Multiple sequence alignment - TraesCS3B01G513300

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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 TraesCS3B01G513300 chr3B 100.000 2257 0 0 1373 3629 756613605 756615861 0.000000e+00 4169
1 TraesCS3B01G513300 chr3B 100.000 1112 0 0 1 1112 756612233 756613344 0.000000e+00 2054
2 TraesCS3B01G513300 chrUn 96.067 1246 46 2 1534 2776 341148701 341147456 0.000000e+00 2026
3 TraesCS3B01G513300 chrUn 95.907 1246 48 2 1534 2776 287225064 287226309 0.000000e+00 2015
4 TraesCS3B01G513300 chrUn 95.907 1246 48 2 1534 2776 287476962 287478207 0.000000e+00 2015
5 TraesCS3B01G513300 chrUn 95.907 1246 48 2 1534 2776 323542291 323541046 0.000000e+00 2015
6 TraesCS3B01G513300 chrUn 96.160 651 25 0 1422 2072 311734961 311735611 0.000000e+00 1064
7 TraesCS3B01G513300 chrUn 96.160 651 25 0 1422 2072 311738835 311739485 0.000000e+00 1064
8 TraesCS3B01G513300 chrUn 92.553 658 41 6 457 1110 311738014 311738667 0.000000e+00 937
9 TraesCS3B01G513300 chrUn 92.401 658 42 6 457 1110 311734140 311734793 0.000000e+00 931
10 TraesCS3B01G513300 chrUn 92.692 520 32 4 571 1088 474549685 474549170 0.000000e+00 745
11 TraesCS3B01G513300 chrUn 92.857 518 27 5 1 510 311733629 311734144 0.000000e+00 743
12 TraesCS3B01G513300 chrUn 92.857 518 28 4 1 510 311737502 311738018 0.000000e+00 743
13 TraesCS3B01G513300 chrUn 77.129 1010 188 30 1427 2413 264010662 264009673 2.460000e-151 545
14 TraesCS3B01G513300 chrUn 77.129 1010 188 30 1427 2413 294197136 294196147 2.460000e-151 545
15 TraesCS3B01G513300 chrUn 80.054 371 38 19 3062 3404 301167384 301167746 3.620000e-60 243
16 TraesCS3B01G513300 chrUn 79.730 370 41 17 3062 3404 287226685 287227047 1.680000e-58 237
17 TraesCS3B01G513300 chrUn 79.730 370 41 17 3062 3404 287478583 287478945 1.680000e-58 237
18 TraesCS3B01G513300 chrUn 79.521 376 43 17 3062 3410 323540670 323540302 1.680000e-58 237
19 TraesCS3B01G513300 chr3D 87.611 1582 151 29 1422 2968 569900453 569902024 0.000000e+00 1794
20 TraesCS3B01G513300 chr3D 81.673 562 85 15 559 1110 569899786 569900339 5.530000e-123 451
21 TraesCS3B01G513300 chr3D 90.299 268 16 6 1379 1636 567399980 567399713 3.470000e-90 342
22 TraesCS3B01G513300 chr3D 90.789 152 13 1 947 1098 567400217 567400067 6.140000e-48 202
23 TraesCS3B01G513300 chr3D 82.488 217 34 3 108 321 569899391 569899606 1.720000e-43 187
24 TraesCS3B01G513300 chr3D 81.429 140 10 5 1 125 569899248 569899386 2.310000e-17 100
25 TraesCS3B01G513300 chr3A 88.913 1362 131 13 1422 2773 702553960 702555311 0.000000e+00 1661
26 TraesCS3B01G513300 chr3A 76.318 1005 193 32 1433 2413 702491458 702492441 2.520000e-136 496
27 TraesCS3B01G513300 chr3A 80.702 570 68 21 547 1110 702553311 702553844 4.360000e-109 405
28 TraesCS3B01G513300 chr5A 77.932 1151 221 24 1431 2559 401317403 401316264 0.000000e+00 688


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 TraesCS3B01G513300 chr3B 756612233 756615861 3628 False 3111.500000 4169 100.000000 1 3629 2 chr3B.!!$F1 3628
1 TraesCS3B01G513300 chrUn 341147456 341148701 1245 True 2026.000000 2026 96.067000 1534 2776 1 chrUn.!!$R3 1242
2 TraesCS3B01G513300 chrUn 287225064 287227047 1983 False 1126.000000 2015 87.818500 1534 3404 2 chrUn.!!$F2 1870
3 TraesCS3B01G513300 chrUn 287476962 287478945 1983 False 1126.000000 2015 87.818500 1534 3404 2 chrUn.!!$F3 1870
4 TraesCS3B01G513300 chrUn 323540302 323542291 1989 True 1126.000000 2015 87.714000 1534 3410 2 chrUn.!!$R5 1876
5 TraesCS3B01G513300 chrUn 311733629 311739485 5856 False 913.666667 1064 93.831333 1 2072 6 chrUn.!!$F4 2071
6 TraesCS3B01G513300 chrUn 474549170 474549685 515 True 745.000000 745 92.692000 571 1088 1 chrUn.!!$R4 517
7 TraesCS3B01G513300 chrUn 264009673 264010662 989 True 545.000000 545 77.129000 1427 2413 1 chrUn.!!$R1 986
8 TraesCS3B01G513300 chrUn 294196147 294197136 989 True 545.000000 545 77.129000 1427 2413 1 chrUn.!!$R2 986
9 TraesCS3B01G513300 chr3D 569899248 569902024 2776 False 633.000000 1794 83.300250 1 2968 4 chr3D.!!$F1 2967
10 TraesCS3B01G513300 chr3D 567399713 567400217 504 True 272.000000 342 90.544000 947 1636 2 chr3D.!!$R1 689
11 TraesCS3B01G513300 chr3A 702553311 702555311 2000 False 1033.000000 1661 84.807500 547 2773 2 chr3A.!!$F2 2226
12 TraesCS3B01G513300 chr3A 702491458 702492441 983 False 496.000000 496 76.318000 1433 2413 1 chr3A.!!$F1 980
13 TraesCS3B01G513300 chr5A 401316264 401317403 1139 True 688.000000 688 77.932000 1431 2559 1 chr5A.!!$R1 1128

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
902 1033 0.179034 CCATCCCCAGTTAGCAGAGC 60.179 60.0 0.00 0.00 0.00 4.09 F
2151 6242 0.101579 CATTCTGATGGCATTGCGCA 59.898 50.0 5.66 5.66 45.17 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2623 6734 1.003545 GCCACGGTCATCAATTCATCG 60.004 52.381 0.00 0.0 0.0 3.84 R
3501 7794 0.235926 GCCTTCGAATAGGAATGCGC 59.764 55.000 7.36 0.0 37.5 6.09 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
26 27 6.404293 GCTCCTTTTTGCCGTGAAATTATCTA 60.404 38.462 0.00 0.00 0.00 1.98
114 130 6.995511 TGGTTAGCATTGTAAGGTGATTAC 57.004 37.500 0.00 0.00 43.54 1.89
158 199 5.187381 TCCACATGTAATACTTTGGACCGTA 59.813 40.000 0.00 0.00 0.00 4.02
238 279 4.371624 TGATTGATCCATATCACCCCAC 57.628 45.455 0.00 0.00 41.87 4.61
245 286 6.511208 TGATCCATATCACCCCACTCATATA 58.489 40.000 0.00 0.00 37.20 0.86
251 292 7.772292 CCATATCACCCCACTCATATATTCTTG 59.228 40.741 0.00 0.00 0.00 3.02
321 362 5.464389 TCCTTCACACGCTACTAAAACTTTC 59.536 40.000 0.00 0.00 0.00 2.62
329 370 7.148373 ACACGCTACTAAAACTTTCTTCAACAA 60.148 33.333 0.00 0.00 0.00 2.83
344 385 5.923684 TCTTCAACAAATAATGGCCGAAAAC 59.076 36.000 0.00 0.00 0.00 2.43
368 409 4.929146 AAGCACCCTAGTTAACTCCAAT 57.071 40.909 12.39 0.00 0.00 3.16
418 459 6.737118 TGTACAACGTCACACTTATGACTTA 58.263 36.000 0.00 0.00 45.73 2.24
420 461 6.706055 ACAACGTCACACTTATGACTTATG 57.294 37.500 4.54 3.53 45.73 1.90
421 462 6.452242 ACAACGTCACACTTATGACTTATGA 58.548 36.000 4.54 0.00 45.73 2.15
422 463 6.365247 ACAACGTCACACTTATGACTTATGAC 59.635 38.462 4.54 0.00 45.73 3.06
423 464 5.408356 ACGTCACACTTATGACTTATGACC 58.592 41.667 4.54 0.00 45.73 4.02
438 479 2.787473 TGACCATCATTGACCACCTC 57.213 50.000 0.00 0.00 0.00 3.85
442 483 3.452627 GACCATCATTGACCACCTCTACT 59.547 47.826 0.00 0.00 0.00 2.57
450 491 3.912248 TGACCACCTCTACTATTCCTCC 58.088 50.000 0.00 0.00 0.00 4.30
489 578 4.650734 TCACATGGTAGCTCATTGTTTGA 58.349 39.130 0.00 0.00 0.00 2.69
499 588 5.005740 AGCTCATTGTTTGACTGCTTGATA 58.994 37.500 0.00 0.00 33.36 2.15
507 596 7.155655 TGTTTGACTGCTTGATATATTTGCA 57.844 32.000 7.61 7.61 0.00 4.08
619 738 7.406553 TCTAAATGAAAATAATGCGAGTTCCG 58.593 34.615 0.00 0.00 42.21 4.30
794 916 5.470098 CAGTGACAGGCTGTTAAACTATTGT 59.530 40.000 22.98 2.27 0.00 2.71
795 917 5.701290 AGTGACAGGCTGTTAAACTATTGTC 59.299 40.000 22.98 4.88 35.48 3.18
902 1033 0.179034 CCATCCCCAGTTAGCAGAGC 60.179 60.000 0.00 0.00 0.00 4.09
916 1047 6.150140 AGTTAGCAGAGCAAAATAAGAACTGG 59.850 38.462 0.00 0.00 0.00 4.00
955 1086 1.673168 CAGTGGCTTCCTAATCTGGC 58.327 55.000 0.00 0.00 0.00 4.85
963 1094 4.224818 GGCTTCCTAATCTGGCTCTATCAT 59.775 45.833 0.00 0.00 0.00 2.45
966 1097 5.735285 TCCTAATCTGGCTCTATCATGTG 57.265 43.478 0.00 0.00 0.00 3.21
981 1112 2.906389 TCATGTGTTCTGGAGGTTAGCT 59.094 45.455 0.00 0.00 0.00 3.32
984 1115 2.038557 TGTGTTCTGGAGGTTAGCTTCC 59.961 50.000 0.30 0.30 40.88 3.46
998 1129 5.314529 GTTAGCTTCCCTCTAACCAAAAGT 58.685 41.667 0.00 0.00 39.75 2.66
1020 1151 1.452833 GGCCTCCAAGCAGATGGTC 60.453 63.158 0.00 0.00 41.46 4.02
1110 1241 4.016444 TGACACTTGGCTTCTCAAAACTT 58.984 39.130 0.00 0.00 0.00 2.66
1111 1242 4.096382 TGACACTTGGCTTCTCAAAACTTC 59.904 41.667 0.00 0.00 0.00 3.01
1518 1732 6.519721 GCTCCTGATAGAAAGAGCCATCATAA 60.520 42.308 0.00 0.00 44.76 1.90
1520 1734 7.982252 TCCTGATAGAAAGAGCCATCATAAAT 58.018 34.615 0.00 0.00 0.00 1.40
1544 5632 1.302752 CAGCAGCAGCACCACCTTA 60.303 57.895 3.17 0.00 45.49 2.69
1580 5668 3.665675 GATCGCGGACTTGGGCTGT 62.666 63.158 6.13 0.00 0.00 4.40
1730 5818 3.060866 ACGGTGGTGAAGAGCCTC 58.939 61.111 0.00 0.00 0.00 4.70
1790 5881 1.084289 GTATTGCACCAGGGTCGTTC 58.916 55.000 0.00 0.00 0.00 3.95
2151 6242 0.101579 CATTCTGATGGCATTGCGCA 59.898 50.000 5.66 5.66 45.17 6.09
2493 6604 3.431766 GGGCCGTGTATGAACAGATAGTT 60.432 47.826 0.00 0.00 44.93 2.24
2623 6734 4.980805 TGTCGGTCGCCAAGGCAC 62.981 66.667 12.19 8.30 42.06 5.01
2628 6739 2.434185 GTCGCCAAGGCACGATGA 60.434 61.111 12.19 0.00 40.90 2.92
2637 6748 3.488047 CCAAGGCACGATGAATTGATGAC 60.488 47.826 0.00 0.00 0.00 3.06
2701 6818 5.647589 CCACATTTGATGAGATTGAACCAG 58.352 41.667 0.00 0.00 0.00 4.00
2719 6836 8.012957 TGAACCAGTAATTTCTTTAAGGCAAA 57.987 30.769 0.00 0.00 0.00 3.68
2720 6837 8.646900 TGAACCAGTAATTTCTTTAAGGCAAAT 58.353 29.630 0.00 0.00 0.00 2.32
2724 6842 9.271828 CCAGTAATTTCTTTAAGGCAAATTGTT 57.728 29.630 11.96 1.88 33.02 2.83
2754 6873 4.403734 TCCTTTGGTTTGTTATCCAGGAC 58.596 43.478 0.00 0.00 35.05 3.85
2777 6896 2.046604 GTTGGTGGCCGGTCTACC 60.047 66.667 19.69 19.69 45.68 3.18
2780 6899 2.046604 GGTGGCCGGTCTACCAAC 60.047 66.667 20.96 11.54 44.91 3.77
2854 7055 9.561069 GCTTCTCCTCTATGTTTATGGATTTTA 57.439 33.333 0.00 0.00 0.00 1.52
2947 7150 0.390472 TACATGTTCATGCCGCGACA 60.390 50.000 8.23 0.48 0.00 4.35
2982 7246 3.056821 TCAGTTATTCAGGTCCGTGACTG 60.057 47.826 4.41 0.00 35.73 3.51
2984 7248 3.056749 AGTTATTCAGGTCCGTGACTGTC 60.057 47.826 0.00 0.00 32.47 3.51
2997 7261 5.242171 TCCGTGACTGTCACTGTATTCTTAA 59.758 40.000 31.34 9.86 44.85 1.85
2998 7262 6.071560 TCCGTGACTGTCACTGTATTCTTAAT 60.072 38.462 31.34 0.00 44.85 1.40
3001 7265 8.162880 CGTGACTGTCACTGTATTCTTAATTTC 58.837 37.037 31.34 6.27 44.85 2.17
3021 7285 5.441718 TTCTGTCCTTAATCATGCTCCTT 57.558 39.130 0.00 0.00 0.00 3.36
3031 7297 3.895232 TCATGCTCCTTACTCTGTTCC 57.105 47.619 0.00 0.00 0.00 3.62
3041 7307 0.617413 ACTCTGTTCCATCAGCCCAG 59.383 55.000 0.00 0.00 35.63 4.45
3042 7308 0.747283 CTCTGTTCCATCAGCCCAGC 60.747 60.000 0.00 0.00 35.63 4.85
3043 7309 1.203441 TCTGTTCCATCAGCCCAGCT 61.203 55.000 0.00 0.00 40.77 4.24
3044 7310 0.543277 CTGTTCCATCAGCCCAGCTA 59.457 55.000 0.00 0.00 36.40 3.32
3045 7311 0.253044 TGTTCCATCAGCCCAGCTAC 59.747 55.000 0.00 0.00 36.40 3.58
3046 7312 0.543749 GTTCCATCAGCCCAGCTACT 59.456 55.000 0.00 0.00 36.40 2.57
3047 7313 1.762957 GTTCCATCAGCCCAGCTACTA 59.237 52.381 0.00 0.00 36.40 1.82
3048 7314 1.414158 TCCATCAGCCCAGCTACTAC 58.586 55.000 0.00 0.00 36.40 2.73
3049 7315 1.123077 CCATCAGCCCAGCTACTACA 58.877 55.000 0.00 0.00 36.40 2.74
3050 7316 1.202580 CCATCAGCCCAGCTACTACAC 60.203 57.143 0.00 0.00 36.40 2.90
3051 7317 1.759445 CATCAGCCCAGCTACTACACT 59.241 52.381 0.00 0.00 36.40 3.55
3052 7318 1.186200 TCAGCCCAGCTACTACACTG 58.814 55.000 0.00 0.00 36.40 3.66
3053 7319 0.460987 CAGCCCAGCTACTACACTGC 60.461 60.000 0.00 0.00 36.40 4.40
3054 7320 0.904865 AGCCCAGCTACTACACTGCA 60.905 55.000 0.00 0.00 36.99 4.41
3055 7321 0.460987 GCCCAGCTACTACACTGCAG 60.461 60.000 13.48 13.48 32.37 4.41
3056 7322 0.898320 CCCAGCTACTACACTGCAGT 59.102 55.000 15.25 15.25 32.37 4.40
3057 7323 1.134965 CCCAGCTACTACACTGCAGTC 60.135 57.143 18.64 3.58 32.37 3.51
3058 7324 1.134965 CCAGCTACTACACTGCAGTCC 60.135 57.143 18.64 0.00 32.37 3.85
3059 7325 1.821753 CAGCTACTACACTGCAGTCCT 59.178 52.381 18.64 7.64 0.00 3.85
3060 7326 1.821753 AGCTACTACACTGCAGTCCTG 59.178 52.381 18.64 9.00 0.00 3.86
3120 7389 0.533755 GCGATGCCCTCATAGTGCTT 60.534 55.000 0.00 0.00 31.96 3.91
3124 7393 0.107508 TGCCCTCATAGTGCTTGAGC 60.108 55.000 0.00 0.00 39.42 4.26
3136 7405 0.886563 GCTTGAGCAAATGCCAGAGT 59.113 50.000 0.94 0.00 43.38 3.24
3137 7406 1.402456 GCTTGAGCAAATGCCAGAGTG 60.402 52.381 0.94 0.00 43.38 3.51
3145 7414 3.425193 GCAAATGCCAGAGTGTAAAAACG 59.575 43.478 0.00 0.00 34.31 3.60
3156 7425 5.527582 AGAGTGTAAAAACGTGAAGATGCTT 59.472 36.000 0.00 0.00 0.00 3.91
3167 7436 4.505922 CGTGAAGATGCTTCTCAGGTAATC 59.494 45.833 2.09 0.00 0.00 1.75
3174 7443 6.545298 AGATGCTTCTCAGGTAATCAAAATCC 59.455 38.462 0.00 0.00 0.00 3.01
3178 7447 6.375455 GCTTCTCAGGTAATCAAAATCCTTCA 59.625 38.462 0.00 0.00 0.00 3.02
3182 7451 6.310941 TCAGGTAATCAAAATCCTTCACCAA 58.689 36.000 0.00 0.00 0.00 3.67
3184 7453 5.185828 AGGTAATCAAAATCCTTCACCAAGC 59.814 40.000 0.00 0.00 0.00 4.01
3185 7454 4.541973 AATCAAAATCCTTCACCAAGCC 57.458 40.909 0.00 0.00 0.00 4.35
3186 7455 2.956132 TCAAAATCCTTCACCAAGCCA 58.044 42.857 0.00 0.00 0.00 4.75
3187 7456 3.509442 TCAAAATCCTTCACCAAGCCAT 58.491 40.909 0.00 0.00 0.00 4.40
3188 7457 3.511146 TCAAAATCCTTCACCAAGCCATC 59.489 43.478 0.00 0.00 0.00 3.51
3189 7458 3.463048 AAATCCTTCACCAAGCCATCT 57.537 42.857 0.00 0.00 0.00 2.90
3190 7459 2.725221 ATCCTTCACCAAGCCATCTC 57.275 50.000 0.00 0.00 0.00 2.75
3191 7460 1.661463 TCCTTCACCAAGCCATCTCT 58.339 50.000 0.00 0.00 0.00 3.10
3198 7487 0.107312 CCAAGCCATCTCTGGACTGG 60.107 60.000 0.00 0.00 46.37 4.00
3206 7495 0.614979 TCTCTGGACTGGGTAGTGGC 60.615 60.000 0.00 0.00 37.25 5.01
3211 7500 1.215647 GACTGGGTAGTGGCTGACG 59.784 63.158 0.00 0.00 37.25 4.35
3240 7529 1.072965 GATACCAAGCTGGGAGGATGG 59.927 57.143 16.25 5.31 43.37 3.51
3247 7536 0.849417 GCTGGGAGGATGGGAGAAAT 59.151 55.000 0.00 0.00 0.00 2.17
3297 7586 5.693104 CACTTACGTCTAGTTGGCTTGTTTA 59.307 40.000 0.00 0.00 0.00 2.01
3303 7592 6.915843 ACGTCTAGTTGGCTTGTTTATTTTTG 59.084 34.615 0.00 0.00 0.00 2.44
3304 7593 6.129194 CGTCTAGTTGGCTTGTTTATTTTTGC 60.129 38.462 0.00 0.00 0.00 3.68
3309 7599 8.499403 AGTTGGCTTGTTTATTTTTGCTTTAA 57.501 26.923 0.00 0.00 0.00 1.52
3358 7651 6.715347 ATCTTTTCACTGTTTTAGCCAAGT 57.285 33.333 0.00 0.00 0.00 3.16
3362 7655 8.691797 TCTTTTCACTGTTTTAGCCAAGTATTT 58.308 29.630 0.00 0.00 0.00 1.40
3363 7656 8.641499 TTTTCACTGTTTTAGCCAAGTATTTG 57.359 30.769 0.00 0.00 0.00 2.32
3364 7657 6.952773 TCACTGTTTTAGCCAAGTATTTGT 57.047 33.333 0.00 0.00 32.21 2.83
3365 7658 6.966021 TCACTGTTTTAGCCAAGTATTTGTC 58.034 36.000 0.00 0.00 32.21 3.18
3366 7659 6.770785 TCACTGTTTTAGCCAAGTATTTGTCT 59.229 34.615 0.00 0.00 32.21 3.41
3367 7660 7.284489 TCACTGTTTTAGCCAAGTATTTGTCTT 59.716 33.333 0.00 0.00 32.21 3.01
3393 7686 3.399440 TTTTCATCCCACAATGCAACC 57.601 42.857 0.00 0.00 0.00 3.77
3398 7691 1.303236 CCCACAATGCAACCGAGGA 60.303 57.895 0.00 0.00 0.00 3.71
3404 7697 1.369091 AATGCAACCGAGGATGACGC 61.369 55.000 3.45 0.00 0.00 5.19
3406 7699 2.511600 CAACCGAGGATGACGCCC 60.512 66.667 0.00 0.00 0.00 6.13
3410 7703 2.202932 CGAGGATGACGCCCAAGG 60.203 66.667 0.00 0.00 0.00 3.61
3411 7704 2.190578 GAGGATGACGCCCAAGGG 59.809 66.667 0.00 0.00 38.57 3.95
3412 7705 2.610859 AGGATGACGCCCAAGGGT 60.611 61.111 7.05 0.00 42.82 4.34
3413 7706 2.198304 GAGGATGACGCCCAAGGGTT 62.198 60.000 7.05 0.00 39.67 4.11
3414 7707 0.912487 AGGATGACGCCCAAGGGTTA 60.912 55.000 7.05 0.00 39.67 2.85
3415 7708 0.746923 GGATGACGCCCAAGGGTTAC 60.747 60.000 7.05 0.00 39.67 2.50
3416 7709 1.078708 ATGACGCCCAAGGGTTACG 60.079 57.895 7.05 4.59 39.67 3.18
3417 7710 1.833787 ATGACGCCCAAGGGTTACGT 61.834 55.000 7.05 7.97 39.67 3.57
3418 7711 1.739196 GACGCCCAAGGGTTACGTC 60.739 63.158 17.03 17.03 45.10 4.34
3419 7712 2.435410 CGCCCAAGGGTTACGTCC 60.435 66.667 7.05 0.00 37.65 4.79
3420 7713 2.951101 CGCCCAAGGGTTACGTCCT 61.951 63.158 7.05 0.00 37.65 3.85
3421 7714 1.606885 CGCCCAAGGGTTACGTCCTA 61.607 60.000 7.05 0.00 37.65 2.94
3422 7715 0.614812 GCCCAAGGGTTACGTCCTAA 59.385 55.000 7.05 0.00 37.65 2.69
3423 7716 1.003464 GCCCAAGGGTTACGTCCTAAA 59.997 52.381 7.05 0.00 37.65 1.85
3424 7717 2.356432 GCCCAAGGGTTACGTCCTAAAT 60.356 50.000 7.05 0.00 37.65 1.40
3425 7718 3.874977 GCCCAAGGGTTACGTCCTAAATT 60.875 47.826 7.05 0.00 37.65 1.82
3426 7719 4.338012 CCCAAGGGTTACGTCCTAAATTT 58.662 43.478 0.00 0.00 33.58 1.82
3427 7720 4.397103 CCCAAGGGTTACGTCCTAAATTTC 59.603 45.833 0.00 0.00 33.58 2.17
3428 7721 5.005094 CCAAGGGTTACGTCCTAAATTTCA 58.995 41.667 0.00 0.00 33.58 2.69
3429 7722 5.123344 CCAAGGGTTACGTCCTAAATTTCAG 59.877 44.000 0.00 0.00 33.58 3.02
3430 7723 4.259356 AGGGTTACGTCCTAAATTTCAGC 58.741 43.478 0.00 0.00 31.86 4.26
3431 7724 4.004982 GGGTTACGTCCTAAATTTCAGCA 58.995 43.478 0.00 0.00 0.00 4.41
3432 7725 4.094442 GGGTTACGTCCTAAATTTCAGCAG 59.906 45.833 0.00 0.00 0.00 4.24
3433 7726 4.933400 GGTTACGTCCTAAATTTCAGCAGA 59.067 41.667 0.00 0.00 0.00 4.26
3434 7727 5.410439 GGTTACGTCCTAAATTTCAGCAGAA 59.590 40.000 0.00 0.00 0.00 3.02
3435 7728 6.304882 GTTACGTCCTAAATTTCAGCAGAAC 58.695 40.000 0.00 0.00 32.39 3.01
3436 7729 4.642429 ACGTCCTAAATTTCAGCAGAACT 58.358 39.130 0.00 0.00 32.39 3.01
3437 7730 5.063880 ACGTCCTAAATTTCAGCAGAACTT 58.936 37.500 0.00 0.00 32.39 2.66
3438 7731 5.179555 ACGTCCTAAATTTCAGCAGAACTTC 59.820 40.000 0.00 0.00 32.39 3.01
3439 7732 5.622378 GTCCTAAATTTCAGCAGAACTTCG 58.378 41.667 0.00 0.00 32.39 3.79
3440 7733 5.408604 GTCCTAAATTTCAGCAGAACTTCGA 59.591 40.000 0.00 0.00 32.39 3.71
3441 7734 5.408604 TCCTAAATTTCAGCAGAACTTCGAC 59.591 40.000 0.00 0.00 32.39 4.20
3442 7735 3.795561 AATTTCAGCAGAACTTCGACG 57.204 42.857 0.00 0.00 32.39 5.12
3443 7736 2.218953 TTTCAGCAGAACTTCGACGT 57.781 45.000 0.00 0.00 32.39 4.34
3444 7737 1.767289 TTCAGCAGAACTTCGACGTC 58.233 50.000 5.18 5.18 0.00 4.34
3445 7738 0.666374 TCAGCAGAACTTCGACGTCA 59.334 50.000 17.16 0.00 0.00 4.35
3446 7739 1.269723 TCAGCAGAACTTCGACGTCAT 59.730 47.619 17.16 0.00 0.00 3.06
3447 7740 1.651138 CAGCAGAACTTCGACGTCATC 59.349 52.381 17.16 5.38 0.00 2.92
3448 7741 0.992802 GCAGAACTTCGACGTCATCC 59.007 55.000 17.16 0.00 0.00 3.51
3449 7742 1.402984 GCAGAACTTCGACGTCATCCT 60.403 52.381 17.16 0.42 0.00 3.24
3450 7743 2.520979 CAGAACTTCGACGTCATCCTC 58.479 52.381 17.16 5.05 0.00 3.71
3451 7744 2.095212 CAGAACTTCGACGTCATCCTCA 60.095 50.000 17.16 0.00 0.00 3.86
3452 7745 2.557056 AGAACTTCGACGTCATCCTCAA 59.443 45.455 17.16 0.00 0.00 3.02
3453 7746 3.005472 AGAACTTCGACGTCATCCTCAAA 59.995 43.478 17.16 0.00 0.00 2.69
3454 7747 3.380479 ACTTCGACGTCATCCTCAAAA 57.620 42.857 17.16 0.00 0.00 2.44
3455 7748 3.724374 ACTTCGACGTCATCCTCAAAAA 58.276 40.909 17.16 0.00 0.00 1.94
3477 7770 8.558973 AAAAATTTCCAAGTTTTGTCATGACA 57.441 26.923 24.56 24.56 37.30 3.58
3478 7771 8.735692 AAAATTTCCAAGTTTTGTCATGACAT 57.264 26.923 28.32 11.57 41.52 3.06
3479 7772 8.735692 AAATTTCCAAGTTTTGTCATGACATT 57.264 26.923 28.32 16.89 41.52 2.71
3480 7773 8.735692 AATTTCCAAGTTTTGTCATGACATTT 57.264 26.923 28.32 16.89 41.52 2.32
3481 7774 8.735692 ATTTCCAAGTTTTGTCATGACATTTT 57.264 26.923 28.32 16.57 41.52 1.82
3482 7775 7.536895 TTCCAAGTTTTGTCATGACATTTTG 57.463 32.000 28.32 24.49 41.52 2.44
3483 7776 5.523188 TCCAAGTTTTGTCATGACATTTTGC 59.477 36.000 28.32 16.27 41.52 3.68
3484 7777 5.277442 CCAAGTTTTGTCATGACATTTTGCC 60.277 40.000 28.32 13.29 41.52 4.52
3485 7778 5.021033 AGTTTTGTCATGACATTTTGCCA 57.979 34.783 28.32 9.66 41.52 4.92
3486 7779 5.613329 AGTTTTGTCATGACATTTTGCCAT 58.387 33.333 28.32 7.57 41.52 4.40
3487 7780 6.056884 AGTTTTGTCATGACATTTTGCCATT 58.943 32.000 28.32 5.90 41.52 3.16
3488 7781 6.543100 AGTTTTGTCATGACATTTTGCCATTT 59.457 30.769 28.32 4.68 41.52 2.32
3489 7782 7.714377 AGTTTTGTCATGACATTTTGCCATTTA 59.286 29.630 28.32 6.85 41.52 1.40
3490 7783 8.505625 GTTTTGTCATGACATTTTGCCATTTAT 58.494 29.630 28.32 0.00 41.52 1.40
3491 7784 8.618702 TTTGTCATGACATTTTGCCATTTATT 57.381 26.923 28.32 0.00 41.52 1.40
3492 7785 8.618702 TTGTCATGACATTTTGCCATTTATTT 57.381 26.923 28.32 0.00 41.52 1.40
3493 7786 8.618702 TGTCATGACATTTTGCCATTTATTTT 57.381 26.923 24.56 0.00 36.21 1.82
3494 7787 8.719648 TGTCATGACATTTTGCCATTTATTTTC 58.280 29.630 24.56 0.00 36.21 2.29
3495 7788 8.177013 GTCATGACATTTTGCCATTTATTTTCC 58.823 33.333 21.07 0.00 0.00 3.13
3496 7789 8.102047 TCATGACATTTTGCCATTTATTTTCCT 58.898 29.630 0.00 0.00 0.00 3.36
3497 7790 8.732531 CATGACATTTTGCCATTTATTTTCCTT 58.267 29.630 0.00 0.00 0.00 3.36
3498 7791 8.097078 TGACATTTTGCCATTTATTTTCCTTG 57.903 30.769 0.00 0.00 0.00 3.61
3499 7792 7.174599 TGACATTTTGCCATTTATTTTCCTTGG 59.825 33.333 0.00 0.00 0.00 3.61
3500 7793 6.433716 ACATTTTGCCATTTATTTTCCTTGGG 59.566 34.615 0.00 0.00 0.00 4.12
3501 7794 4.566426 TTGCCATTTATTTTCCTTGGGG 57.434 40.909 0.00 0.00 0.00 4.96
3502 7795 2.238395 TGCCATTTATTTTCCTTGGGGC 59.762 45.455 0.00 0.00 39.29 5.80
3503 7796 2.741553 GCCATTTATTTTCCTTGGGGCG 60.742 50.000 0.00 0.00 0.00 6.13
3504 7797 2.549926 CATTTATTTTCCTTGGGGCGC 58.450 47.619 0.00 0.00 0.00 6.53
3505 7798 1.633774 TTTATTTTCCTTGGGGCGCA 58.366 45.000 10.83 0.00 0.00 6.09
3506 7799 1.859302 TTATTTTCCTTGGGGCGCAT 58.141 45.000 10.83 0.00 0.00 4.73
3507 7800 1.859302 TATTTTCCTTGGGGCGCATT 58.141 45.000 10.83 0.00 0.00 3.56
3508 7801 0.536724 ATTTTCCTTGGGGCGCATTC 59.463 50.000 10.83 0.00 0.00 2.67
3509 7802 1.540435 TTTTCCTTGGGGCGCATTCC 61.540 55.000 10.83 8.34 0.00 3.01
3510 7803 2.439553 TTTCCTTGGGGCGCATTCCT 62.440 55.000 10.83 0.00 0.00 3.36
3511 7804 1.567208 TTCCTTGGGGCGCATTCCTA 61.567 55.000 10.83 3.63 0.00 2.94
3512 7805 1.151450 CCTTGGGGCGCATTCCTAT 59.849 57.895 10.83 0.00 0.00 2.57
3513 7806 0.468029 CCTTGGGGCGCATTCCTATT 60.468 55.000 10.83 0.00 0.00 1.73
3514 7807 0.954452 CTTGGGGCGCATTCCTATTC 59.046 55.000 10.83 0.00 0.00 1.75
3515 7808 0.817634 TTGGGGCGCATTCCTATTCG 60.818 55.000 10.83 0.00 0.00 3.34
3516 7809 1.070786 GGGGCGCATTCCTATTCGA 59.929 57.895 10.83 0.00 0.00 3.71
3517 7810 0.534203 GGGGCGCATTCCTATTCGAA 60.534 55.000 10.83 0.00 0.00 3.71
3518 7811 0.868406 GGGCGCATTCCTATTCGAAG 59.132 55.000 10.83 0.00 0.00 3.79
3519 7812 0.868406 GGCGCATTCCTATTCGAAGG 59.132 55.000 10.83 0.00 38.06 3.46
3520 7813 0.235926 GCGCATTCCTATTCGAAGGC 59.764 55.000 0.30 0.00 44.08 4.35
3521 7814 0.868406 CGCATTCCTATTCGAAGGCC 59.132 55.000 3.35 0.00 44.54 5.19
3522 7815 0.868406 GCATTCCTATTCGAAGGCCG 59.132 55.000 3.35 0.00 42.27 6.13
3523 7816 1.540363 GCATTCCTATTCGAAGGCCGA 60.540 52.381 3.35 0.00 42.27 5.54
3531 7824 2.199117 TCGAAGGCCGAATGCTAGT 58.801 52.632 0.00 0.00 45.43 2.57
3532 7825 0.535335 TCGAAGGCCGAATGCTAGTT 59.465 50.000 0.00 0.00 45.43 2.24
3533 7826 0.931005 CGAAGGCCGAATGCTAGTTC 59.069 55.000 0.00 0.00 41.76 3.01
3534 7827 1.739035 CGAAGGCCGAATGCTAGTTCA 60.739 52.381 0.00 0.00 41.76 3.18
3535 7828 1.936547 GAAGGCCGAATGCTAGTTCAG 59.063 52.381 0.00 0.00 40.92 3.02
3536 7829 0.905357 AGGCCGAATGCTAGTTCAGT 59.095 50.000 0.00 0.00 40.92 3.41
3537 7830 2.108168 AGGCCGAATGCTAGTTCAGTA 58.892 47.619 0.00 0.00 40.92 2.74
3538 7831 2.700897 AGGCCGAATGCTAGTTCAGTAT 59.299 45.455 0.00 0.00 40.92 2.12
3539 7832 3.134804 AGGCCGAATGCTAGTTCAGTATT 59.865 43.478 0.00 0.00 41.70 1.89
3540 7833 3.877508 GGCCGAATGCTAGTTCAGTATTT 59.122 43.478 0.00 0.00 39.41 1.40
3541 7834 4.335594 GGCCGAATGCTAGTTCAGTATTTT 59.664 41.667 0.00 0.00 39.41 1.82
3542 7835 5.163652 GGCCGAATGCTAGTTCAGTATTTTT 60.164 40.000 0.00 0.00 39.41 1.94
3565 7858 8.830201 TTTTTGCTTGATGTAAATGCATTAGT 57.170 26.923 13.39 0.00 33.50 2.24
3566 7859 8.830201 TTTTGCTTGATGTAAATGCATTAGTT 57.170 26.923 13.39 0.00 33.50 2.24
3567 7860 7.815398 TTGCTTGATGTAAATGCATTAGTTG 57.185 32.000 13.39 0.00 33.50 3.16
3580 7873 3.993920 CATTAGTTGCAAGGTTTTGGCT 58.006 40.909 0.00 0.00 34.79 4.75
3581 7874 5.132897 CATTAGTTGCAAGGTTTTGGCTA 57.867 39.130 0.00 0.00 34.79 3.93
3582 7875 4.577834 TTAGTTGCAAGGTTTTGGCTAC 57.422 40.909 0.00 0.00 34.79 3.58
3583 7876 1.686587 AGTTGCAAGGTTTTGGCTACC 59.313 47.619 0.00 0.00 34.79 3.18
3584 7877 0.671251 TTGCAAGGTTTTGGCTACCG 59.329 50.000 0.00 0.00 40.69 4.02
3585 7878 1.175983 TGCAAGGTTTTGGCTACCGG 61.176 55.000 0.00 0.00 40.69 5.28
3586 7879 0.891904 GCAAGGTTTTGGCTACCGGA 60.892 55.000 9.46 0.00 40.69 5.14
3587 7880 1.834188 CAAGGTTTTGGCTACCGGAT 58.166 50.000 9.46 0.00 40.69 4.18
3588 7881 2.942306 GCAAGGTTTTGGCTACCGGATA 60.942 50.000 9.46 0.00 40.69 2.59
3589 7882 2.681344 CAAGGTTTTGGCTACCGGATAC 59.319 50.000 9.46 0.00 40.69 2.24
3590 7883 1.910671 AGGTTTTGGCTACCGGATACA 59.089 47.619 9.46 0.00 40.69 2.29
3591 7884 2.508300 AGGTTTTGGCTACCGGATACAT 59.492 45.455 9.46 0.00 40.69 2.29
3592 7885 2.616842 GGTTTTGGCTACCGGATACATG 59.383 50.000 9.46 0.00 0.00 3.21
3593 7886 3.537580 GTTTTGGCTACCGGATACATGA 58.462 45.455 9.46 0.00 0.00 3.07
3594 7887 4.134563 GTTTTGGCTACCGGATACATGAT 58.865 43.478 9.46 0.00 0.00 2.45
3595 7888 5.302360 GTTTTGGCTACCGGATACATGATA 58.698 41.667 9.46 0.00 0.00 2.15
3596 7889 5.554437 TTTGGCTACCGGATACATGATAA 57.446 39.130 9.46 0.00 0.00 1.75
3597 7890 5.755409 TTGGCTACCGGATACATGATAAT 57.245 39.130 9.46 0.00 0.00 1.28
3598 7891 5.084818 TGGCTACCGGATACATGATAATG 57.915 43.478 9.46 0.00 0.00 1.90
3599 7892 4.530553 TGGCTACCGGATACATGATAATGT 59.469 41.667 9.46 0.20 38.49 2.71
3600 7893 5.012664 TGGCTACCGGATACATGATAATGTT 59.987 40.000 9.46 0.00 36.08 2.71
3601 7894 5.938125 GGCTACCGGATACATGATAATGTTT 59.062 40.000 9.46 0.00 36.08 2.83
3602 7895 6.128282 GGCTACCGGATACATGATAATGTTTG 60.128 42.308 9.46 0.00 36.08 2.93
3603 7896 6.649141 GCTACCGGATACATGATAATGTTTGA 59.351 38.462 9.46 0.00 36.08 2.69
3604 7897 7.334421 GCTACCGGATACATGATAATGTTTGAT 59.666 37.037 9.46 0.00 36.08 2.57
3605 7898 9.219603 CTACCGGATACATGATAATGTTTGATT 57.780 33.333 9.46 0.00 36.08 2.57
3607 7900 9.219603 ACCGGATACATGATAATGTTTGATTAG 57.780 33.333 9.46 0.00 36.08 1.73
3608 7901 9.219603 CCGGATACATGATAATGTTTGATTAGT 57.780 33.333 0.00 0.00 36.08 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 130 6.260714 TGTGGAAAAAGGACATGATCATATCG 59.739 38.462 8.15 0.00 0.00 2.92
158 199 6.070710 GGTCAACTTTCTACTCTATGGAAGGT 60.071 42.308 0.00 0.00 39.41 3.50
245 286 8.358582 AGCAGAAGGACATTTATTTCAAGAAT 57.641 30.769 0.00 0.00 0.00 2.40
251 292 6.587608 CACCAAAGCAGAAGGACATTTATTTC 59.412 38.462 0.00 0.00 0.00 2.17
266 307 4.232221 CTGCATAAAAGTCACCAAAGCAG 58.768 43.478 0.00 0.00 40.57 4.24
298 339 5.465724 AGAAAGTTTTAGTAGCGTGTGAAGG 59.534 40.000 0.00 0.00 0.00 3.46
321 362 5.164100 CGTTTTCGGCCATTATTTGTTGAAG 60.164 40.000 2.24 0.00 39.94 3.02
329 370 3.057174 TGCTTTCGTTTTCGGCCATTATT 60.057 39.130 2.24 0.00 44.25 1.40
344 385 3.259902 GGAGTTAACTAGGGTGCTTTCG 58.740 50.000 8.42 0.00 0.00 3.46
368 409 2.109128 TGGTCATAAGCTTTTGGGGTGA 59.891 45.455 15.65 4.22 0.00 4.02
418 459 2.848694 AGAGGTGGTCAATGATGGTCAT 59.151 45.455 0.00 0.00 39.09 3.06
420 461 3.452627 AGTAGAGGTGGTCAATGATGGTC 59.547 47.826 0.00 0.00 0.00 4.02
421 462 3.454858 AGTAGAGGTGGTCAATGATGGT 58.545 45.455 0.00 0.00 0.00 3.55
422 463 5.815233 ATAGTAGAGGTGGTCAATGATGG 57.185 43.478 0.00 0.00 0.00 3.51
423 464 6.042552 AGGAATAGTAGAGGTGGTCAATGATG 59.957 42.308 0.00 0.00 0.00 3.07
450 491 6.038603 ACCATGTGATCTTCAAATGATAACCG 59.961 38.462 8.86 0.00 43.22 4.44
489 578 8.906867 ACAACTAATGCAAATATATCAAGCAGT 58.093 29.630 10.96 10.67 38.75 4.40
499 588 8.807948 AAGGAGTGTACAACTAATGCAAATAT 57.192 30.769 0.00 0.00 40.07 1.28
507 596 8.514330 TGAAAACAAAGGAGTGTACAACTAAT 57.486 30.769 0.00 0.00 40.07 1.73
664 785 7.615365 TCCAAAGCCTACATTTCAGACATTTAT 59.385 33.333 0.00 0.00 0.00 1.40
681 803 1.342374 GGGATTCATGGTCCAAAGCCT 60.342 52.381 16.59 0.00 37.49 4.58
682 804 1.114627 GGGATTCATGGTCCAAAGCC 58.885 55.000 16.59 0.00 37.49 4.35
823 945 6.043938 ACTGATTCAAAGGTTACAGGTTAGGA 59.956 38.462 0.00 0.00 0.00 2.94
916 1047 5.065218 CACTGCTAATGATGTACTTGAACCC 59.935 44.000 0.00 0.00 0.00 4.11
955 1086 5.350504 AACCTCCAGAACACATGATAGAG 57.649 43.478 0.00 0.00 0.00 2.43
963 1094 2.038557 GGAAGCTAACCTCCAGAACACA 59.961 50.000 0.00 0.00 0.00 3.72
966 1097 1.909986 AGGGAAGCTAACCTCCAGAAC 59.090 52.381 4.59 0.00 28.88 3.01
981 1112 4.662278 CCATGACTTTTGGTTAGAGGGAA 58.338 43.478 0.00 0.00 0.00 3.97
984 1115 2.755103 GGCCATGACTTTTGGTTAGAGG 59.245 50.000 0.00 0.00 36.57 3.69
993 1124 1.260544 GCTTGGAGGCCATGACTTTT 58.739 50.000 5.01 0.00 31.53 2.27
998 1129 0.106868 CATCTGCTTGGAGGCCATGA 60.107 55.000 5.01 0.00 31.53 3.07
1020 1151 3.290710 CCCTTGTCCTTGGTTCATATGG 58.709 50.000 2.13 0.00 0.00 2.74
1537 5625 5.126067 CCATCTTGTCAGGTAATAAGGTGG 58.874 45.833 0.00 0.00 42.90 4.61
1544 5632 4.697514 CGATCACCATCTTGTCAGGTAAT 58.302 43.478 0.00 0.00 33.49 1.89
1580 5668 2.282180 GCGTTTGGGCCAGAGGAA 60.282 61.111 19.68 2.39 0.00 3.36
1730 5818 2.944557 CATCGACGGAGCGTGACG 60.945 66.667 0.00 0.00 41.37 4.35
1749 5837 3.041940 CACGACAACAGGCCCGTC 61.042 66.667 0.00 0.00 32.50 4.79
1790 5881 5.461078 GCTACTAGTGAAGAGTCTCTCGTAG 59.539 48.000 5.39 11.68 41.73 3.51
2146 6237 1.236616 CCCAGATGTGAAAGTGCGCA 61.237 55.000 5.66 5.66 0.00 6.09
2151 6242 4.647564 AGAATGTCCCAGATGTGAAAGT 57.352 40.909 0.00 0.00 0.00 2.66
2338 6449 5.540719 CCTCCCTTATATCTTCCTTCGAAGT 59.459 44.000 23.03 7.40 45.02 3.01
2493 6604 2.029739 CACATCTCCAAAATGCTGCACA 60.030 45.455 3.57 0.00 0.00 4.57
2551 6662 2.338785 GCAAGCTTCTGTCCAGGCC 61.339 63.158 0.00 0.00 0.00 5.19
2623 6734 1.003545 GCCACGGTCATCAATTCATCG 60.004 52.381 0.00 0.00 0.00 3.84
2628 6739 3.903783 CGGCCACGGTCATCAATT 58.096 55.556 2.24 0.00 36.18 2.32
2719 6836 7.390823 ACAAACCAAAGGAAACTGTTAACAAT 58.609 30.769 10.03 0.00 42.68 2.71
2720 6837 6.760291 ACAAACCAAAGGAAACTGTTAACAA 58.240 32.000 10.03 0.00 42.68 2.83
2724 6842 7.342284 TGGATAACAAACCAAAGGAAACTGTTA 59.658 33.333 0.00 0.00 42.68 2.41
2813 6962 4.891756 AGGAGAAGCAATCCATAAACATGG 59.108 41.667 0.00 0.00 43.01 3.66
2820 6969 6.753913 AACATAGAGGAGAAGCAATCCATA 57.246 37.500 4.88 0.00 39.47 2.74
2822 6971 5.441718 AAACATAGAGGAGAAGCAATCCA 57.558 39.130 4.88 0.00 39.47 3.41
2823 6972 6.429385 CCATAAACATAGAGGAGAAGCAATCC 59.571 42.308 0.00 0.00 37.07 3.01
2906 7109 3.374745 CTTGGACAAACAAGTCATGCAC 58.625 45.455 0.00 0.00 42.18 4.57
2982 7246 8.779354 AGGACAGAAATTAAGAATACAGTGAC 57.221 34.615 0.00 0.00 0.00 3.67
2997 7261 6.011122 AGGAGCATGATTAAGGACAGAAAT 57.989 37.500 0.00 0.00 0.00 2.17
2998 7262 5.441718 AGGAGCATGATTAAGGACAGAAA 57.558 39.130 0.00 0.00 0.00 2.52
3001 7265 5.923204 AGTAAGGAGCATGATTAAGGACAG 58.077 41.667 0.00 0.00 0.00 3.51
3012 7276 3.616956 TGGAACAGAGTAAGGAGCATG 57.383 47.619 0.00 0.00 0.00 4.06
3021 7285 6.959044 TAGCTGGGCTGATGGAACAGAGTA 62.959 50.000 0.00 0.00 40.64 2.59
3031 7297 1.759445 AGTGTAGTAGCTGGGCTGATG 59.241 52.381 0.00 0.00 40.10 3.07
3041 7307 2.285827 CAGGACTGCAGTGTAGTAGC 57.714 55.000 27.27 7.57 0.00 3.58
3058 7324 3.327626 GCTGATCCTGATCACTATGCAG 58.672 50.000 5.74 0.00 42.42 4.41
3059 7325 2.288640 CGCTGATCCTGATCACTATGCA 60.289 50.000 15.19 0.00 42.42 3.96
3060 7326 2.288702 ACGCTGATCCTGATCACTATGC 60.289 50.000 5.74 7.25 42.42 3.14
3081 7347 1.595929 GAACCAGTCGTTCGCCCAA 60.596 57.895 0.00 0.00 41.51 4.12
3120 7389 2.857186 TACACTCTGGCATTTGCTCA 57.143 45.000 2.12 0.00 41.70 4.26
3124 7393 4.440758 CACGTTTTTACACTCTGGCATTTG 59.559 41.667 0.00 0.00 0.00 2.32
3136 7405 5.525745 TGAGAAGCATCTTCACGTTTTTACA 59.474 36.000 8.98 0.00 35.54 2.41
3137 7406 5.985781 TGAGAAGCATCTTCACGTTTTTAC 58.014 37.500 8.98 0.00 35.54 2.01
3145 7414 5.423015 TGATTACCTGAGAAGCATCTTCAC 58.577 41.667 8.98 3.67 35.54 3.18
3156 7425 6.180472 GGTGAAGGATTTTGATTACCTGAGA 58.820 40.000 0.00 0.00 32.73 3.27
3167 7436 3.512724 AGATGGCTTGGTGAAGGATTTTG 59.487 43.478 0.00 0.00 0.00 2.44
3174 7443 1.280133 TCCAGAGATGGCTTGGTGAAG 59.720 52.381 0.00 0.00 0.00 3.02
3178 7447 0.617413 CAGTCCAGAGATGGCTTGGT 59.383 55.000 0.00 0.00 0.00 3.67
3182 7451 0.339859 TACCCAGTCCAGAGATGGCT 59.660 55.000 0.00 0.00 32.46 4.75
3184 7453 1.759445 CACTACCCAGTCCAGAGATGG 59.241 57.143 0.00 0.00 30.46 3.51
3185 7454 1.759445 CCACTACCCAGTCCAGAGATG 59.241 57.143 0.00 0.00 30.46 2.90
3186 7455 1.967274 GCCACTACCCAGTCCAGAGAT 60.967 57.143 0.00 0.00 30.46 2.75
3187 7456 0.614979 GCCACTACCCAGTCCAGAGA 60.615 60.000 0.00 0.00 30.46 3.10
3188 7457 0.616111 AGCCACTACCCAGTCCAGAG 60.616 60.000 0.00 0.00 30.46 3.35
3189 7458 0.904865 CAGCCACTACCCAGTCCAGA 60.905 60.000 0.00 0.00 30.46 3.86
3190 7459 0.904865 TCAGCCACTACCCAGTCCAG 60.905 60.000 0.00 0.00 30.46 3.86
3191 7460 1.157513 TCAGCCACTACCCAGTCCA 59.842 57.895 0.00 0.00 30.46 4.02
3198 7487 0.460284 CATGGACGTCAGCCACTACC 60.460 60.000 18.91 0.00 38.44 3.18
3206 7495 0.597637 GGTATCGCCATGGACGTCAG 60.598 60.000 18.40 6.40 37.17 3.51
3317 7607 8.514594 TGAAAAGATTATTTGAGCAAGTCGATT 58.485 29.630 0.00 0.00 0.00 3.34
3320 7610 7.269937 CAGTGAAAAGATTATTTGAGCAAGTCG 59.730 37.037 0.00 0.00 0.00 4.18
3321 7611 8.078596 ACAGTGAAAAGATTATTTGAGCAAGTC 58.921 33.333 0.00 0.00 0.00 3.01
3335 7628 6.715347 ACTTGGCTAAAACAGTGAAAAGAT 57.285 33.333 0.00 0.00 0.00 2.40
3339 7632 7.777095 ACAAATACTTGGCTAAAACAGTGAAA 58.223 30.769 0.00 0.00 36.82 2.69
3362 7655 7.831691 TTGTGGGATGAAAATAGAAAAGACA 57.168 32.000 0.00 0.00 0.00 3.41
3363 7656 7.276438 GCATTGTGGGATGAAAATAGAAAAGAC 59.724 37.037 0.00 0.00 0.00 3.01
3364 7657 7.039152 TGCATTGTGGGATGAAAATAGAAAAGA 60.039 33.333 0.00 0.00 0.00 2.52
3365 7658 7.098477 TGCATTGTGGGATGAAAATAGAAAAG 58.902 34.615 0.00 0.00 0.00 2.27
3366 7659 7.002250 TGCATTGTGGGATGAAAATAGAAAA 57.998 32.000 0.00 0.00 0.00 2.29
3367 7660 6.602410 TGCATTGTGGGATGAAAATAGAAA 57.398 33.333 0.00 0.00 0.00 2.52
3372 7665 3.617045 CGGTTGCATTGTGGGATGAAAAT 60.617 43.478 0.00 0.00 0.00 1.82
3382 7675 1.131126 GTCATCCTCGGTTGCATTGTG 59.869 52.381 0.00 0.00 0.00 3.33
3393 7686 2.202932 CCTTGGGCGTCATCCTCG 60.203 66.667 0.00 0.00 0.00 4.63
3398 7691 1.078708 CGTAACCCTTGGGCGTCAT 60.079 57.895 5.46 0.00 0.00 3.06
3404 7697 3.639672 ATTTAGGACGTAACCCTTGGG 57.360 47.619 3.77 3.77 35.30 4.12
3406 7699 5.391629 GCTGAAATTTAGGACGTAACCCTTG 60.392 44.000 0.00 0.00 35.30 3.61
3410 7703 4.933400 TCTGCTGAAATTTAGGACGTAACC 59.067 41.667 0.00 0.00 0.00 2.85
3411 7704 6.147328 AGTTCTGCTGAAATTTAGGACGTAAC 59.853 38.462 7.68 0.00 33.52 2.50
3412 7705 6.228258 AGTTCTGCTGAAATTTAGGACGTAA 58.772 36.000 7.68 0.00 33.52 3.18
3413 7706 5.790593 AGTTCTGCTGAAATTTAGGACGTA 58.209 37.500 7.68 0.00 33.52 3.57
3414 7707 4.642429 AGTTCTGCTGAAATTTAGGACGT 58.358 39.130 7.68 0.00 33.52 4.34
3415 7708 5.613358 AAGTTCTGCTGAAATTTAGGACG 57.387 39.130 12.47 0.00 37.20 4.79
3416 7709 5.408604 TCGAAGTTCTGCTGAAATTTAGGAC 59.591 40.000 18.09 6.35 40.05 3.85
3417 7710 5.408604 GTCGAAGTTCTGCTGAAATTTAGGA 59.591 40.000 18.09 13.38 40.05 2.94
3418 7711 5.622378 GTCGAAGTTCTGCTGAAATTTAGG 58.378 41.667 18.09 11.70 40.05 2.69
3419 7712 5.107453 ACGTCGAAGTTCTGCTGAAATTTAG 60.107 40.000 18.09 15.14 40.05 1.85
3420 7713 4.748102 ACGTCGAAGTTCTGCTGAAATTTA 59.252 37.500 18.09 8.82 40.05 1.40
3421 7714 3.560068 ACGTCGAAGTTCTGCTGAAATTT 59.440 39.130 18.09 11.11 40.05 1.82
3422 7715 3.131396 ACGTCGAAGTTCTGCTGAAATT 58.869 40.909 17.26 17.26 42.22 1.82
3423 7716 2.731976 GACGTCGAAGTTCTGCTGAAAT 59.268 45.455 5.24 3.83 33.52 2.17
3424 7717 2.124903 GACGTCGAAGTTCTGCTGAAA 58.875 47.619 5.24 0.00 33.52 2.69
3425 7718 1.066454 TGACGTCGAAGTTCTGCTGAA 59.934 47.619 11.62 1.33 0.00 3.02
3426 7719 0.666374 TGACGTCGAAGTTCTGCTGA 59.334 50.000 11.62 0.00 0.00 4.26
3427 7720 1.651138 GATGACGTCGAAGTTCTGCTG 59.349 52.381 11.62 0.00 0.00 4.41
3428 7721 1.402984 GGATGACGTCGAAGTTCTGCT 60.403 52.381 11.62 0.00 0.00 4.24
3429 7722 0.992802 GGATGACGTCGAAGTTCTGC 59.007 55.000 11.62 0.00 0.00 4.26
3430 7723 2.095212 TGAGGATGACGTCGAAGTTCTG 60.095 50.000 11.62 0.00 34.17 3.02
3431 7724 2.160205 TGAGGATGACGTCGAAGTTCT 58.840 47.619 11.62 0.74 34.17 3.01
3432 7725 2.631418 TGAGGATGACGTCGAAGTTC 57.369 50.000 11.62 0.00 34.17 3.01
3433 7726 3.380479 TTTGAGGATGACGTCGAAGTT 57.620 42.857 11.62 0.00 34.17 2.66
3434 7727 3.380479 TTTTGAGGATGACGTCGAAGT 57.620 42.857 11.62 2.87 34.17 3.01
3452 7745 8.558973 TGTCATGACAAAACTTGGAAATTTTT 57.441 26.923 26.02 0.00 38.93 1.94
3453 7746 8.735692 ATGTCATGACAAAACTTGGAAATTTT 57.264 26.923 31.00 7.11 45.41 1.82
3454 7747 8.735692 AATGTCATGACAAAACTTGGAAATTT 57.264 26.923 31.00 13.70 45.41 1.82
3455 7748 8.735692 AAATGTCATGACAAAACTTGGAAATT 57.264 26.923 31.00 13.90 45.41 1.82
3456 7749 8.614346 CAAAATGTCATGACAAAACTTGGAAAT 58.386 29.630 31.00 8.43 45.41 2.17
3457 7750 7.413877 GCAAAATGTCATGACAAAACTTGGAAA 60.414 33.333 31.00 4.59 45.41 3.13
3458 7751 6.036953 GCAAAATGTCATGACAAAACTTGGAA 59.963 34.615 31.00 5.13 45.41 3.53
3459 7752 5.523188 GCAAAATGTCATGACAAAACTTGGA 59.477 36.000 31.00 5.90 45.41 3.53
3460 7753 5.277442 GGCAAAATGTCATGACAAAACTTGG 60.277 40.000 31.00 19.05 45.41 3.61
3461 7754 5.293814 TGGCAAAATGTCATGACAAAACTTG 59.706 36.000 31.00 26.67 45.41 3.16
3462 7755 5.426504 TGGCAAAATGTCATGACAAAACTT 58.573 33.333 31.00 18.27 45.41 2.66
3463 7756 5.021033 TGGCAAAATGTCATGACAAAACT 57.979 34.783 31.00 13.12 45.41 2.66
3464 7757 5.927954 ATGGCAAAATGTCATGACAAAAC 57.072 34.783 31.00 18.08 41.79 2.43
3465 7758 6.939132 AAATGGCAAAATGTCATGACAAAA 57.061 29.167 31.00 9.79 42.67 2.44
3466 7759 8.618702 AATAAATGGCAAAATGTCATGACAAA 57.381 26.923 31.00 10.58 42.67 2.83
3467 7760 8.618702 AAATAAATGGCAAAATGTCATGACAA 57.381 26.923 31.00 14.18 42.67 3.18
3468 7761 8.618702 AAAATAAATGGCAAAATGTCATGACA 57.381 26.923 29.67 29.67 42.67 3.58
3469 7762 8.177013 GGAAAATAAATGGCAAAATGTCATGAC 58.823 33.333 19.27 19.27 42.67 3.06
3470 7763 8.102047 AGGAAAATAAATGGCAAAATGTCATGA 58.898 29.630 0.00 0.00 42.67 3.07
3471 7764 8.271312 AGGAAAATAAATGGCAAAATGTCATG 57.729 30.769 0.00 0.00 42.67 3.07
3472 7765 8.732531 CAAGGAAAATAAATGGCAAAATGTCAT 58.267 29.630 0.00 0.00 45.92 3.06
3473 7766 7.174599 CCAAGGAAAATAAATGGCAAAATGTCA 59.825 33.333 0.00 0.00 35.91 3.58
3474 7767 7.361971 CCCAAGGAAAATAAATGGCAAAATGTC 60.362 37.037 0.00 0.00 0.00 3.06
3475 7768 6.433716 CCCAAGGAAAATAAATGGCAAAATGT 59.566 34.615 0.00 0.00 0.00 2.71
3476 7769 6.127675 CCCCAAGGAAAATAAATGGCAAAATG 60.128 38.462 0.00 0.00 33.47 2.32
3477 7770 5.951148 CCCCAAGGAAAATAAATGGCAAAAT 59.049 36.000 0.00 0.00 33.47 1.82
3478 7771 5.320277 CCCCAAGGAAAATAAATGGCAAAA 58.680 37.500 0.00 0.00 33.47 2.44
3479 7772 4.809007 GCCCCAAGGAAAATAAATGGCAAA 60.809 41.667 0.00 0.00 36.40 3.68
3480 7773 3.308046 GCCCCAAGGAAAATAAATGGCAA 60.308 43.478 0.00 0.00 36.40 4.52
3481 7774 2.238395 GCCCCAAGGAAAATAAATGGCA 59.762 45.455 0.00 0.00 36.40 4.92
3482 7775 2.741553 CGCCCCAAGGAAAATAAATGGC 60.742 50.000 0.00 0.00 33.47 4.40
3483 7776 2.741553 GCGCCCCAAGGAAAATAAATGG 60.742 50.000 0.00 0.00 33.47 3.16
3484 7777 2.093764 TGCGCCCCAAGGAAAATAAATG 60.094 45.455 4.18 0.00 33.47 2.32
3485 7778 2.183679 TGCGCCCCAAGGAAAATAAAT 58.816 42.857 4.18 0.00 33.47 1.40
3486 7779 1.633774 TGCGCCCCAAGGAAAATAAA 58.366 45.000 4.18 0.00 33.47 1.40
3487 7780 1.859302 ATGCGCCCCAAGGAAAATAA 58.141 45.000 4.18 0.00 33.47 1.40
3488 7781 1.754226 GAATGCGCCCCAAGGAAAATA 59.246 47.619 4.18 0.00 33.47 1.40
3489 7782 0.536724 GAATGCGCCCCAAGGAAAAT 59.463 50.000 4.18 0.00 33.47 1.82
3490 7783 1.540435 GGAATGCGCCCCAAGGAAAA 61.540 55.000 4.18 0.00 33.47 2.29
3491 7784 1.981853 GGAATGCGCCCCAAGGAAA 60.982 57.895 4.18 0.00 33.47 3.13
3492 7785 1.567208 TAGGAATGCGCCCCAAGGAA 61.567 55.000 4.18 0.00 33.47 3.36
3493 7786 1.352622 ATAGGAATGCGCCCCAAGGA 61.353 55.000 4.18 0.00 33.47 3.36
3494 7787 0.468029 AATAGGAATGCGCCCCAAGG 60.468 55.000 4.18 0.00 0.00 3.61
3495 7788 0.954452 GAATAGGAATGCGCCCCAAG 59.046 55.000 4.18 0.00 0.00 3.61
3496 7789 0.817634 CGAATAGGAATGCGCCCCAA 60.818 55.000 4.18 0.00 0.00 4.12
3497 7790 1.227823 CGAATAGGAATGCGCCCCA 60.228 57.895 4.18 0.00 0.00 4.96
3498 7791 0.534203 TTCGAATAGGAATGCGCCCC 60.534 55.000 4.18 3.31 33.81 5.80
3499 7792 0.868406 CTTCGAATAGGAATGCGCCC 59.132 55.000 4.18 0.00 33.81 6.13
3500 7793 0.868406 CCTTCGAATAGGAATGCGCC 59.132 55.000 4.18 0.00 37.50 6.53
3501 7794 0.235926 GCCTTCGAATAGGAATGCGC 59.764 55.000 7.36 0.00 37.50 6.09
3502 7795 0.868406 GGCCTTCGAATAGGAATGCG 59.132 55.000 7.36 0.00 38.11 4.73
3503 7796 0.868406 CGGCCTTCGAATAGGAATGC 59.132 55.000 7.36 0.00 42.43 3.56
3504 7797 2.526304 TCGGCCTTCGAATAGGAATG 57.474 50.000 7.36 0.00 45.86 2.67
3513 7806 0.535335 AACTAGCATTCGGCCTTCGA 59.465 50.000 0.00 0.00 46.50 3.71
3514 7807 0.931005 GAACTAGCATTCGGCCTTCG 59.069 55.000 0.00 0.00 46.50 3.79
3515 7808 1.936547 CTGAACTAGCATTCGGCCTTC 59.063 52.381 0.00 0.00 46.50 3.46
3516 7809 1.279271 ACTGAACTAGCATTCGGCCTT 59.721 47.619 0.00 0.00 46.50 4.35
3517 7810 0.905357 ACTGAACTAGCATTCGGCCT 59.095 50.000 0.00 0.00 46.50 5.19
3518 7811 2.596904 TACTGAACTAGCATTCGGCC 57.403 50.000 0.00 0.00 46.50 6.13
3519 7812 5.485662 AAAATACTGAACTAGCATTCGGC 57.514 39.130 2.58 0.00 38.35 5.54
3540 7833 8.830201 ACTAATGCATTTACATCAAGCAAAAA 57.170 26.923 18.75 0.00 38.85 1.94
3541 7834 8.710551 CAACTAATGCATTTACATCAAGCAAAA 58.289 29.630 18.75 0.00 38.85 2.44
3542 7835 8.242085 CAACTAATGCATTTACATCAAGCAAA 57.758 30.769 18.75 0.00 38.85 3.68
3543 7836 7.815398 CAACTAATGCATTTACATCAAGCAA 57.185 32.000 18.75 0.00 38.85 3.91
3559 7852 3.993920 AGCCAAAACCTTGCAACTAATG 58.006 40.909 0.00 0.00 0.00 1.90
3560 7853 4.021456 GGTAGCCAAAACCTTGCAACTAAT 60.021 41.667 0.00 0.00 33.97 1.73
3561 7854 3.319689 GGTAGCCAAAACCTTGCAACTAA 59.680 43.478 0.00 0.00 33.97 2.24
3562 7855 2.888414 GGTAGCCAAAACCTTGCAACTA 59.112 45.455 0.00 0.00 33.97 2.24
3563 7856 1.686587 GGTAGCCAAAACCTTGCAACT 59.313 47.619 0.00 0.00 33.97 3.16
3564 7857 1.601914 CGGTAGCCAAAACCTTGCAAC 60.602 52.381 0.00 0.00 34.66 4.17
3565 7858 0.671251 CGGTAGCCAAAACCTTGCAA 59.329 50.000 0.00 0.00 34.66 4.08
3566 7859 1.175983 CCGGTAGCCAAAACCTTGCA 61.176 55.000 0.00 0.00 34.66 4.08
3567 7860 0.891904 TCCGGTAGCCAAAACCTTGC 60.892 55.000 0.00 0.00 34.66 4.01
3568 7861 1.834188 ATCCGGTAGCCAAAACCTTG 58.166 50.000 0.00 0.00 34.66 3.61
3569 7862 2.306512 TGTATCCGGTAGCCAAAACCTT 59.693 45.455 0.00 0.00 34.66 3.50
3570 7863 1.910671 TGTATCCGGTAGCCAAAACCT 59.089 47.619 0.00 0.00 34.66 3.50
3571 7864 2.406596 TGTATCCGGTAGCCAAAACC 57.593 50.000 0.00 0.00 0.00 3.27
3572 7865 3.537580 TCATGTATCCGGTAGCCAAAAC 58.462 45.455 0.00 0.00 0.00 2.43
3573 7866 3.916359 TCATGTATCCGGTAGCCAAAA 57.084 42.857 0.00 0.00 0.00 2.44
3574 7867 5.554437 TTATCATGTATCCGGTAGCCAAA 57.446 39.130 0.00 0.00 0.00 3.28
3575 7868 5.012664 ACATTATCATGTATCCGGTAGCCAA 59.987 40.000 0.00 0.00 42.24 4.52
3576 7869 4.530553 ACATTATCATGTATCCGGTAGCCA 59.469 41.667 0.00 0.00 42.24 4.75
3577 7870 5.086104 ACATTATCATGTATCCGGTAGCC 57.914 43.478 0.00 0.00 42.24 3.93
3578 7871 6.649141 TCAAACATTATCATGTATCCGGTAGC 59.351 38.462 0.00 0.00 43.34 3.58
3579 7872 8.777865 ATCAAACATTATCATGTATCCGGTAG 57.222 34.615 0.00 0.00 43.34 3.18
3581 7874 9.219603 CTAATCAAACATTATCATGTATCCGGT 57.780 33.333 0.00 0.00 43.34 5.28
3582 7875 9.219603 ACTAATCAAACATTATCATGTATCCGG 57.780 33.333 0.00 0.00 43.34 5.14


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

AutoCloner maintained by Alex Coulton.