Multiple sequence alignment - TraesCS5D01G417300

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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 TraesCS5D01G417300 chr5D 100.000 9296 0 0 1 9296 479451436 479460731 0.000000e+00 17167.0
1 TraesCS5D01G417300 chr5D 84.127 126 14 6 4503 4625 479456060 479455938 5.900000e-22 117.0
2 TraesCS5D01G417300 chr5D 100.000 39 0 0 5865 5903 479457222 479457260 1.290000e-08 73.1
3 TraesCS5D01G417300 chr5D 100.000 39 0 0 5787 5825 479457300 479457338 1.290000e-08 73.1
4 TraesCS5D01G417300 chr5D 100.000 34 0 0 4506 4539 418585311 418585278 7.790000e-06 63.9
5 TraesCS5D01G417300 chr5B 95.115 3050 113 21 5375 8398 587124761 587127800 0.000000e+00 4774.0
6 TraesCS5D01G417300 chr5B 91.433 3105 128 54 1 3022 587119530 587122579 0.000000e+00 4133.0
7 TraesCS5D01G417300 chr5B 91.463 1511 70 24 3057 4548 587122576 587124046 0.000000e+00 2021.0
8 TraesCS5D01G417300 chr5B 93.750 752 27 12 4549 5286 587124015 587124760 0.000000e+00 1110.0
9 TraesCS5D01G417300 chr5B 85.714 707 54 20 8430 9091 587127801 587128505 0.000000e+00 702.0
10 TraesCS5D01G417300 chr5B 88.571 210 16 6 5908 6111 359142632 359142839 2.000000e-61 248.0
11 TraesCS5D01G417300 chr5B 85.892 241 7 7 9075 9296 587128526 587128758 2.020000e-56 231.0
12 TraesCS5D01G417300 chr5B 94.118 51 2 1 4506 4555 606020248 606020198 1.000000e-09 76.8
13 TraesCS5D01G417300 chr5B 100.000 39 0 0 5865 5903 587125178 587125216 1.290000e-08 73.1
14 TraesCS5D01G417300 chr5A 91.453 3440 141 60 5904 9295 598076956 598080290 0.000000e+00 4582.0
15 TraesCS5D01G417300 chr5A 86.161 3035 223 80 85 3017 598071188 598074127 0.000000e+00 3096.0
16 TraesCS5D01G417300 chr5A 88.903 784 53 12 4629 5379 598075608 598076390 0.000000e+00 935.0
17 TraesCS5D01G417300 chr5A 85.995 864 59 27 3709 4510 598074745 598075608 0.000000e+00 869.0
18 TraesCS5D01G417300 chr5A 92.580 283 13 6 5441 5722 598076415 598076690 5.230000e-107 399.0
19 TraesCS5D01G417300 chr5A 87.665 227 17 7 3418 3641 598074514 598074732 4.310000e-63 254.0
20 TraesCS5D01G417300 chr5A 97.143 35 1 0 4503 4537 703658323 703658357 1.010000e-04 60.2
21 TraesCS5D01G417300 chr3B 86.024 415 50 6 5969 6381 732153107 732153515 1.110000e-118 438.0
22 TraesCS5D01G417300 chr2B 86.058 416 49 7 5969 6381 727216559 727216150 1.110000e-118 438.0
23 TraesCS5D01G417300 chr2B 85.817 416 48 7 5969 6381 733058650 733059057 1.850000e-116 431.0
24 TraesCS5D01G417300 chr2B 82.927 123 14 6 4506 4627 331012829 331012713 4.590000e-18 104.0
25 TraesCS5D01G417300 chr7D 86.861 274 26 7 5906 6171 497016444 497016173 1.960000e-76 298.0
26 TraesCS5D01G417300 chr6A 88.128 219 24 2 5481 5698 506641109 506641326 9.260000e-65 259.0
27 TraesCS5D01G417300 chr6A 89.474 76 6 1 4549 4624 457394200 457394273 2.760000e-15 95.3
28 TraesCS5D01G417300 chr6D 86.818 220 25 4 5481 5698 365844333 365844550 9.330000e-60 243.0
29 TraesCS5D01G417300 chr6D 81.752 274 20 10 5906 6171 454986926 454986675 1.580000e-47 202.0
30 TraesCS5D01G417300 chr6D 89.474 76 6 1 4549 4624 319699818 319699891 2.760000e-15 95.3
31 TraesCS5D01G417300 chr2D 92.913 127 8 1 5969 6095 85829398 85829523 5.730000e-42 183.0
32 TraesCS5D01G417300 chr2D 91.406 128 10 1 6588 6714 85829804 85829931 3.450000e-39 174.0
33 TraesCS5D01G417300 chr2D 83.740 123 13 6 4506 4627 218045298 218045414 9.870000e-20 110.0
34 TraesCS5D01G417300 chr3A 85.366 123 11 4 4506 4627 437869555 437869439 4.560000e-23 121.0
35 TraesCS5D01G417300 chr3A 79.618 157 8 13 4491 4634 41615093 41615238 3.570000e-14 91.6
36 TraesCS5D01G417300 chr3A 80.000 125 16 8 4503 4621 41615229 41615108 5.980000e-12 84.2
37 TraesCS5D01G417300 chr3A 97.222 36 1 0 4503 4538 661983514 661983549 2.800000e-05 62.1
38 TraesCS5D01G417300 chr4D 93.506 77 4 1 4549 4625 298241464 298241389 7.630000e-21 113.0
39 TraesCS5D01G417300 chr4D 97.959 49 1 0 4502 4550 298241388 298241436 1.660000e-12 86.1
40 TraesCS5D01G417300 chr6B 92.208 77 3 2 4549 4623 60597081 60597006 1.280000e-18 106.0
41 TraesCS5D01G417300 chr6B 89.474 76 8 0 4549 4624 503536395 503536320 7.680000e-16 97.1
42 TraesCS5D01G417300 chr6B 97.778 45 1 0 4506 4550 436805395 436805439 2.780000e-10 78.7
43 TraesCS5D01G417300 chr3D 92.105 76 2 4 4560 4634 426873419 426873347 4.590000e-18 104.0
44 TraesCS5D01G417300 chr1A 97.500 40 1 0 4506 4545 10076184 10076145 1.670000e-07 69.4


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 TraesCS5D01G417300 chr5D 479451436 479460731 9295 False 5771.066667 17167 100.000000 1 9296 3 chr5D.!!$F1 9295
1 TraesCS5D01G417300 chr5B 587119530 587128758 9228 False 1863.442857 4774 91.909571 1 9296 7 chr5B.!!$F2 9295
2 TraesCS5D01G417300 chr5A 598071188 598080290 9102 False 1689.166667 4582 88.792833 85 9295 6 chr5A.!!$F2 9210

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
28 29 0.168788 CTTTCGCCATTCGTGCACAT 59.831 50.000 18.64 0.00 39.67 3.21 F
568 621 0.537188 CTGTGGATGGAGTAACCGCT 59.463 55.000 0.00 0.00 42.61 5.52 F
581 634 0.765510 AACCGCTGTTCCTTCCTTCT 59.234 50.000 0.00 0.00 0.00 2.85 F
1273 1375 0.813821 GAGACCTGGCTTGATTTGGC 59.186 55.000 0.00 0.00 0.00 4.52 F
2122 2268 0.868406 CCACTTGTTTCTGCTCCGTC 59.132 55.000 0.00 0.00 0.00 4.79 F
3074 3267 0.247185 ACGGCAAAAATGATGGCAGG 59.753 50.000 0.00 0.00 43.00 4.85 F
3682 3938 0.111639 GTGCCCCAACTTGTTAGGGA 59.888 55.000 18.71 6.53 45.80 4.20 F
5136 5468 0.393537 ATGCCTTGGCTGCTAGTGTC 60.394 55.000 13.18 0.00 0.00 3.67 F
6083 6581 0.829333 TTTTGGGCTGCTGCTTTTCA 59.171 45.000 15.64 6.47 39.59 2.69 F
6532 7030 1.329292 CGTTTCTTTCGGTTGAGTGCA 59.671 47.619 0.00 0.00 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1135 1237 0.601046 ACACAGCAGGATCACACACG 60.601 55.000 0.00 0.00 0.00 4.49 R
1561 1677 1.534163 CAGCATATGAGCCCATTGTCG 59.466 52.381 6.97 0.00 34.31 4.35 R
2506 2663 1.740025 GACAAGGTCCAGCAATACAGC 59.260 52.381 0.00 0.00 0.00 4.40 R
3056 3249 0.531657 TCCTGCCATCATTTTTGCCG 59.468 50.000 0.00 0.00 0.00 5.69 R
3084 3277 1.149627 CCGTCCCCAAACTTCCACA 59.850 57.895 0.00 0.00 0.00 4.17 R
3909 4165 2.162408 GACTGTCACATTAAGGCCTTGC 59.838 50.000 28.77 8.36 0.00 4.01 R
5506 5871 1.135721 GGGAATCAACAGGCATGCTTC 59.864 52.381 18.92 11.12 0.00 3.86 R
6836 7360 0.725686 CGCTCAACTGATGCTCCTTG 59.274 55.000 0.00 0.00 0.00 3.61 R
7679 8204 1.135460 GCAGCCAACTTCAGAATCTGC 60.135 52.381 5.18 0.00 38.62 4.26 R
8517 9078 1.375908 GGAGTGCGCCATGTCAGAA 60.376 57.895 4.18 0.00 0.00 3.02 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
18 19 2.496942 CCAGAATGCCTTTCGCCAT 58.503 52.632 0.00 0.00 39.46 4.40
28 29 0.168788 CTTTCGCCATTCGTGCACAT 59.831 50.000 18.64 0.00 39.67 3.21
163 176 1.451936 CGGGCAGGGAAAGGATAGG 59.548 63.158 0.00 0.00 0.00 2.57
405 446 3.706373 CCACCACCTCCACCTCCG 61.706 72.222 0.00 0.00 0.00 4.63
429 481 2.443016 CCTCCTCCTCCTCCCACG 60.443 72.222 0.00 0.00 0.00 4.94
449 501 1.148498 CCCGCTTCATCTAACCCCC 59.852 63.158 0.00 0.00 0.00 5.40
505 557 2.517402 TCGTGCCACCCACCAAAC 60.517 61.111 0.00 0.00 41.53 2.93
508 560 1.836604 GTGCCACCCACCAAACCAT 60.837 57.895 0.00 0.00 38.55 3.55
517 569 0.947960 CACCAAACCATACACACGCA 59.052 50.000 0.00 0.00 0.00 5.24
519 571 0.947960 CCAAACCATACACACGCACA 59.052 50.000 0.00 0.00 0.00 4.57
520 572 1.334599 CCAAACCATACACACGCACAC 60.335 52.381 0.00 0.00 0.00 3.82
523 575 2.313909 CCATACACACGCACACGCA 61.314 57.895 0.00 0.00 45.53 5.24
524 576 1.154672 CATACACACGCACACGCAC 60.155 57.895 0.00 0.00 45.53 5.34
525 577 1.592939 ATACACACGCACACGCACA 60.593 52.632 0.00 0.00 45.53 4.57
526 578 1.827315 ATACACACGCACACGCACAC 61.827 55.000 0.00 0.00 45.53 3.82
568 621 0.537188 CTGTGGATGGAGTAACCGCT 59.463 55.000 0.00 0.00 42.61 5.52
581 634 0.765510 AACCGCTGTTCCTTCCTTCT 59.234 50.000 0.00 0.00 0.00 2.85
723 807 2.131067 CGGCAGGGTTGGTTTGGTT 61.131 57.895 0.00 0.00 0.00 3.67
754 839 4.340246 CAGGAGGCCACTGCAGCA 62.340 66.667 15.27 0.00 40.13 4.41
1054 1154 1.519455 GCCACGCTGCAGGTAGTAG 60.519 63.158 17.12 0.16 0.00 2.57
1064 1164 1.069358 GCAGGTAGTAGCACATCCTCC 59.931 57.143 1.58 0.00 0.00 4.30
1153 1255 1.904852 GCGTGTGTGATCCTGCTGTG 61.905 60.000 0.00 0.00 0.00 3.66
1257 1359 6.768483 TGATGACAAGGTAAACATTCAGAGA 58.232 36.000 0.00 0.00 0.00 3.10
1273 1375 0.813821 GAGACCTGGCTTGATTTGGC 59.186 55.000 0.00 0.00 0.00 4.52
1292 1394 1.811941 GCTGGGCCATGAACTAGTAGC 60.812 57.143 6.72 0.00 0.00 3.58
1295 1400 2.576191 TGGGCCATGAACTAGTAGCTTT 59.424 45.455 0.00 0.00 0.00 3.51
1310 1416 1.963515 AGCTTTTGTCATGGGTGGTTC 59.036 47.619 0.00 0.00 0.00 3.62
1322 1428 2.441001 TGGGTGGTTCAATTTTGCCATT 59.559 40.909 0.00 0.00 33.20 3.16
1348 1454 9.241919 TGATGGTAATGGTAATATTGCTATTGG 57.758 33.333 20.33 0.00 0.00 3.16
1349 1455 8.593945 ATGGTAATGGTAATATTGCTATTGGG 57.406 34.615 20.33 0.00 0.00 4.12
1350 1456 7.531317 TGGTAATGGTAATATTGCTATTGGGT 58.469 34.615 20.33 2.28 0.00 4.51
1352 1458 9.523168 GGTAATGGTAATATTGCTATTGGGTAA 57.477 33.333 20.33 2.68 0.00 2.85
1561 1677 2.758009 TGAATTGCTTGGCTTGCTTTC 58.242 42.857 4.23 7.38 0.00 2.62
1740 1860 2.294979 TGCTCATGCTTTGGATAGCTG 58.705 47.619 0.00 0.00 41.76 4.24
1741 1861 1.001597 GCTCATGCTTTGGATAGCTGC 60.002 52.381 0.00 0.00 41.76 5.25
1752 1872 2.304470 TGGATAGCTGCAGGTTGTAACA 59.696 45.455 25.47 13.20 0.00 2.41
1848 1969 4.083324 GGTATGCTACCTAACGCGTATACA 60.083 45.833 14.46 4.75 45.52 2.29
1950 2096 8.859090 TGGACATTTGTTGAACTTTATCTTCAT 58.141 29.630 0.00 0.00 0.00 2.57
2122 2268 0.868406 CCACTTGTTTCTGCTCCGTC 59.132 55.000 0.00 0.00 0.00 4.79
2203 2350 3.299340 AGGTTAGTTGTAGTCACTGCG 57.701 47.619 0.00 0.00 0.00 5.18
2272 2419 1.759445 AGATCATGCGAGCACCTAGTT 59.241 47.619 0.00 0.00 0.00 2.24
2489 2646 6.394809 ACAAGTCGTGTAACATCATACATCA 58.605 36.000 0.00 0.00 39.29 3.07
2799 2969 6.012658 TGTTTTGATGACCTGCAAATACTC 57.987 37.500 0.00 0.00 34.36 2.59
2880 3052 7.195374 TGTAATAGGTTGGACTAAGAGCATT 57.805 36.000 0.00 0.00 0.00 3.56
2899 3071 4.634199 CATTTCCAACAGCAGACCAAAAT 58.366 39.130 0.00 0.00 0.00 1.82
2970 3144 5.126869 TCACCAGAAAATCTTGTGCTTTTCA 59.873 36.000 6.69 0.00 39.27 2.69
3012 3186 1.726791 GCACACGAAACATGACGATCT 59.273 47.619 15.38 0.00 0.00 2.75
3022 3196 4.570663 GACGATCTGACGGCGGGG 62.571 72.222 13.24 0.15 37.61 5.73
3024 3198 3.606662 CGATCTGACGGCGGGGAT 61.607 66.667 13.24 11.42 0.00 3.85
3026 3200 4.241555 ATCTGACGGCGGGGATGC 62.242 66.667 13.24 0.00 0.00 3.91
3074 3267 0.247185 ACGGCAAAAATGATGGCAGG 59.753 50.000 0.00 0.00 43.00 4.85
3105 3298 2.031465 GAAGTTTGGGGACGGCGA 59.969 61.111 16.62 0.00 0.00 5.54
3119 3312 4.980805 GCGACGTGGTGCTTGGGA 62.981 66.667 0.00 0.00 0.00 4.37
3234 3429 3.813724 GGATGGCCCTGGGAGTGG 61.814 72.222 19.27 0.00 0.00 4.00
3240 3435 4.039092 CCCTGGGAGTGGTGGCAG 62.039 72.222 7.01 0.00 0.00 4.85
3300 3531 3.194062 GCTGCAGCAGTTTTGGTTTTTA 58.806 40.909 33.36 0.00 41.59 1.52
3329 3583 9.853555 CAAATCACTTGTAGCAATATTTTGGTA 57.146 29.630 4.01 4.01 43.12 3.25
3464 3718 1.002430 TGGTCTGCTGTTGGAGATGTC 59.998 52.381 0.00 0.00 42.48 3.06
3586 3840 2.290641 CACAACCCAGCAAGTTCAGTAC 59.709 50.000 0.00 0.00 0.00 2.73
3678 3934 0.397187 TAGCGTGCCCCAACTTGTTA 59.603 50.000 0.00 0.00 0.00 2.41
3679 3935 0.889186 AGCGTGCCCCAACTTGTTAG 60.889 55.000 0.00 0.00 0.00 2.34
3682 3938 0.111639 GTGCCCCAACTTGTTAGGGA 59.888 55.000 18.71 6.53 45.80 4.20
3686 3942 2.514803 CCCCAACTTGTTAGGGAACTG 58.485 52.381 10.80 0.00 45.80 3.16
3702 3958 3.883489 GGAACTGAAGGCTTAGTTGTTGT 59.117 43.478 19.70 3.56 37.27 3.32
3706 3962 4.335594 ACTGAAGGCTTAGTTGTTGTTGTC 59.664 41.667 0.00 0.00 0.00 3.18
3724 3980 9.357652 GTTGTTGTCGTAAGGTTATTATCACTA 57.642 33.333 0.00 0.00 38.47 2.74
4028 4297 5.030295 GCCATCATCAAATTTACACTCACG 58.970 41.667 0.00 0.00 0.00 4.35
4272 4574 2.148916 TCACACTTAGTCAGTTGCCG 57.851 50.000 0.00 0.00 30.92 5.69
4274 4576 2.159014 TCACACTTAGTCAGTTGCCGTT 60.159 45.455 0.00 0.00 30.92 4.44
4340 4645 3.306780 CCGTCCAGGTCTGTTTGATAAGT 60.307 47.826 0.00 0.00 34.51 2.24
4343 4648 5.105877 CGTCCAGGTCTGTTTGATAAGTCTA 60.106 44.000 0.00 0.00 0.00 2.59
4347 4652 7.234782 TCCAGGTCTGTTTGATAAGTCTAAAGA 59.765 37.037 0.00 0.00 0.00 2.52
4348 4653 7.547370 CCAGGTCTGTTTGATAAGTCTAAAGAG 59.453 40.741 0.00 0.00 0.00 2.85
4545 4863 9.274065 CAAAATATAAGACGTTTTTGTAGGCTC 57.726 33.333 11.08 0.00 35.41 4.70
4546 4864 8.556213 AAATATAAGACGTTTTTGTAGGCTCA 57.444 30.769 0.00 0.00 0.00 4.26
4548 4866 4.547406 AAGACGTTTTTGTAGGCTCAAC 57.453 40.909 0.00 0.00 0.00 3.18
4549 4867 3.805207 AGACGTTTTTGTAGGCTCAACT 58.195 40.909 0.00 0.00 0.00 3.16
4550 4868 3.808174 AGACGTTTTTGTAGGCTCAACTC 59.192 43.478 0.00 0.00 0.00 3.01
4552 4870 3.942748 ACGTTTTTGTAGGCTCAACTCAA 59.057 39.130 0.00 0.00 0.00 3.02
4553 4871 4.396790 ACGTTTTTGTAGGCTCAACTCAAA 59.603 37.500 0.00 0.00 0.00 2.69
4554 4872 5.106078 ACGTTTTTGTAGGCTCAACTCAAAA 60.106 36.000 0.00 0.60 36.60 2.44
4555 4873 5.977129 CGTTTTTGTAGGCTCAACTCAAAAT 59.023 36.000 0.00 0.00 37.66 1.82
4556 4874 7.136119 CGTTTTTGTAGGCTCAACTCAAAATA 58.864 34.615 0.00 0.00 37.66 1.40
4561 4879 9.733556 TTTGTAGGCTCAACTCAAAATATAAGA 57.266 29.630 0.00 0.00 0.00 2.10
4562 4880 8.718102 TGTAGGCTCAACTCAAAATATAAGAC 57.282 34.615 0.00 0.00 0.00 3.01
4563 4881 6.910536 AGGCTCAACTCAAAATATAAGACG 57.089 37.500 0.00 0.00 0.00 4.18
4564 4882 6.640518 AGGCTCAACTCAAAATATAAGACGA 58.359 36.000 0.00 0.00 0.00 4.20
4565 4883 7.275920 AGGCTCAACTCAAAATATAAGACGAT 58.724 34.615 0.00 0.00 0.00 3.73
4566 4884 7.770897 AGGCTCAACTCAAAATATAAGACGATT 59.229 33.333 0.00 0.00 0.00 3.34
4567 4885 8.398665 GGCTCAACTCAAAATATAAGACGATTT 58.601 33.333 0.00 0.00 0.00 2.17
4568 4886 9.774742 GCTCAACTCAAAATATAAGACGATTTT 57.225 29.630 0.00 0.00 36.02 1.82
4574 4892 9.651718 CTCAAAATATAAGACGATTTTGTAGGC 57.348 33.333 15.77 0.00 46.25 3.93
4575 4893 9.391006 TCAAAATATAAGACGATTTTGTAGGCT 57.609 29.630 15.77 0.00 46.25 4.58
4583 4901 8.421673 AAGACGATTTTGTAGGCTAGTTTATC 57.578 34.615 0.00 0.00 0.00 1.75
4584 4902 6.985059 AGACGATTTTGTAGGCTAGTTTATCC 59.015 38.462 0.00 0.00 0.00 2.59
4585 4903 6.885922 ACGATTTTGTAGGCTAGTTTATCCT 58.114 36.000 0.00 0.00 0.00 3.24
4586 4904 8.015185 ACGATTTTGTAGGCTAGTTTATCCTA 57.985 34.615 0.00 0.00 0.00 2.94
4594 4912 6.980051 AGGCTAGTTTATCCTACAAAAACG 57.020 37.500 0.00 0.00 37.99 3.60
4623 4941 9.851686 TTATATTTTGAGACGGAGGTAGTACTA 57.148 33.333 0.00 0.00 0.00 1.82
4624 4942 8.937207 ATATTTTGAGACGGAGGTAGTACTAT 57.063 34.615 5.75 0.00 0.00 2.12
4625 4943 7.657023 ATTTTGAGACGGAGGTAGTACTATT 57.343 36.000 5.75 0.00 0.00 1.73
4626 4944 7.472334 TTTTGAGACGGAGGTAGTACTATTT 57.528 36.000 5.75 0.00 0.00 1.40
4627 4945 6.690194 TTGAGACGGAGGTAGTACTATTTC 57.310 41.667 5.75 6.93 0.00 2.17
5000 5327 9.591404 GTTATCTATGATTTGCTTGAGAAATCG 57.409 33.333 0.00 0.00 41.03 3.34
5089 5421 3.782656 GGTTTACACCTCTTCCTTCCA 57.217 47.619 0.00 0.00 40.44 3.53
5136 5468 0.393537 ATGCCTTGGCTGCTAGTGTC 60.394 55.000 13.18 0.00 0.00 3.67
5170 5502 7.306807 GCCTTCTTTTGTGTTATTTGCTTCTTC 60.307 37.037 0.00 0.00 0.00 2.87
5177 5509 8.770438 TTGTGTTATTTGCTTCTTCTTTTTGT 57.230 26.923 0.00 0.00 0.00 2.83
5179 5511 9.862371 TGTGTTATTTGCTTCTTCTTTTTGTTA 57.138 25.926 0.00 0.00 0.00 2.41
5278 5638 5.247110 AGGACATGAGTAGATCTTGTTGTGT 59.753 40.000 0.00 1.38 44.10 3.72
5295 5655 7.636259 TGTTGTGTTTTTAAGCTGCAATATC 57.364 32.000 1.02 0.00 0.00 1.63
5298 5658 8.764287 GTTGTGTTTTTAAGCTGCAATATCTTT 58.236 29.630 1.02 0.00 0.00 2.52
5300 5660 9.973450 TGTGTTTTTAAGCTGCAATATCTTTTA 57.027 25.926 1.02 0.00 0.00 1.52
5359 5719 7.816945 AAAATGCTGATTTTATCTGGTTTCG 57.183 32.000 0.00 0.00 39.53 3.46
5364 5724 6.861055 TGCTGATTTTATCTGGTTTCGTTTTC 59.139 34.615 0.00 0.00 0.00 2.29
5371 5731 4.625972 TCTGGTTTCGTTTTCCAAAGAC 57.374 40.909 0.00 0.00 0.00 3.01
5432 5792 2.200373 AAGAATTGGTCCTCGGGTTG 57.800 50.000 0.00 0.00 0.00 3.77
5433 5793 1.358152 AGAATTGGTCCTCGGGTTGA 58.642 50.000 0.00 0.00 0.00 3.18
5434 5794 1.702957 AGAATTGGTCCTCGGGTTGAA 59.297 47.619 0.00 0.00 0.00 2.69
5435 5795 2.308866 AGAATTGGTCCTCGGGTTGAAT 59.691 45.455 0.00 0.00 0.00 2.57
5491 5856 5.628193 GCAACATTCAGTATCTATTGCATGC 59.372 40.000 11.82 11.82 40.46 4.06
5538 5903 2.560981 GTTGATTCCCATCGGTTTTGGT 59.439 45.455 0.00 0.00 31.99 3.67
5879 6377 6.201044 GCAAGCTACGATCTTTAATCTGCTAA 59.799 38.462 0.00 0.00 0.00 3.09
6083 6581 0.829333 TTTTGGGCTGCTGCTTTTCA 59.171 45.000 15.64 6.47 39.59 2.69
6123 6621 7.639850 GCAAAAGTAAGCTGAAAACAATTTTCC 59.360 33.333 10.66 0.00 46.49 3.13
6283 6781 5.538849 TGTTCCATATCGCAACAGGTATA 57.461 39.130 0.00 0.00 0.00 1.47
6530 7028 2.033151 GGTCGTTTCTTTCGGTTGAGTG 60.033 50.000 0.00 0.00 0.00 3.51
6531 7029 1.595794 TCGTTTCTTTCGGTTGAGTGC 59.404 47.619 0.00 0.00 0.00 4.40
6532 7030 1.329292 CGTTTCTTTCGGTTGAGTGCA 59.671 47.619 0.00 0.00 0.00 4.57
6533 7031 2.716398 GTTTCTTTCGGTTGAGTGCAC 58.284 47.619 9.40 9.40 0.00 4.57
6534 7032 2.031258 TTCTTTCGGTTGAGTGCACA 57.969 45.000 21.04 0.00 0.00 4.57
6535 7033 2.031258 TCTTTCGGTTGAGTGCACAA 57.969 45.000 21.04 3.51 0.00 3.33
6536 7034 1.668751 TCTTTCGGTTGAGTGCACAAC 59.331 47.619 21.04 15.24 46.20 3.32
6549 7047 3.128188 ACAACCGCACACGCAACA 61.128 55.556 0.00 0.00 38.40 3.33
6809 7333 4.122337 TGTCACTTTCTAGGGTGAGGTA 57.878 45.455 12.09 3.32 42.13 3.08
6836 7360 6.152379 CCAGTTGAAAAAGGAATTAGCTGAC 58.848 40.000 0.00 0.00 0.00 3.51
6980 7504 5.183904 AGCACTGTTTGAACTTGAAGAAACT 59.816 36.000 0.00 0.00 31.03 2.66
7052 7576 1.544759 CCACAGGTGGGTAACTTGACC 60.545 57.143 10.67 0.00 46.81 4.02
7117 7641 6.931281 GCAGCTATTTCCTACATCTATTGTCA 59.069 38.462 0.00 0.00 39.87 3.58
7126 7650 7.492524 TCCTACATCTATTGTCACAACAGATC 58.507 38.462 8.43 0.00 39.87 2.75
7164 7688 3.515502 ACTATGTACAGTGCAGTGATGGT 59.484 43.478 28.02 15.37 0.00 3.55
7212 7736 6.434028 AGAAGGATTATACAGTTTTGCAAGCA 59.566 34.615 0.00 0.00 0.00 3.91
7227 7751 4.334552 TGCAAGCATTAACATCAAGGAGA 58.665 39.130 0.00 0.00 0.00 3.71
7330 7854 5.561725 GCTCTCTTACCTTGAAGCAAACTTG 60.562 44.000 0.00 0.00 35.82 3.16
7351 7875 5.789643 TGCATGGCTATTTATCCTTTTCC 57.210 39.130 0.00 0.00 0.00 3.13
7367 7891 7.465900 TCCTTTTCCCTGTAGGATATTGAAT 57.534 36.000 0.00 0.00 46.94 2.57
7378 7902 8.613060 TGTAGGATATTGAATTGAATGAGAGC 57.387 34.615 0.00 0.00 0.00 4.09
7483 8007 3.327757 ACAGGCTTCTTGTGAGTAATCCA 59.672 43.478 0.00 0.00 0.00 3.41
7497 8021 9.787435 TGTGAGTAATCCACAAAGTTTTAGTAT 57.213 29.630 0.00 0.00 41.07 2.12
7679 8204 2.224769 TGGAACAGGGCTAAACCAGAAG 60.225 50.000 0.00 0.00 42.05 2.85
7984 8509 2.086610 AAACAATGGGCAAGTGGAGT 57.913 45.000 0.00 0.00 0.00 3.85
7985 8510 1.620822 AACAATGGGCAAGTGGAGTC 58.379 50.000 0.00 0.00 0.00 3.36
8103 8628 4.142381 GCAGGCAAAGGAAGGTAATTGTAG 60.142 45.833 0.00 0.00 0.00 2.74
8110 8640 5.862678 AGGAAGGTAATTGTAGCTCTCTC 57.137 43.478 0.00 0.00 37.06 3.20
8111 8641 5.524535 AGGAAGGTAATTGTAGCTCTCTCT 58.475 41.667 0.00 0.00 37.06 3.10
8123 8653 4.454728 AGCTCTCTCTTCTACAAGCAAG 57.545 45.455 0.00 0.00 32.25 4.01
8260 8793 9.806203 TTTAATCTTGGCATGAACTATGATTTG 57.194 29.630 7.20 0.00 39.21 2.32
8310 8845 4.640771 AAGGTAGAGGAAGCACATCAAA 57.359 40.909 0.00 0.00 0.00 2.69
8463 9012 7.786943 TCCTGGATCTGATAAGAGATGTTACTT 59.213 37.037 0.00 0.00 32.57 2.24
8517 9078 4.263905 TGGTCATTTTGGTGCCTCTAGATT 60.264 41.667 0.00 0.00 0.00 2.40
8519 9080 5.163612 GGTCATTTTGGTGCCTCTAGATTTC 60.164 44.000 0.00 0.00 0.00 2.17
8536 9099 2.046988 CTGACATGGCGCACTCCA 60.047 61.111 10.83 0.00 40.97 3.86
8572 9139 4.218852 AGTTGTTAGTCTCCTGTAGTCAGC 59.781 45.833 0.00 0.00 40.09 4.26
8689 9256 1.079503 GCTGCGACTCTTAACCCTTG 58.920 55.000 0.00 0.00 0.00 3.61
8701 9268 4.761739 TCTTAACCCTTGATCAAGCAAGTG 59.238 41.667 27.01 14.33 42.84 3.16
8708 9275 1.202915 TGATCAAGCAAGTGAAGCCCA 60.203 47.619 0.00 0.00 0.00 5.36
8735 9302 0.245539 ACACGGTGGTCTATGAACGG 59.754 55.000 13.48 0.00 0.00 4.44
8740 9307 2.159156 CGGTGGTCTATGAACGGAATCA 60.159 50.000 0.00 0.00 0.00 2.57
8742 9309 3.118738 GGTGGTCTATGAACGGAATCACT 60.119 47.826 0.00 0.00 30.82 3.41
8748 9315 7.123098 TGGTCTATGAACGGAATCACTAGTAAA 59.877 37.037 0.00 0.00 30.82 2.01
8749 9316 7.648510 GGTCTATGAACGGAATCACTAGTAAAG 59.351 40.741 0.00 0.00 30.82 1.85
8750 9317 8.189460 GTCTATGAACGGAATCACTAGTAAAGT 58.811 37.037 0.00 0.00 39.81 2.66
8783 9355 9.588096 AAAGATTACCTAGGAAAACTTCAACAT 57.412 29.630 17.98 0.00 0.00 2.71
8803 9375 7.556275 TCAACATATGAAAAGGACATTCCCTAC 59.444 37.037 10.38 0.00 33.87 3.18
8809 9381 4.302559 AAAGGACATTCCCTACTGTTCC 57.697 45.455 0.00 0.00 37.19 3.62
8850 9422 4.377738 CGTTTGGCATCGAGATGGATTATG 60.378 45.833 14.13 0.00 39.16 1.90
8872 9444 5.607477 TGATGATCCCGTTTACTATCCAAC 58.393 41.667 0.00 0.00 0.00 3.77
8873 9445 4.049546 TGATCCCGTTTACTATCCAACG 57.950 45.455 0.00 0.00 44.34 4.10
8875 9447 3.959535 TCCCGTTTACTATCCAACGTT 57.040 42.857 0.00 0.00 43.43 3.99
8876 9448 4.270245 TCCCGTTTACTATCCAACGTTT 57.730 40.909 0.00 0.00 43.43 3.60
8877 9449 4.640364 TCCCGTTTACTATCCAACGTTTT 58.360 39.130 0.00 0.00 43.43 2.43
8878 9450 4.690280 TCCCGTTTACTATCCAACGTTTTC 59.310 41.667 0.00 0.00 43.43 2.29
8879 9451 4.434593 CCCGTTTACTATCCAACGTTTTCG 60.435 45.833 0.00 0.00 43.43 3.46
8932 9561 2.811317 CGCGGACAGAGCCTGAAC 60.811 66.667 0.00 3.43 35.18 3.18
8965 9594 0.508641 CGAGACCGTTGCTCAAACAG 59.491 55.000 0.00 0.00 38.84 3.16
8978 9607 3.605486 GCTCAAACAGCGATGAAATGAAC 59.395 43.478 8.12 0.22 38.76 3.18
9034 9663 3.230976 TGCTGGGAGATACGTATGATGT 58.769 45.455 13.97 0.00 0.00 3.06
9093 9755 2.503356 GGAGCAGTATAGGATGGATGGG 59.497 54.545 0.00 0.00 0.00 4.00
9195 9857 6.834969 GGGATCTCATCTCATCTCATCTCATA 59.165 42.308 0.00 0.00 0.00 2.15
9205 9867 2.498885 TCTCATCTCATATGCGGATGGG 59.501 50.000 24.63 23.28 38.79 4.00
9257 9938 4.003788 CCTGGACTGACGCCCGTT 62.004 66.667 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.705337 GGGTCGATGTGCACGAATGG 61.705 60.000 13.13 2.52 41.31 3.16
18 19 0.250124 AAAGGGTCGATGTGCACGAA 60.250 50.000 13.13 0.00 41.31 3.85
28 29 0.036765 CGGGATGAACAAAGGGTCGA 60.037 55.000 0.00 0.00 0.00 4.20
185 198 3.234630 TACAGTCCTGCACACCGCC 62.235 63.158 0.00 0.00 41.33 6.13
314 352 1.074850 GAAGGGGAGAGGAGAGGGG 60.075 68.421 0.00 0.00 0.00 4.79
318 356 0.324460 GAACGGAAGGGGAGAGGAGA 60.324 60.000 0.00 0.00 0.00 3.71
319 357 1.331399 GGAACGGAAGGGGAGAGGAG 61.331 65.000 0.00 0.00 0.00 3.69
320 358 1.305887 GGAACGGAAGGGGAGAGGA 60.306 63.158 0.00 0.00 0.00 3.71
429 481 1.526225 GGGTTAGATGAAGCGGGGC 60.526 63.158 0.00 0.00 36.33 5.80
449 501 1.227380 CGAAGCGGATTCAGGGGAG 60.227 63.158 6.81 0.00 37.83 4.30
505 557 2.474266 GCGTGTGCGTGTGTATGG 59.526 61.111 0.00 0.00 40.81 2.74
568 621 1.838073 GCCCGGAGAAGGAAGGAACA 61.838 60.000 0.73 0.00 0.00 3.18
709 792 0.336737 TCCACAACCAAACCAACCCT 59.663 50.000 0.00 0.00 0.00 4.34
710 793 0.462375 GTCCACAACCAAACCAACCC 59.538 55.000 0.00 0.00 0.00 4.11
723 807 3.625897 CCTGCTCACCGGTCCACA 61.626 66.667 2.59 1.22 0.00 4.17
757 842 1.814169 CGAAAAGGAGCCCGCTACC 60.814 63.158 0.00 0.00 0.00 3.18
1051 1151 1.789523 TAGTGGGGAGGATGTGCTAC 58.210 55.000 0.00 0.00 0.00 3.58
1054 1154 1.202818 GGATTAGTGGGGAGGATGTGC 60.203 57.143 0.00 0.00 0.00 4.57
1055 1155 2.126882 TGGATTAGTGGGGAGGATGTG 58.873 52.381 0.00 0.00 0.00 3.21
1056 1156 2.127708 GTGGATTAGTGGGGAGGATGT 58.872 52.381 0.00 0.00 0.00 3.06
1064 1164 2.332063 AATCGCAGTGGATTAGTGGG 57.668 50.000 5.37 0.00 42.38 4.61
1135 1237 0.601046 ACACAGCAGGATCACACACG 60.601 55.000 0.00 0.00 0.00 4.49
1136 1238 1.151668 GACACAGCAGGATCACACAC 58.848 55.000 0.00 0.00 0.00 3.82
1153 1255 0.676782 ACGGCCACCTGCAAATAGAC 60.677 55.000 2.24 0.00 43.89 2.59
1257 1359 0.901580 CCAGCCAAATCAAGCCAGGT 60.902 55.000 0.00 0.00 0.00 4.00
1273 1375 1.765314 AGCTACTAGTTCATGGCCCAG 59.235 52.381 0.00 0.00 0.00 4.45
1292 1394 4.605640 ATTGAACCACCCATGACAAAAG 57.394 40.909 0.00 0.00 0.00 2.27
1295 1400 4.701765 CAAAATTGAACCACCCATGACAA 58.298 39.130 0.00 0.00 0.00 3.18
1322 1428 9.241919 CCAATAGCAATATTACCATTACCATCA 57.758 33.333 0.00 0.00 0.00 3.07
1336 1442 6.838612 ACAACACCATTACCCAATAGCAATAT 59.161 34.615 0.00 0.00 0.00 1.28
1338 1444 5.022787 ACAACACCATTACCCAATAGCAAT 58.977 37.500 0.00 0.00 0.00 3.56
1339 1445 4.219507 CACAACACCATTACCCAATAGCAA 59.780 41.667 0.00 0.00 0.00 3.91
1341 1447 3.428862 GCACAACACCATTACCCAATAGC 60.429 47.826 0.00 0.00 0.00 2.97
1342 1448 4.016444 AGCACAACACCATTACCCAATAG 58.984 43.478 0.00 0.00 0.00 1.73
1343 1449 4.040936 AGCACAACACCATTACCCAATA 57.959 40.909 0.00 0.00 0.00 1.90
1346 1452 1.959985 CAAGCACAACACCATTACCCA 59.040 47.619 0.00 0.00 0.00 4.51
1348 1454 4.217550 ACATACAAGCACAACACCATTACC 59.782 41.667 0.00 0.00 0.00 2.85
1349 1455 5.371115 ACATACAAGCACAACACCATTAC 57.629 39.130 0.00 0.00 0.00 1.89
1350 1456 6.264292 AGAAACATACAAGCACAACACCATTA 59.736 34.615 0.00 0.00 0.00 1.90
1352 1458 4.584325 AGAAACATACAAGCACAACACCAT 59.416 37.500 0.00 0.00 0.00 3.55
1354 1460 4.537015 GAGAAACATACAAGCACAACACC 58.463 43.478 0.00 0.00 0.00 4.16
1561 1677 1.534163 CAGCATATGAGCCCATTGTCG 59.466 52.381 6.97 0.00 34.31 4.35
1740 1860 5.124776 TGCCAATAGTATTGTTACAACCTGC 59.875 40.000 19.18 12.88 0.00 4.85
1741 1861 6.751514 TGCCAATAGTATTGTTACAACCTG 57.248 37.500 19.18 4.41 0.00 4.00
1752 1872 5.101628 CGTTTTGCACATGCCAATAGTATT 58.898 37.500 0.49 0.00 41.18 1.89
1848 1969 3.399305 AGTCCTTTTCCCTGAAACCAGAT 59.601 43.478 0.00 0.00 30.83 2.90
2122 2268 4.379339 TTTTTCTCAAAAAGGGGTGACG 57.621 40.909 0.00 0.00 35.84 4.35
2167 2314 8.962679 ACAACTAACCTACAGATTTTTCAAACA 58.037 29.630 0.00 0.00 0.00 2.83
2272 2419 7.573710 AGTTATGTATCCAATAACTTCCAGCA 58.426 34.615 3.56 0.00 37.72 4.41
2465 2621 6.394809 TGATGTATGATGTTACACGACTTGT 58.605 36.000 0.00 0.00 42.84 3.16
2489 2646 8.711457 GCAATACAGCATTAACTTTTTCAACAT 58.289 29.630 0.00 0.00 0.00 2.71
2506 2663 1.740025 GACAAGGTCCAGCAATACAGC 59.260 52.381 0.00 0.00 0.00 4.40
2853 3023 7.723324 TGCTCTTAGTCCAACCTATTACATAC 58.277 38.462 0.00 0.00 0.00 2.39
2880 3052 4.440880 CAAATTTTGGTCTGCTGTTGGAA 58.559 39.130 0.97 0.00 0.00 3.53
2905 3077 3.568430 CACCCCTAAACTGAGTTTTGGTC 59.432 47.826 27.97 0.00 43.28 4.02
2906 3078 3.562182 CACCCCTAAACTGAGTTTTGGT 58.438 45.455 27.97 21.98 43.28 3.67
2907 3079 2.890945 CCACCCCTAAACTGAGTTTTGG 59.109 50.000 25.11 25.11 43.99 3.28
2916 3090 3.445987 CTTCTCTCTCCACCCCTAAACT 58.554 50.000 0.00 0.00 0.00 2.66
2970 3144 5.052481 GCTTCTCAAAATTTTGGTCTGCTT 58.948 37.500 26.45 0.00 38.66 3.91
3031 3224 3.839432 CGAGTTCCTCCCCGCCTC 61.839 72.222 0.00 0.00 0.00 4.70
3056 3249 0.531657 TCCTGCCATCATTTTTGCCG 59.468 50.000 0.00 0.00 0.00 5.69
3074 3267 2.511600 CTTCCACACCGCCGGATC 60.512 66.667 11.71 0.00 0.00 3.36
3084 3277 1.149627 CCGTCCCCAAACTTCCACA 59.850 57.895 0.00 0.00 0.00 4.17
3105 3298 2.047274 CGATCCCAAGCACCACGT 60.047 61.111 0.00 0.00 0.00 4.49
3234 3429 4.729918 CACCCTGAGCCCTGCCAC 62.730 72.222 0.00 0.00 0.00 5.01
3238 3433 2.985456 GTCTCACCCTGAGCCCTG 59.015 66.667 0.00 0.00 43.95 4.45
3239 3434 2.681778 CGTCTCACCCTGAGCCCT 60.682 66.667 0.00 0.00 43.95 5.19
3240 3435 3.775654 CCGTCTCACCCTGAGCCC 61.776 72.222 0.00 0.00 43.95 5.19
3300 3531 9.630098 CAAAATATTGCTACAAGTGATTTGACT 57.370 29.630 0.00 0.00 39.21 3.41
3346 3600 3.306502 CCAATACCTATATGGCGACCGTT 60.307 47.826 0.00 0.00 40.22 4.44
3391 3645 1.584724 TTTTTGGTCTTTTGGGGCCA 58.415 45.000 4.39 0.00 0.00 5.36
3413 3667 5.105554 ACAGCCATGACACAAAAACTGTTAA 60.106 36.000 0.00 0.00 35.47 2.01
3414 3668 4.400884 ACAGCCATGACACAAAAACTGTTA 59.599 37.500 0.00 0.00 35.47 2.41
3603 3857 7.031372 ACAAACATATTAGCATCAGTTTGCAG 58.969 34.615 13.74 0.00 45.69 4.41
3636 3892 6.418057 AGAGCTGAAACCCATAAGATCTAG 57.582 41.667 0.00 0.00 33.84 2.43
3678 3934 2.711547 ACAACTAAGCCTTCAGTTCCCT 59.288 45.455 0.00 0.00 32.72 4.20
3679 3935 3.141767 ACAACTAAGCCTTCAGTTCCC 57.858 47.619 0.00 0.00 32.72 3.97
3682 3938 4.705023 ACAACAACAACTAAGCCTTCAGTT 59.295 37.500 0.00 0.00 35.38 3.16
3686 3942 3.311596 ACGACAACAACAACTAAGCCTTC 59.688 43.478 0.00 0.00 0.00 3.46
3724 3980 9.412460 TCTCATTCTTGCAGTTTCCATATATTT 57.588 29.630 0.00 0.00 0.00 1.40
3909 4165 2.162408 GACTGTCACATTAAGGCCTTGC 59.838 50.000 28.77 8.36 0.00 4.01
4028 4297 5.295540 GCAACTTATGAGATCCTTCAGAACC 59.704 44.000 0.00 0.00 0.00 3.62
4274 4576 9.790344 AACCATTTGAACAATCATTAAATTGGA 57.210 25.926 5.17 0.00 40.28 3.53
4340 4645 4.488126 GCACATGCACAAACTCTTTAGA 57.512 40.909 0.00 0.00 41.59 2.10
4559 4877 6.985059 GGATAAACTAGCCTACAAAATCGTCT 59.015 38.462 0.00 0.00 0.00 4.18
4560 4878 6.985059 AGGATAAACTAGCCTACAAAATCGTC 59.015 38.462 0.00 0.00 44.08 4.20
4561 4879 6.885922 AGGATAAACTAGCCTACAAAATCGT 58.114 36.000 0.00 0.00 44.08 3.73
4570 4888 7.614494 ACGTTTTTGTAGGATAAACTAGCCTA 58.386 34.615 0.00 0.00 44.08 3.93
4572 4890 6.592994 AGACGTTTTTGTAGGATAAACTAGCC 59.407 38.462 0.00 0.00 31.33 3.93
4573 4891 7.592439 AGACGTTTTTGTAGGATAAACTAGC 57.408 36.000 0.00 0.00 31.33 3.42
4594 4912 7.714703 ACTACCTCCGTCTCAAAATATAAGAC 58.285 38.462 0.00 0.00 36.82 3.01
4623 4941 9.974980 AAAACACCGTTACTGAATAAATGAAAT 57.025 25.926 0.00 0.00 0.00 2.17
4624 4942 9.804758 AAAAACACCGTTACTGAATAAATGAAA 57.195 25.926 0.00 0.00 0.00 2.69
4625 4943 9.239002 CAAAAACACCGTTACTGAATAAATGAA 57.761 29.630 0.00 0.00 0.00 2.57
4626 4944 7.380065 GCAAAAACACCGTTACTGAATAAATGA 59.620 33.333 0.00 0.00 0.00 2.57
4627 4945 7.381139 AGCAAAAACACCGTTACTGAATAAATG 59.619 33.333 0.00 0.00 0.00 2.32
4641 4959 5.560966 ATCCAAGTATAGCAAAAACACCG 57.439 39.130 0.00 0.00 0.00 4.94
5000 5327 2.508586 GAAGCTCCAGGTGACCCGAC 62.509 65.000 0.00 0.00 35.12 4.79
5136 5468 4.326504 ACACAAAAGAAGGCCAGAATTG 57.673 40.909 5.01 6.13 0.00 2.32
5341 5701 7.367285 TGGAAAACGAAACCAGATAAAATCAG 58.633 34.615 0.00 0.00 0.00 2.90
5343 5703 8.582433 TTTGGAAAACGAAACCAGATAAAATC 57.418 30.769 0.00 0.00 35.08 2.17
5351 5711 4.364415 TGTCTTTGGAAAACGAAACCAG 57.636 40.909 0.00 0.00 35.08 4.00
5356 5716 3.628487 ACCGAATGTCTTTGGAAAACGAA 59.372 39.130 0.00 0.00 38.07 3.85
5359 5719 4.561735 TGACCGAATGTCTTTGGAAAAC 57.438 40.909 0.00 0.00 44.75 2.43
5364 5724 3.753272 ACAAGATGACCGAATGTCTTTGG 59.247 43.478 0.00 0.00 44.75 3.28
5412 5772 2.107552 TCAACCCGAGGACCAATTCTTT 59.892 45.455 0.00 0.00 0.00 2.52
5433 5793 7.410120 AGACAAAACACAAGAAAGAAGGATT 57.590 32.000 0.00 0.00 0.00 3.01
5434 5794 8.519799 TTAGACAAAACACAAGAAAGAAGGAT 57.480 30.769 0.00 0.00 0.00 3.24
5435 5795 7.931578 TTAGACAAAACACAAGAAAGAAGGA 57.068 32.000 0.00 0.00 0.00 3.36
5506 5871 1.135721 GGGAATCAACAGGCATGCTTC 59.864 52.381 18.92 11.12 0.00 3.86
6083 6581 6.514048 GCTTACTTTTGCTGACAGAGTGAAAT 60.514 38.462 6.65 0.00 0.00 2.17
6123 6621 1.134848 GTAGCCCTCTCACTGCTCAAG 60.135 57.143 0.00 0.00 36.57 3.02
6283 6781 6.377080 TCTGATAGTAGAATGTCCACCTGAT 58.623 40.000 0.00 0.00 0.00 2.90
6317 6815 6.586344 CCACTGTCACATAACTAGAATGGAT 58.414 40.000 0.00 0.00 0.00 3.41
6633 7156 9.542462 TCGTTCCAATATTTTTCTATACAGGAG 57.458 33.333 0.00 0.00 0.00 3.69
6809 7333 6.019108 AGCTAATTCCTTTTTCAACTGGGAT 58.981 36.000 0.00 0.00 0.00 3.85
6836 7360 0.725686 CGCTCAACTGATGCTCCTTG 59.274 55.000 0.00 0.00 0.00 3.61
6980 7504 1.549620 TCCATCCGGTTACGCTTGTTA 59.450 47.619 0.00 0.00 39.22 2.41
7052 7576 7.290842 TGAAAGAGTTCTCGAAAAATTGATCG 58.709 34.615 6.77 6.77 40.31 3.69
7117 7641 7.389053 GTGTGGAATTTCTAAGAGATCTGTTGT 59.611 37.037 15.08 0.00 0.00 3.32
7126 7650 9.307121 CTGTACATAGTGTGGAATTTCTAAGAG 57.693 37.037 0.00 0.00 0.00 2.85
7170 7694 4.282449 TCCTTCTCGTTCACCTGAATACAA 59.718 41.667 0.00 0.00 36.33 2.41
7171 7695 3.830178 TCCTTCTCGTTCACCTGAATACA 59.170 43.478 0.00 0.00 36.33 2.29
7185 7709 6.662414 TGCAAAACTGTATAATCCTTCTCG 57.338 37.500 0.00 0.00 0.00 4.04
7212 7736 9.965902 AGAATAACTTGTCTCCTTGATGTTAAT 57.034 29.630 0.00 0.00 0.00 1.40
7330 7854 4.835056 AGGGAAAAGGATAAATAGCCATGC 59.165 41.667 0.00 0.00 33.22 4.06
7351 7875 9.217278 CTCTCATTCAATTCAATATCCTACAGG 57.783 37.037 0.00 0.00 0.00 4.00
7367 7891 3.760693 GCCTACGGCTCTCATTCAA 57.239 52.632 0.00 0.00 46.69 2.69
7378 7902 2.890847 CTTGGAGCTGACGCCTACGG 62.891 65.000 0.00 0.00 46.04 4.02
7483 8007 8.919145 TGGATGGAAAACATACTAAAACTTTGT 58.081 29.630 0.00 0.00 41.31 2.83
7496 8020 9.471702 GGATATCATATTCTGGATGGAAAACAT 57.528 33.333 4.83 0.00 44.18 2.71
7497 8021 7.890127 GGGATATCATATTCTGGATGGAAAACA 59.110 37.037 4.83 0.00 0.00 2.83
7679 8204 1.135460 GCAGCCAACTTCAGAATCTGC 60.135 52.381 5.18 0.00 38.62 4.26
7984 8509 3.181469 GGTAGAATGGTATGGCGTTGAGA 60.181 47.826 0.00 0.00 0.00 3.27
7985 8510 3.131396 GGTAGAATGGTATGGCGTTGAG 58.869 50.000 0.00 0.00 0.00 3.02
8103 8628 4.186856 ACTTGCTTGTAGAAGAGAGAGC 57.813 45.455 3.33 0.00 0.00 4.09
8123 8653 6.088824 CAGTTTCAAGAATATGGAGTGCAAC 58.911 40.000 0.00 0.00 0.00 4.17
8177 8709 6.718454 CCTTAATGGAAGATGCTACCATCATT 59.282 38.462 0.00 0.00 43.47 2.57
8260 8793 1.402852 GCACGAATCCTGGAAAAAGGC 60.403 52.381 0.00 0.00 37.24 4.35
8310 8845 4.188462 TGACTCGTGTGTCTTGTTGAATT 58.812 39.130 0.00 0.00 37.79 2.17
8463 9012 3.146066 CAACAGCTTGGCCTAAACTACA 58.854 45.455 3.32 0.00 0.00 2.74
8517 9078 1.375908 GGAGTGCGCCATGTCAGAA 60.376 57.895 4.18 0.00 0.00 3.02
8519 9080 2.046988 TGGAGTGCGCCATGTCAG 60.047 61.111 4.18 0.00 31.66 3.51
8572 9139 3.618780 GAGACAGGGTGCAGCAGGG 62.619 68.421 19.06 8.62 0.00 4.45
8689 9256 1.471684 CTGGGCTTCACTTGCTTGATC 59.528 52.381 0.00 0.00 0.00 2.92
8701 9268 2.035442 GTGTTCGGAGCTGGGCTTC 61.035 63.158 0.00 0.00 39.88 3.86
8735 9302 7.387948 TCTTTGCAAGGACTTTACTAGTGATTC 59.612 37.037 7.24 0.00 37.17 2.52
8740 9307 7.606839 GGTAATCTTTGCAAGGACTTTACTAGT 59.393 37.037 23.35 0.00 40.71 2.57
8742 9309 7.686434 AGGTAATCTTTGCAAGGACTTTACTA 58.314 34.615 23.35 6.62 0.00 1.82
8748 9315 4.783227 TCCTAGGTAATCTTTGCAAGGACT 59.217 41.667 14.09 5.47 28.82 3.85
8749 9316 5.099042 TCCTAGGTAATCTTTGCAAGGAC 57.901 43.478 14.09 1.80 28.82 3.85
8750 9317 5.772393 TTCCTAGGTAATCTTTGCAAGGA 57.228 39.130 14.17 14.17 30.83 3.36
8775 9347 7.123247 AGGGAATGTCCTTTTCATATGTTGAAG 59.877 37.037 1.90 5.72 39.97 3.02
8783 9355 6.636454 ACAGTAGGGAATGTCCTTTTCATA 57.364 37.500 0.00 0.00 38.30 2.15
8839 9411 5.768980 AACGGGATCATCATAATCCATCT 57.231 39.130 4.66 0.00 43.85 2.90
8840 9412 7.106239 AGTAAACGGGATCATCATAATCCATC 58.894 38.462 4.66 0.00 43.85 3.51
8850 9422 4.684703 CGTTGGATAGTAAACGGGATCATC 59.315 45.833 0.00 0.00 44.08 2.92
8888 9460 6.656945 TCGCTGTAAAAATAGTACGCAAAAA 58.343 32.000 0.00 0.00 0.00 1.94
8889 9461 6.225703 TCGCTGTAAAAATAGTACGCAAAA 57.774 33.333 0.00 0.00 0.00 2.44
8890 9462 5.842619 TCGCTGTAAAAATAGTACGCAAA 57.157 34.783 0.00 0.00 0.00 3.68
8891 9463 5.842619 TTCGCTGTAAAAATAGTACGCAA 57.157 34.783 0.00 0.00 0.00 4.85
8892 9464 5.610975 GTTTCGCTGTAAAAATAGTACGCA 58.389 37.500 0.00 0.00 0.00 5.24
8893 9465 4.715905 CGTTTCGCTGTAAAAATAGTACGC 59.284 41.667 0.00 0.00 0.00 4.42
8918 9547 2.746362 CTCATTTGTTCAGGCTCTGTCC 59.254 50.000 2.68 0.00 32.61 4.02
8919 9548 3.668447 TCTCATTTGTTCAGGCTCTGTC 58.332 45.455 2.68 0.00 32.61 3.51
8932 9561 2.346847 CGGTCTCGAAAGCTCTCATTTG 59.653 50.000 0.00 0.00 39.00 2.32
8965 9594 3.605486 GCTGTTCTTGTTCATTTCATCGC 59.395 43.478 0.00 0.00 0.00 4.58
8978 9607 2.135139 TGTAACTGCTCGCTGTTCTTG 58.865 47.619 15.80 0.00 38.64 3.02
9034 9663 3.516700 TGTCCTTGAGCTCAATCATCAGA 59.483 43.478 28.57 15.26 35.02 3.27
9070 9699 3.176411 CATCCATCCTATACTGCTCCCA 58.824 50.000 0.00 0.00 0.00 4.37
9093 9755 1.656818 CGCAACACATGATCCCCCAC 61.657 60.000 0.00 0.00 0.00 4.61
9122 9784 4.096081 AGTTGTTAGTGCTAGCTAGTACCG 59.904 45.833 30.96 5.53 39.36 4.02
9257 9938 0.402887 TGTGGTCTCGAGAGTGGGTA 59.597 55.000 17.22 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.