Multiple sequence alignment - TraesCS4A01G437600

Loading Multiple Alignment...

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 TraesCS4A01G437600 chr4A 100.000 3197 0 0 1 3197 707306501 707303305 0.000000e+00 5904.0
1 TraesCS4A01G437600 chr4A 81.665 1309 205 23 996 2301 707487577 707488853 0.000000e+00 1055.0
2 TraesCS4A01G437600 chr4A 81.473 1317 211 22 996 2310 707674804 707676089 0.000000e+00 1050.0
3 TraesCS4A01G437600 chr4A 81.473 1317 211 22 996 2310 707702263 707703548 0.000000e+00 1050.0
4 TraesCS4A01G437600 chr4A 81.093 1317 216 22 996 2310 706089789 706088504 0.000000e+00 1022.0
5 TraesCS4A01G437600 chr4A 80.942 1317 218 21 996 2310 705953813 705952528 0.000000e+00 1011.0
6 TraesCS4A01G437600 chr4A 87.527 465 40 8 2710 3170 707514028 707514478 3.650000e-144 521.0
7 TraesCS4A01G437600 chr4A 91.398 186 16 0 1784 1969 707513846 707514031 4.090000e-64 255.0
8 TraesCS4A01G437600 chr4A 90.741 108 10 0 889 996 707487312 707487419 9.240000e-31 145.0
9 TraesCS4A01G437600 chr7D 89.741 2125 159 31 996 3108 24326434 24328511 0.000000e+00 2662.0
10 TraesCS4A01G437600 chr7D 82.420 1314 199 18 998 2310 24021239 24019957 0.000000e+00 1118.0
11 TraesCS4A01G437600 chr7D 81.611 1316 208 20 998 2310 24118804 24117520 0.000000e+00 1059.0
12 TraesCS4A01G437600 chr7D 80.681 999 111 52 19 996 24119891 24118954 0.000000e+00 701.0
13 TraesCS4A01G437600 chr7D 92.308 104 7 1 878 981 24325945 24326047 2.570000e-31 147.0
14 TraesCS4A01G437600 chr7D 92.929 99 7 0 885 983 24021487 24021389 9.240000e-31 145.0
15 TraesCS4A01G437600 chr7D 86.792 106 12 2 19 124 91113004 91113107 2.010000e-22 117.0
16 TraesCS4A01G437600 chrUn 80.942 1317 218 21 996 2310 220049451 220048166 0.000000e+00 1011.0
17 TraesCS4A01G437600 chrUn 86.792 106 12 2 19 124 310171238 310171341 2.010000e-22 117.0
18 TraesCS4A01G437600 chr5D 83.486 109 15 3 18 125 425036140 425036246 7.300000e-17 99.0
19 TraesCS4A01G437600 chr5A 77.108 166 36 2 1904 2068 576950287 576950451 9.440000e-16 95.3
20 TraesCS4A01G437600 chr7A 81.188 101 17 2 24 124 75402860 75402762 2.640000e-11 80.5
21 TraesCS4A01G437600 chr6B 87.143 70 7 2 59 128 120703399 120703332 9.510000e-11 78.7


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 TraesCS4A01G437600 chr4A 707303305 707306501 3196 True 5904.0 5904 100.0000 1 3197 1 chr4A.!!$R3 3196
1 TraesCS4A01G437600 chr4A 707674804 707676089 1285 False 1050.0 1050 81.4730 996 2310 1 chr4A.!!$F1 1314
2 TraesCS4A01G437600 chr4A 707702263 707703548 1285 False 1050.0 1050 81.4730 996 2310 1 chr4A.!!$F2 1314
3 TraesCS4A01G437600 chr4A 706088504 706089789 1285 True 1022.0 1022 81.0930 996 2310 1 chr4A.!!$R2 1314
4 TraesCS4A01G437600 chr4A 705952528 705953813 1285 True 1011.0 1011 80.9420 996 2310 1 chr4A.!!$R1 1314
5 TraesCS4A01G437600 chr4A 707487312 707488853 1541 False 600.0 1055 86.2030 889 2301 2 chr4A.!!$F3 1412
6 TraesCS4A01G437600 chr4A 707513846 707514478 632 False 388.0 521 89.4625 1784 3170 2 chr4A.!!$F4 1386
7 TraesCS4A01G437600 chr7D 24325945 24328511 2566 False 1404.5 2662 91.0245 878 3108 2 chr7D.!!$F2 2230
8 TraesCS4A01G437600 chr7D 24117520 24119891 2371 True 880.0 1059 81.1460 19 2310 2 chr7D.!!$R2 2291
9 TraesCS4A01G437600 chr7D 24019957 24021487 1530 True 631.5 1118 87.6745 885 2310 2 chr7D.!!$R1 1425
10 TraesCS4A01G437600 chrUn 220048166 220049451 1285 True 1011.0 1011 80.9420 996 2310 1 chrUn.!!$R1 1314

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
867 873 0.039074 AAGTGACGAGACAGAAGCCG 60.039 55.0 0.0 0.0 0.0 5.52 F
887 904 0.396417 CGTGAGTCTCCCATCTCCCT 60.396 60.0 0.0 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 2684 0.034670 GCTCCAGCACCTTCAGGATT 60.035 55.000 0.00 0.0 41.59 3.01 R
2716 3345 1.141019 GTCGCGGATTCAGGTAGCA 59.859 57.895 6.13 0.0 0.00 3.49 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
49 50 0.603707 CAGCAACGCCTTCAGGAAGA 60.604 55.000 10.52 0.00 40.79 2.87
57 58 2.218603 GCCTTCAGGAAGAAAACGACA 58.781 47.619 10.52 0.00 40.79 4.35
58 59 2.031944 GCCTTCAGGAAGAAAACGACAC 60.032 50.000 10.52 0.00 40.79 3.67
68 69 2.476619 AGAAAACGACACTCAAGCATCG 59.523 45.455 0.00 0.00 40.39 3.84
76 77 0.388649 ACTCAAGCATCGTCGTCACC 60.389 55.000 0.00 0.00 0.00 4.02
90 91 1.004320 TCACCGAATCCAACCACCG 60.004 57.895 0.00 0.00 0.00 4.94
114 115 5.818336 GGAGGCTAGATTTCTAGGTTTTCAC 59.182 44.000 14.75 0.00 44.63 3.18
128 129 3.105937 GTTTTCACCGTGAAGAACAAGC 58.894 45.455 21.62 7.36 37.70 4.01
130 131 0.534203 TCACCGTGAAGAACAAGCCC 60.534 55.000 0.00 0.00 0.00 5.19
143 144 1.628846 ACAAGCCCGTTTCATAGTCCT 59.371 47.619 0.00 0.00 0.00 3.85
145 146 2.403252 AGCCCGTTTCATAGTCCTTG 57.597 50.000 0.00 0.00 0.00 3.61
155 156 7.604164 CCGTTTCATAGTCCTTGCATATCTATT 59.396 37.037 0.00 0.00 0.00 1.73
170 171 7.602644 TGCATATCTATTTCCGTTTCATAGTCC 59.397 37.037 0.00 0.00 0.00 3.85
171 172 7.602644 GCATATCTATTTCCGTTTCATAGTCCA 59.397 37.037 0.00 0.00 0.00 4.02
176 177 0.304705 CCGTTTCATAGTCCATGCGC 59.695 55.000 0.00 0.00 34.35 6.09
181 182 2.445565 TCATAGTCCATGCGCTGATC 57.554 50.000 9.73 1.63 34.35 2.92
184 185 3.766051 TCATAGTCCATGCGCTGATCTAT 59.234 43.478 9.73 11.79 34.35 1.98
188 189 3.056962 AGTCCATGCGCTGATCTATGTAG 60.057 47.826 9.73 0.00 0.00 2.74
194 195 7.035612 CCATGCGCTGATCTATGTAGTTTATA 58.964 38.462 9.73 0.00 0.00 0.98
208 209 6.482835 TGTAGTTTATATTCACGTTGCATGC 58.517 36.000 11.82 11.82 0.00 4.06
209 210 5.818136 AGTTTATATTCACGTTGCATGCT 57.182 34.783 20.33 0.00 0.00 3.79
212 213 7.757526 AGTTTATATTCACGTTGCATGCTTAA 58.242 30.769 20.33 2.28 0.00 1.85
218 219 4.195416 TCACGTTGCATGCTTAATATGGA 58.805 39.130 20.33 3.69 0.00 3.41
221 222 6.073276 TCACGTTGCATGCTTAATATGGATAC 60.073 38.462 20.33 0.00 0.00 2.24
244 245 4.767409 CAGGGTATCGAATATGAGGAGTGA 59.233 45.833 0.00 0.00 0.00 3.41
245 246 4.767928 AGGGTATCGAATATGAGGAGTGAC 59.232 45.833 0.00 0.00 0.00 3.67
246 247 4.379603 GGGTATCGAATATGAGGAGTGACG 60.380 50.000 0.00 0.00 0.00 4.35
247 248 2.776312 TCGAATATGAGGAGTGACGC 57.224 50.000 0.00 0.00 0.00 5.19
248 249 1.002792 TCGAATATGAGGAGTGACGCG 60.003 52.381 3.53 3.53 0.00 6.01
249 250 1.268589 CGAATATGAGGAGTGACGCGT 60.269 52.381 13.85 13.85 0.00 6.01
250 251 2.386249 GAATATGAGGAGTGACGCGTC 58.614 52.381 31.66 31.66 0.00 5.19
251 252 1.389555 ATATGAGGAGTGACGCGTCA 58.610 50.000 36.40 36.40 37.24 4.35
252 253 1.170442 TATGAGGAGTGACGCGTCAA 58.830 50.000 40.60 25.76 41.85 3.18
253 254 0.317160 ATGAGGAGTGACGCGTCAAA 59.683 50.000 40.60 19.59 41.85 2.69
254 255 0.103390 TGAGGAGTGACGCGTCAAAA 59.897 50.000 40.60 18.79 41.85 2.44
255 256 1.214367 GAGGAGTGACGCGTCAAAAA 58.786 50.000 40.60 18.38 41.85 1.94
276 277 0.107508 AATGAGGAGTGCGGATGTGG 60.108 55.000 0.00 0.00 0.00 4.17
289 290 3.003689 GCGGATGTGGAGGACATAAATTG 59.996 47.826 0.00 0.00 45.90 2.32
300 301 3.620488 GACATAAATTGAGGAGTGCCCA 58.380 45.455 0.00 0.00 37.41 5.36
304 305 1.067295 AATTGAGGAGTGCCCAGTCA 58.933 50.000 5.56 0.00 37.41 3.41
305 306 1.067295 ATTGAGGAGTGCCCAGTCAA 58.933 50.000 5.56 0.00 34.73 3.18
306 307 1.067295 TTGAGGAGTGCCCAGTCAAT 58.933 50.000 5.56 0.00 37.41 2.57
307 308 0.325933 TGAGGAGTGCCCAGTCAATG 59.674 55.000 5.56 0.00 37.41 2.82
308 309 1.001641 AGGAGTGCCCAGTCAATGC 60.002 57.895 5.56 0.00 37.41 3.56
309 310 1.303561 GGAGTGCCCAGTCAATGCA 60.304 57.895 5.56 0.00 32.47 3.96
310 311 0.682209 GGAGTGCCCAGTCAATGCAT 60.682 55.000 0.00 0.00 37.34 3.96
311 312 0.454600 GAGTGCCCAGTCAATGCATG 59.545 55.000 0.00 0.00 37.34 4.06
312 313 0.251474 AGTGCCCAGTCAATGCATGT 60.251 50.000 0.00 0.00 37.34 3.21
313 314 0.108992 GTGCCCAGTCAATGCATGTG 60.109 55.000 0.00 0.98 37.34 3.21
314 315 1.252215 TGCCCAGTCAATGCATGTGG 61.252 55.000 0.00 5.31 0.00 4.17
315 316 0.966875 GCCCAGTCAATGCATGTGGA 60.967 55.000 15.75 5.73 28.73 4.02
316 317 0.813184 CCCAGTCAATGCATGTGGAC 59.187 55.000 15.75 15.40 28.73 4.02
317 318 0.448990 CCAGTCAATGCATGTGGACG 59.551 55.000 16.22 12.44 35.49 4.79
318 319 0.179181 CAGTCAATGCATGTGGACGC 60.179 55.000 16.22 0.00 35.49 5.19
319 320 1.226101 GTCAATGCATGTGGACGCG 60.226 57.895 3.53 3.53 0.00 6.01
320 321 2.577644 CAATGCATGTGGACGCGC 60.578 61.111 5.73 0.00 0.00 6.86
321 322 3.055110 AATGCATGTGGACGCGCA 61.055 55.556 5.73 0.00 39.01 6.09
322 323 3.326889 AATGCATGTGGACGCGCAC 62.327 57.895 5.73 8.14 37.17 5.34
346 347 1.660052 CGTGTCCGTGAGCATTTTGTG 60.660 52.381 0.00 0.00 0.00 3.33
370 372 6.039616 GCAGTTGTTGACTTGGAATTGTAAA 58.960 36.000 0.00 0.00 36.10 2.01
397 399 4.070630 GAAGCATTCCTGTGATCTAGCT 57.929 45.455 0.00 0.00 39.83 3.32
407 409 5.011431 TCCTGTGATCTAGCTGTATGAATGG 59.989 44.000 0.00 0.00 0.00 3.16
412 414 6.763135 GTGATCTAGCTGTATGAATGGTTTCA 59.237 38.462 0.00 0.00 45.57 2.69
429 431 4.703093 GGTTTCATTTTCAATACGAGGGGA 59.297 41.667 0.00 0.00 0.00 4.81
431 433 3.527533 TCATTTTCAATACGAGGGGACG 58.472 45.455 0.00 0.00 39.31 4.79
447 449 0.739813 GACGAATTCGGTGACCCTGG 60.740 60.000 29.79 0.61 44.95 4.45
450 452 0.539986 GAATTCGGTGACCCTGGCTA 59.460 55.000 0.00 0.00 0.00 3.93
522 524 6.309712 TGAGACTTTTCAATGCTCTTTGAG 57.690 37.500 0.00 0.00 36.97 3.02
532 534 6.993079 TCAATGCTCTTTGAGAAGTAGTACA 58.007 36.000 2.52 0.00 34.41 2.90
548 550 4.021102 AGTACAAGTTCTCAATGTGGGG 57.979 45.455 0.00 0.00 0.00 4.96
549 551 3.650942 AGTACAAGTTCTCAATGTGGGGA 59.349 43.478 0.00 0.00 0.00 4.81
550 552 2.863809 ACAAGTTCTCAATGTGGGGAC 58.136 47.619 0.00 0.00 0.00 4.46
561 563 5.328565 TCAATGTGGGGACAATAACATCAA 58.671 37.500 0.00 0.00 46.06 2.57
575 577 8.141268 ACAATAACATCAAAGGACGTGAATTTT 58.859 29.630 0.00 0.00 0.00 1.82
580 582 6.863126 ACATCAAAGGACGTGAATTTTCAATC 59.137 34.615 0.00 0.00 39.21 2.67
594 596 6.743575 ATTTTCAATCCTCTTTGAGTACCG 57.256 37.500 0.00 0.00 36.97 4.02
610 612 1.078848 CCGGTTCTCAAGCTCCAGG 60.079 63.158 0.00 0.00 0.00 4.45
620 622 1.001378 CAAGCTCCAGGGTGAAAAACG 60.001 52.381 0.00 0.00 0.00 3.60
626 628 2.105821 TCCAGGGTGAAAAACGATCACT 59.894 45.455 6.62 0.00 45.13 3.41
635 637 4.935205 TGAAAAACGATCACTACCTCCATG 59.065 41.667 0.00 0.00 0.00 3.66
639 641 2.690497 ACGATCACTACCTCCATGTGAG 59.310 50.000 0.00 4.67 42.81 3.51
640 642 2.544694 CGATCACTACCTCCATGTGAGC 60.545 54.545 0.00 0.00 42.81 4.26
649 651 3.196901 ACCTCCATGTGAGCGTATGTAAA 59.803 43.478 5.86 0.00 39.98 2.01
660 662 6.645415 GTGAGCGTATGTAAAATATGGTAGCT 59.355 38.462 0.00 0.00 0.00 3.32
661 663 6.645003 TGAGCGTATGTAAAATATGGTAGCTG 59.355 38.462 0.00 0.00 0.00 4.24
665 667 7.456253 CGTATGTAAAATATGGTAGCTGATGC 58.544 38.462 0.00 0.00 40.05 3.91
671 673 1.337384 ATGGTAGCTGATGCGGGTCA 61.337 55.000 0.00 0.00 45.42 4.02
672 674 1.337384 TGGTAGCTGATGCGGGTCAT 61.337 55.000 0.00 0.00 45.42 3.06
680 682 2.083774 TGATGCGGGTCATTCAACTTC 58.916 47.619 0.00 0.00 35.05 3.01
686 688 2.084546 GGGTCATTCAACTTCGGAAGG 58.915 52.381 20.97 5.30 0.00 3.46
695 697 7.881232 TCATTCAACTTCGGAAGGTTAGTAAAT 59.119 33.333 20.97 6.91 0.00 1.40
696 698 9.158233 CATTCAACTTCGGAAGGTTAGTAAATA 57.842 33.333 20.97 0.00 0.00 1.40
697 699 8.767478 TTCAACTTCGGAAGGTTAGTAAATAG 57.233 34.615 20.97 0.62 0.00 1.73
698 700 7.899973 TCAACTTCGGAAGGTTAGTAAATAGT 58.100 34.615 20.97 0.00 0.00 2.12
699 701 9.023962 TCAACTTCGGAAGGTTAGTAAATAGTA 57.976 33.333 20.97 0.00 0.00 1.82
700 702 9.643693 CAACTTCGGAAGGTTAGTAAATAGTAA 57.356 33.333 20.97 0.00 0.00 2.24
702 704 9.866798 ACTTCGGAAGGTTAGTAAATAGTAAAG 57.133 33.333 20.97 0.00 0.00 1.85
758 763 7.360361 ACATCGTGTATTTGTTTTTCTTCTCC 58.640 34.615 0.00 0.00 0.00 3.71
810 815 2.419297 GGGAGTACTTGATGTGGCTCAG 60.419 54.545 0.00 0.00 35.34 3.35
817 822 0.463204 TGATGTGGCTCAGCTCTAGC 59.537 55.000 8.78 8.78 42.49 3.42
830 836 4.837298 TCAGCTCTAGCCTCAATCATATGT 59.163 41.667 1.90 0.00 43.38 2.29
833 839 5.543405 AGCTCTAGCCTCAATCATATGTCTT 59.457 40.000 1.90 0.00 43.38 3.01
835 841 6.106648 TCTAGCCTCAATCATATGTCTTGG 57.893 41.667 15.79 9.26 0.00 3.61
837 843 3.117776 AGCCTCAATCATATGTCTTGGCA 60.118 43.478 21.46 0.00 40.18 4.92
849 855 5.664294 ATGTCTTGGCAAGATATTTGCAA 57.336 34.783 30.70 11.09 46.58 4.08
853 859 4.766373 TCTTGGCAAGATATTTGCAAGTGA 59.234 37.500 25.38 0.00 46.58 3.41
854 860 4.439305 TGGCAAGATATTTGCAAGTGAC 57.561 40.909 18.16 0.00 46.58 3.67
855 861 3.119884 TGGCAAGATATTTGCAAGTGACG 60.120 43.478 18.16 0.00 46.58 4.35
856 862 3.126858 GGCAAGATATTTGCAAGTGACGA 59.873 43.478 18.16 0.00 46.58 4.20
857 863 4.337763 GCAAGATATTTGCAAGTGACGAG 58.662 43.478 4.47 0.00 44.34 4.18
858 864 4.093408 GCAAGATATTTGCAAGTGACGAGA 59.907 41.667 4.47 0.00 44.34 4.04
860 866 4.820897 AGATATTTGCAAGTGACGAGACA 58.179 39.130 4.47 0.00 0.00 3.41
862 868 2.595124 TTTGCAAGTGACGAGACAGA 57.405 45.000 0.00 0.00 0.00 3.41
863 869 2.595124 TTGCAAGTGACGAGACAGAA 57.405 45.000 0.00 0.00 0.00 3.02
864 870 2.140065 TGCAAGTGACGAGACAGAAG 57.860 50.000 0.00 0.00 0.00 2.85
867 873 0.039074 AAGTGACGAGACAGAAGCCG 60.039 55.000 0.00 0.00 0.00 5.52
868 874 2.089349 GTGACGAGACAGAAGCCGC 61.089 63.158 0.00 0.00 0.00 6.53
869 875 2.876645 GACGAGACAGAAGCCGCG 60.877 66.667 0.00 0.00 0.00 6.46
871 877 3.175240 CGAGACAGAAGCCGCGTG 61.175 66.667 4.92 0.00 0.00 5.34
872 878 2.258591 GAGACAGAAGCCGCGTGA 59.741 61.111 4.92 0.00 0.00 4.35
873 879 1.803519 GAGACAGAAGCCGCGTGAG 60.804 63.158 4.92 0.00 0.00 3.51
874 880 2.049063 GACAGAAGCCGCGTGAGT 60.049 61.111 4.92 0.00 0.00 3.41
876 882 2.259818 CAGAAGCCGCGTGAGTCT 59.740 61.111 4.92 0.00 0.00 3.24
881 898 4.148825 GCCGCGTGAGTCTCCCAT 62.149 66.667 4.92 0.00 0.00 4.00
887 904 0.396417 CGTGAGTCTCCCATCTCCCT 60.396 60.000 0.00 0.00 0.00 4.20
906 923 6.014840 TCTCCCTCACGTCTTTAAATACTTGT 60.015 38.462 9.17 0.00 0.00 3.16
916 933 5.187186 TCTTTAAATACTTGTCGCCTCCTCT 59.813 40.000 0.00 0.00 0.00 3.69
954 971 7.683704 GCACATAAATCATTTGATCAGCCTCTT 60.684 37.037 0.00 0.00 32.75 2.85
983 1000 4.799564 TTGCTTTGTTCTTCACAAGGTT 57.200 36.364 0.00 0.00 46.37 3.50
985 1002 2.860136 GCTTTGTTCTTCACAAGGTTGC 59.140 45.455 0.00 0.00 46.37 4.17
1028 1623 2.707849 GCAACAGCATCCCAGCCAG 61.708 63.158 0.00 0.00 34.23 4.85
1045 1640 2.268920 GCACCTTGGGCGAGATCA 59.731 61.111 0.00 0.00 0.00 2.92
1047 1642 1.900351 CACCTTGGGCGAGATCAGA 59.100 57.895 0.00 0.00 0.00 3.27
1210 1805 1.507141 CGCCAAACTATGCCGGATCC 61.507 60.000 5.05 0.00 0.00 3.36
1234 1829 3.796667 GTCGAGAGGCGTTTCTTCT 57.203 52.632 0.00 0.00 41.80 2.85
1255 1850 2.283532 ACACCGAGGAGCTGCTCT 60.284 61.111 29.52 12.14 0.00 4.09
1359 1954 4.740822 GCCATTGCCGAGTGGGGT 62.741 66.667 0.00 0.00 36.00 4.95
1363 1958 1.985662 ATTGCCGAGTGGGGTCGTA 60.986 57.895 0.00 0.00 38.32 3.43
1449 2044 2.756283 CGCCTCGTCTCCCTCCTT 60.756 66.667 0.00 0.00 0.00 3.36
1599 2194 0.814010 AGCTCACCGTCGCTGTTTTT 60.814 50.000 0.00 0.00 34.69 1.94
1725 2320 0.831711 GCCCCCTGTTCAACATGGTT 60.832 55.000 10.63 0.00 32.78 3.67
1769 2364 2.126071 CACCGAGCACGTACCCAG 60.126 66.667 2.18 0.00 37.88 4.45
1776 2371 1.153168 GCACGTACCCAGGATGCAT 60.153 57.895 0.00 0.00 36.30 3.96
1788 2383 1.402896 GGATGCATCTCGGGAGTGGA 61.403 60.000 25.28 0.00 0.00 4.02
1809 2404 1.062587 GGCATCGACTGGAACATTTCG 59.937 52.381 0.00 0.00 42.72 3.46
1818 2413 3.006110 ACTGGAACATTTCGAACGGACTA 59.994 43.478 0.00 0.00 38.20 2.59
2016 2614 0.737715 CGGCTAGCAGAACTGTGGTC 60.738 60.000 18.24 0.00 0.00 4.02
2086 2684 0.461339 GGTCAGGCGCCGAAGAATAA 60.461 55.000 23.20 0.00 0.00 1.40
2097 2695 4.200092 GCCGAAGAATAAATCCTGAAGGT 58.800 43.478 0.00 0.00 36.34 3.50
2196 2794 2.358615 CTGCACGCTGCCACCTAA 60.359 61.111 7.38 0.00 44.23 2.69
2202 2800 0.688487 ACGCTGCCACCTAAGGTAAA 59.312 50.000 0.00 0.00 32.11 2.01
2214 2812 6.239204 CCACCTAAGGTAAACCCAAGAAAAAG 60.239 42.308 0.00 0.00 32.11 2.27
2216 2814 7.068962 CACCTAAGGTAAACCCAAGAAAAAGAA 59.931 37.037 0.00 0.00 32.11 2.52
2218 2816 5.509716 AGGTAAACCCAAGAAAAAGAACG 57.490 39.130 0.00 0.00 36.42 3.95
2231 2829 3.383620 AAAGAACGAAAATGCATGGCA 57.616 38.095 0.00 0.00 44.86 4.92
2232 2830 2.352503 AGAACGAAAATGCATGGCAC 57.647 45.000 0.00 0.00 43.04 5.01
2233 2831 1.612950 AGAACGAAAATGCATGGCACA 59.387 42.857 0.00 0.00 43.04 4.57
2250 2848 5.752650 TGGCACATACAGAGTAGTACTAGT 58.247 41.667 10.09 10.09 0.00 2.57
2302 2925 9.378504 TGCAACCTTTTATATTTCCATATCCAT 57.621 29.630 0.00 0.00 0.00 3.41
2315 2938 9.818270 ATTTCCATATCCATATGTCACTTTGAT 57.182 29.630 1.24 0.00 38.73 2.57
2321 2944 9.911788 ATATCCATATGTCACTTTGATATTCCC 57.088 33.333 1.24 0.00 30.70 3.97
2322 2945 7.147958 TCCATATGTCACTTTGATATTCCCA 57.852 36.000 1.24 0.00 30.70 4.37
2323 2946 7.758609 TCCATATGTCACTTTGATATTCCCAT 58.241 34.615 1.24 0.00 30.70 4.00
2324 2947 8.889445 TCCATATGTCACTTTGATATTCCCATA 58.111 33.333 1.24 0.00 30.70 2.74
2325 2948 9.690913 CCATATGTCACTTTGATATTCCCATAT 57.309 33.333 1.24 0.00 30.70 1.78
2327 2950 9.911788 ATATGTCACTTTGATATTCCCATATCC 57.088 33.333 0.77 0.00 40.51 2.59
2349 2972 7.728847 TCCATATGTCACTTTGATATTTCCG 57.271 36.000 1.24 0.00 30.70 4.30
2353 2976 8.830580 CATATGTCACTTTGATATTTCCGTCTT 58.169 33.333 0.00 0.00 30.70 3.01
2388 3016 2.942376 GTGAACATGTGTGGTGTGAGAA 59.058 45.455 0.00 0.00 0.00 2.87
2393 3021 3.072330 ACATGTGTGGTGTGAGAATGGTA 59.928 43.478 0.00 0.00 0.00 3.25
2406 3034 6.995686 TGTGAGAATGGTATTGTAAGTTGTGT 59.004 34.615 0.00 0.00 0.00 3.72
2419 3047 8.556213 TTGTAAGTTGTGTAAGAGTGAGTTTT 57.444 30.769 0.00 0.00 0.00 2.43
2503 3132 3.861276 TCCGTACTGTGTGGATTACTG 57.139 47.619 0.00 0.00 0.00 2.74
2504 3133 3.159472 TCCGTACTGTGTGGATTACTGT 58.841 45.455 0.00 0.00 35.02 3.55
2510 3139 8.019669 CCGTACTGTGTGGATTACTGTATATAC 58.980 40.741 5.89 5.89 35.75 1.47
2511 3140 8.019669 CGTACTGTGTGGATTACTGTATATACC 58.980 40.741 10.38 0.00 35.75 2.73
2530 3159 4.948341 ACCTGTTGTTAAATTTGGGGAC 57.052 40.909 0.00 0.00 0.00 4.46
2567 3196 7.121168 TGAATTGACATGTTTCCTCTGGAATAC 59.879 37.037 0.00 3.16 41.71 1.89
2582 3211 6.086785 CTGGAATACAGGCCTAACTAGTAC 57.913 45.833 3.98 0.00 43.70 2.73
2650 3279 3.739300 CGAAAGAGGAAGTACAAGCGAAA 59.261 43.478 0.00 0.00 0.00 3.46
2654 3283 4.894784 AGAGGAAGTACAAGCGAAAATGA 58.105 39.130 0.00 0.00 0.00 2.57
2658 3287 6.381801 AGGAAGTACAAGCGAAAATGAAATG 58.618 36.000 0.00 0.00 0.00 2.32
2681 3310 3.995705 GCACAAGCATATCTCTCCTCATC 59.004 47.826 0.00 0.00 41.58 2.92
2740 3369 1.353103 CTGAATCCGCGACATTGCC 59.647 57.895 8.23 0.00 0.00 4.52
2750 3379 0.179084 CGACATTGCCCAGTACCGAT 60.179 55.000 0.00 0.00 0.00 4.18
2805 3434 3.304391 GCACACAATTCTTGCCGAGTAAA 60.304 43.478 0.00 0.00 0.00 2.01
2806 3435 4.791411 GCACACAATTCTTGCCGAGTAAAA 60.791 41.667 0.00 0.00 0.00 1.52
2807 3436 5.277825 CACACAATTCTTGCCGAGTAAAAA 58.722 37.500 0.00 0.00 0.00 1.94
3017 3652 9.398170 CATCCTTCCTATTTTGTTTTATATGCG 57.602 33.333 0.00 0.00 0.00 4.73
3119 3754 7.123547 TGGGTTGAAAAGTCTTATTTGTGTTCT 59.876 33.333 0.00 0.00 0.00 3.01
3129 3764 9.429359 AGTCTTATTTGTGTTCTTGAGACTATG 57.571 33.333 0.00 0.00 40.37 2.23
3130 3765 9.209175 GTCTTATTTGTGTTCTTGAGACTATGT 57.791 33.333 0.00 0.00 31.89 2.29
3131 3766 9.424319 TCTTATTTGTGTTCTTGAGACTATGTC 57.576 33.333 0.00 0.00 0.00 3.06
3132 3767 9.429359 CTTATTTGTGTTCTTGAGACTATGTCT 57.571 33.333 0.00 0.00 46.42 3.41
3134 3769 8.994429 ATTTGTGTTCTTGAGACTATGTCTAG 57.006 34.615 0.00 0.00 43.53 2.43
3175 3810 7.875971 AGAAAGGAATTACAAATATCGATGGC 58.124 34.615 8.54 0.00 0.00 4.40
3176 3811 5.862924 AGGAATTACAAATATCGATGGCG 57.137 39.130 8.54 0.00 39.35 5.69
3177 3812 5.305585 AGGAATTACAAATATCGATGGCGT 58.694 37.500 8.54 2.62 38.98 5.68
3178 3813 5.763204 AGGAATTACAAATATCGATGGCGTT 59.237 36.000 8.54 0.00 38.98 4.84
3179 3814 5.851177 GGAATTACAAATATCGATGGCGTTG 59.149 40.000 8.54 9.06 38.98 4.10
3180 3815 6.293190 GGAATTACAAATATCGATGGCGTTGA 60.293 38.462 8.54 0.00 38.98 3.18
3181 3816 3.944422 ACAAATATCGATGGCGTTGAC 57.056 42.857 8.54 0.00 38.98 3.18
3182 3817 2.284150 ACAAATATCGATGGCGTTGACG 59.716 45.455 8.54 0.00 43.27 4.35
3183 3818 2.502213 AATATCGATGGCGTTGACGA 57.498 45.000 8.54 0.00 43.02 4.20
3184 3819 2.051879 ATATCGATGGCGTTGACGAG 57.948 50.000 8.54 0.00 43.02 4.18
3185 3820 0.030235 TATCGATGGCGTTGACGAGG 59.970 55.000 8.54 0.00 43.02 4.63
3186 3821 2.629050 ATCGATGGCGTTGACGAGGG 62.629 60.000 7.85 0.00 43.02 4.30
3187 3822 2.577059 GATGGCGTTGACGAGGGA 59.423 61.111 7.85 0.00 43.02 4.20
3188 3823 1.079405 GATGGCGTTGACGAGGGAA 60.079 57.895 7.85 0.00 43.02 3.97
3189 3824 1.359459 GATGGCGTTGACGAGGGAAC 61.359 60.000 7.85 0.00 43.02 3.62
3190 3825 2.741211 GGCGTTGACGAGGGAACC 60.741 66.667 7.85 0.00 45.51 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.105778 TCAATGTCGCAGTGGTGTCA 59.894 50.000 7.28 0.00 29.97 3.58
1 2 1.129251 CATCAATGTCGCAGTGGTGTC 59.871 52.381 10.87 0.00 36.08 3.67
2 3 1.159285 CATCAATGTCGCAGTGGTGT 58.841 50.000 10.87 0.00 36.08 4.16
3 4 1.159285 ACATCAATGTCGCAGTGGTG 58.841 50.000 15.53 15.53 44.63 4.17
4 5 1.896220 AACATCAATGTCGCAGTGGT 58.104 45.000 7.28 0.00 40.80 4.16
6 7 4.289342 TGAAAAACATCAATGTCGCAGTG 58.711 39.130 0.00 1.69 40.80 3.66
7 8 4.566545 TGAAAAACATCAATGTCGCAGT 57.433 36.364 0.00 0.00 40.80 4.40
8 9 4.739228 TGTTGAAAAACATCAATGTCGCAG 59.261 37.500 0.00 0.00 41.09 5.18
9 10 4.676546 TGTTGAAAAACATCAATGTCGCA 58.323 34.783 0.00 0.00 41.09 5.10
10 11 4.375305 GCTGTTGAAAAACATCAATGTCGC 60.375 41.667 0.00 0.00 41.09 5.19
11 12 4.739228 TGCTGTTGAAAAACATCAATGTCG 59.261 37.500 0.00 0.00 41.09 4.35
12 13 6.413269 GTTGCTGTTGAAAAACATCAATGTC 58.587 36.000 10.08 0.00 39.81 3.06
13 14 5.005586 CGTTGCTGTTGAAAAACATCAATGT 59.994 36.000 14.63 0.00 39.81 2.71
14 15 5.425398 CGTTGCTGTTGAAAAACATCAATG 58.575 37.500 10.08 10.55 39.81 2.82
15 16 4.025813 GCGTTGCTGTTGAAAAACATCAAT 60.026 37.500 10.08 0.00 39.81 2.57
16 17 3.305629 GCGTTGCTGTTGAAAAACATCAA 59.694 39.130 4.30 4.30 36.71 2.57
17 18 2.857152 GCGTTGCTGTTGAAAAACATCA 59.143 40.909 0.00 0.00 31.47 3.07
49 50 2.210116 ACGATGCTTGAGTGTCGTTTT 58.790 42.857 0.00 0.00 43.97 2.43
57 58 0.388649 GGTGACGACGATGCTTGAGT 60.389 55.000 0.00 0.00 0.00 3.41
58 59 2.363807 GGTGACGACGATGCTTGAG 58.636 57.895 0.00 0.00 0.00 3.02
76 77 1.449601 CCTCCGGTGGTTGGATTCG 60.450 63.158 14.67 0.00 34.32 3.34
90 91 5.818336 GTGAAAACCTAGAAATCTAGCCTCC 59.182 44.000 11.25 1.68 43.47 4.30
106 107 3.691498 CTTGTTCTTCACGGTGAAAACC 58.309 45.455 26.92 18.28 35.73 3.27
114 115 1.164041 AACGGGCTTGTTCTTCACGG 61.164 55.000 0.00 0.00 0.00 4.94
116 117 1.673920 TGAAACGGGCTTGTTCTTCAC 59.326 47.619 0.00 0.00 0.00 3.18
118 119 3.751698 ACTATGAAACGGGCTTGTTCTTC 59.248 43.478 0.00 0.00 0.00 2.87
121 122 2.418976 GGACTATGAAACGGGCTTGTTC 59.581 50.000 0.00 0.00 0.00 3.18
128 129 2.107950 TGCAAGGACTATGAAACGGG 57.892 50.000 0.00 0.00 0.00 5.28
130 131 8.539770 AATAGATATGCAAGGACTATGAAACG 57.460 34.615 0.00 0.00 0.00 3.60
143 144 8.902540 ACTATGAAACGGAAATAGATATGCAA 57.097 30.769 0.00 0.00 0.00 4.08
145 146 7.602644 TGGACTATGAAACGGAAATAGATATGC 59.397 37.037 0.00 0.00 0.00 3.14
155 156 2.276201 CGCATGGACTATGAAACGGAA 58.724 47.619 2.48 0.00 39.21 4.30
170 171 6.957984 ATAAACTACATAGATCAGCGCATG 57.042 37.500 11.47 5.81 0.00 4.06
171 172 9.307121 GAATATAAACTACATAGATCAGCGCAT 57.693 33.333 11.47 0.00 0.00 4.73
181 182 9.797473 CATGCAACGTGAATATAAACTACATAG 57.203 33.333 0.00 0.00 0.00 2.23
184 185 6.315144 AGCATGCAACGTGAATATAAACTACA 59.685 34.615 21.98 0.00 0.00 2.74
188 189 7.962934 TTAAGCATGCAACGTGAATATAAAC 57.037 32.000 21.98 0.00 0.00 2.01
194 195 5.299028 TCCATATTAAGCATGCAACGTGAAT 59.701 36.000 21.98 6.48 0.00 2.57
204 205 7.439356 CGATACCCTGTATCCATATTAAGCATG 59.561 40.741 8.28 0.00 0.00 4.06
212 213 9.083422 CTCATATTCGATACCCTGTATCCATAT 57.917 37.037 8.28 7.71 0.00 1.78
218 219 6.378564 CACTCCTCATATTCGATACCCTGTAT 59.621 42.308 0.00 0.00 0.00 2.29
221 222 4.767409 TCACTCCTCATATTCGATACCCTG 59.233 45.833 0.00 0.00 0.00 4.45
230 231 2.223502 TGACGCGTCACTCCTCATATTC 60.224 50.000 36.40 7.88 34.14 1.75
231 232 1.749063 TGACGCGTCACTCCTCATATT 59.251 47.619 36.40 0.00 34.14 1.28
234 235 0.317160 TTTGACGCGTCACTCCTCAT 59.683 50.000 39.38 0.00 39.66 2.90
254 255 2.489329 CACATCCGCACTCCTCATTTTT 59.511 45.455 0.00 0.00 0.00 1.94
255 256 2.086869 CACATCCGCACTCCTCATTTT 58.913 47.619 0.00 0.00 0.00 1.82
256 257 1.679944 CCACATCCGCACTCCTCATTT 60.680 52.381 0.00 0.00 0.00 2.32
257 258 0.107508 CCACATCCGCACTCCTCATT 60.108 55.000 0.00 0.00 0.00 2.57
258 259 0.977627 TCCACATCCGCACTCCTCAT 60.978 55.000 0.00 0.00 0.00 2.90
259 260 1.607801 CTCCACATCCGCACTCCTCA 61.608 60.000 0.00 0.00 0.00 3.86
260 261 1.142748 CTCCACATCCGCACTCCTC 59.857 63.158 0.00 0.00 0.00 3.71
261 262 2.362369 CCTCCACATCCGCACTCCT 61.362 63.158 0.00 0.00 0.00 3.69
262 263 2.187946 CCTCCACATCCGCACTCC 59.812 66.667 0.00 0.00 0.00 3.85
263 264 1.153549 GTCCTCCACATCCGCACTC 60.154 63.158 0.00 0.00 0.00 3.51
264 265 1.267574 ATGTCCTCCACATCCGCACT 61.268 55.000 0.00 0.00 42.62 4.40
265 266 0.464036 TATGTCCTCCACATCCGCAC 59.536 55.000 0.00 0.00 42.62 5.34
266 267 1.199615 TTATGTCCTCCACATCCGCA 58.800 50.000 0.00 0.00 42.62 5.69
267 268 2.325583 TTTATGTCCTCCACATCCGC 57.674 50.000 0.00 0.00 42.62 5.54
268 269 4.450976 TCAATTTATGTCCTCCACATCCG 58.549 43.478 0.00 0.00 42.62 4.18
269 270 4.823989 CCTCAATTTATGTCCTCCACATCC 59.176 45.833 0.00 0.00 42.62 3.51
270 271 5.684704 TCCTCAATTTATGTCCTCCACATC 58.315 41.667 0.00 0.00 42.62 3.06
276 277 3.879892 GGCACTCCTCAATTTATGTCCTC 59.120 47.826 0.00 0.00 0.00 3.71
283 284 2.642311 TGACTGGGCACTCCTCAATTTA 59.358 45.455 0.00 0.00 36.20 1.40
289 290 1.028868 GCATTGACTGGGCACTCCTC 61.029 60.000 0.00 0.00 36.20 3.71
300 301 1.638388 CGCGTCCACATGCATTGACT 61.638 55.000 15.15 0.00 33.65 3.41
304 305 3.055110 TGCGCGTCCACATGCATT 61.055 55.556 8.43 0.00 33.65 3.56
305 306 3.803082 GTGCGCGTCCACATGCAT 61.803 61.111 8.43 0.00 39.85 3.96
342 343 2.441410 TCCAAGTCAACAACTGCACAA 58.559 42.857 0.00 0.00 38.58 3.33
343 344 2.121291 TCCAAGTCAACAACTGCACA 57.879 45.000 0.00 0.00 38.58 4.57
346 347 4.045636 ACAATTCCAAGTCAACAACTGC 57.954 40.909 0.00 0.00 38.58 4.40
347 348 6.475402 GGTTTACAATTCCAAGTCAACAACTG 59.525 38.462 0.00 0.00 38.58 3.16
348 349 6.569780 GGTTTACAATTCCAAGTCAACAACT 58.430 36.000 0.00 0.00 41.10 3.16
359 361 4.138290 TGCTTCTTCGGTTTACAATTCCA 58.862 39.130 0.00 0.00 0.00 3.53
370 372 1.347707 TCACAGGAATGCTTCTTCGGT 59.652 47.619 0.00 0.00 0.00 4.69
407 409 5.637809 GTCCCCTCGTATTGAAAATGAAAC 58.362 41.667 0.00 0.00 0.00 2.78
412 414 3.899052 TCGTCCCCTCGTATTGAAAAT 57.101 42.857 0.00 0.00 0.00 1.82
415 417 3.735820 CGAATTCGTCCCCTCGTATTGAA 60.736 47.826 19.67 0.00 32.74 2.69
422 424 1.518572 CACCGAATTCGTCCCCTCG 60.519 63.158 25.10 11.21 37.74 4.63
429 431 1.295423 CCAGGGTCACCGAATTCGT 59.705 57.895 25.10 11.51 43.47 3.85
431 433 0.539986 TAGCCAGGGTCACCGAATTC 59.460 55.000 0.00 0.00 43.47 2.17
494 496 7.521871 AAGAGCATTGAAAAGTCTCAAAGAT 57.478 32.000 0.00 0.00 38.75 2.40
522 524 6.369065 CCCACATTGAGAACTTGTACTACTTC 59.631 42.308 0.00 0.00 0.00 3.01
532 534 3.593442 TTGTCCCCACATTGAGAACTT 57.407 42.857 0.00 0.00 30.55 2.66
542 544 4.085733 CCTTTGATGTTATTGTCCCCACA 58.914 43.478 0.00 0.00 0.00 4.17
543 545 4.157840 GTCCTTTGATGTTATTGTCCCCAC 59.842 45.833 0.00 0.00 0.00 4.61
544 546 4.340617 GTCCTTTGATGTTATTGTCCCCA 58.659 43.478 0.00 0.00 0.00 4.96
548 550 5.856126 TCACGTCCTTTGATGTTATTGTC 57.144 39.130 0.00 0.00 38.70 3.18
549 551 6.817765 ATTCACGTCCTTTGATGTTATTGT 57.182 33.333 0.00 0.00 38.70 2.71
550 552 8.519492 AAAATTCACGTCCTTTGATGTTATTG 57.481 30.769 0.00 0.00 38.70 1.90
561 563 5.316987 AGAGGATTGAAAATTCACGTCCTT 58.683 37.500 21.21 13.18 45.34 3.36
575 577 3.170717 ACCGGTACTCAAAGAGGATTGA 58.829 45.455 4.49 0.00 37.70 2.57
580 582 2.561419 TGAGAACCGGTACTCAAAGAGG 59.439 50.000 8.00 0.00 39.68 3.69
594 596 0.322008 CACCCTGGAGCTTGAGAACC 60.322 60.000 0.00 0.00 0.00 3.62
610 612 3.683340 GGAGGTAGTGATCGTTTTTCACC 59.317 47.826 0.46 0.00 43.62 4.02
620 622 2.544694 CGCTCACATGGAGGTAGTGATC 60.545 54.545 11.63 0.00 44.22 2.92
626 628 2.384828 ACATACGCTCACATGGAGGTA 58.615 47.619 11.63 11.43 44.22 3.08
635 637 6.645415 AGCTACCATATTTTACATACGCTCAC 59.355 38.462 0.00 0.00 0.00 3.51
639 641 7.456253 CATCAGCTACCATATTTTACATACGC 58.544 38.462 0.00 0.00 0.00 4.42
640 642 7.456253 GCATCAGCTACCATATTTTACATACG 58.544 38.462 0.00 0.00 37.91 3.06
649 651 1.699634 ACCCGCATCAGCTACCATATT 59.300 47.619 0.00 0.00 39.10 1.28
660 662 2.083774 GAAGTTGAATGACCCGCATCA 58.916 47.619 0.00 0.00 35.78 3.07
661 663 1.062587 CGAAGTTGAATGACCCGCATC 59.937 52.381 0.00 0.00 35.78 3.91
665 667 1.732259 CTTCCGAAGTTGAATGACCCG 59.268 52.381 0.00 0.00 0.00 5.28
671 673 9.379791 CTATTTACTAACCTTCCGAAGTTGAAT 57.620 33.333 7.37 1.52 0.00 2.57
672 674 8.370182 ACTATTTACTAACCTTCCGAAGTTGAA 58.630 33.333 7.37 0.00 0.00 2.69
732 734 8.500773 GGAGAAGAAAAACAAATACACGATGTA 58.499 33.333 0.00 0.00 37.24 2.29
733 735 7.012894 TGGAGAAGAAAAACAAATACACGATGT 59.987 33.333 0.00 0.00 0.00 3.06
734 736 7.359595 TGGAGAAGAAAAACAAATACACGATG 58.640 34.615 0.00 0.00 0.00 3.84
735 737 7.504924 TGGAGAAGAAAAACAAATACACGAT 57.495 32.000 0.00 0.00 0.00 3.73
736 738 6.928979 TGGAGAAGAAAAACAAATACACGA 57.071 33.333 0.00 0.00 0.00 4.35
737 739 7.979115 TTTGGAGAAGAAAAACAAATACACG 57.021 32.000 0.00 0.00 0.00 4.49
772 777 3.583526 ACTCCCTTTCCTCCAAAGTAGAC 59.416 47.826 0.00 0.00 40.15 2.59
777 782 4.041691 TCAAGTACTCCCTTTCCTCCAAAG 59.958 45.833 0.00 0.00 41.30 2.77
810 815 5.404466 AGACATATGATTGAGGCTAGAGC 57.596 43.478 10.38 0.00 41.14 4.09
817 822 5.128205 TCTTGCCAAGACATATGATTGAGG 58.872 41.667 20.02 11.93 31.20 3.86
830 836 4.766373 TCACTTGCAAATATCTTGCCAAGA 59.234 37.500 10.01 10.01 44.32 3.02
833 839 3.119884 CGTCACTTGCAAATATCTTGCCA 60.120 43.478 15.43 7.67 44.32 4.92
835 841 4.093408 TCTCGTCACTTGCAAATATCTTGC 59.907 41.667 0.00 12.76 45.11 4.01
837 843 5.237815 TGTCTCGTCACTTGCAAATATCTT 58.762 37.500 0.00 0.00 0.00 2.40
849 855 1.581954 CGGCTTCTGTCTCGTCACT 59.418 57.895 0.00 0.00 0.00 3.41
853 859 3.671411 ACGCGGCTTCTGTCTCGT 61.671 61.111 12.47 0.00 0.00 4.18
854 860 3.175240 CACGCGGCTTCTGTCTCG 61.175 66.667 12.47 0.00 0.00 4.04
855 861 1.803519 CTCACGCGGCTTCTGTCTC 60.804 63.158 12.47 0.00 0.00 3.36
856 862 2.259818 CTCACGCGGCTTCTGTCT 59.740 61.111 12.47 0.00 0.00 3.41
857 863 2.049063 ACTCACGCGGCTTCTGTC 60.049 61.111 12.47 0.00 0.00 3.51
858 864 2.049063 GACTCACGCGGCTTCTGT 60.049 61.111 12.47 0.00 0.00 3.41
860 866 2.569134 GAGACTCACGCGGCTTCT 59.431 61.111 12.47 6.25 0.00 2.85
862 868 4.070552 GGGAGACTCACGCGGCTT 62.071 66.667 12.47 0.00 0.00 4.35
864 870 4.148825 ATGGGAGACTCACGCGGC 62.149 66.667 12.47 0.00 0.00 6.53
867 873 1.439644 GGAGATGGGAGACTCACGC 59.560 63.158 4.53 0.00 35.17 5.34
868 874 0.396417 AGGGAGATGGGAGACTCACG 60.396 60.000 4.53 0.00 40.92 4.35
869 875 1.342474 TGAGGGAGATGGGAGACTCAC 60.342 57.143 4.53 0.07 36.88 3.51
871 877 1.408969 GTGAGGGAGATGGGAGACTC 58.591 60.000 0.00 0.00 0.00 3.36
872 878 0.396417 CGTGAGGGAGATGGGAGACT 60.396 60.000 0.00 0.00 0.00 3.24
873 879 0.684805 ACGTGAGGGAGATGGGAGAC 60.685 60.000 0.00 0.00 0.00 3.36
874 880 0.395862 GACGTGAGGGAGATGGGAGA 60.396 60.000 0.00 0.00 0.00 3.71
876 882 0.041238 AAGACGTGAGGGAGATGGGA 59.959 55.000 0.00 0.00 0.00 4.37
880 897 6.793505 AGTATTTAAAGACGTGAGGGAGAT 57.206 37.500 7.29 0.00 0.00 2.75
881 898 6.014840 ACAAGTATTTAAAGACGTGAGGGAGA 60.015 38.462 27.75 0.00 34.13 3.71
887 904 4.386652 GGCGACAAGTATTTAAAGACGTGA 59.613 41.667 27.75 0.00 34.13 4.35
906 923 1.152652 GGGAGATGAGAGGAGGCGA 60.153 63.158 0.00 0.00 0.00 5.54
916 933 3.342377 TTTATGTGCGTTGGGAGATGA 57.658 42.857 0.00 0.00 0.00 2.92
954 971 1.040339 AGAACAAAGCAAACGGGGCA 61.040 50.000 0.00 0.00 0.00 5.36
983 1000 2.121538 ATGGTCGAGCGAGCTAGCA 61.122 57.895 21.36 3.77 42.49 3.49
985 1002 1.007964 CCATGGTCGAGCGAGCTAG 60.008 63.158 20.60 13.36 42.49 3.42
1013 1608 3.654143 TGCTGGCTGGGATGCTGT 61.654 61.111 0.00 0.00 0.00 4.40
1028 1623 1.817099 CTGATCTCGCCCAAGGTGC 60.817 63.158 0.00 0.00 32.51 5.01
1234 1829 2.646175 GCAGCTCCTCGGTGTGGTA 61.646 63.158 0.00 0.00 42.99 3.25
1347 1942 3.376078 GTACGACCCCACTCGGCA 61.376 66.667 0.00 0.00 38.02 5.69
1449 2044 0.977627 AGACATCATGGCGGAGACCA 60.978 55.000 0.00 0.00 45.82 4.02
1610 2205 2.723231 TCGAAGGTGTCCGACTCAA 58.277 52.632 0.00 0.00 0.00 3.02
1615 2210 2.567497 GGGTGTCGAAGGTGTCCGA 61.567 63.158 0.00 0.00 0.00 4.55
1673 2268 3.443045 GGTCAGCCGCCACAATGG 61.443 66.667 0.00 0.00 41.55 3.16
1710 2305 0.039256 CCGCAACCATGTTGAACAGG 60.039 55.000 10.94 3.13 0.00 4.00
1764 2359 2.446848 CCCGAGATGCATCCTGGGT 61.447 63.158 31.91 13.96 37.12 4.51
1769 2364 1.070445 CCACTCCCGAGATGCATCC 59.930 63.158 23.06 13.29 0.00 3.51
1776 2371 1.758514 GATGCCTCCACTCCCGAGA 60.759 63.158 0.00 0.00 0.00 4.04
1788 2383 2.359900 GAAATGTTCCAGTCGATGCCT 58.640 47.619 0.00 0.00 0.00 4.75
1809 2404 0.391263 CCAGCCTTGGTAGTCCGTTC 60.391 60.000 0.00 0.00 39.79 3.95
2001 2599 2.822561 CTCTCTGACCACAGTTCTGCTA 59.177 50.000 0.00 0.00 43.81 3.49
2016 2614 3.254060 CAACATGTTCCCGTACTCTCTG 58.746 50.000 8.48 0.00 0.00 3.35
2086 2684 0.034670 GCTCCAGCACCTTCAGGATT 60.035 55.000 0.00 0.00 41.59 3.01
2114 2712 2.058593 CCCCCACTCTTCATTAAGGC 57.941 55.000 0.00 0.00 33.22 4.35
2196 2794 5.195185 TCGTTCTTTTTCTTGGGTTTACCT 58.805 37.500 0.00 0.00 41.11 3.08
2202 2800 4.808895 GCATTTTCGTTCTTTTTCTTGGGT 59.191 37.500 0.00 0.00 0.00 4.51
2214 2812 2.063156 TGTGCCATGCATTTTCGTTC 57.937 45.000 0.00 0.00 41.91 3.95
2216 2814 2.491298 TGTATGTGCCATGCATTTTCGT 59.509 40.909 0.00 0.00 41.91 3.85
2218 2816 4.142315 ACTCTGTATGTGCCATGCATTTTC 60.142 41.667 0.00 0.00 41.91 2.29
2302 2925 8.889445 TGGATATGGGAATATCAAAGTGACATA 58.111 33.333 7.75 0.00 35.71 2.29
2305 2928 9.911788 ATATGGATATGGGAATATCAAAGTGAC 57.088 33.333 7.75 0.00 35.71 3.67
2310 2933 9.685276 GTGACATATGGATATGGGAATATCAAA 57.315 33.333 7.80 0.00 43.38 2.69
2311 2934 9.061252 AGTGACATATGGATATGGGAATATCAA 57.939 33.333 7.80 0.00 43.38 2.57
2312 2935 8.628368 AGTGACATATGGATATGGGAATATCA 57.372 34.615 7.80 2.63 43.38 2.15
2313 2936 9.911788 AAAGTGACATATGGATATGGGAATATC 57.088 33.333 7.80 0.00 43.38 1.63
2314 2937 9.690913 CAAAGTGACATATGGATATGGGAATAT 57.309 33.333 7.80 0.00 43.38 1.28
2315 2938 8.889445 TCAAAGTGACATATGGATATGGGAATA 58.111 33.333 7.80 0.00 43.38 1.75
2316 2939 7.758609 TCAAAGTGACATATGGATATGGGAAT 58.241 34.615 7.80 0.00 43.38 3.01
2317 2940 7.147958 TCAAAGTGACATATGGATATGGGAA 57.852 36.000 7.80 0.00 43.38 3.97
2318 2941 6.762077 TCAAAGTGACATATGGATATGGGA 57.238 37.500 7.80 0.00 43.38 4.37
2319 2942 9.690913 AATATCAAAGTGACATATGGATATGGG 57.309 33.333 7.80 0.00 43.38 4.00
2323 2946 9.435688 CGGAAATATCAAAGTGACATATGGATA 57.564 33.333 7.80 3.20 0.00 2.59
2324 2947 7.939039 ACGGAAATATCAAAGTGACATATGGAT 59.061 33.333 7.80 0.98 0.00 3.41
2325 2948 7.279615 ACGGAAATATCAAAGTGACATATGGA 58.720 34.615 7.80 0.00 0.00 3.41
2326 2949 7.442364 AGACGGAAATATCAAAGTGACATATGG 59.558 37.037 7.80 0.00 0.00 2.74
2327 2950 8.370493 AGACGGAAATATCAAAGTGACATATG 57.630 34.615 0.00 0.00 0.00 1.78
2349 2972 2.984471 TCACATCGCTTACGTGAAAGAC 59.016 45.455 0.00 0.00 41.18 3.01
2353 2976 2.745102 TGTTCACATCGCTTACGTGAA 58.255 42.857 0.00 0.00 44.95 3.18
2358 2981 3.424829 CCACACATGTTCACATCGCTTAC 60.425 47.826 0.00 0.00 33.61 2.34
2388 3016 8.372459 TCACTCTTACACAACTTACAATACCAT 58.628 33.333 0.00 0.00 0.00 3.55
2393 3021 8.732746 AAACTCACTCTTACACAACTTACAAT 57.267 30.769 0.00 0.00 0.00 2.71
2467 3096 9.338622 CACAGTACGGATATCATATACTCCATA 57.661 37.037 4.83 0.00 0.00 2.74
2468 3097 7.834681 ACACAGTACGGATATCATATACTCCAT 59.165 37.037 4.83 0.00 0.00 3.41
2469 3098 7.120726 CACACAGTACGGATATCATATACTCCA 59.879 40.741 4.83 0.00 0.00 3.86
2470 3099 7.415318 CCACACAGTACGGATATCATATACTCC 60.415 44.444 4.83 0.00 0.00 3.85
2471 3100 7.336176 TCCACACAGTACGGATATCATATACTC 59.664 40.741 4.83 0.00 0.00 2.59
2472 3101 7.173032 TCCACACAGTACGGATATCATATACT 58.827 38.462 4.83 6.07 0.00 2.12
2473 3102 7.387119 TCCACACAGTACGGATATCATATAC 57.613 40.000 4.83 3.90 0.00 1.47
2474 3103 8.589701 AATCCACACAGTACGGATATCATATA 57.410 34.615 4.83 0.00 38.62 0.86
2485 3114 8.019669 GGTATATACAGTAATCCACACAGTACG 58.980 40.741 14.70 0.00 0.00 3.67
2489 3118 7.952671 ACAGGTATATACAGTAATCCACACAG 58.047 38.462 14.70 0.00 0.00 3.66
2503 3132 9.411189 TCCCCAAATTTAACAACAGGTATATAC 57.589 33.333 4.14 4.14 0.00 1.47
2504 3133 9.411189 GTCCCCAAATTTAACAACAGGTATATA 57.589 33.333 0.00 0.00 0.00 0.86
2510 3139 3.859252 GCGTCCCCAAATTTAACAACAGG 60.859 47.826 0.00 0.00 0.00 4.00
2511 3140 3.005367 AGCGTCCCCAAATTTAACAACAG 59.995 43.478 0.00 0.00 0.00 3.16
2519 3148 1.966762 CAGCAGCGTCCCCAAATTT 59.033 52.632 0.00 0.00 0.00 1.82
2567 3196 5.615925 AATTCAGGTACTAGTTAGGCCTG 57.384 43.478 17.99 20.27 44.55 4.85
2582 3211 8.611654 AATTTTGAATTCCAGTGAAATTCAGG 57.388 30.769 15.88 0.00 33.57 3.86
2618 3247 7.158697 TGTACTTCCTCTTTCGATGAAATCAA 58.841 34.615 0.00 0.00 45.97 2.57
2629 3258 5.668558 TTTTCGCTTGTACTTCCTCTTTC 57.331 39.130 0.00 0.00 0.00 2.62
2630 3259 5.763204 TCATTTTCGCTTGTACTTCCTCTTT 59.237 36.000 0.00 0.00 0.00 2.52
2632 3261 4.894784 TCATTTTCGCTTGTACTTCCTCT 58.105 39.130 0.00 0.00 0.00 3.69
2635 3264 5.572896 CCATTTCATTTTCGCTTGTACTTCC 59.427 40.000 0.00 0.00 0.00 3.46
2650 3279 5.597182 AGAGATATGCTTGTGCCATTTCATT 59.403 36.000 0.00 0.00 38.71 2.57
2654 3283 3.887716 GGAGAGATATGCTTGTGCCATTT 59.112 43.478 0.00 0.00 38.71 2.32
2658 3287 2.103771 TGAGGAGAGATATGCTTGTGCC 59.896 50.000 0.00 0.00 38.71 5.01
2671 3300 8.231692 TGTCTGACTATAAAAGATGAGGAGAG 57.768 38.462 9.51 0.00 0.00 3.20
2711 3340 2.545952 CGCGGATTCAGGTAGCAATACT 60.546 50.000 0.00 0.00 0.00 2.12
2716 3345 1.141019 GTCGCGGATTCAGGTAGCA 59.859 57.895 6.13 0.00 0.00 3.49
2808 3437 9.631257 AAGAATTTCTTGTCAATGGGAATTTTT 57.369 25.926 10.82 0.00 34.98 1.94
2809 3438 9.631257 AAAGAATTTCTTGTCAATGGGAATTTT 57.369 25.926 12.27 0.00 36.71 1.82
2810 3439 9.059260 CAAAGAATTTCTTGTCAATGGGAATTT 57.941 29.630 12.27 0.00 36.71 1.82
2811 3440 8.212995 ACAAAGAATTTCTTGTCAATGGGAATT 58.787 29.630 12.27 0.00 36.71 2.17
2812 3441 7.738847 ACAAAGAATTTCTTGTCAATGGGAAT 58.261 30.769 12.27 0.00 36.71 3.01
2814 3443 6.729690 ACAAAGAATTTCTTGTCAATGGGA 57.270 33.333 12.27 0.00 36.71 4.37
2815 3444 6.985645 TCAACAAAGAATTTCTTGTCAATGGG 59.014 34.615 12.27 4.53 35.77 4.00
2826 3455 3.730715 CACGGCACTCAACAAAGAATTTC 59.269 43.478 0.00 0.00 35.03 2.17
2827 3456 3.380004 TCACGGCACTCAACAAAGAATTT 59.620 39.130 0.00 0.00 40.26 1.82
3060 3695 9.998106 ACAATGTTTCTATGTACTTACAGTTCT 57.002 29.630 0.00 0.00 39.92 3.01
3081 3716 9.108284 AGACTTTTCAACCCAATTTTAACAATG 57.892 29.630 0.00 0.00 0.00 2.82
3119 3754 7.005296 GGGATAAGGTCTAGACATAGTCTCAA 58.995 42.308 23.91 4.77 42.40 3.02
3161 3796 2.284150 CGTCAACGCCATCGATATTTGT 59.716 45.455 0.00 0.00 39.41 2.83
3170 3805 1.079405 TTCCCTCGTCAACGCCATC 60.079 57.895 0.00 0.00 39.60 3.51
3171 3806 1.375523 GTTCCCTCGTCAACGCCAT 60.376 57.895 0.00 0.00 39.60 4.40
3172 3807 2.029964 GTTCCCTCGTCAACGCCA 59.970 61.111 0.00 0.00 39.60 5.69
3173 3808 2.741211 GGTTCCCTCGTCAACGCC 60.741 66.667 0.00 0.00 39.60 5.68
3174 3809 3.110178 CGGTTCCCTCGTCAACGC 61.110 66.667 0.00 0.00 39.60 4.84
3175 3810 3.110178 GCGGTTCCCTCGTCAACG 61.110 66.667 0.00 0.00 41.45 4.10
3176 3811 1.566018 CTTGCGGTTCCCTCGTCAAC 61.566 60.000 0.00 0.00 0.00 3.18
3177 3812 1.301401 CTTGCGGTTCCCTCGTCAA 60.301 57.895 0.00 0.00 0.00 3.18
3178 3813 2.342279 CTTGCGGTTCCCTCGTCA 59.658 61.111 0.00 0.00 0.00 4.35
3179 3814 3.119096 GCTTGCGGTTCCCTCGTC 61.119 66.667 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.