Multiple sequence alignment - TraesCS6B01G010200

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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 TraesCS6B01G010200 chr6B 100.000 4933 0 0 1 4933 6194713 6199645 0.000000e+00 9110.0
1 TraesCS6B01G010200 chr6D 93.938 2326 102 20 1760 4066 3028786 3031091 0.000000e+00 3478.0
2 TraesCS6B01G010200 chr6D 95.986 872 34 1 892 1762 3026493 3027364 0.000000e+00 1415.0
3 TraesCS6B01G010200 chr6D 92.842 922 33 6 1 894 3025515 3026431 0.000000e+00 1306.0
4 TraesCS6B01G010200 chr6D 93.095 391 26 1 4543 4933 3031412 3031801 5.540000e-159 571.0
5 TraesCS6B01G010200 chr6D 96.537 231 8 0 4064 4294 3031127 3031357 2.790000e-102 383.0
6 TraesCS6B01G010200 chr6D 86.182 275 29 6 2970 3243 388990613 388990879 6.250000e-74 289.0
7 TraesCS6B01G010200 chr7A 88.043 1681 195 3 1219 2894 540755656 540757335 0.000000e+00 1986.0
8 TraesCS6B01G010200 chr7A 88.051 1632 189 4 1268 2894 540771592 540773222 0.000000e+00 1929.0
9 TraesCS6B01G010200 chr7A 90.180 998 98 0 1897 2894 540283208 540284205 0.000000e+00 1301.0
10 TraesCS6B01G010200 chr7A 85.280 428 63 0 1308 1735 539853010 539853437 4.530000e-120 442.0
11 TraesCS6B01G010200 chr7D 88.165 1673 184 10 1231 2894 459607713 459606046 0.000000e+00 1980.0
12 TraesCS6B01G010200 chr7D 88.012 1685 187 8 1221 2894 459433474 459431794 0.000000e+00 1978.0
13 TraesCS6B01G010200 chr7D 87.463 1683 205 3 1217 2894 459466303 459464622 0.000000e+00 1934.0
14 TraesCS6B01G010200 chr7D 86.449 428 58 0 1308 1735 459746676 459746249 2.080000e-128 470.0
15 TraesCS6B01G010200 chr7B 87.812 1682 197 5 1219 2894 481617926 481616247 0.000000e+00 1964.0
16 TraesCS6B01G010200 chr7B 77.402 1093 223 18 1821 2894 481624776 481623689 3.240000e-176 628.0
17 TraesCS6B01G010200 chr6A 88.529 401 24 14 1 383 1961255 1960859 2.690000e-127 466.0
18 TraesCS6B01G010200 chr6A 89.235 353 23 8 415 766 1960863 1960525 1.270000e-115 427.0
19 TraesCS6B01G010200 chr6A 87.121 264 26 4 2980 3243 596368539 596368794 4.830000e-75 292.0
20 TraesCS6B01G010200 chr6A 97.368 38 1 0 3928 3965 94094186 94094223 1.150000e-06 65.8
21 TraesCS6B01G010200 chr3D 91.373 255 12 7 2980 3232 309921815 309921569 1.700000e-89 340.0
22 TraesCS6B01G010200 chr3D 87.500 264 25 6 2980 3243 111256784 111257039 1.040000e-76 298.0
23 TraesCS6B01G010200 chr3D 86.716 271 29 4 2973 3243 586578930 586579193 1.340000e-75 294.0
24 TraesCS6B01G010200 chr3D 78.931 318 51 14 5 314 157179869 157180178 8.370000e-48 202.0
25 TraesCS6B01G010200 chr3D 96.190 105 4 0 2 106 157102556 157102660 6.560000e-39 172.0
26 TraesCS6B01G010200 chr5D 87.547 265 26 5 2980 3243 321547485 321547743 2.890000e-77 300.0
27 TraesCS6B01G010200 chr5D 90.476 105 10 0 2 106 62528280 62528176 6.660000e-29 139.0
28 TraesCS6B01G010200 chr5D 95.349 43 2 0 3928 3970 382515239 382515197 8.860000e-08 69.4
29 TraesCS6B01G010200 chr3A 86.891 267 27 4 2980 3246 363589488 363589230 4.830000e-75 292.0
30 TraesCS6B01G010200 chr3A 90.374 187 13 4 437 623 171173452 171173271 1.770000e-59 241.0
31 TraesCS6B01G010200 chr3A 79.257 323 52 13 2 317 171138046 171137732 1.390000e-50 211.0
32 TraesCS6B01G010200 chr3A 89.796 147 12 1 440 586 171137657 171137514 8.430000e-43 185.0
33 TraesCS6B01G010200 chr3A 94.286 105 6 0 2 106 171173911 171173807 1.420000e-35 161.0
34 TraesCS6B01G010200 chr3A 91.892 111 8 1 915 1024 697447667 697447777 2.380000e-33 154.0
35 TraesCS6B01G010200 chr3A 90.323 62 3 1 726 784 171173189 171173128 1.470000e-10 78.7
36 TraesCS6B01G010200 chr3A 87.037 54 5 2 3919 3970 105578421 105578368 5.330000e-05 60.2
37 TraesCS6B01G010200 chr5A 86.742 264 27 6 2980 3243 547605701 547605446 2.250000e-73 287.0
38 TraesCS6B01G010200 chr3B 81.361 338 36 14 3 314 228209238 228209574 2.950000e-62 250.0
39 TraesCS6B01G010200 chr3B 90.374 187 13 3 437 623 228209725 228209906 1.770000e-59 241.0
40 TraesCS6B01G010200 chr3B 89.231 65 4 1 723 784 228210001 228210065 1.470000e-10 78.7
41 TraesCS6B01G010200 chr3B 91.667 48 1 1 3917 3964 62725501 62725457 4.120000e-06 63.9
42 TraesCS6B01G010200 chr4D 94.393 107 5 1 918 1024 83148204 83148099 3.950000e-36 163.0
43 TraesCS6B01G010200 chr4B 94.393 107 5 1 918 1024 117778890 117778785 3.950000e-36 163.0
44 TraesCS6B01G010200 chr4A 92.241 116 8 1 909 1024 560995587 560995473 3.950000e-36 163.0
45 TraesCS6B01G010200 chr2D 93.519 108 7 0 917 1024 335687113 335687006 1.420000e-35 161.0
46 TraesCS6B01G010200 chr2D 95.238 42 1 1 3924 3964 616138870 616138829 1.150000e-06 65.8
47 TraesCS6B01G010200 chr2A 92.593 108 8 0 917 1024 446069394 446069287 6.610000e-34 156.0
48 TraesCS6B01G010200 chr2A 95.349 43 2 0 3928 3970 773951983 773951941 8.860000e-08 69.4
49 TraesCS6B01G010200 chr2B 91.667 108 9 0 917 1024 403699491 403699384 3.080000e-32 150.0
50 TraesCS6B01G010200 chr1B 90.826 109 10 0 918 1026 406351979 406351871 3.980000e-31 147.0
51 TraesCS6B01G010200 chr1B 95.238 42 1 1 3924 3964 660817476 660817517 1.150000e-06 65.8
52 TraesCS6B01G010200 chr5B 93.617 47 2 1 3919 3964 281821532 281821578 8.860000e-08 69.4


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 TraesCS6B01G010200 chr6B 6194713 6199645 4932 False 9110.0 9110 100.0000 1 4933 1 chr6B.!!$F1 4932
1 TraesCS6B01G010200 chr6D 3025515 3031801 6286 False 1430.6 3478 94.4796 1 4933 5 chr6D.!!$F2 4932
2 TraesCS6B01G010200 chr7A 540755656 540757335 1679 False 1986.0 1986 88.0430 1219 2894 1 chr7A.!!$F3 1675
3 TraesCS6B01G010200 chr7A 540771592 540773222 1630 False 1929.0 1929 88.0510 1268 2894 1 chr7A.!!$F4 1626
4 TraesCS6B01G010200 chr7A 540283208 540284205 997 False 1301.0 1301 90.1800 1897 2894 1 chr7A.!!$F2 997
5 TraesCS6B01G010200 chr7D 459606046 459607713 1667 True 1980.0 1980 88.1650 1231 2894 1 chr7D.!!$R3 1663
6 TraesCS6B01G010200 chr7D 459431794 459433474 1680 True 1978.0 1978 88.0120 1221 2894 1 chr7D.!!$R1 1673
7 TraesCS6B01G010200 chr7D 459464622 459466303 1681 True 1934.0 1934 87.4630 1217 2894 1 chr7D.!!$R2 1677
8 TraesCS6B01G010200 chr7B 481616247 481617926 1679 True 1964.0 1964 87.8120 1219 2894 1 chr7B.!!$R1 1675
9 TraesCS6B01G010200 chr7B 481623689 481624776 1087 True 628.0 628 77.4020 1821 2894 1 chr7B.!!$R2 1073
10 TraesCS6B01G010200 chr6A 1960525 1961255 730 True 446.5 466 88.8820 1 766 2 chr6A.!!$R1 765

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
530 553 0.034059 ACAGTGTTCTTCTCGCCCTG 59.966 55.000 0.00 0.0 0.00 4.45 F
1122 1232 0.179145 ACTAGTTTCGATGGACGCCG 60.179 55.000 0.00 0.0 42.26 6.46 F
2323 3883 1.283029 CCAATCCCAGCTTCTCTTCCA 59.717 52.381 0.00 0.0 0.00 3.53 F
3237 4797 0.104120 GCTGGCCAAAAAGAAACCGT 59.896 50.000 7.01 0.0 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 3859 0.033699 GAGAAGCTGGGATTGGGCTT 60.034 55.0 0.0 0.0 46.99 4.35 R
2563 4123 0.038166 CCCTTAGCCAAAGCCACTCA 59.962 55.0 0.0 0.0 41.25 3.41 R
3619 5179 0.038892 TCGTTAAAGCTCGGCTCGTT 60.039 50.0 0.0 0.0 38.25 3.85 R
4538 6154 0.457443 GCCTATTGGAGCACTTTGGC 59.543 55.0 0.0 0.0 34.57 4.52 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
150 157 1.943340 GGCAAGAAAGATCGATGGACC 59.057 52.381 0.54 0.00 0.00 4.46
153 160 3.521560 CAAGAAAGATCGATGGACCGAA 58.478 45.455 0.54 0.00 42.22 4.30
161 168 1.132199 CGATGGACCGAACGACGAAG 61.132 60.000 0.00 0.00 45.77 3.79
229 241 2.726351 GCTCTTCTGGTCCTCGGGG 61.726 68.421 0.00 0.00 0.00 5.73
274 286 0.606401 CCCATGTCTTGAGCAACCGT 60.606 55.000 0.00 0.00 0.00 4.83
291 303 1.151668 CGTTGCACCTTCTCTTCCAG 58.848 55.000 0.00 0.00 0.00 3.86
320 332 3.443045 CCCATTCCTGTGGCGCAC 61.443 66.667 10.83 6.37 37.96 5.34
349 366 3.892527 CGTTAATCATGTACGCGTGAA 57.107 42.857 24.59 10.43 43.10 3.18
355 378 3.715618 TCATGTACGCGTGAACAAATC 57.284 42.857 24.59 2.60 37.67 2.17
384 407 8.624028 GTTTGAAAATAAGTACATTTCGTTCCG 58.376 33.333 0.00 0.00 36.17 4.30
405 428 3.366121 CGACACACATAGAAGAAGCACAG 59.634 47.826 0.00 0.00 0.00 3.66
410 433 1.561542 CATAGAAGAAGCACAGGGGGT 59.438 52.381 0.00 0.00 0.00 4.95
513 536 1.679311 GACTCCATGCCTCCACACA 59.321 57.895 0.00 0.00 0.00 3.72
530 553 0.034059 ACAGTGTTCTTCTCGCCCTG 59.966 55.000 0.00 0.00 0.00 4.45
651 674 2.359975 GCGGGGGAGTTCAAGGTG 60.360 66.667 0.00 0.00 0.00 4.00
721 766 1.026718 AGGAAAAATCTGAGCGGCGG 61.027 55.000 9.78 0.00 0.00 6.13
805 850 5.812642 CCAGATGTGTCCAAGATGTTAGTAC 59.187 44.000 0.00 0.00 0.00 2.73
930 1039 2.633481 ACACCAACTACTCCCTCTGTTC 59.367 50.000 0.00 0.00 0.00 3.18
935 1044 4.284746 CCAACTACTCCCTCTGTTCTCTTT 59.715 45.833 0.00 0.00 0.00 2.52
978 1087 1.789464 GACAGAGCACAAGACAGTTCG 59.211 52.381 0.00 0.00 0.00 3.95
1054 1163 5.545658 TGGAGTATTTCATTTCGCAAGTC 57.454 39.130 0.00 0.00 39.48 3.01
1088 1198 4.724279 ACCACCTCCAAGTCAAAACTAT 57.276 40.909 0.00 0.00 33.48 2.12
1101 1211 5.049405 AGTCAAAACTATTTCAGTCGGCAAG 60.049 40.000 0.00 0.00 36.04 4.01
1104 1214 2.076863 ACTATTTCAGTCGGCAAGCAC 58.923 47.619 0.00 0.00 28.33 4.40
1108 1218 0.679505 TTCAGTCGGCAAGCACTAGT 59.320 50.000 0.00 0.00 0.00 2.57
1110 1220 1.070134 TCAGTCGGCAAGCACTAGTTT 59.930 47.619 0.00 0.00 0.00 2.66
1122 1232 0.179145 ACTAGTTTCGATGGACGCCG 60.179 55.000 0.00 0.00 42.26 6.46
1128 1238 2.947118 TTCGATGGACGCCGAATCCG 62.947 60.000 0.00 0.00 39.49 4.18
1290 1404 6.116126 ACTTTGATTTCTACACTCCATAGCC 58.884 40.000 0.00 0.00 0.00 3.93
1300 1418 2.035576 CACTCCATAGCCGTAACCTACC 59.964 54.545 0.00 0.00 0.00 3.18
1417 1535 7.025963 GCAAGGAAACTGAAAATGATAGACAG 58.974 38.462 0.00 0.00 42.68 3.51
1457 1575 2.267324 GACTCTCAGGCCCAGCAC 59.733 66.667 0.00 0.00 0.00 4.40
1480 1598 4.095483 CGAGTTTTAGCTTCATGGAGCAAT 59.905 41.667 27.76 10.85 45.12 3.56
1537 1655 2.006772 CAGCAAACCGTATCCTCGC 58.993 57.895 0.00 0.00 0.00 5.03
1783 3327 4.949856 ACATATGTCAATCTTGGGGTGAAC 59.050 41.667 1.41 0.00 0.00 3.18
1829 3373 3.584848 GTCCCTGGCATATAGTTCATCCT 59.415 47.826 0.00 0.00 0.00 3.24
1850 3394 4.201950 CCTTCCGAATACTTTGGCTCAATG 60.202 45.833 0.00 0.00 33.95 2.82
1892 3436 1.902938 GCCAAAGGCTCTCTTCAACT 58.097 50.000 0.00 0.00 46.69 3.16
1993 3552 7.450903 CCCCTATTGAATACCTCGATTTAAGT 58.549 38.462 0.00 0.00 30.20 2.24
2239 3799 1.427753 CTTGTTGGAAGGTTACCCCCT 59.572 52.381 10.91 0.00 35.96 4.79
2323 3883 1.283029 CCAATCCCAGCTTCTCTTCCA 59.717 52.381 0.00 0.00 0.00 3.53
2328 3888 2.443255 TCCCAGCTTCTCTTCCAAAAGT 59.557 45.455 0.00 0.00 33.95 2.66
2439 3999 4.635765 TGATTTGTCATACAACAGGCTAGC 59.364 41.667 6.04 6.04 37.90 3.42
2563 4123 7.014711 TCGATAGGCAATCTTTCTGATAGTCTT 59.985 37.037 0.00 0.00 34.45 3.01
2610 4170 4.277476 CAAATTTCTGGGCCTATACCACA 58.723 43.478 4.53 0.00 33.63 4.17
2719 4279 1.414181 CACCGCTTGGTCCATCTATCT 59.586 52.381 0.00 0.00 45.05 1.98
2883 4443 2.820787 ACCTTCGTCAGAACTCACTAGG 59.179 50.000 0.00 0.00 32.15 3.02
2986 4546 2.022527 ACCTCTCCTATTTGCTCCCTCT 60.023 50.000 0.00 0.00 0.00 3.69
3209 4769 6.516739 TTGTGTAGTTTGACATTGACCAAA 57.483 33.333 0.00 0.00 0.00 3.28
3222 4782 7.980662 TGACATTGACCAAATTTTATATGCTGG 59.019 33.333 0.00 0.00 0.00 4.85
3223 4783 6.762661 ACATTGACCAAATTTTATATGCTGGC 59.237 34.615 0.00 0.00 0.00 4.85
3229 4789 6.944862 ACCAAATTTTATATGCTGGCCAAAAA 59.055 30.769 7.01 10.16 0.00 1.94
3235 4795 2.549064 ATGCTGGCCAAAAAGAAACC 57.451 45.000 7.01 0.00 0.00 3.27
3237 4797 0.104120 GCTGGCCAAAAAGAAACCGT 59.896 50.000 7.01 0.00 0.00 4.83
3238 4798 1.851658 CTGGCCAAAAAGAAACCGTG 58.148 50.000 7.01 0.00 0.00 4.94
3248 4808 0.981183 AGAAACCGTGGGAGCACATA 59.019 50.000 0.00 0.00 0.00 2.29
3258 4818 4.009675 GTGGGAGCACATACTTTGATGAA 58.990 43.478 0.00 0.00 0.00 2.57
3359 4919 5.216614 AGTAGGGTGTTTTGTCTTCTCTC 57.783 43.478 0.00 0.00 0.00 3.20
3397 4957 5.646793 CAGTGTTGTTCTGATGGATGAAGAT 59.353 40.000 0.00 0.00 35.20 2.40
3398 4958 6.820152 CAGTGTTGTTCTGATGGATGAAGATA 59.180 38.462 0.00 0.00 35.20 1.98
3412 4972 8.737168 TGGATGAAGATAACCAATACTTTCAG 57.263 34.615 0.00 0.00 0.00 3.02
3413 4973 8.328758 TGGATGAAGATAACCAATACTTTCAGT 58.671 33.333 0.00 0.00 0.00 3.41
3433 4993 2.064434 TTCAATGTGTGCACCTTCCA 57.936 45.000 15.69 6.23 0.00 3.53
3461 5021 1.333931 CATGCGCTACTTACTCTCCGA 59.666 52.381 9.73 0.00 0.00 4.55
3518 5078 3.662759 TTGTTGGAACTCTCCCAAAGT 57.337 42.857 0.00 0.00 44.41 2.66
3543 5103 4.584029 GATCACATCGAAACACACGAAT 57.416 40.909 0.00 0.00 42.80 3.34
3548 5108 0.231024 TCGAAACACACGAATGCACG 59.769 50.000 0.00 0.00 36.84 5.34
3563 5123 2.329379 TGCACGCGAACAAAAACTTTT 58.671 38.095 15.93 0.00 0.00 2.27
3596 5156 2.483491 GTCTCGTACCCTCTAATAGGCG 59.517 54.545 0.00 0.00 45.03 5.52
3607 5167 4.261197 CCTCTAATAGGCGCAAAATCAACC 60.261 45.833 10.83 0.00 38.97 3.77
3613 5173 1.953017 CGCAAAATCAACCGACCCA 59.047 52.632 0.00 0.00 0.00 4.51
3614 5174 0.312416 CGCAAAATCAACCGACCCAA 59.688 50.000 0.00 0.00 0.00 4.12
3615 5175 1.665735 CGCAAAATCAACCGACCCAAG 60.666 52.381 0.00 0.00 0.00 3.61
3616 5176 1.934849 GCAAAATCAACCGACCCAAGC 60.935 52.381 0.00 0.00 0.00 4.01
3617 5177 1.613437 CAAAATCAACCGACCCAAGCT 59.387 47.619 0.00 0.00 0.00 3.74
3618 5178 1.995376 AAATCAACCGACCCAAGCTT 58.005 45.000 0.00 0.00 0.00 3.74
3619 5179 2.871096 AATCAACCGACCCAAGCTTA 57.129 45.000 0.00 0.00 0.00 3.09
3620 5180 2.871096 ATCAACCGACCCAAGCTTAA 57.129 45.000 0.00 0.00 0.00 1.85
3621 5181 1.886886 TCAACCGACCCAAGCTTAAC 58.113 50.000 0.00 0.00 0.00 2.01
3622 5182 0.515564 CAACCGACCCAAGCTTAACG 59.484 55.000 0.00 2.79 0.00 3.18
3623 5183 0.393820 AACCGACCCAAGCTTAACGA 59.606 50.000 0.00 0.00 0.00 3.85
3624 5184 0.037605 ACCGACCCAAGCTTAACGAG 60.038 55.000 0.00 0.73 0.00 4.18
3686 5246 2.224450 CGGTAATCCCACCCCTAATCAC 60.224 54.545 0.00 0.00 34.90 3.06
3695 5255 1.572415 ACCCCTAATCACGGACTAGGA 59.428 52.381 9.21 0.00 33.87 2.94
3720 5280 5.455392 TCAACAGCTAACACGAACTAGTAC 58.545 41.667 0.00 0.00 0.00 2.73
3723 5283 6.081872 ACAGCTAACACGAACTAGTACTTT 57.918 37.500 0.00 0.00 0.00 2.66
3779 5339 6.034044 CACGACTAGCACTTCTATTTTGACTC 59.966 42.308 0.00 0.00 0.00 3.36
3780 5340 6.093404 CGACTAGCACTTCTATTTTGACTCA 58.907 40.000 0.00 0.00 0.00 3.41
3831 5391 2.354821 CCTAAACTAATCACCGGCAAGC 59.645 50.000 0.00 0.00 0.00 4.01
3851 5411 2.862921 GCCCGATCACTTCCTAATCGTC 60.863 54.545 0.00 0.00 40.41 4.20
3867 5427 2.089980 TCGTCCAGAACTAGCCTACAC 58.910 52.381 0.00 0.00 0.00 2.90
3905 5465 2.258897 CCATGCATGCAACGCACA 59.741 55.556 26.68 0.00 43.04 4.57
3907 5467 0.738063 CCATGCATGCAACGCACATT 60.738 50.000 26.68 1.67 43.04 2.71
3908 5468 0.368567 CATGCATGCAACGCACATTG 59.631 50.000 26.68 11.98 43.04 2.82
3915 5475 3.383026 CAACGCACATTGCACCTAC 57.617 52.632 0.00 0.00 45.36 3.18
3916 5476 0.109781 CAACGCACATTGCACCTACC 60.110 55.000 0.00 0.00 45.36 3.18
3917 5477 1.241315 AACGCACATTGCACCTACCC 61.241 55.000 0.00 0.00 45.36 3.69
3918 5478 1.377202 CGCACATTGCACCTACCCT 60.377 57.895 0.00 0.00 45.36 4.34
3920 5480 1.256812 GCACATTGCACCTACCCTTT 58.743 50.000 0.00 0.00 44.26 3.11
3922 5482 2.037121 GCACATTGCACCTACCCTTTTT 59.963 45.455 0.00 0.00 44.26 1.94
3959 5534 5.904362 AGCAAGGTGATATTCTTGGTTTC 57.096 39.130 10.99 0.64 45.69 2.78
3965 5540 4.941873 GGTGATATTCTTGGTTTCGTCCTT 59.058 41.667 0.00 0.00 0.00 3.36
3981 5556 4.338682 TCGTCCTTCTTATAGGTTCTCTGC 59.661 45.833 0.00 0.00 36.63 4.26
3983 5558 5.394224 CGTCCTTCTTATAGGTTCTCTGCAA 60.394 44.000 0.00 0.00 36.63 4.08
3984 5559 6.407202 GTCCTTCTTATAGGTTCTCTGCAAA 58.593 40.000 0.00 0.00 36.63 3.68
4014 5589 6.761242 TCAGTCCCTTCACATATAATTTCGTG 59.239 38.462 0.00 0.00 0.00 4.35
4016 5591 4.819630 TCCCTTCACATATAATTTCGTGCC 59.180 41.667 0.00 0.00 0.00 5.01
4019 5594 5.333339 CCTTCACATATAATTTCGTGCCTCG 60.333 44.000 0.00 0.00 41.41 4.63
4020 5595 4.689071 TCACATATAATTTCGTGCCTCGT 58.311 39.130 0.00 0.00 40.80 4.18
4021 5596 5.113383 TCACATATAATTTCGTGCCTCGTT 58.887 37.500 0.00 0.00 40.80 3.85
4103 5719 3.318839 CCGGTTTACCATCCGTATAGACA 59.681 47.826 0.00 0.00 44.51 3.41
4255 5871 0.402121 GTTCTTCCAGCTGGGTTCCT 59.598 55.000 32.23 0.00 38.11 3.36
4272 5888 5.493809 GGTTCCTACCTGCTACAAACATTA 58.506 41.667 0.00 0.00 41.53 1.90
4294 5910 5.776173 AAAAACGGTTACATGATGGAACA 57.224 34.783 21.12 0.00 42.93 3.18
4310 5926 5.181690 TGGAACACAACAAGCTTAATGTC 57.818 39.130 12.09 4.11 0.00 3.06
4311 5927 4.887071 TGGAACACAACAAGCTTAATGTCT 59.113 37.500 12.09 4.58 0.00 3.41
4312 5928 5.359576 TGGAACACAACAAGCTTAATGTCTT 59.640 36.000 12.09 8.22 0.00 3.01
4313 5929 5.915196 GGAACACAACAAGCTTAATGTCTTC 59.085 40.000 16.65 16.65 0.00 2.87
4314 5930 6.238759 GGAACACAACAAGCTTAATGTCTTCT 60.239 38.462 20.70 7.14 0.00 2.85
4315 5931 6.699575 ACACAACAAGCTTAATGTCTTCTT 57.300 33.333 12.09 0.00 0.00 2.52
4316 5932 7.100458 ACACAACAAGCTTAATGTCTTCTTT 57.900 32.000 12.09 0.00 0.00 2.52
4317 5933 7.547227 ACACAACAAGCTTAATGTCTTCTTTT 58.453 30.769 12.09 0.00 0.00 2.27
4318 5934 8.034804 ACACAACAAGCTTAATGTCTTCTTTTT 58.965 29.630 12.09 0.00 0.00 1.94
4319 5935 9.515020 CACAACAAGCTTAATGTCTTCTTTTTA 57.485 29.630 12.09 0.00 0.00 1.52
4330 5946 8.729805 AATGTCTTCTTTTTAATTTGTTGGCA 57.270 26.923 0.00 0.00 0.00 4.92
4331 5947 8.907222 ATGTCTTCTTTTTAATTTGTTGGCAT 57.093 26.923 0.00 0.00 0.00 4.40
4332 5948 8.140677 TGTCTTCTTTTTAATTTGTTGGCATG 57.859 30.769 0.00 0.00 0.00 4.06
4333 5949 7.071414 GTCTTCTTTTTAATTTGTTGGCATGC 58.929 34.615 9.90 9.90 0.00 4.06
4334 5950 6.765036 TCTTCTTTTTAATTTGTTGGCATGCA 59.235 30.769 21.36 2.54 0.00 3.96
4374 5990 3.744940 ATCATGGTGGCCCAATATAGG 57.255 47.619 0.00 0.00 46.04 2.57
4399 6015 9.530633 GGAATTACAATATATAAGCGGAGTAGG 57.469 37.037 0.00 0.00 0.00 3.18
4404 6020 7.556844 ACAATATATAAGCGGAGTAGGATTGG 58.443 38.462 0.00 0.00 0.00 3.16
4405 6021 7.180408 ACAATATATAAGCGGAGTAGGATTGGT 59.820 37.037 0.00 0.00 0.00 3.67
4406 6022 3.753294 ATAAGCGGAGTAGGATTGGTG 57.247 47.619 0.00 0.00 0.00 4.17
4407 6023 1.276622 AAGCGGAGTAGGATTGGTGT 58.723 50.000 0.00 0.00 0.00 4.16
4408 6024 0.537188 AGCGGAGTAGGATTGGTGTG 59.463 55.000 0.00 0.00 0.00 3.82
4409 6025 0.535335 GCGGAGTAGGATTGGTGTGA 59.465 55.000 0.00 0.00 0.00 3.58
4410 6026 1.739371 GCGGAGTAGGATTGGTGTGAC 60.739 57.143 0.00 0.00 0.00 3.67
4411 6027 1.134788 CGGAGTAGGATTGGTGTGACC 60.135 57.143 0.00 0.00 39.22 4.02
4412 6028 2.188817 GGAGTAGGATTGGTGTGACCT 58.811 52.381 0.00 0.00 39.58 3.85
4413 6029 2.168728 GGAGTAGGATTGGTGTGACCTC 59.831 54.545 0.00 0.00 39.58 3.85
4414 6030 3.100671 GAGTAGGATTGGTGTGACCTCT 58.899 50.000 0.00 0.00 39.58 3.69
4415 6031 3.100671 AGTAGGATTGGTGTGACCTCTC 58.899 50.000 0.00 0.00 39.58 3.20
4416 6032 2.334006 AGGATTGGTGTGACCTCTCT 57.666 50.000 0.00 0.00 39.58 3.10
4417 6033 2.183679 AGGATTGGTGTGACCTCTCTC 58.816 52.381 0.00 0.00 39.58 3.20
4418 6034 1.902508 GGATTGGTGTGACCTCTCTCA 59.097 52.381 0.00 0.00 39.58 3.27
4419 6035 2.503356 GGATTGGTGTGACCTCTCTCAT 59.497 50.000 0.00 0.00 39.58 2.90
4420 6036 3.529533 GATTGGTGTGACCTCTCTCATG 58.470 50.000 0.00 0.00 39.58 3.07
4421 6037 2.309136 TGGTGTGACCTCTCTCATGA 57.691 50.000 0.00 0.00 39.58 3.07
4422 6038 2.608623 TGGTGTGACCTCTCTCATGAA 58.391 47.619 0.00 0.00 39.58 2.57
4423 6039 3.176411 TGGTGTGACCTCTCTCATGAAT 58.824 45.455 0.00 0.00 39.58 2.57
4424 6040 4.352893 TGGTGTGACCTCTCTCATGAATA 58.647 43.478 0.00 0.00 39.58 1.75
4425 6041 4.160439 TGGTGTGACCTCTCTCATGAATAC 59.840 45.833 0.00 0.00 39.58 1.89
4426 6042 4.160439 GGTGTGACCTCTCTCATGAATACA 59.840 45.833 0.00 0.00 34.73 2.29
4427 6043 5.337571 GGTGTGACCTCTCTCATGAATACAA 60.338 44.000 0.00 0.00 34.73 2.41
4428 6044 6.166279 GTGTGACCTCTCTCATGAATACAAA 58.834 40.000 0.00 0.00 0.00 2.83
4429 6045 6.650807 GTGTGACCTCTCTCATGAATACAAAA 59.349 38.462 0.00 0.00 0.00 2.44
4430 6046 7.335422 GTGTGACCTCTCTCATGAATACAAAAT 59.665 37.037 0.00 0.00 0.00 1.82
4431 6047 8.539544 TGTGACCTCTCTCATGAATACAAAATA 58.460 33.333 0.00 0.00 0.00 1.40
4432 6048 9.383519 GTGACCTCTCTCATGAATACAAAATAA 57.616 33.333 0.00 0.00 0.00 1.40
4433 6049 9.958180 TGACCTCTCTCATGAATACAAAATAAA 57.042 29.630 0.00 0.00 0.00 1.40
4457 6073 6.588719 TTCAAATTGATTGGGTTAGACTGG 57.411 37.500 0.00 0.00 39.62 4.00
4458 6074 5.640147 TCAAATTGATTGGGTTAGACTGGT 58.360 37.500 0.00 0.00 39.62 4.00
4459 6075 5.710099 TCAAATTGATTGGGTTAGACTGGTC 59.290 40.000 0.00 0.00 39.62 4.02
4460 6076 4.927267 ATTGATTGGGTTAGACTGGTCA 57.073 40.909 3.51 0.00 0.00 4.02
4461 6077 4.927267 TTGATTGGGTTAGACTGGTCAT 57.073 40.909 3.51 0.00 0.00 3.06
4462 6078 4.927267 TGATTGGGTTAGACTGGTCATT 57.073 40.909 3.51 0.00 0.00 2.57
4463 6079 5.255397 TGATTGGGTTAGACTGGTCATTT 57.745 39.130 3.51 0.00 0.00 2.32
4464 6080 5.009631 TGATTGGGTTAGACTGGTCATTTG 58.990 41.667 3.51 0.00 0.00 2.32
4465 6081 4.715534 TTGGGTTAGACTGGTCATTTGA 57.284 40.909 3.51 0.00 0.00 2.69
4466 6082 4.927267 TGGGTTAGACTGGTCATTTGAT 57.073 40.909 3.51 0.00 0.00 2.57
4467 6083 5.255397 TGGGTTAGACTGGTCATTTGATT 57.745 39.130 3.51 0.00 0.00 2.57
4468 6084 5.009631 TGGGTTAGACTGGTCATTTGATTG 58.990 41.667 3.51 0.00 0.00 2.67
4469 6085 5.222027 TGGGTTAGACTGGTCATTTGATTGA 60.222 40.000 3.51 0.00 0.00 2.57
4470 6086 5.888161 GGGTTAGACTGGTCATTTGATTGAT 59.112 40.000 3.51 0.00 0.00 2.57
4471 6087 6.378280 GGGTTAGACTGGTCATTTGATTGATT 59.622 38.462 3.51 0.00 0.00 2.57
4472 6088 7.253422 GGTTAGACTGGTCATTTGATTGATTG 58.747 38.462 3.51 0.00 0.00 2.67
4473 6089 5.909621 AGACTGGTCATTTGATTGATTGG 57.090 39.130 3.51 0.00 0.00 3.16
4474 6090 4.708421 AGACTGGTCATTTGATTGATTGGG 59.292 41.667 3.51 0.00 0.00 4.12
4475 6091 3.196254 ACTGGTCATTTGATTGATTGGGC 59.804 43.478 0.00 0.00 0.00 5.36
4476 6092 3.443052 TGGTCATTTGATTGATTGGGCT 58.557 40.909 0.00 0.00 0.00 5.19
4477 6093 3.196039 TGGTCATTTGATTGATTGGGCTG 59.804 43.478 0.00 0.00 0.00 4.85
4478 6094 3.431207 GGTCATTTGATTGATTGGGCTGG 60.431 47.826 0.00 0.00 0.00 4.85
4479 6095 3.448301 GTCATTTGATTGATTGGGCTGGA 59.552 43.478 0.00 0.00 0.00 3.86
4480 6096 3.448301 TCATTTGATTGATTGGGCTGGAC 59.552 43.478 0.00 0.00 0.00 4.02
4481 6097 2.601240 TTGATTGATTGGGCTGGACA 57.399 45.000 0.00 0.00 0.00 4.02
4482 6098 2.601240 TGATTGATTGGGCTGGACAA 57.399 45.000 0.00 0.00 0.00 3.18
4483 6099 2.170166 TGATTGATTGGGCTGGACAAC 58.830 47.619 0.00 0.00 0.00 3.32
4484 6100 1.133025 GATTGATTGGGCTGGACAACG 59.867 52.381 0.00 0.00 0.00 4.10
4485 6101 0.893270 TTGATTGGGCTGGACAACGG 60.893 55.000 0.00 0.00 0.00 4.44
4506 6122 4.461784 GAGCTCGAACTCCACGAC 57.538 61.111 4.41 0.00 35.88 4.34
4507 6123 1.512310 GAGCTCGAACTCCACGACG 60.512 63.158 4.41 0.00 35.88 5.12
4508 6124 2.185103 GAGCTCGAACTCCACGACGT 62.185 60.000 4.41 0.00 35.88 4.34
4509 6125 1.796749 GCTCGAACTCCACGACGTC 60.797 63.158 5.18 5.18 35.88 4.34
4510 6126 1.154263 CTCGAACTCCACGACGTCC 60.154 63.158 10.58 0.00 35.88 4.79
4511 6127 2.501222 CGAACTCCACGACGTCCG 60.501 66.667 10.58 7.90 45.44 4.79
4512 6128 2.804090 GAACTCCACGACGTCCGC 60.804 66.667 10.58 0.00 43.32 5.54
4513 6129 4.353437 AACTCCACGACGTCCGCC 62.353 66.667 10.58 0.00 43.32 6.13
4552 6168 2.192861 CCACGCCAAAGTGCTCCAA 61.193 57.895 0.00 0.00 40.59 3.53
4569 6185 1.306654 AATAGGCTCACCCGTCCCA 60.307 57.895 0.00 0.00 39.21 4.37
4598 6214 3.043998 CTCCAGATCCGGAGTAGGG 57.956 63.158 15.88 9.12 46.48 3.53
4600 6216 2.565645 CCAGATCCGGAGTAGGGCG 61.566 68.421 11.34 0.00 0.00 6.13
4619 6235 3.049080 GCCCAATCCTCTCGCCCTT 62.049 63.158 0.00 0.00 0.00 3.95
4622 6238 1.821332 CAATCCTCTCGCCCTTGGC 60.821 63.158 0.00 0.00 46.75 4.52
4696 6312 1.670949 GCAGATGCCAGAGTCGGAGA 61.671 60.000 5.36 0.00 34.31 3.71
4762 6378 2.361104 TCTTCCCGCCAATGTGCC 60.361 61.111 0.00 0.00 0.00 5.01
4764 6380 4.292145 TTCCCGCCAATGTGCCCA 62.292 61.111 0.00 0.00 0.00 5.36
4850 6466 1.423056 GAGACGGACGGTAGACACG 59.577 63.158 0.00 0.00 37.36 4.49
4855 6471 4.487412 GACGGTAGACACGCCCGG 62.487 72.222 0.00 0.00 45.85 5.73
4870 6486 1.270041 GCCCGGTGAAAAATGCAAAGA 60.270 47.619 0.00 0.00 0.00 2.52
4875 6491 3.123050 GGTGAAAAATGCAAAGACGCTT 58.877 40.909 0.00 0.00 0.00 4.68
4896 6512 3.535561 TCGGATCAGGATTTGAAGCTTC 58.464 45.455 19.89 19.89 39.77 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 2.647683 TGCCACATAAGACACCAACA 57.352 45.000 0.00 0.00 0.00 3.33
150 157 2.396508 GCGTCATATACTTCGTCGTTCG 59.603 50.000 0.00 0.00 41.41 3.95
153 160 1.945394 AGGCGTCATATACTTCGTCGT 59.055 47.619 0.00 0.00 33.09 4.34
161 168 2.124903 CAACGGTGAGGCGTCATATAC 58.875 52.381 12.93 0.00 34.36 1.47
162 169 1.067974 CCAACGGTGAGGCGTCATATA 59.932 52.381 12.93 0.00 34.36 0.86
163 170 0.179084 CCAACGGTGAGGCGTCATAT 60.179 55.000 12.93 0.00 34.36 1.78
164 171 1.216977 CCAACGGTGAGGCGTCATA 59.783 57.895 12.93 0.00 34.36 2.15
165 172 2.047274 CCAACGGTGAGGCGTCAT 60.047 61.111 12.93 0.00 34.36 3.06
166 173 3.542676 ACCAACGGTGAGGCGTCA 61.543 61.111 0.00 4.68 32.98 4.35
229 241 1.210155 GATGTTCCACAAGGTGCGC 59.790 57.895 0.00 0.00 35.89 6.09
291 303 3.090532 AATGGGCGGAGGGGAGTC 61.091 66.667 0.00 0.00 0.00 3.36
384 407 3.681897 CCTGTGCTTCTTCTATGTGTGTC 59.318 47.826 0.00 0.00 0.00 3.67
405 428 1.005394 CACGAGTACACACACCCCC 60.005 63.158 0.00 0.00 0.00 5.40
410 433 2.094130 TGTTGTTCCACGAGTACACACA 60.094 45.455 0.00 0.00 0.00 3.72
513 536 1.674057 CCAGGGCGAGAAGAACACT 59.326 57.895 0.00 0.00 0.00 3.55
633 656 2.852075 ACCTTGAACTCCCCCGCA 60.852 61.111 0.00 0.00 0.00 5.69
636 659 1.152830 TTGCACCTTGAACTCCCCC 59.847 57.895 0.00 0.00 0.00 5.40
651 674 4.246458 CTCTCAACCTAGTACCAAGTTGC 58.754 47.826 12.35 0.00 39.51 4.17
888 933 3.239587 TGTGAGCATGCATTTGGAATG 57.760 42.857 21.98 0.00 0.00 2.67
960 1069 2.140065 TCGAACTGTCTTGTGCTCTG 57.860 50.000 0.00 0.00 0.00 3.35
978 1087 1.873591 ACGTTTTGGACAGCTGACATC 59.126 47.619 23.35 7.58 0.00 3.06
1017 1126 0.391263 CTCCAACGCCAACTACTCCC 60.391 60.000 0.00 0.00 0.00 4.30
1054 1163 1.338020 GAGGTGGTTGTTCAAAGCCAG 59.662 52.381 0.00 0.00 0.00 4.85
1088 1198 1.070134 ACTAGTGCTTGCCGACTGAAA 59.930 47.619 0.00 0.00 0.00 2.69
1101 1211 0.645868 GCGTCCATCGAAACTAGTGC 59.354 55.000 0.00 0.00 42.86 4.40
1104 1214 0.099968 TCGGCGTCCATCGAAACTAG 59.900 55.000 6.85 0.00 42.86 2.57
1108 1218 0.808453 GGATTCGGCGTCCATCGAAA 60.808 55.000 11.28 0.00 46.25 3.46
1110 1220 2.415843 GGATTCGGCGTCCATCGA 59.584 61.111 11.28 0.00 42.86 3.59
1122 1232 6.228273 TGCTTTTGAATCGATATCGGATTC 57.772 37.500 26.31 26.31 40.29 2.52
1128 1238 5.898606 CACGACTTGCTTTTGAATCGATATC 59.101 40.000 0.00 0.00 33.88 1.63
1235 1345 3.003897 GCAGGAGGATGTCTAAGTACTCG 59.996 52.174 0.00 0.00 0.00 4.18
1290 1404 1.651987 CATGGCTGTGGTAGGTTACG 58.348 55.000 0.00 0.00 0.00 3.18
1300 1418 1.721664 CGGAAGATGGCATGGCTGTG 61.722 60.000 21.08 0.00 0.00 3.66
1417 1535 0.540597 ACTTGAAGCAAAGGAGGGCC 60.541 55.000 0.00 0.00 0.00 5.80
1457 1575 3.002791 TGCTCCATGAAGCTAAAACTCG 58.997 45.455 5.24 0.00 42.94 4.18
1480 1598 4.213270 CACTCGCAAACATCAAAGGACTTA 59.787 41.667 0.00 0.00 0.00 2.24
1537 1655 2.741985 TCCAGCGCAATCACACGG 60.742 61.111 11.47 0.00 0.00 4.94
1746 1866 2.437281 ACATATGTGAGAGAAGGGCTGG 59.563 50.000 7.78 0.00 0.00 4.85
1783 3327 0.105039 GGATGACCCCTGTTAGAGCG 59.895 60.000 0.00 0.00 0.00 5.03
1829 3373 3.694072 CCATTGAGCCAAAGTATTCGGAA 59.306 43.478 0.00 0.00 0.00 4.30
1850 3394 3.826729 AGTTTTCCACCAAGACTATTGCC 59.173 43.478 0.00 0.00 0.00 4.52
1892 3436 5.649395 GGGAAATGTCAACAAGAGATGATGA 59.351 40.000 0.00 0.00 38.38 2.92
2239 3799 6.964807 TTCGGGAGTGTGTAGCTAATATTA 57.035 37.500 0.00 0.00 0.00 0.98
2299 3859 0.033699 GAGAAGCTGGGATTGGGCTT 60.034 55.000 0.00 0.00 46.99 4.35
2300 3860 0.918310 AGAGAAGCTGGGATTGGGCT 60.918 55.000 0.00 0.00 37.99 5.19
2323 3883 4.638865 AGCTGACGAAGGTTGTAAACTTTT 59.361 37.500 0.00 0.00 46.78 2.27
2328 3888 5.362263 AGTAAAGCTGACGAAGGTTGTAAA 58.638 37.500 7.81 0.00 45.87 2.01
2439 3999 4.772100 ACATAAATCCCCAGTTTCCTGTTG 59.228 41.667 0.00 0.00 36.95 3.33
2563 4123 0.038166 CCCTTAGCCAAAGCCACTCA 59.962 55.000 0.00 0.00 41.25 3.41
2719 4279 3.982475 TGACAGTTTGTTGTGTGCAAAA 58.018 36.364 0.00 0.00 37.54 2.44
2785 4345 6.906157 ATGTTGTTCTCATCCAGTTTCAAT 57.094 33.333 0.00 0.00 0.00 2.57
2894 4454 8.809478 GTTTCCGCATTACAGTTTTTCTTAAAA 58.191 29.630 0.00 0.00 0.00 1.52
2896 4456 7.708998 AGTTTCCGCATTACAGTTTTTCTTAA 58.291 30.769 0.00 0.00 0.00 1.85
2953 4513 1.202940 AGGAGAGGTCAAAAGGGTTGC 60.203 52.381 0.00 0.00 0.00 4.17
2986 4546 9.120538 ACTTTATCTGCAGACTAAAAAGAAACA 57.879 29.630 30.11 6.96 0.00 2.83
3200 4760 6.126825 TGGCCAGCATATAAAATTTGGTCAAT 60.127 34.615 0.00 0.00 37.37 2.57
3209 4769 7.336679 GGTTTCTTTTTGGCCAGCATATAAAAT 59.663 33.333 5.11 0.00 0.00 1.82
3222 4782 0.747852 TCCCACGGTTTCTTTTTGGC 59.252 50.000 0.00 0.00 0.00 4.52
3223 4783 1.269569 GCTCCCACGGTTTCTTTTTGG 60.270 52.381 0.00 0.00 0.00 3.28
3229 4789 0.981183 TATGTGCTCCCACGGTTTCT 59.019 50.000 0.00 0.00 45.04 2.52
3235 4795 2.093306 TCAAAGTATGTGCTCCCACG 57.907 50.000 0.00 0.00 45.04 4.94
3237 4797 3.998913 TCATCAAAGTATGTGCTCCCA 57.001 42.857 0.00 0.00 0.00 4.37
3238 4798 3.378427 GGTTCATCAAAGTATGTGCTCCC 59.622 47.826 0.00 0.00 0.00 4.30
3277 4837 3.028850 CACATGGATTTCTGGGCATTCT 58.971 45.455 0.00 0.00 0.00 2.40
3282 4842 3.448301 TGATTTCACATGGATTTCTGGGC 59.552 43.478 0.00 0.00 0.00 5.36
3284 4844 5.506815 CCGATGATTTCACATGGATTTCTGG 60.507 44.000 0.00 0.00 0.00 3.86
3327 4887 6.298361 ACAAAACACCCTACTAACCGTAATT 58.702 36.000 0.00 0.00 0.00 1.40
3412 4972 2.100584 TGGAAGGTGCACACATTGAAAC 59.899 45.455 20.43 0.00 35.27 2.78
3413 4973 2.361757 CTGGAAGGTGCACACATTGAAA 59.638 45.455 20.43 0.00 35.27 2.69
3415 4975 1.133823 ACTGGAAGGTGCACACATTGA 60.134 47.619 20.43 0.00 39.30 2.57
3540 5100 2.116366 AGTTTTTGTTCGCGTGCATTC 58.884 42.857 5.77 0.00 0.00 2.67
3543 5103 1.983972 AAAGTTTTTGTTCGCGTGCA 58.016 40.000 5.77 3.31 0.00 4.57
3548 5108 3.485051 CCTTGGCAAAAGTTTTTGTTCGC 60.485 43.478 16.21 0.00 46.92 4.70
3563 5123 0.608856 TACGAGACGTACCCTTGGCA 60.609 55.000 0.00 0.00 41.54 4.92
3583 5143 3.476552 TGATTTTGCGCCTATTAGAGGG 58.523 45.455 4.18 0.00 46.81 4.30
3593 5153 1.443702 GGTCGGTTGATTTTGCGCC 60.444 57.895 4.18 0.00 0.00 6.53
3596 5156 1.934849 GCTTGGGTCGGTTGATTTTGC 60.935 52.381 0.00 0.00 0.00 3.68
3616 5176 2.027688 CGTTAAAGCTCGGCTCGTTAAG 59.972 50.000 0.00 0.00 38.25 1.85
3617 5177 1.987770 CGTTAAAGCTCGGCTCGTTAA 59.012 47.619 0.00 0.17 38.25 2.01
3618 5178 1.199789 TCGTTAAAGCTCGGCTCGTTA 59.800 47.619 0.00 0.00 38.25 3.18
3619 5179 0.038892 TCGTTAAAGCTCGGCTCGTT 60.039 50.000 0.00 0.00 38.25 3.85
3620 5180 0.456312 CTCGTTAAAGCTCGGCTCGT 60.456 55.000 0.00 0.00 38.25 4.18
3621 5181 1.743855 GCTCGTTAAAGCTCGGCTCG 61.744 60.000 0.00 0.00 38.25 5.03
3622 5182 1.743855 CGCTCGTTAAAGCTCGGCTC 61.744 60.000 0.00 0.00 38.25 4.70
3623 5183 1.805945 CGCTCGTTAAAGCTCGGCT 60.806 57.895 0.00 0.00 42.56 5.52
3624 5184 2.695646 CGCTCGTTAAAGCTCGGC 59.304 61.111 0.00 0.00 40.23 5.54
3625 5185 2.695646 GCGCTCGTTAAAGCTCGG 59.304 61.111 0.00 0.00 40.23 4.63
3626 5186 2.313374 CGCGCTCGTTAAAGCTCG 59.687 61.111 5.56 0.00 43.07 5.03
3667 5227 2.224450 CCGTGATTAGGGGTGGGATTAC 60.224 54.545 0.00 0.00 0.00 1.89
3672 5232 0.981277 AGTCCGTGATTAGGGGTGGG 60.981 60.000 0.00 0.00 32.66 4.61
3686 5246 1.178276 AGCTGTTGAGTCCTAGTCCG 58.822 55.000 0.00 0.00 0.00 4.79
3695 5255 3.454371 AGTTCGTGTTAGCTGTTGAGT 57.546 42.857 0.00 0.00 0.00 3.41
3720 5280 8.360390 AGGAAAGCTACTTTTGTATTGGAAAAG 58.640 33.333 0.00 0.00 43.27 2.27
3723 5283 8.789762 GTTAGGAAAGCTACTTTTGTATTGGAA 58.210 33.333 0.00 0.00 33.49 3.53
3831 5391 2.288273 GGACGATTAGGAAGTGATCGGG 60.288 54.545 9.39 0.00 46.34 5.14
3851 5411 5.599999 ATTACTGTGTAGGCTAGTTCTGG 57.400 43.478 0.00 0.00 0.00 3.86
3867 5427 6.325919 TGGCAACTCAAAAAGGTATTACTG 57.674 37.500 0.00 0.00 37.61 2.74
3930 5490 9.646522 ACCAAGAATATCACCTTGCTTTATTAT 57.353 29.630 0.00 0.00 38.65 1.28
3959 5534 4.098044 TGCAGAGAACCTATAAGAAGGACG 59.902 45.833 0.00 0.00 39.15 4.79
3965 5540 9.295825 TGAAAATTTTGCAGAGAACCTATAAGA 57.704 29.630 8.47 0.00 0.00 2.10
3990 5565 6.511767 GCACGAAATTATATGTGAAGGGACTG 60.512 42.308 0.00 0.00 33.15 3.51
4170 5786 7.676947 TGTTGTGACTAGCTTAAATAAGAGGT 58.323 34.615 4.39 0.00 35.33 3.85
4255 5871 6.262720 ACCGTTTTTAATGTTTGTAGCAGGTA 59.737 34.615 0.00 0.00 0.00 3.08
4272 5888 5.067936 TGTGTTCCATCATGTAACCGTTTTT 59.932 36.000 0.00 0.00 0.00 1.94
4304 5920 9.823647 TGCCAACAAATTAAAAAGAAGACATTA 57.176 25.926 0.00 0.00 0.00 1.90
4305 5921 8.729805 TGCCAACAAATTAAAAAGAAGACATT 57.270 26.923 0.00 0.00 0.00 2.71
4306 5922 8.776470 CATGCCAACAAATTAAAAAGAAGACAT 58.224 29.630 0.00 0.00 0.00 3.06
4307 5923 7.254727 GCATGCCAACAAATTAAAAAGAAGACA 60.255 33.333 6.36 0.00 0.00 3.41
4308 5924 7.071414 GCATGCCAACAAATTAAAAAGAAGAC 58.929 34.615 6.36 0.00 0.00 3.01
4309 5925 6.765036 TGCATGCCAACAAATTAAAAAGAAGA 59.235 30.769 16.68 0.00 0.00 2.87
4310 5926 6.852345 GTGCATGCCAACAAATTAAAAAGAAG 59.148 34.615 16.68 0.00 0.00 2.85
4311 5927 6.317140 TGTGCATGCCAACAAATTAAAAAGAA 59.683 30.769 16.68 0.00 0.00 2.52
4312 5928 5.819379 TGTGCATGCCAACAAATTAAAAAGA 59.181 32.000 16.68 0.00 0.00 2.52
4313 5929 6.057627 TGTGCATGCCAACAAATTAAAAAG 57.942 33.333 16.68 0.00 0.00 2.27
4314 5930 6.630444 ATGTGCATGCCAACAAATTAAAAA 57.370 29.167 16.68 0.00 0.00 1.94
4315 5931 6.630444 AATGTGCATGCCAACAAATTAAAA 57.370 29.167 16.68 0.00 0.00 1.52
4316 5932 6.630444 AAATGTGCATGCCAACAAATTAAA 57.370 29.167 16.68 0.00 0.00 1.52
4317 5933 7.918536 ATAAATGTGCATGCCAACAAATTAA 57.081 28.000 16.68 0.57 0.00 1.40
4318 5934 7.918536 AATAAATGTGCATGCCAACAAATTA 57.081 28.000 16.68 16.04 0.00 1.40
4319 5935 6.821031 AATAAATGTGCATGCCAACAAATT 57.179 29.167 16.68 14.56 0.00 1.82
4320 5936 6.821031 AAATAAATGTGCATGCCAACAAAT 57.179 29.167 16.68 9.35 0.00 2.32
4321 5937 6.261603 TCAAAATAAATGTGCATGCCAACAAA 59.738 30.769 16.68 4.65 0.00 2.83
4322 5938 5.761726 TCAAAATAAATGTGCATGCCAACAA 59.238 32.000 16.68 0.00 0.00 2.83
4323 5939 5.303165 TCAAAATAAATGTGCATGCCAACA 58.697 33.333 16.68 14.43 0.00 3.33
4324 5940 5.163834 CCTCAAAATAAATGTGCATGCCAAC 60.164 40.000 16.68 8.33 0.00 3.77
4325 5941 4.936411 CCTCAAAATAAATGTGCATGCCAA 59.064 37.500 16.68 3.14 0.00 4.52
4326 5942 4.020396 ACCTCAAAATAAATGTGCATGCCA 60.020 37.500 16.68 13.21 0.00 4.92
4327 5943 4.506758 ACCTCAAAATAAATGTGCATGCC 58.493 39.130 16.68 7.25 0.00 4.40
4328 5944 5.413499 AGACCTCAAAATAAATGTGCATGC 58.587 37.500 11.82 11.82 0.00 4.06
4329 5945 6.860080 AGAGACCTCAAAATAAATGTGCATG 58.140 36.000 0.00 0.00 0.00 4.06
4330 5946 8.757982 ATAGAGACCTCAAAATAAATGTGCAT 57.242 30.769 0.00 0.00 0.00 3.96
4331 5947 7.828717 TGATAGAGACCTCAAAATAAATGTGCA 59.171 33.333 0.00 0.00 0.00 4.57
4332 5948 8.213518 TGATAGAGACCTCAAAATAAATGTGC 57.786 34.615 0.00 0.00 0.00 4.57
4334 5950 9.347240 CCATGATAGAGACCTCAAAATAAATGT 57.653 33.333 0.00 0.00 0.00 2.71
4359 5975 4.993028 TGTAATTCCTATATTGGGCCACC 58.007 43.478 5.23 0.00 37.24 4.61
4391 6007 1.134788 GGTCACACCAATCCTACTCCG 60.135 57.143 0.00 0.00 38.42 4.63
4392 6008 2.168728 GAGGTCACACCAATCCTACTCC 59.831 54.545 0.00 0.00 41.95 3.85
4393 6009 3.100671 AGAGGTCACACCAATCCTACTC 58.899 50.000 0.00 0.00 41.95 2.59
4394 6010 3.100671 GAGAGGTCACACCAATCCTACT 58.899 50.000 0.00 0.00 41.95 2.57
4395 6011 3.100671 AGAGAGGTCACACCAATCCTAC 58.899 50.000 0.00 0.00 41.95 3.18
4396 6012 3.245622 TGAGAGAGGTCACACCAATCCTA 60.246 47.826 0.00 0.00 41.95 2.94
4397 6013 2.183679 GAGAGAGGTCACACCAATCCT 58.816 52.381 0.00 0.00 41.95 3.24
4398 6014 1.902508 TGAGAGAGGTCACACCAATCC 59.097 52.381 0.00 0.00 41.95 3.01
4399 6015 3.196469 TCATGAGAGAGGTCACACCAATC 59.804 47.826 0.00 0.00 41.95 2.67
4400 6016 3.176411 TCATGAGAGAGGTCACACCAAT 58.824 45.455 0.00 0.00 41.95 3.16
4401 6017 2.608623 TCATGAGAGAGGTCACACCAA 58.391 47.619 0.00 0.00 41.95 3.67
4402 6018 2.309136 TCATGAGAGAGGTCACACCA 57.691 50.000 0.00 0.00 41.95 4.17
4403 6019 3.902881 ATTCATGAGAGAGGTCACACC 57.097 47.619 0.00 0.00 38.99 4.16
4404 6020 5.330455 TGTATTCATGAGAGAGGTCACAC 57.670 43.478 0.00 0.00 0.00 3.82
4405 6021 6.358974 TTTGTATTCATGAGAGAGGTCACA 57.641 37.500 0.00 0.00 0.00 3.58
4406 6022 7.856145 ATTTTGTATTCATGAGAGAGGTCAC 57.144 36.000 0.00 0.00 0.00 3.67
4407 6023 9.958180 TTTATTTTGTATTCATGAGAGAGGTCA 57.042 29.630 0.00 0.00 0.00 4.02
4431 6047 8.096414 CCAGTCTAACCCAATCAATTTGAATTT 58.904 33.333 2.68 0.00 37.53 1.82
4432 6048 7.235399 ACCAGTCTAACCCAATCAATTTGAATT 59.765 33.333 2.68 0.00 37.53 2.17
4433 6049 6.725834 ACCAGTCTAACCCAATCAATTTGAAT 59.274 34.615 2.68 0.00 37.53 2.57
4434 6050 6.074648 ACCAGTCTAACCCAATCAATTTGAA 58.925 36.000 2.68 0.00 37.53 2.69
4435 6051 5.640147 ACCAGTCTAACCCAATCAATTTGA 58.360 37.500 0.75 0.75 37.53 2.69
4436 6052 5.476599 TGACCAGTCTAACCCAATCAATTTG 59.523 40.000 0.00 0.00 34.93 2.32
4437 6053 5.640147 TGACCAGTCTAACCCAATCAATTT 58.360 37.500 0.00 0.00 0.00 1.82
4438 6054 5.255397 TGACCAGTCTAACCCAATCAATT 57.745 39.130 0.00 0.00 0.00 2.32
4439 6055 4.927267 TGACCAGTCTAACCCAATCAAT 57.073 40.909 0.00 0.00 0.00 2.57
4440 6056 4.927267 ATGACCAGTCTAACCCAATCAA 57.073 40.909 0.00 0.00 0.00 2.57
4441 6057 4.927267 AATGACCAGTCTAACCCAATCA 57.073 40.909 0.00 0.00 0.00 2.57
4442 6058 5.253330 TCAAATGACCAGTCTAACCCAATC 58.747 41.667 0.00 0.00 0.00 2.67
4443 6059 5.255397 TCAAATGACCAGTCTAACCCAAT 57.745 39.130 0.00 0.00 0.00 3.16
4444 6060 4.715534 TCAAATGACCAGTCTAACCCAA 57.284 40.909 0.00 0.00 0.00 4.12
4445 6061 4.927267 ATCAAATGACCAGTCTAACCCA 57.073 40.909 0.00 0.00 0.00 4.51
4446 6062 5.253330 TCAATCAAATGACCAGTCTAACCC 58.747 41.667 0.00 0.00 0.00 4.11
4447 6063 7.253422 CAATCAATCAAATGACCAGTCTAACC 58.747 38.462 0.00 0.00 30.82 2.85
4448 6064 7.253422 CCAATCAATCAAATGACCAGTCTAAC 58.747 38.462 0.00 0.00 30.82 2.34
4449 6065 6.377996 CCCAATCAATCAAATGACCAGTCTAA 59.622 38.462 0.00 0.00 30.82 2.10
4450 6066 5.887598 CCCAATCAATCAAATGACCAGTCTA 59.112 40.000 0.00 0.00 30.82 2.59
4451 6067 4.708421 CCCAATCAATCAAATGACCAGTCT 59.292 41.667 0.00 0.00 30.82 3.24
4452 6068 4.678840 GCCCAATCAATCAAATGACCAGTC 60.679 45.833 0.00 0.00 30.82 3.51
4453 6069 3.196254 GCCCAATCAATCAAATGACCAGT 59.804 43.478 0.00 0.00 30.82 4.00
4454 6070 3.449737 AGCCCAATCAATCAAATGACCAG 59.550 43.478 0.00 0.00 30.82 4.00
4455 6071 3.196039 CAGCCCAATCAATCAAATGACCA 59.804 43.478 0.00 0.00 30.82 4.02
4456 6072 3.431207 CCAGCCCAATCAATCAAATGACC 60.431 47.826 0.00 0.00 30.82 4.02
4457 6073 3.448301 TCCAGCCCAATCAATCAAATGAC 59.552 43.478 0.00 0.00 30.82 3.06
4458 6074 3.448301 GTCCAGCCCAATCAATCAAATGA 59.552 43.478 0.00 0.00 0.00 2.57
4459 6075 3.196039 TGTCCAGCCCAATCAATCAAATG 59.804 43.478 0.00 0.00 0.00 2.32
4460 6076 3.443052 TGTCCAGCCCAATCAATCAAAT 58.557 40.909 0.00 0.00 0.00 2.32
4461 6077 2.886913 TGTCCAGCCCAATCAATCAAA 58.113 42.857 0.00 0.00 0.00 2.69
4462 6078 2.562298 GTTGTCCAGCCCAATCAATCAA 59.438 45.455 0.00 0.00 0.00 2.57
4463 6079 2.170166 GTTGTCCAGCCCAATCAATCA 58.830 47.619 0.00 0.00 0.00 2.57
4464 6080 1.133025 CGTTGTCCAGCCCAATCAATC 59.867 52.381 0.00 0.00 0.00 2.67
4465 6081 1.176527 CGTTGTCCAGCCCAATCAAT 58.823 50.000 0.00 0.00 0.00 2.57
4466 6082 0.893270 CCGTTGTCCAGCCCAATCAA 60.893 55.000 0.00 0.00 0.00 2.57
4467 6083 1.303236 CCGTTGTCCAGCCCAATCA 60.303 57.895 0.00 0.00 0.00 2.57
4468 6084 2.700773 GCCGTTGTCCAGCCCAATC 61.701 63.158 0.00 0.00 0.00 2.67
4469 6085 2.676471 GCCGTTGTCCAGCCCAAT 60.676 61.111 0.00 0.00 0.00 3.16
4480 6096 4.735132 TTCGAGCTCCCGCCGTTG 62.735 66.667 8.47 0.00 36.60 4.10
4481 6097 4.736896 GTTCGAGCTCCCGCCGTT 62.737 66.667 8.47 0.00 36.60 4.44
4483 6099 4.856607 GAGTTCGAGCTCCCGCCG 62.857 72.222 17.67 0.00 36.60 6.46
4489 6105 1.512310 CGTCGTGGAGTTCGAGCTC 60.512 63.158 19.92 19.92 37.99 4.09
4490 6106 2.185103 GACGTCGTGGAGTTCGAGCT 62.185 60.000 0.63 0.00 37.99 4.09
4491 6107 1.796749 GACGTCGTGGAGTTCGAGC 60.797 63.158 0.63 0.00 37.99 5.03
4492 6108 1.154263 GGACGTCGTGGAGTTCGAG 60.154 63.158 9.92 0.00 37.99 4.04
4493 6109 2.949106 GGACGTCGTGGAGTTCGA 59.051 61.111 9.92 0.00 34.91 3.71
4494 6110 2.501222 CGGACGTCGTGGAGTTCG 60.501 66.667 9.92 0.52 32.74 3.95
4495 6111 2.804090 GCGGACGTCGTGGAGTTC 60.804 66.667 9.92 0.00 41.72 3.01
4496 6112 4.353437 GGCGGACGTCGTGGAGTT 62.353 66.667 9.92 0.00 41.72 3.01
4532 6148 4.389576 GAGCACTTTGGCGTGGCG 62.390 66.667 0.00 0.00 39.27 5.69
4533 6149 4.043200 GGAGCACTTTGGCGTGGC 62.043 66.667 0.00 0.00 39.27 5.01
4534 6150 1.526575 ATTGGAGCACTTTGGCGTGG 61.527 55.000 0.00 0.00 39.27 4.94
4535 6151 1.131126 CTATTGGAGCACTTTGGCGTG 59.869 52.381 0.00 0.00 39.27 5.34
4536 6152 1.453155 CTATTGGAGCACTTTGGCGT 58.547 50.000 0.00 0.00 39.27 5.68
4537 6153 0.734889 CCTATTGGAGCACTTTGGCG 59.265 55.000 0.00 0.00 39.27 5.69
4538 6154 0.457443 GCCTATTGGAGCACTTTGGC 59.543 55.000 0.00 0.00 34.57 4.52
4539 6155 2.019984 GAGCCTATTGGAGCACTTTGG 58.980 52.381 0.00 0.00 34.57 3.28
4540 6156 2.421424 GTGAGCCTATTGGAGCACTTTG 59.579 50.000 0.00 0.00 36.58 2.77
4541 6157 2.619074 GGTGAGCCTATTGGAGCACTTT 60.619 50.000 14.76 0.00 38.29 2.66
4542 6158 1.065126 GGTGAGCCTATTGGAGCACTT 60.065 52.381 14.76 0.00 38.29 3.16
4543 6159 0.543749 GGTGAGCCTATTGGAGCACT 59.456 55.000 14.76 0.00 38.29 4.40
4544 6160 0.464554 GGGTGAGCCTATTGGAGCAC 60.465 60.000 0.00 4.00 37.84 4.40
4552 6168 2.064581 GTGGGACGGGTGAGCCTAT 61.065 63.158 0.00 0.00 34.45 2.57
4569 6185 2.601666 TCTGGAGGCGTGCAGAGT 60.602 61.111 24.31 0.00 45.50 3.24
4600 6216 4.570874 GGGCGAGAGGATTGGGCC 62.571 72.222 0.00 0.00 43.01 5.80
4724 6340 4.154347 GGACTCTGCCTCAGCCCG 62.154 72.222 0.00 0.00 38.69 6.13
4725 6341 4.154347 CGGACTCTGCCTCAGCCC 62.154 72.222 0.00 0.00 38.69 5.19
4762 6378 1.033574 GGTCGACAGGGATAGAGTGG 58.966 60.000 18.91 0.00 0.00 4.00
4764 6380 0.465824 CGGGTCGACAGGGATAGAGT 60.466 60.000 18.91 0.00 0.00 3.24
4765 6381 1.173444 CCGGGTCGACAGGGATAGAG 61.173 65.000 18.91 0.00 0.00 2.43
4800 6416 4.373116 AACGGCGCATGACCTCGT 62.373 61.111 10.83 4.47 35.48 4.18
4831 6447 1.799383 GTGTCTACCGTCCGTCTCC 59.201 63.158 0.00 0.00 0.00 3.71
4841 6457 2.438951 TTTCACCGGGCGTGTCTACC 62.439 60.000 6.32 0.00 43.51 3.18
4850 6466 1.147473 CTTTGCATTTTTCACCGGGC 58.853 50.000 6.32 0.00 0.00 6.13
4855 6471 3.121696 CGAAGCGTCTTTGCATTTTTCAC 60.122 43.478 0.00 0.00 37.31 3.18
4870 6486 1.207089 TCAAATCCTGATCCGAAGCGT 59.793 47.619 0.00 0.00 0.00 5.07
4875 6491 3.535561 GAAGCTTCAAATCCTGATCCGA 58.464 45.455 21.67 0.00 32.78 4.55
4896 6512 3.181967 CCTTCACGAGGCGCTTCG 61.182 66.667 36.01 36.01 45.70 3.79
4904 6520 3.548268 GCGTTCTATTTCTCCTTCACGAG 59.452 47.826 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.