Multiple sequence alignment - TraesCS5A01G442200

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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 TraesCS5A01G442200 chr5A 100.000 6935 0 0 1 6935 622774490 622767556 0.000000e+00 12807.0
1 TraesCS5A01G442200 chr5A 86.957 92 6 3 4444 4529 566333878 566333969 1.590000e-16 99.0
2 TraesCS5A01G442200 chr5B 95.624 3565 134 9 2427 5981 617823315 617819763 0.000000e+00 5699.0
3 TraesCS5A01G442200 chr5B 89.755 2450 158 45 11 2394 617825896 617823474 0.000000e+00 3048.0
4 TraesCS5A01G442200 chr5B 90.551 508 37 7 6394 6900 617819385 617818888 0.000000e+00 662.0
5 TraesCS5A01G442200 chr5B 93.393 333 18 3 6065 6394 617819751 617819420 2.250000e-134 490.0
6 TraesCS5A01G442200 chr5D 95.342 3585 120 17 2427 5987 498492295 498488734 0.000000e+00 5651.0
7 TraesCS5A01G442200 chr5D 87.787 2440 142 70 37 2394 498494880 498492515 0.000000e+00 2712.0
8 TraesCS5A01G442200 chr5D 92.288 389 25 3 6394 6781 498488376 498487992 1.320000e-151 547.0
9 TraesCS5A01G442200 chr5D 93.272 327 15 5 6068 6394 498488730 498488411 6.290000e-130 475.0
10 TraesCS5A01G442200 chr5D 90.805 87 7 1 6846 6931 498487975 498487889 1.580000e-21 115.0
11 TraesCS5A01G442200 chr2A 87.786 131 12 2 4399 4529 727182214 727182088 4.330000e-32 150.0
12 TraesCS5A01G442200 chr2A 96.774 62 1 1 6004 6065 42473838 42473778 1.230000e-17 102.0
13 TraesCS5A01G442200 chrUn 85.401 137 19 1 4401 4537 230305064 230304929 2.610000e-29 141.0
14 TraesCS5A01G442200 chrUn 85.401 137 19 1 4401 4537 347349736 347349601 2.610000e-29 141.0
15 TraesCS5A01G442200 chr1B 84.672 137 20 1 4401 4537 59996060 59996195 1.210000e-27 135.0
16 TraesCS5A01G442200 chr1B 88.095 84 7 3 5983 6065 476018790 476018871 5.730000e-16 97.1
17 TraesCS5A01G442200 chr6B 81.818 121 17 4 4405 4525 694181280 694181165 5.730000e-16 97.1
18 TraesCS5A01G442200 chr2D 86.667 90 9 3 5977 6065 17068450 17068363 5.730000e-16 97.1
19 TraesCS5A01G442200 chr2D 85.542 83 9 3 5984 6065 246547753 246547673 4.460000e-12 84.2
20 TraesCS5A01G442200 chr4D 87.059 85 7 4 5984 6067 430895595 430895676 7.410000e-15 93.5
21 TraesCS5A01G442200 chr4D 85.542 83 9 3 5984 6065 11573292 11573372 4.460000e-12 84.2
22 TraesCS5A01G442200 chr2B 91.304 69 5 1 5997 6065 657933891 657933824 7.410000e-15 93.5
23 TraesCS5A01G442200 chr3B 86.747 83 8 3 5984 6065 809833041 809833121 9.580000e-14 89.8
24 TraesCS5A01G442200 chr6A 85.882 85 9 3 5982 6065 536234010 536233928 3.450000e-13 87.9
25 TraesCS5A01G442200 chr7A 84.884 86 9 4 4439 4522 209158285 209158202 4.460000e-12 84.2


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 TraesCS5A01G442200 chr5A 622767556 622774490 6934 True 12807.00 12807 100.00000 1 6935 1 chr5A.!!$R1 6934
1 TraesCS5A01G442200 chr5B 617818888 617825896 7008 True 2474.75 5699 92.33075 11 6900 4 chr5B.!!$R1 6889
2 TraesCS5A01G442200 chr5D 498487889 498494880 6991 True 1900.00 5651 91.89880 37 6931 5 chr5D.!!$R1 6894

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
172 182 0.036765 AAATCGTACCCTCGCAAGCA 60.037 50.000 0.0 0.0 37.18 3.91 F
726 758 0.102481 TCGGATGACTTCGCCTAAGC 59.898 55.000 0.0 0.0 38.93 3.09 F
729 761 0.178068 GATGACTTCGCCTAAGCCCA 59.822 55.000 0.0 0.0 38.93 5.36 F
2125 2229 0.036010 ATTCTGGTGTGAAGCGAGGG 60.036 55.000 0.0 0.0 0.00 4.30 F
2305 2412 0.036105 TGCATCGCCAGTTCAGTCAT 60.036 50.000 0.0 0.0 0.00 3.06 F
2839 3147 1.764571 AAGGAAGTGCGGTGCCTACA 61.765 55.000 0.0 0.0 0.00 2.74 F
3612 3921 2.147958 GTGTCAACGGGCTGTCAATTA 58.852 47.619 0.0 0.0 0.00 1.40 F
5345 5656 1.339929 GGCAACGGTTTGAGGAACAAT 59.660 47.619 0.0 0.0 40.13 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1182 1233 0.674895 ACAATCAAGAGCCGGAGCAC 60.675 55.000 5.05 0.00 43.56 4.40 R
1685 1776 1.000731 GGCACAGAGATGCTAGCTAGG 59.999 57.143 22.10 6.16 45.38 3.02 R
2282 2389 1.978712 CTGAACTGGCGATGCAGCAG 61.979 60.000 1.53 0.00 39.27 4.24 R
3379 3687 0.035152 CACATGCCTAAGGGTGCTCA 60.035 55.000 0.00 0.00 34.45 4.26 R
3459 3767 0.314935 CTCCACACCCACAACAATGC 59.685 55.000 0.00 0.00 0.00 3.56 R
4804 5114 3.874543 GGCCAAAACTACCCAACAAAAAG 59.125 43.478 0.00 0.00 0.00 2.27 R
5443 5754 2.109425 ATGAGGTTACTTGGGCGTTC 57.891 50.000 0.00 0.00 0.00 3.95 R
6441 6795 0.827368 CCTCACTGCTCCTCCTAACC 59.173 60.000 0.00 0.00 0.00 2.85 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
22 23 5.490472 CAGCGATTAATAACATTGCATGC 57.510 39.130 11.82 11.82 33.90 4.06
26 27 5.860182 GCGATTAATAACATTGCATGCTCAT 59.140 36.000 20.33 8.21 31.99 2.90
27 28 6.183359 GCGATTAATAACATTGCATGCTCATG 60.183 38.462 20.33 21.32 41.60 3.07
66 67 5.823045 ACTACTCAAGTGGCATAATAAAGGC 59.177 40.000 0.00 0.00 36.93 4.35
78 79 7.549134 TGGCATAATAAAGGCATATAAGAGACG 59.451 37.037 0.00 0.00 35.21 4.18
86 87 4.752101 AGGCATATAAGAGACGATTTGCAC 59.248 41.667 0.00 0.00 33.30 4.57
90 91 1.882912 AAGAGACGATTTGCACAGCA 58.117 45.000 0.00 0.00 36.47 4.41
91 92 2.105006 AGAGACGATTTGCACAGCAT 57.895 45.000 0.00 0.00 38.76 3.79
94 95 3.558829 AGAGACGATTTGCACAGCATATG 59.441 43.478 0.00 0.00 38.76 1.78
97 107 4.271049 AGACGATTTGCACAGCATATGTAC 59.729 41.667 4.29 0.00 41.41 2.90
99 109 3.245048 CGATTTGCACAGCATATGTACGA 59.755 43.478 4.29 0.00 41.41 3.43
102 112 0.852777 GCACAGCATATGTACGACGG 59.147 55.000 4.29 0.00 41.41 4.79
103 113 1.801395 GCACAGCATATGTACGACGGT 60.801 52.381 4.29 0.00 41.41 4.83
107 117 2.724690 CAGCATATGTACGACGGTAAGC 59.275 50.000 4.29 0.00 0.00 3.09
124 134 2.496899 AGCGATCCAGACCACATTTT 57.503 45.000 0.00 0.00 0.00 1.82
127 137 2.096496 GCGATCCAGACCACATTTTCAG 59.904 50.000 0.00 0.00 0.00 3.02
128 138 2.096496 CGATCCAGACCACATTTTCAGC 59.904 50.000 0.00 0.00 0.00 4.26
131 141 3.499338 TCCAGACCACATTTTCAGCAAT 58.501 40.909 0.00 0.00 0.00 3.56
132 142 4.661222 TCCAGACCACATTTTCAGCAATA 58.339 39.130 0.00 0.00 0.00 1.90
133 143 4.701651 TCCAGACCACATTTTCAGCAATAG 59.298 41.667 0.00 0.00 0.00 1.73
136 146 6.449698 CAGACCACATTTTCAGCAATAGTTT 58.550 36.000 0.00 0.00 0.00 2.66
147 157 6.360370 TCAGCAATAGTTTCTAACCAGAGT 57.640 37.500 0.00 0.00 30.73 3.24
148 158 6.769512 TCAGCAATAGTTTCTAACCAGAGTT 58.230 36.000 0.00 0.00 40.15 3.01
149 159 6.650807 TCAGCAATAGTTTCTAACCAGAGTTG 59.349 38.462 0.00 0.00 36.68 3.16
150 160 5.412904 AGCAATAGTTTCTAACCAGAGTTGC 59.587 40.000 0.00 0.00 36.68 4.17
151 161 5.181245 GCAATAGTTTCTAACCAGAGTTGCA 59.819 40.000 0.00 0.00 38.37 4.08
152 162 6.621596 GCAATAGTTTCTAACCAGAGTTGCAG 60.622 42.308 0.00 0.00 38.37 4.41
154 164 5.036117 AGTTTCTAACCAGAGTTGCAGAA 57.964 39.130 0.00 0.00 36.68 3.02
155 165 5.437060 AGTTTCTAACCAGAGTTGCAGAAA 58.563 37.500 0.00 0.00 37.85 2.52
156 166 6.064717 AGTTTCTAACCAGAGTTGCAGAAAT 58.935 36.000 7.00 0.00 40.27 2.17
157 167 6.205658 AGTTTCTAACCAGAGTTGCAGAAATC 59.794 38.462 7.00 0.00 40.27 2.17
158 168 4.245660 TCTAACCAGAGTTGCAGAAATCG 58.754 43.478 0.00 0.00 36.68 3.34
159 169 2.550830 ACCAGAGTTGCAGAAATCGT 57.449 45.000 0.00 0.00 31.28 3.73
160 170 3.678056 ACCAGAGTTGCAGAAATCGTA 57.322 42.857 0.00 0.00 31.28 3.43
163 173 2.673368 CAGAGTTGCAGAAATCGTACCC 59.327 50.000 0.00 0.00 31.28 3.69
164 174 2.567615 AGAGTTGCAGAAATCGTACCCT 59.432 45.455 0.00 0.00 31.28 4.34
166 176 1.659098 GTTGCAGAAATCGTACCCTCG 59.341 52.381 0.00 0.00 0.00 4.63
167 177 0.459585 TGCAGAAATCGTACCCTCGC 60.460 55.000 0.00 0.00 0.00 5.03
168 178 0.459585 GCAGAAATCGTACCCTCGCA 60.460 55.000 0.00 0.00 0.00 5.10
169 179 2.004583 CAGAAATCGTACCCTCGCAA 57.995 50.000 0.00 0.00 0.00 4.85
170 180 1.927174 CAGAAATCGTACCCTCGCAAG 59.073 52.381 0.00 0.00 0.00 4.01
171 181 0.651031 GAAATCGTACCCTCGCAAGC 59.349 55.000 0.00 0.00 37.18 4.01
172 182 0.036765 AAATCGTACCCTCGCAAGCA 60.037 50.000 0.00 0.00 37.18 3.91
196 213 3.181439 CCAAACTGAGAAGAGGGGAAAGT 60.181 47.826 0.00 0.00 0.00 2.66
198 215 4.893829 AACTGAGAAGAGGGGAAAGTAC 57.106 45.455 0.00 0.00 0.00 2.73
199 216 3.858135 ACTGAGAAGAGGGGAAAGTACA 58.142 45.455 0.00 0.00 0.00 2.90
200 217 4.232091 ACTGAGAAGAGGGGAAAGTACAA 58.768 43.478 0.00 0.00 0.00 2.41
201 218 4.284746 ACTGAGAAGAGGGGAAAGTACAAG 59.715 45.833 0.00 0.00 0.00 3.16
202 219 3.008049 TGAGAAGAGGGGAAAGTACAAGC 59.992 47.826 0.00 0.00 0.00 4.01
253 272 0.895559 CCTTGTTGGGCTGGAACTCC 60.896 60.000 0.00 0.00 0.00 3.85
293 312 1.099879 CCCCGTCTACTCTACCCACG 61.100 65.000 0.00 0.00 0.00 4.94
299 318 3.087781 GTCTACTCTACCCACGAAAGGT 58.912 50.000 0.00 0.00 41.64 3.50
306 325 2.249844 ACCCACGAAAGGTAACACAG 57.750 50.000 0.00 0.00 35.24 3.66
323 346 2.005451 ACAGAGCAAGCAAGATTAGCG 58.995 47.619 0.00 0.00 37.01 4.26
335 358 1.173913 GATTAGCGCCAACCAAACCT 58.826 50.000 2.29 0.00 0.00 3.50
362 385 0.108424 ACTCGAGTCAGCAATGGAGC 60.108 55.000 13.58 0.00 0.00 4.70
363 386 0.809241 CTCGAGTCAGCAATGGAGCC 60.809 60.000 3.62 0.00 34.23 4.70
364 387 1.078918 CGAGTCAGCAATGGAGCCA 60.079 57.895 0.00 0.00 34.23 4.75
365 388 1.088340 CGAGTCAGCAATGGAGCCAG 61.088 60.000 0.00 0.00 34.23 4.85
367 390 2.044650 TCAGCAATGGAGCCAGCC 60.045 61.111 0.00 0.00 34.23 4.85
370 393 1.228956 AGCAATGGAGCCAGCCAAA 60.229 52.632 0.00 0.00 42.16 3.28
371 394 0.616679 AGCAATGGAGCCAGCCAAAT 60.617 50.000 0.00 0.00 42.16 2.32
372 395 0.251073 GCAATGGAGCCAGCCAAATT 59.749 50.000 0.00 0.00 42.16 1.82
373 396 1.481772 GCAATGGAGCCAGCCAAATTA 59.518 47.619 0.00 0.00 42.16 1.40
374 397 2.093553 GCAATGGAGCCAGCCAAATTAA 60.094 45.455 0.00 0.00 42.16 1.40
375 398 3.524541 CAATGGAGCCAGCCAAATTAAC 58.475 45.455 0.00 0.00 42.16 2.01
376 399 1.555967 TGGAGCCAGCCAAATTAACC 58.444 50.000 0.00 0.00 34.31 2.85
377 400 1.077005 TGGAGCCAGCCAAATTAACCT 59.923 47.619 0.00 0.00 34.31 3.50
380 403 0.455815 GCCAGCCAAATTAACCTCCG 59.544 55.000 0.00 0.00 0.00 4.63
381 404 1.953311 GCCAGCCAAATTAACCTCCGA 60.953 52.381 0.00 0.00 0.00 4.55
516 542 1.935194 CAGCAGCTCATCATCGCAG 59.065 57.895 0.00 0.00 0.00 5.18
517 543 1.888172 AGCAGCTCATCATCGCAGC 60.888 57.895 0.00 0.00 38.71 5.25
539 565 3.005261 CCCATTCCAACATCGAAACAACA 59.995 43.478 0.00 0.00 0.00 3.33
724 756 0.744874 CCTCGGATGACTTCGCCTAA 59.255 55.000 0.00 0.00 0.00 2.69
725 757 1.269309 CCTCGGATGACTTCGCCTAAG 60.269 57.143 0.00 0.00 41.33 2.18
726 758 0.102481 TCGGATGACTTCGCCTAAGC 59.898 55.000 0.00 0.00 38.93 3.09
727 759 0.876342 CGGATGACTTCGCCTAAGCC 60.876 60.000 0.00 0.00 38.93 4.35
728 760 0.533085 GGATGACTTCGCCTAAGCCC 60.533 60.000 0.00 0.00 38.93 5.19
729 761 0.178068 GATGACTTCGCCTAAGCCCA 59.822 55.000 0.00 0.00 38.93 5.36
756 788 4.351054 GGTCCCACCCCACAGCAG 62.351 72.222 0.00 0.00 30.04 4.24
765 800 0.895559 CCCCACAGCAGGAGGAAAAC 60.896 60.000 0.00 0.00 0.00 2.43
778 813 2.990514 GAGGAAAACAGAGAGAAGCGAC 59.009 50.000 0.00 0.00 0.00 5.19
781 816 0.959553 AAACAGAGAGAAGCGACGGA 59.040 50.000 0.00 0.00 0.00 4.69
906 941 0.468648 CCTAGCTAAAACCCCCTCGG 59.531 60.000 0.00 0.00 37.81 4.63
938 973 2.359107 CCTCCGCTTTGCTCTGCA 60.359 61.111 0.00 0.00 36.47 4.41
944 979 2.866028 CTTTGCTCTGCACTCCGC 59.134 61.111 0.00 0.00 38.71 5.54
955 990 1.889105 CACTCCGCAATCCCATCCG 60.889 63.158 0.00 0.00 0.00 4.18
957 992 1.889105 CTCCGCAATCCCATCCGTG 60.889 63.158 0.00 0.00 0.00 4.94
962 997 0.815615 GCAATCCCATCCGTGTCTCC 60.816 60.000 0.00 0.00 0.00 3.71
989 1024 1.810030 CTCGGCGAAACCCTAGCAC 60.810 63.158 12.13 0.00 33.26 4.40
1111 1159 2.095252 GTCTCGAAGAAGTGCGCCC 61.095 63.158 4.18 0.00 34.09 6.13
1132 1180 3.118223 CCCCTTCCTCGCTTCTTCTTATT 60.118 47.826 0.00 0.00 0.00 1.40
1182 1233 2.283351 GCTCTTGCTTGCTTGTTTGTTG 59.717 45.455 0.00 0.00 36.03 3.33
1285 1339 4.082523 CGCCGGCTCAAGGAGGAA 62.083 66.667 26.68 0.00 0.00 3.36
1413 1491 6.460781 TGAAACACTAATATCTCCGTGTGTT 58.539 36.000 0.00 0.00 46.28 3.32
1414 1492 6.367695 TGAAACACTAATATCTCCGTGTGTTG 59.632 38.462 9.54 0.00 44.45 3.33
1415 1493 5.401531 ACACTAATATCTCCGTGTGTTGT 57.598 39.130 0.00 0.00 38.99 3.32
1439 1517 4.076394 TCTTTTAATTGTTGTAGGCGGCT 58.924 39.130 18.33 18.33 0.00 5.52
1522 1610 7.233389 ACATGGATCCTACTGTATGTCATAC 57.767 40.000 14.23 14.98 36.29 2.39
1523 1611 7.013220 ACATGGATCCTACTGTATGTCATACT 58.987 38.462 20.91 7.15 36.70 2.12
1526 1614 5.775701 GGATCCTACTGTATGTCATACTGGT 59.224 44.000 25.14 21.73 38.53 4.00
1542 1630 2.256461 GTGCCGCTTTCTTGCTGG 59.744 61.111 0.00 0.00 0.00 4.85
1543 1631 3.673484 TGCCGCTTTCTTGCTGGC 61.673 61.111 12.65 12.65 45.55 4.85
1577 1668 2.438868 ATTGCGTTCTTTCCCTTTGC 57.561 45.000 0.00 0.00 0.00 3.68
1590 1681 0.804989 CCTTTGCGGGATGTTCTGAC 59.195 55.000 0.00 0.00 0.00 3.51
1643 1734 0.548682 ACAGGCTCAGGACCCTTGAT 60.549 55.000 0.00 0.00 0.00 2.57
1685 1776 3.139077 CAACCCCTATCCGCATAAGTTC 58.861 50.000 0.00 0.00 0.00 3.01
1811 1902 3.181418 CCATTGCCCTGGGGAGTATTATT 60.181 47.826 16.03 0.00 37.50 1.40
1841 1932 2.821969 GACATGGTTTTGATCTGTGGCT 59.178 45.455 0.00 0.00 0.00 4.75
1982 2085 0.961019 TGTCTGTTTGGATGGCTTGC 59.039 50.000 0.00 0.00 0.00 4.01
2003 2106 3.507622 GCCACTTTTCAGCCTGTCTATTT 59.492 43.478 0.00 0.00 0.00 1.40
2004 2107 4.021981 GCCACTTTTCAGCCTGTCTATTTT 60.022 41.667 0.00 0.00 0.00 1.82
2005 2108 5.464168 CCACTTTTCAGCCTGTCTATTTTG 58.536 41.667 0.00 0.00 0.00 2.44
2034 2137 8.404107 TCAGTACCGATCTCATGAAATGTATA 57.596 34.615 0.00 0.00 46.80 1.47
2060 2164 6.074648 ACTTCCATTCTCACATTTTTACCCA 58.925 36.000 0.00 0.00 0.00 4.51
2125 2229 0.036010 ATTCTGGTGTGAAGCGAGGG 60.036 55.000 0.00 0.00 0.00 4.30
2188 2295 9.086336 GCTTTGCTTGCAACTTAATTGATTATA 57.914 29.630 7.60 0.00 41.23 0.98
2282 2389 6.404712 ACTTAATCAGCTACTTAAACACGC 57.595 37.500 0.00 0.00 0.00 5.34
2305 2412 0.036105 TGCATCGCCAGTTCAGTCAT 60.036 50.000 0.00 0.00 0.00 3.06
2322 2429 3.947196 AGTCATTTGTGTTTGCAGTCTGA 59.053 39.130 3.32 0.00 0.00 3.27
2326 2433 5.978919 TCATTTGTGTTTGCAGTCTGATTTC 59.021 36.000 3.32 0.00 0.00 2.17
2332 2439 6.262944 TGTGTTTGCAGTCTGATTTCATACTT 59.737 34.615 3.32 0.00 31.96 2.24
2489 2791 9.749490 GCTGGTTTGTTTAACTTTTTCTTTAAC 57.251 29.630 0.00 0.00 36.93 2.01
2555 2862 4.328440 GTCTGATGACTTGGAATTCTCACG 59.672 45.833 5.23 2.56 39.94 4.35
2691 2998 6.626302 TGTTCGAAAGTTGGTTCTTGAAATT 58.374 32.000 0.00 0.00 0.00 1.82
2703 3010 7.841956 TGGTTCTTGAAATTACTGTTTTTCCA 58.158 30.769 11.16 0.00 32.14 3.53
2748 3056 3.006967 GTCTGCAGTCTTTCCTCTGGTTA 59.993 47.826 14.67 0.00 32.94 2.85
2768 3076 6.993902 TGGTTACTTAAGTCTTAGTTGGGTTG 59.006 38.462 12.39 0.00 0.00 3.77
2839 3147 1.764571 AAGGAAGTGCGGTGCCTACA 61.765 55.000 0.00 0.00 0.00 2.74
2872 3180 5.221641 CCCAGGAATGTGTAGGAATATCGAA 60.222 44.000 0.00 0.00 0.00 3.71
2881 3189 9.832445 ATGTGTAGGAATATCGAAAAGTATGTT 57.168 29.630 0.00 0.00 0.00 2.71
2913 3221 4.453819 CCAGGTTTGTTCTCATTCTGACTC 59.546 45.833 0.00 0.00 0.00 3.36
2992 3300 9.420551 GTAGTAACTGTTAGGGATATTGCATAC 57.579 37.037 0.00 0.00 0.00 2.39
3281 3589 6.774354 ATCAGTTTTAGCACATTTTTGCAG 57.226 33.333 0.00 0.00 45.62 4.41
3379 3687 3.092301 GGCAGGTCTTTGAAGGCTTTAT 58.908 45.455 0.00 0.00 0.00 1.40
3404 3712 3.496692 GCACCCTTAGGCATGTGATATGA 60.497 47.826 9.74 0.00 36.11 2.15
3458 3766 6.418057 TTGCTAAATCTCACCCATTTGTTT 57.582 33.333 0.00 0.00 0.00 2.83
3459 3767 5.782047 TGCTAAATCTCACCCATTTGTTTG 58.218 37.500 0.00 0.00 0.00 2.93
3555 3864 8.034804 GGTATTTCTAATTTGCATGACCAAGTT 58.965 33.333 0.00 0.00 0.00 2.66
3594 3903 7.482654 TGTGACTTTCAGTTATCTCTTTGTG 57.517 36.000 0.00 0.00 0.00 3.33
3612 3921 2.147958 GTGTCAACGGGCTGTCAATTA 58.852 47.619 0.00 0.00 0.00 1.40
3617 3926 4.075682 TCAACGGGCTGTCAATTATGAAA 58.924 39.130 0.00 0.00 37.30 2.69
3788 4097 3.550437 ATCTTCAAGACCCGATCCAAG 57.450 47.619 0.00 0.00 0.00 3.61
3821 4130 6.128391 CGTTTATTCGAAGGTTTCTTGATGGA 60.128 38.462 3.35 0.00 32.52 3.41
4107 4416 7.620888 AGGAATGAAGGGATTGATTTAACACAT 59.379 33.333 0.00 0.00 0.00 3.21
4128 4437 7.094634 ACACATAATCCTGAATTCACAACAGTC 60.095 37.037 3.38 0.00 0.00 3.51
4205 4514 6.762187 GCCATGATATCTGGTGAGAATCTATG 59.238 42.308 17.32 4.31 36.10 2.23
4252 4561 9.290483 CCTTTGTAACTTTCTTCTTTTTCTGTC 57.710 33.333 0.00 0.00 0.00 3.51
4381 4691 3.645434 TCACGCCTCCCTTTAGGTAATA 58.355 45.455 0.00 0.00 39.02 0.98
4442 4752 6.846325 AAAGCTTGTCTTACACTTGTCTAC 57.154 37.500 0.00 0.00 33.88 2.59
4446 4756 7.841956 AGCTTGTCTTACACTTGTCTACATAT 58.158 34.615 0.00 0.00 0.00 1.78
4621 4931 6.705381 CAGAAGGATAGACATGATTGAAGGAC 59.295 42.308 0.00 0.00 0.00 3.85
4772 5082 7.330946 GCTTGACAAGGTTTTACTTTTGACTTT 59.669 33.333 16.80 0.00 0.00 2.66
4781 5091 5.845391 TTACTTTTGACTTTTGGGGACTG 57.155 39.130 0.00 0.00 0.00 3.51
4804 5114 5.158101 CATCTGATGCTGTGTCTTCATTC 57.842 43.478 4.47 0.00 0.00 2.67
4836 5147 6.075984 TGGGTAGTTTTGGCCATACTTTTTA 58.924 36.000 21.92 5.70 0.00 1.52
4877 5188 2.627699 GGTGAAGAAAGTTGCATTCCCA 59.372 45.455 0.00 0.00 0.00 4.37
4894 5205 5.806955 TTCCCATAGAACCCCTTATTTGT 57.193 39.130 0.00 0.00 0.00 2.83
4896 5207 4.134563 CCCATAGAACCCCTTATTTGTCG 58.865 47.826 0.00 0.00 0.00 4.35
4951 5262 4.319177 ACTAAACTCACAATCTCAGTGGC 58.681 43.478 0.00 0.00 37.58 5.01
4958 5269 5.587844 ACTCACAATCTCAGTGGCATTATTC 59.412 40.000 0.00 0.00 37.58 1.75
5223 5534 9.845214 AGGTATGTCCTATTCTTCATATAGGTT 57.155 33.333 8.36 0.33 46.10 3.50
5236 5547 9.434275 TCTTCATATAGGTTCTTTGATACCTGA 57.566 33.333 4.11 0.00 44.34 3.86
5260 5571 5.118990 TCTCATTTATGCTGGCTTACACTC 58.881 41.667 0.00 0.00 0.00 3.51
5345 5656 1.339929 GGCAACGGTTTGAGGAACAAT 59.660 47.619 0.00 0.00 40.13 2.71
5355 5666 6.376177 GGTTTGAGGAACAATTAAAGGTACG 58.624 40.000 0.00 0.00 40.13 3.67
5418 5729 4.980573 TGTAATTCTTGCTGTAACCACCT 58.019 39.130 0.00 0.00 0.00 4.00
5421 5732 2.839486 TCTTGCTGTAACCACCTCAG 57.161 50.000 0.00 0.00 0.00 3.35
5443 5754 2.483877 TCTGTATGCTTTGAACTTGGCG 59.516 45.455 0.00 0.00 0.00 5.69
5460 5771 1.632948 GCGAACGCCCAAGTAACCTC 61.633 60.000 8.03 0.00 34.56 3.85
5578 5892 1.493446 GGAAGGGGGTACACTTATGGG 59.507 57.143 0.00 0.00 0.00 4.00
5632 5946 4.882671 TGAGTTGCTTGTTGAGAAGTTC 57.117 40.909 0.00 0.00 0.00 3.01
5637 5951 7.229306 TGAGTTGCTTGTTGAGAAGTTCAATAT 59.771 33.333 5.50 0.00 46.85 1.28
5742 6059 0.033011 AGTATGGACTGCCTCCGACT 60.033 55.000 0.00 1.08 43.03 4.18
5812 6129 3.256704 TCCCAGAACATCAAGGTTAGGT 58.743 45.455 0.00 0.00 0.00 3.08
5822 6139 8.664669 AACATCAAGGTTAGGTTATTTCCATT 57.335 30.769 0.00 0.00 0.00 3.16
5866 6183 5.290643 GTGCAACACTTTTTGACTTGCATTA 59.709 36.000 6.64 0.00 46.45 1.90
5969 6286 1.934589 TCAACAGGTCTGTGAACACG 58.065 50.000 4.22 0.00 44.13 4.49
5989 6306 7.025485 ACACGCTACTTTATCTAGTACTTCC 57.975 40.000 0.00 0.00 0.00 3.46
5990 6307 6.827762 ACACGCTACTTTATCTAGTACTTCCT 59.172 38.462 0.00 0.00 0.00 3.36
5991 6308 7.012232 ACACGCTACTTTATCTAGTACTTCCTC 59.988 40.741 0.00 0.00 0.00 3.71
5992 6309 7.227116 CACGCTACTTTATCTAGTACTTCCTCT 59.773 40.741 0.00 0.00 0.00 3.69
5993 6310 7.774625 ACGCTACTTTATCTAGTACTTCCTCTT 59.225 37.037 0.00 0.00 0.00 2.85
5994 6311 8.623030 CGCTACTTTATCTAGTACTTCCTCTTT 58.377 37.037 0.00 0.00 0.00 2.52
6031 6348 6.518208 AGAGCGTTTAGATCACTCTTTAGT 57.482 37.500 0.00 0.00 37.82 2.24
6045 6362 5.652518 ACTCTTTAGTGATCTAAACGCTCC 58.347 41.667 0.00 0.00 40.05 4.70
6046 6363 5.419471 ACTCTTTAGTGATCTAAACGCTCCT 59.581 40.000 0.00 0.00 40.05 3.69
6047 6364 6.602406 ACTCTTTAGTGATCTAAACGCTCCTA 59.398 38.462 0.00 0.00 40.05 2.94
6048 6365 7.285858 ACTCTTTAGTGATCTAAACGCTCCTAT 59.714 37.037 0.00 0.00 40.05 2.57
6049 6366 8.687292 TCTTTAGTGATCTAAACGCTCCTATA 57.313 34.615 0.00 0.00 40.05 1.31
6050 6367 9.298250 TCTTTAGTGATCTAAACGCTCCTATAT 57.702 33.333 0.00 0.00 40.05 0.86
6051 6368 9.915629 CTTTAGTGATCTAAACGCTCCTATATT 57.084 33.333 0.00 0.00 40.05 1.28
6053 6370 9.909644 TTAGTGATCTAAACGCTCCTATATTTC 57.090 33.333 0.00 0.00 33.79 2.17
6054 6371 8.184304 AGTGATCTAAACGCTCCTATATTTCT 57.816 34.615 0.00 0.00 0.00 2.52
6055 6372 8.643324 AGTGATCTAAACGCTCCTATATTTCTT 58.357 33.333 0.00 0.00 0.00 2.52
6056 6373 9.262358 GTGATCTAAACGCTCCTATATTTCTTT 57.738 33.333 0.00 0.00 0.00 2.52
6060 6377 9.745880 TCTAAACGCTCCTATATTTCTTTACAG 57.254 33.333 0.00 0.00 0.00 2.74
6061 6378 9.745880 CTAAACGCTCCTATATTTCTTTACAGA 57.254 33.333 0.00 0.00 0.00 3.41
6062 6379 8.649973 AAACGCTCCTATATTTCTTTACAGAG 57.350 34.615 0.00 0.00 0.00 3.35
6063 6380 6.750148 ACGCTCCTATATTTCTTTACAGAGG 58.250 40.000 0.00 0.00 0.00 3.69
6082 6399 1.737793 GGGGATAACTCTTTGTGTGCG 59.262 52.381 0.00 0.00 0.00 5.34
6087 6404 4.201724 GGATAACTCTTTGTGTGCGACATC 60.202 45.833 0.00 0.00 33.40 3.06
6170 6487 8.322091 AGTTACTTGTCTAATCTTGCATAACCT 58.678 33.333 0.00 0.00 0.00 3.50
6189 6506 3.181471 ACCTAGTCTTGCGGATCATGAAG 60.181 47.826 0.00 0.00 31.67 3.02
6195 6512 2.768253 TGCGGATCATGAAGTGTCTT 57.232 45.000 0.00 0.00 0.00 3.01
6203 6520 3.213506 TCATGAAGTGTCTTGGGTGTTG 58.786 45.455 0.00 0.00 31.39 3.33
6211 6528 2.162608 TGTCTTGGGTGTTGACAAAACG 59.837 45.455 2.38 0.00 37.71 3.60
6350 6667 5.659463 TGCAGAAGTAATTTTGTTTGCTGT 58.341 33.333 0.00 0.00 0.00 4.40
6389 6708 7.173907 GGATTATGACATGACAATACAAGGAGG 59.826 40.741 0.00 0.00 0.00 4.30
6441 6795 4.506288 GGGTTGTTGAAAATTTGAACTCCG 59.494 41.667 9.26 0.00 0.00 4.63
6475 6830 3.560481 CAGTGAGGCATATGAAGCAAGAG 59.440 47.826 6.97 0.00 0.00 2.85
6480 6835 2.877168 GGCATATGAAGCAAGAGTCAGG 59.123 50.000 6.97 0.00 0.00 3.86
6492 6847 0.392327 GAGTCAGGAGGAGCCAAAGC 60.392 60.000 0.00 0.00 40.02 3.51
6522 6877 7.432350 ACATGTTTGCTTGTTTTCTTTTTGA 57.568 28.000 0.00 0.00 30.04 2.69
6523 6878 8.042944 ACATGTTTGCTTGTTTTCTTTTTGAT 57.957 26.923 0.00 0.00 30.04 2.57
6524 6879 7.964011 ACATGTTTGCTTGTTTTCTTTTTGATG 59.036 29.630 0.00 0.00 30.04 3.07
6564 6919 7.816640 AGTGCTTGGTATTGTTATACACTTTG 58.183 34.615 0.00 0.00 38.71 2.77
6611 6966 3.191669 TGCGTCTTATTTGTATGGACCG 58.808 45.455 0.00 0.00 0.00 4.79
6630 6985 0.469144 GCTAGAGCTAGAGGTGCCCT 60.469 60.000 8.65 0.00 38.21 5.19
6691 7046 0.468648 GGGTAGGATGAAAGGTCCCG 59.531 60.000 0.00 0.00 36.36 5.14
6713 7068 4.675146 CGGAAGTTGGCATTCGAATCAAAT 60.675 41.667 7.92 7.17 0.00 2.32
6714 7069 5.170748 GGAAGTTGGCATTCGAATCAAATT 58.829 37.500 19.07 19.07 31.51 1.82
6715 7070 5.639082 GGAAGTTGGCATTCGAATCAAATTT 59.361 36.000 19.64 14.08 29.48 1.82
6717 7072 6.710692 AGTTGGCATTCGAATCAAATTTTC 57.289 33.333 7.92 0.00 0.00 2.29
6727 7082 9.716507 ATTCGAATCAAATTTTCTACAATACCG 57.283 29.630 4.39 0.00 0.00 4.02
6844 7199 1.004044 CAACTCCAGATTGGTGCTCCT 59.996 52.381 6.34 0.00 39.03 3.69
6864 7219 3.624777 CTGGTGGCAGTGGAGATATTTT 58.375 45.455 0.00 0.00 0.00 1.82
6873 7228 8.325787 TGGCAGTGGAGATATTTTAAGTTCTAA 58.674 33.333 0.00 0.00 0.00 2.10
6893 7248 7.186021 TCTAATTCGTTCCAAGACAAACTTC 57.814 36.000 0.00 0.00 36.61 3.01
6924 7279 9.420118 AGTTTGGCCAAGTTCATATAAATATCA 57.580 29.630 19.48 0.00 0.00 2.15
6927 7282 8.759481 TGGCCAAGTTCATATAAATATCAACA 57.241 30.769 0.61 0.00 0.00 3.33
6928 7283 9.365906 TGGCCAAGTTCATATAAATATCAACAT 57.634 29.630 0.61 0.00 0.00 2.71
6929 7284 9.846248 GGCCAAGTTCATATAAATATCAACATC 57.154 33.333 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 8.465999 AGTAGTGTAATCTATCTATGCATGAGC 58.534 37.037 10.16 0.00 42.57 4.26
26 27 9.355916 ACTTGAGTAGTGTAATCTATCTATGCA 57.644 33.333 0.00 0.00 35.19 3.96
63 64 4.752101 GTGCAAATCGTCTCTTATATGCCT 59.248 41.667 0.00 0.00 0.00 4.75
66 67 5.234972 TGCTGTGCAAATCGTCTCTTATATG 59.765 40.000 0.00 0.00 34.76 1.78
78 79 4.518217 GTCGTACATATGCTGTGCAAATC 58.482 43.478 1.58 0.00 43.62 2.17
83 84 0.852777 CCGTCGTACATATGCTGTGC 59.147 55.000 1.58 0.00 38.92 4.57
86 87 2.724690 GCTTACCGTCGTACATATGCTG 59.275 50.000 1.58 0.00 0.00 4.41
90 91 3.120060 GGATCGCTTACCGTCGTACATAT 60.120 47.826 0.00 0.00 38.35 1.78
91 92 2.224079 GGATCGCTTACCGTCGTACATA 59.776 50.000 0.00 0.00 38.35 2.29
94 95 0.378257 TGGATCGCTTACCGTCGTAC 59.622 55.000 0.00 0.00 38.35 3.67
97 107 0.591741 GTCTGGATCGCTTACCGTCG 60.592 60.000 0.00 0.00 38.35 5.12
99 109 0.968901 TGGTCTGGATCGCTTACCGT 60.969 55.000 0.00 0.00 38.35 4.83
102 112 2.604046 ATGTGGTCTGGATCGCTTAC 57.396 50.000 0.00 0.00 0.00 2.34
103 113 3.627395 AAATGTGGTCTGGATCGCTTA 57.373 42.857 0.00 0.00 0.00 3.09
107 117 2.096496 GCTGAAAATGTGGTCTGGATCG 59.904 50.000 0.00 0.00 0.00 3.69
124 134 6.360370 ACTCTGGTTAGAAACTATTGCTGA 57.640 37.500 0.00 0.00 31.21 4.26
127 137 5.181245 TGCAACTCTGGTTAGAAACTATTGC 59.819 40.000 0.00 0.00 39.26 3.56
128 138 6.650807 TCTGCAACTCTGGTTAGAAACTATTG 59.349 38.462 0.00 0.00 33.88 1.90
131 141 5.801531 TCTGCAACTCTGGTTAGAAACTA 57.198 39.130 0.00 0.00 33.88 2.24
132 142 4.689612 TCTGCAACTCTGGTTAGAAACT 57.310 40.909 0.00 0.00 33.88 2.66
133 143 5.751243 TTTCTGCAACTCTGGTTAGAAAC 57.249 39.130 0.00 0.00 36.20 2.78
136 146 4.245660 CGATTTCTGCAACTCTGGTTAGA 58.754 43.478 0.00 0.00 33.88 2.10
147 157 2.004583 CGAGGGTACGATTTCTGCAA 57.995 50.000 0.00 0.00 35.09 4.08
148 158 0.459585 GCGAGGGTACGATTTCTGCA 60.460 55.000 0.00 0.00 35.09 4.41
149 159 0.459585 TGCGAGGGTACGATTTCTGC 60.460 55.000 0.00 0.00 35.09 4.26
150 160 1.927174 CTTGCGAGGGTACGATTTCTG 59.073 52.381 0.00 0.00 35.09 3.02
151 161 1.739371 GCTTGCGAGGGTACGATTTCT 60.739 52.381 2.37 0.00 35.09 2.52
152 162 0.651031 GCTTGCGAGGGTACGATTTC 59.349 55.000 2.37 0.00 35.09 2.17
154 164 0.460284 CTGCTTGCGAGGGTACGATT 60.460 55.000 2.37 0.00 35.09 3.34
155 165 1.141881 CTGCTTGCGAGGGTACGAT 59.858 57.895 2.37 0.00 35.09 3.73
156 166 2.571757 CTGCTTGCGAGGGTACGA 59.428 61.111 2.37 0.00 35.09 3.43
157 167 3.188786 GCTGCTTGCGAGGGTACG 61.189 66.667 2.37 0.00 0.00 3.67
158 168 2.820037 GGCTGCTTGCGAGGGTAC 60.820 66.667 2.37 0.00 44.05 3.34
159 169 2.404566 TTTGGCTGCTTGCGAGGGTA 62.405 55.000 2.37 0.00 44.05 3.69
160 170 3.790416 TTTGGCTGCTTGCGAGGGT 62.790 57.895 2.37 0.00 44.05 4.34
163 173 1.081641 CAGTTTGGCTGCTTGCGAG 60.082 57.895 0.00 0.00 44.05 5.03
164 174 1.509644 CTCAGTTTGGCTGCTTGCGA 61.510 55.000 0.00 0.00 44.66 5.10
166 176 0.670162 TTCTCAGTTTGGCTGCTTGC 59.330 50.000 0.00 0.00 44.66 4.01
167 177 2.224606 TCTTCTCAGTTTGGCTGCTTG 58.775 47.619 0.00 0.00 44.66 4.01
168 178 2.502295 CTCTTCTCAGTTTGGCTGCTT 58.498 47.619 0.00 0.00 44.66 3.91
169 179 1.271271 CCTCTTCTCAGTTTGGCTGCT 60.271 52.381 0.00 0.00 44.66 4.24
170 180 1.163554 CCTCTTCTCAGTTTGGCTGC 58.836 55.000 0.00 0.00 44.66 5.25
171 181 1.612726 CCCCTCTTCTCAGTTTGGCTG 60.613 57.143 0.00 0.00 46.34 4.85
172 182 0.695347 CCCCTCTTCTCAGTTTGGCT 59.305 55.000 0.00 0.00 0.00 4.75
196 213 2.158827 TCACAAGGTGAGCTTGCTTGTA 60.159 45.455 22.83 2.92 37.67 2.41
198 215 1.311859 TCACAAGGTGAGCTTGCTTG 58.688 50.000 22.83 15.00 37.67 4.01
199 216 3.806941 TCACAAGGTGAGCTTGCTT 57.193 47.368 22.83 3.00 37.67 3.91
220 239 3.936203 AAGGGCGACGTGCTTCCA 61.936 61.111 0.00 0.00 45.43 3.53
253 272 1.144936 GATGGGGAAGACGCTCCTG 59.855 63.158 0.00 0.00 35.63 3.86
293 312 2.878406 TGCTTGCTCTGTGTTACCTTTC 59.122 45.455 0.00 0.00 0.00 2.62
299 318 4.393062 GCTAATCTTGCTTGCTCTGTGTTA 59.607 41.667 0.00 0.00 0.00 2.41
306 325 0.028637 GGCGCTAATCTTGCTTGCTC 59.971 55.000 7.64 0.00 0.00 4.26
323 346 3.910490 TGCGCAGGTTTGGTTGGC 61.910 61.111 5.66 0.00 0.00 4.52
335 358 3.558099 CTGACTCGAGTGGTGCGCA 62.558 63.158 25.58 5.66 0.00 6.09
362 385 1.743394 GTCGGAGGTTAATTTGGCTGG 59.257 52.381 0.00 0.00 0.00 4.85
363 386 1.743394 GGTCGGAGGTTAATTTGGCTG 59.257 52.381 0.00 0.00 0.00 4.85
364 387 1.633945 AGGTCGGAGGTTAATTTGGCT 59.366 47.619 0.00 0.00 0.00 4.75
365 388 2.124277 AGGTCGGAGGTTAATTTGGC 57.876 50.000 0.00 0.00 0.00 4.52
367 390 4.189231 CAGGTAGGTCGGAGGTTAATTTG 58.811 47.826 0.00 0.00 0.00 2.32
370 393 2.395619 CCAGGTAGGTCGGAGGTTAAT 58.604 52.381 0.00 0.00 0.00 1.40
371 394 1.620524 CCCAGGTAGGTCGGAGGTTAA 60.621 57.143 0.00 0.00 34.66 2.01
372 395 0.032813 CCCAGGTAGGTCGGAGGTTA 60.033 60.000 0.00 0.00 34.66 2.85
373 396 1.305887 CCCAGGTAGGTCGGAGGTT 60.306 63.158 0.00 0.00 34.66 3.50
374 397 2.363361 CCCAGGTAGGTCGGAGGT 59.637 66.667 0.00 0.00 34.66 3.85
375 398 3.155167 GCCCAGGTAGGTCGGAGG 61.155 72.222 0.00 0.00 34.66 4.30
376 399 3.528370 CGCCCAGGTAGGTCGGAG 61.528 72.222 0.00 0.00 34.66 4.63
377 400 4.371417 ACGCCCAGGTAGGTCGGA 62.371 66.667 0.00 0.00 34.66 4.55
380 403 3.834799 CCGACGCCCAGGTAGGTC 61.835 72.222 0.00 0.00 34.66 3.85
381 404 4.691359 ACCGACGCCCAGGTAGGT 62.691 66.667 0.00 0.00 40.52 3.08
502 528 2.053259 ATGGGCTGCGATGATGAGCT 62.053 55.000 0.00 0.00 33.03 4.09
503 529 1.170919 AATGGGCTGCGATGATGAGC 61.171 55.000 0.00 0.00 0.00 4.26
504 530 0.873054 GAATGGGCTGCGATGATGAG 59.127 55.000 0.00 0.00 0.00 2.90
516 542 1.543802 TGTTTCGATGTTGGAATGGGC 59.456 47.619 0.00 0.00 0.00 5.36
517 543 3.005261 TGTTGTTTCGATGTTGGAATGGG 59.995 43.478 0.00 0.00 0.00 4.00
742 774 4.039092 CTCCTGCTGTGGGGTGGG 62.039 72.222 0.00 0.00 0.00 4.61
743 775 4.039092 CCTCCTGCTGTGGGGTGG 62.039 72.222 0.00 0.00 0.00 4.61
744 776 2.067932 TTTCCTCCTGCTGTGGGGTG 62.068 60.000 0.00 0.00 0.00 4.61
745 777 1.360393 TTTTCCTCCTGCTGTGGGGT 61.360 55.000 0.00 0.00 0.00 4.95
746 778 0.895559 GTTTTCCTCCTGCTGTGGGG 60.896 60.000 0.00 0.00 0.00 4.96
756 788 2.028930 TCGCTTCTCTCTGTTTTCCTCC 60.029 50.000 0.00 0.00 0.00 4.30
765 800 0.794981 CGTTCCGTCGCTTCTCTCTG 60.795 60.000 0.00 0.00 0.00 3.35
816 851 2.295696 GTGCGCGTAAGTTTTTCTGAC 58.704 47.619 8.43 0.00 41.68 3.51
818 853 1.003331 TGGTGCGCGTAAGTTTTTCTG 60.003 47.619 8.43 0.00 41.68 3.02
865 900 4.648626 TTGCTTGGCTCCTGCGCT 62.649 61.111 9.73 0.00 40.82 5.92
871 906 0.251165 TAGGGTTGTTGCTTGGCTCC 60.251 55.000 0.00 0.00 0.00 4.70
938 973 2.367202 ACGGATGGGATTGCGGAGT 61.367 57.895 0.00 0.00 34.45 3.85
944 979 0.179045 GGGAGACACGGATGGGATTG 60.179 60.000 0.00 0.00 0.00 2.67
955 990 4.026357 AGGGGGAGGGGGAGACAC 62.026 72.222 0.00 0.00 0.00 3.67
957 992 4.862823 CGAGGGGGAGGGGGAGAC 62.863 77.778 0.00 0.00 0.00 3.36
1080 1128 3.213402 GAGACCCTCGGCTCCTCG 61.213 72.222 0.00 0.00 0.00 4.63
1093 1141 2.095252 GGGCGCACTTCTTCGAGAC 61.095 63.158 10.83 0.00 0.00 3.36
1111 1159 3.828875 ATAAGAAGAAGCGAGGAAGGG 57.171 47.619 0.00 0.00 0.00 3.95
1132 1180 2.278336 CGCGCGAAACGGAGGATA 60.278 61.111 28.94 0.00 43.93 2.59
1182 1233 0.674895 ACAATCAAGAGCCGGAGCAC 60.675 55.000 5.05 0.00 43.56 4.40
1285 1339 5.303971 CATCACACCTTGTTCTTCTTCTCT 58.696 41.667 0.00 0.00 0.00 3.10
1324 1379 2.995939 TGCATCAGAAAAGTAGCACGAG 59.004 45.455 0.00 0.00 0.00 4.18
1413 1491 5.278071 CCGCCTACAACAATTAAAAGACACA 60.278 40.000 0.00 0.00 0.00 3.72
1414 1492 5.151389 CCGCCTACAACAATTAAAAGACAC 58.849 41.667 0.00 0.00 0.00 3.67
1415 1493 4.320641 GCCGCCTACAACAATTAAAAGACA 60.321 41.667 0.00 0.00 0.00 3.41
1522 1610 2.256461 GCAAGAAAGCGGCACCAG 59.744 61.111 1.45 0.00 0.00 4.00
1523 1611 2.203337 AGCAAGAAAGCGGCACCA 60.203 55.556 1.45 0.00 40.15 4.17
1526 1614 3.673484 GCCAGCAAGAAAGCGGCA 61.673 61.111 1.45 0.00 46.23 5.69
1542 1630 3.489785 ACGCAATTCAGCTAATAGTACGC 59.510 43.478 0.00 0.00 0.00 4.42
1543 1631 5.459107 AGAACGCAATTCAGCTAATAGTACG 59.541 40.000 0.00 0.00 40.09 3.67
1577 1668 1.739466 CACATTGGTCAGAACATCCCG 59.261 52.381 0.00 0.00 0.00 5.14
1582 1673 4.439974 GCAAGAAACACATTGGTCAGAACA 60.440 41.667 0.00 0.00 0.00 3.18
1590 1681 2.400399 CTGCAGCAAGAAACACATTGG 58.600 47.619 0.00 0.00 0.00 3.16
1685 1776 1.000731 GGCACAGAGATGCTAGCTAGG 59.999 57.143 22.10 6.16 45.38 3.02
1811 1902 7.884877 ACAGATCAAAACCATGTCTAATCTCAA 59.115 33.333 0.00 0.00 0.00 3.02
1827 1918 6.652481 TGAAAAACAAAAGCCACAGATCAAAA 59.348 30.769 0.00 0.00 0.00 2.44
1841 1932 6.552445 TGATCCTCCCTTTGAAAAACAAAA 57.448 33.333 0.00 0.00 45.97 2.44
1982 2085 5.464168 CAAAATAGACAGGCTGAAAAGTGG 58.536 41.667 23.66 0.23 0.00 4.00
2003 2106 4.827284 TCATGAGATCGGTACTGATAGCAA 59.173 41.667 17.26 4.48 0.00 3.91
2004 2107 4.398319 TCATGAGATCGGTACTGATAGCA 58.602 43.478 17.26 16.99 0.00 3.49
2005 2108 5.378292 TTCATGAGATCGGTACTGATAGC 57.622 43.478 17.26 12.24 0.00 2.97
2060 2164 4.553678 TCCAACTCCGAGGTCCTATTAAT 58.446 43.478 0.00 0.00 0.00 1.40
2125 2229 8.739972 GGAATTCCACATATACCAACAATATCC 58.260 37.037 20.04 0.00 35.64 2.59
2188 2295 9.054922 CAAAGTTAAAATTTGGATGTGGATGTT 57.945 29.630 0.00 0.00 34.66 2.71
2206 2313 8.528044 AACTGGTATGGTTCTTTCAAAGTTAA 57.472 30.769 0.00 0.00 0.00 2.01
2209 2316 6.635030 GAACTGGTATGGTTCTTTCAAAGT 57.365 37.500 0.00 0.00 39.68 2.66
2282 2389 1.978712 CTGAACTGGCGATGCAGCAG 61.979 60.000 1.53 0.00 39.27 4.24
2305 2412 5.321959 TGAAATCAGACTGCAAACACAAA 57.678 34.783 0.00 0.00 0.00 2.83
2460 2755 8.697846 AAGAAAAAGTTAAACAAACCAGCTAC 57.302 30.769 0.00 0.00 39.03 3.58
2494 2801 9.685828 GCAAAAAGAAACAACCTACATGTATAA 57.314 29.630 5.91 0.00 0.00 0.98
2555 2862 9.294030 CTATTGCTTTTTCCTGATGATTAACAC 57.706 33.333 0.00 0.00 0.00 3.32
2654 2961 4.576463 ACTTTCGAACAGATTCTGCTTTGT 59.424 37.500 13.64 1.83 34.37 2.83
2656 2963 5.506317 CCAACTTTCGAACAGATTCTGCTTT 60.506 40.000 13.64 1.45 34.37 3.51
2691 2998 5.999205 AATGCATGGATGGAAAAACAGTA 57.001 34.783 0.00 0.00 0.00 2.74
2703 3010 9.193806 AGACTGAAAAATAAGTAATGCATGGAT 57.806 29.630 0.00 0.00 0.00 3.41
2748 3056 6.709397 GCTAACAACCCAACTAAGACTTAAGT 59.291 38.462 8.13 8.13 0.00 2.24
2839 3147 1.002017 CATTCCTGGGGCCCATTGT 59.998 57.895 28.95 10.01 30.82 2.71
2872 3180 4.141018 ACCTGGTCCCTCAAAACATACTTT 60.141 41.667 0.00 0.00 0.00 2.66
2881 3189 2.243736 AGAACAAACCTGGTCCCTCAAA 59.756 45.455 0.00 0.00 40.48 2.69
2992 3300 8.099364 AGAAGGAAAATATGCATATAACACCG 57.901 34.615 19.39 0.00 0.00 4.94
3009 3317 9.457436 GTTCCCTACATGTAAATAAGAAGGAAA 57.543 33.333 7.06 0.00 30.83 3.13
3379 3687 0.035152 CACATGCCTAAGGGTGCTCA 60.035 55.000 0.00 0.00 34.45 4.26
3458 3766 0.396278 TCCACACCCACAACAATGCA 60.396 50.000 0.00 0.00 0.00 3.96
3459 3767 0.314935 CTCCACACCCACAACAATGC 59.685 55.000 0.00 0.00 0.00 3.56
3555 3864 7.619965 TGAAAGTCACATCCATCAACACTATA 58.380 34.615 0.00 0.00 0.00 1.31
3594 3903 3.006940 TCATAATTGACAGCCCGTTGAC 58.993 45.455 0.00 0.00 0.00 3.18
3612 3921 2.093341 GGTGGCATGCTGGATTTTTCAT 60.093 45.455 18.92 0.00 0.00 2.57
3617 3926 1.276989 CAAAGGTGGCATGCTGGATTT 59.723 47.619 18.92 11.10 0.00 2.17
3788 4097 6.404712 AACCTTCGAATAAACGAGACAATC 57.595 37.500 0.00 0.00 43.04 2.67
4107 4416 5.789521 TCGACTGTTGTGAATTCAGGATTA 58.210 37.500 8.80 0.00 34.02 1.75
4128 4437 4.684242 TCTGCATACGCCATATAAAACTCG 59.316 41.667 0.00 0.00 37.32 4.18
4205 4514 7.888250 AAGGAAGAAGGAAAATATGGATGAC 57.112 36.000 0.00 0.00 0.00 3.06
4381 4691 8.376270 GGGAGTACATCTTAATTATGCCTACTT 58.624 37.037 0.00 0.00 0.00 2.24
4421 4731 5.531122 TGTAGACAAGTGTAAGACAAGCT 57.469 39.130 0.00 0.00 0.00 3.74
4772 5082 3.888424 CATCAGATGCAGTCCCCAA 57.112 52.632 0.00 0.00 0.00 4.12
4804 5114 3.874543 GGCCAAAACTACCCAACAAAAAG 59.125 43.478 0.00 0.00 0.00 2.27
4836 5147 4.637534 CACCAAGCACTTGTCATATAAGCT 59.362 41.667 9.41 0.00 38.85 3.74
4853 5164 4.301628 GGAATGCAACTTTCTTCACCAAG 58.698 43.478 0.00 0.00 0.00 3.61
4877 5188 5.687166 TGACGACAAATAAGGGGTTCTAT 57.313 39.130 0.00 0.00 0.00 1.98
4917 5228 9.103048 GATTGTGAGTTTAGTTTTCATAACACG 57.897 33.333 0.00 0.00 0.00 4.49
4958 5269 6.583912 ACGGTAATTTAGATCATGACAACG 57.416 37.500 0.00 0.00 0.00 4.10
5223 5534 8.435187 AGCATAAATGAGATCAGGTATCAAAGA 58.565 33.333 0.00 0.00 37.03 2.52
5236 5547 5.688807 AGTGTAAGCCAGCATAAATGAGAT 58.311 37.500 0.00 0.00 0.00 2.75
5260 5571 5.293814 CACCTAGAAGACATTTGCAGATCAG 59.706 44.000 0.00 0.00 0.00 2.90
5345 5656 5.049267 GGCAGATTCAAACACGTACCTTTAA 60.049 40.000 0.00 0.00 0.00 1.52
5355 5666 2.161211 GCTCTCAGGCAGATTCAAACAC 59.839 50.000 0.00 0.00 0.00 3.32
5418 5729 4.756642 CCAAGTTCAAAGCATACAGACTGA 59.243 41.667 10.08 0.00 0.00 3.41
5421 5732 3.667960 CGCCAAGTTCAAAGCATACAGAC 60.668 47.826 0.00 0.00 0.00 3.51
5443 5754 2.109425 ATGAGGTTACTTGGGCGTTC 57.891 50.000 0.00 0.00 0.00 3.95
5549 5863 2.124411 GTACCCCCTTCCATAGCTTCA 58.876 52.381 0.00 0.00 0.00 3.02
5578 5892 2.744202 CAATGCGGGCTCCATTAGTATC 59.256 50.000 0.65 0.00 32.03 2.24
5637 5951 9.983024 TCCTGGAATATTGTAAGACCATAAAAA 57.017 29.630 0.00 0.00 0.00 1.94
5642 5956 6.043243 ACGATCCTGGAATATTGTAAGACCAT 59.957 38.462 0.00 0.00 0.00 3.55
5651 5968 5.410746 CCAGATTGACGATCCTGGAATATTG 59.589 44.000 0.00 0.00 36.20 1.90
5742 6059 1.886730 TTCCCAAACCCCAACCACCA 61.887 55.000 0.00 0.00 0.00 4.17
5822 6139 5.221204 TGCACTGCATGAAAGAACACAAATA 60.221 36.000 0.00 0.00 31.71 1.40
6022 6339 5.419471 AGGAGCGTTTAGATCACTAAAGAGT 59.581 40.000 0.00 0.00 45.42 3.24
6023 6340 5.897050 AGGAGCGTTTAGATCACTAAAGAG 58.103 41.667 0.00 0.00 45.42 2.85
6024 6341 5.916661 AGGAGCGTTTAGATCACTAAAGA 57.083 39.130 0.00 0.00 45.42 2.52
6025 6342 9.915629 AATATAGGAGCGTTTAGATCACTAAAG 57.084 33.333 0.00 0.00 45.42 1.85
6027 6344 9.909644 GAAATATAGGAGCGTTTAGATCACTAA 57.090 33.333 0.00 0.00 36.90 2.24
6028 6345 9.298250 AGAAATATAGGAGCGTTTAGATCACTA 57.702 33.333 0.00 0.00 36.90 2.74
6029 6346 8.184304 AGAAATATAGGAGCGTTTAGATCACT 57.816 34.615 0.00 0.00 36.90 3.41
6030 6347 8.819643 AAGAAATATAGGAGCGTTTAGATCAC 57.180 34.615 0.00 0.00 36.90 3.06
6034 6351 9.745880 CTGTAAAGAAATATAGGAGCGTTTAGA 57.254 33.333 0.00 0.00 0.00 2.10
6035 6352 9.745880 TCTGTAAAGAAATATAGGAGCGTTTAG 57.254 33.333 0.00 0.00 0.00 1.85
6036 6353 9.745880 CTCTGTAAAGAAATATAGGAGCGTTTA 57.254 33.333 0.00 0.00 0.00 2.01
6037 6354 7.711339 CCTCTGTAAAGAAATATAGGAGCGTTT 59.289 37.037 0.00 0.00 0.00 3.60
6038 6355 7.210873 CCTCTGTAAAGAAATATAGGAGCGTT 58.789 38.462 0.00 0.00 0.00 4.84
6039 6356 6.239345 CCCTCTGTAAAGAAATATAGGAGCGT 60.239 42.308 0.00 0.00 0.00 5.07
6040 6357 6.159988 CCCTCTGTAAAGAAATATAGGAGCG 58.840 44.000 0.00 0.00 0.00 5.03
6041 6358 6.270231 TCCCCTCTGTAAAGAAATATAGGAGC 59.730 42.308 0.00 0.00 0.00 4.70
6042 6359 7.857404 TCCCCTCTGTAAAGAAATATAGGAG 57.143 40.000 0.00 0.00 0.00 3.69
6043 6360 9.907819 TTATCCCCTCTGTAAAGAAATATAGGA 57.092 33.333 0.00 0.00 0.00 2.94
6044 6361 9.945904 GTTATCCCCTCTGTAAAGAAATATAGG 57.054 37.037 0.00 0.00 0.00 2.57
6047 6364 9.453830 AGAGTTATCCCCTCTGTAAAGAAATAT 57.546 33.333 0.00 0.00 37.88 1.28
6048 6365 8.855804 AGAGTTATCCCCTCTGTAAAGAAATA 57.144 34.615 0.00 0.00 37.88 1.40
6049 6366 7.757242 AGAGTTATCCCCTCTGTAAAGAAAT 57.243 36.000 0.00 0.00 37.88 2.17
6050 6367 7.569599 AAGAGTTATCCCCTCTGTAAAGAAA 57.430 36.000 0.00 0.00 39.22 2.52
6051 6368 7.017254 ACAAAGAGTTATCCCCTCTGTAAAGAA 59.983 37.037 0.00 0.00 39.22 2.52
6052 6369 6.500751 ACAAAGAGTTATCCCCTCTGTAAAGA 59.499 38.462 0.00 0.00 39.22 2.52
6053 6370 6.595716 CACAAAGAGTTATCCCCTCTGTAAAG 59.404 42.308 0.00 0.00 39.22 1.85
6054 6371 6.043938 ACACAAAGAGTTATCCCCTCTGTAAA 59.956 38.462 0.00 0.00 39.22 2.01
6055 6372 5.546499 ACACAAAGAGTTATCCCCTCTGTAA 59.454 40.000 0.00 0.00 39.22 2.41
6056 6373 5.046591 CACACAAAGAGTTATCCCCTCTGTA 60.047 44.000 0.00 0.00 39.22 2.74
6057 6374 3.910627 ACACAAAGAGTTATCCCCTCTGT 59.089 43.478 0.00 0.00 39.22 3.41
6058 6375 4.256920 CACACAAAGAGTTATCCCCTCTG 58.743 47.826 0.00 0.00 39.22 3.35
6059 6376 3.307762 GCACACAAAGAGTTATCCCCTCT 60.308 47.826 0.00 0.00 40.99 3.69
6060 6377 3.010420 GCACACAAAGAGTTATCCCCTC 58.990 50.000 0.00 0.00 0.00 4.30
6061 6378 2.615493 CGCACACAAAGAGTTATCCCCT 60.615 50.000 0.00 0.00 0.00 4.79
6062 6379 1.737793 CGCACACAAAGAGTTATCCCC 59.262 52.381 0.00 0.00 0.00 4.81
6063 6380 2.415512 GTCGCACACAAAGAGTTATCCC 59.584 50.000 0.00 0.00 0.00 3.85
6082 6399 1.726248 GCGGGTTTGCATTTTGATGTC 59.274 47.619 0.00 0.00 34.15 3.06
6087 6404 0.950071 CCCAGCGGGTTTGCATTTTG 60.950 55.000 1.11 0.00 38.25 2.44
6170 6487 3.195610 ACACTTCATGATCCGCAAGACTA 59.804 43.478 0.00 0.00 43.02 2.59
6189 6506 3.507786 GTTTTGTCAACACCCAAGACAC 58.492 45.455 0.00 0.00 41.53 3.67
6195 6512 3.082548 TCTTTCGTTTTGTCAACACCCA 58.917 40.909 0.00 0.00 0.00 4.51
6203 6520 6.659776 AGCACTATTTCTCTTTCGTTTTGTC 58.340 36.000 0.00 0.00 0.00 3.18
6211 6528 8.491331 AGAAATCTGAGCACTATTTCTCTTTC 57.509 34.615 14.54 0.00 43.18 2.62
6272 6589 6.957631 ACAAACTGATCCATGGTATAACAGA 58.042 36.000 22.15 0.00 0.00 3.41
6350 6667 3.114606 TCATAATCCTCCAACCTCAGCA 58.885 45.455 0.00 0.00 0.00 4.41
6389 6708 7.178074 CACGCAAAAGTAGCTTATACCTAAAC 58.822 38.462 0.00 0.00 0.00 2.01
6441 6795 0.827368 CCTCACTGCTCCTCCTAACC 59.173 60.000 0.00 0.00 0.00 2.85
6475 6830 1.743252 CGCTTTGGCTCCTCCTGAC 60.743 63.158 0.00 0.00 36.09 3.51
6480 6835 1.079127 TAGCACGCTTTGGCTCCTC 60.079 57.895 0.00 0.00 41.41 3.71
6492 6847 2.686558 ACAAGCAAACATGTAGCACG 57.313 45.000 21.03 14.71 0.00 5.34
6522 6877 9.341078 ACCAAGCACTAAATTTTGATTTTTCAT 57.659 25.926 6.63 0.00 0.00 2.57
6523 6878 8.729805 ACCAAGCACTAAATTTTGATTTTTCA 57.270 26.923 6.63 0.00 0.00 2.69
6564 6919 3.314541 AGTGTTACACGGAGATCCAAC 57.685 47.619 10.00 0.00 39.64 3.77
6630 6985 4.517285 CTGGCTACAAGCATAAGAGGAAA 58.483 43.478 0.78 0.00 44.75 3.13
6691 7046 3.848272 TTGATTCGAATGCCAACTTCC 57.152 42.857 16.96 0.00 0.00 3.46
6713 7068 6.096001 GGTCCTCTAGTCGGTATTGTAGAAAA 59.904 42.308 0.00 0.00 0.00 2.29
6714 7069 5.591877 GGTCCTCTAGTCGGTATTGTAGAAA 59.408 44.000 0.00 0.00 0.00 2.52
6715 7070 5.128919 GGTCCTCTAGTCGGTATTGTAGAA 58.871 45.833 0.00 0.00 0.00 2.10
6717 7072 3.819902 GGGTCCTCTAGTCGGTATTGTAG 59.180 52.174 0.00 0.00 0.00 2.74
6726 7081 5.185442 AGTTTTCTTTAGGGTCCTCTAGTCG 59.815 44.000 0.00 0.00 0.00 4.18
6727 7082 6.608539 AGTTTTCTTTAGGGTCCTCTAGTC 57.391 41.667 0.00 0.00 0.00 2.59
6817 7172 1.280133 CCAATCTGGAGTTGCTCAGGA 59.720 52.381 0.00 0.00 40.96 3.86
6844 7199 3.737559 AAAATATCTCCACTGCCACCA 57.262 42.857 0.00 0.00 0.00 4.17
6864 7219 8.553696 GTTTGTCTTGGAACGAATTAGAACTTA 58.446 33.333 0.00 0.00 0.00 2.24
6873 7228 4.881850 ACAGAAGTTTGTCTTGGAACGAAT 59.118 37.500 0.00 0.00 36.40 3.34
6893 7248 4.853924 ATGAACTTGGCCAAACTTACAG 57.146 40.909 20.91 8.32 0.00 2.74


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

AutoCloner maintained by Alex Coulton.