Multiple sequence alignment - TraesCS5B01G191500

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 TraesCS5B01G191500 chr5B 100.000 4009 0 0 1 4009 345052530 345048522 0.000000e+00 7404
1 TraesCS5B01G191500 chr5B 94.949 99 3 2 3740 3837 344951861 344951764 1.930000e-33 154
2 TraesCS5B01G191500 chr5D 90.526 2871 155 36 1 2808 302019681 302016865 0.000000e+00 3687
3 TraesCS5B01G191500 chr5D 96.505 372 12 1 2807 3177 302016704 302016333 7.360000e-172 614
4 TraesCS5B01G191500 chr5D 86.057 459 36 14 3556 4005 302016087 302015648 6.070000e-128 468
5 TraesCS5B01G191500 chr5D 87.037 270 16 10 3224 3487 302016330 302016074 1.820000e-73 287
6 TraesCS5B01G191500 chr5D 94.915 177 8 1 1 176 328392636 328392812 3.950000e-70 276
7 TraesCS5B01G191500 chr5A 92.050 1673 111 13 1757 3422 395836866 395838523 0.000000e+00 2333
8 TraesCS5B01G191500 chr5A 88.817 1699 103 27 1 1629 395834961 395836642 0.000000e+00 2004
9 TraesCS5B01G191500 chr5A 81.758 455 35 22 3556 4009 395838588 395838995 1.780000e-88 337
10 TraesCS5B01G191500 chr5A 85.345 116 12 4 3800 3915 395847311 395847421 9.100000e-22 115
11 TraesCS5B01G191500 chr7D 94.545 165 9 0 4 168 55446122 55445958 5.140000e-64 255
12 TraesCS5B01G191500 chr6A 90.960 177 14 2 1 176 536911854 536911679 1.860000e-58 237
13 TraesCS5B01G191500 chr3B 97.810 137 3 0 4 140 612294763 612294627 1.860000e-58 237


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 TraesCS5B01G191500 chr5B 345048522 345052530 4008 True 7404 7404 100.000000 1 4009 1 chr5B.!!$R2 4008
1 TraesCS5B01G191500 chr5D 302015648 302019681 4033 True 1264 3687 90.031250 1 4005 4 chr5D.!!$R1 4004
2 TraesCS5B01G191500 chr5A 395834961 395838995 4034 False 1558 2333 87.541667 1 4009 3 chr5A.!!$F2 4008

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
433 434 0.035056 ATGGGAGGTTGAAGAAGCCG 60.035 55.0 0.00 0.00 0.00 5.52 F
644 657 0.323908 AAGAGGGTGAGGAGACGAGG 60.324 60.0 0.00 0.00 0.00 4.63 F
1399 1479 0.039708 TGCATCGCAGCGAGAGATAG 60.040 55.0 24.08 9.35 39.91 2.08 F
1400 1480 0.239613 GCATCGCAGCGAGAGATAGA 59.760 55.0 24.08 0.00 39.91 1.98 F
1649 1852 0.602562 TATGTGCAAAGCTTGTGCCC 59.397 50.0 22.41 15.71 41.49 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1301 1365 0.757188 ACCCTGAGCTACCTCGGATG 60.757 60.000 1.24 0.00 45.56 3.51 R
1515 1610 0.810648 TGTCGCCAATGAATCAAGCC 59.189 50.000 0.00 0.00 0.00 4.35 R
2469 2683 1.897802 AGCATGGAAAAGAAGGGCAAG 59.102 47.619 0.00 0.00 0.00 4.01 R
2535 2749 1.936547 GCCCTCTCTTAAACTGATGCG 59.063 52.381 0.00 0.00 0.00 4.73 R
3552 3948 0.622136 TCAGATGCAGGCAACATCCT 59.378 50.000 14.02 2.41 44.08 3.24 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
343 344 1.746991 GAGGAGCCCGCTTTTCAGG 60.747 63.158 0.00 0.00 0.00 3.86
433 434 0.035056 ATGGGAGGTTGAAGAAGCCG 60.035 55.000 0.00 0.00 0.00 5.52
602 615 1.288037 AGGGTTTAGGGATTTGGGAGC 59.712 52.381 0.00 0.00 0.00 4.70
606 619 1.681229 TTAGGGATTTGGGAGCCAGT 58.319 50.000 0.00 0.00 33.81 4.00
619 632 2.290323 GGAGCCAGTTAGGATGTGTTGT 60.290 50.000 0.00 0.00 41.22 3.32
622 635 2.226437 GCCAGTTAGGATGTGTTGTGTG 59.774 50.000 0.00 0.00 41.22 3.82
626 639 3.137544 AGTTAGGATGTGTTGTGTGGGAA 59.862 43.478 0.00 0.00 0.00 3.97
637 650 0.836400 GTGTGGGAAGAGGGTGAGGA 60.836 60.000 0.00 0.00 0.00 3.71
644 657 0.323908 AAGAGGGTGAGGAGACGAGG 60.324 60.000 0.00 0.00 0.00 4.63
676 689 4.598894 CGGAGGAGGCAGCGGATG 62.599 72.222 0.00 0.00 0.00 3.51
777 803 3.827898 GACGTCTCAGCGGGGAGG 61.828 72.222 8.70 4.81 35.58 4.30
778 804 4.361971 ACGTCTCAGCGGGGAGGA 62.362 66.667 13.47 0.00 35.58 3.71
779 805 3.522731 CGTCTCAGCGGGGAGGAG 61.523 72.222 0.00 0.00 35.58 3.69
817 843 1.279496 TCAGCCTTGTGAGGTAGCAT 58.721 50.000 0.00 0.00 45.44 3.79
863 889 1.529244 GCGCAGGCCCCATCTTATT 60.529 57.895 0.30 0.00 0.00 1.40
866 892 2.795329 CGCAGGCCCCATCTTATTATT 58.205 47.619 0.00 0.00 0.00 1.40
867 893 2.749621 CGCAGGCCCCATCTTATTATTC 59.250 50.000 0.00 0.00 0.00 1.75
876 902 3.686726 CCATCTTATTATTCCGAGCAGGC 59.313 47.826 0.00 0.00 40.77 4.85
892 918 2.658285 CAGGCAAGCCCATATCTCAAA 58.342 47.619 7.62 0.00 36.58 2.69
893 919 3.025978 CAGGCAAGCCCATATCTCAAAA 58.974 45.455 7.62 0.00 36.58 2.44
984 1027 0.386113 GCGCTAGGGTTCTACAGAGG 59.614 60.000 8.77 0.00 0.00 3.69
985 1028 2.022754 GCGCTAGGGTTCTACAGAGGA 61.023 57.143 8.77 0.00 0.00 3.71
986 1029 1.950909 CGCTAGGGTTCTACAGAGGAG 59.049 57.143 0.00 0.00 0.00 3.69
987 1030 2.684334 CGCTAGGGTTCTACAGAGGAGT 60.684 54.545 0.00 0.00 0.00 3.85
988 1031 3.367321 GCTAGGGTTCTACAGAGGAGTT 58.633 50.000 0.00 0.00 0.00 3.01
989 1032 3.131400 GCTAGGGTTCTACAGAGGAGTTG 59.869 52.174 0.00 0.00 0.00 3.16
990 1033 3.261818 AGGGTTCTACAGAGGAGTTGT 57.738 47.619 0.00 0.00 0.00 3.32
991 1034 3.588569 AGGGTTCTACAGAGGAGTTGTT 58.411 45.455 0.00 0.00 0.00 2.83
992 1035 3.325135 AGGGTTCTACAGAGGAGTTGTTG 59.675 47.826 0.00 0.00 0.00 3.33
993 1036 3.071167 GGGTTCTACAGAGGAGTTGTTGT 59.929 47.826 0.00 0.00 0.00 3.32
994 1037 4.058817 GGTTCTACAGAGGAGTTGTTGTG 58.941 47.826 0.00 0.00 0.00 3.33
995 1038 4.443034 GGTTCTACAGAGGAGTTGTTGTGT 60.443 45.833 0.00 0.00 0.00 3.72
1138 1181 2.043852 GGCTCGAGGAGGAGTCCA 60.044 66.667 15.58 0.00 46.80 4.02
1160 1203 2.202440 CACCACGTACGCTCTCCG 60.202 66.667 16.72 0.00 44.21 4.63
1191 1234 2.766313 TGCTTGCACTAGTCGATTGTT 58.234 42.857 0.00 0.00 0.00 2.83
1192 1235 2.736721 TGCTTGCACTAGTCGATTGTTC 59.263 45.455 0.00 0.00 0.00 3.18
1194 1237 3.061429 GCTTGCACTAGTCGATTGTTCTC 59.939 47.826 0.00 0.00 0.00 2.87
1207 1250 4.152938 CGATTGTTCTCTGAGTCAATTGCA 59.847 41.667 21.32 0.00 31.87 4.08
1213 1256 3.001414 CTCTGAGTCAATTGCAGTGGAG 58.999 50.000 0.00 2.34 0.00 3.86
1221 1264 1.203441 ATTGCAGTGGAGCTGGAGGA 61.203 55.000 0.00 0.00 46.16 3.71
1227 1270 2.066393 TGGAGCTGGAGGAATCGGG 61.066 63.158 0.00 0.00 0.00 5.14
1247 1290 4.675671 CGGGATCATCGGCTTAGATCTTAC 60.676 50.000 0.00 0.00 38.51 2.34
1248 1291 4.464597 GGGATCATCGGCTTAGATCTTACT 59.535 45.833 0.00 0.00 38.51 2.24
1249 1292 5.046950 GGGATCATCGGCTTAGATCTTACTT 60.047 44.000 0.00 0.00 38.51 2.24
1250 1293 6.153000 GGGATCATCGGCTTAGATCTTACTTA 59.847 42.308 0.00 0.00 38.51 2.24
1251 1294 7.254852 GGATCATCGGCTTAGATCTTACTTAG 58.745 42.308 0.00 0.00 38.51 2.18
1252 1295 7.094118 GGATCATCGGCTTAGATCTTACTTAGT 60.094 40.741 0.00 0.00 38.51 2.24
1253 1296 8.865420 ATCATCGGCTTAGATCTTACTTAGTA 57.135 34.615 0.00 0.00 0.00 1.82
1254 1297 8.325421 TCATCGGCTTAGATCTTACTTAGTAG 57.675 38.462 0.00 0.00 0.00 2.57
1255 1298 7.937942 TCATCGGCTTAGATCTTACTTAGTAGT 59.062 37.037 0.00 0.00 38.44 2.73
1256 1299 9.217278 CATCGGCTTAGATCTTACTTAGTAGTA 57.783 37.037 0.00 0.00 35.78 1.82
1257 1300 9.962809 ATCGGCTTAGATCTTACTTAGTAGTAT 57.037 33.333 0.00 0.00 36.76 2.12
1258 1301 9.434420 TCGGCTTAGATCTTACTTAGTAGTATC 57.566 37.037 0.00 7.53 36.76 2.24
1259 1302 9.217278 CGGCTTAGATCTTACTTAGTAGTATCA 57.783 37.037 0.00 3.38 36.76 2.15
1306 1370 7.713764 TTACAATATGATGTGTTCTCATCCG 57.286 36.000 10.84 0.00 42.24 4.18
1307 1371 5.917462 ACAATATGATGTGTTCTCATCCGA 58.083 37.500 10.84 2.09 42.24 4.55
1318 1382 0.958091 CTCATCCGAGGTAGCTCAGG 59.042 60.000 21.17 20.52 35.44 3.86
1319 1383 0.468214 TCATCCGAGGTAGCTCAGGG 60.468 60.000 21.17 14.80 0.00 4.45
1335 1403 4.035208 GCTCAGGGTTGTTATATTCAACGG 59.965 45.833 13.46 8.48 43.93 4.44
1354 1422 8.737168 TCAACGGATTGAAAAATCATAGATCT 57.263 30.769 0.00 0.00 41.99 2.75
1356 1424 9.869844 CAACGGATTGAAAAATCATAGATCTAC 57.130 33.333 4.10 0.00 38.15 2.59
1357 1425 8.299262 ACGGATTGAAAAATCATAGATCTACG 57.701 34.615 4.10 0.00 0.00 3.51
1399 1479 0.039708 TGCATCGCAGCGAGAGATAG 60.040 55.000 24.08 9.35 39.91 2.08
1400 1480 0.239613 GCATCGCAGCGAGAGATAGA 59.760 55.000 24.08 0.00 39.91 1.98
1401 1481 1.135431 GCATCGCAGCGAGAGATAGAT 60.135 52.381 24.08 0.00 39.91 1.98
1402 1482 2.096657 GCATCGCAGCGAGAGATAGATA 59.903 50.000 24.08 0.00 39.91 1.98
1403 1483 3.243035 GCATCGCAGCGAGAGATAGATAT 60.243 47.826 24.08 0.00 39.91 1.63
1423 1518 6.617371 AGATATGGTGTAGATTCATATCCCCC 59.383 42.308 14.95 0.00 45.13 5.40
1428 1523 5.711976 GGTGTAGATTCATATCCCCCATTTG 59.288 44.000 0.00 0.00 0.00 2.32
1433 1528 1.147608 TCATATCCCCCATTTGGCCTG 59.852 52.381 3.32 0.00 0.00 4.85
1487 1582 8.642432 TCTAGTACTGGAAATTATCATCAGTGG 58.358 37.037 6.45 0.00 38.84 4.00
1613 1715 6.342111 CAGTCTCAACTTTTATAGAGGACCC 58.658 44.000 0.00 0.00 31.71 4.46
1631 1733 1.434555 CCGAATTCTGCACACGGTTA 58.565 50.000 3.52 0.00 38.97 2.85
1632 1734 2.006888 CCGAATTCTGCACACGGTTAT 58.993 47.619 3.52 0.00 38.97 1.89
1641 1844 1.685302 CACACGGTTATGTGCAAAGC 58.315 50.000 0.00 0.00 43.29 3.51
1648 1851 2.061028 GTTATGTGCAAAGCTTGTGCC 58.939 47.619 22.41 16.55 41.49 5.01
1649 1852 0.602562 TATGTGCAAAGCTTGTGCCC 59.397 50.000 22.41 15.71 41.49 5.36
1673 1876 2.462456 ATGACTGCATGTGACTTCGT 57.538 45.000 0.00 0.00 32.31 3.85
1686 1889 6.202516 TGTGACTTCGTCAAAAAGGAAAAT 57.797 33.333 0.00 0.00 44.49 1.82
1728 1932 2.078849 TCACTACTCATGTTGTGCCG 57.921 50.000 6.02 0.00 45.10 5.69
1763 1975 3.181487 GGCGCAGAAAATGTATGGTCATT 60.181 43.478 10.83 0.00 39.35 2.57
1764 1976 4.036262 GGCGCAGAAAATGTATGGTCATTA 59.964 41.667 10.83 0.00 37.09 1.90
1834 2046 9.393512 ACATCCATGAATTTTGTTTCTTCAAAA 57.606 25.926 0.00 6.98 46.47 2.44
1861 2074 1.882623 CCTTTGGAGTTTGGAGTGAGC 59.117 52.381 0.00 0.00 0.00 4.26
1880 2093 1.110442 CGCAGAGGAGAGAGAATGGT 58.890 55.000 0.00 0.00 0.00 3.55
1969 2182 8.329203 AGTGTAAGCTTTCTTTCAGATTTAGG 57.671 34.615 3.20 0.00 31.60 2.69
1988 2201 7.833285 TTTAGGTTTCTGCCTTTCAAGTTAT 57.167 32.000 0.00 0.00 39.94 1.89
2226 2440 3.760684 AGATGCTAGCCTGGTTTCTTTTG 59.239 43.478 13.29 0.00 0.00 2.44
2277 2491 8.732746 TCCTTTGTGAAGAGGCTATAATTAAC 57.267 34.615 0.00 0.00 34.71 2.01
2368 2582 0.615850 AGGCTAGCCACCTCAACTTC 59.384 55.000 34.70 3.73 38.92 3.01
2369 2583 0.615850 GGCTAGCCACCTCAACTTCT 59.384 55.000 29.33 0.00 35.81 2.85
2370 2584 1.003696 GGCTAGCCACCTCAACTTCTT 59.996 52.381 29.33 0.00 35.81 2.52
2371 2585 2.351455 GCTAGCCACCTCAACTTCTTC 58.649 52.381 2.29 0.00 0.00 2.87
2385 2599 7.489757 CCTCAACTTCTTCTCGATACCTAAAAG 59.510 40.741 0.00 0.00 0.00 2.27
2435 2649 0.768221 AGAGAGCCAACTTGTCCCCA 60.768 55.000 0.00 0.00 0.00 4.96
2444 2658 3.819245 CTTGTCCCCAAGTTCCACA 57.181 52.632 0.00 0.00 42.61 4.17
2469 2683 7.011389 CACCTTGGTTTTTCATTCCTTCTTTTC 59.989 37.037 0.00 0.00 0.00 2.29
2493 2707 1.067354 CCCTTCTTTTCCATGCTGTGC 60.067 52.381 0.00 0.00 0.00 4.57
2494 2708 1.614903 CCTTCTTTTCCATGCTGTGCA 59.385 47.619 0.00 0.00 44.86 4.57
2535 2749 5.244626 AGGCTTAACCATATTGATTGGCATC 59.755 40.000 0.00 0.00 43.14 3.91
2536 2750 5.156355 GCTTAACCATATTGATTGGCATCG 58.844 41.667 0.00 0.00 37.81 3.84
2537 2751 3.648339 AACCATATTGATTGGCATCGC 57.352 42.857 0.00 0.00 37.81 4.58
2538 2752 2.585330 ACCATATTGATTGGCATCGCA 58.415 42.857 0.00 0.00 37.81 5.10
2539 2753 3.159472 ACCATATTGATTGGCATCGCAT 58.841 40.909 0.00 0.00 37.81 4.73
2557 2771 3.181475 CGCATCAGTTTAAGAGAGGGCTA 60.181 47.826 0.00 0.00 0.00 3.93
2610 2824 9.282247 CTTGTACAATTCAATTTATCAGTGCTC 57.718 33.333 9.13 0.00 0.00 4.26
2635 2853 5.763876 ACTAGCCTTTATCCACTGAGTTT 57.236 39.130 0.00 0.00 0.00 2.66
2636 2854 5.491982 ACTAGCCTTTATCCACTGAGTTTG 58.508 41.667 0.00 0.00 0.00 2.93
2637 2855 4.640771 AGCCTTTATCCACTGAGTTTGA 57.359 40.909 0.00 0.00 0.00 2.69
2638 2856 5.184892 AGCCTTTATCCACTGAGTTTGAT 57.815 39.130 0.74 0.74 0.00 2.57
2639 2857 6.313519 AGCCTTTATCCACTGAGTTTGATA 57.686 37.500 0.00 0.00 0.00 2.15
2673 2891 9.994432 GTTCTACTAATCTCATGTTCCAAAATG 57.006 33.333 0.00 0.00 0.00 2.32
2674 2892 8.737168 TCTACTAATCTCATGTTCCAAAATGG 57.263 34.615 0.00 0.00 39.43 3.16
2707 2925 3.565902 ACTTGCTAGTCTTTCACCTTTGC 59.434 43.478 0.00 0.00 0.00 3.68
2738 2956 4.190772 CCAGTGGTTTGAAACTGCAAATT 58.809 39.130 8.09 0.00 42.03 1.82
2822 3202 5.860611 TCCATTCTATAATACCGTGGTTGG 58.139 41.667 0.00 0.00 0.00 3.77
2825 3205 6.940298 CCATTCTATAATACCGTGGTTGGATT 59.060 38.462 0.00 0.00 0.00 3.01
2843 3223 7.441836 GTTGGATTGGTTTCTATTTCCTTTGT 58.558 34.615 0.00 0.00 0.00 2.83
2859 3239 6.723298 TCCTTTGTTTTATTCAAGGCTTCA 57.277 33.333 0.00 0.00 0.00 3.02
2892 3272 7.698130 GGTAAAGTCAACACAGCATATTTGATC 59.302 37.037 0.00 0.00 30.96 2.92
3114 3495 8.900983 AGGATCTTCACTCTAAAGAATATTGC 57.099 34.615 0.00 0.00 36.41 3.56
3140 3521 6.172136 TCAAATAATTTGGGCATGTATGGG 57.828 37.500 0.00 0.00 40.98 4.00
3252 3633 5.000012 ACTCTACGGTTGAGATCAATCAC 58.000 43.478 23.09 0.00 36.80 3.06
3258 3639 3.018856 GGTTGAGATCAATCACCATGCA 58.981 45.455 0.91 0.00 36.96 3.96
3260 3641 4.418392 GTTGAGATCAATCACCATGCAAC 58.582 43.478 0.00 0.00 38.24 4.17
3261 3642 3.959293 TGAGATCAATCACCATGCAACT 58.041 40.909 0.00 0.00 0.00 3.16
3264 3645 5.761726 TGAGATCAATCACCATGCAACTATC 59.238 40.000 0.00 0.00 0.00 2.08
3265 3646 4.753610 AGATCAATCACCATGCAACTATCG 59.246 41.667 0.00 0.00 0.00 2.92
3267 3648 3.871006 TCAATCACCATGCAACTATCGTC 59.129 43.478 0.00 0.00 0.00 4.20
3269 3650 3.610040 TCACCATGCAACTATCGTCTT 57.390 42.857 0.00 0.00 0.00 3.01
3270 3651 3.261580 TCACCATGCAACTATCGTCTTG 58.738 45.455 0.00 0.00 0.00 3.02
3299 3680 5.128663 AGGTTTTGTCTGGCAGTAATTTGTT 59.871 36.000 15.27 0.00 0.00 2.83
3332 3713 3.971245 TTTTTATGGCACCATTCACCC 57.029 42.857 7.63 0.00 37.82 4.61
3354 3737 7.065683 CACCCCCATTGTTTTTATGAAATTAGC 59.934 37.037 0.00 0.00 0.00 3.09
3359 3742 8.161610 CCATTGTTTTTATGAAATTAGCGTGTG 58.838 33.333 0.00 0.00 0.00 3.82
3361 3744 7.616103 TGTTTTTATGAAATTAGCGTGTGTG 57.384 32.000 0.00 0.00 0.00 3.82
3439 3825 5.179045 CAAGTGCTTCTTGTCAATCTTGT 57.821 39.130 11.95 0.00 45.89 3.16
3442 3828 6.212888 AGTGCTTCTTGTCAATCTTGTTTT 57.787 33.333 0.00 0.00 0.00 2.43
3471 3867 4.201910 CCCCACTAATCTTTGTAATGCACG 60.202 45.833 0.00 0.00 0.00 5.34
3480 3876 6.307031 TCTTTGTAATGCACGTATGTTGTT 57.693 33.333 0.00 0.00 0.00 2.83
3481 3877 6.367421 TCTTTGTAATGCACGTATGTTGTTC 58.633 36.000 0.00 0.00 0.00 3.18
3482 3878 4.314948 TGTAATGCACGTATGTTGTTCG 57.685 40.909 0.00 0.00 0.00 3.95
3483 3879 2.241259 AATGCACGTATGTTGTTCGC 57.759 45.000 0.00 0.00 0.00 4.70
3484 3880 1.152510 ATGCACGTATGTTGTTCGCA 58.847 45.000 0.00 0.11 0.00 5.10
3485 3881 1.152510 TGCACGTATGTTGTTCGCAT 58.847 45.000 0.00 0.00 0.00 4.73
3486 3882 1.533299 TGCACGTATGTTGTTCGCATT 59.467 42.857 0.00 0.00 0.00 3.56
3487 3883 2.737252 TGCACGTATGTTGTTCGCATTA 59.263 40.909 0.00 0.00 0.00 1.90
3488 3884 3.372514 TGCACGTATGTTGTTCGCATTAT 59.627 39.130 0.00 0.00 0.00 1.28
3489 3885 4.142795 TGCACGTATGTTGTTCGCATTATT 60.143 37.500 0.00 0.00 0.00 1.40
3490 3886 4.202158 GCACGTATGTTGTTCGCATTATTG 59.798 41.667 0.00 0.00 0.00 1.90
3491 3887 5.320723 CACGTATGTTGTTCGCATTATTGT 58.679 37.500 0.00 0.00 0.00 2.71
3492 3888 5.447846 CACGTATGTTGTTCGCATTATTGTC 59.552 40.000 0.00 0.00 0.00 3.18
3493 3889 5.350365 ACGTATGTTGTTCGCATTATTGTCT 59.650 36.000 0.00 0.00 0.00 3.41
3494 3890 5.896432 CGTATGTTGTTCGCATTATTGTCTC 59.104 40.000 0.00 0.00 0.00 3.36
3495 3891 4.320667 TGTTGTTCGCATTATTGTCTCG 57.679 40.909 0.00 0.00 0.00 4.04
3496 3892 3.991121 TGTTGTTCGCATTATTGTCTCGA 59.009 39.130 0.00 0.00 0.00 4.04
3497 3893 4.091365 TGTTGTTCGCATTATTGTCTCGAG 59.909 41.667 5.93 5.93 0.00 4.04
3498 3894 3.845178 TGTTCGCATTATTGTCTCGAGT 58.155 40.909 13.13 0.00 0.00 4.18
3499 3895 4.242475 TGTTCGCATTATTGTCTCGAGTT 58.758 39.130 13.13 0.00 0.00 3.01
3500 3896 5.404096 TGTTCGCATTATTGTCTCGAGTTA 58.596 37.500 13.13 0.00 0.00 2.24
3501 3897 5.287752 TGTTCGCATTATTGTCTCGAGTTAC 59.712 40.000 13.13 4.71 0.00 2.50
3502 3898 4.989044 TCGCATTATTGTCTCGAGTTACA 58.011 39.130 13.13 7.64 0.00 2.41
3503 3899 5.404096 TCGCATTATTGTCTCGAGTTACAA 58.596 37.500 18.64 18.64 39.73 2.41
3504 3900 5.287752 TCGCATTATTGTCTCGAGTTACAAC 59.712 40.000 18.70 7.87 38.35 3.32
3505 3901 5.061684 CGCATTATTGTCTCGAGTTACAACA 59.938 40.000 18.70 10.26 38.35 3.33
3506 3902 6.400621 CGCATTATTGTCTCGAGTTACAACAA 60.401 38.462 18.70 17.42 38.35 2.83
3507 3903 7.295201 GCATTATTGTCTCGAGTTACAACAAA 58.705 34.615 18.70 16.05 38.35 2.83
3508 3904 7.962918 GCATTATTGTCTCGAGTTACAACAAAT 59.037 33.333 18.70 17.18 38.35 2.32
3514 3910 9.658475 TTGTCTCGAGTTACAACAAATAAATTG 57.342 29.630 13.13 0.00 44.95 2.32
3515 3911 9.047371 TGTCTCGAGTTACAACAAATAAATTGA 57.953 29.630 13.13 0.00 41.85 2.57
3516 3912 9.314501 GTCTCGAGTTACAACAAATAAATTGAC 57.685 33.333 13.13 0.00 41.85 3.18
3517 3913 9.268268 TCTCGAGTTACAACAAATAAATTGACT 57.732 29.630 13.13 0.00 41.85 3.41
3518 3914 9.318041 CTCGAGTTACAACAAATAAATTGACTG 57.682 33.333 3.62 0.00 41.85 3.51
3519 3915 7.801315 TCGAGTTACAACAAATAAATTGACTGC 59.199 33.333 0.00 0.00 41.85 4.40
3520 3916 7.589587 CGAGTTACAACAAATAAATTGACTGCA 59.410 33.333 0.00 0.00 41.85 4.41
3521 3917 8.801715 AGTTACAACAAATAAATTGACTGCAG 57.198 30.769 13.48 13.48 41.85 4.41
3522 3918 8.629158 AGTTACAACAAATAAATTGACTGCAGA 58.371 29.630 23.35 0.00 41.85 4.26
3523 3919 9.243637 GTTACAACAAATAAATTGACTGCAGAA 57.756 29.630 23.35 5.34 41.85 3.02
3524 3920 9.979578 TTACAACAAATAAATTGACTGCAGAAT 57.020 25.926 23.35 7.87 41.85 2.40
3525 3921 8.891671 ACAACAAATAAATTGACTGCAGAATT 57.108 26.923 23.35 13.98 41.85 2.17
3526 3922 9.328845 ACAACAAATAAATTGACTGCAGAATTT 57.671 25.926 23.35 22.76 41.85 1.82
3527 3923 9.801714 CAACAAATAAATTGACTGCAGAATTTC 57.198 29.630 23.35 8.02 41.85 2.17
3528 3924 9.545105 AACAAATAAATTGACTGCAGAATTTCA 57.455 25.926 23.35 10.95 41.85 2.69
3529 3925 9.545105 ACAAATAAATTGACTGCAGAATTTCAA 57.455 25.926 23.35 19.47 41.85 2.69
3531 3927 9.768662 AAATAAATTGACTGCAGAATTTCAAGT 57.231 25.926 23.35 15.79 34.42 3.16
3532 3928 9.768662 AATAAATTGACTGCAGAATTTCAAGTT 57.231 25.926 24.41 24.41 39.07 2.66
3534 3930 8.579682 AAATTGACTGCAGAATTTCAAGTTAC 57.420 30.769 23.35 0.00 35.23 2.50
3535 3931 6.691754 TTGACTGCAGAATTTCAAGTTACA 57.308 33.333 23.35 0.00 0.00 2.41
3536 3932 6.691754 TGACTGCAGAATTTCAAGTTACAA 57.308 33.333 23.35 0.00 0.00 2.41
3537 3933 6.494842 TGACTGCAGAATTTCAAGTTACAAC 58.505 36.000 23.35 0.00 0.00 3.32
3538 3934 6.094742 TGACTGCAGAATTTCAAGTTACAACA 59.905 34.615 23.35 0.00 0.00 3.33
3539 3935 6.862209 ACTGCAGAATTTCAAGTTACAACAA 58.138 32.000 23.35 0.00 0.00 2.83
3540 3936 7.319646 ACTGCAGAATTTCAAGTTACAACAAA 58.680 30.769 23.35 0.00 0.00 2.83
3541 3937 7.981225 ACTGCAGAATTTCAAGTTACAACAAAT 59.019 29.630 23.35 0.00 0.00 2.32
3542 3938 9.462174 CTGCAGAATTTCAAGTTACAACAAATA 57.538 29.630 8.42 0.00 0.00 1.40
3543 3939 9.809096 TGCAGAATTTCAAGTTACAACAAATAA 57.191 25.926 0.00 0.00 0.00 1.40
3552 3948 9.809096 TCAAGTTACAACAAATAAAAGAATGCA 57.191 25.926 0.00 0.00 0.00 3.96
3554 3950 8.816640 AGTTACAACAAATAAAAGAATGCAGG 57.183 30.769 0.00 0.00 0.00 4.85
3555 3951 8.637986 AGTTACAACAAATAAAAGAATGCAGGA 58.362 29.630 0.00 0.00 0.00 3.86
3556 3952 9.423061 GTTACAACAAATAAAAGAATGCAGGAT 57.577 29.630 0.00 0.00 0.00 3.24
3557 3953 7.894376 ACAACAAATAAAAGAATGCAGGATG 57.106 32.000 0.00 0.00 40.87 3.51
3558 3954 7.444299 ACAACAAATAAAAGAATGCAGGATGT 58.556 30.769 0.00 0.00 39.31 3.06
3559 3955 7.933033 ACAACAAATAAAAGAATGCAGGATGTT 59.067 29.630 0.00 0.00 39.31 2.71
3560 3956 7.894376 ACAAATAAAAGAATGCAGGATGTTG 57.106 32.000 0.00 0.00 39.31 3.33
3561 3957 6.369615 ACAAATAAAAGAATGCAGGATGTTGC 59.630 34.615 0.00 0.00 44.33 4.17
3593 3989 9.152327 TCTGATTGATGATTACTGTAGAATCCT 57.848 33.333 1.89 0.00 33.18 3.24
3637 4033 6.423905 TGACTGTAGACTTTCAAGTTACATGC 59.576 38.462 11.69 9.09 39.88 4.06
3657 4056 7.354257 ACATGCAACAAATAAAAAGATTGTGC 58.646 30.769 0.00 0.00 37.36 4.57
3659 4058 7.551035 TGCAACAAATAAAAAGATTGTGCTT 57.449 28.000 0.00 0.00 37.36 3.91
3660 4059 8.654230 TGCAACAAATAAAAAGATTGTGCTTA 57.346 26.923 0.00 0.00 37.36 3.09
3661 4060 8.547069 TGCAACAAATAAAAAGATTGTGCTTAC 58.453 29.630 0.00 0.00 37.36 2.34
3662 4061 8.547069 GCAACAAATAAAAAGATTGTGCTTACA 58.453 29.630 0.00 0.00 37.36 2.41
3669 4068 9.696917 ATAAAAAGATTGTGCTTACAAGAAAGG 57.303 29.630 0.00 0.00 32.69 3.11
3670 4069 6.959639 AAAGATTGTGCTTACAAGAAAGGA 57.040 33.333 0.00 0.00 32.69 3.36
3671 4070 6.566197 AAGATTGTGCTTACAAGAAAGGAG 57.434 37.500 0.00 0.00 32.69 3.69
3672 4071 4.457257 AGATTGTGCTTACAAGAAAGGAGC 59.543 41.667 0.00 0.00 32.69 4.70
3673 4072 3.207265 TGTGCTTACAAGAAAGGAGCA 57.793 42.857 0.00 0.00 40.70 4.26
3675 4074 3.492102 TGCTTACAAGAAAGGAGCACT 57.508 42.857 0.00 0.00 38.33 4.40
3676 4075 3.141398 TGCTTACAAGAAAGGAGCACTG 58.859 45.455 0.00 0.00 38.33 3.66
3681 4080 3.209410 ACAAGAAAGGAGCACTGACAAG 58.791 45.455 0.00 0.00 0.00 3.16
3698 4097 0.598065 AAGAAAGGAACACGGCATGC 59.402 50.000 9.90 9.90 0.00 4.06
3764 4163 4.231273 AGCCAATAAAAAGGAAACCCACT 58.769 39.130 0.00 0.00 0.00 4.00
3777 4176 3.356529 AACCCACTAGAAGCAATCTGG 57.643 47.619 0.00 2.28 42.10 3.86
3831 4231 1.202568 AGCAAGCAACTCAAAAAGGCC 60.203 47.619 0.00 0.00 0.00 5.19
3932 4338 4.954118 TGGTGGACCAGACCGGCT 62.954 66.667 0.00 0.00 42.01 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 1.292541 GGACTTCGACGGCTCCTTT 59.707 57.895 0.00 0.00 0.00 3.11
602 615 2.813754 CCACACAACACATCCTAACTGG 59.186 50.000 0.00 0.00 37.10 4.00
606 619 3.392947 TCTTCCCACACAACACATCCTAA 59.607 43.478 0.00 0.00 0.00 2.69
619 632 0.545309 CTCCTCACCCTCTTCCCACA 60.545 60.000 0.00 0.00 0.00 4.17
622 635 1.324005 CGTCTCCTCACCCTCTTCCC 61.324 65.000 0.00 0.00 0.00 3.97
626 639 1.304952 CCTCGTCTCCTCACCCTCT 59.695 63.158 0.00 0.00 0.00 3.69
777 803 2.481289 AGCCCAGCTTCTGTTAACTC 57.519 50.000 7.22 0.00 33.89 3.01
778 804 2.959465 AAGCCCAGCTTCTGTTAACT 57.041 45.000 7.22 0.00 46.77 2.24
810 836 1.749063 GTTAAAGGCCCACATGCTACC 59.251 52.381 0.00 0.00 0.00 3.18
817 843 2.282603 GCCCGTTAAAGGCCCACA 60.283 61.111 0.00 0.00 45.16 4.17
847 873 3.092301 GGAATAATAAGATGGGGCCTGC 58.908 50.000 0.84 0.00 0.00 4.85
852 878 4.256920 CTGCTCGGAATAATAAGATGGGG 58.743 47.826 0.00 0.00 0.00 4.96
854 880 3.686726 GCCTGCTCGGAATAATAAGATGG 59.313 47.826 0.00 0.00 33.16 3.51
855 881 4.318332 TGCCTGCTCGGAATAATAAGATG 58.682 43.478 0.00 0.00 33.16 2.90
856 882 4.623932 TGCCTGCTCGGAATAATAAGAT 57.376 40.909 0.00 0.00 33.16 2.40
857 883 4.380531 CTTGCCTGCTCGGAATAATAAGA 58.619 43.478 0.00 0.00 33.16 2.10
863 889 1.153168 GGCTTGCCTGCTCGGAATA 60.153 57.895 4.11 0.00 33.16 1.75
867 893 2.687418 ATATGGGCTTGCCTGCTCGG 62.687 60.000 11.71 0.00 35.92 4.63
876 902 4.272489 TGAGGTTTTGAGATATGGGCTTG 58.728 43.478 0.00 0.00 0.00 4.01
892 918 1.110442 CGGAGCAGAGAGATGAGGTT 58.890 55.000 0.00 0.00 0.00 3.50
893 919 0.257328 TCGGAGCAGAGAGATGAGGT 59.743 55.000 0.00 0.00 0.00 3.85
960 1003 2.487532 TAGAACCCTAGCGCGAGGC 61.488 63.158 29.13 16.61 44.05 4.70
963 1006 0.393402 TCTGTAGAACCCTAGCGCGA 60.393 55.000 12.10 0.00 0.00 5.87
984 1027 0.238289 CCATCGCCACACAACAACTC 59.762 55.000 0.00 0.00 0.00 3.01
985 1028 1.795170 GCCATCGCCACACAACAACT 61.795 55.000 0.00 0.00 0.00 3.16
986 1029 1.371635 GCCATCGCCACACAACAAC 60.372 57.895 0.00 0.00 0.00 3.32
987 1030 2.902419 CGCCATCGCCACACAACAA 61.902 57.895 0.00 0.00 0.00 2.83
988 1031 3.353029 CGCCATCGCCACACAACA 61.353 61.111 0.00 0.00 0.00 3.33
989 1032 2.903547 AACGCCATCGCCACACAAC 61.904 57.895 0.00 0.00 39.84 3.32
990 1033 2.593148 AACGCCATCGCCACACAA 60.593 55.556 0.00 0.00 39.84 3.33
991 1034 3.353029 CAACGCCATCGCCACACA 61.353 61.111 0.00 0.00 39.84 3.72
992 1035 3.047280 TCAACGCCATCGCCACAC 61.047 61.111 0.00 0.00 39.84 3.82
993 1036 3.047280 GTCAACGCCATCGCCACA 61.047 61.111 0.00 0.00 39.84 4.17
994 1037 3.799755 GGTCAACGCCATCGCCAC 61.800 66.667 0.00 0.00 39.84 5.01
995 1038 3.834013 TTGGTCAACGCCATCGCCA 62.834 57.895 0.00 0.00 38.48 5.69
1177 1220 5.106515 TGACTCAGAGAACAATCGACTAGTG 60.107 44.000 3.79 0.00 0.00 2.74
1191 1234 2.634453 TCCACTGCAATTGACTCAGAGA 59.366 45.455 10.34 7.17 0.00 3.10
1192 1235 3.001414 CTCCACTGCAATTGACTCAGAG 58.999 50.000 10.34 5.88 0.00 3.35
1194 1237 1.467734 GCTCCACTGCAATTGACTCAG 59.532 52.381 10.34 9.69 0.00 3.35
1207 1250 1.333636 CCGATTCCTCCAGCTCCACT 61.334 60.000 0.00 0.00 0.00 4.00
1213 1256 0.689623 ATGATCCCGATTCCTCCAGC 59.310 55.000 0.00 0.00 0.00 4.85
1221 1264 2.248248 TCTAAGCCGATGATCCCGATT 58.752 47.619 6.23 4.08 0.00 3.34
1227 1270 7.822658 ACTAAGTAAGATCTAAGCCGATGATC 58.177 38.462 0.00 0.00 37.46 2.92
1247 1290 7.925483 AGAGCAAAGCAATCTGATACTACTAAG 59.075 37.037 0.00 0.00 0.00 2.18
1248 1291 7.786030 AGAGCAAAGCAATCTGATACTACTAA 58.214 34.615 0.00 0.00 0.00 2.24
1249 1292 7.353414 AGAGCAAAGCAATCTGATACTACTA 57.647 36.000 0.00 0.00 0.00 1.82
1250 1293 6.232581 AGAGCAAAGCAATCTGATACTACT 57.767 37.500 0.00 0.00 0.00 2.57
1251 1294 6.917217 AAGAGCAAAGCAATCTGATACTAC 57.083 37.500 0.00 0.00 0.00 2.73
1252 1295 6.881065 ACAAAGAGCAAAGCAATCTGATACTA 59.119 34.615 0.00 0.00 0.00 1.82
1253 1296 5.709164 ACAAAGAGCAAAGCAATCTGATACT 59.291 36.000 0.00 0.00 0.00 2.12
1254 1297 5.798934 CACAAAGAGCAAAGCAATCTGATAC 59.201 40.000 0.00 0.00 0.00 2.24
1255 1298 5.706833 TCACAAAGAGCAAAGCAATCTGATA 59.293 36.000 0.00 0.00 0.00 2.15
1256 1299 4.521639 TCACAAAGAGCAAAGCAATCTGAT 59.478 37.500 0.00 0.00 0.00 2.90
1257 1300 3.884693 TCACAAAGAGCAAAGCAATCTGA 59.115 39.130 0.00 0.00 0.00 3.27
1258 1301 4.233123 TCACAAAGAGCAAAGCAATCTG 57.767 40.909 0.00 0.00 0.00 2.90
1259 1302 4.924305 TTCACAAAGAGCAAAGCAATCT 57.076 36.364 0.00 0.00 0.00 2.40
1260 1303 6.535274 AATTTCACAAAGAGCAAAGCAATC 57.465 33.333 0.00 0.00 0.00 2.67
1261 1304 6.985645 TGTAATTTCACAAAGAGCAAAGCAAT 59.014 30.769 0.00 0.00 0.00 3.56
1262 1305 6.336566 TGTAATTTCACAAAGAGCAAAGCAA 58.663 32.000 0.00 0.00 0.00 3.91
1263 1306 5.900425 TGTAATTTCACAAAGAGCAAAGCA 58.100 33.333 0.00 0.00 0.00 3.91
1301 1365 0.757188 ACCCTGAGCTACCTCGGATG 60.757 60.000 1.24 0.00 45.56 3.51
1306 1370 5.810080 ATATAACAACCCTGAGCTACCTC 57.190 43.478 0.00 0.00 38.62 3.85
1307 1371 5.665812 TGAATATAACAACCCTGAGCTACCT 59.334 40.000 0.00 0.00 0.00 3.08
1399 1479 6.386927 TGGGGGATATGAATCTACACCATATC 59.613 42.308 0.00 0.00 43.92 1.63
1400 1480 6.279405 TGGGGGATATGAATCTACACCATAT 58.721 40.000 0.00 0.00 36.51 1.78
1401 1481 5.670899 TGGGGGATATGAATCTACACCATA 58.329 41.667 0.00 0.00 32.29 2.74
1402 1482 4.512298 TGGGGGATATGAATCTACACCAT 58.488 43.478 0.00 0.00 32.29 3.55
1403 1483 3.948126 TGGGGGATATGAATCTACACCA 58.052 45.455 0.00 0.00 32.29 4.17
1423 1518 7.330262 AGAATTTATACCAAACAGGCCAAATG 58.670 34.615 5.01 0.00 43.14 2.32
1515 1610 0.810648 TGTCGCCAATGAATCAAGCC 59.189 50.000 0.00 0.00 0.00 4.35
1613 1715 2.415168 ACATAACCGTGTGCAGAATTCG 59.585 45.455 0.00 0.00 0.00 3.34
1631 1733 1.368579 GGGCACAAGCTTTGCACAT 59.631 52.632 24.87 0.00 43.35 3.21
1632 1734 2.813901 GGGCACAAGCTTTGCACA 59.186 55.556 24.87 0.00 43.35 4.57
1641 1844 2.492881 TGCAGTCATATTTGGGCACAAG 59.507 45.455 0.00 0.00 37.97 3.16
1648 1851 5.571784 AAGTCACATGCAGTCATATTTGG 57.428 39.130 0.00 0.00 0.00 3.28
1649 1852 5.163824 ACGAAGTCACATGCAGTCATATTTG 60.164 40.000 0.00 0.00 29.74 2.32
1673 1876 7.416964 TCAGAGGTTCAATTTTCCTTTTTGA 57.583 32.000 0.00 0.00 0.00 2.69
1686 1889 7.280876 GTGAATAGTATGCATTCAGAGGTTCAA 59.719 37.037 3.54 0.00 41.73 2.69
1736 1940 3.003689 CCATACATTTTCTGCGCCCTAAG 59.996 47.826 4.18 0.00 0.00 2.18
1739 1943 1.340991 ACCATACATTTTCTGCGCCCT 60.341 47.619 4.18 0.00 0.00 5.19
1784 1996 7.821846 TGTTCATCATGCTATAAAGTGTACACA 59.178 33.333 27.06 7.89 0.00 3.72
1834 2046 1.687996 CCAAACTCCAAAGGGGTGTGT 60.688 52.381 5.55 0.00 42.43 3.72
1861 2074 1.110442 ACCATTCTCTCTCCTCTGCG 58.890 55.000 0.00 0.00 0.00 5.18
1880 2093 4.979197 GTGAAATGGTTTTGTGCGTAATCA 59.021 37.500 0.00 0.00 0.00 2.57
2102 2315 4.035558 CGCAATATTTCAGGCTTTCAGCTA 59.964 41.667 0.00 0.00 41.99 3.32
2226 2440 8.803201 AGAAATAAAAGCACAAAGAAAGCTAC 57.197 30.769 0.00 0.00 37.70 3.58
2330 2544 6.192970 AGCCTAGCATGTGTAATCCTTTAT 57.807 37.500 0.00 0.00 0.00 1.40
2368 2582 5.277058 GCACATGCTTTTAGGTATCGAGAAG 60.277 44.000 0.00 0.00 38.21 2.85
2369 2583 4.570772 GCACATGCTTTTAGGTATCGAGAA 59.429 41.667 0.00 0.00 38.21 2.87
2370 2584 4.119862 GCACATGCTTTTAGGTATCGAGA 58.880 43.478 0.00 0.00 38.21 4.04
2371 2585 3.248602 GGCACATGCTTTTAGGTATCGAG 59.751 47.826 3.48 0.00 41.70 4.04
2444 2658 6.560003 AAAGAAGGAATGAAAAACCAAGGT 57.440 33.333 0.00 0.00 0.00 3.50
2469 2683 1.897802 AGCATGGAAAAGAAGGGCAAG 59.102 47.619 0.00 0.00 0.00 4.01
2493 2707 2.165030 GCCTTCACATCAGGAACCAATG 59.835 50.000 0.00 0.00 32.41 2.82
2494 2708 2.042162 AGCCTTCACATCAGGAACCAAT 59.958 45.455 0.00 0.00 32.41 3.16
2535 2749 1.936547 GCCCTCTCTTAAACTGATGCG 59.063 52.381 0.00 0.00 0.00 4.73
2536 2750 3.274095 AGCCCTCTCTTAAACTGATGC 57.726 47.619 0.00 0.00 0.00 3.91
2537 2751 4.742138 GCCTAGCCCTCTCTTAAACTGATG 60.742 50.000 0.00 0.00 0.00 3.07
2538 2752 3.389656 GCCTAGCCCTCTCTTAAACTGAT 59.610 47.826 0.00 0.00 0.00 2.90
2539 2753 2.766828 GCCTAGCCCTCTCTTAAACTGA 59.233 50.000 0.00 0.00 0.00 3.41
2596 2810 7.130681 AGGCTAGTTAGAGCACTGATAAATT 57.869 36.000 0.00 0.00 44.76 1.82
2604 2818 4.962995 TGGATAAAGGCTAGTTAGAGCACT 59.037 41.667 0.00 0.00 44.76 4.40
2610 2824 6.472686 ACTCAGTGGATAAAGGCTAGTTAG 57.527 41.667 0.00 0.00 0.00 2.34
2707 2925 3.417069 TCAAACCACTGGGACATAGTG 57.583 47.619 0.00 0.00 43.94 2.74
2796 3014 7.447238 CCAACCACGGTATTATAGAATGGAATT 59.553 37.037 0.00 0.00 40.93 2.17
2815 3195 5.480422 AGGAAATAGAAACCAATCCAACCAC 59.520 40.000 0.00 0.00 0.00 4.16
2818 3198 7.441836 ACAAAGGAAATAGAAACCAATCCAAC 58.558 34.615 0.00 0.00 0.00 3.77
2859 3239 6.707290 TGCTGTGTTGACTTTACCATAGTAT 58.293 36.000 0.00 0.00 0.00 2.12
2892 3272 6.726299 TCAAAGATATAGTAGGTGGGGATCAG 59.274 42.308 0.00 0.00 0.00 2.90
3114 3495 7.173562 CCCATACATGCCCAAATTATTTGATTG 59.826 37.037 18.13 11.63 43.26 2.67
3140 3521 2.691409 TAGAACCCACATGCAGCTAC 57.309 50.000 0.00 0.00 0.00 3.58
3260 3641 9.186323 CAGACAAAACCTATATCAAGACGATAG 57.814 37.037 0.00 0.00 39.98 2.08
3261 3642 8.141909 CCAGACAAAACCTATATCAAGACGATA 58.858 37.037 0.00 0.00 40.90 2.92
3264 3645 5.006746 GCCAGACAAAACCTATATCAAGACG 59.993 44.000 0.00 0.00 0.00 4.18
3265 3646 5.880332 TGCCAGACAAAACCTATATCAAGAC 59.120 40.000 0.00 0.00 0.00 3.01
3267 3648 5.882557 ACTGCCAGACAAAACCTATATCAAG 59.117 40.000 0.00 0.00 0.00 3.02
3269 3650 5.435686 ACTGCCAGACAAAACCTATATCA 57.564 39.130 0.00 0.00 0.00 2.15
3270 3651 8.451908 AATTACTGCCAGACAAAACCTATATC 57.548 34.615 0.00 0.00 0.00 1.63
3332 3713 7.330700 ACACGCTAATTTCATAAAAACAATGGG 59.669 33.333 0.00 0.00 0.00 4.00
3354 3737 5.620822 CACATACATGAAGAAAACACACACG 59.379 40.000 0.00 0.00 0.00 4.49
3361 3744 9.485591 CGTAAATACCACATACATGAAGAAAAC 57.514 33.333 0.00 0.00 0.00 2.43
3442 3828 7.093945 GCATTACAAAGATTAGTGGGGAAGAAA 60.094 37.037 0.00 0.00 0.00 2.52
3445 3831 5.652014 TGCATTACAAAGATTAGTGGGGAAG 59.348 40.000 0.00 0.00 0.00 3.46
3448 3834 4.201910 CGTGCATTACAAAGATTAGTGGGG 60.202 45.833 0.00 0.00 0.00 4.96
3471 3867 5.896432 CGAGACAATAATGCGAACAACATAC 59.104 40.000 0.00 0.00 0.00 2.39
3480 3876 4.989044 TGTAACTCGAGACAATAATGCGA 58.011 39.130 21.68 0.00 0.00 5.10
3481 3877 5.061684 TGTTGTAACTCGAGACAATAATGCG 59.938 40.000 21.68 0.00 37.84 4.73
3482 3878 6.403333 TGTTGTAACTCGAGACAATAATGC 57.597 37.500 21.68 8.28 37.84 3.56
3488 3884 9.658475 CAATTTATTTGTTGTAACTCGAGACAA 57.342 29.630 21.68 17.10 33.23 3.18
3489 3885 9.047371 TCAATTTATTTGTTGTAACTCGAGACA 57.953 29.630 21.68 11.42 36.65 3.41
3490 3886 9.314501 GTCAATTTATTTGTTGTAACTCGAGAC 57.685 33.333 21.68 8.51 36.65 3.36
3491 3887 9.268268 AGTCAATTTATTTGTTGTAACTCGAGA 57.732 29.630 21.68 0.00 36.65 4.04
3492 3888 9.318041 CAGTCAATTTATTTGTTGTAACTCGAG 57.682 33.333 11.84 11.84 36.65 4.04
3493 3889 7.801315 GCAGTCAATTTATTTGTTGTAACTCGA 59.199 33.333 0.00 0.00 36.65 4.04
3494 3890 7.589587 TGCAGTCAATTTATTTGTTGTAACTCG 59.410 33.333 0.00 0.00 36.65 4.18
3495 3891 8.795786 TGCAGTCAATTTATTTGTTGTAACTC 57.204 30.769 0.00 0.00 36.65 3.01
3496 3892 8.629158 TCTGCAGTCAATTTATTTGTTGTAACT 58.371 29.630 14.67 0.00 36.65 2.24
3497 3893 8.795786 TCTGCAGTCAATTTATTTGTTGTAAC 57.204 30.769 14.67 0.00 36.65 2.50
3498 3894 9.979578 ATTCTGCAGTCAATTTATTTGTTGTAA 57.020 25.926 14.67 0.00 36.65 2.41
3499 3895 9.979578 AATTCTGCAGTCAATTTATTTGTTGTA 57.020 25.926 14.67 0.00 36.65 2.41
3500 3896 8.891671 AATTCTGCAGTCAATTTATTTGTTGT 57.108 26.923 14.67 0.00 36.65 3.32
3501 3897 9.801714 GAAATTCTGCAGTCAATTTATTTGTTG 57.198 29.630 20.21 0.00 33.31 3.33
3502 3898 9.545105 TGAAATTCTGCAGTCAATTTATTTGTT 57.455 25.926 20.21 3.41 33.31 2.83
3503 3899 9.545105 TTGAAATTCTGCAGTCAATTTATTTGT 57.455 25.926 20.21 3.98 33.31 2.83
3505 3901 9.768662 ACTTGAAATTCTGCAGTCAATTTATTT 57.231 25.926 20.21 12.64 33.31 1.40
3506 3902 9.768662 AACTTGAAATTCTGCAGTCAATTTATT 57.231 25.926 20.21 12.47 33.31 1.40
3508 3904 9.677567 GTAACTTGAAATTCTGCAGTCAATTTA 57.322 29.630 20.21 18.36 33.31 1.40
3509 3905 8.196771 TGTAACTTGAAATTCTGCAGTCAATTT 58.803 29.630 20.27 20.27 35.38 1.82
3510 3906 7.715657 TGTAACTTGAAATTCTGCAGTCAATT 58.284 30.769 14.67 10.45 30.06 2.32
3511 3907 7.275888 TGTAACTTGAAATTCTGCAGTCAAT 57.724 32.000 14.67 4.05 30.06 2.57
3512 3908 6.691754 TGTAACTTGAAATTCTGCAGTCAA 57.308 33.333 14.67 14.64 0.00 3.18
3513 3909 6.094742 TGTTGTAACTTGAAATTCTGCAGTCA 59.905 34.615 14.67 7.16 0.00 3.41
3514 3910 6.494842 TGTTGTAACTTGAAATTCTGCAGTC 58.505 36.000 14.67 4.21 0.00 3.51
3515 3911 6.449635 TGTTGTAACTTGAAATTCTGCAGT 57.550 33.333 14.67 0.00 0.00 4.40
3516 3912 7.754069 TTTGTTGTAACTTGAAATTCTGCAG 57.246 32.000 7.63 7.63 0.00 4.41
3517 3913 9.809096 TTATTTGTTGTAACTTGAAATTCTGCA 57.191 25.926 0.00 0.00 0.00 4.41
3526 3922 9.809096 TGCATTCTTTTATTTGTTGTAACTTGA 57.191 25.926 0.00 0.00 0.00 3.02
3528 3924 9.260002 CCTGCATTCTTTTATTTGTTGTAACTT 57.740 29.630 0.00 0.00 0.00 2.66
3529 3925 8.637986 TCCTGCATTCTTTTATTTGTTGTAACT 58.362 29.630 0.00 0.00 0.00 2.24
3530 3926 8.810652 TCCTGCATTCTTTTATTTGTTGTAAC 57.189 30.769 0.00 0.00 0.00 2.50
3531 3927 9.421806 CATCCTGCATTCTTTTATTTGTTGTAA 57.578 29.630 0.00 0.00 0.00 2.41
3532 3928 8.584157 ACATCCTGCATTCTTTTATTTGTTGTA 58.416 29.630 0.00 0.00 0.00 2.41
3533 3929 7.444299 ACATCCTGCATTCTTTTATTTGTTGT 58.556 30.769 0.00 0.00 0.00 3.32
3534 3930 7.894376 ACATCCTGCATTCTTTTATTTGTTG 57.106 32.000 0.00 0.00 0.00 3.33
3535 3931 7.095102 GCAACATCCTGCATTCTTTTATTTGTT 60.095 33.333 0.00 0.00 42.17 2.83
3536 3932 6.369615 GCAACATCCTGCATTCTTTTATTTGT 59.630 34.615 0.00 0.00 42.17 2.83
3537 3933 6.183360 GGCAACATCCTGCATTCTTTTATTTG 60.183 38.462 0.00 0.00 44.52 2.32
3538 3934 5.876460 GGCAACATCCTGCATTCTTTTATTT 59.124 36.000 0.00 0.00 44.52 1.40
3539 3935 5.188359 AGGCAACATCCTGCATTCTTTTATT 59.812 36.000 0.00 0.00 44.52 1.40
3540 3936 4.713321 AGGCAACATCCTGCATTCTTTTAT 59.287 37.500 0.00 0.00 44.52 1.40
3541 3937 4.082081 CAGGCAACATCCTGCATTCTTTTA 60.082 41.667 0.00 0.00 46.11 1.52
3542 3938 2.901839 AGGCAACATCCTGCATTCTTTT 59.098 40.909 0.00 0.00 44.52 2.27
3543 3939 2.232941 CAGGCAACATCCTGCATTCTTT 59.767 45.455 0.00 0.00 46.11 2.52
3544 3940 1.822990 CAGGCAACATCCTGCATTCTT 59.177 47.619 0.00 0.00 46.11 2.52
3545 3941 1.471119 CAGGCAACATCCTGCATTCT 58.529 50.000 0.00 0.00 46.11 2.40
3552 3948 0.622136 TCAGATGCAGGCAACATCCT 59.378 50.000 14.02 2.41 44.08 3.24
3553 3949 1.688772 ATCAGATGCAGGCAACATCC 58.311 50.000 14.02 0.51 44.08 3.51
3554 3950 2.686405 TCAATCAGATGCAGGCAACATC 59.314 45.455 10.73 10.73 43.49 3.06
3555 3951 2.730382 TCAATCAGATGCAGGCAACAT 58.270 42.857 0.00 0.00 41.41 2.71
3556 3952 2.203470 TCAATCAGATGCAGGCAACA 57.797 45.000 0.00 0.00 41.41 3.33
3557 3953 3.079960 CATCAATCAGATGCAGGCAAC 57.920 47.619 0.00 0.00 46.90 4.17
3649 4048 4.457257 GCTCCTTTCTTGTAAGCACAATCT 59.543 41.667 0.00 0.00 43.58 2.40
3650 4049 4.216257 TGCTCCTTTCTTGTAAGCACAATC 59.784 41.667 0.00 0.00 43.58 2.67
3653 4052 3.207265 TGCTCCTTTCTTGTAAGCACA 57.793 42.857 0.00 0.00 38.01 4.57
3655 4054 3.141398 CAGTGCTCCTTTCTTGTAAGCA 58.859 45.455 0.00 0.00 40.45 3.91
3656 4055 3.187432 GTCAGTGCTCCTTTCTTGTAAGC 59.813 47.826 0.00 0.00 0.00 3.09
3657 4056 4.380531 TGTCAGTGCTCCTTTCTTGTAAG 58.619 43.478 0.00 0.00 0.00 2.34
3659 4058 4.100963 TCTTGTCAGTGCTCCTTTCTTGTA 59.899 41.667 0.00 0.00 0.00 2.41
3660 4059 3.118261 TCTTGTCAGTGCTCCTTTCTTGT 60.118 43.478 0.00 0.00 0.00 3.16
3661 4060 3.470709 TCTTGTCAGTGCTCCTTTCTTG 58.529 45.455 0.00 0.00 0.00 3.02
3662 4061 3.845781 TCTTGTCAGTGCTCCTTTCTT 57.154 42.857 0.00 0.00 0.00 2.52
3663 4062 3.845781 TTCTTGTCAGTGCTCCTTTCT 57.154 42.857 0.00 0.00 0.00 2.52
3664 4063 3.251972 CCTTTCTTGTCAGTGCTCCTTTC 59.748 47.826 0.00 0.00 0.00 2.62
3665 4064 3.117888 TCCTTTCTTGTCAGTGCTCCTTT 60.118 43.478 0.00 0.00 0.00 3.11
3666 4065 2.439507 TCCTTTCTTGTCAGTGCTCCTT 59.560 45.455 0.00 0.00 0.00 3.36
3667 4066 2.050144 TCCTTTCTTGTCAGTGCTCCT 58.950 47.619 0.00 0.00 0.00 3.69
3668 4067 2.550180 GTTCCTTTCTTGTCAGTGCTCC 59.450 50.000 0.00 0.00 0.00 4.70
3669 4068 3.002759 GTGTTCCTTTCTTGTCAGTGCTC 59.997 47.826 0.00 0.00 0.00 4.26
3670 4069 2.945668 GTGTTCCTTTCTTGTCAGTGCT 59.054 45.455 0.00 0.00 0.00 4.40
3671 4070 2.286418 CGTGTTCCTTTCTTGTCAGTGC 60.286 50.000 0.00 0.00 0.00 4.40
3672 4071 2.287915 CCGTGTTCCTTTCTTGTCAGTG 59.712 50.000 0.00 0.00 0.00 3.66
3673 4072 2.561569 CCGTGTTCCTTTCTTGTCAGT 58.438 47.619 0.00 0.00 0.00 3.41
3674 4073 1.264288 GCCGTGTTCCTTTCTTGTCAG 59.736 52.381 0.00 0.00 0.00 3.51
3675 4074 1.305201 GCCGTGTTCCTTTCTTGTCA 58.695 50.000 0.00 0.00 0.00 3.58
3676 4075 1.305201 TGCCGTGTTCCTTTCTTGTC 58.695 50.000 0.00 0.00 0.00 3.18
3681 4080 0.109597 CTGCATGCCGTGTTCCTTTC 60.110 55.000 16.68 0.00 0.00 2.62
3698 4097 0.171903 GGCTTGGCTTGTATGCACTG 59.828 55.000 0.00 0.00 34.04 3.66
3764 4163 4.365514 TGGTTTGTCCAGATTGCTTCTA 57.634 40.909 0.00 0.00 41.93 2.10
3777 4176 2.190161 GCTTTCGGTTGTTGGTTTGTC 58.810 47.619 0.00 0.00 0.00 3.18
3785 4184 3.749609 GTGTACATAGGCTTTCGGTTGTT 59.250 43.478 0.00 0.00 0.00 2.83
3846 4247 1.400846 TGCTTCGCGTGTTTGGTTTAA 59.599 42.857 5.77 0.00 0.00 1.52
3847 4248 1.015109 TGCTTCGCGTGTTTGGTTTA 58.985 45.000 5.77 0.00 0.00 2.01
3851 4252 0.729140 GGATTGCTTCGCGTGTTTGG 60.729 55.000 5.77 0.00 0.00 3.28
3859 4260 3.786635 TCTTTAGAGAGGATTGCTTCGC 58.213 45.455 0.00 0.00 0.00 4.70
3892 4293 7.036829 CCATTGATTCACATGTTCATTGCTTA 58.963 34.615 12.38 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.