Multiple sequence alignment - TraesCS2A01G521800

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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 TraesCS2A01G521800 chr2A 100.000 4094 0 0 620 4713 744491640 744495733 0.000000e+00 7561.0
1 TraesCS2A01G521800 chr2A 100.000 338 0 0 1 338 744491021 744491358 4.000000e-175 625.0
2 TraesCS2A01G521800 chr2D 95.298 3360 88 24 620 3923 612364641 612367986 0.000000e+00 5265.0
3 TraesCS2A01G521800 chr2D 88.435 294 26 5 4194 4480 612367985 612368277 9.710000e-92 348.0
4 TraesCS2A01G521800 chr2D 88.688 221 17 5 124 338 612363966 612364184 3.620000e-66 263.0
5 TraesCS2A01G521800 chr2D 82.770 296 39 7 3915 4200 196792491 196792198 2.180000e-63 254.0
6 TraesCS2A01G521800 chr2D 82.500 280 25 13 3924 4200 510215253 510214995 1.710000e-54 224.0
7 TraesCS2A01G521800 chr2D 94.949 99 5 0 1 99 26502326 26502228 6.310000e-34 156.0
8 TraesCS2A01G521800 chr2D 93.137 102 6 1 1 101 640202581 640202480 1.060000e-31 148.0
9 TraesCS2A01G521800 chr2B 94.443 3365 111 26 620 3923 747236926 747240275 0.000000e+00 5108.0
10 TraesCS2A01G521800 chr2B 86.038 530 60 10 4194 4713 747240274 747240799 1.480000e-154 556.0
11 TraesCS2A01G521800 chr2B 91.732 254 17 3 89 338 747236302 747236555 2.700000e-92 350.0
12 TraesCS2A01G521800 chr2B 84.965 286 32 4 3924 4200 679249239 679248956 3.590000e-71 279.0
13 TraesCS2A01G521800 chr2B 83.444 302 34 9 3912 4200 380820625 380820327 2.800000e-67 267.0
14 TraesCS2A01G521800 chr2B 92.308 104 7 1 1 103 106094949 106094846 3.800000e-31 147.0
15 TraesCS2A01G521800 chr3B 86.963 1304 156 8 984 2283 584811391 584812684 0.000000e+00 1454.0
16 TraesCS2A01G521800 chr3B 85.132 1325 147 32 2280 3577 584812778 584814079 0.000000e+00 1310.0
17 TraesCS2A01G521800 chr3A 86.810 1304 158 8 984 2283 587635765 587637058 0.000000e+00 1443.0
18 TraesCS2A01G521800 chr3A 83.965 1478 167 44 2280 3718 587637139 587638585 0.000000e+00 1352.0
19 TraesCS2A01G521800 chr3D 86.503 1304 162 8 984 2283 445858186 445859479 0.000000e+00 1421.0
20 TraesCS2A01G521800 chr3D 87.591 822 71 17 2758 3577 445860077 445860869 0.000000e+00 924.0
21 TraesCS2A01G521800 chr3D 86.190 420 49 4 2280 2693 445859573 445859989 3.350000e-121 446.0
22 TraesCS2A01G521800 chr3D 83.513 279 31 8 3933 4200 269287999 269287725 3.640000e-61 246.0
23 TraesCS2A01G521800 chr1A 85.458 1004 142 4 1283 2284 497243267 497242266 0.000000e+00 1042.0
24 TraesCS2A01G521800 chr1A 78.891 1298 210 46 2278 3551 497242176 497240919 0.000000e+00 821.0
25 TraesCS2A01G521800 chr1A 86.559 186 19 3 1098 1283 497243524 497243345 2.880000e-47 200.0
26 TraesCS2A01G521800 chr1B 84.746 1003 151 2 1283 2284 538868158 538867157 0.000000e+00 1003.0
27 TraesCS2A01G521800 chr1B 80.253 790 127 16 2766 3551 538866570 538865806 6.840000e-158 568.0
28 TraesCS2A01G521800 chr1B 83.623 403 51 14 2278 2677 538867077 538866687 9.640000e-97 364.0
29 TraesCS2A01G521800 chr1B 86.559 186 19 3 1098 1283 538868408 538868229 2.880000e-47 200.0
30 TraesCS2A01G521800 chr1D 84.646 1003 152 2 1283 2284 401134707 401133706 0.000000e+00 998.0
31 TraesCS2A01G521800 chr1D 79.205 1308 194 53 2278 3551 401133630 401132367 0.000000e+00 837.0
32 TraesCS2A01G521800 chr1D 86.559 186 19 3 1098 1283 401134973 401134794 2.880000e-47 200.0
33 TraesCS2A01G521800 chr6A 86.063 287 28 6 3924 4200 575277456 575277172 9.910000e-77 298.0
34 TraesCS2A01G521800 chr4A 85.121 289 31 5 3924 4202 429650373 429650087 7.720000e-73 285.0
35 TraesCS2A01G521800 chr4A 80.952 84 16 0 3036 3119 641291417 641291334 3.040000e-07 67.6
36 TraesCS2A01G521800 chr6D 84.912 285 31 5 3926 4200 202942610 202942892 1.290000e-70 278.0
37 TraesCS2A01G521800 chr6D 82.517 286 38 8 3929 4204 183017194 183017477 1.690000e-59 241.0
38 TraesCS2A01G521800 chr7B 84.321 287 35 4 3924 4200 508983048 508982762 6.010000e-69 272.0
39 TraesCS2A01G521800 chr7B 83.959 293 32 10 3921 4202 3865523 3865811 2.800000e-67 267.0
40 TraesCS2A01G521800 chr6B 80.986 284 40 10 3930 4202 151599317 151599597 3.690000e-51 213.0
41 TraesCS2A01G521800 chr6B 97.059 34 1 0 234 267 479080497 479080464 1.830000e-04 58.4
42 TraesCS2A01G521800 chr5D 75.741 371 74 13 1366 1728 531291688 531292050 6.270000e-39 172.0
43 TraesCS2A01G521800 chr7D 83.333 186 21 6 4025 4200 585612114 585612299 3.770000e-36 163.0
44 TraesCS2A01G521800 chr7D 95.789 95 3 1 1 95 149135989 149136082 8.170000e-33 152.0
45 TraesCS2A01G521800 chr7D 94.845 97 5 0 1 97 426431962 426431866 8.170000e-33 152.0
46 TraesCS2A01G521800 chr7D 90.351 114 9 2 1 112 5033872 5033985 1.060000e-31 148.0
47 TraesCS2A01G521800 chr7D 89.167 120 9 3 1 120 213758608 213758493 3.800000e-31 147.0
48 TraesCS2A01G521800 chr7A 95.789 95 4 0 1 95 77161657 77161563 2.270000e-33 154.0
49 TraesCS2A01G521800 chr4D 90.741 108 9 1 1 108 109243774 109243880 4.920000e-30 143.0


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 TraesCS2A01G521800 chr2A 744491021 744495733 4712 False 4093.000000 7561 100.000000 1 4713 2 chr2A.!!$F1 4712
1 TraesCS2A01G521800 chr2D 612363966 612368277 4311 False 1958.666667 5265 90.807000 124 4480 3 chr2D.!!$F1 4356
2 TraesCS2A01G521800 chr2B 747236302 747240799 4497 False 2004.666667 5108 90.737667 89 4713 3 chr2B.!!$F1 4624
3 TraesCS2A01G521800 chr3B 584811391 584814079 2688 False 1382.000000 1454 86.047500 984 3577 2 chr3B.!!$F1 2593
4 TraesCS2A01G521800 chr3A 587635765 587638585 2820 False 1397.500000 1443 85.387500 984 3718 2 chr3A.!!$F1 2734
5 TraesCS2A01G521800 chr3D 445858186 445860869 2683 False 930.333333 1421 86.761333 984 3577 3 chr3D.!!$F1 2593
6 TraesCS2A01G521800 chr1A 497240919 497243524 2605 True 687.666667 1042 83.636000 1098 3551 3 chr1A.!!$R1 2453
7 TraesCS2A01G521800 chr1B 538865806 538868408 2602 True 533.750000 1003 83.795250 1098 3551 4 chr1B.!!$R1 2453
8 TraesCS2A01G521800 chr1D 401132367 401134973 2606 True 678.333333 998 83.470000 1098 3551 3 chr1D.!!$R1 2453

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
899 1090 1.370587 CTGTCTCTCTCCGTCGTCCC 61.371 65.000 0.00 0.00 0.0 4.46 F
2055 2371 0.252284 TCCTCCTCCCGCTCTTCTTT 60.252 55.000 0.00 0.00 0.0 2.52 F
2101 2417 2.108157 GCATGATACGCGACCCCA 59.892 61.111 15.93 5.32 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2527 0.391661 TGTTCATGAGGAAGCCGAGC 60.392 55.0 0.00 0.00 35.82 5.03 R
2857 3328 0.611200 TGTGGAACGGGATCACGATT 59.389 50.0 26.96 14.55 42.39 3.34 R
3924 4432 0.690762 ACCGGTGCATTGTAAGAGGT 59.309 50.0 6.12 0.00 0.00 3.85 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
34 35 8.885494 AGAGTATAGATTCACTCATTTTGCTC 57.115 34.615 4.70 0.00 42.99 4.26
35 36 7.930865 AGAGTATAGATTCACTCATTTTGCTCC 59.069 37.037 4.70 0.00 42.99 4.70
36 37 5.998454 ATAGATTCACTCATTTTGCTCCG 57.002 39.130 0.00 0.00 0.00 4.63
37 38 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
38 39 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
39 40 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
40 41 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
41 42 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
42 43 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
43 44 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
44 45 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
45 46 5.351465 CACTCATTTTGCTCCGTATGTAGTT 59.649 40.000 0.00 0.00 0.00 2.24
46 47 6.533723 CACTCATTTTGCTCCGTATGTAGTTA 59.466 38.462 0.00 0.00 0.00 2.24
47 48 6.534079 ACTCATTTTGCTCCGTATGTAGTTAC 59.466 38.462 0.00 0.00 0.00 2.50
48 49 5.813672 TCATTTTGCTCCGTATGTAGTTACC 59.186 40.000 0.00 0.00 0.00 2.85
49 50 5.410355 TTTTGCTCCGTATGTAGTTACCT 57.590 39.130 0.00 0.00 0.00 3.08
50 51 6.528537 TTTTGCTCCGTATGTAGTTACCTA 57.471 37.500 0.00 0.00 0.00 3.08
51 52 6.720112 TTTGCTCCGTATGTAGTTACCTAT 57.280 37.500 0.00 0.00 0.00 2.57
52 53 6.720112 TTGCTCCGTATGTAGTTACCTATT 57.280 37.500 0.00 0.00 0.00 1.73
53 54 6.080648 TGCTCCGTATGTAGTTACCTATTG 57.919 41.667 0.00 0.00 0.00 1.90
54 55 5.010314 TGCTCCGTATGTAGTTACCTATTGG 59.990 44.000 0.00 0.00 39.83 3.16
55 56 5.242393 GCTCCGTATGTAGTTACCTATTGGA 59.758 44.000 0.00 0.00 37.04 3.53
56 57 6.239120 GCTCCGTATGTAGTTACCTATTGGAA 60.239 42.308 0.00 0.00 37.04 3.53
57 58 7.525029 GCTCCGTATGTAGTTACCTATTGGAAT 60.525 40.741 0.00 0.00 37.04 3.01
58 59 7.889469 TCCGTATGTAGTTACCTATTGGAATC 58.111 38.462 0.00 0.00 37.04 2.52
59 60 7.727186 TCCGTATGTAGTTACCTATTGGAATCT 59.273 37.037 0.00 0.00 37.04 2.40
60 61 8.027771 CCGTATGTAGTTACCTATTGGAATCTC 58.972 40.741 0.00 0.00 37.04 2.75
61 62 8.794553 CGTATGTAGTTACCTATTGGAATCTCT 58.205 37.037 0.00 0.00 37.04 3.10
65 66 9.931698 TGTAGTTACCTATTGGAATCTCTAGAA 57.068 33.333 0.00 0.00 37.04 2.10
68 69 9.716556 AGTTACCTATTGGAATCTCTAGAAAGA 57.283 33.333 0.00 0.00 37.04 2.52
69 70 9.752961 GTTACCTATTGGAATCTCTAGAAAGAC 57.247 37.037 0.00 0.00 37.04 3.01
70 71 9.716556 TTACCTATTGGAATCTCTAGAAAGACT 57.283 33.333 0.00 0.00 37.04 3.24
71 72 8.616799 ACCTATTGGAATCTCTAGAAAGACTT 57.383 34.615 0.00 0.00 37.04 3.01
72 73 9.716556 ACCTATTGGAATCTCTAGAAAGACTTA 57.283 33.333 0.00 0.00 37.04 2.24
85 86 9.595823 TCTAGAAAGACTTATATTTTGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
86 87 9.595823 CTAGAAAGACTTATATTTTGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
87 88 8.494016 AGAAAGACTTATATTTTGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
91 92 7.048512 AGACTTATATTTTGGAACGGAGGAAG 58.951 38.462 0.00 0.00 0.00 3.46
94 95 7.985752 ACTTATATTTTGGAACGGAGGAAGTAG 59.014 37.037 0.00 0.00 0.00 2.57
199 205 8.433421 AATGATACCGTGATACCACTAAAAAG 57.567 34.615 0.00 0.00 41.06 2.27
200 206 7.172868 TGATACCGTGATACCACTAAAAAGA 57.827 36.000 0.00 0.00 41.06 2.52
204 210 7.571080 ACCGTGATACCACTAAAAAGAAAAA 57.429 32.000 0.00 0.00 41.06 1.94
299 305 8.522178 ACTTCAAATCCGATTTCGAGATATAC 57.478 34.615 15.19 0.00 43.02 1.47
703 885 3.620488 TGGTGCCAGAAATAGGATGAAC 58.380 45.455 0.00 0.00 0.00 3.18
706 888 5.059833 GGTGCCAGAAATAGGATGAACTAG 58.940 45.833 0.00 0.00 0.00 2.57
708 890 5.525378 GTGCCAGAAATAGGATGAACTAGTG 59.475 44.000 0.00 0.00 0.00 2.74
754 939 4.078516 GCGCCCGACCCTTACTGT 62.079 66.667 0.00 0.00 0.00 3.55
779 964 4.504858 ACCTCACAATTCGTGGTAGATTC 58.495 43.478 7.78 0.00 46.36 2.52
899 1090 1.370587 CTGTCTCTCTCCGTCGTCCC 61.371 65.000 0.00 0.00 0.00 4.46
924 1115 3.571588 GCTAGCTGCGCCTCAAGC 61.572 66.667 7.70 7.23 38.52 4.01
1044 1270 3.400590 GTCGACGTGGTTGCGGTC 61.401 66.667 0.00 0.00 35.98 4.79
1245 1471 3.878519 CTCGTCGTCCTCCTCCGC 61.879 72.222 0.00 0.00 0.00 5.54
1287 1603 4.292178 GCTGAGATCCTCGCCGGG 62.292 72.222 2.18 0.00 32.35 5.73
1344 1660 3.831637 TGGGCCAGCCTGGTGTTT 61.832 61.111 13.35 0.00 40.46 2.83
1779 2095 3.073735 CTCTGGGTGCTCCTCGCT 61.074 66.667 4.53 0.00 40.11 4.93
2055 2371 0.252284 TCCTCCTCCCGCTCTTCTTT 60.252 55.000 0.00 0.00 0.00 2.52
2101 2417 2.108157 GCATGATACGCGACCCCA 59.892 61.111 15.93 5.32 0.00 4.96
2295 2721 2.338620 CAGGTGCTGGACGACGAA 59.661 61.111 0.00 0.00 0.00 3.85
2397 2823 2.259204 CGCCTCGTCGGGTACAAA 59.741 61.111 0.00 0.00 0.00 2.83
2857 3328 4.238385 GACAAGCACGTGTCGCTA 57.762 55.556 18.38 0.00 39.29 4.26
3508 3988 4.552278 GACATGCTCGTGTCGTCA 57.448 55.556 6.49 0.00 39.12 4.35
3740 4232 1.885163 CGTAGGGGTCTTCGGCTGTT 61.885 60.000 0.00 0.00 31.49 3.16
3750 4242 2.290367 TCTTCGGCTGTTGTGTGATTTG 59.710 45.455 0.00 0.00 0.00 2.32
3789 4289 6.152323 TCCCTGTAGTGAGTGTAACAGTATTC 59.848 42.308 0.00 0.00 41.43 1.75
3800 4300 9.646427 GAGTGTAACAGTATTCTTCTTTCAGAT 57.354 33.333 0.00 0.00 41.43 2.90
3804 4304 9.355215 GTAACAGTATTCTTCTTTCAGATTCGA 57.645 33.333 0.00 0.00 0.00 3.71
3822 4322 2.809696 TCGATTCGTGTAGTGTGTGAGA 59.190 45.455 5.89 0.00 0.00 3.27
3864 4366 3.595173 TCTGTTATGTGATGAACGGTGG 58.405 45.455 0.00 0.00 34.23 4.61
3907 4415 6.494491 TCAACAATTTCCAGGTGATCAATCTT 59.506 34.615 0.00 0.00 0.00 2.40
3921 4429 7.227512 GGTGATCAATCTTCGAACCAGATAAAT 59.772 37.037 0.00 0.00 30.35 1.40
3922 4430 8.616076 GTGATCAATCTTCGAACCAGATAAATT 58.384 33.333 0.00 0.00 30.35 1.82
3923 4431 8.615211 TGATCAATCTTCGAACCAGATAAATTG 58.385 33.333 0.00 0.00 30.35 2.32
3924 4432 8.737168 ATCAATCTTCGAACCAGATAAATTGA 57.263 30.769 0.00 0.00 30.35 2.57
3925 4433 7.974675 TCAATCTTCGAACCAGATAAATTGAC 58.025 34.615 0.00 0.00 30.35 3.18
3926 4434 6.927294 ATCTTCGAACCAGATAAATTGACC 57.073 37.500 0.00 0.00 0.00 4.02
3927 4435 6.049955 TCTTCGAACCAGATAAATTGACCT 57.950 37.500 0.00 0.00 0.00 3.85
3928 4436 6.106673 TCTTCGAACCAGATAAATTGACCTC 58.893 40.000 0.00 0.00 0.00 3.85
3929 4437 5.677319 TCGAACCAGATAAATTGACCTCT 57.323 39.130 0.00 0.00 0.00 3.69
3930 4438 6.049955 TCGAACCAGATAAATTGACCTCTT 57.950 37.500 0.00 0.00 0.00 2.85
3931 4439 7.177832 TCGAACCAGATAAATTGACCTCTTA 57.822 36.000 0.00 0.00 0.00 2.10
3932 4440 7.039882 TCGAACCAGATAAATTGACCTCTTAC 58.960 38.462 0.00 0.00 0.00 2.34
3933 4441 6.816640 CGAACCAGATAAATTGACCTCTTACA 59.183 38.462 0.00 0.00 0.00 2.41
3934 4442 7.333423 CGAACCAGATAAATTGACCTCTTACAA 59.667 37.037 0.00 0.00 0.00 2.41
3935 4443 9.178758 GAACCAGATAAATTGACCTCTTACAAT 57.821 33.333 0.00 0.00 38.18 2.71
3936 4444 8.511604 ACCAGATAAATTGACCTCTTACAATG 57.488 34.615 0.00 0.00 36.92 2.82
3937 4445 7.067494 ACCAGATAAATTGACCTCTTACAATGC 59.933 37.037 0.00 0.00 36.92 3.56
3938 4446 7.067372 CCAGATAAATTGACCTCTTACAATGCA 59.933 37.037 0.00 0.00 36.92 3.96
3939 4447 7.912250 CAGATAAATTGACCTCTTACAATGCAC 59.088 37.037 0.00 0.00 36.92 4.57
3940 4448 5.391312 AAATTGACCTCTTACAATGCACC 57.609 39.130 0.00 0.00 36.92 5.01
3941 4449 2.093306 TGACCTCTTACAATGCACCG 57.907 50.000 0.00 0.00 0.00 4.94
3942 4450 1.338674 TGACCTCTTACAATGCACCGG 60.339 52.381 0.00 0.00 0.00 5.28
3943 4451 0.690762 ACCTCTTACAATGCACCGGT 59.309 50.000 0.00 0.00 0.00 5.28
3944 4452 1.086696 CCTCTTACAATGCACCGGTG 58.913 55.000 30.66 30.66 0.00 4.94
3958 4466 2.802816 CACCGGTGCTAAGATAAGATGC 59.197 50.000 24.02 0.00 0.00 3.91
3959 4467 2.700897 ACCGGTGCTAAGATAAGATGCT 59.299 45.455 6.12 0.00 0.00 3.79
3960 4468 3.895656 ACCGGTGCTAAGATAAGATGCTA 59.104 43.478 6.12 0.00 0.00 3.49
3961 4469 4.344102 ACCGGTGCTAAGATAAGATGCTAA 59.656 41.667 6.12 0.00 0.00 3.09
3962 4470 4.926238 CCGGTGCTAAGATAAGATGCTAAG 59.074 45.833 0.00 0.00 0.00 2.18
3963 4471 4.387256 CGGTGCTAAGATAAGATGCTAAGC 59.613 45.833 0.00 0.00 0.00 3.09
3964 4472 5.300752 GGTGCTAAGATAAGATGCTAAGCA 58.699 41.667 0.00 0.00 44.86 3.91
3995 4503 9.438228 AAAGAGTTATAAGCAACTAAAGTCTCC 57.562 33.333 0.00 0.00 38.86 3.71
3996 4504 8.135382 AGAGTTATAAGCAACTAAAGTCTCCA 57.865 34.615 0.00 0.00 38.86 3.86
3997 4505 8.594550 AGAGTTATAAGCAACTAAAGTCTCCAA 58.405 33.333 0.00 0.00 38.86 3.53
3998 4506 9.384764 GAGTTATAAGCAACTAAAGTCTCCAAT 57.615 33.333 0.00 0.00 38.86 3.16
4003 4511 7.817418 AAGCAACTAAAGTCTCCAATACAAA 57.183 32.000 0.00 0.00 0.00 2.83
4004 4512 7.440523 AGCAACTAAAGTCTCCAATACAAAG 57.559 36.000 0.00 0.00 0.00 2.77
4005 4513 6.431234 AGCAACTAAAGTCTCCAATACAAAGG 59.569 38.462 0.00 0.00 0.00 3.11
4006 4514 6.206829 GCAACTAAAGTCTCCAATACAAAGGT 59.793 38.462 0.00 0.00 0.00 3.50
4007 4515 7.584987 CAACTAAAGTCTCCAATACAAAGGTG 58.415 38.462 0.00 0.00 0.00 4.00
4008 4516 5.705905 ACTAAAGTCTCCAATACAAAGGTGC 59.294 40.000 0.00 0.00 0.00 5.01
4009 4517 4.373156 AAGTCTCCAATACAAAGGTGCT 57.627 40.909 0.00 0.00 0.00 4.40
4010 4518 4.373156 AGTCTCCAATACAAAGGTGCTT 57.627 40.909 0.00 0.00 0.00 3.91
4011 4519 5.499004 AGTCTCCAATACAAAGGTGCTTA 57.501 39.130 0.00 0.00 0.00 3.09
4012 4520 5.876357 AGTCTCCAATACAAAGGTGCTTAA 58.124 37.500 0.00 0.00 0.00 1.85
4013 4521 5.705905 AGTCTCCAATACAAAGGTGCTTAAC 59.294 40.000 0.00 0.00 0.00 2.01
4014 4522 5.705905 GTCTCCAATACAAAGGTGCTTAACT 59.294 40.000 0.00 0.00 0.00 2.24
4015 4523 6.206829 GTCTCCAATACAAAGGTGCTTAACTT 59.793 38.462 0.00 0.00 0.00 2.66
4016 4524 6.775629 TCTCCAATACAAAGGTGCTTAACTTT 59.224 34.615 0.00 0.00 37.40 2.66
4017 4525 7.286775 TCTCCAATACAAAGGTGCTTAACTTTT 59.713 33.333 0.00 0.00 38.52 2.27
4018 4526 7.787028 TCCAATACAAAGGTGCTTAACTTTTT 58.213 30.769 0.00 0.00 36.02 1.94
4019 4527 7.923878 TCCAATACAAAGGTGCTTAACTTTTTC 59.076 33.333 0.00 0.00 36.02 2.29
4020 4528 7.926018 CCAATACAAAGGTGCTTAACTTTTTCT 59.074 33.333 0.00 0.00 36.02 2.52
4021 4529 9.959749 CAATACAAAGGTGCTTAACTTTTTCTA 57.040 29.630 0.00 0.00 36.02 2.10
4023 4531 6.504398 ACAAAGGTGCTTAACTTTTTCTAGC 58.496 36.000 0.00 0.00 36.02 3.42
4024 4532 6.321435 ACAAAGGTGCTTAACTTTTTCTAGCT 59.679 34.615 0.00 0.00 36.02 3.32
4025 4533 7.501225 ACAAAGGTGCTTAACTTTTTCTAGCTA 59.499 33.333 0.00 0.00 36.02 3.32
4026 4534 8.349983 CAAAGGTGCTTAACTTTTTCTAGCTAA 58.650 33.333 0.00 0.00 36.02 3.09
4027 4535 7.674471 AGGTGCTTAACTTTTTCTAGCTAAG 57.326 36.000 0.00 0.00 33.15 2.18
4028 4536 7.225011 AGGTGCTTAACTTTTTCTAGCTAAGT 58.775 34.615 0.00 0.00 33.76 2.24
4029 4537 8.373220 AGGTGCTTAACTTTTTCTAGCTAAGTA 58.627 33.333 0.00 0.00 32.17 2.24
4030 4538 9.163899 GGTGCTTAACTTTTTCTAGCTAAGTAT 57.836 33.333 0.00 0.00 32.17 2.12
4032 4540 9.379791 TGCTTAACTTTTTCTAGCTAAGTATCC 57.620 33.333 0.00 0.00 32.17 2.59
4033 4541 9.602568 GCTTAACTTTTTCTAGCTAAGTATCCT 57.397 33.333 0.00 0.00 32.17 3.24
4067 4575 9.461312 TGATTTAGCAACTAAAGTTATCCATGT 57.539 29.630 6.04 0.00 38.97 3.21
4072 4580 8.225603 AGCAACTAAAGTTATCCATGTATTGG 57.774 34.615 0.00 0.00 40.83 3.16
4073 4581 7.834181 AGCAACTAAAGTTATCCATGTATTGGT 59.166 33.333 0.00 0.00 40.54 3.67
4074 4582 7.915397 GCAACTAAAGTTATCCATGTATTGGTG 59.085 37.037 0.00 0.00 40.54 4.17
4075 4583 8.405531 CAACTAAAGTTATCCATGTATTGGTGG 58.594 37.037 0.00 0.00 40.54 4.61
4105 4613 8.722342 TTTCATTTAAGTGTATTTTCTCACGC 57.278 30.769 0.00 0.00 39.25 5.34
4106 4614 7.667043 TCATTTAAGTGTATTTTCTCACGCT 57.333 32.000 0.00 0.00 39.25 5.07
4107 4615 8.094798 TCATTTAAGTGTATTTTCTCACGCTT 57.905 30.769 5.90 5.90 45.03 4.68
4108 4616 8.015087 TCATTTAAGTGTATTTTCTCACGCTTG 58.985 33.333 10.00 0.00 43.40 4.01
4109 4617 6.854496 TTAAGTGTATTTTCTCACGCTTGT 57.146 33.333 10.00 0.00 43.40 3.16
4110 4618 4.992381 AGTGTATTTTCTCACGCTTGTC 57.008 40.909 0.00 0.00 39.25 3.18
4111 4619 4.377021 AGTGTATTTTCTCACGCTTGTCA 58.623 39.130 0.00 0.00 39.25 3.58
4112 4620 4.997395 AGTGTATTTTCTCACGCTTGTCAT 59.003 37.500 0.00 0.00 39.25 3.06
4113 4621 5.470098 AGTGTATTTTCTCACGCTTGTCATT 59.530 36.000 0.00 0.00 39.25 2.57
4114 4622 5.565259 GTGTATTTTCTCACGCTTGTCATTG 59.435 40.000 0.00 0.00 0.00 2.82
4115 4623 4.836125 ATTTTCTCACGCTTGTCATTGT 57.164 36.364 0.00 0.00 0.00 2.71
4116 4624 4.630894 TTTTCTCACGCTTGTCATTGTT 57.369 36.364 0.00 0.00 0.00 2.83
4117 4625 4.630894 TTTCTCACGCTTGTCATTGTTT 57.369 36.364 0.00 0.00 0.00 2.83
4118 4626 4.630894 TTCTCACGCTTGTCATTGTTTT 57.369 36.364 0.00 0.00 0.00 2.43
4119 4627 4.630894 TCTCACGCTTGTCATTGTTTTT 57.369 36.364 0.00 0.00 0.00 1.94
4136 4644 2.259266 TTTTCCTCGGGTTACCACAC 57.741 50.000 2.98 0.00 36.13 3.82
4137 4645 0.397564 TTTCCTCGGGTTACCACACC 59.602 55.000 2.98 0.00 36.13 4.16
4146 4654 3.434940 GGTTACCACACCCATCTTTCT 57.565 47.619 0.00 0.00 0.00 2.52
4147 4655 3.344515 GGTTACCACACCCATCTTTCTC 58.655 50.000 0.00 0.00 0.00 2.87
4148 4656 3.344515 GTTACCACACCCATCTTTCTCC 58.655 50.000 0.00 0.00 0.00 3.71
4149 4657 1.747444 ACCACACCCATCTTTCTCCT 58.253 50.000 0.00 0.00 0.00 3.69
4150 4658 1.630878 ACCACACCCATCTTTCTCCTC 59.369 52.381 0.00 0.00 0.00 3.71
4151 4659 1.912043 CCACACCCATCTTTCTCCTCT 59.088 52.381 0.00 0.00 0.00 3.69
4152 4660 2.307098 CCACACCCATCTTTCTCCTCTT 59.693 50.000 0.00 0.00 0.00 2.85
4153 4661 3.519510 CCACACCCATCTTTCTCCTCTTA 59.480 47.826 0.00 0.00 0.00 2.10
4154 4662 4.019321 CCACACCCATCTTTCTCCTCTTAA 60.019 45.833 0.00 0.00 0.00 1.85
4155 4663 5.339530 CCACACCCATCTTTCTCCTCTTAAT 60.340 44.000 0.00 0.00 0.00 1.40
4156 4664 6.183347 CACACCCATCTTTCTCCTCTTAATT 58.817 40.000 0.00 0.00 0.00 1.40
4157 4665 7.338710 CACACCCATCTTTCTCCTCTTAATTA 58.661 38.462 0.00 0.00 0.00 1.40
4158 4666 7.281100 CACACCCATCTTTCTCCTCTTAATTAC 59.719 40.741 0.00 0.00 0.00 1.89
4159 4667 6.768381 CACCCATCTTTCTCCTCTTAATTACC 59.232 42.308 0.00 0.00 0.00 2.85
4160 4668 6.678857 ACCCATCTTTCTCCTCTTAATTACCT 59.321 38.462 0.00 0.00 0.00 3.08
4161 4669 7.184753 ACCCATCTTTCTCCTCTTAATTACCTT 59.815 37.037 0.00 0.00 0.00 3.50
4162 4670 7.500559 CCCATCTTTCTCCTCTTAATTACCTTG 59.499 40.741 0.00 0.00 0.00 3.61
4163 4671 7.012799 CCATCTTTCTCCTCTTAATTACCTTGC 59.987 40.741 0.00 0.00 0.00 4.01
4164 4672 6.415573 TCTTTCTCCTCTTAATTACCTTGCC 58.584 40.000 0.00 0.00 0.00 4.52
4165 4673 5.772393 TTCTCCTCTTAATTACCTTGCCA 57.228 39.130 0.00 0.00 0.00 4.92
4166 4674 5.099042 TCTCCTCTTAATTACCTTGCCAC 57.901 43.478 0.00 0.00 0.00 5.01
4167 4675 4.534500 TCTCCTCTTAATTACCTTGCCACA 59.466 41.667 0.00 0.00 0.00 4.17
4168 4676 5.191722 TCTCCTCTTAATTACCTTGCCACAT 59.808 40.000 0.00 0.00 0.00 3.21
4169 4677 5.437060 TCCTCTTAATTACCTTGCCACATC 58.563 41.667 0.00 0.00 0.00 3.06
4170 4678 5.045213 TCCTCTTAATTACCTTGCCACATCA 60.045 40.000 0.00 0.00 0.00 3.07
4171 4679 5.829924 CCTCTTAATTACCTTGCCACATCAT 59.170 40.000 0.00 0.00 0.00 2.45
4172 4680 6.322201 CCTCTTAATTACCTTGCCACATCATT 59.678 38.462 0.00 0.00 0.00 2.57
4173 4681 7.147846 CCTCTTAATTACCTTGCCACATCATTT 60.148 37.037 0.00 0.00 0.00 2.32
4174 4682 8.133024 TCTTAATTACCTTGCCACATCATTTT 57.867 30.769 0.00 0.00 0.00 1.82
4175 4683 8.592809 TCTTAATTACCTTGCCACATCATTTTT 58.407 29.630 0.00 0.00 0.00 1.94
4192 4700 1.555967 TTTTTGCCTACATGGGAGCC 58.444 50.000 0.00 0.00 37.50 4.70
4205 4713 1.559682 TGGGAGCCTTAGCACTTTAGG 59.440 52.381 0.00 0.00 43.56 2.69
4238 4746 7.631717 AGTTGACTGATTTTCTAATTAGGGC 57.368 36.000 12.54 0.00 33.02 5.19
4239 4747 7.406104 AGTTGACTGATTTTCTAATTAGGGCT 58.594 34.615 12.54 0.00 33.02 5.19
4257 4767 5.295152 AGGGCTAGTCGATTTATTTTACCG 58.705 41.667 0.00 0.00 0.00 4.02
4264 4774 7.837202 AGTCGATTTATTTTACCGTTGATCA 57.163 32.000 0.00 0.00 0.00 2.92
4265 4775 8.259049 AGTCGATTTATTTTACCGTTGATCAA 57.741 30.769 3.38 3.38 0.00 2.57
4267 4777 9.155053 GTCGATTTATTTTACCGTTGATCAATC 57.845 33.333 12.12 4.81 0.00 2.67
4285 4795 1.220206 CCTCCAAGATGCGTGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
4288 4798 0.321346 TCCAAGATGCGTGCTCTTCA 59.679 50.000 0.00 0.00 30.60 3.02
4291 4801 2.163010 CCAAGATGCGTGCTCTTCATTT 59.837 45.455 0.00 0.00 30.60 2.32
4360 4875 1.597027 CCACTGTTTCGGCTCGGTT 60.597 57.895 0.00 0.00 0.00 4.44
4392 4907 1.448985 GCTGAAGCCCGTTACATGAA 58.551 50.000 0.00 0.00 34.31 2.57
4393 4908 1.810151 GCTGAAGCCCGTTACATGAAA 59.190 47.619 0.00 0.00 34.31 2.69
4415 4930 9.461312 TGAAATCTTATAGGCTTGTTTGTATGT 57.539 29.630 0.00 0.00 0.00 2.29
4421 4936 6.648879 ATAGGCTTGTTTGTATGTGTTGTT 57.351 33.333 0.00 0.00 0.00 2.83
4471 4987 8.357290 AGTGGGTAATTTTATGGGTAGTTTTC 57.643 34.615 0.00 0.00 0.00 2.29
4486 5002 3.347216 AGTTTTCGGATGTTGGATGAGG 58.653 45.455 0.00 0.00 0.00 3.86
4672 5192 5.650266 ACCAACGCAAATAATTCACTATCCA 59.350 36.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.973450 GAGCAAAATGAGTGAATCTATACTCTA 57.027 33.333 0.00 0.00 42.86 2.43
10 11 7.095857 CGGAGCAAAATGAGTGAATCTATACTC 60.096 40.741 0.00 0.00 42.77 2.59
12 13 6.480320 ACGGAGCAAAATGAGTGAATCTATAC 59.520 38.462 0.00 0.00 0.00 1.47
13 14 6.582636 ACGGAGCAAAATGAGTGAATCTATA 58.417 36.000 0.00 0.00 0.00 1.31
14 15 5.431765 ACGGAGCAAAATGAGTGAATCTAT 58.568 37.500 0.00 0.00 0.00 1.98
15 16 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
16 17 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
17 18 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
18 19 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
19 20 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
20 21 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
21 22 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
22 23 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
23 24 6.018994 GGTAACTACATACGGAGCAAAATGAG 60.019 42.308 0.00 0.00 0.00 2.90
24 25 5.813672 GGTAACTACATACGGAGCAAAATGA 59.186 40.000 0.00 0.00 0.00 2.57
25 26 6.044512 GGTAACTACATACGGAGCAAAATG 57.955 41.667 0.00 0.00 0.00 2.32
43 44 9.752961 GTCTTTCTAGAGATTCCAATAGGTAAC 57.247 37.037 0.00 0.00 35.89 2.50
44 45 9.716556 AGTCTTTCTAGAGATTCCAATAGGTAA 57.283 33.333 0.00 0.00 35.89 2.85
45 46 9.716556 AAGTCTTTCTAGAGATTCCAATAGGTA 57.283 33.333 0.00 0.00 35.89 3.08
46 47 8.616799 AAGTCTTTCTAGAGATTCCAATAGGT 57.383 34.615 0.00 0.00 35.89 3.08
59 60 9.595823 CCGTTCCAAAATATAAGTCTTTCTAGA 57.404 33.333 0.00 0.00 0.00 2.43
60 61 9.595823 TCCGTTCCAAAATATAAGTCTTTCTAG 57.404 33.333 0.00 0.00 0.00 2.43
61 62 9.595823 CTCCGTTCCAAAATATAAGTCTTTCTA 57.404 33.333 0.00 0.00 0.00 2.10
62 63 7.553044 CCTCCGTTCCAAAATATAAGTCTTTCT 59.447 37.037 0.00 0.00 0.00 2.52
63 64 7.551617 TCCTCCGTTCCAAAATATAAGTCTTTC 59.448 37.037 0.00 0.00 0.00 2.62
64 65 7.399634 TCCTCCGTTCCAAAATATAAGTCTTT 58.600 34.615 0.00 0.00 0.00 2.52
65 66 6.954232 TCCTCCGTTCCAAAATATAAGTCTT 58.046 36.000 0.00 0.00 0.00 3.01
66 67 6.555463 TCCTCCGTTCCAAAATATAAGTCT 57.445 37.500 0.00 0.00 0.00 3.24
67 68 6.822170 ACTTCCTCCGTTCCAAAATATAAGTC 59.178 38.462 0.00 0.00 0.00 3.01
68 69 6.718294 ACTTCCTCCGTTCCAAAATATAAGT 58.282 36.000 0.00 0.00 0.00 2.24
69 70 8.202137 TCTACTTCCTCCGTTCCAAAATATAAG 58.798 37.037 0.00 0.00 0.00 1.73
70 71 8.081517 TCTACTTCCTCCGTTCCAAAATATAA 57.918 34.615 0.00 0.00 0.00 0.98
71 72 7.664552 TCTACTTCCTCCGTTCCAAAATATA 57.335 36.000 0.00 0.00 0.00 0.86
72 73 6.555463 TCTACTTCCTCCGTTCCAAAATAT 57.445 37.500 0.00 0.00 0.00 1.28
73 74 6.070424 ACATCTACTTCCTCCGTTCCAAAATA 60.070 38.462 0.00 0.00 0.00 1.40
74 75 4.903045 TCTACTTCCTCCGTTCCAAAAT 57.097 40.909 0.00 0.00 0.00 1.82
75 76 4.041198 ACATCTACTTCCTCCGTTCCAAAA 59.959 41.667 0.00 0.00 0.00 2.44
76 77 3.581332 ACATCTACTTCCTCCGTTCCAAA 59.419 43.478 0.00 0.00 0.00 3.28
77 78 3.170717 ACATCTACTTCCTCCGTTCCAA 58.829 45.455 0.00 0.00 0.00 3.53
78 79 2.816411 ACATCTACTTCCTCCGTTCCA 58.184 47.619 0.00 0.00 0.00 3.53
79 80 4.996788 TTACATCTACTTCCTCCGTTCC 57.003 45.455 0.00 0.00 0.00 3.62
80 81 6.040166 TGGTATTACATCTACTTCCTCCGTTC 59.960 42.308 0.00 0.00 0.00 3.95
81 82 5.895534 TGGTATTACATCTACTTCCTCCGTT 59.104 40.000 0.00 0.00 0.00 4.44
82 83 5.301298 GTGGTATTACATCTACTTCCTCCGT 59.699 44.000 0.00 0.00 0.00 4.69
83 84 5.535406 AGTGGTATTACATCTACTTCCTCCG 59.465 44.000 0.00 0.00 0.00 4.63
84 85 6.980416 AGTGGTATTACATCTACTTCCTCC 57.020 41.667 0.00 0.00 0.00 4.30
85 86 8.461249 TGTAGTGGTATTACATCTACTTCCTC 57.539 38.462 18.98 0.00 34.13 3.71
86 87 8.861086 CATGTAGTGGTATTACATCTACTTCCT 58.139 37.037 18.98 7.36 39.16 3.36
87 88 8.639761 ACATGTAGTGGTATTACATCTACTTCC 58.360 37.037 18.98 0.00 39.16 3.46
299 305 7.603404 TGGATTTGCCATTTTTGTTTCTCTATG 59.397 33.333 0.00 0.00 43.33 2.23
629 811 6.414732 TGAACCAAGGTGTCTATAATTCCTG 58.585 40.000 0.00 0.00 0.00 3.86
779 964 2.036733 TGACCGGTCACCTTAGTTTCTG 59.963 50.000 33.23 0.00 34.14 3.02
899 1090 2.887568 CGCAGCTAGCTGAACGGG 60.888 66.667 41.87 22.82 46.30 5.28
924 1115 0.106819 CTGGGGAAGGAAGATGGCAG 60.107 60.000 0.00 0.00 0.00 4.85
1044 1270 1.275657 GTTCTGCGTCGTGGTGTTG 59.724 57.895 0.00 0.00 0.00 3.33
1234 1460 3.471806 GAAGGGGCGGAGGAGGAC 61.472 72.222 0.00 0.00 0.00 3.85
1380 1696 3.635268 GAAGAGCAGCCCCAGGTGG 62.635 68.421 0.00 0.00 41.94 4.61
1779 2095 2.847234 AGCACGAAGGTCACCCCA 60.847 61.111 0.00 0.00 34.66 4.96
2101 2417 4.457496 CAGCAGGCCGACGGTGAT 62.457 66.667 16.73 2.09 32.37 3.06
2211 2527 0.391661 TGTTCATGAGGAAGCCGAGC 60.392 55.000 0.00 0.00 35.82 5.03
2295 2721 1.809619 CACCATCACCGCGAACGAT 60.810 57.895 8.23 2.97 43.93 3.73
2857 3328 0.611200 TGTGGAACGGGATCACGATT 59.389 50.000 26.96 14.55 42.39 3.34
3508 3988 1.194781 ACACCGCCATGGAGAAGTCT 61.195 55.000 18.40 0.00 42.00 3.24
3538 4018 1.594021 CACCACGTACTGCTGCACA 60.594 57.895 0.00 0.00 0.00 4.57
3671 4163 1.133325 AGACCATCTGCTATCCCTCGT 60.133 52.381 0.00 0.00 0.00 4.18
3800 4300 3.251487 TCTCACACACTACACGAATCGAA 59.749 43.478 10.55 0.00 0.00 3.71
3804 4304 4.883083 ACAATCTCACACACTACACGAAT 58.117 39.130 0.00 0.00 0.00 3.34
3864 4366 6.942532 TGTTGATGAGTAAGCCAATAATCC 57.057 37.500 0.00 0.00 0.00 3.01
3907 4415 5.677319 AGAGGTCAATTTATCTGGTTCGA 57.323 39.130 0.00 0.00 0.00 3.71
3921 4429 2.422597 CGGTGCATTGTAAGAGGTCAA 58.577 47.619 0.00 0.00 0.00 3.18
3922 4430 1.338674 CCGGTGCATTGTAAGAGGTCA 60.339 52.381 0.00 0.00 0.00 4.02
3923 4431 1.338769 ACCGGTGCATTGTAAGAGGTC 60.339 52.381 6.12 0.00 0.00 3.85
3924 4432 0.690762 ACCGGTGCATTGTAAGAGGT 59.309 50.000 6.12 0.00 0.00 3.85
3925 4433 1.086696 CACCGGTGCATTGTAAGAGG 58.913 55.000 24.02 0.00 0.00 3.69
3937 4445 2.802816 GCATCTTATCTTAGCACCGGTG 59.197 50.000 30.66 30.66 0.00 4.94
3938 4446 2.700897 AGCATCTTATCTTAGCACCGGT 59.299 45.455 0.00 0.00 0.00 5.28
3939 4447 3.393089 AGCATCTTATCTTAGCACCGG 57.607 47.619 0.00 0.00 0.00 5.28
3940 4448 4.387256 GCTTAGCATCTTATCTTAGCACCG 59.613 45.833 0.00 0.00 35.68 4.94
3941 4449 5.300752 TGCTTAGCATCTTATCTTAGCACC 58.699 41.667 1.39 0.00 39.22 5.01
3969 4477 9.438228 GGAGACTTTAGTTGCTTATAACTCTTT 57.562 33.333 0.00 0.00 41.01 2.52
3970 4478 8.594550 TGGAGACTTTAGTTGCTTATAACTCTT 58.405 33.333 0.00 0.00 41.01 2.85
3971 4479 8.135382 TGGAGACTTTAGTTGCTTATAACTCT 57.865 34.615 0.00 0.00 41.01 3.24
3972 4480 8.773404 TTGGAGACTTTAGTTGCTTATAACTC 57.227 34.615 0.00 0.00 41.01 3.01
3977 4485 9.515226 TTTGTATTGGAGACTTTAGTTGCTTAT 57.485 29.630 0.00 0.00 0.00 1.73
3978 4486 8.911918 TTTGTATTGGAGACTTTAGTTGCTTA 57.088 30.769 0.00 0.00 0.00 3.09
3979 4487 7.040409 CCTTTGTATTGGAGACTTTAGTTGCTT 60.040 37.037 0.00 0.00 0.00 3.91
3980 4488 6.431234 CCTTTGTATTGGAGACTTTAGTTGCT 59.569 38.462 0.00 0.00 0.00 3.91
3981 4489 6.206829 ACCTTTGTATTGGAGACTTTAGTTGC 59.793 38.462 0.00 0.00 0.00 4.17
3982 4490 7.584987 CACCTTTGTATTGGAGACTTTAGTTG 58.415 38.462 0.00 0.00 0.00 3.16
3983 4491 6.206829 GCACCTTTGTATTGGAGACTTTAGTT 59.793 38.462 0.00 0.00 0.00 2.24
3984 4492 5.705905 GCACCTTTGTATTGGAGACTTTAGT 59.294 40.000 0.00 0.00 0.00 2.24
3985 4493 5.940470 AGCACCTTTGTATTGGAGACTTTAG 59.060 40.000 0.00 0.00 0.00 1.85
3986 4494 5.876357 AGCACCTTTGTATTGGAGACTTTA 58.124 37.500 0.00 0.00 0.00 1.85
3987 4495 4.729868 AGCACCTTTGTATTGGAGACTTT 58.270 39.130 0.00 0.00 0.00 2.66
3988 4496 4.373156 AGCACCTTTGTATTGGAGACTT 57.627 40.909 0.00 0.00 0.00 3.01
3989 4497 4.373156 AAGCACCTTTGTATTGGAGACT 57.627 40.909 0.00 0.00 0.00 3.24
3990 4498 5.705905 AGTTAAGCACCTTTGTATTGGAGAC 59.294 40.000 0.00 0.00 0.00 3.36
3991 4499 5.876357 AGTTAAGCACCTTTGTATTGGAGA 58.124 37.500 0.00 0.00 0.00 3.71
3992 4500 6.575162 AAGTTAAGCACCTTTGTATTGGAG 57.425 37.500 0.00 0.00 0.00 3.86
3993 4501 6.969993 AAAGTTAAGCACCTTTGTATTGGA 57.030 33.333 0.00 0.00 30.03 3.53
3994 4502 7.926018 AGAAAAAGTTAAGCACCTTTGTATTGG 59.074 33.333 0.00 0.00 31.54 3.16
3995 4503 8.871686 AGAAAAAGTTAAGCACCTTTGTATTG 57.128 30.769 0.00 0.00 31.54 1.90
3997 4505 8.297426 GCTAGAAAAAGTTAAGCACCTTTGTAT 58.703 33.333 0.00 0.00 31.54 2.29
3998 4506 7.501225 AGCTAGAAAAAGTTAAGCACCTTTGTA 59.499 33.333 0.00 0.00 35.63 2.41
3999 4507 6.321435 AGCTAGAAAAAGTTAAGCACCTTTGT 59.679 34.615 0.00 0.00 35.63 2.83
4000 4508 6.739112 AGCTAGAAAAAGTTAAGCACCTTTG 58.261 36.000 0.00 0.00 35.63 2.77
4001 4509 6.961360 AGCTAGAAAAAGTTAAGCACCTTT 57.039 33.333 0.00 0.00 35.63 3.11
4002 4510 7.720074 ACTTAGCTAGAAAAAGTTAAGCACCTT 59.280 33.333 0.00 0.00 41.43 3.50
4003 4511 7.225011 ACTTAGCTAGAAAAAGTTAAGCACCT 58.775 34.615 0.00 0.00 41.43 4.00
4004 4512 7.436430 ACTTAGCTAGAAAAAGTTAAGCACC 57.564 36.000 0.00 0.00 41.43 5.01
4006 4514 9.379791 GGATACTTAGCTAGAAAAAGTTAAGCA 57.620 33.333 4.24 0.00 41.43 3.91
4041 4549 9.461312 ACATGGATAACTTTAGTTGCTAAATCA 57.539 29.630 5.41 0.00 38.90 2.57
4079 4587 9.176181 GCGTGAGAAAATACACTTAAATGAAAA 57.824 29.630 0.00 0.00 35.23 2.29
4080 4588 8.564574 AGCGTGAGAAAATACACTTAAATGAAA 58.435 29.630 0.00 0.00 35.23 2.69
4081 4589 8.094798 AGCGTGAGAAAATACACTTAAATGAA 57.905 30.769 0.00 0.00 35.23 2.57
4082 4590 7.667043 AGCGTGAGAAAATACACTTAAATGA 57.333 32.000 0.00 0.00 35.23 2.57
4083 4591 7.803189 ACAAGCGTGAGAAAATACACTTAAATG 59.197 33.333 6.65 0.00 35.23 2.32
4084 4592 7.871853 ACAAGCGTGAGAAAATACACTTAAAT 58.128 30.769 6.65 0.00 35.23 1.40
4085 4593 7.011576 TGACAAGCGTGAGAAAATACACTTAAA 59.988 33.333 6.65 0.00 35.23 1.52
4086 4594 6.480651 TGACAAGCGTGAGAAAATACACTTAA 59.519 34.615 6.65 0.00 35.23 1.85
4087 4595 5.986741 TGACAAGCGTGAGAAAATACACTTA 59.013 36.000 6.65 0.00 35.23 2.24
4088 4596 4.814234 TGACAAGCGTGAGAAAATACACTT 59.186 37.500 6.65 0.00 35.23 3.16
4089 4597 4.377021 TGACAAGCGTGAGAAAATACACT 58.623 39.130 6.65 0.00 35.23 3.55
4090 4598 4.725556 TGACAAGCGTGAGAAAATACAC 57.274 40.909 6.65 0.00 0.00 2.90
4091 4599 5.238432 ACAATGACAAGCGTGAGAAAATACA 59.762 36.000 6.65 0.00 0.00 2.29
4092 4600 5.689819 ACAATGACAAGCGTGAGAAAATAC 58.310 37.500 6.65 0.00 0.00 1.89
4093 4601 5.940192 ACAATGACAAGCGTGAGAAAATA 57.060 34.783 6.65 0.00 0.00 1.40
4094 4602 4.836125 ACAATGACAAGCGTGAGAAAAT 57.164 36.364 6.65 0.00 0.00 1.82
4095 4603 4.630894 AACAATGACAAGCGTGAGAAAA 57.369 36.364 6.65 0.00 0.00 2.29
4096 4604 4.630894 AAACAATGACAAGCGTGAGAAA 57.369 36.364 6.65 0.00 0.00 2.52
4097 4605 4.630894 AAAACAATGACAAGCGTGAGAA 57.369 36.364 6.65 0.00 0.00 2.87
4098 4606 4.630894 AAAAACAATGACAAGCGTGAGA 57.369 36.364 6.65 0.00 0.00 3.27
4116 4624 2.574450 GTGTGGTAACCCGAGGAAAAA 58.426 47.619 0.00 0.00 0.00 1.94
4117 4625 1.202794 GGTGTGGTAACCCGAGGAAAA 60.203 52.381 0.00 0.00 33.79 2.29
4118 4626 0.397564 GGTGTGGTAACCCGAGGAAA 59.602 55.000 0.00 0.00 33.79 3.13
4119 4627 2.060370 GGTGTGGTAACCCGAGGAA 58.940 57.895 0.00 0.00 33.79 3.36
4120 4628 3.795905 GGTGTGGTAACCCGAGGA 58.204 61.111 0.00 0.00 33.79 3.71
4126 4634 3.344515 GAGAAAGATGGGTGTGGTAACC 58.655 50.000 0.00 0.00 39.71 2.85
4127 4635 3.009143 AGGAGAAAGATGGGTGTGGTAAC 59.991 47.826 0.00 0.00 0.00 2.50
4128 4636 3.256704 AGGAGAAAGATGGGTGTGGTAA 58.743 45.455 0.00 0.00 0.00 2.85
4129 4637 2.838202 GAGGAGAAAGATGGGTGTGGTA 59.162 50.000 0.00 0.00 0.00 3.25
4130 4638 1.630878 GAGGAGAAAGATGGGTGTGGT 59.369 52.381 0.00 0.00 0.00 4.16
4131 4639 1.912043 AGAGGAGAAAGATGGGTGTGG 59.088 52.381 0.00 0.00 0.00 4.17
4132 4640 3.710209 AAGAGGAGAAAGATGGGTGTG 57.290 47.619 0.00 0.00 0.00 3.82
4133 4641 6.394345 AATTAAGAGGAGAAAGATGGGTGT 57.606 37.500 0.00 0.00 0.00 4.16
4134 4642 6.768381 GGTAATTAAGAGGAGAAAGATGGGTG 59.232 42.308 0.00 0.00 0.00 4.61
4135 4643 6.678857 AGGTAATTAAGAGGAGAAAGATGGGT 59.321 38.462 0.00 0.00 0.00 4.51
4136 4644 7.142995 AGGTAATTAAGAGGAGAAAGATGGG 57.857 40.000 0.00 0.00 0.00 4.00
4137 4645 7.012799 GCAAGGTAATTAAGAGGAGAAAGATGG 59.987 40.741 0.00 0.00 0.00 3.51
4138 4646 7.012799 GGCAAGGTAATTAAGAGGAGAAAGATG 59.987 40.741 0.00 0.00 0.00 2.90
4139 4647 7.057264 GGCAAGGTAATTAAGAGGAGAAAGAT 58.943 38.462 0.00 0.00 0.00 2.40
4140 4648 6.012858 TGGCAAGGTAATTAAGAGGAGAAAGA 60.013 38.462 0.00 0.00 0.00 2.52
4141 4649 6.094186 GTGGCAAGGTAATTAAGAGGAGAAAG 59.906 42.308 0.00 0.00 0.00 2.62
4142 4650 5.944007 GTGGCAAGGTAATTAAGAGGAGAAA 59.056 40.000 0.00 0.00 0.00 2.52
4143 4651 5.013704 TGTGGCAAGGTAATTAAGAGGAGAA 59.986 40.000 0.00 0.00 0.00 2.87
4144 4652 4.534500 TGTGGCAAGGTAATTAAGAGGAGA 59.466 41.667 0.00 0.00 0.00 3.71
4145 4653 4.843728 TGTGGCAAGGTAATTAAGAGGAG 58.156 43.478 0.00 0.00 0.00 3.69
4146 4654 4.919774 TGTGGCAAGGTAATTAAGAGGA 57.080 40.909 0.00 0.00 0.00 3.71
4147 4655 5.192927 TGATGTGGCAAGGTAATTAAGAGG 58.807 41.667 0.00 0.00 0.00 3.69
4148 4656 6.949352 ATGATGTGGCAAGGTAATTAAGAG 57.051 37.500 0.00 0.00 0.00 2.85
4149 4657 7.716799 AAATGATGTGGCAAGGTAATTAAGA 57.283 32.000 0.00 0.00 0.00 2.10
4150 4658 8.776376 AAAAATGATGTGGCAAGGTAATTAAG 57.224 30.769 0.00 0.00 0.00 1.85
4173 4681 1.077005 AGGCTCCCATGTAGGCAAAAA 59.923 47.619 17.61 0.00 41.75 1.94
4174 4682 0.704076 AGGCTCCCATGTAGGCAAAA 59.296 50.000 17.61 0.00 41.75 2.44
4175 4683 0.704076 AAGGCTCCCATGTAGGCAAA 59.296 50.000 17.61 0.00 41.75 3.68
4176 4684 1.490490 CTAAGGCTCCCATGTAGGCAA 59.510 52.381 17.61 7.39 41.75 4.52
4177 4685 1.131638 CTAAGGCTCCCATGTAGGCA 58.868 55.000 17.61 1.64 41.75 4.75
4178 4686 0.250510 GCTAAGGCTCCCATGTAGGC 60.251 60.000 9.99 9.99 39.70 3.93
4179 4687 1.131638 TGCTAAGGCTCCCATGTAGG 58.868 55.000 0.00 0.00 39.59 3.18
4180 4688 1.765314 AGTGCTAAGGCTCCCATGTAG 59.235 52.381 0.00 0.00 39.59 2.74
4181 4689 1.879575 AGTGCTAAGGCTCCCATGTA 58.120 50.000 0.00 0.00 39.59 2.29
4182 4690 0.995024 AAGTGCTAAGGCTCCCATGT 59.005 50.000 0.00 0.00 39.59 3.21
4183 4691 2.134789 AAAGTGCTAAGGCTCCCATG 57.865 50.000 0.00 0.00 39.59 3.66
4184 4692 2.173569 CCTAAAGTGCTAAGGCTCCCAT 59.826 50.000 0.00 0.00 39.59 4.00
4185 4693 1.559682 CCTAAAGTGCTAAGGCTCCCA 59.440 52.381 0.00 0.00 39.59 4.37
4186 4694 1.560146 ACCTAAAGTGCTAAGGCTCCC 59.440 52.381 0.00 0.00 39.59 4.30
4187 4695 3.705072 TCTACCTAAAGTGCTAAGGCTCC 59.295 47.826 0.00 0.00 39.59 4.70
4188 4696 5.163395 ACATCTACCTAAAGTGCTAAGGCTC 60.163 44.000 0.00 0.00 39.59 4.70
4189 4697 4.717280 ACATCTACCTAAAGTGCTAAGGCT 59.283 41.667 0.00 0.00 39.59 4.58
4190 4698 5.024785 ACATCTACCTAAAGTGCTAAGGC 57.975 43.478 0.00 0.00 33.42 4.35
4191 4699 7.783042 ACTTACATCTACCTAAAGTGCTAAGG 58.217 38.462 0.00 0.00 36.42 2.69
4192 4700 9.088512 CAACTTACATCTACCTAAAGTGCTAAG 57.911 37.037 0.00 0.00 31.09 2.18
4238 4746 9.027129 TGATCAACGGTAAAATAAATCGACTAG 57.973 33.333 0.00 0.00 0.00 2.57
4239 4747 8.929827 TGATCAACGGTAAAATAAATCGACTA 57.070 30.769 0.00 0.00 0.00 2.59
4249 4759 5.505780 TGGAGGATTGATCAACGGTAAAAT 58.494 37.500 11.07 0.00 0.00 1.82
4257 4767 3.003068 CGCATCTTGGAGGATTGATCAAC 59.997 47.826 11.07 4.95 0.00 3.18
4264 4774 0.254178 AGCACGCATCTTGGAGGATT 59.746 50.000 0.00 0.00 0.00 3.01
4265 4775 0.179062 GAGCACGCATCTTGGAGGAT 60.179 55.000 0.00 0.00 0.00 3.24
4267 4777 0.392193 AAGAGCACGCATCTTGGAGG 60.392 55.000 0.00 0.00 35.70 4.30
4295 4805 2.983907 TGACGGTACACCAACAGAAA 57.016 45.000 0.00 0.00 35.14 2.52
4300 4810 3.549221 CCAAAACATGACGGTACACCAAC 60.549 47.826 0.00 0.00 35.14 3.77
4310 4825 2.791383 TTTCAGCCCAAAACATGACG 57.209 45.000 0.00 0.00 0.00 4.35
4360 4875 2.446435 GCTTCAGCCCAATAAGGAACA 58.554 47.619 0.00 0.00 41.22 3.18
4389 4904 9.461312 ACATACAAACAAGCCTATAAGATTTCA 57.539 29.630 0.00 0.00 0.00 2.69
4392 4907 8.807948 ACACATACAAACAAGCCTATAAGATT 57.192 30.769 0.00 0.00 0.00 2.40
4393 4908 8.677300 CAACACATACAAACAAGCCTATAAGAT 58.323 33.333 0.00 0.00 0.00 2.40
4449 4965 6.602803 TCCGAAAACTACCCATAAAATTACCC 59.397 38.462 0.00 0.00 0.00 3.69
4471 4987 3.275617 TTTACCCTCATCCAACATCCG 57.724 47.619 0.00 0.00 0.00 4.18
4486 5002 6.833839 TGATACTTGCGTGTTTACATTTACC 58.166 36.000 0.00 0.00 0.00 2.85
4585 5102 4.211164 TGAACTTTGTACTGAGATTGCACG 59.789 41.667 0.00 0.00 0.00 5.34
4633 5153 6.256912 TGCGTTGGTATTAACTTTTTAGGG 57.743 37.500 0.00 0.00 0.00 3.53
4634 5154 8.751302 ATTTGCGTTGGTATTAACTTTTTAGG 57.249 30.769 0.00 0.00 0.00 2.69
4640 5160 9.349145 GTGAATTATTTGCGTTGGTATTAACTT 57.651 29.630 0.00 0.00 0.00 2.66
4641 5161 8.736244 AGTGAATTATTTGCGTTGGTATTAACT 58.264 29.630 0.00 0.00 0.00 2.24
4649 5169 6.130298 TGGATAGTGAATTATTTGCGTTGG 57.870 37.500 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.