Multiple sequence alignment - TraesCS3D01G406400

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 TraesCS3D01G406400 chr3D 100.000 2893 0 0 1 2893 520320244 520317352 0.000000e+00 5343.0
1 TraesCS3D01G406400 chr3D 78.185 1201 210 31 1217 2405 569900433 569901593 0.000000e+00 719.0
2 TraesCS3D01G406400 chr3D 93.333 105 7 0 474 578 320429139 320429035 3.860000e-34 156.0
3 TraesCS3D01G406400 chr3D 75.424 354 53 19 996 1324 520153061 520153405 1.080000e-29 141.0
4 TraesCS3D01G406400 chr3D 97.436 39 1 0 2855 2893 413671630 413671668 1.860000e-07 67.6
5 TraesCS3D01G406400 chr3B 89.577 1938 145 37 569 2491 684766920 684768815 0.000000e+00 2407.0
6 TraesCS3D01G406400 chr3B 89.340 197 10 2 2647 2832 684768994 684769190 1.340000e-58 237.0
7 TraesCS3D01G406400 chr3B 92.929 99 6 1 2531 2628 684768811 684768909 3.000000e-30 143.0
8 TraesCS3D01G406400 chr3B 90.385 52 2 3 2842 2893 675408297 675408249 6.690000e-07 65.8
9 TraesCS3D01G406400 chr3B 95.122 41 2 0 2853 2893 676889330 676889290 6.690000e-07 65.8
10 TraesCS3D01G406400 chr3A 88.988 1907 155 33 569 2460 655887050 655885184 0.000000e+00 2307.0
11 TraesCS3D01G406400 chr3A 88.239 1624 141 32 925 2538 655631641 655633224 0.000000e+00 1895.0
12 TraesCS3D01G406400 chr3A 77.575 1204 215 36 1217 2405 702553940 702555103 0.000000e+00 676.0
13 TraesCS3D01G406400 chr3A 76.112 1147 237 31 1286 2413 655629028 655630156 1.500000e-157 566.0
14 TraesCS3D01G406400 chr3A 90.419 334 30 2 142 475 655887380 655887049 3.420000e-119 438.0
15 TraesCS3D01G406400 chr3A 87.123 365 39 6 569 929 655631097 655631457 9.650000e-110 407.0
16 TraesCS3D01G406400 chr3A 91.064 235 20 1 241 475 655630863 655631096 1.670000e-82 316.0
17 TraesCS3D01G406400 chr3A 88.660 194 13 4 2648 2832 655633938 655634131 8.060000e-56 228.0
18 TraesCS3D01G406400 chr3A 72.672 655 130 26 1315 1963 655894626 655894015 3.830000e-39 172.0
19 TraesCS3D01G406400 chr3A 75.424 354 53 20 996 1324 655572422 655572766 1.080000e-29 141.0
20 TraesCS3D01G406400 chr3A 85.827 127 12 4 1 127 636539069 636538949 2.340000e-26 130.0
21 TraesCS3D01G406400 chr3A 87.500 112 11 3 975 1086 702556067 702556175 3.030000e-25 126.0
22 TraesCS3D01G406400 chr5A 78.356 1460 261 36 977 2413 401317672 401316245 0.000000e+00 894.0
23 TraesCS3D01G406400 chr5D 77.877 1460 260 34 977 2413 297736863 297738282 0.000000e+00 848.0
24 TraesCS3D01G406400 chr5D 91.818 110 9 0 466 575 134782102 134782211 1.390000e-33 154.0
25 TraesCS3D01G406400 chr5D 95.122 41 2 0 2853 2893 407664697 407664737 6.690000e-07 65.8
26 TraesCS3D01G406400 chrUn 77.134 1535 270 49 977 2473 250030312 250031803 0.000000e+00 815.0
27 TraesCS3D01G406400 chr5B 77.347 799 164 13 1621 2413 338481845 338482632 9.450000e-125 457.0
28 TraesCS3D01G406400 chr5B 80.460 609 86 20 977 1570 338481249 338481839 4.430000e-118 435.0
29 TraesCS3D01G406400 chr5B 91.667 108 9 0 473 580 474772888 474772781 1.800000e-32 150.0
30 TraesCS3D01G406400 chr1A 92.899 169 12 0 2020 2188 468083091 468083259 2.230000e-61 246.0
31 TraesCS3D01G406400 chr1A 91.919 99 7 1 2531 2628 468082989 468083087 1.400000e-28 137.0
32 TraesCS3D01G406400 chr1A 100.000 34 0 0 2458 2491 468082960 468082993 2.410000e-06 63.9
33 TraesCS3D01G406400 chr7A 95.146 103 5 0 469 571 61816023 61815921 2.310000e-36 163.0
34 TraesCS3D01G406400 chr2D 93.458 107 6 1 466 571 389095035 389094929 1.070000e-34 158.0
35 TraesCS3D01G406400 chr2B 93.396 106 7 0 473 578 63293188 63293083 1.070000e-34 158.0
36 TraesCS3D01G406400 chr2A 94.175 103 6 0 473 575 68155823 68155925 1.070000e-34 158.0
37 TraesCS3D01G406400 chr7D 89.167 120 11 2 452 570 190163237 190163119 6.460000e-32 148.0
38 TraesCS3D01G406400 chr4D 89.831 118 8 4 456 570 482704094 482704210 6.460000e-32 148.0
39 TraesCS3D01G406400 chr6A 95.122 41 2 0 2853 2893 400135570 400135530 6.690000e-07 65.8
40 TraesCS3D01G406400 chr4B 95.122 41 2 0 2853 2893 63102829 63102789 6.690000e-07 65.8
41 TraesCS3D01G406400 chr4B 94.737 38 2 0 2856 2893 554313273 554313236 3.110000e-05 60.2
42 TraesCS3D01G406400 chr1B 97.368 38 1 0 2853 2890 684270122 684270159 6.690000e-07 65.8
43 TraesCS3D01G406400 chr6D 94.737 38 2 0 2856 2893 412462235 412462272 3.110000e-05 60.2


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 TraesCS3D01G406400 chr3D 520317352 520320244 2892 True 5343.0 5343 100.000000 1 2893 1 chr3D.!!$R2 2892
1 TraesCS3D01G406400 chr3D 569900433 569901593 1160 False 719.0 719 78.185000 1217 2405 1 chr3D.!!$F3 1188
2 TraesCS3D01G406400 chr3B 684766920 684769190 2270 False 929.0 2407 90.615333 569 2832 3 chr3B.!!$F1 2263
3 TraesCS3D01G406400 chr3A 655885184 655887380 2196 True 1372.5 2307 89.703500 142 2460 2 chr3A.!!$R3 2318
4 TraesCS3D01G406400 chr3A 655629028 655634131 5103 False 682.4 1895 86.239600 241 2832 5 chr3A.!!$F2 2591
5 TraesCS3D01G406400 chr3A 702553940 702556175 2235 False 401.0 676 82.537500 975 2405 2 chr3A.!!$F3 1430
6 TraesCS3D01G406400 chr5A 401316245 401317672 1427 True 894.0 894 78.356000 977 2413 1 chr5A.!!$R1 1436
7 TraesCS3D01G406400 chr5D 297736863 297738282 1419 False 848.0 848 77.877000 977 2413 1 chr5D.!!$F2 1436
8 TraesCS3D01G406400 chrUn 250030312 250031803 1491 False 815.0 815 77.134000 977 2473 1 chrUn.!!$F1 1496
9 TraesCS3D01G406400 chr5B 338481249 338482632 1383 False 446.0 457 78.903500 977 2413 2 chr5B.!!$F1 1436

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
136 137 0.313043 CAGTGCAAGCAAACCCAGAG 59.687 55.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 4025 0.109597 CTTTGTCAATCACGCCCTGC 60.11 55.0 0.0 0.0 0.0 4.85 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
23 24 5.547465 CCCAAACAGTAGTGACAGATAACA 58.453 41.667 4.09 0.00 0.00 2.41
24 25 5.639506 CCCAAACAGTAGTGACAGATAACAG 59.360 44.000 4.09 0.00 0.00 3.16
26 27 7.099764 CCAAACAGTAGTGACAGATAACAGAT 58.900 38.462 4.09 0.00 0.00 2.90
28 29 8.438513 CAAACAGTAGTGACAGATAACAGATTG 58.561 37.037 4.09 0.00 0.00 2.67
29 30 7.468141 ACAGTAGTGACAGATAACAGATTGA 57.532 36.000 4.09 0.00 0.00 2.57
30 31 7.542890 ACAGTAGTGACAGATAACAGATTGAG 58.457 38.462 4.09 0.00 0.00 3.02
31 32 7.394641 ACAGTAGTGACAGATAACAGATTGAGA 59.605 37.037 4.09 0.00 0.00 3.27
32 33 8.246871 CAGTAGTGACAGATAACAGATTGAGAA 58.753 37.037 0.00 0.00 0.00 2.87
33 34 8.465999 AGTAGTGACAGATAACAGATTGAGAAG 58.534 37.037 0.00 0.00 0.00 2.85
34 35 6.105333 AGTGACAGATAACAGATTGAGAAGC 58.895 40.000 0.00 0.00 0.00 3.86
35 36 5.871524 GTGACAGATAACAGATTGAGAAGCA 59.128 40.000 0.00 0.00 0.00 3.91
36 37 5.871524 TGACAGATAACAGATTGAGAAGCAC 59.128 40.000 0.00 0.00 0.00 4.40
38 39 6.413052 ACAGATAACAGATTGAGAAGCACAT 58.587 36.000 0.00 0.00 0.00 3.21
39 40 6.883217 ACAGATAACAGATTGAGAAGCACATT 59.117 34.615 0.00 0.00 0.00 2.71
40 41 7.148289 ACAGATAACAGATTGAGAAGCACATTG 60.148 37.037 0.00 0.00 0.00 2.82
41 42 7.065443 CAGATAACAGATTGAGAAGCACATTGA 59.935 37.037 0.00 0.00 0.00 2.57
42 43 5.368256 AACAGATTGAGAAGCACATTGAC 57.632 39.130 0.00 0.00 0.00 3.18
43 44 3.755378 ACAGATTGAGAAGCACATTGACC 59.245 43.478 0.00 0.00 0.00 4.02
44 45 3.754850 CAGATTGAGAAGCACATTGACCA 59.245 43.478 0.00 0.00 0.00 4.02
45 46 4.398358 CAGATTGAGAAGCACATTGACCAT 59.602 41.667 0.00 0.00 0.00 3.55
46 47 5.587443 CAGATTGAGAAGCACATTGACCATA 59.413 40.000 0.00 0.00 0.00 2.74
47 48 6.262496 CAGATTGAGAAGCACATTGACCATAT 59.738 38.462 0.00 0.00 0.00 1.78
48 49 6.832384 AGATTGAGAAGCACATTGACCATATT 59.168 34.615 0.00 0.00 0.00 1.28
49 50 7.994911 AGATTGAGAAGCACATTGACCATATTA 59.005 33.333 0.00 0.00 0.00 0.98
51 52 8.523915 TTGAGAAGCACATTGACCATATTATT 57.476 30.769 0.00 0.00 0.00 1.40
52 53 7.933396 TGAGAAGCACATTGACCATATTATTG 58.067 34.615 0.00 0.00 0.00 1.90
53 54 6.742109 AGAAGCACATTGACCATATTATTGC 58.258 36.000 0.00 0.00 0.00 3.56
54 55 5.458041 AGCACATTGACCATATTATTGCC 57.542 39.130 0.00 0.00 0.00 4.52
55 56 4.281688 AGCACATTGACCATATTATTGCCC 59.718 41.667 0.00 0.00 0.00 5.36
56 57 4.561326 GCACATTGACCATATTATTGCCCC 60.561 45.833 0.00 0.00 0.00 5.80
57 58 4.021192 CACATTGACCATATTATTGCCCCC 60.021 45.833 0.00 0.00 0.00 5.40
58 59 3.981516 TTGACCATATTATTGCCCCCA 57.018 42.857 0.00 0.00 0.00 4.96
59 60 3.981516 TGACCATATTATTGCCCCCAA 57.018 42.857 0.00 0.00 35.01 4.12
60 61 4.484026 TGACCATATTATTGCCCCCAAT 57.516 40.909 0.00 0.00 43.74 3.16
61 62 5.607168 TGACCATATTATTGCCCCCAATA 57.393 39.130 0.00 0.00 41.68 1.90
69 70 2.043046 GCCCCCAATAAGCAGCCA 60.043 61.111 0.00 0.00 0.00 4.75
70 71 1.685421 GCCCCCAATAAGCAGCCAA 60.685 57.895 0.00 0.00 0.00 4.52
71 72 1.264045 GCCCCCAATAAGCAGCCAAA 61.264 55.000 0.00 0.00 0.00 3.28
74 75 1.622811 CCCCAATAAGCAGCCAAAACA 59.377 47.619 0.00 0.00 0.00 2.83
75 76 2.354003 CCCCAATAAGCAGCCAAAACAG 60.354 50.000 0.00 0.00 0.00 3.16
77 78 3.578688 CCAATAAGCAGCCAAAACAGTC 58.421 45.455 0.00 0.00 0.00 3.51
78 79 3.005684 CCAATAAGCAGCCAAAACAGTCA 59.994 43.478 0.00 0.00 0.00 3.41
79 80 4.322198 CCAATAAGCAGCCAAAACAGTCAT 60.322 41.667 0.00 0.00 0.00 3.06
80 81 4.708726 ATAAGCAGCCAAAACAGTCATC 57.291 40.909 0.00 0.00 0.00 2.92
82 83 0.961019 GCAGCCAAAACAGTCATCCA 59.039 50.000 0.00 0.00 0.00 3.41
85 86 1.547372 AGCCAAAACAGTCATCCATGC 59.453 47.619 0.00 0.00 0.00 4.06
86 87 1.547372 GCCAAAACAGTCATCCATGCT 59.453 47.619 0.00 0.00 0.00 3.79
87 88 2.028748 GCCAAAACAGTCATCCATGCTT 60.029 45.455 0.00 0.00 0.00 3.91
88 89 3.581755 CCAAAACAGTCATCCATGCTTG 58.418 45.455 0.00 0.00 0.00 4.01
89 90 3.256383 CCAAAACAGTCATCCATGCTTGA 59.744 43.478 0.22 0.00 0.00 3.02
90 91 4.482386 CAAAACAGTCATCCATGCTTGAG 58.518 43.478 0.22 0.00 0.00 3.02
91 92 1.747709 ACAGTCATCCATGCTTGAGC 58.252 50.000 0.22 0.00 42.50 4.26
122 123 4.639135 AGAAAAGTTGAACTTCCAGTGC 57.361 40.909 11.44 0.00 37.47 4.40
123 124 4.016444 AGAAAAGTTGAACTTCCAGTGCA 58.984 39.130 11.44 0.00 37.47 4.57
124 125 4.462483 AGAAAAGTTGAACTTCCAGTGCAA 59.538 37.500 11.44 0.00 41.32 4.08
125 126 4.376340 AAAGTTGAACTTCCAGTGCAAG 57.624 40.909 11.44 0.00 44.04 4.01
126 127 1.678101 AGTTGAACTTCCAGTGCAAGC 59.322 47.619 0.00 0.00 44.04 4.01
128 129 1.761449 TGAACTTCCAGTGCAAGCAA 58.239 45.000 0.00 0.00 28.77 3.91
129 130 2.098614 TGAACTTCCAGTGCAAGCAAA 58.901 42.857 0.00 0.00 28.77 3.68
131 132 0.746659 ACTTCCAGTGCAAGCAAACC 59.253 50.000 0.00 0.00 0.00 3.27
133 134 0.685785 TTCCAGTGCAAGCAAACCCA 60.686 50.000 0.00 0.00 0.00 4.51
134 135 1.108727 TCCAGTGCAAGCAAACCCAG 61.109 55.000 0.00 0.00 0.00 4.45
135 136 1.108727 CCAGTGCAAGCAAACCCAGA 61.109 55.000 0.00 0.00 0.00 3.86
136 137 0.313043 CAGTGCAAGCAAACCCAGAG 59.687 55.000 0.00 0.00 0.00 3.35
137 138 1.006922 GTGCAAGCAAACCCAGAGC 60.007 57.895 0.00 0.00 0.00 4.09
139 140 2.935740 GCAAGCAAACCCAGAGCCC 61.936 63.158 0.00 0.00 0.00 5.19
140 141 1.531365 CAAGCAAACCCAGAGCCCA 60.531 57.895 0.00 0.00 0.00 5.36
163 164 2.969821 AATACAACCCAAGCAGGTGA 57.030 45.000 0.00 0.00 40.05 4.02
196 197 4.021894 AGAGAAGCGTTGAGTGTCAAGTAT 60.022 41.667 0.00 0.00 37.00 2.12
230 231 7.519649 GCATTGTCTACCTAATCTGATTTCTGC 60.520 40.741 8.38 0.90 0.00 4.26
231 232 6.544928 TGTCTACCTAATCTGATTTCTGCA 57.455 37.500 8.38 0.00 0.00 4.41
242 243 6.053632 TCTGATTTCTGCAGATTCAAGGTA 57.946 37.500 19.04 7.06 37.46 3.08
243 244 6.656902 TCTGATTTCTGCAGATTCAAGGTAT 58.343 36.000 19.04 1.47 37.46 2.73
244 245 6.541278 TCTGATTTCTGCAGATTCAAGGTATG 59.459 38.462 19.04 10.50 37.46 2.39
275 1871 3.558674 GCTCCAAGCAAAGCCTCTA 57.441 52.632 0.00 0.00 41.89 2.43
284 1880 3.615155 AGCAAAGCCTCTATCTCCAAAC 58.385 45.455 0.00 0.00 0.00 2.93
352 1948 4.391830 TCGAAACAATATGCTCACAACTCC 59.608 41.667 0.00 0.00 0.00 3.85
358 1954 1.523758 ATGCTCACAACTCCGGTTTC 58.476 50.000 0.00 0.00 32.73 2.78
371 1967 4.720273 ACTCCGGTTTCCAGGTATATTCTT 59.280 41.667 0.00 0.00 0.00 2.52
374 1970 5.883673 TCCGGTTTCCAGGTATATTCTTTTG 59.116 40.000 0.00 0.00 0.00 2.44
393 1989 7.442656 TCTTTTGTTCTCTTGACTAAGTAGGG 58.557 38.462 0.00 0.00 35.38 3.53
404 2000 4.282703 TGACTAAGTAGGGGTGAAACAGTC 59.717 45.833 0.00 0.00 39.98 3.51
442 2038 7.231925 TCCAGTGCATTAATTCATTCATATGCT 59.768 33.333 0.00 0.00 39.19 3.79
448 2044 8.086522 GCATTAATTCATTCATATGCTTGGTCT 58.913 33.333 0.00 0.00 36.39 3.85
449 2045 9.976511 CATTAATTCATTCATATGCTTGGTCTT 57.023 29.630 0.00 0.00 0.00 3.01
455 2051 8.070034 TCATTCATATGCTTGGTCTTCAATTT 57.930 30.769 0.00 0.00 34.45 1.82
477 2073 5.818136 TTTTGGCTGCTTGATGTATACTC 57.182 39.130 4.17 0.36 0.00 2.59
478 2074 3.475566 TGGCTGCTTGATGTATACTCC 57.524 47.619 4.17 0.00 0.00 3.85
479 2075 2.104792 TGGCTGCTTGATGTATACTCCC 59.895 50.000 4.17 0.00 0.00 4.30
480 2076 2.370189 GGCTGCTTGATGTATACTCCCT 59.630 50.000 4.17 0.00 0.00 4.20
481 2077 3.578716 GGCTGCTTGATGTATACTCCCTA 59.421 47.826 4.17 0.00 0.00 3.53
482 2078 4.040461 GGCTGCTTGATGTATACTCCCTAA 59.960 45.833 4.17 0.00 0.00 2.69
483 2079 5.233988 GCTGCTTGATGTATACTCCCTAAG 58.766 45.833 4.17 3.62 0.00 2.18
484 2080 5.221541 GCTGCTTGATGTATACTCCCTAAGT 60.222 44.000 4.17 0.00 42.33 2.24
485 2081 6.406692 TGCTTGATGTATACTCCCTAAGTC 57.593 41.667 4.17 1.00 39.55 3.01
486 2082 5.304614 TGCTTGATGTATACTCCCTAAGTCC 59.695 44.000 4.17 0.00 39.55 3.85
487 2083 5.279556 GCTTGATGTATACTCCCTAAGTCCC 60.280 48.000 4.17 0.00 39.55 4.46
488 2084 5.412617 TGATGTATACTCCCTAAGTCCCA 57.587 43.478 4.17 0.00 39.55 4.37
489 2085 5.784023 TGATGTATACTCCCTAAGTCCCAA 58.216 41.667 4.17 0.00 39.55 4.12
490 2086 6.206787 TGATGTATACTCCCTAAGTCCCAAA 58.793 40.000 4.17 0.00 39.55 3.28
491 2087 6.674861 TGATGTATACTCCCTAAGTCCCAAAA 59.325 38.462 4.17 0.00 39.55 2.44
492 2088 7.349859 TGATGTATACTCCCTAAGTCCCAAAAT 59.650 37.037 4.17 0.00 39.55 1.82
493 2089 8.808240 ATGTATACTCCCTAAGTCCCAAAATA 57.192 34.615 4.17 0.00 39.55 1.40
494 2090 8.626917 TGTATACTCCCTAAGTCCCAAAATAA 57.373 34.615 4.17 0.00 39.55 1.40
495 2091 8.711170 TGTATACTCCCTAAGTCCCAAAATAAG 58.289 37.037 4.17 0.00 39.55 1.73
496 2092 7.766736 ATACTCCCTAAGTCCCAAAATAAGT 57.233 36.000 0.00 0.00 39.55 2.24
497 2093 5.816682 ACTCCCTAAGTCCCAAAATAAGTG 58.183 41.667 0.00 0.00 30.02 3.16
498 2094 5.312443 ACTCCCTAAGTCCCAAAATAAGTGT 59.688 40.000 0.00 0.00 30.02 3.55
499 2095 5.812286 TCCCTAAGTCCCAAAATAAGTGTC 58.188 41.667 0.00 0.00 0.00 3.67
500 2096 5.550403 TCCCTAAGTCCCAAAATAAGTGTCT 59.450 40.000 0.00 0.00 0.00 3.41
501 2097 5.880887 CCCTAAGTCCCAAAATAAGTGTCTC 59.119 44.000 0.00 0.00 0.00 3.36
502 2098 6.472887 CCTAAGTCCCAAAATAAGTGTCTCA 58.527 40.000 0.00 0.00 0.00 3.27
503 2099 6.940298 CCTAAGTCCCAAAATAAGTGTCTCAA 59.060 38.462 0.00 0.00 0.00 3.02
504 2100 6.635030 AAGTCCCAAAATAAGTGTCTCAAC 57.365 37.500 0.00 0.00 0.00 3.18
505 2101 5.070685 AGTCCCAAAATAAGTGTCTCAACC 58.929 41.667 0.00 0.00 0.00 3.77
506 2102 4.825085 GTCCCAAAATAAGTGTCTCAACCA 59.175 41.667 0.00 0.00 0.00 3.67
507 2103 5.476945 GTCCCAAAATAAGTGTCTCAACCAT 59.523 40.000 0.00 0.00 0.00 3.55
508 2104 6.657541 GTCCCAAAATAAGTGTCTCAACCATA 59.342 38.462 0.00 0.00 0.00 2.74
509 2105 6.884295 TCCCAAAATAAGTGTCTCAACCATAG 59.116 38.462 0.00 0.00 0.00 2.23
510 2106 6.659242 CCCAAAATAAGTGTCTCAACCATAGT 59.341 38.462 0.00 0.00 0.00 2.12
511 2107 7.827236 CCCAAAATAAGTGTCTCAACCATAGTA 59.173 37.037 0.00 0.00 0.00 1.82
512 2108 8.665685 CCAAAATAAGTGTCTCAACCATAGTAC 58.334 37.037 0.00 0.00 0.00 2.73
513 2109 9.214957 CAAAATAAGTGTCTCAACCATAGTACA 57.785 33.333 0.00 0.00 0.00 2.90
514 2110 9.787435 AAAATAAGTGTCTCAACCATAGTACAA 57.213 29.630 0.00 0.00 0.00 2.41
515 2111 8.773404 AATAAGTGTCTCAACCATAGTACAAC 57.227 34.615 0.00 0.00 0.00 3.32
516 2112 6.420913 AAGTGTCTCAACCATAGTACAACT 57.579 37.500 0.00 0.00 0.00 3.16
517 2113 6.420913 AGTGTCTCAACCATAGTACAACTT 57.579 37.500 0.00 0.00 0.00 2.66
518 2114 6.827727 AGTGTCTCAACCATAGTACAACTTT 58.172 36.000 0.00 0.00 0.00 2.66
519 2115 6.706270 AGTGTCTCAACCATAGTACAACTTTG 59.294 38.462 0.00 0.00 0.00 2.77
520 2116 6.482308 GTGTCTCAACCATAGTACAACTTTGT 59.518 38.462 0.00 0.00 44.86 2.83
521 2117 7.654520 GTGTCTCAACCATAGTACAACTTTGTA 59.345 37.037 0.00 0.00 42.35 2.41
556 2152 9.965824 AGTACAAAATTGAGACACTTATTTTGG 57.034 29.630 21.75 9.08 45.43 3.28
557 2153 9.191995 GTACAAAATTGAGACACTTATTTTGGG 57.808 33.333 21.75 10.11 45.43 4.12
558 2154 8.017418 ACAAAATTGAGACACTTATTTTGGGA 57.983 30.769 21.75 0.00 45.43 4.37
559 2155 7.926018 ACAAAATTGAGACACTTATTTTGGGAC 59.074 33.333 21.75 0.00 45.43 4.46
560 2156 5.880054 ATTGAGACACTTATTTTGGGACG 57.120 39.130 0.00 0.00 0.00 4.79
561 2157 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
562 2158 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
563 2159 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
564 2160 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
565 2161 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
566 2162 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
567 2163 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
583 2179 5.565045 CGGAGGGAGTATGTATTAGTTCTGC 60.565 48.000 0.00 0.00 0.00 4.26
615 2211 3.820467 TGAACAATCGCAATTCCAGAAGT 59.180 39.130 0.00 0.00 0.00 3.01
623 2219 6.422776 TCGCAATTCCAGAAGTTATTTCTC 57.577 37.500 0.00 0.00 44.34 2.87
628 2224 8.131731 GCAATTCCAGAAGTTATTTCTCCATAC 58.868 37.037 0.00 0.00 44.34 2.39
636 2232 7.491696 AGAAGTTATTTCTCCATACGCACTAAC 59.508 37.037 0.00 0.00 42.54 2.34
637 2233 5.747197 AGTTATTTCTCCATACGCACTAACG 59.253 40.000 0.00 0.00 39.50 3.18
644 2240 3.432933 TCCATACGCACTAACGAAAAACC 59.567 43.478 0.00 0.00 36.70 3.27
650 2246 3.486209 CGCACTAACGAAAAACCAAGTGT 60.486 43.478 0.00 0.00 37.31 3.55
651 2247 3.789224 GCACTAACGAAAAACCAAGTGTG 59.211 43.478 0.00 0.00 37.31 3.82
656 2252 2.159435 ACGAAAAACCAAGTGTGCAGTC 60.159 45.455 0.00 0.00 0.00 3.51
659 2255 1.724582 AAACCAAGTGTGCAGTCGGC 61.725 55.000 0.00 0.00 45.13 5.54
673 2269 3.766151 CAGTCGGCGTAAATAGAGAACA 58.234 45.455 6.85 0.00 0.00 3.18
677 2273 5.124457 AGTCGGCGTAAATAGAGAACACTAA 59.876 40.000 6.85 0.00 0.00 2.24
746 2352 9.075678 AGAATGTCTATTTCATTGGATTCCATC 57.924 33.333 6.15 0.00 35.94 3.51
749 2355 8.229253 TGTCTATTTCATTGGATTCCATCTTG 57.771 34.615 6.15 5.46 31.53 3.02
767 2373 8.112822 TCCATCTTGGACAATTTAACCAGATAA 58.887 33.333 0.00 0.00 42.67 1.75
819 2427 0.459934 CTCTGCTAGTGACAGGCTGC 60.460 60.000 15.89 8.22 35.78 5.25
850 2460 3.438216 TGCTGATCAGAATTTGACCCA 57.562 42.857 27.04 8.27 38.99 4.51
851 2461 3.765381 TGCTGATCAGAATTTGACCCAA 58.235 40.909 27.04 0.00 38.99 4.12
852 2462 3.760151 TGCTGATCAGAATTTGACCCAAG 59.240 43.478 27.04 0.00 38.99 3.61
856 2466 4.158949 TGATCAGAATTTGACCCAAGCATG 59.841 41.667 0.00 0.00 38.99 4.06
870 2480 3.186909 CAAGCATGCATGTCTTTCCATG 58.813 45.455 26.79 14.49 44.07 3.66
872 2482 3.093814 AGCATGCATGTCTTTCCATGAA 58.906 40.909 26.79 0.00 43.99 2.57
874 2484 3.431856 CATGCATGTCTTTCCATGAACG 58.568 45.455 18.91 0.00 43.99 3.95
887 2497 6.820470 TTCCATGAACGTTTTAAGCTTTTG 57.180 33.333 3.20 0.00 0.00 2.44
901 2511 8.432110 TTTAAGCTTTTGAAAATCCAACCTTC 57.568 30.769 3.20 0.00 0.00 3.46
909 2519 4.584325 TGAAAATCCAACCTTCCAACTCAG 59.416 41.667 0.00 0.00 0.00 3.35
919 2529 1.886886 TCCAACTCAGGCGGTTTAAC 58.113 50.000 0.00 0.00 0.00 2.01
939 2737 3.233507 ACTGTTGATTGAACCCATTGCT 58.766 40.909 0.00 0.00 33.07 3.91
942 2740 5.304101 ACTGTTGATTGAACCCATTGCTTTA 59.696 36.000 0.00 0.00 33.07 1.85
944 2742 5.304101 TGTTGATTGAACCCATTGCTTTACT 59.696 36.000 0.00 0.00 33.07 2.24
983 2782 7.430441 CAGATTAAGGACTCTACCTAGCTTTC 58.570 42.308 0.00 0.00 39.62 2.62
989 2788 4.024670 GACTCTACCTAGCTTTCCTCCAA 58.975 47.826 0.00 0.00 0.00 3.53
990 2789 4.027437 ACTCTACCTAGCTTTCCTCCAAG 58.973 47.826 0.00 0.00 0.00 3.61
1010 2809 3.010413 GCAAAGCCATGGCCTCCAC 62.010 63.158 33.14 15.38 43.17 4.02
1062 2863 2.098117 GGAAACAAGCTATGCTCGCAAT 59.902 45.455 0.00 0.00 38.25 3.56
1086 2887 2.364647 CGGTATTCAGGTACCTTCTCCC 59.635 54.545 13.15 7.94 41.61 4.30
1122 2936 9.851686 AATTCATCAATCTATGCTAACCTGTTA 57.148 29.630 0.00 0.00 0.00 2.41
1125 2939 9.494271 TCATCAATCTATGCTAACCTGTTATTC 57.506 33.333 0.00 0.00 0.00 1.75
1147 2962 6.020971 TCGACACTTGCTTTCTCAATACTA 57.979 37.500 0.00 0.00 0.00 1.82
1149 2964 6.531594 TCGACACTTGCTTTCTCAATACTATG 59.468 38.462 0.00 0.00 0.00 2.23
1197 3019 3.442977 GCCTTTCATTGCTGAGACTGAAT 59.557 43.478 0.00 0.00 31.68 2.57
1210 3032 7.712639 TGCTGAGACTGAATAGAATTATTGGTC 59.287 37.037 0.00 0.00 33.47 4.02
1211 3033 7.172361 GCTGAGACTGAATAGAATTATTGGTCC 59.828 40.741 0.00 0.00 33.60 4.46
1212 3034 8.324191 TGAGACTGAATAGAATTATTGGTCCT 57.676 34.615 0.00 0.00 33.60 3.85
1213 3035 8.206867 TGAGACTGAATAGAATTATTGGTCCTG 58.793 37.037 0.00 0.00 33.60 3.86
1214 3036 6.995091 AGACTGAATAGAATTATTGGTCCTGC 59.005 38.462 0.00 0.00 33.60 4.85
1215 3037 6.904626 ACTGAATAGAATTATTGGTCCTGCT 58.095 36.000 0.00 0.00 29.67 4.24
1334 3167 1.146637 CTGATAGAAGCAGCCATCGC 58.853 55.000 0.00 0.00 0.00 4.58
1503 3336 0.317160 CGGAAGTGTGTGTGCTCCTA 59.683 55.000 0.00 0.00 0.00 2.94
1598 3476 1.073125 TGTTGTGACGGTTGGGATCAT 59.927 47.619 0.00 0.00 0.00 2.45
1658 3536 2.163010 CCATGCATCTTTTCTGCTCGTT 59.837 45.455 0.00 0.00 40.34 3.85
1659 3537 2.975410 TGCATCTTTTCTGCTCGTTG 57.025 45.000 0.00 0.00 40.34 4.10
1730 3609 6.487689 GGATCGATCCATTTCCATTAAGTC 57.512 41.667 34.65 5.58 46.38 3.01
1735 3614 5.466728 CGATCCATTTCCATTAAGTCGTCAT 59.533 40.000 0.00 0.00 0.00 3.06
1783 3665 3.131223 CAGGCTCCTGAAGATCTAACGAA 59.869 47.826 10.33 0.00 46.30 3.85
1839 3721 0.323629 TAGGCGTGAAAGGTTCCCTG 59.676 55.000 0.00 0.00 32.13 4.45
1844 3726 1.749286 CGTGAAAGGTTCCCTGTGGTT 60.749 52.381 0.00 0.00 32.13 3.67
1888 3778 9.617523 ACAATTCAGGAAAGATTTCACATTTTT 57.382 25.926 7.56 0.00 38.92 1.94
1926 3816 1.079658 AGAACTAGTTCCAGGAGGCCT 59.920 52.381 28.05 3.86 40.33 5.19
1938 3828 0.389025 GGAGGCCTGTTGGTTGTTTG 59.611 55.000 12.00 0.00 35.27 2.93
1981 3871 1.393883 GACCGTGCTTCGAAATTCTCC 59.606 52.381 0.00 0.00 42.86 3.71
2012 3902 6.038050 GTGGGAAATCTTTGCTCAGATTCTAG 59.962 42.308 10.33 0.00 41.78 2.43
2118 4025 1.431488 CGGTCTCGTGCCATGATTGG 61.431 60.000 0.00 0.00 46.66 3.16
2139 4046 0.537143 AGGGCGTGATTGACAAAGCA 60.537 50.000 0.00 0.00 36.57 3.91
2163 4070 2.961526 ATGATTCGTTCTACGTGCCT 57.038 45.000 0.00 0.00 43.14 4.75
2177 4084 1.740380 CGTGCCTGTCTATGGACCTTG 60.740 57.143 6.77 0.00 41.47 3.61
2181 4088 2.678190 GCCTGTCTATGGACCTTGTGAC 60.678 54.545 6.77 1.23 41.47 3.67
2342 4249 3.042887 CGATAGTCGTGCATCATTTCGA 58.957 45.455 0.00 0.00 34.72 3.71
2500 4428 2.189784 TCGCTCGTCGAGGGAGAT 59.810 61.111 31.27 0.00 44.59 2.75
2528 4457 3.084039 TGATGAGACTGAAACATTGCCC 58.916 45.455 0.00 0.00 0.00 5.36
2564 4493 5.240121 GGGAAAATGCATGTCAAATTCACT 58.760 37.500 0.00 0.00 0.00 3.41
2598 5013 3.057315 CACATCCCTTTTGTGTCATGTCC 60.057 47.826 0.00 0.00 39.66 4.02
2614 5029 6.878923 TGTCATGTCCGTTTTCAATAAGATCT 59.121 34.615 0.00 0.00 0.00 2.75
2617 5032 5.000591 TGTCCGTTTTCAATAAGATCTGCA 58.999 37.500 0.00 0.00 0.00 4.41
2741 5290 4.080695 TCACATCTTCTCCTTGCTGCTATT 60.081 41.667 0.00 0.00 0.00 1.73
2742 5291 4.639310 CACATCTTCTCCTTGCTGCTATTT 59.361 41.667 0.00 0.00 0.00 1.40
2814 5437 2.911280 GCGCGTACGTGCTCATAC 59.089 61.111 38.55 15.20 46.85 2.39
2832 5455 0.909610 ACGGCAATGAGGAGGAGGAA 60.910 55.000 0.00 0.00 0.00 3.36
2836 5459 2.291217 GGCAATGAGGAGGAGGAAAAGT 60.291 50.000 0.00 0.00 0.00 2.66
2837 5460 3.013219 GCAATGAGGAGGAGGAAAAGTC 58.987 50.000 0.00 0.00 0.00 3.01
2838 5461 3.265791 CAATGAGGAGGAGGAAAAGTCG 58.734 50.000 0.00 0.00 0.00 4.18
2839 5462 1.267121 TGAGGAGGAGGAAAAGTCGG 58.733 55.000 0.00 0.00 0.00 4.79
2842 5465 2.038689 GAGGAGGAGGAAAAGTCGGTTT 59.961 50.000 0.00 0.00 0.00 3.27
2864 5487 3.451141 TTTGTGTGTGGAAATGAAGGC 57.549 42.857 0.00 0.00 0.00 4.35
2865 5488 0.950836 TGTGTGTGGAAATGAAGGCG 59.049 50.000 0.00 0.00 0.00 5.52
2867 5490 2.147958 GTGTGTGGAAATGAAGGCGTA 58.852 47.619 0.00 0.00 0.00 4.42
2868 5491 2.095919 GTGTGTGGAAATGAAGGCGTAC 60.096 50.000 0.00 0.00 0.00 3.67
2869 5492 1.467342 GTGTGGAAATGAAGGCGTACC 59.533 52.381 0.00 0.00 0.00 3.34
2870 5493 1.092348 GTGGAAATGAAGGCGTACCC 58.908 55.000 0.00 0.00 36.11 3.69
2871 5494 0.034863 TGGAAATGAAGGCGTACCCC 60.035 55.000 0.00 0.00 36.11 4.95
2872 5495 1.093496 GGAAATGAAGGCGTACCCCG 61.093 60.000 0.00 0.00 36.11 5.73
2873 5496 1.078001 AAATGAAGGCGTACCCCGG 60.078 57.895 0.00 0.00 36.11 5.73
2883 5506 3.161450 TACCCCGGCCTCTGCATC 61.161 66.667 0.00 0.00 40.13 3.91
2884 5507 3.993865 TACCCCGGCCTCTGCATCA 62.994 63.158 0.00 0.00 40.13 3.07
2886 5509 2.519622 CCCCGGCCTCTGCATCATA 61.520 63.158 0.00 0.00 40.13 2.15
2887 5510 1.451504 CCCGGCCTCTGCATCATAA 59.548 57.895 0.00 0.00 40.13 1.90
2888 5511 0.037303 CCCGGCCTCTGCATCATAAT 59.963 55.000 0.00 0.00 40.13 1.28
2889 5512 1.162698 CCGGCCTCTGCATCATAATG 58.837 55.000 0.00 0.00 40.13 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.455647 TCTGTTATCTGTCACTACTGTTTGG 58.544 40.000 0.00 0.00 0.00 3.28
5 6 7.394641 TCTCAATCTGTTATCTGTCACTACTGT 59.605 37.037 0.00 0.00 0.00 3.55
6 7 7.766283 TCTCAATCTGTTATCTGTCACTACTG 58.234 38.462 0.00 0.00 0.00 2.74
7 8 7.946381 TCTCAATCTGTTATCTGTCACTACT 57.054 36.000 0.00 0.00 0.00 2.57
8 9 7.221838 GCTTCTCAATCTGTTATCTGTCACTAC 59.778 40.741 0.00 0.00 0.00 2.73
9 10 7.093771 TGCTTCTCAATCTGTTATCTGTCACTA 60.094 37.037 0.00 0.00 0.00 2.74
12 13 5.871524 GTGCTTCTCAATCTGTTATCTGTCA 59.128 40.000 0.00 0.00 0.00 3.58
13 14 5.871524 TGTGCTTCTCAATCTGTTATCTGTC 59.128 40.000 0.00 0.00 0.00 3.51
14 15 5.798132 TGTGCTTCTCAATCTGTTATCTGT 58.202 37.500 0.00 0.00 0.00 3.41
15 16 6.922247 ATGTGCTTCTCAATCTGTTATCTG 57.078 37.500 0.00 0.00 0.00 2.90
17 18 7.185453 GTCAATGTGCTTCTCAATCTGTTATC 58.815 38.462 0.00 0.00 0.00 1.75
19 20 5.412594 GGTCAATGTGCTTCTCAATCTGTTA 59.587 40.000 0.00 0.00 0.00 2.41
20 21 4.217118 GGTCAATGTGCTTCTCAATCTGTT 59.783 41.667 0.00 0.00 0.00 3.16
22 23 3.754850 TGGTCAATGTGCTTCTCAATCTG 59.245 43.478 0.00 0.00 0.00 2.90
23 24 4.025040 TGGTCAATGTGCTTCTCAATCT 57.975 40.909 0.00 0.00 0.00 2.40
24 25 4.978083 ATGGTCAATGTGCTTCTCAATC 57.022 40.909 0.00 0.00 0.00 2.67
26 27 8.407832 CAATAATATGGTCAATGTGCTTCTCAA 58.592 33.333 0.00 0.00 0.00 3.02
28 29 6.860023 GCAATAATATGGTCAATGTGCTTCTC 59.140 38.462 0.00 0.00 0.00 2.87
29 30 6.239120 GGCAATAATATGGTCAATGTGCTTCT 60.239 38.462 0.00 0.00 0.00 2.85
30 31 5.922544 GGCAATAATATGGTCAATGTGCTTC 59.077 40.000 0.00 0.00 0.00 3.86
31 32 5.221501 GGGCAATAATATGGTCAATGTGCTT 60.222 40.000 0.00 0.00 0.00 3.91
32 33 4.281688 GGGCAATAATATGGTCAATGTGCT 59.718 41.667 0.00 0.00 0.00 4.40
33 34 4.559153 GGGCAATAATATGGTCAATGTGC 58.441 43.478 0.00 0.00 0.00 4.57
34 35 4.021192 GGGGGCAATAATATGGTCAATGTG 60.021 45.833 0.00 0.00 0.00 3.21
35 36 4.159557 GGGGGCAATAATATGGTCAATGT 58.840 43.478 0.00 0.00 0.00 2.71
36 37 4.158786 TGGGGGCAATAATATGGTCAATG 58.841 43.478 0.00 0.00 0.00 2.82
38 39 3.981516 TGGGGGCAATAATATGGTCAA 57.018 42.857 0.00 0.00 0.00 3.18
39 40 3.981516 TTGGGGGCAATAATATGGTCA 57.018 42.857 0.00 0.00 0.00 4.02
40 41 5.105351 GCTTATTGGGGGCAATAATATGGTC 60.105 44.000 0.00 0.00 36.70 4.02
41 42 4.777366 GCTTATTGGGGGCAATAATATGGT 59.223 41.667 0.00 0.00 36.70 3.55
42 43 4.776837 TGCTTATTGGGGGCAATAATATGG 59.223 41.667 0.00 0.00 36.70 2.74
43 44 5.625197 GCTGCTTATTGGGGGCAATAATATG 60.625 44.000 0.00 0.00 36.70 1.78
44 45 4.467438 GCTGCTTATTGGGGGCAATAATAT 59.533 41.667 0.00 0.00 36.70 1.28
45 46 3.831911 GCTGCTTATTGGGGGCAATAATA 59.168 43.478 0.00 0.00 36.70 0.98
46 47 2.634453 GCTGCTTATTGGGGGCAATAAT 59.366 45.455 0.00 0.00 36.70 1.28
47 48 2.038659 GCTGCTTATTGGGGGCAATAA 58.961 47.619 0.00 0.00 36.14 1.40
48 49 1.703411 GCTGCTTATTGGGGGCAATA 58.297 50.000 0.00 0.00 35.49 1.90
49 50 1.050421 GGCTGCTTATTGGGGGCAAT 61.050 55.000 0.00 0.00 35.49 3.56
51 52 2.043046 GGCTGCTTATTGGGGGCA 60.043 61.111 0.00 0.00 34.66 5.36
52 53 1.264045 TTTGGCTGCTTATTGGGGGC 61.264 55.000 0.00 0.00 0.00 5.80
53 54 1.066215 GTTTTGGCTGCTTATTGGGGG 60.066 52.381 0.00 0.00 0.00 5.40
54 55 1.622811 TGTTTTGGCTGCTTATTGGGG 59.377 47.619 0.00 0.00 0.00 4.96
55 56 2.299867 ACTGTTTTGGCTGCTTATTGGG 59.700 45.455 0.00 0.00 0.00 4.12
56 57 3.005684 TGACTGTTTTGGCTGCTTATTGG 59.994 43.478 0.00 0.00 0.00 3.16
57 58 4.241590 TGACTGTTTTGGCTGCTTATTG 57.758 40.909 0.00 0.00 0.00 1.90
58 59 4.082026 GGATGACTGTTTTGGCTGCTTATT 60.082 41.667 0.00 0.00 0.00 1.40
59 60 3.445096 GGATGACTGTTTTGGCTGCTTAT 59.555 43.478 0.00 0.00 0.00 1.73
60 61 2.819608 GGATGACTGTTTTGGCTGCTTA 59.180 45.455 0.00 0.00 0.00 3.09
61 62 1.615392 GGATGACTGTTTTGGCTGCTT 59.385 47.619 0.00 0.00 0.00 3.91
62 63 1.251251 GGATGACTGTTTTGGCTGCT 58.749 50.000 0.00 0.00 0.00 4.24
63 64 0.961019 TGGATGACTGTTTTGGCTGC 59.039 50.000 0.00 0.00 0.00 5.25
64 65 2.673043 GCATGGATGACTGTTTTGGCTG 60.673 50.000 0.00 0.00 0.00 4.85
65 66 1.547372 GCATGGATGACTGTTTTGGCT 59.453 47.619 0.00 0.00 0.00 4.75
66 67 1.547372 AGCATGGATGACTGTTTTGGC 59.453 47.619 0.00 0.00 0.00 4.52
69 70 3.057033 GCTCAAGCATGGATGACTGTTTT 60.057 43.478 0.00 0.00 41.59 2.43
70 71 2.490903 GCTCAAGCATGGATGACTGTTT 59.509 45.455 0.00 0.00 41.59 2.83
71 72 2.089980 GCTCAAGCATGGATGACTGTT 58.910 47.619 0.00 0.00 41.59 3.16
115 116 1.076412 TGGGTTTGCTTGCACTGGA 60.076 52.632 0.00 0.00 0.00 3.86
117 118 0.313043 CTCTGGGTTTGCTTGCACTG 59.687 55.000 0.00 0.00 0.00 3.66
118 119 1.458639 GCTCTGGGTTTGCTTGCACT 61.459 55.000 0.00 0.00 0.00 4.40
119 120 1.006922 GCTCTGGGTTTGCTTGCAC 60.007 57.895 0.00 0.00 0.00 4.57
120 121 2.202395 GGCTCTGGGTTTGCTTGCA 61.202 57.895 0.00 0.00 0.00 4.08
122 123 1.530013 CTGGGCTCTGGGTTTGCTTG 61.530 60.000 0.00 0.00 0.00 4.01
123 124 1.228675 CTGGGCTCTGGGTTTGCTT 60.229 57.895 0.00 0.00 0.00 3.91
124 125 1.719063 TTCTGGGCTCTGGGTTTGCT 61.719 55.000 0.00 0.00 0.00 3.91
125 126 0.827507 TTTCTGGGCTCTGGGTTTGC 60.828 55.000 0.00 0.00 0.00 3.68
126 127 1.703411 TTTTCTGGGCTCTGGGTTTG 58.297 50.000 0.00 0.00 0.00 2.93
128 129 2.378547 TGTATTTTCTGGGCTCTGGGTT 59.621 45.455 0.00 0.00 0.00 4.11
129 130 1.992557 TGTATTTTCTGGGCTCTGGGT 59.007 47.619 0.00 0.00 0.00 4.51
131 132 2.755103 GGTTGTATTTTCTGGGCTCTGG 59.245 50.000 0.00 0.00 0.00 3.86
133 134 2.378547 TGGGTTGTATTTTCTGGGCTCT 59.621 45.455 0.00 0.00 0.00 4.09
134 135 2.802719 TGGGTTGTATTTTCTGGGCTC 58.197 47.619 0.00 0.00 0.00 4.70
135 136 2.990740 TGGGTTGTATTTTCTGGGCT 57.009 45.000 0.00 0.00 0.00 5.19
136 137 2.353704 GCTTGGGTTGTATTTTCTGGGC 60.354 50.000 0.00 0.00 0.00 5.36
137 138 2.896685 TGCTTGGGTTGTATTTTCTGGG 59.103 45.455 0.00 0.00 0.00 4.45
139 140 3.573967 ACCTGCTTGGGTTGTATTTTCTG 59.426 43.478 1.69 0.00 41.11 3.02
140 141 3.573967 CACCTGCTTGGGTTGTATTTTCT 59.426 43.478 1.69 0.00 41.11 2.52
163 164 4.569943 TCAACGCTTCTCTTTTCTATGCT 58.430 39.130 0.00 0.00 0.00 3.79
196 197 1.977854 AGGTAGACAATGCTGACACCA 59.022 47.619 0.00 0.00 0.00 4.17
230 231 6.763610 GGTCTAAACTCCATACCTTGAATCTG 59.236 42.308 0.00 0.00 0.00 2.90
231 232 6.674419 AGGTCTAAACTCCATACCTTGAATCT 59.326 38.462 0.00 0.00 37.25 2.40
237 238 4.104831 AGCAGGTCTAAACTCCATACCTT 58.895 43.478 0.00 0.00 38.51 3.50
239 240 3.181464 GGAGCAGGTCTAAACTCCATACC 60.181 52.174 3.07 0.00 46.57 2.73
240 241 4.061357 GGAGCAGGTCTAAACTCCATAC 57.939 50.000 3.07 0.00 46.57 2.39
263 1859 3.009473 TGTTTGGAGATAGAGGCTTTGCT 59.991 43.478 0.00 0.00 0.00 3.91
275 1871 1.444933 TCCACCACCTGTTTGGAGAT 58.555 50.000 0.00 0.00 39.24 2.75
284 1880 4.139786 CCTTGATTCATATCCACCACCTG 58.860 47.826 0.00 0.00 0.00 4.00
326 1922 3.580731 TGTGAGCATATTGTTTCGACGA 58.419 40.909 0.00 0.00 0.00 4.20
352 1948 6.753107 ACAAAAGAATATACCTGGAAACCG 57.247 37.500 0.00 0.00 0.00 4.44
358 1954 8.669243 GTCAAGAGAACAAAAGAATATACCTGG 58.331 37.037 0.00 0.00 0.00 4.45
371 1967 5.605488 ACCCCTACTTAGTCAAGAGAACAAA 59.395 40.000 0.00 0.00 35.60 2.83
374 1970 4.771054 TCACCCCTACTTAGTCAAGAGAAC 59.229 45.833 0.00 0.00 35.60 3.01
388 1984 1.975680 TCCAGACTGTTTCACCCCTAC 59.024 52.381 0.93 0.00 0.00 3.18
393 1989 6.094186 GGAGAAATAATCCAGACTGTTTCACC 59.906 42.308 14.44 13.57 36.79 4.02
455 2051 4.640201 GGAGTATACATCAAGCAGCCAAAA 59.360 41.667 5.50 0.00 0.00 2.44
475 2071 5.816682 ACACTTATTTTGGGACTTAGGGAG 58.183 41.667 0.00 0.00 0.00 4.30
476 2072 5.550403 AGACACTTATTTTGGGACTTAGGGA 59.450 40.000 0.00 0.00 0.00 4.20
477 2073 5.816682 AGACACTTATTTTGGGACTTAGGG 58.183 41.667 0.00 0.00 0.00 3.53
478 2074 6.472887 TGAGACACTTATTTTGGGACTTAGG 58.527 40.000 0.00 0.00 0.00 2.69
479 2075 7.094762 GGTTGAGACACTTATTTTGGGACTTAG 60.095 40.741 0.00 0.00 0.00 2.18
480 2076 6.713450 GGTTGAGACACTTATTTTGGGACTTA 59.287 38.462 0.00 0.00 0.00 2.24
481 2077 5.535030 GGTTGAGACACTTATTTTGGGACTT 59.465 40.000 0.00 0.00 0.00 3.01
482 2078 5.070685 GGTTGAGACACTTATTTTGGGACT 58.929 41.667 0.00 0.00 0.00 3.85
483 2079 4.825085 TGGTTGAGACACTTATTTTGGGAC 59.175 41.667 0.00 0.00 0.00 4.46
484 2080 5.055265 TGGTTGAGACACTTATTTTGGGA 57.945 39.130 0.00 0.00 0.00 4.37
485 2081 5.982890 ATGGTTGAGACACTTATTTTGGG 57.017 39.130 0.00 0.00 0.00 4.12
486 2082 7.687941 ACTATGGTTGAGACACTTATTTTGG 57.312 36.000 0.00 0.00 0.00 3.28
487 2083 9.214957 TGTACTATGGTTGAGACACTTATTTTG 57.785 33.333 0.00 0.00 0.00 2.44
488 2084 9.787435 TTGTACTATGGTTGAGACACTTATTTT 57.213 29.630 0.00 0.00 0.00 1.82
489 2085 9.216117 GTTGTACTATGGTTGAGACACTTATTT 57.784 33.333 0.00 0.00 0.00 1.40
490 2086 8.594550 AGTTGTACTATGGTTGAGACACTTATT 58.405 33.333 0.00 0.00 0.00 1.40
491 2087 8.135382 AGTTGTACTATGGTTGAGACACTTAT 57.865 34.615 0.00 0.00 0.00 1.73
492 2088 7.534723 AGTTGTACTATGGTTGAGACACTTA 57.465 36.000 0.00 0.00 0.00 2.24
493 2089 6.420913 AGTTGTACTATGGTTGAGACACTT 57.579 37.500 0.00 0.00 0.00 3.16
494 2090 6.420913 AAGTTGTACTATGGTTGAGACACT 57.579 37.500 0.00 0.00 0.00 3.55
495 2091 6.482308 ACAAAGTTGTACTATGGTTGAGACAC 59.518 38.462 0.00 0.00 40.16 3.67
496 2092 6.588204 ACAAAGTTGTACTATGGTTGAGACA 58.412 36.000 0.00 0.00 40.16 3.41
530 2126 9.965824 CCAAAATAAGTGTCTCAATTTTGTACT 57.034 29.630 14.67 0.00 43.14 2.73
531 2127 9.191995 CCCAAAATAAGTGTCTCAATTTTGTAC 57.808 33.333 14.67 0.00 43.14 2.90
532 2128 9.137459 TCCCAAAATAAGTGTCTCAATTTTGTA 57.863 29.630 14.67 4.20 43.14 2.41
533 2129 7.926018 GTCCCAAAATAAGTGTCTCAATTTTGT 59.074 33.333 14.67 0.00 43.14 2.83
534 2130 7.114811 CGTCCCAAAATAAGTGTCTCAATTTTG 59.885 37.037 10.80 10.80 43.77 2.44
535 2131 7.145323 CGTCCCAAAATAAGTGTCTCAATTTT 58.855 34.615 0.00 0.00 33.07 1.82
536 2132 6.294508 CCGTCCCAAAATAAGTGTCTCAATTT 60.295 38.462 0.00 0.00 0.00 1.82
537 2133 5.183140 CCGTCCCAAAATAAGTGTCTCAATT 59.817 40.000 0.00 0.00 0.00 2.32
538 2134 4.700213 CCGTCCCAAAATAAGTGTCTCAAT 59.300 41.667 0.00 0.00 0.00 2.57
539 2135 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
540 2136 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
541 2137 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
542 2138 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
543 2139 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
544 2140 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
545 2141 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
546 2142 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
547 2143 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
548 2144 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
549 2145 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
550 2146 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
551 2147 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
552 2148 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
553 2149 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
554 2150 0.928505 TACATACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
555 2151 2.305858 ATACATACTCCCTCCGTCCC 57.694 55.000 0.00 0.00 0.00 4.46
556 2152 4.405548 ACTAATACATACTCCCTCCGTCC 58.594 47.826 0.00 0.00 0.00 4.79
557 2153 5.769162 AGAACTAATACATACTCCCTCCGTC 59.231 44.000 0.00 0.00 0.00 4.79
558 2154 5.535406 CAGAACTAATACATACTCCCTCCGT 59.465 44.000 0.00 0.00 0.00 4.69
559 2155 5.565045 GCAGAACTAATACATACTCCCTCCG 60.565 48.000 0.00 0.00 0.00 4.63
560 2156 5.304614 TGCAGAACTAATACATACTCCCTCC 59.695 44.000 0.00 0.00 0.00 4.30
561 2157 6.041069 ACTGCAGAACTAATACATACTCCCTC 59.959 42.308 23.35 0.00 0.00 4.30
562 2158 5.900123 ACTGCAGAACTAATACATACTCCCT 59.100 40.000 23.35 0.00 0.00 4.20
563 2159 6.163135 ACTGCAGAACTAATACATACTCCC 57.837 41.667 23.35 0.00 0.00 4.30
564 2160 6.018669 GCAACTGCAGAACTAATACATACTCC 60.019 42.308 23.35 0.00 41.59 3.85
565 2161 6.758886 AGCAACTGCAGAACTAATACATACTC 59.241 38.462 23.35 0.00 45.16 2.59
566 2162 6.644347 AGCAACTGCAGAACTAATACATACT 58.356 36.000 23.35 0.00 45.16 2.12
567 2163 6.910536 AGCAACTGCAGAACTAATACATAC 57.089 37.500 23.35 0.00 45.16 2.39
583 2179 2.046313 GCGATTGTTCACAAGCAACTG 58.954 47.619 8.55 0.00 41.91 3.16
615 2211 5.893687 TCGTTAGTGCGTATGGAGAAATAA 58.106 37.500 0.00 0.00 0.00 1.40
623 2219 3.186817 TGGTTTTTCGTTAGTGCGTATGG 59.813 43.478 0.00 0.00 0.00 2.74
628 2224 3.033185 CACTTGGTTTTTCGTTAGTGCG 58.967 45.455 0.00 0.00 0.00 5.34
636 2232 2.450160 GACTGCACACTTGGTTTTTCG 58.550 47.619 0.00 0.00 0.00 3.46
637 2233 2.450160 CGACTGCACACTTGGTTTTTC 58.550 47.619 0.00 0.00 0.00 2.29
644 2240 1.218875 TTACGCCGACTGCACACTTG 61.219 55.000 0.00 0.00 41.33 3.16
650 2246 1.746787 TCTCTATTTACGCCGACTGCA 59.253 47.619 0.00 0.00 41.33 4.41
651 2247 2.486951 TCTCTATTTACGCCGACTGC 57.513 50.000 0.00 0.00 0.00 4.40
656 2252 6.823678 ATTTAGTGTTCTCTATTTACGCCG 57.176 37.500 0.00 0.00 0.00 6.46
778 2384 7.814107 CAGAGGCAACAATTTTTAATTAGCAGA 59.186 33.333 0.00 0.00 41.41 4.26
793 2401 1.416030 TGTCACTAGCAGAGGCAACAA 59.584 47.619 0.00 0.00 44.61 2.83
797 2405 2.280835 CCTGTCACTAGCAGAGGCA 58.719 57.895 0.00 0.00 44.61 4.75
850 2460 3.093814 TCATGGAAAGACATGCATGCTT 58.906 40.909 26.53 24.17 45.52 3.91
851 2461 2.730382 TCATGGAAAGACATGCATGCT 58.270 42.857 26.53 20.12 45.52 3.79
852 2462 3.184541 GTTCATGGAAAGACATGCATGC 58.815 45.455 26.53 18.25 45.52 4.06
856 2466 3.559238 AACGTTCATGGAAAGACATGC 57.441 42.857 0.00 0.00 46.02 4.06
870 2480 7.901002 TGGATTTTCAAAAGCTTAAAACGTTC 58.099 30.769 0.00 0.00 0.00 3.95
872 2482 7.201574 GGTTGGATTTTCAAAAGCTTAAAACGT 60.202 33.333 0.00 0.00 0.00 3.99
874 2484 8.208718 AGGTTGGATTTTCAAAAGCTTAAAAC 57.791 30.769 0.00 0.00 0.00 2.43
887 2497 4.021981 CCTGAGTTGGAAGGTTGGATTTTC 60.022 45.833 0.00 0.00 0.00 2.29
901 2511 1.535462 CAGTTAAACCGCCTGAGTTGG 59.465 52.381 0.00 0.00 0.00 3.77
909 2519 3.907894 TCAATCAACAGTTAAACCGCC 57.092 42.857 0.00 0.00 0.00 6.13
919 2529 3.947910 AGCAATGGGTTCAATCAACAG 57.052 42.857 0.00 0.00 36.61 3.16
983 2782 0.815734 CATGGCTTTGCTCTTGGAGG 59.184 55.000 0.00 0.00 0.00 4.30
989 2788 1.379576 GAGGCCATGGCTTTGCTCT 60.380 57.895 34.70 22.38 38.98 4.09
990 2789 2.421399 GGAGGCCATGGCTTTGCTC 61.421 63.158 34.70 29.00 38.98 4.26
1086 2887 9.917872 GCATAGATTGATGAATTAATCGAGATG 57.082 33.333 0.00 4.22 37.71 2.90
1122 2936 5.934625 AGTATTGAGAAAGCAAGTGTCGAAT 59.065 36.000 0.00 0.00 0.00 3.34
1125 2939 6.311445 ACATAGTATTGAGAAAGCAAGTGTCG 59.689 38.462 0.00 0.00 0.00 4.35
1160 2975 9.748708 GCAATGAAAGGCTATATTATGAACAAA 57.251 29.630 0.00 0.00 0.00 2.83
1168 2983 7.658982 CAGTCTCAGCAATGAAAGGCTATATTA 59.341 37.037 0.00 0.00 38.56 0.98
1197 3019 9.209048 TCTTAACTAGCAGGACCAATAATTCTA 57.791 33.333 0.00 0.00 0.00 2.10
1213 3035 7.442666 AGCTAAATGGTATGCTTCTTAACTAGC 59.557 37.037 0.00 0.00 37.89 3.42
1214 3036 8.894768 AGCTAAATGGTATGCTTCTTAACTAG 57.105 34.615 0.00 0.00 30.96 2.57
1503 3336 1.202758 TCGTTGTCAGGCAGGTCATTT 60.203 47.619 0.00 0.00 0.00 2.32
1598 3476 0.391927 CTCATAAAACGACCCCGGCA 60.392 55.000 0.00 0.00 40.78 5.69
1728 3607 6.603095 AGATTTTGCTTACAGAAATGACGAC 58.397 36.000 0.00 0.00 0.00 4.34
1730 3609 9.214953 GATAAGATTTTGCTTACAGAAATGACG 57.785 33.333 0.00 0.00 33.53 4.35
1783 3665 0.175073 GTACGCCGGAATCCAGTTCT 59.825 55.000 5.05 0.00 37.01 3.01
1833 3715 0.110486 GCCTCAAGAACCACAGGGAA 59.890 55.000 0.00 0.00 38.05 3.97
1839 3721 2.162408 GTGCATAAGCCTCAAGAACCAC 59.838 50.000 0.00 0.00 41.13 4.16
1844 3726 3.138884 TGTTGTGCATAAGCCTCAAGA 57.861 42.857 0.00 0.00 41.13 3.02
1888 3778 4.040952 AGTTCTTTGGCTCTCAGCTCTAAA 59.959 41.667 0.00 0.00 41.99 1.85
1891 3781 1.977129 AGTTCTTTGGCTCTCAGCTCT 59.023 47.619 0.00 0.00 41.99 4.09
1926 3816 0.610174 TGCAAGGCAAACAACCAACA 59.390 45.000 0.00 0.00 34.76 3.33
1928 3818 3.756739 CTGCAAGGCAAACAACCAA 57.243 47.368 0.00 0.00 38.41 3.67
2012 3902 1.222936 CCTCTGAGGCCATGACACC 59.777 63.158 11.42 0.00 0.00 4.16
2118 4025 0.109597 CTTTGTCAATCACGCCCTGC 60.110 55.000 0.00 0.00 0.00 4.85
2139 4046 4.565564 GGCACGTAGAACGAATCATACTTT 59.434 41.667 6.44 0.00 46.05 2.66
2163 4070 2.521126 TCGTCACAAGGTCCATAGACA 58.479 47.619 0.00 0.00 45.48 3.41
2177 4084 2.811317 CCCGCAGCTCTTCGTCAC 60.811 66.667 0.00 0.00 0.00 3.67
2181 4088 1.299773 GATCTCCCGCAGCTCTTCG 60.300 63.158 0.00 0.00 0.00 3.79
2342 4249 6.096423 CCTCACAAATTCATCCATCACATCTT 59.904 38.462 0.00 0.00 0.00 2.40
2389 4296 1.210204 TCCTGCAAGCTTCCCTCCAT 61.210 55.000 0.00 0.00 0.00 3.41
2500 4428 8.186163 GCAATGTTTCAGTCTCATCAAATATGA 58.814 33.333 0.00 0.00 40.57 2.15
2528 4457 3.623510 GCATTTTCCCCTAGAAACGAGAG 59.376 47.826 0.00 0.00 44.20 3.20
2564 4493 8.465999 CACAAAAGGGATGTGCTTTATTACATA 58.534 33.333 0.00 0.00 41.42 2.29
2598 5013 7.466805 TCTCATTGCAGATCTTATTGAAAACG 58.533 34.615 0.00 0.00 0.00 3.60
2614 5029 4.325972 TGTTGCTAGTCAATCTCATTGCA 58.674 39.130 3.47 0.00 40.05 4.08
2617 5032 4.582869 TGCTGTTGCTAGTCAATCTCATT 58.417 39.130 3.47 0.00 40.48 2.57
2741 5290 7.138081 CAGAAACAAACATACATACTGTGCAA 58.862 34.615 0.00 0.00 0.00 4.08
2742 5291 6.293900 CCAGAAACAAACATACATACTGTGCA 60.294 38.462 0.00 0.00 0.00 4.57
2755 5304 2.096819 GTCAAGCGACCAGAAACAAACA 59.903 45.455 0.00 0.00 36.02 2.83
2814 5437 0.253044 TTTCCTCCTCCTCATTGCCG 59.747 55.000 0.00 0.00 0.00 5.69
2842 5465 4.187694 GCCTTCATTTCCACACACAAAAA 58.812 39.130 0.00 0.00 0.00 1.94
2845 5468 1.336440 CGCCTTCATTTCCACACACAA 59.664 47.619 0.00 0.00 0.00 3.33
2846 5469 0.950836 CGCCTTCATTTCCACACACA 59.049 50.000 0.00 0.00 0.00 3.72
2847 5470 0.951558 ACGCCTTCATTTCCACACAC 59.048 50.000 0.00 0.00 0.00 3.82
2849 5472 1.467342 GGTACGCCTTCATTTCCACAC 59.533 52.381 0.00 0.00 0.00 3.82
2850 5473 1.612199 GGGTACGCCTTCATTTCCACA 60.612 52.381 0.00 0.00 34.45 4.17
2851 5474 1.092348 GGGTACGCCTTCATTTCCAC 58.908 55.000 0.00 0.00 34.45 4.02
2852 5475 0.034863 GGGGTACGCCTTCATTTCCA 60.035 55.000 21.18 0.00 34.11 3.53
2853 5476 1.093496 CGGGGTACGCCTTCATTTCC 61.093 60.000 24.89 0.00 38.40 3.13
2855 5478 1.078001 CCGGGGTACGCCTTCATTT 60.078 57.895 24.89 0.00 42.52 2.32
2856 5479 2.587889 CCGGGGTACGCCTTCATT 59.412 61.111 24.89 0.00 42.52 2.57
2857 5480 4.171103 GCCGGGGTACGCCTTCAT 62.171 66.667 24.89 0.00 42.52 2.57
2865 5488 3.462199 GATGCAGAGGCCGGGGTAC 62.462 68.421 2.18 0.00 40.13 3.34
2868 5491 2.055689 TTATGATGCAGAGGCCGGGG 62.056 60.000 2.18 0.00 40.13 5.73
2869 5492 0.037303 ATTATGATGCAGAGGCCGGG 59.963 55.000 2.18 0.00 40.13 5.73
2870 5493 1.162698 CATTATGATGCAGAGGCCGG 58.837 55.000 0.00 0.00 40.13 6.13
2871 5494 2.174363 TCATTATGATGCAGAGGCCG 57.826 50.000 0.00 0.00 40.13 6.13


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

AutoCloner maintained by Alex Coulton.