Multiple sequence alignment - TraesCS5A01G027000

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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 TraesCS5A01G027000 chr5A 100.000 9102 0 0 1 9102 22280489 22271388 0.000000e+00 16809.0
1 TraesCS5A01G027000 chr5D 96.694 8107 161 39 657 8720 33708114 33700072 0.000000e+00 13387.0
2 TraesCS5A01G027000 chr5D 88.490 669 62 9 4 662 33710285 33709622 0.000000e+00 795.0
3 TraesCS5A01G027000 chr5D 85.321 327 32 8 2418 2744 497146268 497145958 3.170000e-84 324.0
4 TraesCS5A01G027000 chr5D 84.709 327 34 7 2418 2744 497235038 497234728 6.860000e-81 313.0
5 TraesCS5A01G027000 chr5D 84.242 330 36 7 2415 2744 497456622 497456935 3.190000e-79 307.0
6 TraesCS5A01G027000 chr5D 83.180 327 31 10 2418 2744 497109480 497109178 2.500000e-70 278.0
7 TraesCS5A01G027000 chr5D 87.958 191 15 5 8758 8940 33700070 33699880 1.540000e-52 219.0
8 TraesCS5A01G027000 chr5B 92.871 4980 228 57 1 4907 24925639 24920714 0.000000e+00 7112.0
9 TraesCS5A01G027000 chr5B 95.418 3754 106 23 4941 8667 24920713 24916999 0.000000e+00 5919.0
10 TraesCS5A01G027000 chr5B 91.124 1014 46 9 2923 3919 79771845 79770859 0.000000e+00 1334.0
11 TraesCS5A01G027000 chr5B 94.316 563 25 6 2923 3483 473797785 473797228 0.000000e+00 856.0
12 TraesCS5A01G027000 chr5B 89.974 379 24 3 8684 9048 24916527 24916149 2.300000e-130 477.0
13 TraesCS5A01G027000 chr2B 91.510 1013 43 8 2923 3919 467488509 467489494 0.000000e+00 1354.0
14 TraesCS5A01G027000 chr2B 90.000 70 4 3 3926 3993 265428432 265428500 4.530000e-13 87.9
15 TraesCS5A01G027000 chr2B 87.342 79 4 3 3926 4003 551568356 551568429 1.630000e-12 86.1
16 TraesCS5A01G027000 chr2B 86.250 80 5 3 3922 4001 6259573 6259500 2.110000e-11 82.4
17 TraesCS5A01G027000 chr6B 91.420 1014 43 9 2923 3919 481038802 481039788 0.000000e+00 1351.0
18 TraesCS5A01G027000 chr6B 91.313 1013 45 8 2923 3919 123888825 123887840 0.000000e+00 1343.0
19 TraesCS5A01G027000 chr6B 95.495 666 28 2 2923 3588 218966167 218965504 0.000000e+00 1062.0
20 TraesCS5A01G027000 chr7B 91.313 1013 45 8 2923 3919 513731615 513730630 0.000000e+00 1343.0
21 TraesCS5A01G027000 chr1A 91.313 1013 45 8 2923 3919 278156592 278157577 0.000000e+00 1343.0
22 TraesCS5A01G027000 chr1A 96.875 32 1 0 900 931 561347184 561347153 5.000000e-03 54.7
23 TraesCS5A01G027000 chrUn 89.821 560 29 6 3363 3919 410374700 410374166 0.000000e+00 693.0
24 TraesCS5A01G027000 chr3D 88.251 366 39 3 2418 2783 129679076 129678715 1.400000e-117 435.0
25 TraesCS5A01G027000 chr3D 83.243 370 36 9 2840 3207 129678709 129678364 5.300000e-82 316.0
26 TraesCS5A01G027000 chr3D 100.000 35 0 0 5207 5241 559647138 559647104 2.120000e-06 65.8
27 TraesCS5A01G027000 chr6D 84.404 327 45 5 2421 2744 438551472 438551149 5.300000e-82 316.0
28 TraesCS5A01G027000 chr6D 88.462 78 7 1 3925 4002 88889036 88888961 9.730000e-15 93.5
29 TraesCS5A01G027000 chr2D 84.545 330 35 7 2415 2744 80982375 80982688 6.860000e-81 313.0
30 TraesCS5A01G027000 chr2D 92.754 69 4 1 3926 3993 213702944 213703012 2.090000e-16 99.0
31 TraesCS5A01G027000 chr2A 91.781 73 4 2 3922 3993 241968110 241968181 5.820000e-17 100.0
32 TraesCS5A01G027000 chr3A 87.179 78 8 2 3926 4002 365354962 365355038 4.530000e-13 87.9
33 TraesCS5A01G027000 chr6A 100.000 28 0 0 900 927 336011140 336011113 1.700000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G027000 chr5A 22271388 22280489 9101 True 16809.000000 16809 100.000000 1 9102 1 chr5A.!!$R1 9101
1 TraesCS5A01G027000 chr5D 33699880 33710285 10405 True 4800.333333 13387 91.047333 4 8940 3 chr5D.!!$R4 8936
2 TraesCS5A01G027000 chr5B 24916149 24925639 9490 True 4502.666667 7112 92.754333 1 9048 3 chr5B.!!$R3 9047
3 TraesCS5A01G027000 chr5B 79770859 79771845 986 True 1334.000000 1334 91.124000 2923 3919 1 chr5B.!!$R1 996
4 TraesCS5A01G027000 chr5B 473797228 473797785 557 True 856.000000 856 94.316000 2923 3483 1 chr5B.!!$R2 560
5 TraesCS5A01G027000 chr2B 467488509 467489494 985 False 1354.000000 1354 91.510000 2923 3919 1 chr2B.!!$F2 996
6 TraesCS5A01G027000 chr6B 481038802 481039788 986 False 1351.000000 1351 91.420000 2923 3919 1 chr6B.!!$F1 996
7 TraesCS5A01G027000 chr6B 123887840 123888825 985 True 1343.000000 1343 91.313000 2923 3919 1 chr6B.!!$R1 996
8 TraesCS5A01G027000 chr6B 218965504 218966167 663 True 1062.000000 1062 95.495000 2923 3588 1 chr6B.!!$R2 665
9 TraesCS5A01G027000 chr7B 513730630 513731615 985 True 1343.000000 1343 91.313000 2923 3919 1 chr7B.!!$R1 996
10 TraesCS5A01G027000 chr1A 278156592 278157577 985 False 1343.000000 1343 91.313000 2923 3919 1 chr1A.!!$F1 996
11 TraesCS5A01G027000 chrUn 410374166 410374700 534 True 693.000000 693 89.821000 3363 3919 1 chrUn.!!$R1 556
12 TraesCS5A01G027000 chr3D 129678364 129679076 712 True 375.500000 435 85.747000 2418 3207 2 chr3D.!!$R2 789

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
252 256 0.179137 TCTCGTGGAAGCATGCTACG 60.179 55.000 27.63 27.63 36.20 3.51 F
525 544 0.250727 TTTCCTTGCGAAGAGGTGGG 60.251 55.000 0.00 0.00 35.71 4.61 F
1571 3145 0.572125 GTGCGCGGGTTATTACGTAC 59.428 55.000 8.83 0.00 34.24 3.67 F
1821 3399 1.012486 GGGTAACTGTCCGTTGCTCG 61.012 60.000 0.00 0.00 38.18 5.03 F
2122 3700 1.668793 GCAATGTGCAACCAAGCCC 60.669 57.895 0.00 0.00 44.26 5.19 F
2910 4489 2.675658 TCCCCTCCTTGTTTTGAAGG 57.324 50.000 0.00 0.00 43.61 3.46 F
3615 5212 3.431912 GCTTTTAAGCGGGTTGAAATTGG 59.568 43.478 9.79 1.67 42.88 3.16 F
4930 6540 1.075374 TGGGTTCTGCCTGCTATTTGT 59.925 47.619 0.00 0.00 37.43 2.83 F
5873 7483 0.804989 CAGGCAATTCCGTTGGACTC 59.195 55.000 0.00 0.00 40.77 3.36 F
6453 8084 0.255890 TCCCCTGCATGCTTCCTTAC 59.744 55.000 20.33 0.00 0.00 2.34 F
7834 9469 1.746615 CTGCATGTGCTTAGCCCGT 60.747 57.895 0.29 0.00 42.66 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 3173 0.179129 GCGCCAACCATCAGATTTGG 60.179 55.000 8.94 8.94 42.43 3.28 R
1616 3190 0.321653 ACCTAAAGCTTCACTGGGCG 60.322 55.000 0.00 0.00 0.00 6.13 R
2910 4489 1.264288 CAACACTGCCGAGAAACCTTC 59.736 52.381 0.00 0.00 0.00 3.46 R
2921 4500 3.131400 TCCTTTACAAAACCAACACTGCC 59.869 43.478 0.00 0.00 0.00 4.85 R
3425 5022 4.469657 TGTTGCAGGAGGAAATAACAGTT 58.530 39.130 0.00 0.00 0.00 3.16 R
4879 6489 2.268920 CCAGGCACCACATAGCGT 59.731 61.111 0.00 0.00 0.00 5.07 R
5192 6802 1.053835 TGGGCAGGAGTGTTGTCTGA 61.054 55.000 0.00 0.00 0.00 3.27 R
5903 7530 0.174162 AAAGATGCATTGCCTTCCGC 59.826 50.000 6.12 0.00 38.31 5.54 R
7783 9417 0.472471 AGTCAGCGGGGAAAAGAACA 59.528 50.000 0.00 0.00 0.00 3.18 R
8085 9739 0.036732 GGCTCACAAGTCATCACCCA 59.963 55.000 0.00 0.00 0.00 4.51 R
8926 11071 0.035725 CCTGTTCTGAGAGCATGCCA 60.036 55.000 15.66 4.33 0.00 4.92 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
26 27 5.451937 CGTGCCTAATCTTCTCATAGGTTGA 60.452 44.000 0.00 0.00 38.75 3.18
41 42 8.918202 TCATAGGTTGATTCCATATAAACACC 57.082 34.615 0.00 0.00 0.00 4.16
44 45 4.578928 GGTTGATTCCATATAAACACCGCT 59.421 41.667 0.00 0.00 0.00 5.52
51 52 6.130298 TCCATATAAACACCGCTCATTTTG 57.870 37.500 0.00 0.00 0.00 2.44
55 57 3.791973 AAACACCGCTCATTTTGTTGA 57.208 38.095 0.00 0.00 32.54 3.18
79 81 7.395772 TGACACATGGAAAATATGGAGCTAAAA 59.604 33.333 0.00 0.00 0.00 1.52
89 91 8.747538 AAATATGGAGCTAAAATTCGGTAGTT 57.252 30.769 0.00 0.00 0.00 2.24
124 126 5.086058 CGGTTCCGTGTTTCTAAATTCATG 58.914 41.667 2.82 0.00 0.00 3.07
152 154 2.719798 CGCTCATTTCCATTTTAGGCG 58.280 47.619 0.00 0.00 0.00 5.52
155 157 3.438360 CTCATTTCCATTTTAGGCGTGC 58.562 45.455 0.00 0.00 0.00 5.34
156 158 2.165437 TCATTTCCATTTTAGGCGTGCC 59.835 45.455 1.67 1.67 0.00 5.01
157 159 0.892063 TTTCCATTTTAGGCGTGCCC 59.108 50.000 7.39 0.00 36.58 5.36
158 160 1.309499 TTCCATTTTAGGCGTGCCCG 61.309 55.000 7.39 0.00 39.21 6.13
177 179 2.388232 CCCGCCACTGCTAACGTTC 61.388 63.158 2.82 0.00 34.43 3.95
208 212 1.999735 GTGTCATGACGTATGGTGTGG 59.000 52.381 20.54 0.00 37.39 4.17
223 227 1.153289 GTGGCGAGTGGATGAGCAT 60.153 57.895 0.00 0.00 0.00 3.79
244 248 2.504244 CCGACGTCTCGTGGAAGC 60.504 66.667 14.70 0.00 41.37 3.86
252 256 0.179137 TCTCGTGGAAGCATGCTACG 60.179 55.000 27.63 27.63 36.20 3.51
257 261 2.703409 GAAGCATGCTACGCCACG 59.297 61.111 23.00 0.00 0.00 4.94
262 266 2.509336 ATGCTACGCCACGACAGC 60.509 61.111 10.05 10.05 38.29 4.40
274 278 4.250305 GACAGCCCGTGGTGGTGT 62.250 66.667 1.43 10.60 46.27 4.16
287 291 4.595538 GGTGTGGGTGTCGTGCGA 62.596 66.667 0.00 0.00 0.00 5.10
297 301 3.394800 GTCGTGCGACAGTGACATA 57.605 52.632 18.32 0.00 44.02 2.29
305 309 4.152402 GTGCGACAGTGACATATTCTTTGT 59.848 41.667 0.00 0.00 0.00 2.83
328 332 3.233980 AGGCACAGAGACACCGCA 61.234 61.111 0.00 0.00 0.00 5.69
337 341 1.073216 GAGACACCGCAGATGACACG 61.073 60.000 0.00 0.00 0.00 4.49
339 343 2.738139 CACCGCAGATGACACGCA 60.738 61.111 0.00 0.00 0.00 5.24
347 351 2.541588 GCAGATGACACGCAAAAACTGT 60.542 45.455 0.00 0.00 0.00 3.55
348 352 3.038017 CAGATGACACGCAAAAACTGTG 58.962 45.455 0.00 0.00 41.62 3.66
369 381 1.804748 GGTTTTCGTCGAGAAGGCATT 59.195 47.619 0.00 0.00 40.40 3.56
487 506 3.202097 GTGGAGAAGCAAGAATCTAGCC 58.798 50.000 0.00 0.00 0.00 3.93
497 516 4.213059 GCAAGAATCTAGCCTGCAAGATAC 59.787 45.833 0.00 0.00 34.07 2.24
525 544 0.250727 TTTCCTTGCGAAGAGGTGGG 60.251 55.000 0.00 0.00 35.71 4.61
573 592 1.153647 TCGAGTGCCATTACTGCCG 60.154 57.895 0.00 0.00 0.00 5.69
575 594 1.220749 GAGTGCCATTACTGCCGGA 59.779 57.895 5.05 0.00 0.00 5.14
576 595 1.078426 AGTGCCATTACTGCCGGAC 60.078 57.895 5.05 0.00 0.00 4.79
577 596 1.376683 GTGCCATTACTGCCGGACA 60.377 57.895 5.05 1.09 0.00 4.02
635 655 5.527582 CCTAGACAACCATATTCCTTTTCGG 59.472 44.000 0.00 0.00 0.00 4.30
961 2526 2.125106 GTCTCCAAATCCGCCGCT 60.125 61.111 0.00 0.00 0.00 5.52
1122 2688 2.509336 CACCGGTAAGCGCTCCAG 60.509 66.667 12.06 3.09 0.00 3.86
1152 2722 1.304547 CCTAGCCCTCCGATCCGAT 60.305 63.158 0.00 0.00 0.00 4.18
1543 3115 8.159447 AGATGCATTTGTAATGCCTAGATTCTA 58.841 33.333 18.60 0.00 43.94 2.10
1544 3116 8.874744 ATGCATTTGTAATGCCTAGATTCTAT 57.125 30.769 18.60 3.07 43.94 1.98
1545 3117 8.102800 TGCATTTGTAATGCCTAGATTCTATG 57.897 34.615 18.60 0.00 43.94 2.23
1547 3119 7.533426 CATTTGTAATGCCTAGATTCTATGCC 58.467 38.462 15.60 4.10 0.00 4.40
1548 3120 4.820897 TGTAATGCCTAGATTCTATGCCG 58.179 43.478 15.60 0.00 0.00 5.69
1549 3121 4.283467 TGTAATGCCTAGATTCTATGCCGT 59.717 41.667 15.60 8.05 0.00 5.68
1550 3122 2.820059 TGCCTAGATTCTATGCCGTG 57.180 50.000 15.60 0.00 0.00 4.94
1571 3145 0.572125 GTGCGCGGGTTATTACGTAC 59.428 55.000 8.83 0.00 34.24 3.67
1599 3173 7.201556 CGATGATGCATGGTATTAGTATTGGAC 60.202 40.741 2.46 0.00 0.00 4.02
1650 3226 5.416952 AGCTTTAGGTATCATATGCATTGCC 59.583 40.000 3.54 0.00 0.00 4.52
1663 3239 3.814625 TGCATTGCCCTGTCGATTAATA 58.185 40.909 6.12 0.00 0.00 0.98
1750 3328 1.909986 AGGGAGTTAGAGAACCAAGCC 59.090 52.381 0.00 0.00 36.08 4.35
1773 3351 6.096282 GCCTTGTGCCCTATGTTTCTAAAATA 59.904 38.462 0.00 0.00 0.00 1.40
1821 3399 1.012486 GGGTAACTGTCCGTTGCTCG 61.012 60.000 0.00 0.00 38.18 5.03
1889 3467 3.208747 AGGCGGATGGATTATTTCGTT 57.791 42.857 0.00 0.00 0.00 3.85
2038 3616 7.378804 GTTTATTAGTGACACGCTTACTAACG 58.621 38.462 0.00 0.00 39.06 3.18
2057 3635 7.208080 ACTAACGGTCAGTGATGGATTATTAC 58.792 38.462 0.00 0.00 0.00 1.89
2122 3700 1.668793 GCAATGTGCAACCAAGCCC 60.669 57.895 0.00 0.00 44.26 5.19
2299 3878 6.910536 ATATGGTTTGTCGTTTCATCTCTC 57.089 37.500 0.00 0.00 0.00 3.20
2504 4083 6.897966 AGTTCAGACCAAGAGATCTGGTATTA 59.102 38.462 0.00 0.00 42.25 0.98
2733 4312 4.526970 TGATTTTCTCACCTAGGCATTCC 58.473 43.478 9.30 0.00 0.00 3.01
2910 4489 2.675658 TCCCCTCCTTGTTTTGAAGG 57.324 50.000 0.00 0.00 43.61 3.46
2921 4500 4.893424 TGTTTTGAAGGAAGGTTTCTCG 57.107 40.909 0.00 0.00 0.00 4.04
2972 4551 6.730960 ATGTTTTCATGCATGAATTTCACC 57.269 33.333 35.87 18.42 45.30 4.02
3006 4585 6.115450 AGAAAACGGTGTTGTTCTAACTTC 57.885 37.500 0.00 0.00 0.00 3.01
3133 4714 9.952341 GAATGTGTAAAGTTTTGTGTTTCTTTC 57.048 29.630 0.00 0.00 33.22 2.62
3134 4715 9.705290 AATGTGTAAAGTTTTGTGTTTCTTTCT 57.295 25.926 0.00 0.00 33.22 2.52
3135 4716 9.705290 ATGTGTAAAGTTTTGTGTTTCTTTCTT 57.295 25.926 0.00 0.00 33.22 2.52
3583 5180 8.199449 GTGCACATGGGTAGTAAGTAACTAATA 58.801 37.037 13.17 0.00 42.37 0.98
3615 5212 3.431912 GCTTTTAAGCGGGTTGAAATTGG 59.568 43.478 9.79 1.67 42.88 3.16
3955 5563 6.128795 CCTCTGTCTCAAAATGTAAGACGTTC 60.129 42.308 0.00 0.00 41.84 3.95
4823 6433 5.238583 ACTTGCTACTGTGTTAATCCTGTC 58.761 41.667 0.00 0.00 0.00 3.51
4879 6489 3.153919 GGTCTAGTTTGGTTTGCATCCA 58.846 45.455 6.99 6.99 0.00 3.41
4930 6540 1.075374 TGGGTTCTGCCTGCTATTTGT 59.925 47.619 0.00 0.00 37.43 2.83
4987 6597 1.227883 CCTGCATAGCTCAGGCCAG 60.228 63.158 5.01 0.00 43.88 4.85
5105 6715 5.977129 TGATGCGTCAGTTATGTGTATACTG 59.023 40.000 3.97 0.00 0.00 2.74
5175 6785 1.275291 TCACCAGGCTAGAAAACTCGG 59.725 52.381 0.00 0.00 0.00 4.63
5192 6802 2.365237 GAAGTCCTAGGCCCGGGT 60.365 66.667 24.63 5.39 0.00 5.28
5196 6806 3.352748 TCCTAGGCCCGGGTCAGA 61.353 66.667 30.48 18.41 0.00 3.27
5204 6814 1.004918 CCCGGGTCAGACAACACTC 60.005 63.158 14.18 0.00 0.00 3.51
5278 6888 6.480763 TGCTTATATTTCTTGAGGGTGTTGA 58.519 36.000 0.00 0.00 0.00 3.18
5281 6891 9.120538 GCTTATATTTCTTGAGGGTGTTGATTA 57.879 33.333 0.00 0.00 0.00 1.75
5309 6919 7.812648 TCCTTTGTATTATTTTCACACTTCCG 58.187 34.615 0.00 0.00 0.00 4.30
5709 7319 9.618890 TTCTATTTCCTGTGGATGAATTAAGAG 57.381 33.333 0.00 0.00 0.00 2.85
5777 7387 8.926092 AGCCATTTCCTAGTCCTTTTAATATC 57.074 34.615 0.00 0.00 0.00 1.63
5809 7419 0.982852 CAGTGAGGGGCTGGGTATCA 60.983 60.000 0.00 0.00 0.00 2.15
5873 7483 0.804989 CAGGCAATTCCGTTGGACTC 59.195 55.000 0.00 0.00 40.77 3.36
5881 7491 1.946984 TCCGTTGGACTCCCTATTGT 58.053 50.000 0.00 0.00 0.00 2.71
5891 7518 3.833070 GACTCCCTATTGTCCATACCGAT 59.167 47.826 0.00 0.00 0.00 4.18
5892 7519 3.833070 ACTCCCTATTGTCCATACCGATC 59.167 47.826 0.00 0.00 0.00 3.69
5893 7520 3.170717 TCCCTATTGTCCATACCGATCC 58.829 50.000 0.00 0.00 0.00 3.36
5894 7521 2.903784 CCCTATTGTCCATACCGATCCA 59.096 50.000 0.00 0.00 0.00 3.41
5895 7522 3.519510 CCCTATTGTCCATACCGATCCAT 59.480 47.826 0.00 0.00 0.00 3.41
5896 7523 4.019321 CCCTATTGTCCATACCGATCCATT 60.019 45.833 0.00 0.00 0.00 3.16
5897 7524 5.514834 CCCTATTGTCCATACCGATCCATTT 60.515 44.000 0.00 0.00 0.00 2.32
5898 7525 6.296202 CCCTATTGTCCATACCGATCCATTTA 60.296 42.308 0.00 0.00 0.00 1.40
5899 7526 7.165485 CCTATTGTCCATACCGATCCATTTAA 58.835 38.462 0.00 0.00 0.00 1.52
5900 7527 7.829211 CCTATTGTCCATACCGATCCATTTAAT 59.171 37.037 0.00 0.00 0.00 1.40
5901 7528 9.231297 CTATTGTCCATACCGATCCATTTAATT 57.769 33.333 0.00 0.00 0.00 1.40
5902 7529 6.875948 TGTCCATACCGATCCATTTAATTG 57.124 37.500 0.00 0.00 0.00 2.32
5903 7530 5.767665 TGTCCATACCGATCCATTTAATTGG 59.232 40.000 9.69 9.69 38.18 3.16
5904 7531 4.764823 TCCATACCGATCCATTTAATTGGC 59.235 41.667 10.91 0.00 36.66 4.52
5905 7532 4.379394 CCATACCGATCCATTTAATTGGCG 60.379 45.833 10.91 9.59 36.66 5.69
5906 7533 1.953686 ACCGATCCATTTAATTGGCGG 59.046 47.619 23.00 23.00 43.78 6.13
5907 7534 2.226330 CCGATCCATTTAATTGGCGGA 58.774 47.619 21.41 4.74 41.97 5.54
5908 7535 2.621055 CCGATCCATTTAATTGGCGGAA 59.379 45.455 21.41 4.45 41.97 4.30
5909 7536 3.304659 CCGATCCATTTAATTGGCGGAAG 60.305 47.826 21.41 8.74 41.97 3.46
5910 7537 3.304659 CGATCCATTTAATTGGCGGAAGG 60.305 47.826 10.91 0.00 36.66 3.46
6072 7701 5.757850 ATGGTCGATTTTTATTCTGGCTC 57.242 39.130 0.00 0.00 0.00 4.70
6453 8084 0.255890 TCCCCTGCATGCTTCCTTAC 59.744 55.000 20.33 0.00 0.00 2.34
7105 8739 7.975616 GGCATGCTATTTTTCTTGAATACTGAA 59.024 33.333 18.92 0.00 0.00 3.02
7219 8853 5.709164 GCAGGATAATGGTCTCAAGCAATAT 59.291 40.000 0.00 0.00 36.29 1.28
7260 8894 3.260884 TCGCTTCCTGAGGTTTACAAGAT 59.739 43.478 0.00 0.00 0.00 2.40
7609 9243 7.481798 CACCTAAAAAGATTTTCATACAGTCGC 59.518 37.037 0.00 0.00 0.00 5.19
7783 9417 9.098355 CACTACACTGCATATGTTTATGTAAGT 57.902 33.333 8.87 2.78 37.99 2.24
7834 9469 1.746615 CTGCATGTGCTTAGCCCGT 60.747 57.895 0.29 0.00 42.66 5.28
7879 9530 2.030185 GTCAGCTTCTCACACGAGGTAA 60.030 50.000 0.00 0.00 39.95 2.85
8085 9739 2.442272 ATCAGGAGTAGCGGCGGT 60.442 61.111 18.21 18.21 0.00 5.68
8327 9983 6.071672 GCTGATAACTGCAGATATAGACAGGA 60.072 42.308 23.35 0.00 40.01 3.86
8389 10045 4.202202 TGCGTTTGAAACCCATGATTTTCT 60.202 37.500 15.75 0.00 33.61 2.52
8406 10062 0.704076 TCTTGGGGTGGAGAAATGGG 59.296 55.000 0.00 0.00 0.00 4.00
8459 10123 3.909732 TGTTCCCTTGGTTGTTTCTGAT 58.090 40.909 0.00 0.00 0.00 2.90
8498 10162 2.872245 TGCTGCTAATATTTGGCTCGAC 59.128 45.455 0.00 3.28 38.08 4.20
8515 10179 8.902540 TGGCTCGACAAAGAATTTATATACAT 57.097 30.769 0.00 0.00 35.03 2.29
8516 10180 8.773645 TGGCTCGACAAAGAATTTATATACATG 58.226 33.333 0.00 0.00 35.03 3.21
8517 10181 8.230486 GGCTCGACAAAGAATTTATATACATGG 58.770 37.037 0.00 0.00 35.03 3.66
8519 10183 9.273016 CTCGACAAAGAATTTATATACATGGGT 57.727 33.333 0.00 0.00 35.03 4.51
8520 10184 9.621629 TCGACAAAGAATTTATATACATGGGTT 57.378 29.630 0.00 0.00 35.03 4.11
8521 10185 9.878599 CGACAAAGAATTTATATACATGGGTTC 57.121 33.333 0.00 0.00 35.03 3.62
8608 10283 1.336702 ACGTACGAATGTTGGCGGTTA 60.337 47.619 24.41 0.00 0.00 2.85
8720 10850 3.485394 TGCTAAGTCCATTGAACTTGCA 58.515 40.909 0.00 4.07 37.52 4.08
8722 10852 3.671702 GCTAAGTCCATTGAACTTGCAGC 60.672 47.826 0.00 0.00 37.52 5.25
8725 10855 0.599558 TCCATTGAACTTGCAGCTGC 59.400 50.000 31.89 31.89 42.50 5.25
8741 10871 1.079405 TGCGGAACTCAATCGTCCC 60.079 57.895 0.00 0.00 0.00 4.46
8745 10875 1.356938 GGAACTCAATCGTCCCGAAC 58.643 55.000 0.00 0.00 39.99 3.95
8756 10886 1.014564 GTCCCGAACTCCTTCGCAAG 61.015 60.000 0.00 0.00 46.72 4.01
8835 10966 2.051345 GTTTGACGGCAAGCGTGG 60.051 61.111 2.76 0.00 35.04 4.94
8936 11081 3.951769 GGGGCAGTTGGCATGCTCT 62.952 63.158 18.92 10.87 43.93 4.09
8953 11098 2.221981 GCTCTCAGAACAGGTTCAAACG 59.778 50.000 14.06 0.86 41.84 3.60
9008 11153 3.161067 TGAGGGAGAAGACTCTGTTCTG 58.839 50.000 0.00 0.00 42.28 3.02
9020 11165 2.737783 CTCTGTTCTGCTCAAGCTTCAG 59.262 50.000 0.00 1.03 42.66 3.02
9041 11186 1.133388 CCCTATACCCAGTCCACGGTA 60.133 57.143 0.00 0.00 38.94 4.02
9042 11187 1.959282 CCTATACCCAGTCCACGGTAC 59.041 57.143 0.00 0.00 37.44 3.34
9048 11193 1.669049 CCAGTCCACGGTACCGCATA 61.669 60.000 33.62 16.21 44.19 3.14
9049 11194 0.526954 CAGTCCACGGTACCGCATAC 60.527 60.000 33.62 25.80 44.19 2.39
9050 11195 0.966875 AGTCCACGGTACCGCATACA 60.967 55.000 33.62 10.93 44.19 2.29
9051 11196 0.803380 GTCCACGGTACCGCATACAC 60.803 60.000 33.62 18.56 44.19 2.90
9052 11197 0.966875 TCCACGGTACCGCATACACT 60.967 55.000 33.62 10.05 44.19 3.55
9053 11198 0.526954 CCACGGTACCGCATACACTC 60.527 60.000 33.62 0.00 44.19 3.51
9054 11199 0.864377 CACGGTACCGCATACACTCG 60.864 60.000 33.62 6.75 44.19 4.18
9055 11200 1.026182 ACGGTACCGCATACACTCGA 61.026 55.000 33.62 0.00 44.19 4.04
9056 11201 0.309922 CGGTACCGCATACACTCGAT 59.690 55.000 23.44 0.00 35.23 3.59
9057 11202 1.532437 CGGTACCGCATACACTCGATA 59.468 52.381 23.44 0.00 35.23 2.92
9058 11203 2.161012 CGGTACCGCATACACTCGATAT 59.839 50.000 23.44 0.00 35.23 1.63
9059 11204 3.365666 CGGTACCGCATACACTCGATATT 60.366 47.826 23.44 0.00 35.23 1.28
9060 11205 4.164294 GGTACCGCATACACTCGATATTC 58.836 47.826 0.00 0.00 35.23 1.75
9061 11206 3.299340 ACCGCATACACTCGATATTCC 57.701 47.619 0.00 0.00 0.00 3.01
9062 11207 2.626266 ACCGCATACACTCGATATTCCA 59.374 45.455 0.00 0.00 0.00 3.53
9063 11208 3.258372 ACCGCATACACTCGATATTCCAT 59.742 43.478 0.00 0.00 0.00 3.41
9064 11209 3.614176 CCGCATACACTCGATATTCCATG 59.386 47.826 0.00 0.00 0.00 3.66
9065 11210 4.237724 CGCATACACTCGATATTCCATGT 58.762 43.478 0.00 0.00 0.00 3.21
9066 11211 4.324669 CGCATACACTCGATATTCCATGTC 59.675 45.833 0.00 0.00 0.00 3.06
9067 11212 5.473931 GCATACACTCGATATTCCATGTCT 58.526 41.667 0.00 0.00 0.00 3.41
9068 11213 5.574830 GCATACACTCGATATTCCATGTCTC 59.425 44.000 0.00 0.00 0.00 3.36
9069 11214 6.571344 GCATACACTCGATATTCCATGTCTCT 60.571 42.308 0.00 0.00 0.00 3.10
9070 11215 5.446143 ACACTCGATATTCCATGTCTCTC 57.554 43.478 0.00 0.00 0.00 3.20
9071 11216 4.889995 ACACTCGATATTCCATGTCTCTCA 59.110 41.667 0.00 0.00 0.00 3.27
9072 11217 5.360999 ACACTCGATATTCCATGTCTCTCAA 59.639 40.000 0.00 0.00 0.00 3.02
9073 11218 5.689514 CACTCGATATTCCATGTCTCTCAAC 59.310 44.000 0.00 0.00 0.00 3.18
9074 11219 5.596361 ACTCGATATTCCATGTCTCTCAACT 59.404 40.000 0.00 0.00 0.00 3.16
9075 11220 5.836347 TCGATATTCCATGTCTCTCAACTG 58.164 41.667 0.00 0.00 0.00 3.16
9076 11221 5.594317 TCGATATTCCATGTCTCTCAACTGA 59.406 40.000 0.00 0.00 0.00 3.41
9077 11222 6.096846 TCGATATTCCATGTCTCTCAACTGAA 59.903 38.462 0.00 0.00 0.00 3.02
9078 11223 6.420306 CGATATTCCATGTCTCTCAACTGAAG 59.580 42.308 0.00 0.00 0.00 3.02
9079 11224 3.325293 TCCATGTCTCTCAACTGAAGC 57.675 47.619 0.00 0.00 0.00 3.86
9080 11225 2.027745 TCCATGTCTCTCAACTGAAGCC 60.028 50.000 0.00 0.00 0.00 4.35
9081 11226 2.289882 CCATGTCTCTCAACTGAAGCCA 60.290 50.000 0.00 0.00 0.00 4.75
9082 11227 3.607741 CATGTCTCTCAACTGAAGCCAT 58.392 45.455 0.00 0.00 0.00 4.40
9083 11228 4.383444 CCATGTCTCTCAACTGAAGCCATA 60.383 45.833 0.00 0.00 0.00 2.74
9084 11229 4.193826 TGTCTCTCAACTGAAGCCATAC 57.806 45.455 0.00 0.00 0.00 2.39
9085 11230 3.578282 TGTCTCTCAACTGAAGCCATACA 59.422 43.478 0.00 0.00 0.00 2.29
9086 11231 3.929610 GTCTCTCAACTGAAGCCATACAC 59.070 47.826 0.00 0.00 0.00 2.90
9087 11232 3.578282 TCTCTCAACTGAAGCCATACACA 59.422 43.478 0.00 0.00 0.00 3.72
9088 11233 3.664107 TCTCAACTGAAGCCATACACAC 58.336 45.455 0.00 0.00 0.00 3.82
9089 11234 2.744202 CTCAACTGAAGCCATACACACC 59.256 50.000 0.00 0.00 0.00 4.16
9090 11235 2.105649 TCAACTGAAGCCATACACACCA 59.894 45.455 0.00 0.00 0.00 4.17
9091 11236 2.479566 ACTGAAGCCATACACACCAG 57.520 50.000 0.00 0.00 0.00 4.00
9092 11237 1.977854 ACTGAAGCCATACACACCAGA 59.022 47.619 0.00 0.00 0.00 3.86
9093 11238 2.573462 ACTGAAGCCATACACACCAGAT 59.427 45.455 0.00 0.00 0.00 2.90
9094 11239 3.009473 ACTGAAGCCATACACACCAGATT 59.991 43.478 0.00 0.00 0.00 2.40
9095 11240 4.225042 ACTGAAGCCATACACACCAGATTA 59.775 41.667 0.00 0.00 0.00 1.75
9096 11241 5.104360 ACTGAAGCCATACACACCAGATTAT 60.104 40.000 0.00 0.00 0.00 1.28
9097 11242 5.125356 TGAAGCCATACACACCAGATTATG 58.875 41.667 0.00 0.00 0.00 1.90
9098 11243 3.480470 AGCCATACACACCAGATTATGC 58.520 45.455 0.00 0.00 0.00 3.14
9099 11244 3.137176 AGCCATACACACCAGATTATGCT 59.863 43.478 0.00 0.00 0.00 3.79
9100 11245 3.499918 GCCATACACACCAGATTATGCTC 59.500 47.826 0.00 0.00 0.00 4.26
9101 11246 4.744867 GCCATACACACCAGATTATGCTCT 60.745 45.833 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.578928 GCGGTGTTTATATGGAATCAACCT 59.421 41.667 0.00 0.00 0.00 3.50
26 27 6.959639 AAATGAGCGGTGTTTATATGGAAT 57.040 33.333 0.00 0.00 0.00 3.01
36 37 2.425312 TGTCAACAAAATGAGCGGTGTT 59.575 40.909 0.00 0.00 34.60 3.32
41 42 2.981805 CCATGTGTCAACAAAATGAGCG 59.018 45.455 8.08 0.00 40.46 5.03
44 45 9.205719 CATATTTTCCATGTGTCAACAAAATGA 57.794 29.630 8.08 0.00 40.46 2.57
51 52 5.126061 AGCTCCATATTTTCCATGTGTCAAC 59.874 40.000 0.00 0.00 0.00 3.18
55 57 7.716799 TTTTAGCTCCATATTTTCCATGTGT 57.283 32.000 0.00 0.00 0.00 3.72
79 81 4.677250 CGTGGAAGAGCTAAACTACCGAAT 60.677 45.833 0.00 0.00 0.00 3.34
89 91 0.245539 CGGAACCGTGGAAGAGCTAA 59.754 55.000 4.99 0.00 34.35 3.09
111 113 4.574828 GCGCTAGGGTCATGAATTTAGAAA 59.425 41.667 8.77 0.00 0.00 2.52
124 126 0.178068 TGGAAATGAGCGCTAGGGTC 59.822 55.000 11.50 5.95 43.52 4.46
166 168 0.985549 GCTGAGTCGAACGTTAGCAG 59.014 55.000 12.42 10.68 0.00 4.24
177 179 1.657594 GTCATGACACATGCTGAGTCG 59.342 52.381 21.07 0.00 40.18 4.18
208 212 1.816679 TGCATGCTCATCCACTCGC 60.817 57.895 20.33 0.00 0.00 5.03
257 261 4.250305 ACACCACCACGGGCTGTC 62.250 66.667 0.00 0.00 40.22 3.51
262 266 4.947147 CACCCACACCACCACGGG 62.947 72.222 0.00 0.00 44.88 5.28
270 274 4.595538 TCGCACGACACCCACACC 62.596 66.667 0.00 0.00 0.00 4.16
287 291 6.530120 TGGTACACAAAGAATATGTCACTGT 58.470 36.000 0.00 0.00 0.00 3.55
297 301 3.149196 CTGTGCCTGGTACACAAAGAAT 58.851 45.455 13.90 0.00 46.71 2.40
305 309 0.679505 GTGTCTCTGTGCCTGGTACA 59.320 55.000 16.85 16.85 0.00 2.90
328 332 2.033299 CCACAGTTTTTGCGTGTCATCT 59.967 45.455 0.00 0.00 0.00 2.90
347 351 0.601841 GCCTTCTCGACGAAAACCCA 60.602 55.000 0.00 0.00 0.00 4.51
348 352 0.601841 TGCCTTCTCGACGAAAACCC 60.602 55.000 0.00 0.00 0.00 4.11
356 360 4.192317 ACCTTCATTAATGCCTTCTCGAC 58.808 43.478 10.76 0.00 0.00 4.20
438 456 6.366315 TGTAGTGTGTCGTTTTGCTTTTAT 57.634 33.333 0.00 0.00 0.00 1.40
454 472 2.352814 GCTTCTCCACGTGATGTAGTGT 60.353 50.000 19.30 0.00 36.69 3.55
487 506 5.692204 AGGAAAATCGATACGTATCTTGCAG 59.308 40.000 28.06 15.30 0.00 4.41
497 516 3.550275 TCTTCGCAAGGAAAATCGATACG 59.450 43.478 0.00 0.00 33.34 3.06
573 592 1.836802 AGAGGAGGAAGAGCATTGTCC 59.163 52.381 0.00 0.00 0.00 4.02
575 594 1.065564 GCAGAGGAGGAAGAGCATTGT 60.066 52.381 0.00 0.00 0.00 2.71
576 595 1.666054 GCAGAGGAGGAAGAGCATTG 58.334 55.000 0.00 0.00 0.00 2.82
577 596 0.545646 GGCAGAGGAGGAAGAGCATT 59.454 55.000 0.00 0.00 0.00 3.56
705 2238 3.432592 GCTGTCTCTCTTACCGGTTTTTC 59.567 47.826 15.04 0.00 0.00 2.29
706 2239 3.181458 TGCTGTCTCTCTTACCGGTTTTT 60.181 43.478 15.04 0.00 0.00 1.94
707 2240 2.367567 TGCTGTCTCTCTTACCGGTTTT 59.632 45.455 15.04 0.00 0.00 2.43
709 2242 1.546476 CTGCTGTCTCTCTTACCGGTT 59.454 52.381 15.04 0.00 0.00 4.44
710 2243 1.178276 CTGCTGTCTCTCTTACCGGT 58.822 55.000 13.98 13.98 0.00 5.28
711 2244 0.457851 CCTGCTGTCTCTCTTACCGG 59.542 60.000 0.00 0.00 0.00 5.28
712 2245 0.179124 GCCTGCTGTCTCTCTTACCG 60.179 60.000 0.00 0.00 0.00 4.02
713 2246 0.179124 CGCCTGCTGTCTCTCTTACC 60.179 60.000 0.00 0.00 0.00 2.85
714 2247 0.811915 TCGCCTGCTGTCTCTCTTAC 59.188 55.000 0.00 0.00 0.00 2.34
1122 2688 0.395311 GGGCTAGGGTTAGGGTTTGC 60.395 60.000 0.00 0.00 0.00 3.68
1491 3061 3.862877 TTCATCCAATCCATGATCCGT 57.137 42.857 0.00 0.00 30.26 4.69
1548 3120 2.454464 TAATAACCCGCGCACGCAC 61.454 57.895 16.04 0.00 42.06 5.34
1549 3121 2.125633 TAATAACCCGCGCACGCA 60.126 55.556 16.04 0.00 42.06 5.24
1550 3122 2.322081 GTAATAACCCGCGCACGC 59.678 61.111 8.75 4.64 38.22 5.34
1571 3145 2.995939 ACTAATACCATGCATCATCGCG 59.004 45.455 0.00 0.00 33.35 5.87
1599 3173 0.179129 GCGCCAACCATCAGATTTGG 60.179 55.000 8.94 8.94 42.43 3.28
1616 3190 0.321653 ACCTAAAGCTTCACTGGGCG 60.322 55.000 0.00 0.00 0.00 6.13
1650 3226 6.458206 CCAAACCACATGTATTAATCGACAGG 60.458 42.308 0.00 2.31 33.69 4.00
1663 3239 4.112634 ACCTATTGACCAAACCACATGT 57.887 40.909 0.00 0.00 0.00 3.21
1750 3328 7.148086 TGCTATTTTAGAAACATAGGGCACAAG 60.148 37.037 0.00 0.00 0.00 3.16
1773 3351 1.076906 ACCTGAGACTACCGGTGCT 59.923 57.895 19.93 11.99 0.00 4.40
1883 3461 5.464057 AGACGACACAACAATATCAACGAAA 59.536 36.000 0.00 0.00 0.00 3.46
1889 3467 4.084066 GCACAAGACGACACAACAATATCA 60.084 41.667 0.00 0.00 0.00 2.15
2122 3700 1.497991 TTGACGCCAAAGAACTCTCG 58.502 50.000 0.00 0.00 0.00 4.04
2299 3878 2.572191 TCGGCTATGGTAGACAAACG 57.428 50.000 0.00 0.00 31.54 3.60
2329 3908 9.420118 AGCATAAAGTGAACCAATAAATATCCA 57.580 29.630 0.00 0.00 0.00 3.41
2504 4083 6.155049 AGGAATAAATGCAACAGGCTAAATGT 59.845 34.615 0.00 0.00 45.15 2.71
2733 4312 4.686972 TGCCATTAGACTTGAGAGAATCG 58.313 43.478 0.00 0.00 42.67 3.34
2910 4489 1.264288 CAACACTGCCGAGAAACCTTC 59.736 52.381 0.00 0.00 0.00 3.46
2921 4500 3.131400 TCCTTTACAAAACCAACACTGCC 59.869 43.478 0.00 0.00 0.00 4.85
2972 4551 5.924475 ACACCGTTTTCTTATGAACTGAG 57.076 39.130 0.00 0.00 31.02 3.35
3006 4585 9.653287 TGAGTTGTCCTGATATGTTAAAAGTAG 57.347 33.333 0.00 0.00 0.00 2.57
3347 4944 7.732593 AGTGGCTAGGAGATAAAAGACTATGAT 59.267 37.037 0.00 0.00 0.00 2.45
3425 5022 4.469657 TGTTGCAGGAGGAAATAACAGTT 58.530 39.130 0.00 0.00 0.00 3.16
3539 5136 5.982516 TGTGCACATGAAAATTTAAGTGACC 59.017 36.000 17.42 5.92 0.00 4.02
3615 5212 6.166982 AGAAGATGCGGGCTATAAATACTTC 58.833 40.000 0.00 0.00 0.00 3.01
4676 6285 9.581099 TGTCTTTCAGAAAACAAGAAATTTACC 57.419 29.630 0.00 0.00 31.58 2.85
4823 6433 7.080099 CAGGATTCTGGCATTGTAAATTATCG 58.920 38.462 0.00 0.00 37.36 2.92
4879 6489 2.268920 CCAGGCACCACATAGCGT 59.731 61.111 0.00 0.00 0.00 5.07
4914 6524 3.640967 ACCAAAACAAATAGCAGGCAGAA 59.359 39.130 0.00 0.00 0.00 3.02
5175 6785 2.365237 ACCCGGGCCTAGGACTTC 60.365 66.667 24.08 0.00 0.00 3.01
5192 6802 1.053835 TGGGCAGGAGTGTTGTCTGA 61.054 55.000 0.00 0.00 0.00 3.27
5702 7312 8.709308 ACAGCAGATAACCAGTAATCTCTTAAT 58.291 33.333 0.00 0.00 29.93 1.40
5709 7319 8.894768 AATCTAACAGCAGATAACCAGTAATC 57.105 34.615 0.00 0.00 34.08 1.75
5777 7387 1.210478 CCTCACTGACACCCCTAATGG 59.790 57.143 0.00 0.00 0.00 3.16
5809 7419 4.147321 AGGTGTTGATGATTTGACTTGCT 58.853 39.130 0.00 0.00 0.00 3.91
5873 7483 2.903784 TGGATCGGTATGGACAATAGGG 59.096 50.000 0.00 0.00 0.00 3.53
5881 7491 4.764823 GCCAATTAAATGGATCGGTATGGA 59.235 41.667 14.00 0.00 43.54 3.41
5888 7515 3.304659 CCTTCCGCCAATTAAATGGATCG 60.305 47.826 14.00 8.03 43.54 3.69
5891 7518 1.754226 GCCTTCCGCCAATTAAATGGA 59.246 47.619 14.00 0.00 43.54 3.41
5892 7519 1.480137 TGCCTTCCGCCAATTAAATGG 59.520 47.619 5.09 5.09 43.70 3.16
5893 7520 2.957491 TGCCTTCCGCCAATTAAATG 57.043 45.000 0.00 0.00 36.24 2.32
5894 7521 3.795877 CATTGCCTTCCGCCAATTAAAT 58.204 40.909 0.00 0.00 36.24 1.40
5895 7522 2.676463 GCATTGCCTTCCGCCAATTAAA 60.676 45.455 0.00 0.00 36.24 1.52
5896 7523 1.134848 GCATTGCCTTCCGCCAATTAA 60.135 47.619 0.00 0.00 36.24 1.40
5897 7524 0.459489 GCATTGCCTTCCGCCAATTA 59.541 50.000 0.00 0.00 36.24 1.40
5898 7525 1.218854 GCATTGCCTTCCGCCAATT 59.781 52.632 0.00 0.00 36.24 2.32
5899 7526 1.332144 ATGCATTGCCTTCCGCCAAT 61.332 50.000 6.12 0.00 36.24 3.16
5900 7527 1.947597 GATGCATTGCCTTCCGCCAA 61.948 55.000 6.12 0.00 36.24 4.52
5901 7528 2.362760 ATGCATTGCCTTCCGCCA 60.363 55.556 6.12 0.00 36.24 5.69
5902 7529 1.669999 AAGATGCATTGCCTTCCGCC 61.670 55.000 6.12 0.00 36.24 6.13
5903 7530 0.174162 AAAGATGCATTGCCTTCCGC 59.826 50.000 6.12 0.00 38.31 5.54
5904 7531 3.996150 ATAAAGATGCATTGCCTTCCG 57.004 42.857 6.12 0.00 0.00 4.30
5905 7532 4.275936 ACGTATAAAGATGCATTGCCTTCC 59.724 41.667 6.12 0.00 0.00 3.46
5906 7533 5.424121 ACGTATAAAGATGCATTGCCTTC 57.576 39.130 6.12 3.46 0.00 3.46
5907 7534 5.835113 AACGTATAAAGATGCATTGCCTT 57.165 34.783 6.12 0.00 0.00 4.35
5908 7535 7.445402 AGAATAACGTATAAAGATGCATTGCCT 59.555 33.333 6.12 0.00 0.00 4.75
5909 7536 7.584987 AGAATAACGTATAAAGATGCATTGCC 58.415 34.615 6.12 0.00 0.00 4.52
5910 7537 8.895845 CAAGAATAACGTATAAAGATGCATTGC 58.104 33.333 0.00 0.46 0.00 3.56
5911 7538 9.935682 ACAAGAATAACGTATAAAGATGCATTG 57.064 29.630 0.00 0.00 0.00 2.82
6028 7655 1.148867 ACCCACATTCATTCCACCCAA 59.851 47.619 0.00 0.00 0.00 4.12
6072 7701 7.920682 AGTTTGACAAAGCATACAAGTTAAAGG 59.079 33.333 0.00 0.00 0.00 3.11
6712 8343 4.489679 AAAGAAAACAGACGATGAAGGC 57.510 40.909 0.00 0.00 0.00 4.35
6749 8380 6.261381 CGTAAGAAGGCTCTATCTGTACTTCT 59.739 42.308 0.00 0.00 44.51 2.85
6750 8381 6.432107 CGTAAGAAGGCTCTATCTGTACTTC 58.568 44.000 0.00 0.00 43.02 3.01
7219 8853 5.253330 AGCGAATCCAAAGAATCAAGGTTA 58.747 37.500 0.00 0.00 0.00 2.85
7260 8894 2.547218 GGTCTCCTTGTAAACAGCACGA 60.547 50.000 0.00 0.00 0.00 4.35
7783 9417 0.472471 AGTCAGCGGGGAAAAGAACA 59.528 50.000 0.00 0.00 0.00 3.18
8046 9700 7.896811 TGATGTTGTACAATCAGTAGACTCTT 58.103 34.615 12.26 0.00 32.19 2.85
8085 9739 0.036732 GGCTCACAAGTCATCACCCA 59.963 55.000 0.00 0.00 0.00 4.51
8153 9807 1.471684 CTGGATCTTTCTTGGCAGCAC 59.528 52.381 0.00 0.00 0.00 4.40
8200 9854 2.808244 CCGCACAACAAAATGTCAGTT 58.192 42.857 0.00 0.00 0.00 3.16
8327 9983 2.280552 CCAACAGCCAGCCTGCATT 61.281 57.895 0.00 0.00 45.78 3.56
8389 10045 1.780327 CCCCATTTCTCCACCCCAA 59.220 57.895 0.00 0.00 0.00 4.12
8396 10052 8.390921 TGATAAATTATCTACCCCCATTTCTCC 58.609 37.037 13.45 0.00 36.17 3.71
8459 10123 1.879372 GCAGGAGTTCACAGTGCATGA 60.879 52.381 0.00 0.00 34.18 3.07
8515 10179 2.685897 CAAGGACGACAAAAAGAACCCA 59.314 45.455 0.00 0.00 0.00 4.51
8516 10180 2.686405 ACAAGGACGACAAAAAGAACCC 59.314 45.455 0.00 0.00 0.00 4.11
8517 10181 4.102649 CAACAAGGACGACAAAAAGAACC 58.897 43.478 0.00 0.00 0.00 3.62
8519 10183 3.129638 CCCAACAAGGACGACAAAAAGAA 59.870 43.478 0.00 0.00 41.22 2.52
8520 10184 2.685897 CCCAACAAGGACGACAAAAAGA 59.314 45.455 0.00 0.00 41.22 2.52
8521 10185 2.685897 TCCCAACAAGGACGACAAAAAG 59.314 45.455 0.00 0.00 41.22 2.27
8608 10283 2.556189 TGCACGTTATTGAGGCAAACAT 59.444 40.909 0.00 0.00 0.00 2.71
8720 10850 0.737715 GACGATTGAGTTCCGCAGCT 60.738 55.000 0.00 0.00 0.00 4.24
8722 10852 1.084370 GGGACGATTGAGTTCCGCAG 61.084 60.000 0.00 0.00 28.68 5.18
8745 10875 3.181967 CGGTCGCTTGCGAAGGAG 61.182 66.667 19.36 7.45 0.00 3.69
8752 10882 4.389576 CAAGGTGCGGTCGCTTGC 62.390 66.667 16.36 6.73 42.51 4.01
8835 10966 1.093159 CCTGAGAGCAAGATGTTGGC 58.907 55.000 4.57 0.00 33.87 4.52
8926 11071 0.035725 CCTGTTCTGAGAGCATGCCA 60.036 55.000 15.66 4.33 0.00 4.92
8931 11076 3.206150 GTTTGAACCTGTTCTGAGAGCA 58.794 45.455 11.03 0.00 40.14 4.26
8936 11081 2.992124 TCCGTTTGAACCTGTTCTGA 57.008 45.000 11.03 0.00 40.14 3.27
8953 11098 2.100605 ACGATTTCTGTCAGCCTTCC 57.899 50.000 0.00 0.00 0.00 3.46
8992 11137 3.932545 TGAGCAGAACAGAGTCTTCTC 57.067 47.619 0.00 0.00 38.11 2.87
8995 11140 2.368221 AGCTTGAGCAGAACAGAGTCTT 59.632 45.455 5.70 0.00 45.16 3.01
9008 11153 2.488952 GTATAGGGCTGAAGCTTGAGC 58.511 52.381 27.41 27.41 41.70 4.26
9020 11165 1.746517 CGTGGACTGGGTATAGGGC 59.253 63.158 0.00 0.00 0.00 5.19
9041 11186 2.626266 TGGAATATCGAGTGTATGCGGT 59.374 45.455 0.00 0.00 0.00 5.68
9042 11187 3.297830 TGGAATATCGAGTGTATGCGG 57.702 47.619 0.00 0.00 0.00 5.69
9048 11193 4.889995 TGAGAGACATGGAATATCGAGTGT 59.110 41.667 0.00 0.00 0.00 3.55
9049 11194 5.444663 TGAGAGACATGGAATATCGAGTG 57.555 43.478 0.00 0.00 0.00 3.51
9050 11195 5.596361 AGTTGAGAGACATGGAATATCGAGT 59.404 40.000 0.00 0.00 0.00 4.18
9051 11196 5.919707 CAGTTGAGAGACATGGAATATCGAG 59.080 44.000 0.00 0.00 0.00 4.04
9052 11197 5.594317 TCAGTTGAGAGACATGGAATATCGA 59.406 40.000 0.00 0.00 0.00 3.59
9053 11198 5.836347 TCAGTTGAGAGACATGGAATATCG 58.164 41.667 0.00 0.00 0.00 2.92
9054 11199 6.202570 GCTTCAGTTGAGAGACATGGAATATC 59.797 42.308 0.00 0.00 0.00 1.63
9055 11200 6.054295 GCTTCAGTTGAGAGACATGGAATAT 58.946 40.000 0.00 0.00 0.00 1.28
9056 11201 5.423015 GCTTCAGTTGAGAGACATGGAATA 58.577 41.667 0.00 0.00 0.00 1.75
9057 11202 4.260170 GCTTCAGTTGAGAGACATGGAAT 58.740 43.478 0.00 0.00 0.00 3.01
9058 11203 3.557898 GGCTTCAGTTGAGAGACATGGAA 60.558 47.826 0.00 0.00 0.00 3.53
9059 11204 2.027745 GGCTTCAGTTGAGAGACATGGA 60.028 50.000 0.00 0.00 0.00 3.41
9060 11205 2.289882 TGGCTTCAGTTGAGAGACATGG 60.290 50.000 0.00 0.00 0.00 3.66
9061 11206 3.049708 TGGCTTCAGTTGAGAGACATG 57.950 47.619 0.00 0.00 0.00 3.21
9062 11207 3.996921 ATGGCTTCAGTTGAGAGACAT 57.003 42.857 6.76 6.76 0.00 3.06
9063 11208 3.578282 TGTATGGCTTCAGTTGAGAGACA 59.422 43.478 3.48 3.48 0.00 3.41
9064 11209 3.929610 GTGTATGGCTTCAGTTGAGAGAC 59.070 47.826 0.00 0.00 0.00 3.36
9065 11210 3.578282 TGTGTATGGCTTCAGTTGAGAGA 59.422 43.478 0.00 0.00 0.00 3.10
9066 11211 3.681897 GTGTGTATGGCTTCAGTTGAGAG 59.318 47.826 0.00 0.00 0.00 3.20
9067 11212 3.557054 GGTGTGTATGGCTTCAGTTGAGA 60.557 47.826 0.00 0.00 0.00 3.27
9068 11213 2.744202 GGTGTGTATGGCTTCAGTTGAG 59.256 50.000 0.00 0.00 0.00 3.02
9069 11214 2.105649 TGGTGTGTATGGCTTCAGTTGA 59.894 45.455 0.00 0.00 0.00 3.18
9070 11215 2.485426 CTGGTGTGTATGGCTTCAGTTG 59.515 50.000 0.00 0.00 0.00 3.16
9071 11216 2.371841 TCTGGTGTGTATGGCTTCAGTT 59.628 45.455 0.00 0.00 0.00 3.16
9072 11217 1.977854 TCTGGTGTGTATGGCTTCAGT 59.022 47.619 0.00 0.00 0.00 3.41
9073 11218 2.768253 TCTGGTGTGTATGGCTTCAG 57.232 50.000 0.00 0.00 0.00 3.02
9074 11219 3.719268 AATCTGGTGTGTATGGCTTCA 57.281 42.857 0.00 0.00 0.00 3.02
9075 11220 4.023707 GCATAATCTGGTGTGTATGGCTTC 60.024 45.833 0.00 0.00 0.00 3.86
9076 11221 3.885297 GCATAATCTGGTGTGTATGGCTT 59.115 43.478 0.00 0.00 0.00 4.35
9077 11222 3.137176 AGCATAATCTGGTGTGTATGGCT 59.863 43.478 0.00 0.00 33.34 4.75
9078 11223 3.480470 AGCATAATCTGGTGTGTATGGC 58.520 45.455 0.00 0.00 33.34 4.40
9079 11224 4.965814 AGAGCATAATCTGGTGTGTATGG 58.034 43.478 0.00 0.00 35.19 2.74


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

AutoCloner maintained by Alex Coulton.