Multiple sequence alignment - TraesCS1B01G217000

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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 TraesCS1B01G217000 chr1B 100.000 6468 0 0 1 6468 393081197 393074730 0.000000e+00 11945
1 TraesCS1B01G217000 chr1A 95.848 3589 82 25 2125 5691 364229528 364225985 0.000000e+00 5740
2 TraesCS1B01G217000 chr1A 88.709 2037 115 46 1 1990 364231486 364229518 0.000000e+00 2381
3 TraesCS1B01G217000 chr1A 91.603 131 6 1 5879 6004 364225944 364225814 6.670000e-40 176
4 TraesCS1B01G217000 chr1D 93.681 2342 77 26 4157 6468 292081269 292078969 0.000000e+00 3439
5 TraesCS1B01G217000 chr1D 97.013 2042 26 10 2125 4161 292083312 292081301 0.000000e+00 3400
6 TraesCS1B01G217000 chr1D 90.797 2021 114 35 1 1990 292085281 292083302 0.000000e+00 2636
7 TraesCS1B01G217000 chr1D 91.667 432 33 3 6040 6468 285624178 285623747 4.320000e-166 595
8 TraesCS1B01G217000 chr1D 91.822 428 29 6 6040 6462 319444549 319444123 5.580000e-165 592
9 TraesCS1B01G217000 chr1D 91.415 431 34 3 6040 6467 250352794 250352364 7.220000e-164 588
10 TraesCS1B01G217000 chr1D 91.224 433 34 4 6040 6468 258019043 258018611 2.600000e-163 586
11 TraesCS1B01G217000 chr1D 89.764 127 11 2 1987 2112 409046170 409046295 1.870000e-35 161
12 TraesCS1B01G217000 chr4D 91.494 435 34 3 6037 6468 305111547 305111981 4.320000e-166 595
13 TraesCS1B01G217000 chr4D 91.667 432 33 3 6040 6468 469626030 469625599 4.320000e-166 595
14 TraesCS1B01G217000 chr4D 90.076 131 11 2 1976 2106 105237935 105237807 1.120000e-37 169
15 TraesCS1B01G217000 chr3D 91.667 432 33 3 6040 6468 516679562 516679131 4.320000e-166 595
16 TraesCS1B01G217000 chr3D 93.220 118 8 0 1989 2106 194109952 194110069 2.400000e-39 174
17 TraesCS1B01G217000 chr2D 91.647 431 32 3 6040 6466 167886459 167886029 1.550000e-165 593
18 TraesCS1B01G217000 chr4B 93.600 125 7 1 1990 2114 527282635 527282512 1.110000e-42 185
19 TraesCS1B01G217000 chr7A 93.220 118 8 0 1989 2106 17475387 17475504 2.400000e-39 174
20 TraesCS1B01G217000 chr6D 91.270 126 10 1 1984 2109 429436349 429436225 3.100000e-38 171
21 TraesCS1B01G217000 chr6D 92.373 118 9 0 1990 2107 452541856 452541973 1.120000e-37 169
22 TraesCS1B01G217000 chr5D 92.308 117 9 0 1990 2106 519214290 519214174 4.010000e-37 167
23 TraesCS1B01G217000 chr5D 90.323 124 12 0 1984 2107 439217751 439217628 5.190000e-36 163


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 TraesCS1B01G217000 chr1B 393074730 393081197 6467 True 11945.000000 11945 100.000000 1 6468 1 chr1B.!!$R1 6467
1 TraesCS1B01G217000 chr1A 364225814 364231486 5672 True 2765.666667 5740 92.053333 1 6004 3 chr1A.!!$R1 6003
2 TraesCS1B01G217000 chr1D 292078969 292085281 6312 True 3158.333333 3439 93.830333 1 6468 3 chr1D.!!$R5 6467

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
892 950 0.240945 CACGGCCGATTTGCTTCTTT 59.759 50.0 35.90 0.0 0.00 2.52 F
1292 1353 1.006832 GTGCACACCACACGGATATC 58.993 55.0 13.17 0.0 44.06 1.63 F
2013 2076 0.030369 CCTCCGTCCGGAAATACTCG 59.970 60.0 5.23 3.9 44.66 4.18 F
2109 2172 0.258194 ACGGACGGAGGGAGTATCTT 59.742 55.0 0.00 0.0 33.73 2.40 F
3403 3481 0.389025 CAAACCCCTGGAGCAACAAC 59.611 55.0 0.00 0.0 0.00 3.32 F
4827 4952 0.110486 ACACCTTGATTCCACCGCTT 59.890 50.0 0.00 0.0 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2057 0.030369 CGAGTATTTCCGGACGGAGG 59.970 60.000 13.64 0.0 46.06 4.30 R
2764 2842 1.613630 AGGGCCACTGGTAGGAGTG 60.614 63.158 6.18 0.0 42.68 3.51 R
3487 3565 1.019673 ACAGGCAATTATCAGCAGCG 58.980 50.000 0.00 0.0 0.00 5.18 R
4019 4097 3.058983 TGTTAACTTGCATCGCAACAGAG 60.059 43.478 7.22 0.0 43.99 3.35 R
5383 5510 0.617820 ACAGGGAGATTACGGGCAGT 60.618 55.000 0.00 0.0 0.00 4.40 R
6253 6404 0.759959 TCTAAAACCCACCTGCGTGA 59.240 50.000 0.00 0.0 43.14 4.35 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
55 57 3.345508 AGAAAGACGGATTAACACCCC 57.654 47.619 0.00 0.00 0.00 4.95
63 65 1.064537 GGATTAACACCCCGCCCTTTA 60.065 52.381 0.00 0.00 0.00 1.85
81 83 2.672961 TACACATCCCGCTTCAGAAG 57.327 50.000 5.72 5.72 0.00 2.85
154 164 1.679153 CCAACACAACCTAAAACCGCT 59.321 47.619 0.00 0.00 0.00 5.52
168 178 5.854010 AAAACCGCTAGATCTGATGACTA 57.146 39.130 5.18 0.00 0.00 2.59
179 189 6.925211 AGATCTGATGACTAACGAGACAAAA 58.075 36.000 0.00 0.00 31.07 2.44
180 190 7.032580 AGATCTGATGACTAACGAGACAAAAG 58.967 38.462 0.00 0.00 31.07 2.27
181 191 5.470368 TCTGATGACTAACGAGACAAAAGG 58.530 41.667 0.00 0.00 31.07 3.11
198 208 4.748144 GGGCCACCTGCTTCCCAG 62.748 72.222 4.39 0.00 40.92 4.45
211 229 2.910199 CTTCCCAGCATCTTCGATTGA 58.090 47.619 0.00 0.00 0.00 2.57
215 233 2.223112 CCCAGCATCTTCGATTGAAACG 60.223 50.000 0.00 0.00 32.66 3.60
221 239 1.719246 TCTTCGATTGAAACGCTGTCG 59.281 47.619 0.00 0.00 42.43 4.35
222 240 0.787787 TTCGATTGAAACGCTGTCGG 59.212 50.000 0.00 0.00 40.69 4.79
239 257 0.251608 CGGGGTGGGGAAGAAACATT 60.252 55.000 0.00 0.00 0.00 2.71
250 268 5.817296 GGGGAAGAAACATTGCCAAATTATC 59.183 40.000 0.00 0.00 42.13 1.75
267 297 4.201679 CCTGACGCGCCACCGATA 62.202 66.667 5.73 0.00 36.29 2.92
269 299 3.693382 CTGACGCGCCACCGATACA 62.693 63.158 5.73 0.00 36.29 2.29
270 300 2.507547 GACGCGCCACCGATACAA 60.508 61.111 5.73 0.00 36.29 2.41
298 340 1.172180 TGAAGAACAAAGCCCAGCCG 61.172 55.000 0.00 0.00 0.00 5.52
308 350 3.003113 GCCCAGCCGAACTACTCGT 62.003 63.158 0.00 0.00 46.65 4.18
348 391 3.592814 CATCGCCTCCCGTCGCTA 61.593 66.667 0.00 0.00 38.35 4.26
372 416 1.000496 CGATTAACGGAGGGTAGAGGC 60.000 57.143 0.00 0.00 38.46 4.70
406 450 0.625849 AACGAAGATGGGGGCAGAAT 59.374 50.000 0.00 0.00 0.00 2.40
452 496 0.902531 GGGATGAGAAGGGAACGTGA 59.097 55.000 0.00 0.00 0.00 4.35
467 511 1.289109 CGTGAGGCGAAACGGTTCAT 61.289 55.000 14.64 0.00 44.77 2.57
494 538 1.123077 CGGTGAGGATTCTGATGGGA 58.877 55.000 0.00 0.00 0.00 4.37
500 544 3.181447 TGAGGATTCTGATGGGAATGAGC 60.181 47.826 0.00 0.00 36.24 4.26
508 552 4.141344 TCTGATGGGAATGAGCATGAATGA 60.141 41.667 0.00 0.00 0.00 2.57
520 564 1.669265 CATGAATGAGTGCGATGCTGT 59.331 47.619 0.00 0.00 0.00 4.40
523 567 1.326852 GAATGAGTGCGATGCTGTCAG 59.673 52.381 0.00 0.00 0.00 3.51
554 598 3.957497 ACACAGTGATTTTGGCCTTGTAA 59.043 39.130 7.81 0.00 0.00 2.41
555 599 4.588528 ACACAGTGATTTTGGCCTTGTAAT 59.411 37.500 7.81 0.00 0.00 1.89
556 600 5.772672 ACACAGTGATTTTGGCCTTGTAATA 59.227 36.000 7.81 0.00 0.00 0.98
564 608 5.450818 TTTGGCCTTGTAATATCACCTCT 57.549 39.130 3.32 0.00 0.00 3.69
577 621 2.832838 TCACCTCTGGGAGCAAAGATA 58.167 47.619 0.00 0.00 36.25 1.98
578 622 3.181329 TCACCTCTGGGAGCAAAGATAA 58.819 45.455 0.00 0.00 36.25 1.75
579 623 3.782523 TCACCTCTGGGAGCAAAGATAAT 59.217 43.478 0.00 0.00 36.25 1.28
580 624 4.228210 TCACCTCTGGGAGCAAAGATAATT 59.772 41.667 0.00 0.00 36.25 1.40
581 625 4.578105 CACCTCTGGGAGCAAAGATAATTC 59.422 45.833 0.00 0.00 36.25 2.17
582 626 4.140536 CCTCTGGGAGCAAAGATAATTCC 58.859 47.826 0.00 0.00 33.58 3.01
583 627 4.140536 CTCTGGGAGCAAAGATAATTCCC 58.859 47.826 0.89 0.89 46.27 3.97
584 628 3.117512 TCTGGGAGCAAAGATAATTCCCC 60.118 47.826 5.47 0.00 45.64 4.81
585 629 2.858768 TGGGAGCAAAGATAATTCCCCT 59.141 45.455 5.47 0.00 45.64 4.79
586 630 4.051478 TGGGAGCAAAGATAATTCCCCTA 58.949 43.478 5.47 0.00 45.64 3.53
587 631 4.104738 TGGGAGCAAAGATAATTCCCCTAG 59.895 45.833 5.47 0.00 45.64 3.02
588 632 4.351111 GGGAGCAAAGATAATTCCCCTAGA 59.649 45.833 0.00 0.00 41.36 2.43
589 633 5.309638 GGAGCAAAGATAATTCCCCTAGAC 58.690 45.833 0.00 0.00 0.00 2.59
590 634 5.072464 GGAGCAAAGATAATTCCCCTAGACT 59.928 44.000 0.00 0.00 0.00 3.24
591 635 6.270231 GGAGCAAAGATAATTCCCCTAGACTA 59.730 42.308 0.00 0.00 0.00 2.59
600 644 9.847224 GATAATTCCCCTAGACTAACAATCAAA 57.153 33.333 0.00 0.00 0.00 2.69
603 647 4.081309 TCCCCTAGACTAACAATCAAACCG 60.081 45.833 0.00 0.00 0.00 4.44
652 699 0.726827 TTGAGATTCGCACAATCCGC 59.273 50.000 2.43 0.00 0.00 5.54
654 701 0.811616 GAGATTCGCACAATCCGCCT 60.812 55.000 2.43 0.00 0.00 5.52
670 717 1.534729 GCCTGAAAATTCCACGGACT 58.465 50.000 0.00 0.00 0.00 3.85
723 770 1.139095 CCCCTGACTCGAACGCTAC 59.861 63.158 0.00 0.00 0.00 3.58
789 847 0.457853 CACCCGTATCACACCTCACG 60.458 60.000 0.00 0.00 0.00 4.35
790 848 4.806571 CCGTATCACACCTCACGG 57.193 61.111 0.00 0.00 46.85 4.94
868 926 0.464452 CTCCGCCGTTAAATCCCTCT 59.536 55.000 0.00 0.00 0.00 3.69
892 950 0.240945 CACGGCCGATTTGCTTCTTT 59.759 50.000 35.90 0.00 0.00 2.52
989 1050 2.787249 CAGAACCCAATCGCAGCG 59.213 61.111 9.06 9.06 0.00 5.18
1141 1202 2.116125 AAGTTCACCCTGCAGGCC 59.884 61.111 28.39 11.42 40.58 5.19
1291 1352 3.153024 GTGCACACCACACGGATAT 57.847 52.632 13.17 0.00 44.06 1.63
1292 1353 1.006832 GTGCACACCACACGGATATC 58.993 55.000 13.17 0.00 44.06 1.63
1325 1386 2.593436 CGGTTTGGCTTCGGTGGT 60.593 61.111 0.00 0.00 0.00 4.16
1326 1387 1.301874 CGGTTTGGCTTCGGTGGTA 60.302 57.895 0.00 0.00 0.00 3.25
1470 1532 1.308998 GATTGGTTGATGCGGGTAGG 58.691 55.000 0.00 0.00 0.00 3.18
1518 1580 5.527582 GGATACCGTCAGCATAGATGTTTTT 59.472 40.000 0.00 0.00 0.00 1.94
1547 1610 5.426504 CATAGAAGATGGTGAAGCTGAAGT 58.573 41.667 0.00 0.00 0.00 3.01
1565 1628 1.269998 AGTAAGCTTCTCTTGTCGCGT 59.730 47.619 0.00 0.00 36.25 6.01
1593 1656 4.932268 TTTAATTCCAAGCGTTACGGAG 57.068 40.909 6.94 0.00 0.00 4.63
1646 1709 7.928167 TCATTACATAGCTACAGGTGAAATCTG 59.072 37.037 0.00 0.00 38.16 2.90
1846 1909 4.819105 TGTTACTCTGGGGAAGTATGTG 57.181 45.455 0.00 0.00 0.00 3.21
1853 1916 5.946377 ACTCTGGGGAAGTATGTGAAATTTC 59.054 40.000 11.41 11.41 0.00 2.17
1907 1970 3.660865 TCGTAAACTGAGAAAGCCTTCC 58.339 45.455 0.00 0.00 31.28 3.46
1999 2062 9.603921 TTATTTTACAAAATAGTACTCCCTCCG 57.396 33.333 0.00 0.00 40.70 4.63
2000 2063 6.610075 TTTACAAAATAGTACTCCCTCCGT 57.390 37.500 0.00 0.00 0.00 4.69
2001 2064 4.732672 ACAAAATAGTACTCCCTCCGTC 57.267 45.455 0.00 0.00 0.00 4.79
2002 2065 3.450096 ACAAAATAGTACTCCCTCCGTCC 59.550 47.826 0.00 0.00 0.00 4.79
2003 2066 1.978454 AATAGTACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
2004 2067 0.110104 ATAGTACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
2005 2068 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
2006 2069 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2007 2070 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2008 2071 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2009 2072 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2010 2073 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2011 2074 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2012 2075 0.388294 CCCTCCGTCCGGAAATACTC 59.612 60.000 5.23 0.00 44.66 2.59
2013 2076 0.030369 CCTCCGTCCGGAAATACTCG 59.970 60.000 5.23 3.90 44.66 4.18
2014 2077 0.737219 CTCCGTCCGGAAATACTCGT 59.263 55.000 5.23 0.00 44.66 4.18
2015 2078 0.734889 TCCGTCCGGAAATACTCGTC 59.265 55.000 5.23 0.00 42.05 4.20
2016 2079 0.590732 CCGTCCGGAAATACTCGTCG 60.591 60.000 5.23 1.25 37.50 5.12
2017 2080 0.590732 CGTCCGGAAATACTCGTCGG 60.591 60.000 5.23 0.00 41.80 4.79
2018 2081 0.734889 GTCCGGAAATACTCGTCGGA 59.265 55.000 5.23 0.00 46.06 4.55
2019 2082 1.019673 TCCGGAAATACTCGTCGGAG 58.980 55.000 0.00 0.00 43.84 4.63
2020 2083 1.019673 CCGGAAATACTCGTCGGAGA 58.980 55.000 0.00 0.00 43.27 3.71
2021 2084 1.402968 CCGGAAATACTCGTCGGAGAA 59.597 52.381 0.00 0.00 43.27 2.87
2022 2085 2.159338 CCGGAAATACTCGTCGGAGAAA 60.159 50.000 0.00 0.00 43.27 2.52
2023 2086 3.490419 CCGGAAATACTCGTCGGAGAAAT 60.490 47.826 0.00 0.00 43.27 2.17
2024 2087 4.261322 CCGGAAATACTCGTCGGAGAAATA 60.261 45.833 0.00 0.00 43.27 1.40
2025 2088 5.276270 CGGAAATACTCGTCGGAGAAATAA 58.724 41.667 0.00 0.00 43.27 1.40
2026 2089 5.745294 CGGAAATACTCGTCGGAGAAATAAA 59.255 40.000 0.00 0.00 43.27 1.40
2027 2090 6.420008 CGGAAATACTCGTCGGAGAAATAAAT 59.580 38.462 0.00 0.00 43.27 1.40
2028 2091 7.564988 GGAAATACTCGTCGGAGAAATAAATG 58.435 38.462 0.00 0.00 43.27 2.32
2029 2092 7.224167 GGAAATACTCGTCGGAGAAATAAATGT 59.776 37.037 0.00 0.00 43.27 2.71
2030 2093 9.241317 GAAATACTCGTCGGAGAAATAAATGTA 57.759 33.333 0.00 0.00 43.27 2.29
2031 2094 9.760077 AAATACTCGTCGGAGAAATAAATGTAT 57.240 29.630 0.00 0.00 43.27 2.29
2032 2095 8.967552 ATACTCGTCGGAGAAATAAATGTATC 57.032 34.615 0.00 0.00 43.27 2.24
2033 2096 7.040473 ACTCGTCGGAGAAATAAATGTATCT 57.960 36.000 0.00 0.00 43.27 1.98
2034 2097 8.162878 ACTCGTCGGAGAAATAAATGTATCTA 57.837 34.615 0.00 0.00 43.27 1.98
2035 2098 8.291032 ACTCGTCGGAGAAATAAATGTATCTAG 58.709 37.037 0.00 0.00 43.27 2.43
2036 2099 8.387190 TCGTCGGAGAAATAAATGTATCTAGA 57.613 34.615 0.00 0.00 39.69 2.43
2037 2100 8.288208 TCGTCGGAGAAATAAATGTATCTAGAC 58.712 37.037 0.00 0.00 39.69 2.59
2038 2101 7.268659 CGTCGGAGAAATAAATGTATCTAGACG 59.731 40.741 13.55 13.55 41.75 4.18
2039 2102 8.074972 GTCGGAGAAATAAATGTATCTAGACGT 58.925 37.037 0.00 0.00 39.69 4.34
2040 2103 9.276590 TCGGAGAAATAAATGTATCTAGACGTA 57.723 33.333 0.00 0.00 0.00 3.57
2077 2140 8.355169 AGATACATCCATTTTCATTCATTTCCG 58.645 33.333 0.00 0.00 0.00 4.30
2078 2141 5.111293 ACATCCATTTTCATTCATTTCCGC 58.889 37.500 0.00 0.00 0.00 5.54
2079 2142 3.768406 TCCATTTTCATTCATTTCCGCG 58.232 40.909 0.00 0.00 0.00 6.46
2080 2143 3.441922 TCCATTTTCATTCATTTCCGCGA 59.558 39.130 8.23 0.00 0.00 5.87
2081 2144 3.547468 CCATTTTCATTCATTTCCGCGAC 59.453 43.478 8.23 0.00 0.00 5.19
2082 2145 3.906014 TTTTCATTCATTTCCGCGACA 57.094 38.095 8.23 0.00 0.00 4.35
2083 2146 3.906014 TTTCATTCATTTCCGCGACAA 57.094 38.095 8.23 0.00 0.00 3.18
2084 2147 3.469899 TTCATTCATTTCCGCGACAAG 57.530 42.857 8.23 0.00 0.00 3.16
2085 2148 2.422597 TCATTCATTTCCGCGACAAGT 58.577 42.857 8.23 0.00 0.00 3.16
2086 2149 3.591023 TCATTCATTTCCGCGACAAGTA 58.409 40.909 8.23 0.00 0.00 2.24
2087 2150 3.997681 TCATTCATTTCCGCGACAAGTAA 59.002 39.130 8.23 0.00 0.00 2.24
2088 2151 4.634004 TCATTCATTTCCGCGACAAGTAAT 59.366 37.500 8.23 1.19 0.00 1.89
2089 2152 5.123186 TCATTCATTTCCGCGACAAGTAATT 59.877 36.000 8.23 0.00 0.00 1.40
2090 2153 6.314152 TCATTCATTTCCGCGACAAGTAATTA 59.686 34.615 8.23 0.00 0.00 1.40
2091 2154 5.459110 TCATTTCCGCGACAAGTAATTAC 57.541 39.130 8.23 7.57 0.00 1.89
2092 2155 3.976468 TTTCCGCGACAAGTAATTACG 57.024 42.857 8.23 0.00 0.00 3.18
2093 2156 1.912001 TCCGCGACAAGTAATTACGG 58.088 50.000 8.23 8.99 40.47 4.02
2094 2157 1.472082 TCCGCGACAAGTAATTACGGA 59.528 47.619 8.23 8.28 45.18 4.69
2095 2158 1.585214 CCGCGACAAGTAATTACGGAC 59.415 52.381 8.23 6.39 41.61 4.79
2096 2159 1.251002 CGCGACAAGTAATTACGGACG 59.749 52.381 21.00 21.00 0.00 4.79
2097 2160 1.585214 GCGACAAGTAATTACGGACGG 59.415 52.381 23.89 12.68 0.00 4.79
2098 2161 2.731968 GCGACAAGTAATTACGGACGGA 60.732 50.000 23.89 0.00 0.00 4.69
2099 2162 3.103738 CGACAAGTAATTACGGACGGAG 58.896 50.000 19.08 7.09 0.00 4.63
2100 2163 3.442100 GACAAGTAATTACGGACGGAGG 58.558 50.000 9.91 0.00 0.00 4.30
2101 2164 2.167075 ACAAGTAATTACGGACGGAGGG 59.833 50.000 9.91 0.00 0.00 4.30
2102 2165 2.428171 CAAGTAATTACGGACGGAGGGA 59.572 50.000 9.91 0.00 0.00 4.20
2103 2166 2.305009 AGTAATTACGGACGGAGGGAG 58.695 52.381 9.91 0.00 0.00 4.30
2104 2167 2.027385 GTAATTACGGACGGAGGGAGT 58.973 52.381 0.00 0.00 0.00 3.85
2105 2168 2.442236 AATTACGGACGGAGGGAGTA 57.558 50.000 0.00 0.00 0.00 2.59
2106 2169 2.671896 ATTACGGACGGAGGGAGTAT 57.328 50.000 0.00 0.00 0.00 2.12
2107 2170 1.972872 TTACGGACGGAGGGAGTATC 58.027 55.000 0.00 0.00 0.00 2.24
2108 2171 1.135094 TACGGACGGAGGGAGTATCT 58.865 55.000 0.00 0.00 33.73 1.98
2109 2172 0.258194 ACGGACGGAGGGAGTATCTT 59.742 55.000 0.00 0.00 33.73 2.40
2110 2173 1.341778 ACGGACGGAGGGAGTATCTTT 60.342 52.381 0.00 0.00 33.73 2.52
2111 2174 1.755380 CGGACGGAGGGAGTATCTTTT 59.245 52.381 0.00 0.00 33.73 2.27
2112 2175 2.167900 CGGACGGAGGGAGTATCTTTTT 59.832 50.000 0.00 0.00 33.73 1.94
2134 2197 5.517322 TTTTTGCGGGTGTACAAAATAGT 57.483 34.783 0.00 0.00 43.23 2.12
2506 2584 5.582269 ACGATGAGATGAACGATTGATTTGT 59.418 36.000 0.00 0.00 0.00 2.83
2513 2591 8.142994 AGATGAACGATTGATTTGTGGTATAC 57.857 34.615 0.00 0.00 0.00 1.47
2520 2598 7.715249 ACGATTGATTTGTGGTATACTAGCAAT 59.285 33.333 2.25 4.70 37.99 3.56
2764 2842 2.118294 AGCCCCCAAGCTTCAACC 59.882 61.111 0.00 0.00 41.41 3.77
2953 3031 0.744874 ACATGCCAATGATGCAGAGC 59.255 50.000 0.00 0.00 42.92 4.09
3403 3481 0.389025 CAAACCCCTGGAGCAACAAC 59.611 55.000 0.00 0.00 0.00 3.32
3487 3565 9.174166 ACATGTGGTAGTATTTTTATTCTCACC 57.826 33.333 0.00 0.00 0.00 4.02
3592 3670 3.177884 AGGGCTGGTGCAACTGGA 61.178 61.111 10.91 0.00 41.91 3.86
4019 4097 1.541588 CCAGAGGCTTTGCAGGTAAAC 59.458 52.381 0.00 0.00 0.00 2.01
4163 4279 4.705991 ACCTAGCCAGTGAGTAACTCTAAC 59.294 45.833 0.00 0.00 36.83 2.34
4365 4487 8.899427 TCTTTATGCATAATCTCTTCTTCCTG 57.101 34.615 19.51 0.00 0.00 3.86
4571 4695 8.208718 TGTTGTAGCATTAGAATCATTACCAC 57.791 34.615 0.00 0.00 0.00 4.16
4589 4713 2.742053 CCACCTGTTCATTGGTAACTCG 59.258 50.000 0.00 0.00 34.79 4.18
4603 4727 4.523943 TGGTAACTCGAAACTACTAAGGCA 59.476 41.667 0.00 0.00 37.61 4.75
4725 4849 8.996024 TTCTGAATCATGTGATACGTTTCTTA 57.004 30.769 7.53 0.00 33.73 2.10
4758 4883 2.802719 GGTTGCCTCTGACCCAAATAA 58.197 47.619 0.00 0.00 0.00 1.40
4818 4943 7.633789 AGATTGTAGTTCCATACACCTTGATT 58.366 34.615 0.00 0.00 35.44 2.57
4827 4952 0.110486 ACACCTTGATTCCACCGCTT 59.890 50.000 0.00 0.00 0.00 4.68
4828 4953 0.523072 CACCTTGATTCCACCGCTTG 59.477 55.000 0.00 0.00 0.00 4.01
4933 5060 2.431430 TTGACTGCAGAGCGCTCG 60.431 61.111 30.39 24.66 43.06 5.03
4978 5105 5.247862 TGCAATGCAGAGATCTTAAGTTCA 58.752 37.500 2.72 0.00 33.32 3.18
5174 5301 5.255687 TGAGAATTTGCCTGCTCTTATTGA 58.744 37.500 0.00 0.00 0.00 2.57
5180 5307 2.305635 TGCCTGCTCTTATTGAGTTCCA 59.694 45.455 0.00 0.00 44.41 3.53
5205 5332 3.564225 GGCTGATATTAGTTTCCCCGTTG 59.436 47.826 0.00 0.00 0.00 4.10
5300 5427 1.734477 CGCAGAGAATATCCGGGCG 60.734 63.158 0.00 0.67 37.21 6.13
5383 5510 5.509163 GCCAGTAGATAAAACGAGCCAGATA 60.509 44.000 0.00 0.00 0.00 1.98
5597 5726 5.272283 TCCTTTAAGTGTCGAGTCAACTT 57.728 39.130 7.70 7.70 0.00 2.66
5598 5727 5.047847 TCCTTTAAGTGTCGAGTCAACTTG 58.952 41.667 11.30 0.00 0.00 3.16
5786 5932 8.575589 ACAGCAGTACATTTTTGTCATATTTCA 58.424 29.630 0.00 0.00 0.00 2.69
5877 6023 9.799106 AGGGTGGTTGAAATCATATATTAGAAG 57.201 33.333 0.00 0.00 0.00 2.85
6117 6268 4.888823 TGGTCATACATCCAATGTGAATGG 59.111 41.667 2.88 0.00 44.60 3.16
6179 6330 7.548196 AATATTGATGCCAAAAGATGCAAAG 57.452 32.000 0.00 0.00 41.50 2.77
6244 6395 5.008613 AGGTTATATTGGTGTAAAGCGCATG 59.991 40.000 11.47 0.00 0.00 4.06
6253 6404 4.537015 GTGTAAAGCGCATGAAGAAACTT 58.463 39.130 11.47 0.00 0.00 2.66
6256 6407 2.977405 AGCGCATGAAGAAACTTCAC 57.023 45.000 11.47 4.68 0.00 3.18
6263 6414 1.939934 TGAAGAAACTTCACGCAGGTG 59.060 47.619 9.67 0.00 45.78 4.00
6270 6421 1.134037 ACTTCACGCAGGTGGGTTTTA 60.134 47.619 0.00 0.00 44.50 1.52
6272 6423 0.759959 TCACGCAGGTGGGTTTTAGA 59.240 50.000 0.00 0.00 44.50 2.10
6273 6424 1.141254 TCACGCAGGTGGGTTTTAGAA 59.859 47.619 0.00 0.00 44.50 2.10
6274 6425 2.159382 CACGCAGGTGGGTTTTAGAAT 58.841 47.619 0.00 0.00 40.58 2.40
6275 6426 2.161609 CACGCAGGTGGGTTTTAGAATC 59.838 50.000 0.00 0.00 40.58 2.52
6276 6427 2.224670 ACGCAGGTGGGTTTTAGAATCA 60.225 45.455 0.00 0.00 38.04 2.57
6277 6428 2.161609 CGCAGGTGGGTTTTAGAATCAC 59.838 50.000 0.00 0.00 0.00 3.06
6278 6429 3.421844 GCAGGTGGGTTTTAGAATCACT 58.578 45.455 0.00 0.00 0.00 3.41
6279 6430 3.826729 GCAGGTGGGTTTTAGAATCACTT 59.173 43.478 0.00 0.00 0.00 3.16
6280 6431 4.321230 GCAGGTGGGTTTTAGAATCACTTG 60.321 45.833 0.00 0.00 38.10 3.16
6281 6432 5.070001 CAGGTGGGTTTTAGAATCACTTGA 58.930 41.667 8.00 0.00 37.54 3.02
6282 6433 5.711976 CAGGTGGGTTTTAGAATCACTTGAT 59.288 40.000 8.00 0.00 37.54 2.57
6283 6434 6.209391 CAGGTGGGTTTTAGAATCACTTGATT 59.791 38.462 4.07 4.07 46.54 2.57
6284 6435 7.393234 CAGGTGGGTTTTAGAATCACTTGATTA 59.607 37.037 4.42 0.00 44.14 1.75
6285 6436 8.116026 AGGTGGGTTTTAGAATCACTTGATTAT 58.884 33.333 4.42 4.52 44.14 1.28
6344 6495 5.715070 CAAGATGACTAAACTCCGTTCTCT 58.285 41.667 0.00 0.00 0.00 3.10
6346 6497 5.010933 AGATGACTAAACTCCGTTCTCTGA 58.989 41.667 0.00 0.00 0.00 3.27
6349 6500 5.909477 TGACTAAACTCCGTTCTCTGAAAA 58.091 37.500 0.00 0.00 0.00 2.29
6440 6591 2.614983 ACGCGGCGGTATCATTATTTTT 59.385 40.909 27.37 0.00 0.00 1.94
6449 6600 6.238266 GCGGTATCATTATTTTTCGACCTTCA 60.238 38.462 0.00 0.00 0.00 3.02
6460 6611 8.792830 ATTTTTCGACCTTCAGAGATGATTTA 57.207 30.769 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 8.648968 CCGTCTTTCTTCTTTTGTTCTATACTC 58.351 37.037 0.00 0.00 0.00 2.59
23 24 9.550406 TTAATCCGTCTTTCTTCTTTTGTTCTA 57.450 29.630 0.00 0.00 0.00 2.10
55 57 2.469516 GCGGGATGTGTAAAGGGCG 61.470 63.158 0.00 0.00 0.00 6.13
63 65 0.674895 GCTTCTGAAGCGGGATGTGT 60.675 55.000 24.86 0.00 45.74 3.72
128 134 4.082136 GGTTTTAGGTTGTGTTGGTGTTCA 60.082 41.667 0.00 0.00 0.00 3.18
154 164 7.625828 TTTGTCTCGTTAGTCATCAGATCTA 57.374 36.000 0.00 0.00 0.00 1.98
168 178 0.822121 GTGGCCCCTTTTGTCTCGTT 60.822 55.000 0.00 0.00 0.00 3.85
181 191 4.748144 CTGGGAAGCAGGTGGCCC 62.748 72.222 0.00 4.21 46.50 5.80
198 208 2.159653 ACAGCGTTTCAATCGAAGATGC 60.160 45.455 0.00 0.00 45.12 3.91
203 221 0.787787 CCGACAGCGTTTCAATCGAA 59.212 50.000 0.00 0.00 34.77 3.71
211 229 4.636435 CCCACCCCGACAGCGTTT 62.636 66.667 0.00 0.00 35.23 3.60
215 233 4.410400 CTTCCCCACCCCGACAGC 62.410 72.222 0.00 0.00 0.00 4.40
221 239 1.266178 CAATGTTTCTTCCCCACCCC 58.734 55.000 0.00 0.00 0.00 4.95
222 240 0.608130 GCAATGTTTCTTCCCCACCC 59.392 55.000 0.00 0.00 0.00 4.61
239 257 1.013596 CGCGTCAGGATAATTTGGCA 58.986 50.000 0.00 0.00 0.00 4.92
250 268 4.201679 TATCGGTGGCGCGTCAGG 62.202 66.667 16.68 9.95 0.00 3.86
267 297 3.678056 TGTTCTTCATAGAGGCGTTGT 57.322 42.857 0.00 0.00 0.00 3.32
269 299 3.437049 GCTTTGTTCTTCATAGAGGCGTT 59.563 43.478 0.00 0.00 0.00 4.84
270 300 3.003480 GCTTTGTTCTTCATAGAGGCGT 58.997 45.455 0.00 0.00 0.00 5.68
298 340 3.607777 CTGCTCCGACGAGTAGTTC 57.392 57.895 0.00 0.00 42.23 3.01
348 391 1.955080 CTACCCTCCGTTAATCGCTCT 59.045 52.381 0.00 0.00 38.35 4.09
383 427 2.354729 CCCCCATCTTCGTTGGCA 59.645 61.111 0.00 0.00 32.60 4.92
391 435 0.259938 GACCATTCTGCCCCCATCTT 59.740 55.000 0.00 0.00 0.00 2.40
406 450 2.038813 TGATCTGGGAGGCGACCA 59.961 61.111 3.26 3.26 36.38 4.02
452 496 2.332654 GCCATGAACCGTTTCGCCT 61.333 57.895 0.00 0.00 34.04 5.52
467 511 2.028125 GAATCCTCACCGATCCGCCA 62.028 60.000 0.00 0.00 0.00 5.69
494 538 2.635714 TCGCACTCATTCATGCTCATT 58.364 42.857 0.00 0.00 39.79 2.57
500 544 1.669265 ACAGCATCGCACTCATTCATG 59.331 47.619 0.00 0.00 0.00 3.07
508 552 1.217511 CTCCTGACAGCATCGCACT 59.782 57.895 0.00 0.00 0.00 4.40
520 564 1.211703 TCACTGTGTTTTGGCTCCTGA 59.788 47.619 7.79 0.00 0.00 3.86
523 567 3.733443 AAATCACTGTGTTTTGGCTCC 57.267 42.857 14.25 0.00 0.00 4.70
554 598 3.387962 TCTTTGCTCCCAGAGGTGATAT 58.612 45.455 0.00 0.00 0.00 1.63
555 599 2.832838 TCTTTGCTCCCAGAGGTGATA 58.167 47.619 0.00 0.00 0.00 2.15
556 600 1.661463 TCTTTGCTCCCAGAGGTGAT 58.339 50.000 0.00 0.00 0.00 3.06
564 608 2.858768 AGGGGAATTATCTTTGCTCCCA 59.141 45.455 7.70 0.00 46.59 4.37
577 621 6.890268 GGTTTGATTGTTAGTCTAGGGGAATT 59.110 38.462 0.00 0.00 0.00 2.17
578 622 6.424032 GGTTTGATTGTTAGTCTAGGGGAAT 58.576 40.000 0.00 0.00 0.00 3.01
579 623 5.570034 CGGTTTGATTGTTAGTCTAGGGGAA 60.570 44.000 0.00 0.00 0.00 3.97
580 624 4.081309 CGGTTTGATTGTTAGTCTAGGGGA 60.081 45.833 0.00 0.00 0.00 4.81
581 625 4.081309 TCGGTTTGATTGTTAGTCTAGGGG 60.081 45.833 0.00 0.00 0.00 4.79
582 626 5.080969 TCGGTTTGATTGTTAGTCTAGGG 57.919 43.478 0.00 0.00 0.00 3.53
583 627 5.962433 TCTCGGTTTGATTGTTAGTCTAGG 58.038 41.667 0.00 0.00 0.00 3.02
584 628 5.517054 GCTCTCGGTTTGATTGTTAGTCTAG 59.483 44.000 0.00 0.00 0.00 2.43
585 629 5.408356 GCTCTCGGTTTGATTGTTAGTCTA 58.592 41.667 0.00 0.00 0.00 2.59
586 630 4.246458 GCTCTCGGTTTGATTGTTAGTCT 58.754 43.478 0.00 0.00 0.00 3.24
587 631 3.371285 GGCTCTCGGTTTGATTGTTAGTC 59.629 47.826 0.00 0.00 0.00 2.59
588 632 3.244422 TGGCTCTCGGTTTGATTGTTAGT 60.244 43.478 0.00 0.00 0.00 2.24
589 633 3.334691 TGGCTCTCGGTTTGATTGTTAG 58.665 45.455 0.00 0.00 0.00 2.34
590 634 3.007506 TCTGGCTCTCGGTTTGATTGTTA 59.992 43.478 0.00 0.00 0.00 2.41
591 635 2.154462 CTGGCTCTCGGTTTGATTGTT 58.846 47.619 0.00 0.00 0.00 2.83
600 644 0.251209 TGTACAGTCTGGCTCTCGGT 60.251 55.000 4.53 0.00 0.00 4.69
603 647 2.096174 CGTAGTGTACAGTCTGGCTCTC 59.904 54.545 6.44 0.00 0.00 3.20
652 699 1.732259 CGAGTCCGTGGAATTTTCAGG 59.268 52.381 0.00 0.00 0.00 3.86
682 729 1.134068 GGTGCCTTCTCTATTCCCACC 60.134 57.143 0.00 0.00 35.10 4.61
697 744 3.403558 GAGTCAGGGGAGGGTGCC 61.404 72.222 0.00 0.00 0.00 5.01
698 745 3.775654 CGAGTCAGGGGAGGGTGC 61.776 72.222 0.00 0.00 0.00 5.01
771 826 1.888018 CGTGAGGTGTGATACGGGT 59.112 57.895 0.00 0.00 33.27 5.28
892 950 5.714806 GGAGAGAGAAGAAAGAGAGGAGAAA 59.285 44.000 0.00 0.00 0.00 2.52
1291 1352 2.788640 CGCGACCTTATTCCCCGGA 61.789 63.158 0.73 0.00 0.00 5.14
1292 1353 2.279918 CGCGACCTTATTCCCCGG 60.280 66.667 0.00 0.00 0.00 5.73
1325 1386 2.112297 GGGCCGGCCAATTCGATA 59.888 61.111 44.46 0.00 37.98 2.92
1326 1387 4.894896 GGGGCCGGCCAATTCGAT 62.895 66.667 44.46 0.00 37.98 3.59
1396 1457 1.730501 ACTGTTGCATCTGATCCACG 58.269 50.000 8.47 0.00 0.00 4.94
1470 1532 0.107831 TCACTAACACACCCCACTGC 59.892 55.000 0.00 0.00 0.00 4.40
1476 1538 3.598019 TCCGTTATCACTAACACACCC 57.402 47.619 0.00 0.00 37.65 4.61
1518 1580 7.015584 TCAGCTTCACCATCTTCTATGCTATAA 59.984 37.037 0.00 0.00 0.00 0.98
1547 1610 1.268625 TGACGCGACAAGAGAAGCTTA 59.731 47.619 15.93 0.00 34.31 3.09
1565 1628 5.365403 AACGCTTGGAATTAAATTCGTGA 57.635 34.783 0.00 0.00 40.17 4.35
1593 1656 3.249080 TGCACAAGTAACGGAAGCTAAAC 59.751 43.478 0.00 0.00 0.00 2.01
1646 1709 7.383102 TCAAGCAAATCCAGTAAATCTCTTC 57.617 36.000 0.00 0.00 0.00 2.87
1750 1813 4.794169 ACTACATTCAACAATCAAACGCC 58.206 39.130 0.00 0.00 0.00 5.68
1887 1950 2.412089 CGGAAGGCTTTCTCAGTTTACG 59.588 50.000 8.61 0.00 33.68 3.18
1907 1970 8.765219 CATTAGGATTCAACTATAAACTCCACG 58.235 37.037 0.00 0.00 0.00 4.94
1948 2011 5.223449 AGTCGACCATTTAGGAACAAGAA 57.777 39.130 13.01 0.00 41.22 2.52
1950 2013 5.238583 AGAAGTCGACCATTTAGGAACAAG 58.761 41.667 13.01 0.00 41.22 3.16
1990 2053 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
1991 2054 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1992 2055 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1993 2056 0.388294 GAGTATTTCCGGACGGAGGG 59.612 60.000 13.64 0.00 46.06 4.30
1994 2057 0.030369 CGAGTATTTCCGGACGGAGG 59.970 60.000 13.64 0.00 46.06 4.30
1995 2058 0.737219 ACGAGTATTTCCGGACGGAG 59.263 55.000 13.64 3.15 46.06 4.63
1996 2059 0.734889 GACGAGTATTTCCGGACGGA 59.265 55.000 1.83 9.76 43.52 4.69
1997 2060 0.590732 CGACGAGTATTTCCGGACGG 60.591 60.000 1.83 3.96 0.00 4.79
1998 2061 0.590732 CCGACGAGTATTTCCGGACG 60.591 60.000 1.83 5.89 42.49 4.79
1999 2062 0.734889 TCCGACGAGTATTTCCGGAC 59.265 55.000 1.83 0.00 43.47 4.79
2000 2063 1.019673 CTCCGACGAGTATTTCCGGA 58.980 55.000 0.00 0.00 45.74 5.14
2001 2064 1.019673 TCTCCGACGAGTATTTCCGG 58.980 55.000 0.00 0.00 41.36 5.14
2002 2065 2.838386 TTCTCCGACGAGTATTTCCG 57.162 50.000 0.00 0.00 37.40 4.30
2003 2066 7.224167 ACATTTATTTCTCCGACGAGTATTTCC 59.776 37.037 0.00 0.00 37.40 3.13
2004 2067 8.128016 ACATTTATTTCTCCGACGAGTATTTC 57.872 34.615 0.00 0.00 37.40 2.17
2005 2068 9.760077 ATACATTTATTTCTCCGACGAGTATTT 57.240 29.630 0.00 0.00 37.40 1.40
2006 2069 9.408069 GATACATTTATTTCTCCGACGAGTATT 57.592 33.333 0.00 0.00 37.40 1.89
2007 2070 8.794553 AGATACATTTATTTCTCCGACGAGTAT 58.205 33.333 0.00 0.00 37.40 2.12
2008 2071 8.162878 AGATACATTTATTTCTCCGACGAGTA 57.837 34.615 0.00 0.00 37.40 2.59
2009 2072 7.040473 AGATACATTTATTTCTCCGACGAGT 57.960 36.000 0.00 0.00 37.40 4.18
2010 2073 8.504815 TCTAGATACATTTATTTCTCCGACGAG 58.495 37.037 0.00 0.00 37.48 4.18
2011 2074 8.288208 GTCTAGATACATTTATTTCTCCGACGA 58.712 37.037 0.00 0.00 0.00 4.20
2012 2075 7.268659 CGTCTAGATACATTTATTTCTCCGACG 59.731 40.741 0.00 0.00 36.68 5.12
2013 2076 8.074972 ACGTCTAGATACATTTATTTCTCCGAC 58.925 37.037 0.00 0.00 0.00 4.79
2014 2077 8.162878 ACGTCTAGATACATTTATTTCTCCGA 57.837 34.615 0.00 0.00 0.00 4.55
2051 2114 8.355169 CGGAAATGAATGAAAATGGATGTATCT 58.645 33.333 0.00 0.00 0.00 1.98
2052 2115 7.115378 GCGGAAATGAATGAAAATGGATGTATC 59.885 37.037 0.00 0.00 0.00 2.24
2053 2116 6.925165 GCGGAAATGAATGAAAATGGATGTAT 59.075 34.615 0.00 0.00 0.00 2.29
2054 2117 6.272318 GCGGAAATGAATGAAAATGGATGTA 58.728 36.000 0.00 0.00 0.00 2.29
2055 2118 5.111293 GCGGAAATGAATGAAAATGGATGT 58.889 37.500 0.00 0.00 0.00 3.06
2056 2119 4.207635 CGCGGAAATGAATGAAAATGGATG 59.792 41.667 0.00 0.00 0.00 3.51
2057 2120 4.097741 TCGCGGAAATGAATGAAAATGGAT 59.902 37.500 6.13 0.00 0.00 3.41
2058 2121 3.441922 TCGCGGAAATGAATGAAAATGGA 59.558 39.130 6.13 0.00 0.00 3.41
2059 2122 3.547468 GTCGCGGAAATGAATGAAAATGG 59.453 43.478 6.13 0.00 0.00 3.16
2060 2123 4.165036 TGTCGCGGAAATGAATGAAAATG 58.835 39.130 6.13 0.00 0.00 2.32
2061 2124 4.433186 TGTCGCGGAAATGAATGAAAAT 57.567 36.364 6.13 0.00 0.00 1.82
2062 2125 3.906014 TGTCGCGGAAATGAATGAAAA 57.094 38.095 6.13 0.00 0.00 2.29
2063 2126 3.252215 ACTTGTCGCGGAAATGAATGAAA 59.748 39.130 6.13 0.00 0.00 2.69
2064 2127 2.811431 ACTTGTCGCGGAAATGAATGAA 59.189 40.909 6.13 0.00 0.00 2.57
2065 2128 2.422597 ACTTGTCGCGGAAATGAATGA 58.577 42.857 6.13 0.00 0.00 2.57
2066 2129 2.900122 ACTTGTCGCGGAAATGAATG 57.100 45.000 6.13 0.00 0.00 2.67
2067 2130 5.560966 AATTACTTGTCGCGGAAATGAAT 57.439 34.783 6.13 0.00 0.00 2.57
2068 2131 5.444877 CGTAATTACTTGTCGCGGAAATGAA 60.445 40.000 13.56 0.00 0.00 2.57
2069 2132 4.031991 CGTAATTACTTGTCGCGGAAATGA 59.968 41.667 13.56 0.00 0.00 2.57
2070 2133 4.260670 CGTAATTACTTGTCGCGGAAATG 58.739 43.478 13.56 0.00 0.00 2.32
2071 2134 3.307782 CCGTAATTACTTGTCGCGGAAAT 59.692 43.478 13.56 0.00 40.04 2.17
2072 2135 2.667481 CCGTAATTACTTGTCGCGGAAA 59.333 45.455 13.56 0.00 40.04 3.13
2073 2136 2.094803 TCCGTAATTACTTGTCGCGGAA 60.095 45.455 13.56 0.00 42.86 4.30
2074 2137 1.472082 TCCGTAATTACTTGTCGCGGA 59.528 47.619 13.56 10.01 43.47 5.54
2075 2138 1.585214 GTCCGTAATTACTTGTCGCGG 59.415 52.381 13.56 7.89 39.13 6.46
2076 2139 1.251002 CGTCCGTAATTACTTGTCGCG 59.749 52.381 13.56 0.00 0.00 5.87
2077 2140 1.585214 CCGTCCGTAATTACTTGTCGC 59.415 52.381 13.56 0.00 0.00 5.19
2078 2141 3.103738 CTCCGTCCGTAATTACTTGTCG 58.896 50.000 13.56 12.43 0.00 4.35
2079 2142 3.442100 CCTCCGTCCGTAATTACTTGTC 58.558 50.000 13.56 2.48 0.00 3.18
2080 2143 2.167075 CCCTCCGTCCGTAATTACTTGT 59.833 50.000 13.56 0.00 0.00 3.16
2081 2144 2.428171 TCCCTCCGTCCGTAATTACTTG 59.572 50.000 13.56 5.06 0.00 3.16
2082 2145 2.692041 CTCCCTCCGTCCGTAATTACTT 59.308 50.000 13.56 0.00 0.00 2.24
2083 2146 2.305009 CTCCCTCCGTCCGTAATTACT 58.695 52.381 13.56 0.00 0.00 2.24
2084 2147 2.027385 ACTCCCTCCGTCCGTAATTAC 58.973 52.381 5.47 5.47 0.00 1.89
2085 2148 2.442236 ACTCCCTCCGTCCGTAATTA 57.558 50.000 0.00 0.00 0.00 1.40
2086 2149 2.442236 TACTCCCTCCGTCCGTAATT 57.558 50.000 0.00 0.00 0.00 1.40
2087 2150 2.107901 AGATACTCCCTCCGTCCGTAAT 59.892 50.000 0.00 0.00 0.00 1.89
2088 2151 1.492176 AGATACTCCCTCCGTCCGTAA 59.508 52.381 0.00 0.00 0.00 3.18
2089 2152 1.135094 AGATACTCCCTCCGTCCGTA 58.865 55.000 0.00 0.00 0.00 4.02
2090 2153 0.258194 AAGATACTCCCTCCGTCCGT 59.742 55.000 0.00 0.00 0.00 4.69
2091 2154 1.400737 AAAGATACTCCCTCCGTCCG 58.599 55.000 0.00 0.00 0.00 4.79
2092 2155 3.908643 AAAAAGATACTCCCTCCGTCC 57.091 47.619 0.00 0.00 0.00 4.79
2112 2175 5.163540 ACACTATTTTGTACACCCGCAAAAA 60.164 36.000 0.00 0.00 44.38 1.94
2113 2176 4.338682 ACACTATTTTGTACACCCGCAAAA 59.661 37.500 0.00 5.16 44.99 2.44
2114 2177 3.884091 ACACTATTTTGTACACCCGCAAA 59.116 39.130 0.00 0.00 33.40 3.68
2115 2178 3.478509 ACACTATTTTGTACACCCGCAA 58.521 40.909 0.00 0.00 0.00 4.85
2116 2179 3.068560 GACACTATTTTGTACACCCGCA 58.931 45.455 0.00 0.00 0.00 5.69
2117 2180 3.068560 TGACACTATTTTGTACACCCGC 58.931 45.455 0.00 0.00 0.00 6.13
2118 2181 5.873179 AATGACACTATTTTGTACACCCG 57.127 39.130 0.00 0.00 0.00 5.28
2119 2182 7.675962 TGTAATGACACTATTTTGTACACCC 57.324 36.000 0.00 0.00 0.00 4.61
2120 2183 8.019094 GGTTGTAATGACACTATTTTGTACACC 58.981 37.037 0.00 0.00 34.48 4.16
2121 2184 8.561212 TGGTTGTAATGACACTATTTTGTACAC 58.439 33.333 0.00 0.00 34.48 2.90
2122 2185 8.561212 GTGGTTGTAATGACACTATTTTGTACA 58.439 33.333 0.00 0.00 34.48 2.90
2123 2186 8.561212 TGTGGTTGTAATGACACTATTTTGTAC 58.439 33.333 0.00 0.00 34.48 2.90
2124 2187 8.678593 TGTGGTTGTAATGACACTATTTTGTA 57.321 30.769 0.00 0.00 34.48 2.41
2125 2188 7.284489 ACTGTGGTTGTAATGACACTATTTTGT 59.716 33.333 0.00 0.00 34.48 2.83
2126 2189 7.648142 ACTGTGGTTGTAATGACACTATTTTG 58.352 34.615 0.00 0.00 34.48 2.44
2127 2190 7.500892 TGACTGTGGTTGTAATGACACTATTTT 59.499 33.333 0.00 0.00 34.48 1.82
2128 2191 6.995686 TGACTGTGGTTGTAATGACACTATTT 59.004 34.615 0.00 0.00 34.48 1.40
2129 2192 6.426937 GTGACTGTGGTTGTAATGACACTATT 59.573 38.462 0.00 0.00 34.48 1.73
2130 2193 5.932303 GTGACTGTGGTTGTAATGACACTAT 59.068 40.000 0.00 0.00 34.48 2.12
2131 2194 5.069914 AGTGACTGTGGTTGTAATGACACTA 59.930 40.000 0.00 0.00 34.48 2.74
2132 2195 4.127171 GTGACTGTGGTTGTAATGACACT 58.873 43.478 0.00 0.00 34.48 3.55
2133 2196 4.024893 CAGTGACTGTGGTTGTAATGACAC 60.025 45.833 4.01 0.00 34.48 3.67
2134 2197 4.126437 CAGTGACTGTGGTTGTAATGACA 58.874 43.478 4.01 0.00 0.00 3.58
2499 2577 7.121907 TGCAAATTGCTAGTATACCACAAATCA 59.878 33.333 19.34 0.00 45.31 2.57
2506 2584 7.735917 AGATAGTGCAAATTGCTAGTATACCA 58.264 34.615 19.34 0.00 45.31 3.25
2513 2591 7.545362 ACAGTAAGATAGTGCAAATTGCTAG 57.455 36.000 19.34 0.00 45.31 3.42
2764 2842 1.613630 AGGGCCACTGGTAGGAGTG 60.614 63.158 6.18 0.00 42.68 3.51
2953 3031 7.761704 CGTATTAGATCAGGGTTATTCATGAGG 59.238 40.741 0.00 0.00 0.00 3.86
3403 3481 9.866798 AAAACTCTAAATAACTAGAACCTACCG 57.133 33.333 0.00 0.00 0.00 4.02
3487 3565 1.019673 ACAGGCAATTATCAGCAGCG 58.980 50.000 0.00 0.00 0.00 5.18
4019 4097 3.058983 TGTTAACTTGCATCGCAACAGAG 60.059 43.478 7.22 0.00 43.99 3.35
4163 4279 5.413833 GGGGTGATACAATGATGCTATTGAG 59.586 44.000 13.33 0.00 39.79 3.02
4365 4487 8.375506 TCAAACCTGACATAGTAATCCATATCC 58.624 37.037 0.00 0.00 0.00 2.59
4571 4695 4.755123 AGTTTCGAGTTACCAATGAACAGG 59.245 41.667 0.00 0.00 0.00 4.00
4725 4849 2.302733 GAGGCAACCCATTTCCATTTGT 59.697 45.455 0.00 0.00 37.17 2.83
4827 4952 8.133024 AGACATTACAAATAAAAATGGCTCCA 57.867 30.769 0.00 0.00 43.88 3.86
4954 5081 5.706833 TGAACTTAAGATCTCTGCATTGCAA 59.293 36.000 13.18 0.00 38.41 4.08
4959 5086 6.543430 AGACTGAACTTAAGATCTCTGCAT 57.457 37.500 10.09 0.00 0.00 3.96
5018 5145 4.994852 GTGCCTGTATTTGTTCAGACACTA 59.005 41.667 4.82 0.00 40.23 2.74
5174 5301 5.552870 AACTAATATCAGCCGATGGAACT 57.447 39.130 0.00 0.00 32.73 3.01
5180 5307 3.306780 CGGGGAAACTAATATCAGCCGAT 60.307 47.826 0.00 0.00 35.50 4.18
5205 5332 2.393764 CGGTGGCACTGAAATTTTGAC 58.606 47.619 21.95 0.00 0.00 3.18
5300 5427 1.751927 CCCAGAAGTGGCCATCAGC 60.752 63.158 9.72 0.00 43.44 4.26
5383 5510 0.617820 ACAGGGAGATTACGGGCAGT 60.618 55.000 0.00 0.00 0.00 4.40
5443 5570 9.511272 ACGGGAAAAAGTTAACTGTATTATTCT 57.489 29.630 9.34 0.00 0.00 2.40
5618 5747 7.284489 ACCTACATTGTTTGTGTCTATTGTGTT 59.716 33.333 0.00 0.00 39.48 3.32
6085 6236 5.808366 TGGATGTATGACCATAGAAGGAC 57.192 43.478 0.00 0.00 0.00 3.85
6086 6237 6.329986 ACATTGGATGTATGACCATAGAAGGA 59.670 38.462 0.00 0.00 42.78 3.36
6194 6345 1.666888 GCAGTGCCACAAGTATGTTGC 60.667 52.381 2.85 0.00 45.77 4.17
6244 6395 1.264288 CCACCTGCGTGAAGTTTCTTC 59.736 52.381 2.95 2.95 43.14 2.87
6253 6404 0.759959 TCTAAAACCCACCTGCGTGA 59.240 50.000 0.00 0.00 43.14 4.35
6256 6407 2.161609 GTGATTCTAAAACCCACCTGCG 59.838 50.000 0.00 0.00 0.00 5.18
6292 6443 5.945191 TGAGGCATGATTCACAAGTATCAAA 59.055 36.000 0.00 0.00 35.56 2.69
6307 6458 2.171870 TCATCTTGCTCATGAGGCATGA 59.828 45.455 23.89 24.11 46.84 3.07
6319 6470 3.963428 ACGGAGTTTAGTCATCTTGCT 57.037 42.857 0.00 0.00 37.78 3.91
6349 6500 3.550437 AGTCATTAGCTCGCTCCATTT 57.450 42.857 0.00 0.00 0.00 2.32
6388 6539 2.293399 CTCATCGGACCACATACATCGA 59.707 50.000 0.00 0.00 0.00 3.59
6403 6554 1.071894 CGCGTGCTTCAATACTCATCG 60.072 52.381 0.00 0.00 0.00 3.84
6426 6577 8.433421 TCTGAAGGTCGAAAAATAATGATACC 57.567 34.615 0.00 0.00 0.00 2.73
6427 6578 9.314321 TCTCTGAAGGTCGAAAAATAATGATAC 57.686 33.333 0.00 0.00 0.00 2.24
6440 6591 5.105351 TGCTTAAATCATCTCTGAAGGTCGA 60.105 40.000 0.00 0.00 34.37 4.20


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

AutoCloner maintained by Alex Coulton.