Multiple sequence alignment - TraesCS2D01G333000

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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 TraesCS2D01G333000 chr2D 100.000 4869 0 0 1001 5869 426926221 426931089 0.000000e+00 8992.0
1 TraesCS2D01G333000 chr2D 100.000 650 0 0 1 650 426925221 426925870 0.000000e+00 1201.0
2 TraesCS2D01G333000 chr2D 83.974 156 23 2 3124 3278 476962731 476962885 1.320000e-31 148.0
3 TraesCS2D01G333000 chr2D 83.974 156 23 2 3124 3278 477072420 477072574 1.320000e-31 148.0
4 TraesCS2D01G333000 chr2D 93.846 65 3 1 2691 2755 426927596 426927659 4.840000e-16 97.1
5 TraesCS2D01G333000 chr2D 89.062 64 7 0 3215 3278 476984457 476984520 4.880000e-11 80.5
6 TraesCS2D01G333000 chr2A 94.666 4331 168 21 1001 5293 562101231 562096926 0.000000e+00 6660.0
7 TraesCS2D01G333000 chr2A 97.696 651 14 1 4165 4814 561848859 561848209 0.000000e+00 1118.0
8 TraesCS2D01G333000 chr2A 97.755 579 10 1 5291 5869 562096787 562096212 0.000000e+00 994.0
9 TraesCS2D01G333000 chr2A 97.015 335 7 3 316 650 562101598 562101267 1.430000e-155 560.0
10 TraesCS2D01G333000 chr2A 93.182 308 15 6 15 317 73157219 73156913 1.160000e-121 448.0
11 TraesCS2D01G333000 chr2A 82.880 368 28 12 4814 5153 561847954 561847594 1.240000e-76 298.0
12 TraesCS2D01G333000 chr2A 78.421 380 46 16 5505 5869 561847183 561846825 1.280000e-51 215.0
13 TraesCS2D01G333000 chr2A 85.897 156 20 2 3124 3278 619245735 619245889 1.310000e-36 165.0
14 TraesCS2D01G333000 chr2B 95.061 2065 69 9 3081 5135 503752793 503754834 0.000000e+00 3217.0
15 TraesCS2D01G333000 chr2B 92.655 1307 57 12 1040 2326 503750715 503752002 0.000000e+00 1845.0
16 TraesCS2D01G333000 chr2B 90.184 489 38 9 1842 2326 33564407 33564889 3.860000e-176 628.0
17 TraesCS2D01G333000 chr2B 97.035 371 11 0 5499 5869 503754972 503755342 4.990000e-175 625.0
18 TraesCS2D01G333000 chr2B 89.592 490 39 11 1842 2326 84216580 84217062 3.890000e-171 612.0
19 TraesCS2D01G333000 chr2B 96.656 299 9 1 316 614 503750084 503750381 4.090000e-136 496.0
20 TraesCS2D01G333000 chr2B 81.960 449 31 14 2691 3091 503752204 503752650 9.420000e-88 335.0
21 TraesCS2D01G333000 chr2B 93.659 205 9 3 2397 2598 503752002 503752205 2.660000e-78 303.0
22 TraesCS2D01G333000 chr2B 93.069 202 10 3 2397 2595 33564889 33565089 5.750000e-75 292.0
23 TraesCS2D01G333000 chr2B 83.056 301 22 10 2691 2965 84217264 84217561 4.540000e-61 246.0
24 TraesCS2D01G333000 chr2B 94.545 110 6 0 5395 5504 503754832 503754941 2.810000e-38 171.0
25 TraesCS2D01G333000 chr2B 85.000 160 23 1 3119 3278 558295275 558295433 1.690000e-35 161.0
26 TraesCS2D01G333000 chr6B 89.980 489 39 9 1842 2326 203235516 203235998 1.800000e-174 623.0
27 TraesCS2D01G333000 chr1B 89.366 489 42 9 1842 2326 31301101 31301583 1.810000e-169 606.0
28 TraesCS2D01G333000 chr1B 93.069 303 18 3 15 314 518538736 518538434 1.940000e-119 440.0
29 TraesCS2D01G333000 chr1B 92.683 205 11 3 2397 2598 31301583 31301786 5.750000e-75 292.0
30 TraesCS2D01G333000 chr1B 92.344 209 11 4 2398 2602 240275131 240274924 5.750000e-75 292.0
31 TraesCS2D01G333000 chr1B 83.113 302 22 8 2691 2965 31301785 31302084 1.260000e-61 248.0
32 TraesCS2D01G333000 chr7B 89.278 485 43 8 1844 2326 627395139 627394662 3.030000e-167 599.0
33 TraesCS2D01G333000 chr7B 87.526 489 50 10 1842 2326 724080028 724080509 6.650000e-154 555.0
34 TraesCS2D01G333000 chr7B 87.526 489 50 10 1842 2326 724133882 724134363 6.650000e-154 555.0
35 TraesCS2D01G333000 chr7B 95.050 303 12 3 15 314 65449003 65449305 1.910000e-129 473.0
36 TraesCS2D01G333000 chr7B 93.069 303 18 3 15 314 405063176 405062874 1.940000e-119 440.0
37 TraesCS2D01G333000 chr7B 93.269 208 10 3 2397 2601 627394662 627394456 2.660000e-78 303.0
38 TraesCS2D01G333000 chr7B 83.893 298 20 8 2691 2962 627394460 627394165 5.830000e-65 259.0
39 TraesCS2D01G333000 chr4B 88.753 489 45 9 1842 2326 650566666 650567148 1.820000e-164 590.0
40 TraesCS2D01G333000 chr4B 92.344 209 11 4 2398 2602 171196497 171196704 5.750000e-75 292.0
41 TraesCS2D01G333000 chr4B 92.683 205 11 3 2397 2598 650567148 650567351 5.750000e-75 292.0
42 TraesCS2D01G333000 chr4B 82.917 240 13 9 2691 2904 650567350 650567587 2.160000e-44 191.0
43 TraesCS2D01G333000 chr7D 93.399 303 17 3 15 314 148145171 148145473 4.170000e-121 446.0
44 TraesCS2D01G333000 chr7D 92.787 305 19 3 13 314 536314997 536314693 6.980000e-119 438.0
45 TraesCS2D01G333000 chr4A 93.377 302 18 2 14 313 48029946 48029645 4.170000e-121 446.0
46 TraesCS2D01G333000 chr6D 93.069 303 18 3 15 314 454120973 454120671 1.940000e-119 440.0
47 TraesCS2D01G333000 chr3D 92.787 305 19 3 13 314 481230419 481230115 6.980000e-119 438.0
48 TraesCS2D01G333000 chr3B 91.866 209 12 4 2398 2602 814726066 814726273 2.680000e-73 287.0
49 TraesCS2D01G333000 chrUn 84.053 301 20 8 2691 2965 467114736 467114438 1.250000e-66 265.0
50 TraesCS2D01G333000 chr5B 82.781 302 22 9 2691 2965 698087772 698088070 5.880000e-60 243.0
51 TraesCS2D01G333000 chr5A 89.720 107 9 2 2596 2700 593465891 593465785 1.030000e-27 135.0


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 TraesCS2D01G333000 chr2D 426925221 426931089 5868 False 3430.033333 8992 97.948667 1 5869 3 chr2D.!!$F4 5868
1 TraesCS2D01G333000 chr2A 562096212 562101598 5386 True 2738.000000 6660 96.478667 316 5869 3 chr2A.!!$R3 5553
2 TraesCS2D01G333000 chr2A 561846825 561848859 2034 True 543.666667 1118 86.332333 4165 5869 3 chr2A.!!$R2 1704
3 TraesCS2D01G333000 chr2B 503750084 503755342 5258 False 998.857143 3217 93.081571 316 5869 7 chr2B.!!$F4 5553
4 TraesCS2D01G333000 chr2B 33564407 33565089 682 False 460.000000 628 91.626500 1842 2595 2 chr2B.!!$F2 753
5 TraesCS2D01G333000 chr2B 84216580 84217561 981 False 429.000000 612 86.324000 1842 2965 2 chr2B.!!$F3 1123
6 TraesCS2D01G333000 chr1B 31301101 31302084 983 False 382.000000 606 88.387333 1842 2965 3 chr1B.!!$F1 1123
7 TraesCS2D01G333000 chr7B 627394165 627395139 974 True 387.000000 599 88.813333 1844 2962 3 chr7B.!!$R2 1118
8 TraesCS2D01G333000 chr4B 650566666 650567587 921 False 357.666667 590 88.117667 1842 2904 3 chr4B.!!$F2 1062

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
459 460 0.035317 AATCTCACAGCGGCAGAACA 59.965 50.000 1.45 0.00 0.00 3.18 F
1382 1401 0.028770 TTCTTGGACGTTTTGCGCTG 59.971 50.000 9.73 0.00 46.11 5.18 F
1966 1986 2.221169 TCTGCACTGTGCTGTTTAAGG 58.779 47.619 30.43 11.98 45.31 2.69 F
3765 4004 1.261238 GCCTACCTCTGCTGACCTGT 61.261 60.000 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 1500 0.317160 GGCGGAAAACTCAAAAGGGG 59.683 55.000 0.00 0.0 0.0 4.79 R
2393 2428 1.775385 AACCCCAAAACCTGACAGTG 58.225 50.000 0.93 0.0 0.0 3.66 R
3876 4118 3.495001 GCAGCACGTAGAAAGAAAGAACT 59.505 43.478 0.00 0.0 0.0 3.01 R
5094 5646 0.476808 TCAGGGTCTTTTGGGGCCTA 60.477 55.000 0.84 0.0 0.0 3.93 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
23 24 4.640771 TGAAATATGCCATACTCCCTCC 57.359 45.455 0.00 0.00 0.00 4.30
24 25 3.007940 TGAAATATGCCATACTCCCTCCG 59.992 47.826 0.00 0.00 0.00 4.63
25 26 2.327325 ATATGCCATACTCCCTCCGT 57.673 50.000 0.00 0.00 0.00 4.69
26 27 1.629043 TATGCCATACTCCCTCCGTC 58.371 55.000 0.00 0.00 0.00 4.79
27 28 1.122019 ATGCCATACTCCCTCCGTCC 61.122 60.000 0.00 0.00 0.00 4.79
28 29 2.857744 GCCATACTCCCTCCGTCCG 61.858 68.421 0.00 0.00 0.00 4.79
29 30 2.201022 CCATACTCCCTCCGTCCGG 61.201 68.421 0.00 0.00 0.00 5.14
30 31 1.455217 CATACTCCCTCCGTCCGGT 60.455 63.158 0.00 0.00 36.47 5.28
31 32 1.455217 ATACTCCCTCCGTCCGGTG 60.455 63.158 0.00 3.10 36.47 4.94
32 33 1.929860 ATACTCCCTCCGTCCGGTGA 61.930 60.000 0.00 0.00 36.47 4.02
33 34 2.141011 TACTCCCTCCGTCCGGTGAA 62.141 60.000 0.00 0.00 36.47 3.18
34 35 2.678934 TCCCTCCGTCCGGTGAAG 60.679 66.667 0.00 0.00 36.47 3.02
35 36 2.678934 CCCTCCGTCCGGTGAAGA 60.679 66.667 0.00 0.00 36.47 2.87
36 37 2.711922 CCCTCCGTCCGGTGAAGAG 61.712 68.421 0.00 3.95 36.47 2.85
37 38 1.977544 CCTCCGTCCGGTGAAGAGT 60.978 63.158 0.00 0.00 36.47 3.24
38 39 1.213013 CTCCGTCCGGTGAAGAGTG 59.787 63.158 0.00 0.00 36.47 3.51
39 40 1.524863 CTCCGTCCGGTGAAGAGTGT 61.525 60.000 0.00 0.00 36.47 3.55
40 41 0.250858 TCCGTCCGGTGAAGAGTGTA 60.251 55.000 0.00 0.00 36.47 2.90
41 42 0.815734 CCGTCCGGTGAAGAGTGTAT 59.184 55.000 0.00 0.00 0.00 2.29
42 43 2.019249 CCGTCCGGTGAAGAGTGTATA 58.981 52.381 0.00 0.00 0.00 1.47
43 44 2.621998 CCGTCCGGTGAAGAGTGTATAT 59.378 50.000 0.00 0.00 0.00 0.86
44 45 3.304525 CCGTCCGGTGAAGAGTGTATATC 60.305 52.174 0.00 0.00 0.00 1.63
45 46 3.564644 CGTCCGGTGAAGAGTGTATATCT 59.435 47.826 0.00 0.00 0.00 1.98
46 47 4.753610 CGTCCGGTGAAGAGTGTATATCTA 59.246 45.833 0.00 0.00 0.00 1.98
47 48 5.237996 CGTCCGGTGAAGAGTGTATATCTAA 59.762 44.000 0.00 0.00 0.00 2.10
48 49 6.238566 CGTCCGGTGAAGAGTGTATATCTAAA 60.239 42.308 0.00 0.00 0.00 1.85
49 50 7.521748 CGTCCGGTGAAGAGTGTATATCTAAAT 60.522 40.741 0.00 0.00 0.00 1.40
50 51 8.142551 GTCCGGTGAAGAGTGTATATCTAAATT 58.857 37.037 0.00 0.00 0.00 1.82
51 52 8.701895 TCCGGTGAAGAGTGTATATCTAAATTT 58.298 33.333 0.00 0.00 0.00 1.82
52 53 9.326413 CCGGTGAAGAGTGTATATCTAAATTTT 57.674 33.333 0.00 0.00 0.00 1.82
76 77 8.934023 TTTTAGGACAAATTATGGAGTTGAGT 57.066 30.769 0.00 0.00 36.83 3.41
80 81 8.934023 AGGACAAATTATGGAGTTGAGTAAAA 57.066 30.769 0.00 0.00 36.83 1.52
81 82 9.362151 AGGACAAATTATGGAGTTGAGTAAAAA 57.638 29.630 0.00 0.00 36.83 1.94
102 103 1.868469 TGCATTGAAAAGGTGCAAGC 58.132 45.000 0.00 0.00 44.99 4.01
103 104 1.150827 GCATTGAAAAGGTGCAAGCC 58.849 50.000 0.00 0.00 38.68 4.35
104 105 1.540797 GCATTGAAAAGGTGCAAGCCA 60.541 47.619 0.00 0.00 38.68 4.75
105 106 2.137523 CATTGAAAAGGTGCAAGCCAC 58.862 47.619 0.00 0.00 43.90 5.01
106 107 1.484038 TTGAAAAGGTGCAAGCCACT 58.516 45.000 0.00 0.00 44.08 4.00
107 108 2.356665 TGAAAAGGTGCAAGCCACTA 57.643 45.000 0.00 0.00 44.08 2.74
108 109 2.875296 TGAAAAGGTGCAAGCCACTAT 58.125 42.857 0.00 0.00 44.08 2.12
109 110 2.819608 TGAAAAGGTGCAAGCCACTATC 59.180 45.455 0.00 0.00 44.08 2.08
110 111 2.887151 AAAGGTGCAAGCCACTATCT 57.113 45.000 0.00 0.00 44.08 1.98
111 112 2.409948 AAGGTGCAAGCCACTATCTC 57.590 50.000 0.00 0.00 44.08 2.75
112 113 1.577736 AGGTGCAAGCCACTATCTCT 58.422 50.000 0.00 0.00 44.08 3.10
113 114 1.484240 AGGTGCAAGCCACTATCTCTC 59.516 52.381 0.00 0.00 44.08 3.20
114 115 1.484240 GGTGCAAGCCACTATCTCTCT 59.516 52.381 0.00 0.00 44.08 3.10
115 116 2.482839 GGTGCAAGCCACTATCTCTCTC 60.483 54.545 0.00 0.00 44.08 3.20
116 117 1.759445 TGCAAGCCACTATCTCTCTCC 59.241 52.381 0.00 0.00 0.00 3.71
117 118 2.038659 GCAAGCCACTATCTCTCTCCT 58.961 52.381 0.00 0.00 0.00 3.69
118 119 2.035832 GCAAGCCACTATCTCTCTCCTC 59.964 54.545 0.00 0.00 0.00 3.71
119 120 3.565307 CAAGCCACTATCTCTCTCCTCT 58.435 50.000 0.00 0.00 0.00 3.69
120 121 3.960102 CAAGCCACTATCTCTCTCCTCTT 59.040 47.826 0.00 0.00 0.00 2.85
121 122 4.264373 AGCCACTATCTCTCTCCTCTTT 57.736 45.455 0.00 0.00 0.00 2.52
122 123 5.396057 AGCCACTATCTCTCTCCTCTTTA 57.604 43.478 0.00 0.00 0.00 1.85
123 124 5.772004 AGCCACTATCTCTCTCCTCTTTAA 58.228 41.667 0.00 0.00 0.00 1.52
124 125 6.381250 AGCCACTATCTCTCTCCTCTTTAAT 58.619 40.000 0.00 0.00 0.00 1.40
125 126 6.843861 AGCCACTATCTCTCTCCTCTTTAATT 59.156 38.462 0.00 0.00 0.00 1.40
126 127 8.007742 AGCCACTATCTCTCTCCTCTTTAATTA 58.992 37.037 0.00 0.00 0.00 1.40
127 128 8.085909 GCCACTATCTCTCTCCTCTTTAATTAC 58.914 40.741 0.00 0.00 0.00 1.89
128 129 8.581578 CCACTATCTCTCTCCTCTTTAATTACC 58.418 40.741 0.00 0.00 0.00 2.85
129 130 8.581578 CACTATCTCTCTCCTCTTTAATTACCC 58.418 40.741 0.00 0.00 0.00 3.69
130 131 8.290277 ACTATCTCTCTCCTCTTTAATTACCCA 58.710 37.037 0.00 0.00 0.00 4.51
131 132 6.793505 TCTCTCTCCTCTTTAATTACCCAC 57.206 41.667 0.00 0.00 0.00 4.61
132 133 5.661759 TCTCTCTCCTCTTTAATTACCCACC 59.338 44.000 0.00 0.00 0.00 4.61
133 134 4.720273 TCTCTCCTCTTTAATTACCCACCC 59.280 45.833 0.00 0.00 0.00 4.61
134 135 4.706616 TCTCCTCTTTAATTACCCACCCT 58.293 43.478 0.00 0.00 0.00 4.34
135 136 4.720273 TCTCCTCTTTAATTACCCACCCTC 59.280 45.833 0.00 0.00 0.00 4.30
136 137 3.784202 TCCTCTTTAATTACCCACCCTCC 59.216 47.826 0.00 0.00 0.00 4.30
137 138 3.526019 CCTCTTTAATTACCCACCCTCCA 59.474 47.826 0.00 0.00 0.00 3.86
138 139 4.017867 CCTCTTTAATTACCCACCCTCCAA 60.018 45.833 0.00 0.00 0.00 3.53
139 140 5.340863 CCTCTTTAATTACCCACCCTCCAAT 60.341 44.000 0.00 0.00 0.00 3.16
140 141 5.515106 TCTTTAATTACCCACCCTCCAATG 58.485 41.667 0.00 0.00 0.00 2.82
141 142 5.254267 TCTTTAATTACCCACCCTCCAATGA 59.746 40.000 0.00 0.00 0.00 2.57
142 143 3.669939 AATTACCCACCCTCCAATGAG 57.330 47.619 0.00 0.00 38.42 2.90
143 144 0.623723 TTACCCACCCTCCAATGAGC 59.376 55.000 0.00 0.00 37.29 4.26
144 145 0.253160 TACCCACCCTCCAATGAGCT 60.253 55.000 0.00 0.00 37.29 4.09
145 146 0.253160 ACCCACCCTCCAATGAGCTA 60.253 55.000 0.00 0.00 37.29 3.32
146 147 0.918983 CCCACCCTCCAATGAGCTAA 59.081 55.000 0.00 0.00 37.29 3.09
147 148 1.133976 CCCACCCTCCAATGAGCTAAG 60.134 57.143 0.00 0.00 37.29 2.18
148 149 1.561542 CCACCCTCCAATGAGCTAAGT 59.438 52.381 0.00 0.00 37.29 2.24
149 150 2.636830 CACCCTCCAATGAGCTAAGTG 58.363 52.381 0.00 0.00 37.29 3.16
150 151 1.065126 ACCCTCCAATGAGCTAAGTGC 60.065 52.381 0.00 0.00 43.29 4.40
151 152 1.065199 CCCTCCAATGAGCTAAGTGCA 60.065 52.381 0.00 0.00 45.94 4.57
152 153 2.422519 CCCTCCAATGAGCTAAGTGCAT 60.423 50.000 0.00 0.00 45.94 3.96
153 154 3.181451 CCCTCCAATGAGCTAAGTGCATA 60.181 47.826 0.00 0.00 45.94 3.14
154 155 4.506271 CCCTCCAATGAGCTAAGTGCATAT 60.506 45.833 0.00 0.00 45.94 1.78
155 156 5.280164 CCCTCCAATGAGCTAAGTGCATATA 60.280 44.000 0.00 0.00 45.94 0.86
156 157 5.873712 CCTCCAATGAGCTAAGTGCATATAG 59.126 44.000 0.00 0.00 45.94 1.31
157 158 6.295518 CCTCCAATGAGCTAAGTGCATATAGA 60.296 42.308 11.64 0.00 45.94 1.98
158 159 7.066307 TCCAATGAGCTAAGTGCATATAGAA 57.934 36.000 11.64 0.00 45.94 2.10
159 160 7.508687 TCCAATGAGCTAAGTGCATATAGAAA 58.491 34.615 11.64 0.00 45.94 2.52
160 161 8.159447 TCCAATGAGCTAAGTGCATATAGAAAT 58.841 33.333 11.64 1.17 45.94 2.17
161 162 8.790718 CCAATGAGCTAAGTGCATATAGAAATT 58.209 33.333 11.64 5.87 45.94 1.82
171 172 9.905713 AAGTGCATATAGAAATTAAGAAGACCA 57.094 29.630 0.00 0.00 0.00 4.02
174 175 9.851686 TGCATATAGAAATTAAGAAGACCATGT 57.148 29.630 0.00 0.00 0.00 3.21
181 182 9.965902 AGAAATTAAGAAGACCATGTGTAGATT 57.034 29.630 0.00 0.00 0.00 2.40
182 183 9.994432 GAAATTAAGAAGACCATGTGTAGATTG 57.006 33.333 0.00 0.00 0.00 2.67
183 184 6.985188 TTAAGAAGACCATGTGTAGATTGC 57.015 37.500 0.00 0.00 0.00 3.56
184 185 4.833478 AGAAGACCATGTGTAGATTGCT 57.167 40.909 0.00 0.00 0.00 3.91
185 186 5.939764 AGAAGACCATGTGTAGATTGCTA 57.060 39.130 0.00 0.00 0.00 3.49
186 187 6.491714 AGAAGACCATGTGTAGATTGCTAT 57.508 37.500 0.00 0.00 0.00 2.97
187 188 6.893583 AGAAGACCATGTGTAGATTGCTATT 58.106 36.000 0.00 0.00 0.00 1.73
188 189 6.765036 AGAAGACCATGTGTAGATTGCTATTG 59.235 38.462 0.00 0.00 0.00 1.90
189 190 5.371526 AGACCATGTGTAGATTGCTATTGG 58.628 41.667 0.00 0.00 0.00 3.16
190 191 5.104360 AGACCATGTGTAGATTGCTATTGGT 60.104 40.000 0.00 0.00 34.25 3.67
191 192 5.126067 ACCATGTGTAGATTGCTATTGGTC 58.874 41.667 0.00 0.00 29.85 4.02
192 193 5.104360 ACCATGTGTAGATTGCTATTGGTCT 60.104 40.000 0.00 0.00 29.85 3.85
193 194 5.824624 CCATGTGTAGATTGCTATTGGTCTT 59.175 40.000 0.00 0.00 0.00 3.01
194 195 6.238566 CCATGTGTAGATTGCTATTGGTCTTG 60.239 42.308 0.00 0.00 0.00 3.02
195 196 6.048732 TGTGTAGATTGCTATTGGTCTTGA 57.951 37.500 0.00 0.00 0.00 3.02
196 197 6.653020 TGTGTAGATTGCTATTGGTCTTGAT 58.347 36.000 0.00 0.00 0.00 2.57
197 198 7.112122 TGTGTAGATTGCTATTGGTCTTGATT 58.888 34.615 0.00 0.00 0.00 2.57
198 199 8.264347 TGTGTAGATTGCTATTGGTCTTGATTA 58.736 33.333 0.00 0.00 0.00 1.75
199 200 8.552034 GTGTAGATTGCTATTGGTCTTGATTAC 58.448 37.037 0.00 0.00 0.00 1.89
200 201 7.715249 TGTAGATTGCTATTGGTCTTGATTACC 59.285 37.037 0.00 0.00 37.53 2.85
201 202 5.760253 AGATTGCTATTGGTCTTGATTACCG 59.240 40.000 0.00 0.00 40.08 4.02
202 203 4.481368 TGCTATTGGTCTTGATTACCGT 57.519 40.909 0.00 0.00 40.08 4.83
203 204 4.188462 TGCTATTGGTCTTGATTACCGTG 58.812 43.478 0.00 0.00 40.08 4.94
204 205 4.189231 GCTATTGGTCTTGATTACCGTGT 58.811 43.478 0.00 0.00 40.08 4.49
205 206 4.034048 GCTATTGGTCTTGATTACCGTGTG 59.966 45.833 0.00 0.00 40.08 3.82
206 207 3.755112 TTGGTCTTGATTACCGTGTGA 57.245 42.857 0.00 0.00 40.08 3.58
207 208 3.973206 TGGTCTTGATTACCGTGTGAT 57.027 42.857 0.00 0.00 40.08 3.06
208 209 3.595173 TGGTCTTGATTACCGTGTGATG 58.405 45.455 0.00 0.00 40.08 3.07
209 210 3.259625 TGGTCTTGATTACCGTGTGATGA 59.740 43.478 0.00 0.00 40.08 2.92
210 211 3.865745 GGTCTTGATTACCGTGTGATGAG 59.134 47.826 0.00 0.00 0.00 2.90
211 212 4.381612 GGTCTTGATTACCGTGTGATGAGA 60.382 45.833 0.00 0.00 0.00 3.27
212 213 4.800993 GTCTTGATTACCGTGTGATGAGAG 59.199 45.833 0.00 0.00 0.00 3.20
213 214 4.705023 TCTTGATTACCGTGTGATGAGAGA 59.295 41.667 0.00 0.00 0.00 3.10
214 215 4.639135 TGATTACCGTGTGATGAGAGAG 57.361 45.455 0.00 0.00 0.00 3.20
215 216 4.270008 TGATTACCGTGTGATGAGAGAGA 58.730 43.478 0.00 0.00 0.00 3.10
216 217 4.705023 TGATTACCGTGTGATGAGAGAGAA 59.295 41.667 0.00 0.00 0.00 2.87
217 218 4.703645 TTACCGTGTGATGAGAGAGAAG 57.296 45.455 0.00 0.00 0.00 2.85
218 219 2.520069 ACCGTGTGATGAGAGAGAAGT 58.480 47.619 0.00 0.00 0.00 3.01
219 220 3.687125 ACCGTGTGATGAGAGAGAAGTA 58.313 45.455 0.00 0.00 0.00 2.24
220 221 4.274147 ACCGTGTGATGAGAGAGAAGTAT 58.726 43.478 0.00 0.00 0.00 2.12
221 222 4.707448 ACCGTGTGATGAGAGAGAAGTATT 59.293 41.667 0.00 0.00 0.00 1.89
222 223 5.186021 ACCGTGTGATGAGAGAGAAGTATTT 59.814 40.000 0.00 0.00 0.00 1.40
223 224 6.102663 CCGTGTGATGAGAGAGAAGTATTTT 58.897 40.000 0.00 0.00 0.00 1.82
224 225 6.591834 CCGTGTGATGAGAGAGAAGTATTTTT 59.408 38.462 0.00 0.00 0.00 1.94
256 257 9.912634 TTTTAAAGTGCATTGGAAAGATAGAAG 57.087 29.630 0.00 0.00 0.00 2.85
257 258 8.635765 TTAAAGTGCATTGGAAAGATAGAAGT 57.364 30.769 0.00 0.00 0.00 3.01
258 259 9.733556 TTAAAGTGCATTGGAAAGATAGAAGTA 57.266 29.630 0.00 0.00 0.00 2.24
259 260 7.617041 AAGTGCATTGGAAAGATAGAAGTAC 57.383 36.000 0.00 0.00 0.00 2.73
260 261 6.711277 AGTGCATTGGAAAGATAGAAGTACA 58.289 36.000 0.00 0.00 0.00 2.90
261 262 7.341805 AGTGCATTGGAAAGATAGAAGTACAT 58.658 34.615 0.00 0.00 0.00 2.29
262 263 7.831193 AGTGCATTGGAAAGATAGAAGTACATT 59.169 33.333 0.00 0.00 0.00 2.71
263 264 8.462016 GTGCATTGGAAAGATAGAAGTACATTT 58.538 33.333 0.00 0.00 0.00 2.32
264 265 9.023962 TGCATTGGAAAGATAGAAGTACATTTT 57.976 29.630 0.00 0.00 0.00 1.82
265 266 9.860898 GCATTGGAAAGATAGAAGTACATTTTT 57.139 29.630 0.00 0.00 0.00 1.94
302 303 9.961265 TTAAACCTATATGTACACTCTTCATCG 57.039 33.333 0.00 0.00 0.00 3.84
303 304 6.576662 ACCTATATGTACACTCTTCATCGG 57.423 41.667 0.00 0.00 0.00 4.18
304 305 6.304624 ACCTATATGTACACTCTTCATCGGA 58.695 40.000 0.00 0.00 0.00 4.55
305 306 6.207025 ACCTATATGTACACTCTTCATCGGAC 59.793 42.308 0.00 0.00 0.00 4.79
306 307 2.913777 TGTACACTCTTCATCGGACG 57.086 50.000 0.00 0.00 0.00 4.79
307 308 1.471287 TGTACACTCTTCATCGGACGG 59.529 52.381 0.00 0.00 0.00 4.79
308 309 1.741706 GTACACTCTTCATCGGACGGA 59.258 52.381 0.00 0.00 0.00 4.69
309 310 0.811915 ACACTCTTCATCGGACGGAG 59.188 55.000 0.00 0.00 32.57 4.63
310 311 0.101399 CACTCTTCATCGGACGGAGG 59.899 60.000 0.00 0.00 31.35 4.30
311 312 1.038130 ACTCTTCATCGGACGGAGGG 61.038 60.000 0.00 0.00 31.35 4.30
312 313 0.752009 CTCTTCATCGGACGGAGGGA 60.752 60.000 0.00 0.00 0.00 4.20
313 314 0.752009 TCTTCATCGGACGGAGGGAG 60.752 60.000 0.00 0.00 33.17 4.30
314 315 2.356818 CTTCATCGGACGGAGGGAGC 62.357 65.000 0.00 0.00 0.00 4.70
328 329 3.531538 GAGGGAGCACACGAATTATTGA 58.468 45.455 0.00 0.00 0.00 2.57
459 460 0.035317 AATCTCACAGCGGCAGAACA 59.965 50.000 1.45 0.00 0.00 3.18
511 512 0.614415 TGCCAATGGACCATTCCCAC 60.614 55.000 17.16 7.42 42.01 4.61
521 522 1.374947 CATTCCCACACACCGGACT 59.625 57.895 9.46 0.00 0.00 3.85
575 576 2.173669 GGATGCGACATGGTCCACG 61.174 63.158 0.00 0.00 0.00 4.94
1138 1141 7.218025 CGAGCAAATCGTGAGAAATCTCGAG 62.218 48.000 5.93 5.93 46.62 4.04
1186 1189 1.156736 CGTTTCTTGCGGGTTCTGAT 58.843 50.000 0.00 0.00 0.00 2.90
1286 1289 3.802139 CAGGTAATGCGCGAGAAATCTTA 59.198 43.478 12.10 0.00 0.00 2.10
1292 1295 1.593469 GCGCGAGAAATCTTAGGGTTC 59.407 52.381 12.10 0.00 0.00 3.62
1301 1304 5.550403 AGAAATCTTAGGGTTCTTGGTGGTA 59.450 40.000 0.00 0.00 0.00 3.25
1382 1401 0.028770 TTCTTGGACGTTTTGCGCTG 59.971 50.000 9.73 0.00 46.11 5.18
1528 1547 3.888934 TGCTCTTTTGATGCGTTTCTTC 58.111 40.909 0.00 0.00 0.00 2.87
1561 1580 3.624300 CGCATCTCTTCTGCCGCG 61.624 66.667 0.00 0.00 36.24 6.46
1911 1931 6.148150 ACGTGAGTAGTTGAAACTGTTTGAAA 59.852 34.615 11.03 2.38 46.88 2.69
1925 1945 5.971202 ACTGTTTGAAAATGTAGTTGCTTCG 59.029 36.000 0.00 0.00 0.00 3.79
1966 1986 2.221169 TCTGCACTGTGCTGTTTAAGG 58.779 47.619 30.43 11.98 45.31 2.69
1981 2001 7.604164 TGCTGTTTAAGGAGTTTCTAGATGAAG 59.396 37.037 0.00 0.00 35.89 3.02
2003 2023 6.128138 AGGTGTATAGTGCCTTTTCTTCTT 57.872 37.500 0.00 0.00 0.00 2.52
2071 2105 7.436673 TGTTTGAAGTACAATTGTTACCAATGC 59.563 33.333 17.78 11.50 40.42 3.56
2312 2347 7.040755 TGTGGACAGTATTTGAACTTAATGGTG 60.041 37.037 0.00 0.00 0.00 4.17
2434 2469 9.965824 GGGTTTTGATTATTGGTATGAAGTATG 57.034 33.333 0.00 0.00 0.00 2.39
2462 2500 8.792633 CAGGATCTTATTTACACCAAGTTTCAA 58.207 33.333 0.00 0.00 0.00 2.69
2535 2573 5.741982 GTGGACAATATTTGAACGTAATGGC 59.258 40.000 0.00 0.00 0.00 4.40
2610 2648 7.001674 CAGAATAGATGTACTACCTCTGGTCT 58.998 42.308 4.67 4.49 38.90 3.85
2622 2660 4.327680 ACCTCTGGTCTGCTTTAATTGTC 58.672 43.478 0.00 0.00 0.00 3.18
2626 2664 2.811431 TGGTCTGCTTTAATTGTCGTGG 59.189 45.455 0.00 0.00 0.00 4.94
2665 2703 2.901249 ACAAAGTTGTGTACAGCTCGT 58.099 42.857 0.00 0.93 40.49 4.18
2678 2716 4.584029 ACAGCTCGTGACAATAATTTCG 57.416 40.909 0.00 0.00 0.00 3.46
2749 2793 8.837389 GGGTTTTGACTATTGGTATGAAGTATC 58.163 37.037 0.00 0.00 0.00 2.24
2792 2837 6.922957 TGCTCATGAACCATTACTTTGTTTTC 59.077 34.615 0.00 0.00 0.00 2.29
2802 2847 9.014297 ACCATTACTTTGTTTTCTTCCATCTAG 57.986 33.333 0.00 0.00 0.00 2.43
2908 2973 6.358118 TGCTTAAAGTGCAGTTATTATCGG 57.642 37.500 7.33 0.00 35.31 4.18
2946 3011 5.063204 TCACTGTCCAAAGAAACACCTATG 58.937 41.667 0.00 0.00 0.00 2.23
3023 3107 3.497640 GTGATGCCTGAGTATGATTCAGC 59.502 47.826 0.00 0.00 40.54 4.26
3473 3712 9.301153 TGTATACTATTGATACAATAGCATGCG 57.699 33.333 22.97 0.00 36.95 4.73
3484 3723 3.961480 ATAGCATGCGCCAGTTAGATA 57.039 42.857 13.01 0.00 39.83 1.98
3493 3732 7.254252 GCATGCGCCAGTTAGATATCTATTTAG 60.254 40.741 13.22 4.96 0.00 1.85
3611 3850 7.567571 CGTGTCGCTCAAATGATATATTCTTT 58.432 34.615 0.00 0.00 0.00 2.52
3616 3855 9.144747 TCGCTCAAATGATATATTCTTTAGCTC 57.855 33.333 0.00 0.00 0.00 4.09
3617 3856 8.929746 CGCTCAAATGATATATTCTTTAGCTCA 58.070 33.333 0.00 0.00 0.00 4.26
3640 3879 9.757227 CTCAAGTTATTTTAATTGGTGGAACAA 57.243 29.630 0.00 0.00 44.16 2.83
3765 4004 1.261238 GCCTACCTCTGCTGACCTGT 61.261 60.000 0.00 0.00 0.00 4.00
4307 4549 0.178964 CTTCCAAGAGGGCCAACCAA 60.179 55.000 6.18 0.00 43.89 3.67
4316 4558 4.662961 GCCAACCAAAGGCGCACC 62.663 66.667 10.83 0.00 43.15 5.01
4743 4988 5.699458 AGTACCATAAACCATTGCTATACGC 59.301 40.000 0.00 0.00 39.77 4.42
5139 5691 7.547227 ACTGCTTCTGTTTTTCAAACTACAAT 58.453 30.769 1.33 0.00 0.00 2.71
5221 5807 9.838339 CTATGTAATTAGGGAACAAGAATCACT 57.162 33.333 0.00 0.00 34.26 3.41
5228 5814 5.388654 AGGGAACAAGAATCACTGTTTCAT 58.611 37.500 8.25 0.00 0.00 2.57
5241 5827 9.850628 AATCACTGTTTCATATCTGACATTTTG 57.149 29.630 0.00 0.00 0.00 2.44
5595 6431 6.476706 TGCAATTGACTCGATATACTCAACTG 59.523 38.462 10.34 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.104941 CGGAGGGAGTATGGCATATTTCATA 60.105 44.000 10.92 0.00 0.00 2.15
2 3 3.007940 CGGAGGGAGTATGGCATATTTCA 59.992 47.826 10.92 0.00 0.00 2.69
3 4 3.008049 ACGGAGGGAGTATGGCATATTTC 59.992 47.826 10.92 11.23 0.00 2.17
6 7 2.180276 GACGGAGGGAGTATGGCATAT 58.820 52.381 10.92 0.00 0.00 1.78
7 8 1.629043 GACGGAGGGAGTATGGCATA 58.371 55.000 2.32 2.32 0.00 3.14
8 9 1.122019 GGACGGAGGGAGTATGGCAT 61.122 60.000 4.88 4.88 0.00 4.40
11 12 2.201022 CCGGACGGAGGGAGTATGG 61.201 68.421 4.40 0.00 37.50 2.74
12 13 1.455217 ACCGGACGGAGGGAGTATG 60.455 63.158 18.80 0.00 38.96 2.39
13 14 1.455217 CACCGGACGGAGGGAGTAT 60.455 63.158 18.80 0.00 38.96 2.12
14 15 2.044650 CACCGGACGGAGGGAGTA 60.045 66.667 18.80 0.00 38.96 2.59
15 16 3.518552 TTCACCGGACGGAGGGAGT 62.519 63.158 18.80 0.00 38.96 3.85
16 17 2.678934 TTCACCGGACGGAGGGAG 60.679 66.667 18.80 2.08 38.96 4.30
17 18 2.678934 CTTCACCGGACGGAGGGA 60.679 66.667 18.80 8.89 38.96 4.20
18 19 2.678934 TCTTCACCGGACGGAGGG 60.679 66.667 18.80 6.62 38.96 4.30
19 20 1.977544 ACTCTTCACCGGACGGAGG 60.978 63.158 18.80 9.15 38.96 4.30
20 21 1.213013 CACTCTTCACCGGACGGAG 59.787 63.158 18.80 10.03 38.96 4.63
21 22 0.250858 TACACTCTTCACCGGACGGA 60.251 55.000 18.80 0.00 38.96 4.69
22 23 0.815734 ATACACTCTTCACCGGACGG 59.184 55.000 9.46 9.56 42.03 4.79
23 24 3.564644 AGATATACACTCTTCACCGGACG 59.435 47.826 9.46 0.00 0.00 4.79
24 25 6.630444 TTAGATATACACTCTTCACCGGAC 57.370 41.667 9.46 0.00 0.00 4.79
25 26 7.834881 ATTTAGATATACACTCTTCACCGGA 57.165 36.000 9.46 0.00 0.00 5.14
26 27 8.888579 AAATTTAGATATACACTCTTCACCGG 57.111 34.615 0.00 0.00 0.00 5.28
50 51 9.362151 ACTCAACTCCATAATTTGTCCTAAAAA 57.638 29.630 0.00 0.00 0.00 1.94
51 52 8.934023 ACTCAACTCCATAATTTGTCCTAAAA 57.066 30.769 0.00 0.00 0.00 1.52
55 56 8.934023 TTTTACTCAACTCCATAATTTGTCCT 57.066 30.769 0.00 0.00 0.00 3.85
84 85 1.150827 GGCTTGCACCTTTTCAATGC 58.849 50.000 0.00 0.00 39.88 3.56
85 86 2.137523 GTGGCTTGCACCTTTTCAATG 58.862 47.619 0.00 0.00 0.00 2.82
86 87 2.041701 AGTGGCTTGCACCTTTTCAAT 58.958 42.857 0.00 0.00 0.00 2.57
87 88 1.484038 AGTGGCTTGCACCTTTTCAA 58.516 45.000 0.00 0.00 0.00 2.69
88 89 2.356665 TAGTGGCTTGCACCTTTTCA 57.643 45.000 0.00 0.00 0.00 2.69
89 90 3.084786 AGATAGTGGCTTGCACCTTTTC 58.915 45.455 0.00 0.00 0.00 2.29
90 91 3.084786 GAGATAGTGGCTTGCACCTTTT 58.915 45.455 0.00 0.00 0.00 2.27
91 92 2.307098 AGAGATAGTGGCTTGCACCTTT 59.693 45.455 0.00 0.00 0.00 3.11
92 93 1.912043 AGAGATAGTGGCTTGCACCTT 59.088 47.619 0.00 0.00 0.00 3.50
93 94 1.484240 GAGAGATAGTGGCTTGCACCT 59.516 52.381 0.00 0.00 0.00 4.00
94 95 1.484240 AGAGAGATAGTGGCTTGCACC 59.516 52.381 0.00 0.00 0.00 5.01
95 96 2.482839 GGAGAGAGATAGTGGCTTGCAC 60.483 54.545 0.00 0.00 0.00 4.57
96 97 1.759445 GGAGAGAGATAGTGGCTTGCA 59.241 52.381 0.00 0.00 0.00 4.08
97 98 2.035832 GAGGAGAGAGATAGTGGCTTGC 59.964 54.545 0.00 0.00 0.00 4.01
98 99 3.565307 AGAGGAGAGAGATAGTGGCTTG 58.435 50.000 0.00 0.00 0.00 4.01
99 100 3.971468 AGAGGAGAGAGATAGTGGCTT 57.029 47.619 0.00 0.00 0.00 4.35
100 101 3.971468 AAGAGGAGAGAGATAGTGGCT 57.029 47.619 0.00 0.00 0.00 4.75
101 102 6.664428 ATTAAAGAGGAGAGAGATAGTGGC 57.336 41.667 0.00 0.00 0.00 5.01
102 103 8.581578 GGTAATTAAAGAGGAGAGAGATAGTGG 58.418 40.741 0.00 0.00 0.00 4.00
103 104 8.581578 GGGTAATTAAAGAGGAGAGAGATAGTG 58.418 40.741 0.00 0.00 0.00 2.74
104 105 8.290277 TGGGTAATTAAAGAGGAGAGAGATAGT 58.710 37.037 0.00 0.00 0.00 2.12
105 106 8.581578 GTGGGTAATTAAAGAGGAGAGAGATAG 58.418 40.741 0.00 0.00 0.00 2.08
106 107 7.509659 GGTGGGTAATTAAAGAGGAGAGAGATA 59.490 40.741 0.00 0.00 0.00 1.98
107 108 6.327887 GGTGGGTAATTAAAGAGGAGAGAGAT 59.672 42.308 0.00 0.00 0.00 2.75
108 109 5.661759 GGTGGGTAATTAAAGAGGAGAGAGA 59.338 44.000 0.00 0.00 0.00 3.10
109 110 5.163290 GGGTGGGTAATTAAAGAGGAGAGAG 60.163 48.000 0.00 0.00 0.00 3.20
110 111 4.720273 GGGTGGGTAATTAAAGAGGAGAGA 59.280 45.833 0.00 0.00 0.00 3.10
111 112 4.722279 AGGGTGGGTAATTAAAGAGGAGAG 59.278 45.833 0.00 0.00 0.00 3.20
112 113 4.706616 AGGGTGGGTAATTAAAGAGGAGA 58.293 43.478 0.00 0.00 0.00 3.71
113 114 4.141459 GGAGGGTGGGTAATTAAAGAGGAG 60.141 50.000 0.00 0.00 0.00 3.69
114 115 3.784202 GGAGGGTGGGTAATTAAAGAGGA 59.216 47.826 0.00 0.00 0.00 3.71
115 116 3.526019 TGGAGGGTGGGTAATTAAAGAGG 59.474 47.826 0.00 0.00 0.00 3.69
116 117 4.855298 TGGAGGGTGGGTAATTAAAGAG 57.145 45.455 0.00 0.00 0.00 2.85
117 118 5.254267 TCATTGGAGGGTGGGTAATTAAAGA 59.746 40.000 0.00 0.00 0.00 2.52
118 119 5.515106 TCATTGGAGGGTGGGTAATTAAAG 58.485 41.667 0.00 0.00 0.00 1.85
119 120 5.515106 CTCATTGGAGGGTGGGTAATTAAA 58.485 41.667 0.00 0.00 37.51 1.52
120 121 4.630184 GCTCATTGGAGGGTGGGTAATTAA 60.630 45.833 0.00 0.00 41.67 1.40
121 122 3.117663 GCTCATTGGAGGGTGGGTAATTA 60.118 47.826 0.00 0.00 41.67 1.40
122 123 2.358195 GCTCATTGGAGGGTGGGTAATT 60.358 50.000 0.00 0.00 41.67 1.40
123 124 1.215423 GCTCATTGGAGGGTGGGTAAT 59.785 52.381 0.00 0.00 41.67 1.89
124 125 0.623723 GCTCATTGGAGGGTGGGTAA 59.376 55.000 0.00 0.00 41.67 2.85
125 126 0.253160 AGCTCATTGGAGGGTGGGTA 60.253 55.000 0.00 0.00 41.67 3.69
126 127 0.253160 TAGCTCATTGGAGGGTGGGT 60.253 55.000 0.00 0.00 41.67 4.51
127 128 0.918983 TTAGCTCATTGGAGGGTGGG 59.081 55.000 0.00 0.00 41.67 4.61
128 129 1.561542 ACTTAGCTCATTGGAGGGTGG 59.438 52.381 0.00 0.00 41.67 4.61
129 130 2.636830 CACTTAGCTCATTGGAGGGTG 58.363 52.381 0.00 0.00 41.67 4.61
130 131 1.065126 GCACTTAGCTCATTGGAGGGT 60.065 52.381 0.00 0.00 41.67 4.34
131 132 1.065199 TGCACTTAGCTCATTGGAGGG 60.065 52.381 0.00 0.00 45.94 4.30
132 133 2.408271 TGCACTTAGCTCATTGGAGG 57.592 50.000 0.00 0.00 45.94 4.30
133 134 6.695429 TCTATATGCACTTAGCTCATTGGAG 58.305 40.000 0.00 0.00 45.94 3.86
134 135 6.670695 TCTATATGCACTTAGCTCATTGGA 57.329 37.500 0.00 0.00 45.94 3.53
135 136 7.734924 TTTCTATATGCACTTAGCTCATTGG 57.265 36.000 0.00 0.00 45.94 3.16
145 146 9.905713 TGGTCTTCTTAATTTCTATATGCACTT 57.094 29.630 0.00 0.00 0.00 3.16
148 149 9.851686 ACATGGTCTTCTTAATTTCTATATGCA 57.148 29.630 0.00 0.00 0.00 3.96
155 156 9.965902 AATCTACACATGGTCTTCTTAATTTCT 57.034 29.630 0.00 0.00 0.00 2.52
156 157 9.994432 CAATCTACACATGGTCTTCTTAATTTC 57.006 33.333 0.00 0.00 0.00 2.17
157 158 8.462016 GCAATCTACACATGGTCTTCTTAATTT 58.538 33.333 0.00 0.00 0.00 1.82
158 159 7.831193 AGCAATCTACACATGGTCTTCTTAATT 59.169 33.333 0.00 0.00 0.00 1.40
159 160 7.341805 AGCAATCTACACATGGTCTTCTTAAT 58.658 34.615 0.00 0.00 0.00 1.40
160 161 6.711277 AGCAATCTACACATGGTCTTCTTAA 58.289 36.000 0.00 0.00 0.00 1.85
161 162 6.299805 AGCAATCTACACATGGTCTTCTTA 57.700 37.500 0.00 0.00 0.00 2.10
162 163 5.171339 AGCAATCTACACATGGTCTTCTT 57.829 39.130 0.00 0.00 0.00 2.52
163 164 4.833478 AGCAATCTACACATGGTCTTCT 57.167 40.909 0.00 0.00 0.00 2.85
164 165 6.017605 CCAATAGCAATCTACACATGGTCTTC 60.018 42.308 0.00 0.00 0.00 2.87
165 166 5.824624 CCAATAGCAATCTACACATGGTCTT 59.175 40.000 0.00 0.00 0.00 3.01
166 167 5.104360 ACCAATAGCAATCTACACATGGTCT 60.104 40.000 0.00 0.00 31.09 3.85
167 168 5.126067 ACCAATAGCAATCTACACATGGTC 58.874 41.667 0.00 0.00 31.09 4.02
168 169 5.104360 AGACCAATAGCAATCTACACATGGT 60.104 40.000 0.00 0.00 35.42 3.55
169 170 5.371526 AGACCAATAGCAATCTACACATGG 58.628 41.667 0.00 0.00 0.00 3.66
170 171 6.539826 TCAAGACCAATAGCAATCTACACATG 59.460 38.462 0.00 0.00 0.00 3.21
171 172 6.653020 TCAAGACCAATAGCAATCTACACAT 58.347 36.000 0.00 0.00 0.00 3.21
172 173 6.048732 TCAAGACCAATAGCAATCTACACA 57.951 37.500 0.00 0.00 0.00 3.72
173 174 7.559590 AATCAAGACCAATAGCAATCTACAC 57.440 36.000 0.00 0.00 0.00 2.90
174 175 7.715249 GGTAATCAAGACCAATAGCAATCTACA 59.285 37.037 0.00 0.00 36.91 2.74
175 176 7.095607 CGGTAATCAAGACCAATAGCAATCTAC 60.096 40.741 0.00 0.00 36.72 2.59
176 177 6.929049 CGGTAATCAAGACCAATAGCAATCTA 59.071 38.462 0.00 0.00 36.72 1.98
177 178 5.760253 CGGTAATCAAGACCAATAGCAATCT 59.240 40.000 0.00 0.00 36.72 2.40
178 179 5.527582 ACGGTAATCAAGACCAATAGCAATC 59.472 40.000 0.00 0.00 36.72 2.67
179 180 5.296780 CACGGTAATCAAGACCAATAGCAAT 59.703 40.000 0.00 0.00 36.72 3.56
180 181 4.634004 CACGGTAATCAAGACCAATAGCAA 59.366 41.667 0.00 0.00 36.72 3.91
181 182 4.188462 CACGGTAATCAAGACCAATAGCA 58.812 43.478 0.00 0.00 36.72 3.49
182 183 4.034048 CACACGGTAATCAAGACCAATAGC 59.966 45.833 0.00 0.00 36.72 2.97
183 184 5.416083 TCACACGGTAATCAAGACCAATAG 58.584 41.667 0.00 0.00 36.72 1.73
184 185 5.408880 TCACACGGTAATCAAGACCAATA 57.591 39.130 0.00 0.00 36.72 1.90
185 186 4.280436 TCACACGGTAATCAAGACCAAT 57.720 40.909 0.00 0.00 36.72 3.16
186 187 3.755112 TCACACGGTAATCAAGACCAA 57.245 42.857 0.00 0.00 36.72 3.67
187 188 3.259625 TCATCACACGGTAATCAAGACCA 59.740 43.478 0.00 0.00 36.72 4.02
188 189 3.857052 TCATCACACGGTAATCAAGACC 58.143 45.455 0.00 0.00 0.00 3.85
189 190 4.744570 TCTCATCACACGGTAATCAAGAC 58.255 43.478 0.00 0.00 0.00 3.01
190 191 4.705023 TCTCTCATCACACGGTAATCAAGA 59.295 41.667 0.00 0.00 0.00 3.02
191 192 4.998788 TCTCTCATCACACGGTAATCAAG 58.001 43.478 0.00 0.00 0.00 3.02
192 193 4.705023 TCTCTCTCATCACACGGTAATCAA 59.295 41.667 0.00 0.00 0.00 2.57
193 194 4.270008 TCTCTCTCATCACACGGTAATCA 58.730 43.478 0.00 0.00 0.00 2.57
194 195 4.902443 TCTCTCTCATCACACGGTAATC 57.098 45.455 0.00 0.00 0.00 1.75
195 196 4.707448 ACTTCTCTCTCATCACACGGTAAT 59.293 41.667 0.00 0.00 0.00 1.89
196 197 4.079970 ACTTCTCTCTCATCACACGGTAA 58.920 43.478 0.00 0.00 0.00 2.85
197 198 3.687125 ACTTCTCTCTCATCACACGGTA 58.313 45.455 0.00 0.00 0.00 4.02
198 199 2.520069 ACTTCTCTCTCATCACACGGT 58.480 47.619 0.00 0.00 0.00 4.83
199 200 4.909696 ATACTTCTCTCTCATCACACGG 57.090 45.455 0.00 0.00 0.00 4.94
200 201 7.588143 AAAAATACTTCTCTCTCATCACACG 57.412 36.000 0.00 0.00 0.00 4.49
230 231 9.912634 CTTCTATCTTTCCAATGCACTTTAAAA 57.087 29.630 0.00 0.00 0.00 1.52
231 232 9.077885 ACTTCTATCTTTCCAATGCACTTTAAA 57.922 29.630 0.00 0.00 0.00 1.52
232 233 8.635765 ACTTCTATCTTTCCAATGCACTTTAA 57.364 30.769 0.00 0.00 0.00 1.52
233 234 9.162764 GTACTTCTATCTTTCCAATGCACTTTA 57.837 33.333 0.00 0.00 0.00 1.85
234 235 7.665559 TGTACTTCTATCTTTCCAATGCACTTT 59.334 33.333 0.00 0.00 0.00 2.66
235 236 7.168219 TGTACTTCTATCTTTCCAATGCACTT 58.832 34.615 0.00 0.00 0.00 3.16
236 237 6.711277 TGTACTTCTATCTTTCCAATGCACT 58.289 36.000 0.00 0.00 0.00 4.40
237 238 6.985188 TGTACTTCTATCTTTCCAATGCAC 57.015 37.500 0.00 0.00 0.00 4.57
238 239 8.579850 AAATGTACTTCTATCTTTCCAATGCA 57.420 30.769 0.00 0.00 0.00 3.96
239 240 9.860898 AAAAATGTACTTCTATCTTTCCAATGC 57.139 29.630 0.00 0.00 0.00 3.56
276 277 9.961265 CGATGAAGAGTGTACATATAGGTTTAA 57.039 33.333 0.00 0.00 0.00 1.52
277 278 8.573885 CCGATGAAGAGTGTACATATAGGTTTA 58.426 37.037 0.00 0.00 0.00 2.01
278 279 7.287005 TCCGATGAAGAGTGTACATATAGGTTT 59.713 37.037 0.00 0.00 0.00 3.27
279 280 6.776116 TCCGATGAAGAGTGTACATATAGGTT 59.224 38.462 0.00 0.00 0.00 3.50
280 281 6.207025 GTCCGATGAAGAGTGTACATATAGGT 59.793 42.308 0.00 0.00 0.00 3.08
281 282 6.613233 GTCCGATGAAGAGTGTACATATAGG 58.387 44.000 0.00 0.00 0.00 2.57
282 283 6.307915 CGTCCGATGAAGAGTGTACATATAG 58.692 44.000 0.00 0.00 0.00 1.31
283 284 5.180680 CCGTCCGATGAAGAGTGTACATATA 59.819 44.000 0.00 0.00 0.00 0.86
284 285 4.023107 CCGTCCGATGAAGAGTGTACATAT 60.023 45.833 0.00 0.00 0.00 1.78
285 286 3.314357 CCGTCCGATGAAGAGTGTACATA 59.686 47.826 0.00 0.00 0.00 2.29
286 287 2.099263 CCGTCCGATGAAGAGTGTACAT 59.901 50.000 0.00 0.00 0.00 2.29
287 288 1.471287 CCGTCCGATGAAGAGTGTACA 59.529 52.381 0.00 0.00 0.00 2.90
288 289 1.741706 TCCGTCCGATGAAGAGTGTAC 59.258 52.381 0.00 0.00 0.00 2.90
289 290 2.014857 CTCCGTCCGATGAAGAGTGTA 58.985 52.381 0.00 0.00 0.00 2.90
290 291 0.811915 CTCCGTCCGATGAAGAGTGT 59.188 55.000 0.00 0.00 0.00 3.55
291 292 0.101399 CCTCCGTCCGATGAAGAGTG 59.899 60.000 0.00 0.00 0.00 3.51
292 293 1.038130 CCCTCCGTCCGATGAAGAGT 61.038 60.000 0.00 0.00 0.00 3.24
293 294 0.752009 TCCCTCCGTCCGATGAAGAG 60.752 60.000 0.00 0.00 0.00 2.85
294 295 0.752009 CTCCCTCCGTCCGATGAAGA 60.752 60.000 0.00 0.00 0.00 2.87
295 296 1.736586 CTCCCTCCGTCCGATGAAG 59.263 63.158 0.00 0.00 0.00 3.02
296 297 2.423898 GCTCCCTCCGTCCGATGAA 61.424 63.158 0.00 0.00 0.00 2.57
297 298 2.833582 GCTCCCTCCGTCCGATGA 60.834 66.667 0.00 0.00 0.00 2.92
298 299 3.147595 TGCTCCCTCCGTCCGATG 61.148 66.667 0.00 0.00 0.00 3.84
299 300 3.148279 GTGCTCCCTCCGTCCGAT 61.148 66.667 0.00 0.00 0.00 4.18
300 301 4.671590 TGTGCTCCCTCCGTCCGA 62.672 66.667 0.00 0.00 0.00 4.55
301 302 4.436998 GTGTGCTCCCTCCGTCCG 62.437 72.222 0.00 0.00 0.00 4.79
302 303 4.436998 CGTGTGCTCCCTCCGTCC 62.437 72.222 0.00 0.00 0.00 4.79
303 304 2.227089 ATTCGTGTGCTCCCTCCGTC 62.227 60.000 0.00 0.00 0.00 4.79
304 305 1.827399 AATTCGTGTGCTCCCTCCGT 61.827 55.000 0.00 0.00 0.00 4.69
305 306 0.174845 TAATTCGTGTGCTCCCTCCG 59.825 55.000 0.00 0.00 0.00 4.63
306 307 2.614057 CAATAATTCGTGTGCTCCCTCC 59.386 50.000 0.00 0.00 0.00 4.30
307 308 3.531538 TCAATAATTCGTGTGCTCCCTC 58.468 45.455 0.00 0.00 0.00 4.30
308 309 3.627395 TCAATAATTCGTGTGCTCCCT 57.373 42.857 0.00 0.00 0.00 4.20
309 310 3.938963 TCTTCAATAATTCGTGTGCTCCC 59.061 43.478 0.00 0.00 0.00 4.30
310 311 5.351465 TCTTCTTCAATAATTCGTGTGCTCC 59.649 40.000 0.00 0.00 0.00 4.70
311 312 6.244275 GTCTTCTTCAATAATTCGTGTGCTC 58.756 40.000 0.00 0.00 0.00 4.26
312 313 5.163953 CGTCTTCTTCAATAATTCGTGTGCT 60.164 40.000 0.00 0.00 0.00 4.40
313 314 5.015733 CGTCTTCTTCAATAATTCGTGTGC 58.984 41.667 0.00 0.00 0.00 4.57
314 315 6.234213 GTCGTCTTCTTCAATAATTCGTGTG 58.766 40.000 0.00 0.00 0.00 3.82
328 329 0.878961 GTTGGCCACGTCGTCTTCTT 60.879 55.000 3.88 0.00 0.00 2.52
459 460 4.992688 TGATGTTTTTGACTTTTGAGCGT 58.007 34.783 0.00 0.00 0.00 5.07
463 464 4.564769 GCCGTTGATGTTTTTGACTTTTGA 59.435 37.500 0.00 0.00 0.00 2.69
521 522 3.399181 GGTGGACGGGCAGGATGA 61.399 66.667 0.00 0.00 39.69 2.92
1286 1289 1.982958 ACGAATACCACCAAGAACCCT 59.017 47.619 0.00 0.00 0.00 4.34
1292 1295 3.365969 GGAAAGCAACGAATACCACCAAG 60.366 47.826 0.00 0.00 0.00 3.61
1301 1304 1.602323 TGCGGGGAAAGCAACGAAT 60.602 52.632 0.00 0.00 42.18 3.34
1382 1401 1.452108 CTGCTCCCGGAAATCCACC 60.452 63.158 0.73 0.00 35.14 4.61
1481 1500 0.317160 GGCGGAAAACTCAAAAGGGG 59.683 55.000 0.00 0.00 0.00 4.79
1482 1501 1.036707 TGGCGGAAAACTCAAAAGGG 58.963 50.000 0.00 0.00 0.00 3.95
1528 1547 1.586564 GCGGATCGGTGAGAACTCG 60.587 63.158 1.93 0.00 0.00 4.18
1752 1771 1.021390 CGTAGCCTTCACAGCCCAAG 61.021 60.000 0.00 0.00 0.00 3.61
1925 1945 2.225068 TCGTAAGCAAGATAGCAGGC 57.775 50.000 0.00 0.00 36.85 4.85
1966 1986 7.650104 GCACTATACACCTTCATCTAGAAACTC 59.350 40.741 0.00 0.00 35.40 3.01
1981 2001 6.612306 CAAAGAAGAAAAGGCACTATACACC 58.388 40.000 0.00 0.00 38.49 4.16
2029 2063 0.323360 AACATGCTGTTACCGGCCAT 60.323 50.000 0.00 0.00 39.09 4.40
2385 2420 2.592102 AACCTGACAGTGCCAATCAT 57.408 45.000 0.93 0.00 0.00 2.45
2393 2428 1.775385 AACCCCAAAACCTGACAGTG 58.225 50.000 0.93 0.00 0.00 3.66
2434 2469 7.923414 AACTTGGTGTAAATAAGATCCTGTC 57.077 36.000 0.00 0.00 0.00 3.51
2435 2470 7.942341 TGAAACTTGGTGTAAATAAGATCCTGT 59.058 33.333 0.00 0.00 0.00 4.00
2436 2471 8.335532 TGAAACTTGGTGTAAATAAGATCCTG 57.664 34.615 0.00 0.00 0.00 3.86
2535 2573 7.144722 TCATGCTTTCATAACCAACTAGTTG 57.855 36.000 25.79 25.79 40.13 3.16
2610 2648 3.410631 TCCTCCACGACAATTAAAGCA 57.589 42.857 0.00 0.00 0.00 3.91
2622 2660 2.842394 ATCGCAGCAGTTCCTCCACG 62.842 60.000 0.00 0.00 0.00 4.94
2626 2664 2.099263 TGTACTATCGCAGCAGTTCCTC 59.901 50.000 0.00 0.00 0.00 3.71
2665 2703 6.233905 TCCTCTGATCCGAAATTATTGTCA 57.766 37.500 0.00 0.00 0.00 3.58
2678 2716 6.092807 GCACGGAAATAATATTCCTCTGATCC 59.907 42.308 4.71 0.00 45.54 3.36
2749 2793 4.047822 GAGCACAAGAATATCCTCTGTCG 58.952 47.826 0.00 0.00 0.00 4.35
3170 3408 5.657826 AAGTGTGTGCATTTATTGGCATA 57.342 34.783 0.00 0.00 42.75 3.14
3173 3411 4.083908 CCAAAAGTGTGTGCATTTATTGGC 60.084 41.667 0.00 0.00 32.28 4.52
3318 3557 5.525745 CGCATATAGACAACATTGTGGGTTA 59.474 40.000 1.07 0.00 42.43 2.85
3354 3593 6.319658 ACCACAAGAGGATAATGCAAACTATG 59.680 38.462 0.00 0.00 0.00 2.23
3415 3654 8.036575 ACAATGTACAGCATATGCAAAGAATTT 58.963 29.630 28.62 11.27 45.16 1.82
3611 3850 8.871629 TCCACCAATTAAAATAACTTGAGCTA 57.128 30.769 0.00 0.00 0.00 3.32
3707 3946 8.579850 AAATTAGGATTCAGTGATAACAGCAA 57.420 30.769 0.00 0.00 0.00 3.91
3876 4118 3.495001 GCAGCACGTAGAAAGAAAGAACT 59.505 43.478 0.00 0.00 0.00 3.01
4307 4549 2.045926 GACATGAGGGTGCGCCTT 60.046 61.111 17.49 8.94 34.45 4.35
4316 4558 1.202615 ACTCATCGCATGGACATGAGG 60.203 52.381 15.99 6.92 45.37 3.86
4897 5418 9.733219 AACAGAACCAAATTTTATGCAAAAATG 57.267 25.926 15.56 9.08 37.20 2.32
5094 5646 0.476808 TCAGGGTCTTTTGGGGCCTA 60.477 55.000 0.84 0.00 0.00 3.93
5139 5691 4.356405 TTCTCAGCAGAATCAAACTGGA 57.644 40.909 0.00 0.00 33.38 3.86
5217 5794 8.620116 TCAAAATGTCAGATATGAAACAGTGA 57.380 30.769 0.00 0.00 0.00 3.41
5246 5832 9.461312 TCTTAAGCCTCATTATTTGTAACACAT 57.539 29.630 0.00 0.00 0.00 3.21
5320 6047 7.989170 TGTGACATCATATTCAGTAGCTTCAAT 59.011 33.333 0.00 0.00 0.00 2.57
5481 6271 8.912787 ACACTTTGACGAATAGATTGTACTAG 57.087 34.615 0.00 0.00 0.00 2.57
5595 6431 7.832769 AGGTAGTAAAGAAGAAGAGTGATGTC 58.167 38.462 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.