Multiple sequence alignment - TraesCS5A01G134500

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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 TraesCS5A01G134500 chr5A 100.000 6279 0 0 1 6279 303288127 303281849 0.000000e+00 11596
1 TraesCS5A01G134500 chr5A 100.000 272 0 0 6607 6878 303281521 303281250 2.860000e-138 503
2 TraesCS5A01G134500 chr5A 87.097 279 36 0 513 791 372645338 372645060 4.000000e-82 316
3 TraesCS5A01G134500 chr5A 86.380 279 38 0 511 789 564816593 564816871 8.670000e-79 305
4 TraesCS5A01G134500 chr5B 96.007 2354 54 11 3941 6279 243918648 243916320 0.000000e+00 3790
5 TraesCS5A01G134500 chr5B 94.517 1696 44 12 1975 3652 243920312 243918648 0.000000e+00 2571
6 TraesCS5A01G134500 chr5B 92.584 445 18 7 785 1227 243920730 243920299 5.860000e-175 625
7 TraesCS5A01G134500 chr5B 93.836 146 9 0 6733 6878 243916006 243915861 3.230000e-53 220
8 TraesCS5A01G134500 chr5B 93.103 145 10 0 4 148 243921454 243921310 5.400000e-51 213
9 TraesCS5A01G134500 chr5B 90.714 140 8 1 6739 6878 243911856 243911722 1.520000e-41 182
10 TraesCS5A01G134500 chr5B 94.690 113 6 0 6607 6719 243916174 243916062 7.090000e-40 176
11 TraesCS5A01G134500 chr5D 97.134 2233 49 5 3941 6163 221313008 221310781 0.000000e+00 3755
12 TraesCS5A01G134500 chr5D 95.616 1688 34 15 1975 3652 221314665 221313008 0.000000e+00 2671
13 TraesCS5A01G134500 chr5D 94.144 444 14 4 785 1227 221315084 221314652 0.000000e+00 665
14 TraesCS5A01G134500 chr5D 89.572 374 38 1 1 373 221315665 221315292 2.250000e-129 473
15 TraesCS5A01G134500 chr5D 91.096 146 13 0 6733 6878 221308529 221308384 1.510000e-46 198
16 TraesCS5A01G134500 chr5D 95.536 112 3 2 6158 6269 221308850 221308741 1.970000e-40 178
17 TraesCS5A01G134500 chr1A 99.200 750 6 0 1224 1973 560400540 560399791 0.000000e+00 1352
18 TraesCS5A01G134500 chr6B 98.933 750 8 0 1224 1973 199925910 199925161 0.000000e+00 1341
19 TraesCS5A01G134500 chr6B 96.282 753 24 2 1225 1973 647702467 647701715 0.000000e+00 1232
20 TraesCS5A01G134500 chr3A 98.398 749 12 0 1225 1973 189499 188751 0.000000e+00 1317
21 TraesCS5A01G134500 chr3A 96.644 298 7 3 3648 3943 733914468 733914172 6.200000e-135 492
22 TraesCS5A01G134500 chr3A 96.610 295 8 2 3650 3943 733909635 733909342 8.020000e-134 488
23 TraesCS5A01G134500 chr3A 96.610 295 8 2 3650 3943 733912730 733912437 8.020000e-134 488
24 TraesCS5A01G134500 chr3A 95.146 309 8 6 3639 3942 698037303 698036997 1.340000e-131 481
25 TraesCS5A01G134500 chr3A 87.455 279 35 0 511 789 745374431 745374153 8.610000e-84 322
26 TraesCS5A01G134500 chr3A 87.097 279 36 0 511 789 474958391 474958113 4.000000e-82 316
27 TraesCS5A01G134500 chr3D 97.463 749 18 1 1225 1973 598597560 598596813 0.000000e+00 1277
28 TraesCS5A01G134500 chr2A 96.005 751 26 3 1226 1973 640096380 640097129 0.000000e+00 1218
29 TraesCS5A01G134500 chr2D 94.980 757 37 1 1217 1973 629193018 629193773 0.000000e+00 1186
30 TraesCS5A01G134500 chr2D 88.530 279 29 3 507 784 468000106 468000382 1.110000e-87 335
31 TraesCS5A01G134500 chr4B 89.424 747 74 4 1229 1973 78201566 78202309 0.000000e+00 937
32 TraesCS5A01G134500 chr1B 88.070 746 86 3 1231 1973 688754311 688755056 0.000000e+00 881
33 TraesCS5A01G134500 chr4A 98.635 293 3 1 3650 3942 558704830 558704539 1.020000e-142 518
34 TraesCS5A01G134500 chr6A 97.260 292 7 1 3651 3942 23964079 23963789 1.720000e-135 494
35 TraesCS5A01G134500 chr6A 96.928 293 7 2 3651 3942 472393649 472393940 2.230000e-134 490
36 TraesCS5A01G134500 chr7A 96.296 297 9 2 3649 3944 134024133 134023838 2.880000e-133 486
37 TraesCS5A01G134500 chr7A 88.727 275 31 0 513 787 80986606 80986880 3.070000e-88 337
38 TraesCS5A01G134500 chr7A 87.273 275 33 2 513 787 403934052 403934324 5.180000e-81 313
39 TraesCS5A01G134500 chrUn 96.587 293 9 1 3649 3941 87096100 87095809 1.040000e-132 484
40 TraesCS5A01G134500 chr7B 87.943 282 28 4 511 790 254091347 254091070 1.850000e-85 327
41 TraesCS5A01G134500 chr6D 87.500 280 32 1 510 789 440419866 440419590 3.100000e-83 320


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 TraesCS5A01G134500 chr5A 303281250 303288127 6877 True 6049.500000 11596 100.000000 1 6878 2 chr5A.!!$R2 6877
1 TraesCS5A01G134500 chr5B 243915861 243921454 5593 True 1265.833333 3790 94.122833 4 6878 6 chr5B.!!$R2 6874
2 TraesCS5A01G134500 chr5D 221308384 221315665 7281 True 1323.333333 3755 93.849667 1 6878 6 chr5D.!!$R1 6877
3 TraesCS5A01G134500 chr1A 560399791 560400540 749 True 1352.000000 1352 99.200000 1224 1973 1 chr1A.!!$R1 749
4 TraesCS5A01G134500 chr6B 199925161 199925910 749 True 1341.000000 1341 98.933000 1224 1973 1 chr6B.!!$R1 749
5 TraesCS5A01G134500 chr6B 647701715 647702467 752 True 1232.000000 1232 96.282000 1225 1973 1 chr6B.!!$R2 748
6 TraesCS5A01G134500 chr3A 188751 189499 748 True 1317.000000 1317 98.398000 1225 1973 1 chr3A.!!$R1 748
7 TraesCS5A01G134500 chr3A 733909342 733914468 5126 True 489.333333 492 96.621333 3648 3943 3 chr3A.!!$R5 295
8 TraesCS5A01G134500 chr3D 598596813 598597560 747 True 1277.000000 1277 97.463000 1225 1973 1 chr3D.!!$R1 748
9 TraesCS5A01G134500 chr2A 640096380 640097129 749 False 1218.000000 1218 96.005000 1226 1973 1 chr2A.!!$F1 747
10 TraesCS5A01G134500 chr2D 629193018 629193773 755 False 1186.000000 1186 94.980000 1217 1973 1 chr2D.!!$F2 756
11 TraesCS5A01G134500 chr4B 78201566 78202309 743 False 937.000000 937 89.424000 1229 1973 1 chr4B.!!$F1 744
12 TraesCS5A01G134500 chr1B 688754311 688755056 745 False 881.000000 881 88.070000 1231 1973 1 chr1B.!!$F1 742

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
881 1196 0.399075 AACGGAGGTAAACACCCCTG 59.601 55.000 0.00 0.0 0.00 4.45 F
1975 2303 0.463116 AACAAGGTGTTCGACGGCTT 60.463 50.000 0.00 0.0 35.27 4.35 F
1976 2304 0.463116 ACAAGGTGTTCGACGGCTTT 60.463 50.000 0.00 0.0 0.00 3.51 F
1977 2305 0.661020 CAAGGTGTTCGACGGCTTTT 59.339 50.000 0.00 0.0 0.00 2.27 F
1978 2306 1.868498 CAAGGTGTTCGACGGCTTTTA 59.132 47.619 0.00 0.0 0.00 1.52 F
1979 2307 2.467566 AGGTGTTCGACGGCTTTTAT 57.532 45.000 0.00 0.0 0.00 1.40 F
1980 2308 2.774687 AGGTGTTCGACGGCTTTTATT 58.225 42.857 0.00 0.0 0.00 1.40 F
1984 2312 2.801679 TGTTCGACGGCTTTTATTTCGT 59.198 40.909 0.00 0.0 38.62 3.85 F
3144 3490 3.066380 TGTTATGCATATGTAGGCTGCG 58.934 45.455 7.36 0.0 38.75 5.18 F
5114 9574 1.029408 TGTGTTCCCTGTGTGTGTGC 61.029 55.000 0.00 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 2496 2.929531 TTCAACTTCTTTTGCGCACA 57.070 40.000 11.12 0.0 0.00 4.57 R
2895 3241 0.465097 GATGGGGTGAGTGCCATCTG 60.465 60.000 0.00 0.0 36.92 2.90 R
3617 3963 2.028020 AGCAAGGTAAGGTGTGACTAGC 60.028 50.000 0.00 0.0 0.00 3.42 R
3673 4019 6.672218 TGTTGAGAGAAATATCTTAGTGGGGA 59.328 38.462 0.00 0.0 35.54 4.81 R
4323 8772 5.938125 AGCAACCGATTAGTGTTCTACATTT 59.062 36.000 0.00 0.0 0.00 2.32 R
4440 8900 5.017294 TCAGACACGTTGCCATGATTATA 57.983 39.130 0.00 0.0 0.00 0.98 R
4598 9058 7.530426 AAATTTCCAAGTAAAGCAGATCACT 57.470 32.000 0.00 0.0 0.00 3.41 R
4900 9360 4.689062 AGATCCAAACTAGAGGACCTCAA 58.311 43.478 23.60 0.0 36.60 3.02 R
5619 10079 0.534412 CCCTCGCTGATTCTGTCTGT 59.466 55.000 0.00 0.0 0.00 3.41 R
6784 13251 0.398381 GAGAGCCACCCCTGAGAGAT 60.398 60.000 0.00 0.0 0.00 2.75 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
35 36 2.417379 CGAACTCCATCCTTCACATCGT 60.417 50.000 0.00 0.00 0.00 3.73
65 66 2.749076 TCATGCTTTGTGAATCCTTCCG 59.251 45.455 0.00 0.00 0.00 4.30
130 131 2.515057 GTGGTGTGGTGCGGACAA 60.515 61.111 9.96 0.00 0.00 3.18
135 136 3.698463 GTGGTGCGGACAACGTCG 61.698 66.667 9.96 0.00 46.52 5.12
136 137 3.902086 TGGTGCGGACAACGTCGA 61.902 61.111 9.96 0.00 46.52 4.20
156 157 2.729028 AGCCGCACTTAAATACCCAT 57.271 45.000 0.00 0.00 0.00 4.00
164 165 2.585432 ACTTAAATACCCATGGGCAGGT 59.415 45.455 31.73 14.08 40.31 4.00
198 199 1.683011 CCTCCTTTCAATCCGGTGCAT 60.683 52.381 0.00 0.00 0.00 3.96
216 217 2.838693 GAGTCGGGGTAGGCTCCC 60.839 72.222 12.14 12.14 46.31 4.30
248 488 2.609350 CCGAAATTGCATTGAAGTGGG 58.391 47.619 0.00 0.00 0.00 4.61
271 511 2.428085 TTCGCCGATTCATCCGGGA 61.428 57.895 0.00 0.00 46.55 5.14
296 537 1.003928 TGCTCTGGCTGACATCATGTT 59.996 47.619 0.00 0.00 39.59 2.71
297 538 1.400846 GCTCTGGCTGACATCATGTTG 59.599 52.381 2.12 2.12 35.22 3.33
300 541 2.038820 TCTGGCTGACATCATGTTGTGA 59.961 45.455 14.06 5.05 42.06 3.58
321 562 1.227118 TCACGCACGCTCTGAAACA 60.227 52.632 0.00 0.00 0.00 2.83
322 563 0.808060 TCACGCACGCTCTGAAACAA 60.808 50.000 0.00 0.00 0.00 2.83
332 573 2.808543 GCTCTGAAACAACTTGACCGAT 59.191 45.455 0.00 0.00 0.00 4.18
406 683 1.303091 ACTTGCGTCCGGTTTATGGC 61.303 55.000 0.00 0.00 0.00 4.40
438 752 0.661552 CGTGTCCGTAGACCGATGAT 59.338 55.000 0.00 0.00 42.81 2.45
460 774 2.036217 CATCGCGTTGGATTATTTGCG 58.964 47.619 5.77 0.00 46.27 4.85
495 809 3.280295 TCGGTCCAAAAGTTTACTTGCA 58.720 40.909 0.00 0.00 36.12 4.08
509 823 0.971386 CTTGCATTTTGAGGGTGCCT 59.029 50.000 0.00 0.00 38.06 4.75
510 824 1.345415 CTTGCATTTTGAGGGTGCCTT 59.655 47.619 0.00 0.00 38.06 4.35
511 825 2.300956 TGCATTTTGAGGGTGCCTTA 57.699 45.000 0.00 0.00 38.06 2.69
512 826 2.603021 TGCATTTTGAGGGTGCCTTAA 58.397 42.857 0.00 0.00 38.06 1.85
513 827 2.562298 TGCATTTTGAGGGTGCCTTAAG 59.438 45.455 0.00 0.00 38.06 1.85
514 828 2.094026 GCATTTTGAGGGTGCCTTAAGG 60.094 50.000 17.81 17.81 30.89 2.69
528 842 4.608948 CCTTAAGGCTAGTCATAGTGGG 57.391 50.000 9.00 0.00 0.00 4.61
529 843 4.223953 CCTTAAGGCTAGTCATAGTGGGA 58.776 47.826 9.00 0.00 0.00 4.37
530 844 4.654262 CCTTAAGGCTAGTCATAGTGGGAA 59.346 45.833 9.00 0.00 0.00 3.97
531 845 5.221541 CCTTAAGGCTAGTCATAGTGGGAAG 60.222 48.000 9.00 0.00 0.00 3.46
532 846 3.406512 AGGCTAGTCATAGTGGGAAGT 57.593 47.619 0.00 0.00 0.00 3.01
533 847 4.537945 AGGCTAGTCATAGTGGGAAGTA 57.462 45.455 0.00 0.00 0.00 2.24
534 848 4.880164 AGGCTAGTCATAGTGGGAAGTAA 58.120 43.478 0.00 0.00 0.00 2.24
535 849 4.650131 AGGCTAGTCATAGTGGGAAGTAAC 59.350 45.833 0.00 0.00 0.00 2.50
536 850 4.650131 GGCTAGTCATAGTGGGAAGTAACT 59.350 45.833 0.00 0.00 0.00 2.24
537 851 5.128991 GGCTAGTCATAGTGGGAAGTAACTT 59.871 44.000 0.00 0.00 0.00 2.66
538 852 6.323225 GGCTAGTCATAGTGGGAAGTAACTTA 59.677 42.308 0.00 0.00 0.00 2.24
539 853 7.427214 GCTAGTCATAGTGGGAAGTAACTTAG 58.573 42.308 0.00 0.00 0.00 2.18
540 854 7.284944 GCTAGTCATAGTGGGAAGTAACTTAGA 59.715 40.741 0.00 0.00 0.00 2.10
541 855 7.407393 AGTCATAGTGGGAAGTAACTTAGAC 57.593 40.000 0.00 0.00 33.07 2.59
542 856 7.183460 AGTCATAGTGGGAAGTAACTTAGACT 58.817 38.462 0.00 0.00 35.89 3.24
543 857 8.334734 AGTCATAGTGGGAAGTAACTTAGACTA 58.665 37.037 0.00 0.00 37.46 2.59
544 858 8.623030 GTCATAGTGGGAAGTAACTTAGACTAG 58.377 40.741 0.00 0.00 31.58 2.57
545 859 8.334734 TCATAGTGGGAAGTAACTTAGACTAGT 58.665 37.037 0.00 0.00 0.00 2.57
546 860 6.837471 AGTGGGAAGTAACTTAGACTAGTG 57.163 41.667 0.00 0.00 0.00 2.74
547 861 6.313324 AGTGGGAAGTAACTTAGACTAGTGT 58.687 40.000 0.00 0.00 0.00 3.55
548 862 6.433716 AGTGGGAAGTAACTTAGACTAGTGTC 59.566 42.308 0.00 0.00 43.22 3.67
560 874 3.575630 GACTAGTGTCTTGCGAATGACA 58.424 45.455 8.01 8.01 40.39 3.58
565 879 3.660501 TGTCTTGCGAATGACACTAGT 57.339 42.857 8.01 0.00 38.15 2.57
566 880 3.575630 TGTCTTGCGAATGACACTAGTC 58.424 45.455 8.01 0.00 45.19 2.59
567 881 3.255888 TGTCTTGCGAATGACACTAGTCT 59.744 43.478 8.01 0.00 45.20 3.24
568 882 4.457949 TGTCTTGCGAATGACACTAGTCTA 59.542 41.667 8.01 0.00 45.20 2.59
569 883 5.125578 TGTCTTGCGAATGACACTAGTCTAT 59.874 40.000 8.01 0.00 45.20 1.98
570 884 5.457148 GTCTTGCGAATGACACTAGTCTATG 59.543 44.000 4.57 0.00 45.20 2.23
571 885 4.983671 TGCGAATGACACTAGTCTATGT 57.016 40.909 0.00 0.00 45.20 2.29
572 886 5.324784 TGCGAATGACACTAGTCTATGTT 57.675 39.130 0.00 0.00 45.20 2.71
573 887 6.445357 TGCGAATGACACTAGTCTATGTTA 57.555 37.500 0.00 0.00 45.20 2.41
574 888 6.263344 TGCGAATGACACTAGTCTATGTTAC 58.737 40.000 0.00 0.00 45.20 2.50
575 889 6.095021 TGCGAATGACACTAGTCTATGTTACT 59.905 38.462 0.00 0.00 45.20 2.24
576 890 7.281549 TGCGAATGACACTAGTCTATGTTACTA 59.718 37.037 0.00 0.00 45.20 1.82
577 891 7.587028 GCGAATGACACTAGTCTATGTTACTAC 59.413 40.741 0.00 0.00 45.20 2.73
578 892 8.068977 CGAATGACACTAGTCTATGTTACTACC 58.931 40.741 0.00 0.00 45.20 3.18
579 893 9.122779 GAATGACACTAGTCTATGTTACTACCT 57.877 37.037 0.00 0.00 45.20 3.08
580 894 9.476928 AATGACACTAGTCTATGTTACTACCTT 57.523 33.333 0.00 0.00 45.20 3.50
581 895 8.874744 TGACACTAGTCTATGTTACTACCTTT 57.125 34.615 0.00 0.00 45.20 3.11
582 896 9.964354 TGACACTAGTCTATGTTACTACCTTTA 57.036 33.333 0.00 0.00 45.20 1.85
589 903 9.417561 AGTCTATGTTACTACCTTTATAGTGCA 57.582 33.333 0.00 0.00 36.09 4.57
594 908 8.542497 TGTTACTACCTTTATAGTGCAAAGTG 57.458 34.615 0.00 0.00 36.09 3.16
595 909 8.152246 TGTTACTACCTTTATAGTGCAAAGTGT 58.848 33.333 0.00 0.00 36.09 3.55
596 910 8.996271 GTTACTACCTTTATAGTGCAAAGTGTT 58.004 33.333 0.00 0.00 36.09 3.32
602 916 9.953565 ACCTTTATAGTGCAAAGTGTTATAGAA 57.046 29.630 0.00 0.00 32.23 2.10
641 955 9.799106 ATGGTTGCATTTATTAGCTTATAGACT 57.201 29.630 0.00 0.00 0.00 3.24
642 956 9.627123 TGGTTGCATTTATTAGCTTATAGACTT 57.373 29.630 0.00 0.00 0.00 3.01
672 986 7.624360 TTTTTGAGAAATACTATGCGATGGT 57.376 32.000 0.00 0.00 0.00 3.55
673 987 8.725405 TTTTTGAGAAATACTATGCGATGGTA 57.275 30.769 0.00 0.00 0.00 3.25
674 988 8.725405 TTTTGAGAAATACTATGCGATGGTAA 57.275 30.769 0.00 0.00 29.82 2.85
675 989 7.709269 TTGAGAAATACTATGCGATGGTAAC 57.291 36.000 0.00 0.00 29.82 2.50
720 1034 7.907214 TTTCTTTCCTCATTAACTAGCTGTC 57.093 36.000 0.00 0.00 0.00 3.51
721 1035 6.605471 TCTTTCCTCATTAACTAGCTGTCA 57.395 37.500 0.00 0.00 0.00 3.58
722 1036 7.187824 TCTTTCCTCATTAACTAGCTGTCAT 57.812 36.000 0.00 0.00 0.00 3.06
723 1037 8.306313 TCTTTCCTCATTAACTAGCTGTCATA 57.694 34.615 0.00 0.00 0.00 2.15
724 1038 8.928448 TCTTTCCTCATTAACTAGCTGTCATAT 58.072 33.333 0.00 0.00 0.00 1.78
728 1042 8.307483 TCCTCATTAACTAGCTGTCATATAAGC 58.693 37.037 0.00 0.00 39.82 3.09
729 1043 8.090831 CCTCATTAACTAGCTGTCATATAAGCA 58.909 37.037 0.00 0.00 42.06 3.91
730 1044 9.481340 CTCATTAACTAGCTGTCATATAAGCAA 57.519 33.333 0.00 0.00 42.06 3.91
731 1045 9.830975 TCATTAACTAGCTGTCATATAAGCAAA 57.169 29.630 0.00 0.00 42.06 3.68
736 1050 8.511604 ACTAGCTGTCATATAAGCAAATTTGT 57.488 30.769 19.03 3.40 42.06 2.83
737 1051 8.616076 ACTAGCTGTCATATAAGCAAATTTGTC 58.384 33.333 19.03 11.45 42.06 3.18
738 1052 7.636150 AGCTGTCATATAAGCAAATTTGTCT 57.364 32.000 19.03 13.38 42.06 3.41
739 1053 8.059798 AGCTGTCATATAAGCAAATTTGTCTT 57.940 30.769 22.55 22.55 42.06 3.01
740 1054 7.972277 AGCTGTCATATAAGCAAATTTGTCTTG 59.028 33.333 25.23 15.83 42.06 3.02
741 1055 7.970061 GCTGTCATATAAGCAAATTTGTCTTGA 59.030 33.333 25.23 17.19 39.31 3.02
742 1056 9.844790 CTGTCATATAAGCAAATTTGTCTTGAA 57.155 29.630 25.23 17.72 0.00 2.69
771 1085 8.712285 TGTTATGTTACTTGCTATGTTACTCC 57.288 34.615 0.00 0.00 0.00 3.85
772 1086 7.767198 TGTTATGTTACTTGCTATGTTACTCCC 59.233 37.037 0.00 0.00 0.00 4.30
773 1087 5.748670 TGTTACTTGCTATGTTACTCCCA 57.251 39.130 0.00 0.00 0.00 4.37
774 1088 5.484715 TGTTACTTGCTATGTTACTCCCAC 58.515 41.667 0.00 0.00 0.00 4.61
775 1089 3.629142 ACTTGCTATGTTACTCCCACC 57.371 47.619 0.00 0.00 0.00 4.61
776 1090 2.910319 ACTTGCTATGTTACTCCCACCA 59.090 45.455 0.00 0.00 0.00 4.17
777 1091 3.523564 ACTTGCTATGTTACTCCCACCAT 59.476 43.478 0.00 0.00 0.00 3.55
778 1092 3.558931 TGCTATGTTACTCCCACCATG 57.441 47.619 0.00 0.00 0.00 3.66
779 1093 3.111484 TGCTATGTTACTCCCACCATGA 58.889 45.455 0.00 0.00 0.00 3.07
780 1094 3.118408 TGCTATGTTACTCCCACCATGAC 60.118 47.826 0.00 0.00 0.00 3.06
781 1095 3.744530 GCTATGTTACTCCCACCATGACC 60.745 52.174 0.00 0.00 0.00 4.02
782 1096 1.735926 TGTTACTCCCACCATGACCA 58.264 50.000 0.00 0.00 0.00 4.02
783 1097 1.628340 TGTTACTCCCACCATGACCAG 59.372 52.381 0.00 0.00 0.00 4.00
784 1098 0.618458 TTACTCCCACCATGACCAGC 59.382 55.000 0.00 0.00 0.00 4.85
805 1119 5.990668 AGCCTAACTGAAAATAGACCGAAT 58.009 37.500 0.00 0.00 0.00 3.34
810 1124 7.438459 CCTAACTGAAAATAGACCGAATCGAAT 59.562 37.037 3.36 0.00 0.00 3.34
813 1127 7.685594 ACTGAAAATAGACCGAATCGAATTTC 58.314 34.615 3.36 6.12 30.79 2.17
820 1135 3.361786 ACCGAATCGAATTTCCCCAAAT 58.638 40.909 3.36 0.00 33.27 2.32
855 1170 1.269723 CGGACCTGAAAGAAAAAGCCC 59.730 52.381 0.00 0.00 34.07 5.19
856 1171 1.269723 GGACCTGAAAGAAAAAGCCCG 59.730 52.381 0.00 0.00 34.07 6.13
858 1173 2.621526 GACCTGAAAGAAAAAGCCCGAA 59.378 45.455 0.00 0.00 34.07 4.30
859 1174 3.230976 ACCTGAAAGAAAAAGCCCGAAT 58.769 40.909 0.00 0.00 34.07 3.34
860 1175 3.641436 ACCTGAAAGAAAAAGCCCGAATT 59.359 39.130 0.00 0.00 34.07 2.17
861 1176 4.830600 ACCTGAAAGAAAAAGCCCGAATTA 59.169 37.500 0.00 0.00 34.07 1.40
862 1177 5.303333 ACCTGAAAGAAAAAGCCCGAATTAA 59.697 36.000 0.00 0.00 34.07 1.40
863 1178 6.183360 ACCTGAAAGAAAAAGCCCGAATTAAA 60.183 34.615 0.00 0.00 34.07 1.52
864 1179 6.145534 CCTGAAAGAAAAAGCCCGAATTAAAC 59.854 38.462 0.00 0.00 34.07 2.01
865 1180 5.688176 TGAAAGAAAAAGCCCGAATTAAACG 59.312 36.000 0.00 0.00 0.00 3.60
866 1181 8.931012 CTGAAAGAAAAAGCCCGAATTAAACGG 61.931 40.741 14.73 14.73 43.34 4.44
881 1196 0.399075 AACGGAGGTAAACACCCCTG 59.601 55.000 0.00 0.00 0.00 4.45
1138 1453 2.042831 GTGCTGCGGGCTCTGAATT 61.043 57.895 0.00 0.00 42.39 2.17
1190 1506 5.527033 AGAGCACTTTTCTCTTGCAAATTC 58.473 37.500 0.00 0.00 37.63 2.17
1195 1511 4.097892 ACTTTTCTCTTGCAAATTCGGTGT 59.902 37.500 0.00 0.00 0.00 4.16
1202 1518 3.296322 TGCAAATTCGGTGTGGAATTC 57.704 42.857 0.00 0.00 43.81 2.17
1212 1528 0.605319 TGTGGAATTCCTGTGCCGAC 60.605 55.000 24.73 13.13 36.82 4.79
1217 1533 3.078837 GGAATTCCTGTGCCGACTTTTA 58.921 45.455 17.73 0.00 0.00 1.52
1353 1672 2.501223 TACTCAAGTGCTTCGCCCCG 62.501 60.000 0.00 0.00 0.00 5.73
1523 1848 3.585289 TGGGTCTTCCTGTTAGCATTGTA 59.415 43.478 0.00 0.00 36.20 2.41
1868 2196 1.370587 GACGCCGCTGAGTAGAGACT 61.371 60.000 0.00 0.00 39.20 3.24
1973 2301 1.155424 TCAACAAGGTGTTCGACGGC 61.155 55.000 0.00 0.00 38.77 5.68
1974 2302 1.145377 AACAAGGTGTTCGACGGCT 59.855 52.632 0.00 0.00 35.27 5.52
1975 2303 0.463116 AACAAGGTGTTCGACGGCTT 60.463 50.000 0.00 0.00 35.27 4.35
1976 2304 0.463116 ACAAGGTGTTCGACGGCTTT 60.463 50.000 0.00 0.00 0.00 3.51
1977 2305 0.661020 CAAGGTGTTCGACGGCTTTT 59.339 50.000 0.00 0.00 0.00 2.27
1978 2306 1.868498 CAAGGTGTTCGACGGCTTTTA 59.132 47.619 0.00 0.00 0.00 1.52
1979 2307 2.467566 AGGTGTTCGACGGCTTTTAT 57.532 45.000 0.00 0.00 0.00 1.40
1980 2308 2.774687 AGGTGTTCGACGGCTTTTATT 58.225 42.857 0.00 0.00 0.00 1.40
1981 2309 3.143728 AGGTGTTCGACGGCTTTTATTT 58.856 40.909 0.00 0.00 0.00 1.40
1982 2310 3.187842 AGGTGTTCGACGGCTTTTATTTC 59.812 43.478 0.00 0.00 0.00 2.17
1983 2311 3.150731 GTGTTCGACGGCTTTTATTTCG 58.849 45.455 0.00 0.00 0.00 3.46
1984 2312 2.801679 TGTTCGACGGCTTTTATTTCGT 59.198 40.909 0.00 0.00 38.62 3.85
1985 2313 3.248125 TGTTCGACGGCTTTTATTTCGTT 59.752 39.130 0.00 0.00 35.91 3.85
1986 2314 4.213674 GTTCGACGGCTTTTATTTCGTTT 58.786 39.130 0.00 0.00 35.91 3.60
1987 2315 4.471157 TCGACGGCTTTTATTTCGTTTT 57.529 36.364 0.00 0.00 35.91 2.43
1988 2316 4.212911 TCGACGGCTTTTATTTCGTTTTG 58.787 39.130 0.00 0.00 35.91 2.44
2013 2341 6.554334 AAAAGAAAGCAATTAGTCACGCTA 57.446 33.333 0.00 0.00 33.45 4.26
2047 2375 3.718434 AGGGCAATCTGAGGATACATGAA 59.282 43.478 0.00 0.00 41.41 2.57
2091 2419 3.194755 TGGAGCAGCGAAGTGAATTAGTA 59.805 43.478 0.00 0.00 0.00 1.82
2092 2420 3.799420 GGAGCAGCGAAGTGAATTAGTAG 59.201 47.826 0.00 0.00 0.00 2.57
2093 2421 4.425520 GAGCAGCGAAGTGAATTAGTAGT 58.574 43.478 0.00 0.00 0.00 2.73
2094 2422 4.177026 AGCAGCGAAGTGAATTAGTAGTG 58.823 43.478 0.00 0.00 0.00 2.74
2095 2423 3.927142 GCAGCGAAGTGAATTAGTAGTGT 59.073 43.478 0.00 0.00 0.00 3.55
2096 2424 4.389077 GCAGCGAAGTGAATTAGTAGTGTT 59.611 41.667 0.00 0.00 0.00 3.32
2097 2425 5.107065 GCAGCGAAGTGAATTAGTAGTGTTT 60.107 40.000 0.00 0.00 0.00 2.83
2098 2426 6.565999 GCAGCGAAGTGAATTAGTAGTGTTTT 60.566 38.462 0.00 0.00 0.00 2.43
2099 2427 7.352739 CAGCGAAGTGAATTAGTAGTGTTTTT 58.647 34.615 0.00 0.00 0.00 1.94
2168 2496 4.289672 TGTTCTGCTCCCCTTCTTTAATCT 59.710 41.667 0.00 0.00 0.00 2.40
2231 2567 4.771590 TTTTCTGAATCTGATTGCGCTT 57.228 36.364 9.73 0.00 0.00 4.68
2407 2747 8.523915 AAATATGCAAATCTGTACCAAGATGA 57.476 30.769 0.00 0.00 36.99 2.92
2739 3080 4.820716 TCTATACAACCCGCTCTAGTCTTC 59.179 45.833 0.00 0.00 0.00 2.87
2803 3144 3.956199 CCATGCCAGAAGGTTGTTATCAT 59.044 43.478 0.00 0.00 37.19 2.45
2895 3241 4.692625 CGGTAATCCTGATTGATGACCATC 59.307 45.833 8.03 3.17 43.91 3.51
2925 3271 5.178797 CACTCACCCCATCTACAGTTTTAG 58.821 45.833 0.00 0.00 0.00 1.85
3058 3404 5.841267 ATGCCCCTTTTGTTTATCCTTTT 57.159 34.783 0.00 0.00 0.00 2.27
3144 3490 3.066380 TGTTATGCATATGTAGGCTGCG 58.934 45.455 7.36 0.00 38.75 5.18
3631 3977 3.389983 AGTTGGTTGCTAGTCACACCTTA 59.610 43.478 13.73 5.73 31.46 2.69
3642 3988 4.579869 AGTCACACCTTACCTTGCTATTG 58.420 43.478 0.00 0.00 0.00 1.90
3810 4156 9.347934 CATGCATGCATGTAAAAATTTCATTTT 57.652 25.926 40.30 11.70 46.20 1.82
3875 4221 8.859090 ACTATTGTTTCAAGAATTCATGTTCCA 58.141 29.630 8.44 2.12 0.00 3.53
4440 8900 9.803315 GACACTGGATTTTTCTAAGAAAAACTT 57.197 29.630 0.00 0.00 42.04 2.66
4900 9360 4.456280 TTCACTCATCGCTTACATCACT 57.544 40.909 0.00 0.00 0.00 3.41
5010 9470 4.507710 ACTTGTGATATGCGAGAACATGT 58.492 39.130 0.00 0.00 0.00 3.21
5019 9479 2.094026 TGCGAGAACATGTGTCTAGCAT 60.094 45.455 26.08 2.73 37.24 3.79
5113 9573 1.458398 TTGTGTTCCCTGTGTGTGTG 58.542 50.000 0.00 0.00 0.00 3.82
5114 9574 1.029408 TGTGTTCCCTGTGTGTGTGC 61.029 55.000 0.00 0.00 0.00 4.57
5619 10079 3.211288 GCTAGAGCCGAGCTTGGA 58.789 61.111 25.25 1.06 39.88 3.53
5880 10340 1.067142 ACGCGCAAGAATGACTAGGAA 60.067 47.619 5.73 0.00 43.02 3.36
5885 10345 3.536570 GCAAGAATGACTAGGAAGGTCC 58.463 50.000 0.00 0.00 36.58 4.46
5886 10346 3.786635 CAAGAATGACTAGGAAGGTCCG 58.213 50.000 0.00 0.00 42.75 4.79
5898 10358 2.161030 GAAGGTCCGTGTGAGTCTAGT 58.839 52.381 0.00 0.00 0.00 2.57
5922 10382 2.564504 ACTCTGATGCAAGTGCTACTGA 59.435 45.455 4.69 7.13 42.66 3.41
5991 10451 5.367945 TTGTGGTTAAGAGACAACCTTCT 57.632 39.130 5.89 0.00 44.83 2.85
6073 10533 2.447047 AGGGGATGGTCTCTTTGTGTTT 59.553 45.455 0.00 0.00 0.00 2.83
6074 10534 2.558359 GGGGATGGTCTCTTTGTGTTTG 59.442 50.000 0.00 0.00 0.00 2.93
6075 10535 3.222603 GGGATGGTCTCTTTGTGTTTGT 58.777 45.455 0.00 0.00 0.00 2.83
6168 12574 2.700897 TGTTCAGGGCCTAAGATCTAGC 59.299 50.000 5.28 0.00 0.00 3.42
6264 12675 2.168728 CTCGACTCCCTCCCCTAAAAAG 59.831 54.545 0.00 0.00 0.00 2.27
6644 13057 1.653094 GATGAAATGGACGCGCCCAA 61.653 55.000 20.71 1.06 40.04 4.12
6683 13096 2.202878 ATCCATTCGCGACCACGG 60.203 61.111 9.15 7.17 40.15 4.94
6802 13269 0.043940 AATCTCTCAGGGGTGGCTCT 59.956 55.000 0.00 0.00 0.00 4.09
6804 13271 1.305633 CTCTCAGGGGTGGCTCTCA 60.306 63.158 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.348064 TGTGAAGGATGGAGTTCGGT 58.652 50.000 0.00 0.00 0.00 4.69
15 16 2.932614 CACGATGTGAAGGATGGAGTTC 59.067 50.000 0.00 0.00 35.23 3.01
35 36 2.426381 TCACAAAGCATGACAAAGCACA 59.574 40.909 0.00 0.00 0.00 4.57
42 43 4.771590 GAAGGATTCACAAAGCATGACA 57.228 40.909 0.00 0.00 46.62 3.58
130 131 0.598158 TTTAAGTGCGGCTTCGACGT 60.598 50.000 0.00 0.00 35.91 4.34
135 136 2.361789 TGGGTATTTAAGTGCGGCTTC 58.638 47.619 0.00 0.00 38.57 3.86
136 137 2.500392 TGGGTATTTAAGTGCGGCTT 57.500 45.000 0.00 0.00 41.05 4.35
156 157 4.308458 CGTCCGTTCACCTGCCCA 62.308 66.667 0.00 0.00 0.00 5.36
164 165 2.028484 GAGGTGCACGTCCGTTCA 59.972 61.111 25.46 0.00 0.00 3.18
198 199 2.043248 GGAGCCTACCCCGACTCA 60.043 66.667 0.00 0.00 0.00 3.41
226 227 2.609984 CCACTTCAATGCAATTTCGGCA 60.610 45.455 0.00 0.00 46.66 5.69
261 501 2.435938 GCAACGCTCCCGGATGAA 60.436 61.111 0.73 0.00 39.22 2.57
271 511 2.358003 GTCAGCCAGAGCAACGCT 60.358 61.111 0.00 0.00 43.88 5.07
296 537 1.949133 GAGCGTGCGTGACTTCACA 60.949 57.895 9.94 0.00 46.75 3.58
297 538 1.661821 AGAGCGTGCGTGACTTCAC 60.662 57.895 0.00 0.00 43.15 3.18
300 541 0.529773 TTTCAGAGCGTGCGTGACTT 60.530 50.000 0.19 0.00 0.00 3.01
308 549 2.286418 GGTCAAGTTGTTTCAGAGCGTG 60.286 50.000 2.11 0.00 0.00 5.34
310 551 1.070577 CGGTCAAGTTGTTTCAGAGCG 60.071 52.381 2.11 0.00 42.47 5.03
321 562 4.690748 CCGCATATTCATATCGGTCAAGTT 59.309 41.667 0.00 0.00 33.15 2.66
322 563 4.245660 CCGCATATTCATATCGGTCAAGT 58.754 43.478 0.00 0.00 33.15 3.16
373 615 1.057208 CAAGTCACACGTATGCGCG 59.943 57.895 0.00 0.00 42.83 6.86
406 683 2.022129 GACACGTCCGCTTGTCTGG 61.022 63.158 0.00 0.00 39.77 3.86
438 752 2.794282 GCAAATAATCCAACGCGATGCA 60.794 45.455 15.93 0.00 0.00 3.96
484 798 4.501400 GCACCCTCAAAATGCAAGTAAACT 60.501 41.667 0.00 0.00 39.23 2.66
509 823 5.278061 ACTTCCCACTATGACTAGCCTTAA 58.722 41.667 0.00 0.00 0.00 1.85
510 824 4.880164 ACTTCCCACTATGACTAGCCTTA 58.120 43.478 0.00 0.00 0.00 2.69
511 825 3.725634 ACTTCCCACTATGACTAGCCTT 58.274 45.455 0.00 0.00 0.00 4.35
512 826 3.406512 ACTTCCCACTATGACTAGCCT 57.593 47.619 0.00 0.00 0.00 4.58
513 827 4.650131 AGTTACTTCCCACTATGACTAGCC 59.350 45.833 0.00 0.00 0.00 3.93
514 828 5.855740 AGTTACTTCCCACTATGACTAGC 57.144 43.478 0.00 0.00 0.00 3.42
515 829 8.623030 GTCTAAGTTACTTCCCACTATGACTAG 58.377 40.741 0.00 0.00 0.00 2.57
516 830 8.334734 AGTCTAAGTTACTTCCCACTATGACTA 58.665 37.037 0.00 0.00 35.61 2.59
517 831 7.183460 AGTCTAAGTTACTTCCCACTATGACT 58.817 38.462 0.00 1.98 34.02 3.41
518 832 7.407393 AGTCTAAGTTACTTCCCACTATGAC 57.593 40.000 0.00 0.00 0.00 3.06
519 833 8.334734 ACTAGTCTAAGTTACTTCCCACTATGA 58.665 37.037 0.00 0.00 0.00 2.15
520 834 8.407064 CACTAGTCTAAGTTACTTCCCACTATG 58.593 40.741 0.00 4.33 0.00 2.23
521 835 8.114743 ACACTAGTCTAAGTTACTTCCCACTAT 58.885 37.037 0.00 0.00 0.00 2.12
522 836 7.465116 ACACTAGTCTAAGTTACTTCCCACTA 58.535 38.462 0.00 5.84 0.00 2.74
523 837 6.313324 ACACTAGTCTAAGTTACTTCCCACT 58.687 40.000 0.00 4.98 0.00 4.00
524 838 6.587206 ACACTAGTCTAAGTTACTTCCCAC 57.413 41.667 0.00 0.00 0.00 4.61
525 839 6.830873 GACACTAGTCTAAGTTACTTCCCA 57.169 41.667 0.00 0.00 41.64 4.37
545 859 3.255888 AGACTAGTGTCATTCGCAAGACA 59.744 43.478 0.00 0.00 46.27 3.41
546 860 3.839293 AGACTAGTGTCATTCGCAAGAC 58.161 45.455 0.00 0.00 46.27 3.01
547 861 5.125578 ACATAGACTAGTGTCATTCGCAAGA 59.874 40.000 0.00 0.00 45.46 3.02
548 862 5.344066 ACATAGACTAGTGTCATTCGCAAG 58.656 41.667 0.00 0.00 45.20 4.01
549 863 5.324784 ACATAGACTAGTGTCATTCGCAA 57.675 39.130 0.00 0.00 45.20 4.85
550 864 4.983671 ACATAGACTAGTGTCATTCGCA 57.016 40.909 0.00 0.00 45.20 5.10
551 865 6.496571 AGTAACATAGACTAGTGTCATTCGC 58.503 40.000 0.00 0.00 45.20 4.70
552 866 8.068977 GGTAGTAACATAGACTAGTGTCATTCG 58.931 40.741 0.00 0.00 45.20 3.34
553 867 9.122779 AGGTAGTAACATAGACTAGTGTCATTC 57.877 37.037 0.00 0.00 45.20 2.67
554 868 9.476928 AAGGTAGTAACATAGACTAGTGTCATT 57.523 33.333 0.00 0.00 45.20 2.57
555 869 9.476928 AAAGGTAGTAACATAGACTAGTGTCAT 57.523 33.333 0.00 0.00 45.20 3.06
556 870 8.874744 AAAGGTAGTAACATAGACTAGTGTCA 57.125 34.615 0.00 0.00 45.20 3.58
563 877 9.417561 TGCACTATAAAGGTAGTAACATAGACT 57.582 33.333 0.00 0.00 33.29 3.24
568 882 9.162764 CACTTTGCACTATAAAGGTAGTAACAT 57.837 33.333 0.00 0.00 38.99 2.71
569 883 8.152246 ACACTTTGCACTATAAAGGTAGTAACA 58.848 33.333 0.00 0.00 38.99 2.41
570 884 8.543862 ACACTTTGCACTATAAAGGTAGTAAC 57.456 34.615 0.00 0.00 38.99 2.50
576 890 9.953565 TTCTATAACACTTTGCACTATAAAGGT 57.046 29.630 0.00 0.00 38.99 3.50
615 929 9.799106 AGTCTATAAGCTAATAAATGCAACCAT 57.201 29.630 0.00 0.00 0.00 3.55
616 930 9.627123 AAGTCTATAAGCTAATAAATGCAACCA 57.373 29.630 0.00 0.00 0.00 3.67
648 962 7.624360 ACCATCGCATAGTATTTCTCAAAAA 57.376 32.000 0.00 0.00 0.00 1.94
649 963 8.609176 GTTACCATCGCATAGTATTTCTCAAAA 58.391 33.333 0.00 0.00 0.00 2.44
650 964 7.766738 TGTTACCATCGCATAGTATTTCTCAAA 59.233 33.333 0.00 0.00 0.00 2.69
651 965 7.269316 TGTTACCATCGCATAGTATTTCTCAA 58.731 34.615 0.00 0.00 0.00 3.02
652 966 6.811954 TGTTACCATCGCATAGTATTTCTCA 58.188 36.000 0.00 0.00 0.00 3.27
653 967 7.891183 ATGTTACCATCGCATAGTATTTCTC 57.109 36.000 0.00 0.00 0.00 2.87
654 968 9.944376 ATTATGTTACCATCGCATAGTATTTCT 57.056 29.630 0.00 0.00 32.29 2.52
664 978 9.811995 GGAGTAATATATTATGTTACCATCGCA 57.188 33.333 15.64 0.00 37.50 5.10
665 979 9.811995 TGGAGTAATATATTATGTTACCATCGC 57.188 33.333 15.64 6.78 37.50 4.58
694 1008 9.601217 GACAGCTAGTTAATGAGGAAAGAAATA 57.399 33.333 0.00 0.00 0.00 1.40
695 1009 8.103305 TGACAGCTAGTTAATGAGGAAAGAAAT 58.897 33.333 0.00 0.00 0.00 2.17
696 1010 7.450074 TGACAGCTAGTTAATGAGGAAAGAAA 58.550 34.615 0.00 0.00 0.00 2.52
697 1011 7.004555 TGACAGCTAGTTAATGAGGAAAGAA 57.995 36.000 0.00 0.00 0.00 2.52
698 1012 6.605471 TGACAGCTAGTTAATGAGGAAAGA 57.395 37.500 0.00 0.00 0.00 2.52
702 1016 8.307483 GCTTATATGACAGCTAGTTAATGAGGA 58.693 37.037 0.00 0.00 32.87 3.71
703 1017 8.090831 TGCTTATATGACAGCTAGTTAATGAGG 58.909 37.037 0.00 0.00 36.92 3.86
704 1018 9.481340 TTGCTTATATGACAGCTAGTTAATGAG 57.519 33.333 0.00 0.00 36.92 2.90
705 1019 9.830975 TTTGCTTATATGACAGCTAGTTAATGA 57.169 29.630 0.00 0.00 36.92 2.57
710 1024 8.960591 ACAAATTTGCTTATATGACAGCTAGTT 58.039 29.630 18.12 0.00 36.92 2.24
711 1025 8.511604 ACAAATTTGCTTATATGACAGCTAGT 57.488 30.769 18.12 0.00 36.92 2.57
712 1026 8.834465 AGACAAATTTGCTTATATGACAGCTAG 58.166 33.333 18.12 0.00 36.92 3.42
713 1027 8.737168 AGACAAATTTGCTTATATGACAGCTA 57.263 30.769 18.12 0.00 36.92 3.32
714 1028 7.636150 AGACAAATTTGCTTATATGACAGCT 57.364 32.000 18.12 0.00 36.92 4.24
715 1029 7.970061 TCAAGACAAATTTGCTTATATGACAGC 59.030 33.333 18.12 0.00 36.49 4.40
716 1030 9.844790 TTCAAGACAAATTTGCTTATATGACAG 57.155 29.630 18.12 7.94 0.00 3.51
745 1059 9.326413 GGAGTAACATAGCAAGTAACATAACAT 57.674 33.333 0.00 0.00 0.00 2.71
746 1060 7.767198 GGGAGTAACATAGCAAGTAACATAACA 59.233 37.037 0.00 0.00 0.00 2.41
747 1061 7.767198 TGGGAGTAACATAGCAAGTAACATAAC 59.233 37.037 0.00 0.00 0.00 1.89
748 1062 7.767198 GTGGGAGTAACATAGCAAGTAACATAA 59.233 37.037 0.00 0.00 0.00 1.90
749 1063 7.270047 GTGGGAGTAACATAGCAAGTAACATA 58.730 38.462 0.00 0.00 0.00 2.29
750 1064 6.113411 GTGGGAGTAACATAGCAAGTAACAT 58.887 40.000 0.00 0.00 0.00 2.71
751 1065 5.484715 GTGGGAGTAACATAGCAAGTAACA 58.515 41.667 0.00 0.00 0.00 2.41
752 1066 4.874396 GGTGGGAGTAACATAGCAAGTAAC 59.126 45.833 0.00 0.00 0.00 2.50
753 1067 4.532916 TGGTGGGAGTAACATAGCAAGTAA 59.467 41.667 0.00 0.00 0.00 2.24
754 1068 4.098155 TGGTGGGAGTAACATAGCAAGTA 58.902 43.478 0.00 0.00 0.00 2.24
755 1069 2.910319 TGGTGGGAGTAACATAGCAAGT 59.090 45.455 0.00 0.00 0.00 3.16
756 1070 3.627395 TGGTGGGAGTAACATAGCAAG 57.373 47.619 0.00 0.00 0.00 4.01
757 1071 3.521531 TCATGGTGGGAGTAACATAGCAA 59.478 43.478 0.00 0.00 0.00 3.91
758 1072 3.111484 TCATGGTGGGAGTAACATAGCA 58.889 45.455 0.00 0.00 0.00 3.49
759 1073 3.467803 GTCATGGTGGGAGTAACATAGC 58.532 50.000 0.00 0.00 0.00 2.97
760 1074 3.454447 TGGTCATGGTGGGAGTAACATAG 59.546 47.826 0.00 0.00 0.00 2.23
761 1075 3.454447 CTGGTCATGGTGGGAGTAACATA 59.546 47.826 0.00 0.00 0.00 2.29
762 1076 2.239654 CTGGTCATGGTGGGAGTAACAT 59.760 50.000 0.00 0.00 0.00 2.71
763 1077 1.628340 CTGGTCATGGTGGGAGTAACA 59.372 52.381 0.00 0.00 0.00 2.41
764 1078 1.679032 GCTGGTCATGGTGGGAGTAAC 60.679 57.143 0.00 0.00 0.00 2.50
765 1079 0.618458 GCTGGTCATGGTGGGAGTAA 59.382 55.000 0.00 0.00 0.00 2.24
766 1080 1.271840 GGCTGGTCATGGTGGGAGTA 61.272 60.000 0.00 0.00 0.00 2.59
767 1081 2.606587 GGCTGGTCATGGTGGGAGT 61.607 63.158 0.00 0.00 0.00 3.85
768 1082 0.982852 TAGGCTGGTCATGGTGGGAG 60.983 60.000 0.00 0.00 0.00 4.30
769 1083 0.548926 TTAGGCTGGTCATGGTGGGA 60.549 55.000 0.00 0.00 0.00 4.37
770 1084 0.394352 GTTAGGCTGGTCATGGTGGG 60.394 60.000 0.00 0.00 0.00 4.61
771 1085 0.620556 AGTTAGGCTGGTCATGGTGG 59.379 55.000 0.00 0.00 0.00 4.61
772 1086 1.278985 TCAGTTAGGCTGGTCATGGTG 59.721 52.381 0.00 0.00 45.08 4.17
773 1087 1.656587 TCAGTTAGGCTGGTCATGGT 58.343 50.000 0.00 0.00 45.08 3.55
774 1088 2.787473 TTCAGTTAGGCTGGTCATGG 57.213 50.000 0.00 0.00 45.08 3.66
775 1089 6.037610 GTCTATTTTCAGTTAGGCTGGTCATG 59.962 42.308 0.00 0.00 45.08 3.07
776 1090 6.116126 GTCTATTTTCAGTTAGGCTGGTCAT 58.884 40.000 0.00 0.00 45.08 3.06
777 1091 5.488341 GTCTATTTTCAGTTAGGCTGGTCA 58.512 41.667 0.00 0.00 45.08 4.02
778 1092 4.876679 GGTCTATTTTCAGTTAGGCTGGTC 59.123 45.833 0.00 0.00 45.08 4.02
779 1093 4.623171 CGGTCTATTTTCAGTTAGGCTGGT 60.623 45.833 0.00 0.00 45.08 4.00
780 1094 3.871594 CGGTCTATTTTCAGTTAGGCTGG 59.128 47.826 0.00 0.00 45.08 4.85
781 1095 4.755411 TCGGTCTATTTTCAGTTAGGCTG 58.245 43.478 0.00 0.00 46.34 4.85
782 1096 5.416271 TTCGGTCTATTTTCAGTTAGGCT 57.584 39.130 0.00 0.00 0.00 4.58
783 1097 5.050972 CGATTCGGTCTATTTTCAGTTAGGC 60.051 44.000 0.00 0.00 0.00 3.93
784 1098 6.270815 TCGATTCGGTCTATTTTCAGTTAGG 58.729 40.000 6.18 0.00 0.00 2.69
805 1119 5.623368 CGATTTTGGATTTGGGGAAATTCGA 60.623 40.000 0.00 0.00 35.07 3.71
810 1124 4.345257 TCAACGATTTTGGATTTGGGGAAA 59.655 37.500 0.00 0.00 0.00 3.13
813 1127 3.584834 GTCAACGATTTTGGATTTGGGG 58.415 45.455 0.00 0.00 0.00 4.96
855 1170 4.142838 GGGTGTTTACCTCCGTTTAATTCG 60.143 45.833 0.00 0.00 46.66 3.34
856 1171 4.156556 GGGGTGTTTACCTCCGTTTAATTC 59.843 45.833 0.00 0.00 46.66 2.17
858 1173 3.689347 GGGGTGTTTACCTCCGTTTAAT 58.311 45.455 0.00 0.00 46.66 1.40
859 1174 3.138884 GGGGTGTTTACCTCCGTTTAA 57.861 47.619 0.00 0.00 46.66 1.52
860 1175 2.857186 GGGGTGTTTACCTCCGTTTA 57.143 50.000 0.00 0.00 46.66 2.01
861 1176 3.731716 GGGGTGTTTACCTCCGTTT 57.268 52.632 0.00 0.00 46.66 3.60
867 1182 1.145571 TGAAGCAGGGGTGTTTACCT 58.854 50.000 0.00 0.00 46.66 3.08
868 1183 1.244816 GTGAAGCAGGGGTGTTTACC 58.755 55.000 0.00 0.00 46.76 2.85
869 1184 1.880027 CTGTGAAGCAGGGGTGTTTAC 59.120 52.381 0.00 0.00 41.42 2.01
881 1196 1.800586 TCGACTTGCAATCTGTGAAGC 59.199 47.619 0.00 0.00 0.00 3.86
1138 1453 5.957842 ATTGAAAGCTTAACATGACGGAA 57.042 34.783 0.00 0.00 0.00 4.30
1190 1506 1.586154 GGCACAGGAATTCCACACCG 61.586 60.000 26.22 11.07 38.89 4.94
1195 1511 0.400213 AAGTCGGCACAGGAATTCCA 59.600 50.000 26.22 0.39 38.89 3.53
1202 1518 2.482721 ACGAAATAAAAGTCGGCACAGG 59.517 45.455 0.00 0.00 41.56 4.00
1353 1672 1.017387 CCTCGCTTTGGAGTATTGCC 58.983 55.000 0.00 0.00 31.98 4.52
1523 1848 0.034059 CGTCAAAGAGTGGTGGAGCT 59.966 55.000 0.00 0.00 0.00 4.09
1868 2196 7.882791 ACATAACATGGAAATTCACTACTGACA 59.117 33.333 0.00 0.00 33.60 3.58
1979 2307 9.965748 CTAATTGCTTTCTTTTTCAAAACGAAA 57.034 25.926 12.52 12.52 41.95 3.46
1980 2308 9.145865 ACTAATTGCTTTCTTTTTCAAAACGAA 57.854 25.926 0.00 0.00 0.00 3.85
1981 2309 8.696410 ACTAATTGCTTTCTTTTTCAAAACGA 57.304 26.923 0.00 0.00 0.00 3.85
1982 2310 8.591312 TGACTAATTGCTTTCTTTTTCAAAACG 58.409 29.630 0.00 0.00 0.00 3.60
1983 2311 9.689075 GTGACTAATTGCTTTCTTTTTCAAAAC 57.311 29.630 0.00 0.00 0.00 2.43
1984 2312 8.591312 CGTGACTAATTGCTTTCTTTTTCAAAA 58.409 29.630 0.00 0.00 0.00 2.44
1985 2313 7.253950 GCGTGACTAATTGCTTTCTTTTTCAAA 60.254 33.333 0.00 0.00 0.00 2.69
1986 2314 6.198216 GCGTGACTAATTGCTTTCTTTTTCAA 59.802 34.615 0.00 0.00 0.00 2.69
1987 2315 5.685511 GCGTGACTAATTGCTTTCTTTTTCA 59.314 36.000 0.00 0.00 0.00 2.69
1988 2316 5.915196 AGCGTGACTAATTGCTTTCTTTTTC 59.085 36.000 0.00 0.00 32.89 2.29
2013 2341 6.351711 CCTCAGATTGCCCTTAGATCGAATAT 60.352 42.308 0.00 0.00 0.00 1.28
2047 2375 3.255642 AGCAACATACAAAGCGATTTGGT 59.744 39.130 27.82 14.70 36.30 3.67
2102 2430 9.968743 GCAATAAACACTACTAATTATATCCGC 57.031 33.333 0.00 0.00 0.00 5.54
2168 2496 2.929531 TTCAACTTCTTTTGCGCACA 57.070 40.000 11.12 0.00 0.00 4.57
2231 2567 6.041409 TGAAACTAATTCCATTGCCTTCACAA 59.959 34.615 0.00 0.00 37.22 3.33
2407 2747 6.147328 GCAGTGAGGTTTTAGAACTTATTCGT 59.853 38.462 0.00 0.00 40.04 3.85
2803 3144 8.615360 ATGCTTTTCTAGGCTATCAGGATATA 57.385 34.615 0.00 0.00 0.00 0.86
2895 3241 0.465097 GATGGGGTGAGTGCCATCTG 60.465 60.000 0.00 0.00 36.92 2.90
2925 3271 4.748600 GCCCTCGTAACCAGTTATATGAAC 59.251 45.833 0.00 0.00 0.00 3.18
3617 3963 2.028020 AGCAAGGTAAGGTGTGACTAGC 60.028 50.000 0.00 0.00 0.00 3.42
3673 4019 6.672218 TGTTGAGAGAAATATCTTAGTGGGGA 59.328 38.462 0.00 0.00 35.54 4.81
4323 8772 5.938125 AGCAACCGATTAGTGTTCTACATTT 59.062 36.000 0.00 0.00 0.00 2.32
4440 8900 5.017294 TCAGACACGTTGCCATGATTATA 57.983 39.130 0.00 0.00 0.00 0.98
4598 9058 7.530426 AAATTTCCAAGTAAAGCAGATCACT 57.470 32.000 0.00 0.00 0.00 3.41
4900 9360 4.689062 AGATCCAAACTAGAGGACCTCAA 58.311 43.478 23.60 0.00 36.60 3.02
5010 9470 1.205655 GTCTGACTGCCATGCTAGACA 59.794 52.381 0.00 0.00 35.75 3.41
5019 9479 1.979155 CTCGGAGGTCTGACTGCCA 60.979 63.158 7.85 1.04 0.00 4.92
5084 9544 1.152830 GGAACACAAAGCAGGGGGA 59.847 57.895 0.00 0.00 0.00 4.81
5114 9574 1.080569 GCGCAATGGTCAACCCTTG 60.081 57.895 0.30 11.53 42.30 3.61
5446 9906 5.500931 GCAGTACAACACGAGATTATTCAGC 60.501 44.000 0.00 0.00 0.00 4.26
5616 10076 1.203287 CTCGCTGATTCTGTCTGTCCA 59.797 52.381 0.00 0.00 0.00 4.02
5619 10079 0.534412 CCCTCGCTGATTCTGTCTGT 59.466 55.000 0.00 0.00 0.00 3.41
5880 10340 1.887198 CAACTAGACTCACACGGACCT 59.113 52.381 0.00 0.00 0.00 3.85
5898 10358 2.556144 AGCACTTGCATCAGAGTCAA 57.444 45.000 3.62 0.00 45.16 3.18
5922 10382 0.592637 TTGTCGTGTCGGTATGTCGT 59.407 50.000 0.00 0.00 0.00 4.34
6073 10533 5.316167 ACTGCAGTTCCAATCTTCATAACA 58.684 37.500 15.25 0.00 0.00 2.41
6074 10534 5.886960 ACTGCAGTTCCAATCTTCATAAC 57.113 39.130 15.25 0.00 0.00 1.89
6075 10535 6.489700 TGAAACTGCAGTTCCAATCTTCATAA 59.510 34.615 31.20 6.48 37.25 1.90
6168 12574 9.731819 AACAGTAGTAATACAACACGAGATATG 57.268 33.333 2.81 0.00 0.00 1.78
6644 13057 0.824759 GGAATAGAGTGGACAGCGGT 59.175 55.000 0.00 0.00 0.00 5.68
6683 13096 4.168291 CCGGCTGGAGCTCCTTCC 62.168 72.222 32.28 28.13 41.70 3.46
6784 13251 0.398381 GAGAGCCACCCCTGAGAGAT 60.398 60.000 0.00 0.00 0.00 2.75
6785 13252 1.000993 GAGAGCCACCCCTGAGAGA 59.999 63.158 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.