Multiple sequence alignment - TraesCS2B01G234600

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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 TraesCS2B01G234600 chr2B 100.000 7105 0 0 1 7105 233276158 233269054 0.000000e+00 13121.0
1 TraesCS2B01G234600 chr2D 95.525 2838 77 20 1190 3999 176171197 176168382 0.000000e+00 4492.0
2 TraesCS2B01G234600 chr2D 92.301 2208 94 17 4510 6668 176166996 176164816 0.000000e+00 3066.0
3 TraesCS2B01G234600 chr2D 96.187 577 13 5 615 1185 176171811 176171238 0.000000e+00 935.0
4 TraesCS2B01G234600 chr2D 88.512 383 24 9 4095 4473 176167362 176166996 5.060000e-121 446.0
5 TraesCS2B01G234600 chr2D 82.825 361 18 9 6773 7105 176164533 176164189 4.200000e-72 283.0
6 TraesCS2B01G234600 chr2D 87.218 133 6 3 4115 4236 190032886 190032754 2.670000e-29 141.0
7 TraesCS2B01G234600 chr2D 91.753 97 6 1 6670 6764 176164780 176164684 4.470000e-27 134.0
8 TraesCS2B01G234600 chr2D 89.216 102 6 4 3994 4090 176168354 176168253 9.680000e-24 122.0
9 TraesCS2B01G234600 chr2A 95.070 2840 91 19 1190 4005 187965434 187962620 0.000000e+00 4423.0
10 TraesCS2B01G234600 chr2A 95.469 1280 53 4 4594 5871 187957283 187956007 0.000000e+00 2037.0
11 TraesCS2B01G234600 chr2A 95.156 578 19 3 615 1185 187966057 187965482 0.000000e+00 904.0
12 TraesCS2B01G234600 chr2A 87.023 655 32 12 6163 6767 187955525 187954874 0.000000e+00 689.0
13 TraesCS2B01G234600 chr2A 88.684 380 26 9 4095 4473 187961620 187961257 1.410000e-121 448.0
14 TraesCS2B01G234600 chr2A 95.595 227 7 1 5931 6154 187955816 187955590 1.880000e-95 361.0
15 TraesCS2B01G234600 chr2A 81.467 259 11 5 6842 7079 187953815 187953573 2.040000e-40 178.0
16 TraesCS2B01G234600 chr2A 92.857 98 4 2 3996 4090 187962600 187962503 9.610000e-29 139.0
17 TraesCS2B01G234600 chr2A 94.595 37 2 0 6183 6219 187955585 187955549 2.770000e-04 58.4
18 TraesCS2B01G234600 chr2A 100.000 29 0 0 6670 6698 24689912 24689940 4.000000e-03 54.7
19 TraesCS2B01G234600 chr2A 100.000 29 0 0 6670 6698 537253122 537253094 4.000000e-03 54.7
20 TraesCS2B01G234600 chr1B 93.082 636 25 4 1 617 684276091 684276726 0.000000e+00 913.0
21 TraesCS2B01G234600 chr1B 88.799 616 62 5 2 615 671275200 671275810 0.000000e+00 749.0
22 TraesCS2B01G234600 chr1B 85.668 621 79 9 1 616 20317289 20317904 0.000000e+00 645.0
23 TraesCS2B01G234600 chr1B 93.478 46 3 0 4115 4160 288405111 288405156 1.280000e-07 69.4
24 TraesCS2B01G234600 chr1B 94.595 37 2 0 6662 6698 646128874 646128910 2.770000e-04 58.4
25 TraesCS2B01G234600 chr1A 88.462 624 60 11 2 617 72424006 72423387 0.000000e+00 743.0
26 TraesCS2B01G234600 chr6A 88.301 624 64 9 2 619 614416259 614415639 0.000000e+00 739.0
27 TraesCS2B01G234600 chr6A 91.489 47 3 1 4111 4156 522610892 522610938 5.950000e-06 63.9
28 TraesCS2B01G234600 chr6B 87.680 625 69 6 2 618 21292336 21292960 0.000000e+00 721.0
29 TraesCS2B01G234600 chr6B 94.792 192 6 1 6770 6961 594649497 594649684 5.390000e-76 296.0
30 TraesCS2B01G234600 chr6B 94.792 192 6 1 6770 6961 594650787 594650600 5.390000e-76 296.0
31 TraesCS2B01G234600 chr5A 87.118 621 66 14 2 616 297719665 297720277 0.000000e+00 691.0
32 TraesCS2B01G234600 chr5A 92.632 95 7 0 4142 4236 596562878 596562784 3.460000e-28 137.0
33 TraesCS2B01G234600 chr5A 83.871 124 19 1 4112 4235 433540394 433540272 4.500000e-22 117.0
34 TraesCS2B01G234600 chr3A 84.927 617 78 9 2 616 692532305 692532908 1.690000e-170 610.0
35 TraesCS2B01G234600 chr3A 84.677 620 66 14 2 617 102689471 102688877 6.140000e-165 592.0
36 TraesCS2B01G234600 chr4A 81.564 358 59 7 5457 5809 671920628 671920273 9.020000e-74 289.0
37 TraesCS2B01G234600 chr4A 91.837 98 7 1 4142 4238 594088169 594088266 1.240000e-27 135.0
38 TraesCS2B01G234600 chr7B 82.297 209 33 4 5457 5663 195988926 195988720 2.040000e-40 178.0
39 TraesCS2B01G234600 chr3B 82.297 209 33 4 5457 5663 279755549 279755755 2.040000e-40 178.0
40 TraesCS2B01G234600 chr3B 91.176 102 7 2 4145 4244 571762298 571762197 3.460000e-28 137.0
41 TraesCS2B01G234600 chr3B 97.143 35 0 1 6670 6703 112281254 112281220 2.770000e-04 58.4
42 TraesCS2B01G234600 chr4D 91.339 127 10 1 4108 4233 354879614 354879740 9.480000e-39 172.0
43 TraesCS2B01G234600 chr4D 88.732 71 8 0 6020 6090 67461942 67461872 3.530000e-13 87.9
44 TraesCS2B01G234600 chr4B 81.340 209 35 4 5457 5663 338504213 338504007 4.410000e-37 167.0
45 TraesCS2B01G234600 chr4B 88.571 70 7 1 6022 6090 99964870 99964801 4.570000e-12 84.2
46 TraesCS2B01G234600 chr5B 90.196 102 9 1 4142 4242 341584441 341584542 1.610000e-26 132.0
47 TraesCS2B01G234600 chr5B 96.970 33 0 1 6672 6703 300097182 300097214 4.000000e-03 54.7
48 TraesCS2B01G234600 chr3D 97.143 35 0 1 6670 6703 67481301 67481267 2.770000e-04 58.4
49 TraesCS2B01G234600 chr7A 100.000 29 0 0 6670 6698 731652194 731652222 4.000000e-03 54.7
50 TraesCS2B01G234600 chr1D 100.000 28 0 0 6670 6697 112472006 112471979 1.300000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G234600 chr2B 233269054 233276158 7104 True 13121.000000 13121 100.000000 1 7105 1 chr2B.!!$R1 7104
1 TraesCS2B01G234600 chr2D 176164189 176171811 7622 True 1354.000000 4492 90.902714 615 7105 7 chr2D.!!$R2 6490
2 TraesCS2B01G234600 chr2A 187953573 187966057 12484 True 1026.377778 4423 91.768444 615 7079 9 chr2A.!!$R2 6464
3 TraesCS2B01G234600 chr1B 684276091 684276726 635 False 913.000000 913 93.082000 1 617 1 chr1B.!!$F5 616
4 TraesCS2B01G234600 chr1B 671275200 671275810 610 False 749.000000 749 88.799000 2 615 1 chr1B.!!$F4 613
5 TraesCS2B01G234600 chr1B 20317289 20317904 615 False 645.000000 645 85.668000 1 616 1 chr1B.!!$F1 615
6 TraesCS2B01G234600 chr1A 72423387 72424006 619 True 743.000000 743 88.462000 2 617 1 chr1A.!!$R1 615
7 TraesCS2B01G234600 chr6A 614415639 614416259 620 True 739.000000 739 88.301000 2 619 1 chr6A.!!$R1 617
8 TraesCS2B01G234600 chr6B 21292336 21292960 624 False 721.000000 721 87.680000 2 618 1 chr6B.!!$F1 616
9 TraesCS2B01G234600 chr5A 297719665 297720277 612 False 691.000000 691 87.118000 2 616 1 chr5A.!!$F1 614
10 TraesCS2B01G234600 chr3A 692532305 692532908 603 False 610.000000 610 84.927000 2 616 1 chr3A.!!$F1 614
11 TraesCS2B01G234600 chr3A 102688877 102689471 594 True 592.000000 592 84.677000 2 617 1 chr3A.!!$R1 615

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
263 267 1.000283 CAAATAGCGGCAAACACCCAA 60.000 47.619 1.45 0.00 0.00 4.12 F
270 274 1.358759 GCAAACACCCAACCGACAG 59.641 57.895 0.00 0.00 0.00 3.51 F
273 277 1.746220 CAAACACCCAACCGACAGAAA 59.254 47.619 0.00 0.00 0.00 2.52 F
1083 1128 2.034558 CGGCTTCAGGTTTGATTGTGTT 59.965 45.455 0.00 0.00 32.27 3.32 F
2109 2201 3.562973 CCGGAGATGATGAAAATGTCCAG 59.437 47.826 0.00 0.00 37.33 3.86 F
2761 2853 3.502211 AGTCAAACCGAAGCATTACAAGG 59.498 43.478 0.00 0.00 0.00 3.61 F
4299 5350 0.114168 TCCACCAAGGGATTGGGTTG 59.886 55.000 11.47 1.99 46.23 3.77 F
4572 5636 0.103208 GAGACAGCCCACGTGGATAG 59.897 60.000 36.07 24.32 37.39 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 1233 0.252197 AACAAGGGCGATCACTACCC 59.748 55.000 2.57 2.57 44.62 3.69 R
2200 2292 1.111277 GCACCCCCAATAATCACCAC 58.889 55.000 0.00 0.00 0.00 4.16 R
2208 2300 1.133009 ACTTGGTTTGCACCCCCAATA 60.133 47.619 10.43 0.00 43.49 1.90 R
2446 2538 0.596082 CCTGCAAGTTTTACACCCCG 59.404 55.000 0.00 0.00 0.00 5.73 R
3023 3117 0.744281 ACAAGCCAACTGGTTTTCCG 59.256 50.000 0.00 0.00 44.36 4.30 R
4553 5617 0.103208 CTATCCACGTGGGCTGTCTC 59.897 60.000 33.40 0.00 36.21 3.36 R
5136 10092 0.532640 TTGTCGCACAGCATCAGTGT 60.533 50.000 0.00 0.00 39.17 3.55 R
6491 11679 0.749454 ACGCCTGGCATTCATCTTCC 60.749 55.000 20.29 0.00 0.00 3.46 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
32 33 2.297129 GGCTCCTCCTGCAGAACCT 61.297 63.158 17.39 0.00 0.00 3.50
203 206 1.846007 TGCCAACAGTTTCAACCAGT 58.154 45.000 0.00 0.00 0.00 4.00
263 267 1.000283 CAAATAGCGGCAAACACCCAA 60.000 47.619 1.45 0.00 0.00 4.12
267 271 2.902846 CGGCAAACACCCAACCGA 60.903 61.111 0.00 0.00 46.71 4.69
269 273 2.122167 GGCAAACACCCAACCGACA 61.122 57.895 0.00 0.00 0.00 4.35
270 274 1.358759 GCAAACACCCAACCGACAG 59.641 57.895 0.00 0.00 0.00 3.51
273 277 1.746220 CAAACACCCAACCGACAGAAA 59.254 47.619 0.00 0.00 0.00 2.52
383 387 2.097825 GTTCAAGGCATCATTCAGGCT 58.902 47.619 0.00 0.00 43.06 4.58
474 478 5.777223 CCACCATGAGAAGTCCATATAGAGA 59.223 44.000 0.00 0.00 0.00 3.10
507 534 6.905076 TGTTCTTCTTCTTTTCGTTTTCATCG 59.095 34.615 0.00 0.00 0.00 3.84
564 594 4.285775 CCACCCTTTGTATTTTCCCATTGT 59.714 41.667 0.00 0.00 0.00 2.71
689 720 2.140717 GAACGACCACACGATTTTCCT 58.859 47.619 0.00 0.00 37.03 3.36
729 768 4.680237 CAACGAGCCCGACCAGCA 62.680 66.667 0.00 0.00 39.50 4.41
887 932 3.814615 CTCCCGCCATACGCATGCT 62.815 63.158 17.13 5.50 41.76 3.79
1083 1128 2.034558 CGGCTTCAGGTTTGATTGTGTT 59.965 45.455 0.00 0.00 32.27 3.32
1182 1227 7.568199 AAAATACGGCAATTTAGCATCTACT 57.432 32.000 0.00 0.00 35.83 2.57
1197 1285 5.028549 CATCTACTGCTTTGGGTAGTGAT 57.971 43.478 0.00 0.00 40.92 3.06
1309 1397 9.421399 ACCCAATAATTATTCCTTTTCCAGTAG 57.579 33.333 7.76 0.00 0.00 2.57
1383 1471 4.082026 GCACAACTGAAAATATCTTGGGCT 60.082 41.667 0.00 0.00 38.77 5.19
1387 1475 5.441718 ACTGAAAATATCTTGGGCTCTGA 57.558 39.130 0.00 0.00 0.00 3.27
1448 1538 3.726557 TGAAGTGCTGATCCCAGATTT 57.273 42.857 0.00 0.00 43.02 2.17
1719 1810 5.955355 CCTAGGGTTCTATTCCCATCTCTAG 59.045 48.000 0.00 0.00 46.82 2.43
1766 1857 6.986231 TGTTCATATTACTGGCTCACTACATG 59.014 38.462 0.00 0.00 0.00 3.21
1767 1858 6.101650 TCATATTACTGGCTCACTACATGG 57.898 41.667 0.00 0.00 0.00 3.66
1768 1859 5.838521 TCATATTACTGGCTCACTACATGGA 59.161 40.000 0.00 0.00 0.00 3.41
1769 1860 6.326323 TCATATTACTGGCTCACTACATGGAA 59.674 38.462 0.00 0.00 0.00 3.53
1770 1861 5.636903 ATTACTGGCTCACTACATGGAAT 57.363 39.130 0.00 0.00 0.00 3.01
1883 1974 5.664294 ATACATTTTTCTTGCATGGCAGA 57.336 34.783 0.00 0.00 40.61 4.26
1901 1992 7.991084 TGGCAGATCATTTCTATCTAATTGG 57.009 36.000 0.00 0.00 32.40 3.16
1969 2060 6.855836 TCTTGTATTCTTGCATTCATGGTTC 58.144 36.000 0.00 0.00 0.00 3.62
2000 2092 4.818005 TGCAGGCAGTACATGATATTCAAG 59.182 41.667 0.00 0.00 0.00 3.02
2020 2112 6.999950 TCAAGTACTGTAGCTACCATGAAAA 58.000 36.000 21.01 0.00 0.00 2.29
2021 2113 7.620880 TCAAGTACTGTAGCTACCATGAAAAT 58.379 34.615 21.01 0.00 0.00 1.82
2022 2114 8.755028 TCAAGTACTGTAGCTACCATGAAAATA 58.245 33.333 21.01 0.00 0.00 1.40
2023 2115 9.378551 CAAGTACTGTAGCTACCATGAAAATAA 57.621 33.333 21.01 0.00 0.00 1.40
2024 2116 8.943909 AGTACTGTAGCTACCATGAAAATAAC 57.056 34.615 21.01 2.95 0.00 1.89
2025 2117 8.537016 AGTACTGTAGCTACCATGAAAATAACA 58.463 33.333 21.01 0.00 0.00 2.41
2026 2118 7.611213 ACTGTAGCTACCATGAAAATAACAC 57.389 36.000 21.01 0.00 0.00 3.32
2109 2201 3.562973 CCGGAGATGATGAAAATGTCCAG 59.437 47.826 0.00 0.00 37.33 3.86
2175 2267 6.990341 TGATGTCTTACCATGTGAGATTTG 57.010 37.500 0.00 0.00 31.20 2.32
2188 2280 5.324409 TGTGAGATTTGCCTCCTGTATTTT 58.676 37.500 0.00 0.00 32.32 1.82
2200 2292 6.980397 GCCTCCTGTATTTTTACATGGATTTG 59.020 38.462 0.00 0.00 31.67 2.32
2208 2300 9.651913 GTATTTTTACATGGATTTGTGGTGATT 57.348 29.630 0.00 0.00 0.00 2.57
2386 2478 7.284489 AGCTTTGTAAAGGTCAAGTTTGTATCA 59.716 33.333 3.40 0.00 42.60 2.15
2443 2535 8.325787 TGTTTGAGATAATTGGTAGGAGCTTAA 58.674 33.333 0.00 0.00 0.00 1.85
2446 2538 7.727181 TGAGATAATTGGTAGGAGCTTAAGAC 58.273 38.462 6.67 0.00 0.00 3.01
2761 2853 3.502211 AGTCAAACCGAAGCATTACAAGG 59.498 43.478 0.00 0.00 0.00 3.61
2821 2913 6.602803 TGCCATATGAGAACTTAAGCATGAAA 59.397 34.615 3.65 0.00 0.00 2.69
2822 2914 7.122501 TGCCATATGAGAACTTAAGCATGAAAA 59.877 33.333 3.65 0.00 0.00 2.29
2915 3008 5.767168 GGAGAAACCAATAGATGCTATGCTT 59.233 40.000 0.00 0.00 38.79 3.91
2919 3012 9.189156 AGAAACCAATAGATGCTATGCTTAAAA 57.811 29.630 0.00 0.00 0.00 1.52
2920 3013 9.237846 GAAACCAATAGATGCTATGCTTAAAAC 57.762 33.333 0.00 0.00 0.00 2.43
2921 3014 6.959361 ACCAATAGATGCTATGCTTAAAACG 58.041 36.000 0.00 0.00 0.00 3.60
2922 3015 5.853282 CCAATAGATGCTATGCTTAAAACGC 59.147 40.000 0.00 0.00 0.00 4.84
2923 3016 6.293626 CCAATAGATGCTATGCTTAAAACGCT 60.294 38.462 0.00 0.00 0.00 5.07
2924 3017 7.095229 CCAATAGATGCTATGCTTAAAACGCTA 60.095 37.037 0.00 0.00 0.00 4.26
2962 3056 4.731313 AGGGTTCAAATATGGGAGGATC 57.269 45.455 0.00 0.00 0.00 3.36
2984 3078 8.242053 GGATCCAAATATTCATGAATGCACTAG 58.758 37.037 27.59 13.50 32.50 2.57
3001 3095 7.019774 TGCACTAGAAAATGTGAGCATAATC 57.980 36.000 0.00 0.00 36.38 1.75
3071 3165 3.316308 CCAACAGACCCTTTTGACTGAAG 59.684 47.826 0.00 0.00 34.88 3.02
3189 3283 5.851047 GCTTTTGCTTAGTGATTGCATTT 57.149 34.783 0.00 0.00 43.35 2.32
3192 3286 6.542574 TTTTGCTTAGTGATTGCATTTTGG 57.457 33.333 0.00 0.00 36.55 3.28
3225 3319 5.048713 GGAAATGATGACGTTCTTCCAACTT 60.049 40.000 0.00 0.00 0.00 2.66
3345 3439 2.079170 TGCAAAATGGTCAAGGGACA 57.921 45.000 0.00 0.00 46.17 4.02
3358 3452 5.765182 GGTCAAGGGACATATGGAAAGTATG 59.235 44.000 7.80 0.00 46.17 2.39
3403 3497 9.182214 ACACAAGAGATAAGCATCAATTATGTT 57.818 29.630 0.00 0.00 37.93 2.71
3438 3532 2.351738 GGTGCAGTGCAATGAGGTAAAC 60.352 50.000 21.67 2.68 41.47 2.01
3468 3562 8.546083 AAAACATTTAAGGGCATCCATGTATA 57.454 30.769 0.00 0.00 34.83 1.47
3473 3567 8.641541 CATTTAAGGGCATCCATGTATACTTTT 58.358 33.333 4.17 0.00 34.83 2.27
3524 3618 5.484173 TCTCTTTCGCATCGCAATAAAAT 57.516 34.783 0.00 0.00 0.00 1.82
3685 3799 3.131046 AGACATCGTAGATGACATGTGCA 59.869 43.478 15.91 1.26 45.12 4.57
3819 3933 4.037446 TCAGGTGTCACAAAAAGTAATGCC 59.963 41.667 5.12 0.00 0.00 4.40
3820 3934 3.004315 AGGTGTCACAAAAAGTAATGCCG 59.996 43.478 5.12 0.00 0.00 5.69
3955 4070 6.717289 ACTACTGCCTTTGAATGTATACCAA 58.283 36.000 0.00 0.00 0.00 3.67
4050 4199 7.103641 GTCTCTGGTGGATATGTCTGTAAAAA 58.896 38.462 0.00 0.00 0.00 1.94
4090 4243 5.749462 ACTAAATGTTCCTAAGCAGCATCT 58.251 37.500 0.00 0.00 0.00 2.90
4093 5143 4.978083 ATGTTCCTAAGCAGCATCTTTG 57.022 40.909 0.00 0.00 0.00 2.77
4099 5149 1.999648 AAGCAGCATCTTTGTTGGGA 58.000 45.000 0.00 0.00 34.88 4.37
4108 5158 6.012745 AGCATCTTTGTTGGGATTTCTTACT 58.987 36.000 0.00 0.00 0.00 2.24
4136 5186 3.344515 GCCTTGTTCGGTTAATCCTCTT 58.655 45.455 0.00 0.00 0.00 2.85
4144 5194 2.421529 CGGTTAATCCTCTTCCCAAGGG 60.422 54.545 0.00 0.00 34.46 3.95
4167 5217 4.202253 GGATTGGAGGGGATTTTGTATTGC 60.202 45.833 0.00 0.00 0.00 3.56
4199 5249 1.622499 CCCCTCAATCCCTGCCAAT 59.378 57.895 0.00 0.00 0.00 3.16
4204 5254 0.925720 TCAATCCCTGCCAATCCCCT 60.926 55.000 0.00 0.00 0.00 4.79
4206 5256 0.262876 AATCCCTGCCAATCCCCTTC 59.737 55.000 0.00 0.00 0.00 3.46
4276 5327 4.893829 GGATCTAATCCCCTAGTGGAAC 57.106 50.000 0.00 0.00 43.88 3.62
4278 5329 5.652324 GGATCTAATCCCCTAGTGGAACTA 58.348 45.833 0.00 0.00 45.17 2.24
4279 5330 6.082707 GGATCTAATCCCCTAGTGGAACTAA 58.917 44.000 0.00 0.00 45.79 2.24
4280 5331 6.731448 GGATCTAATCCCCTAGTGGAACTAAT 59.269 42.308 0.00 0.00 45.79 1.73
4281 5332 7.093245 GGATCTAATCCCCTAGTGGAACTAATC 60.093 44.444 0.00 0.52 45.79 1.75
4297 5348 2.819272 ATCCACCAAGGGATTGGGT 58.181 52.632 11.47 0.00 45.42 4.51
4298 5349 1.092549 ATCCACCAAGGGATTGGGTT 58.907 50.000 11.47 0.00 45.42 4.11
4299 5350 0.114168 TCCACCAAGGGATTGGGTTG 59.886 55.000 11.47 1.99 46.23 3.77
4300 5351 0.114168 CCACCAAGGGATTGGGTTGA 59.886 55.000 11.47 0.00 46.23 3.18
4350 5410 3.954662 ACACAATCCCCATCCCTACTAT 58.045 45.455 0.00 0.00 0.00 2.12
4352 5412 4.171234 CACAATCCCCATCCCTACTATCT 58.829 47.826 0.00 0.00 0.00 1.98
4364 5424 7.456725 CATCCCTACTATCTCATTTGGTTGAT 58.543 38.462 0.00 0.00 0.00 2.57
4378 5438 4.868172 TGGTTGATCCAGATTCAATCCT 57.132 40.909 0.00 0.00 41.93 3.24
4382 5442 6.331042 TGGTTGATCCAGATTCAATCCTCTAT 59.669 38.462 0.00 0.00 41.93 1.98
4409 5469 6.187682 ACTATAAATTGTCCCTCCCAGTTTG 58.812 40.000 0.00 0.00 0.00 2.93
4473 5537 0.623723 TCTGGCCCCTGTGGAATTAC 59.376 55.000 0.00 0.00 35.39 1.89
4474 5538 0.748005 CTGGCCCCTGTGGAATTACG 60.748 60.000 0.00 0.00 35.39 3.18
4475 5539 2.119029 GGCCCCTGTGGAATTACGC 61.119 63.158 0.00 0.00 35.39 4.42
4476 5540 2.469516 GCCCCTGTGGAATTACGCG 61.470 63.158 3.53 3.53 35.39 6.01
4477 5541 1.817941 CCCCTGTGGAATTACGCGG 60.818 63.158 12.47 2.77 35.39 6.46
4478 5542 1.078708 CCCTGTGGAATTACGCGGT 60.079 57.895 12.47 0.00 0.00 5.68
4479 5543 0.675522 CCCTGTGGAATTACGCGGTT 60.676 55.000 12.47 1.51 0.00 4.44
4480 5544 1.161843 CCTGTGGAATTACGCGGTTT 58.838 50.000 12.47 0.00 0.00 3.27
4481 5545 1.135803 CCTGTGGAATTACGCGGTTTG 60.136 52.381 12.47 0.00 0.00 2.93
4482 5546 0.875728 TGTGGAATTACGCGGTTTGG 59.124 50.000 12.47 0.00 0.00 3.28
4483 5547 0.169451 GTGGAATTACGCGGTTTGGG 59.831 55.000 12.47 0.00 0.00 4.12
4484 5548 1.138036 GGAATTACGCGGTTTGGGC 59.862 57.895 12.47 0.00 0.00 5.36
4485 5549 1.138036 GAATTACGCGGTTTGGGCC 59.862 57.895 12.47 0.00 0.00 5.80
4492 5556 2.026879 CGGTTTGGGCCGTTGTTG 59.973 61.111 0.00 0.00 46.11 3.33
4493 5557 2.776913 CGGTTTGGGCCGTTGTTGT 61.777 57.895 0.00 0.00 46.11 3.32
4494 5558 1.066752 GGTTTGGGCCGTTGTTGTC 59.933 57.895 0.00 0.00 0.00 3.18
4495 5559 1.066752 GTTTGGGCCGTTGTTGTCC 59.933 57.895 0.00 0.00 0.00 4.02
4496 5560 2.128507 TTTGGGCCGTTGTTGTCCC 61.129 57.895 0.00 0.00 39.22 4.46
4497 5561 4.589675 TGGGCCGTTGTTGTCCCC 62.590 66.667 0.00 0.00 37.97 4.81
4503 5567 3.656045 GTTGTTGTCCCCGCCGTG 61.656 66.667 0.00 0.00 0.00 4.94
4504 5568 3.862991 TTGTTGTCCCCGCCGTGA 61.863 61.111 0.00 0.00 0.00 4.35
4505 5569 3.185299 TTGTTGTCCCCGCCGTGAT 62.185 57.895 0.00 0.00 0.00 3.06
4506 5570 2.818274 GTTGTCCCCGCCGTGATC 60.818 66.667 0.00 0.00 0.00 2.92
4507 5571 4.090588 TTGTCCCCGCCGTGATCC 62.091 66.667 0.00 0.00 0.00 3.36
4509 5573 4.090588 GTCCCCGCCGTGATCCAA 62.091 66.667 0.00 0.00 0.00 3.53
4533 5597 8.361139 CAAACCAAACAATGTAAGTATAACCCA 58.639 33.333 0.00 0.00 0.00 4.51
4552 5616 1.343465 CACGTGTAACAGTTCCCCTCT 59.657 52.381 7.58 0.00 35.74 3.69
4553 5617 1.343465 ACGTGTAACAGTTCCCCTCTG 59.657 52.381 0.00 0.00 35.74 3.35
4554 5618 1.616865 CGTGTAACAGTTCCCCTCTGA 59.383 52.381 0.00 0.00 35.74 3.27
4558 5622 2.103153 AACAGTTCCCCTCTGAGACA 57.897 50.000 6.17 0.00 36.81 3.41
4571 5635 0.613572 TGAGACAGCCCACGTGGATA 60.614 55.000 36.07 9.29 37.39 2.59
4572 5636 0.103208 GAGACAGCCCACGTGGATAG 59.897 60.000 36.07 24.32 37.39 2.08
4592 5656 0.257039 AGTGTGATCCCTGGCATTCC 59.743 55.000 0.00 0.00 0.00 3.01
4607 9562 3.592059 GCATTCCACGTGGTTTAGACTA 58.408 45.455 32.74 9.47 36.34 2.59
4637 9592 6.451064 AACAAGACCTAAGGTTGTTTTGAG 57.549 37.500 0.00 0.00 34.25 3.02
4724 9680 4.083431 GGCATAGTGAATCAGTGATCATGC 60.083 45.833 18.65 18.65 36.42 4.06
4768 9724 8.867097 TCATAATTTCCTGTATAGTCTGTACCC 58.133 37.037 4.48 0.00 0.00 3.69
4769 9725 5.786264 ATTTCCTGTATAGTCTGTACCCG 57.214 43.478 4.48 0.00 0.00 5.28
4782 9738 5.052481 GTCTGTACCCGTCAACTTTTACTT 58.948 41.667 0.00 0.00 0.00 2.24
4785 9741 6.258507 TCTGTACCCGTCAACTTTTACTTTTC 59.741 38.462 0.00 0.00 0.00 2.29
4786 9742 5.879223 TGTACCCGTCAACTTTTACTTTTCA 59.121 36.000 0.00 0.00 0.00 2.69
4790 9746 7.324935 ACCCGTCAACTTTTACTTTTCATTTT 58.675 30.769 0.00 0.00 0.00 1.82
4792 9748 9.471084 CCCGTCAACTTTTACTTTTCATTTTAT 57.529 29.630 0.00 0.00 0.00 1.40
4848 9804 5.108187 AGCATGTGGTGACATTCTAGATT 57.892 39.130 0.00 0.00 46.14 2.40
4853 9809 9.056005 GCATGTGGTGACATTCTAGATTATTAA 57.944 33.333 0.00 0.00 46.14 1.40
4919 9875 6.987386 AGATATACGCTCAAGCTTCTGTTAT 58.013 36.000 0.00 0.00 39.32 1.89
4978 9934 5.972935 TCTGCCGTGTTCAGATTTAAGATA 58.027 37.500 0.00 0.00 35.81 1.98
5023 9979 6.183347 AGCACTTGCCAGTATTTCTAGAAAT 58.817 36.000 28.75 28.75 43.38 2.17
5293 10249 4.630644 TTTGATCTCTTTCTCCAGTGCT 57.369 40.909 0.00 0.00 0.00 4.40
5361 10317 5.413309 GAGAGAATTCTCCTTGGAGACAA 57.587 43.478 28.01 6.23 45.11 3.18
5436 10392 1.238439 ATGGTTCAAACTGAGGTGCG 58.762 50.000 0.00 0.00 0.00 5.34
5450 10406 1.531149 AGGTGCGTTCTGTTTCATTCG 59.469 47.619 0.00 0.00 0.00 3.34
5606 10566 6.853872 TCGTTTGTTACAATGCAAGTGATTAC 59.146 34.615 7.69 3.68 34.17 1.89
5622 10582 5.354234 AGTGATTACCTACAATTTCAAGGCG 59.646 40.000 0.00 0.00 33.42 5.52
5726 10686 9.810545 CAGGGTAAATTAGTTTTTCTTTTGTCA 57.189 29.630 0.00 0.00 0.00 3.58
5752 10712 6.437755 TCCCTCATCCTTGAATTTGATCATT 58.562 36.000 0.00 0.00 0.00 2.57
5835 10795 8.434733 ACTTTCTTGGTGTAAGTCTTTAACTC 57.565 34.615 0.00 0.00 37.17 3.01
5890 10876 6.818644 GTCATGTGTATAGAATGAGTTGTGGT 59.181 38.462 0.00 0.00 31.21 4.16
5891 10877 7.010552 GTCATGTGTATAGAATGAGTTGTGGTC 59.989 40.741 0.00 0.00 31.21 4.02
5914 10900 6.879458 GTCAGTAATTCCAATACACAGTTCCT 59.121 38.462 0.00 0.00 0.00 3.36
5985 11079 7.711846 TGTTTATTGCATGAACAGTTTAGTGT 58.288 30.769 0.00 0.00 34.37 3.55
6018 11112 8.404765 TGTGTATTTAGATGTTGTATTGGCATG 58.595 33.333 0.00 0.00 0.00 4.06
6020 11114 8.620416 TGTATTTAGATGTTGTATTGGCATGTC 58.380 33.333 0.00 0.00 0.00 3.06
6110 11204 1.412710 TCGTCAGGCCATTGAGGTATC 59.587 52.381 5.01 0.00 40.61 2.24
6159 11253 3.928211 CAGTGTCGCTGCAAATACATAC 58.072 45.455 0.00 0.00 38.52 2.39
6175 11327 9.868389 CAAATACATACACTTGTATATGCTGTG 57.132 33.333 12.86 12.86 40.94 3.66
6241 11393 1.903183 AGGAAGAACTGGACTGCTACC 59.097 52.381 0.00 0.00 0.00 3.18
6296 11448 2.144482 GCATCTTGTTGCTTGTTGCT 57.856 45.000 0.00 0.00 43.37 3.91
6335 11487 3.825585 TGCATTAAGATCACTTTGCCACA 59.174 39.130 0.00 0.00 38.40 4.17
6339 11509 5.885230 TTAAGATCACTTTGCCACATCAG 57.115 39.130 0.00 0.00 37.53 2.90
6398 11575 3.137544 AGTTTACAACATCTGGTGGACCA 59.862 43.478 0.00 0.00 45.30 4.02
6491 11679 7.461182 TTTATATTGTTTCCCAAGACACCAG 57.539 36.000 0.00 0.00 36.25 4.00
6513 11701 1.888215 AGATGAATGCCAGGCGTATG 58.112 50.000 6.58 0.00 0.00 2.39
6623 11811 2.567615 GTGGGAGCCTTTCTCAGAGTTA 59.432 50.000 0.00 0.00 43.70 2.24
6698 11922 7.222999 ACATAAGAGCGTTTAGATCACTAAAGC 59.777 37.037 0.00 0.00 45.42 3.51
6704 11928 4.031426 CGTTTAGATCACTAAAGCGTGACC 59.969 45.833 0.00 0.00 45.74 4.02
6719 11943 3.325870 CGTGACCACTAGCAAAATCTCA 58.674 45.455 0.00 0.00 0.00 3.27
6750 11974 0.686224 GCTATGCATCTCAGGGAGCT 59.314 55.000 0.19 0.00 0.00 4.09
6757 11981 2.744494 GCATCTCAGGGAGCTTAACTGG 60.744 54.545 11.69 5.07 33.19 4.00
6771 12149 2.833631 AACTGGACCGACCTTTGTAG 57.166 50.000 0.00 0.00 39.86 2.74
6782 12160 1.148310 CCTTTGTAGGCACTGTCACG 58.852 55.000 0.00 0.00 41.52 4.35
6807 12185 2.568003 GGTCCAAACCAGCTTAGCC 58.432 57.895 0.00 0.00 45.68 3.93
6839 12367 1.472878 GAGACGAGCACCACTACATCA 59.527 52.381 0.00 0.00 0.00 3.07
6855 13068 7.401860 CACTACATCATCTGGTTTCGTAAATG 58.598 38.462 0.00 0.00 0.00 2.32
6866 13079 0.449786 TCGTAAATGTGCATTGCCCG 59.550 50.000 6.12 2.39 0.00 6.13
6926 13142 4.033776 GCAGCCTAGCCACCCACA 62.034 66.667 0.00 0.00 0.00 4.17
6927 13143 2.270205 CAGCCTAGCCACCCACAG 59.730 66.667 0.00 0.00 0.00 3.66
6928 13144 3.011517 AGCCTAGCCACCCACAGG 61.012 66.667 0.00 0.00 40.04 4.00
6954 13170 0.810648 AGGCACGCAATATGTGGTTG 59.189 50.000 0.00 0.00 37.80 3.77
6958 13174 1.729517 CACGCAATATGTGGTTGTCGA 59.270 47.619 8.72 0.00 33.69 4.20
6967 13183 1.153127 TGGTTGTCGAAGCCGGTTT 60.153 52.632 1.95 1.95 36.24 3.27
7077 13311 2.539338 GCTCGCTCGATCGTCCTCT 61.539 63.158 15.94 0.00 0.00 3.69
7083 13317 4.315122 CGATCGTCCTCTCCGCCG 62.315 72.222 7.03 0.00 0.00 6.46
7086 13320 3.989838 ATCGTCCTCTCCGCCGTGA 62.990 63.158 0.00 0.00 0.00 4.35
7087 13321 4.477975 CGTCCTCTCCGCCGTGAC 62.478 72.222 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.211865 AGTCTATCGCACGTCCATAGAA 58.788 45.455 8.52 0.00 32.22 2.10
203 206 3.691118 GCTATCTTCATGGAACTGTTGCA 59.309 43.478 17.03 17.03 34.77 4.08
263 267 1.375326 GGCCCTCTTTTCTGTCGGT 59.625 57.895 0.00 0.00 0.00 4.69
267 271 0.185901 TTGCTGGCCCTCTTTTCTGT 59.814 50.000 0.00 0.00 0.00 3.41
269 273 1.553706 CATTGCTGGCCCTCTTTTCT 58.446 50.000 0.00 0.00 0.00 2.52
270 274 0.108472 GCATTGCTGGCCCTCTTTTC 60.108 55.000 0.00 0.00 0.00 2.29
273 277 2.363406 GGCATTGCTGGCCCTCTT 60.363 61.111 8.82 0.00 45.87 2.85
383 387 5.066375 CCAAAGTTCAATGGATTGCTCGATA 59.934 40.000 0.00 0.00 39.12 2.92
483 505 6.357240 CCGATGAAAACGAAAAGAAGAAGAAC 59.643 38.462 0.00 0.00 31.90 3.01
507 534 3.756117 AGGACCAATCAGTTCAAGAACC 58.244 45.455 9.20 0.00 42.06 3.62
564 594 4.380444 GGCGTTTCATTGATAAGCAGGAAA 60.380 41.667 14.54 0.00 32.61 3.13
689 720 1.124780 TGGTGAGGTTGACGAGGAAA 58.875 50.000 0.00 0.00 0.00 3.13
743 788 3.649277 CTTGGAGAGGGACGCGGTG 62.649 68.421 12.47 0.00 0.00 4.94
976 1021 1.146637 GCATAGCTTGATCTGCTCGG 58.853 55.000 15.12 10.71 41.46 4.63
1042 1087 1.034356 TTGGAACTCGTCGGACAAGA 58.966 50.000 9.10 0.00 0.00 3.02
1182 1227 0.392461 GGCGATCACTACCCAAAGCA 60.392 55.000 0.00 0.00 0.00 3.91
1185 1230 0.988832 AAGGGCGATCACTACCCAAA 59.011 50.000 11.49 0.00 46.88 3.28
1187 1232 0.907704 ACAAGGGCGATCACTACCCA 60.908 55.000 11.49 0.00 46.88 4.51
1188 1233 0.252197 AACAAGGGCGATCACTACCC 59.748 55.000 2.57 2.57 44.62 3.69
1309 1397 9.331282 AGAATTTTGTAAGACATATACCTCTGC 57.669 33.333 0.00 0.00 0.00 4.26
1383 1471 4.365514 TGTAAGGAAAGGCACATTCAGA 57.634 40.909 0.00 0.00 37.84 3.27
1387 1475 3.778265 ACCATGTAAGGAAAGGCACATT 58.222 40.909 0.00 0.00 29.31 2.71
1448 1538 4.452825 TCCACAATGGTTCACGTAAAAGA 58.547 39.130 0.00 0.00 39.03 2.52
1742 1833 6.425114 CCATGTAGTGAGCCAGTAATATGAAC 59.575 42.308 0.00 0.00 0.00 3.18
1750 1841 4.030216 TCATTCCATGTAGTGAGCCAGTA 58.970 43.478 0.00 0.00 0.00 2.74
1766 1857 8.424918 TCTAAACAGATCTACTTCCATCATTCC 58.575 37.037 0.00 0.00 0.00 3.01
1767 1858 9.255304 GTCTAAACAGATCTACTTCCATCATTC 57.745 37.037 0.00 0.00 0.00 2.67
1768 1859 8.762645 TGTCTAAACAGATCTACTTCCATCATT 58.237 33.333 0.00 0.00 0.00 2.57
1769 1860 8.311395 TGTCTAAACAGATCTACTTCCATCAT 57.689 34.615 0.00 0.00 0.00 2.45
1770 1861 7.718334 TGTCTAAACAGATCTACTTCCATCA 57.282 36.000 0.00 0.00 0.00 3.07
1771 1862 9.606631 AATTGTCTAAACAGATCTACTTCCATC 57.393 33.333 0.00 0.00 36.57 3.51
1772 1863 9.965902 AAATTGTCTAAACAGATCTACTTCCAT 57.034 29.630 0.00 0.00 36.57 3.41
1773 1864 9.793259 AAAATTGTCTAAACAGATCTACTTCCA 57.207 29.630 0.00 0.00 36.57 3.53
1862 1953 5.185442 TGATCTGCCATGCAAGAAAAATGTA 59.815 36.000 0.00 0.00 38.41 2.29
1883 1974 8.416329 GCCAAACACCAATTAGATAGAAATGAT 58.584 33.333 0.00 0.00 0.00 2.45
2000 2092 8.601476 GTGTTATTTTCATGGTAGCTACAGTAC 58.399 37.037 24.75 8.44 0.00 2.73
2040 2132 3.544834 CGTCGCCAGCAGATATGAAAAAG 60.545 47.826 0.00 0.00 0.00 2.27
2109 2201 1.424493 GGCAGCATCACGAGCTACAC 61.424 60.000 0.00 0.00 41.14 2.90
2175 2267 6.715347 AATCCATGTAAAAATACAGGAGGC 57.285 37.500 2.52 0.00 34.03 4.70
2188 2280 7.147759 CCCAATAATCACCACAAATCCATGTAA 60.148 37.037 0.00 0.00 30.84 2.41
2200 2292 1.111277 GCACCCCCAATAATCACCAC 58.889 55.000 0.00 0.00 0.00 4.16
2208 2300 1.133009 ACTTGGTTTGCACCCCCAATA 60.133 47.619 10.43 0.00 43.49 1.90
2386 2478 5.188359 AGAAAGCCAAAAGGAACATGCATAT 59.812 36.000 0.00 0.00 0.00 1.78
2443 2535 1.134037 TGCAAGTTTTACACCCCGTCT 60.134 47.619 0.00 0.00 0.00 4.18
2446 2538 0.596082 CCTGCAAGTTTTACACCCCG 59.404 55.000 0.00 0.00 0.00 5.73
2481 2573 5.248020 TGGGTGGAAATAAATCTTGCAACAT 59.752 36.000 0.00 0.00 33.82 2.71
2650 2742 3.387374 TGACTGGGTTTCATTTGCACATT 59.613 39.130 0.00 0.00 0.00 2.71
2699 2791 5.071788 CCTCCCTGGTTCATATAAGTAAGCA 59.928 44.000 0.00 0.00 0.00 3.91
2714 2806 1.595311 TATTGTCATGCCTCCCTGGT 58.405 50.000 0.00 0.00 38.35 4.00
2761 2853 8.970691 AGTTTGCTAATGATGTAATGTTGTTC 57.029 30.769 0.00 0.00 0.00 3.18
2962 3056 9.806203 TTTTCTAGTGCATTCATGAATATTTGG 57.194 29.630 20.32 9.21 0.00 3.28
2984 3078 5.653507 TGCAAGGATTATGCTCACATTTTC 58.346 37.500 0.00 0.00 44.14 2.29
3023 3117 0.744281 ACAAGCCAACTGGTTTTCCG 59.256 50.000 0.00 0.00 44.36 4.30
3053 3147 2.575532 TGCTTCAGTCAAAAGGGTCTG 58.424 47.619 0.00 0.00 0.00 3.51
3071 3165 5.105187 AGCTTCAAAAATCCCCTAAAGATGC 60.105 40.000 0.00 0.00 0.00 3.91
3130 3224 4.321452 GCCGCAAAATATGACATCCATCAT 60.321 41.667 0.00 0.00 42.13 2.45
3182 3276 5.860941 TTCCTACTGTTTCCAAAATGCAA 57.139 34.783 0.00 0.00 0.00 4.08
3189 3283 5.411361 CGTCATCATTTCCTACTGTTTCCAA 59.589 40.000 0.00 0.00 0.00 3.53
3192 3286 6.369065 AGAACGTCATCATTTCCTACTGTTTC 59.631 38.462 0.00 0.00 0.00 2.78
3225 3319 5.012239 AGCACAGAGAAAGCCAATTGATAA 58.988 37.500 7.12 0.00 0.00 1.75
3358 3452 8.041323 TCTTGTGTCCTTCCTAATCTTAACATC 58.959 37.037 0.00 0.00 0.00 3.06
3403 3497 2.591429 CACCTCCACAGCACGCAA 60.591 61.111 0.00 0.00 0.00 4.85
3438 3532 8.614346 CATGGATGCCCTTAAATGTTTTAAATG 58.386 33.333 0.00 0.00 0.00 2.32
3487 3581 6.073222 TGCGAAAGAGAAACAATCCTTAAGAC 60.073 38.462 3.36 0.00 0.00 3.01
3491 3585 5.063438 CGATGCGAAAGAGAAACAATCCTTA 59.937 40.000 0.00 0.00 0.00 2.69
3566 3680 3.945921 GCCCTGTCATAAGAACTAAACCC 59.054 47.826 0.00 0.00 0.00 4.11
3800 3914 3.959943 ACGGCATTACTTTTTGTGACAC 58.040 40.909 0.00 0.00 0.00 3.67
3819 3933 5.566623 CCTTGTTTCATTCTCATGATGACG 58.433 41.667 0.00 0.00 39.28 4.35
3820 3934 5.106038 TGCCTTGTTTCATTCTCATGATGAC 60.106 40.000 0.00 0.00 39.28 3.06
3955 4070 7.066142 TCATATGCCTTGTATTTACCATGGTT 58.934 34.615 25.38 7.89 0.00 3.67
4004 4119 9.950496 AGAGACATTAAAGATGTACATCACTTT 57.050 29.630 32.01 25.65 40.22 2.66
4005 4120 9.376075 CAGAGACATTAAAGATGTACATCACTT 57.624 33.333 32.01 25.66 40.22 3.16
4090 4243 7.039993 GCCTAAAGAGTAAGAAATCCCAACAAA 60.040 37.037 0.00 0.00 0.00 2.83
4093 5143 5.357314 GGCCTAAAGAGTAAGAAATCCCAAC 59.643 44.000 0.00 0.00 0.00 3.77
4099 5149 6.371825 CGAACAAGGCCTAAAGAGTAAGAAAT 59.628 38.462 5.16 0.00 0.00 2.17
4108 5158 2.943036 AACCGAACAAGGCCTAAAGA 57.057 45.000 5.16 0.00 33.69 2.52
4144 5194 4.202253 GCAATACAAAATCCCCTCCAATCC 60.202 45.833 0.00 0.00 0.00 3.01
4199 5249 1.753903 TGAGGTGGATTTGAAGGGGA 58.246 50.000 0.00 0.00 0.00 4.81
4204 5254 2.882137 GTTCGGTTGAGGTGGATTTGAA 59.118 45.455 0.00 0.00 0.00 2.69
4206 5256 2.226330 TGTTCGGTTGAGGTGGATTTG 58.774 47.619 0.00 0.00 0.00 2.32
4285 5336 3.382546 GTGATGATCAACCCAATCCCTTG 59.617 47.826 0.00 0.00 0.00 3.61
4286 5337 3.270433 AGTGATGATCAACCCAATCCCTT 59.730 43.478 0.00 0.00 0.00 3.95
4287 5338 2.854967 AGTGATGATCAACCCAATCCCT 59.145 45.455 0.00 0.00 0.00 4.20
4288 5339 3.303351 AGTGATGATCAACCCAATCCC 57.697 47.619 0.00 0.00 0.00 3.85
4289 5340 4.019174 ACAAGTGATGATCAACCCAATCC 58.981 43.478 0.00 0.00 0.00 3.01
4290 5341 4.701651 TGACAAGTGATGATCAACCCAATC 59.298 41.667 0.00 0.00 0.00 2.67
4291 5342 4.460382 GTGACAAGTGATGATCAACCCAAT 59.540 41.667 0.00 0.00 0.00 3.16
4292 5343 3.820467 GTGACAAGTGATGATCAACCCAA 59.180 43.478 0.00 0.00 0.00 4.12
4293 5344 3.072915 AGTGACAAGTGATGATCAACCCA 59.927 43.478 0.00 0.00 0.00 4.51
4294 5345 3.679389 AGTGACAAGTGATGATCAACCC 58.321 45.455 0.00 0.00 0.00 4.11
4295 5346 4.318332 TGAGTGACAAGTGATGATCAACC 58.682 43.478 0.00 0.00 0.00 3.77
4296 5347 5.929697 TTGAGTGACAAGTGATGATCAAC 57.070 39.130 0.00 0.00 34.20 3.18
4297 5348 5.645067 GGATTGAGTGACAAGTGATGATCAA 59.355 40.000 0.00 0.00 42.02 2.57
4298 5349 5.181009 GGATTGAGTGACAAGTGATGATCA 58.819 41.667 0.00 0.00 42.02 2.92
4299 5350 4.574013 GGGATTGAGTGACAAGTGATGATC 59.426 45.833 0.00 0.00 42.02 2.92
4300 5351 4.226846 AGGGATTGAGTGACAAGTGATGAT 59.773 41.667 0.00 0.00 42.02 2.45
4378 5438 8.461854 TGGGAGGGACAATTTATAGTCTATAGA 58.538 37.037 0.00 0.00 35.18 1.98
4382 5442 6.449956 ACTGGGAGGGACAATTTATAGTCTA 58.550 40.000 0.00 0.00 35.18 2.59
4389 5449 4.463050 ACAAACTGGGAGGGACAATTTA 57.537 40.909 0.00 0.00 0.00 1.40
4409 5469 1.862602 AATCCACGGAGGCGCAAAAC 61.863 55.000 10.83 0.00 37.29 2.43
4476 5540 1.066752 GACAACAACGGCCCAAACC 59.933 57.895 0.00 0.00 0.00 3.27
4477 5541 1.066752 GGACAACAACGGCCCAAAC 59.933 57.895 0.00 0.00 0.00 2.93
4478 5542 2.128507 GGGACAACAACGGCCCAAA 61.129 57.895 0.00 0.00 40.39 3.28
4479 5543 2.519780 GGGACAACAACGGCCCAA 60.520 61.111 0.00 0.00 40.39 4.12
4480 5544 4.589675 GGGGACAACAACGGCCCA 62.590 66.667 3.81 0.00 42.52 5.36
4486 5550 3.656045 CACGGCGGGGACAACAAC 61.656 66.667 13.24 0.00 0.00 3.32
4487 5551 3.185299 ATCACGGCGGGGACAACAA 62.185 57.895 10.28 0.00 0.00 2.83
4488 5552 3.599285 GATCACGGCGGGGACAACA 62.599 63.158 10.28 0.00 0.00 3.33
4489 5553 2.818274 GATCACGGCGGGGACAAC 60.818 66.667 10.28 0.00 0.00 3.32
4490 5554 4.090588 GGATCACGGCGGGGACAA 62.091 66.667 10.28 0.00 0.00 3.18
4492 5556 3.615509 TTTGGATCACGGCGGGGAC 62.616 63.158 10.28 3.30 0.00 4.46
4493 5557 3.323286 TTTGGATCACGGCGGGGA 61.323 61.111 10.28 7.78 0.00 4.81
4494 5558 3.131478 GTTTGGATCACGGCGGGG 61.131 66.667 10.28 0.92 0.00 5.73
4495 5559 3.131478 GGTTTGGATCACGGCGGG 61.131 66.667 13.24 7.61 0.00 6.13
4496 5560 1.519751 TTTGGTTTGGATCACGGCGG 61.520 55.000 13.24 0.00 0.00 6.13
4497 5561 0.386731 GTTTGGTTTGGATCACGGCG 60.387 55.000 4.80 4.80 0.00 6.46
4498 5562 0.671251 TGTTTGGTTTGGATCACGGC 59.329 50.000 0.00 0.00 0.00 5.68
4499 5563 3.243704 ACATTGTTTGGTTTGGATCACGG 60.244 43.478 0.00 0.00 0.00 4.94
4500 5564 3.976169 ACATTGTTTGGTTTGGATCACG 58.024 40.909 0.00 0.00 0.00 4.35
4501 5565 6.512297 ACTTACATTGTTTGGTTTGGATCAC 58.488 36.000 0.00 0.00 0.00 3.06
4502 5566 6.723298 ACTTACATTGTTTGGTTTGGATCA 57.277 33.333 0.00 0.00 0.00 2.92
4505 5569 8.578151 GGTTATACTTACATTGTTTGGTTTGGA 58.422 33.333 0.00 0.00 0.00 3.53
4506 5570 7.815549 GGGTTATACTTACATTGTTTGGTTTGG 59.184 37.037 0.00 0.00 0.00 3.28
4507 5571 8.361139 TGGGTTATACTTACATTGTTTGGTTTG 58.639 33.333 0.00 0.00 0.00 2.93
4508 5572 8.361889 GTGGGTTATACTTACATTGTTTGGTTT 58.638 33.333 0.00 0.00 0.00 3.27
4509 5573 7.308710 CGTGGGTTATACTTACATTGTTTGGTT 60.309 37.037 0.00 0.00 0.00 3.67
4530 5594 0.604511 GGGGAACTGTTACACGTGGG 60.605 60.000 21.57 6.83 0.00 4.61
4533 5597 1.343465 CAGAGGGGAACTGTTACACGT 59.657 52.381 4.94 0.00 0.00 4.49
4552 5616 0.613572 TATCCACGTGGGCTGTCTCA 60.614 55.000 33.40 12.86 36.21 3.27
4553 5617 0.103208 CTATCCACGTGGGCTGTCTC 59.897 60.000 33.40 0.00 36.21 3.36
4554 5618 0.324368 TCTATCCACGTGGGCTGTCT 60.324 55.000 33.40 13.93 36.21 3.41
4558 5622 0.614979 ACACTCTATCCACGTGGGCT 60.615 55.000 33.40 22.75 36.21 5.19
4571 5635 1.211457 GAATGCCAGGGATCACACTCT 59.789 52.381 0.00 0.00 0.00 3.24
4572 5636 1.673168 GAATGCCAGGGATCACACTC 58.327 55.000 0.00 0.00 0.00 3.51
4607 9562 6.370453 ACAACCTTAGGTCTTGTTTGGTTAT 58.630 36.000 3.62 0.00 33.12 1.89
4620 9575 4.790718 ACTCCTCAAAACAACCTTAGGT 57.209 40.909 0.00 0.00 37.65 3.08
4696 9652 6.433716 TGATCACTGATTCACTATGCCAAAAA 59.566 34.615 0.00 0.00 0.00 1.94
4724 9680 0.729116 GAAGTGGCACGTCATGATGG 59.271 55.000 25.35 9.08 0.00 3.51
4808 9764 9.113838 CCACATGCTTCTTCTATAACTACATTT 57.886 33.333 0.00 0.00 0.00 2.32
4824 9780 4.507710 TCTAGAATGTCACCACATGCTTC 58.492 43.478 0.84 0.00 45.75 3.86
4848 9804 5.674052 AAATGGTGCAGCATGGTTTAATA 57.326 34.783 30.51 0.00 35.86 0.98
4853 9809 2.899256 AGTTAAATGGTGCAGCATGGTT 59.101 40.909 30.51 23.14 35.86 3.67
4854 9810 2.231964 CAGTTAAATGGTGCAGCATGGT 59.768 45.455 30.51 22.77 35.86 3.55
4936 9892 4.318332 CAGAAATGAAGACCACTACAGCA 58.682 43.478 0.00 0.00 0.00 4.41
5036 9992 7.121974 TGAAAAACAACGATCAGAAGATCTC 57.878 36.000 0.00 0.00 46.84 2.75
5132 10088 1.000233 CGCACAGCATCAGTGTTTGC 61.000 55.000 11.34 11.34 39.17 3.68
5136 10092 0.532640 TTGTCGCACAGCATCAGTGT 60.533 50.000 0.00 0.00 39.17 3.55
5293 10249 1.547675 GCACCAGTTCTCCCAATTCCA 60.548 52.381 0.00 0.00 0.00 3.53
5395 10351 1.726853 CAGTTCGCTGGGACCTAAAG 58.273 55.000 0.00 0.00 41.40 1.85
5436 10392 7.033791 TGATAGGAGTACGAATGAAACAGAAC 58.966 38.462 0.00 0.00 0.00 3.01
5622 10582 3.641437 TTACACAGCAGGCAATGTTTC 57.359 42.857 5.87 0.00 0.00 2.78
5726 10686 6.437755 TGATCAAATTCAAGGATGAGGGAAT 58.562 36.000 0.00 0.00 36.78 3.01
5752 10712 3.706855 TGCTATGGCAGGTGTCGA 58.293 55.556 0.00 0.00 44.28 4.20
5835 10795 7.772332 ATAAGATACTAAACCAGCTTCGTTG 57.228 36.000 0.00 0.00 0.00 4.10
5881 10867 6.653320 TGTATTGGAATTACTGACCACAACTC 59.347 38.462 0.00 0.00 33.20 3.01
5890 10876 7.016153 AGGAACTGTGTATTGGAATTACTGA 57.984 36.000 0.00 0.00 37.18 3.41
5914 10900 5.066375 GCAGTATTAGATGCAATGGTCAACA 59.934 40.000 0.00 0.00 42.11 3.33
6110 11204 3.726607 CATCTTGCAGCCTACCTTAGAG 58.273 50.000 0.00 0.00 0.00 2.43
6241 11393 3.493503 GGAAATAGAAGGGCGACAATACG 59.506 47.826 0.00 0.00 0.00 3.06
6335 11487 7.445402 ACAAGCAGTTGTCTTAACAATACTGAT 59.555 33.333 12.32 5.34 43.88 2.90
6398 11575 3.055891 GGAATGGGCTGTTTACATGCTTT 60.056 43.478 0.00 0.00 0.00 3.51
6491 11679 0.749454 ACGCCTGGCATTCATCTTCC 60.749 55.000 20.29 0.00 0.00 3.46
6513 11701 5.403766 CGATGCATTGGTCTCATCTAACTAC 59.596 44.000 5.98 0.00 35.64 2.73
6673 11895 7.559845 GCTTTAGTGATCTAAACGCTCTTATG 58.440 38.462 0.00 0.00 40.05 1.90
6698 11922 3.325870 TGAGATTTTGCTAGTGGTCACG 58.674 45.455 0.00 0.00 36.20 4.35
6704 11928 2.540361 GCCGCATGAGATTTTGCTAGTG 60.540 50.000 0.00 0.00 36.71 2.74
6750 11974 3.007182 CCTACAAAGGTCGGTCCAGTTAA 59.993 47.826 0.00 0.00 38.19 2.01
6757 11981 0.320697 AGTGCCTACAAAGGTCGGTC 59.679 55.000 0.00 0.00 45.64 4.79
6771 12149 2.031163 AGGCTTCGTGACAGTGCC 59.969 61.111 0.00 0.00 43.52 5.01
6839 12367 5.401550 CAATGCACATTTACGAAACCAGAT 58.598 37.500 0.00 0.00 0.00 2.90
6954 13170 2.556287 CAGCAAACCGGCTTCGAC 59.444 61.111 0.00 0.00 42.71 4.20
7011 13245 1.378119 CAGGCTTGCAGATGAGGCA 60.378 57.895 11.74 0.00 40.58 4.75
7064 13298 2.634777 GCGGAGAGGACGATCGAG 59.365 66.667 24.34 3.50 0.00 4.04


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

AutoCloner maintained by Alex Coulton.