Multiple sequence alignment - TraesCS5B01G479100

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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 TraesCS5B01G479100 chr5B 100.000 4391 0 0 1 4391 650545112 650549502 0.000000e+00 8109.0
1 TraesCS5B01G479100 chr5B 90.347 259 6 5 2274 2523 650547305 650547553 5.480000e-84 322.0
2 TraesCS5B01G479100 chr5B 90.347 259 6 5 2194 2442 650547385 650547634 5.480000e-84 322.0
3 TraesCS5B01G479100 chr5B 92.308 169 5 1 2363 2523 650547305 650547473 2.640000e-57 233.0
4 TraesCS5B01G479100 chr5B 92.308 169 5 1 2194 2362 650547474 650547634 2.640000e-57 233.0
5 TraesCS5B01G479100 chr5B 88.976 127 14 0 2599 2725 266005268 266005394 1.630000e-34 158.0
6 TraesCS5B01G479100 chr5B 98.750 80 0 1 2443 2522 650547305 650547383 1.650000e-29 141.0
7 TraesCS5B01G479100 chr5B 98.750 80 0 1 2194 2272 650547554 650547633 1.650000e-29 141.0
8 TraesCS5B01G479100 chr5D 92.792 1526 79 17 81 1595 517839476 517840981 0.000000e+00 2180.0
9 TraesCS5B01G479100 chr5D 97.076 684 18 2 2443 3126 517841618 517842299 0.000000e+00 1151.0
10 TraesCS5B01G479100 chr5D 89.744 546 22 17 3279 3811 517842747 517843271 0.000000e+00 667.0
11 TraesCS5B01G479100 chr5D 94.118 425 24 1 1607 2031 517840964 517841387 0.000000e+00 645.0
12 TraesCS5B01G479100 chr5D 94.649 299 7 3 1981 2272 517841400 517841696 5.180000e-124 455.0
13 TraesCS5B01G479100 chr5D 84.900 351 14 9 3837 4180 517843380 517843698 7.090000e-83 318.0
14 TraesCS5B01G479100 chr5D 90.503 179 8 6 3148 3319 517842570 517842746 1.230000e-55 228.0
15 TraesCS5B01G479100 chr5D 89.062 128 14 0 2598 2725 238711624 238711497 4.550000e-35 159.0
16 TraesCS5B01G479100 chr5D 86.517 89 3 1 2274 2362 517841618 517841697 6.050000e-14 89.8
17 TraesCS5B01G479100 chr5D 97.297 37 1 0 3126 3162 517842539 517842575 3.670000e-06 63.9
18 TraesCS5B01G479100 chr5A 91.924 1585 71 31 2274 3838 645262156 645263703 0.000000e+00 2165.0
19 TraesCS5B01G479100 chr5A 93.079 838 45 4 1607 2442 645261569 645262395 0.000000e+00 1214.0
20 TraesCS5B01G479100 chr5A 93.248 785 47 5 815 1595 645260804 645261586 0.000000e+00 1151.0
21 TraesCS5B01G479100 chr5A 93.843 536 19 6 294 817 645259833 645260366 0.000000e+00 795.0
22 TraesCS5B01G479100 chr5A 87.865 445 32 12 3837 4271 645263763 645264195 1.820000e-138 503.0
23 TraesCS5B01G479100 chr5A 86.486 259 23 10 1 250 645259582 645259837 1.560000e-69 274.0
24 TraesCS5B01G479100 chr5A 92.547 161 11 1 2363 2523 645262156 645262315 3.420000e-56 230.0
25 TraesCS5B01G479100 chr5A 91.124 169 6 1 2194 2362 645262236 645262395 2.060000e-53 220.0
26 TraesCS5B01G479100 chr5A 89.474 152 14 2 1090 1240 315494733 315494883 1.610000e-44 191.0
27 TraesCS5B01G479100 chr5A 89.062 128 14 0 2598 2725 315495850 315495977 4.550000e-35 159.0
28 TraesCS5B01G479100 chr5A 100.000 79 0 0 2194 2272 645262316 645262394 3.540000e-31 147.0
29 TraesCS5B01G479100 chr5A 93.827 81 4 1 2443 2523 645262156 645262235 2.140000e-23 121.0
30 TraesCS5B01G479100 chr3A 92.073 164 13 0 1081 1244 584276534 584276697 9.500000e-57 231.0
31 TraesCS5B01G479100 chr3D 91.463 164 14 0 1081 1244 443258969 443259132 4.420000e-55 226.0
32 TraesCS5B01G479100 chr3B 90.854 164 15 0 1081 1244 581026438 581026601 2.060000e-53 220.0
33 TraesCS5B01G479100 chr3B 91.473 129 11 0 2599 2727 581029962 581030090 1.250000e-40 178.0
34 TraesCS5B01G479100 chr1D 90.854 164 15 0 1081 1244 403238768 403238605 2.060000e-53 220.0
35 TraesCS5B01G479100 chr1B 90.854 164 15 0 1081 1244 541469864 541469701 2.060000e-53 220.0
36 TraesCS5B01G479100 chr1A 90.854 164 15 0 1081 1244 498454134 498453971 2.060000e-53 220.0
37 TraesCS5B01G479100 chr2D 92.254 142 11 0 2590 2731 277680323 277680464 7.450000e-48 202.0
38 TraesCS5B01G479100 chr2A 92.806 139 10 0 2593 2731 293936397 293936259 7.450000e-48 202.0


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 TraesCS5B01G479100 chr5B 650545112 650549502 4390 False 1357.285714 8109 94.687143 1 4391 7 chr5B.!!$F2 4390
1 TraesCS5B01G479100 chr5D 517839476 517843698 4222 False 644.188889 2180 91.955111 81 4180 9 chr5D.!!$F1 4099
2 TraesCS5B01G479100 chr5A 645259582 645264195 4613 False 682.000000 2165 92.394300 1 4271 10 chr5A.!!$F2 4270

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
164 174 0.243636 GGGACATCCAAACCAAAGCG 59.756 55.0 0.00 0.0 37.91 4.68 F
618 639 0.257616 CTCTCCCCCTTCTCTCTCGT 59.742 60.0 0.00 0.0 0.00 4.18 F
1833 2305 0.744771 GCCACTACAACCAGCTAGCC 60.745 60.0 12.13 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1173 1636 1.290134 AGAGGATGGTGGTCTTTCCC 58.710 55.000 0.00 0.0 34.77 3.97 R
2178 2712 2.287788 ACAATTCAGTTTCAAGGCGCAG 60.288 45.455 10.83 0.0 0.00 5.18 R
3805 4654 0.314935 GTCTTTGCCATGTGGGTGTG 59.685 55.000 0.54 0.0 39.65 3.82 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
20 21 0.518636 CTCACCAATGACGCTTGTGG 59.481 55.000 0.00 0.00 37.17 4.17
32 33 0.322008 GCTTGTGGAAGGAGACCCTG 60.322 60.000 0.00 0.00 43.48 4.45
44 45 2.036256 ACCCTGTCCATGGCAAGC 59.964 61.111 6.96 0.00 0.00 4.01
60 61 2.619074 GCAAGCCTAGATCACCACCTTT 60.619 50.000 0.00 0.00 0.00 3.11
65 66 3.181470 GCCTAGATCACCACCTTTCTCTC 60.181 52.174 0.00 0.00 0.00 3.20
106 108 2.039613 AGAAAGGAGACCAAGGCAAGAG 59.960 50.000 0.00 0.00 0.00 2.85
108 110 1.130054 AGGAGACCAAGGCAAGAGCA 61.130 55.000 0.00 0.00 44.61 4.26
113 115 0.829182 ACCAAGGCAAGAGCAAAGGG 60.829 55.000 0.00 0.00 44.61 3.95
120 122 1.335051 GCAAGAGCAAAGGGAACGAAC 60.335 52.381 0.00 0.00 41.58 3.95
122 124 2.554032 CAAGAGCAAAGGGAACGAACAT 59.446 45.455 0.00 0.00 0.00 2.71
124 126 1.880027 GAGCAAAGGGAACGAACATGT 59.120 47.619 0.00 0.00 0.00 3.21
125 127 2.293399 GAGCAAAGGGAACGAACATGTT 59.707 45.455 11.78 11.78 34.02 2.71
138 148 1.003355 CATGTTGGGAGTGGCGACT 60.003 57.895 0.00 0.00 33.98 4.18
143 153 1.066430 GTTGGGAGTGGCGACTATGAA 60.066 52.381 0.00 0.00 30.16 2.57
164 174 0.243636 GGGACATCCAAACCAAAGCG 59.756 55.000 0.00 0.00 37.91 4.68
173 183 4.643463 TCCAAACCAAAGCGACTAATACA 58.357 39.130 0.00 0.00 0.00 2.29
184 194 2.292569 CGACTAATACAGGCTCGCCTAA 59.707 50.000 10.61 2.34 46.28 2.69
227 237 3.195698 GTTCCCAGTCGCGATGGC 61.196 66.667 23.79 9.18 36.43 4.40
253 263 2.610438 ATCAACATTTCCTGTGGGCT 57.390 45.000 0.00 0.00 38.39 5.19
269 279 6.313519 TGTGGGCTTAGAGTTTTATGAGAT 57.686 37.500 0.00 0.00 0.00 2.75
270 280 7.419057 CCTGTGGGCTTAGAGTTTTATGAGATA 60.419 40.741 0.00 0.00 0.00 1.98
271 281 7.272978 TGTGGGCTTAGAGTTTTATGAGATAC 58.727 38.462 0.00 0.00 0.00 2.24
272 282 7.125811 TGTGGGCTTAGAGTTTTATGAGATACT 59.874 37.037 0.00 0.00 0.00 2.12
273 283 7.654116 GTGGGCTTAGAGTTTTATGAGATACTC 59.346 40.741 0.00 0.00 37.79 2.59
274 284 7.156000 GGGCTTAGAGTTTTATGAGATACTCC 58.844 42.308 0.00 0.00 38.17 3.85
306 316 3.926616 ACGGTATTCTGTGTCTTTCTGG 58.073 45.455 0.00 0.00 0.00 3.86
309 319 4.994852 CGGTATTCTGTGTCTTTCTGGAAA 59.005 41.667 0.00 0.00 0.00 3.13
434 449 5.501156 AGAAAAGGTGAGCGAGGAAATTAT 58.499 37.500 0.00 0.00 0.00 1.28
570 585 1.552226 CCTCGCGTCGCTTAAATACA 58.448 50.000 16.36 0.00 0.00 2.29
618 639 0.257616 CTCTCCCCCTTCTCTCTCGT 59.742 60.000 0.00 0.00 0.00 4.18
787 810 3.060020 GCGAGATCCGTCCGTTCCA 62.060 63.158 5.66 0.00 41.15 3.53
851 1314 1.604593 GGGATCCATGGCCATTCCG 60.605 63.158 23.01 10.99 37.80 4.30
957 1420 4.090588 TGATCCCGTGGCCGTTCC 62.091 66.667 0.00 0.00 0.00 3.62
1007 1470 5.542779 GTGTAGATCTAGCGAAATGGGATT 58.457 41.667 1.64 0.00 0.00 3.01
1052 1515 1.673665 CTGTGTTGCAGGAGAGGCC 60.674 63.158 0.00 0.00 41.42 5.19
1403 1870 8.848474 TTGCCTAAATAACTGCTAGAATATCC 57.152 34.615 0.00 0.00 0.00 2.59
1413 1880 7.468141 ACTGCTAGAATATCCAATATGACGA 57.532 36.000 0.00 0.00 0.00 4.20
1426 1893 8.089625 TCCAATATGACGATATCAATGGGTAT 57.910 34.615 3.12 0.00 41.93 2.73
1469 1937 9.758651 AAAAATGGTTAGGTAGTTTTGTTCATC 57.241 29.630 0.00 0.00 0.00 2.92
1487 1955 1.649321 TCAGGATCTCTGTGCAGGTT 58.351 50.000 9.98 0.00 43.76 3.50
1514 1985 6.525629 GGGTAGTGCACTTATGTTCATAGAT 58.474 40.000 27.06 0.00 0.00 1.98
1541 2012 7.915293 ATATATGGACAAAACGACAGACAAA 57.085 32.000 0.00 0.00 0.00 2.83
1599 2070 9.947433 TTATAACCATATAAACATAAGACCCCG 57.053 33.333 0.00 0.00 32.36 5.73
1600 2071 4.648651 ACCATATAAACATAAGACCCCGC 58.351 43.478 0.00 0.00 0.00 6.13
1601 2072 4.103469 ACCATATAAACATAAGACCCCGCA 59.897 41.667 0.00 0.00 0.00 5.69
1602 2073 5.067273 CCATATAAACATAAGACCCCGCAA 58.933 41.667 0.00 0.00 0.00 4.85
1603 2074 5.533154 CCATATAAACATAAGACCCCGCAAA 59.467 40.000 0.00 0.00 0.00 3.68
1604 2075 6.039941 CCATATAAACATAAGACCCCGCAAAA 59.960 38.462 0.00 0.00 0.00 2.44
1605 2076 5.986501 ATAAACATAAGACCCCGCAAAAA 57.013 34.783 0.00 0.00 0.00 1.94
1650 2121 1.794714 TCCTGGGCTAGATGTCCTTC 58.205 55.000 0.00 0.00 42.07 3.46
1654 2125 1.686325 GGGCTAGATGTCCTTCGGCA 61.686 60.000 0.00 0.00 37.49 5.69
1713 2184 3.317603 AACAAATGCCTACATGCCAAC 57.682 42.857 0.00 0.00 36.36 3.77
1716 2187 0.819582 AATGCCTACATGCCAACAGC 59.180 50.000 0.00 0.00 44.14 4.40
1833 2305 0.744771 GCCACTACAACCAGCTAGCC 60.745 60.000 12.13 0.00 0.00 3.93
1897 2369 6.258507 CCTTTTGTAAATTGACTGCTTGCTTT 59.741 34.615 0.00 0.00 0.00 3.51
1899 2371 5.512753 TGTAAATTGACTGCTTGCTTTGA 57.487 34.783 0.00 0.00 0.00 2.69
1917 2389 8.694581 TGCTTTGAATGTCATTGGATGATATA 57.305 30.769 1.88 0.00 39.74 0.86
1978 2450 2.819608 GTGCTAAAAGGCAAGACCATCA 59.180 45.455 0.00 0.00 44.18 3.07
2048 2582 7.495279 ACATTTGTTAATCTGCAACACATGTTT 59.505 29.630 12.34 0.00 46.97 2.83
2055 2589 2.020720 TGCAACACATGTTTTCTCCGT 58.979 42.857 0.00 0.00 35.83 4.69
2229 2763 6.485830 AGTACCTGCAATGTATGATGTACT 57.514 37.500 0.00 0.00 35.81 2.73
2242 2776 8.392372 TGTATGATGTACTAGTATCTCACACC 57.608 38.462 16.90 2.91 0.00 4.16
2299 2833 9.855021 GAATTGTTTTTATAGTACCTGCAATGT 57.145 29.630 0.00 0.00 0.00 2.71
2307 2841 9.899661 TTTATAGTACCTGCAATGTAATGAACT 57.100 29.630 6.34 1.49 0.00 3.01
2311 2845 8.213518 AGTACCTGCAATGTAATGAACTAATG 57.786 34.615 0.00 0.00 0.00 1.90
2312 2846 8.046708 AGTACCTGCAATGTAATGAACTAATGA 58.953 33.333 0.00 0.00 0.00 2.57
2313 2847 7.886629 ACCTGCAATGTAATGAACTAATGAT 57.113 32.000 0.00 0.00 0.00 2.45
2314 2848 7.709947 ACCTGCAATGTAATGAACTAATGATG 58.290 34.615 0.00 0.00 0.00 3.07
2315 2849 7.340232 ACCTGCAATGTAATGAACTAATGATGT 59.660 33.333 0.00 0.00 0.00 3.06
2316 2850 8.839343 CCTGCAATGTAATGAACTAATGATGTA 58.161 33.333 0.00 0.00 0.00 2.29
2317 2851 9.655769 CTGCAATGTAATGAACTAATGATGTAC 57.344 33.333 0.00 0.00 0.00 2.90
2318 2852 9.394767 TGCAATGTAATGAACTAATGATGTACT 57.605 29.630 0.00 0.00 0.00 2.73
2331 2865 9.069082 ACTAATGATGTACTAGTATCTCACACC 57.931 37.037 15.58 0.81 0.00 4.16
2332 2866 9.290988 CTAATGATGTACTAGTATCTCACACCT 57.709 37.037 15.58 7.21 0.00 4.00
2334 2868 9.642343 AATGATGTACTAGTATCTCACACCTAA 57.358 33.333 15.58 0.00 0.00 2.69
2335 2869 9.815306 ATGATGTACTAGTATCTCACACCTAAT 57.185 33.333 15.58 1.37 0.00 1.73
2336 2870 9.642343 TGATGTACTAGTATCTCACACCTAATT 57.358 33.333 5.75 0.00 0.00 1.40
2339 2873 9.696572 TGTACTAGTATCTCACACCTAATTTCT 57.303 33.333 5.75 0.00 0.00 2.52
2348 2882 8.141298 TCTCACACCTAATTTCTAATACACCA 57.859 34.615 0.00 0.00 0.00 4.17
2349 2883 8.768397 TCTCACACCTAATTTCTAATACACCAT 58.232 33.333 0.00 0.00 0.00 3.55
2350 2884 8.731275 TCACACCTAATTTCTAATACACCATG 57.269 34.615 0.00 0.00 0.00 3.66
2351 2885 7.773224 TCACACCTAATTTCTAATACACCATGG 59.227 37.037 11.19 11.19 0.00 3.66
2352 2886 7.773224 CACACCTAATTTCTAATACACCATGGA 59.227 37.037 21.47 0.00 0.00 3.41
2353 2887 8.333235 ACACCTAATTTCTAATACACCATGGAA 58.667 33.333 21.47 3.43 0.00 3.53
2354 2888 8.621286 CACCTAATTTCTAATACACCATGGAAC 58.379 37.037 21.47 0.00 0.00 3.62
2383 2917 6.327279 AGGAATTGTTTTTGTAGTACCTGC 57.673 37.500 0.00 0.00 0.00 4.85
2384 2918 5.830991 AGGAATTGTTTTTGTAGTACCTGCA 59.169 36.000 0.00 0.00 0.00 4.41
2385 2919 6.322712 AGGAATTGTTTTTGTAGTACCTGCAA 59.677 34.615 0.00 0.00 34.54 4.08
2386 2920 7.015195 AGGAATTGTTTTTGTAGTACCTGCAAT 59.985 33.333 0.00 0.00 36.13 3.56
2387 2921 8.301002 GGAATTGTTTTTGTAGTACCTGCAATA 58.699 33.333 0.00 0.00 36.13 1.90
2398 2932 9.309224 TGTAGTACCTGCAATATATGATGTACT 57.691 33.333 13.62 13.62 39.87 2.73
2727 3261 3.464907 CACAGGATGCTGAATGAGGTAG 58.535 50.000 22.24 0.00 42.53 3.18
2741 3275 8.824756 TGAATGAGGTAGATTCTTACACTACT 57.175 34.615 0.00 0.00 37.32 2.57
2745 3279 8.645814 TGAGGTAGATTCTTACACTACTCAAA 57.354 34.615 0.00 0.00 37.32 2.69
2991 3525 9.897744 TGCTTGTCTTTTCTGTATTTTAAGATG 57.102 29.630 0.00 0.00 0.00 2.90
3121 3658 6.804677 TGGCTTGGTAATGCATATTGTTTAG 58.195 36.000 0.00 0.00 0.00 1.85
3265 4053 5.998454 CAAGGTATGCATAGACTTCCTTG 57.002 43.478 26.23 26.23 42.40 3.61
3277 4068 2.544267 GACTTCCTTGTCGGTTGTCTTG 59.456 50.000 0.00 0.00 35.14 3.02
3285 4076 4.349663 TGTCGGTTGTCTTGAAAACTTG 57.650 40.909 3.99 0.00 0.00 3.16
3322 4161 2.675519 GCAGTCTCCATCTGCGAAG 58.324 57.895 2.28 0.00 46.39 3.79
3326 4165 2.414481 CAGTCTCCATCTGCGAAGTTTG 59.586 50.000 0.00 0.00 0.00 2.93
3334 4173 4.675114 CCATCTGCGAAGTTTGTTTACAAC 59.325 41.667 0.00 0.00 35.28 3.32
3359 4198 5.768317 ACTTGTTTGTCGGTTGATTAATGG 58.232 37.500 0.00 0.00 0.00 3.16
3377 4217 1.269174 TGGCATCCATTTGAACGTGTG 59.731 47.619 0.00 0.00 0.00 3.82
3527 4367 5.412594 TGTGTATTTTCCTGAGATCAACAGC 59.587 40.000 12.47 1.47 34.47 4.40
3601 4441 7.175104 TGTATTTTGAGCCCTAAGATGTTTCT 58.825 34.615 0.00 0.00 0.00 2.52
3602 4442 7.669722 TGTATTTTGAGCCCTAAGATGTTTCTT 59.330 33.333 0.00 0.00 44.44 2.52
3603 4443 6.575162 TTTTGAGCCCTAAGATGTTTCTTC 57.425 37.500 0.00 0.00 41.36 2.87
3652 4492 8.500773 TCCTGTTCAATTTCGTAATAAGTGTTC 58.499 33.333 0.00 0.00 0.00 3.18
3662 4510 5.580691 TCGTAATAAGTGTTCCAAGCATCTG 59.419 40.000 0.00 0.00 0.00 2.90
3666 4514 2.775890 AGTGTTCCAAGCATCTGTCTG 58.224 47.619 0.00 0.00 0.00 3.51
3700 4549 5.787380 CCTGTATATATTCAGCACTGCTCA 58.213 41.667 12.58 0.00 36.40 4.26
3722 4571 6.417327 TCAACTTTTATTTGCGCATTTGTTG 58.583 32.000 12.75 18.12 34.31 3.33
3735 4584 1.698506 TTTGTTGGTAGCACTTGGGG 58.301 50.000 0.00 0.00 0.00 4.96
3744 4593 3.454812 GGTAGCACTTGGGGAAGAAGATA 59.545 47.826 0.00 0.00 0.00 1.98
3745 4594 4.080526 GGTAGCACTTGGGGAAGAAGATAA 60.081 45.833 0.00 0.00 0.00 1.75
3746 4595 4.227864 AGCACTTGGGGAAGAAGATAAG 57.772 45.455 0.00 0.00 0.00 1.73
3763 4612 9.685828 AGAAGATAAGAGTACGATATGCTTTTC 57.314 33.333 0.00 0.00 0.00 2.29
3764 4613 9.464714 GAAGATAAGAGTACGATATGCTTTTCA 57.535 33.333 0.00 0.00 0.00 2.69
3765 4614 8.804688 AGATAAGAGTACGATATGCTTTTCAC 57.195 34.615 0.00 0.00 0.00 3.18
3766 4615 8.414003 AGATAAGAGTACGATATGCTTTTCACA 58.586 33.333 0.00 0.00 0.00 3.58
3767 4616 9.197694 GATAAGAGTACGATATGCTTTTCACAT 57.802 33.333 0.00 0.00 0.00 3.21
3768 4617 7.849804 AAGAGTACGATATGCTTTTCACATT 57.150 32.000 0.00 0.00 0.00 2.71
3769 4618 8.942338 AAGAGTACGATATGCTTTTCACATTA 57.058 30.769 0.00 0.00 0.00 1.90
3770 4619 8.354011 AGAGTACGATATGCTTTTCACATTAC 57.646 34.615 0.00 0.00 0.00 1.89
3792 4641 5.759059 ACTTTGATGAGGATAAGCATGGAA 58.241 37.500 0.00 0.00 0.00 3.53
3804 4653 2.358939 GCATGGAACTGCTCAAAAGG 57.641 50.000 0.00 0.00 39.12 3.11
3805 4654 1.670967 GCATGGAACTGCTCAAAAGGC 60.671 52.381 0.00 0.00 39.12 4.35
3806 4655 1.614903 CATGGAACTGCTCAAAAGGCA 59.385 47.619 0.00 0.00 38.10 4.75
3807 4656 1.032014 TGGAACTGCTCAAAAGGCAC 58.968 50.000 0.00 0.00 35.71 5.01
3808 4657 1.032014 GGAACTGCTCAAAAGGCACA 58.968 50.000 0.00 0.00 35.71 4.57
3810 4659 0.746659 AACTGCTCAAAAGGCACACC 59.253 50.000 0.00 0.00 35.71 4.16
3813 4662 1.363807 GCTCAAAAGGCACACCCAC 59.636 57.895 0.00 0.00 36.11 4.61
3815 4664 1.331214 CTCAAAAGGCACACCCACAT 58.669 50.000 0.00 0.00 36.11 3.21
3816 4665 1.000060 CTCAAAAGGCACACCCACATG 60.000 52.381 0.00 0.00 36.11 3.21
3818 4667 1.757423 AAAAGGCACACCCACATGGC 61.757 55.000 0.00 0.00 41.52 4.40
3819 4668 2.943369 AAAGGCACACCCACATGGCA 62.943 55.000 0.00 0.00 43.55 4.92
3833 4695 2.154462 CATGGCAAAGACGAGAAGGTT 58.846 47.619 0.00 0.00 0.00 3.50
3858 4789 7.784037 TCCTTAAGTCGGCATACAAAGTTATA 58.216 34.615 0.97 0.00 0.00 0.98
3870 4801 4.839121 ACAAAGTTATAATCAGGTGCGGA 58.161 39.130 0.00 0.00 0.00 5.54
3905 4836 3.131400 AGTTAGGAGCTCGATCTGGAAAC 59.869 47.826 7.83 1.62 0.00 2.78
3958 4889 2.425143 ATGTGGCGAAACATCATCCT 57.575 45.000 0.00 0.00 35.92 3.24
3974 4905 2.983402 TCCTTCGCGTAGGAATATCG 57.017 50.000 29.46 4.41 41.33 2.92
3975 4906 1.068748 TCCTTCGCGTAGGAATATCGC 60.069 52.381 29.46 0.00 41.33 4.58
3976 4907 1.068472 CCTTCGCGTAGGAATATCGCT 60.068 52.381 25.94 0.00 46.31 4.93
3979 4910 1.129998 TCGCGTAGGAATATCGCTAGC 59.870 52.381 5.77 4.06 46.31 3.42
3980 4911 1.130749 CGCGTAGGAATATCGCTAGCT 59.869 52.381 13.93 0.00 46.31 3.32
4031 4962 2.436646 CGTGCGGCCTTGAGGAAT 60.437 61.111 0.00 0.00 37.39 3.01
4033 4964 0.742990 CGTGCGGCCTTGAGGAATAA 60.743 55.000 0.00 0.00 37.39 1.40
4034 4965 1.680338 GTGCGGCCTTGAGGAATAAT 58.320 50.000 0.00 0.00 37.39 1.28
4064 5002 4.681781 CGATCTCCACCTGAATAACTTGCT 60.682 45.833 0.00 0.00 0.00 3.91
4180 5125 2.125350 CACCTTCCAGCTCTCGGC 60.125 66.667 0.00 0.00 42.19 5.54
4216 5161 5.862678 TGGTCGGAATTATACTCATCACA 57.137 39.130 0.00 0.00 0.00 3.58
4218 5163 7.533289 TGGTCGGAATTATACTCATCACATA 57.467 36.000 0.00 0.00 0.00 2.29
4262 5210 1.002134 CAAGGGAAGCCACGACCAT 60.002 57.895 0.00 0.00 0.00 3.55
4271 5219 0.178068 GCCACGACCATAGGTGATGT 59.822 55.000 0.00 0.00 35.25 3.06
4272 5220 1.406887 GCCACGACCATAGGTGATGTT 60.407 52.381 0.00 0.00 35.25 2.71
4273 5221 2.279741 CCACGACCATAGGTGATGTTG 58.720 52.381 0.00 0.00 35.25 3.33
4274 5222 2.093711 CCACGACCATAGGTGATGTTGA 60.094 50.000 0.00 0.00 35.25 3.18
4275 5223 3.595173 CACGACCATAGGTGATGTTGAA 58.405 45.455 0.00 0.00 35.25 2.69
4276 5224 4.191544 CACGACCATAGGTGATGTTGAAT 58.808 43.478 0.00 0.00 35.25 2.57
4277 5225 4.034394 CACGACCATAGGTGATGTTGAATG 59.966 45.833 0.00 0.00 35.25 2.67
4278 5226 4.191544 CGACCATAGGTGATGTTGAATGT 58.808 43.478 0.00 0.00 35.25 2.71
4279 5227 4.271049 CGACCATAGGTGATGTTGAATGTC 59.729 45.833 0.00 0.00 35.25 3.06
4280 5228 5.431765 GACCATAGGTGATGTTGAATGTCT 58.568 41.667 0.00 0.00 35.25 3.41
4281 5229 5.819991 ACCATAGGTGATGTTGAATGTCTT 58.180 37.500 0.00 0.00 32.98 3.01
4282 5230 6.248433 ACCATAGGTGATGTTGAATGTCTTT 58.752 36.000 0.00 0.00 32.98 2.52
4283 5231 6.721208 ACCATAGGTGATGTTGAATGTCTTTT 59.279 34.615 0.00 0.00 32.98 2.27
4284 5232 7.233348 ACCATAGGTGATGTTGAATGTCTTTTT 59.767 33.333 0.00 0.00 32.98 1.94
4317 5265 2.652313 TTTTTGCGGGGAGGTGATG 58.348 52.632 0.00 0.00 0.00 3.07
4318 5266 1.531739 TTTTTGCGGGGAGGTGATGC 61.532 55.000 0.00 0.00 0.00 3.91
4319 5267 2.424842 TTTTGCGGGGAGGTGATGCT 62.425 55.000 0.00 0.00 0.00 3.79
4320 5268 3.626996 TTGCGGGGAGGTGATGCTG 62.627 63.158 0.00 0.00 0.00 4.41
4321 5269 3.785859 GCGGGGAGGTGATGCTGA 61.786 66.667 0.00 0.00 0.00 4.26
4322 5270 2.989639 CGGGGAGGTGATGCTGAA 59.010 61.111 0.00 0.00 0.00 3.02
4323 5271 1.528824 CGGGGAGGTGATGCTGAAT 59.471 57.895 0.00 0.00 0.00 2.57
4324 5272 0.816825 CGGGGAGGTGATGCTGAATG 60.817 60.000 0.00 0.00 0.00 2.67
4325 5273 0.257039 GGGGAGGTGATGCTGAATGT 59.743 55.000 0.00 0.00 0.00 2.71
4326 5274 1.673168 GGGAGGTGATGCTGAATGTC 58.327 55.000 0.00 0.00 0.00 3.06
4327 5275 1.293924 GGAGGTGATGCTGAATGTCG 58.706 55.000 0.00 0.00 0.00 4.35
4328 5276 1.134699 GGAGGTGATGCTGAATGTCGA 60.135 52.381 0.00 0.00 0.00 4.20
4329 5277 1.929836 GAGGTGATGCTGAATGTCGAC 59.070 52.381 9.11 9.11 0.00 4.20
4330 5278 0.647410 GGTGATGCTGAATGTCGACG 59.353 55.000 11.62 0.00 0.00 5.12
4331 5279 0.025513 GTGATGCTGAATGTCGACGC 59.974 55.000 11.62 8.25 0.00 5.19
4332 5280 1.083806 TGATGCTGAATGTCGACGCC 61.084 55.000 11.62 2.90 0.00 5.68
4333 5281 1.079197 ATGCTGAATGTCGACGCCA 60.079 52.632 11.62 7.55 0.00 5.69
4334 5282 1.361668 ATGCTGAATGTCGACGCCAC 61.362 55.000 11.62 3.15 0.00 5.01
4335 5283 1.738099 GCTGAATGTCGACGCCACT 60.738 57.895 11.62 0.00 0.00 4.00
4336 5284 1.291877 GCTGAATGTCGACGCCACTT 61.292 55.000 11.62 0.00 0.00 3.16
4337 5285 1.148310 CTGAATGTCGACGCCACTTT 58.852 50.000 11.62 0.00 0.00 2.66
4338 5286 2.333926 CTGAATGTCGACGCCACTTTA 58.666 47.619 11.62 0.00 0.00 1.85
4339 5287 2.930040 CTGAATGTCGACGCCACTTTAT 59.070 45.455 11.62 0.00 0.00 1.40
4340 5288 2.927477 TGAATGTCGACGCCACTTTATC 59.073 45.455 11.62 0.00 0.00 1.75
4341 5289 1.935933 ATGTCGACGCCACTTTATCC 58.064 50.000 11.62 0.00 0.00 2.59
4342 5290 0.108520 TGTCGACGCCACTTTATCCC 60.109 55.000 11.62 0.00 0.00 3.85
4343 5291 0.108520 GTCGACGCCACTTTATCCCA 60.109 55.000 0.00 0.00 0.00 4.37
4344 5292 0.609151 TCGACGCCACTTTATCCCAA 59.391 50.000 0.00 0.00 0.00 4.12
4345 5293 1.002201 TCGACGCCACTTTATCCCAAA 59.998 47.619 0.00 0.00 0.00 3.28
4346 5294 1.129811 CGACGCCACTTTATCCCAAAC 59.870 52.381 0.00 0.00 0.00 2.93
4347 5295 2.433436 GACGCCACTTTATCCCAAACT 58.567 47.619 0.00 0.00 0.00 2.66
4348 5296 3.602483 GACGCCACTTTATCCCAAACTA 58.398 45.455 0.00 0.00 0.00 2.24
4349 5297 3.606687 ACGCCACTTTATCCCAAACTAG 58.393 45.455 0.00 0.00 0.00 2.57
4350 5298 3.262405 ACGCCACTTTATCCCAAACTAGA 59.738 43.478 0.00 0.00 0.00 2.43
4351 5299 3.871594 CGCCACTTTATCCCAAACTAGAG 59.128 47.826 0.00 0.00 0.00 2.43
4352 5300 4.200092 GCCACTTTATCCCAAACTAGAGG 58.800 47.826 0.00 0.00 0.00 3.69
4353 5301 4.324331 GCCACTTTATCCCAAACTAGAGGT 60.324 45.833 0.00 0.00 0.00 3.85
4354 5302 5.186198 CCACTTTATCCCAAACTAGAGGTG 58.814 45.833 0.00 0.00 0.00 4.00
4355 5303 5.045869 CCACTTTATCCCAAACTAGAGGTGA 60.046 44.000 0.00 0.00 0.00 4.02
4356 5304 6.353082 CCACTTTATCCCAAACTAGAGGTGAT 60.353 42.308 0.00 3.88 0.00 3.06
4357 5305 6.540189 CACTTTATCCCAAACTAGAGGTGATG 59.460 42.308 0.00 0.00 0.00 3.07
4358 5306 5.630415 TTATCCCAAACTAGAGGTGATGG 57.370 43.478 0.00 0.00 36.23 3.51
4359 5307 2.717639 CCCAAACTAGAGGTGATGGG 57.282 55.000 0.00 0.97 44.24 4.00
4360 5308 1.212935 CCCAAACTAGAGGTGATGGGG 59.787 57.143 0.00 0.00 45.11 4.96
4361 5309 1.408822 CCAAACTAGAGGTGATGGGGC 60.409 57.143 0.00 0.00 34.18 5.80
4362 5310 0.919710 AAACTAGAGGTGATGGGGCC 59.080 55.000 0.00 0.00 0.00 5.80
4363 5311 0.044855 AACTAGAGGTGATGGGGCCT 59.955 55.000 0.84 0.00 37.91 5.19
4364 5312 0.692419 ACTAGAGGTGATGGGGCCTG 60.692 60.000 0.84 0.00 34.81 4.85
4365 5313 1.384502 TAGAGGTGATGGGGCCTGG 60.385 63.158 0.84 0.00 34.81 4.45
4366 5314 2.914734 TAGAGGTGATGGGGCCTGGG 62.915 65.000 0.84 0.00 34.81 4.45
4384 5332 2.825836 CCGCATTGCTCAGGGGTC 60.826 66.667 7.12 0.00 33.55 4.46
4385 5333 2.270205 CGCATTGCTCAGGGGTCT 59.730 61.111 7.12 0.00 0.00 3.85
4386 5334 2.110967 CGCATTGCTCAGGGGTCTG 61.111 63.158 7.12 0.00 42.21 3.51
4387 5335 2.413142 GCATTGCTCAGGGGTCTGC 61.413 63.158 0.16 0.00 40.69 4.26
4388 5336 1.751927 CATTGCTCAGGGGTCTGCC 60.752 63.158 0.00 0.00 40.69 4.85
4389 5337 1.927527 ATTGCTCAGGGGTCTGCCT 60.928 57.895 0.00 0.00 40.69 4.75
4390 5338 1.504275 ATTGCTCAGGGGTCTGCCTT 61.504 55.000 0.00 0.00 40.69 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.523072 CCTTCCACAAGCGTCATTGG 59.477 55.000 2.96 0.00 34.36 3.16
20 21 0.543749 CCATGGACAGGGTCTCCTTC 59.456 60.000 5.56 0.00 42.67 3.46
32 33 1.141657 TGATCTAGGCTTGCCATGGAC 59.858 52.381 18.40 7.64 0.00 4.02
44 45 3.386402 GGAGAGAAAGGTGGTGATCTAGG 59.614 52.174 0.00 0.00 0.00 3.02
60 61 0.039764 ACACGGGAGACATGGAGAGA 59.960 55.000 0.00 0.00 0.00 3.10
65 66 1.676678 ATCGGACACGGGAGACATGG 61.677 60.000 0.00 0.00 41.39 3.66
106 108 2.393764 CAACATGTTCGTTCCCTTTGC 58.606 47.619 8.48 0.00 0.00 3.68
108 110 1.960689 CCCAACATGTTCGTTCCCTTT 59.039 47.619 8.48 0.00 0.00 3.11
113 115 1.535462 CCACTCCCAACATGTTCGTTC 59.465 52.381 8.48 0.00 0.00 3.95
120 122 0.249120 TAGTCGCCACTCCCAACATG 59.751 55.000 0.00 0.00 33.62 3.21
122 124 0.249120 CATAGTCGCCACTCCCAACA 59.751 55.000 0.00 0.00 33.62 3.33
124 126 1.271856 TTCATAGTCGCCACTCCCAA 58.728 50.000 0.00 0.00 33.62 4.12
125 127 1.207089 CTTTCATAGTCGCCACTCCCA 59.793 52.381 0.00 0.00 33.62 4.37
138 148 4.666412 TGGTTTGGATGTCCCTTTCATA 57.334 40.909 0.00 0.00 35.38 2.15
143 153 1.970640 GCTTTGGTTTGGATGTCCCTT 59.029 47.619 0.00 0.00 35.38 3.95
184 194 1.982938 GAGCCCGGTGTCTACCTGT 60.983 63.158 0.00 0.00 45.22 4.00
250 260 7.958088 AGGAGTATCTCATAAAACTCTAAGCC 58.042 38.462 0.00 0.00 38.69 4.35
269 279 9.755804 CAGAATACCGTATACGATATAGGAGTA 57.244 37.037 26.37 16.09 43.02 2.59
270 280 8.263640 ACAGAATACCGTATACGATATAGGAGT 58.736 37.037 26.37 14.52 43.02 3.85
271 281 8.549548 CACAGAATACCGTATACGATATAGGAG 58.450 40.741 26.37 12.04 43.02 3.69
272 282 8.043113 ACACAGAATACCGTATACGATATAGGA 58.957 37.037 26.37 6.35 43.02 2.94
273 283 8.206325 ACACAGAATACCGTATACGATATAGG 57.794 38.462 26.37 13.67 43.02 2.57
274 284 9.096160 AGACACAGAATACCGTATACGATATAG 57.904 37.037 26.37 14.28 43.02 1.31
281 291 6.696148 CCAGAAAGACACAGAATACCGTATAC 59.304 42.308 0.00 0.00 0.00 1.47
461 476 2.100584 TCCATTGCCCGCAACAATAATC 59.899 45.455 3.85 0.00 38.88 1.75
618 639 2.747686 GGCGGAAACAGGAGGTCA 59.252 61.111 0.00 0.00 0.00 4.02
759 782 1.005630 GGATCTCGCGAATGGAGGG 60.006 63.158 11.33 0.00 32.34 4.30
957 1420 4.856801 CAGATCCGGCCCCCAACG 62.857 72.222 0.00 0.00 0.00 4.10
986 1449 5.172205 GGAATCCCATTTCGCTAGATCTAC 58.828 45.833 0.00 0.00 0.00 2.59
1052 1515 3.393970 TGCTCTTCCTCCCGGCTG 61.394 66.667 0.00 0.00 0.00 4.85
1131 1594 1.691434 AGGATCCGCATCTCCTTCTTC 59.309 52.381 5.98 0.00 38.81 2.87
1173 1636 1.290134 AGAGGATGGTGGTCTTTCCC 58.710 55.000 0.00 0.00 34.77 3.97
1303 1770 2.872858 GTTCCGCTACAGATTCCCAATC 59.127 50.000 0.00 0.00 38.20 2.67
1403 1870 8.722480 ACATACCCATTGATATCGTCATATTG 57.278 34.615 0.00 0.00 36.54 1.90
1411 1878 6.697395 TCCAACTACATACCCATTGATATCG 58.303 40.000 0.00 0.00 0.00 2.92
1413 1880 8.218423 TCATCCAACTACATACCCATTGATAT 57.782 34.615 0.00 0.00 0.00 1.63
1417 1884 6.537355 AGATCATCCAACTACATACCCATTG 58.463 40.000 0.00 0.00 0.00 2.82
1487 1955 3.510753 TGAACATAAGTGCACTACCCGTA 59.489 43.478 22.01 8.85 0.00 4.02
1523 1994 4.272504 TCAGATTTGTCTGTCGTTTTGTCC 59.727 41.667 5.45 0.00 38.75 4.02
1528 1999 6.867662 AAATCTCAGATTTGTCTGTCGTTT 57.132 33.333 12.08 3.29 38.75 3.60
1541 2012 7.876936 ATGCAACAACTGATAAATCTCAGAT 57.123 32.000 8.01 0.00 44.48 2.90
1545 2016 8.976986 AAGAAATGCAACAACTGATAAATCTC 57.023 30.769 0.00 0.00 0.00 2.75
1553 2024 9.677567 GTTATAAGAAAGAAATGCAACAACTGA 57.322 29.630 0.00 0.00 0.00 3.41
1555 2026 8.637986 TGGTTATAAGAAAGAAATGCAACAACT 58.362 29.630 0.00 0.00 0.00 3.16
1611 2082 8.531982 CCCAGGATCGATTTTCTTATGTCTATA 58.468 37.037 0.00 0.00 0.00 1.31
1612 2083 7.390027 CCCAGGATCGATTTTCTTATGTCTAT 58.610 38.462 0.00 0.00 0.00 1.98
1613 2084 6.741521 GCCCAGGATCGATTTTCTTATGTCTA 60.742 42.308 0.00 0.00 0.00 2.59
1614 2085 5.615289 CCCAGGATCGATTTTCTTATGTCT 58.385 41.667 0.00 0.00 0.00 3.41
1615 2086 4.214332 GCCCAGGATCGATTTTCTTATGTC 59.786 45.833 0.00 0.00 0.00 3.06
1616 2087 4.137543 GCCCAGGATCGATTTTCTTATGT 58.862 43.478 0.00 0.00 0.00 2.29
1617 2088 4.392940 AGCCCAGGATCGATTTTCTTATG 58.607 43.478 0.00 0.00 0.00 1.90
1618 2089 4.713792 AGCCCAGGATCGATTTTCTTAT 57.286 40.909 0.00 0.00 0.00 1.73
1630 2101 2.334023 GAAGGACATCTAGCCCAGGAT 58.666 52.381 0.00 0.00 0.00 3.24
1650 2121 3.982576 AAAGTAACTGGAACTTTGCCG 57.017 42.857 8.32 0.00 43.66 5.69
1654 2125 6.370453 ACCATACCAAAGTAACTGGAACTTT 58.630 36.000 0.00 4.42 45.64 2.66
1713 2184 7.584108 TGTTTGTTACTATCAATGACTTGCTG 58.416 34.615 0.00 0.00 32.11 4.41
1742 2213 3.136443 TGACTTCCTGTTGGCATATAGGG 59.864 47.826 10.95 0.65 0.00 3.53
1833 2305 5.661056 TCAGTGTACTTTGAGATAGGGTG 57.339 43.478 0.00 0.00 0.00 4.61
1884 2356 2.950975 TGACATTCAAAGCAAGCAGTCA 59.049 40.909 0.00 0.00 32.91 3.41
1897 2369 9.917129 GCAAATTATATCATCCAATGACATTCA 57.083 29.630 0.00 0.00 43.01 2.57
1899 2371 8.872134 TGGCAAATTATATCATCCAATGACATT 58.128 29.630 0.00 0.00 43.01 2.71
1917 2389 7.173218 CACACGAGGATATTATACTGGCAAATT 59.827 37.037 0.00 0.00 0.00 1.82
2008 2480 5.712152 AACAAATGTCCAAATCTGACCTC 57.288 39.130 0.00 0.00 31.60 3.85
2178 2712 2.287788 ACAATTCAGTTTCAAGGCGCAG 60.288 45.455 10.83 0.00 0.00 5.18
2305 2839 9.069082 GGTGTGAGATACTAGTACATCATTAGT 57.931 37.037 17.44 0.00 34.36 2.24
2306 2840 9.290988 AGGTGTGAGATACTAGTACATCATTAG 57.709 37.037 17.44 0.00 0.00 1.73
2308 2842 9.642343 TTAGGTGTGAGATACTAGTACATCATT 57.358 33.333 17.44 9.57 0.00 2.57
2309 2843 9.815306 ATTAGGTGTGAGATACTAGTACATCAT 57.185 33.333 17.44 8.03 0.00 2.45
2310 2844 9.642343 AATTAGGTGTGAGATACTAGTACATCA 57.358 33.333 4.31 9.52 0.00 3.07
2313 2847 9.696572 AGAAATTAGGTGTGAGATACTAGTACA 57.303 33.333 4.31 0.00 0.00 2.90
2322 2856 8.768397 TGGTGTATTAGAAATTAGGTGTGAGAT 58.232 33.333 0.00 0.00 0.00 2.75
2323 2857 8.141298 TGGTGTATTAGAAATTAGGTGTGAGA 57.859 34.615 0.00 0.00 0.00 3.27
2324 2858 8.830580 CATGGTGTATTAGAAATTAGGTGTGAG 58.169 37.037 0.00 0.00 0.00 3.51
2325 2859 7.773224 CCATGGTGTATTAGAAATTAGGTGTGA 59.227 37.037 2.57 0.00 0.00 3.58
2326 2860 7.773224 TCCATGGTGTATTAGAAATTAGGTGTG 59.227 37.037 12.58 0.00 0.00 3.82
2327 2861 7.867921 TCCATGGTGTATTAGAAATTAGGTGT 58.132 34.615 12.58 0.00 0.00 4.16
2328 2862 8.621286 GTTCCATGGTGTATTAGAAATTAGGTG 58.379 37.037 12.58 0.00 0.00 4.00
2329 2863 8.333235 TGTTCCATGGTGTATTAGAAATTAGGT 58.667 33.333 12.58 0.00 0.00 3.08
2330 2864 8.746052 TGTTCCATGGTGTATTAGAAATTAGG 57.254 34.615 12.58 0.00 0.00 2.69
2337 2871 9.387397 TCCTATATTGTTCCATGGTGTATTAGA 57.613 33.333 12.58 0.00 0.00 2.10
2340 2874 9.881773 AATTCCTATATTGTTCCATGGTGTATT 57.118 29.630 12.58 0.00 0.00 1.89
2341 2875 9.300681 CAATTCCTATATTGTTCCATGGTGTAT 57.699 33.333 12.58 6.93 32.17 2.29
2342 2876 8.278639 ACAATTCCTATATTGTTCCATGGTGTA 58.721 33.333 12.58 0.00 44.18 2.90
2343 2877 7.125391 ACAATTCCTATATTGTTCCATGGTGT 58.875 34.615 12.58 0.00 44.18 4.16
2344 2878 7.587037 ACAATTCCTATATTGTTCCATGGTG 57.413 36.000 12.58 0.00 44.18 4.17
2357 2891 9.169592 GCAGGTACTACAAAAACAATTCCTATA 57.830 33.333 0.00 0.00 36.02 1.31
2358 2892 7.668052 TGCAGGTACTACAAAAACAATTCCTAT 59.332 33.333 0.00 0.00 36.02 2.57
2359 2893 6.999272 TGCAGGTACTACAAAAACAATTCCTA 59.001 34.615 0.00 0.00 36.02 2.94
2360 2894 5.830991 TGCAGGTACTACAAAAACAATTCCT 59.169 36.000 0.00 0.00 36.02 3.36
2361 2895 6.079424 TGCAGGTACTACAAAAACAATTCC 57.921 37.500 0.00 0.00 36.02 3.01
2362 2896 9.855021 ATATTGCAGGTACTACAAAAACAATTC 57.145 29.630 0.00 0.00 45.63 2.17
2366 2900 9.674068 TCATATATTGCAGGTACTACAAAAACA 57.326 29.630 0.00 0.00 45.63 2.83
2369 2903 9.845740 ACATCATATATTGCAGGTACTACAAAA 57.154 29.630 0.00 0.00 45.63 2.44
2371 2905 9.923143 GTACATCATATATTGCAGGTACTACAA 57.077 33.333 0.00 0.00 46.63 2.41
2372 2906 9.309224 AGTACATCATATATTGCAGGTACTACA 57.691 33.333 9.99 0.00 36.02 2.74
2375 2909 9.535170 ACTAGTACATCATATATTGCAGGTACT 57.465 33.333 13.82 13.82 37.10 2.73
2402 2936 8.768397 TGGTGTATTAGAAATTAGGTGTGAGAT 58.232 33.333 0.00 0.00 0.00 2.75
2407 2941 7.867921 TCCATGGTGTATTAGAAATTAGGTGT 58.132 34.615 12.58 0.00 0.00 4.16
2469 3003 9.642343 TTAGGTGTGAGATACTAGTACATCATT 57.358 33.333 17.44 9.57 0.00 2.57
2727 3261 6.107343 GGACCCTTTGAGTAGTGTAAGAATC 58.893 44.000 0.00 0.00 0.00 2.52
2741 3275 1.002069 ATGCAGATGGGACCCTTTGA 58.998 50.000 13.00 0.00 0.00 2.69
2745 3279 1.898863 AGTAATGCAGATGGGACCCT 58.101 50.000 13.00 0.00 0.00 4.34
2797 3331 3.206150 ACCAGTGAACATGTGAACTGTC 58.794 45.455 27.02 11.67 38.68 3.51
2991 3525 9.896645 ATAATGACAAGGATGACCATCATATAC 57.103 33.333 11.59 1.62 37.20 1.47
3000 3534 5.239525 GCCAGTTATAATGACAAGGATGACC 59.760 44.000 0.00 0.00 0.00 4.02
3076 3613 1.386533 AGGGCAGCAGATCAATTTCG 58.613 50.000 0.00 0.00 0.00 3.46
3242 4029 5.431765 CAAGGAAGTCTATGCATACCTTGT 58.568 41.667 28.56 10.19 44.15 3.16
3265 4053 3.105937 GCAAGTTTTCAAGACAACCGAC 58.894 45.455 0.00 0.00 0.00 4.79
3359 4198 1.068333 AGCACACGTTCAAATGGATGC 60.068 47.619 0.00 5.15 32.95 3.91
3377 4217 4.159120 GACGAAAATTTAGGACTGCAAGC 58.841 43.478 0.00 0.00 37.60 4.01
3527 4367 2.811101 CCGGAGCTGGCTCAGTAG 59.189 66.667 21.75 10.89 44.40 2.57
3601 4441 7.727181 ACTCTCTTTAGCTGTTTACTTCAGAA 58.273 34.615 0.00 0.00 35.20 3.02
3602 4442 7.291411 ACTCTCTTTAGCTGTTTACTTCAGA 57.709 36.000 0.00 0.00 35.20 3.27
3603 4443 6.588373 GGACTCTCTTTAGCTGTTTACTTCAG 59.412 42.308 0.00 0.00 36.18 3.02
3652 4492 4.669206 AGATAGACAGACAGATGCTTGG 57.331 45.455 0.00 0.00 0.00 3.61
3666 4514 9.906660 GCTGAATATATACAGGCATAGATAGAC 57.093 37.037 0.00 0.00 35.05 2.59
3700 4549 5.295540 ACCAACAAATGCGCAAATAAAAGTT 59.704 32.000 17.11 9.90 0.00 2.66
3722 4571 1.628846 TCTTCTTCCCCAAGTGCTACC 59.371 52.381 0.00 0.00 0.00 3.18
3735 4584 9.685828 AAAGCATATCGTACTCTTATCTTCTTC 57.314 33.333 0.00 0.00 0.00 2.87
3744 4593 7.849804 AATGTGAAAAGCATATCGTACTCTT 57.150 32.000 0.00 0.00 0.00 2.85
3745 4594 8.198109 AGTAATGTGAAAAGCATATCGTACTCT 58.802 33.333 0.00 0.00 0.00 3.24
3746 4595 8.354011 AGTAATGTGAAAAGCATATCGTACTC 57.646 34.615 0.00 0.00 0.00 2.59
3762 4611 7.337938 TGCTTATCCTCATCAAAGTAATGTGA 58.662 34.615 0.00 0.00 0.00 3.58
3763 4612 7.558161 TGCTTATCCTCATCAAAGTAATGTG 57.442 36.000 0.00 0.00 0.00 3.21
3764 4613 7.230108 CCATGCTTATCCTCATCAAAGTAATGT 59.770 37.037 0.00 0.00 0.00 2.71
3765 4614 7.446319 TCCATGCTTATCCTCATCAAAGTAATG 59.554 37.037 0.00 0.00 0.00 1.90
3766 4615 7.520798 TCCATGCTTATCCTCATCAAAGTAAT 58.479 34.615 0.00 0.00 0.00 1.89
3767 4616 6.899089 TCCATGCTTATCCTCATCAAAGTAA 58.101 36.000 0.00 0.00 0.00 2.24
3768 4617 6.499106 TCCATGCTTATCCTCATCAAAGTA 57.501 37.500 0.00 0.00 0.00 2.24
3769 4618 5.378230 TCCATGCTTATCCTCATCAAAGT 57.622 39.130 0.00 0.00 0.00 2.66
3770 4619 5.826737 AGTTCCATGCTTATCCTCATCAAAG 59.173 40.000 0.00 0.00 0.00 2.77
3792 4641 1.109323 GGGTGTGCCTTTTGAGCAGT 61.109 55.000 0.00 0.00 41.87 4.40
3802 4651 2.943369 TTTGCCATGTGGGTGTGCCT 62.943 55.000 0.54 0.00 39.65 4.75
3804 4653 1.005867 CTTTGCCATGTGGGTGTGC 60.006 57.895 0.54 0.00 39.65 4.57
3805 4654 0.314935 GTCTTTGCCATGTGGGTGTG 59.685 55.000 0.54 0.00 39.65 3.82
3806 4655 1.172180 CGTCTTTGCCATGTGGGTGT 61.172 55.000 0.54 0.00 39.65 4.16
3807 4656 0.888736 TCGTCTTTGCCATGTGGGTG 60.889 55.000 0.54 0.00 39.65 4.61
3808 4657 0.606401 CTCGTCTTTGCCATGTGGGT 60.606 55.000 0.54 0.00 39.65 4.51
3810 4659 1.466167 CTTCTCGTCTTTGCCATGTGG 59.534 52.381 0.00 0.00 38.53 4.17
3813 4662 1.813513 ACCTTCTCGTCTTTGCCATG 58.186 50.000 0.00 0.00 0.00 3.66
3815 4664 1.542547 GGAACCTTCTCGTCTTTGCCA 60.543 52.381 0.00 0.00 0.00 4.92
3816 4665 1.157585 GGAACCTTCTCGTCTTTGCC 58.842 55.000 0.00 0.00 0.00 4.52
3818 4667 5.298347 ACTTAAGGAACCTTCTCGTCTTTG 58.702 41.667 9.50 0.00 37.47 2.77
3819 4668 5.539979 GACTTAAGGAACCTTCTCGTCTTT 58.460 41.667 9.50 0.00 37.47 2.52
3833 4695 4.546829 ACTTTGTATGCCGACTTAAGGA 57.453 40.909 7.53 0.00 0.00 3.36
3858 4789 1.683011 CCTTCCAATCCGCACCTGATT 60.683 52.381 0.00 0.00 32.77 2.57
3870 4801 4.538089 AGCTCCTAACTTTCTCCTTCCAAT 59.462 41.667 0.00 0.00 0.00 3.16
3905 4836 2.673523 CCTCCCTGGGCAGTTCTG 59.326 66.667 8.22 0.00 0.00 3.02
3974 4905 3.605749 TTCCACACCGCCAGCTAGC 62.606 63.158 6.62 6.62 0.00 3.42
3975 4906 1.741770 GTTCCACACCGCCAGCTAG 60.742 63.158 0.00 0.00 0.00 3.42
3976 4907 1.764571 AAGTTCCACACCGCCAGCTA 61.765 55.000 0.00 0.00 0.00 3.32
3979 4910 0.817634 TCAAAGTTCCACACCGCCAG 60.818 55.000 0.00 0.00 0.00 4.85
3980 4911 0.179004 ATCAAAGTTCCACACCGCCA 60.179 50.000 0.00 0.00 0.00 5.69
4023 4954 4.593206 AGATCGGGCACTATTATTCCTCAA 59.407 41.667 0.00 0.00 0.00 3.02
4024 4955 4.160329 AGATCGGGCACTATTATTCCTCA 58.840 43.478 0.00 0.00 0.00 3.86
4025 4956 4.382147 GGAGATCGGGCACTATTATTCCTC 60.382 50.000 0.00 0.00 0.00 3.71
4029 4960 3.008049 GGTGGAGATCGGGCACTATTATT 59.992 47.826 0.00 0.00 0.00 1.40
4031 4962 1.968493 GGTGGAGATCGGGCACTATTA 59.032 52.381 0.00 0.00 0.00 0.98
4033 4964 0.105453 AGGTGGAGATCGGGCACTAT 60.105 55.000 0.00 0.00 0.00 2.12
4034 4965 1.043116 CAGGTGGAGATCGGGCACTA 61.043 60.000 0.00 0.00 0.00 2.74
4064 5002 1.741401 CGCATCCTCGTTTGCTCCA 60.741 57.895 0.00 0.00 36.71 3.86
4180 5125 2.046314 ACCATTCCCCGACAAGCG 60.046 61.111 0.00 0.00 40.47 4.68
4181 5126 2.106683 CGACCATTCCCCGACAAGC 61.107 63.158 0.00 0.00 0.00 4.01
4182 5127 1.449601 CCGACCATTCCCCGACAAG 60.450 63.158 0.00 0.00 0.00 3.16
4183 5128 1.481901 TTCCGACCATTCCCCGACAA 61.482 55.000 0.00 0.00 0.00 3.18
4184 5129 1.268992 ATTCCGACCATTCCCCGACA 61.269 55.000 0.00 0.00 0.00 4.35
4185 5130 0.107361 AATTCCGACCATTCCCCGAC 60.107 55.000 0.00 0.00 0.00 4.79
4186 5131 1.498264 TAATTCCGACCATTCCCCGA 58.502 50.000 0.00 0.00 0.00 5.14
4187 5132 2.561478 ATAATTCCGACCATTCCCCG 57.439 50.000 0.00 0.00 0.00 5.73
4216 5161 2.250924 AGGCAGCTTTGTTTGGCTTAT 58.749 42.857 0.00 0.00 46.63 1.73
4218 5163 2.519937 AGGCAGCTTTGTTTGGCTT 58.480 47.368 0.00 0.00 46.63 4.35
4257 5205 5.431765 AGACATTCAACATCACCTATGGTC 58.568 41.667 0.00 0.00 40.16 4.02
4299 5247 1.531739 GCATCACCTCCCCGCAAAAA 61.532 55.000 0.00 0.00 0.00 1.94
4300 5248 1.976474 GCATCACCTCCCCGCAAAA 60.976 57.895 0.00 0.00 0.00 2.44
4301 5249 2.361104 GCATCACCTCCCCGCAAA 60.361 61.111 0.00 0.00 0.00 3.68
4302 5250 3.329889 AGCATCACCTCCCCGCAA 61.330 61.111 0.00 0.00 0.00 4.85
4303 5251 4.100084 CAGCATCACCTCCCCGCA 62.100 66.667 0.00 0.00 0.00 5.69
4304 5252 2.615227 ATTCAGCATCACCTCCCCGC 62.615 60.000 0.00 0.00 0.00 6.13
4305 5253 0.816825 CATTCAGCATCACCTCCCCG 60.817 60.000 0.00 0.00 0.00 5.73
4306 5254 0.257039 ACATTCAGCATCACCTCCCC 59.743 55.000 0.00 0.00 0.00 4.81
4307 5255 1.673168 GACATTCAGCATCACCTCCC 58.327 55.000 0.00 0.00 0.00 4.30
4308 5256 1.134699 TCGACATTCAGCATCACCTCC 60.135 52.381 0.00 0.00 0.00 4.30
4309 5257 1.929836 GTCGACATTCAGCATCACCTC 59.070 52.381 11.55 0.00 0.00 3.85
4310 5258 1.737029 CGTCGACATTCAGCATCACCT 60.737 52.381 17.16 0.00 0.00 4.00
4311 5259 0.647410 CGTCGACATTCAGCATCACC 59.353 55.000 17.16 0.00 0.00 4.02
4312 5260 0.025513 GCGTCGACATTCAGCATCAC 59.974 55.000 17.16 0.00 0.00 3.06
4313 5261 1.083806 GGCGTCGACATTCAGCATCA 61.084 55.000 17.16 0.00 0.00 3.07
4314 5262 1.083806 TGGCGTCGACATTCAGCATC 61.084 55.000 17.16 0.00 0.00 3.91
4315 5263 1.079197 TGGCGTCGACATTCAGCAT 60.079 52.632 17.16 0.00 0.00 3.79
4316 5264 2.027073 GTGGCGTCGACATTCAGCA 61.027 57.895 17.16 0.00 0.00 4.41
4317 5265 1.291877 AAGTGGCGTCGACATTCAGC 61.292 55.000 17.16 10.08 0.00 4.26
4318 5266 1.148310 AAAGTGGCGTCGACATTCAG 58.852 50.000 17.16 0.00 0.00 3.02
4319 5267 2.442212 TAAAGTGGCGTCGACATTCA 57.558 45.000 17.16 7.35 0.00 2.57
4320 5268 2.284417 GGATAAAGTGGCGTCGACATTC 59.716 50.000 17.16 4.64 0.00 2.67
4321 5269 2.277084 GGATAAAGTGGCGTCGACATT 58.723 47.619 17.16 0.00 0.00 2.71
4322 5270 1.472728 GGGATAAAGTGGCGTCGACAT 60.473 52.381 17.16 0.00 0.00 3.06
4323 5271 0.108520 GGGATAAAGTGGCGTCGACA 60.109 55.000 17.16 0.00 0.00 4.35
4324 5272 0.108520 TGGGATAAAGTGGCGTCGAC 60.109 55.000 5.18 5.18 0.00 4.20
4325 5273 0.609151 TTGGGATAAAGTGGCGTCGA 59.391 50.000 0.00 0.00 0.00 4.20
4326 5274 1.129811 GTTTGGGATAAAGTGGCGTCG 59.870 52.381 0.00 0.00 0.00 5.12
4327 5275 2.433436 AGTTTGGGATAAAGTGGCGTC 58.567 47.619 0.00 0.00 0.00 5.19
4328 5276 2.579410 AGTTTGGGATAAAGTGGCGT 57.421 45.000 0.00 0.00 0.00 5.68
4329 5277 3.869065 TCTAGTTTGGGATAAAGTGGCG 58.131 45.455 0.00 0.00 0.00 5.69
4330 5278 4.200092 CCTCTAGTTTGGGATAAAGTGGC 58.800 47.826 0.00 0.00 0.00 5.01
4331 5279 5.045869 TCACCTCTAGTTTGGGATAAAGTGG 60.046 44.000 0.00 0.00 0.00 4.00
4332 5280 6.049955 TCACCTCTAGTTTGGGATAAAGTG 57.950 41.667 0.00 0.00 0.00 3.16
4333 5281 6.353082 CCATCACCTCTAGTTTGGGATAAAGT 60.353 42.308 0.00 0.00 0.00 2.66
4334 5282 6.058183 CCATCACCTCTAGTTTGGGATAAAG 58.942 44.000 0.00 0.00 0.00 1.85
4335 5283 5.104109 CCCATCACCTCTAGTTTGGGATAAA 60.104 44.000 0.00 0.00 46.23 1.40
4336 5284 4.412199 CCCATCACCTCTAGTTTGGGATAA 59.588 45.833 0.00 0.00 46.23 1.75
4337 5285 3.973973 CCCATCACCTCTAGTTTGGGATA 59.026 47.826 0.00 0.00 46.23 2.59
4338 5286 2.780010 CCCATCACCTCTAGTTTGGGAT 59.220 50.000 0.00 0.07 46.23 3.85
4339 5287 2.196595 CCCATCACCTCTAGTTTGGGA 58.803 52.381 0.00 0.00 46.23 4.37
4340 5288 1.212935 CCCCATCACCTCTAGTTTGGG 59.787 57.143 0.00 0.00 44.28 4.12
4341 5289 1.408822 GCCCCATCACCTCTAGTTTGG 60.409 57.143 0.00 0.00 0.00 3.28
4342 5290 1.408822 GGCCCCATCACCTCTAGTTTG 60.409 57.143 0.00 0.00 0.00 2.93
4343 5291 0.919710 GGCCCCATCACCTCTAGTTT 59.080 55.000 0.00 0.00 0.00 2.66
4344 5292 0.044855 AGGCCCCATCACCTCTAGTT 59.955 55.000 0.00 0.00 0.00 2.24
4345 5293 0.692419 CAGGCCCCATCACCTCTAGT 60.692 60.000 0.00 0.00 32.56 2.57
4346 5294 1.414061 CCAGGCCCCATCACCTCTAG 61.414 65.000 0.00 0.00 32.56 2.43
4347 5295 1.384502 CCAGGCCCCATCACCTCTA 60.385 63.158 0.00 0.00 32.56 2.43
4348 5296 2.693864 CCAGGCCCCATCACCTCT 60.694 66.667 0.00 0.00 32.56 3.69
4349 5297 3.813724 CCCAGGCCCCATCACCTC 61.814 72.222 0.00 0.00 32.56 3.85
4362 5310 3.515286 CTGAGCAATGCGGCCCAG 61.515 66.667 0.00 2.76 0.00 4.45
4367 5315 2.825836 GACCCCTGAGCAATGCGG 60.826 66.667 0.00 0.00 0.00 5.69
4368 5316 2.110967 CAGACCCCTGAGCAATGCG 61.111 63.158 0.00 0.00 43.02 4.73
4369 5317 2.413142 GCAGACCCCTGAGCAATGC 61.413 63.158 0.00 0.00 43.02 3.56
4370 5318 1.751927 GGCAGACCCCTGAGCAATG 60.752 63.158 0.00 0.00 43.02 2.82
4371 5319 1.504275 AAGGCAGACCCCTGAGCAAT 61.504 55.000 0.00 0.00 43.02 3.56
4372 5320 2.156098 AAGGCAGACCCCTGAGCAA 61.156 57.895 0.00 0.00 43.02 3.91
4373 5321 2.530151 AAGGCAGACCCCTGAGCA 60.530 61.111 0.00 0.00 43.02 4.26


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

AutoCloner maintained by Alex Coulton.