Multiple sequence alignment - TraesCS5A01G334200

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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 TraesCS5A01G334200 chr5A 100.000 4208 0 0 1 4208 543930687 543926480 0.000000e+00 7771.0
1 TraesCS5A01G334200 chr5B 92.043 2149 131 16 94 2224 517577700 517575574 0.000000e+00 2985.0
2 TraesCS5A01G334200 chr5B 90.343 1253 90 19 2210 3448 517575211 517573976 0.000000e+00 1615.0
3 TraesCS5A01G334200 chr5B 87.706 667 43 19 3564 4198 517573972 517573313 0.000000e+00 741.0
4 TraesCS5A01G334200 chr5D 88.857 2082 137 40 2168 4187 428386470 428384422 0.000000e+00 2471.0
5 TraesCS5A01G334200 chr5D 92.647 1564 90 16 111 1666 428388817 428387271 0.000000e+00 2228.0
6 TraesCS5A01G334200 chrUn 91.724 1015 59 9 1464 2464 220215124 220216127 0.000000e+00 1386.0
7 TraesCS5A01G334200 chr2B 90.427 867 57 10 1464 2316 35017499 35016645 0.000000e+00 1118.0
8 TraesCS5A01G334200 chr2B 75.234 214 44 7 2100 2312 514855143 514855348 4.480000e-15 93.5
9 TraesCS5A01G334200 chr7A 90.311 867 58 10 1464 2316 671182114 671181260 0.000000e+00 1112.0
10 TraesCS5A01G334200 chr6B 90.311 867 58 10 1464 2316 623377327 623378181 0.000000e+00 1112.0
11 TraesCS5A01G334200 chr6B 81.343 134 22 3 2181 2313 222680189 222680058 5.750000e-19 106.0
12 TraesCS5A01G334200 chr4A 90.311 867 58 10 1464 2316 609391207 609392061 0.000000e+00 1112.0
13 TraesCS5A01G334200 chr4A 90.081 867 59 12 1464 2316 609307591 609308444 0.000000e+00 1099.0
14 TraesCS5A01G334200 chr4A 79.259 135 24 4 2179 2311 179057335 179057203 1.610000e-14 91.6
15 TraesCS5A01G334200 chr7B 90.196 867 59 10 1464 2316 747634820 747635674 0.000000e+00 1107.0
16 TraesCS5A01G334200 chr3B 90.081 867 59 12 1464 2316 89592978 89593831 0.000000e+00 1099.0
17 TraesCS5A01G334200 chr3B 97.500 40 1 0 3737 3776 481625397 481625358 7.550000e-08 69.4
18 TraesCS5A01G334200 chr6D 80.420 143 25 3 2172 2313 124941395 124941255 5.750000e-19 106.0
19 TraesCS5A01G334200 chr2A 76.168 214 42 7 2100 2312 550549091 550548886 2.070000e-18 104.0
20 TraesCS5A01G334200 chr4D 78.322 143 29 2 2170 2311 301756423 301756564 1.610000e-14 91.6
21 TraesCS5A01G334200 chr4B 94.595 37 1 1 9 45 363309560 363309595 5.880000e-04 56.5


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 TraesCS5A01G334200 chr5A 543926480 543930687 4207 True 7771.000000 7771 100.000000 1 4208 1 chr5A.!!$R1 4207
1 TraesCS5A01G334200 chr5B 517573313 517577700 4387 True 1780.333333 2985 90.030667 94 4198 3 chr5B.!!$R1 4104
2 TraesCS5A01G334200 chr5D 428384422 428388817 4395 True 2349.500000 2471 90.752000 111 4187 2 chr5D.!!$R1 4076
3 TraesCS5A01G334200 chrUn 220215124 220216127 1003 False 1386.000000 1386 91.724000 1464 2464 1 chrUn.!!$F1 1000
4 TraesCS5A01G334200 chr2B 35016645 35017499 854 True 1118.000000 1118 90.427000 1464 2316 1 chr2B.!!$R1 852
5 TraesCS5A01G334200 chr7A 671181260 671182114 854 True 1112.000000 1112 90.311000 1464 2316 1 chr7A.!!$R1 852
6 TraesCS5A01G334200 chr6B 623377327 623378181 854 False 1112.000000 1112 90.311000 1464 2316 1 chr6B.!!$F1 852
7 TraesCS5A01G334200 chr4A 609391207 609392061 854 False 1112.000000 1112 90.311000 1464 2316 1 chr4A.!!$F2 852
8 TraesCS5A01G334200 chr4A 609307591 609308444 853 False 1099.000000 1099 90.081000 1464 2316 1 chr4A.!!$F1 852
9 TraesCS5A01G334200 chr7B 747634820 747635674 854 False 1107.000000 1107 90.196000 1464 2316 1 chr7B.!!$F1 852
10 TraesCS5A01G334200 chr3B 89592978 89593831 853 False 1099.000000 1099 90.081000 1464 2316 1 chr3B.!!$F1 852

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
102 103 0.033228 CAGCTGCCCCGAGAAGATAG 59.967 60.0 0.00 0.00 0.00 2.08 F
191 204 0.321671 TAAGGTGCCTGCACTCTGTC 59.678 55.0 20.52 4.96 45.52 3.51 F
320 335 0.573987 GAGCGACGCCGTAAATTACC 59.426 55.0 17.79 0.00 38.24 2.85 F
1834 2075 0.742281 CTGAGTCCCGATGGTTGCAG 60.742 60.0 0.00 0.00 0.00 4.41 F
2025 2268 1.860676 GTGCACCTACACTGAACGAA 58.139 50.0 5.22 0.00 37.58 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1452 1473 0.581529 CTCGCGTTGTGAAGCTTTCA 59.418 50.00 5.77 0.33 37.33 2.69 R
1979 2222 1.238439 AGGATTGTTCACTGCCAACG 58.762 50.00 0.00 0.00 0.00 4.10 R
2195 2531 4.768145 TCGACAACAGCAAATTAGTTTCG 58.232 39.13 0.00 0.00 32.48 3.46 R
2767 3481 0.373716 CGTACTTGCGCTTTCCCATC 59.626 55.00 9.73 0.00 0.00 3.51 R
4003 4772 0.321346 TGAGATGAGAAAGCACCGCA 59.679 50.00 0.00 0.00 0.00 5.69 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
46 47 7.448748 TTTCAAAAGAAACAGGACTATAGCC 57.551 36.000 0.00 2.38 0.00 3.93
47 48 6.374417 TCAAAAGAAACAGGACTATAGCCT 57.626 37.500 9.23 9.23 35.75 4.58
48 49 6.779860 TCAAAAGAAACAGGACTATAGCCTT 58.220 36.000 11.64 0.79 32.12 4.35
49 50 7.231467 TCAAAAGAAACAGGACTATAGCCTTT 58.769 34.615 11.64 6.47 32.12 3.11
50 51 8.380099 TCAAAAGAAACAGGACTATAGCCTTTA 58.620 33.333 11.64 0.00 32.12 1.85
51 52 8.669243 CAAAAGAAACAGGACTATAGCCTTTAG 58.331 37.037 11.64 5.62 32.12 1.85
52 53 7.735326 AAGAAACAGGACTATAGCCTTTAGA 57.265 36.000 11.64 0.00 32.12 2.10
53 54 7.735326 AGAAACAGGACTATAGCCTTTAGAA 57.265 36.000 11.64 0.00 32.12 2.10
54 55 7.787028 AGAAACAGGACTATAGCCTTTAGAAG 58.213 38.462 11.64 4.52 32.12 2.85
67 68 5.665916 CCTTTAGAAGGCCAATTGACATT 57.334 39.130 5.01 0.00 42.78 2.71
68 69 5.413499 CCTTTAGAAGGCCAATTGACATTG 58.587 41.667 5.01 0.00 42.78 2.82
69 70 5.185635 CCTTTAGAAGGCCAATTGACATTGA 59.814 40.000 5.01 0.00 41.14 2.57
70 71 5.643379 TTAGAAGGCCAATTGACATTGAC 57.357 39.130 5.01 0.00 42.35 3.18
71 72 3.771216 AGAAGGCCAATTGACATTGACT 58.229 40.909 5.01 0.00 42.35 3.41
72 73 4.154942 AGAAGGCCAATTGACATTGACTT 58.845 39.130 5.01 3.00 42.35 3.01
73 74 4.590222 AGAAGGCCAATTGACATTGACTTT 59.410 37.500 5.01 0.00 42.35 2.66
74 75 4.961438 AGGCCAATTGACATTGACTTTT 57.039 36.364 5.01 0.00 42.35 2.27
75 76 4.634199 AGGCCAATTGACATTGACTTTTG 58.366 39.130 5.01 0.00 42.35 2.44
76 77 4.344679 AGGCCAATTGACATTGACTTTTGA 59.655 37.500 5.01 0.00 42.35 2.69
77 78 5.012354 AGGCCAATTGACATTGACTTTTGAT 59.988 36.000 5.01 0.00 42.35 2.57
78 79 6.211184 AGGCCAATTGACATTGACTTTTGATA 59.789 34.615 5.01 0.00 42.35 2.15
79 80 6.532657 GGCCAATTGACATTGACTTTTGATAG 59.467 38.462 7.12 0.00 42.35 2.08
80 81 7.092716 GCCAATTGACATTGACTTTTGATAGT 58.907 34.615 7.12 0.00 42.35 2.12
81 82 7.599998 GCCAATTGACATTGACTTTTGATAGTT 59.400 33.333 7.12 0.00 42.35 2.24
82 83 9.132521 CCAATTGACATTGACTTTTGATAGTTC 57.867 33.333 7.12 0.00 42.35 3.01
83 84 9.132521 CAATTGACATTGACTTTTGATAGTTCC 57.867 33.333 0.00 0.00 42.35 3.62
84 85 7.815840 TTGACATTGACTTTTGATAGTTCCA 57.184 32.000 0.00 0.00 0.00 3.53
85 86 7.439157 TGACATTGACTTTTGATAGTTCCAG 57.561 36.000 0.00 0.00 0.00 3.86
86 87 6.072508 TGACATTGACTTTTGATAGTTCCAGC 60.073 38.462 0.00 0.00 0.00 4.85
87 88 6.006449 ACATTGACTTTTGATAGTTCCAGCT 58.994 36.000 0.00 0.00 0.00 4.24
88 89 5.947228 TTGACTTTTGATAGTTCCAGCTG 57.053 39.130 6.78 6.78 0.00 4.24
89 90 3.753272 TGACTTTTGATAGTTCCAGCTGC 59.247 43.478 8.66 0.00 0.00 5.25
90 91 3.084786 ACTTTTGATAGTTCCAGCTGCC 58.915 45.455 8.66 0.00 0.00 4.85
91 92 2.128771 TTTGATAGTTCCAGCTGCCC 57.871 50.000 8.66 0.00 0.00 5.36
92 93 0.255890 TTGATAGTTCCAGCTGCCCC 59.744 55.000 8.66 0.00 0.00 5.80
93 94 1.227674 GATAGTTCCAGCTGCCCCG 60.228 63.158 8.66 0.00 0.00 5.73
94 95 1.686325 GATAGTTCCAGCTGCCCCGA 61.686 60.000 8.66 0.00 0.00 5.14
95 96 1.690219 ATAGTTCCAGCTGCCCCGAG 61.690 60.000 8.66 0.00 0.00 4.63
96 97 2.798445 TAGTTCCAGCTGCCCCGAGA 62.798 60.000 8.66 0.00 0.00 4.04
97 98 2.927856 TTCCAGCTGCCCCGAGAA 60.928 61.111 8.66 2.17 0.00 2.87
98 99 2.959484 TTCCAGCTGCCCCGAGAAG 61.959 63.158 8.66 0.00 0.00 2.85
99 100 3.393970 CCAGCTGCCCCGAGAAGA 61.394 66.667 8.66 0.00 0.00 2.87
100 101 2.739996 CCAGCTGCCCCGAGAAGAT 61.740 63.158 8.66 0.00 0.00 2.40
101 102 1.402896 CCAGCTGCCCCGAGAAGATA 61.403 60.000 8.66 0.00 0.00 1.98
102 103 0.033228 CAGCTGCCCCGAGAAGATAG 59.967 60.000 0.00 0.00 0.00 2.08
103 104 1.301322 GCTGCCCCGAGAAGATAGC 60.301 63.158 0.00 0.00 0.00 2.97
104 105 2.032860 GCTGCCCCGAGAAGATAGCA 62.033 60.000 0.00 0.00 0.00 3.49
105 106 0.683973 CTGCCCCGAGAAGATAGCAT 59.316 55.000 0.00 0.00 0.00 3.79
106 107 1.071385 CTGCCCCGAGAAGATAGCATT 59.929 52.381 0.00 0.00 0.00 3.56
107 108 1.490490 TGCCCCGAGAAGATAGCATTT 59.510 47.619 0.00 0.00 0.00 2.32
108 109 2.092429 TGCCCCGAGAAGATAGCATTTT 60.092 45.455 0.00 0.00 0.00 1.82
109 110 2.952310 GCCCCGAGAAGATAGCATTTTT 59.048 45.455 0.00 0.00 0.00 1.94
182 195 5.220931 GCAACAGAATAGAATAAGGTGCCTG 60.221 44.000 0.00 0.00 0.00 4.85
183 196 4.455606 ACAGAATAGAATAAGGTGCCTGC 58.544 43.478 0.00 0.00 0.00 4.85
184 197 4.080356 ACAGAATAGAATAAGGTGCCTGCA 60.080 41.667 0.00 0.00 0.00 4.41
185 198 4.274459 CAGAATAGAATAAGGTGCCTGCAC 59.726 45.833 13.75 13.75 45.49 4.57
186 199 4.164988 AGAATAGAATAAGGTGCCTGCACT 59.835 41.667 20.52 5.81 45.52 4.40
187 200 2.409948 AGAATAAGGTGCCTGCACTC 57.590 50.000 20.52 10.61 45.52 3.51
188 201 1.912043 AGAATAAGGTGCCTGCACTCT 59.088 47.619 20.52 12.56 45.52 3.24
189 202 2.012673 GAATAAGGTGCCTGCACTCTG 58.987 52.381 20.52 0.00 45.52 3.35
190 203 0.987294 ATAAGGTGCCTGCACTCTGT 59.013 50.000 20.52 5.15 45.52 3.41
191 204 0.321671 TAAGGTGCCTGCACTCTGTC 59.678 55.000 20.52 4.96 45.52 3.51
192 205 1.414061 AAGGTGCCTGCACTCTGTCT 61.414 55.000 20.52 7.13 45.52 3.41
193 206 1.072159 GGTGCCTGCACTCTGTCTT 59.928 57.895 20.52 0.00 45.52 3.01
205 218 6.101997 TGCACTCTGTCTTGTACTTATCATG 58.898 40.000 0.00 0.00 0.00 3.07
225 240 5.874810 TCATGTCACTTGTTCTTATAGGTGC 59.125 40.000 0.00 0.00 0.00 5.01
278 293 1.912043 CCAGTCCAGGATTCAAGGTCT 59.088 52.381 0.00 0.00 0.00 3.85
320 335 0.573987 GAGCGACGCCGTAAATTACC 59.426 55.000 17.79 0.00 38.24 2.85
367 382 5.108517 GCACTTGTTTGATTTTTGTCAGGA 58.891 37.500 0.00 0.00 0.00 3.86
373 388 5.128499 TGTTTGATTTTTGTCAGGACATGGT 59.872 36.000 2.52 0.00 41.52 3.55
421 436 2.280628 CGCAGGAACTCTTGTTATCCC 58.719 52.381 0.00 0.00 34.60 3.85
548 565 6.655078 ACTTATGTGGCTTTTCAAGATTGT 57.345 33.333 0.00 0.00 0.00 2.71
568 585 9.671279 AGATTGTTGATATCACATTCTGTTACA 57.329 29.630 20.05 11.74 0.00 2.41
592 609 2.583024 TTTGGTCTGTGATGGCATGA 57.417 45.000 3.81 0.00 0.00 3.07
610 627 5.712217 CATGATTGGAATTCATGCACAAC 57.288 39.130 7.93 0.00 35.49 3.32
624 641 9.979578 ATTCATGCACAACTCTTTAATTTGTTA 57.020 25.926 0.00 0.00 30.98 2.41
625 642 9.809096 TTCATGCACAACTCTTTAATTTGTTAA 57.191 25.926 0.00 0.00 30.98 2.01
626 643 9.809096 TCATGCACAACTCTTTAATTTGTTAAA 57.191 25.926 0.00 0.00 30.98 1.52
677 694 7.063456 CCACGTATAGCTCATTAATTTGTTCG 58.937 38.462 0.00 0.00 0.00 3.95
686 703 9.764363 AGCTCATTAATTTGTTCGATATCTGTA 57.236 29.630 0.34 0.00 0.00 2.74
728 746 5.767816 TTTTGATGCATCATCTGATCTGG 57.232 39.130 29.13 0.00 41.06 3.86
729 747 4.432980 TTGATGCATCATCTGATCTGGT 57.567 40.909 29.13 0.00 41.06 4.00
730 748 4.432980 TGATGCATCATCTGATCTGGTT 57.567 40.909 25.42 0.00 41.06 3.67
731 749 4.134563 TGATGCATCATCTGATCTGGTTG 58.865 43.478 25.42 0.00 41.06 3.77
732 750 3.918294 TGCATCATCTGATCTGGTTGA 57.082 42.857 0.00 4.54 31.21 3.18
733 751 4.224991 TGCATCATCTGATCTGGTTGAA 57.775 40.909 9.15 0.00 31.21 2.69
734 752 4.591929 TGCATCATCTGATCTGGTTGAAA 58.408 39.130 9.15 0.00 31.21 2.69
735 753 4.397103 TGCATCATCTGATCTGGTTGAAAC 59.603 41.667 9.15 6.35 31.21 2.78
736 754 4.639310 GCATCATCTGATCTGGTTGAAACT 59.361 41.667 9.15 0.00 31.21 2.66
748 767 6.411376 TCTGGTTGAAACTCTGTACTGAAAA 58.589 36.000 3.89 0.00 0.00 2.29
758 777 7.807977 ACTCTGTACTGAAAAATGTTCATGT 57.192 32.000 3.89 0.00 0.00 3.21
811 830 1.675310 CAAGATTGGTGCGGCTCCA 60.675 57.895 19.09 19.09 0.00 3.86
867 886 4.821589 GGCCGCCTTCGTCTCCTG 62.822 72.222 0.71 0.00 0.00 3.86
1050 1069 4.876752 GTCAGGACCACCTCTCCT 57.123 61.111 0.00 0.00 45.94 3.69
1149 1169 3.380637 TCTTTACGGATGCTCTGGTACTC 59.619 47.826 0.00 0.00 0.00 2.59
1269 1290 1.745320 CGAGGTAGGCGCATTACCCT 61.745 60.000 27.13 18.49 41.23 4.34
1405 1426 8.437360 TGTATCTGTCAATGGATGTTGATTAC 57.563 34.615 0.00 0.00 39.99 1.89
1452 1473 2.928396 AACCCCTACAGCCACGCT 60.928 61.111 0.00 0.00 40.77 5.07
1640 1663 4.695217 TCCTTGGTTAAATGCATCGAAC 57.305 40.909 0.00 7.39 0.00 3.95
1657 1680 6.145696 GCATCGAACTCTAGTTTGTAACTGTT 59.854 38.462 9.41 0.00 42.84 3.16
1714 1955 5.121298 GTGATCCACGTTAAGTAAAAGGGAC 59.879 44.000 0.00 0.00 0.00 4.46
1761 2002 5.353123 TGGGTACAGAAATCGCAATTAACTC 59.647 40.000 0.00 0.00 0.00 3.01
1834 2075 0.742281 CTGAGTCCCGATGGTTGCAG 60.742 60.000 0.00 0.00 0.00 4.41
1848 2089 3.282021 GGTTGCAGCCATCTCATTAGAA 58.718 45.455 15.64 0.00 34.73 2.10
1851 2092 5.279384 GTTGCAGCCATCTCATTAGAATTG 58.721 41.667 0.00 0.00 34.73 2.32
1950 2193 4.545208 TGTTTGTCGATCCCTTGTATCA 57.455 40.909 0.00 0.00 0.00 2.15
1952 2195 6.228616 TGTTTGTCGATCCCTTGTATCATA 57.771 37.500 0.00 0.00 0.00 2.15
1979 2222 8.723942 ATCTTACTTCTGTTCACATACATTCC 57.276 34.615 0.00 0.00 0.00 3.01
2025 2268 1.860676 GTGCACCTACACTGAACGAA 58.139 50.000 5.22 0.00 37.58 3.85
2208 2544 7.349711 TGACAGAACTAACGAAACTAATTTGC 58.650 34.615 0.00 0.00 0.00 3.68
2215 2551 7.130269 ACTAACGAAACTAATTTGCTGTTGTC 58.870 34.615 0.00 0.00 0.00 3.18
2224 2560 7.075741 ACTAATTTGCTGTTGTCGATGTTAAC 58.924 34.615 0.00 0.00 0.00 2.01
2226 2939 3.870723 TGCTGTTGTCGATGTTAACAC 57.129 42.857 11.22 4.38 31.64 3.32
2297 3010 8.850156 ACAAAGCTAGAACTTAATGTGATTTGT 58.150 29.630 0.00 0.00 34.72 2.83
2316 3029 6.418057 TTTGTAACGGAGGGAGTAGTTTTA 57.582 37.500 0.00 0.00 0.00 1.52
2352 3066 6.068473 ACCGAAGTTTCAAAATCCAGTTAC 57.932 37.500 0.00 0.00 0.00 2.50
2426 3140 7.150783 AGAAGTAAAGACAATGGCTCAATTC 57.849 36.000 0.00 0.00 0.00 2.17
2494 3208 9.678260 AGAAAAATAGAATCTCAACTGTGCTAT 57.322 29.630 0.00 0.00 0.00 2.97
2501 3215 8.621532 AGAATCTCAACTGTGCTATTTGTTTA 57.378 30.769 0.00 0.00 0.00 2.01
2502 3216 9.236006 AGAATCTCAACTGTGCTATTTGTTTAT 57.764 29.630 0.00 0.00 0.00 1.40
2503 3217 9.495754 GAATCTCAACTGTGCTATTTGTTTATC 57.504 33.333 0.00 0.00 0.00 1.75
2504 3218 7.977789 TCTCAACTGTGCTATTTGTTTATCA 57.022 32.000 0.00 0.00 0.00 2.15
2505 3219 8.565896 TCTCAACTGTGCTATTTGTTTATCAT 57.434 30.769 0.00 0.00 0.00 2.45
2506 3220 9.013229 TCTCAACTGTGCTATTTGTTTATCATT 57.987 29.630 0.00 0.00 0.00 2.57
2507 3221 9.630098 CTCAACTGTGCTATTTGTTTATCATTT 57.370 29.630 0.00 0.00 0.00 2.32
2540 3254 9.903682 ATATTTCTCTTCATTGCCAATTTATCG 57.096 29.630 0.00 0.00 0.00 2.92
2697 3411 4.438336 GCCCGAAATGTAAGCTCTTAAACC 60.438 45.833 0.00 0.00 0.00 3.27
2712 3426 5.833082 TCTTAAACCGTTTATTTGCAGCAA 58.167 33.333 2.83 2.83 0.00 3.91
2713 3427 6.451393 TCTTAAACCGTTTATTTGCAGCAAT 58.549 32.000 9.12 2.06 0.00 3.56
2732 3446 9.495754 GCAGCAATTTTTAGTAGAATTACAGAG 57.504 33.333 0.00 0.00 31.96 3.35
2743 3457 8.709272 AGTAGAATTACAGAGTTAGTATCCCC 57.291 38.462 0.00 0.00 31.96 4.81
2767 3481 5.285651 GGTGTATCTCTCTTCTTTCATCCG 58.714 45.833 0.00 0.00 0.00 4.18
2801 3515 6.090898 GCGCAAGTACGGAGATATTTGATTAT 59.909 38.462 0.30 0.00 41.68 1.28
2828 3542 1.237285 CCGTCCTGTTTCTTGGCTGG 61.237 60.000 0.00 0.00 0.00 4.85
2848 3562 2.349817 GGTGTGATGAGTTTGCTGTTCG 60.350 50.000 0.00 0.00 0.00 3.95
2900 3614 1.072331 TCAGGTTTTCTCAGTCCAGCC 59.928 52.381 0.00 0.00 0.00 4.85
2931 3645 4.192317 AGTCAGAACCACAAGTTTCAGAC 58.808 43.478 0.00 0.00 39.40 3.51
2936 3650 4.989168 AGAACCACAAGTTTCAGACGATAC 59.011 41.667 0.00 0.00 39.40 2.24
2989 3703 1.263356 CCGGACTCTTTCTGGGTGTA 58.737 55.000 0.00 0.00 46.30 2.90
2990 3704 1.067071 CCGGACTCTTTCTGGGTGTAC 60.067 57.143 0.00 0.00 46.30 2.90
3005 3721 4.101898 TGGGTGTACACAGTATGAAGTGTT 59.898 41.667 26.51 0.00 46.04 3.32
3009 3725 4.988540 TGTACACAGTATGAAGTGTTGCTC 59.011 41.667 3.39 0.00 46.04 4.26
3022 3738 1.409790 TGTTGCTCATGCTTGCTTTGT 59.590 42.857 0.00 0.00 40.48 2.83
3039 3755 6.514947 TGCTTTGTGATGCAAAAATTAGAGT 58.485 32.000 0.00 0.00 45.35 3.24
3040 3756 7.656412 TGCTTTGTGATGCAAAAATTAGAGTA 58.344 30.769 0.00 0.00 45.35 2.59
3047 3763 9.162764 GTGATGCAAAAATTAGAGTACCTTCTA 57.837 33.333 0.00 0.00 0.00 2.10
3051 3767 7.658575 TGCAAAAATTAGAGTACCTTCTAACGT 59.341 33.333 6.71 0.00 41.17 3.99
3052 3768 8.167345 GCAAAAATTAGAGTACCTTCTAACGTC 58.833 37.037 6.71 0.00 41.17 4.34
3053 3769 9.199982 CAAAAATTAGAGTACCTTCTAACGTCA 57.800 33.333 6.71 0.00 41.17 4.35
3054 3770 8.983307 AAAATTAGAGTACCTTCTAACGTCAG 57.017 34.615 6.71 0.00 41.17 3.51
3087 3807 4.038402 CAGTTTTTCAGGAAGTTCCATGCT 59.962 41.667 23.87 8.61 39.61 3.79
3156 3876 2.574399 GCCTCGAGAAGCTTCGGT 59.426 61.111 20.43 4.20 40.83 4.69
3192 3912 4.263905 ACCATAGTGAAATCCTTTGGCTCA 60.264 41.667 0.00 0.00 35.25 4.26
3243 3966 0.323725 AGCACCCTCCGCAATCAATT 60.324 50.000 0.00 0.00 0.00 2.32
3250 3973 2.086869 CTCCGCAATCAATTGTCCTGT 58.913 47.619 5.13 0.00 39.88 4.00
3256 3981 4.615682 CGCAATCAATTGTCCTGTGCTTTA 60.616 41.667 5.13 0.00 39.88 1.85
3329 4055 8.564574 TGTATGTTGGACAAGAAATAGTTTGAC 58.435 33.333 0.00 0.00 0.00 3.18
3334 4060 6.353323 TGGACAAGAAATAGTTTGACACTCA 58.647 36.000 0.00 0.00 36.88 3.41
3338 4064 6.263168 ACAAGAAATAGTTTGACACTCAAGGG 59.737 38.462 0.00 0.00 37.70 3.95
3342 4068 3.760580 AGTTTGACACTCAAGGGAGAG 57.239 47.619 0.00 0.00 44.26 3.20
3384 4115 7.938140 TTACTAAGCATTATGCCTTGTTTCT 57.062 32.000 14.10 0.00 46.52 2.52
3389 4120 4.400567 AGCATTATGCCTTGTTTCTCTTCC 59.599 41.667 14.10 0.00 46.52 3.46
3390 4121 4.400567 GCATTATGCCTTGTTTCTCTTCCT 59.599 41.667 5.80 0.00 37.42 3.36
3391 4122 5.105595 GCATTATGCCTTGTTTCTCTTCCTT 60.106 40.000 5.80 0.00 37.42 3.36
3397 4128 5.363580 TGCCTTGTTTCTCTTCCTTCAATTT 59.636 36.000 0.00 0.00 0.00 1.82
3404 4135 6.808008 TTCTCTTCCTTCAATTTAGTGCAG 57.192 37.500 0.00 0.00 0.00 4.41
3408 4139 3.754965 TCCTTCAATTTAGTGCAGCTGT 58.245 40.909 16.64 0.00 0.00 4.40
3414 4145 5.491070 TCAATTTAGTGCAGCTGTAGTGAT 58.509 37.500 21.00 12.21 0.00 3.06
3419 4150 1.938577 GTGCAGCTGTAGTGATCCATG 59.061 52.381 16.64 0.00 0.00 3.66
3421 4152 1.474677 GCAGCTGTAGTGATCCATGCT 60.475 52.381 16.64 0.00 0.00 3.79
3435 4166 2.038952 TCCATGCTGTGCTGTTACTTCT 59.961 45.455 0.00 0.00 0.00 2.85
3442 4173 4.106029 TGTGCTGTTACTTCTATCGTCC 57.894 45.455 0.00 0.00 0.00 4.79
3458 4189 3.357079 CCGCTTGTGTGGGCTGTC 61.357 66.667 0.00 0.00 40.05 3.51
3475 4206 0.107459 GTCTCCTGCCCATCCTGTTC 60.107 60.000 0.00 0.00 0.00 3.18
3556 4287 3.545703 AGTTCCAGTGAAAGTTGAGTGG 58.454 45.455 0.00 0.00 36.37 4.00
3557 4288 2.618709 GTTCCAGTGAAAGTTGAGTGGG 59.381 50.000 4.77 0.00 35.82 4.61
3561 4292 1.564348 AGTGAAAGTTGAGTGGGTGGT 59.436 47.619 0.00 0.00 0.00 4.16
3581 4317 3.823330 GGCATGGCAGCAGCAGAC 61.823 66.667 15.47 0.00 44.61 3.51
3633 4375 4.091939 TGCTGATGCGCTGGCTCT 62.092 61.111 9.73 0.00 43.34 4.09
3634 4376 3.270839 GCTGATGCGCTGGCTCTC 61.271 66.667 9.73 0.00 40.82 3.20
3635 4377 2.960659 CTGATGCGCTGGCTCTCG 60.961 66.667 9.73 0.00 40.82 4.04
3637 4379 2.510238 GATGCGCTGGCTCTCGTT 60.510 61.111 9.73 0.00 40.82 3.85
3656 4403 3.064545 CGTTTCCTCTGCCTTTCATCATC 59.935 47.826 0.00 0.00 0.00 2.92
3751 4504 9.503399 AAATAAATGAATACTCCCTTCGTATCC 57.497 33.333 0.00 0.00 0.00 2.59
3825 4594 7.336176 GGGAGTAAATTTTAGACCCACTACAAG 59.664 40.741 18.22 0.00 36.27 3.16
3912 4681 0.947244 GCAAGACAACTCCACCACAG 59.053 55.000 0.00 0.00 0.00 3.66
3916 4685 0.663153 GACAACTCCACCACAGCAAC 59.337 55.000 0.00 0.00 0.00 4.17
3918 4687 1.102154 CAACTCCACCACAGCAACAA 58.898 50.000 0.00 0.00 0.00 2.83
3947 4716 1.852067 GCAAAACCGGACGTGCAGAT 61.852 55.000 9.46 0.00 36.97 2.90
3991 4760 0.040425 ACGTCATGCCGAGCAAAAAC 60.040 50.000 1.83 1.89 43.62 2.43
3997 4766 4.089923 GTCATGCCGAGCAAAAACAATAAC 59.910 41.667 2.68 0.00 43.62 1.89
3999 4768 4.046938 TGCCGAGCAAAAACAATAACAA 57.953 36.364 0.00 0.00 34.76 2.83
4001 4770 5.053145 TGCCGAGCAAAAACAATAACAAAT 58.947 33.333 0.00 0.00 34.76 2.32
4002 4771 5.176590 TGCCGAGCAAAAACAATAACAAATC 59.823 36.000 0.00 0.00 34.76 2.17
4003 4772 5.405269 GCCGAGCAAAAACAATAACAAATCT 59.595 36.000 0.00 0.00 0.00 2.40
4004 4773 6.616260 GCCGAGCAAAAACAATAACAAATCTG 60.616 38.462 0.00 0.00 0.00 2.90
4005 4774 6.291385 CGAGCAAAAACAATAACAAATCTGC 58.709 36.000 0.00 0.00 0.00 4.26
4006 4775 6.214205 AGCAAAAACAATAACAAATCTGCG 57.786 33.333 0.00 0.00 0.00 5.18
4007 4776 5.177327 AGCAAAAACAATAACAAATCTGCGG 59.823 36.000 0.00 0.00 0.00 5.69
4058 4842 9.545928 AAGCATGATATATTAGTTCTCTCTCCT 57.454 33.333 0.00 0.00 0.00 3.69
4118 4903 5.775701 ACCACTGACAACTCATACTAACTCT 59.224 40.000 0.00 0.00 0.00 3.24
4189 4977 4.084641 CGATTTTCTCGGCTCATCTCATTC 60.085 45.833 0.00 0.00 43.82 2.67
4191 4979 3.724508 TTCTCGGCTCATCTCATTCTC 57.275 47.619 0.00 0.00 0.00 2.87
4194 4982 1.410517 TCGGCTCATCTCATTCTCCAC 59.589 52.381 0.00 0.00 0.00 4.02
4198 4986 2.360483 GCTCATCTCATTCTCCACGAGA 59.640 50.000 0.00 0.00 39.95 4.04
4199 4987 3.795150 GCTCATCTCATTCTCCACGAGAC 60.795 52.174 0.00 0.00 38.51 3.36
4200 4988 2.356069 TCATCTCATTCTCCACGAGACG 59.644 50.000 0.00 0.00 38.51 4.18
4201 4989 1.095600 TCTCATTCTCCACGAGACGG 58.904 55.000 0.00 0.00 38.51 4.79
4202 4990 0.526524 CTCATTCTCCACGAGACGGC 60.527 60.000 0.00 0.00 38.51 5.68
4203 4991 1.215382 CATTCTCCACGAGACGGCA 59.785 57.895 0.00 0.00 38.51 5.69
4204 4992 0.179100 CATTCTCCACGAGACGGCAT 60.179 55.000 0.00 0.00 38.51 4.40
4205 4993 0.179100 ATTCTCCACGAGACGGCATG 60.179 55.000 0.00 0.00 38.51 4.06
4206 4994 1.248101 TTCTCCACGAGACGGCATGA 61.248 55.000 0.00 0.00 38.51 3.07
4207 4995 1.226802 CTCCACGAGACGGCATGAG 60.227 63.158 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 7.231467 AGGCTATAGTCCTGTTTCTTTTGAAA 58.769 34.615 13.07 0.00 38.05 2.69
23 24 6.779860 AGGCTATAGTCCTGTTTCTTTTGAA 58.220 36.000 13.07 0.00 32.51 2.69
24 25 6.374417 AGGCTATAGTCCTGTTTCTTTTGA 57.626 37.500 13.07 0.00 31.53 2.69
25 26 7.454260 AAAGGCTATAGTCCTGTTTCTTTTG 57.546 36.000 14.17 0.00 33.43 2.44
26 27 8.603304 TCTAAAGGCTATAGTCCTGTTTCTTTT 58.397 33.333 14.17 3.61 33.43 2.27
27 28 8.147244 TCTAAAGGCTATAGTCCTGTTTCTTT 57.853 34.615 14.17 4.22 33.43 2.52
28 29 7.735326 TCTAAAGGCTATAGTCCTGTTTCTT 57.265 36.000 14.17 8.54 33.43 2.52
29 30 7.147637 CCTTCTAAAGGCTATAGTCCTGTTTCT 60.148 40.741 14.17 0.00 42.78 2.52
30 31 6.987404 CCTTCTAAAGGCTATAGTCCTGTTTC 59.013 42.308 14.17 0.00 42.78 2.78
31 32 6.890293 CCTTCTAAAGGCTATAGTCCTGTTT 58.110 40.000 14.17 6.03 42.78 2.83
32 33 6.487299 CCTTCTAAAGGCTATAGTCCTGTT 57.513 41.667 14.17 12.54 42.78 3.16
45 46 5.185635 TCAATGTCAATTGGCCTTCTAAAGG 59.814 40.000 7.75 1.20 45.10 3.11
46 47 6.095377 GTCAATGTCAATTGGCCTTCTAAAG 58.905 40.000 7.75 0.00 41.66 1.85
47 48 6.024552 GTCAATGTCAATTGGCCTTCTAAA 57.975 37.500 7.75 0.00 41.66 1.85
48 49 5.643379 GTCAATGTCAATTGGCCTTCTAA 57.357 39.130 7.75 0.00 41.66 2.10
55 56 7.092716 ACTATCAAAAGTCAATGTCAATTGGC 58.907 34.615 2.20 2.20 46.76 4.52
56 57 9.132521 GAACTATCAAAAGTCAATGTCAATTGG 57.867 33.333 5.42 0.00 42.97 3.16
57 58 9.132521 GGAACTATCAAAAGTCAATGTCAATTG 57.867 33.333 0.00 0.00 43.94 2.32
58 59 8.859090 TGGAACTATCAAAAGTCAATGTCAATT 58.141 29.630 0.00 0.00 0.00 2.32
59 60 8.408043 TGGAACTATCAAAAGTCAATGTCAAT 57.592 30.769 0.00 0.00 0.00 2.57
60 61 7.522073 GCTGGAACTATCAAAAGTCAATGTCAA 60.522 37.037 0.00 0.00 0.00 3.18
61 62 6.072508 GCTGGAACTATCAAAAGTCAATGTCA 60.073 38.462 0.00 0.00 0.00 3.58
62 63 6.150140 AGCTGGAACTATCAAAAGTCAATGTC 59.850 38.462 0.00 0.00 0.00 3.06
63 64 6.006449 AGCTGGAACTATCAAAAGTCAATGT 58.994 36.000 0.00 0.00 0.00 2.71
64 65 6.320171 CAGCTGGAACTATCAAAAGTCAATG 58.680 40.000 5.57 0.00 0.00 2.82
65 66 5.105997 GCAGCTGGAACTATCAAAAGTCAAT 60.106 40.000 17.12 0.00 0.00 2.57
66 67 4.216257 GCAGCTGGAACTATCAAAAGTCAA 59.784 41.667 17.12 0.00 0.00 3.18
67 68 3.753272 GCAGCTGGAACTATCAAAAGTCA 59.247 43.478 17.12 0.00 0.00 3.41
68 69 3.127721 GGCAGCTGGAACTATCAAAAGTC 59.872 47.826 17.12 0.00 0.00 3.01
69 70 3.084786 GGCAGCTGGAACTATCAAAAGT 58.915 45.455 17.12 0.00 0.00 2.66
70 71 2.424956 GGGCAGCTGGAACTATCAAAAG 59.575 50.000 17.12 0.00 0.00 2.27
71 72 2.446435 GGGCAGCTGGAACTATCAAAA 58.554 47.619 17.12 0.00 0.00 2.44
72 73 1.340991 GGGGCAGCTGGAACTATCAAA 60.341 52.381 17.12 0.00 0.00 2.69
73 74 0.255890 GGGGCAGCTGGAACTATCAA 59.744 55.000 17.12 0.00 0.00 2.57
74 75 1.915228 GGGGCAGCTGGAACTATCA 59.085 57.895 17.12 0.00 0.00 2.15
75 76 1.227674 CGGGGCAGCTGGAACTATC 60.228 63.158 17.12 0.00 0.00 2.08
76 77 1.689233 TCGGGGCAGCTGGAACTAT 60.689 57.895 17.12 0.00 0.00 2.12
77 78 2.284331 TCGGGGCAGCTGGAACTA 60.284 61.111 17.12 0.00 0.00 2.24
78 79 3.710722 CTCGGGGCAGCTGGAACT 61.711 66.667 17.12 0.00 0.00 3.01
79 80 3.254024 TTCTCGGGGCAGCTGGAAC 62.254 63.158 17.12 0.00 0.00 3.62
80 81 2.927856 TTCTCGGGGCAGCTGGAA 60.928 61.111 17.12 6.29 0.00 3.53
81 82 3.393970 CTTCTCGGGGCAGCTGGA 61.394 66.667 17.12 2.81 0.00 3.86
82 83 1.402896 TATCTTCTCGGGGCAGCTGG 61.403 60.000 17.12 0.00 0.00 4.85
83 84 0.033228 CTATCTTCTCGGGGCAGCTG 59.967 60.000 10.11 10.11 0.00 4.24
84 85 1.753368 GCTATCTTCTCGGGGCAGCT 61.753 60.000 0.00 0.00 0.00 4.24
85 86 1.301322 GCTATCTTCTCGGGGCAGC 60.301 63.158 0.00 0.00 0.00 5.25
86 87 0.683973 ATGCTATCTTCTCGGGGCAG 59.316 55.000 0.00 0.00 33.23 4.85
87 88 1.131638 AATGCTATCTTCTCGGGGCA 58.868 50.000 0.00 0.00 0.00 5.36
88 89 2.262423 AAATGCTATCTTCTCGGGGC 57.738 50.000 0.00 0.00 0.00 5.80
89 90 4.199310 TGAAAAATGCTATCTTCTCGGGG 58.801 43.478 0.00 0.00 0.00 5.73
90 91 5.123820 TGTTGAAAAATGCTATCTTCTCGGG 59.876 40.000 0.00 0.00 0.00 5.14
91 92 6.092670 TCTGTTGAAAAATGCTATCTTCTCGG 59.907 38.462 0.00 0.00 0.00 4.63
92 93 7.065216 TCTGTTGAAAAATGCTATCTTCTCG 57.935 36.000 0.00 0.00 0.00 4.04
93 94 9.286946 CAATCTGTTGAAAAATGCTATCTTCTC 57.713 33.333 0.00 0.00 37.53 2.87
94 95 9.017509 TCAATCTGTTGAAAAATGCTATCTTCT 57.982 29.630 0.00 0.00 41.22 2.85
95 96 9.286946 CTCAATCTGTTGAAAAATGCTATCTTC 57.713 33.333 0.00 0.00 43.39 2.87
96 97 8.800332 ACTCAATCTGTTGAAAAATGCTATCTT 58.200 29.630 0.00 0.00 43.39 2.40
97 98 8.345724 ACTCAATCTGTTGAAAAATGCTATCT 57.654 30.769 0.00 0.00 43.39 1.98
102 103 8.749499 GCATATACTCAATCTGTTGAAAAATGC 58.251 33.333 9.54 9.54 43.39 3.56
105 106 7.970061 GCAGCATATACTCAATCTGTTGAAAAA 59.030 33.333 0.00 0.00 43.39 1.94
106 107 7.415541 GGCAGCATATACTCAATCTGTTGAAAA 60.416 37.037 0.00 0.00 43.39 2.29
107 108 6.038603 GGCAGCATATACTCAATCTGTTGAAA 59.961 38.462 0.00 0.00 43.39 2.69
108 109 5.528690 GGCAGCATATACTCAATCTGTTGAA 59.471 40.000 0.00 0.00 43.39 2.69
109 110 5.059161 GGCAGCATATACTCAATCTGTTGA 58.941 41.667 0.00 0.00 41.89 3.18
182 195 6.102663 ACATGATAAGTACAAGACAGAGTGC 58.897 40.000 0.00 0.00 0.00 4.40
183 196 7.274468 GTGACATGATAAGTACAAGACAGAGTG 59.726 40.741 0.00 0.00 0.00 3.51
184 197 7.177568 AGTGACATGATAAGTACAAGACAGAGT 59.822 37.037 0.00 0.00 0.00 3.24
185 198 7.542890 AGTGACATGATAAGTACAAGACAGAG 58.457 38.462 0.00 0.00 0.00 3.35
186 199 7.468141 AGTGACATGATAAGTACAAGACAGA 57.532 36.000 0.00 0.00 0.00 3.41
187 200 7.600375 ACAAGTGACATGATAAGTACAAGACAG 59.400 37.037 0.00 0.00 0.00 3.51
188 201 7.441836 ACAAGTGACATGATAAGTACAAGACA 58.558 34.615 0.00 0.00 0.00 3.41
189 202 7.891183 ACAAGTGACATGATAAGTACAAGAC 57.109 36.000 0.00 0.00 0.00 3.01
190 203 8.367911 AGAACAAGTGACATGATAAGTACAAGA 58.632 33.333 0.00 0.00 0.00 3.02
191 204 8.539770 AGAACAAGTGACATGATAAGTACAAG 57.460 34.615 0.00 0.00 0.00 3.16
192 205 8.902540 AAGAACAAGTGACATGATAAGTACAA 57.097 30.769 0.00 0.00 0.00 2.41
205 218 4.833390 AGGCACCTATAAGAACAAGTGAC 58.167 43.478 0.00 0.00 33.33 3.67
225 240 1.747355 CCCAGAGCACTTGCAATAAGG 59.253 52.381 0.00 0.00 45.16 2.69
278 293 1.223487 GCGGATGCCCTGGAAAGTA 59.777 57.895 0.00 0.00 33.98 2.24
302 317 0.807275 GGGTAATTTACGGCGTCGCT 60.807 55.000 19.21 2.02 40.63 4.93
320 335 3.314331 ACCAGACGGCAGAGTGGG 61.314 66.667 12.25 3.97 34.07 4.61
388 403 4.385825 AGTTCCTGCGTATGAAACTTTGA 58.614 39.130 0.00 0.00 0.00 2.69
389 404 4.452455 AGAGTTCCTGCGTATGAAACTTTG 59.548 41.667 0.00 0.00 0.00 2.77
421 436 2.125350 GCCGCCTCTGAGTTCAGG 60.125 66.667 9.13 2.71 43.91 3.86
473 488 5.639931 GCTTATTCCGTTCTCAAACTTCTCT 59.360 40.000 0.00 0.00 32.95 3.10
474 489 5.408604 TGCTTATTCCGTTCTCAAACTTCTC 59.591 40.000 0.00 0.00 32.95 2.87
476 491 5.179555 AGTGCTTATTCCGTTCTCAAACTTC 59.820 40.000 0.00 0.00 32.95 3.01
478 493 4.642429 AGTGCTTATTCCGTTCTCAAACT 58.358 39.130 0.00 0.00 32.95 2.66
479 494 6.312918 TCATAGTGCTTATTCCGTTCTCAAAC 59.687 38.462 0.00 0.00 0.00 2.93
480 495 6.403049 TCATAGTGCTTATTCCGTTCTCAAA 58.597 36.000 0.00 0.00 0.00 2.69
489 506 9.453572 TGGATTAATCATCATAGTGCTTATTCC 57.546 33.333 17.07 0.00 34.26 3.01
526 543 7.147312 TCAACAATCTTGAAAAGCCACATAAG 58.853 34.615 0.00 0.00 45.70 1.73
592 609 5.733620 AAGAGTTGTGCATGAATTCCAAT 57.266 34.783 2.27 0.00 0.00 3.16
646 663 6.745159 TTAATGAGCTATACGTGGCAAAAA 57.255 33.333 0.00 0.00 33.68 1.94
659 676 9.764363 ACAGATATCGAACAAATTAATGAGCTA 57.236 29.630 0.00 0.00 0.00 3.32
708 726 4.432980 ACCAGATCAGATGATGCATCAA 57.567 40.909 31.79 16.85 42.72 2.57
710 728 4.386711 TCAACCAGATCAGATGATGCATC 58.613 43.478 20.14 20.14 40.80 3.91
712 730 3.918294 TCAACCAGATCAGATGATGCA 57.082 42.857 0.00 0.00 34.37 3.96
713 731 4.639310 AGTTTCAACCAGATCAGATGATGC 59.361 41.667 0.00 0.00 34.37 3.91
714 732 6.037281 CAGAGTTTCAACCAGATCAGATGATG 59.963 42.308 0.00 0.00 34.37 3.07
715 733 6.114089 CAGAGTTTCAACCAGATCAGATGAT 58.886 40.000 0.00 0.00 37.51 2.45
716 734 5.012458 ACAGAGTTTCAACCAGATCAGATGA 59.988 40.000 0.00 0.00 0.00 2.92
717 735 5.243981 ACAGAGTTTCAACCAGATCAGATG 58.756 41.667 0.00 0.00 0.00 2.90
718 736 5.495926 ACAGAGTTTCAACCAGATCAGAT 57.504 39.130 0.00 0.00 0.00 2.90
720 738 5.636965 CAGTACAGAGTTTCAACCAGATCAG 59.363 44.000 0.00 0.00 0.00 2.90
721 739 5.304357 TCAGTACAGAGTTTCAACCAGATCA 59.696 40.000 0.00 0.00 0.00 2.92
722 740 5.784177 TCAGTACAGAGTTTCAACCAGATC 58.216 41.667 0.00 0.00 0.00 2.75
723 741 5.808366 TCAGTACAGAGTTTCAACCAGAT 57.192 39.130 0.00 0.00 0.00 2.90
725 743 6.677781 TTTTCAGTACAGAGTTTCAACCAG 57.322 37.500 0.00 0.00 0.00 4.00
726 744 7.122055 ACATTTTTCAGTACAGAGTTTCAACCA 59.878 33.333 0.00 0.00 0.00 3.67
727 745 7.480810 ACATTTTTCAGTACAGAGTTTCAACC 58.519 34.615 0.00 0.00 0.00 3.77
728 746 8.911247 AACATTTTTCAGTACAGAGTTTCAAC 57.089 30.769 0.00 0.00 0.00 3.18
729 747 8.735315 TGAACATTTTTCAGTACAGAGTTTCAA 58.265 29.630 0.00 0.00 0.00 2.69
730 748 8.275015 TGAACATTTTTCAGTACAGAGTTTCA 57.725 30.769 0.00 0.00 0.00 2.69
731 749 9.173939 CATGAACATTTTTCAGTACAGAGTTTC 57.826 33.333 0.00 0.00 0.00 2.78
732 750 8.686334 ACATGAACATTTTTCAGTACAGAGTTT 58.314 29.630 0.00 0.00 0.00 2.66
733 751 8.131100 CACATGAACATTTTTCAGTACAGAGTT 58.869 33.333 0.00 0.00 0.00 3.01
734 752 7.498900 TCACATGAACATTTTTCAGTACAGAGT 59.501 33.333 0.00 0.00 0.00 3.24
735 753 7.800380 GTCACATGAACATTTTTCAGTACAGAG 59.200 37.037 0.00 0.00 0.00 3.35
736 754 7.518211 CGTCACATGAACATTTTTCAGTACAGA 60.518 37.037 0.00 0.00 0.00 3.41
748 767 3.187227 GCTTCAGACGTCACATGAACATT 59.813 43.478 19.50 0.00 0.00 2.71
758 777 1.538204 GGTTCAGTGCTTCAGACGTCA 60.538 52.381 19.50 0.00 0.00 4.35
806 825 1.448013 GTCTACCGGTGCTTGGAGC 60.448 63.158 19.93 0.00 42.82 4.70
936 955 3.345808 GCAGTTGAAGCGGCGACA 61.346 61.111 12.98 4.18 0.00 4.35
1117 1136 3.873952 GCATCCGTAAAGAAGATCAGCTT 59.126 43.478 0.00 0.00 40.25 3.74
1149 1169 4.072088 GCGGGTTGTTCTGCGACG 62.072 66.667 0.00 0.00 32.16 5.12
1269 1290 3.005897 GCCTAGATCTAGATTGCCACGAA 59.994 47.826 28.04 0.00 35.21 3.85
1369 1390 6.823182 CCATTGACAGATACAACAAGATACCA 59.177 38.462 0.00 0.00 0.00 3.25
1433 1454 2.267961 CGTGGCTGTAGGGGTTCC 59.732 66.667 0.00 0.00 0.00 3.62
1452 1473 0.581529 CTCGCGTTGTGAAGCTTTCA 59.418 50.000 5.77 0.33 37.33 2.69
1640 1663 7.597743 ACGTCCATTAACAGTTACAAACTAGAG 59.402 37.037 0.00 0.00 40.46 2.43
1714 1955 7.083858 CCACACAACATGGAATTTGTAACTAG 58.916 38.462 0.00 0.00 39.87 2.57
1761 2002 1.400846 CTTTGCATAGCAGAGTGGCAG 59.599 52.381 1.76 0.00 40.61 4.85
1797 2038 3.898123 CTCAGCTGGAAACCCTATAGCTA 59.102 47.826 15.13 0.00 42.38 3.32
1848 2089 9.595955 ACAGACCCATGTGAATTGAGTCTCAAT 62.596 40.741 20.33 20.33 39.21 2.57
1851 2092 3.937706 CAGACCCATGTGAATTGAGTCTC 59.062 47.826 0.00 0.00 30.99 3.36
1963 2206 3.426159 GCCAACGGAATGTATGTGAACAG 60.426 47.826 0.00 0.00 31.70 3.16
1979 2222 1.238439 AGGATTGTTCACTGCCAACG 58.762 50.000 0.00 0.00 0.00 4.10
2025 2268 7.282450 GTCGGATATAGAAGACCCAAAAATGTT 59.718 37.037 0.00 0.00 0.00 2.71
2195 2531 4.768145 TCGACAACAGCAAATTAGTTTCG 58.232 39.130 0.00 0.00 32.48 3.46
2208 2544 7.678194 AAAAATGTGTTAACATCGACAACAG 57.322 32.000 12.26 0.00 46.58 3.16
2297 3010 8.592809 TGTAAATTAAAACTACTCCCTCCGTTA 58.407 33.333 0.00 0.00 0.00 3.18
2331 3045 6.142320 GCAAGTAACTGGATTTTGAAACTTCG 59.858 38.462 0.00 0.00 0.00 3.79
2352 3066 3.466836 TGTGACTCTGTGTAAAGGCAAG 58.533 45.455 0.00 0.00 30.78 4.01
2417 3131 9.213799 CTAATATACTCTTTCTGGAATTGAGCC 57.786 37.037 11.10 0.00 0.00 4.70
2426 3140 8.370940 TGCAGGAATCTAATATACTCTTTCTGG 58.629 37.037 0.00 0.00 0.00 3.86
2445 3159 6.048732 TCACTTGACATTATACTGCAGGAA 57.951 37.500 19.93 9.51 0.00 3.36
2508 3222 9.638176 ATTGGCAATGAAGAGAAATATTACTCT 57.362 29.630 12.82 0.00 44.03 3.24
2557 3271 9.665719 TCATAGTTCATGAATTGTTAGCAGTAA 57.334 29.630 12.12 0.00 40.80 2.24
2561 3275 7.920160 TGTCATAGTTCATGAATTGTTAGCA 57.080 32.000 12.12 3.73 45.28 3.49
2646 3360 6.408869 TGCATCTTTCACATCAAGATCAGTA 58.591 36.000 0.00 0.00 38.67 2.74
2697 3411 9.123709 TCTACTAAAAATTGCTGCAAATAAACG 57.876 29.630 20.06 9.41 0.00 3.60
2732 3446 4.405548 AGAGATACACCGGGGATACTAAC 58.594 47.826 12.96 0.00 0.00 2.34
2734 3448 3.915073 AGAGAGATACACCGGGGATACTA 59.085 47.826 12.96 0.00 0.00 1.82
2743 3457 5.285651 GGATGAAAGAAGAGAGATACACCG 58.714 45.833 0.00 0.00 0.00 4.94
2767 3481 0.373716 CGTACTTGCGCTTTCCCATC 59.626 55.000 9.73 0.00 0.00 3.51
2808 3522 1.073199 AGCCAAGAAACAGGACGGG 59.927 57.895 0.00 0.00 0.00 5.28
2828 3542 2.287915 ACGAACAGCAAACTCATCACAC 59.712 45.455 0.00 0.00 0.00 3.82
2866 3580 1.663695 ACCTGACACTTTCCACGTTG 58.336 50.000 0.00 0.00 0.00 4.10
2873 3587 4.273724 GGACTGAGAAAACCTGACACTTTC 59.726 45.833 0.00 0.00 0.00 2.62
2949 3663 7.008332 TCCGGAATTTAGGAGTATCATCACTA 58.992 38.462 0.00 0.00 36.25 2.74
2950 3664 5.839063 TCCGGAATTTAGGAGTATCATCACT 59.161 40.000 0.00 0.00 36.25 3.41
2951 3665 5.927115 GTCCGGAATTTAGGAGTATCATCAC 59.073 44.000 5.23 0.00 37.18 3.06
2952 3666 5.839063 AGTCCGGAATTTAGGAGTATCATCA 59.161 40.000 5.23 0.00 38.35 3.07
2953 3667 6.209788 AGAGTCCGGAATTTAGGAGTATCATC 59.790 42.308 5.23 0.00 40.08 2.92
2954 3668 6.078664 AGAGTCCGGAATTTAGGAGTATCAT 58.921 40.000 5.23 0.00 40.08 2.45
2968 3682 0.685097 CACCCAGAAAGAGTCCGGAA 59.315 55.000 5.23 0.00 0.00 4.30
2972 3686 2.367567 TGTGTACACCCAGAAAGAGTCC 59.632 50.000 22.91 0.00 0.00 3.85
2990 3704 4.670992 GCATGAGCAACACTTCATACTGTG 60.671 45.833 0.00 0.00 41.58 3.66
2994 3710 4.409570 CAAGCATGAGCAACACTTCATAC 58.590 43.478 0.00 0.00 45.49 2.39
3005 3721 1.320507 TCACAAAGCAAGCATGAGCA 58.679 45.000 0.00 0.00 45.49 4.26
3009 3725 2.073117 TGCATCACAAAGCAAGCATG 57.927 45.000 0.00 0.00 37.90 4.06
3022 3738 9.733556 TTAGAAGGTACTCTAATTTTTGCATCA 57.266 29.630 1.47 0.00 38.49 3.07
3039 3755 5.243283 AGAAAAGAGCTGACGTTAGAAGGTA 59.757 40.000 12.13 0.00 0.00 3.08
3040 3756 4.039366 AGAAAAGAGCTGACGTTAGAAGGT 59.961 41.667 12.13 2.24 0.00 3.50
3047 3763 3.460857 ACTGAGAAAAGAGCTGACGTT 57.539 42.857 0.00 0.00 0.00 3.99
3051 3767 5.297776 CCTGAAAAACTGAGAAAAGAGCTGA 59.702 40.000 0.00 0.00 0.00 4.26
3052 3768 5.297776 TCCTGAAAAACTGAGAAAAGAGCTG 59.702 40.000 0.00 0.00 0.00 4.24
3053 3769 5.440610 TCCTGAAAAACTGAGAAAAGAGCT 58.559 37.500 0.00 0.00 0.00 4.09
3054 3770 5.757850 TCCTGAAAAACTGAGAAAAGAGC 57.242 39.130 0.00 0.00 0.00 4.09
3087 3807 3.975083 GACGGCGTCCACGTATGCA 62.975 63.158 28.72 0.00 45.68 3.96
3156 3876 0.457443 CTATGGTGCTCACTCTCGCA 59.543 55.000 0.00 0.00 0.00 5.10
3186 3906 2.997315 CCGACAGTCCCTGAGCCA 60.997 66.667 0.00 0.00 35.18 4.75
3192 3912 2.854963 GGTTTTTAACCGACAGTCCCT 58.145 47.619 0.00 0.00 42.62 4.20
3250 3973 1.202782 TGCCGGTTAAGGTGTAAAGCA 60.203 47.619 1.90 0.00 0.00 3.91
3256 3981 1.058284 TAGGTTGCCGGTTAAGGTGT 58.942 50.000 1.90 0.00 0.00 4.16
3329 4055 3.900601 AGCCATATACTCTCCCTTGAGTG 59.099 47.826 7.34 0.00 45.70 3.51
3334 4060 6.558775 TCAATAACAGCCATATACTCTCCCTT 59.441 38.462 0.00 0.00 0.00 3.95
3384 4115 4.456911 CAGCTGCACTAAATTGAAGGAAGA 59.543 41.667 0.00 0.00 0.00 2.87
3389 4120 5.409520 TCACTACAGCTGCACTAAATTGAAG 59.590 40.000 15.27 0.00 0.00 3.02
3390 4121 5.304778 TCACTACAGCTGCACTAAATTGAA 58.695 37.500 15.27 0.00 0.00 2.69
3391 4122 4.893608 TCACTACAGCTGCACTAAATTGA 58.106 39.130 15.27 2.58 0.00 2.57
3397 4128 2.456577 TGGATCACTACAGCTGCACTA 58.543 47.619 15.27 0.00 0.00 2.74
3404 4135 1.938577 CACAGCATGGATCACTACAGC 59.061 52.381 0.00 0.00 43.62 4.40
3408 4139 1.556451 ACAGCACAGCATGGATCACTA 59.444 47.619 0.00 0.00 43.62 2.74
3414 4145 2.038952 AGAAGTAACAGCACAGCATGGA 59.961 45.455 0.00 0.00 43.62 3.41
3419 4150 3.512680 ACGATAGAAGTAACAGCACAGC 58.487 45.455 0.00 0.00 41.38 4.40
3421 4152 3.427098 CGGACGATAGAAGTAACAGCACA 60.427 47.826 0.00 0.00 41.38 4.57
3435 4166 1.216977 CCCACACAAGCGGACGATA 59.783 57.895 0.00 0.00 0.00 2.92
3442 4173 2.281070 AGACAGCCCACACAAGCG 60.281 61.111 0.00 0.00 0.00 4.68
3458 4189 1.225704 GGAACAGGATGGGCAGGAG 59.774 63.158 0.00 0.00 43.62 3.69
3511 4242 1.683011 CCCTAGTCACCCATGCTTTGG 60.683 57.143 0.00 0.00 46.00 3.28
3556 4287 2.658422 CTGCCATGCCAAACCACC 59.342 61.111 0.00 0.00 0.00 4.61
3557 4288 2.047939 GCTGCCATGCCAAACCAC 60.048 61.111 0.00 0.00 0.00 4.16
3561 4292 2.918276 TGCTGCTGCCATGCCAAA 60.918 55.556 13.47 0.00 38.71 3.28
3633 4375 2.038426 TGATGAAAGGCAGAGGAAACGA 59.962 45.455 0.00 0.00 0.00 3.85
3634 4376 2.426522 TGATGAAAGGCAGAGGAAACG 58.573 47.619 0.00 0.00 0.00 3.60
3635 4377 4.012374 TGATGATGAAAGGCAGAGGAAAC 58.988 43.478 0.00 0.00 0.00 2.78
3637 4379 3.371273 CCTGATGATGAAAGGCAGAGGAA 60.371 47.826 0.00 0.00 0.00 3.36
3656 4403 1.330655 ATACCTGTCGGCTCCACCTG 61.331 60.000 0.00 0.00 35.61 4.00
3737 4490 7.850935 TCTTATATTTGGATACGAAGGGAGT 57.149 36.000 0.00 0.00 45.12 3.85
3795 4564 4.853276 TGGGTCTAAAATTTACTCCCTCCA 59.147 41.667 16.14 6.78 35.00 3.86
3809 4578 6.503560 TTCCTTTCTTGTAGTGGGTCTAAA 57.496 37.500 0.00 0.00 0.00 1.85
3825 4594 8.138074 GGCTCACCAATATTATCTTTTCCTTTC 58.862 37.037 0.00 0.00 35.26 2.62
3912 4681 3.561155 TTTGCGTTTCGAAATTGTTGC 57.439 38.095 14.69 13.11 0.00 4.17
3916 4685 2.097637 CCGGTTTTGCGTTTCGAAATTG 60.098 45.455 14.69 10.97 31.17 2.32
3918 4687 1.334243 TCCGGTTTTGCGTTTCGAAAT 59.666 42.857 14.69 0.00 31.17 2.17
3974 4743 2.132740 TTGTTTTTGCTCGGCATGAC 57.867 45.000 0.00 0.00 38.76 3.06
3986 4755 5.050431 GCACCGCAGATTTGTTATTGTTTTT 60.050 36.000 0.00 0.00 0.00 1.94
3991 4760 3.492421 AGCACCGCAGATTTGTTATTG 57.508 42.857 0.00 0.00 0.00 1.90
3997 4766 1.536766 TGAGAAAGCACCGCAGATTTG 59.463 47.619 0.00 0.00 0.00 2.32
3999 4768 2.012673 GATGAGAAAGCACCGCAGATT 58.987 47.619 0.00 0.00 0.00 2.40
4001 4770 0.610174 AGATGAGAAAGCACCGCAGA 59.390 50.000 0.00 0.00 0.00 4.26
4002 4771 1.005340 GAGATGAGAAAGCACCGCAG 58.995 55.000 0.00 0.00 0.00 5.18
4003 4772 0.321346 TGAGATGAGAAAGCACCGCA 59.679 50.000 0.00 0.00 0.00 5.69
4004 4773 1.005340 CTGAGATGAGAAAGCACCGC 58.995 55.000 0.00 0.00 0.00 5.68
4005 4774 2.094286 AGTCTGAGATGAGAAAGCACCG 60.094 50.000 0.00 0.00 0.00 4.94
4006 4775 3.608316 AGTCTGAGATGAGAAAGCACC 57.392 47.619 0.00 0.00 0.00 5.01
4007 4776 5.323371 ACTAGTCTGAGATGAGAAAGCAC 57.677 43.478 0.00 0.00 0.00 4.40
4118 4903 3.760151 AGCTGAAAACATAGCATGCTTCA 59.240 39.130 28.02 20.26 42.29 3.02
4148 4934 7.492344 AGAAAATCGACTGAAAGCAACAAAAAT 59.508 29.630 0.00 0.00 37.60 1.82
4176 4964 1.410517 TCGTGGAGAATGAGATGAGCC 59.589 52.381 0.00 0.00 0.00 4.70
4177 4965 2.360483 TCTCGTGGAGAATGAGATGAGC 59.640 50.000 0.00 0.00 44.46 4.26
4189 4977 1.226802 CTCATGCCGTCTCGTGGAG 60.227 63.158 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.