Multiple sequence alignment - TraesCS1B01G300100

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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 TraesCS1B01G300100 chr1B 100.000 4789 0 0 1 4789 520816642 520811854 0.000000e+00 8844.0
1 TraesCS1B01G300100 chr1D 91.633 1984 107 26 375 2338 387434874 387432930 0.000000e+00 2689.0
2 TraesCS1B01G300100 chr1D 90.239 922 43 24 3070 3983 387432026 387431144 0.000000e+00 1160.0
3 TraesCS1B01G300100 chr1D 81.901 547 79 12 3987 4519 285110091 285110631 1.220000e-120 444.0
4 TraesCS1B01G300100 chr1D 81.509 530 67 22 3981 4491 127840442 127839925 1.600000e-109 407.0
5 TraesCS1B01G300100 chr1D 85.013 387 38 9 1 370 387435337 387434954 4.520000e-100 375.0
6 TraesCS1B01G300100 chr1D 86.614 127 14 3 3985 4110 49955595 49955471 2.320000e-28 137.0
7 TraesCS1B01G300100 chr1A 89.355 1907 142 34 1153 3041 487103329 487101466 0.000000e+00 2340.0
8 TraesCS1B01G300100 chr1A 93.369 935 36 18 3058 3983 487101395 487100478 0.000000e+00 1360.0
9 TraesCS1B01G300100 chr1A 94.196 672 24 6 375 1032 487104060 487103390 0.000000e+00 1011.0
10 TraesCS1B01G300100 chr1A 85.019 267 33 7 4525 4787 23017536 23017799 1.020000e-66 265.0
11 TraesCS1B01G300100 chr1A 83.636 275 35 10 4519 4787 10434809 10434539 2.860000e-62 250.0
12 TraesCS1B01G300100 chr1A 97.674 43 1 0 1059 1101 487103384 487103342 1.850000e-09 75.0
13 TraesCS1B01G300100 chr2D 87.183 671 70 13 4126 4789 103478525 103479186 0.000000e+00 749.0
14 TraesCS1B01G300100 chr2D 83.641 434 58 12 4246 4677 573838256 573838678 3.470000e-106 396.0
15 TraesCS1B01G300100 chr2D 79.890 547 57 27 3979 4520 625626959 625626461 7.630000e-93 351.0
16 TraesCS1B01G300100 chr5B 86.510 682 62 18 4133 4789 463161564 463160888 0.000000e+00 723.0
17 TraesCS1B01G300100 chr5B 80.364 550 80 18 3990 4520 398441622 398441082 4.490000e-105 392.0
18 TraesCS1B01G300100 chr5B 85.000 260 31 8 4534 4789 15329074 15329329 1.710000e-64 257.0
19 TraesCS1B01G300100 chr6B 78.129 823 129 36 3985 4785 415462491 415463284 4.340000e-130 475.0
20 TraesCS1B01G300100 chr6D 81.919 542 78 14 3985 4512 473301600 473301065 1.580000e-119 440.0
21 TraesCS1B01G300100 chr6D 80.901 466 58 20 4062 4512 143661245 143660796 5.940000e-89 339.0
22 TraesCS1B01G300100 chr6D 84.615 260 33 7 4534 4789 143660489 143660233 7.960000e-63 252.0
23 TraesCS1B01G300100 chr6D 87.755 49 6 0 4062 4110 473300506 473300554 1.860000e-04 58.4
24 TraesCS1B01G300100 chr7A 81.970 538 74 21 3988 4512 100549325 100549852 7.360000e-118 435.0
25 TraesCS1B01G300100 chr7A 84.672 274 33 9 4519 4787 100550172 100550441 1.020000e-66 265.0
26 TraesCS1B01G300100 chr4D 77.146 827 122 43 3985 4789 318469855 318470636 7.410000e-113 418.0
27 TraesCS1B01G300100 chr4D 76.259 834 139 43 3981 4789 117711795 117710996 5.810000e-104 388.0
28 TraesCS1B01G300100 chr4D 74.329 857 136 49 3985 4789 318471024 318470200 2.180000e-73 287.0
29 TraesCS1B01G300100 chr4D 79.070 215 39 5 3985 4197 506609920 506609710 5.000000e-30 143.0
30 TraesCS1B01G300100 chr4D 85.333 75 11 0 1700 1774 498686114 498686040 1.430000e-10 78.7
31 TraesCS1B01G300100 chr4B 77.051 841 117 45 3986 4788 613291644 613292446 9.590000e-112 414.0
32 TraesCS1B01G300100 chr4B 80.328 549 77 21 3981 4512 179845536 179845002 2.090000e-103 387.0
33 TraesCS1B01G300100 chr4B 85.333 75 11 0 1700 1774 640824013 640823939 1.430000e-10 78.7
34 TraesCS1B01G300100 chr2A 80.917 545 78 23 3985 4512 742780761 742780226 1.600000e-109 407.0
35 TraesCS1B01G300100 chr5A 80.699 544 80 20 3985 4512 239404553 239404019 2.690000e-107 399.0
36 TraesCS1B01G300100 chr5A 83.102 432 56 12 3985 4406 43543636 43543212 1.260000e-100 377.0
37 TraesCS1B01G300100 chr7B 91.186 295 21 4 4321 4615 498966560 498966271 3.470000e-106 396.0
38 TraesCS1B01G300100 chr7B 78.926 503 81 16 3985 4471 466711208 466711701 7.730000e-83 318.0
39 TraesCS1B01G300100 chr4A 75.747 837 137 44 3981 4789 641478661 641479459 1.270000e-95 361.0
40 TraesCS1B01G300100 chr4A 79.740 538 69 25 3985 4512 25796094 25795587 2.120000e-93 353.0
41 TraesCS1B01G300100 chr4A 79.923 518 52 30 3986 4499 641479888 641479419 2.760000e-87 333.0
42 TraesCS1B01G300100 chr3D 81.104 471 66 16 4063 4519 611021703 611021242 5.890000e-94 355.0
43 TraesCS1B01G300100 chr3D 78.277 534 80 23 3985 4512 507767927 507767424 1.290000e-80 311.0
44 TraesCS1B01G300100 chr3D 71.184 760 148 48 4053 4782 494651040 494651758 1.810000e-24 124.0
45 TraesCS1B01G300100 chr7D 86.486 259 30 5 4534 4789 265265990 265266246 3.650000e-71 279.0


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 TraesCS1B01G300100 chr1B 520811854 520816642 4788 True 8844.0 8844 100.000000 1 4789 1 chr1B.!!$R1 4788
1 TraesCS1B01G300100 chr1D 387431144 387435337 4193 True 1408.0 2689 88.961667 1 3983 3 chr1D.!!$R3 3982
2 TraesCS1B01G300100 chr1D 285110091 285110631 540 False 444.0 444 81.901000 3987 4519 1 chr1D.!!$F1 532
3 TraesCS1B01G300100 chr1D 127839925 127840442 517 True 407.0 407 81.509000 3981 4491 1 chr1D.!!$R2 510
4 TraesCS1B01G300100 chr1A 487100478 487104060 3582 True 1196.5 2340 93.648500 375 3983 4 chr1A.!!$R2 3608
5 TraesCS1B01G300100 chr2D 103478525 103479186 661 False 749.0 749 87.183000 4126 4789 1 chr2D.!!$F1 663
6 TraesCS1B01G300100 chr5B 463160888 463161564 676 True 723.0 723 86.510000 4133 4789 1 chr5B.!!$R2 656
7 TraesCS1B01G300100 chr5B 398441082 398441622 540 True 392.0 392 80.364000 3990 4520 1 chr5B.!!$R1 530
8 TraesCS1B01G300100 chr6B 415462491 415463284 793 False 475.0 475 78.129000 3985 4785 1 chr6B.!!$F1 800
9 TraesCS1B01G300100 chr6D 473301065 473301600 535 True 440.0 440 81.919000 3985 4512 1 chr6D.!!$R1 527
10 TraesCS1B01G300100 chr6D 143660233 143661245 1012 True 295.5 339 82.758000 4062 4789 2 chr6D.!!$R2 727
11 TraesCS1B01G300100 chr7A 100549325 100550441 1116 False 350.0 435 83.321000 3988 4787 2 chr7A.!!$F1 799
12 TraesCS1B01G300100 chr4D 318469855 318470636 781 False 418.0 418 77.146000 3985 4789 1 chr4D.!!$F1 804
13 TraesCS1B01G300100 chr4D 117710996 117711795 799 True 388.0 388 76.259000 3981 4789 1 chr4D.!!$R1 808
14 TraesCS1B01G300100 chr4D 318470200 318471024 824 True 287.0 287 74.329000 3985 4789 1 chr4D.!!$R2 804
15 TraesCS1B01G300100 chr4B 613291644 613292446 802 False 414.0 414 77.051000 3986 4788 1 chr4B.!!$F1 802
16 TraesCS1B01G300100 chr4B 179845002 179845536 534 True 387.0 387 80.328000 3981 4512 1 chr4B.!!$R1 531
17 TraesCS1B01G300100 chr2A 742780226 742780761 535 True 407.0 407 80.917000 3985 4512 1 chr2A.!!$R1 527
18 TraesCS1B01G300100 chr5A 239404019 239404553 534 True 399.0 399 80.699000 3985 4512 1 chr5A.!!$R2 527
19 TraesCS1B01G300100 chr4A 641478661 641479459 798 False 361.0 361 75.747000 3981 4789 1 chr4A.!!$F1 808
20 TraesCS1B01G300100 chr4A 25795587 25796094 507 True 353.0 353 79.740000 3985 4512 1 chr4A.!!$R1 527
21 TraesCS1B01G300100 chr3D 507767424 507767927 503 True 311.0 311 78.277000 3985 4512 1 chr3D.!!$R1 527

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
37 38 0.106419 GGGGGAGTTTGGTTGTGTCA 60.106 55.000 0.00 0.00 0.00 3.58 F
413 505 0.106708 TCCCTGCAACAGTCAGTGAC 59.893 55.000 15.78 15.78 0.00 3.67 F
874 982 0.536006 ACTTGTTCACTGCAGGCTCC 60.536 55.000 19.93 3.70 0.00 4.70 F
2378 2500 1.202758 AGACAAAATGGTGGCAGACGA 60.203 47.619 0.00 0.00 0.00 4.20 F
2505 2634 0.027979 CGTGCGCACAAATATGGGAG 59.972 55.000 37.03 15.14 34.56 4.30 F
2623 2754 0.030195 TCCCATGGGAGCACCTGATA 60.030 55.000 30.62 2.96 39.76 2.15 F
3607 4118 0.102663 TCAACGTCAAGGTACGCACA 59.897 50.000 0.00 0.00 46.71 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1800 1.079543 CACCTCCTCGCTGGTCTTG 60.080 63.158 0.00 0.00 33.75 3.02 R
2410 2533 0.172578 TGGGAGCGTGTCTCAATACG 59.827 55.000 0.00 0.00 43.70 3.06 R
2487 2616 0.248621 GCTCCCATATTTGTGCGCAC 60.249 55.000 33.11 33.11 0.00 5.34 R
3349 3860 0.107703 GGTCGATCATCACCTTGGCA 60.108 55.000 0.00 0.00 0.00 4.92 R
3613 4124 0.248215 GATCTGCGTTCAATTGGCGG 60.248 55.000 19.35 13.96 0.00 6.13 R
3658 4178 0.741221 GATCCGGCGCTCAGTTTCTT 60.741 55.000 7.64 0.00 0.00 2.52 R
4683 5974 9.658475 TGTTGAATAAGTATTTGAAAACTGTCG 57.342 29.630 0.00 0.00 0.00 4.35 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 2.356125 CCACAGTCAAGATGTAAGGGGG 60.356 54.545 0.00 0.00 0.00 5.40
24 25 2.840651 ACAGTCAAGATGTAAGGGGGAG 59.159 50.000 0.00 0.00 0.00 4.30
36 37 0.185175 AGGGGGAGTTTGGTTGTGTC 59.815 55.000 0.00 0.00 0.00 3.67
37 38 0.106419 GGGGGAGTTTGGTTGTGTCA 60.106 55.000 0.00 0.00 0.00 3.58
42 43 3.751698 GGGAGTTTGGTTGTGTCACTATC 59.248 47.826 4.27 0.00 0.00 2.08
48 49 2.224426 TGGTTGTGTCACTATCCACCAC 60.224 50.000 4.27 0.00 0.00 4.16
55 56 2.093973 GTCACTATCCACCACAGGACAG 60.094 54.545 0.00 0.00 41.30 3.51
68 69 4.003648 CACAGGACAGGGATAAACACTTC 58.996 47.826 0.00 0.00 0.00 3.01
111 113 4.355588 TGGTTGAGGGAAAAGGAAGGATAA 59.644 41.667 0.00 0.00 0.00 1.75
151 153 8.665685 CGTGGAAATATTCTACTAAAAGTTGCT 58.334 33.333 5.30 0.00 38.81 3.91
160 162 2.737252 ACTAAAAGTTGCTCGCTACAGC 59.263 45.455 6.29 0.00 40.13 4.40
179 194 1.679032 GCACTTACATCCTGACCCCAC 60.679 57.143 0.00 0.00 0.00 4.61
205 220 1.227674 GAGCTATGACCAAGGGCCG 60.228 63.158 0.00 0.00 0.00 6.13
213 228 0.826256 GACCAAGGGCCGGTTCTTTT 60.826 55.000 1.90 0.00 36.69 2.27
218 233 0.112412 AGGGCCGGTTCTTTTGATGT 59.888 50.000 1.90 0.00 0.00 3.06
219 234 0.243636 GGGCCGGTTCTTTTGATGTG 59.756 55.000 1.90 0.00 0.00 3.21
223 238 3.501950 GCCGGTTCTTTTGATGTGATTC 58.498 45.455 1.90 0.00 0.00 2.52
228 243 6.082338 CGGTTCTTTTGATGTGATTCTGAAG 58.918 40.000 0.00 0.00 0.00 3.02
251 266 1.356059 TCATGGTCCGGGGAATCAAAA 59.644 47.619 0.00 0.00 0.00 2.44
253 268 2.137810 TGGTCCGGGGAATCAAAATC 57.862 50.000 0.00 0.00 0.00 2.17
254 269 1.356059 TGGTCCGGGGAATCAAAATCA 59.644 47.619 0.00 0.00 0.00 2.57
255 270 2.024464 TGGTCCGGGGAATCAAAATCAT 60.024 45.455 0.00 0.00 0.00 2.45
259 274 5.451381 GGTCCGGGGAATCAAAATCATAAAC 60.451 44.000 0.00 0.00 0.00 2.01
260 275 4.336993 TCCGGGGAATCAAAATCATAAACG 59.663 41.667 0.00 0.00 0.00 3.60
273 288 9.162793 CAAAATCATAAACGAACTCATCTATGC 57.837 33.333 0.00 0.00 0.00 3.14
278 293 1.414181 ACGAACTCATCTATGCCCCAG 59.586 52.381 0.00 0.00 0.00 4.45
282 297 2.711174 ACTCATCTATGCCCCAGGAAT 58.289 47.619 0.00 0.00 0.00 3.01
285 300 0.326264 ATCTATGCCCCAGGAATCGC 59.674 55.000 0.00 0.00 0.00 4.58
299 314 2.158813 GGAATCGCCTAGAATCAACCCA 60.159 50.000 0.00 0.00 30.39 4.51
301 316 0.830648 TCGCCTAGAATCAACCCAGG 59.169 55.000 0.00 0.00 0.00 4.45
306 321 2.037772 CCTAGAATCAACCCAGGATCGG 59.962 54.545 0.00 0.00 0.00 4.18
308 323 2.196595 AGAATCAACCCAGGATCGGAA 58.803 47.619 0.00 0.00 0.00 4.30
315 330 1.774254 ACCCAGGATCGGAATGCAATA 59.226 47.619 0.00 0.00 0.00 1.90
316 331 2.224621 ACCCAGGATCGGAATGCAATAG 60.225 50.000 0.00 0.00 0.00 1.73
318 333 3.496692 CCCAGGATCGGAATGCAATAGAA 60.497 47.826 0.00 0.00 0.00 2.10
319 334 4.330250 CCAGGATCGGAATGCAATAGAAT 58.670 43.478 0.00 0.00 0.00 2.40
320 335 4.394300 CCAGGATCGGAATGCAATAGAATC 59.606 45.833 0.00 0.00 0.00 2.52
321 336 4.092529 CAGGATCGGAATGCAATAGAATCG 59.907 45.833 0.00 0.00 0.00 3.34
322 337 3.997021 GGATCGGAATGCAATAGAATCGT 59.003 43.478 0.00 0.00 0.00 3.73
333 350 4.438744 GCAATAGAATCGTGGAAACTTGGG 60.439 45.833 0.00 0.00 0.00 4.12
342 359 2.820197 GTGGAAACTTGGGGATTCTGAC 59.180 50.000 0.00 0.00 0.00 3.51
346 363 2.990066 ACTTGGGGATTCTGACGATC 57.010 50.000 0.00 0.00 0.00 3.69
365 382 1.628846 TCCTAGCCAGTCCCTCAAAAC 59.371 52.381 0.00 0.00 0.00 2.43
370 387 3.103742 AGCCAGTCCCTCAAAACAAAAA 58.896 40.909 0.00 0.00 0.00 1.94
371 388 3.711190 AGCCAGTCCCTCAAAACAAAAAT 59.289 39.130 0.00 0.00 0.00 1.82
372 389 3.809279 GCCAGTCCCTCAAAACAAAAATG 59.191 43.478 0.00 0.00 0.00 2.32
388 480 0.958822 AATGTGGCCCAAAACGACTC 59.041 50.000 0.00 0.00 0.00 3.36
402 494 0.389817 CGACTCGTTCATCCCTGCAA 60.390 55.000 0.00 0.00 0.00 4.08
408 500 1.877680 CGTTCATCCCTGCAACAGTCA 60.878 52.381 0.00 0.00 0.00 3.41
413 505 0.106708 TCCCTGCAACAGTCAGTGAC 59.893 55.000 15.78 15.78 0.00 3.67
416 508 1.835483 CTGCAACAGTCAGTGACGCC 61.835 60.000 17.40 6.24 37.67 5.68
444 536 1.887854 TGTTGTATCCTGACGACCGAA 59.112 47.619 0.00 0.00 33.38 4.30
487 579 2.899256 CAGAAAAGATTTTGCCCCCTCA 59.101 45.455 0.00 0.00 0.00 3.86
501 600 1.753073 CCCCTCAGGCAATCATGTTTC 59.247 52.381 0.00 0.00 0.00 2.78
562 662 4.599047 TGCTACCACCCAAAAGAAAATG 57.401 40.909 0.00 0.00 0.00 2.32
760 860 2.175811 GTGGCGCGGTGAATTCAC 59.824 61.111 27.16 27.16 45.72 3.18
788 888 3.194755 ACCCTTTTCAATTAATGCGTCCC 59.805 43.478 0.00 0.00 0.00 4.46
874 982 0.536006 ACTTGTTCACTGCAGGCTCC 60.536 55.000 19.93 3.70 0.00 4.70
891 999 4.735132 CTCTTCCGGCGGACGCAA 62.735 66.667 31.23 13.63 44.11 4.85
1101 1212 5.576447 ATCAGTTTCGGAAGTGTTTGTTT 57.424 34.783 11.08 0.00 37.45 2.83
1102 1213 6.510478 CGATCAGTTTCGGAAGTGTTTGTTTA 60.510 38.462 11.08 0.00 37.45 2.01
1103 1214 6.114221 TCAGTTTCGGAAGTGTTTGTTTAG 57.886 37.500 11.08 0.00 37.45 1.85
1104 1215 5.644636 TCAGTTTCGGAAGTGTTTGTTTAGT 59.355 36.000 11.08 0.00 37.45 2.24
1105 1216 5.963586 CAGTTTCGGAAGTGTTTGTTTAGTC 59.036 40.000 2.83 0.00 32.61 2.59
1106 1217 5.644636 AGTTTCGGAAGTGTTTGTTTAGTCA 59.355 36.000 0.00 0.00 0.00 3.41
1107 1218 6.149807 AGTTTCGGAAGTGTTTGTTTAGTCAA 59.850 34.615 0.00 0.00 0.00 3.18
1108 1219 5.728351 TCGGAAGTGTTTGTTTAGTCAAG 57.272 39.130 0.00 0.00 0.00 3.02
1111 1222 5.064198 CGGAAGTGTTTGTTTAGTCAAGTGA 59.936 40.000 0.00 0.00 0.00 3.41
1112 1223 6.238374 CGGAAGTGTTTGTTTAGTCAAGTGAT 60.238 38.462 0.00 0.00 0.00 3.06
1113 1224 7.042321 CGGAAGTGTTTGTTTAGTCAAGTGATA 60.042 37.037 0.00 0.00 0.00 2.15
1114 1225 8.283291 GGAAGTGTTTGTTTAGTCAAGTGATAG 58.717 37.037 0.00 0.00 0.00 2.08
1115 1226 8.958119 AAGTGTTTGTTTAGTCAAGTGATAGA 57.042 30.769 0.00 0.00 0.00 1.98
1116 1227 8.366671 AGTGTTTGTTTAGTCAAGTGATAGAC 57.633 34.615 0.00 0.00 35.02 2.59
1128 1239 2.959707 AGTGATAGACTAAGCTTCGGGG 59.040 50.000 0.00 0.00 30.86 5.73
1129 1240 2.694109 GTGATAGACTAAGCTTCGGGGT 59.306 50.000 0.00 0.00 0.00 4.95
1130 1241 3.132467 GTGATAGACTAAGCTTCGGGGTT 59.868 47.826 0.00 0.00 39.19 4.11
1131 1242 3.773119 TGATAGACTAAGCTTCGGGGTTT 59.227 43.478 0.00 0.00 36.91 3.27
1132 1243 4.224370 TGATAGACTAAGCTTCGGGGTTTT 59.776 41.667 0.00 0.00 36.91 2.43
1133 1244 2.779506 AGACTAAGCTTCGGGGTTTTG 58.220 47.619 0.00 0.00 36.91 2.44
1134 1245 2.105993 AGACTAAGCTTCGGGGTTTTGT 59.894 45.455 0.00 0.00 36.91 2.83
1135 1246 3.325716 AGACTAAGCTTCGGGGTTTTGTA 59.674 43.478 0.00 0.00 36.91 2.41
1136 1247 3.405831 ACTAAGCTTCGGGGTTTTGTAC 58.594 45.455 0.00 0.00 36.91 2.90
1149 1260 4.093703 GGGTTTTGTACTTTTGTTGGTTGC 59.906 41.667 0.00 0.00 0.00 4.17
1150 1261 4.093703 GGTTTTGTACTTTTGTTGGTTGCC 59.906 41.667 0.00 0.00 0.00 4.52
1827 1938 6.370718 CCTACGTCCAAAGGGTATTTATATGC 59.629 42.308 0.00 0.00 34.93 3.14
1855 1966 3.510388 TCTCACTCGCTACCATTTCAG 57.490 47.619 0.00 0.00 0.00 3.02
1864 1979 5.516996 TCGCTACCATTTCAGTATAGTTCG 58.483 41.667 0.00 0.00 0.00 3.95
2008 2123 5.854010 TTATGTCTAAGTCGATGGAGCTT 57.146 39.130 0.00 0.00 0.00 3.74
2010 2125 3.849911 TGTCTAAGTCGATGGAGCTTTG 58.150 45.455 0.00 0.00 0.00 2.77
2072 2187 7.235079 TGGTAACATAAAAATTCCAGACCTCA 58.765 34.615 0.00 0.00 46.17 3.86
2075 2190 7.454260 AACATAAAAATTCCAGACCTCAGTC 57.546 36.000 0.00 0.00 43.89 3.51
2091 2206 7.484035 ACCTCAGTCGAATATCTAAAATTGC 57.516 36.000 0.00 0.00 0.00 3.56
2131 2246 6.983474 TTCGATCTATCAAATTGCACTGAA 57.017 33.333 0.00 0.00 0.00 3.02
2149 2264 8.646356 TGCACTGAATTTTAAAGAAATTATGCG 58.354 29.630 15.30 0.00 36.68 4.73
2182 2297 9.508642 AAATTTGGTTTGGAACTAGTTCAAAAA 57.491 25.926 30.87 26.23 42.29 1.94
2236 2351 7.992754 ATCTTGCTTAAGATATGTCAATCCC 57.007 36.000 6.67 0.00 37.72 3.85
2246 2361 6.072649 AGATATGTCAATCCCATTTGCATCA 58.927 36.000 0.00 0.00 30.99 3.07
2279 2400 6.509523 TTCCCTTCTTCCTCTACTTTGAAA 57.490 37.500 0.00 0.00 0.00 2.69
2286 2407 3.735591 TCCTCTACTTTGAAACCAACCG 58.264 45.455 0.00 0.00 0.00 4.44
2300 2421 1.801771 CCAACCGCGATTACTTTGACA 59.198 47.619 8.23 0.00 0.00 3.58
2303 2424 4.472286 CAACCGCGATTACTTTGACAATT 58.528 39.130 8.23 0.00 0.00 2.32
2318 2439 8.973182 ACTTTGACAATTTTAGGGTTAACTTGA 58.027 29.630 5.42 0.00 0.00 3.02
2346 2468 4.122046 ACATGCTCAAGGTTTTCTTTTGC 58.878 39.130 0.00 0.00 32.41 3.68
2359 2481 8.520835 GGTTTTCTTTTGCTATCAAAACCTAG 57.479 34.615 14.57 0.00 46.70 3.02
2360 2482 8.357402 GGTTTTCTTTTGCTATCAAAACCTAGA 58.643 33.333 14.57 0.00 46.70 2.43
2361 2483 9.181805 GTTTTCTTTTGCTATCAAAACCTAGAC 57.818 33.333 0.40 0.00 44.58 2.59
2362 2484 8.458573 TTTCTTTTGCTATCAAAACCTAGACA 57.541 30.769 0.40 0.00 44.58 3.41
2366 2488 9.696917 CTTTTGCTATCAAAACCTAGACAAAAT 57.303 29.630 0.40 0.00 44.58 1.82
2378 2500 1.202758 AGACAAAATGGTGGCAGACGA 60.203 47.619 0.00 0.00 0.00 4.20
2385 2507 2.029844 GGTGGCAGACGAAGCAGAC 61.030 63.158 0.00 0.00 0.00 3.51
2392 2514 2.857152 GCAGACGAAGCAGACTAGAATG 59.143 50.000 0.00 0.00 0.00 2.67
2422 2545 6.757010 ACCTTGAATATCACGTATTGAGACAC 59.243 38.462 0.00 0.00 37.77 3.67
2438 2561 3.790437 ACGCTCCCATGCTCCAGG 61.790 66.667 0.00 0.00 0.00 4.45
2458 2586 1.895707 CGGGCCATTGGATCTCAGC 60.896 63.158 6.95 0.00 0.00 4.26
2462 2590 1.595466 GCCATTGGATCTCAGCTCTG 58.405 55.000 6.95 0.00 0.00 3.35
2487 2616 3.512680 GTCATAGTCAAGTCCTTGGACG 58.487 50.000 13.41 1.79 40.78 4.79
2491 2620 1.300620 TCAAGTCCTTGGACGTGCG 60.301 57.895 24.11 11.03 40.78 5.34
2505 2634 0.027979 CGTGCGCACAAATATGGGAG 59.972 55.000 37.03 15.14 34.56 4.30
2509 2638 0.664761 CGCACAAATATGGGAGCCTG 59.335 55.000 0.00 0.00 34.56 4.85
2621 2752 2.124768 TCCCATGGGAGCACCTGA 59.875 61.111 30.62 4.68 39.76 3.86
2622 2753 1.308128 TCCCATGGGAGCACCTGAT 60.308 57.895 30.62 0.00 39.76 2.90
2623 2754 0.030195 TCCCATGGGAGCACCTGATA 60.030 55.000 30.62 2.96 39.76 2.15
2624 2755 1.070604 CCCATGGGAGCACCTGATAT 58.929 55.000 28.27 0.00 41.11 1.63
2625 2756 1.426598 CCCATGGGAGCACCTGATATT 59.573 52.381 28.27 0.00 41.11 1.28
2626 2757 2.553904 CCCATGGGAGCACCTGATATTC 60.554 54.545 28.27 0.00 41.11 1.75
2627 2758 2.374504 CCATGGGAGCACCTGATATTCT 59.625 50.000 2.85 0.00 41.11 2.40
2628 2759 3.181436 CCATGGGAGCACCTGATATTCTT 60.181 47.826 2.85 0.00 41.11 2.52
2629 2760 3.845781 TGGGAGCACCTGATATTCTTC 57.154 47.619 0.00 0.00 41.11 2.87
2630 2761 2.439507 TGGGAGCACCTGATATTCTTCC 59.560 50.000 0.00 0.00 41.11 3.46
2631 2762 2.439507 GGGAGCACCTGATATTCTTCCA 59.560 50.000 0.00 0.00 35.85 3.53
2632 2763 3.073650 GGGAGCACCTGATATTCTTCCAT 59.926 47.826 0.00 0.00 35.85 3.41
2633 2764 4.287067 GGGAGCACCTGATATTCTTCCATA 59.713 45.833 0.00 0.00 35.85 2.74
2634 2765 5.241662 GGAGCACCTGATATTCTTCCATAC 58.758 45.833 0.00 0.00 0.00 2.39
2635 2766 5.234466 AGCACCTGATATTCTTCCATACC 57.766 43.478 0.00 0.00 0.00 2.73
2636 2767 4.042187 AGCACCTGATATTCTTCCATACCC 59.958 45.833 0.00 0.00 0.00 3.69
2637 2768 4.807643 GCACCTGATATTCTTCCATACCCC 60.808 50.000 0.00 0.00 0.00 4.95
2651 2782 7.404980 TCTTCCATACCCCAGAGTACTATTTTT 59.595 37.037 0.00 0.00 0.00 1.94
2708 2839 4.425577 AATTTTCAGTCAACATCGAGGC 57.574 40.909 0.00 0.00 0.00 4.70
2719 2850 3.765051 TCGAGGCCCATCGATCTC 58.235 61.111 12.70 0.00 46.20 2.75
2720 2851 1.903890 TCGAGGCCCATCGATCTCC 60.904 63.158 12.70 0.00 46.20 3.71
2740 2871 2.820197 CCATGATGAGATCCATGCAAGG 59.180 50.000 0.19 0.19 38.95 3.61
2750 2881 6.664816 TGAGATCCATGCAAGGTTTTATCTTT 59.335 34.615 8.03 0.00 0.00 2.52
2754 2885 4.423732 CATGCAAGGTTTTATCTTTCCCG 58.576 43.478 0.00 0.00 0.00 5.14
2760 2891 2.608090 GGTTTTATCTTTCCCGAGCTCG 59.392 50.000 29.06 29.06 39.44 5.03
2786 2929 9.373603 GGAAAACAAACACTACCATTTTTACTT 57.626 29.630 0.00 0.00 0.00 2.24
2809 2952 9.979578 ACTTGATAAACAAATTTTCATAGCACA 57.020 25.926 0.00 0.00 38.08 4.57
2823 2966 8.883954 TTTCATAGCACAATGAACATTTTTGA 57.116 26.923 8.22 0.65 43.69 2.69
2905 3048 5.887754 AGACATAGGCACTCCCTTTAAAAA 58.112 37.500 0.00 0.00 43.06 1.94
2916 3059 7.915923 GCACTCCCTTTAAAAATTCATAGCTAC 59.084 37.037 0.00 0.00 0.00 3.58
2958 3102 8.926092 TCTTAGCTAGTTAGATCTTAGATGCA 57.074 34.615 0.00 0.00 0.00 3.96
2959 3103 8.788806 TCTTAGCTAGTTAGATCTTAGATGCAC 58.211 37.037 0.00 0.00 0.00 4.57
3054 3207 9.831682 TGATATACCAGTACACCTAATCCATAA 57.168 33.333 0.00 0.00 0.00 1.90
3058 3211 6.420638 ACCAGTACACCTAATCCATAAAACC 58.579 40.000 0.00 0.00 0.00 3.27
3059 3212 5.826208 CCAGTACACCTAATCCATAAAACCC 59.174 44.000 0.00 0.00 0.00 4.11
3321 3832 2.185608 GAGCCTCTCGTTCCCTGC 59.814 66.667 0.00 0.00 0.00 4.85
3607 4118 0.102663 TCAACGTCAAGGTACGCACA 59.897 50.000 0.00 0.00 46.71 4.57
3608 4119 0.231279 CAACGTCAAGGTACGCACAC 59.769 55.000 0.00 0.00 46.71 3.82
3634 4154 1.064505 CGCCAATTGAACGCAGATCAT 59.935 47.619 7.12 0.00 39.55 2.45
3635 4155 2.724349 GCCAATTGAACGCAGATCATC 58.276 47.619 7.12 0.00 39.55 2.92
3636 4156 2.852143 GCCAATTGAACGCAGATCATCG 60.852 50.000 7.12 0.00 39.55 3.84
3637 4157 2.609002 CCAATTGAACGCAGATCATCGA 59.391 45.455 7.12 0.00 39.55 3.59
3638 4158 3.249320 CCAATTGAACGCAGATCATCGAT 59.751 43.478 7.12 0.00 39.55 3.59
3639 4159 4.452447 CAATTGAACGCAGATCATCGATC 58.548 43.478 12.54 10.63 39.55 3.69
3640 4160 1.758783 TGAACGCAGATCATCGATCG 58.241 50.000 9.36 9.36 43.17 3.69
3641 4161 1.333619 TGAACGCAGATCATCGATCGA 59.666 47.619 21.86 21.86 43.17 3.59
3642 4162 2.030805 TGAACGCAGATCATCGATCGAT 60.031 45.455 24.60 24.60 43.17 3.59
3643 4163 2.254918 ACGCAGATCATCGATCGATC 57.745 50.000 27.20 17.48 43.17 3.69
3652 4172 2.462898 CGATCGATCGTGCATGCG 59.537 61.111 33.95 11.64 44.74 4.73
3653 4173 2.295765 CGATCGATCGTGCATGCGT 61.296 57.895 33.95 0.00 44.74 5.24
3654 4174 0.996727 CGATCGATCGTGCATGCGTA 60.997 55.000 33.95 0.49 44.74 4.42
3655 4175 1.340658 GATCGATCGTGCATGCGTAT 58.659 50.000 15.94 6.06 0.00 3.06
3656 4176 1.058270 GATCGATCGTGCATGCGTATG 59.942 52.381 15.94 9.36 37.36 2.39
3672 4192 1.086696 TATGCAAGAAACTGAGCGCC 58.913 50.000 2.29 0.00 0.00 6.53
3677 4197 0.741221 AAGAAACTGAGCGCCGGATC 60.741 55.000 5.05 0.00 0.00 3.36
3805 4330 5.437060 GTTATGAGCCATCCCTTTACTCAA 58.563 41.667 0.00 0.00 40.49 3.02
3891 4418 6.884836 CCCTTAATTATATTTTCCTCCCTCGG 59.115 42.308 0.00 0.00 0.00 4.63
3912 4439 6.174760 TCGGGTACTTGTGCTTAATTGTATT 58.825 36.000 0.00 0.00 0.00 1.89
3983 4510 6.051074 TGATTAGATGTACAATGAGTGGCTG 58.949 40.000 0.00 0.00 0.00 4.85
4232 4838 2.615493 CCTTTAGGTCGACAGGTGCATT 60.615 50.000 18.91 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.644151 ACCAAACTCCCCCTTACATCT 58.356 47.619 0.00 0.00 0.00 2.90
22 23 4.213482 GTGGATAGTGACACAACCAAACTC 59.787 45.833 16.08 4.89 37.54 3.01
24 25 3.252458 GGTGGATAGTGACACAACCAAAC 59.748 47.826 16.08 10.72 39.31 2.93
36 37 1.208052 CCTGTCCTGTGGTGGATAGTG 59.792 57.143 6.57 0.00 41.80 2.74
37 38 1.573108 CCTGTCCTGTGGTGGATAGT 58.427 55.000 6.57 0.00 41.80 2.12
42 43 1.285280 TTATCCCTGTCCTGTGGTGG 58.715 55.000 0.00 0.00 0.00 4.61
48 49 4.508662 GAGAAGTGTTTATCCCTGTCCTG 58.491 47.826 0.00 0.00 0.00 3.86
55 56 4.569719 TCCTTGGAGAAGTGTTTATCCC 57.430 45.455 0.00 0.00 42.77 3.85
68 69 0.036010 AACGAGTGGCATCCTTGGAG 60.036 55.000 0.00 0.00 0.00 3.86
111 113 5.888982 ATTTCCACGTATCTGGTTATCCT 57.111 39.130 0.00 0.00 32.50 3.24
139 141 2.737252 GCTGTAGCGAGCAACTTTTAGT 59.263 45.455 0.00 0.00 38.95 2.24
151 153 2.100197 AGGATGTAAGTGCTGTAGCGA 58.900 47.619 0.00 0.00 45.83 4.93
160 162 1.628340 TGTGGGGTCAGGATGTAAGTG 59.372 52.381 0.00 0.00 37.40 3.16
161 163 1.909302 CTGTGGGGTCAGGATGTAAGT 59.091 52.381 0.00 0.00 37.40 2.24
162 164 1.909302 ACTGTGGGGTCAGGATGTAAG 59.091 52.381 0.00 0.00 39.48 2.34
163 165 1.628340 CACTGTGGGGTCAGGATGTAA 59.372 52.381 0.00 0.00 39.48 2.41
164 166 1.275666 CACTGTGGGGTCAGGATGTA 58.724 55.000 0.00 0.00 39.48 2.29
179 194 0.982852 TGGTCATAGCTCCCCCACTG 60.983 60.000 0.00 0.00 0.00 3.66
205 220 7.206981 TCTTCAGAATCACATCAAAAGAACC 57.793 36.000 0.00 0.00 0.00 3.62
223 238 1.475751 CCCCGGACCATGATTCTTCAG 60.476 57.143 0.73 0.00 34.73 3.02
228 243 1.142870 TGATTCCCCGGACCATGATTC 59.857 52.381 0.73 0.00 0.00 2.52
234 249 1.356059 TGATTTTGATTCCCCGGACCA 59.644 47.619 0.73 0.00 0.00 4.02
251 266 5.934625 GGGCATAGATGAGTTCGTTTATGAT 59.065 40.000 13.23 0.00 33.96 2.45
253 268 4.452455 GGGGCATAGATGAGTTCGTTTATG 59.548 45.833 7.26 7.26 34.73 1.90
254 269 4.102524 TGGGGCATAGATGAGTTCGTTTAT 59.897 41.667 0.00 0.00 0.00 1.40
255 270 3.452990 TGGGGCATAGATGAGTTCGTTTA 59.547 43.478 0.00 0.00 0.00 2.01
259 274 1.270518 CCTGGGGCATAGATGAGTTCG 60.271 57.143 0.00 0.00 0.00 3.95
260 275 2.050144 TCCTGGGGCATAGATGAGTTC 58.950 52.381 0.00 0.00 0.00 3.01
270 285 1.770110 TAGGCGATTCCTGGGGCAT 60.770 57.895 0.00 0.00 46.98 4.40
273 288 1.002544 GATTCTAGGCGATTCCTGGGG 59.997 57.143 0.00 0.00 46.98 4.96
278 293 2.158813 TGGGTTGATTCTAGGCGATTCC 60.159 50.000 0.00 0.00 0.00 3.01
282 297 0.830648 CCTGGGTTGATTCTAGGCGA 59.169 55.000 0.00 0.00 0.00 5.54
285 300 2.037772 CCGATCCTGGGTTGATTCTAGG 59.962 54.545 0.00 0.00 0.00 3.02
297 312 3.407424 TCTATTGCATTCCGATCCTGG 57.593 47.619 0.00 0.00 0.00 4.45
299 314 4.248859 CGATTCTATTGCATTCCGATCCT 58.751 43.478 0.00 0.00 0.00 3.24
301 316 4.143030 CCACGATTCTATTGCATTCCGATC 60.143 45.833 0.00 0.00 0.00 3.69
306 321 6.124088 AGTTTCCACGATTCTATTGCATTC 57.876 37.500 0.00 0.00 0.00 2.67
308 323 5.163622 CCAAGTTTCCACGATTCTATTGCAT 60.164 40.000 0.00 0.00 0.00 3.96
315 330 1.702957 TCCCCAAGTTTCCACGATTCT 59.297 47.619 0.00 0.00 0.00 2.40
316 331 2.194201 TCCCCAAGTTTCCACGATTC 57.806 50.000 0.00 0.00 0.00 2.52
318 333 2.308866 AGAATCCCCAAGTTTCCACGAT 59.691 45.455 0.00 0.00 0.00 3.73
319 334 1.702957 AGAATCCCCAAGTTTCCACGA 59.297 47.619 0.00 0.00 0.00 4.35
320 335 1.812571 CAGAATCCCCAAGTTTCCACG 59.187 52.381 0.00 0.00 0.00 4.94
321 336 2.820197 GTCAGAATCCCCAAGTTTCCAC 59.180 50.000 0.00 0.00 0.00 4.02
322 337 2.552155 CGTCAGAATCCCCAAGTTTCCA 60.552 50.000 0.00 0.00 0.00 3.53
333 350 1.964223 TGGCTAGGATCGTCAGAATCC 59.036 52.381 0.00 0.00 34.77 3.01
342 359 0.468214 TGAGGGACTGGCTAGGATCG 60.468 60.000 0.85 0.00 41.55 3.69
346 363 1.351017 TGTTTTGAGGGACTGGCTAGG 59.649 52.381 0.85 0.00 41.55 3.02
365 382 2.286563 GTCGTTTTGGGCCACATTTTTG 59.713 45.455 5.23 0.00 0.00 2.44
370 387 1.234615 CGAGTCGTTTTGGGCCACAT 61.235 55.000 5.23 0.00 0.00 3.21
371 388 1.890041 CGAGTCGTTTTGGGCCACA 60.890 57.895 5.23 0.00 0.00 4.17
372 389 1.890510 ACGAGTCGTTTTGGGCCAC 60.891 57.895 13.56 0.00 36.35 5.01
388 480 0.798776 GACTGTTGCAGGGATGAACG 59.201 55.000 1.08 0.00 35.51 3.95
402 494 4.664677 GCCGGCGTCACTGACTGT 62.665 66.667 12.58 0.00 0.00 3.55
416 508 1.153901 AGGATACAACACGTCGCCG 60.154 57.895 0.00 0.00 41.41 6.46
427 519 1.830279 ACTTCGGTCGTCAGGATACA 58.170 50.000 0.00 0.00 41.41 2.29
487 579 2.783135 AGACACGAAACATGATTGCCT 58.217 42.857 0.00 0.00 0.00 4.75
501 600 0.318441 TCTTCAGGGAGCAAGACACG 59.682 55.000 0.00 0.00 0.00 4.49
544 644 6.155393 ACTGTTTCATTTTCTTTTGGGTGGTA 59.845 34.615 0.00 0.00 0.00 3.25
562 662 5.752955 GGCTCAAGAGATCTATCACTGTTTC 59.247 44.000 0.00 0.00 0.00 2.78
603 703 1.135141 TCGACATGTGACGATGCATGA 60.135 47.619 2.46 0.00 43.60 3.07
760 860 4.383010 GCATTAATTGAAAAGGGTGGAGGG 60.383 45.833 0.00 0.00 0.00 4.30
763 863 3.829601 ACGCATTAATTGAAAAGGGTGGA 59.170 39.130 0.00 0.00 0.00 4.02
874 982 4.735132 TTGCGTCCGCCGGAAGAG 62.735 66.667 23.30 11.43 42.27 2.85
891 999 4.892965 TGCAAGGCCGGTGTGCTT 62.893 61.111 21.45 0.00 39.09 3.91
1050 1160 3.670377 GGCCAGGCGGAAACACAC 61.670 66.667 5.00 0.00 0.00 3.82
1051 1161 3.505790 ATGGCCAGGCGGAAACACA 62.506 57.895 13.05 0.00 0.00 3.72
1052 1162 2.676471 ATGGCCAGGCGGAAACAC 60.676 61.111 13.05 0.00 0.00 3.32
1053 1163 2.676121 CATGGCCAGGCGGAAACA 60.676 61.111 13.05 0.00 0.00 2.83
1054 1164 4.133796 GCATGGCCAGGCGGAAAC 62.134 66.667 28.54 0.00 0.00 2.78
1101 1212 6.038382 CCGAAGCTTAGTCTATCACTTGACTA 59.962 42.308 0.00 0.00 42.67 2.59
1102 1213 5.163602 CCGAAGCTTAGTCTATCACTTGACT 60.164 44.000 0.00 0.00 44.56 3.41
1103 1214 5.038033 CCGAAGCTTAGTCTATCACTTGAC 58.962 45.833 0.00 0.00 36.43 3.18
1104 1215 4.098044 CCCGAAGCTTAGTCTATCACTTGA 59.902 45.833 0.00 0.00 36.43 3.02
1105 1216 4.363999 CCCGAAGCTTAGTCTATCACTTG 58.636 47.826 0.00 0.00 36.43 3.16
1106 1217 3.385111 CCCCGAAGCTTAGTCTATCACTT 59.615 47.826 0.00 0.00 36.43 3.16
1107 1218 2.959707 CCCCGAAGCTTAGTCTATCACT 59.040 50.000 0.00 0.00 39.41 3.41
1108 1219 2.694109 ACCCCGAAGCTTAGTCTATCAC 59.306 50.000 0.00 0.00 0.00 3.06
1111 1222 4.019591 ACAAAACCCCGAAGCTTAGTCTAT 60.020 41.667 0.00 0.00 0.00 1.98
1112 1223 3.325716 ACAAAACCCCGAAGCTTAGTCTA 59.674 43.478 0.00 0.00 0.00 2.59
1113 1224 2.105993 ACAAAACCCCGAAGCTTAGTCT 59.894 45.455 0.00 0.00 0.00 3.24
1114 1225 2.501261 ACAAAACCCCGAAGCTTAGTC 58.499 47.619 0.00 0.00 0.00 2.59
1115 1226 2.651382 ACAAAACCCCGAAGCTTAGT 57.349 45.000 0.00 0.00 0.00 2.24
1116 1227 3.671716 AGTACAAAACCCCGAAGCTTAG 58.328 45.455 0.00 0.00 0.00 2.18
1128 1239 4.691216 TGGCAACCAACAAAAGTACAAAAC 59.309 37.500 0.00 0.00 0.00 2.43
1129 1240 4.894784 TGGCAACCAACAAAAGTACAAAA 58.105 34.783 0.00 0.00 0.00 2.44
1130 1241 4.537135 TGGCAACCAACAAAAGTACAAA 57.463 36.364 0.00 0.00 0.00 2.83
1131 1242 4.437239 CATGGCAACCAACAAAAGTACAA 58.563 39.130 0.00 0.00 36.95 2.41
1132 1243 3.181471 CCATGGCAACCAACAAAAGTACA 60.181 43.478 0.00 0.00 36.95 2.90
1133 1244 3.181470 ACCATGGCAACCAACAAAAGTAC 60.181 43.478 13.04 0.00 36.95 2.73
1134 1245 3.034635 ACCATGGCAACCAACAAAAGTA 58.965 40.909 13.04 0.00 36.95 2.24
1135 1246 1.836802 ACCATGGCAACCAACAAAAGT 59.163 42.857 13.04 0.00 36.95 2.66
1136 1247 2.482864 GACCATGGCAACCAACAAAAG 58.517 47.619 13.04 0.00 36.95 2.27
1149 1260 1.521010 CTGCTCAGAGCGACCATGG 60.521 63.158 17.81 11.19 46.26 3.66
1150 1261 1.521010 CCTGCTCAGAGCGACCATG 60.521 63.158 17.81 3.62 46.26 3.66
1689 1800 1.079543 CACCTCCTCGCTGGTCTTG 60.080 63.158 0.00 0.00 33.75 3.02
1753 1864 4.098654 CCTGAGGTAATCGTTCATCTGTCT 59.901 45.833 0.00 0.00 0.00 3.41
1827 1938 1.923204 GTAGCGAGTGAGATGTGCAAG 59.077 52.381 0.00 0.00 0.00 4.01
1855 1966 2.279136 CACTGCAAGCGACGAACTATAC 59.721 50.000 0.00 0.00 37.60 1.47
1864 1979 1.264020 TGAAATGTCACTGCAAGCGAC 59.736 47.619 3.48 3.48 45.91 5.19
1905 2020 7.455641 TTTTGTGGAGTACTGTTCTTTTCAA 57.544 32.000 0.00 0.00 0.00 2.69
2004 2119 2.936919 TGTGATGTCTCCACAAAGCT 57.063 45.000 0.00 0.00 41.07 3.74
2008 2123 3.324556 TGAGTCATGTGATGTCTCCACAA 59.675 43.478 0.00 0.00 46.12 3.33
2010 2125 3.257393 GTGAGTCATGTGATGTCTCCAC 58.743 50.000 0.00 0.00 42.32 4.02
2072 2187 8.723942 ACTTCAGCAATTTTAGATATTCGACT 57.276 30.769 0.00 0.00 0.00 4.18
2075 2190 9.994432 AAGAACTTCAGCAATTTTAGATATTCG 57.006 29.630 0.00 0.00 0.00 3.34
2088 2203 5.067153 TCGAAATCCAAAAGAACTTCAGCAA 59.933 36.000 0.00 0.00 0.00 3.91
2089 2204 4.578516 TCGAAATCCAAAAGAACTTCAGCA 59.421 37.500 0.00 0.00 0.00 4.41
2090 2205 5.108385 TCGAAATCCAAAAGAACTTCAGC 57.892 39.130 0.00 0.00 0.00 4.26
2091 2206 7.138692 AGATCGAAATCCAAAAGAACTTCAG 57.861 36.000 0.00 0.00 31.78 3.02
2145 2260 8.499967 GTTCCAAACCAAATTTAAATTACGCAT 58.500 29.630 13.68 0.00 0.00 4.73
2146 2261 7.711339 AGTTCCAAACCAAATTTAAATTACGCA 59.289 29.630 13.68 0.00 0.00 5.24
2181 2296 8.485578 TTGTAACCTTAAAATTCCTGTCCATT 57.514 30.769 0.00 0.00 0.00 3.16
2182 2297 8.485578 TTTGTAACCTTAAAATTCCTGTCCAT 57.514 30.769 0.00 0.00 0.00 3.41
2216 2331 7.470424 GCAAATGGGATTGACATATCTTAAGCA 60.470 37.037 0.00 0.00 31.84 3.91
2246 2361 6.497640 AGAGGAAGAAGGGAAAAAGCATAAT 58.502 36.000 0.00 0.00 0.00 1.28
2252 2373 6.998673 TCAAAGTAGAGGAAGAAGGGAAAAAG 59.001 38.462 0.00 0.00 0.00 2.27
2258 2379 5.004448 GGTTTCAAAGTAGAGGAAGAAGGG 58.996 45.833 0.00 0.00 0.00 3.95
2262 2383 5.374071 GGTTGGTTTCAAAGTAGAGGAAGA 58.626 41.667 0.00 0.00 34.28 2.87
2279 2400 1.802365 GTCAAAGTAATCGCGGTTGGT 59.198 47.619 16.41 0.00 0.00 3.67
2286 2407 6.617879 ACCCTAAAATTGTCAAAGTAATCGC 58.382 36.000 0.00 0.00 0.00 4.58
2300 2421 9.423964 TGTAAACCTCAAGTTAACCCTAAAATT 57.576 29.630 0.88 0.00 37.88 1.82
2303 2424 7.040271 GCATGTAAACCTCAAGTTAACCCTAAA 60.040 37.037 0.88 0.00 37.88 1.85
2318 2439 5.140454 AGAAAACCTTGAGCATGTAAACCT 58.860 37.500 0.00 0.00 0.00 3.50
2346 2468 7.538575 CCACCATTTTGTCTAGGTTTTGATAG 58.461 38.462 0.00 0.00 30.44 2.08
2356 2478 2.416547 CGTCTGCCACCATTTTGTCTAG 59.583 50.000 0.00 0.00 0.00 2.43
2357 2479 2.037902 TCGTCTGCCACCATTTTGTCTA 59.962 45.455 0.00 0.00 0.00 2.59
2358 2480 1.202758 TCGTCTGCCACCATTTTGTCT 60.203 47.619 0.00 0.00 0.00 3.41
2359 2481 1.234821 TCGTCTGCCACCATTTTGTC 58.765 50.000 0.00 0.00 0.00 3.18
2360 2482 1.608590 CTTCGTCTGCCACCATTTTGT 59.391 47.619 0.00 0.00 0.00 2.83
2361 2483 1.666888 GCTTCGTCTGCCACCATTTTG 60.667 52.381 0.00 0.00 0.00 2.44
2362 2484 0.598065 GCTTCGTCTGCCACCATTTT 59.402 50.000 0.00 0.00 0.00 1.82
2366 2488 2.031012 CTGCTTCGTCTGCCACCA 59.969 61.111 0.00 0.00 0.00 4.17
2378 2500 4.561752 AGGTATCCCATTCTAGTCTGCTT 58.438 43.478 0.00 0.00 0.00 3.91
2385 2507 7.761704 CGTGATATTCAAGGTATCCCATTCTAG 59.238 40.741 0.00 0.00 0.00 2.43
2392 2514 7.383687 TCAATACGTGATATTCAAGGTATCCC 58.616 38.462 0.00 0.00 31.31 3.85
2400 2523 5.231357 GCGTGTCTCAATACGTGATATTCAA 59.769 40.000 0.00 0.00 41.51 2.69
2410 2533 0.172578 TGGGAGCGTGTCTCAATACG 59.827 55.000 0.00 0.00 43.70 3.06
2413 2536 0.745845 GCATGGGAGCGTGTCTCAAT 60.746 55.000 0.00 0.00 39.90 2.57
2422 2545 4.559063 CCCTGGAGCATGGGAGCG 62.559 72.222 0.00 0.00 46.15 5.03
2438 2561 2.595754 GAGATCCAATGGCCCGCC 60.596 66.667 0.00 0.00 0.00 6.13
2446 2574 1.489649 CCACCAGAGCTGAGATCCAAT 59.510 52.381 0.00 0.00 0.00 3.16
2458 2586 3.118956 GGACTTGACTATGACCACCAGAG 60.119 52.174 0.00 0.00 39.88 3.35
2462 2590 3.600388 CAAGGACTTGACTATGACCACC 58.400 50.000 6.19 0.00 42.93 4.61
2487 2616 0.248621 GCTCCCATATTTGTGCGCAC 60.249 55.000 33.11 33.11 0.00 5.34
2491 2620 1.035139 CCAGGCTCCCATATTTGTGC 58.965 55.000 0.00 0.00 0.00 4.57
2506 2635 2.261215 GCAGAAAACTGCCTCCAGG 58.739 57.895 10.58 0.00 43.99 4.45
2521 2652 2.420022 CGGAGGGTCTGTAAATTTGCAG 59.580 50.000 25.24 25.24 41.49 4.41
2536 2667 0.464373 CAATGGTCATGGTCGGAGGG 60.464 60.000 0.00 0.00 0.00 4.30
2583 2714 2.890612 CATGCTCCCATGCTCCAAA 58.109 52.632 0.00 0.00 42.08 3.28
2606 2737 2.374504 AGAATATCAGGTGCTCCCATGG 59.625 50.000 4.14 4.14 34.66 3.66
2607 2738 3.784511 AGAATATCAGGTGCTCCCATG 57.215 47.619 0.00 0.00 34.66 3.66
2608 2739 3.073650 GGAAGAATATCAGGTGCTCCCAT 59.926 47.826 0.00 0.00 34.66 4.00
2609 2740 2.439507 GGAAGAATATCAGGTGCTCCCA 59.560 50.000 0.00 0.00 34.66 4.37
2610 2741 2.439507 TGGAAGAATATCAGGTGCTCCC 59.560 50.000 0.00 0.00 0.00 4.30
2611 2742 3.845781 TGGAAGAATATCAGGTGCTCC 57.154 47.619 0.00 0.00 0.00 4.70
2612 2743 5.241662 GGTATGGAAGAATATCAGGTGCTC 58.758 45.833 0.00 0.00 0.00 4.26
2613 2744 4.042187 GGGTATGGAAGAATATCAGGTGCT 59.958 45.833 0.00 0.00 0.00 4.40
2615 2746 4.350816 TGGGGTATGGAAGAATATCAGGTG 59.649 45.833 0.00 0.00 0.00 4.00
2616 2747 4.577096 TGGGGTATGGAAGAATATCAGGT 58.423 43.478 0.00 0.00 0.00 4.00
2619 2750 5.476983 ACTCTGGGGTATGGAAGAATATCA 58.523 41.667 0.00 0.00 0.00 2.15
2620 2751 6.726764 AGTACTCTGGGGTATGGAAGAATATC 59.273 42.308 0.00 0.00 0.00 1.63
2621 2752 6.635021 AGTACTCTGGGGTATGGAAGAATAT 58.365 40.000 0.00 0.00 0.00 1.28
2622 2753 6.039415 AGTACTCTGGGGTATGGAAGAATA 57.961 41.667 0.00 0.00 0.00 1.75
2623 2754 4.897051 AGTACTCTGGGGTATGGAAGAAT 58.103 43.478 0.00 0.00 0.00 2.40
2624 2755 4.348020 AGTACTCTGGGGTATGGAAGAA 57.652 45.455 0.00 0.00 0.00 2.52
2625 2756 5.681494 ATAGTACTCTGGGGTATGGAAGA 57.319 43.478 0.00 0.00 0.00 2.87
2626 2757 6.749036 AAATAGTACTCTGGGGTATGGAAG 57.251 41.667 0.00 0.00 0.00 3.46
2627 2758 7.519347 AAAAATAGTACTCTGGGGTATGGAA 57.481 36.000 0.00 0.00 0.00 3.53
2708 2839 2.830321 TCTCATCATGGAGATCGATGGG 59.170 50.000 0.54 4.84 38.95 4.00
2719 2850 2.820197 CCTTGCATGGATCTCATCATGG 59.180 50.000 13.33 10.39 40.59 3.66
2720 2851 3.487372 ACCTTGCATGGATCTCATCATG 58.513 45.455 24.48 5.57 42.47 3.07
2740 2871 3.927552 CGAGCTCGGGAAAGATAAAAC 57.072 47.619 28.40 0.00 35.37 2.43
2754 2885 3.059120 GGTAGTGTTTGTTTTCCGAGCTC 60.059 47.826 2.73 2.73 0.00 4.09
2760 2891 8.936070 AGTAAAAATGGTAGTGTTTGTTTTCC 57.064 30.769 0.00 0.00 0.00 3.13
2790 2933 9.107177 TGTTCATTGTGCTATGAAAATTTGTTT 57.893 25.926 9.79 0.00 43.88 2.83
2802 2945 8.362639 ACTCTTCAAAAATGTTCATTGTGCTAT 58.637 29.630 0.00 0.00 0.00 2.97
2856 2999 9.991388 TCGGTCACCTAAAAATTAATAAATTCG 57.009 29.630 0.00 0.00 34.12 3.34
2863 3006 9.326413 CTATGTCTCGGTCACCTAAAAATTAAT 57.674 33.333 0.00 0.00 0.00 1.40
2876 3019 1.103803 GAGTGCCTATGTCTCGGTCA 58.896 55.000 0.00 0.00 0.00 4.02
2880 3023 1.115467 AAGGGAGTGCCTATGTCTCG 58.885 55.000 2.47 0.00 0.00 4.04
2905 3048 4.682778 TTGCGGGTAAGTAGCTATGAAT 57.317 40.909 0.00 0.00 0.00 2.57
2933 3077 8.788806 GTGCATCTAAGATCTAACTAGCTAAGA 58.211 37.037 0.00 0.00 0.00 2.10
3054 3207 7.364320 GCCATATGTTACCAAAGTTATGGGTTT 60.364 37.037 1.24 0.00 45.18 3.27
3057 3210 5.596361 TGCCATATGTTACCAAAGTTATGGG 59.404 40.000 1.24 0.00 45.18 4.00
3058 3211 6.503524 GTGCCATATGTTACCAAAGTTATGG 58.496 40.000 1.24 0.00 46.38 2.74
3059 3212 6.037720 TCGTGCCATATGTTACCAAAGTTATG 59.962 38.462 1.24 0.00 0.00 1.90
3232 3737 4.760047 GATGTCGCCGGCACCACT 62.760 66.667 28.98 11.47 0.00 4.00
3289 3800 1.108132 GGCTCGGGGAGACGTAGAAT 61.108 60.000 0.00 0.00 34.94 2.40
3349 3860 0.107703 GGTCGATCATCACCTTGGCA 60.108 55.000 0.00 0.00 0.00 4.92
3394 3905 2.119611 TTCTCGGCCACCTCCTCA 59.880 61.111 2.24 0.00 0.00 3.86
3611 4122 3.969642 CTGCGTTCAATTGGCGGGC 62.970 63.158 19.35 12.63 0.00 6.13
3612 4123 1.656818 ATCTGCGTTCAATTGGCGGG 61.657 55.000 19.35 7.96 33.89 6.13
3613 4124 0.248215 GATCTGCGTTCAATTGGCGG 60.248 55.000 19.35 13.96 0.00 6.13
3615 4126 2.724349 GATGATCTGCGTTCAATTGGC 58.276 47.619 5.42 1.73 0.00 4.52
3620 4140 2.119457 CGATCGATGATCTGCGTTCAA 58.881 47.619 10.26 0.00 36.96 2.69
3636 4156 1.058270 CATACGCATGCACGATCGATC 59.942 52.381 24.34 15.68 36.70 3.69
3637 4157 1.063031 CATACGCATGCACGATCGAT 58.937 50.000 24.34 0.00 36.70 3.59
3638 4158 2.505447 CATACGCATGCACGATCGA 58.495 52.632 24.34 0.00 36.70 3.59
3650 4170 1.527793 CGCTCAGTTTCTTGCATACGC 60.528 52.381 0.00 0.00 39.24 4.42
3651 4171 1.527793 GCGCTCAGTTTCTTGCATACG 60.528 52.381 0.00 0.00 0.00 3.06
3652 4172 1.202076 GGCGCTCAGTTTCTTGCATAC 60.202 52.381 7.64 0.00 0.00 2.39
3653 4173 1.086696 GGCGCTCAGTTTCTTGCATA 58.913 50.000 7.64 0.00 0.00 3.14
3654 4174 1.878775 GGCGCTCAGTTTCTTGCAT 59.121 52.632 7.64 0.00 0.00 3.96
3655 4175 2.606961 CGGCGCTCAGTTTCTTGCA 61.607 57.895 7.64 0.00 0.00 4.08
3656 4176 2.174349 CGGCGCTCAGTTTCTTGC 59.826 61.111 7.64 0.00 0.00 4.01
3657 4177 1.021390 ATCCGGCGCTCAGTTTCTTG 61.021 55.000 7.64 0.00 0.00 3.02
3658 4178 0.741221 GATCCGGCGCTCAGTTTCTT 60.741 55.000 7.64 0.00 0.00 2.52
3659 4179 1.153549 GATCCGGCGCTCAGTTTCT 60.154 57.895 7.64 0.00 0.00 2.52
3660 4180 2.517450 CGATCCGGCGCTCAGTTTC 61.517 63.158 7.64 0.00 0.00 2.78
3661 4181 2.501223 TTCGATCCGGCGCTCAGTTT 62.501 55.000 7.64 0.00 0.00 2.66
3662 4182 2.298158 ATTCGATCCGGCGCTCAGTT 62.298 55.000 7.64 0.00 0.00 3.16
3663 4183 2.298158 AATTCGATCCGGCGCTCAGT 62.298 55.000 7.64 0.00 0.00 3.41
3664 4184 1.592669 AATTCGATCCGGCGCTCAG 60.593 57.895 7.64 0.00 0.00 3.35
3665 4185 1.882625 CAATTCGATCCGGCGCTCA 60.883 57.895 7.64 0.00 0.00 4.26
3668 4188 3.272334 AGCAATTCGATCCGGCGC 61.272 61.111 0.00 0.00 0.00 6.53
3672 4192 1.398041 TCAAAGCAGCAATTCGATCCG 59.602 47.619 0.00 0.00 0.00 4.18
3677 4197 4.973396 TCTAACATCAAAGCAGCAATTCG 58.027 39.130 0.00 0.00 0.00 3.34
3725 4246 4.632458 GCGCCGACGATCTCCTCC 62.632 72.222 0.00 0.00 43.93 4.30
3789 4310 4.526970 TCAATCTTGAGTAAAGGGATGGC 58.473 43.478 0.00 0.00 36.46 4.40
3805 4330 3.667497 TCGACAACAGAAGCTCAATCT 57.333 42.857 0.00 0.00 0.00 2.40
3867 4392 6.884836 CCCGAGGGAGGAAAATATAATTAAGG 59.115 42.308 0.84 0.00 37.50 2.69
3912 4439 4.808895 GGAACAGTGCATATCGTCATACAA 59.191 41.667 0.00 0.00 0.00 2.41
3926 4453 1.269831 ACGAGAGTGAAGGAACAGTGC 60.270 52.381 0.00 0.00 46.97 4.40
4046 4576 9.269453 GTAGGCCGACTGAGTATTATTATTTTT 57.731 33.333 9.01 0.00 0.00 1.94
4232 4838 6.074648 ACCTATTCAACAGAAAAATGGGTGA 58.925 36.000 2.10 0.00 41.16 4.02
4683 5974 9.658475 TGTTGAATAAGTATTTGAAAACTGTCG 57.342 29.630 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.