Multiple sequence alignment - TraesCS1D01G089900

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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 TraesCS1D01G089900 chr1D 100.000 3553 0 0 1 3553 75914179 75917731 0.000000e+00 6562
1 TraesCS1D01G089900 chr1D 94.270 1780 79 13 735 2511 75767975 75766216 0.000000e+00 2700
2 TraesCS1D01G089900 chr1D 90.235 1874 98 31 690 2511 75841829 75839989 0.000000e+00 2368
3 TraesCS1D01G089900 chr1D 96.587 293 7 3 3261 3553 140213336 140213625 1.920000e-132 483
4 TraesCS1D01G089900 chr1A 92.745 1847 97 26 691 2511 76539443 76537608 0.000000e+00 2634
5 TraesCS1D01G089900 chr1A 93.898 1737 80 19 792 2524 76728540 76730254 0.000000e+00 2597
6 TraesCS1D01G089900 chr1A 92.225 746 43 7 1 732 76725773 76726517 0.000000e+00 1042
7 TraesCS1D01G089900 chr1A 77.220 259 36 10 240 490 76540429 76540186 2.880000e-26 130
8 TraesCS1D01G089900 chr1B 90.404 2032 127 36 606 2610 119578579 119580569 0.000000e+00 2610
9 TraesCS1D01G089900 chr1B 93.451 1756 74 18 758 2511 119494752 119493036 0.000000e+00 2567
10 TraesCS1D01G089900 chr1B 94.017 1404 76 8 843 2243 119250100 119248702 0.000000e+00 2121
11 TraesCS1D01G089900 chr1B 93.273 996 66 1 1516 2511 119219553 119218559 0.000000e+00 1467
12 TraesCS1D01G089900 chr1B 94.366 284 16 0 2236 2519 119248322 119248039 1.510000e-118 436
13 TraesCS1D01G089900 chr1B 94.604 278 13 1 1 276 119577631 119577908 2.530000e-116 429
14 TraesCS1D01G089900 chr1B 91.135 282 13 4 276 546 119578288 119578568 4.330000e-99 372
15 TraesCS1D01G089900 chr1B 78.742 461 44 30 241 671 119250772 119250336 3.520000e-65 259
16 TraesCS1D01G089900 chr1B 95.238 63 3 0 222 284 119292770 119292708 2.260000e-17 100
17 TraesCS1D01G089900 chr2D 97.010 669 20 0 2615 3283 8972387 8971719 0.000000e+00 1125
18 TraesCS1D01G089900 chr2D 96.856 668 18 3 2616 3283 575684953 575685617 0.000000e+00 1114
19 TraesCS1D01G089900 chr2D 98.227 282 4 1 3272 3553 303134041 303133761 3.190000e-135 492
20 TraesCS1D01G089900 chr2D 86.833 281 30 7 2612 2890 572033372 572033097 1.240000e-79 307
21 TraesCS1D01G089900 chr2D 87.778 180 17 3 2940 3119 575685445 575685619 4.650000e-49 206
22 TraesCS1D01G089900 chr2D 85.556 180 21 3 2940 3119 8971891 8971717 2.180000e-42 183
23 TraesCS1D01G089900 chr6D 96.269 670 25 0 2614 3283 452911403 452910734 0.000000e+00 1099
24 TraesCS1D01G089900 chr6D 98.929 280 2 1 3275 3553 465810544 465810823 1.900000e-137 499
25 TraesCS1D01G089900 chr6D 87.222 180 18 3 2940 3119 452910906 452910732 2.160000e-47 200
26 TraesCS1D01G089900 chr7D 95.958 668 24 1 2616 3283 619113542 619114206 0.000000e+00 1081
27 TraesCS1D01G089900 chr7D 81.538 780 122 13 1731 2508 9390913 9390154 1.080000e-174 623
28 TraesCS1D01G089900 chr7D 99.278 277 2 0 3277 3553 596419271 596419547 5.300000e-138 501
29 TraesCS1D01G089900 chr7D 97.902 286 4 2 3269 3553 396592492 396592776 8.860000e-136 494
30 TraesCS1D01G089900 chr7D 86.594 276 31 6 2616 2890 575145667 575145397 2.070000e-77 300
31 TraesCS1D01G089900 chr7D 78.796 382 77 4 1063 1442 9393707 9393328 1.640000e-63 254
32 TraesCS1D01G089900 chr5A 89.806 412 23 1 2872 3283 28397215 28396823 8.800000e-141 510
33 TraesCS1D01G089900 chr5A 94.737 266 12 2 2616 2880 28419778 28419514 2.550000e-111 412
34 TraesCS1D01G089900 chr5A 87.222 180 18 3 2940 3119 28396995 28396821 2.160000e-47 200
35 TraesCS1D01G089900 chr4D 100.000 274 0 0 3280 3553 35785465 35785738 1.140000e-139 507
36 TraesCS1D01G089900 chr4D 99.638 276 0 1 3279 3553 402932776 402932501 1.470000e-138 503
37 TraesCS1D01G089900 chr5D 99.278 277 1 1 3278 3553 148805404 148805128 1.900000e-137 499
38 TraesCS1D01G089900 chr5D 81.081 444 63 15 2617 3059 443905916 443905493 5.680000e-88 335
39 TraesCS1D01G089900 chr5D 80.952 441 66 14 2616 3056 456594113 456594535 2.040000e-87 333
40 TraesCS1D01G089900 chr3D 100.000 270 0 0 3284 3553 309260478 309260209 1.900000e-137 499
41 TraesCS1D01G089900 chr7A 79.841 377 70 6 1069 1442 9264086 9263713 1.630000e-68 270


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 TraesCS1D01G089900 chr1D 75914179 75917731 3552 False 6562.000000 6562 100.000000 1 3553 1 chr1D.!!$F1 3552
1 TraesCS1D01G089900 chr1D 75766216 75767975 1759 True 2700.000000 2700 94.270000 735 2511 1 chr1D.!!$R1 1776
2 TraesCS1D01G089900 chr1D 75839989 75841829 1840 True 2368.000000 2368 90.235000 690 2511 1 chr1D.!!$R2 1821
3 TraesCS1D01G089900 chr1A 76725773 76730254 4481 False 1819.500000 2597 93.061500 1 2524 2 chr1A.!!$F1 2523
4 TraesCS1D01G089900 chr1A 76537608 76540429 2821 True 1382.000000 2634 84.982500 240 2511 2 chr1A.!!$R1 2271
5 TraesCS1D01G089900 chr1B 119493036 119494752 1716 True 2567.000000 2567 93.451000 758 2511 1 chr1B.!!$R3 1753
6 TraesCS1D01G089900 chr1B 119218559 119219553 994 True 1467.000000 1467 93.273000 1516 2511 1 chr1B.!!$R1 995
7 TraesCS1D01G089900 chr1B 119577631 119580569 2938 False 1137.000000 2610 92.047667 1 2610 3 chr1B.!!$F1 2609
8 TraesCS1D01G089900 chr1B 119248039 119250772 2733 True 938.666667 2121 89.041667 241 2519 3 chr1B.!!$R4 2278
9 TraesCS1D01G089900 chr2D 575684953 575685619 666 False 660.000000 1114 92.317000 2616 3283 2 chr2D.!!$F1 667
10 TraesCS1D01G089900 chr2D 8971717 8972387 670 True 654.000000 1125 91.283000 2615 3283 2 chr2D.!!$R3 668
11 TraesCS1D01G089900 chr6D 452910732 452911403 671 True 649.500000 1099 91.745500 2614 3283 2 chr6D.!!$R1 669
12 TraesCS1D01G089900 chr7D 619113542 619114206 664 False 1081.000000 1081 95.958000 2616 3283 1 chr7D.!!$F3 667
13 TraesCS1D01G089900 chr7D 9390154 9393707 3553 True 438.500000 623 80.167000 1063 2508 2 chr7D.!!$R2 1445

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
875 3837 0.179078 TGCCGTCAACGTTACCAACT 60.179 50.0 0.0 0.0 37.74 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2598 8178 0.173708 CTCGGTTCAGGAGCAGGTAC 59.826 60.0 0.0 0.0 0.0 3.34 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
131 134 1.914051 CTCGCGTCACAGATGTACTTG 59.086 52.381 5.77 0.00 0.00 3.16
166 169 1.404477 AAACAAAACATGCTACGCGC 58.596 45.000 5.73 0.00 39.77 6.86
262 265 3.044059 GCAACCATGAGACCAGCGC 62.044 63.158 0.00 0.00 0.00 5.92
284 671 3.948473 CCGGTCGATCTCATCCATACTAT 59.052 47.826 0.00 0.00 0.00 2.12
301 688 2.818432 ACTATTACTACCGGCCTGATCG 59.182 50.000 0.00 0.00 0.00 3.69
513 930 3.640498 GGTAGCTCCGTATATATTCCCCC 59.360 52.174 0.00 0.00 0.00 5.40
540 957 0.730834 CAGAGGCGACAGACACGAAG 60.731 60.000 0.00 0.00 0.00 3.79
574 993 4.207955 TCCAGCCACTACATACTAGTCTG 58.792 47.826 0.00 1.93 0.00 3.51
675 1258 4.682787 TGAAACATGCCGTAGACTGATAG 58.317 43.478 0.00 0.00 0.00 2.08
722 1679 2.182030 GGAAGGCCGACGAGTCAG 59.818 66.667 0.00 0.00 0.00 3.51
732 1693 0.179097 GACGAGTCAGGAGGGAATGC 60.179 60.000 0.00 0.00 0.00 3.56
742 3340 1.612463 GGAGGGAATGCTCGTACGTAT 59.388 52.381 16.05 5.92 0.00 3.06
774 3384 4.746309 TGGCATGCCAGCAGGACC 62.746 66.667 35.59 6.59 41.89 4.46
782 3392 2.743718 CAGCAGGACCGTTCACCT 59.256 61.111 0.00 0.00 36.92 4.00
875 3837 0.179078 TGCCGTCAACGTTACCAACT 60.179 50.000 0.00 0.00 37.74 3.16
998 3963 2.899256 ACACTAACCTACGCTAACCCAA 59.101 45.455 0.00 0.00 0.00 4.12
999 3964 3.256558 CACTAACCTACGCTAACCCAAC 58.743 50.000 0.00 0.00 0.00 3.77
1000 3965 2.899256 ACTAACCTACGCTAACCCAACA 59.101 45.455 0.00 0.00 0.00 3.33
1001 3966 2.174363 AACCTACGCTAACCCAACAC 57.826 50.000 0.00 0.00 0.00 3.32
1037 4022 1.612156 CCACACAACACAAACACACG 58.388 50.000 0.00 0.00 0.00 4.49
1082 4075 1.672356 AGCAATGGCAGTGACGGTC 60.672 57.895 20.42 0.00 44.61 4.79
1157 4152 0.036022 GCAAGAAGGTGCCTCTCACT 59.964 55.000 0.00 0.00 44.98 3.41
1340 4335 4.657824 CACCTCAACGACGCCGGT 62.658 66.667 1.90 0.00 40.78 5.28
1473 4470 6.426025 AGGAAGAGTATTTTTACACGTCCAAC 59.574 38.462 14.23 0.00 39.91 3.77
1504 4532 8.866956 AGTTTCTACACGTAACATAAAGCATAC 58.133 33.333 1.35 0.00 0.00 2.39
1513 4567 8.585881 ACGTAACATAAAGCATACCAGATATCT 58.414 33.333 0.00 0.00 0.00 1.98
1806 6999 3.181494 CGGCGTATGATCACCGGAATATA 60.181 47.826 9.46 0.00 41.95 0.86
1853 7046 1.343478 CCACTCCTATGGTGTCCTCCT 60.343 57.143 0.00 0.00 34.77 3.69
2508 8088 3.906218 AGCAGATATGCTACTCCATGGAA 59.094 43.478 14.39 0.00 44.28 3.53
2589 8169 7.633361 ATGTACACGAGTAACACTACAAAAG 57.367 36.000 0.00 0.00 30.67 2.27
2607 8187 6.164176 ACAAAAGTGTAGTATGTACCTGCTC 58.836 40.000 0.00 0.00 35.72 4.26
2608 8188 5.340439 AAAGTGTAGTATGTACCTGCTCC 57.660 43.478 0.00 0.00 0.00 4.70
2609 8189 4.252570 AGTGTAGTATGTACCTGCTCCT 57.747 45.455 0.00 0.00 0.00 3.69
2610 8190 3.954904 AGTGTAGTATGTACCTGCTCCTG 59.045 47.826 0.00 0.00 0.00 3.86
2611 8191 3.952323 GTGTAGTATGTACCTGCTCCTGA 59.048 47.826 0.00 0.00 0.00 3.86
2612 8192 4.401519 GTGTAGTATGTACCTGCTCCTGAA 59.598 45.833 0.00 0.00 0.00 3.02
2708 8288 6.458342 CCAAAAATCACTAATTCCGAGGCTAC 60.458 42.308 0.00 0.00 0.00 3.58
2781 8361 2.204090 AAGTGGGTCCCGGTGGAT 60.204 61.111 2.65 0.00 44.28 3.41
2785 8365 2.284493 GGGTCCCGGTGGATAGGA 59.716 66.667 0.00 0.00 44.28 2.94
2905 8485 4.642466 AAAAGAAAGAGGAGGGAATCGT 57.358 40.909 0.00 0.00 0.00 3.73
3283 8863 3.710722 CTGGACAAGGAGCCGGCT 61.711 66.667 33.48 33.48 0.00 5.52
3284 8864 3.965539 CTGGACAAGGAGCCGGCTG 62.966 68.421 38.41 23.53 0.00 4.85
3285 8865 3.706373 GGACAAGGAGCCGGCTGA 61.706 66.667 38.41 0.00 0.00 4.26
3286 8866 2.347490 GACAAGGAGCCGGCTGAA 59.653 61.111 38.41 0.00 0.00 3.02
3287 8867 1.743252 GACAAGGAGCCGGCTGAAG 60.743 63.158 38.41 22.54 0.00 3.02
3288 8868 2.437359 CAAGGAGCCGGCTGAAGG 60.437 66.667 38.41 17.25 0.00 3.46
3289 8869 2.607750 AAGGAGCCGGCTGAAGGA 60.608 61.111 38.41 0.00 0.00 3.36
3290 8870 2.224159 AAGGAGCCGGCTGAAGGAA 61.224 57.895 38.41 0.00 0.00 3.36
3291 8871 1.779061 AAGGAGCCGGCTGAAGGAAA 61.779 55.000 38.41 0.00 0.00 3.13
3292 8872 1.077429 GGAGCCGGCTGAAGGAAAT 60.077 57.895 38.41 6.10 0.00 2.17
3293 8873 0.180406 GGAGCCGGCTGAAGGAAATA 59.820 55.000 38.41 0.00 0.00 1.40
3294 8874 1.202818 GGAGCCGGCTGAAGGAAATAT 60.203 52.381 38.41 4.41 0.00 1.28
3295 8875 1.876156 GAGCCGGCTGAAGGAAATATG 59.124 52.381 38.41 0.00 0.00 1.78
3296 8876 0.312102 GCCGGCTGAAGGAAATATGC 59.688 55.000 22.15 0.00 0.00 3.14
3297 8877 0.954452 CCGGCTGAAGGAAATATGCC 59.046 55.000 0.00 0.00 37.24 4.40
3298 8878 0.954452 CGGCTGAAGGAAATATGCCC 59.046 55.000 0.00 0.00 37.29 5.36
3299 8879 1.477558 CGGCTGAAGGAAATATGCCCT 60.478 52.381 0.00 0.00 37.29 5.19
3300 8880 2.224523 CGGCTGAAGGAAATATGCCCTA 60.225 50.000 0.00 0.00 37.29 3.53
3301 8881 3.416156 GGCTGAAGGAAATATGCCCTAG 58.584 50.000 0.00 0.00 34.81 3.02
3302 8882 3.073062 GGCTGAAGGAAATATGCCCTAGA 59.927 47.826 0.00 0.00 34.81 2.43
3303 8883 4.322567 GCTGAAGGAAATATGCCCTAGAG 58.677 47.826 0.00 0.00 31.36 2.43
3304 8884 4.805609 GCTGAAGGAAATATGCCCTAGAGG 60.806 50.000 0.00 0.00 39.47 3.69
3379 8959 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
3380 8960 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
3381 8961 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
3382 8962 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
3383 8963 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
3384 8964 6.879993 TGCTAGAATTGTATTAACCGGAAACA 59.120 34.615 9.46 1.34 0.00 2.83
3385 8965 7.554835 TGCTAGAATTGTATTAACCGGAAACAT 59.445 33.333 9.46 0.00 0.00 2.71
3386 8966 7.855904 GCTAGAATTGTATTAACCGGAAACATG 59.144 37.037 9.46 0.00 0.00 3.21
3387 8967 7.931578 AGAATTGTATTAACCGGAAACATGA 57.068 32.000 9.46 0.00 0.00 3.07
3388 8968 8.519799 AGAATTGTATTAACCGGAAACATGAT 57.480 30.769 9.46 0.00 0.00 2.45
3389 8969 9.621629 AGAATTGTATTAACCGGAAACATGATA 57.378 29.630 9.46 0.00 0.00 2.15
3390 8970 9.659830 GAATTGTATTAACCGGAAACATGATAC 57.340 33.333 9.46 7.13 0.00 2.24
3391 8971 8.740123 ATTGTATTAACCGGAAACATGATACA 57.260 30.769 9.46 9.57 0.00 2.29
3392 8972 8.740123 TTGTATTAACCGGAAACATGATACAT 57.260 30.769 9.46 0.00 31.27 2.29
3393 8973 8.148807 TGTATTAACCGGAAACATGATACATG 57.851 34.615 9.46 9.72 0.00 3.21
3394 8974 7.771361 TGTATTAACCGGAAACATGATACATGT 59.229 33.333 9.46 10.94 0.00 3.21
3395 8975 4.963276 AACCGGAAACATGATACATGTG 57.037 40.909 9.46 7.59 31.80 3.21
3396 8976 3.950397 ACCGGAAACATGATACATGTGT 58.050 40.909 9.46 11.88 31.80 3.72
3397 8977 3.689161 ACCGGAAACATGATACATGTGTG 59.311 43.478 9.46 4.81 31.80 3.82
3398 8978 3.938334 CCGGAAACATGATACATGTGTGA 59.062 43.478 16.29 0.00 31.80 3.58
3399 8979 4.394610 CCGGAAACATGATACATGTGTGAA 59.605 41.667 16.29 0.00 31.80 3.18
3400 8980 5.066375 CCGGAAACATGATACATGTGTGAAT 59.934 40.000 16.29 0.00 31.80 2.57
3401 8981 6.259829 CCGGAAACATGATACATGTGTGAATA 59.740 38.462 16.29 0.00 31.80 1.75
3402 8982 7.125755 CGGAAACATGATACATGTGTGAATAC 58.874 38.462 16.29 1.40 31.80 1.89
3403 8983 7.201600 CGGAAACATGATACATGTGTGAATACA 60.202 37.037 16.29 0.00 34.63 2.29
3404 8984 8.623903 GGAAACATGATACATGTGTGAATACAT 58.376 33.333 16.29 0.00 41.77 2.29
3408 8988 9.481340 ACATGATACATGTGTGAATACATAGAC 57.519 33.333 15.11 0.00 39.17 2.59
3409 8989 9.480053 CATGATACATGTGTGAATACATAGACA 57.520 33.333 9.11 0.00 39.17 3.41
3411 8991 9.883142 TGATACATGTGTGAATACATAGACAAA 57.117 29.630 9.11 0.00 39.17 2.83
3413 8993 7.977789 ACATGTGTGAATACATAGACAAACA 57.022 32.000 0.00 0.00 39.17 2.83
3414 8994 8.032952 ACATGTGTGAATACATAGACAAACAG 57.967 34.615 0.00 0.00 39.17 3.16
3415 8995 7.877612 ACATGTGTGAATACATAGACAAACAGA 59.122 33.333 0.00 0.00 39.17 3.41
3416 8996 7.889589 TGTGTGAATACATAGACAAACAGAG 57.110 36.000 0.00 0.00 39.39 3.35
3417 8997 7.441836 TGTGTGAATACATAGACAAACAGAGT 58.558 34.615 0.00 0.00 39.39 3.24
3418 8998 7.384932 TGTGTGAATACATAGACAAACAGAGTG 59.615 37.037 0.00 0.00 39.39 3.51
3419 8999 7.385205 GTGTGAATACATAGACAAACAGAGTGT 59.615 37.037 0.00 0.00 39.39 3.55
3420 9000 7.598869 TGTGAATACATAGACAAACAGAGTGTC 59.401 37.037 0.00 0.00 44.75 3.67
3421 9001 7.598869 GTGAATACATAGACAAACAGAGTGTCA 59.401 37.037 7.26 0.00 46.44 3.58
3422 9002 7.598869 TGAATACATAGACAAACAGAGTGTCAC 59.401 37.037 7.26 0.00 46.44 3.67
3423 9003 5.537300 ACATAGACAAACAGAGTGTCACT 57.463 39.130 4.81 4.81 46.44 3.41
3424 9004 6.650427 ACATAGACAAACAGAGTGTCACTA 57.350 37.500 5.21 0.00 46.44 2.74
3425 9005 6.682746 ACATAGACAAACAGAGTGTCACTAG 58.317 40.000 5.21 4.44 46.44 2.57
3426 9006 6.265649 ACATAGACAAACAGAGTGTCACTAGT 59.734 38.462 5.21 5.11 46.44 2.57
3427 9007 7.447545 ACATAGACAAACAGAGTGTCACTAGTA 59.552 37.037 5.21 0.00 46.44 1.82
3428 9008 6.902771 AGACAAACAGAGTGTCACTAGTAT 57.097 37.500 5.21 0.00 46.44 2.12
3429 9009 6.682746 AGACAAACAGAGTGTCACTAGTATG 58.317 40.000 5.21 5.56 46.44 2.39
3430 9010 5.230942 ACAAACAGAGTGTCACTAGTATGC 58.769 41.667 5.21 0.00 0.00 3.14
3431 9011 4.457834 AACAGAGTGTCACTAGTATGCC 57.542 45.455 5.21 0.00 0.00 4.40
3432 9012 3.702792 ACAGAGTGTCACTAGTATGCCT 58.297 45.455 5.21 0.00 0.00 4.75
3433 9013 3.697045 ACAGAGTGTCACTAGTATGCCTC 59.303 47.826 5.21 0.00 0.00 4.70
3434 9014 3.951037 CAGAGTGTCACTAGTATGCCTCT 59.049 47.826 5.21 1.89 0.00 3.69
3435 9015 5.126779 CAGAGTGTCACTAGTATGCCTCTA 58.873 45.833 5.21 0.00 0.00 2.43
3436 9016 5.008217 CAGAGTGTCACTAGTATGCCTCTAC 59.992 48.000 5.21 0.00 0.00 2.59
3437 9017 5.104277 AGAGTGTCACTAGTATGCCTCTACT 60.104 44.000 5.21 0.00 36.04 2.57
3438 9018 5.511363 AGTGTCACTAGTATGCCTCTACTT 58.489 41.667 2.87 0.00 33.96 2.24
3439 9019 5.358442 AGTGTCACTAGTATGCCTCTACTTG 59.642 44.000 2.87 0.00 33.96 3.16
3440 9020 5.357314 GTGTCACTAGTATGCCTCTACTTGA 59.643 44.000 0.00 0.18 33.96 3.02
3441 9021 5.357314 TGTCACTAGTATGCCTCTACTTGAC 59.643 44.000 0.00 11.98 38.64 3.18
3442 9022 5.591067 GTCACTAGTATGCCTCTACTTGACT 59.409 44.000 0.00 0.00 36.95 3.41
3443 9023 6.766944 GTCACTAGTATGCCTCTACTTGACTA 59.233 42.308 0.00 0.00 36.95 2.59
3444 9024 6.993308 TCACTAGTATGCCTCTACTTGACTAG 59.007 42.308 0.00 0.00 40.35 2.57
3445 9025 5.766174 ACTAGTATGCCTCTACTTGACTAGC 59.234 44.000 0.00 0.00 38.86 3.42
3446 9026 4.798882 AGTATGCCTCTACTTGACTAGCT 58.201 43.478 0.00 0.00 0.00 3.32
3447 9027 4.825085 AGTATGCCTCTACTTGACTAGCTC 59.175 45.833 0.00 0.00 0.00 4.09
3448 9028 2.017782 TGCCTCTACTTGACTAGCTCG 58.982 52.381 0.00 0.00 0.00 5.03
3449 9029 2.018515 GCCTCTACTTGACTAGCTCGT 58.981 52.381 0.00 0.00 0.00 4.18
3450 9030 2.424246 GCCTCTACTTGACTAGCTCGTT 59.576 50.000 0.00 0.00 0.00 3.85
3451 9031 3.732471 GCCTCTACTTGACTAGCTCGTTG 60.732 52.174 0.00 0.00 0.00 4.10
3452 9032 3.690139 CCTCTACTTGACTAGCTCGTTGA 59.310 47.826 0.00 0.00 0.00 3.18
3453 9033 4.336993 CCTCTACTTGACTAGCTCGTTGAT 59.663 45.833 0.00 0.00 0.00 2.57
3454 9034 5.487153 TCTACTTGACTAGCTCGTTGATC 57.513 43.478 0.00 0.00 0.00 2.92
3455 9035 4.941873 TCTACTTGACTAGCTCGTTGATCA 59.058 41.667 0.00 0.00 0.00 2.92
3456 9036 4.521130 ACTTGACTAGCTCGTTGATCAA 57.479 40.909 3.38 3.38 0.00 2.57
3457 9037 4.883083 ACTTGACTAGCTCGTTGATCAAA 58.117 39.130 10.35 0.00 0.00 2.69
3458 9038 4.926238 ACTTGACTAGCTCGTTGATCAAAG 59.074 41.667 10.35 12.64 0.00 2.77
3459 9039 4.783764 TGACTAGCTCGTTGATCAAAGA 57.216 40.909 20.62 20.62 0.00 2.52
3460 9040 5.330455 TGACTAGCTCGTTGATCAAAGAT 57.670 39.130 21.83 12.82 0.00 2.40
3461 9041 5.105063 TGACTAGCTCGTTGATCAAAGATG 58.895 41.667 21.83 16.63 0.00 2.90
3462 9042 4.437239 ACTAGCTCGTTGATCAAAGATGG 58.563 43.478 21.83 14.18 0.00 3.51
3463 9043 3.340814 AGCTCGTTGATCAAAGATGGT 57.659 42.857 21.83 17.63 0.00 3.55
3464 9044 3.679389 AGCTCGTTGATCAAAGATGGTT 58.321 40.909 21.83 8.86 0.00 3.67
3465 9045 4.832248 AGCTCGTTGATCAAAGATGGTTA 58.168 39.130 21.83 1.90 0.00 2.85
3466 9046 5.431765 AGCTCGTTGATCAAAGATGGTTAT 58.568 37.500 21.83 4.91 0.00 1.89
3467 9047 5.295292 AGCTCGTTGATCAAAGATGGTTATG 59.705 40.000 21.83 11.16 0.00 1.90
3468 9048 5.065218 GCTCGTTGATCAAAGATGGTTATGT 59.935 40.000 21.83 0.00 0.00 2.29
3469 9049 6.403636 GCTCGTTGATCAAAGATGGTTATGTT 60.404 38.462 21.83 0.00 0.00 2.71
3470 9050 7.447374 TCGTTGATCAAAGATGGTTATGTTT 57.553 32.000 18.50 0.00 30.61 2.83
3471 9051 7.526608 TCGTTGATCAAAGATGGTTATGTTTC 58.473 34.615 18.50 0.00 28.23 2.78
3472 9052 6.747280 CGTTGATCAAAGATGGTTATGTTTCC 59.253 38.462 15.34 0.00 28.23 3.13
3473 9053 7.362056 CGTTGATCAAAGATGGTTATGTTTCCT 60.362 37.037 15.34 0.00 28.23 3.36
3474 9054 8.956426 GTTGATCAAAGATGGTTATGTTTCCTA 58.044 33.333 10.35 0.00 28.23 2.94
3475 9055 8.737168 TGATCAAAGATGGTTATGTTTCCTAG 57.263 34.615 0.00 0.00 28.23 3.02
3476 9056 7.283127 TGATCAAAGATGGTTATGTTTCCTAGC 59.717 37.037 0.00 0.00 28.23 3.42
3477 9057 5.885912 TCAAAGATGGTTATGTTTCCTAGCC 59.114 40.000 0.00 0.00 28.23 3.93
3478 9058 5.450818 AAGATGGTTATGTTTCCTAGCCA 57.549 39.130 0.00 0.00 34.50 4.75
3479 9059 5.653255 AGATGGTTATGTTTCCTAGCCAT 57.347 39.130 0.00 0.00 41.28 4.40
3480 9060 6.763715 AGATGGTTATGTTTCCTAGCCATA 57.236 37.500 0.00 0.00 39.44 2.74
3481 9061 6.773638 AGATGGTTATGTTTCCTAGCCATAG 58.226 40.000 0.00 0.00 39.44 2.23
3482 9062 6.558775 AGATGGTTATGTTTCCTAGCCATAGA 59.441 38.462 0.00 0.00 39.44 1.98
3483 9063 5.925509 TGGTTATGTTTCCTAGCCATAGAC 58.074 41.667 0.00 0.00 0.00 2.59
3484 9064 5.427157 TGGTTATGTTTCCTAGCCATAGACA 59.573 40.000 0.00 0.00 0.00 3.41
3485 9065 6.101150 TGGTTATGTTTCCTAGCCATAGACAT 59.899 38.462 0.00 0.00 32.04 3.06
3486 9066 6.428159 GGTTATGTTTCCTAGCCATAGACATG 59.572 42.308 0.00 0.00 30.64 3.21
3487 9067 5.894298 ATGTTTCCTAGCCATAGACATGA 57.106 39.130 0.00 0.00 33.67 3.07
3488 9068 5.282055 TGTTTCCTAGCCATAGACATGAG 57.718 43.478 0.00 0.00 33.67 2.90
3489 9069 4.716784 TGTTTCCTAGCCATAGACATGAGT 59.283 41.667 0.00 0.00 33.67 3.41
3490 9070 5.189736 TGTTTCCTAGCCATAGACATGAGTT 59.810 40.000 0.00 0.00 33.67 3.01
3491 9071 4.944619 TCCTAGCCATAGACATGAGTTG 57.055 45.455 0.00 0.00 33.67 3.16
3492 9072 4.290093 TCCTAGCCATAGACATGAGTTGT 58.710 43.478 0.00 0.00 42.79 3.32
3506 9086 6.611381 ACATGAGTTGTCATTTGATTAACGG 58.389 36.000 0.00 0.00 40.84 4.44
3507 9087 5.621197 TGAGTTGTCATTTGATTAACGGG 57.379 39.130 0.00 0.00 32.73 5.28
3508 9088 5.309638 TGAGTTGTCATTTGATTAACGGGA 58.690 37.500 0.00 0.00 32.73 5.14
3509 9089 5.943416 TGAGTTGTCATTTGATTAACGGGAT 59.057 36.000 0.00 0.00 32.73 3.85
3510 9090 6.093495 TGAGTTGTCATTTGATTAACGGGATC 59.907 38.462 0.00 0.00 32.73 3.36
3511 9091 5.943416 AGTTGTCATTTGATTAACGGGATCA 59.057 36.000 0.00 0.00 32.73 2.92
3512 9092 6.603201 AGTTGTCATTTGATTAACGGGATCAT 59.397 34.615 0.00 0.00 33.82 2.45
3513 9093 7.773224 AGTTGTCATTTGATTAACGGGATCATA 59.227 33.333 0.00 0.00 33.82 2.15
3514 9094 8.567948 GTTGTCATTTGATTAACGGGATCATAT 58.432 33.333 0.00 0.00 33.82 1.78
3515 9095 8.322906 TGTCATTTGATTAACGGGATCATATC 57.677 34.615 0.00 0.00 33.82 1.63
3516 9096 7.936301 TGTCATTTGATTAACGGGATCATATCA 59.064 33.333 0.00 0.00 33.82 2.15
3517 9097 8.950210 GTCATTTGATTAACGGGATCATATCAT 58.050 33.333 0.00 0.00 33.82 2.45
3518 9098 9.519191 TCATTTGATTAACGGGATCATATCATT 57.481 29.630 0.00 0.00 33.82 2.57
3521 9101 9.448438 TTTGATTAACGGGATCATATCATTAGG 57.552 33.333 0.00 0.00 33.82 2.69
3522 9102 8.374184 TGATTAACGGGATCATATCATTAGGA 57.626 34.615 0.00 0.00 0.00 2.94
3523 9103 8.478066 TGATTAACGGGATCATATCATTAGGAG 58.522 37.037 0.00 0.00 0.00 3.69
3524 9104 8.609617 ATTAACGGGATCATATCATTAGGAGA 57.390 34.615 0.00 0.00 0.00 3.71
3525 9105 6.935240 AACGGGATCATATCATTAGGAGAA 57.065 37.500 0.00 0.00 0.00 2.87
3526 9106 7.502060 AACGGGATCATATCATTAGGAGAAT 57.498 36.000 0.00 0.00 0.00 2.40
3527 9107 6.882656 ACGGGATCATATCATTAGGAGAATG 58.117 40.000 0.00 0.00 0.00 2.67
3528 9108 6.669591 ACGGGATCATATCATTAGGAGAATGA 59.330 38.462 2.66 2.66 40.50 2.57
3529 9109 7.346698 ACGGGATCATATCATTAGGAGAATGAT 59.653 37.037 15.12 15.12 46.01 2.45
3530 9110 7.656542 CGGGATCATATCATTAGGAGAATGATG 59.343 40.741 18.59 8.24 44.49 3.07
3531 9111 8.492782 GGGATCATATCATTAGGAGAATGATGT 58.507 37.037 18.59 11.75 44.49 3.06
3538 9118 8.618702 ATCATTAGGAGAATGATGTGATTGAC 57.381 34.615 11.08 0.00 43.52 3.18
3539 9119 7.799081 TCATTAGGAGAATGATGTGATTGACT 58.201 34.615 0.00 0.00 32.21 3.41
3540 9120 8.270030 TCATTAGGAGAATGATGTGATTGACTT 58.730 33.333 0.00 0.00 32.21 3.01
3541 9121 7.854557 TTAGGAGAATGATGTGATTGACTTG 57.145 36.000 0.00 0.00 0.00 3.16
3542 9122 6.058553 AGGAGAATGATGTGATTGACTTGA 57.941 37.500 0.00 0.00 0.00 3.02
3543 9123 5.879223 AGGAGAATGATGTGATTGACTTGAC 59.121 40.000 0.00 0.00 0.00 3.18
3544 9124 5.065731 GGAGAATGATGTGATTGACTTGACC 59.934 44.000 0.00 0.00 0.00 4.02
3545 9125 4.946157 AGAATGATGTGATTGACTTGACCC 59.054 41.667 0.00 0.00 0.00 4.46
3546 9126 3.786368 TGATGTGATTGACTTGACCCA 57.214 42.857 0.00 0.00 0.00 4.51
3547 9127 4.305539 TGATGTGATTGACTTGACCCAT 57.694 40.909 0.00 0.00 0.00 4.00
3548 9128 4.665451 TGATGTGATTGACTTGACCCATT 58.335 39.130 0.00 0.00 0.00 3.16
3549 9129 4.701651 TGATGTGATTGACTTGACCCATTC 59.298 41.667 0.00 0.00 0.00 2.67
3550 9130 3.420893 TGTGATTGACTTGACCCATTCC 58.579 45.455 0.00 0.00 0.00 3.01
3551 9131 2.420022 GTGATTGACTTGACCCATTCCG 59.580 50.000 0.00 0.00 0.00 4.30
3552 9132 2.039746 TGATTGACTTGACCCATTCCGT 59.960 45.455 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 72 2.677037 CGGTGTGAACCACTTCCCTATC 60.677 54.545 0.00 0.00 43.94 2.08
131 134 0.721483 GTTTACTCACAAGTGCGCGC 60.721 55.000 27.26 27.26 36.92 6.86
166 169 2.983136 CGATCTTCCTGAATCGATTCCG 59.017 50.000 30.16 24.69 38.67 4.30
262 265 2.163509 AGTATGGATGAGATCGACCGG 58.836 52.381 0.00 0.00 0.00 5.28
284 671 0.742505 CACGATCAGGCCGGTAGTAA 59.257 55.000 1.90 0.00 0.00 2.24
513 930 2.221981 GTCTGTCGCCTCTGAGTTTTTG 59.778 50.000 3.66 0.00 0.00 2.44
540 957 3.412386 AGTGGCTGGAACATCAGTAAAC 58.588 45.455 0.00 0.00 38.20 2.01
541 958 3.788227 AGTGGCTGGAACATCAGTAAA 57.212 42.857 0.00 0.00 38.20 2.01
574 993 1.475682 CCGTAACTAGACCCCACTGAC 59.524 57.143 0.00 0.00 0.00 3.51
675 1258 2.164219 TCCCCTCGTCAATACAACGTAC 59.836 50.000 0.00 0.00 40.86 3.67
716 1673 0.103937 CGAGCATTCCCTCCTGACTC 59.896 60.000 0.00 0.00 0.00 3.36
718 1675 1.112113 TACGAGCATTCCCTCCTGAC 58.888 55.000 0.00 0.00 0.00 3.51
722 1679 1.027357 TACGTACGAGCATTCCCTCC 58.973 55.000 24.41 0.00 0.00 4.30
732 1693 4.499399 CAGAATGGTGTTCATACGTACGAG 59.501 45.833 24.41 11.35 34.44 4.18
774 3384 5.289675 CAGAGATTAGTAAAGCAGGTGAACG 59.710 44.000 0.00 0.00 0.00 3.95
782 3392 2.550978 GGCGCAGAGATTAGTAAAGCA 58.449 47.619 10.83 0.00 0.00 3.91
875 3837 5.860941 TTGGCTGGTTAGTCAAAAATTGA 57.139 34.783 0.00 0.00 44.98 2.57
998 3963 1.396996 GCTCGTTGTCTTGTGTTGTGT 59.603 47.619 0.00 0.00 0.00 3.72
999 3964 1.268032 GGCTCGTTGTCTTGTGTTGTG 60.268 52.381 0.00 0.00 0.00 3.33
1000 3965 1.014352 GGCTCGTTGTCTTGTGTTGT 58.986 50.000 0.00 0.00 0.00 3.32
1001 3966 1.013596 TGGCTCGTTGTCTTGTGTTG 58.986 50.000 0.00 0.00 0.00 3.33
1082 4075 1.057822 CGTGCTCTGCGTGATTTCG 59.942 57.895 0.00 0.00 0.00 3.46
1187 4182 3.908081 GCGAAGACGGCCGGGATA 61.908 66.667 31.76 0.00 40.15 2.59
1340 4335 1.301716 GGCCTCGAGAACAAGCACA 60.302 57.895 15.71 0.00 0.00 4.57
1504 4532 7.691213 TCAACCCTAGAGTACTAGATATCTGG 58.309 42.308 15.79 14.91 46.34 3.86
1513 4567 6.212791 AGCATGTTTTCAACCCTAGAGTACTA 59.787 38.462 0.00 0.00 0.00 1.82
1547 4602 0.664761 CTGCAACCCAACAGTGTCAG 59.335 55.000 0.00 0.00 0.00 3.51
1806 6999 1.188219 TGAGCTCGCCCTTGAACTCT 61.188 55.000 9.64 0.00 33.30 3.24
1853 7046 3.054875 CAGGTTCTTGATCCTGTCCATGA 60.055 47.826 15.86 0.00 44.19 3.07
1878 7071 1.296392 CTCATCCGGGAAGTGCACA 59.704 57.895 21.04 0.00 0.00 4.57
1920 7113 4.742201 CTACAGCGCGTGCCCACT 62.742 66.667 19.02 0.00 44.31 4.00
2566 8146 6.563422 ACTTTTGTAGTGTTACTCGTGTACA 58.437 36.000 0.00 0.00 35.19 2.90
2589 8169 3.952323 TCAGGAGCAGGTACATACTACAC 59.048 47.826 0.00 0.00 0.00 2.90
2594 8174 2.481449 CGGTTCAGGAGCAGGTACATAC 60.481 54.545 0.00 0.00 0.00 2.39
2595 8175 1.754803 CGGTTCAGGAGCAGGTACATA 59.245 52.381 0.00 0.00 0.00 2.29
2596 8176 0.537188 CGGTTCAGGAGCAGGTACAT 59.463 55.000 0.00 0.00 0.00 2.29
2598 8178 0.173708 CTCGGTTCAGGAGCAGGTAC 59.826 60.000 0.00 0.00 0.00 3.34
2599 8179 0.251653 ACTCGGTTCAGGAGCAGGTA 60.252 55.000 0.00 0.00 34.87 3.08
2600 8180 1.534235 ACTCGGTTCAGGAGCAGGT 60.534 57.895 0.00 0.00 34.87 4.00
2601 8181 1.079543 CACTCGGTTCAGGAGCAGG 60.080 63.158 0.00 0.00 34.87 4.85
2604 8184 1.734465 CAATTCACTCGGTTCAGGAGC 59.266 52.381 0.00 0.00 34.87 4.70
2607 8187 1.466167 CTGCAATTCACTCGGTTCAGG 59.534 52.381 0.00 0.00 0.00 3.86
2608 8188 2.416747 TCTGCAATTCACTCGGTTCAG 58.583 47.619 0.00 0.00 0.00 3.02
2609 8189 2.542020 TCTGCAATTCACTCGGTTCA 57.458 45.000 0.00 0.00 0.00 3.18
2610 8190 3.896648 TTTCTGCAATTCACTCGGTTC 57.103 42.857 0.00 0.00 0.00 3.62
2611 8191 3.380004 TGTTTTCTGCAATTCACTCGGTT 59.620 39.130 0.00 0.00 0.00 4.44
2612 8192 2.948979 TGTTTTCTGCAATTCACTCGGT 59.051 40.909 0.00 0.00 0.00 4.69
2781 8361 0.613572 TGTCCTGCCACGTCATCCTA 60.614 55.000 0.00 0.00 0.00 2.94
2785 8365 1.277842 TGTTATGTCCTGCCACGTCAT 59.722 47.619 0.00 0.00 0.00 3.06
2905 8485 0.313987 TGCTCTCTTTCGCGAACTCA 59.686 50.000 23.33 6.26 0.00 3.41
2916 8496 2.359230 GGCCGTTGCTGCTCTCTT 60.359 61.111 0.00 0.00 37.74 2.85
3038 8618 3.953775 CGGTGGAGCCAGGGTGTT 61.954 66.667 0.00 0.00 36.97 3.32
3180 8760 1.748403 GGTGTGTGGCTCTGAGACA 59.252 57.895 9.67 9.67 0.00 3.41
3222 8802 0.321919 ACGACTGGAGTACGCCTGTA 60.322 55.000 24.32 1.25 39.79 2.74
3283 8863 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
3295 8875 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19
3353 8933 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.00 35.82 1.75
3354 8934 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
3355 8935 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
3356 8936 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
3357 8937 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
3358 8938 7.554835 TGTTTCCGGTTAATACAATTCTAGCAT 59.445 33.333 0.00 0.00 0.00 3.79
3359 8939 6.879993 TGTTTCCGGTTAATACAATTCTAGCA 59.120 34.615 0.00 0.00 0.00 3.49
3360 8940 7.311364 TGTTTCCGGTTAATACAATTCTAGC 57.689 36.000 0.00 0.00 0.00 3.42
3361 8941 9.104965 TCATGTTTCCGGTTAATACAATTCTAG 57.895 33.333 0.00 0.00 0.00 2.43
3362 8942 9.621629 ATCATGTTTCCGGTTAATACAATTCTA 57.378 29.630 0.00 0.00 0.00 2.10
3363 8943 7.931578 TCATGTTTCCGGTTAATACAATTCT 57.068 32.000 0.00 0.00 0.00 2.40
3364 8944 9.659830 GTATCATGTTTCCGGTTAATACAATTC 57.340 33.333 0.00 0.00 0.00 2.17
3365 8945 9.179909 TGTATCATGTTTCCGGTTAATACAATT 57.820 29.630 0.00 0.00 0.00 2.32
3366 8946 8.740123 TGTATCATGTTTCCGGTTAATACAAT 57.260 30.769 0.00 0.00 0.00 2.71
3367 8947 8.616942 CATGTATCATGTTTCCGGTTAATACAA 58.383 33.333 0.00 0.00 33.52 2.41
3368 8948 7.771361 ACATGTATCATGTTTCCGGTTAATACA 59.229 33.333 0.00 7.97 34.10 2.29
3369 8949 8.067784 CACATGTATCATGTTTCCGGTTAATAC 58.932 37.037 11.89 2.60 0.00 1.89
3370 8950 7.771361 ACACATGTATCATGTTTCCGGTTAATA 59.229 33.333 11.89 0.00 0.00 0.98
3371 8951 6.601613 ACACATGTATCATGTTTCCGGTTAAT 59.398 34.615 11.89 0.00 0.00 1.40
3372 8952 5.941058 ACACATGTATCATGTTTCCGGTTAA 59.059 36.000 11.89 0.00 0.00 2.01
3373 8953 5.352846 CACACATGTATCATGTTTCCGGTTA 59.647 40.000 11.89 0.00 0.00 2.85
3374 8954 4.155826 CACACATGTATCATGTTTCCGGTT 59.844 41.667 11.89 0.00 0.00 4.44
3375 8955 3.689161 CACACATGTATCATGTTTCCGGT 59.311 43.478 11.89 5.17 0.00 5.28
3376 8956 3.938334 TCACACATGTATCATGTTTCCGG 59.062 43.478 11.89 0.00 0.00 5.14
3377 8957 5.544136 TTCACACATGTATCATGTTTCCG 57.456 39.130 11.89 4.94 0.00 4.30
3378 8958 7.984391 TGTATTCACACATGTATCATGTTTCC 58.016 34.615 11.89 0.00 0.00 3.13
3382 8962 9.481340 GTCTATGTATTCACACATGTATCATGT 57.519 33.333 9.21 9.21 39.46 3.21
3383 8963 9.480053 TGTCTATGTATTCACACATGTATCATG 57.520 33.333 0.00 7.99 39.46 3.07
3385 8965 9.883142 TTTGTCTATGTATTCACACATGTATCA 57.117 29.630 0.00 0.00 39.46 2.15
3387 8967 9.665719 TGTTTGTCTATGTATTCACACATGTAT 57.334 29.630 0.00 0.00 39.46 2.29
3388 8968 9.150348 CTGTTTGTCTATGTATTCACACATGTA 57.850 33.333 0.00 0.00 39.46 2.29
3389 8969 7.877612 TCTGTTTGTCTATGTATTCACACATGT 59.122 33.333 0.00 0.00 39.46 3.21
3390 8970 8.255394 TCTGTTTGTCTATGTATTCACACATG 57.745 34.615 0.00 0.00 39.46 3.21
3391 8971 8.097038 ACTCTGTTTGTCTATGTATTCACACAT 58.903 33.333 0.00 0.00 41.88 3.21
3392 8972 7.384932 CACTCTGTTTGTCTATGTATTCACACA 59.615 37.037 0.00 0.00 37.54 3.72
3393 8973 7.385205 ACACTCTGTTTGTCTATGTATTCACAC 59.615 37.037 0.00 0.00 37.54 3.82
3394 8974 7.441836 ACACTCTGTTTGTCTATGTATTCACA 58.558 34.615 0.00 0.00 39.52 3.58
3395 8975 7.598869 TGACACTCTGTTTGTCTATGTATTCAC 59.401 37.037 11.01 0.00 43.30 3.18
3396 8976 7.598869 GTGACACTCTGTTTGTCTATGTATTCA 59.401 37.037 0.00 0.00 43.30 2.57
3397 8977 7.815068 AGTGACACTCTGTTTGTCTATGTATTC 59.185 37.037 1.07 0.00 43.30 1.75
3398 8978 7.671302 AGTGACACTCTGTTTGTCTATGTATT 58.329 34.615 1.07 0.00 43.30 1.89
3399 8979 7.233389 AGTGACACTCTGTTTGTCTATGTAT 57.767 36.000 1.07 0.00 43.30 2.29
3400 8980 6.650427 AGTGACACTCTGTTTGTCTATGTA 57.350 37.500 1.07 0.00 43.30 2.29
3401 8981 5.537300 AGTGACACTCTGTTTGTCTATGT 57.463 39.130 1.07 0.00 43.30 2.29
3402 8982 6.682746 ACTAGTGACACTCTGTTTGTCTATG 58.317 40.000 12.39 0.00 43.30 2.23
3403 8983 6.902771 ACTAGTGACACTCTGTTTGTCTAT 57.097 37.500 12.39 0.00 43.30 1.98
3404 8984 7.575155 GCATACTAGTGACACTCTGTTTGTCTA 60.575 40.741 12.39 0.00 43.30 2.59
3405 8985 6.682746 CATACTAGTGACACTCTGTTTGTCT 58.317 40.000 12.39 0.00 43.30 3.41
3406 8986 5.346281 GCATACTAGTGACACTCTGTTTGTC 59.654 44.000 12.39 9.81 43.22 3.18
3407 8987 5.230942 GCATACTAGTGACACTCTGTTTGT 58.769 41.667 12.39 5.61 0.00 2.83
3408 8988 4.627467 GGCATACTAGTGACACTCTGTTTG 59.373 45.833 12.39 16.63 0.00 2.93
3409 8989 4.528596 AGGCATACTAGTGACACTCTGTTT 59.471 41.667 12.39 5.23 0.00 2.83
3410 8990 4.090090 AGGCATACTAGTGACACTCTGTT 58.910 43.478 12.39 0.00 0.00 3.16
3411 8991 3.697045 GAGGCATACTAGTGACACTCTGT 59.303 47.826 12.39 14.35 0.00 3.41
3412 8992 3.951037 AGAGGCATACTAGTGACACTCTG 59.049 47.826 12.39 9.04 33.23 3.35
3413 8993 4.243793 AGAGGCATACTAGTGACACTCT 57.756 45.455 12.39 10.40 0.00 3.24
3414 8994 5.127491 AGTAGAGGCATACTAGTGACACTC 58.873 45.833 12.39 8.31 34.21 3.51
3415 8995 5.118729 AGTAGAGGCATACTAGTGACACT 57.881 43.478 13.68 13.68 34.21 3.55
3416 8996 5.357314 TCAAGTAGAGGCATACTAGTGACAC 59.643 44.000 5.39 0.00 34.90 3.67
3417 8997 5.357314 GTCAAGTAGAGGCATACTAGTGACA 59.643 44.000 19.41 0.00 40.28 3.58
3418 8998 5.591067 AGTCAAGTAGAGGCATACTAGTGAC 59.409 44.000 17.97 17.97 40.57 3.67
3419 8999 5.756918 AGTCAAGTAGAGGCATACTAGTGA 58.243 41.667 5.39 2.59 34.90 3.41
3420 9000 6.293735 GCTAGTCAAGTAGAGGCATACTAGTG 60.294 46.154 5.39 0.00 38.02 2.74
3421 9001 5.766174 GCTAGTCAAGTAGAGGCATACTAGT 59.234 44.000 0.00 0.00 38.02 2.57
3422 9002 6.001460 AGCTAGTCAAGTAGAGGCATACTAG 58.999 44.000 0.00 0.00 38.50 2.57
3423 9003 5.942961 AGCTAGTCAAGTAGAGGCATACTA 58.057 41.667 3.23 0.00 34.90 1.82
3424 9004 4.798882 AGCTAGTCAAGTAGAGGCATACT 58.201 43.478 0.00 0.00 37.61 2.12
3425 9005 4.319911 CGAGCTAGTCAAGTAGAGGCATAC 60.320 50.000 0.00 0.00 0.00 2.39
3426 9006 3.815962 CGAGCTAGTCAAGTAGAGGCATA 59.184 47.826 0.00 0.00 0.00 3.14
3427 9007 2.621055 CGAGCTAGTCAAGTAGAGGCAT 59.379 50.000 0.00 0.00 0.00 4.40
3428 9008 2.017782 CGAGCTAGTCAAGTAGAGGCA 58.982 52.381 0.00 0.00 0.00 4.75
3429 9009 2.018515 ACGAGCTAGTCAAGTAGAGGC 58.981 52.381 0.00 0.00 0.00 4.70
3430 9010 3.690139 TCAACGAGCTAGTCAAGTAGAGG 59.310 47.826 0.00 0.00 0.00 3.69
3431 9011 4.948608 TCAACGAGCTAGTCAAGTAGAG 57.051 45.455 0.00 0.00 0.00 2.43
3432 9012 4.941873 TGATCAACGAGCTAGTCAAGTAGA 59.058 41.667 0.00 0.00 0.00 2.59
3433 9013 5.236655 TGATCAACGAGCTAGTCAAGTAG 57.763 43.478 0.00 0.00 0.00 2.57
3434 9014 5.638596 TTGATCAACGAGCTAGTCAAGTA 57.361 39.130 3.38 0.00 0.00 2.24
3435 9015 4.521130 TTGATCAACGAGCTAGTCAAGT 57.479 40.909 3.38 0.00 0.00 3.16
3436 9016 5.164233 TCTTTGATCAACGAGCTAGTCAAG 58.836 41.667 7.89 0.00 0.00 3.02
3437 9017 5.134202 TCTTTGATCAACGAGCTAGTCAA 57.866 39.130 7.89 0.00 0.00 3.18
3438 9018 4.783764 TCTTTGATCAACGAGCTAGTCA 57.216 40.909 7.89 0.00 0.00 3.41
3439 9019 4.505922 CCATCTTTGATCAACGAGCTAGTC 59.494 45.833 18.24 0.00 0.00 2.59
3440 9020 4.081420 ACCATCTTTGATCAACGAGCTAGT 60.081 41.667 18.24 10.56 0.00 2.57
3441 9021 4.437239 ACCATCTTTGATCAACGAGCTAG 58.563 43.478 18.24 8.24 0.00 3.42
3442 9022 4.471904 ACCATCTTTGATCAACGAGCTA 57.528 40.909 18.24 0.00 0.00 3.32
3443 9023 3.340814 ACCATCTTTGATCAACGAGCT 57.659 42.857 18.24 2.03 0.00 4.09
3444 9024 5.065218 ACATAACCATCTTTGATCAACGAGC 59.935 40.000 18.24 0.00 0.00 5.03
3445 9025 6.668541 ACATAACCATCTTTGATCAACGAG 57.331 37.500 18.24 10.23 0.00 4.18
3446 9026 7.361713 GGAAACATAACCATCTTTGATCAACGA 60.362 37.037 16.08 16.08 0.00 3.85
3447 9027 6.747280 GGAAACATAACCATCTTTGATCAACG 59.253 38.462 7.89 6.62 0.00 4.10
3448 9028 7.830739 AGGAAACATAACCATCTTTGATCAAC 58.169 34.615 7.89 0.00 0.00 3.18
3449 9029 9.177608 CTAGGAAACATAACCATCTTTGATCAA 57.822 33.333 3.38 3.38 0.00 2.57
3450 9030 7.283127 GCTAGGAAACATAACCATCTTTGATCA 59.717 37.037 0.00 0.00 0.00 2.92
3451 9031 7.255277 GGCTAGGAAACATAACCATCTTTGATC 60.255 40.741 0.00 0.00 0.00 2.92
3452 9032 6.547510 GGCTAGGAAACATAACCATCTTTGAT 59.452 38.462 0.00 0.00 0.00 2.57
3453 9033 5.885912 GGCTAGGAAACATAACCATCTTTGA 59.114 40.000 0.00 0.00 0.00 2.69
3454 9034 5.652014 TGGCTAGGAAACATAACCATCTTTG 59.348 40.000 0.00 0.00 0.00 2.77
3455 9035 5.826643 TGGCTAGGAAACATAACCATCTTT 58.173 37.500 0.00 0.00 0.00 2.52
3456 9036 5.450818 TGGCTAGGAAACATAACCATCTT 57.549 39.130 0.00 0.00 0.00 2.40
3457 9037 5.653255 ATGGCTAGGAAACATAACCATCT 57.347 39.130 0.00 0.00 30.76 2.90
3458 9038 6.651225 GTCTATGGCTAGGAAACATAACCATC 59.349 42.308 0.00 0.00 37.58 3.51
3459 9039 6.101150 TGTCTATGGCTAGGAAACATAACCAT 59.899 38.462 0.00 0.00 39.62 3.55
3460 9040 5.427157 TGTCTATGGCTAGGAAACATAACCA 59.573 40.000 0.00 0.00 0.00 3.67
3461 9041 5.925509 TGTCTATGGCTAGGAAACATAACC 58.074 41.667 0.00 0.00 0.00 2.85
3462 9042 7.217200 TCATGTCTATGGCTAGGAAACATAAC 58.783 38.462 0.00 0.00 34.97 1.89
3463 9043 7.071196 ACTCATGTCTATGGCTAGGAAACATAA 59.929 37.037 0.00 0.00 34.97 1.90
3464 9044 6.554982 ACTCATGTCTATGGCTAGGAAACATA 59.445 38.462 0.00 0.00 34.97 2.29
3465 9045 5.367937 ACTCATGTCTATGGCTAGGAAACAT 59.632 40.000 0.00 0.00 34.97 2.71
3466 9046 4.716784 ACTCATGTCTATGGCTAGGAAACA 59.283 41.667 0.00 0.00 34.97 2.83
3467 9047 5.283457 ACTCATGTCTATGGCTAGGAAAC 57.717 43.478 0.00 0.00 34.97 2.78
3468 9048 5.189736 ACAACTCATGTCTATGGCTAGGAAA 59.810 40.000 0.00 0.00 37.96 3.13
3469 9049 4.716784 ACAACTCATGTCTATGGCTAGGAA 59.283 41.667 0.00 0.00 37.96 3.36
3470 9050 4.290093 ACAACTCATGTCTATGGCTAGGA 58.710 43.478 0.00 0.00 37.96 2.94
3471 9051 4.679373 ACAACTCATGTCTATGGCTAGG 57.321 45.455 0.00 0.00 37.96 3.02
3483 9063 6.029607 CCCGTTAATCAAATGACAACTCATG 58.970 40.000 7.65 0.00 37.20 3.07
3484 9064 5.943416 TCCCGTTAATCAAATGACAACTCAT 59.057 36.000 7.65 0.00 38.94 2.90
3485 9065 5.309638 TCCCGTTAATCAAATGACAACTCA 58.690 37.500 7.65 0.00 0.00 3.41
3486 9066 5.873179 TCCCGTTAATCAAATGACAACTC 57.127 39.130 7.65 0.00 0.00 3.01
3487 9067 5.943416 TGATCCCGTTAATCAAATGACAACT 59.057 36.000 0.00 0.00 30.37 3.16
3488 9068 6.189677 TGATCCCGTTAATCAAATGACAAC 57.810 37.500 0.00 0.00 30.37 3.32
3489 9069 8.690203 ATATGATCCCGTTAATCAAATGACAA 57.310 30.769 0.00 0.00 36.75 3.18
3490 9070 7.936301 TGATATGATCCCGTTAATCAAATGACA 59.064 33.333 0.00 0.00 36.75 3.58
3491 9071 8.322906 TGATATGATCCCGTTAATCAAATGAC 57.677 34.615 0.00 0.00 36.75 3.06
3492 9072 9.519191 AATGATATGATCCCGTTAATCAAATGA 57.481 29.630 0.00 0.00 36.75 2.57
3495 9075 9.448438 CCTAATGATATGATCCCGTTAATCAAA 57.552 33.333 0.00 0.00 36.75 2.69
3496 9076 8.821817 TCCTAATGATATGATCCCGTTAATCAA 58.178 33.333 0.00 0.00 36.75 2.57
3497 9077 8.374184 TCCTAATGATATGATCCCGTTAATCA 57.626 34.615 0.00 0.00 37.53 2.57
3498 9078 8.696374 TCTCCTAATGATATGATCCCGTTAATC 58.304 37.037 0.00 0.00 0.00 1.75
3499 9079 8.609617 TCTCCTAATGATATGATCCCGTTAAT 57.390 34.615 0.00 0.00 0.00 1.40
3500 9080 8.430573 TTCTCCTAATGATATGATCCCGTTAA 57.569 34.615 0.00 0.00 0.00 2.01
3501 9081 8.478066 CATTCTCCTAATGATATGATCCCGTTA 58.522 37.037 0.00 0.00 0.00 3.18
3502 9082 6.935240 TTCTCCTAATGATATGATCCCGTT 57.065 37.500 0.00 0.00 0.00 4.44
3503 9083 6.669591 TCATTCTCCTAATGATATGATCCCGT 59.330 38.462 0.00 0.00 32.21 5.28
3504 9084 7.117285 TCATTCTCCTAATGATATGATCCCG 57.883 40.000 0.00 0.00 32.21 5.14
3505 9085 8.492782 ACATCATTCTCCTAATGATATGATCCC 58.507 37.037 11.71 0.00 43.38 3.85
3506 9086 9.327628 CACATCATTCTCCTAATGATATGATCC 57.672 37.037 11.68 0.00 41.59 3.36
3512 9092 9.716531 GTCAATCACATCATTCTCCTAATGATA 57.283 33.333 11.71 0.02 43.38 2.15
3513 9093 8.438373 AGTCAATCACATCATTCTCCTAATGAT 58.562 33.333 7.28 7.28 45.40 2.45
3514 9094 7.799081 AGTCAATCACATCATTCTCCTAATGA 58.201 34.615 3.13 3.13 40.50 2.57
3515 9095 8.343366 CAAGTCAATCACATCATTCTCCTAATG 58.657 37.037 0.00 0.00 0.00 1.90
3516 9096 8.270030 TCAAGTCAATCACATCATTCTCCTAAT 58.730 33.333 0.00 0.00 0.00 1.73
3517 9097 7.550551 GTCAAGTCAATCACATCATTCTCCTAA 59.449 37.037 0.00 0.00 0.00 2.69
3518 9098 7.044181 GTCAAGTCAATCACATCATTCTCCTA 58.956 38.462 0.00 0.00 0.00 2.94
3519 9099 5.879223 GTCAAGTCAATCACATCATTCTCCT 59.121 40.000 0.00 0.00 0.00 3.69
3520 9100 5.065731 GGTCAAGTCAATCACATCATTCTCC 59.934 44.000 0.00 0.00 0.00 3.71
3521 9101 5.065731 GGGTCAAGTCAATCACATCATTCTC 59.934 44.000 0.00 0.00 0.00 2.87
3522 9102 4.946157 GGGTCAAGTCAATCACATCATTCT 59.054 41.667 0.00 0.00 0.00 2.40
3523 9103 4.701651 TGGGTCAAGTCAATCACATCATTC 59.298 41.667 0.00 0.00 0.00 2.67
3524 9104 4.665451 TGGGTCAAGTCAATCACATCATT 58.335 39.130 0.00 0.00 0.00 2.57
3525 9105 4.305539 TGGGTCAAGTCAATCACATCAT 57.694 40.909 0.00 0.00 0.00 2.45
3526 9106 3.786368 TGGGTCAAGTCAATCACATCA 57.214 42.857 0.00 0.00 0.00 3.07
3527 9107 4.096984 GGAATGGGTCAAGTCAATCACATC 59.903 45.833 0.00 0.00 0.00 3.06
3528 9108 4.019174 GGAATGGGTCAAGTCAATCACAT 58.981 43.478 0.00 0.00 0.00 3.21
3529 9109 3.420893 GGAATGGGTCAAGTCAATCACA 58.579 45.455 0.00 0.00 0.00 3.58
3530 9110 2.420022 CGGAATGGGTCAAGTCAATCAC 59.580 50.000 0.00 0.00 0.00 3.06
3531 9111 2.039746 ACGGAATGGGTCAAGTCAATCA 59.960 45.455 0.00 0.00 0.00 2.57
3532 9112 2.711542 ACGGAATGGGTCAAGTCAATC 58.288 47.619 0.00 0.00 0.00 2.67
3533 9113 2.879103 ACGGAATGGGTCAAGTCAAT 57.121 45.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.