Multiple sequence alignment - TraesCS2A01G115300

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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 TraesCS2A01G115300 chr2A 100.000 2981 0 0 1 2981 65815061 65812081 0.000000e+00 5505.0
1 TraesCS2A01G115300 chr2A 98.466 717 11 0 2265 2981 65768072 65767356 0.000000e+00 1264.0
2 TraesCS2A01G115300 chr2A 98.187 717 13 0 2265 2981 65742238 65741522 0.000000e+00 1253.0
3 TraesCS2A01G115300 chr2A 97.490 717 18 0 2265 2981 65705491 65704775 0.000000e+00 1225.0
4 TraesCS2A01G115300 chr2A 90.909 55 4 1 176 230 75929288 75929235 4.120000e-09 73.1
5 TraesCS2A01G115300 chr2B 87.932 1417 75 53 761 2115 101453455 101454837 0.000000e+00 1581.0
6 TraesCS2A01G115300 chr2B 84.177 316 19 15 323 624 101455557 101455259 8.140000e-71 278.0
7 TraesCS2A01G115300 chr2B 81.763 329 12 19 1970 2284 101434349 101434055 6.430000e-57 231.0
8 TraesCS2A01G115300 chr2B 87.766 188 11 4 1 188 101455801 101455626 3.010000e-50 209.0
9 TraesCS2A01G115300 chr2B 80.565 283 12 18 2017 2284 101420409 101420155 8.490000e-41 178.0
10 TraesCS2A01G115300 chr2D 88.041 1062 56 37 762 1778 68905278 68904243 0.000000e+00 1192.0
11 TraesCS2A01G115300 chr2D 81.761 477 33 21 237 691 68905824 68905380 1.700000e-92 350.0
12 TraesCS2A01G115300 chr2D 82.487 394 35 16 1746 2124 68904245 68903871 6.200000e-82 315.0
13 TraesCS2A01G115300 chr2D 82.979 188 20 7 1 188 68906019 68905844 3.080000e-35 159.0
14 TraesCS2A01G115300 chr2D 90.991 111 6 2 2174 2284 69148452 69148558 2.390000e-31 147.0
15 TraesCS2A01G115300 chr3A 92.407 698 49 4 2285 2981 735411747 735411053 0.000000e+00 992.0
16 TraesCS2A01G115300 chr3A 89.193 694 61 5 2284 2977 721821402 721822081 0.000000e+00 854.0
17 TraesCS2A01G115300 chr3A 77.049 305 56 8 1000 1303 692607299 692607008 2.380000e-36 163.0
18 TraesCS2A01G115300 chr3A 93.617 47 3 0 184 230 129482455 129482501 1.480000e-08 71.3
19 TraesCS2A01G115300 chr3B 92.253 697 51 3 2285 2981 815301439 815302132 0.000000e+00 985.0
20 TraesCS2A01G115300 chr3B 92.361 144 11 0 2838 2981 799926115 799926258 3.890000e-49 206.0
21 TraesCS2A01G115300 chr3B 76.792 293 52 10 1000 1290 738685649 738685371 1.850000e-32 150.0
22 TraesCS2A01G115300 chr7B 91.903 704 52 4 2278 2981 749295831 749296529 0.000000e+00 979.0
23 TraesCS2A01G115300 chr7B 95.349 43 1 1 187 228 1050201 1050159 1.920000e-07 67.6
24 TraesCS2A01G115300 chr1D 90.531 697 53 6 2284 2978 418336385 418337070 0.000000e+00 909.0
25 TraesCS2A01G115300 chr1D 89.796 49 4 1 182 230 390668776 390668729 8.920000e-06 62.1
26 TraesCS2A01G115300 chr4A 89.971 688 53 7 2307 2981 668792064 668791380 0.000000e+00 874.0
27 TraesCS2A01G115300 chr4A 97.368 38 1 0 193 230 604837659 604837622 6.900000e-07 65.8
28 TraesCS2A01G115300 chr4A 100.000 35 0 0 194 228 656810378 656810412 6.900000e-07 65.8
29 TraesCS2A01G115300 chr3D 78.361 305 52 9 1000 1303 555454752 555454461 5.070000e-43 185.0
30 TraesCS2A01G115300 chr1A 97.619 42 1 0 187 228 16424622 16424663 4.120000e-09 73.1
31 TraesCS2A01G115300 chr6A 100.000 38 0 0 193 230 478304737 478304774 1.480000e-08 71.3
32 TraesCS2A01G115300 chr7A 93.182 44 3 0 187 230 63718068 63718111 6.900000e-07 65.8


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 TraesCS2A01G115300 chr2A 65812081 65815061 2980 True 5505.0 5505 100.0000 1 2981 1 chr2A.!!$R4 2980
1 TraesCS2A01G115300 chr2A 65767356 65768072 716 True 1264.0 1264 98.4660 2265 2981 1 chr2A.!!$R3 716
2 TraesCS2A01G115300 chr2A 65741522 65742238 716 True 1253.0 1253 98.1870 2265 2981 1 chr2A.!!$R2 716
3 TraesCS2A01G115300 chr2A 65704775 65705491 716 True 1225.0 1225 97.4900 2265 2981 1 chr2A.!!$R1 716
4 TraesCS2A01G115300 chr2B 101453455 101454837 1382 False 1581.0 1581 87.9320 761 2115 1 chr2B.!!$F1 1354
5 TraesCS2A01G115300 chr2B 101455259 101455801 542 True 243.5 278 85.9715 1 624 2 chr2B.!!$R3 623
6 TraesCS2A01G115300 chr2D 68903871 68906019 2148 True 504.0 1192 83.8170 1 2124 4 chr2D.!!$R1 2123
7 TraesCS2A01G115300 chr3A 735411053 735411747 694 True 992.0 992 92.4070 2285 2981 1 chr3A.!!$R2 696
8 TraesCS2A01G115300 chr3A 721821402 721822081 679 False 854.0 854 89.1930 2284 2977 1 chr3A.!!$F2 693
9 TraesCS2A01G115300 chr3B 815301439 815302132 693 False 985.0 985 92.2530 2285 2981 1 chr3B.!!$F2 696
10 TraesCS2A01G115300 chr7B 749295831 749296529 698 False 979.0 979 91.9030 2278 2981 1 chr7B.!!$F1 703
11 TraesCS2A01G115300 chr1D 418336385 418337070 685 False 909.0 909 90.5310 2284 2978 1 chr1D.!!$F1 694
12 TraesCS2A01G115300 chr4A 668791380 668792064 684 True 874.0 874 89.9710 2307 2981 1 chr4A.!!$R2 674

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
734 761 0.036732 TGCCGGAATTCAGAAGTGCT 59.963 50.0 5.05 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 2354 0.108756 GCGGGGAGATATACTTCGCC 60.109 60.0 9.98 9.98 37.1 5.54 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
19 20 1.067295 TTGAACCCATCAGCTGACCT 58.933 50.000 20.97 0.00 39.77 3.85
20 21 0.325933 TGAACCCATCAGCTGACCTG 59.674 55.000 20.97 14.59 43.17 4.00
21 22 1.001641 AACCCATCAGCTGACCTGC 60.002 57.895 20.97 0.00 41.50 4.85
52 53 0.451383 TGCCAATTATGCACTGCGAC 59.549 50.000 0.00 0.00 32.85 5.19
73 74 0.940126 GTGTTGCTCACTGTCACTGG 59.060 55.000 5.59 0.00 43.13 4.00
79 80 1.947678 GCTCACTGTCACTGGGATTGG 60.948 57.143 0.00 0.00 0.00 3.16
91 92 1.854939 TGGGATTGGGATGAGCTTCAT 59.145 47.619 0.00 0.00 40.34 2.57
102 103 3.207669 GCTTCATGCTCCTGGCCG 61.208 66.667 0.00 0.00 40.92 6.13
103 104 2.270205 CTTCATGCTCCTGGCCGT 59.730 61.111 0.00 0.00 40.92 5.68
104 105 1.522092 CTTCATGCTCCTGGCCGTA 59.478 57.895 0.00 0.00 40.92 4.02
105 106 0.811616 CTTCATGCTCCTGGCCGTAC 60.812 60.000 0.00 0.00 40.92 3.67
114 115 1.389609 CCTGGCCGTACGTAGTCCAT 61.390 60.000 15.21 0.00 43.93 3.41
154 155 2.009774 CATGGAGGTCACGAAATCACC 58.990 52.381 0.00 0.00 0.00 4.02
188 189 5.531287 GGTCAAAGTTGGTCAAGTGAAGTAT 59.469 40.000 0.00 0.00 0.00 2.12
189 190 6.039382 GGTCAAAGTTGGTCAAGTGAAGTATT 59.961 38.462 0.00 0.00 0.00 1.89
191 192 7.973944 GTCAAAGTTGGTCAAGTGAAGTATTTT 59.026 33.333 0.00 0.00 0.00 1.82
192 193 8.188139 TCAAAGTTGGTCAAGTGAAGTATTTTC 58.812 33.333 0.00 0.00 0.00 2.29
194 195 7.497925 AGTTGGTCAAGTGAAGTATTTTCTC 57.502 36.000 0.00 0.00 0.00 2.87
195 196 6.486993 AGTTGGTCAAGTGAAGTATTTTCTCC 59.513 38.462 0.00 0.00 0.00 3.71
196 197 4.994852 TGGTCAAGTGAAGTATTTTCTCCG 59.005 41.667 0.00 0.00 0.00 4.63
197 198 4.995487 GGTCAAGTGAAGTATTTTCTCCGT 59.005 41.667 0.00 0.00 0.00 4.69
198 199 5.469084 GGTCAAGTGAAGTATTTTCTCCGTT 59.531 40.000 0.00 0.00 0.00 4.44
200 201 7.415229 GTCAAGTGAAGTATTTTCTCCGTTTT 58.585 34.615 0.00 0.00 0.00 2.43
201 202 8.553696 GTCAAGTGAAGTATTTTCTCCGTTTTA 58.446 33.333 0.00 0.00 0.00 1.52
202 203 9.111613 TCAAGTGAAGTATTTTCTCCGTTTTAA 57.888 29.630 0.00 0.00 0.00 1.52
203 204 9.724839 CAAGTGAAGTATTTTCTCCGTTTTAAA 57.275 29.630 0.00 0.00 0.00 1.52
215 216 9.496873 TTTCTCCGTTTTAAAATAGATGACTCA 57.503 29.630 3.52 0.00 0.00 3.41
216 217 9.496873 TTCTCCGTTTTAAAATAGATGACTCAA 57.503 29.630 3.52 0.00 0.00 3.02
217 218 9.667107 TCTCCGTTTTAAAATAGATGACTCAAT 57.333 29.630 3.52 0.00 0.00 2.57
246 247 4.923281 ACTAACTATTTCGTTTAACCGCGT 59.077 37.500 4.92 0.00 0.00 6.01
247 248 6.090129 ACTAACTATTTCGTTTAACCGCGTA 58.910 36.000 4.92 0.00 0.00 4.42
257 258 0.604578 TAACCGCGTACTGCTTTCCT 59.395 50.000 4.92 0.00 43.27 3.36
260 261 2.100631 CGCGTACTGCTTTCCTGGG 61.101 63.158 0.00 0.00 43.27 4.45
286 290 5.655532 AGGAACTGATGCTATGCAAATTTCT 59.344 36.000 0.00 0.00 39.20 2.52
297 301 5.859205 ATGCAAATTTCTAAGGGTGGATC 57.141 39.130 0.00 0.00 0.00 3.36
299 303 4.023291 GCAAATTTCTAAGGGTGGATCCA 58.977 43.478 11.44 11.44 38.11 3.41
300 304 4.466015 GCAAATTTCTAAGGGTGGATCCAA 59.534 41.667 18.20 0.00 38.11 3.53
301 305 5.129320 GCAAATTTCTAAGGGTGGATCCAAT 59.871 40.000 18.20 5.92 38.11 3.16
302 306 6.683861 GCAAATTTCTAAGGGTGGATCCAATC 60.684 42.308 18.20 11.88 38.11 2.67
388 392 1.600076 CAAGCAGCTCAGTGGCACT 60.600 57.895 15.88 15.88 34.17 4.40
390 394 3.735029 GCAGCTCAGTGGCACTGC 61.735 66.667 36.65 27.86 45.54 4.40
401 405 0.608856 TGGCACTGCTACCCAACATG 60.609 55.000 0.00 0.00 0.00 3.21
406 410 1.066430 ACTGCTACCCAACATGGTACG 60.066 52.381 0.00 0.00 39.91 3.67
407 411 0.391927 TGCTACCCAACATGGTACGC 60.392 55.000 0.00 0.00 39.91 4.42
408 412 0.391927 GCTACCCAACATGGTACGCA 60.392 55.000 0.00 0.00 39.91 5.24
410 414 2.210116 CTACCCAACATGGTACGCATC 58.790 52.381 0.00 0.00 39.91 3.91
462 482 2.961522 TTTCGTTTTGGATGCTCGTC 57.038 45.000 0.00 0.00 0.00 4.20
463 483 1.153353 TTCGTTTTGGATGCTCGTCC 58.847 50.000 1.20 1.20 38.81 4.79
470 490 0.037326 TGGATGCTCGTCCAGTTGAC 60.037 55.000 6.72 0.00 43.20 3.18
477 497 4.554163 GTCCAGTTGACGACTCGG 57.446 61.111 2.98 0.00 36.10 4.63
479 499 0.313043 GTCCAGTTGACGACTCGGAA 59.687 55.000 12.82 0.00 37.33 4.30
480 500 0.596577 TCCAGTTGACGACTCGGAAG 59.403 55.000 2.98 0.00 36.10 3.46
481 501 0.596577 CCAGTTGACGACTCGGAAGA 59.403 55.000 2.98 0.00 36.10 2.87
532 554 3.031013 TCCTTTGGAGATGCATAGACGA 58.969 45.455 0.00 0.00 0.00 4.20
535 557 5.304357 TCCTTTGGAGATGCATAGACGAATA 59.696 40.000 0.00 0.00 0.00 1.75
536 558 5.636965 CCTTTGGAGATGCATAGACGAATAG 59.363 44.000 0.00 0.00 0.00 1.73
537 559 6.405278 TTTGGAGATGCATAGACGAATAGA 57.595 37.500 0.00 0.00 0.00 1.98
538 560 6.596309 TTGGAGATGCATAGACGAATAGAT 57.404 37.500 0.00 0.00 0.00 1.98
539 561 5.958955 TGGAGATGCATAGACGAATAGATG 58.041 41.667 0.00 0.00 0.00 2.90
540 562 5.478332 TGGAGATGCATAGACGAATAGATGT 59.522 40.000 0.00 0.00 0.00 3.06
553 578 9.126151 AGACGAATAGATGTATGTATATCCAGG 57.874 37.037 0.00 0.00 0.00 4.45
554 579 8.239038 ACGAATAGATGTATGTATATCCAGGG 57.761 38.462 0.00 0.00 0.00 4.45
555 580 7.287927 ACGAATAGATGTATGTATATCCAGGGG 59.712 40.741 0.00 0.00 0.00 4.79
556 581 7.287927 CGAATAGATGTATGTATATCCAGGGGT 59.712 40.741 0.00 0.00 0.00 4.95
596 623 2.409378 GCATGCAAACAAAAGATGACCG 59.591 45.455 14.21 0.00 0.00 4.79
618 645 3.636381 CCTCTTTGAACTTTGAAGCAGC 58.364 45.455 0.00 0.00 0.00 5.25
625 652 5.835113 TGAACTTTGAAGCAGCTTAGTTT 57.165 34.783 18.70 6.96 0.00 2.66
626 653 5.821204 TGAACTTTGAAGCAGCTTAGTTTC 58.179 37.500 18.70 13.54 0.00 2.78
627 654 5.590259 TGAACTTTGAAGCAGCTTAGTTTCT 59.410 36.000 18.70 2.13 31.06 2.52
628 655 6.765989 TGAACTTTGAAGCAGCTTAGTTTCTA 59.234 34.615 18.70 9.23 31.06 2.10
629 656 7.282224 TGAACTTTGAAGCAGCTTAGTTTCTAA 59.718 33.333 18.70 5.74 31.06 2.10
630 657 7.751768 ACTTTGAAGCAGCTTAGTTTCTAAT 57.248 32.000 7.92 0.00 31.06 1.73
631 658 8.848474 ACTTTGAAGCAGCTTAGTTTCTAATA 57.152 30.769 7.92 0.00 31.06 0.98
632 659 9.284968 ACTTTGAAGCAGCTTAGTTTCTAATAA 57.715 29.630 7.92 0.00 31.06 1.40
685 712 7.995289 TCAAAAACAGAAACAGCTTATTCTCA 58.005 30.769 7.62 0.00 33.73 3.27
686 713 8.632679 TCAAAAACAGAAACAGCTTATTCTCAT 58.367 29.630 7.62 0.00 33.73 2.90
688 715 8.807667 AAAACAGAAACAGCTTATTCTCATTG 57.192 30.769 7.62 2.06 33.73 2.82
690 717 6.006449 ACAGAAACAGCTTATTCTCATTGGT 58.994 36.000 7.62 1.51 33.73 3.67
692 719 7.014615 ACAGAAACAGCTTATTCTCATTGGTTT 59.985 33.333 7.62 0.00 33.73 3.27
693 720 7.869429 CAGAAACAGCTTATTCTCATTGGTTTT 59.131 33.333 7.62 0.00 33.73 2.43
694 721 9.077885 AGAAACAGCTTATTCTCATTGGTTTTA 57.922 29.630 5.17 0.00 30.16 1.52
695 722 9.346725 GAAACAGCTTATTCTCATTGGTTTTAG 57.653 33.333 1.78 0.00 0.00 1.85
696 723 8.635765 AACAGCTTATTCTCATTGGTTTTAGA 57.364 30.769 0.00 0.00 0.00 2.10
697 724 8.814038 ACAGCTTATTCTCATTGGTTTTAGAT 57.186 30.769 0.00 0.00 0.00 1.98
698 725 9.905713 ACAGCTTATTCTCATTGGTTTTAGATA 57.094 29.630 0.00 0.00 0.00 1.98
704 731 7.807977 TTCTCATTGGTTTTAGATAGATGGC 57.192 36.000 0.00 0.00 0.00 4.40
705 732 7.141758 TCTCATTGGTTTTAGATAGATGGCT 57.858 36.000 0.00 0.00 0.00 4.75
706 733 7.220030 TCTCATTGGTTTTAGATAGATGGCTC 58.780 38.462 0.00 0.00 0.00 4.70
707 734 6.899089 TCATTGGTTTTAGATAGATGGCTCA 58.101 36.000 0.00 0.00 0.00 4.26
708 735 6.767902 TCATTGGTTTTAGATAGATGGCTCAC 59.232 38.462 0.00 0.00 0.00 3.51
709 736 5.036117 TGGTTTTAGATAGATGGCTCACC 57.964 43.478 0.00 0.00 0.00 4.02
734 761 0.036732 TGCCGGAATTCAGAAGTGCT 59.963 50.000 5.05 0.00 0.00 4.40
749 776 9.842775 TTCAGAAGTGCTATTTGATCTGAATAT 57.157 29.630 10.91 0.00 44.50 1.28
795 876 3.378427 CCGGAAGTTTCCCATCTGAATTC 59.622 47.826 0.00 0.00 44.67 2.17
804 885 6.566079 TTCCCATCTGAATTCTCACATAGT 57.434 37.500 7.05 0.00 0.00 2.12
815 896 9.912634 TGAATTCTCACATAGTTTTTGGAATTC 57.087 29.630 7.05 14.31 43.39 2.17
846 930 4.419200 ACACCTCCTCCTCCTATACATACA 59.581 45.833 0.00 0.00 0.00 2.29
853 937 5.222275 CCTCCTCCTATACATACACTACCCA 60.222 48.000 0.00 0.00 0.00 4.51
881 965 2.437200 GCTGCATACCTCTCAGCTAG 57.563 55.000 6.24 0.00 46.93 3.42
882 966 1.605202 GCTGCATACCTCTCAGCTAGC 60.605 57.143 6.62 6.62 46.93 3.42
884 968 2.364970 CTGCATACCTCTCAGCTAGCTT 59.635 50.000 16.46 1.38 0.00 3.74
890 974 1.206610 CCTCTCAGCTAGCTTCAAGCA 59.793 52.381 16.46 0.00 45.56 3.91
892 976 3.332919 CTCTCAGCTAGCTTCAAGCAAA 58.667 45.455 16.46 0.00 45.56 3.68
909 1016 4.962836 AGCACACCAGCACCTGCC 62.963 66.667 0.00 0.00 43.38 4.85
921 1028 1.069049 GCACCTGCCAATCAAACACTT 59.931 47.619 0.00 0.00 34.31 3.16
922 1029 2.746269 CACCTGCCAATCAAACACTTG 58.254 47.619 0.00 0.00 0.00 3.16
923 1030 1.069049 ACCTGCCAATCAAACACTTGC 59.931 47.619 0.00 0.00 32.14 4.01
927 1034 1.866601 GCCAATCAAACACTTGCAACC 59.133 47.619 0.00 0.00 32.14 3.77
930 1037 3.125316 CAATCAAACACTTGCAACCAGG 58.875 45.455 0.00 0.00 32.14 4.45
931 1038 2.136298 TCAAACACTTGCAACCAGGA 57.864 45.000 0.00 0.00 32.14 3.86
946 1058 5.537188 CAACCAGGACATCTATCTAGCTTC 58.463 45.833 0.00 0.00 0.00 3.86
948 1060 5.401750 ACCAGGACATCTATCTAGCTTCAT 58.598 41.667 0.00 0.00 0.00 2.57
952 1064 7.319646 CAGGACATCTATCTAGCTTCATTACC 58.680 42.308 0.00 0.00 0.00 2.85
954 1066 8.394822 AGGACATCTATCTAGCTTCATTACCTA 58.605 37.037 0.00 0.00 0.00 3.08
968 1080 6.068461 TCATTACCTAGAGAGTGAGTGAGT 57.932 41.667 0.00 0.00 0.00 3.41
969 1081 5.883115 TCATTACCTAGAGAGTGAGTGAGTG 59.117 44.000 0.00 0.00 0.00 3.51
970 1082 5.500546 TTACCTAGAGAGTGAGTGAGTGA 57.499 43.478 0.00 0.00 0.00 3.41
971 1083 3.950397 ACCTAGAGAGTGAGTGAGTGAG 58.050 50.000 0.00 0.00 0.00 3.51
972 1084 3.329520 ACCTAGAGAGTGAGTGAGTGAGT 59.670 47.826 0.00 0.00 0.00 3.41
974 1086 3.500448 AGAGAGTGAGTGAGTGAGTGA 57.500 47.619 0.00 0.00 0.00 3.41
975 1087 3.411446 AGAGAGTGAGTGAGTGAGTGAG 58.589 50.000 0.00 0.00 0.00 3.51
977 1089 2.884012 AGAGTGAGTGAGTGAGTGAGTG 59.116 50.000 0.00 0.00 0.00 3.51
978 1090 2.881513 GAGTGAGTGAGTGAGTGAGTGA 59.118 50.000 0.00 0.00 0.00 3.41
979 1091 2.884012 AGTGAGTGAGTGAGTGAGTGAG 59.116 50.000 0.00 0.00 0.00 3.51
980 1092 1.611006 TGAGTGAGTGAGTGAGTGAGC 59.389 52.381 0.00 0.00 0.00 4.26
981 1093 1.885887 GAGTGAGTGAGTGAGTGAGCT 59.114 52.381 0.00 0.00 0.00 4.09
982 1094 1.885887 AGTGAGTGAGTGAGTGAGCTC 59.114 52.381 6.82 6.82 41.97 4.09
983 1095 1.067915 GTGAGTGAGTGAGTGAGCTCC 60.068 57.143 12.15 2.40 40.95 4.70
984 1096 1.252175 GAGTGAGTGAGTGAGCTCCA 58.748 55.000 12.15 0.00 40.95 3.86
1012 1124 1.227556 GGTAGCATGGCGTACAGGG 60.228 63.158 0.00 0.00 0.00 4.45
1089 1201 2.099831 CTCGAGGTGTACGCCGTC 59.900 66.667 19.53 15.33 0.00 4.79
1185 1297 3.616721 ACCACGCTCCGCTTCACT 61.617 61.111 0.00 0.00 0.00 3.41
1296 1408 4.477975 GTCGTCCCGCTCACCGAG 62.478 72.222 0.00 0.00 40.02 4.63
1506 1645 2.738521 GCTGCCGCTCACGAAGAA 60.739 61.111 0.00 0.00 43.93 2.52
1507 1646 2.734673 GCTGCCGCTCACGAAGAAG 61.735 63.158 0.00 0.00 43.93 2.85
1554 1693 3.186047 CGGCCGTCGTTCCATCAC 61.186 66.667 19.50 0.00 0.00 3.06
1659 1798 2.261361 CACATGTCGTCCTCGCCA 59.739 61.111 0.00 0.00 36.96 5.69
1680 1819 0.456312 CGTCTCCGCGGGATTATAGC 60.456 60.000 27.83 9.18 0.00 2.97
1852 2033 2.074339 GAACGCGAGGAATAACGGCG 62.074 60.000 15.93 4.80 36.10 6.46
1857 2038 4.157120 AGGAATAACGGCGGCGCT 62.157 61.111 32.57 23.00 0.00 5.92
1984 2171 1.298938 GCCGCCGTGTACTAGCTAC 60.299 63.158 0.00 0.00 0.00 3.58
1986 2173 1.586422 CCGCCGTGTACTAGCTACTA 58.414 55.000 0.00 0.00 0.00 1.82
1988 2175 1.070041 CGCCGTGTACTAGCTACTAGC 60.070 57.143 0.00 0.00 42.84 3.42
1991 2178 2.548904 CCGTGTACTAGCTACTAGCCAG 59.451 54.545 4.32 3.23 43.77 4.85
1992 2179 2.031857 CGTGTACTAGCTACTAGCCAGC 60.032 54.545 8.54 8.54 43.77 4.85
1993 2180 2.950309 GTGTACTAGCTACTAGCCAGCA 59.050 50.000 16.79 4.90 43.77 4.41
1994 2181 3.570550 GTGTACTAGCTACTAGCCAGCAT 59.429 47.826 16.79 6.64 43.77 3.79
1995 2182 3.570125 TGTACTAGCTACTAGCCAGCATG 59.430 47.826 16.79 11.60 43.77 4.06
1996 2183 1.342819 ACTAGCTACTAGCCAGCATGC 59.657 52.381 10.51 10.51 43.77 4.06
1997 2184 1.342496 CTAGCTACTAGCCAGCATGCA 59.658 52.381 21.98 0.00 43.77 3.96
1998 2185 0.179062 AGCTACTAGCCAGCATGCAC 60.179 55.000 21.98 8.95 43.77 4.57
1999 2186 0.462581 GCTACTAGCCAGCATGCACA 60.463 55.000 21.98 0.00 38.93 4.57
2000 2187 1.813092 GCTACTAGCCAGCATGCACAT 60.813 52.381 21.98 5.19 38.93 3.21
2001 2188 2.141517 CTACTAGCCAGCATGCACATC 58.858 52.381 21.98 5.81 31.97 3.06
2081 2277 4.461198 ACTCCTACTTGGAAGTTTTGGTG 58.539 43.478 0.00 2.89 45.63 4.17
2108 2305 1.547292 GCAAGATCGAGCTAGCGCAG 61.547 60.000 18.87 11.04 39.10 5.18
2136 2337 1.353103 GCTTCCATGCGGTTCATCG 59.647 57.895 0.00 0.00 31.79 3.84
2144 2345 3.487202 CGGTTCATCGCCACGGTG 61.487 66.667 0.00 0.00 39.56 4.94
2145 2346 2.358247 GGTTCATCGCCACGGTGT 60.358 61.111 7.45 0.00 39.21 4.16
2146 2347 2.677003 GGTTCATCGCCACGGTGTG 61.677 63.158 7.45 0.00 39.21 3.82
2147 2348 3.047280 TTCATCGCCACGGTGTGC 61.047 61.111 7.45 9.17 39.21 4.57
2148 2349 3.816367 TTCATCGCCACGGTGTGCA 62.816 57.895 17.58 8.43 39.21 4.57
2149 2350 4.088762 CATCGCCACGGTGTGCAC 62.089 66.667 10.75 10.75 32.87 4.57
2150 2351 4.617520 ATCGCCACGGTGTGCACA 62.618 61.111 17.42 17.42 31.34 4.57
2151 2352 4.840005 TCGCCACGGTGTGCACAA 62.840 61.111 23.59 2.55 31.34 3.33
2152 2353 4.605967 CGCCACGGTGTGCACAAC 62.606 66.667 25.30 25.30 31.34 3.32
2158 2359 3.578272 GGTGTGCACAACGGCGAA 61.578 61.111 23.59 0.00 36.28 4.70
2159 2360 2.052237 GTGTGCACAACGGCGAAG 60.052 61.111 23.59 7.98 36.28 3.79
2160 2361 2.512745 TGTGCACAACGGCGAAGT 60.513 55.556 19.28 8.75 36.28 3.01
2161 2362 1.227292 TGTGCACAACGGCGAAGTA 60.227 52.632 19.28 0.00 36.28 2.24
2162 2363 0.601576 TGTGCACAACGGCGAAGTAT 60.602 50.000 19.28 0.00 36.28 2.12
2163 2364 1.336980 TGTGCACAACGGCGAAGTATA 60.337 47.619 19.28 0.95 36.28 1.47
2164 2365 1.931172 GTGCACAACGGCGAAGTATAT 59.069 47.619 16.62 0.00 36.28 0.86
2165 2366 2.034001 GTGCACAACGGCGAAGTATATC 60.034 50.000 16.62 2.64 36.28 1.63
2166 2367 2.159156 TGCACAACGGCGAAGTATATCT 60.159 45.455 16.62 0.00 36.28 1.98
2167 2368 2.471743 GCACAACGGCGAAGTATATCTC 59.528 50.000 16.62 0.00 0.00 2.75
2168 2369 3.050619 CACAACGGCGAAGTATATCTCC 58.949 50.000 16.62 0.00 0.00 3.71
2169 2370 2.035576 ACAACGGCGAAGTATATCTCCC 59.964 50.000 16.62 0.00 0.00 4.30
2170 2371 1.254954 ACGGCGAAGTATATCTCCCC 58.745 55.000 16.62 0.00 0.00 4.81
2171 2372 0.170561 CGGCGAAGTATATCTCCCCG 59.829 60.000 0.00 0.00 0.00 5.73
2172 2373 0.108756 GGCGAAGTATATCTCCCCGC 60.109 60.000 0.00 0.00 38.05 6.13
2173 2374 0.108756 GCGAAGTATATCTCCCCGCC 60.109 60.000 0.00 0.00 35.24 6.13
2174 2375 0.170561 CGAAGTATATCTCCCCGCCG 59.829 60.000 0.00 0.00 0.00 6.46
2175 2376 0.108756 GAAGTATATCTCCCCGCCGC 60.109 60.000 0.00 0.00 0.00 6.53
2176 2377 1.542187 AAGTATATCTCCCCGCCGCC 61.542 60.000 0.00 0.00 0.00 6.13
2177 2378 3.066190 TATATCTCCCCGCCGCCG 61.066 66.667 0.00 0.00 0.00 6.46
2198 2399 4.090057 GCTCTGCGCCCACGTTTC 62.090 66.667 4.18 0.00 42.83 2.78
2199 2400 3.423154 CTCTGCGCCCACGTTTCC 61.423 66.667 4.18 0.00 42.83 3.13
2224 2425 4.622456 CGGGCGTGCGCTTGTTTT 62.622 61.111 16.21 0.00 41.60 2.43
2225 2426 2.279186 GGGCGTGCGCTTGTTTTT 60.279 55.556 16.21 0.00 41.60 1.94
2616 2821 2.406130 CCATGAAACTGCGCATGTTTT 58.594 42.857 27.04 19.87 40.11 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.526575 AATTGGCAGCCGTTGGTCTG 61.527 55.000 7.03 3.79 32.70 3.51
28 29 0.680921 AGTGCATAATTGGCAGCCGT 60.681 50.000 7.03 0.00 42.85 5.68
73 74 1.612463 GCATGAAGCTCATCCCAATCC 59.388 52.381 0.00 0.00 34.28 3.01
91 92 2.361483 TACGTACGGCCAGGAGCA 60.361 61.111 21.06 0.00 46.50 4.26
102 103 2.389962 TGGCCAAATGGACTACGTAC 57.610 50.000 0.61 0.00 45.91 3.67
103 104 2.355310 CCTTGGCCAAATGGACTACGTA 60.355 50.000 20.91 0.00 45.91 3.57
104 105 1.613255 CCTTGGCCAAATGGACTACGT 60.613 52.381 20.91 0.00 45.91 3.57
105 106 1.094785 CCTTGGCCAAATGGACTACG 58.905 55.000 20.91 4.02 45.91 3.51
154 155 4.199310 ACCAACTTTGACCGATATGGATG 58.801 43.478 0.00 0.00 42.00 3.51
189 190 9.496873 TGAGTCATCTATTTTAAAACGGAGAAA 57.503 29.630 1.97 0.00 0.00 2.52
191 192 9.667107 ATTGAGTCATCTATTTTAAAACGGAGA 57.333 29.630 1.97 7.08 0.00 3.71
219 220 8.742188 CGCGGTTAAACGAAATAGTTAGTATAA 58.258 33.333 18.94 0.00 35.47 0.98
220 221 7.913297 ACGCGGTTAAACGAAATAGTTAGTATA 59.087 33.333 18.94 0.00 35.47 1.47
221 222 6.751888 ACGCGGTTAAACGAAATAGTTAGTAT 59.248 34.615 18.94 0.00 35.47 2.12
222 223 6.090129 ACGCGGTTAAACGAAATAGTTAGTA 58.910 36.000 18.94 0.00 35.47 1.82
223 224 4.923281 ACGCGGTTAAACGAAATAGTTAGT 59.077 37.500 18.94 0.00 35.47 2.24
224 225 5.440260 ACGCGGTTAAACGAAATAGTTAG 57.560 39.130 18.94 0.00 35.47 2.34
225 226 6.033407 CAGTACGCGGTTAAACGAAATAGTTA 59.967 38.462 18.94 0.00 35.47 2.24
226 227 4.923281 AGTACGCGGTTAAACGAAATAGTT 59.077 37.500 18.94 0.00 35.47 2.24
227 228 4.324402 CAGTACGCGGTTAAACGAAATAGT 59.676 41.667 18.94 9.97 35.47 2.12
228 229 4.776922 GCAGTACGCGGTTAAACGAAATAG 60.777 45.833 18.94 4.25 35.47 1.73
229 230 3.060628 GCAGTACGCGGTTAAACGAAATA 59.939 43.478 18.94 1.93 35.47 1.40
230 231 2.159801 GCAGTACGCGGTTAAACGAAAT 60.160 45.455 18.94 2.99 35.47 2.17
231 232 1.192090 GCAGTACGCGGTTAAACGAAA 59.808 47.619 18.94 0.00 35.47 3.46
232 233 0.783579 GCAGTACGCGGTTAAACGAA 59.216 50.000 18.94 0.00 35.47 3.85
233 234 2.433637 GCAGTACGCGGTTAAACGA 58.566 52.632 18.94 0.00 35.47 3.85
257 258 1.134007 CATAGCATCAGTTCCTGCCCA 60.134 52.381 0.00 0.00 39.22 5.36
260 261 1.671979 TGCATAGCATCAGTTCCTGC 58.328 50.000 0.00 0.00 38.69 4.85
268 269 5.893255 ACCCTTAGAAATTTGCATAGCATCA 59.107 36.000 0.00 0.00 38.76 3.07
297 301 4.456911 GCATAGTGTGGATATGTGGATTGG 59.543 45.833 0.00 0.00 33.90 3.16
299 303 5.573380 AGCATAGTGTGGATATGTGGATT 57.427 39.130 0.00 0.00 33.90 3.01
300 304 6.296087 CCTTAGCATAGTGTGGATATGTGGAT 60.296 42.308 0.00 0.00 33.90 3.41
301 305 5.012046 CCTTAGCATAGTGTGGATATGTGGA 59.988 44.000 0.00 0.00 33.90 4.02
302 306 5.221722 ACCTTAGCATAGTGTGGATATGTGG 60.222 44.000 0.00 0.00 33.90 4.17
303 307 5.698089 CACCTTAGCATAGTGTGGATATGTG 59.302 44.000 0.00 0.00 33.90 3.21
304 308 5.602561 TCACCTTAGCATAGTGTGGATATGT 59.397 40.000 0.00 0.00 33.90 2.29
305 309 6.101650 TCACCTTAGCATAGTGTGGATATG 57.898 41.667 0.00 0.00 34.40 1.78
306 310 6.498303 TGATCACCTTAGCATAGTGTGGATAT 59.502 38.462 0.00 0.00 33.21 1.63
307 311 5.838521 TGATCACCTTAGCATAGTGTGGATA 59.161 40.000 0.00 0.00 33.21 2.59
308 312 4.655649 TGATCACCTTAGCATAGTGTGGAT 59.344 41.667 0.00 0.00 33.21 3.41
309 313 4.030216 TGATCACCTTAGCATAGTGTGGA 58.970 43.478 0.00 0.00 33.21 4.02
310 314 4.122776 GTGATCACCTTAGCATAGTGTGG 58.877 47.826 15.31 0.00 33.21 4.17
388 392 0.391927 GCGTACCATGTTGGGTAGCA 60.392 55.000 0.00 0.00 43.83 3.49
389 393 0.391927 TGCGTACCATGTTGGGTAGC 60.392 55.000 0.00 0.00 43.83 3.58
390 394 2.158957 AGATGCGTACCATGTTGGGTAG 60.159 50.000 2.07 0.00 43.83 3.18
401 405 1.290203 CATGTCACCAGATGCGTACC 58.710 55.000 0.00 0.00 0.00 3.34
406 410 0.169672 GCACACATGTCACCAGATGC 59.830 55.000 0.00 0.00 0.00 3.91
407 411 1.198408 GTGCACACATGTCACCAGATG 59.802 52.381 13.17 0.00 30.92 2.90
408 412 1.527034 GTGCACACATGTCACCAGAT 58.473 50.000 13.17 0.00 30.92 2.90
410 414 1.570967 CGTGCACACATGTCACCAG 59.429 57.895 18.64 0.00 32.48 4.00
462 482 0.596577 TCTTCCGAGTCGTCAACTGG 59.403 55.000 12.31 0.00 38.74 4.00
463 483 1.401670 CCTCTTCCGAGTCGTCAACTG 60.402 57.143 12.31 0.00 38.74 3.16
470 490 0.733729 CTACCACCTCTTCCGAGTCG 59.266 60.000 5.29 5.29 35.43 4.18
471 491 0.456628 GCTACCACCTCTTCCGAGTC 59.543 60.000 0.00 0.00 35.43 3.36
477 497 4.691216 CAGTTAAAGTGCTACCACCTCTTC 59.309 45.833 0.00 0.00 43.09 2.87
479 499 3.901844 TCAGTTAAAGTGCTACCACCTCT 59.098 43.478 0.00 0.00 43.09 3.69
480 500 3.995048 GTCAGTTAAAGTGCTACCACCTC 59.005 47.826 0.00 0.00 43.09 3.85
481 501 3.389983 TGTCAGTTAAAGTGCTACCACCT 59.610 43.478 0.00 0.00 43.09 4.00
483 503 4.378459 GCATGTCAGTTAAAGTGCTACCAC 60.378 45.833 0.00 0.00 42.39 4.16
484 504 3.751175 GCATGTCAGTTAAAGTGCTACCA 59.249 43.478 0.00 0.00 0.00 3.25
486 506 4.213270 TGTGCATGTCAGTTAAAGTGCTAC 59.787 41.667 0.00 0.00 33.95 3.58
487 507 4.213270 GTGTGCATGTCAGTTAAAGTGCTA 59.787 41.667 0.00 0.00 33.95 3.49
488 508 3.003689 GTGTGCATGTCAGTTAAAGTGCT 59.996 43.478 0.00 0.00 33.95 4.40
489 509 3.003689 AGTGTGCATGTCAGTTAAAGTGC 59.996 43.478 0.00 0.00 0.00 4.40
490 510 4.319766 GGAGTGTGCATGTCAGTTAAAGTG 60.320 45.833 0.00 0.00 0.00 3.16
530 552 7.287927 ACCCCTGGATATACATACATCTATTCG 59.712 40.741 0.00 0.00 0.00 3.34
532 554 8.933522 AACCCCTGGATATACATACATCTATT 57.066 34.615 0.00 0.00 0.00 1.73
535 557 8.933522 ATAAACCCCTGGATATACATACATCT 57.066 34.615 0.00 0.00 0.00 2.90
536 558 8.211629 GGATAAACCCCTGGATATACATACATC 58.788 40.741 0.00 0.00 0.00 3.06
537 559 7.686790 TGGATAAACCCCTGGATATACATACAT 59.313 37.037 0.00 0.00 38.00 2.29
538 560 7.026247 TGGATAAACCCCTGGATATACATACA 58.974 38.462 0.00 0.00 38.00 2.29
539 561 7.037873 TGTGGATAAACCCCTGGATATACATAC 60.038 40.741 0.00 0.00 38.00 2.39
540 562 7.026247 TGTGGATAAACCCCTGGATATACATA 58.974 38.462 0.00 0.00 38.00 2.29
554 579 1.917872 TGGGTTGCTGTGGATAAACC 58.082 50.000 0.00 0.00 41.14 3.27
555 580 3.508744 CATGGGTTGCTGTGGATAAAC 57.491 47.619 0.00 0.00 0.00 2.01
596 623 3.636381 CTGCTTCAAAGTTCAAAGAGGC 58.364 45.455 2.27 0.00 34.18 4.70
661 688 8.807667 ATGAGAATAAGCTGTTTCTGTTTTTG 57.192 30.769 14.35 0.00 32.46 2.44
685 712 6.064717 GGTGAGCCATCTATCTAAAACCAAT 58.935 40.000 0.00 0.00 34.09 3.16
686 713 5.045213 TGGTGAGCCATCTATCTAAAACCAA 60.045 40.000 0.00 0.00 40.46 3.67
688 715 5.036117 TGGTGAGCCATCTATCTAAAACC 57.964 43.478 0.00 0.00 40.46 3.27
702 729 2.903855 CGGCATGGATGGTGAGCC 60.904 66.667 0.00 0.00 41.86 4.70
703 730 2.903855 CCGGCATGGATGGTGAGC 60.904 66.667 0.00 0.00 42.00 4.26
704 731 2.910360 TCCGGCATGGATGGTGAG 59.090 61.111 0.00 0.00 43.74 3.51
712 739 1.402968 CACTTCTGAATTCCGGCATGG 59.597 52.381 2.27 0.00 40.09 3.66
713 740 1.202222 GCACTTCTGAATTCCGGCATG 60.202 52.381 2.27 0.00 0.00 4.06
714 741 1.098050 GCACTTCTGAATTCCGGCAT 58.902 50.000 2.27 0.00 0.00 4.40
715 742 0.036732 AGCACTTCTGAATTCCGGCA 59.963 50.000 2.27 0.00 0.00 5.69
716 743 2.024176 TAGCACTTCTGAATTCCGGC 57.976 50.000 2.27 0.00 0.00 6.13
717 744 4.635765 TCAAATAGCACTTCTGAATTCCGG 59.364 41.667 2.27 0.00 0.00 5.14
746 773 8.950210 GCTGGTTGCATACAGAATTATGTATAT 58.050 33.333 21.90 4.26 43.01 0.86
747 774 7.390440 GGCTGGTTGCATACAGAATTATGTATA 59.610 37.037 21.90 8.20 43.01 1.47
748 775 6.207417 GGCTGGTTGCATACAGAATTATGTAT 59.793 38.462 17.89 17.89 45.17 2.29
749 776 5.530915 GGCTGGTTGCATACAGAATTATGTA 59.469 40.000 14.86 14.86 45.15 2.29
750 777 4.339247 GGCTGGTTGCATACAGAATTATGT 59.661 41.667 18.99 11.02 45.15 2.29
751 778 4.261741 GGGCTGGTTGCATACAGAATTATG 60.262 45.833 18.99 0.00 45.15 1.90
753 780 3.287222 GGGCTGGTTGCATACAGAATTA 58.713 45.455 18.99 0.00 45.15 1.40
754 781 2.102578 GGGCTGGTTGCATACAGAATT 58.897 47.619 18.99 0.00 45.15 2.17
755 782 1.767759 GGGCTGGTTGCATACAGAAT 58.232 50.000 18.99 0.00 45.15 2.40
756 783 0.676466 CGGGCTGGTTGCATACAGAA 60.676 55.000 18.99 0.00 45.15 3.02
757 784 1.078497 CGGGCTGGTTGCATACAGA 60.078 57.895 18.99 0.00 45.15 3.41
759 786 2.045438 CCGGGCTGGTTGCATACA 60.045 61.111 3.48 0.00 45.15 2.29
795 876 6.624423 CCCAGAATTCCAAAAACTATGTGAG 58.376 40.000 0.65 0.00 0.00 3.51
804 885 1.696884 GTGGGCCCAGAATTCCAAAAA 59.303 47.619 29.55 0.00 0.00 1.94
815 896 3.721706 GAGGAGGTGTGGGCCCAG 61.722 72.222 29.55 0.00 0.00 4.45
853 937 0.987294 AGGTATGCAGCACCTTGAGT 59.013 50.000 15.40 0.00 44.18 3.41
882 966 1.866880 GCTGGTGTGCTTTGCTTGAAG 60.867 52.381 0.00 0.00 0.00 3.02
884 968 1.036481 TGCTGGTGTGCTTTGCTTGA 61.036 50.000 0.00 0.00 0.00 3.02
890 974 2.492773 GCAGGTGCTGGTGTGCTTT 61.493 57.895 0.00 0.00 38.21 3.51
892 976 4.962836 GGCAGGTGCTGGTGTGCT 62.963 66.667 1.26 0.00 41.70 4.40
909 1016 3.125316 CCTGGTTGCAAGTGTTTGATTG 58.875 45.455 0.00 0.00 36.36 2.67
921 1028 3.070159 GCTAGATAGATGTCCTGGTTGCA 59.930 47.826 0.00 0.00 0.00 4.08
922 1029 3.323403 AGCTAGATAGATGTCCTGGTTGC 59.677 47.826 0.00 0.00 0.00 4.17
923 1030 5.069648 TGAAGCTAGATAGATGTCCTGGTTG 59.930 44.000 0.00 0.00 0.00 3.77
927 1034 7.178274 AGGTAATGAAGCTAGATAGATGTCCTG 59.822 40.741 0.00 0.00 32.98 3.86
946 1058 5.883115 TCACTCACTCACTCTCTAGGTAATG 59.117 44.000 0.00 0.00 0.00 1.90
948 1060 5.013287 ACTCACTCACTCACTCTCTAGGTAA 59.987 44.000 0.00 0.00 0.00 2.85
952 1064 4.574892 TCACTCACTCACTCACTCTCTAG 58.425 47.826 0.00 0.00 0.00 2.43
954 1066 3.181445 ACTCACTCACTCACTCACTCTCT 60.181 47.826 0.00 0.00 0.00 3.10
968 1080 0.319728 GCTTGGAGCTCACTCACTCA 59.680 55.000 17.19 0.00 45.42 3.41
969 1081 3.135942 GCTTGGAGCTCACTCACTC 57.864 57.895 17.19 0.00 45.42 3.51
979 1091 1.202475 GCTACCTGTCTAGCTTGGAGC 60.202 57.143 0.00 0.00 42.84 4.70
980 1092 2.103373 TGCTACCTGTCTAGCTTGGAG 58.897 52.381 0.00 0.00 40.02 3.86
981 1093 2.231716 TGCTACCTGTCTAGCTTGGA 57.768 50.000 0.00 0.00 40.02 3.53
982 1094 2.831333 CATGCTACCTGTCTAGCTTGG 58.169 52.381 0.00 0.00 39.53 3.61
983 1095 2.831333 CCATGCTACCTGTCTAGCTTG 58.169 52.381 0.00 0.00 41.40 4.01
984 1096 1.139853 GCCATGCTACCTGTCTAGCTT 59.860 52.381 0.00 0.00 40.02 3.74
990 1102 0.174845 TGTACGCCATGCTACCTGTC 59.825 55.000 0.00 0.00 0.00 3.51
991 1103 0.175760 CTGTACGCCATGCTACCTGT 59.824 55.000 0.00 0.00 0.00 4.00
995 1107 0.810031 CACCCTGTACGCCATGCTAC 60.810 60.000 0.00 0.00 0.00 3.58
1353 1465 1.445582 GTGGTAGACGGCGAACTGG 60.446 63.158 16.62 0.00 0.00 4.00
1640 1779 3.545481 GCGAGGACGACATGTGCG 61.545 66.667 1.15 9.63 44.84 5.34
1668 1807 0.177141 TATGCCCGCTATAATCCCGC 59.823 55.000 0.00 0.00 0.00 6.13
1695 1840 1.514873 CTTTGAAAGCGGCGGATGC 60.515 57.895 9.78 0.00 41.71 3.91
1696 1841 1.137404 CCTTTGAAAGCGGCGGATG 59.863 57.895 9.78 0.00 0.00 3.51
1697 1842 2.700773 GCCTTTGAAAGCGGCGGAT 61.701 57.895 9.78 0.00 33.64 4.18
1793 1968 3.605749 TTGTACCCGGCTGCTGCTC 62.606 63.158 15.64 4.88 39.59 4.26
1827 2008 0.179156 TATTCCTCGCGTTCGTCCAC 60.179 55.000 5.77 0.00 36.96 4.02
1835 2016 2.581409 CGCCGTTATTCCTCGCGT 60.581 61.111 5.77 0.00 0.00 6.01
1836 2017 3.327754 CCGCCGTTATTCCTCGCG 61.328 66.667 0.00 0.00 0.00 5.87
1857 2038 4.738998 CCCATGCGGCCCAAGTCA 62.739 66.667 0.00 0.00 0.00 3.41
1970 2157 2.548904 CTGGCTAGTAGCTAGTACACGG 59.451 54.545 23.55 6.99 43.76 4.94
1971 2158 3.881780 CTGGCTAGTAGCTAGTACACG 57.118 52.381 23.55 2.03 43.76 4.49
1984 2171 0.464916 TGGATGTGCATGCTGGCTAG 60.465 55.000 20.33 0.00 34.04 3.42
1986 2173 1.076265 ATGGATGTGCATGCTGGCT 60.076 52.632 20.33 0.45 34.04 4.75
1988 2175 0.816421 TCGATGGATGTGCATGCTGG 60.816 55.000 20.33 0.00 0.00 4.85
1991 2178 1.019673 AACTCGATGGATGTGCATGC 58.980 50.000 11.82 11.82 0.00 4.06
1992 2179 2.282407 TCAACTCGATGGATGTGCATG 58.718 47.619 0.00 0.00 0.00 4.06
1993 2180 2.696989 TCAACTCGATGGATGTGCAT 57.303 45.000 0.00 0.00 0.00 3.96
1994 2181 2.093553 TGATCAACTCGATGGATGTGCA 60.094 45.455 0.00 0.00 33.17 4.57
1995 2182 2.286294 GTGATCAACTCGATGGATGTGC 59.714 50.000 0.00 0.00 33.17 4.57
1996 2183 3.790091 AGTGATCAACTCGATGGATGTG 58.210 45.455 0.00 0.00 31.64 3.21
1997 2184 4.478206 AAGTGATCAACTCGATGGATGT 57.522 40.909 0.00 0.00 38.56 3.06
1998 2185 8.593492 TTAATAAGTGATCAACTCGATGGATG 57.407 34.615 0.00 0.00 38.56 3.51
1999 2186 9.784531 AATTAATAAGTGATCAACTCGATGGAT 57.215 29.630 0.00 0.00 38.56 3.41
2062 2258 2.296190 GCCACCAAAACTTCCAAGTAGG 59.704 50.000 0.00 0.00 38.57 3.18
2063 2259 2.031157 CGCCACCAAAACTTCCAAGTAG 60.031 50.000 0.00 0.00 38.57 2.57
2064 2260 1.950909 CGCCACCAAAACTTCCAAGTA 59.049 47.619 0.00 0.00 38.57 2.24
2065 2261 0.744281 CGCCACCAAAACTTCCAAGT 59.256 50.000 0.00 0.00 42.04 3.16
2066 2262 1.028905 TCGCCACCAAAACTTCCAAG 58.971 50.000 0.00 0.00 0.00 3.61
2067 2263 0.741915 GTCGCCACCAAAACTTCCAA 59.258 50.000 0.00 0.00 0.00 3.53
2127 2328 3.487202 CACCGTGGCGATGAACCG 61.487 66.667 0.00 0.00 0.00 4.44
2128 2329 2.358247 ACACCGTGGCGATGAACC 60.358 61.111 3.03 0.00 0.00 3.62
2129 2330 2.860293 CACACCGTGGCGATGAAC 59.140 61.111 3.03 0.00 0.00 3.18
2130 2331 3.047280 GCACACCGTGGCGATGAA 61.047 61.111 3.03 0.00 33.64 2.57
2131 2332 4.306967 TGCACACCGTGGCGATGA 62.307 61.111 3.03 0.00 33.64 2.92
2132 2333 4.088762 GTGCACACCGTGGCGATG 62.089 66.667 13.17 0.00 33.64 3.84
2133 2334 4.617520 TGTGCACACCGTGGCGAT 62.618 61.111 17.42 0.00 33.64 4.58
2134 2335 4.840005 TTGTGCACACCGTGGCGA 62.840 61.111 21.56 0.00 33.64 5.54
2135 2336 4.605967 GTTGTGCACACCGTGGCG 62.606 66.667 21.56 0.00 33.64 5.69
2136 2337 4.605967 CGTTGTGCACACCGTGGC 62.606 66.667 26.41 9.11 33.64 5.01
2137 2338 3.947841 CCGTTGTGCACACCGTGG 61.948 66.667 30.76 20.31 33.64 4.94
2138 2339 4.605967 GCCGTTGTGCACACCGTG 62.606 66.667 30.76 23.29 36.51 4.94
2141 2342 3.521308 CTTCGCCGTTGTGCACACC 62.521 63.158 21.56 12.58 0.00 4.16
2142 2343 1.492319 TACTTCGCCGTTGTGCACAC 61.492 55.000 21.56 13.79 0.00 3.82
2143 2344 0.601576 ATACTTCGCCGTTGTGCACA 60.602 50.000 17.42 17.42 0.00 4.57
2144 2345 1.352114 TATACTTCGCCGTTGTGCAC 58.648 50.000 10.75 10.75 0.00 4.57
2145 2346 2.159156 AGATATACTTCGCCGTTGTGCA 60.159 45.455 0.00 0.00 0.00 4.57
2146 2347 2.470821 AGATATACTTCGCCGTTGTGC 58.529 47.619 0.00 0.00 0.00 4.57
2147 2348 3.050619 GGAGATATACTTCGCCGTTGTG 58.949 50.000 0.00 0.00 0.00 3.33
2148 2349 2.035576 GGGAGATATACTTCGCCGTTGT 59.964 50.000 0.00 0.00 36.53 3.32
2149 2350 2.609737 GGGGAGATATACTTCGCCGTTG 60.610 54.545 5.87 0.00 36.53 4.10
2150 2351 1.617357 GGGGAGATATACTTCGCCGTT 59.383 52.381 5.87 0.00 36.53 4.44
2151 2352 1.254954 GGGGAGATATACTTCGCCGT 58.745 55.000 5.87 0.00 36.53 5.68
2153 2354 0.108756 GCGGGGAGATATACTTCGCC 60.109 60.000 9.98 9.98 37.10 5.54
2154 2355 0.108756 GGCGGGGAGATATACTTCGC 60.109 60.000 0.00 0.00 39.76 4.70
2155 2356 0.170561 CGGCGGGGAGATATACTTCG 59.829 60.000 0.00 0.00 0.00 3.79
2156 2357 0.108756 GCGGCGGGGAGATATACTTC 60.109 60.000 9.78 0.00 0.00 3.01
2157 2358 1.542187 GGCGGCGGGGAGATATACTT 61.542 60.000 9.78 0.00 0.00 2.24
2158 2359 1.982938 GGCGGCGGGGAGATATACT 60.983 63.158 9.78 0.00 0.00 2.12
2159 2360 2.577593 GGCGGCGGGGAGATATAC 59.422 66.667 9.78 0.00 0.00 1.47
2160 2361 3.066190 CGGCGGCGGGGAGATATA 61.066 66.667 25.36 0.00 0.00 0.86
2182 2383 3.423154 GGAAACGTGGGCGCAGAG 61.423 66.667 10.83 3.98 42.83 3.35
2207 2408 4.622456 AAAACAAGCGCACGCCCG 62.622 61.111 11.47 5.56 43.17 6.13
2208 2409 2.279186 AAAAACAAGCGCACGCCC 60.279 55.556 11.47 0.00 43.17 6.13
2260 2461 9.298250 TGAGGCTCGTCTCTTATTATTTATACT 57.702 33.333 10.42 0.00 34.98 2.12
2261 2462 9.562583 CTGAGGCTCGTCTCTTATTATTTATAC 57.437 37.037 10.42 0.00 34.98 1.47
2262 2463 8.740906 CCTGAGGCTCGTCTCTTATTATTTATA 58.259 37.037 10.42 0.00 34.98 0.98
2263 2464 7.310113 CCCTGAGGCTCGTCTCTTATTATTTAT 60.310 40.741 10.42 0.00 34.98 1.40
2275 2476 2.681778 CCACCCTGAGGCTCGTCT 60.682 66.667 10.42 0.00 36.11 4.18
2498 2699 2.760385 GCGCCCTACACCTCCTCT 60.760 66.667 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.