Multiple sequence alignment - TraesCS5D01G215200

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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 TraesCS5D01G215200 chr5D 100.000 4558 0 0 1 4558 324580093 324584650 0.000000e+00 8418.0
1 TraesCS5D01G215200 chr5D 100.000 3834 0 0 5508 9341 324585600 324589433 0.000000e+00 7081.0
2 TraesCS5D01G215200 chr5D 91.656 791 38 5 1 764 14641260 14642049 0.000000e+00 1070.0
3 TraesCS5D01G215200 chr5D 91.049 782 40 7 1 754 555499872 555500651 0.000000e+00 1029.0
4 TraesCS5D01G215200 chr5D 100.000 546 0 0 4818 5363 324584910 324585455 0.000000e+00 1009.0
5 TraesCS5D01G215200 chr5B 93.791 2287 63 16 5508 7754 376333119 376335366 0.000000e+00 3363.0
6 TraesCS5D01G215200 chr5B 95.640 1858 56 11 773 2620 376326401 376328243 0.000000e+00 2959.0
7 TraesCS5D01G215200 chr5B 95.993 1822 52 8 2724 4534 376330508 376332319 0.000000e+00 2940.0
8 TraesCS5D01G215200 chr5B 93.018 845 43 11 7755 8586 376335399 376336240 0.000000e+00 1219.0
9 TraesCS5D01G215200 chr5B 92.754 552 22 5 4818 5363 376332509 376333048 0.000000e+00 782.0
10 TraesCS5D01G215200 chr5B 86.838 623 34 14 8748 9341 376336275 376336878 0.000000e+00 652.0
11 TraesCS5D01G215200 chr5B 94.643 112 6 0 2621 2732 376328310 376328421 3.470000e-39 174.0
12 TraesCS5D01G215200 chr5A 96.476 1873 41 7 2683 4534 422064303 422066171 0.000000e+00 3070.0
13 TraesCS5D01G215200 chr5A 96.353 1700 55 4 930 2626 422062389 422064084 0.000000e+00 2789.0
14 TraesCS5D01G215200 chr5A 95.196 1457 36 15 5508 6936 422067104 422068554 0.000000e+00 2272.0
15 TraesCS5D01G215200 chr5A 91.621 728 50 7 8618 9341 422075897 422076617 0.000000e+00 996.0
16 TraesCS5D01G215200 chr5A 93.863 554 25 3 4818 5363 422066481 422067033 0.000000e+00 826.0
17 TraesCS5D01G215200 chr5A 94.118 510 18 5 8064 8571 422075409 422075908 0.000000e+00 765.0
18 TraesCS5D01G215200 chr5A 93.567 513 11 9 6921 7433 422068671 422069161 0.000000e+00 745.0
19 TraesCS5D01G215200 chr5A 87.242 533 31 17 7441 7943 422069265 422069790 2.930000e-159 573.0
20 TraesCS5D01G215200 chr5A 97.015 67 2 0 8004 8070 422069789 422069855 7.670000e-21 113.0
21 TraesCS5D01G215200 chr5A 91.667 72 6 0 779 850 422062298 422062369 5.970000e-17 100.0
22 TraesCS5D01G215200 chr5A 97.368 38 1 0 7975 8012 588845524 588845487 2.180000e-06 65.8
23 TraesCS5D01G215200 chr5A 93.023 43 3 0 7932 7974 429169655 429169697 7.830000e-06 63.9
24 TraesCS5D01G215200 chr5A 100.000 28 0 0 3904 3931 143574354 143574381 1.700000e-02 52.8
25 TraesCS5D01G215200 chr2D 92.555 779 29 5 1 751 486303979 486304756 0.000000e+00 1090.0
26 TraesCS5D01G215200 chr2D 91.763 777 38 4 1 752 623949566 623950341 0.000000e+00 1057.0
27 TraesCS5D01G215200 chr2D 90.152 792 46 6 1 762 559833251 559834040 0.000000e+00 1002.0
28 TraesCS5D01G215200 chr2D 83.133 83 13 1 7923 8005 2047551 2047632 3.620000e-09 75.0
29 TraesCS5D01G215200 chr2D 100.000 36 0 0 7973 8008 17068391 17068356 6.050000e-07 67.6
30 TraesCS5D01G215200 chr2D 95.122 41 2 0 7973 8013 302248045 302248005 2.180000e-06 65.8
31 TraesCS5D01G215200 chr1D 92.436 780 30 4 1 751 426586072 426585293 0.000000e+00 1086.0
32 TraesCS5D01G215200 chr1D 90.909 792 41 7 1 762 307826091 307825301 0.000000e+00 1035.0
33 TraesCS5D01G215200 chr1D 89.367 790 32 6 1 760 469382171 469382938 0.000000e+00 946.0
34 TraesCS5D01G215200 chr4D 92.506 774 31 3 1 747 498513895 498514668 0.000000e+00 1083.0
35 TraesCS5D01G215200 chr4D 97.368 38 1 0 7973 8010 494787228 494787191 2.180000e-06 65.8
36 TraesCS5D01G215200 chr4D 100.000 33 0 0 7942 7974 427325373 427325405 2.820000e-05 62.1
37 TraesCS5D01G215200 chr6D 92.159 778 33 6 1 751 460306057 460306833 0.000000e+00 1074.0
38 TraesCS5D01G215200 chr6D 97.368 38 1 0 7952 7989 361536699 361536736 2.180000e-06 65.8
39 TraesCS5D01G215200 chr6D 100.000 33 0 0 7942 7974 8901112 8901080 2.820000e-05 62.1
40 TraesCS5D01G215200 chr3D 91.923 780 32 13 1 751 214958953 214959730 0.000000e+00 1062.0
41 TraesCS5D01G215200 chr3D 91.114 754 37 10 1 729 425153508 425152760 0.000000e+00 994.0
42 TraesCS5D01G215200 chr3D 83.721 86 6 6 3904 3981 197994051 197993966 3.620000e-09 75.0
43 TraesCS5D01G215200 chr7D 91.571 783 35 7 1 754 114467562 114468342 0.000000e+00 1051.0
44 TraesCS5D01G215200 chr7D 90.990 788 39 6 1 760 26718484 26719267 0.000000e+00 1033.0
45 TraesCS5D01G215200 chr7D 95.616 593 19 3 1 587 603599053 603598462 0.000000e+00 944.0
46 TraesCS5D01G215200 chr7D 88.679 265 7 4 510 751 630792496 630792232 1.520000e-77 302.0
47 TraesCS5D01G215200 chr7D 87.342 79 8 2 3904 3981 274696573 274696650 1.290000e-13 89.8
48 TraesCS5D01G215200 chr7D 100.000 28 0 0 3905 3932 583447032 583447005 1.700000e-02 52.8
49 TraesCS5D01G215200 chr4B 90.204 786 44 9 1 759 446199240 446200019 0.000000e+00 994.0
50 TraesCS5D01G215200 chr7B 91.089 101 7 2 8597 8697 256222300 256222202 1.640000e-27 135.0
51 TraesCS5D01G215200 chr7B 83.544 79 11 2 3904 3981 263111211 263111134 1.300000e-08 73.1
52 TraesCS5D01G215200 chr7B 85.294 68 5 3 7938 8005 13758324 13758262 2.180000e-06 65.8
53 TraesCS5D01G215200 chr7B 100.000 33 0 0 7942 7974 4613764 4613732 2.820000e-05 62.1
54 TraesCS5D01G215200 chr3A 85.333 75 6 4 3904 3973 314623560 314623486 1.300000e-08 73.1
55 TraesCS5D01G215200 chr6A 100.000 35 0 0 7973 8007 536233956 536233922 2.180000e-06 65.8
56 TraesCS5D01G215200 chr6A 90.000 50 5 0 7927 7976 591898975 591899024 2.180000e-06 65.8
57 TraesCS5D01G215200 chrUn 100.000 33 0 0 7973 8005 94750552 94750584 2.820000e-05 62.1
58 TraesCS5D01G215200 chr7A 100.000 28 0 0 3905 3932 675071976 675071949 1.700000e-02 52.8
59 TraesCS5D01G215200 chr6B 100.000 28 0 0 2599 2626 668897423 668897450 1.700000e-02 52.8


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 TraesCS5D01G215200 chr5D 324580093 324589433 9340 False 5502.666667 8418 100.000000 1 9341 3 chr5D.!!$F3 9340
1 TraesCS5D01G215200 chr5D 14641260 14642049 789 False 1070.000000 1070 91.656000 1 764 1 chr5D.!!$F1 763
2 TraesCS5D01G215200 chr5D 555499872 555500651 779 False 1029.000000 1029 91.049000 1 754 1 chr5D.!!$F2 753
3 TraesCS5D01G215200 chr5B 376326401 376336878 10477 False 1727.000000 3363 93.239571 773 9341 7 chr5B.!!$F1 8568
4 TraesCS5D01G215200 chr5A 422062298 422069855 7557 False 1311.000000 3070 93.922375 779 8070 8 chr5A.!!$F3 7291
5 TraesCS5D01G215200 chr5A 422075409 422076617 1208 False 880.500000 996 92.869500 8064 9341 2 chr5A.!!$F4 1277
6 TraesCS5D01G215200 chr2D 486303979 486304756 777 False 1090.000000 1090 92.555000 1 751 1 chr2D.!!$F2 750
7 TraesCS5D01G215200 chr2D 623949566 623950341 775 False 1057.000000 1057 91.763000 1 752 1 chr2D.!!$F4 751
8 TraesCS5D01G215200 chr2D 559833251 559834040 789 False 1002.000000 1002 90.152000 1 762 1 chr2D.!!$F3 761
9 TraesCS5D01G215200 chr1D 426585293 426586072 779 True 1086.000000 1086 92.436000 1 751 1 chr1D.!!$R2 750
10 TraesCS5D01G215200 chr1D 307825301 307826091 790 True 1035.000000 1035 90.909000 1 762 1 chr1D.!!$R1 761
11 TraesCS5D01G215200 chr1D 469382171 469382938 767 False 946.000000 946 89.367000 1 760 1 chr1D.!!$F1 759
12 TraesCS5D01G215200 chr4D 498513895 498514668 773 False 1083.000000 1083 92.506000 1 747 1 chr4D.!!$F2 746
13 TraesCS5D01G215200 chr6D 460306057 460306833 776 False 1074.000000 1074 92.159000 1 751 1 chr6D.!!$F2 750
14 TraesCS5D01G215200 chr3D 214958953 214959730 777 False 1062.000000 1062 91.923000 1 751 1 chr3D.!!$F1 750
15 TraesCS5D01G215200 chr3D 425152760 425153508 748 True 994.000000 994 91.114000 1 729 1 chr3D.!!$R2 728
16 TraesCS5D01G215200 chr7D 114467562 114468342 780 False 1051.000000 1051 91.571000 1 754 1 chr7D.!!$F2 753
17 TraesCS5D01G215200 chr7D 26718484 26719267 783 False 1033.000000 1033 90.990000 1 760 1 chr7D.!!$F1 759
18 TraesCS5D01G215200 chr7D 603598462 603599053 591 True 944.000000 944 95.616000 1 587 1 chr7D.!!$R2 586
19 TraesCS5D01G215200 chr4B 446199240 446200019 779 False 994.000000 994 90.204000 1 759 1 chr4B.!!$F1 758

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
954 1021 0.109412 GACCGATCGTGTTTCCGTCT 60.109 55.000 15.09 0.0 0.00 4.18 F
955 1022 0.109412 ACCGATCGTGTTTCCGTCTC 60.109 55.000 15.09 0.0 0.00 3.36 F
1334 1401 2.028130 CCAAGTGAGTCCGCTCTATCT 58.972 52.381 0.00 0.0 42.13 1.98 F
2135 2212 3.813724 CCTTGTATCTCATGCACCATCTG 59.186 47.826 0.00 0.0 0.00 2.90 F
3224 5558 2.362077 GCAAAACTTCAGGCCTCTTTCA 59.638 45.455 0.00 0.0 0.00 2.69 F
4076 6420 0.824109 TCGGAAGGAATCAGATGCGT 59.176 50.000 0.00 0.0 0.00 5.24 F
4553 6908 0.039617 GCGATGATCCTGGAGAGACG 60.040 60.000 1.52 7.1 0.00 4.18 F
5085 7472 0.405585 CCAGGGGAAAAAGCTCCTCA 59.594 55.000 0.00 0.0 36.32 3.86 F
5112 7501 1.372683 CTGGTCCAGTGTGTCAGGG 59.627 63.158 11.09 0.0 0.00 4.45 F
6509 8931 2.978978 TGAGGAGGTTGGTTCTGATTCA 59.021 45.455 0.00 0.0 0.00 2.57 F
7434 9990 0.727970 TGTTTTCACACCGACAACCG 59.272 50.000 0.00 0.0 34.04 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2624 2768 2.290514 ACTGGCACTGTGACATAGCAAT 60.291 45.455 18.08 0.00 39.59 3.56 R
2656 2800 4.098349 ACGTAATTCCGTAATGAGGCTACA 59.902 41.667 0.00 0.00 39.73 2.74 R
2883 5217 5.409826 ACTGAAAACACGAAGATCAGATTCC 59.590 40.000 7.98 0.00 39.85 3.01 R
3963 6307 1.410882 GCACCTCCTCATCTAGGTCAC 59.589 57.143 0.00 0.00 44.43 3.67 R
4534 6889 0.039617 CGTCTCTCCAGGATCATCGC 60.040 60.000 0.00 0.00 0.00 4.58 R
4947 7334 0.393267 CGTCCTTATTTTCCCCCGCA 60.393 55.000 0.00 0.00 0.00 5.69 R
5979 8393 1.616374 GAGGCGTTTTCCCCATTTTCA 59.384 47.619 0.00 0.00 0.00 2.69 R
6996 9552 1.805345 GCATGAGCCATATCTGCAGAC 59.195 52.381 20.97 5.79 33.13 3.51 R
7042 9598 9.185680 ACCCATAAACTGATCCAAAAATACTAC 57.814 33.333 0.00 0.00 0.00 2.73 R
7700 10356 0.392193 CTTGGTGGAGCTGCCTAGTG 60.392 60.000 1.53 0.00 37.63 2.74 R
8991 11705 0.250684 TGCACCACACCGATTGACAT 60.251 50.000 0.00 0.00 0.00 3.06 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
352 366 1.552337 CTGCAGTAGACCAGACCACAT 59.448 52.381 5.25 0.00 0.00 3.21
503 541 3.059461 GCACTTAAACGAACATGGACGAA 60.059 43.478 17.79 4.27 0.00 3.85
545 585 2.736682 GCGCGCGGTAAAGTGTCAT 61.737 57.895 33.06 0.00 0.00 3.06
555 595 0.398696 AAAGTGTCATGTGGGGCGTA 59.601 50.000 0.00 0.00 0.00 4.42
558 598 3.192922 GTCATGTGGGGCGTACGC 61.193 66.667 31.54 31.54 41.06 4.42
617 680 1.373246 CGCGTGTAAAAGGGACCGA 60.373 57.895 0.00 0.00 0.00 4.69
670 737 0.748367 TTTGCCCACACACAAGCGTA 60.748 50.000 0.00 0.00 0.00 4.42
678 745 0.673333 CACACAAGCGTATGGGCTGA 60.673 55.000 0.00 0.00 43.93 4.26
754 821 0.651031 GCAGTTATCGGCGTCCTTTC 59.349 55.000 6.85 0.00 0.00 2.62
764 831 1.000843 GGCGTCCTTTCTTTTTGGCAT 59.999 47.619 0.00 0.00 0.00 4.40
765 832 2.061028 GCGTCCTTTCTTTTTGGCATG 58.939 47.619 0.00 0.00 0.00 4.06
766 833 2.676076 CGTCCTTTCTTTTTGGCATGG 58.324 47.619 0.00 0.00 0.00 3.66
767 834 2.295909 CGTCCTTTCTTTTTGGCATGGA 59.704 45.455 0.00 0.00 0.00 3.41
768 835 3.056607 CGTCCTTTCTTTTTGGCATGGAT 60.057 43.478 0.00 0.00 0.00 3.41
769 836 4.248058 GTCCTTTCTTTTTGGCATGGATG 58.752 43.478 0.00 0.00 0.00 3.51
770 837 3.903090 TCCTTTCTTTTTGGCATGGATGT 59.097 39.130 0.00 0.00 0.00 3.06
771 838 4.021192 TCCTTTCTTTTTGGCATGGATGTC 60.021 41.667 0.00 0.00 0.00 3.06
777 844 1.626686 TTGGCATGGATGTCCGTTTT 58.373 45.000 0.00 0.00 39.43 2.43
806 873 2.539142 CGTTGAAGACCTCGGAGATACG 60.539 54.545 6.58 0.00 33.89 3.06
815 882 3.050619 CCTCGGAGATACGCATTGTAAC 58.949 50.000 6.58 0.00 36.44 2.50
821 888 4.092383 GGAGATACGCATTGTAACACGTTT 59.908 41.667 0.00 0.00 39.78 3.60
853 920 7.041576 TCGAAGTCGTGCTACACATAATATACT 60.042 37.037 0.00 0.00 40.80 2.12
854 921 7.059602 CGAAGTCGTGCTACACATAATATACTG 59.940 40.741 0.00 0.00 33.40 2.74
857 924 6.802348 GTCGTGCTACACATAATATACTGGAG 59.198 42.308 0.00 0.00 33.40 3.86
859 926 7.662669 TCGTGCTACACATAATATACTGGAGTA 59.337 37.037 0.00 0.00 33.40 2.59
860 927 7.749570 CGTGCTACACATAATATACTGGAGTAC 59.250 40.741 0.00 2.43 33.40 2.73
861 928 7.749570 GTGCTACACATAATATACTGGAGTACG 59.250 40.741 0.00 0.00 34.08 3.67
862 929 7.662669 TGCTACACATAATATACTGGAGTACGA 59.337 37.037 0.00 0.00 32.72 3.43
863 930 8.176365 GCTACACATAATATACTGGAGTACGAG 58.824 40.741 0.00 0.00 32.72 4.18
954 1021 0.109412 GACCGATCGTGTTTCCGTCT 60.109 55.000 15.09 0.00 0.00 4.18
955 1022 0.109412 ACCGATCGTGTTTCCGTCTC 60.109 55.000 15.09 0.00 0.00 3.36
1160 1227 3.230134 GACTGGATCTATCTCCTGCTGT 58.770 50.000 0.00 0.00 37.67 4.40
1222 1289 4.143333 GCGGGGTTCGAGCAGCTA 62.143 66.667 0.00 0.00 42.43 3.32
1334 1401 2.028130 CCAAGTGAGTCCGCTCTATCT 58.972 52.381 0.00 0.00 42.13 1.98
1528 1595 5.735766 ACCAAGGTGAGCTCTTAGTTATTC 58.264 41.667 16.19 0.00 0.00 1.75
1569 1636 6.823182 TGTCCTGAAACATCGATTGATAATGT 59.177 34.615 0.00 0.00 35.20 2.71
1682 1749 4.054671 ACAGAGTCTTGCTTCTTCTTTCG 58.945 43.478 0.00 0.00 0.00 3.46
1906 1973 4.755123 AGACAGGTTGGTGATAAAAACTCG 59.245 41.667 0.00 0.00 0.00 4.18
2135 2212 3.813724 CCTTGTATCTCATGCACCATCTG 59.186 47.826 0.00 0.00 0.00 2.90
2242 2319 4.724279 TCCTTAAACTGAAGGGCTTTCT 57.276 40.909 10.86 0.00 45.35 2.52
2248 2325 7.176690 CCTTAAACTGAAGGGCTTTCTTTATCA 59.823 37.037 10.86 0.00 42.12 2.15
2324 2401 4.092116 AGAGCATTTTGGGCCTATAGTC 57.908 45.455 4.53 0.00 0.00 2.59
2428 2505 7.173218 CCATACTGCAATGTAAATTCGGTATCT 59.827 37.037 0.00 0.00 0.00 1.98
2429 2506 6.604735 ACTGCAATGTAAATTCGGTATCTC 57.395 37.500 0.00 0.00 0.00 2.75
2497 2574 5.622378 GCTAGTTGTTTACAGATTGCAGTC 58.378 41.667 0.00 0.00 0.00 3.51
2656 2800 7.165485 TGTCACAGTGCCAGTACTAAATAATT 58.835 34.615 0.00 0.00 0.00 1.40
2883 5217 3.376234 AGGTGATTTGACTGCATTGATCG 59.624 43.478 0.00 0.00 0.00 3.69
3171 5505 2.845967 CACACGTTCTGAACAAAACTGC 59.154 45.455 19.56 0.00 0.00 4.40
3224 5558 2.362077 GCAAAACTTCAGGCCTCTTTCA 59.638 45.455 0.00 0.00 0.00 2.69
3230 5564 4.446371 ACTTCAGGCCTCTTTCATTATCG 58.554 43.478 0.00 0.00 0.00 2.92
3691 6028 3.149899 GCTGCAGCTGTGTGATACT 57.850 52.632 31.33 0.00 38.21 2.12
3936 6280 4.512914 GCCTGGCCCATCTCCACC 62.513 72.222 7.66 0.00 0.00 4.61
4076 6420 0.824109 TCGGAAGGAATCAGATGCGT 59.176 50.000 0.00 0.00 0.00 5.24
4144 6488 1.379977 TGCCCGAGTCGAGGAAGAT 60.380 57.895 15.64 0.00 0.00 2.40
4485 6839 4.404073 ACAAAGGCATACAAAAGTCCAACA 59.596 37.500 0.00 0.00 0.00 3.33
4526 6881 8.630917 CAAAGCATTAGGATTTTCAGAGATCAT 58.369 33.333 0.00 0.00 31.52 2.45
4534 6889 6.993308 AGGATTTTCAGAGATCATGACATCTG 59.007 38.462 23.84 23.84 40.42 2.90
4535 6890 6.293516 GGATTTTCAGAGATCATGACATCTGC 60.294 42.308 24.54 14.86 39.21 4.26
4538 6893 3.573110 TCAGAGATCATGACATCTGCGAT 59.427 43.478 24.54 0.00 39.21 4.58
4540 6895 3.573110 AGAGATCATGACATCTGCGATGA 59.427 43.478 20.36 0.00 32.94 2.92
4541 6896 4.221041 AGAGATCATGACATCTGCGATGAT 59.779 41.667 20.36 3.21 38.08 2.45
4542 6897 4.496360 AGATCATGACATCTGCGATGATC 58.504 43.478 20.36 16.82 46.20 2.92
4544 6899 2.631545 TCATGACATCTGCGATGATCCT 59.368 45.455 20.36 8.35 0.00 3.24
4547 6902 1.342496 GACATCTGCGATGATCCTGGA 59.658 52.381 20.36 0.00 0.00 3.86
4548 6903 1.343789 ACATCTGCGATGATCCTGGAG 59.656 52.381 20.36 0.00 0.00 3.86
4550 6905 1.326328 TCTGCGATGATCCTGGAGAG 58.674 55.000 1.52 0.00 0.00 3.20
4551 6906 1.133668 TCTGCGATGATCCTGGAGAGA 60.134 52.381 1.52 0.00 0.00 3.10
4552 6907 1.000385 CTGCGATGATCCTGGAGAGAC 60.000 57.143 1.52 0.00 0.00 3.36
4553 6908 0.039617 GCGATGATCCTGGAGAGACG 60.040 60.000 1.52 7.10 0.00 4.18
4557 6912 1.098129 TGATCCTGGAGAGACGAGCG 61.098 60.000 1.52 0.00 0.00 5.03
4896 7283 2.654079 CGTTGGCAGGGCTCTCTCT 61.654 63.158 0.00 0.00 0.00 3.10
5054 7441 1.004745 CTCTGGTTGGGCAGTTACCAT 59.995 52.381 0.00 0.00 40.89 3.55
5085 7472 0.405585 CCAGGGGAAAAAGCTCCTCA 59.594 55.000 0.00 0.00 36.32 3.86
5087 7474 2.558350 CCAGGGGAAAAAGCTCCTCATT 60.558 50.000 0.00 0.00 36.32 2.57
5101 7488 1.619654 CTCATTGTTTGGCTGGTCCA 58.380 50.000 0.00 0.00 44.85 4.02
5108 7497 2.828868 TGGCTGGTCCAGTGTGTC 59.171 61.111 20.24 2.88 40.72 3.67
5112 7501 1.372683 CTGGTCCAGTGTGTCAGGG 59.627 63.158 11.09 0.00 0.00 4.45
5259 7648 5.050490 GTGGCTCGATTCACTATTACATGT 58.950 41.667 2.69 2.69 0.00 3.21
5295 7684 3.324846 TGTCAGAGCCAAGCTTCTAGAAA 59.675 43.478 6.63 0.00 39.88 2.52
5978 8392 6.594788 AATGTGTGGATTCTGCAATTTAGT 57.405 33.333 0.00 0.00 0.00 2.24
5979 8393 6.594788 ATGTGTGGATTCTGCAATTTAGTT 57.405 33.333 0.00 0.00 0.00 2.24
6048 8465 4.734695 GCTTATAGTGTTGCTGGATTTGGC 60.735 45.833 0.00 0.00 0.00 4.52
6078 8495 8.701895 TCGTACTCCCTACAATATCTCATTTTT 58.298 33.333 0.00 0.00 0.00 1.94
6095 8512 9.636789 TCTCATTTTTCTCATGGATGATTGTAT 57.363 29.630 0.00 0.00 36.02 2.29
6363 8785 6.569179 AACAAATACGTATTGCTGTCCTTT 57.431 33.333 21.00 5.59 0.00 3.11
6509 8931 2.978978 TGAGGAGGTTGGTTCTGATTCA 59.021 45.455 0.00 0.00 0.00 2.57
6593 9015 5.982890 ACCATTCAAATTCCAAGGTACAG 57.017 39.130 0.00 0.00 0.00 2.74
6684 9106 9.906660 TTTTCACATTACCTGATTTTATGTCAC 57.093 29.630 0.00 0.00 0.00 3.67
7042 9598 7.122650 CCTTGCACCCCAATTATATGGTAATAG 59.877 40.741 0.00 0.00 38.91 1.73
7309 9865 7.285401 CCCTATTACAATTGTGGATTAGCTTGT 59.715 37.037 21.42 0.00 0.00 3.16
7310 9866 9.337396 CCTATTACAATTGTGGATTAGCTTGTA 57.663 33.333 21.42 0.00 0.00 2.41
7312 9868 8.807948 ATTACAATTGTGGATTAGCTTGTAGT 57.192 30.769 21.42 0.00 32.52 2.73
7313 9869 9.899661 ATTACAATTGTGGATTAGCTTGTAGTA 57.100 29.630 21.42 0.00 32.52 1.82
7314 9870 9.727859 TTACAATTGTGGATTAGCTTGTAGTAA 57.272 29.630 21.42 0.00 32.52 2.24
7315 9871 8.630054 ACAATTGTGGATTAGCTTGTAGTAAA 57.370 30.769 11.07 0.00 0.00 2.01
7316 9872 8.512138 ACAATTGTGGATTAGCTTGTAGTAAAC 58.488 33.333 11.07 0.00 0.00 2.01
7317 9873 8.730680 CAATTGTGGATTAGCTTGTAGTAAACT 58.269 33.333 0.00 0.00 0.00 2.66
7318 9874 9.953565 AATTGTGGATTAGCTTGTAGTAAACTA 57.046 29.630 0.00 0.00 0.00 2.24
7319 9875 9.953565 ATTGTGGATTAGCTTGTAGTAAACTAA 57.046 29.630 0.00 0.00 0.00 2.24
7320 9876 9.781633 TTGTGGATTAGCTTGTAGTAAACTAAA 57.218 29.630 0.00 0.00 0.00 1.85
7321 9877 9.953565 TGTGGATTAGCTTGTAGTAAACTAAAT 57.046 29.630 0.00 0.00 0.00 1.40
7340 9896 2.584835 TCAAGTTGCCATAACTGCCT 57.415 45.000 0.00 0.00 0.00 4.75
7360 9916 7.550906 ACTGCCTTTCTCAACTTATACTTGATC 59.449 37.037 0.00 0.00 0.00 2.92
7373 9929 8.454106 ACTTATACTTGATCTTGTGATTGCAAC 58.546 33.333 0.00 0.00 32.19 4.17
7374 9930 6.822667 ATACTTGATCTTGTGATTGCAACA 57.177 33.333 0.00 0.00 32.19 3.33
7375 9931 5.717078 ACTTGATCTTGTGATTGCAACAT 57.283 34.783 0.00 0.00 32.19 2.71
7401 9957 5.731599 AGAGTACTAACGACAAGATACCG 57.268 43.478 0.00 0.00 0.00 4.02
7433 9989 2.095161 TGTTGTTTTCACACCGACAACC 60.095 45.455 13.61 0.30 46.87 3.77
7434 9990 0.727970 TGTTTTCACACCGACAACCG 59.272 50.000 0.00 0.00 34.04 4.44
7654 10310 3.738281 AGGAGAGCCAATTCGTATGAACG 60.738 47.826 0.00 0.00 43.26 3.95
7700 10356 6.509418 TTTTGAGCTCCACCAAACATATAC 57.491 37.500 12.15 0.00 32.67 1.47
7740 10396 4.360563 AGATACATGTCGTTTTAGCTCCG 58.639 43.478 0.00 0.00 0.00 4.63
7760 10448 4.826733 TCCGCCAAACATATATCAGCAATT 59.173 37.500 0.00 0.00 0.00 2.32
7948 10636 9.636789 AACAAGTAAAAATACAACTTACTCCCT 57.363 29.630 0.00 0.00 35.36 4.20
7949 10637 9.063615 ACAAGTAAAAATACAACTTACTCCCTG 57.936 33.333 0.00 0.00 35.36 4.45
8172 10862 2.097466 GTCAACAATCGGGCCAATACTG 59.903 50.000 4.39 0.00 0.00 2.74
8280 10970 5.971792 CGACGTCAACTACTCATATGAACAT 59.028 40.000 17.16 0.00 0.00 2.71
8351 11041 3.722908 AGACTGCTGAGGTGTAGTAGA 57.277 47.619 0.00 0.00 33.21 2.59
8352 11042 3.349022 AGACTGCTGAGGTGTAGTAGAC 58.651 50.000 0.00 0.00 33.21 2.59
8354 11044 2.290134 ACTGCTGAGGTGTAGTAGACGA 60.290 50.000 0.00 0.00 32.96 4.20
8356 11046 1.401199 GCTGAGGTGTAGTAGACGACC 59.599 57.143 0.00 0.00 32.43 4.79
8358 11048 3.280295 CTGAGGTGTAGTAGACGACCAT 58.720 50.000 0.00 0.00 33.84 3.55
8359 11049 4.449131 CTGAGGTGTAGTAGACGACCATA 58.551 47.826 0.00 0.00 33.84 2.74
8360 11050 5.045012 TGAGGTGTAGTAGACGACCATAT 57.955 43.478 0.00 0.00 33.84 1.78
8361 11051 6.178607 TGAGGTGTAGTAGACGACCATATA 57.821 41.667 0.00 0.00 33.84 0.86
8458 11153 9.901724 GTATGTTAGTGAAGACGTGAATAAATG 57.098 33.333 0.00 0.00 0.00 2.32
8586 11284 0.721718 AGTTAGACATCGCGCTTTGC 59.278 50.000 5.56 0.00 41.47 3.68
8587 11285 0.442310 GTTAGACATCGCGCTTTGCA 59.558 50.000 5.56 0.00 46.97 4.08
8588 11286 0.442310 TTAGACATCGCGCTTTGCAC 59.558 50.000 5.56 1.32 46.97 4.57
8589 11287 0.389817 TAGACATCGCGCTTTGCACT 60.390 50.000 5.56 8.58 46.97 4.40
8591 11289 0.247301 GACATCGCGCTTTGCACTAC 60.247 55.000 5.56 0.00 46.97 2.73
8592 11290 0.670546 ACATCGCGCTTTGCACTACT 60.671 50.000 5.56 0.00 46.97 2.57
8593 11291 0.443869 CATCGCGCTTTGCACTACTT 59.556 50.000 5.56 0.00 46.97 2.24
8594 11292 1.135972 CATCGCGCTTTGCACTACTTT 60.136 47.619 5.56 0.00 46.97 2.66
8595 11293 0.941542 TCGCGCTTTGCACTACTTTT 59.058 45.000 5.56 0.00 46.97 2.27
8597 11295 1.408422 GCGCTTTGCACTACTTTTGG 58.592 50.000 0.00 0.00 45.45 3.28
8599 11297 2.351738 GCGCTTTGCACTACTTTTGGAT 60.352 45.455 0.00 0.00 45.45 3.41
8600 11298 3.857010 GCGCTTTGCACTACTTTTGGATT 60.857 43.478 0.00 0.00 45.45 3.01
8601 11299 3.670055 CGCTTTGCACTACTTTTGGATTG 59.330 43.478 0.00 0.00 0.00 2.67
8602 11300 3.989817 GCTTTGCACTACTTTTGGATTGG 59.010 43.478 0.00 0.00 0.00 3.16
8603 11301 4.261994 GCTTTGCACTACTTTTGGATTGGA 60.262 41.667 0.00 0.00 0.00 3.53
8604 11302 5.452078 TTTGCACTACTTTTGGATTGGAG 57.548 39.130 0.00 0.00 0.00 3.86
8605 11303 3.420893 TGCACTACTTTTGGATTGGAGG 58.579 45.455 0.00 0.00 0.00 4.30
8607 11305 3.356290 CACTACTTTTGGATTGGAGGGG 58.644 50.000 0.00 0.00 0.00 4.79
8608 11306 3.010138 CACTACTTTTGGATTGGAGGGGA 59.990 47.826 0.00 0.00 0.00 4.81
8609 11307 3.858638 ACTACTTTTGGATTGGAGGGGAT 59.141 43.478 0.00 0.00 0.00 3.85
8611 11309 4.146245 ACTTTTGGATTGGAGGGGATTT 57.854 40.909 0.00 0.00 0.00 2.17
8612 11310 3.840078 ACTTTTGGATTGGAGGGGATTTG 59.160 43.478 0.00 0.00 0.00 2.32
8614 11312 3.386932 TTGGATTGGAGGGGATTTGAG 57.613 47.619 0.00 0.00 0.00 3.02
8615 11313 2.572340 TGGATTGGAGGGGATTTGAGA 58.428 47.619 0.00 0.00 0.00 3.27
8616 11314 2.511218 TGGATTGGAGGGGATTTGAGAG 59.489 50.000 0.00 0.00 0.00 3.20
8617 11315 2.780010 GGATTGGAGGGGATTTGAGAGA 59.220 50.000 0.00 0.00 0.00 3.10
8618 11316 3.203040 GGATTGGAGGGGATTTGAGAGAA 59.797 47.826 0.00 0.00 0.00 2.87
8620 11318 4.953781 TTGGAGGGGATTTGAGAGAATT 57.046 40.909 0.00 0.00 0.00 2.17
8621 11319 4.953781 TGGAGGGGATTTGAGAGAATTT 57.046 40.909 0.00 0.00 0.00 1.82
8622 11320 5.275263 TGGAGGGGATTTGAGAGAATTTT 57.725 39.130 0.00 0.00 0.00 1.82
8623 11321 5.018809 TGGAGGGGATTTGAGAGAATTTTG 58.981 41.667 0.00 0.00 0.00 2.44
8624 11322 5.222316 TGGAGGGGATTTGAGAGAATTTTGA 60.222 40.000 0.00 0.00 0.00 2.69
8625 11323 5.126222 GGAGGGGATTTGAGAGAATTTTGAC 59.874 44.000 0.00 0.00 0.00 3.18
8626 11324 5.896963 AGGGGATTTGAGAGAATTTTGACT 58.103 37.500 0.00 0.00 0.00 3.41
8627 11325 6.318112 AGGGGATTTGAGAGAATTTTGACTT 58.682 36.000 0.00 0.00 0.00 3.01
8631 11329 8.576442 GGGATTTGAGAGAATTTTGACTTGTAA 58.424 33.333 0.00 0.00 0.00 2.41
8647 11345 8.934023 TGACTTGTAAGGGATTAAATTCACTT 57.066 30.769 0.00 0.00 42.04 3.16
8648 11346 9.010029 TGACTTGTAAGGGATTAAATTCACTTC 57.990 33.333 0.00 0.00 38.65 3.01
8650 11348 9.362151 ACTTGTAAGGGATTAAATTCACTTCAA 57.638 29.630 0.00 2.73 38.65 2.69
8658 11356 5.659440 TTAAATTCACTTCAATCCCTGCC 57.341 39.130 0.00 0.00 0.00 4.85
8659 11357 2.905415 ATTCACTTCAATCCCTGCCA 57.095 45.000 0.00 0.00 0.00 4.92
8662 11360 2.956132 TCACTTCAATCCCTGCCAAAA 58.044 42.857 0.00 0.00 0.00 2.44
8685 11383 3.089284 CCCCTTCAAATACCTGTCAACC 58.911 50.000 0.00 0.00 0.00 3.77
8695 11393 1.507141 CCTGTCAACCGAACACAGCC 61.507 60.000 0.00 0.00 36.91 4.85
8718 11416 1.000955 AGAGAGTACGCCAAAGGTGTG 59.999 52.381 12.22 0.00 46.65 3.82
8725 11423 2.978018 GCCAAAGGTGTGCCGTAGC 61.978 63.158 0.00 0.00 40.50 3.58
8728 11426 0.960364 CAAAGGTGTGCCGTAGCCAT 60.960 55.000 0.00 0.00 40.50 4.40
8751 11449 8.581578 CCATAAATAGTTTTACAACACCCTTGT 58.418 33.333 0.00 0.00 35.05 3.16
8855 11569 4.037222 TCCAATATGCCCACTCAGTAGAA 58.963 43.478 0.00 0.00 0.00 2.10
8989 11703 3.057315 GCAGTAAGCCAGCATTTCTTGAA 60.057 43.478 0.00 0.00 37.23 2.69
8991 11705 4.022935 CAGTAAGCCAGCATTTCTTGAACA 60.023 41.667 0.00 0.00 0.00 3.18
9029 11746 7.710907 GTGGTGCAGATAACTAACATTGATCTA 59.289 37.037 0.00 0.00 0.00 1.98
9059 11776 4.082125 CTGAAAACCCTATGCCAAGTCTT 58.918 43.478 0.00 0.00 0.00 3.01
9091 11814 3.385749 CTGATACGGGGCAAGCCGT 62.386 63.158 11.02 11.02 44.90 5.68
9211 11935 6.771188 GACAAGATCCATACCAATTACTCG 57.229 41.667 0.00 0.00 0.00 4.18
9229 11953 3.951680 ACTCGTCAAAACCCAAGTCAATT 59.048 39.130 0.00 0.00 0.00 2.32
9323 12050 1.630878 GGAGTGATGGAGGTCTTGGTT 59.369 52.381 0.00 0.00 0.00 3.67
9329 12056 3.650942 TGATGGAGGTCTTGGTTGTAGTT 59.349 43.478 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 105 4.334552 ACATATGGCAACTGACATGTTCA 58.665 39.130 8.36 0.00 44.95 3.18
282 296 2.235402 GCCACCTACTAACACTAGGCAA 59.765 50.000 0.00 0.00 40.50 4.52
390 406 3.228188 TGCCATCTCAGGTCAAAGTTT 57.772 42.857 0.00 0.00 0.00 2.66
555 595 4.093952 CGTACCTCGTGGTCGCGT 62.094 66.667 13.38 0.00 44.78 6.01
558 598 2.789917 CCTCGTACCTCGTGGTCG 59.210 66.667 13.38 15.64 44.78 4.79
608 671 1.441695 TTTTTCCCTCTCGGTCCCTT 58.558 50.000 0.00 0.00 0.00 3.95
670 737 1.063183 GCCTAAGAGGATCAGCCCAT 58.937 55.000 0.00 0.00 37.67 4.00
678 745 1.556911 CTGTGTGGTGCCTAAGAGGAT 59.443 52.381 0.00 0.00 37.67 3.24
754 821 1.545582 ACGGACATCCATGCCAAAAAG 59.454 47.619 0.00 0.00 35.14 2.27
764 831 2.623535 CGGATACAAAACGGACATCCA 58.376 47.619 0.00 0.00 35.85 3.41
765 832 1.329599 GCGGATACAAAACGGACATCC 59.670 52.381 0.00 0.00 33.28 3.51
766 833 1.005347 CGCGGATACAAAACGGACATC 60.005 52.381 0.00 0.00 0.00 3.06
767 834 1.003851 CGCGGATACAAAACGGACAT 58.996 50.000 0.00 0.00 0.00 3.06
768 835 0.319727 ACGCGGATACAAAACGGACA 60.320 50.000 12.47 0.00 0.00 4.02
769 836 0.792031 AACGCGGATACAAAACGGAC 59.208 50.000 12.47 0.00 0.00 4.79
770 837 0.791422 CAACGCGGATACAAAACGGA 59.209 50.000 12.47 0.00 0.00 4.69
771 838 0.791422 TCAACGCGGATACAAAACGG 59.209 50.000 12.47 0.00 0.00 4.44
777 844 0.892755 AGGTCTTCAACGCGGATACA 59.107 50.000 12.47 0.00 0.00 2.29
806 873 4.486025 CGAATACGAAACGTGTTACAATGC 59.514 41.667 7.05 0.00 40.86 3.56
821 888 6.139845 TGTGTAGCACGACTTCGAATACGA 62.140 45.833 23.58 0.00 41.03 3.43
853 920 8.459911 TCTTTTGATGTATATCTCGTACTCCA 57.540 34.615 0.89 0.00 34.31 3.86
854 921 9.745880 TTTCTTTTGATGTATATCTCGTACTCC 57.254 33.333 0.89 0.00 34.31 3.85
881 948 6.201615 CCGCCGTATCTCTCGTATATTATGTA 59.798 42.308 0.00 0.00 0.00 2.29
893 960 0.102481 TTTGCTCCGCCGTATCTCTC 59.898 55.000 0.00 0.00 0.00 3.20
894 961 0.535335 TTTTGCTCCGCCGTATCTCT 59.465 50.000 0.00 0.00 0.00 3.10
954 1021 3.691342 CGCGGAGGTGGGAACTGA 61.691 66.667 0.00 0.00 0.00 3.41
955 1022 4.760047 CCGCGGAGGTGGGAACTG 62.760 72.222 24.07 0.00 40.28 3.16
1115 1182 4.450419 CAGATCAGTTCAGTTCACTTCACC 59.550 45.833 0.00 0.00 0.00 4.02
1160 1227 1.125093 TCTTCTCCCACCGGAAGCAA 61.125 55.000 9.46 0.00 37.86 3.91
1222 1289 2.835431 CACTCCTCCCGCTCCGAT 60.835 66.667 0.00 0.00 0.00 4.18
1413 1480 3.447918 ACCTACCAAACATCGATACCG 57.552 47.619 0.00 0.00 37.07 4.02
1528 1595 4.216902 TCAGGACACAATTGCTCTGAAATG 59.783 41.667 5.05 0.00 34.24 2.32
1569 1636 0.383949 GAACCGCTGTTCCTGCAAAA 59.616 50.000 9.67 0.00 44.20 2.44
1665 1732 2.802816 TCTGCGAAAGAAGAAGCAAGAC 59.197 45.455 0.00 0.00 44.70 3.01
1763 1830 3.744530 GCACCCTACCAGCAATAGTAAGG 60.745 52.174 0.00 0.00 0.00 2.69
1927 2000 9.860898 GAGTAATTTTCAAAGGCTTCACAATAT 57.139 29.630 0.00 0.00 0.00 1.28
2078 2155 8.367660 AGAAACTGAATGGAGATACAGAAGTA 57.632 34.615 0.00 0.00 34.88 2.24
2135 2212 8.360390 ACAAAGGATAATTCAAGGTTGTCTTTC 58.640 33.333 0.00 0.00 32.41 2.62
2242 2319 4.839121 ACCGAGTAACAAGGCATGATAAA 58.161 39.130 0.00 0.00 0.00 1.40
2248 2325 3.259876 TGAACTACCGAGTAACAAGGCAT 59.740 43.478 0.00 0.00 33.58 4.40
2324 2401 9.092876 GATGAAACTTCCAGAATAGTGTTCTAG 57.907 37.037 1.36 0.00 0.00 2.43
2428 2505 6.773976 AGTTCAAAAAGTGGAGAACAATGA 57.226 33.333 0.00 0.00 42.01 2.57
2429 2506 8.971321 CATAAGTTCAAAAAGTGGAGAACAATG 58.029 33.333 0.00 0.00 42.01 2.82
2474 2551 5.390991 GGACTGCAATCTGTAAACAACTAGC 60.391 44.000 0.00 0.00 0.00 3.42
2615 2692 5.755375 ACTGTGACATAGCAATTTAGGATCG 59.245 40.000 0.00 0.00 0.00 3.69
2624 2768 2.290514 ACTGGCACTGTGACATAGCAAT 60.291 45.455 18.08 0.00 39.59 3.56
2656 2800 4.098349 ACGTAATTCCGTAATGAGGCTACA 59.902 41.667 0.00 0.00 39.73 2.74
2669 2813 7.533426 AGGTAGCATTATAGTACGTAATTCCG 58.467 38.462 0.00 0.00 0.00 4.30
2690 2929 6.011451 ACCAGGGTTAAATCCAAACATAGGTA 60.011 38.462 0.00 0.00 0.00 3.08
2883 5217 5.409826 ACTGAAAACACGAAGATCAGATTCC 59.590 40.000 7.98 0.00 39.85 3.01
2993 5327 6.690530 CCTCTTCAAACTGAAAATTATGGCA 58.309 36.000 0.00 0.00 35.73 4.92
2994 5328 5.578336 GCCTCTTCAAACTGAAAATTATGGC 59.422 40.000 0.00 0.00 35.73 4.40
3224 5558 5.775701 ACTAGGTGGAGCATTCTACGATAAT 59.224 40.000 0.00 0.00 35.79 1.28
3230 5564 6.183360 TGGATAAACTAGGTGGAGCATTCTAC 60.183 42.308 0.00 0.00 34.32 2.59
3963 6307 1.410882 GCACCTCCTCATCTAGGTCAC 59.589 57.143 0.00 0.00 44.43 3.67
4076 6420 2.414179 CGCCCGATACGGTAAGCA 59.586 61.111 9.28 0.00 46.80 3.91
4485 6839 5.824904 ATGCTTTGATCGTCATAGCTTTT 57.175 34.783 21.19 10.63 46.80 2.27
4526 6881 1.069668 CCAGGATCATCGCAGATGTCA 59.930 52.381 15.04 1.90 45.12 3.58
4534 6889 0.039617 CGTCTCTCCAGGATCATCGC 60.040 60.000 0.00 0.00 0.00 4.58
4535 6890 1.535028 CTCGTCTCTCCAGGATCATCG 59.465 57.143 0.00 0.00 0.00 3.84
4538 6893 1.098129 CGCTCGTCTCTCCAGGATCA 61.098 60.000 0.00 0.00 0.00 2.92
4540 6895 3.834726 CGCTCGTCTCTCCAGGAT 58.165 61.111 0.00 0.00 0.00 3.24
4896 7283 1.132657 TCTCTCCCCTACAAACCCACA 60.133 52.381 0.00 0.00 0.00 4.17
4943 7330 2.024846 TCCTTATTTTCCCCCGCATCAA 60.025 45.455 0.00 0.00 0.00 2.57
4947 7334 0.393267 CGTCCTTATTTTCCCCCGCA 60.393 55.000 0.00 0.00 0.00 5.69
5011 7398 2.202810 TGTCGCGTGTTGCAGTCA 60.203 55.556 5.77 0.00 46.97 3.41
5101 7488 2.147387 GTCCCCACCCTGACACACT 61.147 63.158 0.00 0.00 0.00 3.55
5112 7501 4.048470 GAAGCCCCCTGTCCCCAC 62.048 72.222 0.00 0.00 0.00 4.61
5259 7648 1.132977 TCTGACAAGTAGTGGGACCCA 60.133 52.381 9.95 9.95 0.00 4.51
5295 7684 3.295973 ACCAAACCAGCAACACATTAGT 58.704 40.909 0.00 0.00 0.00 2.24
5978 8392 2.036604 GAGGCGTTTTCCCCATTTTCAA 59.963 45.455 0.00 0.00 0.00 2.69
5979 8393 1.616374 GAGGCGTTTTCCCCATTTTCA 59.384 47.619 0.00 0.00 0.00 2.69
6048 8465 7.160049 TGAGATATTGTAGGGAGTACGAGTAG 58.840 42.308 0.00 0.00 33.87 2.57
6095 8512 3.282021 GAGGCAATGTAGAAGCAATGGA 58.718 45.455 0.00 0.00 0.00 3.41
6299 8721 4.757149 AGCTTCATTGACCAACTACACTTC 59.243 41.667 0.00 0.00 0.00 3.01
6363 8785 3.810310 ATCGGGACTTTGTTGCAAAAA 57.190 38.095 0.00 0.00 0.00 1.94
6593 9015 4.079253 TGCTGGGTGAAGGAAATTAGTTC 58.921 43.478 0.00 0.00 35.28 3.01
6684 9106 6.205101 AGCAGATAAGCAGAAAGAAAATGG 57.795 37.500 0.00 0.00 36.85 3.16
6749 9171 6.041523 AGGGTGTGCAATAACTGTTACAATTT 59.958 34.615 1.73 0.00 0.00 1.82
6750 9172 5.538433 AGGGTGTGCAATAACTGTTACAATT 59.462 36.000 1.73 0.00 0.00 2.32
6754 9176 6.563222 TTAAGGGTGTGCAATAACTGTTAC 57.437 37.500 1.73 0.00 0.00 2.50
6996 9552 1.805345 GCATGAGCCATATCTGCAGAC 59.195 52.381 20.97 5.79 33.13 3.51
7042 9598 9.185680 ACCCATAAACTGATCCAAAAATACTAC 57.814 33.333 0.00 0.00 0.00 2.73
7310 9866 9.297037 AGTTATGGCAACTTGATTTAGTTTACT 57.703 29.630 0.00 0.00 36.24 2.24
7311 9867 9.341899 CAGTTATGGCAACTTGATTTAGTTTAC 57.658 33.333 0.00 0.00 36.24 2.01
7312 9868 8.026607 GCAGTTATGGCAACTTGATTTAGTTTA 58.973 33.333 0.00 0.00 36.24 2.01
7313 9869 6.868339 GCAGTTATGGCAACTTGATTTAGTTT 59.132 34.615 0.00 0.00 36.24 2.66
7314 9870 6.389906 GCAGTTATGGCAACTTGATTTAGTT 58.610 36.000 0.00 0.00 38.87 2.24
7315 9871 5.954335 GCAGTTATGGCAACTTGATTTAGT 58.046 37.500 0.00 0.00 37.61 2.24
7340 9896 9.996554 TCACAAGATCAAGTATAAGTTGAGAAA 57.003 29.630 0.00 0.00 40.49 2.52
7360 9916 9.102757 AGTACTCTTATATGTTGCAATCACAAG 57.897 33.333 0.59 3.60 0.00 3.16
7375 9931 8.982685 CGGTATCTTGTCGTTAGTACTCTTATA 58.017 37.037 0.00 0.00 0.00 0.98
7401 9957 6.371389 GTGTGAAAACAACATAAGAGTAGGC 58.629 40.000 0.00 0.00 0.00 3.93
7462 10114 8.259411 TCAGCATCTACAATGCCAATTAATTTT 58.741 29.630 6.40 0.00 45.59 1.82
7465 10117 6.964807 TCAGCATCTACAATGCCAATTAAT 57.035 33.333 6.40 0.00 45.59 1.40
7503 10158 4.580580 CACTTCTTTAAGTTTGACCAGGCT 59.419 41.667 0.00 0.00 43.60 4.58
7654 10310 3.578688 CAATGCTTTACTGGGCAAACTC 58.421 45.455 0.00 0.00 41.90 3.01
7680 10336 4.225042 AGTGTATATGTTTGGTGGAGCTCA 59.775 41.667 17.19 0.00 0.00 4.26
7700 10356 0.392193 CTTGGTGGAGCTGCCTAGTG 60.392 60.000 1.53 0.00 37.63 2.74
7740 10396 8.918658 CAATACAATTGCTGATATATGTTTGGC 58.081 33.333 5.05 0.00 0.00 4.52
7991 10679 6.550163 AGCTTATCTAATACTCCCTCCGTAA 58.450 40.000 0.00 0.00 0.00 3.18
8172 10862 1.296727 GAATACCAACACCGCTAGCC 58.703 55.000 9.66 0.00 0.00 3.93
8271 10961 9.358406 TCAAAATATGCCTTGAGATGTTCATAT 57.642 29.630 0.00 0.00 35.27 1.78
8280 10970 8.246180 GTGAATTCTTCAAAATATGCCTTGAGA 58.754 33.333 7.05 0.00 42.15 3.27
8354 11044 5.133221 GTTCTGCTGACCCAATTATATGGT 58.867 41.667 0.00 0.00 38.91 3.55
8356 11046 5.240183 CAGGTTCTGCTGACCCAATTATATG 59.760 44.000 9.82 0.00 0.00 1.78
8358 11048 4.227300 ACAGGTTCTGCTGACCCAATTATA 59.773 41.667 9.82 0.00 34.37 0.98
8359 11049 3.010584 ACAGGTTCTGCTGACCCAATTAT 59.989 43.478 9.82 0.00 34.37 1.28
8360 11050 2.375174 ACAGGTTCTGCTGACCCAATTA 59.625 45.455 9.82 0.00 34.37 1.40
8361 11051 1.145738 ACAGGTTCTGCTGACCCAATT 59.854 47.619 9.82 0.00 34.37 2.32
8518 11216 5.049198 TTCTCGAGCTAGAAAAACGTGAGTA 60.049 40.000 7.81 0.00 36.44 2.59
8564 11262 3.542291 GCAAAGCGCGATGTCTAACTTAG 60.542 47.826 12.10 0.00 0.00 2.18
8577 11275 1.044725 CAAAAGTAGTGCAAAGCGCG 58.955 50.000 0.00 0.00 46.97 6.86
8586 11284 3.010138 TCCCCTCCAATCCAAAAGTAGTG 59.990 47.826 0.00 0.00 0.00 2.74
8587 11285 3.265489 TCCCCTCCAATCCAAAAGTAGT 58.735 45.455 0.00 0.00 0.00 2.73
8588 11286 4.526438 ATCCCCTCCAATCCAAAAGTAG 57.474 45.455 0.00 0.00 0.00 2.57
8589 11287 4.965283 AATCCCCTCCAATCCAAAAGTA 57.035 40.909 0.00 0.00 0.00 2.24
8591 11289 4.095946 TCAAATCCCCTCCAATCCAAAAG 58.904 43.478 0.00 0.00 0.00 2.27
8592 11290 4.095946 CTCAAATCCCCTCCAATCCAAAA 58.904 43.478 0.00 0.00 0.00 2.44
8593 11291 3.336391 TCTCAAATCCCCTCCAATCCAAA 59.664 43.478 0.00 0.00 0.00 3.28
8594 11292 2.925653 TCTCAAATCCCCTCCAATCCAA 59.074 45.455 0.00 0.00 0.00 3.53
8595 11293 2.511218 CTCTCAAATCCCCTCCAATCCA 59.489 50.000 0.00 0.00 0.00 3.41
8597 11295 4.510167 TTCTCTCAAATCCCCTCCAATC 57.490 45.455 0.00 0.00 0.00 2.67
8599 11297 4.953781 AATTCTCTCAAATCCCCTCCAA 57.046 40.909 0.00 0.00 0.00 3.53
8600 11298 4.953781 AAATTCTCTCAAATCCCCTCCA 57.046 40.909 0.00 0.00 0.00 3.86
8601 11299 5.126222 GTCAAAATTCTCTCAAATCCCCTCC 59.874 44.000 0.00 0.00 0.00 4.30
8602 11300 5.948758 AGTCAAAATTCTCTCAAATCCCCTC 59.051 40.000 0.00 0.00 0.00 4.30
8603 11301 5.896963 AGTCAAAATTCTCTCAAATCCCCT 58.103 37.500 0.00 0.00 0.00 4.79
8604 11302 6.015095 ACAAGTCAAAATTCTCTCAAATCCCC 60.015 38.462 0.00 0.00 0.00 4.81
8605 11303 6.986250 ACAAGTCAAAATTCTCTCAAATCCC 58.014 36.000 0.00 0.00 0.00 3.85
8607 11305 9.617975 CCTTACAAGTCAAAATTCTCTCAAATC 57.382 33.333 0.00 0.00 0.00 2.17
8608 11306 8.579863 CCCTTACAAGTCAAAATTCTCTCAAAT 58.420 33.333 0.00 0.00 0.00 2.32
8609 11307 7.777910 TCCCTTACAAGTCAAAATTCTCTCAAA 59.222 33.333 0.00 0.00 0.00 2.69
8611 11309 6.837312 TCCCTTACAAGTCAAAATTCTCTCA 58.163 36.000 0.00 0.00 0.00 3.27
8612 11310 7.929941 ATCCCTTACAAGTCAAAATTCTCTC 57.070 36.000 0.00 0.00 0.00 3.20
8620 11318 9.362151 AGTGAATTTAATCCCTTACAAGTCAAA 57.638 29.630 0.00 0.00 0.00 2.69
8621 11319 8.934023 AGTGAATTTAATCCCTTACAAGTCAA 57.066 30.769 0.00 0.00 0.00 3.18
8622 11320 8.934023 AAGTGAATTTAATCCCTTACAAGTCA 57.066 30.769 0.00 0.00 0.00 3.41
8623 11321 9.010029 TGAAGTGAATTTAATCCCTTACAAGTC 57.990 33.333 0.00 0.00 0.00 3.01
8624 11322 8.934023 TGAAGTGAATTTAATCCCTTACAAGT 57.066 30.769 0.00 0.00 0.00 3.16
8642 11340 2.627699 GTTTTGGCAGGGATTGAAGTGA 59.372 45.455 0.00 0.00 0.00 3.41
8647 11345 0.544120 GGGGTTTTGGCAGGGATTGA 60.544 55.000 0.00 0.00 0.00 2.57
8648 11346 1.552799 GGGGGTTTTGGCAGGGATTG 61.553 60.000 0.00 0.00 0.00 2.67
8650 11348 1.750087 AAGGGGGTTTTGGCAGGGAT 61.750 55.000 0.00 0.00 0.00 3.85
8651 11349 2.380571 GAAGGGGGTTTTGGCAGGGA 62.381 60.000 0.00 0.00 0.00 4.20
8654 11352 1.127343 TTTGAAGGGGGTTTTGGCAG 58.873 50.000 0.00 0.00 0.00 4.85
8655 11353 1.813102 ATTTGAAGGGGGTTTTGGCA 58.187 45.000 0.00 0.00 0.00 4.92
8656 11354 2.027561 GGTATTTGAAGGGGGTTTTGGC 60.028 50.000 0.00 0.00 0.00 4.52
8658 11356 3.901222 ACAGGTATTTGAAGGGGGTTTTG 59.099 43.478 0.00 0.00 0.00 2.44
8659 11357 4.157246 GACAGGTATTTGAAGGGGGTTTT 58.843 43.478 0.00 0.00 0.00 2.43
8662 11360 2.354328 TGACAGGTATTTGAAGGGGGT 58.646 47.619 0.00 0.00 0.00 4.95
8685 11383 3.728268 CGTACTCTCTAAGGCTGTGTTCG 60.728 52.174 0.00 0.00 0.00 3.95
8695 11393 3.056749 ACACCTTTGGCGTACTCTCTAAG 60.057 47.826 0.00 0.00 0.00 2.18
8718 11416 6.607735 TGTAAAACTATTTATGGCTACGGC 57.392 37.500 0.00 0.00 33.76 5.68
8725 11423 8.581578 ACAAGGGTGTTGTAAAACTATTTATGG 58.418 33.333 0.00 0.00 32.58 2.74
8728 11426 7.285858 AGCACAAGGGTGTTGTAAAACTATTTA 59.714 33.333 0.00 0.00 46.95 1.40
8776 11474 0.696501 AGTATTGGTGGGGTGTGTCC 59.303 55.000 0.00 0.00 0.00 4.02
8822 11520 5.010012 GTGGGCATATTGGAATTAAGACAGG 59.990 44.000 0.00 0.00 0.00 4.00
8881 11595 5.129485 TGGCACCTTTGGAAATAAAGAAACA 59.871 36.000 0.00 0.00 39.46 2.83
8928 11642 1.897560 AAGGACAAAAGGAGCTTCGG 58.102 50.000 0.00 0.00 0.00 4.30
8964 11678 2.026449 AGAAATGCTGGCTTACTGCTCT 60.026 45.455 0.00 0.00 43.66 4.09
8986 11700 2.150390 CCACACCGATTGACATGTTCA 58.850 47.619 0.00 0.00 0.00 3.18
8989 11703 1.522668 CACCACACCGATTGACATGT 58.477 50.000 0.00 0.00 0.00 3.21
8991 11705 0.250684 TGCACCACACCGATTGACAT 60.251 50.000 0.00 0.00 0.00 3.06
9029 11746 4.280929 GGCATAGGGTTTTCAGTGAACTTT 59.719 41.667 4.68 0.00 0.00 2.66
9059 11776 1.879380 GTATCAGTGTGCCAACAAGCA 59.121 47.619 0.00 0.00 38.27 3.91
9091 11814 5.512942 TCATGAAGATTGGACCACCTTTA 57.487 39.130 9.10 6.33 37.04 1.85
9121 11845 6.773976 TCCTTGTGTTTCTTCTCAAAACAT 57.226 33.333 4.90 0.00 45.42 2.71
9211 11935 6.923508 CCTCTTAAATTGACTTGGGTTTTGAC 59.076 38.462 0.00 0.00 0.00 3.18
9229 11953 4.021229 TGGATCTAAGACGCACCTCTTAA 58.979 43.478 0.00 0.00 33.30 1.85


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

AutoCloner maintained by Alex Coulton.