Multiple sequence alignment - TraesCS4B01G362000

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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 TraesCS4B01G362000 chr4B 100.000 4944 0 0 1 4944 650971572 650976515 0.000000e+00 9130.0
1 TraesCS4B01G362000 chr4B 88.983 590 22 6 3492 4042 651906938 651906353 0.000000e+00 689.0
2 TraesCS4B01G362000 chr4B 97.248 218 6 0 4461 4678 651752179 651752396 2.170000e-98 370.0
3 TraesCS4B01G362000 chr4B 95.897 195 7 1 2884 3078 651771057 651771250 1.030000e-81 315.0
4 TraesCS4B01G362000 chr4B 90.411 219 21 0 4705 4923 649529217 649529435 6.260000e-74 289.0
5 TraesCS4B01G362000 chr4B 88.584 219 25 0 4705 4923 649532168 649531950 2.930000e-67 267.0
6 TraesCS4B01G362000 chr4B 95.758 165 5 1 3142 3304 651908971 651908807 1.060000e-66 265.0
7 TraesCS4B01G362000 chr4B 94.444 162 5 3 3341 3500 651908806 651908647 3.820000e-61 246.0
8 TraesCS4B01G362000 chr4B 96.226 53 2 0 3087 3139 651913613 651913561 2.450000e-13 87.9
9 TraesCS4B01G362000 chr5A 94.128 4070 130 27 1 4021 688984238 688988247 0.000000e+00 6091.0
10 TraesCS4B01G362000 chr5A 94.599 611 7 9 4112 4696 688988246 688988856 0.000000e+00 922.0
11 TraesCS4B01G362000 chr5A 90.833 120 11 0 2768 2887 480631422 480631541 1.420000e-35 161.0
12 TraesCS4B01G362000 chr4D 94.747 1504 45 12 1 1481 504339863 504341355 0.000000e+00 2309.0
13 TraesCS4B01G362000 chr4D 95.310 1258 44 5 1524 2772 504341353 504342604 0.000000e+00 1982.0
14 TraesCS4B01G362000 chr4D 94.000 1200 31 9 2884 4049 504342601 504343793 0.000000e+00 1779.0
15 TraesCS4B01G362000 chr4D 91.085 931 41 21 1200 2122 505229183 505228287 0.000000e+00 1221.0
16 TraesCS4B01G362000 chr4D 98.176 603 11 0 4076 4678 504343791 504344393 0.000000e+00 1053.0
17 TraesCS4B01G362000 chr4D 95.681 602 20 4 2884 3481 505193566 505192967 0.000000e+00 963.0
18 TraesCS4B01G362000 chr4D 92.647 544 24 5 2239 2772 505194100 505193563 0.000000e+00 769.0
19 TraesCS4B01G362000 chr4D 89.445 559 28 2 3531 4058 505192967 505192409 0.000000e+00 676.0
20 TraesCS4B01G362000 chr4D 91.260 389 16 5 4076 4464 505192420 505192050 9.490000e-142 514.0
21 TraesCS4B01G362000 chr4D 99.020 204 2 0 4475 4678 505190208 505190005 2.810000e-97 366.0
22 TraesCS4B01G362000 chr4D 96.703 91 2 1 2112 2201 505194186 505194096 3.080000e-32 150.0
23 TraesCS4B01G362000 chr3A 94.477 344 16 1 3678 4021 691210002 691210342 1.220000e-145 527.0
24 TraesCS4B01G362000 chr3A 97.727 132 3 0 4112 4243 691210341 691210472 1.380000e-55 228.0
25 TraesCS4B01G362000 chr7B 94.186 344 17 1 3678 4021 630508371 630508711 5.670000e-144 521.0
26 TraesCS4B01G362000 chr7B 96.970 132 4 0 4112 4243 6963803 6963934 6.440000e-54 222.0
27 TraesCS4B01G362000 chr7B 96.212 132 5 0 4112 4243 630508710 630508841 3.000000e-52 217.0
28 TraesCS4B01G362000 chr5B 94.186 344 17 1 3678 4021 23307041 23306701 5.670000e-144 521.0
29 TraesCS4B01G362000 chr5B 91.121 214 18 1 4706 4918 530922696 530922483 6.260000e-74 289.0
30 TraesCS4B01G362000 chr6A 93.605 344 18 2 3678 4021 245228678 245228339 1.230000e-140 510.0
31 TraesCS4B01G362000 chr6A 89.316 234 23 2 4709 4941 93889012 93888780 4.840000e-75 292.0
32 TraesCS4B01G362000 chr6A 89.450 218 23 0 4703 4920 66269664 66269447 4.880000e-70 276.0
33 TraesCS4B01G362000 chr6A 96.947 131 4 0 4112 4242 245228340 245228210 2.320000e-53 220.0
34 TraesCS4B01G362000 chr6A 95.556 135 6 0 4112 4246 53686252 53686118 3.000000e-52 217.0
35 TraesCS4B01G362000 chr6A 96.212 132 5 0 4112 4243 62872572 62872703 3.000000e-52 217.0
36 TraesCS4B01G362000 chr3B 93.605 344 19 1 3678 4021 185527438 185527778 1.230000e-140 510.0
37 TraesCS4B01G362000 chr3B 96.970 132 4 0 4112 4243 185527777 185527908 6.440000e-54 222.0
38 TraesCS4B01G362000 chr4A 92.694 219 16 0 4705 4923 611198300 611198518 2.870000e-82 316.0
39 TraesCS4B01G362000 chr4A 83.200 250 32 9 2416 2659 1512869 1512624 2.320000e-53 220.0
40 TraesCS4B01G362000 chr4A 92.941 85 6 0 764 848 723510643 723510727 1.870000e-24 124.0
41 TraesCS4B01G362000 chr2A 90.000 220 21 1 4704 4923 277334659 277334441 2.910000e-72 283.0
42 TraesCS4B01G362000 chr2A 89.431 123 13 0 2768 2890 137121475 137121353 6.630000e-34 156.0
43 TraesCS4B01G362000 chr3D 89.815 216 22 0 4708 4923 32355404 32355619 1.360000e-70 278.0
44 TraesCS4B01G362000 chr2B 88.362 232 25 2 4714 4944 665149667 665149897 1.360000e-70 278.0
45 TraesCS4B01G362000 chr2B 90.110 91 9 0 4020 4110 74002833 74002923 8.690000e-23 119.0
46 TraesCS4B01G362000 chr2B 88.660 97 11 0 4017 4113 164901375 164901471 8.690000e-23 119.0
47 TraesCS4B01G362000 chr7D 90.625 128 10 2 2763 2890 33478576 33478451 8.510000e-38 169.0
48 TraesCS4B01G362000 chr7D 88.542 96 7 3 4020 4113 479747784 479747877 4.040000e-21 113.0
49 TraesCS4B01G362000 chr7D 87.500 96 12 0 4020 4115 235576920 235577015 1.450000e-20 111.0
50 TraesCS4B01G362000 chr2D 90.984 122 11 0 2767 2888 441085887 441085766 1.100000e-36 165.0
51 TraesCS4B01G362000 chr2D 91.525 118 10 0 2771 2888 610294415 610294532 3.960000e-36 163.0
52 TraesCS4B01G362000 chr2D 88.660 97 11 0 4017 4113 114517563 114517659 8.690000e-23 119.0
53 TraesCS4B01G362000 chr6B 91.525 118 10 0 2770 2887 188191525 188191642 3.960000e-36 163.0
54 TraesCS4B01G362000 chr1B 90.323 124 12 0 2768 2891 3240090 3239967 3.960000e-36 163.0
55 TraesCS4B01G362000 chr7A 85.417 144 19 2 2760 2901 17417377 17417234 1.110000e-31 148.0
56 TraesCS4B01G362000 chr5D 89.691 97 8 2 4020 4115 530605393 530605298 6.720000e-24 122.0
57 TraesCS4B01G362000 chr1A 89.362 94 10 0 4020 4113 508144323 508144416 8.690000e-23 119.0
58 TraesCS4B01G362000 chr1A 88.000 100 7 4 4016 4113 566218176 566218080 4.040000e-21 113.0


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 TraesCS4B01G362000 chr4B 650971572 650976515 4943 False 9130.00 9130 100.000000 1 4944 1 chr4B.!!$F2 4943
1 TraesCS4B01G362000 chr4B 651906353 651908971 2618 True 400.00 689 93.061667 3142 4042 3 chr4B.!!$R3 900
2 TraesCS4B01G362000 chr5A 688984238 688988856 4618 False 3506.50 6091 94.363500 1 4696 2 chr5A.!!$F2 4695
3 TraesCS4B01G362000 chr4D 504339863 504344393 4530 False 1780.75 2309 95.558250 1 4678 4 chr4D.!!$F1 4677
4 TraesCS4B01G362000 chr4D 505228287 505229183 896 True 1221.00 1221 91.085000 1200 2122 1 chr4D.!!$R1 922
5 TraesCS4B01G362000 chr4D 505190005 505194186 4181 True 573.00 963 94.126000 2112 4678 6 chr4D.!!$R2 2566

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
917 962 0.252197 GGCCATTGGAGTACTCGGTT 59.748 55.000 16.56 0.73 0.00 4.44 F
2342 2426 1.948834 TCCTGAACCAATGCATATGCG 59.051 47.619 22.21 10.66 45.83 4.73 F
2879 2963 2.094390 CCGACAAGTATTTCCGGACAGA 60.094 50.000 1.83 0.00 42.49 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2422 2506 0.598065 AAAGCTGACCGACCAAATGC 59.402 50.000 0.00 0.00 0.00 3.56 R
3249 3335 1.062365 CATTGCATGGTACCGCACG 59.938 57.895 13.36 5.25 35.48 5.34 R
4718 8420 0.112412 CAAGTTAGGGCACTTGGGGT 59.888 55.000 0.00 0.00 46.84 4.95 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
216 236 7.672983 TTCTGTTGATTTGATTAGGAGTGAC 57.327 36.000 0.00 0.00 0.00 3.67
221 241 8.567948 TGTTGATTTGATTAGGAGTGACTTTTC 58.432 33.333 0.00 0.00 0.00 2.29
267 287 1.338020 GGATGCCGGATTCAATTGGAC 59.662 52.381 5.05 0.00 0.00 4.02
352 372 0.692476 CCCATCACCACAGAGTCCAA 59.308 55.000 0.00 0.00 0.00 3.53
450 470 6.257193 GCTTATTGCCATTGAATCTTTGAAGG 59.743 38.462 0.00 0.00 35.15 3.46
501 522 7.099764 CGCATACTAGATTTCCCAATATGTCT 58.900 38.462 0.00 0.00 0.00 3.41
525 547 4.384056 CCACTGCTCTTTGGTCCATATAG 58.616 47.826 0.00 0.00 0.00 1.31
527 553 4.813161 CACTGCTCTTTGGTCCATATAGTG 59.187 45.833 0.00 0.00 0.00 2.74
616 642 1.334556 TCAGCTGTTGAATGTGTGTGC 59.665 47.619 14.67 0.00 31.34 4.57
747 773 4.252073 GGCAATTTTGATTATGCACCACA 58.748 39.130 0.00 0.00 40.51 4.17
749 775 5.354792 GGCAATTTTGATTATGCACCACATT 59.645 36.000 0.00 0.00 40.38 2.71
750 776 6.252281 GCAATTTTGATTATGCACCACATTG 58.748 36.000 0.00 0.00 40.38 2.82
751 777 6.092396 GCAATTTTGATTATGCACCACATTGA 59.908 34.615 0.00 0.00 40.38 2.57
752 778 7.675403 GCAATTTTGATTATGCACCACATTGAG 60.675 37.037 0.00 0.00 40.38 3.02
753 779 5.981088 TTTGATTATGCACCACATTGAGT 57.019 34.783 0.00 0.00 40.38 3.41
754 780 7.459795 TTTTGATTATGCACCACATTGAGTA 57.540 32.000 0.00 0.00 40.38 2.59
755 781 7.459795 TTTGATTATGCACCACATTGAGTAA 57.540 32.000 0.00 0.00 40.38 2.24
756 782 7.459795 TTGATTATGCACCACATTGAGTAAA 57.540 32.000 0.00 0.00 40.38 2.01
757 783 7.459795 TGATTATGCACCACATTGAGTAAAA 57.540 32.000 0.00 0.00 40.38 1.52
758 784 7.537715 TGATTATGCACCACATTGAGTAAAAG 58.462 34.615 0.00 0.00 40.38 2.27
759 785 4.789012 ATGCACCACATTGAGTAAAAGG 57.211 40.909 0.00 0.00 34.40 3.11
760 786 2.890311 TGCACCACATTGAGTAAAAGGG 59.110 45.455 0.00 0.00 0.00 3.95
761 787 2.890945 GCACCACATTGAGTAAAAGGGT 59.109 45.455 0.00 0.00 0.00 4.34
762 788 3.320826 GCACCACATTGAGTAAAAGGGTT 59.679 43.478 0.00 0.00 0.00 4.11
763 789 4.202212 GCACCACATTGAGTAAAAGGGTTT 60.202 41.667 0.00 0.00 0.00 3.27
764 790 5.683770 GCACCACATTGAGTAAAAGGGTTTT 60.684 40.000 0.00 0.00 36.67 2.43
765 791 6.461788 GCACCACATTGAGTAAAAGGGTTTTA 60.462 38.462 0.00 0.00 34.19 1.52
766 792 7.145323 CACCACATTGAGTAAAAGGGTTTTAG 58.855 38.462 0.00 0.00 35.91 1.85
767 793 7.013846 CACCACATTGAGTAAAAGGGTTTTAGA 59.986 37.037 0.00 0.00 35.91 2.10
777 822 8.803235 AGTAAAAGGGTTTTAGATGTGAAATCC 58.197 33.333 1.41 1.41 35.91 3.01
917 962 0.252197 GGCCATTGGAGTACTCGGTT 59.748 55.000 16.56 0.73 0.00 4.44
1045 1090 2.781681 AAAACCAGAGGTATGACCCG 57.218 50.000 0.00 0.00 39.75 5.28
1055 1100 4.134563 GAGGTATGACCCGTGCATTTATT 58.865 43.478 0.00 0.00 39.75 1.40
1078 1123 3.383185 AGTTTGGAATTCGTTTGCCTTGA 59.617 39.130 0.00 0.00 0.00 3.02
1229 1274 6.384258 TGTCGAGAAATTGTCAAAAATGGA 57.616 33.333 0.00 0.00 0.00 3.41
1356 1401 4.320870 CTCCAACAAGGTACCGTATGTTT 58.679 43.478 22.93 11.53 39.02 2.83
1432 1483 2.009774 CTTCAACCCATGGACATCGTC 58.990 52.381 15.22 0.00 0.00 4.20
1517 1581 8.737168 TTACTTTCTCACCATAAGGATGATTG 57.263 34.615 0.00 0.00 38.69 2.67
1526 1590 5.533903 ACCATAAGGATGATTGTCTGAATGC 59.466 40.000 0.00 0.00 38.69 3.56
1584 1648 7.016153 ACTTGGATGTTGTATTCTGTTAGGA 57.984 36.000 0.00 0.00 0.00 2.94
1645 1709 9.528489 TGTTCCAGTTATCTTATTAGGCTTTTT 57.472 29.630 0.00 0.00 0.00 1.94
1859 1923 3.592059 TGACTTAACGGAGGCATGTAAC 58.408 45.455 0.00 0.00 27.08 2.50
1905 1969 9.358872 GCAGGAGTTTTCTTTATTAATTTGAGG 57.641 33.333 0.00 0.00 0.00 3.86
2342 2426 1.948834 TCCTGAACCAATGCATATGCG 59.051 47.619 22.21 10.66 45.83 4.73
2422 2506 5.128827 TCCCTGCCAGTTAGTAGTAATTGAG 59.871 44.000 12.98 4.98 29.39 3.02
2461 2545 5.301298 GCTTTTCATGAGCTCCCATATTTCT 59.699 40.000 12.15 0.00 37.18 2.52
2468 2552 5.674525 TGAGCTCCCATATTTCTGTAACTG 58.325 41.667 12.15 0.00 0.00 3.16
2475 2559 7.466804 TCCCATATTTCTGTAACTGGTTTCTT 58.533 34.615 0.00 0.00 0.00 2.52
2512 2596 3.873910 ACGGATTTTATGTCTGACTGGG 58.126 45.455 9.51 0.00 0.00 4.45
2612 2696 9.262358 GGTACTGTAAAGCTTTAGATTATCTGG 57.738 37.037 19.16 7.01 0.00 3.86
2806 2890 6.934645 TCTGAAAATACTTGTCGGAGAAATGT 59.065 34.615 0.00 0.00 39.69 2.71
2821 2905 6.797513 CGGAGAAATGTATGTATCTAGACGTG 59.202 42.308 0.00 0.00 0.00 4.49
2838 2922 9.531942 TCTAGACGTGTTTTAGTTCAAAATACA 57.468 29.630 0.00 0.00 44.24 2.29
2879 2963 2.094390 CCGACAAGTATTTCCGGACAGA 60.094 50.000 1.83 0.00 42.49 3.41
2959 3043 4.724399 TGAGCTTGGTTACCATTTCAAGA 58.276 39.130 4.38 0.00 38.96 3.02
3022 3106 4.750021 TCTCCATCAGTCTTTCCTCATG 57.250 45.455 0.00 0.00 0.00 3.07
3249 3335 1.002011 GTTCAGGAGGAAGGTGCCC 60.002 63.158 0.00 0.00 35.82 5.36
3406 3492 5.908247 AGGAAGAGCTTGATAGGTAAGGAAT 59.092 40.000 0.00 0.00 30.79 3.01
3507 5312 1.783979 TGGGTTGAAGTGTTATGGGGT 59.216 47.619 0.00 0.00 0.00 4.95
3593 5412 0.258774 ACCCCTGTTTGTGCTCACTT 59.741 50.000 1.47 0.00 0.00 3.16
3749 5594 5.277974 CGAATTTACTGCCCATATTCCTGTG 60.278 44.000 0.00 0.00 0.00 3.66
3766 5611 4.503314 GCCAAAGCCCTCATGCGC 62.503 66.667 0.00 0.00 36.02 6.09
3774 5619 0.038892 GCCCTCATGCGCATTAATGG 60.039 55.000 22.81 18.97 0.00 3.16
3979 5824 6.042208 AGTGAGTATAGAATTTAGCCCACTCC 59.958 42.308 0.00 0.00 32.15 3.85
4028 5873 5.848833 AGGTTTTACATACTACTCCCTCG 57.151 43.478 0.00 0.00 0.00 4.63
4042 5887 4.351127 ACTCCCTCGGTCCCATAATATAC 58.649 47.826 0.00 0.00 0.00 1.47
4046 5891 4.202121 CCCTCGGTCCCATAATATACGATG 60.202 50.000 0.00 0.00 0.00 3.84
4047 5892 4.401519 CCTCGGTCCCATAATATACGATGT 59.598 45.833 0.00 0.00 0.00 3.06
4048 5893 5.105473 CCTCGGTCCCATAATATACGATGTT 60.105 44.000 0.00 0.00 0.00 2.71
4049 5894 6.095860 CCTCGGTCCCATAATATACGATGTTA 59.904 42.308 0.00 0.00 0.00 2.41
4050 5895 7.201884 CCTCGGTCCCATAATATACGATGTTAT 60.202 40.741 0.00 0.00 0.00 1.89
4051 5896 8.070034 TCGGTCCCATAATATACGATGTTATT 57.930 34.615 0.00 0.00 0.00 1.40
4052 5897 9.187996 TCGGTCCCATAATATACGATGTTATTA 57.812 33.333 0.00 0.00 0.00 0.98
4053 5898 9.241317 CGGTCCCATAATATACGATGTTATTAC 57.759 37.037 0.00 0.00 0.00 1.89
4067 5912 9.249457 ACGATGTTATTACAACAGATGTATGAG 57.751 33.333 0.00 0.00 43.84 2.90
4068 5913 9.249457 CGATGTTATTACAACAGATGTATGAGT 57.751 33.333 0.00 0.00 43.84 3.41
4086 5931 9.830294 TGTATGAGTATATCGGTTGTAATAACG 57.170 33.333 0.00 0.00 0.00 3.18
4183 6028 2.025981 TGCACCAGCTCATTCCATAACT 60.026 45.455 0.00 0.00 42.74 2.24
4208 6075 6.376864 TGGGTCAAGTGATAATTTGTATGTGG 59.623 38.462 0.00 0.00 0.00 4.17
4235 6102 2.493278 GGGTTCAATCACAGGTGAATGG 59.507 50.000 15.37 5.19 43.58 3.16
4271 6138 1.470494 GCAAGCTGAAGCCTAGGAAAC 59.530 52.381 14.75 2.64 43.38 2.78
4390 6257 4.248058 CATCTGTTTCCCTTTGCCATTTC 58.752 43.478 0.00 0.00 0.00 2.17
4696 8398 4.274705 TGTGTTGCTGACGTTGAAATACAT 59.725 37.500 8.12 0.00 0.00 2.29
4697 8399 5.467063 TGTGTTGCTGACGTTGAAATACATA 59.533 36.000 8.12 0.00 0.00 2.29
4698 8400 5.788531 GTGTTGCTGACGTTGAAATACATAC 59.211 40.000 0.00 0.00 0.00 2.39
4699 8401 5.467063 TGTTGCTGACGTTGAAATACATACA 59.533 36.000 0.00 0.00 0.00 2.29
4700 8402 5.778161 TGCTGACGTTGAAATACATACAG 57.222 39.130 0.00 0.00 0.00 2.74
4701 8403 4.629634 TGCTGACGTTGAAATACATACAGG 59.370 41.667 0.00 0.00 0.00 4.00
4702 8404 4.868171 GCTGACGTTGAAATACATACAGGA 59.132 41.667 0.00 0.00 0.00 3.86
4703 8405 5.350365 GCTGACGTTGAAATACATACAGGAA 59.650 40.000 0.00 0.00 0.00 3.36
4704 8406 6.128391 GCTGACGTTGAAATACATACAGGAAA 60.128 38.462 0.00 0.00 0.00 3.13
4705 8407 7.572353 GCTGACGTTGAAATACATACAGGAAAA 60.572 37.037 0.00 0.00 0.00 2.29
4706 8408 8.330466 TGACGTTGAAATACATACAGGAAAAT 57.670 30.769 0.00 0.00 0.00 1.82
4707 8409 8.233868 TGACGTTGAAATACATACAGGAAAATG 58.766 33.333 0.00 0.00 0.00 2.32
4708 8410 8.330466 ACGTTGAAATACATACAGGAAAATGA 57.670 30.769 0.00 0.00 0.00 2.57
4709 8411 8.450964 ACGTTGAAATACATACAGGAAAATGAG 58.549 33.333 0.00 0.00 0.00 2.90
4710 8412 7.910162 CGTTGAAATACATACAGGAAAATGAGG 59.090 37.037 0.00 0.00 0.00 3.86
4711 8413 8.739972 GTTGAAATACATACAGGAAAATGAGGT 58.260 33.333 0.00 0.00 0.00 3.85
4712 8414 9.967451 TTGAAATACATACAGGAAAATGAGGTA 57.033 29.630 0.00 0.00 0.00 3.08
4713 8415 9.967451 TGAAATACATACAGGAAAATGAGGTAA 57.033 29.630 0.00 0.00 0.00 2.85
4717 8419 9.726438 ATACATACAGGAAAATGAGGTAATAGC 57.274 33.333 0.00 0.00 0.00 2.97
4718 8420 7.573710 ACATACAGGAAAATGAGGTAATAGCA 58.426 34.615 0.00 0.00 0.00 3.49
4719 8421 7.499232 ACATACAGGAAAATGAGGTAATAGCAC 59.501 37.037 0.00 0.00 0.00 4.40
4720 8422 5.193679 ACAGGAAAATGAGGTAATAGCACC 58.806 41.667 0.00 0.00 39.02 5.01
4721 8423 4.580580 CAGGAAAATGAGGTAATAGCACCC 59.419 45.833 0.00 0.00 39.62 4.61
4722 8424 3.889538 GGAAAATGAGGTAATAGCACCCC 59.110 47.826 0.00 0.00 39.62 4.95
4723 8425 4.532834 GAAAATGAGGTAATAGCACCCCA 58.467 43.478 0.00 0.00 39.62 4.96
4724 8426 4.601406 AAATGAGGTAATAGCACCCCAA 57.399 40.909 0.00 0.00 39.62 4.12
4725 8427 3.864789 ATGAGGTAATAGCACCCCAAG 57.135 47.619 0.00 0.00 39.62 3.61
4726 8428 2.557869 TGAGGTAATAGCACCCCAAGT 58.442 47.619 0.00 0.00 39.62 3.16
4734 8436 4.415783 CACCCCAAGTGCCCTAAC 57.584 61.111 0.00 0.00 40.28 2.34
4735 8437 1.767692 CACCCCAAGTGCCCTAACT 59.232 57.895 0.00 0.00 40.28 2.24
4736 8438 0.112412 CACCCCAAGTGCCCTAACTT 59.888 55.000 0.00 0.00 40.28 2.66
4745 8447 2.584835 TGCCCTAACTTGCACAGAAT 57.415 45.000 0.00 0.00 31.31 2.40
4746 8448 2.161855 TGCCCTAACTTGCACAGAATG 58.838 47.619 0.00 0.00 46.00 2.67
4764 8466 7.827819 CAGAATGTGACGATTTAGTCCTAAA 57.172 36.000 2.21 2.21 40.26 1.85
4765 8467 7.899974 CAGAATGTGACGATTTAGTCCTAAAG 58.100 38.462 5.78 0.00 40.26 1.85
4766 8468 7.545965 CAGAATGTGACGATTTAGTCCTAAAGT 59.454 37.037 5.78 0.00 40.26 2.66
4767 8469 8.095169 AGAATGTGACGATTTAGTCCTAAAGTT 58.905 33.333 5.78 0.00 40.26 2.66
4768 8470 7.596749 ATGTGACGATTTAGTCCTAAAGTTG 57.403 36.000 5.78 1.48 40.26 3.16
4769 8471 5.407387 TGTGACGATTTAGTCCTAAAGTTGC 59.593 40.000 5.78 0.00 40.26 4.17
4770 8472 5.407387 GTGACGATTTAGTCCTAAAGTTGCA 59.593 40.000 5.78 0.00 40.26 4.08
4771 8473 5.992829 TGACGATTTAGTCCTAAAGTTGCAA 59.007 36.000 0.00 0.00 40.26 4.08
4772 8474 6.483974 TGACGATTTAGTCCTAAAGTTGCAAA 59.516 34.615 0.00 0.00 40.26 3.68
4773 8475 7.012515 TGACGATTTAGTCCTAAAGTTGCAAAA 59.987 33.333 0.00 0.00 40.26 2.44
4774 8476 7.136772 ACGATTTAGTCCTAAAGTTGCAAAAC 58.863 34.615 0.00 0.00 38.30 2.43
4775 8477 7.012989 ACGATTTAGTCCTAAAGTTGCAAAACT 59.987 33.333 0.00 0.00 38.30 2.66
4776 8478 7.860872 CGATTTAGTCCTAAAGTTGCAAAACTT 59.139 33.333 0.00 0.00 44.25 2.66
4777 8479 8.871686 ATTTAGTCCTAAAGTTGCAAAACTTG 57.128 30.769 0.00 0.00 41.76 3.16
4778 8480 7.633193 TTAGTCCTAAAGTTGCAAAACTTGA 57.367 32.000 0.00 0.00 41.76 3.02
4779 8481 5.891451 AGTCCTAAAGTTGCAAAACTTGAC 58.109 37.500 0.00 6.44 41.76 3.18
4780 8482 5.652452 AGTCCTAAAGTTGCAAAACTTGACT 59.348 36.000 13.19 13.19 41.76 3.41
4781 8483 5.971792 GTCCTAAAGTTGCAAAACTTGACTC 59.028 40.000 0.00 0.00 41.76 3.36
4782 8484 5.067283 TCCTAAAGTTGCAAAACTTGACTCC 59.933 40.000 0.00 0.00 41.76 3.85
4783 8485 4.799564 AAAGTTGCAAAACTTGACTCCA 57.200 36.364 0.00 0.00 41.76 3.86
4784 8486 3.782889 AGTTGCAAAACTTGACTCCAC 57.217 42.857 0.00 0.00 0.00 4.02
4785 8487 2.427095 AGTTGCAAAACTTGACTCCACC 59.573 45.455 0.00 0.00 0.00 4.61
4786 8488 2.136298 TGCAAAACTTGACTCCACCA 57.864 45.000 0.00 0.00 0.00 4.17
4787 8489 2.665165 TGCAAAACTTGACTCCACCAT 58.335 42.857 0.00 0.00 0.00 3.55
4788 8490 3.826524 TGCAAAACTTGACTCCACCATA 58.173 40.909 0.00 0.00 0.00 2.74
4789 8491 3.568007 TGCAAAACTTGACTCCACCATAC 59.432 43.478 0.00 0.00 0.00 2.39
4790 8492 3.057526 GCAAAACTTGACTCCACCATACC 60.058 47.826 0.00 0.00 0.00 2.73
4791 8493 4.141287 CAAAACTTGACTCCACCATACCA 58.859 43.478 0.00 0.00 0.00 3.25
4792 8494 3.418684 AACTTGACTCCACCATACCAC 57.581 47.619 0.00 0.00 0.00 4.16
4793 8495 2.334977 ACTTGACTCCACCATACCACA 58.665 47.619 0.00 0.00 0.00 4.17
4794 8496 2.708861 ACTTGACTCCACCATACCACAA 59.291 45.455 0.00 0.00 0.00 3.33
4795 8497 2.851263 TGACTCCACCATACCACAAC 57.149 50.000 0.00 0.00 0.00 3.32
4796 8498 2.334977 TGACTCCACCATACCACAACT 58.665 47.619 0.00 0.00 0.00 3.16
4797 8499 2.708861 TGACTCCACCATACCACAACTT 59.291 45.455 0.00 0.00 0.00 2.66
4798 8500 3.074412 GACTCCACCATACCACAACTTG 58.926 50.000 0.00 0.00 0.00 3.16
4799 8501 1.812571 CTCCACCATACCACAACTTGC 59.187 52.381 0.00 0.00 0.00 4.01
4800 8502 1.143889 TCCACCATACCACAACTTGCA 59.856 47.619 0.00 0.00 0.00 4.08
4801 8503 1.269448 CCACCATACCACAACTTGCAC 59.731 52.381 0.00 0.00 0.00 4.57
4802 8504 1.269448 CACCATACCACAACTTGCACC 59.731 52.381 0.00 0.00 0.00 5.01
4803 8505 1.144913 ACCATACCACAACTTGCACCT 59.855 47.619 0.00 0.00 0.00 4.00
4804 8506 2.238521 CCATACCACAACTTGCACCTT 58.761 47.619 0.00 0.00 0.00 3.50
4805 8507 3.181438 ACCATACCACAACTTGCACCTTA 60.181 43.478 0.00 0.00 0.00 2.69
4806 8508 4.016444 CCATACCACAACTTGCACCTTAT 58.984 43.478 0.00 0.00 0.00 1.73
4807 8509 4.142403 CCATACCACAACTTGCACCTTATG 60.142 45.833 0.00 0.00 0.00 1.90
4808 8510 2.944129 ACCACAACTTGCACCTTATGT 58.056 42.857 0.00 0.00 0.00 2.29
4823 8525 6.575244 ACCTTATGTGATGATTTAGTCCCA 57.425 37.500 0.00 0.00 0.00 4.37
4824 8526 6.595682 ACCTTATGTGATGATTTAGTCCCAG 58.404 40.000 0.00 0.00 0.00 4.45
4825 8527 6.000219 CCTTATGTGATGATTTAGTCCCAGG 59.000 44.000 0.00 0.00 0.00 4.45
4826 8528 6.409695 CCTTATGTGATGATTTAGTCCCAGGT 60.410 42.308 0.00 0.00 0.00 4.00
4827 8529 4.487714 TGTGATGATTTAGTCCCAGGTC 57.512 45.455 0.00 0.00 0.00 3.85
4828 8530 3.843619 TGTGATGATTTAGTCCCAGGTCA 59.156 43.478 0.00 0.00 0.00 4.02
4829 8531 4.288366 TGTGATGATTTAGTCCCAGGTCAA 59.712 41.667 0.00 0.00 0.00 3.18
4830 8532 5.044919 TGTGATGATTTAGTCCCAGGTCAAT 60.045 40.000 0.00 0.00 0.00 2.57
4831 8533 5.529060 GTGATGATTTAGTCCCAGGTCAATC 59.471 44.000 0.00 0.00 0.00 2.67
4832 8534 5.191522 TGATGATTTAGTCCCAGGTCAATCA 59.808 40.000 0.00 0.00 35.64 2.57
4833 8535 4.843728 TGATTTAGTCCCAGGTCAATCAC 58.156 43.478 0.00 0.00 0.00 3.06
4834 8536 4.288366 TGATTTAGTCCCAGGTCAATCACA 59.712 41.667 0.00 0.00 0.00 3.58
4835 8537 3.981071 TTAGTCCCAGGTCAATCACAG 57.019 47.619 0.00 0.00 0.00 3.66
4836 8538 0.326264 AGTCCCAGGTCAATCACAGC 59.674 55.000 0.00 0.00 0.00 4.40
4837 8539 0.326264 GTCCCAGGTCAATCACAGCT 59.674 55.000 0.00 0.00 0.00 4.24
4838 8540 0.615331 TCCCAGGTCAATCACAGCTC 59.385 55.000 0.00 0.00 0.00 4.09
4839 8541 0.742281 CCCAGGTCAATCACAGCTCG 60.742 60.000 0.00 0.00 0.00 5.03
4840 8542 1.364626 CCAGGTCAATCACAGCTCGC 61.365 60.000 0.00 0.00 0.00 5.03
4841 8543 1.078848 AGGTCAATCACAGCTCGCC 60.079 57.895 0.00 0.00 0.00 5.54
4842 8544 1.375908 GGTCAATCACAGCTCGCCA 60.376 57.895 0.00 0.00 0.00 5.69
4843 8545 0.955428 GGTCAATCACAGCTCGCCAA 60.955 55.000 0.00 0.00 0.00 4.52
4844 8546 1.089920 GTCAATCACAGCTCGCCAAT 58.910 50.000 0.00 0.00 0.00 3.16
4845 8547 1.470098 GTCAATCACAGCTCGCCAATT 59.530 47.619 0.00 0.00 0.00 2.32
4846 8548 1.469703 TCAATCACAGCTCGCCAATTG 59.530 47.619 0.00 0.00 0.00 2.32
4847 8549 0.813184 AATCACAGCTCGCCAATTGG 59.187 50.000 20.81 20.81 38.53 3.16
4858 8560 2.269978 CCAATTGGCAGACAGGTGG 58.730 57.895 12.53 0.00 0.00 4.61
4859 8561 1.588082 CAATTGGCAGACAGGTGGC 59.412 57.895 0.00 0.00 43.25 5.01
4860 8562 0.896940 CAATTGGCAGACAGGTGGCT 60.897 55.000 0.00 0.00 43.34 4.75
4866 8568 3.314331 AGACAGGTGGCTGGACCG 61.314 66.667 0.00 0.00 43.94 4.79
4867 8569 4.394712 GACAGGTGGCTGGACCGG 62.395 72.222 0.00 0.00 43.94 5.28
4869 8571 4.394712 CAGGTGGCTGGACCGGTC 62.395 72.222 27.04 27.04 43.94 4.79
4870 8572 4.954118 AGGTGGCTGGACCGGTCA 62.954 66.667 34.40 19.72 43.94 4.02
4871 8573 3.948719 GGTGGCTGGACCGGTCAA 61.949 66.667 34.40 24.54 43.94 3.18
4872 8574 2.668550 GTGGCTGGACCGGTCAAC 60.669 66.667 34.40 22.17 43.94 3.18
4873 8575 4.308458 TGGCTGGACCGGTCAACG 62.308 66.667 34.40 22.00 43.94 4.10
4875 8577 4.980805 GCTGGACCGGTCAACGCA 62.981 66.667 34.40 21.79 42.52 5.24
4876 8578 3.041940 CTGGACCGGTCAACGCAC 61.042 66.667 34.40 17.23 42.52 5.34
4877 8579 4.953868 TGGACCGGTCAACGCACG 62.954 66.667 34.40 0.00 42.52 5.34
4882 8584 3.636043 CGGTCAACGCACGCACTT 61.636 61.111 0.00 0.00 34.82 3.16
4883 8585 2.713154 GGTCAACGCACGCACTTT 59.287 55.556 0.00 0.00 0.00 2.66
4884 8586 1.063488 GGTCAACGCACGCACTTTT 59.937 52.632 0.00 0.00 0.00 2.27
4885 8587 1.199852 GGTCAACGCACGCACTTTTG 61.200 55.000 0.00 0.00 0.00 2.44
4886 8588 1.585002 TCAACGCACGCACTTTTGC 60.585 52.632 0.00 0.00 46.21 3.68
4897 8599 1.285578 CACTTTTGCACAAAACCCCG 58.714 50.000 4.47 0.00 35.57 5.73
4898 8600 0.899019 ACTTTTGCACAAAACCCCGT 59.101 45.000 4.47 0.00 35.57 5.28
4899 8601 1.285578 CTTTTGCACAAAACCCCGTG 58.714 50.000 4.47 0.00 35.57 4.94
4903 8605 3.213402 CACAAAACCCCGTGCCGT 61.213 61.111 0.00 0.00 0.00 5.68
4904 8606 2.440613 ACAAAACCCCGTGCCGTT 60.441 55.556 0.00 0.00 0.00 4.44
4905 8607 2.053277 ACAAAACCCCGTGCCGTTT 61.053 52.632 0.00 0.00 33.69 3.60
4906 8608 1.299544 CAAAACCCCGTGCCGTTTC 60.300 57.895 0.00 0.00 31.09 2.78
4907 8609 2.491897 AAAACCCCGTGCCGTTTCC 61.492 57.895 0.00 0.00 31.09 3.13
4908 8610 2.914756 AAAACCCCGTGCCGTTTCCT 62.915 55.000 0.00 0.00 31.09 3.36
4909 8611 2.914756 AAACCCCGTGCCGTTTCCTT 62.915 55.000 0.00 0.00 0.00 3.36
4910 8612 2.596338 CCCCGTGCCGTTTCCTTT 60.596 61.111 0.00 0.00 0.00 3.11
4911 8613 2.197605 CCCCGTGCCGTTTCCTTTT 61.198 57.895 0.00 0.00 0.00 2.27
4912 8614 0.890090 CCCCGTGCCGTTTCCTTTTA 60.890 55.000 0.00 0.00 0.00 1.52
4913 8615 1.170442 CCCGTGCCGTTTCCTTTTAT 58.830 50.000 0.00 0.00 0.00 1.40
4914 8616 1.131693 CCCGTGCCGTTTCCTTTTATC 59.868 52.381 0.00 0.00 0.00 1.75
4915 8617 1.807742 CCGTGCCGTTTCCTTTTATCA 59.192 47.619 0.00 0.00 0.00 2.15
4916 8618 2.226912 CCGTGCCGTTTCCTTTTATCAA 59.773 45.455 0.00 0.00 0.00 2.57
4917 8619 3.231160 CGTGCCGTTTCCTTTTATCAAC 58.769 45.455 0.00 0.00 0.00 3.18
4918 8620 3.571571 GTGCCGTTTCCTTTTATCAACC 58.428 45.455 0.00 0.00 0.00 3.77
4919 8621 2.559231 TGCCGTTTCCTTTTATCAACCC 59.441 45.455 0.00 0.00 0.00 4.11
4920 8622 2.414957 GCCGTTTCCTTTTATCAACCCG 60.415 50.000 0.00 0.00 0.00 5.28
4921 8623 2.414957 CCGTTTCCTTTTATCAACCCGC 60.415 50.000 0.00 0.00 0.00 6.13
4922 8624 2.226912 CGTTTCCTTTTATCAACCCGCA 59.773 45.455 0.00 0.00 0.00 5.69
4923 8625 3.304794 CGTTTCCTTTTATCAACCCGCAA 60.305 43.478 0.00 0.00 0.00 4.85
4924 8626 4.617298 CGTTTCCTTTTATCAACCCGCAAT 60.617 41.667 0.00 0.00 0.00 3.56
4925 8627 5.392165 CGTTTCCTTTTATCAACCCGCAATA 60.392 40.000 0.00 0.00 0.00 1.90
4926 8628 6.569780 GTTTCCTTTTATCAACCCGCAATAT 58.430 36.000 0.00 0.00 0.00 1.28
4927 8629 7.467539 CGTTTCCTTTTATCAACCCGCAATATA 60.468 37.037 0.00 0.00 0.00 0.86
4928 8630 7.504924 TTCCTTTTATCAACCCGCAATATAG 57.495 36.000 0.00 0.00 0.00 1.31
4929 8631 5.472137 TCCTTTTATCAACCCGCAATATAGC 59.528 40.000 0.00 0.00 0.00 2.97
4930 8632 5.240623 CCTTTTATCAACCCGCAATATAGCA 59.759 40.000 0.00 0.00 0.00 3.49
4931 8633 5.682943 TTTATCAACCCGCAATATAGCAC 57.317 39.130 0.00 0.00 0.00 4.40
4932 8634 2.700722 TCAACCCGCAATATAGCACA 57.299 45.000 0.00 0.00 0.00 4.57
4933 8635 2.285083 TCAACCCGCAATATAGCACAC 58.715 47.619 0.00 0.00 0.00 3.82
4934 8636 1.333619 CAACCCGCAATATAGCACACC 59.666 52.381 0.00 0.00 0.00 4.16
4935 8637 0.837272 ACCCGCAATATAGCACACCT 59.163 50.000 0.00 0.00 0.00 4.00
4936 8638 1.229428 CCCGCAATATAGCACACCTG 58.771 55.000 0.00 0.00 0.00 4.00
4937 8639 1.202639 CCCGCAATATAGCACACCTGA 60.203 52.381 0.00 0.00 0.00 3.86
4938 8640 2.560504 CCGCAATATAGCACACCTGAA 58.439 47.619 0.00 0.00 0.00 3.02
4939 8641 3.141398 CCGCAATATAGCACACCTGAAT 58.859 45.455 0.00 0.00 0.00 2.57
4940 8642 3.565482 CCGCAATATAGCACACCTGAATT 59.435 43.478 0.00 0.00 0.00 2.17
4941 8643 4.754618 CCGCAATATAGCACACCTGAATTA 59.245 41.667 0.00 0.00 0.00 1.40
4942 8644 5.238432 CCGCAATATAGCACACCTGAATTAA 59.762 40.000 0.00 0.00 0.00 1.40
4943 8645 6.238621 CCGCAATATAGCACACCTGAATTAAA 60.239 38.462 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 129 2.277084 CTAAACGGATGGGAAACGAGG 58.723 52.381 0.00 0.00 0.00 4.63
180 196 2.778299 TCAACAGAAATTCGTCCCTGG 58.222 47.619 0.00 0.00 0.00 4.45
216 236 2.781681 ACAGTCGTATGGGGGAAAAG 57.218 50.000 0.00 0.00 0.00 2.27
221 241 0.107361 GGGAAACAGTCGTATGGGGG 60.107 60.000 0.00 0.00 0.00 5.40
267 287 3.347216 ACGTCAATGGGAAGGAATTGAG 58.653 45.455 0.00 0.00 42.02 3.02
333 353 0.692476 TTGGACTCTGTGGTGATGGG 59.308 55.000 0.00 0.00 0.00 4.00
352 372 8.918202 TTAATGGTTTCAGTGAACTATTGTCT 57.082 30.769 18.42 4.47 39.85 3.41
450 470 6.420306 CGCCTTACTCTGATATATGATGATGC 59.580 42.308 0.00 0.00 0.00 3.91
501 522 1.228245 GGACCAAAGAGCAGTGGCA 60.228 57.895 0.00 0.00 44.61 4.92
525 547 7.958053 TTAGTTACTGTTTTAAGAGGAGCAC 57.042 36.000 0.00 0.00 0.00 4.40
527 553 8.496751 CAGTTTAGTTACTGTTTTAAGAGGAGC 58.503 37.037 0.00 0.00 40.48 4.70
747 773 8.934023 TCACATCTAAAACCCTTTTACTCAAT 57.066 30.769 0.00 0.00 34.19 2.57
749 775 8.754991 TTTCACATCTAAAACCCTTTTACTCA 57.245 30.769 0.00 0.00 34.19 3.41
750 776 9.841880 GATTTCACATCTAAAACCCTTTTACTC 57.158 33.333 0.00 0.00 34.19 2.59
751 777 8.803235 GGATTTCACATCTAAAACCCTTTTACT 58.197 33.333 0.00 0.00 34.19 2.24
752 778 8.033038 GGGATTTCACATCTAAAACCCTTTTAC 58.967 37.037 6.64 0.00 42.64 2.01
753 779 8.129496 GGGATTTCACATCTAAAACCCTTTTA 57.871 34.615 6.64 0.00 42.64 1.52
754 780 7.004555 GGGATTTCACATCTAAAACCCTTTT 57.995 36.000 6.64 0.00 42.64 2.27
755 781 6.605471 GGGATTTCACATCTAAAACCCTTT 57.395 37.500 6.64 0.00 42.64 3.11
758 784 5.510430 AGAGGGATTTCACATCTAAAACCC 58.490 41.667 5.93 5.93 44.95 4.11
759 785 6.659242 TGAAGAGGGATTTCACATCTAAAACC 59.341 38.462 0.00 0.00 30.03 3.27
760 786 7.607991 TCTGAAGAGGGATTTCACATCTAAAAC 59.392 37.037 0.00 0.00 31.66 2.43
761 787 7.689299 TCTGAAGAGGGATTTCACATCTAAAA 58.311 34.615 0.00 0.00 31.66 1.52
762 788 7.257790 TCTGAAGAGGGATTTCACATCTAAA 57.742 36.000 0.00 0.00 31.66 1.85
763 789 6.874278 TCTGAAGAGGGATTTCACATCTAA 57.126 37.500 0.00 0.00 31.66 2.10
764 790 8.591940 CATATCTGAAGAGGGATTTCACATCTA 58.408 37.037 0.00 0.00 31.66 1.98
765 791 5.972327 ATCTGAAGAGGGATTTCACATCT 57.028 39.130 0.00 0.00 31.66 2.90
766 792 6.654161 CCATATCTGAAGAGGGATTTCACATC 59.346 42.308 0.00 0.00 31.66 3.06
767 793 6.102321 ACCATATCTGAAGAGGGATTTCACAT 59.898 38.462 1.23 0.00 31.66 3.21
777 822 6.426328 GCAAGTGATAACCATATCTGAAGAGG 59.574 42.308 0.00 0.00 38.99 3.69
917 962 8.445361 AGTAACTCCTTTTTAGGTATTCCTCA 57.555 34.615 0.00 0.00 43.94 3.86
1045 1090 8.460831 AACGAATTCCAAACTAATAAATGCAC 57.539 30.769 0.00 0.00 0.00 4.57
1055 1100 4.580995 TCAAGGCAAACGAATTCCAAACTA 59.419 37.500 0.00 0.00 0.00 2.24
1229 1274 5.424252 AGCATGATTTTTGGATGATCCTGTT 59.576 36.000 13.44 0.00 37.46 3.16
1356 1401 2.038863 TGGAGAGGCCAGGAAGTTAA 57.961 50.000 5.01 0.00 43.33 2.01
1407 1458 1.075212 TGTCCATGGGTTGAAGATGCA 59.925 47.619 13.02 0.00 0.00 3.96
1416 1467 2.838202 ACTTAGACGATGTCCATGGGTT 59.162 45.455 13.02 0.00 32.18 4.11
1497 1561 6.156775 TCAGACAATCATCCTTATGGTGAGAA 59.843 38.462 0.00 0.00 33.61 2.87
1501 1565 6.514541 GCATTCAGACAATCATCCTTATGGTG 60.515 42.308 0.00 0.00 33.61 4.17
1552 1616 2.925724 ACAACATCCAAGTCGGTGAAA 58.074 42.857 0.00 0.00 35.57 2.69
1595 1659 6.369065 CAGAGGTAAGCTTGTCGACTATTTTT 59.631 38.462 17.92 7.50 0.00 1.94
1597 1661 5.047235 ACAGAGGTAAGCTTGTCGACTATTT 60.047 40.000 17.92 9.23 0.00 1.40
1598 1662 4.463186 ACAGAGGTAAGCTTGTCGACTATT 59.537 41.667 17.92 8.50 0.00 1.73
1859 1923 5.458041 TGCTGATCCTCAAAAAGAAAAGG 57.542 39.130 0.00 0.00 0.00 3.11
2298 2382 7.384932 GGACAGCAACTTTTGTTAGCAATTTAT 59.615 33.333 0.00 0.00 41.35 1.40
2319 2403 3.243301 GCATATGCATTGGTTCAGGACAG 60.243 47.826 22.84 0.00 41.59 3.51
2342 2426 7.573968 ACTTGATCCTTGAAATATAGCCAAC 57.426 36.000 0.00 0.00 0.00 3.77
2422 2506 0.598065 AAAGCTGACCGACCAAATGC 59.402 50.000 0.00 0.00 0.00 3.56
2461 2545 3.201266 ACCCAGTGAAGAAACCAGTTACA 59.799 43.478 0.00 0.00 0.00 2.41
2468 2552 0.668535 GTGCACCCAGTGAAGAAACC 59.331 55.000 5.22 0.00 35.23 3.27
2475 2559 1.369692 CGTAAGGTGCACCCAGTGA 59.630 57.895 32.29 10.40 35.23 3.41
2512 2596 8.721019 TTCAAAAGCCAATTCCAATCATTATC 57.279 30.769 0.00 0.00 0.00 1.75
2612 2696 0.811616 CTACTGGGCAGCGAATCACC 60.812 60.000 0.00 0.00 0.00 4.02
2838 2922 8.801882 TGTCGGAGAAATGGATAAAAGTTTAT 57.198 30.769 0.00 0.00 39.69 1.40
2959 3043 6.379703 TGCTTGCATTGTAGGTATTGGTTTAT 59.620 34.615 0.00 0.00 0.00 1.40
3022 3106 1.734465 GACAGCTGGTTACATGCAGTC 59.266 52.381 19.93 8.04 36.43 3.51
3162 3246 9.620660 CATACACTGAAAAATTAGGGTTACAAC 57.379 33.333 0.00 0.00 31.89 3.32
3249 3335 1.062365 CATTGCATGGTACCGCACG 59.938 57.895 13.36 5.25 35.48 5.34
3476 3566 6.994421 ACACTTCAACCCATTAGGAAAAAT 57.006 33.333 0.00 0.00 39.89 1.82
3593 5412 2.995939 CAGCGACTTCTATTGAACAGCA 59.004 45.455 0.00 0.00 0.00 4.41
3766 5611 6.277605 TCAGAAATGAAGCATGCCATTAATG 58.722 36.000 18.66 18.36 33.13 1.90
3774 5619 4.746115 TGTTTGTTCAGAAATGAAGCATGC 59.254 37.500 10.51 10.51 0.00 4.06
3979 5824 7.012327 TCTGTTCTTCCAAAACTACATTCAGTG 59.988 37.037 0.00 0.00 0.00 3.66
4042 5887 9.249457 ACTCATACATCTGTTGTAATAACATCG 57.751 33.333 2.95 0.00 43.84 3.84
4050 5895 9.074576 ACCGATATACTCATACATCTGTTGTAA 57.925 33.333 2.95 0.00 43.84 2.41
4051 5896 8.631480 ACCGATATACTCATACATCTGTTGTA 57.369 34.615 1.40 1.40 44.71 2.41
4052 5897 7.526142 ACCGATATACTCATACATCTGTTGT 57.474 36.000 0.00 0.00 42.62 3.32
4053 5898 7.867909 ACAACCGATATACTCATACATCTGTTG 59.132 37.037 12.94 12.94 42.95 3.33
4054 5899 7.952671 ACAACCGATATACTCATACATCTGTT 58.047 34.615 0.00 0.00 0.00 3.16
4055 5900 7.526142 ACAACCGATATACTCATACATCTGT 57.474 36.000 0.00 0.00 0.00 3.41
4060 5905 9.830294 CGTTATTACAACCGATATACTCATACA 57.170 33.333 0.00 0.00 0.00 2.29
4061 5906 9.831737 ACGTTATTACAACCGATATACTCATAC 57.168 33.333 0.00 0.00 0.00 2.39
4063 5908 8.790718 AGACGTTATTACAACCGATATACTCAT 58.209 33.333 0.00 0.00 0.00 2.90
4064 5909 8.158169 AGACGTTATTACAACCGATATACTCA 57.842 34.615 0.00 0.00 0.00 3.41
4086 5931 5.021458 TCCCTCCGTCCCATAATATAAGAC 58.979 45.833 0.00 0.00 0.00 3.01
4183 6028 6.376864 CCACATACAAATTATCACTTGACCCA 59.623 38.462 0.00 0.00 0.00 4.51
4208 6075 1.926511 CTGTGATTGAACCCTGCGGC 61.927 60.000 0.00 0.00 0.00 6.53
4271 6138 2.068519 TCGAAGCTGTATGTGCACAAG 58.931 47.619 25.72 17.91 0.00 3.16
4696 8398 6.354130 GGTGCTATTACCTCATTTTCCTGTA 58.646 40.000 0.00 0.00 37.74 2.74
4697 8399 5.193679 GGTGCTATTACCTCATTTTCCTGT 58.806 41.667 0.00 0.00 37.74 4.00
4698 8400 4.580580 GGGTGCTATTACCTCATTTTCCTG 59.419 45.833 0.00 0.00 40.66 3.86
4699 8401 4.386424 GGGGTGCTATTACCTCATTTTCCT 60.386 45.833 0.00 0.00 41.08 3.36
4700 8402 3.889538 GGGGTGCTATTACCTCATTTTCC 59.110 47.826 0.00 0.00 41.08 3.13
4701 8403 4.532834 TGGGGTGCTATTACCTCATTTTC 58.467 43.478 0.00 0.00 46.11 2.29
4702 8404 4.601406 TGGGGTGCTATTACCTCATTTT 57.399 40.909 0.00 0.00 46.11 1.82
4707 8409 2.919228 CACTTGGGGTGCTATTACCTC 58.081 52.381 0.00 0.00 41.82 3.85
4717 8419 2.159230 CAAGTTAGGGCACTTGGGGTG 61.159 57.143 0.00 0.00 46.84 4.61
4718 8420 0.112412 CAAGTTAGGGCACTTGGGGT 59.888 55.000 0.00 0.00 46.84 4.95
4719 8421 2.961424 CAAGTTAGGGCACTTGGGG 58.039 57.895 0.00 0.00 46.84 4.96
4726 8428 2.161855 CATTCTGTGCAAGTTAGGGCA 58.838 47.619 0.00 0.00 37.77 5.36
4727 8429 2.095059 CACATTCTGTGCAAGTTAGGGC 60.095 50.000 0.00 0.00 41.89 5.19
4728 8430 3.837213 CACATTCTGTGCAAGTTAGGG 57.163 47.619 0.00 0.00 41.89 3.53
4738 8440 7.330946 TTTAGGACTAAATCGTCACATTCTGTG 59.669 37.037 0.80 0.80 38.53 3.66
4739 8441 5.407407 AGGACTAAATCGTCACATTCTGT 57.593 39.130 0.00 0.00 35.63 3.41
4740 8442 7.545965 ACTTTAGGACTAAATCGTCACATTCTG 59.454 37.037 5.09 0.00 34.86 3.02
4741 8443 7.612677 ACTTTAGGACTAAATCGTCACATTCT 58.387 34.615 5.09 0.00 34.86 2.40
4742 8444 7.829378 ACTTTAGGACTAAATCGTCACATTC 57.171 36.000 5.09 0.00 34.86 2.67
4743 8445 7.360946 GCAACTTTAGGACTAAATCGTCACATT 60.361 37.037 5.09 0.00 34.86 2.71
4744 8446 6.092259 GCAACTTTAGGACTAAATCGTCACAT 59.908 38.462 5.09 0.00 34.86 3.21
4745 8447 5.407387 GCAACTTTAGGACTAAATCGTCACA 59.593 40.000 5.09 0.00 34.86 3.58
4746 8448 5.407387 TGCAACTTTAGGACTAAATCGTCAC 59.593 40.000 5.09 0.00 34.86 3.67
4747 8449 5.543714 TGCAACTTTAGGACTAAATCGTCA 58.456 37.500 5.09 0.71 34.86 4.35
4748 8450 6.476243 TTGCAACTTTAGGACTAAATCGTC 57.524 37.500 0.00 0.00 34.86 4.20
4749 8451 6.870971 TTTGCAACTTTAGGACTAAATCGT 57.129 33.333 0.00 0.00 34.86 3.73
4750 8452 7.360361 AGTTTTGCAACTTTAGGACTAAATCG 58.640 34.615 0.00 0.00 40.66 3.34
4764 8466 2.427095 GGTGGAGTCAAGTTTTGCAACT 59.573 45.455 0.00 0.00 45.89 3.16
4765 8467 2.165437 TGGTGGAGTCAAGTTTTGCAAC 59.835 45.455 0.00 0.00 0.00 4.17
4766 8468 2.451490 TGGTGGAGTCAAGTTTTGCAA 58.549 42.857 0.00 0.00 0.00 4.08
4767 8469 2.136298 TGGTGGAGTCAAGTTTTGCA 57.864 45.000 0.00 0.00 0.00 4.08
4768 8470 3.057526 GGTATGGTGGAGTCAAGTTTTGC 60.058 47.826 0.00 0.00 0.00 3.68
4769 8471 4.023193 GTGGTATGGTGGAGTCAAGTTTTG 60.023 45.833 0.00 0.00 0.00 2.44
4770 8472 4.142038 GTGGTATGGTGGAGTCAAGTTTT 58.858 43.478 0.00 0.00 0.00 2.43
4771 8473 3.137544 TGTGGTATGGTGGAGTCAAGTTT 59.862 43.478 0.00 0.00 0.00 2.66
4772 8474 2.708861 TGTGGTATGGTGGAGTCAAGTT 59.291 45.455 0.00 0.00 0.00 2.66
4773 8475 2.334977 TGTGGTATGGTGGAGTCAAGT 58.665 47.619 0.00 0.00 0.00 3.16
4774 8476 3.074412 GTTGTGGTATGGTGGAGTCAAG 58.926 50.000 0.00 0.00 0.00 3.02
4775 8477 2.708861 AGTTGTGGTATGGTGGAGTCAA 59.291 45.455 0.00 0.00 0.00 3.18
4776 8478 2.334977 AGTTGTGGTATGGTGGAGTCA 58.665 47.619 0.00 0.00 0.00 3.41
4777 8479 3.074412 CAAGTTGTGGTATGGTGGAGTC 58.926 50.000 0.00 0.00 0.00 3.36
4778 8480 2.814097 GCAAGTTGTGGTATGGTGGAGT 60.814 50.000 4.48 0.00 0.00 3.85
4779 8481 1.812571 GCAAGTTGTGGTATGGTGGAG 59.187 52.381 4.48 0.00 0.00 3.86
4780 8482 1.143889 TGCAAGTTGTGGTATGGTGGA 59.856 47.619 4.48 0.00 0.00 4.02
4781 8483 1.269448 GTGCAAGTTGTGGTATGGTGG 59.731 52.381 4.48 0.00 0.00 4.61
4782 8484 1.269448 GGTGCAAGTTGTGGTATGGTG 59.731 52.381 4.48 0.00 0.00 4.17
4783 8485 1.144913 AGGTGCAAGTTGTGGTATGGT 59.855 47.619 4.48 0.00 0.00 3.55
4784 8486 1.909700 AGGTGCAAGTTGTGGTATGG 58.090 50.000 4.48 0.00 0.00 2.74
4785 8487 4.458989 ACATAAGGTGCAAGTTGTGGTATG 59.541 41.667 4.48 8.22 0.00 2.39
4786 8488 4.458989 CACATAAGGTGCAAGTTGTGGTAT 59.541 41.667 4.48 0.00 41.36 2.73
4787 8489 3.818210 CACATAAGGTGCAAGTTGTGGTA 59.182 43.478 4.48 0.00 41.36 3.25
4788 8490 2.622942 CACATAAGGTGCAAGTTGTGGT 59.377 45.455 4.48 0.00 41.36 4.16
4789 8491 3.287312 CACATAAGGTGCAAGTTGTGG 57.713 47.619 4.48 0.00 41.36 4.17
4800 8502 6.409695 CCTGGGACTAAATCATCACATAAGGT 60.410 42.308 0.00 0.00 0.00 3.50
4801 8503 6.000219 CCTGGGACTAAATCATCACATAAGG 59.000 44.000 0.00 0.00 0.00 2.69
4802 8504 6.595682 ACCTGGGACTAAATCATCACATAAG 58.404 40.000 0.00 0.00 0.00 1.73
4803 8505 6.157820 TGACCTGGGACTAAATCATCACATAA 59.842 38.462 0.00 0.00 0.00 1.90
4804 8506 5.665360 TGACCTGGGACTAAATCATCACATA 59.335 40.000 0.00 0.00 0.00 2.29
4805 8507 4.474651 TGACCTGGGACTAAATCATCACAT 59.525 41.667 0.00 0.00 0.00 3.21
4806 8508 3.843619 TGACCTGGGACTAAATCATCACA 59.156 43.478 0.00 0.00 0.00 3.58
4807 8509 4.487714 TGACCTGGGACTAAATCATCAC 57.512 45.455 0.00 0.00 0.00 3.06
4808 8510 5.191522 TGATTGACCTGGGACTAAATCATCA 59.808 40.000 0.00 0.00 31.08 3.07
4809 8511 5.529060 GTGATTGACCTGGGACTAAATCATC 59.471 44.000 0.00 0.00 36.67 2.92
4810 8512 5.044919 TGTGATTGACCTGGGACTAAATCAT 60.045 40.000 0.00 0.00 36.67 2.45
4811 8513 4.288366 TGTGATTGACCTGGGACTAAATCA 59.712 41.667 0.00 3.51 33.02 2.57
4812 8514 4.843728 TGTGATTGACCTGGGACTAAATC 58.156 43.478 0.00 0.96 0.00 2.17
4813 8515 4.848357 CTGTGATTGACCTGGGACTAAAT 58.152 43.478 0.00 0.00 0.00 1.40
4814 8516 3.559171 GCTGTGATTGACCTGGGACTAAA 60.559 47.826 0.00 0.00 0.00 1.85
4815 8517 2.027192 GCTGTGATTGACCTGGGACTAA 60.027 50.000 0.00 0.00 0.00 2.24
4816 8518 1.555075 GCTGTGATTGACCTGGGACTA 59.445 52.381 0.00 0.00 0.00 2.59
4817 8519 0.326264 GCTGTGATTGACCTGGGACT 59.674 55.000 0.00 0.00 0.00 3.85
4818 8520 0.326264 AGCTGTGATTGACCTGGGAC 59.674 55.000 0.00 0.00 0.00 4.46
4819 8521 0.615331 GAGCTGTGATTGACCTGGGA 59.385 55.000 0.00 0.00 0.00 4.37
4820 8522 0.742281 CGAGCTGTGATTGACCTGGG 60.742 60.000 0.00 0.00 0.00 4.45
4821 8523 1.364626 GCGAGCTGTGATTGACCTGG 61.365 60.000 0.00 0.00 0.00 4.45
4822 8524 1.364626 GGCGAGCTGTGATTGACCTG 61.365 60.000 0.00 0.00 0.00 4.00
4823 8525 1.078848 GGCGAGCTGTGATTGACCT 60.079 57.895 0.00 0.00 0.00 3.85
4824 8526 0.955428 TTGGCGAGCTGTGATTGACC 60.955 55.000 0.00 0.00 0.00 4.02
4825 8527 1.089920 ATTGGCGAGCTGTGATTGAC 58.910 50.000 0.00 0.00 0.00 3.18
4826 8528 1.469703 CAATTGGCGAGCTGTGATTGA 59.530 47.619 0.00 0.00 0.00 2.57
4827 8529 1.468565 CCAATTGGCGAGCTGTGATTG 60.469 52.381 12.53 0.00 0.00 2.67
4828 8530 0.813184 CCAATTGGCGAGCTGTGATT 59.187 50.000 12.53 0.00 0.00 2.57
4829 8531 2.485677 CCAATTGGCGAGCTGTGAT 58.514 52.632 12.53 0.00 0.00 3.06
4830 8532 3.985877 CCAATTGGCGAGCTGTGA 58.014 55.556 12.53 0.00 0.00 3.58
4840 8542 1.880819 GCCACCTGTCTGCCAATTGG 61.881 60.000 20.81 20.81 38.53 3.16
4841 8543 0.896940 AGCCACCTGTCTGCCAATTG 60.897 55.000 0.00 0.00 0.00 2.32
4842 8544 0.896940 CAGCCACCTGTCTGCCAATT 60.897 55.000 0.00 0.00 34.31 2.32
4843 8545 1.303888 CAGCCACCTGTCTGCCAAT 60.304 57.895 0.00 0.00 34.31 3.16
4844 8546 2.113774 CAGCCACCTGTCTGCCAA 59.886 61.111 0.00 0.00 34.31 4.52
4845 8547 3.957586 CCAGCCACCTGTCTGCCA 61.958 66.667 0.00 0.00 37.38 4.92
4846 8548 3.640407 TCCAGCCACCTGTCTGCC 61.640 66.667 0.00 0.00 37.38 4.85
4847 8549 2.359230 GTCCAGCCACCTGTCTGC 60.359 66.667 0.00 0.00 37.38 4.26
4848 8550 2.348998 GGTCCAGCCACCTGTCTG 59.651 66.667 0.00 0.00 37.38 3.51
4849 8551 3.314331 CGGTCCAGCCACCTGTCT 61.314 66.667 0.00 0.00 37.38 3.41
4850 8552 4.394712 CCGGTCCAGCCACCTGTC 62.395 72.222 0.00 0.00 37.38 3.51
4852 8554 4.394712 GACCGGTCCAGCCACCTG 62.395 72.222 24.75 0.00 38.85 4.00
4853 8555 4.954118 TGACCGGTCCAGCCACCT 62.954 66.667 31.19 0.00 36.97 4.00
4854 8556 3.948719 TTGACCGGTCCAGCCACC 61.949 66.667 31.19 5.34 36.97 4.61
4855 8557 2.668550 GTTGACCGGTCCAGCCAC 60.669 66.667 31.19 15.68 36.97 5.01
4856 8558 4.308458 CGTTGACCGGTCCAGCCA 62.308 66.667 31.19 10.73 36.97 4.75
4858 8560 4.980805 TGCGTTGACCGGTCCAGC 62.981 66.667 31.19 29.37 36.94 4.85
4859 8561 3.041940 GTGCGTTGACCGGTCCAG 61.042 66.667 31.19 21.84 36.94 3.86
4860 8562 4.953868 CGTGCGTTGACCGGTCCA 62.954 66.667 31.19 18.97 36.94 4.02
4865 8567 2.640736 AAAAGTGCGTGCGTTGACCG 62.641 55.000 0.00 0.00 40.40 4.79
4866 8568 1.063488 AAAAGTGCGTGCGTTGACC 59.937 52.632 0.00 0.00 0.00 4.02
4867 8569 1.797388 GCAAAAGTGCGTGCGTTGAC 61.797 55.000 0.00 0.00 41.93 3.18
4868 8570 1.585002 GCAAAAGTGCGTGCGTTGA 60.585 52.632 0.00 0.00 41.93 3.18
4869 8571 2.912744 GCAAAAGTGCGTGCGTTG 59.087 55.556 0.00 0.00 41.93 4.10
4878 8580 1.285578 CGGGGTTTTGTGCAAAAGTG 58.714 50.000 9.98 0.00 40.53 3.16
4879 8581 0.899019 ACGGGGTTTTGTGCAAAAGT 59.101 45.000 9.98 3.02 40.53 2.66
4880 8582 1.285578 CACGGGGTTTTGTGCAAAAG 58.714 50.000 9.98 2.47 40.53 2.27
4881 8583 3.442996 CACGGGGTTTTGTGCAAAA 57.557 47.368 6.04 6.04 37.90 2.44
4897 8599 3.571571 GGTTGATAAAAGGAAACGGCAC 58.428 45.455 0.00 0.00 0.00 5.01
4898 8600 2.559231 GGGTTGATAAAAGGAAACGGCA 59.441 45.455 0.00 0.00 0.00 5.69
4899 8601 2.414957 CGGGTTGATAAAAGGAAACGGC 60.415 50.000 0.00 0.00 0.00 5.68
4900 8602 2.414957 GCGGGTTGATAAAAGGAAACGG 60.415 50.000 0.00 0.00 0.00 4.44
4901 8603 2.226912 TGCGGGTTGATAAAAGGAAACG 59.773 45.455 0.00 0.00 0.00 3.60
4902 8604 3.926821 TGCGGGTTGATAAAAGGAAAC 57.073 42.857 0.00 0.00 0.00 2.78
4903 8605 6.783708 ATATTGCGGGTTGATAAAAGGAAA 57.216 33.333 0.00 0.00 0.00 3.13
4904 8606 6.016610 GCTATATTGCGGGTTGATAAAAGGAA 60.017 38.462 0.00 0.00 0.00 3.36
4905 8607 5.472137 GCTATATTGCGGGTTGATAAAAGGA 59.528 40.000 0.00 0.00 0.00 3.36
4906 8608 5.240623 TGCTATATTGCGGGTTGATAAAAGG 59.759 40.000 4.70 0.00 35.36 3.11
4907 8609 6.142817 GTGCTATATTGCGGGTTGATAAAAG 58.857 40.000 4.70 0.00 35.36 2.27
4908 8610 5.590663 TGTGCTATATTGCGGGTTGATAAAA 59.409 36.000 4.70 0.00 35.36 1.52
4909 8611 5.008217 GTGTGCTATATTGCGGGTTGATAAA 59.992 40.000 4.70 0.00 35.36 1.40
4910 8612 4.513692 GTGTGCTATATTGCGGGTTGATAA 59.486 41.667 4.70 0.00 35.36 1.75
4911 8613 4.062293 GTGTGCTATATTGCGGGTTGATA 58.938 43.478 4.70 0.00 35.36 2.15
4912 8614 2.878406 GTGTGCTATATTGCGGGTTGAT 59.122 45.455 4.70 0.00 35.36 2.57
4913 8615 2.285083 GTGTGCTATATTGCGGGTTGA 58.715 47.619 4.70 0.00 35.36 3.18
4914 8616 1.333619 GGTGTGCTATATTGCGGGTTG 59.666 52.381 4.70 0.00 35.36 3.77
4915 8617 1.211949 AGGTGTGCTATATTGCGGGTT 59.788 47.619 4.70 0.00 35.36 4.11
4916 8618 0.837272 AGGTGTGCTATATTGCGGGT 59.163 50.000 4.70 0.00 35.36 5.28
4917 8619 1.202639 TCAGGTGTGCTATATTGCGGG 60.203 52.381 4.70 0.00 35.36 6.13
4918 8620 2.238942 TCAGGTGTGCTATATTGCGG 57.761 50.000 4.70 0.00 35.36 5.69
4919 8621 4.818534 AATTCAGGTGTGCTATATTGCG 57.181 40.909 4.70 0.00 35.36 4.85


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

AutoCloner maintained by Alex Coulton.