Multiple sequence alignment - TraesCS5B01G201700

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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 TraesCS5B01G201700 chr5B 100.000 6560 0 0 1 6560 366004466 366011025 0.000000e+00 12115.0
1 TraesCS5B01G201700 chr5B 99.793 483 1 0 343 825 214106794 214106312 0.000000e+00 887.0
2 TraesCS5B01G201700 chr5B 99.723 361 1 0 1 361 214107167 214106807 0.000000e+00 662.0
3 TraesCS5B01G201700 chr5D 94.985 3071 76 28 3094 6097 316243485 316246544 0.000000e+00 4747.0
4 TraesCS5B01G201700 chr5D 94.016 2189 85 23 823 2990 316241330 316243493 0.000000e+00 3275.0
5 TraesCS5B01G201700 chr5D 90.212 378 25 4 6084 6456 316246493 316246863 3.560000e-132 483.0
6 TraesCS5B01G201700 chr5A 93.986 2145 49 25 3094 5168 410801215 410803349 0.000000e+00 3173.0
7 TraesCS5B01G201700 chr5A 92.207 1835 85 23 825 2647 410798831 410800619 0.000000e+00 2543.0
8 TraesCS5B01G201700 chr5A 96.107 899 26 5 5206 6097 410803350 410804246 0.000000e+00 1458.0
9 TraesCS5B01G201700 chr5A 97.661 342 8 0 2649 2990 410800882 410801223 7.330000e-164 588.0
10 TraesCS5B01G201700 chr5A 86.053 337 25 7 6211 6547 410804434 410804748 6.300000e-90 342.0
11 TraesCS5B01G201700 chr5A 90.000 110 3 1 6104 6213 410804220 410804321 1.150000e-27 135.0
12 TraesCS5B01G201700 chr3A 96.328 817 0 1 1 787 19965921 19966737 0.000000e+00 1315.0
13 TraesCS5B01G201700 chr3A 99.793 482 1 0 343 824 19966897 19967378 0.000000e+00 885.0
14 TraesCS5B01G201700 chr3A 99.791 479 1 0 345 823 19967389 19967867 0.000000e+00 880.0
15 TraesCS5B01G201700 chr3A 100.000 206 0 0 1 206 19965377 19965582 1.330000e-101 381.0
16 TraesCS5B01G201700 chr3A 92.473 186 13 1 641 825 19965257 19965072 1.400000e-66 265.0
17 TraesCS5B01G201700 chr3A 100.000 137 0 0 225 361 19966748 19966884 3.040000e-63 254.0
18 TraesCS5B01G201700 chr4B 99.793 482 1 0 343 824 123919745 123919264 0.000000e+00 885.0
19 TraesCS5B01G201700 chr4B 100.000 361 0 0 1 361 123920118 123919758 0.000000e+00 667.0
20 TraesCS5B01G201700 chr4B 84.946 279 32 6 551 823 95086679 95086405 2.330000e-69 274.0
21 TraesCS5B01G201700 chr4B 91.848 184 14 1 641 823 123920238 123920421 8.440000e-64 255.0
22 TraesCS5B01G201700 chr4A 99.472 379 2 0 450 828 729826950 729827328 0.000000e+00 689.0
23 TraesCS5B01G201700 chr4A 100.000 360 0 0 1 360 729826534 729826893 0.000000e+00 665.0
24 TraesCS5B01G201700 chr4A 100.000 50 0 0 343 392 729826903 729826952 7.000000e-15 93.5


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 TraesCS5B01G201700 chr5B 366004466 366011025 6559 False 12115.000000 12115 100.0000 1 6560 1 chr5B.!!$F1 6559
1 TraesCS5B01G201700 chr5B 214106312 214107167 855 True 774.500000 887 99.7580 1 825 2 chr5B.!!$R1 824
2 TraesCS5B01G201700 chr5D 316241330 316246863 5533 False 2835.000000 4747 93.0710 823 6456 3 chr5D.!!$F1 5633
3 TraesCS5B01G201700 chr5A 410798831 410804748 5917 False 1373.166667 3173 92.6690 825 6547 6 chr5A.!!$F1 5722
4 TraesCS5B01G201700 chr3A 19965377 19967867 2490 False 743.000000 1315 99.1824 1 824 5 chr3A.!!$F1 823
5 TraesCS5B01G201700 chr4B 123919264 123920118 854 True 776.000000 885 99.8965 1 824 2 chr4B.!!$R2 823
6 TraesCS5B01G201700 chr4A 729826534 729827328 794 False 482.500000 689 99.8240 1 828 3 chr4A.!!$F1 827

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
454 1637 0.676782 AAACCTGTACGGCCAGATGC 60.677 55.0 2.24 0.00 34.23 3.91 F
1180 2378 0.315568 GCGAGATTAGCCGGTCTCAT 59.684 55.0 17.25 6.47 40.65 2.90 F
2006 3210 0.467844 ACAGTCTTTGCACATGGGCA 60.468 50.0 21.25 21.25 43.19 5.36 F
2823 4294 0.106819 GGGCTCAGCATCTGACCAAT 60.107 55.0 0.00 0.00 35.39 3.16 F
3088 4559 0.395173 AAGGTGCCTGTTTTGACGGT 60.395 50.0 0.00 0.00 0.00 4.83 F
4773 6301 0.383949 TGCTGTCCGCCAAAAAGAAC 59.616 50.0 0.00 0.00 38.05 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1469 2672 0.617413 ATCAGTCCACTTGGCTCCAG 59.383 55.000 0.00 0.00 34.44 3.86 R
2707 4178 0.252197 AACACATAGGAGGGCCGAAC 59.748 55.000 0.00 0.00 39.96 3.95 R
3069 4540 0.395173 ACCGTCAAAACAGGCACCTT 60.395 50.000 0.00 0.00 0.00 3.50 R
3952 5438 1.704628 TGTGATGGTGTCCTGGAACAT 59.295 47.619 0.00 3.62 38.20 2.71 R
4906 6446 0.527600 GCACAGCATACGATGGTCGA 60.528 55.000 6.34 0.00 43.74 4.20 R
6482 8155 0.388649 GTGCACCACGTTCTCTCGAT 60.389 55.000 5.22 0.00 34.70 3.59 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
454 1637 0.676782 AAACCTGTACGGCCAGATGC 60.677 55.000 2.24 0.00 34.23 3.91
1129 2316 3.138128 CCCCGTTTCAATCCCGCC 61.138 66.667 0.00 0.00 0.00 6.13
1134 2321 1.402325 CCGTTTCAATCCCGCCTTTTC 60.402 52.381 0.00 0.00 0.00 2.29
1138 2325 0.404040 TCAATCCCGCCTTTTCTGGT 59.596 50.000 0.00 0.00 0.00 4.00
1140 2327 0.676782 AATCCCGCCTTTTCTGGTCG 60.677 55.000 0.00 0.00 0.00 4.79
1142 2329 3.431725 CCGCCTTTTCTGGTCGGC 61.432 66.667 0.00 0.00 38.89 5.54
1144 2331 2.358247 GCCTTTTCTGGTCGGCGA 60.358 61.111 4.99 4.99 32.22 5.54
1145 2332 1.745489 GCCTTTTCTGGTCGGCGAT 60.745 57.895 14.79 0.00 32.22 4.58
1146 2333 1.305930 GCCTTTTCTGGTCGGCGATT 61.306 55.000 14.79 0.00 32.22 3.34
1147 2334 2.010043 GCCTTTTCTGGTCGGCGATTA 61.010 52.381 14.79 4.17 32.22 1.75
1148 2335 1.933853 CCTTTTCTGGTCGGCGATTAG 59.066 52.381 14.79 14.72 0.00 1.73
1151 2338 0.974010 TTCTGGTCGGCGATTAGGGT 60.974 55.000 14.79 0.00 0.00 4.34
1152 2339 1.067582 CTGGTCGGCGATTAGGGTC 59.932 63.158 14.79 0.00 0.00 4.46
1153 2340 1.672854 CTGGTCGGCGATTAGGGTCA 61.673 60.000 14.79 2.76 0.00 4.02
1154 2341 1.067582 GGTCGGCGATTAGGGTCAG 59.932 63.158 14.79 0.00 0.00 3.51
1180 2378 0.315568 GCGAGATTAGCCGGTCTCAT 59.684 55.000 17.25 6.47 40.65 2.90
1186 2384 1.557099 TTAGCCGGTCTCATGTGAGT 58.443 50.000 1.90 0.00 42.60 3.41
1188 2386 0.687354 AGCCGGTCTCATGTGAGTTT 59.313 50.000 1.90 0.00 42.60 2.66
1208 2406 2.705821 CGAGCTGGAGGAACGCTCT 61.706 63.158 0.00 0.00 45.95 4.09
1275 2473 1.304052 TGGTCAAAAGGGATGCCGG 60.304 57.895 0.00 0.00 0.00 6.13
1288 2486 2.203351 GCCGGCCCCCTAGATTTG 60.203 66.667 18.11 0.00 0.00 2.32
1306 2504 7.789273 AGATTTGTTTTGCATGTGAAATTGA 57.211 28.000 0.00 0.00 0.00 2.57
1307 2505 8.211116 AGATTTGTTTTGCATGTGAAATTGAA 57.789 26.923 0.00 0.00 0.00 2.69
1308 2506 8.339714 AGATTTGTTTTGCATGTGAAATTGAAG 58.660 29.630 0.00 0.00 0.00 3.02
1337 2540 8.642935 TCTGGTTGATGTGGATTTGTTATTAA 57.357 30.769 0.00 0.00 0.00 1.40
1357 2560 4.428615 AAGAGACTTTAGAGCGTCAGAC 57.571 45.455 0.00 0.00 32.68 3.51
1392 2595 3.433740 GGAGGTTAGAATGGACCATGGTC 60.434 52.174 33.14 33.14 43.87 4.02
1393 2596 2.170607 AGGTTAGAATGGACCATGGTCG 59.829 50.000 33.24 2.15 45.41 4.79
1394 2597 2.561569 GTTAGAATGGACCATGGTCGG 58.438 52.381 33.24 1.60 45.41 4.79
1396 2599 0.914417 AGAATGGACCATGGTCGGGT 60.914 55.000 33.24 22.26 45.41 5.28
1413 2616 1.153549 GTCTCGGGTGAGTGATGGC 60.154 63.158 0.00 0.00 43.09 4.40
1469 2672 6.992063 TCTTGACCTGCTCTGAATTTAATC 57.008 37.500 0.00 0.00 0.00 1.75
1672 2875 7.240897 TGATCTTAGGCAATATTTATGGGCTT 58.759 34.615 6.37 0.00 39.26 4.35
1726 2929 5.479716 TTCTTTTTGACGAGAAACCTGTC 57.520 39.130 0.00 0.00 0.00 3.51
1828 3031 8.402472 AGTAATTTCGACACAAAGATTCACAAA 58.598 29.630 0.00 0.00 0.00 2.83
1924 3127 9.995003 CTTGAATTACTTCTCTAGCCTGAATAT 57.005 33.333 0.00 0.00 32.29 1.28
1952 3155 5.125739 ACAAAGTCCGTTAAAATCAACCACA 59.874 36.000 0.00 0.00 0.00 4.17
2006 3210 0.467844 ACAGTCTTTGCACATGGGCA 60.468 50.000 21.25 21.25 43.19 5.36
2011 3215 3.465218 TTTGCACATGGGCAGGGGT 62.465 57.895 23.95 0.00 45.88 4.95
2053 3257 1.202582 AGAGGATCCGTTGTCTTGTCG 59.797 52.381 5.98 0.00 33.66 4.35
2121 3325 1.346068 GGAGCTGAAGTGAAGTCCTGT 59.654 52.381 0.00 0.00 0.00 4.00
2197 3401 1.414158 AACCCCACATCTCGATCGAT 58.586 50.000 19.78 0.94 0.00 3.59
2270 3474 2.289002 GGCTGATTTTGTCTCCGCTATG 59.711 50.000 0.00 0.00 0.00 2.23
2281 3485 2.094182 TCTCCGCTATGACCAAGACAAC 60.094 50.000 0.00 0.00 0.00 3.32
2282 3486 1.621317 TCCGCTATGACCAAGACAACA 59.379 47.619 0.00 0.00 0.00 3.33
2295 3499 0.526739 GACAACAAACAACGGCACCC 60.527 55.000 0.00 0.00 0.00 4.61
2306 3510 8.322828 ACAAACAACGGCACCCATATATATATA 58.677 33.333 4.90 4.92 0.00 0.86
2308 3512 9.914834 AAACAACGGCACCCATATATATATATT 57.085 29.630 11.83 0.00 0.00 1.28
2504 3711 3.914771 TCCCTTCCATTCATGATTTCCC 58.085 45.455 0.00 0.00 0.00 3.97
2523 3730 2.282180 CCCTCAACCACCCCAACG 60.282 66.667 0.00 0.00 0.00 4.10
2533 3740 1.038130 CACCCCAACGGTTTCCAACA 61.038 55.000 0.00 0.00 45.36 3.33
2576 3783 5.823209 TTGTGTCTTCATGCATTGATAGG 57.177 39.130 0.00 0.00 33.34 2.57
2603 3810 4.382147 GGAAAGTTGTGTACAAGGCCAAAA 60.382 41.667 5.01 0.00 36.39 2.44
2629 3836 3.292460 GCCAGACCTGAGAGTATACAGT 58.708 50.000 5.50 0.00 32.93 3.55
2634 3841 1.269309 CCTGAGAGTATACAGTGCCGC 60.269 57.143 5.50 0.00 32.93 6.53
2647 3854 4.858680 GCCGCACCCCTAAGAGCC 62.859 72.222 0.00 0.00 0.00 4.70
2707 4178 1.079543 CTCTCGCCCAGAGTTGTGG 60.080 63.158 0.00 0.00 46.86 4.17
2798 4269 6.418057 AAGGCTCAGGATCTCATAGTAAAG 57.582 41.667 0.00 0.00 0.00 1.85
2823 4294 0.106819 GGGCTCAGCATCTGACCAAT 60.107 55.000 0.00 0.00 35.39 3.16
2892 4363 4.806247 GCCATAGTAGTTTCTGTAGCAGTG 59.194 45.833 0.00 0.00 32.61 3.66
2990 4461 2.299297 GTTGCGCTCCCTAGTACCATAT 59.701 50.000 9.73 0.00 0.00 1.78
2993 4464 3.699538 TGCGCTCCCTAGTACCATATATG 59.300 47.826 9.73 5.68 0.00 1.78
2994 4465 3.700038 GCGCTCCCTAGTACCATATATGT 59.300 47.826 11.73 3.03 0.00 2.29
2995 4466 4.885907 GCGCTCCCTAGTACCATATATGTA 59.114 45.833 11.73 2.14 0.00 2.29
2996 4467 5.221009 GCGCTCCCTAGTACCATATATGTAC 60.221 48.000 11.73 12.69 0.00 2.90
2997 4468 5.884232 CGCTCCCTAGTACCATATATGTACA 59.116 44.000 19.04 0.00 0.00 2.90
2998 4469 6.376299 CGCTCCCTAGTACCATATATGTACAA 59.624 42.308 19.04 0.00 0.00 2.41
2999 4470 7.094075 CGCTCCCTAGTACCATATATGTACAAA 60.094 40.741 19.04 10.94 0.00 2.83
3000 4471 8.759782 GCTCCCTAGTACCATATATGTACAAAT 58.240 37.037 19.04 0.00 0.00 2.32
3025 4496 7.753309 AACAATTGTATGTACTTTACCAGCA 57.247 32.000 12.39 0.00 32.02 4.41
3026 4497 7.753309 ACAATTGTATGTACTTTACCAGCAA 57.247 32.000 9.97 0.00 0.00 3.91
3027 4498 8.348285 ACAATTGTATGTACTTTACCAGCAAT 57.652 30.769 9.97 0.00 0.00 3.56
3028 4499 8.802267 ACAATTGTATGTACTTTACCAGCAATT 58.198 29.630 9.97 0.00 35.01 2.32
3029 4500 9.075519 CAATTGTATGTACTTTACCAGCAATTG 57.924 33.333 0.00 0.00 39.80 2.32
3030 4501 7.753309 TTGTATGTACTTTACCAGCAATTGT 57.247 32.000 7.40 0.00 0.00 2.71
3031 4502 7.139896 TGTATGTACTTTACCAGCAATTGTG 57.860 36.000 7.40 4.35 0.00 3.33
3032 4503 6.712998 TGTATGTACTTTACCAGCAATTGTGT 59.287 34.615 7.40 5.11 0.00 3.72
3033 4504 7.878644 TGTATGTACTTTACCAGCAATTGTGTA 59.121 33.333 7.40 4.15 0.00 2.90
3034 4505 6.795098 TGTACTTTACCAGCAATTGTGTAG 57.205 37.500 7.40 1.20 0.00 2.74
3035 4506 6.292923 TGTACTTTACCAGCAATTGTGTAGT 58.707 36.000 7.40 6.47 0.00 2.73
3036 4507 7.443477 TGTACTTTACCAGCAATTGTGTAGTA 58.557 34.615 7.40 5.64 0.00 1.82
3037 4508 7.932491 TGTACTTTACCAGCAATTGTGTAGTAA 59.068 33.333 7.40 7.65 0.00 2.24
3038 4509 7.996098 ACTTTACCAGCAATTGTGTAGTAAT 57.004 32.000 7.40 0.00 0.00 1.89
3040 4511 9.681062 ACTTTACCAGCAATTGTGTAGTAATAT 57.319 29.630 7.40 0.64 0.00 1.28
3041 4512 9.935682 CTTTACCAGCAATTGTGTAGTAATATG 57.064 33.333 7.40 2.15 0.00 1.78
3042 4513 6.377327 ACCAGCAATTGTGTAGTAATATGC 57.623 37.500 7.40 0.00 0.00 3.14
3043 4514 5.885352 ACCAGCAATTGTGTAGTAATATGCA 59.115 36.000 7.40 0.00 35.11 3.96
3044 4515 6.183360 ACCAGCAATTGTGTAGTAATATGCAC 60.183 38.462 7.40 0.00 36.46 4.57
3045 4516 6.038603 CCAGCAATTGTGTAGTAATATGCACT 59.961 38.462 7.40 0.00 36.81 4.40
3046 4517 7.415541 CCAGCAATTGTGTAGTAATATGCACTT 60.416 37.037 7.40 0.00 36.81 3.16
3047 4518 7.970061 CAGCAATTGTGTAGTAATATGCACTTT 59.030 33.333 7.40 0.00 36.81 2.66
3048 4519 9.173021 AGCAATTGTGTAGTAATATGCACTTTA 57.827 29.630 7.40 0.00 36.81 1.85
3049 4520 9.438291 GCAATTGTGTAGTAATATGCACTTTAG 57.562 33.333 7.40 0.00 36.81 1.85
3052 4523 8.487313 TTGTGTAGTAATATGCACTTTAGTGG 57.513 34.615 11.55 0.00 45.72 4.00
3053 4524 6.537301 TGTGTAGTAATATGCACTTTAGTGGC 59.463 38.462 11.55 5.02 45.72 5.01
3054 4525 6.537301 GTGTAGTAATATGCACTTTAGTGGCA 59.463 38.462 11.55 9.91 45.72 4.92
3055 4526 7.065324 GTGTAGTAATATGCACTTTAGTGGCAA 59.935 37.037 11.55 3.20 45.72 4.52
3056 4527 7.608376 TGTAGTAATATGCACTTTAGTGGCAAA 59.392 33.333 11.55 0.00 45.72 3.68
3057 4528 6.852664 AGTAATATGCACTTTAGTGGCAAAC 58.147 36.000 11.55 7.65 45.72 2.93
3058 4529 5.720371 AATATGCACTTTAGTGGCAAACA 57.280 34.783 11.55 1.51 45.72 2.83
3059 4530 5.920193 ATATGCACTTTAGTGGCAAACAT 57.080 34.783 11.55 8.16 45.72 2.71
3060 4531 3.367992 TGCACTTTAGTGGCAAACATG 57.632 42.857 11.55 0.00 45.72 3.21
3061 4532 2.692557 TGCACTTTAGTGGCAAACATGT 59.307 40.909 11.55 0.00 45.72 3.21
3062 4533 3.052036 GCACTTTAGTGGCAAACATGTG 58.948 45.455 11.55 0.00 45.72 3.21
3063 4534 3.052036 CACTTTAGTGGCAAACATGTGC 58.948 45.455 0.00 0.00 42.10 4.57
3064 4535 2.692557 ACTTTAGTGGCAAACATGTGCA 59.307 40.909 10.16 0.00 46.81 4.57
3065 4536 3.321682 ACTTTAGTGGCAAACATGTGCAT 59.678 39.130 10.16 0.00 46.81 3.96
3066 4537 3.300852 TTAGTGGCAAACATGTGCATG 57.699 42.857 10.16 10.31 46.81 4.06
3076 4547 2.282701 CATGTGCATGTTAAGGTGCC 57.717 50.000 8.95 2.90 40.56 5.01
3077 4548 1.820519 CATGTGCATGTTAAGGTGCCT 59.179 47.619 8.95 0.00 40.56 4.75
3078 4549 1.246649 TGTGCATGTTAAGGTGCCTG 58.753 50.000 8.95 0.00 40.56 4.85
3079 4550 1.247567 GTGCATGTTAAGGTGCCTGT 58.752 50.000 8.95 0.00 40.56 4.00
3080 4551 1.613437 GTGCATGTTAAGGTGCCTGTT 59.387 47.619 8.95 0.00 40.56 3.16
3081 4552 2.035832 GTGCATGTTAAGGTGCCTGTTT 59.964 45.455 8.95 0.00 40.56 2.83
3082 4553 2.697751 TGCATGTTAAGGTGCCTGTTTT 59.302 40.909 8.95 0.00 40.56 2.43
3083 4554 3.059166 GCATGTTAAGGTGCCTGTTTTG 58.941 45.455 0.00 0.00 35.35 2.44
3084 4555 3.243704 GCATGTTAAGGTGCCTGTTTTGA 60.244 43.478 0.00 0.00 35.35 2.69
3085 4556 4.298332 CATGTTAAGGTGCCTGTTTTGAC 58.702 43.478 0.00 0.00 0.00 3.18
3086 4557 2.356382 TGTTAAGGTGCCTGTTTTGACG 59.644 45.455 0.00 0.00 0.00 4.35
3087 4558 1.600023 TAAGGTGCCTGTTTTGACGG 58.400 50.000 0.00 0.00 0.00 4.79
3088 4559 0.395173 AAGGTGCCTGTTTTGACGGT 60.395 50.000 0.00 0.00 0.00 4.83
3089 4560 0.470766 AGGTGCCTGTTTTGACGGTA 59.529 50.000 0.00 0.00 0.00 4.02
3090 4561 1.073284 AGGTGCCTGTTTTGACGGTAT 59.927 47.619 0.00 0.00 0.00 2.73
3091 4562 1.199097 GGTGCCTGTTTTGACGGTATG 59.801 52.381 0.00 0.00 0.00 2.39
3092 4563 2.147958 GTGCCTGTTTTGACGGTATGA 58.852 47.619 0.00 0.00 0.00 2.15
3093 4564 2.550606 GTGCCTGTTTTGACGGTATGAA 59.449 45.455 0.00 0.00 0.00 2.57
3094 4565 2.811431 TGCCTGTTTTGACGGTATGAAG 59.189 45.455 0.00 0.00 0.00 3.02
3095 4566 2.812011 GCCTGTTTTGACGGTATGAAGT 59.188 45.455 0.00 0.00 0.00 3.01
3096 4567 3.998341 GCCTGTTTTGACGGTATGAAGTA 59.002 43.478 0.00 0.00 0.00 2.24
3097 4568 4.142966 GCCTGTTTTGACGGTATGAAGTAC 60.143 45.833 0.00 0.00 0.00 2.73
3098 4569 4.992319 CCTGTTTTGACGGTATGAAGTACA 59.008 41.667 0.00 0.00 34.87 2.90
3099 4570 5.642063 CCTGTTTTGACGGTATGAAGTACAT 59.358 40.000 0.00 0.00 42.39 2.29
3100 4571 6.183360 CCTGTTTTGACGGTATGAAGTACATC 60.183 42.308 0.00 0.00 40.07 3.06
3101 4572 5.640357 TGTTTTGACGGTATGAAGTACATCC 59.360 40.000 0.00 0.00 40.07 3.51
3102 4573 5.408880 TTTGACGGTATGAAGTACATCCA 57.591 39.130 0.00 0.00 40.07 3.41
3103 4574 5.607939 TTGACGGTATGAAGTACATCCAT 57.392 39.130 0.00 0.00 40.07 3.41
3167 4651 6.849588 ACGGTTTATCGAACTTAAGTTTGT 57.150 33.333 27.38 19.37 39.75 2.83
3187 4671 2.279935 TTTCTGCGGTACCACCAATT 57.720 45.000 13.54 0.00 38.47 2.32
3198 4682 6.448006 CGGTACCACCAATTTTATTGTTTCA 58.552 36.000 13.54 0.00 38.47 2.69
3274 4758 3.106827 TCCTGATGGCTGTGATCAAGTA 58.893 45.455 0.00 0.00 29.44 2.24
3700 5186 9.257651 GCTTAATTAATCGTACCAGTATTCACT 57.742 33.333 0.00 0.00 34.42 3.41
3749 5235 9.591792 AGGTTAGTTCTATATTTGTTAACCGAC 57.408 33.333 2.48 0.00 41.96 4.79
3826 5312 4.680407 AGATATGGGTATACGGCTAACCA 58.320 43.478 5.83 5.83 42.56 3.67
3851 5337 6.422333 TGTGGTATATGATTCCAGAAAGCAA 58.578 36.000 0.00 0.00 36.73 3.91
4112 5598 2.430248 TCTGATGCATGGCAGTTGAT 57.570 45.000 2.46 0.00 43.65 2.57
4234 5726 4.870426 ACTAGTGAAATGCTGTTGATACCG 59.130 41.667 0.00 0.00 0.00 4.02
4246 5738 6.183360 TGCTGTTGATACCGTTTTGTACTTTT 60.183 34.615 0.00 0.00 0.00 2.27
4292 5784 1.279846 TGATCTGCTGCATGGTCTTCA 59.720 47.619 1.31 0.00 0.00 3.02
4315 5834 7.428020 TCATTACAGTTTAGACACGTTGTACT 58.572 34.615 0.00 0.00 0.00 2.73
4625 6153 0.533032 GGTGCTCTCCTGGAGTGTAC 59.467 60.000 28.00 28.00 43.62 2.90
4762 6290 1.663379 TATCTCACCCGTGCTGTCCG 61.663 60.000 0.00 0.00 0.00 4.79
4773 6301 0.383949 TGCTGTCCGCCAAAAAGAAC 59.616 50.000 0.00 0.00 38.05 3.01
4890 6430 6.952773 AGTTGCCACACTATTGTTTCTTAA 57.047 33.333 0.00 0.00 31.66 1.85
4903 6443 7.816945 ATTGTTTCTTAATTTCTGATTGGCG 57.183 32.000 0.00 0.00 0.00 5.69
4904 6444 5.160641 TGTTTCTTAATTTCTGATTGGCGC 58.839 37.500 0.00 0.00 0.00 6.53
4905 6445 5.160641 GTTTCTTAATTTCTGATTGGCGCA 58.839 37.500 10.83 0.00 0.00 6.09
4906 6446 5.581126 TTCTTAATTTCTGATTGGCGCAT 57.419 34.783 10.83 0.00 0.00 4.73
4907 6447 5.173774 TCTTAATTTCTGATTGGCGCATC 57.826 39.130 10.83 5.07 0.00 3.91
4908 6448 2.480224 AATTTCTGATTGGCGCATCG 57.520 45.000 10.83 1.69 0.00 3.84
4909 6449 1.667236 ATTTCTGATTGGCGCATCGA 58.333 45.000 10.83 4.11 0.00 3.59
5118 6659 4.939052 ATAATCCGTAACTGTGCTAGCT 57.061 40.909 17.23 0.00 0.00 3.32
5128 6669 6.020599 CGTAACTGTGCTAGCTGTATTTAGTG 60.021 42.308 17.23 0.31 0.00 2.74
5291 6832 4.124851 TCAGGACCTCGCTTCTATTTTC 57.875 45.455 0.00 0.00 0.00 2.29
5316 6857 8.865090 TCTTTATCTCTGACTCTGTTCTCTTTT 58.135 33.333 0.00 0.00 0.00 2.27
5317 6858 8.824159 TTTATCTCTGACTCTGTTCTCTTTTG 57.176 34.615 0.00 0.00 0.00 2.44
5529 7070 0.104120 CATCAGGCGGTTATCGGACA 59.896 55.000 0.00 0.00 39.69 4.02
5587 7128 3.111853 TCACTGGTGCTACTGTCTTTG 57.888 47.619 0.00 0.00 0.00 2.77
5625 7166 7.226441 ACATATTAAGATGGCAGTGCTCATAA 58.774 34.615 16.11 9.51 0.00 1.90
5680 7222 0.107654 AGGCTATGTTTCCTCACCGC 60.108 55.000 0.00 0.00 0.00 5.68
5685 7227 0.108585 ATGTTTCCTCACCGCACACT 59.891 50.000 0.00 0.00 0.00 3.55
5695 7237 1.735920 CCGCACACTCTGCTCTGTC 60.736 63.158 0.00 0.00 44.64 3.51
6065 7613 2.290960 GCCAAGTAACAGGATCCTGGTT 60.291 50.000 38.54 30.31 41.95 3.67
6066 7614 3.054655 GCCAAGTAACAGGATCCTGGTTA 60.055 47.826 38.54 29.45 41.95 2.85
6067 7615 4.514401 CCAAGTAACAGGATCCTGGTTAC 58.486 47.826 38.54 35.22 41.95 2.50
6068 7616 4.181578 CAAGTAACAGGATCCTGGTTACG 58.818 47.826 38.54 25.52 41.95 3.18
6069 7617 3.438183 AGTAACAGGATCCTGGTTACGT 58.562 45.455 38.54 26.35 41.95 3.57
6070 7618 4.603131 AGTAACAGGATCCTGGTTACGTA 58.397 43.478 38.54 19.67 41.95 3.57
6071 7619 5.018809 AGTAACAGGATCCTGGTTACGTAA 58.981 41.667 38.54 18.94 41.95 3.18
6072 7620 4.895668 AACAGGATCCTGGTTACGTAAA 57.104 40.909 38.54 0.00 41.95 2.01
6073 7621 5.231702 AACAGGATCCTGGTTACGTAAAA 57.768 39.130 38.54 0.56 41.95 1.52
6074 7622 5.623169 AACAGGATCCTGGTTACGTAAAAA 58.377 37.500 38.54 0.18 41.95 1.94
6097 7645 6.449830 AAAAGGTACTAACAGGATCCTTGT 57.550 37.500 13.00 11.20 38.49 3.16
6214 7767 6.097554 ACCTCTGGTACTGAATTCTGATACAG 59.902 42.308 18.13 18.49 35.46 2.74
6215 7768 6.322456 CCTCTGGTACTGAATTCTGATACAGA 59.678 42.308 18.13 20.79 35.75 3.41
6216 7769 7.015098 CCTCTGGTACTGAATTCTGATACAGAT 59.985 40.741 23.08 6.43 36.74 2.90
6217 7770 7.720442 TCTGGTACTGAATTCTGATACAGATG 58.280 38.462 18.13 8.38 35.30 2.90
6327 8000 0.319555 ACGTGTCGATGGTGTTCTGG 60.320 55.000 0.00 0.00 0.00 3.86
6328 8001 0.038618 CGTGTCGATGGTGTTCTGGA 60.039 55.000 0.00 0.00 0.00 3.86
6329 8002 1.404181 CGTGTCGATGGTGTTCTGGAT 60.404 52.381 0.00 0.00 0.00 3.41
6330 8003 2.699954 GTGTCGATGGTGTTCTGGATT 58.300 47.619 0.00 0.00 0.00 3.01
6331 8004 2.416547 GTGTCGATGGTGTTCTGGATTG 59.583 50.000 0.00 0.00 0.00 2.67
6373 8046 4.951094 AGTATTAGACCCTGGATATCTCGC 59.049 45.833 2.05 0.00 0.00 5.03
6377 8050 2.126307 CCTGGATATCTCGCCGCG 60.126 66.667 6.39 6.39 0.00 6.46
6399 8072 0.243365 CCTTGGCTAACGCAATGCAA 59.757 50.000 5.91 0.00 38.10 4.08
6404 8077 1.470890 GGCTAACGCAATGCAAACCTA 59.529 47.619 5.91 0.00 38.10 3.08
6406 8079 2.769376 CTAACGCAATGCAAACCTACG 58.231 47.619 5.91 0.00 0.00 3.51
6438 8111 0.528033 TTTTTGTCGTCGAGGCGTCA 60.528 50.000 7.26 0.00 0.00 4.35
6442 8115 1.081641 GTCGTCGAGGCGTCAGAAA 60.082 57.895 7.26 0.00 0.00 2.52
6444 8117 1.801913 CGTCGAGGCGTCAGAAAGG 60.802 63.158 7.26 0.00 0.00 3.11
6447 8120 0.391597 TCGAGGCGTCAGAAAGGTTT 59.608 50.000 7.26 0.00 0.00 3.27
6448 8121 0.512952 CGAGGCGTCAGAAAGGTTTG 59.487 55.000 7.26 0.00 0.00 2.93
6464 8137 4.950050 AGGTTTGCCTTGATACTATCGAG 58.050 43.478 6.38 6.38 44.18 4.04
6465 8138 3.495001 GGTTTGCCTTGATACTATCGAGC 59.505 47.826 7.58 3.65 39.10 5.03
6466 8139 4.119862 GTTTGCCTTGATACTATCGAGCA 58.880 43.478 7.58 5.81 39.10 4.26
6467 8140 4.607293 TTGCCTTGATACTATCGAGCAT 57.393 40.909 7.58 0.00 39.10 3.79
6468 8141 4.179926 TGCCTTGATACTATCGAGCATC 57.820 45.455 7.58 0.00 39.10 3.91
6504 8177 1.512926 GAGAGAACGTGGTGCACATT 58.487 50.000 20.43 6.88 33.40 2.71
6507 8180 1.601903 GAGAACGTGGTGCACATTGAA 59.398 47.619 20.43 0.00 33.40 2.69
6511 8184 0.040157 CGTGGTGCACATTGAAGTGG 60.040 55.000 20.43 0.00 39.87 4.00
6522 8195 2.067932 TTGAAGTGGGCTGTGGAGGG 62.068 60.000 0.00 0.00 0.00 4.30
6530 8203 1.374252 GCTGTGGAGGGTACACACG 60.374 63.158 0.00 0.00 43.35 4.49
6533 8206 1.374252 GTGGAGGGTACACACGCAG 60.374 63.158 0.00 0.00 39.99 5.18
6543 8216 0.657840 ACACACGCAGAAGAGTTTGC 59.342 50.000 0.00 0.00 36.97 3.68
6544 8217 0.657312 CACACGCAGAAGAGTTTGCA 59.343 50.000 0.00 0.00 40.28 4.08
6545 8218 0.657840 ACACGCAGAAGAGTTTGCAC 59.342 50.000 0.00 0.00 40.28 4.57
6546 8219 0.657312 CACGCAGAAGAGTTTGCACA 59.343 50.000 0.00 0.00 40.28 4.57
6547 8220 1.063912 CACGCAGAAGAGTTTGCACAA 59.936 47.619 0.00 0.00 40.28 3.33
6548 8221 1.949525 ACGCAGAAGAGTTTGCACAAT 59.050 42.857 0.00 0.00 40.28 2.71
6549 8222 2.287188 ACGCAGAAGAGTTTGCACAATG 60.287 45.455 0.00 0.00 40.28 2.82
6550 8223 2.287188 CGCAGAAGAGTTTGCACAATGT 60.287 45.455 0.00 0.00 40.28 2.71
6551 8224 3.709987 GCAGAAGAGTTTGCACAATGTT 58.290 40.909 0.00 0.00 40.02 2.71
6552 8225 3.732721 GCAGAAGAGTTTGCACAATGTTC 59.267 43.478 2.31 2.31 40.02 3.18
6553 8226 4.734402 GCAGAAGAGTTTGCACAATGTTCA 60.734 41.667 11.94 0.00 40.02 3.18
6554 8227 4.974275 CAGAAGAGTTTGCACAATGTTCAG 59.026 41.667 11.94 1.22 0.00 3.02
6555 8228 4.641989 AGAAGAGTTTGCACAATGTTCAGT 59.358 37.500 11.94 0.00 0.00 3.41
6556 8229 4.989279 AGAGTTTGCACAATGTTCAGTT 57.011 36.364 0.00 0.00 0.00 3.16
6557 8230 4.675510 AGAGTTTGCACAATGTTCAGTTG 58.324 39.130 0.00 0.00 0.00 3.16
6558 8231 3.784338 AGTTTGCACAATGTTCAGTTGG 58.216 40.909 0.00 0.00 0.00 3.77
6559 8232 2.865551 GTTTGCACAATGTTCAGTTGGG 59.134 45.455 0.00 0.00 33.15 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1116 2303 2.352715 CCAGAAAAGGCGGGATTGAAAC 60.353 50.000 0.00 0.00 0.00 2.78
1129 2316 1.933853 CCTAATCGCCGACCAGAAAAG 59.066 52.381 0.00 0.00 0.00 2.27
1134 2321 1.067582 GACCCTAATCGCCGACCAG 59.932 63.158 0.00 0.00 0.00 4.00
1138 2325 2.792947 GGCTGACCCTAATCGCCGA 61.793 63.158 0.00 0.00 31.75 5.54
1140 2327 2.280186 CGGCTGACCCTAATCGCC 60.280 66.667 0.00 0.00 35.94 5.54
1142 2329 4.732106 GTCGGCTGACCCTAATCG 57.268 61.111 15.20 0.00 39.30 3.34
1151 2338 2.060004 CTAATCTCGCGGTCGGCTGA 62.060 60.000 6.13 0.00 40.44 4.26
1152 2339 1.658717 CTAATCTCGCGGTCGGCTG 60.659 63.158 6.13 0.00 40.44 4.85
1153 2340 2.722487 CTAATCTCGCGGTCGGCT 59.278 61.111 6.13 0.00 40.44 5.52
1154 2341 3.030882 GCTAATCTCGCGGTCGGC 61.031 66.667 6.13 0.00 36.13 5.54
1180 2378 1.272490 CCTCCAGCTCGTAAACTCACA 59.728 52.381 0.00 0.00 0.00 3.58
1186 2384 0.389426 GCGTTCCTCCAGCTCGTAAA 60.389 55.000 0.00 0.00 0.00 2.01
1188 2386 1.654954 GAGCGTTCCTCCAGCTCGTA 61.655 60.000 0.81 0.00 46.14 3.43
1208 2406 4.919774 TGGGAACAGCAATTTCTACCTA 57.080 40.909 0.00 0.00 35.01 3.08
1275 2473 1.899142 TGCAAAACAAATCTAGGGGGC 59.101 47.619 0.00 0.00 0.00 5.80
1280 2478 8.980610 TCAATTTCACATGCAAAACAAATCTAG 58.019 29.630 0.00 0.00 0.00 2.43
1288 2486 8.553696 AGAATTCTTCAATTTCACATGCAAAAC 58.446 29.630 0.88 0.00 31.94 2.43
1306 2504 6.268387 ACAAATCCACATCAACCAGAATTCTT 59.732 34.615 4.86 0.00 0.00 2.52
1307 2505 5.776716 ACAAATCCACATCAACCAGAATTCT 59.223 36.000 0.88 0.88 0.00 2.40
1308 2506 6.029346 ACAAATCCACATCAACCAGAATTC 57.971 37.500 0.00 0.00 0.00 2.17
1337 2540 2.417239 CGTCTGACGCTCTAAAGTCTCT 59.583 50.000 17.94 0.00 38.16 3.10
1392 2595 2.052690 ATCACTCACCCGAGACCCG 61.053 63.158 0.00 0.00 42.34 5.28
1393 2596 1.517832 CATCACTCACCCGAGACCC 59.482 63.158 0.00 0.00 42.34 4.46
1394 2597 1.517832 CCATCACTCACCCGAGACC 59.482 63.158 0.00 0.00 42.34 3.85
1396 2599 1.191489 TTGCCATCACTCACCCGAGA 61.191 55.000 0.00 0.00 42.34 4.04
1397 2600 1.021390 GTTGCCATCACTCACCCGAG 61.021 60.000 0.00 0.00 45.49 4.63
1469 2672 0.617413 ATCAGTCCACTTGGCTCCAG 59.383 55.000 0.00 0.00 34.44 3.86
1581 2784 8.936864 GTCTATCGGTCTTGGGATAATTTAATG 58.063 37.037 0.00 0.00 0.00 1.90
1582 2785 8.881262 AGTCTATCGGTCTTGGGATAATTTAAT 58.119 33.333 0.00 0.00 0.00 1.40
1583 2786 8.258850 AGTCTATCGGTCTTGGGATAATTTAA 57.741 34.615 0.00 0.00 0.00 1.52
1726 2929 2.500509 TGTTTTGCCTGGTTTAAGCG 57.499 45.000 0.00 0.00 0.00 4.68
1952 3155 1.161843 CCACACGGCGGATTACTTTT 58.838 50.000 13.24 0.00 0.00 2.27
2011 3215 1.558167 TTGCCAAGCTCGGGGTGATA 61.558 55.000 6.52 0.00 0.00 2.15
2121 3325 1.632920 TGGTCAACCATGGCACTATGA 59.367 47.619 13.04 6.18 42.01 2.15
2221 3425 7.633553 GCATAATAATTGTCCTCCTTTGCCTTT 60.634 37.037 0.00 0.00 0.00 3.11
2270 3474 2.792749 CCGTTGTTTGTTGTCTTGGTC 58.207 47.619 0.00 0.00 0.00 4.02
2281 3485 5.957842 ATATATATGGGTGCCGTTGTTTG 57.042 39.130 0.00 0.00 0.00 2.93
2282 3486 9.914834 AATATATATATATGGGTGCCGTTGTTT 57.085 29.630 14.65 0.00 0.00 2.83
2306 3510 4.225042 GGGGGAGGCTGATTTTACAAAAAT 59.775 41.667 0.00 0.00 0.00 1.82
2308 3512 3.169908 GGGGGAGGCTGATTTTACAAAA 58.830 45.455 0.00 0.00 0.00 2.44
2504 3711 3.189646 TTGGGGTGGTTGAGGGGG 61.190 66.667 0.00 0.00 0.00 5.40
2533 3740 6.359617 CACAATACTTTTTGCGTTTTCTCGAT 59.640 34.615 0.00 0.00 0.00 3.59
2576 3783 4.499188 GGCCTTGTACACAACTTTCCTTTC 60.499 45.833 0.00 0.00 0.00 2.62
2603 3810 0.474660 ACTCTCAGGTCTGGCCCTTT 60.475 55.000 0.00 0.00 38.26 3.11
2629 3836 4.096003 GCTCTTAGGGGTGCGGCA 62.096 66.667 0.00 0.00 0.00 5.69
2634 3841 2.592308 GCCTGGCTCTTAGGGGTG 59.408 66.667 12.43 0.00 35.80 4.61
2697 4168 1.966451 GGGCCGAACCACAACTCTG 60.966 63.158 0.00 0.00 42.05 3.35
2698 4169 2.113243 GAGGGCCGAACCACAACTCT 62.113 60.000 0.00 0.00 42.05 3.24
2699 4170 1.671379 GAGGGCCGAACCACAACTC 60.671 63.158 0.00 0.00 42.05 3.01
2707 4178 0.252197 AACACATAGGAGGGCCGAAC 59.748 55.000 0.00 0.00 39.96 3.95
2798 4269 1.209019 TCAGATGCTGAGCCCTTCTTC 59.791 52.381 0.23 0.00 35.39 2.87
2892 4363 6.452242 CCAAAACCCAAATAGTTACAACTCC 58.548 40.000 0.00 0.00 40.37 3.85
2999 4470 9.456147 TGCTGGTAAAGTACATACAATTGTTAT 57.544 29.630 17.78 5.63 0.00 1.89
3000 4471 8.850007 TGCTGGTAAAGTACATACAATTGTTA 57.150 30.769 17.78 0.00 0.00 2.41
3001 4472 7.753309 TGCTGGTAAAGTACATACAATTGTT 57.247 32.000 17.78 0.92 0.00 2.83
3002 4473 7.753309 TTGCTGGTAAAGTACATACAATTGT 57.247 32.000 16.68 16.68 0.00 2.71
3003 4474 9.075519 CAATTGCTGGTAAAGTACATACAATTG 57.924 33.333 3.24 3.24 41.44 2.32
3004 4475 8.802267 ACAATTGCTGGTAAAGTACATACAATT 58.198 29.630 5.05 0.00 36.77 2.32
3005 4476 8.243426 CACAATTGCTGGTAAAGTACATACAAT 58.757 33.333 5.05 0.00 31.49 2.71
3006 4477 7.229707 ACACAATTGCTGGTAAAGTACATACAA 59.770 33.333 5.05 0.00 0.00 2.41
3007 4478 6.712998 ACACAATTGCTGGTAAAGTACATACA 59.287 34.615 5.05 0.00 0.00 2.29
3008 4479 7.141100 ACACAATTGCTGGTAAAGTACATAC 57.859 36.000 5.05 0.00 0.00 2.39
3009 4480 8.098286 ACTACACAATTGCTGGTAAAGTACATA 58.902 33.333 5.05 0.00 0.00 2.29
3010 4481 6.940298 ACTACACAATTGCTGGTAAAGTACAT 59.060 34.615 5.05 0.00 0.00 2.29
3011 4482 6.292923 ACTACACAATTGCTGGTAAAGTACA 58.707 36.000 5.05 0.00 0.00 2.90
3012 4483 6.796705 ACTACACAATTGCTGGTAAAGTAC 57.203 37.500 5.05 0.00 0.00 2.73
3014 4485 7.996098 ATTACTACACAATTGCTGGTAAAGT 57.004 32.000 5.05 5.89 0.00 2.66
3015 4486 9.935682 CATATTACTACACAATTGCTGGTAAAG 57.064 33.333 5.05 0.23 0.00 1.85
3016 4487 8.402472 GCATATTACTACACAATTGCTGGTAAA 58.598 33.333 5.05 0.00 0.00 2.01
3017 4488 7.554476 TGCATATTACTACACAATTGCTGGTAA 59.446 33.333 5.05 9.78 0.00 2.85
3018 4489 7.011950 GTGCATATTACTACACAATTGCTGGTA 59.988 37.037 5.05 5.30 33.23 3.25
3019 4490 5.885352 TGCATATTACTACACAATTGCTGGT 59.115 36.000 5.05 4.33 0.00 4.00
3020 4491 6.038603 AGTGCATATTACTACACAATTGCTGG 59.961 38.462 5.05 0.00 35.47 4.85
3021 4492 7.019774 AGTGCATATTACTACACAATTGCTG 57.980 36.000 5.05 5.95 35.47 4.41
3022 4493 7.630242 AAGTGCATATTACTACACAATTGCT 57.370 32.000 5.05 0.00 35.47 3.91
3023 4494 9.438291 CTAAAGTGCATATTACTACACAATTGC 57.562 33.333 5.05 0.00 35.47 3.56
3026 4497 9.109393 CCACTAAAGTGCATATTACTACACAAT 57.891 33.333 4.53 0.00 44.34 2.71
3027 4498 7.065324 GCCACTAAAGTGCATATTACTACACAA 59.935 37.037 4.53 0.00 44.34 3.33
3028 4499 6.537301 GCCACTAAAGTGCATATTACTACACA 59.463 38.462 4.53 0.00 44.34 3.72
3029 4500 6.537301 TGCCACTAAAGTGCATATTACTACAC 59.463 38.462 4.53 0.00 44.34 2.90
3030 4501 6.645306 TGCCACTAAAGTGCATATTACTACA 58.355 36.000 4.53 0.00 44.34 2.74
3031 4502 7.548196 TTGCCACTAAAGTGCATATTACTAC 57.452 36.000 4.53 0.00 44.34 2.73
3032 4503 7.608376 TGTTTGCCACTAAAGTGCATATTACTA 59.392 33.333 4.53 0.00 44.34 1.82
3033 4504 6.432783 TGTTTGCCACTAAAGTGCATATTACT 59.567 34.615 4.53 0.00 44.34 2.24
3034 4505 6.616947 TGTTTGCCACTAAAGTGCATATTAC 58.383 36.000 4.53 4.57 44.34 1.89
3035 4506 6.825944 TGTTTGCCACTAAAGTGCATATTA 57.174 33.333 4.53 0.00 44.34 0.98
3036 4507 5.720371 TGTTTGCCACTAAAGTGCATATT 57.280 34.783 4.53 0.00 44.34 1.28
3037 4508 5.185635 ACATGTTTGCCACTAAAGTGCATAT 59.814 36.000 4.53 1.12 44.34 1.78
3038 4509 4.522405 ACATGTTTGCCACTAAAGTGCATA 59.478 37.500 4.53 0.34 44.34 3.14
3039 4510 3.321682 ACATGTTTGCCACTAAAGTGCAT 59.678 39.130 4.53 0.24 44.34 3.96
3040 4511 2.692557 ACATGTTTGCCACTAAAGTGCA 59.307 40.909 4.53 4.21 44.34 4.57
3041 4512 3.052036 CACATGTTTGCCACTAAAGTGC 58.948 45.455 0.00 1.74 44.34 4.40
3042 4513 3.052036 GCACATGTTTGCCACTAAAGTG 58.948 45.455 0.00 3.02 45.23 3.16
3043 4514 2.692557 TGCACATGTTTGCCACTAAAGT 59.307 40.909 0.00 0.00 42.25 2.66
3044 4515 3.367992 TGCACATGTTTGCCACTAAAG 57.632 42.857 0.00 0.00 42.25 1.85
3045 4516 3.651206 CATGCACATGTTTGCCACTAAA 58.349 40.909 0.00 0.00 42.25 1.85
3046 4517 3.300852 CATGCACATGTTTGCCACTAA 57.699 42.857 0.00 0.00 42.25 2.24
3048 4519 3.898380 CATGCACATGTTTGCCACT 57.102 47.368 0.00 0.00 42.25 4.00
3057 4528 1.820519 AGGCACCTTAACATGCACATG 59.179 47.619 9.06 9.06 43.93 3.21
3058 4529 1.820519 CAGGCACCTTAACATGCACAT 59.179 47.619 8.14 0.00 43.93 3.21
3059 4530 1.246649 CAGGCACCTTAACATGCACA 58.753 50.000 8.14 0.00 43.93 4.57
3060 4531 1.247567 ACAGGCACCTTAACATGCAC 58.752 50.000 8.14 0.00 43.93 4.57
3061 4532 1.993956 AACAGGCACCTTAACATGCA 58.006 45.000 8.14 0.00 43.93 3.96
3062 4533 3.059166 CAAAACAGGCACCTTAACATGC 58.941 45.455 0.00 0.00 41.29 4.06
3063 4534 4.298332 GTCAAAACAGGCACCTTAACATG 58.702 43.478 0.00 0.00 0.00 3.21
3064 4535 3.004315 CGTCAAAACAGGCACCTTAACAT 59.996 43.478 0.00 0.00 0.00 2.71
3065 4536 2.356382 CGTCAAAACAGGCACCTTAACA 59.644 45.455 0.00 0.00 0.00 2.41
3066 4537 2.287368 CCGTCAAAACAGGCACCTTAAC 60.287 50.000 0.00 0.00 0.00 2.01
3067 4538 1.950909 CCGTCAAAACAGGCACCTTAA 59.049 47.619 0.00 0.00 0.00 1.85
3068 4539 1.134037 ACCGTCAAAACAGGCACCTTA 60.134 47.619 0.00 0.00 0.00 2.69
3069 4540 0.395173 ACCGTCAAAACAGGCACCTT 60.395 50.000 0.00 0.00 0.00 3.50
3070 4541 0.470766 TACCGTCAAAACAGGCACCT 59.529 50.000 0.00 0.00 0.00 4.00
3071 4542 1.199097 CATACCGTCAAAACAGGCACC 59.801 52.381 0.00 0.00 0.00 5.01
3072 4543 2.147958 TCATACCGTCAAAACAGGCAC 58.852 47.619 0.00 0.00 0.00 5.01
3073 4544 2.552599 TCATACCGTCAAAACAGGCA 57.447 45.000 0.00 0.00 0.00 4.75
3074 4545 2.812011 ACTTCATACCGTCAAAACAGGC 59.188 45.455 0.00 0.00 0.00 4.85
3075 4546 4.992319 TGTACTTCATACCGTCAAAACAGG 59.008 41.667 0.00 0.00 32.16 4.00
3076 4547 6.183360 GGATGTACTTCATACCGTCAAAACAG 60.183 42.308 10.60 0.00 36.83 3.16
3077 4548 5.640357 GGATGTACTTCATACCGTCAAAACA 59.360 40.000 10.60 0.00 36.83 2.83
3078 4549 5.640357 TGGATGTACTTCATACCGTCAAAAC 59.360 40.000 10.60 0.00 36.59 2.43
3079 4550 5.795972 TGGATGTACTTCATACCGTCAAAA 58.204 37.500 10.60 0.00 36.59 2.44
3080 4551 5.408880 TGGATGTACTTCATACCGTCAAA 57.591 39.130 10.60 0.00 36.59 2.69
3081 4552 5.607939 ATGGATGTACTTCATACCGTCAA 57.392 39.130 10.60 0.00 36.59 3.18
3082 4553 5.607939 AATGGATGTACTTCATACCGTCA 57.392 39.130 10.60 0.00 36.59 4.35
3083 4554 6.046593 TCAAATGGATGTACTTCATACCGTC 58.953 40.000 10.60 0.00 36.59 4.79
3084 4555 5.984725 TCAAATGGATGTACTTCATACCGT 58.015 37.500 10.60 0.00 36.59 4.83
3085 4556 6.280643 TCTCAAATGGATGTACTTCATACCG 58.719 40.000 10.60 0.00 36.59 4.02
3086 4557 7.987458 TCTTCTCAAATGGATGTACTTCATACC 59.013 37.037 10.60 0.00 36.59 2.73
3087 4558 8.821894 GTCTTCTCAAATGGATGTACTTCATAC 58.178 37.037 10.60 0.00 36.83 2.39
3088 4559 8.539544 TGTCTTCTCAAATGGATGTACTTCATA 58.460 33.333 10.60 0.18 36.83 2.15
3089 4560 7.397221 TGTCTTCTCAAATGGATGTACTTCAT 58.603 34.615 10.60 1.50 39.77 2.57
3090 4561 6.768483 TGTCTTCTCAAATGGATGTACTTCA 58.232 36.000 10.60 0.00 0.00 3.02
3091 4562 7.672983 TTGTCTTCTCAAATGGATGTACTTC 57.327 36.000 0.10 0.10 0.00 3.01
3092 4563 8.641498 ATTTGTCTTCTCAAATGGATGTACTT 57.359 30.769 4.25 0.00 43.50 2.24
3102 4573 8.842358 AAAATGATGCATTTGTCTTCTCAAAT 57.158 26.923 0.00 0.00 42.32 2.32
3103 4574 7.385752 GGAAAATGATGCATTTGTCTTCTCAAA 59.614 33.333 0.00 0.00 42.32 2.69
3159 4643 4.035441 GTGGTACCGCAGAAAACAAACTTA 59.965 41.667 20.74 0.00 0.00 2.24
3167 4651 2.279935 ATTGGTGGTACCGCAGAAAA 57.720 45.000 26.20 14.59 42.58 2.29
3237 4721 6.538021 GCCATCAGGAATTACTAGAGCATATG 59.462 42.308 0.00 0.00 36.89 1.78
3427 4913 2.702592 AGACCAACGACCAAGTGAAA 57.297 45.000 0.00 0.00 0.00 2.69
3668 5154 8.589335 ACTGGTACGATTAATTAAGCATACTG 57.411 34.615 16.45 12.69 0.00 2.74
3700 5186 8.052748 ACCTATGCAAATCCATACTTTTACTCA 58.947 33.333 0.00 0.00 0.00 3.41
3747 5233 4.342378 TGAGGACTGGCATAACATAGAGTC 59.658 45.833 0.00 0.00 0.00 3.36
3749 5235 4.343526 ACTGAGGACTGGCATAACATAGAG 59.656 45.833 0.00 0.00 0.00 2.43
3826 5312 6.604171 TGCTTTCTGGAATCATATACCACAT 58.396 36.000 0.00 0.00 0.00 3.21
3851 5337 3.726607 GATCAAGAATCCAGAGCGACAT 58.273 45.455 0.00 0.00 0.00 3.06
3952 5438 1.704628 TGTGATGGTGTCCTGGAACAT 59.295 47.619 0.00 3.62 38.20 2.71
4112 5598 7.716560 TGAATAGAGAAGCAATGCAAATAGCTA 59.283 33.333 8.35 0.00 45.94 3.32
4246 5738 9.407380 ACCTTGACATCAACATATAATAAAGCA 57.593 29.630 0.00 0.00 0.00 3.91
4292 5784 8.652810 AAAGTACAACGTGTCTAAACTGTAAT 57.347 30.769 0.00 0.00 0.00 1.89
4625 6153 6.176183 ACCATCAGTGAAGGAAACTCATTAG 58.824 40.000 20.95 0.00 42.68 1.73
4762 6290 7.770801 AAGAAGTTTACATGTTCTTTTTGGC 57.229 32.000 2.30 0.00 37.25 4.52
4820 6348 8.499162 CAAAAACACCACTTTATCAAAAACACA 58.501 29.630 0.00 0.00 0.00 3.72
4882 6422 5.160641 TGCGCCAATCAGAAATTAAGAAAC 58.839 37.500 4.18 0.00 0.00 2.78
4890 6430 1.331756 GTCGATGCGCCAATCAGAAAT 59.668 47.619 4.18 0.00 0.00 2.17
4901 6441 1.775344 CATACGATGGTCGATGCGC 59.225 57.895 0.00 0.00 43.74 6.09
4903 6443 0.786581 CAGCATACGATGGTCGATGC 59.213 55.000 19.38 19.38 45.06 3.91
4904 6444 1.788886 CACAGCATACGATGGTCGATG 59.211 52.381 6.34 6.84 43.74 3.84
4905 6445 1.869754 GCACAGCATACGATGGTCGAT 60.870 52.381 6.34 0.00 43.74 3.59
4906 6446 0.527600 GCACAGCATACGATGGTCGA 60.528 55.000 6.34 0.00 43.74 4.20
4907 6447 0.805711 TGCACAGCATACGATGGTCG 60.806 55.000 0.00 0.00 39.29 4.79
4908 6448 3.064079 TGCACAGCATACGATGGTC 57.936 52.632 0.00 0.00 39.29 4.02
4932 6472 4.356405 TTCAAGAGTCAAATCCTGCAGA 57.644 40.909 17.39 1.21 0.00 4.26
5118 6659 6.220930 GTGTTCAGACTGGACACTAAATACA 58.779 40.000 31.67 0.67 40.28 2.29
5128 6669 5.899120 TGATACTAGTGTTCAGACTGGAC 57.101 43.478 6.97 6.97 0.00 4.02
5260 6801 3.572255 AGCGAGGTCCTGATAAGAGATTC 59.428 47.826 0.00 0.00 0.00 2.52
5291 6832 8.924691 CAAAAGAGAACAGAGTCAGAGATAAAG 58.075 37.037 0.00 0.00 0.00 1.85
5529 7070 3.837355 ACCAACAAGAGAAAGCAGGAAT 58.163 40.909 0.00 0.00 0.00 3.01
5587 7128 7.331193 CCATCTTAATATGTAAGCGGGTACTTC 59.669 40.741 0.00 0.00 0.00 3.01
5625 7166 3.636764 GGTGGAGAAAAACACAAGGTCAT 59.363 43.478 0.00 0.00 39.31 3.06
5680 7222 1.006922 TGCGACAGAGCAGAGTGTG 60.007 57.895 0.00 0.00 42.92 3.82
5695 7237 3.314357 GGCCTTTAGGGTAAAGTAATGCG 59.686 47.826 0.00 0.00 42.73 4.73
5847 7391 1.513158 CACTGCACTAGAGTCCCCG 59.487 63.158 0.00 0.00 0.00 5.73
5871 7415 2.449464 CCATGAAAGATGGAACCAGCA 58.551 47.619 11.62 0.00 41.64 4.41
6073 7621 6.849151 ACAAGGATCCTGTTAGTACCTTTTT 58.151 36.000 17.02 0.00 35.88 1.94
6074 7622 6.449830 ACAAGGATCCTGTTAGTACCTTTT 57.550 37.500 17.02 0.00 35.88 2.27
6075 7623 6.449830 AACAAGGATCCTGTTAGTACCTTT 57.550 37.500 17.02 0.00 35.88 3.11
6076 7624 6.350780 CGTAACAAGGATCCTGTTAGTACCTT 60.351 42.308 24.94 9.83 38.10 3.50
6077 7625 5.126707 CGTAACAAGGATCCTGTTAGTACCT 59.873 44.000 24.94 10.34 0.00 3.08
6078 7626 5.105595 ACGTAACAAGGATCCTGTTAGTACC 60.106 44.000 24.94 16.96 0.00 3.34
6079 7627 5.958955 ACGTAACAAGGATCCTGTTAGTAC 58.041 41.667 24.94 18.87 0.00 2.73
6080 7628 7.701539 TTACGTAACAAGGATCCTGTTAGTA 57.298 36.000 24.94 23.24 0.00 1.82
6081 7629 6.594788 TTACGTAACAAGGATCCTGTTAGT 57.405 37.500 24.94 23.84 0.00 2.24
6082 7630 7.894376 TTTTACGTAACAAGGATCCTGTTAG 57.106 36.000 24.94 21.31 0.00 2.34
6144 7697 3.136626 GCATATGAAACACCTACCCCTCT 59.863 47.826 6.97 0.00 0.00 3.69
6214 7767 9.125026 ACATATACCAGGTCTGAAATTTTCATC 57.875 33.333 12.04 8.59 39.30 2.92
6215 7768 8.906867 CACATATACCAGGTCTGAAATTTTCAT 58.093 33.333 12.04 0.00 39.30 2.57
6216 7769 8.106462 TCACATATACCAGGTCTGAAATTTTCA 58.894 33.333 11.19 11.19 38.17 2.69
6217 7770 8.506168 TCACATATACCAGGTCTGAAATTTTC 57.494 34.615 0.00 2.05 0.00 2.29
6327 8000 0.665369 GCAGTGCAACACCAGCAATC 60.665 55.000 11.09 0.00 44.64 2.67
6328 8001 1.111116 AGCAGTGCAACACCAGCAAT 61.111 50.000 19.20 0.00 44.64 3.56
6329 8002 1.753848 AGCAGTGCAACACCAGCAA 60.754 52.632 19.20 0.00 44.64 3.91
6330 8003 2.124193 AGCAGTGCAACACCAGCA 60.124 55.556 19.20 0.00 41.43 4.41
6331 8004 2.333938 CAGCAGTGCAACACCAGC 59.666 61.111 19.20 5.02 41.43 4.85
6353 8026 3.100671 GGCGAGATATCCAGGGTCTAAT 58.899 50.000 0.00 0.00 0.00 1.73
6373 8046 2.818274 GTTAGCCAAGGGACGCGG 60.818 66.667 12.47 0.00 0.00 6.46
6377 8050 0.451783 CATTGCGTTAGCCAAGGGAC 59.548 55.000 0.00 0.00 44.33 4.46
6399 8072 1.035139 ACAACTGACGGTCGTAGGTT 58.965 50.000 3.34 2.31 0.00 3.50
6438 8111 6.351881 TCGATAGTATCAAGGCAAACCTTTCT 60.352 38.462 10.71 0.00 46.47 2.52
6442 8115 4.740934 GCTCGATAGTATCAAGGCAAACCT 60.741 45.833 10.71 0.00 43.78 3.50
6444 8117 4.119862 TGCTCGATAGTATCAAGGCAAAC 58.880 43.478 10.71 0.00 37.40 2.93
6447 8120 3.366374 CGATGCTCGATAGTATCAAGGCA 60.366 47.826 17.79 17.79 43.02 4.75
6448 8121 3.119814 TCGATGCTCGATAGTATCAAGGC 60.120 47.826 10.71 10.46 44.82 4.35
6473 8146 4.684703 CCACGTTCTCTCGATAGTGTTTTT 59.315 41.667 0.00 0.00 37.40 1.94
6474 8147 4.235360 CCACGTTCTCTCGATAGTGTTTT 58.765 43.478 0.00 0.00 37.40 2.43
6475 8148 3.255149 ACCACGTTCTCTCGATAGTGTTT 59.745 43.478 0.00 0.00 37.40 2.83
6482 8155 0.388649 GTGCACCACGTTCTCTCGAT 60.389 55.000 5.22 0.00 34.70 3.59
6487 8160 1.225855 TCAATGTGCACCACGTTCTC 58.774 50.000 15.69 0.00 40.99 2.87
6497 8170 0.467844 ACAGCCCACTTCAATGTGCA 60.468 50.000 0.00 0.00 36.68 4.57
6504 8177 2.528818 CCCTCCACAGCCCACTTCA 61.529 63.158 0.00 0.00 0.00 3.02
6507 8180 1.918800 GTACCCTCCACAGCCCACT 60.919 63.158 0.00 0.00 0.00 4.00
6511 8184 1.003718 GTGTGTACCCTCCACAGCC 60.004 63.158 0.00 0.00 43.05 4.85
6522 8195 2.348591 GCAAACTCTTCTGCGTGTGTAC 60.349 50.000 0.00 0.00 0.00 2.90
6530 8203 3.360249 ACATTGTGCAAACTCTTCTGC 57.640 42.857 0.00 0.00 39.09 4.26
6533 8206 4.925068 ACTGAACATTGTGCAAACTCTTC 58.075 39.130 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.