Multiple sequence alignment - TraesCS1D01G100800

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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 TraesCS1D01G100800 chr1D 100.000 2882 0 0 1 2882 88243676 88240795 0.000000e+00 5323.0
1 TraesCS1D01G100800 chr1D 90.634 694 35 14 2 693 88281827 88281162 0.000000e+00 894.0
2 TraesCS1D01G100800 chr1D 90.750 573 36 11 2315 2881 190482816 190483377 0.000000e+00 749.0
3 TraesCS1D01G100800 chr1D 88.776 588 50 7 2310 2882 22271640 22272226 0.000000e+00 706.0
4 TraesCS1D01G100800 chr1D 88.489 417 29 9 2 413 87904417 87904819 1.200000e-133 486.0
5 TraesCS1D01G100800 chr1D 88.489 417 29 9 2 413 88215200 88215602 1.200000e-133 486.0
6 TraesCS1D01G100800 chr1D 88.000 225 14 9 471 693 88215804 88216017 1.330000e-63 254.0
7 TraesCS1D01G100800 chr1D 83.444 151 13 6 1000 1147 88216304 88216445 2.330000e-26 130.0
8 TraesCS1D01G100800 chr1D 84.444 135 6 11 471 603 87905022 87905143 5.040000e-23 119.0
9 TraesCS1D01G100800 chr1A 91.457 2025 93 25 2 1993 84795939 84793962 0.000000e+00 2708.0
10 TraesCS1D01G100800 chr1A 85.294 612 34 10 2 604 85005823 85005259 5.350000e-162 580.0
11 TraesCS1D01G100800 chr1A 87.290 417 34 8 2 413 84621702 84622104 2.620000e-125 459.0
12 TraesCS1D01G100800 chr1A 87.050 417 35 8 2 413 84484505 84484907 1.220000e-123 453.0
13 TraesCS1D01G100800 chr1A 90.741 216 20 0 478 693 84622323 84622538 3.630000e-74 289.0
14 TraesCS1D01G100800 chr1A 90.278 216 21 0 478 693 84485125 84485340 1.690000e-72 283.0
15 TraesCS1D01G100800 chr1A 93.750 48 2 1 804 851 84485526 84485572 1.430000e-08 71.3
16 TraesCS1D01G100800 chr1A 93.750 48 2 1 804 851 84622727 84622773 1.430000e-08 71.3
17 TraesCS1D01G100800 chr4D 90.039 1807 98 24 2 1790 464797232 464795490 0.000000e+00 2265.0
18 TraesCS1D01G100800 chr4D 88.245 587 51 9 2312 2882 487201950 487201366 0.000000e+00 686.0
19 TraesCS1D01G100800 chr4D 88.095 168 7 5 1816 1978 464795494 464795335 1.360000e-43 187.0
20 TraesCS1D01G100800 chr1B 92.968 1351 45 20 690 1993 142133063 142131716 0.000000e+00 1923.0
21 TraesCS1D01G100800 chr1B 92.529 522 27 5 21 535 142133748 142133232 0.000000e+00 737.0
22 TraesCS1D01G100800 chr1B 84.507 710 44 21 3 693 141845744 141846406 2.420000e-180 641.0
23 TraesCS1D01G100800 chr1B 93.811 307 15 1 2 308 142094512 142094814 2.620000e-125 459.0
24 TraesCS1D01G100800 chr1B 86.998 423 32 14 3 413 142038253 142038664 3.390000e-124 455.0
25 TraesCS1D01G100800 chr1B 94.059 101 6 0 1994 2094 484457751 484457651 1.380000e-33 154.0
26 TraesCS1D01G100800 chr1B 82.051 117 12 5 999 1115 142103366 142103473 1.100000e-14 91.6
27 TraesCS1D01G100800 chr2B 89.950 597 38 6 2307 2882 757533764 757533169 0.000000e+00 750.0
28 TraesCS1D01G100800 chr2D 89.882 593 34 7 2315 2882 623460681 623460090 0.000000e+00 739.0
29 TraesCS1D01G100800 chr2D 93.069 101 7 0 1994 2094 89224327 89224427 6.430000e-32 148.0
30 TraesCS1D01G100800 chr2D 93.069 101 7 0 1994 2094 104868266 104868166 6.430000e-32 148.0
31 TraesCS1D01G100800 chr5D 89.825 570 45 9 2308 2873 481943544 481944104 0.000000e+00 719.0
32 TraesCS1D01G100800 chr7A 88.435 588 50 7 2312 2882 398909868 398910454 0.000000e+00 693.0
33 TraesCS1D01G100800 chr7A 86.947 452 43 11 2312 2759 686198009 686198448 7.170000e-136 494.0
34 TraesCS1D01G100800 chr6D 88.165 583 57 4 2312 2882 114771936 114772518 0.000000e+00 684.0
35 TraesCS1D01G100800 chr6D 82.491 554 77 14 2312 2853 21358994 21359539 4.350000e-128 468.0
36 TraesCS1D01G100800 chr2A 85.223 582 73 7 2312 2882 554107493 554108072 1.150000e-163 586.0
37 TraesCS1D01G100800 chr3A 85.395 582 62 15 2308 2882 719975167 719975732 1.490000e-162 582.0
38 TraesCS1D01G100800 chr5A 82.169 544 80 12 2313 2846 5976073 5975537 4.380000e-123 451.0
39 TraesCS1D01G100800 chr4A 94.059 101 6 0 1994 2094 5254928 5255028 1.380000e-33 154.0
40 TraesCS1D01G100800 chr3D 94.000 100 6 0 1995 2094 434935877 434935778 4.970000e-33 152.0
41 TraesCS1D01G100800 chr3D 94.000 100 6 0 1995 2094 436196337 436196436 4.970000e-33 152.0
42 TraesCS1D01G100800 chr7B 93.069 101 7 0 1994 2094 634277186 634277286 6.430000e-32 148.0
43 TraesCS1D01G100800 chr6B 93.069 101 7 0 1994 2094 513615493 513615393 6.430000e-32 148.0
44 TraesCS1D01G100800 chr4B 93.069 101 7 0 1994 2094 553536803 553536703 6.430000e-32 148.0
45 TraesCS1D01G100800 chr3B 90.244 82 7 1 479 559 535704347 535704266 3.930000e-19 106.0


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 TraesCS1D01G100800 chr1D 88240795 88243676 2881 True 5323.0 5323 100.000000 1 2882 1 chr1D.!!$R1 2881
1 TraesCS1D01G100800 chr1D 88281162 88281827 665 True 894.0 894 90.634000 2 693 1 chr1D.!!$R2 691
2 TraesCS1D01G100800 chr1D 190482816 190483377 561 False 749.0 749 90.750000 2315 2881 1 chr1D.!!$F2 566
3 TraesCS1D01G100800 chr1D 22271640 22272226 586 False 706.0 706 88.776000 2310 2882 1 chr1D.!!$F1 572
4 TraesCS1D01G100800 chr1D 87904417 87905143 726 False 302.5 486 86.466500 2 603 2 chr1D.!!$F3 601
5 TraesCS1D01G100800 chr1D 88215200 88216445 1245 False 290.0 486 86.644333 2 1147 3 chr1D.!!$F4 1145
6 TraesCS1D01G100800 chr1A 84793962 84795939 1977 True 2708.0 2708 91.457000 2 1993 1 chr1A.!!$R1 1991
7 TraesCS1D01G100800 chr1A 85005259 85005823 564 True 580.0 580 85.294000 2 604 1 chr1A.!!$R2 602
8 TraesCS1D01G100800 chr1A 84621702 84622773 1071 False 273.1 459 90.593667 2 851 3 chr1A.!!$F2 849
9 TraesCS1D01G100800 chr1A 84484505 84485572 1067 False 269.1 453 90.359333 2 851 3 chr1A.!!$F1 849
10 TraesCS1D01G100800 chr4D 464795335 464797232 1897 True 1226.0 2265 89.067000 2 1978 2 chr4D.!!$R2 1976
11 TraesCS1D01G100800 chr4D 487201366 487201950 584 True 686.0 686 88.245000 2312 2882 1 chr4D.!!$R1 570
12 TraesCS1D01G100800 chr1B 142131716 142133748 2032 True 1330.0 1923 92.748500 21 1993 2 chr1B.!!$R2 1972
13 TraesCS1D01G100800 chr1B 141845744 141846406 662 False 641.0 641 84.507000 3 693 1 chr1B.!!$F1 690
14 TraesCS1D01G100800 chr2B 757533169 757533764 595 True 750.0 750 89.950000 2307 2882 1 chr2B.!!$R1 575
15 TraesCS1D01G100800 chr2D 623460090 623460681 591 True 739.0 739 89.882000 2315 2882 1 chr2D.!!$R2 567
16 TraesCS1D01G100800 chr5D 481943544 481944104 560 False 719.0 719 89.825000 2308 2873 1 chr5D.!!$F1 565
17 TraesCS1D01G100800 chr7A 398909868 398910454 586 False 693.0 693 88.435000 2312 2882 1 chr7A.!!$F1 570
18 TraesCS1D01G100800 chr6D 114771936 114772518 582 False 684.0 684 88.165000 2312 2882 1 chr6D.!!$F2 570
19 TraesCS1D01G100800 chr6D 21358994 21359539 545 False 468.0 468 82.491000 2312 2853 1 chr6D.!!$F1 541
20 TraesCS1D01G100800 chr2A 554107493 554108072 579 False 586.0 586 85.223000 2312 2882 1 chr2A.!!$F1 570
21 TraesCS1D01G100800 chr3A 719975167 719975732 565 False 582.0 582 85.395000 2308 2882 1 chr3A.!!$F1 574
22 TraesCS1D01G100800 chr5A 5975537 5976073 536 True 451.0 451 82.169000 2313 2846 1 chr5A.!!$R1 533

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
867 1214 2.094803 TCACACAAACACAAAGTGCCTG 60.095 45.455 0.0 0.0 36.98 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2197 2608 0.040336 TAGAGAATAGCTTCGCCGCG 60.04 55.0 6.39 6.39 36.45 6.46 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
39 40 3.291584 TGCGAGACCAGATCACTTCTAT 58.708 45.455 0.00 0.00 31.77 1.98
420 463 9.119418 ACTGTAGCATGCAAATTACATTACATA 57.881 29.630 21.98 0.00 0.00 2.29
425 468 8.640651 AGCATGCAAATTACATTACATAATGGA 58.359 29.630 21.98 4.69 45.54 3.41
426 469 8.918658 GCATGCAAATTACATTACATAATGGAG 58.081 33.333 14.21 0.00 45.54 3.86
427 470 8.918658 CATGCAAATTACATTACATAATGGAGC 58.081 33.333 14.53 7.46 45.54 4.70
428 471 8.236585 TGCAAATTACATTACATAATGGAGCT 57.763 30.769 14.53 0.00 45.54 4.09
429 472 9.348476 TGCAAATTACATTACATAATGGAGCTA 57.652 29.630 14.53 0.00 45.54 3.32
490 750 2.489722 GGCCAAGTTTCTGAATCTGGTC 59.510 50.000 0.00 7.79 0.00 4.02
589 849 3.710209 AGATGTGAAGTCCAAGGAAGG 57.290 47.619 0.00 0.00 0.00 3.46
610 870 6.899393 AGGAAAACAAATGCTGAATGTCTA 57.101 33.333 0.00 0.00 0.00 2.59
615 875 6.882610 AACAAATGCTGAATGTCTAAGACA 57.117 33.333 0.00 0.00 46.90 3.41
652 912 6.561614 TCTACTACTAGCAACTTGGATTTCG 58.438 40.000 0.00 0.00 0.00 3.46
659 919 2.287368 GCAACTTGGATTTCGTCGGTTT 60.287 45.455 0.00 0.00 0.00 3.27
752 1099 7.016072 ACAATACAATGAAAAAGGGAACATCCA 59.984 33.333 0.00 0.00 38.64 3.41
867 1214 2.094803 TCACACAAACACAAAGTGCCTG 60.095 45.455 0.00 0.00 36.98 4.85
901 1248 3.192422 AGATTAGGCTCGATCAATCCTCG 59.808 47.826 11.83 0.00 37.47 4.63
1278 1660 2.360475 GCAGGCGGCTTCTTCCTT 60.360 61.111 9.66 0.00 40.25 3.36
1287 1669 1.908483 CTTCTTCCTTCCTCCGGGG 59.092 63.158 0.00 0.00 0.00 5.73
1395 1786 4.498520 CTCACCGGCGACTGCGAT 62.499 66.667 9.30 0.00 44.10 4.58
1994 2405 7.618502 TTGTGTTGACATAATACATGTACCC 57.381 36.000 7.96 0.00 31.52 3.69
1995 2406 5.813157 TGTGTTGACATAATACATGTACCCG 59.187 40.000 7.96 0.00 31.52 5.28
1996 2407 5.235616 GTGTTGACATAATACATGTACCCGG 59.764 44.000 7.96 0.00 31.52 5.73
1997 2408 3.997762 TGACATAATACATGTACCCGGC 58.002 45.455 7.96 0.00 31.52 6.13
1998 2409 2.991190 GACATAATACATGTACCCGGCG 59.009 50.000 7.96 0.00 31.52 6.46
1999 2410 2.629137 ACATAATACATGTACCCGGCGA 59.371 45.455 9.30 0.00 0.00 5.54
2000 2411 3.259876 ACATAATACATGTACCCGGCGAT 59.740 43.478 9.30 0.00 0.00 4.58
2001 2412 4.463539 ACATAATACATGTACCCGGCGATA 59.536 41.667 9.30 0.00 0.00 2.92
2002 2413 3.308438 AATACATGTACCCGGCGATAC 57.692 47.619 9.30 11.43 0.00 2.24
2003 2414 0.592637 TACATGTACCCGGCGATACG 59.407 55.000 9.30 1.80 0.00 3.06
2015 2426 3.659850 CGATACGCATTCAGTGGGA 57.340 52.632 0.00 0.00 43.02 4.37
2016 2427 1.491670 CGATACGCATTCAGTGGGAG 58.508 55.000 0.00 0.00 43.02 4.30
2017 2428 1.869754 CGATACGCATTCAGTGGGAGG 60.870 57.143 0.00 0.00 43.02 4.30
2018 2429 1.412710 GATACGCATTCAGTGGGAGGA 59.587 52.381 0.00 0.00 43.02 3.71
2019 2430 0.824109 TACGCATTCAGTGGGAGGAG 59.176 55.000 0.00 0.00 43.02 3.69
2020 2431 0.904865 ACGCATTCAGTGGGAGGAGA 60.905 55.000 0.00 0.00 43.02 3.71
2021 2432 0.460987 CGCATTCAGTGGGAGGAGAC 60.461 60.000 0.00 0.00 43.02 3.36
2022 2433 0.460987 GCATTCAGTGGGAGGAGACG 60.461 60.000 0.00 0.00 0.00 4.18
2023 2434 0.898320 CATTCAGTGGGAGGAGACGT 59.102 55.000 0.00 0.00 0.00 4.34
2024 2435 1.276421 CATTCAGTGGGAGGAGACGTT 59.724 52.381 0.00 0.00 0.00 3.99
2025 2436 0.966920 TTCAGTGGGAGGAGACGTTC 59.033 55.000 0.00 0.00 0.00 3.95
2037 2448 4.806571 ACGTTCCCGTCGATGATG 57.193 55.556 6.11 0.00 46.28 3.07
2038 2449 2.186155 ACGTTCCCGTCGATGATGA 58.814 52.632 6.11 0.00 46.28 2.92
2039 2450 0.100682 ACGTTCCCGTCGATGATGAG 59.899 55.000 6.11 0.00 46.28 2.90
2040 2451 0.595053 CGTTCCCGTCGATGATGAGG 60.595 60.000 6.11 0.00 0.00 3.86
2041 2452 0.460311 GTTCCCGTCGATGATGAGGT 59.540 55.000 6.11 0.00 0.00 3.85
2042 2453 0.459899 TTCCCGTCGATGATGAGGTG 59.540 55.000 6.11 0.00 0.00 4.00
2043 2454 1.592669 CCCGTCGATGATGAGGTGC 60.593 63.158 6.11 0.00 0.00 5.01
2044 2455 1.439228 CCGTCGATGATGAGGTGCT 59.561 57.895 6.11 0.00 0.00 4.40
2045 2456 0.179100 CCGTCGATGATGAGGTGCTT 60.179 55.000 6.11 0.00 0.00 3.91
2046 2457 1.067060 CCGTCGATGATGAGGTGCTTA 59.933 52.381 6.11 0.00 0.00 3.09
2047 2458 2.120232 CGTCGATGATGAGGTGCTTAC 58.880 52.381 0.00 0.00 0.00 2.34
2048 2459 2.479560 CGTCGATGATGAGGTGCTTACA 60.480 50.000 0.00 0.00 0.00 2.41
2049 2460 3.119291 GTCGATGATGAGGTGCTTACAG 58.881 50.000 0.00 0.00 0.00 2.74
2050 2461 2.760650 TCGATGATGAGGTGCTTACAGT 59.239 45.455 0.00 0.00 0.00 3.55
2051 2462 2.862536 CGATGATGAGGTGCTTACAGTG 59.137 50.000 0.00 0.00 0.00 3.66
2052 2463 3.429410 CGATGATGAGGTGCTTACAGTGA 60.429 47.826 0.00 0.00 0.00 3.41
2053 2464 3.319137 TGATGAGGTGCTTACAGTGAC 57.681 47.619 0.00 0.00 0.00 3.67
2054 2465 2.899900 TGATGAGGTGCTTACAGTGACT 59.100 45.455 0.00 0.00 0.00 3.41
2055 2466 3.056536 TGATGAGGTGCTTACAGTGACTC 60.057 47.826 0.00 0.00 0.00 3.36
2056 2467 1.618837 TGAGGTGCTTACAGTGACTCC 59.381 52.381 0.00 0.00 0.00 3.85
2057 2468 1.618837 GAGGTGCTTACAGTGACTCCA 59.381 52.381 0.00 0.00 0.00 3.86
2058 2469 2.234908 GAGGTGCTTACAGTGACTCCAT 59.765 50.000 0.00 0.00 0.00 3.41
2059 2470 3.441101 AGGTGCTTACAGTGACTCCATA 58.559 45.455 0.00 0.00 0.00 2.74
2060 2471 3.838317 AGGTGCTTACAGTGACTCCATAA 59.162 43.478 0.00 0.00 0.00 1.90
2061 2472 4.286032 AGGTGCTTACAGTGACTCCATAAA 59.714 41.667 0.00 0.00 0.00 1.40
2062 2473 5.045578 AGGTGCTTACAGTGACTCCATAAAT 60.046 40.000 0.00 0.00 0.00 1.40
2063 2474 5.648092 GGTGCTTACAGTGACTCCATAAATT 59.352 40.000 0.00 0.00 0.00 1.82
2064 2475 6.151144 GGTGCTTACAGTGACTCCATAAATTT 59.849 38.462 0.00 0.00 0.00 1.82
2065 2476 7.309194 GGTGCTTACAGTGACTCCATAAATTTT 60.309 37.037 0.00 0.00 0.00 1.82
2066 2477 8.726988 GTGCTTACAGTGACTCCATAAATTTTA 58.273 33.333 0.00 0.00 0.00 1.52
2067 2478 9.290988 TGCTTACAGTGACTCCATAAATTTTAA 57.709 29.630 0.00 0.00 0.00 1.52
2068 2479 9.774742 GCTTACAGTGACTCCATAAATTTTAAG 57.225 33.333 0.00 0.00 0.00 1.85
2072 2483 9.739276 ACAGTGACTCCATAAATTTTAAGATGA 57.261 29.630 0.00 0.00 0.00 2.92
2079 2490 9.778993 CTCCATAAATTTTAAGATGATATGCCG 57.221 33.333 0.00 0.00 0.00 5.69
2080 2491 8.739039 TCCATAAATTTTAAGATGATATGCCGG 58.261 33.333 0.00 0.00 0.00 6.13
2081 2492 7.489113 CCATAAATTTTAAGATGATATGCCGGC 59.511 37.037 22.73 22.73 0.00 6.13
2082 2493 6.655078 AAATTTTAAGATGATATGCCGGCT 57.345 33.333 29.70 15.76 0.00 5.52
2083 2494 5.886960 ATTTTAAGATGATATGCCGGCTC 57.113 39.130 29.70 17.89 0.00 4.70
2084 2495 4.350368 TTTAAGATGATATGCCGGCTCA 57.650 40.909 29.70 23.34 0.00 4.26
2085 2496 2.469274 AAGATGATATGCCGGCTCAG 57.531 50.000 29.70 0.00 0.00 3.35
2086 2497 1.346062 AGATGATATGCCGGCTCAGT 58.654 50.000 29.70 13.44 0.00 3.41
2087 2498 1.274728 AGATGATATGCCGGCTCAGTC 59.725 52.381 29.70 19.55 0.00 3.51
2088 2499 1.274728 GATGATATGCCGGCTCAGTCT 59.725 52.381 29.70 8.26 0.00 3.24
2089 2500 1.123077 TGATATGCCGGCTCAGTCTT 58.877 50.000 29.70 5.10 0.00 3.01
2090 2501 1.486310 TGATATGCCGGCTCAGTCTTT 59.514 47.619 29.70 3.35 0.00 2.52
2091 2502 2.139118 GATATGCCGGCTCAGTCTTTC 58.861 52.381 29.70 9.22 0.00 2.62
2092 2503 0.179111 TATGCCGGCTCAGTCTTTCG 60.179 55.000 29.70 0.00 0.00 3.46
2093 2504 2.815647 GCCGGCTCAGTCTTTCGG 60.816 66.667 22.15 0.00 43.13 4.30
2094 2505 2.657237 CCGGCTCAGTCTTTCGGT 59.343 61.111 0.00 0.00 36.38 4.69
2095 2506 1.888018 CCGGCTCAGTCTTTCGGTA 59.112 57.895 0.00 0.00 36.38 4.02
2096 2507 0.458025 CCGGCTCAGTCTTTCGGTAC 60.458 60.000 0.00 0.00 36.38 3.34
2097 2508 0.458025 CGGCTCAGTCTTTCGGTACC 60.458 60.000 0.16 0.16 0.00 3.34
2098 2509 0.606604 GGCTCAGTCTTTCGGTACCA 59.393 55.000 13.54 0.00 0.00 3.25
2099 2510 1.207329 GGCTCAGTCTTTCGGTACCAT 59.793 52.381 13.54 0.00 0.00 3.55
2100 2511 2.271800 GCTCAGTCTTTCGGTACCATG 58.728 52.381 13.54 0.00 0.00 3.66
2101 2512 2.271800 CTCAGTCTTTCGGTACCATGC 58.728 52.381 13.54 0.00 0.00 4.06
2102 2513 1.621317 TCAGTCTTTCGGTACCATGCA 59.379 47.619 13.54 0.00 0.00 3.96
2103 2514 2.037902 TCAGTCTTTCGGTACCATGCAA 59.962 45.455 13.54 0.00 0.00 4.08
2104 2515 2.811431 CAGTCTTTCGGTACCATGCAAA 59.189 45.455 13.54 4.13 0.00 3.68
2105 2516 3.252215 CAGTCTTTCGGTACCATGCAAAA 59.748 43.478 13.54 3.34 0.00 2.44
2106 2517 3.886505 AGTCTTTCGGTACCATGCAAAAA 59.113 39.130 13.54 1.65 0.00 1.94
2107 2518 4.522789 AGTCTTTCGGTACCATGCAAAAAT 59.477 37.500 13.54 0.00 0.00 1.82
2108 2519 5.708230 AGTCTTTCGGTACCATGCAAAAATA 59.292 36.000 13.54 0.00 0.00 1.40
2109 2520 6.377146 AGTCTTTCGGTACCATGCAAAAATAT 59.623 34.615 13.54 0.00 0.00 1.28
2110 2521 7.554835 AGTCTTTCGGTACCATGCAAAAATATA 59.445 33.333 13.54 0.00 0.00 0.86
2111 2522 8.185505 GTCTTTCGGTACCATGCAAAAATATAA 58.814 33.333 13.54 0.00 0.00 0.98
2112 2523 8.740906 TCTTTCGGTACCATGCAAAAATATAAA 58.259 29.630 13.54 0.00 0.00 1.40
2113 2524 9.528018 CTTTCGGTACCATGCAAAAATATAAAT 57.472 29.630 13.54 0.00 0.00 1.40
2161 2572 7.931578 AAAATACATGAACTATTTGACCGGA 57.068 32.000 9.46 0.00 0.00 5.14
2162 2573 7.931578 AAATACATGAACTATTTGACCGGAA 57.068 32.000 9.46 0.00 0.00 4.30
2163 2574 7.931578 AATACATGAACTATTTGACCGGAAA 57.068 32.000 9.46 0.00 0.00 3.13
2164 2575 7.931578 ATACATGAACTATTTGACCGGAAAA 57.068 32.000 9.46 9.19 0.00 2.29
2165 2576 6.642707 ACATGAACTATTTGACCGGAAAAA 57.357 33.333 9.46 8.77 0.00 1.94
2190 2601 7.961326 AAAATTCATGTACCATTTAGAGGCT 57.039 32.000 0.00 0.00 0.00 4.58
2191 2602 9.474313 AAAAATTCATGTACCATTTAGAGGCTA 57.526 29.630 0.00 0.00 0.00 3.93
2192 2603 9.474313 AAAATTCATGTACCATTTAGAGGCTAA 57.526 29.630 0.00 0.00 0.00 3.09
2193 2604 9.474313 AAATTCATGTACCATTTAGAGGCTAAA 57.526 29.630 2.49 2.49 0.00 1.85
2194 2605 8.682936 ATTCATGTACCATTTAGAGGCTAAAG 57.317 34.615 5.92 0.00 0.00 1.85
2195 2606 7.195374 TCATGTACCATTTAGAGGCTAAAGT 57.805 36.000 5.92 2.67 0.00 2.66
2196 2607 7.047891 TCATGTACCATTTAGAGGCTAAAGTG 58.952 38.462 5.92 0.00 0.00 3.16
2197 2608 5.183228 TGTACCATTTAGAGGCTAAAGTGC 58.817 41.667 5.92 4.08 0.00 4.40
2198 2609 3.270877 ACCATTTAGAGGCTAAAGTGCG 58.729 45.455 5.92 0.00 0.00 5.34
2199 2610 2.032178 CCATTTAGAGGCTAAAGTGCGC 59.968 50.000 0.00 0.00 0.00 6.09
2200 2611 1.355971 TTTAGAGGCTAAAGTGCGCG 58.644 50.000 0.00 0.00 0.00 6.86
2201 2612 0.459585 TTAGAGGCTAAAGTGCGCGG 60.460 55.000 8.83 0.00 0.00 6.46
2202 2613 2.901051 TAGAGGCTAAAGTGCGCGGC 62.901 60.000 8.83 0.00 0.00 6.53
2205 2616 3.784412 GCTAAAGTGCGCGGCGAA 61.784 61.111 28.54 14.49 0.00 4.70
2206 2617 2.395690 CTAAAGTGCGCGGCGAAG 59.604 61.111 28.54 4.43 0.00 3.79
2224 2635 5.914085 CGAAGCTATTCTCTATTTGTGGG 57.086 43.478 0.00 0.00 32.93 4.61
2225 2636 5.601662 CGAAGCTATTCTCTATTTGTGGGA 58.398 41.667 0.00 0.00 32.93 4.37
2226 2637 6.226787 CGAAGCTATTCTCTATTTGTGGGAT 58.773 40.000 0.00 0.00 32.93 3.85
2227 2638 6.708054 CGAAGCTATTCTCTATTTGTGGGATT 59.292 38.462 0.00 0.00 32.93 3.01
2228 2639 7.872993 CGAAGCTATTCTCTATTTGTGGGATTA 59.127 37.037 0.00 0.00 32.93 1.75
2229 2640 9.561069 GAAGCTATTCTCTATTTGTGGGATTAA 57.439 33.333 0.00 0.00 32.33 1.40
2230 2641 9.566432 AAGCTATTCTCTATTTGTGGGATTAAG 57.434 33.333 0.00 0.00 0.00 1.85
2231 2642 8.160106 AGCTATTCTCTATTTGTGGGATTAAGG 58.840 37.037 0.00 0.00 0.00 2.69
2232 2643 7.391833 GCTATTCTCTATTTGTGGGATTAAGGG 59.608 40.741 0.00 0.00 0.00 3.95
2233 2644 6.652205 TTCTCTATTTGTGGGATTAAGGGT 57.348 37.500 0.00 0.00 0.00 4.34
2234 2645 6.248569 TCTCTATTTGTGGGATTAAGGGTC 57.751 41.667 0.00 0.00 0.00 4.46
2235 2646 5.970640 TCTCTATTTGTGGGATTAAGGGTCT 59.029 40.000 0.00 0.00 0.00 3.85
2236 2647 6.001449 TCTATTTGTGGGATTAAGGGTCTG 57.999 41.667 0.00 0.00 0.00 3.51
2237 2648 4.675063 ATTTGTGGGATTAAGGGTCTGT 57.325 40.909 0.00 0.00 0.00 3.41
2238 2649 4.463050 TTTGTGGGATTAAGGGTCTGTT 57.537 40.909 0.00 0.00 0.00 3.16
2239 2650 4.463050 TTGTGGGATTAAGGGTCTGTTT 57.537 40.909 0.00 0.00 0.00 2.83
2240 2651 5.586155 TTGTGGGATTAAGGGTCTGTTTA 57.414 39.130 0.00 0.00 0.00 2.01
2241 2652 5.174037 TGTGGGATTAAGGGTCTGTTTAG 57.826 43.478 0.00 0.00 0.00 1.85
2242 2653 4.600111 TGTGGGATTAAGGGTCTGTTTAGT 59.400 41.667 0.00 0.00 0.00 2.24
2243 2654 5.073965 TGTGGGATTAAGGGTCTGTTTAGTT 59.926 40.000 0.00 0.00 0.00 2.24
2244 2655 5.414765 GTGGGATTAAGGGTCTGTTTAGTTG 59.585 44.000 0.00 0.00 0.00 3.16
2245 2656 5.311121 TGGGATTAAGGGTCTGTTTAGTTGA 59.689 40.000 0.00 0.00 0.00 3.18
2246 2657 6.011981 TGGGATTAAGGGTCTGTTTAGTTGAT 60.012 38.462 0.00 0.00 0.00 2.57
2247 2658 6.318900 GGGATTAAGGGTCTGTTTAGTTGATG 59.681 42.308 0.00 0.00 0.00 3.07
2248 2659 6.884836 GGATTAAGGGTCTGTTTAGTTGATGT 59.115 38.462 0.00 0.00 0.00 3.06
2249 2660 7.065923 GGATTAAGGGTCTGTTTAGTTGATGTC 59.934 40.741 0.00 0.00 0.00 3.06
2250 2661 4.287766 AGGGTCTGTTTAGTTGATGTCC 57.712 45.455 0.00 0.00 0.00 4.02
2251 2662 3.910627 AGGGTCTGTTTAGTTGATGTCCT 59.089 43.478 0.00 0.00 0.00 3.85
2252 2663 4.020128 AGGGTCTGTTTAGTTGATGTCCTC 60.020 45.833 0.00 0.00 0.00 3.71
2253 2664 4.262894 GGGTCTGTTTAGTTGATGTCCTCA 60.263 45.833 0.00 0.00 0.00 3.86
2254 2665 5.491982 GGTCTGTTTAGTTGATGTCCTCAT 58.508 41.667 0.00 0.00 36.95 2.90
2272 2683 2.876091 CATCACAAGATGCTTGGCTTG 58.124 47.619 11.40 0.00 44.61 4.01
2273 2684 2.275134 TCACAAGATGCTTGGCTTGA 57.725 45.000 11.40 4.04 43.11 3.02
2274 2685 2.585330 TCACAAGATGCTTGGCTTGAA 58.415 42.857 11.40 0.00 43.11 2.69
2275 2686 2.555325 TCACAAGATGCTTGGCTTGAAG 59.445 45.455 11.40 0.00 43.11 3.02
2285 2696 3.966215 GCTTGAAGCCTGCGTGTA 58.034 55.556 5.74 0.00 34.48 2.90
2286 2697 1.497722 GCTTGAAGCCTGCGTGTAC 59.502 57.895 5.74 0.00 34.48 2.90
2287 2698 1.912371 GCTTGAAGCCTGCGTGTACC 61.912 60.000 5.74 0.00 34.48 3.34
2288 2699 1.298859 CTTGAAGCCTGCGTGTACCC 61.299 60.000 0.00 0.00 0.00 3.69
2289 2700 2.436115 GAAGCCTGCGTGTACCCC 60.436 66.667 0.00 0.00 0.00 4.95
2290 2701 3.246112 AAGCCTGCGTGTACCCCA 61.246 61.111 0.00 0.00 0.00 4.96
2291 2702 2.536997 GAAGCCTGCGTGTACCCCAT 62.537 60.000 0.00 0.00 0.00 4.00
2292 2703 2.513897 GCCTGCGTGTACCCCATC 60.514 66.667 0.00 0.00 0.00 3.51
2293 2704 2.189521 CCTGCGTGTACCCCATCC 59.810 66.667 0.00 0.00 0.00 3.51
2294 2705 2.665089 CCTGCGTGTACCCCATCCA 61.665 63.158 0.00 0.00 0.00 3.41
2295 2706 1.153369 CTGCGTGTACCCCATCCAG 60.153 63.158 0.00 0.00 0.00 3.86
2296 2707 1.610967 TGCGTGTACCCCATCCAGA 60.611 57.895 0.00 0.00 0.00 3.86
2297 2708 1.153429 GCGTGTACCCCATCCAGAC 60.153 63.158 0.00 0.00 0.00 3.51
2298 2709 1.141019 CGTGTACCCCATCCAGACG 59.859 63.158 0.00 0.00 0.00 4.18
2299 2710 1.153429 GTGTACCCCATCCAGACGC 60.153 63.158 0.00 0.00 0.00 5.19
2300 2711 2.106332 GTACCCCATCCAGACGCG 59.894 66.667 3.53 3.53 0.00 6.01
2301 2712 2.363276 TACCCCATCCAGACGCGT 60.363 61.111 13.85 13.85 0.00 6.01
2302 2713 2.717044 TACCCCATCCAGACGCGTG 61.717 63.158 20.70 2.10 0.00 5.34
2303 2714 4.838152 CCCCATCCAGACGCGTGG 62.838 72.222 20.70 14.02 39.19 4.94
2308 2719 2.596338 TCCAGACGCGTGGAGTCA 60.596 61.111 20.70 0.00 41.99 3.41
2309 2720 2.126307 CCAGACGCGTGGAGTCAG 60.126 66.667 20.70 0.00 40.44 3.51
2310 2721 2.126307 CAGACGCGTGGAGTCAGG 60.126 66.667 20.70 0.00 40.84 3.86
2335 2746 2.851071 GCATCTCTAGCCGCGTCCT 61.851 63.158 4.92 3.24 0.00 3.85
2406 2818 3.450115 GTCGCGTCCCCAGTAGCT 61.450 66.667 5.77 0.00 0.00 3.32
2500 2932 2.203294 AAGCGAAAAGGGGCGTGT 60.203 55.556 0.00 0.00 0.00 4.49
2759 3228 1.218316 GGAAGTTCAGCGACGGGAT 59.782 57.895 5.01 0.00 0.00 3.85
2761 3230 0.389948 GAAGTTCAGCGACGGGATGT 60.390 55.000 0.00 0.00 32.65 3.06
2865 3340 3.441290 CCGAGTCCGAGGCGACTT 61.441 66.667 0.00 0.00 43.22 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 0.332632 CTCCAAATCCAGCTTCCCCA 59.667 55.000 0.00 0.00 0.00 4.96
285 297 8.684973 ACTAACACAGTAATTAAGCTAACTCG 57.315 34.615 0.00 0.00 34.98 4.18
328 348 4.325501 CCATAAACTAAGTTTGGGCCCCTA 60.326 45.833 22.27 3.97 36.37 3.53
420 463 2.907458 ACTTGGCCTTTAGCTCCATT 57.093 45.000 3.32 0.00 43.05 3.16
425 468 3.295973 TGTTCAAACTTGGCCTTTAGCT 58.704 40.909 3.32 0.00 43.05 3.32
426 469 3.726291 TGTTCAAACTTGGCCTTTAGC 57.274 42.857 3.32 0.00 42.60 3.09
427 470 5.415221 TGTTTGTTCAAACTTGGCCTTTAG 58.585 37.500 22.90 0.94 33.95 1.85
428 471 5.407407 TGTTTGTTCAAACTTGGCCTTTA 57.593 34.783 22.90 3.54 33.95 1.85
429 472 4.278975 TGTTTGTTCAAACTTGGCCTTT 57.721 36.364 22.90 0.00 33.95 3.11
430 473 3.971245 TGTTTGTTCAAACTTGGCCTT 57.029 38.095 22.90 0.00 33.95 4.35
490 750 2.854777 CAGACCGTTCATAGAAAGCTCG 59.145 50.000 0.00 0.00 0.00 5.03
564 824 6.094603 CCTTCCTTGGACTTCACATCTATTTG 59.905 42.308 0.00 0.00 0.00 2.32
589 849 7.862372 TGTCTTAGACATTCAGCATTTGTTTTC 59.138 33.333 11.42 0.00 37.67 2.29
652 912 0.163146 GTGCGTTGCTCTAAACCGAC 59.837 55.000 0.00 0.00 0.00 4.79
659 919 3.371898 CAGATTTCATGTGCGTTGCTCTA 59.628 43.478 0.00 0.00 0.00 2.43
727 1045 7.331687 GTGGATGTTCCCTTTTTCATTGTATTG 59.668 37.037 0.00 0.00 35.03 1.90
752 1099 7.323420 GCCAAGAAAGCTTAGGATTTTTATGT 58.677 34.615 0.00 0.00 30.71 2.29
901 1248 2.169842 GCAACTGCAGAGAAGAGGC 58.830 57.895 23.35 8.78 41.59 4.70
948 1304 5.743117 AGGAGACCTGAAATGAAGATGAAG 58.257 41.667 0.00 0.00 29.57 3.02
1954 2363 6.575942 GTCAACACAAAATATTACACACCGTC 59.424 38.462 0.00 0.00 0.00 4.79
1955 2364 6.038382 TGTCAACACAAAATATTACACACCGT 59.962 34.615 0.00 0.00 0.00 4.83
1997 2408 1.491670 CTCCCACTGAATGCGTATCG 58.508 55.000 0.00 0.00 0.00 2.92
1998 2409 1.412710 TCCTCCCACTGAATGCGTATC 59.587 52.381 0.00 0.00 0.00 2.24
1999 2410 1.414181 CTCCTCCCACTGAATGCGTAT 59.586 52.381 0.00 0.00 0.00 3.06
2000 2411 0.824109 CTCCTCCCACTGAATGCGTA 59.176 55.000 0.00 0.00 0.00 4.42
2001 2412 0.904865 TCTCCTCCCACTGAATGCGT 60.905 55.000 0.00 0.00 0.00 5.24
2002 2413 0.460987 GTCTCCTCCCACTGAATGCG 60.461 60.000 0.00 0.00 0.00 4.73
2003 2414 0.460987 CGTCTCCTCCCACTGAATGC 60.461 60.000 0.00 0.00 0.00 3.56
2004 2415 0.898320 ACGTCTCCTCCCACTGAATG 59.102 55.000 0.00 0.00 0.00 2.67
2005 2416 1.550976 GAACGTCTCCTCCCACTGAAT 59.449 52.381 0.00 0.00 0.00 2.57
2006 2417 0.966920 GAACGTCTCCTCCCACTGAA 59.033 55.000 0.00 0.00 0.00 3.02
2007 2418 0.898789 GGAACGTCTCCTCCCACTGA 60.899 60.000 8.87 0.00 41.61 3.41
2008 2419 1.592223 GGAACGTCTCCTCCCACTG 59.408 63.158 8.87 0.00 41.61 3.66
2009 2420 4.115270 GGAACGTCTCCTCCCACT 57.885 61.111 8.87 0.00 41.61 4.00
2022 2433 0.460311 ACCTCATCATCGACGGGAAC 59.540 55.000 0.00 0.00 0.00 3.62
2023 2434 0.459899 CACCTCATCATCGACGGGAA 59.540 55.000 0.00 0.00 0.00 3.97
2024 2435 2.016393 GCACCTCATCATCGACGGGA 62.016 60.000 0.00 0.00 0.00 5.14
2025 2436 1.592669 GCACCTCATCATCGACGGG 60.593 63.158 0.00 0.00 0.00 5.28
2026 2437 0.179100 AAGCACCTCATCATCGACGG 60.179 55.000 0.00 0.00 0.00 4.79
2027 2438 2.120232 GTAAGCACCTCATCATCGACG 58.880 52.381 0.00 0.00 0.00 5.12
2028 2439 3.119291 CTGTAAGCACCTCATCATCGAC 58.881 50.000 0.00 0.00 0.00 4.20
2029 2440 2.760650 ACTGTAAGCACCTCATCATCGA 59.239 45.455 0.00 0.00 37.60 3.59
2030 2441 2.862536 CACTGTAAGCACCTCATCATCG 59.137 50.000 0.00 0.00 37.60 3.84
2031 2442 3.868077 GTCACTGTAAGCACCTCATCATC 59.132 47.826 0.00 0.00 37.60 2.92
2032 2443 3.517100 AGTCACTGTAAGCACCTCATCAT 59.483 43.478 0.00 0.00 37.60 2.45
2033 2444 2.899900 AGTCACTGTAAGCACCTCATCA 59.100 45.455 0.00 0.00 37.60 3.07
2034 2445 3.516615 GAGTCACTGTAAGCACCTCATC 58.483 50.000 0.00 0.00 37.60 2.92
2035 2446 2.234908 GGAGTCACTGTAAGCACCTCAT 59.765 50.000 0.00 0.00 37.60 2.90
2036 2447 1.618837 GGAGTCACTGTAAGCACCTCA 59.381 52.381 0.00 0.00 37.60 3.86
2037 2448 1.618837 TGGAGTCACTGTAAGCACCTC 59.381 52.381 0.00 0.00 37.60 3.85
2038 2449 1.717032 TGGAGTCACTGTAAGCACCT 58.283 50.000 0.00 0.00 37.60 4.00
2039 2450 2.770164 ATGGAGTCACTGTAAGCACC 57.230 50.000 0.00 0.00 37.60 5.01
2040 2451 6.743575 AATTTATGGAGTCACTGTAAGCAC 57.256 37.500 0.00 0.00 37.60 4.40
2041 2452 7.759489 AAAATTTATGGAGTCACTGTAAGCA 57.241 32.000 0.00 0.00 37.60 3.91
2042 2453 9.774742 CTTAAAATTTATGGAGTCACTGTAAGC 57.225 33.333 0.00 0.00 37.60 3.09
2046 2457 9.739276 TCATCTTAAAATTTATGGAGTCACTGT 57.261 29.630 0.00 0.00 0.00 3.55
2053 2464 9.778993 CGGCATATCATCTTAAAATTTATGGAG 57.221 33.333 0.00 0.00 0.00 3.86
2054 2465 8.739039 CCGGCATATCATCTTAAAATTTATGGA 58.261 33.333 0.00 0.00 0.00 3.41
2055 2466 7.489113 GCCGGCATATCATCTTAAAATTTATGG 59.511 37.037 24.80 0.00 0.00 2.74
2056 2467 8.246180 AGCCGGCATATCATCTTAAAATTTATG 58.754 33.333 31.54 0.00 0.00 1.90
2057 2468 8.353423 AGCCGGCATATCATCTTAAAATTTAT 57.647 30.769 31.54 0.00 0.00 1.40
2058 2469 7.446931 TGAGCCGGCATATCATCTTAAAATTTA 59.553 33.333 31.54 0.00 0.00 1.40
2059 2470 6.265196 TGAGCCGGCATATCATCTTAAAATTT 59.735 34.615 31.54 0.00 0.00 1.82
2060 2471 5.769662 TGAGCCGGCATATCATCTTAAAATT 59.230 36.000 31.54 0.00 0.00 1.82
2061 2472 5.316167 TGAGCCGGCATATCATCTTAAAAT 58.684 37.500 31.54 0.06 0.00 1.82
2062 2473 4.713553 TGAGCCGGCATATCATCTTAAAA 58.286 39.130 31.54 0.00 0.00 1.52
2063 2474 4.202357 ACTGAGCCGGCATATCATCTTAAA 60.202 41.667 31.54 0.00 0.00 1.52
2064 2475 3.324846 ACTGAGCCGGCATATCATCTTAA 59.675 43.478 31.54 0.00 0.00 1.85
2065 2476 2.899900 ACTGAGCCGGCATATCATCTTA 59.100 45.455 31.54 0.00 0.00 2.10
2066 2477 1.696336 ACTGAGCCGGCATATCATCTT 59.304 47.619 31.54 3.33 0.00 2.40
2067 2478 1.274728 GACTGAGCCGGCATATCATCT 59.725 52.381 31.54 11.40 0.00 2.90
2068 2479 1.274728 AGACTGAGCCGGCATATCATC 59.725 52.381 31.54 19.98 0.00 2.92
2069 2480 1.346062 AGACTGAGCCGGCATATCAT 58.654 50.000 31.54 13.17 0.00 2.45
2070 2481 1.123077 AAGACTGAGCCGGCATATCA 58.877 50.000 31.54 22.44 0.00 2.15
2071 2482 2.139118 GAAAGACTGAGCCGGCATATC 58.861 52.381 31.54 18.63 0.00 1.63
2072 2483 1.539065 CGAAAGACTGAGCCGGCATAT 60.539 52.381 31.54 8.11 0.00 1.78
2073 2484 0.179111 CGAAAGACTGAGCCGGCATA 60.179 55.000 31.54 16.21 0.00 3.14
2074 2485 1.448540 CGAAAGACTGAGCCGGCAT 60.449 57.895 31.54 14.28 0.00 4.40
2075 2486 2.048222 CGAAAGACTGAGCCGGCA 60.048 61.111 31.54 7.98 0.00 5.69
2076 2487 2.221906 TACCGAAAGACTGAGCCGGC 62.222 60.000 21.89 21.89 43.56 6.13
2077 2488 0.458025 GTACCGAAAGACTGAGCCGG 60.458 60.000 0.00 0.00 45.09 6.13
2078 2489 0.458025 GGTACCGAAAGACTGAGCCG 60.458 60.000 0.00 0.00 0.00 5.52
2079 2490 0.606604 TGGTACCGAAAGACTGAGCC 59.393 55.000 7.57 0.00 0.00 4.70
2080 2491 2.271800 CATGGTACCGAAAGACTGAGC 58.728 52.381 7.57 0.00 0.00 4.26
2081 2492 2.271800 GCATGGTACCGAAAGACTGAG 58.728 52.381 7.57 0.00 0.00 3.35
2082 2493 1.621317 TGCATGGTACCGAAAGACTGA 59.379 47.619 7.57 0.00 0.00 3.41
2083 2494 2.093306 TGCATGGTACCGAAAGACTG 57.907 50.000 7.57 0.00 0.00 3.51
2084 2495 2.851263 TTGCATGGTACCGAAAGACT 57.149 45.000 7.57 0.00 0.00 3.24
2085 2496 3.907894 TTTTGCATGGTACCGAAAGAC 57.092 42.857 7.57 0.00 0.00 3.01
2086 2497 6.767524 ATATTTTTGCATGGTACCGAAAGA 57.232 33.333 7.57 0.00 0.00 2.52
2087 2498 8.918961 TTTATATTTTTGCATGGTACCGAAAG 57.081 30.769 7.57 0.00 0.00 2.62
2136 2547 8.343168 TCCGGTCAAATAGTTCATGTATTTTT 57.657 30.769 0.00 0.00 29.39 1.94
2137 2548 7.931578 TCCGGTCAAATAGTTCATGTATTTT 57.068 32.000 0.00 0.00 29.39 1.82
2138 2549 7.931578 TTCCGGTCAAATAGTTCATGTATTT 57.068 32.000 0.00 0.00 31.54 1.40
2139 2550 7.931578 TTTCCGGTCAAATAGTTCATGTATT 57.068 32.000 0.00 0.00 0.00 1.89
2140 2551 7.931578 TTTTCCGGTCAAATAGTTCATGTAT 57.068 32.000 0.00 0.00 0.00 2.29
2141 2552 7.747155 TTTTTCCGGTCAAATAGTTCATGTA 57.253 32.000 0.00 0.00 0.00 2.29
2142 2553 6.642707 TTTTTCCGGTCAAATAGTTCATGT 57.357 33.333 0.00 0.00 0.00 3.21
2175 2586 4.270325 CGCACTTTAGCCTCTAAATGGTAC 59.730 45.833 0.17 0.00 0.00 3.34
2176 2587 4.439057 CGCACTTTAGCCTCTAAATGGTA 58.561 43.478 0.17 0.00 0.00 3.25
2177 2588 3.270877 CGCACTTTAGCCTCTAAATGGT 58.729 45.455 0.17 0.00 0.00 3.55
2178 2589 2.032178 GCGCACTTTAGCCTCTAAATGG 59.968 50.000 0.30 0.00 0.00 3.16
2179 2590 2.285834 CGCGCACTTTAGCCTCTAAATG 60.286 50.000 8.75 3.30 0.00 2.32
2180 2591 1.933853 CGCGCACTTTAGCCTCTAAAT 59.066 47.619 8.75 0.00 0.00 1.40
2181 2592 1.355971 CGCGCACTTTAGCCTCTAAA 58.644 50.000 8.75 0.00 0.00 1.85
2182 2593 0.459585 CCGCGCACTTTAGCCTCTAA 60.460 55.000 8.75 0.00 0.00 2.10
2183 2594 1.141019 CCGCGCACTTTAGCCTCTA 59.859 57.895 8.75 0.00 0.00 2.43
2184 2595 2.125512 CCGCGCACTTTAGCCTCT 60.126 61.111 8.75 0.00 0.00 3.69
2185 2596 3.865830 GCCGCGCACTTTAGCCTC 61.866 66.667 8.75 0.00 0.00 4.70
2188 2599 3.702334 CTTCGCCGCGCACTTTAGC 62.702 63.158 8.75 0.00 0.00 3.09
2189 2600 2.395690 CTTCGCCGCGCACTTTAG 59.604 61.111 8.75 0.00 0.00 1.85
2190 2601 2.822418 TAGCTTCGCCGCGCACTTTA 62.822 55.000 8.75 0.00 34.40 1.85
2192 2603 4.735132 TAGCTTCGCCGCGCACTT 62.735 61.111 8.75 0.00 34.40 3.16
2193 2604 4.514577 ATAGCTTCGCCGCGCACT 62.515 61.111 8.75 7.54 34.40 4.40
2194 2605 3.492980 GAATAGCTTCGCCGCGCAC 62.493 63.158 8.75 0.00 34.40 5.34
2195 2606 3.261951 GAATAGCTTCGCCGCGCA 61.262 61.111 8.75 0.00 34.40 6.09
2196 2607 2.933203 GAGAATAGCTTCGCCGCGC 61.933 63.158 8.21 0.00 36.45 6.86
2197 2608 0.040336 TAGAGAATAGCTTCGCCGCG 60.040 55.000 6.39 6.39 36.45 6.46
2198 2609 2.355717 ATAGAGAATAGCTTCGCCGC 57.644 50.000 0.00 0.00 36.45 6.53
2199 2610 4.051922 ACAAATAGAGAATAGCTTCGCCG 58.948 43.478 0.00 0.00 36.45 6.46
2200 2611 4.212214 CCACAAATAGAGAATAGCTTCGCC 59.788 45.833 0.00 0.00 36.45 5.54
2201 2612 4.212214 CCCACAAATAGAGAATAGCTTCGC 59.788 45.833 0.00 0.00 36.45 4.70
2202 2613 5.601662 TCCCACAAATAGAGAATAGCTTCG 58.398 41.667 0.00 0.00 36.45 3.79
2203 2614 9.561069 TTAATCCCACAAATAGAGAATAGCTTC 57.439 33.333 0.00 0.00 0.00 3.86
2204 2615 9.566432 CTTAATCCCACAAATAGAGAATAGCTT 57.434 33.333 0.00 0.00 0.00 3.74
2205 2616 8.160106 CCTTAATCCCACAAATAGAGAATAGCT 58.840 37.037 0.00 0.00 0.00 3.32
2206 2617 7.391833 CCCTTAATCCCACAAATAGAGAATAGC 59.608 40.741 0.00 0.00 0.00 2.97
2207 2618 8.440771 ACCCTTAATCCCACAAATAGAGAATAG 58.559 37.037 0.00 0.00 0.00 1.73
2208 2619 8.344939 ACCCTTAATCCCACAAATAGAGAATA 57.655 34.615 0.00 0.00 0.00 1.75
2209 2620 7.129504 AGACCCTTAATCCCACAAATAGAGAAT 59.870 37.037 0.00 0.00 0.00 2.40
2210 2621 6.447084 AGACCCTTAATCCCACAAATAGAGAA 59.553 38.462 0.00 0.00 0.00 2.87
2211 2622 5.970640 AGACCCTTAATCCCACAAATAGAGA 59.029 40.000 0.00 0.00 0.00 3.10
2212 2623 6.058183 CAGACCCTTAATCCCACAAATAGAG 58.942 44.000 0.00 0.00 0.00 2.43
2213 2624 5.491078 ACAGACCCTTAATCCCACAAATAGA 59.509 40.000 0.00 0.00 0.00 1.98
2214 2625 5.755849 ACAGACCCTTAATCCCACAAATAG 58.244 41.667 0.00 0.00 0.00 1.73
2215 2626 5.789574 ACAGACCCTTAATCCCACAAATA 57.210 39.130 0.00 0.00 0.00 1.40
2216 2627 4.675063 ACAGACCCTTAATCCCACAAAT 57.325 40.909 0.00 0.00 0.00 2.32
2217 2628 4.463050 AACAGACCCTTAATCCCACAAA 57.537 40.909 0.00 0.00 0.00 2.83
2218 2629 4.463050 AAACAGACCCTTAATCCCACAA 57.537 40.909 0.00 0.00 0.00 3.33
2219 2630 4.600111 ACTAAACAGACCCTTAATCCCACA 59.400 41.667 0.00 0.00 0.00 4.17
2220 2631 5.175388 ACTAAACAGACCCTTAATCCCAC 57.825 43.478 0.00 0.00 0.00 4.61
2221 2632 5.311121 TCAACTAAACAGACCCTTAATCCCA 59.689 40.000 0.00 0.00 0.00 4.37
2222 2633 5.812286 TCAACTAAACAGACCCTTAATCCC 58.188 41.667 0.00 0.00 0.00 3.85
2223 2634 6.884836 ACATCAACTAAACAGACCCTTAATCC 59.115 38.462 0.00 0.00 0.00 3.01
2224 2635 7.065923 GGACATCAACTAAACAGACCCTTAATC 59.934 40.741 0.00 0.00 0.00 1.75
2225 2636 6.884836 GGACATCAACTAAACAGACCCTTAAT 59.115 38.462 0.00 0.00 0.00 1.40
2226 2637 6.043938 AGGACATCAACTAAACAGACCCTTAA 59.956 38.462 0.00 0.00 0.00 1.85
2227 2638 5.546499 AGGACATCAACTAAACAGACCCTTA 59.454 40.000 0.00 0.00 0.00 2.69
2228 2639 4.351111 AGGACATCAACTAAACAGACCCTT 59.649 41.667 0.00 0.00 0.00 3.95
2229 2640 3.910627 AGGACATCAACTAAACAGACCCT 59.089 43.478 0.00 0.00 0.00 4.34
2230 2641 4.254492 GAGGACATCAACTAAACAGACCC 58.746 47.826 0.00 0.00 0.00 4.46
2231 2642 4.894784 TGAGGACATCAACTAAACAGACC 58.105 43.478 0.00 0.00 34.02 3.85
2253 2664 2.799017 TCAAGCCAAGCATCTTGTGAT 58.201 42.857 5.92 0.00 40.27 3.06
2254 2665 2.275134 TCAAGCCAAGCATCTTGTGA 57.725 45.000 5.92 1.23 40.27 3.58
2255 2666 2.925306 GCTTCAAGCCAAGCATCTTGTG 60.925 50.000 0.00 0.00 46.93 3.33
2256 2667 1.271656 GCTTCAAGCCAAGCATCTTGT 59.728 47.619 0.00 0.00 46.93 3.16
2257 2668 1.992170 GCTTCAAGCCAAGCATCTTG 58.008 50.000 0.00 0.00 46.93 3.02
2268 2679 1.497722 GTACACGCAGGCTTCAAGC 59.502 57.895 0.00 0.00 41.46 4.01
2269 2680 1.298859 GGGTACACGCAGGCTTCAAG 61.299 60.000 0.00 0.00 0.00 3.02
2270 2681 1.302192 GGGTACACGCAGGCTTCAA 60.302 57.895 0.00 0.00 0.00 2.69
2271 2682 2.345991 GGGTACACGCAGGCTTCA 59.654 61.111 0.00 0.00 0.00 3.02
2272 2683 2.436115 GGGGTACACGCAGGCTTC 60.436 66.667 0.00 0.00 0.00 3.86
2273 2684 2.536997 GATGGGGTACACGCAGGCTT 62.537 60.000 0.00 0.00 45.87 4.35
2274 2685 3.009115 ATGGGGTACACGCAGGCT 61.009 61.111 0.00 0.00 45.87 4.58
2275 2686 2.513897 GATGGGGTACACGCAGGC 60.514 66.667 0.00 0.00 45.87 4.85
2276 2687 2.189521 GGATGGGGTACACGCAGG 59.810 66.667 0.00 0.00 45.87 4.85
2277 2688 1.153369 CTGGATGGGGTACACGCAG 60.153 63.158 0.00 0.00 45.87 5.18
2278 2689 1.610967 TCTGGATGGGGTACACGCA 60.611 57.895 0.00 0.00 46.77 5.24
2279 2690 1.153429 GTCTGGATGGGGTACACGC 60.153 63.158 0.00 0.00 0.00 5.34
2280 2691 1.141019 CGTCTGGATGGGGTACACG 59.859 63.158 0.00 0.00 0.00 4.49
2281 2692 1.153429 GCGTCTGGATGGGGTACAC 60.153 63.158 0.00 0.00 0.00 2.90
2282 2693 2.717044 CGCGTCTGGATGGGGTACA 61.717 63.158 0.00 0.00 0.00 2.90
2283 2694 2.106332 CGCGTCTGGATGGGGTAC 59.894 66.667 0.00 0.00 0.00 3.34
2284 2695 2.363276 ACGCGTCTGGATGGGGTA 60.363 61.111 5.58 0.00 34.93 3.69
2285 2696 4.082523 CACGCGTCTGGATGGGGT 62.083 66.667 9.86 1.48 34.93 4.95
2286 2697 4.838152 CCACGCGTCTGGATGGGG 62.838 72.222 9.86 0.00 34.93 4.96
2287 2698 3.723235 CTCCACGCGTCTGGATGGG 62.723 68.421 17.72 10.76 39.72 4.00
2288 2699 2.202797 CTCCACGCGTCTGGATGG 60.203 66.667 17.72 11.54 39.72 3.51
2289 2700 1.517257 GACTCCACGCGTCTGGATG 60.517 63.158 17.72 13.89 39.72 3.51
2290 2701 1.938657 CTGACTCCACGCGTCTGGAT 61.939 60.000 17.72 9.08 39.72 3.41
2291 2702 2.596338 TGACTCCACGCGTCTGGA 60.596 61.111 9.86 14.17 38.05 3.86
2292 2703 2.126307 CTGACTCCACGCGTCTGG 60.126 66.667 9.86 9.58 32.70 3.86
2293 2704 2.126307 CCTGACTCCACGCGTCTG 60.126 66.667 9.86 3.30 32.70 3.51
2294 2705 4.057428 GCCTGACTCCACGCGTCT 62.057 66.667 9.86 0.00 32.70 4.18
2295 2706 2.209064 TTAGCCTGACTCCACGCGTC 62.209 60.000 9.86 0.00 31.07 5.19
2296 2707 2.214181 CTTAGCCTGACTCCACGCGT 62.214 60.000 5.58 5.58 31.07 6.01
2297 2708 1.517257 CTTAGCCTGACTCCACGCG 60.517 63.158 3.53 3.53 31.07 6.01
2298 2709 0.179124 CTCTTAGCCTGACTCCACGC 60.179 60.000 0.00 0.00 0.00 5.34
2299 2710 0.179124 GCTCTTAGCCTGACTCCACG 60.179 60.000 0.00 0.00 34.48 4.94
2300 2711 0.898320 TGCTCTTAGCCTGACTCCAC 59.102 55.000 0.00 0.00 41.51 4.02
2301 2712 1.759445 GATGCTCTTAGCCTGACTCCA 59.241 52.381 0.00 0.00 41.51 3.86
2302 2713 2.035832 GAGATGCTCTTAGCCTGACTCC 59.964 54.545 0.00 0.00 41.51 3.85
2303 2714 2.958355 AGAGATGCTCTTAGCCTGACTC 59.042 50.000 0.00 0.00 41.51 3.36
2304 2715 3.030873 AGAGATGCTCTTAGCCTGACT 57.969 47.619 0.00 0.00 41.51 3.41
2305 2716 3.305335 GCTAGAGATGCTCTTAGCCTGAC 60.305 52.174 1.88 0.00 41.51 3.51
2306 2717 2.890311 GCTAGAGATGCTCTTAGCCTGA 59.110 50.000 1.88 0.00 41.51 3.86
2307 2718 2.029110 GGCTAGAGATGCTCTTAGCCTG 60.029 54.545 23.08 5.81 44.38 4.85
2308 2719 2.247358 GGCTAGAGATGCTCTTAGCCT 58.753 52.381 23.08 7.57 44.38 4.58
2309 2720 1.067915 CGGCTAGAGATGCTCTTAGCC 60.068 57.143 21.79 21.79 44.35 3.93
2310 2721 1.668628 GCGGCTAGAGATGCTCTTAGC 60.669 57.143 1.88 9.08 41.50 3.09
2335 2746 1.360393 ACCTGGAAAGGGCCTGTTGA 61.360 55.000 6.92 0.00 0.00 3.18
2406 2818 3.408020 CGAGCCGGCGAAAAACGA 61.408 61.111 23.20 0.00 45.77 3.85
2478 2909 2.855514 GCCCCTTTTCGCTTGTGCA 61.856 57.895 0.00 0.00 39.64 4.57
2550 3010 2.780010 GGAGGAATGGAGAGAATGGGAA 59.220 50.000 0.00 0.00 0.00 3.97
2759 3228 4.953868 CGGTCGGCGGTGACAACA 62.954 66.667 7.21 0.00 40.72 3.33


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

AutoCloner maintained by Alex Coulton.