Multiple sequence alignment - TraesCS5D01G486300

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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 TraesCS5D01G486300 chr5D 100.000 2328 0 0 2153 4480 521483294 521485621 0.000000e+00 4300.0
1 TraesCS5D01G486300 chr5D 100.000 1873 0 0 1 1873 521481142 521483014 0.000000e+00 3459.0
2 TraesCS5D01G486300 chr5D 91.608 286 20 3 4198 4480 9470486 9470202 4.200000e-105 392.0
3 TraesCS5D01G486300 chr5D 91.135 282 20 2 4199 4480 422764614 422764890 1.180000e-100 377.0
4 TraesCS5D01G486300 chr5B 90.453 1215 48 27 685 1873 657727970 657729142 0.000000e+00 1539.0
5 TraesCS5D01G486300 chr5B 89.390 1131 83 21 2742 3863 657729812 657730914 0.000000e+00 1389.0
6 TraesCS5D01G486300 chr5B 91.335 1004 52 7 2981 3976 657880138 657881114 0.000000e+00 1339.0
7 TraesCS5D01G486300 chr5B 95.171 497 16 2 2158 2646 657876745 657877241 0.000000e+00 778.0
8 TraesCS5D01G486300 chr5B 88.504 548 47 13 1 544 657727203 657727738 0.000000e+00 649.0
9 TraesCS5D01G486300 chr5B 89.976 409 26 6 2271 2671 657729287 657729688 8.590000e-142 514.0
10 TraesCS5D01G486300 chr5B 92.527 281 19 2 4201 4480 400520672 400520393 6.980000e-108 401.0
11 TraesCS5D01G486300 chr5B 91.786 280 22 1 4201 4479 403853047 403852768 5.430000e-104 388.0
12 TraesCS5D01G486300 chr5B 95.455 220 8 2 3976 4194 657881151 657881369 2.560000e-92 350.0
13 TraesCS5D01G486300 chr5B 84.262 305 23 16 983 1286 657733592 657733872 1.590000e-69 274.0
14 TraesCS5D01G486300 chr5B 92.424 132 10 0 1727 1858 657876546 657876677 5.920000e-44 189.0
15 TraesCS5D01G486300 chr5A 91.246 1051 32 25 690 1735 649804900 649805895 0.000000e+00 1376.0
16 TraesCS5D01G486300 chr5A 89.990 979 44 16 3007 3976 649806536 649807469 0.000000e+00 1216.0
17 TraesCS5D01G486300 chr5A 88.621 457 36 5 142 593 649804220 649804665 3.940000e-150 542.0
18 TraesCS5D01G486300 chr5A 91.135 282 20 2 4199 4480 655090872 655091148 1.180000e-100 377.0
19 TraesCS5D01G486300 chr5A 95.408 196 9 0 2271 2466 649805995 649806190 3.360000e-81 313.0
20 TraesCS5D01G486300 chr5A 80.935 278 27 13 2520 2784 564441099 564440835 3.540000e-46 196.0
21 TraesCS5D01G486300 chr5A 86.982 169 15 3 4026 4194 649811339 649811500 2.750000e-42 183.0
22 TraesCS5D01G486300 chr5A 91.489 47 4 0 192 238 60131307 60131261 1.040000e-06 65.8
23 TraesCS5D01G486300 chr3D 85.988 1042 102 23 2733 3767 301738692 301737688 0.000000e+00 1075.0
24 TraesCS5D01G486300 chr3D 92.058 277 20 2 4205 4480 113029137 113028862 5.430000e-104 388.0
25 TraesCS5D01G486300 chr3D 100.000 32 0 0 204 235 66121978 66121947 4.840000e-05 60.2
26 TraesCS5D01G486300 chr3D 100.000 32 0 0 204 235 66137775 66137744 4.840000e-05 60.2
27 TraesCS5D01G486300 chr2D 85.893 1042 103 22 2733 3767 565532612 565533616 0.000000e+00 1070.0
28 TraesCS5D01G486300 chr2D 90.559 286 22 3 4195 4480 442040973 442041253 1.520000e-99 374.0
29 TraesCS5D01G486300 chr2D 88.679 53 3 3 599 650 2616460 2616410 1.350000e-05 62.1
30 TraesCS5D01G486300 chr3B 85.096 1040 128 23 2735 3767 706921544 706920525 0.000000e+00 1037.0
31 TraesCS5D01G486300 chr3B 84.270 445 35 12 2231 2671 430932810 430932397 6.980000e-108 401.0
32 TraesCS5D01G486300 chr3B 79.668 241 34 11 1628 1858 430933172 430932937 4.640000e-35 159.0
33 TraesCS5D01G486300 chr3B 96.970 33 1 0 203 235 109797043 109797011 6.260000e-04 56.5
34 TraesCS5D01G486300 chr4A 83.799 1037 120 27 2743 3767 702700310 702701310 0.000000e+00 941.0
35 TraesCS5D01G486300 chr4A 87.414 437 44 5 1280 1706 298171369 298170934 4.030000e-135 492.0
36 TraesCS5D01G486300 chr4A 84.719 445 33 12 2231 2671 60969307 60968894 3.220000e-111 412.0
37 TraesCS5D01G486300 chr4A 85.329 334 38 7 2742 3072 298169483 298169158 7.180000e-88 335.0
38 TraesCS5D01G486300 chr4A 79.412 204 27 11 1665 1858 60969632 60969434 3.640000e-26 130.0
39 TraesCS5D01G486300 chr4A 94.231 52 3 0 599 650 472195651 472195600 3.710000e-11 80.5
40 TraesCS5D01G486300 chr7A 85.138 942 98 24 2733 3667 577678332 577677426 0.000000e+00 926.0
41 TraesCS5D01G486300 chr7A 84.719 445 33 12 2231 2671 586272638 586272225 3.220000e-111 412.0
42 TraesCS5D01G486300 chr7A 79.253 241 35 10 1628 1858 586273000 586272765 2.160000e-33 154.0
43 TraesCS5D01G486300 chr7A 97.561 41 0 1 613 652 230594995 230595035 8.040000e-08 69.4
44 TraesCS5D01G486300 chr2A 84.926 942 100 23 2733 3667 182860521 182861427 0.000000e+00 915.0
45 TraesCS5D01G486300 chr2A 90.977 266 24 0 1280 1545 424508359 424508094 4.260000e-95 359.0
46 TraesCS5D01G486300 chr2A 81.752 274 30 11 2403 2671 424507197 424506939 1.260000e-50 211.0
47 TraesCS5D01G486300 chr2A 79.710 276 29 14 2520 2785 30690330 30690588 1.660000e-39 174.0
48 TraesCS5D01G486300 chr2A 89.362 47 4 1 605 650 600526568 600526614 1.740000e-04 58.4
49 TraesCS5D01G486300 chr1A 84.004 944 104 25 2733 3667 450979997 450980902 0.000000e+00 863.0
50 TraesCS5D01G486300 chr1A 88.462 52 5 1 599 650 71685559 71685609 1.350000e-05 62.1
51 TraesCS5D01G486300 chr7D 82.185 595 60 17 1280 1858 336234206 336234770 1.890000e-128 470.0
52 TraesCS5D01G486300 chr7D 85.894 397 39 7 2247 2634 336235640 336236028 1.500000e-109 407.0
53 TraesCS5D01G486300 chr3A 84.494 445 34 12 2231 2671 662208339 662207926 1.500000e-109 407.0
54 TraesCS5D01G486300 chr3A 80.935 278 27 13 2521 2785 679990922 679991186 3.540000e-46 196.0
55 TraesCS5D01G486300 chr3A 88.462 52 5 1 599 650 18824256 18824206 1.350000e-05 62.1
56 TraesCS5D01G486300 chr4D 92.334 287 18 3 4198 4480 3217910 3217624 5.400000e-109 405.0
57 TraesCS5D01G486300 chr4D 81.720 279 25 14 2520 2785 255551700 255551965 4.540000e-50 209.0
58 TraesCS5D01G486300 chr4D 90.385 52 4 1 599 650 294089273 294089323 2.890000e-07 67.6
59 TraesCS5D01G486300 chr1D 92.336 274 16 2 4205 4478 25761632 25761364 7.030000e-103 385.0
60 TraesCS5D01G486300 chr6D 82.437 279 24 13 2520 2785 225587886 225587620 2.100000e-53 220.0
61 TraesCS5D01G486300 chr6A 82.437 279 24 13 2520 2785 347392011 347391745 2.100000e-53 220.0
62 TraesCS5D01G486300 chr6A 81.004 279 24 16 2520 2784 29436764 29437027 1.270000e-45 195.0
63 TraesCS5D01G486300 chr6A 91.667 48 3 1 604 650 139422164 139422211 1.040000e-06 65.8
64 TraesCS5D01G486300 chr6A 88.679 53 6 0 599 651 539645334 539645386 1.040000e-06 65.8
65 TraesCS5D01G486300 chr6A 87.234 47 6 0 192 238 555487184 555487138 2.000000e-03 54.7
66 TraesCS5D01G486300 chrUn 90.361 166 15 1 2231 2395 374971050 374970885 2.710000e-52 217.0
67 TraesCS5D01G486300 chrUn 79.253 241 35 11 1628 1858 374971412 374971177 2.160000e-33 154.0
68 TraesCS5D01G486300 chrUn 92.308 39 2 1 194 231 35202964 35202926 2.000000e-03 54.7
69 TraesCS5D01G486300 chrUn 92.308 39 2 1 194 231 236914358 236914396 2.000000e-03 54.7
70 TraesCS5D01G486300 chr2B 82.079 279 25 14 2520 2785 707738548 707738814 9.760000e-52 215.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G486300 chr5D 521481142 521485621 4479 False 3879.5 4300 100.00000 1 4480 2 chr5D.!!$F2 4479
1 TraesCS5D01G486300 chr5B 657727203 657733872 6669 False 873.0 1539 88.51700 1 3863 5 chr5B.!!$F1 3862
2 TraesCS5D01G486300 chr5B 657876546 657881369 4823 False 664.0 1339 93.59625 1727 4194 4 chr5B.!!$F2 2467
3 TraesCS5D01G486300 chr5A 649804220 649811500 7280 False 726.0 1376 90.44940 142 4194 5 chr5A.!!$F2 4052
4 TraesCS5D01G486300 chr3D 301737688 301738692 1004 True 1075.0 1075 85.98800 2733 3767 1 chr3D.!!$R4 1034
5 TraesCS5D01G486300 chr2D 565532612 565533616 1004 False 1070.0 1070 85.89300 2733 3767 1 chr2D.!!$F2 1034
6 TraesCS5D01G486300 chr3B 706920525 706921544 1019 True 1037.0 1037 85.09600 2735 3767 1 chr3B.!!$R2 1032
7 TraesCS5D01G486300 chr3B 430932397 430933172 775 True 280.0 401 81.96900 1628 2671 2 chr3B.!!$R3 1043
8 TraesCS5D01G486300 chr4A 702700310 702701310 1000 False 941.0 941 83.79900 2743 3767 1 chr4A.!!$F1 1024
9 TraesCS5D01G486300 chr4A 298169158 298171369 2211 True 413.5 492 86.37150 1280 3072 2 chr4A.!!$R3 1792
10 TraesCS5D01G486300 chr4A 60968894 60969632 738 True 271.0 412 82.06550 1665 2671 2 chr4A.!!$R2 1006
11 TraesCS5D01G486300 chr7A 577677426 577678332 906 True 926.0 926 85.13800 2733 3667 1 chr7A.!!$R1 934
12 TraesCS5D01G486300 chr7A 586272225 586273000 775 True 283.0 412 81.98600 1628 2671 2 chr7A.!!$R2 1043
13 TraesCS5D01G486300 chr2A 182860521 182861427 906 False 915.0 915 84.92600 2733 3667 1 chr2A.!!$F2 934
14 TraesCS5D01G486300 chr2A 424506939 424508359 1420 True 285.0 359 86.36450 1280 2671 2 chr2A.!!$R1 1391
15 TraesCS5D01G486300 chr1A 450979997 450980902 905 False 863.0 863 84.00400 2733 3667 1 chr1A.!!$F2 934
16 TraesCS5D01G486300 chr7D 336234206 336236028 1822 False 438.5 470 84.03950 1280 2634 2 chr7D.!!$F1 1354

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
876 1047 0.031314 CTCGATAGCCGTGCACTCAT 59.969 55.000 16.19 2.45 39.75 2.90 F
882 1053 0.321671 AGCCGTGCACTCATACACTT 59.678 50.000 16.19 0.00 34.58 3.16 F
883 1054 0.721718 GCCGTGCACTCATACACTTC 59.278 55.000 16.19 0.00 34.58 3.01 F
886 1057 1.391485 CGTGCACTCATACACTTCAGC 59.609 52.381 16.19 0.00 34.58 4.26 F
1707 2030 1.453762 GGGGTGAGAGATACGACCGG 61.454 65.000 0.00 0.00 0.00 5.28 F
3005 7136 0.870393 CACATCCTCAGCACACACAC 59.130 55.000 0.00 0.00 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2630 3845 1.440476 GCATGAATTGCCCCTGCTC 59.560 57.895 0.00 0.00 46.15 4.26 R
2719 3949 2.029244 CAGCGGTATACTGTTTTGCTCG 59.971 50.000 13.23 1.25 0.00 5.03 R
2875 4156 2.918656 GACGAATGTCGATGCATGAG 57.081 50.000 2.46 0.00 43.74 2.90 R
2886 4167 0.038166 ATTGCCAGGGTGACGAATGT 59.962 50.000 0.00 0.00 0.00 2.71 R
3298 7437 0.802494 AGCAAGCGAAATGGTTACCG 59.198 50.000 0.00 0.00 36.29 4.02 R
3983 8187 0.171455 AAGTCGCCTCAGATCGTCAC 59.829 55.000 0.00 0.00 0.00 3.67 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
56 57 2.409870 CGTTGGCAGCCATCCTTCC 61.410 63.158 17.09 0.00 31.53 3.46
79 80 3.726291 ACAAAAATGACCGACCCAAAG 57.274 42.857 0.00 0.00 0.00 2.77
81 82 3.067601 ACAAAAATGACCGACCCAAAGTC 59.932 43.478 0.00 0.00 42.54 3.01
90 91 1.305201 GACCCAAAGTCGAAAGCACA 58.695 50.000 0.00 0.00 35.30 4.57
91 92 1.002792 GACCCAAAGTCGAAAGCACAC 60.003 52.381 0.00 0.00 35.30 3.82
92 93 1.021202 CCCAAAGTCGAAAGCACACA 58.979 50.000 0.00 0.00 0.00 3.72
93 94 1.608590 CCCAAAGTCGAAAGCACACAT 59.391 47.619 0.00 0.00 0.00 3.21
94 95 2.811431 CCCAAAGTCGAAAGCACACATA 59.189 45.455 0.00 0.00 0.00 2.29
95 96 3.252215 CCCAAAGTCGAAAGCACACATAA 59.748 43.478 0.00 0.00 0.00 1.90
96 97 4.082787 CCCAAAGTCGAAAGCACACATAAT 60.083 41.667 0.00 0.00 0.00 1.28
97 98 5.460646 CCAAAGTCGAAAGCACACATAATT 58.539 37.500 0.00 0.00 0.00 1.40
98 99 5.343058 CCAAAGTCGAAAGCACACATAATTG 59.657 40.000 0.00 0.00 0.00 2.32
99 100 4.083581 AGTCGAAAGCACACATAATTGC 57.916 40.909 0.00 0.00 39.16 3.56
100 101 3.501828 AGTCGAAAGCACACATAATTGCA 59.498 39.130 0.00 0.00 41.48 4.08
101 102 4.023279 AGTCGAAAGCACACATAATTGCAA 60.023 37.500 0.00 0.00 41.48 4.08
105 106 7.220683 GTCGAAAGCACACATAATTGCAATATT 59.779 33.333 13.39 0.86 41.48 1.28
146 148 8.462143 TCTAAGACTTAGTTAGTTTGATTGCG 57.538 34.615 19.39 0.00 37.17 4.85
164 166 7.703328 TGATTGCGTTAGGAAAATAAAGGATC 58.297 34.615 0.00 0.00 0.00 3.36
184 186 5.189145 GGATCCTTTCAAAGTACTACCTCCA 59.811 44.000 3.84 0.00 0.00 3.86
282 285 0.844661 ACCCTGTAATCCCCACTGCA 60.845 55.000 0.00 0.00 0.00 4.41
303 306 6.396829 GCATAGGGCACTTCTAATTCAAAT 57.603 37.500 0.00 0.00 43.97 2.32
305 308 6.736794 GCATAGGGCACTTCTAATTCAAATGG 60.737 42.308 0.00 0.00 43.97 3.16
312 315 9.087424 GGCACTTCTAATTCAAATGGATTTTAC 57.913 33.333 0.00 0.00 0.00 2.01
313 316 9.638239 GCACTTCTAATTCAAATGGATTTTACA 57.362 29.630 0.00 0.00 0.00 2.41
372 375 5.076182 TCTCCTCATAGATCATGTGACTCC 58.924 45.833 0.00 0.00 35.96 3.85
375 378 6.798766 TCCTCATAGATCATGTGACTCCTAT 58.201 40.000 0.00 0.00 35.96 2.57
429 432 4.379339 TTTTGGAAGAAAGTTTCACCCG 57.621 40.909 17.65 0.00 0.00 5.28
540 549 3.559238 TCAAGAGAAAAATGCCGCTTC 57.441 42.857 0.00 0.00 0.00 3.86
547 556 4.488879 AGAAAAATGCCGCTTCAATCTTC 58.511 39.130 0.00 0.00 0.00 2.87
555 564 3.670523 GCCGCTTCAATCTTCTGTTTTTC 59.329 43.478 0.00 0.00 0.00 2.29
563 572 8.749841 TTCAATCTTCTGTTTTTCGTTTTCAA 57.250 26.923 0.00 0.00 0.00 2.69
565 574 8.026607 TCAATCTTCTGTTTTTCGTTTTCAAGT 58.973 29.630 0.00 0.00 0.00 3.16
646 791 6.500589 TTCTATCCTATGAACCAAAGGAGG 57.499 41.667 0.00 0.00 42.53 4.30
648 793 1.564348 TCCTATGAACCAAAGGAGGCC 59.436 52.381 0.00 0.00 34.46 5.19
649 794 1.566231 CCTATGAACCAAAGGAGGCCT 59.434 52.381 3.86 3.86 33.87 5.19
652 797 1.075601 TGAACCAAAGGAGGCCTGAT 58.924 50.000 12.00 0.00 32.13 2.90
653 798 1.428912 TGAACCAAAGGAGGCCTGATT 59.571 47.619 12.00 0.28 32.13 2.57
655 800 1.075601 ACCAAAGGAGGCCTGATTGA 58.924 50.000 12.00 0.00 32.13 2.57
656 801 1.428912 ACCAAAGGAGGCCTGATTGAA 59.571 47.619 12.00 0.00 32.13 2.69
657 802 2.097825 CCAAAGGAGGCCTGATTGAAG 58.902 52.381 12.00 0.00 32.13 3.02
658 803 1.475682 CAAAGGAGGCCTGATTGAAGC 59.524 52.381 12.00 0.00 32.13 3.86
659 804 0.700564 AAGGAGGCCTGATTGAAGCA 59.299 50.000 12.00 0.00 32.13 3.91
663 825 2.299867 GGAGGCCTGATTGAAGCAAAAA 59.700 45.455 12.00 0.00 0.00 1.94
810 981 8.064814 GCGAATCAATGAAATCTTAGGTTCTAC 58.935 37.037 0.00 0.00 0.00 2.59
811 982 9.319143 CGAATCAATGAAATCTTAGGTTCTACT 57.681 33.333 0.00 0.00 0.00 2.57
853 1024 3.612247 CTGGAAGCCACCTCCCACG 62.612 68.421 0.00 0.00 0.00 4.94
875 1046 1.313091 ACTCGATAGCCGTGCACTCA 61.313 55.000 16.19 0.00 39.75 3.41
876 1047 0.031314 CTCGATAGCCGTGCACTCAT 59.969 55.000 16.19 2.45 39.75 2.90
877 1048 1.266989 CTCGATAGCCGTGCACTCATA 59.733 52.381 16.19 4.79 39.75 2.15
879 1050 1.269051 CGATAGCCGTGCACTCATACA 60.269 52.381 16.19 0.00 0.00 2.29
880 1051 2.128035 GATAGCCGTGCACTCATACAC 58.872 52.381 16.19 0.00 0.00 2.90
881 1052 1.182667 TAGCCGTGCACTCATACACT 58.817 50.000 16.19 4.06 34.58 3.55
882 1053 0.321671 AGCCGTGCACTCATACACTT 59.678 50.000 16.19 0.00 34.58 3.16
883 1054 0.721718 GCCGTGCACTCATACACTTC 59.278 55.000 16.19 0.00 34.58 3.01
884 1055 1.939381 GCCGTGCACTCATACACTTCA 60.939 52.381 16.19 0.00 34.58 3.02
885 1056 1.995484 CCGTGCACTCATACACTTCAG 59.005 52.381 16.19 0.00 34.58 3.02
886 1057 1.391485 CGTGCACTCATACACTTCAGC 59.609 52.381 16.19 0.00 34.58 4.26
887 1058 2.416747 GTGCACTCATACACTTCAGCA 58.583 47.619 10.32 0.00 33.92 4.41
888 1059 2.414481 GTGCACTCATACACTTCAGCAG 59.586 50.000 10.32 0.00 33.92 4.24
889 1060 2.037641 TGCACTCATACACTTCAGCAGT 59.962 45.455 0.00 0.00 35.35 4.40
890 1061 3.070018 GCACTCATACACTTCAGCAGTT 58.930 45.455 0.00 0.00 30.92 3.16
891 1062 3.120408 GCACTCATACACTTCAGCAGTTG 60.120 47.826 0.00 0.00 30.92 3.16
892 1063 3.434641 CACTCATACACTTCAGCAGTTGG 59.565 47.826 0.00 0.00 30.92 3.77
906 1077 2.353208 GCAGTTGGACTTCATCGTCTCT 60.353 50.000 0.00 0.00 34.38 3.10
952 1134 2.283676 TCAGTCCCCAGTCGACCC 60.284 66.667 13.01 0.00 0.00 4.46
959 1141 3.041940 CCAGTCGACCCGCAACAC 61.042 66.667 13.01 0.00 0.00 3.32
960 1142 3.041940 CAGTCGACCCGCAACACC 61.042 66.667 13.01 0.00 0.00 4.16
961 1143 3.542676 AGTCGACCCGCAACACCA 61.543 61.111 13.01 0.00 0.00 4.17
962 1144 3.343421 GTCGACCCGCAACACCAC 61.343 66.667 3.51 0.00 0.00 4.16
1190 1378 3.636231 TTGACCAGGGACCTGCGG 61.636 66.667 12.90 3.05 42.35 5.69
1215 1403 1.644786 CGGAGGCCACCGTTTGATTC 61.645 60.000 30.94 2.94 46.70 2.52
1470 1680 4.042311 TCAGAGTTCAGTCCTCTCAGTACT 59.958 45.833 0.00 0.00 37.18 2.73
1489 1699 2.126424 GGTGGCGTCTGTCTCGTC 60.126 66.667 0.00 0.00 0.00 4.20
1706 2029 1.783031 CGGGGTGAGAGATACGACCG 61.783 65.000 0.00 0.00 34.57 4.79
1707 2030 1.453762 GGGGTGAGAGATACGACCGG 61.454 65.000 0.00 0.00 0.00 5.28
1745 2082 6.928492 CAGTTACTAACCATGCCAAAAACAAT 59.072 34.615 0.00 0.00 0.00 2.71
2227 3232 6.843069 AAGGACATGTTGTAAAATTGTTGC 57.157 33.333 0.00 0.00 0.00 4.17
2228 3233 6.160576 AGGACATGTTGTAAAATTGTTGCT 57.839 33.333 0.00 0.00 0.00 3.91
2229 3234 5.984926 AGGACATGTTGTAAAATTGTTGCTG 59.015 36.000 0.00 0.00 0.00 4.41
2230 3235 5.982516 GGACATGTTGTAAAATTGTTGCTGA 59.017 36.000 0.00 0.00 0.00 4.26
2231 3236 6.478344 GGACATGTTGTAAAATTGTTGCTGAA 59.522 34.615 0.00 0.00 0.00 3.02
2232 3237 7.171337 GGACATGTTGTAAAATTGTTGCTGAAT 59.829 33.333 0.00 0.00 0.00 2.57
2233 3238 8.436046 ACATGTTGTAAAATTGTTGCTGAATT 57.564 26.923 0.00 0.00 0.00 2.17
2234 3239 8.336806 ACATGTTGTAAAATTGTTGCTGAATTG 58.663 29.630 0.00 0.00 0.00 2.32
2235 3240 7.840342 TGTTGTAAAATTGTTGCTGAATTGT 57.160 28.000 0.00 0.00 0.00 2.71
2236 3241 8.261492 TGTTGTAAAATTGTTGCTGAATTGTT 57.739 26.923 0.00 0.00 0.00 2.83
2466 3650 3.334583 TCTTCGCTTGCTTGAAGGTAT 57.665 42.857 9.27 0.00 41.48 2.73
2467 3651 3.674997 TCTTCGCTTGCTTGAAGGTATT 58.325 40.909 9.27 0.00 41.48 1.89
2468 3652 4.072131 TCTTCGCTTGCTTGAAGGTATTT 58.928 39.130 9.27 0.00 41.48 1.40
2470 3654 4.159377 TCGCTTGCTTGAAGGTATTTTG 57.841 40.909 0.00 0.00 31.56 2.44
2515 3717 6.858993 GCTCTGGTCATAGTTTTAGATCTACG 59.141 42.308 0.67 0.00 0.00 3.51
2630 3845 5.911752 AGAATGTTATGAGTAGCAGACTGG 58.088 41.667 4.26 0.00 39.06 4.00
2673 3888 7.151999 AGTTGTACAAACTGAACACATTTGA 57.848 32.000 10.51 0.00 36.91 2.69
2676 3891 8.868916 GTTGTACAAACTGAACACATTTGATTT 58.131 29.630 10.51 0.00 36.91 2.17
2679 3894 7.992180 ACAAACTGAACACATTTGATTTCTC 57.008 32.000 11.34 0.00 36.91 2.87
2681 3896 7.703621 ACAAACTGAACACATTTGATTTCTCAG 59.296 33.333 11.34 0.00 36.91 3.35
2682 3897 7.572523 AACTGAACACATTTGATTTCTCAGA 57.427 32.000 2.95 0.00 34.51 3.27
2684 3899 7.420800 ACTGAACACATTTGATTTCTCAGAAC 58.579 34.615 2.95 0.00 34.51 3.01
2727 3957 5.461032 AATTACCAAATGGACGAGCAAAA 57.539 34.783 6.42 0.00 38.94 2.44
2728 3958 2.793278 ACCAAATGGACGAGCAAAAC 57.207 45.000 6.42 0.00 38.94 2.43
2849 4130 5.002464 ACATAACAATTCCTCTGCATTGC 57.998 39.130 0.46 0.46 34.26 3.56
2884 4165 8.358148 ACATAGATTGAAAAATCCTCATGCATC 58.642 33.333 0.00 0.00 0.00 3.91
2886 4167 5.591472 AGATTGAAAAATCCTCATGCATCGA 59.409 36.000 0.00 0.00 0.00 3.59
2906 4188 1.176527 CATTCGTCACCCTGGCAATT 58.823 50.000 0.00 0.00 0.00 2.32
2910 4192 2.156098 TCGTCACCCTGGCAATTTAAC 58.844 47.619 0.00 0.00 0.00 2.01
2932 4214 7.636150 AACTTATCTGCATTTGCTATTCAGT 57.364 32.000 3.94 0.00 42.66 3.41
2934 4216 8.915057 ACTTATCTGCATTTGCTATTCAGTAT 57.085 30.769 3.94 0.00 42.66 2.12
2968 4250 2.687425 TGGTTCAGTGTGTGATTGGTTG 59.313 45.455 0.00 0.00 34.17 3.77
2969 4251 2.687935 GGTTCAGTGTGTGATTGGTTGT 59.312 45.455 0.00 0.00 34.17 3.32
2996 7125 8.899427 ACTATGATAATGAAACACATCCTCAG 57.101 34.615 0.00 0.00 38.38 3.35
2997 7126 6.630444 ATGATAATGAAACACATCCTCAGC 57.370 37.500 0.00 0.00 38.38 4.26
2998 7127 5.499313 TGATAATGAAACACATCCTCAGCA 58.501 37.500 0.00 0.00 38.38 4.41
2999 7128 5.355071 TGATAATGAAACACATCCTCAGCAC 59.645 40.000 0.00 0.00 38.38 4.40
3005 7136 0.870393 CACATCCTCAGCACACACAC 59.130 55.000 0.00 0.00 0.00 3.82
3192 7331 4.435970 TCGCCGAGCTCTACCCCA 62.436 66.667 12.85 0.00 0.00 4.96
3259 7398 8.139350 ACATGATATGTTTGGAGCACAATAATG 58.861 33.333 0.00 0.00 41.63 1.90
3292 7431 1.001520 ACGACATGAACGGACCATTGA 59.998 47.619 17.43 0.00 34.93 2.57
3375 7514 3.071206 GGCTGGTGAGAGCGGAGA 61.071 66.667 0.00 0.00 40.13 3.71
3599 7761 4.100189 CCAGTGCTAGACCTTATAGTTGCT 59.900 45.833 0.00 0.00 0.00 3.91
3707 7873 0.389948 GTTGCGAGGAAGATCACCGT 60.390 55.000 0.00 0.00 0.00 4.83
3789 7955 7.872113 ATGAAACTAAAAATGCCCACAAAAA 57.128 28.000 0.00 0.00 0.00 1.94
3806 7972 2.050477 AAACGGATTTCTTTGCGCAG 57.950 45.000 11.31 0.00 33.30 5.18
3824 7990 3.730061 CGCAGATTCAGTTTCATGGCTTC 60.730 47.826 0.00 0.00 0.00 3.86
3829 7995 2.783135 TCAGTTTCATGGCTTCAGGTC 58.217 47.619 0.00 0.00 0.00 3.85
3983 8187 2.489971 TCCTTGGACGCTAAACACTTG 58.510 47.619 0.00 0.00 0.00 3.16
4071 12974 2.544685 CCGAGGACAAGCAGTTCATAG 58.455 52.381 0.00 0.00 0.00 2.23
4083 12986 3.314635 GCAGTTCATAGCTTAAGCATGCT 59.685 43.478 28.39 16.30 45.16 3.79
4084 12987 4.512944 GCAGTTCATAGCTTAAGCATGCTA 59.487 41.667 28.39 12.88 44.47 3.49
4086 12989 6.369890 GCAGTTCATAGCTTAAGCATGCTATA 59.630 38.462 28.39 12.63 46.82 1.31
4087 12990 7.065563 GCAGTTCATAGCTTAAGCATGCTATAT 59.934 37.037 28.39 13.52 46.82 0.86
4088 12991 9.591792 CAGTTCATAGCTTAAGCATGCTATATA 57.408 33.333 28.39 7.11 46.82 0.86
4174 13084 6.969993 AATAACACACCCAACAACATTAGT 57.030 33.333 0.00 0.00 0.00 2.24
4196 13106 6.698380 AGTTTACAAGGCCATCTATATACCG 58.302 40.000 5.01 0.00 0.00 4.02
4197 13107 3.611766 ACAAGGCCATCTATATACCGC 57.388 47.619 5.01 0.00 0.00 5.68
4198 13108 2.094182 ACAAGGCCATCTATATACCGCG 60.094 50.000 5.01 0.00 0.00 6.46
4199 13109 0.460311 AGGCCATCTATATACCGCGC 59.540 55.000 5.01 0.00 0.00 6.86
4200 13110 0.529992 GGCCATCTATATACCGCGCC 60.530 60.000 0.00 0.00 0.00 6.53
4203 13113 0.104304 CATCTATATACCGCGCCCCC 59.896 60.000 0.00 0.00 0.00 5.40
4204 13114 1.389609 ATCTATATACCGCGCCCCCG 61.390 60.000 0.00 0.00 37.57 5.73
4222 13132 4.135153 CGTCGCTCCTCTGGGGTG 62.135 72.222 0.00 0.00 36.25 4.61
4224 13134 2.680352 TCGCTCCTCTGGGGTGAC 60.680 66.667 0.00 0.00 36.25 3.67
4225 13135 2.681778 CGCTCCTCTGGGGTGACT 60.682 66.667 0.00 0.00 36.25 3.41
4227 13137 2.716017 GCTCCTCTGGGGTGACTCG 61.716 68.421 0.00 0.00 36.25 4.18
4229 14165 3.077556 CCTCTGGGGTGACTCGGG 61.078 72.222 0.00 0.00 37.98 5.14
4245 14181 4.815108 GGCGGCCCCAACCCTAAG 62.815 72.222 8.12 0.00 0.00 2.18
4248 14184 2.362503 GGCCCCAACCCTAAGCAC 60.363 66.667 0.00 0.00 0.00 4.40
4249 14185 2.362503 GCCCCAACCCTAAGCACC 60.363 66.667 0.00 0.00 0.00 5.01
4253 14189 3.124921 CAACCCTAAGCACCGCCG 61.125 66.667 0.00 0.00 0.00 6.46
4254 14190 4.404098 AACCCTAAGCACCGCCGG 62.404 66.667 0.00 0.00 0.00 6.13
4272 14208 4.845307 CCCCCTTCCCCCTCCCTC 62.845 77.778 0.00 0.00 0.00 4.30
4274 14210 4.038804 CCCTTCCCCCTCCCTCCA 62.039 72.222 0.00 0.00 0.00 3.86
4276 14212 2.787866 CTTCCCCCTCCCTCCAGA 59.212 66.667 0.00 0.00 0.00 3.86
4277 14213 1.319799 CTTCCCCCTCCCTCCAGAT 59.680 63.158 0.00 0.00 0.00 2.90
4278 14214 0.766288 CTTCCCCCTCCCTCCAGATC 60.766 65.000 0.00 0.00 0.00 2.75
4280 14216 1.152139 CCCCCTCCCTCCAGATCTC 60.152 68.421 0.00 0.00 0.00 2.75
4281 14217 1.532794 CCCCTCCCTCCAGATCTCG 60.533 68.421 0.00 0.00 0.00 4.04
4283 14219 2.206536 CCTCCCTCCAGATCTCGCC 61.207 68.421 0.00 0.00 0.00 5.54
4284 14220 2.519541 TCCCTCCAGATCTCGCCG 60.520 66.667 0.00 0.00 0.00 6.46
4285 14221 4.292178 CCCTCCAGATCTCGCCGC 62.292 72.222 0.00 0.00 0.00 6.53
4286 14222 4.292178 CCTCCAGATCTCGCCGCC 62.292 72.222 0.00 0.00 0.00 6.13
4287 14223 3.531207 CTCCAGATCTCGCCGCCA 61.531 66.667 0.00 0.00 0.00 5.69
4288 14224 3.781770 CTCCAGATCTCGCCGCCAC 62.782 68.421 0.00 0.00 0.00 5.01
4289 14225 4.899239 CCAGATCTCGCCGCCACC 62.899 72.222 0.00 0.00 0.00 4.61
4290 14226 4.147449 CAGATCTCGCCGCCACCA 62.147 66.667 0.00 0.00 0.00 4.17
4293 14229 3.781770 GATCTCGCCGCCACCAGAG 62.782 68.421 0.00 0.00 0.00 3.35
4295 14231 3.842923 CTCGCCGCCACCAGAGAT 61.843 66.667 0.00 0.00 32.84 2.75
4296 14232 2.441348 TCGCCGCCACCAGAGATA 60.441 61.111 0.00 0.00 0.00 1.98
4297 14233 1.810606 CTCGCCGCCACCAGAGATAT 61.811 60.000 0.00 0.00 32.84 1.63
4298 14234 1.373497 CGCCGCCACCAGAGATATC 60.373 63.158 0.00 0.00 0.00 1.63
4299 14235 1.810606 CGCCGCCACCAGAGATATCT 61.811 60.000 4.47 4.47 0.00 1.98
4300 14236 0.320247 GCCGCCACCAGAGATATCTG 60.320 60.000 10.74 10.50 37.48 2.90
4301 14237 0.320247 CCGCCACCAGAGATATCTGC 60.320 60.000 10.74 5.18 36.46 4.26
4302 14238 0.678395 CGCCACCAGAGATATCTGCT 59.322 55.000 10.74 4.49 36.46 4.24
4307 14243 2.924757 CCAGAGATATCTGCTGGCAA 57.075 50.000 25.40 0.00 42.30 4.52
4308 14244 2.768698 CCAGAGATATCTGCTGGCAAG 58.231 52.381 25.40 11.73 42.30 4.01
4328 14264 3.315521 CGCGCGTCATCGAGGAAG 61.316 66.667 24.19 8.68 39.71 3.46
4329 14265 2.956964 GCGCGTCATCGAGGAAGG 60.957 66.667 14.53 5.19 39.71 3.46
4330 14266 2.490217 CGCGTCATCGAGGAAGGT 59.510 61.111 14.53 0.00 39.71 3.50
4334 14270 1.519455 GTCATCGAGGAAGGTGGCG 60.519 63.158 0.00 0.00 0.00 5.69
4336 14272 4.162690 ATCGAGGAAGGTGGCGGC 62.163 66.667 0.00 0.00 0.00 6.53
4358 14294 4.717313 CTGGCTGCTGCTGCCTCA 62.717 66.667 38.41 24.90 46.43 3.86
4373 14309 3.303135 TCACGCGGAGAGCTTGGT 61.303 61.111 12.47 0.00 44.25 3.67
4375 14311 3.616721 ACGCGGAGAGCTTGGTGT 61.617 61.111 12.47 0.00 45.59 4.16
4376 14312 3.114616 CGCGGAGAGCTTGGTGTG 61.115 66.667 0.00 0.00 45.59 3.82
4377 14313 3.426568 GCGGAGAGCTTGGTGTGC 61.427 66.667 0.00 0.00 44.04 4.57
4378 14314 2.743928 CGGAGAGCTTGGTGTGCC 60.744 66.667 0.00 0.00 0.00 5.01
4379 14315 2.743928 GGAGAGCTTGGTGTGCCG 60.744 66.667 0.00 0.00 37.67 5.69
4380 14316 2.743928 GAGAGCTTGGTGTGCCGG 60.744 66.667 0.00 0.00 37.67 6.13
4381 14317 4.335647 AGAGCTTGGTGTGCCGGG 62.336 66.667 2.18 0.00 37.67 5.73
4403 14339 4.722700 CAGCCCCGGTCAAGGTGG 62.723 72.222 0.00 0.00 0.00 4.61
4423 14359 4.388499 GGCGCCTTTCCTGACGGA 62.388 66.667 22.15 0.00 37.60 4.69
4424 14360 2.815647 GCGCCTTTCCTGACGGAG 60.816 66.667 0.00 0.00 41.25 4.63
4425 14361 2.125512 CGCCTTTCCTGACGGAGG 60.126 66.667 0.00 0.00 44.45 4.30
4426 14362 2.269241 GCCTTTCCTGACGGAGGG 59.731 66.667 3.12 0.00 43.06 4.30
4427 14363 2.593956 GCCTTTCCTGACGGAGGGT 61.594 63.158 3.12 0.00 43.06 4.34
4428 14364 1.296715 CCTTTCCTGACGGAGGGTG 59.703 63.158 3.12 0.00 43.06 4.61
4429 14365 1.296715 CTTTCCTGACGGAGGGTGG 59.703 63.158 3.12 0.00 43.06 4.61
4430 14366 2.804828 CTTTCCTGACGGAGGGTGGC 62.805 65.000 3.12 0.00 43.06 5.01
4431 14367 3.846405 TTCCTGACGGAGGGTGGCT 62.846 63.158 3.12 0.00 43.06 4.75
4432 14368 4.087892 CCTGACGGAGGGTGGCTG 62.088 72.222 0.00 0.00 38.36 4.85
4433 14369 4.767255 CTGACGGAGGGTGGCTGC 62.767 72.222 0.00 0.00 0.00 5.25
4452 14388 4.717313 GGGGTGTGGCCGGTCTTC 62.717 72.222 7.97 0.54 38.44 2.87
4453 14389 4.717313 GGGTGTGGCCGGTCTTCC 62.717 72.222 7.97 6.91 38.44 3.46
4454 14390 3.637273 GGTGTGGCCGGTCTTCCT 61.637 66.667 7.97 0.00 0.00 3.36
4455 14391 2.047179 GTGTGGCCGGTCTTCCTC 60.047 66.667 7.97 0.00 0.00 3.71
4456 14392 3.691342 TGTGGCCGGTCTTCCTCG 61.691 66.667 7.97 0.00 0.00 4.63
4461 14397 2.125512 CCGGTCTTCCTCGGCTTG 60.126 66.667 0.00 0.00 39.78 4.01
4462 14398 2.815647 CGGTCTTCCTCGGCTTGC 60.816 66.667 0.00 0.00 0.00 4.01
4463 14399 2.815647 GGTCTTCCTCGGCTTGCG 60.816 66.667 0.00 0.00 0.00 4.85
4464 14400 2.048127 GTCTTCCTCGGCTTGCGT 60.048 61.111 0.00 0.00 0.00 5.24
4465 14401 2.048222 TCTTCCTCGGCTTGCGTG 60.048 61.111 0.00 0.00 0.00 5.34
4466 14402 3.121030 CTTCCTCGGCTTGCGTGG 61.121 66.667 0.00 0.00 0.00 4.94
4467 14403 4.697756 TTCCTCGGCTTGCGTGGG 62.698 66.667 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.166011 GATGGCTGCCAACGACGC 62.166 66.667 27.24 7.31 36.95 5.19
56 57 3.444703 TGGGTCGGTCATTTTTGTTTG 57.555 42.857 0.00 0.00 0.00 2.93
79 80 3.820689 TGCAATTATGTGTGCTTTCGAC 58.179 40.909 0.00 0.00 41.48 4.20
81 82 7.453980 AATATTGCAATTATGTGTGCTTTCG 57.546 32.000 18.75 0.00 41.48 3.46
120 121 9.088512 CGCAATCAAACTAACTAAGTCTTAGAT 57.911 33.333 23.62 15.52 37.50 1.98
128 129 7.591006 TCCTAACGCAATCAAACTAACTAAG 57.409 36.000 0.00 0.00 0.00 2.18
131 132 6.870971 TTTCCTAACGCAATCAAACTAACT 57.129 33.333 0.00 0.00 0.00 2.24
207 209 6.045072 ACCTCCGTATCAAAATGTAAGACA 57.955 37.500 0.00 0.00 0.00 3.41
282 285 6.672593 TCCATTTGAATTAGAAGTGCCCTAT 58.327 36.000 0.00 0.00 0.00 2.57
429 432 5.864628 AAAAAGTAGGAAGATGTTCGAGC 57.135 39.130 0.00 0.00 32.92 5.03
519 527 3.507233 TGAAGCGGCATTTTTCTCTTGAT 59.493 39.130 1.45 0.00 0.00 2.57
540 549 8.103924 CACTTGAAAACGAAAAACAGAAGATTG 58.896 33.333 0.00 0.00 0.00 2.67
547 556 7.099666 TGAAACACTTGAAAACGAAAAACAG 57.900 32.000 0.00 0.00 0.00 3.16
555 564 7.289587 AGGATTTTTGAAACACTTGAAAACG 57.710 32.000 0.00 0.00 28.93 3.60
614 759 9.964354 TTGGTTCATAGGATAGAAATATCATGG 57.036 33.333 0.00 0.00 0.00 3.66
642 787 1.549203 TTTGCTTCAATCAGGCCTCC 58.451 50.000 0.00 0.00 0.00 4.30
677 839 5.355596 GCTGTCTGCTTGATTCATAGTAGT 58.644 41.667 10.96 0.00 38.95 2.73
678 840 4.749099 GGCTGTCTGCTTGATTCATAGTAG 59.251 45.833 1.44 7.26 42.39 2.57
679 841 4.406972 AGGCTGTCTGCTTGATTCATAGTA 59.593 41.667 1.44 0.00 42.39 1.82
681 843 3.806380 AGGCTGTCTGCTTGATTCATAG 58.194 45.455 1.44 0.00 42.39 2.23
682 844 3.920231 AGGCTGTCTGCTTGATTCATA 57.080 42.857 1.44 0.00 42.39 2.15
812 983 8.049721 CCAGAACCTAAGATTCTTTTGTAGGAT 58.950 37.037 16.46 7.46 34.08 3.24
814 985 7.394816 TCCAGAACCTAAGATTCTTTTGTAGG 58.605 38.462 3.86 7.72 34.08 3.18
815 986 8.848474 TTCCAGAACCTAAGATTCTTTTGTAG 57.152 34.615 3.86 0.00 34.08 2.74
816 987 7.390718 GCTTCCAGAACCTAAGATTCTTTTGTA 59.609 37.037 3.86 0.00 34.08 2.41
818 989 6.349694 GGCTTCCAGAACCTAAGATTCTTTTG 60.350 42.308 3.86 0.00 34.08 2.44
823 994 3.942115 GTGGCTTCCAGAACCTAAGATTC 59.058 47.826 0.00 0.00 32.34 2.52
826 997 1.628846 GGTGGCTTCCAGAACCTAAGA 59.371 52.381 0.00 0.00 32.34 2.10
853 1024 2.962253 GCACGGCTATCGAGTGGC 60.962 66.667 4.20 4.25 42.43 5.01
875 1046 4.202357 TGAAGTCCAACTGCTGAAGTGTAT 60.202 41.667 0.00 0.00 39.81 2.29
876 1047 3.133901 TGAAGTCCAACTGCTGAAGTGTA 59.866 43.478 0.00 0.00 39.81 2.90
877 1048 2.092968 TGAAGTCCAACTGCTGAAGTGT 60.093 45.455 0.00 0.00 39.81 3.55
879 1050 3.406764 GATGAAGTCCAACTGCTGAAGT 58.593 45.455 0.00 0.00 42.60 3.01
880 1051 2.414481 CGATGAAGTCCAACTGCTGAAG 59.586 50.000 0.00 0.00 0.00 3.02
881 1052 2.224281 ACGATGAAGTCCAACTGCTGAA 60.224 45.455 0.00 0.00 0.00 3.02
882 1053 1.344438 ACGATGAAGTCCAACTGCTGA 59.656 47.619 0.00 0.00 0.00 4.26
883 1054 1.728971 GACGATGAAGTCCAACTGCTG 59.271 52.381 0.00 0.00 35.22 4.41
884 1055 1.620819 AGACGATGAAGTCCAACTGCT 59.379 47.619 0.00 0.00 41.83 4.24
885 1056 1.996191 GAGACGATGAAGTCCAACTGC 59.004 52.381 0.00 0.00 41.83 4.40
886 1057 3.584406 AGAGACGATGAAGTCCAACTG 57.416 47.619 0.00 0.00 41.83 3.16
887 1058 3.056465 GGAAGAGACGATGAAGTCCAACT 60.056 47.826 0.00 0.00 41.83 3.16
888 1059 3.056465 AGGAAGAGACGATGAAGTCCAAC 60.056 47.826 0.00 0.00 41.83 3.77
889 1060 3.165875 AGGAAGAGACGATGAAGTCCAA 58.834 45.455 0.00 0.00 41.83 3.53
890 1061 2.755655 GAGGAAGAGACGATGAAGTCCA 59.244 50.000 0.00 0.00 41.83 4.02
891 1062 2.755655 TGAGGAAGAGACGATGAAGTCC 59.244 50.000 0.00 0.00 41.83 3.85
892 1063 3.428316 GGTGAGGAAGAGACGATGAAGTC 60.428 52.174 0.00 0.00 41.23 3.01
965 1147 3.582120 GTGTGTGTGTGGCGTGGG 61.582 66.667 0.00 0.00 0.00 4.61
996 1180 0.460987 CAACTCCTGTCGCCATCTCC 60.461 60.000 0.00 0.00 0.00 3.71
1443 1647 2.495669 GAGAGGACTGAACTCTGAAGGG 59.504 54.545 9.81 0.00 44.89 3.95
1470 1680 3.680786 CGAGACAGACGCCACCCA 61.681 66.667 0.00 0.00 0.00 4.51
1489 1699 2.032528 TCCTTCTGCGGCCACAAG 59.967 61.111 2.24 0.00 0.00 3.16
1706 2029 4.830826 AGTAACTGCACTTTTGTAAGCC 57.169 40.909 0.00 0.00 34.60 4.35
1707 2030 6.140786 GGTTAGTAACTGCACTTTTGTAAGC 58.859 40.000 12.65 0.00 34.60 3.09
1790 2127 2.550830 AGTAACCAACTGGACTGCAG 57.449 50.000 13.48 13.48 36.93 4.41
1817 2155 7.692460 TTCATCTCATCAAACAAACTATGCT 57.308 32.000 0.00 0.00 0.00 3.79
2167 2571 9.919416 TTTCTGTCCATTGATCCAAATAGAATA 57.081 29.630 0.00 0.00 0.00 1.75
2227 3232 7.894376 AAATGGTTGCATCTTAACAATTCAG 57.106 32.000 0.00 0.00 32.03 3.02
2228 3233 8.674263 AAAAATGGTTGCATCTTAACAATTCA 57.326 26.923 0.00 0.00 32.03 2.57
2229 3234 8.992073 AGAAAAATGGTTGCATCTTAACAATTC 58.008 29.630 0.00 0.00 32.03 2.17
2230 3235 8.776470 CAGAAAAATGGTTGCATCTTAACAATT 58.224 29.630 0.00 0.00 34.07 2.32
2231 3236 7.095102 GCAGAAAAATGGTTGCATCTTAACAAT 60.095 33.333 0.00 0.00 36.59 2.71
2232 3237 6.202570 GCAGAAAAATGGTTGCATCTTAACAA 59.797 34.615 0.00 0.00 36.59 2.83
2233 3238 5.695816 GCAGAAAAATGGTTGCATCTTAACA 59.304 36.000 0.00 0.00 36.59 2.41
2234 3239 5.120674 GGCAGAAAAATGGTTGCATCTTAAC 59.879 40.000 0.00 0.00 38.27 2.01
2235 3240 5.237048 GGCAGAAAAATGGTTGCATCTTAA 58.763 37.500 0.00 0.00 38.27 1.85
2236 3241 4.617995 CGGCAGAAAAATGGTTGCATCTTA 60.618 41.667 0.00 0.00 38.27 2.10
2466 3650 9.013229 AGCATTATCAAGACTACATGAACAAAA 57.987 29.630 0.00 0.00 0.00 2.44
2467 3651 8.565896 AGCATTATCAAGACTACATGAACAAA 57.434 30.769 0.00 0.00 0.00 2.83
2468 3652 8.043113 AGAGCATTATCAAGACTACATGAACAA 58.957 33.333 0.00 0.00 0.00 2.83
2470 3654 7.042187 CCAGAGCATTATCAAGACTACATGAAC 60.042 40.741 0.00 0.00 0.00 3.18
2515 3717 8.169977 TCATCTGGCAAATTATGAAATACTCC 57.830 34.615 0.00 0.00 0.00 3.85
2630 3845 1.440476 GCATGAATTGCCCCTGCTC 59.560 57.895 0.00 0.00 46.15 4.26
2648 3863 7.026562 TCAAATGTGTTCAGTTTGTACAACTG 58.973 34.615 22.04 22.04 46.67 3.16
2650 3865 7.985634 ATCAAATGTGTTCAGTTTGTACAAC 57.014 32.000 8.07 4.01 35.09 3.32
2673 3888 9.981460 AGGTTATGAATTTAGGTTCTGAGAAAT 57.019 29.630 0.00 0.00 0.00 2.17
2694 3924 8.732531 CGTCCATTTGGTAATTTCTTAAGGTTA 58.267 33.333 1.85 0.00 36.34 2.85
2704 3934 5.461032 TTTGCTCGTCCATTTGGTAATTT 57.539 34.783 0.00 0.00 36.34 1.82
2710 3940 2.034558 ACTGTTTTGCTCGTCCATTTGG 59.965 45.455 0.00 0.00 0.00 3.28
2719 3949 2.029244 CAGCGGTATACTGTTTTGCTCG 59.971 50.000 13.23 1.25 0.00 5.03
2728 3958 7.539022 CAGAATATTCAGTACAGCGGTATACTG 59.461 40.741 23.58 23.58 46.46 2.74
2858 4139 7.649533 TGCATGAGGATTTTTCAATCTATGT 57.350 32.000 0.00 0.00 39.17 2.29
2875 4156 2.918656 GACGAATGTCGATGCATGAG 57.081 50.000 2.46 0.00 43.74 2.90
2886 4167 0.038166 ATTGCCAGGGTGACGAATGT 59.962 50.000 0.00 0.00 0.00 2.71
2906 4188 9.177608 ACTGAATAGCAAATGCAGATAAGTTAA 57.822 29.630 12.72 0.00 45.16 2.01
2932 4214 8.783093 CACACTGAACCAGACAAGAAAAATATA 58.217 33.333 0.45 0.00 35.18 0.86
2934 4216 6.601613 ACACACTGAACCAGACAAGAAAAATA 59.398 34.615 0.45 0.00 35.18 1.40
2936 4218 4.764823 ACACACTGAACCAGACAAGAAAAA 59.235 37.500 0.45 0.00 35.18 1.94
2996 7125 1.068588 TGTGTAGAGAGGTGTGTGTGC 59.931 52.381 0.00 0.00 0.00 4.57
2997 7126 2.743938 GTGTGTAGAGAGGTGTGTGTG 58.256 52.381 0.00 0.00 0.00 3.82
2998 7127 1.337071 CGTGTGTAGAGAGGTGTGTGT 59.663 52.381 0.00 0.00 0.00 3.72
2999 7128 1.930817 GCGTGTGTAGAGAGGTGTGTG 60.931 57.143 0.00 0.00 0.00 3.82
3005 7136 1.153745 GCCTGCGTGTGTAGAGAGG 60.154 63.158 0.00 0.00 0.00 3.69
3259 7398 4.661993 TCATGTCGTTGTTTGCTATGAC 57.338 40.909 0.00 0.00 37.06 3.06
3292 7431 2.358984 AAATGGTTACCGCCGCGT 60.359 55.556 12.58 2.59 0.00 6.01
3298 7437 0.802494 AGCAAGCGAAATGGTTACCG 59.198 50.000 0.00 0.00 36.29 4.02
3375 7514 2.172483 ATCAGCTTCTTCGGCACCGT 62.172 55.000 9.23 0.00 40.74 4.83
3516 7658 1.676967 CCAGCAACAGAGGGGAAGC 60.677 63.158 0.00 0.00 0.00 3.86
3707 7873 8.992349 TCTCTCTTATCCTGGACAATTATTCAA 58.008 33.333 0.00 0.00 0.00 2.69
3789 7955 1.453155 ATCTGCGCAAAGAAATCCGT 58.547 45.000 13.05 0.00 0.00 4.69
3806 7972 3.760684 ACCTGAAGCCATGAAACTGAATC 59.239 43.478 0.00 0.00 0.00 2.52
3824 7990 3.563808 TGAAAAGATTTGACACGGACCTG 59.436 43.478 0.00 0.00 0.00 4.00
3829 7995 3.057315 AGCCATGAAAAGATTTGACACGG 60.057 43.478 0.00 0.00 0.00 4.94
3905 8071 4.219033 GCAGTTTTGTACAATTCACTCCG 58.781 43.478 9.56 3.30 0.00 4.63
3983 8187 0.171455 AAGTCGCCTCAGATCGTCAC 59.829 55.000 0.00 0.00 0.00 3.67
4042 12909 2.289444 TGCTTGTCCTCGGGTTAAGAAG 60.289 50.000 10.54 0.00 0.00 2.85
4084 12987 9.881649 CTCATGTTGGCTGTAATGACTATATAT 57.118 33.333 0.00 0.00 0.00 0.86
4085 12988 9.088987 TCTCATGTTGGCTGTAATGACTATATA 57.911 33.333 0.00 0.00 0.00 0.86
4086 12989 7.966812 TCTCATGTTGGCTGTAATGACTATAT 58.033 34.615 0.00 0.00 0.00 0.86
4087 12990 7.360113 TCTCATGTTGGCTGTAATGACTATA 57.640 36.000 0.00 0.00 0.00 1.31
4088 12991 6.239217 TCTCATGTTGGCTGTAATGACTAT 57.761 37.500 0.00 0.00 0.00 2.12
4156 13066 6.137794 TGTAAACTAATGTTGTTGGGTGTG 57.862 37.500 0.00 0.00 36.39 3.82
4174 13084 5.484715 GCGGTATATAGATGGCCTTGTAAA 58.515 41.667 3.32 0.00 0.00 2.01
4205 13115 4.135153 CACCCCAGAGGAGCGACG 62.135 72.222 0.00 0.00 39.89 5.12
4207 13117 2.680352 GTCACCCCAGAGGAGCGA 60.680 66.667 0.00 0.00 39.89 4.93
4208 13118 2.681778 AGTCACCCCAGAGGAGCG 60.682 66.667 0.00 0.00 39.89 5.03
4209 13119 2.716017 CGAGTCACCCCAGAGGAGC 61.716 68.421 0.00 0.00 39.89 4.70
4210 13120 2.055042 CCGAGTCACCCCAGAGGAG 61.055 68.421 0.00 0.00 39.89 3.69
4212 13122 3.077556 CCCGAGTCACCCCAGAGG 61.078 72.222 0.00 0.00 43.78 3.69
4213 13123 3.775654 GCCCGAGTCACCCCAGAG 61.776 72.222 0.00 0.00 0.00 3.35
4232 14168 2.362503 GGTGCTTAGGGTTGGGGC 60.363 66.667 0.00 0.00 0.00 5.80
4235 14171 2.750237 GGCGGTGCTTAGGGTTGG 60.750 66.667 0.00 0.00 0.00 3.77
4257 14193 4.038804 TGGAGGGAGGGGGAAGGG 62.039 72.222 0.00 0.00 0.00 3.95
4260 14196 1.238896 AGATCTGGAGGGAGGGGGAA 61.239 60.000 0.00 0.00 0.00 3.97
4265 14201 2.206536 GGCGAGATCTGGAGGGAGG 61.207 68.421 9.17 0.00 0.00 4.30
4267 14203 2.519541 CGGCGAGATCTGGAGGGA 60.520 66.667 9.17 0.00 0.00 4.20
4268 14204 4.292178 GCGGCGAGATCTGGAGGG 62.292 72.222 12.98 0.00 0.00 4.30
4269 14205 4.292178 GGCGGCGAGATCTGGAGG 62.292 72.222 12.98 0.16 0.00 4.30
4270 14206 3.531207 TGGCGGCGAGATCTGGAG 61.531 66.667 12.98 2.78 0.00 3.86
4271 14207 3.838271 GTGGCGGCGAGATCTGGA 61.838 66.667 12.98 0.00 0.00 3.86
4272 14208 4.899239 GGTGGCGGCGAGATCTGG 62.899 72.222 12.98 0.00 0.00 3.86
4274 14210 3.842923 CTGGTGGCGGCGAGATCT 61.843 66.667 12.98 0.00 0.00 2.75
4276 14212 3.842923 CTCTGGTGGCGGCGAGAT 61.843 66.667 12.98 0.00 0.00 2.75
4277 14213 2.904178 TATCTCTGGTGGCGGCGAGA 62.904 60.000 12.98 14.81 36.99 4.04
4278 14214 1.810606 ATATCTCTGGTGGCGGCGAG 61.811 60.000 12.98 4.79 0.00 5.03
4280 14216 1.373497 GATATCTCTGGTGGCGGCG 60.373 63.158 0.51 0.51 0.00 6.46
4281 14217 0.320247 CAGATATCTCTGGTGGCGGC 60.320 60.000 1.03 0.00 44.40 6.53
4290 14226 2.547299 GCTTGCCAGCAGATATCTCT 57.453 50.000 4.63 0.66 46.49 3.10
4311 14247 3.315521 CTTCCTCGATGACGCGCG 61.316 66.667 30.96 30.96 39.58 6.86
4313 14249 1.874019 CACCTTCCTCGATGACGCG 60.874 63.158 3.53 3.53 39.58 6.01
4314 14250 1.519455 CCACCTTCCTCGATGACGC 60.519 63.158 0.00 0.00 39.58 5.19
4315 14251 1.519455 GCCACCTTCCTCGATGACG 60.519 63.158 0.00 0.00 41.26 4.35
4316 14252 1.519455 CGCCACCTTCCTCGATGAC 60.519 63.158 0.00 0.00 0.00 3.06
4317 14253 2.721167 CCGCCACCTTCCTCGATGA 61.721 63.158 0.00 0.00 0.00 2.92
4318 14254 2.202932 CCGCCACCTTCCTCGATG 60.203 66.667 0.00 0.00 0.00 3.84
4319 14255 4.162690 GCCGCCACCTTCCTCGAT 62.163 66.667 0.00 0.00 0.00 3.59
4357 14293 3.114616 CACCAAGCTCTCCGCGTG 61.115 66.667 4.92 0.00 45.96 5.34
4358 14294 3.616721 ACACCAAGCTCTCCGCGT 61.617 61.111 4.92 0.00 45.59 6.01
4359 14295 3.114616 CACACCAAGCTCTCCGCG 61.115 66.667 0.00 0.00 45.59 6.46
4360 14296 3.426568 GCACACCAAGCTCTCCGC 61.427 66.667 0.00 0.00 39.57 5.54
4362 14298 2.743928 CGGCACACCAAGCTCTCC 60.744 66.667 0.00 0.00 34.57 3.71
4364 14300 4.335647 CCCGGCACACCAAGCTCT 62.336 66.667 0.00 0.00 34.57 4.09
4386 14322 4.722700 CCACCTTGACCGGGGCTG 62.723 72.222 6.32 0.00 0.00 4.85
4406 14342 4.388499 TCCGTCAGGAAAGGCGCC 62.388 66.667 21.89 21.89 45.12 6.53
4415 14351 4.087892 CAGCCACCCTCCGTCAGG 62.088 72.222 0.00 0.00 43.01 3.86
4416 14352 4.767255 GCAGCCACCCTCCGTCAG 62.767 72.222 0.00 0.00 0.00 3.51
4435 14371 4.717313 GAAGACCGGCCACACCCC 62.717 72.222 0.00 0.00 33.26 4.95
4436 14372 4.717313 GGAAGACCGGCCACACCC 62.717 72.222 0.00 0.00 33.26 4.61
4437 14373 3.607370 GAGGAAGACCGGCCACACC 62.607 68.421 0.00 0.00 41.83 4.16
4438 14374 2.047179 GAGGAAGACCGGCCACAC 60.047 66.667 0.00 0.00 41.83 3.82
4439 14375 3.691342 CGAGGAAGACCGGCCACA 61.691 66.667 0.00 0.00 41.83 4.17
4440 14376 4.452733 CCGAGGAAGACCGGCCAC 62.453 72.222 0.00 0.00 41.83 5.01
4445 14381 2.815647 GCAAGCCGAGGAAGACCG 60.816 66.667 0.00 0.00 41.83 4.79
4446 14382 2.815647 CGCAAGCCGAGGAAGACC 60.816 66.667 0.00 0.00 40.02 3.85
4447 14383 2.048127 ACGCAAGCCGAGGAAGAC 60.048 61.111 0.00 0.00 45.62 3.01
4448 14384 2.048222 CACGCAAGCCGAGGAAGA 60.048 61.111 0.00 0.00 45.62 2.87


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

AutoCloner maintained by Alex Coulton.