Multiple sequence alignment - TraesCS5D01G098700

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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 TraesCS5D01G098700 chr5D 100.000 5074 0 0 1 5074 110346786 110351859 0.000000e+00 9371.0
1 TraesCS5D01G098700 chr5D 86.567 4273 458 60 7 4235 110365258 110369458 0.000000e+00 4604.0
2 TraesCS5D01G098700 chr5D 71.947 1294 333 23 2043 3324 109943919 109942644 8.080000e-93 351.0
3 TraesCS5D01G098700 chr5B 96.400 4250 129 9 1 4241 122439716 122435482 0.000000e+00 6979.0
4 TraesCS5D01G098700 chr5B 83.374 409 44 8 4412 4817 382316273 382316660 1.740000e-94 357.0
5 TraesCS5D01G098700 chr5B 75.616 730 166 10 2059 2782 122831377 122832100 8.080000e-93 351.0
6 TraesCS5D01G098700 chr5B 83.429 175 26 3 4240 4412 680999570 680999743 5.260000e-35 159.0
7 TraesCS5D01G098700 chr5A 88.168 4344 404 56 7 4319 116588312 116584048 0.000000e+00 5073.0
8 TraesCS5D01G098700 chr5A 97.297 2886 73 2 676 3558 116698873 116695990 0.000000e+00 4892.0
9 TraesCS5D01G098700 chr5A 97.839 2221 42 3 145 2362 116781248 116779031 0.000000e+00 3831.0
10 TraesCS5D01G098700 chr5A 96.703 1941 58 3 2380 4319 116776535 116774600 0.000000e+00 3225.0
11 TraesCS5D01G098700 chr5A 96.143 726 27 1 3595 4319 116695993 116695268 0.000000e+00 1184.0
12 TraesCS5D01G098700 chr5A 97.970 394 8 0 145 538 116699264 116698871 0.000000e+00 684.0
13 TraesCS5D01G098700 chr5A 93.200 250 16 1 4825 5074 116773891 116773643 2.890000e-97 366.0
14 TraesCS5D01G098700 chr5A 83.133 415 56 9 4414 4824 544220196 544220600 2.890000e-97 366.0
15 TraesCS5D01G098700 chr5A 92.800 250 17 1 4825 5074 116694559 116694311 1.340000e-95 361.0
16 TraesCS5D01G098700 chr5A 98.658 149 2 0 1 149 116802735 116802587 1.080000e-66 265.0
17 TraesCS5D01G098700 chr5A 71.464 813 209 16 2518 3324 117388437 117389232 1.440000e-45 195.0
18 TraesCS5D01G098700 chr5A 81.166 223 33 7 4410 4627 610330038 610329820 2.430000e-38 171.0
19 TraesCS5D01G098700 chr5A 96.809 94 2 1 4319 4412 116774526 116774434 6.800000e-34 156.0
20 TraesCS5D01G098700 chr5A 95.745 94 3 1 4319 4412 116695194 116695102 3.160000e-32 150.0
21 TraesCS5D01G098700 chr5A 96.341 82 2 1 4319 4400 116583974 116583894 3.190000e-27 134.0
22 TraesCS5D01G098700 chr5A 92.045 88 6 1 4325 4412 116694913 116694827 6.900000e-24 122.0
23 TraesCS5D01G098700 chr5A 92.683 82 6 0 4824 4905 116774167 116774086 8.920000e-23 119.0
24 TraesCS5D01G098700 chr5A 91.463 82 7 0 4824 4905 116695110 116695029 4.150000e-21 113.0
25 TraesCS5D01G098700 chr5A 91.463 82 7 0 4824 4905 116774442 116774361 4.150000e-21 113.0
26 TraesCS5D01G098700 chr5A 90.244 82 8 0 4824 4905 116694835 116694754 1.930000e-19 108.0
27 TraesCS5D01G098700 chrUn 97.656 384 6 1 847 1227 480886713 480887096 0.000000e+00 656.0
28 TraesCS5D01G098700 chr1D 92.689 424 13 6 4413 4823 203869481 203869899 3.380000e-166 595.0
29 TraesCS5D01G098700 chr1A 92.788 416 19 9 4413 4823 532969628 532969219 4.370000e-165 592.0
30 TraesCS5D01G098700 chr1A 92.417 422 15 5 4410 4817 37618815 37619233 2.040000e-163 586.0
31 TraesCS5D01G098700 chr1A 90.110 455 22 8 4402 4839 147685096 147684648 2.050000e-158 569.0
32 TraesCS5D01G098700 chr6D 92.417 422 15 5 4412 4819 3319207 3319625 2.040000e-163 586.0
33 TraesCS5D01G098700 chr4A 92.399 421 15 5 4411 4817 737301687 737302104 7.320000e-163 584.0
34 TraesCS5D01G098700 chr3B 94.503 382 14 4 4444 4823 66625463 66625087 2.630000e-162 582.0
35 TraesCS5D01G098700 chr3B 86.957 69 7 2 2044 2111 829213233 829213300 5.450000e-10 76.8
36 TraesCS5D01G098700 chr3B 83.333 66 11 0 2044 2109 817011814 817011749 1.530000e-05 62.1
37 TraesCS5D01G098700 chr2D 94.241 382 19 3 4444 4824 448507258 448507637 9.470000e-162 580.0
38 TraesCS5D01G098700 chr7A 94.241 382 17 4 4444 4823 692756627 692756249 3.410000e-161 579.0
39 TraesCS5D01G098700 chr7A 84.514 381 47 10 4410 4784 23153585 23153959 2.890000e-97 366.0
40 TraesCS5D01G098700 chr7A 83.761 117 17 2 4828 4944 251474540 251474426 5.370000e-20 110.0
41 TraesCS5D01G098700 chr7D 85.851 417 49 7 4413 4826 630308322 630307913 7.800000e-118 435.0
42 TraesCS5D01G098700 chr7D 92.188 64 0 1 4413 4476 13383978 13383920 9.050000e-13 86.1
43 TraesCS5D01G098700 chr7B 84.514 381 46 11 4410 4784 65348273 65347900 1.040000e-96 364.0
44 TraesCS5D01G098700 chr1B 81.419 296 41 11 4412 4705 624841141 624840858 3.950000e-56 230.0
45 TraesCS5D01G098700 chr6A 84.112 107 14 3 4228 4333 596145325 596145221 3.230000e-17 100.0
46 TraesCS5D01G098700 chr3A 80.189 106 19 2 4229 4333 662827326 662827430 1.510000e-10 78.7
47 TraesCS5D01G098700 chr3D 97.727 44 0 1 377 419 573703596 573703639 1.960000e-09 75.0


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 TraesCS5D01G098700 chr5D 110346786 110351859 5073 False 9371.000000 9371 100.000000 1 5074 1 chr5D.!!$F1 5073
1 TraesCS5D01G098700 chr5D 110365258 110369458 4200 False 4604.000000 4604 86.567000 7 4235 1 chr5D.!!$F2 4228
2 TraesCS5D01G098700 chr5D 109942644 109943919 1275 True 351.000000 351 71.947000 2043 3324 1 chr5D.!!$R1 1281
3 TraesCS5D01G098700 chr5B 122435482 122439716 4234 True 6979.000000 6979 96.400000 1 4241 1 chr5B.!!$R1 4240
4 TraesCS5D01G098700 chr5B 122831377 122832100 723 False 351.000000 351 75.616000 2059 2782 1 chr5B.!!$F1 723
5 TraesCS5D01G098700 chr5A 116583894 116588312 4418 True 2603.500000 5073 92.254500 7 4400 2 chr5A.!!$R3 4393
6 TraesCS5D01G098700 chr5A 116773643 116781248 7605 True 1301.666667 3831 94.782833 145 5074 6 chr5A.!!$R5 4929
7 TraesCS5D01G098700 chr5A 116694311 116699264 4953 True 951.750000 4892 94.213375 145 5074 8 chr5A.!!$R4 4929

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
456 466 2.132996 CCCTCTCATCTCCAGCGCT 61.133 63.158 2.64 2.64 0.00 5.92 F
1186 1201 3.303938 GAGGTTGAGGATCCTGATGAGA 58.696 50.000 22.02 0.00 33.83 3.27 F
1495 1517 1.247567 ACCAGCATTTTTCACCGAGG 58.752 50.000 0.00 0.00 0.00 4.63 F
3392 5913 2.299013 TGCAGATAACTTGGTCGTGTCT 59.701 45.455 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 1465 0.179073 TGCTTATCCTGCTCGGCTTC 60.179 55.0 0.00 0.0 0.00 3.86 R
2819 5338 4.619394 GCATGATAGTTCAGGGATAGTCGG 60.619 50.0 0.00 0.0 34.26 4.79 R
3395 5916 1.908344 TGAGCATGCCTAGTTTGCAA 58.092 45.0 15.66 0.0 42.92 4.08 R
4810 7416 0.172803 GCATACCGAGAGTGGACGTT 59.827 55.0 0.00 0.0 0.00 3.99 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
40 42 9.676129 TTATCTAGTCAGGGAAGATATTTCCTT 57.324 33.333 0.00 0.00 38.61 3.36
41 43 7.366847 TCTAGTCAGGGAAGATATTTCCTTG 57.633 40.000 16.10 16.10 44.28 3.61
63 68 3.242739 GCCCAGAATATAAAGCACACACG 60.243 47.826 0.00 0.00 0.00 4.49
89 94 5.477984 TCCCAAGAATTGTCTTTCATTGAGG 59.522 40.000 0.00 0.00 46.99 3.86
456 466 2.132996 CCCTCTCATCTCCAGCGCT 61.133 63.158 2.64 2.64 0.00 5.92
997 1009 4.724279 AAAACTCAACCCACAGATAGGT 57.276 40.909 0.00 0.00 38.27 3.08
1186 1201 3.303938 GAGGTTGAGGATCCTGATGAGA 58.696 50.000 22.02 0.00 33.83 3.27
1233 1248 3.353557 ACGAGAGCTGTCCTACAACATA 58.646 45.455 5.11 0.00 0.00 2.29
1275 1290 4.308458 CTGTCCCCGTGTGGCGAA 62.308 66.667 0.00 0.00 44.77 4.70
1383 1405 6.275335 TGCCAAGAAAATCAAAGTTCTCAAG 58.725 36.000 0.00 0.00 32.90 3.02
1443 1465 3.748048 ACAAGGTTGATGATGTTGTCTCG 59.252 43.478 0.00 0.00 0.00 4.04
1495 1517 1.247567 ACCAGCATTTTTCACCGAGG 58.752 50.000 0.00 0.00 0.00 4.63
1686 1708 3.202097 TGAATGTCAAGCTTTCGTGTCA 58.798 40.909 0.00 0.00 34.93 3.58
2693 5212 4.037208 CCAGTTGAAATCCAGTATGATGGC 59.963 45.833 0.00 0.00 39.69 4.40
2819 5338 7.275920 ACTCACTTCCATATGATAAGGTTCAC 58.724 38.462 17.11 0.00 0.00 3.18
2935 5454 2.313234 CGAAGCTGAACACATGCTTTG 58.687 47.619 0.00 0.00 45.56 2.77
3188 5709 5.689819 CAACTGGCATGTCTGTTAGTTAAC 58.310 41.667 20.33 0.00 32.84 2.01
3300 5821 3.007920 AGGAGCTGGGCAGTCTGG 61.008 66.667 1.14 0.00 0.00 3.86
3358 5879 5.929992 GGCACATAAGTAGTACAAACAGTGA 59.070 40.000 2.52 0.00 0.00 3.41
3387 5908 4.122776 AGCTTATGCAGATAACTTGGTCG 58.877 43.478 3.16 0.00 42.74 4.79
3392 5913 2.299013 TGCAGATAACTTGGTCGTGTCT 59.701 45.455 0.00 0.00 0.00 3.41
3395 5916 4.810790 CAGATAACTTGGTCGTGTCTCTT 58.189 43.478 0.00 0.00 0.00 2.85
3653 6174 3.589288 ACCTGCCCTCTCTGTTATTTCTT 59.411 43.478 0.00 0.00 0.00 2.52
3681 6202 1.268899 CTTCAAGAACAGCAAGGCCTG 59.731 52.381 5.69 1.10 38.78 4.85
3826 6347 1.860326 GGTTCCATTTAATGCGCATGC 59.140 47.619 26.09 7.91 43.20 4.06
3917 6438 5.231357 CGTTGAGATAGTTTGTTATAGCGCA 59.769 40.000 11.47 0.00 0.00 6.09
4171 6700 1.415200 GGCACTTAGAGGGGTAGAGG 58.585 60.000 0.00 0.00 0.00 3.69
4182 6711 0.470268 GGGTAGAGGCTGGAGTAGGG 60.470 65.000 0.00 0.00 0.00 3.53
4283 6815 8.389779 TGCTGCGGAAATATAAAGATTGATTA 57.610 30.769 0.00 0.00 0.00 1.75
4353 6959 6.262273 ACTTTCGGAAGTAATTGTGTGTGAAT 59.738 34.615 7.51 0.00 44.13 2.57
4412 7018 6.813152 GCAACAATTATATTGGGGTATGCATC 59.187 38.462 0.19 0.00 0.00 3.91
4413 7019 6.757897 ACAATTATATTGGGGTATGCATCG 57.242 37.500 0.19 0.00 0.00 3.84
4415 7021 5.708736 ATTATATTGGGGTATGCATCGGA 57.291 39.130 0.19 0.00 0.00 4.55
4418 7024 5.912149 ATATTGGGGTATGCATCGGATAT 57.088 39.130 0.19 0.00 0.00 1.63
4419 7025 4.591321 ATTGGGGTATGCATCGGATATT 57.409 40.909 0.19 0.00 0.00 1.28
4420 7026 3.348647 TGGGGTATGCATCGGATATTG 57.651 47.619 0.19 0.00 0.00 1.90
4421 7027 2.642311 TGGGGTATGCATCGGATATTGT 59.358 45.455 0.19 0.00 0.00 2.71
4422 7028 3.270877 GGGGTATGCATCGGATATTGTC 58.729 50.000 0.19 0.00 0.00 3.18
4424 7030 4.565652 GGGGTATGCATCGGATATTGTCTT 60.566 45.833 0.19 0.00 0.00 3.01
4426 7032 5.106555 GGGTATGCATCGGATATTGTCTTTG 60.107 44.000 0.19 0.00 0.00 2.77
4428 7034 4.149511 TGCATCGGATATTGTCTTTGGA 57.850 40.909 0.00 0.00 0.00 3.53
4429 7035 4.129380 TGCATCGGATATTGTCTTTGGAG 58.871 43.478 0.00 0.00 0.00 3.86
4430 7036 3.499918 GCATCGGATATTGTCTTTGGAGG 59.500 47.826 0.00 0.00 0.00 4.30
4431 7037 3.194005 TCGGATATTGTCTTTGGAGGC 57.806 47.619 0.00 0.00 0.00 4.70
4432 7038 2.158813 TCGGATATTGTCTTTGGAGGCC 60.159 50.000 0.00 0.00 0.00 5.19
4434 7040 2.158813 GGATATTGTCTTTGGAGGCCGA 60.159 50.000 0.00 0.00 0.00 5.54
4435 7041 2.691409 TATTGTCTTTGGAGGCCGAG 57.309 50.000 0.00 0.00 0.00 4.63
4436 7042 0.678048 ATTGTCTTTGGAGGCCGAGC 60.678 55.000 0.00 0.00 0.00 5.03
4437 7043 1.768684 TTGTCTTTGGAGGCCGAGCT 61.769 55.000 0.00 0.00 0.00 4.09
4438 7044 1.448717 GTCTTTGGAGGCCGAGCTC 60.449 63.158 2.73 2.73 0.00 4.09
4440 7046 2.927856 TTTGGAGGCCGAGCTCCA 60.928 61.111 8.47 7.35 46.84 3.86
4442 7048 3.473647 TGGAGGCCGAGCTCCATG 61.474 66.667 8.47 0.00 44.02 3.66
4444 7050 3.157252 GAGGCCGAGCTCCATGGA 61.157 66.667 15.27 15.27 0.00 3.41
4445 7051 2.688666 AGGCCGAGCTCCATGGAA 60.689 61.111 17.00 0.00 0.00 3.53
4446 7052 2.257409 GAGGCCGAGCTCCATGGAAA 62.257 60.000 17.00 0.00 0.00 3.13
4447 7053 1.378514 GGCCGAGCTCCATGGAAAA 60.379 57.895 17.00 0.00 0.00 2.29
4450 7056 1.478105 GCCGAGCTCCATGGAAAATTT 59.522 47.619 17.00 0.00 0.00 1.82
4452 7058 3.514645 CCGAGCTCCATGGAAAATTTTG 58.485 45.455 17.00 3.03 0.00 2.44
4453 7059 3.193267 CCGAGCTCCATGGAAAATTTTGA 59.807 43.478 17.00 0.00 0.00 2.69
4454 7060 4.321899 CCGAGCTCCATGGAAAATTTTGAA 60.322 41.667 17.00 0.00 0.00 2.69
4455 7061 5.413499 CGAGCTCCATGGAAAATTTTGAAT 58.587 37.500 17.00 0.00 0.00 2.57
4457 7063 6.369615 CGAGCTCCATGGAAAATTTTGAATTT 59.630 34.615 17.00 0.00 0.00 1.82
4458 7064 7.095102 CGAGCTCCATGGAAAATTTTGAATTTT 60.095 33.333 17.00 10.24 34.30 1.82
4459 7065 7.878036 AGCTCCATGGAAAATTTTGAATTTTG 58.122 30.769 17.00 0.00 32.03 2.44
4460 7066 7.503230 AGCTCCATGGAAAATTTTGAATTTTGT 59.497 29.630 17.00 1.09 32.03 2.83
4461 7067 7.804600 GCTCCATGGAAAATTTTGAATTTTGTC 59.195 33.333 17.00 8.24 32.03 3.18
4465 7071 9.881529 CATGGAAAATTTTGAATTTTGTCGAAT 57.118 25.926 8.47 1.56 32.03 3.34
4528 7134 8.574251 AAACACACATAATATGAAGGCTAACA 57.426 30.769 7.33 0.00 0.00 2.41
4530 7136 7.109501 ACACACATAATATGAAGGCTAACACA 58.890 34.615 7.33 0.00 0.00 3.72
4531 7137 7.065803 ACACACATAATATGAAGGCTAACACAC 59.934 37.037 7.33 0.00 0.00 3.82
4532 7138 6.542370 ACACATAATATGAAGGCTAACACACC 59.458 38.462 7.33 0.00 0.00 4.16
4533 7139 6.767902 CACATAATATGAAGGCTAACACACCT 59.232 38.462 7.33 0.00 38.14 4.00
4534 7140 7.931407 CACATAATATGAAGGCTAACACACCTA 59.069 37.037 7.33 0.00 34.31 3.08
4535 7141 8.660435 ACATAATATGAAGGCTAACACACCTAT 58.340 33.333 7.33 0.00 34.31 2.57
4536 7142 8.939929 CATAATATGAAGGCTAACACACCTATG 58.060 37.037 0.00 0.00 34.31 2.23
4537 7143 4.844349 ATGAAGGCTAACACACCTATGT 57.156 40.909 0.00 0.00 40.80 2.29
4552 7158 5.650543 CACCTATGTGTAAATTTTCAGGGC 58.349 41.667 0.00 0.00 37.72 5.19
4553 7159 5.184864 CACCTATGTGTAAATTTTCAGGGCA 59.815 40.000 0.00 0.00 37.72 5.36
4554 7160 5.777732 ACCTATGTGTAAATTTTCAGGGCAA 59.222 36.000 0.00 0.00 0.00 4.52
4555 7161 6.268847 ACCTATGTGTAAATTTTCAGGGCAAA 59.731 34.615 0.00 0.00 0.00 3.68
4556 7162 7.158021 CCTATGTGTAAATTTTCAGGGCAAAA 58.842 34.615 0.00 0.00 0.00 2.44
4557 7163 7.823799 CCTATGTGTAAATTTTCAGGGCAAAAT 59.176 33.333 0.00 0.00 37.53 1.82
4558 7164 9.868277 CTATGTGTAAATTTTCAGGGCAAAATA 57.132 29.630 0.00 0.00 35.35 1.40
4560 7166 8.600449 TGTGTAAATTTTCAGGGCAAAATAAG 57.400 30.769 0.00 0.00 35.35 1.73
4561 7167 8.207545 TGTGTAAATTTTCAGGGCAAAATAAGT 58.792 29.630 0.00 0.00 35.35 2.24
4562 7168 9.051679 GTGTAAATTTTCAGGGCAAAATAAGTT 57.948 29.630 0.00 0.00 35.35 2.66
4563 7169 9.050601 TGTAAATTTTCAGGGCAAAATAAGTTG 57.949 29.630 0.00 0.00 35.35 3.16
4564 7170 9.267084 GTAAATTTTCAGGGCAAAATAAGTTGA 57.733 29.630 0.00 0.00 35.35 3.18
4565 7171 8.744568 AAATTTTCAGGGCAAAATAAGTTGAA 57.255 26.923 0.00 0.00 35.35 2.69
4566 7172 8.744568 AATTTTCAGGGCAAAATAAGTTGAAA 57.255 26.923 0.00 0.00 35.35 2.69
4567 7173 8.922931 ATTTTCAGGGCAAAATAAGTTGAAAT 57.077 26.923 0.00 0.00 34.77 2.17
4568 7174 7.727331 TTTCAGGGCAAAATAAGTTGAAATG 57.273 32.000 0.00 0.00 30.67 2.32
4569 7175 6.662865 TCAGGGCAAAATAAGTTGAAATGA 57.337 33.333 0.00 0.00 0.00 2.57
4570 7176 6.690530 TCAGGGCAAAATAAGTTGAAATGAG 58.309 36.000 0.00 0.00 0.00 2.90
4571 7177 5.870978 CAGGGCAAAATAAGTTGAAATGAGG 59.129 40.000 0.00 0.00 0.00 3.86
4572 7178 5.046376 AGGGCAAAATAAGTTGAAATGAGGG 60.046 40.000 0.00 0.00 0.00 4.30
4573 7179 5.279960 GGGCAAAATAAGTTGAAATGAGGGT 60.280 40.000 0.00 0.00 0.00 4.34
4574 7180 6.230472 GGCAAAATAAGTTGAAATGAGGGTT 58.770 36.000 0.00 0.00 0.00 4.11
4575 7181 6.147656 GGCAAAATAAGTTGAAATGAGGGTTG 59.852 38.462 0.00 0.00 0.00 3.77
4576 7182 6.705825 GCAAAATAAGTTGAAATGAGGGTTGT 59.294 34.615 0.00 0.00 0.00 3.32
4577 7183 7.307337 GCAAAATAAGTTGAAATGAGGGTTGTG 60.307 37.037 0.00 0.00 0.00 3.33
4578 7184 3.733443 AAGTTGAAATGAGGGTTGTGC 57.267 42.857 0.00 0.00 0.00 4.57
4579 7185 2.665165 AGTTGAAATGAGGGTTGTGCA 58.335 42.857 0.00 0.00 0.00 4.57
4580 7186 3.030291 AGTTGAAATGAGGGTTGTGCAA 58.970 40.909 0.00 0.00 0.00 4.08
4581 7187 3.450457 AGTTGAAATGAGGGTTGTGCAAA 59.550 39.130 0.00 0.00 0.00 3.68
4582 7188 4.081198 AGTTGAAATGAGGGTTGTGCAAAA 60.081 37.500 0.00 0.00 0.00 2.44
4583 7189 4.478206 TGAAATGAGGGTTGTGCAAAAA 57.522 36.364 0.00 0.00 0.00 1.94
4602 7208 5.372343 AAAAAGACAAATCTGGGGCTTTT 57.628 34.783 0.00 0.00 35.69 2.27
4603 7209 5.372343 AAAAGACAAATCTGGGGCTTTTT 57.628 34.783 0.00 0.00 34.48 1.94
4604 7210 6.493189 AAAAGACAAATCTGGGGCTTTTTA 57.507 33.333 0.00 0.00 34.48 1.52
4605 7211 6.493189 AAAGACAAATCTGGGGCTTTTTAA 57.507 33.333 0.00 0.00 34.48 1.52
4606 7212 5.468540 AGACAAATCTGGGGCTTTTTAAC 57.531 39.130 0.00 0.00 32.29 2.01
4607 7213 4.898861 AGACAAATCTGGGGCTTTTTAACA 59.101 37.500 0.00 0.00 32.29 2.41
4608 7214 4.956085 ACAAATCTGGGGCTTTTTAACAC 58.044 39.130 0.00 0.00 0.00 3.32
4609 7215 4.407296 ACAAATCTGGGGCTTTTTAACACA 59.593 37.500 0.00 0.00 0.00 3.72
4610 7216 5.071653 ACAAATCTGGGGCTTTTTAACACAT 59.928 36.000 0.00 0.00 0.00 3.21
4611 7217 4.806640 ATCTGGGGCTTTTTAACACATG 57.193 40.909 0.00 0.00 0.00 3.21
4612 7218 3.838565 TCTGGGGCTTTTTAACACATGA 58.161 40.909 0.00 0.00 0.00 3.07
4620 7226 8.135529 GGGGCTTTTTAACACATGATACTATTC 58.864 37.037 0.00 0.00 0.00 1.75
4629 7235 5.846164 ACACATGATACTATTCATCCTCCCA 59.154 40.000 0.00 0.00 34.09 4.37
4630 7236 6.013898 ACACATGATACTATTCATCCTCCCAG 60.014 42.308 0.00 0.00 34.09 4.45
4631 7237 5.486775 ACATGATACTATTCATCCTCCCAGG 59.513 44.000 0.00 0.00 34.09 4.45
4633 7239 1.439543 ACTATTCATCCTCCCAGGCC 58.560 55.000 0.00 0.00 34.61 5.19
4636 7242 0.481567 ATTCATCCTCCCAGGCCATG 59.518 55.000 5.01 0.00 34.61 3.66
4640 7246 1.133262 CATCCTCCCAGGCCATGAATT 60.133 52.381 5.01 0.00 34.61 2.17
4641 7247 1.009997 TCCTCCCAGGCCATGAATTT 58.990 50.000 5.01 0.00 34.61 1.82
4642 7248 1.117150 CCTCCCAGGCCATGAATTTG 58.883 55.000 5.01 0.00 0.00 2.32
4643 7249 1.620524 CCTCCCAGGCCATGAATTTGT 60.621 52.381 5.01 0.00 0.00 2.83
4644 7250 1.753073 CTCCCAGGCCATGAATTTGTC 59.247 52.381 5.01 0.00 0.00 3.18
4645 7251 1.358787 TCCCAGGCCATGAATTTGTCT 59.641 47.619 5.01 0.00 0.00 3.41
4646 7252 2.181975 CCCAGGCCATGAATTTGTCTT 58.818 47.619 5.01 0.00 0.00 3.01
4648 7254 3.008266 CCCAGGCCATGAATTTGTCTTTT 59.992 43.478 5.01 0.00 0.00 2.27
4649 7255 4.505390 CCCAGGCCATGAATTTGTCTTTTT 60.505 41.667 5.01 0.00 0.00 1.94
4671 7277 5.766150 TTTGTACAGGTCACATTTCAAGG 57.234 39.130 0.00 0.00 0.00 3.61
4672 7278 4.431416 TGTACAGGTCACATTTCAAGGT 57.569 40.909 0.00 0.00 0.00 3.50
4673 7279 4.787551 TGTACAGGTCACATTTCAAGGTT 58.212 39.130 0.00 0.00 0.00 3.50
4674 7280 5.197451 TGTACAGGTCACATTTCAAGGTTT 58.803 37.500 0.00 0.00 0.00 3.27
4675 7281 5.654650 TGTACAGGTCACATTTCAAGGTTTT 59.345 36.000 0.00 0.00 0.00 2.43
4676 7282 5.675684 ACAGGTCACATTTCAAGGTTTTT 57.324 34.783 0.00 0.00 0.00 1.94
4677 7283 5.660460 ACAGGTCACATTTCAAGGTTTTTC 58.340 37.500 0.00 0.00 0.00 2.29
4679 7285 6.127083 ACAGGTCACATTTCAAGGTTTTTCAT 60.127 34.615 0.00 0.00 0.00 2.57
4680 7286 6.762661 CAGGTCACATTTCAAGGTTTTTCATT 59.237 34.615 0.00 0.00 0.00 2.57
4681 7287 6.986231 AGGTCACATTTCAAGGTTTTTCATTC 59.014 34.615 0.00 0.00 0.00 2.67
4683 7289 8.141268 GGTCACATTTCAAGGTTTTTCATTCTA 58.859 33.333 0.00 0.00 0.00 2.10
4717 7323 9.502091 ACACACATAGACATAACATACTTGTTT 57.498 29.630 0.00 0.00 43.57 2.83
4724 7330 8.615878 AGACATAACATACTTGTTTACTTGCA 57.384 30.769 0.00 0.00 43.57 4.08
4725 7331 8.504005 AGACATAACATACTTGTTTACTTGCAC 58.496 33.333 0.00 0.00 43.57 4.57
4726 7332 8.160521 ACATAACATACTTGTTTACTTGCACA 57.839 30.769 0.00 0.00 43.57 4.57
4730 7336 8.940768 AACATACTTGTTTACTTGCACAATTT 57.059 26.923 0.00 0.00 43.57 1.82
4732 7338 9.377312 ACATACTTGTTTACTTGCACAATTTTT 57.623 25.926 0.00 0.00 32.50 1.94
4767 7373 9.952188 TTTTTGAAACCGAAAAGTTTGAATTTT 57.048 22.222 0.00 0.00 40.01 1.82
4768 7374 8.941127 TTTGAAACCGAAAAGTTTGAATTTTG 57.059 26.923 0.00 0.00 40.01 2.44
4769 7375 7.891183 TGAAACCGAAAAGTTTGAATTTTGA 57.109 28.000 0.00 0.00 40.01 2.69
4770 7376 8.485976 TGAAACCGAAAAGTTTGAATTTTGAT 57.514 26.923 0.00 0.00 40.01 2.57
4771 7377 8.940952 TGAAACCGAAAAGTTTGAATTTTGATT 58.059 25.926 0.00 0.00 40.01 2.57
4772 7378 9.767684 GAAACCGAAAAGTTTGAATTTTGATTT 57.232 25.926 0.00 0.00 40.01 2.17
4773 7379 9.553418 AAACCGAAAAGTTTGAATTTTGATTTG 57.447 25.926 0.00 0.00 38.51 2.32
4774 7380 8.262715 ACCGAAAAGTTTGAATTTTGATTTGT 57.737 26.923 0.00 0.00 30.22 2.83
4775 7381 8.726068 ACCGAAAAGTTTGAATTTTGATTTGTT 58.274 25.926 0.00 0.00 30.22 2.83
4776 7382 9.553418 CCGAAAAGTTTGAATTTTGATTTGTTT 57.447 25.926 0.00 0.00 30.22 2.83
4806 7412 3.554342 CTCCATGGCTCCCGGGAG 61.554 72.222 41.29 41.29 44.56 4.30
4814 7420 4.016706 CTCCCGGGAGCCAAACGT 62.017 66.667 36.90 0.00 35.31 3.99
4815 7421 3.952628 CTCCCGGGAGCCAAACGTC 62.953 68.421 36.90 0.00 35.31 4.34
4817 7423 4.323477 CCGGGAGCCAAACGTCCA 62.323 66.667 0.00 0.00 34.14 4.02
4818 7424 3.047877 CGGGAGCCAAACGTCCAC 61.048 66.667 0.00 0.00 34.14 4.02
4819 7425 2.430367 GGGAGCCAAACGTCCACT 59.570 61.111 0.00 0.00 34.14 4.00
4820 7426 1.671379 GGGAGCCAAACGTCCACTC 60.671 63.158 0.00 0.00 34.14 3.51
4821 7427 1.371558 GGAGCCAAACGTCCACTCT 59.628 57.895 0.00 0.00 32.55 3.24
4822 7428 0.670854 GGAGCCAAACGTCCACTCTC 60.671 60.000 0.00 0.00 32.55 3.20
4880 7486 3.417101 TGACGTGGCTTATTTGGTGATT 58.583 40.909 0.00 0.00 0.00 2.57
4882 7488 5.004448 TGACGTGGCTTATTTGGTGATTTA 58.996 37.500 0.00 0.00 0.00 1.40
4894 7500 1.952296 GGTGATTTAGAGGGCTGCATG 59.048 52.381 0.50 0.00 0.00 4.06
4896 7502 2.615912 GTGATTTAGAGGGCTGCATGTC 59.384 50.000 0.50 0.00 0.00 3.06
4904 7784 1.284198 AGGGCTGCATGTCAAGAGAAT 59.716 47.619 0.50 0.00 0.00 2.40
4905 7785 1.674962 GGGCTGCATGTCAAGAGAATC 59.325 52.381 0.50 0.00 0.00 2.52
4915 7795 6.035866 GCATGTCAAGAGAATCAGAGTTAGTG 59.964 42.308 0.00 0.00 37.82 2.74
4917 7797 5.047021 TGTCAAGAGAATCAGAGTTAGTGGG 60.047 44.000 0.00 0.00 37.82 4.61
4918 7798 4.467795 TCAAGAGAATCAGAGTTAGTGGGG 59.532 45.833 0.00 0.00 37.82 4.96
5000 7880 1.609208 TGGGTTTTTGCAGCTCTCTC 58.391 50.000 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 3.694072 GTGTGTGCTTTATATTCTGGGCA 59.306 43.478 0.00 0.00 0.00 5.36
41 43 3.242739 CGTGTGTGCTTTATATTCTGGGC 60.243 47.826 0.00 0.00 0.00 5.36
63 68 6.748132 TCAATGAAAGACAATTCTTGGGAAC 58.252 36.000 0.00 0.00 41.56 3.62
89 94 1.396815 CGAGGTTTCGTCGAACAAAGC 60.397 52.381 7.29 3.18 43.12 3.51
170 175 9.245481 CTTTTACCACCTATTTTATACAACCCA 57.755 33.333 0.00 0.00 0.00 4.51
855 866 0.608130 ATAGTGAGTGCGCAGGTGAA 59.392 50.000 12.22 0.00 0.00 3.18
997 1009 1.852309 ACATACAATGGCCTCCATCCA 59.148 47.619 3.32 0.00 44.40 3.41
1233 1248 3.195610 TGAAACTGTCGATGCCATACTCT 59.804 43.478 0.00 0.00 0.00 3.24
1383 1405 4.480386 GCTAACCTCAATAGCATCTTGC 57.520 45.455 0.91 0.00 44.11 4.01
1443 1465 0.179073 TGCTTATCCTGCTCGGCTTC 60.179 55.000 0.00 0.00 0.00 3.86
1495 1517 0.674895 ATGCCAACGAGCCTCTTCAC 60.675 55.000 0.00 0.00 0.00 3.18
1499 1521 0.254178 ATCAATGCCAACGAGCCTCT 59.746 50.000 0.00 0.00 0.00 3.69
1686 1708 0.549469 AGTCGGGTTTTTGGGACACT 59.451 50.000 0.00 0.00 39.29 3.55
2819 5338 4.619394 GCATGATAGTTCAGGGATAGTCGG 60.619 50.000 0.00 0.00 34.26 4.79
2935 5454 7.636326 TCTTACGGATTGAAAGTTTGAAAGAC 58.364 34.615 0.00 0.00 0.00 3.01
3300 5821 5.643777 TCAGCTCAAGTATTCTTAGTTTGGC 59.356 40.000 0.00 0.00 32.07 4.52
3358 5879 7.415989 CCAAGTTATCTGCATAAGCTTTCATGT 60.416 37.037 3.20 0.00 42.74 3.21
3387 5908 2.878406 TGCCTAGTTTGCAAAGAGACAC 59.122 45.455 13.26 0.00 35.40 3.67
3392 5913 2.489329 GAGCATGCCTAGTTTGCAAAGA 59.511 45.455 15.66 2.65 42.92 2.52
3395 5916 1.908344 TGAGCATGCCTAGTTTGCAA 58.092 45.000 15.66 0.00 42.92 4.08
3653 6174 5.649395 CCTTGCTGTTCTTGAAGATATCCAA 59.351 40.000 0.00 0.00 0.00 3.53
3681 6202 4.261114 GCTGCTGATAATGAGCCTTTCTTC 60.261 45.833 0.00 0.00 35.43 2.87
3826 6347 1.949525 CACCACTCAAAGGGAACACAG 59.050 52.381 0.00 0.00 0.00 3.66
3874 6395 1.126846 CGTGGAGATGTTTGAGCGAAC 59.873 52.381 0.00 0.00 0.00 3.95
3917 6438 1.670059 CCTCCACCTCCCTAACCTTT 58.330 55.000 0.00 0.00 0.00 3.11
4092 6616 4.280174 GGCCTACGAGAATGAATAGTACCA 59.720 45.833 0.00 0.00 0.00 3.25
4171 6700 2.383442 TCCTACATCCCTACTCCAGC 57.617 55.000 0.00 0.00 0.00 4.85
4182 6711 2.887152 GTTTCCATGCCCATCCTACATC 59.113 50.000 0.00 0.00 0.00 3.06
4303 6835 9.162764 GTAATAGCTTTTGATTTAGGTCACTCA 57.837 33.333 0.00 0.00 0.00 3.41
4314 6846 8.336801 ACTTCCGAAAGTAATAGCTTTTGATT 57.663 30.769 0.00 0.00 43.98 2.57
4353 6959 4.569162 GTCCAGCGTACATGCATACTTTTA 59.431 41.667 0.00 0.00 37.31 1.52
4365 6971 0.249120 CTCCAATGGTCCAGCGTACA 59.751 55.000 0.00 0.00 0.00 2.90
4412 7018 2.222027 GGCCTCCAAAGACAATATCCG 58.778 52.381 0.00 0.00 0.00 4.18
4413 7019 2.158813 TCGGCCTCCAAAGACAATATCC 60.159 50.000 0.00 0.00 0.00 2.59
4415 7021 2.746472 GCTCGGCCTCCAAAGACAATAT 60.746 50.000 0.00 0.00 0.00 1.28
4418 7024 1.302511 GCTCGGCCTCCAAAGACAA 60.303 57.895 0.00 0.00 0.00 3.18
4419 7025 2.172483 GAGCTCGGCCTCCAAAGACA 62.172 60.000 0.00 0.00 0.00 3.41
4420 7026 1.448717 GAGCTCGGCCTCCAAAGAC 60.449 63.158 0.00 0.00 0.00 3.01
4421 7027 2.982130 GAGCTCGGCCTCCAAAGA 59.018 61.111 0.00 0.00 0.00 2.52
4428 7034 1.852157 TTTTCCATGGAGCTCGGCCT 61.852 55.000 15.53 0.00 0.00 5.19
4429 7035 0.753111 ATTTTCCATGGAGCTCGGCC 60.753 55.000 15.53 0.00 0.00 6.13
4430 7036 1.106285 AATTTTCCATGGAGCTCGGC 58.894 50.000 15.53 0.00 0.00 5.54
4431 7037 3.193267 TCAAAATTTTCCATGGAGCTCGG 59.807 43.478 15.53 3.50 0.00 4.63
4432 7038 4.439305 TCAAAATTTTCCATGGAGCTCG 57.561 40.909 15.53 1.64 0.00 5.03
4434 7040 7.503230 ACAAAATTCAAAATTTTCCATGGAGCT 59.497 29.630 15.53 0.49 0.00 4.09
4435 7041 7.650890 ACAAAATTCAAAATTTTCCATGGAGC 58.349 30.769 15.53 0.00 0.00 4.70
4436 7042 8.011106 CGACAAAATTCAAAATTTTCCATGGAG 58.989 33.333 15.53 1.18 0.00 3.86
4437 7043 7.712639 TCGACAAAATTCAAAATTTTCCATGGA 59.287 29.630 11.44 11.44 0.00 3.41
4438 7044 7.859598 TCGACAAAATTCAAAATTTTCCATGG 58.140 30.769 4.97 4.97 0.00 3.66
4501 7107 9.855021 GTTAGCCTTCATATTATGTGTGTTTTT 57.145 29.630 3.67 0.00 0.00 1.94
4504 7110 7.609918 TGTGTTAGCCTTCATATTATGTGTGTT 59.390 33.333 3.67 0.00 0.00 3.32
4505 7111 7.065803 GTGTGTTAGCCTTCATATTATGTGTGT 59.934 37.037 3.67 0.00 0.00 3.72
4506 7112 7.409697 GTGTGTTAGCCTTCATATTATGTGTG 58.590 38.462 3.67 0.00 0.00 3.82
4508 7114 6.767902 AGGTGTGTTAGCCTTCATATTATGTG 59.232 38.462 3.67 0.00 0.00 3.21
4509 7115 6.900194 AGGTGTGTTAGCCTTCATATTATGT 58.100 36.000 3.67 0.00 0.00 2.29
4510 7116 8.939929 CATAGGTGTGTTAGCCTTCATATTATG 58.060 37.037 0.00 0.00 36.38 1.90
4511 7117 8.660435 ACATAGGTGTGTTAGCCTTCATATTAT 58.340 33.333 0.00 0.00 37.14 1.28
4512 7118 8.029782 ACATAGGTGTGTTAGCCTTCATATTA 57.970 34.615 0.00 0.00 37.14 0.98
4513 7119 6.900194 ACATAGGTGTGTTAGCCTTCATATT 58.100 36.000 0.00 0.00 37.14 1.28
4515 7121 5.950544 ACATAGGTGTGTTAGCCTTCATA 57.049 39.130 0.00 0.00 37.14 2.15
4530 7136 5.329399 TGCCCTGAAAATTTACACATAGGT 58.671 37.500 0.00 0.00 0.00 3.08
4531 7137 5.913137 TGCCCTGAAAATTTACACATAGG 57.087 39.130 0.00 0.00 0.00 2.57
4532 7138 8.776376 ATTTTGCCCTGAAAATTTACACATAG 57.224 30.769 0.00 0.00 32.70 2.23
4534 7140 9.218440 CTTATTTTGCCCTGAAAATTTACACAT 57.782 29.630 0.00 0.00 36.94 3.21
4535 7141 8.207545 ACTTATTTTGCCCTGAAAATTTACACA 58.792 29.630 0.00 0.00 36.94 3.72
4536 7142 8.601845 ACTTATTTTGCCCTGAAAATTTACAC 57.398 30.769 0.00 0.00 36.94 2.90
4537 7143 9.050601 CAACTTATTTTGCCCTGAAAATTTACA 57.949 29.630 0.00 0.00 36.94 2.41
4538 7144 9.267084 TCAACTTATTTTGCCCTGAAAATTTAC 57.733 29.630 0.00 0.00 36.94 2.01
4539 7145 9.838339 TTCAACTTATTTTGCCCTGAAAATTTA 57.162 25.926 0.00 0.00 36.94 1.40
4540 7146 8.744568 TTCAACTTATTTTGCCCTGAAAATTT 57.255 26.923 0.00 0.00 36.94 1.82
4541 7147 8.744568 TTTCAACTTATTTTGCCCTGAAAATT 57.255 26.923 0.00 0.00 36.94 1.82
4542 7148 8.785946 CATTTCAACTTATTTTGCCCTGAAAAT 58.214 29.630 0.00 0.00 38.69 1.82
4543 7149 7.989741 TCATTTCAACTTATTTTGCCCTGAAAA 59.010 29.630 0.00 0.00 35.59 2.29
4544 7150 7.504403 TCATTTCAACTTATTTTGCCCTGAAA 58.496 30.769 0.00 0.00 36.19 2.69
4545 7151 7.060383 TCATTTCAACTTATTTTGCCCTGAA 57.940 32.000 0.00 0.00 0.00 3.02
4546 7152 6.295236 CCTCATTTCAACTTATTTTGCCCTGA 60.295 38.462 0.00 0.00 0.00 3.86
4547 7153 5.870978 CCTCATTTCAACTTATTTTGCCCTG 59.129 40.000 0.00 0.00 0.00 4.45
4548 7154 5.046376 CCCTCATTTCAACTTATTTTGCCCT 60.046 40.000 0.00 0.00 0.00 5.19
4549 7155 5.178061 CCCTCATTTCAACTTATTTTGCCC 58.822 41.667 0.00 0.00 0.00 5.36
4550 7156 5.793817 ACCCTCATTTCAACTTATTTTGCC 58.206 37.500 0.00 0.00 0.00 4.52
4551 7157 6.705825 ACAACCCTCATTTCAACTTATTTTGC 59.294 34.615 0.00 0.00 0.00 3.68
4552 7158 7.307337 GCACAACCCTCATTTCAACTTATTTTG 60.307 37.037 0.00 0.00 0.00 2.44
4553 7159 6.705825 GCACAACCCTCATTTCAACTTATTTT 59.294 34.615 0.00 0.00 0.00 1.82
4554 7160 6.183360 TGCACAACCCTCATTTCAACTTATTT 60.183 34.615 0.00 0.00 0.00 1.40
4555 7161 5.304101 TGCACAACCCTCATTTCAACTTATT 59.696 36.000 0.00 0.00 0.00 1.40
4556 7162 4.832266 TGCACAACCCTCATTTCAACTTAT 59.168 37.500 0.00 0.00 0.00 1.73
4557 7163 4.211125 TGCACAACCCTCATTTCAACTTA 58.789 39.130 0.00 0.00 0.00 2.24
4558 7164 3.030291 TGCACAACCCTCATTTCAACTT 58.970 40.909 0.00 0.00 0.00 2.66
4559 7165 2.665165 TGCACAACCCTCATTTCAACT 58.335 42.857 0.00 0.00 0.00 3.16
4560 7166 3.451141 TTGCACAACCCTCATTTCAAC 57.549 42.857 0.00 0.00 0.00 3.18
4561 7167 4.478206 TTTTGCACAACCCTCATTTCAA 57.522 36.364 0.00 0.00 0.00 2.69
4562 7168 4.478206 TTTTTGCACAACCCTCATTTCA 57.522 36.364 0.00 0.00 0.00 2.69
4580 7186 5.372343 AAAAGCCCCAGATTTGTCTTTTT 57.628 34.783 0.00 0.00 31.97 1.94
4581 7187 5.372343 AAAAAGCCCCAGATTTGTCTTTT 57.628 34.783 0.00 0.00 35.89 2.27
4582 7188 6.126911 TGTTAAAAAGCCCCAGATTTGTCTTT 60.127 34.615 0.00 0.00 30.45 2.52
4583 7189 5.365314 TGTTAAAAAGCCCCAGATTTGTCTT 59.635 36.000 0.00 0.00 30.45 3.01
4584 7190 4.898861 TGTTAAAAAGCCCCAGATTTGTCT 59.101 37.500 0.00 0.00 30.45 3.41
4585 7191 4.988540 GTGTTAAAAAGCCCCAGATTTGTC 59.011 41.667 0.00 0.00 30.45 3.18
4586 7192 4.407296 TGTGTTAAAAAGCCCCAGATTTGT 59.593 37.500 0.00 0.00 30.45 2.83
4587 7193 4.954875 TGTGTTAAAAAGCCCCAGATTTG 58.045 39.130 0.00 0.00 30.45 2.32
4588 7194 5.306678 TCATGTGTTAAAAAGCCCCAGATTT 59.693 36.000 0.00 0.00 31.52 2.17
4589 7195 4.837860 TCATGTGTTAAAAAGCCCCAGATT 59.162 37.500 0.00 0.00 0.00 2.40
4590 7196 4.415596 TCATGTGTTAAAAAGCCCCAGAT 58.584 39.130 0.00 0.00 0.00 2.90
4591 7197 3.838565 TCATGTGTTAAAAAGCCCCAGA 58.161 40.909 0.00 0.00 0.00 3.86
4592 7198 4.806640 ATCATGTGTTAAAAAGCCCCAG 57.193 40.909 0.00 0.00 0.00 4.45
4593 7199 5.329399 AGTATCATGTGTTAAAAAGCCCCA 58.671 37.500 0.00 0.00 0.00 4.96
4594 7200 5.914898 AGTATCATGTGTTAAAAAGCCCC 57.085 39.130 0.00 0.00 0.00 5.80
4595 7201 8.682710 TGAATAGTATCATGTGTTAAAAAGCCC 58.317 33.333 0.00 0.00 0.00 5.19
4601 7207 9.778741 GGAGGATGAATAGTATCATGTGTTAAA 57.221 33.333 0.00 0.00 40.08 1.52
4602 7208 8.375506 GGGAGGATGAATAGTATCATGTGTTAA 58.624 37.037 0.00 0.00 40.08 2.01
4603 7209 7.512402 TGGGAGGATGAATAGTATCATGTGTTA 59.488 37.037 0.00 0.00 40.08 2.41
4604 7210 6.329986 TGGGAGGATGAATAGTATCATGTGTT 59.670 38.462 0.00 0.00 40.08 3.32
4605 7211 5.846164 TGGGAGGATGAATAGTATCATGTGT 59.154 40.000 0.00 0.00 40.08 3.72
4606 7212 6.364568 TGGGAGGATGAATAGTATCATGTG 57.635 41.667 0.00 0.00 40.08 3.21
4607 7213 5.486775 CCTGGGAGGATGAATAGTATCATGT 59.513 44.000 0.00 0.00 40.08 3.21
4608 7214 5.628666 GCCTGGGAGGATGAATAGTATCATG 60.629 48.000 0.00 0.00 40.08 3.07
4609 7215 4.472833 GCCTGGGAGGATGAATAGTATCAT 59.527 45.833 0.00 0.00 42.62 2.45
4610 7216 3.840666 GCCTGGGAGGATGAATAGTATCA 59.159 47.826 0.00 0.00 37.67 2.15
4611 7217 3.198853 GGCCTGGGAGGATGAATAGTATC 59.801 52.174 0.00 0.00 37.67 2.24
4612 7218 3.185455 GGCCTGGGAGGATGAATAGTAT 58.815 50.000 0.00 0.00 37.67 2.12
4620 7226 0.481567 ATTCATGGCCTGGGAGGATG 59.518 55.000 3.32 0.00 37.67 3.51
4623 7229 1.117150 CAAATTCATGGCCTGGGAGG 58.883 55.000 3.32 0.00 38.80 4.30
4648 7254 5.654650 ACCTTGAAATGTGACCTGTACAAAA 59.345 36.000 0.00 0.00 0.00 2.44
4649 7255 5.197451 ACCTTGAAATGTGACCTGTACAAA 58.803 37.500 0.00 0.00 0.00 2.83
4651 7257 4.431416 ACCTTGAAATGTGACCTGTACA 57.569 40.909 0.00 0.00 0.00 2.90
4652 7258 5.767816 AAACCTTGAAATGTGACCTGTAC 57.232 39.130 0.00 0.00 0.00 2.90
4653 7259 6.378564 TGAAAAACCTTGAAATGTGACCTGTA 59.621 34.615 0.00 0.00 0.00 2.74
4654 7260 5.186797 TGAAAAACCTTGAAATGTGACCTGT 59.813 36.000 0.00 0.00 0.00 4.00
4655 7261 5.659463 TGAAAAACCTTGAAATGTGACCTG 58.341 37.500 0.00 0.00 0.00 4.00
4656 7262 5.930837 TGAAAAACCTTGAAATGTGACCT 57.069 34.783 0.00 0.00 0.00 3.85
4658 7264 9.528018 TTAGAATGAAAAACCTTGAAATGTGAC 57.472 29.630 0.00 0.00 0.00 3.67
4706 7312 8.940768 AAAATTGTGCAAGTAAACAAGTATGT 57.059 26.923 0.00 0.00 43.14 2.29
4741 7347 9.952188 AAAATTCAAACTTTTCGGTTTCAAAAA 57.048 22.222 0.00 0.00 37.32 1.94
4742 7348 9.387123 CAAAATTCAAACTTTTCGGTTTCAAAA 57.613 25.926 0.00 0.00 37.32 2.44
4743 7349 8.774586 TCAAAATTCAAACTTTTCGGTTTCAAA 58.225 25.926 0.00 0.00 37.32 2.69
4747 7353 9.553418 CAAATCAAAATTCAAACTTTTCGGTTT 57.447 25.926 0.00 0.00 39.62 3.27
4789 7395 3.554342 CTCCCGGGAGCCATGGAG 61.554 72.222 36.90 12.91 36.38 3.86
4797 7403 3.952628 GACGTTTGGCTCCCGGGAG 62.953 68.421 41.29 41.29 44.56 4.30
4798 7404 4.011517 GACGTTTGGCTCCCGGGA 62.012 66.667 25.06 25.06 0.00 5.14
4800 7406 4.323477 TGGACGTTTGGCTCCCGG 62.323 66.667 0.00 0.00 0.00 5.73
4801 7407 3.047877 GTGGACGTTTGGCTCCCG 61.048 66.667 0.00 0.00 0.00 5.14
4802 7408 1.671379 GAGTGGACGTTTGGCTCCC 60.671 63.158 0.00 0.00 0.00 4.30
4803 7409 0.670854 GAGAGTGGACGTTTGGCTCC 60.671 60.000 0.00 0.00 0.00 4.70
4804 7410 1.009389 CGAGAGTGGACGTTTGGCTC 61.009 60.000 0.00 0.00 0.00 4.70
4805 7411 1.006102 CGAGAGTGGACGTTTGGCT 60.006 57.895 0.00 0.00 0.00 4.75
4806 7412 2.027625 CCGAGAGTGGACGTTTGGC 61.028 63.158 0.00 0.00 0.00 4.52
4807 7413 0.599558 TACCGAGAGTGGACGTTTGG 59.400 55.000 0.00 0.00 0.00 3.28
4808 7414 2.259618 CATACCGAGAGTGGACGTTTG 58.740 52.381 0.00 0.00 0.00 2.93
4809 7415 1.403780 GCATACCGAGAGTGGACGTTT 60.404 52.381 0.00 0.00 0.00 3.60
4810 7416 0.172803 GCATACCGAGAGTGGACGTT 59.827 55.000 0.00 0.00 0.00 3.99
4811 7417 0.963856 TGCATACCGAGAGTGGACGT 60.964 55.000 0.00 0.00 0.00 4.34
4812 7418 0.385751 ATGCATACCGAGAGTGGACG 59.614 55.000 0.00 0.00 0.00 4.79
4813 7419 1.137086 ACATGCATACCGAGAGTGGAC 59.863 52.381 0.00 0.00 0.00 4.02
4814 7420 1.136891 CACATGCATACCGAGAGTGGA 59.863 52.381 0.00 0.00 0.00 4.02
4815 7421 1.575244 CACATGCATACCGAGAGTGG 58.425 55.000 0.00 0.00 0.00 4.00
4816 7422 0.933097 GCACATGCATACCGAGAGTG 59.067 55.000 0.00 2.53 41.59 3.51
4817 7423 0.826715 AGCACATGCATACCGAGAGT 59.173 50.000 6.64 0.00 45.16 3.24
4818 7424 2.223805 TGTAGCACATGCATACCGAGAG 60.224 50.000 6.64 0.00 45.16 3.20
4819 7425 1.754226 TGTAGCACATGCATACCGAGA 59.246 47.619 6.64 0.00 45.16 4.04
4820 7426 2.223537 TGTAGCACATGCATACCGAG 57.776 50.000 6.64 0.00 45.16 4.63
4821 7427 2.682155 TTGTAGCACATGCATACCGA 57.318 45.000 6.64 0.00 45.16 4.69
4822 7428 3.755965 TTTTGTAGCACATGCATACCG 57.244 42.857 6.64 0.00 45.16 4.02
4854 7460 3.627577 ACCAAATAAGCCACGTCATCATC 59.372 43.478 0.00 0.00 0.00 2.92
4880 7486 1.908619 TCTTGACATGCAGCCCTCTAA 59.091 47.619 0.00 0.00 0.00 2.10
4882 7488 0.252479 CTCTTGACATGCAGCCCTCT 59.748 55.000 0.00 0.00 0.00 3.69
4894 7500 5.415221 CCCACTAACTCTGATTCTCTTGAC 58.585 45.833 0.00 0.00 0.00 3.18
4896 7502 4.467795 TCCCCACTAACTCTGATTCTCTTG 59.532 45.833 0.00 0.00 0.00 3.02
4904 7784 7.989947 AATAGTTTATCCCCACTAACTCTGA 57.010 36.000 0.00 0.00 33.28 3.27
4905 7785 9.765795 CTAAATAGTTTATCCCCACTAACTCTG 57.234 37.037 0.00 0.00 33.28 3.35
4942 7822 3.362706 AGGACGCTGAACAGTAATCCTA 58.637 45.455 16.19 0.00 35.70 2.94
4944 7824 2.674796 AGGACGCTGAACAGTAATCC 57.325 50.000 3.77 7.97 0.00 3.01
5000 7880 1.009900 CTAGTAGGCTTCGTCGGCG 60.010 63.158 1.15 1.15 39.92 6.46


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

AutoCloner maintained by Alex Coulton.