Multiple sequence alignment - TraesCS5D01G341000

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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 TraesCS5D01G341000 chr5D 100.000 4598 0 0 1 4598 429288426 429293023 0.000000e+00 8492.0
1 TraesCS5D01G341000 chr5D 86.340 388 49 3 233 616 483568156 483567769 1.980000e-113 420.0
2 TraesCS5D01G341000 chr5D 86.040 351 27 10 2010 2344 423009221 423008877 1.570000e-94 357.0
3 TraesCS5D01G341000 chr5A 93.981 1977 64 23 2010 3977 545074707 545076637 0.000000e+00 2940.0
4 TraesCS5D01G341000 chr5A 90.132 1287 88 20 733 2011 545073407 545074662 0.000000e+00 1637.0
5 TraesCS5D01G341000 chr5A 82.785 1458 124 63 904 2309 545058593 545059975 0.000000e+00 1184.0
6 TraesCS5D01G341000 chr5A 87.671 511 41 11 3301 3791 545060714 545061222 3.990000e-160 575.0
7 TraesCS5D01G341000 chr5A 86.154 520 40 13 411 908 545057434 545057943 2.440000e-147 532.0
8 TraesCS5D01G341000 chr5A 89.245 437 31 9 4162 4598 545077636 545078056 2.440000e-147 532.0
9 TraesCS5D01G341000 chr5A 84.597 422 38 11 2365 2778 545059971 545060373 1.200000e-105 394.0
10 TraesCS5D01G341000 chr5A 90.141 213 19 1 196 406 545057058 545057270 4.530000e-70 276.0
11 TraesCS5D01G341000 chr5A 90.909 143 9 4 4003 4142 545077252 545077393 6.070000e-44 189.0
12 TraesCS5D01G341000 chr5A 86.713 143 13 3 58 196 123000509 123000649 2.220000e-33 154.0
13 TraesCS5D01G341000 chr5A 93.750 48 3 0 4175 4222 545077577 545077624 6.380000e-09 73.1
14 TraesCS5D01G341000 chr5B 95.357 1809 47 8 2010 3798 518482497 518484288 0.000000e+00 2841.0
15 TraesCS5D01G341000 chr5B 89.900 1297 89 22 733 2014 518481192 518482461 0.000000e+00 1631.0
16 TraesCS5D01G341000 chr5B 88.466 893 75 18 2917 3791 518474906 518475788 0.000000e+00 1053.0
17 TraesCS5D01G341000 chr5B 82.277 1168 110 47 942 2083 518472399 518473495 0.000000e+00 920.0
18 TraesCS5D01G341000 chr5B 82.240 884 93 35 1486 2344 310664639 310663795 0.000000e+00 704.0
19 TraesCS5D01G341000 chr5B 91.972 436 29 5 4169 4598 518486835 518487270 1.410000e-169 606.0
20 TraesCS5D01G341000 chr5B 91.536 319 17 9 3828 4142 518484281 518484593 9.140000e-117 431.0
21 TraesCS5D01G341000 chr5B 90.604 149 14 0 2494 2642 518473834 518473982 1.010000e-46 198.0
22 TraesCS5D01G341000 chr5B 90.588 85 8 0 817 901 518472304 518472388 3.760000e-21 113.0
23 TraesCS5D01G341000 chr5B 94.737 38 2 0 4144 4181 518484755 518484792 4.970000e-05 60.2
24 TraesCS5D01G341000 chr7D 81.279 1736 183 62 2014 3649 2037981 2036288 0.000000e+00 1275.0
25 TraesCS5D01G341000 chr7D 78.614 837 107 38 920 1712 2039037 2038229 5.350000e-134 488.0
26 TraesCS5D01G341000 chr4A 81.043 1725 174 75 2014 3649 742607367 742605707 0.000000e+00 1232.0
27 TraesCS5D01G341000 chr4A 78.701 770 99 38 920 1650 742608470 742607727 1.950000e-123 453.0
28 TraesCS5D01G341000 chr4A 83.726 424 51 9 1145 1553 742652148 742651728 7.220000e-103 385.0
29 TraesCS5D01G341000 chr4A 85.500 200 25 2 1 196 476719016 476718817 6.030000e-49 206.0
30 TraesCS5D01G341000 chr4A 85.915 142 14 3 59 196 406758134 406758273 3.710000e-31 147.0
31 TraesCS5D01G341000 chr4A 78.378 111 14 4 2326 2432 742651210 742651106 3.840000e-06 63.9
32 TraesCS5D01G341000 chrUn 82.271 1224 116 45 2121 3285 81435328 81436509 0.000000e+00 965.0
33 TraesCS5D01G341000 chrUn 82.271 1224 116 45 2121 3285 336021890 336023071 0.000000e+00 965.0
34 TraesCS5D01G341000 chrUn 78.512 847 105 45 917 1709 81434100 81434923 6.920000e-133 484.0
35 TraesCS5D01G341000 chrUn 83.430 344 35 15 3312 3648 81436605 81436933 2.690000e-77 300.0
36 TraesCS5D01G341000 chrUn 83.430 344 35 15 3312 3648 336023167 336023495 2.690000e-77 300.0
37 TraesCS5D01G341000 chr2D 81.214 692 96 18 1403 2089 639858292 639857630 1.130000e-145 527.0
38 TraesCS5D01G341000 chr2D 82.046 479 52 20 1883 2340 1714470 1714005 1.210000e-100 377.0
39 TraesCS5D01G341000 chr2D 84.000 200 27 3 1 196 370123558 370123756 2.180000e-43 187.0
40 TraesCS5D01G341000 chr2D 81.176 170 28 4 447 614 360030116 360030283 2.890000e-27 134.0
41 TraesCS5D01G341000 chr2B 87.047 386 47 2 233 615 449523584 449523969 2.540000e-117 433.0
42 TraesCS5D01G341000 chr2B 81.346 520 58 18 1428 1932 747755716 747756211 2.010000e-103 387.0
43 TraesCS5D01G341000 chr2B 87.013 77 10 0 1 77 439559788 439559864 2.280000e-13 87.9
44 TraesCS5D01G341000 chr3B 82.543 527 56 18 1428 1940 818195135 818195639 9.140000e-117 431.0
45 TraesCS5D01G341000 chr3B 82.617 512 56 16 1443 1940 818230891 818231383 5.500000e-114 422.0
46 TraesCS5D01G341000 chr3B 86.620 142 14 3 58 195 528719149 528719289 7.970000e-33 152.0
47 TraesCS5D01G341000 chr3B 85.526 76 11 0 1 76 546155662 546155737 3.810000e-11 80.5
48 TraesCS5D01G341000 chr3B 88.462 52 6 0 186 237 314388708 314388759 3.840000e-06 63.9
49 TraesCS5D01G341000 chr3A 86.856 388 48 2 233 617 85547207 85547594 9.140000e-117 431.0
50 TraesCS5D01G341000 chr7B 86.154 390 50 3 233 619 692788554 692788166 7.120000e-113 418.0
51 TraesCS5D01G341000 chr1B 81.733 531 61 15 1430 1946 39295028 39294520 1.190000e-110 411.0
52 TraesCS5D01G341000 chr1B 85.788 387 50 4 233 616 214569820 214569436 5.540000e-109 405.0
53 TraesCS5D01G341000 chr1A 81.733 531 61 15 1430 1946 22788409 22787901 1.190000e-110 411.0
54 TraesCS5D01G341000 chr1A 85.751 386 46 4 233 615 555806987 555807366 2.580000e-107 399.0
55 TraesCS5D01G341000 chr1A 86.167 347 25 11 2010 2340 291730601 291730940 2.040000e-93 353.0
56 TraesCS5D01G341000 chr1A 85.920 348 25 12 2010 2340 292014096 292014436 2.630000e-92 350.0
57 TraesCS5D01G341000 chr1A 85.879 347 25 12 2010 2340 293321398 293321060 9.470000e-92 348.0
58 TraesCS5D01G341000 chr1A 90.789 76 7 0 1 76 465102757 465102682 8.140000e-18 102.0
59 TraesCS5D01G341000 chr6D 78.198 688 89 29 1409 2089 217173268 217172635 2.600000e-102 383.0
60 TraesCS5D01G341000 chr6D 77.391 690 114 24 1406 2089 260812668 260812015 5.620000e-99 372.0
61 TraesCS5D01G341000 chr6D 82.500 200 31 2 1 196 307822571 307822372 6.120000e-39 172.0
62 TraesCS5D01G341000 chr4B 87.795 254 30 1 364 616 428460965 428461218 3.480000e-76 296.0
63 TraesCS5D01G341000 chr4B 86.111 144 14 4 58 197 412686328 412686187 2.870000e-32 150.0
64 TraesCS5D01G341000 chr3D 86.713 143 13 4 58 196 548486657 548486797 2.220000e-33 154.0
65 TraesCS5D01G341000 chr2A 80.928 194 33 2 7 196 501054675 501054868 2.870000e-32 150.0
66 TraesCS5D01G341000 chr7A 89.744 78 6 2 1 77 430144355 430144431 1.050000e-16 99.0
67 TraesCS5D01G341000 chr6A 88.158 76 9 0 3 78 305435689 305435614 1.760000e-14 91.6


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 TraesCS5D01G341000 chr5D 429288426 429293023 4597 False 8492.00 8492 100.000000 1 4598 1 chr5D.!!$F1 4597
1 TraesCS5D01G341000 chr5A 545073407 545078056 4649 False 1074.22 2940 91.603400 733 4598 5 chr5A.!!$F3 3865
2 TraesCS5D01G341000 chr5A 545057058 545061222 4164 False 592.20 1184 86.269600 196 3791 5 chr5A.!!$F2 3595
3 TraesCS5D01G341000 chr5B 518481192 518487270 6078 False 1113.84 2841 92.700400 733 4598 5 chr5B.!!$F2 3865
4 TraesCS5D01G341000 chr5B 310663795 310664639 844 True 704.00 704 82.240000 1486 2344 1 chr5B.!!$R1 858
5 TraesCS5D01G341000 chr5B 518472304 518475788 3484 False 571.00 1053 87.983750 817 3791 4 chr5B.!!$F1 2974
6 TraesCS5D01G341000 chr7D 2036288 2039037 2749 True 881.50 1275 79.946500 920 3649 2 chr7D.!!$R1 2729
7 TraesCS5D01G341000 chr4A 742605707 742608470 2763 True 842.50 1232 79.872000 920 3649 2 chr4A.!!$R2 2729
8 TraesCS5D01G341000 chr4A 742651106 742652148 1042 True 224.45 385 81.052000 1145 2432 2 chr4A.!!$R3 1287
9 TraesCS5D01G341000 chrUn 336021890 336023495 1605 False 632.50 965 82.850500 2121 3648 2 chrUn.!!$F2 1527
10 TraesCS5D01G341000 chrUn 81434100 81436933 2833 False 583.00 965 81.404333 917 3648 3 chrUn.!!$F1 2731
11 TraesCS5D01G341000 chr2D 639857630 639858292 662 True 527.00 527 81.214000 1403 2089 1 chr2D.!!$R2 686
12 TraesCS5D01G341000 chr3B 818195135 818195639 504 False 431.00 431 82.543000 1428 1940 1 chr3B.!!$F4 512
13 TraesCS5D01G341000 chr1B 39294520 39295028 508 True 411.00 411 81.733000 1430 1946 1 chr1B.!!$R1 516
14 TraesCS5D01G341000 chr1A 22787901 22788409 508 True 411.00 411 81.733000 1430 1946 1 chr1A.!!$R1 516
15 TraesCS5D01G341000 chr6D 217172635 217173268 633 True 383.00 383 78.198000 1409 2089 1 chr6D.!!$R1 680
16 TraesCS5D01G341000 chr6D 260812015 260812668 653 True 372.00 372 77.391000 1406 2089 1 chr6D.!!$R2 683

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
121 122 0.036590 CGGAAGGGTTTCGGGGTTTA 59.963 55.000 0.00 0.00 33.98 2.01 F
462 624 0.179004 TGGGTGTGTTTGTAGGGCTG 60.179 55.000 0.00 0.00 0.00 4.85 F
660 823 0.317854 CTGCGACAGAGTCACGTCAA 60.318 55.000 11.83 1.07 32.44 3.18 F
724 887 1.464198 AAGGAGGAAGGCACCCTGT 60.464 57.895 2.29 0.00 32.13 4.00 F
1185 2057 2.720758 CGCCGTCGTCTTCTGCTTG 61.721 63.158 0.00 0.00 0.00 4.01 F
1704 2671 3.122613 GTGCTGCTATGTATCGATCAAGC 59.877 47.826 0.00 7.68 0.00 4.01 F
2952 5072 0.107897 AACATTATCGTGCCAGCCGA 60.108 50.000 5.84 5.84 38.89 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1480 2382 0.409484 AGGATTTGGGGGAGGTTGTG 59.591 55.000 0.00 0.00 0.00 3.33 R
1825 2858 2.026822 CAGATAGCACAGTCCCCACTTT 60.027 50.000 0.00 0.00 0.00 2.66 R
1966 3024 2.040947 TGAACATGCATGGTAACCTCCA 59.959 45.455 29.41 14.04 42.01 3.86 R
1967 3025 2.684881 CTGAACATGCATGGTAACCTCC 59.315 50.000 29.41 11.50 0.00 4.30 R
2213 3467 3.960755 AGTCCCCTGTTTTCCTTGAAAAG 59.039 43.478 2.42 0.00 41.32 2.27 R
3427 5623 3.659786 TGAGTGTAGTATGTGTTGGTGC 58.340 45.455 0.00 0.00 0.00 5.01 R
4327 9374 0.379669 GCCATGGCGATTGAGAAGTG 59.620 55.000 23.48 0.00 0.00 3.16 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 9.912634 CACAAACTTAAGGAAATCACAATATGT 57.087 29.630 7.53 0.00 0.00 2.29
31 32 9.520515 ACTTAAGGAAATCACAATATGTTGAGT 57.479 29.630 9.40 0.00 38.71 3.41
32 33 9.778993 CTTAAGGAAATCACAATATGTTGAGTG 57.221 33.333 9.40 0.00 38.71 3.51
33 34 7.765695 AAGGAAATCACAATATGTTGAGTGT 57.234 32.000 9.40 0.00 38.71 3.55
34 35 7.765695 AGGAAATCACAATATGTTGAGTGTT 57.234 32.000 9.40 0.54 38.71 3.32
35 36 8.862325 AGGAAATCACAATATGTTGAGTGTTA 57.138 30.769 9.40 0.00 38.71 2.41
36 37 8.950210 AGGAAATCACAATATGTTGAGTGTTAG 58.050 33.333 9.40 0.00 38.71 2.34
37 38 8.730680 GGAAATCACAATATGTTGAGTGTTAGT 58.269 33.333 9.40 0.00 38.71 2.24
40 41 8.948631 ATCACAATATGTTGAGTGTTAGTAGG 57.051 34.615 9.40 0.00 38.71 3.18
41 42 8.129496 TCACAATATGTTGAGTGTTAGTAGGA 57.871 34.615 9.40 0.00 38.71 2.94
42 43 8.033038 TCACAATATGTTGAGTGTTAGTAGGAC 58.967 37.037 9.40 0.00 38.71 3.85
43 44 7.817478 CACAATATGTTGAGTGTTAGTAGGACA 59.183 37.037 9.40 0.00 38.71 4.02
44 45 8.540388 ACAATATGTTGAGTGTTAGTAGGACAT 58.460 33.333 9.40 0.00 38.71 3.06
45 46 8.820933 CAATATGTTGAGTGTTAGTAGGACATG 58.179 37.037 0.00 0.00 37.53 3.21
46 47 4.566004 TGTTGAGTGTTAGTAGGACATGC 58.434 43.478 0.00 0.00 0.00 4.06
47 48 4.039852 TGTTGAGTGTTAGTAGGACATGCA 59.960 41.667 0.00 0.00 0.00 3.96
48 49 5.178797 GTTGAGTGTTAGTAGGACATGCAT 58.821 41.667 0.00 0.00 0.00 3.96
49 50 6.071051 TGTTGAGTGTTAGTAGGACATGCATA 60.071 38.462 0.00 0.00 0.00 3.14
50 51 6.538945 TGAGTGTTAGTAGGACATGCATAA 57.461 37.500 0.00 0.00 0.00 1.90
51 52 7.124573 TGAGTGTTAGTAGGACATGCATAAT 57.875 36.000 0.00 0.00 0.00 1.28
52 53 6.986231 TGAGTGTTAGTAGGACATGCATAATG 59.014 38.462 0.00 0.00 42.48 1.90
53 54 7.124573 AGTGTTAGTAGGACATGCATAATGA 57.875 36.000 0.00 0.00 38.72 2.57
54 55 7.212976 AGTGTTAGTAGGACATGCATAATGAG 58.787 38.462 0.00 0.00 38.72 2.90
55 56 6.425114 GTGTTAGTAGGACATGCATAATGAGG 59.575 42.308 0.00 0.00 38.72 3.86
56 57 6.326323 TGTTAGTAGGACATGCATAATGAGGA 59.674 38.462 0.00 0.00 38.72 3.71
57 58 5.894298 AGTAGGACATGCATAATGAGGAA 57.106 39.130 0.00 0.00 38.72 3.36
58 59 6.252599 AGTAGGACATGCATAATGAGGAAA 57.747 37.500 0.00 0.00 38.72 3.13
59 60 6.845908 AGTAGGACATGCATAATGAGGAAAT 58.154 36.000 0.00 0.00 38.72 2.17
60 61 7.977818 AGTAGGACATGCATAATGAGGAAATA 58.022 34.615 0.00 0.00 38.72 1.40
61 62 8.609483 AGTAGGACATGCATAATGAGGAAATAT 58.391 33.333 0.00 0.00 38.72 1.28
62 63 9.236006 GTAGGACATGCATAATGAGGAAATATT 57.764 33.333 0.00 0.00 38.72 1.28
63 64 8.716674 AGGACATGCATAATGAGGAAATATTT 57.283 30.769 0.00 0.00 38.72 1.40
64 65 8.582437 AGGACATGCATAATGAGGAAATATTTG 58.418 33.333 5.17 0.00 38.72 2.32
65 66 8.362639 GGACATGCATAATGAGGAAATATTTGT 58.637 33.333 5.17 0.00 38.72 2.83
66 67 9.188588 GACATGCATAATGAGGAAATATTTGTG 57.811 33.333 5.17 0.00 38.72 3.33
67 68 8.916062 ACATGCATAATGAGGAAATATTTGTGA 58.084 29.630 5.17 0.00 38.72 3.58
68 69 9.752961 CATGCATAATGAGGAAATATTTGTGAA 57.247 29.630 5.17 0.00 38.72 3.18
85 86 9.887406 TATTTGTGAAATAGTTTCGAAAGGAAC 57.113 29.630 11.66 0.00 42.55 3.62
89 90 4.812308 GTTTCGAAAGGAACGGCG 57.188 55.556 11.66 4.80 40.28 6.46
90 91 1.936658 GTTTCGAAAGGAACGGCGT 59.063 52.632 11.66 6.77 40.28 5.68
91 92 0.305617 GTTTCGAAAGGAACGGCGTT 59.694 50.000 27.15 27.15 40.28 4.84
92 93 1.015868 TTTCGAAAGGAACGGCGTTT 58.984 45.000 27.48 10.92 37.30 3.60
93 94 0.582960 TTCGAAAGGAACGGCGTTTC 59.417 50.000 27.48 25.30 44.08 2.78
94 95 4.812308 GAAAGGAACGGCGTTTCG 57.188 55.556 27.48 0.00 40.31 3.46
95 96 1.205820 GAAAGGAACGGCGTTTCGG 59.794 57.895 27.48 0.00 40.31 4.30
96 97 2.178892 GAAAGGAACGGCGTTTCGGG 62.179 60.000 27.48 0.00 40.31 5.14
97 98 2.946172 AAAGGAACGGCGTTTCGGGT 62.946 55.000 27.48 12.64 29.08 5.28
98 99 2.946172 AAGGAACGGCGTTTCGGGTT 62.946 55.000 27.48 12.38 0.00 4.11
99 100 2.552768 GAACGGCGTTTCGGGTTC 59.447 61.111 27.48 8.40 32.92 3.62
100 101 2.203042 AACGGCGTTTCGGGTTCA 60.203 55.556 21.19 0.00 0.00 3.18
101 102 2.434225 GAACGGCGTTTCGGGTTCAC 62.434 60.000 27.48 6.65 38.82 3.18
102 103 3.719144 CGGCGTTTCGGGTTCACC 61.719 66.667 0.00 0.00 0.00 4.02
119 120 2.433004 CGGAAGGGTTTCGGGGTT 59.567 61.111 0.00 0.00 33.98 4.11
120 121 1.228337 CGGAAGGGTTTCGGGGTTT 60.228 57.895 0.00 0.00 33.98 3.27
121 122 0.036590 CGGAAGGGTTTCGGGGTTTA 59.963 55.000 0.00 0.00 33.98 2.01
122 123 1.538047 GGAAGGGTTTCGGGGTTTAC 58.462 55.000 0.00 0.00 33.98 2.01
123 124 1.538047 GAAGGGTTTCGGGGTTTACC 58.462 55.000 0.00 0.00 39.11 2.85
131 132 2.115695 GGGGTTTACCGGGCAACA 59.884 61.111 17.16 0.00 41.60 3.33
132 133 2.270257 GGGGTTTACCGGGCAACAC 61.270 63.158 17.16 14.27 41.60 3.32
133 134 2.270257 GGGTTTACCGGGCAACACC 61.270 63.158 17.16 12.59 36.71 4.16
134 135 1.528776 GGTTTACCGGGCAACACCA 60.529 57.895 17.16 0.00 42.05 4.17
135 136 1.520600 GGTTTACCGGGCAACACCAG 61.521 60.000 17.16 0.00 42.05 4.00
140 141 4.734652 CGGGCAACACCAGGTATT 57.265 55.556 0.00 0.00 42.05 1.89
141 142 3.865477 CGGGCAACACCAGGTATTA 57.135 52.632 0.00 0.00 42.05 0.98
142 143 1.375551 CGGGCAACACCAGGTATTAC 58.624 55.000 0.00 0.00 42.05 1.89
143 144 1.758936 GGGCAACACCAGGTATTACC 58.241 55.000 4.57 4.57 42.05 2.85
144 145 1.375551 GGCAACACCAGGTATTACCG 58.624 55.000 7.21 2.98 44.90 4.02
145 146 1.065998 GGCAACACCAGGTATTACCGA 60.066 52.381 7.21 0.00 44.90 4.69
146 147 2.420967 GGCAACACCAGGTATTACCGAT 60.421 50.000 7.21 0.00 44.90 4.18
147 148 3.181463 GGCAACACCAGGTATTACCGATA 60.181 47.826 7.21 0.00 44.90 2.92
148 149 4.444536 GCAACACCAGGTATTACCGATAA 58.555 43.478 7.21 0.00 44.90 1.75
149 150 4.877251 GCAACACCAGGTATTACCGATAAA 59.123 41.667 7.21 0.00 44.90 1.40
150 151 5.529800 GCAACACCAGGTATTACCGATAAAT 59.470 40.000 7.21 0.00 44.90 1.40
151 152 6.707161 GCAACACCAGGTATTACCGATAAATA 59.293 38.462 7.21 0.00 44.90 1.40
152 153 7.227116 GCAACACCAGGTATTACCGATAAATAA 59.773 37.037 7.21 0.00 44.90 1.40
153 154 9.280174 CAACACCAGGTATTACCGATAAATAAT 57.720 33.333 7.21 0.00 44.90 1.28
176 177 3.570912 ATAGGTGGGAAATGTTACCGG 57.429 47.619 0.00 0.00 38.24 5.28
177 178 1.364269 AGGTGGGAAATGTTACCGGA 58.636 50.000 9.46 0.00 38.24 5.14
178 179 1.280998 AGGTGGGAAATGTTACCGGAG 59.719 52.381 9.46 0.00 38.24 4.63
179 180 1.279846 GGTGGGAAATGTTACCGGAGA 59.720 52.381 9.46 0.00 0.00 3.71
180 181 2.092592 GGTGGGAAATGTTACCGGAGAT 60.093 50.000 9.46 0.00 0.00 2.75
181 182 2.943033 GTGGGAAATGTTACCGGAGATG 59.057 50.000 9.46 0.00 0.00 2.90
182 183 2.574369 TGGGAAATGTTACCGGAGATGT 59.426 45.455 9.46 0.00 0.00 3.06
183 184 3.009695 TGGGAAATGTTACCGGAGATGTT 59.990 43.478 9.46 0.00 0.00 2.71
184 185 3.626217 GGGAAATGTTACCGGAGATGTTC 59.374 47.826 9.46 4.20 0.00 3.18
185 186 4.258543 GGAAATGTTACCGGAGATGTTCA 58.741 43.478 9.46 0.00 0.00 3.18
186 187 4.698304 GGAAATGTTACCGGAGATGTTCAA 59.302 41.667 9.46 0.00 0.00 2.69
187 188 5.357032 GGAAATGTTACCGGAGATGTTCAAT 59.643 40.000 9.46 0.00 0.00 2.57
188 189 6.127730 GGAAATGTTACCGGAGATGTTCAATT 60.128 38.462 9.46 0.00 0.00 2.32
189 190 7.066525 GGAAATGTTACCGGAGATGTTCAATTA 59.933 37.037 9.46 0.00 0.00 1.40
190 191 7.931578 AATGTTACCGGAGATGTTCAATTAA 57.068 32.000 9.46 0.00 0.00 1.40
191 192 8.519799 AATGTTACCGGAGATGTTCAATTAAT 57.480 30.769 9.46 0.00 0.00 1.40
192 193 9.621629 AATGTTACCGGAGATGTTCAATTAATA 57.378 29.630 9.46 0.00 0.00 0.98
193 194 9.621629 ATGTTACCGGAGATGTTCAATTAATAA 57.378 29.630 9.46 0.00 0.00 1.40
194 195 9.621629 TGTTACCGGAGATGTTCAATTAATAAT 57.378 29.630 9.46 0.00 0.00 1.28
258 259 4.006319 CTCTCAGGGGCAAAACTAAGAAG 58.994 47.826 0.00 0.00 0.00 2.85
267 268 3.003378 GCAAAACTAAGAAGAGTGGCGTT 59.997 43.478 0.00 0.00 0.00 4.84
273 274 2.892784 AGAAGAGTGGCGTTATAGGC 57.107 50.000 0.00 0.00 37.19 3.93
286 287 3.381949 GTTATAGGCAAGGCGTCTGTAG 58.618 50.000 0.00 0.00 0.00 2.74
290 291 1.374758 GCAAGGCGTCTGTAGCTGT 60.375 57.895 0.00 0.00 34.52 4.40
302 305 3.519107 TCTGTAGCTGTTTGGGATGATCA 59.481 43.478 0.00 0.00 0.00 2.92
315 318 3.369892 GGGATGATCATCGGTCTATTGGG 60.370 52.174 25.60 0.00 38.69 4.12
320 323 0.600255 CATCGGTCTATTGGGCGGTC 60.600 60.000 0.00 0.00 0.00 4.79
332 335 2.818169 GGCGGTCCATATGGCCTGA 61.818 63.158 24.11 5.41 42.29 3.86
348 351 1.610102 CCTGACTTGGGCTTGTCTCTG 60.610 57.143 0.00 0.00 34.57 3.35
357 360 2.508526 GGCTTGTCTCTGTGGATTTGT 58.491 47.619 0.00 0.00 0.00 2.83
365 368 3.322541 TCTCTGTGGATTTGTCGGTGTTA 59.677 43.478 0.00 0.00 0.00 2.41
389 392 1.122019 ACTTCGGTGGAGGTGCTCTT 61.122 55.000 0.00 0.00 30.32 2.85
390 393 0.671781 CTTCGGTGGAGGTGCTCTTG 60.672 60.000 0.00 0.00 0.00 3.02
394 397 1.270625 CGGTGGAGGTGCTCTTGTTAA 60.271 52.381 0.00 0.00 0.00 2.01
401 404 4.506095 GGAGGTGCTCTTGTTAAGGGTTTA 60.506 45.833 0.00 0.00 0.00 2.01
406 409 5.633601 GTGCTCTTGTTAAGGGTTTATTTGC 59.366 40.000 0.00 0.00 0.00 3.68
407 410 4.857037 GCTCTTGTTAAGGGTTTATTTGCG 59.143 41.667 0.00 0.00 0.00 4.85
426 588 3.119245 TGCGATGTAGTAGTTTGGAGGTC 60.119 47.826 0.00 0.00 0.00 3.85
435 597 1.079405 TTTGGAGGTCGATGGTCGC 60.079 57.895 0.00 0.00 40.21 5.19
437 599 1.945354 TTGGAGGTCGATGGTCGCTC 61.945 60.000 0.00 0.00 40.21 5.03
462 624 0.179004 TGGGTGTGTTTGTAGGGCTG 60.179 55.000 0.00 0.00 0.00 4.85
474 636 3.567797 GGGCTGATCGTGCGCTTC 61.568 66.667 9.73 0.35 39.74 3.86
477 639 2.806856 GCTGATCGTGCGCTTCTGG 61.807 63.158 9.73 0.00 0.00 3.86
507 669 2.293170 CTCTCTGAGTAGTCCGCATGA 58.707 52.381 4.32 0.00 0.00 3.07
508 670 2.290367 CTCTCTGAGTAGTCCGCATGAG 59.710 54.545 4.32 0.00 0.00 2.90
519 682 2.351726 GTCCGCATGAGATTGGTTGTAC 59.648 50.000 0.00 0.00 0.00 2.90
523 686 2.939640 GCATGAGATTGGTTGTACCGGT 60.940 50.000 13.98 13.98 42.58 5.28
528 691 4.070009 GAGATTGGTTGTACCGGTTTTCT 58.930 43.478 15.04 3.71 42.58 2.52
529 692 4.070009 AGATTGGTTGTACCGGTTTTCTC 58.930 43.478 15.04 0.66 42.58 2.87
531 694 1.202794 TGGTTGTACCGGTTTTCTCCC 60.203 52.381 15.04 6.58 42.58 4.30
543 706 5.952526 GGTTTTCTCCCGATTTTCTGTTA 57.047 39.130 0.00 0.00 0.00 2.41
552 715 7.551617 TCTCCCGATTTTCTGTTAATTAACTCC 59.448 37.037 24.81 3.98 37.12 3.85
565 728 9.793259 TGTTAATTAACTCCACAATTCTCTTCT 57.207 29.630 24.81 0.00 37.12 2.85
582 745 8.771920 TTCTCTTCTGCTTAATTAATCAACGA 57.228 30.769 0.00 0.00 0.00 3.85
584 747 8.035394 TCTCTTCTGCTTAATTAATCAACGAGT 58.965 33.333 14.70 0.00 0.00 4.18
600 763 2.814336 ACGAGTCAAATCTTTTGCCTCC 59.186 45.455 5.69 0.00 0.00 4.30
601 764 2.162408 CGAGTCAAATCTTTTGCCTCCC 59.838 50.000 5.69 0.00 0.00 4.30
605 768 5.393866 AGTCAAATCTTTTGCCTCCCTTTA 58.606 37.500 0.00 0.00 0.00 1.85
606 769 5.838521 AGTCAAATCTTTTGCCTCCCTTTAA 59.161 36.000 0.00 0.00 0.00 1.52
607 770 6.326323 AGTCAAATCTTTTGCCTCCCTTTAAA 59.674 34.615 0.00 0.00 0.00 1.52
608 771 6.989759 GTCAAATCTTTTGCCTCCCTTTAAAA 59.010 34.615 0.00 0.00 0.00 1.52
609 772 7.497579 GTCAAATCTTTTGCCTCCCTTTAAAAA 59.502 33.333 0.00 0.00 0.00 1.94
610 773 8.217111 TCAAATCTTTTGCCTCCCTTTAAAAAT 58.783 29.630 0.00 0.00 0.00 1.82
611 774 9.500785 CAAATCTTTTGCCTCCCTTTAAAAATA 57.499 29.630 0.00 0.00 0.00 1.40
620 783 9.425577 TGCCTCCCTTTAAAAATAAAATAAACG 57.574 29.630 0.00 0.00 0.00 3.60
632 795 7.710766 AATAAAATAAACGAGACGATCCTCC 57.289 36.000 0.00 0.00 0.00 4.30
639 802 1.791103 GAGACGATCCTCCCTGCGAG 61.791 65.000 0.00 0.00 38.46 5.03
640 803 3.492311 GACGATCCTCCCTGCGAGC 62.492 68.421 0.00 0.00 37.27 5.03
641 804 4.292178 CGATCCTCCCTGCGAGCC 62.292 72.222 0.00 0.00 37.27 4.70
642 805 2.841988 GATCCTCCCTGCGAGCCT 60.842 66.667 0.00 0.00 37.27 4.58
650 813 4.426112 CTGCGAGCCTGCGACAGA 62.426 66.667 8.20 0.00 37.50 3.41
651 814 4.426112 TGCGAGCCTGCGACAGAG 62.426 66.667 8.20 1.16 37.81 3.35
660 823 0.317854 CTGCGACAGAGTCACGTCAA 60.318 55.000 11.83 1.07 32.44 3.18
724 887 1.464198 AAGGAGGAAGGCACCCTGT 60.464 57.895 2.29 0.00 32.13 4.00
1072 1914 3.494048 GCTGGTAGATGAATGAGGAGTGG 60.494 52.174 0.00 0.00 0.00 4.00
1185 2057 2.720758 CGCCGTCGTCTTCTGCTTG 61.721 63.158 0.00 0.00 0.00 4.01
1659 2618 6.631971 TTGTGTGATACATTGTGTGTGATT 57.368 33.333 0.00 0.00 42.24 2.57
1704 2671 3.122613 GTGCTGCTATGTATCGATCAAGC 59.877 47.826 0.00 7.68 0.00 4.01
1835 2868 5.585820 TTGTAACAAAAGAAAGTGGGGAC 57.414 39.130 0.00 0.00 0.00 4.46
1958 3016 7.764141 CATGTAATGGTGGGATCATATGAAA 57.236 36.000 9.99 0.00 41.79 2.69
1959 3017 8.357290 CATGTAATGGTGGGATCATATGAAAT 57.643 34.615 9.99 0.00 41.79 2.17
1960 3018 7.764141 TGTAATGGTGGGATCATATGAAATG 57.236 36.000 9.99 0.00 0.00 2.32
1961 3019 7.525165 TGTAATGGTGGGATCATATGAAATGA 58.475 34.615 9.99 0.00 0.00 2.57
1963 3021 9.028284 GTAATGGTGGGATCATATGAAATGATT 57.972 33.333 9.99 5.03 38.73 2.57
1965 3023 9.604569 AATGGTGGGATCATATGAAATGATTAA 57.395 29.630 9.99 0.00 38.73 1.40
1966 3024 9.778479 ATGGTGGGATCATATGAAATGATTAAT 57.222 29.630 9.99 0.00 38.73 1.40
1967 3025 9.027202 TGGTGGGATCATATGAAATGATTAATG 57.973 33.333 9.99 0.00 38.73 1.90
1968 3026 8.472413 GGTGGGATCATATGAAATGATTAATGG 58.528 37.037 9.99 0.00 38.73 3.16
2024 3197 8.356657 CAATTTTTGTGGTACCTTCTAATCACA 58.643 33.333 14.36 3.25 33.97 3.58
2051 3224 7.067532 TGAACGCATATGTTAGTTAGTTTGG 57.932 36.000 4.29 0.00 30.75 3.28
2350 3624 6.926630 AAGGATGTCTTTCTCTAGTTGAGT 57.073 37.500 1.45 0.00 43.13 3.41
2398 3672 8.970691 AATGAATCGTCTAAAAACCTTCATTG 57.029 30.769 6.77 0.00 37.03 2.82
2952 5072 0.107897 AACATTATCGTGCCAGCCGA 60.108 50.000 5.84 5.84 38.89 5.54
3248 5374 5.476091 AGAAGAACAGGAAGTAAGTCTGG 57.524 43.478 0.00 0.00 33.19 3.86
3427 5623 0.107703 TCGCCAAGGCTACCAATGAG 60.108 55.000 9.73 0.00 39.32 2.90
3945 6178 0.317603 GCATGCCTGCGATGTGAATC 60.318 55.000 6.36 0.00 38.92 2.52
3946 6179 1.018910 CATGCCTGCGATGTGAATCA 58.981 50.000 0.00 0.00 0.00 2.57
3947 6180 1.402613 CATGCCTGCGATGTGAATCAA 59.597 47.619 0.00 0.00 0.00 2.57
4014 6790 6.582636 TGTAAGAGCACTGAAGAAGAAGAAA 58.417 36.000 0.00 0.00 0.00 2.52
4017 6793 7.579761 AAGAGCACTGAAGAAGAAGAAAAAT 57.420 32.000 0.00 0.00 0.00 1.82
4129 6961 0.693049 AGGTGTTTCCGAAGATGGCT 59.307 50.000 0.00 0.00 41.99 4.75
4142 6974 4.319046 CGAAGATGGCTTTTGGACGATATG 60.319 45.833 0.00 0.00 33.61 1.78
4213 7312 3.709653 TCTTCTGGGCCGTAAAGTATGAT 59.290 43.478 0.00 0.00 0.00 2.45
4215 7314 2.367567 TCTGGGCCGTAAAGTATGATCC 59.632 50.000 0.00 0.00 0.00 3.36
4241 9288 1.001974 TGGTCATCTGGAACACCTTCG 59.998 52.381 0.00 0.00 38.63 3.79
4244 9291 3.600388 GTCATCTGGAACACCTTCGATT 58.400 45.455 0.00 0.00 0.00 3.34
4322 9369 6.603940 AAAACATACCATGCATTGTAACCT 57.396 33.333 14.02 0.00 0.00 3.50
4323 9370 5.835113 AACATACCATGCATTGTAACCTC 57.165 39.130 14.02 0.00 0.00 3.85
4324 9371 4.854173 ACATACCATGCATTGTAACCTCA 58.146 39.130 14.02 0.00 0.00 3.86
4325 9372 5.260424 ACATACCATGCATTGTAACCTCAA 58.740 37.500 14.02 0.00 0.00 3.02
4326 9373 5.893255 ACATACCATGCATTGTAACCTCAAT 59.107 36.000 14.02 0.00 38.38 2.57
4327 9374 4.989279 ACCATGCATTGTAACCTCAATC 57.011 40.909 0.69 0.00 36.10 2.67
4328 9375 4.343231 ACCATGCATTGTAACCTCAATCA 58.657 39.130 0.69 0.00 36.10 2.57
4329 9376 4.158394 ACCATGCATTGTAACCTCAATCAC 59.842 41.667 0.69 0.00 36.10 3.06
4330 9377 4.400251 CCATGCATTGTAACCTCAATCACT 59.600 41.667 0.00 0.00 36.10 3.41
4331 9378 5.105635 CCATGCATTGTAACCTCAATCACTT 60.106 40.000 0.00 0.00 36.10 3.16
4394 9453 3.568538 CGCCTTTTCACCAGAGATTTTG 58.431 45.455 0.00 0.00 0.00 2.44
4397 9456 4.746611 GCCTTTTCACCAGAGATTTTGTTG 59.253 41.667 0.00 0.00 0.00 3.33
4398 9457 5.451798 GCCTTTTCACCAGAGATTTTGTTGA 60.452 40.000 0.00 0.00 0.00 3.18
4403 9462 7.826260 TTCACCAGAGATTTTGTTGAAAAAC 57.174 32.000 0.00 0.00 34.72 2.43
4429 9491 6.762077 TGTCCATAATAGACCCATTGATCA 57.238 37.500 0.00 0.00 33.09 2.92
4501 9566 7.114811 CGAAACAGAATAAAATGGGACTTGTTG 59.885 37.037 0.00 0.00 0.00 3.33
4502 9567 6.976934 ACAGAATAAAATGGGACTTGTTGT 57.023 33.333 0.00 0.00 0.00 3.32
4503 9568 7.360113 ACAGAATAAAATGGGACTTGTTGTT 57.640 32.000 0.00 0.00 0.00 2.83
4504 9569 7.791029 ACAGAATAAAATGGGACTTGTTGTTT 58.209 30.769 0.00 0.00 0.00 2.83
4505 9570 8.919145 ACAGAATAAAATGGGACTTGTTGTTTA 58.081 29.630 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.520515 ACTCAACATATTGTGATTTCCTTAAGT 57.479 29.630 0.97 0.00 37.11 2.24
7 8 9.295825 ACACTCAACATATTGTGATTTCCTTAA 57.704 29.630 0.00 0.00 37.11 1.85
8 9 8.862325 ACACTCAACATATTGTGATTTCCTTA 57.138 30.769 0.00 0.00 37.11 2.69
9 10 7.765695 ACACTCAACATATTGTGATTTCCTT 57.234 32.000 0.00 0.00 37.11 3.36
10 11 7.765695 AACACTCAACATATTGTGATTTCCT 57.234 32.000 0.00 0.00 37.11 3.36
11 12 8.730680 ACTAACACTCAACATATTGTGATTTCC 58.269 33.333 0.00 0.00 37.11 3.13
14 15 9.383519 CCTACTAACACTCAACATATTGTGATT 57.616 33.333 0.00 0.00 37.11 2.57
15 16 8.758829 TCCTACTAACACTCAACATATTGTGAT 58.241 33.333 0.00 0.00 37.11 3.06
16 17 8.033038 GTCCTACTAACACTCAACATATTGTGA 58.967 37.037 0.00 0.00 37.11 3.58
17 18 7.817478 TGTCCTACTAACACTCAACATATTGTG 59.183 37.037 0.00 0.00 37.11 3.33
18 19 7.903145 TGTCCTACTAACACTCAACATATTGT 58.097 34.615 0.00 0.00 37.11 2.71
19 20 8.820933 CATGTCCTACTAACACTCAACATATTG 58.179 37.037 0.00 0.00 37.14 1.90
20 21 7.495934 GCATGTCCTACTAACACTCAACATATT 59.504 37.037 0.00 0.00 0.00 1.28
21 22 6.986817 GCATGTCCTACTAACACTCAACATAT 59.013 38.462 0.00 0.00 0.00 1.78
22 23 6.071051 TGCATGTCCTACTAACACTCAACATA 60.071 38.462 0.00 0.00 0.00 2.29
23 24 5.178797 GCATGTCCTACTAACACTCAACAT 58.821 41.667 0.00 0.00 0.00 2.71
24 25 4.039852 TGCATGTCCTACTAACACTCAACA 59.960 41.667 0.00 0.00 0.00 3.33
25 26 4.566004 TGCATGTCCTACTAACACTCAAC 58.434 43.478 0.00 0.00 0.00 3.18
26 27 4.882842 TGCATGTCCTACTAACACTCAA 57.117 40.909 0.00 0.00 0.00 3.02
27 28 6.538945 TTATGCATGTCCTACTAACACTCA 57.461 37.500 10.16 0.00 0.00 3.41
28 29 7.210174 TCATTATGCATGTCCTACTAACACTC 58.790 38.462 10.16 0.00 34.06 3.51
29 30 7.124573 TCATTATGCATGTCCTACTAACACT 57.875 36.000 10.16 0.00 34.06 3.55
30 31 6.425114 CCTCATTATGCATGTCCTACTAACAC 59.575 42.308 10.16 0.00 34.06 3.32
31 32 6.326323 TCCTCATTATGCATGTCCTACTAACA 59.674 38.462 10.16 0.00 34.06 2.41
32 33 6.759272 TCCTCATTATGCATGTCCTACTAAC 58.241 40.000 10.16 0.00 34.06 2.34
33 34 6.994421 TCCTCATTATGCATGTCCTACTAA 57.006 37.500 10.16 0.00 34.06 2.24
34 35 6.994421 TTCCTCATTATGCATGTCCTACTA 57.006 37.500 10.16 0.00 34.06 1.82
35 36 5.894298 TTCCTCATTATGCATGTCCTACT 57.106 39.130 10.16 0.00 34.06 2.57
36 37 8.798859 ATATTTCCTCATTATGCATGTCCTAC 57.201 34.615 10.16 0.00 34.06 3.18
37 38 9.812347 AAATATTTCCTCATTATGCATGTCCTA 57.188 29.630 10.16 0.00 34.06 2.94
38 39 8.582437 CAAATATTTCCTCATTATGCATGTCCT 58.418 33.333 10.16 0.00 34.06 3.85
39 40 8.362639 ACAAATATTTCCTCATTATGCATGTCC 58.637 33.333 10.16 0.00 34.06 4.02
40 41 9.188588 CACAAATATTTCCTCATTATGCATGTC 57.811 33.333 10.16 0.00 34.06 3.06
41 42 8.916062 TCACAAATATTTCCTCATTATGCATGT 58.084 29.630 10.16 0.00 34.06 3.21
42 43 9.752961 TTCACAAATATTTCCTCATTATGCATG 57.247 29.630 10.16 0.00 0.00 4.06
59 60 9.887406 GTTCCTTTCGAAACTATTTCACAAATA 57.113 29.630 6.47 0.00 39.63 1.40
60 61 7.589954 CGTTCCTTTCGAAACTATTTCACAAAT 59.410 33.333 6.47 0.00 39.63 2.32
61 62 6.908284 CGTTCCTTTCGAAACTATTTCACAAA 59.092 34.615 6.47 0.38 39.63 2.83
62 63 6.423862 CGTTCCTTTCGAAACTATTTCACAA 58.576 36.000 6.47 0.00 39.63 3.33
63 64 5.049954 CCGTTCCTTTCGAAACTATTTCACA 60.050 40.000 6.47 0.00 39.63 3.58
64 65 5.379827 CCGTTCCTTTCGAAACTATTTCAC 58.620 41.667 6.47 0.00 39.63 3.18
65 66 4.083696 GCCGTTCCTTTCGAAACTATTTCA 60.084 41.667 6.47 0.00 39.63 2.69
66 67 4.400845 GCCGTTCCTTTCGAAACTATTTC 58.599 43.478 6.47 0.00 36.32 2.17
67 68 3.120442 CGCCGTTCCTTTCGAAACTATTT 60.120 43.478 6.47 0.00 30.39 1.40
68 69 2.414138 CGCCGTTCCTTTCGAAACTATT 59.586 45.455 6.47 0.00 30.39 1.73
69 70 1.997606 CGCCGTTCCTTTCGAAACTAT 59.002 47.619 6.47 0.00 30.39 2.12
70 71 1.269726 ACGCCGTTCCTTTCGAAACTA 60.270 47.619 6.47 0.00 30.39 2.24
71 72 0.531311 ACGCCGTTCCTTTCGAAACT 60.531 50.000 6.47 0.00 30.39 2.66
72 73 0.305617 AACGCCGTTCCTTTCGAAAC 59.694 50.000 6.47 0.00 30.39 2.78
73 74 1.003652 GAAACGCCGTTCCTTTCGAAA 60.004 47.619 10.71 10.71 30.39 3.46
74 75 0.582960 GAAACGCCGTTCCTTTCGAA 59.417 50.000 1.60 0.00 0.00 3.71
75 76 1.550659 CGAAACGCCGTTCCTTTCGA 61.551 55.000 14.60 0.00 45.84 3.71
76 77 1.154727 CGAAACGCCGTTCCTTTCG 60.155 57.895 1.60 5.07 40.04 3.46
77 78 1.205820 CCGAAACGCCGTTCCTTTC 59.794 57.895 1.60 0.00 0.00 2.62
78 79 2.255881 CCCGAAACGCCGTTCCTTT 61.256 57.895 1.60 0.00 0.00 3.11
79 80 2.667199 CCCGAAACGCCGTTCCTT 60.667 61.111 1.60 0.00 0.00 3.36
80 81 3.465258 AACCCGAAACGCCGTTCCT 62.465 57.895 1.60 0.00 0.00 3.36
81 82 2.958204 GAACCCGAAACGCCGTTCC 61.958 63.158 1.60 0.00 32.48 3.62
82 83 2.246042 TGAACCCGAAACGCCGTTC 61.246 57.895 1.60 0.00 36.16 3.95
83 84 2.203042 TGAACCCGAAACGCCGTT 60.203 55.556 0.00 0.00 0.00 4.44
84 85 2.968697 GTGAACCCGAAACGCCGT 60.969 61.111 0.00 0.00 0.00 5.68
85 86 3.719144 GGTGAACCCGAAACGCCG 61.719 66.667 0.00 0.00 0.00 6.46
101 102 2.702040 AAACCCCGAAACCCTTCCGG 62.702 60.000 0.00 0.00 37.81 5.14
102 103 0.036590 TAAACCCCGAAACCCTTCCG 59.963 55.000 0.00 0.00 0.00 4.30
103 104 1.538047 GTAAACCCCGAAACCCTTCC 58.462 55.000 0.00 0.00 0.00 3.46
104 105 1.538047 GGTAAACCCCGAAACCCTTC 58.462 55.000 0.00 0.00 0.00 3.46
105 106 3.751767 GGTAAACCCCGAAACCCTT 57.248 52.632 0.00 0.00 0.00 3.95
114 115 2.115695 TGTTGCCCGGTAAACCCC 59.884 61.111 12.51 0.00 0.00 4.95
115 116 2.270257 GGTGTTGCCCGGTAAACCC 61.270 63.158 12.51 9.86 0.00 4.11
116 117 1.520600 CTGGTGTTGCCCGGTAAACC 61.521 60.000 12.51 7.30 36.04 3.27
117 118 1.520600 CCTGGTGTTGCCCGGTAAAC 61.521 60.000 0.00 5.03 36.92 2.01
118 119 1.228306 CCTGGTGTTGCCCGGTAAA 60.228 57.895 0.00 0.00 36.92 2.01
119 120 2.432563 CCTGGTGTTGCCCGGTAA 59.567 61.111 0.00 0.00 36.92 2.85
122 123 0.253610 TAATACCTGGTGTTGCCCGG 59.746 55.000 17.85 0.00 45.98 5.73
123 124 1.375551 GTAATACCTGGTGTTGCCCG 58.624 55.000 17.85 0.00 36.04 6.13
124 125 1.758936 GGTAATACCTGGTGTTGCCC 58.241 55.000 25.85 17.63 34.52 5.36
125 126 1.065998 TCGGTAATACCTGGTGTTGCC 60.066 52.381 26.18 26.18 36.45 4.52
126 127 2.389962 TCGGTAATACCTGGTGTTGC 57.610 50.000 17.85 16.08 35.66 4.17
127 128 8.665643 TTATTTATCGGTAATACCTGGTGTTG 57.334 34.615 17.85 2.82 35.66 3.33
150 151 8.542080 CCGGTAACATTTCCCACCTATATATTA 58.458 37.037 0.00 0.00 0.00 0.98
151 152 7.238096 TCCGGTAACATTTCCCACCTATATATT 59.762 37.037 0.00 0.00 0.00 1.28
152 153 6.731919 TCCGGTAACATTTCCCACCTATATAT 59.268 38.462 0.00 0.00 0.00 0.86
153 154 6.083383 TCCGGTAACATTTCCCACCTATATA 58.917 40.000 0.00 0.00 0.00 0.86
154 155 4.909088 TCCGGTAACATTTCCCACCTATAT 59.091 41.667 0.00 0.00 0.00 0.86
155 156 4.296912 TCCGGTAACATTTCCCACCTATA 58.703 43.478 0.00 0.00 0.00 1.31
156 157 3.116959 TCCGGTAACATTTCCCACCTAT 58.883 45.455 0.00 0.00 0.00 2.57
157 158 2.502538 CTCCGGTAACATTTCCCACCTA 59.497 50.000 0.00 0.00 0.00 3.08
158 159 1.280998 CTCCGGTAACATTTCCCACCT 59.719 52.381 0.00 0.00 0.00 4.00
159 160 1.279846 TCTCCGGTAACATTTCCCACC 59.720 52.381 0.00 0.00 0.00 4.61
160 161 2.773993 TCTCCGGTAACATTTCCCAC 57.226 50.000 0.00 0.00 0.00 4.61
161 162 2.574369 ACATCTCCGGTAACATTTCCCA 59.426 45.455 0.00 0.00 0.00 4.37
162 163 3.277142 ACATCTCCGGTAACATTTCCC 57.723 47.619 0.00 0.00 0.00 3.97
163 164 4.258543 TGAACATCTCCGGTAACATTTCC 58.741 43.478 0.00 0.00 0.00 3.13
164 165 5.873179 TTGAACATCTCCGGTAACATTTC 57.127 39.130 0.00 0.00 0.00 2.17
165 166 6.834168 AATTGAACATCTCCGGTAACATTT 57.166 33.333 0.00 0.00 0.00 2.32
166 167 7.931578 TTAATTGAACATCTCCGGTAACATT 57.068 32.000 0.00 0.00 0.00 2.71
167 168 9.621629 TTATTAATTGAACATCTCCGGTAACAT 57.378 29.630 0.00 0.00 0.00 2.71
168 169 9.621629 ATTATTAATTGAACATCTCCGGTAACA 57.378 29.630 0.00 0.00 0.00 2.41
171 172 9.431887 GCTATTATTAATTGAACATCTCCGGTA 57.568 33.333 0.00 0.00 0.00 4.02
172 173 7.390718 GGCTATTATTAATTGAACATCTCCGGT 59.609 37.037 0.00 0.00 0.00 5.28
173 174 7.607991 AGGCTATTATTAATTGAACATCTCCGG 59.392 37.037 0.00 0.00 0.00 5.14
174 175 8.553459 AGGCTATTATTAATTGAACATCTCCG 57.447 34.615 0.00 0.00 0.00 4.63
222 223 3.496331 CCTGAGAGCCTTTTAAAACCCA 58.504 45.455 0.00 0.00 0.00 4.51
227 228 1.427368 TGCCCCTGAGAGCCTTTTAAA 59.573 47.619 0.00 0.00 0.00 1.52
258 259 1.583054 CCTTGCCTATAACGCCACTC 58.417 55.000 0.00 0.00 0.00 3.51
267 268 1.340248 GCTACAGACGCCTTGCCTATA 59.660 52.381 0.00 0.00 0.00 1.31
273 274 1.195448 CAAACAGCTACAGACGCCTTG 59.805 52.381 0.00 0.00 0.00 3.61
286 287 1.605710 CCGATGATCATCCCAAACAGC 59.394 52.381 26.30 2.99 34.40 4.40
290 291 5.308014 CAATAGACCGATGATCATCCCAAA 58.692 41.667 26.30 11.36 34.40 3.28
302 305 1.746517 GACCGCCCAATAGACCGAT 59.253 57.895 0.00 0.00 0.00 4.18
320 323 0.825010 GCCCAAGTCAGGCCATATGG 60.825 60.000 18.07 18.07 45.16 2.74
332 335 0.109342 CCACAGAGACAAGCCCAAGT 59.891 55.000 0.00 0.00 0.00 3.16
339 342 2.738846 CCGACAAATCCACAGAGACAAG 59.261 50.000 0.00 0.00 0.00 3.16
348 351 2.482721 CCACTAACACCGACAAATCCAC 59.517 50.000 0.00 0.00 0.00 4.02
357 360 0.599558 CCGAAGTCCACTAACACCGA 59.400 55.000 0.00 0.00 0.00 4.69
365 368 1.152312 ACCTCCACCGAAGTCCACT 60.152 57.895 0.00 0.00 0.00 4.00
389 392 5.968528 ACATCGCAAATAAACCCTTAACA 57.031 34.783 0.00 0.00 0.00 2.41
390 393 7.080353 ACTACATCGCAAATAAACCCTTAAC 57.920 36.000 0.00 0.00 0.00 2.01
394 397 5.985911 ACTACTACATCGCAAATAAACCCT 58.014 37.500 0.00 0.00 0.00 4.34
401 404 4.876107 CCTCCAAACTACTACATCGCAAAT 59.124 41.667 0.00 0.00 0.00 2.32
406 409 3.376234 TCGACCTCCAAACTACTACATCG 59.624 47.826 0.00 0.00 0.00 3.84
407 410 4.978083 TCGACCTCCAAACTACTACATC 57.022 45.455 0.00 0.00 0.00 3.06
426 588 2.126071 AACACGGAGCGACCATCG 60.126 61.111 4.10 0.00 43.89 3.84
435 597 0.380378 CAAACACACCCAACACGGAG 59.620 55.000 0.00 0.00 36.56 4.63
437 599 1.332375 CTACAAACACACCCAACACGG 59.668 52.381 0.00 0.00 0.00 4.94
462 624 0.737715 AACTCCAGAAGCGCACGATC 60.738 55.000 11.47 1.85 0.00 3.69
474 636 1.066358 TCAGAGAGCATGCAACTCCAG 60.066 52.381 28.50 23.51 34.56 3.86
477 639 2.383368 ACTCAGAGAGCATGCAACTC 57.617 50.000 26.46 26.46 32.04 3.01
507 669 4.070009 GAGAAAACCGGTACAACCAATCT 58.930 43.478 8.00 2.73 38.47 2.40
508 670 3.189910 GGAGAAAACCGGTACAACCAATC 59.810 47.826 8.00 0.00 38.47 2.67
523 686 9.902196 GTTAATTAACAGAAAATCGGGAGAAAA 57.098 29.630 20.95 0.00 38.09 2.29
528 691 7.120138 GTGGAGTTAATTAACAGAAAATCGGGA 59.880 37.037 26.06 3.58 38.62 5.14
529 692 7.094549 TGTGGAGTTAATTAACAGAAAATCGGG 60.095 37.037 26.06 0.00 38.62 5.14
531 694 9.840427 ATTGTGGAGTTAATTAACAGAAAATCG 57.160 29.630 26.06 0.00 38.62 3.34
539 702 9.793259 AGAAGAGAATTGTGGAGTTAATTAACA 57.207 29.630 26.06 6.94 38.62 2.41
543 706 6.944862 AGCAGAAGAGAATTGTGGAGTTAATT 59.055 34.615 0.00 0.00 0.00 1.40
565 728 8.946085 AGATTTGACTCGTTGATTAATTAAGCA 58.054 29.630 11.99 11.99 0.00 3.91
578 741 4.489679 GAGGCAAAAGATTTGACTCGTT 57.510 40.909 19.60 0.00 43.76 3.85
582 745 3.532641 AGGGAGGCAAAAGATTTGACT 57.467 42.857 10.82 10.82 41.23 3.41
584 747 6.739331 TTTAAAGGGAGGCAAAAGATTTGA 57.261 33.333 6.99 0.00 0.00 2.69
605 768 9.983804 GAGGATCGTCTCGTTTATTTTATTTTT 57.016 29.630 8.17 0.00 0.00 1.94
606 769 8.610035 GGAGGATCGTCTCGTTTATTTTATTTT 58.390 33.333 14.65 0.00 34.37 1.82
607 770 7.226128 GGGAGGATCGTCTCGTTTATTTTATTT 59.774 37.037 14.65 0.00 34.37 1.40
608 771 6.704937 GGGAGGATCGTCTCGTTTATTTTATT 59.295 38.462 14.65 0.00 34.37 1.40
609 772 6.041751 AGGGAGGATCGTCTCGTTTATTTTAT 59.958 38.462 14.65 0.00 34.37 1.40
610 773 5.361857 AGGGAGGATCGTCTCGTTTATTTTA 59.638 40.000 14.65 0.00 34.37 1.52
611 774 4.161754 AGGGAGGATCGTCTCGTTTATTTT 59.838 41.667 14.65 0.00 34.37 1.82
612 775 3.705072 AGGGAGGATCGTCTCGTTTATTT 59.295 43.478 14.65 0.00 34.37 1.40
613 776 3.068307 CAGGGAGGATCGTCTCGTTTATT 59.932 47.826 14.65 0.00 34.37 1.40
615 778 2.022195 CAGGGAGGATCGTCTCGTTTA 58.978 52.381 14.65 0.00 34.37 2.01
619 782 2.725008 GCAGGGAGGATCGTCTCG 59.275 66.667 14.65 8.65 34.37 4.04
620 783 1.791103 CTCGCAGGGAGGATCGTCTC 61.791 65.000 14.65 11.21 39.22 3.36
622 785 2.725008 CTCGCAGGGAGGATCGTC 59.275 66.667 6.88 6.88 39.22 4.20
639 802 2.807045 CGTGACTCTGTCGCAGGC 60.807 66.667 11.08 0.00 42.42 4.85
640 803 1.442857 GACGTGACTCTGTCGCAGG 60.443 63.158 11.08 0.00 42.42 4.85
641 804 0.317854 TTGACGTGACTCTGTCGCAG 60.318 55.000 11.08 1.02 42.42 5.18
642 805 0.594028 GTTGACGTGACTCTGTCGCA 60.594 55.000 11.08 0.00 42.42 5.10
646 809 1.399714 TCAGGTTGACGTGACTCTGT 58.600 50.000 0.00 0.00 36.04 3.41
647 810 2.128035 GTTCAGGTTGACGTGACTCTG 58.872 52.381 6.06 2.09 40.03 3.35
648 811 2.032620 AGTTCAGGTTGACGTGACTCT 58.967 47.619 6.06 5.73 40.03 3.24
649 812 2.510768 AGTTCAGGTTGACGTGACTC 57.489 50.000 6.06 3.84 40.03 3.36
650 813 2.936498 CAAAGTTCAGGTTGACGTGACT 59.064 45.455 6.06 5.05 40.03 3.41
651 814 2.933906 TCAAAGTTCAGGTTGACGTGAC 59.066 45.455 6.06 0.00 40.03 3.67
660 823 3.213206 TCAGCATGTCAAAGTTCAGGT 57.787 42.857 0.00 0.00 37.40 4.00
724 887 3.461773 GCGTGAGGCCCTCTGCTA 61.462 66.667 12.94 0.00 40.92 3.49
808 971 3.972276 TTGGTTTGCGCTTCGGGC 61.972 61.111 9.73 0.00 41.94 6.13
813 976 4.622456 CGCGGTTGGTTTGCGCTT 62.622 61.111 9.73 0.00 45.67 4.68
890 1073 1.395954 GAAATAGGTCGCGGTTGGTTC 59.604 52.381 6.13 0.00 0.00 3.62
1092 1937 2.781923 TGGTCCGCCATTATGATGATG 58.218 47.619 0.00 0.00 40.46 3.07
1444 2346 0.965866 AAGTCCTCCTGCGACGATGA 60.966 55.000 0.00 0.00 35.33 2.92
1445 2347 0.526524 GAAGTCCTCCTGCGACGATG 60.527 60.000 0.00 0.00 35.33 3.84
1446 2348 1.810532 GAAGTCCTCCTGCGACGAT 59.189 57.895 0.00 0.00 35.33 3.73
1480 2382 0.409484 AGGATTTGGGGGAGGTTGTG 59.591 55.000 0.00 0.00 0.00 3.33
1659 2618 4.504864 CCACCCACTGAATTTAGTCACTGA 60.505 45.833 0.00 0.00 0.00 3.41
1704 2671 8.504812 TCATTCTCTCCTCTCTATATCATTCG 57.495 38.462 0.00 0.00 0.00 3.34
1789 2814 5.492855 ACAATGTAGGTAGTAGTGCCAAA 57.507 39.130 7.49 0.00 0.00 3.28
1825 2858 2.026822 CAGATAGCACAGTCCCCACTTT 60.027 50.000 0.00 0.00 0.00 2.66
1934 2992 7.764141 TTTCATATGATCCCACCATTACATG 57.236 36.000 6.17 0.00 0.00 3.21
1935 2993 8.172070 TCATTTCATATGATCCCACCATTACAT 58.828 33.333 6.17 0.00 0.00 2.29
1936 2994 7.525165 TCATTTCATATGATCCCACCATTACA 58.475 34.615 6.17 0.00 0.00 2.41
1937 2995 8.585471 ATCATTTCATATGATCCCACCATTAC 57.415 34.615 6.17 0.00 33.86 1.89
1939 2997 9.604569 TTAATCATTTCATATGATCCCACCATT 57.395 29.630 6.17 2.43 37.75 3.16
1940 2998 9.778479 ATTAATCATTTCATATGATCCCACCAT 57.222 29.630 6.17 0.00 37.75 3.55
1941 2999 9.027202 CATTAATCATTTCATATGATCCCACCA 57.973 33.333 6.17 0.00 37.75 4.17
1942 3000 8.472413 CCATTAATCATTTCATATGATCCCACC 58.528 37.037 6.17 0.00 37.75 4.61
1943 3001 9.246670 TCCATTAATCATTTCATATGATCCCAC 57.753 33.333 6.17 0.00 37.75 4.61
1958 3016 5.704354 TGCATGGTAACCTCCATTAATCAT 58.296 37.500 0.00 0.00 44.75 2.45
1959 3017 5.122707 TGCATGGTAACCTCCATTAATCA 57.877 39.130 0.00 0.00 44.75 2.57
1960 3018 5.536161 ACATGCATGGTAACCTCCATTAATC 59.464 40.000 29.41 0.00 44.75 1.75
1961 3019 5.457686 ACATGCATGGTAACCTCCATTAAT 58.542 37.500 29.41 0.48 44.75 1.40
1963 3021 4.518278 ACATGCATGGTAACCTCCATTA 57.482 40.909 29.41 0.00 44.75 1.90
1966 3024 2.040947 TGAACATGCATGGTAACCTCCA 59.959 45.455 29.41 14.04 42.01 3.86
1967 3025 2.684881 CTGAACATGCATGGTAACCTCC 59.315 50.000 29.41 11.50 0.00 4.30
1968 3026 3.347216 ACTGAACATGCATGGTAACCTC 58.653 45.455 29.41 12.23 0.00 3.85
2024 3197 9.554724 CAAACTAACTAACATATGCGTTCAATT 57.445 29.630 1.58 0.00 0.00 2.32
2051 3224 8.909708 TTTGCTTTTTATGTGATGTATACAGC 57.090 30.769 14.20 14.20 0.00 4.40
2102 3280 4.382793 GGGTTCACTGGTTCTGTAGTATCC 60.383 50.000 0.00 0.00 0.00 2.59
2213 3467 3.960755 AGTCCCCTGTTTTCCTTGAAAAG 59.039 43.478 2.42 0.00 41.32 2.27
2952 5072 4.097135 CAGAAGAGTAGTCGATGTCATGGT 59.903 45.833 0.00 0.00 0.00 3.55
3427 5623 3.659786 TGAGTGTAGTATGTGTTGGTGC 58.340 45.455 0.00 0.00 0.00 5.01
3513 5710 9.330063 CACTGTCTATATGCAAAAGGAATAAGA 57.670 33.333 0.00 0.00 0.00 2.10
3515 5712 7.555914 TGCACTGTCTATATGCAAAAGGAATAA 59.444 33.333 0.00 0.00 45.96 1.40
3978 6213 9.890629 TTCAGTGCTCTTACATGTTTAGAATAT 57.109 29.630 2.30 0.00 0.00 1.28
3979 6214 9.371136 CTTCAGTGCTCTTACATGTTTAGAATA 57.629 33.333 2.30 0.00 0.00 1.75
4014 6790 9.725019 TCACAAATGAGTGTATCTTGTCTATTT 57.275 29.630 0.00 0.00 40.37 1.40
4017 6793 8.753133 AGATCACAAATGAGTGTATCTTGTCTA 58.247 33.333 0.00 0.00 38.57 2.59
4055 6884 5.357089 GCAATAATTATGCACGAATTTGCG 58.643 37.500 12.33 4.59 46.20 4.85
4129 6961 3.128415 CACACCATGCATATCGTCCAAAA 59.872 43.478 0.00 0.00 0.00 2.44
4172 7164 6.900568 GAAGATGCCTTCGATATAATCCAG 57.099 41.667 0.00 0.00 39.36 3.86
4213 7312 3.330405 TGTTCCAGATGACCATTTCAGGA 59.670 43.478 0.00 0.00 37.77 3.86
4215 7314 3.441572 GGTGTTCCAGATGACCATTTCAG 59.558 47.826 0.00 0.00 37.77 3.02
4316 9363 5.220491 GCGATTGAGAAGTGATTGAGGTTAC 60.220 44.000 0.00 0.00 0.00 2.50
4321 9368 3.264947 TGGCGATTGAGAAGTGATTGAG 58.735 45.455 0.00 0.00 0.00 3.02
4322 9369 3.333029 TGGCGATTGAGAAGTGATTGA 57.667 42.857 0.00 0.00 0.00 2.57
4323 9370 3.242969 CCATGGCGATTGAGAAGTGATTG 60.243 47.826 0.00 0.00 0.00 2.67
4324 9371 2.947652 CCATGGCGATTGAGAAGTGATT 59.052 45.455 0.00 0.00 0.00 2.57
4325 9372 2.569059 CCATGGCGATTGAGAAGTGAT 58.431 47.619 0.00 0.00 0.00 3.06
4326 9373 2.013563 GCCATGGCGATTGAGAAGTGA 61.014 52.381 23.48 0.00 0.00 3.41
4327 9374 0.379669 GCCATGGCGATTGAGAAGTG 59.620 55.000 23.48 0.00 0.00 3.16
4328 9375 0.749454 GGCCATGGCGATTGAGAAGT 60.749 55.000 29.90 0.00 43.06 3.01
4329 9376 1.450531 GGGCCATGGCGATTGAGAAG 61.451 60.000 29.90 0.00 43.06 2.85
4330 9377 1.453745 GGGCCATGGCGATTGAGAA 60.454 57.895 29.90 0.00 43.06 2.87
4331 9378 1.998444 ATGGGCCATGGCGATTGAGA 61.998 55.000 29.90 8.82 43.06 3.27
4394 9453 9.353999 GGTCTATTATGGACATTGTTTTTCAAC 57.646 33.333 10.71 0.00 38.97 3.18
4397 9456 8.062065 TGGGTCTATTATGGACATTGTTTTTC 57.938 34.615 10.71 0.00 35.61 2.29
4398 9457 8.608185 ATGGGTCTATTATGGACATTGTTTTT 57.392 30.769 10.71 0.00 35.61 1.94
4403 9462 7.666804 TGATCAATGGGTCTATTATGGACATTG 59.333 37.037 10.71 11.72 35.61 2.82
4417 9479 3.960571 CCCAGGATATGATCAATGGGTC 58.039 50.000 18.26 6.45 45.62 4.46
4429 9491 1.379776 AGCCATCATGCCCAGGATAT 58.620 50.000 0.00 0.00 29.85 1.63
4501 9566 4.504858 ACCTGATGGAAGTCGTCATAAAC 58.495 43.478 0.00 0.00 40.30 2.01
4502 9567 4.466370 AGACCTGATGGAAGTCGTCATAAA 59.534 41.667 0.00 0.00 40.30 1.40
4503 9568 4.023980 AGACCTGATGGAAGTCGTCATAA 58.976 43.478 0.00 0.00 40.30 1.90
4504 9569 3.632333 AGACCTGATGGAAGTCGTCATA 58.368 45.455 0.00 0.00 40.30 2.15
4505 9570 2.461695 AGACCTGATGGAAGTCGTCAT 58.538 47.619 0.00 0.00 40.30 3.06


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

AutoCloner maintained by Alex Coulton.