Multiple sequence alignment - TraesCS5D01G129300

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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 TraesCS5D01G129300 chr5D 100.000 2945 0 0 1516 4460 202906025 202908969 0.000000e+00 5439.0
1 TraesCS5D01G129300 chr5D 100.000 1388 0 0 1 1388 202904510 202905897 0.000000e+00 2564.0
2 TraesCS5D01G129300 chr5D 84.239 184 24 3 3160 3343 436546896 436546718 1.650000e-39 174.0
3 TraesCS5D01G129300 chr5D 89.552 134 12 2 2995 3127 436547032 436546900 7.670000e-38 169.0
4 TraesCS5D01G129300 chr5D 92.308 39 3 0 246 284 150823914 150823876 6.230000e-04 56.5
5 TraesCS5D01G129300 chr5B 94.138 2644 89 24 1516 4116 208709551 208706931 0.000000e+00 3964.0
6 TraesCS5D01G129300 chr5B 93.777 707 40 4 1 705 208711134 208710430 0.000000e+00 1059.0
7 TraesCS5D01G129300 chr5B 94.127 647 23 4 744 1388 208710224 208709591 0.000000e+00 970.0
8 TraesCS5D01G129300 chr5B 88.421 95 9 2 2995 3088 100836921 100837014 3.650000e-21 113.0
9 TraesCS5D01G129300 chr5B 91.304 46 4 0 3625 3670 90985801 90985756 3.720000e-06 63.9
10 TraesCS5D01G129300 chr5B 92.308 39 3 0 246 284 194210302 194210340 6.230000e-04 56.5
11 TraesCS5D01G129300 chr5A 95.677 1920 54 12 1516 3411 219687542 219689456 0.000000e+00 3059.0
12 TraesCS5D01G129300 chr5A 90.994 533 43 5 147 678 219677966 219678494 0.000000e+00 713.0
13 TraesCS5D01G129300 chr5A 96.040 404 15 1 3714 4116 219691341 219691744 0.000000e+00 656.0
14 TraesCS5D01G129300 chr5A 86.493 422 19 17 805 1217 219682114 219682506 3.190000e-116 429.0
15 TraesCS5D01G129300 chr5A 88.793 348 33 4 4115 4460 644174775 644175118 5.330000e-114 422.0
16 TraesCS5D01G129300 chr5A 95.364 151 7 0 1 151 219653514 219653664 1.600000e-59 241.0
17 TraesCS5D01G129300 chr5A 99.167 120 1 0 1269 1388 219687384 219687503 2.700000e-52 217.0
18 TraesCS5D01G129300 chr5A 95.935 123 2 1 3399 3518 219689542 219689664 3.520000e-46 196.0
19 TraesCS5D01G129300 chr5A 82.796 186 8 4 3509 3678 219691162 219691339 1.290000e-30 145.0
20 TraesCS5D01G129300 chr3D 88.796 357 35 4 4107 4460 500251281 500250927 2.460000e-117 433.0
21 TraesCS5D01G129300 chr3D 88.473 347 34 5 4115 4458 90820421 90820764 8.930000e-112 414.0
22 TraesCS5D01G129300 chr3D 87.464 351 39 3 4111 4458 40757591 40757243 2.500000e-107 399.0
23 TraesCS5D01G129300 chr2A 87.896 347 41 1 4115 4460 768446669 768446323 1.490000e-109 407.0
24 TraesCS5D01G129300 chr2A 87.679 349 40 2 4115 4460 528136737 528137085 1.930000e-108 403.0
25 TraesCS5D01G129300 chr2A 86.628 344 43 3 4119 4460 376112587 376112245 1.170000e-100 377.0
26 TraesCS5D01G129300 chr2A 93.056 72 5 0 1139 1210 528101460 528101389 6.100000e-19 106.0
27 TraesCS5D01G129300 chr1D 87.393 349 38 4 4115 4458 7063747 7063400 3.230000e-106 396.0
28 TraesCS5D01G129300 chr1D 87.106 349 43 2 4113 4460 41443011 41443358 1.160000e-105 394.0
29 TraesCS5D01G129300 chr1D 89.286 140 12 1 2991 3127 241967655 241967516 5.930000e-39 172.0
30 TraesCS5D01G129300 chr2D 80.656 305 42 10 3216 3512 74123787 74124082 2.090000e-53 220.0
31 TraesCS5D01G129300 chr4A 80.537 298 44 8 3216 3512 211671587 211671871 2.700000e-52 217.0
32 TraesCS5D01G129300 chr4A 83.152 184 25 5 3160 3343 256956136 256955959 3.570000e-36 163.0
33 TraesCS5D01G129300 chr4A 90.991 111 10 0 3019 3129 257295306 257295196 2.780000e-32 150.0
34 TraesCS5D01G129300 chr3A 79.221 308 50 8 3206 3512 530086362 530086656 7.560000e-48 202.0
35 TraesCS5D01G129300 chr3A 100.000 33 0 0 3640 3672 629668915 629668883 1.340000e-05 62.1
36 TraesCS5D01G129300 chr6B 80.505 277 40 8 3216 3491 511279288 511279025 2.720000e-47 200.0
37 TraesCS5D01G129300 chr6B 100.000 34 0 0 3640 3673 157668213 157668246 3.720000e-06 63.9
38 TraesCS5D01G129300 chr3B 90.000 140 11 1 2991 3127 273250204 273250343 1.270000e-40 178.0
39 TraesCS5D01G129300 chr3B 100.000 33 0 0 3640 3672 648925296 648925264 1.340000e-05 62.1
40 TraesCS5D01G129300 chr3B 92.857 42 1 2 3634 3673 799204631 799204590 4.820000e-05 60.2
41 TraesCS5D01G129300 chr6A 86.395 147 19 1 3206 3351 86625674 86625528 4.620000e-35 159.0
42 TraesCS5D01G129300 chr4B 92.135 89 7 0 1122 1210 378000872 378000960 4.680000e-25 126.0
43 TraesCS5D01G129300 chr4B 100.000 30 0 0 1057 1086 203186366 203186337 6.230000e-04 56.5
44 TraesCS5D01G129300 chr1B 92.683 41 3 0 3640 3680 593924345 593924385 4.820000e-05 60.2
45 TraesCS5D01G129300 chr1A 97.222 36 0 1 3640 3674 553539195 553539160 4.820000e-05 60.2


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 TraesCS5D01G129300 chr5D 202904510 202908969 4459 False 4001.500000 5439 100.0000 1 4460 2 chr5D.!!$F1 4459
1 TraesCS5D01G129300 chr5B 208706931 208711134 4203 True 1997.666667 3964 94.0140 1 4116 3 chr5B.!!$R2 4115
2 TraesCS5D01G129300 chr5A 219687384 219691744 4360 False 854.600000 3059 93.9230 1269 4116 5 chr5A.!!$F4 2847
3 TraesCS5D01G129300 chr5A 219677966 219682506 4540 False 571.000000 713 88.7435 147 1217 2 chr5A.!!$F3 1070

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
887 4552 0.874390 TTCATCTGTTTCGCTGCCAC 59.126 50.0 0.0 0.0 0.00 5.01 F
1875 5568 0.450983 GCCAGAGCAGACTTTGATGC 59.549 55.0 0.0 0.0 42.87 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 5871 0.671251 GCAACCGACCCAATCACAAA 59.329 50.0 0.00 0.0 0.00 2.83 R
3465 7276 0.167908 TGAACCGCGCAATGCTTAAG 59.832 50.0 8.75 0.0 43.27 1.85 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
101 103 3.197927 AGCCATTACCAATTCCCCAAA 57.802 42.857 0.00 0.00 0.00 3.28
114 116 5.552430 ATTCCCCAAATACTCCCTCTTTT 57.448 39.130 0.00 0.00 0.00 2.27
121 123 6.724441 CCCAAATACTCCCTCTTTTAAAGGTT 59.276 38.462 4.77 0.00 31.51 3.50
129 131 5.529800 TCCCTCTTTTAAAGGTTTGAACTCG 59.470 40.000 4.77 0.00 31.51 4.18
132 134 6.056428 TCTTTTAAAGGTTTGAACTCGAGC 57.944 37.500 13.61 0.00 0.00 5.03
212 214 3.916989 ACCAGAGGGGAAGTACTTTGATT 59.083 43.478 10.02 0.00 41.15 2.57
243 245 5.449588 CCCTTACACAATCATGATGCTCAAC 60.450 44.000 9.46 0.00 0.00 3.18
325 327 1.965414 TGCCACCTCTATCCTTTGGA 58.035 50.000 0.00 0.00 35.55 3.53
342 344 2.217750 TGGAACACACATTCTTCACCG 58.782 47.619 0.00 0.00 0.00 4.94
366 369 3.181545 GCAAACCAATGCATTTTACGTCG 60.182 43.478 9.83 0.00 45.70 5.12
395 398 1.440618 TGTCACCCCACCAATAGTGT 58.559 50.000 0.00 0.00 45.74 3.55
406 409 5.360714 CCCACCAATAGTGTGAAATAGCATT 59.639 40.000 0.00 0.00 45.74 3.56
422 425 4.434545 AGCATTAGTGATCCTCTTGCAT 57.565 40.909 14.75 0.00 34.97 3.96
452 455 6.373216 TCTTCGGGAATTTGAATACGTTCATT 59.627 34.615 0.00 0.00 43.49 2.57
492 495 1.604278 GGGCCATCGCTTTAATCAGAC 59.396 52.381 4.39 0.00 34.44 3.51
645 649 3.189702 AGAAAGAGAAAGAGACTCCGTCG 59.810 47.826 0.00 0.00 37.67 5.12
649 653 3.436359 AGAGAAAGAGACTCCGTCGTTAC 59.564 47.826 0.00 0.00 37.67 2.50
655 659 2.163010 GAGACTCCGTCGTTACATCCAA 59.837 50.000 0.00 0.00 37.67 3.53
705 2398 6.680810 TCAACATTTGTATTGAGGCTGAAAG 58.319 36.000 0.00 0.00 31.29 2.62
706 2399 5.649782 ACATTTGTATTGAGGCTGAAAGG 57.350 39.130 0.00 0.00 0.00 3.11
721 2414 6.830873 GCTGAAAGGCCATAGAATAATCAT 57.169 37.500 5.01 0.00 0.00 2.45
722 2415 6.850555 GCTGAAAGGCCATAGAATAATCATC 58.149 40.000 5.01 0.00 0.00 2.92
723 2416 6.127786 GCTGAAAGGCCATAGAATAATCATCC 60.128 42.308 5.01 0.00 0.00 3.51
724 2417 5.939883 TGAAAGGCCATAGAATAATCATCCG 59.060 40.000 5.01 0.00 0.00 4.18
725 2418 3.878778 AGGCCATAGAATAATCATCCGC 58.121 45.455 5.01 0.00 0.00 5.54
726 2419 2.945668 GGCCATAGAATAATCATCCGCC 59.054 50.000 0.00 0.00 0.00 6.13
727 2420 2.945668 GCCATAGAATAATCATCCGCCC 59.054 50.000 0.00 0.00 0.00 6.13
729 2422 4.446371 CCATAGAATAATCATCCGCCCTC 58.554 47.826 0.00 0.00 0.00 4.30
730 2423 4.080919 CCATAGAATAATCATCCGCCCTCA 60.081 45.833 0.00 0.00 0.00 3.86
732 2425 6.183361 CCATAGAATAATCATCCGCCCTCATA 60.183 42.308 0.00 0.00 0.00 2.15
733 2426 5.762179 AGAATAATCATCCGCCCTCATAA 57.238 39.130 0.00 0.00 0.00 1.90
734 2427 6.319048 AGAATAATCATCCGCCCTCATAAT 57.681 37.500 0.00 0.00 0.00 1.28
735 2428 6.352516 AGAATAATCATCCGCCCTCATAATC 58.647 40.000 0.00 0.00 0.00 1.75
738 2431 2.179427 TCATCCGCCCTCATAATCGAT 58.821 47.619 0.00 0.00 0.00 3.59
741 2434 1.021390 CCGCCCTCATAATCGATGGC 61.021 60.000 11.21 11.21 41.72 4.40
742 2435 1.021390 CGCCCTCATAATCGATGGCC 61.021 60.000 14.54 0.00 42.02 5.36
764 2624 4.637534 CCCAAGGCCATAGAATAATCATCG 59.362 45.833 5.01 0.00 0.00 3.84
887 4552 0.874390 TTCATCTGTTTCGCTGCCAC 59.126 50.000 0.00 0.00 0.00 5.01
919 4584 4.641645 CCAGCAGCACCACGGGAA 62.642 66.667 0.00 0.00 0.00 3.97
932 4597 2.046285 CGGGAATCCCAAGTGCACC 61.046 63.158 19.81 0.00 45.83 5.01
933 4598 1.076549 GGGAATCCCAAGTGCACCA 59.923 57.895 14.67 0.00 44.65 4.17
966 4631 1.165907 ACCATCCACAAGCACACACG 61.166 55.000 0.00 0.00 0.00 4.49
967 4632 0.884259 CCATCCACAAGCACACACGA 60.884 55.000 0.00 0.00 0.00 4.35
968 4633 1.159285 CATCCACAAGCACACACGAT 58.841 50.000 0.00 0.00 0.00 3.73
970 4635 0.943835 TCCACAAGCACACACGATCG 60.944 55.000 14.88 14.88 0.00 3.69
976 4641 4.468545 CACACACGATCGCGCACG 62.469 66.667 16.60 19.29 42.48 5.34
1554 5228 3.589988 CACGCTGTTCTGTTCCTATCTT 58.410 45.455 0.00 0.00 0.00 2.40
1662 5355 4.749245 ATGACGTGGAAATGTTTCTGAC 57.251 40.909 0.00 2.87 37.35 3.51
1669 5362 4.214332 GTGGAAATGTTTCTGACTCTCACC 59.786 45.833 5.56 0.00 37.35 4.02
1722 5415 1.811965 CAATGCGTGAAGGTCAATCCA 59.188 47.619 0.00 0.00 39.02 3.41
1750 5443 1.525784 CGCAGAAGCAAGTTCGATTCG 60.526 52.381 0.00 0.00 42.27 3.34
1875 5568 0.450983 GCCAGAGCAGACTTTGATGC 59.549 55.000 0.00 0.00 42.87 3.91
2028 5723 3.619038 CAGGCGATAAGAAACTTCTGACC 59.381 47.826 0.00 0.00 37.65 4.02
2086 5781 5.163663 GCTCTAGAATCTCAGATGATACCCG 60.164 48.000 0.00 0.00 0.00 5.28
2176 5871 7.628234 AGATGAAGTGATTAAAGTGGATCTGT 58.372 34.615 0.00 0.00 0.00 3.41
2249 5944 6.546403 GGGAAGGGTGAGGTAATTATTTTCTC 59.454 42.308 0.00 0.00 0.00 2.87
2268 5963 0.870393 CGCACATGCAGTTGAAGAGT 59.130 50.000 4.49 0.00 42.21 3.24
2338 6033 2.361757 TGTTGACCTTTGCCAATGTCAG 59.638 45.455 8.31 0.00 38.37 3.51
2396 6091 2.747446 TCTACTGCGCCATTTTCCTTTC 59.253 45.455 4.18 0.00 0.00 2.62
2513 6208 9.347934 CGCTTCTTATCTGTAGTTTATCTATGG 57.652 37.037 0.00 0.00 0.00 2.74
2517 6212 8.512956 TCTTATCTGTAGTTTATCTATGGACGC 58.487 37.037 0.00 0.00 0.00 5.19
2518 6213 5.449107 TCTGTAGTTTATCTATGGACGCC 57.551 43.478 0.00 0.00 0.00 5.68
2732 6436 2.564471 GCATGAGTGCCAGCTTTCT 58.436 52.632 0.00 0.00 45.76 2.52
2733 6437 1.742761 GCATGAGTGCCAGCTTTCTA 58.257 50.000 0.00 0.00 45.76 2.10
2734 6438 2.295885 GCATGAGTGCCAGCTTTCTAT 58.704 47.619 0.00 0.00 45.76 1.98
2735 6439 2.686915 GCATGAGTGCCAGCTTTCTATT 59.313 45.455 0.00 0.00 45.76 1.73
2736 6440 3.129988 GCATGAGTGCCAGCTTTCTATTT 59.870 43.478 0.00 0.00 45.76 1.40
2842 6546 6.461092 CGCTAGAAATGGTTGAGATACTGGTA 60.461 42.308 0.00 0.00 0.00 3.25
2887 6594 4.271049 ACAATCCTGCTTGTATTTCGATCG 59.729 41.667 9.36 9.36 37.58 3.69
2918 6625 7.194112 TCAAAGAACCATCTATGTGGACATA 57.806 36.000 0.00 0.00 42.02 2.29
2943 6650 4.130118 GTGCCTCTTCTTTTCTGAAGTGA 58.870 43.478 7.59 0.00 42.76 3.41
2999 6706 8.475639 TGAAAGATTGAGTAGTAACCTATCCAC 58.524 37.037 0.00 0.00 0.00 4.02
3199 6906 6.019779 TCGCTTGGTAAAGTTGCAAATAAT 57.980 33.333 0.00 0.00 35.69 1.28
3200 6907 7.119992 TCTCGCTTGGTAAAGTTGCAAATAATA 59.880 33.333 0.00 0.00 35.69 0.98
3201 6908 7.247728 TCGCTTGGTAAAGTTGCAAATAATAG 58.752 34.615 0.00 0.00 35.69 1.73
3224 6931 4.177537 TCTTCCACCACCAGATTTTGAA 57.822 40.909 0.00 0.00 0.00 2.69
3525 8843 6.050432 AGACGTGTTTACAAAAGGTCATACA 58.950 36.000 0.00 0.00 0.00 2.29
3552 8870 1.272490 TCTTCTTCGTTGAGTCGGCAT 59.728 47.619 0.00 0.00 0.00 4.40
3553 8871 2.069273 CTTCTTCGTTGAGTCGGCATT 58.931 47.619 0.00 0.00 0.00 3.56
3554 8872 1.710013 TCTTCGTTGAGTCGGCATTC 58.290 50.000 0.00 0.00 0.00 2.67
3555 8873 0.366871 CTTCGTTGAGTCGGCATTCG 59.633 55.000 0.00 0.00 40.90 3.34
3556 8874 1.011968 TTCGTTGAGTCGGCATTCGG 61.012 55.000 0.00 0.00 39.77 4.30
3557 8875 2.785258 GTTGAGTCGGCATTCGGC 59.215 61.111 0.00 0.00 45.07 5.54
3591 8913 2.631012 CTAGGCTGTTCCCATGGCCC 62.631 65.000 6.09 0.00 45.07 5.80
3692 9026 6.218108 ACTAGAAAACGGGTTCTATACTGG 57.782 41.667 9.66 2.74 38.96 4.00
3693 9027 5.954150 ACTAGAAAACGGGTTCTATACTGGA 59.046 40.000 9.66 0.00 38.96 3.86
3889 9223 3.390135 TGCGTCTTTTGTCCTTCACTAG 58.610 45.455 0.00 0.00 0.00 2.57
3947 9281 0.108804 TTGTGGTTTGCGCGGAAAAA 60.109 45.000 27.46 15.08 0.00 1.94
3948 9282 0.103208 TGTGGTTTGCGCGGAAAAAT 59.897 45.000 27.46 0.00 0.00 1.82
3956 9290 1.068610 TGCGCGGAAAAATGAAGAAGG 60.069 47.619 8.83 0.00 0.00 3.46
3986 9320 2.290641 ACAGGTTGTGAACGCTGAAATC 59.709 45.455 10.18 0.00 35.23 2.17
4054 9388 6.747280 CCTAATTTGAACGTGTGAATGGATTC 59.253 38.462 0.00 0.00 37.31 2.52
4099 9434 1.694696 GTGTCCTTGAGACCCTGTCTT 59.305 52.381 0.00 0.00 43.53 3.01
4105 9440 4.467795 TCCTTGAGACCCTGTCTTAATCTG 59.532 45.833 2.47 0.00 43.53 2.90
4110 9445 0.830648 CCCTGTCTTAATCTGCCGGA 59.169 55.000 5.05 0.00 0.00 5.14
4116 9451 2.427453 GTCTTAATCTGCCGGACTCAGA 59.573 50.000 5.05 9.53 43.79 3.27
4117 9452 2.690497 TCTTAATCTGCCGGACTCAGAG 59.310 50.000 5.05 0.00 43.02 3.35
4118 9453 0.747255 TAATCTGCCGGACTCAGAGC 59.253 55.000 5.05 0.00 43.02 4.09
4119 9454 1.260538 AATCTGCCGGACTCAGAGCA 61.261 55.000 5.05 0.00 43.02 4.26
4120 9455 1.047596 ATCTGCCGGACTCAGAGCAT 61.048 55.000 5.05 0.00 43.02 3.79
4121 9456 1.227205 CTGCCGGACTCAGAGCATC 60.227 63.158 5.05 0.00 34.16 3.91
4132 9467 4.434685 GAGCATCTCCAAGAGCCG 57.565 61.111 0.00 0.00 0.00 5.52
4133 9468 1.519719 GAGCATCTCCAAGAGCCGT 59.480 57.895 0.00 0.00 0.00 5.68
4134 9469 0.809241 GAGCATCTCCAAGAGCCGTG 60.809 60.000 0.00 0.00 0.00 4.94
4135 9470 2.467826 GCATCTCCAAGAGCCGTGC 61.468 63.158 0.00 0.00 0.00 5.34
4136 9471 1.220206 CATCTCCAAGAGCCGTGCT 59.780 57.895 0.00 0.00 43.88 4.40
4137 9472 0.461548 CATCTCCAAGAGCCGTGCTA 59.538 55.000 0.00 0.00 39.88 3.49
4138 9473 1.069823 CATCTCCAAGAGCCGTGCTAT 59.930 52.381 0.00 0.00 39.88 2.97
4139 9474 2.067365 TCTCCAAGAGCCGTGCTATA 57.933 50.000 0.00 0.00 39.88 1.31
4140 9475 2.598565 TCTCCAAGAGCCGTGCTATAT 58.401 47.619 0.00 0.00 39.88 0.86
4141 9476 3.763057 TCTCCAAGAGCCGTGCTATATA 58.237 45.455 0.00 0.00 39.88 0.86
4142 9477 4.149598 TCTCCAAGAGCCGTGCTATATAA 58.850 43.478 0.00 0.00 39.88 0.98
4143 9478 4.218635 TCTCCAAGAGCCGTGCTATATAAG 59.781 45.833 0.00 0.00 39.88 1.73
4151 9486 4.470876 GCTATATAAGCGCCGCGA 57.529 55.556 18.91 0.00 42.53 5.87
4152 9487 2.959275 GCTATATAAGCGCCGCGAT 58.041 52.632 18.91 7.57 42.53 4.58
4153 9488 0.572590 GCTATATAAGCGCCGCGATG 59.427 55.000 18.91 0.00 42.53 3.84
4154 9489 1.797713 GCTATATAAGCGCCGCGATGA 60.798 52.381 18.91 2.81 42.53 2.92
4155 9490 2.526077 CTATATAAGCGCCGCGATGAA 58.474 47.619 18.91 2.40 0.00 2.57
4156 9491 1.790755 ATATAAGCGCCGCGATGAAA 58.209 45.000 18.91 0.00 0.00 2.69
4157 9492 1.573026 TATAAGCGCCGCGATGAAAA 58.427 45.000 18.91 0.00 0.00 2.29
4158 9493 0.730265 ATAAGCGCCGCGATGAAAAA 59.270 45.000 18.91 0.00 0.00 1.94
4159 9494 0.730265 TAAGCGCCGCGATGAAAAAT 59.270 45.000 18.91 0.00 0.00 1.82
4160 9495 0.523335 AAGCGCCGCGATGAAAAATC 60.523 50.000 18.91 0.00 0.00 2.17
4161 9496 1.226267 GCGCCGCGATGAAAAATCA 60.226 52.632 18.91 0.00 0.00 2.57
4162 9497 1.196130 GCGCCGCGATGAAAAATCAG 61.196 55.000 18.91 0.00 0.00 2.90
4163 9498 0.096976 CGCCGCGATGAAAAATCAGT 59.903 50.000 8.23 0.00 0.00 3.41
4164 9499 1.538276 GCCGCGATGAAAAATCAGTG 58.462 50.000 8.23 0.00 0.00 3.66
4165 9500 1.135689 GCCGCGATGAAAAATCAGTGT 60.136 47.619 8.23 0.00 0.00 3.55
4166 9501 2.668279 GCCGCGATGAAAAATCAGTGTT 60.668 45.455 8.23 0.00 0.00 3.32
4167 9502 3.564511 CCGCGATGAAAAATCAGTGTTT 58.435 40.909 8.23 0.00 0.00 2.83
4168 9503 3.980775 CCGCGATGAAAAATCAGTGTTTT 59.019 39.130 8.23 0.00 32.94 2.43
4169 9504 4.444056 CCGCGATGAAAAATCAGTGTTTTT 59.556 37.500 8.23 12.81 42.29 1.94
4194 9529 3.917760 GCTATCGCTCCGGGTGCT 61.918 66.667 17.98 4.03 0.00 4.40
4195 9530 2.336809 CTATCGCTCCGGGTGCTC 59.663 66.667 17.98 0.00 0.00 4.26
4196 9531 3.214250 CTATCGCTCCGGGTGCTCC 62.214 68.421 17.98 0.00 0.00 4.70
4200 9535 4.767255 GCTCCGGGTGCTCCAGTG 62.767 72.222 13.59 0.00 34.36 3.66
4201 9536 4.087892 CTCCGGGTGCTCCAGTGG 62.088 72.222 1.40 1.40 34.36 4.00
4202 9537 4.631740 TCCGGGTGCTCCAGTGGA 62.632 66.667 12.40 12.40 34.36 4.02
4203 9538 3.636231 CCGGGTGCTCCAGTGGAA 61.636 66.667 14.17 0.00 34.36 3.53
4204 9539 2.046892 CGGGTGCTCCAGTGGAAG 60.047 66.667 14.17 8.66 34.36 3.46
4205 9540 2.360475 GGGTGCTCCAGTGGAAGC 60.360 66.667 14.17 18.06 35.00 3.86
4206 9541 2.743928 GGTGCTCCAGTGGAAGCG 60.744 66.667 14.17 2.66 31.72 4.68
4207 9542 2.031163 GTGCTCCAGTGGAAGCGT 59.969 61.111 14.17 0.00 31.72 5.07
4208 9543 1.292223 GTGCTCCAGTGGAAGCGTA 59.708 57.895 14.17 0.00 31.72 4.42
4209 9544 0.320421 GTGCTCCAGTGGAAGCGTAA 60.320 55.000 14.17 1.19 31.72 3.18
4210 9545 0.394938 TGCTCCAGTGGAAGCGTAAA 59.605 50.000 14.17 0.86 31.72 2.01
4211 9546 1.202710 TGCTCCAGTGGAAGCGTAAAA 60.203 47.619 14.17 0.51 31.72 1.52
4212 9547 1.877443 GCTCCAGTGGAAGCGTAAAAA 59.123 47.619 14.17 0.00 0.00 1.94
4213 9548 2.488153 GCTCCAGTGGAAGCGTAAAAAT 59.512 45.455 14.17 0.00 0.00 1.82
4214 9549 3.426292 GCTCCAGTGGAAGCGTAAAAATC 60.426 47.826 14.17 0.00 0.00 2.17
4215 9550 2.739913 TCCAGTGGAAGCGTAAAAATCG 59.260 45.455 10.20 0.00 0.00 3.34
4221 9556 3.645309 GCGTAAAAATCGCGCGCG 61.645 61.111 44.84 44.84 43.94 6.86
4222 9557 3.645309 CGTAAAAATCGCGCGCGC 61.645 61.111 45.41 42.65 39.59 6.86
4233 9568 3.536394 CGCGCGCGGCATATCTAG 61.536 66.667 43.28 13.53 43.84 2.43
4234 9569 2.430921 GCGCGCGGCATATCTAGT 60.431 61.111 33.06 0.00 42.87 2.57
4235 9570 2.022129 GCGCGCGGCATATCTAGTT 61.022 57.895 33.06 0.00 42.87 2.24
4236 9571 1.945776 GCGCGCGGCATATCTAGTTC 61.946 60.000 33.06 5.61 42.87 3.01
4237 9572 0.663269 CGCGCGGCATATCTAGTTCA 60.663 55.000 24.84 0.00 0.00 3.18
4238 9573 1.063806 GCGCGGCATATCTAGTTCAG 58.936 55.000 8.83 0.00 0.00 3.02
4239 9574 1.063806 CGCGGCATATCTAGTTCAGC 58.936 55.000 0.00 0.00 0.00 4.26
4240 9575 1.063806 GCGGCATATCTAGTTCAGCG 58.936 55.000 0.00 0.00 0.00 5.18
4241 9576 1.063806 CGGCATATCTAGTTCAGCGC 58.936 55.000 0.00 0.00 0.00 5.92
4242 9577 1.063806 GGCATATCTAGTTCAGCGCG 58.936 55.000 0.00 0.00 0.00 6.86
4243 9578 0.436531 GCATATCTAGTTCAGCGCGC 59.563 55.000 26.66 26.66 0.00 6.86
4244 9579 0.705094 CATATCTAGTTCAGCGCGCG 59.295 55.000 28.44 28.44 0.00 6.86
4245 9580 0.387367 ATATCTAGTTCAGCGCGCGG 60.387 55.000 33.06 26.50 0.00 6.46
4246 9581 2.402282 TATCTAGTTCAGCGCGCGGG 62.402 60.000 33.06 23.76 0.00 6.13
4278 9613 4.252242 CGCGTCGCTTATTTGCTG 57.748 55.556 16.36 0.00 0.00 4.41
4279 9614 1.419922 CGCGTCGCTTATTTGCTGT 59.580 52.632 16.36 0.00 0.00 4.40
4280 9615 0.853224 CGCGTCGCTTATTTGCTGTG 60.853 55.000 16.36 0.00 0.00 3.66
4281 9616 1.128147 GCGTCGCTTATTTGCTGTGC 61.128 55.000 10.68 0.00 0.00 4.57
4282 9617 0.521242 CGTCGCTTATTTGCTGTGCC 60.521 55.000 0.00 0.00 0.00 5.01
4283 9618 0.521242 GTCGCTTATTTGCTGTGCCG 60.521 55.000 0.00 0.00 0.00 5.69
4284 9619 1.869132 CGCTTATTTGCTGTGCCGC 60.869 57.895 0.00 0.00 0.00 6.53
4285 9620 1.508088 GCTTATTTGCTGTGCCGCT 59.492 52.632 0.00 0.00 0.00 5.52
4286 9621 0.524180 GCTTATTTGCTGTGCCGCTC 60.524 55.000 0.00 0.00 0.00 5.03
4287 9622 1.089920 CTTATTTGCTGTGCCGCTCT 58.910 50.000 0.00 0.00 0.00 4.09
4288 9623 1.063174 CTTATTTGCTGTGCCGCTCTC 59.937 52.381 0.00 0.00 0.00 3.20
4289 9624 1.083806 TATTTGCTGTGCCGCTCTCG 61.084 55.000 0.00 0.00 0.00 4.04
4300 9635 4.560856 GCTCTCGCGCGATGGACT 62.561 66.667 34.86 0.00 0.00 3.85
4301 9636 2.352915 CTCTCGCGCGATGGACTC 60.353 66.667 34.86 0.00 0.00 3.36
4302 9637 2.824489 TCTCGCGCGATGGACTCT 60.824 61.111 34.86 0.00 0.00 3.24
4303 9638 2.352915 CTCGCGCGATGGACTCTC 60.353 66.667 34.86 0.00 0.00 3.20
4304 9639 4.237809 TCGCGCGATGGACTCTCG 62.238 66.667 31.40 0.00 39.11 4.04
4305 9640 4.237809 CGCGCGATGGACTCTCGA 62.238 66.667 28.94 0.00 38.38 4.04
4306 9641 2.352915 GCGCGATGGACTCTCGAG 60.353 66.667 12.10 5.93 38.38 4.04
4307 9642 2.352915 CGCGATGGACTCTCGAGC 60.353 66.667 7.81 0.00 38.38 5.03
4308 9643 2.352915 GCGATGGACTCTCGAGCG 60.353 66.667 7.81 3.64 37.08 5.03
4309 9644 2.352915 CGATGGACTCTCGAGCGC 60.353 66.667 7.81 0.00 38.38 5.92
4310 9645 2.829206 CGATGGACTCTCGAGCGCT 61.829 63.158 11.27 11.27 38.38 5.92
4311 9646 1.008995 GATGGACTCTCGAGCGCTC 60.009 63.158 27.64 27.64 0.00 5.03
4324 9659 3.105782 CGCTCGCTCGCAACTTCA 61.106 61.111 0.00 0.00 0.00 3.02
4325 9660 2.472049 GCTCGCTCGCAACTTCAC 59.528 61.111 0.00 0.00 0.00 3.18
4326 9661 3.016474 GCTCGCTCGCAACTTCACC 62.016 63.158 0.00 0.00 0.00 4.02
4327 9662 1.373497 CTCGCTCGCAACTTCACCT 60.373 57.895 0.00 0.00 0.00 4.00
4328 9663 0.109272 CTCGCTCGCAACTTCACCTA 60.109 55.000 0.00 0.00 0.00 3.08
4329 9664 0.388134 TCGCTCGCAACTTCACCTAC 60.388 55.000 0.00 0.00 0.00 3.18
4330 9665 1.352156 CGCTCGCAACTTCACCTACC 61.352 60.000 0.00 0.00 0.00 3.18
4331 9666 1.019805 GCTCGCAACTTCACCTACCC 61.020 60.000 0.00 0.00 0.00 3.69
4332 9667 0.391263 CTCGCAACTTCACCTACCCC 60.391 60.000 0.00 0.00 0.00 4.95
4333 9668 1.122632 TCGCAACTTCACCTACCCCA 61.123 55.000 0.00 0.00 0.00 4.96
4334 9669 0.035439 CGCAACTTCACCTACCCCAT 60.035 55.000 0.00 0.00 0.00 4.00
4335 9670 1.751437 GCAACTTCACCTACCCCATC 58.249 55.000 0.00 0.00 0.00 3.51
4336 9671 1.682087 GCAACTTCACCTACCCCATCC 60.682 57.143 0.00 0.00 0.00 3.51
4337 9672 1.633432 CAACTTCACCTACCCCATCCA 59.367 52.381 0.00 0.00 0.00 3.41
4338 9673 1.584724 ACTTCACCTACCCCATCCAG 58.415 55.000 0.00 0.00 0.00 3.86
4339 9674 0.181350 CTTCACCTACCCCATCCAGC 59.819 60.000 0.00 0.00 0.00 4.85
4340 9675 1.279025 TTCACCTACCCCATCCAGCC 61.279 60.000 0.00 0.00 0.00 4.85
4341 9676 2.768344 ACCTACCCCATCCAGCCG 60.768 66.667 0.00 0.00 0.00 5.52
4342 9677 4.256180 CCTACCCCATCCAGCCGC 62.256 72.222 0.00 0.00 0.00 6.53
4343 9678 4.609018 CTACCCCATCCAGCCGCG 62.609 72.222 0.00 0.00 0.00 6.46
4400 9735 2.434774 GGTTCCCCGGCATATCCC 59.565 66.667 0.00 0.00 0.00 3.85
4401 9736 2.434774 GTTCCCCGGCATATCCCC 59.565 66.667 0.00 0.00 0.00 4.81
4402 9737 3.246112 TTCCCCGGCATATCCCCG 61.246 66.667 0.00 4.68 45.17 5.73
4428 9763 4.214327 CGGCTTCCTCCGCCTCTC 62.214 72.222 0.00 0.00 45.37 3.20
4429 9764 2.762043 GGCTTCCTCCGCCTCTCT 60.762 66.667 0.00 0.00 44.17 3.10
4430 9765 2.791868 GGCTTCCTCCGCCTCTCTC 61.792 68.421 0.00 0.00 44.17 3.20
4431 9766 1.756561 GCTTCCTCCGCCTCTCTCT 60.757 63.158 0.00 0.00 0.00 3.10
4432 9767 0.466555 GCTTCCTCCGCCTCTCTCTA 60.467 60.000 0.00 0.00 0.00 2.43
4433 9768 1.604604 CTTCCTCCGCCTCTCTCTAG 58.395 60.000 0.00 0.00 0.00 2.43
4434 9769 0.920438 TTCCTCCGCCTCTCTCTAGT 59.080 55.000 0.00 0.00 0.00 2.57
4435 9770 0.470766 TCCTCCGCCTCTCTCTAGTC 59.529 60.000 0.00 0.00 0.00 2.59
4436 9771 0.181587 CCTCCGCCTCTCTCTAGTCA 59.818 60.000 0.00 0.00 0.00 3.41
4437 9772 1.305201 CTCCGCCTCTCTCTAGTCAC 58.695 60.000 0.00 0.00 0.00 3.67
4438 9773 0.107116 TCCGCCTCTCTCTAGTCACC 60.107 60.000 0.00 0.00 0.00 4.02
4439 9774 1.440938 CCGCCTCTCTCTAGTCACCG 61.441 65.000 0.00 0.00 0.00 4.94
4440 9775 1.731093 GCCTCTCTCTAGTCACCGC 59.269 63.158 0.00 0.00 0.00 5.68
4441 9776 1.730451 GCCTCTCTCTAGTCACCGCC 61.730 65.000 0.00 0.00 0.00 6.13
4442 9777 1.440938 CCTCTCTCTAGTCACCGCCG 61.441 65.000 0.00 0.00 0.00 6.46
4443 9778 2.054140 CTCTCTCTAGTCACCGCCGC 62.054 65.000 0.00 0.00 0.00 6.53
4444 9779 3.127352 CTCTCTAGTCACCGCCGCC 62.127 68.421 0.00 0.00 0.00 6.13
4445 9780 4.208686 CTCTAGTCACCGCCGCCC 62.209 72.222 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.226620 TGGGAGGATTGTTAGACCCTAAAC 59.773 45.833 0.00 0.00 38.28 2.01
47 48 2.661176 TGGGAGGATTGTTAGACCCT 57.339 50.000 0.00 0.00 38.28 4.34
48 49 3.732048 TTTGGGAGGATTGTTAGACCC 57.268 47.619 0.00 0.00 37.99 4.46
101 103 8.225416 AGTTCAAACCTTTAAAAGAGGGAGTAT 58.775 33.333 0.00 0.00 38.65 2.12
114 116 2.105134 TGGGCTCGAGTTCAAACCTTTA 59.895 45.455 15.13 0.00 0.00 1.85
121 123 0.881118 GCATTTGGGCTCGAGTTCAA 59.119 50.000 15.13 15.18 0.00 2.69
132 134 2.408271 TGTCTAGCAGAGCATTTGGG 57.592 50.000 0.00 0.00 0.00 4.12
212 214 3.500448 TGATTGTGTAAGGGTGCTTCA 57.500 42.857 0.00 0.00 0.00 3.02
243 245 2.159517 GCTAAACAATGTTGGAGGCTCG 60.160 50.000 8.69 0.00 0.00 5.03
274 276 5.391060 GTGATATGCACGGTTTTAGTCTC 57.609 43.478 0.00 0.00 37.83 3.36
325 327 1.333619 GCACGGTGAAGAATGTGTGTT 59.666 47.619 13.29 0.00 34.86 3.32
395 398 6.484643 GCAAGAGGATCACTAATGCTATTTCA 59.515 38.462 0.00 0.00 35.35 2.69
406 409 7.439356 CGAAGAAAATATGCAAGAGGATCACTA 59.561 37.037 0.00 0.00 37.82 2.74
422 425 8.271312 ACGTATTCAAATTCCCGAAGAAAATA 57.729 30.769 0.00 0.00 38.21 1.40
452 455 1.128200 AAGCCATCCCTACGTATGCA 58.872 50.000 0.00 0.00 0.00 3.96
492 495 7.978925 ACTTTATCTTATGATGGTAAGGAGGG 58.021 38.462 1.45 0.00 33.48 4.30
655 659 5.469760 GCAAAAGTGAAGGTATGCCAAATTT 59.530 36.000 1.54 0.00 37.19 1.82
705 2398 2.945668 GGCGGATGATTATTCTATGGCC 59.054 50.000 0.00 0.00 0.00 5.36
706 2399 2.945668 GGGCGGATGATTATTCTATGGC 59.054 50.000 0.00 0.00 0.00 4.40
707 2400 4.080919 TGAGGGCGGATGATTATTCTATGG 60.081 45.833 0.00 0.00 0.00 2.74
708 2401 5.089970 TGAGGGCGGATGATTATTCTATG 57.910 43.478 0.00 0.00 0.00 2.23
709 2402 5.965033 ATGAGGGCGGATGATTATTCTAT 57.035 39.130 0.00 0.00 0.00 1.98
710 2403 6.867519 TTATGAGGGCGGATGATTATTCTA 57.132 37.500 0.00 0.00 0.00 2.10
712 2405 5.235186 CGATTATGAGGGCGGATGATTATTC 59.765 44.000 0.00 0.00 0.00 1.75
713 2406 5.104941 TCGATTATGAGGGCGGATGATTATT 60.105 40.000 0.00 0.00 0.00 1.40
714 2407 4.405680 TCGATTATGAGGGCGGATGATTAT 59.594 41.667 0.00 0.00 0.00 1.28
715 2408 3.767131 TCGATTATGAGGGCGGATGATTA 59.233 43.478 0.00 0.00 0.00 1.75
718 2411 1.627864 TCGATTATGAGGGCGGATGA 58.372 50.000 0.00 0.00 0.00 2.92
719 2412 2.274437 CATCGATTATGAGGGCGGATG 58.726 52.381 0.00 0.00 37.86 3.51
720 2413 1.208052 CCATCGATTATGAGGGCGGAT 59.792 52.381 0.00 0.00 37.86 4.18
721 2414 0.608130 CCATCGATTATGAGGGCGGA 59.392 55.000 0.00 0.00 37.86 5.54
722 2415 3.143675 CCATCGATTATGAGGGCGG 57.856 57.895 0.00 0.00 37.86 6.13
725 2418 0.692476 TGGGCCATCGATTATGAGGG 59.308 55.000 0.00 0.00 42.62 4.30
726 2419 2.430465 CTTGGGCCATCGATTATGAGG 58.570 52.381 7.26 0.00 37.86 3.86
727 2420 2.430465 CCTTGGGCCATCGATTATGAG 58.570 52.381 7.26 0.00 37.86 2.90
729 2422 0.883833 GCCTTGGGCCATCGATTATG 59.116 55.000 7.26 0.00 44.06 1.90
730 2423 3.346426 GCCTTGGGCCATCGATTAT 57.654 52.632 7.26 0.00 44.06 1.28
741 2434 4.637534 CGATGATTATTCTATGGCCTTGGG 59.362 45.833 3.32 0.00 0.00 4.12
742 2435 5.491070 TCGATGATTATTCTATGGCCTTGG 58.509 41.667 3.32 0.00 0.00 3.61
748 2608 9.664332 AAAGGATTCTCGATGATTATTCTATGG 57.336 33.333 0.00 0.00 0.00 2.74
764 2624 5.974751 TGCAAACACGTTAAAAAGGATTCTC 59.025 36.000 0.00 0.00 0.00 2.87
916 4581 0.251341 ACTGGTGCACTTGGGATTCC 60.251 55.000 17.98 0.00 0.00 3.01
919 4584 4.828409 CACTGGTGCACTTGGGAT 57.172 55.556 17.98 0.00 0.00 3.85
938 4603 1.763546 TTGTGGATGGTGAGCACGGA 61.764 55.000 0.00 0.00 0.00 4.69
939 4604 1.300971 CTTGTGGATGGTGAGCACGG 61.301 60.000 0.00 0.00 0.00 4.94
1254 4928 0.543410 TCTTCCACTTCCACGCCCTA 60.543 55.000 0.00 0.00 0.00 3.53
1638 5331 6.147821 AGTCAGAAACATTTCCACGTCATTAG 59.852 38.462 0.68 0.00 37.92 1.73
1662 5355 2.234908 CAACCTCCCTAACTGGTGAGAG 59.765 54.545 0.00 0.00 36.10 3.20
1669 5362 0.974383 ACGTCCAACCTCCCTAACTG 59.026 55.000 0.00 0.00 0.00 3.16
1722 5415 1.364626 CTTGCTTCTGCGGCGAATCT 61.365 55.000 12.98 0.00 43.34 2.40
1875 5568 4.002906 TGGTATGGAAAGCTATAAGCCG 57.997 45.455 0.00 0.00 43.77 5.52
2176 5871 0.671251 GCAACCGACCCAATCACAAA 59.329 50.000 0.00 0.00 0.00 2.83
2249 5944 0.870393 ACTCTTCAACTGCATGTGCG 59.130 50.000 0.01 0.00 45.83 5.34
2396 6091 8.433421 ACCGTTTGTATAGTTCTCCATTTATG 57.567 34.615 0.00 0.00 0.00 1.90
2513 6208 2.069273 CAAATCCCTATGATCGGCGTC 58.931 52.381 6.85 4.58 31.61 5.19
2517 6212 3.332919 CTCTGCAAATCCCTATGATCGG 58.667 50.000 0.00 0.00 31.61 4.18
2518 6213 2.740981 GCTCTGCAAATCCCTATGATCG 59.259 50.000 0.00 0.00 31.61 3.69
2736 6440 9.376075 TGCTGACAAATATTTTGAGAAAAACAA 57.624 25.926 6.96 0.00 33.47 2.83
2887 6594 7.809806 CCACATAGATGGTTCTTTGAAGAAAAC 59.190 37.037 7.69 5.41 45.77 2.43
2918 6625 3.845781 TCAGAAAAGAAGAGGCACAGT 57.154 42.857 0.00 0.00 0.00 3.55
2943 6650 8.194769 AGAAACTAACGAATCACCAATTGTTTT 58.805 29.630 4.43 0.00 0.00 2.43
3199 6906 5.250543 TCAAAATCTGGTGGTGGAAGATCTA 59.749 40.000 0.00 0.00 30.35 1.98
3200 6907 4.043310 TCAAAATCTGGTGGTGGAAGATCT 59.957 41.667 0.00 0.00 30.35 2.75
3201 6908 4.335416 TCAAAATCTGGTGGTGGAAGATC 58.665 43.478 0.00 0.00 30.35 2.75
3224 6931 2.092429 TCCCTGCACAAACAGAAGTTCT 60.092 45.455 0.00 0.00 40.25 3.01
3465 7276 0.167908 TGAACCGCGCAATGCTTAAG 59.832 50.000 8.75 0.00 43.27 1.85
3505 7316 8.185505 TGAAACTGTATGACCTTTTGTAAACAC 58.814 33.333 0.00 0.00 0.00 3.32
3525 8843 4.681942 CGACTCAACGAAGAAGATGAAACT 59.318 41.667 0.00 0.00 35.09 2.66
3552 8870 3.537580 AGTACTCTTTTGTGTTGCCGAA 58.462 40.909 0.00 0.00 0.00 4.30
3553 8871 3.188159 AGTACTCTTTTGTGTTGCCGA 57.812 42.857 0.00 0.00 0.00 5.54
3554 8872 3.432252 CCTAGTACTCTTTTGTGTTGCCG 59.568 47.826 0.00 0.00 0.00 5.69
3555 8873 3.188667 GCCTAGTACTCTTTTGTGTTGCC 59.811 47.826 0.00 0.00 0.00 4.52
3556 8874 4.065789 AGCCTAGTACTCTTTTGTGTTGC 58.934 43.478 0.00 0.00 0.00 4.17
3557 8875 5.057149 ACAGCCTAGTACTCTTTTGTGTTG 58.943 41.667 0.00 0.00 0.00 3.33
3558 8876 5.291905 ACAGCCTAGTACTCTTTTGTGTT 57.708 39.130 0.00 0.00 0.00 3.32
3562 8880 4.254492 GGGAACAGCCTAGTACTCTTTTG 58.746 47.826 0.00 0.00 36.66 2.44
3566 8884 2.921834 TGGGAACAGCCTAGTACTCT 57.078 50.000 0.00 0.00 36.66 3.24
3591 8913 5.909621 ATTTGAGGACAGACCATCAAATG 57.090 39.130 18.90 0.00 44.54 2.32
3692 9026 6.721571 TGAGTAACATTTCCGAATTCTGTC 57.278 37.500 3.52 0.00 0.00 3.51
3693 9027 6.710744 AGTTGAGTAACATTTCCGAATTCTGT 59.289 34.615 3.52 0.00 39.30 3.41
3889 9223 3.058914 CGACAAATTGGTCACAACTCTCC 60.059 47.826 13.42 0.00 39.87 3.71
3947 9281 5.885465 ACCTGTCATCTTTTCCTTCTTCAT 58.115 37.500 0.00 0.00 0.00 2.57
3948 9282 5.310409 ACCTGTCATCTTTTCCTTCTTCA 57.690 39.130 0.00 0.00 0.00 3.02
3956 9290 4.527564 CGTTCACAACCTGTCATCTTTTC 58.472 43.478 0.00 0.00 0.00 2.29
3986 9320 6.348050 GGCTAGATCATTCGGCTGAATTTTAG 60.348 42.308 18.34 13.81 42.14 1.85
4054 9388 5.412904 GGTCCAAGAAATACAGGAGACAAAG 59.587 44.000 0.00 0.00 0.00 2.77
4099 9434 0.747255 GCTCTGAGTCCGGCAGATTA 59.253 55.000 10.25 0.00 41.20 1.75
4105 9440 1.067250 GAGATGCTCTGAGTCCGGC 59.933 63.158 6.53 0.00 0.00 6.13
4110 9445 1.481772 GCTCTTGGAGATGCTCTGAGT 59.518 52.381 6.53 0.00 31.22 3.41
4116 9451 1.220206 CACGGCTCTTGGAGATGCT 59.780 57.895 0.00 0.00 0.00 3.79
4117 9452 2.467826 GCACGGCTCTTGGAGATGC 61.468 63.158 0.00 1.79 31.35 3.91
4118 9453 0.461548 TAGCACGGCTCTTGGAGATG 59.538 55.000 1.46 0.00 40.44 2.90
4119 9454 1.418334 ATAGCACGGCTCTTGGAGAT 58.582 50.000 1.46 0.00 40.44 2.75
4120 9455 2.067365 TATAGCACGGCTCTTGGAGA 57.933 50.000 1.46 0.00 40.44 3.71
4121 9456 4.489810 CTTATATAGCACGGCTCTTGGAG 58.510 47.826 1.46 0.00 40.44 3.86
4122 9457 4.521130 CTTATATAGCACGGCTCTTGGA 57.479 45.455 1.46 0.00 40.44 3.53
4134 9469 0.572590 CATCGCGGCGCTTATATAGC 59.427 55.000 30.54 0.00 46.83 2.97
4135 9470 2.188837 TCATCGCGGCGCTTATATAG 57.811 50.000 30.54 12.47 0.00 1.31
4136 9471 2.640346 TTCATCGCGGCGCTTATATA 57.360 45.000 30.54 11.48 0.00 0.86
4137 9472 1.790755 TTTCATCGCGGCGCTTATAT 58.209 45.000 30.54 14.57 0.00 0.86
4138 9473 1.573026 TTTTCATCGCGGCGCTTATA 58.427 45.000 30.54 12.80 0.00 0.98
4139 9474 0.730265 TTTTTCATCGCGGCGCTTAT 59.270 45.000 30.54 19.77 0.00 1.73
4140 9475 0.730265 ATTTTTCATCGCGGCGCTTA 59.270 45.000 30.54 18.26 0.00 3.09
4141 9476 0.523335 GATTTTTCATCGCGGCGCTT 60.523 50.000 30.54 14.58 0.00 4.68
4142 9477 1.062525 GATTTTTCATCGCGGCGCT 59.937 52.632 30.54 9.46 0.00 5.92
4143 9478 1.196130 CTGATTTTTCATCGCGGCGC 61.196 55.000 24.21 24.21 0.00 6.53
4144 9479 0.096976 ACTGATTTTTCATCGCGGCG 59.903 50.000 17.70 17.70 0.00 6.46
4145 9480 1.135689 ACACTGATTTTTCATCGCGGC 60.136 47.619 6.13 0.00 0.00 6.53
4146 9481 2.900122 ACACTGATTTTTCATCGCGG 57.100 45.000 6.13 0.00 0.00 6.46
4147 9482 5.559694 AAAAACACTGATTTTTCATCGCG 57.440 34.783 0.00 0.00 37.21 5.87
4178 9513 2.336809 GAGCACCCGGAGCGATAG 59.663 66.667 0.73 0.00 37.01 2.08
4179 9514 3.224324 GGAGCACCCGGAGCGATA 61.224 66.667 0.73 0.00 37.01 2.92
4183 9518 4.767255 CACTGGAGCACCCGGAGC 62.767 72.222 0.73 6.94 44.44 4.70
4184 9519 4.087892 CCACTGGAGCACCCGGAG 62.088 72.222 0.73 0.00 44.44 4.63
4185 9520 4.631740 TCCACTGGAGCACCCGGA 62.632 66.667 0.73 5.17 44.44 5.14
4187 9522 2.046892 CTTCCACTGGAGCACCCG 60.047 66.667 0.00 0.00 37.93 5.28
4188 9523 2.360475 GCTTCCACTGGAGCACCC 60.360 66.667 12.23 0.00 31.21 4.61
4189 9524 2.167398 TACGCTTCCACTGGAGCACC 62.167 60.000 15.58 0.00 31.21 5.01
4190 9525 0.320421 TTACGCTTCCACTGGAGCAC 60.320 55.000 15.58 3.28 31.21 4.40
4191 9526 0.394938 TTTACGCTTCCACTGGAGCA 59.605 50.000 15.58 0.00 31.21 4.26
4192 9527 1.519408 TTTTACGCTTCCACTGGAGC 58.481 50.000 0.00 3.96 31.21 4.70
4193 9528 3.181520 CGATTTTTACGCTTCCACTGGAG 60.182 47.826 0.00 0.00 31.21 3.86
4194 9529 2.739913 CGATTTTTACGCTTCCACTGGA 59.260 45.455 0.00 0.00 0.00 3.86
4195 9530 3.117434 CGATTTTTACGCTTCCACTGG 57.883 47.619 0.00 0.00 0.00 4.00
4216 9551 3.536394 CTAGATATGCCGCGCGCG 61.536 66.667 43.73 43.73 42.08 6.86
4217 9552 1.945776 GAACTAGATATGCCGCGCGC 61.946 60.000 27.36 23.91 38.31 6.86
4218 9553 0.663269 TGAACTAGATATGCCGCGCG 60.663 55.000 25.67 25.67 0.00 6.86
4219 9554 1.063806 CTGAACTAGATATGCCGCGC 58.936 55.000 0.00 0.00 0.00 6.86
4220 9555 1.063806 GCTGAACTAGATATGCCGCG 58.936 55.000 0.00 0.00 0.00 6.46
4221 9556 1.063806 CGCTGAACTAGATATGCCGC 58.936 55.000 0.00 0.00 0.00 6.53
4222 9557 1.063806 GCGCTGAACTAGATATGCCG 58.936 55.000 0.00 0.00 0.00 5.69
4223 9558 1.063806 CGCGCTGAACTAGATATGCC 58.936 55.000 5.56 0.00 0.00 4.40
4224 9559 0.436531 GCGCGCTGAACTAGATATGC 59.563 55.000 26.67 0.00 0.00 3.14
4225 9560 0.705094 CGCGCGCTGAACTAGATATG 59.295 55.000 30.48 4.24 0.00 1.78
4226 9561 0.387367 CCGCGCGCTGAACTAGATAT 60.387 55.000 30.48 0.00 0.00 1.63
4227 9562 1.008881 CCGCGCGCTGAACTAGATA 60.009 57.895 30.48 0.00 0.00 1.98
4228 9563 2.278857 CCGCGCGCTGAACTAGAT 60.279 61.111 30.48 0.00 0.00 1.98
4229 9564 4.492160 CCCGCGCGCTGAACTAGA 62.492 66.667 30.48 0.00 0.00 2.43
4261 9596 0.853224 CACAGCAAATAAGCGACGCG 60.853 55.000 15.18 3.53 40.15 6.01
4262 9597 1.128147 GCACAGCAAATAAGCGACGC 61.128 55.000 13.03 13.03 40.15 5.19
4263 9598 0.521242 GGCACAGCAAATAAGCGACG 60.521 55.000 0.00 0.00 40.15 5.12
4264 9599 0.521242 CGGCACAGCAAATAAGCGAC 60.521 55.000 0.00 0.00 40.15 5.19
4265 9600 1.793581 CGGCACAGCAAATAAGCGA 59.206 52.632 0.00 0.00 40.15 4.93
4266 9601 1.869132 GCGGCACAGCAAATAAGCG 60.869 57.895 0.00 0.00 40.15 4.68
4267 9602 0.524180 GAGCGGCACAGCAAATAAGC 60.524 55.000 1.45 0.00 40.15 3.09
4268 9603 1.063174 GAGAGCGGCACAGCAAATAAG 59.937 52.381 1.45 0.00 40.15 1.73
4269 9604 1.086696 GAGAGCGGCACAGCAAATAA 58.913 50.000 1.45 0.00 40.15 1.40
4270 9605 1.083806 CGAGAGCGGCACAGCAAATA 61.084 55.000 1.45 0.00 40.15 1.40
4271 9606 2.393768 CGAGAGCGGCACAGCAAAT 61.394 57.895 1.45 0.00 40.15 2.32
4272 9607 3.043713 CGAGAGCGGCACAGCAAA 61.044 61.111 1.45 0.00 40.15 3.68
4284 9619 2.352915 GAGTCCATCGCGCGAGAG 60.353 66.667 36.99 29.46 0.00 3.20
4285 9620 2.824489 AGAGTCCATCGCGCGAGA 60.824 61.111 36.99 26.61 0.00 4.04
4286 9621 2.352915 GAGAGTCCATCGCGCGAG 60.353 66.667 36.99 26.56 0.00 5.03
4287 9622 4.237809 CGAGAGTCCATCGCGCGA 62.238 66.667 36.65 36.65 44.23 5.87
4291 9626 2.352915 CGCTCGAGAGTCCATCGC 60.353 66.667 18.75 0.00 39.98 4.58
4292 9627 2.352915 GCGCTCGAGAGTCCATCG 60.353 66.667 18.75 9.36 41.50 3.84
4293 9628 1.008995 GAGCGCTCGAGAGTCCATC 60.009 63.158 23.61 6.83 0.00 3.51
4294 9629 3.115556 GAGCGCTCGAGAGTCCAT 58.884 61.111 23.61 0.53 0.00 3.41
4307 9642 3.105782 TGAAGTTGCGAGCGAGCG 61.106 61.111 0.00 0.00 40.67 5.03
4308 9643 2.472049 GTGAAGTTGCGAGCGAGC 59.528 61.111 0.00 0.00 37.71 5.03
4309 9644 0.109272 TAGGTGAAGTTGCGAGCGAG 60.109 55.000 0.00 0.00 0.00 5.03
4310 9645 0.388134 GTAGGTGAAGTTGCGAGCGA 60.388 55.000 0.00 0.00 0.00 4.93
4311 9646 1.352156 GGTAGGTGAAGTTGCGAGCG 61.352 60.000 0.00 0.00 0.00 5.03
4312 9647 1.019805 GGGTAGGTGAAGTTGCGAGC 61.020 60.000 0.00 0.00 0.00 5.03
4313 9648 0.391263 GGGGTAGGTGAAGTTGCGAG 60.391 60.000 0.00 0.00 0.00 5.03
4314 9649 1.122632 TGGGGTAGGTGAAGTTGCGA 61.123 55.000 0.00 0.00 0.00 5.10
4315 9650 0.035439 ATGGGGTAGGTGAAGTTGCG 60.035 55.000 0.00 0.00 0.00 4.85
4316 9651 1.682087 GGATGGGGTAGGTGAAGTTGC 60.682 57.143 0.00 0.00 0.00 4.17
4317 9652 1.633432 TGGATGGGGTAGGTGAAGTTG 59.367 52.381 0.00 0.00 0.00 3.16
4318 9653 1.916181 CTGGATGGGGTAGGTGAAGTT 59.084 52.381 0.00 0.00 0.00 2.66
4319 9654 1.584724 CTGGATGGGGTAGGTGAAGT 58.415 55.000 0.00 0.00 0.00 3.01
4320 9655 0.181350 GCTGGATGGGGTAGGTGAAG 59.819 60.000 0.00 0.00 0.00 3.02
4321 9656 1.279025 GGCTGGATGGGGTAGGTGAA 61.279 60.000 0.00 0.00 0.00 3.18
4322 9657 1.692749 GGCTGGATGGGGTAGGTGA 60.693 63.158 0.00 0.00 0.00 4.02
4323 9658 2.919043 GGCTGGATGGGGTAGGTG 59.081 66.667 0.00 0.00 0.00 4.00
4324 9659 2.768344 CGGCTGGATGGGGTAGGT 60.768 66.667 0.00 0.00 0.00 3.08
4325 9660 4.256180 GCGGCTGGATGGGGTAGG 62.256 72.222 0.00 0.00 0.00 3.18
4326 9661 4.609018 CGCGGCTGGATGGGGTAG 62.609 72.222 0.00 0.00 0.00 3.18
4384 9719 2.434774 GGGGATATGCCGGGGAAC 59.565 66.667 7.23 0.00 37.63 3.62
4385 9720 3.246112 CGGGGATATGCCGGGGAA 61.246 66.667 12.39 0.00 37.63 3.97
4413 9748 0.466555 TAGAGAGAGGCGGAGGAAGC 60.467 60.000 0.00 0.00 0.00 3.86
4414 9749 1.133915 ACTAGAGAGAGGCGGAGGAAG 60.134 57.143 0.00 0.00 0.00 3.46
4415 9750 0.920438 ACTAGAGAGAGGCGGAGGAA 59.080 55.000 0.00 0.00 0.00 3.36
4416 9751 0.470766 GACTAGAGAGAGGCGGAGGA 59.529 60.000 0.00 0.00 0.00 3.71
4417 9752 0.181587 TGACTAGAGAGAGGCGGAGG 59.818 60.000 0.00 0.00 0.00 4.30
4418 9753 1.305201 GTGACTAGAGAGAGGCGGAG 58.695 60.000 0.00 0.00 0.00 4.63
4419 9754 0.107116 GGTGACTAGAGAGAGGCGGA 60.107 60.000 0.00 0.00 0.00 5.54
4420 9755 1.440938 CGGTGACTAGAGAGAGGCGG 61.441 65.000 0.00 0.00 0.00 6.13
4421 9756 2.018544 CGGTGACTAGAGAGAGGCG 58.981 63.158 0.00 0.00 0.00 5.52
4422 9757 1.730451 GGCGGTGACTAGAGAGAGGC 61.730 65.000 0.00 0.00 0.00 4.70
4423 9758 1.440938 CGGCGGTGACTAGAGAGAGG 61.441 65.000 0.00 0.00 0.00 3.69
4424 9759 2.018544 CGGCGGTGACTAGAGAGAG 58.981 63.158 0.00 0.00 0.00 3.20
4425 9760 2.113433 GCGGCGGTGACTAGAGAGA 61.113 63.158 9.78 0.00 0.00 3.10
4426 9761 2.409651 GCGGCGGTGACTAGAGAG 59.590 66.667 9.78 0.00 0.00 3.20
4427 9762 3.138798 GGCGGCGGTGACTAGAGA 61.139 66.667 9.78 0.00 0.00 3.10
4428 9763 4.208686 GGGCGGCGGTGACTAGAG 62.209 72.222 9.78 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.