Multiple sequence alignment - TraesCS2D01G168100

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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 TraesCS2D01G168100 chr2D 100.000 5013 0 0 1 5013 111587673 111592685 0.000000e+00 9258.0
1 TraesCS2D01G168100 chr2D 85.532 1645 164 43 627 2244 112098952 112100549 0.000000e+00 1652.0
2 TraesCS2D01G168100 chr2D 86.587 999 97 26 705 1677 112181370 112180383 0.000000e+00 1068.0
3 TraesCS2D01G168100 chr2D 81.505 1103 137 30 2568 3626 112179530 112178451 0.000000e+00 845.0
4 TraesCS2D01G168100 chr2D 83.085 739 85 23 2259 2988 112100601 112101308 1.970000e-178 636.0
5 TraesCS2D01G168100 chr2D 84.844 640 59 26 3657 4267 112101766 112102396 1.190000e-170 610.0
6 TraesCS2D01G168100 chr2D 86.580 462 34 17 1791 2244 112180279 112179838 7.550000e-133 484.0
7 TraesCS2D01G168100 chr2D 89.572 374 34 2 3894 4262 112178119 112177746 2.110000e-128 470.0
8 TraesCS2D01G168100 chr2D 83.613 476 72 5 302 774 112283212 112282740 4.610000e-120 442.0
9 TraesCS2D01G168100 chr2D 81.356 413 45 19 3260 3655 112101324 112101721 1.750000e-79 307.0
10 TraesCS2D01G168100 chr2D 89.952 209 12 4 2265 2468 112179786 112179582 1.380000e-65 261.0
11 TraesCS2D01G168100 chr2D 90.805 174 11 1 4682 4850 112102664 112102837 1.400000e-55 228.0
12 TraesCS2D01G168100 chr2D 82.645 242 38 4 295 534 112289576 112289337 1.410000e-50 211.0
13 TraesCS2D01G168100 chr2D 88.971 136 12 2 4284 4416 112102384 112102519 1.120000e-36 165.0
14 TraesCS2D01G168100 chr2D 91.429 105 3 1 4909 5013 112103577 112103675 6.770000e-29 139.0
15 TraesCS2D01G168100 chr2D 85.714 91 10 3 181 271 112186200 112186113 5.340000e-15 93.5
16 TraesCS2D01G168100 chr2A 93.366 2276 100 27 1 2244 111920942 111923198 0.000000e+00 3319.0
17 TraesCS2D01G168100 chr2A 84.479 1527 157 50 539 2002 113312436 113310927 0.000000e+00 1434.0
18 TraesCS2D01G168100 chr2A 84.786 1492 151 49 565 2002 112744385 112745854 0.000000e+00 1428.0
19 TraesCS2D01G168100 chr2A 90.048 1035 89 8 2641 3668 111923578 111924605 0.000000e+00 1328.0
20 TraesCS2D01G168100 chr2A 94.514 638 18 10 3642 4267 111924627 111925259 0.000000e+00 968.0
21 TraesCS2D01G168100 chr2A 84.534 569 63 18 3267 3820 112746880 112747438 1.590000e-149 540.0
22 TraesCS2D01G168100 chr2A 90.051 392 27 8 3886 4267 112747459 112747848 9.690000e-137 497.0
23 TraesCS2D01G168100 chr2A 89.125 377 32 5 3896 4267 113309512 113309140 1.270000e-125 460.0
24 TraesCS2D01G168100 chr2A 92.138 318 19 3 2238 2550 111923235 111923551 1.280000e-120 444.0
25 TraesCS2D01G168100 chr2A 82.083 480 76 6 302 774 113344548 113344072 7.820000e-108 401.0
26 TraesCS2D01G168100 chr2A 97.321 224 6 0 4790 5013 111925575 111925798 1.020000e-101 381.0
27 TraesCS2D01G168100 chr2A 86.262 313 42 1 2608 2919 112746501 112746813 6.220000e-89 339.0
28 TraesCS2D01G168100 chr2A 86.262 313 42 1 2608 2919 113310300 113309988 6.220000e-89 339.0
29 TraesCS2D01G168100 chr2A 78.445 566 77 33 3334 3887 113196994 113196462 1.350000e-85 327.0
30 TraesCS2D01G168100 chr2A 85.714 301 32 7 2259 2555 112746196 112746489 1.750000e-79 307.0
31 TraesCS2D01G168100 chr2A 85.906 298 31 7 2262 2555 113310602 113310312 1.750000e-79 307.0
32 TraesCS2D01G168100 chr2A 81.551 374 44 15 3267 3626 113309921 113309559 8.210000e-73 285.0
33 TraesCS2D01G168100 chr2A 94.545 165 4 1 2080 2244 112745961 112746120 3.000000e-62 250.0
34 TraesCS2D01G168100 chr2A 94.545 165 4 1 2080 2244 113310820 113310661 3.000000e-62 250.0
35 TraesCS2D01G168100 chr2A 91.813 171 7 4 4284 4447 111925247 111925417 1.090000e-56 231.0
36 TraesCS2D01G168100 chr2A 82.946 258 39 5 553 807 113343539 113343284 1.400000e-55 228.0
37 TraesCS2D01G168100 chr2A 81.176 255 45 2 283 534 113343777 113343523 8.510000e-48 202.0
38 TraesCS2D01G168100 chr2A 79.693 261 48 3 282 537 113319644 113319384 3.080000e-42 183.0
39 TraesCS2D01G168100 chr2A 81.124 249 26 9 4612 4848 112748258 112748497 3.990000e-41 180.0
40 TraesCS2D01G168100 chr2A 97.000 100 3 0 4529 4628 111925415 111925514 8.630000e-38 169.0
41 TraesCS2D01G168100 chr2A 89.524 105 5 2 4909 5013 112749182 112749280 1.460000e-25 128.0
42 TraesCS2D01G168100 chr2A 96.667 60 2 0 4684 4743 111925514 111925573 3.190000e-17 100.0
43 TraesCS2D01G168100 chr2A 81.600 125 13 5 4302 4416 112747959 112748083 1.490000e-15 95.3
44 TraesCS2D01G168100 chr2A 83.516 91 12 2 181 271 113318467 113318380 1.160000e-11 82.4
45 TraesCS2D01G168100 chr2A 92.308 52 4 0 4577 4628 113250358 113250307 1.940000e-09 75.0
46 TraesCS2D01G168100 chr2B 95.537 1703 64 5 2568 4267 161723927 161725620 0.000000e+00 2713.0
47 TraesCS2D01G168100 chr2B 89.470 1339 80 22 487 1822 161721916 161723196 0.000000e+00 1635.0
48 TraesCS2D01G168100 chr2B 80.295 2167 265 96 1791 3887 162447987 162445913 0.000000e+00 1487.0
49 TraesCS2D01G168100 chr2B 86.709 1091 95 32 725 1779 162007423 162008499 0.000000e+00 1166.0
50 TraesCS2D01G168100 chr2B 85.670 977 85 38 741 1687 162449043 162448092 0.000000e+00 977.0
51 TraesCS2D01G168100 chr2B 84.189 740 92 17 2259 2988 162009023 162009747 0.000000e+00 695.0
52 TraesCS2D01G168100 chr2B 85.141 498 53 13 3328 3815 162009946 162010432 1.620000e-134 490.0
53 TraesCS2D01G168100 chr2B 89.974 379 33 2 3894 4267 162445875 162445497 7.550000e-133 484.0
54 TraesCS2D01G168100 chr2B 90.186 377 23 7 3896 4267 162010632 162010999 3.510000e-131 479.0
55 TraesCS2D01G168100 chr2B 92.236 322 21 2 2238 2555 161723623 161723944 2.130000e-123 453.0
56 TraesCS2D01G168100 chr2B 91.429 315 11 2 4714 5013 161725909 161726222 7.760000e-113 418.0
57 TraesCS2D01G168100 chr2B 79.920 498 75 9 295 789 162497549 162497074 4.810000e-90 342.0
58 TraesCS2D01G168100 chr2B 85.000 320 35 6 1930 2244 161723281 161723592 3.770000e-81 313.0
59 TraesCS2D01G168100 chr2B 86.111 288 37 3 1 287 161721459 161721744 1.750000e-79 307.0
60 TraesCS2D01G168100 chr2B 85.271 258 34 4 553 807 162496550 162496294 3.850000e-66 263.0
61 TraesCS2D01G168100 chr2B 91.860 172 6 2 2081 2244 162008806 162008977 3.020000e-57 233.0
62 TraesCS2D01G168100 chr2B 82.927 246 20 8 4612 4850 162011196 162011426 8.510000e-48 202.0
63 TraesCS2D01G168100 chr2B 83.105 219 32 4 306 521 162495488 162495272 1.420000e-45 195.0
64 TraesCS2D01G168100 chr2B 90.909 143 8 4 4531 4668 161725777 161725919 2.380000e-43 187.0
65 TraesCS2D01G168100 chr2B 80.252 238 45 1 302 537 162483234 162482997 1.430000e-40 178.0
66 TraesCS2D01G168100 chr2B 88.148 135 14 1 4284 4416 162010987 162011121 5.190000e-35 159.0
67 TraesCS2D01G168100 chr2B 92.453 106 7 1 1791 1896 162008568 162008672 3.130000e-32 150.0
68 TraesCS2D01G168100 chr2B 92.381 105 2 1 4909 5013 162012126 162012224 1.450000e-30 145.0
69 TraesCS2D01G168100 chr2B 91.579 95 8 0 4439 4533 214532779 214532873 1.130000e-26 132.0
70 TraesCS2D01G168100 chr2B 75.956 183 35 8 95 274 162497960 162497784 8.940000e-13 86.1
71 TraesCS2D01G168100 chr2B 82.796 93 8 4 181 269 162495822 162495734 5.380000e-10 76.8
72 TraesCS2D01G168100 chr2B 97.561 41 1 0 1904 1944 161723226 161723266 2.500000e-08 71.3
73 TraesCS2D01G168100 chr2B 81.522 92 12 3 181 271 162482288 162482201 2.500000e-08 71.3
74 TraesCS2D01G168100 chr7B 95.294 85 4 0 4448 4532 747110341 747110257 8.750000e-28 135.0
75 TraesCS2D01G168100 chr7D 93.258 89 6 0 4448 4536 4011448 4011360 1.130000e-26 132.0
76 TraesCS2D01G168100 chr5B 93.333 90 5 1 4444 4533 144134325 144134413 1.130000e-26 132.0
77 TraesCS2D01G168100 chr3B 93.258 89 6 0 4448 4536 612117734 612117822 1.130000e-26 132.0
78 TraesCS2D01G168100 chrUn 94.118 85 5 0 4448 4532 459259778 459259694 4.070000e-26 130.0
79 TraesCS2D01G168100 chrUn 91.398 93 8 0 4440 4532 36436883 36436975 1.460000e-25 128.0
80 TraesCS2D01G168100 chr4A 90.816 98 7 2 4435 4532 39531531 39531436 4.070000e-26 130.0
81 TraesCS2D01G168100 chr3D 85.345 116 15 2 4426 4539 434025904 434025789 8.820000e-23 119.0
82 TraesCS2D01G168100 chr6A 82.524 103 18 0 1380 1482 535154205 535154103 1.920000e-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 TraesCS2D01G168100 chr2D 111587673 111592685 5012 False 9258.000000 9258 100.000000 1 5013 1 chr2D.!!$F1 5012
1 TraesCS2D01G168100 chr2D 112177746 112181370 3624 True 625.600000 1068 86.839200 705 4262 5 chr2D.!!$R4 3557
2 TraesCS2D01G168100 chr2D 112098952 112103675 4723 False 533.857143 1652 86.574571 627 5013 7 chr2D.!!$F2 4386
3 TraesCS2D01G168100 chr2A 111920942 111925798 4856 False 867.500000 3319 94.108375 1 5013 8 chr2A.!!$F1 5012
4 TraesCS2D01G168100 chr2A 113309140 113312436 3296 True 512.500000 1434 86.978000 539 4267 6 chr2A.!!$R3 3728
5 TraesCS2D01G168100 chr2A 112744385 112749280 4895 False 418.255556 1428 86.460000 565 5013 9 chr2A.!!$F2 4448
6 TraesCS2D01G168100 chr2A 113196462 113196994 532 True 327.000000 327 78.445000 3334 3887 1 chr2A.!!$R1 553
7 TraesCS2D01G168100 chr2A 113343284 113344548 1264 True 277.000000 401 82.068333 283 807 3 chr2A.!!$R5 524
8 TraesCS2D01G168100 chr2B 162445497 162449043 3546 True 982.666667 1487 85.313000 741 4267 3 chr2B.!!$R1 3526
9 TraesCS2D01G168100 chr2B 161721459 161726222 4763 False 762.162500 2713 91.031625 1 5013 8 chr2B.!!$F2 5012
10 TraesCS2D01G168100 chr2B 162007423 162012224 4801 False 413.222222 1166 88.221556 725 5013 9 chr2B.!!$F3 4288

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
179 180 0.034477 AGAAACCGCCCTAACCCATG 60.034 55.000 0.00 0.00 0.00 3.66 F
854 1652 0.684535 CCCCAACCATCAAACCAACC 59.315 55.000 0.00 0.00 0.00 3.77 F
855 1653 0.684535 CCCAACCATCAAACCAACCC 59.315 55.000 0.00 0.00 0.00 4.11 F
2071 3062 0.893447 GTAGTACTTCCGCCCACAGT 59.107 55.000 0.00 0.00 0.00 3.55 F
2282 3373 1.194772 CGTGAAAGAGTCTTTTCGGCC 59.805 52.381 18.96 6.91 39.39 6.13 F
3423 4735 0.456142 CAGACGAGGATGCGTTCGAA 60.456 55.000 7.00 0.00 45.72 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 2944 0.405973 AAAGGGTCCCTGCCTTTCTC 59.594 55.000 12.53 0.0 32.13 2.87 R
2311 3409 0.167470 CAATCACGCAGCTCACAAGG 59.833 55.000 0.00 0.0 0.00 3.61 R
2807 3938 1.555533 ACCTTTCTTCCCTCGGTGATC 59.444 52.381 0.00 0.0 0.00 2.92 R
3343 4655 0.962356 CCCGCAAAGCCTGTGAAGAT 60.962 55.000 0.00 0.0 37.79 2.40 R
3975 5614 1.312815 GTTGCTCTTCACCAGCTTGT 58.687 50.000 0.00 0.0 37.79 3.16 R
4680 6538 1.069568 TGCATTTACGAACTGTTGGCG 60.070 47.619 0.00 0.0 0.00 5.69 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
22 23 1.917336 TAGCCCCATCCCAAACGTCC 61.917 60.000 0.00 0.00 0.00 4.79
30 31 4.142249 CCCATCCCAAACGTCCTTTTATTC 60.142 45.833 0.00 0.00 0.00 1.75
45 46 9.901172 GTCCTTTTATTCTCCTTCTAATAACCA 57.099 33.333 0.00 0.00 29.58 3.67
92 93 8.586570 TTTCAGTAACCGTCGTTTCTAATAAA 57.413 30.769 0.00 0.00 33.17 1.40
179 180 0.034477 AGAAACCGCCCTAACCCATG 60.034 55.000 0.00 0.00 0.00 3.66
201 202 5.754782 TGGTTTAGCCATCACAACTCATAT 58.245 37.500 0.00 0.00 43.61 1.78
204 205 6.765989 GGTTTAGCCATCACAACTCATATACA 59.234 38.462 0.00 0.00 37.17 2.29
372 376 5.378332 TCCCGGTTTTCATTAAAGAAGACA 58.622 37.500 13.90 0.00 35.11 3.41
653 1447 4.920340 CGCCTCATTATAACTCTAGCAGTG 59.080 45.833 0.00 0.00 34.56 3.66
854 1652 0.684535 CCCCAACCATCAAACCAACC 59.315 55.000 0.00 0.00 0.00 3.77
855 1653 0.684535 CCCAACCATCAAACCAACCC 59.315 55.000 0.00 0.00 0.00 4.11
1251 2058 2.482142 CCAAGAGGAGTGGATCGTAAGC 60.482 54.545 0.00 0.00 38.54 3.09
1299 2111 1.352687 GTGCTTTCTTTCCCTCCCTCT 59.647 52.381 0.00 0.00 0.00 3.69
1307 2132 1.885049 TTCCCTCCCTCTCTTCATGG 58.115 55.000 0.00 0.00 0.00 3.66
1450 2275 2.516460 CCGATCGTCGAGGACCCT 60.516 66.667 15.09 0.00 43.74 4.34
1678 2510 2.099263 GCGATGCAGAGACAAGGTACTA 59.901 50.000 0.00 0.00 38.49 1.82
1679 2511 3.243569 GCGATGCAGAGACAAGGTACTAT 60.244 47.826 0.00 0.00 38.49 2.12
1680 2512 4.023107 GCGATGCAGAGACAAGGTACTATA 60.023 45.833 0.00 0.00 38.49 1.31
1681 2513 5.453648 CGATGCAGAGACAAGGTACTATAC 58.546 45.833 0.00 0.00 38.49 1.47
1686 2518 6.607600 TGCAGAGACAAGGTACTATACATTCT 59.392 38.462 0.00 0.00 38.49 2.40
1699 2531 9.408069 GTACTATACATTCTAGTGCCAACATAC 57.592 37.037 0.00 0.00 31.96 2.39
1770 2606 8.946935 GCATTTATTTTTGTTGTTGCTTTCTTC 58.053 29.630 0.00 0.00 0.00 2.87
1798 2704 1.841334 TTTTTCCCCCTCTCCTCCAA 58.159 50.000 0.00 0.00 0.00 3.53
1834 2741 3.357203 GGAATCTTCCAGGTTCCCTTTC 58.643 50.000 4.62 0.00 46.76 2.62
1849 2757 2.946990 CCCTTTCGTAATATTTGGGCGT 59.053 45.455 0.00 0.00 0.00 5.68
1935 2843 5.475719 ACGCTATACACACAACAGTACATT 58.524 37.500 0.00 0.00 0.00 2.71
2001 2944 1.755179 ATTTCCGCCCACAGAATGAG 58.245 50.000 0.00 0.00 39.69 2.90
2045 3036 1.448717 GCTCGGTTGCCTCTTCTCC 60.449 63.158 0.00 0.00 0.00 3.71
2055 3046 1.134551 GCCTCTTCTCCCTTGCAGTAG 60.135 57.143 0.00 0.00 0.00 2.57
2057 3048 3.366396 CCTCTTCTCCCTTGCAGTAGTA 58.634 50.000 0.00 0.00 0.00 1.82
2058 3049 3.131400 CCTCTTCTCCCTTGCAGTAGTAC 59.869 52.174 0.00 0.00 0.00 2.73
2061 3052 4.463186 TCTTCTCCCTTGCAGTAGTACTTC 59.537 45.833 0.00 0.00 0.00 3.01
2063 3054 1.822990 TCCCTTGCAGTAGTACTTCCG 59.177 52.381 0.00 0.00 0.00 4.30
2064 3055 1.641577 CCTTGCAGTAGTACTTCCGC 58.358 55.000 0.00 0.00 0.00 5.54
2065 3056 1.641577 CTTGCAGTAGTACTTCCGCC 58.358 55.000 0.00 0.00 0.00 6.13
2067 3058 0.901114 TGCAGTAGTACTTCCGCCCA 60.901 55.000 0.00 0.00 0.00 5.36
2070 3061 1.135083 CAGTAGTACTTCCGCCCACAG 60.135 57.143 0.00 0.00 0.00 3.66
2071 3062 0.893447 GTAGTACTTCCGCCCACAGT 59.107 55.000 0.00 0.00 0.00 3.55
2073 3064 1.861982 AGTACTTCCGCCCACAGTAT 58.138 50.000 0.00 0.00 0.00 2.12
2074 3065 2.185387 AGTACTTCCGCCCACAGTATT 58.815 47.619 0.00 0.00 0.00 1.89
2075 3066 2.570302 AGTACTTCCGCCCACAGTATTT 59.430 45.455 0.00 0.00 0.00 1.40
2076 3067 2.579410 ACTTCCGCCCACAGTATTTT 57.421 45.000 0.00 0.00 0.00 1.82
2077 3068 2.871453 ACTTCCGCCCACAGTATTTTT 58.129 42.857 0.00 0.00 0.00 1.94
2103 3119 6.183360 TGCACTGTATTTGTATTTATGGGCTG 60.183 38.462 0.00 0.00 0.00 4.85
2110 3133 3.641046 TGTATTTATGGGCTGGTGCAAT 58.359 40.909 0.00 0.00 41.91 3.56
2112 3135 4.582656 TGTATTTATGGGCTGGTGCAATAC 59.417 41.667 0.00 0.00 41.91 1.89
2272 3363 1.521423 CGCTTTTCGTCGTGAAAGAGT 59.479 47.619 20.22 0.00 46.72 3.24
2279 3370 3.040795 TCGTCGTGAAAGAGTCTTTTCG 58.959 45.455 24.78 24.78 39.39 3.46
2280 3371 2.153247 CGTCGTGAAAGAGTCTTTTCGG 59.847 50.000 27.41 17.63 39.39 4.30
2281 3372 2.096860 GTCGTGAAAGAGTCTTTTCGGC 60.097 50.000 27.41 25.13 39.39 5.54
2282 3373 1.194772 CGTGAAAGAGTCTTTTCGGCC 59.805 52.381 18.96 6.91 39.39 6.13
2284 3375 1.420138 TGAAAGAGTCTTTTCGGCCCT 59.580 47.619 18.96 0.00 39.39 5.19
2285 3376 2.635915 TGAAAGAGTCTTTTCGGCCCTA 59.364 45.455 18.96 0.00 39.39 3.53
2311 3409 6.931243 TTTTTGTTCGCGGTAATTAAATCC 57.069 33.333 6.13 0.00 0.00 3.01
2444 3542 1.202651 ACCTGACCTTGTCTTTCACCG 60.203 52.381 0.00 0.00 33.15 4.94
2489 3592 9.450807 AAACTTTCTGAGACGAAACAAATAATG 57.549 29.630 0.00 0.00 0.00 1.90
2524 3629 4.886496 ACTAGTAACCTTGGTGTCCTTC 57.114 45.455 0.00 0.00 0.00 3.46
2545 3650 2.961526 TTCTCGCTATCAAGTCCACC 57.038 50.000 0.00 0.00 0.00 4.61
2550 3657 1.740380 CGCTATCAAGTCCACCACTGG 60.740 57.143 0.00 0.00 39.23 4.00
2551 3658 1.279271 GCTATCAAGTCCACCACTGGT 59.721 52.381 0.00 0.00 38.90 4.00
2552 3659 2.500098 GCTATCAAGTCCACCACTGGTA 59.500 50.000 0.00 0.00 38.90 3.25
2553 3660 3.679083 GCTATCAAGTCCACCACTGGTAC 60.679 52.174 0.00 0.00 38.90 3.34
2554 3661 2.097110 TCAAGTCCACCACTGGTACT 57.903 50.000 0.00 0.00 38.90 2.73
2555 3662 2.404559 TCAAGTCCACCACTGGTACTT 58.595 47.619 9.72 9.72 37.92 2.24
2556 3663 2.775384 TCAAGTCCACCACTGGTACTTT 59.225 45.455 12.11 0.00 36.53 2.66
2557 3664 3.201266 TCAAGTCCACCACTGGTACTTTT 59.799 43.478 12.11 0.00 36.53 2.27
2558 3665 4.409574 TCAAGTCCACCACTGGTACTTTTA 59.590 41.667 12.11 3.66 36.53 1.52
2559 3666 5.072600 TCAAGTCCACCACTGGTACTTTTAT 59.927 40.000 12.11 0.00 36.53 1.40
2560 3667 5.161943 AGTCCACCACTGGTACTTTTATC 57.838 43.478 0.00 0.00 38.90 1.75
2561 3668 4.019591 AGTCCACCACTGGTACTTTTATCC 60.020 45.833 0.00 0.00 38.90 2.59
2562 3669 3.911260 TCCACCACTGGTACTTTTATCCA 59.089 43.478 0.00 0.00 38.90 3.41
2563 3670 4.351407 TCCACCACTGGTACTTTTATCCAA 59.649 41.667 0.00 0.00 38.90 3.53
2564 3671 5.074115 CCACCACTGGTACTTTTATCCAAA 58.926 41.667 0.00 0.00 32.11 3.28
2565 3672 5.536916 CCACCACTGGTACTTTTATCCAAAA 59.463 40.000 0.00 0.00 32.11 2.44
2566 3673 6.041069 CCACCACTGGTACTTTTATCCAAAAA 59.959 38.462 0.00 0.00 31.34 1.94
2631 3761 4.329545 TGACAAGTCTGGCCCGGC 62.330 66.667 0.00 0.00 0.00 6.13
2652 3783 3.554960 GCTGGATCGATTGCAGGTGTATA 60.555 47.826 14.64 0.00 43.57 1.47
3231 4407 6.639686 GGTGTTTTCTTTAAAGGAAATCGACC 59.360 38.462 21.73 21.21 36.02 4.79
3300 4601 3.937706 AGTTGCTACTTCATGCATGTCTC 59.062 43.478 25.43 10.84 39.07 3.36
3320 4621 8.048534 TGTCTCGTTACTTACTTGCTACTAAT 57.951 34.615 0.00 0.00 0.00 1.73
3423 4735 0.456142 CAGACGAGGATGCGTTCGAA 60.456 55.000 7.00 0.00 45.72 3.71
3436 4752 1.818850 GTTCGAAGTATAGTGCGCGA 58.181 50.000 12.10 0.26 0.00 5.87
3496 4816 4.069304 TCCGATCCGTTGAAAGAACAAAT 58.931 39.130 0.00 0.00 0.00 2.32
3633 4971 2.093447 AGCCTGCTGAGGTATACACAAC 60.093 50.000 5.01 1.07 42.15 3.32
3762 5203 5.336102 ACCTACCTACCTAAAGCAACTACA 58.664 41.667 0.00 0.00 0.00 2.74
3853 5304 2.180432 AACTGCTTCCCGGTAAAGTC 57.820 50.000 13.58 7.95 31.20 3.01
4071 5710 4.797743 TGGAGATCGAGCAGGCTATATAT 58.202 43.478 2.38 0.00 0.00 0.86
4140 5787 8.304596 TGTCTTTCGTTTCATCTAGTAGAACAT 58.695 33.333 3.45 0.00 0.00 2.71
4211 5866 1.452833 CTTGCTAGGCCTTGGCTCC 60.453 63.158 24.30 7.16 39.70 4.70
4259 5914 2.354821 CGCAAGGTCTTGTAATTAGCCC 59.645 50.000 11.71 0.00 42.31 5.19
4267 5922 5.422145 GTCTTGTAATTAGCCCTCCGTTAA 58.578 41.667 0.00 0.00 0.00 2.01
4269 5924 6.541278 GTCTTGTAATTAGCCCTCCGTTAATT 59.459 38.462 0.00 0.00 40.02 1.40
4270 5925 7.066645 GTCTTGTAATTAGCCCTCCGTTAATTT 59.933 37.037 0.00 0.00 38.41 1.82
4271 5926 7.612633 TCTTGTAATTAGCCCTCCGTTAATTTT 59.387 33.333 0.00 0.00 38.41 1.82
4273 5928 7.540299 TGTAATTAGCCCTCCGTTAATTTTTG 58.460 34.615 0.00 0.00 38.41 2.44
4276 5931 4.948341 AGCCCTCCGTTAATTTTTGTTT 57.052 36.364 0.00 0.00 0.00 2.83
4277 5932 5.284861 AGCCCTCCGTTAATTTTTGTTTT 57.715 34.783 0.00 0.00 0.00 2.43
4278 5933 5.053811 AGCCCTCCGTTAATTTTTGTTTTG 58.946 37.500 0.00 0.00 0.00 2.44
4279 5934 4.319190 GCCCTCCGTTAATTTTTGTTTTGC 60.319 41.667 0.00 0.00 0.00 3.68
4280 5935 4.084797 CCCTCCGTTAATTTTTGTTTTGCG 60.085 41.667 0.00 0.00 0.00 4.85
4281 5936 4.740695 CCTCCGTTAATTTTTGTTTTGCGA 59.259 37.500 0.00 0.00 0.00 5.10
4282 5937 5.232414 CCTCCGTTAATTTTTGTTTTGCGAA 59.768 36.000 0.00 0.00 0.00 4.70
4284 5939 7.115095 CCTCCGTTAATTTTTGTTTTGCGAATA 59.885 33.333 0.00 0.00 0.00 1.75
4285 5940 7.998141 TCCGTTAATTTTTGTTTTGCGAATAG 58.002 30.769 0.00 0.00 0.00 1.73
4348 6082 1.633945 GCCCTCCTTTTTCTCACCCTA 59.366 52.381 0.00 0.00 0.00 3.53
4358 6092 8.098912 TCCTTTTTCTCACCCTACACTATAAAC 58.901 37.037 0.00 0.00 0.00 2.01
4446 6287 8.041323 AGTTATTGCTGTGCTAGTATTGTTAGT 58.959 33.333 0.00 0.00 0.00 2.24
4447 6288 8.665685 GTTATTGCTGTGCTAGTATTGTTAGTT 58.334 33.333 0.00 0.00 0.00 2.24
4448 6289 9.878667 TTATTGCTGTGCTAGTATTGTTAGTTA 57.121 29.630 0.00 0.00 0.00 2.24
4449 6290 7.591006 TTGCTGTGCTAGTATTGTTAGTTAC 57.409 36.000 0.00 0.00 0.00 2.50
4450 6291 6.931838 TGCTGTGCTAGTATTGTTAGTTACT 58.068 36.000 0.00 0.00 33.41 2.24
4451 6292 7.033791 TGCTGTGCTAGTATTGTTAGTTACTC 58.966 38.462 0.00 0.00 31.37 2.59
4452 6293 6.476053 GCTGTGCTAGTATTGTTAGTTACTCC 59.524 42.308 0.00 0.00 31.37 3.85
4453 6294 6.870769 TGTGCTAGTATTGTTAGTTACTCCC 58.129 40.000 0.00 0.00 31.37 4.30
4454 6295 6.438108 TGTGCTAGTATTGTTAGTTACTCCCA 59.562 38.462 0.00 0.00 31.37 4.37
4455 6296 6.755607 GTGCTAGTATTGTTAGTTACTCCCAC 59.244 42.308 0.00 0.00 31.37 4.61
4456 6297 6.666546 TGCTAGTATTGTTAGTTACTCCCACT 59.333 38.462 0.00 0.00 31.37 4.00
4457 6298 6.979238 GCTAGTATTGTTAGTTACTCCCACTG 59.021 42.308 0.00 0.00 31.37 3.66
4458 6299 6.930068 AGTATTGTTAGTTACTCCCACTGT 57.070 37.500 0.00 0.00 0.00 3.55
4459 6300 9.182214 CTAGTATTGTTAGTTACTCCCACTGTA 57.818 37.037 0.00 0.00 31.37 2.74
4460 6301 8.426569 AGTATTGTTAGTTACTCCCACTGTAA 57.573 34.615 0.00 0.00 0.00 2.41
4461 6302 8.873144 AGTATTGTTAGTTACTCCCACTGTAAA 58.127 33.333 0.00 0.00 32.58 2.01
4462 6303 7.974482 ATTGTTAGTTACTCCCACTGTAAAC 57.026 36.000 0.00 0.00 32.58 2.01
4463 6304 6.736110 TGTTAGTTACTCCCACTGTAAACT 57.264 37.500 0.00 0.00 32.58 2.66
4464 6305 7.838079 TGTTAGTTACTCCCACTGTAAACTA 57.162 36.000 0.00 0.00 32.58 2.24
4465 6306 8.248904 TGTTAGTTACTCCCACTGTAAACTAA 57.751 34.615 0.00 0.00 32.58 2.24
4466 6307 8.873144 TGTTAGTTACTCCCACTGTAAACTAAT 58.127 33.333 8.27 0.00 32.82 1.73
4475 6316 9.245962 CTCCCACTGTAAACTAATATAAGAACG 57.754 37.037 0.00 0.00 0.00 3.95
4476 6317 8.752187 TCCCACTGTAAACTAATATAAGAACGT 58.248 33.333 0.00 0.00 0.00 3.99
4477 6318 9.374838 CCCACTGTAAACTAATATAAGAACGTT 57.625 33.333 0.00 0.00 0.00 3.99
4505 6346 9.310716 AGATCACTATTTTAGTAACCTAAACGC 57.689 33.333 0.00 0.00 41.64 4.84
4506 6347 9.310716 GATCACTATTTTAGTAACCTAAACGCT 57.689 33.333 0.00 0.00 41.64 5.07
4507 6348 8.693542 TCACTATTTTAGTAACCTAAACGCTC 57.306 34.615 0.00 0.00 41.64 5.03
4508 6349 8.526147 TCACTATTTTAGTAACCTAAACGCTCT 58.474 33.333 0.00 0.00 41.64 4.09
4509 6350 9.148104 CACTATTTTAGTAACCTAAACGCTCTT 57.852 33.333 0.00 0.00 41.64 2.85
4522 6363 9.028185 ACCTAAACGCTCTTATATTTCTTTACG 57.972 33.333 0.00 0.00 0.00 3.18
4523 6364 8.485591 CCTAAACGCTCTTATATTTCTTTACGG 58.514 37.037 0.00 0.00 0.00 4.02
4524 6365 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
4525 6366 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
4526 6367 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
4527 6368 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
4528 6369 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
4529 6370 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
4570 6411 1.937223 CGTTGTAACTGTTGCTGGTGA 59.063 47.619 9.94 0.00 0.00 4.02
4646 6504 0.613260 CCCTAGCCAAGTGCACAGTA 59.387 55.000 21.04 1.74 44.83 2.74
4663 6521 4.703897 ACAGTACATGTGTATGGGTATGC 58.296 43.478 9.11 0.00 41.91 3.14
4664 6522 4.163268 ACAGTACATGTGTATGGGTATGCA 59.837 41.667 9.11 0.00 41.91 3.96
4665 6523 4.751600 CAGTACATGTGTATGGGTATGCAG 59.248 45.833 9.11 0.00 38.66 4.41
4666 6524 3.931907 ACATGTGTATGGGTATGCAGT 57.068 42.857 0.00 0.00 38.66 4.40
4667 6525 3.544684 ACATGTGTATGGGTATGCAGTG 58.455 45.455 0.00 0.00 38.66 3.66
4675 6533 1.026718 GGGTATGCAGTGCACAGACC 61.027 60.000 26.64 26.64 43.04 3.85
4680 6538 0.950555 TGCAGTGCACAGACCGATTC 60.951 55.000 21.04 0.00 31.71 2.52
4719 6577 2.079158 CATGGACCGATCATGTATGCC 58.921 52.381 0.00 0.00 37.72 4.40
4734 6592 2.936919 ATGCCTGTGTGAGAAGTCAA 57.063 45.000 0.00 0.00 33.27 3.18
4795 6653 2.837031 CTTGCCCCTGTACGGCCAAT 62.837 60.000 2.24 0.00 46.48 3.16
4878 6755 0.595053 CGAGCATGCGACCGATTACT 60.595 55.000 20.09 0.00 0.00 2.24
5009 7611 0.030235 TCACGTGTCACGACCAAGAG 59.970 55.000 30.95 11.29 46.05 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 1.153229 GGCGGGATAAAAGCGACCT 60.153 57.895 0.00 0.00 0.00 3.85
179 180 6.765989 TGTATATGAGTTGTGATGGCTAAACC 59.234 38.462 0.00 0.00 39.84 3.27
372 376 5.891551 ACTAAACACAGAAATGGGTTGAAGT 59.108 36.000 0.00 1.88 35.33 3.01
782 1578 2.693864 CCTGGCCCACCTCTGGAT 60.694 66.667 0.00 0.00 40.55 3.41
854 1652 3.368501 TGGAGGGAGGAGAGGGGG 61.369 72.222 0.00 0.00 0.00 5.40
855 1653 2.041405 GTGGAGGGAGGAGAGGGG 60.041 72.222 0.00 0.00 0.00 4.79
865 1663 1.685820 GTTTCTGGGGAGTGGAGGG 59.314 63.158 0.00 0.00 0.00 4.30
1156 1963 2.187946 CAGAGACCCGGCCATCAC 59.812 66.667 2.24 0.00 0.00 3.06
1233 2040 2.445682 AGCTTACGATCCACTCCTCT 57.554 50.000 0.00 0.00 0.00 3.69
1251 2058 2.933906 GCCATGGATGCATGTCAAAAAG 59.066 45.455 23.60 9.27 0.00 2.27
1279 2091 1.352687 AGAGGGAGGGAAAGAAAGCAC 59.647 52.381 0.00 0.00 0.00 4.40
1307 2132 4.670347 GATTCAGGCAAAGATTCTTCAGC 58.330 43.478 12.79 12.79 0.00 4.26
1339 2164 1.296392 CTCCAATGCTGACGGGTGA 59.704 57.895 0.00 0.00 0.00 4.02
1485 2310 1.269998 AGAAGACACGAAACGAGGGAG 59.730 52.381 0.00 0.00 0.00 4.30
1677 2509 7.368198 TGGTATGTTGGCACTAGAATGTATA 57.632 36.000 0.00 0.00 0.00 1.47
1678 2510 6.247229 TGGTATGTTGGCACTAGAATGTAT 57.753 37.500 0.00 0.00 0.00 2.29
1679 2511 5.685520 TGGTATGTTGGCACTAGAATGTA 57.314 39.130 0.00 0.00 0.00 2.29
1680 2512 4.568072 TGGTATGTTGGCACTAGAATGT 57.432 40.909 0.00 0.00 0.00 2.71
1681 2513 4.516698 GGATGGTATGTTGGCACTAGAATG 59.483 45.833 0.00 0.00 0.00 2.67
1686 2518 1.140052 CGGGATGGTATGTTGGCACTA 59.860 52.381 0.00 0.00 0.00 2.74
1699 2531 2.910688 AATGTAGCACTACGGGATGG 57.089 50.000 3.52 0.00 38.85 3.51
1834 2741 6.020995 GTGAAAATCAACGCCCAAATATTACG 60.021 38.462 0.00 0.00 0.00 3.18
1849 2757 1.271934 CATGTGGGCGGTGAAAATCAA 59.728 47.619 0.00 0.00 0.00 2.57
1935 2843 0.528466 CGCTCGCTATGCCTCTTTGA 60.528 55.000 0.00 0.00 0.00 2.69
1983 2926 0.690192 TCTCATTCTGTGGGCGGAAA 59.310 50.000 0.00 0.00 42.60 3.13
2001 2944 0.405973 AAAGGGTCCCTGCCTTTCTC 59.594 55.000 12.53 0.00 32.13 2.87
2045 3036 1.641577 GCGGAAGTACTACTGCAAGG 58.358 55.000 0.00 0.00 39.30 3.61
2055 3046 2.685850 AATACTGTGGGCGGAAGTAC 57.314 50.000 0.00 0.00 0.00 2.73
2057 3048 2.579410 AAAATACTGTGGGCGGAAGT 57.421 45.000 0.00 0.00 0.00 3.01
2074 3065 9.429359 CCCATAAATACAAATACAGTGCAAAAA 57.571 29.630 0.00 0.00 0.00 1.94
2075 3066 7.547370 GCCCATAAATACAAATACAGTGCAAAA 59.453 33.333 0.00 0.00 0.00 2.44
2076 3067 7.038659 GCCCATAAATACAAATACAGTGCAAA 58.961 34.615 0.00 0.00 0.00 3.68
2077 3068 6.379703 AGCCCATAAATACAAATACAGTGCAA 59.620 34.615 0.00 0.00 0.00 4.08
2078 3069 5.890985 AGCCCATAAATACAAATACAGTGCA 59.109 36.000 0.00 0.00 0.00 4.57
2103 3119 1.330521 CACCTGCGTATGTATTGCACC 59.669 52.381 0.00 0.00 34.42 5.01
2110 3133 3.671008 AGTTGAACACCTGCGTATGTA 57.329 42.857 0.00 0.00 0.00 2.29
2112 3135 3.003275 ACAAAGTTGAACACCTGCGTATG 59.997 43.478 0.00 0.00 0.00 2.39
2308 3406 1.376424 CACGCAGCTCACAAGGGAT 60.376 57.895 0.00 0.00 0.00 3.85
2311 3409 0.167470 CAATCACGCAGCTCACAAGG 59.833 55.000 0.00 0.00 0.00 3.61
2444 3542 7.803279 AAGTTTAATTAATCTCGATCCCACC 57.197 36.000 8.83 0.00 0.00 4.61
2489 3592 6.944096 AGGTTACTAGTAGTTGATTGGGAAC 58.056 40.000 8.40 4.14 0.00 3.62
2524 3629 3.190874 GGTGGACTTGATAGCGAGAAAG 58.809 50.000 1.25 0.00 0.00 2.62
2568 3675 8.517175 AGTAGCTAGTACTACCAGTAGTGGACT 61.517 44.444 23.82 17.07 42.65 3.85
2569 3676 6.407979 AGTAGCTAGTACTACCAGTAGTGGAC 60.408 46.154 23.82 10.60 42.65 4.02
2570 3677 5.664908 AGTAGCTAGTACTACCAGTAGTGGA 59.335 44.000 23.82 6.12 42.65 4.02
2571 3678 5.759273 CAGTAGCTAGTACTACCAGTAGTGG 59.241 48.000 18.55 15.45 45.25 4.00
2572 3679 6.580788 TCAGTAGCTAGTACTACCAGTAGTG 58.419 44.000 18.55 5.00 45.25 2.74
2574 3681 8.805175 TCTATCAGTAGCTAGTACTACCAGTAG 58.195 40.741 0.00 3.25 42.97 2.57
2575 3682 8.718158 TCTATCAGTAGCTAGTACTACCAGTA 57.282 38.462 0.00 0.00 42.97 2.74
2576 3683 7.615039 TCTATCAGTAGCTAGTACTACCAGT 57.385 40.000 0.00 0.00 42.97 4.00
2631 3761 2.602257 TACACCTGCAATCGATCCAG 57.398 50.000 15.46 15.46 0.00 3.86
2762 3893 2.610859 GCCTTCACCTCCCTCCCA 60.611 66.667 0.00 0.00 0.00 4.37
2765 3896 3.003763 ACCGCCTTCACCTCCCTC 61.004 66.667 0.00 0.00 0.00 4.30
2807 3938 1.555533 ACCTTTCTTCCCTCGGTGATC 59.444 52.381 0.00 0.00 0.00 2.92
3122 4297 8.647796 TCTTTTCTTGGTCTCTCATGTAGTTTA 58.352 33.333 0.00 0.00 0.00 2.01
3210 4386 5.008811 TGCGGTCGATTTCCTTTAAAGAAAA 59.991 36.000 16.98 9.53 36.83 2.29
3231 4407 1.206578 CTAAACAACGGGCTGTGCG 59.793 57.895 0.00 0.00 0.00 5.34
3278 4474 3.937706 GAGACATGCATGAAGTAGCAACT 59.062 43.478 32.75 15.12 44.88 3.16
3343 4655 0.962356 CCCGCAAAGCCTGTGAAGAT 60.962 55.000 0.00 0.00 37.79 2.40
3423 4735 2.031069 CAGGTGTATCGCGCACTATACT 60.031 50.000 19.30 1.74 37.07 2.12
3436 4752 2.699954 CGCAAAAGAGGACAGGTGTAT 58.300 47.619 0.00 0.00 0.00 2.29
3496 4816 2.232756 TGCAAAAGAGCGTCAGTACA 57.767 45.000 0.00 0.00 37.31 2.90
3853 5304 7.541783 TCATTGCTTTATTTCTCCAAACAATCG 59.458 33.333 0.00 0.00 0.00 3.34
3975 5614 1.312815 GTTGCTCTTCACCAGCTTGT 58.687 50.000 0.00 0.00 37.79 3.16
4211 5866 8.576936 GAAGGATACAGTAATAGAAACCTTCG 57.423 38.462 0.00 0.00 40.45 3.79
4259 5914 5.874892 TCGCAAAACAAAAATTAACGGAG 57.125 34.783 0.00 0.00 0.00 4.63
4267 5922 5.408299 GGAAGGCTATTCGCAAAACAAAAAT 59.592 36.000 0.00 0.00 41.67 1.82
4269 5924 4.303282 GGAAGGCTATTCGCAAAACAAAA 58.697 39.130 0.00 0.00 41.67 2.44
4270 5925 3.305744 GGGAAGGCTATTCGCAAAACAAA 60.306 43.478 12.21 0.00 41.67 2.83
4271 5926 2.230266 GGGAAGGCTATTCGCAAAACAA 59.770 45.455 12.21 0.00 41.67 2.83
4273 5928 2.092323 AGGGAAGGCTATTCGCAAAAC 58.908 47.619 17.07 0.00 41.67 2.43
4276 5931 3.857157 ATAAGGGAAGGCTATTCGCAA 57.143 42.857 17.07 8.50 41.67 4.85
4277 5932 3.857157 AATAAGGGAAGGCTATTCGCA 57.143 42.857 17.07 3.19 41.67 5.10
4278 5933 3.685272 GCTAATAAGGGAAGGCTATTCGC 59.315 47.826 10.02 10.02 38.13 4.70
4279 5934 5.153950 AGCTAATAAGGGAAGGCTATTCG 57.846 43.478 0.00 0.00 0.00 3.34
4280 5935 7.766738 GTCATAGCTAATAAGGGAAGGCTATTC 59.233 40.741 0.00 0.00 39.83 1.75
4281 5936 7.237679 TGTCATAGCTAATAAGGGAAGGCTATT 59.762 37.037 0.00 0.00 39.83 1.73
4282 5937 6.730977 TGTCATAGCTAATAAGGGAAGGCTAT 59.269 38.462 0.00 0.00 41.67 2.97
4284 5939 4.907875 TGTCATAGCTAATAAGGGAAGGCT 59.092 41.667 0.00 0.00 0.00 4.58
4285 5940 5.012148 TCTGTCATAGCTAATAAGGGAAGGC 59.988 44.000 0.00 0.00 0.00 4.35
4287 5942 8.997323 CATTTCTGTCATAGCTAATAAGGGAAG 58.003 37.037 0.00 0.00 0.00 3.46
4288 5943 7.939039 CCATTTCTGTCATAGCTAATAAGGGAA 59.061 37.037 0.00 0.00 0.00 3.97
4289 5944 7.453393 CCATTTCTGTCATAGCTAATAAGGGA 58.547 38.462 0.00 0.00 0.00 4.20
4290 5945 6.656693 CCCATTTCTGTCATAGCTAATAAGGG 59.343 42.308 0.00 0.00 0.00 3.95
4291 5946 7.453393 TCCCATTTCTGTCATAGCTAATAAGG 58.547 38.462 0.00 0.00 0.00 2.69
4292 5947 8.153550 ACTCCCATTTCTGTCATAGCTAATAAG 58.846 37.037 0.00 0.00 0.00 1.73
4293 5948 7.933577 CACTCCCATTTCTGTCATAGCTAATAA 59.066 37.037 0.00 0.00 0.00 1.40
4295 5950 6.100279 TCACTCCCATTTCTGTCATAGCTAAT 59.900 38.462 0.00 0.00 0.00 1.73
4296 5951 5.425217 TCACTCCCATTTCTGTCATAGCTAA 59.575 40.000 0.00 0.00 0.00 3.09
4298 5953 3.776969 TCACTCCCATTTCTGTCATAGCT 59.223 43.478 0.00 0.00 0.00 3.32
4374 6123 7.333174 TCACATCATAACAAGCTAACGATGAAA 59.667 33.333 12.59 1.98 34.34 2.69
4449 6290 9.245962 CGTTCTTATATTAGTTTACAGTGGGAG 57.754 37.037 0.00 0.00 0.00 4.30
4450 6291 8.752187 ACGTTCTTATATTAGTTTACAGTGGGA 58.248 33.333 0.00 0.00 0.00 4.37
4451 6292 8.937634 ACGTTCTTATATTAGTTTACAGTGGG 57.062 34.615 0.00 0.00 0.00 4.61
4496 6337 9.028185 CGTAAAGAAATATAAGAGCGTTTAGGT 57.972 33.333 0.00 0.00 0.00 3.08
4497 6338 8.485591 CCGTAAAGAAATATAAGAGCGTTTAGG 58.514 37.037 0.00 0.00 0.00 2.69
4498 6339 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
4499 6340 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
4500 6341 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
4501 6342 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
4502 6343 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
4503 6344 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
4504 6345 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
4505 6346 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
4506 6347 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
4507 6348 9.640963 CATACTCCCTCCGTAAAGAAATATAAG 57.359 37.037 0.00 0.00 0.00 1.73
4508 6349 9.151177 ACATACTCCCTCCGTAAAGAAATATAA 57.849 33.333 0.00 0.00 0.00 0.98
4509 6350 8.716674 ACATACTCCCTCCGTAAAGAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
4510 6351 7.613551 ACATACTCCCTCCGTAAAGAAATAT 57.386 36.000 0.00 0.00 0.00 1.28
4511 6352 7.270047 CAACATACTCCCTCCGTAAAGAAATA 58.730 38.462 0.00 0.00 0.00 1.40
4512 6353 5.952347 ACATACTCCCTCCGTAAAGAAAT 57.048 39.130 0.00 0.00 0.00 2.17
4513 6354 5.484715 CAACATACTCCCTCCGTAAAGAAA 58.515 41.667 0.00 0.00 0.00 2.52
4514 6355 4.622220 GCAACATACTCCCTCCGTAAAGAA 60.622 45.833 0.00 0.00 0.00 2.52
4515 6356 3.118884 GCAACATACTCCCTCCGTAAAGA 60.119 47.826 0.00 0.00 0.00 2.52
4516 6357 3.195661 GCAACATACTCCCTCCGTAAAG 58.804 50.000 0.00 0.00 0.00 1.85
4517 6358 2.568062 TGCAACATACTCCCTCCGTAAA 59.432 45.455 0.00 0.00 0.00 2.01
4518 6359 2.181125 TGCAACATACTCCCTCCGTAA 58.819 47.619 0.00 0.00 0.00 3.18
4519 6360 1.855295 TGCAACATACTCCCTCCGTA 58.145 50.000 0.00 0.00 0.00 4.02
4520 6361 1.134401 CATGCAACATACTCCCTCCGT 60.134 52.381 0.00 0.00 0.00 4.69
4521 6362 1.586422 CATGCAACATACTCCCTCCG 58.414 55.000 0.00 0.00 0.00 4.63
4522 6363 1.212935 ACCATGCAACATACTCCCTCC 59.787 52.381 0.00 0.00 0.00 4.30
4523 6364 2.717639 ACCATGCAACATACTCCCTC 57.282 50.000 0.00 0.00 0.00 4.30
4524 6365 2.172717 GGTACCATGCAACATACTCCCT 59.827 50.000 7.15 0.00 0.00 4.20
4525 6366 2.172717 AGGTACCATGCAACATACTCCC 59.827 50.000 15.94 0.00 0.00 4.30
4526 6367 3.206150 CAGGTACCATGCAACATACTCC 58.794 50.000 15.94 0.00 0.00 3.85
4527 6368 3.206150 CCAGGTACCATGCAACATACTC 58.794 50.000 15.94 0.00 0.00 2.59
4528 6369 2.576191 ACCAGGTACCATGCAACATACT 59.424 45.455 15.94 0.00 0.00 2.12
4529 6370 2.943033 GACCAGGTACCATGCAACATAC 59.057 50.000 15.94 0.00 0.00 2.39
4646 6504 3.544684 CACTGCATACCCATACACATGT 58.455 45.455 0.00 0.00 0.00 3.21
4663 6521 1.959899 GCGAATCGGTCTGTGCACTG 61.960 60.000 19.41 18.10 0.00 3.66
4664 6522 1.738099 GCGAATCGGTCTGTGCACT 60.738 57.895 19.41 0.00 0.00 4.40
4665 6523 2.740714 GGCGAATCGGTCTGTGCAC 61.741 63.158 10.75 10.75 0.00 4.57
4666 6524 2.434185 GGCGAATCGGTCTGTGCA 60.434 61.111 4.35 0.00 0.00 4.57
4667 6525 2.032634 TTGGCGAATCGGTCTGTGC 61.033 57.895 4.35 0.00 0.00 4.57
4675 6533 1.342555 TACGAACTGTTGGCGAATCG 58.657 50.000 8.38 0.00 36.45 3.34
4680 6538 1.069568 TGCATTTACGAACTGTTGGCG 60.070 47.619 0.00 0.00 0.00 5.69
4719 6577 5.116180 TGGTAGTTTTGACTTCTCACACAG 58.884 41.667 0.00 0.00 0.00 3.66
4734 6592 4.607239 TGGTAGCTAGCTACTGGTAGTTT 58.393 43.478 39.86 11.64 45.88 2.66
4795 6653 2.942752 GCATTGATCTGAAGGTGCAGGA 60.943 50.000 0.00 0.00 36.55 3.86
4878 6755 1.309950 CTACTCGATCCGCCTTCTCA 58.690 55.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.