTTAGGCTGGA 59.960 50.000 0.00 0.00 0.00 3.86
3410 3538 3.339141 GGACTTGAACTTTAGGCTGGAG 58.661 50.000 0.00 0.00 0.00 3.86
3411 3539 3.008049 GGACTTGAACTTTAGGCTGGAGA 59.992 47.826 0.00 0.00 0.00 3.71
3412 3540 4.323868 GGACTTGAACTTTAGGCTGGAGAT 60.324 45.833 0.00 0.00 0.00 2.75
3413 3541 5.104900 GGACTTGAACTTTAGGCTGGAGATA 60.105 44.000 0.00 0.00 0.00 1.98
3414 3542 5.735766 ACTTGAACTTTAGGCTGGAGATAC 58.264 41.667 0.00 0.00 0.00 2.24
3415 3543 4.755266 TGAACTTTAGGCTGGAGATACC 57.245 45.455 0.00 0.00 39.54 2.73
3417 3545 4.081087 TGAACTTTAGGCTGGAGATACCAC 60.081 45.833 0.00 0.00 44.64 4.16
3418 3546 3.725634 ACTTTAGGCTGGAGATACCACT 58.274 45.455 0.00 0.00 44.64 4.00
3419 3547 4.880164 ACTTTAGGCTGGAGATACCACTA 58.120 43.478 0.00 0.00 44.64 2.74
3420 3548 5.468658 ACTTTAGGCTGGAGATACCACTAT 58.531 41.667 0.00 0.00 44.64 2.12
3421 3549 5.540719 ACTTTAGGCTGGAGATACCACTATC 59.459 44.000 0.00 0.00 44.64 2.08
3422 3550 2.896039 AGGCTGGAGATACCACTATCC 58.104 52.381 0.00 0.00 44.64 2.59
3423 3551 1.903183 GGCTGGAGATACCACTATCCC 59.097 57.143 0.00 0.00 44.64 3.85
3424 3552 2.493687 GGCTGGAGATACCACTATCCCT 60.494 54.545 0.00 0.00 44.64 4.20
3425 3553 2.829120 GCTGGAGATACCACTATCCCTC 59.171 54.545 0.00 0.00 44.64 4.30
3426 3554 3.501385 GCTGGAGATACCACTATCCCTCT 60.501 52.174 0.00 0.00 44.64 3.69
3427 3555 4.263994 GCTGGAGATACCACTATCCCTCTA 60.264 50.000 0.00 0.00 44.64 2.43
3428 3556 5.752332 GCTGGAGATACCACTATCCCTCTAA 60.752 48.000 0.00 0.00 44.64 2.10
3429 3557 5.642165 TGGAGATACCACTATCCCTCTAAC 58.358 45.833 0.00 0.00 44.64 2.34
3430 3558 5.018149 GGAGATACCACTATCCCTCTAACC 58.982 50.000 0.00 0.00 38.79 2.85
3431 3559 5.459241 GGAGATACCACTATCCCTCTAACCA 60.459 48.000 0.00 0.00 38.79 3.67
3432 3560 6.234404 AGATACCACTATCCCTCTAACCAT 57.766 41.667 0.00 0.00 30.40 3.55
3433 3561 6.635021 AGATACCACTATCCCTCTAACCATT 58.365 40.000 0.00 0.00 30.40 3.16
3434 3562 6.726764 AGATACCACTATCCCTCTAACCATTC 59.273 42.308 0.00 0.00 30.40 2.67
3435 3563 4.897051 ACCACTATCCCTCTAACCATTCT 58.103 43.478 0.00 0.00 0.00 2.40
3483 3611 8.868522 ATGAAGTTACTCAATTTCATCTGGAA 57.131 30.769 3.19 0.00 43.66 3.53
3485 3613 9.300681 TGAAGTTACTCAATTTCATCTGGAATT 57.699 29.630 0.00 0.00 35.98 2.17
3486 3614 9.780413 GAAGTTACTCAATTTCATCTGGAATTC 57.220 33.333 0.00 0.00 34.91 2.17
3487 3615 8.868522 AGTTACTCAATTTCATCTGGAATTCA 57.131 30.769 7.93 0.00 34.91 2.57
3488 3616 9.471702 AGTTACTCAATTTCATCTGGAATTCAT 57.528 29.630 7.93 0.00 34.91 2.57
3489 3617 9.727627 GTTACTCAATTTCATCTGGAATTCATC 57.272 33.333 7.93 0.00 34.91 2.92
3545 5512 6.721321 TCATGTCGAAGGTTAAACTTTTGTC 58.279 36.000 7.31 2.45 0.00 3.18
3556 5523 3.715628 AACTTTTGTCATCTGGCACAC 57.284 42.857 0.00 0.00 0.00 3.82
3557 5524 2.653726 ACTTTTGTCATCTGGCACACA 58.346 42.857 0.00 0.00 0.00 3.72
3629 5599 9.832445 GATCCTATCCTTCTTTATGTTGTGTTA 57.168 33.333 0.00 0.00 0.00 2.41
3734 5714 5.418840 AGTTGCCCACATTTTGGTTATAGAG 59.581 40.000 0.00 0.00 45.25 2.43
3754 5734 4.009002 GAGGAGACAACCGTTACTACTCT 58.991 47.826 16.42 5.60 37.36 3.24
3785 5765 9.757227 TTTTAAGTTAAGCAACCGTTACTACTA 57.243 29.630 0.00 0.00 35.05 1.82
3786 5766 8.970691 TTAAGTTAAGCAACCGTTACTACTAG 57.029 34.615 0.00 0.00 35.05 2.57
3787 5767 5.958955 AGTTAAGCAACCGTTACTACTAGG 58.041 41.667 0.00 0.00 35.05 3.02
3788 5768 5.711976 AGTTAAGCAACCGTTACTACTAGGA 59.288 40.000 0.00 0.00 35.05 2.94
3789 5769 4.715527 AAGCAACCGTTACTACTAGGAG 57.284 45.455 0.00 0.00 0.00 3.69
3790 5770 2.426381 AGCAACCGTTACTACTAGGAGC 59.574 50.000 0.36 0.00 0.00 4.70
3791 5771 2.480932 GCAACCGTTACTACTAGGAGCC 60.481 54.545 0.36 0.00 0.00 4.70
3792 5772 1.673168 ACCGTTACTACTAGGAGCCG 58.327 55.000 0.36 1.99 0.00 5.52
3793 5773 0.950116 CCGTTACTACTAGGAGCCGG 59.050 60.000 12.39 12.39 0.00 6.13
3794 5774 1.673168 CGTTACTACTAGGAGCCGGT 58.327 55.000 0.36 0.00 0.00 5.28
3795 5775 1.601430 CGTTACTACTAGGAGCCGGTC 59.399 57.143 0.36 0.00 0.00 4.79
3796 5776 2.648059 GTTACTACTAGGAGCCGGTCA 58.352 52.381 0.36 0.00 0.00 4.02
3797 5777 3.220940 GTTACTACTAGGAGCCGGTCAT 58.779 50.000 0.36 0.00 0.00 3.06
3798 5778 4.392940 GTTACTACTAGGAGCCGGTCATA 58.607 47.826 0.36 0.63 0.00 2.15
3799 5779 3.143211 ACTACTAGGAGCCGGTCATAG 57.857 52.381 15.77 15.77 43.88 2.23
3803 5783 2.588620 CTAGGAGCCGGTCATAGTTCT 58.411 52.381 10.43 0.00 35.24 3.01
3813 5812 6.985059 AGCCGGTCATAGTTCTTAAGATAAAC 59.015 38.462 5.89 1.68 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 1.153823 GCTACTGGTCGACGCACAT 60.154 57.895 9.92 1.14 0.00 3.21
104 105 4.697828 TGATGCTATTGGTCGTGCTAAAAA 59.302 37.500 0.00 0.00 0.00 1.94
105 106 4.257731 TGATGCTATTGGTCGTGCTAAAA 58.742 39.130 0.00 0.00 0.00 1.52
106 107 3.867857 TGATGCTATTGGTCGTGCTAAA 58.132 40.909 0.00 0.00 0.00 1.85
107 108 3.535280 TGATGCTATTGGTCGTGCTAA 57.465 42.857 0.00 0.00 0.00 3.09
108 109 3.751479 ATGATGCTATTGGTCGTGCTA 57.249 42.857 0.00 0.00 0.00 3.49
109 110 2.627515 ATGATGCTATTGGTCGTGCT 57.372 45.000 0.00 0.00 0.00 4.40
110 111 2.874701 AGAATGATGCTATTGGTCGTGC 59.125 45.455 0.00 0.00 0.00 5.34
111 112 3.249320 CCAGAATGATGCTATTGGTCGTG 59.751 47.826 0.00 0.00 39.69 4.35
112 113 3.470709 CCAGAATGATGCTATTGGTCGT 58.529 45.455 0.00 0.00 39.69 4.34
143 144 0.999406 CATCGGCTAGTGTGAAACCG 59.001 55.000 0.00 0.00 45.15 4.44
159 160 2.417243 CGTCAATTTTCTTGGGCCCATC 60.417 50.000 29.23 0.00 0.00 3.51
189 190 3.940209 TTTTAGCCAAACTGCTGATGG 57.060 42.857 13.16 13.16 42.77 3.51
216 217 6.170675 AGAAGATGAATACAACAAACTCGC 57.829 37.500 0.00 0.00 0.00 5.03
258 259 7.838884 TGATTTCATTCAACCTCAATAATGCA 58.161 30.769 0.00 0.00 30.99 3.96
259 260 8.706492 TTGATTTCATTCAACCTCAATAATGC 57.294 30.769 0.00 0.00 30.82 3.56
269 270 5.933463 TGCAAGGAATTGATTTCATTCAACC 59.067 36.000 0.00 0.00 36.25 3.77
270 271 6.401796 GCTGCAAGGAATTGATTTCATTCAAC 60.402 38.462 0.00 0.00 36.25 3.18
274 275 5.155278 TGCTGCAAGGAATTGATTTCATT 57.845 34.783 0.00 0.00 38.82 2.57
497 523 6.959311 ACTGCGCGTATTAAATTTGTCTAAAG 59.041 34.615 8.43 0.00 0.00 1.85
498 524 6.833839 ACTGCGCGTATTAAATTTGTCTAAA 58.166 32.000 8.43 0.00 0.00 1.85
508 534 7.583401 CGGATTTTATTTACTGCGCGTATTAAA 59.417 33.333 18.79 18.79 0.00 1.52
509 535 7.042858 TCGGATTTTATTTACTGCGCGTATTAA 60.043 33.333 8.43 5.29 0.00 1.40
515 541 3.531982 CTCGGATTTTATTTACTGCGCG 58.468 45.455 0.00 0.00 0.00 6.86
518 544 5.123936 ACTCCCTCGGATTTTATTTACTGC 58.876 41.667 0.00 0.00 0.00 4.40
519 545 7.438459 CACTACTCCCTCGGATTTTATTTACTG 59.562 40.741 0.00 0.00 0.00 2.74
531 557 2.301009 GTTTTTCCACTACTCCCTCGGA 59.699 50.000 0.00 0.00 0.00 4.55
533 559 2.029649 TCGTTTTTCCACTACTCCCTCG 60.030 50.000 0.00 0.00 0.00 4.63
552 584 1.217882 AGACGTTGCAAAAGGTCTCG 58.782 50.000 18.26 11.28 42.25 4.04
631 663 1.081509 CATGGGAAACGTTGGTGCG 60.082 57.895 0.00 0.00 37.94 5.34
765 816 0.170561 CCGGAGACAGGTAGACAACG 59.829 60.000 0.00 0.00 0.00 4.10
773 824 3.923645 TGGGACCCGGAGACAGGT 61.924 66.667 0.73 0.00 39.75 4.00
774 825 3.391382 GTGGGACCCGGAGACAGG 61.391 72.222 0.73 0.00 0.00 4.00
859 919 0.391263 GAAGGCGATCGGGTGAAGTT 60.391 55.000 18.30 0.00 0.00 2.66
860 920 1.218316 GAAGGCGATCGGGTGAAGT 59.782 57.895 18.30 0.00 0.00 3.01
900 971 2.467880 GAGAGTGATTGGAGGTGGGTA 58.532 52.381 0.00 0.00 0.00 3.69
927 1015 1.895231 ACGGACGAAGGTTTTGGGC 60.895 57.895 0.00 0.00 0.00 5.36
958 1046 4.150454 AGGGAGGGAGGAGAGCGG 62.150 72.222 0.00 0.00 0.00 5.52
1113 1201 1.218047 GATGCCCAGTAGCGACACA 59.782 57.895 0.00 0.00 34.65 3.72
1122 1210 1.078426 GCCGTAGTTGATGCCCAGT 60.078 57.895 0.00 0.00 0.00 4.00
1476 1564 4.243008 TTGTCGAGGTTGGCCGCA 62.243 61.111 0.00 0.00 40.50 5.69
1650 1738 0.729116 CGTCGGAGTAGGCGAAGTAA 59.271 55.000 0.00 0.00 0.00 2.24
1869 1957 3.533691 GCCTTCTCGTTCGCGTCG 61.534 66.667 5.77 12.96 42.11 5.12
1908 1996 0.102663 TCACGTTGCTGTTGTACCGA 59.897 50.000 0.00 0.00 0.00 4.69
2200 2288 4.063689 AGCATGAACAAGTGACAGAGAAG 58.936 43.478 0.00 0.00 0.00 2.85
2211 2299 5.633830 AGGTCAATGTAAGCATGAACAAG 57.366 39.130 0.00 0.00 35.15 3.16
2236 2324 2.338809 AGTGTCATCTCCTTTCCACCA 58.661 47.619 0.00 0.00 0.00 4.17
2239 2327 3.498481 CCCAAAGTGTCATCTCCTTTCCA 60.498 47.826 0.00 0.00 0.00 3.53
2486 2589 6.875726 CCTGAGAATGATGTCAAGTTTCTACA 59.124 38.462 0.00 0.00 0.00 2.74
2491 2594 6.547141 TGAAACCTGAGAATGATGTCAAGTTT 59.453 34.615 3.30 3.30 42.74 2.66
2543 2648 8.148351 ACTTATTTAGTTTGGAAGCCTTTTTCC 58.852 33.333 0.00 0.00 39.65 3.13
2570 2687 7.255871 GGAGTCACCGGATCTACTATTTTGTAT 60.256 40.741 9.46 0.00 0.00 2.29
2571 2688 6.040166 GGAGTCACCGGATCTACTATTTTGTA 59.960 42.308 9.46 0.00 0.00 2.41
2572 2689 5.163437 GGAGTCACCGGATCTACTATTTTGT 60.163 44.000 9.46 0.00 0.00 2.83
2573 2690 5.163447 TGGAGTCACCGGATCTACTATTTTG 60.163 44.000 9.46 0.00 42.61 2.44
2574 2691 4.960469 TGGAGTCACCGGATCTACTATTTT 59.040 41.667 9.46 0.00 42.61 1.82
2575 2692 4.543689 TGGAGTCACCGGATCTACTATTT 58.456 43.478 9.46 0.00 42.61 1.40
2576 2693 4.180377 TGGAGTCACCGGATCTACTATT 57.820 45.455 9.46 0.00 42.61 1.73
2577 2694 3.878237 TGGAGTCACCGGATCTACTAT 57.122 47.619 9.46 0.00 42.61 2.12
2587 2704 0.534412 ATCTCTTGCTGGAGTCACCG 59.466 55.000 0.00 0.00 42.61 4.94
2633 2750 8.881743 GCATTTGGCATTTTGACTATCAAATAA 58.118 29.630 4.90 0.00 43.11 1.40
2636 2753 5.348179 CGCATTTGGCATTTTGACTATCAAA 59.652 36.000 0.00 0.00 42.83 2.69
2681 2798 2.599659 CGTAAAGAACACCTACCGGAC 58.400 52.381 9.46 0.00 0.00 4.79
2687 2804 0.614812 GGCCCCGTAAAGAACACCTA 59.385 55.000 0.00 0.00 0.00 3.08
2699 2816 2.046314 CAAACAGATCGGCCCCGT 60.046 61.111 6.61 0.00 40.74 5.28
2704 2821 3.253432 AGAAAAAGGACAAACAGATCGGC 59.747 43.478 0.00 0.00 0.00 5.54
2770 2887 4.167554 AGCAACAAACAAACGAGAAACA 57.832 36.364 0.00 0.00 0.00 2.83
2786 2903 4.051237 GACCCTTTTGAATCACAAGCAAC 58.949 43.478 3.74 0.00 39.77 4.17
2788 2905 2.293122 CGACCCTTTTGAATCACAAGCA 59.707 45.455 3.74 0.00 39.77 3.91
2939 3061 6.214412 CAGGCAGTTATATTCCCTTCCTATCT 59.786 42.308 0.00 0.00 0.00 1.98
2947 3069 3.072184 CAGAGCAGGCAGTTATATTCCCT 59.928 47.826 0.00 0.00 0.00 4.20
2948 3070 3.406764 CAGAGCAGGCAGTTATATTCCC 58.593 50.000 0.00 0.00 0.00 3.97
3049 3177 0.032117 ACCCAGATCCACATCTCGGA 60.032 55.000 2.97 0.00 39.26 4.55
3074 3202 7.357777 CGATGCCATCAAATTAATCGTTTCATG 60.358 37.037 5.40 0.00 33.92 3.07
3102 3230 4.319766 GGCACCAAGATGAAATACATAGCG 60.320 45.833 0.00 0.00 39.56 4.26
3168 3296 8.350852 TCTATTAAAGGGCAATTAAAACCGAA 57.649 30.769 0.00 0.00 0.00 4.30
3260 3388 5.677319 TCTCAAGATGATAGGAAAACGGT 57.323 39.130 0.00 0.00 0.00 4.83
3263 3391 9.314321 TCGTAAATCTCAAGATGATAGGAAAAC 57.686 33.333 0.00 0.00 34.49 2.43
3264 3392 9.534565 CTCGTAAATCTCAAGATGATAGGAAAA 57.465 33.333 0.00 0.00 34.49 2.29
3266 3394 7.287927 ACCTCGTAAATCTCAAGATGATAGGAA 59.712 37.037 11.21 0.43 34.49 3.36
3269 3397 7.652727 TGACCTCGTAAATCTCAAGATGATAG 58.347 38.462 0.00 0.00 34.49 2.08
3270 3398 7.582667 TGACCTCGTAAATCTCAAGATGATA 57.417 36.000 0.00 0.00 34.49 2.15
3271 3399 6.471233 TGACCTCGTAAATCTCAAGATGAT 57.529 37.500 0.00 0.00 34.49 2.45
3272 3400 5.914898 TGACCTCGTAAATCTCAAGATGA 57.085 39.130 0.00 0.00 34.49 2.92
3273 3401 5.400782 CGATGACCTCGTAAATCTCAAGATG 59.599 44.000 0.00 0.00 42.56 2.90
3274 3402 5.524284 CGATGACCTCGTAAATCTCAAGAT 58.476 41.667 0.00 0.00 42.56 2.40
3275 3403 4.921547 CGATGACCTCGTAAATCTCAAGA 58.078 43.478 0.00 0.00 42.56 3.02
3288 3416 2.017559 AAGGCGCCTACGATGACCTC 62.018 60.000 33.07 0.00 43.93 3.85
3289 3417 1.614241 AAAGGCGCCTACGATGACCT 61.614 55.000 33.07 7.71 43.93 3.85
3290 3418 0.743345 AAAAGGCGCCTACGATGACC 60.743 55.000 33.07 0.00 43.93 4.02
3291 3419 0.651031 GAAAAGGCGCCTACGATGAC 59.349 55.000 33.07 13.19 43.93 3.06
3292 3420 0.248012 TGAAAAGGCGCCTACGATGA 59.752 50.000 33.07 9.17 43.93 2.92
3293 3421 1.003545 CATGAAAAGGCGCCTACGATG 60.004 52.381 33.07 23.62 43.93 3.84
3294 3422 1.299541 CATGAAAAGGCGCCTACGAT 58.700 50.000 33.07 16.42 43.93 3.73
3295 3423 0.742990 CCATGAAAAGGCGCCTACGA 60.743 55.000 33.07 14.82 43.93 3.43
3296 3424 0.742990 TCCATGAAAAGGCGCCTACG 60.743 55.000 33.07 14.14 44.07 3.51
3297 3425 0.733150 GTCCATGAAAAGGCGCCTAC 59.267 55.000 33.07 23.56 0.00 3.18
3298 3426 0.326595 TGTCCATGAAAAGGCGCCTA 59.673 50.000 33.07 15.54 0.00 3.93
3299 3427 0.962356 CTGTCCATGAAAAGGCGCCT 60.962 55.000 27.08 27.08 0.00 5.52
3300 3428 1.508088 CTGTCCATGAAAAGGCGCC 59.492 57.895 21.89 21.89 0.00 6.53
3301 3429 0.960364 TCCTGTCCATGAAAAGGCGC 60.960 55.000 0.00 0.00 0.00 6.53
3302 3430 1.200020 GTTCCTGTCCATGAAAAGGCG 59.800 52.381 0.00 0.00 0.00 5.52
3303 3431 1.200020 CGTTCCTGTCCATGAAAAGGC 59.800 52.381 0.00 0.00 0.00 4.35
3304 3432 2.504367 ACGTTCCTGTCCATGAAAAGG 58.496 47.619 0.00 0.00 0.00 3.11
3305 3433 4.537015 GAAACGTTCCTGTCCATGAAAAG 58.463 43.478 0.00 0.00 0.00 2.27
3306 3434 3.316868 GGAAACGTTCCTGTCCATGAAAA 59.683 43.478 11.11 0.00 46.57 2.29
3307 3435 2.882137 GGAAACGTTCCTGTCCATGAAA 59.118 45.455 11.11 0.00 46.57 2.69
3308 3436 2.500229 GGAAACGTTCCTGTCCATGAA 58.500 47.619 11.11 0.00 46.57 2.57
3309 3437 2.178912 GGAAACGTTCCTGTCCATGA 57.821 50.000 11.11 0.00 46.57 3.07
3319 3447 4.338964 TGTTTTTAGGGGAAGGAAACGTTC 59.661 41.667 0.00 0.00 33.98 3.95
3320 3448 4.098349 GTGTTTTTAGGGGAAGGAAACGTT 59.902 41.667 0.00 0.00 33.98 3.99
3321 3449 3.633525 GTGTTTTTAGGGGAAGGAAACGT 59.366 43.478 0.00 0.00 33.98 3.99
3322 3450 3.633065 TGTGTTTTTAGGGGAAGGAAACG 59.367 43.478 0.00 0.00 33.98 3.60
3323 3451 5.564063 CGATGTGTTTTTAGGGGAAGGAAAC 60.564 44.000 0.00 0.00 0.00 2.78
3324 3452 4.521256 CGATGTGTTTTTAGGGGAAGGAAA 59.479 41.667 0.00 0.00 0.00 3.13
3325 3453 4.076394 CGATGTGTTTTTAGGGGAAGGAA 58.924 43.478 0.00 0.00 0.00 3.36
3326 3454 3.681593 CGATGTGTTTTTAGGGGAAGGA 58.318 45.455 0.00 0.00 0.00 3.36
3327 3455 2.163613 GCGATGTGTTTTTAGGGGAAGG 59.836 50.000 0.00 0.00 0.00 3.46
3328 3456 2.163613 GGCGATGTGTTTTTAGGGGAAG 59.836 50.000 0.00 0.00 0.00 3.46
3329 3457 2.164338 GGCGATGTGTTTTTAGGGGAA 58.836 47.619 0.00 0.00 0.00 3.97
3330 3458 1.828979 GGCGATGTGTTTTTAGGGGA 58.171 50.000 0.00 0.00 0.00 4.81
3331 3459 0.450184 CGGCGATGTGTTTTTAGGGG 59.550 55.000 0.00 0.00 0.00 4.79
3332 3460 1.444836 TCGGCGATGTGTTTTTAGGG 58.555 50.000 4.99 0.00 0.00 3.53
3333 3461 3.546002 TTTCGGCGATGTGTTTTTAGG 57.454 42.857 11.76 0.00 0.00 2.69
3334 3462 4.557301 GGATTTTCGGCGATGTGTTTTTAG 59.443 41.667 11.76 0.00 0.00 1.85
3335 3463 4.216687 AGGATTTTCGGCGATGTGTTTTTA 59.783 37.500 11.76 0.00 0.00 1.52
3336 3464 3.005367 AGGATTTTCGGCGATGTGTTTTT 59.995 39.130 11.76 0.00 0.00 1.94
3337 3465 2.556622 AGGATTTTCGGCGATGTGTTTT 59.443 40.909 11.76 0.00 0.00 2.43
3338 3466 2.095263 CAGGATTTTCGGCGATGTGTTT 60.095 45.455 11.76 0.00 0.00 2.83
3339 3467 1.468520 CAGGATTTTCGGCGATGTGTT 59.531 47.619 11.76 0.00 0.00 3.32
3340 3468 1.086696 CAGGATTTTCGGCGATGTGT 58.913 50.000 11.76 0.00 0.00 3.72
3341 3469 1.368641 TCAGGATTTTCGGCGATGTG 58.631 50.000 11.76 2.41 0.00 3.21
3342 3470 2.107950 TTCAGGATTTTCGGCGATGT 57.892 45.000 11.76 0.00 0.00 3.06
3343 3471 3.698029 ATTTCAGGATTTTCGGCGATG 57.302 42.857 11.76 4.79 0.00 3.84
3344 3472 5.828299 TTTATTTCAGGATTTTCGGCGAT 57.172 34.783 11.76 0.00 0.00 4.58
3345 3473 5.828299 ATTTATTTCAGGATTTTCGGCGA 57.172 34.783 4.99 4.99 0.00 5.54
3346 3474 6.033341 TGAATTTATTTCAGGATTTTCGGCG 58.967 36.000 0.00 0.00 39.44 6.46
3361 3489 9.101655 GGTGCTTGCATTATTTCTGAATTTATT 57.898 29.630 0.00 0.00 0.00 1.40
3362 3490 7.436080 CGGTGCTTGCATTATTTCTGAATTTAT 59.564 33.333 0.00 0.00 0.00 1.40
3363 3491 6.751425 CGGTGCTTGCATTATTTCTGAATTTA 59.249 34.615 0.00 0.00 0.00 1.40
3364 3492 5.577945 CGGTGCTTGCATTATTTCTGAATTT 59.422 36.000 0.00 0.00 0.00 1.82
3365 3493 5.104374 CGGTGCTTGCATTATTTCTGAATT 58.896 37.500 0.00 0.00 0.00 2.17
3366 3494 4.440525 CCGGTGCTTGCATTATTTCTGAAT 60.441 41.667 0.00 0.00 0.00 2.57
3367 3495 3.119531 CCGGTGCTTGCATTATTTCTGAA 60.120 43.478 0.00 0.00 0.00 3.02
3368 3496 2.423185 CCGGTGCTTGCATTATTTCTGA 59.577 45.455 0.00 0.00 0.00 3.27
3369 3497 2.480073 CCCGGTGCTTGCATTATTTCTG 60.480 50.000 0.00 0.00 0.00 3.02
3370 3498 1.750778 CCCGGTGCTTGCATTATTTCT 59.249 47.619 0.00 0.00 0.00 2.52
3371 3499 1.748493 TCCCGGTGCTTGCATTATTTC 59.252 47.619 0.00 0.00 0.00 2.17
3372 3500 1.476488 GTCCCGGTGCTTGCATTATTT 59.524 47.619 0.00 0.00 0.00 1.40
3373 3501 1.102978 GTCCCGGTGCTTGCATTATT 58.897 50.000 0.00 0.00 0.00 1.40
3374 3502 0.255890 AGTCCCGGTGCTTGCATTAT 59.744 50.000 0.00 0.00 0.00 1.28
3375 3503 0.037590 AAGTCCCGGTGCTTGCATTA 59.962 50.000 0.00 0.00 0.00 1.90
3376 3504 1.228552 AAGTCCCGGTGCTTGCATT 60.229 52.632 0.00 0.00 0.00 3.56
3377 3505 1.973281 CAAGTCCCGGTGCTTGCAT 60.973 57.895 18.22 0.00 36.17 3.96
3378 3506 2.594303 CAAGTCCCGGTGCTTGCA 60.594 61.111 18.22 0.00 36.17 4.08
3379 3507 1.896660 TTCAAGTCCCGGTGCTTGC 60.897 57.895 22.82 0.00 41.15 4.01
3380 3508 0.535102 AGTTCAAGTCCCGGTGCTTG 60.535 55.000 22.05 22.05 42.32 4.01
3381 3509 0.182775 AAGTTCAAGTCCCGGTGCTT 59.817 50.000 0.00 0.67 0.00 3.91
3382 3510 0.182775 AAAGTTCAAGTCCCGGTGCT 59.817 50.000 0.00 0.00 0.00 4.40
3383 3511 1.804748 CTAAAGTTCAAGTCCCGGTGC 59.195 52.381 0.00 0.00 0.00 5.01
3384 3512 2.423577 CCTAAAGTTCAAGTCCCGGTG 58.576 52.381 0.00 0.00 0.00 4.94
3385 3513 1.271217 GCCTAAAGTTCAAGTCCCGGT 60.271 52.381 0.00 0.00 0.00 5.28
3386 3514 1.003233 AGCCTAAAGTTCAAGTCCCGG 59.997 52.381 0.00 0.00 0.00 5.73
3387 3515 2.076863 CAGCCTAAAGTTCAAGTCCCG 58.923 52.381 0.00 0.00 0.00 5.14
3388 3516 2.039879 TCCAGCCTAAAGTTCAAGTCCC 59.960 50.000 0.00 0.00 0.00 4.46
3389 3517 3.008049 TCTCCAGCCTAAAGTTCAAGTCC 59.992 47.826 0.00 0.00 0.00 3.85
3390 3518 4.273148 TCTCCAGCCTAAAGTTCAAGTC 57.727 45.455 0.00 0.00 0.00 3.01
3391 3519 4.917906 ATCTCCAGCCTAAAGTTCAAGT 57.082 40.909 0.00 0.00 0.00 3.16
3392 3520 5.119694 GGTATCTCCAGCCTAAAGTTCAAG 58.880 45.833 0.00 0.00 35.97 3.02
3393 3521 4.534500 TGGTATCTCCAGCCTAAAGTTCAA 59.466 41.667 0.00 0.00 41.93 2.69
3394 3522 4.101114 TGGTATCTCCAGCCTAAAGTTCA 58.899 43.478 0.00 0.00 41.93 3.18
3395 3523 4.755266 TGGTATCTCCAGCCTAAAGTTC 57.245 45.455 0.00 0.00 41.93 3.01
3406 3534 5.459241 GGTTAGAGGGATAGTGGTATCTCCA 60.459 48.000 0.00 0.00 45.01 3.86
3407 3535 5.018149 GGTTAGAGGGATAGTGGTATCTCC 58.982 50.000 0.00 0.00 36.87 3.71
3408 3536 5.642165 TGGTTAGAGGGATAGTGGTATCTC 58.358 45.833 0.00 0.00 36.48 2.75
3409 3537 5.681494 TGGTTAGAGGGATAGTGGTATCT 57.319 43.478 0.00 0.00 36.11 1.98
3410 3538 6.726764 AGAATGGTTAGAGGGATAGTGGTATC 59.273 42.308 0.00 0.00 35.19 2.24
3411 3539 6.635021 AGAATGGTTAGAGGGATAGTGGTAT 58.365 40.000 0.00 0.00 0.00 2.73
3412 3540 6.039415 AGAATGGTTAGAGGGATAGTGGTA 57.961 41.667 0.00 0.00 0.00 3.25
3413 3541 4.897051 AGAATGGTTAGAGGGATAGTGGT 58.103 43.478 0.00 0.00 0.00 4.16
3414 3542 4.284746 GGAGAATGGTTAGAGGGATAGTGG 59.715 50.000 0.00 0.00 0.00 4.00
3415 3543 5.151454 AGGAGAATGGTTAGAGGGATAGTG 58.849 45.833 0.00 0.00 0.00 2.74
3416 3544 5.426325 AGGAGAATGGTTAGAGGGATAGT 57.574 43.478 0.00 0.00 0.00 2.12
3417 3545 6.239743 GGAAAGGAGAATGGTTAGAGGGATAG 60.240 46.154 0.00 0.00 0.00 2.08
3418 3546 5.607171 GGAAAGGAGAATGGTTAGAGGGATA 59.393 44.000 0.00 0.00 0.00 2.59
3419 3547 4.413851 GGAAAGGAGAATGGTTAGAGGGAT 59.586 45.833 0.00 0.00 0.00 3.85
3420 3548 3.780850 GGAAAGGAGAATGGTTAGAGGGA 59.219 47.826 0.00 0.00 0.00 4.20
3421 3549 3.523564 TGGAAAGGAGAATGGTTAGAGGG 59.476 47.826 0.00 0.00 0.00 4.30
3422 3550 4.844349 TGGAAAGGAGAATGGTTAGAGG 57.156 45.455 0.00 0.00 0.00 3.69
3423 3551 8.807948 TTATTTGGAAAGGAGAATGGTTAGAG 57.192 34.615 0.00 0.00 0.00 2.43
3424 3552 9.189156 CATTATTTGGAAAGGAGAATGGTTAGA 57.811 33.333 0.00 0.00 0.00 2.10
3425 3553 9.189156 TCATTATTTGGAAAGGAGAATGGTTAG 57.811 33.333 0.00 0.00 0.00 2.34
3426 3554 9.540538 TTCATTATTTGGAAAGGAGAATGGTTA 57.459 29.630 0.00 0.00 0.00 2.85
3427 3555 8.434589 TTCATTATTTGGAAAGGAGAATGGTT 57.565 30.769 0.00 0.00 0.00 3.67
3428 3556 8.434589 TTTCATTATTTGGAAAGGAGAATGGT 57.565 30.769 0.00 0.00 0.00 3.55
3429 3557 9.895138 ATTTTCATTATTTGGAAAGGAGAATGG 57.105 29.630 0.00 0.00 36.25 3.16
3514 3651 3.340814 AACCTTCGACATGAGCAATCT 57.659 42.857 0.00 0.00 0.00 2.40
3524 3661 6.540914 AGATGACAAAAGTTTAACCTTCGACA 59.459 34.615 0.00 0.00 0.00 4.35
3545 5512 1.395954 CTGATCGTTGTGTGCCAGATG 59.604 52.381 0.00 0.00 0.00 2.90
3556 5523 4.094887 ACCGAATCCATTTTCTGATCGTTG 59.905 41.667 0.00 0.00 0.00 4.10
3557 5524 4.261801 ACCGAATCCATTTTCTGATCGTT 58.738 39.130 0.00 0.00 0.00 3.85
3629 5599 5.268118 TGAATCTCGTATCTGACTGCAAT 57.732 39.130 0.00 0.00 0.00 3.56
3665 5641 9.195411 ACTCAATTAACAATGCACAACATAAAG 57.805 29.630 0.00 0.00 38.34 1.85
3666 5642 8.976471 CACTCAATTAACAATGCACAACATAAA 58.024 29.630 0.00 0.00 38.34 1.40
3734 5714 4.780275 AAGAGTAGTAACGGTTGTCTCC 57.220 45.455 3.07 0.00 0.00 3.71
3768 5748 3.119209 GCTCCTAGTAGTAACGGTTGCTT 60.119 47.826 16.50 2.82 0.00 3.91
3785 5765 1.867363 AAGAACTATGACCGGCTCCT 58.133 50.000 0.00 0.00 0.00 3.69
3786 5766 3.383825 TCTTAAGAACTATGACCGGCTCC 59.616 47.826 0.00 0.00 0.00 4.70
3787 5767 4.650754 TCTTAAGAACTATGACCGGCTC 57.349 45.455 0.00 0.00 0.00 4.70
3788 5768 6.726490 TTATCTTAAGAACTATGACCGGCT 57.274 37.500 9.71 0.00 0.00 5.52
3789 5769 6.759827 TGTTTATCTTAAGAACTATGACCGGC 59.240 38.462 9.71 0.00 0.00 6.13
3790 5770 8.712285 TTGTTTATCTTAAGAACTATGACCGG 57.288 34.615 9.71 0.00 0.00 5.28
3813 5812 9.132521 CTGTTTTTAGCAAGGAGTGATAATTTG 57.867 33.333 0.00 0.00 37.90 2.32


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

AutoCloner maintained by Alex Coulton.