Multiple sequence alignment - TraesCS7D01G032500

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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 TraesCS7D01G032500 chr7D 100.000 2542 0 0 2862 5403 16781955 16779414 0.000000e+00 4695.0
1 TraesCS7D01G032500 chr7D 100.000 2536 0 0 1 2536 16784816 16782281 0.000000e+00 4684.0
2 TraesCS7D01G032500 chr7D 90.669 643 56 3 3696 4336 744288 744928 0.000000e+00 852.0
3 TraesCS7D01G032500 chr7D 100.000 416 0 0 5727 6142 16779090 16778675 0.000000e+00 769.0
4 TraesCS7D01G032500 chr7D 95.000 60 3 0 5864 5923 179903473 179903414 1.820000e-15 95.3
5 TraesCS7D01G032500 chr7A 94.220 2578 93 28 2862 5403 16018636 16016079 0.000000e+00 3884.0
6 TraesCS7D01G032500 chr7A 88.753 1885 104 52 68 1889 16024352 16022513 0.000000e+00 2207.0
7 TraesCS7D01G032500 chr7A 90.719 668 31 22 1883 2536 16019309 16018659 0.000000e+00 861.0
8 TraesCS7D01G032500 chr7A 84.790 835 65 28 3011 3807 627407039 627407849 0.000000e+00 782.0
9 TraesCS7D01G032500 chr7A 92.698 493 22 10 3091 3581 75989983 75990463 0.000000e+00 699.0
10 TraesCS7D01G032500 chr7A 92.308 494 24 10 3091 3581 647085571 647086053 0.000000e+00 689.0
11 TraesCS7D01G032500 chr7A 93.878 343 10 4 5805 6141 16015978 16015641 1.980000e-139 507.0
12 TraesCS7D01G032500 chr7A 89.401 217 17 3 59 269 16024803 16024587 1.010000e-67 268.0
13 TraesCS7D01G032500 chr4A 93.747 2015 78 21 3403 5403 717309209 717307229 0.000000e+00 2979.0
14 TraesCS7D01G032500 chr4A 85.951 2534 157 82 57 2536 717312436 717310048 0.000000e+00 2523.0
15 TraesCS7D01G032500 chr4A 89.747 712 67 4 3623 4333 50232337 50233043 0.000000e+00 905.0
16 TraesCS7D01G032500 chr4A 88.158 532 21 20 2862 3356 717310016 717309490 4.100000e-166 595.0
17 TraesCS7D01G032500 chr4A 94.000 200 9 3 5938 6134 717306994 717306795 3.600000e-77 300.0
18 TraesCS7D01G032500 chr4A 87.981 208 17 5 5938 6141 664802359 664802562 7.960000e-59 239.0
19 TraesCS7D01G032500 chr4A 82.353 204 19 11 5735 5923 717307180 717306979 1.770000e-35 161.0
20 TraesCS7D01G032500 chr3D 92.245 735 50 4 3612 4344 413347371 413346642 0.000000e+00 1035.0
21 TraesCS7D01G032500 chr3D 88.889 198 14 5 5937 6130 494021247 494021440 2.860000e-58 237.0
22 TraesCS7D01G032500 chr3D 94.915 59 3 0 5864 5922 491030374 491030432 6.560000e-15 93.5
23 TraesCS7D01G032500 chr5D 86.603 836 52 28 3011 3807 289561426 289562240 0.000000e+00 869.0
24 TraesCS7D01G032500 chr6B 90.187 642 61 2 3696 4336 284281936 284282576 0.000000e+00 835.0
25 TraesCS7D01G032500 chr6B 88.942 208 15 4 5938 6141 546842863 546842660 3.680000e-62 250.0
26 TraesCS7D01G032500 chr6B 82.778 180 11 9 3043 3209 388992491 388992319 6.420000e-30 143.0
27 TraesCS7D01G032500 chr5A 93.061 490 20 10 3094 3581 178108767 178108290 0.000000e+00 704.0
28 TraesCS7D01G032500 chr3A 92.857 490 21 10 3094 3581 349330126 349329649 0.000000e+00 699.0
29 TraesCS7D01G032500 chr3A 92.653 490 22 10 3094 3581 457850092 457849615 0.000000e+00 693.0
30 TraesCS7D01G032500 chr1A 92.668 491 22 10 3094 3581 33946465 33945986 0.000000e+00 695.0
31 TraesCS7D01G032500 chr1A 92.638 489 24 8 3094 3581 411207450 411206973 0.000000e+00 693.0
32 TraesCS7D01G032500 chr2A 92.292 493 24 10 3091 3581 138092649 138093129 0.000000e+00 688.0
33 TraesCS7D01G032500 chr6A 92.019 426 30 3 3713 4135 159243380 159242956 4.100000e-166 595.0
34 TraesCS7D01G032500 chr3B 92.822 404 27 2 3696 4098 238017989 238018391 8.870000e-163 584.0
35 TraesCS7D01G032500 chr3B 85.403 459 24 22 2862 3293 737694811 737694369 2.630000e-118 436.0
36 TraesCS7D01G032500 chr3B 88.934 244 11 7 2293 2525 737695088 737694850 2.800000e-73 287.0
37 TraesCS7D01G032500 chr3B 95.082 122 6 0 4215 4336 222545264 222545385 6.280000e-45 193.0
38 TraesCS7D01G032500 chr2B 84.130 586 41 25 3011 3559 610244526 610245096 2.540000e-143 520.0
39 TraesCS7D01G032500 chr2B 85.153 458 26 21 2863 3293 60386301 60385859 1.220000e-116 431.0
40 TraesCS7D01G032500 chr2B 88.115 244 13 7 2293 2525 60386578 60386340 6.060000e-70 276.0
41 TraesCS7D01G032500 chr2B 87.981 208 17 4 5938 6141 99485541 99485338 7.960000e-59 239.0
42 TraesCS7D01G032500 chr2B 82.424 165 15 7 3047 3204 302398918 302399075 1.390000e-26 132.0
43 TraesCS7D01G032500 chr1B 91.803 366 27 2 3696 4059 50641605 50641241 1.980000e-139 507.0
44 TraesCS7D01G032500 chr4B 88.942 208 15 4 5938 6141 439419118 439418915 3.680000e-62 250.0
45 TraesCS7D01G032500 chr4D 88.832 197 14 5 5938 6130 47427459 47427651 1.030000e-57 235.0
46 TraesCS7D01G032500 chr4D 91.765 85 6 1 3011 3094 446552798 446552714 3.890000e-22 117.0
47 TraesCS7D01G032500 chr4D 94.915 59 3 0 5864 5922 42557911 42557969 6.560000e-15 93.5
48 TraesCS7D01G032500 chr4D 94.915 59 3 0 5864 5922 396187250 396187192 6.560000e-15 93.5
49 TraesCS7D01G032500 chr4D 97.297 37 1 0 5822 5858 42557832 42557868 5.140000e-06 63.9
50 TraesCS7D01G032500 chr4D 97.297 37 1 0 5822 5858 47427336 47427372 5.140000e-06 63.9
51 TraesCS7D01G032500 chr4D 97.297 37 1 0 5822 5858 240093284 240093248 5.140000e-06 63.9
52 TraesCS7D01G032500 chr4D 97.297 37 1 0 5822 5858 396187329 396187293 5.140000e-06 63.9
53 TraesCS7D01G032500 chr1D 88.832 197 14 6 5938 6130 45673082 45673274 1.030000e-57 235.0
54 TraesCS7D01G032500 chr1D 94.915 59 3 0 5864 5922 26717654 26717712 6.560000e-15 93.5
55 TraesCS7D01G032500 chr5B 92.086 139 11 0 4204 4342 702404459 702404321 4.860000e-46 196.0
56 TraesCS7D01G032500 chr5B 81.421 183 11 13 3043 3209 69573408 69573233 1.800000e-25 128.0
57 TraesCS7D01G032500 chr6D 94.915 59 3 0 5864 5922 342994610 342994552 6.560000e-15 93.5
58 TraesCS7D01G032500 chr6D 94.915 59 3 0 5864 5922 447162045 447161987 6.560000e-15 93.5
59 TraesCS7D01G032500 chr6D 80.189 106 11 4 5822 5922 83729174 83729274 3.070000e-08 71.3
60 TraesCS7D01G032500 chr6D 79.808 104 15 4 5822 5922 179684545 179684445 3.070000e-08 71.3
61 TraesCS7D01G032500 chr6D 97.297 37 1 0 5822 5858 342994689 342994653 5.140000e-06 63.9
62 TraesCS7D01G032500 chr6D 97.297 37 1 0 5822 5858 430807085 430807121 5.140000e-06 63.9


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 TraesCS7D01G032500 chr7D 16778675 16784816 6141 True 3382.666667 4695 100.0000 1 6142 3 chr7D.!!$R2 6141
1 TraesCS7D01G032500 chr7D 744288 744928 640 False 852.000000 852 90.6690 3696 4336 1 chr7D.!!$F1 640
2 TraesCS7D01G032500 chr7A 16015641 16024803 9162 True 1545.400000 3884 91.3942 59 6141 5 chr7A.!!$R1 6082
3 TraesCS7D01G032500 chr7A 627407039 627407849 810 False 782.000000 782 84.7900 3011 3807 1 chr7A.!!$F2 796
4 TraesCS7D01G032500 chr4A 717306795 717312436 5641 True 1311.600000 2979 88.8418 57 6134 5 chr4A.!!$R1 6077
5 TraesCS7D01G032500 chr4A 50232337 50233043 706 False 905.000000 905 89.7470 3623 4333 1 chr4A.!!$F1 710
6 TraesCS7D01G032500 chr3D 413346642 413347371 729 True 1035.000000 1035 92.2450 3612 4344 1 chr3D.!!$R1 732
7 TraesCS7D01G032500 chr5D 289561426 289562240 814 False 869.000000 869 86.6030 3011 3807 1 chr5D.!!$F1 796
8 TraesCS7D01G032500 chr6B 284281936 284282576 640 False 835.000000 835 90.1870 3696 4336 1 chr6B.!!$F1 640
9 TraesCS7D01G032500 chr3B 737694369 737695088 719 True 361.500000 436 87.1685 2293 3293 2 chr3B.!!$R1 1000
10 TraesCS7D01G032500 chr2B 610244526 610245096 570 False 520.000000 520 84.1300 3011 3559 1 chr2B.!!$F2 548
11 TraesCS7D01G032500 chr2B 60385859 60386578 719 True 353.500000 431 86.6340 2293 3293 2 chr2B.!!$R2 1000

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 56 0.178955 TGTACTCCTTCCGTCCCACA 60.179 55.000 0.00 0.0 0.00 4.17 F
1725 2250 0.196118 TTTCCCTCCCCTGTTCCTCT 59.804 55.000 0.00 0.0 0.00 3.69 F
1910 5652 1.427368 ACCCAGTGTCTGCCCAAAATA 59.573 47.619 0.00 0.0 0.00 1.40 F
3365 7191 0.473694 TCTTGGGCCTGGTCTTCTCA 60.474 55.000 4.53 0.0 0.00 3.27 F
3608 7691 0.916086 TGACACCCCAACTCACACTT 59.084 50.000 0.00 0.0 0.00 3.16 F
4465 8554 0.330941 TACAGCATGACCATTGGCCA 59.669 50.000 0.00 0.0 39.69 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 2420 0.847373 TTTTGGGCAGACACTGGGTA 59.153 50.000 0.00 0.0 31.21 3.69 R
3052 6842 0.733909 GCATGGAAGCAAGTTTCGCC 60.734 55.000 0.00 0.0 0.00 5.54 R
3758 7844 1.133790 GGCATGACTGAACCTTGCATC 59.866 52.381 0.00 0.0 36.69 3.91 R
4465 8554 0.844661 TCCAATGGCCTGTGGGTAGT 60.845 55.000 21.07 0.0 35.46 2.73 R
4967 9056 1.077858 GAGGAAGCTGCCCAGGAAG 60.078 63.158 7.30 0.0 0.00 3.46 R
6029 10149 4.389890 TGTAAGAAAATGGCCATGATGC 57.610 40.909 21.63 10.5 0.00 3.91 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
24 25 5.146010 GAGATCCAGTGGATATCCTCAAC 57.854 47.826 29.18 13.79 42.62 3.18
25 26 4.560739 AGATCCAGTGGATATCCTCAACA 58.439 43.478 24.89 7.11 43.27 3.33
26 27 4.971282 AGATCCAGTGGATATCCTCAACAA 59.029 41.667 24.89 6.93 43.27 2.83
27 28 4.487714 TCCAGTGGATATCCTCAACAAC 57.512 45.455 22.35 10.99 36.82 3.32
28 29 3.199946 TCCAGTGGATATCCTCAACAACC 59.800 47.826 22.35 0.00 36.82 3.77
29 30 3.545703 CAGTGGATATCCTCAACAACCC 58.454 50.000 22.35 0.00 36.82 4.11
30 31 3.054434 CAGTGGATATCCTCAACAACCCA 60.054 47.826 22.35 0.00 36.82 4.51
31 32 3.591527 AGTGGATATCCTCAACAACCCAA 59.408 43.478 22.35 0.00 36.82 4.12
32 33 4.044065 AGTGGATATCCTCAACAACCCAAA 59.956 41.667 22.35 0.00 36.82 3.28
33 34 4.770010 GTGGATATCCTCAACAACCCAAAA 59.230 41.667 22.35 0.00 36.82 2.44
34 35 5.422012 GTGGATATCCTCAACAACCCAAAAT 59.578 40.000 22.35 0.00 36.82 1.82
35 36 6.605594 GTGGATATCCTCAACAACCCAAAATA 59.394 38.462 22.35 0.00 36.82 1.40
36 37 7.287696 GTGGATATCCTCAACAACCCAAAATAT 59.712 37.037 22.35 0.00 36.82 1.28
37 38 7.287466 TGGATATCCTCAACAACCCAAAATATG 59.713 37.037 22.35 0.00 36.82 1.78
38 39 7.287696 GGATATCCTCAACAACCCAAAATATGT 59.712 37.037 14.97 0.00 0.00 2.29
39 40 9.349713 GATATCCTCAACAACCCAAAATATGTA 57.650 33.333 0.00 0.00 0.00 2.29
40 41 6.827586 TCCTCAACAACCCAAAATATGTAC 57.172 37.500 0.00 0.00 0.00 2.90
41 42 6.548321 TCCTCAACAACCCAAAATATGTACT 58.452 36.000 0.00 0.00 0.00 2.73
42 43 6.657541 TCCTCAACAACCCAAAATATGTACTC 59.342 38.462 0.00 0.00 0.00 2.59
43 44 6.127730 CCTCAACAACCCAAAATATGTACTCC 60.128 42.308 0.00 0.00 0.00 3.85
44 45 6.548321 TCAACAACCCAAAATATGTACTCCT 58.452 36.000 0.00 0.00 0.00 3.69
45 46 7.007723 TCAACAACCCAAAATATGTACTCCTT 58.992 34.615 0.00 0.00 0.00 3.36
46 47 7.175990 TCAACAACCCAAAATATGTACTCCTTC 59.824 37.037 0.00 0.00 0.00 3.46
47 48 5.949952 ACAACCCAAAATATGTACTCCTTCC 59.050 40.000 0.00 0.00 0.00 3.46
48 49 4.777463 ACCCAAAATATGTACTCCTTCCG 58.223 43.478 0.00 0.00 0.00 4.30
49 50 4.226620 ACCCAAAATATGTACTCCTTCCGT 59.773 41.667 0.00 0.00 0.00 4.69
50 51 4.814771 CCCAAAATATGTACTCCTTCCGTC 59.185 45.833 0.00 0.00 0.00 4.79
51 52 4.814771 CCAAAATATGTACTCCTTCCGTCC 59.185 45.833 0.00 0.00 0.00 4.79
52 53 4.684484 AAATATGTACTCCTTCCGTCCC 57.316 45.455 0.00 0.00 0.00 4.46
53 54 2.832643 TATGTACTCCTTCCGTCCCA 57.167 50.000 0.00 0.00 0.00 4.37
54 55 1.192428 ATGTACTCCTTCCGTCCCAC 58.808 55.000 0.00 0.00 0.00 4.61
55 56 0.178955 TGTACTCCTTCCGTCCCACA 60.179 55.000 0.00 0.00 0.00 4.17
56 57 0.971386 GTACTCCTTCCGTCCCACAA 59.029 55.000 0.00 0.00 0.00 3.33
57 58 1.553704 GTACTCCTTCCGTCCCACAAT 59.446 52.381 0.00 0.00 0.00 2.71
65 66 4.342951 CCTTCCGTCCCACAATATACTACA 59.657 45.833 0.00 0.00 0.00 2.74
108 109 1.222300 TGTCCGGTCAATGAAACACG 58.778 50.000 0.00 0.00 0.00 4.49
145 146 2.747446 CACCTGTCCGTTTTTCCCATAG 59.253 50.000 0.00 0.00 0.00 2.23
188 194 7.711339 GGATATCCTCGACAACTCATACTTTTT 59.289 37.037 14.97 0.00 0.00 1.94
207 214 2.014010 TACCTTGTTCCCCTACACGT 57.986 50.000 0.00 0.00 0.00 4.49
210 217 2.148768 CCTTGTTCCCCTACACGTTTC 58.851 52.381 0.00 0.00 0.00 2.78
214 221 2.768503 TTCCCCTACACGTTTCGCCG 62.769 60.000 0.00 0.00 0.00 6.46
269 276 5.734634 ACCCTAATCTTGTACCCATTACCTT 59.265 40.000 0.00 0.00 0.00 3.50
277 284 5.266733 TGTACCCATTACCTTTACGCTAG 57.733 43.478 0.00 0.00 0.00 3.42
278 285 3.832615 ACCCATTACCTTTACGCTAGG 57.167 47.619 0.00 0.00 38.79 3.02
282 289 4.383335 CCCATTACCTTTACGCTAGGACAA 60.383 45.833 5.19 0.38 36.58 3.18
283 290 4.809426 CCATTACCTTTACGCTAGGACAAG 59.191 45.833 5.19 0.00 36.58 3.16
284 291 5.394883 CCATTACCTTTACGCTAGGACAAGA 60.395 44.000 5.19 0.00 36.58 3.02
293 300 2.701107 GCTAGGACAAGACTCCAAACC 58.299 52.381 0.00 0.00 31.94 3.27
295 302 3.617775 GCTAGGACAAGACTCCAAACCTC 60.618 52.174 0.00 0.00 31.94 3.85
297 745 1.149148 GACAAGACTCCAAACCTCGC 58.851 55.000 0.00 0.00 0.00 5.03
303 751 2.501723 AGACTCCAAACCTCGCATACAT 59.498 45.455 0.00 0.00 0.00 2.29
317 765 2.101917 GCATACATTCTTTGCCAGCCAT 59.898 45.455 0.00 0.00 0.00 4.40
355 816 4.284829 TCACACAATGCTCTACCATCAA 57.715 40.909 0.00 0.00 0.00 2.57
356 817 4.650734 TCACACAATGCTCTACCATCAAA 58.349 39.130 0.00 0.00 0.00 2.69
362 823 5.047164 ACAATGCTCTACCATCAAAATTGCA 60.047 36.000 0.00 0.00 0.00 4.08
428 890 6.076298 CGAAAACGCACAGTAAGTAAACAAAG 60.076 38.462 0.00 0.00 0.00 2.77
430 892 6.425577 AACGCACAGTAAGTAAACAAAGAA 57.574 33.333 0.00 0.00 0.00 2.52
431 893 6.044512 ACGCACAGTAAGTAAACAAAGAAG 57.955 37.500 0.00 0.00 0.00 2.85
433 895 6.482308 ACGCACAGTAAGTAAACAAAGAAGAT 59.518 34.615 0.00 0.00 0.00 2.40
436 898 8.342634 GCACAGTAAGTAAACAAAGAAGATGAA 58.657 33.333 0.00 0.00 0.00 2.57
459 925 8.428063 TGAAAAACAAAATCCATCAGTTGGTAT 58.572 29.630 0.00 0.00 46.52 2.73
492 958 4.637276 ACACCGAAGTCACATGTTCATTA 58.363 39.130 0.00 0.00 0.00 1.90
559 1030 1.338200 ACTCATCCGCTCTCCAAACAC 60.338 52.381 0.00 0.00 0.00 3.32
594 1065 3.705289 GCATGGGTTGGGTTGGGC 61.705 66.667 0.00 0.00 0.00 5.36
667 1155 2.126346 GCTCCAATGGCAACGCAC 60.126 61.111 0.00 0.00 42.51 5.34
669 1157 1.081242 CTCCAATGGCAACGCACAC 60.081 57.895 0.00 0.00 42.51 3.82
673 1161 2.855514 AATGGCAACGCACACCACC 61.856 57.895 0.00 0.00 35.99 4.61
678 1166 3.804329 AACGCACACCACCCCACT 61.804 61.111 0.00 0.00 0.00 4.00
686 1174 2.195683 CCACCCCACTGCACACTT 59.804 61.111 0.00 0.00 0.00 3.16
692 1180 1.650912 CCACTGCACACTTCACAGC 59.349 57.895 0.00 0.00 34.72 4.40
693 1181 0.816825 CCACTGCACACTTCACAGCT 60.817 55.000 0.00 0.00 34.72 4.24
727 1215 0.697658 CCCCAAAACCCCATTGCATT 59.302 50.000 0.00 0.00 0.00 3.56
762 1250 2.548547 GCCACCTTTTCCCCTCCCT 61.549 63.158 0.00 0.00 0.00 4.20
774 1262 2.180308 TCCCCTCCCTATTTCTCTCTCC 59.820 54.545 0.00 0.00 0.00 3.71
785 1273 3.374042 TTCTCTCTCCACCCTCTACTG 57.626 52.381 0.00 0.00 0.00 2.74
800 1288 1.946768 CTACTGCTCCCGAGAAGAGAG 59.053 57.143 6.71 0.20 36.10 3.20
801 1289 0.329931 ACTGCTCCCGAGAAGAGAGA 59.670 55.000 6.71 0.00 36.10 3.10
827 1315 0.912006 AGAGAGGAGGAACCCAAGGC 60.912 60.000 0.00 0.00 40.05 4.35
978 1485 2.747460 CTGCGGCTGCCTGCTTAA 60.747 61.111 26.88 12.83 41.78 1.85
1480 1997 5.289675 CACGAGATGTCCATGTAAGAAGAAC 59.710 44.000 0.00 0.00 0.00 3.01
1481 1998 5.047306 ACGAGATGTCCATGTAAGAAGAACA 60.047 40.000 0.00 0.00 0.00 3.18
1482 1999 5.869344 CGAGATGTCCATGTAAGAAGAACAA 59.131 40.000 0.00 0.00 0.00 2.83
1483 2000 6.035435 CGAGATGTCCATGTAAGAAGAACAAG 59.965 42.308 0.00 0.00 0.00 3.16
1484 2001 7.009179 AGATGTCCATGTAAGAAGAACAAGA 57.991 36.000 0.00 0.00 0.00 3.02
1485 2002 7.628234 AGATGTCCATGTAAGAAGAACAAGAT 58.372 34.615 0.00 0.00 0.00 2.40
1516 2033 1.230853 TCTCCCCACTCCCTCCCTA 60.231 63.158 0.00 0.00 0.00 3.53
1538 2056 6.546034 CCTACTTCTCTCCCAAAGTTTTGAAA 59.454 38.462 6.18 0.00 40.55 2.69
1565 2083 2.783510 TGGGGTTTCTCTCCTCTGTTTT 59.216 45.455 0.00 0.00 37.63 2.43
1618 2137 0.252239 AGGGGTTTTGGGCCAGATTC 60.252 55.000 6.23 0.00 0.00 2.52
1652 2171 1.341209 CAGTTTCTTGGGGTGCTTTCC 59.659 52.381 0.00 0.00 0.00 3.13
1698 2223 7.650903 ACAGATTTGCAGATTTGTTTTCTTCTC 59.349 33.333 7.51 0.00 0.00 2.87
1702 2227 4.520492 TGCAGATTTGTTTTCTTCTCCCTC 59.480 41.667 0.00 0.00 0.00 4.30
1725 2250 0.196118 TTTCCCTCCCCTGTTCCTCT 59.804 55.000 0.00 0.00 0.00 3.69
1814 2345 9.901172 TTTATGGGAAGTAGTAATCTTTCCTTC 57.099 33.333 4.88 0.00 40.29 3.46
1817 2348 6.447084 TGGGAAGTAGTAATCTTTCCTTCCAT 59.553 38.462 15.75 0.00 40.29 3.41
1820 2351 8.894731 GGAAGTAGTAATCTTTCCTTCCATTTC 58.105 37.037 10.52 0.00 38.98 2.17
1857 2388 7.201444 CGCCAGTGATTTTTCTTGTAGTACTAG 60.201 40.741 1.87 5.49 0.00 2.57
1871 2402 8.591114 TTGTAGTACTAGCACTATTTTCCTCT 57.409 34.615 6.11 0.00 33.71 3.69
1872 2403 8.223177 TGTAGTACTAGCACTATTTTCCTCTC 57.777 38.462 6.11 0.00 33.71 3.20
1889 2420 4.707448 TCCTCTCGAGCTTGTTCTTATCTT 59.293 41.667 7.81 0.00 0.00 2.40
1910 5652 1.427368 ACCCAGTGTCTGCCCAAAATA 59.573 47.619 0.00 0.00 0.00 1.40
1944 5686 3.506810 TCTTGTTTTTGTCTGCAAACGG 58.493 40.909 0.00 0.00 43.47 4.44
1966 5714 2.191641 GCATGGTGCTCCCTCCTC 59.808 66.667 1.59 0.00 40.96 3.71
2009 5757 3.812053 TGCGGATTTCAATTTGTTTTGGG 59.188 39.130 0.00 0.00 0.00 4.12
2032 5780 4.899239 CTCCTGCCGCATCCCGTC 62.899 72.222 0.00 0.00 34.38 4.79
2040 5788 1.443407 CGCATCCCGTCATCTCCTT 59.557 57.895 0.00 0.00 0.00 3.36
2062 5810 8.540388 TCCTTTGTACTTCTGCTCACTATTATT 58.460 33.333 0.00 0.00 0.00 1.40
2063 5811 8.821894 CCTTTGTACTTCTGCTCACTATTATTC 58.178 37.037 0.00 0.00 0.00 1.75
2064 5812 9.371136 CTTTGTACTTCTGCTCACTATTATTCA 57.629 33.333 0.00 0.00 0.00 2.57
2153 5902 6.543831 ACAAGTATATGATTTTCCCTGTCTGC 59.456 38.462 0.00 0.00 0.00 4.26
2155 5904 6.294473 AGTATATGATTTTCCCTGTCTGCTG 58.706 40.000 0.00 0.00 0.00 4.41
2194 5943 1.624487 TATTGCGGCGTATATGCGAG 58.376 50.000 17.83 10.64 35.06 5.03
2196 5945 3.479269 GCGGCGTATATGCGAGGC 61.479 66.667 17.83 14.27 35.06 4.70
2234 5983 4.696479 AGGAGAAATGATAGGATGCGTT 57.304 40.909 0.00 0.00 0.00 4.84
2235 5984 4.384056 AGGAGAAATGATAGGATGCGTTG 58.616 43.478 0.00 0.00 0.00 4.10
2238 5987 4.526970 AGAAATGATAGGATGCGTTGGTT 58.473 39.130 0.00 0.00 0.00 3.67
2258 6007 5.905331 TGGTTATACCTCAGAGATTCCATGT 59.095 40.000 0.00 0.00 39.58 3.21
2449 6210 5.007682 TCGCAGCTAAATATTATTTCCCCC 58.992 41.667 4.94 0.00 0.00 5.40
2911 6688 5.146010 TGCCTGTGAAAATAAAACCCATC 57.854 39.130 0.00 0.00 0.00 3.51
2941 6721 4.231718 TCTTTTTGTAACGTTGGGATGC 57.768 40.909 11.99 0.00 0.00 3.91
2943 6723 3.634568 TTTTGTAACGTTGGGATGCTG 57.365 42.857 11.99 0.00 0.00 4.41
3020 6810 6.042143 CCATAAGTGTGAAATTTATGGGCAC 58.958 40.000 8.60 3.71 45.10 5.01
3052 6842 2.880890 CCCATTAAATTCGGCCTCTGAG 59.119 50.000 0.00 0.00 0.00 3.35
3101 6899 7.446013 GCTTCAGATAGTACACAGATACTACCT 59.554 40.741 0.00 0.00 39.80 3.08
3184 6995 9.912634 TTTTCATTTCCTATGAGTGATGTTTTC 57.087 29.630 0.00 0.00 0.00 2.29
3185 6996 8.868522 TTCATTTCCTATGAGTGATGTTTTCT 57.131 30.769 0.00 0.00 0.00 2.52
3187 6998 7.554118 TCATTTCCTATGAGTGATGTTTTCTCC 59.446 37.037 0.00 0.00 0.00 3.71
3188 6999 5.359194 TCCTATGAGTGATGTTTTCTCCC 57.641 43.478 0.00 0.00 0.00 4.30
3189 7000 5.032846 TCCTATGAGTGATGTTTTCTCCCT 58.967 41.667 0.00 0.00 0.00 4.20
3190 7001 6.202331 TCCTATGAGTGATGTTTTCTCCCTA 58.798 40.000 0.00 0.00 0.00 3.53
3191 7002 6.325028 TCCTATGAGTGATGTTTTCTCCCTAG 59.675 42.308 0.00 0.00 0.00 3.02
3300 7126 2.027561 TGTCCCACTTTTGATAGGACCG 60.028 50.000 5.12 0.00 45.26 4.79
3365 7191 0.473694 TCTTGGGCCTGGTCTTCTCA 60.474 55.000 4.53 0.00 0.00 3.27
3381 7207 1.564348 TCTCACCCCTTTATGCCCTTC 59.436 52.381 0.00 0.00 0.00 3.46
3408 7468 3.754965 TGAACAGGAAAAGAGGGTGATG 58.245 45.455 0.00 0.00 0.00 3.07
3469 7552 6.482973 CCCACAAAAATTGTTAGTTGATGCTT 59.517 34.615 0.00 0.00 43.23 3.91
3606 7689 1.608590 CATTGACACCCCAACTCACAC 59.391 52.381 0.00 0.00 0.00 3.82
3608 7691 0.916086 TGACACCCCAACTCACACTT 59.084 50.000 0.00 0.00 0.00 3.16
3609 7692 1.308998 GACACCCCAACTCACACTTG 58.691 55.000 0.00 0.00 0.00 3.16
3709 7794 4.678509 TTTAACTAGGCTGAAATGTGCG 57.321 40.909 0.00 0.00 0.00 5.34
3711 7796 2.185004 ACTAGGCTGAAATGTGCGTT 57.815 45.000 0.00 0.00 0.00 4.84
3748 7833 9.008965 TCAGCATTGTTGTACTTATTTACATGT 57.991 29.630 2.69 2.69 31.98 3.21
3749 7834 9.064804 CAGCATTGTTGTACTTATTTACATGTG 57.935 33.333 9.11 0.00 31.98 3.21
3750 7835 8.792633 AGCATTGTTGTACTTATTTACATGTGT 58.207 29.630 9.11 0.00 31.98 3.72
4079 8168 1.186267 AGACGGTCTGGGTGTTCCTC 61.186 60.000 10.41 0.00 36.20 3.71
4382 8471 3.535629 CTGCCACGGCCTCTTCACA 62.536 63.158 5.42 0.00 41.09 3.58
4400 8489 3.137385 AAACAGGCCCAGCAGCTCA 62.137 57.895 0.00 0.00 0.00 4.26
4465 8554 0.330941 TACAGCATGACCATTGGCCA 59.669 50.000 0.00 0.00 39.69 5.36
4481 8570 1.691219 CCACTACCCACAGGCCATT 59.309 57.895 5.01 0.00 36.11 3.16
4505 8594 1.109323 GCTTGGTGGCAGTGTTCCTT 61.109 55.000 0.00 0.00 0.00 3.36
4514 8603 3.960102 TGGCAGTGTTCCTTTCATCTTTT 59.040 39.130 0.00 0.00 0.00 2.27
4964 9053 2.361737 GGAGGGTCCTTTGCTGCC 60.362 66.667 0.00 0.00 32.53 4.85
5012 9101 1.014044 TCGTGCTCATCTTCGGCAAC 61.014 55.000 0.00 0.00 37.73 4.17
5027 9116 1.154413 CAACGTCAGCAACATCGGC 60.154 57.895 0.00 0.00 0.00 5.54
5368 9472 4.870426 GCTAGCAGCTCTGTTAATGTGTTA 59.130 41.667 10.63 0.00 38.45 2.41
5369 9473 5.351465 GCTAGCAGCTCTGTTAATGTGTTAA 59.649 40.000 10.63 0.00 38.45 2.01
5370 9474 6.128282 GCTAGCAGCTCTGTTAATGTGTTAAA 60.128 38.462 10.63 0.00 38.45 1.52
5371 9475 6.824305 AGCAGCTCTGTTAATGTGTTAAAT 57.176 33.333 0.00 0.00 31.94 1.40
5372 9476 7.219484 AGCAGCTCTGTTAATGTGTTAAATT 57.781 32.000 0.00 0.00 31.94 1.82
5373 9477 7.308435 AGCAGCTCTGTTAATGTGTTAAATTC 58.692 34.615 0.00 0.00 31.94 2.17
5769 9874 5.794687 TGCTTCGTGATTTATGTCGAAAT 57.205 34.783 0.00 0.00 40.74 2.17
5783 9888 9.553418 TTTATGTCGAAATTGTGATTGTGTATG 57.447 29.630 0.00 0.00 0.00 2.39
5786 9891 6.651225 TGTCGAAATTGTGATTGTGTATGGTA 59.349 34.615 0.00 0.00 0.00 3.25
5824 9929 1.246056 GCAATCTGCCTGGTGCTTCA 61.246 55.000 0.00 0.00 42.00 3.02
5832 9944 2.012673 GCCTGGTGCTTCATTCTAGTG 58.987 52.381 0.00 0.00 36.87 2.74
5845 9957 4.019771 TCATTCTAGTGTACCATTGTGGCA 60.020 41.667 0.00 0.00 42.67 4.92
5931 10049 9.605275 TGAATGAAAACATTATGGTTGTTGAAA 57.395 25.926 0.00 0.00 37.38 2.69
5934 10052 9.829507 ATGAAAACATTATGGTTGTTGAAAAGA 57.170 25.926 0.00 0.00 37.38 2.52
5935 10053 9.658799 TGAAAACATTATGGTTGTTGAAAAGAA 57.341 25.926 0.00 0.00 37.38 2.52
6024 10144 8.308931 ACTTTGCATGAAAACACATCATTATCT 58.691 29.630 0.00 0.00 35.38 1.98
6029 10149 4.096231 TGAAAACACATCATTATCTGGGCG 59.904 41.667 0.00 0.00 0.00 6.13
6141 10262 6.839124 AATTGTTGATGCTAATGACCTTCA 57.161 33.333 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.756203 TGAGGATATCCACTGGATCTCT 57.244 45.455 23.81 10.03 42.11 3.10
2 3 4.590647 TGTTGAGGATATCCACTGGATCTC 59.409 45.833 23.81 13.52 42.11 2.75
3 4 4.560739 TGTTGAGGATATCCACTGGATCT 58.439 43.478 23.81 4.67 42.11 2.75
4 5 4.963318 TGTTGAGGATATCCACTGGATC 57.037 45.455 23.81 11.49 42.11 3.36
6 7 3.199946 GGTTGTTGAGGATATCCACTGGA 59.800 47.826 23.81 0.00 38.89 3.86
7 8 3.545703 GGTTGTTGAGGATATCCACTGG 58.454 50.000 23.81 0.00 38.89 4.00
8 9 3.054434 TGGGTTGTTGAGGATATCCACTG 60.054 47.826 23.81 0.00 38.89 3.66
9 10 3.189606 TGGGTTGTTGAGGATATCCACT 58.810 45.455 23.81 3.63 38.89 4.00
10 11 3.644966 TGGGTTGTTGAGGATATCCAC 57.355 47.619 23.81 17.83 38.89 4.02
11 12 4.666412 TTTGGGTTGTTGAGGATATCCA 57.334 40.909 23.81 0.58 38.89 3.41
12 13 7.287696 ACATATTTTGGGTTGTTGAGGATATCC 59.712 37.037 14.41 14.41 0.00 2.59
13 14 8.237811 ACATATTTTGGGTTGTTGAGGATATC 57.762 34.615 0.00 0.00 0.00 1.63
14 15 9.131791 GTACATATTTTGGGTTGTTGAGGATAT 57.868 33.333 0.00 0.00 0.00 1.63
15 16 8.333235 AGTACATATTTTGGGTTGTTGAGGATA 58.667 33.333 0.00 0.00 0.00 2.59
16 17 7.182060 AGTACATATTTTGGGTTGTTGAGGAT 58.818 34.615 0.00 0.00 0.00 3.24
17 18 6.548321 AGTACATATTTTGGGTTGTTGAGGA 58.452 36.000 0.00 0.00 0.00 3.71
18 19 6.127730 GGAGTACATATTTTGGGTTGTTGAGG 60.128 42.308 0.00 0.00 0.00 3.86
19 20 6.659242 AGGAGTACATATTTTGGGTTGTTGAG 59.341 38.462 0.00 0.00 0.00 3.02
20 21 6.548321 AGGAGTACATATTTTGGGTTGTTGA 58.452 36.000 0.00 0.00 0.00 3.18
21 22 6.834168 AGGAGTACATATTTTGGGTTGTTG 57.166 37.500 0.00 0.00 0.00 3.33
22 23 6.436218 GGAAGGAGTACATATTTTGGGTTGTT 59.564 38.462 0.00 0.00 0.00 2.83
23 24 5.949952 GGAAGGAGTACATATTTTGGGTTGT 59.050 40.000 0.00 0.00 0.00 3.32
24 25 5.065988 CGGAAGGAGTACATATTTTGGGTTG 59.934 44.000 0.00 0.00 0.00 3.77
25 26 5.190677 CGGAAGGAGTACATATTTTGGGTT 58.809 41.667 0.00 0.00 0.00 4.11
26 27 4.226620 ACGGAAGGAGTACATATTTTGGGT 59.773 41.667 0.00 0.00 0.00 4.51
27 28 4.777463 ACGGAAGGAGTACATATTTTGGG 58.223 43.478 0.00 0.00 0.00 4.12
28 29 4.814771 GGACGGAAGGAGTACATATTTTGG 59.185 45.833 0.00 0.00 0.00 3.28
29 30 4.814771 GGGACGGAAGGAGTACATATTTTG 59.185 45.833 0.00 0.00 0.00 2.44
30 31 4.472108 TGGGACGGAAGGAGTACATATTTT 59.528 41.667 0.00 0.00 0.00 1.82
31 32 4.035112 TGGGACGGAAGGAGTACATATTT 58.965 43.478 0.00 0.00 0.00 1.40
32 33 3.387050 GTGGGACGGAAGGAGTACATATT 59.613 47.826 0.00 0.00 0.00 1.28
33 34 2.963782 GTGGGACGGAAGGAGTACATAT 59.036 50.000 0.00 0.00 0.00 1.78
34 35 2.291735 TGTGGGACGGAAGGAGTACATA 60.292 50.000 0.00 0.00 0.00 2.29
35 36 1.192428 GTGGGACGGAAGGAGTACAT 58.808 55.000 0.00 0.00 0.00 2.29
36 37 0.178955 TGTGGGACGGAAGGAGTACA 60.179 55.000 0.00 0.00 0.00 2.90
37 38 0.971386 TTGTGGGACGGAAGGAGTAC 59.029 55.000 0.00 0.00 0.00 2.73
38 39 1.946984 ATTGTGGGACGGAAGGAGTA 58.053 50.000 0.00 0.00 0.00 2.59
39 40 1.946984 TATTGTGGGACGGAAGGAGT 58.053 50.000 0.00 0.00 0.00 3.85
40 41 3.641906 AGTATATTGTGGGACGGAAGGAG 59.358 47.826 0.00 0.00 0.00 3.69
41 42 3.649843 AGTATATTGTGGGACGGAAGGA 58.350 45.455 0.00 0.00 0.00 3.36
42 43 4.342951 TGTAGTATATTGTGGGACGGAAGG 59.657 45.833 0.00 0.00 0.00 3.46
43 44 5.524971 TGTAGTATATTGTGGGACGGAAG 57.475 43.478 0.00 0.00 0.00 3.46
44 45 5.936187 TTGTAGTATATTGTGGGACGGAA 57.064 39.130 0.00 0.00 0.00 4.30
45 46 7.600231 TTATTGTAGTATATTGTGGGACGGA 57.400 36.000 0.00 0.00 0.00 4.69
46 47 8.145767 TCTTTATTGTAGTATATTGTGGGACGG 58.854 37.037 0.00 0.00 0.00 4.79
47 48 9.706691 ATCTTTATTGTAGTATATTGTGGGACG 57.293 33.333 0.00 0.00 0.00 4.79
91 92 1.600013 CAACGTGTTTCATTGACCGGA 59.400 47.619 9.46 0.00 0.00 5.14
108 109 2.031682 CAGGTGTAAAGTGCAGCTCAAC 60.032 50.000 0.00 0.00 41.99 3.18
145 146 6.894103 AGGATATCCTTTGCATCCATATTTCC 59.106 38.462 19.18 1.79 46.09 3.13
188 194 2.014010 ACGTGTAGGGGAACAAGGTA 57.986 50.000 0.00 0.00 33.76 3.08
207 214 2.188062 ATCTAACAAACCCGGCGAAA 57.812 45.000 9.30 0.00 0.00 3.46
210 217 2.624636 AGTTATCTAACAAACCCGGCG 58.375 47.619 0.00 0.00 38.62 6.46
214 221 6.127814 GGGCTTTGTAGTTATCTAACAAACCC 60.128 42.308 15.46 15.46 38.62 4.11
269 276 2.799017 TGGAGTCTTGTCCTAGCGTAA 58.201 47.619 0.00 0.00 37.52 3.18
277 284 1.797025 CGAGGTTTGGAGTCTTGTCC 58.203 55.000 0.00 0.00 37.10 4.02
278 285 1.149148 GCGAGGTTTGGAGTCTTGTC 58.851 55.000 0.00 0.00 0.00 3.18
282 289 1.899814 TGTATGCGAGGTTTGGAGTCT 59.100 47.619 0.00 0.00 0.00 3.24
283 290 2.380084 TGTATGCGAGGTTTGGAGTC 57.620 50.000 0.00 0.00 0.00 3.36
284 291 3.055094 AGAATGTATGCGAGGTTTGGAGT 60.055 43.478 0.00 0.00 0.00 3.85
293 300 2.540361 GCTGGCAAAGAATGTATGCGAG 60.540 50.000 4.88 4.88 45.23 5.03
295 302 1.534595 GGCTGGCAAAGAATGTATGCG 60.535 52.381 0.00 0.00 40.94 4.73
297 745 3.243636 GGATGGCTGGCAAAGAATGTATG 60.244 47.826 8.35 0.00 0.00 2.39
303 751 1.477553 GATGGATGGCTGGCAAAGAA 58.522 50.000 8.35 0.00 0.00 2.52
332 788 5.612725 TGATGGTAGAGCATTGTGTGATA 57.387 39.130 0.00 0.00 0.00 2.15
355 816 3.665745 AAGCGGAGTGAATTGCAATTT 57.334 38.095 24.81 10.25 0.00 1.82
356 817 3.005684 TGAAAGCGGAGTGAATTGCAATT 59.994 39.130 24.33 24.33 0.00 2.32
362 823 0.517316 GCGTGAAAGCGGAGTGAATT 59.483 50.000 0.00 0.00 0.00 2.17
387 849 2.697431 TTCGTGTAAATTGCTGGTGC 57.303 45.000 0.00 0.00 40.20 5.01
428 890 8.822652 ACTGATGGATTTTGTTTTTCATCTTC 57.177 30.769 0.00 0.00 34.03 2.87
430 892 8.597662 CAACTGATGGATTTTGTTTTTCATCT 57.402 30.769 0.00 0.00 34.03 2.90
459 925 4.216257 GTGACTTCGGTGTACCTACAAGTA 59.784 45.833 8.85 0.00 38.04 2.24
549 1020 0.813610 CACCACTGCGTGTTTGGAGA 60.814 55.000 7.68 0.00 34.24 3.71
577 1048 3.705289 GCCCAACCCAACCCATGC 61.705 66.667 0.00 0.00 0.00 4.06
667 1155 2.906897 GTGTGCAGTGGGGTGGTG 60.907 66.667 0.00 0.00 0.00 4.17
669 1157 1.898574 GAAGTGTGCAGTGGGGTGG 60.899 63.158 0.00 0.00 0.00 4.61
673 1161 1.789078 GCTGTGAAGTGTGCAGTGGG 61.789 60.000 0.00 0.00 33.18 4.61
678 1166 0.755079 AGAGAGCTGTGAAGTGTGCA 59.245 50.000 0.00 0.00 0.00 4.57
686 1174 3.118408 GGTAGAGAGAGAGAGAGCTGTGA 60.118 52.174 0.00 0.00 0.00 3.58
692 1180 2.131854 TGGGGGTAGAGAGAGAGAGAG 58.868 57.143 0.00 0.00 0.00 3.20
693 1181 2.288598 TGGGGGTAGAGAGAGAGAGA 57.711 55.000 0.00 0.00 0.00 3.10
762 1250 5.450453 CAGTAGAGGGTGGAGAGAGAAATA 58.550 45.833 0.00 0.00 0.00 1.40
774 1262 1.379977 TCGGGAGCAGTAGAGGGTG 60.380 63.158 0.00 0.00 0.00 4.61
785 1273 1.676006 CTCTTCTCTCTTCTCGGGAGC 59.324 57.143 0.00 0.00 0.00 4.70
800 1288 3.288092 GGTTCCTCCTCTCTCTCTCTTC 58.712 54.545 0.00 0.00 0.00 2.87
801 1289 2.024369 GGGTTCCTCCTCTCTCTCTCTT 60.024 54.545 0.00 0.00 36.25 2.85
966 1473 0.035056 TCCTCCTTTAAGCAGGCAGC 60.035 55.000 0.00 0.00 46.19 5.25
967 1474 1.407989 CCTCCTCCTTTAAGCAGGCAG 60.408 57.143 0.00 0.00 33.35 4.85
968 1475 0.620556 CCTCCTCCTTTAAGCAGGCA 59.379 55.000 0.00 0.00 33.35 4.75
969 1476 0.912486 TCCTCCTCCTTTAAGCAGGC 59.088 55.000 0.00 0.00 33.35 4.85
970 1477 1.488393 CCTCCTCCTCCTTTAAGCAGG 59.512 57.143 0.00 0.00 34.86 4.85
971 1478 1.488393 CCCTCCTCCTCCTTTAAGCAG 59.512 57.143 0.00 0.00 0.00 4.24
972 1479 1.584724 CCCTCCTCCTCCTTTAAGCA 58.415 55.000 0.00 0.00 0.00 3.91
974 1481 0.466124 CGCCCTCCTCCTCCTTTAAG 59.534 60.000 0.00 0.00 0.00 1.85
975 1482 0.981277 CCGCCCTCCTCCTCCTTTAA 60.981 60.000 0.00 0.00 0.00 1.52
976 1483 1.382695 CCGCCCTCCTCCTCCTTTA 60.383 63.158 0.00 0.00 0.00 1.85
977 1484 2.689034 CCGCCCTCCTCCTCCTTT 60.689 66.667 0.00 0.00 0.00 3.11
978 1485 4.806339 CCCGCCCTCCTCCTCCTT 62.806 72.222 0.00 0.00 0.00 3.36
1095 1609 4.394712 ACGGCCGCCTTCTCCTTG 62.395 66.667 28.58 0.00 0.00 3.61
1484 2001 1.566231 GGGGAGAGGGATGTTGTTCAT 59.434 52.381 0.00 0.00 39.77 2.57
1485 2002 0.991920 GGGGAGAGGGATGTTGTTCA 59.008 55.000 0.00 0.00 0.00 3.18
1516 2033 7.423844 AATTTCAAAACTTTGGGAGAGAAGT 57.576 32.000 2.49 0.00 38.66 3.01
1565 2083 1.679153 GAAACGGCCAAGAACTCCAAA 59.321 47.619 2.24 0.00 0.00 3.28
1568 2086 1.266989 CAAGAAACGGCCAAGAACTCC 59.733 52.381 2.24 0.00 0.00 3.85
1569 2087 1.947456 ACAAGAAACGGCCAAGAACTC 59.053 47.619 2.24 0.00 0.00 3.01
1652 2171 1.306482 TGGAGGAGGGGAGCTGAAG 60.306 63.158 0.00 0.00 0.00 3.02
1698 2223 1.777272 CAGGGGAGGGAAAATAGAGGG 59.223 57.143 0.00 0.00 0.00 4.30
1702 2227 2.853077 AGGAACAGGGGAGGGAAAATAG 59.147 50.000 0.00 0.00 0.00 1.73
1725 2250 3.351740 TGGCTCAAACTTGTGTGAAAGA 58.648 40.909 0.00 0.00 0.00 2.52
1814 2345 1.160137 GCGCATAGCCCTAGAAATGG 58.840 55.000 0.30 0.00 40.81 3.16
1857 2388 3.172229 AGCTCGAGAGGAAAATAGTGC 57.828 47.619 18.75 0.00 0.00 4.40
1871 2402 4.464951 TGGGTAAGATAAGAACAAGCTCGA 59.535 41.667 0.00 0.00 0.00 4.04
1872 2403 4.755411 TGGGTAAGATAAGAACAAGCTCG 58.245 43.478 0.00 0.00 0.00 5.03
1889 2420 0.847373 TTTTGGGCAGACACTGGGTA 59.153 50.000 0.00 0.00 31.21 3.69
1917 5659 5.132897 TGCAGACAAAAACAAGAACACTT 57.867 34.783 0.00 0.00 0.00 3.16
1918 5660 4.782019 TGCAGACAAAAACAAGAACACT 57.218 36.364 0.00 0.00 0.00 3.55
1919 5661 5.608146 GTTTGCAGACAAAAACAAGAACAC 58.392 37.500 1.83 0.00 46.94 3.32
1920 5662 4.384247 CGTTTGCAGACAAAAACAAGAACA 59.616 37.500 8.25 0.00 46.94 3.18
1944 5686 4.512914 GGGAGCACCATGCCTCCC 62.513 72.222 21.35 21.35 46.52 4.30
1986 5734 4.319405 CCCAAAACAAATTGAAATCCGCAC 60.319 41.667 0.00 0.00 31.84 5.34
2032 5780 4.629200 GTGAGCAGAAGTACAAAGGAGATG 59.371 45.833 0.00 0.00 0.00 2.90
2040 5788 9.534565 GATGAATAATAGTGAGCAGAAGTACAA 57.465 33.333 0.00 0.00 0.00 2.41
2062 5810 5.798125 TGGGCAAAAACAAATACTGATGA 57.202 34.783 0.00 0.00 0.00 2.92
2063 5811 7.437793 AAATGGGCAAAAACAAATACTGATG 57.562 32.000 0.00 0.00 0.00 3.07
2064 5812 8.462589 AAAAATGGGCAAAAACAAATACTGAT 57.537 26.923 0.00 0.00 0.00 2.90
2114 5863 7.158697 TCATATACTTGTACTTGCACACAGTT 58.841 34.615 0.00 0.00 0.00 3.16
2153 5902 4.284550 CACCCACACCCACCCCAG 62.285 72.222 0.00 0.00 0.00 4.45
2194 5943 5.780793 TCTCCTATCTCCTAGGTATTTTGCC 59.219 44.000 9.08 0.00 46.38 4.52
2196 5945 9.717942 CATTTCTCCTATCTCCTAGGTATTTTG 57.282 37.037 9.08 0.00 46.38 2.44
2234 5983 5.905331 ACATGGAATCTCTGAGGTATAACCA 59.095 40.000 4.59 6.67 41.95 3.67
2235 5984 6.426646 ACATGGAATCTCTGAGGTATAACC 57.573 41.667 4.59 1.25 38.99 2.85
2238 5987 7.306013 AGGTAACATGGAATCTCTGAGGTATA 58.694 38.462 4.59 0.00 41.41 1.47
2258 6007 0.901827 TGGAGATGCAAGCGAGGTAA 59.098 50.000 0.00 0.00 0.00 2.85
2358 6107 3.553302 CCTCACTGAGCTATCTGCATCTG 60.553 52.174 0.00 0.00 45.94 2.90
2428 6189 4.157840 CCGGGGGAAATAATATTTAGCTGC 59.842 45.833 0.00 0.00 0.00 5.25
2449 6210 6.696411 AGATATAGGCAGAGAGAAAAATCCG 58.304 40.000 0.00 0.00 0.00 4.18
2911 6688 7.114811 CCCAACGTTACAAAAAGATTCATTCAG 59.885 37.037 0.00 0.00 0.00 3.02
2941 6721 1.769026 TCTACTGCTGCTCCTACCAG 58.231 55.000 0.00 0.00 0.00 4.00
2943 6723 3.611766 TTTTCTACTGCTGCTCCTACC 57.388 47.619 0.00 0.00 0.00 3.18
3020 6810 4.319477 CGAATTTAATGGGATACACAGGCG 60.319 45.833 0.00 0.00 39.74 5.52
3052 6842 0.733909 GCATGGAAGCAAGTTTCGCC 60.734 55.000 0.00 0.00 0.00 5.54
3055 6845 2.670509 GCAGAGCATGGAAGCAAGTTTC 60.671 50.000 0.00 0.00 36.85 2.78
3143 6947 7.337942 AGGAAATGAAAATCTGTCATCAGTACC 59.662 37.037 0.00 0.00 41.91 3.34
3185 6996 6.027025 TGCTATTTTCTCTCCTACTAGGGA 57.973 41.667 2.04 0.00 35.59 4.20
3187 6998 6.969993 ACTGCTATTTTCTCTCCTACTAGG 57.030 41.667 0.00 0.00 36.46 3.02
3188 6999 7.308951 GGCTACTGCTATTTTCTCTCCTACTAG 60.309 44.444 0.00 0.00 39.59 2.57
3189 7000 6.490721 GGCTACTGCTATTTTCTCTCCTACTA 59.509 42.308 0.00 0.00 39.59 1.82
3190 7001 5.303333 GGCTACTGCTATTTTCTCTCCTACT 59.697 44.000 0.00 0.00 39.59 2.57
3191 7002 5.069251 TGGCTACTGCTATTTTCTCTCCTAC 59.931 44.000 0.00 0.00 39.59 3.18
3238 7061 6.505700 TCACTAGATCTATCCATCACCCTAGA 59.494 42.308 2.11 0.00 0.00 2.43
3300 7126 2.095053 GCTTTCGAGCACTCATTTCCTC 59.905 50.000 0.00 0.00 34.41 3.71
3365 7191 1.987080 AGAGAAGGGCATAAAGGGGT 58.013 50.000 0.00 0.00 0.00 4.95
3408 7468 4.361451 CTTGTGCATGATTACAAGGGTC 57.639 45.455 20.95 0.00 46.16 4.46
3446 7506 6.847289 GCAAGCATCAACTAACAATTTTTGTG 59.153 34.615 0.00 0.00 44.59 3.33
3606 7689 6.155475 TCATTACACAAGGGGAAAAACAAG 57.845 37.500 0.00 0.00 0.00 3.16
3608 7691 5.205056 ACTCATTACACAAGGGGAAAAACA 58.795 37.500 0.00 0.00 0.00 2.83
3609 7692 5.784578 ACTCATTACACAAGGGGAAAAAC 57.215 39.130 0.00 0.00 0.00 2.43
3711 7796 9.066892 AGTACAACAATGCTGAGAAGATAAAAA 57.933 29.630 0.00 0.00 0.00 1.94
3735 7820 9.820229 CATCGTAAAACACACATGTAAATAAGT 57.180 29.630 0.00 0.00 38.45 2.24
3748 7833 3.628032 TGAACCTTGCATCGTAAAACACA 59.372 39.130 0.00 0.00 0.00 3.72
3749 7834 4.217754 TGAACCTTGCATCGTAAAACAC 57.782 40.909 0.00 0.00 0.00 3.32
3750 7835 3.880490 ACTGAACCTTGCATCGTAAAACA 59.120 39.130 0.00 0.00 0.00 2.83
3758 7844 1.133790 GGCATGACTGAACCTTGCATC 59.866 52.381 0.00 0.00 36.69 3.91
4079 8168 3.648009 GGCGATGAAGAGGATGTAGAAG 58.352 50.000 0.00 0.00 0.00 2.85
4370 8459 2.247790 CCTGTTTGTGAAGAGGCCG 58.752 57.895 0.00 0.00 39.21 6.13
4382 8471 2.282745 GAGCTGCTGGGCCTGTTT 60.283 61.111 7.01 0.00 0.00 2.83
4400 8489 1.378514 GAATGCGGTGGTGGGTGAT 60.379 57.895 0.00 0.00 0.00 3.06
4465 8554 0.844661 TCCAATGGCCTGTGGGTAGT 60.845 55.000 21.07 0.00 35.46 2.73
4481 8570 1.529010 CACTGCCACCAAGCTTCCA 60.529 57.895 0.00 0.00 0.00 3.53
4505 8594 3.181468 TGCACATTGTGGCAAAAGATGAA 60.181 39.130 18.05 0.00 37.03 2.57
4514 8603 1.270274 GTGAAGATGCACATTGTGGCA 59.730 47.619 18.05 15.57 45.23 4.92
4646 8735 1.943046 GCGCGGATGATGATCTGGATT 60.943 52.381 8.83 0.00 35.70 3.01
4922 9011 4.435970 CCAGGGCCAGCAGATGCA 62.436 66.667 6.18 0.00 45.16 3.96
4967 9056 1.077858 GAGGAAGCTGCCCAGGAAG 60.078 63.158 7.30 0.00 0.00 3.46
5012 9101 4.505217 GCGCCGATGTTGCTGACG 62.505 66.667 0.00 0.00 0.00 4.35
5048 9137 1.225704 GTCCTCCATGCCCTTGAGG 59.774 63.158 8.28 8.28 45.77 3.86
5126 9215 3.963525 ATCAATCATACCCTCCCCCTA 57.036 47.619 0.00 0.00 0.00 3.53
5741 9846 5.220472 CGACATAAATCACGAAGCATGACTT 60.220 40.000 0.00 0.00 42.98 3.01
5782 9887 7.103641 TGCACCACAAGTTTTTATTTTTACCA 58.896 30.769 0.00 0.00 0.00 3.25
5783 9888 7.541122 TGCACCACAAGTTTTTATTTTTACC 57.459 32.000 0.00 0.00 0.00 2.85
5786 9891 8.397148 CAGATTGCACCACAAGTTTTTATTTTT 58.603 29.630 0.00 0.00 42.87 1.94
5845 9957 6.964807 TGACAGATTTGCATATATGGCTTT 57.035 33.333 16.92 0.00 0.00 3.51
5927 10045 9.334947 TGCCATATGTTTTCATTTTTCTTTTCA 57.665 25.926 1.24 0.00 41.25 2.69
5931 10049 7.452562 AGGTGCCATATGTTTTCATTTTTCTT 58.547 30.769 1.24 0.00 41.25 2.52
5932 10050 7.008021 AGGTGCCATATGTTTTCATTTTTCT 57.992 32.000 1.24 0.00 41.25 2.52
5933 10051 7.520686 CAAGGTGCCATATGTTTTCATTTTTC 58.479 34.615 1.24 0.00 41.25 2.29
5934 10052 6.072563 GCAAGGTGCCATATGTTTTCATTTTT 60.073 34.615 1.24 0.00 38.34 1.94
5935 10053 5.412286 GCAAGGTGCCATATGTTTTCATTTT 59.588 36.000 1.24 0.00 38.34 1.82
6024 10144 4.526348 ATGGCCATGATGCGCCCA 62.526 61.111 20.04 2.73 45.07 5.36
6029 10149 4.389890 TGTAAGAAAATGGCCATGATGC 57.610 40.909 21.63 10.50 0.00 3.91


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

AutoCloner maintained by Alex Coulton.