Multiple sequence alignment - TraesCS5D01G059700

Loading Multiple Alignment...

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 TraesCS5D01G059700 chr5D 100.000 6627 0 0 1 6627 56460829 56454203 0.000000e+00 12238.0
1 TraesCS5D01G059700 chr5D 81.366 161 21 6 3036 3188 37140911 37140752 9.020000e-24 122.0
2 TraesCS5D01G059700 chr5D 95.588 68 3 0 6560 6627 497231085 497231018 7.030000e-20 110.0
3 TraesCS5D01G059700 chr5D 94.366 71 4 0 6557 6627 497253975 497254045 7.030000e-20 110.0
4 TraesCS5D01G059700 chr5D 94.366 71 4 0 6557 6627 497392578 497392648 7.030000e-20 110.0
5 TraesCS5D01G059700 chr5D 94.366 71 4 0 6557 6627 497393608 497393678 7.030000e-20 110.0
6 TraesCS5D01G059700 chr5B 93.675 6672 248 67 2 6566 59171188 59164584 0.000000e+00 9823.0
7 TraesCS5D01G059700 chr5B 91.954 87 5 2 3036 3121 59168289 59168204 3.250000e-23 121.0
8 TraesCS5D01G059700 chr5A 93.607 2362 102 20 3377 5700 44986241 44983891 0.000000e+00 3480.0
9 TraesCS5D01G059700 chr5A 92.919 1158 39 15 962 2095 44988348 44987210 0.000000e+00 1644.0
10 TraesCS5D01G059700 chr5A 93.128 713 34 11 2133 2834 44987215 44986507 0.000000e+00 1031.0
11 TraesCS5D01G059700 chr5A 92.245 490 30 4 488 973 44988849 44988364 0.000000e+00 688.0
12 TraesCS5D01G059700 chr5A 92.694 219 12 3 5692 5909 44983869 44983654 4.990000e-81 313.0
13 TraesCS5D01G059700 chr5A 84.360 211 22 9 2012 2215 26142332 26142126 5.240000e-46 196.0
14 TraesCS5D01G059700 chr5A 82.629 213 22 5 5958 6167 44983556 44983356 2.460000e-39 174.0
15 TraesCS5D01G059700 chr5A 88.406 138 12 3 3085 3218 44986402 44986265 5.320000e-36 163.0
16 TraesCS5D01G059700 chr5A 87.050 139 13 3 1 138 44991217 44991083 1.150000e-32 152.0
17 TraesCS5D01G059700 chr5A 89.720 107 7 1 2925 3031 44986510 44986408 4.170000e-27 134.0
18 TraesCS5D01G059700 chr5A 86.667 90 9 3 3034 3121 26138442 26138354 5.470000e-16 97.1
19 TraesCS5D01G059700 chr5A 100.000 37 0 0 3085 3121 44986511 44986475 1.190000e-07 69.4
20 TraesCS5D01G059700 chr2A 79.235 183 31 7 1017 1195 708058382 708058561 3.250000e-23 121.0
21 TraesCS5D01G059700 chr2A 97.015 67 2 0 6561 6627 196283770 196283836 5.430000e-21 113.0
22 TraesCS5D01G059700 chr2A 87.500 72 6 3 1027 1097 54882373 54882442 5.510000e-11 80.5
23 TraesCS5D01G059700 chr2A 90.323 62 3 3 1036 1095 54955478 54955418 1.980000e-10 78.7
24 TraesCS5D01G059700 chr3D 94.595 74 3 1 6552 6625 565969252 565969324 5.430000e-21 113.0
25 TraesCS5D01G059700 chrUn 94.366 71 4 0 6557 6627 329701210 329701280 7.030000e-20 110.0
26 TraesCS5D01G059700 chr1B 93.243 74 4 1 6552 6625 484293208 484293280 2.530000e-19 108.0
27 TraesCS5D01G059700 chr2D 77.660 188 31 8 1017 1195 568801327 568801512 3.270000e-18 104.0
28 TraesCS5D01G059700 chr2D 77.108 166 22 13 1036 1198 54487979 54487827 1.530000e-11 82.4
29 TraesCS5D01G059700 chr3A 83.784 111 12 5 6523 6627 60544595 60544485 4.230000e-17 100.0
30 TraesCS5D01G059700 chr2B 78.182 165 20 13 1036 1197 85177910 85177759 2.540000e-14 91.6
31 TraesCS5D01G059700 chr1D 86.667 60 6 2 1035 1093 359666065 359666007 1.540000e-06 65.8


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 TraesCS5D01G059700 chr5D 56454203 56460829 6626 True 12238.00 12238 100.0000 1 6627 1 chr5D.!!$R2 6626
1 TraesCS5D01G059700 chr5B 59164584 59171188 6604 True 4972.00 9823 92.8145 2 6566 2 chr5B.!!$R1 6564
2 TraesCS5D01G059700 chr5A 44983356 44991217 7861 True 784.84 3480 91.2398 1 6167 10 chr5A.!!$R2 6166

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
937 2837 1.280421 AGCACAACTCCATTCCTCTCC 59.720 52.381 0.00 0.00 0.00 3.71 F
1940 3899 1.571457 TCAAGTGGGGGACTTCCAAAA 59.429 47.619 0.00 0.00 43.52 2.44 F
2894 4952 0.038618 AAAAGAATTTGGCGCCGTCC 60.039 50.000 23.90 8.98 39.02 4.79 F
3235 5297 0.391661 ATCCTGACACATGGCACGAC 60.392 55.000 0.00 0.00 0.00 4.34 F
3425 5487 0.611896 ACTTCCATTGAAAGGGGCCG 60.612 55.000 0.00 0.00 0.00 6.13 F
3645 5710 0.613777 ACCTTAGCGGCTACTGCTTT 59.386 50.000 9.68 0.00 43.71 3.51 F
4828 6915 1.073763 TCTTAGCCAGCTTTCTTGCCA 59.926 47.619 0.00 0.00 31.81 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2875 4933 0.038618 GGACGGCGCCAAATTCTTTT 60.039 50.000 28.98 0.0 0.00 2.27 R
3780 5845 0.038526 CCGACACAGTAGCTCGGTTT 60.039 55.000 0.00 0.0 41.75 3.27 R
3816 5881 0.623324 CCACCACCCTATCCTTCCCA 60.623 60.000 0.00 0.0 0.00 4.37 R
4957 7047 2.027837 GCATCCAACCAAGCATTTTCCT 60.028 45.455 0.00 0.0 0.00 3.36 R
5293 7384 1.078143 GGTGGTGTCCATGAGAGGC 60.078 63.158 0.00 0.0 35.28 4.70 R
5501 7604 3.199946 AGGACCTTCTTGTCACAGTTCAA 59.800 43.478 0.00 0.0 36.97 2.69 R
6602 8813 0.044855 AACTCTGGTGGGCTAGGGAT 59.955 55.000 0.00 0.0 0.00 3.85 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
156 186 7.857456 ACATATTAAGTGACATTCTGTACCCA 58.143 34.615 0.00 0.00 0.00 4.51
157 187 8.494433 ACATATTAAGTGACATTCTGTACCCAT 58.506 33.333 0.00 0.00 0.00 4.00
197 227 1.999735 TCAATTTGGAGATCGACACGC 59.000 47.619 0.00 0.00 0.00 5.34
397 598 9.901172 AAAGAAACTTCTACTTTACCAGAAAGA 57.099 29.630 4.14 0.00 36.28 2.52
427 628 7.201875 GCTCTCCTAGAGAAACAAACTAGCTAT 60.202 40.741 8.11 0.00 45.07 2.97
744 2644 3.127533 GCTAGCTTGTGGCCGGTG 61.128 66.667 7.70 0.00 43.05 4.94
811 2711 7.549134 GGAAGAAAAGGCGAAATGGAAATAAAT 59.451 33.333 0.00 0.00 0.00 1.40
819 2719 7.768582 AGGCGAAATGGAAATAAATAAAAAGGG 59.231 33.333 0.00 0.00 0.00 3.95
820 2720 7.406553 GCGAAATGGAAATAAATAAAAAGGGC 58.593 34.615 0.00 0.00 0.00 5.19
821 2721 7.466725 GCGAAATGGAAATAAATAAAAAGGGCC 60.467 37.037 0.00 0.00 0.00 5.80
929 2829 2.346766 TGACACAAGCACAACTCCAT 57.653 45.000 0.00 0.00 0.00 3.41
930 2830 2.653726 TGACACAAGCACAACTCCATT 58.346 42.857 0.00 0.00 0.00 3.16
937 2837 1.280421 AGCACAACTCCATTCCTCTCC 59.720 52.381 0.00 0.00 0.00 3.71
1107 3046 4.379243 CTCGCGCCCAAGGTCACT 62.379 66.667 0.00 0.00 0.00 3.41
1231 3172 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1318 3263 4.037858 CATGGATGCATATCGATCGAGA 57.962 45.455 23.84 19.95 30.42 4.04
1319 3264 3.772060 TGGATGCATATCGATCGAGAG 57.228 47.619 23.84 15.65 33.98 3.20
1320 3265 3.347216 TGGATGCATATCGATCGAGAGA 58.653 45.455 23.84 11.51 38.26 3.10
1400 3345 7.465916 GCCTTTTCTGTTCAATCCAACTTTTTC 60.466 37.037 0.00 0.00 0.00 2.29
1409 3354 3.021177 TCCAACTTTTTCCGTTCCCTT 57.979 42.857 0.00 0.00 0.00 3.95
1588 3536 2.432510 CCTCCTCCAGCGTTTCTTCTAT 59.567 50.000 0.00 0.00 0.00 1.98
1715 3668 6.650120 ACTTGACTTGGAGTACTCTTTGAAA 58.350 36.000 21.88 9.35 0.00 2.69
1722 3675 5.984725 TGGAGTACTCTTTGAAACTTCACA 58.015 37.500 21.88 4.38 36.83 3.58
1749 3706 6.095432 AGAATAGTTCTAGTAGGCATGCAG 57.905 41.667 21.36 7.90 38.49 4.41
1783 3742 5.948992 ACTGGAACTGCTAGTGATTTTTC 57.051 39.130 0.00 0.00 36.90 2.29
1784 3743 5.625150 ACTGGAACTGCTAGTGATTTTTCT 58.375 37.500 0.00 0.00 36.90 2.52
1786 3745 7.224297 ACTGGAACTGCTAGTGATTTTTCTTA 58.776 34.615 0.00 0.00 36.90 2.10
1787 3746 7.885399 ACTGGAACTGCTAGTGATTTTTCTTAT 59.115 33.333 0.00 0.00 36.90 1.73
1788 3747 9.383519 CTGGAACTGCTAGTGATTTTTCTTATA 57.616 33.333 0.00 0.00 0.00 0.98
1789 3748 9.905713 TGGAACTGCTAGTGATTTTTCTTATAT 57.094 29.630 0.00 0.00 0.00 0.86
1940 3899 1.571457 TCAAGTGGGGGACTTCCAAAA 59.429 47.619 0.00 0.00 43.52 2.44
2021 3980 9.495572 ACTCGAATCTAGAATCTTTTTCTTGTT 57.504 29.630 6.26 0.00 0.00 2.83
2074 4033 4.401202 TCTCACCTTCAGATGCATACGTAA 59.599 41.667 0.00 0.00 0.00 3.18
2131 4091 8.997621 AAAAATGATCTCTAAGCTTACGTACA 57.002 30.769 0.86 0.63 0.00 2.90
2176 4136 7.998383 TCCTATCTAATTTGGTGTATTGTGCAT 59.002 33.333 0.00 0.00 0.00 3.96
2226 4187 4.630894 ATGTATGATCTCTAGCTAGCGC 57.369 45.455 16.35 0.00 0.00 5.92
2450 4412 6.345096 TGAAATTTCAGGCCTTCTAAAAGG 57.655 37.500 16.91 0.00 42.45 3.11
2633 4599 4.037923 ACATGTGGTTCAACATTCCTTGTC 59.962 41.667 0.00 0.00 38.75 3.18
2638 4604 3.300009 GTTCAACATTCCTTGTCTTGCG 58.700 45.455 0.00 0.00 37.68 4.85
2834 4892 6.052360 GTGGGCTAAAAGGAAATGAAAAACA 58.948 36.000 0.00 0.00 0.00 2.83
2835 4893 6.202762 GTGGGCTAAAAGGAAATGAAAAACAG 59.797 38.462 0.00 0.00 0.00 3.16
2836 4894 6.126911 TGGGCTAAAAGGAAATGAAAAACAGT 60.127 34.615 0.00 0.00 0.00 3.55
2837 4895 7.070074 TGGGCTAAAAGGAAATGAAAAACAGTA 59.930 33.333 0.00 0.00 0.00 2.74
2838 4896 7.598869 GGGCTAAAAGGAAATGAAAAACAGTAG 59.401 37.037 0.00 0.00 0.00 2.57
2839 4897 8.141909 GGCTAAAAGGAAATGAAAAACAGTAGT 58.858 33.333 0.00 0.00 0.00 2.73
2892 4950 3.978460 AAAAAGAATTTGGCGCCGT 57.022 42.105 23.90 7.56 39.02 5.68
2893 4951 1.778334 AAAAAGAATTTGGCGCCGTC 58.222 45.000 23.90 16.06 39.02 4.79
2894 4952 0.038618 AAAAGAATTTGGCGCCGTCC 60.039 50.000 23.90 8.98 39.02 4.79
2895 4953 1.175983 AAAGAATTTGGCGCCGTCCA 61.176 50.000 23.90 5.42 36.60 4.02
2896 4954 1.586154 AAGAATTTGGCGCCGTCCAG 61.586 55.000 23.90 0.00 37.44 3.86
2897 4955 2.033448 AATTTGGCGCCGTCCAGA 59.967 55.556 23.90 0.00 37.44 3.86
2898 4956 1.376609 GAATTTGGCGCCGTCCAGAT 61.377 55.000 23.90 1.19 37.44 2.90
2899 4957 0.965363 AATTTGGCGCCGTCCAGATT 60.965 50.000 23.90 8.23 36.46 2.40
2900 4958 0.965363 ATTTGGCGCCGTCCAGATTT 60.965 50.000 23.90 0.00 37.44 2.17
2901 4959 1.861542 TTTGGCGCCGTCCAGATTTG 61.862 55.000 23.90 0.00 37.44 2.32
2902 4960 2.435938 GGCGCCGTCCAGATTTGA 60.436 61.111 12.58 0.00 0.00 2.69
2903 4961 2.038269 GGCGCCGTCCAGATTTGAA 61.038 57.895 12.58 0.00 0.00 2.69
2904 4962 1.134694 GCGCCGTCCAGATTTGAAC 59.865 57.895 0.00 0.00 0.00 3.18
2905 4963 1.794222 CGCCGTCCAGATTTGAACC 59.206 57.895 0.00 0.00 0.00 3.62
2906 4964 0.953471 CGCCGTCCAGATTTGAACCA 60.953 55.000 0.00 0.00 0.00 3.67
2907 4965 0.804989 GCCGTCCAGATTTGAACCAG 59.195 55.000 0.00 0.00 0.00 4.00
2908 4966 1.610624 GCCGTCCAGATTTGAACCAGA 60.611 52.381 0.00 0.00 0.00 3.86
2909 4967 2.350522 CCGTCCAGATTTGAACCAGAG 58.649 52.381 0.00 0.00 0.00 3.35
2910 4968 2.028112 CCGTCCAGATTTGAACCAGAGA 60.028 50.000 0.00 0.00 0.00 3.10
2911 4969 3.369892 CCGTCCAGATTTGAACCAGAGAT 60.370 47.826 0.00 0.00 0.00 2.75
2912 4970 3.868077 CGTCCAGATTTGAACCAGAGATC 59.132 47.826 0.00 0.00 0.00 2.75
2913 4971 4.382470 CGTCCAGATTTGAACCAGAGATCT 60.382 45.833 0.00 0.00 0.00 2.75
2914 4972 5.495640 GTCCAGATTTGAACCAGAGATCTT 58.504 41.667 0.00 0.00 0.00 2.40
2915 4973 5.584251 GTCCAGATTTGAACCAGAGATCTTC 59.416 44.000 0.00 0.00 0.00 2.87
2916 4974 5.249163 TCCAGATTTGAACCAGAGATCTTCA 59.751 40.000 0.00 0.00 0.00 3.02
2917 4975 5.585445 CCAGATTTGAACCAGAGATCTTCAG 59.415 44.000 0.00 0.00 0.00 3.02
2918 4976 5.064962 CAGATTTGAACCAGAGATCTTCAGC 59.935 44.000 0.00 0.00 0.00 4.26
2919 4977 2.662006 TGAACCAGAGATCTTCAGCG 57.338 50.000 0.00 0.00 0.00 5.18
2920 4978 1.895798 TGAACCAGAGATCTTCAGCGT 59.104 47.619 0.00 0.00 0.00 5.07
2921 4979 2.266554 GAACCAGAGATCTTCAGCGTG 58.733 52.381 0.00 0.00 0.00 5.34
2922 4980 1.261480 ACCAGAGATCTTCAGCGTGT 58.739 50.000 0.00 0.00 0.00 4.49
2923 4981 1.067283 ACCAGAGATCTTCAGCGTGTG 60.067 52.381 0.00 0.00 0.00 3.82
2924 4982 1.203287 CCAGAGATCTTCAGCGTGTGA 59.797 52.381 0.00 0.00 0.00 3.58
2925 4983 2.353109 CCAGAGATCTTCAGCGTGTGAA 60.353 50.000 0.00 2.88 43.26 3.18
2926 4984 3.320626 CAGAGATCTTCAGCGTGTGAAA 58.679 45.455 0.00 0.00 44.83 2.69
2927 4985 3.122613 CAGAGATCTTCAGCGTGTGAAAC 59.877 47.826 0.00 0.69 44.83 2.78
2947 5005 1.404391 CGGACGTGCTAGACCAACTAT 59.596 52.381 5.27 0.00 0.00 2.12
2963 5021 4.561938 CCAACTATACCACGACACCTTTCA 60.562 45.833 0.00 0.00 0.00 2.69
2964 5022 4.451629 ACTATACCACGACACCTTTCAG 57.548 45.455 0.00 0.00 0.00 3.02
3062 5120 3.315140 TGGCATCGTCCGGGTTCA 61.315 61.111 0.00 0.00 0.00 3.18
3128 5186 1.610038 CACCACGACACCTGTACAGTA 59.390 52.381 21.18 0.00 0.00 2.74
3195 5256 1.874129 TTATGACGTCACCCTGGGAT 58.126 50.000 22.71 4.68 0.00 3.85
3222 5284 3.115390 CCCTTTCCCTGTCTAATCCTGA 58.885 50.000 0.00 0.00 0.00 3.86
3223 5285 3.118223 CCCTTTCCCTGTCTAATCCTGAC 60.118 52.174 0.00 0.00 35.21 3.51
3225 5287 4.508662 CTTTCCCTGTCTAATCCTGACAC 58.491 47.826 0.00 0.00 39.23 3.67
3226 5288 3.184382 TCCCTGTCTAATCCTGACACA 57.816 47.619 0.00 0.00 39.23 3.72
3227 5289 3.724478 TCCCTGTCTAATCCTGACACAT 58.276 45.455 0.00 0.00 39.23 3.21
3228 5290 3.452264 TCCCTGTCTAATCCTGACACATG 59.548 47.826 0.00 0.00 39.23 3.21
3229 5291 3.432749 CCCTGTCTAATCCTGACACATGG 60.433 52.174 0.00 0.00 39.23 3.66
3230 5292 3.201290 CTGTCTAATCCTGACACATGGC 58.799 50.000 0.00 0.00 39.23 4.40
3231 5293 2.571202 TGTCTAATCCTGACACATGGCA 59.429 45.455 0.00 0.00 39.23 4.92
3232 5294 2.939103 GTCTAATCCTGACACATGGCAC 59.061 50.000 0.00 0.00 34.80 5.01
3233 5295 1.935873 CTAATCCTGACACATGGCACG 59.064 52.381 0.00 0.00 0.00 5.34
3235 5297 0.391661 ATCCTGACACATGGCACGAC 60.392 55.000 0.00 0.00 0.00 4.34
3236 5298 2.382746 CCTGACACATGGCACGACG 61.383 63.158 0.00 0.00 0.00 5.12
3237 5299 2.356913 TGACACATGGCACGACGG 60.357 61.111 0.00 0.00 0.00 4.79
3238 5300 3.118454 GACACATGGCACGACGGG 61.118 66.667 0.00 0.00 0.00 5.28
3239 5301 4.697756 ACACATGGCACGACGGGG 62.698 66.667 0.00 0.00 0.00 5.73
3241 5303 4.388499 ACATGGCACGACGGGGAC 62.388 66.667 0.00 0.00 0.00 4.46
3256 5318 2.539338 GGACGGCGACAAACTGCAA 61.539 57.895 16.62 0.00 0.00 4.08
3347 5409 2.298446 ACATCTAGGATGGCATGTCTCG 59.702 50.000 3.81 0.00 0.00 4.04
3361 5423 2.290464 TGTCTCGCTCTAACCTCTAGC 58.710 52.381 0.00 0.00 0.00 3.42
3383 5445 4.437239 CTCTACCACTTGCTCATCGATTT 58.563 43.478 0.00 0.00 0.00 2.17
3425 5487 0.611896 ACTTCCATTGAAAGGGGCCG 60.612 55.000 0.00 0.00 0.00 6.13
3471 5533 0.764752 GGGGGAGGGTCGATGAGATT 60.765 60.000 0.00 0.00 0.00 2.40
3538 5601 2.616376 TGTCAATGTCACCGTCAAAAGG 59.384 45.455 0.00 0.00 0.00 3.11
3619 5682 4.216687 GTCATCGTTTATTTGTGGGACCAA 59.783 41.667 0.00 0.00 0.00 3.67
3627 5690 7.274686 CGTTTATTTGTGGGACCAATTTGATAC 59.725 37.037 0.00 0.00 0.00 2.24
3645 5710 0.613777 ACCTTAGCGGCTACTGCTTT 59.386 50.000 9.68 0.00 43.71 3.51
3741 5806 4.497507 GGCGGCAAAGAATGGTATTTCTAC 60.498 45.833 3.07 0.00 34.89 2.59
3816 5881 1.392710 CGGGATACTGGAAGGCGACT 61.393 60.000 0.00 0.00 41.20 4.18
4160 6225 4.686554 GCACAACCAATCGTATAGGAGATC 59.313 45.833 1.16 0.00 0.00 2.75
4172 6237 4.935352 ATAGGAGATCTCTTGCAGTGTC 57.065 45.455 21.81 2.41 0.00 3.67
4244 6309 3.843027 AGATGGACTTCTTGACCTGTCAT 59.157 43.478 0.03 0.00 39.64 3.06
4253 6318 6.378280 ACTTCTTGACCTGTCATTTTCTGTTT 59.622 34.615 0.03 0.00 39.64 2.83
4367 6435 1.331447 GGTTTTGTTGCGGTAGACGTT 59.669 47.619 0.00 0.00 46.52 3.99
4384 6452 9.460906 GGTAGACGTTCTATTTAATAAGGACTG 57.539 37.037 0.00 0.00 30.76 3.51
4618 6692 8.854979 TCTTGATGTTATGATTTTTATTGCGG 57.145 30.769 0.00 0.00 0.00 5.69
4665 6752 1.793258 CATGGAATGCGCTCCTCTAG 58.207 55.000 15.89 1.20 37.62 2.43
4704 6791 9.716556 ACTGATAGAGACCGGGAATAAATATAT 57.283 33.333 6.32 0.00 0.00 0.86
4710 6797 9.046846 AGAGACCGGGAATAAATATATGATTCA 57.953 33.333 6.32 0.00 32.30 2.57
4775 6862 3.713858 TGCAAACAAGTTGGTCATCTG 57.286 42.857 7.96 0.00 37.73 2.90
4828 6915 1.073763 TCTTAGCCAGCTTTCTTGCCA 59.926 47.619 0.00 0.00 31.81 4.92
4829 6916 1.888512 CTTAGCCAGCTTTCTTGCCAA 59.111 47.619 0.00 0.00 31.81 4.52
4830 6917 1.993956 TAGCCAGCTTTCTTGCCAAA 58.006 45.000 0.00 0.00 31.81 3.28
4959 7049 8.421002 TCTTACCAATTCTCCAAAAGAAAAAGG 58.579 33.333 0.00 0.00 46.85 3.11
4989 7079 2.496871 TGGTTGGATGCATGAACCAATC 59.503 45.455 26.90 22.63 44.84 2.67
5127 7217 4.322801 GCACCTACCATTGAACTACTGACT 60.323 45.833 0.00 0.00 0.00 3.41
5251 7342 2.162681 CCAAGGAACCTCACCAACATC 58.837 52.381 0.00 0.00 0.00 3.06
5293 7384 3.596066 CTCCTCACCACCACTGCCG 62.596 68.421 0.00 0.00 0.00 5.69
5501 7604 2.123382 GCTACCTAGACCCCGCCT 60.123 66.667 0.00 0.00 0.00 5.52
5665 7768 3.838120 TCGAGACAACATAAGCAGACAG 58.162 45.455 0.00 0.00 0.00 3.51
5861 7995 5.171339 AGAACCACTCTAATGATTGCTGT 57.829 39.130 0.00 0.00 30.22 4.40
5900 8034 2.175878 ACAGGTTGCAGTGATCAGAC 57.824 50.000 0.00 0.00 0.00 3.51
5902 8036 2.074576 CAGGTTGCAGTGATCAGACAG 58.925 52.381 0.00 0.00 0.00 3.51
5969 8169 6.349694 GGAATTCTGAATGTTCTTCCCTCAAC 60.350 42.308 3.22 0.00 0.00 3.18
6091 8292 8.888579 ATTCCACATAAATAGTACTGTAGCAC 57.111 34.615 5.39 0.00 0.00 4.40
6134 8335 2.169978 TCAGAATCAGTCCAGATGCAGG 59.830 50.000 0.00 0.00 0.00 4.85
6144 8347 2.226315 AGATGCAGGACAGGTGCCA 61.226 57.895 0.00 0.00 40.43 4.92
6176 8379 9.877178 ATTCATTTAGAAAAGTATCACGAGACT 57.123 29.630 0.00 0.00 40.22 3.24
6177 8380 8.912787 TCATTTAGAAAAGTATCACGAGACTC 57.087 34.615 0.00 0.00 30.64 3.36
6178 8381 8.520351 TCATTTAGAAAAGTATCACGAGACTCA 58.480 33.333 2.82 0.00 30.64 3.41
6179 8382 8.587950 CATTTAGAAAAGTATCACGAGACTCAC 58.412 37.037 2.82 0.00 30.64 3.51
6180 8383 5.707242 AGAAAAGTATCACGAGACTCACA 57.293 39.130 2.82 0.00 30.64 3.58
6181 8384 6.085555 AGAAAAGTATCACGAGACTCACAA 57.914 37.500 2.82 0.00 30.64 3.33
6198 8401 1.258427 CAATATGTTGCGTGGTTGCG 58.742 50.000 0.00 0.00 37.81 4.85
6378 8588 3.429272 CCATCCGATCCACAAAACATTGG 60.429 47.826 0.00 0.00 0.00 3.16
6383 8593 2.969628 TCCACAAAACATTGGCGTTT 57.030 40.000 0.00 0.00 40.79 3.60
6387 8597 3.492756 CCACAAAACATTGGCGTTTTAGG 59.507 43.478 1.80 4.19 45.05 2.69
6396 8606 7.457024 ACATTGGCGTTTTAGGTATAGTTTT 57.543 32.000 0.00 0.00 0.00 2.43
6401 8611 5.163723 GGCGTTTTAGGTATAGTTTTGGTCC 60.164 44.000 0.00 0.00 0.00 4.46
6475 8686 3.937706 GTGGATCTATGCATAGATGTGCC 59.062 47.826 40.73 34.47 46.98 5.01
6485 8696 3.243636 GCATAGATGTGCCCCTCAAAATG 60.244 47.826 0.00 0.00 39.18 2.32
6563 8774 5.298347 AGACTAACTCAAAGTTACACCTGC 58.702 41.667 0.00 0.00 39.51 4.85
6566 8777 3.188159 ACTCAAAGTTACACCTGCGAA 57.812 42.857 0.00 0.00 0.00 4.70
6567 8778 2.870411 ACTCAAAGTTACACCTGCGAAC 59.130 45.455 0.00 0.00 0.00 3.95
6568 8779 2.215196 TCAAAGTTACACCTGCGAACC 58.785 47.619 0.00 0.00 0.00 3.62
6569 8780 1.944024 CAAAGTTACACCTGCGAACCA 59.056 47.619 0.00 0.00 0.00 3.67
6570 8781 2.335316 AAGTTACACCTGCGAACCAA 57.665 45.000 0.00 0.00 0.00 3.67
6571 8782 1.589803 AGTTACACCTGCGAACCAAC 58.410 50.000 0.00 0.00 0.00 3.77
6572 8783 0.589708 GTTACACCTGCGAACCAACC 59.410 55.000 0.00 0.00 0.00 3.77
6573 8784 0.470766 TTACACCTGCGAACCAACCT 59.529 50.000 0.00 0.00 0.00 3.50
6574 8785 0.250124 TACACCTGCGAACCAACCTG 60.250 55.000 0.00 0.00 0.00 4.00
6575 8786 1.525995 CACCTGCGAACCAACCTGT 60.526 57.895 0.00 0.00 0.00 4.00
6576 8787 1.525995 ACCTGCGAACCAACCTGTG 60.526 57.895 0.00 0.00 0.00 3.66
6589 8800 2.879103 ACCTGTGGTTGGATGGTTAG 57.121 50.000 0.00 0.00 27.29 2.34
6590 8801 2.344592 ACCTGTGGTTGGATGGTTAGA 58.655 47.619 0.00 0.00 27.29 2.10
6591 8802 2.305927 ACCTGTGGTTGGATGGTTAGAG 59.694 50.000 0.00 0.00 27.29 2.43
6592 8803 2.356125 CCTGTGGTTGGATGGTTAGAGG 60.356 54.545 0.00 0.00 0.00 3.69
6593 8804 2.571653 CTGTGGTTGGATGGTTAGAGGA 59.428 50.000 0.00 0.00 0.00 3.71
6594 8805 2.983192 TGTGGTTGGATGGTTAGAGGAA 59.017 45.455 0.00 0.00 0.00 3.36
6595 8806 3.244770 TGTGGTTGGATGGTTAGAGGAAC 60.245 47.826 0.00 0.00 37.31 3.62
6597 8808 3.009033 TGGTTGGATGGTTAGAGGAACTG 59.991 47.826 0.00 0.00 41.55 3.16
6598 8809 3.009143 GGTTGGATGGTTAGAGGAACTGT 59.991 47.826 0.00 0.00 41.55 3.55
6599 8810 3.981071 TGGATGGTTAGAGGAACTGTG 57.019 47.619 0.00 0.00 41.55 3.66
6600 8811 2.571653 TGGATGGTTAGAGGAACTGTGG 59.428 50.000 0.00 0.00 41.55 4.17
6601 8812 2.572104 GGATGGTTAGAGGAACTGTGGT 59.428 50.000 0.00 0.00 41.55 4.16
6602 8813 3.773119 GGATGGTTAGAGGAACTGTGGTA 59.227 47.826 0.00 0.00 41.55 3.25
6603 8814 4.409247 GGATGGTTAGAGGAACTGTGGTAT 59.591 45.833 0.00 0.00 41.55 2.73
6604 8815 5.453480 GGATGGTTAGAGGAACTGTGGTATC 60.453 48.000 0.00 0.00 41.55 2.24
6605 8816 3.773119 TGGTTAGAGGAACTGTGGTATCC 59.227 47.826 0.00 0.00 41.55 2.59
6606 8817 3.134262 GGTTAGAGGAACTGTGGTATCCC 59.866 52.174 0.00 0.00 41.55 3.85
6607 8818 2.950990 AGAGGAACTGTGGTATCCCT 57.049 50.000 0.00 0.00 41.55 4.20
6608 8819 5.206587 GTTAGAGGAACTGTGGTATCCCTA 58.793 45.833 0.00 0.00 41.55 3.53
6609 8820 3.917300 AGAGGAACTGTGGTATCCCTAG 58.083 50.000 0.00 0.00 41.55 3.02
6610 8821 2.365941 GAGGAACTGTGGTATCCCTAGC 59.634 54.545 0.00 0.00 41.55 3.42
6611 8822 1.416772 GGAACTGTGGTATCCCTAGCC 59.583 57.143 0.00 0.00 0.00 3.93
6612 8823 1.416772 GAACTGTGGTATCCCTAGCCC 59.583 57.143 0.00 0.00 0.00 5.19
6613 8824 0.341961 ACTGTGGTATCCCTAGCCCA 59.658 55.000 0.00 0.00 0.00 5.36
6614 8825 0.759346 CTGTGGTATCCCTAGCCCAC 59.241 60.000 0.00 0.00 46.04 4.61
6615 8826 0.693092 TGTGGTATCCCTAGCCCACC 60.693 60.000 5.31 3.75 45.41 4.61
6616 8827 0.693092 GTGGTATCCCTAGCCCACCA 60.693 60.000 0.00 0.00 41.20 4.17
6617 8828 0.399949 TGGTATCCCTAGCCCACCAG 60.400 60.000 0.00 0.00 34.40 4.00
6618 8829 0.105142 GGTATCCCTAGCCCACCAGA 60.105 60.000 0.00 0.00 0.00 3.86
6619 8830 1.343069 GTATCCCTAGCCCACCAGAG 58.657 60.000 0.00 0.00 0.00 3.35
6620 8831 0.941963 TATCCCTAGCCCACCAGAGT 59.058 55.000 0.00 0.00 0.00 3.24
6621 8832 0.044855 ATCCCTAGCCCACCAGAGTT 59.955 55.000 0.00 0.00 0.00 3.01
6622 8833 0.617820 TCCCTAGCCCACCAGAGTTC 60.618 60.000 0.00 0.00 0.00 3.01
6623 8834 0.909610 CCCTAGCCCACCAGAGTTCA 60.910 60.000 0.00 0.00 0.00 3.18
6624 8835 0.984230 CCTAGCCCACCAGAGTTCAA 59.016 55.000 0.00 0.00 0.00 2.69
6625 8836 1.065854 CCTAGCCCACCAGAGTTCAAG 60.066 57.143 0.00 0.00 0.00 3.02
6626 8837 1.625818 CTAGCCCACCAGAGTTCAAGT 59.374 52.381 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 8.580720 TGCAATAAATTTTGTCCTACTTGCTAA 58.419 29.630 0.00 0.00 37.81 3.09
156 186 3.424703 ACAGCACTTGCATTACCAGAAT 58.575 40.909 3.62 0.00 45.16 2.40
157 187 2.813754 GACAGCACTTGCATTACCAGAA 59.186 45.455 3.62 0.00 45.16 3.02
322 361 9.921637 TCAAACTTTCAAAACTTTGACTAATGT 57.078 25.926 4.38 0.00 45.99 2.71
397 598 5.071115 AGTTTGTTTCTCTAGGAGAGCAAGT 59.929 40.000 0.00 6.20 42.04 3.16
427 628 3.330126 ACTATGAAGTAGCCTAGGCCA 57.670 47.619 30.42 20.25 43.17 5.36
478 679 4.718940 ATGCCATTTTAGGAGGAAAACG 57.281 40.909 0.00 0.00 31.35 3.60
537 2427 2.105649 TGGCTCCACTTGTCAATGTGTA 59.894 45.455 11.65 0.02 32.76 2.90
567 2457 2.945668 GCTAGCTATCCAACACCAAAGG 59.054 50.000 7.70 0.00 0.00 3.11
744 2644 2.049063 ACGTCAGCGCAAGAGACC 60.049 61.111 11.47 0.00 42.83 3.85
811 2711 7.415086 TCTTCACCTATTATTGGCCCTTTTTA 58.585 34.615 0.00 0.00 0.00 1.52
819 2719 6.039829 CCTTTTCCTCTTCACCTATTATTGGC 59.960 42.308 0.00 0.00 0.00 4.52
820 2720 6.039829 GCCTTTTCCTCTTCACCTATTATTGG 59.960 42.308 0.00 0.00 0.00 3.16
821 2721 6.830838 AGCCTTTTCCTCTTCACCTATTATTG 59.169 38.462 0.00 0.00 0.00 1.90
929 2829 2.622977 GCAAGAGAGAGAGGGAGAGGAA 60.623 54.545 0.00 0.00 0.00 3.36
930 2830 1.064017 GCAAGAGAGAGAGGGAGAGGA 60.064 57.143 0.00 0.00 0.00 3.71
937 2837 2.348660 CAAGCAAGCAAGAGAGAGAGG 58.651 52.381 0.00 0.00 0.00 3.69
1107 3046 2.347490 GAGAAGCCGACCTTGCCA 59.653 61.111 0.00 0.00 32.78 4.92
1231 3172 1.069022 CACTTCACATCGGTGCAAAGG 60.069 52.381 13.40 1.81 44.87 3.11
1318 3263 2.105821 CCACCGTCCTATCTCTCTCTCT 59.894 54.545 0.00 0.00 0.00 3.10
1319 3264 2.105134 TCCACCGTCCTATCTCTCTCTC 59.895 54.545 0.00 0.00 0.00 3.20
1320 3265 2.105821 CTCCACCGTCCTATCTCTCTCT 59.894 54.545 0.00 0.00 0.00 3.10
1329 3274 2.893215 TTTCTCTCTCCACCGTCCTA 57.107 50.000 0.00 0.00 0.00 2.94
1400 3345 3.320826 ACAAAATCAAAGGAAGGGAACGG 59.679 43.478 0.00 0.00 0.00 4.44
1566 3514 0.391793 GAAGAAACGCTGGAGGAGGG 60.392 60.000 0.00 0.00 40.53 4.30
1567 3515 0.610687 AGAAGAAACGCTGGAGGAGG 59.389 55.000 0.00 0.00 0.00 4.30
1568 3516 3.452474 CATAGAAGAAACGCTGGAGGAG 58.548 50.000 0.00 0.00 0.00 3.69
1570 3518 1.936547 GCATAGAAGAAACGCTGGAGG 59.063 52.381 0.00 0.00 0.00 4.30
1588 3536 1.374252 GGAGAAAGAACTCCGCGCA 60.374 57.895 8.75 0.00 45.30 6.09
1722 3675 7.829211 TGCATGCCTACTAGAACTATTCTTTTT 59.171 33.333 16.68 0.00 41.14 1.94
1786 3745 9.305555 AGATTGCAAATAGCTATGGAACAATAT 57.694 29.630 7.09 9.53 44.38 1.28
1787 3746 8.696043 AGATTGCAAATAGCTATGGAACAATA 57.304 30.769 7.09 0.00 44.38 1.90
1788 3747 7.592885 AGATTGCAAATAGCTATGGAACAAT 57.407 32.000 17.58 17.58 44.38 2.71
1789 3748 7.408756 AAGATTGCAAATAGCTATGGAACAA 57.591 32.000 7.09 10.07 44.38 2.83
1940 3899 9.528489 TTGGTAAAGGCTATAACTCTTTCATTT 57.472 29.630 0.00 0.00 33.44 2.32
2021 3980 2.108075 TGGGAAGCTGGAATTGTGAAGA 59.892 45.455 0.00 0.00 0.00 2.87
2176 4136 6.824704 CCAAGGGGACACGAAATAATAGTTTA 59.175 38.462 0.00 0.00 35.59 2.01
2397 4358 4.385754 GCCTTGGAGTAAATGGAAGATCCT 60.386 45.833 0.00 0.00 37.46 3.24
2476 4440 9.851686 TTAGAAGACCAGAAATTGTATGCATAT 57.148 29.630 10.16 0.00 0.00 1.78
2633 4599 8.168681 ACGTTGGAAATAAAATAAATCGCAAG 57.831 30.769 0.00 0.00 0.00 4.01
2697 4664 6.769512 TCCCCATAAAGTAGTGCATAGATTC 58.230 40.000 0.00 0.00 0.00 2.52
2735 4702 6.885952 TGTGCAACAGTAATTTAAAGGCTA 57.114 33.333 0.00 0.00 45.67 3.93
2802 4769 7.453126 TCATTTCCTTTTAGCCCACTGAATTAA 59.547 33.333 0.00 0.00 0.00 1.40
2803 4770 6.951198 TCATTTCCTTTTAGCCCACTGAATTA 59.049 34.615 0.00 0.00 0.00 1.40
2874 4932 1.604438 GGACGGCGCCAAATTCTTTTT 60.604 47.619 28.98 0.00 0.00 1.94
2875 4933 0.038618 GGACGGCGCCAAATTCTTTT 60.039 50.000 28.98 0.00 0.00 2.27
2876 4934 1.175983 TGGACGGCGCCAAATTCTTT 61.176 50.000 28.98 0.00 34.31 2.52
2877 4935 1.586154 CTGGACGGCGCCAAATTCTT 61.586 55.000 28.98 0.00 37.52 2.52
2878 4936 2.033448 TGGACGGCGCCAAATTCT 59.967 55.556 28.98 0.00 34.31 2.40
2879 4937 1.376609 ATCTGGACGGCGCCAAATTC 61.377 55.000 28.98 16.07 37.52 2.17
2880 4938 0.965363 AATCTGGACGGCGCCAAATT 60.965 50.000 28.98 16.91 37.52 1.82
2881 4939 0.965363 AAATCTGGACGGCGCCAAAT 60.965 50.000 28.98 11.48 37.52 2.32
2882 4940 1.602323 AAATCTGGACGGCGCCAAA 60.602 52.632 28.98 10.92 37.52 3.28
2883 4941 2.033448 AAATCTGGACGGCGCCAA 59.967 55.556 28.98 7.65 37.52 4.52
2884 4942 2.739849 TTCAAATCTGGACGGCGCCA 62.740 55.000 28.98 19.17 36.30 5.69
2885 4943 2.038269 TTCAAATCTGGACGGCGCC 61.038 57.895 19.07 19.07 0.00 6.53
2886 4944 1.134694 GTTCAAATCTGGACGGCGC 59.865 57.895 6.90 0.00 0.00 6.53
2887 4945 0.953471 TGGTTCAAATCTGGACGGCG 60.953 55.000 4.80 4.80 30.85 6.46
2888 4946 0.804989 CTGGTTCAAATCTGGACGGC 59.195 55.000 0.00 0.00 30.85 5.68
2889 4947 2.028112 TCTCTGGTTCAAATCTGGACGG 60.028 50.000 0.00 0.00 30.85 4.79
2890 4948 3.319137 TCTCTGGTTCAAATCTGGACG 57.681 47.619 0.00 0.00 30.85 4.79
2891 4949 5.096443 AGATCTCTGGTTCAAATCTGGAC 57.904 43.478 0.00 0.00 0.00 4.02
2892 4950 5.249163 TGAAGATCTCTGGTTCAAATCTGGA 59.751 40.000 0.00 0.00 0.00 3.86
2893 4951 5.494724 TGAAGATCTCTGGTTCAAATCTGG 58.505 41.667 0.00 0.00 0.00 3.86
2894 4952 5.064962 GCTGAAGATCTCTGGTTCAAATCTG 59.935 44.000 0.00 0.00 30.00 2.90
2895 4953 5.184711 GCTGAAGATCTCTGGTTCAAATCT 58.815 41.667 0.00 0.00 30.00 2.40
2896 4954 4.033817 CGCTGAAGATCTCTGGTTCAAATC 59.966 45.833 0.00 0.00 30.00 2.17
2897 4955 3.937706 CGCTGAAGATCTCTGGTTCAAAT 59.062 43.478 0.00 0.00 30.00 2.32
2898 4956 3.244215 ACGCTGAAGATCTCTGGTTCAAA 60.244 43.478 0.00 0.00 30.00 2.69
2899 4957 2.300152 ACGCTGAAGATCTCTGGTTCAA 59.700 45.455 0.00 0.00 30.00 2.69
2900 4958 1.895798 ACGCTGAAGATCTCTGGTTCA 59.104 47.619 0.00 0.00 0.00 3.18
2901 4959 2.266554 CACGCTGAAGATCTCTGGTTC 58.733 52.381 0.00 0.00 0.00 3.62
2902 4960 1.620819 ACACGCTGAAGATCTCTGGTT 59.379 47.619 0.00 0.00 0.00 3.67
2903 4961 1.067283 CACACGCTGAAGATCTCTGGT 60.067 52.381 0.00 0.00 0.00 4.00
2904 4962 1.203287 TCACACGCTGAAGATCTCTGG 59.797 52.381 0.00 0.00 0.00 3.86
2905 4963 2.643933 TCACACGCTGAAGATCTCTG 57.356 50.000 0.00 0.00 0.00 3.35
2906 4964 3.321497 GTTTCACACGCTGAAGATCTCT 58.679 45.455 0.00 0.00 40.12 3.10
2907 4965 2.091277 CGTTTCACACGCTGAAGATCTC 59.909 50.000 0.00 0.00 43.37 2.75
2908 4966 2.061773 CGTTTCACACGCTGAAGATCT 58.938 47.619 0.00 0.00 43.37 2.75
2909 4967 2.493997 CGTTTCACACGCTGAAGATC 57.506 50.000 0.00 0.00 43.37 2.75
2919 4977 0.782384 CTAGCACGTCCGTTTCACAC 59.218 55.000 0.00 0.00 0.00 3.82
2920 4978 0.669619 TCTAGCACGTCCGTTTCACA 59.330 50.000 0.00 0.00 0.00 3.58
2921 4979 1.058404 GTCTAGCACGTCCGTTTCAC 58.942 55.000 0.00 0.00 0.00 3.18
2922 4980 0.038892 GGTCTAGCACGTCCGTTTCA 60.039 55.000 0.00 0.00 0.00 2.69
2923 4981 0.038892 TGGTCTAGCACGTCCGTTTC 60.039 55.000 0.00 0.00 0.00 2.78
2924 4982 0.390124 TTGGTCTAGCACGTCCGTTT 59.610 50.000 0.00 0.00 0.00 3.60
2925 4983 0.319297 GTTGGTCTAGCACGTCCGTT 60.319 55.000 0.00 0.00 0.00 4.44
2926 4984 1.177256 AGTTGGTCTAGCACGTCCGT 61.177 55.000 0.00 0.00 0.00 4.69
2927 4985 0.806868 TAGTTGGTCTAGCACGTCCG 59.193 55.000 0.00 0.00 0.00 4.79
2928 4986 3.243334 GGTATAGTTGGTCTAGCACGTCC 60.243 52.174 0.00 0.00 31.67 4.79
2947 5005 2.696707 AGAACTGAAAGGTGTCGTGGTA 59.303 45.455 0.00 0.00 39.30 3.25
3062 5120 0.608640 ACGCTGAAGATCTCCGGTTT 59.391 50.000 0.00 0.00 0.00 3.27
3162 5223 2.482721 CGTCATAATTGGCCCGGTAATC 59.517 50.000 0.00 0.00 0.00 1.75
3171 5232 1.670811 CAGGGTGACGTCATAATTGGC 59.329 52.381 23.12 6.52 0.00 4.52
3195 5256 1.304381 GACAGGGAAAGGGCATGCA 60.304 57.895 21.36 0.00 0.00 3.96
3222 5284 4.697756 CCCCGTCGTGCCATGTGT 62.698 66.667 0.00 0.00 0.00 3.72
3223 5285 4.386951 TCCCCGTCGTGCCATGTG 62.387 66.667 0.00 0.00 0.00 3.21
3233 5295 4.668118 TTTGTCGCCGTCCCCGTC 62.668 66.667 0.00 0.00 0.00 4.79
3235 5297 4.675029 AGTTTGTCGCCGTCCCCG 62.675 66.667 0.00 0.00 0.00 5.73
3236 5298 3.047877 CAGTTTGTCGCCGTCCCC 61.048 66.667 0.00 0.00 0.00 4.81
3237 5299 3.723348 GCAGTTTGTCGCCGTCCC 61.723 66.667 0.00 0.00 0.00 4.46
3238 5300 2.054140 TTTGCAGTTTGTCGCCGTCC 62.054 55.000 0.00 0.00 0.00 4.79
3239 5301 0.248296 TTTTGCAGTTTGTCGCCGTC 60.248 50.000 0.00 0.00 0.00 4.79
3241 5303 1.052287 GATTTTGCAGTTTGTCGCCG 58.948 50.000 0.00 0.00 0.00 6.46
3242 5304 1.418373 GGATTTTGCAGTTTGTCGCC 58.582 50.000 0.00 0.00 0.00 5.54
3243 5305 1.269517 TGGGATTTTGCAGTTTGTCGC 60.270 47.619 0.00 0.00 0.00 5.19
3256 5318 1.679680 CGAGCATGCAAGATGGGATTT 59.320 47.619 21.98 0.00 0.00 2.17
3347 5409 3.566742 GTGGTAGAGCTAGAGGTTAGAGC 59.433 52.174 0.00 0.00 36.42 4.09
3361 5423 3.724508 ATCGATGAGCAAGTGGTAGAG 57.275 47.619 0.00 0.00 0.00 2.43
3383 5445 8.015185 AGTCGGCTTATTTACCACTAGAAATA 57.985 34.615 0.00 0.00 0.00 1.40
3471 5533 3.528853 ACGGAACAGACCACGTCA 58.471 55.556 0.00 0.00 33.92 4.35
3538 5601 5.529060 GGGTTTCTCCATCATGTGTTCTATC 59.471 44.000 0.00 0.00 38.11 2.08
3590 5653 5.218885 CCACAAATAAACGATGACAAAGCA 58.781 37.500 0.00 0.00 0.00 3.91
3597 5660 4.022413 TGGTCCCACAAATAAACGATGA 57.978 40.909 0.00 0.00 0.00 2.92
3619 5682 4.632153 CAGTAGCCGCTAAGGTATCAAAT 58.368 43.478 0.46 0.00 43.70 2.32
3627 5690 1.398390 CAAAAGCAGTAGCCGCTAAGG 59.602 52.381 0.46 0.00 43.56 2.69
3726 5791 7.127339 TCCTTTAGGCTGTAGAAATACCATTCT 59.873 37.037 0.00 0.00 37.98 2.40
3741 5806 4.154918 GCATATTTCCGATCCTTTAGGCTG 59.845 45.833 0.00 0.00 34.44 4.85
3780 5845 0.038526 CCGACACAGTAGCTCGGTTT 60.039 55.000 0.00 0.00 41.75 3.27
3816 5881 0.623324 CCACCACCCTATCCTTCCCA 60.623 60.000 0.00 0.00 0.00 4.37
3915 5980 3.493334 CCTGTATTCATGCATCACCCAT 58.507 45.455 0.00 0.00 0.00 4.00
3937 6002 1.748122 GCTCATGTGCACCCTCCAG 60.748 63.158 15.69 4.28 0.00 3.86
4160 6225 3.397482 ACAAGCTTAGACACTGCAAGAG 58.603 45.455 0.00 0.00 37.43 2.85
4192 6257 5.225899 ACAGTACGTCAAACTTGAAAACC 57.774 39.130 0.00 0.00 39.21 3.27
4618 6692 7.295930 GTGGTGTGTCTACTTTTATGCTTAAC 58.704 38.462 0.00 0.00 0.00 2.01
4665 6752 6.586844 GGTCTCTATCAGTTGTAAGTGTGTTC 59.413 42.308 0.00 0.00 0.00 3.18
4743 6830 2.937469 TGTTTGCAAAGTCACCACAG 57.063 45.000 13.26 0.00 0.00 3.66
4775 6862 5.871396 TCCACTTCACTATCCTGGATTAC 57.129 43.478 15.55 0.00 0.00 1.89
4957 7047 2.027837 GCATCCAACCAAGCATTTTCCT 60.028 45.455 0.00 0.00 0.00 3.36
4959 7049 3.042871 TGCATCCAACCAAGCATTTTC 57.957 42.857 0.00 0.00 31.05 2.29
5127 7217 7.134362 AGGATCAAGAAGAGAGCATTGATTA 57.866 36.000 0.00 0.00 41.27 1.75
5293 7384 1.078143 GGTGGTGTCCATGAGAGGC 60.078 63.158 0.00 0.00 35.28 4.70
5501 7604 3.199946 AGGACCTTCTTGTCACAGTTCAA 59.800 43.478 0.00 0.00 36.97 2.69
5843 7977 7.212976 ACATACTACAGCAATCATTAGAGTGG 58.787 38.462 0.00 0.00 40.08 4.00
5861 7995 8.818622 ACCTGTACTTCTGAATGTACATACTA 57.181 34.615 21.74 0.00 45.05 1.82
5900 8034 3.474600 GGGGACATCAATGACTGATCTG 58.525 50.000 0.00 0.00 43.28 2.90
5902 8036 2.441001 AGGGGGACATCAATGACTGATC 59.559 50.000 0.00 0.00 43.28 2.92
5969 8169 5.327091 GTTCTCAATCAACCATGATGTTCG 58.673 41.667 0.00 0.00 45.60 3.95
6134 8335 2.229792 TGAATTTCACTGGCACCTGTC 58.770 47.619 0.00 0.00 0.00 3.51
6178 8381 1.400888 CGCAACCACGCAACATATTGT 60.401 47.619 0.00 0.00 38.17 2.71
6179 8382 1.258427 CGCAACCACGCAACATATTG 58.742 50.000 0.00 0.00 38.99 1.90
6180 8383 3.692998 CGCAACCACGCAACATATT 57.307 47.368 0.00 0.00 0.00 1.28
6276 8485 2.352030 CGCACGTACTACCAAAAGAGGA 60.352 50.000 0.00 0.00 0.00 3.71
6378 8588 5.412286 TGGACCAAAACTATACCTAAAACGC 59.588 40.000 0.00 0.00 0.00 4.84
6396 8606 9.110502 GTGGTAAAAATGTAAAATTTTGGACCA 57.889 29.630 13.76 17.93 41.02 4.02
6444 8654 8.328055 TCTATGCATAGATCCACATATCCAAT 57.672 34.615 28.69 0.00 34.63 3.16
6475 8686 7.281040 ACATGATATACAAGCATTTTGAGGG 57.719 36.000 0.00 0.00 0.00 4.30
6542 8753 4.056050 CGCAGGTGTAACTTTGAGTTAGT 58.944 43.478 1.02 0.00 40.95 2.24
6570 8781 2.305927 CTCTAACCATCCAACCACAGGT 59.694 50.000 0.00 0.00 37.65 4.00
6571 8782 2.356125 CCTCTAACCATCCAACCACAGG 60.356 54.545 0.00 0.00 0.00 4.00
6572 8783 2.571653 TCCTCTAACCATCCAACCACAG 59.428 50.000 0.00 0.00 0.00 3.66
6573 8784 2.626785 TCCTCTAACCATCCAACCACA 58.373 47.619 0.00 0.00 0.00 4.17
6574 8785 3.009143 AGTTCCTCTAACCATCCAACCAC 59.991 47.826 0.00 0.00 39.03 4.16
6575 8786 3.009033 CAGTTCCTCTAACCATCCAACCA 59.991 47.826 0.00 0.00 39.03 3.67
6576 8787 3.009143 ACAGTTCCTCTAACCATCCAACC 59.991 47.826 0.00 0.00 39.03 3.77
6577 8788 4.003648 CACAGTTCCTCTAACCATCCAAC 58.996 47.826 0.00 0.00 39.03 3.77
6578 8789 3.009033 CCACAGTTCCTCTAACCATCCAA 59.991 47.826 0.00 0.00 39.03 3.53
6579 8790 2.571653 CCACAGTTCCTCTAACCATCCA 59.428 50.000 0.00 0.00 39.03 3.41
6580 8791 2.572104 ACCACAGTTCCTCTAACCATCC 59.428 50.000 0.00 0.00 39.03 3.51
6581 8792 3.983044 ACCACAGTTCCTCTAACCATC 57.017 47.619 0.00 0.00 39.03 3.51
6582 8793 4.409247 GGATACCACAGTTCCTCTAACCAT 59.591 45.833 0.00 0.00 39.03 3.55
6583 8794 3.773119 GGATACCACAGTTCCTCTAACCA 59.227 47.826 0.00 0.00 39.03 3.67
6584 8795 4.403585 GGATACCACAGTTCCTCTAACC 57.596 50.000 0.00 0.00 39.03 2.85
6600 8811 1.343069 CTCTGGTGGGCTAGGGATAC 58.657 60.000 0.00 0.00 0.00 2.24
6601 8812 0.941963 ACTCTGGTGGGCTAGGGATA 59.058 55.000 0.00 0.00 0.00 2.59
6602 8813 0.044855 AACTCTGGTGGGCTAGGGAT 59.955 55.000 0.00 0.00 0.00 3.85
6603 8814 0.617820 GAACTCTGGTGGGCTAGGGA 60.618 60.000 0.00 0.00 0.00 4.20
6604 8815 0.909610 TGAACTCTGGTGGGCTAGGG 60.910 60.000 0.00 0.00 0.00 3.53
6605 8816 0.984230 TTGAACTCTGGTGGGCTAGG 59.016 55.000 0.00 0.00 0.00 3.02
6606 8817 1.625818 ACTTGAACTCTGGTGGGCTAG 59.374 52.381 0.00 0.00 0.00 3.42
6607 8818 1.729586 ACTTGAACTCTGGTGGGCTA 58.270 50.000 0.00 0.00 0.00 3.93
6608 8819 2.544768 ACTTGAACTCTGGTGGGCT 58.455 52.632 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.