Multiple sequence alignment - TraesCS4D01G264500

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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 TraesCS4D01G264500 chr4D 100.000 5369 0 0 1 5369 435016328 435010960 0.000000e+00 9915
1 TraesCS4D01G264500 chr4B 89.056 3929 186 102 416 4235 535089388 535085595 0.000000e+00 4649
2 TraesCS4D01G264500 chr4B 91.004 667 46 9 4694 5354 535085195 535084537 0.000000e+00 887
3 TraesCS4D01G264500 chr4B 87.461 319 27 8 1 317 535090392 535090085 6.610000e-94 355
4 TraesCS4D01G264500 chr4B 99.048 105 1 0 4267 4371 535085596 535085492 7.100000e-44 189
5 TraesCS4D01G264500 chr4A 91.850 2184 92 27 3246 5369 36391194 36389037 0.000000e+00 2968
6 TraesCS4D01G264500 chr4A 86.574 2160 114 56 1134 3193 36393388 36391305 0.000000e+00 2220
7 TraesCS4D01G264500 chr4A 87.407 540 28 18 541 1062 36393940 36393423 7.750000e-163 584
8 TraesCS4D01G264500 chr4A 91.475 305 21 4 1 301 36394887 36394584 1.080000e-111 414
9 TraesCS4D01G264500 chr3A 84.713 314 30 9 1327 1625 549333093 549333403 1.130000e-76 298
10 TraesCS4D01G264500 chr3B 83.439 314 34 9 1327 1625 599815674 599815364 5.300000e-70 276


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 TraesCS4D01G264500 chr4D 435010960 435016328 5368 True 9915.0 9915 100.00000 1 5369 1 chr4D.!!$R1 5368
1 TraesCS4D01G264500 chr4B 535084537 535090392 5855 True 1520.0 4649 91.64225 1 5354 4 chr4B.!!$R1 5353
2 TraesCS4D01G264500 chr4A 36389037 36394887 5850 True 1546.5 2968 89.32650 1 5369 4 chr4A.!!$R1 5368

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
519 1233 0.249489 ATGCATCTAGCCGTTCGTCC 60.249 55.0 0.00 0.0 44.83 4.79 F
1062 1804 0.230260 GTCGCGCTTTTCGTTGTGTA 59.770 50.0 5.56 0.0 41.07 2.90 F
2418 3274 0.390472 CCCACGGCAGTCTCTTTCTC 60.390 60.0 0.00 0.0 0.00 2.87 F
2796 3664 0.625849 CACCTGGCCAACCCTAATCT 59.374 55.0 7.01 0.0 33.59 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 2967 0.182061 TGGGATGCAGAGCAAGGATC 59.818 55.0 0.00 0.0 43.62 3.36 R
2435 3293 0.252479 AGGCAGTCATGGAAGCAGAG 59.748 55.0 0.00 0.0 0.00 3.35 R
3390 4348 0.534873 TCGATCGCTCATGGAAACCA 59.465 50.0 11.09 0.0 38.19 3.67 R
4696 5735 0.315886 TTGCGTCGTGTACCAGTCAT 59.684 50.0 0.00 0.0 0.00 3.06 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
92 97 2.301870 TGTGTGACCCAATCTGTACTCC 59.698 50.000 0.00 0.00 0.00 3.85
93 98 2.301870 GTGTGACCCAATCTGTACTCCA 59.698 50.000 0.00 0.00 0.00 3.86
227 234 2.807676 CTAATTGTCAAGGCCAGGGTT 58.192 47.619 5.01 0.00 0.00 4.11
268 275 0.814010 AGCTGGTTTTCGCGTTCTGT 60.814 50.000 5.77 0.00 0.00 3.41
286 293 7.059488 GCGTTCTGTAACTTCAACATATGTTTG 59.941 37.037 18.50 13.55 32.89 2.93
306 313 7.244898 TGTTTGTGTACATTATTATTCGGTGC 58.755 34.615 0.00 0.00 0.00 5.01
309 319 7.010697 TGTGTACATTATTATTCGGTGCAAG 57.989 36.000 0.00 0.00 0.00 4.01
311 321 7.011016 TGTGTACATTATTATTCGGTGCAAGAG 59.989 37.037 0.00 0.00 0.00 2.85
312 322 5.424121 ACATTATTATTCGGTGCAAGAGC 57.576 39.130 0.00 0.00 42.57 4.09
364 597 6.072286 ACAAGATGCAAATTACTCTTCACCTG 60.072 38.462 0.00 0.00 0.00 4.00
366 599 2.819608 TGCAAATTACTCTTCACCTGGC 59.180 45.455 0.00 0.00 0.00 4.85
395 1099 2.328819 AGCTAGCCATGCTCTGAAAG 57.671 50.000 12.13 0.00 40.44 2.62
396 1100 1.836166 AGCTAGCCATGCTCTGAAAGA 59.164 47.619 12.13 0.00 43.69 2.52
397 1101 2.238144 AGCTAGCCATGCTCTGAAAGAA 59.762 45.455 12.13 0.00 46.34 2.52
398 1102 3.012518 GCTAGCCATGCTCTGAAAGAAA 58.987 45.455 2.29 0.00 46.34 2.52
399 1103 3.181502 GCTAGCCATGCTCTGAAAGAAAC 60.182 47.826 2.29 0.00 46.34 2.78
400 1104 3.151912 AGCCATGCTCTGAAAGAAACT 57.848 42.857 0.00 0.00 46.34 2.66
401 1105 3.080319 AGCCATGCTCTGAAAGAAACTC 58.920 45.455 0.00 0.00 46.34 3.01
418 1129 3.039252 ACTCTCACCTCCAGGATAAGG 57.961 52.381 0.00 0.00 38.94 2.69
470 1183 0.517316 GACGCATGGTTTGGTGAGAC 59.483 55.000 0.00 0.00 0.00 3.36
472 1185 0.948623 CGCATGGTTTGGTGAGACGA 60.949 55.000 0.00 0.00 0.00 4.20
473 1186 1.453155 GCATGGTTTGGTGAGACGAT 58.547 50.000 0.00 0.00 0.00 3.73
474 1187 1.131126 GCATGGTTTGGTGAGACGATG 59.869 52.381 0.00 0.00 35.77 3.84
477 1190 1.270625 TGGTTTGGTGAGACGATGGAC 60.271 52.381 0.00 0.00 0.00 4.02
478 1191 1.439679 GTTTGGTGAGACGATGGACC 58.560 55.000 0.00 0.00 0.00 4.46
480 1193 0.320374 TTGGTGAGACGATGGACCAC 59.680 55.000 0.00 0.00 38.22 4.16
481 1194 0.830023 TGGTGAGACGATGGACCACA 60.830 55.000 0.00 0.00 33.44 4.17
485 1199 2.125106 GACGATGGACCACAGCCC 60.125 66.667 0.00 0.00 29.76 5.19
501 1215 1.197812 GCCCTTGCCAGGAAAATCAT 58.802 50.000 5.14 0.00 44.19 2.45
502 1216 1.134610 GCCCTTGCCAGGAAAATCATG 60.135 52.381 5.14 0.00 44.19 3.07
506 1220 3.454375 CTTGCCAGGAAAATCATGCATC 58.546 45.455 0.00 0.00 0.00 3.91
510 1224 3.305199 GCCAGGAAAATCATGCATCTAGC 60.305 47.826 0.00 0.00 45.96 3.42
512 1226 3.058432 CAGGAAAATCATGCATCTAGCCG 60.058 47.826 0.00 0.00 44.83 5.52
513 1227 2.880890 GGAAAATCATGCATCTAGCCGT 59.119 45.455 0.00 0.00 44.83 5.68
516 1230 1.788258 ATCATGCATCTAGCCGTTCG 58.212 50.000 0.00 0.00 44.83 3.95
517 1231 0.459899 TCATGCATCTAGCCGTTCGT 59.540 50.000 0.00 0.00 44.83 3.85
519 1233 0.249489 ATGCATCTAGCCGTTCGTCC 60.249 55.000 0.00 0.00 44.83 4.79
521 1235 1.146358 GCATCTAGCCGTTCGTCCAC 61.146 60.000 0.00 0.00 37.23 4.02
522 1236 0.456221 CATCTAGCCGTTCGTCCACT 59.544 55.000 0.00 0.00 0.00 4.00
523 1237 1.674441 CATCTAGCCGTTCGTCCACTA 59.326 52.381 0.00 0.00 0.00 2.74
524 1238 1.376543 TCTAGCCGTTCGTCCACTAG 58.623 55.000 0.00 0.00 33.22 2.57
528 1242 0.807496 GCCGTTCGTCCACTAGTAGT 59.193 55.000 0.00 0.00 0.00 2.73
533 1247 3.681897 CGTTCGTCCACTAGTAGTACACT 59.318 47.826 1.57 0.00 41.62 3.55
539 1253 2.527100 CACTAGTAGTACACTTGGCGC 58.473 52.381 1.57 0.00 38.80 6.53
582 1297 2.030274 GGACACCCGAAACCAAGATTTG 60.030 50.000 0.00 0.00 0.00 2.32
583 1298 1.339929 ACACCCGAAACCAAGATTTGC 59.660 47.619 0.00 0.00 0.00 3.68
584 1299 0.966179 ACCCGAAACCAAGATTTGCC 59.034 50.000 0.00 0.00 0.00 4.52
586 1301 0.965439 CCGAAACCAAGATTTGCCCA 59.035 50.000 0.00 0.00 0.00 5.36
587 1302 1.550072 CCGAAACCAAGATTTGCCCAT 59.450 47.619 0.00 0.00 0.00 4.00
588 1303 2.609350 CGAAACCAAGATTTGCCCATG 58.391 47.619 0.00 0.00 0.00 3.66
611 1327 2.388232 GGACAAACCGTGCCTAGCG 61.388 63.158 0.00 0.00 0.00 4.26
788 1515 6.942163 AGGCTCTTCTATAAATCCAGCATA 57.058 37.500 0.00 0.00 0.00 3.14
789 1516 7.507797 AGGCTCTTCTATAAATCCAGCATAT 57.492 36.000 0.00 0.00 0.00 1.78
790 1517 8.615360 AGGCTCTTCTATAAATCCAGCATATA 57.385 34.615 0.00 0.00 0.00 0.86
791 1518 9.223291 AGGCTCTTCTATAAATCCAGCATATAT 57.777 33.333 0.00 0.00 0.00 0.86
871 1600 3.651423 AGCCCTATAAATACACCCAGGAC 59.349 47.826 0.00 0.00 0.00 3.85
902 1631 0.671251 CTTGCCTCCTAGAGCTACCG 59.329 60.000 0.00 0.00 0.00 4.02
936 1672 0.312416 AGCTATAGCAACCTCGCTCG 59.688 55.000 26.07 0.00 42.62 5.03
937 1673 1.278849 GCTATAGCAACCTCGCTCGC 61.279 60.000 20.01 0.00 42.62 5.03
939 1675 0.673985 TATAGCAACCTCGCTCGCAT 59.326 50.000 0.00 0.00 42.62 4.73
940 1676 0.598680 ATAGCAACCTCGCTCGCATC 60.599 55.000 0.00 0.00 42.62 3.91
941 1677 1.944234 TAGCAACCTCGCTCGCATCA 61.944 55.000 0.00 0.00 42.62 3.07
944 1680 1.448540 AACCTCGCTCGCATCAAGG 60.449 57.895 0.00 0.00 0.00 3.61
946 1682 1.153568 CCTCGCTCGCATCAAGGAA 60.154 57.895 0.00 0.00 0.00 3.36
947 1683 0.531532 CCTCGCTCGCATCAAGGAAT 60.532 55.000 0.00 0.00 0.00 3.01
972 1708 2.168936 CTGAATCAAGAGGCTCTCAGCT 59.831 50.000 19.03 3.05 41.99 4.24
976 1712 0.896923 CAAGAGGCTCTCAGCTGACT 59.103 55.000 19.03 8.45 41.99 3.41
990 1728 0.457851 CTGACTAGTCCAAGGCTCCG 59.542 60.000 20.11 0.00 0.00 4.63
1037 1779 9.579768 CATGATCTCCAAGTATATACTTACTGC 57.420 37.037 24.29 13.70 44.19 4.40
1038 1780 8.706322 TGATCTCCAAGTATATACTTACTGCA 57.294 34.615 24.29 15.59 44.19 4.41
1039 1781 9.314133 TGATCTCCAAGTATATACTTACTGCAT 57.686 33.333 24.29 14.09 44.19 3.96
1062 1804 0.230260 GTCGCGCTTTTCGTTGTGTA 59.770 50.000 5.56 0.00 41.07 2.90
1063 1805 0.928922 TCGCGCTTTTCGTTGTGTAA 59.071 45.000 5.56 0.00 41.07 2.41
1068 1810 4.029625 CGCGCTTTTCGTTGTGTAAATATG 60.030 41.667 5.56 0.00 41.07 1.78
1082 1824 8.986477 TGTGTAAATATGTAGATCATGGATCG 57.014 34.615 0.00 0.00 43.17 3.69
1097 1843 0.510359 GATCGATGATCCTTGCGTGC 59.490 55.000 0.54 0.00 33.37 5.34
1100 1846 1.136110 TCGATGATCCTTGCGTGCTAA 59.864 47.619 0.00 0.00 0.00 3.09
1101 1847 2.138320 CGATGATCCTTGCGTGCTAAT 58.862 47.619 0.00 0.00 0.00 1.73
1102 1848 2.545526 CGATGATCCTTGCGTGCTAATT 59.454 45.455 0.00 0.00 0.00 1.40
1103 1849 3.002656 CGATGATCCTTGCGTGCTAATTT 59.997 43.478 0.00 0.00 0.00 1.82
1104 1850 4.531332 GATGATCCTTGCGTGCTAATTTC 58.469 43.478 0.00 0.00 0.00 2.17
1105 1851 3.342719 TGATCCTTGCGTGCTAATTTCA 58.657 40.909 0.00 0.00 0.00 2.69
1106 1852 3.126858 TGATCCTTGCGTGCTAATTTCAC 59.873 43.478 0.00 0.00 0.00 3.18
1115 1861 4.537936 GTGCTAATTTCACGAAGGGATC 57.462 45.455 0.00 0.00 0.00 3.36
1132 1878 7.736447 AAGGGATCGATCTTAATTTGATCAC 57.264 36.000 23.96 11.40 40.03 3.06
1141 1887 7.630987 CGATCTTAATTTGATCACGTGTGTAAC 59.369 37.037 16.51 4.58 40.03 2.50
1151 1897 2.607635 CACGTGTGTAACTGCTGTTTCT 59.392 45.455 14.54 0.00 38.04 2.52
1168 1914 6.090628 GCTGTTTCTGTTGTTTTGTTTGATCA 59.909 34.615 0.00 0.00 0.00 2.92
1214 1969 0.770499 TCCTTCCACTGGATGTTGCA 59.230 50.000 0.00 0.00 0.00 4.08
1240 1995 2.840651 CTGTGAAGAAGGGACCAGGTAT 59.159 50.000 0.00 0.00 0.00 2.73
1241 1996 2.571653 TGTGAAGAAGGGACCAGGTATG 59.428 50.000 0.00 0.00 0.00 2.39
1337 2114 2.032178 GCATCCTAACAATTCAGCGTCC 59.968 50.000 0.00 0.00 0.00 4.79
1372 2149 2.096496 GTCGCAATCCAAACATGGAGAG 59.904 50.000 3.69 0.10 41.88 3.20
1417 2194 3.692576 CGGAGGTACGTACAGAAGATTG 58.307 50.000 26.02 4.65 0.00 2.67
1627 2405 4.262079 GCCATGGCCGAGGTATATATACTC 60.262 50.000 27.24 14.34 32.78 2.59
1664 2442 9.193133 CTTCCATATATTACTTCTAACACCACG 57.807 37.037 0.00 0.00 0.00 4.94
1712 2490 0.958382 TACCCTTGAACATGCGTGCC 60.958 55.000 5.64 0.00 0.00 5.01
1723 2505 3.076621 ACATGCGTGCCTATATGAATGG 58.923 45.455 5.64 0.00 28.49 3.16
1729 2511 4.036262 GCGTGCCTATATGAATGGAAAACA 59.964 41.667 0.00 0.00 0.00 2.83
1857 2649 0.682209 AGGCATCCACGTACGTACCT 60.682 55.000 22.34 18.36 0.00 3.08
1941 2754 3.755112 TGCCCAATAATTGCATGGATG 57.245 42.857 4.81 0.00 36.27 3.51
1953 2766 5.925506 TTGCATGGATGTTTCTGATGATT 57.074 34.783 0.00 0.00 0.00 2.57
1956 2769 6.334989 TGCATGGATGTTTCTGATGATTTTC 58.665 36.000 0.00 0.00 0.00 2.29
1971 2784 5.539582 TGATTTTCGTACAAGGCATACAC 57.460 39.130 0.00 0.00 0.00 2.90
1995 2815 2.028561 ACAAAGGGAATGGTTGGCAT 57.971 45.000 0.00 0.00 0.00 4.40
2015 2835 8.746052 TGGCATAACCATAATATATACAAGGC 57.254 34.615 0.00 0.00 46.36 4.35
2016 2836 8.332487 TGGCATAACCATAATATATACAAGGCA 58.668 33.333 0.00 0.00 46.36 4.75
2017 2837 9.184523 GGCATAACCATAATATATACAAGGCAA 57.815 33.333 0.00 0.00 38.86 4.52
2119 2956 5.771666 ACAAGTCATTGATCACCAAGAACAT 59.228 36.000 0.00 0.00 38.83 2.71
2120 2957 6.942005 ACAAGTCATTGATCACCAAGAACATA 59.058 34.615 0.00 0.00 38.83 2.29
2121 2958 7.613022 ACAAGTCATTGATCACCAAGAACATAT 59.387 33.333 0.00 0.00 38.83 1.78
2122 2959 9.112725 CAAGTCATTGATCACCAAGAACATATA 57.887 33.333 0.00 0.00 38.83 0.86
2130 2967 8.082242 TGATCACCAAGAACATATATACTGTCG 58.918 37.037 0.00 0.00 0.00 4.35
2191 3037 7.641411 CGAATGCACCAAACAATTTCTATAGAG 59.359 37.037 2.02 0.00 0.00 2.43
2243 3089 2.029649 TCCTCACTGGTTAACTACACGC 60.030 50.000 5.42 0.00 37.07 5.34
2367 3217 4.142609 TCTGAAGCTCCATCATACAACC 57.857 45.455 0.00 0.00 0.00 3.77
2401 3257 4.262617 GACTTGTCAAACCCTTATCTCCC 58.737 47.826 0.00 0.00 0.00 4.30
2403 3259 3.713826 TGTCAAACCCTTATCTCCCAC 57.286 47.619 0.00 0.00 0.00 4.61
2418 3274 0.390472 CCCACGGCAGTCTCTTTCTC 60.390 60.000 0.00 0.00 0.00 2.87
2429 3285 5.163561 GCAGTCTCTTTCTCTACATGCTACT 60.164 44.000 0.00 0.00 0.00 2.57
2430 3286 6.038825 GCAGTCTCTTTCTCTACATGCTACTA 59.961 42.308 0.00 0.00 0.00 1.82
2431 3287 7.414436 CAGTCTCTTTCTCTACATGCTACTAC 58.586 42.308 0.00 0.00 0.00 2.73
2432 3288 7.066404 CAGTCTCTTTCTCTACATGCTACTACA 59.934 40.741 0.00 0.00 0.00 2.74
2435 3293 8.625651 TCTCTTTCTCTACATGCTACTACATTC 58.374 37.037 0.00 0.00 0.00 2.67
2448 3306 5.452496 GCTACTACATTCTCTGCTTCCATGA 60.452 44.000 0.00 0.00 0.00 3.07
2449 3307 4.764172 ACTACATTCTCTGCTTCCATGAC 58.236 43.478 0.00 0.00 0.00 3.06
2479 3337 4.083696 CCATGCAATGCAAACTTTCTTTCC 60.084 41.667 13.45 0.00 44.97 3.13
2493 3351 1.202927 TCTTTCCTTGTCAAGCCCTGG 60.203 52.381 7.09 0.00 0.00 4.45
2509 3371 1.615116 CCTGGCTGCATCTTTTCCTCA 60.615 52.381 0.50 0.00 0.00 3.86
2550 3413 5.598417 CCCCTAAAATTGGAAGTGGATAAGG 59.402 44.000 0.00 0.00 0.00 2.69
2689 3557 1.299468 CCACGGCTGATACTCTCGC 60.299 63.158 0.00 0.00 0.00 5.03
2691 3559 2.727647 CGGCTGATACTCTCGCGC 60.728 66.667 0.00 0.00 0.00 6.86
2705 3573 1.531578 CTCGCGCACTAGTCTATGCTA 59.468 52.381 8.75 0.00 39.79 3.49
2706 3574 1.531578 TCGCGCACTAGTCTATGCTAG 59.468 52.381 8.75 0.00 42.96 3.42
2707 3575 1.531578 CGCGCACTAGTCTATGCTAGA 59.468 52.381 8.75 0.00 40.54 2.43
2739 3607 6.552859 TGTGCTCGATCTTTAATTTGTGAA 57.447 33.333 0.00 0.00 0.00 3.18
2749 3617 9.861138 GATCTTTAATTTGTGAAGATCGATCAG 57.139 33.333 26.47 10.61 44.68 2.90
2750 3618 9.605275 ATCTTTAATTTGTGAAGATCGATCAGA 57.395 29.630 26.47 15.22 37.92 3.27
2751 3619 9.435688 TCTTTAATTTGTGAAGATCGATCAGAA 57.564 29.630 26.47 10.34 27.32 3.02
2754 3622 7.854557 AATTTGTGAAGATCGATCAGAATCA 57.145 32.000 26.47 19.84 31.19 2.57
2778 3646 2.948315 TGTTTGTTGCACTACATCTGCA 59.052 40.909 0.00 0.00 42.95 4.41
2796 3664 0.625849 CACCTGGCCAACCCTAATCT 59.374 55.000 7.01 0.00 33.59 2.40
2958 3838 1.502640 GACGACTGAGACCCGACAG 59.497 63.158 0.00 0.00 39.65 3.51
3013 3903 4.575645 ACTTACTTCTACGTAGCTAGCTGG 59.424 45.833 27.68 20.06 0.00 4.85
3077 3967 9.191479 TGAAGGATTAACTGTGGTAAAAGAAAA 57.809 29.630 0.00 0.00 0.00 2.29
3127 4017 6.567602 ATTTCCTCCTATTCTTGCAGTACT 57.432 37.500 0.00 0.00 0.00 2.73
3198 4156 5.009110 GCAAGGCCAGAAGGTAATTAAGATC 59.991 44.000 5.01 0.00 37.19 2.75
3205 4163 7.633772 GCCAGAAGGTAATTAAGATCTCTGACA 60.634 40.741 0.00 0.00 37.19 3.58
3254 4212 5.944135 CACGATCACGAAATTAACTAACACG 59.056 40.000 0.00 0.00 42.66 4.49
3255 4213 4.947933 CGATCACGAAATTAACTAACACGC 59.052 41.667 0.00 0.00 42.66 5.34
3385 4343 1.288127 GCCTGCAGGTTCAGCAAAG 59.712 57.895 32.81 4.74 42.17 2.77
3390 4348 1.458639 GCAGGTTCAGCAAAGCCACT 61.459 55.000 0.00 0.00 35.94 4.00
3402 4360 1.915141 AAGCCACTGGTTTCCATGAG 58.085 50.000 0.00 0.00 30.82 2.90
3426 4384 0.584876 CGAGGTTCGGTGTTCAAACC 59.415 55.000 0.00 0.00 42.27 3.27
3427 4385 0.949397 GAGGTTCGGTGTTCAAACCC 59.051 55.000 0.00 0.00 42.82 4.11
3428 4386 0.816421 AGGTTCGGTGTTCAAACCCG 60.816 55.000 13.34 13.34 42.82 5.28
3429 4387 1.009335 GTTCGGTGTTCAAACCCGC 60.009 57.895 14.22 3.00 40.33 6.13
3432 4390 1.161563 TCGGTGTTCAAACCCGCTTC 61.162 55.000 14.22 0.00 40.33 3.86
3433 4391 1.281656 GGTGTTCAAACCCGCTTCG 59.718 57.895 0.00 0.00 33.79 3.79
3436 4394 1.281656 GTTCAAACCCGCTTCGGTG 59.718 57.895 4.47 0.00 46.80 4.94
3437 4395 1.146485 TTCAAACCCGCTTCGGTGA 59.854 52.632 4.47 0.00 46.80 4.02
3438 4396 0.464013 TTCAAACCCGCTTCGGTGAA 60.464 50.000 4.47 5.30 46.80 3.18
3439 4397 0.250553 TCAAACCCGCTTCGGTGAAT 60.251 50.000 4.47 0.00 46.80 2.57
3441 4399 0.536460 AAACCCGCTTCGGTGAATGT 60.536 50.000 4.47 0.00 46.80 2.71
3445 4403 2.014128 CCCGCTTCGGTGAATGTAAAT 58.986 47.619 4.47 0.00 46.80 1.40
3470 4433 3.065371 CACCTTGTGTTTCTCCTTGTGAC 59.935 47.826 0.00 0.00 0.00 3.67
4380 5361 2.186125 GCCTAAACCCTCCGTCGG 59.814 66.667 4.39 4.39 0.00 4.79
4445 5427 6.223120 TGCTTACTCATTCATGTATACGCAT 58.777 36.000 0.00 0.00 0.00 4.73
4473 5455 1.252015 CGTACAATAACGCTGCGAGAC 59.748 52.381 30.47 13.02 35.87 3.36
4539 5578 9.551734 TCATATATGTATGCTCTAATGAATGCC 57.448 33.333 12.42 0.00 38.05 4.40
4558 5597 5.671463 TGCCCATTGGTTAATATAGGGAA 57.329 39.130 1.20 0.00 31.66 3.97
4559 5598 5.390387 TGCCCATTGGTTAATATAGGGAAC 58.610 41.667 1.20 0.00 31.66 3.62
4560 5599 5.103473 TGCCCATTGGTTAATATAGGGAACA 60.103 40.000 1.20 0.00 31.66 3.18
4561 5600 6.016555 GCCCATTGGTTAATATAGGGAACAT 58.983 40.000 1.20 0.00 31.66 2.71
4564 5603 7.335924 CCCATTGGTTAATATAGGGAACATACG 59.664 40.741 1.20 0.00 31.66 3.06
4565 5604 7.881232 CCATTGGTTAATATAGGGAACATACGT 59.119 37.037 0.00 0.00 0.00 3.57
4566 5605 8.932791 CATTGGTTAATATAGGGAACATACGTC 58.067 37.037 0.00 0.00 0.00 4.34
4568 5607 7.663827 TGGTTAATATAGGGAACATACGTCAG 58.336 38.462 0.00 0.00 0.00 3.51
4569 5608 6.589139 GGTTAATATAGGGAACATACGTCAGC 59.411 42.308 0.00 0.00 0.00 4.26
4571 5610 1.753930 TAGGGAACATACGTCAGCGA 58.246 50.000 0.00 0.00 42.00 4.93
4572 5611 0.892755 AGGGAACATACGTCAGCGAA 59.107 50.000 0.00 0.00 42.00 4.70
4576 5615 2.471749 GGAACATACGTCAGCGAAAACG 60.472 50.000 0.00 0.00 44.22 3.60
4580 5619 2.851104 CGTCAGCGAAAACGTCCC 59.149 61.111 0.00 0.00 41.33 4.46
4581 5620 1.952133 CGTCAGCGAAAACGTCCCA 60.952 57.895 0.00 0.00 41.33 4.37
4582 5621 1.568025 GTCAGCGAAAACGTCCCAC 59.432 57.895 0.00 0.00 0.00 4.61
4585 5624 1.663702 AGCGAAAACGTCCCACGAG 60.664 57.895 2.48 0.00 46.05 4.18
4586 5625 2.851104 CGAAAACGTCCCACGAGC 59.149 61.111 2.48 0.00 46.05 5.03
4587 5626 2.664436 CGAAAACGTCCCACGAGCC 61.664 63.158 2.48 0.00 46.05 4.70
4588 5627 1.301479 GAAAACGTCCCACGAGCCT 60.301 57.895 2.48 0.00 46.05 4.58
4589 5628 1.566018 GAAAACGTCCCACGAGCCTG 61.566 60.000 2.48 0.00 46.05 4.85
4590 5629 2.319890 AAAACGTCCCACGAGCCTGT 62.320 55.000 2.48 0.00 46.05 4.00
4591 5630 1.466025 AAACGTCCCACGAGCCTGTA 61.466 55.000 2.48 0.00 46.05 2.74
4592 5631 1.255667 AACGTCCCACGAGCCTGTAT 61.256 55.000 2.48 0.00 46.05 2.29
4593 5632 1.255667 ACGTCCCACGAGCCTGTATT 61.256 55.000 2.48 0.00 46.05 1.89
4594 5633 0.742505 CGTCCCACGAGCCTGTATTA 59.257 55.000 0.00 0.00 46.05 0.98
4606 5645 9.309516 CACGAGCCTGTATTAGTCTAAATAAAA 57.690 33.333 0.00 0.00 0.00 1.52
4626 5665 2.474816 AGCACTCGTGTTCTCAAAGAC 58.525 47.619 0.00 0.00 0.00 3.01
4629 5668 3.706698 CACTCGTGTTCTCAAAGACTGA 58.293 45.455 0.00 0.00 0.00 3.41
4630 5669 3.487574 CACTCGTGTTCTCAAAGACTGAC 59.512 47.826 0.00 0.00 0.00 3.51
4631 5670 3.053455 CTCGTGTTCTCAAAGACTGACC 58.947 50.000 0.00 0.00 0.00 4.02
4632 5671 2.135933 CGTGTTCTCAAAGACTGACCC 58.864 52.381 0.00 0.00 0.00 4.46
4664 5703 9.854668 ACAGTCTACACTTACATATACTGATCT 57.145 33.333 0.00 0.00 37.22 2.75
4696 5735 9.238368 ACGAATCCCTCAAAAGAAAAATACATA 57.762 29.630 0.00 0.00 0.00 2.29
4703 5742 9.793252 CCTCAAAAGAAAAATACATATGACTGG 57.207 33.333 10.38 0.00 0.00 4.00
4711 5750 7.766219 AAAATACATATGACTGGTACACGAC 57.234 36.000 10.38 0.00 0.00 4.34
4762 5801 7.504403 AGATAGATTGTTTTCAGATCCACGAT 58.496 34.615 0.00 0.00 0.00 3.73
4763 5802 8.642432 AGATAGATTGTTTTCAGATCCACGATA 58.358 33.333 0.00 0.00 0.00 2.92
4766 5805 8.335532 AGATTGTTTTCAGATCCACGATAAAA 57.664 30.769 0.00 0.00 0.00 1.52
4797 5837 5.835819 AGAGACCTGGATCTTATTTCGATCA 59.164 40.000 0.00 0.00 39.17 2.92
4807 5847 7.905493 GGATCTTATTTCGATCAGACAAACAAC 59.095 37.037 0.00 0.00 39.17 3.32
4868 5908 1.429463 TTCCTCTTCGCTTTCTTCGC 58.571 50.000 0.00 0.00 0.00 4.70
4876 5916 2.744768 GCTTTCTTCGCCCTCGCTG 61.745 63.158 0.00 0.00 35.26 5.18
5038 6082 7.446931 TGCAGAACCAATCTTAGTACAATTTGA 59.553 33.333 2.79 0.00 35.73 2.69
5071 6116 9.895138 ATAGATTTTGCCAAAATTCTAATGCTT 57.105 25.926 16.03 3.05 40.97 3.91
5081 6126 7.010183 CCAAAATTCTAATGCTTTGAGATGCAG 59.990 37.037 0.00 0.00 42.74 4.41
5125 6170 3.002246 GTGACTTTGAAACACTCGATGCA 59.998 43.478 0.00 0.00 0.00 3.96
5137 6182 0.250252 TCGATGCACTTGACAGCCAA 60.250 50.000 0.00 0.00 0.00 4.52
5173 6218 3.559655 TGATTATCTCGGTGCCATTTTCG 59.440 43.478 0.00 0.00 0.00 3.46
5272 6320 8.839914 CATTACGTAAATGAAACATGTTCTGTG 58.160 33.333 12.39 0.00 46.81 3.66
5308 6356 4.274459 GCTAGTTAATGTGAAGGGCAGATG 59.726 45.833 0.00 0.00 29.77 2.90
5361 6409 9.064706 ACTAAGATGATTGAATGCTGGATAAAG 57.935 33.333 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 75 2.301870 TGGAGTACAGATTGGGTCACAC 59.698 50.000 0.00 0.00 0.00 3.82
81 84 8.635765 AAAAACATACATGTGGAGTACAGATT 57.364 30.769 9.11 0.00 43.80 2.40
140 147 5.183228 TCATATGATCATGGCATGTGCTAG 58.817 41.667 25.62 11.76 41.70 3.42
143 150 4.983671 ATCATATGATCATGGCATGTGC 57.016 40.909 25.62 18.54 35.59 4.57
173 180 6.037720 TCAACTTTCACAGAAATAGCAAACGA 59.962 34.615 0.00 0.00 0.00 3.85
175 182 9.334693 CTATCAACTTTCACAGAAATAGCAAAC 57.665 33.333 0.00 0.00 0.00 2.93
227 234 1.732809 TCGCGACAACTGTTGTTTGAA 59.267 42.857 25.35 10.74 45.52 2.69
242 249 1.733041 CGAAAACCAGCTCTCGCGA 60.733 57.895 9.26 9.26 42.32 5.87
286 293 7.241663 TCTTGCACCGAATAATAATGTACAC 57.758 36.000 0.00 0.00 0.00 2.90
343 576 4.439289 GCCAGGTGAAGAGTAATTTGCATC 60.439 45.833 0.00 0.00 0.00 3.91
345 578 2.819608 GCCAGGTGAAGAGTAATTTGCA 59.180 45.455 0.00 0.00 0.00 4.08
390 1094 3.071602 CCTGGAGGTGAGAGTTTCTTTCA 59.928 47.826 0.00 0.00 0.00 2.69
395 1099 4.141824 CCTTATCCTGGAGGTGAGAGTTTC 60.142 50.000 1.52 0.00 36.34 2.78
396 1100 3.777522 CCTTATCCTGGAGGTGAGAGTTT 59.222 47.826 1.52 0.00 36.34 2.66
397 1101 3.012959 TCCTTATCCTGGAGGTGAGAGTT 59.987 47.826 1.52 0.00 34.57 3.01
398 1102 2.587777 TCCTTATCCTGGAGGTGAGAGT 59.412 50.000 1.52 0.00 34.57 3.24
399 1103 3.230134 CTCCTTATCCTGGAGGTGAGAG 58.770 54.545 1.52 1.14 45.39 3.20
400 1104 3.320610 CTCCTTATCCTGGAGGTGAGA 57.679 52.381 1.52 0.00 45.39 3.27
436 1147 2.503331 TGCGTCTGAATTTGGTGATGT 58.497 42.857 0.00 0.00 0.00 3.06
437 1148 3.431856 CATGCGTCTGAATTTGGTGATG 58.568 45.455 0.00 0.00 0.00 3.07
438 1149 2.424601 CCATGCGTCTGAATTTGGTGAT 59.575 45.455 0.00 0.00 0.00 3.06
440 1151 1.541147 ACCATGCGTCTGAATTTGGTG 59.459 47.619 0.00 0.00 36.18 4.17
470 1183 1.746615 CAAGGGCTGTGGTCCATCG 60.747 63.158 0.00 0.00 40.27 3.84
472 1185 2.036256 GCAAGGGCTGTGGTCCAT 59.964 61.111 0.00 0.00 40.27 3.41
473 1186 4.284550 GGCAAGGGCTGTGGTCCA 62.285 66.667 0.00 0.00 40.27 4.02
474 1187 4.284550 TGGCAAGGGCTGTGGTCC 62.285 66.667 0.00 0.00 40.87 4.46
477 1190 3.512154 TTCCTGGCAAGGGCTGTGG 62.512 63.158 7.48 0.00 44.62 4.17
478 1191 1.114722 TTTTCCTGGCAAGGGCTGTG 61.115 55.000 7.48 0.00 44.62 3.66
480 1193 0.533951 GATTTTCCTGGCAAGGGCTG 59.466 55.000 7.48 0.00 44.62 4.85
481 1194 0.114954 TGATTTTCCTGGCAAGGGCT 59.885 50.000 7.48 0.00 44.62 5.19
485 1199 3.132289 AGATGCATGATTTTCCTGGCAAG 59.868 43.478 2.46 0.00 34.64 4.01
501 1215 1.141019 GGACGAACGGCTAGATGCA 59.859 57.895 0.00 0.00 45.15 3.96
502 1216 1.141019 TGGACGAACGGCTAGATGC 59.859 57.895 0.00 0.00 41.94 3.91
506 1220 1.093159 ACTAGTGGACGAACGGCTAG 58.907 55.000 0.00 7.63 36.25 3.42
510 1224 3.002791 TGTACTACTAGTGGACGAACGG 58.997 50.000 13.86 0.00 0.00 4.44
512 1226 5.388944 CAAGTGTACTACTAGTGGACGAAC 58.611 45.833 13.86 5.76 39.18 3.95
513 1227 4.456911 CCAAGTGTACTACTAGTGGACGAA 59.543 45.833 13.86 0.00 38.90 3.85
516 1230 3.427233 CGCCAAGTGTACTACTAGTGGAC 60.427 52.174 13.86 6.96 38.90 4.02
517 1231 2.751259 CGCCAAGTGTACTACTAGTGGA 59.249 50.000 13.86 0.00 38.90 4.02
519 1233 2.527100 GCGCCAAGTGTACTACTAGTG 58.473 52.381 5.39 0.00 39.18 2.74
521 1235 1.823828 CGCGCCAAGTGTACTACTAG 58.176 55.000 0.00 0.00 39.18 2.57
522 1236 0.179156 GCGCGCCAAGTGTACTACTA 60.179 55.000 23.24 0.00 39.18 1.82
523 1237 1.445582 GCGCGCCAAGTGTACTACT 60.446 57.895 23.24 0.00 42.89 2.57
524 1238 2.785105 CGCGCGCCAAGTGTACTAC 61.785 63.158 27.72 0.00 0.00 2.73
528 1242 3.408020 GAACGCGCGCCAAGTGTA 61.408 61.111 32.58 0.00 0.00 2.90
569 1284 2.355007 CCCATGGGCAAATCTTGGTTTC 60.355 50.000 20.41 0.00 0.00 2.78
611 1327 2.185004 TGCAGTTTAGGCAGTCTTCC 57.815 50.000 0.00 0.00 36.11 3.46
788 1515 4.125703 CAAGAGAAGAAGGCGAGCAATAT 58.874 43.478 0.00 0.00 0.00 1.28
789 1516 3.525537 CAAGAGAAGAAGGCGAGCAATA 58.474 45.455 0.00 0.00 0.00 1.90
790 1517 2.354259 CAAGAGAAGAAGGCGAGCAAT 58.646 47.619 0.00 0.00 0.00 3.56
791 1518 1.800805 CAAGAGAAGAAGGCGAGCAA 58.199 50.000 0.00 0.00 0.00 3.91
799 1526 2.985406 GCAACTGGCAAGAGAAGAAG 57.015 50.000 0.00 0.00 43.97 2.85
871 1600 1.821136 GGAGGCAAGAAACAATGGAGG 59.179 52.381 0.00 0.00 0.00 4.30
926 1655 1.448540 CCTTGATGCGAGCGAGGTT 60.449 57.895 0.00 0.00 33.09 3.50
934 1670 3.893326 TCAGAGAATTCCTTGATGCGA 57.107 42.857 0.65 0.00 0.00 5.10
936 1672 6.318144 TCTTGATTCAGAGAATTCCTTGATGC 59.682 38.462 0.65 2.96 0.00 3.91
937 1673 7.012515 CCTCTTGATTCAGAGAATTCCTTGATG 59.987 40.741 0.65 0.00 42.81 3.07
939 1675 6.413052 CCTCTTGATTCAGAGAATTCCTTGA 58.587 40.000 0.65 3.64 42.81 3.02
940 1676 5.066246 GCCTCTTGATTCAGAGAATTCCTTG 59.934 44.000 0.65 1.07 42.81 3.61
941 1677 5.044993 AGCCTCTTGATTCAGAGAATTCCTT 60.045 40.000 0.65 0.00 42.81 3.36
944 1680 5.673514 AGAGCCTCTTGATTCAGAGAATTC 58.326 41.667 12.10 0.00 42.81 2.17
946 1682 4.715792 TGAGAGCCTCTTGATTCAGAGAAT 59.284 41.667 0.00 0.00 42.81 2.40
947 1683 4.092279 TGAGAGCCTCTTGATTCAGAGAA 58.908 43.478 0.00 0.00 42.81 2.87
972 1708 0.970937 CCGGAGCCTTGGACTAGTCA 60.971 60.000 23.91 7.95 0.00 3.41
976 1712 1.686325 GATGCCGGAGCCTTGGACTA 61.686 60.000 5.05 0.00 38.69 2.59
1036 1778 1.521423 ACGAAAAGCGCGACTATATGC 59.479 47.619 12.10 0.00 46.04 3.14
1037 1779 3.000078 ACAACGAAAAGCGCGACTATATG 60.000 43.478 12.10 0.57 46.04 1.78
1038 1780 3.000078 CACAACGAAAAGCGCGACTATAT 60.000 43.478 12.10 0.00 46.04 0.86
1039 1781 2.343246 CACAACGAAAAGCGCGACTATA 59.657 45.455 12.10 0.00 46.04 1.31
1041 1783 0.505231 CACAACGAAAAGCGCGACTA 59.495 50.000 12.10 0.00 46.04 2.59
1042 1784 1.275657 CACAACGAAAAGCGCGACT 59.724 52.632 12.10 3.13 46.04 4.18
1043 1785 0.230260 TACACAACGAAAAGCGCGAC 59.770 50.000 12.10 0.04 46.04 5.19
1082 1824 4.035558 TGAAATTAGCACGCAAGGATCATC 59.964 41.667 0.00 0.00 46.39 2.92
1107 1853 7.359598 CGTGATCAAATTAAGATCGATCCCTTC 60.360 40.741 21.66 0.00 43.73 3.46
1108 1854 6.425114 CGTGATCAAATTAAGATCGATCCCTT 59.575 38.462 21.66 12.84 43.73 3.95
1109 1855 5.928839 CGTGATCAAATTAAGATCGATCCCT 59.071 40.000 21.66 11.88 43.73 4.20
1110 1856 5.696724 ACGTGATCAAATTAAGATCGATCCC 59.303 40.000 21.66 0.00 43.73 3.85
1111 1857 6.201044 ACACGTGATCAAATTAAGATCGATCC 59.799 38.462 25.01 4.34 43.73 3.36
1112 1858 7.059817 CACACGTGATCAAATTAAGATCGATC 58.940 38.462 25.01 17.91 43.73 3.69
1113 1859 6.535150 ACACACGTGATCAAATTAAGATCGAT 59.465 34.615 25.01 0.00 43.73 3.59
1114 1860 5.867174 ACACACGTGATCAAATTAAGATCGA 59.133 36.000 25.01 0.00 43.73 3.59
1115 1861 6.094739 ACACACGTGATCAAATTAAGATCG 57.905 37.500 25.01 0.00 43.73 3.69
1116 1862 8.656849 AGTTACACACGTGATCAAATTAAGATC 58.343 33.333 25.01 11.83 41.72 2.75
1117 1863 8.443160 CAGTTACACACGTGATCAAATTAAGAT 58.557 33.333 25.01 0.00 0.00 2.40
1118 1864 7.570507 GCAGTTACACACGTGATCAAATTAAGA 60.571 37.037 25.01 0.00 0.00 2.10
1119 1865 6.519761 GCAGTTACACACGTGATCAAATTAAG 59.480 38.462 25.01 3.86 0.00 1.85
1120 1866 6.203915 AGCAGTTACACACGTGATCAAATTAA 59.796 34.615 25.01 5.49 0.00 1.40
1121 1867 5.699001 AGCAGTTACACACGTGATCAAATTA 59.301 36.000 25.01 0.00 0.00 1.40
1122 1868 4.515191 AGCAGTTACACACGTGATCAAATT 59.485 37.500 25.01 4.84 0.00 1.82
1123 1869 4.065088 AGCAGTTACACACGTGATCAAAT 58.935 39.130 25.01 8.63 0.00 2.32
1124 1870 3.247411 CAGCAGTTACACACGTGATCAAA 59.753 43.478 25.01 7.87 0.00 2.69
1125 1871 2.799978 CAGCAGTTACACACGTGATCAA 59.200 45.455 25.01 9.39 0.00 2.57
1126 1872 2.223947 ACAGCAGTTACACACGTGATCA 60.224 45.455 25.01 2.84 0.00 2.92
1127 1873 2.404215 ACAGCAGTTACACACGTGATC 58.596 47.619 25.01 7.27 0.00 2.92
1132 1878 2.607635 ACAGAAACAGCAGTTACACACG 59.392 45.455 0.00 0.00 36.84 4.49
1141 1887 5.404968 TCAAACAAAACAACAGAAACAGCAG 59.595 36.000 0.00 0.00 0.00 4.24
1151 1897 5.523188 GCTTGGATGATCAAACAAAACAACA 59.477 36.000 14.07 0.00 0.00 3.33
1214 1969 1.353091 GTCCCTTCTTCACAGGAGGT 58.647 55.000 0.00 0.00 44.12 3.85
1240 1995 6.016276 GCTACAAGGATCAAAGAAAGAAACCA 60.016 38.462 0.00 0.00 0.00 3.67
1241 1996 6.016276 TGCTACAAGGATCAAAGAAAGAAACC 60.016 38.462 0.00 0.00 0.00 3.27
1242 1997 6.970484 TGCTACAAGGATCAAAGAAAGAAAC 58.030 36.000 0.00 0.00 0.00 2.78
1243 1998 7.765695 ATGCTACAAGGATCAAAGAAAGAAA 57.234 32.000 0.00 0.00 0.00 2.52
1244 1999 7.765695 AATGCTACAAGGATCAAAGAAAGAA 57.234 32.000 0.00 0.00 0.00 2.52
1372 2149 2.667473 TAAGTAGCCGTTCTGAAGCC 57.333 50.000 0.00 0.00 0.00 4.35
1417 2194 3.091545 TCAAATGGCAGTGAAATCCCTC 58.908 45.455 0.00 0.00 0.00 4.30
1664 2442 9.384764 AGGAATTTAGCTTCTACTTACATGTTC 57.615 33.333 2.30 0.00 0.00 3.18
1712 2490 9.603298 CGATCATGTTGTTTTCCATTCATATAG 57.397 33.333 0.00 0.00 0.00 1.31
1723 2505 8.667987 TGCTATAAAACGATCATGTTGTTTTC 57.332 30.769 20.32 12.22 46.65 2.29
1729 2511 8.131100 CCATTTCTGCTATAAAACGATCATGTT 58.869 33.333 0.00 0.00 0.00 2.71
1857 2649 2.694213 TGTATTTCGCTAGCACTGCAA 58.306 42.857 16.45 0.00 0.00 4.08
1915 2728 2.277969 TGCAATTATTGGGCATTTGCG 58.722 42.857 7.08 0.00 44.23 4.85
1941 2754 5.795441 GCCTTGTACGAAAATCATCAGAAAC 59.205 40.000 0.00 0.00 0.00 2.78
1953 2766 7.266400 TGTATATGTGTATGCCTTGTACGAAA 58.734 34.615 0.00 0.00 0.00 3.46
1956 2769 7.307160 CCTTTGTATATGTGTATGCCTTGTACG 60.307 40.741 0.00 0.00 0.00 3.67
1971 2784 4.648762 TGCCAACCATTCCCTTTGTATATG 59.351 41.667 0.00 0.00 0.00 1.78
2009 2829 0.771127 TAGCCAGGTTCTTGCCTTGT 59.229 50.000 0.00 0.00 36.58 3.16
2014 2834 1.474143 CCTAGCTAGCCAGGTTCTTGC 60.474 57.143 19.99 0.00 33.61 4.01
2015 2835 1.834263 ACCTAGCTAGCCAGGTTCTTG 59.166 52.381 26.91 4.79 42.68 3.02
2016 2836 2.255770 ACCTAGCTAGCCAGGTTCTT 57.744 50.000 26.91 6.62 42.68 2.52
2119 2956 5.106118 GCAGAGCAAGGATCGACAGTATATA 60.106 44.000 0.00 0.00 0.00 0.86
2120 2957 4.321601 GCAGAGCAAGGATCGACAGTATAT 60.322 45.833 0.00 0.00 0.00 0.86
2121 2958 3.004839 GCAGAGCAAGGATCGACAGTATA 59.995 47.826 0.00 0.00 0.00 1.47
2122 2959 2.223923 GCAGAGCAAGGATCGACAGTAT 60.224 50.000 0.00 0.00 0.00 2.12
2130 2967 0.182061 TGGGATGCAGAGCAAGGATC 59.818 55.000 0.00 0.00 43.62 3.36
2191 3037 7.864307 ACGTCACGCTAATTATTACCTAATC 57.136 36.000 0.00 0.00 0.00 1.75
2196 3042 7.080099 TCAGATACGTCACGCTAATTATTACC 58.920 38.462 0.00 0.00 0.00 2.85
2197 3043 8.670804 ATCAGATACGTCACGCTAATTATTAC 57.329 34.615 0.00 0.00 0.00 1.89
2198 3044 7.966753 GGATCAGATACGTCACGCTAATTATTA 59.033 37.037 0.00 0.00 0.00 0.98
2199 3045 6.807230 GGATCAGATACGTCACGCTAATTATT 59.193 38.462 0.00 0.00 0.00 1.40
2200 3046 6.151312 AGGATCAGATACGTCACGCTAATTAT 59.849 38.462 0.00 0.00 0.00 1.28
2201 3047 5.472478 AGGATCAGATACGTCACGCTAATTA 59.528 40.000 0.00 0.00 0.00 1.40
2202 3048 4.278669 AGGATCAGATACGTCACGCTAATT 59.721 41.667 0.00 0.00 0.00 1.40
2243 3089 1.726791 GGTCTTCTGTGCACGTGTATG 59.273 52.381 18.38 10.09 0.00 2.39
2367 3217 2.349590 TGACAAGTCCAATCTGATGCG 58.650 47.619 0.00 0.00 0.00 4.73
2401 3257 2.229062 TGTAGAGAAAGAGACTGCCGTG 59.771 50.000 0.00 0.00 0.00 4.94
2403 3259 3.443037 CATGTAGAGAAAGAGACTGCCG 58.557 50.000 0.00 0.00 0.00 5.69
2418 3274 6.083098 AGCAGAGAATGTAGTAGCATGTAG 57.917 41.667 0.00 0.00 0.00 2.74
2429 3285 4.763073 CAGTCATGGAAGCAGAGAATGTA 58.237 43.478 0.00 0.00 0.00 2.29
2430 3286 3.607741 CAGTCATGGAAGCAGAGAATGT 58.392 45.455 0.00 0.00 0.00 2.71
2431 3287 2.355132 GCAGTCATGGAAGCAGAGAATG 59.645 50.000 0.00 0.00 0.00 2.67
2432 3288 2.641305 GCAGTCATGGAAGCAGAGAAT 58.359 47.619 0.00 0.00 0.00 2.40
2435 3293 0.252479 AGGCAGTCATGGAAGCAGAG 59.748 55.000 0.00 0.00 0.00 3.35
2448 3306 0.323633 TGCATTGCATGGTAGGCAGT 60.324 50.000 7.38 0.00 43.05 4.40
2449 3307 0.818938 TTGCATTGCATGGTAGGCAG 59.181 50.000 12.95 0.00 43.05 4.85
2493 3351 3.015327 ACAGATGAGGAAAAGATGCAGC 58.985 45.455 0.00 0.00 0.00 5.25
2499 3357 2.430465 GCAGCACAGATGAGGAAAAGA 58.570 47.619 0.00 0.00 0.00 2.52
2500 3358 1.471684 GGCAGCACAGATGAGGAAAAG 59.528 52.381 0.00 0.00 0.00 2.27
2509 3371 1.604593 GGGTTGTGGCAGCACAGAT 60.605 57.895 0.00 0.00 36.35 2.90
2550 3413 7.859325 TGCAAGTACACCTAAATAATCTTCC 57.141 36.000 0.00 0.00 0.00 3.46
2705 3573 2.839486 TCGAGCACAAATCTGGTTCT 57.161 45.000 0.00 0.00 0.00 3.01
2706 3574 3.265791 AGATCGAGCACAAATCTGGTTC 58.734 45.455 2.38 0.00 0.00 3.62
2707 3575 3.340814 AGATCGAGCACAAATCTGGTT 57.659 42.857 2.38 0.00 0.00 3.67
2739 3607 6.111382 ACAAACATGTGATTCTGATCGATCT 58.889 36.000 25.02 5.76 34.91 2.75
2749 3617 5.518812 TGTAGTGCAACAAACATGTGATTC 58.481 37.500 0.00 0.00 41.43 2.52
2750 3618 5.512753 TGTAGTGCAACAAACATGTGATT 57.487 34.783 0.00 0.00 41.43 2.57
2751 3619 5.474532 AGATGTAGTGCAACAAACATGTGAT 59.525 36.000 0.00 0.00 43.08 3.06
2752 3620 4.821260 AGATGTAGTGCAACAAACATGTGA 59.179 37.500 0.00 0.00 43.08 3.58
2753 3621 4.913345 CAGATGTAGTGCAACAAACATGTG 59.087 41.667 0.00 11.88 44.18 3.21
2754 3622 4.557296 GCAGATGTAGTGCAACAAACATGT 60.557 41.667 8.65 0.00 43.08 3.21
2778 3646 1.005924 CAAGATTAGGGTTGGCCAGGT 59.994 52.381 5.11 0.00 36.17 4.00
2796 3664 7.759489 AGCATTTTCAGTGTACTTATTCCAA 57.241 32.000 0.00 0.00 0.00 3.53
2816 3684 5.552870 AGTAATACGGGATCTGAAAGCAT 57.447 39.130 0.00 0.00 0.00 3.79
2825 3693 5.416326 AGCTGATCAGTAGTAATACGGGATC 59.584 44.000 23.38 21.07 36.79 3.36
2829 3697 6.528423 GCATTAGCTGATCAGTAGTAATACGG 59.472 42.308 23.38 12.63 37.91 4.02
2875 3743 3.064820 CCGGCCACATAAAATACAGTGTC 59.935 47.826 2.24 0.00 0.00 3.67
3084 3974 9.353431 AGGAAATTTTGTAAGCCATGAAATTTT 57.647 25.926 11.03 4.85 38.98 1.82
3127 4017 1.355971 GGAGTTGATAACGCAAGCGA 58.644 50.000 22.30 0.00 42.83 4.93
3198 4156 8.768957 TTAATCATCTCTTGTTTCTGTCAGAG 57.231 34.615 2.12 0.00 0.00 3.35
3205 4163 6.402222 AGACGCTTAATCATCTCTTGTTTCT 58.598 36.000 0.00 0.00 0.00 2.52
3371 4329 1.006922 GTGGCTTTGCTGAACCTGC 60.007 57.895 0.00 0.00 0.00 4.85
3385 4343 1.885871 GCTCATGGAAACCAGTGGC 59.114 57.895 9.78 0.00 36.75 5.01
3390 4348 0.534873 TCGATCGCTCATGGAAACCA 59.465 50.000 11.09 0.00 38.19 3.67
3402 4360 1.411493 GAACACCGAACCTCGATCGC 61.411 60.000 11.09 0.00 43.74 4.58
3427 4385 3.616821 TGAGATTTACATTCACCGAAGCG 59.383 43.478 0.00 0.00 0.00 4.68
3428 4386 4.898370 GTGAGATTTACATTCACCGAAGC 58.102 43.478 0.00 0.00 36.17 3.86
3434 4392 6.560253 ACACAAGGTGAGATTTACATTCAC 57.440 37.500 2.98 0.00 40.29 3.18
3436 4394 7.875971 AGAAACACAAGGTGAGATTTACATTC 58.124 34.615 2.98 0.00 36.96 2.67
3437 4395 7.040409 GGAGAAACACAAGGTGAGATTTACATT 60.040 37.037 2.98 0.00 36.96 2.71
3438 4396 6.431234 GGAGAAACACAAGGTGAGATTTACAT 59.569 38.462 2.98 0.00 36.96 2.29
3439 4397 5.763204 GGAGAAACACAAGGTGAGATTTACA 59.237 40.000 2.98 0.00 36.96 2.41
3441 4399 6.187727 AGGAGAAACACAAGGTGAGATTTA 57.812 37.500 2.98 0.00 36.96 1.40
3445 4403 3.199946 ACAAGGAGAAACACAAGGTGAGA 59.800 43.478 2.98 0.00 36.96 3.27
3470 4433 2.874694 CGCCCGAACATCATCTGCG 61.875 63.158 0.00 0.00 33.90 5.18
4417 5398 8.708742 GCGTATACATGAATGAGTAAGCAAATA 58.291 33.333 0.00 0.00 31.89 1.40
4418 5399 7.226523 TGCGTATACATGAATGAGTAAGCAAAT 59.773 33.333 0.00 0.00 35.21 2.32
4539 5578 7.881232 ACGTATGTTCCCTATATTAACCAATGG 59.119 37.037 0.00 0.00 0.00 3.16
4554 5593 1.717194 TTTCGCTGACGTATGTTCCC 58.283 50.000 0.00 0.00 41.18 3.97
4571 5610 1.597027 CAGGCTCGTGGGACGTTTT 60.597 57.895 0.00 0.00 43.14 2.43
4572 5611 1.466025 TACAGGCTCGTGGGACGTTT 61.466 55.000 0.00 0.00 43.14 3.60
4576 5615 1.755380 ACTAATACAGGCTCGTGGGAC 59.245 52.381 0.00 0.00 0.00 4.46
4577 5616 2.029623 GACTAATACAGGCTCGTGGGA 58.970 52.381 0.00 0.00 0.00 4.37
4578 5617 2.032620 AGACTAATACAGGCTCGTGGG 58.967 52.381 0.00 0.00 38.86 4.61
4579 5618 4.913335 TTAGACTAATACAGGCTCGTGG 57.087 45.455 0.00 0.00 38.86 4.94
4580 5619 8.867112 TTTATTTAGACTAATACAGGCTCGTG 57.133 34.615 0.00 0.00 38.86 4.35
4581 5620 9.530633 CTTTTATTTAGACTAATACAGGCTCGT 57.469 33.333 0.00 0.00 38.86 4.18
4582 5621 8.488764 GCTTTTATTTAGACTAATACAGGCTCG 58.511 37.037 0.00 0.00 38.86 5.03
4583 5622 9.326413 TGCTTTTATTTAGACTAATACAGGCTC 57.674 33.333 0.00 0.00 38.86 4.70
4585 5624 9.110502 AGTGCTTTTATTTAGACTAATACAGGC 57.889 33.333 0.00 0.00 0.00 4.85
4588 5627 9.865321 ACGAGTGCTTTTATTTAGACTAATACA 57.135 29.630 0.00 0.00 0.00 2.29
4590 5629 9.865321 ACACGAGTGCTTTTATTTAGACTAATA 57.135 29.630 2.76 0.00 0.00 0.98
4591 5630 8.773404 ACACGAGTGCTTTTATTTAGACTAAT 57.227 30.769 2.76 0.00 0.00 1.73
4592 5631 8.597662 AACACGAGTGCTTTTATTTAGACTAA 57.402 30.769 2.76 0.00 0.00 2.24
4593 5632 8.086522 AGAACACGAGTGCTTTTATTTAGACTA 58.913 33.333 2.76 0.00 24.49 2.59
4594 5633 6.929606 AGAACACGAGTGCTTTTATTTAGACT 59.070 34.615 2.76 0.00 24.49 3.24
4606 5645 2.101582 AGTCTTTGAGAACACGAGTGCT 59.898 45.455 2.76 0.00 35.88 4.40
4661 5700 5.614324 TTTGAGGGATTCGTGTATCAGAT 57.386 39.130 0.00 0.00 0.00 2.90
4662 5701 5.186992 TCTTTTGAGGGATTCGTGTATCAGA 59.813 40.000 0.00 0.00 0.00 3.27
4663 5702 5.419542 TCTTTTGAGGGATTCGTGTATCAG 58.580 41.667 0.00 0.00 0.00 2.90
4664 5703 5.414789 TCTTTTGAGGGATTCGTGTATCA 57.585 39.130 0.00 0.00 0.00 2.15
4665 5704 6.737254 TTTCTTTTGAGGGATTCGTGTATC 57.263 37.500 0.00 0.00 0.00 2.24
4666 5705 7.519032 TTTTTCTTTTGAGGGATTCGTGTAT 57.481 32.000 0.00 0.00 0.00 2.29
4696 5735 0.315886 TTGCGTCGTGTACCAGTCAT 59.684 50.000 0.00 0.00 0.00 3.06
4698 5737 1.615107 GCTTGCGTCGTGTACCAGTC 61.615 60.000 0.00 0.00 0.00 3.51
4703 5742 1.154654 GCTTGCTTGCGTCGTGTAC 60.155 57.895 0.00 0.00 0.00 2.90
4711 5750 1.980844 CACTTGTATTGCTTGCTTGCG 59.019 47.619 0.00 0.00 35.36 4.85
4762 5801 5.548056 AGATCCAGGTCTCTTGAGGTTTTTA 59.452 40.000 0.00 0.00 0.00 1.52
4763 5802 4.352298 AGATCCAGGTCTCTTGAGGTTTTT 59.648 41.667 0.00 0.00 0.00 1.94
4766 5805 3.197927 AGATCCAGGTCTCTTGAGGTT 57.802 47.619 0.00 0.00 0.00 3.50
4797 5837 4.050553 CGCAAAATGATGGTTGTTTGTCT 58.949 39.130 0.00 0.00 34.24 3.41
4807 5847 3.548014 GGATTACCGACGCAAAATGATGG 60.548 47.826 0.00 0.00 0.00 3.51
4876 5916 2.568623 ACATGAACCACTTGGACCTC 57.431 50.000 0.00 0.00 38.94 3.85
5012 6056 7.446931 TCAAATTGTACTAAGATTGGTTCTGCA 59.553 33.333 0.00 0.00 33.93 4.41
5038 6082 9.205513 AGAATTTTGGCAAAATCTATCCATACT 57.794 29.630 31.79 16.32 40.05 2.12
5071 6116 2.346766 ACAACCACACTGCATCTCAA 57.653 45.000 0.00 0.00 0.00 3.02
5081 6126 3.002553 CCTGTAAACGGTAACAACCACAC 59.997 47.826 0.00 0.00 0.00 3.82
5137 6182 5.078411 AGATAATCAACGTGCAGAACTCT 57.922 39.130 0.00 0.00 0.00 3.24
5173 6218 3.754188 CTGAAAGCATACTCCAAGTGC 57.246 47.619 0.00 0.00 39.10 4.40
5272 6320 6.037610 CACATTAACTAGCCTGGATTCTTCAC 59.962 42.308 0.00 0.00 0.00 3.18
5308 6356 2.289320 TGCAATACCCAAATTGTGCACC 60.289 45.455 15.69 0.00 38.78 5.01


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

AutoCloner maintained by Alex Coulton.