Multiple sequence alignment - TraesCS1A01G440100

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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 TraesCS1A01G440100 chr1A 100.000 3152 0 0 1 3152 589249494 589246343 0.000000e+00 5821.0
1 TraesCS1A01G440100 chr1A 95.735 211 4 4 2292 2498 395198099 395198308 5.040000e-88 335.0
2 TraesCS1A01G440100 chr1D 92.515 1149 56 10 919 2048 491589856 491588719 0.000000e+00 1618.0
3 TraesCS1A01G440100 chr1D 90.559 572 38 5 1 571 491597304 491596748 0.000000e+00 743.0
4 TraesCS1A01G440100 chr1D 90.941 563 32 7 2592 3152 491588197 491587652 0.000000e+00 739.0
5 TraesCS1A01G440100 chr1D 84.804 204 22 6 572 773 491595468 491595272 2.480000e-46 196.0
6 TraesCS1A01G440100 chr1D 98.214 56 1 0 2497 2552 491588663 491588608 7.190000e-17 99.0
7 TraesCS1A01G440100 chr6A 85.631 1204 163 10 960 2157 9364565 9365764 0.000000e+00 1256.0
8 TraesCS1A01G440100 chr6A 99.476 191 1 0 2309 2499 189563478 189563668 6.470000e-92 348.0
9 TraesCS1A01G440100 chr6A 95.238 42 1 1 2512 2552 30557023 30556982 7.300000e-07 65.8
10 TraesCS1A01G440100 chr1B 95.207 772 36 1 1 771 683539726 683538955 0.000000e+00 1219.0
11 TraesCS1A01G440100 chr1B 92.000 675 24 12 784 1432 683538888 683538218 0.000000e+00 920.0
12 TraesCS1A01G440100 chr1B 93.478 46 1 2 2512 2555 662161039 662161084 2.030000e-07 67.6
13 TraesCS1A01G440100 chr1B 95.238 42 1 1 2512 2552 662158485 662158526 7.300000e-07 65.8
14 TraesCS1A01G440100 chr6D 82.948 1167 178 16 977 2128 8987208 8988368 0.000000e+00 1033.0
15 TraesCS1A01G440100 chr6D 78.385 1263 247 23 968 2212 15358355 15357101 0.000000e+00 797.0
16 TraesCS1A01G440100 chr6D 78.537 1230 233 28 999 2211 8894056 8895271 0.000000e+00 780.0
17 TraesCS1A01G440100 chr6D 95.238 42 1 1 2512 2552 8816473 8816514 7.300000e-07 65.8
18 TraesCS1A01G440100 chr6D 95.122 41 1 1 2512 2551 8513089 8513049 2.620000e-06 63.9
19 TraesCS1A01G440100 chr6D 95.122 41 1 1 2512 2551 8819615 8819655 2.620000e-06 63.9
20 TraesCS1A01G440100 chr2B 81.234 1199 201 19 950 2131 800420976 800419785 0.000000e+00 946.0
21 TraesCS1A01G440100 chr2B 97.980 198 3 1 2310 2507 763841081 763841277 3.010000e-90 342.0
22 TraesCS1A01G440100 chr2B 100.000 33 0 0 2512 2544 89503469 89503501 9.440000e-06 62.1
23 TraesCS1A01G440100 chrUn 82.273 1100 169 20 999 2087 101167998 101169082 0.000000e+00 928.0
24 TraesCS1A01G440100 chrUn 84.071 452 41 12 2700 3150 71395591 71396012 1.050000e-109 407.0
25 TraesCS1A01G440100 chr7D 80.137 1168 208 20 999 2154 161390651 161391806 0.000000e+00 850.0
26 TraesCS1A01G440100 chr7B 80.348 1150 195 26 1019 2154 123655594 123656726 0.000000e+00 843.0
27 TraesCS1A01G440100 chr4B 99.479 192 1 0 2307 2498 545868208 545868017 1.800000e-92 350.0
28 TraesCS1A01G440100 chr4B 98.469 196 3 0 2308 2503 634327395 634327590 2.330000e-91 346.0
29 TraesCS1A01G440100 chr4A 99.476 191 1 0 2307 2497 31161985 31161795 6.470000e-92 348.0
30 TraesCS1A01G440100 chr2A 98.964 193 2 0 2306 2498 334889482 334889674 2.330000e-91 346.0
31 TraesCS1A01G440100 chr2A 95.349 215 8 2 2282 2495 718356341 718356554 1.080000e-89 340.0
32 TraesCS1A01G440100 chr6B 95.261 211 9 1 2282 2492 557419309 557419518 1.810000e-87 333.0
33 TraesCS1A01G440100 chr6B 95.238 42 1 1 2512 2552 16258741 16258782 7.300000e-07 65.8


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 TraesCS1A01G440100 chr1A 589246343 589249494 3151 True 5821.000000 5821 100.0000 1 3152 1 chr1A.!!$R1 3151
1 TraesCS1A01G440100 chr1D 491587652 491589856 2204 True 818.666667 1618 93.8900 919 3152 3 chr1D.!!$R1 2233
2 TraesCS1A01G440100 chr1D 491595272 491597304 2032 True 469.500000 743 87.6815 1 773 2 chr1D.!!$R2 772
3 TraesCS1A01G440100 chr6A 9364565 9365764 1199 False 1256.000000 1256 85.6310 960 2157 1 chr6A.!!$F1 1197
4 TraesCS1A01G440100 chr1B 683538218 683539726 1508 True 1069.500000 1219 93.6035 1 1432 2 chr1B.!!$R1 1431
5 TraesCS1A01G440100 chr6D 8987208 8988368 1160 False 1033.000000 1033 82.9480 977 2128 1 chr6D.!!$F2 1151
6 TraesCS1A01G440100 chr6D 15357101 15358355 1254 True 797.000000 797 78.3850 968 2212 1 chr6D.!!$R2 1244
7 TraesCS1A01G440100 chr6D 8894056 8895271 1215 False 780.000000 780 78.5370 999 2211 1 chr6D.!!$F1 1212
8 TraesCS1A01G440100 chr2B 800419785 800420976 1191 True 946.000000 946 81.2340 950 2131 1 chr2B.!!$R1 1181
9 TraesCS1A01G440100 chrUn 101167998 101169082 1084 False 928.000000 928 82.2730 999 2087 1 chrUn.!!$F2 1088
10 TraesCS1A01G440100 chr7D 161390651 161391806 1155 False 850.000000 850 80.1370 999 2154 1 chr7D.!!$F1 1155
11 TraesCS1A01G440100 chr7B 123655594 123656726 1132 False 843.000000 843 80.3480 1019 2154 1 chr7B.!!$F1 1135

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
456 458 0.178975 TTCCCCCGCATTCTGTTTGT 60.179 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 3734 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.0 0.0 0.0 44.78 4.85 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
43 44 3.181508 GCCGTTATAGTCTCGAGATAGGC 60.182 52.174 19.90 19.31 0.00 3.93
46 47 2.863132 ATAGTCTCGAGATAGGCCGT 57.137 50.000 19.90 0.55 0.00 5.68
123 124 2.105134 ACCAACCTTACGTCCACATTGA 59.895 45.455 0.00 0.00 0.00 2.57
301 303 1.068333 CCACACCATTCTTCAAAGCCG 60.068 52.381 0.00 0.00 0.00 5.52
305 307 0.179189 CCATTCTTCAAAGCCGTCGC 60.179 55.000 0.00 0.00 0.00 5.19
442 444 1.047801 ACATGTGCAACCTTTTCCCC 58.952 50.000 0.00 0.00 34.36 4.81
456 458 0.178975 TTCCCCCGCATTCTGTTTGT 60.179 50.000 0.00 0.00 0.00 2.83
550 552 1.228245 GATGTGTGCTGTGGGTGGT 60.228 57.895 0.00 0.00 0.00 4.16
567 569 3.814991 TCGAGCTAGGCGACTCAG 58.185 61.111 0.00 0.00 43.67 3.35
606 1887 5.023533 TGTTCTTTCGATCCCATAGAAGG 57.976 43.478 0.00 0.00 0.00 3.46
615 1896 2.274542 TCCCATAGAAGGTTGGAAGCA 58.725 47.619 0.00 0.00 34.81 3.91
686 1967 7.148787 CGAAACTCTAGTGGTATTCTGTTCAAC 60.149 40.741 0.00 0.00 0.00 3.18
715 1996 9.338622 ACAATGTTACCTATAAGTATCTTTGCC 57.661 33.333 13.20 0.00 34.06 4.52
728 2009 7.035840 AGTATCTTTGCCATTGAATTGCTAG 57.964 36.000 2.85 1.23 0.00 3.42
799 2108 9.573133 ACATTTTACTATGAGTATTTTGCTTGC 57.427 29.630 0.00 0.00 29.64 4.01
800 2109 9.571810 CATTTTACTATGAGTATTTTGCTTGCA 57.428 29.630 0.00 0.00 29.64 4.08
802 2111 9.973450 TTTTACTATGAGTATTTTGCTTGCAAA 57.027 25.926 15.66 15.66 29.64 3.68
844 2178 5.836821 TTTGTAGATGTGAGTCGCTCTAT 57.163 39.130 5.11 0.00 0.00 1.98
864 2198 1.477553 TCCAGCCCATTTTCAGATGC 58.522 50.000 0.00 0.00 0.00 3.91
881 2215 2.675423 CGGGAGACACTGACGGGA 60.675 66.667 0.00 0.00 0.00 5.14
1043 2414 4.463879 CACCCAGCTGCTCCCTCG 62.464 72.222 8.66 0.00 0.00 4.63
1308 2692 2.032528 CCCAAGTTCCTCTGCGCA 59.967 61.111 10.98 10.98 0.00 6.09
1329 2713 2.284995 GTGGAGAGGACCCTGGCT 60.285 66.667 0.00 0.00 0.00 4.75
1598 2988 2.009051 CGATATTGTCAGGCTGTGCAA 58.991 47.619 21.91 21.91 0.00 4.08
1727 3117 0.445436 CAAGCTGTCGCATTCCTCAC 59.555 55.000 0.00 0.00 39.10 3.51
1749 3139 1.470098 CAGGAGAAAATCACCGCCAAG 59.530 52.381 0.00 0.00 32.07 3.61
2023 3415 7.005902 TCATGACCGGGACTACTATAATACAA 58.994 38.462 6.32 0.00 0.00 2.41
2077 3469 5.513233 AGTTCATATGCCCTCACAAGAAAT 58.487 37.500 0.00 0.00 0.00 2.17
2128 3520 1.073897 GCTTGCAGAGGGGAAGTGT 59.926 57.895 0.00 0.00 45.83 3.55
2132 3524 2.584391 GCAGAGGGGAAGTGTCCGT 61.584 63.158 0.00 0.00 46.04 4.69
2133 3525 1.293498 CAGAGGGGAAGTGTCCGTG 59.707 63.158 0.00 0.00 46.04 4.94
2141 3533 2.093447 GGGAAGTGTCCGTGAGATTCAT 60.093 50.000 0.00 0.00 46.04 2.57
2144 3536 4.985409 GGAAGTGTCCGTGAGATTCATATC 59.015 45.833 0.00 0.00 33.05 1.63
2146 3538 5.193663 AGTGTCCGTGAGATTCATATCTG 57.806 43.478 0.00 0.00 41.23 2.90
2157 3549 6.261603 TGAGATTCATATCTGCATGAACCAAC 59.738 38.462 2.68 0.00 45.22 3.77
2164 3556 1.180456 TGCATGAACCAACAGCAGGG 61.180 55.000 0.00 0.00 0.00 4.45
2166 3558 0.599558 CATGAACCAACAGCAGGGTG 59.400 55.000 0.00 0.00 37.50 4.61
2168 3560 0.033601 TGAACCAACAGCAGGGTGTT 60.034 50.000 10.79 10.79 41.47 3.32
2187 3581 7.494298 AGGGTGTTGAATTTTGAAAATGTGTAC 59.506 33.333 3.62 2.08 0.00 2.90
2188 3582 7.494298 GGGTGTTGAATTTTGAAAATGTGTACT 59.506 33.333 3.62 0.00 0.00 2.73
2191 3585 7.547019 TGTTGAATTTTGAAAATGTGTACTGCA 59.453 29.630 3.62 0.00 0.00 4.41
2212 3606 2.421424 ACAATGAAGATTTCGCTCTGCC 59.579 45.455 0.00 0.00 0.00 4.85
2213 3607 2.408271 ATGAAGATTTCGCTCTGCCA 57.592 45.000 0.00 0.00 0.00 4.92
2214 3608 1.442769 TGAAGATTTCGCTCTGCCAC 58.557 50.000 0.00 0.00 0.00 5.01
2215 3609 0.729690 GAAGATTTCGCTCTGCCACC 59.270 55.000 0.00 0.00 0.00 4.61
2216 3610 0.678048 AAGATTTCGCTCTGCCACCC 60.678 55.000 0.00 0.00 0.00 4.61
2217 3611 1.377202 GATTTCGCTCTGCCACCCA 60.377 57.895 0.00 0.00 0.00 4.51
2218 3612 0.960364 GATTTCGCTCTGCCACCCAA 60.960 55.000 0.00 0.00 0.00 4.12
2219 3613 0.323725 ATTTCGCTCTGCCACCCAAT 60.324 50.000 0.00 0.00 0.00 3.16
2220 3614 0.326595 TTTCGCTCTGCCACCCAATA 59.673 50.000 0.00 0.00 0.00 1.90
2221 3615 0.326595 TTCGCTCTGCCACCCAATAA 59.673 50.000 0.00 0.00 0.00 1.40
2222 3616 0.326595 TCGCTCTGCCACCCAATAAA 59.673 50.000 0.00 0.00 0.00 1.40
2223 3617 0.734889 CGCTCTGCCACCCAATAAAG 59.265 55.000 0.00 0.00 0.00 1.85
2224 3618 1.106285 GCTCTGCCACCCAATAAAGG 58.894 55.000 0.00 0.00 0.00 3.11
2225 3619 1.616994 GCTCTGCCACCCAATAAAGGT 60.617 52.381 0.00 0.00 38.48 3.50
2226 3620 2.807676 CTCTGCCACCCAATAAAGGTT 58.192 47.619 0.00 0.00 34.56 3.50
2227 3621 3.165071 CTCTGCCACCCAATAAAGGTTT 58.835 45.455 0.00 0.00 34.56 3.27
2228 3622 3.161866 TCTGCCACCCAATAAAGGTTTC 58.838 45.455 0.00 0.00 34.56 2.78
2229 3623 2.233676 CTGCCACCCAATAAAGGTTTCC 59.766 50.000 0.00 0.00 34.56 3.13
2230 3624 2.158234 TGCCACCCAATAAAGGTTTCCT 60.158 45.455 0.00 0.00 34.56 3.36
2232 3626 3.306710 GCCACCCAATAAAGGTTTCCTTG 60.307 47.826 1.62 0.00 43.92 3.61
2233 3627 3.901222 CCACCCAATAAAGGTTTCCTTGT 59.099 43.478 1.62 0.00 43.92 3.16
2234 3628 4.346709 CCACCCAATAAAGGTTTCCTTGTT 59.653 41.667 1.62 0.00 43.92 2.83
2235 3629 5.510690 CCACCCAATAAAGGTTTCCTTGTTC 60.511 44.000 1.62 0.00 43.92 3.18
2236 3630 5.304357 CACCCAATAAAGGTTTCCTTGTTCT 59.696 40.000 1.62 0.00 43.92 3.01
2237 3631 5.903010 ACCCAATAAAGGTTTCCTTGTTCTT 59.097 36.000 1.62 0.00 43.92 2.52
2238 3632 6.385759 ACCCAATAAAGGTTTCCTTGTTCTTT 59.614 34.615 1.62 0.00 43.92 2.52
2239 3633 7.092623 ACCCAATAAAGGTTTCCTTGTTCTTTT 60.093 33.333 1.62 0.00 43.92 2.27
2240 3634 7.773224 CCCAATAAAGGTTTCCTTGTTCTTTTT 59.227 33.333 1.62 0.00 43.92 1.94
2241 3635 8.611757 CCAATAAAGGTTTCCTTGTTCTTTTTG 58.388 33.333 1.62 0.00 43.92 2.44
2242 3636 9.161629 CAATAAAGGTTTCCTTGTTCTTTTTGT 57.838 29.630 1.62 0.00 43.92 2.83
2279 3673 2.705658 TCCTGCTATTGTATGTCCCCTG 59.294 50.000 0.00 0.00 0.00 4.45
2280 3674 2.439507 CCTGCTATTGTATGTCCCCTGT 59.560 50.000 0.00 0.00 0.00 4.00
2281 3675 3.117888 CCTGCTATTGTATGTCCCCTGTT 60.118 47.826 0.00 0.00 0.00 3.16
2308 3702 4.842574 TGAATCTGTTGCATGCTACCTTA 58.157 39.130 25.88 13.61 0.00 2.69
2309 3703 4.877823 TGAATCTGTTGCATGCTACCTTAG 59.122 41.667 25.88 17.79 0.00 2.18
2310 3704 4.760530 ATCTGTTGCATGCTACCTTAGA 57.239 40.909 25.88 21.68 0.00 2.10
2311 3705 4.551702 TCTGTTGCATGCTACCTTAGAA 57.448 40.909 25.88 8.40 0.00 2.10
2312 3706 4.507710 TCTGTTGCATGCTACCTTAGAAG 58.492 43.478 25.88 16.54 0.00 2.85
2323 3717 0.548510 CCTTAGAAGGGGAGCCTTGG 59.451 60.000 0.00 0.00 42.66 3.61
2324 3718 0.106967 CTTAGAAGGGGAGCCTTGGC 60.107 60.000 2.97 2.97 0.00 4.52
2325 3719 1.910580 TTAGAAGGGGAGCCTTGGCG 61.911 60.000 5.95 0.00 0.00 5.69
2333 3727 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
2334 3728 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
2335 3729 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
2336 3730 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
2337 3731 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
2338 3732 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
2339 3733 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
2344 3738 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
2345 3739 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
2346 3740 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
2347 3741 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
2348 3742 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
2349 3743 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
2350 3744 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2351 3745 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2352 3746 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2353 3747 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2354 3748 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2355 3749 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2356 3750 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2357 3751 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2358 3752 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2373 3767 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
2374 3768 1.351017 TGAGGTCATGGGTTCAAGTCC 59.649 52.381 0.00 0.00 0.00 3.85
2375 3769 1.630878 GAGGTCATGGGTTCAAGTCCT 59.369 52.381 0.00 0.00 0.00 3.85
2376 3770 1.352352 AGGTCATGGGTTCAAGTCCTG 59.648 52.381 0.00 0.00 0.00 3.86
2377 3771 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
2378 3772 1.351017 GTCATGGGTTCAAGTCCTGGA 59.649 52.381 0.00 0.00 0.00 3.86
2379 3773 2.061848 TCATGGGTTCAAGTCCTGGAA 58.938 47.619 0.00 0.00 0.00 3.53
2380 3774 2.445145 TCATGGGTTCAAGTCCTGGAAA 59.555 45.455 0.00 0.00 0.00 3.13
2381 3775 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
2382 3776 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
2396 3790 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
2397 3791 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
2398 3792 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
2399 3793 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
2400 3794 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
2401 3795 6.430000 GGAAACAGCCTCTTACAGAAATGTAA 59.570 38.462 1.31 1.31 33.73 2.41
2403 3797 5.491982 ACAGCCTCTTACAGAAATGTAAGG 58.508 41.667 21.68 12.72 46.67 2.69
2404 3798 5.248477 ACAGCCTCTTACAGAAATGTAAGGA 59.752 40.000 21.68 11.60 46.67 3.36
2405 3799 6.173339 CAGCCTCTTACAGAAATGTAAGGAA 58.827 40.000 21.68 8.22 46.67 3.36
2406 3800 6.655003 CAGCCTCTTACAGAAATGTAAGGAAA 59.345 38.462 21.68 7.67 46.67 3.13
2407 3801 6.881602 AGCCTCTTACAGAAATGTAAGGAAAG 59.118 38.462 21.68 14.39 46.67 2.62
2408 3802 6.094186 GCCTCTTACAGAAATGTAAGGAAAGG 59.906 42.308 21.68 20.70 46.67 3.11
2409 3803 6.094186 CCTCTTACAGAAATGTAAGGAAAGGC 59.906 42.308 21.68 0.00 46.67 4.35
2410 3804 6.779860 TCTTACAGAAATGTAAGGAAAGGCT 58.220 36.000 21.68 0.00 46.67 4.58
2411 3805 6.655003 TCTTACAGAAATGTAAGGAAAGGCTG 59.345 38.462 21.68 0.00 46.67 4.85
2412 3806 3.507622 ACAGAAATGTAAGGAAAGGCTGC 59.492 43.478 0.00 0.00 0.00 5.25
2413 3807 2.749621 AGAAATGTAAGGAAAGGCTGCG 59.250 45.455 0.00 0.00 0.00 5.18
2414 3808 2.200373 AATGTAAGGAAAGGCTGCGT 57.800 45.000 0.00 0.00 0.00 5.24
2415 3809 3.343941 AATGTAAGGAAAGGCTGCGTA 57.656 42.857 0.00 0.00 0.00 4.42
2416 3810 2.088950 TGTAAGGAAAGGCTGCGTAC 57.911 50.000 0.00 0.00 32.24 3.67
2417 3811 1.621814 TGTAAGGAAAGGCTGCGTACT 59.378 47.619 0.00 0.00 32.71 2.73
2418 3812 2.827322 TGTAAGGAAAGGCTGCGTACTA 59.173 45.455 0.00 0.00 32.71 1.82
2419 3813 3.449737 TGTAAGGAAAGGCTGCGTACTAT 59.550 43.478 0.00 0.00 32.71 2.12
2420 3814 4.646040 TGTAAGGAAAGGCTGCGTACTATA 59.354 41.667 0.00 0.00 32.71 1.31
2421 3815 4.323553 AAGGAAAGGCTGCGTACTATAG 57.676 45.455 0.00 0.00 0.00 1.31
2422 3816 3.563223 AGGAAAGGCTGCGTACTATAGA 58.437 45.455 6.78 0.00 0.00 1.98
2423 3817 3.318557 AGGAAAGGCTGCGTACTATAGAC 59.681 47.826 6.78 0.00 0.00 2.59
2424 3818 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
2425 3819 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
2426 3820 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
2427 3821 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
2428 3822 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
2429 3823 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
2430 3824 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
2431 3825 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
2432 3826 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
2433 3827 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
2438 3832 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2439 3833 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2440 3834 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2441 3835 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2442 3836 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2443 3837 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2444 3838 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2445 3839 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2446 3840 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
2447 3841 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
2448 3842 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
2449 3843 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
2450 3844 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
2451 3845 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
2452 3846 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
2453 3847 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
2454 3848 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2455 3849 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
2456 3850 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2457 3851 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2482 3876 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
2483 3877 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
2484 3878 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
2485 3879 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
2486 3880 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
2487 3881 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
2488 3882 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
2489 3883 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
2490 3884 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
2491 3885 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
2572 3978 7.006509 TCCTTTTGAACTTCTTCATCCTCATT 58.993 34.615 0.00 0.00 36.26 2.57
2573 3979 7.506938 TCCTTTTGAACTTCTTCATCCTCATTT 59.493 33.333 0.00 0.00 36.26 2.32
2578 3984 8.868522 TGAACTTCTTCATCCTCATTTAATGT 57.131 30.769 4.77 0.00 31.00 2.71
2579 3985 9.300681 TGAACTTCTTCATCCTCATTTAATGTT 57.699 29.630 4.77 0.00 31.00 2.71
2580 3986 9.565213 GAACTTCTTCATCCTCATTTAATGTTG 57.435 33.333 4.77 0.12 0.00 3.33
2582 3988 8.734386 ACTTCTTCATCCTCATTTAATGTTGAC 58.266 33.333 4.77 0.00 0.00 3.18
2584 3990 8.044060 TCTTCATCCTCATTTAATGTTGACAC 57.956 34.615 4.77 0.00 0.00 3.67
2586 3992 7.381766 TCATCCTCATTTAATGTTGACACAG 57.618 36.000 4.77 0.00 35.94 3.66
2588 3994 6.801539 TCCTCATTTAATGTTGACACAGTC 57.198 37.500 4.77 0.00 35.94 3.51
2589 3995 5.705441 TCCTCATTTAATGTTGACACAGTCC 59.295 40.000 4.77 0.00 35.94 3.85
2590 3996 5.707298 CCTCATTTAATGTTGACACAGTCCT 59.293 40.000 4.77 0.00 35.94 3.85
2598 4363 3.389656 TGTTGACACAGTCCTCATGGTAA 59.610 43.478 0.00 0.00 34.23 2.85
2628 4393 3.941483 TCAATCGAATTTCTGAGGGCTTC 59.059 43.478 0.00 0.00 0.00 3.86
2637 4402 1.712977 CTGAGGGCTTCATCTTGCGC 61.713 60.000 0.00 0.00 41.52 6.09
2639 4404 2.439156 GGGCTTCATCTTGCGCCT 60.439 61.111 4.18 0.00 42.13 5.52
2656 4421 4.212425 TGCGCCTTTTATACATACAATCCG 59.788 41.667 4.18 0.00 0.00 4.18
2667 4432 3.802139 ACATACAATCCGTACATTGCTCG 59.198 43.478 5.97 0.00 37.28 5.03
2709 4474 5.582269 GCTGTCTTTAGATGACAAGTGCATA 59.418 40.000 0.00 0.00 42.85 3.14
2722 4487 6.070481 TGACAAGTGCATAACTCCCAAGTATA 60.070 38.462 0.00 0.00 38.56 1.47
2725 4490 6.412362 AGTGCATAACTCCCAAGTATAGAG 57.588 41.667 0.00 0.00 31.64 2.43
2861 4626 7.575414 TTTGCTTATACACTCCTTTCACAAA 57.425 32.000 0.00 0.00 0.00 2.83
2876 4641 2.777692 TCACAAAGGAGGAGAAGTGGTT 59.222 45.455 0.00 0.00 0.00 3.67
2903 4668 1.000731 TGCAAAACAGGGCATGCTTAC 59.999 47.619 18.92 8.53 39.49 2.34
2940 4707 6.273825 ACTACTTCAAGGATAACACATAGCG 58.726 40.000 0.00 0.00 0.00 4.26
2963 4730 0.743097 GCCATTCCTGGATCAGTTGC 59.257 55.000 0.00 0.00 46.37 4.17
2972 4739 1.026182 GGATCAGTTGCGGTGCATCA 61.026 55.000 0.00 0.00 38.76 3.07
2974 4741 0.736636 ATCAGTTGCGGTGCATCATG 59.263 50.000 0.00 0.00 38.76 3.07
2979 4746 2.355756 AGTTGCGGTGCATCATGTATTC 59.644 45.455 0.00 0.00 38.76 1.75
2984 4751 4.761227 TGCGGTGCATCATGTATTCATATT 59.239 37.500 0.00 0.00 31.71 1.28
3016 4783 6.693315 AGACTAGTAGACTTGATGAGCTTC 57.307 41.667 3.59 0.00 0.00 3.86
3022 4789 4.750021 AGACTTGATGAGCTTCAGCATA 57.250 40.909 0.75 0.00 42.81 3.14
3025 4792 3.620374 ACTTGATGAGCTTCAGCATAACG 59.380 43.478 0.75 0.00 42.81 3.18
3043 4810 2.561569 ACGACTGTGCAAGTAAAAGCT 58.438 42.857 0.00 0.00 40.07 3.74
3044 4811 2.544267 ACGACTGTGCAAGTAAAAGCTC 59.456 45.455 0.00 0.00 40.07 4.09
3045 4812 2.802816 CGACTGTGCAAGTAAAAGCTCT 59.197 45.455 0.00 0.00 40.07 4.09
3046 4813 3.363378 CGACTGTGCAAGTAAAAGCTCTG 60.363 47.826 0.00 0.00 40.07 3.35
3047 4814 3.808728 ACTGTGCAAGTAAAAGCTCTGA 58.191 40.909 0.00 0.00 37.36 3.27
3048 4815 4.199310 ACTGTGCAAGTAAAAGCTCTGAA 58.801 39.130 0.00 0.00 37.36 3.02
3049 4816 4.640201 ACTGTGCAAGTAAAAGCTCTGAAA 59.360 37.500 0.00 0.00 37.36 2.69
3050 4817 5.173774 TGTGCAAGTAAAAGCTCTGAAAG 57.826 39.130 0.00 0.00 0.00 2.62
3051 4818 4.881273 TGTGCAAGTAAAAGCTCTGAAAGA 59.119 37.500 0.00 0.00 43.69 2.52
3099 4866 6.560253 TCAGAGCTCTTGACAAAATAAACC 57.440 37.500 15.27 0.00 0.00 3.27
3102 4869 5.827797 AGAGCTCTTGACAAAATAAACCACA 59.172 36.000 11.45 0.00 0.00 4.17
3137 4904 3.181510 GGCACCAAAATCGACTGTACATC 60.182 47.826 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 9.712359 GGTCTTAAGCATAGTTTTAAATAACGG 57.288 33.333 0.00 0.00 33.26 4.44
203 205 4.591321 AGGAGGACATAAGCAAAATGGA 57.409 40.909 0.00 0.00 0.00 3.41
442 444 1.002900 ACGTCAACAAACAGAATGCGG 60.003 47.619 0.00 0.00 42.53 5.69
456 458 3.063485 TGAATGCGATGAAGAACGTCAA 58.937 40.909 0.00 0.00 34.46 3.18
550 552 1.820056 CCTGAGTCGCCTAGCTCGA 60.820 63.158 0.00 0.00 34.67 4.04
567 569 7.516312 CGAAAGAACAAATAATAGTACGAGCCC 60.516 40.741 0.00 0.00 0.00 5.19
606 1887 5.531634 TGAATTTGTTCATCTGCTTCCAAC 58.468 37.500 0.00 0.00 0.00 3.77
694 1975 9.555727 TCAATGGCAAAGATACTTATAGGTAAC 57.444 33.333 0.00 0.00 0.00 2.50
712 1993 3.720949 GCATCTAGCAATTCAATGGCA 57.279 42.857 0.00 0.00 44.79 4.92
801 2110 8.862325 ACAAAAACTCAGATTTTTCCCTTTTT 57.138 26.923 0.00 0.00 39.25 1.94
802 2111 9.599866 CTACAAAAACTCAGATTTTTCCCTTTT 57.400 29.630 0.00 0.00 39.25 2.27
806 2139 8.360390 ACATCTACAAAAACTCAGATTTTTCCC 58.640 33.333 0.00 0.00 39.25 3.97
809 2142 9.956720 CTCACATCTACAAAAACTCAGATTTTT 57.043 29.630 0.00 0.00 41.38 1.94
825 2158 4.276183 TGGAATAGAGCGACTCACATCTAC 59.724 45.833 9.09 0.00 32.06 2.59
844 2178 1.826720 GCATCTGAAAATGGGCTGGAA 59.173 47.619 0.00 0.00 0.00 3.53
864 2198 2.675423 TCCCGTCAGTGTCTCCCG 60.675 66.667 0.00 0.00 0.00 5.14
881 2215 3.971702 GCTGACCAAGTGGCCCCT 61.972 66.667 0.00 0.00 39.32 4.79
1043 2414 1.331399 GGAGGTGGAGGCAGAGGTAC 61.331 65.000 0.00 0.00 0.00 3.34
1308 2692 2.120718 AGGGTCCTCTCCACGCTT 59.879 61.111 0.00 0.00 33.45 4.68
1727 3117 1.032114 GGCGGTGATTTTCTCCTGGG 61.032 60.000 0.00 0.00 0.00 4.45
1749 3139 2.440539 TCTTCTTCAAGTGCTCGACC 57.559 50.000 0.00 0.00 0.00 4.79
1752 3142 3.124297 GGAACATCTTCTTCAAGTGCTCG 59.876 47.826 0.00 0.00 0.00 5.03
2023 3415 1.107114 ACCTTCTCGCTGATCACGAT 58.893 50.000 16.87 3.85 39.12 3.73
2128 3520 4.281688 TCATGCAGATATGAATCTCACGGA 59.718 41.667 0.00 0.00 40.65 4.69
2132 3524 5.932455 TGGTTCATGCAGATATGAATCTCA 58.068 37.500 11.30 5.42 45.67 3.27
2133 3525 6.261603 TGTTGGTTCATGCAGATATGAATCTC 59.738 38.462 11.30 6.33 45.67 2.75
2141 3533 3.070476 TGCTGTTGGTTCATGCAGATA 57.930 42.857 0.00 0.00 0.00 1.98
2144 3536 3.786809 CTGCTGTTGGTTCATGCAG 57.213 52.632 0.00 0.00 43.71 4.41
2146 3538 1.181098 ACCCTGCTGTTGGTTCATGC 61.181 55.000 0.00 0.00 0.00 4.06
2157 3549 3.731652 TCAAAATTCAACACCCTGCTG 57.268 42.857 0.00 0.00 0.00 4.41
2164 3556 7.845622 GCAGTACACATTTTCAAAATTCAACAC 59.154 33.333 0.00 0.00 0.00 3.32
2166 3558 7.904094 TGCAGTACACATTTTCAAAATTCAAC 58.096 30.769 0.00 0.00 0.00 3.18
2187 3581 3.126514 AGAGCGAAATCTTCATTGTGCAG 59.873 43.478 0.00 0.00 0.00 4.41
2188 3582 3.076621 AGAGCGAAATCTTCATTGTGCA 58.923 40.909 0.00 0.00 0.00 4.57
2191 3585 2.421424 GGCAGAGCGAAATCTTCATTGT 59.579 45.455 0.00 0.00 0.00 2.71
2195 3589 1.442769 GTGGCAGAGCGAAATCTTCA 58.557 50.000 0.00 0.00 0.00 3.02
2196 3590 0.729690 GGTGGCAGAGCGAAATCTTC 59.270 55.000 0.00 0.00 0.00 2.87
2200 3594 0.323725 ATTGGGTGGCAGAGCGAAAT 60.324 50.000 0.00 0.00 0.00 2.17
2212 3606 5.304357 AGAACAAGGAAACCTTTATTGGGTG 59.696 40.000 0.00 0.00 41.69 4.61
2213 3607 5.464069 AGAACAAGGAAACCTTTATTGGGT 58.536 37.500 0.00 0.00 41.69 4.51
2214 3608 6.419484 AAGAACAAGGAAACCTTTATTGGG 57.581 37.500 0.00 0.00 41.69 4.12
2215 3609 8.611757 CAAAAAGAACAAGGAAACCTTTATTGG 58.388 33.333 0.00 0.00 41.69 3.16
2216 3610 9.161629 ACAAAAAGAACAAGGAAACCTTTATTG 57.838 29.630 0.00 0.00 41.69 1.90
2219 3613 9.642327 GTTACAAAAAGAACAAGGAAACCTTTA 57.358 29.630 0.00 0.00 41.69 1.85
2220 3614 8.372459 AGTTACAAAAAGAACAAGGAAACCTTT 58.628 29.630 0.00 0.00 41.69 3.11
2221 3615 7.903145 AGTTACAAAAAGAACAAGGAAACCTT 58.097 30.769 0.00 0.00 45.88 3.50
2222 3616 7.476540 AGTTACAAAAAGAACAAGGAAACCT 57.523 32.000 0.00 0.00 33.87 3.50
2287 3681 5.118990 TCTAAGGTAGCATGCAACAGATTC 58.881 41.667 21.98 0.00 0.00 2.52
2315 3709 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
2316 3710 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
2317 3711 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
2318 3712 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
2319 3713 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
2320 3714 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
2321 3715 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
2322 3716 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
2326 3720 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
2327 3721 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
2328 3722 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
2329 3723 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
2330 3724 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2331 3725 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2332 3726 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
2333 3727 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
2334 3728 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2335 3729 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
2336 3730 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
2337 3731 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2338 3732 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2339 3733 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2340 3734 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2341 3735 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2353 3747 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
2354 3748 1.351017 GGACTTGAACCCATGACCTCA 59.649 52.381 0.00 0.00 32.45 3.86
2355 3749 1.630878 AGGACTTGAACCCATGACCTC 59.369 52.381 0.00 0.00 37.82 3.85
2356 3750 1.352352 CAGGACTTGAACCCATGACCT 59.648 52.381 0.00 0.00 40.96 3.85
2357 3751 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
2358 3752 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
2359 3753 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
2360 3754 2.558359 GTTTCCAGGACTTGAACCCATG 59.442 50.000 0.00 0.00 0.00 3.66
2361 3755 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
2362 3756 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
2363 3757 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2364 3758 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2365 3759 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2366 3760 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2367 3761 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2368 3762 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2369 3763 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2370 3764 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
2371 3765 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
2372 3766 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
2373 3767 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
2374 3768 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
2388 3782 5.183140 GCAGCCTTTCCTTACATTTCTGTAA 59.817 40.000 0.00 0.00 43.80 2.41
2389 3783 4.700213 GCAGCCTTTCCTTACATTTCTGTA 59.300 41.667 0.00 0.00 36.79 2.74
2390 3784 3.507622 GCAGCCTTTCCTTACATTTCTGT 59.492 43.478 0.00 0.00 39.49 3.41
2391 3785 3.426695 CGCAGCCTTTCCTTACATTTCTG 60.427 47.826 0.00 0.00 0.00 3.02
2392 3786 2.749621 CGCAGCCTTTCCTTACATTTCT 59.250 45.455 0.00 0.00 0.00 2.52
2393 3787 2.488153 ACGCAGCCTTTCCTTACATTTC 59.512 45.455 0.00 0.00 0.00 2.17
2394 3788 2.514803 ACGCAGCCTTTCCTTACATTT 58.485 42.857 0.00 0.00 0.00 2.32
2395 3789 2.200373 ACGCAGCCTTTCCTTACATT 57.800 45.000 0.00 0.00 0.00 2.71
2396 3790 2.236395 AGTACGCAGCCTTTCCTTACAT 59.764 45.455 0.00 0.00 0.00 2.29
2397 3791 1.621814 AGTACGCAGCCTTTCCTTACA 59.378 47.619 0.00 0.00 0.00 2.41
2398 3792 2.381725 AGTACGCAGCCTTTCCTTAC 57.618 50.000 0.00 0.00 0.00 2.34
2399 3793 5.009410 GTCTATAGTACGCAGCCTTTCCTTA 59.991 44.000 0.00 0.00 0.00 2.69
2400 3794 3.958798 TCTATAGTACGCAGCCTTTCCTT 59.041 43.478 0.00 0.00 0.00 3.36
2401 3795 3.318557 GTCTATAGTACGCAGCCTTTCCT 59.681 47.826 0.00 0.00 0.00 3.36
2402 3796 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
2403 3797 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
2404 3798 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
2405 3799 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
2406 3800 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
2407 3801 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
2408 3802 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
2409 3803 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
2410 3804 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
2411 3805 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
2412 3806 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
2422 3816 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2423 3817 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2424 3818 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2425 3819 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2426 3820 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2427 3821 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2428 3822 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2429 3823 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
2430 3824 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
2431 3825 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2432 3826 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2433 3827 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2434 3828 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2435 3829 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2436 3830 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2437 3831 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
2438 3832 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
2439 3833 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
2440 3834 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
2452 3846 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2455 3849 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2456 3850 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2457 3851 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2458 3852 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2464 3858 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
2465 3859 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
2466 3860 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
2467 3861 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
2468 3862 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
2493 3887 4.069304 ACGACTAAGGTAGCATGCAAAAA 58.931 39.130 21.98 0.00 0.00 1.94
2494 3888 3.670625 ACGACTAAGGTAGCATGCAAAA 58.329 40.909 21.98 1.32 0.00 2.44
2495 3889 3.328382 ACGACTAAGGTAGCATGCAAA 57.672 42.857 21.98 4.29 0.00 3.68
2496 3890 3.000041 CAACGACTAAGGTAGCATGCAA 59.000 45.455 21.98 0.00 0.00 4.08
2497 3891 2.616960 CAACGACTAAGGTAGCATGCA 58.383 47.619 21.98 2.77 0.00 3.96
2498 3892 1.327764 GCAACGACTAAGGTAGCATGC 59.672 52.381 10.51 10.51 31.49 4.06
2499 3893 2.893637 AGCAACGACTAAGGTAGCATG 58.106 47.619 0.00 0.00 0.00 4.06
2500 3894 4.308899 CTAGCAACGACTAAGGTAGCAT 57.691 45.455 0.00 0.00 0.00 3.79
2501 3895 3.777465 CTAGCAACGACTAAGGTAGCA 57.223 47.619 0.00 0.00 0.00 3.49
2503 3897 3.243134 GGAGCTAGCAACGACTAAGGTAG 60.243 52.174 18.83 0.00 36.66 3.18
2504 3898 2.686915 GGAGCTAGCAACGACTAAGGTA 59.313 50.000 18.83 0.00 0.00 3.08
2505 3899 1.477295 GGAGCTAGCAACGACTAAGGT 59.523 52.381 18.83 0.00 0.00 3.50
2506 3900 1.751924 AGGAGCTAGCAACGACTAAGG 59.248 52.381 18.83 0.00 0.00 2.69
2507 3901 2.423892 TCAGGAGCTAGCAACGACTAAG 59.576 50.000 18.83 0.00 0.00 2.18
2508 3902 2.443416 TCAGGAGCTAGCAACGACTAA 58.557 47.619 18.83 0.00 0.00 2.24
2509 3903 2.124277 TCAGGAGCTAGCAACGACTA 57.876 50.000 18.83 0.00 0.00 2.59
2510 3904 1.135915 CATCAGGAGCTAGCAACGACT 59.864 52.381 18.83 4.19 0.00 4.18
2572 3978 5.003160 CCATGAGGACTGTGTCAACATTAA 58.997 41.667 0.00 0.00 34.06 1.40
2573 3979 4.041567 ACCATGAGGACTGTGTCAACATTA 59.958 41.667 0.00 0.00 38.69 1.90
2577 3983 2.550830 ACCATGAGGACTGTGTCAAC 57.449 50.000 0.00 0.00 38.69 3.18
2578 3984 4.698201 TTTACCATGAGGACTGTGTCAA 57.302 40.909 0.00 0.00 38.69 3.18
2579 3985 4.698201 TTTTACCATGAGGACTGTGTCA 57.302 40.909 0.00 0.00 38.69 3.58
2580 3986 9.561069 AATATATTTTACCATGAGGACTGTGTC 57.439 33.333 0.00 0.00 38.69 3.67
2582 3988 9.559732 TGAATATATTTTACCATGAGGACTGTG 57.440 33.333 0.00 0.00 38.69 3.66
2619 4384 1.746615 GCGCAAGATGAAGCCCTCA 60.747 57.895 0.30 0.00 43.02 3.86
2628 4393 6.299023 TGTATGTATAAAAGGCGCAAGATG 57.701 37.500 10.83 0.00 43.02 2.90
2639 4404 9.332502 AGCAATGTACGGATTGTATGTATAAAA 57.667 29.630 7.52 0.00 35.98 1.52
2656 4421 1.398390 CCTTGAAGGCGAGCAATGTAC 59.602 52.381 0.00 0.00 0.00 2.90
2709 4474 4.353777 TGACAGCTCTATACTTGGGAGTT 58.646 43.478 0.00 0.00 37.33 3.01
2722 4487 2.005451 GCATCGACAAATGACAGCTCT 58.995 47.619 0.00 0.00 0.00 4.09
2725 4490 0.804364 TGGCATCGACAAATGACAGC 59.196 50.000 0.00 0.00 39.77 4.40
2754 4519 9.847224 CATTTAGTGGGTTCCAGTTACTATTAT 57.153 33.333 0.00 0.00 38.30 1.28
2762 4527 5.255397 TGATCATTTAGTGGGTTCCAGTT 57.745 39.130 0.00 0.00 38.30 3.16
2861 4626 1.202818 GCACAAACCACTTCTCCTCCT 60.203 52.381 0.00 0.00 0.00 3.69
2876 4641 0.461693 GCCCTGTTTTGCAAGCACAA 60.462 50.000 12.99 0.00 0.00 3.33
2940 4707 3.567478 ACTGATCCAGGAATGGCTTAC 57.433 47.619 0.00 0.00 35.51 2.34
2953 4720 1.026182 TGATGCACCGCAACTGATCC 61.026 55.000 0.00 0.00 43.62 3.36
2963 4730 7.137490 AGAAATATGAATACATGATGCACCG 57.863 36.000 0.00 0.00 37.87 4.94
2984 4751 9.168451 CATCAAGTCTACTAGTCTAGTGAAGAA 57.832 37.037 20.78 4.16 39.81 2.52
3016 4783 1.800586 ACTTGCACAGTCGTTATGCTG 59.199 47.619 0.00 0.00 40.13 4.41
3022 4789 2.943033 AGCTTTTACTTGCACAGTCGTT 59.057 40.909 5.04 0.00 36.88 3.85
3025 4792 3.809832 TCAGAGCTTTTACTTGCACAGTC 59.190 43.478 5.04 0.00 36.88 3.51
3064 4831 9.155975 TGTCAAGAGCTCTGAAATTACTTTATC 57.844 33.333 19.06 1.89 0.00 1.75
3102 4869 2.733945 GTGCCGCCCACAACATTT 59.266 55.556 0.26 0.00 44.06 2.32
3111 4878 3.059386 TCGATTTTGGTGCCGCCC 61.059 61.111 0.00 0.00 36.04 6.13
3115 4882 2.147958 TGTACAGTCGATTTTGGTGCC 58.852 47.619 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.