Multiple sequence alignment - TraesCS7D01G166700

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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 TraesCS7D01G166700 chr7D 100.000 4124 0 0 1 4124 117462162 117466285 0.000000e+00 7616.0
1 TraesCS7D01G166700 chr7D 94.253 174 10 0 3204 3377 235502406 235502579 2.440000e-67 267.0
2 TraesCS7D01G166700 chr7D 93.642 173 10 1 3194 3366 147465256 147465085 1.470000e-64 257.0
3 TraesCS7D01G166700 chr7A 92.828 2663 121 28 518 3137 121843810 121846445 0.000000e+00 3795.0
4 TraesCS7D01G166700 chr7A 93.162 234 16 0 5 238 121843295 121843528 1.100000e-90 344.0
5 TraesCS7D01G166700 chr7A 93.365 211 8 1 295 499 121843615 121843825 1.440000e-79 307.0
6 TraesCS7D01G166700 chr4B 91.276 2178 145 21 969 3126 574169250 574171402 0.000000e+00 2928.0
7 TraesCS7D01G166700 chr4D 92.019 2080 132 17 1050 3126 459383308 459385356 0.000000e+00 2891.0
8 TraesCS7D01G166700 chr4D 94.643 168 8 1 3199 3366 433364771 433364937 4.090000e-65 259.0
9 TraesCS7D01G166700 chr4D 89.583 48 3 2 2376 2422 417608630 417608584 4.450000e-05 60.2
10 TraesCS7D01G166700 chr4A 91.820 1198 71 13 1950 3126 9401145 9399954 0.000000e+00 1644.0
11 TraesCS7D01G166700 chr4A 91.639 897 58 10 1050 1940 9402010 9401125 0.000000e+00 1225.0
12 TraesCS7D01G166700 chr4A 83.333 120 15 3 14 129 9405308 9405190 5.640000e-19 106.0
13 TraesCS7D01G166700 chr6B 89.404 755 62 13 3369 4119 554344690 554343950 0.000000e+00 935.0
14 TraesCS7D01G166700 chr6B 84.942 777 90 22 3362 4123 612844540 612845304 0.000000e+00 761.0
15 TraesCS7D01G166700 chrUn 86.979 768 80 13 3368 4124 308643419 308644177 0.000000e+00 846.0
16 TraesCS7D01G166700 chr6A 86.979 768 80 13 3368 4124 607135834 607136592 0.000000e+00 846.0
17 TraesCS7D01G166700 chr6A 86.962 767 81 12 3368 4124 607274249 607275006 0.000000e+00 845.0
18 TraesCS7D01G166700 chr2B 86.086 769 81 19 3368 4123 666726005 666726760 0.000000e+00 804.0
19 TraesCS7D01G166700 chr5B 85.919 767 88 15 3368 4124 43815043 43815799 0.000000e+00 800.0
20 TraesCS7D01G166700 chr5B 76.336 524 98 24 2283 2793 107370402 107370912 1.470000e-64 257.0
21 TraesCS7D01G166700 chr1D 85.436 769 90 16 3368 4124 228043937 228043179 0.000000e+00 780.0
22 TraesCS7D01G166700 chr1D 73.191 1078 240 36 1492 2550 268000658 267999611 1.100000e-90 344.0
23 TraesCS7D01G166700 chr1D 96.951 164 5 0 3203 3366 311986611 311986774 4.060000e-70 276.0
24 TraesCS7D01G166700 chr1D 84.375 192 26 3 2239 2428 294227201 294227390 7.040000e-43 185.0
25 TraesCS7D01G166700 chr1D 82.828 198 34 0 2231 2428 382917964 382917767 1.180000e-40 178.0
26 TraesCS7D01G166700 chr1D 100.000 31 0 0 1558 1588 192569800 192569830 1.600000e-04 58.4
27 TraesCS7D01G166700 chr5D 86.345 725 80 15 3366 4085 438337887 438338597 0.000000e+00 773.0
28 TraesCS7D01G166700 chr5D 76.571 525 98 23 2283 2793 98228654 98229167 8.790000e-67 265.0
29 TraesCS7D01G166700 chr5D 95.732 164 7 0 3204 3367 431780588 431780425 8.790000e-67 265.0
30 TraesCS7D01G166700 chr5D 92.222 180 13 1 3194 3372 398757413 398757234 1.900000e-63 254.0
31 TraesCS7D01G166700 chr7B 94.301 193 6 1 295 487 77800112 77800299 1.450000e-74 291.0
32 TraesCS7D01G166700 chr7B 91.667 120 10 0 13 132 77799800 77799919 2.550000e-37 167.0
33 TraesCS7D01G166700 chr7B 95.652 69 3 0 170 238 77799915 77799983 1.210000e-20 111.0
34 TraesCS7D01G166700 chr3D 95.808 167 7 0 3204 3370 486424949 486424783 1.890000e-68 270.0
35 TraesCS7D01G166700 chr2D 94.253 174 8 2 3203 3376 391812509 391812338 8.790000e-67 265.0
36 TraesCS7D01G166700 chr2D 94.048 168 8 2 3200 3367 631626555 631626390 1.900000e-63 254.0
37 TraesCS7D01G166700 chr5A 76.038 530 104 21 2283 2799 105416187 105415668 1.900000e-63 254.0
38 TraesCS7D01G166700 chr3A 81.313 198 37 0 2231 2428 63469631 63469828 1.190000e-35 161.0
39 TraesCS7D01G166700 chr1A 100.000 31 0 0 1558 1588 238678453 238678483 1.600000e-04 58.4


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 TraesCS7D01G166700 chr7D 117462162 117466285 4123 False 7616.000000 7616 100.000000 1 4124 1 chr7D.!!$F1 4123
1 TraesCS7D01G166700 chr7A 121843295 121846445 3150 False 1482.000000 3795 93.118333 5 3137 3 chr7A.!!$F1 3132
2 TraesCS7D01G166700 chr4B 574169250 574171402 2152 False 2928.000000 2928 91.276000 969 3126 1 chr4B.!!$F1 2157
3 TraesCS7D01G166700 chr4D 459383308 459385356 2048 False 2891.000000 2891 92.019000 1050 3126 1 chr4D.!!$F2 2076
4 TraesCS7D01G166700 chr4A 9399954 9405308 5354 True 991.666667 1644 88.930667 14 3126 3 chr4A.!!$R1 3112
5 TraesCS7D01G166700 chr6B 554343950 554344690 740 True 935.000000 935 89.404000 3369 4119 1 chr6B.!!$R1 750
6 TraesCS7D01G166700 chr6B 612844540 612845304 764 False 761.000000 761 84.942000 3362 4123 1 chr6B.!!$F1 761
7 TraesCS7D01G166700 chrUn 308643419 308644177 758 False 846.000000 846 86.979000 3368 4124 1 chrUn.!!$F1 756
8 TraesCS7D01G166700 chr6A 607135834 607136592 758 False 846.000000 846 86.979000 3368 4124 1 chr6A.!!$F1 756
9 TraesCS7D01G166700 chr6A 607274249 607275006 757 False 845.000000 845 86.962000 3368 4124 1 chr6A.!!$F2 756
10 TraesCS7D01G166700 chr2B 666726005 666726760 755 False 804.000000 804 86.086000 3368 4123 1 chr2B.!!$F1 755
11 TraesCS7D01G166700 chr5B 43815043 43815799 756 False 800.000000 800 85.919000 3368 4124 1 chr5B.!!$F1 756
12 TraesCS7D01G166700 chr5B 107370402 107370912 510 False 257.000000 257 76.336000 2283 2793 1 chr5B.!!$F2 510
13 TraesCS7D01G166700 chr1D 228043179 228043937 758 True 780.000000 780 85.436000 3368 4124 1 chr1D.!!$R1 756
14 TraesCS7D01G166700 chr1D 267999611 268000658 1047 True 344.000000 344 73.191000 1492 2550 1 chr1D.!!$R2 1058
15 TraesCS7D01G166700 chr5D 438337887 438338597 710 False 773.000000 773 86.345000 3366 4085 1 chr5D.!!$F2 719
16 TraesCS7D01G166700 chr5D 98228654 98229167 513 False 265.000000 265 76.571000 2283 2793 1 chr5D.!!$F1 510
17 TraesCS7D01G166700 chr5A 105415668 105416187 519 True 254.000000 254 76.038000 2283 2799 1 chr5A.!!$R1 516

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
284 762 0.963962 AGCCAAGTTCTAACCGTCGA 59.036 50.0 0.0 0.0 0.0 4.20 F
1833 4621 0.885879 ACATGTACGTCGGCTTCTCA 59.114 50.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 4985 0.112412 AACCACCCGAGCCAAGAAAT 59.888 50.0 0.00 0.0 0.00 2.17 R
3164 6029 0.109272 TTCGCTAGCTCACCGAACTG 60.109 55.0 13.93 0.0 36.23 3.16 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
31 32 3.368571 GTGGGAACAGCAGCCTGC 61.369 66.667 9.13 9.13 44.46 4.85
53 54 4.689812 GCATCGAGCAGATAATCAATCACT 59.310 41.667 0.00 0.00 44.79 3.41
98 103 1.407979 ACGTATTCTAGGACCTTGGCG 59.592 52.381 0.00 4.20 0.00 5.69
123 128 1.097547 AATGGAGATTTCTGCGCCCG 61.098 55.000 4.18 0.00 37.10 6.13
152 411 5.682862 TGTACAGTAGACGTTTCTTTCGTTC 59.317 40.000 0.00 0.00 41.64 3.95
153 412 4.047142 ACAGTAGACGTTTCTTTCGTTCC 58.953 43.478 0.00 0.00 41.64 3.62
158 417 1.067516 ACGTTTCTTTCGTTCCGGAGA 59.932 47.619 3.34 0.00 38.38 3.71
170 429 3.854669 CGGAGAAGGAGGGCGCAT 61.855 66.667 10.83 0.00 0.00 4.73
228 487 2.930682 GGAATCTGCTGTTCTAACCGTC 59.069 50.000 0.00 0.00 0.00 4.79
278 756 3.498777 GTCCAAGTCAGCCAAGTTCTAAC 59.501 47.826 0.00 0.00 0.00 2.34
280 758 2.457366 AGTCAGCCAAGTTCTAACCG 57.543 50.000 0.00 0.00 0.00 4.44
282 760 2.067013 GTCAGCCAAGTTCTAACCGTC 58.933 52.381 0.00 0.00 0.00 4.79
283 761 1.068474 CAGCCAAGTTCTAACCGTCG 58.932 55.000 0.00 0.00 0.00 5.12
284 762 0.963962 AGCCAAGTTCTAACCGTCGA 59.036 50.000 0.00 0.00 0.00 4.20
285 763 1.066136 GCCAAGTTCTAACCGTCGAC 58.934 55.000 5.18 5.18 0.00 4.20
286 764 1.334054 CCAAGTTCTAACCGTCGACG 58.666 55.000 30.33 30.33 39.44 5.12
352 888 4.637276 TCAGTTCCATTTTTCGTGCTCTA 58.363 39.130 0.00 0.00 0.00 2.43
398 935 2.325583 TTGACTGACTTGGCGTTTCT 57.674 45.000 0.00 0.00 0.00 2.52
435 978 1.930908 GCACAGGGAAGTGATGCTGC 61.931 60.000 0.00 0.00 42.05 5.25
499 1042 9.010366 GTGCTCTTTTAATCACGATTTTAATCC 57.990 33.333 0.00 0.00 32.50 3.01
500 1043 8.956426 TGCTCTTTTAATCACGATTTTAATCCT 58.044 29.630 0.00 0.00 32.50 3.24
501 1044 9.788960 GCTCTTTTAATCACGATTTTAATCCTT 57.211 29.630 0.00 0.00 32.50 3.36
528 1071 5.452078 TTTTTGCAGGAAATCACGATCTT 57.548 34.783 0.00 0.00 0.00 2.40
529 1072 6.567687 TTTTTGCAGGAAATCACGATCTTA 57.432 33.333 0.00 0.00 0.00 2.10
530 1073 6.567687 TTTTGCAGGAAATCACGATCTTAA 57.432 33.333 0.00 0.00 0.00 1.85
531 1074 6.757897 TTTGCAGGAAATCACGATCTTAAT 57.242 33.333 0.00 0.00 0.00 1.40
532 1075 5.991328 TGCAGGAAATCACGATCTTAATC 57.009 39.130 0.00 0.00 0.00 1.75
533 1076 4.816385 TGCAGGAAATCACGATCTTAATCC 59.184 41.667 0.00 0.00 0.00 3.01
534 1077 5.059833 GCAGGAAATCACGATCTTAATCCT 58.940 41.667 0.00 0.00 36.52 3.24
548 1091 6.305272 TCTTAATCCTGAGCTCACATCTTT 57.695 37.500 13.74 5.21 0.00 2.52
550 1093 3.557228 ATCCTGAGCTCACATCTTTCC 57.443 47.619 13.74 0.00 0.00 3.13
552 1095 1.649664 CTGAGCTCACATCTTTCCCG 58.350 55.000 13.74 0.00 0.00 5.14
558 1101 2.766313 CTCACATCTTTCCCGTGAACA 58.234 47.619 0.00 0.00 39.07 3.18
559 1102 2.738846 CTCACATCTTTCCCGTGAACAG 59.261 50.000 0.00 0.00 39.07 3.16
696 1239 2.097036 CAATGCTCCTGAATGCTTCCA 58.903 47.619 0.00 0.00 0.00 3.53
703 1246 4.201990 GCTCCTGAATGCTTCCAACAATAG 60.202 45.833 0.00 0.00 0.00 1.73
710 1253 6.922957 TGAATGCTTCCAACAATAGTGTTTTC 59.077 34.615 5.68 6.63 46.01 2.29
711 1254 5.843673 TGCTTCCAACAATAGTGTTTTCA 57.156 34.783 5.68 0.00 46.01 2.69
715 1258 6.292328 GCTTCCAACAATAGTGTTTTCAAAGC 60.292 38.462 17.82 17.82 46.01 3.51
720 1263 7.011295 CCAACAATAGTGTTTTCAAAGCATTGT 59.989 33.333 5.68 0.12 46.01 2.71
789 1336 4.449870 TTTTGCGTGCAATGAAAACATC 57.550 36.364 8.26 0.00 27.64 3.06
798 1345 5.640357 GTGCAATGAAAACATCCATCAATGT 59.360 36.000 0.00 0.00 41.60 2.71
863 1437 2.327325 TTACTGTTCAGGAGGGAGCT 57.673 50.000 4.82 0.00 0.00 4.09
886 1460 1.975660 AAGCTCGGGTGCAAAAACTA 58.024 45.000 0.00 0.00 34.99 2.24
893 1467 1.002142 GGGTGCAAAAACTACACGTCC 60.002 52.381 0.00 0.00 35.11 4.79
936 1510 1.865340 GCGGCTAGCGCTTTTTATACT 59.135 47.619 18.68 0.00 35.41 2.12
937 1511 2.348591 GCGGCTAGCGCTTTTTATACTG 60.349 50.000 18.68 3.85 35.41 2.74
960 3724 9.930693 ACTGTACCAATTAAAAAGAAACAACAA 57.069 25.926 0.00 0.00 0.00 2.83
962 3726 9.152595 TGTACCAATTAAAAAGAAACAACAACC 57.847 29.630 0.00 0.00 0.00 3.77
984 3748 1.209127 GCGACCAACCAATCAACGG 59.791 57.895 0.00 0.00 0.00 4.44
990 3754 2.962421 ACCAACCAATCAACGGTGAAAT 59.038 40.909 7.51 0.00 37.30 2.17
1019 3783 7.158697 ACGGATATGCTGCTTATACATAACAA 58.841 34.615 15.57 0.00 30.57 2.83
1037 3801 5.888412 AACAAACAAGAAATCATTGTCGC 57.112 34.783 0.00 0.00 39.91 5.19
1038 3802 4.298332 ACAAACAAGAAATCATTGTCGCC 58.702 39.130 0.00 0.00 39.91 5.54
1042 3806 1.755179 AGAAATCATTGTCGCCCCTG 58.245 50.000 0.00 0.00 0.00 4.45
1046 3822 2.202236 ATCATTGTCGCCCCTGCACT 62.202 55.000 0.00 0.00 37.32 4.40
1048 3824 3.196207 ATTGTCGCCCCTGCACTGT 62.196 57.895 0.00 0.00 37.32 3.55
1167 3946 2.376109 GTCGACTTCATCTACCAGGGA 58.624 52.381 8.70 0.00 0.00 4.20
1479 4258 3.692406 GTCCTCGGGCCGAACACT 61.692 66.667 30.59 0.00 34.74 3.55
1481 4260 1.380785 TCCTCGGGCCGAACACTAT 60.381 57.895 30.59 0.00 34.74 2.12
1530 4309 1.162181 TCGAGTTCGACACGGTCACT 61.162 55.000 0.00 2.02 44.22 3.41
1627 4412 2.964174 CCGCGTACTACACCACCA 59.036 61.111 4.92 0.00 0.00 4.17
1833 4621 0.885879 ACATGTACGTCGGCTTCTCA 59.114 50.000 0.00 0.00 0.00 3.27
2091 4913 1.197430 AACTGGAGGACTGGGAGCTG 61.197 60.000 0.00 0.00 0.00 4.24
2094 4916 2.063378 GGAGGACTGGGAGCTGGAG 61.063 68.421 0.00 0.00 0.00 3.86
2157 4985 2.291043 GGGGTTCAAGGAGAGCGGA 61.291 63.158 0.00 0.00 0.00 5.54
2928 5790 1.452108 GGGCATGGTGTGTAGCCTC 60.452 63.158 0.00 0.00 46.23 4.70
3075 5940 1.135915 CTCTCCTCCATGACCTTGTCG 59.864 57.143 0.00 0.00 34.95 4.35
3087 5952 2.203523 TTGTCGTCCTCCGGTGGA 60.204 61.111 21.30 21.30 37.11 4.02
3101 5966 2.434185 TGGAACCATGTCGCTCGC 60.434 61.111 0.00 0.00 0.00 5.03
3114 5979 4.519437 CTCGCCTCGCAGCATGGA 62.519 66.667 4.94 0.00 35.86 3.41
3126 5991 2.187946 CATGGAGGTCGGTGAGCC 59.812 66.667 0.00 0.00 0.00 4.70
3137 6002 1.968493 TCGGTGAGCCAGGGAATATAC 59.032 52.381 0.00 0.00 34.09 1.47
3138 6003 1.971357 CGGTGAGCCAGGGAATATACT 59.029 52.381 0.00 0.00 34.09 2.12
3139 6004 2.289072 CGGTGAGCCAGGGAATATACTG 60.289 54.545 0.00 0.00 34.09 2.74
3140 6005 2.706190 GGTGAGCCAGGGAATATACTGT 59.294 50.000 0.00 0.00 32.90 3.55
3141 6006 3.901844 GGTGAGCCAGGGAATATACTGTA 59.098 47.826 0.00 0.00 32.90 2.74
3142 6007 4.021016 GGTGAGCCAGGGAATATACTGTAG 60.021 50.000 0.00 0.00 32.90 2.74
3143 6008 4.833380 GTGAGCCAGGGAATATACTGTAGA 59.167 45.833 0.00 0.00 32.90 2.59
3144 6009 5.304614 GTGAGCCAGGGAATATACTGTAGAA 59.695 44.000 0.00 0.00 32.90 2.10
3145 6010 6.014156 GTGAGCCAGGGAATATACTGTAGAAT 60.014 42.308 0.00 0.00 32.90 2.40
3146 6011 6.558775 TGAGCCAGGGAATATACTGTAGAATT 59.441 38.462 0.00 0.00 32.90 2.17
3147 6012 7.072454 TGAGCCAGGGAATATACTGTAGAATTT 59.928 37.037 0.00 0.00 32.90 1.82
3148 6013 7.454225 AGCCAGGGAATATACTGTAGAATTTC 58.546 38.462 0.00 0.00 32.90 2.17
3149 6014 7.293535 AGCCAGGGAATATACTGTAGAATTTCT 59.706 37.037 4.03 4.03 32.90 2.52
3150 6015 7.939588 GCCAGGGAATATACTGTAGAATTTCTT 59.060 37.037 3.86 0.00 32.90 2.52
3151 6016 9.853177 CCAGGGAATATACTGTAGAATTTCTTT 57.147 33.333 3.86 0.00 32.90 2.52
3170 6035 1.593196 TTTTCCAGCAGGTCAGTTCG 58.407 50.000 0.00 0.00 35.89 3.95
3171 6036 0.250295 TTTCCAGCAGGTCAGTTCGG 60.250 55.000 0.00 0.00 35.89 4.30
3172 6037 1.407656 TTCCAGCAGGTCAGTTCGGT 61.408 55.000 0.00 0.00 35.89 4.69
3173 6038 1.669115 CCAGCAGGTCAGTTCGGTG 60.669 63.158 0.00 0.00 0.00 4.94
3174 6039 1.367471 CAGCAGGTCAGTTCGGTGA 59.633 57.895 0.00 0.00 0.00 4.02
3175 6040 0.668706 CAGCAGGTCAGTTCGGTGAG 60.669 60.000 0.00 0.00 0.00 3.51
3176 6041 2.029844 GCAGGTCAGTTCGGTGAGC 61.030 63.158 4.89 4.89 43.88 4.26
3179 6044 3.723554 GGTCAGTTCGGTGAGCTAG 57.276 57.895 0.00 0.00 40.98 3.42
3180 6045 0.458716 GGTCAGTTCGGTGAGCTAGC 60.459 60.000 6.62 6.62 40.98 3.42
3193 6058 5.593010 GGTGAGCTAGCGAATATATTAGGG 58.407 45.833 9.55 0.00 0.00 3.53
3194 6059 5.127356 GGTGAGCTAGCGAATATATTAGGGT 59.873 44.000 9.55 6.77 0.00 4.34
3195 6060 6.351117 GGTGAGCTAGCGAATATATTAGGGTT 60.351 42.308 9.55 0.00 0.00 4.11
3196 6061 7.147949 GGTGAGCTAGCGAATATATTAGGGTTA 60.148 40.741 9.55 0.00 0.00 2.85
3197 6062 8.248945 GTGAGCTAGCGAATATATTAGGGTTAA 58.751 37.037 9.55 0.00 0.00 2.01
3198 6063 8.978472 TGAGCTAGCGAATATATTAGGGTTAAT 58.022 33.333 9.55 0.00 34.04 1.40
3199 6064 9.819267 GAGCTAGCGAATATATTAGGGTTAATT 57.181 33.333 9.55 0.00 31.97 1.40
3213 6078 6.651975 AGGGTTAATTAGATACTCACTCCG 57.348 41.667 0.00 0.00 0.00 4.63
3214 6079 6.134754 AGGGTTAATTAGATACTCACTCCGT 58.865 40.000 0.00 0.00 0.00 4.69
3215 6080 6.610425 AGGGTTAATTAGATACTCACTCCGTT 59.390 38.462 0.00 0.00 0.00 4.44
3216 6081 7.125356 AGGGTTAATTAGATACTCACTCCGTTT 59.875 37.037 0.00 0.00 0.00 3.60
3217 6082 7.437565 GGGTTAATTAGATACTCACTCCGTTTC 59.562 40.741 0.00 0.00 0.00 2.78
3218 6083 8.196103 GGTTAATTAGATACTCACTCCGTTTCT 58.804 37.037 0.00 0.00 0.00 2.52
3230 6095 8.968969 ACTCACTCCGTTTCTAAATATAAGTCT 58.031 33.333 0.00 0.00 0.00 3.24
3231 6096 9.804758 CTCACTCCGTTTCTAAATATAAGTCTT 57.195 33.333 0.00 0.00 0.00 3.01
3260 6125 8.873215 AGAGATTTTACTATGAACCACATACG 57.127 34.615 0.00 0.00 40.07 3.06
3261 6126 7.926555 AGAGATTTTACTATGAACCACATACGG 59.073 37.037 0.00 0.00 40.07 4.02
3262 6127 7.788026 AGATTTTACTATGAACCACATACGGA 58.212 34.615 0.00 0.00 40.07 4.69
3263 6128 8.429641 AGATTTTACTATGAACCACATACGGAT 58.570 33.333 0.00 0.00 40.07 4.18
3264 6129 7.780008 TTTTACTATGAACCACATACGGATG 57.220 36.000 5.94 5.94 40.07 3.51
3266 6131 7.585579 TTACTATGAACCACATACGGATGTA 57.414 36.000 14.23 0.00 44.82 2.29
3267 6132 6.665992 ACTATGAACCACATACGGATGTAT 57.334 37.500 14.23 5.54 44.82 2.29
3268 6133 7.770366 ACTATGAACCACATACGGATGTATA 57.230 36.000 14.23 6.48 44.82 1.47
3269 6134 8.362464 ACTATGAACCACATACGGATGTATAT 57.638 34.615 14.23 1.68 44.82 0.86
3270 6135 9.470399 ACTATGAACCACATACGGATGTATATA 57.530 33.333 14.23 7.10 44.82 0.86
3271 6136 9.952188 CTATGAACCACATACGGATGTATATAG 57.048 37.037 14.23 12.28 44.82 1.31
3272 6137 8.589701 ATGAACCACATACGGATGTATATAGA 57.410 34.615 14.23 0.00 44.82 1.98
3273 6138 8.589701 TGAACCACATACGGATGTATATAGAT 57.410 34.615 14.23 0.00 44.82 1.98
3274 6139 8.466798 TGAACCACATACGGATGTATATAGATG 58.533 37.037 14.23 0.00 44.82 2.90
3275 6140 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
3276 6141 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
3277 6142 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
3278 6143 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
3279 6144 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
3280 6145 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
3284 6149 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
3306 6171 7.093322 AGTGTAGATTCATTCATTTTGCTCC 57.907 36.000 0.00 0.00 0.00 4.70
3307 6172 5.967674 GTGTAGATTCATTCATTTTGCTCCG 59.032 40.000 0.00 0.00 0.00 4.63
3308 6173 5.647658 TGTAGATTCATTCATTTTGCTCCGT 59.352 36.000 0.00 0.00 0.00 4.69
3309 6174 6.821160 TGTAGATTCATTCATTTTGCTCCGTA 59.179 34.615 0.00 0.00 0.00 4.02
3310 6175 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
3311 6176 8.988934 GTAGATTCATTCATTTTGCTCCGTATA 58.011 33.333 0.00 0.00 0.00 1.47
3312 6177 8.627208 AGATTCATTCATTTTGCTCCGTATAT 57.373 30.769 0.00 0.00 0.00 0.86
3313 6178 9.725019 AGATTCATTCATTTTGCTCCGTATATA 57.275 29.630 0.00 0.00 0.00 0.86
3314 6179 9.979270 GATTCATTCATTTTGCTCCGTATATAG 57.021 33.333 0.00 0.00 0.00 1.31
3315 6180 8.902540 TTCATTCATTTTGCTCCGTATATAGT 57.097 30.769 0.00 0.00 0.00 2.12
3316 6181 8.534333 TCATTCATTTTGCTCCGTATATAGTC 57.466 34.615 0.00 0.00 0.00 2.59
3317 6182 7.602644 TCATTCATTTTGCTCCGTATATAGTCC 59.397 37.037 0.00 0.00 0.00 3.85
3318 6183 6.413783 TCATTTTGCTCCGTATATAGTCCA 57.586 37.500 0.00 0.00 0.00 4.02
3319 6184 6.220930 TCATTTTGCTCCGTATATAGTCCAC 58.779 40.000 0.00 0.00 0.00 4.02
3320 6185 4.595762 TTTGCTCCGTATATAGTCCACC 57.404 45.455 0.00 0.00 0.00 4.61
3321 6186 3.520691 TGCTCCGTATATAGTCCACCT 57.479 47.619 0.00 0.00 0.00 4.00
3322 6187 4.645863 TGCTCCGTATATAGTCCACCTA 57.354 45.455 0.00 0.00 0.00 3.08
3323 6188 4.586884 TGCTCCGTATATAGTCCACCTAG 58.413 47.826 0.00 0.00 0.00 3.02
3324 6189 4.042560 TGCTCCGTATATAGTCCACCTAGT 59.957 45.833 0.00 0.00 0.00 2.57
3325 6190 4.395542 GCTCCGTATATAGTCCACCTAGTG 59.604 50.000 0.00 0.00 0.00 2.74
3326 6191 5.802465 CTCCGTATATAGTCCACCTAGTGA 58.198 45.833 0.00 0.00 35.23 3.41
3327 6192 6.191657 TCCGTATATAGTCCACCTAGTGAA 57.808 41.667 0.00 0.00 35.23 3.18
3328 6193 6.604171 TCCGTATATAGTCCACCTAGTGAAA 58.396 40.000 0.00 0.00 35.23 2.69
3329 6194 7.236529 TCCGTATATAGTCCACCTAGTGAAAT 58.763 38.462 0.00 0.00 35.23 2.17
3330 6195 7.392673 TCCGTATATAGTCCACCTAGTGAAATC 59.607 40.741 0.00 0.00 35.23 2.17
3331 6196 7.393796 CCGTATATAGTCCACCTAGTGAAATCT 59.606 40.741 0.00 0.00 35.23 2.40
3332 6197 8.452534 CGTATATAGTCCACCTAGTGAAATCTC 58.547 40.741 0.00 0.00 35.23 2.75
3333 6198 9.523168 GTATATAGTCCACCTAGTGAAATCTCT 57.477 37.037 0.00 0.00 35.23 3.10
3335 6200 7.826918 ATAGTCCACCTAGTGAAATCTCTAC 57.173 40.000 0.00 0.00 35.23 2.59
3336 6201 5.580998 AGTCCACCTAGTGAAATCTCTACA 58.419 41.667 0.00 0.00 35.23 2.74
3337 6202 6.017192 AGTCCACCTAGTGAAATCTCTACAA 58.983 40.000 0.00 0.00 35.23 2.41
3338 6203 6.497259 AGTCCACCTAGTGAAATCTCTACAAA 59.503 38.462 0.00 0.00 35.23 2.83
3339 6204 6.814146 GTCCACCTAGTGAAATCTCTACAAAG 59.186 42.308 0.00 0.00 35.23 2.77
3340 6205 6.724441 TCCACCTAGTGAAATCTCTACAAAGA 59.276 38.462 0.00 0.00 35.23 2.52
3341 6206 6.814146 CCACCTAGTGAAATCTCTACAAAGAC 59.186 42.308 0.00 0.00 35.23 3.01
3342 6207 7.310113 CCACCTAGTGAAATCTCTACAAAGACT 60.310 40.741 0.00 0.00 35.23 3.24
3343 6208 8.091449 CACCTAGTGAAATCTCTACAAAGACTT 58.909 37.037 0.00 0.00 35.23 3.01
3344 6209 9.310449 ACCTAGTGAAATCTCTACAAAGACTTA 57.690 33.333 0.00 0.00 0.00 2.24
3360 6225 9.379791 ACAAAGACTTATATTTAGGAACGGAAG 57.620 33.333 0.00 0.00 0.00 3.46
3361 6226 8.827677 CAAAGACTTATATTTAGGAACGGAAGG 58.172 37.037 0.00 0.00 0.00 3.46
3362 6227 7.909485 AGACTTATATTTAGGAACGGAAGGA 57.091 36.000 0.00 0.00 0.00 3.36
3363 6228 7.953752 AGACTTATATTTAGGAACGGAAGGAG 58.046 38.462 0.00 0.00 0.00 3.69
3364 6229 7.564292 AGACTTATATTTAGGAACGGAAGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
3384 6249 7.104290 AGGAGTACCTTTAGCTACATTTTCAC 58.896 38.462 0.00 0.00 45.36 3.18
3452 6317 0.445436 CGTGCTTTGAGATCTGTGCC 59.555 55.000 0.00 0.00 0.00 5.01
3487 6354 7.945033 TTTTCTGTTCAATTCTATTGTTGCC 57.055 32.000 0.00 0.00 0.00 4.52
3587 6454 2.554893 GTTGCACCCGTTTAATTCTGGA 59.445 45.455 0.00 0.00 0.00 3.86
3588 6455 2.156098 TGCACCCGTTTAATTCTGGAC 58.844 47.619 0.00 0.00 0.00 4.02
3671 6543 8.585018 GCTTTTTGGCTGGGTGTAATTATATAT 58.415 33.333 0.00 0.00 0.00 0.86
3775 6651 4.806881 GCAAAGTTGTGCGTTAGTTTTTC 58.193 39.130 0.00 0.00 34.21 2.29
3832 6715 7.359595 TCAACACCACTAATTCATTCTTTTCG 58.640 34.615 0.00 0.00 0.00 3.46
3835 6718 7.936584 ACACCACTAATTCATTCTTTTCGAAA 58.063 30.769 6.47 6.47 34.79 3.46
3983 6875 5.309323 TGCATAGTTCTAAAAAGCGCAAT 57.691 34.783 11.47 0.00 0.00 3.56
4043 6936 8.498358 GTTTGCTTTAGATTCTTTTTCCCATTG 58.502 33.333 0.00 0.00 0.00 2.82
4085 6979 6.610075 ACCAATGCCACTAATTCATTCTTT 57.390 33.333 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.260230 TCCCACCACACCAACATGTT 59.740 50.000 4.92 4.92 0.00 2.71
2 3 0.673437 GTTCCCACCACACCAACATG 59.327 55.000 0.00 0.00 0.00 3.21
31 32 6.157904 AGAGTGATTGATTATCTGCTCGATG 58.842 40.000 0.00 0.00 39.12 3.84
32 33 6.343716 AGAGTGATTGATTATCTGCTCGAT 57.656 37.500 0.00 0.00 39.12 3.59
53 54 1.504359 CCTACGCGTTTTGGTCAAGA 58.496 50.000 20.78 0.00 0.00 3.02
98 103 2.287427 CGCAGAAATCTCCATTGATGCC 60.287 50.000 0.00 0.00 33.55 4.40
123 128 4.243270 AGAAACGTCTACTGTACATTGCC 58.757 43.478 0.00 0.00 29.93 4.52
153 412 3.798954 GATGCGCCCTCCTTCTCCG 62.799 68.421 4.18 0.00 0.00 4.63
158 417 1.383248 ACCTAGATGCGCCCTCCTT 60.383 57.895 4.18 0.00 0.00 3.36
252 730 0.671781 CTTGGCTGACTTGGACGGAG 60.672 60.000 0.00 0.00 0.00 4.63
255 733 0.868406 GAACTTGGCTGACTTGGACG 59.132 55.000 0.00 0.00 0.00 4.79
256 734 2.262423 AGAACTTGGCTGACTTGGAC 57.738 50.000 0.00 0.00 0.00 4.02
257 735 3.496160 GGTTAGAACTTGGCTGACTTGGA 60.496 47.826 0.00 0.00 0.00 3.53
258 736 2.814336 GGTTAGAACTTGGCTGACTTGG 59.186 50.000 0.00 0.00 0.00 3.61
259 737 2.480419 CGGTTAGAACTTGGCTGACTTG 59.520 50.000 0.00 0.00 0.00 3.16
261 739 1.692519 ACGGTTAGAACTTGGCTGACT 59.307 47.619 0.00 0.00 0.00 3.41
262 740 2.067013 GACGGTTAGAACTTGGCTGAC 58.933 52.381 0.00 0.00 0.00 3.51
282 760 4.851991 GCAATCAGCAAGACAACCGTCG 62.852 54.545 0.00 0.00 44.75 5.12
283 761 1.400242 GCAATCAGCAAGACAACCGTC 60.400 52.381 0.00 0.00 44.79 4.79
284 762 0.593128 GCAATCAGCAAGACAACCGT 59.407 50.000 0.00 0.00 44.79 4.83
285 763 3.389741 GCAATCAGCAAGACAACCG 57.610 52.632 0.00 0.00 44.79 4.44
352 888 5.296780 ACTTGACACGAGTGAATGAAAATGT 59.703 36.000 10.50 0.00 0.00 2.71
398 935 1.514678 GCGTGTGCCATTCCAAGTCA 61.515 55.000 0.00 0.00 33.98 3.41
506 1049 5.452078 AAGATCGTGATTTCCTGCAAAAA 57.548 34.783 0.00 0.00 0.00 1.94
507 1050 6.567687 TTAAGATCGTGATTTCCTGCAAAA 57.432 33.333 0.00 0.00 0.00 2.44
508 1051 6.183360 GGATTAAGATCGTGATTTCCTGCAAA 60.183 38.462 0.00 0.00 32.84 3.68
509 1052 5.296780 GGATTAAGATCGTGATTTCCTGCAA 59.703 40.000 0.00 0.00 32.84 4.08
510 1053 4.816385 GGATTAAGATCGTGATTTCCTGCA 59.184 41.667 0.00 0.00 32.84 4.41
511 1054 5.049818 CAGGATTAAGATCGTGATTTCCTGC 60.050 44.000 14.93 0.00 46.19 4.85
512 1055 6.283694 TCAGGATTAAGATCGTGATTTCCTG 58.716 40.000 18.48 18.48 46.55 3.86
513 1056 6.485830 TCAGGATTAAGATCGTGATTTCCT 57.514 37.500 7.48 0.00 46.55 3.36
520 1063 4.047822 GTGAGCTCAGGATTAAGATCGTG 58.952 47.826 18.89 3.42 45.20 4.35
521 1064 3.701542 TGTGAGCTCAGGATTAAGATCGT 59.298 43.478 18.89 0.00 30.59 3.73
522 1065 4.313277 TGTGAGCTCAGGATTAAGATCG 57.687 45.455 18.89 0.00 30.59 3.69
523 1066 6.100404 AGATGTGAGCTCAGGATTAAGATC 57.900 41.667 18.89 6.82 0.00 2.75
524 1067 6.497624 AAGATGTGAGCTCAGGATTAAGAT 57.502 37.500 18.89 0.00 0.00 2.40
525 1068 5.946942 AAGATGTGAGCTCAGGATTAAGA 57.053 39.130 18.89 0.00 0.00 2.10
526 1069 5.526846 GGAAAGATGTGAGCTCAGGATTAAG 59.473 44.000 18.89 0.00 0.00 1.85
527 1070 5.431765 GGAAAGATGTGAGCTCAGGATTAA 58.568 41.667 18.89 0.00 0.00 1.40
528 1071 4.141620 GGGAAAGATGTGAGCTCAGGATTA 60.142 45.833 18.89 1.71 0.00 1.75
529 1072 3.371380 GGGAAAGATGTGAGCTCAGGATT 60.371 47.826 18.89 8.21 0.00 3.01
530 1073 2.172293 GGGAAAGATGTGAGCTCAGGAT 59.828 50.000 18.89 12.40 0.00 3.24
531 1074 1.556911 GGGAAAGATGTGAGCTCAGGA 59.443 52.381 18.89 7.30 0.00 3.86
532 1075 1.741732 CGGGAAAGATGTGAGCTCAGG 60.742 57.143 18.89 0.00 0.00 3.86
533 1076 1.066573 ACGGGAAAGATGTGAGCTCAG 60.067 52.381 18.89 3.52 0.00 3.35
534 1077 0.976641 ACGGGAAAGATGTGAGCTCA 59.023 50.000 13.74 13.74 0.00 4.26
629 1172 8.090250 CATTTCCACAAATGTCATTTTGTCAT 57.910 30.769 8.12 0.00 45.54 3.06
663 1206 9.729281 ATTCAGGAGCATTGATTTTGTATTTTT 57.271 25.926 0.00 0.00 0.00 1.94
668 1211 5.419788 AGCATTCAGGAGCATTGATTTTGTA 59.580 36.000 0.00 0.00 0.00 2.41
685 1228 6.403866 AAACACTATTGTTGGAAGCATTCA 57.596 33.333 0.00 0.00 46.06 2.57
686 1229 6.922957 TGAAAACACTATTGTTGGAAGCATTC 59.077 34.615 0.00 0.00 45.69 2.67
696 1239 8.491331 AACAATGCTTTGAAAACACTATTGTT 57.509 26.923 18.35 7.99 40.78 2.83
725 1268 5.678583 TCATGAAAATGTGGGCAAAGAAAA 58.321 33.333 0.00 0.00 0.00 2.29
729 1272 4.998672 ACATTCATGAAAATGTGGGCAAAG 59.001 37.500 13.09 0.00 45.68 2.77
836 1404 7.039993 GCTCCCTCCTGAACAGTAAAATAAAAA 60.040 37.037 1.18 0.00 0.00 1.94
837 1405 6.433093 GCTCCCTCCTGAACAGTAAAATAAAA 59.567 38.462 1.18 0.00 0.00 1.52
841 1409 3.589288 AGCTCCCTCCTGAACAGTAAAAT 59.411 43.478 1.18 0.00 0.00 1.82
863 1437 1.681538 TTTTGCACCCGAGCTTACAA 58.318 45.000 0.00 0.00 34.99 2.41
873 1447 1.002142 GGACGTGTAGTTTTTGCACCC 60.002 52.381 0.00 0.00 39.00 4.61
876 1450 0.305313 GCGGACGTGTAGTTTTTGCA 59.695 50.000 0.00 0.00 0.00 4.08
934 1508 9.930693 TTGTTGTTTCTTTTTAATTGGTACAGT 57.069 25.926 0.00 0.00 42.39 3.55
936 1510 9.152595 GGTTGTTGTTTCTTTTTAATTGGTACA 57.847 29.630 0.00 0.00 0.00 2.90
937 1511 9.152595 TGGTTGTTGTTTCTTTTTAATTGGTAC 57.847 29.630 0.00 0.00 0.00 3.34
951 3715 1.601914 GGTCGCCATGGTTGTTGTTTC 60.602 52.381 14.67 0.00 0.00 2.78
953 3717 0.753479 TGGTCGCCATGGTTGTTGTT 60.753 50.000 14.67 0.00 0.00 2.83
954 3718 0.753479 TTGGTCGCCATGGTTGTTGT 60.753 50.000 14.67 0.00 31.53 3.32
955 3719 0.318614 GTTGGTCGCCATGGTTGTTG 60.319 55.000 14.67 0.00 31.53 3.33
956 3720 1.460273 GGTTGGTCGCCATGGTTGTT 61.460 55.000 14.67 0.00 31.53 2.83
957 3721 1.901464 GGTTGGTCGCCATGGTTGT 60.901 57.895 14.67 0.00 31.53 3.32
960 3724 0.965363 GATTGGTTGGTCGCCATGGT 60.965 55.000 14.67 0.00 35.71 3.55
962 3726 0.887247 TTGATTGGTTGGTCGCCATG 59.113 50.000 0.00 0.00 35.71 3.66
984 3748 3.548818 GCAGCATATCCGTTGGATTTCAC 60.549 47.826 3.27 0.00 39.79 3.18
990 3754 3.769739 ATAAGCAGCATATCCGTTGGA 57.230 42.857 0.00 0.00 35.55 3.53
1019 3783 2.231235 GGGGCGACAATGATTTCTTGTT 59.769 45.455 0.00 0.00 36.98 2.83
1037 3801 1.003355 CTGGTGTACAGTGCAGGGG 60.003 63.158 0.00 0.00 42.42 4.79
1038 3802 4.701663 CTGGTGTACAGTGCAGGG 57.298 61.111 0.00 0.00 42.42 4.45
1046 3822 1.270094 CGCTGGAACTTCTGGTGTACA 60.270 52.381 0.00 0.00 0.00 2.90
1048 3824 1.272490 CTCGCTGGAACTTCTGGTGTA 59.728 52.381 0.00 0.00 0.00 2.90
1232 4011 3.414700 CGCTGTCGTTGGTGAGCC 61.415 66.667 0.00 0.00 0.00 4.70
1300 4079 2.433318 GCTCTGGCTGTCACCGAC 60.433 66.667 0.00 0.00 35.22 4.79
1304 4083 2.740055 CACCGCTCTGGCTGTCAC 60.740 66.667 0.00 0.00 43.94 3.67
1328 4107 2.282958 TGAAGGAGGAGACCGCGT 60.283 61.111 4.92 0.00 34.73 6.01
1530 4309 1.839994 GTCTCATTCATCCCCAGGTCA 59.160 52.381 0.00 0.00 0.00 4.02
1634 4419 3.787001 CCTTCCTGTCCTCCCCGC 61.787 72.222 0.00 0.00 0.00 6.13
2091 4913 1.988982 GAATCCTCTGGGGGTGCTCC 61.989 65.000 0.00 0.00 35.33 4.70
2094 4916 1.649271 ATGGAATCCTCTGGGGGTGC 61.649 60.000 0.00 0.00 35.33 5.01
2157 4985 0.112412 AACCACCCGAGCCAAGAAAT 59.888 50.000 0.00 0.00 0.00 2.17
2433 5286 4.357279 AGCACCTTGCCCTGCTCC 62.357 66.667 0.00 0.00 46.52 4.70
2435 5288 3.573229 TGAGCACCTTGCCCTGCT 61.573 61.111 0.00 0.00 46.52 4.24
2436 5289 3.368571 GTGAGCACCTTGCCCTGC 61.369 66.667 0.00 0.00 46.52 4.85
2438 5291 3.560251 ACGTGAGCACCTTGCCCT 61.560 61.111 0.00 0.00 46.52 5.19
2907 5769 1.299648 GCTACACACCATGCCCAGA 59.700 57.895 0.00 0.00 0.00 3.86
3009 5871 2.490165 GGGATCCGAGAACACGAGA 58.510 57.895 5.45 0.00 35.09 4.04
3087 5952 2.125512 GAGGCGAGCGACATGGTT 60.126 61.111 0.00 0.00 0.00 3.67
3097 5962 4.519437 TCCATGCTGCGAGGCGAG 62.519 66.667 5.41 0.00 34.52 5.03
3107 5972 3.023949 GCTCACCGACCTCCATGCT 62.024 63.158 0.00 0.00 0.00 3.79
3114 5979 3.723803 TATTCCCTGGCTCACCGACCT 62.724 57.143 0.00 0.00 39.70 3.85
3150 6015 1.946768 CGAACTGACCTGCTGGAAAAA 59.053 47.619 17.64 0.00 37.04 1.94
3151 6016 1.593196 CGAACTGACCTGCTGGAAAA 58.407 50.000 17.64 0.24 37.04 2.29
3152 6017 0.250295 CCGAACTGACCTGCTGGAAA 60.250 55.000 17.64 2.81 37.04 3.13
3153 6018 1.371183 CCGAACTGACCTGCTGGAA 59.629 57.895 17.64 3.18 37.04 3.53
3154 6019 1.837051 ACCGAACTGACCTGCTGGA 60.837 57.895 17.64 0.00 37.04 3.86
3155 6020 1.669115 CACCGAACTGACCTGCTGG 60.669 63.158 8.29 8.29 39.83 4.85
3156 6021 0.668706 CTCACCGAACTGACCTGCTG 60.669 60.000 0.00 0.00 0.00 4.41
3157 6022 1.668294 CTCACCGAACTGACCTGCT 59.332 57.895 0.00 0.00 0.00 4.24
3158 6023 2.029844 GCTCACCGAACTGACCTGC 61.030 63.158 0.00 0.00 0.00 4.85
3159 6024 0.888619 TAGCTCACCGAACTGACCTG 59.111 55.000 0.00 0.00 0.00 4.00
3160 6025 1.178276 CTAGCTCACCGAACTGACCT 58.822 55.000 0.00 0.00 0.00 3.85
3161 6026 0.458716 GCTAGCTCACCGAACTGACC 60.459 60.000 7.70 0.00 0.00 4.02
3162 6027 0.798771 CGCTAGCTCACCGAACTGAC 60.799 60.000 13.93 0.00 0.00 3.51
3163 6028 0.958876 TCGCTAGCTCACCGAACTGA 60.959 55.000 13.93 0.00 0.00 3.41
3164 6029 0.109272 TTCGCTAGCTCACCGAACTG 60.109 55.000 13.93 0.00 36.23 3.16
3165 6030 0.818296 ATTCGCTAGCTCACCGAACT 59.182 50.000 13.93 5.71 42.76 3.01
3166 6031 2.486951 TATTCGCTAGCTCACCGAAC 57.513 50.000 13.93 0.00 42.76 3.95
3167 6032 5.386958 AATATATTCGCTAGCTCACCGAA 57.613 39.130 13.93 15.32 43.87 4.30
3168 6033 5.066117 CCTAATATATTCGCTAGCTCACCGA 59.934 44.000 13.93 0.00 0.00 4.69
3169 6034 5.274718 CCTAATATATTCGCTAGCTCACCG 58.725 45.833 13.93 0.00 0.00 4.94
3170 6035 5.127356 ACCCTAATATATTCGCTAGCTCACC 59.873 44.000 13.93 0.00 0.00 4.02
3171 6036 6.210287 ACCCTAATATATTCGCTAGCTCAC 57.790 41.667 13.93 0.00 0.00 3.51
3172 6037 6.852420 AACCCTAATATATTCGCTAGCTCA 57.148 37.500 13.93 0.00 0.00 4.26
3173 6038 9.819267 AATTAACCCTAATATATTCGCTAGCTC 57.181 33.333 13.93 0.00 0.00 4.09
3187 6052 8.804204 CGGAGTGAGTATCTAATTAACCCTAAT 58.196 37.037 0.00 0.00 34.92 1.73
3188 6053 7.781693 ACGGAGTGAGTATCTAATTAACCCTAA 59.218 37.037 0.00 0.00 42.51 2.69
3189 6054 7.293073 ACGGAGTGAGTATCTAATTAACCCTA 58.707 38.462 0.00 0.00 42.51 3.53
3190 6055 6.134754 ACGGAGTGAGTATCTAATTAACCCT 58.865 40.000 0.00 0.00 42.51 4.34
3191 6056 6.402456 ACGGAGTGAGTATCTAATTAACCC 57.598 41.667 0.00 0.00 42.51 4.11
3192 6057 8.196103 AGAAACGGAGTGAGTATCTAATTAACC 58.804 37.037 0.00 0.00 45.00 2.85
3204 6069 8.968969 AGACTTATATTTAGAAACGGAGTGAGT 58.031 33.333 0.00 0.00 45.00 3.41
3205 6070 9.804758 AAGACTTATATTTAGAAACGGAGTGAG 57.195 33.333 0.00 0.00 45.00 3.51
3234 6099 9.961265 CGTATGTGGTTCATAGTAAAATCTCTA 57.039 33.333 0.00 0.00 39.36 2.43
3235 6100 7.926555 CCGTATGTGGTTCATAGTAAAATCTCT 59.073 37.037 0.00 0.00 39.36 3.10
3236 6101 7.924412 TCCGTATGTGGTTCATAGTAAAATCTC 59.076 37.037 0.00 0.00 39.36 2.75
3237 6102 7.788026 TCCGTATGTGGTTCATAGTAAAATCT 58.212 34.615 0.00 0.00 39.36 2.40
3238 6103 8.495949 CATCCGTATGTGGTTCATAGTAAAATC 58.504 37.037 0.00 0.00 39.36 2.17
3239 6104 7.990886 ACATCCGTATGTGGTTCATAGTAAAAT 59.009 33.333 0.00 0.00 44.79 1.82
3240 6105 7.332557 ACATCCGTATGTGGTTCATAGTAAAA 58.667 34.615 0.00 0.00 44.79 1.52
3241 6106 6.880484 ACATCCGTATGTGGTTCATAGTAAA 58.120 36.000 0.00 0.00 44.79 2.01
3242 6107 6.474140 ACATCCGTATGTGGTTCATAGTAA 57.526 37.500 0.00 0.00 44.79 2.24
3243 6108 7.770366 ATACATCCGTATGTGGTTCATAGTA 57.230 36.000 3.56 0.00 45.99 1.82
3244 6109 6.665992 ATACATCCGTATGTGGTTCATAGT 57.334 37.500 3.56 0.00 45.99 2.12
3245 6110 9.952188 CTATATACATCCGTATGTGGTTCATAG 57.048 37.037 3.56 0.80 45.99 2.23
3246 6111 9.689501 TCTATATACATCCGTATGTGGTTCATA 57.310 33.333 3.56 0.00 45.99 2.15
3247 6112 8.589701 TCTATATACATCCGTATGTGGTTCAT 57.410 34.615 3.56 0.00 45.99 2.57
3248 6113 8.466798 CATCTATATACATCCGTATGTGGTTCA 58.533 37.037 3.56 0.00 45.99 3.18
3249 6114 7.435488 GCATCTATATACATCCGTATGTGGTTC 59.565 40.741 3.56 0.00 45.99 3.62
3250 6115 7.093509 TGCATCTATATACATCCGTATGTGGTT 60.094 37.037 3.56 0.00 45.99 3.67
3251 6116 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
3252 6117 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
3253 6118 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
3258 6123 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
3280 6145 8.677300 GGAGCAAAATGAATGAATCTACACTTA 58.323 33.333 0.00 0.00 0.00 2.24
3281 6146 7.542025 GGAGCAAAATGAATGAATCTACACTT 58.458 34.615 0.00 0.00 0.00 3.16
3282 6147 6.183360 CGGAGCAAAATGAATGAATCTACACT 60.183 38.462 0.00 0.00 0.00 3.55
3283 6148 5.967674 CGGAGCAAAATGAATGAATCTACAC 59.032 40.000 0.00 0.00 0.00 2.90
3284 6149 5.647658 ACGGAGCAAAATGAATGAATCTACA 59.352 36.000 0.00 0.00 0.00 2.74
3285 6150 6.124088 ACGGAGCAAAATGAATGAATCTAC 57.876 37.500 0.00 0.00 0.00 2.59
3286 6151 9.725019 ATATACGGAGCAAAATGAATGAATCTA 57.275 29.630 0.00 0.00 0.00 1.98
3287 6152 6.949352 ATACGGAGCAAAATGAATGAATCT 57.051 33.333 0.00 0.00 0.00 2.40
3288 6153 9.979270 CTATATACGGAGCAAAATGAATGAATC 57.021 33.333 0.00 0.00 0.00 2.52
3289 6154 9.507329 ACTATATACGGAGCAAAATGAATGAAT 57.493 29.630 0.00 0.00 0.00 2.57
3290 6155 8.902540 ACTATATACGGAGCAAAATGAATGAA 57.097 30.769 0.00 0.00 0.00 2.57
3291 6156 7.602644 GGACTATATACGGAGCAAAATGAATGA 59.397 37.037 0.00 0.00 0.00 2.57
3292 6157 7.387673 TGGACTATATACGGAGCAAAATGAATG 59.612 37.037 0.00 0.00 0.00 2.67
3293 6158 7.387948 GTGGACTATATACGGAGCAAAATGAAT 59.612 37.037 0.00 0.00 0.00 2.57
3294 6159 6.704493 GTGGACTATATACGGAGCAAAATGAA 59.296 38.462 0.00 0.00 0.00 2.57
3295 6160 6.220930 GTGGACTATATACGGAGCAAAATGA 58.779 40.000 0.00 0.00 0.00 2.57
3296 6161 5.408604 GGTGGACTATATACGGAGCAAAATG 59.591 44.000 0.00 0.00 0.00 2.32
3297 6162 5.307196 AGGTGGACTATATACGGAGCAAAAT 59.693 40.000 0.00 0.00 0.00 1.82
3298 6163 4.652421 AGGTGGACTATATACGGAGCAAAA 59.348 41.667 0.00 0.00 0.00 2.44
3299 6164 4.220724 AGGTGGACTATATACGGAGCAAA 58.779 43.478 0.00 0.00 0.00 3.68
3300 6165 3.840991 AGGTGGACTATATACGGAGCAA 58.159 45.455 0.00 0.00 0.00 3.91
3301 6166 3.520691 AGGTGGACTATATACGGAGCA 57.479 47.619 0.00 0.00 0.00 4.26
3302 6167 4.395542 CACTAGGTGGACTATATACGGAGC 59.604 50.000 0.00 0.00 0.00 4.70
3303 6168 5.802465 TCACTAGGTGGACTATATACGGAG 58.198 45.833 0.00 0.00 33.87 4.63
3304 6169 5.830799 TCACTAGGTGGACTATATACGGA 57.169 43.478 0.00 0.00 33.87 4.69
3305 6170 6.889301 TTTCACTAGGTGGACTATATACGG 57.111 41.667 0.00 0.00 33.87 4.02
3306 6171 8.338072 AGATTTCACTAGGTGGACTATATACG 57.662 38.462 0.00 0.00 33.87 3.06
3307 6172 9.523168 AGAGATTTCACTAGGTGGACTATATAC 57.477 37.037 0.00 0.00 33.87 1.47
3309 6174 9.523168 GTAGAGATTTCACTAGGTGGACTATAT 57.477 37.037 0.00 0.00 33.87 0.86
3310 6175 8.500238 TGTAGAGATTTCACTAGGTGGACTATA 58.500 37.037 0.00 0.00 33.87 1.31
3311 6176 7.355101 TGTAGAGATTTCACTAGGTGGACTAT 58.645 38.462 0.00 0.00 33.87 2.12
3312 6177 6.728411 TGTAGAGATTTCACTAGGTGGACTA 58.272 40.000 0.00 0.00 33.87 2.59
3313 6178 5.580998 TGTAGAGATTTCACTAGGTGGACT 58.419 41.667 0.00 0.00 33.87 3.85
3314 6179 5.916661 TGTAGAGATTTCACTAGGTGGAC 57.083 43.478 0.00 0.00 33.87 4.02
3315 6180 6.724441 TCTTTGTAGAGATTTCACTAGGTGGA 59.276 38.462 0.00 0.00 33.87 4.02
3316 6181 6.814146 GTCTTTGTAGAGATTTCACTAGGTGG 59.186 42.308 0.00 0.00 33.87 4.61
3317 6182 7.607250 AGTCTTTGTAGAGATTTCACTAGGTG 58.393 38.462 0.00 0.00 34.45 4.00
3318 6183 7.784470 AGTCTTTGTAGAGATTTCACTAGGT 57.216 36.000 0.00 0.00 0.00 3.08
3334 6199 9.379791 CTTCCGTTCCTAAATATAAGTCTTTGT 57.620 33.333 0.00 0.00 0.00 2.83
3335 6200 8.827677 CCTTCCGTTCCTAAATATAAGTCTTTG 58.172 37.037 0.00 0.00 0.00 2.77
3336 6201 8.765517 TCCTTCCGTTCCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
3337 6202 8.315220 TCCTTCCGTTCCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
3338 6203 7.564292 ACTCCTTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
3339 6204 7.724287 ACTCCTTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
3340 6205 7.672122 ACTCCTTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
3341 6206 8.087136 GGTACTCCTTCCGTTCCTAAATATAAG 58.913 40.741 0.00 0.00 0.00 1.73
3342 6207 7.786464 AGGTACTCCTTCCGTTCCTAAATATAA 59.214 37.037 0.00 0.00 42.12 0.98
3343 6208 7.300658 AGGTACTCCTTCCGTTCCTAAATATA 58.699 38.462 0.00 0.00 42.12 0.86
3344 6209 6.141790 AGGTACTCCTTCCGTTCCTAAATAT 58.858 40.000 0.00 0.00 42.12 1.28
3345 6210 5.522641 AGGTACTCCTTCCGTTCCTAAATA 58.477 41.667 0.00 0.00 42.12 1.40
3346 6211 4.359996 AGGTACTCCTTCCGTTCCTAAAT 58.640 43.478 0.00 0.00 42.12 1.40
3347 6212 3.782992 AGGTACTCCTTCCGTTCCTAAA 58.217 45.455 0.00 0.00 42.12 1.85
3348 6213 3.463048 AGGTACTCCTTCCGTTCCTAA 57.537 47.619 0.00 0.00 42.12 2.69
3359 6224 7.038231 AGTGAAAATGTAGCTAAAGGTACTCCT 60.038 37.037 17.50 6.33 46.08 3.69
3360 6225 7.104290 AGTGAAAATGTAGCTAAAGGTACTCC 58.896 38.462 17.50 5.83 46.08 3.85
3361 6226 8.549338 AAGTGAAAATGTAGCTAAAGGTACTC 57.451 34.615 17.50 9.19 46.08 2.59
3388 6253 8.717821 CGACTGACCATAAAATGAAAAGTTAGA 58.282 33.333 0.00 0.00 0.00 2.10
3472 6339 3.806625 CCCAGGGCAACAATAGAATTG 57.193 47.619 0.00 0.00 39.74 2.32
3487 6354 3.379445 CTTGCAGGCAAGCCCAGG 61.379 66.667 19.77 0.00 45.38 4.45
3494 6361 1.473677 CAATCGATTCCTTGCAGGCAA 59.526 47.619 7.92 6.53 34.61 4.52
3495 6362 1.097232 CAATCGATTCCTTGCAGGCA 58.903 50.000 7.92 0.00 34.61 4.75
3496 6363 1.064654 GTCAATCGATTCCTTGCAGGC 59.935 52.381 7.92 0.00 34.61 4.85
3497 6364 1.328680 CGTCAATCGATTCCTTGCAGG 59.671 52.381 7.92 0.00 42.86 4.85
3498 6365 1.267732 GCGTCAATCGATTCCTTGCAG 60.268 52.381 7.92 0.00 42.86 4.41
3550 6417 4.936891 GTGCAACCAAGACAAAGAAATCT 58.063 39.130 0.00 0.00 0.00 2.40
3646 6518 9.912634 CATATATAATTACACCCAGCCAAAAAG 57.087 33.333 0.00 0.00 0.00 2.27
3807 6684 7.227711 TCGAAAAGAATGAATTAGTGGTGTTGA 59.772 33.333 0.00 0.00 0.00 3.18
3940 6830 7.213216 TGCAAGAATAAGCATACAAAAGTGA 57.787 32.000 0.00 0.00 35.51 3.41
4011 6903 8.822652 AAAAAGAATCTAAAGCAAACATGGAG 57.177 30.769 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.