Multiple sequence alignment - TraesCS5D01G273300

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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 TraesCS5D01G273300 chr5D 100.000 4495 0 0 1 4495 376177403 376181897 0.000000e+00 8301
1 TraesCS5D01G273300 chr5D 75.097 2325 530 36 1053 3357 278137562 278139857 0.000000e+00 1040
2 TraesCS5D01G273300 chr5D 97.443 352 7 1 4146 4495 496196483 496196834 2.310000e-167 599
3 TraesCS5D01G273300 chr5B 96.650 3701 91 13 1 3684 449128892 449132576 0.000000e+00 6117
4 TraesCS5D01G273300 chr5B 75.651 2304 512 34 1053 3336 316152143 316154417 0.000000e+00 1101
5 TraesCS5D01G273300 chr5B 88.110 471 46 7 3683 4145 449132793 449133261 6.570000e-153 551
6 TraesCS5D01G273300 chr5B 90.991 111 10 0 1560 1670 37449588 37449478 2.800000e-32 150
7 TraesCS5D01G273300 chr5B 89.565 115 12 0 1738 1852 37449478 37449364 3.620000e-31 147
8 TraesCS5D01G273300 chr5A 97.628 2993 62 7 692 3683 477221791 477224775 0.000000e+00 5125
9 TraesCS5D01G273300 chr5A 75.097 2325 530 35 1053 3357 367269835 367272130 0.000000e+00 1040
10 TraesCS5D01G273300 chr5A 92.553 470 27 7 3683 4145 477224977 477225445 0.000000e+00 667
11 TraesCS5D01G273300 chr5A 88.571 455 35 7 246 692 477221401 477221846 1.840000e-148 536
12 TraesCS5D01G273300 chr5A 89.328 253 14 2 1 240 477221071 477221323 5.650000e-79 305
13 TraesCS5D01G273300 chr1D 97.734 353 7 1 4144 4495 463059256 463059608 1.380000e-169 606
14 TraesCS5D01G273300 chr6D 97.727 352 6 1 4146 4495 49841289 49840938 4.970000e-169 604
15 TraesCS5D01G273300 chr3D 97.727 352 5 2 4146 4495 305633653 305634003 1.790000e-168 603
16 TraesCS5D01G273300 chr3D 97.143 350 10 0 4146 4495 53408553 53408902 3.870000e-165 592
17 TraesCS5D01G273300 chr7D 97.436 351 8 1 4146 4495 4651656 4651306 8.320000e-167 597
18 TraesCS5D01G273300 chr7D 97.143 350 10 0 4146 4495 638389958 638390307 3.870000e-165 592
19 TraesCS5D01G273300 chr2D 97.159 352 8 1 4146 4495 81324170 81323819 1.080000e-165 593
20 TraesCS5D01G273300 chr4D 97.143 350 10 0 4146 4495 95828768 95828419 3.870000e-165 592
21 TraesCS5D01G273300 chr1B 91.743 109 9 0 1738 1846 633293451 633293559 7.790000e-33 152
22 TraesCS5D01G273300 chr1B 94.521 73 4 0 1557 1629 633291771 633291843 3.680000e-21 113


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 TraesCS5D01G273300 chr5D 376177403 376181897 4494 False 8301.00 8301 100.000 1 4495 1 chr5D.!!$F2 4494
1 TraesCS5D01G273300 chr5D 278137562 278139857 2295 False 1040.00 1040 75.097 1053 3357 1 chr5D.!!$F1 2304
2 TraesCS5D01G273300 chr5B 449128892 449133261 4369 False 3334.00 6117 92.380 1 4145 2 chr5B.!!$F2 4144
3 TraesCS5D01G273300 chr5B 316152143 316154417 2274 False 1101.00 1101 75.651 1053 3336 1 chr5B.!!$F1 2283
4 TraesCS5D01G273300 chr5A 477221071 477225445 4374 False 1658.25 5125 92.020 1 4145 4 chr5A.!!$F2 4144
5 TraesCS5D01G273300 chr5A 367269835 367272130 2295 False 1040.00 1040 75.097 1053 3357 1 chr5A.!!$F1 2304

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
81 82 0.033405 TCCGTCCTTTCCGAGATCCT 60.033 55.0 0.0 0.0 0.00 3.24 F
84 85 0.753867 GTCCTTTCCGAGATCCTCCC 59.246 60.0 0.0 0.0 0.00 4.30 F
1978 2092 0.754217 AGCATGTGATGGTGGATGGC 60.754 55.0 0.0 0.0 39.92 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 2092 0.967887 TGGTCTCCTTCCTCTGCTCG 60.968 60.000 0.00 0.00 0.00 5.03 R
2743 2860 3.623060 CACCCATGATACGGAAGAAGTTG 59.377 47.826 0.00 0.00 0.00 3.16 R
4238 4594 0.032615 ATCTCCAGGAGAGGCGTCTT 60.033 55.000 23.96 2.93 42.26 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 0.033405 TCCGTCCTTTCCGAGATCCT 60.033 55.000 0.00 0.00 0.00 3.24
84 85 0.753867 GTCCTTTCCGAGATCCTCCC 59.246 60.000 0.00 0.00 0.00 4.30
110 112 0.807667 GATCGCGTGCTGGAATCTGT 60.808 55.000 5.77 0.00 0.00 3.41
264 289 3.307480 GGAGCTGCTAGGGTTTTACAAGA 60.307 47.826 0.15 0.00 0.00 3.02
394 480 3.131396 CAGCGATTAGTTAAATCCCGCT 58.869 45.455 11.39 11.39 46.30 5.52
448 546 5.470845 AGTTCATATGCGCTGTTTTAGTC 57.529 39.130 9.73 0.00 0.00 2.59
529 627 4.272991 GCTAGCTGTTCTTCATGATCCAAG 59.727 45.833 7.70 0.00 0.00 3.61
624 724 5.482908 ACTGTTGTCCTGCTTGATAAGTAG 58.517 41.667 0.44 0.44 40.44 2.57
625 725 5.012148 ACTGTTGTCCTGCTTGATAAGTAGT 59.988 40.000 6.05 0.00 39.29 2.73
659 759 6.535508 GGATTTATGTTGTAGTGTCCTCAGTC 59.464 42.308 0.00 0.00 0.00 3.51
742 842 3.060473 GCTATACTTGTCGCGGATGTTTC 60.060 47.826 6.13 0.00 0.00 2.78
761 864 6.506147 TGTTTCTTTCAAGATTGGTGATGTG 58.494 36.000 0.00 0.00 34.49 3.21
762 865 6.320926 TGTTTCTTTCAAGATTGGTGATGTGA 59.679 34.615 0.00 0.00 34.49 3.58
763 866 7.014518 TGTTTCTTTCAAGATTGGTGATGTGAT 59.985 33.333 0.00 0.00 34.49 3.06
764 867 6.505044 TCTTTCAAGATTGGTGATGTGATG 57.495 37.500 0.00 0.00 0.00 3.07
765 868 6.005823 TCTTTCAAGATTGGTGATGTGATGT 58.994 36.000 0.00 0.00 0.00 3.06
766 869 7.167535 TCTTTCAAGATTGGTGATGTGATGTA 58.832 34.615 0.00 0.00 0.00 2.29
767 870 6.990341 TTCAAGATTGGTGATGTGATGTAG 57.010 37.500 0.00 0.00 0.00 2.74
768 871 6.298441 TCAAGATTGGTGATGTGATGTAGA 57.702 37.500 0.00 0.00 0.00 2.59
769 872 6.892485 TCAAGATTGGTGATGTGATGTAGAT 58.108 36.000 0.00 0.00 0.00 1.98
770 873 6.764560 TCAAGATTGGTGATGTGATGTAGATG 59.235 38.462 0.00 0.00 0.00 2.90
798 901 2.621998 CCACATGGCAGATGGAGAATTC 59.378 50.000 13.27 0.00 35.33 2.17
918 1021 6.472686 TTGCCTACAACAACCATTTAAAGT 57.527 33.333 0.00 0.00 0.00 2.66
932 1035 7.088272 ACCATTTAAAGTCCGTGCTTATTTTC 58.912 34.615 0.00 0.00 0.00 2.29
1978 2092 0.754217 AGCATGTGATGGTGGATGGC 60.754 55.000 0.00 0.00 39.92 4.40
2743 2860 0.455005 GCATGAGAAAGAGCAAGGCC 59.545 55.000 0.00 0.00 0.00 5.19
2812 2929 3.383620 AGATGGTTCGATCAGATCTGC 57.616 47.619 18.36 4.04 0.00 4.26
2866 2983 6.611236 TGATCCATGTCCTCTTTGTGATACTA 59.389 38.462 0.00 0.00 0.00 1.82
3049 3166 0.396695 TCCCTACATCTCGTCCACCC 60.397 60.000 0.00 0.00 0.00 4.61
3058 3175 2.506217 CGTCCACCCGACATCGTG 60.506 66.667 0.00 0.00 42.07 4.35
3208 3325 0.391661 TGACCTTCTGCTTCATCGCC 60.392 55.000 0.00 0.00 0.00 5.54
3388 3508 2.656085 GTCTCTTATCGCTCCGTGATG 58.344 52.381 0.49 0.00 34.45 3.07
3401 3521 4.838152 TGATGCGGCGCCTTCCTC 62.838 66.667 30.82 17.70 0.00 3.71
3523 3643 4.097286 TGTTTGTAGTCTTTTCAGTTGCCC 59.903 41.667 0.00 0.00 0.00 5.36
3525 3645 1.197036 GTAGTCTTTTCAGTTGCCCGC 59.803 52.381 0.00 0.00 0.00 6.13
3539 3659 1.890041 CCCGCGTGTCTGTTTTGGA 60.890 57.895 4.92 0.00 0.00 3.53
3542 3662 0.375454 CGCGTGTCTGTTTTGGAACA 59.625 50.000 0.00 0.00 43.23 3.18
3587 3707 1.462283 CTGAAACGCCTGATGTGTGAG 59.538 52.381 0.00 0.00 37.86 3.51
3737 4079 1.939934 CGTCAGTTGCTTCAGTTGGAA 59.060 47.619 0.00 0.00 0.00 3.53
3763 4105 2.972713 TGCCAGTATTGGGATCCTACTC 59.027 50.000 12.58 2.07 45.16 2.59
3775 4119 4.767409 GGGATCCTACTCTTTTTGCACTTT 59.233 41.667 12.58 0.00 0.00 2.66
3811 4156 2.289072 CCTTCACTCGCCCGAATATGAT 60.289 50.000 0.00 0.00 0.00 2.45
3855 4200 5.602145 TCCCAAATTTGAATGTCAACTCCTT 59.398 36.000 19.86 0.00 35.89 3.36
3908 4254 4.618489 CGCTTGTCCATGAATTTCTGTTTC 59.382 41.667 0.00 0.00 0.00 2.78
3934 4282 7.420184 TGATCGATATACATGCGTTCAAAAT 57.580 32.000 0.00 0.00 32.75 1.82
3955 4303 9.132521 CAAAATTCAACTTCTTAGGCTGTAATG 57.867 33.333 0.00 0.00 0.00 1.90
4063 4411 5.607939 AGGTATGTGTGTCGGAAATATCA 57.392 39.130 0.00 0.00 0.00 2.15
4100 4451 6.377327 TGCTTACAGTTTTCCTCTCAAAAG 57.623 37.500 0.00 0.00 0.00 2.27
4156 4512 7.939784 TCATGCTAGTTAGTGTTAGAAGAGA 57.060 36.000 0.00 0.00 0.00 3.10
4157 4513 7.990917 TCATGCTAGTTAGTGTTAGAAGAGAG 58.009 38.462 0.00 0.00 0.00 3.20
4158 4514 7.829706 TCATGCTAGTTAGTGTTAGAAGAGAGA 59.170 37.037 0.00 0.00 0.00 3.10
4159 4515 7.618502 TGCTAGTTAGTGTTAGAAGAGAGAG 57.381 40.000 0.00 0.00 0.00 3.20
4160 4516 7.395617 TGCTAGTTAGTGTTAGAAGAGAGAGA 58.604 38.462 0.00 0.00 0.00 3.10
4161 4517 7.551262 TGCTAGTTAGTGTTAGAAGAGAGAGAG 59.449 40.741 0.00 0.00 0.00 3.20
4162 4518 7.767198 GCTAGTTAGTGTTAGAAGAGAGAGAGA 59.233 40.741 0.00 0.00 0.00 3.10
4163 4519 9.314321 CTAGTTAGTGTTAGAAGAGAGAGAGAG 57.686 40.741 0.00 0.00 0.00 3.20
4164 4520 7.913789 AGTTAGTGTTAGAAGAGAGAGAGAGA 58.086 38.462 0.00 0.00 0.00 3.10
4165 4521 8.548877 AGTTAGTGTTAGAAGAGAGAGAGAGAT 58.451 37.037 0.00 0.00 0.00 2.75
4166 4522 9.174166 GTTAGTGTTAGAAGAGAGAGAGAGATT 57.826 37.037 0.00 0.00 0.00 2.40
4167 4523 7.630242 AGTGTTAGAAGAGAGAGAGAGATTG 57.370 40.000 0.00 0.00 0.00 2.67
4168 4524 7.175104 AGTGTTAGAAGAGAGAGAGAGATTGT 58.825 38.462 0.00 0.00 0.00 2.71
4169 4525 7.669722 AGTGTTAGAAGAGAGAGAGAGATTGTT 59.330 37.037 0.00 0.00 0.00 2.83
4170 4526 7.754924 GTGTTAGAAGAGAGAGAGAGATTGTTG 59.245 40.741 0.00 0.00 0.00 3.33
4171 4527 5.329035 AGAAGAGAGAGAGAGATTGTTGC 57.671 43.478 0.00 0.00 0.00 4.17
4172 4528 3.781079 AGAGAGAGAGAGATTGTTGCG 57.219 47.619 0.00 0.00 0.00 4.85
4173 4529 2.426738 AGAGAGAGAGAGATTGTTGCGG 59.573 50.000 0.00 0.00 0.00 5.69
4174 4530 2.425312 GAGAGAGAGAGATTGTTGCGGA 59.575 50.000 0.00 0.00 0.00 5.54
4175 4531 2.828520 AGAGAGAGAGATTGTTGCGGAA 59.171 45.455 0.00 0.00 0.00 4.30
4176 4532 3.450457 AGAGAGAGAGATTGTTGCGGAAT 59.550 43.478 0.00 0.00 0.00 3.01
4177 4533 4.646945 AGAGAGAGAGATTGTTGCGGAATA 59.353 41.667 0.00 0.00 0.00 1.75
4178 4534 5.304101 AGAGAGAGAGATTGTTGCGGAATAT 59.696 40.000 0.00 0.00 0.00 1.28
4179 4535 5.295950 AGAGAGAGATTGTTGCGGAATATG 58.704 41.667 0.00 0.00 0.00 1.78
4180 4536 5.069648 AGAGAGAGATTGTTGCGGAATATGA 59.930 40.000 0.00 0.00 0.00 2.15
4181 4537 5.862845 AGAGAGATTGTTGCGGAATATGAT 58.137 37.500 0.00 0.00 0.00 2.45
4182 4538 5.699915 AGAGAGATTGTTGCGGAATATGATG 59.300 40.000 0.00 0.00 0.00 3.07
4183 4539 4.758674 AGAGATTGTTGCGGAATATGATGG 59.241 41.667 0.00 0.00 0.00 3.51
4184 4540 4.717877 AGATTGTTGCGGAATATGATGGA 58.282 39.130 0.00 0.00 0.00 3.41
4185 4541 5.319453 AGATTGTTGCGGAATATGATGGAT 58.681 37.500 0.00 0.00 0.00 3.41
4186 4542 4.834357 TTGTTGCGGAATATGATGGATG 57.166 40.909 0.00 0.00 0.00 3.51
4187 4543 3.819368 TGTTGCGGAATATGATGGATGT 58.181 40.909 0.00 0.00 0.00 3.06
4188 4544 4.967036 TGTTGCGGAATATGATGGATGTA 58.033 39.130 0.00 0.00 0.00 2.29
4189 4545 5.559770 TGTTGCGGAATATGATGGATGTAT 58.440 37.500 0.00 0.00 0.00 2.29
4190 4546 6.003326 TGTTGCGGAATATGATGGATGTATT 58.997 36.000 0.00 0.00 0.00 1.89
4191 4547 7.164803 TGTTGCGGAATATGATGGATGTATTA 58.835 34.615 0.00 0.00 0.00 0.98
4192 4548 7.828717 TGTTGCGGAATATGATGGATGTATTAT 59.171 33.333 0.00 0.00 0.00 1.28
4193 4549 8.677300 GTTGCGGAATATGATGGATGTATTATT 58.323 33.333 0.00 0.00 0.00 1.40
4194 4550 8.212317 TGCGGAATATGATGGATGTATTATTG 57.788 34.615 0.00 0.00 0.00 1.90
4195 4551 8.046107 TGCGGAATATGATGGATGTATTATTGA 58.954 33.333 0.00 0.00 0.00 2.57
4196 4552 8.554528 GCGGAATATGATGGATGTATTATTGAG 58.445 37.037 0.00 0.00 0.00 3.02
4197 4553 8.554528 CGGAATATGATGGATGTATTATTGAGC 58.445 37.037 0.00 0.00 0.00 4.26
4198 4554 8.844244 GGAATATGATGGATGTATTATTGAGCC 58.156 37.037 0.00 0.00 0.00 4.70
4199 4555 9.624373 GAATATGATGGATGTATTATTGAGCCT 57.376 33.333 0.00 0.00 0.00 4.58
4200 4556 9.624373 AATATGATGGATGTATTATTGAGCCTC 57.376 33.333 0.00 0.00 0.00 4.70
4201 4557 5.482006 TGATGGATGTATTATTGAGCCTCG 58.518 41.667 0.00 0.00 0.00 4.63
4202 4558 5.245977 TGATGGATGTATTATTGAGCCTCGA 59.754 40.000 0.00 0.00 0.00 4.04
4203 4559 5.139435 TGGATGTATTATTGAGCCTCGAG 57.861 43.478 5.13 5.13 0.00 4.04
4204 4560 4.021104 TGGATGTATTATTGAGCCTCGAGG 60.021 45.833 27.83 27.83 38.53 4.63
4205 4561 4.499183 GATGTATTATTGAGCCTCGAGGG 58.501 47.826 32.06 14.53 35.18 4.30
4221 4577 4.586884 TCGAGGGCGAGTATATATTGAGT 58.413 43.478 0.00 0.00 42.51 3.41
4222 4578 5.737860 TCGAGGGCGAGTATATATTGAGTA 58.262 41.667 0.00 0.00 42.51 2.59
4223 4579 5.583854 TCGAGGGCGAGTATATATTGAGTAC 59.416 44.000 0.00 0.00 42.51 2.73
4224 4580 5.353400 CGAGGGCGAGTATATATTGAGTACA 59.647 44.000 0.00 0.00 40.82 2.90
4225 4581 6.128090 CGAGGGCGAGTATATATTGAGTACAA 60.128 42.308 0.00 0.00 40.82 2.41
4226 4582 7.159322 AGGGCGAGTATATATTGAGTACAAG 57.841 40.000 0.00 0.00 39.46 3.16
4227 4583 6.946583 AGGGCGAGTATATATTGAGTACAAGA 59.053 38.462 0.00 0.00 39.46 3.02
4228 4584 7.028361 GGGCGAGTATATATTGAGTACAAGAC 58.972 42.308 0.00 0.00 39.46 3.01
4229 4585 7.094291 GGGCGAGTATATATTGAGTACAAGACT 60.094 40.741 0.00 0.00 42.90 3.24
4230 4586 8.298140 GGCGAGTATATATTGAGTACAAGACTT 58.702 37.037 0.00 0.00 39.06 3.01
4231 4587 9.119329 GCGAGTATATATTGAGTACAAGACTTG 57.881 37.037 13.77 13.77 39.06 3.16
4237 4593 3.402628 TGAGTACAAGACTTGAAGGGC 57.597 47.619 21.95 7.38 39.06 5.19
4238 4594 2.703536 TGAGTACAAGACTTGAAGGGCA 59.296 45.455 21.95 9.66 39.06 5.36
4239 4595 3.135712 TGAGTACAAGACTTGAAGGGCAA 59.864 43.478 21.95 0.00 39.06 4.52
4241 4597 9.536554 ATTGAGTACAAGACTTGAAGGGCAAGA 62.537 40.741 21.95 0.25 46.11 3.02
4253 4609 2.125350 GCAAGACGCCTCTCCTGG 60.125 66.667 0.00 0.00 32.94 4.45
4254 4610 2.650116 GCAAGACGCCTCTCCTGGA 61.650 63.158 0.00 0.00 32.94 3.86
4255 4611 1.515020 CAAGACGCCTCTCCTGGAG 59.485 63.158 17.84 17.84 41.51 3.86
4256 4612 0.967887 CAAGACGCCTCTCCTGGAGA 60.968 60.000 24.27 24.27 44.45 3.71
4257 4613 0.032615 AAGACGCCTCTCCTGGAGAT 60.033 55.000 25.82 11.94 44.45 2.75
4258 4614 0.847373 AGACGCCTCTCCTGGAGATA 59.153 55.000 25.82 5.90 44.45 1.98
4259 4615 1.215673 AGACGCCTCTCCTGGAGATAA 59.784 52.381 25.82 5.14 44.45 1.75
4260 4616 1.611491 GACGCCTCTCCTGGAGATAAG 59.389 57.143 25.82 20.06 44.45 1.73
4261 4617 0.965439 CGCCTCTCCTGGAGATAAGG 59.035 60.000 25.82 22.92 44.45 2.69
4262 4618 1.755977 CGCCTCTCCTGGAGATAAGGT 60.756 57.143 25.82 0.00 44.45 3.50
4263 4619 2.489255 CGCCTCTCCTGGAGATAAGGTA 60.489 54.545 25.82 2.89 44.45 3.08
4264 4620 3.161866 GCCTCTCCTGGAGATAAGGTAG 58.838 54.545 25.82 12.58 44.45 3.18
4265 4621 3.773560 CCTCTCCTGGAGATAAGGTAGG 58.226 54.545 25.82 17.38 44.45 3.18
4266 4622 3.399644 CCTCTCCTGGAGATAAGGTAGGA 59.600 52.174 25.82 0.96 44.45 2.94
4269 4625 4.456662 TCCTGGAGATAAGGTAGGAGAC 57.543 50.000 0.00 0.00 36.14 3.36
4270 4626 3.150767 CCTGGAGATAAGGTAGGAGACG 58.849 54.545 0.00 0.00 0.00 4.18
4271 4627 3.150767 CTGGAGATAAGGTAGGAGACGG 58.849 54.545 0.00 0.00 0.00 4.79
4272 4628 2.781757 TGGAGATAAGGTAGGAGACGGA 59.218 50.000 0.00 0.00 0.00 4.69
4273 4629 3.398292 TGGAGATAAGGTAGGAGACGGAT 59.602 47.826 0.00 0.00 0.00 4.18
4274 4630 4.140994 TGGAGATAAGGTAGGAGACGGATT 60.141 45.833 0.00 0.00 0.00 3.01
4275 4631 5.074102 TGGAGATAAGGTAGGAGACGGATTA 59.926 44.000 0.00 0.00 0.00 1.75
4276 4632 5.415389 GGAGATAAGGTAGGAGACGGATTAC 59.585 48.000 0.00 0.00 0.00 1.89
4277 4633 5.950023 AGATAAGGTAGGAGACGGATTACA 58.050 41.667 0.00 0.00 0.00 2.41
4278 4634 6.371278 AGATAAGGTAGGAGACGGATTACAA 58.629 40.000 0.00 0.00 0.00 2.41
4279 4635 6.837568 AGATAAGGTAGGAGACGGATTACAAA 59.162 38.462 0.00 0.00 0.00 2.83
4280 4636 5.952347 AAGGTAGGAGACGGATTACAAAT 57.048 39.130 0.00 0.00 0.00 2.32
4281 4637 5.532664 AGGTAGGAGACGGATTACAAATC 57.467 43.478 0.00 0.00 0.00 2.17
4282 4638 4.344390 AGGTAGGAGACGGATTACAAATCC 59.656 45.833 8.37 8.37 34.90 3.01
4283 4639 4.344390 GGTAGGAGACGGATTACAAATCCT 59.656 45.833 14.93 0.00 39.06 3.24
4284 4640 5.537674 GGTAGGAGACGGATTACAAATCCTA 59.462 44.000 14.93 0.00 37.00 2.94
4285 4641 6.041296 GGTAGGAGACGGATTACAAATCCTAA 59.959 42.308 14.93 0.00 39.11 2.69
4286 4642 6.555463 AGGAGACGGATTACAAATCCTAAA 57.445 37.500 14.93 0.00 33.99 1.85
4287 4643 6.346896 AGGAGACGGATTACAAATCCTAAAC 58.653 40.000 14.93 5.95 33.99 2.01
4288 4644 6.156429 AGGAGACGGATTACAAATCCTAAACT 59.844 38.462 14.93 9.19 33.99 2.66
4289 4645 7.343833 AGGAGACGGATTACAAATCCTAAACTA 59.656 37.037 14.93 0.00 33.99 2.24
4290 4646 7.437565 GGAGACGGATTACAAATCCTAAACTAC 59.562 40.741 14.93 7.18 36.07 2.73
4291 4647 7.270779 AGACGGATTACAAATCCTAAACTACC 58.729 38.462 14.93 0.00 36.07 3.18
4292 4648 6.949715 ACGGATTACAAATCCTAAACTACCA 58.050 36.000 14.93 0.00 36.07 3.25
4293 4649 7.396418 ACGGATTACAAATCCTAAACTACCAA 58.604 34.615 14.93 0.00 36.07 3.67
4294 4650 7.884354 ACGGATTACAAATCCTAAACTACCAAA 59.116 33.333 14.93 0.00 36.07 3.28
4295 4651 8.899771 CGGATTACAAATCCTAAACTACCAAAT 58.100 33.333 14.93 0.00 36.07 2.32
4301 4657 9.582648 ACAAATCCTAAACTACCAAATACAAGT 57.417 29.630 0.00 0.00 0.00 3.16
4306 4662 8.488668 TCCTAAACTACCAAATACAAGTATCCC 58.511 37.037 0.00 0.00 0.00 3.85
4307 4663 8.269317 CCTAAACTACCAAATACAAGTATCCCA 58.731 37.037 0.00 0.00 0.00 4.37
4308 4664 9.675464 CTAAACTACCAAATACAAGTATCCCAA 57.325 33.333 0.00 0.00 0.00 4.12
4309 4665 8.943594 AAACTACCAAATACAAGTATCCCAAA 57.056 30.769 0.00 0.00 0.00 3.28
4310 4666 9.541884 AAACTACCAAATACAAGTATCCCAAAT 57.458 29.630 0.00 0.00 0.00 2.32
4327 4683 7.510675 TCCCAAATATATCTCTAACATCCCC 57.489 40.000 0.00 0.00 0.00 4.81
4328 4684 6.447084 TCCCAAATATATCTCTAACATCCCCC 59.553 42.308 0.00 0.00 0.00 5.40
4356 4712 3.408020 GCGGTAGCGTTGCGAACA 61.408 61.111 16.63 0.00 0.00 3.18
4357 4713 2.945615 GCGGTAGCGTTGCGAACAA 61.946 57.895 16.63 0.00 0.00 2.83
4365 4721 3.329231 TTGCGAACAACAGGAGCG 58.671 55.556 0.00 0.00 0.00 5.03
4366 4722 1.522806 TTGCGAACAACAGGAGCGT 60.523 52.632 0.00 0.00 0.00 5.07
4367 4723 1.495584 TTGCGAACAACAGGAGCGTC 61.496 55.000 0.00 0.00 0.00 5.19
4368 4724 3.000080 GCGAACAACAGGAGCGTCG 62.000 63.158 0.00 0.00 0.00 5.12
4369 4725 2.853914 GAACAACAGGAGCGTCGC 59.146 61.111 9.80 9.80 0.00 5.19
4370 4726 3.000080 GAACAACAGGAGCGTCGCG 62.000 63.158 12.30 0.00 0.00 5.87
4372 4728 4.717629 CAACAGGAGCGTCGCGGA 62.718 66.667 12.30 0.00 0.00 5.54
4373 4729 4.719369 AACAGGAGCGTCGCGGAC 62.719 66.667 12.30 6.16 0.00 4.79
4382 4738 2.796651 GTCGCGGACGGTCATACT 59.203 61.111 6.13 0.00 40.63 2.12
4383 4739 1.585521 GTCGCGGACGGTCATACTG 60.586 63.158 6.13 0.00 40.63 2.74
4384 4740 1.746239 TCGCGGACGGTCATACTGA 60.746 57.895 6.13 0.00 40.63 3.41
4385 4741 1.138036 CGCGGACGGTCATACTGAA 59.862 57.895 10.76 0.00 34.97 3.02
4386 4742 0.866061 CGCGGACGGTCATACTGAAG 60.866 60.000 10.76 0.00 34.97 3.02
4387 4743 0.454600 GCGGACGGTCATACTGAAGA 59.545 55.000 10.76 0.00 0.00 2.87
4388 4744 1.534175 GCGGACGGTCATACTGAAGAG 60.534 57.143 10.76 0.00 0.00 2.85
4389 4745 2.014857 CGGACGGTCATACTGAAGAGA 58.985 52.381 10.76 0.00 0.00 3.10
4390 4746 2.422479 CGGACGGTCATACTGAAGAGAA 59.578 50.000 10.76 0.00 0.00 2.87
4391 4747 3.066900 CGGACGGTCATACTGAAGAGAAT 59.933 47.826 10.76 0.00 0.00 2.40
4392 4748 4.275196 CGGACGGTCATACTGAAGAGAATA 59.725 45.833 10.76 0.00 0.00 1.75
4393 4749 5.561145 CGGACGGTCATACTGAAGAGAATAG 60.561 48.000 10.76 0.00 0.00 1.73
4394 4750 5.189659 ACGGTCATACTGAAGAGAATAGC 57.810 43.478 0.00 0.00 0.00 2.97
4395 4751 4.645136 ACGGTCATACTGAAGAGAATAGCA 59.355 41.667 0.00 0.00 0.00 3.49
4396 4752 5.218885 CGGTCATACTGAAGAGAATAGCAG 58.781 45.833 0.00 0.00 34.65 4.24
4397 4753 4.987912 GGTCATACTGAAGAGAATAGCAGC 59.012 45.833 0.00 0.00 31.74 5.25
4398 4754 4.987912 GTCATACTGAAGAGAATAGCAGCC 59.012 45.833 0.00 0.00 31.74 4.85
4399 4755 2.593346 ACTGAAGAGAATAGCAGCCG 57.407 50.000 0.00 0.00 31.74 5.52
4400 4756 2.103373 ACTGAAGAGAATAGCAGCCGA 58.897 47.619 0.00 0.00 31.74 5.54
4401 4757 2.159170 ACTGAAGAGAATAGCAGCCGAC 60.159 50.000 0.00 0.00 31.74 4.79
4402 4758 1.202302 TGAAGAGAATAGCAGCCGACG 60.202 52.381 0.00 0.00 0.00 5.12
4403 4759 0.103208 AAGAGAATAGCAGCCGACGG 59.897 55.000 10.29 10.29 0.00 4.79
4404 4760 0.752009 AGAGAATAGCAGCCGACGGA 60.752 55.000 20.50 0.00 0.00 4.69
4405 4761 0.595310 GAGAATAGCAGCCGACGGAC 60.595 60.000 20.50 9.27 0.00 4.79
4406 4762 1.038130 AGAATAGCAGCCGACGGACT 61.038 55.000 20.50 13.67 0.00 3.85
4407 4763 0.872021 GAATAGCAGCCGACGGACTG 60.872 60.000 24.90 24.90 36.96 3.51
4408 4764 1.320344 AATAGCAGCCGACGGACTGA 61.320 55.000 30.10 17.32 35.90 3.41
4409 4765 2.005960 ATAGCAGCCGACGGACTGAC 62.006 60.000 30.10 22.89 35.90 3.51
4410 4766 4.357947 GCAGCCGACGGACTGACA 62.358 66.667 30.10 0.00 35.90 3.58
4411 4767 2.573869 CAGCCGACGGACTGACAT 59.426 61.111 24.96 0.00 35.90 3.06
4412 4768 1.517257 CAGCCGACGGACTGACATC 60.517 63.158 24.96 4.43 35.90 3.06
4413 4769 2.202756 GCCGACGGACTGACATCC 60.203 66.667 20.50 0.00 35.16 3.51
4414 4770 2.494918 CCGACGGACTGACATCCC 59.505 66.667 8.64 0.00 35.03 3.85
4415 4771 2.494918 CGACGGACTGACATCCCC 59.505 66.667 0.00 0.00 35.03 4.81
4416 4772 2.901042 GACGGACTGACATCCCCC 59.099 66.667 0.00 0.00 35.03 5.40
4445 4801 4.873129 CGGGAGCATCGTGGACGG 62.873 72.222 0.00 0.00 40.29 4.79
4446 4802 3.771160 GGGAGCATCGTGGACGGT 61.771 66.667 0.00 0.00 40.29 4.83
4451 4807 3.179265 CATCGTGGACGGTGTCGC 61.179 66.667 4.23 0.00 44.76 5.19
4452 4808 4.771356 ATCGTGGACGGTGTCGCG 62.771 66.667 0.00 0.00 40.63 5.87
4472 4828 2.429571 GCGGACGCGTTGACTGTA 60.430 61.111 15.53 0.00 0.00 2.74
4473 4829 2.434134 GCGGACGCGTTGACTGTAG 61.434 63.158 15.53 0.00 0.00 2.74
4474 4830 1.208358 CGGACGCGTTGACTGTAGA 59.792 57.895 15.53 0.00 0.00 2.59
4475 4831 0.793478 CGGACGCGTTGACTGTAGAG 60.793 60.000 15.53 0.00 0.00 2.43
4476 4832 0.456312 GGACGCGTTGACTGTAGAGG 60.456 60.000 15.53 0.00 0.00 3.69
4477 4833 0.520404 GACGCGTTGACTGTAGAGGA 59.480 55.000 15.53 0.00 0.00 3.71
4478 4834 0.956633 ACGCGTTGACTGTAGAGGAA 59.043 50.000 5.58 0.00 0.00 3.36
4479 4835 1.068472 ACGCGTTGACTGTAGAGGAAG 60.068 52.381 5.58 0.00 0.00 3.46
4480 4836 1.351153 GCGTTGACTGTAGAGGAAGC 58.649 55.000 0.00 0.00 0.00 3.86
4481 4837 1.997669 CGTTGACTGTAGAGGAAGCC 58.002 55.000 0.00 0.00 0.00 4.35
4482 4838 1.732732 CGTTGACTGTAGAGGAAGCCG 60.733 57.143 0.00 0.00 0.00 5.52
4483 4839 1.544691 GTTGACTGTAGAGGAAGCCGA 59.455 52.381 0.00 0.00 0.00 5.54
4484 4840 1.174783 TGACTGTAGAGGAAGCCGAC 58.825 55.000 0.00 0.00 0.00 4.79
4485 4841 0.099082 GACTGTAGAGGAAGCCGACG 59.901 60.000 0.00 0.00 0.00 5.12
4486 4842 0.322277 ACTGTAGAGGAAGCCGACGA 60.322 55.000 0.00 0.00 0.00 4.20
4487 4843 0.378962 CTGTAGAGGAAGCCGACGAG 59.621 60.000 0.00 0.00 0.00 4.18
4488 4844 0.322277 TGTAGAGGAAGCCGACGAGT 60.322 55.000 0.00 0.00 0.00 4.18
4489 4845 0.810016 GTAGAGGAAGCCGACGAGTT 59.190 55.000 0.00 0.00 0.00 3.01
4490 4846 0.809385 TAGAGGAAGCCGACGAGTTG 59.191 55.000 0.00 0.00 0.00 3.16
4491 4847 2.048127 AGGAAGCCGACGAGTTGC 60.048 61.111 0.00 0.00 0.00 4.17
4492 4848 2.048127 GGAAGCCGACGAGTTGCT 60.048 61.111 0.00 0.00 36.79 3.91
4493 4849 2.095252 GGAAGCCGACGAGTTGCTC 61.095 63.158 0.00 0.00 33.36 4.26
4494 4850 1.372997 GAAGCCGACGAGTTGCTCA 60.373 57.895 0.00 0.00 33.36 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.079750 GGCCAGGAGTCGAGAACAC 60.080 63.158 0.00 0.00 0.00 3.32
81 82 1.215382 CACGCGATCTGAACAGGGA 59.785 57.895 15.93 0.00 0.00 4.20
84 85 1.690283 CCAGCACGCGATCTGAACAG 61.690 60.000 25.46 11.06 32.26 3.16
110 112 1.372499 GGACTGCGCACTCACGTAA 60.372 57.895 5.66 0.00 34.88 3.18
224 239 1.051812 CCGCACCTAGATCCTCCATT 58.948 55.000 0.00 0.00 0.00 3.16
448 546 4.833390 CTTTAACTACCAGTCCAGGAAGG 58.167 47.826 7.53 7.53 39.47 3.46
645 745 3.688235 ACTACTGGACTGAGGACACTAC 58.312 50.000 0.00 0.00 0.00 2.73
652 752 6.777213 ACAAGTATAACTACTGGACTGAGG 57.223 41.667 0.00 0.00 38.23 3.86
659 759 5.762825 TCCGCTACAAGTATAACTACTGG 57.237 43.478 0.00 0.00 38.23 4.00
701 801 1.932604 GCGACTGAACTGAGGACACTG 60.933 57.143 0.00 0.00 0.00 3.66
742 842 6.263516 ACATCACATCACCAATCTTGAAAG 57.736 37.500 0.00 0.00 0.00 2.62
761 864 4.339247 CCATGTGGGGAAAACATCTACATC 59.661 45.833 0.00 0.00 36.10 3.06
762 865 4.280819 CCATGTGGGGAAAACATCTACAT 58.719 43.478 0.00 0.00 36.10 2.29
763 866 3.696045 CCATGTGGGGAAAACATCTACA 58.304 45.455 0.00 0.00 36.10 2.74
764 867 2.427095 GCCATGTGGGGAAAACATCTAC 59.573 50.000 0.54 0.00 36.10 2.59
765 868 2.042297 TGCCATGTGGGGAAAACATCTA 59.958 45.455 0.54 0.00 36.10 1.98
766 869 1.203162 TGCCATGTGGGGAAAACATCT 60.203 47.619 0.54 0.00 36.10 2.90
767 870 1.205417 CTGCCATGTGGGGAAAACATC 59.795 52.381 0.54 0.00 36.08 3.06
768 871 1.203162 TCTGCCATGTGGGGAAAACAT 60.203 47.619 0.54 0.00 36.08 2.71
769 872 0.187117 TCTGCCATGTGGGGAAAACA 59.813 50.000 0.54 0.00 36.08 2.83
770 873 1.205417 CATCTGCCATGTGGGGAAAAC 59.795 52.381 0.54 0.00 36.08 2.43
830 933 4.344679 ACCTTTGCAATCAACAATTCAGGA 59.655 37.500 12.26 0.00 30.83 3.86
1570 1684 3.757248 ATCGCCAGGGATTGACGCC 62.757 63.158 0.00 0.00 32.22 5.68
1978 2092 0.967887 TGGTCTCCTTCCTCTGCTCG 60.968 60.000 0.00 0.00 0.00 5.03
2743 2860 3.623060 CACCCATGATACGGAAGAAGTTG 59.377 47.826 0.00 0.00 0.00 3.16
2812 2929 3.906980 AGTGGGTTCCTCCAGTGG 58.093 61.111 1.40 1.40 38.90 4.00
2866 2983 5.301551 CAGTATCAGCTCAGGATACAAGACT 59.698 44.000 19.37 3.33 46.06 3.24
2956 3073 2.815211 CGAGTGTCCATGTGCGGG 60.815 66.667 0.00 0.00 0.00 6.13
3085 3202 2.038813 TGGATCCTCCCAGCGACA 59.961 61.111 14.23 0.00 35.03 4.35
3401 3521 3.081133 CATCGAGCCACCGAAACG 58.919 61.111 0.00 0.00 42.22 3.60
3523 3643 0.375454 TGTTCCAAAACAGACACGCG 59.625 50.000 3.53 3.53 40.45 6.01
3539 3659 5.245075 TCAACAGGAAAGGTTCAAAACTGTT 59.755 36.000 0.00 0.00 45.38 3.16
3542 3662 4.142469 CGTCAACAGGAAAGGTTCAAAACT 60.142 41.667 0.00 0.00 0.00 2.66
3697 4039 5.105595 TGACGATAGATCAGCATTCCTATGG 60.106 44.000 0.00 0.00 41.38 2.74
3737 4079 0.921896 ATCCCAATACTGGCAGCAGT 59.078 50.000 15.89 0.00 41.99 4.40
3763 4105 5.916883 CACTCCATCTGTAAAGTGCAAAAAG 59.083 40.000 0.00 0.00 33.42 2.27
3775 4119 4.160329 AGTGAAGGAACACTCCATCTGTA 58.840 43.478 0.00 0.00 46.36 2.74
3811 4156 4.949856 GGGAGATAAATGCCAAACTCTTCA 59.050 41.667 0.00 0.00 0.00 3.02
3855 4200 4.516321 CCTCAACATATCGATTGGCATTCA 59.484 41.667 1.71 0.00 0.00 2.57
3908 4254 6.452244 TTGAACGCATGTATATCGATCAAG 57.548 37.500 0.00 0.00 39.08 3.02
3924 4272 5.117135 GCCTAAGAAGTTGAATTTTGAACGC 59.883 40.000 0.00 0.00 29.32 4.84
3934 4282 5.312895 TGCATTACAGCCTAAGAAGTTGAA 58.687 37.500 0.00 0.00 0.00 2.69
3955 4303 5.349543 CAGGAGCCAATTAGTTTTTGAATGC 59.650 40.000 0.00 0.00 0.00 3.56
4033 4381 4.098960 TCCGACACACATACCTAAATCCTC 59.901 45.833 0.00 0.00 0.00 3.71
4063 4411 2.366266 TGTAAGCAAGTACGTGGACCTT 59.634 45.455 10.87 7.90 0.00 3.50
4100 4451 3.912496 AAAGCATTAGGGGCAATTTCC 57.088 42.857 0.00 0.00 0.00 3.13
4145 4501 7.576666 GCAACAATCTCTCTCTCTCTTCTAACA 60.577 40.741 0.00 0.00 0.00 2.41
4146 4502 6.751888 GCAACAATCTCTCTCTCTCTTCTAAC 59.248 42.308 0.00 0.00 0.00 2.34
4147 4503 6.404184 CGCAACAATCTCTCTCTCTCTTCTAA 60.404 42.308 0.00 0.00 0.00 2.10
4148 4504 5.065859 CGCAACAATCTCTCTCTCTCTTCTA 59.934 44.000 0.00 0.00 0.00 2.10
4149 4505 4.142403 CGCAACAATCTCTCTCTCTCTTCT 60.142 45.833 0.00 0.00 0.00 2.85
4150 4506 4.104776 CGCAACAATCTCTCTCTCTCTTC 58.895 47.826 0.00 0.00 0.00 2.87
4151 4507 3.119173 CCGCAACAATCTCTCTCTCTCTT 60.119 47.826 0.00 0.00 0.00 2.85
4152 4508 2.426738 CCGCAACAATCTCTCTCTCTCT 59.573 50.000 0.00 0.00 0.00 3.10
4153 4509 2.425312 TCCGCAACAATCTCTCTCTCTC 59.575 50.000 0.00 0.00 0.00 3.20
4154 4510 2.451490 TCCGCAACAATCTCTCTCTCT 58.549 47.619 0.00 0.00 0.00 3.10
4155 4511 2.949451 TCCGCAACAATCTCTCTCTC 57.051 50.000 0.00 0.00 0.00 3.20
4156 4512 3.902881 ATTCCGCAACAATCTCTCTCT 57.097 42.857 0.00 0.00 0.00 3.10
4157 4513 5.292765 TCATATTCCGCAACAATCTCTCTC 58.707 41.667 0.00 0.00 0.00 3.20
4158 4514 5.282055 TCATATTCCGCAACAATCTCTCT 57.718 39.130 0.00 0.00 0.00 3.10
4159 4515 5.106791 CCATCATATTCCGCAACAATCTCTC 60.107 44.000 0.00 0.00 0.00 3.20
4160 4516 4.758674 CCATCATATTCCGCAACAATCTCT 59.241 41.667 0.00 0.00 0.00 3.10
4161 4517 4.756642 TCCATCATATTCCGCAACAATCTC 59.243 41.667 0.00 0.00 0.00 2.75
4162 4518 4.717877 TCCATCATATTCCGCAACAATCT 58.282 39.130 0.00 0.00 0.00 2.40
4163 4519 5.048504 ACATCCATCATATTCCGCAACAATC 60.049 40.000 0.00 0.00 0.00 2.67
4164 4520 4.828939 ACATCCATCATATTCCGCAACAAT 59.171 37.500 0.00 0.00 0.00 2.71
4165 4521 4.206375 ACATCCATCATATTCCGCAACAA 58.794 39.130 0.00 0.00 0.00 2.83
4166 4522 3.819368 ACATCCATCATATTCCGCAACA 58.181 40.909 0.00 0.00 0.00 3.33
4167 4523 6.500684 AATACATCCATCATATTCCGCAAC 57.499 37.500 0.00 0.00 0.00 4.17
4168 4524 8.676401 CAATAATACATCCATCATATTCCGCAA 58.324 33.333 0.00 0.00 0.00 4.85
4169 4525 8.046107 TCAATAATACATCCATCATATTCCGCA 58.954 33.333 0.00 0.00 0.00 5.69
4170 4526 8.437360 TCAATAATACATCCATCATATTCCGC 57.563 34.615 0.00 0.00 0.00 5.54
4171 4527 8.554528 GCTCAATAATACATCCATCATATTCCG 58.445 37.037 0.00 0.00 0.00 4.30
4172 4528 8.844244 GGCTCAATAATACATCCATCATATTCC 58.156 37.037 0.00 0.00 0.00 3.01
4173 4529 9.624373 AGGCTCAATAATACATCCATCATATTC 57.376 33.333 0.00 0.00 0.00 1.75
4174 4530 9.624373 GAGGCTCAATAATACATCCATCATATT 57.376 33.333 10.25 0.00 0.00 1.28
4175 4531 7.930325 CGAGGCTCAATAATACATCCATCATAT 59.070 37.037 15.95 0.00 0.00 1.78
4176 4532 7.124147 TCGAGGCTCAATAATACATCCATCATA 59.876 37.037 15.95 0.00 0.00 2.15
4177 4533 6.070596 TCGAGGCTCAATAATACATCCATCAT 60.071 38.462 15.95 0.00 0.00 2.45
4178 4534 5.245977 TCGAGGCTCAATAATACATCCATCA 59.754 40.000 15.95 0.00 0.00 3.07
4179 4535 5.724328 TCGAGGCTCAATAATACATCCATC 58.276 41.667 15.95 0.00 0.00 3.51
4180 4536 5.337894 CCTCGAGGCTCAATAATACATCCAT 60.338 44.000 20.67 0.00 0.00 3.41
4181 4537 4.021104 CCTCGAGGCTCAATAATACATCCA 60.021 45.833 20.67 0.00 0.00 3.41
4182 4538 4.499183 CCTCGAGGCTCAATAATACATCC 58.501 47.826 20.67 0.00 0.00 3.51
4183 4539 4.499183 CCCTCGAGGCTCAATAATACATC 58.501 47.826 26.87 0.00 0.00 3.06
4184 4540 4.543590 CCCTCGAGGCTCAATAATACAT 57.456 45.455 26.87 0.00 0.00 2.29
4199 4555 4.586884 ACTCAATATATACTCGCCCTCGA 58.413 43.478 0.00 0.00 43.28 4.04
4200 4556 4.966965 ACTCAATATATACTCGCCCTCG 57.033 45.455 0.00 0.00 0.00 4.63
4201 4557 6.754702 TGTACTCAATATATACTCGCCCTC 57.245 41.667 0.00 0.00 0.00 4.30
4202 4558 6.946583 TCTTGTACTCAATATATACTCGCCCT 59.053 38.462 0.00 0.00 32.82 5.19
4203 4559 7.028361 GTCTTGTACTCAATATATACTCGCCC 58.972 42.308 0.00 0.00 32.82 6.13
4204 4560 7.818642 AGTCTTGTACTCAATATATACTCGCC 58.181 38.462 0.00 0.00 30.33 5.54
4205 4561 9.119329 CAAGTCTTGTACTCAATATATACTCGC 57.881 37.037 4.27 0.00 37.50 5.03
4211 4567 7.934120 GCCCTTCAAGTCTTGTACTCAATATAT 59.066 37.037 12.30 0.00 37.50 0.86
4212 4568 7.093068 TGCCCTTCAAGTCTTGTACTCAATATA 60.093 37.037 12.30 0.00 37.50 0.86
4213 4569 6.116126 GCCCTTCAAGTCTTGTACTCAATAT 58.884 40.000 12.30 0.00 37.50 1.28
4214 4570 5.012664 TGCCCTTCAAGTCTTGTACTCAATA 59.987 40.000 12.30 0.00 37.50 1.90
4215 4571 4.202461 TGCCCTTCAAGTCTTGTACTCAAT 60.202 41.667 12.30 0.00 37.50 2.57
4216 4572 3.135712 TGCCCTTCAAGTCTTGTACTCAA 59.864 43.478 12.30 0.00 37.50 3.02
4217 4573 2.703536 TGCCCTTCAAGTCTTGTACTCA 59.296 45.455 12.30 3.52 37.50 3.41
4218 4574 3.402628 TGCCCTTCAAGTCTTGTACTC 57.597 47.619 12.30 1.19 37.50 2.59
4219 4575 3.744660 CTTGCCCTTCAAGTCTTGTACT 58.255 45.455 12.30 0.00 45.48 2.73
4236 4592 2.125350 CCAGGAGAGGCGTCTTGC 60.125 66.667 10.79 0.00 45.38 4.01
4237 4593 0.967887 TCTCCAGGAGAGGCGTCTTG 60.968 60.000 15.98 5.77 43.44 3.02
4238 4594 0.032615 ATCTCCAGGAGAGGCGTCTT 60.033 55.000 23.96 2.93 42.26 3.01
4239 4595 0.847373 TATCTCCAGGAGAGGCGTCT 59.153 55.000 23.96 9.04 42.26 4.18
4240 4596 1.611491 CTTATCTCCAGGAGAGGCGTC 59.389 57.143 23.96 0.00 42.26 5.19
4241 4597 1.698506 CTTATCTCCAGGAGAGGCGT 58.301 55.000 23.96 10.20 42.26 5.68
4242 4598 0.965439 CCTTATCTCCAGGAGAGGCG 59.035 60.000 23.96 13.57 42.26 5.52
4243 4599 2.095604 ACCTTATCTCCAGGAGAGGC 57.904 55.000 23.96 0.00 42.26 4.70
4244 4600 3.399644 TCCTACCTTATCTCCAGGAGAGG 59.600 52.174 23.96 20.74 42.26 3.69
4245 4601 4.733077 TCCTACCTTATCTCCAGGAGAG 57.267 50.000 23.96 12.91 42.26 3.20
4248 4604 3.181442 CGTCTCCTACCTTATCTCCAGGA 60.181 52.174 0.00 0.00 35.14 3.86
4249 4605 3.150767 CGTCTCCTACCTTATCTCCAGG 58.849 54.545 0.00 0.00 37.45 4.45
4250 4606 3.150767 CCGTCTCCTACCTTATCTCCAG 58.849 54.545 0.00 0.00 0.00 3.86
4251 4607 2.781757 TCCGTCTCCTACCTTATCTCCA 59.218 50.000 0.00 0.00 0.00 3.86
4252 4608 3.505480 TCCGTCTCCTACCTTATCTCC 57.495 52.381 0.00 0.00 0.00 3.71
4253 4609 6.002704 TGTAATCCGTCTCCTACCTTATCTC 58.997 44.000 0.00 0.00 0.00 2.75
4254 4610 5.950023 TGTAATCCGTCTCCTACCTTATCT 58.050 41.667 0.00 0.00 0.00 1.98
4255 4611 6.645790 TTGTAATCCGTCTCCTACCTTATC 57.354 41.667 0.00 0.00 0.00 1.75
4256 4612 7.256225 GGATTTGTAATCCGTCTCCTACCTTAT 60.256 40.741 2.90 0.00 0.00 1.73
4257 4613 6.041296 GGATTTGTAATCCGTCTCCTACCTTA 59.959 42.308 2.90 0.00 0.00 2.69
4258 4614 5.163332 GGATTTGTAATCCGTCTCCTACCTT 60.163 44.000 2.90 0.00 0.00 3.50
4259 4615 4.344390 GGATTTGTAATCCGTCTCCTACCT 59.656 45.833 2.90 0.00 0.00 3.08
4260 4616 4.344390 AGGATTTGTAATCCGTCTCCTACC 59.656 45.833 11.65 0.00 42.87 3.18
4261 4617 5.532664 AGGATTTGTAATCCGTCTCCTAC 57.467 43.478 11.65 0.00 42.87 3.18
4262 4618 7.343833 AGTTTAGGATTTGTAATCCGTCTCCTA 59.656 37.037 11.65 0.00 42.87 2.94
4263 4619 6.156429 AGTTTAGGATTTGTAATCCGTCTCCT 59.844 38.462 11.65 0.00 42.87 3.69
4264 4620 6.346896 AGTTTAGGATTTGTAATCCGTCTCC 58.653 40.000 11.65 2.79 42.87 3.71
4265 4621 7.437565 GGTAGTTTAGGATTTGTAATCCGTCTC 59.562 40.741 11.65 5.97 42.87 3.36
4266 4622 7.093201 TGGTAGTTTAGGATTTGTAATCCGTCT 60.093 37.037 11.65 10.74 42.87 4.18
4267 4623 7.043565 TGGTAGTTTAGGATTTGTAATCCGTC 58.956 38.462 11.65 5.43 42.87 4.79
4268 4624 6.949715 TGGTAGTTTAGGATTTGTAATCCGT 58.050 36.000 11.65 4.83 42.87 4.69
4269 4625 7.852971 TTGGTAGTTTAGGATTTGTAATCCG 57.147 36.000 11.65 0.00 42.87 4.18
4275 4631 9.582648 ACTTGTATTTGGTAGTTTAGGATTTGT 57.417 29.630 0.00 0.00 0.00 2.83
4280 4636 8.488668 GGGATACTTGTATTTGGTAGTTTAGGA 58.511 37.037 0.00 0.00 0.00 2.94
4281 4637 8.269317 TGGGATACTTGTATTTGGTAGTTTAGG 58.731 37.037 0.00 0.00 0.00 2.69
4282 4638 9.675464 TTGGGATACTTGTATTTGGTAGTTTAG 57.325 33.333 0.00 0.00 0.00 1.85
4284 4640 8.943594 TTTGGGATACTTGTATTTGGTAGTTT 57.056 30.769 0.00 0.00 0.00 2.66
4301 4657 9.225682 GGGGATGTTAGAGATATATTTGGGATA 57.774 37.037 0.00 0.00 0.00 2.59
4302 4658 7.129504 GGGGGATGTTAGAGATATATTTGGGAT 59.870 40.741 0.00 0.00 0.00 3.85
4303 4659 6.447084 GGGGGATGTTAGAGATATATTTGGGA 59.553 42.308 0.00 0.00 0.00 4.37
4304 4660 6.663734 GGGGGATGTTAGAGATATATTTGGG 58.336 44.000 0.00 0.00 0.00 4.12
4330 4686 2.651232 CGCTACCGCTACGACTGC 60.651 66.667 0.00 0.00 0.00 4.40
4331 4687 1.132199 CAACGCTACCGCTACGACTG 61.132 60.000 0.00 0.00 38.22 3.51
4332 4688 1.136147 CAACGCTACCGCTACGACT 59.864 57.895 0.00 0.00 38.22 4.18
4333 4689 2.502965 GCAACGCTACCGCTACGAC 61.503 63.158 0.00 0.00 38.22 4.34
4334 4690 2.202518 GCAACGCTACCGCTACGA 60.203 61.111 0.00 0.00 38.22 3.43
4335 4691 3.604202 CGCAACGCTACCGCTACG 61.604 66.667 0.00 0.00 38.22 3.51
4336 4692 1.802715 TTCGCAACGCTACCGCTAC 60.803 57.895 0.00 0.00 38.22 3.58
4337 4693 1.802715 GTTCGCAACGCTACCGCTA 60.803 57.895 0.00 0.00 38.22 4.26
4338 4694 3.110178 GTTCGCAACGCTACCGCT 61.110 61.111 0.00 0.00 38.22 5.52
4339 4695 2.945615 TTGTTCGCAACGCTACCGC 61.946 57.895 0.00 0.00 38.22 5.68
4340 4696 1.154727 GTTGTTCGCAACGCTACCG 60.155 57.895 0.00 0.00 46.47 4.02
4341 4697 4.812308 GTTGTTCGCAACGCTACC 57.188 55.556 0.00 0.00 46.47 3.18
4348 4704 1.495584 GACGCTCCTGTTGTTCGCAA 61.496 55.000 0.00 0.00 34.21 4.85
4349 4705 1.954146 GACGCTCCTGTTGTTCGCA 60.954 57.895 0.00 0.00 0.00 5.10
4350 4706 2.853914 GACGCTCCTGTTGTTCGC 59.146 61.111 0.00 0.00 0.00 4.70
4351 4707 3.000080 GCGACGCTCCTGTTGTTCG 62.000 63.158 13.73 0.00 0.00 3.95
4352 4708 2.853914 GCGACGCTCCTGTTGTTC 59.146 61.111 13.73 0.00 0.00 3.18
4353 4709 3.036084 CGCGACGCTCCTGTTGTT 61.036 61.111 19.02 0.00 0.00 2.83
4355 4711 4.717629 TCCGCGACGCTCCTGTTG 62.718 66.667 19.02 0.00 0.00 3.33
4356 4712 4.719369 GTCCGCGACGCTCCTGTT 62.719 66.667 19.02 0.00 0.00 3.16
4365 4721 1.585521 CAGTATGACCGTCCGCGAC 60.586 63.158 8.23 2.72 39.69 5.19
4366 4722 1.746239 TCAGTATGACCGTCCGCGA 60.746 57.895 8.23 0.00 42.56 5.87
4367 4723 2.795973 TCAGTATGACCGTCCGCG 59.204 61.111 0.00 0.00 42.56 6.46
4377 4733 3.986572 CGGCTGCTATTCTCTTCAGTATG 59.013 47.826 0.00 0.00 37.54 2.39
4378 4734 3.891977 TCGGCTGCTATTCTCTTCAGTAT 59.108 43.478 0.00 0.00 0.00 2.12
4379 4735 3.066900 GTCGGCTGCTATTCTCTTCAGTA 59.933 47.826 0.00 0.00 0.00 2.74
4380 4736 2.103373 TCGGCTGCTATTCTCTTCAGT 58.897 47.619 0.00 0.00 0.00 3.41
4381 4737 2.468831 GTCGGCTGCTATTCTCTTCAG 58.531 52.381 0.00 0.00 0.00 3.02
4382 4738 1.202302 CGTCGGCTGCTATTCTCTTCA 60.202 52.381 0.00 0.00 0.00 3.02
4383 4739 1.482278 CGTCGGCTGCTATTCTCTTC 58.518 55.000 0.00 0.00 0.00 2.87
4384 4740 0.103208 CCGTCGGCTGCTATTCTCTT 59.897 55.000 0.00 0.00 0.00 2.85
4385 4741 0.752009 TCCGTCGGCTGCTATTCTCT 60.752 55.000 6.34 0.00 0.00 3.10
4386 4742 0.595310 GTCCGTCGGCTGCTATTCTC 60.595 60.000 6.34 0.00 0.00 2.87
4387 4743 1.038130 AGTCCGTCGGCTGCTATTCT 61.038 55.000 6.34 0.00 0.00 2.40
4388 4744 0.872021 CAGTCCGTCGGCTGCTATTC 60.872 60.000 18.45 0.00 0.00 1.75
4389 4745 1.141881 CAGTCCGTCGGCTGCTATT 59.858 57.895 18.45 0.00 0.00 1.73
4390 4746 1.753078 TCAGTCCGTCGGCTGCTAT 60.753 57.895 22.99 0.00 33.09 2.97
4391 4747 2.360726 TCAGTCCGTCGGCTGCTA 60.361 61.111 22.99 10.39 33.09 3.49
4392 4748 4.057428 GTCAGTCCGTCGGCTGCT 62.057 66.667 22.99 12.16 33.09 4.24
4393 4749 3.649277 ATGTCAGTCCGTCGGCTGC 62.649 63.158 22.99 19.04 33.09 5.25
4394 4750 1.517257 GATGTCAGTCCGTCGGCTG 60.517 63.158 22.23 22.23 0.00 4.85
4395 4751 2.711922 GGATGTCAGTCCGTCGGCT 61.712 63.158 6.34 4.26 0.00 5.52
4396 4752 2.202756 GGATGTCAGTCCGTCGGC 60.203 66.667 6.34 1.61 0.00 5.54
4397 4753 2.494918 GGGATGTCAGTCCGTCGG 59.505 66.667 4.39 4.39 39.26 4.79
4398 4754 2.494918 GGGGATGTCAGTCCGTCG 59.505 66.667 0.00 0.00 39.26 5.12
4399 4755 2.901042 GGGGGATGTCAGTCCGTC 59.099 66.667 0.00 0.00 39.26 4.79
4418 4774 2.707529 GATGCTCCCGCTAGGACTGC 62.708 65.000 0.00 0.00 40.93 4.40
4419 4775 1.365633 GATGCTCCCGCTAGGACTG 59.634 63.158 0.00 0.00 40.93 3.51
4420 4776 2.196925 CGATGCTCCCGCTAGGACT 61.197 63.158 0.00 0.00 40.93 3.85
4421 4777 2.336809 CGATGCTCCCGCTAGGAC 59.663 66.667 0.00 0.00 40.93 3.85
4422 4778 2.123854 ACGATGCTCCCGCTAGGA 60.124 61.111 0.00 0.00 44.91 2.94
4423 4779 2.028190 CACGATGCTCCCGCTAGG 59.972 66.667 0.00 0.00 36.97 3.02
4424 4780 2.028190 CCACGATGCTCCCGCTAG 59.972 66.667 0.00 0.00 36.97 3.42
4425 4781 2.441348 TCCACGATGCTCCCGCTA 60.441 61.111 0.00 0.00 36.97 4.26
4426 4782 4.148825 GTCCACGATGCTCCCGCT 62.149 66.667 0.00 0.00 36.97 5.52
4428 4784 4.873129 CCGTCCACGATGCTCCCG 62.873 72.222 0.00 0.00 43.02 5.14
4429 4785 3.771160 ACCGTCCACGATGCTCCC 61.771 66.667 0.00 0.00 43.02 4.30
4430 4786 2.509336 CACCGTCCACGATGCTCC 60.509 66.667 0.00 0.00 43.02 4.70
4431 4787 1.805945 GACACCGTCCACGATGCTC 60.806 63.158 0.00 0.00 36.00 4.26
4432 4788 2.261671 GACACCGTCCACGATGCT 59.738 61.111 0.00 0.00 36.00 3.79
4433 4789 3.179265 CGACACCGTCCACGATGC 61.179 66.667 0.00 0.00 36.00 3.91
4434 4790 3.179265 GCGACACCGTCCACGATG 61.179 66.667 0.00 0.00 43.02 3.84
4435 4791 4.771356 CGCGACACCGTCCACGAT 62.771 66.667 0.00 0.00 43.02 3.73
4455 4811 2.429571 TACAGTCAACGCGTCCGC 60.430 61.111 14.44 5.40 38.22 5.54
4456 4812 0.793478 CTCTACAGTCAACGCGTCCG 60.793 60.000 14.44 7.35 41.14 4.79
4457 4813 0.456312 CCTCTACAGTCAACGCGTCC 60.456 60.000 14.44 3.44 0.00 4.79
4458 4814 0.520404 TCCTCTACAGTCAACGCGTC 59.480 55.000 14.44 0.00 0.00 5.19
4459 4815 0.956633 TTCCTCTACAGTCAACGCGT 59.043 50.000 5.58 5.58 0.00 6.01
4460 4816 1.618861 CTTCCTCTACAGTCAACGCG 58.381 55.000 3.53 3.53 0.00 6.01
4461 4817 1.351153 GCTTCCTCTACAGTCAACGC 58.649 55.000 0.00 0.00 0.00 4.84
4462 4818 1.732732 CGGCTTCCTCTACAGTCAACG 60.733 57.143 0.00 0.00 0.00 4.10
4463 4819 1.544691 TCGGCTTCCTCTACAGTCAAC 59.455 52.381 0.00 0.00 0.00 3.18
4464 4820 1.544691 GTCGGCTTCCTCTACAGTCAA 59.455 52.381 0.00 0.00 0.00 3.18
4465 4821 1.174783 GTCGGCTTCCTCTACAGTCA 58.825 55.000 0.00 0.00 0.00 3.41
4466 4822 0.099082 CGTCGGCTTCCTCTACAGTC 59.901 60.000 0.00 0.00 0.00 3.51
4467 4823 0.322277 TCGTCGGCTTCCTCTACAGT 60.322 55.000 0.00 0.00 0.00 3.55
4468 4824 0.378962 CTCGTCGGCTTCCTCTACAG 59.621 60.000 0.00 0.00 0.00 2.74
4469 4825 0.322277 ACTCGTCGGCTTCCTCTACA 60.322 55.000 0.00 0.00 0.00 2.74
4470 4826 0.810016 AACTCGTCGGCTTCCTCTAC 59.190 55.000 0.00 0.00 0.00 2.59
4471 4827 0.809385 CAACTCGTCGGCTTCCTCTA 59.191 55.000 0.00 0.00 0.00 2.43
4472 4828 1.587054 CAACTCGTCGGCTTCCTCT 59.413 57.895 0.00 0.00 0.00 3.69
4473 4829 2.095252 GCAACTCGTCGGCTTCCTC 61.095 63.158 0.00 0.00 0.00 3.71
4474 4830 2.048127 GCAACTCGTCGGCTTCCT 60.048 61.111 0.00 0.00 0.00 3.36
4475 4831 2.048127 AGCAACTCGTCGGCTTCC 60.048 61.111 0.00 0.00 33.21 3.46
4476 4832 1.372997 TGAGCAACTCGTCGGCTTC 60.373 57.895 0.00 0.00 38.15 3.86
4477 4833 2.734591 TGAGCAACTCGTCGGCTT 59.265 55.556 0.00 0.00 38.15 4.35


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

AutoCloner maintained by Alex Coulton.