Multiple sequence alignment - TraesCS5A01G314800

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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 TraesCS5A01G314800 chr5A 100.000 3830 0 0 1 3830 525118885 525115056 0.000000e+00 7073.0
1 TraesCS5A01G314800 chr5A 81.643 572 96 7 3168 3730 665889401 665888830 2.080000e-127 466.0
2 TraesCS5A01G314800 chr5A 84.722 72 11 0 2731 2802 382564062 382563991 5.310000e-09 73.1
3 TraesCS5A01G314800 chr5B 85.974 3572 261 117 326 3784 497906288 497902844 0.000000e+00 3600.0
4 TraesCS5A01G314800 chr5B 77.053 414 66 19 3428 3825 683402665 683402265 1.080000e-50 211.0
5 TraesCS5A01G314800 chr5B 87.640 178 15 5 8 183 497906647 497906475 2.330000e-47 200.0
6 TraesCS5A01G314800 chr5B 97.727 44 0 1 214 257 497906398 497906356 1.480000e-09 75.0
7 TraesCS5A01G314800 chr5B 83.784 74 12 0 2730 2803 330846571 330846498 1.910000e-08 71.3
8 TraesCS5A01G314800 chr5D 87.384 3020 158 107 279 3172 413068919 413065997 0.000000e+00 3260.0
9 TraesCS5A01G314800 chr5D 86.497 2755 182 82 977 3630 413068170 413065505 0.000000e+00 2852.0
10 TraesCS5A01G314800 chr5D 80.282 284 15 10 8 259 413069656 413069382 3.930000e-40 176.0
11 TraesCS5A01G314800 chr5D 90.598 117 10 1 3714 3830 413065333 413065218 1.840000e-33 154.0
12 TraesCS5A01G314800 chr5D 97.333 75 1 1 185 259 413069068 413068995 4.020000e-25 126.0
13 TraesCS5A01G314800 chr5D 81.319 91 16 1 2713 2803 290072206 290072117 5.310000e-09 73.1
14 TraesCS5A01G314800 chr7D 82.043 607 95 10 3186 3784 167512342 167512942 4.420000e-139 505.0
15 TraesCS5A01G314800 chr7D 87.500 64 8 0 3721 3784 153061674 153061611 1.480000e-09 75.0
16 TraesCS5A01G314800 chr3D 80.984 610 102 8 3183 3784 518544748 518544145 4.480000e-129 472.0
17 TraesCS5A01G314800 chr3D 77.533 681 122 20 3168 3830 49480059 49480726 7.760000e-102 381.0
18 TraesCS5A01G314800 chr2A 79.904 627 107 12 3168 3784 707230345 707230962 3.510000e-120 442.0
19 TraesCS5A01G314800 chr4D 79.393 626 114 10 3168 3784 287536928 287537547 9.830000e-116 427.0
20 TraesCS5A01G314800 chr4D 77.816 586 122 4 3168 3745 439740860 439740275 4.710000e-94 355.0
21 TraesCS5A01G314800 chr4D 79.487 117 21 1 3714 3830 475042673 475042560 3.170000e-11 80.5
22 TraesCS5A01G314800 chr4D 80.000 110 19 1 3721 3830 434930482 434930588 1.140000e-10 78.7
23 TraesCS5A01G314800 chr1A 79.393 626 113 13 3168 3784 73129899 73130517 9.830000e-116 427.0
24 TraesCS5A01G314800 chr2B 81.720 93 15 2 3693 3784 680509323 680509414 4.100000e-10 76.8
25 TraesCS5A01G314800 chr3A 78.632 117 22 1 3714 3830 62259360 62259473 1.480000e-09 75.0
26 TraesCS5A01G314800 chr2D 77.778 126 24 3 3641 3764 414385598 414385475 1.480000e-09 75.0


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 TraesCS5A01G314800 chr5A 525115056 525118885 3829 True 7073.000000 7073 100.0000 1 3830 1 chr5A.!!$R2 3829
1 TraesCS5A01G314800 chr5A 665888830 665889401 571 True 466.000000 466 81.6430 3168 3730 1 chr5A.!!$R3 562
2 TraesCS5A01G314800 chr5B 497902844 497906647 3803 True 1291.666667 3600 90.4470 8 3784 3 chr5B.!!$R3 3776
3 TraesCS5A01G314800 chr5D 413065218 413069656 4438 True 1313.600000 3260 88.4188 8 3830 5 chr5D.!!$R2 3822
4 TraesCS5A01G314800 chr7D 167512342 167512942 600 False 505.000000 505 82.0430 3186 3784 1 chr7D.!!$F1 598
5 TraesCS5A01G314800 chr3D 518544145 518544748 603 True 472.000000 472 80.9840 3183 3784 1 chr3D.!!$R1 601
6 TraesCS5A01G314800 chr3D 49480059 49480726 667 False 381.000000 381 77.5330 3168 3830 1 chr3D.!!$F1 662
7 TraesCS5A01G314800 chr2A 707230345 707230962 617 False 442.000000 442 79.9040 3168 3784 1 chr2A.!!$F1 616
8 TraesCS5A01G314800 chr4D 287536928 287537547 619 False 427.000000 427 79.3930 3168 3784 1 chr4D.!!$F1 616
9 TraesCS5A01G314800 chr4D 439740275 439740860 585 True 355.000000 355 77.8160 3168 3745 1 chr4D.!!$R1 577
10 TraesCS5A01G314800 chr1A 73129899 73130517 618 False 427.000000 427 79.3930 3168 3784 1 chr1A.!!$F1 616

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
442 966 0.096976 GATGGCAACGTTGGTGATCG 59.903 55.0 28.33 2.69 42.51 3.69 F
1300 1884 0.101399 GCTTCTTCGATCCTGCTCGA 59.899 55.0 0.00 0.00 45.32 4.04 F
2387 3021 0.105964 TACCACAAGTGCGCTTCTGT 59.894 50.0 10.18 3.89 31.49 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 2302 0.036577 CTGAAGAGCAGGGGACAGTG 60.037 60.0 0.0 0.0 41.07 3.66 R
2458 3092 0.179111 TGCCGTATGCCTTCTCGAAG 60.179 55.0 0.0 0.0 40.16 3.79 R
3575 4285 0.098376 CGTCCTACTACACCAGCGAC 59.902 60.0 0.0 0.0 0.00 5.19 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.753867 GAAGACCGGATTCCTCCTCC 59.246 60.000 9.46 0.00 39.65 4.30
74 79 2.124193 CTGCCGCCCCATCAATCA 60.124 61.111 0.00 0.00 0.00 2.57
75 80 2.124193 TGCCGCCCCATCAATCAG 60.124 61.111 0.00 0.00 0.00 2.90
79 84 0.179009 CCGCCCCATCAATCAGACAT 60.179 55.000 0.00 0.00 0.00 3.06
80 85 0.949397 CGCCCCATCAATCAGACATG 59.051 55.000 0.00 0.00 0.00 3.21
81 86 1.475571 CGCCCCATCAATCAGACATGA 60.476 52.381 0.00 0.00 40.50 3.07
82 87 2.658285 GCCCCATCAATCAGACATGAA 58.342 47.619 0.00 0.00 39.39 2.57
83 88 3.025978 GCCCCATCAATCAGACATGAAA 58.974 45.455 0.00 0.00 39.39 2.69
85 90 4.018490 CCCCATCAATCAGACATGAAACA 58.982 43.478 0.00 0.00 39.39 2.83
86 91 4.097437 CCCCATCAATCAGACATGAAACAG 59.903 45.833 0.00 0.00 39.39 3.16
129 139 4.839668 TTTTTCCCTTTACCGTGTCATG 57.160 40.909 0.00 0.00 0.00 3.07
183 583 0.250727 CTGGGGCACGGAAAAGAAGA 60.251 55.000 0.00 0.00 0.00 2.87
184 584 0.183971 TGGGGCACGGAAAAGAAGAA 59.816 50.000 0.00 0.00 0.00 2.52
208 628 1.826487 GTGGTTGTTCCCCGCACTT 60.826 57.895 0.00 0.00 34.77 3.16
257 706 1.082300 CACGACTCTGCACGTACGT 60.082 57.895 16.72 16.72 40.76 3.57
258 707 0.164432 CACGACTCTGCACGTACGTA 59.836 55.000 22.34 5.54 40.76 3.57
259 708 0.441533 ACGACTCTGCACGTACGTAG 59.558 55.000 22.34 17.01 40.92 3.51
261 710 1.655597 CGACTCTGCACGTACGTAGTA 59.344 52.381 22.34 13.59 45.11 1.82
273 722 1.032114 ACGTAGTAGGTACCACGCCC 61.032 60.000 19.23 2.25 43.35 6.13
274 723 0.749454 CGTAGTAGGTACCACGCCCT 60.749 60.000 15.94 4.48 34.90 5.19
275 724 0.743097 GTAGTAGGTACCACGCCCTG 59.257 60.000 15.94 0.00 32.08 4.45
276 725 1.039233 TAGTAGGTACCACGCCCTGC 61.039 60.000 15.94 0.00 34.05 4.85
277 726 2.038329 TAGGTACCACGCCCTGCT 59.962 61.111 15.94 0.00 32.08 4.24
298 810 1.196200 CCTGAAAACGTTGGTTTGCG 58.804 50.000 0.00 0.00 45.35 4.85
332 851 4.135153 CCTCCTGACTCGTGCCGG 62.135 72.222 0.00 0.00 0.00 6.13
397 918 1.356398 TCCGGCCCATAATTATTCCCC 59.644 52.381 0.00 0.00 0.00 4.81
400 921 2.225017 CGGCCCATAATTATTCCCCTGT 60.225 50.000 0.00 0.00 0.00 4.00
428 949 2.663188 GATGGAGACGGCGATGGC 60.663 66.667 16.62 0.00 38.90 4.40
442 966 0.096976 GATGGCAACGTTGGTGATCG 59.903 55.000 28.33 2.69 42.51 3.69
443 967 1.305219 ATGGCAACGTTGGTGATCGG 61.305 55.000 28.33 1.91 42.51 4.18
444 968 2.686816 GGCAACGTTGGTGATCGGG 61.687 63.158 28.33 1.15 0.00 5.14
445 969 2.867472 CAACGTTGGTGATCGGGC 59.133 61.111 20.71 0.00 0.00 6.13
446 970 2.740826 AACGTTGGTGATCGGGCG 60.741 61.111 0.00 0.00 0.00 6.13
447 971 4.752879 ACGTTGGTGATCGGGCGG 62.753 66.667 0.00 0.00 0.00 6.13
601 1125 1.403647 CGCGGTTCCTCACATCACTTA 60.404 52.381 0.00 0.00 0.00 2.24
653 1177 2.724377 CGATAGAGCTGCCTCGCA 59.276 61.111 0.00 0.00 43.05 5.10
671 1195 2.279851 GCGTGCCAAAACCCCAAC 60.280 61.111 0.00 0.00 0.00 3.77
679 1203 2.035449 GCCAAAACCCCAACACTAACTC 59.965 50.000 0.00 0.00 0.00 3.01
722 1253 8.008513 TCCCAAAACTAACTATAGTAGCAGAG 57.991 38.462 5.65 2.02 41.57 3.35
760 1291 1.576356 GATCGATCGCCTTTTGAGCT 58.424 50.000 11.09 0.00 0.00 4.09
762 1293 0.460284 TCGATCGCCTTTTGAGCTCC 60.460 55.000 12.15 0.00 0.00 4.70
844 1378 3.056749 ACGCAATTACTCCTATCCCGATC 60.057 47.826 0.00 0.00 0.00 3.69
878 1419 2.953284 AGACTATAGCTCGTGGCCTA 57.047 50.000 3.32 0.00 43.05 3.93
926 1479 4.369182 CAGTCTATAAATCTTTCGGCGGT 58.631 43.478 7.21 0.00 0.00 5.68
990 1574 1.299541 CACGGAGAGAGAGAGAGAGC 58.700 60.000 0.00 0.00 0.00 4.09
1252 1836 8.613060 ATTCATCTTCGTACGTATACTCCTAA 57.387 34.615 16.05 0.00 0.00 2.69
1279 1863 2.572284 CCCACCGTCGTCTCCTTC 59.428 66.667 0.00 0.00 0.00 3.46
1285 1869 0.456995 CCGTCGTCTCCTTCAGCTTC 60.457 60.000 0.00 0.00 0.00 3.86
1299 1883 0.102120 AGCTTCTTCGATCCTGCTCG 59.898 55.000 0.00 0.00 39.99 5.03
1300 1884 0.101399 GCTTCTTCGATCCTGCTCGA 59.899 55.000 0.00 0.00 45.32 4.04
1328 1936 4.848357 AGTTCTGTACCCTGATTGATTGG 58.152 43.478 0.00 0.00 0.00 3.16
1339 1947 5.068198 CCCTGATTGATTGGTAGATTGGTTG 59.932 44.000 0.00 0.00 0.00 3.77
1354 1962 0.608130 GGTTGGGTGAATTTCAGGGC 59.392 55.000 0.00 0.00 0.00 5.19
1418 2026 4.171754 CAAGCGGTACTACCTAGTTGTTC 58.828 47.826 3.68 0.00 35.66 3.18
1419 2027 2.421424 AGCGGTACTACCTAGTTGTTCG 59.579 50.000 3.68 0.00 35.66 3.95
1420 2028 2.420022 GCGGTACTACCTAGTTGTTCGA 59.580 50.000 3.68 0.00 35.66 3.71
1421 2029 3.065925 GCGGTACTACCTAGTTGTTCGAT 59.934 47.826 3.68 0.00 35.66 3.59
1422 2030 4.787882 GCGGTACTACCTAGTTGTTCGATC 60.788 50.000 3.68 0.00 35.66 3.69
1426 2034 5.831702 ACTACCTAGTTGTTCGATCGATT 57.168 39.130 20.18 5.35 31.13 3.34
1431 2039 4.681942 CCTAGTTGTTCGATCGATTCATCC 59.318 45.833 20.18 13.61 0.00 3.51
1432 2040 4.392921 AGTTGTTCGATCGATTCATCCT 57.607 40.909 20.18 15.31 0.00 3.24
1435 2043 4.385358 TGTTCGATCGATTCATCCTTCA 57.615 40.909 20.18 0.00 0.00 3.02
1445 2053 1.942776 TCATCCTTCAGTCAGGAGCA 58.057 50.000 0.00 0.00 46.60 4.26
1447 2055 2.433604 TCATCCTTCAGTCAGGAGCATC 59.566 50.000 0.00 0.00 46.60 3.91
1448 2056 1.942776 TCCTTCAGTCAGGAGCATCA 58.057 50.000 0.00 0.00 38.11 3.07
1457 2065 5.356190 TCAGTCAGGAGCATCAATTTGATTC 59.644 40.000 9.19 5.09 34.28 2.52
1460 2068 3.702548 CAGGAGCATCAATTTGATTCCCA 59.297 43.478 19.70 0.00 35.40 4.37
1501 2112 0.385098 GACTAACCGTTTTGCCGTGC 60.385 55.000 0.00 0.00 0.00 5.34
1685 2299 1.536940 CGTAAAACCCCAATCCCGTT 58.463 50.000 0.00 0.00 0.00 4.44
1688 2302 1.552578 AAAACCCCAATCCCGTTAGC 58.447 50.000 0.00 0.00 0.00 3.09
1713 2331 0.469070 CCCCTGCTCTTCAGAGATGG 59.531 60.000 8.09 8.02 45.72 3.51
1714 2332 0.179051 CCCTGCTCTTCAGAGATGGC 60.179 60.000 8.09 0.00 45.72 4.40
1718 2336 0.529555 GCTCTTCAGAGATGGCCGAC 60.530 60.000 8.09 0.00 44.74 4.79
1732 2350 1.203928 GCCGACGATCTTCAGTGATG 58.796 55.000 0.00 0.00 0.00 3.07
1735 2353 1.576356 GACGATCTTCAGTGATGGCC 58.424 55.000 0.00 0.00 0.00 5.36
1746 2364 0.883833 GTGATGGCCCTGACACTTTG 59.116 55.000 0.00 0.00 0.00 2.77
1752 2370 1.272147 GGCCCTGACACTTTGGAGAAT 60.272 52.381 0.00 0.00 0.00 2.40
1753 2371 1.815003 GCCCTGACACTTTGGAGAATG 59.185 52.381 0.00 0.00 0.00 2.67
1755 2373 3.490348 CCCTGACACTTTGGAGAATGTT 58.510 45.455 0.00 0.00 0.00 2.71
1756 2374 3.891366 CCCTGACACTTTGGAGAATGTTT 59.109 43.478 0.00 0.00 0.00 2.83
1757 2375 4.022849 CCCTGACACTTTGGAGAATGTTTC 60.023 45.833 0.00 0.00 0.00 2.78
1758 2376 4.022849 CCTGACACTTTGGAGAATGTTTCC 60.023 45.833 0.00 0.00 35.20 3.13
1759 2377 4.792068 TGACACTTTGGAGAATGTTTCCT 58.208 39.130 0.00 0.00 35.67 3.36
1760 2378 5.935945 TGACACTTTGGAGAATGTTTCCTA 58.064 37.500 0.00 0.00 35.67 2.94
1995 2629 0.740868 ACTGGCGTCGATGTGATTGG 60.741 55.000 6.48 0.00 0.00 3.16
2199 2833 1.507174 GAGCTCAACGTCTACGGCT 59.493 57.895 9.40 5.63 44.95 5.52
2348 2982 2.104963 GCCCAATTAACAACCAACCCAA 59.895 45.455 0.00 0.00 0.00 4.12
2349 2983 3.734463 CCCAATTAACAACCAACCCAAC 58.266 45.455 0.00 0.00 0.00 3.77
2350 2984 3.495276 CCCAATTAACAACCAACCCAACC 60.495 47.826 0.00 0.00 0.00 3.77
2351 2985 3.495276 CCAATTAACAACCAACCCAACCC 60.495 47.826 0.00 0.00 0.00 4.11
2352 2986 2.544844 TTAACAACCAACCCAACCCA 57.455 45.000 0.00 0.00 0.00 4.51
2354 2988 1.334384 AACAACCAACCCAACCCAGC 61.334 55.000 0.00 0.00 0.00 4.85
2373 3007 1.733526 GCCCGGCATCATTTACCAC 59.266 57.895 3.91 0.00 0.00 4.16
2375 3009 1.468985 CCCGGCATCATTTACCACAA 58.531 50.000 0.00 0.00 0.00 3.33
2376 3010 1.405105 CCCGGCATCATTTACCACAAG 59.595 52.381 0.00 0.00 0.00 3.16
2377 3011 2.091541 CCGGCATCATTTACCACAAGT 58.908 47.619 0.00 0.00 0.00 3.16
2378 3012 2.159393 CCGGCATCATTTACCACAAGTG 60.159 50.000 0.00 0.00 0.00 3.16
2379 3013 2.731968 CGGCATCATTTACCACAAGTGC 60.732 50.000 0.00 0.00 0.00 4.40
2380 3014 2.518949 GCATCATTTACCACAAGTGCG 58.481 47.619 0.00 0.00 0.00 5.34
2383 3017 2.226330 TCATTTACCACAAGTGCGCTT 58.774 42.857 9.73 6.71 34.82 4.68
2384 3018 2.225491 TCATTTACCACAAGTGCGCTTC 59.775 45.455 10.18 1.40 31.49 3.86
2385 3019 1.961793 TTTACCACAAGTGCGCTTCT 58.038 45.000 10.18 4.18 31.49 2.85
2386 3020 1.225855 TTACCACAAGTGCGCTTCTG 58.774 50.000 10.18 9.04 31.49 3.02
2387 3021 0.105964 TACCACAAGTGCGCTTCTGT 59.894 50.000 10.18 3.89 31.49 3.41
2458 3092 2.202987 CTGGAGATGGTGAGCGCC 60.203 66.667 2.29 0.00 0.00 6.53
2489 3123 0.034337 ATACGGCAAGGTTGACACGT 59.966 50.000 10.74 10.74 35.35 4.49
2511 3145 6.015434 ACGTTCTTCTTTGCCCTTGATATTTT 60.015 34.615 0.00 0.00 0.00 1.82
2520 3164 3.638160 GCCCTTGATATTTTGCCTGATGA 59.362 43.478 0.00 0.00 0.00 2.92
2524 3168 6.536224 CCCTTGATATTTTGCCTGATGAAAAC 59.464 38.462 0.00 0.00 0.00 2.43
2528 3172 1.698506 TTTGCCTGATGAAAACGGGT 58.301 45.000 0.00 0.00 37.49 5.28
2529 3173 1.243902 TTGCCTGATGAAAACGGGTC 58.756 50.000 0.00 0.00 37.49 4.46
2540 3184 1.410004 AAACGGGTCTGAGACTGACA 58.590 50.000 12.92 0.00 34.69 3.58
2577 3221 2.819595 CCGGTGAAGATGTGCCCG 60.820 66.667 0.00 0.00 38.39 6.13
2657 3301 1.591863 GCTGGAGGTAACCGATCGC 60.592 63.158 10.32 0.00 37.17 4.58
2658 3302 1.067582 CTGGAGGTAACCGATCGCC 59.932 63.158 10.32 5.40 37.17 5.54
2661 3305 1.588139 GAGGTAACCGATCGCCGTG 60.588 63.158 10.32 0.00 36.31 4.94
2662 3306 1.996786 GAGGTAACCGATCGCCGTGA 61.997 60.000 10.32 0.00 36.31 4.35
2664 3308 1.416050 GGTAACCGATCGCCGTGAAC 61.416 60.000 10.32 5.77 36.31 3.18
2665 3309 0.733566 GTAACCGATCGCCGTGAACA 60.734 55.000 10.32 0.00 36.31 3.18
2666 3310 0.733566 TAACCGATCGCCGTGAACAC 60.734 55.000 10.32 0.00 36.31 3.32
2667 3311 3.186047 CCGATCGCCGTGAACACC 61.186 66.667 10.32 0.00 36.31 4.16
2668 3312 2.431771 CGATCGCCGTGAACACCA 60.432 61.111 0.26 0.00 0.00 4.17
2669 3313 2.444624 CGATCGCCGTGAACACCAG 61.445 63.158 0.26 0.00 0.00 4.00
2670 3314 1.374252 GATCGCCGTGAACACCAGT 60.374 57.895 0.00 0.00 0.00 4.00
2671 3315 1.352156 GATCGCCGTGAACACCAGTC 61.352 60.000 0.00 0.00 0.00 3.51
2701 3358 3.113322 TCGAGCGAGATGGATTAAAACG 58.887 45.455 0.00 0.00 0.00 3.60
2702 3359 2.858344 CGAGCGAGATGGATTAAAACGT 59.142 45.455 0.00 0.00 0.00 3.99
2705 3362 2.351726 GCGAGATGGATTAAAACGTGCT 59.648 45.455 0.00 0.00 0.00 4.40
2706 3363 3.554324 GCGAGATGGATTAAAACGTGCTA 59.446 43.478 0.00 0.00 0.00 3.49
2796 3467 0.675837 GGGCCAAGAAGAACCCGTAC 60.676 60.000 4.39 0.00 31.32 3.67
2831 3505 4.458708 GACGCTGAAAACAAAGACTGATC 58.541 43.478 0.00 0.00 0.00 2.92
2834 3508 3.498397 GCTGAAAACAAAGACTGATCCGA 59.502 43.478 0.00 0.00 0.00 4.55
2836 3510 5.611796 TGAAAACAAAGACTGATCCGATG 57.388 39.130 0.00 0.00 0.00 3.84
2837 3511 4.455533 TGAAAACAAAGACTGATCCGATGG 59.544 41.667 0.00 0.00 0.00 3.51
2917 3593 4.486125 AAGTGTGCCCAGAAAATGTTTT 57.514 36.364 0.00 0.00 0.00 2.43
3062 3739 2.414691 GCCGTCATCTGCTTCCTTTTTC 60.415 50.000 0.00 0.00 0.00 2.29
3087 3764 5.141182 TCCTTCCAATTATAGAGCGAGACT 58.859 41.667 0.00 0.00 0.00 3.24
3125 3802 8.637986 TCATTACAAACTTTTTACTGCTTGGAT 58.362 29.630 0.00 0.00 0.00 3.41
3127 3804 6.715347 ACAAACTTTTTACTGCTTGGATCT 57.285 33.333 0.00 0.00 0.00 2.75
3145 3822 3.851458 TCTATAGTACTCGCAGGGTGA 57.149 47.619 0.00 0.00 0.00 4.02
3159 3836 1.423921 AGGGTGAGTTTGGTTACCTGG 59.576 52.381 2.07 0.00 33.71 4.45
3179 3882 5.004361 TGGATCATTTTTGGGTCTGGTTA 57.996 39.130 0.00 0.00 0.00 2.85
3182 3885 6.327626 TGGATCATTTTTGGGTCTGGTTAAAA 59.672 34.615 0.00 0.00 0.00 1.52
3183 3886 7.017056 TGGATCATTTTTGGGTCTGGTTAAAAT 59.983 33.333 0.00 0.00 0.00 1.82
3223 3929 2.904697 TTGCATGTTGATTGGTTGCA 57.095 40.000 0.00 0.00 41.22 4.08
3241 3948 0.549950 CATGCATCCCCTCTCCTTGT 59.450 55.000 0.00 0.00 0.00 3.16
3413 4122 4.321966 TGGACGGTGATTGCGGCA 62.322 61.111 0.00 0.00 0.00 5.69
3461 4170 2.730733 GGGCGAGCGATCTCATCA 59.269 61.111 0.00 0.00 39.30 3.07
3521 4230 3.305720 AGGAAGTCTGTGTGGAGTAACA 58.694 45.455 0.00 0.00 0.00 2.41
3536 4245 5.201243 GGAGTAACAAATAGGAGGGCATTT 58.799 41.667 0.00 0.00 0.00 2.32
3576 4286 2.914695 AAAATGCAGTGTGCCATTGT 57.085 40.000 0.00 0.00 44.23 2.71
3577 4287 2.443887 AAATGCAGTGTGCCATTGTC 57.556 45.000 0.00 0.00 44.23 3.18
3579 4289 2.126734 GCAGTGTGCCATTGTCGC 60.127 61.111 0.00 0.00 37.42 5.19
3597 4368 1.930908 GCTGGTGTAGTAGGACGCGT 61.931 60.000 13.85 13.85 0.00 6.01
3598 4369 0.179171 CTGGTGTAGTAGGACGCGTG 60.179 60.000 20.70 0.00 0.00 5.34
3599 4370 1.515736 GGTGTAGTAGGACGCGTGC 60.516 63.158 24.26 24.26 0.00 5.34
3603 4374 1.742880 TAGTAGGACGCGTGCGAGT 60.743 57.895 25.16 23.95 42.83 4.18
3652 4621 0.886563 GCCGGTATAGTAGGACGCAT 59.113 55.000 1.90 0.00 0.00 4.73
3673 4642 1.536073 CGTGGAGGCTGAGAGGAACA 61.536 60.000 0.00 0.00 0.00 3.18
3680 4649 1.066858 GGCTGAGAGGAACAATGTCGA 60.067 52.381 0.00 0.00 0.00 4.20
3681 4650 1.996191 GCTGAGAGGAACAATGTCGAC 59.004 52.381 9.11 9.11 0.00 4.20
3682 4651 2.254459 CTGAGAGGAACAATGTCGACG 58.746 52.381 11.62 0.00 0.00 5.12
3683 4652 1.883926 TGAGAGGAACAATGTCGACGA 59.116 47.619 11.62 0.00 0.00 4.20
3684 4653 2.492088 TGAGAGGAACAATGTCGACGAT 59.508 45.455 11.62 2.87 0.00 3.73
3685 4654 2.854777 GAGAGGAACAATGTCGACGATG 59.145 50.000 11.62 14.33 0.00 3.84
3686 4655 1.927174 GAGGAACAATGTCGACGATGG 59.073 52.381 20.30 11.50 0.00 3.51
3687 4656 0.373716 GGAACAATGTCGACGATGGC 59.626 55.000 20.30 13.24 0.00 4.40
3688 4657 1.359848 GAACAATGTCGACGATGGCT 58.640 50.000 20.30 10.00 0.00 4.75
3689 4658 1.732259 GAACAATGTCGACGATGGCTT 59.268 47.619 20.30 9.63 0.00 4.35
3690 4659 1.808411 ACAATGTCGACGATGGCTTT 58.192 45.000 20.30 1.57 0.00 3.51
3691 4660 1.464608 ACAATGTCGACGATGGCTTTG 59.535 47.619 20.30 5.99 0.00 2.77
3692 4661 1.086696 AATGTCGACGATGGCTTTGG 58.913 50.000 11.62 0.00 0.00 3.28
3693 4662 0.036388 ATGTCGACGATGGCTTTGGT 60.036 50.000 11.62 0.00 0.00 3.67
3694 4663 0.948623 TGTCGACGATGGCTTTGGTG 60.949 55.000 11.62 0.00 0.00 4.17
3695 4664 0.949105 GTCGACGATGGCTTTGGTGT 60.949 55.000 0.00 0.00 0.00 4.16
3696 4665 0.604073 TCGACGATGGCTTTGGTGTA 59.396 50.000 0.00 0.00 0.00 2.90
3697 4666 0.999406 CGACGATGGCTTTGGTGTAG 59.001 55.000 0.00 0.00 0.00 2.74
3698 4667 1.671850 CGACGATGGCTTTGGTGTAGT 60.672 52.381 0.00 0.00 0.00 2.73
3699 4668 2.416296 CGACGATGGCTTTGGTGTAGTA 60.416 50.000 0.00 0.00 0.00 1.82
3700 4669 3.187700 GACGATGGCTTTGGTGTAGTAG 58.812 50.000 0.00 0.00 0.00 2.57
3701 4670 2.093658 ACGATGGCTTTGGTGTAGTAGG 60.094 50.000 0.00 0.00 0.00 3.18
3702 4671 2.167693 CGATGGCTTTGGTGTAGTAGGA 59.832 50.000 0.00 0.00 0.00 2.94
3703 4672 3.181465 CGATGGCTTTGGTGTAGTAGGAT 60.181 47.826 0.00 0.00 0.00 3.24
3704 4673 4.038763 CGATGGCTTTGGTGTAGTAGGATA 59.961 45.833 0.00 0.00 0.00 2.59
3705 4674 5.279506 CGATGGCTTTGGTGTAGTAGGATAT 60.280 44.000 0.00 0.00 0.00 1.63
3706 4675 5.290493 TGGCTTTGGTGTAGTAGGATATG 57.710 43.478 0.00 0.00 0.00 1.78
3707 4676 4.102524 TGGCTTTGGTGTAGTAGGATATGG 59.897 45.833 0.00 0.00 0.00 2.74
3708 4677 4.505039 GGCTTTGGTGTAGTAGGATATGGG 60.505 50.000 0.00 0.00 0.00 4.00
3709 4678 4.347000 GCTTTGGTGTAGTAGGATATGGGA 59.653 45.833 0.00 0.00 0.00 4.37
3710 4679 5.742255 GCTTTGGTGTAGTAGGATATGGGAC 60.742 48.000 0.00 0.00 0.00 4.46
3724 4693 1.279496 TGGGACATGAGACCAAGAGG 58.721 55.000 0.00 0.00 42.21 3.69
3725 4694 1.203300 TGGGACATGAGACCAAGAGGA 60.203 52.381 0.00 0.00 38.69 3.71
3726 4695 1.909302 GGGACATGAGACCAAGAGGAA 59.091 52.381 0.00 0.00 38.69 3.36
3727 4696 2.355209 GGGACATGAGACCAAGAGGAAC 60.355 54.545 0.00 0.00 38.69 3.62
3728 4697 2.611518 GACATGAGACCAAGAGGAACG 58.388 52.381 0.00 0.00 38.69 3.95
3729 4698 2.231478 GACATGAGACCAAGAGGAACGA 59.769 50.000 0.00 0.00 38.69 3.85
3730 4699 2.834549 ACATGAGACCAAGAGGAACGAT 59.165 45.455 0.00 0.00 38.69 3.73
3731 4700 3.193263 CATGAGACCAAGAGGAACGATG 58.807 50.000 0.00 0.00 38.69 3.84
3732 4701 2.248248 TGAGACCAAGAGGAACGATGT 58.752 47.619 0.00 0.00 38.69 3.06
3733 4702 2.231478 TGAGACCAAGAGGAACGATGTC 59.769 50.000 0.00 0.00 38.69 3.06
3734 4703 2.231478 GAGACCAAGAGGAACGATGTCA 59.769 50.000 0.00 0.00 38.69 3.58
3773 4742 0.415429 AGGACATGGGACAGGAGACT 59.585 55.000 0.00 0.00 46.40 3.24
3784 4757 3.274601 AGGAGACTGAGAGGAACGG 57.725 57.895 0.00 0.00 41.13 4.44
3826 4799 2.842496 TCGGACACTAGAGAGGAGGTTA 59.158 50.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.107017 AATCCGGTCTTCATGGGCTG 60.107 55.000 0.00 0.00 0.00 4.85
2 3 0.819666 GGAATCCGGTCTTCATGGGC 60.820 60.000 17.32 1.30 0.00 5.36
3 4 0.839946 AGGAATCCGGTCTTCATGGG 59.160 55.000 17.32 0.00 0.00 4.00
4 5 1.202698 GGAGGAATCCGGTCTTCATGG 60.203 57.143 17.32 0.00 0.00 3.66
5 6 1.765314 AGGAGGAATCCGGTCTTCATG 59.235 52.381 17.32 0.00 34.28 3.07
6 7 2.043227 GAGGAGGAATCCGGTCTTCAT 58.957 52.381 17.32 12.36 34.28 2.57
27 28 2.584143 GACGATAACGGCCGTGGG 60.584 66.667 34.95 22.58 42.35 4.61
74 79 1.202639 TGCACGACCTGTTTCATGTCT 60.203 47.619 0.00 0.00 29.16 3.41
75 80 1.225855 TGCACGACCTGTTTCATGTC 58.774 50.000 0.00 0.00 0.00 3.06
79 84 1.202639 AGACATGCACGACCTGTTTCA 60.203 47.619 0.00 0.00 0.00 2.69
80 85 1.512926 AGACATGCACGACCTGTTTC 58.487 50.000 0.00 0.00 0.00 2.78
81 86 1.967319 AAGACATGCACGACCTGTTT 58.033 45.000 0.00 0.00 0.00 2.83
82 87 2.831685 TAAGACATGCACGACCTGTT 57.168 45.000 0.00 0.00 0.00 3.16
83 88 2.418746 GGATAAGACATGCACGACCTGT 60.419 50.000 0.00 0.00 0.00 4.00
85 90 2.111384 AGGATAAGACATGCACGACCT 58.889 47.619 0.00 0.00 0.00 3.85
86 91 2.604046 AGGATAAGACATGCACGACC 57.396 50.000 0.00 0.00 0.00 4.79
115 125 1.468127 TGCATGCATGACACGGTAAAG 59.532 47.619 30.64 0.00 0.00 1.85
119 129 1.875514 GATATGCATGCATGACACGGT 59.124 47.619 37.43 16.54 37.82 4.83
121 131 1.136169 CGGATATGCATGCATGACACG 60.136 52.381 37.43 29.64 37.82 4.49
122 132 1.875514 ACGGATATGCATGCATGACAC 59.124 47.619 37.43 24.67 37.82 3.67
123 133 2.145536 GACGGATATGCATGCATGACA 58.854 47.619 37.43 24.96 37.82 3.58
124 134 1.466167 GGACGGATATGCATGCATGAC 59.534 52.381 37.43 28.85 37.82 3.06
125 135 1.812235 GGACGGATATGCATGCATGA 58.188 50.000 37.43 23.29 37.82 3.07
126 136 0.445043 CGGACGGATATGCATGCATG 59.555 55.000 37.43 24.90 37.82 4.06
127 137 0.674581 CCGGACGGATATGCATGCAT 60.675 55.000 33.92 33.92 37.70 3.96
128 138 1.301637 CCGGACGGATATGCATGCA 60.302 57.895 25.04 25.04 37.50 3.96
129 139 2.680913 GCCGGACGGATATGCATGC 61.681 63.158 15.99 11.82 37.50 4.06
257 706 1.039233 GCAGGGCGTGGTACCTACTA 61.039 60.000 14.36 0.00 34.71 1.82
258 707 2.356780 GCAGGGCGTGGTACCTACT 61.357 63.158 14.36 1.14 34.71 2.57
259 708 1.896122 AAGCAGGGCGTGGTACCTAC 61.896 60.000 14.36 8.80 35.15 3.18
260 709 1.610554 GAAGCAGGGCGTGGTACCTA 61.611 60.000 14.36 0.00 35.15 3.08
261 710 2.928396 AAGCAGGGCGTGGTACCT 60.928 61.111 14.36 0.00 35.15 3.08
262 711 2.436115 GAAGCAGGGCGTGGTACC 60.436 66.667 12.66 4.43 35.15 3.34
273 722 1.676006 ACCAACGTTTTCAGGAAGCAG 59.324 47.619 9.21 0.00 0.00 4.24
274 723 1.757682 ACCAACGTTTTCAGGAAGCA 58.242 45.000 9.21 0.00 0.00 3.91
275 724 2.857748 CAAACCAACGTTTTCAGGAAGC 59.142 45.455 9.21 0.00 40.28 3.86
276 725 2.857748 GCAAACCAACGTTTTCAGGAAG 59.142 45.455 9.21 0.70 40.28 3.46
277 726 2.732597 CGCAAACCAACGTTTTCAGGAA 60.733 45.455 9.21 0.00 40.28 3.36
298 810 2.053277 GGGGTCCTCTCTCGTCACC 61.053 68.421 0.00 0.00 0.00 4.02
397 918 1.227764 CCATCGGCCTCATCCACAG 60.228 63.158 0.00 0.00 0.00 3.66
400 921 1.075301 TCTCCATCGGCCTCATCCA 60.075 57.895 0.00 0.00 0.00 3.41
428 949 2.867472 GCCCGATCACCAACGTTG 59.133 61.111 21.47 21.47 0.00 4.10
549 1073 1.724581 GCAACCAACAACGCGCTAC 60.725 57.895 5.73 0.00 0.00 3.58
601 1125 1.227438 CGATGTTCCCGGCCGTAAT 60.227 57.895 26.12 9.67 0.00 1.89
653 1177 2.443016 TTGGGGTTTTGGCACGCT 60.443 55.556 0.00 0.00 0.00 5.07
695 1223 8.818860 TCTGCTACTATAGTTAGTTTTGGGAAA 58.181 33.333 11.40 0.00 39.42 3.13
697 1225 7.837689 TCTCTGCTACTATAGTTAGTTTTGGGA 59.162 37.037 11.40 0.00 39.42 4.37
722 1253 0.661780 CGGCCGATCTCGTCTTGATC 60.662 60.000 24.07 0.00 37.53 2.92
760 1291 0.908910 TGGCTTTCCTATCGCTTGGA 59.091 50.000 0.00 0.00 0.00 3.53
762 1293 1.062587 CGTTGGCTTTCCTATCGCTTG 59.937 52.381 0.00 0.00 0.00 4.01
800 1331 6.631847 CGTGAATATTCGTTCTGATCTTGAC 58.368 40.000 10.80 0.00 0.00 3.18
858 1392 2.953284 AGGCCACGAGCTATAGTCTA 57.047 50.000 5.01 0.00 43.05 2.59
859 1393 2.953284 TAGGCCACGAGCTATAGTCT 57.047 50.000 5.01 0.00 43.05 3.24
860 1394 3.349022 AGATAGGCCACGAGCTATAGTC 58.651 50.000 5.01 0.00 43.05 2.59
861 1395 3.443145 AGATAGGCCACGAGCTATAGT 57.557 47.619 5.01 0.00 43.05 2.12
862 1396 3.181505 CGAAGATAGGCCACGAGCTATAG 60.182 52.174 5.01 0.00 43.05 1.31
863 1397 2.747989 CGAAGATAGGCCACGAGCTATA 59.252 50.000 5.01 0.00 43.05 1.31
864 1398 1.542030 CGAAGATAGGCCACGAGCTAT 59.458 52.381 5.01 0.00 43.05 2.97
952 1505 0.676736 GTTCCGTTGGGGATTTTGCA 59.323 50.000 0.00 0.00 46.62 4.08
990 1574 2.013483 GATCGCCATCTGTCGCTCG 61.013 63.158 0.00 0.00 0.00 5.03
1218 1802 0.305922 CGAAGATGAATTGGAGGCGC 59.694 55.000 0.00 0.00 0.00 6.53
1271 1855 3.443976 GATCGAAGAAGCTGAAGGAGAC 58.556 50.000 0.00 0.00 43.58 3.36
1273 1857 2.430332 AGGATCGAAGAAGCTGAAGGAG 59.570 50.000 0.00 0.00 43.58 3.69
1274 1858 2.167281 CAGGATCGAAGAAGCTGAAGGA 59.833 50.000 0.00 0.00 43.58 3.36
1275 1859 2.548875 CAGGATCGAAGAAGCTGAAGG 58.451 52.381 0.00 0.00 43.58 3.46
1276 1860 1.932511 GCAGGATCGAAGAAGCTGAAG 59.067 52.381 0.00 0.00 43.58 3.02
1277 1861 1.552337 AGCAGGATCGAAGAAGCTGAA 59.448 47.619 5.21 0.00 43.58 3.02
1279 1863 1.569708 GAGCAGGATCGAAGAAGCTG 58.430 55.000 9.97 0.00 43.58 4.24
1308 1916 4.927267 ACCAATCAATCAGGGTACAGAA 57.073 40.909 0.00 0.00 0.00 3.02
1311 1919 6.356556 CAATCTACCAATCAATCAGGGTACA 58.643 40.000 0.00 0.00 34.88 2.90
1328 1936 5.105756 CCTGAAATTCACCCAACCAATCTAC 60.106 44.000 0.00 0.00 0.00 2.59
1339 1947 1.313091 GGTCGCCCTGAAATTCACCC 61.313 60.000 0.00 0.00 0.00 4.61
1354 1962 1.405463 TCATCCTTGATCGTCAGGTCG 59.595 52.381 5.55 0.00 0.00 4.79
1400 2008 4.551603 CGATCGAACAACTAGGTAGTACCG 60.552 50.000 10.26 3.24 44.90 4.02
1405 2013 5.817988 TGAATCGATCGAACAACTAGGTAG 58.182 41.667 23.50 0.00 0.00 3.18
1409 2017 5.524284 AGGATGAATCGATCGAACAACTAG 58.476 41.667 23.50 0.00 0.00 2.57
1418 2026 3.969899 TGACTGAAGGATGAATCGATCG 58.030 45.455 9.36 9.36 0.00 3.69
1419 2027 4.038522 TCCTGACTGAAGGATGAATCGATC 59.961 45.833 0.00 0.00 41.60 3.69
1420 2028 3.963374 TCCTGACTGAAGGATGAATCGAT 59.037 43.478 0.00 0.00 41.60 3.59
1421 2029 3.365472 TCCTGACTGAAGGATGAATCGA 58.635 45.455 0.00 0.00 41.60 3.59
1422 2030 3.715495 CTCCTGACTGAAGGATGAATCG 58.285 50.000 4.70 0.00 45.41 3.34
1426 2034 1.942776 TGCTCCTGACTGAAGGATGA 58.057 50.000 4.70 0.00 45.41 2.92
1431 2039 4.698780 TCAAATTGATGCTCCTGACTGAAG 59.301 41.667 0.00 0.00 0.00 3.02
1432 2040 4.654915 TCAAATTGATGCTCCTGACTGAA 58.345 39.130 0.00 0.00 0.00 3.02
1435 2043 4.643784 GGAATCAAATTGATGCTCCTGACT 59.356 41.667 15.83 0.00 37.15 3.41
1445 2053 4.441913 GCCACGATTGGGAATCAAATTGAT 60.442 41.667 2.07 2.07 44.15 2.57
1447 2055 3.189285 GCCACGATTGGGAATCAAATTG 58.811 45.455 0.00 0.00 44.15 2.32
1448 2056 2.159254 CGCCACGATTGGGAATCAAATT 60.159 45.455 0.00 0.00 44.15 1.82
1457 2065 1.284982 GATCGATCGCCACGATTGGG 61.285 60.000 11.09 4.42 47.00 4.12
1460 2068 0.660595 GTCGATCGATCGCCACGATT 60.661 55.000 36.58 0.00 47.00 3.34
1479 2090 0.437295 CGGCAAAACGGTTAGTCTCG 59.563 55.000 0.00 0.00 0.00 4.04
1480 2091 1.193874 CACGGCAAAACGGTTAGTCTC 59.806 52.381 0.00 0.00 38.39 3.36
1481 2092 1.223187 CACGGCAAAACGGTTAGTCT 58.777 50.000 0.00 0.00 38.39 3.24
1482 2093 0.385098 GCACGGCAAAACGGTTAGTC 60.385 55.000 0.00 0.00 38.39 2.59
1484 2095 1.439693 CGCACGGCAAAACGGTTAG 60.440 57.895 0.00 0.00 38.39 2.34
1501 2112 2.031807 CGTACCTGGTGATCAGTAGTCG 59.968 54.545 10.23 0.00 41.83 4.18
1575 2189 1.252215 TGCGGTTGTACATCTCCGGA 61.252 55.000 24.98 22.09 42.71 5.14
1688 2302 0.036577 CTGAAGAGCAGGGGACAGTG 60.037 60.000 0.00 0.00 41.07 3.66
1713 2331 1.203928 CATCACTGAAGATCGTCGGC 58.796 55.000 16.33 0.00 0.00 5.54
1714 2332 1.845266 CCATCACTGAAGATCGTCGG 58.155 55.000 15.02 15.02 0.00 4.79
1718 2336 0.467384 AGGGCCATCACTGAAGATCG 59.533 55.000 6.18 0.00 0.00 3.69
1732 2350 0.110486 TTCTCCAAAGTGTCAGGGCC 59.890 55.000 0.00 0.00 0.00 5.80
1735 2353 4.022849 GGAAACATTCTCCAAAGTGTCAGG 60.023 45.833 0.00 0.00 32.77 3.86
1746 2364 4.010349 CCAACTGGTAGGAAACATTCTCC 58.990 47.826 0.00 0.00 0.00 3.71
1950 2574 7.024768 CGAAAAGGTTAGATTAATTGCCGAAA 58.975 34.615 0.00 0.00 0.00 3.46
1951 2575 6.372103 TCGAAAAGGTTAGATTAATTGCCGAA 59.628 34.615 0.00 0.00 0.00 4.30
1995 2629 2.510238 CTCCAGGTACAGCTGCGC 60.510 66.667 15.27 0.00 0.00 6.09
2199 2833 3.814268 GCGGGTGCGGTAGTCGTA 61.814 66.667 0.00 0.00 41.72 3.43
2351 2985 2.186160 TAAATGATGCCGGGCGCTG 61.186 57.895 15.40 0.00 38.78 5.18
2352 2986 2.186826 GTAAATGATGCCGGGCGCT 61.187 57.895 15.40 3.77 38.78 5.92
2354 2988 1.821759 TGGTAAATGATGCCGGGCG 60.822 57.895 15.40 0.00 36.40 6.13
2356 2990 1.405105 CTTGTGGTAAATGATGCCGGG 59.595 52.381 2.18 0.00 36.40 5.73
2357 2991 2.091541 ACTTGTGGTAAATGATGCCGG 58.908 47.619 0.00 0.00 36.40 6.13
2360 2994 2.518949 CGCACTTGTGGTAAATGATGC 58.481 47.619 2.81 0.00 0.00 3.91
2361 2995 2.162208 AGCGCACTTGTGGTAAATGATG 59.838 45.455 11.47 0.00 34.17 3.07
2373 3007 2.529151 ACAAAAACAGAAGCGCACTTG 58.471 42.857 11.47 6.85 35.82 3.16
2375 3009 1.742831 TGACAAAAACAGAAGCGCACT 59.257 42.857 11.47 5.61 0.00 4.40
2376 3010 2.111756 CTGACAAAAACAGAAGCGCAC 58.888 47.619 11.47 2.78 37.54 5.34
2377 3011 1.065401 CCTGACAAAAACAGAAGCGCA 59.935 47.619 11.47 0.00 37.54 6.09
2378 3012 1.758783 CCTGACAAAAACAGAAGCGC 58.241 50.000 0.00 0.00 37.54 5.92
2379 3013 1.334869 AGCCTGACAAAAACAGAAGCG 59.665 47.619 0.00 0.00 37.54 4.68
2380 3014 2.099756 ACAGCCTGACAAAAACAGAAGC 59.900 45.455 0.00 0.00 37.54 3.86
2383 3017 2.423185 CACACAGCCTGACAAAAACAGA 59.577 45.455 0.00 0.00 37.54 3.41
2384 3018 2.480073 CCACACAGCCTGACAAAAACAG 60.480 50.000 0.00 0.00 35.43 3.16
2385 3019 1.476085 CCACACAGCCTGACAAAAACA 59.524 47.619 0.00 0.00 0.00 2.83
2386 3020 1.802508 GCCACACAGCCTGACAAAAAC 60.803 52.381 0.00 0.00 0.00 2.43
2387 3021 0.459489 GCCACACAGCCTGACAAAAA 59.541 50.000 0.00 0.00 0.00 1.94
2458 3092 0.179111 TGCCGTATGCCTTCTCGAAG 60.179 55.000 0.00 0.00 40.16 3.79
2485 3119 1.946768 TCAAGGGCAAAGAAGAACGTG 59.053 47.619 0.00 0.00 0.00 4.49
2489 3123 6.165577 GCAAAATATCAAGGGCAAAGAAGAA 58.834 36.000 0.00 0.00 0.00 2.52
2511 3145 0.400213 AGACCCGTTTTCATCAGGCA 59.600 50.000 0.00 0.00 0.00 4.75
2520 3164 1.760613 TGTCAGTCTCAGACCCGTTTT 59.239 47.619 0.00 0.00 35.15 2.43
2524 3168 2.232452 AGAAATGTCAGTCTCAGACCCG 59.768 50.000 0.00 0.00 35.15 5.28
2528 3172 2.902486 AGCCAGAAATGTCAGTCTCAGA 59.098 45.455 0.00 0.00 0.00 3.27
2529 3173 3.001414 CAGCCAGAAATGTCAGTCTCAG 58.999 50.000 0.00 0.00 0.00 3.35
2577 3221 4.610714 GAATCGCCCGGCCTCCTC 62.611 72.222 3.10 0.00 0.00 3.71
2657 3301 1.066858 AGCTATGACTGGTGTTCACGG 60.067 52.381 0.00 0.00 0.00 4.94
2658 3302 2.370281 AGCTATGACTGGTGTTCACG 57.630 50.000 0.00 0.00 0.00 4.35
2661 3305 4.933330 TCGATAAGCTATGACTGGTGTTC 58.067 43.478 0.00 0.00 0.00 3.18
2662 3306 4.938080 CTCGATAAGCTATGACTGGTGTT 58.062 43.478 0.00 0.00 0.00 3.32
2701 3358 1.586154 AAAGCGGCACACCATAGCAC 61.586 55.000 1.45 0.00 34.57 4.40
2702 3359 1.303236 AAAGCGGCACACCATAGCA 60.303 52.632 1.45 0.00 34.57 3.49
2705 3362 1.303236 AGCAAAGCGGCACACCATA 60.303 52.632 1.45 0.00 35.83 2.74
2706 3363 2.598394 AGCAAAGCGGCACACCAT 60.598 55.556 1.45 0.00 35.83 3.55
2809 3480 3.944422 TCAGTCTTTGTTTTCAGCGTC 57.056 42.857 0.00 0.00 0.00 5.19
2934 3610 9.924010 AGTTCCATCTTGAATAGTAGTACTAGT 57.076 33.333 15.08 14.57 33.66 2.57
2937 3613 9.256228 TCAAGTTCCATCTTGAATAGTAGTACT 57.744 33.333 8.14 8.14 46.88 2.73
2949 3625 3.254166 CACCCAACTCAAGTTCCATCTTG 59.746 47.826 0.00 0.00 44.08 3.02
3062 3739 5.923684 GTCTCGCTCTATAATTGGAAGGAAG 59.076 44.000 0.00 0.00 0.00 3.46
3087 3764 6.741992 AGTTTGTAATGATTCGCTTCATCA 57.258 33.333 1.15 0.00 35.29 3.07
3125 3802 3.136077 ACTCACCCTGCGAGTACTATAGA 59.864 47.826 6.78 0.00 41.91 1.98
3127 3804 3.572632 ACTCACCCTGCGAGTACTATA 57.427 47.619 0.00 0.00 41.91 1.31
3136 3813 0.872388 GTAACCAAACTCACCCTGCG 59.128 55.000 0.00 0.00 0.00 5.18
3145 3822 6.239572 CCAAAAATGATCCAGGTAACCAAACT 60.240 38.462 0.00 0.00 37.17 2.66
3179 3882 6.334102 TGACGGTTTTTGCCTGTATATTTT 57.666 33.333 0.00 0.00 0.00 1.82
3182 3885 6.329496 CAAATGACGGTTTTTGCCTGTATAT 58.671 36.000 5.07 0.00 0.00 0.86
3183 3886 5.704888 CAAATGACGGTTTTTGCCTGTATA 58.295 37.500 5.07 0.00 0.00 1.47
3185 3888 3.971150 CAAATGACGGTTTTTGCCTGTA 58.029 40.909 5.07 0.00 0.00 2.74
3186 3889 2.820330 CAAATGACGGTTTTTGCCTGT 58.180 42.857 5.07 0.00 0.00 4.00
3223 3929 2.196742 TACAAGGAGAGGGGATGCAT 57.803 50.000 0.00 0.00 0.00 3.96
3413 4122 1.873903 GCTTGTCATATCGGATGCGGT 60.874 52.381 6.82 0.77 0.00 5.68
3418 4127 1.686587 TCCGTGCTTGTCATATCGGAT 59.313 47.619 0.00 0.00 41.45 4.18
3424 4133 0.457853 GCGACTCCGTGCTTGTCATA 60.458 55.000 0.00 0.00 38.24 2.15
3502 4211 6.369065 CCTATTTGTTACTCCACACAGACTTC 59.631 42.308 0.00 0.00 0.00 3.01
3521 4230 3.463329 TCTGCCTAAATGCCCTCCTATTT 59.537 43.478 0.00 0.00 0.00 1.40
3536 4245 5.698741 TTTTCTTCATCATCCTCTGCCTA 57.301 39.130 0.00 0.00 0.00 3.93
3572 4282 2.165845 GTCCTACTACACCAGCGACAAT 59.834 50.000 0.00 0.00 0.00 2.71
3573 4283 1.542915 GTCCTACTACACCAGCGACAA 59.457 52.381 0.00 0.00 0.00 3.18
3574 4284 1.171308 GTCCTACTACACCAGCGACA 58.829 55.000 0.00 0.00 0.00 4.35
3575 4285 0.098376 CGTCCTACTACACCAGCGAC 59.902 60.000 0.00 0.00 0.00 5.19
3576 4286 1.651240 GCGTCCTACTACACCAGCGA 61.651 60.000 0.00 0.00 0.00 4.93
3577 4287 1.226603 GCGTCCTACTACACCAGCG 60.227 63.158 0.00 0.00 0.00 5.18
3579 4289 0.179171 CACGCGTCCTACTACACCAG 60.179 60.000 9.86 0.00 0.00 4.00
3597 4368 0.319083 TTCTTTTCGGCCTACTCGCA 59.681 50.000 0.00 0.00 0.00 5.10
3598 4369 1.327764 CATTCTTTTCGGCCTACTCGC 59.672 52.381 0.00 0.00 0.00 5.03
3599 4370 2.603560 GTCATTCTTTTCGGCCTACTCG 59.396 50.000 0.00 0.00 0.00 4.18
3603 4374 3.194861 CATCGTCATTCTTTTCGGCCTA 58.805 45.455 0.00 0.00 0.00 3.93
3630 4599 0.947244 CGTCCTACTATACCGGCGTT 59.053 55.000 6.01 0.00 0.00 4.84
3636 4605 1.978542 CGCATGCGTCCTACTATACC 58.021 55.000 31.33 0.00 34.35 2.73
3652 4621 3.385384 CCTCTCAGCCTCCACGCA 61.385 66.667 0.00 0.00 0.00 5.24
3656 4625 1.280133 CATTGTTCCTCTCAGCCTCCA 59.720 52.381 0.00 0.00 0.00 3.86
3673 4642 1.086696 CCAAAGCCATCGTCGACATT 58.913 50.000 17.16 0.00 0.00 2.71
3680 4649 2.093658 CCTACTACACCAAAGCCATCGT 60.094 50.000 0.00 0.00 0.00 3.73
3681 4650 2.167693 TCCTACTACACCAAAGCCATCG 59.832 50.000 0.00 0.00 0.00 3.84
3682 4651 3.906720 TCCTACTACACCAAAGCCATC 57.093 47.619 0.00 0.00 0.00 3.51
3683 4652 5.221925 CCATATCCTACTACACCAAAGCCAT 60.222 44.000 0.00 0.00 0.00 4.40
3684 4653 4.102524 CCATATCCTACTACACCAAAGCCA 59.897 45.833 0.00 0.00 0.00 4.75
3685 4654 4.505039 CCCATATCCTACTACACCAAAGCC 60.505 50.000 0.00 0.00 0.00 4.35
3686 4655 4.347000 TCCCATATCCTACTACACCAAAGC 59.653 45.833 0.00 0.00 0.00 3.51
3687 4656 5.365605 TGTCCCATATCCTACTACACCAAAG 59.634 44.000 0.00 0.00 0.00 2.77
3688 4657 5.282129 TGTCCCATATCCTACTACACCAAA 58.718 41.667 0.00 0.00 0.00 3.28
3689 4658 4.886163 TGTCCCATATCCTACTACACCAA 58.114 43.478 0.00 0.00 0.00 3.67
3690 4659 4.546224 TGTCCCATATCCTACTACACCA 57.454 45.455 0.00 0.00 0.00 4.17
3691 4660 5.084519 TCATGTCCCATATCCTACTACACC 58.915 45.833 0.00 0.00 0.00 4.16
3692 4661 6.010850 TCTCATGTCCCATATCCTACTACAC 58.989 44.000 0.00 0.00 0.00 2.90
3693 4662 6.010850 GTCTCATGTCCCATATCCTACTACA 58.989 44.000 0.00 0.00 0.00 2.74
3694 4663 5.419471 GGTCTCATGTCCCATATCCTACTAC 59.581 48.000 0.00 0.00 0.00 2.73
3695 4664 5.075900 TGGTCTCATGTCCCATATCCTACTA 59.924 44.000 0.00 0.00 0.00 1.82
3696 4665 4.140686 TGGTCTCATGTCCCATATCCTACT 60.141 45.833 0.00 0.00 0.00 2.57
3697 4666 4.160329 TGGTCTCATGTCCCATATCCTAC 58.840 47.826 0.00 0.00 0.00 3.18
3698 4667 4.485653 TGGTCTCATGTCCCATATCCTA 57.514 45.455 0.00 0.00 0.00 2.94
3699 4668 3.350992 TGGTCTCATGTCCCATATCCT 57.649 47.619 0.00 0.00 0.00 3.24
3700 4669 3.648067 TCTTGGTCTCATGTCCCATATCC 59.352 47.826 0.00 0.00 0.00 2.59
3701 4670 4.262808 CCTCTTGGTCTCATGTCCCATATC 60.263 50.000 0.00 0.00 0.00 1.63
3702 4671 3.649981 CCTCTTGGTCTCATGTCCCATAT 59.350 47.826 0.00 0.00 0.00 1.78
3703 4672 3.041211 CCTCTTGGTCTCATGTCCCATA 58.959 50.000 0.00 0.00 0.00 2.74
3704 4673 1.842562 CCTCTTGGTCTCATGTCCCAT 59.157 52.381 0.00 0.00 0.00 4.00
3705 4674 1.203300 TCCTCTTGGTCTCATGTCCCA 60.203 52.381 0.00 0.00 34.23 4.37
3706 4675 1.573108 TCCTCTTGGTCTCATGTCCC 58.427 55.000 0.00 0.00 34.23 4.46
3707 4676 2.675317 CGTTCCTCTTGGTCTCATGTCC 60.675 54.545 0.00 0.00 34.23 4.02
3708 4677 2.231478 TCGTTCCTCTTGGTCTCATGTC 59.769 50.000 0.00 0.00 34.23 3.06
3709 4678 2.248248 TCGTTCCTCTTGGTCTCATGT 58.752 47.619 0.00 0.00 34.23 3.21
3710 4679 3.193263 CATCGTTCCTCTTGGTCTCATG 58.807 50.000 0.00 0.00 34.23 3.07
3711 4680 2.834549 ACATCGTTCCTCTTGGTCTCAT 59.165 45.455 0.00 0.00 34.23 2.90
3712 4681 2.231478 GACATCGTTCCTCTTGGTCTCA 59.769 50.000 0.00 0.00 34.23 3.27
3713 4682 2.231478 TGACATCGTTCCTCTTGGTCTC 59.769 50.000 0.00 0.00 34.23 3.36
3714 4683 2.232452 CTGACATCGTTCCTCTTGGTCT 59.768 50.000 0.00 0.00 34.23 3.85
3715 4684 2.611518 CTGACATCGTTCCTCTTGGTC 58.388 52.381 0.00 0.00 34.23 4.02
3716 4685 1.338200 GCTGACATCGTTCCTCTTGGT 60.338 52.381 0.00 0.00 34.23 3.67
3717 4686 1.363744 GCTGACATCGTTCCTCTTGG 58.636 55.000 0.00 0.00 0.00 3.61
3718 4687 0.994995 CGCTGACATCGTTCCTCTTG 59.005 55.000 0.00 0.00 0.00 3.02
3719 4688 0.888619 TCGCTGACATCGTTCCTCTT 59.111 50.000 0.00 0.00 0.00 2.85
3720 4689 1.107114 ATCGCTGACATCGTTCCTCT 58.893 50.000 0.00 0.00 0.00 3.69
3721 4690 1.203928 CATCGCTGACATCGTTCCTC 58.796 55.000 0.00 0.00 0.00 3.71
3722 4691 0.179100 CCATCGCTGACATCGTTCCT 60.179 55.000 0.00 0.00 0.00 3.36
3723 4692 1.766143 GCCATCGCTGACATCGTTCC 61.766 60.000 0.00 0.00 0.00 3.62
3724 4693 0.807667 AGCCATCGCTGACATCGTTC 60.808 55.000 0.00 0.00 46.19 3.95
3725 4694 1.219124 AGCCATCGCTGACATCGTT 59.781 52.632 0.00 0.00 46.19 3.85
3726 4695 2.895680 AGCCATCGCTGACATCGT 59.104 55.556 0.00 0.00 46.19 3.73
3773 4742 0.966920 GTTCCTCACCGTTCCTCTCA 59.033 55.000 0.00 0.00 0.00 3.27
3784 4757 2.263077 CTACACTCGCATGTTCCTCAC 58.737 52.381 0.00 0.00 33.85 3.51


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

AutoCloner maintained by Alex Coulton.