Multiple sequence alignment - TraesCS6A01G010100

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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 TraesCS6A01G010100 chr6A 100.000 6765 0 0 1 6765 4598507 4591743 0.000000e+00 12493.0
1 TraesCS6A01G010100 chr6A 93.241 2530 147 14 3210 5726 4771424 4768906 0.000000e+00 3703.0
2 TraesCS6A01G010100 chr6A 96.387 2242 66 7 557 2793 4773902 4771671 0.000000e+00 3677.0
3 TraesCS6A01G010100 chr6A 92.617 2086 136 11 3655 5726 4181373 4183454 0.000000e+00 2983.0
4 TraesCS6A01G010100 chr6A 92.474 2086 139 11 3655 5726 4207053 4209134 0.000000e+00 2966.0
5 TraesCS6A01G010100 chr6A 99.521 1043 5 0 5723 6765 4211351 4212393 0.000000e+00 1899.0
6 TraesCS6A01G010100 chr6A 99.425 1043 6 0 5723 6765 4160758 4161800 0.000000e+00 1893.0
7 TraesCS6A01G010100 chr6A 99.425 1043 6 0 5723 6765 4185586 4186628 0.000000e+00 1893.0
8 TraesCS6A01G010100 chr6A 93.192 1278 46 13 698 1948 4226960 4228223 0.000000e+00 1840.0
9 TraesCS6A01G010100 chr6A 93.114 1278 47 13 698 1948 4176476 4177739 0.000000e+00 1834.0
10 TraesCS6A01G010100 chr6A 92.958 1278 49 13 698 1948 4151582 4152845 0.000000e+00 1823.0
11 TraesCS6A01G010100 chr6A 92.958 1278 49 13 698 1948 4201716 4202979 0.000000e+00 1823.0
12 TraesCS6A01G010100 chr6A 99.550 667 3 0 6099 6765 4136356 4137022 0.000000e+00 1216.0
13 TraesCS6A01G010100 chr6A 97.133 593 12 3 5723 6311 4767932 4767341 0.000000e+00 996.0
14 TraesCS6A01G010100 chr6A 88.727 479 47 4 93 565 4614928 4614451 4.550000e-161 579.0
15 TraesCS6A01G010100 chr6A 85.348 273 30 3 284 548 4774227 4773957 2.400000e-69 274.0
16 TraesCS6A01G010100 chr6A 85.981 214 23 4 557 769 4614287 4614080 8.830000e-54 222.0
17 TraesCS6A01G010100 chr6D 91.169 2378 180 12 3356 5709 5179845 5177474 0.000000e+00 3201.0
18 TraesCS6A01G010100 chr6D 90.344 2382 196 16 3354 5709 5063452 5065825 0.000000e+00 3094.0
19 TraesCS6A01G010100 chr6D 90.923 2005 166 9 3731 5726 5367526 5365529 0.000000e+00 2680.0
20 TraesCS6A01G010100 chr6D 87.325 2067 219 20 3694 5726 5196873 5194816 0.000000e+00 2326.0
21 TraesCS6A01G010100 chr6D 85.804 2064 234 24 3694 5726 5151616 5149581 0.000000e+00 2134.0
22 TraesCS6A01G010100 chr6D 90.336 1428 108 4 589 2015 5058568 5059966 0.000000e+00 1845.0
23 TraesCS6A01G010100 chr6D 94.291 1051 48 6 5723 6765 5192687 5191641 0.000000e+00 1598.0
24 TraesCS6A01G010100 chr6D 88.531 1212 106 5 807 2015 5183658 5182477 0.000000e+00 1437.0
25 TraesCS6A01G010100 chr6D 92.243 954 66 4 3731 4681 5368586 5367638 0.000000e+00 1345.0
26 TraesCS6A01G010100 chr6D 85.276 1141 110 24 889 1998 5729581 5728468 0.000000e+00 1123.0
27 TraesCS6A01G010100 chr6D 87.772 965 90 17 5726 6667 5136515 5135556 0.000000e+00 1103.0
28 TraesCS6A01G010100 chr6D 87.854 601 60 10 2046 2637 5182490 5181894 0.000000e+00 693.0
29 TraesCS6A01G010100 chr6D 87.500 600 62 12 2046 2637 5059953 5060547 0.000000e+00 680.0
30 TraesCS6A01G010100 chr6D 94.390 410 21 2 5770 6178 5068076 5068484 4.450000e-176 628.0
31 TraesCS6A01G010100 chr6D 87.102 566 52 7 1 558 5057955 5058507 7.450000e-174 621.0
32 TraesCS6A01G010100 chr6D 94.984 319 12 1 6016 6334 5068601 5068915 1.310000e-136 497.0
33 TraesCS6A01G010100 chr6D 82.060 563 83 13 1 559 5437845 5437297 1.330000e-126 464.0
34 TraesCS6A01G010100 chr6D 94.118 306 12 6 6363 6665 5068912 5069214 1.720000e-125 460.0
35 TraesCS6A01G010100 chr6D 80.241 415 62 14 6264 6677 5363109 5362714 1.850000e-75 294.0
36 TraesCS6A01G010100 chr6D 88.442 199 15 5 557 750 5437255 5437060 4.080000e-57 233.0
37 TraesCS6A01G010100 chr6D 83.898 118 16 2 633 750 5436891 5436777 7.170000e-20 110.0
38 TraesCS6A01G010100 chr6D 86.207 58 6 2 3552 3607 162298038 162298095 2.040000e-05 62.1
39 TraesCS6A01G010100 chr6D 87.037 54 6 1 3552 3604 162297070 162297017 7.330000e-05 60.2
40 TraesCS6A01G010100 chr6B 87.042 2454 263 29 3305 5724 10727423 10724991 0.000000e+00 2719.0
41 TraesCS6A01G010100 chr6B 87.328 1089 121 10 816 1899 10730958 10729882 0.000000e+00 1230.0
42 TraesCS6A01G010100 chr6B 80.141 1279 221 25 560 1822 9791769 9790508 0.000000e+00 924.0
43 TraesCS6A01G010100 chr6B 88.612 562 41 13 1 558 9792360 9791818 0.000000e+00 662.0
44 TraesCS6A01G010100 chr6B 90.303 495 36 5 5726 6219 10722917 10722434 7.400000e-179 638.0
45 TraesCS6A01G010100 chr6B 86.530 438 47 8 121 551 9348306 9347874 7.940000e-129 472.0
46 TraesCS6A01G010100 chr6B 93.354 316 15 3 6456 6765 10722431 10722116 4.780000e-126 462.0
47 TraesCS6A01G010100 chr6B 79.487 663 85 24 2007 2637 10728705 10728062 2.260000e-114 424.0
48 TraesCS6A01G010100 chr6B 85.437 206 23 4 5718 5922 10058058 10058257 2.470000e-49 207.0
49 TraesCS6A01G010100 chr6B 95.935 123 5 0 628 750 9338115 9337993 4.140000e-47 200.0
50 TraesCS6A01G010100 chr6B 88.679 53 5 1 3553 3604 2796057 2796109 5.660000e-06 63.9
51 TraesCS6A01G010100 chr6B 100.000 28 0 0 557 584 9338162 9338135 1.200000e-02 52.8
52 TraesCS6A01G010100 chrUn 85.574 2544 314 28 3220 5720 87339641 87342174 0.000000e+00 2615.0
53 TraesCS6A01G010100 chrUn 85.123 2030 242 28 3733 5726 305210877 305212882 0.000000e+00 2021.0
54 TraesCS6A01G010100 chrUn 92.958 1278 49 13 698 1948 345034608 345035871 0.000000e+00 1823.0
55 TraesCS6A01G010100 chrUn 87.679 1185 136 6 816 1998 87336287 87337463 0.000000e+00 1371.0
56 TraesCS6A01G010100 chrUn 100.000 340 0 0 6426 6765 377972648 377972309 4.450000e-176 628.0
57 TraesCS6A01G010100 chrUn 89.848 394 28 4 177 558 364737473 364737866 4.710000e-136 496.0
58 TraesCS6A01G010100 chrUn 84.198 405 42 12 2007 2407 87338514 87338900 2.300000e-99 374.0
59 TraesCS6A01G010100 chrUn 81.337 359 34 8 6343 6688 325286090 325286428 1.870000e-65 261.0
60 TraesCS6A01G010100 chrUn 84.158 202 18 3 557 758 364737914 364738101 4.170000e-42 183.0
61 TraesCS6A01G010100 chr4A 90.351 228 22 0 2940 3167 390876388 390876615 3.970000e-77 300.0
62 TraesCS6A01G010100 chr4A 88.312 231 27 0 2940 3170 390906759 390906989 1.860000e-70 278.0
63 TraesCS6A01G010100 chr4A 92.647 68 5 0 2871 2938 390876184 390876251 1.550000e-16 99.0
64 TraesCS6A01G010100 chr7B 88.511 235 26 1 2940 3173 615663012 615662778 3.990000e-72 283.0
65 TraesCS6A01G010100 chr7B 96.491 57 2 0 6690 6746 562372112 562372168 2.010000e-15 95.3
66 TraesCS6A01G010100 chr7B 89.552 67 7 0 2870 2936 720696374 720696440 1.210000e-12 86.1
67 TraesCS6A01G010100 chr7B 80.198 101 15 4 2246 2344 32124084 32123987 3.380000e-08 71.3
68 TraesCS6A01G010100 chr2B 88.085 235 27 1 2940 3174 717876079 717876312 1.860000e-70 278.0
69 TraesCS6A01G010100 chr2B 78.676 136 27 2 1573 1707 798158625 798158491 9.340000e-14 89.8
70 TraesCS6A01G010100 chr2B 77.698 139 31 0 1569 1707 798194767 798194629 1.210000e-12 86.1
71 TraesCS6A01G010100 chr2B 88.235 68 6 1 2868 2935 647385886 647385951 5.620000e-11 80.5
72 TraesCS6A01G010100 chr5B 87.983 233 28 0 2940 3172 491030045 491029813 6.680000e-70 276.0
73 TraesCS6A01G010100 chr5B 92.063 63 5 0 2870 2932 491030189 491030127 9.340000e-14 89.8
74 TraesCS6A01G010100 chr5B 90.323 62 6 0 2873 2934 6919845 6919784 1.560000e-11 82.4
75 TraesCS6A01G010100 chr2D 86.076 237 33 0 2940 3176 628983541 628983305 8.710000e-64 255.0
76 TraesCS6A01G010100 chr2D 77.698 139 31 0 1569 1707 639363501 639363363 1.210000e-12 86.1
77 TraesCS6A01G010100 chr2D 91.379 58 5 0 6690 6747 29833275 29833218 5.620000e-11 80.5
78 TraesCS6A01G010100 chr3A 85.774 239 32 2 2936 3173 20999821 21000058 1.130000e-62 252.0
79 TraesCS6A01G010100 chr3A 97.959 49 1 0 2870 2918 12149604 12149556 1.210000e-12 86.1
80 TraesCS6A01G010100 chr2A 85.593 236 34 0 2941 3176 765290149 765289914 1.460000e-61 248.0
81 TraesCS6A01G010100 chr2A 80.189 106 19 2 2240 2344 766884314 766884210 2.020000e-10 78.7
82 TraesCS6A01G010100 chr3D 85.356 239 33 2 2940 3177 561088780 561089017 5.240000e-61 246.0
83 TraesCS6A01G010100 chr3D 97.959 49 1 0 2870 2918 561088634 561088682 1.210000e-12 86.1
84 TraesCS6A01G010100 chr3D 87.692 65 5 3 2448 2512 90177162 90177223 9.410000e-09 73.1
85 TraesCS6A01G010100 chr3D 95.122 41 2 0 2304 2344 77350138 77350178 1.570000e-06 65.8
86 TraesCS6A01G010100 chr5A 90.769 65 6 0 2870 2934 18815424 18815488 3.360000e-13 87.9
87 TraesCS6A01G010100 chr7A 95.918 49 2 0 2870 2918 686005107 686005155 5.620000e-11 80.5
88 TraesCS6A01G010100 chr1B 88.679 53 5 1 3553 3604 679367122 679367174 5.660000e-06 63.9
89 TraesCS6A01G010100 chr1D 86.792 53 7 0 3553 3605 233311697 233311645 7.330000e-05 60.2


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 TraesCS6A01G010100 chr6A 4591743 4598507 6764 True 12493.000000 12493 100.000000 1 6765 1 chr6A.!!$R1 6764
1 TraesCS6A01G010100 chr6A 4207053 4212393 5340 False 2432.500000 2966 95.997500 3655 6765 2 chr6A.!!$F7 3110
2 TraesCS6A01G010100 chr6A 4176476 4186628 10152 False 2236.666667 2983 95.052000 698 6765 3 chr6A.!!$F6 6067
3 TraesCS6A01G010100 chr6A 4767341 4774227 6886 True 2162.500000 3703 93.027250 284 6311 4 chr6A.!!$R3 6027
4 TraesCS6A01G010100 chr6A 4160758 4161800 1042 False 1893.000000 1893 99.425000 5723 6765 1 chr6A.!!$F3 1042
5 TraesCS6A01G010100 chr6A 4226960 4228223 1263 False 1840.000000 1840 93.192000 698 1948 1 chr6A.!!$F5 1250
6 TraesCS6A01G010100 chr6A 4151582 4152845 1263 False 1823.000000 1823 92.958000 698 1948 1 chr6A.!!$F2 1250
7 TraesCS6A01G010100 chr6A 4201716 4202979 1263 False 1823.000000 1823 92.958000 698 1948 1 chr6A.!!$F4 1250
8 TraesCS6A01G010100 chr6A 4136356 4137022 666 False 1216.000000 1216 99.550000 6099 6765 1 chr6A.!!$F1 666
9 TraesCS6A01G010100 chr6A 4614080 4614928 848 True 400.500000 579 87.354000 93 769 2 chr6A.!!$R2 676
10 TraesCS6A01G010100 chr6D 5149581 5151616 2035 True 2134.000000 2134 85.804000 3694 5726 1 chr6D.!!$R2 2032
11 TraesCS6A01G010100 chr6D 5191641 5196873 5232 True 1962.000000 2326 90.808000 3694 6765 2 chr6D.!!$R6 3071
12 TraesCS6A01G010100 chr6D 5177474 5183658 6184 True 1777.000000 3201 89.184667 807 5709 3 chr6D.!!$R5 4902
13 TraesCS6A01G010100 chr6D 5362714 5368586 5872 True 1439.666667 2680 87.802333 3731 6677 3 chr6D.!!$R7 2946
14 TraesCS6A01G010100 chr6D 5728468 5729581 1113 True 1123.000000 1123 85.276000 889 1998 1 chr6D.!!$R3 1109
15 TraesCS6A01G010100 chr6D 5057955 5069214 11259 False 1117.857143 3094 91.253429 1 6665 7 chr6D.!!$F2 6664
16 TraesCS6A01G010100 chr6D 5135556 5136515 959 True 1103.000000 1103 87.772000 5726 6667 1 chr6D.!!$R1 941
17 TraesCS6A01G010100 chr6D 5436777 5437845 1068 True 269.000000 464 84.800000 1 750 3 chr6D.!!$R8 749
18 TraesCS6A01G010100 chr6B 10722116 10730958 8842 True 1094.600000 2719 87.502800 816 6765 5 chr6B.!!$R4 5949
19 TraesCS6A01G010100 chr6B 9790508 9792360 1852 True 793.000000 924 84.376500 1 1822 2 chr6B.!!$R3 1821
20 TraesCS6A01G010100 chrUn 305210877 305212882 2005 False 2021.000000 2021 85.123000 3733 5726 1 chrUn.!!$F1 1993
21 TraesCS6A01G010100 chrUn 345034608 345035871 1263 False 1823.000000 1823 92.958000 698 1948 1 chrUn.!!$F3 1250
22 TraesCS6A01G010100 chrUn 87336287 87342174 5887 False 1453.333333 2615 85.817000 816 5720 3 chrUn.!!$F4 4904
23 TraesCS6A01G010100 chrUn 364737473 364738101 628 False 339.500000 496 87.003000 177 758 2 chrUn.!!$F5 581

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
486 534 0.105039 CGGTCCCTAGTGCTCCAATC 59.895 60.0 0.00 0.0 0.00 2.67 F
526 586 0.108709 TCAAAATTGCCGCTCCATGC 60.109 50.0 0.00 0.0 38.57 4.06 F
2029 5932 0.734309 TGCCAAGCTATCAATGCACG 59.266 50.0 0.00 0.0 0.00 5.34 F
2986 8317 0.109132 CGGAAGGATGCTTTTGCCAC 60.109 55.0 0.00 0.0 46.87 5.01 F
3127 9004 0.038599 GGGGGAATGGTAAACACGGT 59.961 55.0 0.00 0.0 0.00 4.83 F
4124 12028 0.189574 TGAGGCCATTGGTTTTGGGA 59.810 50.0 5.01 0.0 34.66 4.37 F
4622 12541 0.673333 TGTAGACTGCCGTGCCAATG 60.673 55.0 0.00 0.0 0.00 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 2241 2.233922 TGTCTTCCTTAGTGTAGCTGGC 59.766 50.000 0.00 0.00 0.00 4.85 R
2508 6447 0.321298 TGTAGGCAGCCGGTTTCTTC 60.321 55.000 5.55 0.00 0.00 2.87 R
3108 8985 0.038599 ACCGTGTTTACCATTCCCCC 59.961 55.000 0.00 0.00 0.00 5.40 R
3991 10798 0.321671 TGGTAGTCACTTCAGCAGGC 59.678 55.000 0.00 0.00 0.00 4.85 R
4823 12743 0.533755 GGCGGCAGCTCACTTATCAT 60.534 55.000 9.17 0.00 44.37 2.45 R
5045 12965 1.005097 AGATTCCACCAGAGCATTGCA 59.995 47.619 11.91 0.00 0.00 4.08 R
6409 19759 1.609932 GTGTCGTTGAATGCATGCAG 58.390 50.000 26.69 11.27 0.00 4.41 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
34 35 4.621510 GCCCATGTGAAAATCTTCTTTCCC 60.622 45.833 0.00 0.00 34.91 3.97
45 46 8.768501 AAAATCTTCTTTCCCCATTATCTACC 57.231 34.615 0.00 0.00 0.00 3.18
47 48 6.248569 TCTTCTTTCCCCATTATCTACCAC 57.751 41.667 0.00 0.00 0.00 4.16
68 69 4.021894 CACAATCCTTCTATAGAGGGTCCG 60.022 50.000 25.60 17.94 41.55 4.79
74 75 4.944930 CCTTCTATAGAGGGTCCGATAGTG 59.055 50.000 20.27 0.00 36.63 2.74
76 77 5.837770 TCTATAGAGGGTCCGATAGTGAA 57.162 43.478 0.00 0.00 0.00 3.18
152 153 6.998074 ACAACACCTTTAAGAGAATCATGACA 59.002 34.615 0.00 0.00 37.82 3.58
190 196 4.142687 GGTTCAACAAATGGAGGACATACG 60.143 45.833 0.00 0.00 39.40 3.06
311 340 9.667107 TTGTGTCTGCTAGCTAATATTAAAAGT 57.333 29.630 17.23 0.00 0.00 2.66
330 359 3.424703 AGTACAACCTCGGTAGCAACTA 58.575 45.455 0.00 0.00 0.00 2.24
354 383 2.047179 GACAGCCCCACCGAGAAC 60.047 66.667 0.00 0.00 0.00 3.01
371 401 6.812160 ACCGAGAACACTTTGATATTGTAGTC 59.188 38.462 0.00 0.00 0.00 2.59
384 414 7.977904 TGATATTGTAGTCTTGCACAAATCTG 58.022 34.615 0.00 0.00 38.11 2.90
398 428 5.696822 CACAAATCTGGAGACTGTTTCATG 58.303 41.667 0.54 0.00 0.00 3.07
468 501 2.478894 CCTGGTAGCAAGTAACAACACG 59.521 50.000 0.00 0.00 0.00 4.49
486 534 0.105039 CGGTCCCTAGTGCTCCAATC 59.895 60.000 0.00 0.00 0.00 2.67
526 586 0.108709 TCAAAATTGCCGCTCCATGC 60.109 50.000 0.00 0.00 38.57 4.06
551 611 7.698130 GCATATACACTTCAGTTTTGAACCATC 59.302 37.037 0.00 0.00 38.37 3.51
634 906 0.784778 GTCTGACAGTGCGCACTAAC 59.215 55.000 40.17 32.81 40.20 2.34
686 958 0.894835 TAGAGATGCTTGGCACGTGA 59.105 50.000 22.23 0.00 43.04 4.35
1638 1988 4.223477 ACCCTTGCAAAAGCATTGTATGAT 59.777 37.500 0.00 0.00 0.00 2.45
1873 2241 3.136443 TCTTTATGTCACCTATGCCCAGG 59.864 47.826 0.00 0.00 41.87 4.45
1874 2242 0.764890 TATGTCACCTATGCCCAGGC 59.235 55.000 0.38 0.38 39.53 4.85
1875 2243 1.999634 ATGTCACCTATGCCCAGGCC 62.000 60.000 6.14 0.00 39.53 5.19
1876 2244 2.286045 TCACCTATGCCCAGGCCA 60.286 61.111 5.01 0.00 39.53 5.36
2025 5928 5.922739 TTACGTATGCCAAGCTATCAATG 57.077 39.130 0.00 0.00 0.00 2.82
2029 5932 0.734309 TGCCAAGCTATCAATGCACG 59.266 50.000 0.00 0.00 0.00 5.34
2118 6024 6.257849 TCAAGATTAATACCAACAGTCGCATC 59.742 38.462 0.00 0.00 0.00 3.91
2170 6103 4.567159 CGGTCAACTATCTCTAGTTTTGCC 59.433 45.833 0.00 0.00 44.07 4.52
2175 6108 6.426937 TCAACTATCTCTAGTTTTGCCACAAC 59.573 38.462 0.00 0.00 44.07 3.32
2286 6224 3.153919 GGGCTAGTGGTCACAAAAATCA 58.846 45.455 3.82 0.00 0.00 2.57
2508 6447 5.770162 CAGGTAGGGCCCAAATATTTTCTAG 59.230 44.000 27.56 0.00 38.26 2.43
2516 6455 7.265673 GGCCCAAATATTTTCTAGAAGAAACC 58.734 38.462 5.12 0.00 43.25 3.27
2813 6854 0.547553 AATATTTGTACGCCCCGGGT 59.452 50.000 21.85 2.88 0.00 5.28
2852 6893 6.757010 ACATTGTGCACTGTAGCTATAGTTAC 59.243 38.462 19.45 19.54 34.99 2.50
2861 6902 6.896307 ACTGTAGCTATAGTTACTGAAGGGTT 59.104 38.462 28.27 11.28 35.42 4.11
2862 6903 7.399478 ACTGTAGCTATAGTTACTGAAGGGTTT 59.601 37.037 28.27 10.76 35.42 3.27
2863 6904 8.142485 TGTAGCTATAGTTACTGAAGGGTTTT 57.858 34.615 22.52 0.00 33.63 2.43
2864 6905 8.038944 TGTAGCTATAGTTACTGAAGGGTTTTG 58.961 37.037 22.52 0.00 33.63 2.44
2867 8198 6.035758 GCTATAGTTACTGAAGGGTTTTGACG 59.964 42.308 0.84 0.00 0.00 4.35
2870 8201 1.578583 ACTGAAGGGTTTTGACGTCG 58.421 50.000 11.62 0.00 0.00 5.12
2874 8205 3.207778 TGAAGGGTTTTGACGTCGAAAT 58.792 40.909 28.84 16.14 32.39 2.17
2883 8214 7.208429 GGTTTTGACGTCGAAATTTAAAATCG 58.792 34.615 28.84 16.38 37.90 3.34
2884 8215 7.111870 GGTTTTGACGTCGAAATTTAAAATCGA 59.888 33.333 28.84 19.49 42.71 3.59
2885 8216 8.462938 GTTTTGACGTCGAAATTTAAAATCGAA 58.537 29.630 28.84 10.91 45.92 3.71
2886 8217 8.544409 TTTGACGTCGAAATTTAAAATCGAAA 57.456 26.923 22.96 14.73 45.92 3.46
2887 8218 8.716619 TTGACGTCGAAATTTAAAATCGAAAT 57.283 26.923 22.96 16.67 45.92 2.17
2888 8219 8.716619 TGACGTCGAAATTTAAAATCGAAATT 57.283 26.923 22.96 14.11 45.92 1.82
2889 8220 9.171701 TGACGTCGAAATTTAAAATCGAAATTT 57.828 25.926 22.96 12.37 45.92 1.82
2890 8221 9.431044 GACGTCGAAATTTAAAATCGAAATTTG 57.569 29.630 22.96 15.51 45.92 2.32
2891 8222 9.171701 ACGTCGAAATTTAAAATCGAAATTTGA 57.828 25.926 22.96 5.41 45.92 2.69
2892 8223 9.981943 CGTCGAAATTTAAAATCGAAATTTGAA 57.018 25.926 22.96 7.76 45.92 2.69
2924 8255 7.925703 ATTTTTGACGTCGATATAGATTCGT 57.074 32.000 11.62 1.97 37.82 3.85
2925 8256 6.727569 TTTTGACGTCGATATAGATTCGTG 57.272 37.500 11.62 0.00 37.82 4.35
2929 8260 5.679792 TGACGTCGATATAGATTCGTGTTTG 59.320 40.000 11.62 0.00 37.82 2.93
2931 8262 5.680229 ACGTCGATATAGATTCGTGTTTGAC 59.320 40.000 0.00 0.00 37.82 3.18
2932 8263 5.907945 CGTCGATATAGATTCGTGTTTGACT 59.092 40.000 0.00 0.00 37.82 3.41
2933 8264 6.085198 CGTCGATATAGATTCGTGTTTGACTC 59.915 42.308 0.00 0.00 37.82 3.36
2934 8265 6.910972 GTCGATATAGATTCGTGTTTGACTCA 59.089 38.462 0.00 0.00 37.82 3.41
2935 8266 7.431376 GTCGATATAGATTCGTGTTTGACTCAA 59.569 37.037 0.00 0.00 37.82 3.02
2936 8267 7.644157 TCGATATAGATTCGTGTTTGACTCAAG 59.356 37.037 0.00 0.00 37.82 3.02
2938 8269 9.469807 GATATAGATTCGTGTTTGACTCAAGAT 57.530 33.333 0.00 0.00 0.00 2.40
2939 8270 7.763172 ATAGATTCGTGTTTGACTCAAGATC 57.237 36.000 0.00 0.00 0.00 2.75
2940 8271 5.541845 AGATTCGTGTTTGACTCAAGATCA 58.458 37.500 0.00 0.00 0.00 2.92
2941 8272 5.636965 AGATTCGTGTTTGACTCAAGATCAG 59.363 40.000 0.00 0.00 0.00 2.90
2942 8273 4.584327 TCGTGTTTGACTCAAGATCAGA 57.416 40.909 0.00 0.00 0.00 3.27
2943 8274 4.299155 TCGTGTTTGACTCAAGATCAGAC 58.701 43.478 0.00 0.00 33.04 3.51
2944 8275 4.038042 TCGTGTTTGACTCAAGATCAGACT 59.962 41.667 0.00 0.00 33.47 3.24
2945 8276 4.384247 CGTGTTTGACTCAAGATCAGACTC 59.616 45.833 0.00 0.00 33.47 3.36
2946 8277 4.384247 GTGTTTGACTCAAGATCAGACTCG 59.616 45.833 0.00 0.00 33.47 4.18
2948 8279 5.221244 TGTTTGACTCAAGATCAGACTCGAA 60.221 40.000 0.00 0.00 33.47 3.71
2949 8280 4.427096 TGACTCAAGATCAGACTCGAAC 57.573 45.455 0.00 0.00 0.00 3.95
2950 8281 3.191581 TGACTCAAGATCAGACTCGAACC 59.808 47.826 0.00 0.00 0.00 3.62
2951 8282 3.157881 ACTCAAGATCAGACTCGAACCA 58.842 45.455 0.00 0.00 0.00 3.67
2952 8283 3.192422 ACTCAAGATCAGACTCGAACCAG 59.808 47.826 0.00 0.00 0.00 4.00
2953 8284 2.094494 TCAAGATCAGACTCGAACCAGC 60.094 50.000 0.00 0.00 0.00 4.85
2955 8286 0.452184 GATCAGACTCGAACCAGCGA 59.548 55.000 0.00 0.00 38.74 4.93
2956 8287 0.171455 ATCAGACTCGAACCAGCGAC 59.829 55.000 0.00 0.00 36.17 5.19
2957 8288 0.889638 TCAGACTCGAACCAGCGACT 60.890 55.000 0.00 0.00 36.17 4.18
2959 8290 1.088306 AGACTCGAACCAGCGACTAG 58.912 55.000 0.00 0.00 36.17 2.57
2980 8311 2.871096 TGGTAACGGAAGGATGCTTT 57.129 45.000 0.00 0.00 42.51 3.51
2981 8312 3.149005 TGGTAACGGAAGGATGCTTTT 57.851 42.857 0.00 0.00 42.51 2.27
2984 8315 0.603065 AACGGAAGGATGCTTTTGCC 59.397 50.000 0.00 0.00 46.87 4.52
2986 8317 0.109132 CGGAAGGATGCTTTTGCCAC 60.109 55.000 0.00 0.00 46.87 5.01
2987 8318 1.260544 GGAAGGATGCTTTTGCCACT 58.739 50.000 0.00 0.00 46.87 4.00
2989 8320 2.424956 GGAAGGATGCTTTTGCCACTAG 59.575 50.000 0.00 0.00 46.87 2.57
2990 8321 2.134789 AGGATGCTTTTGCCACTAGG 57.865 50.000 0.00 0.00 46.87 3.02
3001 8332 2.992476 CCACTAGGCCACTACCTGT 58.008 57.895 5.01 0.00 41.34 4.00
3002 8333 0.824759 CCACTAGGCCACTACCTGTC 59.175 60.000 5.01 0.00 41.34 3.51
3005 8336 0.456221 CTAGGCCACTACCTGTCGTG 59.544 60.000 5.01 0.00 41.34 4.35
3006 8337 0.251474 TAGGCCACTACCTGTCGTGT 60.251 55.000 5.01 0.00 41.34 4.49
3007 8338 1.119574 AGGCCACTACCTGTCGTGTT 61.120 55.000 5.01 0.00 39.13 3.32
3008 8339 0.949105 GGCCACTACCTGTCGTGTTG 60.949 60.000 0.00 0.00 0.00 3.33
3009 8340 0.249741 GCCACTACCTGTCGTGTTGT 60.250 55.000 1.92 0.00 0.00 3.32
3010 8341 1.779569 CCACTACCTGTCGTGTTGTC 58.220 55.000 1.92 0.00 0.00 3.18
3012 8343 2.288825 CCACTACCTGTCGTGTTGTCAT 60.289 50.000 1.92 0.00 0.00 3.06
3014 8345 4.166523 CACTACCTGTCGTGTTGTCATAG 58.833 47.826 0.00 0.00 0.00 2.23
3017 8348 3.914312 ACCTGTCGTGTTGTCATAGAAG 58.086 45.455 0.00 0.00 0.00 2.85
3018 8349 3.321111 ACCTGTCGTGTTGTCATAGAAGT 59.679 43.478 0.00 0.00 0.00 3.01
3019 8350 3.675225 CCTGTCGTGTTGTCATAGAAGTG 59.325 47.826 0.00 0.00 0.00 3.16
3022 8353 4.923281 TGTCGTGTTGTCATAGAAGTGATG 59.077 41.667 0.00 0.00 0.00 3.07
3023 8354 4.327357 GTCGTGTTGTCATAGAAGTGATGG 59.673 45.833 0.00 0.00 0.00 3.51
3025 8356 4.091945 CGTGTTGTCATAGAAGTGATGGTG 59.908 45.833 0.00 0.00 0.00 4.17
3027 8358 5.120830 GTGTTGTCATAGAAGTGATGGTGTC 59.879 44.000 0.00 0.00 0.00 3.67
3029 8360 6.210584 TGTTGTCATAGAAGTGATGGTGTCTA 59.789 38.462 0.00 0.00 0.00 2.59
3030 8361 7.093333 TGTTGTCATAGAAGTGATGGTGTCTAT 60.093 37.037 0.00 0.00 34.38 1.98
3031 8362 7.423844 TGTCATAGAAGTGATGGTGTCTATT 57.576 36.000 0.00 0.00 32.26 1.73
3032 8363 7.851228 TGTCATAGAAGTGATGGTGTCTATTT 58.149 34.615 0.00 0.00 32.26 1.40
3034 8365 9.817809 GTCATAGAAGTGATGGTGTCTATTTAA 57.182 33.333 0.00 0.00 32.26 1.52
3035 8366 9.817809 TCATAGAAGTGATGGTGTCTATTTAAC 57.182 33.333 0.00 0.00 32.26 2.01
3036 8367 9.046296 CATAGAAGTGATGGTGTCTATTTAACC 57.954 37.037 0.00 0.00 32.26 2.85
3038 8369 7.106239 AGAAGTGATGGTGTCTATTTAACCAG 58.894 38.462 0.00 0.00 46.68 4.00
3040 8371 6.407202 AGTGATGGTGTCTATTTAACCAGAC 58.593 40.000 8.18 8.18 46.68 3.51
3047 8378 6.985188 TGTCTATTTAACCAGACAATGAGC 57.015 37.500 13.44 0.00 46.13 4.26
3048 8379 5.580691 TGTCTATTTAACCAGACAATGAGCG 59.419 40.000 13.44 0.00 46.13 5.03
3049 8380 5.581085 GTCTATTTAACCAGACAATGAGCGT 59.419 40.000 9.70 0.00 40.74 5.07
3050 8381 6.092259 GTCTATTTAACCAGACAATGAGCGTT 59.908 38.462 9.70 0.00 40.74 4.84
3051 8382 5.705609 ATTTAACCAGACAATGAGCGTTT 57.294 34.783 0.00 0.00 0.00 3.60
3052 8383 4.481930 TTAACCAGACAATGAGCGTTTG 57.518 40.909 0.00 0.00 0.00 2.93
3059 8936 5.214417 CAGACAATGAGCGTTTGAATTCAA 58.786 37.500 16.91 16.91 0.00 2.69
3066 8943 8.885108 CAATGAGCGTTTGAATTCAAAAATTTC 58.115 29.630 30.07 23.50 46.08 2.17
3113 8990 2.667348 GAGTGTTTCTCGAGGGGGA 58.333 57.895 13.56 0.00 33.25 4.81
3114 8991 0.974383 GAGTGTTTCTCGAGGGGGAA 59.026 55.000 13.56 0.00 33.25 3.97
3115 8992 1.555533 GAGTGTTTCTCGAGGGGGAAT 59.444 52.381 13.56 0.00 33.25 3.01
3116 8993 1.279271 AGTGTTTCTCGAGGGGGAATG 59.721 52.381 13.56 0.00 0.00 2.67
3117 8994 0.618458 TGTTTCTCGAGGGGGAATGG 59.382 55.000 13.56 0.00 0.00 3.16
3118 8995 0.618981 GTTTCTCGAGGGGGAATGGT 59.381 55.000 13.56 0.00 0.00 3.55
3119 8996 1.835531 GTTTCTCGAGGGGGAATGGTA 59.164 52.381 13.56 0.00 0.00 3.25
3120 8997 2.237893 GTTTCTCGAGGGGGAATGGTAA 59.762 50.000 13.56 0.00 0.00 2.85
3121 8998 2.257391 TCTCGAGGGGGAATGGTAAA 57.743 50.000 13.56 0.00 0.00 2.01
3122 8999 1.835531 TCTCGAGGGGGAATGGTAAAC 59.164 52.381 13.56 0.00 0.00 2.01
3123 9000 1.557832 CTCGAGGGGGAATGGTAAACA 59.442 52.381 3.91 0.00 0.00 2.83
3124 9001 1.279846 TCGAGGGGGAATGGTAAACAC 59.720 52.381 0.00 0.00 0.00 3.32
3125 9002 1.746470 GAGGGGGAATGGTAAACACG 58.254 55.000 0.00 0.00 0.00 4.49
3126 9003 0.330267 AGGGGGAATGGTAAACACGG 59.670 55.000 0.00 0.00 0.00 4.94
3127 9004 0.038599 GGGGGAATGGTAAACACGGT 59.961 55.000 0.00 0.00 0.00 4.83
3128 9005 1.281577 GGGGGAATGGTAAACACGGTA 59.718 52.381 0.00 0.00 0.00 4.02
3129 9006 2.290832 GGGGGAATGGTAAACACGGTAA 60.291 50.000 0.00 0.00 0.00 2.85
3130 9007 2.749076 GGGGAATGGTAAACACGGTAAC 59.251 50.000 0.00 0.00 0.00 2.50
3131 9008 2.749076 GGGAATGGTAAACACGGTAACC 59.251 50.000 0.00 0.00 0.00 2.85
3144 9021 1.548973 GGTAACCGCGCGAGATCATG 61.549 60.000 34.63 15.43 0.00 3.07
3151 9028 2.293100 CGCGCGAGATCATGAAATTTC 58.707 47.619 28.94 11.41 0.00 2.17
3152 9029 2.293100 GCGCGAGATCATGAAATTTCG 58.707 47.619 12.10 8.20 36.61 3.46
3156 9033 3.781161 CGAGATCATGAAATTTCGCTCG 58.219 45.455 21.26 21.26 38.12 5.03
3162 9039 1.729284 TGAAATTTCGCTCGGTACCC 58.271 50.000 13.34 0.00 0.00 3.69
3163 9040 1.002201 TGAAATTTCGCTCGGTACCCA 59.998 47.619 13.34 0.00 0.00 4.51
3164 9041 2.078392 GAAATTTCGCTCGGTACCCAA 58.922 47.619 6.25 0.00 0.00 4.12
3165 9042 2.188062 AATTTCGCTCGGTACCCAAA 57.812 45.000 6.25 0.00 0.00 3.28
3166 9043 2.188062 ATTTCGCTCGGTACCCAAAA 57.812 45.000 6.25 0.59 0.00 2.44
3167 9044 1.228533 TTTCGCTCGGTACCCAAAAC 58.771 50.000 6.25 0.00 0.00 2.43
3168 9045 0.945265 TTCGCTCGGTACCCAAAACG 60.945 55.000 6.25 3.76 0.00 3.60
3169 9046 2.865308 GCTCGGTACCCAAAACGC 59.135 61.111 6.25 0.00 0.00 4.84
3264 10000 3.067320 CCGCATCAGAGATCAACACTAGA 59.933 47.826 0.00 0.00 0.00 2.43
3269 10005 5.078411 TCAGAGATCAACACTAGAAAGGC 57.922 43.478 0.00 0.00 0.00 4.35
3288 10024 4.680237 CTCGCCCACGTTGGAGCA 62.680 66.667 10.41 0.00 40.96 4.26
3289 10025 4.980805 TCGCCCACGTTGGAGCAC 62.981 66.667 10.41 0.00 40.96 4.40
3292 10028 4.619227 CCCACGTTGGAGCACCGT 62.619 66.667 0.00 0.00 40.96 4.83
3474 10265 5.163723 GGTCCAATATGTCATAATCATGCCG 60.164 44.000 0.00 0.00 31.73 5.69
3518 10312 7.319646 ACAAGTGTTTTCTCAAATAGCAAACA 58.680 30.769 0.00 0.00 45.27 2.83
3526 10321 8.801715 TTTCTCAAATAGCAAACAATCTTGTC 57.198 30.769 0.00 0.00 41.31 3.18
3567 10371 5.649970 TTAGGAGTGGTAGTTTTGGGAAA 57.350 39.130 0.00 0.00 0.00 3.13
3723 10527 4.114794 GCATTGTTGTGCTTCTTGTTCTT 58.885 39.130 0.00 0.00 41.82 2.52
3729 10533 1.032014 TGCTTCTTGTTCTTGTGGGC 58.968 50.000 0.00 0.00 0.00 5.36
3803 10610 7.923414 AGGTACTTTATTGTTCTTGATGACC 57.077 36.000 0.00 0.00 27.25 4.02
3810 10617 3.931907 TGTTCTTGATGACCTATGGGG 57.068 47.619 0.00 0.00 41.89 4.96
3837 10644 7.513371 AACAAACATGGGAAACGATTAAGTA 57.487 32.000 0.00 0.00 0.00 2.24
3844 10651 6.827586 TGGGAAACGATTAAGTATGCTTTT 57.172 33.333 0.00 0.00 36.22 2.27
3934 10741 2.572290 GGTATCTACCACATGCAACCC 58.428 52.381 0.00 0.00 45.73 4.11
3948 10755 3.509442 TGCAACCCCTTTCTGATGATTT 58.491 40.909 0.00 0.00 0.00 2.17
3957 10764 6.350780 CCCCTTTCTGATGATTTCTCCAAAAG 60.351 42.308 0.00 0.00 0.00 2.27
3991 10798 4.256920 CAAGAACATCTGGTAGTGAAGGG 58.743 47.826 0.00 0.00 0.00 3.95
4039 10882 1.172180 AGAAATGTGGTGGTGTGCCG 61.172 55.000 0.00 0.00 37.67 5.69
4075 10918 1.453155 TAGCTAGCTTGCTTGTTGGC 58.547 50.000 27.19 0.00 43.74 4.52
4108 12012 6.207810 GTGAGGACTGGTCTAAGGTATATGAG 59.792 46.154 0.67 0.00 0.00 2.90
4124 12028 0.189574 TGAGGCCATTGGTTTTGGGA 59.810 50.000 5.01 0.00 34.66 4.37
4157 12061 5.839262 TGACGATGTTCATAACACAAGAC 57.161 39.130 0.00 0.00 45.50 3.01
4344 12248 8.324306 TCAACTTGGAGAGATCTATTTCAACAT 58.676 33.333 0.00 0.00 0.00 2.71
4395 12305 7.594351 GGATAGATCCTGCATATAGTGATGA 57.406 40.000 0.98 0.00 43.73 2.92
4622 12541 0.673333 TGTAGACTGCCGTGCCAATG 60.673 55.000 0.00 0.00 0.00 2.82
4664 12584 4.084223 GCTTTAAAGTACTGCGTGTGCTAA 60.084 41.667 16.38 0.00 40.73 3.09
4682 12602 6.149308 TGTGCTAATTATTGAGGACTGTGTTG 59.851 38.462 0.23 0.00 35.26 3.33
4823 12743 5.989717 AGATATTGGATGTAAGGGGAGGTA 58.010 41.667 0.00 0.00 0.00 3.08
4978 12898 1.308998 AGTGCCCAAACTTCTTCACG 58.691 50.000 0.00 0.00 0.00 4.35
5045 12965 4.713814 TCAGTGAAATAGAGGAGTCTGCAT 59.286 41.667 0.00 0.00 33.84 3.96
5050 12970 4.434545 AATAGAGGAGTCTGCATGCAAT 57.565 40.909 22.88 10.69 33.84 3.56
5073 12993 1.911357 TCTGGTGGAATCTCTGTGCAT 59.089 47.619 0.00 0.00 0.00 3.96
5098 13018 3.771479 TGCACAAGATCCATAGTCTGACT 59.229 43.478 15.57 15.57 0.00 3.41
5105 13034 6.865834 AGATCCATAGTCTGACTGTCTTTT 57.134 37.500 20.19 1.09 0.00 2.27
5137 13066 4.759782 AGTATTCGGTTGTCCTCAATCAG 58.240 43.478 0.00 0.00 34.63 2.90
5150 13079 3.269178 CTCAATCAGAGCTTGGAAGACC 58.731 50.000 0.00 0.00 37.59 3.85
5153 13082 2.015456 TCAGAGCTTGGAAGACCTGA 57.985 50.000 0.00 6.92 35.31 3.86
5377 13306 4.568152 ATCATATACTTTTGGCGGCAAC 57.432 40.909 25.48 0.00 0.00 4.17
5407 13336 3.405831 CAAGCTGAGATTCTTGTGGACA 58.594 45.455 0.00 0.00 36.01 4.02
5416 13345 7.000472 TGAGATTCTTGTGGACAAAGAAGATT 59.000 34.615 5.04 0.00 35.15 2.40
6409 19759 1.435577 CAAATGCCAGCTTTGCCTTC 58.564 50.000 2.68 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.564660 AGAAGATTTTCACATGGGCCAATATTA 59.435 33.333 11.89 0.00 35.70 0.98
45 46 4.021894 CGGACCCTCTATAGAAGGATTGTG 60.022 50.000 22.02 7.01 30.26 3.33
47 48 4.408276 TCGGACCCTCTATAGAAGGATTG 58.592 47.826 22.02 11.33 30.26 2.67
68 69 1.335324 GCCATTGCGCCATTCACTATC 60.335 52.381 4.18 0.00 0.00 2.08
74 75 0.596600 CTGATGCCATTGCGCCATTC 60.597 55.000 4.18 0.00 41.78 2.67
76 77 1.038681 TTCTGATGCCATTGCGCCAT 61.039 50.000 4.18 0.00 41.78 4.40
91 92 8.365399 TGTGTTCTCTACTATTTTGTGTTCTG 57.635 34.615 0.00 0.00 0.00 3.02
152 153 1.202830 TGAACCCAACAACGGCTACAT 60.203 47.619 0.00 0.00 0.00 2.29
213 219 6.434018 AATCTAGTAACAGAGACGGTGTAC 57.566 41.667 0.00 0.00 0.00 2.90
306 335 3.756933 TGCTACCGAGGTTGTACTTTT 57.243 42.857 0.00 0.00 0.00 2.27
311 340 4.708421 AGAATAGTTGCTACCGAGGTTGTA 59.292 41.667 0.00 0.00 0.00 2.41
330 359 1.903877 CGGTGGGGCTGTCAGAGAAT 61.904 60.000 3.32 0.00 0.00 2.40
354 383 7.132694 TGTGCAAGACTACAATATCAAAGTG 57.867 36.000 0.00 0.00 0.00 3.16
371 401 3.144506 ACAGTCTCCAGATTTGTGCAAG 58.855 45.455 0.00 0.00 0.00 4.01
384 414 7.454260 AACTATTTTCCATGAAACAGTCTCC 57.546 36.000 0.00 0.00 30.66 3.71
468 501 1.139853 CTGATTGGAGCACTAGGGACC 59.860 57.143 0.00 0.00 0.00 4.46
509 561 4.917474 GCATGGAGCGGCAATTTT 57.083 50.000 1.45 0.00 0.00 1.82
526 586 8.729756 TGATGGTTCAAAACTGAAGTGTATATG 58.270 33.333 0.00 0.00 0.00 1.78
551 611 0.386476 TCTGCAGCCAGCTTTTTGTG 59.614 50.000 9.47 0.00 45.94 3.33
596 854 2.915137 TGGCCGGCCCTTTGTTTC 60.915 61.111 41.75 15.00 34.56 2.78
621 888 0.721718 GGCTTAGTTAGTGCGCACTG 59.278 55.000 44.69 30.48 42.52 3.66
634 906 3.886505 TGGTTTGTTGGTTAGTGGCTTAG 59.113 43.478 0.00 0.00 0.00 2.18
686 958 0.183492 ACGTGATGGGCATTGGCTAT 59.817 50.000 8.86 8.86 40.87 2.97
695 967 1.450312 CAAGGAGGACGTGATGGGC 60.450 63.158 0.00 0.00 0.00 5.36
1638 1988 8.955388 TGACATTCATATTTTGTGCTAAGCTTA 58.045 29.630 5.94 5.94 0.00 3.09
1873 2241 2.233922 TGTCTTCCTTAGTGTAGCTGGC 59.766 50.000 0.00 0.00 0.00 4.85
1874 2242 4.537135 TTGTCTTCCTTAGTGTAGCTGG 57.463 45.455 0.00 0.00 0.00 4.85
1875 2243 9.416794 CATATATTGTCTTCCTTAGTGTAGCTG 57.583 37.037 0.00 0.00 0.00 4.24
1876 2244 9.148879 ACATATATTGTCTTCCTTAGTGTAGCT 57.851 33.333 0.00 0.00 30.89 3.32
1925 2334 8.034804 GCCAAGTTGTTTATTGATTTGGACTAT 58.965 33.333 1.45 0.00 36.56 2.12
2025 5928 7.969387 TTAATTTGATTTTCTAGATGCGTGC 57.031 32.000 0.00 0.00 0.00 5.34
2118 6024 7.630242 AGTAATCCATGTAACCAATCAGTTG 57.370 36.000 0.00 0.00 35.05 3.16
2223 6156 6.816136 TGCCATTTAATCGAGTCTTCATCTA 58.184 36.000 0.00 0.00 0.00 1.98
2224 6157 5.674525 TGCCATTTAATCGAGTCTTCATCT 58.325 37.500 0.00 0.00 0.00 2.90
2442 6381 2.912956 ACCTAATGGTCAAAGCTCAGGA 59.087 45.455 0.00 0.00 44.78 3.86
2508 6447 0.321298 TGTAGGCAGCCGGTTTCTTC 60.321 55.000 5.55 0.00 0.00 2.87
2813 6854 3.490933 GCACAATGTAGCTACGAGGATGA 60.491 47.826 18.74 0.00 0.00 2.92
2846 6887 5.280654 ACGTCAAAACCCTTCAGTAACTA 57.719 39.130 0.00 0.00 0.00 2.24
2852 6893 1.860676 TCGACGTCAAAACCCTTCAG 58.139 50.000 17.16 0.00 0.00 3.02
2861 6902 8.544409 TTTCGATTTTAAATTTCGACGTCAAA 57.456 26.923 17.16 14.74 41.18 2.69
2862 6903 8.716619 ATTTCGATTTTAAATTTCGACGTCAA 57.283 26.923 17.16 3.31 41.18 3.18
2863 6904 8.716619 AATTTCGATTTTAAATTTCGACGTCA 57.283 26.923 17.16 0.00 41.18 4.35
2864 6905 9.431044 CAAATTTCGATTTTAAATTTCGACGTC 57.569 29.630 18.10 5.18 41.99 4.34
2900 8231 7.434307 ACACGAATCTATATCGACGTCAAAAAT 59.566 33.333 17.16 5.71 42.76 1.82
2903 8234 5.813717 ACACGAATCTATATCGACGTCAAA 58.186 37.500 17.16 2.91 42.76 2.69
2904 8235 5.413969 ACACGAATCTATATCGACGTCAA 57.586 39.130 17.16 0.00 42.76 3.18
2906 8237 5.905733 TCAAACACGAATCTATATCGACGTC 59.094 40.000 5.18 5.18 42.76 4.34
2907 8238 5.680229 GTCAAACACGAATCTATATCGACGT 59.320 40.000 2.65 0.00 42.76 4.34
2908 8239 5.907945 AGTCAAACACGAATCTATATCGACG 59.092 40.000 2.65 0.00 42.76 5.12
2909 8240 6.910972 TGAGTCAAACACGAATCTATATCGAC 59.089 38.462 2.65 0.00 42.76 4.20
2910 8241 7.023197 TGAGTCAAACACGAATCTATATCGA 57.977 36.000 2.65 0.00 42.76 3.59
2911 8242 7.644157 TCTTGAGTCAAACACGAATCTATATCG 59.356 37.037 7.06 0.00 45.47 2.92
2912 8243 8.858003 TCTTGAGTCAAACACGAATCTATATC 57.142 34.615 7.06 0.00 31.39 1.63
2913 8244 9.469807 GATCTTGAGTCAAACACGAATCTATAT 57.530 33.333 7.06 0.00 31.39 0.86
2916 8247 6.687604 TGATCTTGAGTCAAACACGAATCTA 58.312 36.000 7.06 0.00 31.39 1.98
2917 8248 5.541845 TGATCTTGAGTCAAACACGAATCT 58.458 37.500 7.06 0.00 31.39 2.40
2918 8249 5.635280 TCTGATCTTGAGTCAAACACGAATC 59.365 40.000 7.06 4.57 0.00 2.52
2920 8251 4.745125 GTCTGATCTTGAGTCAAACACGAA 59.255 41.667 7.06 0.00 0.00 3.85
2921 8252 4.038042 AGTCTGATCTTGAGTCAAACACGA 59.962 41.667 7.06 0.98 0.00 4.35
2922 8253 4.302455 AGTCTGATCTTGAGTCAAACACG 58.698 43.478 7.06 0.00 0.00 4.49
2923 8254 4.384247 CGAGTCTGATCTTGAGTCAAACAC 59.616 45.833 7.06 1.97 34.51 3.32
2924 8255 4.278419 TCGAGTCTGATCTTGAGTCAAACA 59.722 41.667 7.06 6.91 34.51 2.83
2925 8256 4.799678 TCGAGTCTGATCTTGAGTCAAAC 58.200 43.478 7.06 1.07 34.51 2.93
2929 8260 3.191581 TGGTTCGAGTCTGATCTTGAGTC 59.808 47.826 11.57 11.57 0.00 3.36
2931 8262 3.768406 CTGGTTCGAGTCTGATCTTGAG 58.232 50.000 0.00 0.00 0.00 3.02
2932 8263 2.094494 GCTGGTTCGAGTCTGATCTTGA 60.094 50.000 0.00 0.00 0.00 3.02
2933 8264 2.266554 GCTGGTTCGAGTCTGATCTTG 58.733 52.381 0.00 0.00 0.00 3.02
2934 8265 1.135257 CGCTGGTTCGAGTCTGATCTT 60.135 52.381 0.00 0.00 0.00 2.40
2935 8266 0.453793 CGCTGGTTCGAGTCTGATCT 59.546 55.000 0.00 0.00 0.00 2.75
2936 8267 0.452184 TCGCTGGTTCGAGTCTGATC 59.548 55.000 0.00 0.00 34.09 2.92
2938 8269 0.889638 AGTCGCTGGTTCGAGTCTGA 60.890 55.000 0.00 0.00 37.57 3.27
2939 8270 0.803117 TAGTCGCTGGTTCGAGTCTG 59.197 55.000 0.00 0.00 41.72 3.51
2940 8271 1.088306 CTAGTCGCTGGTTCGAGTCT 58.912 55.000 0.00 0.00 41.72 3.24
2941 8272 0.523757 GCTAGTCGCTGGTTCGAGTC 60.524 60.000 0.00 0.00 41.72 3.36
2942 8273 1.507174 GCTAGTCGCTGGTTCGAGT 59.493 57.895 0.00 0.00 43.64 4.18
2943 8274 4.386245 GCTAGTCGCTGGTTCGAG 57.614 61.111 0.00 0.00 39.34 4.04
2952 8283 0.171903 TTCCGTTACCAGCTAGTCGC 59.828 55.000 0.00 0.00 39.57 5.19
2953 8284 1.202268 CCTTCCGTTACCAGCTAGTCG 60.202 57.143 0.00 0.00 0.00 4.18
2955 8286 2.226962 TCCTTCCGTTACCAGCTAGT 57.773 50.000 0.00 0.00 0.00 2.57
2956 8287 2.803492 GCATCCTTCCGTTACCAGCTAG 60.803 54.545 0.00 0.00 0.00 3.42
2957 8288 1.138266 GCATCCTTCCGTTACCAGCTA 59.862 52.381 0.00 0.00 0.00 3.32
2959 8290 0.107654 AGCATCCTTCCGTTACCAGC 60.108 55.000 0.00 0.00 0.00 4.85
2960 8291 2.403252 AAGCATCCTTCCGTTACCAG 57.597 50.000 0.00 0.00 0.00 4.00
2961 8292 2.817258 CAAAAGCATCCTTCCGTTACCA 59.183 45.455 0.00 0.00 0.00 3.25
2962 8293 2.415491 GCAAAAGCATCCTTCCGTTACC 60.415 50.000 0.00 0.00 0.00 2.85
2966 8297 0.539438 TGGCAAAAGCATCCTTCCGT 60.539 50.000 0.00 0.00 0.00 4.69
2967 8298 0.109132 GTGGCAAAAGCATCCTTCCG 60.109 55.000 0.00 0.00 0.00 4.30
2969 8300 2.424956 CCTAGTGGCAAAAGCATCCTTC 59.575 50.000 0.00 0.00 0.00 3.46
2984 8315 0.456221 CGACAGGTAGTGGCCTAGTG 59.544 60.000 3.32 0.00 37.04 2.74
2986 8317 0.456221 CACGACAGGTAGTGGCCTAG 59.544 60.000 3.32 0.00 37.04 3.02
2987 8318 0.251474 ACACGACAGGTAGTGGCCTA 60.251 55.000 15.42 0.00 39.93 3.93
2989 8320 0.949105 CAACACGACAGGTAGTGGCC 60.949 60.000 15.42 0.00 39.93 5.36
2990 8321 0.249741 ACAACACGACAGGTAGTGGC 60.250 55.000 15.42 0.00 39.93 5.01
2991 8322 1.067974 TGACAACACGACAGGTAGTGG 59.932 52.381 15.42 3.32 39.93 4.00
2992 8323 2.502213 TGACAACACGACAGGTAGTG 57.498 50.000 10.52 10.52 41.13 2.74
2993 8324 4.077108 TCTATGACAACACGACAGGTAGT 58.923 43.478 0.00 0.00 0.00 2.73
2994 8325 4.696899 TCTATGACAACACGACAGGTAG 57.303 45.455 0.00 0.00 0.00 3.18
2995 8326 4.521639 ACTTCTATGACAACACGACAGGTA 59.478 41.667 0.00 0.00 0.00 3.08
2997 8328 3.675225 CACTTCTATGACAACACGACAGG 59.325 47.826 0.00 0.00 0.00 4.00
2998 8329 4.546570 TCACTTCTATGACAACACGACAG 58.453 43.478 0.00 0.00 0.00 3.51
2999 8330 4.577834 TCACTTCTATGACAACACGACA 57.422 40.909 0.00 0.00 0.00 4.35
3001 8332 4.021456 ACCATCACTTCTATGACAACACGA 60.021 41.667 0.00 0.00 0.00 4.35
3002 8333 4.091945 CACCATCACTTCTATGACAACACG 59.908 45.833 0.00 0.00 0.00 4.49
3005 8336 5.482908 AGACACCATCACTTCTATGACAAC 58.517 41.667 0.00 0.00 0.00 3.32
3006 8337 5.745312 AGACACCATCACTTCTATGACAA 57.255 39.130 0.00 0.00 0.00 3.18
3007 8338 7.423844 AATAGACACCATCACTTCTATGACA 57.576 36.000 0.00 0.00 32.70 3.58
3008 8339 9.817809 TTAAATAGACACCATCACTTCTATGAC 57.182 33.333 0.00 0.00 32.70 3.06
3009 8340 9.817809 GTTAAATAGACACCATCACTTCTATGA 57.182 33.333 0.00 0.00 32.70 2.15
3010 8341 9.046296 GGTTAAATAGACACCATCACTTCTATG 57.954 37.037 0.00 0.00 32.70 2.23
3012 8343 8.141298 TGGTTAAATAGACACCATCACTTCTA 57.859 34.615 0.00 0.00 35.57 2.10
3014 8345 7.064728 GTCTGGTTAAATAGACACCATCACTTC 59.935 40.741 12.92 0.00 42.18 3.01
3017 8348 6.170506 TGTCTGGTTAAATAGACACCATCAC 58.829 40.000 15.39 2.38 45.97 3.06
3018 8349 6.367374 TGTCTGGTTAAATAGACACCATCA 57.633 37.500 15.39 1.87 45.97 3.07
3025 8356 5.581085 ACGCTCATTGTCTGGTTAAATAGAC 59.419 40.000 11.53 11.53 42.77 2.59
3027 8358 6.422776 AACGCTCATTGTCTGGTTAAATAG 57.577 37.500 0.00 0.00 0.00 1.73
3029 8360 5.240623 TCAAACGCTCATTGTCTGGTTAAAT 59.759 36.000 0.00 0.00 0.00 1.40
3030 8361 4.576873 TCAAACGCTCATTGTCTGGTTAAA 59.423 37.500 0.00 0.00 0.00 1.52
3031 8362 4.130857 TCAAACGCTCATTGTCTGGTTAA 58.869 39.130 0.00 0.00 0.00 2.01
3032 8363 3.734463 TCAAACGCTCATTGTCTGGTTA 58.266 40.909 0.00 0.00 0.00 2.85
3034 8365 2.254546 TCAAACGCTCATTGTCTGGT 57.745 45.000 0.00 0.00 0.00 4.00
3035 8366 3.837213 ATTCAAACGCTCATTGTCTGG 57.163 42.857 0.00 0.00 0.00 3.86
3036 8367 4.786507 TGAATTCAAACGCTCATTGTCTG 58.213 39.130 5.45 0.00 0.00 3.51
3037 8368 5.437289 TTGAATTCAAACGCTCATTGTCT 57.563 34.783 18.45 0.00 32.11 3.41
3038 8369 6.509317 TTTTGAATTCAAACGCTCATTGTC 57.491 33.333 28.78 0.00 44.56 3.18
3040 8371 8.770850 AAATTTTTGAATTCAAACGCTCATTG 57.229 26.923 28.78 0.00 44.56 2.82
3042 8373 8.140677 TGAAATTTTTGAATTCAAACGCTCAT 57.859 26.923 28.78 15.26 44.56 2.90
3044 8375 8.819152 TTTGAAATTTTTGAATTCAAACGCTC 57.181 26.923 28.78 21.76 43.99 5.03
3045 8376 9.786105 ATTTTGAAATTTTTGAATTCAAACGCT 57.214 22.222 28.78 15.76 46.72 5.07
3075 8952 3.664486 CTCGTACCGAGCAAAATATCTCG 59.336 47.826 0.20 4.83 46.75 4.04
3095 8972 0.974383 TTCCCCCTCGAGAAACACTC 59.026 55.000 15.71 0.00 41.79 3.51
3097 8974 1.679032 CCATTCCCCCTCGAGAAACAC 60.679 57.143 15.71 0.00 0.00 3.32
3098 8975 0.618458 CCATTCCCCCTCGAGAAACA 59.382 55.000 15.71 0.00 0.00 2.83
3099 8976 0.618981 ACCATTCCCCCTCGAGAAAC 59.381 55.000 15.71 0.00 0.00 2.78
3100 8977 2.257391 TACCATTCCCCCTCGAGAAA 57.743 50.000 15.71 2.99 0.00 2.52
3101 8978 2.237893 GTTTACCATTCCCCCTCGAGAA 59.762 50.000 15.71 0.00 0.00 2.87
3102 8979 1.835531 GTTTACCATTCCCCCTCGAGA 59.164 52.381 15.71 0.00 0.00 4.04
3103 8980 1.557832 TGTTTACCATTCCCCCTCGAG 59.442 52.381 5.13 5.13 0.00 4.04
3104 8981 1.279846 GTGTTTACCATTCCCCCTCGA 59.720 52.381 0.00 0.00 0.00 4.04
3105 8982 1.746470 GTGTTTACCATTCCCCCTCG 58.254 55.000 0.00 0.00 0.00 4.63
3106 8983 1.680860 CCGTGTTTACCATTCCCCCTC 60.681 57.143 0.00 0.00 0.00 4.30
3107 8984 0.330267 CCGTGTTTACCATTCCCCCT 59.670 55.000 0.00 0.00 0.00 4.79
3108 8985 0.038599 ACCGTGTTTACCATTCCCCC 59.961 55.000 0.00 0.00 0.00 5.40
3109 8986 2.749076 GTTACCGTGTTTACCATTCCCC 59.251 50.000 0.00 0.00 0.00 4.81
3110 8987 2.749076 GGTTACCGTGTTTACCATTCCC 59.251 50.000 0.00 0.00 0.00 3.97
3111 8988 2.416202 CGGTTACCGTGTTTACCATTCC 59.584 50.000 16.53 0.00 42.73 3.01
3112 8989 3.727780 CGGTTACCGTGTTTACCATTC 57.272 47.619 16.53 0.00 42.73 2.67
3125 9002 1.299926 ATGATCTCGCGCGGTTACC 60.300 57.895 31.69 15.70 0.00 2.85
3126 9003 0.594028 TCATGATCTCGCGCGGTTAC 60.594 55.000 31.69 18.93 0.00 2.50
3127 9004 0.101579 TTCATGATCTCGCGCGGTTA 59.898 50.000 31.69 16.07 0.00 2.85
3128 9005 0.739462 TTTCATGATCTCGCGCGGTT 60.739 50.000 31.69 15.10 0.00 4.44
3129 9006 0.530650 ATTTCATGATCTCGCGCGGT 60.531 50.000 31.69 16.64 0.00 5.68
3130 9007 0.583438 AATTTCATGATCTCGCGCGG 59.417 50.000 31.69 20.60 0.00 6.46
3131 9008 2.293100 GAAATTTCATGATCTCGCGCG 58.707 47.619 26.76 26.76 0.00 6.86
3132 9009 2.293100 CGAAATTTCATGATCTCGCGC 58.707 47.619 17.99 0.00 0.00 6.86
3133 9010 2.293100 GCGAAATTTCATGATCTCGCG 58.707 47.619 17.99 0.00 41.71 5.87
3135 9012 3.362401 CCGAGCGAAATTTCATGATCTCG 60.362 47.826 22.59 22.59 41.01 4.04
3136 9013 3.557595 ACCGAGCGAAATTTCATGATCTC 59.442 43.478 17.99 12.86 0.00 2.75
3138 9015 3.951979 ACCGAGCGAAATTTCATGATC 57.048 42.857 17.99 9.61 0.00 2.92
3162 9039 0.110238 CGTCATGGACCAGCGTTTTG 60.110 55.000 0.00 0.00 0.00 2.44
3163 9040 0.250124 TCGTCATGGACCAGCGTTTT 60.250 50.000 0.00 0.00 0.00 2.43
3164 9041 0.670546 CTCGTCATGGACCAGCGTTT 60.671 55.000 0.00 0.00 0.00 3.60
3165 9042 1.079819 CTCGTCATGGACCAGCGTT 60.080 57.895 0.00 0.00 0.00 4.84
3166 9043 2.573869 CTCGTCATGGACCAGCGT 59.426 61.111 0.00 0.00 0.00 5.07
3167 9044 2.021068 ATCCTCGTCATGGACCAGCG 62.021 60.000 0.00 4.96 36.30 5.18
3168 9045 0.531532 CATCCTCGTCATGGACCAGC 60.532 60.000 0.00 0.00 36.30 4.85
3169 9046 0.826715 ACATCCTCGTCATGGACCAG 59.173 55.000 0.00 0.00 36.30 4.00
3199 9915 1.234821 CGAGATCCTCTCTTCTCCGG 58.765 60.000 0.00 0.00 41.26 5.14
3290 10026 0.863538 CTCGAGATGCTTCCGTCACG 60.864 60.000 6.58 0.00 40.79 4.35
3291 10027 0.526524 CCTCGAGATGCTTCCGTCAC 60.527 60.000 15.71 0.00 0.00 3.67
3292 10028 0.965866 ACCTCGAGATGCTTCCGTCA 60.966 55.000 15.71 0.00 0.00 4.35
3293 10029 0.526524 CACCTCGAGATGCTTCCGTC 60.527 60.000 15.71 0.00 0.00 4.79
3294 10030 1.513158 CACCTCGAGATGCTTCCGT 59.487 57.895 15.71 0.00 0.00 4.69
3348 10120 4.489771 CCATCACCCCCTGTCGGC 62.490 72.222 0.00 0.00 0.00 5.54
3474 10265 8.024865 ACACTTGTTGTTAGTTGGTTAAAGTTC 58.975 33.333 0.00 0.00 33.09 3.01
3504 10298 6.373779 ACGACAAGATTGTTTGCTATTTGAG 58.626 36.000 0.00 0.00 42.43 3.02
3506 10300 6.742718 CCTACGACAAGATTGTTTGCTATTTG 59.257 38.462 0.00 0.00 42.43 2.32
3518 10312 9.594478 AAATTTTGAAAAACCTACGACAAGATT 57.406 25.926 0.00 0.00 0.00 2.40
3526 10321 9.524106 ACTCCTAAAAATTTTGAAAAACCTACG 57.476 29.630 3.73 0.00 0.00 3.51
3604 10408 8.784994 GTTCTTATGATCTACCGAGTCTTGATA 58.215 37.037 0.00 0.00 0.00 2.15
3723 10527 6.934645 GCAAACTATCTAATATACTGCCCACA 59.065 38.462 0.00 0.00 0.00 4.17
3803 10610 4.605183 TCCCATGTTTGTTTACCCCATAG 58.395 43.478 0.00 0.00 0.00 2.23
3810 10617 7.863877 ACTTAATCGTTTCCCATGTTTGTTTAC 59.136 33.333 0.00 0.00 0.00 2.01
3813 10620 6.399639 ACTTAATCGTTTCCCATGTTTGTT 57.600 33.333 0.00 0.00 0.00 2.83
3934 10741 6.210185 ACCTTTTGGAGAAATCATCAGAAAGG 59.790 38.462 8.93 8.93 44.07 3.11
3991 10798 0.321671 TGGTAGTCACTTCAGCAGGC 59.678 55.000 0.00 0.00 0.00 4.85
4108 12012 1.627834 TCATTCCCAAAACCAATGGCC 59.372 47.619 0.00 0.00 36.58 5.36
4124 12028 8.607459 GTTATGAACATCGTCATTCTCTTCATT 58.393 33.333 0.00 0.00 39.07 2.57
4622 12541 1.106285 CTCAAAAGCAGGGGCATACC 58.894 55.000 0.00 0.00 44.61 2.73
4664 12584 5.181245 CCGAAACAACACAGTCCTCAATAAT 59.819 40.000 0.00 0.00 0.00 1.28
4682 12602 5.382618 TCAAGACTACTACCTTCCGAAAC 57.617 43.478 0.00 0.00 0.00 2.78
4823 12743 0.533755 GGCGGCAGCTCACTTATCAT 60.534 55.000 9.17 0.00 44.37 2.45
4978 12898 2.561478 TTGTCAGCTTACCCACCTTC 57.439 50.000 0.00 0.00 0.00 3.46
4987 12907 3.818773 GCACCCTTAACTTTGTCAGCTTA 59.181 43.478 0.00 0.00 0.00 3.09
5045 12965 1.005097 AGATTCCACCAGAGCATTGCA 59.995 47.619 11.91 0.00 0.00 4.08
5050 12970 1.277273 CACAGAGATTCCACCAGAGCA 59.723 52.381 0.00 0.00 0.00 4.26
5057 12977 2.286872 CAGGATGCACAGAGATTCCAC 58.713 52.381 3.24 0.00 0.00 4.02
5073 12993 3.133542 CAGACTATGGATCTTGTGCAGGA 59.866 47.826 0.00 0.00 0.00 3.86
5098 13018 6.073276 CCGAATACTCAACATCACAAAAGACA 60.073 38.462 0.00 0.00 0.00 3.41
5105 13034 4.637276 ACAACCGAATACTCAACATCACA 58.363 39.130 0.00 0.00 0.00 3.58
5137 13066 1.609320 GGTGTCAGGTCTTCCAAGCTC 60.609 57.143 0.00 0.00 35.89 4.09
5150 13079 2.146342 CAGCTTTGTACAGGGTGTCAG 58.854 52.381 16.66 1.11 0.00 3.51
5153 13082 2.547218 CGTACAGCTTTGTACAGGGTGT 60.547 50.000 26.58 26.58 43.39 4.16
5377 13306 3.993081 AGAATCTCAGCTTGTGAAACTCG 59.007 43.478 0.00 0.00 38.04 4.18
5407 13336 5.771666 TCCAACAGCAATCTCAATCTTCTTT 59.228 36.000 0.00 0.00 0.00 2.52
5416 13345 2.639347 TCCTTCTCCAACAGCAATCTCA 59.361 45.455 0.00 0.00 0.00 3.27
6409 19759 1.609932 GTGTCGTTGAATGCATGCAG 58.390 50.000 26.69 11.27 0.00 4.41


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

AutoCloner maintained by Alex Coulton.