Multiple sequence alignment - TraesCS1D01G321300

Loading Multiple Alignment...

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 TraesCS1D01G321300 chr1D 100.000 4299 0 0 1 4299 414774612 414778910 0.000000e+00 7939.0
1 TraesCS1D01G321300 chr1D 79.498 239 42 4 3808 4044 467929954 467930187 3.440000e-36 163.0
2 TraesCS1D01G321300 chr1D 76.491 285 52 13 1349 1624 461486977 461486699 1.610000e-29 141.0
3 TraesCS1D01G321300 chr1A 89.963 4055 225 75 1 3981 511499020 511502966 0.000000e+00 5066.0
4 TraesCS1D01G321300 chr1A 76.678 283 55 10 1349 1624 552951834 552951556 3.460000e-31 147.0
5 TraesCS1D01G321300 chr1A 80.537 149 25 4 1099 1245 552952082 552951936 1.260000e-20 111.0
6 TraesCS1D01G321300 chr1A 95.161 62 3 0 4233 4294 511584996 511585057 9.840000e-17 99.0
7 TraesCS1D01G321300 chr1B 93.525 1668 67 18 481 2129 560250912 560252557 0.000000e+00 2444.0
8 TraesCS1D01G321300 chr1B 89.963 1355 79 29 2165 3485 560252660 560253991 0.000000e+00 1696.0
9 TraesCS1D01G321300 chr1B 83.770 764 96 13 3554 4299 560254019 560254772 0.000000e+00 699.0
10 TraesCS1D01G321300 chr1B 94.276 297 13 4 1 296 560226065 560226358 6.560000e-123 451.0
11 TraesCS1D01G321300 chr1B 76.087 276 51 13 1349 1615 634601099 634601368 3.490000e-26 130.0
12 TraesCS1D01G321300 chr1B 75.397 126 27 4 1501 1624 634413629 634413506 1.670000e-04 58.4
13 TraesCS1D01G321300 chr7D 86.636 217 26 2 1329 1542 65600817 65600601 2.000000e-58 237.0
14 TraesCS1D01G321300 chr7D 81.364 220 35 3 3783 4001 45001747 45001533 1.590000e-39 174.0
15 TraesCS1D01G321300 chr7D 86.806 144 17 2 1828 1971 68791068 68791209 4.450000e-35 159.0
16 TraesCS1D01G321300 chr7D 79.904 209 33 8 1043 1245 68790247 68790452 1.250000e-30 145.0
17 TraesCS1D01G321300 chr7A 86.636 217 26 2 1329 1542 69901825 69902041 2.000000e-58 237.0
18 TraesCS1D01G321300 chr7A 80.663 181 32 3 1067 1245 71146022 71145843 2.080000e-28 137.0
19 TraesCS1D01G321300 chrUn 86.239 218 25 4 1329 1542 84039759 84039543 9.300000e-57 231.0
20 TraesCS1D01G321300 chr2D 81.739 230 33 7 3790 4017 119762870 119763092 2.640000e-42 183.0
21 TraesCS1D01G321300 chr3D 84.270 178 26 2 1075 1251 110310928 110310752 5.720000e-39 172.0
22 TraesCS1D01G321300 chr3D 90.909 55 5 0 1570 1624 110244771 110244717 1.660000e-09 75.0
23 TraesCS1D01G321300 chr3B 77.259 321 53 15 3729 4044 420930282 420929977 2.060000e-38 171.0
24 TraesCS1D01G321300 chr3B 83.616 177 29 0 1075 1251 161461454 161461278 2.660000e-37 167.0
25 TraesCS1D01G321300 chr3B 90.909 55 5 0 1570 1624 161377728 161377674 1.660000e-09 75.0
26 TraesCS1D01G321300 chr3A 84.091 176 28 0 1075 1250 120175455 120175630 2.060000e-38 171.0
27 TraesCS1D01G321300 chr3A 81.657 169 31 0 1082 1250 120166185 120166353 1.610000e-29 141.0
28 TraesCS1D01G321300 chr3A 90.909 55 5 0 1570 1624 120224184 120224238 1.660000e-09 75.0
29 TraesCS1D01G321300 chr3A 73.333 180 43 5 3095 3271 120226847 120227024 1.290000e-05 62.1
30 TraesCS1D01G321300 chr2A 77.044 318 54 10 3729 4044 539305007 539305307 9.560000e-37 165.0
31 TraesCS1D01G321300 chr5D 78.277 267 48 6 3792 4056 495915309 495915051 3.440000e-36 163.0
32 TraesCS1D01G321300 chr7B 86.806 144 19 0 1828 1971 9751281 9751424 1.240000e-35 161.0
33 TraesCS1D01G321300 chr4B 77.372 274 57 4 3729 4001 660947059 660947328 1.600000e-34 158.0
34 TraesCS1D01G321300 chr4B 73.391 233 54 3 3727 3951 653432378 653432146 3.560000e-11 80.5
35 TraesCS1D01G321300 chr5B 78.113 265 44 11 3780 4042 398385665 398385413 5.760000e-34 156.0
36 TraesCS1D01G321300 chr4D 84.536 97 13 2 364 459 81384889 81384794 1.270000e-15 95.3


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 TraesCS1D01G321300 chr1D 414774612 414778910 4298 False 7939 7939 100.000 1 4299 1 chr1D.!!$F1 4298
1 TraesCS1D01G321300 chr1A 511499020 511502966 3946 False 5066 5066 89.963 1 3981 1 chr1A.!!$F1 3980
2 TraesCS1D01G321300 chr1B 560250912 560254772 3860 False 1613 2444 89.086 481 4299 3 chr1B.!!$F3 3818

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
466 471 0.040425 GGACATTTGTGCACACGGAC 60.040 55.0 21.56 11.78 36.33 4.79 F
1262 1280 0.252197 CTTGGTACCTGCCTACCACC 59.748 60.0 14.36 0.00 44.91 4.61 F
1295 1313 0.676466 CTGTAAAGATGGTGGCCGCA 60.676 55.0 19.98 4.65 0.00 5.69 F
3048 3192 0.621571 AGGACAAGCAGGATGGGCTA 60.622 55.0 0.00 0.00 41.66 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2057 0.178068 GGCGTACATGATCCTGGTGT 59.822 55.0 0.0 0.0 0.00 4.16 R
2250 2366 0.255890 CCGGACAGGGATGTTTGGAT 59.744 55.0 0.0 0.0 35.97 3.41 R
3056 3200 0.613292 AACCACACACACCAAAGCCA 60.613 50.0 0.0 0.0 0.00 4.75 R
4119 4289 0.104120 ACCGGCCTTTGCAAGAAAAC 59.896 50.0 0.0 0.0 40.13 2.43 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 5.714047 TGCATGTGTTAGAGAGTAAGACAG 58.286 41.667 0.00 0.00 34.83 3.51
68 69 4.704057 GGACAAGCCAATCTGAAGAATCTT 59.296 41.667 0.00 0.00 36.34 2.40
94 95 6.810182 GTCTTAGTTACCGTTCTGCAATCTTA 59.190 38.462 0.00 0.00 0.00 2.10
95 96 7.330208 GTCTTAGTTACCGTTCTGCAATCTTAA 59.670 37.037 0.00 0.00 0.00 1.85
101 102 6.870971 ACCGTTCTGCAATCTTAAAACTTA 57.129 33.333 0.00 0.00 0.00 2.24
135 136 1.191647 CGACGTTTGTTGACCACTAGC 59.808 52.381 0.00 0.00 0.00 3.42
141 142 0.179070 TGTTGACCACTAGCGTGCAA 60.179 50.000 0.00 0.00 39.86 4.08
147 150 1.568612 CCACTAGCGTGCAACCACTG 61.569 60.000 0.00 0.00 39.86 3.66
166 169 2.553602 CTGCTGTTGTTGAATGGTGCTA 59.446 45.455 0.00 0.00 0.00 3.49
186 189 2.614829 TTAAGCCTCACCTAATCGCC 57.385 50.000 0.00 0.00 0.00 5.54
189 192 1.223487 GCCTCACCTAATCGCCCAA 59.777 57.895 0.00 0.00 0.00 4.12
195 198 3.211045 TCACCTAATCGCCCAATTTAGC 58.789 45.455 0.00 0.00 0.00 3.09
222 227 4.071961 ACTATGTGCGATGAAGGCATAA 57.928 40.909 0.00 0.00 43.19 1.90
227 232 4.422840 TGTGCGATGAAGGCATAAAAATG 58.577 39.130 0.00 0.00 43.19 2.32
257 262 3.609103 ATCTGAAAGTGAAACGTGTGC 57.391 42.857 0.00 0.00 45.86 4.57
268 273 6.094719 AGTGAAACGTGTGCGATAACTAATA 58.905 36.000 0.00 0.00 45.86 0.98
302 307 0.736325 TAGAAAAGAGAGCCGCGTGC 60.736 55.000 4.92 8.57 41.71 5.34
317 322 0.872451 CGTGCGGTATCGGTTGCATA 60.872 55.000 0.00 0.00 39.85 3.14
318 323 1.292061 GTGCGGTATCGGTTGCATAA 58.708 50.000 0.00 0.00 39.85 1.90
333 338 5.221028 GGTTGCATAATTCGATCATCCAACA 60.221 40.000 13.52 0.00 33.62 3.33
379 384 2.558795 CACGAGAAGAGAAGGAGGACAA 59.441 50.000 0.00 0.00 0.00 3.18
392 397 1.146263 GGACAATAGGGCGGGACAG 59.854 63.158 0.00 0.00 0.00 3.51
395 400 0.759346 ACAATAGGGCGGGACAGATC 59.241 55.000 0.00 0.00 0.00 2.75
403 408 2.557317 GGCGGGACAGATCGAAATAAA 58.443 47.619 0.00 0.00 0.00 1.40
413 418 5.142265 CAGATCGAAATAAATGGACGCATG 58.858 41.667 0.00 0.00 0.00 4.06
415 420 4.530094 TCGAAATAAATGGACGCATGAC 57.470 40.909 0.00 0.00 0.00 3.06
417 422 4.574421 TCGAAATAAATGGACGCATGACAT 59.426 37.500 0.00 0.00 0.00 3.06
420 425 2.127271 AAATGGACGCATGACATGGA 57.873 45.000 17.03 0.00 0.00 3.41
421 426 1.382522 AATGGACGCATGACATGGAC 58.617 50.000 17.03 7.50 0.00 4.02
447 452 1.134226 GTCTCCCGTTACAACACACG 58.866 55.000 0.00 0.00 36.12 4.49
459 464 1.098869 AACACACGGACATTTGTGCA 58.901 45.000 3.11 0.00 45.92 4.57
460 465 0.380378 ACACACGGACATTTGTGCAC 59.620 50.000 10.75 10.75 45.92 4.57
461 466 0.380024 CACACGGACATTTGTGCACA 59.620 50.000 17.42 17.42 39.71 4.57
462 467 0.380378 ACACGGACATTTGTGCACAC 59.620 50.000 21.56 7.52 39.71 3.82
463 468 0.657077 CACGGACATTTGTGCACACG 60.657 55.000 21.56 20.48 36.05 4.49
464 469 1.082169 CGGACATTTGTGCACACGG 60.082 57.895 21.56 14.27 36.05 4.94
465 470 1.502990 CGGACATTTGTGCACACGGA 61.503 55.000 21.56 9.21 36.05 4.69
466 471 0.040425 GGACATTTGTGCACACGGAC 60.040 55.000 21.56 11.78 36.33 4.79
467 472 0.660488 GACATTTGTGCACACGGACA 59.340 50.000 21.56 0.39 42.36 4.02
468 473 1.266718 GACATTTGTGCACACGGACAT 59.733 47.619 21.56 2.87 43.63 3.06
469 474 1.680735 ACATTTGTGCACACGGACATT 59.319 42.857 21.56 0.00 43.63 2.71
470 475 2.100584 ACATTTGTGCACACGGACATTT 59.899 40.909 21.56 0.00 43.63 2.32
471 476 2.200792 TTTGTGCACACGGACATTTG 57.799 45.000 21.56 0.00 43.63 2.32
472 477 1.098869 TTGTGCACACGGACATTTGT 58.901 45.000 21.56 0.00 43.63 2.83
473 478 0.380024 TGTGCACACGGACATTTGTG 59.620 50.000 17.42 0.00 45.01 3.33
574 583 4.574599 AAAATGTCTTTCTTTCGCTGCT 57.425 36.364 0.00 0.00 0.00 4.24
602 611 9.708092 GGGCCTAAAATATCTAGTTACAAGTAG 57.292 37.037 0.84 0.00 34.04 2.57
618 627 1.548269 AGTAGCTCTCACCTGTCAAGC 59.452 52.381 0.00 0.00 0.00 4.01
919 929 2.000701 ATCCCAACGGATCTGCCCA 61.001 57.895 0.00 0.00 46.77 5.36
920 930 1.570857 ATCCCAACGGATCTGCCCAA 61.571 55.000 0.00 0.00 46.77 4.12
921 931 1.304052 CCCAACGGATCTGCCCAAA 60.304 57.895 0.00 0.00 0.00 3.28
934 947 1.341089 TGCCCAAAGTAACCACACACA 60.341 47.619 0.00 0.00 0.00 3.72
935 948 1.066454 GCCCAAAGTAACCACACACAC 59.934 52.381 0.00 0.00 0.00 3.82
936 949 1.679153 CCCAAAGTAACCACACACACC 59.321 52.381 0.00 0.00 0.00 4.16
937 950 2.370349 CCAAAGTAACCACACACACCA 58.630 47.619 0.00 0.00 0.00 4.17
938 951 2.755655 CCAAAGTAACCACACACACCAA 59.244 45.455 0.00 0.00 0.00 3.67
939 952 3.428316 CCAAAGTAACCACACACACCAAC 60.428 47.826 0.00 0.00 0.00 3.77
940 953 2.791347 AGTAACCACACACACCAACA 57.209 45.000 0.00 0.00 0.00 3.33
941 954 3.074675 AGTAACCACACACACCAACAA 57.925 42.857 0.00 0.00 0.00 2.83
957 971 1.511254 CAATCGTCGTCTCGTGCGA 60.511 57.895 11.53 11.53 38.73 5.10
1014 1032 2.969238 GCCATGGCGACGATGAGG 60.969 66.667 23.48 0.00 0.00 3.86
1245 1263 0.456312 GCGTCATCGTCGACTTCCTT 60.456 55.000 14.70 0.00 39.49 3.36
1253 1271 1.402456 CGTCGACTTCCTTGGTACCTG 60.402 57.143 14.36 5.99 0.00 4.00
1262 1280 0.252197 CTTGGTACCTGCCTACCACC 59.748 60.000 14.36 0.00 44.91 4.61
1264 1282 1.614226 GGTACCTGCCTACCACCCA 60.614 63.158 4.06 0.00 36.84 4.51
1270 1288 0.824759 CTGCCTACCACCCAGTCTAC 59.175 60.000 0.00 0.00 0.00 2.59
1275 1293 3.091545 CCTACCACCCAGTCTACGTAAA 58.908 50.000 0.00 0.00 0.00 2.01
1288 1306 7.088905 CAGTCTACGTAAACTGTAAAGATGGT 58.911 38.462 18.91 0.00 38.44 3.55
1294 1312 0.676782 ACTGTAAAGATGGTGGCCGC 60.677 55.000 8.12 8.12 0.00 6.53
1295 1313 0.676466 CTGTAAAGATGGTGGCCGCA 60.676 55.000 19.98 4.65 0.00 5.69
1727 1745 1.697432 CCTACTTTGTCCACCACCTCA 59.303 52.381 0.00 0.00 0.00 3.86
1729 1747 1.213296 ACTTTGTCCACCACCTCACT 58.787 50.000 0.00 0.00 0.00 3.41
1795 1835 7.445096 TGATCATCTGACACTGTGTTAATTTGT 59.555 33.333 15.54 0.24 0.00 2.83
2017 2057 1.865045 TCCAGAGGACCTACCCCCA 60.865 63.158 0.00 0.00 40.05 4.96
2095 2138 4.392138 CCCTCAGAATTTCGGTAAGTTGAC 59.608 45.833 0.00 0.00 0.00 3.18
2096 2139 4.994852 CCTCAGAATTTCGGTAAGTTGACA 59.005 41.667 0.00 0.00 0.00 3.58
2107 2150 3.866910 GGTAAGTTGACACAGTTTCGTCA 59.133 43.478 0.00 0.00 40.30 4.35
2119 2162 6.964934 ACACAGTTTCGTCATCAAAACTTTAC 59.035 34.615 0.00 0.00 41.67 2.01
2145 2258 9.445878 CAAGTTACATCTATCCATATCAAGCAT 57.554 33.333 0.00 0.00 0.00 3.79
2152 2265 9.189723 CATCTATCCATATCAAGCATACATACG 57.810 37.037 0.00 0.00 0.00 3.06
2155 2268 9.452065 CTATCCATATCAAGCATACATACGTAC 57.548 37.037 0.00 0.00 0.00 3.67
2156 2269 7.222000 TCCATATCAAGCATACATACGTACA 57.778 36.000 0.00 0.00 0.00 2.90
2158 2271 7.973944 TCCATATCAAGCATACATACGTACATC 59.026 37.037 0.00 0.00 0.00 3.06
2159 2272 7.976175 CCATATCAAGCATACATACGTACATCT 59.024 37.037 0.00 0.00 0.00 2.90
2160 2273 9.358872 CATATCAAGCATACATACGTACATCTT 57.641 33.333 0.00 0.00 0.00 2.40
2161 2274 7.875316 ATCAAGCATACATACGTACATCTTC 57.125 36.000 0.00 0.00 0.00 2.87
2162 2275 7.039313 TCAAGCATACATACGTACATCTTCT 57.961 36.000 0.00 0.00 0.00 2.85
2184 2297 8.415950 TTCTTATGTTTAAAATCTTGCTCCCA 57.584 30.769 0.00 0.00 0.00 4.37
2196 2309 3.578456 CTCCCACACGGTGCATTC 58.422 61.111 8.30 0.00 31.34 2.67
2211 2327 4.094887 GGTGCATTCTTGTACTACATGTGG 59.905 45.833 9.11 8.41 38.40 4.17
2250 2366 1.301423 GTGTAAAGTCGTTGTGCCCA 58.699 50.000 0.00 0.00 0.00 5.36
2251 2367 1.877443 GTGTAAAGTCGTTGTGCCCAT 59.123 47.619 0.00 0.00 0.00 4.00
2281 2397 4.704833 GTCCGGAGCAGCAAGGCA 62.705 66.667 3.06 0.00 35.83 4.75
2440 2565 1.854163 GCTACCTAGCTACTCCGCGG 61.854 65.000 22.12 22.12 45.62 6.46
2472 2601 6.430925 TCCATTTATCCAAAGTTGAGTCACAG 59.569 38.462 0.00 0.00 0.00 3.66
2474 2603 6.861065 TTTATCCAAAGTTGAGTCACAGTC 57.139 37.500 0.00 0.00 0.00 3.51
2476 2605 2.503765 TCCAAAGTTGAGTCACAGTCCA 59.496 45.455 0.00 0.00 0.00 4.02
2506 2635 4.358494 TGACGTAGAGAAAAGCTAGCTC 57.642 45.455 19.65 5.97 0.00 4.09
2507 2636 3.128938 TGACGTAGAGAAAAGCTAGCTCC 59.871 47.826 19.65 10.50 0.00 4.70
2508 2637 3.090037 ACGTAGAGAAAAGCTAGCTCCA 58.910 45.455 19.65 0.00 0.00 3.86
2535 2666 3.615496 GCATGCACAATAAGCTTTGGAAG 59.385 43.478 14.21 0.00 0.00 3.46
2706 2844 1.151668 CATGCCCATCTAGCTAACGC 58.848 55.000 0.00 0.00 0.00 4.84
2708 2846 0.758734 TGCCCATCTAGCTAACGCAT 59.241 50.000 0.00 0.00 39.10 4.73
2709 2847 1.151668 GCCCATCTAGCTAACGCATG 58.848 55.000 0.00 0.00 39.10 4.06
2710 2848 1.151668 CCCATCTAGCTAACGCATGC 58.848 55.000 7.91 7.91 39.10 4.06
2711 2849 1.541015 CCCATCTAGCTAACGCATGCA 60.541 52.381 19.57 0.00 39.10 3.96
2712 2850 1.528586 CCATCTAGCTAACGCATGCAC 59.471 52.381 19.57 0.88 39.10 4.57
2761 2900 5.277202 CGTGACAGTGTGCGTATAGTATAGT 60.277 44.000 0.00 0.00 0.00 2.12
2762 2901 6.074142 CGTGACAGTGTGCGTATAGTATAGTA 60.074 42.308 0.00 0.00 0.00 1.82
2763 2902 7.359849 CGTGACAGTGTGCGTATAGTATAGTAT 60.360 40.741 0.00 5.43 0.00 2.12
2764 2903 8.929746 GTGACAGTGTGCGTATAGTATAGTATA 58.070 37.037 0.00 3.54 0.00 1.47
2802 2941 2.336667 CACTGTACATGCATGTGACGA 58.663 47.619 36.72 18.29 41.89 4.20
2807 2946 1.080435 ACATGCATGTGACGAGCTCG 61.080 55.000 33.45 33.45 41.76 5.03
2849 2988 5.694006 GCGTATAATTTGACAGAGAGATGCT 59.306 40.000 0.00 0.00 0.00 3.79
2853 2992 0.820226 TTGACAGAGAGATGCTCCGG 59.180 55.000 0.00 0.00 45.10 5.14
2872 3011 3.541711 CGGAAAGTCATGTTCACGAAAC 58.458 45.455 0.00 0.00 38.43 2.78
2880 3019 9.825972 AAAGTCATGTTCACGAAACTAATAATG 57.174 29.630 0.00 0.00 38.76 1.90
2957 3096 1.202463 CGTCTCCTCATGGTCATCACC 60.202 57.143 0.00 0.00 44.10 4.02
2958 3097 1.139853 GTCTCCTCATGGTCATCACCC 59.860 57.143 0.00 0.00 42.99 4.61
2959 3098 1.206878 CTCCTCATGGTCATCACCCA 58.793 55.000 0.00 0.00 42.99 4.51
2960 3099 1.773052 CTCCTCATGGTCATCACCCAT 59.227 52.381 0.00 0.00 42.99 4.00
2961 3100 1.770658 TCCTCATGGTCATCACCCATC 59.229 52.381 0.00 0.00 42.99 3.51
2963 3102 2.486727 CCTCATGGTCATCACCCATCAG 60.487 54.545 0.00 0.00 42.99 2.90
2964 3103 2.172082 CTCATGGTCATCACCCATCAGT 59.828 50.000 0.00 0.00 42.99 3.41
2969 3112 2.093658 GGTCATCACCCATCAGTACGTT 60.094 50.000 0.00 0.00 36.54 3.99
3031 3174 7.552687 TGATTGGCAGTAGTAGTAAAATGAAGG 59.447 37.037 0.00 0.00 0.00 3.46
3037 3180 7.413109 GCAGTAGTAGTAAAATGAAGGACAAGC 60.413 40.741 0.00 0.00 0.00 4.01
3039 3182 7.819900 AGTAGTAGTAAAATGAAGGACAAGCAG 59.180 37.037 0.00 0.00 0.00 4.24
3048 3192 0.621571 AGGACAAGCAGGATGGGCTA 60.622 55.000 0.00 0.00 41.66 3.93
3056 3200 5.075493 CAAGCAGGATGGGCTAATAGAAAT 58.925 41.667 0.00 0.00 41.66 2.17
3145 3291 4.518970 CAGGGCAAGTACAACTACAACAAT 59.481 41.667 0.00 0.00 0.00 2.71
3304 3450 1.263484 CGCATCCTGCACTGATCATTC 59.737 52.381 0.00 0.00 45.36 2.67
3307 3453 3.380637 GCATCCTGCACTGATCATTCTTT 59.619 43.478 0.00 0.00 44.26 2.52
3308 3454 4.497674 GCATCCTGCACTGATCATTCTTTC 60.498 45.833 0.00 0.00 44.26 2.62
3313 3459 6.765036 TCCTGCACTGATCATTCTTTCTTATC 59.235 38.462 0.00 0.00 0.00 1.75
3319 3465 8.494347 CACTGATCATTCTTTCTTATCGATTCC 58.506 37.037 1.71 0.00 0.00 3.01
3385 3534 1.066215 TCAAGTGTGGTGGGATCGATG 60.066 52.381 0.54 0.00 0.00 3.84
3397 3558 0.441533 GATCGATGGATGCGTCATGC 59.558 55.000 0.54 4.79 46.70 4.06
3516 3677 4.178956 ACTAGATGTGTTGTTTGGGGTT 57.821 40.909 0.00 0.00 0.00 4.11
3520 3681 5.467035 AGATGTGTTGTTTGGGGTTATTG 57.533 39.130 0.00 0.00 0.00 1.90
3524 3690 5.178797 TGTGTTGTTTGGGGTTATTGTTTG 58.821 37.500 0.00 0.00 0.00 2.93
3543 3709 7.026631 TGTTTGACTGTAAACTGAGGAAATG 57.973 36.000 0.00 0.00 40.36 2.32
3585 3751 6.737254 TTAACCGAACTGAGGAAATGAATC 57.263 37.500 0.00 0.00 0.00 2.52
3586 3752 4.286297 ACCGAACTGAGGAAATGAATCA 57.714 40.909 0.00 0.00 0.00 2.57
3602 3769 6.764308 ATGAATCAAACGAGGTCATCATTT 57.236 33.333 0.00 0.00 0.00 2.32
3605 3772 3.343617 TCAAACGAGGTCATCATTTCCC 58.656 45.455 0.00 0.00 0.00 3.97
3647 3814 3.914364 CGCTTGAGCTTGATTTTGGTAAC 59.086 43.478 1.07 0.00 39.32 2.50
3662 3829 5.811399 TTGGTAACTGATTCCGCATTAAG 57.189 39.130 0.00 0.00 37.61 1.85
3683 3850 2.739609 GCCATTTGCTATGAGGTTTGCC 60.740 50.000 1.56 0.00 36.87 4.52
3687 3854 0.323302 TGCTATGAGGTTTGCCGTCA 59.677 50.000 0.00 0.00 40.50 4.35
3698 3865 3.049912 GTTTGCCGTCAATTTCCTTCAC 58.950 45.455 0.00 0.00 31.33 3.18
3761 3931 1.621814 TGGTTGGACCGTTAGAAGGAG 59.378 52.381 0.00 0.00 42.58 3.69
3774 3944 1.041437 GAAGGAGAGTGGTATCCCCG 58.959 60.000 0.00 0.00 34.18 5.73
3777 3947 1.760875 GAGAGTGGTATCCCCGGCA 60.761 63.158 0.00 0.00 35.15 5.69
3778 3948 1.074471 AGAGTGGTATCCCCGGCAT 60.074 57.895 0.00 0.00 35.15 4.40
3787 3957 1.270907 ATCCCCGGCATATCAGAGTC 58.729 55.000 0.00 0.00 0.00 3.36
3788 3958 0.105709 TCCCCGGCATATCAGAGTCA 60.106 55.000 0.00 0.00 0.00 3.41
3814 3984 4.623932 TCTAGACTTGACATTGGTGCTT 57.376 40.909 0.00 0.00 0.00 3.91
3858 4028 2.545742 GGCCTTTTGACGATGTGCTTTT 60.546 45.455 0.00 0.00 0.00 2.27
3871 4041 1.075601 TGCTTTTGGTGGGAGGAGAT 58.924 50.000 0.00 0.00 0.00 2.75
3877 4047 4.469469 TTTGGTGGGAGGAGATTTTTCT 57.531 40.909 0.00 0.00 0.00 2.52
3951 4121 1.303398 TCGGTCTCTCGAAGGTGCT 60.303 57.895 0.00 0.00 36.12 4.40
3952 4122 0.035725 TCGGTCTCTCGAAGGTGCTA 60.036 55.000 0.00 0.00 36.12 3.49
3953 4123 1.025812 CGGTCTCTCGAAGGTGCTAT 58.974 55.000 0.00 0.00 0.00 2.97
3954 4124 2.158856 TCGGTCTCTCGAAGGTGCTATA 60.159 50.000 0.00 0.00 36.12 1.31
3981 4151 0.668401 GGTAGGGTGTACGTGTGTGC 60.668 60.000 0.00 0.00 0.00 4.57
3982 4152 1.005294 GTAGGGTGTACGTGTGTGCG 61.005 60.000 0.00 0.00 32.77 5.34
3991 4161 2.941891 ACGTGTGTGCGTTCATAAAG 57.058 45.000 0.00 0.00 43.04 1.85
3994 4164 2.732500 CGTGTGTGCGTTCATAAAGGTA 59.267 45.455 0.00 0.00 0.00 3.08
4001 4171 5.406175 TGTGCGTTCATAAAGGTAAGTGTAC 59.594 40.000 0.00 0.00 0.00 2.90
4002 4172 5.406175 GTGCGTTCATAAAGGTAAGTGTACA 59.594 40.000 0.00 0.00 31.21 2.90
4006 4176 6.475207 GTTCATAAAGGTAAGTGTACATGCG 58.525 40.000 0.00 0.00 31.21 4.73
4023 4193 3.733443 TGCGTATGTATGAGCATCTGT 57.267 42.857 0.00 0.00 34.39 3.41
4026 4196 3.426859 GCGTATGTATGAGCATCTGTGTC 59.573 47.826 0.00 0.00 34.92 3.67
4027 4197 4.794329 GCGTATGTATGAGCATCTGTGTCT 60.794 45.833 0.00 0.00 34.92 3.41
4028 4198 5.562890 GCGTATGTATGAGCATCTGTGTCTA 60.563 44.000 0.00 0.00 34.92 2.59
4031 4201 7.694367 CGTATGTATGAGCATCTGTGTCTATAC 59.306 40.741 0.00 0.00 34.92 1.47
4038 4208 6.042638 AGCATCTGTGTCTATACTGTGTTT 57.957 37.500 0.00 0.00 0.00 2.83
4051 4221 6.952773 ATACTGTGTTTAAAAAGTCAGGCA 57.047 33.333 3.45 0.00 0.00 4.75
4055 4225 3.425193 GTGTTTAAAAAGTCAGGCATGCG 59.575 43.478 12.44 0.00 0.00 4.73
4056 4226 3.067461 TGTTTAAAAAGTCAGGCATGCGT 59.933 39.130 12.44 9.84 0.00 5.24
4061 4231 2.698855 AAGTCAGGCATGCGTATCTT 57.301 45.000 13.36 15.98 0.00 2.40
4068 4238 1.643292 CATGCGTATCTTGGTGGCG 59.357 57.895 0.00 0.00 0.00 5.69
4077 4247 1.002134 CTTGGTGGCGGTCATTCCT 60.002 57.895 0.00 0.00 0.00 3.36
4090 4260 4.530875 GGTCATTCCTGATCTTGGATTGT 58.469 43.478 19.62 6.44 36.72 2.71
4094 4264 5.649395 TCATTCCTGATCTTGGATTGTTGAC 59.351 40.000 19.62 0.00 36.72 3.18
4103 4273 2.217750 TGGATTGTTGACGTGGACAAG 58.782 47.619 15.77 0.00 38.95 3.16
4104 4274 2.218603 GGATTGTTGACGTGGACAAGT 58.781 47.619 15.77 7.13 38.95 3.16
4106 4276 2.388310 TTGTTGACGTGGACAAGTGA 57.612 45.000 8.74 0.00 32.43 3.41
4108 4278 0.935196 GTTGACGTGGACAAGTGACC 59.065 55.000 0.00 0.00 0.00 4.02
4124 4294 3.948851 GTGACCTCCACGAAAAGTTTTC 58.051 45.455 16.87 16.87 35.86 2.29
4125 4295 3.626217 GTGACCTCCACGAAAAGTTTTCT 59.374 43.478 22.57 9.78 35.86 2.52
4127 4297 4.095782 TGACCTCCACGAAAAGTTTTCTTG 59.904 41.667 21.83 21.83 40.37 3.02
4128 4298 3.181490 ACCTCCACGAAAAGTTTTCTTGC 60.181 43.478 22.86 2.73 40.37 4.01
4129 4299 3.181491 CCTCCACGAAAAGTTTTCTTGCA 60.181 43.478 22.86 12.29 40.37 4.08
4130 4300 4.420168 CTCCACGAAAAGTTTTCTTGCAA 58.580 39.130 22.86 14.66 40.37 4.08
4137 4321 0.389025 AGTTTTCTTGCAAAGGCCGG 59.611 50.000 0.00 0.00 46.24 6.13
4164 4348 4.926832 CCCGCGGAATACTTTGAAAATTTT 59.073 37.500 30.73 2.28 0.00 1.82
4165 4349 5.164002 CCCGCGGAATACTTTGAAAATTTTG 60.164 40.000 30.73 0.00 0.00 2.44
4186 4370 5.277857 TGAAGTTAATAGCCTAGGTGCTC 57.722 43.478 11.31 0.00 41.68 4.26
4206 4390 1.305718 GAGGACCAGACCAGGCTCT 60.306 63.158 0.00 0.00 0.00 4.09
4231 4415 1.004044 CAGCTGGTCAAGGGTGAAGAT 59.996 52.381 5.57 0.00 34.87 2.40
4234 4418 2.938756 GCTGGTCAAGGGTGAAGATGAG 60.939 54.545 0.00 0.00 34.87 2.90
4246 4430 3.415087 GATGAGGCCAGGGGTGCT 61.415 66.667 5.01 0.00 0.00 4.40
4280 4464 0.312416 CACCGAGGATTAGGAGCTCG 59.688 60.000 7.83 0.00 37.30 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.940126 CCACTGACACAACACAGAGC 59.060 55.000 0.00 0.00 37.54 4.09
68 69 4.325028 TTGCAGAACGGTAACTAAGACA 57.675 40.909 0.00 0.00 0.00 3.41
94 95 5.233689 GTCGCTTCGCCAGTATATAAGTTTT 59.766 40.000 0.00 0.00 0.00 2.43
95 96 4.743644 GTCGCTTCGCCAGTATATAAGTTT 59.256 41.667 0.00 0.00 0.00 2.66
101 102 0.666913 ACGTCGCTTCGCCAGTATAT 59.333 50.000 0.00 0.00 0.00 0.86
109 110 0.985416 GTCAACAAACGTCGCTTCGC 60.985 55.000 0.00 0.00 0.00 4.70
118 119 1.070843 CACGCTAGTGGTCAACAAACG 60.071 52.381 8.42 0.00 44.34 3.60
141 142 1.682854 CCATTCAACAACAGCAGTGGT 59.317 47.619 0.00 0.00 31.62 4.16
147 150 3.855689 ATAGCACCATTCAACAACAGC 57.144 42.857 0.00 0.00 0.00 4.40
166 169 2.224548 GGGCGATTAGGTGAGGCTTAAT 60.225 50.000 0.00 0.00 32.87 1.40
186 189 4.782195 GCACATAGTTCGACGCTAAATTGG 60.782 45.833 0.00 0.00 0.00 3.16
189 192 2.534349 CGCACATAGTTCGACGCTAAAT 59.466 45.455 0.00 0.00 0.00 1.40
195 198 1.822581 TCATCGCACATAGTTCGACG 58.177 50.000 0.00 0.00 33.87 5.12
227 232 8.230486 ACGTTTCACTTTCAGATACATGATTTC 58.770 33.333 0.00 0.00 0.00 2.17
257 262 5.813717 TCGTGCCCGATATATTAGTTATCG 58.186 41.667 6.20 6.20 44.97 2.92
273 278 3.064134 GCTCTCTTTTCTAAATCGTGCCC 59.936 47.826 0.00 0.00 0.00 5.36
302 307 3.054166 TCGAATTATGCAACCGATACCG 58.946 45.455 0.00 0.00 0.00 4.02
303 308 4.688879 TGATCGAATTATGCAACCGATACC 59.311 41.667 10.46 3.30 39.65 2.73
304 309 5.839262 TGATCGAATTATGCAACCGATAC 57.161 39.130 10.46 6.88 39.65 2.24
305 310 5.580691 GGATGATCGAATTATGCAACCGATA 59.419 40.000 10.46 3.43 39.65 2.92
306 311 4.393062 GGATGATCGAATTATGCAACCGAT 59.607 41.667 10.34 10.34 41.85 4.18
307 312 3.745975 GGATGATCGAATTATGCAACCGA 59.254 43.478 0.00 0.00 0.00 4.69
308 313 3.498018 TGGATGATCGAATTATGCAACCG 59.502 43.478 0.00 0.00 0.00 4.44
309 314 5.215160 GTTGGATGATCGAATTATGCAACC 58.785 41.667 22.11 10.14 45.37 3.77
311 316 5.008911 CCTGTTGGATGATCGAATTATGCAA 59.991 40.000 8.88 8.88 34.98 4.08
317 322 3.003394 TGCCTGTTGGATGATCGAATT 57.997 42.857 0.00 0.00 34.57 2.17
318 323 2.715749 TGCCTGTTGGATGATCGAAT 57.284 45.000 0.00 0.00 34.57 3.34
333 338 2.405618 TAGTATGAGCTCCCATGCCT 57.594 50.000 12.15 3.38 30.81 4.75
379 384 0.469331 TTCGATCTGTCCCGCCCTAT 60.469 55.000 0.00 0.00 0.00 2.57
392 397 5.140177 GTCATGCGTCCATTTATTTCGATC 58.860 41.667 0.00 0.00 0.00 3.69
395 400 4.271590 TGTCATGCGTCCATTTATTTCG 57.728 40.909 0.00 0.00 0.00 3.46
403 408 0.252761 TGTCCATGTCATGCGTCCAT 59.747 50.000 7.35 0.00 0.00 3.41
420 425 3.478857 TGTAACGGGAGACATTGTTGT 57.521 42.857 0.00 0.00 39.32 3.32
421 426 3.562141 TGTTGTAACGGGAGACATTGTTG 59.438 43.478 0.00 0.00 0.00 3.33
438 443 1.202245 GCACAAATGTCCGTGTGTTGT 60.202 47.619 5.76 0.00 45.60 3.32
439 444 1.202234 TGCACAAATGTCCGTGTGTTG 60.202 47.619 5.76 0.00 45.60 3.33
447 452 0.040425 GTCCGTGTGCACAAATGTCC 60.040 55.000 23.59 6.98 0.00 4.02
448 453 0.660488 TGTCCGTGTGCACAAATGTC 59.340 50.000 23.59 7.80 0.00 3.06
449 454 1.317613 ATGTCCGTGTGCACAAATGT 58.682 45.000 23.59 2.89 0.00 2.71
459 464 2.543777 ACTAGCACAAATGTCCGTGT 57.456 45.000 0.00 0.00 35.51 4.49
460 465 2.805671 TCAACTAGCACAAATGTCCGTG 59.194 45.455 0.00 0.00 36.18 4.94
461 466 3.120321 TCAACTAGCACAAATGTCCGT 57.880 42.857 0.00 0.00 0.00 4.69
462 467 4.481930 TTTCAACTAGCACAAATGTCCG 57.518 40.909 0.00 0.00 0.00 4.79
463 468 7.865385 TGTTAATTTCAACTAGCACAAATGTCC 59.135 33.333 0.00 0.00 0.00 4.02
464 469 8.795786 TGTTAATTTCAACTAGCACAAATGTC 57.204 30.769 0.00 0.00 0.00 3.06
465 470 9.593134 TTTGTTAATTTCAACTAGCACAAATGT 57.407 25.926 0.00 0.00 30.05 2.71
496 501 5.689383 ACGAACTTTGATGCTAAACACAT 57.311 34.783 0.00 0.00 0.00 3.21
574 583 7.128263 ACTTGTAACTAGATATTTTAGGCCCCA 59.872 37.037 0.00 0.00 0.00 4.96
602 611 1.367659 GATGCTTGACAGGTGAGAGC 58.632 55.000 0.00 0.00 0.00 4.09
618 627 2.009774 GTTGATTGGTCGACTGGGATG 58.990 52.381 16.46 0.00 36.09 3.51
736 745 1.068474 ACTCACGTACGCATCTTTGC 58.932 50.000 16.72 0.00 45.78 3.68
847 857 3.612247 CTTCCCCGGTGGACTGCTG 62.612 68.421 10.84 0.00 45.11 4.41
848 858 3.322466 CTTCCCCGGTGGACTGCT 61.322 66.667 10.84 0.00 45.11 4.24
849 859 4.410400 CCTTCCCCGGTGGACTGC 62.410 72.222 10.84 0.00 45.11 4.40
850 860 4.410400 GCCTTCCCCGGTGGACTG 62.410 72.222 10.84 6.81 45.11 3.51
887 897 0.690762 TGGGATTTATAGGCGGGCTC 59.309 55.000 7.59 0.00 0.00 4.70
915 925 1.066454 GTGTGTGTGGTTACTTTGGGC 59.934 52.381 0.00 0.00 0.00 5.36
919 929 3.422796 TGTTGGTGTGTGTGGTTACTTT 58.577 40.909 0.00 0.00 0.00 2.66
920 930 3.074675 TGTTGGTGTGTGTGGTTACTT 57.925 42.857 0.00 0.00 0.00 2.24
921 931 2.791347 TGTTGGTGTGTGTGGTTACT 57.209 45.000 0.00 0.00 0.00 2.24
934 947 0.313043 ACGAGACGACGATTGTTGGT 59.687 50.000 0.00 0.00 37.03 3.67
935 948 0.708370 CACGAGACGACGATTGTTGG 59.292 55.000 0.00 0.00 37.03 3.77
936 949 0.091344 GCACGAGACGACGATTGTTG 59.909 55.000 0.00 0.00 37.03 3.33
937 950 1.334992 CGCACGAGACGACGATTGTT 61.335 55.000 0.00 0.00 37.03 2.83
938 951 1.796355 CGCACGAGACGACGATTGT 60.796 57.895 0.00 0.00 37.03 2.71
939 952 1.511254 TCGCACGAGACGACGATTG 60.511 57.895 0.00 0.00 35.23 2.67
940 953 2.865308 TCGCACGAGACGACGATT 59.135 55.556 0.00 0.00 35.23 3.34
1179 1197 0.693049 GCTTGAAGAAGGTCTCCCCA 59.307 55.000 0.00 0.00 34.66 4.96
1253 1271 0.969409 ACGTAGACTGGGTGGTAGGC 60.969 60.000 0.00 0.00 0.00 3.93
1262 1280 6.530534 CCATCTTTACAGTTTACGTAGACTGG 59.469 42.308 35.63 23.80 45.78 4.00
1264 1282 7.088905 CACCATCTTTACAGTTTACGTAGACT 58.911 38.462 12.70 12.70 0.00 3.24
1270 1288 3.126343 GGCCACCATCTTTACAGTTTACG 59.874 47.826 0.00 0.00 0.00 3.18
1275 1293 0.676782 GCGGCCACCATCTTTACAGT 60.677 55.000 2.24 0.00 0.00 3.55
1288 1306 1.303970 TTCACCATCATTGCGGCCA 60.304 52.632 2.24 0.00 0.00 5.36
1294 1312 3.894782 TTGTCACGTTCACCATCATTG 57.105 42.857 0.00 0.00 0.00 2.82
1295 1313 3.882888 ACTTTGTCACGTTCACCATCATT 59.117 39.130 0.00 0.00 0.00 2.57
1727 1745 1.751924 GAGCCGGTGAGATTAGTGAGT 59.248 52.381 1.90 0.00 0.00 3.41
1729 1747 1.112113 GGAGCCGGTGAGATTAGTGA 58.888 55.000 1.90 0.00 0.00 3.41
1778 1814 9.654417 AAAATACGTACAAATTAACACAGTGTC 57.346 29.630 6.67 0.00 0.00 3.67
1795 1835 6.546972 TCATGTTCTGCACAAAAATACGTA 57.453 33.333 0.00 0.00 39.50 3.57
2017 2057 0.178068 GGCGTACATGATCCTGGTGT 59.822 55.000 0.00 0.00 0.00 4.16
2119 2162 8.837788 TGCTTGATATGGATAGATGTAACTTG 57.162 34.615 0.00 0.00 0.00 3.16
2128 2241 8.293699 ACGTATGTATGCTTGATATGGATAGA 57.706 34.615 0.00 0.00 0.00 1.98
2129 2242 9.452065 GTACGTATGTATGCTTGATATGGATAG 57.548 37.037 0.00 0.00 32.11 2.08
2134 2247 8.917415 AGATGTACGTATGTATGCTTGATATG 57.083 34.615 0.00 0.00 32.11 1.78
2139 2252 7.700322 AAGAAGATGTACGTATGTATGCTTG 57.300 36.000 0.00 0.00 32.11 4.01
2140 2253 9.411801 CATAAGAAGATGTACGTATGTATGCTT 57.588 33.333 0.00 1.17 32.11 3.91
2158 2271 8.522830 TGGGAGCAAGATTTTAAACATAAGAAG 58.477 33.333 0.00 0.00 0.00 2.85
2159 2272 8.303876 GTGGGAGCAAGATTTTAAACATAAGAA 58.696 33.333 0.00 0.00 0.00 2.52
2160 2273 7.450014 TGTGGGAGCAAGATTTTAAACATAAGA 59.550 33.333 0.00 0.00 0.00 2.10
2161 2274 7.542130 GTGTGGGAGCAAGATTTTAAACATAAG 59.458 37.037 0.00 0.00 0.00 1.73
2162 2275 7.375053 GTGTGGGAGCAAGATTTTAAACATAA 58.625 34.615 0.00 0.00 0.00 1.90
2179 2292 0.606401 AAGAATGCACCGTGTGGGAG 60.606 55.000 0.00 0.00 40.75 4.30
2180 2293 0.888736 CAAGAATGCACCGTGTGGGA 60.889 55.000 0.00 0.00 40.75 4.37
2181 2294 1.172180 ACAAGAATGCACCGTGTGGG 61.172 55.000 8.31 0.00 40.75 4.61
2182 2295 1.196808 GTACAAGAATGCACCGTGTGG 59.803 52.381 15.98 0.00 42.84 4.17
2184 2297 2.543777 AGTACAAGAATGCACCGTGT 57.456 45.000 12.53 12.53 0.00 4.49
2196 2309 6.525578 TTCCTACTCCACATGTAGTACAAG 57.474 41.667 7.16 5.45 36.56 3.16
2211 2327 6.426646 ACACAAGGATGGATATTCCTACTC 57.573 41.667 0.00 0.00 42.90 2.59
2250 2366 0.255890 CCGGACAGGGATGTTTGGAT 59.744 55.000 0.00 0.00 35.97 3.41
2251 2367 0.838554 TCCGGACAGGGATGTTTGGA 60.839 55.000 0.00 0.00 41.52 3.53
2281 2397 5.147330 TCGATTCCTACTTCACATGTGTT 57.853 39.130 24.63 13.06 0.00 3.32
2440 2565 4.514401 ACTTTGGATAAATGGACGTCTCC 58.486 43.478 16.46 13.52 37.04 3.71
2446 2571 6.206634 TGTGACTCAACTTTGGATAAATGGAC 59.793 38.462 0.00 0.00 0.00 4.02
2448 2573 6.207417 ACTGTGACTCAACTTTGGATAAATGG 59.793 38.462 0.00 0.00 0.00 3.16
2472 2601 3.650139 TCTACGTCAAAGAAAGCTGGAC 58.350 45.455 0.00 0.00 0.00 4.02
2474 2603 3.914312 TCTCTACGTCAAAGAAAGCTGG 58.086 45.455 0.00 0.00 0.00 4.85
2476 2605 5.050023 GCTTTTCTCTACGTCAAAGAAAGCT 60.050 40.000 21.37 0.00 39.45 3.74
2506 2635 2.883574 CTTATTGTGCATGCACCTTGG 58.116 47.619 40.01 24.67 45.63 3.61
2507 2636 2.094390 AGCTTATTGTGCATGCACCTTG 60.094 45.455 40.01 27.01 45.63 3.61
2508 2637 2.173519 AGCTTATTGTGCATGCACCTT 58.826 42.857 40.01 30.31 45.63 3.50
2535 2666 5.337975 GGCTAAGAATCCAGGAGACCATATC 60.338 48.000 0.00 0.00 0.00 1.63
2691 2829 1.151668 GCATGCGTTAGCTAGATGGG 58.848 55.000 0.00 0.00 45.42 4.00
2706 2844 8.856247 CATTTCATAATAATTGGATCGTGCATG 58.144 33.333 0.00 0.00 0.00 4.06
2708 2846 8.164058 TCATTTCATAATAATTGGATCGTGCA 57.836 30.769 0.00 0.00 0.00 4.57
2709 2847 7.752239 CCTCATTTCATAATAATTGGATCGTGC 59.248 37.037 0.00 0.00 0.00 5.34
2710 2848 8.239314 CCCTCATTTCATAATAATTGGATCGTG 58.761 37.037 0.00 0.00 0.00 4.35
2711 2849 7.094205 GCCCTCATTTCATAATAATTGGATCGT 60.094 37.037 0.00 0.00 0.00 3.73
2712 2850 7.253422 GCCCTCATTTCATAATAATTGGATCG 58.747 38.462 0.00 0.00 0.00 3.69
2774 2913 5.341707 ACATGCATGTACAGTGCTTTAGCA 61.342 41.667 30.50 0.00 43.72 3.49
2777 2916 4.154015 GTCACATGCATGTACAGTGCTTTA 59.846 41.667 30.92 0.96 42.92 1.85
2788 2927 1.080435 CGAGCTCGTCACATGCATGT 61.080 55.000 26.61 26.61 36.61 3.21
2802 2941 3.181489 CGTTATACCTGGAAAGACGAGCT 60.181 47.826 0.00 0.00 0.00 4.09
2807 2946 2.199236 CGCCGTTATACCTGGAAAGAC 58.801 52.381 0.00 0.00 0.00 3.01
2815 2954 6.514947 TGTCAAATTATACGCCGTTATACCT 58.485 36.000 0.00 0.00 0.00 3.08
2816 2955 6.642131 TCTGTCAAATTATACGCCGTTATACC 59.358 38.462 0.00 0.00 0.00 2.73
2849 2988 1.341852 TCGTGAACATGACTTTCCGGA 59.658 47.619 0.00 0.00 0.00 5.14
2872 3011 4.703575 ACATGGGCATGCTAGCATTATTAG 59.296 41.667 27.59 16.58 42.39 1.73
2880 3019 1.000607 CATGAACATGGGCATGCTAGC 60.001 52.381 18.92 8.10 42.39 3.42
2957 3096 2.347452 CCGCTTTGTAACGTACTGATGG 59.653 50.000 0.00 0.00 0.00 3.51
2958 3097 2.991190 ACCGCTTTGTAACGTACTGATG 59.009 45.455 0.00 0.00 0.00 3.07
2959 3098 3.057033 AGACCGCTTTGTAACGTACTGAT 60.057 43.478 0.00 0.00 0.00 2.90
2960 3099 2.294233 AGACCGCTTTGTAACGTACTGA 59.706 45.455 0.00 0.00 0.00 3.41
2961 3100 2.407361 CAGACCGCTTTGTAACGTACTG 59.593 50.000 0.00 0.00 0.00 2.74
2963 3102 1.723003 CCAGACCGCTTTGTAACGTAC 59.277 52.381 0.00 0.00 0.00 3.67
2964 3103 1.612950 TCCAGACCGCTTTGTAACGTA 59.387 47.619 0.00 0.00 0.00 3.57
2969 3112 1.403647 CGTGATCCAGACCGCTTTGTA 60.404 52.381 0.00 0.00 0.00 2.41
2992 3135 1.586422 CCAATCAGTATGCGTCCTGG 58.414 55.000 0.00 0.00 34.76 4.45
3031 3174 2.355010 ATTAGCCCATCCTGCTTGTC 57.645 50.000 0.00 0.00 40.23 3.18
3037 3180 3.760684 GCCATTTCTATTAGCCCATCCTG 59.239 47.826 0.00 0.00 0.00 3.86
3039 3182 4.039603 AGCCATTTCTATTAGCCCATCC 57.960 45.455 0.00 0.00 0.00 3.51
3048 3192 4.588528 ACACACACCAAAGCCATTTCTATT 59.411 37.500 0.00 0.00 0.00 1.73
3056 3200 0.613292 AACCACACACACCAAAGCCA 60.613 50.000 0.00 0.00 0.00 4.75
3145 3291 3.781307 ATGCCGCACCTCGCCTTA 61.781 61.111 0.00 0.00 37.30 2.69
3352 3498 3.291585 CACACTTGATCAGAAAACGCAC 58.708 45.455 0.00 0.00 0.00 5.34
3397 3558 3.015293 GCTGTCACATCCGCACACG 62.015 63.158 0.00 0.00 39.67 4.49
3403 3564 9.189723 CATCATATATATTAGCTGTCACATCCG 57.810 37.037 0.00 0.00 0.00 4.18
3465 3626 6.884295 AGTTTTATTCATTCATTCTCCGGACA 59.116 34.615 0.00 0.00 0.00 4.02
3496 3657 6.208599 ACAATAACCCCAAACAACACATCTAG 59.791 38.462 0.00 0.00 0.00 2.43
3498 3659 4.898861 ACAATAACCCCAAACAACACATCT 59.101 37.500 0.00 0.00 0.00 2.90
3512 3673 7.266922 TCAGTTTACAGTCAAACAATAACCC 57.733 36.000 1.99 0.00 40.22 4.11
3516 3677 8.740123 TTTCCTCAGTTTACAGTCAAACAATA 57.260 30.769 1.99 0.00 40.22 1.90
3520 3681 6.438763 CCATTTCCTCAGTTTACAGTCAAAC 58.561 40.000 0.00 0.00 38.44 2.93
3524 3690 4.327680 AGCCATTTCCTCAGTTTACAGTC 58.672 43.478 0.00 0.00 0.00 3.51
3556 3722 2.500098 TCCTCAGTTCGGTTAATCAGGG 59.500 50.000 0.00 0.00 0.00 4.45
3567 3733 5.082059 CGTTTGATTCATTTCCTCAGTTCG 58.918 41.667 0.00 0.00 0.00 3.95
3568 3734 6.241207 TCGTTTGATTCATTTCCTCAGTTC 57.759 37.500 0.00 0.00 0.00 3.01
3585 3751 3.127548 CAGGGAAATGATGACCTCGTTTG 59.872 47.826 3.02 0.00 42.01 2.93
3586 3752 3.347216 CAGGGAAATGATGACCTCGTTT 58.653 45.455 0.00 0.00 44.10 3.60
3602 3769 4.501071 GAACTTACGAAACATAGCAGGGA 58.499 43.478 0.00 0.00 0.00 4.20
3605 3772 3.241995 GCGGAACTTACGAAACATAGCAG 60.242 47.826 0.00 0.00 0.00 4.24
3647 3814 3.996150 AATGGCTTAATGCGGAATCAG 57.004 42.857 0.00 0.00 44.05 2.90
3662 3829 2.543641 GCAAACCTCATAGCAAATGGC 58.456 47.619 0.00 0.00 45.30 4.40
3676 3843 2.035321 TGAAGGAAATTGACGGCAAACC 59.965 45.455 8.31 12.46 37.59 3.27
3680 3847 1.243902 GGTGAAGGAAATTGACGGCA 58.756 50.000 0.00 0.00 0.00 5.69
3683 3850 0.168128 GCGGGTGAAGGAAATTGACG 59.832 55.000 0.00 0.00 0.00 4.35
3687 3854 1.185315 CATGGCGGGTGAAGGAAATT 58.815 50.000 0.00 0.00 0.00 1.82
3698 3865 3.186047 GACGACGAACATGGCGGG 61.186 66.667 0.00 8.11 0.00 6.13
3749 3919 3.318557 GGATACCACTCTCCTTCTAACGG 59.681 52.174 0.00 0.00 0.00 4.44
3750 3920 4.571372 GGATACCACTCTCCTTCTAACG 57.429 50.000 0.00 0.00 0.00 3.18
3774 3944 6.699642 GTCTAGAACTTTGACTCTGATATGCC 59.300 42.308 0.00 0.00 0.00 4.40
3777 3947 9.249053 TCAAGTCTAGAACTTTGACTCTGATAT 57.751 33.333 10.08 0.00 46.26 1.63
3778 3948 8.516234 GTCAAGTCTAGAACTTTGACTCTGATA 58.484 37.037 24.61 2.72 46.26 2.15
3787 3957 6.662616 CACCAATGTCAAGTCTAGAACTTTG 58.337 40.000 11.34 11.34 46.26 2.77
3788 3958 5.239525 GCACCAATGTCAAGTCTAGAACTTT 59.760 40.000 0.00 0.00 46.26 2.66
3814 3984 8.891720 GGCCTGAAATAAATTCATAAAAATGCA 58.108 29.630 0.00 0.00 46.62 3.96
3843 4013 1.336440 CCACCAAAAGCACATCGTCAA 59.664 47.619 0.00 0.00 0.00 3.18
3858 4028 2.716424 ACAGAAAAATCTCCTCCCACCA 59.284 45.455 0.00 0.00 0.00 4.17
3871 4041 3.970610 CGTCTTCGTAGTCGACAGAAAAA 59.029 43.478 19.50 8.32 46.03 1.94
3900 4070 4.248859 CATCTTGAGATGGACAAAGTCGT 58.751 43.478 12.20 0.00 46.09 4.34
3922 4092 0.814457 AGAGACCGAGCTGACACATC 59.186 55.000 0.00 0.00 0.00 3.06
3935 4105 5.961396 TTATATAGCACCTTCGAGAGACC 57.039 43.478 0.00 0.00 41.84 3.85
3951 4121 7.118723 CACGTACACCCTACCCCTATTATATA 58.881 42.308 0.00 0.00 0.00 0.86
3952 4122 5.954150 CACGTACACCCTACCCCTATTATAT 59.046 44.000 0.00 0.00 0.00 0.86
3953 4123 5.162991 ACACGTACACCCTACCCCTATTATA 60.163 44.000 0.00 0.00 0.00 0.98
3954 4124 4.154942 CACGTACACCCTACCCCTATTAT 58.845 47.826 0.00 0.00 0.00 1.28
3981 4151 6.475207 GCATGTACACTTACCTTTATGAACG 58.525 40.000 0.00 0.00 0.00 3.95
3982 4152 6.091713 ACGCATGTACACTTACCTTTATGAAC 59.908 38.462 0.00 0.00 0.00 3.18
4001 4171 3.992427 ACAGATGCTCATACATACGCATG 59.008 43.478 0.00 0.00 42.60 4.06
4002 4172 3.992427 CACAGATGCTCATACATACGCAT 59.008 43.478 0.00 0.00 44.97 4.73
4006 4176 8.735315 AGTATAGACACAGATGCTCATACATAC 58.265 37.037 0.00 0.00 0.00 2.39
4023 4193 9.268268 CCTGACTTTTTAAACACAGTATAGACA 57.732 33.333 0.00 0.00 0.00 3.41
4026 4196 8.094798 TGCCTGACTTTTTAAACACAGTATAG 57.905 34.615 0.00 0.00 0.00 1.31
4027 4197 8.511321 CATGCCTGACTTTTTAAACACAGTATA 58.489 33.333 0.00 0.00 0.00 1.47
4028 4198 6.952773 TGCCTGACTTTTTAAACACAGTAT 57.047 33.333 0.00 0.00 0.00 2.12
4031 4201 4.445385 GCATGCCTGACTTTTTAAACACAG 59.555 41.667 6.36 0.00 0.00 3.66
4038 4208 4.513442 AGATACGCATGCCTGACTTTTTA 58.487 39.130 13.15 0.00 0.00 1.52
4051 4221 1.523711 CCGCCACCAAGATACGCAT 60.524 57.895 0.00 0.00 0.00 4.73
4055 4225 1.940613 GAATGACCGCCACCAAGATAC 59.059 52.381 0.00 0.00 0.00 2.24
4056 4226 1.134220 GGAATGACCGCCACCAAGATA 60.134 52.381 0.00 0.00 0.00 1.98
4061 4231 1.561769 ATCAGGAATGACCGCCACCA 61.562 55.000 0.00 0.00 44.74 4.17
4068 4238 4.530875 ACAATCCAAGATCAGGAATGACC 58.469 43.478 22.10 0.00 38.12 4.02
4077 4247 3.073678 CCACGTCAACAATCCAAGATCA 58.926 45.455 0.00 0.00 0.00 2.92
4090 4260 0.828022 AGGTCACTTGTCCACGTCAA 59.172 50.000 0.00 0.00 0.00 3.18
4094 4264 1.745890 TGGAGGTCACTTGTCCACG 59.254 57.895 0.00 0.00 35.36 4.94
4103 4273 3.626217 AGAAAACTTTTCGTGGAGGTCAC 59.374 43.478 8.32 0.00 42.74 3.67
4104 4274 3.881220 AGAAAACTTTTCGTGGAGGTCA 58.119 40.909 8.32 0.00 0.00 4.02
4106 4276 3.181490 GCAAGAAAACTTTTCGTGGAGGT 60.181 43.478 23.29 0.00 0.00 3.85
4108 4278 4.027572 TGCAAGAAAACTTTTCGTGGAG 57.972 40.909 23.29 9.64 0.00 3.86
4114 4284 3.001228 CGGCCTTTGCAAGAAAACTTTTC 59.999 43.478 0.00 6.18 40.13 2.29
4116 4286 2.549926 CGGCCTTTGCAAGAAAACTTT 58.450 42.857 0.00 0.00 40.13 2.66
4119 4289 0.104120 ACCGGCCTTTGCAAGAAAAC 59.896 50.000 0.00 0.00 40.13 2.43
4120 4290 0.827368 AACCGGCCTTTGCAAGAAAA 59.173 45.000 0.00 0.00 40.13 2.29
4124 4294 1.006220 GGAAACCGGCCTTTGCAAG 60.006 57.895 0.00 0.00 40.13 4.01
4125 4295 2.503382 GGGAAACCGGCCTTTGCAA 61.503 57.895 0.00 0.00 43.64 4.08
4137 4321 2.078392 TCAAAGTATTCCGCGGGAAAC 58.922 47.619 27.83 19.82 45.41 2.78
4164 4348 4.714802 TGAGCACCTAGGCTATTAACTTCA 59.285 41.667 9.30 0.00 45.99 3.02
4165 4349 5.069251 TCTGAGCACCTAGGCTATTAACTTC 59.931 44.000 9.30 0.00 45.99 3.01
4177 4361 1.110442 CTGGTCCTCTGAGCACCTAG 58.890 60.000 18.21 10.28 43.72 3.02
4186 4370 1.611851 AGCCTGGTCTGGTCCTCTG 60.612 63.158 0.00 0.00 0.00 3.35
4206 4390 2.528818 CCCTTGACCAGCTGGACCA 61.529 63.158 39.19 29.50 38.94 4.02
4231 4415 1.619363 ATTAGCACCCCTGGCCTCA 60.619 57.895 3.32 0.00 0.00 3.86
4234 4418 1.754234 CACATTAGCACCCCTGGCC 60.754 63.158 0.00 0.00 0.00 5.36
4246 4430 1.600107 GGTGTCCGAGGGCACATTA 59.400 57.895 25.72 0.00 37.35 1.90


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

AutoCloner maintained by Alex Coulton.