Multiple sequence alignment - TraesCS4D01G231800

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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 TraesCS4D01G231800 chr4D 100.000 6768 0 0 1 6768 391715837 391722604 0.000000e+00 12499.0
1 TraesCS4D01G231800 chr4B 95.225 2534 109 10 3739 6265 481601735 481604263 0.000000e+00 3999.0
2 TraesCS4D01G231800 chr4B 95.544 2334 76 11 1136 3461 481598899 481601212 0.000000e+00 3709.0
3 TraesCS4D01G231800 chr4B 89.541 937 48 23 233 1143 481597944 481598856 0.000000e+00 1142.0
4 TraesCS4D01G231800 chr4B 95.035 282 12 1 3463 3742 481601284 481601565 6.230000e-120 442.0
5 TraesCS4D01G231800 chr4A 93.220 2655 138 17 3636 6265 73453018 73455655 0.000000e+00 3868.0
6 TraesCS4D01G231800 chr4A 90.665 2828 179 39 170 2949 73449579 73452369 0.000000e+00 3681.0
7 TraesCS4D01G231800 chr4A 93.398 515 29 5 2948 3461 73452438 73452948 0.000000e+00 758.0
8 TraesCS4D01G231800 chr4A 95.957 470 7 4 6311 6768 73455661 73456130 0.000000e+00 752.0
9 TraesCS4D01G231800 chr4A 82.485 668 77 12 5125 5792 706249868 706249241 3.570000e-152 549.0
10 TraesCS4D01G231800 chr4A 94.521 73 4 0 3501 3573 73452948 73453020 5.550000e-21 113.0
11 TraesCS4D01G231800 chr2D 84.828 725 60 14 5065 5789 364954166 364954840 0.000000e+00 684.0
12 TraesCS4D01G231800 chr2D 94.000 50 3 0 3460 3509 36748720 36748671 7.280000e-10 76.8
13 TraesCS4D01G231800 chr7A 84.066 728 74 12 5065 5792 677847655 677846970 0.000000e+00 664.0
14 TraesCS4D01G231800 chr7A 86.645 307 34 6 4455 4759 677848332 677848031 3.910000e-87 333.0
15 TraesCS4D01G231800 chr7A 96.000 50 0 2 3457 3505 29531945 29531897 5.630000e-11 80.5
16 TraesCS4D01G231800 chr3D 87.885 454 41 7 5065 5518 410515471 410515910 7.780000e-144 521.0
17 TraesCS4D01G231800 chr3D 88.636 308 25 9 4455 4759 410514806 410515106 3.860000e-97 366.0
18 TraesCS4D01G231800 chr3D 89.500 200 18 1 5590 5789 410515933 410516129 4.050000e-62 250.0
19 TraesCS4D01G231800 chr3D 92.727 55 0 4 3458 3510 400683988 400683936 7.280000e-10 76.8
20 TraesCS4D01G231800 chr3D 90.000 60 1 5 3458 3513 124616796 124616854 9.420000e-09 73.1
21 TraesCS4D01G231800 chr1B 91.525 59 1 4 3458 3513 7292032 7291975 2.020000e-10 78.7
22 TraesCS4D01G231800 chr2A 94.118 51 1 2 3458 3506 23630419 23630469 7.280000e-10 76.8
23 TraesCS4D01G231800 chr2A 87.879 66 2 6 3461 3524 751396158 751396097 9.420000e-09 73.1
24 TraesCS4D01G231800 chr3A 85.915 71 1 7 3458 3525 698142986 698143050 4.380000e-07 67.6


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 TraesCS4D01G231800 chr4D 391715837 391722604 6767 False 12499.0 12499 100.000000 1 6768 1 chr4D.!!$F1 6767
1 TraesCS4D01G231800 chr4B 481597944 481604263 6319 False 2323.0 3999 93.836250 233 6265 4 chr4B.!!$F1 6032
2 TraesCS4D01G231800 chr4A 73449579 73456130 6551 False 1834.4 3868 93.552200 170 6768 5 chr4A.!!$F1 6598
3 TraesCS4D01G231800 chr4A 706249241 706249868 627 True 549.0 549 82.485000 5125 5792 1 chr4A.!!$R1 667
4 TraesCS4D01G231800 chr2D 364954166 364954840 674 False 684.0 684 84.828000 5065 5789 1 chr2D.!!$F1 724
5 TraesCS4D01G231800 chr7A 677846970 677848332 1362 True 498.5 664 85.355500 4455 5792 2 chr7A.!!$R2 1337
6 TraesCS4D01G231800 chr3D 410514806 410516129 1323 False 379.0 521 88.673667 4455 5789 3 chr3D.!!$F2 1334

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
573 591 0.036010 CCCAGTTCGCAACTCCTCAT 60.036 55.000 0.00 0.00 40.46 2.90 F
658 682 0.108567 GTCTTCTCCAACCTCTCGCC 60.109 60.000 0.00 0.00 0.00 5.54 F
988 1036 1.194781 AGCCGCTTCCTCCTTCTTCA 61.195 55.000 0.00 0.00 0.00 3.02 F
1121 1181 1.687493 GTCCCTCTCCCAGTCCCAG 60.687 68.421 0.00 0.00 0.00 4.45 F
1457 1572 2.035632 AGCTTCTGGTATTCTCTCCCG 58.964 52.381 0.00 0.00 0.00 5.14 F
1602 1718 2.170187 CTGAATCTTGAGAGGTGAGGGG 59.830 54.545 0.00 0.00 0.00 4.79 F
2360 2489 2.432628 CGGAAGGTCGACAGTGCC 60.433 66.667 18.91 10.94 0.00 5.01 F
3571 3842 3.395639 TGACCGTTTGTGTAGAACCATC 58.604 45.455 0.00 0.00 0.00 3.51 F
3901 4347 0.609151 TGCATCCAAGTTTGCATGGG 59.391 50.000 4.27 0.00 43.54 4.00 F
5273 5826 1.006571 GAAGGTTCGTCTGGTCGCA 60.007 57.895 0.00 0.00 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2306 2435 0.959553 ACTCCGCTTCGAGTTCTTGA 59.040 50.000 0.00 0.0 40.23 3.02 R
2318 2447 1.446099 CACACGCATACACTCCGCT 60.446 57.895 0.00 0.0 0.00 5.52 R
2664 2793 0.393808 ACAGCCAAACCGCCGAATAT 60.394 50.000 0.00 0.0 0.00 1.28 R
2673 2802 4.631131 AGCTTAAAAATGACAGCCAAACC 58.369 39.130 0.00 0.0 32.25 3.27 R
2777 2906 8.918202 TTCTATACTGCCTTTTCTTTTCTTCA 57.082 30.769 0.00 0.0 0.00 3.02 R
3517 3788 3.986996 TCTGATGACTGGATTGAAGCA 57.013 42.857 0.00 0.0 0.00 3.91 R
3871 4317 2.224426 ACTTGGATGCACGTCCTTTACA 60.224 45.455 10.18 0.0 39.12 2.41 R
5344 5897 0.445436 CAGAAAGAGCACGGCATGTC 59.555 55.000 0.00 0.0 0.00 3.06 R
5669 6248 1.068472 CGTAGAGAAGTTGAGTGGCGT 60.068 52.381 0.00 0.0 0.00 5.68 R
6276 6864 0.111061 AGCTGGACATTCCACTGCAA 59.889 50.000 8.64 0.0 42.67 4.08 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
21 22 4.282950 CATCAATTTCCGTGGACAGATG 57.717 45.455 0.00 0.00 0.00 2.90
22 23 3.417069 TCAATTTCCGTGGACAGATGT 57.583 42.857 0.00 0.00 0.00 3.06
23 24 3.334691 TCAATTTCCGTGGACAGATGTC 58.665 45.455 4.33 4.33 44.04 3.06
53 54 9.445786 AAAATTTACGTGTTAGTGTTGAAGATG 57.554 29.630 0.00 0.00 0.00 2.90
54 55 5.585500 TTACGTGTTAGTGTTGAAGATGC 57.415 39.130 0.00 0.00 0.00 3.91
55 56 2.806244 ACGTGTTAGTGTTGAAGATGCC 59.194 45.455 0.00 0.00 0.00 4.40
56 57 2.159627 CGTGTTAGTGTTGAAGATGCCC 59.840 50.000 0.00 0.00 0.00 5.36
57 58 3.412386 GTGTTAGTGTTGAAGATGCCCT 58.588 45.455 0.00 0.00 0.00 5.19
58 59 4.575885 GTGTTAGTGTTGAAGATGCCCTA 58.424 43.478 0.00 0.00 0.00 3.53
59 60 5.001232 GTGTTAGTGTTGAAGATGCCCTAA 58.999 41.667 0.00 0.00 0.00 2.69
60 61 5.648092 GTGTTAGTGTTGAAGATGCCCTAAT 59.352 40.000 0.00 0.00 0.00 1.73
61 62 6.151144 GTGTTAGTGTTGAAGATGCCCTAATT 59.849 38.462 0.00 0.00 0.00 1.40
62 63 6.150976 TGTTAGTGTTGAAGATGCCCTAATTG 59.849 38.462 0.00 0.00 0.00 2.32
63 64 3.445096 AGTGTTGAAGATGCCCTAATTGC 59.555 43.478 0.00 0.00 0.00 3.56
64 65 2.760092 TGTTGAAGATGCCCTAATTGCC 59.240 45.455 0.00 0.00 0.00 4.52
65 66 2.760092 GTTGAAGATGCCCTAATTGCCA 59.240 45.455 0.00 0.00 0.00 4.92
66 67 3.317455 TGAAGATGCCCTAATTGCCAT 57.683 42.857 0.00 0.00 0.00 4.40
67 68 4.451891 TGAAGATGCCCTAATTGCCATA 57.548 40.909 0.00 0.00 0.00 2.74
68 69 4.144297 TGAAGATGCCCTAATTGCCATAC 58.856 43.478 0.00 0.00 0.00 2.39
69 70 2.783135 AGATGCCCTAATTGCCATACG 58.217 47.619 0.00 0.00 0.00 3.06
70 71 2.106511 AGATGCCCTAATTGCCATACGT 59.893 45.455 0.00 0.00 0.00 3.57
71 72 2.428544 TGCCCTAATTGCCATACGTT 57.571 45.000 0.00 0.00 0.00 3.99
72 73 2.294074 TGCCCTAATTGCCATACGTTC 58.706 47.619 0.00 0.00 0.00 3.95
73 74 1.263217 GCCCTAATTGCCATACGTTCG 59.737 52.381 0.00 0.00 0.00 3.95
74 75 2.828877 CCCTAATTGCCATACGTTCGA 58.171 47.619 0.00 0.00 0.00 3.71
75 76 2.542595 CCCTAATTGCCATACGTTCGAC 59.457 50.000 0.00 0.00 0.00 4.20
76 77 2.542595 CCTAATTGCCATACGTTCGACC 59.457 50.000 0.00 0.00 0.00 4.79
77 78 1.003851 AATTGCCATACGTTCGACCG 58.996 50.000 0.00 0.00 0.00 4.79
78 79 0.808453 ATTGCCATACGTTCGACCGG 60.808 55.000 7.43 0.00 0.00 5.28
79 80 2.584143 GCCATACGTTCGACCGGG 60.584 66.667 6.32 0.00 0.00 5.73
80 81 3.067480 GCCATACGTTCGACCGGGA 62.067 63.158 6.32 0.00 0.00 5.14
81 82 1.737816 CCATACGTTCGACCGGGAT 59.262 57.895 6.32 0.00 0.00 3.85
82 83 0.318445 CCATACGTTCGACCGGGATC 60.318 60.000 6.32 0.00 0.00 3.36
83 84 0.659417 CATACGTTCGACCGGGATCG 60.659 60.000 6.32 7.37 43.63 3.69
93 94 3.833645 CGGGATCGAGGGCGTCAA 61.834 66.667 8.06 0.00 39.00 3.18
94 95 2.202892 GGGATCGAGGGCGTCAAC 60.203 66.667 8.06 0.00 38.98 3.18
95 96 2.722201 GGGATCGAGGGCGTCAACT 61.722 63.158 8.06 0.00 38.98 3.16
96 97 1.218316 GGATCGAGGGCGTCAACTT 59.782 57.895 8.06 0.00 38.98 2.66
97 98 0.391263 GGATCGAGGGCGTCAACTTT 60.391 55.000 8.06 0.00 38.98 2.66
98 99 1.439679 GATCGAGGGCGTCAACTTTT 58.560 50.000 8.06 0.00 38.98 2.27
99 100 1.804748 GATCGAGGGCGTCAACTTTTT 59.195 47.619 8.06 0.00 38.98 1.94
118 119 5.838531 TTTTTACCCAAACAATCTCACGT 57.161 34.783 0.00 0.00 0.00 4.49
119 120 5.427036 TTTTACCCAAACAATCTCACGTC 57.573 39.130 0.00 0.00 0.00 4.34
120 121 2.631160 ACCCAAACAATCTCACGTCA 57.369 45.000 0.00 0.00 0.00 4.35
121 122 2.925724 ACCCAAACAATCTCACGTCAA 58.074 42.857 0.00 0.00 0.00 3.18
122 123 3.283751 ACCCAAACAATCTCACGTCAAA 58.716 40.909 0.00 0.00 0.00 2.69
123 124 3.888930 ACCCAAACAATCTCACGTCAAAT 59.111 39.130 0.00 0.00 0.00 2.32
124 125 5.067273 ACCCAAACAATCTCACGTCAAATA 58.933 37.500 0.00 0.00 0.00 1.40
125 126 5.710099 ACCCAAACAATCTCACGTCAAATAT 59.290 36.000 0.00 0.00 0.00 1.28
126 127 6.882140 ACCCAAACAATCTCACGTCAAATATA 59.118 34.615 0.00 0.00 0.00 0.86
127 128 7.556275 ACCCAAACAATCTCACGTCAAATATAT 59.444 33.333 0.00 0.00 0.00 0.86
128 129 9.051679 CCCAAACAATCTCACGTCAAATATATA 57.948 33.333 0.00 0.00 0.00 0.86
154 155 7.315247 TGAAATCCATAAGTTATCACAACGG 57.685 36.000 0.00 0.00 0.00 4.44
155 156 6.882140 TGAAATCCATAAGTTATCACAACGGT 59.118 34.615 0.00 0.00 0.00 4.83
156 157 7.392113 TGAAATCCATAAGTTATCACAACGGTT 59.608 33.333 0.00 0.00 0.00 4.44
157 158 7.696992 AATCCATAAGTTATCACAACGGTTT 57.303 32.000 0.00 0.00 0.00 3.27
158 159 8.795842 AATCCATAAGTTATCACAACGGTTTA 57.204 30.769 0.00 0.00 0.00 2.01
159 160 7.837202 TCCATAAGTTATCACAACGGTTTAG 57.163 36.000 0.00 0.00 0.00 1.85
160 161 6.819649 TCCATAAGTTATCACAACGGTTTAGG 59.180 38.462 0.00 0.00 0.00 2.69
161 162 6.819649 CCATAAGTTATCACAACGGTTTAGGA 59.180 38.462 0.00 0.00 0.00 2.94
162 163 7.497909 CCATAAGTTATCACAACGGTTTAGGAT 59.502 37.037 0.00 0.00 0.00 3.24
163 164 9.537192 CATAAGTTATCACAACGGTTTAGGATA 57.463 33.333 0.00 0.00 0.00 2.59
164 165 9.760077 ATAAGTTATCACAACGGTTTAGGATAG 57.240 33.333 0.00 0.00 0.00 2.08
165 166 7.414222 AGTTATCACAACGGTTTAGGATAGA 57.586 36.000 0.00 0.00 0.00 1.98
166 167 7.263496 AGTTATCACAACGGTTTAGGATAGAC 58.737 38.462 0.00 2.11 0.00 2.59
167 168 5.670792 ATCACAACGGTTTAGGATAGACA 57.329 39.130 0.00 0.00 0.00 3.41
168 169 5.068234 TCACAACGGTTTAGGATAGACAG 57.932 43.478 0.00 0.00 0.00 3.51
175 176 4.443621 GGTTTAGGATAGACAGAAGCACC 58.556 47.826 0.00 0.00 0.00 5.01
214 215 4.820897 TGTGCTCTATACACAAAGGACAG 58.179 43.478 0.00 0.00 44.68 3.51
256 257 9.542462 AGTATATCTTTTGAATAACGCAGCTAA 57.458 29.630 0.00 0.00 0.00 3.09
262 263 4.875544 TGAATAACGCAGCTAAACATCC 57.124 40.909 0.00 0.00 0.00 3.51
282 284 4.633175 TCCTGACACTTTACAACGCAATA 58.367 39.130 0.00 0.00 0.00 1.90
286 288 5.922546 TGACACTTTACAACGCAATATGAC 58.077 37.500 0.00 0.00 0.00 3.06
292 294 6.821665 ACTTTACAACGCAATATGACCATACT 59.178 34.615 0.00 0.00 0.00 2.12
302 304 6.620733 GCAATATGACCATACTAATCGTTGCC 60.621 42.308 9.40 0.00 33.08 4.52
321 326 0.316442 CAGCATATTCCAAGCGTGCG 60.316 55.000 0.00 0.00 40.54 5.34
381 390 7.614124 AAAAGCAGAACACACATGAAAAATT 57.386 28.000 0.00 0.00 0.00 1.82
382 391 8.715191 AAAAGCAGAACACACATGAAAAATTA 57.285 26.923 0.00 0.00 0.00 1.40
383 392 7.698836 AAGCAGAACACACATGAAAAATTAC 57.301 32.000 0.00 0.00 0.00 1.89
454 468 2.223386 ACCACATTTCACCGACAAAACG 60.223 45.455 0.00 0.00 0.00 3.60
573 591 0.036010 CCCAGTTCGCAACTCCTCAT 60.036 55.000 0.00 0.00 40.46 2.90
574 592 1.363744 CCAGTTCGCAACTCCTCATC 58.636 55.000 0.00 0.00 40.46 2.92
575 593 1.338105 CCAGTTCGCAACTCCTCATCA 60.338 52.381 0.00 0.00 40.46 3.07
657 681 0.456995 CGTCTTCTCCAACCTCTCGC 60.457 60.000 0.00 0.00 0.00 5.03
658 682 0.108567 GTCTTCTCCAACCTCTCGCC 60.109 60.000 0.00 0.00 0.00 5.54
659 683 1.219393 CTTCTCCAACCTCTCGCCC 59.781 63.158 0.00 0.00 0.00 6.13
660 684 2.564553 CTTCTCCAACCTCTCGCCCG 62.565 65.000 0.00 0.00 0.00 6.13
661 685 4.821589 CTCCAACCTCTCGCCCGC 62.822 72.222 0.00 0.00 0.00 6.13
722 746 1.912371 GCGCTCTTACCAACTGCACC 61.912 60.000 0.00 0.00 0.00 5.01
817 844 1.757682 GCGAGGAGAGAGAAGAGGAA 58.242 55.000 0.00 0.00 0.00 3.36
915 958 4.432741 GGCAGGACCAAGGAGGCC 62.433 72.222 0.00 0.00 43.14 5.19
963 1011 4.452733 GCCGAGGTGTCCCCTTCG 62.453 72.222 0.00 0.00 46.51 3.79
967 1015 3.003763 AGGTGTCCCCTTCGCCTC 61.004 66.667 0.00 0.00 42.73 4.70
988 1036 1.194781 AGCCGCTTCCTCCTTCTTCA 61.195 55.000 0.00 0.00 0.00 3.02
1115 1175 3.775654 GGTGCGTCCCTCTCCCAG 61.776 72.222 0.00 0.00 0.00 4.45
1116 1176 2.997897 GTGCGTCCCTCTCCCAGT 60.998 66.667 0.00 0.00 0.00 4.00
1121 1181 1.687493 GTCCCTCTCCCAGTCCCAG 60.687 68.421 0.00 0.00 0.00 4.45
1204 1314 3.652057 TCATGAGGATTTGGGAGGTTC 57.348 47.619 0.00 0.00 0.00 3.62
1386 1500 3.662247 AAAGACGAGGACGATGTTTCT 57.338 42.857 0.00 0.00 42.66 2.52
1457 1572 2.035632 AGCTTCTGGTATTCTCTCCCG 58.964 52.381 0.00 0.00 0.00 5.14
1544 1660 4.769215 CTTCCGTTTACAGTTTCCTTTCG 58.231 43.478 0.00 0.00 0.00 3.46
1602 1718 2.170187 CTGAATCTTGAGAGGTGAGGGG 59.830 54.545 0.00 0.00 0.00 4.79
1675 1791 4.098416 GGCTTAAAAATAGCACTGCTTCG 58.902 43.478 9.30 0.00 40.44 3.79
1756 1873 6.590292 TGCTTGCTAGTACAATCTCAAGTTAC 59.410 38.462 0.00 0.00 34.90 2.50
1831 1953 7.839680 AAGTTGAAAATCATAACTGGGAAGT 57.160 32.000 0.00 0.00 35.06 3.01
1836 1958 9.541143 TTGAAAATCATAACTGGGAAGTTTTTC 57.459 29.630 0.00 2.08 33.59 2.29
1929 2057 7.996644 GTGTTCCCAATTTATTAGGAGGTATGA 59.003 37.037 0.00 0.00 29.48 2.15
2077 2206 2.485903 TGCACTAAAACGTGGGTGTAG 58.514 47.619 0.00 0.00 35.47 2.74
2139 2268 9.778741 ATGTGGACGTTATTTGATTATCATAGT 57.221 29.630 0.00 0.00 0.00 2.12
2306 2435 6.456988 GCGAACAAGATAAAGATCGGATGTTT 60.457 38.462 16.10 16.10 37.86 2.83
2318 2447 3.985008 TCGGATGTTTCAAGAACTCGAA 58.015 40.909 0.00 0.00 0.00 3.71
2360 2489 2.432628 CGGAAGGTCGACAGTGCC 60.433 66.667 18.91 10.94 0.00 5.01
2544 2673 4.141620 GGACCTCCTTGAATATGAGCTCAA 60.142 45.833 22.50 10.69 0.00 3.02
2565 2694 7.118390 GCTCAAGTGTCATGTTATTCTAAGTGT 59.882 37.037 0.00 0.00 0.00 3.55
2605 2734 9.383519 GAGACTGAAATATTGGTAGTTCATTGA 57.616 33.333 0.00 0.00 42.12 2.57
2777 2906 7.768643 TGATGGATGGAGATGGGTAAATATTT 58.231 34.615 5.89 5.89 0.00 1.40
3021 3220 7.131498 ACGCCAAACAACGATAAAATACTAA 57.869 32.000 0.00 0.00 0.00 2.24
3112 3313 6.378280 ACCAAAAACTCTTTCAACTGACATCT 59.622 34.615 0.00 0.00 0.00 2.90
3314 3515 7.477144 AATCGAGACGATAAATGCACAAATA 57.523 32.000 7.06 0.00 46.30 1.40
3517 3788 4.656112 AGGGAGTACTTAGTTGCATATGCT 59.344 41.667 27.13 10.98 42.66 3.79
3560 3831 4.345859 TCAGATAGGTTTGACCGTTTGT 57.654 40.909 0.00 0.00 44.90 2.83
3571 3842 3.395639 TGACCGTTTGTGTAGAACCATC 58.604 45.455 0.00 0.00 0.00 3.51
3610 3881 4.461198 ACCTTAACTTCTCACACAAAGGG 58.539 43.478 0.00 0.00 37.03 3.95
3620 3891 6.385649 TCTCACACAAAGGGATTTGTAAAC 57.614 37.500 6.08 0.00 42.69 2.01
3623 3894 7.069331 TCTCACACAAAGGGATTTGTAAACAAT 59.931 33.333 6.08 0.00 42.69 2.71
3624 3895 8.239038 TCACACAAAGGGATTTGTAAACAATA 57.761 30.769 6.08 0.00 42.69 1.90
3643 3916 7.225784 ACAATAAGCATTTGTGTCATAACCA 57.774 32.000 0.00 0.00 36.02 3.67
3644 3917 7.090173 ACAATAAGCATTTGTGTCATAACCAC 58.910 34.615 0.00 0.00 36.02 4.16
3667 3940 4.982999 TGTACGCTTCTCTACTGCTTTAG 58.017 43.478 0.00 0.00 0.00 1.85
3793 4239 5.576447 TTTCCCTTTTTGTTCAGTCTGAC 57.424 39.130 0.78 0.00 0.00 3.51
3871 4317 3.509442 TGGGATGGATTTTGCAAAGACT 58.491 40.909 12.41 1.33 0.00 3.24
3880 4326 5.920840 GGATTTTGCAAAGACTGTAAAGGAC 59.079 40.000 12.41 0.00 40.22 3.85
3901 4347 0.609151 TGCATCCAAGTTTGCATGGG 59.391 50.000 4.27 0.00 43.54 4.00
4000 4446 3.056179 CAGAAAAGAGGACCAGAGTCTCC 60.056 52.174 0.00 0.00 43.05 3.71
4041 4487 4.570772 TGAAACTATGGCAGCGATTAGTTC 59.429 41.667 10.05 6.68 0.00 3.01
4265 4711 2.747446 GGTTTGCCAGCTTTCTATCGAA 59.253 45.455 0.00 0.00 34.09 3.71
4436 4884 2.295349 CAGAAATGCACATATGGAGCCC 59.705 50.000 16.66 6.55 0.00 5.19
4568 5016 5.740290 TCTTGAACGATCCTAGAACCTTT 57.260 39.130 0.00 0.00 0.00 3.11
4647 5095 4.813027 TGCAAAAGCAAATGAGGAATCTC 58.187 39.130 0.00 0.00 40.36 2.75
4907 5419 2.168326 TGAATCTCAAGCGTGCAGAA 57.832 45.000 0.00 0.00 0.00 3.02
4917 5429 2.331451 GTGCAGAAAAAGCGCGGT 59.669 55.556 4.23 4.23 32.37 5.68
4971 5488 4.455606 CTTTCTTCAGTTGGAGGACACTT 58.544 43.478 0.00 0.00 30.34 3.16
5217 5767 5.638657 GCTAGCTCACCATAATCATCAGAAG 59.361 44.000 7.70 0.00 0.00 2.85
5273 5826 1.006571 GAAGGTTCGTCTGGTCGCA 60.007 57.895 0.00 0.00 0.00 5.10
5344 5897 5.922544 AGAAACGATACCGGGTATAAATTCG 59.077 40.000 19.35 19.72 40.78 3.34
5349 5902 5.287752 CGATACCGGGTATAAATTCGACATG 59.712 44.000 19.35 0.00 0.00 3.21
5351 5904 2.482721 CCGGGTATAAATTCGACATGCC 59.517 50.000 0.00 0.00 0.00 4.40
5377 5932 2.965831 TCTTTCTGGCACTACACTCACT 59.034 45.455 0.00 0.00 0.00 3.41
5391 5946 5.791336 ACACTCACTACAGAAGTCATCAA 57.209 39.130 0.00 0.00 35.76 2.57
5414 5969 9.226606 TCAATCTTGTTCATTAATTCTTACCGT 57.773 29.630 0.00 0.00 0.00 4.83
5452 6007 6.600822 AGCTGCAGAATCTATTGCTTAAAGAA 59.399 34.615 20.43 0.00 40.87 2.52
5459 6014 9.746457 AGAATCTATTGCTTAAAGAAAAGGAGT 57.254 29.630 0.00 0.00 0.00 3.85
5620 6199 2.066262 CTTTTGACACCACGCTCGTAT 58.934 47.619 0.00 0.00 0.00 3.06
5669 6248 1.945354 GAACAGGAGGATGACGGCGA 61.945 60.000 16.62 0.00 0.00 5.54
5789 6368 5.700832 TGAGTATGATATCGCCCAACATTTC 59.299 40.000 0.00 0.00 0.00 2.17
5824 6404 1.747355 CCAGGATCTGTTGCATGAACC 59.253 52.381 0.00 0.00 33.07 3.62
5834 6414 1.170442 TGCATGAACCTGTGCTGATG 58.830 50.000 0.00 0.00 41.78 3.07
5871 6451 5.095145 TGACATTTCTGATCAGGGAAGAG 57.905 43.478 22.42 14.95 0.00 2.85
5937 6517 0.171903 GGGCAATTGTGTGCTAGCTG 59.828 55.000 17.23 4.84 44.31 4.24
5988 6569 8.930846 ATTGGACAGGATTTAGATAAGATTGG 57.069 34.615 0.00 0.00 0.00 3.16
6155 6737 6.197096 GCGTATCATCATTTTGGATGTGAAAC 59.803 38.462 0.00 0.00 44.00 2.78
6265 6853 8.271458 TCCACTTTATCTTTTGGAGCATGTATA 58.729 33.333 0.00 0.00 33.02 1.47
6266 6854 8.562892 CCACTTTATCTTTTGGAGCATGTATAG 58.437 37.037 0.00 0.00 0.00 1.31
6267 6855 8.562892 CACTTTATCTTTTGGAGCATGTATAGG 58.437 37.037 0.00 0.00 0.00 2.57
6268 6856 8.494433 ACTTTATCTTTTGGAGCATGTATAGGA 58.506 33.333 0.00 0.00 0.00 2.94
6269 6857 9.342308 CTTTATCTTTTGGAGCATGTATAGGAA 57.658 33.333 0.00 0.00 0.00 3.36
6270 6858 9.866655 TTTATCTTTTGGAGCATGTATAGGAAT 57.133 29.630 0.00 0.00 0.00 3.01
6271 6859 7.756395 ATCTTTTGGAGCATGTATAGGAATG 57.244 36.000 0.00 0.00 0.00 2.67
6272 6860 6.064060 TCTTTTGGAGCATGTATAGGAATGG 58.936 40.000 0.00 0.00 0.00 3.16
6273 6861 3.423539 TGGAGCATGTATAGGAATGGC 57.576 47.619 0.00 0.00 0.00 4.40
6274 6862 2.710471 TGGAGCATGTATAGGAATGGCA 59.290 45.455 0.00 0.00 0.00 4.92
6275 6863 3.077359 GGAGCATGTATAGGAATGGCAC 58.923 50.000 0.00 0.00 0.00 5.01
6276 6864 3.244700 GGAGCATGTATAGGAATGGCACT 60.245 47.826 0.00 0.00 0.00 4.40
6277 6865 4.392940 GAGCATGTATAGGAATGGCACTT 58.607 43.478 0.00 0.00 0.00 3.16
6278 6866 4.139786 AGCATGTATAGGAATGGCACTTG 58.860 43.478 0.00 0.00 0.00 3.16
6279 6867 3.304928 GCATGTATAGGAATGGCACTTGC 60.305 47.826 0.00 0.00 41.14 4.01
6280 6868 3.643199 TGTATAGGAATGGCACTTGCA 57.357 42.857 3.15 0.00 44.36 4.08
6281 6869 3.544684 TGTATAGGAATGGCACTTGCAG 58.455 45.455 3.15 0.00 44.36 4.41
6282 6870 2.814805 ATAGGAATGGCACTTGCAGT 57.185 45.000 3.15 0.00 44.36 4.40
6284 6872 0.896940 AGGAATGGCACTTGCAGTGG 60.897 55.000 15.16 1.13 46.01 4.00
6285 6873 0.895100 GGAATGGCACTTGCAGTGGA 60.895 55.000 15.16 0.00 46.01 4.02
6286 6874 0.961019 GAATGGCACTTGCAGTGGAA 59.039 50.000 15.16 0.00 46.01 3.53
6287 6875 1.547372 GAATGGCACTTGCAGTGGAAT 59.453 47.619 15.16 0.00 46.01 3.01
6288 6876 0.892755 ATGGCACTTGCAGTGGAATG 59.107 50.000 15.16 0.37 46.01 2.67
6289 6877 0.467844 TGGCACTTGCAGTGGAATGT 60.468 50.000 15.16 0.00 46.01 2.71
6290 6878 0.242017 GGCACTTGCAGTGGAATGTC 59.758 55.000 15.16 0.00 46.01 3.06
6291 6879 0.242017 GCACTTGCAGTGGAATGTCC 59.758 55.000 15.16 0.00 46.01 4.02
6292 6880 1.608055 CACTTGCAGTGGAATGTCCA 58.392 50.000 0.00 0.00 45.98 4.02
6293 6881 4.275047 GCACTTGCAGTGGAATGTCCAG 62.275 54.545 15.16 0.00 46.01 3.86
6299 6887 4.728409 TGGAATGTCCAGCTGCTG 57.272 55.556 22.44 22.44 42.67 4.41
6300 6888 1.676635 TGGAATGTCCAGCTGCTGC 60.677 57.895 23.86 11.90 42.67 5.25
6324 6912 7.987458 TGCTGTATTCAACCTCTAGGAATTAAG 59.013 37.037 2.23 0.00 38.94 1.85
6403 6991 7.405469 TGTTGCAACATATGAAAACATGAAC 57.595 32.000 27.96 0.00 34.26 3.18
6548 7137 6.992715 AGTTTTACTCACATGCTGATATACCC 59.007 38.462 0.00 0.00 0.00 3.69
6637 7226 4.219115 GGATCATTCTGGTGGAGAGACTA 58.781 47.826 0.00 0.00 30.18 2.59
6646 7235 3.898123 TGGTGGAGAGACTATATGAAGCC 59.102 47.826 0.00 0.00 0.00 4.35
6744 7344 6.990045 TGGCCAACCTATAATGGATAGATCCT 60.990 42.308 0.61 0.00 40.18 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.691118 ACATCTGTCCACGGAAATTGATG 59.309 43.478 12.96 12.96 36.92 3.07
1 2 3.941483 GACATCTGTCCACGGAAATTGAT 59.059 43.478 0.00 0.00 39.07 2.57
2 3 3.334691 GACATCTGTCCACGGAAATTGA 58.665 45.455 0.00 0.00 39.07 2.57
3 4 3.747099 GACATCTGTCCACGGAAATTG 57.253 47.619 0.00 0.00 39.07 2.32
27 28 9.445786 CATCTTCAACACTAACACGTAAATTTT 57.554 29.630 0.00 0.00 0.00 1.82
28 29 7.589954 GCATCTTCAACACTAACACGTAAATTT 59.410 33.333 0.00 0.00 0.00 1.82
29 30 7.075741 GCATCTTCAACACTAACACGTAAATT 58.924 34.615 0.00 0.00 0.00 1.82
30 31 6.348213 GGCATCTTCAACACTAACACGTAAAT 60.348 38.462 0.00 0.00 0.00 1.40
31 32 5.049954 GGCATCTTCAACACTAACACGTAAA 60.050 40.000 0.00 0.00 0.00 2.01
32 33 4.449743 GGCATCTTCAACACTAACACGTAA 59.550 41.667 0.00 0.00 0.00 3.18
33 34 3.991773 GGCATCTTCAACACTAACACGTA 59.008 43.478 0.00 0.00 0.00 3.57
34 35 2.806244 GGCATCTTCAACACTAACACGT 59.194 45.455 0.00 0.00 0.00 4.49
35 36 2.159627 GGGCATCTTCAACACTAACACG 59.840 50.000 0.00 0.00 0.00 4.49
36 37 3.412386 AGGGCATCTTCAACACTAACAC 58.588 45.455 0.00 0.00 0.00 3.32
37 38 3.788227 AGGGCATCTTCAACACTAACA 57.212 42.857 0.00 0.00 0.00 2.41
38 39 6.555315 CAATTAGGGCATCTTCAACACTAAC 58.445 40.000 0.00 0.00 0.00 2.34
39 40 5.125417 GCAATTAGGGCATCTTCAACACTAA 59.875 40.000 0.00 0.00 0.00 2.24
40 41 4.640201 GCAATTAGGGCATCTTCAACACTA 59.360 41.667 0.00 0.00 0.00 2.74
41 42 3.445096 GCAATTAGGGCATCTTCAACACT 59.555 43.478 0.00 0.00 0.00 3.55
42 43 3.429410 GGCAATTAGGGCATCTTCAACAC 60.429 47.826 0.00 0.00 0.00 3.32
43 44 2.760092 GGCAATTAGGGCATCTTCAACA 59.240 45.455 0.00 0.00 0.00 3.33
44 45 2.760092 TGGCAATTAGGGCATCTTCAAC 59.240 45.455 0.00 0.00 38.55 3.18
45 46 3.098774 TGGCAATTAGGGCATCTTCAA 57.901 42.857 0.00 0.00 38.55 2.69
46 47 2.824689 TGGCAATTAGGGCATCTTCA 57.175 45.000 0.00 0.00 38.55 3.02
53 54 1.263217 CGAACGTATGGCAATTAGGGC 59.737 52.381 0.00 0.00 0.00 5.19
54 55 2.542595 GTCGAACGTATGGCAATTAGGG 59.457 50.000 0.00 0.00 0.00 3.53
55 56 2.542595 GGTCGAACGTATGGCAATTAGG 59.457 50.000 0.00 0.00 0.00 2.69
56 57 2.217847 CGGTCGAACGTATGGCAATTAG 59.782 50.000 16.31 0.00 0.00 1.73
57 58 2.195096 CGGTCGAACGTATGGCAATTA 58.805 47.619 16.31 0.00 0.00 1.40
58 59 1.003851 CGGTCGAACGTATGGCAATT 58.996 50.000 16.31 0.00 0.00 2.32
59 60 0.808453 CCGGTCGAACGTATGGCAAT 60.808 55.000 23.08 0.00 0.00 3.56
60 61 1.446445 CCGGTCGAACGTATGGCAA 60.446 57.895 23.08 0.00 0.00 4.52
61 62 2.182284 CCGGTCGAACGTATGGCA 59.818 61.111 23.08 0.00 0.00 4.92
62 63 2.359570 ATCCCGGTCGAACGTATGGC 62.360 60.000 23.08 0.00 0.00 4.40
63 64 0.318445 GATCCCGGTCGAACGTATGG 60.318 60.000 23.08 16.11 0.00 2.74
64 65 0.659417 CGATCCCGGTCGAACGTATG 60.659 60.000 23.08 10.01 44.06 2.39
65 66 0.815213 TCGATCCCGGTCGAACGTAT 60.815 55.000 23.08 14.81 46.54 3.06
66 67 1.449423 TCGATCCCGGTCGAACGTA 60.449 57.895 23.08 10.05 46.54 3.57
67 68 2.747460 TCGATCCCGGTCGAACGT 60.747 61.111 23.08 2.41 46.54 3.99
76 77 3.833645 TTGACGCCCTCGATCCCG 61.834 66.667 0.00 0.00 39.41 5.14
77 78 2.202892 GTTGACGCCCTCGATCCC 60.203 66.667 0.00 0.00 39.41 3.85
78 79 0.391263 AAAGTTGACGCCCTCGATCC 60.391 55.000 0.00 0.00 39.41 3.36
79 80 1.439679 AAAAGTTGACGCCCTCGATC 58.560 50.000 0.00 0.00 39.41 3.69
80 81 1.892209 AAAAAGTTGACGCCCTCGAT 58.108 45.000 0.00 0.00 39.41 3.59
81 82 3.390003 AAAAAGTTGACGCCCTCGA 57.610 47.368 0.00 0.00 39.41 4.04
96 97 5.357314 TGACGTGAGATTGTTTGGGTAAAAA 59.643 36.000 0.00 0.00 0.00 1.94
97 98 4.882427 TGACGTGAGATTGTTTGGGTAAAA 59.118 37.500 0.00 0.00 0.00 1.52
98 99 4.452825 TGACGTGAGATTGTTTGGGTAAA 58.547 39.130 0.00 0.00 0.00 2.01
99 100 4.074627 TGACGTGAGATTGTTTGGGTAA 57.925 40.909 0.00 0.00 0.00 2.85
100 101 3.755112 TGACGTGAGATTGTTTGGGTA 57.245 42.857 0.00 0.00 0.00 3.69
101 102 2.631160 TGACGTGAGATTGTTTGGGT 57.369 45.000 0.00 0.00 0.00 4.51
102 103 3.980646 TTTGACGTGAGATTGTTTGGG 57.019 42.857 0.00 0.00 0.00 4.12
128 129 8.405531 CCGTTGTGATAACTTATGGATTTCAAT 58.594 33.333 0.00 0.00 0.00 2.57
129 130 7.392113 ACCGTTGTGATAACTTATGGATTTCAA 59.608 33.333 2.23 0.00 0.00 2.69
130 131 6.882140 ACCGTTGTGATAACTTATGGATTTCA 59.118 34.615 2.23 0.00 0.00 2.69
131 132 7.316544 ACCGTTGTGATAACTTATGGATTTC 57.683 36.000 2.23 0.00 0.00 2.17
132 133 7.696992 AACCGTTGTGATAACTTATGGATTT 57.303 32.000 2.23 0.00 0.00 2.17
133 134 7.696992 AAACCGTTGTGATAACTTATGGATT 57.303 32.000 2.23 0.00 0.00 3.01
134 135 7.497909 CCTAAACCGTTGTGATAACTTATGGAT 59.502 37.037 2.23 0.00 0.00 3.41
135 136 6.819649 CCTAAACCGTTGTGATAACTTATGGA 59.180 38.462 2.23 0.00 0.00 3.41
136 137 6.819649 TCCTAAACCGTTGTGATAACTTATGG 59.180 38.462 0.00 0.00 0.00 2.74
137 138 7.837202 TCCTAAACCGTTGTGATAACTTATG 57.163 36.000 0.00 0.00 0.00 1.90
138 139 9.760077 CTATCCTAAACCGTTGTGATAACTTAT 57.240 33.333 0.00 0.00 0.00 1.73
139 140 8.970020 TCTATCCTAAACCGTTGTGATAACTTA 58.030 33.333 0.00 0.00 0.00 2.24
140 141 7.763071 GTCTATCCTAAACCGTTGTGATAACTT 59.237 37.037 0.00 0.00 0.00 2.66
141 142 7.093640 TGTCTATCCTAAACCGTTGTGATAACT 60.094 37.037 0.00 0.00 0.00 2.24
142 143 7.037438 TGTCTATCCTAAACCGTTGTGATAAC 58.963 38.462 0.00 0.00 0.00 1.89
143 144 7.123098 TCTGTCTATCCTAAACCGTTGTGATAA 59.877 37.037 0.00 0.00 0.00 1.75
144 145 6.604396 TCTGTCTATCCTAAACCGTTGTGATA 59.396 38.462 0.00 0.00 0.00 2.15
145 146 5.421056 TCTGTCTATCCTAAACCGTTGTGAT 59.579 40.000 0.00 0.00 0.00 3.06
146 147 4.768448 TCTGTCTATCCTAAACCGTTGTGA 59.232 41.667 0.00 0.00 0.00 3.58
147 148 5.068234 TCTGTCTATCCTAAACCGTTGTG 57.932 43.478 0.00 0.00 0.00 3.33
148 149 5.721232 CTTCTGTCTATCCTAAACCGTTGT 58.279 41.667 0.00 0.00 0.00 3.32
149 150 4.567159 GCTTCTGTCTATCCTAAACCGTTG 59.433 45.833 0.00 0.00 0.00 4.10
150 151 4.222145 TGCTTCTGTCTATCCTAAACCGTT 59.778 41.667 0.00 0.00 0.00 4.44
151 152 3.767673 TGCTTCTGTCTATCCTAAACCGT 59.232 43.478 0.00 0.00 0.00 4.83
152 153 4.113354 GTGCTTCTGTCTATCCTAAACCG 58.887 47.826 0.00 0.00 0.00 4.44
153 154 4.443621 GGTGCTTCTGTCTATCCTAAACC 58.556 47.826 0.00 0.00 0.00 3.27
154 155 4.081087 TGGGTGCTTCTGTCTATCCTAAAC 60.081 45.833 0.00 0.00 0.00 2.01
155 156 4.101114 TGGGTGCTTCTGTCTATCCTAAA 58.899 43.478 0.00 0.00 0.00 1.85
156 157 3.719871 TGGGTGCTTCTGTCTATCCTAA 58.280 45.455 0.00 0.00 0.00 2.69
157 158 3.398318 TGGGTGCTTCTGTCTATCCTA 57.602 47.619 0.00 0.00 0.00 2.94
158 159 2.254152 TGGGTGCTTCTGTCTATCCT 57.746 50.000 0.00 0.00 0.00 3.24
159 160 3.567478 AATGGGTGCTTCTGTCTATCC 57.433 47.619 0.00 0.00 0.00 2.59
160 161 3.879892 GGAAATGGGTGCTTCTGTCTATC 59.120 47.826 0.00 0.00 0.00 2.08
161 162 3.525199 AGGAAATGGGTGCTTCTGTCTAT 59.475 43.478 0.00 0.00 0.00 1.98
162 163 2.912956 AGGAAATGGGTGCTTCTGTCTA 59.087 45.455 0.00 0.00 0.00 2.59
163 164 1.707427 AGGAAATGGGTGCTTCTGTCT 59.293 47.619 0.00 0.00 0.00 3.41
164 165 2.087646 GAGGAAATGGGTGCTTCTGTC 58.912 52.381 0.00 0.00 0.00 3.51
165 166 1.611673 CGAGGAAATGGGTGCTTCTGT 60.612 52.381 0.00 0.00 0.00 3.41
166 167 1.089920 CGAGGAAATGGGTGCTTCTG 58.910 55.000 0.00 0.00 0.00 3.02
167 168 0.035056 CCGAGGAAATGGGTGCTTCT 60.035 55.000 0.00 0.00 0.00 2.85
168 169 0.035439 TCCGAGGAAATGGGTGCTTC 60.035 55.000 0.00 0.00 0.00 3.86
175 176 3.885297 AGCACAATTATCCGAGGAAATGG 59.115 43.478 0.00 0.00 0.00 3.16
214 215 5.416326 AGATATACTCCTATGTCGCACCTTC 59.584 44.000 0.00 0.00 0.00 3.46
249 250 2.704572 AGTGTCAGGATGTTTAGCTGC 58.295 47.619 0.00 0.00 37.40 5.25
256 257 3.250040 GCGTTGTAAAGTGTCAGGATGTT 59.750 43.478 0.00 0.00 37.40 2.71
262 263 6.015504 GTCATATTGCGTTGTAAAGTGTCAG 58.984 40.000 0.00 0.00 0.00 3.51
282 284 4.380531 CTGGCAACGATTAGTATGGTCAT 58.619 43.478 0.00 0.00 42.51 3.06
286 288 2.560504 TGCTGGCAACGATTAGTATGG 58.439 47.619 0.00 0.00 42.51 2.74
292 294 3.814625 TGGAATATGCTGGCAACGATTA 58.185 40.909 0.00 0.00 42.51 1.75
302 304 0.316442 CGCACGCTTGGAATATGCTG 60.316 55.000 0.00 0.00 34.06 4.41
321 326 1.444119 TTTCACGTGAAGCAGTGGGC 61.444 55.000 28.21 0.00 45.30 5.36
381 390 5.868801 CGTATCCGGGTTTCTTTTTACTGTA 59.131 40.000 0.00 0.00 0.00 2.74
382 391 4.692155 CGTATCCGGGTTTCTTTTTACTGT 59.308 41.667 0.00 0.00 0.00 3.55
383 392 4.692155 ACGTATCCGGGTTTCTTTTTACTG 59.308 41.667 0.00 0.00 38.78 2.74
398 412 4.100529 ACTTTTGTCATCGTACGTATCCG 58.899 43.478 16.05 0.00 40.83 4.18
420 434 6.272318 GTGAAATGTGGTGACAAAATCTCAA 58.728 36.000 0.00 0.00 46.06 3.02
454 468 1.068472 TCTCTGTTCGTTTCCGAGAGC 60.068 52.381 0.00 0.00 45.24 4.09
658 682 4.929707 GTGATAAGGCGGGGGCGG 62.930 72.222 0.00 0.00 0.00 6.13
659 683 4.929707 GGTGATAAGGCGGGGGCG 62.930 72.222 0.00 0.00 0.00 6.13
660 684 3.804329 TGGTGATAAGGCGGGGGC 61.804 66.667 0.00 0.00 0.00 5.80
661 685 2.192175 GTGGTGATAAGGCGGGGG 59.808 66.667 0.00 0.00 0.00 5.40
722 746 4.862902 ATATGGATCTCAGTTGAGTCCG 57.137 45.455 17.81 0.00 41.26 4.79
811 838 1.398234 CCCTTCCTCCCCTTCCTCT 59.602 63.158 0.00 0.00 0.00 3.69
817 844 1.852626 CACCAACCCTTCCTCCCCT 60.853 63.158 0.00 0.00 0.00 4.79
898 941 4.432741 GGCCTCCTTGGTCCTGCC 62.433 72.222 0.00 0.00 38.35 4.85
915 958 0.959372 ACTGTACCCGTCGTCCTCTG 60.959 60.000 0.00 0.00 0.00 3.35
963 1011 4.847444 GAGGAAGCGGCTGGAGGC 62.847 72.222 1.81 0.00 40.90 4.70
967 1015 2.124942 GAAGGAGGAAGCGGCTGG 60.125 66.667 1.81 0.00 0.00 4.85
988 1036 1.152567 CGCCCATCTCCTCTCTCCT 60.153 63.158 0.00 0.00 0.00 3.69
1115 1175 1.508088 CCGCATTTGCTTCTGGGAC 59.492 57.895 0.51 0.00 39.32 4.46
1116 1176 2.342650 GCCGCATTTGCTTCTGGGA 61.343 57.895 0.51 0.00 39.32 4.37
1121 1181 1.138247 CAGAGGCCGCATTTGCTTC 59.862 57.895 9.88 0.00 39.32 3.86
1134 1244 2.202987 GGATGCCGCAGACAGAGG 60.203 66.667 0.00 0.00 40.66 3.69
1158 1268 4.645535 AGCAGAGAACAAGCAGTAAATCA 58.354 39.130 0.00 0.00 0.00 2.57
1386 1500 4.023291 GGGCTTTTATGAACAATCCTGGA 58.977 43.478 0.00 0.00 0.00 3.86
1544 1660 5.468540 AATGAAAAGTTCCACCTAAAGCC 57.531 39.130 0.00 0.00 0.00 4.35
1602 1718 2.158740 GGAAAAGTAGATCTCCCTGCCC 60.159 54.545 0.00 0.00 0.00 5.36
1604 1720 4.447290 GAAGGAAAAGTAGATCTCCCTGC 58.553 47.826 0.00 0.00 0.00 4.85
1608 1724 4.471747 AGTGGGAAGGAAAAGTAGATCTCC 59.528 45.833 0.00 0.00 0.00 3.71
1675 1791 3.067742 CAGTGGCTTCAATCATTGGGATC 59.932 47.826 0.00 0.00 34.28 3.36
1771 1893 6.209391 AGTGCTTTGTTATGCTTGTAGGAATT 59.791 34.615 0.00 0.00 0.00 2.17
1896 2021 7.898636 TCCTAATAAATTGGGAACACAGGATTT 59.101 33.333 5.40 0.00 43.32 2.17
1984 2112 5.066505 AGGACTTCTGTTGAATGTTGAACAC 59.933 40.000 0.00 0.00 31.20 3.32
2139 2268 3.772572 TGTCTGCCAGTACCTAATAGCAA 59.227 43.478 0.00 0.00 0.00 3.91
2306 2435 0.959553 ACTCCGCTTCGAGTTCTTGA 59.040 50.000 0.00 0.00 40.23 3.02
2318 2447 1.446099 CACACGCATACACTCCGCT 60.446 57.895 0.00 0.00 0.00 5.52
2467 2596 6.859112 ATTAGAGATTACGGCAGGATATGT 57.141 37.500 0.00 0.00 0.00 2.29
2544 2673 9.507329 AATCAACACTTAGAATAACATGACACT 57.493 29.630 0.00 0.00 0.00 3.55
2664 2793 0.393808 ACAGCCAAACCGCCGAATAT 60.394 50.000 0.00 0.00 0.00 1.28
2673 2802 4.631131 AGCTTAAAAATGACAGCCAAACC 58.369 39.130 0.00 0.00 32.25 3.27
2777 2906 8.918202 TTCTATACTGCCTTTTCTTTTCTTCA 57.082 30.769 0.00 0.00 0.00 3.02
3444 3645 8.950208 AGATCACTAAGTATTTTAGTCAAGGC 57.050 34.615 0.00 0.00 33.30 4.35
3517 3788 3.986996 TCTGATGACTGGATTGAAGCA 57.013 42.857 0.00 0.00 0.00 3.91
3620 3891 7.274033 CAGTGGTTATGACACAAATGCTTATTG 59.726 37.037 0.00 0.00 41.21 1.90
3623 3894 5.767665 ACAGTGGTTATGACACAAATGCTTA 59.232 36.000 0.00 0.00 41.21 3.09
3624 3895 4.584325 ACAGTGGTTATGACACAAATGCTT 59.416 37.500 0.00 0.00 41.21 3.91
3643 3916 2.438411 AGCAGTAGAGAAGCGTACAGT 58.562 47.619 0.00 0.00 0.00 3.55
3644 3917 3.495670 AAGCAGTAGAGAAGCGTACAG 57.504 47.619 0.00 0.00 0.00 2.74
3769 4215 6.036470 GTCAGACTGAACAAAAAGGGAAAAG 58.964 40.000 6.76 0.00 0.00 2.27
3793 4239 7.226720 ACATATACAAATACTTTCTGAAGGCGG 59.773 37.037 0.00 0.00 37.19 6.13
3871 4317 2.224426 ACTTGGATGCACGTCCTTTACA 60.224 45.455 10.18 0.00 39.12 2.41
3901 4347 4.669318 TCGTCGAATTATCTGAGTTGGTC 58.331 43.478 0.00 0.00 0.00 4.02
4000 4446 8.043710 ATAGTTTCACTAAGAGGAATCACCTTG 58.956 37.037 0.00 0.00 40.76 3.61
4041 4487 3.942748 AGTTAGAGAGGCTACGAGACAAG 59.057 47.826 0.00 0.00 0.00 3.16
4334 4782 6.535274 TTTTGCTTAGTTAGTCTTTCGACC 57.465 37.500 0.00 0.00 41.16 4.79
4436 4884 1.142185 CTGGTGCTGTGCTCGTATCG 61.142 60.000 0.00 0.00 0.00 2.92
4568 5016 2.325484 TCCACTAGACCTGCAAGTGAA 58.675 47.619 15.48 0.00 42.59 3.18
4647 5095 7.121907 TCTCTCCATGATATCTTTCCTCGTATG 59.878 40.741 3.98 0.00 0.00 2.39
4847 5359 4.383118 GCACTGTACCTGTTATCATCCTGT 60.383 45.833 0.00 0.00 0.00 4.00
4907 5419 0.509929 GAACGAGTAACCGCGCTTTT 59.490 50.000 5.56 0.00 37.39 2.27
4914 5426 4.449743 TGGAATCTTTTGAACGAGTAACCG 59.550 41.667 0.00 0.00 0.00 4.44
4917 5429 6.764085 TCACTTGGAATCTTTTGAACGAGTAA 59.236 34.615 0.00 0.00 0.00 2.24
5047 5564 4.378978 CCAAATGCGACGTGGATCTTTAAA 60.379 41.667 0.11 0.00 34.05 1.52
5048 5565 3.126171 CCAAATGCGACGTGGATCTTTAA 59.874 43.478 0.11 0.00 34.05 1.52
5049 5566 2.675844 CCAAATGCGACGTGGATCTTTA 59.324 45.455 0.11 0.00 34.05 1.85
5217 5767 3.555139 GCATCAGATCTAGTGTGCTTGAC 59.445 47.826 0.00 0.00 29.93 3.18
5273 5826 6.877236 TCTGAGTTTTTGCTCTTCCAAAATT 58.123 32.000 1.49 0.00 42.36 1.82
5344 5897 0.445436 CAGAAAGAGCACGGCATGTC 59.555 55.000 0.00 0.00 0.00 3.06
5349 5902 2.669569 TGCCAGAAAGAGCACGGC 60.670 61.111 0.00 0.00 43.28 5.68
5377 5932 8.853077 AATGAACAAGATTGATGACTTCTGTA 57.147 30.769 0.00 0.00 0.00 2.74
5391 5946 9.326413 CCTACGGTAAGAATTAATGAACAAGAT 57.674 33.333 0.00 0.00 28.70 2.40
5405 5960 4.038271 TCTTCTGGTCCTACGGTAAGAA 57.962 45.455 0.00 0.77 0.00 2.52
5413 5968 1.276421 TGCAGCTTCTTCTGGTCCTAC 59.724 52.381 0.00 0.00 34.74 3.18
5414 5969 1.552337 CTGCAGCTTCTTCTGGTCCTA 59.448 52.381 0.00 0.00 34.74 2.94
5452 6007 3.140144 TGGACCCAAAGATCAACTCCTTT 59.860 43.478 0.00 0.00 33.29 3.11
5459 6014 3.138283 ACAGACTTGGACCCAAAGATCAA 59.862 43.478 2.84 0.00 35.33 2.57
5620 6199 2.279935 AATTGTTGTACCGGCCAGAA 57.720 45.000 0.00 0.00 0.00 3.02
5669 6248 1.068472 CGTAGAGAAGTTGAGTGGCGT 60.068 52.381 0.00 0.00 0.00 5.68
5789 6368 5.063944 CAGATCCTGGAAATCACTTGTAACG 59.936 44.000 0.00 0.00 0.00 3.18
5824 6404 5.179929 TGTTTACAGATCAACATCAGCACAG 59.820 40.000 0.00 0.00 0.00 3.66
5834 6414 8.506437 TCAGAAATGTCATGTTTACAGATCAAC 58.494 33.333 0.00 0.00 0.00 3.18
5871 6451 1.377333 CTCCCCGCCAAGAAAGTCC 60.377 63.158 0.00 0.00 0.00 3.85
5900 6480 1.473434 CCCAATCTTGACGGTAGCCTC 60.473 57.143 0.00 0.00 0.00 4.70
5937 6517 3.501828 TGTCACACATTAGCATGGTCAAC 59.498 43.478 0.00 0.00 34.27 3.18
5988 6569 4.279671 AGTGCTAGGTCATGTATCTACAGC 59.720 45.833 0.00 0.00 39.92 4.40
6131 6713 7.249858 TGTTTCACATCCAAAATGATGATACG 58.750 34.615 7.93 0.00 43.94 3.06
6139 6721 6.588756 CCATCTCTTGTTTCACATCCAAAATG 59.411 38.462 0.00 0.00 0.00 2.32
6140 6722 6.268387 ACCATCTCTTGTTTCACATCCAAAAT 59.732 34.615 0.00 0.00 0.00 1.82
6177 6759 9.161629 CAGGATACAACACTTTTATGTGATACA 57.838 33.333 1.47 0.00 39.33 2.29
6178 6760 9.162764 ACAGGATACAACACTTTTATGTGATAC 57.837 33.333 1.47 0.00 39.33 2.24
6190 6778 4.471386 AGGCTGAATACAGGATACAACACT 59.529 41.667 0.00 0.00 43.62 3.55
6275 6863 0.524862 GCTGGACATTCCACTGCAAG 59.475 55.000 2.41 0.00 42.67 4.01
6276 6864 0.111061 AGCTGGACATTCCACTGCAA 59.889 50.000 8.64 0.00 42.67 4.08
6277 6865 0.607217 CAGCTGGACATTCCACTGCA 60.607 55.000 5.57 0.00 42.67 4.41
6278 6866 2.177950 CAGCTGGACATTCCACTGC 58.822 57.895 5.57 5.47 42.67 4.40
6279 6867 0.322277 AGCAGCTGGACATTCCACTG 60.322 55.000 17.12 15.11 42.67 3.66
6280 6868 0.322277 CAGCAGCTGGACATTCCACT 60.322 55.000 17.12 0.00 42.67 4.00
6281 6869 1.930908 GCAGCAGCTGGACATTCCAC 61.931 60.000 24.13 0.00 42.67 4.02
6282 6870 1.676635 GCAGCAGCTGGACATTCCA 60.677 57.895 24.13 0.00 45.98 3.53
6283 6871 3.194719 GCAGCAGCTGGACATTCC 58.805 61.111 24.13 1.20 37.91 3.01
6293 6881 1.399791 GAGGTTGAATACAGCAGCAGC 59.600 52.381 0.00 0.00 42.56 5.25
6294 6882 2.983229 AGAGGTTGAATACAGCAGCAG 58.017 47.619 0.00 0.00 0.00 4.24
6295 6883 3.118629 CCTAGAGGTTGAATACAGCAGCA 60.119 47.826 0.00 0.00 0.00 4.41
6296 6884 3.133003 TCCTAGAGGTTGAATACAGCAGC 59.867 47.826 0.00 0.00 36.34 5.25
6297 6885 5.344743 TTCCTAGAGGTTGAATACAGCAG 57.655 43.478 0.00 0.00 36.34 4.24
6298 6886 5.957771 ATTCCTAGAGGTTGAATACAGCA 57.042 39.130 0.00 0.00 36.34 4.41
6299 6887 7.041712 GCTTAATTCCTAGAGGTTGAATACAGC 60.042 40.741 0.00 0.00 36.34 4.40
6300 6888 7.987458 TGCTTAATTCCTAGAGGTTGAATACAG 59.013 37.037 0.00 0.00 36.34 2.74
6301 6889 7.857456 TGCTTAATTCCTAGAGGTTGAATACA 58.143 34.615 0.00 0.00 36.34 2.29
6302 6890 8.910351 ATGCTTAATTCCTAGAGGTTGAATAC 57.090 34.615 0.00 0.00 36.34 1.89
6303 6891 8.713971 TGATGCTTAATTCCTAGAGGTTGAATA 58.286 33.333 0.00 0.00 36.34 1.75
6304 6892 7.577303 TGATGCTTAATTCCTAGAGGTTGAAT 58.423 34.615 0.00 0.00 36.34 2.57
6305 6893 6.957631 TGATGCTTAATTCCTAGAGGTTGAA 58.042 36.000 0.00 0.00 36.34 2.69
6306 6894 6.560003 TGATGCTTAATTCCTAGAGGTTGA 57.440 37.500 0.00 0.00 36.34 3.18
6307 6895 6.994496 TGATGATGCTTAATTCCTAGAGGTTG 59.006 38.462 0.00 0.00 36.34 3.77
6308 6896 7.141758 TGATGATGCTTAATTCCTAGAGGTT 57.858 36.000 0.00 0.00 36.34 3.50
6309 6897 6.753913 TGATGATGCTTAATTCCTAGAGGT 57.246 37.500 0.00 0.00 36.34 3.85
6324 6912 1.263484 CGCCTGTCTGAATGATGATGC 59.737 52.381 0.00 0.00 0.00 3.91
6357 6945 3.954200 TCATATTTTCAGCAGCTGGACA 58.046 40.909 22.62 7.37 31.51 4.02
6403 6991 4.285292 GCCAGACAATTTCATGAATAGCG 58.715 43.478 9.40 1.29 0.00 4.26
6490 7078 4.201832 GCTTCAGAATCAGAGCATGTTCTG 60.202 45.833 28.17 28.17 44.74 3.02
6548 7137 1.906574 TGCCAGACTAGGTTAACCCAG 59.093 52.381 21.30 19.23 36.42 4.45
6646 7235 8.028354 TGGTGAGCTTGTTATAAATGTCAAATG 58.972 33.333 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.