Multiple sequence alignment - TraesCS5A01G038500

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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 TraesCS5A01G038500 chr5A 100.000 3962 0 0 1 3962 35654108 35658069 0.000000e+00 7317.0
1 TraesCS5A01G038500 chr5A 88.136 118 12 2 81 197 168126168 168126052 5.340000e-29 139.0
2 TraesCS5A01G038500 chr5A 100.000 40 0 0 3923 3962 35657979 35658018 1.530000e-09 75.0
3 TraesCS5A01G038500 chr5D 95.329 2676 80 14 713 3378 45018256 45020896 0.000000e+00 4207.0
4 TraesCS5A01G038500 chr5D 89.371 461 24 6 3379 3817 45020946 45021403 1.240000e-154 556.0
5 TraesCS5A01G038500 chr5D 77.796 599 99 24 78 660 45016364 45016944 4.900000e-89 339.0
6 TraesCS5A01G038500 chr5D 77.295 599 102 24 78 660 45017666 45018246 4.940000e-84 322.0
7 TraesCS5A01G038500 chr5D 83.889 180 5 6 713 892 45016954 45017109 2.470000e-32 150.0
8 TraesCS5A01G038500 chr5B 90.075 3355 172 56 78 3380 44857810 44861055 0.000000e+00 4202.0
9 TraesCS5A01G038500 chr5B 83.958 480 35 15 3379 3821 44861110 44861584 4.730000e-114 422.0
10 TraesCS5A01G038500 chr5B 97.826 92 2 0 3821 3912 611822829 611822920 4.100000e-35 159.0
11 TraesCS5A01G038500 chr3B 93.750 96 6 0 3817 3912 448774390 448774485 1.150000e-30 145.0
12 TraesCS5A01G038500 chr7B 87.903 124 12 3 77 199 649324162 649324283 4.130000e-30 143.0
13 TraesCS5A01G038500 chr3A 87.903 124 12 3 77 199 432865104 432864983 4.130000e-30 143.0
14 TraesCS5A01G038500 chr2B 88.333 120 12 2 81 199 131196093 131196211 4.130000e-30 143.0
15 TraesCS5A01G038500 chr2A 94.565 92 5 0 3821 3912 75644919 75644828 4.130000e-30 143.0
16 TraesCS5A01G038500 chr2A 100.000 42 0 0 3921 3962 75644870 75644829 1.180000e-10 78.7
17 TraesCS5A01G038500 chr6B 86.029 136 14 4 77 208 296767556 296767422 1.480000e-29 141.0
18 TraesCS5A01G038500 chr6A 92.708 96 7 0 3817 3912 13150751 13150846 5.340000e-29 139.0
19 TraesCS5A01G038500 chr6A 91.667 96 8 0 3817 3912 13092840 13092935 2.480000e-27 134.0
20 TraesCS5A01G038500 chr6A 87.288 118 13 2 83 199 569397702 569397586 2.480000e-27 134.0
21 TraesCS5A01G038500 chr2D 93.548 93 6 0 3820 3912 500490298 500490206 5.340000e-29 139.0
22 TraesCS5A01G038500 chr7A 87.500 120 13 2 81 199 210794936 210795054 1.920000e-28 137.0
23 TraesCS5A01G038500 chr7A 87.500 120 13 2 81 199 216414331 216414213 1.920000e-28 137.0
24 TraesCS5A01G038500 chr4A 87.288 118 15 0 83 200 540351002 540350885 6.910000e-28 135.0
25 TraesCS5A01G038500 chr1B 93.333 90 6 0 3823 3912 349719312 349719223 2.480000e-27 134.0
26 TraesCS5A01G038500 chr3D 91.398 93 8 0 3820 3912 419842285 419842193 1.160000e-25 128.0
27 TraesCS5A01G038500 chr4D 90.323 93 9 0 3820 3912 278249346 278249254 5.380000e-24 122.0


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 TraesCS5A01G038500 chr5A 35654108 35658069 3961 False 3696.0 7317 100.0000 1 3962 2 chr5A.!!$F1 3961
1 TraesCS5A01G038500 chr5D 45016364 45021403 5039 False 1114.8 4207 84.7360 78 3817 5 chr5D.!!$F1 3739
2 TraesCS5A01G038500 chr5B 44857810 44861584 3774 False 2312.0 4202 87.0165 78 3821 2 chr5B.!!$F2 3743

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
358 367 0.248949 GCGTGGTCGAAGATACCCTC 60.249 60.0 0.0 0.0 40.67 4.30 F
359 368 0.384669 CGTGGTCGAAGATACCCTCC 59.615 60.0 0.0 0.0 40.67 4.30 F
501 533 0.388263 GTCACGACCGTCTTCTTCCC 60.388 60.0 0.0 0.0 0.00 3.97 F
1632 2980 0.459899 CCGATTCCGACATCACCTCA 59.540 55.0 0.0 0.0 38.22 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 3277 0.662619 TCGGCAACTTCAGCTTGTTG 59.337 50.0 15.62 15.62 44.33 3.33 R
2091 3439 0.981277 ACTCAACCCCATCCCTACCG 60.981 60.0 0.00 0.00 0.00 4.02 R
2388 3736 0.251922 ATGCCAGTGGTGCCTCAAAT 60.252 50.0 11.74 0.00 0.00 2.32 R
3104 4452 0.808755 GCCATAAACCCGACAACAGG 59.191 55.0 0.00 0.00 0.00 4.00 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
45 46 4.967084 TTGAGGGCAAAAGTGTAGTAGA 57.033 40.909 0.00 0.00 0.00 2.59
46 47 5.499004 TTGAGGGCAAAAGTGTAGTAGAT 57.501 39.130 0.00 0.00 0.00 1.98
47 48 6.614694 TTGAGGGCAAAAGTGTAGTAGATA 57.385 37.500 0.00 0.00 0.00 1.98
48 49 6.808321 TGAGGGCAAAAGTGTAGTAGATAT 57.192 37.500 0.00 0.00 0.00 1.63
49 50 7.195374 TGAGGGCAAAAGTGTAGTAGATATT 57.805 36.000 0.00 0.00 0.00 1.28
50 51 8.313944 TGAGGGCAAAAGTGTAGTAGATATTA 57.686 34.615 0.00 0.00 0.00 0.98
51 52 8.934697 TGAGGGCAAAAGTGTAGTAGATATTAT 58.065 33.333 0.00 0.00 0.00 1.28
52 53 9.780186 GAGGGCAAAAGTGTAGTAGATATTATT 57.220 33.333 0.00 0.00 0.00 1.40
66 67 9.929180 AGTAGATATTATTTGATGTGTATGCGT 57.071 29.630 0.00 0.00 0.00 5.24
73 74 8.887036 TTATTTGATGTGTATGCGTCTATCTT 57.113 30.769 0.00 0.00 0.00 2.40
74 75 7.792374 ATTTGATGTGTATGCGTCTATCTTT 57.208 32.000 0.00 0.00 0.00 2.52
75 76 6.588348 TTGATGTGTATGCGTCTATCTTTG 57.412 37.500 0.00 0.00 0.00 2.77
76 77 5.901552 TGATGTGTATGCGTCTATCTTTGA 58.098 37.500 0.00 0.00 0.00 2.69
90 91 7.273815 CGTCTATCTTTGAAAGGTTACTCTCAC 59.726 40.741 4.94 0.00 0.00 3.51
91 92 8.308207 GTCTATCTTTGAAAGGTTACTCTCACT 58.692 37.037 4.94 0.00 0.00 3.41
99 100 6.720288 TGAAAGGTTACTCTCACTAGTTAGCT 59.280 38.462 0.00 0.00 38.19 3.32
120 121 4.627900 GCTAGTAGCTTGTTTTCTCAGGTC 59.372 45.833 15.16 0.00 38.45 3.85
129 130 4.957296 TGTTTTCTCAGGTCCTACTTCAC 58.043 43.478 0.00 0.00 0.00 3.18
138 139 1.334243 GTCCTACTTCACGGGATCTCG 59.666 57.143 14.88 14.88 0.00 4.04
159 160 4.098960 TCGGATCACATAGGTTGAGTTACC 59.901 45.833 0.00 0.00 38.53 2.85
161 162 5.395324 CGGATCACATAGGTTGAGTTACCTT 60.395 44.000 0.00 0.00 46.39 3.50
206 208 1.145119 ACCCACCTCCCTCAGTTTTTC 59.855 52.381 0.00 0.00 0.00 2.29
207 209 1.425448 CCCACCTCCCTCAGTTTTTCT 59.575 52.381 0.00 0.00 0.00 2.52
208 210 2.553247 CCCACCTCCCTCAGTTTTTCTC 60.553 54.545 0.00 0.00 0.00 2.87
273 277 9.638176 ATTCAGATATTTCAGTTTTATGCCTCT 57.362 29.630 0.00 0.00 0.00 3.69
287 291 0.525668 GCCTCTATCGTCCACGTGTG 60.526 60.000 15.65 6.24 40.80 3.82
298 302 3.201342 CACGTGTGGACAGAAGAGG 57.799 57.895 7.58 0.00 0.00 3.69
299 303 0.673985 CACGTGTGGACAGAAGAGGA 59.326 55.000 7.58 0.00 0.00 3.71
300 304 1.068588 CACGTGTGGACAGAAGAGGAA 59.931 52.381 7.58 0.00 0.00 3.36
301 305 1.068741 ACGTGTGGACAGAAGAGGAAC 59.931 52.381 0.00 0.00 0.00 3.62
302 306 1.605712 CGTGTGGACAGAAGAGGAACC 60.606 57.143 0.00 0.00 0.00 3.62
321 325 1.356938 CCTTCGTTCTTTCGTAGGCC 58.643 55.000 0.00 0.00 40.30 5.19
329 338 0.529992 CTTTCGTAGGCCGGATCACC 60.530 60.000 5.05 0.00 37.11 4.02
330 339 0.974010 TTTCGTAGGCCGGATCACCT 60.974 55.000 5.05 4.19 40.24 4.00
332 341 2.125326 CGTAGGCCGGATCACCTCA 61.125 63.158 5.05 0.00 37.50 3.86
337 346 1.526887 GCCGGATCACCTCATCCAA 59.473 57.895 5.05 0.00 42.50 3.53
356 365 1.588139 CGCGTGGTCGAAGATACCC 60.588 63.158 0.00 0.00 40.67 3.69
358 367 0.248949 GCGTGGTCGAAGATACCCTC 60.249 60.000 0.00 0.00 40.67 4.30
359 368 0.384669 CGTGGTCGAAGATACCCTCC 59.615 60.000 0.00 0.00 40.67 4.30
363 372 1.152610 TCGAAGATACCCTCCCCGG 60.153 63.158 0.00 0.00 0.00 5.73
364 373 1.457079 CGAAGATACCCTCCCCGGT 60.457 63.158 0.00 0.00 40.13 5.28
365 374 1.461911 CGAAGATACCCTCCCCGGTC 61.462 65.000 0.00 0.00 37.34 4.79
366 375 1.457079 AAGATACCCTCCCCGGTCG 60.457 63.158 0.00 0.00 37.34 4.79
394 423 3.418675 CGAAGAGCGGTCTTTGCTA 57.581 52.632 28.85 0.00 43.50 3.49
402 431 1.021390 CGGTCTTTGCTAGGCAGTGG 61.021 60.000 0.00 0.00 40.61 4.00
421 450 1.004745 GGGCCAAAGAGATGACCTTCA 59.995 52.381 4.39 0.00 0.00 3.02
427 456 1.273759 AGAGATGACCTTCAGCTGCA 58.726 50.000 9.47 0.33 44.01 4.41
461 490 2.297701 AGCGGTCTTTGTTCAACACAT 58.702 42.857 0.00 0.00 34.43 3.21
481 510 8.137745 ACACATGAACAAAGAAATTGGGATAT 57.862 30.769 0.00 0.00 43.66 1.63
485 517 7.773489 TGAACAAAGAAATTGGGATATGTCA 57.227 32.000 0.00 0.00 43.66 3.58
501 533 0.388263 GTCACGACCGTCTTCTTCCC 60.388 60.000 0.00 0.00 0.00 3.97
524 560 2.530177 CGACGCTTGCTCATTTCTCTA 58.470 47.619 0.00 0.00 0.00 2.43
528 564 4.367450 ACGCTTGCTCATTTCTCTATCTC 58.633 43.478 0.00 0.00 0.00 2.75
536 572 7.715657 TGCTCATTTCTCTATCTCTCTCTTTC 58.284 38.462 0.00 0.00 0.00 2.62
537 573 7.147976 GCTCATTTCTCTATCTCTCTCTTTCC 58.852 42.308 0.00 0.00 0.00 3.13
544 580 0.811915 TCTCTCTCTTTCCTTCGCGG 59.188 55.000 6.13 0.00 0.00 6.46
545 581 0.528470 CTCTCTCTTTCCTTCGCGGT 59.472 55.000 6.13 0.00 0.00 5.68
586 622 3.372206 CCATTTCGCGACTCAAGATTCTT 59.628 43.478 9.15 0.00 0.00 2.52
588 624 1.350193 TCGCGACTCAAGATTCTTGC 58.650 50.000 19.53 8.28 0.00 4.01
592 628 1.060266 CGACTCAAGATTCTTGCTGCG 59.940 52.381 19.53 16.93 0.00 5.18
594 630 2.344950 ACTCAAGATTCTTGCTGCGAG 58.655 47.619 19.53 10.76 0.00 5.03
612 648 3.751621 CGAGCATCAATTGGTTTCACTC 58.248 45.455 5.42 2.07 35.82 3.51
616 652 4.586001 AGCATCAATTGGTTTCACTCAAGT 59.414 37.500 5.42 0.00 29.87 3.16
682 719 6.662865 TCCATTTTAGGTTGAATTTGCTGA 57.337 33.333 0.00 0.00 0.00 4.26
688 725 8.592105 TTTTAGGTTGAATTTGCTGATTTGAG 57.408 30.769 0.00 0.00 0.00 3.02
689 726 5.796424 AGGTTGAATTTGCTGATTTGAGT 57.204 34.783 0.00 0.00 0.00 3.41
711 768 3.883631 AAACCGTGTTTGTATTCGTCC 57.116 42.857 1.85 0.00 0.00 4.79
722 779 2.494471 TGTATTCGTCCGGTCAATCACT 59.506 45.455 0.00 0.00 0.00 3.41
723 780 2.762535 ATTCGTCCGGTCAATCACTT 57.237 45.000 0.00 0.00 0.00 3.16
724 781 3.880047 ATTCGTCCGGTCAATCACTTA 57.120 42.857 0.00 0.00 0.00 2.24
796 853 4.898265 TCAACAAAATGGGTGGATTTCAGA 59.102 37.500 0.00 0.00 0.00 3.27
911 2250 2.427506 CCAAACTGCTGGTAGTTCTCC 58.572 52.381 4.70 0.00 39.86 3.71
1076 2424 3.797353 CCCCCAGTCCCATCACCG 61.797 72.222 0.00 0.00 0.00 4.94
1078 2426 3.402681 CCCAGTCCCATCACCGCT 61.403 66.667 0.00 0.00 0.00 5.52
1081 2429 4.101448 AGTCCCATCACCGCTGGC 62.101 66.667 0.00 0.00 32.08 4.85
1082 2430 4.408821 GTCCCATCACCGCTGGCA 62.409 66.667 0.00 0.00 32.08 4.92
1104 2452 2.430465 CTGTCCCCTGATTGACAACTG 58.570 52.381 0.00 0.00 40.71 3.16
1113 2461 2.223226 TGATTGACAACTGTGTTGCGTG 60.223 45.455 9.96 0.00 38.41 5.34
1632 2980 0.459899 CCGATTCCGACATCACCTCA 59.540 55.000 0.00 0.00 38.22 3.86
1965 3313 3.316588 TGCCGACAGAGAAGTATGATCTC 59.683 47.826 0.00 0.00 42.95 2.75
1974 3322 6.427853 CAGAGAAGTATGATCTCGATGACTCT 59.572 42.308 0.00 0.00 46.31 3.24
2007 3355 4.389576 GCAAACAGCTGGTCGCCG 62.390 66.667 19.93 2.23 41.15 6.46
2166 3514 1.325640 CTCATGAATGCGGTGAACTCG 59.674 52.381 0.00 0.00 0.00 4.18
2274 3622 5.772672 GTCTCTGGATGGATACTATGAGTGT 59.227 44.000 0.00 0.00 37.61 3.55
2283 3631 7.043961 TGGATACTATGAGTGTGAGAATGAC 57.956 40.000 0.00 0.00 37.61 3.06
2328 3676 1.134995 CGGAACATGCTGCTGAGTCTA 60.135 52.381 0.00 0.00 0.00 2.59
2364 3712 1.674057 CAAGGAGGACAAGCTCCGT 59.326 57.895 0.00 0.00 45.10 4.69
2373 3721 3.626924 AAGCTCCGTCTGGCCGTT 61.627 61.111 0.00 0.00 34.14 4.44
2388 3736 1.684983 GCCGTTACCTACCTGCTATCA 59.315 52.381 0.00 0.00 0.00 2.15
2402 3750 2.025981 TGCTATCATTTGAGGCACCACT 60.026 45.455 6.83 0.00 33.90 4.00
2463 3811 3.119673 AGTCAGAAGTAGACATGTCTGCG 60.120 47.826 33.76 20.72 45.24 5.18
2499 3847 5.470047 AGAGGATAAAGTCGTTGAACACT 57.530 39.130 0.00 0.00 0.00 3.55
2547 3895 1.610522 AGCAGGAGCAACATTGTTGAC 59.389 47.619 29.04 20.86 45.49 3.18
2883 4231 2.242196 GGAGATTCTCAATGGGGTGGAA 59.758 50.000 15.36 0.00 31.08 3.53
2926 4274 1.209504 TGGGACAGAAAGCGGGATTAG 59.790 52.381 0.00 0.00 0.00 1.73
2927 4275 1.475213 GGGACAGAAAGCGGGATTAGG 60.475 57.143 0.00 0.00 0.00 2.69
2928 4276 1.209747 GGACAGAAAGCGGGATTAGGT 59.790 52.381 0.00 0.00 0.00 3.08
2934 4282 2.516225 GCGGGATTAGGTGGTGGC 60.516 66.667 0.00 0.00 0.00 5.01
2955 4303 2.034879 CAGCAGCAACCTACCACCG 61.035 63.158 0.00 0.00 0.00 4.94
2965 4313 3.531934 ACCTACCACCGCAGTAAATAC 57.468 47.619 0.00 0.00 0.00 1.89
3002 4350 3.737559 TTGATGCTAAGGTGGGATTGT 57.262 42.857 0.00 0.00 0.00 2.71
3003 4351 3.737559 TGATGCTAAGGTGGGATTGTT 57.262 42.857 0.00 0.00 0.00 2.83
3004 4352 3.355378 TGATGCTAAGGTGGGATTGTTG 58.645 45.455 0.00 0.00 0.00 3.33
3138 4486 0.889994 ATGGCGCTGCTTTGAATGAA 59.110 45.000 7.64 0.00 0.00 2.57
3184 4533 4.446371 CAGAGTTCAACTGTTCCAGAAGT 58.554 43.478 0.00 0.00 35.18 3.01
3294 4643 4.537751 TGTTTGAACACCCCTACAATCAA 58.462 39.130 0.00 0.00 33.17 2.57
3317 4666 7.890127 TCAATTCATGGAATCTTAGAACACCTT 59.110 33.333 0.00 0.00 30.29 3.50
3325 4674 7.944554 TGGAATCTTAGAACACCTTTTCTGATT 59.055 33.333 0.00 0.00 36.48 2.57
3387 4794 8.102676 TGAATATCAGTCAAATGTTCCTTCTGA 58.897 33.333 0.00 0.00 35.47 3.27
3458 4865 9.989296 TGGCAATAATAATAACATATAGGCCTT 57.011 29.630 12.58 0.81 33.84 4.35
3495 4903 4.521943 CAGAAGCGCATATTACTGAAAGC 58.478 43.478 11.47 0.00 37.60 3.51
3499 4907 2.975851 GCGCATATTACTGAAAGCATGC 59.024 45.455 10.51 10.51 37.60 4.06
3599 5018 7.254590 GCACAATATATCTTGTTCTGTGGAGTC 60.255 40.741 3.85 0.00 37.25 3.36
3611 5033 1.028868 GTGGAGTCAAGGGAGCATGC 61.029 60.000 10.51 10.51 0.00 4.06
3671 5111 9.696917 CATATTTTTAGCTTTGTTTCCAGAACT 57.303 29.630 0.00 0.00 0.00 3.01
3687 5131 6.042777 TCCAGAACTCTATTACGCTGATTTG 58.957 40.000 0.00 0.00 0.00 2.32
3749 5193 2.363306 TGTGCACAACCTCTGGAATT 57.637 45.000 19.28 0.00 0.00 2.17
3777 5222 7.931015 TTCATGGTAGTAAATGAGGGACTAT 57.069 36.000 0.00 0.00 41.55 2.12
3812 5257 4.523558 ACTACGGGGATATCTAACTGAAGC 59.476 45.833 2.05 0.00 0.00 3.86
3821 5266 8.247562 GGGATATCTAACTGAAGCACTACATAG 58.752 40.741 2.05 0.00 0.00 2.23
3822 5267 8.798402 GGATATCTAACTGAAGCACTACATAGT 58.202 37.037 2.05 0.00 36.90 2.12
3831 5276 1.556564 CACTACATAGTGCCCGTTCG 58.443 55.000 6.13 0.00 46.03 3.95
3832 5277 0.458669 ACTACATAGTGCCCGTTCGG 59.541 55.000 4.08 4.08 34.72 4.30
3833 5278 0.742505 CTACATAGTGCCCGTTCGGA 59.257 55.000 13.08 0.00 0.00 4.55
3834 5279 0.742505 TACATAGTGCCCGTTCGGAG 59.257 55.000 13.08 4.30 0.00 4.63
3835 5280 1.883084 CATAGTGCCCGTTCGGAGC 60.883 63.158 13.08 13.87 0.00 4.70
3836 5281 3.090219 ATAGTGCCCGTTCGGAGCC 62.090 63.158 13.08 8.38 0.00 4.70
3852 5297 3.322466 CCCCTCCGCTCCACAACT 61.322 66.667 0.00 0.00 0.00 3.16
3853 5298 2.266055 CCCTCCGCTCCACAACTC 59.734 66.667 0.00 0.00 0.00 3.01
3854 5299 2.286523 CCCTCCGCTCCACAACTCT 61.287 63.158 0.00 0.00 0.00 3.24
3855 5300 1.079543 CCTCCGCTCCACAACTCTG 60.080 63.158 0.00 0.00 0.00 3.35
3856 5301 1.739562 CTCCGCTCCACAACTCTGC 60.740 63.158 0.00 0.00 0.00 4.26
3857 5302 2.743928 CCGCTCCACAACTCTGCC 60.744 66.667 0.00 0.00 0.00 4.85
3858 5303 2.031012 CGCTCCACAACTCTGCCA 59.969 61.111 0.00 0.00 0.00 4.92
3859 5304 2.320587 CGCTCCACAACTCTGCCAC 61.321 63.158 0.00 0.00 0.00 5.01
3860 5305 2.320587 GCTCCACAACTCTGCCACG 61.321 63.158 0.00 0.00 0.00 4.94
3861 5306 1.669115 CTCCACAACTCTGCCACGG 60.669 63.158 0.00 0.00 0.00 4.94
3862 5307 2.099652 CTCCACAACTCTGCCACGGA 62.100 60.000 0.00 0.00 0.00 4.69
3863 5308 1.669115 CCACAACTCTGCCACGGAG 60.669 63.158 1.86 1.86 42.15 4.63
3864 5309 2.031163 ACAACTCTGCCACGGAGC 59.969 61.111 3.33 0.00 40.26 4.70
3865 5310 3.114616 CAACTCTGCCACGGAGCG 61.115 66.667 3.33 0.00 40.26 5.03
3866 5311 4.379243 AACTCTGCCACGGAGCGG 62.379 66.667 3.33 1.55 40.26 5.52
3885 5330 2.964978 GCGGGCTGCAGTTCAAAT 59.035 55.556 16.64 0.00 45.45 2.32
3886 5331 1.290009 GCGGGCTGCAGTTCAAATT 59.710 52.632 16.64 0.00 45.45 1.82
3887 5332 0.319813 GCGGGCTGCAGTTCAAATTT 60.320 50.000 16.64 0.00 45.45 1.82
3888 5333 1.701704 CGGGCTGCAGTTCAAATTTC 58.298 50.000 16.64 0.00 0.00 2.17
3889 5334 1.669795 CGGGCTGCAGTTCAAATTTCC 60.670 52.381 16.64 4.06 0.00 3.13
3890 5335 1.344114 GGGCTGCAGTTCAAATTTCCA 59.656 47.619 16.64 0.00 0.00 3.53
3891 5336 2.611224 GGGCTGCAGTTCAAATTTCCAG 60.611 50.000 16.64 0.00 0.00 3.86
3892 5337 2.297033 GGCTGCAGTTCAAATTTCCAGA 59.703 45.455 16.64 0.00 0.00 3.86
3893 5338 3.572584 GCTGCAGTTCAAATTTCCAGAG 58.427 45.455 16.64 0.00 0.00 3.35
3894 5339 3.572584 CTGCAGTTCAAATTTCCAGAGC 58.427 45.455 5.25 0.00 0.00 4.09
3895 5340 2.030893 TGCAGTTCAAATTTCCAGAGCG 60.031 45.455 0.00 0.00 0.00 5.03
3896 5341 2.669391 GCAGTTCAAATTTCCAGAGCGG 60.669 50.000 0.00 0.00 0.00 5.52
3897 5342 2.554032 CAGTTCAAATTTCCAGAGCGGT 59.446 45.455 0.00 0.00 35.57 5.68
3898 5343 2.554032 AGTTCAAATTTCCAGAGCGGTG 59.446 45.455 0.00 0.00 35.57 4.94
3899 5344 1.533625 TCAAATTTCCAGAGCGGTGG 58.466 50.000 0.00 1.05 39.19 4.61
3900 5345 1.073125 TCAAATTTCCAGAGCGGTGGA 59.927 47.619 6.01 6.01 45.37 4.02
3905 5350 2.516448 TCCAGAGCGGTGGAATAGG 58.484 57.895 7.56 0.00 44.01 2.57
3906 5351 0.325296 TCCAGAGCGGTGGAATAGGT 60.325 55.000 7.56 0.00 44.01 3.08
3907 5352 0.179073 CCAGAGCGGTGGAATAGGTG 60.179 60.000 0.00 0.00 40.44 4.00
3908 5353 0.811616 CAGAGCGGTGGAATAGGTGC 60.812 60.000 0.00 0.00 0.00 5.01
3909 5354 0.978146 AGAGCGGTGGAATAGGTGCT 60.978 55.000 0.00 0.00 34.96 4.40
3910 5355 0.530870 GAGCGGTGGAATAGGTGCTC 60.531 60.000 0.00 0.00 41.57 4.26
3911 5356 1.523938 GCGGTGGAATAGGTGCTCC 60.524 63.158 0.00 0.00 0.00 4.70
3913 5358 0.179073 CGGTGGAATAGGTGCTCCTG 60.179 60.000 17.65 0.00 44.81 3.86
3914 5359 0.464554 GGTGGAATAGGTGCTCCTGC 60.465 60.000 17.65 6.60 44.81 4.85
3915 5360 0.543749 GTGGAATAGGTGCTCCTGCT 59.456 55.000 17.65 3.92 44.81 4.24
3916 5361 0.833287 TGGAATAGGTGCTCCTGCTC 59.167 55.000 17.65 12.46 44.81 4.26
3931 5376 4.711949 CTCCGCCAGGCTGCAGTT 62.712 66.667 16.64 0.77 37.47 3.16
3932 5377 4.704833 TCCGCCAGGCTGCAGTTC 62.705 66.667 16.64 8.32 37.47 3.01
3934 5379 2.979676 CGCCAGGCTGCAGTTCAA 60.980 61.111 16.64 0.00 0.00 2.69
3935 5380 2.554636 CGCCAGGCTGCAGTTCAAA 61.555 57.895 16.64 0.00 0.00 2.69
3936 5381 1.870055 CGCCAGGCTGCAGTTCAAAT 61.870 55.000 16.64 0.00 0.00 2.32
3937 5382 0.319405 GCCAGGCTGCAGTTCAAATT 59.681 50.000 16.64 0.00 0.00 1.82
3938 5383 1.270465 GCCAGGCTGCAGTTCAAATTT 60.270 47.619 16.64 0.00 0.00 1.82
3939 5384 2.680577 CCAGGCTGCAGTTCAAATTTC 58.319 47.619 16.64 0.00 0.00 2.17
3940 5385 2.611224 CCAGGCTGCAGTTCAAATTTCC 60.611 50.000 16.64 4.27 0.00 3.13
3941 5386 2.036217 CAGGCTGCAGTTCAAATTTCCA 59.964 45.455 16.64 0.00 0.00 3.53
3942 5387 2.298163 AGGCTGCAGTTCAAATTTCCAG 59.702 45.455 16.64 0.00 0.00 3.86
3943 5388 2.297033 GGCTGCAGTTCAAATTTCCAGA 59.703 45.455 16.64 0.00 0.00 3.86
3944 5389 3.572584 GCTGCAGTTCAAATTTCCAGAG 58.427 45.455 16.64 0.00 0.00 3.35
3945 5390 3.572584 CTGCAGTTCAAATTTCCAGAGC 58.427 45.455 5.25 0.00 0.00 4.09
3946 5391 2.030893 TGCAGTTCAAATTTCCAGAGCG 60.031 45.455 0.00 0.00 0.00 5.03
3947 5392 2.669391 GCAGTTCAAATTTCCAGAGCGG 60.669 50.000 0.00 0.00 0.00 5.52
3948 5393 2.554032 CAGTTCAAATTTCCAGAGCGGT 59.446 45.455 0.00 0.00 35.57 5.68
3949 5394 2.554032 AGTTCAAATTTCCAGAGCGGTG 59.446 45.455 0.00 0.00 35.57 4.94
3950 5395 1.533625 TCAAATTTCCAGAGCGGTGG 58.466 50.000 0.00 1.05 39.19 4.61
3951 5396 1.073125 TCAAATTTCCAGAGCGGTGGA 59.927 47.619 6.01 6.01 45.37 4.02
3956 5401 2.516448 TCCAGAGCGGTGGAATAGG 58.484 57.895 7.56 0.00 44.01 2.57
3957 5402 0.325296 TCCAGAGCGGTGGAATAGGT 60.325 55.000 7.56 0.00 44.01 3.08
3958 5403 0.179073 CCAGAGCGGTGGAATAGGTG 60.179 60.000 0.00 0.00 40.44 4.00
3959 5404 0.811616 CAGAGCGGTGGAATAGGTGC 60.812 60.000 0.00 0.00 0.00 5.01
3960 5405 0.978146 AGAGCGGTGGAATAGGTGCT 60.978 55.000 0.00 0.00 34.96 4.40
3961 5406 0.530870 GAGCGGTGGAATAGGTGCTC 60.531 60.000 0.00 0.00 41.57 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.686753 TCTACTACACTTTTGCCCTCAAAA 58.313 37.500 3.60 3.60 46.51 2.44
23 24 5.298989 TCTACTACACTTTTGCCCTCAAA 57.701 39.130 0.00 0.00 40.17 2.69
24 25 4.967084 TCTACTACACTTTTGCCCTCAA 57.033 40.909 0.00 0.00 0.00 3.02
25 26 6.808321 ATATCTACTACACTTTTGCCCTCA 57.192 37.500 0.00 0.00 0.00 3.86
26 27 9.780186 AATAATATCTACTACACTTTTGCCCTC 57.220 33.333 0.00 0.00 0.00 4.30
40 41 9.929180 ACGCATACACATCAAATAATATCTACT 57.071 29.630 0.00 0.00 0.00 2.57
47 48 9.494271 AAGATAGACGCATACACATCAAATAAT 57.506 29.630 0.00 0.00 0.00 1.28
48 49 8.887036 AAGATAGACGCATACACATCAAATAA 57.113 30.769 0.00 0.00 0.00 1.40
49 50 8.764287 CAAAGATAGACGCATACACATCAAATA 58.236 33.333 0.00 0.00 0.00 1.40
50 51 7.495606 TCAAAGATAGACGCATACACATCAAAT 59.504 33.333 0.00 0.00 0.00 2.32
51 52 6.816140 TCAAAGATAGACGCATACACATCAAA 59.184 34.615 0.00 0.00 0.00 2.69
52 53 6.337356 TCAAAGATAGACGCATACACATCAA 58.663 36.000 0.00 0.00 0.00 2.57
53 54 5.901552 TCAAAGATAGACGCATACACATCA 58.098 37.500 0.00 0.00 0.00 3.07
54 55 6.828502 TTCAAAGATAGACGCATACACATC 57.171 37.500 0.00 0.00 0.00 3.06
55 56 6.258727 CCTTTCAAAGATAGACGCATACACAT 59.741 38.462 0.00 0.00 0.00 3.21
56 57 5.580691 CCTTTCAAAGATAGACGCATACACA 59.419 40.000 0.00 0.00 0.00 3.72
57 58 5.581085 ACCTTTCAAAGATAGACGCATACAC 59.419 40.000 0.00 0.00 0.00 2.90
58 59 5.730550 ACCTTTCAAAGATAGACGCATACA 58.269 37.500 0.00 0.00 0.00 2.29
59 60 6.663944 AACCTTTCAAAGATAGACGCATAC 57.336 37.500 0.00 0.00 0.00 2.39
60 61 7.553334 AGTAACCTTTCAAAGATAGACGCATA 58.447 34.615 0.00 0.00 0.00 3.14
61 62 6.407202 AGTAACCTTTCAAAGATAGACGCAT 58.593 36.000 0.00 0.00 0.00 4.73
62 63 5.790593 AGTAACCTTTCAAAGATAGACGCA 58.209 37.500 0.00 0.00 0.00 5.24
63 64 6.100668 AGAGTAACCTTTCAAAGATAGACGC 58.899 40.000 0.00 0.00 0.00 5.19
64 65 7.273815 GTGAGAGTAACCTTTCAAAGATAGACG 59.726 40.741 0.00 0.00 33.97 4.18
65 66 8.308207 AGTGAGAGTAACCTTTCAAAGATAGAC 58.692 37.037 0.00 0.00 33.97 2.59
66 67 8.423906 AGTGAGAGTAACCTTTCAAAGATAGA 57.576 34.615 0.00 0.00 33.97 1.98
67 68 9.796120 CTAGTGAGAGTAACCTTTCAAAGATAG 57.204 37.037 0.00 0.00 33.97 2.08
68 69 9.310449 ACTAGTGAGAGTAACCTTTCAAAGATA 57.690 33.333 0.00 0.00 33.97 1.98
69 70 8.196378 ACTAGTGAGAGTAACCTTTCAAAGAT 57.804 34.615 0.00 0.00 33.97 2.40
70 71 7.598759 ACTAGTGAGAGTAACCTTTCAAAGA 57.401 36.000 0.00 0.00 33.97 2.52
71 72 9.413048 CTAACTAGTGAGAGTAACCTTTCAAAG 57.587 37.037 0.12 0.00 33.97 2.77
72 73 7.871463 GCTAACTAGTGAGAGTAACCTTTCAAA 59.129 37.037 11.84 0.00 33.97 2.69
73 74 7.232941 AGCTAACTAGTGAGAGTAACCTTTCAA 59.767 37.037 11.84 0.00 33.97 2.69
74 75 6.720288 AGCTAACTAGTGAGAGTAACCTTTCA 59.280 38.462 11.84 0.00 29.89 2.69
75 76 7.160547 AGCTAACTAGTGAGAGTAACCTTTC 57.839 40.000 11.84 0.00 0.00 2.62
76 77 8.283699 CTAGCTAACTAGTGAGAGTAACCTTT 57.716 38.462 11.84 0.00 40.97 3.11
99 100 4.838986 AGGACCTGAGAAAACAAGCTACTA 59.161 41.667 0.00 0.00 0.00 1.82
114 115 0.406750 TCCCGTGAAGTAGGACCTGA 59.593 55.000 3.53 0.00 0.00 3.86
115 116 1.409427 GATCCCGTGAAGTAGGACCTG 59.591 57.143 3.53 0.00 30.97 4.00
117 118 1.682323 GAGATCCCGTGAAGTAGGACC 59.318 57.143 0.00 0.00 30.97 4.46
118 119 1.334243 CGAGATCCCGTGAAGTAGGAC 59.666 57.143 0.00 0.00 30.97 3.85
120 121 0.669077 CCGAGATCCCGTGAAGTAGG 59.331 60.000 0.00 0.00 0.00 3.18
129 130 1.474478 CCTATGTGATCCGAGATCCCG 59.526 57.143 10.25 0.00 0.00 5.14
159 160 3.157087 ACCCACTTAAGTTGCCATGAAG 58.843 45.455 5.07 0.00 0.00 3.02
160 161 3.153919 GACCCACTTAAGTTGCCATGAA 58.846 45.455 5.07 0.00 0.00 2.57
161 162 2.375174 AGACCCACTTAAGTTGCCATGA 59.625 45.455 5.07 0.00 0.00 3.07
191 192 6.410942 AAAATTGAGAAAAACTGAGGGAGG 57.589 37.500 0.00 0.00 0.00 4.30
269 273 3.624305 CACACGTGGACGATAGAGG 57.376 57.895 21.57 0.00 43.02 3.69
287 291 1.066787 CGAAGGGTTCCTCTTCTGTCC 60.067 57.143 13.75 0.00 38.66 4.02
290 294 2.841442 AACGAAGGGTTCCTCTTCTG 57.159 50.000 13.75 10.97 38.66 3.02
299 303 2.869237 GCCTACGAAAGAACGAAGGGTT 60.869 50.000 0.00 0.00 42.96 4.11
300 304 1.337541 GCCTACGAAAGAACGAAGGGT 60.338 52.381 0.00 0.00 37.03 4.34
301 305 1.356938 GCCTACGAAAGAACGAAGGG 58.643 55.000 0.00 0.00 37.03 3.95
302 306 1.356938 GGCCTACGAAAGAACGAAGG 58.643 55.000 0.00 0.00 37.03 3.46
321 325 1.154205 GCGTTGGATGAGGTGATCCG 61.154 60.000 0.00 0.00 44.52 4.18
337 346 1.138247 GGTATCTTCGACCACGCGT 59.862 57.895 5.58 5.58 39.58 6.01
345 354 1.152610 CCGGGGAGGGTATCTTCGA 60.153 63.158 0.00 0.00 35.97 3.71
348 357 1.457079 CGACCGGGGAGGGTATCTT 60.457 63.158 6.32 0.00 46.96 2.40
384 413 0.678048 CCCACTGCCTAGCAAAGACC 60.678 60.000 0.00 0.00 38.41 3.85
402 431 2.363683 CTGAAGGTCATCTCTTTGGCC 58.636 52.381 0.00 0.00 41.92 5.36
406 435 2.039480 TGCAGCTGAAGGTCATCTCTTT 59.961 45.455 20.43 0.00 0.00 2.52
421 450 1.140589 CTTCGGTCTCGATGCAGCT 59.859 57.895 0.00 0.00 45.51 4.24
427 456 1.433879 CCGCTTCTTCGGTCTCGAT 59.566 57.895 0.00 0.00 45.51 3.59
442 471 2.032799 TCATGTGTTGAACAAAGACCGC 59.967 45.455 0.00 0.00 43.61 5.68
443 472 3.961477 TCATGTGTTGAACAAAGACCG 57.039 42.857 0.00 0.00 43.61 4.79
452 481 6.538021 CCCAATTTCTTTGTTCATGTGTTGAA 59.462 34.615 0.00 0.00 35.91 2.69
461 490 7.574779 CGTGACATATCCCAATTTCTTTGTTCA 60.575 37.037 0.00 0.00 33.15 3.18
472 501 1.760613 ACGGTCGTGACATATCCCAAT 59.239 47.619 2.00 0.00 0.00 3.16
474 503 0.742505 GACGGTCGTGACATATCCCA 59.257 55.000 0.00 0.00 0.00 4.37
481 510 0.313043 GGAAGAAGACGGTCGTGACA 59.687 55.000 0.16 0.00 0.00 3.58
485 517 2.281295 GGGGGAAGAAGACGGTCGT 61.281 63.158 1.89 0.00 0.00 4.34
501 533 1.982073 GAAATGAGCAAGCGTCGGGG 61.982 60.000 0.00 0.00 0.00 5.73
524 560 1.407258 CCGCGAAGGAAAGAGAGAGAT 59.593 52.381 8.23 0.00 45.00 2.75
528 564 1.797025 AAACCGCGAAGGAAAGAGAG 58.203 50.000 8.23 0.00 45.00 3.20
588 624 2.095110 TGAAACCAATTGATGCTCGCAG 60.095 45.455 7.12 0.00 0.00 5.18
592 628 4.771590 TGAGTGAAACCAATTGATGCTC 57.228 40.909 7.12 6.30 37.80 4.26
594 630 4.874970 ACTTGAGTGAAACCAATTGATGC 58.125 39.130 7.12 0.00 37.80 3.91
597 633 7.448161 ACATCATACTTGAGTGAAACCAATTGA 59.552 33.333 7.12 0.00 37.80 2.57
612 648 7.064609 CCAACACTACCTACAACATCATACTTG 59.935 40.741 0.00 0.00 0.00 3.16
616 652 6.127168 CCTCCAACACTACCTACAACATCATA 60.127 42.308 0.00 0.00 0.00 2.15
654 691 6.147656 GCAAATTCAACCTAAAATGGAACCAG 59.852 38.462 0.00 0.00 0.00 4.00
682 719 7.588488 CGAATACAAACACGGTTTAACTCAAAT 59.412 33.333 0.00 0.00 0.00 2.32
688 725 5.139482 GGACGAATACAAACACGGTTTAAC 58.861 41.667 0.00 0.00 0.00 2.01
689 726 4.084641 CGGACGAATACAAACACGGTTTAA 60.085 41.667 0.00 0.00 0.00 1.52
711 768 5.233050 CAGCAGTCTAATAAGTGATTGACCG 59.767 44.000 0.00 0.00 31.34 4.79
722 779 2.225068 GCTCGCCAGCAGTCTAATAA 57.775 50.000 0.00 0.00 46.06 1.40
723 780 3.967886 GCTCGCCAGCAGTCTAATA 57.032 52.632 0.00 0.00 46.06 0.98
724 781 4.844420 GCTCGCCAGCAGTCTAAT 57.156 55.556 0.00 0.00 46.06 1.73
807 864 8.194104 AGCTCCTTTTCTTTCTTTCTTTCTTTC 58.806 33.333 0.00 0.00 0.00 2.62
808 865 8.072321 AGCTCCTTTTCTTTCTTTCTTTCTTT 57.928 30.769 0.00 0.00 0.00 2.52
810 867 7.041712 CGTAGCTCCTTTTCTTTCTTTCTTTCT 60.042 37.037 0.00 0.00 0.00 2.52
811 868 7.041984 TCGTAGCTCCTTTTCTTTCTTTCTTTC 60.042 37.037 0.00 0.00 0.00 2.62
812 869 6.766467 TCGTAGCTCCTTTTCTTTCTTTCTTT 59.234 34.615 0.00 0.00 0.00 2.52
816 2155 4.998033 CCTCGTAGCTCCTTTTCTTTCTTT 59.002 41.667 0.00 0.00 0.00 2.52
823 2162 1.646189 CAGCCTCGTAGCTCCTTTTC 58.354 55.000 0.00 0.00 42.61 2.29
828 2167 2.801631 ATGGCAGCCTCGTAGCTCC 61.802 63.158 14.15 5.35 42.61 4.70
911 2250 0.533032 GGGAAGTCGGGAACAGAGAG 59.467 60.000 0.00 0.00 0.00 3.20
1064 2412 4.101448 GCCAGCGGTGATGGGACT 62.101 66.667 17.83 0.00 39.79 3.85
1066 2414 4.100084 CTGCCAGCGGTGATGGGA 62.100 66.667 17.83 0.00 39.79 4.37
1078 2426 2.233566 AATCAGGGGACAGCTGCCA 61.234 57.895 23.05 8.03 0.00 4.92
1081 2429 0.325933 TGTCAATCAGGGGACAGCTG 59.674 55.000 13.48 13.48 39.00 4.24
1082 2430 1.067295 TTGTCAATCAGGGGACAGCT 58.933 50.000 0.00 0.00 44.12 4.24
1104 2452 0.792640 CTGGATCAGACACGCAACAC 59.207 55.000 0.00 0.00 32.44 3.32
1206 2554 3.738281 CGTCCATCACCAGGATCTTGTAC 60.738 52.174 3.93 0.00 37.52 2.90
1632 2980 4.104417 GCGACTGCCTCGACGAGT 62.104 66.667 22.61 5.63 46.14 4.18
1929 3277 0.662619 TCGGCAACTTCAGCTTGTTG 59.337 50.000 15.62 15.62 44.33 3.33
1965 3313 2.679837 CCAAAATGGGTCAGAGTCATCG 59.320 50.000 0.00 0.00 32.67 3.84
2007 3355 1.574702 CCTCGGCCACTTTCGGAAAC 61.575 60.000 2.24 0.00 0.00 2.78
2013 3361 2.032620 TCTATCTCCTCGGCCACTTTC 58.967 52.381 2.24 0.00 0.00 2.62
2085 3433 4.235762 CCATCCCTACCGCCACCG 62.236 72.222 0.00 0.00 0.00 4.94
2091 3439 0.981277 ACTCAACCCCATCCCTACCG 60.981 60.000 0.00 0.00 0.00 4.02
2095 3443 1.455822 TCAAACTCAACCCCATCCCT 58.544 50.000 0.00 0.00 0.00 4.20
2274 3622 3.317603 TTCACGAGCATGTCATTCTCA 57.682 42.857 12.18 0.00 0.00 3.27
2283 3631 2.349580 CACAGTACCATTCACGAGCATG 59.650 50.000 0.00 0.00 0.00 4.06
2328 3676 1.920835 GGTGCCCTTCCCTCTGAGT 60.921 63.158 3.66 0.00 0.00 3.41
2364 3712 1.610554 GCAGGTAGGTAACGGCCAGA 61.611 60.000 2.24 0.00 46.39 3.86
2373 3721 4.040461 GCCTCAAATGATAGCAGGTAGGTA 59.960 45.833 4.13 0.00 34.18 3.08
2388 3736 0.251922 ATGCCAGTGGTGCCTCAAAT 60.252 50.000 11.74 0.00 0.00 2.32
2402 3750 1.612462 CCTGCTCAAGTTCAGATGCCA 60.612 52.381 0.00 0.00 32.26 4.92
2463 3811 7.331791 ACTTTATCCTCTTCACATACTGGAAC 58.668 38.462 0.00 0.00 0.00 3.62
2547 3895 1.363744 CGTAAAGCTTCTCTGCCCAG 58.636 55.000 0.00 0.00 0.00 4.45
2695 4043 2.511600 GGCCCGTGGATCGAACAG 60.512 66.667 0.00 0.00 42.86 3.16
2883 4231 2.910199 TCTGCGAGCTGCTGAATAAAT 58.090 42.857 7.01 0.00 46.94 1.40
2934 4282 3.127533 GGTAGGTTGCTGCTGCCG 61.128 66.667 13.47 0.00 38.71 5.69
2955 4303 4.679662 TCTGGTAAGAGCGTATTTACTGC 58.320 43.478 5.51 0.00 31.92 4.40
2965 4313 4.728882 GCATCAAAACATCTGGTAAGAGCG 60.729 45.833 0.00 0.00 35.37 5.03
3002 4350 1.677576 CTGCAACCTGTGAAGCTTCAA 59.322 47.619 29.99 18.36 39.21 2.69
3003 4351 1.311859 CTGCAACCTGTGAAGCTTCA 58.688 50.000 25.16 25.16 34.20 3.02
3004 4352 1.312815 ACTGCAACCTGTGAAGCTTC 58.687 50.000 19.89 19.89 36.11 3.86
3104 4452 0.808755 GCCATAAACCCGACAACAGG 59.191 55.000 0.00 0.00 0.00 4.00
3184 4533 8.631797 CATACATGGACATTTCAACATATTGGA 58.368 33.333 0.00 0.00 36.39 3.53
3294 4643 8.655935 AAAAGGTGTTCTAAGATTCCATGAAT 57.344 30.769 0.00 0.00 34.71 2.57
3387 4794 3.966979 TGGTGAACCATGCATATTGTCT 58.033 40.909 0.00 0.00 42.01 3.41
3440 4847 7.922382 AGCACTGAAGGCCTATATGTTATTAT 58.078 34.615 5.16 0.00 0.00 1.28
3444 4851 6.463897 GGTTAGCACTGAAGGCCTATATGTTA 60.464 42.308 5.16 2.03 0.00 2.41
3445 4852 5.368989 GTTAGCACTGAAGGCCTATATGTT 58.631 41.667 5.16 3.10 0.00 2.71
3446 4853 4.202367 GGTTAGCACTGAAGGCCTATATGT 60.202 45.833 5.16 0.00 0.00 2.29
3490 4897 5.107133 ACTAATTCATTGCTGCATGCTTTC 58.893 37.500 20.33 8.27 43.37 2.62
3495 4903 4.772046 GCAACTAATTCATTGCTGCATG 57.228 40.909 15.82 4.47 46.21 4.06
3517 4925 5.358160 GCTGTTAATGCCTTTCTATTCAGGT 59.642 40.000 0.00 0.00 32.06 4.00
3634 5056 9.858247 CAAAGCTAAAAATATGCAGCAAATATG 57.142 29.630 0.00 0.00 36.47 1.78
3635 5057 9.603921 ACAAAGCTAAAAATATGCAGCAAATAT 57.396 25.926 0.00 0.00 36.47 1.28
3749 5193 7.054124 GTCCCTCATTTACTACCATGAATTGA 58.946 38.462 0.00 0.00 0.00 2.57
3835 5280 3.316573 GAGTTGTGGAGCGGAGGGG 62.317 68.421 0.00 0.00 0.00 4.79
3836 5281 2.266055 GAGTTGTGGAGCGGAGGG 59.734 66.667 0.00 0.00 0.00 4.30
3837 5282 1.079543 CAGAGTTGTGGAGCGGAGG 60.080 63.158 0.00 0.00 0.00 4.30
3838 5283 1.739562 GCAGAGTTGTGGAGCGGAG 60.740 63.158 0.00 0.00 0.00 4.63
3839 5284 2.343758 GCAGAGTTGTGGAGCGGA 59.656 61.111 0.00 0.00 0.00 5.54
3840 5285 2.743928 GGCAGAGTTGTGGAGCGG 60.744 66.667 0.00 0.00 0.00 5.52
3841 5286 2.031012 TGGCAGAGTTGTGGAGCG 59.969 61.111 0.00 0.00 0.00 5.03
3842 5287 2.320587 CGTGGCAGAGTTGTGGAGC 61.321 63.158 0.00 0.00 0.00 4.70
3843 5288 1.669115 CCGTGGCAGAGTTGTGGAG 60.669 63.158 0.00 0.00 0.00 3.86
3844 5289 2.099652 CTCCGTGGCAGAGTTGTGGA 62.100 60.000 0.00 0.00 0.00 4.02
3845 5290 1.669115 CTCCGTGGCAGAGTTGTGG 60.669 63.158 0.00 0.00 0.00 4.17
3846 5291 2.320587 GCTCCGTGGCAGAGTTGTG 61.321 63.158 5.74 0.00 33.69 3.33
3847 5292 2.031163 GCTCCGTGGCAGAGTTGT 59.969 61.111 5.74 0.00 33.69 3.32
3848 5293 3.114616 CGCTCCGTGGCAGAGTTG 61.115 66.667 5.74 0.00 33.69 3.16
3849 5294 4.379243 CCGCTCCGTGGCAGAGTT 62.379 66.667 5.74 0.00 33.69 3.01
3851 5296 4.504916 CTCCGCTCCGTGGCAGAG 62.505 72.222 0.00 0.00 32.51 3.35
3865 5310 4.704833 TGAACTGCAGCCCGCTCC 62.705 66.667 15.27 0.00 43.06 4.70
3866 5311 1.589716 ATTTGAACTGCAGCCCGCTC 61.590 55.000 15.27 3.58 43.06 5.03
3867 5312 1.181098 AATTTGAACTGCAGCCCGCT 61.181 50.000 15.27 0.00 43.06 5.52
3868 5313 0.319813 AAATTTGAACTGCAGCCCGC 60.320 50.000 15.27 0.88 42.89 6.13
3869 5314 1.669795 GGAAATTTGAACTGCAGCCCG 60.670 52.381 15.27 0.00 0.00 6.13
3870 5315 1.344114 TGGAAATTTGAACTGCAGCCC 59.656 47.619 15.27 6.29 0.00 5.19
3871 5316 2.297033 TCTGGAAATTTGAACTGCAGCC 59.703 45.455 15.27 6.70 0.00 4.85
3872 5317 3.572584 CTCTGGAAATTTGAACTGCAGC 58.427 45.455 15.27 0.00 0.00 5.25
3873 5318 3.572584 GCTCTGGAAATTTGAACTGCAG 58.427 45.455 13.48 13.48 0.00 4.41
3874 5319 2.030893 CGCTCTGGAAATTTGAACTGCA 60.031 45.455 0.00 0.00 0.00 4.41
3875 5320 2.589014 CGCTCTGGAAATTTGAACTGC 58.411 47.619 0.00 0.00 0.00 4.40
3876 5321 2.554032 ACCGCTCTGGAAATTTGAACTG 59.446 45.455 0.00 0.00 42.00 3.16
3877 5322 2.554032 CACCGCTCTGGAAATTTGAACT 59.446 45.455 0.00 0.00 42.00 3.01
3878 5323 2.351738 CCACCGCTCTGGAAATTTGAAC 60.352 50.000 0.00 0.00 42.00 3.18
3879 5324 1.885887 CCACCGCTCTGGAAATTTGAA 59.114 47.619 0.00 0.00 42.00 2.69
3880 5325 1.073125 TCCACCGCTCTGGAAATTTGA 59.927 47.619 0.00 0.00 42.00 2.69
3881 5326 1.533625 TCCACCGCTCTGGAAATTTG 58.466 50.000 0.00 0.00 42.00 2.32
3882 5327 2.286365 TTCCACCGCTCTGGAAATTT 57.714 45.000 9.03 0.00 45.61 1.82
3887 5332 0.325296 ACCTATTCCACCGCTCTGGA 60.325 55.000 0.00 0.00 42.00 3.86
3888 5333 0.179073 CACCTATTCCACCGCTCTGG 60.179 60.000 0.00 0.00 46.41 3.86
3889 5334 0.811616 GCACCTATTCCACCGCTCTG 60.812 60.000 0.00 0.00 0.00 3.35
3890 5335 0.978146 AGCACCTATTCCACCGCTCT 60.978 55.000 0.00 0.00 0.00 4.09
3891 5336 0.530870 GAGCACCTATTCCACCGCTC 60.531 60.000 0.00 0.00 39.10 5.03
3892 5337 1.522569 GAGCACCTATTCCACCGCT 59.477 57.895 0.00 0.00 0.00 5.52
3893 5338 1.523938 GGAGCACCTATTCCACCGC 60.524 63.158 0.00 0.00 33.55 5.68
3894 5339 0.179073 CAGGAGCACCTATTCCACCG 60.179 60.000 1.02 0.00 45.94 4.94
3895 5340 0.464554 GCAGGAGCACCTATTCCACC 60.465 60.000 1.02 0.00 45.94 4.61
3896 5341 0.543749 AGCAGGAGCACCTATTCCAC 59.456 55.000 1.02 0.00 45.94 4.02
3897 5342 0.833287 GAGCAGGAGCACCTATTCCA 59.167 55.000 1.02 0.00 45.94 3.53
3898 5343 0.107643 GGAGCAGGAGCACCTATTCC 59.892 60.000 13.80 13.80 46.56 3.01
3899 5344 3.696306 GGAGCAGGAGCACCTATTC 57.304 57.895 1.02 3.53 46.56 1.75
3914 5359 4.711949 AACTGCAGCCTGGCGGAG 62.712 66.667 23.18 22.90 42.91 4.63
3915 5360 4.704833 GAACTGCAGCCTGGCGGA 62.705 66.667 23.18 13.14 42.91 5.54
3917 5362 1.870055 ATTTGAACTGCAGCCTGGCG 61.870 55.000 15.27 9.54 36.28 5.69
3918 5363 0.319405 AATTTGAACTGCAGCCTGGC 59.681 50.000 15.27 11.65 0.00 4.85
3919 5364 2.611224 GGAAATTTGAACTGCAGCCTGG 60.611 50.000 15.27 0.00 0.00 4.45
3920 5365 2.036217 TGGAAATTTGAACTGCAGCCTG 59.964 45.455 15.27 0.00 0.00 4.85
3921 5366 2.298163 CTGGAAATTTGAACTGCAGCCT 59.702 45.455 15.27 0.00 0.00 4.58
3922 5367 2.297033 TCTGGAAATTTGAACTGCAGCC 59.703 45.455 15.27 6.70 0.00 4.85
3923 5368 3.572584 CTCTGGAAATTTGAACTGCAGC 58.427 45.455 15.27 0.00 0.00 5.25
3924 5369 3.572584 GCTCTGGAAATTTGAACTGCAG 58.427 45.455 13.48 13.48 0.00 4.41
3925 5370 2.030893 CGCTCTGGAAATTTGAACTGCA 60.031 45.455 0.00 0.00 0.00 4.41
3926 5371 2.589014 CGCTCTGGAAATTTGAACTGC 58.411 47.619 0.00 0.00 0.00 4.40
3927 5372 2.554032 ACCGCTCTGGAAATTTGAACTG 59.446 45.455 0.00 0.00 42.00 3.16
3928 5373 2.554032 CACCGCTCTGGAAATTTGAACT 59.446 45.455 0.00 0.00 42.00 3.01
3929 5374 2.351738 CCACCGCTCTGGAAATTTGAAC 60.352 50.000 0.00 0.00 42.00 3.18
3930 5375 1.885887 CCACCGCTCTGGAAATTTGAA 59.114 47.619 0.00 0.00 42.00 2.69
3931 5376 1.073125 TCCACCGCTCTGGAAATTTGA 59.927 47.619 0.00 0.00 42.00 2.69
3932 5377 1.533625 TCCACCGCTCTGGAAATTTG 58.466 50.000 0.00 0.00 42.00 2.32
3933 5378 2.286365 TTCCACCGCTCTGGAAATTT 57.714 45.000 9.03 0.00 45.61 1.82
3938 5383 0.325296 ACCTATTCCACCGCTCTGGA 60.325 55.000 0.00 0.00 42.00 3.86
3939 5384 0.179073 CACCTATTCCACCGCTCTGG 60.179 60.000 0.00 0.00 46.41 3.86
3940 5385 0.811616 GCACCTATTCCACCGCTCTG 60.812 60.000 0.00 0.00 0.00 3.35
3941 5386 0.978146 AGCACCTATTCCACCGCTCT 60.978 55.000 0.00 0.00 0.00 4.09
3942 5387 0.530870 GAGCACCTATTCCACCGCTC 60.531 60.000 0.00 0.00 39.10 5.03
3943 5388 1.522569 GAGCACCTATTCCACCGCT 59.477 57.895 0.00 0.00 0.00 5.52
3944 5389 4.126524 GAGCACCTATTCCACCGC 57.873 61.111 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.