Multiple sequence alignment - TraesCS4A01G020100

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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 TraesCS4A01G020100 chr4A 100.000 4329 0 0 1 4329 13749495 13745167 0.000000e+00 7995
1 TraesCS4A01G020100 chr4A 86.802 197 24 2 3574 3768 618191528 618191332 7.290000e-53 219
2 TraesCS4A01G020100 chr4D 89.465 3047 179 73 578 3573 453329812 453332767 0.000000e+00 3718
3 TraesCS4A01G020100 chr4D 84.279 229 14 14 167 384 453329386 453329603 2.040000e-48 204
4 TraesCS4A01G020100 chr4B 91.066 2485 102 45 999 3443 567004315 567006719 0.000000e+00 3249
5 TraesCS4A01G020100 chr4B 76.578 491 51 28 37 473 567003358 567003838 1.220000e-50 211
6 TraesCS4A01G020100 chr1A 93.290 775 37 9 3569 4329 71442286 71443059 0.000000e+00 1129
7 TraesCS4A01G020100 chr5D 85.882 765 94 12 3573 4329 65107219 65106461 0.000000e+00 802
8 TraesCS4A01G020100 chr5D 88.571 280 27 5 3850 4127 62477573 62477297 6.940000e-88 335
9 TraesCS4A01G020100 chr5D 85.890 326 29 11 3573 3884 62477894 62477572 8.970000e-87 331
10 TraesCS4A01G020100 chr1D 84.746 767 78 20 3572 4329 432378957 432378221 0.000000e+00 732
11 TraesCS4A01G020100 chr2A 91.195 318 24 4 3573 3889 761485837 761485523 3.090000e-116 429
12 TraesCS4A01G020100 chr2A 86.269 386 35 12 3566 3936 41149819 41150201 1.870000e-108 403
13 TraesCS4A01G020100 chr5B 85.933 327 29 9 3573 3885 68050141 68050464 2.490000e-87 333
14 TraesCS4A01G020100 chr7D 85.714 196 27 1 3574 3768 85030769 85030574 5.670000e-49 206
15 TraesCS4A01G020100 chr6D 84.865 185 21 6 3574 3756 427748480 427748301 3.440000e-41 180
16 TraesCS4A01G020100 chr2B 77.007 274 48 12 3574 3835 94092332 94092062 4.510000e-30 143


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 TraesCS4A01G020100 chr4A 13745167 13749495 4328 True 7995 7995 100.0000 1 4329 1 chr4A.!!$R1 4328
1 TraesCS4A01G020100 chr4D 453329386 453332767 3381 False 1961 3718 86.8720 167 3573 2 chr4D.!!$F1 3406
2 TraesCS4A01G020100 chr4B 567003358 567006719 3361 False 1730 3249 83.8220 37 3443 2 chr4B.!!$F1 3406
3 TraesCS4A01G020100 chr1A 71442286 71443059 773 False 1129 1129 93.2900 3569 4329 1 chr1A.!!$F1 760
4 TraesCS4A01G020100 chr5D 65106461 65107219 758 True 802 802 85.8820 3573 4329 1 chr5D.!!$R1 756
5 TraesCS4A01G020100 chr5D 62477297 62477894 597 True 333 335 87.2305 3573 4127 2 chr5D.!!$R2 554
6 TraesCS4A01G020100 chr1D 432378221 432378957 736 True 732 732 84.7460 3572 4329 1 chr1D.!!$R1 757

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
22 23 0.031616 AGCCCCAAACAACCCTTGAA 60.032 50.0 0.00 0.0 0.00 2.69 F
571 672 0.033894 GTCCTCTCTCTCCGGGAAGT 60.034 60.0 0.00 0.0 0.00 3.01 F
1412 1561 0.031994 AACAATGGCGCCTGAACAAC 59.968 50.0 29.70 0.0 0.00 3.32 F
2088 2263 0.592637 TGAAGGCAAAGACATGTGCG 59.407 50.0 1.15 0.0 41.85 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 1542 0.031994 GTTGTTCAGGCGCCATTGTT 59.968 50.0 31.54 3.61 0.00 2.83 R
2359 2534 0.110328 CTCGCACTTCAAGCTGCAAG 60.110 55.0 1.02 0.00 32.57 4.01 R
2508 2683 0.245266 GCCTAGGGCGATTAGAGAGC 59.755 60.0 11.72 0.00 39.62 4.09 R
3514 3727 0.177604 GAGCTGGGACTGTCTGATGG 59.822 60.0 7.85 0.00 0.00 3.51 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
17 18 3.964108 AACAGCCCCAAACAACCC 58.036 55.556 0.00 0.00 0.00 4.11
18 19 1.313129 AACAGCCCCAAACAACCCT 59.687 52.632 0.00 0.00 0.00 4.34
19 20 0.326143 AACAGCCCCAAACAACCCTT 60.326 50.000 0.00 0.00 0.00 3.95
20 21 1.048160 ACAGCCCCAAACAACCCTTG 61.048 55.000 0.00 0.00 0.00 3.61
21 22 0.758685 CAGCCCCAAACAACCCTTGA 60.759 55.000 0.00 0.00 0.00 3.02
22 23 0.031616 AGCCCCAAACAACCCTTGAA 60.032 50.000 0.00 0.00 0.00 2.69
23 24 0.833949 GCCCCAAACAACCCTTGAAA 59.166 50.000 0.00 0.00 0.00 2.69
24 25 1.210722 GCCCCAAACAACCCTTGAAAA 59.789 47.619 0.00 0.00 0.00 2.29
25 26 2.356227 GCCCCAAACAACCCTTGAAAAA 60.356 45.455 0.00 0.00 0.00 1.94
54 55 4.867086 AGAGAAGAAGAACCCCAAACAAA 58.133 39.130 0.00 0.00 0.00 2.83
55 56 4.889995 AGAGAAGAAGAACCCCAAACAAAG 59.110 41.667 0.00 0.00 0.00 2.77
56 57 4.867086 AGAAGAAGAACCCCAAACAAAGA 58.133 39.130 0.00 0.00 0.00 2.52
57 58 4.645136 AGAAGAAGAACCCCAAACAAAGAC 59.355 41.667 0.00 0.00 0.00 3.01
58 59 3.976015 AGAAGAACCCCAAACAAAGACA 58.024 40.909 0.00 0.00 0.00 3.41
59 60 4.546674 AGAAGAACCCCAAACAAAGACAT 58.453 39.130 0.00 0.00 0.00 3.06
60 61 5.701224 AGAAGAACCCCAAACAAAGACATA 58.299 37.500 0.00 0.00 0.00 2.29
61 62 6.133356 AGAAGAACCCCAAACAAAGACATAA 58.867 36.000 0.00 0.00 0.00 1.90
63 64 6.994421 AGAACCCCAAACAAAGACATAATT 57.006 33.333 0.00 0.00 0.00 1.40
64 65 8.485578 AAGAACCCCAAACAAAGACATAATTA 57.514 30.769 0.00 0.00 0.00 1.40
65 66 8.485578 AGAACCCCAAACAAAGACATAATTAA 57.514 30.769 0.00 0.00 0.00 1.40
111 120 4.702131 AGGAATTAACACTGCTTGACCATC 59.298 41.667 0.00 0.00 0.00 3.51
114 123 2.592102 AACACTGCTTGACCATCCAT 57.408 45.000 0.00 0.00 0.00 3.41
115 124 1.830279 ACACTGCTTGACCATCCATG 58.170 50.000 0.00 0.00 0.00 3.66
117 126 0.038599 ACTGCTTGACCATCCATGCA 59.961 50.000 0.00 0.00 42.45 3.96
176 200 1.004200 ACGGCCCGTTTCCAGTAAG 60.004 57.895 1.02 0.00 36.35 2.34
243 267 4.314440 TCCTGTGGCGGCACTGAC 62.314 66.667 38.57 18.69 0.00 3.51
245 269 4.662961 CTGTGGCGGCACTGACGA 62.663 66.667 37.33 19.61 35.20 4.20
246 270 4.961511 TGTGGCGGCACTGACGAC 62.962 66.667 37.33 5.59 45.88 4.34
397 454 3.341043 CATCATTCGCCTCGCCGG 61.341 66.667 0.00 0.00 0.00 6.13
517 618 3.118454 CGCCATGGCTCGTTCGTT 61.118 61.111 33.07 0.00 39.32 3.85
518 619 2.785258 GCCATGGCTCGTTCGTTC 59.215 61.111 29.98 0.00 38.26 3.95
519 620 2.750888 GCCATGGCTCGTTCGTTCC 61.751 63.158 29.98 0.00 38.26 3.62
520 621 1.079127 CCATGGCTCGTTCGTTCCT 60.079 57.895 0.00 0.00 0.00 3.36
521 622 0.673644 CCATGGCTCGTTCGTTCCTT 60.674 55.000 0.00 0.00 0.00 3.36
522 623 0.721718 CATGGCTCGTTCGTTCCTTC 59.278 55.000 0.00 0.00 0.00 3.46
523 624 0.736325 ATGGCTCGTTCGTTCCTTCG 60.736 55.000 0.00 0.00 0.00 3.79
524 625 1.080974 GGCTCGTTCGTTCCTTCGA 60.081 57.895 0.00 0.00 38.08 3.71
525 626 1.342796 GGCTCGTTCGTTCCTTCGAC 61.343 60.000 0.00 0.00 39.58 4.20
526 627 1.662845 GCTCGTTCGTTCCTTCGACG 61.663 60.000 0.00 0.00 39.58 5.12
527 628 0.110509 CTCGTTCGTTCCTTCGACGA 60.111 55.000 0.00 0.00 46.60 4.20
532 633 0.242825 TCGTTCCTTCGACGAATGCT 59.757 50.000 11.30 0.00 45.45 3.79
533 634 1.068474 CGTTCCTTCGACGAATGCTT 58.932 50.000 11.30 0.00 42.82 3.91
547 648 3.976942 CGAATGCTTTGGTTCTGTCTTTG 59.023 43.478 0.00 0.00 0.00 2.77
558 659 4.561105 GTTCTGTCTTTGATTCGTCCTCT 58.439 43.478 0.00 0.00 0.00 3.69
559 660 4.442375 TCTGTCTTTGATTCGTCCTCTC 57.558 45.455 0.00 0.00 0.00 3.20
560 661 4.082845 TCTGTCTTTGATTCGTCCTCTCT 58.917 43.478 0.00 0.00 0.00 3.10
561 662 4.156922 TCTGTCTTTGATTCGTCCTCTCTC 59.843 45.833 0.00 0.00 0.00 3.20
562 663 4.082845 TGTCTTTGATTCGTCCTCTCTCT 58.917 43.478 0.00 0.00 0.00 3.10
563 664 4.156922 TGTCTTTGATTCGTCCTCTCTCTC 59.843 45.833 0.00 0.00 0.00 3.20
564 665 3.697045 TCTTTGATTCGTCCTCTCTCTCC 59.303 47.826 0.00 0.00 0.00 3.71
565 666 1.669604 TGATTCGTCCTCTCTCTCCG 58.330 55.000 0.00 0.00 0.00 4.63
567 668 0.466555 ATTCGTCCTCTCTCTCCGGG 60.467 60.000 0.00 0.00 0.00 5.73
568 669 1.559965 TTCGTCCTCTCTCTCCGGGA 61.560 60.000 0.00 0.00 0.00 5.14
569 670 1.077644 CGTCCTCTCTCTCCGGGAA 60.078 63.158 0.00 0.00 0.00 3.97
570 671 1.098712 CGTCCTCTCTCTCCGGGAAG 61.099 65.000 0.00 0.00 0.00 3.46
571 672 0.033894 GTCCTCTCTCTCCGGGAAGT 60.034 60.000 0.00 0.00 0.00 3.01
572 673 0.705253 TCCTCTCTCTCCGGGAAGTT 59.295 55.000 0.00 0.00 0.00 2.66
573 674 1.077334 TCCTCTCTCTCCGGGAAGTTT 59.923 52.381 0.00 0.00 0.00 2.66
574 675 1.903183 CCTCTCTCTCCGGGAAGTTTT 59.097 52.381 0.00 0.00 0.00 2.43
575 676 2.303311 CCTCTCTCTCCGGGAAGTTTTT 59.697 50.000 0.00 0.00 0.00 1.94
617 718 2.911143 CTGGGATTCAGGGACGGG 59.089 66.667 0.00 0.00 39.76 5.28
626 727 2.448931 AGGGACGGGTTGGGTTGA 60.449 61.111 0.00 0.00 0.00 3.18
633 738 2.671963 GGTTGGGTTGAGGCCGAC 60.672 66.667 0.00 0.00 0.00 4.79
641 746 0.788391 GTTGAGGCCGACTGTTTACG 59.212 55.000 0.00 0.00 0.00 3.18
648 753 1.942586 GCCGACTGTTTACGGTCCATT 60.943 52.381 14.49 0.00 46.76 3.16
650 755 1.652124 CGACTGTTTACGGTCCATTCG 59.348 52.381 14.49 1.77 46.76 3.34
690 795 0.238553 GCTGCGAACCACTTTCCTTC 59.761 55.000 0.00 0.00 0.00 3.46
696 801 3.756963 GCGAACCACTTTCCTTCCTTATT 59.243 43.478 0.00 0.00 0.00 1.40
700 805 5.319043 ACCACTTTCCTTCCTTATTGTCA 57.681 39.130 0.00 0.00 0.00 3.58
702 807 7.027874 ACCACTTTCCTTCCTTATTGTCATA 57.972 36.000 0.00 0.00 0.00 2.15
721 826 6.811665 TGTCATAATATCGGTTACAGCTATGC 59.188 38.462 0.00 0.00 0.00 3.14
722 827 6.020599 GTCATAATATCGGTTACAGCTATGCG 60.021 42.308 0.00 0.00 0.00 4.73
724 829 2.882927 ATCGGTTACAGCTATGCGAA 57.117 45.000 0.00 0.00 0.00 4.70
725 830 1.917273 TCGGTTACAGCTATGCGAAC 58.083 50.000 0.00 0.00 0.00 3.95
788 893 1.001393 TCCCCAAATTCACGCCCTC 60.001 57.895 0.00 0.00 0.00 4.30
792 897 0.168128 CCAAATTCACGCCCTCGAAC 59.832 55.000 0.00 0.00 39.41 3.95
811 916 4.084888 CCGCCGAAACTTCCGTGC 62.085 66.667 0.00 0.00 0.00 5.34
851 956 0.898320 AAAGCTAGCTCTTCCGCTGA 59.102 50.000 19.65 0.00 41.12 4.26
872 977 1.822581 GCGCCTTTAAATAACGCCTG 58.177 50.000 14.98 0.00 43.58 4.85
873 978 1.822581 CGCCTTTAAATAACGCCTGC 58.177 50.000 0.00 0.00 0.00 4.85
874 979 1.400494 CGCCTTTAAATAACGCCTGCT 59.600 47.619 0.00 0.00 0.00 4.24
875 980 2.538939 CGCCTTTAAATAACGCCTGCTC 60.539 50.000 0.00 0.00 0.00 4.26
876 981 2.683362 GCCTTTAAATAACGCCTGCTCT 59.317 45.455 0.00 0.00 0.00 4.09
877 982 3.242772 GCCTTTAAATAACGCCTGCTCTC 60.243 47.826 0.00 0.00 0.00 3.20
878 983 3.001330 CCTTTAAATAACGCCTGCTCTCG 59.999 47.826 0.00 0.00 0.00 4.04
879 984 2.953466 TAAATAACGCCTGCTCTCGT 57.047 45.000 0.00 0.00 41.06 4.18
900 1005 1.121407 TGGTCTGGTCTGGTCTGTGG 61.121 60.000 0.00 0.00 0.00 4.17
903 1008 3.596066 CTGGTCTGGTCTGTGGGCG 62.596 68.421 0.00 0.00 0.00 6.13
906 1011 2.203640 TCTGGTCTGTGGGCGACT 60.204 61.111 0.31 0.00 0.00 4.18
920 1025 3.248626 CGACTAGCAGCTGCAGTAG 57.751 57.895 38.24 31.08 45.16 2.57
921 1026 0.453793 CGACTAGCAGCTGCAGTAGT 59.546 55.000 38.24 33.76 45.16 2.73
922 1027 1.671328 CGACTAGCAGCTGCAGTAGTA 59.329 52.381 38.24 21.11 45.16 1.82
933 1041 3.443037 CTGCAGTAGTAGATGACACAGC 58.557 50.000 5.25 0.00 0.00 4.40
955 1063 1.006220 GGCTTTGGTTTTCGCAGGG 60.006 57.895 0.00 0.00 0.00 4.45
989 1097 0.606604 TGGTTCGTAGCAGAGGTTCC 59.393 55.000 0.00 0.00 0.00 3.62
1001 1109 2.267961 GGTTCCGAACCGAGCCAT 59.732 61.111 14.56 0.00 42.62 4.40
1002 1110 2.106683 GGTTCCGAACCGAGCCATG 61.107 63.158 14.56 0.00 42.62 3.66
1004 1112 3.969250 TTCCGAACCGAGCCATGGC 62.969 63.158 30.12 30.12 42.33 4.40
1021 1161 4.170062 CTGATGGCAAGTGCGGCG 62.170 66.667 0.51 0.51 43.26 6.46
1143 1283 1.571936 ACCTACCTCCTCCTCTTCCTC 59.428 57.143 0.00 0.00 0.00 3.71
1161 1301 2.279784 CAAGAGATCGGCCTCGCC 60.280 66.667 0.00 0.00 46.75 5.54
1179 1323 0.107654 CCCCAAGGTACTACTGCTGC 60.108 60.000 0.00 0.00 38.49 5.25
1254 1402 1.885871 GTTCATGCCTTGCAGGGAC 59.114 57.895 20.85 10.63 41.53 4.46
1380 1529 2.089349 GCCGCTCGACAGTGAGAAC 61.089 63.158 0.00 0.00 38.28 3.01
1383 1532 0.109086 CGCTCGACAGTGAGAACCAT 60.109 55.000 0.00 0.00 38.28 3.55
1384 1533 1.354040 GCTCGACAGTGAGAACCATG 58.646 55.000 0.00 0.00 38.28 3.66
1385 1534 1.067565 GCTCGACAGTGAGAACCATGA 60.068 52.381 0.00 0.00 38.28 3.07
1386 1535 2.417924 GCTCGACAGTGAGAACCATGAT 60.418 50.000 0.00 0.00 38.28 2.45
1387 1536 3.854666 CTCGACAGTGAGAACCATGATT 58.145 45.455 0.00 0.00 38.28 2.57
1388 1537 3.849911 TCGACAGTGAGAACCATGATTC 58.150 45.455 0.00 0.00 0.00 2.52
1389 1538 2.932614 CGACAGTGAGAACCATGATTCC 59.067 50.000 0.00 0.00 0.00 3.01
1390 1539 3.617288 CGACAGTGAGAACCATGATTCCA 60.617 47.826 0.00 0.00 0.00 3.53
1391 1540 4.521146 GACAGTGAGAACCATGATTCCAT 58.479 43.478 0.00 0.00 0.00 3.41
1412 1561 0.031994 AACAATGGCGCCTGAACAAC 59.968 50.000 29.70 0.00 0.00 3.32
1429 1596 2.223249 ACAACGTGTGCTGTTTGATCAC 60.223 45.455 0.00 0.00 0.00 3.06
1430 1597 0.944386 ACGTGTGCTGTTTGATCACC 59.056 50.000 0.00 0.00 0.00 4.02
1543 1710 1.525923 CCTCCTCTGCACCATCCTG 59.474 63.158 0.00 0.00 0.00 3.86
1600 1767 2.027625 CTTCTTCGCCGCCGTCTTT 61.028 57.895 0.00 0.00 35.54 2.52
1676 1850 2.297701 TGCCTCCAAACTTTGACTGAC 58.702 47.619 2.87 0.00 0.00 3.51
1710 1885 6.866480 ACAATCTGACAAGTGTTTTGAACAT 58.134 32.000 0.00 0.00 44.35 2.71
1744 1919 1.909700 TGTGTTCCCAATCCTTCTGC 58.090 50.000 0.00 0.00 0.00 4.26
1873 2048 1.813513 CACGGCCATCTTTCTTGACT 58.186 50.000 2.24 0.00 0.00 3.41
1874 2049 2.154462 CACGGCCATCTTTCTTGACTT 58.846 47.619 2.24 0.00 0.00 3.01
1877 2052 2.160417 CGGCCATCTTTCTTGACTTGTC 59.840 50.000 2.24 0.00 0.00 3.18
1905 2080 2.737932 CTTTGCTTCACGCCACTGCC 62.738 60.000 0.00 0.00 38.05 4.85
1931 2106 1.373748 GTGCCAACATGCTTGCCTG 60.374 57.895 0.00 0.00 0.00 4.85
1932 2107 1.833492 TGCCAACATGCTTGCCTGT 60.833 52.632 0.00 0.00 0.00 4.00
1940 2115 3.894759 ACATGCTTGCCTGTTCTATGAT 58.105 40.909 0.00 0.00 0.00 2.45
1950 2125 9.368674 CTTGCCTGTTCTATGATCTCTATTATG 57.631 37.037 0.00 0.00 0.00 1.90
1951 2126 8.427902 TGCCTGTTCTATGATCTCTATTATGT 57.572 34.615 0.00 0.00 0.00 2.29
1952 2127 9.533831 TGCCTGTTCTATGATCTCTATTATGTA 57.466 33.333 0.00 0.00 0.00 2.29
1986 2161 4.081917 ACAACGTGACCCTGAAACAAAAAT 60.082 37.500 0.00 0.00 0.00 1.82
1995 2170 5.304101 ACCCTGAAACAAAAATATGCTGACA 59.696 36.000 0.00 0.00 0.00 3.58
1996 2171 5.865552 CCCTGAAACAAAAATATGCTGACAG 59.134 40.000 0.00 0.00 0.00 3.51
1997 2172 6.449698 CCTGAAACAAAAATATGCTGACAGT 58.550 36.000 3.99 0.00 0.00 3.55
2058 2233 4.166011 GGCATCGCGTTGGCAGTC 62.166 66.667 31.43 10.33 41.53 3.51
2088 2263 0.592637 TGAAGGCAAAGACATGTGCG 59.407 50.000 1.15 0.00 41.85 5.34
2112 2287 5.278315 GGACATTGTTGTTCAGGTAACCTTC 60.278 44.000 0.00 0.00 37.27 3.46
2136 2311 6.428159 TCTCCAAATCAGCTTTGAGTTCTAAC 59.572 38.462 0.00 0.00 45.96 2.34
2237 2412 2.360475 GTGGGGTGCTGCTTCCTC 60.360 66.667 0.00 4.28 0.00 3.71
2276 2451 1.522569 GGAAGAGCCCACGTATGCT 59.477 57.895 10.46 10.46 41.42 3.79
2317 2492 4.691860 AATAGCAGTTCAGAATGTGCAC 57.308 40.909 10.75 10.75 38.44 4.57
2367 2542 1.542915 CTTATGGTGTTGCTTGCAGCT 59.457 47.619 10.50 0.00 42.97 4.24
2426 2601 1.429463 CGTGGAGCTACTGGTTCAAC 58.571 55.000 0.00 0.00 30.07 3.18
2450 2625 0.745468 CCCTCTACTACCAAGTCGCC 59.255 60.000 0.00 0.00 37.15 5.54
2489 2664 3.368843 CCAGATTGATCACCAACGTCTCT 60.369 47.826 0.00 0.00 37.63 3.10
2497 2672 2.960384 TCACCAACGTCTCTCAGGTTAA 59.040 45.455 0.00 0.00 31.69 2.01
2498 2673 3.057734 CACCAACGTCTCTCAGGTTAAC 58.942 50.000 0.00 0.00 31.69 2.01
2499 2674 2.963782 ACCAACGTCTCTCAGGTTAACT 59.036 45.455 5.42 0.00 31.69 2.24
2500 2675 3.387050 ACCAACGTCTCTCAGGTTAACTT 59.613 43.478 5.42 0.00 31.69 2.66
2501 2676 4.586001 ACCAACGTCTCTCAGGTTAACTTA 59.414 41.667 5.42 0.00 31.69 2.24
2502 2677 4.922103 CCAACGTCTCTCAGGTTAACTTAC 59.078 45.833 5.42 0.00 31.69 2.34
2503 2678 5.508489 CCAACGTCTCTCAGGTTAACTTACA 60.508 44.000 5.42 0.00 31.69 2.41
2504 2679 5.118642 ACGTCTCTCAGGTTAACTTACAC 57.881 43.478 5.42 0.00 0.00 2.90
2505 2680 4.022503 ACGTCTCTCAGGTTAACTTACACC 60.023 45.833 5.42 0.00 0.00 4.16
2506 2681 4.617762 CGTCTCTCAGGTTAACTTACACCC 60.618 50.000 5.42 0.00 32.92 4.61
2507 2682 4.527427 GTCTCTCAGGTTAACTTACACCCT 59.473 45.833 5.42 0.00 32.92 4.34
2508 2683 4.527038 TCTCTCAGGTTAACTTACACCCTG 59.473 45.833 5.42 2.70 43.26 4.45
2509 2684 3.007614 TCTCAGGTTAACTTACACCCTGC 59.992 47.826 5.42 0.00 41.96 4.85
2510 2685 2.976882 TCAGGTTAACTTACACCCTGCT 59.023 45.455 5.42 0.00 41.96 4.24
2511 2686 3.007614 TCAGGTTAACTTACACCCTGCTC 59.992 47.826 5.42 0.00 41.96 4.26
2512 2687 3.008049 CAGGTTAACTTACACCCTGCTCT 59.992 47.826 5.42 0.00 36.58 4.09
2513 2688 3.261137 AGGTTAACTTACACCCTGCTCTC 59.739 47.826 5.42 0.00 32.92 3.20
2514 2689 3.261137 GGTTAACTTACACCCTGCTCTCT 59.739 47.826 5.42 0.00 0.00 3.10
2515 2690 4.465305 GGTTAACTTACACCCTGCTCTCTA 59.535 45.833 5.42 0.00 0.00 2.43
2516 2691 5.046807 GGTTAACTTACACCCTGCTCTCTAA 60.047 44.000 5.42 0.00 0.00 2.10
2517 2692 6.351966 GGTTAACTTACACCCTGCTCTCTAAT 60.352 42.308 5.42 0.00 0.00 1.73
2518 2693 5.346181 AACTTACACCCTGCTCTCTAATC 57.654 43.478 0.00 0.00 0.00 1.75
2521 2696 0.249657 CACCCTGCTCTCTAATCGCC 60.250 60.000 0.00 0.00 0.00 5.54
2539 2714 3.118905 GCCCTAGGCTAGATGTTCTTG 57.881 52.381 22.99 3.30 46.69 3.02
2555 2730 6.564709 TGTTCTTGGTGAAGATCATTTCTG 57.435 37.500 0.00 0.00 38.05 3.02
2617 2801 6.150976 TGGTGTGATGAACTTGGATTATGAAC 59.849 38.462 0.00 0.00 0.00 3.18
2736 2944 4.331968 TCATCACCACCAATTTGAGTACC 58.668 43.478 0.00 0.00 0.00 3.34
2755 2963 3.403038 ACCGTGATCTTCTTGGTTCAAG 58.597 45.455 1.53 1.53 42.25 3.02
2767 2975 4.338118 TCTTGGTTCAAGCGTTTGATCTTT 59.662 37.500 15.71 0.00 42.60 2.52
2774 2982 1.455786 AGCGTTTGATCTTTGACGACG 59.544 47.619 12.49 0.00 37.69 5.12
2775 2983 1.461888 GCGTTTGATCTTTGACGACGG 60.462 52.381 0.00 0.00 37.69 4.79
2821 3029 0.604780 TCTGCTGCAGCTTCTTGGTC 60.605 55.000 36.61 7.74 42.66 4.02
3341 3552 1.084370 CGTCTGAATCAGTTCCCGCC 61.084 60.000 10.36 0.00 33.26 6.13
3424 3637 9.231297 TGAAAAAGGAAGGTAAGATAAGATGTG 57.769 33.333 0.00 0.00 0.00 3.21
3453 3666 0.179094 TCGACATGCCGGTGGTAATC 60.179 55.000 1.90 0.00 0.00 1.75
3461 3674 1.595794 GCCGGTGGTAATCGTGTAATG 59.404 52.381 1.90 0.00 0.00 1.90
3471 3684 5.163754 GGTAATCGTGTAATGCAGCTCTTTT 60.164 40.000 0.00 0.00 0.00 2.27
3490 3703 8.473219 GCTCTTTTCAATTAGATTTGGGAAGAT 58.527 33.333 0.00 0.00 32.63 2.40
3491 3704 9.798994 CTCTTTTCAATTAGATTTGGGAAGATG 57.201 33.333 0.00 0.00 32.63 2.90
3492 3705 8.253113 TCTTTTCAATTAGATTTGGGAAGATGC 58.747 33.333 0.00 0.00 30.35 3.91
3493 3706 7.722949 TTTCAATTAGATTTGGGAAGATGCT 57.277 32.000 0.00 0.00 0.00 3.79
3494 3707 6.949352 TCAATTAGATTTGGGAAGATGCTC 57.051 37.500 0.00 0.00 0.00 4.26
3495 3708 5.528690 TCAATTAGATTTGGGAAGATGCTCG 59.471 40.000 0.00 0.00 0.00 5.03
3497 3710 2.911484 AGATTTGGGAAGATGCTCGTC 58.089 47.619 0.00 0.00 0.00 4.20
3498 3711 2.237143 AGATTTGGGAAGATGCTCGTCA 59.763 45.455 0.00 0.00 0.00 4.35
3499 3712 2.099141 TTTGGGAAGATGCTCGTCAG 57.901 50.000 0.00 0.00 0.00 3.51
3500 3713 0.976641 TTGGGAAGATGCTCGTCAGT 59.023 50.000 0.00 0.00 0.00 3.41
3501 3714 0.976641 TGGGAAGATGCTCGTCAGTT 59.023 50.000 0.00 0.00 0.00 3.16
3502 3715 1.338105 TGGGAAGATGCTCGTCAGTTG 60.338 52.381 0.00 0.00 0.00 3.16
3503 3716 1.338200 GGGAAGATGCTCGTCAGTTGT 60.338 52.381 0.00 0.00 0.00 3.32
3504 3717 2.417719 GGAAGATGCTCGTCAGTTGTT 58.582 47.619 0.00 0.00 0.00 2.83
3506 3719 3.994392 GGAAGATGCTCGTCAGTTGTTTA 59.006 43.478 0.00 0.00 0.00 2.01
3508 3721 5.220491 GGAAGATGCTCGTCAGTTGTTTATC 60.220 44.000 0.00 0.00 0.00 1.75
3509 3722 4.820897 AGATGCTCGTCAGTTGTTTATCA 58.179 39.130 0.00 0.00 0.00 2.15
3510 3723 4.627467 AGATGCTCGTCAGTTGTTTATCAC 59.373 41.667 0.00 0.00 0.00 3.06
3511 3724 3.723260 TGCTCGTCAGTTGTTTATCACA 58.277 40.909 0.00 0.00 0.00 3.58
3512 3725 4.314961 TGCTCGTCAGTTGTTTATCACAT 58.685 39.130 0.00 0.00 34.43 3.21
3514 3727 5.347635 TGCTCGTCAGTTGTTTATCACATAC 59.652 40.000 0.00 0.00 34.43 2.39
3515 3728 5.220416 GCTCGTCAGTTGTTTATCACATACC 60.220 44.000 0.00 0.00 34.43 2.73
3516 3729 5.785243 TCGTCAGTTGTTTATCACATACCA 58.215 37.500 0.00 0.00 34.43 3.25
3517 3730 6.403049 TCGTCAGTTGTTTATCACATACCAT 58.597 36.000 0.00 0.00 34.43 3.55
3518 3731 6.533723 TCGTCAGTTGTTTATCACATACCATC 59.466 38.462 0.00 0.00 34.43 3.51
3519 3732 6.312672 CGTCAGTTGTTTATCACATACCATCA 59.687 38.462 0.00 0.00 34.43 3.07
3520 3733 7.464577 CGTCAGTTGTTTATCACATACCATCAG 60.465 40.741 0.00 0.00 34.43 2.90
3521 3734 7.549134 GTCAGTTGTTTATCACATACCATCAGA 59.451 37.037 0.00 0.00 34.43 3.27
3527 3740 4.679373 ATCACATACCATCAGACAGTCC 57.321 45.455 0.00 0.00 0.00 3.85
3545 3758 2.229784 GTCCCAGCTCCAATTTTGAGTG 59.770 50.000 4.21 2.34 0.00 3.51
3549 3763 3.571401 CCAGCTCCAATTTTGAGTGAAGT 59.429 43.478 4.21 0.00 0.00 3.01
3560 3774 1.160137 GAGTGAAGTTTCAGGCGCAT 58.840 50.000 10.83 0.00 37.98 4.73
3569 3783 7.275560 GTGAAGTTTCAGGCGCATAATAAAATT 59.724 33.333 10.83 9.29 37.98 1.82
3599 3813 9.750882 GAGTATTTAACGAAAAACTACCACATC 57.249 33.333 0.00 0.00 0.00 3.06
3605 3819 3.985279 CGAAAAACTACCACATCTCGTCA 59.015 43.478 0.00 0.00 0.00 4.35
3617 3831 3.181475 ACATCTCGTCAAATCGTGCCTAT 60.181 43.478 0.00 0.00 0.00 2.57
3621 3835 5.041287 TCTCGTCAAATCGTGCCTATAAAG 58.959 41.667 0.00 0.00 0.00 1.85
3630 3844 4.751060 TCGTGCCTATAAAGTACCACTTG 58.249 43.478 0.00 0.00 38.66 3.16
3661 3875 9.606631 ATTTGTGCCAAAAACTATCACTTTTTA 57.393 25.926 4.76 0.00 31.15 1.52
3694 3908 5.342806 TCTCAAAAACACTAGTGATTGCG 57.657 39.130 29.30 21.59 0.00 4.85
3790 4046 6.039605 TCCGTTAGATTGACCGTTATGACATA 59.960 38.462 0.00 0.00 0.00 2.29
3812 4068 1.024579 GGGCCCGTATGTCAGTGTTG 61.025 60.000 5.69 0.00 0.00 3.33
3953 4242 6.714278 TCTAATCCTAACAAACCACTAACCC 58.286 40.000 0.00 0.00 0.00 4.11
4031 4324 3.151710 CCAGGCCGTCGGTGGATA 61.152 66.667 14.35 0.00 32.60 2.59
4042 4335 4.517815 GTGGATACGCCGCCGGAA 62.518 66.667 7.68 0.00 41.49 4.30
4161 4454 0.178950 ATGGCTCGCCTCTCCAGATA 60.179 55.000 9.65 0.00 36.94 1.98
4162 4455 0.178950 TGGCTCGCCTCTCCAGATAT 60.179 55.000 9.65 0.00 36.94 1.63
4284 4577 2.257676 GAAGAACTCGTCCGCGGT 59.742 61.111 27.15 3.60 38.89 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.326143 AAGGGTTGTTTGGGGCTGTT 60.326 50.000 0.00 0.00 0.00 3.16
1 2 1.048160 CAAGGGTTGTTTGGGGCTGT 61.048 55.000 0.00 0.00 0.00 4.40
3 4 0.031616 TTCAAGGGTTGTTTGGGGCT 60.032 50.000 0.00 0.00 0.00 5.19
5 6 3.636153 TTTTTCAAGGGTTGTTTGGGG 57.364 42.857 0.00 0.00 0.00 4.96
25 26 5.766590 TGGGGTTCTTCTTCTCTTCTTTTT 58.233 37.500 0.00 0.00 0.00 1.94
26 27 5.388599 TGGGGTTCTTCTTCTCTTCTTTT 57.611 39.130 0.00 0.00 0.00 2.27
27 28 5.388599 TTGGGGTTCTTCTTCTCTTCTTT 57.611 39.130 0.00 0.00 0.00 2.52
28 29 5.133941 GTTTGGGGTTCTTCTTCTCTTCTT 58.866 41.667 0.00 0.00 0.00 2.52
29 30 4.166144 TGTTTGGGGTTCTTCTTCTCTTCT 59.834 41.667 0.00 0.00 0.00 2.85
30 31 4.461198 TGTTTGGGGTTCTTCTTCTCTTC 58.539 43.478 0.00 0.00 0.00 2.87
31 32 4.519906 TGTTTGGGGTTCTTCTTCTCTT 57.480 40.909 0.00 0.00 0.00 2.85
32 33 4.519906 TTGTTTGGGGTTCTTCTTCTCT 57.480 40.909 0.00 0.00 0.00 3.10
33 34 4.887655 TCTTTGTTTGGGGTTCTTCTTCTC 59.112 41.667 0.00 0.00 0.00 2.87
34 35 4.645136 GTCTTTGTTTGGGGTTCTTCTTCT 59.355 41.667 0.00 0.00 0.00 2.85
35 36 4.401202 TGTCTTTGTTTGGGGTTCTTCTTC 59.599 41.667 0.00 0.00 0.00 2.87
64 65 9.930693 CCTTTCTTTCTCTACACTTACAGTATT 57.069 33.333 0.00 0.00 0.00 1.89
65 66 9.310449 TCCTTTCTTTCTCTACACTTACAGTAT 57.690 33.333 0.00 0.00 0.00 2.12
74 79 9.274206 AGTGTTAATTCCTTTCTTTCTCTACAC 57.726 33.333 0.00 0.00 0.00 2.90
79 84 7.208225 AGCAGTGTTAATTCCTTTCTTTCTC 57.792 36.000 0.00 0.00 0.00 2.87
80 85 7.285401 TCAAGCAGTGTTAATTCCTTTCTTTCT 59.715 33.333 0.00 0.00 0.00 2.52
81 86 7.379797 GTCAAGCAGTGTTAATTCCTTTCTTTC 59.620 37.037 0.00 0.00 0.00 2.62
85 90 5.009610 TGGTCAAGCAGTGTTAATTCCTTTC 59.990 40.000 0.00 0.00 0.00 2.62
87 92 4.469657 TGGTCAAGCAGTGTTAATTCCTT 58.530 39.130 0.00 0.00 0.00 3.36
89 94 4.142381 GGATGGTCAAGCAGTGTTAATTCC 60.142 45.833 0.00 0.00 0.00 3.01
111 120 1.254284 TTTTTACCCCGGCTGCATGG 61.254 55.000 0.50 2.19 0.00 3.66
146 170 4.452733 GGCCGTTCAGACTCCGGG 62.453 72.222 0.00 0.00 41.96 5.73
508 609 0.110509 TCGTCGAAGGAACGAACGAG 60.111 55.000 0.14 0.00 43.75 4.18
511 612 1.201780 GCATTCGTCGAAGGAACGAAC 60.202 52.381 22.67 0.65 46.35 3.95
513 614 0.242825 AGCATTCGTCGAAGGAACGA 59.757 50.000 22.67 0.15 40.00 3.85
514 615 1.068474 AAGCATTCGTCGAAGGAACG 58.932 50.000 22.67 5.48 0.00 3.95
515 616 2.412847 CCAAAGCATTCGTCGAAGGAAC 60.413 50.000 22.67 6.49 0.00 3.62
516 617 1.804151 CCAAAGCATTCGTCGAAGGAA 59.196 47.619 22.67 0.30 0.00 3.36
517 618 1.270625 ACCAAAGCATTCGTCGAAGGA 60.271 47.619 22.67 0.00 0.00 3.36
518 619 1.156736 ACCAAAGCATTCGTCGAAGG 58.843 50.000 14.95 14.95 0.00 3.46
519 620 2.480419 AGAACCAAAGCATTCGTCGAAG 59.520 45.455 13.88 6.90 0.00 3.79
520 621 2.223144 CAGAACCAAAGCATTCGTCGAA 59.777 45.455 10.61 10.61 0.00 3.71
521 622 1.798223 CAGAACCAAAGCATTCGTCGA 59.202 47.619 0.00 0.00 0.00 4.20
522 623 1.531149 ACAGAACCAAAGCATTCGTCG 59.469 47.619 0.00 0.00 0.00 5.12
523 624 2.808543 AGACAGAACCAAAGCATTCGTC 59.191 45.455 0.00 0.00 32.97 4.20
524 625 2.851195 AGACAGAACCAAAGCATTCGT 58.149 42.857 0.00 0.00 0.00 3.85
525 626 3.904136 AAGACAGAACCAAAGCATTCG 57.096 42.857 0.00 0.00 0.00 3.34
526 627 5.186996 TCAAAGACAGAACCAAAGCATTC 57.813 39.130 0.00 0.00 0.00 2.67
527 628 5.796424 ATCAAAGACAGAACCAAAGCATT 57.204 34.783 0.00 0.00 0.00 3.56
528 629 5.563475 CGAATCAAAGACAGAACCAAAGCAT 60.563 40.000 0.00 0.00 0.00 3.79
529 630 4.261155 CGAATCAAAGACAGAACCAAAGCA 60.261 41.667 0.00 0.00 0.00 3.91
532 633 4.274950 GGACGAATCAAAGACAGAACCAAA 59.725 41.667 0.00 0.00 0.00 3.28
533 634 3.813166 GGACGAATCAAAGACAGAACCAA 59.187 43.478 0.00 0.00 0.00 3.67
547 648 0.948678 CCGGAGAGAGAGGACGAATC 59.051 60.000 0.00 0.00 0.00 2.52
572 673 6.590357 CGAACTCGCATCTTTCTAAGAAAAA 58.410 36.000 0.00 0.00 41.63 1.94
573 674 6.153212 CGAACTCGCATCTTTCTAAGAAAA 57.847 37.500 0.00 0.00 41.63 2.29
574 675 5.763444 CGAACTCGCATCTTTCTAAGAAA 57.237 39.130 0.00 0.00 41.63 2.52
591 692 0.392193 CTGAATCCCAGCAGCGAACT 60.392 55.000 0.00 0.00 35.89 3.01
592 693 1.372087 CCTGAATCCCAGCAGCGAAC 61.372 60.000 0.00 0.00 41.57 3.95
617 718 1.966451 CAGTCGGCCTCAACCCAAC 60.966 63.158 0.00 0.00 0.00 3.77
633 738 3.061322 TGAACGAATGGACCGTAAACAG 58.939 45.455 0.00 0.00 39.57 3.16
641 746 2.552315 ACACACAATGAACGAATGGACC 59.448 45.455 0.00 0.00 0.00 4.46
648 753 0.579630 GCGACACACACAATGAACGA 59.420 50.000 0.00 0.00 0.00 3.85
650 755 0.991770 GCGCGACACACACAATGAAC 60.992 55.000 12.10 0.00 0.00 3.18
690 795 8.656849 GCTGTAACCGATATTATGACAATAAGG 58.343 37.037 0.00 0.00 31.81 2.69
696 801 6.811665 GCATAGCTGTAACCGATATTATGACA 59.188 38.462 0.00 0.00 0.00 3.58
700 805 6.203808 TCGCATAGCTGTAACCGATATTAT 57.796 37.500 0.00 0.00 0.00 1.28
702 807 4.514781 TCGCATAGCTGTAACCGATATT 57.485 40.909 0.00 0.00 0.00 1.28
714 819 6.056884 AGAAGTAGTACTAGTTCGCATAGCT 58.943 40.000 31.07 17.46 45.49 3.32
721 826 5.564048 AGGCAAGAAGTAGTACTAGTTCG 57.436 43.478 31.07 23.28 45.49 3.95
722 827 6.689554 ACAAGGCAAGAAGTAGTACTAGTTC 58.310 40.000 30.86 30.86 42.78 3.01
724 829 6.667558 AACAAGGCAAGAAGTAGTACTAGT 57.332 37.500 1.87 3.18 0.00 2.57
725 830 9.303537 GAATAACAAGGCAAGAAGTAGTACTAG 57.696 37.037 1.87 0.00 0.00 2.57
788 893 2.667199 AAGTTTCGGCGGGGTTCG 60.667 61.111 7.21 0.00 42.76 3.95
792 897 4.692475 ACGGAAGTTTCGGCGGGG 62.692 66.667 8.74 0.00 46.40 5.73
811 916 0.107654 GAAGGGAGGGATTCGTGTGG 60.108 60.000 0.00 0.00 0.00 4.17
851 956 2.089201 AGGCGTTATTTAAAGGCGCTT 58.911 42.857 23.22 17.46 46.20 4.68
867 972 3.691744 GACCAGACGAGAGCAGGCG 62.692 68.421 0.00 0.00 0.00 5.52
870 975 1.247419 ACCAGACCAGACGAGAGCAG 61.247 60.000 0.00 0.00 0.00 4.24
871 976 1.228583 ACCAGACCAGACGAGAGCA 60.229 57.895 0.00 0.00 0.00 4.26
872 977 0.963355 AGACCAGACCAGACGAGAGC 60.963 60.000 0.00 0.00 0.00 4.09
873 978 0.808125 CAGACCAGACCAGACGAGAG 59.192 60.000 0.00 0.00 0.00 3.20
874 979 0.609406 CCAGACCAGACCAGACGAGA 60.609 60.000 0.00 0.00 0.00 4.04
875 980 0.896019 ACCAGACCAGACCAGACGAG 60.896 60.000 0.00 0.00 0.00 4.18
876 981 0.894184 GACCAGACCAGACCAGACGA 60.894 60.000 0.00 0.00 0.00 4.20
877 982 0.896019 AGACCAGACCAGACCAGACG 60.896 60.000 0.00 0.00 0.00 4.18
878 983 0.605589 CAGACCAGACCAGACCAGAC 59.394 60.000 0.00 0.00 0.00 3.51
879 984 0.188587 ACAGACCAGACCAGACCAGA 59.811 55.000 0.00 0.00 0.00 3.86
900 1005 2.284798 TACTGCAGCTGCTAGTCGCC 62.285 60.000 36.61 8.49 42.66 5.54
903 1008 2.946329 TCTACTACTGCAGCTGCTAGTC 59.054 50.000 32.26 11.76 42.66 2.59
906 1011 3.316588 GTCATCTACTACTGCAGCTGCTA 59.683 47.826 36.61 21.87 42.66 3.49
920 1025 1.281899 GCCGAAGCTGTGTCATCTAC 58.718 55.000 0.00 0.00 35.50 2.59
921 1026 3.741029 GCCGAAGCTGTGTCATCTA 57.259 52.632 0.00 0.00 35.50 1.98
922 1027 4.606071 GCCGAAGCTGTGTCATCT 57.394 55.556 0.00 0.00 35.50 2.90
933 1041 0.030101 TGCGAAAACCAAAGCCGAAG 59.970 50.000 0.00 0.00 0.00 3.79
944 1052 1.200020 CTGAATCACCCCTGCGAAAAC 59.800 52.381 0.00 0.00 0.00 2.43
949 1057 1.134280 AGATTCTGAATCACCCCTGCG 60.134 52.381 27.06 0.00 40.42 5.18
955 1063 4.003648 ACGAACCAAGATTCTGAATCACC 58.996 43.478 27.06 6.35 40.42 4.02
1000 1108 2.412323 CGCACTTGCCATCAGCCAT 61.412 57.895 0.00 0.00 42.71 4.40
1001 1109 3.057548 CGCACTTGCCATCAGCCA 61.058 61.111 0.00 0.00 42.71 4.75
1002 1110 3.818787 CCGCACTTGCCATCAGCC 61.819 66.667 0.00 0.00 42.71 4.85
1004 1112 4.170062 CGCCGCACTTGCCATCAG 62.170 66.667 0.00 0.00 37.91 2.90
1021 1161 3.151022 CTCCACCTCCTCCTCCGC 61.151 72.222 0.00 0.00 0.00 5.54
1022 1162 2.443016 CCTCCACCTCCTCCTCCG 60.443 72.222 0.00 0.00 0.00 4.63
1023 1163 1.382009 GACCTCCACCTCCTCCTCC 60.382 68.421 0.00 0.00 0.00 4.30
1143 1283 2.279784 GCGAGGCCGATCTCTTGG 60.280 66.667 0.00 0.00 38.22 3.61
1161 1301 0.613260 TGCAGCAGTAGTACCTTGGG 59.387 55.000 0.00 0.00 0.00 4.12
1179 1323 3.598019 AAATGGCTGCATTGGTTACTG 57.402 42.857 0.50 0.00 0.00 2.74
1254 1402 2.925395 GAGCATCACGATCGCTGCG 61.925 63.158 23.56 17.25 39.57 5.18
1260 1408 0.599728 GGCCTGAGAGCATCACGATC 60.600 60.000 0.00 0.00 37.82 3.69
1325 1473 5.011090 TCGATCGAGTTGGATTGATTTCT 57.989 39.130 15.15 0.00 33.00 2.52
1326 1475 5.718649 TTCGATCGAGTTGGATTGATTTC 57.281 39.130 18.54 0.00 36.85 2.17
1389 1538 0.527113 TTCAGGCGCCATTGTTCATG 59.473 50.000 31.54 15.77 0.00 3.07
1390 1539 0.527565 GTTCAGGCGCCATTGTTCAT 59.472 50.000 31.54 0.76 0.00 2.57
1391 1540 0.821301 TGTTCAGGCGCCATTGTTCA 60.821 50.000 31.54 17.97 0.00 3.18
1392 1541 0.313672 TTGTTCAGGCGCCATTGTTC 59.686 50.000 31.54 15.76 0.00 3.18
1393 1542 0.031994 GTTGTTCAGGCGCCATTGTT 59.968 50.000 31.54 3.61 0.00 2.83
1394 1543 1.659794 GTTGTTCAGGCGCCATTGT 59.340 52.632 31.54 4.11 0.00 2.71
1395 1544 1.442520 CGTTGTTCAGGCGCCATTG 60.443 57.895 31.54 19.91 0.00 2.82
1396 1545 1.896660 ACGTTGTTCAGGCGCCATT 60.897 52.632 31.54 5.56 0.00 3.16
1397 1546 2.281484 ACGTTGTTCAGGCGCCAT 60.281 55.556 31.54 11.31 0.00 4.40
1398 1547 3.276091 CACGTTGTTCAGGCGCCA 61.276 61.111 31.54 5.56 0.00 5.69
1399 1548 3.276846 ACACGTTGTTCAGGCGCC 61.277 61.111 21.89 21.89 0.00 6.53
1400 1549 2.052237 CACACGTTGTTCAGGCGC 60.052 61.111 0.00 0.00 0.00 6.53
1401 1550 2.052237 GCACACGTTGTTCAGGCG 60.052 61.111 0.00 0.00 0.00 5.52
1402 1551 1.009675 CAGCACACGTTGTTCAGGC 60.010 57.895 0.00 0.00 0.00 4.85
1403 1552 0.732571 AACAGCACACGTTGTTCAGG 59.267 50.000 0.00 0.00 42.19 3.86
1404 1553 2.159585 TCAAACAGCACACGTTGTTCAG 60.160 45.455 3.95 1.51 44.73 3.02
1412 1561 1.195448 GAGGTGATCAAACAGCACACG 59.805 52.381 0.00 0.00 40.20 4.49
1429 1596 4.271816 CGGTCGATCTGCGGGAGG 62.272 72.222 0.00 0.00 41.33 4.30
1430 1597 4.271816 CCGGTCGATCTGCGGGAG 62.272 72.222 0.00 0.00 41.33 4.30
1456 1623 0.167470 CGATGTGCCACAGCTTGAAG 59.833 55.000 11.74 0.00 40.80 3.02
1480 1647 3.471244 GATGCCGACGAGGACCGAG 62.471 68.421 0.00 0.00 45.00 4.63
1543 1710 2.363925 AGGTAGGAGTCGGTGCCC 60.364 66.667 0.00 0.00 0.00 5.36
1600 1767 4.849310 GCCGCCCAGCCGATGTTA 62.849 66.667 0.00 0.00 0.00 2.41
1676 1850 7.132213 ACACTTGTCAGATTGTAAAATGTTCG 58.868 34.615 0.00 0.00 0.00 3.95
1710 1885 6.307776 TGGGAACACAACCAAATATCAGTAA 58.692 36.000 0.00 0.00 32.89 2.24
1721 1896 2.176798 AGAAGGATTGGGAACACAACCA 59.823 45.455 9.63 0.00 42.67 3.67
1798 1973 2.393768 CGTTTCTGCAGCTCGCCAT 61.394 57.895 9.47 0.00 41.33 4.40
1833 2008 0.535335 GTGCATGGTCGTAGGAAGGA 59.465 55.000 0.00 0.00 0.00 3.36
1834 2009 0.806102 CGTGCATGGTCGTAGGAAGG 60.806 60.000 0.00 0.00 0.00 3.46
1835 2010 1.421410 GCGTGCATGGTCGTAGGAAG 61.421 60.000 8.27 0.00 0.00 3.46
1836 2011 1.447140 GCGTGCATGGTCGTAGGAA 60.447 57.895 8.27 0.00 0.00 3.36
1873 2048 3.947196 TGAAGCAAAGAGAAAGCAGACAA 59.053 39.130 0.00 0.00 0.00 3.18
1874 2049 3.313526 GTGAAGCAAAGAGAAAGCAGACA 59.686 43.478 0.00 0.00 0.00 3.41
1877 2052 2.913613 CGTGAAGCAAAGAGAAAGCAG 58.086 47.619 0.00 0.00 0.00 4.24
1905 2080 0.376152 GCATGTTGGCACGAGATGAG 59.624 55.000 0.86 0.00 0.00 2.90
1974 2149 7.140705 TCACTGTCAGCATATTTTTGTTTCAG 58.859 34.615 0.00 0.00 0.00 3.02
1986 2161 2.893489 ACACTCACTCACTGTCAGCATA 59.107 45.455 0.00 0.00 0.00 3.14
1995 2170 5.670485 TGTAATTTGTCACACTCACTCACT 58.330 37.500 0.00 0.00 0.00 3.41
1996 2171 5.050091 CCTGTAATTTGTCACACTCACTCAC 60.050 44.000 0.00 0.00 0.00 3.51
1997 2172 5.056480 CCTGTAATTTGTCACACTCACTCA 58.944 41.667 0.00 0.00 0.00 3.41
2055 2230 4.640771 TGCCTTCACTATTCCAAAGACT 57.359 40.909 0.00 0.00 0.00 3.24
2058 2233 5.241506 TGTCTTTGCCTTCACTATTCCAAAG 59.758 40.000 0.00 0.00 40.04 2.77
2088 2263 4.142038 AGGTTACCTGAACAACAATGTCC 58.858 43.478 1.74 0.00 40.09 4.02
2112 2287 6.205464 TGTTAGAACTCAAAGCTGATTTGGAG 59.795 38.462 17.26 14.66 46.93 3.86
2237 2412 3.716006 CCAGCGTGGAACAGCACG 61.716 66.667 0.00 0.00 40.96 5.34
2258 2433 0.811616 CAGCATACGTGGGCTCTTCC 60.812 60.000 12.18 0.00 38.56 3.46
2314 2489 6.972328 TCTTTCAGAAAACACTGTTTATGTGC 59.028 34.615 7.59 0.00 38.86 4.57
2343 2518 4.619973 CTGCAAGCAACACCATAAGAAAA 58.380 39.130 0.00 0.00 0.00 2.29
2345 2520 3.921119 CTGCAAGCAACACCATAAGAA 57.079 42.857 0.00 0.00 0.00 2.52
2359 2534 0.110328 CTCGCACTTCAAGCTGCAAG 60.110 55.000 1.02 0.00 32.57 4.01
2367 2542 1.795768 CAGTTAGGCTCGCACTTCAA 58.204 50.000 0.00 0.00 0.00 2.69
2426 2601 3.128938 CGACTTGGTAGTAGAGGGTCTTG 59.871 52.174 0.00 0.00 33.84 3.02
2450 2625 0.543277 TGGCAAGCATGTAGAGGAGG 59.457 55.000 0.00 0.00 0.00 4.30
2497 2672 3.381908 CGATTAGAGAGCAGGGTGTAAGT 59.618 47.826 0.00 0.00 0.00 2.24
2498 2673 3.797184 GCGATTAGAGAGCAGGGTGTAAG 60.797 52.174 0.00 0.00 0.00 2.34
2499 2674 2.100916 GCGATTAGAGAGCAGGGTGTAA 59.899 50.000 0.00 0.00 0.00 2.41
2500 2675 1.681793 GCGATTAGAGAGCAGGGTGTA 59.318 52.381 0.00 0.00 0.00 2.90
2501 2676 0.461961 GCGATTAGAGAGCAGGGTGT 59.538 55.000 0.00 0.00 0.00 4.16
2502 2677 0.249657 GGCGATTAGAGAGCAGGGTG 60.250 60.000 0.00 0.00 0.00 4.61
2503 2678 1.403687 GGGCGATTAGAGAGCAGGGT 61.404 60.000 0.00 0.00 0.00 4.34
2504 2679 1.118356 AGGGCGATTAGAGAGCAGGG 61.118 60.000 0.00 0.00 0.00 4.45
2505 2680 1.543802 CTAGGGCGATTAGAGAGCAGG 59.456 57.143 0.00 0.00 0.00 4.85
2506 2681 1.543802 CCTAGGGCGATTAGAGAGCAG 59.456 57.143 0.00 0.00 0.00 4.24
2507 2682 1.621992 CCTAGGGCGATTAGAGAGCA 58.378 55.000 0.00 0.00 0.00 4.26
2508 2683 0.245266 GCCTAGGGCGATTAGAGAGC 59.755 60.000 11.72 0.00 39.62 4.09
2521 2696 3.706594 TCACCAAGAACATCTAGCCTAGG 59.293 47.826 3.67 3.67 0.00 3.02
2539 2714 3.955471 TCCACCAGAAATGATCTTCACC 58.045 45.455 0.00 0.00 35.73 4.02
2555 2730 7.148523 GCAAATCTTCAGAAATCAAATTCCACC 60.149 37.037 0.00 0.00 0.00 4.61
2594 2778 7.023575 GTGTTCATAATCCAAGTTCATCACAC 58.976 38.462 0.00 0.00 0.00 3.82
2595 2779 6.942005 AGTGTTCATAATCCAAGTTCATCACA 59.058 34.615 0.00 0.00 0.00 3.58
2617 2801 4.036734 ACTGCAAACCACAGAACAATAGTG 59.963 41.667 0.00 0.00 38.55 2.74
2631 2815 1.421485 CGATGAGCGACTGCAAACC 59.579 57.895 0.00 0.00 46.23 3.27
2736 2944 2.159787 CGCTTGAACCAAGAAGATCACG 60.160 50.000 10.55 0.00 43.42 4.35
2755 2963 1.461888 CCGTCGTCAAAGATCAAACGC 60.462 52.381 0.00 0.00 35.22 4.84
2767 2975 1.300620 CTGCAGAAACCCGTCGTCA 60.301 57.895 8.42 0.00 0.00 4.35
2774 2982 1.657751 GCCGGAATCTGCAGAAACCC 61.658 60.000 22.50 19.41 0.00 4.11
2775 2983 1.657751 GGCCGGAATCTGCAGAAACC 61.658 60.000 22.50 23.39 0.00 3.27
2821 3029 2.997315 TCCTGGAGCACCACGGAG 60.997 66.667 14.32 0.00 41.77 4.63
3150 3358 4.636435 CGGTGTTGAGCCCCCGTT 62.636 66.667 0.00 0.00 35.78 4.44
3154 3362 2.358737 CTGACGGTGTTGAGCCCC 60.359 66.667 0.00 0.00 0.00 5.80
3209 3417 2.722487 GACGACGATGGCGAGGAT 59.278 61.111 0.00 0.00 41.64 3.24
3341 3552 3.056107 TCTTTCCCACATACGAACAGAGG 60.056 47.826 0.00 0.00 0.00 3.69
3404 3615 7.510685 TGATAGCACATCTTATCTTACCTTCCT 59.489 37.037 0.00 0.00 0.00 3.36
3424 3637 1.063806 GGCATGTCGACGATGATAGC 58.936 55.000 23.42 13.98 0.00 2.97
3453 3666 3.811722 TGAAAAGAGCTGCATTACACG 57.188 42.857 1.02 0.00 0.00 4.49
3461 3674 5.809051 CCCAAATCTAATTGAAAAGAGCTGC 59.191 40.000 0.00 0.00 31.84 5.25
3471 3684 5.528690 CGAGCATCTTCCCAAATCTAATTGA 59.471 40.000 0.00 0.00 31.84 2.57
3490 3703 3.723260 TGTGATAAACAACTGACGAGCA 58.277 40.909 0.00 0.00 35.24 4.26
3491 3704 4.928661 ATGTGATAAACAACTGACGAGC 57.071 40.909 0.00 0.00 43.61 5.03
3492 3705 5.867174 TGGTATGTGATAAACAACTGACGAG 59.133 40.000 0.00 0.00 43.61 4.18
3493 3706 5.785243 TGGTATGTGATAAACAACTGACGA 58.215 37.500 0.00 0.00 43.61 4.20
3494 3707 6.312672 TGATGGTATGTGATAAACAACTGACG 59.687 38.462 0.00 0.00 43.61 4.35
3495 3708 7.549134 TCTGATGGTATGTGATAAACAACTGAC 59.451 37.037 0.00 0.00 43.61 3.51
3497 3710 7.334171 TGTCTGATGGTATGTGATAAACAACTG 59.666 37.037 0.00 0.00 43.61 3.16
3498 3711 7.394016 TGTCTGATGGTATGTGATAAACAACT 58.606 34.615 0.00 0.00 43.61 3.16
3499 3712 7.334421 ACTGTCTGATGGTATGTGATAAACAAC 59.666 37.037 0.00 0.00 43.61 3.32
3500 3713 7.394016 ACTGTCTGATGGTATGTGATAAACAA 58.606 34.615 0.00 0.00 43.61 2.83
3501 3714 6.946340 ACTGTCTGATGGTATGTGATAAACA 58.054 36.000 0.00 0.00 44.79 2.83
3502 3715 6.480320 GGACTGTCTGATGGTATGTGATAAAC 59.520 42.308 7.85 0.00 0.00 2.01
3503 3716 6.408092 GGGACTGTCTGATGGTATGTGATAAA 60.408 42.308 7.85 0.00 0.00 1.40
3504 3717 5.070446 GGGACTGTCTGATGGTATGTGATAA 59.930 44.000 7.85 0.00 0.00 1.75
3506 3719 3.389329 GGGACTGTCTGATGGTATGTGAT 59.611 47.826 7.85 0.00 0.00 3.06
3508 3721 2.501316 TGGGACTGTCTGATGGTATGTG 59.499 50.000 7.85 0.00 0.00 3.21
3509 3722 2.768527 CTGGGACTGTCTGATGGTATGT 59.231 50.000 7.85 0.00 0.00 2.29
3510 3723 2.484417 GCTGGGACTGTCTGATGGTATG 60.484 54.545 7.85 0.00 0.00 2.39
3511 3724 1.765314 GCTGGGACTGTCTGATGGTAT 59.235 52.381 7.85 0.00 0.00 2.73
3512 3725 1.195115 GCTGGGACTGTCTGATGGTA 58.805 55.000 7.85 0.00 0.00 3.25
3514 3727 0.177604 GAGCTGGGACTGTCTGATGG 59.822 60.000 7.85 0.00 0.00 3.51
3515 3728 0.177604 GGAGCTGGGACTGTCTGATG 59.822 60.000 7.85 0.00 0.00 3.07
3516 3729 0.252421 TGGAGCTGGGACTGTCTGAT 60.252 55.000 7.85 0.00 0.00 2.90
3517 3730 0.471780 TTGGAGCTGGGACTGTCTGA 60.472 55.000 7.85 0.00 0.00 3.27
3518 3731 0.617413 ATTGGAGCTGGGACTGTCTG 59.383 55.000 7.85 0.23 0.00 3.51
3519 3732 1.366319 AATTGGAGCTGGGACTGTCT 58.634 50.000 7.85 0.00 0.00 3.41
3520 3733 2.206576 AAATTGGAGCTGGGACTGTC 57.793 50.000 0.00 0.00 0.00 3.51
3521 3734 2.158475 TCAAAATTGGAGCTGGGACTGT 60.158 45.455 0.00 0.00 0.00 3.55
3527 3740 3.571401 ACTTCACTCAAAATTGGAGCTGG 59.429 43.478 0.00 0.00 35.79 4.85
3545 3758 7.487829 TGAATTTTATTATGCGCCTGAAACTTC 59.512 33.333 4.18 8.78 0.00 3.01
3549 3763 6.096141 TCCTGAATTTTATTATGCGCCTGAAA 59.904 34.615 4.18 0.00 0.00 2.69
3569 3783 8.149647 TGGTAGTTTTTCGTTAAATACTCCTGA 58.850 33.333 0.00 0.00 37.79 3.86
3599 3813 4.804139 ACTTTATAGGCACGATTTGACGAG 59.196 41.667 0.00 0.00 38.90 4.18
3605 3819 5.985911 AGTGGTACTTTATAGGCACGATTT 58.014 37.500 0.00 0.00 0.00 2.17
3617 3831 6.975772 GCACAAATTTGTCAAGTGGTACTTTA 59.024 34.615 20.85 0.00 39.91 1.85
3621 3835 4.048504 GGCACAAATTTGTCAAGTGGTAC 58.951 43.478 20.85 3.64 39.91 3.34
3694 3908 7.167468 GTCATAATCATGTTTAATTTCGGCCAC 59.833 37.037 2.24 0.00 33.57 5.01
3790 4046 1.692749 ACTGACATACGGGCCCCAT 60.693 57.895 18.66 7.01 0.00 4.00
3953 4242 3.390311 GGTTAGTGGGTAGGTTAGGGATG 59.610 52.174 0.00 0.00 0.00 3.51
4029 4322 1.006571 CAGTATTCCGGCGGCGTAT 60.007 57.895 30.09 23.08 0.00 3.06
4260 4553 0.316204 GGACGAGTTCTTCCGTGGAA 59.684 55.000 0.68 0.68 39.30 3.53
4284 4577 1.876799 CATTCGGTTGGTGCAGTACAA 59.123 47.619 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.