Multiple sequence alignment - TraesCS2D01G471500

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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 TraesCS2D01G471500 chr2D 100.000 3679 0 0 1 3679 575358463 575362141 0.000000e+00 6794.0
1 TraesCS2D01G471500 chr2D 79.482 463 55 22 1022 1472 140713136 140713570 3.590000e-75 292.0
2 TraesCS2D01G471500 chr2D 80.120 332 55 9 2432 2762 439657372 439657051 1.710000e-58 237.0
3 TraesCS2D01G471500 chr2D 93.827 81 4 1 1904 1983 575360282 575360362 1.790000e-23 121.0
4 TraesCS2D01G471500 chr2D 93.827 81 4 1 1820 1900 575360366 575360445 1.790000e-23 121.0
5 TraesCS2D01G471500 chr2A 94.336 1995 94 8 1 1983 713542713 713544700 0.000000e+00 3040.0
6 TraesCS2D01G471500 chr2A 95.060 1417 62 8 1820 3231 713544622 713546035 0.000000e+00 2222.0
7 TraesCS2D01G471500 chr2A 89.041 219 23 1 3429 3646 713628958 713629176 1.680000e-68 270.0
8 TraesCS2D01G471500 chr2A 92.500 80 6 0 1904 1983 713544539 713544618 8.350000e-22 115.0
9 TraesCS2D01G471500 chr2A 83.019 106 11 5 2432 2537 425831545 425831643 5.060000e-14 89.8
10 TraesCS2D01G471500 chr2B 92.364 1925 114 10 1 1900 691452045 691453961 0.000000e+00 2710.0
11 TraesCS2D01G471500 chr2B 94.631 1341 56 4 1904 3228 691453882 691455222 0.000000e+00 2063.0
12 TraesCS2D01G471500 chr2B 78.339 277 23 19 3300 3550 691462032 691462297 1.060000e-30 145.0
13 TraesCS2D01G471500 chr6A 88.261 903 91 8 1 895 617687099 617686204 0.000000e+00 1066.0
14 TraesCS2D01G471500 chr6A 83.661 814 105 18 2426 3231 617683431 617682638 0.000000e+00 741.0
15 TraesCS2D01G471500 chr6A 82.031 128 10 4 1003 1130 617686075 617685961 3.020000e-16 97.1
16 TraesCS2D01G471500 chr6D 87.364 918 93 10 1 895 472305577 472306494 0.000000e+00 1031.0
17 TraesCS2D01G471500 chr6D 86.250 560 54 9 2426 2974 472307539 472308086 1.470000e-163 586.0
18 TraesCS2D01G471500 chr6D 78.543 508 52 29 985 1472 472306598 472307068 7.780000e-72 281.0
19 TraesCS2D01G471500 chr6D 92.958 71 5 0 2537 2607 472312094 472312164 1.810000e-18 104.0
20 TraesCS2D01G471500 chr6D 92.105 38 2 1 2721 2758 472312197 472312233 7.000000e-03 52.8
21 TraesCS2D01G471500 chr6B 87.078 859 96 8 1 853 716975899 716976748 0.000000e+00 957.0
22 TraesCS2D01G471500 chr6B 82.381 420 62 7 2980 3391 716730555 716730140 4.520000e-94 355.0
23 TraesCS2D01G471500 chr6B 81.522 368 53 9 3026 3392 716820903 716820550 4.650000e-74 289.0
24 TraesCS2D01G471500 chr6B 90.323 217 16 3 2432 2647 716885679 716885467 2.800000e-71 279.0
25 TraesCS2D01G471500 chr6B 84.932 219 28 2 2804 3017 716821267 716821049 2.220000e-52 217.0
26 TraesCS2D01G471500 chr6B 83.260 227 28 7 2580 2804 716855577 716855359 2.240000e-47 200.0
27 TraesCS2D01G471500 chrUn 83.820 377 54 5 3015 3388 74768829 74769201 5.850000e-93 351.0
28 TraesCS2D01G471500 chrUn 81.918 365 39 13 1022 1378 96713519 96713174 2.160000e-72 283.0
29 TraesCS2D01G471500 chr1D 77.949 585 65 31 1022 1569 432955662 432956219 1.280000e-79 307.0
30 TraesCS2D01G471500 chr7D 86.007 293 29 8 1017 1304 24431928 24431643 1.660000e-78 303.0
31 TraesCS2D01G471500 chr7D 79.437 462 58 18 1022 1472 26614936 26614501 3.590000e-75 292.0
32 TraesCS2D01G471500 chr7D 82.192 365 38 13 1022 1378 73007478 73007823 4.650000e-74 289.0
33 TraesCS2D01G471500 chr7D 81.096 365 41 14 1022 1378 190196225 190196569 2.180000e-67 267.0
34 TraesCS2D01G471500 chr5D 83.486 327 28 13 1022 1342 149768664 149768358 7.780000e-72 281.0
35 TraesCS2D01G471500 chr4D 81.644 365 40 13 1022 1378 21035081 21034736 1.010000e-70 278.0
36 TraesCS2D01G471500 chr5B 85.088 114 13 3 1011 1123 674553133 674553243 3.000000e-21 113.0
37 TraesCS2D01G471500 chr7B 83.019 106 11 5 2432 2537 104516237 104516335 5.060000e-14 89.8
38 TraesCS2D01G471500 chr1A 83.019 106 11 5 2432 2537 244553388 244553290 5.060000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G471500 chr2D 575358463 575362141 3678 False 2345.333333 6794 95.884667 1 3679 3 chr2D.!!$F2 3678
1 TraesCS2D01G471500 chr2A 713542713 713546035 3322 False 1792.333333 3040 93.965333 1 3231 3 chr2A.!!$F3 3230
2 TraesCS2D01G471500 chr2B 691452045 691455222 3177 False 2386.500000 2710 93.497500 1 3228 2 chr2B.!!$F2 3227
3 TraesCS2D01G471500 chr6A 617682638 617687099 4461 True 634.700000 1066 84.651000 1 3231 3 chr6A.!!$R1 3230
4 TraesCS2D01G471500 chr6D 472305577 472308086 2509 False 632.666667 1031 84.052333 1 2974 3 chr6D.!!$F1 2973
5 TraesCS2D01G471500 chr6B 716975899 716976748 849 False 957.000000 957 87.078000 1 853 1 chr6B.!!$F1 852
6 TraesCS2D01G471500 chr6B 716820550 716821267 717 True 253.000000 289 83.227000 2804 3392 2 chr6B.!!$R4 588
7 TraesCS2D01G471500 chr1D 432955662 432956219 557 False 307.000000 307 77.949000 1022 1569 1 chr1D.!!$F1 547

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
761 771 0.738389 GACTCTGAGCTTCCTCGAGG 59.262 60.0 26.32 26.32 41.13 4.63 F
1386 2584 0.107508 ATGGCGTCTGGATTGGTCAG 60.108 55.0 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 3306 1.895131 GATGCAATGTTGAACACCCCT 59.105 47.619 0.00 0.0 0.0 4.79 R
3296 5317 1.139853 GTGGTGCTAGAAGGATCCAGG 59.860 57.143 15.82 0.0 0.0 4.45 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
247 248 1.229209 GAGGATGGCCGGGGAGATA 60.229 63.158 2.18 0.00 39.96 1.98
761 771 0.738389 GACTCTGAGCTTCCTCGAGG 59.262 60.000 26.32 26.32 41.13 4.63
938 1006 4.762289 ACAACCAGAAGTCTGAAGAGTT 57.238 40.909 9.95 0.00 46.59 3.01
943 1011 4.282195 ACCAGAAGTCTGAAGAGTTACTGG 59.718 45.833 25.53 25.53 46.59 4.00
950 1018 1.362406 GAAGAGTTACTGGCAGCCGC 61.362 60.000 15.89 4.73 37.44 6.53
992 1060 1.197721 CAAGAACAATCTCCACCACGC 59.802 52.381 0.00 0.00 33.77 5.34
1124 1218 0.612174 TGCGACTGTAAGCCTCCTCT 60.612 55.000 5.47 0.00 37.60 3.69
1150 1248 0.598680 CCTGATCCGGTCAATCGAGC 60.599 60.000 0.00 0.00 36.14 5.03
1191 1289 1.445716 GAGCATGCTCTGACCATGGC 61.446 60.000 35.26 10.02 40.24 4.40
1192 1290 1.453379 GCATGCTCTGACCATGGCT 60.453 57.895 13.04 0.00 40.24 4.75
1193 1291 1.725557 GCATGCTCTGACCATGGCTG 61.726 60.000 13.04 9.05 40.24 4.85
1386 2584 0.107508 ATGGCGTCTGGATTGGTCAG 60.108 55.000 0.00 0.00 0.00 3.51
1392 2590 1.751927 CTGGATTGGTCAGCCCAGC 60.752 63.158 0.00 0.00 46.31 4.85
1418 2616 1.598882 TGAACAACCATACGCTGCAA 58.401 45.000 0.00 0.00 0.00 4.08
1431 2629 2.261345 CGCTGCAATGTATTGTTTGGG 58.739 47.619 0.00 2.70 39.88 4.12
1444 2642 2.234143 TGTTTGGGCATGTGAATTCGA 58.766 42.857 0.04 0.00 0.00 3.71
1520 2799 3.181493 ACTTTCAGTTGCTGTTTGCTCTG 60.181 43.478 0.00 0.00 43.37 3.35
1541 2820 3.455910 TGCCCTGCTCTGTCATTTAGTAT 59.544 43.478 0.00 0.00 0.00 2.12
1577 2857 3.187022 GCAATTTGGTTCACAATTGCCTC 59.813 43.478 15.59 0.00 41.90 4.70
1713 3046 4.992319 CGGACAACTTACATGTCTGGTTAA 59.008 41.667 0.00 0.00 45.99 2.01
1744 3077 5.444663 TGTCAGTATACAGCTATGCTCTG 57.555 43.478 5.50 0.00 36.40 3.35
1780 3114 8.735315 CCTTGTAAATTCCACATGTTATGTACA 58.265 33.333 0.00 0.00 42.70 2.90
1783 3117 9.945904 TGTAAATTCCACATGTTATGTACAGTA 57.054 29.630 0.33 0.00 42.70 2.74
1869 3255 2.291209 TTGCATCAGGTTGACATGGT 57.709 45.000 0.00 0.00 0.00 3.55
1913 3300 0.321564 CAGATGACAGGCGGTTTGGA 60.322 55.000 0.00 0.00 0.00 3.53
1919 3306 1.611491 GACAGGCGGTTTGGATTCAAA 59.389 47.619 0.00 0.00 40.23 2.69
1924 3311 1.627864 CGGTTTGGATTCAAAGGGGT 58.372 50.000 0.00 0.00 42.78 4.95
2005 3475 1.691976 ACCCGCCAGATCGATTAATGA 59.308 47.619 0.00 0.00 0.00 2.57
2182 3888 0.108585 AGAGTCGCATGGGTGTTTGT 59.891 50.000 9.86 0.00 0.00 2.83
2295 4003 1.605710 GATCAATCAGTGCATTCCCCG 59.394 52.381 0.00 0.00 0.00 5.73
2713 4581 0.179163 GGTACTTGGCGCATTGCTTC 60.179 55.000 10.83 0.00 45.43 3.86
2724 4592 3.173599 CGCATTGCTTCGTTGATTGAAT 58.826 40.909 7.12 0.00 0.00 2.57
2814 4683 7.229506 GCAGCCATAGAGATAATTTTAGGTTGT 59.770 37.037 0.00 0.00 0.00 3.32
2822 4691 3.385193 AATTTTAGGTTGTGGTGCTGC 57.615 42.857 0.00 0.00 0.00 5.25
2877 4758 4.808364 GGCATTTTTGTAAACAGAGTTGCA 59.192 37.500 10.12 0.00 0.00 4.08
2942 4823 4.060038 TCTCTTTCTTCATGGTATCCGC 57.940 45.455 0.00 0.00 0.00 5.54
2998 4880 3.326297 AGTTATATCTCTGCTCCTTGGGC 59.674 47.826 0.00 0.00 0.00 5.36
3009 4891 2.967887 GCTCCTTGGGCCATTGAAATAT 59.032 45.455 7.26 0.00 0.00 1.28
3198 5219 8.135382 AGAGGTGCTAGTACTCTGAATTAAAA 57.865 34.615 10.95 0.00 39.92 1.52
3203 5224 6.090358 TGCTAGTACTCTGAATTAAAACGCAC 59.910 38.462 0.00 0.00 0.00 5.34
3231 5252 6.889301 ATGATGCCACCAAGAAATATACTG 57.111 37.500 0.00 0.00 0.00 2.74
3232 5253 4.580167 TGATGCCACCAAGAAATATACTGC 59.420 41.667 0.00 0.00 0.00 4.40
3236 5257 5.067674 TGCCACCAAGAAATATACTGCATTC 59.932 40.000 0.00 0.00 0.00 2.67
3250 5271 7.938140 ATACTGCATTCTAGAGGATAGAGTC 57.062 40.000 0.00 0.00 0.00 3.36
3256 5277 8.606830 TGCATTCTAGAGGATAGAGTCTATGTA 58.393 37.037 17.52 0.00 0.00 2.29
3275 5296 2.930826 AGGTGTCAAGACGTTTGGAT 57.069 45.000 9.54 0.00 0.00 3.41
3286 5307 3.569701 AGACGTTTGGATTTGTGCTTGAT 59.430 39.130 0.00 0.00 0.00 2.57
3290 5311 4.925054 CGTTTGGATTTGTGCTTGATCATT 59.075 37.500 0.00 0.00 0.00 2.57
3293 5314 4.009002 TGGATTTGTGCTTGATCATTCGA 58.991 39.130 0.00 0.00 0.00 3.71
3296 5317 3.476295 TTGTGCTTGATCATTCGAAGC 57.524 42.857 3.35 9.02 42.07 3.86
3299 5320 2.011947 TGCTTGATCATTCGAAGCCTG 58.988 47.619 12.60 0.00 41.21 4.85
3309 5330 2.454336 TCGAAGCCTGGATCCTTCTA 57.546 50.000 14.23 0.00 36.25 2.10
3317 5338 2.114616 CTGGATCCTTCTAGCACCACT 58.885 52.381 14.23 0.00 0.00 4.00
3331 5352 1.303236 CCACTTCCATGCCGGTGAA 60.303 57.895 1.90 0.35 35.57 3.18
3336 5357 1.773856 TTCCATGCCGGTGAACAGGA 61.774 55.000 1.90 0.00 35.57 3.86
3340 5361 1.852157 ATGCCGGTGAACAGGACCAT 61.852 55.000 1.90 0.00 32.68 3.55
3350 5371 2.196382 ACAGGACCATCGTGTCGACG 62.196 60.000 11.62 0.00 41.04 5.12
3353 5374 1.731613 GACCATCGTGTCGACGCAA 60.732 57.895 27.16 11.46 45.68 4.85
3374 5395 1.224592 GGTGCGATTGTCCCATCCT 59.775 57.895 0.00 0.00 0.00 3.24
3377 5398 0.911769 TGCGATTGTCCCATCCTTCT 59.088 50.000 0.00 0.00 0.00 2.85
3388 5409 3.019564 CCCATCCTTCTGTTTCCATGAC 58.980 50.000 0.00 0.00 0.00 3.06
3392 5413 2.076863 CCTTCTGTTTCCATGACGTCC 58.923 52.381 14.12 0.00 0.00 4.79
3393 5414 2.289694 CCTTCTGTTTCCATGACGTCCT 60.290 50.000 14.12 0.00 0.00 3.85
3394 5415 3.403038 CTTCTGTTTCCATGACGTCCTT 58.597 45.455 14.12 0.00 0.00 3.36
3395 5416 2.766313 TCTGTTTCCATGACGTCCTTG 58.234 47.619 14.12 10.70 0.00 3.61
3396 5417 2.367241 TCTGTTTCCATGACGTCCTTGA 59.633 45.455 14.12 1.33 0.00 3.02
3397 5418 2.738846 CTGTTTCCATGACGTCCTTGAG 59.261 50.000 14.12 5.60 0.00 3.02
3398 5419 2.076863 GTTTCCATGACGTCCTTGAGG 58.923 52.381 14.12 7.73 0.00 3.86
3399 5420 1.348064 TTCCATGACGTCCTTGAGGT 58.652 50.000 14.12 0.00 36.34 3.85
3400 5421 2.225382 TCCATGACGTCCTTGAGGTA 57.775 50.000 14.12 0.00 36.34 3.08
3401 5422 1.822990 TCCATGACGTCCTTGAGGTAC 59.177 52.381 14.12 0.00 36.34 3.34
3402 5423 1.548719 CCATGACGTCCTTGAGGTACA 59.451 52.381 14.12 0.00 36.34 2.90
3403 5424 2.607187 CATGACGTCCTTGAGGTACAC 58.393 52.381 14.12 0.00 36.34 2.90
3404 5425 0.963962 TGACGTCCTTGAGGTACACC 59.036 55.000 14.12 0.00 36.34 4.16
3405 5426 0.963962 GACGTCCTTGAGGTACACCA 59.036 55.000 3.51 0.00 38.89 4.17
3406 5427 1.549170 GACGTCCTTGAGGTACACCAT 59.451 52.381 3.51 0.00 38.89 3.55
3407 5428 1.275291 ACGTCCTTGAGGTACACCATG 59.725 52.381 0.38 0.00 38.89 3.66
3408 5429 1.739067 GTCCTTGAGGTACACCATGC 58.261 55.000 0.38 0.00 38.89 4.06
3409 5430 1.279271 GTCCTTGAGGTACACCATGCT 59.721 52.381 0.38 0.00 38.89 3.79
3410 5431 1.278985 TCCTTGAGGTACACCATGCTG 59.721 52.381 0.38 0.00 38.89 4.41
3411 5432 1.089920 CTTGAGGTACACCATGCTGC 58.910 55.000 0.38 0.00 38.89 5.25
3412 5433 0.673333 TTGAGGTACACCATGCTGCG 60.673 55.000 0.38 0.00 38.89 5.18
3413 5434 1.815421 GAGGTACACCATGCTGCGG 60.815 63.158 0.38 0.00 38.89 5.69
3414 5435 2.046314 GGTACACCATGCTGCGGT 60.046 61.111 0.00 0.00 37.16 5.68
3415 5436 1.219664 GGTACACCATGCTGCGGTA 59.780 57.895 0.00 0.00 34.02 4.02
3416 5437 1.087771 GGTACACCATGCTGCGGTAC 61.088 60.000 0.00 4.80 34.02 3.34
3417 5438 0.108329 GTACACCATGCTGCGGTACT 60.108 55.000 0.00 0.00 34.02 2.73
3418 5439 0.108377 TACACCATGCTGCGGTACTG 60.108 55.000 0.00 0.00 34.02 2.74
3419 5440 2.436646 ACCATGCTGCGGTACTGC 60.437 61.111 20.17 20.17 43.16 4.40
3420 5441 2.124983 CCATGCTGCGGTACTGCT 60.125 61.111 26.36 4.19 43.25 4.24
3421 5442 2.466982 CCATGCTGCGGTACTGCTG 61.467 63.158 26.36 25.52 43.25 4.41
3422 5443 1.448365 CATGCTGCGGTACTGCTGA 60.448 57.895 31.01 18.68 43.25 4.26
3423 5444 0.812811 CATGCTGCGGTACTGCTGAT 60.813 55.000 31.01 19.79 43.25 2.90
3424 5445 0.812811 ATGCTGCGGTACTGCTGATG 60.813 55.000 31.01 17.73 43.25 3.07
3425 5446 2.817423 GCTGCGGTACTGCTGATGC 61.817 63.158 31.01 22.27 39.94 3.91
3426 5447 2.125147 TGCGGTACTGCTGATGCC 60.125 61.111 26.36 0.00 38.71 4.40
3427 5448 2.125147 GCGGTACTGCTGATGCCA 60.125 61.111 19.72 0.00 38.71 4.92
3428 5449 1.524621 GCGGTACTGCTGATGCCAT 60.525 57.895 19.72 0.00 38.71 4.40
3429 5450 1.502163 GCGGTACTGCTGATGCCATC 61.502 60.000 19.72 0.00 38.71 3.51
3430 5451 0.882042 CGGTACTGCTGATGCCATCC 60.882 60.000 1.49 0.00 38.71 3.51
3431 5452 0.536006 GGTACTGCTGATGCCATCCC 60.536 60.000 1.49 0.00 38.71 3.85
3432 5453 0.181114 GTACTGCTGATGCCATCCCA 59.819 55.000 1.49 0.00 38.71 4.37
3433 5454 0.471191 TACTGCTGATGCCATCCCAG 59.529 55.000 16.40 16.40 38.71 4.45
3434 5455 1.226542 CTGCTGATGCCATCCCAGT 59.773 57.895 1.49 0.00 38.71 4.00
3435 5456 1.077285 TGCTGATGCCATCCCAGTG 60.077 57.895 1.49 0.00 38.71 3.66
3436 5457 1.826921 GCTGATGCCATCCCAGTGG 60.827 63.158 0.63 0.63 42.35 4.00
3437 5458 1.611419 CTGATGCCATCCCAGTGGT 59.389 57.895 8.74 0.00 41.47 4.16
3438 5459 0.750546 CTGATGCCATCCCAGTGGTG 60.751 60.000 8.74 0.00 41.47 4.17
3439 5460 1.454479 GATGCCATCCCAGTGGTGG 60.454 63.158 13.42 13.42 44.56 4.61
3447 5468 3.068881 CCAGTGGTGGGTCGATGT 58.931 61.111 0.00 0.00 40.67 3.06
3448 5469 1.079127 CCAGTGGTGGGTCGATGTC 60.079 63.158 0.00 0.00 40.67 3.06
3449 5470 1.446099 CAGTGGTGGGTCGATGTCG 60.446 63.158 0.00 0.00 41.45 4.35
3458 5479 2.503158 TCGATGTCGAACCACGCG 60.503 61.111 3.53 3.53 46.30 6.01
3459 5480 2.803670 CGATGTCGAACCACGCGT 60.804 61.111 5.58 5.58 43.02 6.01
3460 5481 2.769617 GATGTCGAACCACGCGTG 59.230 61.111 31.77 31.77 42.26 5.34
3461 5482 3.348967 GATGTCGAACCACGCGTGC 62.349 63.158 33.17 18.74 42.26 5.34
3486 5507 4.807631 TCGAGGCCGATCCGTCCA 62.808 66.667 0.00 0.00 40.30 4.02
3487 5508 3.606662 CGAGGCCGATCCGTCCAT 61.607 66.667 0.00 0.00 40.77 3.41
3488 5509 2.340443 GAGGCCGATCCGTCCATC 59.660 66.667 0.00 0.00 40.77 3.51
3489 5510 3.227792 GAGGCCGATCCGTCCATCC 62.228 68.421 0.00 0.00 40.77 3.51
3490 5511 3.234730 GGCCGATCCGTCCATCCT 61.235 66.667 0.00 0.00 0.00 3.24
3491 5512 2.340443 GCCGATCCGTCCATCCTC 59.660 66.667 0.00 0.00 0.00 3.71
3492 5513 2.645567 CCGATCCGTCCATCCTCG 59.354 66.667 0.00 0.00 0.00 4.63
3493 5514 2.194212 CCGATCCGTCCATCCTCGT 61.194 63.158 0.00 0.00 0.00 4.18
3494 5515 0.887836 CCGATCCGTCCATCCTCGTA 60.888 60.000 0.00 0.00 0.00 3.43
3495 5516 0.517755 CGATCCGTCCATCCTCGTAG 59.482 60.000 0.00 0.00 0.00 3.51
3496 5517 0.241481 GATCCGTCCATCCTCGTAGC 59.759 60.000 0.00 0.00 0.00 3.58
3497 5518 1.516365 ATCCGTCCATCCTCGTAGCG 61.516 60.000 0.00 0.00 0.00 4.26
3498 5519 2.184830 CCGTCCATCCTCGTAGCGA 61.185 63.158 0.00 0.00 0.00 4.93
3507 5528 4.861883 TCGTAGCGAGACTGCAAC 57.138 55.556 0.00 0.00 37.31 4.17
3508 5529 1.211969 TCGTAGCGAGACTGCAACC 59.788 57.895 0.00 0.00 37.31 3.77
3509 5530 1.080772 CGTAGCGAGACTGCAACCA 60.081 57.895 0.00 0.00 37.31 3.67
3510 5531 0.666274 CGTAGCGAGACTGCAACCAA 60.666 55.000 0.00 0.00 37.31 3.67
3511 5532 1.071605 GTAGCGAGACTGCAACCAAG 58.928 55.000 0.00 0.00 37.31 3.61
3512 5533 0.679505 TAGCGAGACTGCAACCAAGT 59.320 50.000 0.00 0.00 37.31 3.16
3513 5534 0.882042 AGCGAGACTGCAACCAAGTG 60.882 55.000 0.00 0.00 37.31 3.16
3514 5535 0.880278 GCGAGACTGCAACCAAGTGA 60.880 55.000 0.00 0.00 34.15 3.41
3515 5536 1.800805 CGAGACTGCAACCAAGTGAT 58.199 50.000 0.00 0.00 0.00 3.06
3516 5537 2.146342 CGAGACTGCAACCAAGTGATT 58.854 47.619 0.00 0.00 0.00 2.57
3517 5538 2.549754 CGAGACTGCAACCAAGTGATTT 59.450 45.455 0.00 0.00 0.00 2.17
3518 5539 3.364366 CGAGACTGCAACCAAGTGATTTC 60.364 47.826 0.00 0.00 0.00 2.17
3519 5540 3.554934 AGACTGCAACCAAGTGATTTCA 58.445 40.909 0.00 0.00 0.00 2.69
3520 5541 3.316308 AGACTGCAACCAAGTGATTTCAC 59.684 43.478 2.41 2.41 46.77 3.18
3529 5550 3.877801 GTGATTTCACCATCGTCGC 57.122 52.632 0.00 0.00 40.85 5.19
3530 5551 1.359848 GTGATTTCACCATCGTCGCT 58.640 50.000 0.00 0.00 40.85 4.93
3531 5552 1.324736 GTGATTTCACCATCGTCGCTC 59.675 52.381 0.00 0.00 40.85 5.03
3532 5553 1.204704 TGATTTCACCATCGTCGCTCT 59.795 47.619 0.00 0.00 0.00 4.09
3533 5554 1.855360 GATTTCACCATCGTCGCTCTC 59.145 52.381 0.00 0.00 0.00 3.20
3534 5555 0.601057 TTTCACCATCGTCGCTCTCA 59.399 50.000 0.00 0.00 0.00 3.27
3535 5556 0.601057 TTCACCATCGTCGCTCTCAA 59.399 50.000 0.00 0.00 0.00 3.02
3536 5557 0.601057 TCACCATCGTCGCTCTCAAA 59.399 50.000 0.00 0.00 0.00 2.69
3537 5558 1.000394 TCACCATCGTCGCTCTCAAAA 60.000 47.619 0.00 0.00 0.00 2.44
3538 5559 1.391485 CACCATCGTCGCTCTCAAAAG 59.609 52.381 0.00 0.00 0.00 2.27
3539 5560 0.371645 CCATCGTCGCTCTCAAAAGC 59.628 55.000 0.00 0.00 38.97 3.51
3540 5561 1.354040 CATCGTCGCTCTCAAAAGCT 58.646 50.000 0.00 0.00 40.23 3.74
3541 5562 1.728971 CATCGTCGCTCTCAAAAGCTT 59.271 47.619 0.00 0.00 40.23 3.74
3542 5563 1.139989 TCGTCGCTCTCAAAAGCTTG 58.860 50.000 0.00 0.00 40.23 4.01
3543 5564 1.139989 CGTCGCTCTCAAAAGCTTGA 58.860 50.000 0.00 0.00 40.23 3.02
3544 5565 1.728971 CGTCGCTCTCAAAAGCTTGAT 59.271 47.619 0.00 0.00 40.78 2.57
3545 5566 2.473540 CGTCGCTCTCAAAAGCTTGATG 60.474 50.000 0.00 2.58 40.78 3.07
3546 5567 2.481952 GTCGCTCTCAAAAGCTTGATGT 59.518 45.455 0.00 0.00 40.78 3.06
3547 5568 3.058639 GTCGCTCTCAAAAGCTTGATGTT 60.059 43.478 0.00 0.00 40.78 2.71
3548 5569 3.187227 TCGCTCTCAAAAGCTTGATGTTC 59.813 43.478 0.00 0.00 40.78 3.18
3549 5570 3.058708 CGCTCTCAAAAGCTTGATGTTCA 60.059 43.478 0.00 0.00 40.78 3.18
3550 5571 4.555313 CGCTCTCAAAAGCTTGATGTTCAA 60.555 41.667 0.00 0.00 40.78 2.69
3565 5586 5.987953 TGATGTTCAAGATACTATCAGCTGC 59.012 40.000 9.47 0.00 0.00 5.25
3566 5587 5.604758 TGTTCAAGATACTATCAGCTGCT 57.395 39.130 9.47 0.82 0.00 4.24
3567 5588 5.595885 TGTTCAAGATACTATCAGCTGCTC 58.404 41.667 9.47 0.00 0.00 4.26
3568 5589 4.862902 TCAAGATACTATCAGCTGCTCC 57.137 45.455 9.47 0.00 0.00 4.70
3569 5590 4.218312 TCAAGATACTATCAGCTGCTCCA 58.782 43.478 9.47 0.00 0.00 3.86
3570 5591 4.651045 TCAAGATACTATCAGCTGCTCCAA 59.349 41.667 9.47 0.00 0.00 3.53
3571 5592 4.870123 AGATACTATCAGCTGCTCCAAG 57.130 45.455 9.47 4.07 0.00 3.61
3572 5593 4.478203 AGATACTATCAGCTGCTCCAAGA 58.522 43.478 9.47 0.00 0.00 3.02
3573 5594 5.085920 AGATACTATCAGCTGCTCCAAGAT 58.914 41.667 9.47 2.07 0.00 2.40
3574 5595 3.749665 ACTATCAGCTGCTCCAAGATC 57.250 47.619 9.47 0.00 0.00 2.75
3575 5596 3.307506 ACTATCAGCTGCTCCAAGATCT 58.692 45.455 9.47 0.00 0.00 2.75
3576 5597 3.710677 ACTATCAGCTGCTCCAAGATCTT 59.289 43.478 9.47 0.88 0.00 2.40
3577 5598 3.648507 ATCAGCTGCTCCAAGATCTTT 57.351 42.857 9.47 0.00 0.00 2.52
3578 5599 2.983229 TCAGCTGCTCCAAGATCTTTC 58.017 47.619 9.47 0.00 0.00 2.62
3579 5600 2.303890 TCAGCTGCTCCAAGATCTTTCA 59.696 45.455 9.47 1.15 0.00 2.69
3580 5601 3.054582 TCAGCTGCTCCAAGATCTTTCAT 60.055 43.478 9.47 0.00 0.00 2.57
3581 5602 3.312973 CAGCTGCTCCAAGATCTTTCATC 59.687 47.826 4.86 0.00 0.00 2.92
3582 5603 3.200385 AGCTGCTCCAAGATCTTTCATCT 59.800 43.478 4.86 0.47 0.00 2.90
3583 5604 4.408270 AGCTGCTCCAAGATCTTTCATCTA 59.592 41.667 4.86 0.00 0.00 1.98
3584 5605 5.104610 AGCTGCTCCAAGATCTTTCATCTAA 60.105 40.000 4.86 0.00 0.00 2.10
3585 5606 5.587844 GCTGCTCCAAGATCTTTCATCTAAA 59.412 40.000 4.86 0.00 0.00 1.85
3586 5607 6.094603 GCTGCTCCAAGATCTTTCATCTAAAA 59.905 38.462 4.86 0.00 0.00 1.52
3587 5608 7.621428 TGCTCCAAGATCTTTCATCTAAAAG 57.379 36.000 4.86 0.00 37.55 2.27
3588 5609 7.170965 TGCTCCAAGATCTTTCATCTAAAAGT 58.829 34.615 4.86 0.00 37.49 2.66
3589 5610 7.667219 TGCTCCAAGATCTTTCATCTAAAAGTT 59.333 33.333 4.86 0.00 37.49 2.66
3590 5611 9.167311 GCTCCAAGATCTTTCATCTAAAAGTTA 57.833 33.333 4.86 0.00 37.49 2.24
3612 5633 9.884814 AGTTATTACATCTCCTATGTAAGTCCT 57.115 33.333 14.00 7.84 44.56 3.85
3613 5634 9.915629 GTTATTACATCTCCTATGTAAGTCCTG 57.084 37.037 14.00 0.00 44.56 3.86
3614 5635 4.946478 ACATCTCCTATGTAAGTCCTGC 57.054 45.455 0.00 0.00 0.00 4.85
3615 5636 4.290093 ACATCTCCTATGTAAGTCCTGCA 58.710 43.478 0.00 0.00 0.00 4.41
3616 5637 4.716784 ACATCTCCTATGTAAGTCCTGCAA 59.283 41.667 0.00 0.00 0.00 4.08
3617 5638 5.163364 ACATCTCCTATGTAAGTCCTGCAAG 60.163 44.000 0.00 0.00 0.00 4.01
3618 5639 4.610333 TCTCCTATGTAAGTCCTGCAAGA 58.390 43.478 0.00 0.00 34.07 3.02
3619 5640 5.211973 TCTCCTATGTAAGTCCTGCAAGAT 58.788 41.667 0.00 0.00 34.07 2.40
3620 5641 5.069648 TCTCCTATGTAAGTCCTGCAAGATG 59.930 44.000 0.00 0.00 34.07 2.90
3621 5642 4.962362 TCCTATGTAAGTCCTGCAAGATGA 59.038 41.667 0.00 0.00 34.07 2.92
3622 5643 5.604231 TCCTATGTAAGTCCTGCAAGATGAT 59.396 40.000 0.00 0.00 34.07 2.45
3623 5644 6.782494 TCCTATGTAAGTCCTGCAAGATGATA 59.218 38.462 0.00 0.00 34.07 2.15
3624 5645 6.870965 CCTATGTAAGTCCTGCAAGATGATAC 59.129 42.308 0.00 0.00 34.07 2.24
3625 5646 5.675684 TGTAAGTCCTGCAAGATGATACA 57.324 39.130 0.00 0.00 34.07 2.29
3626 5647 6.239217 TGTAAGTCCTGCAAGATGATACAT 57.761 37.500 0.00 0.00 34.07 2.29
3627 5648 6.653020 TGTAAGTCCTGCAAGATGATACATT 58.347 36.000 0.00 0.00 34.07 2.71
3628 5649 6.539826 TGTAAGTCCTGCAAGATGATACATTG 59.460 38.462 0.00 0.00 34.07 2.82
3634 5655 3.699067 GCAAGATGATACATTGCACCAC 58.301 45.455 4.38 0.00 46.64 4.16
3635 5656 3.129113 GCAAGATGATACATTGCACCACA 59.871 43.478 4.38 0.00 46.64 4.17
3636 5657 4.380761 GCAAGATGATACATTGCACCACAA 60.381 41.667 4.38 0.00 46.64 3.33
3637 5658 5.337554 CAAGATGATACATTGCACCACAAG 58.662 41.667 0.00 0.00 42.87 3.16
3638 5659 3.949754 AGATGATACATTGCACCACAAGG 59.050 43.478 0.00 0.00 45.51 3.61
3639 5660 2.445427 TGATACATTGCACCACAAGGG 58.555 47.619 0.00 0.00 44.32 3.95
3670 5691 5.984233 TTGAATATATCGGCAAGTCACAC 57.016 39.130 0.00 0.00 0.00 3.82
3671 5692 5.276461 TGAATATATCGGCAAGTCACACT 57.724 39.130 0.00 0.00 0.00 3.55
3672 5693 6.399639 TGAATATATCGGCAAGTCACACTA 57.600 37.500 0.00 0.00 0.00 2.74
3673 5694 6.447162 TGAATATATCGGCAAGTCACACTAG 58.553 40.000 0.00 0.00 0.00 2.57
3674 5695 2.579207 TATCGGCAAGTCACACTAGC 57.421 50.000 0.00 0.00 0.00 3.42
3675 5696 0.608130 ATCGGCAAGTCACACTAGCA 59.392 50.000 0.00 0.00 0.00 3.49
3676 5697 0.608130 TCGGCAAGTCACACTAGCAT 59.392 50.000 0.00 0.00 0.00 3.79
3677 5698 1.822371 TCGGCAAGTCACACTAGCATA 59.178 47.619 0.00 0.00 0.00 3.14
3678 5699 2.232696 TCGGCAAGTCACACTAGCATAA 59.767 45.455 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 244 1.806623 GCTTCCACGCCGACAATATCT 60.807 52.381 0.00 0.00 0.00 1.98
247 248 2.746277 GGCTTCCACGCCGACAAT 60.746 61.111 0.00 0.00 40.79 2.71
527 528 2.687200 CATCACCTCCCCGTCCCA 60.687 66.667 0.00 0.00 0.00 4.37
761 771 3.858989 GCTGCTCTCCTTTCGCGC 61.859 66.667 0.00 0.00 0.00 6.86
1020 1100 2.115911 CAGGAGGAGGAGGACGACG 61.116 68.421 0.00 0.00 0.00 5.12
1114 1203 1.307430 GGGGAGGAAGAGGAGGCTT 60.307 63.158 0.00 0.00 0.00 4.35
1124 1218 1.382695 GACCGGATCAGGGGAGGAA 60.383 63.158 16.73 0.00 35.02 3.36
1150 1248 4.859245 TCAGATCAGAAAGAAATCGTCACG 59.141 41.667 0.00 0.00 0.00 4.35
1191 1289 2.929483 CCACCCATCCCATCCCAG 59.071 66.667 0.00 0.00 0.00 4.45
1192 1290 3.428664 GCCACCCATCCCATCCCA 61.429 66.667 0.00 0.00 0.00 4.37
1193 1291 3.428664 TGCCACCCATCCCATCCC 61.429 66.667 0.00 0.00 0.00 3.85
1231 1329 2.978010 CCCACGCCGCAGAACTTT 60.978 61.111 0.00 0.00 0.00 2.66
1392 2590 0.738389 GTATGGTTGTTCATGGCGGG 59.262 55.000 0.00 0.00 0.00 6.13
1418 2616 5.680594 ATTCACATGCCCAAACAATACAT 57.319 34.783 0.00 0.00 0.00 2.29
1431 2629 4.332543 TCAGTACCATTCGAATTCACATGC 59.667 41.667 8.21 0.00 0.00 4.06
1444 2642 9.334947 CTCATCTTATCAATTGTCAGTACCATT 57.665 33.333 5.13 0.00 0.00 3.16
1520 2799 2.409948 ACTAAATGACAGAGCAGGGC 57.590 50.000 0.00 0.00 0.00 5.19
1558 2837 5.716228 TCATAGAGGCAATTGTGAACCAAAT 59.284 36.000 7.40 0.00 36.44 2.32
1577 2857 5.784750 TGAGCGAAAACATCAGTTCATAG 57.215 39.130 0.00 0.00 36.84 2.23
1648 2972 3.498397 GTGTGCATACTACAAAGCTGTGT 59.502 43.478 15.35 15.35 36.96 3.72
1697 3021 5.106830 GGAAACGGTTAACCAGACATGTAAG 60.107 44.000 24.14 6.39 35.14 2.34
1713 3046 3.368116 GCTGTATACTGACAGGAAACGGT 60.368 47.826 13.44 0.00 45.85 4.83
1744 3077 4.020662 TGGAATTTACAAGGGAATTGGTGC 60.021 41.667 0.00 0.00 43.68 5.01
1780 3114 2.432628 GCGGCTGCACGACTTACT 60.433 61.111 14.08 0.00 42.15 2.24
1913 3300 4.743348 GCAATGTTGAACACCCCTTTGAAT 60.743 41.667 11.51 0.00 0.00 2.57
1919 3306 1.895131 GATGCAATGTTGAACACCCCT 59.105 47.619 0.00 0.00 0.00 4.79
1924 3311 3.635836 TCAACCTGATGCAATGTTGAACA 59.364 39.130 16.43 0.00 42.81 3.18
2005 3475 9.830186 AGTATAACTATAGGATTGTGGAGATGT 57.170 33.333 4.43 0.00 0.00 3.06
2077 3547 2.223479 GCCGCAATTGACAAATACGGAT 60.223 45.455 22.75 0.00 43.39 4.18
2713 4581 8.236586 TCAAAGGAAGTCAATATTCAATCAACG 58.763 33.333 0.00 0.00 0.00 4.10
2763 4632 7.255416 GCCCAAAACAATGTGATTTTACCAATT 60.255 33.333 0.00 0.00 0.00 2.32
2822 4691 8.252417 AGAAGATCTGATACTATATGCTGCAAG 58.748 37.037 6.36 1.79 0.00 4.01
2942 4823 5.649782 AATTGAAGCAGACCACAATTAGG 57.350 39.130 0.00 0.00 39.88 2.69
2998 4880 7.116075 ACACATTCCTCCAATATTTCAATGG 57.884 36.000 0.00 0.00 35.49 3.16
3009 4891 4.009675 GTGCTATCAACACATTCCTCCAA 58.990 43.478 0.00 0.00 37.96 3.53
3128 5148 9.241317 GCAATAATTATCTGTCTGTTCCAAATG 57.759 33.333 0.00 0.00 0.00 2.32
3231 5252 7.938140 ACATAGACTCTATCCTCTAGAATGC 57.062 40.000 0.00 0.00 0.00 3.56
3232 5253 9.613428 CCTACATAGACTCTATCCTCTAGAATG 57.387 40.741 0.00 0.00 0.00 2.67
3236 5257 7.913789 ACACCTACATAGACTCTATCCTCTAG 58.086 42.308 0.00 0.00 0.00 2.43
3250 5271 4.625742 CCAAACGTCTTGACACCTACATAG 59.374 45.833 10.71 0.00 0.00 2.23
3256 5277 2.930826 ATCCAAACGTCTTGACACCT 57.069 45.000 10.71 0.00 0.00 4.00
3275 5296 3.366273 GGCTTCGAATGATCAAGCACAAA 60.366 43.478 16.14 0.03 39.43 2.83
3286 5307 1.500474 AGGATCCAGGCTTCGAATGA 58.500 50.000 15.82 0.00 0.00 2.57
3290 5311 2.311463 CTAGAAGGATCCAGGCTTCGA 58.689 52.381 15.82 4.40 0.00 3.71
3293 5314 1.488393 GTGCTAGAAGGATCCAGGCTT 59.512 52.381 15.82 0.00 0.00 4.35
3296 5317 1.139853 GTGGTGCTAGAAGGATCCAGG 59.860 57.143 15.82 0.00 0.00 4.45
3299 5320 2.158885 GGAAGTGGTGCTAGAAGGATCC 60.159 54.545 2.48 2.48 0.00 3.36
3309 5330 2.360350 CGGCATGGAAGTGGTGCT 60.360 61.111 0.00 0.00 38.83 4.40
3317 5338 1.303236 CCTGTTCACCGGCATGGAA 60.303 57.895 0.00 0.00 42.00 3.53
3331 5352 1.585006 GTCGACACGATGGTCCTGT 59.415 57.895 11.55 0.00 38.42 4.00
3361 5382 4.810720 TGGAAACAGAAGGATGGGACAATC 60.811 45.833 0.00 0.00 37.74 2.67
3363 5384 2.445145 TGGAAACAGAAGGATGGGACAA 59.555 45.455 0.00 0.00 37.74 3.18
3374 5395 7.984864 CCTCAAGGACGTCATGGAAACAGAA 62.985 48.000 18.91 0.00 40.51 3.02
3377 5398 2.549992 CCTCAAGGACGTCATGGAAACA 60.550 50.000 18.91 0.00 41.28 2.83
3388 5409 2.007049 GCATGGTGTACCTCAAGGACG 61.007 57.143 2.30 0.00 38.94 4.79
3392 5413 1.089920 GCAGCATGGTGTACCTCAAG 58.910 55.000 24.73 0.00 35.86 3.02
3393 5414 0.673333 CGCAGCATGGTGTACCTCAA 60.673 55.000 24.73 0.00 35.86 3.02
3394 5415 1.079197 CGCAGCATGGTGTACCTCA 60.079 57.895 24.73 0.00 35.86 3.86
3395 5416 1.815421 CCGCAGCATGGTGTACCTC 60.815 63.158 24.73 7.95 35.86 3.85
3396 5417 1.261938 TACCGCAGCATGGTGTACCT 61.262 55.000 24.73 8.83 40.73 3.08
3397 5418 1.087771 GTACCGCAGCATGGTGTACC 61.088 60.000 24.73 8.66 40.73 3.34
3398 5419 0.108329 AGTACCGCAGCATGGTGTAC 60.108 55.000 24.73 18.48 40.73 2.90
3399 5420 0.108377 CAGTACCGCAGCATGGTGTA 60.108 55.000 24.73 8.08 40.73 2.90
3400 5421 1.375908 CAGTACCGCAGCATGGTGT 60.376 57.895 24.73 9.08 40.73 4.16
3401 5422 2.753966 GCAGTACCGCAGCATGGTG 61.754 63.158 20.52 20.52 40.73 4.17
3402 5423 2.436646 GCAGTACCGCAGCATGGT 60.437 61.111 0.00 0.00 43.62 3.55
3403 5424 2.124983 AGCAGTACCGCAGCATGG 60.125 61.111 3.48 0.00 35.86 3.66
3404 5425 0.812811 ATCAGCAGTACCGCAGCATG 60.813 55.000 3.48 0.00 40.87 4.06
3405 5426 0.812811 CATCAGCAGTACCGCAGCAT 60.813 55.000 3.48 0.00 31.44 3.79
3406 5427 1.448365 CATCAGCAGTACCGCAGCA 60.448 57.895 3.48 0.00 31.44 4.41
3407 5428 2.817423 GCATCAGCAGTACCGCAGC 61.817 63.158 3.48 0.00 41.58 5.25
3408 5429 2.176273 GGCATCAGCAGTACCGCAG 61.176 63.158 3.48 0.00 44.61 5.18
3409 5430 2.125147 GGCATCAGCAGTACCGCA 60.125 61.111 3.48 0.00 44.61 5.69
3410 5431 1.502163 GATGGCATCAGCAGTACCGC 61.502 60.000 22.23 0.00 44.61 5.68
3411 5432 0.882042 GGATGGCATCAGCAGTACCG 60.882 60.000 27.39 0.00 44.61 4.02
3412 5433 0.536006 GGGATGGCATCAGCAGTACC 60.536 60.000 27.39 14.29 44.61 3.34
3413 5434 0.181114 TGGGATGGCATCAGCAGTAC 59.819 55.000 27.39 9.20 44.61 2.73
3414 5435 0.471191 CTGGGATGGCATCAGCAGTA 59.529 55.000 27.39 7.02 44.61 2.74
3415 5436 1.226542 CTGGGATGGCATCAGCAGT 59.773 57.895 27.39 0.00 44.61 4.40
3416 5437 1.101635 CACTGGGATGGCATCAGCAG 61.102 60.000 27.39 11.24 44.61 4.24
3417 5438 1.077285 CACTGGGATGGCATCAGCA 60.077 57.895 27.39 3.46 44.61 4.41
3418 5439 1.826921 CCACTGGGATGGCATCAGC 60.827 63.158 27.39 12.02 36.65 4.26
3419 5440 0.750546 CACCACTGGGATGGCATCAG 60.751 60.000 27.39 19.84 44.33 2.90
3420 5441 1.303948 CACCACTGGGATGGCATCA 59.696 57.895 27.39 9.15 44.33 3.07
3421 5442 1.454479 CCACCACTGGGATGGCATC 60.454 63.158 19.23 19.23 44.33 3.91
3422 5443 2.685366 CCACCACTGGGATGGCAT 59.315 61.111 0.00 0.00 44.33 4.40
3430 5451 1.079127 GACATCGACCCACCACTGG 60.079 63.158 0.00 0.00 37.29 4.00
3431 5452 1.446099 CGACATCGACCCACCACTG 60.446 63.158 0.00 0.00 43.02 3.66
3432 5453 1.605451 TCGACATCGACCCACCACT 60.605 57.895 0.00 0.00 44.22 4.00
3433 5454 2.967397 TCGACATCGACCCACCAC 59.033 61.111 0.00 0.00 44.22 4.16
3442 5463 2.803670 ACGCGTGGTTCGACATCG 60.804 61.111 12.93 0.00 42.86 3.84
3443 5464 2.769617 CACGCGTGGTTCGACATC 59.230 61.111 31.15 0.00 42.86 3.06
3444 5465 3.411351 GCACGCGTGGTTCGACAT 61.411 61.111 37.47 0.00 42.86 3.06
3474 5495 2.340443 GAGGATGGACGGATCGGC 59.660 66.667 0.00 0.00 0.00 5.54
3475 5496 0.887836 TACGAGGATGGACGGATCGG 60.888 60.000 0.00 0.00 37.69 4.18
3476 5497 0.517755 CTACGAGGATGGACGGATCG 59.482 60.000 0.00 0.00 39.22 3.69
3477 5498 0.241481 GCTACGAGGATGGACGGATC 59.759 60.000 0.00 0.00 0.00 3.36
3478 5499 1.516365 CGCTACGAGGATGGACGGAT 61.516 60.000 0.00 0.00 0.00 4.18
3479 5500 2.184830 CGCTACGAGGATGGACGGA 61.185 63.158 0.00 0.00 0.00 4.69
3480 5501 2.184830 TCGCTACGAGGATGGACGG 61.185 63.158 0.00 0.00 0.00 4.79
3481 5502 3.417601 TCGCTACGAGGATGGACG 58.582 61.111 0.00 0.00 0.00 4.79
3490 5511 1.211969 GGTTGCAGTCTCGCTACGA 59.788 57.895 0.00 0.00 38.33 3.43
3491 5512 0.666274 TTGGTTGCAGTCTCGCTACG 60.666 55.000 0.00 0.00 38.33 3.51
3492 5513 1.071605 CTTGGTTGCAGTCTCGCTAC 58.928 55.000 0.00 0.00 36.98 3.58
3493 5514 0.679505 ACTTGGTTGCAGTCTCGCTA 59.320 50.000 0.00 0.00 0.00 4.26
3494 5515 0.882042 CACTTGGTTGCAGTCTCGCT 60.882 55.000 0.00 0.00 0.00 4.93
3495 5516 0.880278 TCACTTGGTTGCAGTCTCGC 60.880 55.000 0.00 0.00 0.00 5.03
3496 5517 1.800805 ATCACTTGGTTGCAGTCTCG 58.199 50.000 0.00 0.00 0.00 4.04
3497 5518 3.565482 TGAAATCACTTGGTTGCAGTCTC 59.435 43.478 0.00 0.00 0.00 3.36
3498 5519 3.316308 GTGAAATCACTTGGTTGCAGTCT 59.684 43.478 6.30 0.00 43.25 3.24
3499 5520 3.550842 GGTGAAATCACTTGGTTGCAGTC 60.551 47.826 12.87 0.00 45.73 3.51
3500 5521 2.362077 GGTGAAATCACTTGGTTGCAGT 59.638 45.455 12.87 0.00 45.73 4.40
3501 5522 2.361757 TGGTGAAATCACTTGGTTGCAG 59.638 45.455 12.87 0.00 45.73 4.41
3502 5523 2.382882 TGGTGAAATCACTTGGTTGCA 58.617 42.857 12.87 0.00 45.73 4.08
3503 5524 3.578688 GATGGTGAAATCACTTGGTTGC 58.421 45.455 12.87 0.00 45.73 4.17
3504 5525 3.253188 ACGATGGTGAAATCACTTGGTTG 59.747 43.478 12.87 4.36 45.73 3.77
3505 5526 3.486383 ACGATGGTGAAATCACTTGGTT 58.514 40.909 12.87 0.00 45.73 3.67
3506 5527 3.074412 GACGATGGTGAAATCACTTGGT 58.926 45.455 12.87 8.45 45.73 3.67
3507 5528 2.094258 CGACGATGGTGAAATCACTTGG 59.906 50.000 12.87 5.74 45.73 3.61
3508 5529 2.474526 GCGACGATGGTGAAATCACTTG 60.475 50.000 12.87 1.75 45.73 3.16
3509 5530 1.732259 GCGACGATGGTGAAATCACTT 59.268 47.619 12.87 1.97 45.73 3.16
3510 5531 1.066858 AGCGACGATGGTGAAATCACT 60.067 47.619 12.87 0.00 45.73 3.41
3511 5532 1.324736 GAGCGACGATGGTGAAATCAC 59.675 52.381 0.00 4.96 45.72 3.06
3512 5533 1.204704 AGAGCGACGATGGTGAAATCA 59.795 47.619 0.00 0.00 0.00 2.57
3513 5534 1.855360 GAGAGCGACGATGGTGAAATC 59.145 52.381 0.00 0.00 0.00 2.17
3514 5535 1.204704 TGAGAGCGACGATGGTGAAAT 59.795 47.619 0.00 0.00 0.00 2.17
3515 5536 0.601057 TGAGAGCGACGATGGTGAAA 59.399 50.000 0.00 0.00 0.00 2.69
3516 5537 0.601057 TTGAGAGCGACGATGGTGAA 59.399 50.000 0.00 0.00 0.00 3.18
3517 5538 0.601057 TTTGAGAGCGACGATGGTGA 59.399 50.000 0.00 0.00 0.00 4.02
3518 5539 1.391485 CTTTTGAGAGCGACGATGGTG 59.609 52.381 0.00 0.00 0.00 4.17
3519 5540 1.714794 CTTTTGAGAGCGACGATGGT 58.285 50.000 0.00 0.00 0.00 3.55
3520 5541 0.371645 GCTTTTGAGAGCGACGATGG 59.628 55.000 0.00 0.00 32.23 3.51
3521 5542 3.865914 GCTTTTGAGAGCGACGATG 57.134 52.632 0.00 0.00 32.23 3.84
3526 5547 8.422696 CTTGAACATCAAGCTTTTGAGAGCGA 62.423 42.308 12.05 0.00 46.03 4.93
3527 5548 6.341888 CTTGAACATCAAGCTTTTGAGAGCG 61.342 44.000 12.05 0.00 46.03 5.03
3528 5549 4.494350 TGAACATCAAGCTTTTGAGAGC 57.506 40.909 12.05 0.00 43.02 4.09
3540 5561 6.481313 GCAGCTGATAGTATCTTGAACATCAA 59.519 38.462 20.43 0.00 34.79 2.57
3541 5562 5.987953 GCAGCTGATAGTATCTTGAACATCA 59.012 40.000 20.43 0.00 0.00 3.07
3542 5563 6.222389 AGCAGCTGATAGTATCTTGAACATC 58.778 40.000 20.43 0.00 0.00 3.06
3543 5564 6.172136 AGCAGCTGATAGTATCTTGAACAT 57.828 37.500 20.43 0.00 0.00 2.71
3544 5565 5.452496 GGAGCAGCTGATAGTATCTTGAACA 60.452 44.000 20.43 0.00 0.00 3.18
3545 5566 4.987912 GGAGCAGCTGATAGTATCTTGAAC 59.012 45.833 20.43 0.00 0.00 3.18
3546 5567 4.651045 TGGAGCAGCTGATAGTATCTTGAA 59.349 41.667 20.43 0.00 0.00 2.69
3547 5568 4.218312 TGGAGCAGCTGATAGTATCTTGA 58.782 43.478 20.43 0.00 0.00 3.02
3548 5569 4.597404 TGGAGCAGCTGATAGTATCTTG 57.403 45.455 20.43 8.18 0.00 3.02
3549 5570 4.898265 TCTTGGAGCAGCTGATAGTATCTT 59.102 41.667 20.43 0.00 0.00 2.40
3550 5571 4.478203 TCTTGGAGCAGCTGATAGTATCT 58.522 43.478 20.43 2.06 0.00 1.98
3551 5572 4.862902 TCTTGGAGCAGCTGATAGTATC 57.137 45.455 20.43 2.97 0.00 2.24
3552 5573 5.085920 AGATCTTGGAGCAGCTGATAGTAT 58.914 41.667 20.43 0.89 0.00 2.12
3553 5574 4.478203 AGATCTTGGAGCAGCTGATAGTA 58.522 43.478 20.43 0.00 0.00 1.82
3554 5575 3.307506 AGATCTTGGAGCAGCTGATAGT 58.692 45.455 20.43 0.00 0.00 2.12
3555 5576 4.339872 AAGATCTTGGAGCAGCTGATAG 57.660 45.455 20.43 5.80 0.00 2.08
3556 5577 4.162888 TGAAAGATCTTGGAGCAGCTGATA 59.837 41.667 20.43 0.00 0.00 2.15
3557 5578 3.054582 TGAAAGATCTTGGAGCAGCTGAT 60.055 43.478 20.43 12.64 0.00 2.90
3558 5579 2.303890 TGAAAGATCTTGGAGCAGCTGA 59.696 45.455 20.43 0.00 0.00 4.26
3559 5580 2.708051 TGAAAGATCTTGGAGCAGCTG 58.292 47.619 10.11 10.11 0.00 4.24
3560 5581 3.200385 AGATGAAAGATCTTGGAGCAGCT 59.800 43.478 9.17 10.23 0.00 4.24
3561 5582 3.543665 AGATGAAAGATCTTGGAGCAGC 58.456 45.455 9.17 8.17 0.00 5.25
3562 5583 7.336427 ACTTTTAGATGAAAGATCTTGGAGCAG 59.664 37.037 9.17 0.00 38.60 4.24
3563 5584 7.170965 ACTTTTAGATGAAAGATCTTGGAGCA 58.829 34.615 9.17 5.93 38.60 4.26
3564 5585 7.622893 ACTTTTAGATGAAAGATCTTGGAGC 57.377 36.000 9.17 1.32 38.60 4.70
3586 5607 9.884814 AGGACTTACATAGGAGATGTAATAACT 57.115 33.333 9.84 6.43 41.78 2.24
3587 5608 9.915629 CAGGACTTACATAGGAGATGTAATAAC 57.084 37.037 9.84 4.73 41.78 1.89
3588 5609 8.585881 GCAGGACTTACATAGGAGATGTAATAA 58.414 37.037 9.84 0.00 41.78 1.40
3589 5610 7.728532 TGCAGGACTTACATAGGAGATGTAATA 59.271 37.037 9.84 0.00 41.78 0.98
3590 5611 6.554982 TGCAGGACTTACATAGGAGATGTAAT 59.445 38.462 9.84 2.73 41.78 1.89
3591 5612 5.897250 TGCAGGACTTACATAGGAGATGTAA 59.103 40.000 9.21 9.21 40.82 2.41
3592 5613 5.454966 TGCAGGACTTACATAGGAGATGTA 58.545 41.667 0.00 0.00 33.76 2.29
3593 5614 4.290093 TGCAGGACTTACATAGGAGATGT 58.710 43.478 0.00 0.00 36.13 3.06
3594 5615 4.944619 TGCAGGACTTACATAGGAGATG 57.055 45.455 0.00 0.00 0.00 2.90
3595 5616 5.211973 TCTTGCAGGACTTACATAGGAGAT 58.788 41.667 0.00 0.00 0.00 2.75
3596 5617 4.610333 TCTTGCAGGACTTACATAGGAGA 58.390 43.478 0.00 0.00 0.00 3.71
3597 5618 5.069648 TCATCTTGCAGGACTTACATAGGAG 59.930 44.000 0.00 0.00 0.00 3.69
3598 5619 4.962362 TCATCTTGCAGGACTTACATAGGA 59.038 41.667 0.00 0.00 0.00 2.94
3599 5620 5.282055 TCATCTTGCAGGACTTACATAGG 57.718 43.478 0.00 0.00 0.00 2.57
3600 5621 7.436933 TGTATCATCTTGCAGGACTTACATAG 58.563 38.462 0.00 0.00 0.00 2.23
3601 5622 7.360113 TGTATCATCTTGCAGGACTTACATA 57.640 36.000 0.00 0.00 0.00 2.29
3602 5623 6.239217 TGTATCATCTTGCAGGACTTACAT 57.761 37.500 0.00 0.00 0.00 2.29
3603 5624 5.675684 TGTATCATCTTGCAGGACTTACA 57.324 39.130 0.00 6.93 0.00 2.41
3604 5625 6.512415 GCAATGTATCATCTTGCAGGACTTAC 60.512 42.308 0.00 4.37 43.62 2.34
3605 5626 5.528690 GCAATGTATCATCTTGCAGGACTTA 59.471 40.000 0.00 0.00 43.62 2.24
3606 5627 4.337555 GCAATGTATCATCTTGCAGGACTT 59.662 41.667 0.00 0.00 43.62 3.01
3607 5628 3.881688 GCAATGTATCATCTTGCAGGACT 59.118 43.478 0.00 0.00 43.62 3.85
3608 5629 4.220533 GCAATGTATCATCTTGCAGGAC 57.779 45.455 0.00 0.00 43.62 3.85
3613 5634 3.129113 TGTGGTGCAATGTATCATCTTGC 59.871 43.478 0.00 0.00 44.25 4.01
3614 5635 4.968812 TGTGGTGCAATGTATCATCTTG 57.031 40.909 0.00 0.00 0.00 3.02
3615 5636 4.400251 CCTTGTGGTGCAATGTATCATCTT 59.600 41.667 0.00 0.00 36.36 2.40
3616 5637 3.949754 CCTTGTGGTGCAATGTATCATCT 59.050 43.478 0.00 0.00 36.36 2.90
3617 5638 3.067180 CCCTTGTGGTGCAATGTATCATC 59.933 47.826 0.00 0.00 36.36 2.92
3618 5639 3.025978 CCCTTGTGGTGCAATGTATCAT 58.974 45.455 0.00 0.00 36.36 2.45
3619 5640 2.445427 CCCTTGTGGTGCAATGTATCA 58.555 47.619 0.00 0.00 36.36 2.15
3635 5656 9.561069 GCCGATATATTCAATATATTGACCCTT 57.439 33.333 24.55 13.64 45.63 3.95
3636 5657 8.713971 TGCCGATATATTCAATATATTGACCCT 58.286 33.333 24.55 15.55 45.63 4.34
3637 5658 8.902540 TGCCGATATATTCAATATATTGACCC 57.097 34.615 24.55 11.01 45.63 4.46
3644 5665 9.366216 GTGTGACTTGCCGATATATTCAATATA 57.634 33.333 0.00 0.00 32.66 0.86
3645 5666 8.097038 AGTGTGACTTGCCGATATATTCAATAT 58.903 33.333 0.00 0.00 0.00 1.28
3646 5667 7.441836 AGTGTGACTTGCCGATATATTCAATA 58.558 34.615 0.00 0.00 0.00 1.90
3647 5668 6.291377 AGTGTGACTTGCCGATATATTCAAT 58.709 36.000 0.00 0.00 0.00 2.57
3648 5669 5.670485 AGTGTGACTTGCCGATATATTCAA 58.330 37.500 0.00 0.00 0.00 2.69
3649 5670 5.276461 AGTGTGACTTGCCGATATATTCA 57.724 39.130 0.00 0.00 0.00 2.57
3650 5671 5.346281 GCTAGTGTGACTTGCCGATATATTC 59.654 44.000 0.00 0.00 40.28 1.75
3651 5672 5.221441 TGCTAGTGTGACTTGCCGATATATT 60.221 40.000 7.53 0.00 44.40 1.28
3652 5673 4.280929 TGCTAGTGTGACTTGCCGATATAT 59.719 41.667 7.53 0.00 44.40 0.86
3653 5674 3.634910 TGCTAGTGTGACTTGCCGATATA 59.365 43.478 7.53 0.00 44.40 0.86
3654 5675 2.430694 TGCTAGTGTGACTTGCCGATAT 59.569 45.455 7.53 0.00 44.40 1.63
3655 5676 1.822371 TGCTAGTGTGACTTGCCGATA 59.178 47.619 7.53 0.00 44.40 2.92
3656 5677 0.608130 TGCTAGTGTGACTTGCCGAT 59.392 50.000 7.53 0.00 44.40 4.18
3657 5678 0.608130 ATGCTAGTGTGACTTGCCGA 59.392 50.000 7.53 0.00 44.40 5.54
3658 5679 2.293677 TATGCTAGTGTGACTTGCCG 57.706 50.000 7.53 0.00 44.40 5.69


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

AutoCloner maintained by Alex Coulton.