Multiple sequence alignment - TraesCS7D01G128300

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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 TraesCS7D01G128300 chr7D 100.000 4449 0 0 1 4449 80504983 80509431 0.000000e+00 8216.0
1 TraesCS7D01G128300 chr7D 87.106 1016 82 30 3437 4437 80709141 80710122 0.000000e+00 1105.0
2 TraesCS7D01G128300 chr7D 93.586 343 18 2 3447 3785 80520237 80520579 3.970000e-140 508.0
3 TraesCS7D01G128300 chr7D 86.159 289 28 8 4021 4299 80520622 80520908 7.230000e-78 302.0
4 TraesCS7D01G128300 chr7D 86.364 110 13 2 4326 4435 80520909 80521016 7.820000e-23 119.0
5 TraesCS7D01G128300 chr7D 100.000 51 0 0 100 150 448687378 448687328 1.320000e-15 95.3
6 TraesCS7D01G128300 chr7D 93.333 45 2 1 2874 2917 80520633 80520589 1.030000e-06 65.8
7 TraesCS7D01G128300 chr7A 89.819 3919 232 69 429 4284 83284772 83288586 0.000000e+00 4872.0
8 TraesCS7D01G128300 chr7B 89.715 3714 217 76 171 3796 27819304 27822940 0.000000e+00 4590.0
9 TraesCS7D01G128300 chr7B 86.189 391 36 12 3912 4287 28055722 28056109 1.490000e-109 407.0
10 TraesCS7D01G128300 chr7B 89.423 208 7 10 4227 4423 27823128 27823331 9.560000e-62 248.0
11 TraesCS7D01G128300 chr7B 95.575 113 5 0 3914 4026 27822953 27823065 9.830000e-42 182.0
12 TraesCS7D01G128300 chr7B 94.203 69 3 1 4064 4132 27823063 27823130 2.190000e-18 104.0
13 TraesCS7D01G128300 chr7B 96.429 56 2 0 95 150 743467976 743467921 4.740000e-15 93.5
14 TraesCS7D01G128300 chr5A 82.927 123 18 3 4326 4447 509042454 509042334 1.690000e-19 108.0
15 TraesCS7D01G128300 chr1D 85.000 100 14 1 4326 4424 223787064 223786965 2.830000e-17 100.0
16 TraesCS7D01G128300 chr1D 81.513 119 21 1 4329 4447 413199163 413199046 3.660000e-16 97.1
17 TraesCS7D01G128300 chr4D 98.148 54 1 0 97 150 191234891 191234838 1.320000e-15 95.3
18 TraesCS7D01G128300 chr1B 84.000 100 15 1 4326 4424 323332661 323332562 1.320000e-15 95.3
19 TraesCS7D01G128300 chr6D 92.308 65 5 0 86 150 422026894 422026958 4.740000e-15 93.5
20 TraesCS7D01G128300 chr3B 98.113 53 1 0 98 150 459409042 459409094 4.740000e-15 93.5
21 TraesCS7D01G128300 chr3B 96.429 56 2 0 96 151 558519854 558519799 4.740000e-15 93.5
22 TraesCS7D01G128300 chr6B 96.364 55 2 0 96 150 48548629 48548683 1.700000e-14 91.6
23 TraesCS7D01G128300 chr6B 90.278 72 3 4 81 150 280098602 280098671 1.700000e-14 91.6
24 TraesCS7D01G128300 chr6A 96.364 55 2 0 96 150 178876043 178875989 1.700000e-14 91.6


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 TraesCS7D01G128300 chr7D 80504983 80509431 4448 False 8216.000000 8216 100.000 1 4449 1 chr7D.!!$F1 4448
1 TraesCS7D01G128300 chr7D 80709141 80710122 981 False 1105.000000 1105 87.106 3437 4437 1 chr7D.!!$F2 1000
2 TraesCS7D01G128300 chr7D 80520237 80521016 779 False 309.666667 508 88.703 3447 4435 3 chr7D.!!$F3 988
3 TraesCS7D01G128300 chr7A 83284772 83288586 3814 False 4872.000000 4872 89.819 429 4284 1 chr7A.!!$F1 3855
4 TraesCS7D01G128300 chr7B 27819304 27823331 4027 False 1281.000000 4590 92.229 171 4423 4 chr7B.!!$F2 4252

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
499 535 0.036199 CGGGGTCAACAATCCGGTTA 60.036 55.0 0.00 0.00 38.93 2.85 F
755 843 0.107945 CAGCTAGGCAAGTCCAGGAC 60.108 60.0 12.25 12.25 37.29 3.85 F
1633 1766 0.110486 ATTGTCGCCTGGTGTTCCTT 59.890 50.0 7.20 0.00 34.23 3.36 F
2570 2716 0.320697 ACCTCCTGAGTTTACGTGGC 59.679 55.0 0.00 0.00 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2156 0.529378 CAGCAAGGAACATCAAGGCC 59.471 55.000 0.0 0.0 0.0 5.19 R
2093 2231 2.401583 TGTGTGGTTAGGCAGCTATG 57.598 50.000 0.0 0.0 0.0 2.23 R
3364 3510 0.099968 CGACGGAACTAGCCATCGAA 59.900 55.000 0.0 0.0 0.0 3.71 R
3861 4029 1.002033 ACAGAAAGCAAAAGCTCAGCG 60.002 47.619 0.0 0.0 0.0 5.18 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
75 76 7.654022 GGATTCCTTTTTGTAATCCATACCA 57.346 36.000 8.15 0.00 45.31 3.25
76 77 8.073467 GGATTCCTTTTTGTAATCCATACCAA 57.927 34.615 8.15 0.00 45.31 3.67
77 78 8.536175 GGATTCCTTTTTGTAATCCATACCAAA 58.464 33.333 8.15 0.00 45.31 3.28
78 79 9.366216 GATTCCTTTTTGTAATCCATACCAAAC 57.634 33.333 0.00 0.00 31.09 2.93
79 80 7.234661 TCCTTTTTGTAATCCATACCAAACC 57.765 36.000 0.00 0.00 31.09 3.27
80 81 6.782988 TCCTTTTTGTAATCCATACCAAACCA 59.217 34.615 0.00 0.00 31.09 3.67
81 82 7.039363 TCCTTTTTGTAATCCATACCAAACCAG 60.039 37.037 0.00 0.00 31.09 4.00
82 83 5.652994 TTTGTAATCCATACCAAACCAGC 57.347 39.130 0.00 0.00 33.27 4.85
83 84 4.308526 TGTAATCCATACCAAACCAGCA 57.691 40.909 0.00 0.00 33.27 4.41
84 85 4.865905 TGTAATCCATACCAAACCAGCAT 58.134 39.130 0.00 0.00 33.27 3.79
85 86 6.007485 TGTAATCCATACCAAACCAGCATA 57.993 37.500 0.00 0.00 33.27 3.14
86 87 6.609876 TGTAATCCATACCAAACCAGCATAT 58.390 36.000 0.00 0.00 33.27 1.78
87 88 7.066142 TGTAATCCATACCAAACCAGCATATT 58.934 34.615 0.00 0.00 33.27 1.28
88 89 7.563188 TGTAATCCATACCAAACCAGCATATTT 59.437 33.333 0.00 0.00 33.27 1.40
89 90 9.073475 GTAATCCATACCAAACCAGCATATTTA 57.927 33.333 0.00 0.00 0.00 1.40
90 91 7.765695 ATCCATACCAAACCAGCATATTTAG 57.234 36.000 0.00 0.00 0.00 1.85
91 92 6.905736 TCCATACCAAACCAGCATATTTAGA 58.094 36.000 0.00 0.00 0.00 2.10
92 93 7.350382 TCCATACCAAACCAGCATATTTAGAA 58.650 34.615 0.00 0.00 0.00 2.10
93 94 7.284489 TCCATACCAAACCAGCATATTTAGAAC 59.716 37.037 0.00 0.00 0.00 3.01
94 95 5.914898 ACCAAACCAGCATATTTAGAACC 57.085 39.130 0.00 0.00 0.00 3.62
95 96 5.329399 ACCAAACCAGCATATTTAGAACCA 58.671 37.500 0.00 0.00 0.00 3.67
96 97 5.777732 ACCAAACCAGCATATTTAGAACCAA 59.222 36.000 0.00 0.00 0.00 3.67
97 98 6.440328 ACCAAACCAGCATATTTAGAACCAAT 59.560 34.615 0.00 0.00 0.00 3.16
98 99 7.038373 ACCAAACCAGCATATTTAGAACCAATT 60.038 33.333 0.00 0.00 0.00 2.32
99 100 7.823799 CCAAACCAGCATATTTAGAACCAATTT 59.176 33.333 0.00 0.00 0.00 1.82
100 101 9.868277 CAAACCAGCATATTTAGAACCAATTTA 57.132 29.630 0.00 0.00 0.00 1.40
112 113 9.681062 TTTAGAACCAATTTATTACTCCCTCTG 57.319 33.333 0.00 0.00 0.00 3.35
113 114 7.272144 AGAACCAATTTATTACTCCCTCTGT 57.728 36.000 0.00 0.00 0.00 3.41
114 115 8.388656 AGAACCAATTTATTACTCCCTCTGTA 57.611 34.615 0.00 0.00 0.00 2.74
115 116 8.832735 AGAACCAATTTATTACTCCCTCTGTAA 58.167 33.333 0.00 0.00 34.87 2.41
116 117 9.457436 GAACCAATTTATTACTCCCTCTGTAAA 57.543 33.333 0.00 0.00 34.20 2.01
117 118 8.803397 ACCAATTTATTACTCCCTCTGTAAAC 57.197 34.615 0.00 0.00 34.20 2.01
118 119 8.612145 ACCAATTTATTACTCCCTCTGTAAACT 58.388 33.333 0.00 0.00 34.20 2.66
129 130 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
130 131 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
131 132 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
158 159 7.934855 AGATTACTAAAGTAGTTCACGGAGA 57.065 36.000 0.00 0.00 40.14 3.71
159 160 7.987649 AGATTACTAAAGTAGTTCACGGAGAG 58.012 38.462 0.00 0.00 40.14 3.20
160 161 7.611079 AGATTACTAAAGTAGTTCACGGAGAGT 59.389 37.037 0.00 0.00 40.14 3.24
161 162 8.798859 ATTACTAAAGTAGTTCACGGAGAGTA 57.201 34.615 0.00 0.00 40.14 2.59
162 163 6.740411 ACTAAAGTAGTTCACGGAGAGTAG 57.260 41.667 0.00 0.00 34.86 2.57
163 164 6.237154 ACTAAAGTAGTTCACGGAGAGTAGT 58.763 40.000 0.00 0.00 34.86 2.73
164 165 7.390027 ACTAAAGTAGTTCACGGAGAGTAGTA 58.610 38.462 0.00 0.00 34.86 1.82
165 166 6.740411 AAAGTAGTTCACGGAGAGTAGTAG 57.260 41.667 0.00 0.00 0.00 2.57
166 167 4.190772 AGTAGTTCACGGAGAGTAGTAGC 58.809 47.826 0.00 0.00 0.00 3.58
167 168 2.008329 AGTTCACGGAGAGTAGTAGCG 58.992 52.381 0.00 0.00 0.00 4.26
168 169 2.005451 GTTCACGGAGAGTAGTAGCGA 58.995 52.381 0.00 0.00 0.00 4.93
169 170 2.391616 TCACGGAGAGTAGTAGCGAA 57.608 50.000 0.00 0.00 0.00 4.70
170 171 2.703416 TCACGGAGAGTAGTAGCGAAA 58.297 47.619 0.00 0.00 0.00 3.46
171 172 3.276857 TCACGGAGAGTAGTAGCGAAAT 58.723 45.455 0.00 0.00 0.00 2.17
172 173 3.311871 TCACGGAGAGTAGTAGCGAAATC 59.688 47.826 0.00 0.00 0.00 2.17
173 174 2.287373 ACGGAGAGTAGTAGCGAAATCG 59.713 50.000 0.00 0.00 43.27 3.34
174 175 2.543012 CGGAGAGTAGTAGCGAAATCGA 59.457 50.000 7.06 0.00 43.02 3.59
175 176 3.002042 CGGAGAGTAGTAGCGAAATCGAA 59.998 47.826 7.06 0.00 43.02 3.71
180 181 5.572126 AGAGTAGTAGCGAAATCGAACAAAC 59.428 40.000 7.06 6.58 43.02 2.93
188 189 3.648009 GAAATCGAACAAACAATGGCCA 58.352 40.909 8.56 8.56 0.00 5.36
205 206 3.181491 TGGCCAGAAAGAAACGTGAAAAG 60.181 43.478 0.00 0.00 0.00 2.27
223 224 1.032794 AGCACGCTCTGGATCGAATA 58.967 50.000 0.00 0.00 0.00 1.75
225 226 1.932604 GCACGCTCTGGATCGAATAGG 60.933 57.143 0.00 0.00 0.00 2.57
226 227 0.315568 ACGCTCTGGATCGAATAGGC 59.684 55.000 0.00 0.00 0.00 3.93
238 239 1.802553 GAATAGGCTGGGTCCCACTA 58.197 55.000 6.47 8.67 0.00 2.74
243 244 1.489560 GGCTGGGTCCCACTACAACT 61.490 60.000 6.47 0.00 0.00 3.16
249 250 2.289257 GGGTCCCACTACAACTGTACAC 60.289 54.545 1.78 0.00 0.00 2.90
252 253 2.366266 TCCCACTACAACTGTACACACC 59.634 50.000 0.00 0.00 0.00 4.16
253 254 2.367567 CCCACTACAACTGTACACACCT 59.632 50.000 0.00 0.00 0.00 4.00
254 255 3.554337 CCCACTACAACTGTACACACCTC 60.554 52.174 0.00 0.00 0.00 3.85
255 256 3.069016 CCACTACAACTGTACACACCTCA 59.931 47.826 0.00 0.00 0.00 3.86
256 257 4.262463 CCACTACAACTGTACACACCTCAT 60.262 45.833 0.00 0.00 0.00 2.90
257 258 4.686091 CACTACAACTGTACACACCTCATG 59.314 45.833 0.00 0.00 0.00 3.07
258 259 3.126001 ACAACTGTACACACCTCATGG 57.874 47.619 0.00 0.00 39.83 3.66
259 260 1.806542 CAACTGTACACACCTCATGGC 59.193 52.381 0.00 0.00 36.63 4.40
302 307 9.481340 GGTCAAAAGAAATTTCTAAAGCTTGAT 57.519 29.630 20.76 0.00 36.28 2.57
318 323 0.184692 TGATTGAGGCCCACACACAA 59.815 50.000 0.00 0.00 0.00 3.33
319 324 1.203038 TGATTGAGGCCCACACACAAT 60.203 47.619 0.00 2.36 34.55 2.71
320 325 2.040947 TGATTGAGGCCCACACACAATA 59.959 45.455 0.00 0.00 32.50 1.90
321 326 2.666272 TTGAGGCCCACACACAATAA 57.334 45.000 0.00 0.00 0.00 1.40
322 327 2.897271 TGAGGCCCACACACAATAAT 57.103 45.000 0.00 0.00 0.00 1.28
351 356 3.492756 CCAAATAAACAAACAAGCCACCG 59.507 43.478 0.00 0.00 0.00 4.94
369 404 0.881159 CGCACCGTACCAGTCCAAAA 60.881 55.000 0.00 0.00 0.00 2.44
370 405 0.589708 GCACCGTACCAGTCCAAAAC 59.410 55.000 0.00 0.00 0.00 2.43
372 407 2.567985 CACCGTACCAGTCCAAAACTT 58.432 47.619 0.00 0.00 35.45 2.66
373 408 2.546789 CACCGTACCAGTCCAAAACTTC 59.453 50.000 0.00 0.00 35.45 3.01
374 409 2.436911 ACCGTACCAGTCCAAAACTTCT 59.563 45.455 0.00 0.00 35.45 2.85
377 412 4.261031 CCGTACCAGTCCAAAACTTCTTTG 60.261 45.833 0.00 0.00 35.45 2.77
382 417 4.805719 CCAGTCCAAAACTTCTTTGCTTTC 59.194 41.667 0.00 0.00 35.45 2.62
383 418 4.500477 CAGTCCAAAACTTCTTTGCTTTCG 59.500 41.667 0.00 0.00 35.45 3.46
393 428 2.096622 CTTTGCTTTCGATGATTCGCG 58.903 47.619 0.00 0.00 45.10 5.87
394 429 1.355005 TTGCTTTCGATGATTCGCGA 58.645 45.000 3.71 3.71 45.10 5.87
395 430 1.355005 TGCTTTCGATGATTCGCGAA 58.645 45.000 25.66 25.66 45.10 4.70
400 435 1.286501 TCGATGATTCGCGAAAAGGG 58.713 50.000 27.23 13.99 45.10 3.95
409 444 4.373348 TTCGCGAAAAGGGAAAGAAAAA 57.627 36.364 21.14 0.00 46.77 1.94
419 454 0.248702 GAAAGAAAAACGCCGCACCA 60.249 50.000 0.00 0.00 0.00 4.17
497 533 2.349755 CGGGGTCAACAATCCGGT 59.650 61.111 0.00 0.00 38.93 5.28
498 534 1.302993 CGGGGTCAACAATCCGGTT 60.303 57.895 0.00 0.00 38.93 4.44
499 535 0.036199 CGGGGTCAACAATCCGGTTA 60.036 55.000 0.00 0.00 38.93 2.85
500 536 1.746470 GGGGTCAACAATCCGGTTAG 58.254 55.000 0.00 0.00 0.00 2.34
501 537 1.092348 GGGTCAACAATCCGGTTAGC 58.908 55.000 0.00 0.00 0.00 3.09
535 581 4.748144 GTCCCCTGCCAGCCCAAG 62.748 72.222 0.00 0.00 0.00 3.61
630 699 3.011760 GCAACGCGGTTTCTCTCGG 62.012 63.158 12.47 0.00 0.00 4.63
655 739 2.973600 GCACCCACGCGTACCAAA 60.974 61.111 13.44 0.00 0.00 3.28
656 740 2.544698 GCACCCACGCGTACCAAAA 61.545 57.895 13.44 0.00 0.00 2.44
657 741 2.023318 CACCCACGCGTACCAAAAA 58.977 52.632 13.44 0.00 0.00 1.94
710 797 3.094062 GCATAGCCGAGCCACCAGA 62.094 63.158 0.00 0.00 0.00 3.86
755 843 0.107945 CAGCTAGGCAAGTCCAGGAC 60.108 60.000 12.25 12.25 37.29 3.85
756 844 0.252467 AGCTAGGCAAGTCCAGGACT 60.252 55.000 17.31 17.31 45.64 3.85
757 845 0.176910 GCTAGGCAAGTCCAGGACTC 59.823 60.000 23.17 11.06 42.59 3.36
786 874 3.681835 GAGGCTGTCACGTCCCGT 61.682 66.667 0.00 0.00 42.36 5.28
793 881 1.674980 GTCACGTCCCGTCTCTCCT 60.675 63.158 0.00 0.00 38.32 3.69
794 882 1.074423 TCACGTCCCGTCTCTCCTT 59.926 57.895 0.00 0.00 38.32 3.36
795 883 0.959372 TCACGTCCCGTCTCTCCTTC 60.959 60.000 0.00 0.00 38.32 3.46
796 884 2.039405 ACGTCCCGTCTCTCCTTCG 61.039 63.158 0.00 0.00 33.69 3.79
797 885 2.039405 CGTCCCGTCTCTCCTTCGT 61.039 63.158 0.00 0.00 0.00 3.85
798 886 1.801983 GTCCCGTCTCTCCTTCGTC 59.198 63.158 0.00 0.00 0.00 4.20
799 887 1.378250 TCCCGTCTCTCCTTCGTCC 60.378 63.158 0.00 0.00 0.00 4.79
800 888 1.378778 CCCGTCTCTCCTTCGTCCT 60.379 63.158 0.00 0.00 0.00 3.85
801 889 0.966370 CCCGTCTCTCCTTCGTCCTT 60.966 60.000 0.00 0.00 0.00 3.36
802 890 0.452585 CCGTCTCTCCTTCGTCCTTC 59.547 60.000 0.00 0.00 0.00 3.46
803 891 0.452585 CGTCTCTCCTTCGTCCTTCC 59.547 60.000 0.00 0.00 0.00 3.46
830 918 4.179599 CTCCTCCCCCTCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
861 966 0.893727 GTCCACCACGCCATTCCTTT 60.894 55.000 0.00 0.00 0.00 3.11
862 967 0.178975 TCCACCACGCCATTCCTTTT 60.179 50.000 0.00 0.00 0.00 2.27
863 968 0.678950 CCACCACGCCATTCCTTTTT 59.321 50.000 0.00 0.00 0.00 1.94
893 998 2.182030 CTCCAAGCGACGACTCCC 59.818 66.667 0.00 0.00 0.00 4.30
902 1007 1.075896 GACGACTCCCTCCATCCCT 60.076 63.158 0.00 0.00 0.00 4.20
903 1008 1.075896 ACGACTCCCTCCATCCCTC 60.076 63.158 0.00 0.00 0.00 4.30
905 1010 1.629297 GACTCCCTCCATCCCTCCT 59.371 63.158 0.00 0.00 0.00 3.69
1080 1190 3.166489 GGGGACGATCTGTAAGTCTTG 57.834 52.381 0.00 0.00 35.42 3.02
1081 1191 2.159085 GGGGACGATCTGTAAGTCTTGG 60.159 54.545 0.00 0.00 35.42 3.61
1082 1192 2.541556 GGACGATCTGTAAGTCTTGGC 58.458 52.381 0.00 0.00 35.42 4.52
1083 1193 2.541556 GACGATCTGTAAGTCTTGGCC 58.458 52.381 0.00 0.00 33.76 5.36
1084 1194 1.899814 ACGATCTGTAAGTCTTGGCCA 59.100 47.619 0.00 0.00 33.76 5.36
1090 1202 0.250597 GTAAGTCTTGGCCAACCCGT 60.251 55.000 16.05 8.63 35.87 5.28
1094 1206 1.076632 TCTTGGCCAACCCGTTGTT 60.077 52.632 16.05 0.00 38.85 2.83
1095 1207 0.684805 TCTTGGCCAACCCGTTGTTT 60.685 50.000 16.05 0.00 38.85 2.83
1098 1210 1.830847 GGCCAACCCGTTGTTTCCT 60.831 57.895 0.00 0.00 38.85 3.36
1106 1218 0.400594 CCGTTGTTTCCTCTTCCCCT 59.599 55.000 0.00 0.00 0.00 4.79
1107 1219 1.626825 CCGTTGTTTCCTCTTCCCCTA 59.373 52.381 0.00 0.00 0.00 3.53
1109 1221 3.270877 CGTTGTTTCCTCTTCCCCTATG 58.729 50.000 0.00 0.00 0.00 2.23
1112 1224 5.077564 GTTGTTTCCTCTTCCCCTATGTTT 58.922 41.667 0.00 0.00 0.00 2.83
1115 1227 5.186942 GTTTCCTCTTCCCCTATGTTTCTC 58.813 45.833 0.00 0.00 0.00 2.87
1116 1228 4.354208 TCCTCTTCCCCTATGTTTCTCT 57.646 45.455 0.00 0.00 0.00 3.10
1119 1231 4.471386 CCTCTTCCCCTATGTTTCTCTGAA 59.529 45.833 0.00 0.00 0.00 3.02
1125 1237 3.274288 CCTATGTTTCTCTGAACTGGGC 58.726 50.000 0.00 0.00 0.00 5.36
1246 1368 3.298958 CCGGCTTGTCTGGCTAGA 58.701 61.111 0.00 0.00 33.73 2.43
1257 1379 2.099263 GTCTGGCTAGATTGTGCTACGA 59.901 50.000 2.00 0.00 34.94 3.43
1264 1386 1.751924 AGATTGTGCTACGAGAGGGTC 59.248 52.381 0.00 0.00 0.00 4.46
1317 1440 1.298859 GAGGCGGTGCTCAATTTCGT 61.299 55.000 0.00 0.00 0.00 3.85
1319 1442 0.800012 GGCGGTGCTCAATTTCGTTA 59.200 50.000 0.00 0.00 0.00 3.18
1323 1446 2.348666 CGGTGCTCAATTTCGTTAGGAG 59.651 50.000 0.00 0.00 0.00 3.69
1324 1447 2.678336 GGTGCTCAATTTCGTTAGGAGG 59.322 50.000 0.00 0.00 0.00 4.30
1325 1448 3.596214 GTGCTCAATTTCGTTAGGAGGA 58.404 45.455 0.00 0.00 0.00 3.71
1336 1466 1.614241 TTAGGAGGAGTTCGGCCTGC 61.614 60.000 0.00 0.00 43.45 4.85
1398 1528 3.039011 GGACTGGGGAAGTAGATGCTAA 58.961 50.000 0.00 0.00 40.07 3.09
1401 1531 4.104831 ACTGGGGAAGTAGATGCTAAAGT 58.895 43.478 0.00 0.00 37.36 2.66
1427 1557 2.787473 TTGGGTGCGAATCTCATCTT 57.213 45.000 0.00 0.00 0.00 2.40
1431 1561 0.579156 GTGCGAATCTCATCTTCCGC 59.421 55.000 0.00 0.00 0.00 5.54
1433 1563 1.202568 TGCGAATCTCATCTTCCGCAT 60.203 47.619 0.00 0.00 31.87 4.73
1457 1587 4.332268 GGTCCAAAACGTGTTGTGTTAGTA 59.668 41.667 17.06 0.00 0.00 1.82
1468 1598 4.580995 TGTTGTGTTAGTATTGGTGTTGGG 59.419 41.667 0.00 0.00 0.00 4.12
1497 1629 4.273148 TCTGTCTTGTTTAAGCCCTCTC 57.727 45.455 0.00 0.00 33.82 3.20
1501 1633 2.028385 TCTTGTTTAAGCCCTCTCGTCC 60.028 50.000 0.00 0.00 33.82 4.79
1502 1634 0.245539 TGTTTAAGCCCTCTCGTCCG 59.754 55.000 0.00 0.00 0.00 4.79
1539 1671 1.519751 TTCGCAATTGTTGTCCCCGG 61.520 55.000 7.40 0.00 0.00 5.73
1585 1718 4.619394 GCTCTCATATGGACATAGAACCGG 60.619 50.000 0.00 0.00 0.00 5.28
1607 1740 6.719370 CCGGAAATTGGGATGGAATCTTATTA 59.281 38.462 0.00 0.00 44.71 0.98
1613 1746 6.433847 TGGGATGGAATCTTATTACGACAT 57.566 37.500 0.00 0.00 44.71 3.06
1633 1766 0.110486 ATTGTCGCCTGGTGTTCCTT 59.890 50.000 7.20 0.00 34.23 3.36
1643 1776 3.568007 CCTGGTGTTCCTTTGATTTTCGA 59.432 43.478 0.00 0.00 34.23 3.71
1645 1778 5.119931 TGGTGTTCCTTTGATTTTCGATG 57.880 39.130 0.00 0.00 34.23 3.84
1651 1784 4.078537 TCCTTTGATTTTCGATGCTTGGA 58.921 39.130 0.00 0.00 0.00 3.53
1652 1785 4.706476 TCCTTTGATTTTCGATGCTTGGAT 59.294 37.500 0.00 0.00 0.00 3.41
1653 1786 5.185635 TCCTTTGATTTTCGATGCTTGGATT 59.814 36.000 0.00 0.00 0.00 3.01
1655 1788 7.035004 CCTTTGATTTTCGATGCTTGGATTTA 58.965 34.615 0.00 0.00 0.00 1.40
1656 1789 7.707893 CCTTTGATTTTCGATGCTTGGATTTAT 59.292 33.333 0.00 0.00 0.00 1.40
1665 1799 5.924254 CGATGCTTGGATTTATGCATGATTT 59.076 36.000 10.16 0.00 44.80 2.17
1687 1821 4.724399 TGTTCAGGAATTAGGAGCACAAA 58.276 39.130 0.00 0.00 0.00 2.83
1733 1868 5.515008 GGGAACTAACTTGGACCTCTGATTT 60.515 44.000 0.00 0.00 0.00 2.17
1740 1875 3.713826 TGGACCTCTGATTTTGTACCC 57.286 47.619 0.00 0.00 0.00 3.69
1758 1893 0.534412 CCGGAGAGTTCATGCTCACT 59.466 55.000 0.00 0.00 37.94 3.41
1769 1904 8.700051 AGAGTTCATGCTCACTATGTAACTAAT 58.300 33.333 3.57 0.00 37.94 1.73
1894 2029 2.982130 GGAGAAGGCTCGCTTGGA 59.018 61.111 0.00 0.00 42.25 3.53
1980 2115 8.493607 CCATTTTATACATTTCCCAATTCCCTT 58.506 33.333 0.00 0.00 0.00 3.95
1981 2116 9.904198 CATTTTATACATTTCCCAATTCCCTTT 57.096 29.630 0.00 0.00 0.00 3.11
1983 2118 7.669089 TTATACATTTCCCAATTCCCTTTCC 57.331 36.000 0.00 0.00 0.00 3.13
1984 2119 3.181329 ACATTTCCCAATTCCCTTTCCC 58.819 45.455 0.00 0.00 0.00 3.97
1985 2120 3.181396 ACATTTCCCAATTCCCTTTCCCT 60.181 43.478 0.00 0.00 0.00 4.20
1986 2121 2.621556 TTCCCAATTCCCTTTCCCTG 57.378 50.000 0.00 0.00 0.00 4.45
1987 2122 1.466858 TCCCAATTCCCTTTCCCTGT 58.533 50.000 0.00 0.00 0.00 4.00
2015 2153 2.965805 TGGGAAGAATGCCAGCTTG 58.034 52.632 0.00 0.00 42.90 4.01
2018 2156 1.407979 GGGAAGAATGCCAGCTTGATG 59.592 52.381 0.00 0.00 32.29 3.07
2093 2231 2.497273 ACTGTTGGGCAAATGCTATTCC 59.503 45.455 5.25 0.00 41.70 3.01
2387 2533 2.283145 AAGATGCACCAGTTCTGCTT 57.717 45.000 0.00 0.00 35.53 3.91
2394 2540 2.287608 GCACCAGTTCTGCTTTTACCAC 60.288 50.000 0.00 0.00 0.00 4.16
2522 2668 4.612264 AATGGAATTTGCTGCAGAAGTT 57.388 36.364 20.43 11.63 26.74 2.66
2570 2716 0.320697 ACCTCCTGAGTTTACGTGGC 59.679 55.000 0.00 0.00 0.00 5.01
2744 2890 4.605573 GCGTGAGTAAACGTCTTCTTTGTC 60.606 45.833 0.00 0.00 45.32 3.18
2763 2909 4.204799 TGTCCGTAGTAGCATGACATAGT 58.795 43.478 0.00 0.00 31.45 2.12
2851 2997 0.400213 TTCACCACCATGAGACACCC 59.600 55.000 0.00 0.00 0.00 4.61
2854 3000 2.230653 CCACCATGAGACACCCCCA 61.231 63.158 0.00 0.00 0.00 4.96
2888 3034 2.159338 AGCATCAAATCGACCAATGTGC 60.159 45.455 0.00 0.00 0.00 4.57
2893 3039 5.079689 TCAAATCGACCAATGTGCTACTA 57.920 39.130 0.00 0.00 0.00 1.82
2899 3045 4.401202 TCGACCAATGTGCTACTAGATTCA 59.599 41.667 0.00 0.00 0.00 2.57
2920 3066 1.178534 ATTTCCAGGCACACGTTGGG 61.179 55.000 3.47 0.00 32.76 4.12
2926 3072 2.258726 GGCACACGTTGGGGACTTC 61.259 63.158 0.00 0.00 0.00 3.01
3007 3153 2.766263 ACGAGGTTATCATGCTCCTGAA 59.234 45.455 0.00 0.00 0.00 3.02
3013 3159 5.057149 GGTTATCATGCTCCTGAATACGTT 58.943 41.667 0.00 0.00 0.00 3.99
3025 3171 5.473846 TCCTGAATACGTTATGTTTGGCAAA 59.526 36.000 8.93 8.93 0.00 3.68
3076 3222 4.778213 TGGCATAATACTTCTGGAGCTT 57.222 40.909 0.00 0.00 0.00 3.74
3115 3261 4.335416 CAGTAGAAAAATCAGGCTCCCAA 58.665 43.478 0.00 0.00 0.00 4.12
3169 3315 3.243771 CGTTGGCGAAAGAGGGTAGATAT 60.244 47.826 0.00 0.00 41.33 1.63
3226 3372 7.893658 AGTATTCCGAGTCTGAACTAAAAAGA 58.106 34.615 0.00 0.00 35.28 2.52
3265 3411 1.887242 GTGCACGCACAGAGAACCA 60.887 57.895 17.03 0.00 45.53 3.67
3346 3492 2.887152 GCTTCTGAGGCTTGAAAAGGAA 59.113 45.455 4.32 0.00 46.35 3.36
3352 3498 2.487372 GAGGCTTGAAAAGGAAGAGCTG 59.513 50.000 0.00 0.00 46.35 4.24
3364 3510 2.092699 GGAAGAGCTGTTTAGGCCAGAT 60.093 50.000 5.01 0.00 31.38 2.90
3684 3843 1.140161 CCAGATGTTTGGGCATGCG 59.860 57.895 12.44 0.00 34.46 4.73
3861 4029 7.095481 GGTTCTTTCTTTTGCAGGATTTTCATC 60.095 37.037 0.00 0.00 0.00 2.92
3895 4065 3.242608 GCTTTCTGTCTTGCGTGTGTTTA 60.243 43.478 0.00 0.00 0.00 2.01
3946 4116 4.888326 AAGAAGCTCTGCCTATCCTATG 57.112 45.455 0.00 0.00 0.00 2.23
4039 4209 9.771534 CAGAATTTAGGGTCCATTTTAAACAAA 57.228 29.630 0.00 0.00 0.00 2.83
4138 4318 0.661780 CGACATAGGCGTGCTAGAGC 60.662 60.000 0.00 0.00 42.50 4.09
4156 4336 4.514401 AGAGCCCCTAATAGTTTGTTTCG 58.486 43.478 0.00 0.00 0.00 3.46
4200 4393 3.832527 AGTAAAACCATGCAGAAGGTGT 58.167 40.909 8.81 1.15 38.37 4.16
4202 4395 0.675633 AAACCATGCAGAAGGTGTGC 59.324 50.000 8.81 0.00 38.37 4.57
4221 4414 2.103094 TGCCTATGTCTCGCTATTTGCT 59.897 45.455 0.00 0.00 40.11 3.91
4313 4511 1.861575 CGAAGCTTCGCTAAATCCTCC 59.138 52.381 33.46 0.00 44.26 4.30
4314 4512 1.861575 GAAGCTTCGCTAAATCCTCCG 59.138 52.381 11.40 0.00 38.25 4.63
4315 4513 0.530870 AGCTTCGCTAAATCCTCCGC 60.531 55.000 0.00 0.00 36.99 5.54
4316 4514 0.810031 GCTTCGCTAAATCCTCCGCA 60.810 55.000 0.00 0.00 0.00 5.69
4317 4515 1.651987 CTTCGCTAAATCCTCCGCAA 58.348 50.000 0.00 0.00 0.00 4.85
4318 4516 2.006888 CTTCGCTAAATCCTCCGCAAA 58.993 47.619 0.00 0.00 0.00 3.68
4319 4517 2.102070 TCGCTAAATCCTCCGCAAAA 57.898 45.000 0.00 0.00 0.00 2.44
4320 4518 2.428491 TCGCTAAATCCTCCGCAAAAA 58.572 42.857 0.00 0.00 0.00 1.94
4321 4519 2.418628 TCGCTAAATCCTCCGCAAAAAG 59.581 45.455 0.00 0.00 0.00 2.27
4322 4520 2.418628 CGCTAAATCCTCCGCAAAAAGA 59.581 45.455 0.00 0.00 0.00 2.52
4323 4521 3.119990 CGCTAAATCCTCCGCAAAAAGAA 60.120 43.478 0.00 0.00 0.00 2.52
4324 4522 4.614993 CGCTAAATCCTCCGCAAAAAGAAA 60.615 41.667 0.00 0.00 0.00 2.52
4425 4655 6.096705 TGGCATTCCTATGAACCTGTTATTTG 59.903 38.462 0.00 0.00 33.37 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 9.416284 GGTATGGATTACAAAAAGGAATCCTAA 57.584 33.333 17.45 5.56 45.97 2.69
49 50 8.561769 TGGTATGGATTACAAAAAGGAATCCTA 58.438 33.333 17.45 7.03 45.97 2.94
50 51 7.418378 TGGTATGGATTACAAAAAGGAATCCT 58.582 34.615 17.45 0.00 45.97 3.24
51 52 7.654022 TGGTATGGATTACAAAAAGGAATCC 57.346 36.000 11.35 11.35 45.99 3.01
52 53 9.366216 GTTTGGTATGGATTACAAAAAGGAATC 57.634 33.333 0.00 0.00 35.86 2.52
53 54 8.318412 GGTTTGGTATGGATTACAAAAAGGAAT 58.682 33.333 0.00 0.00 35.86 3.01
54 55 7.290248 TGGTTTGGTATGGATTACAAAAAGGAA 59.710 33.333 0.00 0.00 35.86 3.36
55 56 6.782988 TGGTTTGGTATGGATTACAAAAAGGA 59.217 34.615 0.00 0.00 35.86 3.36
56 57 6.998802 TGGTTTGGTATGGATTACAAAAAGG 58.001 36.000 0.00 0.00 35.86 3.11
57 58 6.589907 GCTGGTTTGGTATGGATTACAAAAAG 59.410 38.462 0.00 0.00 35.86 2.27
58 59 6.042093 TGCTGGTTTGGTATGGATTACAAAAA 59.958 34.615 0.00 0.00 35.86 1.94
59 60 5.540337 TGCTGGTTTGGTATGGATTACAAAA 59.460 36.000 0.00 0.00 32.37 2.44
60 61 5.080337 TGCTGGTTTGGTATGGATTACAAA 58.920 37.500 0.00 0.00 31.99 2.83
61 62 4.667573 TGCTGGTTTGGTATGGATTACAA 58.332 39.130 0.00 0.00 31.99 2.41
62 63 4.308526 TGCTGGTTTGGTATGGATTACA 57.691 40.909 0.00 0.00 31.99 2.41
63 64 7.524717 AATATGCTGGTTTGGTATGGATTAC 57.475 36.000 0.00 0.00 0.00 1.89
64 65 9.295825 CTAAATATGCTGGTTTGGTATGGATTA 57.704 33.333 0.00 0.00 0.00 1.75
65 66 8.004215 TCTAAATATGCTGGTTTGGTATGGATT 58.996 33.333 0.00 0.00 0.00 3.01
66 67 7.526041 TCTAAATATGCTGGTTTGGTATGGAT 58.474 34.615 0.00 0.00 0.00 3.41
67 68 6.905736 TCTAAATATGCTGGTTTGGTATGGA 58.094 36.000 0.00 0.00 0.00 3.41
68 69 7.425606 GTTCTAAATATGCTGGTTTGGTATGG 58.574 38.462 0.00 0.00 0.00 2.74
69 70 7.068103 TGGTTCTAAATATGCTGGTTTGGTATG 59.932 37.037 0.00 0.00 0.00 2.39
70 71 7.122715 TGGTTCTAAATATGCTGGTTTGGTAT 58.877 34.615 0.00 0.00 0.00 2.73
71 72 6.486056 TGGTTCTAAATATGCTGGTTTGGTA 58.514 36.000 0.00 0.00 0.00 3.25
72 73 5.329399 TGGTTCTAAATATGCTGGTTTGGT 58.671 37.500 0.00 0.00 0.00 3.67
73 74 5.913137 TGGTTCTAAATATGCTGGTTTGG 57.087 39.130 0.00 0.00 0.00 3.28
74 75 8.776376 AAATTGGTTCTAAATATGCTGGTTTG 57.224 30.769 0.00 0.00 0.00 2.93
86 87 9.681062 CAGAGGGAGTAATAAATTGGTTCTAAA 57.319 33.333 0.00 0.00 0.00 1.85
87 88 8.832735 ACAGAGGGAGTAATAAATTGGTTCTAA 58.167 33.333 0.00 0.00 0.00 2.10
88 89 8.388656 ACAGAGGGAGTAATAAATTGGTTCTA 57.611 34.615 0.00 0.00 0.00 2.10
89 90 7.272144 ACAGAGGGAGTAATAAATTGGTTCT 57.728 36.000 0.00 0.00 0.00 3.01
90 91 9.457436 TTTACAGAGGGAGTAATAAATTGGTTC 57.543 33.333 0.00 0.00 32.07 3.62
91 92 9.239551 GTTTACAGAGGGAGTAATAAATTGGTT 57.760 33.333 0.00 0.00 32.07 3.67
92 93 8.612145 AGTTTACAGAGGGAGTAATAAATTGGT 58.388 33.333 0.00 0.00 32.07 3.67
103 104 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
104 105 8.861086 TGCTCTTATATTAGTTTACAGAGGGAG 58.139 37.037 0.00 0.00 0.00 4.30
105 106 8.777578 TGCTCTTATATTAGTTTACAGAGGGA 57.222 34.615 0.00 0.00 0.00 4.20
132 133 9.453572 TCTCCGTGAACTACTTTAGTAATCTAA 57.546 33.333 0.00 0.00 38.26 2.10
133 134 9.107177 CTCTCCGTGAACTACTTTAGTAATCTA 57.893 37.037 0.00 0.00 38.26 1.98
134 135 7.611079 ACTCTCCGTGAACTACTTTAGTAATCT 59.389 37.037 0.00 0.00 38.26 2.40
135 136 7.760437 ACTCTCCGTGAACTACTTTAGTAATC 58.240 38.462 0.00 0.00 38.26 1.75
136 137 7.700022 ACTCTCCGTGAACTACTTTAGTAAT 57.300 36.000 0.00 0.00 38.26 1.89
137 138 7.880195 ACTACTCTCCGTGAACTACTTTAGTAA 59.120 37.037 0.00 0.00 38.26 2.24
138 139 7.390027 ACTACTCTCCGTGAACTACTTTAGTA 58.610 38.462 0.00 0.00 38.26 1.82
139 140 6.237154 ACTACTCTCCGTGAACTACTTTAGT 58.763 40.000 0.00 0.00 41.73 2.24
140 141 6.740411 ACTACTCTCCGTGAACTACTTTAG 57.260 41.667 0.00 0.00 0.00 1.85
141 142 6.314896 GCTACTACTCTCCGTGAACTACTTTA 59.685 42.308 0.00 0.00 0.00 1.85
142 143 5.123661 GCTACTACTCTCCGTGAACTACTTT 59.876 44.000 0.00 0.00 0.00 2.66
143 144 4.635324 GCTACTACTCTCCGTGAACTACTT 59.365 45.833 0.00 0.00 0.00 2.24
144 145 4.190772 GCTACTACTCTCCGTGAACTACT 58.809 47.826 0.00 0.00 0.00 2.57
145 146 3.001127 CGCTACTACTCTCCGTGAACTAC 59.999 52.174 0.00 0.00 0.00 2.73
146 147 3.118992 TCGCTACTACTCTCCGTGAACTA 60.119 47.826 0.00 0.00 0.00 2.24
147 148 2.008329 CGCTACTACTCTCCGTGAACT 58.992 52.381 0.00 0.00 0.00 3.01
148 149 2.005451 TCGCTACTACTCTCCGTGAAC 58.995 52.381 0.00 0.00 0.00 3.18
149 150 2.391616 TCGCTACTACTCTCCGTGAA 57.608 50.000 0.00 0.00 0.00 3.18
150 151 2.391616 TTCGCTACTACTCTCCGTGA 57.608 50.000 0.00 0.00 0.00 4.35
151 152 3.619729 GATTTCGCTACTACTCTCCGTG 58.380 50.000 0.00 0.00 0.00 4.94
152 153 2.287373 CGATTTCGCTACTACTCTCCGT 59.713 50.000 0.00 0.00 0.00 4.69
153 154 2.543012 TCGATTTCGCTACTACTCTCCG 59.457 50.000 0.00 0.00 39.60 4.63
154 155 4.201891 TGTTCGATTTCGCTACTACTCTCC 60.202 45.833 0.00 0.00 39.60 3.71
155 156 4.906423 TGTTCGATTTCGCTACTACTCTC 58.094 43.478 0.00 0.00 39.60 3.20
156 157 4.959596 TGTTCGATTTCGCTACTACTCT 57.040 40.909 0.00 0.00 39.60 3.24
157 158 5.344128 TGTTTGTTCGATTTCGCTACTACTC 59.656 40.000 0.00 0.00 39.60 2.59
158 159 5.224888 TGTTTGTTCGATTTCGCTACTACT 58.775 37.500 0.00 0.00 39.60 2.57
159 160 5.505165 TGTTTGTTCGATTTCGCTACTAC 57.495 39.130 0.00 1.28 39.60 2.73
160 161 6.401688 CCATTGTTTGTTCGATTTCGCTACTA 60.402 38.462 0.00 0.00 39.60 1.82
161 162 5.382303 CATTGTTTGTTCGATTTCGCTACT 58.618 37.500 0.00 0.00 39.60 2.57
162 163 4.553429 CCATTGTTTGTTCGATTTCGCTAC 59.447 41.667 0.00 0.00 39.60 3.58
163 164 4.717991 CCATTGTTTGTTCGATTTCGCTA 58.282 39.130 0.00 0.00 39.60 4.26
164 165 3.564511 CCATTGTTTGTTCGATTTCGCT 58.435 40.909 0.00 0.00 39.60 4.93
165 166 2.090503 GCCATTGTTTGTTCGATTTCGC 59.909 45.455 0.00 0.00 39.60 4.70
166 167 2.661195 GGCCATTGTTTGTTCGATTTCG 59.339 45.455 0.00 0.00 41.45 3.46
167 168 3.648009 TGGCCATTGTTTGTTCGATTTC 58.352 40.909 0.00 0.00 0.00 2.17
168 169 3.320541 TCTGGCCATTGTTTGTTCGATTT 59.679 39.130 5.51 0.00 0.00 2.17
169 170 2.890311 TCTGGCCATTGTTTGTTCGATT 59.110 40.909 5.51 0.00 0.00 3.34
170 171 2.513753 TCTGGCCATTGTTTGTTCGAT 58.486 42.857 5.51 0.00 0.00 3.59
171 172 1.974265 TCTGGCCATTGTTTGTTCGA 58.026 45.000 5.51 0.00 0.00 3.71
172 173 2.791383 TTCTGGCCATTGTTTGTTCG 57.209 45.000 5.51 0.00 0.00 3.95
173 174 4.320608 TCTTTCTGGCCATTGTTTGTTC 57.679 40.909 5.51 0.00 0.00 3.18
174 175 4.751767 TTCTTTCTGGCCATTGTTTGTT 57.248 36.364 5.51 0.00 0.00 2.83
175 176 4.441792 GTTTCTTTCTGGCCATTGTTTGT 58.558 39.130 5.51 0.00 0.00 2.83
180 181 2.293122 TCACGTTTCTTTCTGGCCATTG 59.707 45.455 5.51 0.00 0.00 2.82
205 206 1.413382 CTATTCGATCCAGAGCGTGC 58.587 55.000 5.12 0.00 41.48 5.34
215 216 0.321996 GGGACCCAGCCTATTCGATC 59.678 60.000 5.33 0.00 0.00 3.69
223 224 1.151899 TTGTAGTGGGACCCAGCCT 60.152 57.895 15.52 11.41 32.34 4.58
225 226 0.321653 CAGTTGTAGTGGGACCCAGC 60.322 60.000 15.52 9.27 32.34 4.85
226 227 1.056660 ACAGTTGTAGTGGGACCCAG 58.943 55.000 15.52 1.45 32.34 4.45
238 239 2.810400 GCCATGAGGTGTGTACAGTTGT 60.810 50.000 0.00 0.00 37.19 3.32
243 244 1.295101 CGGCCATGAGGTGTGTACA 59.705 57.895 2.24 0.00 37.19 2.90
272 277 8.695456 AGCTTTAGAAATTTCTTTTGACCAGAA 58.305 29.630 25.02 7.94 38.70 3.02
274 279 8.758715 CAAGCTTTAGAAATTTCTTTTGACCAG 58.241 33.333 25.02 11.64 38.70 4.00
302 307 2.666272 TTATTGTGTGTGGGCCTCAA 57.334 45.000 10.32 5.62 0.00 3.02
334 339 1.103803 TGCGGTGGCTTGTTTGTTTA 58.896 45.000 0.00 0.00 40.82 2.01
335 340 0.459411 GTGCGGTGGCTTGTTTGTTT 60.459 50.000 0.00 0.00 40.82 2.83
338 343 2.027460 GGTGCGGTGGCTTGTTTG 59.973 61.111 0.00 0.00 40.82 2.93
339 344 2.944409 TACGGTGCGGTGGCTTGTTT 62.944 55.000 0.00 0.00 40.82 2.83
342 347 3.419759 GTACGGTGCGGTGGCTTG 61.420 66.667 0.00 0.00 40.82 4.01
343 348 4.692475 GGTACGGTGCGGTGGCTT 62.692 66.667 0.00 0.00 40.82 4.35
383 418 3.374058 TCTTTCCCTTTTCGCGAATCATC 59.626 43.478 24.05 0.00 0.00 2.92
393 428 2.792674 CGGCGTTTTTCTTTCCCTTTTC 59.207 45.455 0.00 0.00 0.00 2.29
394 429 2.816689 CGGCGTTTTTCTTTCCCTTTT 58.183 42.857 0.00 0.00 0.00 2.27
395 430 1.537348 GCGGCGTTTTTCTTTCCCTTT 60.537 47.619 9.37 0.00 0.00 3.11
396 431 0.031585 GCGGCGTTTTTCTTTCCCTT 59.968 50.000 9.37 0.00 0.00 3.95
397 432 1.104577 TGCGGCGTTTTTCTTTCCCT 61.105 50.000 9.37 0.00 0.00 4.20
400 435 0.248702 TGGTGCGGCGTTTTTCTTTC 60.249 50.000 9.37 0.00 0.00 2.62
497 533 4.575885 ACGCACTTTCCATTCTAAGCTAA 58.424 39.130 0.00 0.00 0.00 3.09
498 534 4.181578 GACGCACTTTCCATTCTAAGCTA 58.818 43.478 0.00 0.00 0.00 3.32
499 535 3.003480 GACGCACTTTCCATTCTAAGCT 58.997 45.455 0.00 0.00 0.00 3.74
500 536 2.096013 GGACGCACTTTCCATTCTAAGC 59.904 50.000 0.00 0.00 32.82 3.09
501 537 2.678336 GGGACGCACTTTCCATTCTAAG 59.322 50.000 0.00 0.00 34.45 2.18
612 681 2.470286 CGAGAGAAACCGCGTTGC 59.530 61.111 4.92 0.00 0.00 4.17
613 682 3.011760 GCCGAGAGAAACCGCGTTG 62.012 63.158 4.92 0.00 0.00 4.10
655 739 0.392729 TTGACCCGTCGGTGTTGTTT 60.393 50.000 11.06 0.00 44.88 2.83
656 740 0.812412 CTTGACCCGTCGGTGTTGTT 60.812 55.000 11.06 0.00 44.88 2.83
657 741 1.227438 CTTGACCCGTCGGTGTTGT 60.227 57.895 11.06 0.00 44.88 3.32
695 779 3.075005 GGTCTGGTGGCTCGGCTA 61.075 66.667 0.00 0.00 0.00 3.93
710 797 1.761174 GGTGATCTGGTGTGGTGGT 59.239 57.895 0.00 0.00 0.00 4.16
745 833 3.390280 CTGGAGGAGTCCTGGACTT 57.610 57.895 28.90 15.47 43.53 3.01
786 874 0.408309 TGGGAAGGACGAAGGAGAGA 59.592 55.000 0.00 0.00 0.00 3.10
793 881 1.202722 GGACTTGTTGGGAAGGACGAA 60.203 52.381 0.00 0.00 0.00 3.85
794 882 0.395312 GGACTTGTTGGGAAGGACGA 59.605 55.000 0.00 0.00 0.00 4.20
795 883 0.396811 AGGACTTGTTGGGAAGGACG 59.603 55.000 0.00 0.00 0.00 4.79
796 884 1.271434 GGAGGACTTGTTGGGAAGGAC 60.271 57.143 0.00 0.00 0.00 3.85
797 885 1.064825 GGAGGACTTGTTGGGAAGGA 58.935 55.000 0.00 0.00 0.00 3.36
798 886 1.003696 GAGGAGGACTTGTTGGGAAGG 59.996 57.143 0.00 0.00 0.00 3.46
799 887 1.003696 GGAGGAGGACTTGTTGGGAAG 59.996 57.143 0.00 0.00 0.00 3.46
800 888 1.064825 GGAGGAGGACTTGTTGGGAA 58.935 55.000 0.00 0.00 0.00 3.97
801 889 0.840722 GGGAGGAGGACTTGTTGGGA 60.841 60.000 0.00 0.00 0.00 4.37
802 890 1.685820 GGGAGGAGGACTTGTTGGG 59.314 63.158 0.00 0.00 0.00 4.12
803 891 1.685820 GGGGAGGAGGACTTGTTGG 59.314 63.158 0.00 0.00 0.00 3.77
830 918 2.358737 GTGGACTGGTGGGCGAAG 60.359 66.667 0.00 0.00 0.00 3.79
861 966 1.841334 TGGAGGGGAAGGAAGGAAAA 58.159 50.000 0.00 0.00 0.00 2.29
862 967 1.710809 CTTGGAGGGGAAGGAAGGAAA 59.289 52.381 0.00 0.00 0.00 3.13
863 968 1.372501 CTTGGAGGGGAAGGAAGGAA 58.627 55.000 0.00 0.00 0.00 3.36
864 969 1.208165 GCTTGGAGGGGAAGGAAGGA 61.208 60.000 0.00 0.00 0.00 3.36
865 970 1.304617 GCTTGGAGGGGAAGGAAGG 59.695 63.158 0.00 0.00 0.00 3.46
866 971 1.078143 CGCTTGGAGGGGAAGGAAG 60.078 63.158 0.00 0.00 0.00 3.46
867 972 1.537889 TCGCTTGGAGGGGAAGGAA 60.538 57.895 0.00 0.00 0.00 3.36
868 973 2.121832 TCGCTTGGAGGGGAAGGA 59.878 61.111 0.00 0.00 0.00 3.36
869 974 2.269241 GTCGCTTGGAGGGGAAGG 59.731 66.667 0.00 0.00 0.00 3.46
870 975 2.125512 CGTCGCTTGGAGGGGAAG 60.126 66.667 0.00 0.00 0.00 3.46
871 976 2.602267 TCGTCGCTTGGAGGGGAA 60.602 61.111 0.00 0.00 0.00 3.97
872 977 3.379445 GTCGTCGCTTGGAGGGGA 61.379 66.667 0.00 0.00 0.00 4.81
873 978 3.358076 GAGTCGTCGCTTGGAGGGG 62.358 68.421 0.00 0.00 0.00 4.79
893 998 3.237741 GCGGGAGGAGGGATGGAG 61.238 72.222 0.00 0.00 0.00 3.86
1077 1187 0.249280 GAAACAACGGGTTGGCCAAG 60.249 55.000 21.21 10.35 44.45 3.61
1079 1189 2.128507 GGAAACAACGGGTTGGCCA 61.129 57.895 15.31 0.00 44.45 5.36
1080 1190 1.802337 GAGGAAACAACGGGTTGGCC 61.802 60.000 15.31 12.58 44.45 5.36
1081 1191 0.822121 AGAGGAAACAACGGGTTGGC 60.822 55.000 15.31 4.99 44.45 4.52
1082 1192 1.607148 GAAGAGGAAACAACGGGTTGG 59.393 52.381 15.31 0.00 44.45 3.77
1083 1193 1.607148 GGAAGAGGAAACAACGGGTTG 59.393 52.381 9.87 9.87 45.58 3.77
1084 1194 1.478105 GGGAAGAGGAAACAACGGGTT 60.478 52.381 0.00 0.00 42.98 4.11
1090 1202 5.074515 AGAAACATAGGGGAAGAGGAAACAA 59.925 40.000 0.00 0.00 0.00 2.83
1094 1206 4.471386 CAGAGAAACATAGGGGAAGAGGAA 59.529 45.833 0.00 0.00 0.00 3.36
1095 1207 4.033709 CAGAGAAACATAGGGGAAGAGGA 58.966 47.826 0.00 0.00 0.00 3.71
1098 1210 5.046304 CAGTTCAGAGAAACATAGGGGAAGA 60.046 44.000 0.00 0.00 0.00 2.87
1106 1218 2.354704 CCGCCCAGTTCAGAGAAACATA 60.355 50.000 0.00 0.00 0.00 2.29
1107 1219 1.611673 CCGCCCAGTTCAGAGAAACAT 60.612 52.381 0.00 0.00 0.00 2.71
1109 1221 0.955919 CCCGCCCAGTTCAGAGAAAC 60.956 60.000 0.00 0.00 0.00 2.78
1112 1224 3.706373 GCCCGCCCAGTTCAGAGA 61.706 66.667 0.00 0.00 0.00 3.10
1191 1305 0.802607 CTGGTTAGAGCGAGCGAACC 60.803 60.000 16.99 16.99 41.49 3.62
1246 1368 0.824759 GGACCCTCTCGTAGCACAAT 59.175 55.000 0.00 0.00 0.00 2.71
1317 1440 1.614241 GCAGGCCGAACTCCTCCTAA 61.614 60.000 0.00 0.00 0.00 2.69
1319 1442 3.394836 GCAGGCCGAACTCCTCCT 61.395 66.667 0.00 0.00 0.00 3.69
1323 1446 2.335712 CCAAAGCAGGCCGAACTCC 61.336 63.158 0.00 0.00 0.00 3.85
1324 1447 1.172812 AACCAAAGCAGGCCGAACTC 61.173 55.000 0.00 0.00 0.00 3.01
1325 1448 0.755327 AAACCAAAGCAGGCCGAACT 60.755 50.000 0.00 0.00 0.00 3.01
1336 1466 1.535462 CGCTGGTCCTACAAACCAAAG 59.465 52.381 0.00 0.00 45.86 2.77
1398 1528 3.263941 GCACCCAATCGCGAACTT 58.736 55.556 15.24 0.00 0.00 2.66
1427 1557 1.228003 ACGTTTTGGACCATGCGGA 60.228 52.632 14.46 0.00 35.59 5.54
1431 1561 2.159310 ACACAACACGTTTTGGACCATG 60.159 45.455 18.02 9.39 0.00 3.66
1433 1563 1.535833 ACACAACACGTTTTGGACCA 58.464 45.000 18.02 0.00 0.00 4.02
1457 1587 2.282887 GCGTCCCCCAACACCAAT 60.283 61.111 0.00 0.00 0.00 3.16
1468 1598 1.523758 AAACAAGACAGATGCGTCCC 58.476 50.000 1.23 0.00 36.52 4.46
1497 1629 3.246699 ACTGTTAACATCACAAACGGACG 59.753 43.478 9.13 0.00 34.34 4.79
1501 1633 4.144051 GCGAAACTGTTAACATCACAAACG 59.856 41.667 9.13 9.76 0.00 3.60
1502 1634 5.031578 TGCGAAACTGTTAACATCACAAAC 58.968 37.500 9.13 0.00 0.00 2.93
1546 1678 5.193663 TGAGAGCATGATAGACTAGTTGC 57.806 43.478 6.83 6.83 0.00 4.17
1559 1691 5.873712 GGTTCTATGTCCATATGAGAGCATG 59.126 44.000 3.65 0.00 35.94 4.06
1585 1718 8.290325 GTCGTAATAAGATTCCATCCCAATTTC 58.710 37.037 0.00 0.00 0.00 2.17
1613 1746 0.981183 AGGAACACCAGGCGACAATA 59.019 50.000 0.00 0.00 0.00 1.90
1620 1753 3.653344 GAAAATCAAAGGAACACCAGGC 58.347 45.455 0.00 0.00 0.00 4.85
1633 1766 6.476380 GCATAAATCCAAGCATCGAAAATCAA 59.524 34.615 0.00 0.00 0.00 2.57
1645 1778 6.535865 TGAACAAATCATGCATAAATCCAAGC 59.464 34.615 0.00 0.00 31.50 4.01
1652 1785 9.806203 CTAATTCCTGAACAAATCATGCATAAA 57.194 29.630 0.00 0.00 37.44 1.40
1653 1786 8.415553 CCTAATTCCTGAACAAATCATGCATAA 58.584 33.333 0.00 0.00 37.44 1.90
1655 1788 6.608405 TCCTAATTCCTGAACAAATCATGCAT 59.392 34.615 0.00 0.00 37.44 3.96
1656 1789 5.951148 TCCTAATTCCTGAACAAATCATGCA 59.049 36.000 0.00 0.00 37.44 3.96
1665 1799 4.365514 TTGTGCTCCTAATTCCTGAACA 57.634 40.909 0.00 0.00 0.00 3.18
1687 1821 5.127031 CCCTTTTCCACCGATAACAATTCAT 59.873 40.000 0.00 0.00 0.00 2.57
1733 1868 1.066430 GCATGAACTCTCCGGGTACAA 60.066 52.381 0.00 0.00 0.00 2.41
1740 1875 3.181482 ACATAGTGAGCATGAACTCTCCG 60.181 47.826 0.00 0.00 37.58 4.63
1894 2029 0.608640 CTTGTCCCCAGTAGACGCTT 59.391 55.000 0.00 0.00 37.04 4.68
1980 2115 2.530460 CCATCATGGGAAACAGGGAA 57.470 50.000 0.00 0.00 32.67 3.97
2015 2153 1.135721 GCAAGGAACATCAAGGCCATC 59.864 52.381 5.01 0.00 0.00 3.51
2018 2156 0.529378 CAGCAAGGAACATCAAGGCC 59.471 55.000 0.00 0.00 0.00 5.19
2093 2231 2.401583 TGTGTGGTTAGGCAGCTATG 57.598 50.000 0.00 0.00 0.00 2.23
2107 2245 4.159377 ACTGACAGTTGTTTGTTGTGTG 57.841 40.909 1.07 0.00 0.00 3.82
2329 2475 3.248024 AGGGTGGTCAGTGAGTGATTTA 58.752 45.455 0.00 0.00 37.56 1.40
2371 2517 2.558359 GGTAAAAGCAGAACTGGTGCAT 59.442 45.455 7.28 0.63 43.82 3.96
2387 2533 5.463061 GTGTAAGCAGAGTTAACGTGGTAAA 59.537 40.000 13.81 5.53 0.00 2.01
2522 2668 4.042809 TGCCTTACTCTTCCCAAAGATTCA 59.957 41.667 0.00 0.00 40.68 2.57
2570 2716 3.548745 TCAGGTCCATCAGCACAATAG 57.451 47.619 0.00 0.00 0.00 1.73
2744 2890 8.082852 AGAATTAACTATGTCATGCTACTACGG 58.917 37.037 0.00 0.00 0.00 4.02
2851 2997 4.154176 TGATGCTTCCATGGATTATTGGG 58.846 43.478 17.06 1.67 0.00 4.12
2854 3000 6.491062 TCGATTTGATGCTTCCATGGATTATT 59.509 34.615 17.06 0.99 0.00 1.40
2888 3034 5.988561 GTGCCTGGAAATCTGAATCTAGTAG 59.011 44.000 0.00 0.00 0.00 2.57
2893 3039 3.350833 GTGTGCCTGGAAATCTGAATCT 58.649 45.455 0.00 0.00 0.00 2.40
2899 3045 1.238439 CAACGTGTGCCTGGAAATCT 58.762 50.000 0.00 0.00 0.00 2.40
2920 3066 3.119101 TGAGCTTCATAAGACCGAAGTCC 60.119 47.826 0.00 0.00 44.72 3.85
2926 3072 4.037327 TCTGAGATGAGCTTCATAAGACCG 59.963 45.833 0.00 0.00 37.20 4.79
2983 3129 2.766263 AGGAGCATGATAACCTCGTTGA 59.234 45.455 0.00 0.00 0.00 3.18
2992 3138 7.441836 ACATAACGTATTCAGGAGCATGATAA 58.558 34.615 0.00 0.00 0.00 1.75
3007 3153 5.706369 TGTAGGTTTGCCAAACATAACGTAT 59.294 36.000 20.95 0.54 43.15 3.06
3013 3159 4.279671 CCTGTTGTAGGTTTGCCAAACATA 59.720 41.667 20.95 15.81 43.15 2.29
3076 3222 3.185880 ACTGGCTTTCTCCCACTAGTA 57.814 47.619 0.00 0.00 0.00 1.82
3169 3315 4.756642 AGTTTTGAGTCTGCGATTTCATCA 59.243 37.500 0.00 0.00 0.00 3.07
3226 3372 1.107114 CTAGTCCGATCAGCACCACT 58.893 55.000 0.00 0.00 0.00 4.00
3265 3411 2.550606 GAGCATCGTCGGTCTCTTATCT 59.449 50.000 0.00 0.00 0.00 1.98
3346 3492 2.419297 CGAATCTGGCCTAAACAGCTCT 60.419 50.000 3.32 0.00 35.94 4.09
3364 3510 0.099968 CGACGGAACTAGCCATCGAA 59.900 55.000 0.00 0.00 0.00 3.71
3462 3611 1.581640 TCTACCAATACCTAGGGGCCA 59.418 52.381 14.81 0.00 35.63 5.36
3463 3612 2.258109 CTCTACCAATACCTAGGGGCC 58.742 57.143 14.81 0.00 35.63 5.80
3597 3755 3.971245 AAAGCCAACTCACCTCTCTAG 57.029 47.619 0.00 0.00 0.00 2.43
3684 3843 2.838736 ACACAGTGACAACAGGATGAC 58.161 47.619 7.81 0.00 39.69 3.06
3861 4029 1.002033 ACAGAAAGCAAAAGCTCAGCG 60.002 47.619 0.00 0.00 0.00 5.18
3876 4044 2.286833 GCTAAACACACGCAAGACAGAA 59.713 45.455 0.00 0.00 43.62 3.02
3895 4065 7.215789 ACAGAATATGATCATCTCTTTTCGCT 58.784 34.615 12.53 0.00 0.00 4.93
3946 4116 5.007136 GCTTAGGACAACATGATAGCAAGAC 59.993 44.000 0.00 0.00 0.00 3.01
4039 4209 3.951680 AGGTTGAACTGTTTCGGTGAAAT 59.048 39.130 0.00 0.00 33.97 2.17
4138 4318 6.428771 TGAAGTTCGAAACAAACTATTAGGGG 59.571 38.462 0.00 0.00 35.96 4.79
4182 4364 1.069049 GCACACCTTCTGCATGGTTTT 59.931 47.619 3.78 0.00 33.75 2.43
4200 4393 2.483876 GCAAATAGCGAGACATAGGCA 58.516 47.619 0.00 0.00 0.00 4.75
4221 4414 2.227494 TACTAGGCGGCCCACTACCA 62.227 60.000 17.02 0.00 0.00 3.25
4299 4497 2.102070 TTTGCGGAGGATTTAGCGAA 57.898 45.000 0.00 0.00 0.00 4.70
4300 4498 2.102070 TTTTGCGGAGGATTTAGCGA 57.898 45.000 0.00 0.00 0.00 4.93
4301 4499 2.418628 TCTTTTTGCGGAGGATTTAGCG 59.581 45.455 0.00 0.00 0.00 4.26
4302 4500 4.434713 TTCTTTTTGCGGAGGATTTAGC 57.565 40.909 0.00 0.00 0.00 3.09
4303 4501 6.212955 TGTTTTCTTTTTGCGGAGGATTTAG 58.787 36.000 0.00 0.00 0.00 1.85
4304 4502 6.150396 TGTTTTCTTTTTGCGGAGGATTTA 57.850 33.333 0.00 0.00 0.00 1.40
4305 4503 5.017294 TGTTTTCTTTTTGCGGAGGATTT 57.983 34.783 0.00 0.00 0.00 2.17
4306 4504 4.664150 TGTTTTCTTTTTGCGGAGGATT 57.336 36.364 0.00 0.00 0.00 3.01
4307 4505 4.871933 ATGTTTTCTTTTTGCGGAGGAT 57.128 36.364 0.00 0.00 0.00 3.24
4308 4506 4.320935 GCTATGTTTTCTTTTTGCGGAGGA 60.321 41.667 0.00 0.00 0.00 3.71
4309 4507 3.920412 GCTATGTTTTCTTTTTGCGGAGG 59.080 43.478 0.00 0.00 0.00 4.30
4310 4508 3.920412 GGCTATGTTTTCTTTTTGCGGAG 59.080 43.478 0.00 0.00 0.00 4.63
4311 4509 3.572255 AGGCTATGTTTTCTTTTTGCGGA 59.428 39.130 0.00 0.00 0.00 5.54
4312 4510 3.913089 AGGCTATGTTTTCTTTTTGCGG 58.087 40.909 0.00 0.00 0.00 5.69
4313 4511 3.603770 CGAGGCTATGTTTTCTTTTTGCG 59.396 43.478 0.00 0.00 0.00 4.85
4314 4512 3.364920 GCGAGGCTATGTTTTCTTTTTGC 59.635 43.478 0.00 0.00 0.00 3.68
4315 4513 4.798574 AGCGAGGCTATGTTTTCTTTTTG 58.201 39.130 0.00 0.00 36.99 2.44
4316 4514 6.569179 TTAGCGAGGCTATGTTTTCTTTTT 57.431 33.333 0.00 0.00 41.01 1.94
4317 4515 6.016610 TGTTTAGCGAGGCTATGTTTTCTTTT 60.017 34.615 0.00 0.00 41.01 2.27
4318 4516 5.472137 TGTTTAGCGAGGCTATGTTTTCTTT 59.528 36.000 0.00 0.00 41.01 2.52
4319 4517 5.001232 TGTTTAGCGAGGCTATGTTTTCTT 58.999 37.500 0.00 0.00 41.01 2.52
4320 4518 4.392138 GTGTTTAGCGAGGCTATGTTTTCT 59.608 41.667 0.00 0.00 41.01 2.52
4321 4519 4.648970 GTGTTTAGCGAGGCTATGTTTTC 58.351 43.478 0.00 0.00 41.01 2.29
4322 4520 3.124636 CGTGTTTAGCGAGGCTATGTTTT 59.875 43.478 0.00 0.00 41.01 2.43
4323 4521 2.671396 CGTGTTTAGCGAGGCTATGTTT 59.329 45.455 0.00 0.00 41.01 2.83
4324 4522 2.268298 CGTGTTTAGCGAGGCTATGTT 58.732 47.619 0.00 0.00 41.01 2.71


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

AutoCloner maintained by Alex Coulton.