Multiple sequence alignment - TraesCS7D01G186600

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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 TraesCS7D01G186600 chr7D 100.000 3857 0 0 1 3857 139105305 139109161 0.000000e+00 7123.0
1 TraesCS7D01G186600 chr7D 91.931 347 25 1 1822 2168 139107072 139107415 2.080000e-132 483.0
2 TraesCS7D01G186600 chr7D 91.931 347 25 1 1768 2111 139107126 139107472 2.080000e-132 483.0
3 TraesCS7D01G186600 chr7D 85.238 210 22 3 2231 2431 139182701 139182910 1.400000e-49 207.0
4 TraesCS7D01G186600 chr7D 85.714 168 17 6 2668 2835 139252049 139252209 1.840000e-38 171.0
5 TraesCS7D01G186600 chr7D 92.308 117 9 0 3738 3854 139187104 139187220 2.380000e-37 167.0
6 TraesCS7D01G186600 chr7A 88.946 1945 160 26 1938 3853 139153009 139154927 0.000000e+00 2350.0
7 TraesCS7D01G186600 chr7A 88.312 1309 85 30 740 2001 139151953 139153240 0.000000e+00 1507.0
8 TraesCS7D01G186600 chr7A 85.352 710 46 23 1 693 139151278 139151946 0.000000e+00 682.0
9 TraesCS7D01G186600 chr7A 87.699 439 40 7 2144 2571 139418044 139418479 2.070000e-137 499.0
10 TraesCS7D01G186600 chr7A 90.503 179 14 1 1994 2172 139153008 139153183 2.320000e-57 233.0
11 TraesCS7D01G186600 chr7A 93.333 120 8 0 1768 1887 139153121 139153240 1.100000e-40 178.0
12 TraesCS7D01G186600 chr7A 91.270 126 11 0 2051 2176 139153008 139153133 5.120000e-39 172.0
13 TraesCS7D01G186600 chr7B 88.932 1536 105 23 1881 3392 104517944 104519438 0.000000e+00 1834.0
14 TraesCS7D01G186600 chr7B 85.245 1674 98 63 471 2060 104516611 104518219 0.000000e+00 1585.0
15 TraesCS7D01G186600 chr7B 87.992 483 31 14 1 469 104510184 104510653 2.620000e-151 545.0
16 TraesCS7D01G186600 chr7B 86.076 474 27 17 3388 3857 104522116 104522554 1.250000e-129 473.0
17 TraesCS7D01G186600 chr7B 86.552 290 21 7 1822 2111 104517942 104518213 1.740000e-78 303.0
18 TraesCS7D01G186600 chr7B 93.785 177 11 0 1993 2169 104517942 104518118 2.280000e-67 267.0
19 TraesCS7D01G186600 chr7B 94.737 171 9 0 1938 2108 104517944 104518114 2.280000e-67 267.0
20 TraesCS7D01G186600 chr7B 100.000 38 0 0 2129 2166 104518117 104518154 1.920000e-08 71.3
21 TraesCS7D01G186600 chr1B 85.782 633 83 6 2902 3530 61964665 61965294 0.000000e+00 664.0
22 TraesCS7D01G186600 chr1B 84.339 613 92 3 2908 3518 573579829 573580439 7.130000e-167 597.0
23 TraesCS7D01G186600 chr6D 84.020 607 93 4 2924 3527 62884107 62884712 7.180000e-162 580.0
24 TraesCS7D01G186600 chr3A 83.254 627 101 3 2903 3527 640842096 640842720 1.200000e-159 573.0
25 TraesCS7D01G186600 chr6B 83.333 606 98 3 2927 3530 626462146 626461542 1.210000e-154 556.0
26 TraesCS7D01G186600 chr6B 82.622 633 100 7 2903 3528 93420470 93421099 5.630000e-153 551.0
27 TraesCS7D01G186600 chr2D 82.671 629 98 8 2903 3527 101874672 101874051 7.290000e-152 547.0
28 TraesCS7D01G186600 chr5A 80.929 624 112 6 2908 3527 573833349 573832729 1.610000e-133 486.0


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 TraesCS7D01G186600 chr7D 139105305 139109161 3856 False 2696.333333 7123 94.620667 1 3857 3 chr7D.!!$F4 3856
1 TraesCS7D01G186600 chr7A 139151278 139154927 3649 False 853.666667 2350 89.619333 1 3853 6 chr7A.!!$F2 3852
2 TraesCS7D01G186600 chr7B 104516611 104522554 5943 False 685.757143 1834 90.761000 471 3857 7 chr7B.!!$F2 3386
3 TraesCS7D01G186600 chr1B 61964665 61965294 629 False 664.000000 664 85.782000 2902 3530 1 chr1B.!!$F1 628
4 TraesCS7D01G186600 chr1B 573579829 573580439 610 False 597.000000 597 84.339000 2908 3518 1 chr1B.!!$F2 610
5 TraesCS7D01G186600 chr6D 62884107 62884712 605 False 580.000000 580 84.020000 2924 3527 1 chr6D.!!$F1 603
6 TraesCS7D01G186600 chr3A 640842096 640842720 624 False 573.000000 573 83.254000 2903 3527 1 chr3A.!!$F1 624
7 TraesCS7D01G186600 chr6B 626461542 626462146 604 True 556.000000 556 83.333000 2927 3530 1 chr6B.!!$R1 603
8 TraesCS7D01G186600 chr6B 93420470 93421099 629 False 551.000000 551 82.622000 2903 3528 1 chr6B.!!$F1 625
9 TraesCS7D01G186600 chr2D 101874051 101874672 621 True 547.000000 547 82.671000 2903 3527 1 chr2D.!!$R1 624
10 TraesCS7D01G186600 chr5A 573832729 573833349 620 True 486.000000 486 80.929000 2908 3527 1 chr5A.!!$R1 619

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
58 59 0.037139 GCATGAACCAGGCATTGCAA 60.037 50.0 11.39 0.00 41.05 4.08 F
695 718 0.095417 GTGCAAGAATTCGTCGCTCC 59.905 55.0 14.90 5.37 0.00 4.70 F
1923 2090 0.032952 CCGTCGTCAACAAGGAGGAA 59.967 55.0 0.00 0.00 33.91 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 2071 0.032952 TTCCTCCTTGTTGACGACGG 59.967 55.0 0.00 0.0 0.00 4.79 R
2093 2302 0.035439 ATCGGCGAACACCTGGATTT 60.035 50.0 15.93 0.0 0.00 2.17 R
3141 3376 0.248289 ATCCGTCCCGACAAACGAAT 59.752 50.0 0.00 0.0 45.77 3.34 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 2.610374 CTGACTAGACTACTCGCAGGTC 59.390 54.545 0.00 0.00 0.00 3.85
51 52 0.108520 CAACCATGCATGAACCAGGC 60.109 55.000 28.31 0.00 41.79 4.85
58 59 0.037139 GCATGAACCAGGCATTGCAA 60.037 50.000 11.39 0.00 41.05 4.08
59 60 1.406341 GCATGAACCAGGCATTGCAAT 60.406 47.619 5.99 5.99 41.05 3.56
62 63 0.179129 GAACCAGGCATTGCAATCGG 60.179 55.000 9.53 10.24 0.00 4.18
63 64 0.611618 AACCAGGCATTGCAATCGGA 60.612 50.000 9.53 0.00 0.00 4.55
64 65 1.315257 ACCAGGCATTGCAATCGGAC 61.315 55.000 9.53 1.06 0.00 4.79
65 66 1.063006 CAGGCATTGCAATCGGACG 59.937 57.895 9.53 0.00 0.00 4.79
66 67 2.278142 GGCATTGCAATCGGACGC 60.278 61.111 9.53 9.55 0.00 5.19
67 68 2.278142 GCATTGCAATCGGACGCC 60.278 61.111 9.53 0.00 0.00 5.68
82 83 1.278337 CGCCGACTCGATCTCTCTG 59.722 63.158 0.00 0.00 0.00 3.35
89 90 4.526625 CGACTCGATCTCTCTGAAATGAG 58.473 47.826 0.00 0.00 35.52 2.90
93 94 3.067883 TCGATCTCTCTGAAATGAGCAGG 59.932 47.826 0.00 0.00 34.20 4.85
97 98 2.614520 CTCTCTGAAATGAGCAGGCATG 59.385 50.000 0.00 0.00 34.20 4.06
98 99 1.676529 CTCTGAAATGAGCAGGCATGG 59.323 52.381 0.00 0.00 34.20 3.66
124 125 4.997395 CAGGCTTATCTACTTGTGTTGTGT 59.003 41.667 0.00 0.00 0.00 3.72
132 133 2.755650 ACTTGTGTTGTGTCGATCCTC 58.244 47.619 0.00 0.00 0.00 3.71
153 154 4.756084 CTCGTTTGGAGAAGCAAAGATT 57.244 40.909 0.00 0.00 46.23 2.40
154 155 5.862924 CTCGTTTGGAGAAGCAAAGATTA 57.137 39.130 0.00 0.00 46.23 1.75
155 156 5.862811 CTCGTTTGGAGAAGCAAAGATTAG 58.137 41.667 0.00 0.00 46.23 1.73
156 157 4.154195 TCGTTTGGAGAAGCAAAGATTAGC 59.846 41.667 0.00 0.00 0.00 3.09
157 158 4.083324 CGTTTGGAGAAGCAAAGATTAGCA 60.083 41.667 0.00 0.00 0.00 3.49
179 185 1.134995 AGTAGGCCGTACGTAAAAGCC 60.135 52.381 20.61 20.61 44.20 4.35
198 211 4.527157 GCTCGCGGCGTAGTACGT 62.527 66.667 22.90 0.00 44.73 3.57
273 286 3.495331 TGGCATCTGGCTTTAGACAAAA 58.505 40.909 5.30 0.00 44.01 2.44
283 296 5.650266 TGGCTTTAGACAAAAGAAGTGTTGA 59.350 36.000 1.78 0.00 46.44 3.18
307 320 3.816580 GCTCGGGCTAGCTATAACC 57.183 57.895 15.72 5.75 39.50 2.85
308 321 0.246910 GCTCGGGCTAGCTATAACCC 59.753 60.000 15.72 14.06 39.50 4.11
314 327 3.451890 GGGCTAGCTATAACCCCTATGT 58.548 50.000 15.72 0.00 31.84 2.29
315 328 4.617593 GGGCTAGCTATAACCCCTATGTA 58.382 47.826 15.72 0.00 31.84 2.29
322 335 4.220163 GCTATAACCCCTATGTAAGCGTCT 59.780 45.833 0.00 0.00 0.00 4.18
330 343 1.174783 ATGTAAGCGTCTCTGTCGGT 58.825 50.000 0.00 0.00 40.68 4.69
332 345 1.338973 TGTAAGCGTCTCTGTCGGTTT 59.661 47.619 7.93 0.00 44.47 3.27
333 346 2.223876 TGTAAGCGTCTCTGTCGGTTTT 60.224 45.455 7.93 0.00 44.47 2.43
334 347 1.949465 AAGCGTCTCTGTCGGTTTTT 58.051 45.000 0.00 0.00 44.47 1.94
335 348 1.499049 AGCGTCTCTGTCGGTTTTTC 58.501 50.000 0.00 0.00 35.53 2.29
336 349 1.068741 AGCGTCTCTGTCGGTTTTTCT 59.931 47.619 0.00 0.00 35.53 2.52
337 350 1.865340 GCGTCTCTGTCGGTTTTTCTT 59.135 47.619 0.00 0.00 0.00 2.52
338 351 2.287103 GCGTCTCTGTCGGTTTTTCTTT 59.713 45.455 0.00 0.00 0.00 2.52
339 352 3.242641 GCGTCTCTGTCGGTTTTTCTTTT 60.243 43.478 0.00 0.00 0.00 2.27
340 353 4.729746 GCGTCTCTGTCGGTTTTTCTTTTT 60.730 41.667 0.00 0.00 0.00 1.94
341 354 4.728608 CGTCTCTGTCGGTTTTTCTTTTTG 59.271 41.667 0.00 0.00 0.00 2.44
342 355 5.637809 GTCTCTGTCGGTTTTTCTTTTTGT 58.362 37.500 0.00 0.00 0.00 2.83
343 356 6.090783 GTCTCTGTCGGTTTTTCTTTTTGTT 58.909 36.000 0.00 0.00 0.00 2.83
344 357 6.033513 GTCTCTGTCGGTTTTTCTTTTTGTTG 59.966 38.462 0.00 0.00 0.00 3.33
345 358 6.015027 TCTGTCGGTTTTTCTTTTTGTTGA 57.985 33.333 0.00 0.00 0.00 3.18
402 415 2.044946 GGGCCGAGTTTGGATGCT 60.045 61.111 0.00 0.00 0.00 3.79
409 422 1.741706 CGAGTTTGGATGCTTGATGCT 59.258 47.619 0.00 0.00 43.37 3.79
415 428 1.442526 GGATGCTTGATGCTGGGACG 61.443 60.000 0.00 0.00 43.37 4.79
456 473 2.037121 ACGTTGTCAGATGTCACATCCA 59.963 45.455 14.53 2.62 0.00 3.41
460 477 5.237815 GTTGTCAGATGTCACATCCACTAA 58.762 41.667 14.53 2.92 0.00 2.24
461 478 5.077134 TGTCAGATGTCACATCCACTAAG 57.923 43.478 14.53 0.00 0.00 2.18
462 479 4.772100 TGTCAGATGTCACATCCACTAAGA 59.228 41.667 14.53 0.95 0.00 2.10
463 480 5.423290 TGTCAGATGTCACATCCACTAAGAT 59.577 40.000 14.53 0.00 0.00 2.40
464 481 5.982516 GTCAGATGTCACATCCACTAAGATC 59.017 44.000 14.53 0.00 0.00 2.75
465 482 5.896106 TCAGATGTCACATCCACTAAGATCT 59.104 40.000 14.53 0.00 0.00 2.75
467 484 7.561356 TCAGATGTCACATCCACTAAGATCTAA 59.439 37.037 14.53 0.00 0.00 2.10
468 485 8.366401 CAGATGTCACATCCACTAAGATCTAAT 58.634 37.037 14.53 0.00 0.00 1.73
470 487 7.904558 TGTCACATCCACTAAGATCTAATCT 57.095 36.000 0.00 0.00 42.61 2.40
471 488 8.996651 TGTCACATCCACTAAGATCTAATCTA 57.003 34.615 0.00 0.00 39.08 1.98
472 489 9.421399 TGTCACATCCACTAAGATCTAATCTAA 57.579 33.333 0.00 0.00 39.08 2.10
522 539 5.487488 TGGTTAACTGTAATCCAGGACTGAT 59.513 40.000 5.42 0.00 46.06 2.90
564 585 1.762957 AGTCCCCGATCGATCACAAAT 59.237 47.619 24.40 3.97 0.00 2.32
596 617 6.088541 TCCACTAGTATCAGGTTCCTTACT 57.911 41.667 0.00 7.92 0.00 2.24
632 653 0.602562 TAACCATTGCAGCTGTTGGC 59.397 50.000 23.86 9.18 42.19 4.52
642 663 2.520458 CTGTTGGCTGTTGGGGGA 59.480 61.111 0.00 0.00 0.00 4.81
644 665 0.967380 CTGTTGGCTGTTGGGGGATC 60.967 60.000 0.00 0.00 0.00 3.36
657 680 1.755783 GGGATCGACCACGGGTACT 60.756 63.158 6.41 0.00 41.20 2.73
695 718 0.095417 GTGCAAGAATTCGTCGCTCC 59.905 55.000 14.90 5.37 0.00 4.70
697 720 1.706287 GCAAGAATTCGTCGCTCCCC 61.706 60.000 0.00 0.00 0.00 4.81
710 733 1.032114 GCTCCCCTCCAACAAATCCG 61.032 60.000 0.00 0.00 0.00 4.18
714 737 1.304052 CCTCCAACAAATCCGGGCA 60.304 57.895 0.00 0.00 0.00 5.36
715 738 1.595093 CCTCCAACAAATCCGGGCAC 61.595 60.000 0.00 0.00 0.00 5.01
716 739 0.893270 CTCCAACAAATCCGGGCACA 60.893 55.000 0.00 0.00 0.00 4.57
717 740 1.175983 TCCAACAAATCCGGGCACAC 61.176 55.000 0.00 0.00 0.00 3.82
718 741 1.459455 CCAACAAATCCGGGCACACA 61.459 55.000 0.00 0.00 0.00 3.72
719 742 0.602562 CAACAAATCCGGGCACACAT 59.397 50.000 0.00 0.00 0.00 3.21
720 743 1.815613 CAACAAATCCGGGCACACATA 59.184 47.619 0.00 0.00 0.00 2.29
721 744 2.426738 CAACAAATCCGGGCACACATAT 59.573 45.455 0.00 0.00 0.00 1.78
722 745 3.569194 ACAAATCCGGGCACACATATA 57.431 42.857 0.00 0.00 0.00 0.86
723 746 4.098914 ACAAATCCGGGCACACATATAT 57.901 40.909 0.00 0.00 0.00 0.86
724 747 4.072131 ACAAATCCGGGCACACATATATC 58.928 43.478 0.00 0.00 0.00 1.63
731 774 2.430465 GGCACACATATATCTGCCCAG 58.570 52.381 12.06 0.00 43.01 4.45
859 921 2.440980 GGGCAGGCCAATGACCTC 60.441 66.667 9.72 0.00 45.80 3.85
860 922 2.440980 GGCAGGCCAATGACCTCC 60.441 66.667 5.01 0.00 34.42 4.30
861 923 2.356278 GCAGGCCAATGACCTCCA 59.644 61.111 5.01 0.00 34.42 3.86
862 924 1.304381 GCAGGCCAATGACCTCCAA 60.304 57.895 5.01 0.00 34.42 3.53
1152 1276 4.379243 CGCTGCCCAGTCCTCGTT 62.379 66.667 0.00 0.00 0.00 3.85
1153 1277 2.435059 GCTGCCCAGTCCTCGTTC 60.435 66.667 0.00 0.00 0.00 3.95
1154 1278 2.125912 CTGCCCAGTCCTCGTTCG 60.126 66.667 0.00 0.00 0.00 3.95
1155 1279 2.915659 TGCCCAGTCCTCGTTCGT 60.916 61.111 0.00 0.00 0.00 3.85
1182 1322 2.835701 TTCCACCGATCGCTGAGTGC 62.836 60.000 10.32 0.00 38.57 4.40
1209 1349 2.727544 GTTTTGCTCTGGCCGCAA 59.272 55.556 11.94 11.94 44.83 4.85
1254 1397 3.995506 GATGGGGTGCAAGGGGTCG 62.996 68.421 0.00 0.00 0.00 4.79
1655 1819 0.594284 GCGGACGAGGAAGAATACGG 60.594 60.000 0.00 0.00 0.00 4.02
1656 1820 0.594284 CGGACGAGGAAGAATACGGC 60.594 60.000 0.00 0.00 0.00 5.68
1761 1925 2.757917 GAGCTGTCGCCTCCTCCT 60.758 66.667 0.00 0.00 36.60 3.69
1762 1926 1.454111 GAGCTGTCGCCTCCTCCTA 60.454 63.158 0.00 0.00 36.60 2.94
1857 2024 2.126031 GGAGGAGCCGTCGTCAAC 60.126 66.667 0.00 0.00 39.03 3.18
1881 2048 2.437413 GAGGAAATCCAGGTGTTCACC 58.563 52.381 13.45 13.45 38.89 4.02
1882 2049 1.165270 GGAAATCCAGGTGTTCACCG 58.835 55.000 15.07 10.47 35.64 4.94
1883 2050 1.271163 GGAAATCCAGGTGTTCACCGA 60.271 52.381 15.07 8.75 35.64 4.69
1884 2051 1.804748 GAAATCCAGGTGTTCACCGAC 59.195 52.381 15.07 1.82 34.28 4.79
1885 2052 0.320421 AATCCAGGTGTTCACCGACG 60.320 55.000 15.07 8.67 34.28 5.12
1886 2053 1.469335 ATCCAGGTGTTCACCGACGT 61.469 55.000 15.07 0.00 34.28 4.34
1887 2054 1.663702 CCAGGTGTTCACCGACGTC 60.664 63.158 15.07 5.18 34.28 4.34
1888 2055 2.014554 CAGGTGTTCACCGACGTCG 61.015 63.158 30.33 30.33 39.44 5.12
1889 2056 3.400590 GGTGTTCACCGACGTCGC 61.401 66.667 31.73 18.08 38.18 5.19
1890 2057 3.749373 GTGTTCACCGACGTCGCG 61.749 66.667 31.73 25.16 38.18 5.87
1891 2058 3.951464 TGTTCACCGACGTCGCGA 61.951 61.111 31.73 25.29 38.18 5.87
1892 2059 3.164011 GTTCACCGACGTCGCGAG 61.164 66.667 31.73 21.71 38.18 5.03
1914 2081 4.256813 GGAGGAACCGTCGTCAAC 57.743 61.111 0.00 0.00 39.88 3.18
1915 2082 1.364901 GGAGGAACCGTCGTCAACA 59.635 57.895 0.00 0.00 39.88 3.33
1916 2083 0.249573 GGAGGAACCGTCGTCAACAA 60.250 55.000 0.00 0.00 39.88 2.83
1917 2084 1.137513 GAGGAACCGTCGTCAACAAG 58.862 55.000 0.00 0.00 38.33 3.16
1918 2085 0.249741 AGGAACCGTCGTCAACAAGG 60.250 55.000 0.00 0.00 0.00 3.61
1919 2086 0.249573 GGAACCGTCGTCAACAAGGA 60.250 55.000 0.00 0.00 0.00 3.36
1920 2087 1.137513 GAACCGTCGTCAACAAGGAG 58.862 55.000 0.00 0.00 0.00 3.69
1921 2088 0.249741 AACCGTCGTCAACAAGGAGG 60.250 55.000 0.00 0.00 0.00 4.30
1922 2089 1.111116 ACCGTCGTCAACAAGGAGGA 61.111 55.000 0.00 0.00 31.03 3.71
1923 2090 0.032952 CCGTCGTCAACAAGGAGGAA 59.967 55.000 0.00 0.00 33.91 3.36
1924 2091 1.539496 CCGTCGTCAACAAGGAGGAAA 60.539 52.381 0.00 0.00 33.91 3.13
1925 2092 2.413837 CGTCGTCAACAAGGAGGAAAT 58.586 47.619 0.00 0.00 33.91 2.17
1926 2093 2.412089 CGTCGTCAACAAGGAGGAAATC 59.588 50.000 0.00 0.00 33.91 2.17
1938 2105 2.437413 GAGGAAATCCAGGTGTTCACC 58.563 52.381 13.45 13.45 38.89 4.02
1939 2106 1.165270 GGAAATCCAGGTGTTCACCG 58.835 55.000 15.07 10.47 35.64 4.94
1940 2107 1.271163 GGAAATCCAGGTGTTCACCGA 60.271 52.381 15.07 8.75 35.64 4.69
1941 2108 1.804748 GAAATCCAGGTGTTCACCGAC 59.195 52.381 15.07 1.82 34.28 4.79
1942 2109 0.320421 AATCCAGGTGTTCACCGACG 60.320 55.000 15.07 8.67 34.28 5.12
1943 2110 1.469335 ATCCAGGTGTTCACCGACGT 61.469 55.000 15.07 0.00 34.28 4.34
1944 2111 1.663702 CCAGGTGTTCACCGACGTC 60.664 63.158 15.07 5.18 34.28 4.34
1945 2112 2.014554 CAGGTGTTCACCGACGTCG 61.015 63.158 30.33 30.33 39.44 5.12
1946 2113 3.400590 GGTGTTCACCGACGTCGC 61.401 66.667 31.73 18.08 38.18 5.19
1947 2114 3.749373 GTGTTCACCGACGTCGCG 61.749 66.667 31.73 25.16 38.18 5.87
1948 2115 3.951464 TGTTCACCGACGTCGCGA 61.951 61.111 31.73 25.29 38.18 5.87
1949 2116 3.164011 GTTCACCGACGTCGCGAG 61.164 66.667 31.73 21.71 38.18 5.03
1962 2129 4.244802 GCGAGCGACGGAGGAGAG 62.245 72.222 0.00 0.00 42.83 3.20
1963 2130 2.511829 CGAGCGACGGAGGAGAGA 60.512 66.667 0.00 0.00 38.46 3.10
1964 2131 1.890041 CGAGCGACGGAGGAGAGAT 60.890 63.158 0.00 0.00 38.46 2.75
1965 2132 1.837538 CGAGCGACGGAGGAGAGATC 61.838 65.000 0.00 0.00 38.46 2.75
1966 2133 1.837538 GAGCGACGGAGGAGAGATCG 61.838 65.000 0.00 0.00 35.91 3.69
1967 2134 2.181521 GCGACGGAGGAGAGATCGT 61.182 63.158 0.00 0.00 38.62 3.73
1968 2135 1.935925 CGACGGAGGAGAGATCGTC 59.064 63.158 0.00 0.00 45.61 4.20
1970 2137 3.571748 ACGGAGGAGAGATCGTCAA 57.428 52.632 1.19 0.00 0.00 3.18
1971 2138 1.384525 ACGGAGGAGAGATCGTCAAG 58.615 55.000 1.19 0.00 0.00 3.02
1972 2139 1.065345 ACGGAGGAGAGATCGTCAAGA 60.065 52.381 1.19 0.00 0.00 3.02
1973 2140 2.017782 CGGAGGAGAGATCGTCAAGAA 58.982 52.381 1.19 0.00 0.00 2.52
1974 2141 2.032799 CGGAGGAGAGATCGTCAAGAAG 59.967 54.545 1.19 0.00 0.00 2.85
1975 2142 2.360801 GGAGGAGAGATCGTCAAGAAGG 59.639 54.545 1.19 0.00 0.00 3.46
1976 2143 3.283751 GAGGAGAGATCGTCAAGAAGGA 58.716 50.000 1.19 0.00 0.00 3.36
1977 2144 3.287222 AGGAGAGATCGTCAAGAAGGAG 58.713 50.000 1.19 0.00 0.00 3.69
1978 2145 2.360801 GGAGAGATCGTCAAGAAGGAGG 59.639 54.545 1.19 0.00 0.00 4.30
1979 2146 3.283751 GAGAGATCGTCAAGAAGGAGGA 58.716 50.000 0.00 0.00 36.28 3.71
1980 2147 3.697045 GAGAGATCGTCAAGAAGGAGGAA 59.303 47.826 0.00 0.00 35.56 3.36
1981 2148 4.090090 AGAGATCGTCAAGAAGGAGGAAA 58.910 43.478 0.00 0.00 35.56 3.13
1982 2149 4.714308 AGAGATCGTCAAGAAGGAGGAAAT 59.286 41.667 0.00 0.00 35.56 2.17
1983 2150 5.017294 AGATCGTCAAGAAGGAGGAAATC 57.983 43.478 0.00 0.00 35.56 2.17
2028 2237 4.011517 GGAGGGGCCGTCGTCAAA 62.012 66.667 19.16 0.00 0.00 2.69
2029 2238 2.031465 GAGGGGCCGTCGTCAAAA 59.969 61.111 10.92 0.00 0.00 2.44
2030 2239 1.598685 GAGGGGCCGTCGTCAAAAA 60.599 57.895 10.92 0.00 0.00 1.94
2085 2294 4.452733 GGAGGGGCCGTCGTCAAG 62.453 72.222 19.16 0.00 0.00 3.02
2086 2295 3.379445 GAGGGGCCGTCGTCAAGA 61.379 66.667 10.92 0.00 0.00 3.02
2087 2296 2.920912 AGGGGCCGTCGTCAAGAA 60.921 61.111 0.00 0.00 0.00 2.52
2088 2297 2.434359 GGGGCCGTCGTCAAGAAG 60.434 66.667 0.00 0.00 0.00 2.85
2095 2304 2.433868 CGTCGTCAAGAAGGAGGAAA 57.566 50.000 0.00 0.00 33.91 3.13
2096 2305 2.960819 CGTCGTCAAGAAGGAGGAAAT 58.039 47.619 0.00 0.00 33.91 2.17
2097 2306 2.924290 CGTCGTCAAGAAGGAGGAAATC 59.076 50.000 0.00 0.00 33.91 2.17
2108 2317 1.087501 GAGGAAATCCAGGTGTTCGC 58.912 55.000 1.67 0.00 38.89 4.70
2109 2318 0.322546 AGGAAATCCAGGTGTTCGCC 60.323 55.000 1.67 0.00 38.89 5.54
2110 2319 1.644786 GGAAATCCAGGTGTTCGCCG 61.645 60.000 0.00 0.00 35.64 6.46
2111 2320 0.672401 GAAATCCAGGTGTTCGCCGA 60.672 55.000 0.00 0.00 0.00 5.54
2112 2321 0.035439 AAATCCAGGTGTTCGCCGAT 60.035 50.000 0.00 0.00 0.00 4.18
2113 2322 0.744414 AATCCAGGTGTTCGCCGATG 60.744 55.000 0.00 0.00 0.00 3.84
2114 2323 1.613317 ATCCAGGTGTTCGCCGATGA 61.613 55.000 0.00 0.00 0.00 2.92
2115 2324 1.153369 CCAGGTGTTCGCCGATGAT 60.153 57.895 0.00 0.00 0.00 2.45
2116 2325 1.431488 CCAGGTGTTCGCCGATGATG 61.431 60.000 0.00 0.00 0.00 3.07
2117 2326 1.815421 AGGTGTTCGCCGATGATGC 60.815 57.895 0.00 0.00 0.00 3.91
2124 2333 3.696426 GCCGATGATGCGAGCGAC 61.696 66.667 0.00 0.00 0.00 5.19
2125 2334 3.390017 CCGATGATGCGAGCGACG 61.390 66.667 0.00 0.00 45.66 5.12
2126 2335 3.390017 CGATGATGCGAGCGACGG 61.390 66.667 0.00 0.00 42.83 4.79
2460 2687 2.430244 CAGGTGTTCGTCGACGGG 60.430 66.667 35.05 11.19 40.29 5.28
2760 2987 4.399303 CCAATCTGTTAATGGAACCACTCC 59.601 45.833 0.00 0.00 45.64 3.85
2761 2988 3.713826 TCTGTTAATGGAACCACTCCC 57.286 47.619 0.00 0.00 44.69 4.30
2763 2990 3.009033 TCTGTTAATGGAACCACTCCCTG 59.991 47.826 0.00 0.00 44.69 4.45
2768 2995 2.943036 TGGAACCACTCCCTGTAAAC 57.057 50.000 0.00 0.00 44.69 2.01
2778 3005 3.074538 ACTCCCTGTAAACTGCTTGGATT 59.925 43.478 0.00 0.00 0.00 3.01
2779 3006 4.082125 CTCCCTGTAAACTGCTTGGATTT 58.918 43.478 0.00 0.00 0.00 2.17
2780 3007 3.826157 TCCCTGTAAACTGCTTGGATTTG 59.174 43.478 0.00 0.00 0.00 2.32
2781 3008 3.573967 CCCTGTAAACTGCTTGGATTTGT 59.426 43.478 0.00 0.00 0.00 2.83
2782 3009 4.039124 CCCTGTAAACTGCTTGGATTTGTT 59.961 41.667 0.00 0.00 0.00 2.83
2783 3010 4.984161 CCTGTAAACTGCTTGGATTTGTTG 59.016 41.667 0.00 0.00 0.00 3.33
2795 3022 6.567511 GCTTGGATTTGTTGTTGTTGTTGTTT 60.568 34.615 0.00 0.00 0.00 2.83
2812 3039 5.163663 TGTTGTTTTTAGTGTGCCTTCTCTG 60.164 40.000 0.00 0.00 0.00 3.35
2822 3049 5.600484 AGTGTGCCTTCTCTGTAGCTAATAT 59.400 40.000 0.00 0.00 0.00 1.28
2826 3053 5.712446 TGCCTTCTCTGTAGCTAATATCGAT 59.288 40.000 2.16 2.16 0.00 3.59
3047 3282 2.170012 TTCCTGGTACCTCGGCTTAT 57.830 50.000 14.36 0.00 0.00 1.73
3084 3319 4.807039 TCGTAAAGGCGGCGCTCC 62.807 66.667 32.30 16.35 0.00 4.70
3105 3340 2.040544 CGGATGGTGGCGCTTCTTT 61.041 57.895 7.64 0.00 0.00 2.52
3188 3423 1.076559 TCCCGGCGTAGATTCCTGA 60.077 57.895 6.01 0.00 0.00 3.86
3272 3508 7.479897 AATGTCAGATTCTTCAGATCGATTG 57.520 36.000 0.00 0.15 0.00 2.67
3432 6351 2.914908 GCGGTGGCAATGGTCGTTT 61.915 57.895 0.00 0.00 39.62 3.60
3561 6498 3.075134 AGAGGGAGGAACAGAAATTTGCT 59.925 43.478 0.00 0.00 0.00 3.91
3562 6499 4.289672 AGAGGGAGGAACAGAAATTTGCTA 59.710 41.667 0.00 0.00 0.00 3.49
3567 6504 5.595952 GGAGGAACAGAAATTTGCTATCCAT 59.404 40.000 0.00 0.00 0.00 3.41
3574 6511 5.537295 CAGAAATTTGCTATCCATCCATCCA 59.463 40.000 0.00 0.00 0.00 3.41
3575 6512 6.210784 CAGAAATTTGCTATCCATCCATCCAT 59.789 38.462 0.00 0.00 0.00 3.41
3576 6513 6.436532 AGAAATTTGCTATCCATCCATCCATC 59.563 38.462 0.00 0.00 0.00 3.51
3577 6514 3.726557 TTGCTATCCATCCATCCATCC 57.273 47.619 0.00 0.00 0.00 3.51
3655 6595 6.016777 AGGAATAAACAGTTGCTTGTGAGAAG 60.017 38.462 0.00 0.00 0.00 2.85
3656 6596 6.017109 GGAATAAACAGTTGCTTGTGAGAAGA 60.017 38.462 0.00 0.00 0.00 2.87
3659 6599 2.945668 ACAGTTGCTTGTGAGAAGAACC 59.054 45.455 0.00 0.00 0.00 3.62
3660 6600 2.945008 CAGTTGCTTGTGAGAAGAACCA 59.055 45.455 0.00 0.00 0.00 3.67
3661 6601 2.945668 AGTTGCTTGTGAGAAGAACCAC 59.054 45.455 0.00 0.00 0.00 4.16
3662 6602 2.945668 GTTGCTTGTGAGAAGAACCACT 59.054 45.455 0.00 0.00 34.57 4.00
3663 6603 2.564771 TGCTTGTGAGAAGAACCACTG 58.435 47.619 0.00 0.00 34.57 3.66
3664 6604 1.265365 GCTTGTGAGAAGAACCACTGC 59.735 52.381 0.00 0.00 34.57 4.40
3665 6605 2.564771 CTTGTGAGAAGAACCACTGCA 58.435 47.619 0.00 0.00 34.57 4.41
3666 6606 1.953559 TGTGAGAAGAACCACTGCAC 58.046 50.000 0.00 0.00 34.57 4.57
3667 6607 1.486310 TGTGAGAAGAACCACTGCACT 59.514 47.619 0.00 0.00 34.57 4.40
3668 6608 1.869767 GTGAGAAGAACCACTGCACTG 59.130 52.381 0.00 0.00 0.00 3.66
3669 6609 0.871057 GAGAAGAACCACTGCACTGC 59.129 55.000 0.00 0.00 0.00 4.40
3794 6740 3.758554 GGATTCATACCATGCATGTACCC 59.241 47.826 24.58 10.27 0.00 3.69
3796 6742 1.071542 TCATACCATGCATGTACCCGG 59.928 52.381 24.58 11.22 0.00 5.73
3798 6744 2.332312 TACCATGCATGTACCCGGCC 62.332 60.000 24.58 0.00 0.00 6.13
3826 6772 1.480212 ATGGCCTCGTGACTTGTGGA 61.480 55.000 3.32 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 1.155424 AGAGAGATCGAGTCGGCGTC 61.155 60.000 13.54 8.84 0.00 5.19
63 64 1.153329 AGAGAGATCGAGTCGGCGT 60.153 57.895 13.54 0.00 0.00 5.68
64 65 1.154814 TCAGAGAGATCGAGTCGGCG 61.155 60.000 13.54 0.00 0.00 6.46
65 66 1.018148 TTCAGAGAGATCGAGTCGGC 58.982 55.000 13.54 5.44 0.00 5.54
66 67 3.313803 TCATTTCAGAGAGATCGAGTCGG 59.686 47.826 13.54 0.00 0.00 4.79
67 68 4.526625 CTCATTTCAGAGAGATCGAGTCG 58.473 47.826 6.09 6.09 37.87 4.18
68 69 4.202000 TGCTCATTTCAGAGAGATCGAGTC 60.202 45.833 0.00 0.00 37.87 3.36
69 70 3.698539 TGCTCATTTCAGAGAGATCGAGT 59.301 43.478 0.00 0.00 37.87 4.18
70 71 4.292599 CTGCTCATTTCAGAGAGATCGAG 58.707 47.826 0.00 0.00 37.87 4.04
82 83 0.179119 GTGCCATGCCTGCTCATTTC 60.179 55.000 0.00 0.00 0.00 2.17
93 94 1.876156 GTAGATAAGCCTGTGCCATGC 59.124 52.381 0.00 0.00 38.69 4.06
97 98 2.939103 CACAAGTAGATAAGCCTGTGCC 59.061 50.000 0.00 0.00 38.69 5.01
98 99 3.600388 ACACAAGTAGATAAGCCTGTGC 58.400 45.455 0.00 0.00 37.95 4.57
115 116 2.724977 GAGAGGATCGACACAACACA 57.275 50.000 0.00 0.00 42.67 3.72
132 133 4.756084 AATCTTTGCTTCTCCAAACGAG 57.244 40.909 0.00 0.00 40.30 4.18
146 147 2.609459 CGGCCTACTGTGCTAATCTTTG 59.391 50.000 0.00 0.00 0.00 2.77
149 150 1.486211 ACGGCCTACTGTGCTAATCT 58.514 50.000 0.00 0.00 32.77 2.40
150 151 2.740452 GTACGGCCTACTGTGCTAATC 58.260 52.381 0.00 0.00 36.55 1.75
152 153 0.452987 CGTACGGCCTACTGTGCTAA 59.547 55.000 7.57 0.00 35.77 3.09
153 154 0.677731 ACGTACGGCCTACTGTGCTA 60.678 55.000 21.06 0.00 35.77 3.49
154 155 0.677731 TACGTACGGCCTACTGTGCT 60.678 55.000 21.06 0.00 35.77 4.40
155 156 0.171007 TTACGTACGGCCTACTGTGC 59.829 55.000 21.06 0.00 36.55 4.57
156 157 2.634982 TTTACGTACGGCCTACTGTG 57.365 50.000 21.06 0.00 36.55 3.66
157 158 2.672195 GCTTTTACGTACGGCCTACTGT 60.672 50.000 21.06 7.84 39.33 3.55
194 207 2.359107 ACAGCTCGACCGGACGTA 60.359 61.111 24.75 11.49 34.70 3.57
197 210 3.664223 GACGACAGCTCGACCGGAC 62.664 68.421 9.46 0.00 43.06 4.79
198 211 3.429141 GACGACAGCTCGACCGGA 61.429 66.667 9.46 0.00 43.06 5.14
235 248 0.324091 CCAATCAGAGCTTTGGCCCT 60.324 55.000 0.00 0.00 36.28 5.19
251 264 2.877097 TGTCTAAAGCCAGATGCCAA 57.123 45.000 0.00 0.00 42.71 4.52
273 286 2.614057 CCGAGCTTTGTTCAACACTTCT 59.386 45.455 0.00 0.00 0.00 2.85
299 312 4.220163 AGACGCTTACATAGGGGTTATAGC 59.780 45.833 0.00 0.00 40.94 2.97
300 313 5.711036 AGAGACGCTTACATAGGGGTTATAG 59.289 44.000 0.00 0.00 40.94 1.31
303 316 3.635373 CAGAGACGCTTACATAGGGGTTA 59.365 47.826 0.00 0.00 40.94 2.85
307 320 2.287069 CGACAGAGACGCTTACATAGGG 60.287 54.545 0.00 0.00 42.27 3.53
308 321 2.287069 CCGACAGAGACGCTTACATAGG 60.287 54.545 0.00 0.00 0.00 2.57
314 327 2.806608 AAAACCGACAGAGACGCTTA 57.193 45.000 0.00 0.00 0.00 3.09
315 328 1.865340 GAAAAACCGACAGAGACGCTT 59.135 47.619 0.00 0.00 0.00 4.68
322 335 6.015027 TCAACAAAAAGAAAAACCGACAGA 57.985 33.333 0.00 0.00 0.00 3.41
334 347 8.835439 GCCTTTAATCCAAAATCAACAAAAAGA 58.165 29.630 0.00 0.00 0.00 2.52
335 348 8.839343 AGCCTTTAATCCAAAATCAACAAAAAG 58.161 29.630 0.00 0.00 0.00 2.27
336 349 8.744568 AGCCTTTAATCCAAAATCAACAAAAA 57.255 26.923 0.00 0.00 0.00 1.94
337 350 8.619546 CAAGCCTTTAATCCAAAATCAACAAAA 58.380 29.630 0.00 0.00 0.00 2.44
338 351 7.228308 CCAAGCCTTTAATCCAAAATCAACAAA 59.772 33.333 0.00 0.00 0.00 2.83
339 352 6.709846 CCAAGCCTTTAATCCAAAATCAACAA 59.290 34.615 0.00 0.00 0.00 2.83
340 353 6.229733 CCAAGCCTTTAATCCAAAATCAACA 58.770 36.000 0.00 0.00 0.00 3.33
341 354 5.122239 GCCAAGCCTTTAATCCAAAATCAAC 59.878 40.000 0.00 0.00 0.00 3.18
342 355 5.244755 GCCAAGCCTTTAATCCAAAATCAA 58.755 37.500 0.00 0.00 0.00 2.57
343 356 4.323409 GGCCAAGCCTTTAATCCAAAATCA 60.323 41.667 0.00 0.00 46.69 2.57
344 357 4.191544 GGCCAAGCCTTTAATCCAAAATC 58.808 43.478 0.00 0.00 46.69 2.17
345 358 4.220693 GGCCAAGCCTTTAATCCAAAAT 57.779 40.909 0.00 0.00 46.69 1.82
402 415 1.107945 TCGATACGTCCCAGCATCAA 58.892 50.000 0.00 0.00 0.00 2.57
409 422 1.471119 AGCTTCTTCGATACGTCCCA 58.529 50.000 0.00 0.00 0.00 4.37
415 428 3.240861 CGTGTTGCTAGCTTCTTCGATAC 59.759 47.826 17.23 1.75 0.00 2.24
473 490 9.562583 CAAGCCAAAACGCTTTATTAATTAGTA 57.437 29.630 0.00 0.00 46.97 1.82
474 491 7.544217 CCAAGCCAAAACGCTTTATTAATTAGT 59.456 33.333 0.00 0.00 46.97 2.24
475 492 7.544217 ACCAAGCCAAAACGCTTTATTAATTAG 59.456 33.333 0.00 0.00 46.97 1.73
522 539 6.437755 ACTAATGTATCCAGGGTGTACTACA 58.562 40.000 0.00 0.00 0.00 2.74
564 585 6.377080 ACCTGATACTAGTGGATGAGATGAA 58.623 40.000 5.39 0.00 0.00 2.57
596 617 0.318022 TTACAGCTCGCGTTTCGACA 60.318 50.000 5.77 0.00 43.16 4.35
632 653 1.078426 GTGGTCGATCCCCCAACAG 60.078 63.158 0.00 0.00 34.77 3.16
640 661 1.732308 GAGTACCCGTGGTCGATCC 59.268 63.158 0.00 0.00 37.09 3.36
642 663 2.768492 GCGAGTACCCGTGGTCGAT 61.768 63.158 0.00 0.00 37.09 3.59
644 665 4.824166 CGCGAGTACCCGTGGTCG 62.824 72.222 0.00 0.00 37.09 4.79
657 680 2.433491 CGGTTGATGGGTTCGCGA 60.433 61.111 3.71 3.71 0.00 5.87
695 718 2.052104 GCCCGGATTTGTTGGAGGG 61.052 63.158 0.73 0.00 41.65 4.30
697 720 0.893270 TGTGCCCGGATTTGTTGGAG 60.893 55.000 0.73 0.00 0.00 3.86
714 737 4.163427 AGTAGCTGGGCAGATATATGTGT 58.837 43.478 11.20 0.00 31.46 3.72
715 738 4.815533 AGTAGCTGGGCAGATATATGTG 57.184 45.455 5.50 5.50 31.46 3.21
716 739 4.712337 GGTAGTAGCTGGGCAGATATATGT 59.288 45.833 0.00 0.00 31.46 2.29
717 740 4.202060 CGGTAGTAGCTGGGCAGATATATG 60.202 50.000 0.00 0.00 31.46 1.78
718 741 3.954904 CGGTAGTAGCTGGGCAGATATAT 59.045 47.826 0.00 0.00 31.46 0.86
719 742 3.009805 TCGGTAGTAGCTGGGCAGATATA 59.990 47.826 0.00 0.00 31.46 0.86
720 743 2.171840 CGGTAGTAGCTGGGCAGATAT 58.828 52.381 0.00 0.00 31.46 1.63
721 744 1.144298 TCGGTAGTAGCTGGGCAGATA 59.856 52.381 0.00 0.00 0.00 1.98
722 745 0.106167 TCGGTAGTAGCTGGGCAGAT 60.106 55.000 0.00 0.00 0.00 2.90
723 746 0.323999 TTCGGTAGTAGCTGGGCAGA 60.324 55.000 0.00 0.00 0.00 4.26
724 747 0.179108 GTTCGGTAGTAGCTGGGCAG 60.179 60.000 0.00 0.00 0.00 4.85
728 771 1.436336 CCGGTTCGGTAGTAGCTGG 59.564 63.158 0.00 0.00 42.73 4.85
815 865 2.464459 GCTGTGGAATTCTCGGCCG 61.464 63.158 22.12 22.12 0.00 6.13
817 867 1.377202 TGGCTGTGGAATTCTCGGC 60.377 57.895 19.24 19.24 0.00 5.54
1003 1106 3.771160 GGCGAGATCCGTGGTGGT 61.771 66.667 5.66 0.00 41.15 4.16
1150 1274 0.230515 GGTGGAACGAACGAACGAAC 59.769 55.000 11.97 6.05 38.12 3.95
1151 1275 1.208009 CGGTGGAACGAACGAACGAA 61.208 55.000 11.97 0.00 38.12 3.85
1152 1276 1.658102 CGGTGGAACGAACGAACGA 60.658 57.895 11.97 0.00 38.12 3.85
1153 1277 1.005294 ATCGGTGGAACGAACGAACG 61.005 55.000 0.87 0.00 46.92 3.95
1154 1278 0.712222 GATCGGTGGAACGAACGAAC 59.288 55.000 0.87 0.00 46.92 3.95
1155 1279 3.111536 GATCGGTGGAACGAACGAA 57.888 52.632 0.87 0.00 46.92 3.85
1182 1322 2.032071 AGCAAAACCTCCGTCCGG 59.968 61.111 0.00 0.00 0.00 5.14
1393 1539 2.126850 GAAAGAAACCGCCGCAGC 60.127 61.111 0.00 0.00 0.00 5.25
1394 1540 2.173382 CGAAAGAAACCGCCGCAG 59.827 61.111 0.00 0.00 0.00 5.18
1395 1541 4.020378 GCGAAAGAAACCGCCGCA 62.020 61.111 0.00 0.00 45.06 5.69
1437 1583 4.377760 TCCTTCCCGGACCTCGCT 62.378 66.667 0.73 0.00 36.69 4.93
1634 1789 0.100146 GTATTCTTCCTCGTCCGCGT 59.900 55.000 4.92 0.00 39.49 6.01
1641 1805 1.787155 CAATCGCCGTATTCTTCCTCG 59.213 52.381 0.00 0.00 0.00 4.63
1710 1874 3.547249 GAACGCCGACAGGACGTCA 62.547 63.158 18.91 0.00 45.70 4.35
1857 2024 2.887151 ACACCTGGATTTCCTCCTTG 57.113 50.000 0.00 0.00 45.21 3.61
1897 2064 0.249573 TTGTTGACGACGGTTCCTCC 60.250 55.000 0.00 0.00 0.00 4.30
1898 2065 1.137513 CTTGTTGACGACGGTTCCTC 58.862 55.000 0.00 0.00 0.00 3.71
1899 2066 0.249741 CCTTGTTGACGACGGTTCCT 60.250 55.000 0.00 0.00 0.00 3.36
1900 2067 0.249573 TCCTTGTTGACGACGGTTCC 60.250 55.000 0.00 0.00 0.00 3.62
1901 2068 1.137513 CTCCTTGTTGACGACGGTTC 58.862 55.000 0.00 0.00 0.00 3.62
1902 2069 0.249741 CCTCCTTGTTGACGACGGTT 60.250 55.000 0.00 0.00 0.00 4.44
1903 2070 1.111116 TCCTCCTTGTTGACGACGGT 61.111 55.000 0.00 0.00 0.00 4.83
1904 2071 0.032952 TTCCTCCTTGTTGACGACGG 59.967 55.000 0.00 0.00 0.00 4.79
1905 2072 1.860676 TTTCCTCCTTGTTGACGACG 58.139 50.000 0.00 0.00 0.00 5.12
1906 2073 2.742589 GGATTTCCTCCTTGTTGACGAC 59.257 50.000 0.00 0.00 41.29 4.34
1907 2074 2.370519 TGGATTTCCTCCTTGTTGACGA 59.629 45.455 0.00 0.00 45.21 4.20
1908 2075 2.744202 CTGGATTTCCTCCTTGTTGACG 59.256 50.000 0.00 0.00 45.21 4.35
1909 2076 3.084786 CCTGGATTTCCTCCTTGTTGAC 58.915 50.000 0.00 0.00 45.21 3.18
1910 2077 2.716424 ACCTGGATTTCCTCCTTGTTGA 59.284 45.455 0.00 0.00 45.21 3.18
1911 2078 2.821969 CACCTGGATTTCCTCCTTGTTG 59.178 50.000 0.00 0.00 45.21 3.33
1912 2079 2.447047 ACACCTGGATTTCCTCCTTGTT 59.553 45.455 0.00 0.00 45.21 2.83
1913 2080 2.065799 ACACCTGGATTTCCTCCTTGT 58.934 47.619 0.00 0.00 45.21 3.16
1914 2081 2.887151 ACACCTGGATTTCCTCCTTG 57.113 50.000 0.00 0.00 45.21 3.61
1915 2082 2.716424 TGAACACCTGGATTTCCTCCTT 59.284 45.455 0.00 0.00 45.21 3.36
1916 2083 2.040412 GTGAACACCTGGATTTCCTCCT 59.960 50.000 0.00 0.00 45.21 3.69
1917 2084 2.437413 GTGAACACCTGGATTTCCTCC 58.563 52.381 0.00 0.00 45.19 4.30
1930 2097 3.749373 CGCGACGTCGGTGAACAC 61.749 66.667 36.13 18.23 40.23 3.32
1931 2098 3.867226 CTCGCGACGTCGGTGAACA 62.867 63.158 36.13 11.33 40.23 3.18
1932 2099 3.164011 CTCGCGACGTCGGTGAAC 61.164 66.667 36.13 19.63 40.23 3.18
1945 2112 4.244802 CTCTCCTCCGTCGCTCGC 62.245 72.222 0.00 0.00 38.35 5.03
1946 2113 1.837538 GATCTCTCCTCCGTCGCTCG 61.838 65.000 0.00 0.00 39.52 5.03
1947 2114 1.837538 CGATCTCTCCTCCGTCGCTC 61.838 65.000 0.00 0.00 0.00 5.03
1948 2115 1.890041 CGATCTCTCCTCCGTCGCT 60.890 63.158 0.00 0.00 0.00 4.93
1949 2116 2.108344 GACGATCTCTCCTCCGTCGC 62.108 65.000 0.00 0.00 41.22 5.19
1950 2117 1.935925 GACGATCTCTCCTCCGTCG 59.064 63.158 0.00 0.00 41.22 5.12
1952 2119 1.065345 TCTTGACGATCTCTCCTCCGT 60.065 52.381 0.00 0.00 38.01 4.69
1953 2120 1.669604 TCTTGACGATCTCTCCTCCG 58.330 55.000 0.00 0.00 0.00 4.63
1954 2121 2.360801 CCTTCTTGACGATCTCTCCTCC 59.639 54.545 0.00 0.00 0.00 4.30
1955 2122 3.283751 TCCTTCTTGACGATCTCTCCTC 58.716 50.000 0.00 0.00 0.00 3.71
1956 2123 3.287222 CTCCTTCTTGACGATCTCTCCT 58.713 50.000 0.00 0.00 0.00 3.69
1957 2124 2.360801 CCTCCTTCTTGACGATCTCTCC 59.639 54.545 0.00 0.00 0.00 3.71
1958 2125 3.283751 TCCTCCTTCTTGACGATCTCTC 58.716 50.000 0.00 0.00 0.00 3.20
1959 2126 3.374042 TCCTCCTTCTTGACGATCTCT 57.626 47.619 0.00 0.00 0.00 3.10
1960 2127 4.457834 TTTCCTCCTTCTTGACGATCTC 57.542 45.455 0.00 0.00 0.00 2.75
1961 2128 4.141824 GGATTTCCTCCTTCTTGACGATCT 60.142 45.833 0.00 0.00 41.29 2.75
1962 2129 4.123506 GGATTTCCTCCTTCTTGACGATC 58.876 47.826 0.00 0.00 41.29 3.69
1963 2130 3.519510 TGGATTTCCTCCTTCTTGACGAT 59.480 43.478 0.00 0.00 45.21 3.73
1964 2131 2.903784 TGGATTTCCTCCTTCTTGACGA 59.096 45.455 0.00 0.00 45.21 4.20
1965 2132 3.265791 CTGGATTTCCTCCTTCTTGACG 58.734 50.000 0.00 0.00 45.21 4.35
1966 2133 3.264450 TCCTGGATTTCCTCCTTCTTGAC 59.736 47.826 0.00 0.00 45.21 3.18
1967 2134 3.521126 CTCCTGGATTTCCTCCTTCTTGA 59.479 47.826 0.00 0.00 45.21 3.02
1968 2135 3.883669 CTCCTGGATTTCCTCCTTCTTG 58.116 50.000 0.00 0.00 45.21 3.02
1969 2136 2.240921 GCTCCTGGATTTCCTCCTTCTT 59.759 50.000 0.00 0.00 45.21 2.52
1970 2137 1.843206 GCTCCTGGATTTCCTCCTTCT 59.157 52.381 0.00 0.00 45.21 2.85
1971 2138 1.843206 AGCTCCTGGATTTCCTCCTTC 59.157 52.381 0.00 0.00 45.21 3.46
1972 2139 1.843206 GAGCTCCTGGATTTCCTCCTT 59.157 52.381 0.87 0.00 45.21 3.36
1973 2140 1.506025 GAGCTCCTGGATTTCCTCCT 58.494 55.000 0.87 0.00 45.21 3.69
1974 2141 0.105778 CGAGCTCCTGGATTTCCTCC 59.894 60.000 8.47 0.00 45.19 4.30
1975 2142 0.531753 GCGAGCTCCTGGATTTCCTC 60.532 60.000 8.47 0.65 36.82 3.71
1976 2143 1.524482 GCGAGCTCCTGGATTTCCT 59.476 57.895 8.47 0.00 36.82 3.36
1977 2144 1.524849 GGCGAGCTCCTGGATTTCC 60.525 63.158 8.47 0.00 0.00 3.13
1978 2145 1.884926 CGGCGAGCTCCTGGATTTC 60.885 63.158 8.47 0.00 0.00 2.17
1979 2146 2.187946 CGGCGAGCTCCTGGATTT 59.812 61.111 8.47 0.00 0.00 2.17
1980 2147 2.759973 TCGGCGAGCTCCTGGATT 60.760 61.111 4.99 0.00 0.00 3.01
1981 2148 3.532155 GTCGGCGAGCTCCTGGAT 61.532 66.667 11.20 0.00 0.00 3.41
1984 2151 4.838486 GACGTCGGCGAGCTCCTG 62.838 72.222 20.03 6.42 42.00 3.86
2028 2237 1.713078 AGCACCTGGATTTCCTCCTTT 59.287 47.619 0.00 0.00 45.21 3.11
2029 2238 1.283321 GAGCACCTGGATTTCCTCCTT 59.717 52.381 0.00 0.00 45.21 3.36
2030 2239 0.915364 GAGCACCTGGATTTCCTCCT 59.085 55.000 0.00 0.00 45.21 3.69
2071 2280 2.434359 CTTCTTGACGACGGCCCC 60.434 66.667 0.00 0.00 0.00 5.80
2072 2281 2.434359 CCTTCTTGACGACGGCCC 60.434 66.667 0.00 0.00 0.00 5.80
2073 2282 1.446272 CTCCTTCTTGACGACGGCC 60.446 63.158 0.00 0.00 31.32 6.13
2074 2283 1.446272 CCTCCTTCTTGACGACGGC 60.446 63.158 0.00 0.00 31.32 5.68
2075 2284 0.601558 TTCCTCCTTCTTGACGACGG 59.398 55.000 0.00 0.00 32.48 4.79
2076 2285 2.433868 TTTCCTCCTTCTTGACGACG 57.566 50.000 0.00 0.00 0.00 5.12
2077 2286 3.263261 GGATTTCCTCCTTCTTGACGAC 58.737 50.000 0.00 0.00 41.29 4.34
2078 2287 2.903784 TGGATTTCCTCCTTCTTGACGA 59.096 45.455 0.00 0.00 45.21 4.20
2079 2288 3.265791 CTGGATTTCCTCCTTCTTGACG 58.734 50.000 0.00 0.00 45.21 4.35
2080 2289 3.009584 ACCTGGATTTCCTCCTTCTTGAC 59.990 47.826 0.00 0.00 45.21 3.18
2081 2290 3.009473 CACCTGGATTTCCTCCTTCTTGA 59.991 47.826 0.00 0.00 45.21 3.02
2082 2291 3.245052 ACACCTGGATTTCCTCCTTCTTG 60.245 47.826 0.00 0.00 45.21 3.02
2083 2292 2.989571 ACACCTGGATTTCCTCCTTCTT 59.010 45.455 0.00 0.00 45.21 2.52
2084 2293 2.637165 ACACCTGGATTTCCTCCTTCT 58.363 47.619 0.00 0.00 45.21 2.85
2085 2294 3.348119 GAACACCTGGATTTCCTCCTTC 58.652 50.000 0.00 0.00 45.21 3.46
2086 2295 2.290323 CGAACACCTGGATTTCCTCCTT 60.290 50.000 0.00 0.00 45.21 3.36
2087 2296 1.279271 CGAACACCTGGATTTCCTCCT 59.721 52.381 0.00 0.00 45.21 3.69
2088 2297 1.739067 CGAACACCTGGATTTCCTCC 58.261 55.000 0.00 0.00 45.19 4.30
2089 2298 1.087501 GCGAACACCTGGATTTCCTC 58.912 55.000 0.00 0.00 36.82 3.71
2090 2299 0.322546 GGCGAACACCTGGATTTCCT 60.323 55.000 0.00 0.00 36.82 3.36
2091 2300 1.644786 CGGCGAACACCTGGATTTCC 61.645 60.000 0.00 0.00 0.00 3.13
2092 2301 0.672401 TCGGCGAACACCTGGATTTC 60.672 55.000 7.35 1.21 0.00 2.17
2093 2302 0.035439 ATCGGCGAACACCTGGATTT 60.035 50.000 15.93 0.00 0.00 2.17
2094 2303 0.744414 CATCGGCGAACACCTGGATT 60.744 55.000 15.93 0.00 0.00 3.01
2095 2304 1.153369 CATCGGCGAACACCTGGAT 60.153 57.895 15.93 0.00 0.00 3.41
2096 2305 1.613317 ATCATCGGCGAACACCTGGA 61.613 55.000 15.93 3.59 0.00 3.86
2097 2306 1.153369 ATCATCGGCGAACACCTGG 60.153 57.895 15.93 0.00 0.00 4.45
2098 2307 2.009108 CATCATCGGCGAACACCTG 58.991 57.895 15.93 7.49 0.00 4.00
2099 2308 1.815421 GCATCATCGGCGAACACCT 60.815 57.895 15.93 0.00 0.00 4.00
2100 2309 2.709475 GCATCATCGGCGAACACC 59.291 61.111 15.93 0.00 0.00 4.16
2107 2316 3.696426 GTCGCTCGCATCATCGGC 61.696 66.667 0.00 0.00 0.00 5.54
2108 2317 3.390017 CGTCGCTCGCATCATCGG 61.390 66.667 0.00 0.00 0.00 4.18
2109 2318 3.390017 CCGTCGCTCGCATCATCG 61.390 66.667 0.00 0.00 38.35 3.84
2110 2319 2.013483 CTCCGTCGCTCGCATCATC 61.013 63.158 0.00 0.00 38.35 2.92
2111 2320 2.026734 CTCCGTCGCTCGCATCAT 59.973 61.111 0.00 0.00 38.35 2.45
2112 2321 4.193334 CCTCCGTCGCTCGCATCA 62.193 66.667 0.00 0.00 38.35 3.07
2113 2322 3.815569 CTCCTCCGTCGCTCGCATC 62.816 68.421 0.00 0.00 38.35 3.91
2114 2323 3.893763 CTCCTCCGTCGCTCGCAT 61.894 66.667 0.00 0.00 38.35 4.73
2118 2327 3.492311 GATGGCTCCTCCGTCGCTC 62.492 68.421 0.00 0.00 40.78 5.03
2119 2328 3.532155 GATGGCTCCTCCGTCGCT 61.532 66.667 0.00 0.00 40.78 4.93
2122 2331 2.413765 GACGATGGCTCCTCCGTC 59.586 66.667 14.10 14.10 45.53 4.79
2123 2332 1.949847 CTTGACGATGGCTCCTCCGT 61.950 60.000 0.00 6.03 37.80 4.69
2124 2333 1.227089 CTTGACGATGGCTCCTCCG 60.227 63.158 0.00 0.00 37.80 4.63
2125 2334 0.537188 TTCTTGACGATGGCTCCTCC 59.463 55.000 0.00 0.00 0.00 4.30
2126 2335 1.472376 CCTTCTTGACGATGGCTCCTC 60.472 57.143 0.00 0.00 31.08 3.71
2127 2336 0.539051 CCTTCTTGACGATGGCTCCT 59.461 55.000 0.00 0.00 31.08 3.69
2184 2393 3.374402 CCCTGGAGCACGTCGAGT 61.374 66.667 0.00 0.00 29.03 4.18
2328 2546 1.227380 GCCGTAGCTGGACAGGATG 60.227 63.158 0.00 0.00 38.03 3.51
2760 2987 4.853924 ACAAATCCAAGCAGTTTACAGG 57.146 40.909 0.00 0.00 0.00 4.00
2761 2988 5.591099 ACAACAAATCCAAGCAGTTTACAG 58.409 37.500 0.00 0.00 0.00 2.74
2763 2990 5.810074 ACAACAACAAATCCAAGCAGTTTAC 59.190 36.000 0.00 0.00 0.00 2.01
2768 2995 4.183101 ACAACAACAACAAATCCAAGCAG 58.817 39.130 0.00 0.00 0.00 4.24
2778 3005 7.621991 CACACTAAAAACAACAACAACAACAA 58.378 30.769 0.00 0.00 0.00 2.83
2779 3006 6.292381 GCACACTAAAAACAACAACAACAACA 60.292 34.615 0.00 0.00 0.00 3.33
2780 3007 6.068300 GCACACTAAAAACAACAACAACAAC 58.932 36.000 0.00 0.00 0.00 3.32
2781 3008 5.177696 GGCACACTAAAAACAACAACAACAA 59.822 36.000 0.00 0.00 0.00 2.83
2782 3009 4.686554 GGCACACTAAAAACAACAACAACA 59.313 37.500 0.00 0.00 0.00 3.33
2783 3010 4.926832 AGGCACACTAAAAACAACAACAAC 59.073 37.500 0.00 0.00 0.00 3.32
2795 3022 3.578716 AGCTACAGAGAAGGCACACTAAA 59.421 43.478 0.00 0.00 0.00 1.85
2812 3039 7.090808 TGGATGAACACATCGATATTAGCTAC 58.909 38.462 0.00 0.00 40.66 3.58
3009 3243 1.205460 ATACCCTTTCTGCCACCGGT 61.205 55.000 0.00 0.00 0.00 5.28
3036 3271 3.336088 ACCCTACCTATATAAGCCGAGGT 59.664 47.826 0.00 0.00 44.55 3.85
3047 3282 9.474313 TTTACGAGAACTAAAACCCTACCTATA 57.526 33.333 0.00 0.00 0.00 1.31
3105 3340 1.034356 TCCGGAAGACAGACACGAAA 58.966 50.000 0.00 0.00 0.00 3.46
3141 3376 0.248289 ATCCGTCCCGACAAACGAAT 59.752 50.000 0.00 0.00 45.77 3.34
3170 3405 1.076559 TCAGGAATCTACGCCGGGA 60.077 57.895 2.18 0.00 0.00 5.14
3171 3406 1.067582 GTCAGGAATCTACGCCGGG 59.932 63.158 2.18 0.00 0.00 5.73
3272 3508 3.001330 CGGTCGTAGCCATTGAATCTTTC 59.999 47.826 0.00 0.00 0.00 2.62
3379 3616 4.771356 GCGTCGCTGTCACCGCTA 62.771 66.667 10.68 0.00 42.66 4.26
3432 6351 0.896479 TCGAGATCCGTGGACAACCA 60.896 55.000 0.00 0.00 39.50 3.67
3539 6476 3.075134 AGCAAATTTCTGTTCCTCCCTCT 59.925 43.478 0.00 0.00 0.00 3.69
3540 6477 3.425659 AGCAAATTTCTGTTCCTCCCTC 58.574 45.455 0.00 0.00 0.00 4.30
3561 6498 3.195459 AGCATGGATGGATGGATGGATA 58.805 45.455 0.00 0.00 0.00 2.59
3562 6499 2.000803 AGCATGGATGGATGGATGGAT 58.999 47.619 0.00 0.00 0.00 3.41
3567 6504 1.980765 GTCCTAGCATGGATGGATGGA 59.019 52.381 0.00 0.00 38.52 3.41
3574 6511 1.898472 CGGATCAGTCCTAGCATGGAT 59.102 52.381 0.00 0.00 42.73 3.41
3575 6512 1.332195 CGGATCAGTCCTAGCATGGA 58.668 55.000 0.00 0.00 42.73 3.41
3576 6513 0.320247 GCGGATCAGTCCTAGCATGG 60.320 60.000 0.00 0.00 42.73 3.66
3577 6514 0.678395 AGCGGATCAGTCCTAGCATG 59.322 55.000 0.00 0.00 42.73 4.06
3595 6532 1.226802 CACAGCTCGACCCGATCAG 60.227 63.158 0.00 0.00 34.61 2.90
3631 6568 5.689383 TCTCACAAGCAACTGTTTATTCC 57.311 39.130 0.00 0.00 0.00 3.01
3655 6595 1.526917 AGTGGCAGTGCAGTGGTTC 60.527 57.895 22.71 6.39 0.00 3.62
3656 6596 1.825191 CAGTGGCAGTGCAGTGGTT 60.825 57.895 22.71 0.00 0.00 3.67
3659 6599 4.021631 CGCAGTGGCAGTGCAGTG 62.022 66.667 37.82 23.02 44.55 3.66
3664 6604 3.720193 GTGAGCGCAGTGGCAGTG 61.720 66.667 18.01 18.01 41.24 3.66
3665 6605 4.996434 GGTGAGCGCAGTGGCAGT 62.996 66.667 11.47 0.00 41.24 4.40
3669 6609 4.320456 ACAGGGTGAGCGCAGTGG 62.320 66.667 11.47 0.00 0.00 4.00
3680 6620 1.460305 AGTCAGACAGCCACAGGGT 60.460 57.895 2.66 0.00 36.17 4.34
3798 6744 5.392767 AGTCACGAGGCCATAATATAGTG 57.607 43.478 5.01 0.00 0.00 2.74
3826 6772 0.670546 CCATTTCTGCTCACGACCGT 60.671 55.000 0.00 0.00 0.00 4.83


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

AutoCloner maintained by Alex Coulton.