Multiple sequence alignment - TraesCS1D01G443900

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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 TraesCS1D01G443900 chr1D 100.000 2380 0 0 1 2380 487499110 487496731 0.000000e+00 4396.0
1 TraesCS1D01G443900 chr1D 84.375 384 41 8 1194 1560 487469361 487468980 2.250000e-95 359.0
2 TraesCS1D01G443900 chr1D 81.457 453 46 18 753 1178 487469876 487469435 1.050000e-88 337.0
3 TraesCS1D01G443900 chr1D 91.228 57 5 0 609 665 487439913 487439857 7.050000e-11 78.7
4 TraesCS1D01G443900 chr1D 100.000 30 0 0 1900 1929 391099035 391099064 3.300000e-04 56.5
5 TraesCS1D01G443900 chrUn 94.643 560 24 1 1500 2059 302757271 302756718 0.000000e+00 863.0
6 TraesCS1D01G443900 chrUn 92.570 323 14 4 865 1179 302757995 302757675 2.790000e-124 455.0
7 TraesCS1D01G443900 chrUn 91.875 320 14 1 1192 1499 302757629 302757310 1.010000e-118 436.0
8 TraesCS1D01G443900 chrUn 92.958 284 17 3 2 284 302759112 302758831 6.120000e-111 411.0
9 TraesCS1D01G443900 chrUn 94.922 256 13 0 2056 2311 314413637 314413382 3.680000e-108 401.0
10 TraesCS1D01G443900 chrUn 92.032 251 15 3 570 815 302758243 302757993 4.870000e-92 348.0
11 TraesCS1D01G443900 chrUn 87.209 258 14 13 294 549 302758847 302758607 2.330000e-70 276.0
12 TraesCS1D01G443900 chr1A 93.705 556 23 8 628 1178 585577051 585576503 0.000000e+00 822.0
13 TraesCS1D01G443900 chr1A 96.256 454 15 1 2 453 585577501 585577048 0.000000e+00 743.0
14 TraesCS1D01G443900 chr1A 92.553 470 23 7 1837 2301 585570979 585570517 0.000000e+00 664.0
15 TraesCS1D01G443900 chr1A 94.361 266 13 2 1493 1758 585571259 585570996 7.920000e-110 407.0
16 TraesCS1D01G443900 chr1A 87.613 331 36 4 1188 1514 585576430 585576101 1.730000e-101 379.0
17 TraesCS1D01G443900 chr1A 84.759 374 38 6 1207 1563 585519181 585518810 8.090000e-95 357.0
18 TraesCS1D01G443900 chr1A 81.600 375 42 15 829 1178 585519617 585519245 3.870000e-73 285.0
19 TraesCS1D01G443900 chr1A 90.000 60 6 0 606 665 585452360 585452419 7.050000e-11 78.7
20 TraesCS1D01G443900 chr1B 80.000 845 95 42 753 1554 678844415 678845228 7.430000e-155 556.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G443900 chr1D 487496731 487499110 2379 True 4396.000000 4396 100.000000 1 2380 1 chr1D.!!$R2 2379
1 TraesCS1D01G443900 chr1D 487468980 487469876 896 True 348.000000 359 82.916000 753 1560 2 chr1D.!!$R3 807
2 TraesCS1D01G443900 chrUn 302756718 302759112 2394 True 464.833333 863 91.881167 2 2059 6 chrUn.!!$R2 2057
3 TraesCS1D01G443900 chr1A 585576101 585577501 1400 True 648.000000 822 92.524667 2 1514 3 chr1A.!!$R3 1512
4 TraesCS1D01G443900 chr1A 585570517 585571259 742 True 535.500000 664 93.457000 1493 2301 2 chr1A.!!$R2 808
5 TraesCS1D01G443900 chr1A 585518810 585519617 807 True 321.000000 357 83.179500 829 1563 2 chr1A.!!$R1 734
6 TraesCS1D01G443900 chr1B 678844415 678845228 813 False 556.000000 556 80.000000 753 1554 1 chr1B.!!$F1 801

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
470 992 0.037605 AACAACCAGATCGGACGTCC 60.038 55.0 25.28 25.28 38.63 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1406 2050 0.039764 ACTGATGGTCTCACTCCCGA 59.96 55.0 0.0 0.0 0.0 5.14 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
104 106 7.205297 CAGGATTAAAATTAGCCACAATCAGG 58.795 38.462 0.00 0.00 0.00 3.86
170 172 3.612423 GCAAAATCATACGGGAAGCAAAC 59.388 43.478 0.00 0.00 0.00 2.93
214 216 9.368921 CAAAACTGAAAAGTTTTTGAAACAGTC 57.631 29.630 15.86 0.00 46.15 3.51
308 310 4.381411 AGCGCTAGAGTTATTTGATTCCC 58.619 43.478 8.99 0.00 0.00 3.97
339 343 9.342308 AGATCAGAAGTTGATTTCACAAAACTA 57.658 29.630 0.00 0.00 46.51 2.24
363 367 1.314730 AAAACGGAACCAGCGAACAT 58.685 45.000 0.00 0.00 0.00 2.71
365 369 0.534203 AACGGAACCAGCGAACATGT 60.534 50.000 0.00 0.00 0.00 3.21
366 370 0.319083 ACGGAACCAGCGAACATGTA 59.681 50.000 0.00 0.00 0.00 2.29
367 371 1.270412 ACGGAACCAGCGAACATGTAA 60.270 47.619 0.00 0.00 0.00 2.41
450 972 1.103398 GGTAATCTGGCGCATGGCTT 61.103 55.000 10.83 0.00 42.94 4.35
451 973 1.593196 GTAATCTGGCGCATGGCTTA 58.407 50.000 10.83 0.00 42.94 3.09
452 974 1.946768 GTAATCTGGCGCATGGCTTAA 59.053 47.619 10.83 0.00 42.94 1.85
453 975 0.740737 AATCTGGCGCATGGCTTAAC 59.259 50.000 10.83 0.00 42.94 2.01
454 976 0.394216 ATCTGGCGCATGGCTTAACA 60.394 50.000 10.83 0.00 42.94 2.41
455 977 0.607762 TCTGGCGCATGGCTTAACAA 60.608 50.000 10.83 0.00 42.94 2.83
456 978 0.456653 CTGGCGCATGGCTTAACAAC 60.457 55.000 10.83 0.00 42.94 3.32
457 979 1.153842 GGCGCATGGCTTAACAACC 60.154 57.895 10.83 0.00 42.94 3.77
458 980 1.583986 GCGCATGGCTTAACAACCA 59.416 52.632 0.30 0.00 41.06 3.67
459 981 0.456653 GCGCATGGCTTAACAACCAG 60.457 55.000 0.30 0.00 39.88 4.00
460 982 1.164411 CGCATGGCTTAACAACCAGA 58.836 50.000 0.00 0.00 39.88 3.86
461 983 1.745087 CGCATGGCTTAACAACCAGAT 59.255 47.619 0.00 0.00 39.88 2.90
462 984 2.223340 CGCATGGCTTAACAACCAGATC 60.223 50.000 0.00 0.00 39.88 2.75
463 985 2.223340 GCATGGCTTAACAACCAGATCG 60.223 50.000 0.00 0.00 39.88 3.69
464 986 2.107950 TGGCTTAACAACCAGATCGG 57.892 50.000 2.55 2.55 42.50 4.18
465 987 1.626321 TGGCTTAACAACCAGATCGGA 59.374 47.619 10.05 0.00 38.63 4.55
466 988 2.007608 GGCTTAACAACCAGATCGGAC 58.992 52.381 10.05 0.00 38.63 4.79
467 989 1.659098 GCTTAACAACCAGATCGGACG 59.341 52.381 10.05 3.89 38.63 4.79
468 990 2.929592 GCTTAACAACCAGATCGGACGT 60.930 50.000 10.05 0.00 38.63 4.34
469 991 2.642139 TAACAACCAGATCGGACGTC 57.358 50.000 7.13 7.13 38.63 4.34
470 992 0.037605 AACAACCAGATCGGACGTCC 60.038 55.000 25.28 25.28 38.63 4.79
471 993 1.183030 ACAACCAGATCGGACGTCCA 61.183 55.000 32.80 20.42 38.63 4.02
472 994 0.175760 CAACCAGATCGGACGTCCAT 59.824 55.000 32.80 23.87 38.63 3.41
473 995 0.460311 AACCAGATCGGACGTCCATC 59.540 55.000 32.80 29.05 38.63 3.51
474 996 0.395862 ACCAGATCGGACGTCCATCT 60.396 55.000 32.80 30.46 38.63 2.90
475 997 0.312416 CCAGATCGGACGTCCATCTC 59.688 60.000 30.47 24.15 36.56 2.75
476 998 0.040870 CAGATCGGACGTCCATCTCG 60.041 60.000 30.47 24.28 34.16 4.04
477 999 1.370657 GATCGGACGTCCATCTCGC 60.371 63.158 32.80 12.48 35.14 5.03
478 1000 1.787057 GATCGGACGTCCATCTCGCT 61.787 60.000 32.80 11.12 35.14 4.93
479 1001 1.384989 ATCGGACGTCCATCTCGCTT 61.385 55.000 32.80 7.81 35.14 4.68
480 1002 1.586564 CGGACGTCCATCTCGCTTC 60.587 63.158 32.80 3.24 35.14 3.86
481 1003 1.227002 GGACGTCCATCTCGCTTCC 60.227 63.158 29.75 0.00 35.64 3.46
482 1004 1.668101 GGACGTCCATCTCGCTTCCT 61.668 60.000 29.75 0.00 35.64 3.36
483 1005 1.022735 GACGTCCATCTCGCTTCCTA 58.977 55.000 3.51 0.00 0.00 2.94
484 1006 1.609555 GACGTCCATCTCGCTTCCTAT 59.390 52.381 3.51 0.00 0.00 2.57
485 1007 1.609555 ACGTCCATCTCGCTTCCTATC 59.390 52.381 0.00 0.00 0.00 2.08
486 1008 1.068194 CGTCCATCTCGCTTCCTATCC 60.068 57.143 0.00 0.00 0.00 2.59
487 1009 1.964223 GTCCATCTCGCTTCCTATCCA 59.036 52.381 0.00 0.00 0.00 3.41
488 1010 2.365617 GTCCATCTCGCTTCCTATCCAA 59.634 50.000 0.00 0.00 0.00 3.53
489 1011 2.365617 TCCATCTCGCTTCCTATCCAAC 59.634 50.000 0.00 0.00 0.00 3.77
490 1012 2.398498 CATCTCGCTTCCTATCCAACG 58.602 52.381 0.00 0.00 0.00 4.10
491 1013 0.744874 TCTCGCTTCCTATCCAACGG 59.255 55.000 0.00 0.00 0.00 4.44
492 1014 0.876342 CTCGCTTCCTATCCAACGGC 60.876 60.000 0.00 0.00 0.00 5.68
493 1015 1.153449 CGCTTCCTATCCAACGGCA 60.153 57.895 0.00 0.00 0.00 5.69
494 1016 0.532862 CGCTTCCTATCCAACGGCAT 60.533 55.000 0.00 0.00 0.00 4.40
495 1017 1.270094 CGCTTCCTATCCAACGGCATA 60.270 52.381 0.00 0.00 0.00 3.14
496 1018 2.417719 GCTTCCTATCCAACGGCATAG 58.582 52.381 0.00 0.00 0.00 2.23
497 1019 2.872038 GCTTCCTATCCAACGGCATAGG 60.872 54.545 2.22 2.22 42.24 2.57
498 1020 2.391926 TCCTATCCAACGGCATAGGA 57.608 50.000 6.46 6.46 45.72 2.94
499 1021 1.968493 TCCTATCCAACGGCATAGGAC 59.032 52.381 6.46 0.00 43.89 3.85
500 1022 1.971357 CCTATCCAACGGCATAGGACT 59.029 52.381 2.43 0.00 43.18 3.85
501 1023 3.162666 CCTATCCAACGGCATAGGACTA 58.837 50.000 2.43 0.00 43.18 2.59
502 1024 3.193691 CCTATCCAACGGCATAGGACTAG 59.806 52.174 2.43 0.00 43.18 2.57
503 1025 2.154567 TCCAACGGCATAGGACTAGT 57.845 50.000 0.00 0.00 0.00 2.57
504 1026 2.029623 TCCAACGGCATAGGACTAGTC 58.970 52.381 14.87 14.87 0.00 2.59
505 1027 2.032620 CCAACGGCATAGGACTAGTCT 58.967 52.381 21.88 10.81 0.00 3.24
506 1028 2.034812 CCAACGGCATAGGACTAGTCTC 59.965 54.545 21.88 12.27 0.00 3.36
507 1029 2.688446 CAACGGCATAGGACTAGTCTCA 59.312 50.000 21.88 10.67 0.00 3.27
508 1030 3.231207 ACGGCATAGGACTAGTCTCAT 57.769 47.619 21.88 12.41 0.00 2.90
509 1031 2.887783 ACGGCATAGGACTAGTCTCATG 59.112 50.000 21.88 22.27 0.00 3.07
510 1032 2.230025 CGGCATAGGACTAGTCTCATGG 59.770 54.545 25.38 14.33 0.00 3.66
511 1033 3.501349 GGCATAGGACTAGTCTCATGGA 58.499 50.000 25.38 9.15 0.00 3.41
512 1034 4.093011 GGCATAGGACTAGTCTCATGGAT 58.907 47.826 25.38 10.53 0.00 3.41
513 1035 4.081752 GGCATAGGACTAGTCTCATGGATG 60.082 50.000 25.38 18.49 0.00 3.51
514 1036 4.620332 GCATAGGACTAGTCTCATGGATGC 60.620 50.000 25.38 22.01 0.00 3.91
515 1037 3.037851 AGGACTAGTCTCATGGATGCA 57.962 47.619 21.88 0.00 0.00 3.96
516 1038 3.585360 AGGACTAGTCTCATGGATGCAT 58.415 45.455 21.88 0.00 0.00 3.96
517 1039 3.324268 AGGACTAGTCTCATGGATGCATG 59.676 47.826 20.28 20.28 0.00 4.06
518 1040 3.065655 GACTAGTCTCATGGATGCATGC 58.934 50.000 21.37 11.82 32.87 4.06
519 1041 2.224475 ACTAGTCTCATGGATGCATGCC 60.224 50.000 21.37 11.49 32.87 4.40
520 1042 0.844660 AGTCTCATGGATGCATGCCT 59.155 50.000 21.37 13.64 32.87 4.75
521 1043 2.052468 AGTCTCATGGATGCATGCCTA 58.948 47.619 21.37 7.04 32.87 3.93
522 1044 2.038689 AGTCTCATGGATGCATGCCTAG 59.961 50.000 21.37 14.00 32.87 3.02
523 1045 2.052468 TCTCATGGATGCATGCCTAGT 58.948 47.619 21.37 0.00 32.87 2.57
524 1046 3.007290 GTCTCATGGATGCATGCCTAGTA 59.993 47.826 21.37 3.27 32.87 1.82
525 1047 3.260128 TCTCATGGATGCATGCCTAGTAG 59.740 47.826 21.37 12.65 32.87 2.57
526 1048 2.974794 TCATGGATGCATGCCTAGTAGT 59.025 45.455 21.37 0.00 32.87 2.73
527 1049 3.392285 TCATGGATGCATGCCTAGTAGTT 59.608 43.478 21.37 0.00 32.87 2.24
528 1050 3.198409 TGGATGCATGCCTAGTAGTTG 57.802 47.619 16.68 0.00 0.00 3.16
529 1051 1.876156 GGATGCATGCCTAGTAGTTGC 59.124 52.381 16.68 9.06 0.00 4.17
530 1052 1.876156 GATGCATGCCTAGTAGTTGCC 59.124 52.381 16.68 0.00 32.39 4.52
531 1053 0.107214 TGCATGCCTAGTAGTTGCCC 60.107 55.000 16.68 0.00 32.39 5.36
532 1054 0.181350 GCATGCCTAGTAGTTGCCCT 59.819 55.000 6.36 0.00 0.00 5.19
533 1055 1.408822 GCATGCCTAGTAGTTGCCCTT 60.409 52.381 6.36 0.00 0.00 3.95
534 1056 2.158813 GCATGCCTAGTAGTTGCCCTTA 60.159 50.000 6.36 0.00 0.00 2.69
535 1057 3.496870 GCATGCCTAGTAGTTGCCCTTAT 60.497 47.826 6.36 0.00 0.00 1.73
536 1058 4.718961 CATGCCTAGTAGTTGCCCTTATT 58.281 43.478 0.00 0.00 0.00 1.40
537 1059 5.744887 GCATGCCTAGTAGTTGCCCTTATTA 60.745 44.000 6.36 0.00 0.00 0.98
538 1060 6.476378 CATGCCTAGTAGTTGCCCTTATTAT 58.524 40.000 0.00 0.00 0.00 1.28
539 1061 6.509523 TGCCTAGTAGTTGCCCTTATTATT 57.490 37.500 0.00 0.00 0.00 1.40
540 1062 7.621006 TGCCTAGTAGTTGCCCTTATTATTA 57.379 36.000 0.00 0.00 0.00 0.98
541 1063 8.214721 TGCCTAGTAGTTGCCCTTATTATTAT 57.785 34.615 0.00 0.00 0.00 1.28
542 1064 8.665906 TGCCTAGTAGTTGCCCTTATTATTATT 58.334 33.333 0.00 0.00 0.00 1.40
543 1065 9.516546 GCCTAGTAGTTGCCCTTATTATTATTT 57.483 33.333 0.00 0.00 0.00 1.40
550 1072 9.715119 AGTTGCCCTTATTATTATTTTCTTCCT 57.285 29.630 0.00 0.00 0.00 3.36
598 1120 3.971032 AAAAAGAGAAGCAGAACCGTG 57.029 42.857 0.00 0.00 0.00 4.94
599 1121 2.910688 AAAGAGAAGCAGAACCGTGA 57.089 45.000 0.00 0.00 0.00 4.35
600 1122 2.156343 AAGAGAAGCAGAACCGTGAC 57.844 50.000 0.00 0.00 0.00 3.67
601 1123 0.039074 AGAGAAGCAGAACCGTGACG 60.039 55.000 0.00 0.00 0.00 4.35
602 1124 0.039437 GAGAAGCAGAACCGTGACGA 60.039 55.000 6.54 0.00 0.00 4.20
603 1125 0.387929 AGAAGCAGAACCGTGACGAA 59.612 50.000 6.54 0.00 0.00 3.85
604 1126 1.000955 AGAAGCAGAACCGTGACGAAT 59.999 47.619 6.54 0.00 0.00 3.34
605 1127 2.230508 AGAAGCAGAACCGTGACGAATA 59.769 45.455 6.54 0.00 0.00 1.75
606 1128 2.736144 AGCAGAACCGTGACGAATAA 57.264 45.000 6.54 0.00 0.00 1.40
607 1129 2.607187 AGCAGAACCGTGACGAATAAG 58.393 47.619 6.54 0.00 0.00 1.73
608 1130 2.230508 AGCAGAACCGTGACGAATAAGA 59.769 45.455 6.54 0.00 0.00 2.10
609 1131 2.599082 GCAGAACCGTGACGAATAAGAG 59.401 50.000 6.54 0.00 0.00 2.85
610 1132 3.672511 GCAGAACCGTGACGAATAAGAGA 60.673 47.826 6.54 0.00 0.00 3.10
611 1133 4.099120 CAGAACCGTGACGAATAAGAGAG 58.901 47.826 6.54 0.00 0.00 3.20
612 1134 4.008330 AGAACCGTGACGAATAAGAGAGA 58.992 43.478 6.54 0.00 0.00 3.10
613 1135 4.095185 AGAACCGTGACGAATAAGAGAGAG 59.905 45.833 6.54 0.00 0.00 3.20
614 1136 2.683867 ACCGTGACGAATAAGAGAGAGG 59.316 50.000 6.54 0.00 0.00 3.69
615 1137 2.943690 CCGTGACGAATAAGAGAGAGGA 59.056 50.000 6.54 0.00 0.00 3.71
616 1138 3.377485 CCGTGACGAATAAGAGAGAGGAA 59.623 47.826 6.54 0.00 0.00 3.36
617 1139 4.036971 CCGTGACGAATAAGAGAGAGGAAT 59.963 45.833 6.54 0.00 0.00 3.01
618 1140 5.238868 CCGTGACGAATAAGAGAGAGGAATA 59.761 44.000 6.54 0.00 0.00 1.75
619 1141 6.072397 CCGTGACGAATAAGAGAGAGGAATAT 60.072 42.308 6.54 0.00 0.00 1.28
620 1142 7.119407 CCGTGACGAATAAGAGAGAGGAATATA 59.881 40.741 6.54 0.00 0.00 0.86
621 1143 8.670135 CGTGACGAATAAGAGAGAGGAATATAT 58.330 37.037 0.00 0.00 0.00 0.86
622 1144 9.997482 GTGACGAATAAGAGAGAGGAATATATC 57.003 37.037 0.00 0.00 0.00 1.63
623 1145 9.740710 TGACGAATAAGAGAGAGGAATATATCA 57.259 33.333 0.00 0.00 0.00 2.15
810 1341 9.138062 GTGTAAATCAATTAACAATGATGCACA 57.862 29.630 0.00 12.48 36.44 4.57
821 1352 2.401583 TGATGCACAAGATAAGCCGT 57.598 45.000 0.00 0.00 0.00 5.68
822 1353 2.009051 TGATGCACAAGATAAGCCGTG 58.991 47.619 0.00 0.00 0.00 4.94
893 1435 7.459234 ACTAGCCCTATTCCATTTTACCATAC 58.541 38.462 0.00 0.00 0.00 2.39
968 1521 2.034879 CGCAACGAAGGGTGAGCAT 61.035 57.895 0.00 0.00 32.47 3.79
969 1522 1.503542 GCAACGAAGGGTGAGCATG 59.496 57.895 0.00 0.00 32.47 4.06
1100 1662 1.000955 AGGTTCAGAGCTTGGTACGTG 59.999 52.381 0.00 0.00 0.00 4.49
1112 1678 3.367992 TGGTACGTGCGTTCTCTTAAA 57.632 42.857 1.66 0.00 0.00 1.52
1137 1708 4.757149 AGCATCTACCAGTTTTCACAAGAC 59.243 41.667 0.00 0.00 0.00 3.01
1182 1755 9.738832 TGAGCATGATGAATGTATTTTTATGTG 57.261 29.630 0.00 0.00 38.65 3.21
1184 1757 9.524106 AGCATGATGAATGTATTTTTATGTGTG 57.476 29.630 0.00 0.00 38.65 3.82
1258 1901 0.907486 TTCCCAGATGACTGCCAGAG 59.093 55.000 0.00 0.00 42.25 3.35
1343 1986 0.743688 TAAAACCGTATCCCGCGCTA 59.256 50.000 5.56 0.00 34.38 4.26
1405 2049 3.206150 CATGGCGCTTAATTAGTCCACT 58.794 45.455 7.64 0.00 33.53 4.00
1406 2050 3.343941 TGGCGCTTAATTAGTCCACTT 57.656 42.857 7.64 0.00 0.00 3.16
1609 2309 7.654022 AAATATCACGGACCCATACAAAAAT 57.346 32.000 0.00 0.00 0.00 1.82
1727 2427 2.050350 CGACCTCTCGGCCTTGGTA 61.050 63.158 0.00 0.00 36.16 3.25
1733 2433 1.227674 CTCGGCCTTGGTATCAGCC 60.228 63.158 0.00 0.00 42.18 4.85
1745 2445 1.535462 GTATCAGCCGCACAAACTTGT 59.465 47.619 0.00 0.00 43.36 3.16
1786 2486 2.743928 CAGTGGCTGGGAAGTCGC 60.744 66.667 0.00 0.00 0.00 5.19
1806 2506 2.637595 CCGACGTAGATTAGAAGACGC 58.362 52.381 0.00 0.00 38.86 5.19
1807 2507 2.031314 CCGACGTAGATTAGAAGACGCA 59.969 50.000 0.00 0.00 38.86 5.24
1862 2562 5.277779 CCTTGCAGAACAAAACGTCATAGAA 60.278 40.000 0.00 0.00 37.96 2.10
2043 2747 6.973843 AGACAAACCCGTAGAAAAATAAACC 58.026 36.000 0.00 0.00 0.00 3.27
2070 2774 8.352942 AGACTGGAAAATAAAATCTTGTGACAC 58.647 33.333 0.00 0.00 0.00 3.67
2071 2775 8.006298 ACTGGAAAATAAAATCTTGTGACACA 57.994 30.769 3.56 3.56 0.00 3.72
2072 2776 7.920682 ACTGGAAAATAAAATCTTGTGACACAC 59.079 33.333 8.05 0.00 34.56 3.82
2087 2791 3.265791 GACACACCATCTTCCTCATGTC 58.734 50.000 0.00 0.00 0.00 3.06
2129 2833 1.986378 CAGTCGGAAACATGACGAGAC 59.014 52.381 0.00 2.45 40.05 3.36
2138 2842 0.179134 CATGACGAGACGGGAAGACC 60.179 60.000 0.00 0.00 0.00 3.85
2151 2855 4.472108 ACGGGAAGACCTTATTCCATGTTA 59.528 41.667 7.02 0.00 46.77 2.41
2160 2864 5.163561 ACCTTATTCCATGTTATTGGCAACG 60.164 40.000 0.00 0.00 42.51 4.10
2249 2953 0.988832 ACAGGCGGAGGGAAATGTAA 59.011 50.000 0.00 0.00 0.00 2.41
2254 2958 2.422479 GGCGGAGGGAAATGTAAACTTC 59.578 50.000 0.00 0.00 0.00 3.01
2256 2960 3.119955 GCGGAGGGAAATGTAAACTTCAC 60.120 47.826 0.00 0.00 0.00 3.18
2301 3005 1.338674 CGTTGCCTATCACCAAGGTCA 60.339 52.381 0.00 0.00 36.43 4.02
2302 3006 2.084546 GTTGCCTATCACCAAGGTCAC 58.915 52.381 0.00 0.00 36.43 3.67
2303 3007 0.249120 TGCCTATCACCAAGGTCACG 59.751 55.000 0.00 0.00 36.43 4.35
2304 3008 0.462047 GCCTATCACCAAGGTCACGG 60.462 60.000 0.00 0.00 36.43 4.94
2305 3009 0.178068 CCTATCACCAAGGTCACGGG 59.822 60.000 0.00 0.00 0.00 5.28
2306 3010 1.191535 CTATCACCAAGGTCACGGGA 58.808 55.000 0.00 0.00 0.00 5.14
2307 3011 1.137086 CTATCACCAAGGTCACGGGAG 59.863 57.143 0.00 0.00 0.00 4.30
2309 3013 0.178955 TCACCAAGGTCACGGGAGTA 60.179 55.000 0.00 0.00 44.67 2.59
2310 3014 0.246635 CACCAAGGTCACGGGAGTAG 59.753 60.000 0.00 0.00 44.67 2.57
2311 3015 0.113776 ACCAAGGTCACGGGAGTAGA 59.886 55.000 0.00 0.00 44.67 2.59
2312 3016 1.263356 CCAAGGTCACGGGAGTAGAA 58.737 55.000 0.00 0.00 44.67 2.10
2313 3017 1.204941 CCAAGGTCACGGGAGTAGAAG 59.795 57.143 0.00 0.00 44.67 2.85
2314 3018 1.204941 CAAGGTCACGGGAGTAGAAGG 59.795 57.143 0.00 0.00 44.67 3.46
2315 3019 0.702902 AGGTCACGGGAGTAGAAGGA 59.297 55.000 0.00 0.00 44.67 3.36
2316 3020 1.076677 AGGTCACGGGAGTAGAAGGAA 59.923 52.381 0.00 0.00 44.67 3.36
2317 3021 1.897802 GGTCACGGGAGTAGAAGGAAA 59.102 52.381 0.00 0.00 44.67 3.13
2318 3022 2.094130 GGTCACGGGAGTAGAAGGAAAG 60.094 54.545 0.00 0.00 44.67 2.62
2319 3023 2.824341 GTCACGGGAGTAGAAGGAAAGA 59.176 50.000 0.00 0.00 44.67 2.52
2320 3024 3.257624 GTCACGGGAGTAGAAGGAAAGAA 59.742 47.826 0.00 0.00 44.67 2.52
2321 3025 4.081586 GTCACGGGAGTAGAAGGAAAGAAT 60.082 45.833 0.00 0.00 44.67 2.40
2322 3026 4.530946 TCACGGGAGTAGAAGGAAAGAATT 59.469 41.667 0.00 0.00 44.67 2.17
2323 3027 4.631813 CACGGGAGTAGAAGGAAAGAATTG 59.368 45.833 0.00 0.00 44.67 2.32
2324 3028 4.286291 ACGGGAGTAGAAGGAAAGAATTGT 59.714 41.667 0.00 0.00 44.60 2.71
2325 3029 5.482878 ACGGGAGTAGAAGGAAAGAATTGTA 59.517 40.000 0.00 0.00 44.60 2.41
2326 3030 6.013984 ACGGGAGTAGAAGGAAAGAATTGTAA 60.014 38.462 0.00 0.00 44.60 2.41
2327 3031 7.048512 CGGGAGTAGAAGGAAAGAATTGTAAT 58.951 38.462 0.00 0.00 0.00 1.89
2328 3032 7.011482 CGGGAGTAGAAGGAAAGAATTGTAATG 59.989 40.741 0.00 0.00 0.00 1.90
2329 3033 7.201741 GGGAGTAGAAGGAAAGAATTGTAATGC 60.202 40.741 0.00 0.00 0.00 3.56
2330 3034 7.336931 GGAGTAGAAGGAAAGAATTGTAATGCA 59.663 37.037 0.00 0.00 0.00 3.96
2331 3035 8.045176 AGTAGAAGGAAAGAATTGTAATGCAC 57.955 34.615 0.00 0.00 0.00 4.57
2332 3036 7.885399 AGTAGAAGGAAAGAATTGTAATGCACT 59.115 33.333 0.00 0.00 0.00 4.40
2333 3037 9.162764 GTAGAAGGAAAGAATTGTAATGCACTA 57.837 33.333 0.00 0.00 0.00 2.74
2334 3038 8.273780 AGAAGGAAAGAATTGTAATGCACTAG 57.726 34.615 0.00 0.00 0.00 2.57
2335 3039 8.103305 AGAAGGAAAGAATTGTAATGCACTAGA 58.897 33.333 0.00 0.00 0.00 2.43
2336 3040 8.814038 AAGGAAAGAATTGTAATGCACTAGAT 57.186 30.769 0.00 0.00 0.00 1.98
2337 3041 9.905713 AAGGAAAGAATTGTAATGCACTAGATA 57.094 29.630 0.00 0.00 0.00 1.98
2349 3053 9.593134 GTAATGCACTAGATATTAGATGAAGGG 57.407 37.037 0.00 0.00 0.00 3.95
2350 3054 7.805083 ATGCACTAGATATTAGATGAAGGGT 57.195 36.000 0.00 0.00 0.00 4.34
2351 3055 7.233389 TGCACTAGATATTAGATGAAGGGTC 57.767 40.000 0.00 0.00 0.00 4.46
2352 3056 7.013220 TGCACTAGATATTAGATGAAGGGTCT 58.987 38.462 0.00 0.00 0.00 3.85
2353 3057 7.039434 TGCACTAGATATTAGATGAAGGGTCTG 60.039 40.741 0.00 0.00 0.00 3.51
2354 3058 7.039363 GCACTAGATATTAGATGAAGGGTCTGT 60.039 40.741 0.00 0.00 0.00 3.41
2355 3059 8.519526 CACTAGATATTAGATGAAGGGTCTGTC 58.480 40.741 0.00 0.00 0.00 3.51
2356 3060 6.926630 AGATATTAGATGAAGGGTCTGTCC 57.073 41.667 0.00 0.00 0.00 4.02
2357 3061 6.629156 AGATATTAGATGAAGGGTCTGTCCT 58.371 40.000 0.00 0.00 39.17 3.85
2359 3063 4.826274 TTAGATGAAGGGTCTGTCCTTG 57.174 45.455 9.12 0.00 46.31 3.61
2360 3064 2.625639 AGATGAAGGGTCTGTCCTTGT 58.374 47.619 9.12 0.44 46.31 3.16
2361 3065 3.791320 AGATGAAGGGTCTGTCCTTGTA 58.209 45.455 9.12 1.23 46.31 2.41
2362 3066 4.366267 AGATGAAGGGTCTGTCCTTGTAT 58.634 43.478 9.12 4.94 46.31 2.29
2363 3067 4.785376 AGATGAAGGGTCTGTCCTTGTATT 59.215 41.667 9.12 0.00 46.31 1.89
2364 3068 4.286297 TGAAGGGTCTGTCCTTGTATTG 57.714 45.455 9.12 0.00 46.31 1.90
2365 3069 3.907474 TGAAGGGTCTGTCCTTGTATTGA 59.093 43.478 9.12 0.00 46.31 2.57
2366 3070 4.536090 TGAAGGGTCTGTCCTTGTATTGAT 59.464 41.667 9.12 0.00 46.31 2.57
2367 3071 5.724370 TGAAGGGTCTGTCCTTGTATTGATA 59.276 40.000 9.12 0.00 46.31 2.15
2368 3072 6.386927 TGAAGGGTCTGTCCTTGTATTGATAT 59.613 38.462 9.12 0.00 46.31 1.63
2369 3073 6.831664 AGGGTCTGTCCTTGTATTGATATT 57.168 37.500 0.00 0.00 32.13 1.28
2370 3074 7.931015 AGGGTCTGTCCTTGTATTGATATTA 57.069 36.000 0.00 0.00 32.13 0.98
2371 3075 8.331931 AGGGTCTGTCCTTGTATTGATATTAA 57.668 34.615 0.00 0.00 32.13 1.40
2372 3076 8.949421 AGGGTCTGTCCTTGTATTGATATTAAT 58.051 33.333 0.00 0.00 32.13 1.40
2373 3077 9.574516 GGGTCTGTCCTTGTATTGATATTAATT 57.425 33.333 0.00 0.00 36.25 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.961522 TCGAACAAACGGAGAATTGC 57.038 45.000 0.00 0.00 32.87 3.56
339 343 0.596082 CGCTGGTTCCGTTTTTCCAT 59.404 50.000 0.00 0.00 0.00 3.41
363 367 9.111613 CCTAATTACGTGGGATTTGTTATTACA 57.888 33.333 0.00 0.00 0.00 2.41
365 369 7.774157 TGCCTAATTACGTGGGATTTGTTATTA 59.226 33.333 0.00 0.00 0.00 0.98
366 370 6.603997 TGCCTAATTACGTGGGATTTGTTATT 59.396 34.615 0.00 0.00 0.00 1.40
367 371 6.123651 TGCCTAATTACGTGGGATTTGTTAT 58.876 36.000 0.00 0.00 0.00 1.89
450 972 1.203052 GGACGTCCGATCTGGTTGTTA 59.797 52.381 20.85 0.00 39.52 2.41
451 973 0.037605 GGACGTCCGATCTGGTTGTT 60.038 55.000 20.85 0.00 39.52 2.83
452 974 1.183030 TGGACGTCCGATCTGGTTGT 61.183 55.000 28.70 4.16 39.43 3.32
453 975 0.175760 ATGGACGTCCGATCTGGTTG 59.824 55.000 28.70 1.57 39.43 3.77
454 976 0.460311 GATGGACGTCCGATCTGGTT 59.540 55.000 28.70 6.48 39.43 3.67
455 977 0.395862 AGATGGACGTCCGATCTGGT 60.396 55.000 31.48 18.14 39.43 4.00
456 978 0.312416 GAGATGGACGTCCGATCTGG 59.688 60.000 34.52 0.00 39.43 3.86
457 979 0.040870 CGAGATGGACGTCCGATCTG 60.041 60.000 34.52 26.18 39.43 2.90
458 980 1.787057 GCGAGATGGACGTCCGATCT 61.787 60.000 32.03 32.03 39.43 2.75
459 981 1.370657 GCGAGATGGACGTCCGATC 60.371 63.158 28.70 27.38 39.43 3.69
460 982 1.384989 AAGCGAGATGGACGTCCGAT 61.385 55.000 28.70 21.89 39.43 4.18
461 983 1.989966 GAAGCGAGATGGACGTCCGA 61.990 60.000 28.70 18.27 39.43 4.55
462 984 1.586564 GAAGCGAGATGGACGTCCG 60.587 63.158 28.70 17.38 39.43 4.79
463 985 1.227002 GGAAGCGAGATGGACGTCC 60.227 63.158 28.17 28.17 0.00 4.79
464 986 1.022735 TAGGAAGCGAGATGGACGTC 58.977 55.000 7.13 7.13 0.00 4.34
465 987 1.609555 GATAGGAAGCGAGATGGACGT 59.390 52.381 0.00 0.00 0.00 4.34
466 988 1.068194 GGATAGGAAGCGAGATGGACG 60.068 57.143 0.00 0.00 0.00 4.79
467 989 1.964223 TGGATAGGAAGCGAGATGGAC 59.036 52.381 0.00 0.00 0.00 4.02
468 990 2.365617 GTTGGATAGGAAGCGAGATGGA 59.634 50.000 0.00 0.00 0.00 3.41
469 991 2.760374 GTTGGATAGGAAGCGAGATGG 58.240 52.381 0.00 0.00 0.00 3.51
470 992 2.398498 CGTTGGATAGGAAGCGAGATG 58.602 52.381 0.00 0.00 0.00 2.90
471 993 1.341531 CCGTTGGATAGGAAGCGAGAT 59.658 52.381 0.00 0.00 0.00 2.75
472 994 0.744874 CCGTTGGATAGGAAGCGAGA 59.255 55.000 0.00 0.00 0.00 4.04
473 995 0.876342 GCCGTTGGATAGGAAGCGAG 60.876 60.000 0.00 0.00 0.00 5.03
474 996 1.143183 GCCGTTGGATAGGAAGCGA 59.857 57.895 0.00 0.00 0.00 4.93
475 997 0.532862 ATGCCGTTGGATAGGAAGCG 60.533 55.000 0.00 0.00 0.00 4.68
476 998 2.417719 CTATGCCGTTGGATAGGAAGC 58.582 52.381 0.00 0.00 0.00 3.86
477 999 2.632996 TCCTATGCCGTTGGATAGGAAG 59.367 50.000 17.27 0.00 44.80 3.46
478 1000 2.684943 TCCTATGCCGTTGGATAGGAA 58.315 47.619 17.27 4.86 44.80 3.36
479 1001 1.968493 GTCCTATGCCGTTGGATAGGA 59.032 52.381 16.08 16.08 45.32 2.94
480 1002 1.971357 AGTCCTATGCCGTTGGATAGG 59.029 52.381 12.41 12.41 41.87 2.57
481 1003 3.827302 ACTAGTCCTATGCCGTTGGATAG 59.173 47.826 0.00 0.00 34.22 2.08
482 1004 3.825014 GACTAGTCCTATGCCGTTGGATA 59.175 47.826 12.13 0.00 34.22 2.59
483 1005 2.628657 GACTAGTCCTATGCCGTTGGAT 59.371 50.000 12.13 0.00 34.22 3.41
484 1006 2.029623 GACTAGTCCTATGCCGTTGGA 58.970 52.381 12.13 0.00 0.00 3.53
485 1007 2.032620 AGACTAGTCCTATGCCGTTGG 58.967 52.381 19.38 0.00 0.00 3.77
486 1008 2.688446 TGAGACTAGTCCTATGCCGTTG 59.312 50.000 19.38 0.00 0.00 4.10
487 1009 3.014304 TGAGACTAGTCCTATGCCGTT 57.986 47.619 19.38 0.00 0.00 4.44
488 1010 2.730934 TGAGACTAGTCCTATGCCGT 57.269 50.000 19.38 0.00 0.00 5.68
489 1011 2.230025 CCATGAGACTAGTCCTATGCCG 59.770 54.545 19.38 8.53 0.00 5.69
490 1012 3.501349 TCCATGAGACTAGTCCTATGCC 58.499 50.000 19.38 3.15 0.00 4.40
491 1013 4.620332 GCATCCATGAGACTAGTCCTATGC 60.620 50.000 19.38 18.47 0.00 3.14
492 1014 4.525874 TGCATCCATGAGACTAGTCCTATG 59.474 45.833 19.38 20.68 0.00 2.23
493 1015 4.745351 TGCATCCATGAGACTAGTCCTAT 58.255 43.478 19.38 11.02 0.00 2.57
494 1016 4.184649 TGCATCCATGAGACTAGTCCTA 57.815 45.455 19.38 9.09 0.00 2.94
495 1017 3.037851 TGCATCCATGAGACTAGTCCT 57.962 47.619 19.38 6.89 0.00 3.85
507 1029 3.748083 CAACTACTAGGCATGCATCCAT 58.252 45.455 21.36 4.03 0.00 3.41
508 1030 2.746142 GCAACTACTAGGCATGCATCCA 60.746 50.000 21.36 0.00 37.00 3.41
509 1031 1.876156 GCAACTACTAGGCATGCATCC 59.124 52.381 21.36 1.57 37.00 3.51
510 1032 1.876156 GGCAACTACTAGGCATGCATC 59.124 52.381 21.36 2.42 38.73 3.91
511 1033 1.477558 GGGCAACTACTAGGCATGCAT 60.478 52.381 21.36 16.31 38.73 3.96
512 1034 0.107214 GGGCAACTACTAGGCATGCA 60.107 55.000 21.36 0.00 38.73 3.96
513 1035 0.181350 AGGGCAACTACTAGGCATGC 59.819 55.000 9.90 9.90 36.31 4.06
514 1036 2.717639 AAGGGCAACTACTAGGCATG 57.282 50.000 0.00 0.00 0.00 4.06
515 1037 6.704056 ATAATAAGGGCAACTACTAGGCAT 57.296 37.500 0.00 0.00 0.00 4.40
516 1038 6.509523 AATAATAAGGGCAACTACTAGGCA 57.490 37.500 0.00 0.00 0.00 4.75
517 1039 9.516546 AAATAATAATAAGGGCAACTACTAGGC 57.483 33.333 0.00 0.00 0.00 3.93
524 1046 9.715119 AGGAAGAAAATAATAATAAGGGCAACT 57.285 29.630 0.00 0.00 0.00 3.16
578 1100 3.312697 GTCACGGTTCTGCTTCTCTTTTT 59.687 43.478 0.00 0.00 0.00 1.94
579 1101 2.872858 GTCACGGTTCTGCTTCTCTTTT 59.127 45.455 0.00 0.00 0.00 2.27
580 1102 2.484889 GTCACGGTTCTGCTTCTCTTT 58.515 47.619 0.00 0.00 0.00 2.52
581 1103 1.603172 CGTCACGGTTCTGCTTCTCTT 60.603 52.381 0.00 0.00 0.00 2.85
582 1104 0.039074 CGTCACGGTTCTGCTTCTCT 60.039 55.000 0.00 0.00 0.00 3.10
583 1105 0.039437 TCGTCACGGTTCTGCTTCTC 60.039 55.000 0.00 0.00 0.00 2.87
584 1106 0.387929 TTCGTCACGGTTCTGCTTCT 59.612 50.000 0.00 0.00 0.00 2.85
585 1107 1.429463 ATTCGTCACGGTTCTGCTTC 58.571 50.000 0.00 0.00 0.00 3.86
586 1108 2.736144 TATTCGTCACGGTTCTGCTT 57.264 45.000 0.00 0.00 0.00 3.91
587 1109 2.230508 TCTTATTCGTCACGGTTCTGCT 59.769 45.455 0.00 0.00 0.00 4.24
588 1110 2.599082 CTCTTATTCGTCACGGTTCTGC 59.401 50.000 0.00 0.00 0.00 4.26
589 1111 4.092771 TCTCTTATTCGTCACGGTTCTG 57.907 45.455 0.00 0.00 0.00 3.02
590 1112 4.008330 TCTCTCTTATTCGTCACGGTTCT 58.992 43.478 0.00 0.00 0.00 3.01
591 1113 4.344448 CTCTCTCTTATTCGTCACGGTTC 58.656 47.826 0.00 0.00 0.00 3.62
592 1114 3.128938 CCTCTCTCTTATTCGTCACGGTT 59.871 47.826 0.00 0.00 0.00 4.44
593 1115 2.683867 CCTCTCTCTTATTCGTCACGGT 59.316 50.000 0.00 0.00 0.00 4.83
594 1116 2.943690 TCCTCTCTCTTATTCGTCACGG 59.056 50.000 0.00 0.00 0.00 4.94
595 1117 4.617808 TTCCTCTCTCTTATTCGTCACG 57.382 45.455 0.00 0.00 0.00 4.35
596 1118 9.997482 GATATATTCCTCTCTCTTATTCGTCAC 57.003 37.037 0.00 0.00 0.00 3.67
597 1119 9.740710 TGATATATTCCTCTCTCTTATTCGTCA 57.259 33.333 0.00 0.00 0.00 4.35
607 1129 9.263538 GCATTGATCATGATATATTCCTCTCTC 57.736 37.037 8.54 0.00 34.31 3.20
608 1130 8.769359 TGCATTGATCATGATATATTCCTCTCT 58.231 33.333 8.54 0.00 34.31 3.10
609 1131 8.959705 TGCATTGATCATGATATATTCCTCTC 57.040 34.615 8.54 0.00 34.31 3.20
620 1142 9.602568 GAAGACTATCTATGCATTGATCATGAT 57.397 33.333 23.97 8.25 34.31 2.45
621 1143 8.813951 AGAAGACTATCTATGCATTGATCATGA 58.186 33.333 23.97 8.64 34.31 3.07
622 1144 9.438228 AAGAAGACTATCTATGCATTGATCATG 57.562 33.333 23.97 17.56 35.73 3.07
680 1203 4.384427 GGTGTTCCGGGTCCAATCTTAATA 60.384 45.833 0.00 0.00 0.00 0.98
681 1204 3.617284 GTGTTCCGGGTCCAATCTTAAT 58.383 45.455 0.00 0.00 0.00 1.40
709 1233 3.440522 CGGGTCCAATCTTCTTCCTTTTC 59.559 47.826 0.00 0.00 0.00 2.29
766 1291 6.612247 TTACACGCCAAATATAGTGAATGG 57.388 37.500 1.24 0.00 37.95 3.16
946 1497 0.661020 CTCACCCTTCGTTGCGTTTT 59.339 50.000 0.00 0.00 0.00 2.43
968 1521 1.855295 ATCTTGATGCATTGGCCACA 58.145 45.000 3.88 0.00 40.13 4.17
969 1522 2.973694 AATCTTGATGCATTGGCCAC 57.026 45.000 3.88 0.00 40.13 5.01
1100 1662 5.983720 TGGTAGATGCTATTTAAGAGAACGC 59.016 40.000 0.00 0.00 0.00 4.84
1112 1678 6.595716 GTCTTGTGAAAACTGGTAGATGCTAT 59.404 38.462 0.00 0.00 0.00 2.97
1178 1751 2.556189 ACACACACAAACACACACACAT 59.444 40.909 0.00 0.00 0.00 3.21
1179 1752 1.950216 ACACACACAAACACACACACA 59.050 42.857 0.00 0.00 0.00 3.72
1180 1753 2.287308 ACACACACACAAACACACACAC 60.287 45.455 0.00 0.00 0.00 3.82
1181 1754 1.950216 ACACACACACAAACACACACA 59.050 42.857 0.00 0.00 0.00 3.72
1182 1755 2.287308 ACACACACACACAAACACACAC 60.287 45.455 0.00 0.00 0.00 3.82
1184 1757 2.287308 ACACACACACACACAAACACAC 60.287 45.455 0.00 0.00 0.00 3.82
1186 1759 2.315011 CACACACACACACACAAACAC 58.685 47.619 0.00 0.00 0.00 3.32
1258 1901 0.944386 AATATTGTCCGCGCATGTCC 59.056 50.000 8.75 0.00 0.00 4.02
1343 1986 4.486090 CGTCTCTATAGCAACAACACACT 58.514 43.478 0.00 0.00 0.00 3.55
1405 2049 1.186200 CTGATGGTCTCACTCCCGAA 58.814 55.000 0.00 0.00 0.00 4.30
1406 2050 0.039764 ACTGATGGTCTCACTCCCGA 59.960 55.000 0.00 0.00 0.00 5.14
1464 2122 2.605366 GGCTCACGACTTTGCTAATCTC 59.395 50.000 0.00 0.00 0.00 2.75
1621 2321 9.289303 CCACGGACTTAGATTTAATTTTCAATG 57.711 33.333 0.00 0.00 0.00 2.82
1727 2427 1.032014 AACAAGTTTGTGCGGCTGAT 58.968 45.000 0.00 0.00 41.31 2.90
1733 2433 4.911610 CCTAGATTTCAACAAGTTTGTGCG 59.088 41.667 0.00 0.00 41.31 5.34
1745 2445 8.856153 TGCTTATACAAACACCTAGATTTCAA 57.144 30.769 0.00 0.00 0.00 2.69
1786 2486 2.031314 TGCGTCTTCTAATCTACGTCGG 59.969 50.000 0.00 0.00 37.64 4.79
1806 2506 3.003897 GCTACTTAGATCACTCCCGTCTG 59.996 52.174 0.00 0.00 0.00 3.51
1807 2507 3.215975 GCTACTTAGATCACTCCCGTCT 58.784 50.000 0.00 0.00 0.00 4.18
1822 2522 2.558359 GCAAGGTGGTGATTTGCTACTT 59.442 45.455 1.51 0.00 42.84 2.24
2043 2747 8.352201 TGTCACAAGATTTTATTTTCCAGTCTG 58.648 33.333 0.00 0.00 0.00 3.51
2059 2763 3.328931 AGGAAGATGGTGTGTCACAAGAT 59.671 43.478 7.38 2.38 35.86 2.40
2070 2774 3.450096 TCAGAGACATGAGGAAGATGGTG 59.550 47.826 0.00 0.00 0.00 4.17
2071 2775 3.717576 TCAGAGACATGAGGAAGATGGT 58.282 45.455 0.00 0.00 0.00 3.55
2072 2776 4.440880 GTTCAGAGACATGAGGAAGATGG 58.559 47.826 0.00 0.00 0.00 3.51
2087 2791 1.970447 CTCCTTCGTGTCGTTCAGAG 58.030 55.000 0.00 0.00 0.00 3.35
2129 2833 3.560636 ACATGGAATAAGGTCTTCCCG 57.439 47.619 0.00 0.00 41.29 5.14
2138 2842 5.890334 ACGTTGCCAATAACATGGAATAAG 58.110 37.500 0.00 0.00 43.54 1.73
2243 2947 3.498397 CCTGCACGAGTGAAGTTTACATT 59.502 43.478 10.10 0.00 34.33 2.71
2249 2953 1.071471 CCCCTGCACGAGTGAAGTT 59.929 57.895 10.10 0.00 34.33 2.66
2254 2958 1.513158 CTACTCCCCTGCACGAGTG 59.487 63.158 13.94 0.00 39.64 3.51
2256 2960 0.395311 TACCTACTCCCCTGCACGAG 60.395 60.000 0.00 0.00 0.00 4.18
2301 3005 4.286291 ACAATTCTTTCCTTCTACTCCCGT 59.714 41.667 0.00 0.00 0.00 5.28
2302 3006 4.833390 ACAATTCTTTCCTTCTACTCCCG 58.167 43.478 0.00 0.00 0.00 5.14
2303 3007 7.201741 GCATTACAATTCTTTCCTTCTACTCCC 60.202 40.741 0.00 0.00 0.00 4.30
2304 3008 7.336931 TGCATTACAATTCTTTCCTTCTACTCC 59.663 37.037 0.00 0.00 0.00 3.85
2305 3009 8.178313 GTGCATTACAATTCTTTCCTTCTACTC 58.822 37.037 0.00 0.00 0.00 2.59
2306 3010 7.885399 AGTGCATTACAATTCTTTCCTTCTACT 59.115 33.333 0.00 0.00 0.00 2.57
2307 3011 8.045176 AGTGCATTACAATTCTTTCCTTCTAC 57.955 34.615 0.00 0.00 0.00 2.59
2308 3012 9.383519 CTAGTGCATTACAATTCTTTCCTTCTA 57.616 33.333 0.00 0.00 0.00 2.10
2309 3013 8.103305 TCTAGTGCATTACAATTCTTTCCTTCT 58.897 33.333 0.00 0.00 0.00 2.85
2310 3014 8.268850 TCTAGTGCATTACAATTCTTTCCTTC 57.731 34.615 0.00 0.00 0.00 3.46
2311 3015 8.814038 ATCTAGTGCATTACAATTCTTTCCTT 57.186 30.769 0.00 0.00 0.00 3.36
2323 3027 9.593134 CCCTTCATCTAATATCTAGTGCATTAC 57.407 37.037 0.00 0.00 0.00 1.89
2324 3028 9.326489 ACCCTTCATCTAATATCTAGTGCATTA 57.674 33.333 0.00 0.00 0.00 1.90
2325 3029 8.212259 ACCCTTCATCTAATATCTAGTGCATT 57.788 34.615 0.00 0.00 0.00 3.56
2326 3030 7.677745 AGACCCTTCATCTAATATCTAGTGCAT 59.322 37.037 0.00 0.00 0.00 3.96
2327 3031 7.013220 AGACCCTTCATCTAATATCTAGTGCA 58.987 38.462 0.00 0.00 0.00 4.57
2328 3032 7.039363 ACAGACCCTTCATCTAATATCTAGTGC 60.039 40.741 0.00 0.00 0.00 4.40
2329 3033 8.415950 ACAGACCCTTCATCTAATATCTAGTG 57.584 38.462 0.00 0.00 0.00 2.74
2330 3034 7.672239 GGACAGACCCTTCATCTAATATCTAGT 59.328 40.741 0.00 0.00 0.00 2.57
2331 3035 7.893302 AGGACAGACCCTTCATCTAATATCTAG 59.107 40.741 0.00 0.00 40.05 2.43
2332 3036 7.770662 AGGACAGACCCTTCATCTAATATCTA 58.229 38.462 0.00 0.00 40.05 1.98
2333 3037 6.629156 AGGACAGACCCTTCATCTAATATCT 58.371 40.000 0.00 0.00 40.05 1.98
2334 3038 6.926630 AGGACAGACCCTTCATCTAATATC 57.073 41.667 0.00 0.00 40.05 1.63
2335 3039 6.617371 ACAAGGACAGACCCTTCATCTAATAT 59.383 38.462 0.00 0.00 44.30 1.28
2336 3040 5.964477 ACAAGGACAGACCCTTCATCTAATA 59.036 40.000 0.00 0.00 44.30 0.98
2337 3041 4.785376 ACAAGGACAGACCCTTCATCTAAT 59.215 41.667 0.00 0.00 44.30 1.73
2338 3042 4.168101 ACAAGGACAGACCCTTCATCTAA 58.832 43.478 0.00 0.00 44.30 2.10
2339 3043 3.791320 ACAAGGACAGACCCTTCATCTA 58.209 45.455 0.00 0.00 44.30 1.98
2340 3044 2.625639 ACAAGGACAGACCCTTCATCT 58.374 47.619 0.00 0.00 44.30 2.90
2341 3045 4.762289 ATACAAGGACAGACCCTTCATC 57.238 45.455 0.00 0.00 44.30 2.92
2342 3046 4.536090 TCAATACAAGGACAGACCCTTCAT 59.464 41.667 0.00 0.00 44.30 2.57
2343 3047 3.907474 TCAATACAAGGACAGACCCTTCA 59.093 43.478 0.00 0.00 44.30 3.02
2344 3048 4.553330 TCAATACAAGGACAGACCCTTC 57.447 45.455 0.00 0.00 44.30 3.46
2345 3049 6.831664 ATATCAATACAAGGACAGACCCTT 57.168 37.500 0.00 0.00 46.91 3.95
2346 3050 6.831664 AATATCAATACAAGGACAGACCCT 57.168 37.500 0.00 0.00 40.05 4.34
2347 3051 9.574516 AATTAATATCAATACAAGGACAGACCC 57.425 33.333 0.00 0.00 40.05 4.46


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

AutoCloner maintained by Alex Coulton.