Multiple sequence alignment - TraesCS1D01G348600

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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 TraesCS1D01G348600 chr1D 100.000 4424 0 0 1 4424 435278723 435274300 0.000000e+00 8170.0
1 TraesCS1D01G348600 chr1D 92.424 462 27 5 1740 2195 435253256 435252797 0.000000e+00 652.0
2 TraesCS1D01G348600 chr1D 86.613 493 49 10 1781 2258 452618008 452618498 3.030000e-146 529.0
3 TraesCS1D01G348600 chr1D 89.552 335 31 3 2212 2545 435252386 435252055 5.290000e-114 422.0
4 TraesCS1D01G348600 chr1D 86.857 350 32 6 2837 3178 435170368 435170025 3.230000e-101 379.0
5 TraesCS1D01G348600 chr1D 88.333 300 28 4 2539 2832 435171672 435171374 1.960000e-93 353.0
6 TraesCS1D01G348600 chr1D 84.324 370 37 9 705 1066 452617071 452617427 4.240000e-90 342.0
7 TraesCS1D01G348600 chr1D 78.131 567 80 18 2263 2819 452618619 452619151 1.990000e-83 320.0
8 TraesCS1D01G348600 chr1D 87.398 246 26 5 1337 1579 452617736 452617979 1.210000e-70 278.0
9 TraesCS1D01G348600 chr1D 89.894 188 14 4 4237 4423 452620806 452620989 2.060000e-58 237.0
10 TraesCS1D01G348600 chr1D 91.724 145 11 1 1438 1582 435253396 435253253 2.700000e-47 200.0
11 TraesCS1D01G348600 chr1D 95.556 45 1 1 625 669 435253524 435253481 2.210000e-08 71.3
12 TraesCS1D01G348600 chr1B 89.211 2104 166 30 1739 3817 588505618 588503551 0.000000e+00 2571.0
13 TraesCS1D01G348600 chr1B 87.454 813 45 32 520 1299 588510123 588509335 0.000000e+00 883.0
14 TraesCS1D01G348600 chr1B 83.702 859 109 18 1779 2632 622698272 622699104 0.000000e+00 782.0
15 TraesCS1D01G348600 chr1B 85.714 364 35 11 141 503 588510552 588510205 6.990000e-98 368.0
16 TraesCS1D01G348600 chr1B 85.075 335 35 9 742 1066 622697363 622697692 1.190000e-85 327.0
17 TraesCS1D01G348600 chr1B 97.354 189 5 0 4235 4423 588498464 588498276 5.520000e-84 322.0
18 TraesCS1D01G348600 chr1B 86.000 250 25 5 1337 1582 588505857 588505614 4.390000e-65 259.0
19 TraesCS1D01G348600 chr1B 84.766 256 25 7 1337 1579 622697990 622698244 1.230000e-60 244.0
20 TraesCS1D01G348600 chr1B 92.814 167 12 0 1578 1744 533863226 533863060 4.420000e-60 243.0
21 TraesCS1D01G348600 chr1B 87.368 190 15 3 4234 4423 622700581 622700761 4.480000e-50 209.0
22 TraesCS1D01G348600 chr1B 90.083 121 9 2 4039 4159 588498658 588498541 2.130000e-33 154.0
23 TraesCS1D01G348600 chr1A 96.389 1357 45 3 2840 4192 532778124 532776768 0.000000e+00 2231.0
24 TraesCS1D01G348600 chr1A 90.893 1098 84 12 1739 2825 532779421 532778329 0.000000e+00 1459.0
25 TraesCS1D01G348600 chr1A 82.221 1738 227 48 1779 3494 547382564 547384241 0.000000e+00 1423.0
26 TraesCS1D01G348600 chr1A 89.457 645 43 15 681 1315 532780358 532779729 0.000000e+00 791.0
27 TraesCS1D01G348600 chr1A 96.694 242 6 1 4183 4424 532776414 532776175 6.890000e-108 401.0
28 TraesCS1D01G348600 chr1A 84.324 370 37 9 705 1066 547381627 547381983 4.240000e-90 342.0
29 TraesCS1D01G348600 chr1A 90.698 258 14 3 1334 1582 532779673 532779417 7.090000e-88 335.0
30 TraesCS1D01G348600 chr1A 87.295 244 29 2 1337 1579 547382294 547382536 1.210000e-70 278.0
31 TraesCS1D01G348600 chr1A 86.096 187 17 6 4237 4423 547384892 547385069 4.520000e-45 193.0
32 TraesCS1D01G348600 chr7D 81.503 346 41 18 140 480 410126390 410126063 3.390000e-66 263.0
33 TraesCS1D01G348600 chr7D 93.333 150 6 4 8 153 14654547 14654696 7.450000e-53 219.0
34 TraesCS1D01G348600 chr7D 94.366 142 6 2 8 147 608667419 608667278 2.680000e-52 217.0
35 TraesCS1D01G348600 chr7D 90.506 158 10 3 8 163 56055102 56055256 2.090000e-48 204.0
36 TraesCS1D01G348600 chr4D 95.092 163 7 1 1579 1741 334164391 334164552 5.680000e-64 255.0
37 TraesCS1D01G348600 chr3B 94.375 160 9 0 1582 1741 201028666 201028507 3.420000e-61 246.0
38 TraesCS1D01G348600 chr3B 94.118 51 2 1 161 210 829145462 829145512 4.740000e-10 76.8
39 TraesCS1D01G348600 chr2D 93.413 167 10 1 1578 1744 571079120 571078955 3.420000e-61 246.0
40 TraesCS1D01G348600 chr2D 93.373 166 10 1 1576 1741 218046991 218046827 1.230000e-60 244.0
41 TraesCS1D01G348600 chr2D 89.617 183 17 2 1560 1741 87407344 87407525 9.570000e-57 231.0
42 TraesCS1D01G348600 chr2D 94.406 143 5 3 8 147 411726326 411726184 2.680000e-52 217.0
43 TraesCS1D01G348600 chr2D 92.157 153 7 5 8 157 44329527 44329677 1.250000e-50 211.0
44 TraesCS1D01G348600 chr5A 92.045 176 10 4 1582 1754 558675655 558675481 1.230000e-60 244.0
45 TraesCS1D01G348600 chr6D 90.710 183 14 2 1560 1742 431160650 431160829 1.590000e-59 241.0
46 TraesCS1D01G348600 chr6D 85.000 80 11 1 161 240 315701407 315701485 3.670000e-11 80.5
47 TraesCS1D01G348600 chr3D 92.353 170 12 1 1572 1741 87925993 87926161 1.590000e-59 241.0
48 TraesCS1D01G348600 chr3D 93.197 147 6 4 8 152 566956153 566956297 3.470000e-51 213.0
49 TraesCS1D01G348600 chr3D 90.566 159 9 5 8 164 563044201 563044047 5.800000e-49 206.0
50 TraesCS1D01G348600 chr3D 87.879 66 4 3 146 210 611362731 611362793 1.710000e-09 75.0
51 TraesCS1D01G348600 chr3D 92.453 53 3 1 159 210 611430884 611430936 1.710000e-09 75.0
52 TraesCS1D01G348600 chr5D 93.793 145 7 2 8 150 56451720 56451576 2.680000e-52 217.0
53 TraesCS1D01G348600 chr5D 92.617 149 7 4 8 154 218510987 218510841 1.250000e-50 211.0
54 TraesCS1D01G348600 chr5D 90.278 72 5 2 162 232 281855323 281855393 4.710000e-15 93.5
55 TraesCS1D01G348600 chr7A 89.516 124 13 0 4290 4413 10419857 10419734 1.650000e-34 158.0
56 TraesCS1D01G348600 chr2A 78.761 113 14 4 900 1011 704057347 704057450 2.860000e-07 67.6
57 TraesCS1D01G348600 chr2A 91.489 47 4 0 965 1011 704054986 704055032 1.030000e-06 65.8
58 TraesCS1D01G348600 chr5B 73.762 202 38 13 180 368 509198626 509198427 1.030000e-06 65.8
59 TraesCS1D01G348600 chr2B 79.798 99 11 7 163 255 197153604 197153509 3.690000e-06 63.9


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 TraesCS1D01G348600 chr1D 435274300 435278723 4423 True 8170.000 8170 100.00000 1 4424 1 chr1D.!!$R1 4423
1 TraesCS1D01G348600 chr1D 435170025 435171672 1647 True 366.000 379 87.59500 2539 3178 2 chr1D.!!$R2 639
2 TraesCS1D01G348600 chr1D 452617071 452620989 3918 False 341.200 529 85.27200 705 4423 5 chr1D.!!$F1 3718
3 TraesCS1D01G348600 chr1D 435252055 435253524 1469 True 336.325 652 92.31400 625 2545 4 chr1D.!!$R3 1920
4 TraesCS1D01G348600 chr1B 588503551 588510552 7001 True 1020.250 2571 87.09475 141 3817 4 chr1B.!!$R3 3676
5 TraesCS1D01G348600 chr1B 622697363 622700761 3398 False 390.500 782 85.22775 742 4423 4 chr1B.!!$F1 3681
6 TraesCS1D01G348600 chr1A 532776175 532780358 4183 True 1043.400 2231 92.82620 681 4424 5 chr1A.!!$R1 3743
7 TraesCS1D01G348600 chr1A 547381627 547385069 3442 False 559.000 1423 84.98400 705 4423 4 chr1A.!!$F1 3718

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
675 742 0.096976 CGTTGGCAATTCCTACTGCG 59.903 55.000 1.92 0.0 39.55 5.18 F
676 743 0.179163 GTTGGCAATTCCTACTGCGC 60.179 55.000 1.92 0.0 39.55 6.09 F
677 744 0.322456 TTGGCAATTCCTACTGCGCT 60.322 50.000 9.73 0.0 39.55 5.92 F
1102 1198 1.003118 CTGACCAATCTCCCCGAACAA 59.997 52.381 0.00 0.0 0.00 2.83 F
1345 4922 1.546029 TCACCAGATCACTTGTCTCCG 59.454 52.381 0.00 0.0 0.00 4.63 F
2298 6438 1.676967 GCTGGGCAGGGTTTCTCTG 60.677 63.158 0.00 0.0 35.49 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 6408 1.273048 CTGCCCAGCTACAATTTGCAA 59.727 47.619 0.00 0.00 0.00 4.08 R
2349 6490 1.501169 AAATTTCTTTGGCAGCGTGC 58.499 45.000 1.92 1.92 44.08 5.34 R
2601 6746 8.041919 TGGACCATTTAGTTGATATACGAAACA 58.958 33.333 0.00 0.00 0.00 2.83 R
2740 6924 2.429971 TGTTCAACAAAATGCAGCCAGA 59.570 40.909 0.00 0.00 0.00 3.86 R
3149 8723 1.291877 GAACAGATCAACAGCGCCGT 61.292 55.000 2.29 0.00 0.00 5.68 R
3940 9684 0.699151 CGCAGTGTTCGTGTACGTAC 59.301 55.000 18.90 18.90 39.56 3.67 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
27 28 8.517062 AAGTCCTTTCAGAGATTTCAATATGG 57.483 34.615 0.00 0.00 0.00 2.74
28 29 7.865820 AGTCCTTTCAGAGATTTCAATATGGA 58.134 34.615 0.00 0.00 0.00 3.41
29 30 7.772757 AGTCCTTTCAGAGATTTCAATATGGAC 59.227 37.037 0.00 0.00 38.27 4.02
30 31 7.772757 GTCCTTTCAGAGATTTCAATATGGACT 59.227 37.037 0.00 0.00 35.99 3.85
31 32 8.992349 TCCTTTCAGAGATTTCAATATGGACTA 58.008 33.333 0.00 0.00 0.00 2.59
32 33 9.050601 CCTTTCAGAGATTTCAATATGGACTAC 57.949 37.037 0.00 0.00 0.00 2.73
33 34 9.605275 CTTTCAGAGATTTCAATATGGACTACA 57.395 33.333 0.00 0.00 0.00 2.74
37 38 9.133627 CAGAGATTTCAATATGGACTACATACG 57.866 37.037 0.00 0.00 44.41 3.06
38 39 8.307483 AGAGATTTCAATATGGACTACATACGG 58.693 37.037 0.00 0.00 44.41 4.02
39 40 8.190326 AGATTTCAATATGGACTACATACGGA 57.810 34.615 0.00 0.00 44.41 4.69
40 41 8.307483 AGATTTCAATATGGACTACATACGGAG 58.693 37.037 0.00 0.00 44.41 4.63
41 42 5.386958 TCAATATGGACTACATACGGAGC 57.613 43.478 0.00 0.00 44.41 4.70
42 43 4.830600 TCAATATGGACTACATACGGAGCA 59.169 41.667 0.00 0.00 44.41 4.26
43 44 5.303333 TCAATATGGACTACATACGGAGCAA 59.697 40.000 0.00 0.00 44.41 3.91
44 45 5.801531 ATATGGACTACATACGGAGCAAA 57.198 39.130 0.00 0.00 44.41 3.68
45 46 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
46 47 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
47 48 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
48 49 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
49 50 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
50 51 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
51 52 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
52 53 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
53 54 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
54 55 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
55 56 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
56 57 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
57 58 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
58 59 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
59 60 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
60 61 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
101 102 8.763049 CATACATCCGTATGTGATAGTCATTT 57.237 34.615 3.56 0.00 46.70 2.32
102 103 8.650714 CATACATCCGTATGTGATAGTCATTTG 58.349 37.037 3.56 0.00 46.70 2.32
103 104 6.816136 ACATCCGTATGTGATAGTCATTTGA 58.184 36.000 0.00 0.00 44.79 2.69
104 105 7.272244 ACATCCGTATGTGATAGTCATTTGAA 58.728 34.615 0.00 0.00 44.79 2.69
105 106 7.768582 ACATCCGTATGTGATAGTCATTTGAAA 59.231 33.333 0.00 0.00 44.79 2.69
106 107 8.777413 CATCCGTATGTGATAGTCATTTGAAAT 58.223 33.333 0.00 0.00 0.00 2.17
107 108 8.141835 TCCGTATGTGATAGTCATTTGAAATG 57.858 34.615 11.54 11.54 0.00 2.32
108 109 6.852853 CCGTATGTGATAGTCATTTGAAATGC 59.147 38.462 12.86 8.33 0.00 3.56
109 110 6.852853 CGTATGTGATAGTCATTTGAAATGCC 59.147 38.462 12.86 1.61 0.00 4.40
110 111 7.254898 CGTATGTGATAGTCATTTGAAATGCCT 60.255 37.037 12.86 9.73 0.00 4.75
111 112 9.056005 GTATGTGATAGTCATTTGAAATGCCTA 57.944 33.333 10.59 10.59 0.00 3.93
112 113 7.558161 TGTGATAGTCATTTGAAATGCCTAG 57.442 36.000 13.20 0.00 0.00 3.02
113 114 7.337938 TGTGATAGTCATTTGAAATGCCTAGA 58.662 34.615 13.20 1.78 0.00 2.43
114 115 7.828717 TGTGATAGTCATTTGAAATGCCTAGAA 59.171 33.333 13.20 2.99 0.00 2.10
115 116 8.677300 GTGATAGTCATTTGAAATGCCTAGAAA 58.323 33.333 13.20 0.91 0.00 2.52
116 117 8.896744 TGATAGTCATTTGAAATGCCTAGAAAG 58.103 33.333 13.20 0.00 0.00 2.62
117 118 9.113838 GATAGTCATTTGAAATGCCTAGAAAGA 57.886 33.333 13.20 0.00 0.00 2.52
118 119 7.150783 AGTCATTTGAAATGCCTAGAAAGAC 57.849 36.000 12.86 3.23 0.00 3.01
119 120 6.716628 AGTCATTTGAAATGCCTAGAAAGACA 59.283 34.615 12.86 0.00 0.00 3.41
120 121 7.231317 AGTCATTTGAAATGCCTAGAAAGACAA 59.769 33.333 12.86 0.00 0.00 3.18
121 122 7.540055 GTCATTTGAAATGCCTAGAAAGACAAG 59.460 37.037 12.86 0.00 0.00 3.16
122 123 6.959639 TTTGAAATGCCTAGAAAGACAAGT 57.040 33.333 0.00 0.00 0.00 3.16
123 124 8.514594 CATTTGAAATGCCTAGAAAGACAAGTA 58.485 33.333 4.82 0.00 0.00 2.24
124 125 8.635765 TTTGAAATGCCTAGAAAGACAAGTAT 57.364 30.769 0.00 0.00 0.00 2.12
125 126 8.635765 TTGAAATGCCTAGAAAGACAAGTATT 57.364 30.769 0.00 0.00 0.00 1.89
126 127 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
127 128 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
129 130 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
130 131 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
131 132 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
132 133 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
133 134 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
134 135 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
135 136 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
136 137 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
137 138 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
138 139 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
139 140 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
144 145 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
159 160 9.543783 GGAGGGAGTACATTACATTAACTTAAG 57.456 37.037 0.00 0.00 0.00 1.85
193 195 5.692204 ACACGTTTCAAAAATGTGTTTGTGA 59.308 32.000 19.52 0.00 39.28 3.58
415 417 9.232082 CAATACATATGAAAAATGTACAACGGG 57.768 33.333 10.38 0.00 41.34 5.28
419 421 8.402472 ACATATGAAAAATGTACAACGGGTATG 58.598 33.333 10.38 6.16 35.82 2.39
420 422 5.630661 TGAAAAATGTACAACGGGTATGG 57.369 39.130 0.00 0.00 33.76 2.74
566 632 1.804748 CGAAAAACCCCCGAAGAGAAG 59.195 52.381 0.00 0.00 0.00 2.85
571 637 2.563261 ACCCCCGAAGAGAAGAAAAC 57.437 50.000 0.00 0.00 0.00 2.43
572 638 1.270678 ACCCCCGAAGAGAAGAAAACG 60.271 52.381 0.00 0.00 0.00 3.60
573 639 1.001633 CCCCCGAAGAGAAGAAAACGA 59.998 52.381 0.00 0.00 0.00 3.85
574 640 2.549349 CCCCCGAAGAGAAGAAAACGAA 60.549 50.000 0.00 0.00 0.00 3.85
577 643 4.319549 CCCCGAAGAGAAGAAAACGAAAAG 60.320 45.833 0.00 0.00 0.00 2.27
603 669 2.640826 AGAAACCAGACGGAACCCATAA 59.359 45.455 0.00 0.00 35.59 1.90
611 677 0.372334 CGGAACCCATAAAGCGAACG 59.628 55.000 0.00 0.00 0.00 3.95
612 678 1.729284 GGAACCCATAAAGCGAACGA 58.271 50.000 0.00 0.00 0.00 3.85
618 685 1.468565 CCATAAAGCGAACGAGGACGA 60.469 52.381 0.00 0.00 42.66 4.20
620 687 0.455633 TAAAGCGAACGAGGACGAGC 60.456 55.000 0.00 0.00 42.66 5.03
673 740 1.094785 CCCGTTGGCAATTCCTACTG 58.905 55.000 1.92 0.00 38.26 2.74
675 742 0.096976 CGTTGGCAATTCCTACTGCG 59.903 55.000 1.92 0.00 39.55 5.18
676 743 0.179163 GTTGGCAATTCCTACTGCGC 60.179 55.000 1.92 0.00 39.55 6.09
677 744 0.322456 TTGGCAATTCCTACTGCGCT 60.322 50.000 9.73 0.00 39.55 5.92
678 745 1.026182 TGGCAATTCCTACTGCGCTG 61.026 55.000 13.23 13.23 39.55 5.18
685 759 1.066587 CCTACTGCGCTGGCTCTAC 59.933 63.158 18.98 0.00 40.82 2.59
694 768 1.749638 CTGGCTCTACGACCGGTCT 60.750 63.158 30.92 20.06 0.00 3.85
698 772 1.025647 GCTCTACGACCGGTCTCACT 61.026 60.000 30.92 13.59 0.00 3.41
734 808 3.672295 CTCCTTCTCCAGTGCGCCC 62.672 68.421 4.18 0.00 0.00 6.13
735 809 4.785453 CCTTCTCCAGTGCGCCCC 62.785 72.222 4.18 0.00 0.00 5.80
882 958 3.288290 CGACCCTCCCGGATCTCG 61.288 72.222 0.73 0.00 38.88 4.04
975 1069 2.444706 CGGCTCTCCCATCCAGGA 60.445 66.667 0.00 0.00 41.22 3.86
1034 1128 4.820716 CAGTCCCTGATCAATTCAATCTCC 59.179 45.833 0.00 0.00 32.78 3.71
1035 1129 4.476113 AGTCCCTGATCAATTCAATCTCCA 59.524 41.667 0.00 0.00 32.78 3.86
1067 1162 7.768582 TGCTTATTCTCTCCAAAATATTCGACA 59.231 33.333 0.00 0.00 0.00 4.35
1070 1165 9.667107 TTATTCTCTCCAAAATATTCGACAGTT 57.333 29.630 0.00 0.00 0.00 3.16
1090 1185 5.047092 CAGTTTTGCTTAATCCCTGACCAAT 60.047 40.000 0.00 0.00 0.00 3.16
1091 1186 5.185828 AGTTTTGCTTAATCCCTGACCAATC 59.814 40.000 0.00 0.00 0.00 2.67
1092 1187 4.591321 TTGCTTAATCCCTGACCAATCT 57.409 40.909 0.00 0.00 0.00 2.40
1094 1189 3.117888 TGCTTAATCCCTGACCAATCTCC 60.118 47.826 0.00 0.00 0.00 3.71
1102 1198 1.003118 CTGACCAATCTCCCCGAACAA 59.997 52.381 0.00 0.00 0.00 2.83
1220 1325 3.955771 TTTACCTTTTCGTGCTGTGTC 57.044 42.857 0.00 0.00 0.00 3.67
1235 1340 3.871594 GCTGTGTCGATGGTTAGCTTAAT 59.128 43.478 0.00 0.00 0.00 1.40
1289 1419 6.595772 TGTTGTTGTATGTTTTGAATTGCC 57.404 33.333 0.00 0.00 0.00 4.52
1343 4920 8.821894 GTTTAATATCACCAGATCACTTGTCTC 58.178 37.037 0.00 0.00 35.67 3.36
1345 4922 1.546029 TCACCAGATCACTTGTCTCCG 59.454 52.381 0.00 0.00 0.00 4.63
1408 4992 9.886132 ATAGTCTTCCAATATACTGTCGTTTTT 57.114 29.630 0.00 0.00 0.00 1.94
1436 5035 8.746922 ACATACTTTTACATTTGAACTGCATG 57.253 30.769 0.00 0.00 0.00 4.06
1454 5053 7.056635 ACTGCATGGCTTGTAAGTTCTAATAT 58.943 34.615 2.12 0.00 0.00 1.28
1475 5077 4.270245 TCAAATCACCATTTTGAAGGCC 57.730 40.909 0.00 0.00 39.46 5.19
1517 5119 3.606595 TCTCAACTTGAGCATCTCCAG 57.393 47.619 13.24 0.00 43.95 3.86
1583 5185 8.213518 TGTAAGCATCTCATCTTTTGTATTCC 57.786 34.615 0.00 0.00 0.00 3.01
1584 5186 6.705863 AAGCATCTCATCTTTTGTATTCCC 57.294 37.500 0.00 0.00 0.00 3.97
1585 5187 6.011122 AGCATCTCATCTTTTGTATTCCCT 57.989 37.500 0.00 0.00 0.00 4.20
1586 5188 6.060788 AGCATCTCATCTTTTGTATTCCCTC 58.939 40.000 0.00 0.00 0.00 4.30
1587 5189 5.824624 GCATCTCATCTTTTGTATTCCCTCA 59.175 40.000 0.00 0.00 0.00 3.86
1588 5190 6.017275 GCATCTCATCTTTTGTATTCCCTCAG 60.017 42.308 0.00 0.00 0.00 3.35
1589 5191 6.627087 TCTCATCTTTTGTATTCCCTCAGT 57.373 37.500 0.00 0.00 0.00 3.41
1590 5192 7.020827 TCTCATCTTTTGTATTCCCTCAGTT 57.979 36.000 0.00 0.00 0.00 3.16
1591 5193 7.106239 TCTCATCTTTTGTATTCCCTCAGTTC 58.894 38.462 0.00 0.00 0.00 3.01
1592 5194 6.180472 TCATCTTTTGTATTCCCTCAGTTCC 58.820 40.000 0.00 0.00 0.00 3.62
1593 5195 5.843019 TCTTTTGTATTCCCTCAGTTCCT 57.157 39.130 0.00 0.00 0.00 3.36
1594 5196 6.945636 TCTTTTGTATTCCCTCAGTTCCTA 57.054 37.500 0.00 0.00 0.00 2.94
1595 5197 7.324388 TCTTTTGTATTCCCTCAGTTCCTAA 57.676 36.000 0.00 0.00 0.00 2.69
1596 5198 7.751646 TCTTTTGTATTCCCTCAGTTCCTAAA 58.248 34.615 0.00 0.00 0.00 1.85
1597 5199 8.390921 TCTTTTGTATTCCCTCAGTTCCTAAAT 58.609 33.333 0.00 0.00 0.00 1.40
1598 5200 9.681062 CTTTTGTATTCCCTCAGTTCCTAAATA 57.319 33.333 0.00 0.00 0.00 1.40
1605 5207 8.855804 TTCCCTCAGTTCCTAAATATAAGTCT 57.144 34.615 0.00 0.00 0.00 3.24
1606 5208 8.855804 TCCCTCAGTTCCTAAATATAAGTCTT 57.144 34.615 0.00 0.00 0.00 3.01
1607 5209 9.280456 TCCCTCAGTTCCTAAATATAAGTCTTT 57.720 33.333 0.00 0.00 0.00 2.52
1608 5210 9.907229 CCCTCAGTTCCTAAATATAAGTCTTTT 57.093 33.333 0.00 0.00 0.00 2.27
1626 5228 9.467796 AAGTCTTTTTAGAGATTCCAATAAGGG 57.532 33.333 0.00 0.00 38.24 3.95
1627 5229 8.836735 AGTCTTTTTAGAGATTCCAATAAGGGA 58.163 33.333 0.00 0.00 38.24 4.20
1628 5230 8.894731 GTCTTTTTAGAGATTCCAATAAGGGAC 58.105 37.037 0.00 0.00 36.46 4.46
1631 5233 9.901172 TTTTTAGAGATTCCAATAAGGGACTAC 57.099 33.333 0.00 0.00 38.49 2.73
1632 5234 8.618240 TTTAGAGATTCCAATAAGGGACTACA 57.382 34.615 0.00 0.00 38.49 2.74
1633 5235 8.798975 TTAGAGATTCCAATAAGGGACTACAT 57.201 34.615 0.00 0.00 38.49 2.29
1634 5236 9.892444 TTAGAGATTCCAATAAGGGACTACATA 57.108 33.333 0.00 0.00 38.49 2.29
1635 5237 8.196378 AGAGATTCCAATAAGGGACTACATAC 57.804 38.462 0.00 0.00 38.49 2.39
1636 5238 6.994221 AGATTCCAATAAGGGACTACATACG 58.006 40.000 0.00 0.00 38.49 3.06
1637 5239 5.540400 TTCCAATAAGGGACTACATACGG 57.460 43.478 0.00 0.00 38.49 4.02
1638 5240 4.806892 TCCAATAAGGGACTACATACGGA 58.193 43.478 0.00 0.00 38.49 4.69
1639 5241 4.831155 TCCAATAAGGGACTACATACGGAG 59.169 45.833 0.00 0.00 38.49 4.63
1640 5242 4.557205 CAATAAGGGACTACATACGGAGC 58.443 47.826 0.00 0.00 38.49 4.70
1641 5243 2.154567 AAGGGACTACATACGGAGCA 57.845 50.000 0.00 0.00 38.49 4.26
1642 5244 2.154567 AGGGACTACATACGGAGCAA 57.845 50.000 0.00 0.00 36.02 3.91
1643 5245 2.463752 AGGGACTACATACGGAGCAAA 58.536 47.619 0.00 0.00 36.02 3.68
1644 5246 2.835764 AGGGACTACATACGGAGCAAAA 59.164 45.455 0.00 0.00 36.02 2.44
1645 5247 3.454812 AGGGACTACATACGGAGCAAAAT 59.545 43.478 0.00 0.00 36.02 1.82
1646 5248 3.560068 GGGACTACATACGGAGCAAAATG 59.440 47.826 0.00 0.00 0.00 2.32
1647 5249 4.439057 GGACTACATACGGAGCAAAATGA 58.561 43.478 0.00 0.00 0.00 2.57
1648 5250 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
1649 5251 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
1650 5252 5.488341 ACTACATACGGAGCAAAATGAGTT 58.512 37.500 0.00 0.00 0.00 3.01
1651 5253 6.636705 ACTACATACGGAGCAAAATGAGTTA 58.363 36.000 0.00 0.00 0.00 2.24
1652 5254 7.101054 ACTACATACGGAGCAAAATGAGTTAA 58.899 34.615 0.00 0.00 0.00 2.01
1653 5255 7.769044 ACTACATACGGAGCAAAATGAGTTAAT 59.231 33.333 0.00 0.00 0.00 1.40
1654 5256 7.016361 ACATACGGAGCAAAATGAGTTAATC 57.984 36.000 0.00 0.00 0.00 1.75
1655 5257 6.823689 ACATACGGAGCAAAATGAGTTAATCT 59.176 34.615 0.00 0.00 0.00 2.40
1656 5258 7.985184 ACATACGGAGCAAAATGAGTTAATCTA 59.015 33.333 0.00 0.00 0.00 1.98
1657 5259 6.663944 ACGGAGCAAAATGAGTTAATCTAC 57.336 37.500 0.00 0.00 0.00 2.59
1658 5260 6.170506 ACGGAGCAAAATGAGTTAATCTACA 58.829 36.000 0.00 0.00 0.00 2.74
1659 5261 6.092259 ACGGAGCAAAATGAGTTAATCTACAC 59.908 38.462 0.00 0.00 0.00 2.90
1660 5262 6.313905 CGGAGCAAAATGAGTTAATCTACACT 59.686 38.462 0.00 0.00 0.00 3.55
1661 5263 7.464710 CGGAGCAAAATGAGTTAATCTACACTC 60.465 40.741 0.00 0.00 40.03 3.51
1662 5264 7.550906 GGAGCAAAATGAGTTAATCTACACTCT 59.449 37.037 1.31 0.00 40.24 3.24
1663 5265 9.587772 GAGCAAAATGAGTTAATCTACACTCTA 57.412 33.333 1.31 0.00 40.24 2.43
1664 5266 9.944376 AGCAAAATGAGTTAATCTACACTCTAA 57.056 29.630 1.31 0.00 40.24 2.10
1703 5305 8.645814 ACATCCGTATGTAGTTCATATAGGAA 57.354 34.615 15.57 0.00 44.66 3.36
1704 5306 9.256228 ACATCCGTATGTAGTTCATATAGGAAT 57.744 33.333 15.57 8.51 44.66 3.01
1705 5307 9.737427 CATCCGTATGTAGTTCATATAGGAATC 57.263 37.037 15.57 0.00 44.00 2.52
1706 5308 9.702253 ATCCGTATGTAGTTCATATAGGAATCT 57.298 33.333 15.57 5.50 44.00 2.40
1707 5309 9.175312 TCCGTATGTAGTTCATATAGGAATCTC 57.825 37.037 2.74 0.00 41.25 2.75
1708 5310 9.179909 CCGTATGTAGTTCATATAGGAATCTCT 57.820 37.037 2.74 0.00 40.54 3.10
1739 5341 7.672122 ACTTATATTTAGAAACGGAGGGAGT 57.328 36.000 0.00 0.00 0.00 3.85
1740 5342 8.773033 ACTTATATTTAGAAACGGAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
1741 5343 9.377238 ACTTATATTTAGAAACGGAGGGAGTAT 57.623 33.333 0.00 0.00 0.00 2.12
1746 5348 6.956202 TTAGAAACGGAGGGAGTATTAGAG 57.044 41.667 0.00 0.00 0.00 2.43
1767 5369 6.222389 AGAGATGTTGCATTAGCTAGCTAAG 58.778 40.000 33.88 26.59 41.18 2.18
1776 5383 5.692654 GCATTAGCTAGCTAAGTGGTAAGAC 59.307 44.000 33.88 17.46 41.18 3.01
1818 5426 8.751215 TGGTCTGGTAGGATATTAACCATTAT 57.249 34.615 5.52 0.00 42.23 1.28
1876 5484 2.877168 CCAAAGAGACAGCTATGCATCC 59.123 50.000 0.19 0.00 0.00 3.51
2000 5609 7.988599 AGATGTATCTTAACTCGTCTACTGAGT 59.011 37.037 0.00 0.00 40.27 3.41
2195 5825 6.108015 TGCATCATAATTGGCCTTCTTTTTC 58.892 36.000 3.32 0.00 0.00 2.29
2268 6408 7.944729 AGCTCATTAAATACCATCTTGTTGT 57.055 32.000 0.00 0.00 0.00 3.32
2298 6438 1.676967 GCTGGGCAGGGTTTCTCTG 60.677 63.158 0.00 0.00 35.49 3.35
2299 6439 2.069776 CTGGGCAGGGTTTCTCTGA 58.930 57.895 0.44 0.00 34.36 3.27
2315 6455 7.446625 GGTTTCTCTGATGAGCCATAATACATT 59.553 37.037 0.00 0.00 40.03 2.71
2327 6467 5.538118 CCATAATACATTGCGGTCAGAGTA 58.462 41.667 0.00 0.00 0.00 2.59
2340 6481 4.800993 CGGTCAGAGTATAGCTTGAAGTTG 59.199 45.833 0.00 0.00 0.00 3.16
2349 6490 8.856490 AGTATAGCTTGAAGTTGTTTTGTTTG 57.144 30.769 0.00 0.00 0.00 2.93
2399 6540 3.673809 GCGTGACAGTTTGAGGTACTAAG 59.326 47.826 0.00 0.00 41.55 2.18
2407 6548 8.828688 ACAGTTTGAGGTACTAAGTGTTTATC 57.171 34.615 0.00 0.00 42.08 1.75
2587 6732 8.613922 ACATATTTCTCATCAAAGGGGAAAAT 57.386 30.769 0.00 0.00 31.24 1.82
2601 6746 5.583932 AGGGGAAAATTGTAGCTTGAAGAT 58.416 37.500 0.00 0.00 0.00 2.40
2775 6959 9.823647 ATTTTGTTGAACACACATTTTACCATA 57.176 25.926 0.00 0.00 33.98 2.74
3073 8635 5.390779 GCTTGCGCCAAAATGTTTAAATCAT 60.391 36.000 4.18 0.00 0.00 2.45
3136 8710 5.827666 ACCCAGTTTTTCTATTTGAACACG 58.172 37.500 0.00 0.00 33.88 4.49
3149 8723 3.878160 TGAACACGTATGCTATGGTCA 57.122 42.857 0.00 0.00 37.72 4.02
3545 9149 5.821995 TCTCTGTGATTGTGTTTGAACATCA 59.178 36.000 0.00 0.00 41.59 3.07
3631 9324 0.248498 ACCGTGATGTCGTATCTGCG 60.248 55.000 4.56 7.84 0.00 5.18
3822 9552 7.147312 TGCATTTCTTTTTCGATGAACTTCAT 58.853 30.769 3.80 3.80 40.34 2.57
3913 9657 4.265893 TGCTGTACTGTTGGTTCTCAAAA 58.734 39.130 1.46 0.00 37.08 2.44
3919 9663 8.378172 TGTACTGTTGGTTCTCAAAATAAGAG 57.622 34.615 0.00 0.00 37.08 2.85
3940 9684 5.869888 AGAGAAAAGGTTTGCTATACTGTCG 59.130 40.000 0.00 0.00 0.00 4.35
3959 9703 0.699151 GTACGTACACGAACACTGCG 59.301 55.000 20.67 0.00 43.02 5.18
4026 9804 4.019858 CAAGTATCACTCCAGTCCTCAGA 58.980 47.826 0.00 0.00 0.00 3.27
4073 9894 2.814913 GATTTCTTGGGCCGGGTCGT 62.815 60.000 2.18 0.00 0.00 4.34
4074 9895 1.555477 ATTTCTTGGGCCGGGTCGTA 61.555 55.000 2.18 0.00 0.00 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.618890 CCATATTGAAATCTCTGAAAGGACTTA 57.381 33.333 0.00 0.00 0.00 2.24
2 3 8.331740 TCCATATTGAAATCTCTGAAAGGACTT 58.668 33.333 0.00 0.00 0.00 3.01
3 4 7.772757 GTCCATATTGAAATCTCTGAAAGGACT 59.227 37.037 0.00 0.00 37.06 3.85
4 5 7.772757 AGTCCATATTGAAATCTCTGAAAGGAC 59.227 37.037 0.00 0.00 39.53 3.85
5 6 7.865820 AGTCCATATTGAAATCTCTGAAAGGA 58.134 34.615 0.00 0.00 0.00 3.36
6 7 9.050601 GTAGTCCATATTGAAATCTCTGAAAGG 57.949 37.037 0.00 0.00 0.00 3.11
7 8 9.605275 TGTAGTCCATATTGAAATCTCTGAAAG 57.395 33.333 0.00 0.00 0.00 2.62
11 12 9.133627 CGTATGTAGTCCATATTGAAATCTCTG 57.866 37.037 0.00 0.00 38.29 3.35
12 13 8.307483 CCGTATGTAGTCCATATTGAAATCTCT 58.693 37.037 0.00 0.00 38.29 3.10
13 14 8.304596 TCCGTATGTAGTCCATATTGAAATCTC 58.695 37.037 0.00 0.00 38.29 2.75
14 15 8.190326 TCCGTATGTAGTCCATATTGAAATCT 57.810 34.615 0.00 0.00 38.29 2.40
15 16 7.063544 GCTCCGTATGTAGTCCATATTGAAATC 59.936 40.741 0.00 0.00 38.29 2.17
16 17 6.874134 GCTCCGTATGTAGTCCATATTGAAAT 59.126 38.462 0.00 0.00 38.29 2.17
17 18 6.183360 TGCTCCGTATGTAGTCCATATTGAAA 60.183 38.462 0.00 0.00 38.29 2.69
18 19 5.303333 TGCTCCGTATGTAGTCCATATTGAA 59.697 40.000 0.00 0.00 38.29 2.69
19 20 4.830600 TGCTCCGTATGTAGTCCATATTGA 59.169 41.667 0.00 0.00 38.29 2.57
20 21 5.134202 TGCTCCGTATGTAGTCCATATTG 57.866 43.478 0.00 0.00 38.29 1.90
21 22 5.801531 TTGCTCCGTATGTAGTCCATATT 57.198 39.130 0.00 0.00 38.29 1.28
22 23 5.801531 TTTGCTCCGTATGTAGTCCATAT 57.198 39.130 0.00 0.00 38.29 1.78
23 24 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
24 25 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
25 26 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
26 27 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
27 28 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
28 29 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
29 30 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
30 31 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
31 32 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
32 33 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
33 34 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
34 35 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
35 36 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
36 37 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
37 38 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
38 39 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
77 78 8.585018 TCAAATGACTATCACATACGGATGTAT 58.415 33.333 14.23 10.02 44.82 2.29
78 79 7.947282 TCAAATGACTATCACATACGGATGTA 58.053 34.615 14.23 2.61 44.82 2.29
80 81 7.713764 TTCAAATGACTATCACATACGGATG 57.286 36.000 5.94 5.94 39.16 3.51
81 82 8.777413 CATTTCAAATGACTATCACATACGGAT 58.223 33.333 3.82 0.00 0.00 4.18
82 83 7.254761 GCATTTCAAATGACTATCACATACGGA 60.255 37.037 14.65 0.00 0.00 4.69
83 84 6.852853 GCATTTCAAATGACTATCACATACGG 59.147 38.462 14.65 0.00 0.00 4.02
84 85 6.852853 GGCATTTCAAATGACTATCACATACG 59.147 38.462 14.65 0.00 0.00 3.06
85 86 7.934457 AGGCATTTCAAATGACTATCACATAC 58.066 34.615 17.52 0.00 35.20 2.39
86 87 9.276590 CTAGGCATTTCAAATGACTATCACATA 57.723 33.333 23.50 4.36 38.80 2.29
87 88 7.994911 TCTAGGCATTTCAAATGACTATCACAT 59.005 33.333 23.50 1.77 38.80 3.21
88 89 7.337938 TCTAGGCATTTCAAATGACTATCACA 58.662 34.615 23.50 5.75 38.80 3.58
89 90 7.792374 TCTAGGCATTTCAAATGACTATCAC 57.208 36.000 23.50 0.15 38.80 3.06
90 91 8.806429 TTTCTAGGCATTTCAAATGACTATCA 57.194 30.769 23.50 12.23 38.80 2.15
91 92 9.113838 TCTTTCTAGGCATTTCAAATGACTATC 57.886 33.333 23.50 1.52 38.80 2.08
92 93 8.897752 GTCTTTCTAGGCATTTCAAATGACTAT 58.102 33.333 23.50 4.64 38.80 2.12
93 94 7.882791 TGTCTTTCTAGGCATTTCAAATGACTA 59.117 33.333 22.19 22.19 38.54 2.59
94 95 6.716628 TGTCTTTCTAGGCATTTCAAATGACT 59.283 34.615 22.35 22.35 41.04 3.41
95 96 6.913170 TGTCTTTCTAGGCATTTCAAATGAC 58.087 36.000 14.65 11.48 29.10 3.06
96 97 7.231317 ACTTGTCTTTCTAGGCATTTCAAATGA 59.769 33.333 14.65 0.00 35.56 2.57
97 98 7.373493 ACTTGTCTTTCTAGGCATTTCAAATG 58.627 34.615 5.68 5.68 35.56 2.32
98 99 7.530426 ACTTGTCTTTCTAGGCATTTCAAAT 57.470 32.000 0.00 0.00 35.56 2.32
99 100 6.959639 ACTTGTCTTTCTAGGCATTTCAAA 57.040 33.333 0.00 0.00 35.56 2.69
100 101 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
101 102 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
103 104 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
104 105 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
105 106 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
106 107 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
107 108 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
108 109 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
109 110 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
110 111 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
111 112 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
112 113 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
113 114 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
114 115 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
115 116 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
116 117 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
117 118 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
118 119 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
119 120 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
120 121 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
121 122 4.646492 TGTACTCCCTCCGTTCCTAAATAC 59.354 45.833 0.00 0.00 0.00 1.89
122 123 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
123 124 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
124 125 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
125 126 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
126 127 3.393426 AATGTACTCCCTCCGTTCCTA 57.607 47.619 0.00 0.00 0.00 2.94
127 128 2.249309 AATGTACTCCCTCCGTTCCT 57.751 50.000 0.00 0.00 0.00 3.36
128 129 2.762327 TGTAATGTACTCCCTCCGTTCC 59.238 50.000 0.00 0.00 0.00 3.62
129 130 4.667519 ATGTAATGTACTCCCTCCGTTC 57.332 45.455 0.00 0.00 0.00 3.95
130 131 6.155737 AGTTAATGTAATGTACTCCCTCCGTT 59.844 38.462 0.00 0.00 0.00 4.44
131 132 5.659971 AGTTAATGTAATGTACTCCCTCCGT 59.340 40.000 0.00 0.00 0.00 4.69
132 133 6.158023 AGTTAATGTAATGTACTCCCTCCG 57.842 41.667 0.00 0.00 0.00 4.63
133 134 9.543783 CTTAAGTTAATGTAATGTACTCCCTCC 57.456 37.037 0.00 0.00 0.00 4.30
159 160 8.379902 ACATTTTTGAAACGTGTGAAGATTTTC 58.620 29.630 0.00 0.00 0.00 2.29
324 326 9.194271 ACGTGTTTAACACTTTTTACAAAACAT 57.806 25.926 23.27 0.00 46.46 2.71
325 327 8.571461 ACGTGTTTAACACTTTTTACAAAACA 57.429 26.923 23.27 1.45 46.46 2.83
348 350 9.724839 ATATCCGTTTAACATTTTCCAAATACG 57.275 29.630 0.00 0.00 0.00 3.06
389 391 9.232082 CCCGTTGTACATTTTTCATATGTATTG 57.768 33.333 1.90 0.00 39.78 1.90
452 454 9.890352 TTTTGTTTCCTTTTTCAGTTTTCATTG 57.110 25.926 0.00 0.00 0.00 2.82
566 632 8.160342 GTCTGGTTTCTTTTTCTTTTCGTTTTC 58.840 33.333 0.00 0.00 0.00 2.29
571 637 4.733405 CCGTCTGGTTTCTTTTTCTTTTCG 59.267 41.667 0.00 0.00 0.00 3.46
572 638 5.886992 TCCGTCTGGTTTCTTTTTCTTTTC 58.113 37.500 0.00 0.00 36.30 2.29
573 639 5.907866 TCCGTCTGGTTTCTTTTTCTTTT 57.092 34.783 0.00 0.00 36.30 2.27
574 640 5.393787 GGTTCCGTCTGGTTTCTTTTTCTTT 60.394 40.000 0.00 0.00 36.30 2.52
577 643 3.243301 GGGTTCCGTCTGGTTTCTTTTTC 60.243 47.826 0.00 0.00 36.30 2.29
603 669 2.126424 GCTCGTCCTCGTTCGCTT 60.126 61.111 0.00 0.00 38.33 4.68
611 677 0.100682 TTATCTGCACGCTCGTCCTC 59.899 55.000 0.00 0.00 0.00 3.71
612 678 0.530744 TTTATCTGCACGCTCGTCCT 59.469 50.000 0.00 0.00 0.00 3.85
618 685 0.107017 AGCCCATTTATCTGCACGCT 60.107 50.000 0.00 0.00 0.00 5.07
620 687 0.664761 CCAGCCCATTTATCTGCACG 59.335 55.000 0.00 0.00 0.00 5.34
659 726 1.026182 CAGCGCAGTAGGAATTGCCA 61.026 55.000 11.47 0.00 40.02 4.92
685 759 1.025113 TCTGCTAGTGAGACCGGTCG 61.025 60.000 28.26 14.32 34.09 4.79
694 768 0.972983 GGGAGCTGGTCTGCTAGTGA 60.973 60.000 6.83 0.00 44.17 3.41
698 772 0.041833 AGAAGGGAGCTGGTCTGCTA 59.958 55.000 6.83 0.00 44.17 3.49
882 958 4.890306 GAGGAGGAGGAGGGGGCC 62.890 77.778 0.00 0.00 0.00 5.80
975 1069 1.464376 CCGACGAGTATGGCCCTGAT 61.464 60.000 0.00 0.00 0.00 2.90
1034 1128 5.885230 TTGGAGAGAATAAGCAACACATG 57.115 39.130 0.00 0.00 0.00 3.21
1035 1129 6.899393 TTTTGGAGAGAATAAGCAACACAT 57.101 33.333 0.00 0.00 0.00 3.21
1067 1162 4.112634 TGGTCAGGGATTAAGCAAAACT 57.887 40.909 0.00 0.00 0.00 2.66
1070 1165 4.934356 AGATTGGTCAGGGATTAAGCAAA 58.066 39.130 0.00 0.00 34.47 3.68
1090 1185 2.243810 CCCAAAAATTGTTCGGGGAGA 58.756 47.619 0.00 0.00 37.80 3.71
1091 1186 1.967779 ACCCAAAAATTGTTCGGGGAG 59.032 47.619 10.17 0.00 41.55 4.30
1092 1187 1.964933 GACCCAAAAATTGTTCGGGGA 59.035 47.619 10.17 0.00 41.55 4.81
1094 1189 1.609555 TCGACCCAAAAATTGTTCGGG 59.390 47.619 12.06 12.06 43.02 5.14
1102 1198 7.027161 CGACAAGAATAAATCGACCCAAAAAT 58.973 34.615 0.00 0.00 36.70 1.82
1199 1304 3.242478 CGACACAGCACGAAAAGGTAAAA 60.242 43.478 0.00 0.00 0.00 1.52
1220 1325 7.705325 ACTGTAACTACATTAAGCTAACCATCG 59.295 37.037 0.00 0.00 35.36 3.84
1235 1340 5.074804 TCTAAGACTGGCACTGTAACTACA 58.925 41.667 0.00 0.00 41.64 2.74
1343 4920 3.683581 GCTGAAGCAAGCTAAACGG 57.316 52.632 0.00 0.00 40.20 4.44
1368 4946 4.162509 GGAAGACTATGGCCTAGTTGAAGT 59.837 45.833 3.32 0.00 40.88 3.01
1427 5026 3.503748 AGAACTTACAAGCCATGCAGTTC 59.496 43.478 17.09 17.09 45.05 3.01
1436 5035 9.937175 GTGATTTGATATTAGAACTTACAAGCC 57.063 33.333 0.00 0.00 0.00 4.35
1454 5053 3.645212 TGGCCTTCAAAATGGTGATTTGA 59.355 39.130 3.32 0.00 43.12 2.69
1475 5077 1.511850 TGATGTTGAACCTGTCGCTG 58.488 50.000 0.00 0.00 0.00 5.18
1517 5119 1.676006 CCTGTTCCGACATATTTGGCC 59.324 52.381 0.00 0.00 34.72 5.36
1582 5184 9.907229 AAAAGACTTATATTTAGGAACTGAGGG 57.093 33.333 0.00 0.00 41.52 4.30
1600 5202 9.467796 CCCTTATTGGAATCTCTAAAAAGACTT 57.532 33.333 0.00 0.00 38.35 3.01
1601 5203 8.836735 TCCCTTATTGGAATCTCTAAAAAGACT 58.163 33.333 0.00 0.00 38.35 3.24
1602 5204 8.894731 GTCCCTTATTGGAATCTCTAAAAAGAC 58.105 37.037 0.00 0.00 35.80 3.01
1603 5205 8.836735 AGTCCCTTATTGGAATCTCTAAAAAGA 58.163 33.333 0.00 0.00 35.80 2.52
1605 5207 9.901172 GTAGTCCCTTATTGGAATCTCTAAAAA 57.099 33.333 0.00 0.00 35.80 1.94
1606 5208 9.053472 TGTAGTCCCTTATTGGAATCTCTAAAA 57.947 33.333 0.00 0.00 35.80 1.52
1607 5209 8.618240 TGTAGTCCCTTATTGGAATCTCTAAA 57.382 34.615 0.00 0.00 35.80 1.85
1608 5210 8.798975 ATGTAGTCCCTTATTGGAATCTCTAA 57.201 34.615 0.00 0.00 35.80 2.10
1609 5211 9.310449 GTATGTAGTCCCTTATTGGAATCTCTA 57.690 37.037 0.00 0.00 35.80 2.43
1610 5212 7.039644 CGTATGTAGTCCCTTATTGGAATCTCT 60.040 40.741 0.00 0.00 35.80 3.10
1611 5213 7.091443 CGTATGTAGTCCCTTATTGGAATCTC 58.909 42.308 0.00 0.00 35.80 2.75
1612 5214 6.014499 CCGTATGTAGTCCCTTATTGGAATCT 60.014 42.308 0.00 0.00 35.80 2.40
1613 5215 6.014840 TCCGTATGTAGTCCCTTATTGGAATC 60.015 42.308 0.00 0.00 35.80 2.52
1614 5216 5.842328 TCCGTATGTAGTCCCTTATTGGAAT 59.158 40.000 0.00 0.00 35.80 3.01
1615 5217 5.210430 TCCGTATGTAGTCCCTTATTGGAA 58.790 41.667 0.00 0.00 35.80 3.53
1616 5218 4.806892 TCCGTATGTAGTCCCTTATTGGA 58.193 43.478 0.00 0.00 38.35 3.53
1617 5219 4.560919 GCTCCGTATGTAGTCCCTTATTGG 60.561 50.000 0.00 0.00 0.00 3.16
1618 5220 4.038763 TGCTCCGTATGTAGTCCCTTATTG 59.961 45.833 0.00 0.00 0.00 1.90
1619 5221 4.220724 TGCTCCGTATGTAGTCCCTTATT 58.779 43.478 0.00 0.00 0.00 1.40
1620 5222 3.840991 TGCTCCGTATGTAGTCCCTTAT 58.159 45.455 0.00 0.00 0.00 1.73
1621 5223 3.301794 TGCTCCGTATGTAGTCCCTTA 57.698 47.619 0.00 0.00 0.00 2.69
1622 5224 2.154567 TGCTCCGTATGTAGTCCCTT 57.845 50.000 0.00 0.00 0.00 3.95
1623 5225 2.154567 TTGCTCCGTATGTAGTCCCT 57.845 50.000 0.00 0.00 0.00 4.20
1624 5226 2.973694 TTTGCTCCGTATGTAGTCCC 57.026 50.000 0.00 0.00 0.00 4.46
1625 5227 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
1626 5228 5.109903 ACTCATTTTGCTCCGTATGTAGTC 58.890 41.667 0.00 0.00 0.00 2.59
1627 5229 5.086104 ACTCATTTTGCTCCGTATGTAGT 57.914 39.130 0.00 0.00 0.00 2.73
1628 5230 7.534085 TTAACTCATTTTGCTCCGTATGTAG 57.466 36.000 0.00 0.00 0.00 2.74
1629 5231 7.985184 AGATTAACTCATTTTGCTCCGTATGTA 59.015 33.333 0.00 0.00 0.00 2.29
1630 5232 6.823689 AGATTAACTCATTTTGCTCCGTATGT 59.176 34.615 0.00 0.00 0.00 2.29
1631 5233 7.251704 AGATTAACTCATTTTGCTCCGTATG 57.748 36.000 0.00 0.00 0.00 2.39
1632 5234 7.985184 TGTAGATTAACTCATTTTGCTCCGTAT 59.015 33.333 0.00 0.00 0.00 3.06
1633 5235 7.277098 GTGTAGATTAACTCATTTTGCTCCGTA 59.723 37.037 0.00 0.00 0.00 4.02
1634 5236 6.092259 GTGTAGATTAACTCATTTTGCTCCGT 59.908 38.462 0.00 0.00 0.00 4.69
1635 5237 6.313905 AGTGTAGATTAACTCATTTTGCTCCG 59.686 38.462 0.00 0.00 0.00 4.63
1636 5238 7.550906 AGAGTGTAGATTAACTCATTTTGCTCC 59.449 37.037 5.68 0.00 44.34 4.70
1637 5239 8.485976 AGAGTGTAGATTAACTCATTTTGCTC 57.514 34.615 5.68 0.00 44.34 4.26
1638 5240 9.944376 TTAGAGTGTAGATTAACTCATTTTGCT 57.056 29.630 5.68 0.00 44.34 3.91
1669 5271 9.729281 TGAACTACATACGGATGTATATAGACA 57.271 33.333 20.64 12.87 45.42 3.41
1676 5278 9.916360 TCCTATATGAACTACATACGGATGTAT 57.084 33.333 20.64 7.28 45.42 2.29
1677 5279 9.743581 TTCCTATATGAACTACATACGGATGTA 57.256 33.333 19.32 19.32 44.77 2.29
1679 5281 9.737427 GATTCCTATATGAACTACATACGGATG 57.263 37.037 5.94 5.94 43.12 3.51
1680 5282 9.702253 AGATTCCTATATGAACTACATACGGAT 57.298 33.333 0.00 0.00 43.12 4.18
1681 5283 9.175312 GAGATTCCTATATGAACTACATACGGA 57.825 37.037 0.00 0.00 43.12 4.69
1682 5284 9.179909 AGAGATTCCTATATGAACTACATACGG 57.820 37.037 0.00 0.00 43.12 4.02
1713 5315 9.377238 ACTCCCTCCGTTTCTAAATATAAGTAT 57.623 33.333 0.00 0.00 0.00 2.12
1714 5316 8.773033 ACTCCCTCCGTTTCTAAATATAAGTA 57.227 34.615 0.00 0.00 0.00 2.24
1715 5317 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
1719 5321 9.597681 TCTAATACTCCCTCCGTTTCTAAATAT 57.402 33.333 0.00 0.00 0.00 1.28
1720 5322 9.075678 CTCTAATACTCCCTCCGTTTCTAAATA 57.924 37.037 0.00 0.00 0.00 1.40
1721 5323 7.783596 TCTCTAATACTCCCTCCGTTTCTAAAT 59.216 37.037 0.00 0.00 0.00 1.40
1722 5324 7.121382 TCTCTAATACTCCCTCCGTTTCTAAA 58.879 38.462 0.00 0.00 0.00 1.85
1723 5325 6.666678 TCTCTAATACTCCCTCCGTTTCTAA 58.333 40.000 0.00 0.00 0.00 2.10
1724 5326 6.257994 TCTCTAATACTCCCTCCGTTTCTA 57.742 41.667 0.00 0.00 0.00 2.10
1725 5327 5.126699 TCTCTAATACTCCCTCCGTTTCT 57.873 43.478 0.00 0.00 0.00 2.52
1726 5328 5.302313 ACATCTCTAATACTCCCTCCGTTTC 59.698 44.000 0.00 0.00 0.00 2.78
1727 5329 5.209659 ACATCTCTAATACTCCCTCCGTTT 58.790 41.667 0.00 0.00 0.00 3.60
1728 5330 4.805744 ACATCTCTAATACTCCCTCCGTT 58.194 43.478 0.00 0.00 0.00 4.44
1729 5331 4.456662 ACATCTCTAATACTCCCTCCGT 57.543 45.455 0.00 0.00 0.00 4.69
1730 5332 4.559704 GCAACATCTCTAATACTCCCTCCG 60.560 50.000 0.00 0.00 0.00 4.63
1731 5333 4.345257 TGCAACATCTCTAATACTCCCTCC 59.655 45.833 0.00 0.00 0.00 4.30
1732 5334 5.537300 TGCAACATCTCTAATACTCCCTC 57.463 43.478 0.00 0.00 0.00 4.30
1733 5335 6.506538 AATGCAACATCTCTAATACTCCCT 57.493 37.500 0.00 0.00 0.00 4.20
1734 5336 6.370166 GCTAATGCAACATCTCTAATACTCCC 59.630 42.308 0.00 0.00 39.41 4.30
1735 5337 7.158021 AGCTAATGCAACATCTCTAATACTCC 58.842 38.462 0.00 0.00 42.74 3.85
1736 5338 9.352784 CTAGCTAATGCAACATCTCTAATACTC 57.647 37.037 0.00 0.00 42.74 2.59
1737 5339 7.816995 GCTAGCTAATGCAACATCTCTAATACT 59.183 37.037 7.70 0.00 42.74 2.12
1738 5340 7.816995 AGCTAGCTAATGCAACATCTCTAATAC 59.183 37.037 17.69 0.00 42.74 1.89
1739 5341 7.901029 AGCTAGCTAATGCAACATCTCTAATA 58.099 34.615 17.69 0.00 42.74 0.98
1740 5342 6.767456 AGCTAGCTAATGCAACATCTCTAAT 58.233 36.000 17.69 0.00 42.74 1.73
1741 5343 6.166984 AGCTAGCTAATGCAACATCTCTAA 57.833 37.500 17.69 0.00 42.74 2.10
1742 5344 5.798125 AGCTAGCTAATGCAACATCTCTA 57.202 39.130 17.69 0.00 42.74 2.43
1746 5348 5.049818 CCACTTAGCTAGCTAATGCAACATC 60.050 44.000 31.95 0.00 42.74 3.06
1767 5369 6.374333 TGCCAATCAAGAATAAGTCTTACCAC 59.626 38.462 0.00 0.00 45.25 4.16
1776 5383 5.221185 CCAGACCATGCCAATCAAGAATAAG 60.221 44.000 0.00 0.00 0.00 1.73
1818 5426 4.284829 TCACTGCAATACAAGGACATGA 57.715 40.909 0.00 0.00 0.00 3.07
1894 5502 4.577283 GCAATGGAAAAATATGCCAGCATT 59.423 37.500 10.91 0.00 37.82 3.56
2000 5609 4.757657 TCCTACACGATTTGCAGCTAAAAA 59.242 37.500 0.00 0.00 0.00 1.94
2195 5825 5.008019 GCTTACAAGGTACATGGTCATGATG 59.992 44.000 16.77 0.00 41.20 3.07
2268 6408 1.273048 CTGCCCAGCTACAATTTGCAA 59.727 47.619 0.00 0.00 0.00 4.08
2298 6438 3.753272 ACCGCAATGTATTATGGCTCATC 59.247 43.478 0.00 0.00 0.00 2.92
2299 6439 3.753272 GACCGCAATGTATTATGGCTCAT 59.247 43.478 0.00 0.00 0.00 2.90
2315 6455 2.375146 TCAAGCTATACTCTGACCGCA 58.625 47.619 0.00 0.00 0.00 5.69
2327 6467 6.035975 GTGCAAACAAAACAACTTCAAGCTAT 59.964 34.615 0.00 0.00 0.00 2.97
2349 6490 1.501169 AAATTTCTTTGGCAGCGTGC 58.499 45.000 1.92 1.92 44.08 5.34
2451 6593 9.474920 GTCTCTCATATCACTTGAATAAAGAGG 57.525 37.037 0.00 0.00 39.38 3.69
2556 6700 8.790718 CCCCTTTGATGAGAAATATGTCAATAG 58.209 37.037 0.00 0.00 31.89 1.73
2587 6732 8.942338 ATATACGAAACATCTTCAAGCTACAA 57.058 30.769 0.00 0.00 0.00 2.41
2601 6746 8.041919 TGGACCATTTAGTTGATATACGAAACA 58.958 33.333 0.00 0.00 0.00 2.83
2740 6924 2.429971 TGTTCAACAAAATGCAGCCAGA 59.570 40.909 0.00 0.00 0.00 3.86
3054 8616 8.711457 AGAAAGAATGATTTAAACATTTTGGCG 58.289 29.630 13.58 0.00 37.96 5.69
3136 8710 1.557443 GCGCCGTGACCATAGCATAC 61.557 60.000 0.00 0.00 0.00 2.39
3149 8723 1.291877 GAACAGATCAACAGCGCCGT 61.292 55.000 2.29 0.00 0.00 5.68
3822 9552 8.327271 GGTATATCAGGTAGTGGAGTACAGATA 58.673 40.741 0.00 0.00 31.54 1.98
3913 9657 9.384764 GACAGTATAGCAAACCTTTTCTCTTAT 57.615 33.333 0.00 0.00 0.00 1.73
3919 9663 5.857822 ACGACAGTATAGCAAACCTTTTC 57.142 39.130 0.00 0.00 0.00 2.29
3940 9684 0.699151 CGCAGTGTTCGTGTACGTAC 59.301 55.000 18.90 18.90 39.56 3.67
3959 9703 6.701432 CAAAGGAAATTGCATTCAGACTTC 57.299 37.500 2.65 0.00 0.00 3.01
4048 9827 1.065551 CCGGCCCAAGAAATCGAAATC 59.934 52.381 0.00 0.00 0.00 2.17
4073 9894 1.399744 CCTACCCATCTGCTGCCGTA 61.400 60.000 0.00 0.00 0.00 4.02
4074 9895 2.735772 CCTACCCATCTGCTGCCGT 61.736 63.158 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.