Multiple sequence alignment - TraesCS3D01G087900

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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 TraesCS3D01G087900 chr3D 100.000 8518 0 0 1 8518 44881285 44889802 0.000000e+00 15730.0
1 TraesCS3D01G087900 chr3D 85.830 2583 236 57 261 2786 81721492 81718983 0.000000e+00 2623.0
2 TraesCS3D01G087900 chr3D 86.937 1355 121 31 6512 7834 81715567 81714237 0.000000e+00 1471.0
3 TraesCS3D01G087900 chr3D 86.349 945 89 18 2875 3813 81718917 81718007 0.000000e+00 994.0
4 TraesCS3D01G087900 chr3D 83.043 460 58 14 5583 6036 585989801 585989356 4.790000e-107 399.0
5 TraesCS3D01G087900 chr3D 85.185 405 36 7 5523 5903 536945425 536945829 2.230000e-105 394.0
6 TraesCS3D01G087900 chr3D 86.667 240 31 1 6029 6268 306032989 306033227 1.820000e-66 265.0
7 TraesCS3D01G087900 chr3D 79.456 331 45 18 5513 5827 420445649 420445326 6.700000e-51 213.0
8 TraesCS3D01G087900 chr3D 75.596 545 43 41 5525 6038 306032456 306032941 4.060000e-43 187.0
9 TraesCS3D01G087900 chr3D 84.211 76 12 0 6134 6209 7585169 7585094 3.300000e-09 75.0
10 TraesCS3D01G087900 chr3B 94.301 2720 98 19 1 2691 69810568 69813259 0.000000e+00 4111.0
11 TraesCS3D01G087900 chr3B 84.433 3790 358 111 118 3813 127936812 127933161 0.000000e+00 3517.0
12 TraesCS3D01G087900 chr3B 94.153 1676 60 12 6512 8152 69817146 69818818 0.000000e+00 2518.0
13 TraesCS3D01G087900 chr3B 88.821 1646 106 33 3930 5525 69814537 69816154 0.000000e+00 1949.0
14 TraesCS3D01G087900 chr3B 95.129 1088 51 2 2841 3926 69813409 69814496 0.000000e+00 1714.0
15 TraesCS3D01G087900 chr3B 86.896 1366 108 40 6512 7834 127930626 127929289 0.000000e+00 1465.0
16 TraesCS3D01G087900 chr3B 85.451 543 49 7 5522 6036 543895166 543895706 9.730000e-149 538.0
17 TraesCS3D01G087900 chr3B 80.488 533 82 13 5522 6038 524763895 524763369 1.040000e-103 388.0
18 TraesCS3D01G087900 chr3B 87.611 226 16 7 8256 8477 69819018 69819235 1.420000e-62 252.0
19 TraesCS3D01G087900 chr3B 85.477 241 35 0 6029 6269 543895756 543895996 1.420000e-62 252.0
20 TraesCS3D01G087900 chr3B 92.771 83 5 1 2741 2823 69813268 69813349 1.500000e-22 119.0
21 TraesCS3D01G087900 chr3A 85.608 3613 347 81 262 3813 96250666 96247166 0.000000e+00 3631.0
22 TraesCS3D01G087900 chr3A 96.344 1614 31 4 1246 2847 56668613 56670210 0.000000e+00 2628.0
23 TraesCS3D01G087900 chr3A 95.015 1625 48 12 3930 5545 56671348 56672948 0.000000e+00 2521.0
24 TraesCS3D01G087900 chr3A 95.530 1454 41 11 6512 7949 56674997 56676442 0.000000e+00 2303.0
25 TraesCS3D01G087900 chr3A 96.097 1076 25 4 2861 3931 56670249 56671312 0.000000e+00 1738.0
26 TraesCS3D01G087900 chr3A 87.116 1335 114 33 6512 7816 96243169 96241863 0.000000e+00 1459.0
27 TraesCS3D01G087900 chr3A 88.810 706 56 11 5545 6229 56673979 56674682 0.000000e+00 845.0
28 TraesCS3D01G087900 chr3A 89.643 280 9 8 6250 6509 56674673 56674952 1.060000e-88 339.0
29 TraesCS3D01G087900 chr3A 88.542 192 14 7 8025 8215 56676469 56676653 8.600000e-55 226.0
30 TraesCS3D01G087900 chr6B 84.682 2755 306 58 823 3529 434302853 434300167 0.000000e+00 2643.0
31 TraesCS3D01G087900 chr6B 88.529 1203 83 21 6568 7733 434299766 434298582 0.000000e+00 1406.0
32 TraesCS3D01G087900 chr6B 81.109 487 57 15 3456 3923 434300149 434299679 2.920000e-94 357.0
33 TraesCS3D01G087900 chr6D 84.461 2748 295 63 823 3529 272862875 272860219 0.000000e+00 2588.0
34 TraesCS3D01G087900 chr6D 86.248 749 51 16 7015 7733 272859231 272858505 0.000000e+00 765.0
35 TraesCS3D01G087900 chr6D 90.153 457 28 5 6568 7010 272859818 272859365 5.730000e-161 579.0
36 TraesCS3D01G087900 chr6D 80.040 506 60 18 3439 3923 272860218 272859733 3.810000e-88 337.0
37 TraesCS3D01G087900 chr6D 89.157 83 5 4 4470 4549 181729612 181729531 5.440000e-17 100.0
38 TraesCS3D01G087900 chr6A 84.490 2708 295 66 825 3474 389958866 389956226 0.000000e+00 2558.0
39 TraesCS3D01G087900 chr6A 88.640 1206 81 13 6568 7733 389955775 389954586 0.000000e+00 1417.0
40 TraesCS3D01G087900 chr6A 80.792 505 60 15 3439 3923 389956175 389955688 2.260000e-95 361.0
41 TraesCS3D01G087900 chr6A 78.614 332 24 15 5576 5895 157425359 157425655 8.790000e-40 176.0
42 TraesCS3D01G087900 chr7D 88.972 934 67 17 407 1338 46890563 46891462 0.000000e+00 1122.0
43 TraesCS3D01G087900 chr7D 91.925 322 15 2 1338 1659 46893208 46893518 2.820000e-119 440.0
44 TraesCS3D01G087900 chr7D 90.588 85 5 2 4467 4549 483278737 483278820 9.040000e-20 110.0
45 TraesCS3D01G087900 chr4A 78.642 810 110 32 5523 6277 621735368 621734567 5.980000e-131 479.0
46 TraesCS3D01G087900 chr4A 87.749 351 29 3 6568 6911 706471870 706471527 1.720000e-106 398.0
47 TraesCS3D01G087900 chr4A 84.309 427 42 9 7032 7455 706471531 706471127 2.230000e-105 394.0
48 TraesCS3D01G087900 chr4A 79.754 568 66 15 2866 3422 706493985 706493456 4.860000e-97 366.0
49 TraesCS3D01G087900 chr4A 80.992 121 20 3 6110 6227 147368421 147368301 9.100000e-15 93.5
50 TraesCS3D01G087900 chr2A 82.846 513 63 10 5524 6019 35780872 35780368 3.650000e-118 436.0
51 TraesCS3D01G087900 chr2A 81.698 530 61 16 5540 6036 776149764 776150290 7.960000e-110 409.0
52 TraesCS3D01G087900 chr5D 88.636 308 28 4 5527 5831 562078827 562078524 1.350000e-97 368.0
53 TraesCS3D01G087900 chr5D 91.026 78 5 1 4470 4545 468172109 468172032 4.210000e-18 104.0
54 TraesCS3D01G087900 chr5D 89.744 78 6 1 4470 4545 7616489 7616412 1.960000e-16 99.0
55 TraesCS3D01G087900 chr5D 100.000 28 0 0 5034 5061 556049742 556049715 1.500000e-02 52.8
56 TraesCS3D01G087900 chr5B 79.705 542 73 19 5523 6030 690324029 690324567 2.920000e-94 357.0
57 TraesCS3D01G087900 chr5B 86.235 247 23 5 5540 5785 355666183 355666419 3.050000e-64 257.0
58 TraesCS3D01G087900 chr5B 85.308 211 25 2 5831 6035 355682773 355682983 6.700000e-51 213.0
59 TraesCS3D01G087900 chr5B 90.789 76 5 1 4470 4543 8406964 8406889 5.440000e-17 100.0
60 TraesCS3D01G087900 chr5A 79.174 533 71 18 5520 6019 60098282 60097757 4.930000e-87 333.0
61 TraesCS3D01G087900 chr5A 91.406 128 11 0 5844 5971 219646295 219646168 8.790000e-40 176.0
62 TraesCS3D01G087900 chr5A 83.133 83 14 0 6134 6216 429732808 429732726 9.170000e-10 76.8
63 TraesCS3D01G087900 chr7A 88.938 226 12 3 1810 2035 23791393 23791605 5.070000e-67 267.0
64 TraesCS3D01G087900 chr7A 81.590 239 26 12 6043 6263 107789894 107789656 1.890000e-41 182.0
65 TraesCS3D01G087900 chr1A 89.535 86 4 5 4467 4549 358767508 358767425 4.210000e-18 104.0
66 TraesCS3D01G087900 chr1D 90.789 76 5 1 4470 4543 481697890 481697815 5.440000e-17 100.0
67 TraesCS3D01G087900 chr1D 100.000 28 0 0 2820 2847 42096415 42096442 1.500000e-02 52.8
68 TraesCS3D01G087900 chr7B 81.443 97 18 0 6143 6239 654172152 654172248 7.090000e-11 80.5
69 TraesCS3D01G087900 chr2D 93.333 45 2 1 6030 6074 580009583 580009626 1.980000e-06 65.8
70 TraesCS3D01G087900 chr4D 94.595 37 2 0 2826 2862 10768010 10768046 3.320000e-04 58.4
71 TraesCS3D01G087900 chr2B 90.909 44 3 1 2822 2865 39156811 39156769 3.320000e-04 58.4
72 TraesCS3D01G087900 chr2B 89.130 46 5 0 6049 6094 698962463 698962508 3.320000e-04 58.4
73 TraesCS3D01G087900 chr1B 92.683 41 2 1 2826 2866 277446196 277446157 3.320000e-04 58.4
74 TraesCS3D01G087900 chr4B 94.444 36 1 1 5034 5068 418511648 418511613 4.000000e-03 54.7


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 TraesCS3D01G087900 chr3D 44881285 44889802 8517 False 15730.000000 15730 100.000000 1 8518 1 chr3D.!!$F1 8517
1 TraesCS3D01G087900 chr3D 81714237 81721492 7255 True 1696.000000 2623 86.372000 261 7834 3 chr3D.!!$R4 7573
2 TraesCS3D01G087900 chr3D 306032456 306033227 771 False 226.000000 265 81.131500 5525 6268 2 chr3D.!!$F3 743
3 TraesCS3D01G087900 chr3B 127929289 127936812 7523 True 2491.000000 3517 85.664500 118 7834 2 chr3B.!!$R2 7716
4 TraesCS3D01G087900 chr3B 69810568 69819235 8667 False 1777.166667 4111 92.131000 1 8477 6 chr3B.!!$F1 8476
5 TraesCS3D01G087900 chr3B 543895166 543895996 830 False 395.000000 538 85.464000 5522 6269 2 chr3B.!!$F2 747
6 TraesCS3D01G087900 chr3B 524763369 524763895 526 True 388.000000 388 80.488000 5522 6038 1 chr3B.!!$R1 516
7 TraesCS3D01G087900 chr3A 96241863 96250666 8803 True 2545.000000 3631 86.362000 262 7816 2 chr3A.!!$R1 7554
8 TraesCS3D01G087900 chr3A 56668613 56676653 8040 False 1514.285714 2628 92.854429 1246 8215 7 chr3A.!!$F1 6969
9 TraesCS3D01G087900 chr6B 434298582 434302853 4271 True 1468.666667 2643 84.773333 823 7733 3 chr6B.!!$R1 6910
10 TraesCS3D01G087900 chr6D 272858505 272862875 4370 True 1067.250000 2588 85.225500 823 7733 4 chr6D.!!$R2 6910
11 TraesCS3D01G087900 chr6A 389954586 389958866 4280 True 1445.333333 2558 84.640667 825 7733 3 chr6A.!!$R1 6908
12 TraesCS3D01G087900 chr7D 46890563 46893518 2955 False 781.000000 1122 90.448500 407 1659 2 chr7D.!!$F2 1252
13 TraesCS3D01G087900 chr4A 621734567 621735368 801 True 479.000000 479 78.642000 5523 6277 1 chr4A.!!$R2 754
14 TraesCS3D01G087900 chr4A 706471127 706471870 743 True 396.000000 398 86.029000 6568 7455 2 chr4A.!!$R4 887
15 TraesCS3D01G087900 chr4A 706493456 706493985 529 True 366.000000 366 79.754000 2866 3422 1 chr4A.!!$R3 556
16 TraesCS3D01G087900 chr2A 35780368 35780872 504 True 436.000000 436 82.846000 5524 6019 1 chr2A.!!$R1 495
17 TraesCS3D01G087900 chr2A 776149764 776150290 526 False 409.000000 409 81.698000 5540 6036 1 chr2A.!!$F1 496
18 TraesCS3D01G087900 chr5B 690324029 690324567 538 False 357.000000 357 79.705000 5523 6030 1 chr5B.!!$F3 507
19 TraesCS3D01G087900 chr5A 60097757 60098282 525 True 333.000000 333 79.174000 5520 6019 1 chr5A.!!$R1 499

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
808 920 0.035820 GGCTTGGTACGGATTGGTCA 60.036 55.000 0.00 0.00 0.00 4.02 F
1077 1208 0.179065 ACGAAATAGCTTACCGGGGC 60.179 55.000 6.32 7.37 0.00 5.80 F
1437 3317 2.124236 TTGCCGACAAAACCCCGT 60.124 55.556 0.00 0.00 31.21 5.28 F
1913 3793 2.157738 GCCAACTGAGATTGTGAAGCT 58.842 47.619 0.00 0.00 0.00 3.74 F
3035 5080 1.061546 TTCTTAAACAGCCCGTCCCT 58.938 50.000 0.00 0.00 0.00 4.20 F
4118 8936 0.318699 TTGTGCTCCTCTTGTCGACG 60.319 55.000 11.62 0.00 0.00 5.12 F
4200 9018 0.107459 GTCCATGCCCTCCTCTTGTC 60.107 60.000 0.00 0.00 0.00 3.18 F
5450 10387 0.179181 GATGCGTGGCTGATTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82 F
5805 11808 0.740737 CAAAATGGGGCTCATCGGAC 59.259 55.000 0.00 0.00 34.44 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 3569 2.159531 TCGGGGATTATACGTTATCGCG 60.160 50.000 0.00 0.00 41.18 5.87 R
2927 4963 1.070758 AGCTATGTATGACCCCTTGCG 59.929 52.381 0.00 0.00 0.00 4.85 R
3035 5080 4.220724 ACAGTAGGGTCTTGTAGACAACA 58.779 43.478 8.89 0.00 46.79 3.33 R
3491 5718 0.679505 CTGGTTCGGTCTGACCAAGA 59.320 55.000 25.42 13.27 38.47 3.02 R
4170 8988 0.748005 GGCATGGACAACTACCGCAT 60.748 55.000 0.00 0.00 0.00 4.73 R
5282 10213 1.065102 GCCGCACATCTTCTAGTACGA 59.935 52.381 0.00 0.00 0.00 3.43 R
6140 12804 0.392193 GACAGAGGAGTACGACCGGA 60.392 60.000 9.46 0.00 0.00 5.14 R
6263 12985 0.030235 CGTCTCCTGTGACAACGACA 59.970 55.000 1.61 0.00 36.82 4.35 R
7636 14839 0.243365 GCATCAAATTCCGTGCACCA 59.757 50.000 12.15 0.00 37.52 4.17 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
100 101 2.193087 CTCCCCAAACCAGTACCGGG 62.193 65.000 6.32 0.00 36.59 5.73
232 246 2.356780 GGTCCCGACCCGACTCATT 61.357 63.158 2.16 0.00 45.68 2.57
234 248 2.056223 TCCCGACCCGACTCATTCC 61.056 63.158 0.00 0.00 0.00 3.01
628 692 2.190578 CCCCGACAGCCTCAATCC 59.809 66.667 0.00 0.00 0.00 3.01
704 768 2.939103 CCTGTACATTTGTAGCTCCTGC 59.061 50.000 0.00 0.00 40.05 4.85
722 786 6.662865 TCCTGCTTGGATTTAGAGAGATAG 57.337 41.667 0.00 0.00 40.56 2.08
742 806 1.656095 GGATTCGTTTCACTCTCTGCG 59.344 52.381 0.00 0.00 0.00 5.18
777 841 5.530171 TCCTGCTCTGATTCATTTCATTAGC 59.470 40.000 0.00 0.00 36.12 3.09
778 842 5.413969 TGCTCTGATTCATTTCATTAGCG 57.586 39.130 0.00 0.00 37.35 4.26
808 920 0.035820 GGCTTGGTACGGATTGGTCA 60.036 55.000 0.00 0.00 0.00 4.02
809 921 1.084289 GCTTGGTACGGATTGGTCAC 58.916 55.000 0.00 0.00 0.00 3.67
859 974 1.831343 CGCAGCATTTGAATACCTGC 58.169 50.000 13.93 13.93 43.95 4.85
865 980 5.446741 GCAGCATTTGAATACCTGCAAATTG 60.447 40.000 16.89 0.00 46.00 2.32
926 1041 3.119849 AGTTTGTTGTCTGTGTGCTTGTC 60.120 43.478 0.00 0.00 0.00 3.18
928 1043 2.279741 TGTTGTCTGTGTGCTTGTCTC 58.720 47.619 0.00 0.00 0.00 3.36
930 1045 2.515926 TGTCTGTGTGCTTGTCTCTC 57.484 50.000 0.00 0.00 0.00 3.20
932 1047 2.035193 TGTCTGTGTGCTTGTCTCTCTC 59.965 50.000 0.00 0.00 0.00 3.20
1077 1208 0.179065 ACGAAATAGCTTACCGGGGC 60.179 55.000 6.32 7.37 0.00 5.80
1362 3242 3.002583 TCATCGTCAGCTGCCCCA 61.003 61.111 9.47 0.00 0.00 4.96
1437 3317 2.124236 TTGCCGACAAAACCCCGT 60.124 55.556 0.00 0.00 31.21 5.28
1913 3793 2.157738 GCCAACTGAGATTGTGAAGCT 58.842 47.619 0.00 0.00 0.00 3.74
2250 4145 3.244770 TGTCATGTACCCTTTGAGGTTCC 60.245 47.826 0.00 0.00 41.58 3.62
2749 4706 2.356069 TGACACGTGCTGCAAATTTGTA 59.644 40.909 17.22 14.01 0.00 2.41
2846 4862 3.562108 ACTCCCTCCGTCCCATATTAT 57.438 47.619 0.00 0.00 0.00 1.28
2881 4897 6.018669 GGAGTAGTTAGGATTTCAAGAATGCG 60.019 42.308 0.00 0.00 0.00 4.73
2927 4963 8.662781 TGATTCTTAGTGAACTAATATGTGGC 57.337 34.615 3.47 0.00 37.75 5.01
3035 5080 1.061546 TTCTTAAACAGCCCGTCCCT 58.938 50.000 0.00 0.00 0.00 4.20
3281 5331 3.316308 GTGAACATATGGACCAATGGAGC 59.684 47.826 6.16 0.00 0.00 4.70
3284 5334 2.703536 ACATATGGACCAATGGAGCGTA 59.296 45.455 6.16 0.00 0.00 4.42
3285 5335 2.902705 TATGGACCAATGGAGCGTAC 57.097 50.000 6.16 0.00 0.00 3.67
3289 5339 2.029623 GGACCAATGGAGCGTACTAGA 58.970 52.381 6.16 0.00 0.00 2.43
3486 5712 4.759693 TGTAGCTTGTACTTCATTGGTTGG 59.240 41.667 0.00 0.00 0.00 3.77
3491 5718 2.224426 TGTACTTCATTGGTTGGCTCGT 60.224 45.455 0.00 0.00 0.00 4.18
3788 6040 2.714991 GCCCCCTTTAGCTGCTTGC 61.715 63.158 7.79 0.00 43.29 4.01
3926 6178 0.693049 CACCTGAGGGTAAGCACCTT 59.307 55.000 2.38 0.00 45.41 3.50
3951 8750 7.755591 TCATGCATCATCTCTTTTACAACTTC 58.244 34.615 0.00 0.00 0.00 3.01
4094 8912 1.645034 CTCATGGGTGACAGTTAGCG 58.355 55.000 0.00 0.00 0.00 4.26
4118 8936 0.318699 TTGTGCTCCTCTTGTCGACG 60.319 55.000 11.62 0.00 0.00 5.12
4146 8964 3.706594 TCCACCTAGGATCAAGTCATGTC 59.293 47.826 17.98 0.00 43.07 3.06
4153 8971 5.091261 AGGATCAAGTCATGTCCTTGTAC 57.909 43.478 19.92 15.94 40.15 2.90
4195 9013 1.134371 GTAGTTGTCCATGCCCTCCTC 60.134 57.143 0.00 0.00 0.00 3.71
4200 9018 0.107459 GTCCATGCCCTCCTCTTGTC 60.107 60.000 0.00 0.00 0.00 3.18
4202 9020 1.617018 CCATGCCCTCCTCTTGTCGA 61.617 60.000 0.00 0.00 0.00 4.20
4424 9331 8.880244 ACCAACATAGCTAGATTGATACCATTA 58.120 33.333 17.35 0.00 0.00 1.90
4784 9697 2.033141 GGCCAGAGAAGTGCAGCA 59.967 61.111 0.00 0.00 0.00 4.41
4786 9699 2.039405 GCCAGAGAAGTGCAGCAGG 61.039 63.158 0.00 0.00 0.00 4.85
4966 9895 1.823169 TTAACTCCACCGCGCTCCTT 61.823 55.000 5.56 0.00 0.00 3.36
5027 9956 2.038329 TCCTACCTCACCCCCACG 59.962 66.667 0.00 0.00 0.00 4.94
5147 10076 2.472695 TGTGCGGCTATGAAACTCTT 57.527 45.000 0.00 0.00 0.00 2.85
5282 10213 7.926555 ACTAATTTATGCGTGTGCTTACTAGAT 59.073 33.333 0.00 0.00 43.34 1.98
5394 10331 8.752766 TTACTACCGTAGATGAACAAGAAAAG 57.247 34.615 12.66 0.00 0.00 2.27
5449 10386 1.308069 GGATGCGTGGCTGATTGTGT 61.308 55.000 0.00 0.00 0.00 3.72
5450 10387 0.179181 GATGCGTGGCTGATTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
5558 11548 3.243724 CAGACCCCTTATAAGGCTAGCT 58.756 50.000 24.05 14.94 45.10 3.32
5563 11554 5.088026 ACCCCTTATAAGGCTAGCTCTTAG 58.912 45.833 24.05 14.63 45.10 2.18
5724 11727 9.639601 GAAGTTGATCACCGATACATATATGAA 57.360 33.333 19.63 0.00 0.00 2.57
5805 11808 0.740737 CAAAATGGGGCTCATCGGAC 59.259 55.000 0.00 0.00 34.44 4.79
6094 12740 3.003173 CCTCCCTCTTGACCGGCA 61.003 66.667 0.00 0.00 0.00 5.69
6140 12804 3.151022 GTAGAGCCGAGCCTGCCT 61.151 66.667 0.00 0.00 0.00 4.75
6306 13230 2.448926 TGCGTAATGCTGTACACTGT 57.551 45.000 0.00 0.00 46.63 3.55
6367 13291 0.251787 GGGCTGGGTGGTTCTGATTT 60.252 55.000 0.00 0.00 0.00 2.17
6506 13455 9.051679 GCACCAGATGTTTATTTTTAGGTTTTT 57.948 29.630 0.00 0.00 0.00 1.94
6623 13639 1.079750 GAACTCGGTGAGCAGGACC 60.080 63.158 0.00 0.00 32.04 4.46
6738 13762 8.066612 TCTGATCCTTTCCCAATGAAAAATAC 57.933 34.615 0.00 0.00 42.25 1.89
6954 13991 3.519510 CTCAGGGTGGAGATAAACAGGAA 59.480 47.826 0.00 0.00 37.05 3.36
7000 14037 6.451064 AAGGTAAAAAGCATATACACCTGC 57.549 37.500 0.00 0.00 35.17 4.85
7583 14784 1.597854 CTGTTTCAGCTGGCCGACA 60.598 57.895 15.13 12.15 0.00 4.35
7617 14819 3.104602 CTGGTAGCTGCGCACATGC 62.105 63.158 5.66 9.45 37.78 4.06
7636 14839 3.509442 TGCCAGACATTTTCTCCCAAAT 58.491 40.909 0.00 0.00 28.96 2.32
7659 14875 0.803380 GCACGGAATTTGATGCTGCC 60.803 55.000 0.00 0.00 35.16 4.85
7711 14944 2.044946 CCTTTGGAAGGGAGGCGG 60.045 66.667 0.00 0.00 45.27 6.13
7752 14986 3.682858 CCAAAATCCAGCTGCAAATGAAG 59.317 43.478 8.66 0.00 0.00 3.02
7849 15090 0.914644 TGATGGAGGCTTCTGGAAGG 59.085 55.000 11.61 0.00 38.80 3.46
7949 15190 2.113860 TCCAGCTGCTTTGGTGATAC 57.886 50.000 8.66 0.00 37.61 2.24
7952 15193 2.430465 CAGCTGCTTTGGTGATACTGT 58.570 47.619 0.00 0.00 37.61 3.55
7962 15203 6.371548 GCTTTGGTGATACTGTCTCAATACAA 59.628 38.462 0.00 2.30 0.00 2.41
7980 15221 7.384932 TCAATACAATCCAGTACGCATTATGAG 59.615 37.037 0.00 0.00 0.00 2.90
8005 15246 6.628919 ACTAAAGTATTGGTTTGTGGTGTC 57.371 37.500 0.00 0.00 0.00 3.67
8103 15345 7.423199 TCATTTGTATACACGGATAGACAGAC 58.577 38.462 4.68 0.00 28.58 3.51
8106 15348 5.677567 TGTATACACGGATAGACAGACAGA 58.322 41.667 0.08 0.00 0.00 3.41
8107 15349 6.296803 TGTATACACGGATAGACAGACAGAT 58.703 40.000 0.08 0.00 0.00 2.90
8108 15350 7.447594 TGTATACACGGATAGACAGACAGATA 58.552 38.462 0.08 0.00 0.00 1.98
8111 15353 4.576873 ACACGGATAGACAGACAGATAGTG 59.423 45.833 0.00 0.00 0.00 2.74
8113 15355 4.576873 ACGGATAGACAGACAGATAGTGTG 59.423 45.833 0.00 0.00 46.33 3.82
8179 15559 8.696410 ATTTAATGTATTTTGGCTACGGTTTG 57.304 30.769 0.00 0.00 0.00 2.93
8218 15598 8.417106 CGAATGTATTGCCTAGATATGTAGGAT 58.583 37.037 26.20 15.29 42.18 3.24
8229 15609 7.784073 CCTAGATATGTAGGATGGACTGATCAT 59.216 40.741 19.07 0.00 42.18 2.45
8232 15612 5.999205 ATGTAGGATGGACTGATCATCTC 57.001 43.478 0.00 0.00 40.44 2.75
8233 15613 5.072129 TGTAGGATGGACTGATCATCTCT 57.928 43.478 0.00 10.39 40.44 3.10
8234 15614 6.206180 TGTAGGATGGACTGATCATCTCTA 57.794 41.667 0.00 0.00 40.44 2.43
8235 15615 6.798766 TGTAGGATGGACTGATCATCTCTAT 58.201 40.000 0.00 0.00 40.44 1.98
8236 15616 7.244558 TGTAGGATGGACTGATCATCTCTATT 58.755 38.462 0.00 0.00 40.44 1.73
8237 15617 6.855763 AGGATGGACTGATCATCTCTATTC 57.144 41.667 0.00 0.00 40.44 1.75
8238 15618 6.564099 AGGATGGACTGATCATCTCTATTCT 58.436 40.000 0.00 0.00 40.44 2.40
8239 15619 7.707648 AGGATGGACTGATCATCTCTATTCTA 58.292 38.462 0.00 0.00 40.44 2.10
8240 15620 7.615365 AGGATGGACTGATCATCTCTATTCTAC 59.385 40.741 0.00 0.00 40.44 2.59
8241 15621 7.615365 GGATGGACTGATCATCTCTATTCTACT 59.385 40.741 0.00 0.00 40.44 2.57
8242 15622 9.679661 GATGGACTGATCATCTCTATTCTACTA 57.320 37.037 0.00 0.00 38.30 1.82
8301 15681 1.354368 CTTCCTCCCAAGGCCTTGTTA 59.646 52.381 37.09 25.51 43.02 2.41
8302 15682 1.451449 TCCTCCCAAGGCCTTGTTAA 58.549 50.000 37.09 23.27 43.02 2.01
8304 15684 1.075536 CCTCCCAAGGCCTTGTTAAGT 59.924 52.381 37.09 4.72 38.85 2.24
8307 15687 1.000843 CCCAAGGCCTTGTTAAGTTGC 59.999 52.381 37.09 0.00 38.85 4.17
8308 15688 1.963515 CCAAGGCCTTGTTAAGTTGCT 59.036 47.619 37.09 1.66 38.85 3.91
8310 15690 3.763897 CCAAGGCCTTGTTAAGTTGCTAT 59.236 43.478 37.09 0.94 38.85 2.97
8332 15712 5.675684 TGGATTTAGGGCCAATTCTTTTC 57.324 39.130 6.18 0.00 0.00 2.29
8333 15713 5.341169 TGGATTTAGGGCCAATTCTTTTCT 58.659 37.500 6.18 0.00 0.00 2.52
8334 15714 5.784906 TGGATTTAGGGCCAATTCTTTTCTT 59.215 36.000 6.18 0.00 0.00 2.52
8335 15715 6.272090 TGGATTTAGGGCCAATTCTTTTCTTT 59.728 34.615 6.18 0.00 0.00 2.52
8336 15716 7.168219 GGATTTAGGGCCAATTCTTTTCTTTT 58.832 34.615 6.18 0.00 0.00 2.27
8337 15717 7.119699 GGATTTAGGGCCAATTCTTTTCTTTTG 59.880 37.037 6.18 0.00 0.00 2.44
8338 15718 4.356405 AGGGCCAATTCTTTTCTTTTGG 57.644 40.909 6.18 0.00 41.26 3.28
8339 15719 3.072915 AGGGCCAATTCTTTTCTTTTGGG 59.927 43.478 6.18 0.00 39.21 4.12
8340 15720 3.411446 GGCCAATTCTTTTCTTTTGGGG 58.589 45.455 0.00 0.00 39.21 4.96
8341 15721 3.181445 GGCCAATTCTTTTCTTTTGGGGT 60.181 43.478 0.00 0.00 39.21 4.95
8342 15722 4.460263 GCCAATTCTTTTCTTTTGGGGTT 58.540 39.130 3.01 0.00 39.21 4.11
8343 15723 4.887071 GCCAATTCTTTTCTTTTGGGGTTT 59.113 37.500 3.01 0.00 39.21 3.27
8344 15724 6.058833 GCCAATTCTTTTCTTTTGGGGTTTA 58.941 36.000 3.01 0.00 39.21 2.01
8345 15725 6.714810 GCCAATTCTTTTCTTTTGGGGTTTAT 59.285 34.615 3.01 0.00 39.21 1.40
8346 15726 7.308529 GCCAATTCTTTTCTTTTGGGGTTTATG 60.309 37.037 3.01 0.00 39.21 1.90
8347 15727 7.174772 CCAATTCTTTTCTTTTGGGGTTTATGG 59.825 37.037 0.00 0.00 35.93 2.74
8348 15728 5.222079 TCTTTTCTTTTGGGGTTTATGGC 57.778 39.130 0.00 0.00 0.00 4.40
8349 15729 3.669251 TTTCTTTTGGGGTTTATGGCG 57.331 42.857 0.00 0.00 0.00 5.69
8356 15736 0.609681 GGGGTTTATGGCGGTTGTGA 60.610 55.000 0.00 0.00 0.00 3.58
8376 15756 0.988678 AAATAAGCCGCCTCCTCCCT 60.989 55.000 0.00 0.00 0.00 4.20
8386 15766 2.615391 GCCTCCTCCCTAGCTTATTCT 58.385 52.381 0.00 0.00 0.00 2.40
8481 15865 5.826601 AGGCTGAGCTTTTAAGAATAAGC 57.173 39.130 3.72 2.03 45.46 3.09
8490 15874 6.730175 GCTTTTAAGAATAAGCTAGGAAGGC 58.270 40.000 2.93 0.00 42.62 4.35
8491 15875 6.318900 GCTTTTAAGAATAAGCTAGGAAGGCA 59.681 38.462 2.93 0.00 42.62 4.75
8492 15876 7.467947 GCTTTTAAGAATAAGCTAGGAAGGCAG 60.468 40.741 2.93 0.00 42.62 4.85
8493 15877 3.483808 AGAATAAGCTAGGAAGGCAGC 57.516 47.619 0.00 0.00 38.09 5.25
8496 15880 2.588989 AGCTAGGAAGGCAGCTGC 59.411 61.111 30.88 30.88 46.21 5.25
8497 15881 1.994507 AGCTAGGAAGGCAGCTGCT 60.995 57.895 35.82 19.70 46.21 4.24
8498 15882 1.077858 GCTAGGAAGGCAGCTGCTT 60.078 57.895 35.82 28.28 41.70 3.91
8499 15883 0.179000 GCTAGGAAGGCAGCTGCTTA 59.821 55.000 35.82 19.17 41.70 3.09
8500 15884 1.202746 GCTAGGAAGGCAGCTGCTTAT 60.203 52.381 35.82 22.67 41.70 1.73
8501 15885 2.747799 GCTAGGAAGGCAGCTGCTTATT 60.748 50.000 35.82 26.79 41.70 1.40
8502 15886 2.521547 AGGAAGGCAGCTGCTTATTT 57.478 45.000 35.82 24.02 41.70 1.40
8503 15887 2.373224 AGGAAGGCAGCTGCTTATTTC 58.627 47.619 35.82 28.79 41.70 2.17
8504 15888 1.406898 GGAAGGCAGCTGCTTATTTCC 59.593 52.381 35.82 32.23 41.70 3.13
8505 15889 2.094675 GAAGGCAGCTGCTTATTTCCA 58.905 47.619 35.82 0.00 41.70 3.53
8506 15890 1.467920 AGGCAGCTGCTTATTTCCAC 58.532 50.000 35.82 17.24 41.70 4.02
8507 15891 1.176527 GGCAGCTGCTTATTTCCACA 58.823 50.000 35.82 0.00 41.70 4.17
8508 15892 1.133790 GGCAGCTGCTTATTTCCACAG 59.866 52.381 35.82 0.00 41.70 3.66
8512 15896 0.734889 CTGCTTATTTCCACAGCCGG 59.265 55.000 0.00 0.00 32.11 6.13
8513 15897 1.312371 TGCTTATTTCCACAGCCGGC 61.312 55.000 21.89 21.89 32.11 6.13
8514 15898 2.004808 GCTTATTTCCACAGCCGGCC 62.005 60.000 26.15 5.07 0.00 6.13
8515 15899 0.679640 CTTATTTCCACAGCCGGCCA 60.680 55.000 26.15 0.00 0.00 5.36
8516 15900 0.033601 TTATTTCCACAGCCGGCCAT 60.034 50.000 26.15 8.94 0.00 4.40
8517 15901 0.751277 TATTTCCACAGCCGGCCATG 60.751 55.000 26.15 21.66 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.233980 TGACACGTGGAGGCAGCT 61.234 61.111 21.57 0.00 0.00 4.24
5 6 3.044305 GTGACACGTGGAGGCAGC 61.044 66.667 21.57 0.60 0.00 5.25
91 92 1.756950 TGCTCTAGGCCCGGTACTG 60.757 63.158 0.00 0.00 40.92 2.74
100 101 3.798511 GGTGGGGGTGCTCTAGGC 61.799 72.222 0.00 0.00 42.22 3.93
162 164 1.736645 ATTCGGTTCGGTGCGACTG 60.737 57.895 0.00 0.00 34.89 3.51
223 229 0.978146 AGGTCCTGGGAATGAGTCGG 60.978 60.000 0.00 0.00 0.00 4.79
224 230 0.176680 CAGGTCCTGGGAATGAGTCG 59.823 60.000 11.46 0.00 0.00 4.18
230 244 0.119155 TGGAGTCAGGTCCTGGGAAT 59.881 55.000 19.11 0.00 37.52 3.01
232 246 1.229209 GTGGAGTCAGGTCCTGGGA 60.229 63.158 19.11 0.00 37.52 4.37
234 248 0.610687 GAAGTGGAGTCAGGTCCTGG 59.389 60.000 19.11 0.53 37.52 4.45
281 304 2.803492 CGCTTATCCTTTTCCTCCTCGG 60.803 54.545 0.00 0.00 0.00 4.63
549 611 3.110178 CAAACGACCTCGGCGTCC 61.110 66.667 6.85 0.00 41.75 4.79
628 692 1.063942 GGGATTCACCTTAGGGTTGGG 60.064 57.143 2.32 0.00 44.73 4.12
704 768 7.891561 ACGAATCCTATCTCTCTAAATCCAAG 58.108 38.462 0.00 0.00 0.00 3.61
722 786 1.656095 CGCAGAGAGTGAAACGAATCC 59.344 52.381 0.00 0.00 45.86 3.01
742 806 2.046892 AGCAGGACGGTGACATGC 60.047 61.111 0.00 0.00 43.79 4.06
777 841 3.118454 CAAGCCACCAGCCGTACG 61.118 66.667 8.69 8.69 45.47 3.67
778 842 2.175035 TACCAAGCCACCAGCCGTAC 62.175 60.000 0.00 0.00 45.47 3.67
789 901 0.035820 TGACCAATCCGTACCAAGCC 60.036 55.000 0.00 0.00 0.00 4.35
808 920 1.196104 AGCATTGCAATTGGCCCTGT 61.196 50.000 9.83 0.00 43.89 4.00
809 921 0.825410 TAGCATTGCAATTGGCCCTG 59.175 50.000 9.83 0.00 43.89 4.45
818 933 2.453983 GCAAAACCCTAGCATTGCAA 57.546 45.000 11.91 0.00 45.61 4.08
859 974 1.569708 AGCACACAAACCGCAATTTG 58.430 45.000 7.87 7.87 43.81 2.32
865 980 1.851658 AATGAAAGCACACAAACCGC 58.148 45.000 0.00 0.00 0.00 5.68
926 1041 1.871408 GCCACACACACACAGAGAGAG 60.871 57.143 0.00 0.00 0.00 3.20
928 1043 0.105593 AGCCACACACACACAGAGAG 59.894 55.000 0.00 0.00 0.00 3.20
930 1045 0.179076 TCAGCCACACACACACAGAG 60.179 55.000 0.00 0.00 0.00 3.35
932 1047 0.659427 CTTCAGCCACACACACACAG 59.341 55.000 0.00 0.00 0.00 3.66
981 1108 1.078708 GTTACCAGGCGCCAGCTAA 60.079 57.895 31.54 16.07 44.37 3.09
1328 1462 1.376037 GAGAAACCAGGTGCTCGGG 60.376 63.158 6.91 0.00 36.74 5.14
1437 3317 3.713288 CAACACTGTAGACGTTTCAGGA 58.287 45.455 15.90 0.00 34.02 3.86
1475 3355 2.093764 AGAATAGCTTCGCACTGCTTCT 60.094 45.455 0.00 0.00 40.35 2.85
1689 3569 2.159531 TCGGGGATTATACGTTATCGCG 60.160 50.000 0.00 0.00 41.18 5.87
1913 3793 6.772605 TCTTTCTCCTCAAATGTCATCTTCA 58.227 36.000 0.00 0.00 0.00 3.02
2749 4706 9.856162 TTAAAAAGGTACTCCTAAATGACAAGT 57.144 29.630 0.00 0.00 44.35 3.16
2825 4798 4.350245 CATAATATGGGACGGAGGGAGTA 58.650 47.826 0.00 0.00 0.00 2.59
2854 4870 5.952347 TCTTGAAATCCTAACTACTCCCC 57.048 43.478 0.00 0.00 0.00 4.81
2881 4897 1.953559 TGCGAGGTAATTGCAGGATC 58.046 50.000 0.00 0.00 43.74 3.36
2927 4963 1.070758 AGCTATGTATGACCCCTTGCG 59.929 52.381 0.00 0.00 0.00 4.85
3035 5080 4.220724 ACAGTAGGGTCTTGTAGACAACA 58.779 43.478 8.89 0.00 46.79 3.33
3281 5331 5.128335 AGTGGGGTTTAATCCTTCTAGTACG 59.872 44.000 2.63 0.00 0.00 3.67
3284 5334 7.766736 ATTAGTGGGGTTTAATCCTTCTAGT 57.233 36.000 2.63 0.00 0.00 2.57
3285 5335 8.495260 AGAATTAGTGGGGTTTAATCCTTCTAG 58.505 37.037 2.63 0.00 0.00 2.43
3289 5339 8.177456 AGAAAGAATTAGTGGGGTTTAATCCTT 58.823 33.333 2.63 0.00 0.00 3.36
3491 5718 0.679505 CTGGTTCGGTCTGACCAAGA 59.320 55.000 25.42 13.27 38.47 3.02
3576 5805 6.642950 ACAGCATTAGTAGAACTGAATATCGC 59.357 38.462 0.00 0.00 32.67 4.58
3686 5932 4.072131 TCTGCAGGTTGTTCTGGTATTTC 58.928 43.478 15.13 0.00 35.43 2.17
3788 6040 5.368256 AGATTAAGAACAGCTTGCAACAG 57.632 39.130 0.00 0.00 37.42 3.16
3926 6178 7.413328 CGAAGTTGTAAAAGAGATGATGCATGA 60.413 37.037 2.46 0.00 0.00 3.07
4028 8846 2.871633 TGTGGCTGTATGTCGCATATTG 59.128 45.455 3.46 2.11 35.68 1.90
4088 8906 1.602377 AGGAGCACAAACAACGCTAAC 59.398 47.619 0.00 0.00 35.75 2.34
4094 8912 2.286418 CGACAAGAGGAGCACAAACAAC 60.286 50.000 0.00 0.00 0.00 3.32
4170 8988 0.748005 GGCATGGACAACTACCGCAT 60.748 55.000 0.00 0.00 0.00 4.73
4506 9414 1.127343 AGATGCTTAGGGAGGTGCTC 58.873 55.000 0.00 0.00 0.00 4.26
4546 9454 2.553247 GCAGTTTGGCTATCCCTATCCC 60.553 54.545 0.00 0.00 0.00 3.85
4604 9512 2.233271 CCTCATCCGCCATATTTTGCT 58.767 47.619 0.00 0.00 0.00 3.91
4672 9584 2.297698 TTGTTCGGGAGAGGTGACTA 57.702 50.000 0.00 0.00 44.43 2.59
4898 9827 3.114616 CTCTCAAGTGTGGCGGCG 61.115 66.667 0.51 0.51 0.00 6.46
4946 9875 1.153429 GGAGCGCGGTGGAGTTAAT 60.153 57.895 18.92 0.00 0.00 1.40
5027 9956 1.562672 TAACCCAGCAGAGGAAGGGC 61.563 60.000 0.00 0.00 45.45 5.19
5095 10024 6.506827 GCATGCTGCAGTTTATGAATTTAACG 60.507 38.462 23.06 0.00 44.26 3.18
5147 10076 6.535963 TCATAGAGCAACAAATCAGAGAGA 57.464 37.500 0.00 0.00 0.00 3.10
5235 10165 3.615496 GTGTACACACGACTGTTGTCTTT 59.385 43.478 21.14 0.00 40.86 2.52
5282 10213 1.065102 GCCGCACATCTTCTAGTACGA 59.935 52.381 0.00 0.00 0.00 3.43
5558 11548 3.056607 CGAACCGTAAACCCCTTCTAAGA 60.057 47.826 0.00 0.00 0.00 2.10
5563 11554 1.629345 CGCGAACCGTAAACCCCTTC 61.629 60.000 0.00 0.00 0.00 3.46
6063 12704 3.077556 GAGGCGAAGGAGCTCCCA 61.078 66.667 29.54 0.00 37.41 4.37
6074 12715 3.068691 CGGTCAAGAGGGAGGCGA 61.069 66.667 0.00 0.00 0.00 5.54
6140 12804 0.392193 GACAGAGGAGTACGACCGGA 60.392 60.000 9.46 0.00 0.00 5.14
6248 12970 2.970974 GACAAGGAGCGCAAGTGCC 61.971 63.158 11.47 2.33 41.68 5.01
6251 12973 1.227556 AACGACAAGGAGCGCAAGT 60.228 52.632 11.47 0.00 41.68 3.16
6263 12985 0.030235 CGTCTCCTGTGACAACGACA 59.970 55.000 1.61 0.00 36.82 4.35
6306 13230 2.365105 GACCACCCCCGATCCAGA 60.365 66.667 0.00 0.00 0.00 3.86
6367 13291 0.318441 CTTCCAACCTCTCGCTCACA 59.682 55.000 0.00 0.00 0.00 3.58
6457 13403 0.966920 CACACAAGGTCTCCCTACGT 59.033 55.000 0.00 0.00 41.56 3.57
6458 13405 0.966920 ACACACAAGGTCTCCCTACG 59.033 55.000 0.00 0.00 41.56 3.51
6623 13639 2.049156 TGCAGCCTTCGACTCGTG 60.049 61.111 0.00 0.00 0.00 4.35
6738 13762 3.129988 GTCAGATTTTGCATTCTCCCCTG 59.870 47.826 0.00 0.00 0.00 4.45
6954 13991 1.346062 TCTGCAGTTTCTCCAGCTCT 58.654 50.000 14.67 0.00 0.00 4.09
7583 14784 1.269012 CCAGCAATTTCCCCATGTGT 58.731 50.000 0.00 0.00 0.00 3.72
7617 14819 3.834231 ACCATTTGGGAGAAAATGTCTGG 59.166 43.478 0.96 0.00 43.17 3.86
7636 14839 0.243365 GCATCAAATTCCGTGCACCA 59.757 50.000 12.15 0.00 37.52 4.17
7659 14875 3.009723 AGCACATGATTTAACACCTCCG 58.990 45.455 0.00 0.00 0.00 4.63
7709 14942 2.851071 GCCTCGATCTCTGTCCCCG 61.851 68.421 0.00 0.00 0.00 5.73
7711 14944 1.758514 TGGCCTCGATCTCTGTCCC 60.759 63.158 3.32 0.00 0.00 4.46
7849 15090 3.179939 GCGCGAGTCGGAAGGAAC 61.180 66.667 12.10 0.00 38.94 3.62
7868 15109 1.059098 ACTGAGCCAACATCTGACCA 58.941 50.000 0.00 0.00 0.00 4.02
7949 15190 4.504461 GCGTACTGGATTGTATTGAGACAG 59.496 45.833 0.00 0.00 0.00 3.51
7952 15193 4.729227 TGCGTACTGGATTGTATTGAGA 57.271 40.909 0.00 0.00 0.00 3.27
7962 15203 7.520451 TTAGTACTCATAATGCGTACTGGAT 57.480 36.000 18.22 0.87 45.29 3.41
7980 15221 7.443272 AGACACCACAAACCAATACTTTAGTAC 59.557 37.037 0.00 0.00 32.72 2.73
7990 15231 2.387757 AGCAAGACACCACAAACCAAT 58.612 42.857 0.00 0.00 0.00 3.16
7991 15232 1.846007 AGCAAGACACCACAAACCAA 58.154 45.000 0.00 0.00 0.00 3.67
8005 15246 3.624861 ACTTCACACTCACAGAAAGCAAG 59.375 43.478 0.00 0.00 0.00 4.01
8073 15314 8.325997 GTCTATCCGTGTATACAAATGAACAAC 58.674 37.037 7.25 0.00 0.00 3.32
8108 15350 8.304596 CCTGGTGATAATCGTATAATACACACT 58.695 37.037 0.00 0.00 0.00 3.55
8111 15353 9.565213 GTACCTGGTGATAATCGTATAATACAC 57.435 37.037 10.23 0.00 0.00 2.90
8121 15376 7.450124 ACTATGTAGTACCTGGTGATAATCG 57.550 40.000 10.23 0.00 34.13 3.34
8178 15558 7.247728 GCAATACATTCGAATTAGTCAAACCA 58.752 34.615 8.21 0.00 0.00 3.67
8179 15559 6.691388 GGCAATACATTCGAATTAGTCAAACC 59.309 38.462 8.21 0.28 0.00 3.27
8251 15631 8.289618 GCACTTTAAACAATCTGAACTGACATA 58.710 33.333 0.00 0.00 0.00 2.29
8252 15632 7.141363 GCACTTTAAACAATCTGAACTGACAT 58.859 34.615 0.00 0.00 0.00 3.06
8253 15633 6.094742 TGCACTTTAAACAATCTGAACTGACA 59.905 34.615 0.00 0.00 0.00 3.58
8254 15634 6.494842 TGCACTTTAAACAATCTGAACTGAC 58.505 36.000 0.00 0.00 0.00 3.51
8255 15635 6.691754 TGCACTTTAAACAATCTGAACTGA 57.308 33.333 0.00 0.00 0.00 3.41
8256 15636 7.864379 AGAATGCACTTTAAACAATCTGAACTG 59.136 33.333 0.00 0.00 0.00 3.16
8257 15637 7.945134 AGAATGCACTTTAAACAATCTGAACT 58.055 30.769 0.00 0.00 0.00 3.01
8258 15638 8.579682 AAGAATGCACTTTAAACAATCTGAAC 57.420 30.769 0.00 0.00 0.00 3.18
8259 15639 7.867403 GGAAGAATGCACTTTAAACAATCTGAA 59.133 33.333 0.00 0.00 0.00 3.02
8260 15640 7.231317 AGGAAGAATGCACTTTAAACAATCTGA 59.769 33.333 0.00 0.00 0.00 3.27
8301 15681 3.052944 TGGCCCTAAATCCATAGCAACTT 60.053 43.478 0.00 0.00 0.00 2.66
8302 15682 2.513738 TGGCCCTAAATCCATAGCAACT 59.486 45.455 0.00 0.00 0.00 3.16
8304 15684 3.678965 TTGGCCCTAAATCCATAGCAA 57.321 42.857 0.00 0.00 31.54 3.91
8307 15687 6.983906 AAAGAATTGGCCCTAAATCCATAG 57.016 37.500 0.00 0.00 31.54 2.23
8308 15688 7.132128 AGAAAAGAATTGGCCCTAAATCCATA 58.868 34.615 0.00 0.00 31.54 2.74
8310 15690 5.341169 AGAAAAGAATTGGCCCTAAATCCA 58.659 37.500 0.00 0.00 0.00 3.41
8332 15712 1.262417 ACCGCCATAAACCCCAAAAG 58.738 50.000 0.00 0.00 0.00 2.27
8333 15713 1.344763 CAACCGCCATAAACCCCAAAA 59.655 47.619 0.00 0.00 0.00 2.44
8334 15714 0.969894 CAACCGCCATAAACCCCAAA 59.030 50.000 0.00 0.00 0.00 3.28
8335 15715 0.178958 ACAACCGCCATAAACCCCAA 60.179 50.000 0.00 0.00 0.00 4.12
8336 15716 0.896019 CACAACCGCCATAAACCCCA 60.896 55.000 0.00 0.00 0.00 4.96
8337 15717 0.609681 TCACAACCGCCATAAACCCC 60.610 55.000 0.00 0.00 0.00 4.95
8338 15718 1.249407 TTCACAACCGCCATAAACCC 58.751 50.000 0.00 0.00 0.00 4.11
8339 15719 3.372660 TTTTCACAACCGCCATAAACC 57.627 42.857 0.00 0.00 0.00 3.27
8340 15720 5.061684 GCTTATTTTCACAACCGCCATAAAC 59.938 40.000 0.00 0.00 0.00 2.01
8341 15721 5.164954 GCTTATTTTCACAACCGCCATAAA 58.835 37.500 0.00 0.00 0.00 1.40
8342 15722 4.381079 GGCTTATTTTCACAACCGCCATAA 60.381 41.667 0.00 0.00 36.37 1.90
8343 15723 3.129638 GGCTTATTTTCACAACCGCCATA 59.870 43.478 0.00 0.00 36.37 2.74
8344 15724 2.094234 GGCTTATTTTCACAACCGCCAT 60.094 45.455 0.00 0.00 36.37 4.40
8345 15725 1.271102 GGCTTATTTTCACAACCGCCA 59.729 47.619 0.00 0.00 36.37 5.69
8346 15726 1.731098 CGGCTTATTTTCACAACCGCC 60.731 52.381 0.00 0.00 31.85 6.13
8347 15727 1.613270 CGGCTTATTTTCACAACCGC 58.387 50.000 0.00 0.00 31.85 5.68
8348 15728 1.613270 GCGGCTTATTTTCACAACCG 58.387 50.000 0.00 0.00 41.97 4.44
8349 15729 1.544246 AGGCGGCTTATTTTCACAACC 59.456 47.619 5.25 0.00 0.00 3.77
8356 15736 0.106669 GGGAGGAGGCGGCTTATTTT 60.107 55.000 14.76 0.00 0.00 1.82
8456 15840 7.935520 GCTTATTCTTAAAAGCTCAGCCTAAT 58.064 34.615 0.00 0.00 43.77 1.73
8457 15841 7.321745 GCTTATTCTTAAAAGCTCAGCCTAA 57.678 36.000 0.00 0.00 43.77 2.69
8473 15857 3.483808 GCTGCCTTCCTAGCTTATTCT 57.516 47.619 0.00 0.00 36.99 2.40
8480 15864 0.179000 TAAGCAGCTGCCTTCCTAGC 59.821 55.000 34.39 6.96 43.38 3.42
8481 15865 2.926778 ATAAGCAGCTGCCTTCCTAG 57.073 50.000 34.39 0.00 43.38 3.02
8482 15866 3.545703 GAAATAAGCAGCTGCCTTCCTA 58.454 45.455 34.39 17.90 43.38 2.94
8483 15867 2.373224 GAAATAAGCAGCTGCCTTCCT 58.627 47.619 34.39 17.07 43.38 3.36
8484 15868 1.406898 GGAAATAAGCAGCTGCCTTCC 59.593 52.381 34.39 31.00 43.38 3.46
8485 15869 2.094675 TGGAAATAAGCAGCTGCCTTC 58.905 47.619 34.39 27.23 43.38 3.46
8486 15870 1.821136 GTGGAAATAAGCAGCTGCCTT 59.179 47.619 34.39 26.81 43.38 4.35
8487 15871 1.272092 TGTGGAAATAAGCAGCTGCCT 60.272 47.619 34.39 25.20 43.38 4.75
8488 15872 1.133790 CTGTGGAAATAAGCAGCTGCC 59.866 52.381 34.39 17.92 43.38 4.85
8489 15873 2.556534 CTGTGGAAATAAGCAGCTGC 57.443 50.000 31.53 31.53 42.49 5.25
8493 15877 0.734889 CCGGCTGTGGAAATAAGCAG 59.265 55.000 0.00 0.00 38.73 4.24
8494 15878 1.312371 GCCGGCTGTGGAAATAAGCA 61.312 55.000 22.15 0.00 38.73 3.91
8495 15879 1.433471 GCCGGCTGTGGAAATAAGC 59.567 57.895 22.15 0.00 36.17 3.09
8496 15880 0.679640 TGGCCGGCTGTGGAAATAAG 60.680 55.000 28.56 0.00 0.00 1.73
8497 15881 0.033601 ATGGCCGGCTGTGGAAATAA 60.034 50.000 28.56 0.00 0.00 1.40
8498 15882 0.751277 CATGGCCGGCTGTGGAAATA 60.751 55.000 28.56 1.97 0.00 1.40
8499 15883 2.053865 CATGGCCGGCTGTGGAAAT 61.054 57.895 28.56 6.05 0.00 2.17
8500 15884 2.676121 CATGGCCGGCTGTGGAAA 60.676 61.111 28.56 3.74 0.00 3.13


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

AutoCloner maintained by Alex Coulton.