Multiple sequence alignment - TraesCS1A01G356800

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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 TraesCS1A01G356800 chr1A 100.000 4272 0 0 985 5256 539754407 539758678 0.000000e+00 7890.0
1 TraesCS1A01G356800 chr1A 97.512 844 19 1 1521 2364 570328066 570327225 0.000000e+00 1441.0
2 TraesCS1A01G356800 chr1A 100.000 707 0 0 1 707 539753423 539754129 0.000000e+00 1306.0
3 TraesCS1A01G356800 chr1D 89.302 3898 214 74 985 4781 443816256 443820051 0.000000e+00 4700.0
4 TraesCS1A01G356800 chr1D 83.668 698 51 20 57 707 443815553 443816234 2.710000e-167 599.0
5 TraesCS1A01G356800 chr1D 93.229 192 12 1 5066 5256 443820243 443820434 1.110000e-71 281.0
6 TraesCS1A01G356800 chr1B 91.727 1801 101 24 2969 4766 603294271 603296026 0.000000e+00 2457.0
7 TraesCS1A01G356800 chr1B 87.059 765 51 17 1263 1996 603292368 603293115 0.000000e+00 821.0
8 TraesCS1A01G356800 chr1B 86.111 648 43 16 2101 2737 603293356 603293967 0.000000e+00 654.0
9 TraesCS1A01G356800 chr1B 95.205 292 6 1 985 1268 603285096 603285387 6.200000e-124 455.0
10 TraesCS1A01G356800 chr1B 77.878 443 59 13 10 427 603284252 603284680 6.800000e-59 239.0
11 TraesCS1A01G356800 chr1B 89.552 134 13 1 2778 2910 603294114 603294247 9.050000e-38 169.0
12 TraesCS1A01G356800 chr1B 84.127 189 12 10 5075 5256 603297690 603297867 3.260000e-37 167.0
13 TraesCS1A01G356800 chr1B 90.909 77 4 2 425 498 603284714 603284790 3.350000e-17 100.0
14 TraesCS1A01G356800 chr1B 96.491 57 2 0 4822 4878 603297532 603297588 1.560000e-15 95.3
15 TraesCS1A01G356800 chr2A 98.104 844 15 1 1521 2364 572190687 572189845 0.000000e+00 1469.0
16 TraesCS1A01G356800 chr2A 97.867 844 16 1 1521 2364 545286105 545286946 0.000000e+00 1458.0
17 TraesCS1A01G356800 chr2A 94.994 859 27 3 1521 2364 577098411 577097554 0.000000e+00 1334.0
18 TraesCS1A01G356800 chr2A 86.275 102 11 3 202 302 753717909 753717810 2.000000e-19 108.0
19 TraesCS1A01G356800 chr5A 97.275 844 22 1 1521 2364 103312012 103311170 0.000000e+00 1430.0
20 TraesCS1A01G356800 chr5A 98.396 561 7 1 1804 2364 186818467 186817909 0.000000e+00 985.0
21 TraesCS1A01G356800 chr5A 98.739 555 6 1 1804 2358 506641650 506642203 0.000000e+00 985.0
22 TraesCS1A01G356800 chr5A 98.396 561 7 2 1804 2364 563184626 563184068 0.000000e+00 985.0
23 TraesCS1A01G356800 chr5A 98.043 562 8 2 1804 2364 229663989 229664548 0.000000e+00 974.0
24 TraesCS1A01G356800 chr5A 98.667 75 0 1 1521 1594 186818532 186818458 1.190000e-26 132.0
25 TraesCS1A01G356800 chr5A 98.667 75 0 1 1521 1594 186858377 186858451 1.190000e-26 132.0
26 TraesCS1A01G356800 chr5A 98.667 75 0 1 1521 1594 229663924 229663998 1.190000e-26 132.0
27 TraesCS1A01G356800 chr7B 83.916 143 14 8 148 288 588076960 588076825 1.540000e-25 128.0
28 TraesCS1A01G356800 chr7B 87.838 74 8 1 193 265 413108729 413108802 9.380000e-13 86.1
29 TraesCS1A01G356800 chr7B 76.220 164 20 8 142 303 658214885 658215031 9.440000e-08 69.4
30 TraesCS1A01G356800 chr3B 71.676 519 123 22 3414 3917 795840151 795840660 7.150000e-24 122.0
31 TraesCS1A01G356800 chr5B 76.142 197 43 4 3724 3918 606302207 606302401 3.350000e-17 100.0
32 TraesCS1A01G356800 chr5B 90.909 44 3 1 215 257 644574491 644574534 2.040000e-04 58.4
33 TraesCS1A01G356800 chr5B 83.333 60 7 3 199 257 397955647 397955704 1.000000e-02 52.8
34 TraesCS1A01G356800 chr3D 70.906 519 127 21 3414 3917 593236408 593236917 3.350000e-17 100.0
35 TraesCS1A01G356800 chr4B 77.500 160 33 3 142 299 34729815 34729973 5.600000e-15 93.5
36 TraesCS1A01G356800 chr4B 74.138 232 54 4 3414 3642 11656957 11656729 2.020000e-14 91.6
37 TraesCS1A01G356800 chr4A 74.138 232 54 4 3414 3642 597014971 597015199 2.020000e-14 91.6
38 TraesCS1A01G356800 chr5D 75.127 197 45 4 3724 3918 491528336 491528530 7.250000e-14 89.8
39 TraesCS1A01G356800 chr4D 70.349 516 132 16 3414 3917 6424697 6425203 9.380000e-13 86.1
40 TraesCS1A01G356800 chr6B 92.857 42 1 1 216 257 534512215 534512254 5.680000e-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 TraesCS1A01G356800 chr1A 539753423 539758678 5255 False 4598.000000 7890 100.000000 1 5256 2 chr1A.!!$F1 5255
1 TraesCS1A01G356800 chr1A 570327225 570328066 841 True 1441.000000 1441 97.512000 1521 2364 1 chr1A.!!$R1 843
2 TraesCS1A01G356800 chr1D 443815553 443820434 4881 False 1860.000000 4700 88.733000 57 5256 3 chr1D.!!$F1 5199
3 TraesCS1A01G356800 chr1B 603292368 603297867 5499 False 727.216667 2457 89.177833 1263 5256 6 chr1B.!!$F2 3993
4 TraesCS1A01G356800 chr1B 603284252 603285387 1135 False 264.666667 455 87.997333 10 1268 3 chr1B.!!$F1 1258
5 TraesCS1A01G356800 chr2A 572189845 572190687 842 True 1469.000000 1469 98.104000 1521 2364 1 chr2A.!!$R1 843
6 TraesCS1A01G356800 chr2A 545286105 545286946 841 False 1458.000000 1458 97.867000 1521 2364 1 chr2A.!!$F1 843
7 TraesCS1A01G356800 chr2A 577097554 577098411 857 True 1334.000000 1334 94.994000 1521 2364 1 chr2A.!!$R2 843
8 TraesCS1A01G356800 chr5A 103311170 103312012 842 True 1430.000000 1430 97.275000 1521 2364 1 chr5A.!!$R1 843
9 TraesCS1A01G356800 chr5A 506641650 506642203 553 False 985.000000 985 98.739000 1804 2358 1 chr5A.!!$F2 554
10 TraesCS1A01G356800 chr5A 563184068 563184626 558 True 985.000000 985 98.396000 1804 2364 1 chr5A.!!$R2 560
11 TraesCS1A01G356800 chr5A 186817909 186818532 623 True 558.500000 985 98.531500 1521 2364 2 chr5A.!!$R3 843
12 TraesCS1A01G356800 chr5A 229663924 229664548 624 False 553.000000 974 98.355000 1521 2364 2 chr5A.!!$F3 843

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
55 57 0.741915 TGCACCCTTCGTTCCAAAAC 59.258 50.000 0.0 0.0 0.00 2.43 F
1258 1429 0.404426 GCCTCCCCCTTGTGTTAGTT 59.596 55.000 0.0 0.0 0.00 2.24 F
1376 1573 0.306228 TTGCGTGTCCGAAATGTGTG 59.694 50.000 0.0 0.0 35.63 3.82 F
1459 1660 1.002624 GTGGAGTGGGGATTGCGAA 60.003 57.895 0.0 0.0 0.00 4.70 F
1461 1662 1.299976 GGAGTGGGGATTGCGAAGT 59.700 57.895 0.0 0.0 0.00 3.01 F
3284 3876 0.178990 GGTCAAGGCTGTTGTTCCCT 60.179 55.000 0.0 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1376 1573 0.787908 CGCGCAAACGAACCACATAC 60.788 55.0 8.75 0.00 43.93 2.39 R
2477 2878 0.393537 CACTTGATCAGCCCAGTCCC 60.394 60.0 0.00 0.00 0.00 4.46 R
2776 3329 0.534873 TAACATGACGGCTGCAGCTA 59.465 50.0 35.82 20.72 41.70 3.32 R
3148 3740 0.608856 TGCCAACAGCCACATACCTG 60.609 55.0 0.00 0.00 42.71 4.00 R
3397 3989 0.958091 TGACAACAAAAGGGGCATCG 59.042 50.0 0.00 0.00 0.00 3.84 R
5003 7081 0.044855 AGGTAGACCCATTCCTGCCT 59.955 55.0 0.00 0.00 40.06 4.75 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
27 28 3.782889 GGCAACTATGAATGTCAACCC 57.217 47.619 0.00 0.00 0.00 4.11
35 37 6.779860 ACTATGAATGTCAACCCAAAGTAGT 58.220 36.000 0.00 0.00 0.00 2.73
37 39 5.766150 TGAATGTCAACCCAAAGTAGTTG 57.234 39.130 0.00 0.00 43.78 3.16
39 41 3.006112 TGTCAACCCAAAGTAGTTGCA 57.994 42.857 0.00 0.00 42.46 4.08
44 46 1.216930 ACCCAAAGTAGTTGCACCCTT 59.783 47.619 0.00 0.00 35.74 3.95
50 52 1.154197 GTAGTTGCACCCTTCGTTCC 58.846 55.000 0.00 0.00 0.00 3.62
55 57 0.741915 TGCACCCTTCGTTCCAAAAC 59.258 50.000 0.00 0.00 0.00 2.43
64 66 4.744631 CCTTCGTTCCAAAACAATTGAAGG 59.255 41.667 13.59 6.64 40.11 3.46
75 77 7.862873 CCAAAACAATTGAAGGTCTAGACTTTC 59.137 37.037 30.79 30.79 44.59 2.62
83 85 8.701908 TTGAAGGTCTAGACTTTCTGTAAGTA 57.298 34.615 34.32 18.52 47.00 2.24
307 322 1.255667 TGGAGGGAGTACAAGCCGAC 61.256 60.000 0.00 0.00 0.00 4.79
329 344 5.952033 ACTAAGAAATAGTCACTCACCGTC 58.048 41.667 0.00 0.00 41.04 4.79
331 346 4.175787 AGAAATAGTCACTCACCGTCAC 57.824 45.455 0.00 0.00 0.00 3.67
340 356 3.559655 TCACTCACCGTCACAATTTTCAG 59.440 43.478 0.00 0.00 0.00 3.02
404 437 2.283821 GGGACCCAATTGCCAGCA 60.284 61.111 5.33 0.00 0.00 4.41
469 552 1.405821 CTCCCTTCCTACTGTAGCACG 59.594 57.143 9.35 0.00 0.00 5.34
498 583 1.923204 CGAAGAAATCTCCAGCTGTCG 59.077 52.381 13.81 8.05 0.00 4.35
499 584 2.672478 CGAAGAAATCTCCAGCTGTCGT 60.672 50.000 13.81 0.03 0.00 4.34
500 585 2.663826 AGAAATCTCCAGCTGTCGTC 57.336 50.000 13.81 1.22 0.00 4.20
561 646 2.281761 CCAGCACTCACACCACCC 60.282 66.667 0.00 0.00 0.00 4.61
598 695 4.912395 GCCACAGCCCCAACCACA 62.912 66.667 0.00 0.00 0.00 4.17
599 696 2.912025 CCACAGCCCCAACCACAC 60.912 66.667 0.00 0.00 0.00 3.82
600 697 2.123939 CACAGCCCCAACCACACA 60.124 61.111 0.00 0.00 0.00 3.72
623 720 1.303282 CAAGCACCCTAACCCTCCC 59.697 63.158 0.00 0.00 0.00 4.30
1150 1313 4.316823 ACCACCTCGCCTCCCTCA 62.317 66.667 0.00 0.00 0.00 3.86
1255 1426 2.598787 CCGCCTCCCCCTTGTGTTA 61.599 63.158 0.00 0.00 0.00 2.41
1256 1427 1.078426 CGCCTCCCCCTTGTGTTAG 60.078 63.158 0.00 0.00 0.00 2.34
1257 1428 1.838073 CGCCTCCCCCTTGTGTTAGT 61.838 60.000 0.00 0.00 0.00 2.24
1258 1429 0.404426 GCCTCCCCCTTGTGTTAGTT 59.596 55.000 0.00 0.00 0.00 2.24
1259 1430 1.631898 GCCTCCCCCTTGTGTTAGTTA 59.368 52.381 0.00 0.00 0.00 2.24
1260 1431 2.355818 GCCTCCCCCTTGTGTTAGTTAG 60.356 54.545 0.00 0.00 0.00 2.34
1261 1432 2.910977 CCTCCCCCTTGTGTTAGTTAGT 59.089 50.000 0.00 0.00 0.00 2.24
1314 1489 4.265056 GCCCTGTTCGGTGGGTGT 62.265 66.667 0.00 0.00 45.06 4.16
1318 1493 1.145156 CTGTTCGGTGGGTGTGTCA 59.855 57.895 0.00 0.00 0.00 3.58
1368 1543 2.028484 GTGGAGTTGCGTGTCCGA 59.972 61.111 0.00 0.00 35.37 4.55
1369 1544 1.593209 GTGGAGTTGCGTGTCCGAA 60.593 57.895 0.00 0.00 35.37 4.30
1370 1545 1.144276 TGGAGTTGCGTGTCCGAAA 59.856 52.632 0.00 0.00 35.37 3.46
1376 1573 0.306228 TTGCGTGTCCGAAATGTGTG 59.694 50.000 0.00 0.00 35.63 3.82
1380 1577 2.473868 GCGTGTCCGAAATGTGTGTATG 60.474 50.000 0.00 0.00 35.63 2.39
1390 1587 5.508200 AAATGTGTGTATGTGGTTCGTTT 57.492 34.783 0.00 0.00 0.00 3.60
1459 1660 1.002624 GTGGAGTGGGGATTGCGAA 60.003 57.895 0.00 0.00 0.00 4.70
1461 1662 1.299976 GGAGTGGGGATTGCGAAGT 59.700 57.895 0.00 0.00 0.00 3.01
1511 1712 1.536709 GGTTCATGCGGAATTGATGCC 60.537 52.381 0.00 0.00 37.93 4.40
1613 1836 4.921515 TGACTGCACAATCGAGTTAACTAC 59.078 41.667 8.42 1.72 0.00 2.73
2378 2779 6.678568 ATATCTAGTGCTTCCTGTGCTTAT 57.321 37.500 0.00 0.00 0.00 1.73
2402 2803 5.473162 TGCTGTTTATGTGCTTCAGTGTATT 59.527 36.000 0.00 0.00 0.00 1.89
2462 2863 6.852911 GTTGTGAAAGCTTATTCAAAACGTC 58.147 36.000 15.23 0.54 43.72 4.34
2470 2871 5.408604 AGCTTATTCAAAACGTCGAATGAGT 59.591 36.000 19.28 9.46 37.48 3.41
2477 2878 4.364817 AAACGTCGAATGAGTAAACACG 57.635 40.909 0.00 0.00 0.00 4.49
2508 2910 4.378149 GCTGATCAAGTGCCATATCATTCG 60.378 45.833 0.00 0.00 0.00 3.34
2543 2945 6.459670 TTGTAGATTACCAGCGATAGTCAA 57.540 37.500 0.00 0.00 39.35 3.18
2591 2993 7.494211 ACTGTTTATTACATCCTACATACGCA 58.506 34.615 0.00 0.00 35.85 5.24
2618 3021 8.551205 TGAGAAATTTTACTATGATAGCTTGCG 58.449 33.333 0.00 0.00 0.00 4.85
2622 3025 8.657074 AATTTTACTATGATAGCTTGCGTGTA 57.343 30.769 0.00 0.00 0.00 2.90
2694 3105 3.632145 CCATAATTTGGTACTGCTGGACC 59.368 47.826 17.86 17.86 40.99 4.46
2710 3121 4.578105 GCTGGACCATTTCTAGAATTCAGG 59.422 45.833 5.89 8.47 34.71 3.86
2761 3314 8.364894 TCAGTTAGTTTTGTAGTGAGAAGCATA 58.635 33.333 0.00 0.00 0.00 3.14
2860 3424 6.492007 TGTGTGCTACTAGTAGTGTCTTAC 57.508 41.667 26.76 17.88 35.65 2.34
2881 3445 5.677319 ACTACATTTCTACTGCAGCCTTA 57.323 39.130 15.27 0.00 0.00 2.69
2911 3475 9.911788 ATTTTCCTCTAAGATGATGCTTAAGAA 57.088 29.630 6.67 0.00 30.55 2.52
2912 3476 9.739276 TTTTCCTCTAAGATGATGCTTAAGAAA 57.261 29.630 6.67 0.00 30.55 2.52
2913 3477 9.739276 TTTCCTCTAAGATGATGCTTAAGAAAA 57.261 29.630 6.67 0.00 29.98 2.29
2914 3478 9.739276 TTCCTCTAAGATGATGCTTAAGAAAAA 57.261 29.630 6.67 0.00 30.55 1.94
2960 3532 3.275338 GCACTAGGCCAGATGCGC 61.275 66.667 5.01 0.00 42.61 6.09
2968 3540 2.887568 CCAGATGCGCCGTGACTC 60.888 66.667 4.18 0.00 0.00 3.36
3050 3642 9.055248 GTCTGAAACATTTATTTGAGTTCGATG 57.945 33.333 0.00 0.00 0.00 3.84
3051 3643 8.236586 TCTGAAACATTTATTTGAGTTCGATGG 58.763 33.333 0.00 0.00 0.00 3.51
3052 3644 8.105097 TGAAACATTTATTTGAGTTCGATGGA 57.895 30.769 0.00 0.00 0.00 3.41
3053 3645 8.020819 TGAAACATTTATTTGAGTTCGATGGAC 58.979 33.333 0.00 0.00 0.00 4.02
3054 3646 7.447374 AACATTTATTTGAGTTCGATGGACA 57.553 32.000 0.00 0.00 0.00 4.02
3055 3647 7.630242 ACATTTATTTGAGTTCGATGGACAT 57.370 32.000 0.00 0.00 0.00 3.06
3056 3648 7.475015 ACATTTATTTGAGTTCGATGGACATG 58.525 34.615 0.00 0.00 0.00 3.21
3057 3649 7.121168 ACATTTATTTGAGTTCGATGGACATGT 59.879 33.333 0.00 0.00 0.00 3.21
3058 3650 7.447374 TTTATTTGAGTTCGATGGACATGTT 57.553 32.000 0.00 0.00 0.00 2.71
3059 3651 4.747540 TTTGAGTTCGATGGACATGTTG 57.252 40.909 0.00 0.00 0.00 3.33
3060 3652 3.401033 TGAGTTCGATGGACATGTTGT 57.599 42.857 0.00 0.00 0.00 3.32
3061 3653 3.066380 TGAGTTCGATGGACATGTTGTG 58.934 45.455 0.00 0.00 0.00 3.33
3062 3654 1.806542 AGTTCGATGGACATGTTGTGC 59.193 47.619 0.00 0.00 39.30 4.57
3085 3677 9.816354 GTGCATGTTTTTATTAATTCCACCTAT 57.184 29.630 0.00 0.00 0.00 2.57
3114 3706 8.633075 TTTGCAACTTTTCATCTTAGTTCTTG 57.367 30.769 0.00 0.00 30.08 3.02
3120 3712 8.682936 ACTTTTCATCTTAGTTCTTGTGTGAT 57.317 30.769 0.00 0.00 0.00 3.06
3134 3726 6.631016 TCTTGTGTGATACTCTGGTTACATC 58.369 40.000 0.00 0.00 0.00 3.06
3148 3740 5.848406 TGGTTACATCCATTGGTTTTGTTC 58.152 37.500 1.86 3.59 31.96 3.18
3183 3775 4.240096 GTTGGCAATGAACCATTTCTGAG 58.760 43.478 1.92 0.00 36.96 3.35
3284 3876 0.178990 GGTCAAGGCTGTTGTTCCCT 60.179 55.000 0.00 0.00 0.00 4.20
3442 4034 2.982339 ACCCGTATCTGAGCCTCTAT 57.018 50.000 0.00 0.00 0.00 1.98
3460 4052 5.435291 CTCTATCAGAATGCAAACTTCCCT 58.565 41.667 0.00 0.00 34.76 4.20
3512 4104 0.315251 GCCAGTCTTTGACAAAGGGC 59.685 55.000 24.22 23.40 39.01 5.19
3571 4163 2.484264 CCTTGTTTGGTCGCTAAGGAAG 59.516 50.000 0.00 0.00 40.18 3.46
3670 4262 5.584253 AGTATGCACAGAAGTTCTACGAT 57.416 39.130 4.74 0.00 0.00 3.73
3706 4298 0.468214 TGGCCAAAAATGTCGGGACA 60.468 50.000 0.61 3.69 46.44 4.02
3718 4310 2.284995 GGGACACCTCTGAGGCCT 60.285 66.667 23.43 3.86 39.63 5.19
3723 4315 1.915266 CACCTCTGAGGCCTGGTCA 60.915 63.158 23.43 0.05 39.63 4.02
3751 4343 0.460284 CCTACCTGTTCGCGCTGATT 60.460 55.000 5.56 0.00 0.00 2.57
3880 4472 2.363925 AGGTACCTGCTCGGGGTC 60.364 66.667 15.42 0.00 38.19 4.46
3881 4473 3.468140 GGTACCTGCTCGGGGTCC 61.468 72.222 4.06 0.00 38.19 4.46
3946 4538 5.208294 AGGACTTGAAGGATAGGTACAGA 57.792 43.478 0.00 0.00 0.00 3.41
4198 4790 2.690653 CTTCGGAAAGGGTGGTGCCA 62.691 60.000 0.00 0.00 39.65 4.92
4267 4859 3.866582 ATGTAGGCGAGGCAGGGC 61.867 66.667 0.00 0.00 0.00 5.19
4274 4866 3.385384 CGAGGCAGGGCAGTGAGA 61.385 66.667 0.00 0.00 0.00 3.27
4278 4870 1.673665 GGCAGGGCAGTGAGAACTG 60.674 63.158 0.00 1.45 40.51 3.16
4309 4901 2.869636 GCTGCTGTCAGAAGCTGTTACT 60.870 50.000 23.73 0.00 43.76 2.24
4310 4902 3.615110 GCTGCTGTCAGAAGCTGTTACTA 60.615 47.826 23.73 0.00 43.76 1.82
4319 4911 4.324669 CAGAAGCTGTTACTACATGACACG 59.675 45.833 0.00 0.00 32.86 4.49
4321 4913 2.561419 AGCTGTTACTACATGACACGGT 59.439 45.455 0.00 0.00 32.86 4.83
4324 4916 2.028839 TGTTACTACATGACACGGTGGG 60.029 50.000 13.48 1.72 0.00 4.61
4339 4931 4.424711 GGGGAGCACCGGATTGCA 62.425 66.667 18.29 0.00 45.62 4.08
4411 5004 4.464244 TGGGTGATTGAAGACAGAGTCTAG 59.536 45.833 0.00 0.00 42.59 2.43
4432 5025 3.320541 AGTTTCAGAGGACAGTCTCACAG 59.679 47.826 0.00 0.00 36.30 3.66
4436 5029 2.219325 GAGGACAGTCTCACAGGGCG 62.219 65.000 0.00 0.00 34.13 6.13
4445 5038 2.666190 CACAGGGCGACAGGTGTG 60.666 66.667 3.54 3.54 34.77 3.82
4458 5053 5.385617 CGACAGGTGTGAAATTCTGAATTC 58.614 41.667 15.43 9.92 0.00 2.17
4511 5106 0.322456 TTCTACAGCGGCATGGCTTT 60.322 50.000 18.09 2.81 42.53 3.51
4533 5128 3.135712 TCCAGGTTTCTGTTTGACAGCTA 59.864 43.478 3.26 0.00 45.54 3.32
4534 5129 3.251004 CCAGGTTTCTGTTTGACAGCTAC 59.749 47.826 3.26 4.14 45.54 3.58
4535 5130 3.251004 CAGGTTTCTGTTTGACAGCTACC 59.749 47.826 16.75 16.75 45.54 3.18
4536 5131 3.136626 AGGTTTCTGTTTGACAGCTACCT 59.863 43.478 19.35 19.35 45.88 3.08
4539 5134 4.948341 TTCTGTTTGACAGCTACCTACA 57.052 40.909 3.26 0.00 45.54 2.74
4540 5135 4.948341 TCTGTTTGACAGCTACCTACAA 57.052 40.909 3.26 0.00 45.54 2.41
4552 5149 4.020485 AGCTACCTACAACCTGTTTACTGG 60.020 45.833 4.45 4.45 40.37 4.00
4553 5150 3.136009 ACCTACAACCTGTTTACTGGC 57.864 47.619 5.79 0.00 38.38 4.85
4554 5151 2.709397 ACCTACAACCTGTTTACTGGCT 59.291 45.455 5.79 0.00 38.38 4.75
4556 5153 4.348754 ACCTACAACCTGTTTACTGGCTAA 59.651 41.667 5.79 0.00 38.38 3.09
4571 5168 1.777101 GCTAATAGTCAGCCTGAGCG 58.223 55.000 0.00 0.00 46.67 5.03
4576 5173 1.032794 TAGTCAGCCTGAGCGGTATG 58.967 55.000 0.00 0.00 46.67 2.39
4633 5236 4.501921 GCATTTGCAGATTCGATCTTTTCC 59.498 41.667 0.00 0.00 37.58 3.13
4640 5243 5.289595 CAGATTCGATCTTTTCCGGATGTA 58.710 41.667 4.15 0.00 37.58 2.29
4641 5244 5.928839 CAGATTCGATCTTTTCCGGATGTAT 59.071 40.000 4.15 0.00 37.58 2.29
4642 5245 5.928839 AGATTCGATCTTTTCCGGATGTATG 59.071 40.000 4.15 0.00 35.76 2.39
4778 5381 7.912056 TTTTATCTGTTGATCTCAGTTCCTG 57.088 36.000 14.62 0.00 34.32 3.86
4779 5382 6.611613 TTATCTGTTGATCTCAGTTCCTGT 57.388 37.500 14.62 3.45 34.32 4.00
4780 5383 4.963318 TCTGTTGATCTCAGTTCCTGTT 57.037 40.909 14.62 0.00 34.86 3.16
4781 5384 5.296151 TCTGTTGATCTCAGTTCCTGTTT 57.704 39.130 14.62 0.00 34.86 2.83
4782 5385 5.684704 TCTGTTGATCTCAGTTCCTGTTTT 58.315 37.500 14.62 0.00 34.86 2.43
4783 5386 6.122277 TCTGTTGATCTCAGTTCCTGTTTTT 58.878 36.000 14.62 0.00 34.86 1.94
4812 5415 9.801873 TTTTAAATCTCAGTTCCTGTTCTTTTG 57.198 29.630 0.00 0.00 32.61 2.44
4813 5416 8.519799 TTAAATCTCAGTTCCTGTTCTTTTGT 57.480 30.769 0.00 0.00 32.61 2.83
4814 5417 7.410120 AAATCTCAGTTCCTGTTCTTTTGTT 57.590 32.000 0.00 0.00 32.61 2.83
4815 5418 5.818136 TCTCAGTTCCTGTTCTTTTGTTG 57.182 39.130 0.00 0.00 32.61 3.33
4816 5419 5.496556 TCTCAGTTCCTGTTCTTTTGTTGA 58.503 37.500 0.00 0.00 32.61 3.18
4817 5420 6.122277 TCTCAGTTCCTGTTCTTTTGTTGAT 58.878 36.000 0.00 0.00 32.61 2.57
4831 6884 6.603201 TCTTTTGTTGATCTCAGTTCCTGTTT 59.397 34.615 0.00 0.00 32.61 2.83
4871 6924 2.239400 CCCCAGTTTCAGTTCCCTTTC 58.761 52.381 0.00 0.00 0.00 2.62
4878 6931 4.884164 AGTTTCAGTTCCCTTTCTCTGTTG 59.116 41.667 0.00 0.00 0.00 3.33
4886 6939 5.367945 TCCCTTTCTCTGTTGTACAAGTT 57.632 39.130 8.98 0.00 0.00 2.66
4887 6940 5.123227 TCCCTTTCTCTGTTGTACAAGTTG 58.877 41.667 8.98 0.00 0.00 3.16
4900 6974 3.806949 ACAAGTTGGCTCAGGGAATAA 57.193 42.857 7.96 0.00 0.00 1.40
4940 7014 8.910351 ATTCTAAAGTAGAAACAGTTCTTGCT 57.090 30.769 2.04 0.00 46.81 3.91
4941 7015 8.732746 TTCTAAAGTAGAAACAGTTCTTGCTT 57.267 30.769 0.00 0.00 41.55 3.91
4942 7016 8.732746 TCTAAAGTAGAAACAGTTCTTGCTTT 57.267 30.769 13.70 13.70 41.55 3.51
4946 7020 7.195839 AGTAGAAACAGTTCTTGCTTTCATC 57.804 36.000 0.00 0.00 41.55 2.92
4948 7022 8.150945 AGTAGAAACAGTTCTTGCTTTCATCTA 58.849 33.333 0.00 0.00 41.55 1.98
4949 7023 7.807977 AGAAACAGTTCTTGCTTTCATCTAA 57.192 32.000 0.00 0.00 41.55 2.10
4950 7024 8.225603 AGAAACAGTTCTTGCTTTCATCTAAA 57.774 30.769 0.00 0.00 41.55 1.85
4982 7060 8.499403 ACAGTTCTTGCTTTTCTATATCCTTC 57.501 34.615 0.00 0.00 0.00 3.46
4983 7061 7.554476 ACAGTTCTTGCTTTTCTATATCCTTCC 59.446 37.037 0.00 0.00 0.00 3.46
4991 7069 8.274322 TGCTTTTCTATATCCTTCCTGATGAAA 58.726 33.333 0.00 0.00 31.06 2.69
5001 7079 2.802667 CTGATGAAACGCGAGCCCG 61.803 63.158 15.93 0.00 39.16 6.13
5002 7080 3.564027 GATGAAACGCGAGCCCGG 61.564 66.667 15.93 0.00 36.06 5.73
5003 7081 4.077184 ATGAAACGCGAGCCCGGA 62.077 61.111 15.93 0.00 36.06 5.14
5004 7082 4.735132 TGAAACGCGAGCCCGGAG 62.735 66.667 15.93 0.00 36.06 4.63
5016 7094 3.411517 CCGGAGGCAGGAATGGGT 61.412 66.667 0.00 0.00 46.14 4.51
5025 7103 1.068741 GCAGGAATGGGTCTACCTACG 59.931 57.143 0.00 0.00 41.11 3.51
5026 7104 2.385803 CAGGAATGGGTCTACCTACGT 58.614 52.381 0.00 0.00 41.11 3.57
5029 7107 3.842436 AGGAATGGGTCTACCTACGTTTT 59.158 43.478 0.00 0.00 41.11 2.43
5114 7192 1.519455 GGCCTCAGGTTCGTCGATG 60.519 63.158 0.00 0.00 0.00 3.84
5245 7330 2.344521 AAGGACCGGTGTTTTTGCGC 62.345 55.000 14.63 0.00 0.00 6.09
5251 7336 1.942223 GGTGTTTTTGCGCGGACAC 60.942 57.895 20.19 20.19 41.14 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.687780 TGACATTCATAGTTGCCTCATGAT 58.312 37.500 0.00 0.00 0.00 2.45
1 2 5.101648 TGACATTCATAGTTGCCTCATGA 57.898 39.130 0.00 0.00 0.00 3.07
2 3 5.449588 GGTTGACATTCATAGTTGCCTCATG 60.450 44.000 0.00 0.00 0.00 3.07
3 4 4.641989 GGTTGACATTCATAGTTGCCTCAT 59.358 41.667 0.00 0.00 0.00 2.90
4 5 4.009675 GGTTGACATTCATAGTTGCCTCA 58.990 43.478 0.00 0.00 0.00 3.86
5 6 3.378427 GGGTTGACATTCATAGTTGCCTC 59.622 47.826 0.00 0.00 0.00 4.70
6 7 3.245229 TGGGTTGACATTCATAGTTGCCT 60.245 43.478 0.00 0.00 0.00 4.75
7 8 3.088532 TGGGTTGACATTCATAGTTGCC 58.911 45.455 0.00 0.00 0.00 4.52
8 9 4.782019 TTGGGTTGACATTCATAGTTGC 57.218 40.909 0.00 0.00 0.00 4.17
22 23 1.339929 GGGTGCAACTACTTTGGGTTG 59.660 52.381 0.00 0.00 43.71 3.77
23 24 1.216930 AGGGTGCAACTACTTTGGGTT 59.783 47.619 0.00 0.00 35.51 4.11
26 27 1.535462 CGAAGGGTGCAACTACTTTGG 59.465 52.381 0.00 0.00 34.98 3.28
27 28 2.218603 ACGAAGGGTGCAACTACTTTG 58.781 47.619 0.00 3.99 39.43 2.77
35 37 1.135333 GTTTTGGAACGAAGGGTGCAA 59.865 47.619 0.00 0.00 0.00 4.08
37 39 0.741915 TGTTTTGGAACGAAGGGTGC 59.258 50.000 0.00 0.00 38.65 5.01
39 41 3.702045 TCAATTGTTTTGGAACGAAGGGT 59.298 39.130 5.13 0.00 38.65 4.34
44 46 4.642885 AGACCTTCAATTGTTTTGGAACGA 59.357 37.500 5.13 0.00 38.65 3.85
50 52 8.624776 AGAAAGTCTAGACCTTCAATTGTTTTG 58.375 33.333 27.90 0.00 34.94 2.44
55 57 8.833231 TTACAGAAAGTCTAGACCTTCAATTG 57.167 34.615 27.90 21.32 34.94 2.32
83 85 9.665719 ATGTGGTCAAACTTAAAAGTGAAATTT 57.334 25.926 0.00 0.00 39.66 1.82
86 88 8.062065 AGATGTGGTCAAACTTAAAAGTGAAA 57.938 30.769 0.00 0.00 39.66 2.69
87 89 7.639113 AGATGTGGTCAAACTTAAAAGTGAA 57.361 32.000 0.00 0.00 39.66 3.18
88 90 8.918202 ATAGATGTGGTCAAACTTAAAAGTGA 57.082 30.769 0.00 0.00 39.66 3.41
183 191 8.972127 AGCATCTACTCAACTAGATTTACTTCA 58.028 33.333 0.00 0.00 32.08 3.02
307 322 5.800941 GTGACGGTGAGTGACTATTTCTTAG 59.199 44.000 0.00 0.00 34.02 2.18
319 334 3.559655 TCTGAAAATTGTGACGGTGAGTG 59.440 43.478 0.00 0.00 0.00 3.51
320 335 3.804036 TCTGAAAATTGTGACGGTGAGT 58.196 40.909 0.00 0.00 0.00 3.41
329 344 6.199719 GTGAGCTTTCCTTTCTGAAAATTGTG 59.800 38.462 4.18 0.00 34.06 3.33
331 346 5.400485 CGTGAGCTTTCCTTTCTGAAAATTG 59.600 40.000 4.18 0.00 34.06 2.32
340 356 2.079925 AGCATCGTGAGCTTTCCTTTC 58.920 47.619 0.00 0.00 39.87 2.62
404 437 2.014068 GCTGGATTTCTACGCTGGCTT 61.014 52.381 0.00 0.00 0.00 4.35
447 530 1.343075 TGCTACAGTAGGAAGGGAGGG 60.343 57.143 9.74 0.00 0.00 4.30
451 534 1.405821 CTCGTGCTACAGTAGGAAGGG 59.594 57.143 13.68 7.73 0.00 3.95
469 552 0.107459 AGATTTCTTCGCTGGGGCTC 60.107 55.000 0.00 0.00 36.09 4.70
525 610 2.202690 GTTTTTATGGGGCGCGCC 60.203 61.111 41.63 41.63 0.00 6.53
526 611 2.202690 GGTTTTTATGGGGCGCGC 60.203 61.111 25.94 25.94 0.00 6.86
527 612 2.492560 GGGTTTTTATGGGGCGCG 59.507 61.111 0.00 0.00 0.00 6.86
528 613 1.955495 CTGGGGTTTTTATGGGGCGC 61.955 60.000 0.00 0.00 0.00 6.53
529 614 1.955495 GCTGGGGTTTTTATGGGGCG 61.955 60.000 0.00 0.00 0.00 6.13
530 615 0.907230 TGCTGGGGTTTTTATGGGGC 60.907 55.000 0.00 0.00 0.00 5.80
531 616 0.901827 GTGCTGGGGTTTTTATGGGG 59.098 55.000 0.00 0.00 0.00 4.96
532 617 1.824852 GAGTGCTGGGGTTTTTATGGG 59.175 52.381 0.00 0.00 0.00 4.00
533 618 2.231235 GTGAGTGCTGGGGTTTTTATGG 59.769 50.000 0.00 0.00 0.00 2.74
534 619 2.890311 TGTGAGTGCTGGGGTTTTTATG 59.110 45.455 0.00 0.00 0.00 1.90
535 620 2.890945 GTGTGAGTGCTGGGGTTTTTAT 59.109 45.455 0.00 0.00 0.00 1.40
536 621 2.303175 GTGTGAGTGCTGGGGTTTTTA 58.697 47.619 0.00 0.00 0.00 1.52
537 622 1.111277 GTGTGAGTGCTGGGGTTTTT 58.889 50.000 0.00 0.00 0.00 1.94
595 692 2.912025 GGTGCTTGGGGGTGTGTG 60.912 66.667 0.00 0.00 0.00 3.82
596 693 4.218686 GGGTGCTTGGGGGTGTGT 62.219 66.667 0.00 0.00 0.00 3.72
597 694 2.075355 TTAGGGTGCTTGGGGGTGTG 62.075 60.000 0.00 0.00 0.00 3.82
598 695 1.776710 TTAGGGTGCTTGGGGGTGT 60.777 57.895 0.00 0.00 0.00 4.16
599 696 1.304134 GTTAGGGTGCTTGGGGGTG 60.304 63.158 0.00 0.00 0.00 4.61
600 697 2.544745 GGTTAGGGTGCTTGGGGGT 61.545 63.158 0.00 0.00 0.00 4.95
1221 1384 4.367023 GGCGGTGCGTACCTGACA 62.367 66.667 20.87 0.00 45.22 3.58
1303 1478 2.107343 CGTGACACACCCACCGAA 59.893 61.111 6.37 0.00 0.00 4.30
1332 1507 4.170723 GACCGAAAGTCGCTCCAG 57.829 61.111 0.00 0.00 38.82 3.86
1341 1516 1.566018 GCAACTCCACCGACCGAAAG 61.566 60.000 0.00 0.00 0.00 2.62
1368 1543 5.277825 CAAACGAACCACATACACACATTT 58.722 37.500 0.00 0.00 0.00 2.32
1369 1544 4.791411 GCAAACGAACCACATACACACATT 60.791 41.667 0.00 0.00 0.00 2.71
1370 1545 3.304391 GCAAACGAACCACATACACACAT 60.304 43.478 0.00 0.00 0.00 3.21
1376 1573 0.787908 CGCGCAAACGAACCACATAC 60.788 55.000 8.75 0.00 43.93 2.39
1380 1577 2.501607 TATGCGCGCAAACGAACCAC 62.502 55.000 39.68 0.56 43.93 4.16
1390 1587 0.808125 AAACATTTCCTATGCGCGCA 59.192 45.000 38.27 38.27 0.00 6.09
1444 1645 1.648467 GCACTTCGCAATCCCCACTC 61.648 60.000 0.00 0.00 41.79 3.51
1459 1660 2.027192 ACACATACCCAAATCGAGCACT 60.027 45.455 0.00 0.00 0.00 4.40
1461 1662 2.746904 CAACACATACCCAAATCGAGCA 59.253 45.455 0.00 0.00 0.00 4.26
1473 1674 5.403246 TGAACCAAAACACACAACACATAC 58.597 37.500 0.00 0.00 0.00 2.39
1511 1712 1.493772 CAACAACCAGCACAAGCATG 58.506 50.000 0.00 0.00 45.49 4.06
1613 1836 4.327982 ACATGATGACCCGTATGAAGAG 57.672 45.455 0.00 0.00 0.00 2.85
2043 2436 1.338674 CCCTCTGTGACGGTGCATTAA 60.339 52.381 0.00 0.00 0.00 1.40
2378 2779 3.213506 ACACTGAAGCACATAAACAGCA 58.786 40.909 0.00 0.00 32.67 4.41
2417 2818 9.302345 CACAACAATCGATCTAGTAGTGTAAAT 57.698 33.333 0.00 0.00 0.00 1.40
2418 2819 8.517056 TCACAACAATCGATCTAGTAGTGTAAA 58.483 33.333 0.00 0.00 0.00 2.01
2419 2820 8.047413 TCACAACAATCGATCTAGTAGTGTAA 57.953 34.615 0.00 0.00 0.00 2.41
2420 2821 7.619964 TCACAACAATCGATCTAGTAGTGTA 57.380 36.000 0.00 0.00 0.00 2.90
2421 2822 6.510879 TCACAACAATCGATCTAGTAGTGT 57.489 37.500 0.00 0.00 0.00 3.55
2422 2823 7.463383 GCTTTCACAACAATCGATCTAGTAGTG 60.463 40.741 0.00 4.02 0.00 2.74
2423 2824 6.531948 GCTTTCACAACAATCGATCTAGTAGT 59.468 38.462 0.00 0.00 0.00 2.73
2424 2825 6.754209 AGCTTTCACAACAATCGATCTAGTAG 59.246 38.462 0.00 0.00 0.00 2.57
2425 2826 6.631016 AGCTTTCACAACAATCGATCTAGTA 58.369 36.000 0.00 0.00 0.00 1.82
2426 2827 5.482908 AGCTTTCACAACAATCGATCTAGT 58.517 37.500 0.00 0.00 0.00 2.57
2427 2828 6.414408 AAGCTTTCACAACAATCGATCTAG 57.586 37.500 0.00 0.00 0.00 2.43
2428 2829 8.492673 AATAAGCTTTCACAACAATCGATCTA 57.507 30.769 3.20 0.00 0.00 1.98
2429 2830 6.992063 ATAAGCTTTCACAACAATCGATCT 57.008 33.333 3.20 0.00 0.00 2.75
2430 2831 7.243487 TGAATAAGCTTTCACAACAATCGATC 58.757 34.615 3.20 0.00 30.82 3.69
2431 2832 7.144722 TGAATAAGCTTTCACAACAATCGAT 57.855 32.000 3.20 0.00 30.82 3.59
2432 2833 6.552859 TGAATAAGCTTTCACAACAATCGA 57.447 33.333 3.20 0.00 30.82 3.59
2433 2834 7.621832 TTTGAATAAGCTTTCACAACAATCG 57.378 32.000 3.20 0.00 35.42 3.34
2437 2838 6.326375 ACGTTTTGAATAAGCTTTCACAACA 58.674 32.000 21.39 10.47 42.38 3.33
2459 2860 1.652124 CCCGTGTTTACTCATTCGACG 59.348 52.381 0.00 0.00 0.00 5.12
2462 2863 2.666508 CAGTCCCGTGTTTACTCATTCG 59.333 50.000 0.00 0.00 0.00 3.34
2470 2871 1.122632 TCAGCCCAGTCCCGTGTTTA 61.123 55.000 0.00 0.00 0.00 2.01
2477 2878 0.393537 CACTTGATCAGCCCAGTCCC 60.394 60.000 0.00 0.00 0.00 4.46
2508 2910 9.503427 GCTGGTAATCTACAATTACAAACATTC 57.497 33.333 9.43 0.00 36.49 2.67
2583 2985 9.325198 TCATAGTAAAATTTCTCATGCGTATGT 57.675 29.630 13.39 0.00 35.73 2.29
2588 2990 8.715998 AGCTATCATAGTAAAATTTCTCATGCG 58.284 33.333 0.00 0.00 0.00 4.73
2618 3021 5.984926 CCATGCCATCACCAATAAAATACAC 59.015 40.000 0.00 0.00 0.00 2.90
2622 3025 4.964262 ACTCCATGCCATCACCAATAAAAT 59.036 37.500 0.00 0.00 0.00 1.82
2694 3105 7.334090 TCTGAAGTCCCTGAATTCTAGAAATG 58.666 38.462 9.71 0.33 37.50 2.32
2710 3121 9.471084 GAGCTATAATCTAAACTTCTGAAGTCC 57.529 37.037 22.24 1.82 41.91 3.85
2761 3314 2.749621 GCAGCTACACCAAAAGCACTAT 59.250 45.455 0.00 0.00 41.32 2.12
2776 3329 0.534873 TAACATGACGGCTGCAGCTA 59.465 50.000 35.82 20.72 41.70 3.32
2808 3369 1.096967 TGTGACAGTGGCACTTGCAG 61.097 55.000 28.82 9.40 44.36 4.41
2814 3376 1.949525 AGAACATTGTGACAGTGGCAC 59.050 47.619 22.88 22.88 36.81 5.01
2817 3379 3.817084 ACATGAGAACATTGTGACAGTGG 59.183 43.478 12.73 0.00 34.15 4.00
2860 3424 6.051717 ACATAAGGCTGCAGTAGAAATGTAG 58.948 40.000 16.64 0.00 33.97 2.74
2866 3430 6.542370 GGAAAATACATAAGGCTGCAGTAGAA 59.458 38.462 16.64 0.00 0.00 2.10
2960 3532 2.913777 TGACTATTCACGAGTCACGG 57.086 50.000 1.42 0.00 46.49 4.94
2982 3554 6.037786 AGTCATTGAGGAACTGAATACGAA 57.962 37.500 0.00 0.00 41.10 3.85
3038 3610 4.024133 CACAACATGTCCATCGAACTCAAA 60.024 41.667 0.00 0.00 0.00 2.69
3039 3611 3.498018 CACAACATGTCCATCGAACTCAA 59.502 43.478 0.00 0.00 0.00 3.02
3042 3614 1.806542 GCACAACATGTCCATCGAACT 59.193 47.619 0.00 0.00 0.00 3.01
3054 3646 9.499479 TGGAATTAATAAAAACATGCACAACAT 57.501 25.926 0.00 0.00 40.66 2.71
3055 3647 8.768955 GTGGAATTAATAAAAACATGCACAACA 58.231 29.630 0.00 0.00 0.00 3.33
3056 3648 8.227119 GGTGGAATTAATAAAAACATGCACAAC 58.773 33.333 7.64 0.00 0.00 3.32
3057 3649 8.153550 AGGTGGAATTAATAAAAACATGCACAA 58.846 29.630 7.64 0.00 0.00 3.33
3058 3650 7.675062 AGGTGGAATTAATAAAAACATGCACA 58.325 30.769 7.64 0.00 0.00 4.57
3059 3651 9.816354 ATAGGTGGAATTAATAAAAACATGCAC 57.184 29.630 0.00 0.00 0.00 4.57
3114 3706 5.339008 TGGATGTAACCAGAGTATCACAC 57.661 43.478 0.00 0.00 37.82 3.82
3120 3712 5.772393 AACCAATGGATGTAACCAGAGTA 57.228 39.130 6.16 0.00 43.49 2.59
3134 3726 5.229423 CACATACCTGAACAAAACCAATGG 58.771 41.667 0.00 0.00 0.00 3.16
3148 3740 0.608856 TGCCAACAGCCACATACCTG 60.609 55.000 0.00 0.00 42.71 4.00
3397 3989 0.958091 TGACAACAAAAGGGGCATCG 59.042 50.000 0.00 0.00 0.00 3.84
3403 3995 4.022329 GGGTAGATGTTGACAACAAAAGGG 60.022 45.833 24.00 0.00 45.86 3.95
3442 4034 3.072915 TCAGAGGGAAGTTTGCATTCTGA 59.927 43.478 12.41 12.41 37.93 3.27
3448 4040 3.117888 AGAAGTTCAGAGGGAAGTTTGCA 60.118 43.478 5.50 0.00 46.61 4.08
3460 4052 5.072329 ACCATCAAAGAAGGAGAAGTTCAGA 59.928 40.000 5.50 0.00 0.00 3.27
3670 4262 3.157087 GGCCATCTTCTTCAGAAAACCA 58.843 45.455 0.00 0.00 34.16 3.67
3706 4298 1.915769 GTGACCAGGCCTCAGAGGT 60.916 63.158 18.37 12.20 37.80 3.85
3718 4310 1.594833 GTAGGCGTCCATGTGACCA 59.405 57.895 8.25 0.00 41.18 4.02
3723 4315 0.249398 GAACAGGTAGGCGTCCATGT 59.751 55.000 4.10 0.00 0.00 3.21
3751 4343 0.241213 CGCTCTTCTGGTTCTCGTCA 59.759 55.000 0.00 0.00 0.00 4.35
3904 4496 2.964925 TCGAACACGCACCACTGC 60.965 61.111 0.00 0.00 40.38 4.40
4198 4790 1.961277 CGCGGCCAAAACTCTCAGT 60.961 57.895 2.24 0.00 0.00 3.41
4274 4866 2.224621 ACAGCAGCTTGATGTACCAGTT 60.225 45.455 5.44 0.00 46.11 3.16
4309 4901 1.895020 GCTCCCCACCGTGTCATGTA 61.895 60.000 0.00 0.00 0.00 2.29
4310 4902 3.068881 CTCCCCACCGTGTCATGT 58.931 61.111 0.00 0.00 0.00 3.21
4321 4913 4.424711 GCAATCCGGTGCTCCCCA 62.425 66.667 9.69 0.00 41.51 4.96
4324 4916 1.372087 CTCTTGCAATCCGGTGCTCC 61.372 60.000 17.03 0.00 45.17 4.70
4355 4947 4.321008 CCTTACAGACTCTTGTAGCACGAA 60.321 45.833 0.00 0.00 35.17 3.85
4360 4952 3.594603 TGCCTTACAGACTCTTGTAGC 57.405 47.619 0.00 0.00 35.17 3.58
4363 4955 3.142174 GCTTTGCCTTACAGACTCTTGT 58.858 45.455 0.00 0.00 35.09 3.16
4411 5004 3.553922 CCTGTGAGACTGTCCTCTGAAAC 60.554 52.174 3.76 0.00 34.38 2.78
4432 5025 0.521735 GAATTTCACACCTGTCGCCC 59.478 55.000 0.00 0.00 0.00 6.13
4436 5029 6.205464 TGAGAATTCAGAATTTCACACCTGTC 59.795 38.462 9.84 0.00 0.00 3.51
4458 5053 0.806868 ATGGCAATTGACGTGCTGAG 59.193 50.000 10.34 0.00 41.88 3.35
4501 5096 0.247460 GAAACCTGGAAAGCCATGCC 59.753 55.000 0.00 0.00 44.91 4.40
4530 5125 4.251268 CCAGTAAACAGGTTGTAGGTAGC 58.749 47.826 0.00 0.00 0.00 3.58
4533 5128 2.709397 AGCCAGTAAACAGGTTGTAGGT 59.291 45.455 0.00 0.00 0.00 3.08
4534 5129 3.418684 AGCCAGTAAACAGGTTGTAGG 57.581 47.619 0.00 0.00 0.00 3.18
4535 5130 7.328737 ACTATTAGCCAGTAAACAGGTTGTAG 58.671 38.462 0.00 0.00 0.00 2.74
4536 5131 7.038870 TGACTATTAGCCAGTAAACAGGTTGTA 60.039 37.037 0.00 0.00 0.00 2.41
4539 5134 6.368779 TGACTATTAGCCAGTAAACAGGTT 57.631 37.500 0.00 0.00 0.00 3.50
4540 5135 5.627040 GCTGACTATTAGCCAGTAAACAGGT 60.627 44.000 8.55 0.00 35.15 4.00
4552 5149 1.604185 CCGCTCAGGCTGACTATTAGC 60.604 57.143 14.43 13.34 40.41 3.09
4553 5150 1.683917 ACCGCTCAGGCTGACTATTAG 59.316 52.381 14.43 3.79 46.52 1.73
4554 5151 1.776662 ACCGCTCAGGCTGACTATTA 58.223 50.000 14.43 0.00 46.52 0.98
4556 5153 1.615883 CATACCGCTCAGGCTGACTAT 59.384 52.381 14.43 3.53 46.52 2.12
4571 5168 3.119849 ACAAACTGCTCATTTCGCATACC 60.120 43.478 0.00 0.00 36.70 2.73
4576 5173 2.031682 ACTGACAAACTGCTCATTTCGC 60.032 45.455 0.00 0.00 0.00 4.70
4633 5236 2.742774 TCGCAGTTCATCATACATCCG 58.257 47.619 0.00 0.00 0.00 4.18
4640 5243 5.048504 ACATGTTTCTTTCGCAGTTCATCAT 60.049 36.000 0.00 0.00 0.00 2.45
4641 5244 4.275689 ACATGTTTCTTTCGCAGTTCATCA 59.724 37.500 0.00 0.00 0.00 3.07
4642 5245 4.614284 CACATGTTTCTTTCGCAGTTCATC 59.386 41.667 0.00 0.00 0.00 2.92
4672 5275 1.412710 TCCTTCCGTATGCCTGTCATC 59.587 52.381 0.00 0.00 36.63 2.92
4709 5312 5.010112 TCAGTAACTCAAGGAACAGACAGAG 59.990 44.000 0.00 0.00 0.00 3.35
4797 5400 6.122277 TGAGATCAACAAAAGAACAGGAACT 58.878 36.000 0.00 0.00 43.88 3.01
4798 5401 6.038714 ACTGAGATCAACAAAAGAACAGGAAC 59.961 38.462 0.00 0.00 0.00 3.62
4799 5402 6.122277 ACTGAGATCAACAAAAGAACAGGAA 58.878 36.000 0.00 0.00 0.00 3.36
4800 5403 5.684704 ACTGAGATCAACAAAAGAACAGGA 58.315 37.500 0.00 0.00 0.00 3.86
4802 5405 6.261826 AGGAACTGAGATCAACAAAAGAACAG 59.738 38.462 0.00 0.00 37.18 3.16
4803 5406 6.122277 AGGAACTGAGATCAACAAAAGAACA 58.878 36.000 0.00 0.00 37.18 3.18
4804 5407 6.625873 AGGAACTGAGATCAACAAAAGAAC 57.374 37.500 0.00 0.00 37.18 3.01
4831 6884 1.962412 CAAAGAGCGCACGCAATTAA 58.038 45.000 18.24 0.00 44.88 1.40
4871 6924 3.466836 TGAGCCAACTTGTACAACAGAG 58.533 45.455 3.59 0.00 0.00 3.35
4878 6931 2.561478 TTCCCTGAGCCAACTTGTAC 57.439 50.000 0.00 0.00 0.00 2.90
4886 6939 4.079787 ACAAGCTAATTATTCCCTGAGCCA 60.080 41.667 0.00 0.00 0.00 4.75
4887 6940 4.276926 CACAAGCTAATTATTCCCTGAGCC 59.723 45.833 0.00 0.00 0.00 4.70
4925 6999 7.807977 TTAGATGAAAGCAAGAACTGTTTCT 57.192 32.000 0.00 0.00 44.53 2.52
4926 7000 8.856490 TTTTAGATGAAAGCAAGAACTGTTTC 57.144 30.769 0.00 0.00 0.00 2.78
4956 7030 9.601217 GAAGGATATAGAAAAGCAAGAACTGTA 57.399 33.333 0.00 0.00 0.00 2.74
4963 7041 7.935755 TCATCAGGAAGGATATAGAAAAGCAAG 59.064 37.037 0.00 0.00 0.00 4.01
4979 7057 0.371645 GCTCGCGTTTCATCAGGAAG 59.628 55.000 5.77 0.00 36.72 3.46
4980 7058 1.019278 GGCTCGCGTTTCATCAGGAA 61.019 55.000 5.77 0.00 0.00 3.36
4981 7059 1.447838 GGCTCGCGTTTCATCAGGA 60.448 57.895 5.77 0.00 0.00 3.86
4982 7060 2.464459 GGGCTCGCGTTTCATCAGG 61.464 63.158 5.77 0.00 0.00 3.86
4983 7061 2.802667 CGGGCTCGCGTTTCATCAG 61.803 63.158 5.77 0.00 0.00 2.90
5001 7079 0.470341 GTAGACCCATTCCTGCCTCC 59.530 60.000 0.00 0.00 0.00 4.30
5002 7080 0.470341 GGTAGACCCATTCCTGCCTC 59.530 60.000 0.00 0.00 33.21 4.70
5003 7081 0.044855 AGGTAGACCCATTCCTGCCT 59.955 55.000 0.00 0.00 40.06 4.75
5004 7082 1.416772 GTAGGTAGACCCATTCCTGCC 59.583 57.143 0.00 0.00 36.42 4.85
5005 7083 1.068741 CGTAGGTAGACCCATTCCTGC 59.931 57.143 0.00 0.00 36.42 4.85
5006 7084 2.385803 ACGTAGGTAGACCCATTCCTG 58.614 52.381 0.00 0.00 36.42 3.86
5048 7126 5.130145 GGAGTACTCTGTGTAGGTAGACCTA 59.870 48.000 21.88 4.22 46.48 3.08
5050 7128 4.080413 AGGAGTACTCTGTGTAGGTAGACC 60.080 50.000 21.88 1.22 0.00 3.85
5051 7129 5.101648 AGGAGTACTCTGTGTAGGTAGAC 57.898 47.826 21.88 1.15 0.00 2.59
5052 7130 5.963253 ACTAGGAGTACTCTGTGTAGGTAGA 59.037 44.000 21.88 0.00 0.00 2.59
5053 7131 6.237887 ACTAGGAGTACTCTGTGTAGGTAG 57.762 45.833 21.88 11.67 0.00 3.18
5054 7132 6.633325 AACTAGGAGTACTCTGTGTAGGTA 57.367 41.667 21.88 1.92 0.00 3.08
5055 7133 5.517620 AACTAGGAGTACTCTGTGTAGGT 57.482 43.478 21.88 13.11 0.00 3.08
5056 7134 7.511268 AGATAACTAGGAGTACTCTGTGTAGG 58.489 42.308 21.88 8.42 0.00 3.18
5057 7135 7.658575 GGAGATAACTAGGAGTACTCTGTGTAG 59.341 44.444 21.88 17.64 0.00 2.74
5058 7136 7.347748 AGGAGATAACTAGGAGTACTCTGTGTA 59.652 40.741 21.88 9.03 0.00 2.90
5059 7137 6.159046 AGGAGATAACTAGGAGTACTCTGTGT 59.841 42.308 21.88 14.30 0.00 3.72
5060 7138 6.485313 CAGGAGATAACTAGGAGTACTCTGTG 59.515 46.154 21.88 13.72 0.00 3.66
5061 7139 6.409925 CCAGGAGATAACTAGGAGTACTCTGT 60.410 46.154 21.88 14.93 0.00 3.41
5062 7140 6.001460 CCAGGAGATAACTAGGAGTACTCTG 58.999 48.000 21.88 14.35 0.00 3.35
5063 7141 5.073965 CCCAGGAGATAACTAGGAGTACTCT 59.926 48.000 21.88 10.81 0.00 3.24
5064 7142 5.318630 CCCAGGAGATAACTAGGAGTACTC 58.681 50.000 14.87 14.87 0.00 2.59
5103 7181 1.134367 TGGTGAGATCATCGACGAACC 59.866 52.381 0.00 3.47 0.00 3.62
5114 7192 0.835941 ATGTGGGCTCTGGTGAGATC 59.164 55.000 0.00 0.00 42.73 2.75


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

AutoCloner maintained by Alex Coulton.