Multiple sequence alignment - TraesCS7D01G249400

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 TraesCS7D01G249400 chr7D 100.000 6935 0 0 1 6935 220522130 220515196 0.000000e+00 12807.0
1 TraesCS7D01G249400 chr7D 80.456 307 34 16 5802 6091 618329191 618328894 1.960000e-50 211.0
2 TraesCS7D01G249400 chr7D 94.624 93 3 2 2974 3066 220519070 220518980 7.250000e-30 143.0
3 TraesCS7D01G249400 chr7D 94.624 93 3 2 3061 3151 220519157 220519065 7.250000e-30 143.0
4 TraesCS7D01G249400 chr7B 94.560 3272 119 19 3681 6935 178402765 178405994 0.000000e+00 5001.0
5 TraesCS7D01G249400 chr7B 95.240 2248 91 7 827 3065 178399678 178401918 0.000000e+00 3544.0
6 TraesCS7D01G249400 chr7B 89.271 494 37 4 250 740 178391771 178392251 7.690000e-169 604.0
7 TraesCS7D01G249400 chr7B 86.316 570 45 16 3058 3600 178401826 178402389 2.150000e-164 590.0
8 TraesCS7D01G249400 chr7B 90.000 250 25 0 1 250 178391475 178391724 2.410000e-84 324.0
9 TraesCS7D01G249400 chr7B 85.806 155 22 0 42 196 380994776 380994930 1.550000e-36 165.0
10 TraesCS7D01G249400 chr7A 94.181 2681 103 20 3688 6345 232753392 232750742 0.000000e+00 4037.0
11 TraesCS7D01G249400 chr7A 94.723 2255 97 11 817 3066 232758697 232756460 0.000000e+00 3485.0
12 TraesCS7D01G249400 chr7A 96.759 432 14 0 6504 6935 232750729 232750298 0.000000e+00 721.0
13 TraesCS7D01G249400 chr7A 88.757 507 31 7 250 746 232759175 232758685 1.290000e-166 597.0
14 TraesCS7D01G249400 chr7A 89.067 375 33 5 3226 3599 232756352 232755985 6.340000e-125 459.0
15 TraesCS7D01G249400 chr7A 91.200 250 21 1 1 250 232759468 232759220 8.620000e-89 339.0
16 TraesCS7D01G249400 chr7A 95.294 170 7 1 3058 3227 232756552 232756384 1.150000e-67 268.0
17 TraesCS7D01G249400 chr4B 92.994 157 11 0 6344 6500 135218208 135218052 5.410000e-56 230.0
18 TraesCS7D01G249400 chr4B 90.909 165 14 1 6344 6507 190690805 190690969 3.260000e-53 220.0
19 TraesCS7D01G249400 chr4B 90.476 168 12 2 6345 6511 474400433 474400597 1.170000e-52 219.0
20 TraesCS7D01G249400 chr1A 93.421 152 10 0 6344 6495 566481167 566481016 7.000000e-55 226.0
21 TraesCS7D01G249400 chr3D 90.909 165 13 2 6344 6507 537154704 537154867 3.260000e-53 220.0
22 TraesCS7D01G249400 chr2A 90.419 167 14 2 6344 6509 606381407 606381242 1.170000e-52 219.0
23 TraesCS7D01G249400 chr1D 90.476 168 13 1 6344 6511 463382064 463381900 1.170000e-52 219.0
24 TraesCS7D01G249400 chr2D 87.978 183 16 6 6344 6526 289157299 289157123 1.960000e-50 211.0
25 TraesCS7D01G249400 chr4A 87.742 155 19 0 42 196 429240310 429240464 1.540000e-41 182.0
26 TraesCS7D01G249400 chr5D 87.838 148 15 3 50 196 63772402 63772257 3.330000e-38 171.0
27 TraesCS7D01G249400 chr2B 85.897 156 22 0 41 196 404458597 404458752 4.300000e-37 167.0
28 TraesCS7D01G249400 chr2B 78.528 163 30 5 250 409 101125716 101125556 1.230000e-17 102.0
29 TraesCS7D01G249400 chr6D 86.861 137 17 1 41 176 273274586 273274722 1.200000e-32 152.0
30 TraesCS7D01G249400 chr3B 84.416 154 23 1 44 196 341558625 341558472 4.330000e-32 150.0
31 TraesCS7D01G249400 chr3B 90.566 53 5 0 311 363 704876774 704876722 3.470000e-08 71.3
32 TraesCS7D01G249400 chr3A 83.851 161 23 3 42 200 118443284 118443125 4.330000e-32 150.0
33 TraesCS7D01G249400 chr5B 77.727 220 39 10 246 459 246591332 246591547 7.300000e-25 126.0
34 TraesCS7D01G249400 chr6B 92.593 54 4 0 310 363 659578707 659578760 2.070000e-10 78.7


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 TraesCS7D01G249400 chr7D 220515196 220522130 6934 True 4364.333333 12807 96.416000 1 6935 3 chr7D.!!$R2 6934
1 TraesCS7D01G249400 chr7B 178399678 178405994 6316 False 3045.000000 5001 92.038667 827 6935 3 chr7B.!!$F3 6108
2 TraesCS7D01G249400 chr7B 178391475 178392251 776 False 464.000000 604 89.635500 1 740 2 chr7B.!!$F2 739
3 TraesCS7D01G249400 chr7A 232750298 232759468 9170 True 1415.142857 4037 92.854429 1 6935 7 chr7A.!!$R1 6934

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
207 209 0.112606 AGACCTCCCAAGAGACGACA 59.887 55.0 0.00 0.00 43.39 4.35 F
956 1015 1.184970 ATGCCCCTTTTGACCAACCG 61.185 55.0 0.00 0.00 0.00 4.44 F
1640 1705 0.531532 CCCAGGAGAGCTATGTTGCG 60.532 60.0 0.00 0.00 38.13 4.85 F
1883 1948 0.037326 TAGCAGACCACTTTGCCTCG 60.037 55.0 0.00 0.00 41.17 4.63 F
2667 2735 0.330604 AGGCATGATGTCCACAAGCT 59.669 50.0 0.00 0.00 33.42 3.74 F
2668 2736 0.454600 GGCATGATGTCCACAAGCTG 59.545 55.0 0.00 0.00 33.42 4.24 F
3921 6529 0.675633 ACTGGCAGAAAATGTGGCAC 59.324 50.0 23.66 11.55 44.85 5.01 F
5473 8110 0.176910 GCTGCTTGTAGGGAGGAGAC 59.823 60.0 0.00 0.00 34.87 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 1702 0.034756 ACCTTGATGCACAGTACGCA 59.965 50.000 0.00 0.00 44.94 5.24 R
1883 1948 1.202818 ACACCTTCTGAGACAAAGGGC 60.203 52.381 3.89 0.00 45.27 5.19 R
3277 3379 0.677842 GCATCATGGGCCAATTCTCC 59.322 55.000 11.89 0.00 0.00 3.71 R
3669 4895 2.092323 AGGTTCCCTAAAGCATTTCGC 58.908 47.619 0.00 0.00 40.09 4.70 R
4085 6693 1.202758 GGGTAATCGATGCCATCACCA 60.203 52.381 17.63 0.00 35.05 4.17 R
4140 6748 1.547820 TCATCAGTGACTCTGTCAGGC 59.452 52.381 0.00 0.00 43.57 4.85 R
5516 8153 0.101579 GAGGTACTGCTCTTCCTCGC 59.898 60.000 0.00 0.00 41.55 5.03 R
6689 9339 2.908940 CTGGGATTCATGGCCGGC 60.909 66.667 21.18 21.18 0.00 6.13 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
48 49 4.994852 GGTAGCATTATAAGATTGTCGGCA 59.005 41.667 0.00 0.00 0.00 5.69
83 84 0.264657 TACCCAGATCTGCCTGCCTA 59.735 55.000 17.76 0.00 32.97 3.93
109 110 2.203788 AACCTGGCTCCCTCGACA 60.204 61.111 0.00 0.00 0.00 4.35
205 207 1.203013 TCAAGACCTCCCAAGAGACGA 60.203 52.381 0.00 0.00 43.39 4.20
207 209 0.112606 AGACCTCCCAAGAGACGACA 59.887 55.000 0.00 0.00 43.39 4.35
217 219 2.692557 CAAGAGACGACAGATGGAGGAT 59.307 50.000 0.00 0.00 0.00 3.24
224 226 3.007940 ACGACAGATGGAGGATGAAACAA 59.992 43.478 0.00 0.00 0.00 2.83
246 248 1.468506 TTGGACACCGAGCACTGCTA 61.469 55.000 2.71 0.00 39.88 3.49
286 335 1.197492 GTCGTGCTTGCATGAATGTCA 59.803 47.619 17.65 0.00 0.00 3.58
350 399 8.735315 TCATTCAGTTTGTTGAAGAAGTGTTTA 58.265 29.630 0.00 0.00 40.16 2.01
367 416 3.508012 TGTTTAAAATGTATGCGGGCAGT 59.492 39.130 0.00 0.00 0.00 4.40
368 417 3.773860 TTAAAATGTATGCGGGCAGTG 57.226 42.857 0.00 0.00 0.00 3.66
455 504 5.127491 AGGAAATTTACAGGTTGTCGTTGA 58.873 37.500 2.58 0.00 0.00 3.18
471 520 9.745880 GTTGTCGTTGAAGATATTCTTATAGGA 57.254 33.333 1.19 0.00 36.73 2.94
528 577 6.035650 GTGCATGTAACTAGCTTCAACGATTA 59.964 38.462 0.00 0.00 0.00 1.75
531 580 8.215132 GCATGTAACTAGCTTCAACGATTATAC 58.785 37.037 0.00 0.00 0.00 1.47
600 649 8.936864 CGTAAAATTCTAGACAAGAGATTGGTT 58.063 33.333 0.00 0.00 35.05 3.67
607 656 9.658799 TTCTAGACAAGAGATTGGTTATTTCAG 57.341 33.333 0.00 0.00 35.05 3.02
648 700 9.744468 AAAGCATCTTTTTCTATAAAAACGTGT 57.256 25.926 0.00 0.00 39.16 4.49
670 722 1.694150 CTGAGGTGTGAAGTGGGAGAA 59.306 52.381 0.00 0.00 0.00 2.87
758 817 9.918630 AAAACATCTTACATTTTGAGAATGAGG 57.081 29.630 2.46 0.00 0.00 3.86
759 818 8.641498 AACATCTTACATTTTGAGAATGAGGT 57.359 30.769 2.46 0.00 0.00 3.85
760 819 8.048534 ACATCTTACATTTTGAGAATGAGGTG 57.951 34.615 2.46 0.20 0.00 4.00
761 820 7.121759 ACATCTTACATTTTGAGAATGAGGTGG 59.878 37.037 2.46 0.00 0.00 4.61
762 821 6.542821 TCTTACATTTTGAGAATGAGGTGGT 58.457 36.000 2.46 0.00 0.00 4.16
763 822 6.430925 TCTTACATTTTGAGAATGAGGTGGTG 59.569 38.462 2.46 0.00 0.00 4.17
764 823 3.256631 ACATTTTGAGAATGAGGTGGTGC 59.743 43.478 2.46 0.00 0.00 5.01
765 824 2.655090 TTTGAGAATGAGGTGGTGCA 57.345 45.000 0.00 0.00 0.00 4.57
766 825 2.655090 TTGAGAATGAGGTGGTGCAA 57.345 45.000 0.00 0.00 0.00 4.08
767 826 2.655090 TGAGAATGAGGTGGTGCAAA 57.345 45.000 0.00 0.00 0.00 3.68
768 827 2.942804 TGAGAATGAGGTGGTGCAAAA 58.057 42.857 0.00 0.00 0.00 2.44
769 828 3.295093 TGAGAATGAGGTGGTGCAAAAA 58.705 40.909 0.00 0.00 0.00 1.94
822 881 8.986477 AAATGCTATCCTACAAATCAAACAAC 57.014 30.769 0.00 0.00 0.00 3.32
823 882 6.509418 TGCTATCCTACAAATCAAACAACC 57.491 37.500 0.00 0.00 0.00 3.77
824 883 6.245408 TGCTATCCTACAAATCAAACAACCT 58.755 36.000 0.00 0.00 0.00 3.50
825 884 7.398829 TGCTATCCTACAAATCAAACAACCTA 58.601 34.615 0.00 0.00 0.00 3.08
856 915 7.722949 AAAATCCCAAAGATCAGATTGCTTA 57.277 32.000 0.00 0.00 32.47 3.09
956 1015 1.184970 ATGCCCCTTTTGACCAACCG 61.185 55.000 0.00 0.00 0.00 4.44
973 1032 2.774774 GCTCTCTGCACTTTCGCG 59.225 61.111 0.00 0.00 42.31 5.87
1320 1379 2.203337 TGCCACTGCTTCCACCAC 60.203 61.111 0.00 0.00 38.71 4.16
1359 1418 4.518970 GCCATGTCTTCTTTTACTGGTTGA 59.481 41.667 0.00 0.00 0.00 3.18
1360 1419 5.009610 GCCATGTCTTCTTTTACTGGTTGAA 59.990 40.000 0.00 0.00 0.00 2.69
1437 1497 4.319261 CCAACGTAGCCTAAACAGTTGTTC 60.319 45.833 0.00 0.00 37.25 3.18
1592 1657 8.419076 TGAGCCTTTAAAATTTTCTGACAAAC 57.581 30.769 6.72 0.00 0.00 2.93
1637 1702 2.503356 CTGTTCCCAGGAGAGCTATGTT 59.497 50.000 0.00 0.00 34.90 2.71
1640 1705 0.531532 CCCAGGAGAGCTATGTTGCG 60.532 60.000 0.00 0.00 38.13 4.85
1661 1726 1.331214 ACTGTGCATCAAGGTTTGGG 58.669 50.000 0.00 0.00 0.00 4.12
1774 1839 0.868406 GAGCCGTTTGACCTTGACAG 59.132 55.000 0.00 0.00 0.00 3.51
1777 1842 0.588252 CCGTTTGACCTTGACAGCAG 59.412 55.000 0.00 0.00 0.00 4.24
1814 1879 9.333724 GGAAATAATTCAAATGGCATTGAGAAT 57.666 29.630 24.20 24.20 40.21 2.40
1829 1894 6.259608 GCATTGAGAATGACAGTGCTAATAGT 59.740 38.462 0.00 0.00 43.88 2.12
1883 1948 0.037326 TAGCAGACCACTTTGCCTCG 60.037 55.000 0.00 0.00 41.17 4.63
1988 2053 2.034685 CACAACCAGAGAAGACACTCGA 59.965 50.000 0.00 0.00 41.25 4.04
2160 2225 1.152860 TTGGCAGAGTTTTCCGGCA 60.153 52.632 0.00 0.00 0.00 5.69
2201 2266 5.336150 ACACTGATGTCTATCAAGGACAG 57.664 43.478 0.00 0.00 45.14 3.51
2202 2267 4.118410 CACTGATGTCTATCAAGGACAGC 58.882 47.826 5.34 5.34 46.31 4.40
2527 2593 3.365265 GTTCTTGGTGGCTGGCCG 61.365 66.667 7.14 0.00 39.42 6.13
2557 2623 9.961265 AAAAACAATTTCTACTTGGCTACTTAC 57.039 29.630 0.00 0.00 0.00 2.34
2617 2685 4.889409 TGGCATTTCCTTATGTCTTGGATC 59.111 41.667 0.00 0.00 31.45 3.36
2619 2687 4.816385 GCATTTCCTTATGTCTTGGATCGA 59.184 41.667 0.00 0.00 0.00 3.59
2667 2735 0.330604 AGGCATGATGTCCACAAGCT 59.669 50.000 0.00 0.00 33.42 3.74
2668 2736 0.454600 GGCATGATGTCCACAAGCTG 59.545 55.000 0.00 0.00 33.42 4.24
2690 2758 7.339212 AGCTGTCATACTGTGGCAAATATTAAA 59.661 33.333 0.00 0.00 42.94 1.52
2719 2788 9.771915 AACATTTGTCAAAAAGCAAATAGTTTG 57.228 25.926 1.31 0.00 41.62 2.93
2745 2814 3.009723 ACATTATGGGCACTTCAAGACG 58.990 45.455 0.00 0.00 0.00 4.18
2747 2816 2.672961 TATGGGCACTTCAAGACGAG 57.327 50.000 0.00 0.00 0.00 4.18
2778 2847 9.458727 CCAAGATGCAAGATTACCTATATTGAT 57.541 33.333 0.00 0.00 37.59 2.57
2842 2911 7.956420 TTAATACTTTATCGCGGTCATCATT 57.044 32.000 6.13 0.00 0.00 2.57
2845 2914 4.188462 ACTTTATCGCGGTCATCATTTCA 58.812 39.130 6.13 0.00 0.00 2.69
2851 2920 5.553290 TCGCGGTCATCATTTCATAAAAA 57.447 34.783 6.13 0.00 0.00 1.94
2878 2947 8.980481 AGCCGGGGATTTTTATATCAATATAG 57.020 34.615 2.18 0.00 0.00 1.31
2913 2982 8.506168 TTAATTATCCAATCACAAGAGTCCAC 57.494 34.615 0.00 0.00 0.00 4.02
2949 3018 9.593134 TGCAAGTAAAATGTTAATTCTTGTGTT 57.407 25.926 6.43 0.00 32.03 3.32
2972 3041 6.537453 TCTTCTGTTCTATCCTTGGAAGAG 57.463 41.667 0.00 0.00 35.73 2.85
3048 3117 7.721286 ACTCATTAGTATTTGCAGCTGATAC 57.279 36.000 20.43 16.16 32.84 2.24
3050 3119 5.177511 TCATTAGTATTTGCAGCTGATACGC 59.822 40.000 20.43 0.98 32.81 4.42
3051 3120 3.185246 AGTATTTGCAGCTGATACGCT 57.815 42.857 20.43 4.59 41.90 5.07
3052 3121 4.322080 AGTATTTGCAGCTGATACGCTA 57.678 40.909 20.43 0.00 38.41 4.26
3054 3123 5.300752 AGTATTTGCAGCTGATACGCTATT 58.699 37.500 20.43 0.00 38.41 1.73
3055 3124 4.739046 ATTTGCAGCTGATACGCTATTC 57.261 40.909 20.43 0.00 38.41 1.75
3056 3125 1.770957 TGCAGCTGATACGCTATTCG 58.229 50.000 20.43 0.00 38.41 3.34
3057 3126 1.063806 GCAGCTGATACGCTATTCGG 58.936 55.000 20.43 0.00 43.86 4.30
3058 3127 1.335964 GCAGCTGATACGCTATTCGGA 60.336 52.381 20.43 0.00 43.86 4.55
3059 3128 2.862530 GCAGCTGATACGCTATTCGGAA 60.863 50.000 20.43 0.00 43.86 4.30
3060 3129 2.726760 CAGCTGATACGCTATTCGGAAC 59.273 50.000 8.42 0.00 43.86 3.62
3061 3130 2.361119 AGCTGATACGCTATTCGGAACA 59.639 45.455 0.00 0.00 43.86 3.18
3062 3131 3.120792 GCTGATACGCTATTCGGAACAA 58.879 45.455 0.00 0.00 43.86 2.83
3063 3132 3.554324 GCTGATACGCTATTCGGAACAAA 59.446 43.478 0.00 0.00 43.86 2.83
3064 3133 4.033587 GCTGATACGCTATTCGGAACAAAA 59.966 41.667 0.00 0.00 43.86 2.44
3065 3134 5.446741 GCTGATACGCTATTCGGAACAAAAA 60.447 40.000 0.00 0.00 43.86 1.94
3066 3135 6.102006 TGATACGCTATTCGGAACAAAAAG 57.898 37.500 0.00 0.00 43.86 2.27
3067 3136 3.197434 ACGCTATTCGGAACAAAAAGC 57.803 42.857 0.00 0.00 43.86 3.51
3068 3137 2.812011 ACGCTATTCGGAACAAAAAGCT 59.188 40.909 0.00 0.00 43.86 3.74
3069 3138 3.998341 ACGCTATTCGGAACAAAAAGCTA 59.002 39.130 0.00 0.00 43.86 3.32
3070 3139 4.092968 ACGCTATTCGGAACAAAAAGCTAG 59.907 41.667 0.00 0.00 43.86 3.42
3071 3140 4.328983 CGCTATTCGGAACAAAAAGCTAGA 59.671 41.667 0.00 0.00 33.78 2.43
3072 3141 5.500931 CGCTATTCGGAACAAAAAGCTAGAG 60.501 44.000 0.00 0.00 33.78 2.43
3073 3142 5.351740 GCTATTCGGAACAAAAAGCTAGAGT 59.648 40.000 0.00 0.00 0.00 3.24
3074 3143 6.128254 GCTATTCGGAACAAAAAGCTAGAGTT 60.128 38.462 0.00 0.00 0.00 3.01
3075 3144 6.635030 ATTCGGAACAAAAAGCTAGAGTTT 57.365 33.333 0.00 0.00 0.00 2.66
3076 3145 5.418310 TCGGAACAAAAAGCTAGAGTTTG 57.582 39.130 0.00 2.88 38.06 2.93
3077 3146 3.975035 CGGAACAAAAAGCTAGAGTTTGC 59.025 43.478 11.14 0.00 36.01 3.68
3078 3147 4.497340 CGGAACAAAAAGCTAGAGTTTGCA 60.497 41.667 11.14 0.00 36.01 4.08
3079 3148 4.740205 GGAACAAAAAGCTAGAGTTTGCAC 59.260 41.667 11.14 7.11 36.01 4.57
3080 3149 4.307443 ACAAAAAGCTAGAGTTTGCACC 57.693 40.909 11.14 0.00 36.01 5.01
3081 3150 3.243068 ACAAAAAGCTAGAGTTTGCACCG 60.243 43.478 11.14 0.00 36.01 4.94
3082 3151 2.256117 AAAGCTAGAGTTTGCACCGT 57.744 45.000 0.00 0.00 0.00 4.83
3083 3152 2.256117 AAGCTAGAGTTTGCACCGTT 57.744 45.000 0.00 0.00 0.00 4.44
3084 3153 3.396260 AAGCTAGAGTTTGCACCGTTA 57.604 42.857 0.00 0.00 0.00 3.18
3085 3154 3.611766 AGCTAGAGTTTGCACCGTTAT 57.388 42.857 0.00 0.00 0.00 1.89
3086 3155 3.939066 AGCTAGAGTTTGCACCGTTATT 58.061 40.909 0.00 0.00 0.00 1.40
3087 3156 3.684788 AGCTAGAGTTTGCACCGTTATTG 59.315 43.478 0.00 0.00 0.00 1.90
3088 3157 3.682858 GCTAGAGTTTGCACCGTTATTGA 59.317 43.478 0.00 0.00 0.00 2.57
3089 3158 4.201724 GCTAGAGTTTGCACCGTTATTGAG 60.202 45.833 0.00 0.00 0.00 3.02
3090 3159 3.740115 AGAGTTTGCACCGTTATTGAGT 58.260 40.909 0.00 0.00 0.00 3.41
3091 3160 4.134563 AGAGTTTGCACCGTTATTGAGTT 58.865 39.130 0.00 0.00 0.00 3.01
3092 3161 5.302360 AGAGTTTGCACCGTTATTGAGTTA 58.698 37.500 0.00 0.00 0.00 2.24
3093 3162 5.761234 AGAGTTTGCACCGTTATTGAGTTAA 59.239 36.000 0.00 0.00 0.00 2.01
3094 3163 6.430000 AGAGTTTGCACCGTTATTGAGTTAAT 59.570 34.615 0.00 0.00 0.00 1.40
3095 3164 6.378582 AGTTTGCACCGTTATTGAGTTAATG 58.621 36.000 0.00 0.00 0.00 1.90
3096 3165 6.205853 AGTTTGCACCGTTATTGAGTTAATGA 59.794 34.615 0.00 0.00 0.00 2.57
3097 3166 5.794687 TGCACCGTTATTGAGTTAATGAG 57.205 39.130 0.00 0.00 0.00 2.90
3098 3167 4.094294 TGCACCGTTATTGAGTTAATGAGC 59.906 41.667 0.00 0.00 0.00 4.26
3099 3168 4.332819 GCACCGTTATTGAGTTAATGAGCT 59.667 41.667 0.00 0.00 0.00 4.09
3100 3169 5.163754 GCACCGTTATTGAGTTAATGAGCTT 60.164 40.000 0.00 0.00 0.00 3.74
3101 3170 6.036735 GCACCGTTATTGAGTTAATGAGCTTA 59.963 38.462 0.00 0.00 0.00 3.09
3102 3171 7.254795 GCACCGTTATTGAGTTAATGAGCTTAT 60.255 37.037 0.00 0.00 0.00 1.73
3103 3172 8.276325 CACCGTTATTGAGTTAATGAGCTTATC 58.724 37.037 0.00 0.00 0.00 1.75
3104 3173 8.204836 ACCGTTATTGAGTTAATGAGCTTATCT 58.795 33.333 0.00 0.00 0.00 1.98
3105 3174 8.491152 CCGTTATTGAGTTAATGAGCTTATCTG 58.509 37.037 0.00 0.00 0.00 2.90
3106 3175 8.006590 CGTTATTGAGTTAATGAGCTTATCTGC 58.993 37.037 0.00 0.00 0.00 4.26
3107 3176 8.830580 GTTATTGAGTTAATGAGCTTATCTGCA 58.169 33.333 0.00 0.00 34.99 4.41
3108 3177 6.668541 TTGAGTTAATGAGCTTATCTGCAC 57.331 37.500 0.00 0.00 34.99 4.57
3109 3178 5.118990 TGAGTTAATGAGCTTATCTGCACC 58.881 41.667 0.00 0.00 34.99 5.01
3110 3179 5.104776 TGAGTTAATGAGCTTATCTGCACCT 60.105 40.000 0.00 0.00 34.99 4.00
3111 3180 6.098266 TGAGTTAATGAGCTTATCTGCACCTA 59.902 38.462 0.00 0.00 34.99 3.08
3112 3181 6.284459 AGTTAATGAGCTTATCTGCACCTAC 58.716 40.000 0.00 0.00 34.99 3.18
3113 3182 6.098982 AGTTAATGAGCTTATCTGCACCTACT 59.901 38.462 0.00 0.00 34.99 2.57
3114 3183 4.599047 ATGAGCTTATCTGCACCTACTC 57.401 45.455 0.00 0.00 34.99 2.59
3115 3184 3.365472 TGAGCTTATCTGCACCTACTCA 58.635 45.455 0.00 0.00 34.99 3.41
3116 3185 3.963374 TGAGCTTATCTGCACCTACTCAT 59.037 43.478 0.00 0.00 34.99 2.90
3117 3186 4.406972 TGAGCTTATCTGCACCTACTCATT 59.593 41.667 0.00 0.00 34.99 2.57
3118 3187 5.598417 TGAGCTTATCTGCACCTACTCATTA 59.402 40.000 0.00 0.00 34.99 1.90
3119 3188 6.095432 AGCTTATCTGCACCTACTCATTAG 57.905 41.667 0.00 0.00 34.99 1.73
3120 3189 5.600484 AGCTTATCTGCACCTACTCATTAGT 59.400 40.000 0.00 0.00 36.14 2.24
3121 3190 6.778069 AGCTTATCTGCACCTACTCATTAGTA 59.222 38.462 0.00 0.00 34.69 1.82
3122 3191 7.453126 AGCTTATCTGCACCTACTCATTAGTAT 59.547 37.037 0.00 0.00 35.06 2.12
3123 3192 8.091449 GCTTATCTGCACCTACTCATTAGTATT 58.909 37.037 0.00 0.00 37.57 1.89
3124 3193 9.988815 CTTATCTGCACCTACTCATTAGTATTT 57.011 33.333 0.00 0.00 37.57 1.40
3125 3194 9.764363 TTATCTGCACCTACTCATTAGTATTTG 57.236 33.333 0.00 0.00 37.57 2.32
3126 3195 6.049149 TCTGCACCTACTCATTAGTATTTGC 58.951 40.000 10.86 10.86 41.70 3.68
3127 3196 5.123227 TGCACCTACTCATTAGTATTTGCC 58.877 41.667 13.52 2.54 41.19 4.52
3128 3197 4.211374 GCACCTACTCATTAGTATTTGCCG 59.789 45.833 8.08 0.00 38.62 5.69
3129 3198 4.211374 CACCTACTCATTAGTATTTGCCGC 59.789 45.833 0.00 0.00 37.57 6.53
3130 3199 4.101119 ACCTACTCATTAGTATTTGCCGCT 59.899 41.667 0.00 0.00 37.57 5.52
3131 3200 4.449068 CCTACTCATTAGTATTTGCCGCTG 59.551 45.833 0.00 0.00 37.57 5.18
3132 3201 4.137116 ACTCATTAGTATTTGCCGCTGA 57.863 40.909 0.00 0.00 32.84 4.26
3133 3202 4.513442 ACTCATTAGTATTTGCCGCTGAA 58.487 39.130 0.00 0.00 32.84 3.02
3134 3203 4.332819 ACTCATTAGTATTTGCCGCTGAAC 59.667 41.667 0.00 0.00 32.84 3.18
3135 3204 3.308595 TCATTAGTATTTGCCGCTGAACG 59.691 43.478 0.00 0.00 43.15 3.95
3230 3332 2.851195 AGACGGCATGAACTTGAGTTT 58.149 42.857 0.00 0.00 38.56 2.66
3242 3344 3.365265 GAGTTTGCTGTGGGGGCG 61.365 66.667 0.00 0.00 0.00 6.13
3277 3379 6.587608 GCTTTCCCACTGAATATTGAAAAGTG 59.412 38.462 0.00 1.84 38.36 3.16
3401 3503 5.646692 TGGCTTTACTAGATAATTGCCCT 57.353 39.130 0.00 0.00 39.84 5.19
3420 3522 1.804396 TTGCGTTGCAATGGGTCCAG 61.804 55.000 19.93 0.00 43.99 3.86
3443 3546 7.026562 CAGAAATAATTTGTACGCAATCACCA 58.973 34.615 0.00 0.00 34.18 4.17
3456 3559 4.083324 CGCAATCACCATGATTACATACCC 60.083 45.833 3.81 0.00 44.60 3.69
3465 3569 6.900186 ACCATGATTACATACCCAAAATGGAA 59.100 34.615 4.94 0.00 35.87 3.53
3570 3674 3.127895 TGGTAAACCAATAAGATGTGCGC 59.872 43.478 0.00 0.00 44.35 6.09
3580 3684 0.881118 AGATGTGCGCGGTTTTCAAT 59.119 45.000 8.83 0.00 0.00 2.57
3581 3685 0.984109 GATGTGCGCGGTTTTCAATG 59.016 50.000 8.83 0.00 0.00 2.82
3646 4868 2.407340 GGGGGAGGAGATGATGTACT 57.593 55.000 0.00 0.00 0.00 2.73
3647 4869 3.544698 GGGGGAGGAGATGATGTACTA 57.455 52.381 0.00 0.00 0.00 1.82
3649 4871 4.430441 GGGGGAGGAGATGATGTACTAAT 58.570 47.826 0.00 0.00 0.00 1.73
3669 4895 2.638480 TGTTGGACAAAGGTGAGGAG 57.362 50.000 0.00 0.00 0.00 3.69
3675 4901 2.427506 GACAAAGGTGAGGAGCGAAAT 58.572 47.619 0.00 0.00 0.00 2.17
3676 4902 2.154462 ACAAAGGTGAGGAGCGAAATG 58.846 47.619 0.00 0.00 0.00 2.32
3732 6340 8.223177 GTACAGATGTGAAGTATGTACTACCT 57.777 38.462 0.00 0.00 41.77 3.08
3733 6341 9.334947 GTACAGATGTGAAGTATGTACTACCTA 57.665 37.037 0.00 0.00 41.77 3.08
3734 6342 8.998277 ACAGATGTGAAGTATGTACTACCTAT 57.002 34.615 0.00 0.00 34.99 2.57
3873 6481 6.480320 GGTGTTACAGATCATTAAAGCTCGAT 59.520 38.462 0.00 0.00 0.00 3.59
3921 6529 0.675633 ACTGGCAGAAAATGTGGCAC 59.324 50.000 23.66 11.55 44.85 5.01
4085 6693 1.277557 GGAGCTCGATGCCAGGATTAT 59.722 52.381 7.83 0.00 44.23 1.28
4116 6724 4.460263 CATCGATTACCCCTCCAATTCAA 58.540 43.478 0.00 0.00 0.00 2.69
4140 6748 4.669197 GCACCTTACTTATTGAAGTGCGTG 60.669 45.833 0.00 5.38 45.74 5.34
4167 6775 0.531532 GAGTCACTGATGATGGCGGG 60.532 60.000 0.00 0.00 37.14 6.13
4174 6782 1.529010 GATGATGGCGGGGCAATGA 60.529 57.895 0.00 0.00 0.00 2.57
4212 6820 1.403647 CGCATGAGAAGTTACCGTCCA 60.404 52.381 0.00 0.00 0.00 4.02
4272 6880 2.882137 TGGTGGGAAAGAATGTTTCGTC 59.118 45.455 0.00 0.00 34.02 4.20
4360 6968 0.621609 GGCACATACCACACCCCTTA 59.378 55.000 0.00 0.00 0.00 2.69
4379 6987 6.481976 CCCCTTAACAAGTTTTTGGTGAATTC 59.518 38.462 0.00 0.00 38.66 2.17
4397 7014 8.739972 GGTGAATTCTCTAACAAAATACACCAT 58.260 33.333 7.05 0.00 41.33 3.55
4462 7087 7.717875 TGTTGAGTGGTTATGTTACTAAGCTTT 59.282 33.333 3.20 0.00 31.85 3.51
4485 7110 2.767445 GCGGGGGAACGGCATTTAC 61.767 63.158 0.00 0.00 44.12 2.01
4486 7111 1.078001 CGGGGGAACGGCATTTACT 60.078 57.895 0.00 0.00 0.00 2.24
4487 7112 1.373590 CGGGGGAACGGCATTTACTG 61.374 60.000 0.00 0.00 0.00 2.74
4488 7113 0.323087 GGGGGAACGGCATTTACTGT 60.323 55.000 0.00 0.00 0.00 3.55
4489 7114 1.541379 GGGGAACGGCATTTACTGTT 58.459 50.000 0.00 0.00 41.83 3.16
4490 7115 2.618559 GGGGGAACGGCATTTACTGTTA 60.619 50.000 0.00 0.00 39.25 2.41
4491 7116 3.284617 GGGGAACGGCATTTACTGTTAT 58.715 45.455 0.00 0.00 39.25 1.89
4492 7117 4.453751 GGGGAACGGCATTTACTGTTATA 58.546 43.478 0.00 0.00 39.25 0.98
4493 7118 4.514066 GGGGAACGGCATTTACTGTTATAG 59.486 45.833 0.00 0.00 39.25 1.31
4494 7119 4.024302 GGGAACGGCATTTACTGTTATAGC 60.024 45.833 0.00 0.00 39.25 2.97
4495 7120 4.573201 GGAACGGCATTTACTGTTATAGCA 59.427 41.667 0.00 0.00 39.25 3.49
4496 7121 5.238650 GGAACGGCATTTACTGTTATAGCAT 59.761 40.000 0.00 0.00 39.25 3.79
4497 7122 6.238648 GGAACGGCATTTACTGTTATAGCATT 60.239 38.462 0.00 0.00 39.25 3.56
4498 7123 6.693315 ACGGCATTTACTGTTATAGCATTT 57.307 33.333 0.00 0.00 0.00 2.32
4499 7124 7.795482 ACGGCATTTACTGTTATAGCATTTA 57.205 32.000 0.00 0.00 0.00 1.40
4705 7330 9.431887 GGTAACTTCATTACACTGAATAGTTGA 57.568 33.333 0.00 0.00 44.46 3.18
4729 7354 9.546428 TGATTGATGTCAGTATTATACCTTGTG 57.454 33.333 0.00 0.00 0.00 3.33
4730 7355 7.786178 TTGATGTCAGTATTATACCTTGTGC 57.214 36.000 0.00 0.00 0.00 4.57
4758 7383 3.487372 GAGCCTAGTTGTTTCCCTTTGT 58.513 45.455 0.00 0.00 0.00 2.83
4819 7444 8.047310 ACGAAATATCAACAGGAGAATAAGGTT 58.953 33.333 0.00 0.00 0.00 3.50
4888 7513 4.623932 TGACCTCAACTTTCAGCTACAT 57.376 40.909 0.00 0.00 0.00 2.29
4955 7581 5.275602 CGCTCGATTTCTTGATGCATTTTTC 60.276 40.000 0.00 0.00 0.00 2.29
5019 7654 7.992608 ACATAATCACATAACTGTCCTGCATTA 59.007 33.333 0.00 0.00 31.62 1.90
5186 7821 5.874810 TGTACAACAGATGCCATCTAACTTC 59.125 40.000 6.94 0.00 37.58 3.01
5230 7867 8.246180 GTCATTTGACTGATCAACCATATTTGT 58.754 33.333 0.00 0.00 44.66 2.83
5239 7876 8.984891 TGATCAACCATATTTGTTCATGTTTC 57.015 30.769 0.00 0.00 32.64 2.78
5254 7891 9.184523 TGTTCATGTTTCCTATTTAATTCGGAT 57.815 29.630 0.00 0.00 0.00 4.18
5280 7917 8.404000 TGTGTAGCTATTTTTGTTCCGTAAAAA 58.596 29.630 0.00 0.00 40.17 1.94
5330 7967 7.741027 AGATTTAACTGTGATAGATGGCATG 57.259 36.000 3.81 0.00 0.00 4.06
5413 8050 5.540911 ACTTTCCAGTGCCATTTTGTAATG 58.459 37.500 0.00 0.00 40.70 1.90
5425 8062 6.630188 GCCATTTTGTAATGCCTTCTAACCAT 60.630 38.462 0.00 0.00 39.87 3.55
5473 8110 0.176910 GCTGCTTGTAGGGAGGAGAC 59.823 60.000 0.00 0.00 34.87 3.36
5516 8153 4.379813 GGACAGCACATCAAATAACCACAG 60.380 45.833 0.00 0.00 0.00 3.66
5517 8154 3.057315 ACAGCACATCAAATAACCACAGC 60.057 43.478 0.00 0.00 0.00 4.40
5557 8194 1.762957 CCCTAGTCCGAACATCACCAT 59.237 52.381 0.00 0.00 0.00 3.55
5601 8238 2.476185 CGCGCTCCTAAACTGGAAATTG 60.476 50.000 5.56 0.00 35.43 2.32
5697 8334 2.100087 GACGGAGATCAGAAGGGAAGAC 59.900 54.545 0.00 0.00 0.00 3.01
5703 8340 0.832135 TCAGAAGGGAAGACGTGGCT 60.832 55.000 0.00 0.00 0.00 4.75
5733 8370 2.271957 GCGACGAAGAATACGCGAA 58.728 52.632 15.93 0.00 41.49 4.70
5849 8486 3.072944 GTGTTTTGAGCTCTGCAGAGAT 58.927 45.455 41.20 37.57 44.40 2.75
5955 8592 4.141620 TGAAGCCCTGATGGAGATAGTTTC 60.142 45.833 0.00 0.00 35.39 2.78
6151 8790 6.625873 GGAAGATATCCCAGAACATGTTTC 57.374 41.667 13.36 6.25 43.00 2.78
6177 8816 4.265073 ACTGTCCCAGAAAATATGTCTGC 58.735 43.478 10.05 0.68 41.04 4.26
6417 9064 7.568349 ACATGAGGATGTACACAGACATATTT 58.432 34.615 0.00 0.00 41.27 1.40
6423 9070 8.982723 AGGATGTACACAGACATATTTTAGAGT 58.017 33.333 0.00 0.00 40.18 3.24
6446 9093 3.777106 AGATTCACTCACTTTGCTCCA 57.223 42.857 0.00 0.00 0.00 3.86
6457 9104 6.607600 ACTCACTTTGCTCCATATGTAGTCTA 59.392 38.462 1.24 0.00 0.00 2.59
6474 9121 8.515695 TGTAGTCTATAGTGGAATCTCGAAAA 57.484 34.615 0.00 0.00 0.00 2.29
6485 9132 9.892130 AGTGGAATCTCGAAAAAGACTTATATT 57.108 29.630 0.00 0.00 0.00 1.28
6624 9274 3.503891 TCATGCAAGCATCGACAAATTG 58.496 40.909 4.24 0.00 33.90 2.32
6681 9331 0.744874 CTGCCAGCTGGATTTGATGG 59.255 55.000 37.21 7.81 43.20 3.51
6689 9339 1.945394 CTGGATTTGATGGAAGCCGAG 59.055 52.381 0.00 0.00 37.90 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.822164 ATGCTACCGGCGTTCTAAGT 59.178 50.000 6.01 0.00 45.43 2.24
23 24 4.625742 CCGACAATCTTATAATGCTACCGG 59.374 45.833 0.00 0.00 0.00 5.28
48 49 0.767060 GGTACCCCCGATCCCAGAAT 60.767 60.000 0.00 0.00 0.00 2.40
92 93 2.203788 TGTCGAGGGAGCCAGGTT 60.204 61.111 0.00 0.00 0.00 3.50
181 183 3.008485 GTCTCTTGGGAGGTCTTGATGTT 59.992 47.826 0.00 0.00 39.86 2.71
205 207 3.009916 AGCTTGTTTCATCCTCCATCTGT 59.990 43.478 0.00 0.00 0.00 3.41
207 209 4.015084 CAAGCTTGTTTCATCCTCCATCT 58.985 43.478 18.65 0.00 0.00 2.90
217 219 1.021202 CGGTGTCCAAGCTTGTTTCA 58.979 50.000 24.35 16.37 0.00 2.69
224 226 2.031163 GTGCTCGGTGTCCAAGCT 59.969 61.111 0.51 0.00 36.96 3.74
246 248 7.021196 CACGACGAATTTTCATTAGATTTGGT 58.979 34.615 0.00 0.00 0.00 3.67
286 335 5.243730 ACAGTGCATTTTATACAAAGCTGGT 59.756 36.000 0.00 0.00 0.00 4.00
330 379 9.705290 ACATTTTAAACACTTCTTCAACAAACT 57.295 25.926 0.00 0.00 0.00 2.66
350 399 1.544724 ACACTGCCCGCATACATTTT 58.455 45.000 0.00 0.00 0.00 1.82
412 461 1.354337 CCTGCACTCATCCGTGAACG 61.354 60.000 0.00 0.00 37.06 3.95
422 471 4.326826 CTGTAAATTTCCTCCTGCACTCA 58.673 43.478 0.00 0.00 0.00 3.41
471 520 6.054941 TGAACGCATGGTCATACATTCTATT 58.945 36.000 0.00 0.00 0.00 1.73
547 596 3.386486 TCTGTGTGATGTTGTCCGTTAC 58.614 45.455 0.00 0.00 0.00 2.50
594 643 9.753674 TCATCTTCTTAACCTGAAATAACCAAT 57.246 29.630 0.00 0.00 0.00 3.16
600 649 9.167311 GCTTTCTCATCTTCTTAACCTGAAATA 57.833 33.333 0.00 0.00 0.00 1.40
648 700 1.694150 CTCCCACTTCACACCTCAGAA 59.306 52.381 0.00 0.00 0.00 3.02
746 805 2.655090 TGCACCACCTCATTCTCAAA 57.345 45.000 0.00 0.00 0.00 2.69
747 806 2.655090 TTGCACCACCTCATTCTCAA 57.345 45.000 0.00 0.00 0.00 3.02
748 807 2.655090 TTTGCACCACCTCATTCTCA 57.345 45.000 0.00 0.00 0.00 3.27
796 855 9.423061 GTTGTTTGATTTGTAGGATAGCATTTT 57.577 29.630 0.00 0.00 0.00 1.82
797 856 8.034804 GGTTGTTTGATTTGTAGGATAGCATTT 58.965 33.333 0.00 0.00 0.00 2.32
798 857 7.397192 AGGTTGTTTGATTTGTAGGATAGCATT 59.603 33.333 0.00 0.00 0.00 3.56
799 858 6.891908 AGGTTGTTTGATTTGTAGGATAGCAT 59.108 34.615 0.00 0.00 0.00 3.79
800 859 6.245408 AGGTTGTTTGATTTGTAGGATAGCA 58.755 36.000 0.00 0.00 0.00 3.49
801 860 6.759497 AGGTTGTTTGATTTGTAGGATAGC 57.241 37.500 0.00 0.00 0.00 2.97
802 861 8.786826 TGTAGGTTGTTTGATTTGTAGGATAG 57.213 34.615 0.00 0.00 0.00 2.08
804 863 9.747898 TTATGTAGGTTGTTTGATTTGTAGGAT 57.252 29.630 0.00 0.00 0.00 3.24
805 864 9.575868 TTTATGTAGGTTGTTTGATTTGTAGGA 57.424 29.630 0.00 0.00 0.00 2.94
834 893 7.722949 TTTAAGCAATCTGATCTTTGGGATT 57.277 32.000 0.00 0.00 34.33 3.01
867 926 5.449304 ACCGAGCAAACGATTTCTAAAAAG 58.551 37.500 0.00 0.00 35.09 2.27
918 977 0.612744 TGTGCCGACTGATGGATGAA 59.387 50.000 0.00 0.00 0.00 2.57
956 1015 1.681945 CTCGCGAAAGTGCAGAGAGC 61.682 60.000 11.33 0.00 45.96 4.09
1160 1219 4.065281 CGTTTCCTCGGGCGGACT 62.065 66.667 0.00 0.00 31.44 3.85
1320 1379 3.793144 GCGGCAAGAAGGCTCACG 61.793 66.667 0.00 0.00 41.46 4.35
1592 1657 3.438087 AGAATCCACTTGAAATCGCACAG 59.562 43.478 0.00 0.00 0.00 3.66
1637 1702 0.034756 ACCTTGATGCACAGTACGCA 59.965 50.000 0.00 0.00 44.94 5.24
1640 1705 2.228822 CCCAAACCTTGATGCACAGTAC 59.771 50.000 0.00 0.00 0.00 2.73
1661 1726 2.731348 GGTCGATCGATGAGGCGC 60.731 66.667 22.50 6.07 0.00 6.53
1774 1839 8.706492 TGAATTATTTCCATCAAATTCACTGC 57.294 30.769 5.48 0.00 41.17 4.40
1814 1879 8.389779 TGAAAATTTCACTATTAGCACTGTCA 57.610 30.769 4.03 0.00 34.08 3.58
1829 1894 8.905660 ATGTTTGAACCATCATGAAAATTTCA 57.094 26.923 11.10 11.10 45.01 2.69
1883 1948 1.202818 ACACCTTCTGAGACAAAGGGC 60.203 52.381 3.89 0.00 45.27 5.19
1988 2053 2.037367 TCCAGGCTAGGCACGAGT 59.963 61.111 19.70 0.00 32.26 4.18
2160 2225 3.438087 GTGTCATGTCTGTTGCATAGCTT 59.562 43.478 0.00 0.00 0.00 3.74
2201 2266 3.190535 ACTGACCACCATTTTCATAACGC 59.809 43.478 0.00 0.00 0.00 4.84
2202 2267 5.371115 AACTGACCACCATTTTCATAACG 57.629 39.130 0.00 0.00 0.00 3.18
2470 2536 7.559590 AATATGAAGCTGTATCACAAGTTCC 57.440 36.000 0.00 0.00 0.00 3.62
2557 2623 5.627499 TTTGTGAAGAAGAATCGAATGGG 57.373 39.130 0.00 0.00 0.00 4.00
2617 2685 4.631813 CCCCAAGTTCTCAGTTCTTTATCG 59.368 45.833 0.00 0.00 0.00 2.92
2619 2687 5.843019 TCCCCAAGTTCTCAGTTCTTTAT 57.157 39.130 0.00 0.00 0.00 1.40
2745 2814 2.119801 TCTTGCATCTTGGGCTTCTC 57.880 50.000 0.00 0.00 0.00 2.87
2747 2816 3.067320 GGTAATCTTGCATCTTGGGCTTC 59.933 47.826 0.00 0.00 0.00 3.86
2778 2847 8.426489 ACCAACTACATTCAGTACTTAACAGAA 58.574 33.333 0.00 0.00 37.91 3.02
2790 2859 4.184629 GCAGGTCTACCAACTACATTCAG 58.815 47.826 1.26 0.00 38.89 3.02
2851 2920 6.994421 ATTGATATAAAAATCCCCGGCTTT 57.006 33.333 0.00 0.00 0.00 3.51
2853 2922 8.557450 ACTATATTGATATAAAAATCCCCGGCT 58.443 33.333 0.00 0.00 0.00 5.52
2898 2967 7.554118 CAGTTATATTGGTGGACTCTTGTGATT 59.446 37.037 0.00 0.00 0.00 2.57
2949 3018 5.105146 GCTCTTCCAAGGATAGAACAGAAGA 60.105 44.000 0.00 0.00 36.74 2.87
3048 3117 3.471495 AGCTTTTTGTTCCGAATAGCG 57.529 42.857 0.00 0.00 37.07 4.26
3050 3119 6.969828 ACTCTAGCTTTTTGTTCCGAATAG 57.030 37.500 0.00 0.00 0.00 1.73
3051 3120 7.581476 CAAACTCTAGCTTTTTGTTCCGAATA 58.419 34.615 0.00 0.00 0.00 1.75
3052 3121 6.438763 CAAACTCTAGCTTTTTGTTCCGAAT 58.561 36.000 0.00 0.00 0.00 3.34
3054 3123 4.261031 GCAAACTCTAGCTTTTTGTTCCGA 60.261 41.667 0.00 0.00 33.57 4.55
3055 3124 3.975035 GCAAACTCTAGCTTTTTGTTCCG 59.025 43.478 0.00 0.00 33.57 4.30
3056 3125 4.740205 GTGCAAACTCTAGCTTTTTGTTCC 59.260 41.667 0.00 0.00 33.57 3.62
3057 3126 4.740205 GGTGCAAACTCTAGCTTTTTGTTC 59.260 41.667 0.00 0.00 33.57 3.18
3058 3127 4.682787 GGTGCAAACTCTAGCTTTTTGTT 58.317 39.130 0.00 0.00 33.57 2.83
3059 3128 3.243068 CGGTGCAAACTCTAGCTTTTTGT 60.243 43.478 0.00 0.00 33.57 2.83
3060 3129 3.243068 ACGGTGCAAACTCTAGCTTTTTG 60.243 43.478 0.00 0.00 34.05 2.44
3061 3130 2.949644 ACGGTGCAAACTCTAGCTTTTT 59.050 40.909 0.00 0.00 0.00 1.94
3062 3131 2.572290 ACGGTGCAAACTCTAGCTTTT 58.428 42.857 0.00 0.00 0.00 2.27
3063 3132 2.256117 ACGGTGCAAACTCTAGCTTT 57.744 45.000 0.00 0.00 0.00 3.51
3064 3133 2.256117 AACGGTGCAAACTCTAGCTT 57.744 45.000 0.00 0.00 0.00 3.74
3065 3134 3.611766 ATAACGGTGCAAACTCTAGCT 57.388 42.857 0.00 0.00 0.00 3.32
3066 3135 3.682858 TCAATAACGGTGCAAACTCTAGC 59.317 43.478 0.00 0.00 0.00 3.42
3067 3136 4.929808 ACTCAATAACGGTGCAAACTCTAG 59.070 41.667 0.00 0.00 0.00 2.43
3068 3137 4.890088 ACTCAATAACGGTGCAAACTCTA 58.110 39.130 0.00 0.00 0.00 2.43
3069 3138 3.740115 ACTCAATAACGGTGCAAACTCT 58.260 40.909 0.00 0.00 0.00 3.24
3070 3139 4.483476 AACTCAATAACGGTGCAAACTC 57.517 40.909 0.00 0.00 0.00 3.01
3071 3140 6.205853 TCATTAACTCAATAACGGTGCAAACT 59.794 34.615 0.00 0.00 0.00 2.66
3072 3141 6.375377 TCATTAACTCAATAACGGTGCAAAC 58.625 36.000 0.00 0.00 0.00 2.93
3073 3142 6.561737 TCATTAACTCAATAACGGTGCAAA 57.438 33.333 0.00 0.00 0.00 3.68
3074 3143 5.391523 GCTCATTAACTCAATAACGGTGCAA 60.392 40.000 0.00 0.00 0.00 4.08
3075 3144 4.094294 GCTCATTAACTCAATAACGGTGCA 59.906 41.667 0.00 0.00 0.00 4.57
3076 3145 4.332819 AGCTCATTAACTCAATAACGGTGC 59.667 41.667 0.00 0.00 0.00 5.01
3077 3146 6.422776 AAGCTCATTAACTCAATAACGGTG 57.577 37.500 0.00 0.00 0.00 4.94
3078 3147 8.204836 AGATAAGCTCATTAACTCAATAACGGT 58.795 33.333 0.00 0.00 0.00 4.83
3079 3148 8.491152 CAGATAAGCTCATTAACTCAATAACGG 58.509 37.037 0.00 0.00 0.00 4.44
3080 3149 8.006590 GCAGATAAGCTCATTAACTCAATAACG 58.993 37.037 0.00 0.00 0.00 3.18
3081 3150 8.830580 TGCAGATAAGCTCATTAACTCAATAAC 58.169 33.333 0.00 0.00 34.99 1.89
3082 3151 8.830580 GTGCAGATAAGCTCATTAACTCAATAA 58.169 33.333 0.00 0.00 34.99 1.40
3083 3152 7.442364 GGTGCAGATAAGCTCATTAACTCAATA 59.558 37.037 0.00 0.00 34.99 1.90
3084 3153 6.261826 GGTGCAGATAAGCTCATTAACTCAAT 59.738 38.462 0.00 0.00 34.99 2.57
3085 3154 5.586243 GGTGCAGATAAGCTCATTAACTCAA 59.414 40.000 0.00 0.00 34.99 3.02
3086 3155 5.104776 AGGTGCAGATAAGCTCATTAACTCA 60.105 40.000 0.00 0.00 34.99 3.41
3087 3156 5.363939 AGGTGCAGATAAGCTCATTAACTC 58.636 41.667 0.00 0.00 34.99 3.01
3088 3157 5.365021 AGGTGCAGATAAGCTCATTAACT 57.635 39.130 0.00 0.00 34.99 2.24
3089 3158 6.284459 AGTAGGTGCAGATAAGCTCATTAAC 58.716 40.000 0.00 0.00 34.99 2.01
3090 3159 6.098266 TGAGTAGGTGCAGATAAGCTCATTAA 59.902 38.462 0.00 0.00 34.99 1.40
3091 3160 5.598417 TGAGTAGGTGCAGATAAGCTCATTA 59.402 40.000 0.00 0.00 34.99 1.90
3092 3161 4.406972 TGAGTAGGTGCAGATAAGCTCATT 59.593 41.667 0.00 0.00 34.99 2.57
3093 3162 3.963374 TGAGTAGGTGCAGATAAGCTCAT 59.037 43.478 0.00 0.00 34.99 2.90
3094 3163 3.365472 TGAGTAGGTGCAGATAAGCTCA 58.635 45.455 0.00 0.00 34.99 4.26
3095 3164 4.599047 ATGAGTAGGTGCAGATAAGCTC 57.401 45.455 0.00 0.00 34.99 4.09
3096 3165 5.600484 ACTAATGAGTAGGTGCAGATAAGCT 59.400 40.000 0.00 0.00 32.65 3.74
3097 3166 5.848406 ACTAATGAGTAGGTGCAGATAAGC 58.152 41.667 0.00 0.00 32.65 3.09
3098 3167 9.988815 AAATACTAATGAGTAGGTGCAGATAAG 57.011 33.333 0.00 0.00 41.50 1.73
3099 3168 9.764363 CAAATACTAATGAGTAGGTGCAGATAA 57.236 33.333 0.00 0.00 41.50 1.75
3100 3169 7.872993 GCAAATACTAATGAGTAGGTGCAGATA 59.127 37.037 17.50 0.00 44.17 1.98
3101 3170 6.708054 GCAAATACTAATGAGTAGGTGCAGAT 59.292 38.462 17.50 0.00 44.17 2.90
3102 3171 6.049149 GCAAATACTAATGAGTAGGTGCAGA 58.951 40.000 17.50 0.00 44.17 4.26
3103 3172 5.237344 GGCAAATACTAATGAGTAGGTGCAG 59.763 44.000 21.37 2.16 45.33 4.41
3104 3173 5.123227 GGCAAATACTAATGAGTAGGTGCA 58.877 41.667 21.37 0.00 45.33 4.57
3105 3174 4.211374 CGGCAAATACTAATGAGTAGGTGC 59.789 45.833 15.34 15.34 44.10 5.01
3106 3175 4.211374 GCGGCAAATACTAATGAGTAGGTG 59.789 45.833 0.00 0.00 41.50 4.00
3107 3176 4.101119 AGCGGCAAATACTAATGAGTAGGT 59.899 41.667 1.45 0.00 41.50 3.08
3108 3177 4.449068 CAGCGGCAAATACTAATGAGTAGG 59.551 45.833 1.45 0.00 41.50 3.18
3109 3178 5.289595 TCAGCGGCAAATACTAATGAGTAG 58.710 41.667 1.45 0.00 41.50 2.57
3110 3179 5.270893 TCAGCGGCAAATACTAATGAGTA 57.729 39.130 1.45 0.00 42.41 2.59
3111 3180 4.137116 TCAGCGGCAAATACTAATGAGT 57.863 40.909 1.45 0.00 39.92 3.41
3112 3181 4.550831 CGTTCAGCGGCAAATACTAATGAG 60.551 45.833 1.45 0.00 36.85 2.90
3113 3182 3.308595 CGTTCAGCGGCAAATACTAATGA 59.691 43.478 1.45 0.00 36.85 2.57
3114 3183 3.607439 CGTTCAGCGGCAAATACTAATG 58.393 45.455 1.45 0.00 36.85 1.90
3115 3184 3.944422 CGTTCAGCGGCAAATACTAAT 57.056 42.857 1.45 0.00 36.85 1.73
3127 3196 1.352114 TTTCCGAATACCGTTCAGCG 58.648 50.000 0.00 0.00 40.95 5.18
3128 3197 3.817148 TTTTTCCGAATACCGTTCAGC 57.183 42.857 0.00 0.00 36.31 4.26
3167 3236 7.696992 AAGAACTTTCAGTGGAAGTACAAAA 57.303 32.000 17.36 0.00 33.82 2.44
3213 3282 1.267806 AGCAAACTCAAGTTCATGCCG 59.732 47.619 13.34 0.00 40.67 5.69
3277 3379 0.677842 GCATCATGGGCCAATTCTCC 59.322 55.000 11.89 0.00 0.00 3.71
3339 3441 5.186021 TGAGCTTTCCTTTGTGTACCAAAAA 59.814 36.000 9.73 2.23 42.31 1.94
3342 3444 3.630312 GTGAGCTTTCCTTTGTGTACCAA 59.370 43.478 0.00 0.00 0.00 3.67
3343 3445 3.211045 GTGAGCTTTCCTTTGTGTACCA 58.789 45.455 0.00 0.00 0.00 3.25
3344 3446 3.211045 TGTGAGCTTTCCTTTGTGTACC 58.789 45.455 0.00 0.00 0.00 3.34
3345 3447 4.335594 AGTTGTGAGCTTTCCTTTGTGTAC 59.664 41.667 0.00 0.00 0.00 2.90
3382 3484 5.527582 ACGCAAGGGCAATTATCTAGTAAAG 59.472 40.000 0.00 0.00 46.39 1.85
3416 3518 7.247728 GTGATTGCGTACAAATTATTTCTGGA 58.752 34.615 0.00 0.00 39.77 3.86
3420 3522 7.700234 TCATGGTGATTGCGTACAAATTATTTC 59.300 33.333 0.00 0.00 39.77 2.17
3456 3559 6.372103 TCAATTGGCAGCTAAATTCCATTTTG 59.628 34.615 5.42 0.00 33.82 2.44
3501 3605 6.150976 TGGCAAGTCGATAAATGTTGATTCTT 59.849 34.615 0.00 0.00 0.00 2.52
3630 4852 6.708054 CCAACAATTAGTACATCATCTCCTCC 59.292 42.308 0.00 0.00 0.00 4.30
3632 4854 7.092891 TGTCCAACAATTAGTACATCATCTCCT 60.093 37.037 0.00 0.00 0.00 3.69
3641 4863 6.358178 TCACCTTTGTCCAACAATTAGTACA 58.642 36.000 0.00 0.00 38.00 2.90
3645 4867 5.070001 TCCTCACCTTTGTCCAACAATTAG 58.930 41.667 0.00 0.00 38.00 1.73
3646 4868 5.055265 TCCTCACCTTTGTCCAACAATTA 57.945 39.130 0.00 0.00 38.00 1.40
3647 4869 3.891366 CTCCTCACCTTTGTCCAACAATT 59.109 43.478 0.00 0.00 38.00 2.32
3649 4871 2.930950 CTCCTCACCTTTGTCCAACAA 58.069 47.619 0.00 0.00 36.11 2.83
3669 4895 2.092323 AGGTTCCCTAAAGCATTTCGC 58.908 47.619 0.00 0.00 40.09 4.70
3675 4901 2.901839 AGACGTAAGGTTCCCTAAAGCA 59.098 45.455 0.00 0.00 46.39 3.91
3676 4902 3.606595 AGACGTAAGGTTCCCTAAAGC 57.393 47.619 0.00 0.00 46.39 3.51
3679 4905 8.593945 TCTATAAAAGACGTAAGGTTCCCTAA 57.406 34.615 0.00 0.00 46.39 2.69
3760 6368 9.378551 GAACACACATACCTGTTATCAAGAATA 57.621 33.333 0.00 0.00 31.62 1.75
3807 6415 4.095483 AGAAATTCCTTGCTAATGTGCTCG 59.905 41.667 0.00 0.00 0.00 5.03
3873 6481 5.880332 GCAGGATAAATTGGACACTGACTTA 59.120 40.000 0.00 0.00 0.00 2.24
3921 6529 4.326817 CGGGTTGCAAATTCACAATACATG 59.673 41.667 0.00 0.00 0.00 3.21
4029 6637 5.374071 AGTGATTTCTCATGCAGCATATCA 58.626 37.500 7.82 10.45 32.98 2.15
4085 6693 1.202758 GGGTAATCGATGCCATCACCA 60.203 52.381 17.63 0.00 35.05 4.17
4116 6724 3.684788 CGCACTTCAATAAGTAAGGTGCT 59.315 43.478 12.16 0.00 44.28 4.40
4140 6748 1.547820 TCATCAGTGACTCTGTCAGGC 59.452 52.381 0.00 0.00 43.57 4.85
4164 6772 2.026641 ACATCAGAAATCATTGCCCCG 58.973 47.619 0.00 0.00 0.00 5.73
4167 6775 6.365247 GCAATATGACATCAGAAATCATTGCC 59.635 38.462 13.64 1.87 34.50 4.52
4174 6782 5.239963 TCATGCGCAATATGACATCAGAAAT 59.760 36.000 17.11 0.00 30.03 2.17
4212 6820 2.526873 AGCCACCGTCCTTCCTGT 60.527 61.111 0.00 0.00 0.00 4.00
4272 6880 5.902681 TCTGAACAATACCTCATCCTAACG 58.097 41.667 0.00 0.00 0.00 3.18
4322 6930 8.690203 ATGTGCCACATAATGTTAAGCTATAA 57.310 30.769 8.96 0.00 36.99 0.98
4360 6968 8.527810 TGTTAGAGAATTCACCAAAAACTTGTT 58.472 29.630 8.44 0.00 0.00 2.83
4393 7001 6.740944 AAAAGCAAAAGGGTTAACTATGGT 57.259 33.333 5.42 1.28 35.85 3.55
4498 7123 9.529325 GCACAATTGTACTGAGATATAACAGTA 57.471 33.333 11.53 13.85 44.06 2.74
4499 7124 8.260818 AGCACAATTGTACTGAGATATAACAGT 58.739 33.333 11.53 15.37 46.81 3.55
4705 7330 8.213679 AGCACAAGGTATAATACTGACATCAAT 58.786 33.333 0.00 0.00 0.00 2.57
4729 7354 1.190643 ACAACTAGGCTCCTCTCAGC 58.809 55.000 0.00 0.00 38.84 4.26
4730 7355 3.368948 GGAAACAACTAGGCTCCTCTCAG 60.369 52.174 0.00 0.00 0.00 3.35
4758 7383 2.364970 CCAACCACCTTTTCTGCATCAA 59.635 45.455 0.00 0.00 0.00 2.57
4819 7444 2.231478 TCCAGTTGAAAAACGCCAAACA 59.769 40.909 0.00 0.00 0.00 2.83
4955 7581 7.273320 TCTATACTAACTCCAATTCCAGACG 57.727 40.000 0.00 0.00 0.00 4.18
4997 7632 6.932356 CTAATGCAGGACAGTTATGTGATT 57.068 37.500 0.00 0.00 40.68 2.57
5019 7654 2.555757 GAGCTTTCAGCAATGAACACCT 59.444 45.455 0.00 0.00 45.56 4.00
5089 7724 3.005791 GTGCTGTAATCCTTTTTGCCTGT 59.994 43.478 0.00 0.00 0.00 4.00
5230 7867 9.184523 ACATCCGAATTAAATAGGAAACATGAA 57.815 29.630 0.00 0.00 36.25 2.57
5239 7876 9.436957 AATAGCTACACATCCGAATTAAATAGG 57.563 33.333 0.00 0.00 0.00 2.57
5249 7886 5.353123 GGAACAAAAATAGCTACACATCCGA 59.647 40.000 0.00 0.00 0.00 4.55
5251 7888 5.123344 ACGGAACAAAAATAGCTACACATCC 59.877 40.000 0.00 0.00 0.00 3.51
5254 7891 7.493743 TTTACGGAACAAAAATAGCTACACA 57.506 32.000 0.00 0.00 0.00 3.72
5311 7948 5.129320 AGTCACATGCCATCTATCACAGTTA 59.871 40.000 0.00 0.00 0.00 2.24
5330 7967 1.024271 ACATGTGTGGTGCAAGTCAC 58.976 50.000 0.00 8.58 44.90 3.67
5413 8050 0.103572 TCGCGGTATGGTTAGAAGGC 59.896 55.000 6.13 0.00 0.00 4.35
5425 8062 5.136816 TGCTAATATGGTTTATCGCGGTA 57.863 39.130 6.13 0.00 0.00 4.02
5473 8110 4.621886 GTCCTTCTTTACGCTGTAACTCAG 59.378 45.833 1.47 0.00 46.12 3.35
5516 8153 0.101579 GAGGTACTGCTCTTCCTCGC 59.898 60.000 0.00 0.00 41.55 5.03
5517 8154 1.133407 GTGAGGTACTGCTCTTCCTCG 59.867 57.143 11.60 0.00 46.48 4.63
5601 8238 1.666189 GGTAAGAACTCCATTGCGAGC 59.334 52.381 0.00 0.00 32.79 5.03
5697 8334 4.335647 ACCAGAAGCCCAGCCACG 62.336 66.667 0.00 0.00 0.00 4.94
5703 8340 4.680237 CGTCGCACCAGAAGCCCA 62.680 66.667 0.00 0.00 0.00 5.36
5733 8370 3.077556 CTCTGCCCTACCTGCGGT 61.078 66.667 5.58 5.58 40.16 5.68
5849 8486 1.003355 GCTCTGTTAGGCAGCACCA 60.003 57.895 0.00 0.00 44.66 4.17
5955 8592 4.271696 TGTCCTGTACATTCCTTCACAG 57.728 45.455 0.00 0.00 38.48 3.66
6035 8674 6.150809 ACACAACAACAAATCAAGCCATTTTT 59.849 30.769 0.00 0.00 0.00 1.94
6423 9070 4.040339 TGGAGCAAAGTGAGTGAATCTACA 59.960 41.667 0.00 0.00 0.00 2.74
6433 9080 5.911752 AGACTACATATGGAGCAAAGTGAG 58.088 41.667 15.30 0.00 0.00 3.51
6437 9084 8.031864 CCACTATAGACTACATATGGAGCAAAG 58.968 40.741 15.30 8.09 0.00 2.77
6446 9093 9.961264 TTCGAGATTCCACTATAGACTACATAT 57.039 33.333 6.78 0.00 0.00 1.78
6484 9131 8.597167 CCATGTACATATCTCTCCATTCCTAAA 58.403 37.037 8.32 0.00 0.00 1.85
6485 9132 7.180946 CCCATGTACATATCTCTCCATTCCTAA 59.819 40.741 8.32 0.00 0.00 2.69
6486 9133 6.669591 CCCATGTACATATCTCTCCATTCCTA 59.330 42.308 8.32 0.00 0.00 2.94
6487 9134 5.486775 CCCATGTACATATCTCTCCATTCCT 59.513 44.000 8.32 0.00 0.00 3.36
6488 9135 5.249393 ACCCATGTACATATCTCTCCATTCC 59.751 44.000 8.32 0.00 0.00 3.01
6489 9136 6.014242 TGACCCATGTACATATCTCTCCATTC 60.014 42.308 8.32 0.00 0.00 2.67
6490 9137 5.846164 TGACCCATGTACATATCTCTCCATT 59.154 40.000 8.32 0.00 0.00 3.16
6491 9138 5.406163 TGACCCATGTACATATCTCTCCAT 58.594 41.667 8.32 0.00 0.00 3.41
6492 9139 4.814967 TGACCCATGTACATATCTCTCCA 58.185 43.478 8.32 0.00 0.00 3.86
6493 9140 5.808366 TTGACCCATGTACATATCTCTCC 57.192 43.478 8.32 0.00 0.00 3.71
6689 9339 2.908940 CTGGGATTCATGGCCGGC 60.909 66.667 21.18 21.18 0.00 6.13


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

AutoCloner maintained by Alex Coulton.