Multiple sequence alignment - TraesCS4A01G205100

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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 TraesCS4A01G205100 chr4A 100.000 4655 0 0 1 4655 497443580 497438926 0.000000e+00 8597.0
1 TraesCS4A01G205100 chr4A 91.200 250 20 2 4407 4655 638798959 638798711 5.770000e-89 339.0
2 TraesCS4A01G205100 chr4D 92.504 4429 215 58 1 4364 84548747 84544371 0.000000e+00 6231.0
3 TraesCS4A01G205100 chr4B 93.793 3673 153 34 759 4389 119825178 119821539 0.000000e+00 5450.0
4 TraesCS4A01G205100 chr4B 90.688 494 21 7 227 715 119825749 119825276 6.570000e-178 634.0
5 TraesCS4A01G205100 chr5D 88.564 376 43 0 2960 3335 5816881 5816506 1.530000e-124 457.0
6 TraesCS4A01G205100 chr5D 86.260 393 54 0 2531 2923 5817277 5816885 1.200000e-115 427.0
7 TraesCS4A01G205100 chr2A 74.877 1019 179 61 2326 3313 530380363 530381335 4.370000e-105 392.0
8 TraesCS4A01G205100 chr2A 89.883 257 21 4 4400 4652 102113523 102113268 4.490000e-85 326.0
9 TraesCS4A01G205100 chr2A 90.688 247 19 4 4405 4648 514235800 514235555 4.490000e-85 326.0
10 TraesCS4A01G205100 chr2B 74.669 983 179 53 2326 3279 464466316 464467257 5.690000e-99 372.0
11 TraesCS4A01G205100 chr2D 75.862 812 148 37 2515 3313 392525893 392526669 2.050000e-98 370.0
12 TraesCS4A01G205100 chr5A 91.633 251 17 4 4405 4652 445674971 445675220 1.240000e-90 344.0
13 TraesCS4A01G205100 chr7A 91.200 250 18 3 4405 4651 722081651 722081403 2.080000e-88 337.0
14 TraesCS4A01G205100 chr7A 74.478 670 112 40 2407 3063 464573277 464572654 7.790000e-58 235.0
15 TraesCS4A01G205100 chr1A 90.400 250 20 2 4405 4651 513732052 513731804 4.490000e-85 326.0
16 TraesCS4A01G205100 chr1A 89.883 257 18 5 4405 4655 453126635 453126381 1.620000e-84 324.0
17 TraesCS4A01G205100 chr7B 90.079 252 18 5 4405 4652 592347019 592346771 2.090000e-83 320.0
18 TraesCS4A01G205100 chr7B 75.155 483 89 24 2407 2875 418049671 418049206 1.020000e-46 198.0
19 TraesCS4A01G205100 chr7B 88.991 109 11 1 2956 3063 418049156 418049048 2.920000e-27 134.0
20 TraesCS4A01G205100 chr3A 89.641 251 22 3 4405 4652 63527022 63527271 2.700000e-82 316.0
21 TraesCS4A01G205100 chr7D 75.569 483 87 24 2407 2875 407072271 407071806 4.720000e-50 209.0
22 TraesCS4A01G205100 chr7D 88.991 109 11 1 2956 3063 407071756 407071648 2.920000e-27 134.0
23 TraesCS4A01G205100 chr6D 100.000 28 0 0 3138 3165 429304699 429304726 8.000000e-03 52.8


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 TraesCS4A01G205100 chr4A 497438926 497443580 4654 True 8597 8597 100.0000 1 4655 1 chr4A.!!$R1 4654
1 TraesCS4A01G205100 chr4D 84544371 84548747 4376 True 6231 6231 92.5040 1 4364 1 chr4D.!!$R1 4363
2 TraesCS4A01G205100 chr4B 119821539 119825749 4210 True 3042 5450 92.2405 227 4389 2 chr4B.!!$R1 4162
3 TraesCS4A01G205100 chr5D 5816506 5817277 771 True 442 457 87.4120 2531 3335 2 chr5D.!!$R1 804
4 TraesCS4A01G205100 chr2A 530380363 530381335 972 False 392 392 74.8770 2326 3313 1 chr2A.!!$F1 987
5 TraesCS4A01G205100 chr2B 464466316 464467257 941 False 372 372 74.6690 2326 3279 1 chr2B.!!$F1 953
6 TraesCS4A01G205100 chr2D 392525893 392526669 776 False 370 370 75.8620 2515 3313 1 chr2D.!!$F1 798
7 TraesCS4A01G205100 chr7A 464572654 464573277 623 True 235 235 74.4780 2407 3063 1 chr7A.!!$R1 656

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
678 689 0.109342 ACCTGCTGCTGCTGTTAAGT 59.891 50.000 17.00 6.69 40.48 2.24 F
884 958 0.450983 GCAGAGCTCTGGTGAAATGC 59.549 55.000 37.86 22.24 43.94 3.56 F
1872 1958 1.447838 CGCCGGTCTGCAGTACAAT 60.448 57.895 14.67 0.00 0.00 2.71 F
3544 3669 1.264020 CATTGGAACACACACAGTCGG 59.736 52.381 0.00 0.00 39.29 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2140 2226 0.980231 ATCTTTCTCCTCCTGCCGCT 60.980 55.000 0.00 0.0 0.0 5.52 R
2202 2288 1.081242 GAACTGCAATGCCACCACG 60.081 57.895 1.53 0.0 0.0 4.94 R
3567 3692 0.457853 TCTCCGCGTTTCTGATTCCG 60.458 55.000 4.92 0.0 0.0 4.30 R
4511 4684 0.034476 GCGGTAGGCTGTTATACCCC 59.966 60.000 0.00 0.0 38.6 4.95 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
20 21 2.382519 CCTGAATATCCGTCGAACGTC 58.617 52.381 0.00 0.00 40.58 4.34
21 22 2.034789 CTGAATATCCGTCGAACGTCG 58.965 52.381 6.84 6.84 40.58 5.12
27 28 2.437850 CCGTCGAACGTCGGATTTT 58.562 52.632 22.99 0.00 46.64 1.82
28 29 0.364515 CCGTCGAACGTCGGATTTTC 59.635 55.000 22.99 0.00 46.64 2.29
30 31 1.452773 CGTCGAACGTCGGATTTTCAA 59.547 47.619 0.00 0.00 40.88 2.69
43 44 4.263677 CGGATTTTCAAGCATGACAAATCG 59.736 41.667 20.43 13.14 39.99 3.34
46 47 6.197842 GGATTTTCAAGCATGACAAATCGATC 59.802 38.462 20.43 11.57 39.99 3.69
51 52 4.264543 AGCATGACAAATCGATCGTTTC 57.735 40.909 15.94 2.31 0.00 2.78
57 59 7.621102 CATGACAAATCGATCGTTTCTTATGA 58.379 34.615 15.94 0.00 0.00 2.15
72 74 9.128107 CGTTTCTTATGACAAATTATGTTTGCT 57.872 29.630 5.59 0.00 44.12 3.91
75 77 9.844790 TTCTTATGACAAATTATGTTTGCTGAG 57.155 29.630 5.59 0.00 44.12 3.35
80 82 6.433716 TGACAAATTATGTTTGCTGAGGATGA 59.566 34.615 5.59 0.00 44.12 2.92
83 85 6.839124 AATTATGTTTGCTGAGGATGACAA 57.161 33.333 0.00 0.00 0.00 3.18
93 95 4.154918 GCTGAGGATGACAAGTTTAGTTGG 59.845 45.833 2.66 0.00 0.00 3.77
97 99 5.690865 AGGATGACAAGTTTAGTTGGTGAA 58.309 37.500 2.66 0.00 0.00 3.18
98 100 6.306987 AGGATGACAAGTTTAGTTGGTGAAT 58.693 36.000 2.66 0.00 0.00 2.57
101 103 8.184192 GGATGACAAGTTTAGTTGGTGAATATG 58.816 37.037 2.66 0.00 0.00 1.78
102 104 7.447374 TGACAAGTTTAGTTGGTGAATATGG 57.553 36.000 2.66 0.00 0.00 2.74
109 111 8.374743 AGTTTAGTTGGTGAATATGGCAAATTT 58.625 29.630 0.00 0.00 0.00 1.82
110 112 8.442384 GTTTAGTTGGTGAATATGGCAAATTTG 58.558 33.333 14.03 14.03 0.00 2.32
115 117 5.036737 GGTGAATATGGCAAATTTGTCTCG 58.963 41.667 22.47 0.00 33.01 4.04
116 118 5.393027 GGTGAATATGGCAAATTTGTCTCGT 60.393 40.000 22.47 13.93 33.01 4.18
123 126 4.981674 TGGCAAATTTGTCTCGTTCATTTC 59.018 37.500 22.47 0.29 33.01 2.17
128 131 5.695851 ATTTGTCTCGTTCATTTCTTGCT 57.304 34.783 0.00 0.00 0.00 3.91
130 133 5.845985 TTGTCTCGTTCATTTCTTGCTAG 57.154 39.130 0.00 0.00 0.00 3.42
146 149 9.502091 TTTCTTGCTAGAAAATTGCTCTACTTA 57.498 29.630 18.99 0.00 45.08 2.24
171 174 5.705609 AACTAAATTTGCCATTCTCACGT 57.294 34.783 0.00 0.00 0.00 4.49
180 183 6.993786 TTGCCATTCTCACGTCAATATAAA 57.006 33.333 0.00 0.00 0.00 1.40
184 187 6.360681 GCCATTCTCACGTCAATATAAATTGC 59.639 38.462 0.00 0.00 41.96 3.56
189 192 8.083462 TCTCACGTCAATATAAATTGCCATAC 57.917 34.615 0.00 0.00 41.96 2.39
191 194 8.214721 TCACGTCAATATAAATTGCCATACAA 57.785 30.769 0.00 0.00 41.96 2.41
206 211 4.869861 GCCATACAAAAATTCGATTTGGCT 59.130 37.500 13.07 0.00 41.08 4.75
219 224 3.191371 CGATTTGGCTTGCCTAAAAGTCT 59.809 43.478 13.18 0.00 32.82 3.24
220 225 4.488879 GATTTGGCTTGCCTAAAAGTCTG 58.511 43.478 13.18 0.00 32.82 3.51
223 228 1.464997 GGCTTGCCTAAAAGTCTGACG 59.535 52.381 4.11 0.00 0.00 4.35
225 230 3.323243 GCTTGCCTAAAAGTCTGACGTA 58.677 45.455 1.52 0.00 0.00 3.57
243 248 8.421784 TCTGACGTAAGATTATTAGCATTTCCT 58.578 33.333 0.00 0.00 43.62 3.36
280 285 3.858886 TGGCACATGGGAGGAAAAA 57.141 47.368 0.00 0.00 0.00 1.94
304 315 3.008485 AGTGAGACCAGGCTAAAAAGGAG 59.992 47.826 0.00 0.00 0.00 3.69
343 354 1.668419 ATTAACCACGCAGCATCCTC 58.332 50.000 0.00 0.00 0.00 3.71
363 374 1.268794 CGATCGAGCCTACACCTGAAG 60.269 57.143 10.26 0.00 0.00 3.02
520 531 2.813907 TCTCTCAACTCTCAAGGGAGG 58.186 52.381 1.51 0.00 41.69 4.30
524 535 3.973973 TCTCAACTCTCAAGGGAGGAAAA 59.026 43.478 1.51 0.00 41.69 2.29
525 536 4.599241 TCTCAACTCTCAAGGGAGGAAAAT 59.401 41.667 1.51 0.00 41.69 1.82
530 541 4.018324 ACTCTCAAGGGAGGAAAATAACCC 60.018 45.833 1.51 0.00 41.69 4.11
571 582 4.096382 GCACTATCATTTGTCCGGAATTGT 59.904 41.667 5.23 0.00 0.00 2.71
572 583 5.295787 GCACTATCATTTGTCCGGAATTGTA 59.704 40.000 5.23 0.00 0.00 2.41
576 587 6.773976 ATCATTTGTCCGGAATTGTATTGT 57.226 33.333 5.23 0.00 0.00 2.71
584 595 3.186409 CCGGAATTGTATTGTAGCCATCG 59.814 47.826 0.00 0.00 0.00 3.84
670 681 2.980233 AAACCGACCTGCTGCTGC 60.980 61.111 8.89 8.89 40.20 5.25
676 687 0.950555 CGACCTGCTGCTGCTGTTAA 60.951 55.000 17.00 0.00 40.48 2.01
677 688 0.801251 GACCTGCTGCTGCTGTTAAG 59.199 55.000 17.00 5.09 40.48 1.85
678 689 0.109342 ACCTGCTGCTGCTGTTAAGT 59.891 50.000 17.00 6.69 40.48 2.24
679 690 1.347707 ACCTGCTGCTGCTGTTAAGTA 59.652 47.619 17.00 0.00 40.48 2.24
680 691 2.005451 CCTGCTGCTGCTGTTAAGTAG 58.995 52.381 17.00 2.95 39.03 2.57
681 692 2.005451 CTGCTGCTGCTGTTAAGTAGG 58.995 52.381 17.00 0.00 36.69 3.18
715 726 2.488836 AGGTAGTTTTCCCCGGATGAT 58.511 47.619 0.73 0.00 0.00 2.45
743 770 2.644992 GGAAGCAAGCAACCCACG 59.355 61.111 0.00 0.00 0.00 4.94
768 833 1.002142 CCACATGCACCATGATAAGCG 60.002 52.381 11.78 0.00 43.81 4.68
795 860 4.554723 CGTCTCCCATTTTGTTTCACACTC 60.555 45.833 0.00 0.00 0.00 3.51
828 893 1.302832 CCAGGAGTTGGCAGACACC 60.303 63.158 7.73 7.73 40.87 4.16
840 914 1.766059 AGACACCAGACCAGTGGCA 60.766 57.895 9.78 0.00 46.27 4.92
841 915 1.148273 GACACCAGACCAGTGGCAA 59.852 57.895 9.78 0.00 43.15 4.52
842 916 0.465460 GACACCAGACCAGTGGCAAA 60.465 55.000 9.78 0.00 43.15 3.68
843 917 0.466189 ACACCAGACCAGTGGCAAAG 60.466 55.000 9.78 0.00 41.90 2.77
845 919 1.228367 CCAGACCAGTGGCAAAGCT 60.228 57.895 9.78 0.00 0.00 3.74
884 958 0.450983 GCAGAGCTCTGGTGAAATGC 59.549 55.000 37.86 22.24 43.94 3.56
1066 1152 3.589654 TTCCTCGCCTTGCTCGTGG 62.590 63.158 0.00 0.00 40.67 4.94
1067 1153 4.379243 CCTCGCCTTGCTCGTGGT 62.379 66.667 0.00 0.00 36.27 4.16
1068 1154 3.114616 CTCGCCTTGCTCGTGGTG 61.115 66.667 0.00 0.00 35.34 4.17
1650 1736 2.181021 GGGAGCTACGACGTGGTG 59.819 66.667 13.96 4.76 0.00 4.17
1871 1957 2.048597 CGCCGGTCTGCAGTACAA 60.049 61.111 14.67 0.00 0.00 2.41
1872 1958 1.447838 CGCCGGTCTGCAGTACAAT 60.448 57.895 14.67 0.00 0.00 2.71
1984 2070 4.415332 GCCTCGTCTTCGACCGCA 62.415 66.667 0.00 0.00 41.35 5.69
2106 2192 1.945776 CTTTCGAGCTCAACGTCGCC 61.946 60.000 15.40 0.00 36.11 5.54
2202 2288 2.428071 GCTGCGTTGCTTGTGCTC 60.428 61.111 0.00 0.00 40.48 4.26
2358 2444 1.497278 CGTGGTGGAGCATTTCACG 59.503 57.895 0.00 0.00 43.58 4.35
3544 3669 1.264020 CATTGGAACACACACAGTCGG 59.736 52.381 0.00 0.00 39.29 4.79
3567 3692 0.729690 GGAAAGCAATGCGAGAGGAC 59.270 55.000 0.00 0.00 0.00 3.85
3579 3704 2.531206 CGAGAGGACGGAATCAGAAAC 58.469 52.381 0.00 0.00 0.00 2.78
3630 3755 2.701006 CGCGAATTGACGGCGAAT 59.299 55.556 16.62 0.00 35.93 3.34
3689 3815 2.352960 GGCTAGTCAAAATCAAGGAGCG 59.647 50.000 0.00 0.00 0.00 5.03
3742 3868 2.029518 ACCGGTTTCCGTTCGTCC 59.970 61.111 0.00 0.00 46.80 4.79
3874 4009 2.431260 GCACGCCTGCATTTGGTG 60.431 61.111 2.56 2.65 43.62 4.17
3929 4091 7.653311 GGGGATTCTTTATTGATGTGTAATTGC 59.347 37.037 0.00 0.00 0.00 3.56
3949 4111 6.971527 TTGCGTATAGATTTTTCTTTCCGA 57.028 33.333 0.00 0.00 0.00 4.55
3965 4129 8.882415 TTCTTTCCGAGGATAATTGTGTATAC 57.118 34.615 0.00 0.00 0.00 1.47
3968 4132 6.092955 TCCGAGGATAATTGTGTATACACC 57.907 41.667 28.67 14.46 45.88 4.16
4036 4201 7.293402 TCTTTTTGTTCATGCTTCTGTTTTG 57.707 32.000 0.00 0.00 0.00 2.44
4040 4205 5.512753 TGTTCATGCTTCTGTTTTGCTTA 57.487 34.783 0.00 0.00 0.00 3.09
4041 4206 5.900425 TGTTCATGCTTCTGTTTTGCTTAA 58.100 33.333 0.00 0.00 0.00 1.85
4049 4220 7.153985 TGCTTCTGTTTTGCTTAATAATTGCT 58.846 30.769 0.00 0.00 0.00 3.91
4056 4227 2.286833 TGCTTAATAATTGCTCGTCCGC 59.713 45.455 0.00 0.00 0.00 5.54
4077 4248 4.268644 CGCTGCAACGGGATATAGATATTG 59.731 45.833 0.45 0.00 0.00 1.90
4109 4280 3.000277 TGCAAATTTTCAAGTTTCGCACG 60.000 39.130 0.00 0.00 0.00 5.34
4117 4288 4.430423 GTTTCGCACGCGGCAGAG 62.430 66.667 12.47 1.47 45.17 3.35
4232 4405 8.257306 GCTGATTTTTATATGGTCAAAAGGGAA 58.743 33.333 0.00 0.00 0.00 3.97
4246 4419 7.327975 GTCAAAAGGGAAAAAGGAAAGAAGAA 58.672 34.615 0.00 0.00 0.00 2.52
4270 4443 7.792374 AGAAATCCCTTTTTCTTTTTCTTGC 57.208 32.000 0.00 0.00 41.95 4.01
4286 4459 2.159184 TCTTGCTAGTGCTCATCTTCGG 60.159 50.000 0.00 0.00 40.48 4.30
4344 4517 2.437359 CTTTGCCTGCCTCCTCCG 60.437 66.667 0.00 0.00 0.00 4.63
4361 4534 1.227674 CGGATGCAAGGGGAGTAGC 60.228 63.158 0.00 0.00 0.00 3.58
4395 4568 1.818642 GCTCACTGCTCATTTCTGGT 58.181 50.000 0.00 0.00 38.95 4.00
4396 4569 2.977914 GCTCACTGCTCATTTCTGGTA 58.022 47.619 0.00 0.00 38.95 3.25
4397 4570 3.338249 GCTCACTGCTCATTTCTGGTAA 58.662 45.455 0.00 0.00 38.95 2.85
4398 4571 3.753272 GCTCACTGCTCATTTCTGGTAAA 59.247 43.478 0.00 0.00 38.95 2.01
4399 4572 4.397417 GCTCACTGCTCATTTCTGGTAAAT 59.603 41.667 0.00 0.00 38.95 1.40
4400 4573 5.675575 GCTCACTGCTCATTTCTGGTAAATG 60.676 44.000 4.46 4.46 38.60 2.32
4401 4574 4.701651 TCACTGCTCATTTCTGGTAAATGG 59.298 41.667 9.81 3.66 38.00 3.16
4402 4575 4.019174 ACTGCTCATTTCTGGTAAATGGG 58.981 43.478 9.81 8.00 40.24 4.00
4403 4576 3.364549 TGCTCATTTCTGGTAAATGGGG 58.635 45.455 11.25 6.34 38.29 4.96
4404 4577 2.695147 GCTCATTTCTGGTAAATGGGGG 59.305 50.000 11.25 4.47 38.29 5.40
4421 4594 3.671008 GGGGGCTAAATTTCGTGTTTT 57.329 42.857 0.00 0.00 0.00 2.43
4422 4595 3.322369 GGGGGCTAAATTTCGTGTTTTG 58.678 45.455 0.00 0.00 0.00 2.44
4423 4596 3.006003 GGGGGCTAAATTTCGTGTTTTGA 59.994 43.478 0.00 0.00 0.00 2.69
4424 4597 3.985279 GGGGCTAAATTTCGTGTTTTGAC 59.015 43.478 0.00 0.00 0.00 3.18
4425 4598 3.985279 GGGCTAAATTTCGTGTTTTGACC 59.015 43.478 0.00 0.00 33.51 4.02
4426 4599 3.985279 GGCTAAATTTCGTGTTTTGACCC 59.015 43.478 0.00 0.00 0.00 4.46
4427 4600 4.261867 GGCTAAATTTCGTGTTTTGACCCT 60.262 41.667 0.00 0.00 0.00 4.34
4428 4601 5.286438 GCTAAATTTCGTGTTTTGACCCTT 58.714 37.500 0.00 0.00 0.00 3.95
4429 4602 5.751509 GCTAAATTTCGTGTTTTGACCCTTT 59.248 36.000 0.00 0.00 0.00 3.11
4430 4603 6.256975 GCTAAATTTCGTGTTTTGACCCTTTT 59.743 34.615 0.00 0.00 0.00 2.27
4431 4604 6.656314 AAATTTCGTGTTTTGACCCTTTTC 57.344 33.333 0.00 0.00 0.00 2.29
4432 4605 5.592104 ATTTCGTGTTTTGACCCTTTTCT 57.408 34.783 0.00 0.00 0.00 2.52
4433 4606 4.364415 TTCGTGTTTTGACCCTTTTCTG 57.636 40.909 0.00 0.00 0.00 3.02
4434 4607 3.611970 TCGTGTTTTGACCCTTTTCTGA 58.388 40.909 0.00 0.00 0.00 3.27
4435 4608 4.011023 TCGTGTTTTGACCCTTTTCTGAA 58.989 39.130 0.00 0.00 0.00 3.02
4436 4609 4.459685 TCGTGTTTTGACCCTTTTCTGAAA 59.540 37.500 0.00 0.00 0.00 2.69
4437 4610 4.561213 CGTGTTTTGACCCTTTTCTGAAAC 59.439 41.667 1.58 0.00 0.00 2.78
4438 4611 5.621329 CGTGTTTTGACCCTTTTCTGAAACT 60.621 40.000 1.58 0.00 0.00 2.66
4439 4612 6.163476 GTGTTTTGACCCTTTTCTGAAACTT 58.837 36.000 1.58 0.00 0.00 2.66
4440 4613 7.317390 GTGTTTTGACCCTTTTCTGAAACTTA 58.683 34.615 1.58 0.00 0.00 2.24
4441 4614 7.979537 GTGTTTTGACCCTTTTCTGAAACTTAT 59.020 33.333 1.58 0.00 0.00 1.73
4442 4615 8.536175 TGTTTTGACCCTTTTCTGAAACTTATT 58.464 29.630 1.58 0.00 0.00 1.40
4443 4616 9.378551 GTTTTGACCCTTTTCTGAAACTTATTT 57.621 29.630 1.58 0.00 0.00 1.40
4444 4617 9.952030 TTTTGACCCTTTTCTGAAACTTATTTT 57.048 25.926 1.58 0.00 0.00 1.82
4445 4618 8.940768 TTGACCCTTTTCTGAAACTTATTTTG 57.059 30.769 1.58 0.00 0.00 2.44
4446 4619 8.299990 TGACCCTTTTCTGAAACTTATTTTGA 57.700 30.769 1.58 0.00 0.00 2.69
4447 4620 8.413229 TGACCCTTTTCTGAAACTTATTTTGAG 58.587 33.333 1.58 0.00 30.07 3.02
4448 4621 8.533569 ACCCTTTTCTGAAACTTATTTTGAGA 57.466 30.769 1.58 0.00 35.83 3.27
4449 4622 9.147732 ACCCTTTTCTGAAACTTATTTTGAGAT 57.852 29.630 1.58 0.00 37.30 2.75
4450 4623 9.987272 CCCTTTTCTGAAACTTATTTTGAGATT 57.013 29.630 1.58 0.00 37.30 2.40
4494 4667 7.539712 TTTAATCTGACTCTTTTGCTATCGG 57.460 36.000 0.00 0.00 0.00 4.18
4495 4668 2.893637 TCTGACTCTTTTGCTATCGGC 58.106 47.619 0.00 0.00 42.22 5.54
4504 4677 3.151906 GCTATCGGCAGGGACCAT 58.848 61.111 0.00 0.00 41.35 3.55
4505 4678 2.362242 GCTATCGGCAGGGACCATA 58.638 57.895 0.00 0.00 41.35 2.74
4506 4679 0.247736 GCTATCGGCAGGGACCATAG 59.752 60.000 0.00 0.00 41.35 2.23
4507 4680 0.247736 CTATCGGCAGGGACCATAGC 59.752 60.000 0.00 0.00 0.00 2.97
4508 4681 1.532604 TATCGGCAGGGACCATAGCG 61.533 60.000 0.00 0.00 0.00 4.26
4509 4682 4.609018 CGGCAGGGACCATAGCGG 62.609 72.222 0.00 0.00 42.50 5.52
4520 4693 2.467566 CCATAGCGGTGGGGTATAAC 57.532 55.000 0.00 0.00 37.22 1.89
4521 4694 1.695242 CCATAGCGGTGGGGTATAACA 59.305 52.381 0.00 0.00 37.22 2.41
4522 4695 2.289444 CCATAGCGGTGGGGTATAACAG 60.289 54.545 0.00 0.00 37.22 3.16
4523 4696 0.754472 TAGCGGTGGGGTATAACAGC 59.246 55.000 0.00 0.00 37.70 4.40
4524 4697 1.525306 GCGGTGGGGTATAACAGCC 60.525 63.158 0.00 0.00 44.70 4.85
4525 4698 1.979619 GCGGTGGGGTATAACAGCCT 61.980 60.000 0.00 0.00 44.81 4.58
4526 4699 1.416243 CGGTGGGGTATAACAGCCTA 58.584 55.000 0.00 0.00 44.81 3.93
4529 4702 1.416243 TGGGGTATAACAGCCTACCG 58.584 55.000 0.00 0.00 44.81 4.02
4530 4703 0.034476 GGGGTATAACAGCCTACCGC 59.966 60.000 0.00 0.00 44.81 5.68
4531 4704 0.034476 GGGTATAACAGCCTACCGCC 59.966 60.000 0.00 0.00 41.95 6.13
4532 4705 0.754472 GGTATAACAGCCTACCGCCA 59.246 55.000 0.00 0.00 38.78 5.69
4533 4706 1.139455 GGTATAACAGCCTACCGCCAA 59.861 52.381 0.00 0.00 38.78 4.52
4534 4707 2.480845 GTATAACAGCCTACCGCCAAG 58.519 52.381 0.00 0.00 38.78 3.61
4544 4717 2.742372 CCGCCAAGGTCCTTGACG 60.742 66.667 29.91 28.81 44.49 4.35
4545 4718 2.742372 CGCCAAGGTCCTTGACGG 60.742 66.667 29.91 16.34 42.03 4.79
4546 4719 2.430367 GCCAAGGTCCTTGACGGT 59.570 61.111 29.91 0.00 43.42 4.83
4547 4720 1.675219 GCCAAGGTCCTTGACGGTA 59.325 57.895 29.91 0.00 43.42 4.02
4548 4721 0.391263 GCCAAGGTCCTTGACGGTAG 60.391 60.000 29.91 14.62 43.42 3.18
4549 4722 0.249398 CCAAGGTCCTTGACGGTAGG 59.751 60.000 29.91 10.06 43.42 3.18
4550 4723 0.249398 CAAGGTCCTTGACGGTAGGG 59.751 60.000 25.15 0.00 43.42 3.53
4551 4724 0.178912 AAGGTCCTTGACGGTAGGGT 60.179 55.000 2.38 0.00 32.65 4.34
4552 4725 0.178912 AGGTCCTTGACGGTAGGGTT 60.179 55.000 0.00 0.00 32.65 4.11
4553 4726 1.077663 AGGTCCTTGACGGTAGGGTTA 59.922 52.381 0.00 0.00 32.65 2.85
4554 4727 1.205655 GGTCCTTGACGGTAGGGTTAC 59.794 57.143 0.00 0.00 32.65 2.50
4555 4728 1.895131 GTCCTTGACGGTAGGGTTACA 59.105 52.381 0.00 0.00 33.41 2.41
4556 4729 2.498885 GTCCTTGACGGTAGGGTTACAT 59.501 50.000 0.00 0.00 33.41 2.29
4557 4730 2.498481 TCCTTGACGGTAGGGTTACATG 59.502 50.000 0.00 0.00 33.41 3.21
4558 4731 2.277084 CTTGACGGTAGGGTTACATGC 58.723 52.381 0.00 0.00 0.00 4.06
4559 4732 0.538118 TGACGGTAGGGTTACATGCC 59.462 55.000 0.00 0.00 0.00 4.40
4560 4733 0.179065 GACGGTAGGGTTACATGCCC 60.179 60.000 0.00 0.00 46.43 5.36
4565 4738 4.870190 GGGTTACATGCCCTACCG 57.130 61.111 0.00 0.00 42.81 4.02
4566 4739 1.909975 GGGTTACATGCCCTACCGT 59.090 57.895 0.00 0.00 42.81 4.83
4567 4740 1.122227 GGGTTACATGCCCTACCGTA 58.878 55.000 0.00 0.00 42.81 4.02
4568 4741 1.485895 GGGTTACATGCCCTACCGTAA 59.514 52.381 0.00 0.00 42.81 3.18
4569 4742 2.093021 GGGTTACATGCCCTACCGTAAA 60.093 50.000 0.00 0.00 42.81 2.01
4570 4743 3.608796 GGTTACATGCCCTACCGTAAAA 58.391 45.455 0.00 0.00 0.00 1.52
4571 4744 4.009002 GGTTACATGCCCTACCGTAAAAA 58.991 43.478 0.00 0.00 0.00 1.94
4596 4769 6.787085 ACTTCTAAGTATTGAACACAGTGC 57.213 37.500 0.00 0.00 37.52 4.40
4597 4770 5.405571 ACTTCTAAGTATTGAACACAGTGCG 59.594 40.000 0.00 0.00 37.52 5.34
4598 4771 4.878439 TCTAAGTATTGAACACAGTGCGT 58.122 39.130 0.00 0.00 0.00 5.24
4599 4772 8.889598 ACTTCTAAGTATTGAACACAGTGCGTG 61.890 40.741 0.00 0.00 43.96 5.34
4606 4779 4.360027 CACAGTGCGTGCTCGTGC 62.360 66.667 10.18 1.71 39.19 5.34
4609 4782 3.680786 AGTGCGTGCTCGTGCCTA 61.681 61.111 10.18 0.00 39.49 3.93
4610 4783 3.479269 GTGCGTGCTCGTGCCTAC 61.479 66.667 10.18 0.00 39.49 3.18
4611 4784 4.735132 TGCGTGCTCGTGCCTACC 62.735 66.667 10.18 0.00 39.49 3.18
4616 4789 4.752879 GCTCGTGCCTACCGCCAA 62.753 66.667 0.00 0.00 36.24 4.52
4617 4790 2.509336 CTCGTGCCTACCGCCAAG 60.509 66.667 0.00 0.00 36.24 3.61
4618 4791 4.752879 TCGTGCCTACCGCCAAGC 62.753 66.667 0.00 0.00 36.24 4.01
4621 4794 4.715523 TGCCTACCGCCAAGCACC 62.716 66.667 0.00 0.00 36.24 5.01
4622 4795 4.410400 GCCTACCGCCAAGCACCT 62.410 66.667 0.00 0.00 0.00 4.00
4623 4796 2.351276 CCTACCGCCAAGCACCTT 59.649 61.111 0.00 0.00 0.00 3.50
4624 4797 2.040544 CCTACCGCCAAGCACCTTG 61.041 63.158 0.00 0.00 40.75 3.61
4631 4804 3.578456 CAAGCACCTTGGCGGTAG 58.422 61.111 0.00 0.00 46.94 3.18
4632 4805 2.040544 CAAGCACCTTGGCGGTAGG 61.041 63.158 0.00 0.00 46.94 3.18
4633 4806 3.268103 AAGCACCTTGGCGGTAGGG 62.268 63.158 5.31 0.00 46.94 3.53
4634 4807 4.029809 GCACCTTGGCGGTAGGGT 62.030 66.667 5.31 0.00 46.94 4.34
4635 4808 2.754375 CACCTTGGCGGTAGGGTT 59.246 61.111 5.31 0.00 46.94 4.11
4636 4809 1.674322 CACCTTGGCGGTAGGGTTG 60.674 63.158 5.31 0.00 46.94 3.77
4637 4810 2.151388 ACCTTGGCGGTAGGGTTGT 61.151 57.895 5.31 0.00 46.73 3.32
4638 4811 1.674322 CCTTGGCGGTAGGGTTGTG 60.674 63.158 0.00 0.00 0.00 3.33
4639 4812 2.281900 TTGGCGGTAGGGTTGTGC 60.282 61.111 0.00 0.00 0.00 4.57
4640 4813 3.121406 TTGGCGGTAGGGTTGTGCA 62.121 57.895 0.00 0.00 0.00 4.57
4641 4814 2.746277 GGCGGTAGGGTTGTGCAG 60.746 66.667 0.00 0.00 0.00 4.41
4642 4815 2.746277 GCGGTAGGGTTGTGCAGG 60.746 66.667 0.00 0.00 0.00 4.85
4643 4816 2.746277 CGGTAGGGTTGTGCAGGC 60.746 66.667 0.00 0.00 0.00 4.85
4644 4817 2.757077 GGTAGGGTTGTGCAGGCT 59.243 61.111 0.00 0.00 0.00 4.58
4645 4818 1.895020 CGGTAGGGTTGTGCAGGCTA 61.895 60.000 0.00 0.00 0.00 3.93
4646 4819 0.392595 GGTAGGGTTGTGCAGGCTAC 60.393 60.000 0.00 0.00 0.00 3.58
4647 4820 0.392595 GTAGGGTTGTGCAGGCTACC 60.393 60.000 0.00 0.00 0.00 3.18
4648 4821 1.895020 TAGGGTTGTGCAGGCTACCG 61.895 60.000 0.00 0.00 0.00 4.02
4649 4822 3.431725 GGTTGTGCAGGCTACCGC 61.432 66.667 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.458064 GCTTGAAAATCCGACGTTCGA 59.542 47.619 8.63 0.00 43.74 3.71
13 14 1.193650 TGCTTGAAAATCCGACGTTCG 59.806 47.619 0.00 0.00 40.07 3.95
15 16 2.811431 TCATGCTTGAAAATCCGACGTT 59.189 40.909 0.00 0.00 0.00 3.99
20 21 4.263677 CGATTTGTCATGCTTGAAAATCCG 59.736 41.667 24.45 18.51 36.83 4.18
21 22 5.401550 TCGATTTGTCATGCTTGAAAATCC 58.598 37.500 24.45 13.89 36.83 3.01
24 25 5.088068 CGATCGATTTGTCATGCTTGAAAA 58.912 37.500 10.26 2.24 32.48 2.29
27 28 3.261580 ACGATCGATTTGTCATGCTTGA 58.738 40.909 24.34 0.00 0.00 3.02
28 29 3.663464 ACGATCGATTTGTCATGCTTG 57.337 42.857 24.34 0.00 0.00 4.01
30 31 3.935203 AGAAACGATCGATTTGTCATGCT 59.065 39.130 24.34 4.78 0.00 3.79
46 47 9.128107 AGCAAACATAATTTGTCATAAGAAACG 57.872 29.630 1.71 0.00 37.68 3.60
51 52 8.461222 TCCTCAGCAAACATAATTTGTCATAAG 58.539 33.333 1.71 0.00 37.68 1.73
57 59 6.209192 TGTCATCCTCAGCAAACATAATTTGT 59.791 34.615 1.71 0.00 41.53 2.83
72 74 5.063204 CACCAACTAAACTTGTCATCCTCA 58.937 41.667 0.00 0.00 0.00 3.86
75 77 6.575162 ATTCACCAACTAAACTTGTCATCC 57.425 37.500 0.00 0.00 0.00 3.51
80 82 5.772672 TGCCATATTCACCAACTAAACTTGT 59.227 36.000 0.00 0.00 0.00 3.16
83 85 6.909550 TTTGCCATATTCACCAACTAAACT 57.090 33.333 0.00 0.00 0.00 2.66
93 95 5.640732 ACGAGACAAATTTGCCATATTCAC 58.359 37.500 18.12 5.08 0.00 3.18
97 99 5.895636 TGAACGAGACAAATTTGCCATAT 57.104 34.783 18.12 0.00 0.00 1.78
98 100 5.895636 ATGAACGAGACAAATTTGCCATA 57.104 34.783 18.12 0.00 0.00 2.74
101 103 5.222631 AGAAATGAACGAGACAAATTTGCC 58.777 37.500 18.12 7.29 0.00 4.52
102 104 6.575132 CAAGAAATGAACGAGACAAATTTGC 58.425 36.000 18.12 10.76 0.00 3.68
109 111 5.134202 TCTAGCAAGAAATGAACGAGACA 57.866 39.130 0.00 0.00 0.00 3.41
110 112 6.467723 TTTCTAGCAAGAAATGAACGAGAC 57.532 37.500 0.00 0.00 44.85 3.36
123 126 8.256611 TGTAAGTAGAGCAATTTTCTAGCAAG 57.743 34.615 0.00 0.00 0.00 4.01
157 160 6.993786 TTTATATTGACGTGAGAATGGCAA 57.006 33.333 0.00 0.00 0.00 4.52
160 163 6.857964 GGCAATTTATATTGACGTGAGAATGG 59.142 38.462 9.76 0.00 43.12 3.16
180 183 6.183360 GCCAAATCGAATTTTTGTATGGCAAT 60.183 34.615 8.00 0.00 35.28 3.56
184 187 6.672836 GCAAGCCAAATCGAATTTTTGTATGG 60.673 38.462 8.68 0.00 33.23 2.74
189 192 3.747529 AGGCAAGCCAAATCGAATTTTTG 59.252 39.130 14.40 3.48 38.92 2.44
191 194 3.683365 AGGCAAGCCAAATCGAATTTT 57.317 38.095 14.40 0.00 38.92 1.82
196 199 3.153919 ACTTTTAGGCAAGCCAAATCGA 58.846 40.909 14.40 0.00 38.92 3.59
197 200 3.191371 AGACTTTTAGGCAAGCCAAATCG 59.809 43.478 14.40 8.41 38.92 3.34
206 211 5.204409 TCTTACGTCAGACTTTTAGGCAA 57.796 39.130 0.00 0.00 0.00 4.52
219 224 8.958119 AAGGAAATGCTAATAATCTTACGTCA 57.042 30.769 0.00 0.00 0.00 4.35
250 255 5.732633 TCCCATGTGCCATTTTCATTAAAG 58.267 37.500 0.00 0.00 0.00 1.85
280 285 4.141251 TCCTTTTTAGCCTGGTCTCACTTT 60.141 41.667 0.00 0.00 0.00 2.66
304 315 3.915437 TTCTTCTTTGAATGGAACGGC 57.085 42.857 0.00 0.00 0.00 5.68
343 354 0.738975 TTCAGGTGTAGGCTCGATCG 59.261 55.000 9.36 9.36 0.00 3.69
520 531 1.596895 TTGCCGCCCGGGTTATTTTC 61.597 55.000 24.63 1.44 38.44 2.29
524 535 3.723922 ACTTGCCGCCCGGGTTAT 61.724 61.111 24.63 0.00 38.44 1.89
525 536 4.708386 CACTTGCCGCCCGGGTTA 62.708 66.667 24.63 2.86 38.44 2.85
545 556 1.942657 CCGGACAAATGATAGTGCCTG 59.057 52.381 0.00 0.00 0.00 4.85
571 582 1.522668 GCATGGCGATGGCTACAATA 58.477 50.000 10.93 0.00 39.81 1.90
572 583 2.334307 GCATGGCGATGGCTACAAT 58.666 52.632 10.93 0.00 39.81 2.71
584 595 1.447838 TTTCGTCTCTCCGCATGGC 60.448 57.895 0.00 0.00 34.14 4.40
670 681 5.657302 ACCACCATCTACTCCTACTTAACAG 59.343 44.000 0.00 0.00 0.00 3.16
676 687 3.792684 ACCTACCACCATCTACTCCTACT 59.207 47.826 0.00 0.00 0.00 2.57
677 688 4.181799 ACCTACCACCATCTACTCCTAC 57.818 50.000 0.00 0.00 0.00 3.18
678 689 4.980342 ACTACCTACCACCATCTACTCCTA 59.020 45.833 0.00 0.00 0.00 2.94
679 690 3.792684 ACTACCTACCACCATCTACTCCT 59.207 47.826 0.00 0.00 0.00 3.69
680 691 4.181799 ACTACCTACCACCATCTACTCC 57.818 50.000 0.00 0.00 0.00 3.85
681 692 6.406737 GGAAAACTACCTACCACCATCTACTC 60.407 46.154 0.00 0.00 0.00 2.59
715 726 1.243902 CTTGCTTCCCGGCTTGTTTA 58.756 50.000 0.00 0.00 0.00 2.01
743 770 1.038681 TCATGGTGCATGTGGGCATC 61.039 55.000 0.00 0.00 46.92 3.91
768 833 3.813166 TGAAACAAAATGGGAGACGAGTC 59.187 43.478 0.00 0.00 0.00 3.36
795 860 3.390639 ACTCCTGGAGAAGATAATGGCTG 59.609 47.826 29.71 0.00 33.32 4.85
828 893 1.808945 CTTAGCTTTGCCACTGGTCTG 59.191 52.381 0.00 0.00 0.00 3.51
840 914 2.907458 ATTCCCACCAGCTTAGCTTT 57.093 45.000 3.00 0.00 36.40 3.51
841 915 2.846827 ACTATTCCCACCAGCTTAGCTT 59.153 45.455 3.00 0.00 36.40 3.74
842 916 2.482494 ACTATTCCCACCAGCTTAGCT 58.518 47.619 0.00 0.00 40.77 3.32
843 917 2.945668 CAACTATTCCCACCAGCTTAGC 59.054 50.000 0.00 0.00 0.00 3.09
845 919 2.356741 GCCAACTATTCCCACCAGCTTA 60.357 50.000 0.00 0.00 0.00 3.09
884 958 2.240500 GCCGCCTACTTCATCGCAG 61.241 63.158 0.00 0.00 0.00 5.18
1723 1809 1.008194 CGTTCTCACCGTCCAACGA 60.008 57.895 0.24 0.00 46.05 3.85
1726 1812 2.029964 GGCGTTCTCACCGTCCAA 59.970 61.111 0.00 0.00 0.00 3.53
1871 1957 4.457496 CCTGCGCCTGGACGTCAT 62.457 66.667 18.91 0.00 34.88 3.06
2106 2192 4.697756 TTCGCTGCCTTGGGGACG 62.698 66.667 0.00 0.00 33.58 4.79
2140 2226 0.980231 ATCTTTCTCCTCCTGCCGCT 60.980 55.000 0.00 0.00 0.00 5.52
2202 2288 1.081242 GAACTGCAATGCCACCACG 60.081 57.895 1.53 0.00 0.00 4.94
2267 2353 3.099211 ATCGCGGCAAGCTCATCCT 62.099 57.895 6.13 0.00 45.59 3.24
3501 3626 3.302347 CTCGCGTGGCTTCCTTCCT 62.302 63.158 5.77 0.00 0.00 3.36
3502 3627 2.815647 CTCGCGTGGCTTCCTTCC 60.816 66.667 5.77 0.00 0.00 3.46
3503 3628 2.048127 ACTCGCGTGGCTTCCTTC 60.048 61.111 13.32 0.00 0.00 3.46
3504 3629 2.048127 GACTCGCGTGGCTTCCTT 60.048 61.111 13.32 0.00 0.00 3.36
3544 3669 1.019278 TCTCGCATTGCTTTCCGTCC 61.019 55.000 7.12 0.00 0.00 4.79
3567 3692 0.457853 TCTCCGCGTTTCTGATTCCG 60.458 55.000 4.92 0.00 0.00 4.30
3579 3704 1.790387 CTTTGGCTTCTTCTCCGCG 59.210 57.895 0.00 0.00 0.00 6.46
3614 3739 1.577578 GAAAATTCGCCGTCAATTCGC 59.422 47.619 0.00 0.00 0.00 4.70
3627 3752 0.794605 GCAGCTCGCCACGAAAATTC 60.795 55.000 0.00 0.00 34.74 2.17
3630 3755 2.280797 AGCAGCTCGCCACGAAAA 60.281 55.556 0.00 0.00 44.04 2.29
3696 3822 1.194772 GCTGTGGAGTTGTTAACGAGC 59.805 52.381 0.26 0.00 36.23 5.03
3758 3884 1.911269 ATTTTGCCCCGGTTCACCC 60.911 57.895 0.00 0.00 0.00 4.61
3872 4007 7.010091 CCAATGAAACAACCAAAGAGTAAACAC 59.990 37.037 0.00 0.00 0.00 3.32
3874 4009 6.478673 CCCAATGAAACAACCAAAGAGTAAAC 59.521 38.462 0.00 0.00 0.00 2.01
3929 4091 7.948278 ATCCTCGGAAAGAAAAATCTATACG 57.052 36.000 0.00 0.00 0.00 3.06
4005 4170 8.658609 CAGAAGCATGAACAAAAAGAAAAGAAA 58.341 29.630 0.00 0.00 0.00 2.52
4006 4171 7.818930 ACAGAAGCATGAACAAAAAGAAAAGAA 59.181 29.630 0.00 0.00 0.00 2.52
4007 4172 7.322664 ACAGAAGCATGAACAAAAAGAAAAGA 58.677 30.769 0.00 0.00 0.00 2.52
4008 4173 7.529880 ACAGAAGCATGAACAAAAAGAAAAG 57.470 32.000 0.00 0.00 0.00 2.27
4026 4191 7.538678 ACGAGCAATTATTAAGCAAAACAGAAG 59.461 33.333 0.00 0.00 0.00 2.85
4036 4201 2.544267 AGCGGACGAGCAATTATTAAGC 59.456 45.455 0.00 0.00 40.15 3.09
4040 4205 0.657840 GCAGCGGACGAGCAATTATT 59.342 50.000 0.00 0.00 40.15 1.40
4041 4206 0.461870 TGCAGCGGACGAGCAATTAT 60.462 50.000 9.25 0.00 40.15 1.28
4056 4227 5.178061 TGCAATATCTATATCCCGTTGCAG 58.822 41.667 5.84 0.00 43.58 4.41
4097 4268 4.306471 TGCCGCGTGCGAAACTTG 62.306 61.111 16.91 0.00 45.60 3.16
4117 4288 1.303317 ACATGTTCCCAACTCCCGC 60.303 57.895 0.00 0.00 0.00 6.13
4120 4291 2.859165 TCAGACATGTTCCCAACTCC 57.141 50.000 0.00 0.00 0.00 3.85
4165 4338 6.687105 GGATGTACTCAATTGTTTCGCATTAC 59.313 38.462 5.13 0.00 0.00 1.89
4232 4405 7.921041 AAGGGATTTCTTCTTCTTTCCTTTT 57.079 32.000 0.00 0.00 0.00 2.27
4344 4517 1.424638 TAGCTACTCCCCTTGCATCC 58.575 55.000 0.00 0.00 0.00 3.51
4401 4574 3.006003 TCAAAACACGAAATTTAGCCCCC 59.994 43.478 0.00 0.00 0.00 5.40
4402 4575 3.985279 GTCAAAACACGAAATTTAGCCCC 59.015 43.478 0.00 0.00 0.00 5.80
4403 4576 3.985279 GGTCAAAACACGAAATTTAGCCC 59.015 43.478 0.00 0.00 0.00 5.19
4404 4577 3.985279 GGGTCAAAACACGAAATTTAGCC 59.015 43.478 0.00 0.00 0.00 3.93
4405 4578 4.866921 AGGGTCAAAACACGAAATTTAGC 58.133 39.130 0.00 0.00 32.44 3.09
4406 4579 7.704899 AGAAAAGGGTCAAAACACGAAATTTAG 59.295 33.333 0.00 0.00 32.44 1.85
4407 4580 7.489757 CAGAAAAGGGTCAAAACACGAAATTTA 59.510 33.333 0.00 0.00 32.44 1.40
4408 4581 6.312672 CAGAAAAGGGTCAAAACACGAAATTT 59.687 34.615 0.00 0.00 32.44 1.82
4409 4582 5.810074 CAGAAAAGGGTCAAAACACGAAATT 59.190 36.000 0.00 0.00 32.44 1.82
4410 4583 5.126384 TCAGAAAAGGGTCAAAACACGAAAT 59.874 36.000 0.00 0.00 32.44 2.17
4411 4584 4.459685 TCAGAAAAGGGTCAAAACACGAAA 59.540 37.500 0.00 0.00 32.44 3.46
4412 4585 4.011023 TCAGAAAAGGGTCAAAACACGAA 58.989 39.130 0.00 0.00 32.44 3.85
4413 4586 3.611970 TCAGAAAAGGGTCAAAACACGA 58.388 40.909 0.00 0.00 32.44 4.35
4414 4587 4.364415 TTCAGAAAAGGGTCAAAACACG 57.636 40.909 0.00 0.00 32.44 4.49
4415 4588 5.720202 AGTTTCAGAAAAGGGTCAAAACAC 58.280 37.500 0.00 0.00 32.28 3.32
4416 4589 5.993748 AGTTTCAGAAAAGGGTCAAAACA 57.006 34.783 0.00 0.00 32.28 2.83
4417 4590 8.942338 AATAAGTTTCAGAAAAGGGTCAAAAC 57.058 30.769 0.00 0.00 0.00 2.43
4418 4591 9.952030 AAAATAAGTTTCAGAAAAGGGTCAAAA 57.048 25.926 0.00 0.00 0.00 2.44
4419 4592 9.377312 CAAAATAAGTTTCAGAAAAGGGTCAAA 57.623 29.630 0.00 0.00 0.00 2.69
4420 4593 8.754080 TCAAAATAAGTTTCAGAAAAGGGTCAA 58.246 29.630 0.00 0.00 0.00 3.18
4421 4594 8.299990 TCAAAATAAGTTTCAGAAAAGGGTCA 57.700 30.769 0.00 0.00 0.00 4.02
4422 4595 8.630037 TCTCAAAATAAGTTTCAGAAAAGGGTC 58.370 33.333 0.00 0.00 0.00 4.46
4423 4596 8.533569 TCTCAAAATAAGTTTCAGAAAAGGGT 57.466 30.769 0.00 0.00 0.00 4.34
4424 4597 9.987272 AATCTCAAAATAAGTTTCAGAAAAGGG 57.013 29.630 0.00 0.00 0.00 3.95
4468 4641 8.450964 CCGATAGCAAAAGAGTCAGATTAAAAA 58.549 33.333 0.00 0.00 0.00 1.94
4469 4642 7.414098 GCCGATAGCAAAAGAGTCAGATTAAAA 60.414 37.037 0.00 0.00 42.97 1.52
4470 4643 6.037172 GCCGATAGCAAAAGAGTCAGATTAAA 59.963 38.462 0.00 0.00 42.97 1.52
4471 4644 5.523916 GCCGATAGCAAAAGAGTCAGATTAA 59.476 40.000 0.00 0.00 42.97 1.40
4472 4645 5.050490 GCCGATAGCAAAAGAGTCAGATTA 58.950 41.667 0.00 0.00 42.97 1.75
4473 4646 3.873952 GCCGATAGCAAAAGAGTCAGATT 59.126 43.478 0.00 0.00 42.97 2.40
4474 4647 3.462021 GCCGATAGCAAAAGAGTCAGAT 58.538 45.455 0.00 0.00 42.97 2.90
4475 4648 2.893637 GCCGATAGCAAAAGAGTCAGA 58.106 47.619 0.00 0.00 42.97 3.27
4487 4660 0.247736 CTATGGTCCCTGCCGATAGC 59.752 60.000 0.00 0.00 44.14 2.97
4488 4661 0.247736 GCTATGGTCCCTGCCGATAG 59.752 60.000 0.00 0.00 0.00 2.08
4489 4662 1.532604 CGCTATGGTCCCTGCCGATA 61.533 60.000 0.00 0.00 0.00 2.92
4490 4663 2.872388 CGCTATGGTCCCTGCCGAT 61.872 63.158 0.00 0.00 0.00 4.18
4491 4664 3.536917 CGCTATGGTCCCTGCCGA 61.537 66.667 0.00 0.00 0.00 5.54
4492 4665 4.609018 CCGCTATGGTCCCTGCCG 62.609 72.222 0.00 0.00 0.00 5.69
4501 4674 1.695242 TGTTATACCCCACCGCTATGG 59.305 52.381 0.00 0.00 46.41 2.74
4502 4675 2.870435 GCTGTTATACCCCACCGCTATG 60.870 54.545 0.00 0.00 0.00 2.23
4503 4676 1.346722 GCTGTTATACCCCACCGCTAT 59.653 52.381 0.00 0.00 0.00 2.97
4504 4677 0.754472 GCTGTTATACCCCACCGCTA 59.246 55.000 0.00 0.00 0.00 4.26
4505 4678 1.525442 GCTGTTATACCCCACCGCT 59.475 57.895 0.00 0.00 0.00 5.52
4506 4679 1.525306 GGCTGTTATACCCCACCGC 60.525 63.158 0.00 0.00 0.00 5.68
4507 4680 1.069668 GTAGGCTGTTATACCCCACCG 59.930 57.143 0.00 0.00 0.00 4.94
4508 4681 1.419012 GGTAGGCTGTTATACCCCACC 59.581 57.143 0.00 0.00 36.26 4.61
4509 4682 1.069668 CGGTAGGCTGTTATACCCCAC 59.930 57.143 0.00 0.00 38.60 4.61
4510 4683 1.416243 CGGTAGGCTGTTATACCCCA 58.584 55.000 0.00 0.00 38.60 4.96
4511 4684 0.034476 GCGGTAGGCTGTTATACCCC 59.966 60.000 0.00 0.00 38.60 4.95
4512 4685 0.034476 GGCGGTAGGCTGTTATACCC 59.966 60.000 0.00 0.00 42.94 3.69
4513 4686 0.754472 TGGCGGTAGGCTGTTATACC 59.246 55.000 0.00 0.00 44.18 2.73
4514 4687 2.480845 CTTGGCGGTAGGCTGTTATAC 58.519 52.381 0.00 0.00 44.18 1.47
4515 4688 1.414919 CCTTGGCGGTAGGCTGTTATA 59.585 52.381 0.00 0.00 44.18 0.98
4516 4689 0.180406 CCTTGGCGGTAGGCTGTTAT 59.820 55.000 0.00 0.00 44.18 1.89
4517 4690 1.196104 ACCTTGGCGGTAGGCTGTTA 61.196 55.000 0.00 0.00 46.73 2.41
4518 4691 2.351276 CCTTGGCGGTAGGCTGTT 59.649 61.111 0.00 0.00 44.18 3.16
4519 4692 2.928396 ACCTTGGCGGTAGGCTGT 60.928 61.111 0.00 0.00 46.73 4.40
4529 4702 0.391263 CTACCGTCAAGGACCTTGGC 60.391 60.000 29.76 27.99 45.00 4.52
4530 4703 0.249398 CCTACCGTCAAGGACCTTGG 59.751 60.000 29.76 18.75 45.00 3.61
4531 4704 0.249398 CCCTACCGTCAAGGACCTTG 59.751 60.000 25.87 25.87 45.00 3.61
4532 4705 0.178912 ACCCTACCGTCAAGGACCTT 60.179 55.000 0.00 0.00 45.00 3.50
4533 4706 0.178912 AACCCTACCGTCAAGGACCT 60.179 55.000 0.00 0.00 45.00 3.85
4534 4707 1.205655 GTAACCCTACCGTCAAGGACC 59.794 57.143 0.00 0.00 45.00 4.46
4535 4708 1.895131 TGTAACCCTACCGTCAAGGAC 59.105 52.381 0.00 0.00 45.00 3.85
4536 4709 2.307496 TGTAACCCTACCGTCAAGGA 57.693 50.000 0.00 0.00 45.00 3.36
4538 4711 2.277084 GCATGTAACCCTACCGTCAAG 58.723 52.381 0.00 0.00 0.00 3.02
4539 4712 1.065998 GGCATGTAACCCTACCGTCAA 60.066 52.381 0.00 0.00 0.00 3.18
4540 4713 0.538118 GGCATGTAACCCTACCGTCA 59.462 55.000 0.00 0.00 0.00 4.35
4541 4714 0.179065 GGGCATGTAACCCTACCGTC 60.179 60.000 0.00 0.00 44.68 4.79
4542 4715 1.909975 GGGCATGTAACCCTACCGT 59.090 57.895 0.00 0.00 44.68 4.83
4543 4716 4.870190 GGGCATGTAACCCTACCG 57.130 61.111 0.00 0.00 44.68 4.02
4549 4722 2.985957 TTACGGTAGGGCATGTAACC 57.014 50.000 0.00 0.00 0.00 2.85
4570 4743 8.129211 GCACTGTGTTCAATACTTAGAAGTTTT 58.871 33.333 9.86 0.00 40.37 2.43
4571 4744 7.518370 CGCACTGTGTTCAATACTTAGAAGTTT 60.518 37.037 9.86 0.00 40.37 2.66
4572 4745 6.073765 CGCACTGTGTTCAATACTTAGAAGTT 60.074 38.462 9.86 0.00 40.37 2.66
4573 4746 5.405571 CGCACTGTGTTCAATACTTAGAAGT 59.594 40.000 9.86 0.00 42.91 3.01
4574 4747 5.405571 ACGCACTGTGTTCAATACTTAGAAG 59.594 40.000 9.86 0.00 0.00 2.85
4575 4748 5.176774 CACGCACTGTGTTCAATACTTAGAA 59.823 40.000 9.86 0.00 43.88 2.10
4576 4749 4.684242 CACGCACTGTGTTCAATACTTAGA 59.316 41.667 9.86 0.00 43.88 2.10
4577 4750 4.946255 CACGCACTGTGTTCAATACTTAG 58.054 43.478 9.86 0.00 43.88 2.18
4578 4751 4.983215 CACGCACTGTGTTCAATACTTA 57.017 40.909 9.86 0.00 43.88 2.24
4579 4752 3.878086 CACGCACTGTGTTCAATACTT 57.122 42.857 9.86 0.00 43.88 2.24
4591 4764 3.914605 TAGGCACGAGCACGCACTG 62.915 63.158 7.26 0.00 44.61 3.66
4592 4765 3.680786 TAGGCACGAGCACGCACT 61.681 61.111 7.26 1.98 44.61 4.40
4593 4766 3.479269 GTAGGCACGAGCACGCAC 61.479 66.667 7.26 0.00 44.61 5.34
4594 4767 4.735132 GGTAGGCACGAGCACGCA 62.735 66.667 7.26 0.00 44.61 5.24
4605 4778 3.920093 AAGGTGCTTGGCGGTAGGC 62.920 63.158 0.00 0.00 44.11 3.93
4606 4779 2.040544 CAAGGTGCTTGGCGGTAGG 61.041 63.158 0.00 0.00 37.77 3.18
4607 4780 3.578456 CAAGGTGCTTGGCGGTAG 58.422 61.111 0.00 0.00 37.77 3.18
4621 4794 2.332654 GCACAACCCTACCGCCAAG 61.333 63.158 0.00 0.00 0.00 3.61
4622 4795 2.281900 GCACAACCCTACCGCCAA 60.282 61.111 0.00 0.00 0.00 4.52
4623 4796 3.545124 CTGCACAACCCTACCGCCA 62.545 63.158 0.00 0.00 0.00 5.69
4624 4797 2.746277 CTGCACAACCCTACCGCC 60.746 66.667 0.00 0.00 0.00 6.13
4625 4798 2.746277 CCTGCACAACCCTACCGC 60.746 66.667 0.00 0.00 0.00 5.68
4626 4799 1.895020 TAGCCTGCACAACCCTACCG 61.895 60.000 0.00 0.00 0.00 4.02
4627 4800 0.392595 GTAGCCTGCACAACCCTACC 60.393 60.000 0.00 0.00 0.00 3.18
4628 4801 0.392595 GGTAGCCTGCACAACCCTAC 60.393 60.000 0.00 0.00 0.00 3.18
4629 4802 1.895020 CGGTAGCCTGCACAACCCTA 61.895 60.000 0.00 0.00 0.00 3.53
4630 4803 2.757077 GGTAGCCTGCACAACCCT 59.243 61.111 0.00 0.00 0.00 4.34
4631 4804 2.746277 CGGTAGCCTGCACAACCC 60.746 66.667 0.00 0.00 0.00 4.11
4632 4805 3.431725 GCGGTAGCCTGCACAACC 61.432 66.667 0.00 0.00 37.42 3.77


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

AutoCloner maintained by Alex Coulton.