Multiple sequence alignment - TraesCS4B01G197600

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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 TraesCS4B01G197600 chr4B 100.000 5064 0 0 1 5064 426115166 426110103 0.000000e+00 9352
1 TraesCS4B01G197600 chr4B 89.177 656 63 6 2351 3000 300054843 300054190 0.000000e+00 811
2 TraesCS4B01G197600 chr4D 91.673 2630 139 29 698 3263 344117272 344114659 0.000000e+00 3570
3 TraesCS4B01G197600 chr4D 90.923 1344 79 17 3523 4841 344114491 344113166 0.000000e+00 1766
4 TraesCS4B01G197600 chr4D 91.045 402 32 3 4 405 344118272 344117875 1.600000e-149 540
5 TraesCS4B01G197600 chr4D 93.818 275 15 2 424 698 344117896 344117624 3.650000e-111 412
6 TraesCS4B01G197600 chr4A 93.662 1499 65 15 424 1900 121498198 121499688 0.000000e+00 2215
7 TraesCS4B01G197600 chr4A 89.922 1538 98 28 3160 4668 121501320 121502829 0.000000e+00 1929
8 TraesCS4B01G197600 chr4A 89.015 1320 86 22 1896 3158 121499866 121501183 0.000000e+00 1580
9 TraesCS4B01G197600 chr4A 90.123 405 23 7 1 405 121497832 121498219 1.260000e-140 510
10 TraesCS4B01G197600 chr4A 90.455 220 20 1 4707 4925 121502829 121503048 6.410000e-74 289
11 TraesCS4B01G197600 chr2A 88.737 657 65 7 2351 3001 761160475 761161128 0.000000e+00 795
12 TraesCS4B01G197600 chr2A 86.308 577 64 11 3050 3617 197516531 197515961 9.320000e-172 614
13 TraesCS4B01G197600 chr2A 87.719 285 27 7 2349 2628 197523447 197523166 4.890000e-85 326
14 TraesCS4B01G197600 chr2A 89.873 237 22 2 2627 2862 197523135 197522900 2.290000e-78 303
15 TraesCS4B01G197600 chr2A 90.714 140 12 1 2862 3000 197516678 197516539 8.660000e-43 185
16 TraesCS4B01G197600 chr6B 95.116 430 13 4 610 1032 131278170 131278598 0.000000e+00 671
17 TraesCS4B01G197600 chr6B 85.306 490 57 11 3147 3628 363767255 363767737 4.560000e-135 492
18 TraesCS4B01G197600 chr2B 80.943 530 57 17 1814 2303 238654835 238654310 3.700000e-101 379
19 TraesCS4B01G197600 chr2B 88.380 284 27 4 2349 2628 238654309 238654028 2.260000e-88 337
20 TraesCS4B01G197600 chr2B 87.352 253 26 4 3051 3302 238650138 238649891 8.300000e-73 285
21 TraesCS4B01G197600 chr2B 92.105 190 14 1 2812 3000 238650336 238650147 3.010000e-67 267
22 TraesCS4B01G197600 chr2B 86.047 172 23 1 2637 2808 238653925 238653755 3.110000e-42 183
23 TraesCS4B01G197600 chr2D 89.825 285 22 5 2349 2628 182384952 182384670 4.820000e-95 359
24 TraesCS4B01G197600 chr3A 87.365 277 32 1 2030 2303 746903883 746904159 1.060000e-81 315


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 TraesCS4B01G197600 chr4B 426110103 426115166 5063 True 9352.0 9352 100.00000 1 5064 1 chr4B.!!$R2 5063
1 TraesCS4B01G197600 chr4B 300054190 300054843 653 True 811.0 811 89.17700 2351 3000 1 chr4B.!!$R1 649
2 TraesCS4B01G197600 chr4D 344113166 344118272 5106 True 1572.0 3570 91.86475 4 4841 4 chr4D.!!$R1 4837
3 TraesCS4B01G197600 chr4A 121497832 121503048 5216 False 1304.6 2215 90.63540 1 4925 5 chr4A.!!$F1 4924
4 TraesCS4B01G197600 chr2A 761160475 761161128 653 False 795.0 795 88.73700 2351 3001 1 chr2A.!!$F1 650
5 TraesCS4B01G197600 chr2A 197515961 197516678 717 True 399.5 614 88.51100 2862 3617 2 chr2A.!!$R1 755
6 TraesCS4B01G197600 chr2A 197522900 197523447 547 True 314.5 326 88.79600 2349 2862 2 chr2A.!!$R2 513
7 TraesCS4B01G197600 chr2B 238649891 238654835 4944 True 290.2 379 86.96540 1814 3302 5 chr2B.!!$R1 1488

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
434 435 0.535328 TTTTTGCGGGTGACGGATCA 60.535 50.000 0.00 0.00 44.30 2.92 F
527 528 2.684881 AGTAGCTAAAAAGCATGCGCAT 59.315 40.909 19.28 19.28 42.27 4.73 F
1284 1658 2.279784 CTCGCCAAGATCTCCGCC 60.280 66.667 0.00 0.00 0.00 6.13 F
1768 2144 0.409484 AGTTGGGCTGGGCAATAGTT 59.591 50.000 0.00 0.00 0.00 2.24 F
3254 7535 1.149174 AGCTGTGTCAACCCCAGTG 59.851 57.895 0.00 0.00 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1658 1.153667 GCAGAAGACGAGGCTGAGG 60.154 63.158 0.00 0.00 0.00 3.86 R
1395 1769 1.412710 ACGGTCATGATGTAGGCGAAT 59.587 47.619 0.00 0.00 0.00 3.34 R
2339 2956 2.474735 CCTGTAAATTTGGTTTGCGCAC 59.525 45.455 11.12 0.00 35.45 5.34 R
3517 7805 1.067425 TGCTTTAGGTGTATCACGCGT 60.067 47.619 5.58 5.58 34.83 6.01 R
4662 8979 0.038890 TTCCCGAAATGGCCACATCA 59.961 50.000 8.16 0.00 35.94 3.07 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
86 87 5.394663 GCTAGAGCAACCCATATCGATATGT 60.395 44.000 32.89 19.73 38.67 2.29
114 115 1.524393 GACACGTTCCCAAACCCGT 60.524 57.895 0.00 0.00 31.27 5.28
139 140 1.507141 GCGACGATTATGGCCCCTTG 61.507 60.000 0.00 0.00 0.00 3.61
151 152 1.619704 GGCCCCTTGTGCCTTATCTTT 60.620 52.381 0.00 0.00 45.70 2.52
169 170 6.662414 ATCTTTCAATCTATTTTGTCGCGA 57.338 33.333 3.71 3.71 0.00 5.87
219 220 3.305335 GGCAACGGATCACAACTCATTTT 60.305 43.478 0.00 0.00 0.00 1.82
280 281 3.604314 CGTCAATGCCATTTGTTTGCAAC 60.604 43.478 0.00 0.00 38.69 4.17
334 335 2.441750 TGGTGACCCCTTATGCCTTATC 59.558 50.000 0.00 0.00 0.00 1.75
337 338 4.386424 GGTGACCCCTTATGCCTTATCTTT 60.386 45.833 0.00 0.00 0.00 2.52
341 342 6.030727 ACCCCTTATGCCTTATCTTTCAAT 57.969 37.500 0.00 0.00 0.00 2.57
346 347 9.525826 CCCTTATGCCTTATCTTTCAATCTATT 57.474 33.333 0.00 0.00 0.00 1.73
388 389 3.244422 TGCCTTAAACTCAACTCGGTGAT 60.244 43.478 0.00 0.00 0.00 3.06
408 409 5.807909 TGATGGATCACAACTCATTTCTCA 58.192 37.500 0.00 0.00 0.00 3.27
409 410 6.420638 TGATGGATCACAACTCATTTCTCAT 58.579 36.000 0.00 0.00 0.00 2.90
410 411 7.567458 TGATGGATCACAACTCATTTCTCATA 58.433 34.615 0.00 0.00 0.00 2.15
411 412 8.215736 TGATGGATCACAACTCATTTCTCATAT 58.784 33.333 0.00 0.00 0.00 1.78
412 413 9.716531 GATGGATCACAACTCATTTCTCATATA 57.283 33.333 0.00 0.00 0.00 0.86
432 433 4.484987 TTTTTGCGGGTGACGGAT 57.515 50.000 0.00 0.00 44.30 4.18
433 434 2.249692 TTTTTGCGGGTGACGGATC 58.750 52.632 0.00 0.00 44.30 3.36
434 435 0.535328 TTTTTGCGGGTGACGGATCA 60.535 50.000 0.00 0.00 44.30 2.92
455 456 5.981174 TCACAGCTCATTTATGTCTCATCA 58.019 37.500 0.00 0.00 0.00 3.07
457 458 7.052248 TCACAGCTCATTTATGTCTCATCAAT 58.948 34.615 0.00 0.00 0.00 2.57
481 482 5.248020 TCCAATGTCAGTAATTTTGGGCATT 59.752 36.000 3.59 1.24 37.89 3.56
523 524 4.588278 CGGTTAGTAGCTAAAAAGCATGC 58.412 43.478 10.51 10.51 37.25 4.06
527 528 2.684881 AGTAGCTAAAAAGCATGCGCAT 59.315 40.909 19.28 19.28 42.27 4.73
1074 1448 3.119096 GGGCGCTTCTTCACGGTC 61.119 66.667 7.64 0.00 0.00 4.79
1146 1520 4.097418 ACAAGTACCTCCTCAGCAACTAT 58.903 43.478 0.00 0.00 0.00 2.12
1284 1658 2.279784 CTCGCCAAGATCTCCGCC 60.280 66.667 0.00 0.00 0.00 6.13
1395 1769 1.294138 CCCTTTCTTCACCGCCGTA 59.706 57.895 0.00 0.00 0.00 4.02
1660 2036 9.436957 CACAATAGTGTCTAATTACTTGGACTT 57.563 33.333 10.04 2.79 41.87 3.01
1671 2047 9.901172 CTAATTACTTGGACTTAAATGGTAGGT 57.099 33.333 0.00 0.00 0.00 3.08
1672 2048 8.575649 AATTACTTGGACTTAAATGGTAGGTG 57.424 34.615 0.00 0.00 0.00 4.00
1677 2053 4.224370 TGGACTTAAATGGTAGGTGACTCC 59.776 45.833 0.00 0.00 43.67 3.85
1681 2057 2.642171 AATGGTAGGTGACTCCCTCA 57.358 50.000 0.00 0.00 43.67 3.86
1722 2098 4.989168 GTCTGATACGTCCACAACTTTCTT 59.011 41.667 0.00 0.00 0.00 2.52
1723 2099 6.154445 GTCTGATACGTCCACAACTTTCTTA 58.846 40.000 0.00 0.00 0.00 2.10
1732 2108 6.293698 GTCCACAACTTTCTTAACTAGGGAA 58.706 40.000 0.00 0.00 0.00 3.97
1768 2144 0.409484 AGTTGGGCTGGGCAATAGTT 59.591 50.000 0.00 0.00 0.00 2.24
1769 2145 1.638589 AGTTGGGCTGGGCAATAGTTA 59.361 47.619 0.00 0.00 0.00 2.24
1792 2175 1.983691 CCTCATGTCCAGGCATCCTAT 59.016 52.381 0.00 0.00 29.64 2.57
1793 2176 3.176411 CCTCATGTCCAGGCATCCTATA 58.824 50.000 0.00 0.00 29.64 1.31
1803 2186 8.278639 TGTCCAGGCATCCTATAATCTTTTAAA 58.721 33.333 0.00 0.00 29.64 1.52
1826 2209 3.840666 AGCCATTTAGTTGTCTGGAGAGA 59.159 43.478 0.00 0.00 0.00 3.10
1846 2229 5.643777 AGAGAAATCCGGTTGACTAATTGTG 59.356 40.000 0.00 0.00 0.00 3.33
1855 2238 5.619757 CGGTTGACTAATTGTGTGCATGATT 60.620 40.000 0.00 0.00 0.00 2.57
1856 2239 5.801947 GGTTGACTAATTGTGTGCATGATTC 59.198 40.000 0.00 0.00 0.00 2.52
1857 2240 6.380995 GTTGACTAATTGTGTGCATGATTCA 58.619 36.000 0.00 0.00 0.00 2.57
1858 2241 6.762702 TGACTAATTGTGTGCATGATTCAT 57.237 33.333 0.00 0.00 0.00 2.57
1859 2242 7.862512 TGACTAATTGTGTGCATGATTCATA 57.137 32.000 0.00 0.00 0.00 2.15
1860 2243 8.454570 TGACTAATTGTGTGCATGATTCATAT 57.545 30.769 0.00 0.00 0.00 1.78
1867 2250 6.500041 TGTGTGCATGATTCATATGTCATTG 58.500 36.000 1.90 2.95 32.98 2.82
1868 2251 5.918576 GTGTGCATGATTCATATGTCATTGG 59.081 40.000 1.90 0.00 32.98 3.16
1887 2270 4.453454 GGGGGATTGGTTTGGGTC 57.547 61.111 0.00 0.00 0.00 4.46
1927 2492 3.071874 TCTGCCATAAAACTCCACAGG 57.928 47.619 0.00 0.00 0.00 4.00
1965 2538 6.811954 TCCAAATTGACCTTTACAGGAAAAC 58.188 36.000 0.79 0.00 44.19 2.43
1970 2543 3.141272 TGACCTTTACAGGAAAACCCCAT 59.859 43.478 0.79 0.00 44.19 4.00
2000 2573 6.573664 TTGTATCTCAACTTCATGGGTTTG 57.426 37.500 0.00 0.00 0.00 2.93
2002 2575 6.774673 TGTATCTCAACTTCATGGGTTTGTA 58.225 36.000 0.00 0.00 0.00 2.41
2003 2576 7.227873 TGTATCTCAACTTCATGGGTTTGTAA 58.772 34.615 0.00 0.00 0.00 2.41
2119 2720 9.613428 TTTGTCCATTAGTCCTTATGATGTTAG 57.387 33.333 0.00 0.00 0.00 2.34
2140 2752 8.511321 TGTTAGTTGTGGCATTATTAAGTTGAG 58.489 33.333 0.00 0.00 0.00 3.02
2161 2773 3.818787 CTTGCGATGGGTGCTGCC 61.819 66.667 0.00 0.00 0.00 4.85
2283 2895 9.694137 GTATCTTCTGTAGTTAGTGAACTGTTT 57.306 33.333 0.00 0.00 45.74 2.83
2326 2943 5.310451 AGCTGGATTTGCATGTTTTTCATT 58.690 33.333 0.00 0.00 34.09 2.57
2475 3092 4.159135 GTCGTCTGAGGGGTAATCAGTTTA 59.841 45.833 3.14 0.00 43.79 2.01
2486 3106 8.778059 AGGGGTAATCAGTTTATCTCATTTGTA 58.222 33.333 0.00 0.00 0.00 2.41
2621 3245 9.192642 TGTGTATACTTCTAGGCTTTGTGTATA 57.807 33.333 4.17 0.00 0.00 1.47
2872 7006 8.025445 ACTCTTGCTTGTCATATTTTGTCAATC 58.975 33.333 0.00 0.00 33.79 2.67
2929 7063 1.472878 TGACTCTGCAGGTACGTCATC 59.527 52.381 15.13 1.18 30.41 2.92
3022 7167 5.351948 ACTTGTTTTACATGTGGCCTTTT 57.648 34.783 9.11 0.00 35.51 2.27
3048 7193 5.185635 TGCCAAAATCTCTTCCATTAACCTG 59.814 40.000 0.00 0.00 0.00 4.00
3066 7211 3.181434 ACCTGCCACCTTGTAGATTTGAA 60.181 43.478 0.00 0.00 0.00 2.69
3107 7253 8.833231 AACGATCTGGAATTATTATTCGTGAT 57.167 30.769 9.18 9.18 40.91 3.06
3111 7257 9.442047 GATCTGGAATTATTATTCGTGATCCTT 57.558 33.333 17.83 1.08 40.10 3.36
3140 7286 4.911514 TTCACATACGCAGCAGAGTATA 57.088 40.909 5.24 0.00 38.47 1.47
3178 7459 3.290948 TGTACCTTTTGAGGCAACACT 57.709 42.857 0.00 0.00 41.41 3.55
3181 7462 2.949447 ACCTTTTGAGGCAACACTGAT 58.051 42.857 0.00 0.00 41.41 2.90
3254 7535 1.149174 AGCTGTGTCAACCCCAGTG 59.851 57.895 0.00 0.00 0.00 3.66
3309 7590 9.257651 GCCACTATATCGTTTTACTAGAAATGT 57.742 33.333 0.00 0.00 0.00 2.71
3374 7659 3.859386 CACAGCTTCAGGTTTTGTTGAAC 59.141 43.478 0.00 0.00 30.66 3.18
3387 7672 6.909895 GGTTTTGTTGAACCATTTTGTTATGC 59.090 34.615 2.08 0.00 46.66 3.14
3389 7674 5.188327 TGTTGAACCATTTTGTTATGCGA 57.812 34.783 0.00 0.00 0.00 5.10
3397 7682 4.685628 CCATTTTGTTATGCGAGCTTGTTT 59.314 37.500 2.14 0.00 0.00 2.83
3400 7685 3.536158 TGTTATGCGAGCTTGTTTCAC 57.464 42.857 2.14 0.00 0.00 3.18
3422 7707 6.770746 ACTGTTAAGTGGAGTATACACGAT 57.229 37.500 5.50 0.00 43.41 3.73
3423 7708 7.166691 ACTGTTAAGTGGAGTATACACGATT 57.833 36.000 5.50 0.00 43.41 3.34
3424 7709 7.033791 ACTGTTAAGTGGAGTATACACGATTG 58.966 38.462 5.50 0.00 43.41 2.67
3430 7717 8.836268 AAGTGGAGTATACACGATTGTTTTTA 57.164 30.769 5.50 0.00 43.41 1.52
3485 7773 7.315247 TGTGTTAATAGTATTGGCATGTGTC 57.685 36.000 5.61 0.00 0.00 3.67
3517 7805 4.338118 GCCCATAACTAAATGTAGCTTGCA 59.662 41.667 0.00 0.00 0.00 4.08
3518 7806 5.733373 GCCCATAACTAAATGTAGCTTGCAC 60.733 44.000 0.00 0.00 0.00 4.57
3520 7808 3.471495 AACTAAATGTAGCTTGCACGC 57.529 42.857 7.16 7.16 0.00 5.34
3532 7822 0.244178 TTGCACGCGTGATACACCTA 59.756 50.000 41.19 16.98 0.00 3.08
3543 7833 5.963586 GCGTGATACACCTAAAGCATTTTAC 59.036 40.000 0.00 0.00 40.09 2.01
3621 7913 7.404980 ACCAAAACTCTAGAAATATCCCTGGTA 59.595 37.037 0.00 0.00 0.00 3.25
3624 7916 7.989947 AACTCTAGAAATATCCCTGGTACAA 57.010 36.000 0.00 0.00 38.70 2.41
3653 7946 9.703892 TGTTTTGGAATTTACATTACCATTCTG 57.296 29.630 0.00 0.00 0.00 3.02
3676 7969 7.069455 TCTGGTGAACTGCTATTATTGTAGCTA 59.931 37.037 7.35 0.00 45.70 3.32
3685 7978 9.440773 CTGCTATTATTGTAGCTATGGAATTCA 57.559 33.333 7.93 0.00 45.70 2.57
3696 7989 6.550163 AGCTATGGAATTCATATTGGCTCTT 58.450 36.000 7.93 0.00 34.36 2.85
3701 7994 7.281040 TGGAATTCATATTGGCTCTTTGATC 57.719 36.000 7.93 0.00 0.00 2.92
3704 7997 8.365647 GGAATTCATATTGGCTCTTTGATCATT 58.634 33.333 7.93 0.00 0.00 2.57
3748 8041 4.761235 ATTTGTCTGCATCTGTTGAGTG 57.239 40.909 0.00 0.00 0.00 3.51
3758 8051 6.408869 TGCATCTGTTGAGTGAATATCTCAA 58.591 36.000 4.56 4.56 45.66 3.02
3809 8102 3.315191 GCACTTGGTGAACTATGTGTTGT 59.685 43.478 12.32 0.00 39.30 3.32
3822 8115 3.650070 TGTGTTGTGTTTTTGCTCACA 57.350 38.095 0.00 0.00 41.81 3.58
3868 8161 6.043938 ACCAGTAGATAAGTCCTTGGTTTCAA 59.956 38.462 0.00 0.00 32.24 2.69
3877 8170 4.956075 AGTCCTTGGTTTCAACAAATGAGT 59.044 37.500 0.00 0.00 39.77 3.41
3882 8175 3.450457 TGGTTTCAACAAATGAGTGGCTT 59.550 39.130 0.00 0.00 39.77 4.35
3884 8177 3.731652 TTCAACAAATGAGTGGCTTGG 57.268 42.857 0.00 0.00 39.77 3.61
3893 8186 2.722094 TGAGTGGCTTGGCGATTTAAT 58.278 42.857 0.00 0.00 0.00 1.40
3899 8192 7.094805 TGAGTGGCTTGGCGATTTAATATATTC 60.095 37.037 0.00 0.00 0.00 1.75
3905 8198 7.268447 GCTTGGCGATTTAATATATTCACGTTC 59.732 37.037 0.00 2.99 0.00 3.95
3964 8257 4.153117 GCAGTTGTCGTCTCAATTCTGATT 59.847 41.667 0.00 0.00 0.00 2.57
4051 8344 4.497473 TTACAGTGAATCCAAAAAGCGG 57.503 40.909 0.00 0.00 0.00 5.52
4133 8426 4.020218 GGTGCCCAGAGCTAATATATGACA 60.020 45.833 0.00 0.00 44.23 3.58
4358 8652 5.209977 ACGCTTAGTTTTCGGAAATTGTTC 58.790 37.500 3.67 0.00 0.00 3.18
4361 8655 6.565999 CGCTTAGTTTTCGGAAATTGTTCTCT 60.566 38.462 3.67 0.00 33.92 3.10
4435 8729 1.000827 TGCATGTACCAAACTTTGCCG 60.001 47.619 0.00 0.00 37.22 5.69
4478 8772 8.669946 TTATGACACTGAATTTGTTGACACTA 57.330 30.769 0.00 0.00 0.00 2.74
4485 8779 9.173939 CACTGAATTTGTTGACACTATTCTTTC 57.826 33.333 14.29 0.00 32.61 2.62
4568 8865 4.066490 CTGAGGGAGCTCATCAAATGATC 58.934 47.826 17.19 0.71 38.85 2.92
4569 8866 3.065655 GAGGGAGCTCATCAAATGATCG 58.934 50.000 17.19 0.00 38.85 3.69
4570 8867 2.149578 GGGAGCTCATCAAATGATCGG 58.850 52.381 17.19 0.00 38.85 4.18
4612 8929 3.726291 TGAAGCTTTGTAAGGGCAAAC 57.274 42.857 0.00 0.00 34.95 2.93
4613 8930 3.027412 TGAAGCTTTGTAAGGGCAAACA 58.973 40.909 0.00 0.00 34.95 2.83
4637 8954 2.821366 CCGGATGCTGTGTCTGCC 60.821 66.667 0.00 0.00 0.00 4.85
4638 8955 2.267006 CGGATGCTGTGTCTGCCT 59.733 61.111 0.00 0.00 0.00 4.75
4640 8957 1.748122 GGATGCTGTGTCTGCCTGG 60.748 63.158 0.00 0.00 0.00 4.45
4641 8958 1.002868 GATGCTGTGTCTGCCTGGT 60.003 57.895 0.00 0.00 0.00 4.00
4642 8959 1.303074 ATGCTGTGTCTGCCTGGTG 60.303 57.895 0.00 0.00 0.00 4.17
4644 8961 1.670406 GCTGTGTCTGCCTGGTGAG 60.670 63.158 0.00 0.00 0.00 3.51
4645 8962 1.670406 CTGTGTCTGCCTGGTGAGC 60.670 63.158 0.00 0.00 0.00 4.26
4646 8963 2.387476 CTGTGTCTGCCTGGTGAGCA 62.387 60.000 0.00 0.00 38.82 4.26
4654 8971 1.202867 TGCCTGGTGAGCAAATGTGTA 60.203 47.619 0.00 0.00 37.28 2.90
4662 8979 5.181748 GGTGAGCAAATGTGTAATCTCTCT 58.818 41.667 0.00 0.00 0.00 3.10
4665 8982 6.538021 GTGAGCAAATGTGTAATCTCTCTGAT 59.462 38.462 0.00 0.00 36.89 2.90
4666 8983 6.537660 TGAGCAAATGTGTAATCTCTCTGATG 59.462 38.462 0.00 0.00 35.21 3.07
4667 8984 6.413052 AGCAAATGTGTAATCTCTCTGATGT 58.587 36.000 0.00 0.00 35.21 3.06
4668 8985 6.315642 AGCAAATGTGTAATCTCTCTGATGTG 59.684 38.462 0.00 0.00 35.21 3.21
4669 8986 6.457934 GCAAATGTGTAATCTCTCTGATGTGG 60.458 42.308 0.00 0.00 35.21 4.17
4670 8987 4.128925 TGTGTAATCTCTCTGATGTGGC 57.871 45.455 0.00 0.00 35.21 5.01
4671 8988 3.118629 TGTGTAATCTCTCTGATGTGGCC 60.119 47.826 0.00 0.00 35.21 5.36
4672 8989 3.106827 TGTAATCTCTCTGATGTGGCCA 58.893 45.455 0.00 0.00 35.21 5.36
4673 8990 3.713248 TGTAATCTCTCTGATGTGGCCAT 59.287 43.478 9.72 0.00 35.21 4.40
4674 8991 3.947612 AATCTCTCTGATGTGGCCATT 57.052 42.857 9.72 0.00 35.21 3.16
4726 9045 8.981659 TGAGACTTCTATTCTGGTGAATTATGA 58.018 33.333 0.00 0.00 42.37 2.15
4785 9104 7.551974 AGGTATTCATCTCTTGATTTGTCTGTG 59.448 37.037 0.00 0.00 33.34 3.66
4812 9131 9.521503 GACAAATTTCAAGCTAAAACTTTCTCT 57.478 29.630 0.00 0.00 0.00 3.10
4829 9148 0.953727 TCTGCAACACACTTCCATGC 59.046 50.000 0.00 0.00 37.52 4.06
4865 9184 0.378257 ATCGCGGTGCATGACAAATC 59.622 50.000 6.13 0.00 0.00 2.17
4879 9198 0.311790 CAAATCGCACAACTGCAGGT 59.688 50.000 19.93 9.19 44.50 4.00
4891 9210 1.216444 TGCAGGTAAGCAGAGCTCG 59.784 57.895 8.37 4.60 38.25 5.03
4894 9213 2.202946 GGTAAGCAGAGCTCGGGC 60.203 66.667 21.31 21.31 38.25 6.13
4905 9224 0.827925 AGCTCGGGCCGATATCAAGA 60.828 55.000 31.23 3.96 39.73 3.02
4911 9231 3.813166 TCGGGCCGATATCAAGATTTTTC 59.187 43.478 27.46 0.00 0.00 2.29
4913 9233 4.083802 CGGGCCGATATCAAGATTTTTCTC 60.084 45.833 24.41 0.00 0.00 2.87
4915 9235 5.532779 GGGCCGATATCAAGATTTTTCTCTT 59.467 40.000 3.12 0.00 35.88 2.85
4925 9245 7.077605 TCAAGATTTTTCTCTTACACATTGCG 58.922 34.615 0.00 0.00 33.73 4.85
4926 9246 6.560253 AGATTTTTCTCTTACACATTGCGT 57.440 33.333 0.00 0.00 0.00 5.24
4927 9247 7.149080 CAAGATTTTTCTCTTACACATTGCGTG 60.149 37.037 0.00 0.00 41.31 5.34
4937 9257 3.755965 CACATTGCGTGCCTAAATACA 57.244 42.857 0.00 0.00 39.19 2.29
4938 9258 3.683989 CACATTGCGTGCCTAAATACAG 58.316 45.455 0.00 0.00 39.19 2.74
4939 9259 3.126858 CACATTGCGTGCCTAAATACAGT 59.873 43.478 0.00 0.00 39.19 3.55
4940 9260 3.756434 ACATTGCGTGCCTAAATACAGTT 59.244 39.130 0.00 0.00 0.00 3.16
4941 9261 4.217550 ACATTGCGTGCCTAAATACAGTTT 59.782 37.500 0.00 0.00 0.00 2.66
4942 9262 3.822594 TGCGTGCCTAAATACAGTTTG 57.177 42.857 0.00 0.00 0.00 2.93
4943 9263 3.403968 TGCGTGCCTAAATACAGTTTGA 58.596 40.909 0.00 0.00 0.00 2.69
4944 9264 3.187637 TGCGTGCCTAAATACAGTTTGAC 59.812 43.478 0.00 0.00 0.00 3.18
4945 9265 3.435671 GCGTGCCTAAATACAGTTTGACT 59.564 43.478 0.00 0.00 0.00 3.41
4946 9266 4.628333 GCGTGCCTAAATACAGTTTGACTA 59.372 41.667 0.00 0.00 0.00 2.59
4947 9267 5.220416 GCGTGCCTAAATACAGTTTGACTAG 60.220 44.000 0.00 0.00 0.00 2.57
4948 9268 5.220416 CGTGCCTAAATACAGTTTGACTAGC 60.220 44.000 0.00 0.00 0.00 3.42
4949 9269 5.064834 GTGCCTAAATACAGTTTGACTAGCC 59.935 44.000 0.00 0.00 0.00 3.93
4950 9270 4.270325 GCCTAAATACAGTTTGACTAGCCG 59.730 45.833 0.00 0.00 0.00 5.52
4951 9271 5.657474 CCTAAATACAGTTTGACTAGCCGA 58.343 41.667 0.00 0.00 0.00 5.54
4952 9272 6.281405 CCTAAATACAGTTTGACTAGCCGAT 58.719 40.000 0.00 0.00 0.00 4.18
4953 9273 6.761714 CCTAAATACAGTTTGACTAGCCGATT 59.238 38.462 0.00 0.00 0.00 3.34
4954 9274 6.663944 AAATACAGTTTGACTAGCCGATTC 57.336 37.500 0.00 0.00 0.00 2.52
4955 9275 2.973945 ACAGTTTGACTAGCCGATTCC 58.026 47.619 0.00 0.00 0.00 3.01
4956 9276 2.301870 ACAGTTTGACTAGCCGATTCCA 59.698 45.455 0.00 0.00 0.00 3.53
4957 9277 3.244422 ACAGTTTGACTAGCCGATTCCAA 60.244 43.478 0.00 0.00 0.00 3.53
4958 9278 3.751175 CAGTTTGACTAGCCGATTCCAAA 59.249 43.478 0.00 0.00 0.00 3.28
4959 9279 4.215399 CAGTTTGACTAGCCGATTCCAAAA 59.785 41.667 0.00 0.00 0.00 2.44
4960 9280 5.010282 AGTTTGACTAGCCGATTCCAAAAT 58.990 37.500 0.00 0.00 0.00 1.82
4961 9281 5.123979 AGTTTGACTAGCCGATTCCAAAATC 59.876 40.000 0.00 0.00 38.34 2.17
4962 9282 3.541632 TGACTAGCCGATTCCAAAATCC 58.458 45.455 0.00 0.00 38.46 3.01
4963 9283 3.199946 TGACTAGCCGATTCCAAAATCCT 59.800 43.478 0.00 0.00 38.46 3.24
4964 9284 4.407621 TGACTAGCCGATTCCAAAATCCTA 59.592 41.667 0.00 0.00 38.46 2.94
4965 9285 5.071788 TGACTAGCCGATTCCAAAATCCTAT 59.928 40.000 0.00 0.00 38.46 2.57
4966 9286 5.941788 ACTAGCCGATTCCAAAATCCTATT 58.058 37.500 0.00 0.00 38.46 1.73
4967 9287 5.765182 ACTAGCCGATTCCAAAATCCTATTG 59.235 40.000 0.00 0.00 38.46 1.90
4968 9288 3.319122 AGCCGATTCCAAAATCCTATTGC 59.681 43.478 0.00 0.00 38.46 3.56
4969 9289 3.853307 GCCGATTCCAAAATCCTATTGCG 60.853 47.826 0.00 0.00 38.46 4.85
4970 9290 3.315191 CCGATTCCAAAATCCTATTGCGT 59.685 43.478 0.00 0.00 38.46 5.24
4971 9291 4.282068 CGATTCCAAAATCCTATTGCGTG 58.718 43.478 0.00 0.00 38.46 5.34
4972 9292 3.502191 TTCCAAAATCCTATTGCGTGC 57.498 42.857 0.00 0.00 0.00 5.34
4973 9293 1.748493 TCCAAAATCCTATTGCGTGCC 59.252 47.619 0.00 0.00 0.00 5.01
4974 9294 1.750778 CCAAAATCCTATTGCGTGCCT 59.249 47.619 0.00 0.00 0.00 4.75
4975 9295 2.948979 CCAAAATCCTATTGCGTGCCTA 59.051 45.455 0.00 0.00 0.00 3.93
4976 9296 3.380004 CCAAAATCCTATTGCGTGCCTAA 59.620 43.478 0.00 0.00 0.00 2.69
4977 9297 4.142271 CCAAAATCCTATTGCGTGCCTAAA 60.142 41.667 0.00 0.00 0.00 1.85
4978 9298 5.451798 CCAAAATCCTATTGCGTGCCTAAAT 60.452 40.000 0.00 0.00 0.00 1.40
4979 9299 6.238897 CCAAAATCCTATTGCGTGCCTAAATA 60.239 38.462 0.00 0.00 0.00 1.40
4980 9300 5.941948 AATCCTATTGCGTGCCTAAATAC 57.058 39.130 0.00 0.00 0.00 1.89
4981 9301 4.409718 TCCTATTGCGTGCCTAAATACA 57.590 40.909 0.00 0.00 0.00 2.29
4982 9302 4.377021 TCCTATTGCGTGCCTAAATACAG 58.623 43.478 0.00 0.00 0.00 2.74
4983 9303 3.498397 CCTATTGCGTGCCTAAATACAGG 59.502 47.826 0.00 0.00 38.86 4.00
4984 9304 2.772077 TTGCGTGCCTAAATACAGGA 57.228 45.000 0.00 0.00 38.00 3.86
4985 9305 2.309528 TGCGTGCCTAAATACAGGAG 57.690 50.000 0.00 0.00 38.00 3.69
4986 9306 1.828595 TGCGTGCCTAAATACAGGAGA 59.171 47.619 0.00 0.00 38.00 3.71
4987 9307 2.235155 TGCGTGCCTAAATACAGGAGAA 59.765 45.455 0.00 0.00 38.00 2.87
4988 9308 3.118408 TGCGTGCCTAAATACAGGAGAAT 60.118 43.478 0.00 0.00 38.00 2.40
4989 9309 4.100344 TGCGTGCCTAAATACAGGAGAATA 59.900 41.667 0.00 0.00 38.00 1.75
4990 9310 4.686554 GCGTGCCTAAATACAGGAGAATAG 59.313 45.833 0.00 0.00 38.00 1.73
4991 9311 5.739358 GCGTGCCTAAATACAGGAGAATAGT 60.739 44.000 0.00 0.00 38.00 2.12
4992 9312 6.516194 GCGTGCCTAAATACAGGAGAATAGTA 60.516 42.308 0.00 0.00 38.00 1.82
4993 9313 7.603651 CGTGCCTAAATACAGGAGAATAGTAT 58.396 38.462 0.00 0.00 38.00 2.12
4994 9314 7.542477 CGTGCCTAAATACAGGAGAATAGTATG 59.458 40.741 0.00 0.00 38.00 2.39
4995 9315 8.368668 GTGCCTAAATACAGGAGAATAGTATGT 58.631 37.037 0.00 0.00 38.00 2.29
4996 9316 8.934697 TGCCTAAATACAGGAGAATAGTATGTT 58.065 33.333 0.00 0.00 38.00 2.71
4997 9317 9.425577 GCCTAAATACAGGAGAATAGTATGTTC 57.574 37.037 0.00 0.00 38.00 3.18
5047 9367 9.631452 TGCTCAAGTAATCTCATTCGATAATAG 57.369 33.333 0.00 0.00 0.00 1.73
5048 9368 9.632807 GCTCAAGTAATCTCATTCGATAATAGT 57.367 33.333 0.00 0.00 0.00 2.12
5050 9370 9.914131 TCAAGTAATCTCATTCGATAATAGTGG 57.086 33.333 0.00 0.00 0.00 4.00
5051 9371 9.914131 CAAGTAATCTCATTCGATAATAGTGGA 57.086 33.333 0.00 0.00 0.00 4.02
5053 9373 9.303116 AGTAATCTCATTCGATAATAGTGGAGT 57.697 33.333 0.00 0.00 0.00 3.85
5054 9374 9.915629 GTAATCTCATTCGATAATAGTGGAGTT 57.084 33.333 0.00 0.00 0.00 3.01
5055 9375 8.824159 AATCTCATTCGATAATAGTGGAGTTG 57.176 34.615 0.00 0.00 0.00 3.16
5056 9376 7.582667 TCTCATTCGATAATAGTGGAGTTGA 57.417 36.000 0.00 0.00 0.00 3.18
5057 9377 7.426410 TCTCATTCGATAATAGTGGAGTTGAC 58.574 38.462 0.00 0.00 0.00 3.18
5058 9378 6.513180 TCATTCGATAATAGTGGAGTTGACC 58.487 40.000 0.00 0.00 0.00 4.02
5059 9379 4.931661 TCGATAATAGTGGAGTTGACCC 57.068 45.455 0.00 0.00 0.00 4.46
5060 9380 3.317149 TCGATAATAGTGGAGTTGACCCG 59.683 47.826 0.00 0.00 0.00 5.28
5061 9381 3.317149 CGATAATAGTGGAGTTGACCCGA 59.683 47.826 0.00 0.00 0.00 5.14
5062 9382 4.022242 CGATAATAGTGGAGTTGACCCGAT 60.022 45.833 0.00 0.00 0.00 4.18
5063 9383 5.509163 CGATAATAGTGGAGTTGACCCGATT 60.509 44.000 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 7.040340 TGGGAACGTGTCATTTACAAAACATAT 60.040 33.333 0.00 0.00 40.63 1.78
86 87 5.578005 TTGGGAACGTGTCATTTACAAAA 57.422 34.783 0.00 0.00 40.63 2.44
114 115 1.539496 GGCCATAATCGTCGCAACCTA 60.539 52.381 0.00 0.00 0.00 3.08
139 140 9.508567 GACAAAATAGATTGAAAGATAAGGCAC 57.491 33.333 0.00 0.00 34.38 5.01
151 152 5.168569 ACTCTTCGCGACAAAATAGATTGA 58.831 37.500 9.15 0.00 34.38 2.57
169 170 3.805207 AGTTTAAGGCACGTCAACTCTT 58.195 40.909 0.00 0.00 0.00 2.85
211 212 8.812513 TTGGATCAATGAGATGTAAAATGAGT 57.187 30.769 0.00 0.00 37.00 3.41
290 291 2.811799 GCAACTTGCGGGTTTGGT 59.188 55.556 0.00 0.00 31.71 3.67
334 335 4.864247 CCCCGCAACAAAATAGATTGAAAG 59.136 41.667 0.00 0.00 34.38 2.62
337 338 3.691575 TCCCCGCAACAAAATAGATTGA 58.308 40.909 0.00 0.00 34.38 2.57
341 342 1.353022 ACCTCCCCGCAACAAAATAGA 59.647 47.619 0.00 0.00 0.00 1.98
346 347 1.527380 GTCACCTCCCCGCAACAAA 60.527 57.895 0.00 0.00 0.00 2.83
348 349 4.308458 CGTCACCTCCCCGCAACA 62.308 66.667 0.00 0.00 0.00 3.33
349 350 4.309950 ACGTCACCTCCCCGCAAC 62.310 66.667 0.00 0.00 0.00 4.17
415 416 0.535328 TGATCCGTCACCCGCAAAAA 60.535 50.000 0.00 0.00 34.38 1.94
416 417 1.071642 TGATCCGTCACCCGCAAAA 59.928 52.632 0.00 0.00 34.38 2.44
417 418 2.744377 TGATCCGTCACCCGCAAA 59.256 55.556 0.00 0.00 34.38 3.68
425 426 2.768253 AAATGAGCTGTGATCCGTCA 57.232 45.000 0.00 0.00 0.00 4.35
426 427 4.122776 ACATAAATGAGCTGTGATCCGTC 58.877 43.478 0.00 0.00 0.00 4.79
427 428 4.122776 GACATAAATGAGCTGTGATCCGT 58.877 43.478 0.00 0.00 0.00 4.69
428 429 4.375272 AGACATAAATGAGCTGTGATCCG 58.625 43.478 0.00 0.00 0.00 4.18
429 430 5.363101 TGAGACATAAATGAGCTGTGATCC 58.637 41.667 0.00 0.00 0.00 3.36
430 431 6.704937 TGATGAGACATAAATGAGCTGTGATC 59.295 38.462 0.00 0.00 0.00 2.92
431 432 6.589135 TGATGAGACATAAATGAGCTGTGAT 58.411 36.000 0.00 0.00 0.00 3.06
432 433 5.981174 TGATGAGACATAAATGAGCTGTGA 58.019 37.500 0.00 0.00 0.00 3.58
433 434 6.673154 TTGATGAGACATAAATGAGCTGTG 57.327 37.500 0.00 0.00 0.00 3.66
434 435 6.485984 GGATTGATGAGACATAAATGAGCTGT 59.514 38.462 0.00 0.00 0.00 4.40
435 436 6.485648 TGGATTGATGAGACATAAATGAGCTG 59.514 38.462 0.00 0.00 0.00 4.24
436 437 6.598503 TGGATTGATGAGACATAAATGAGCT 58.401 36.000 0.00 0.00 0.00 4.09
455 456 5.248020 TGCCCAAAATTACTGACATTGGATT 59.752 36.000 5.05 0.00 42.46 3.01
457 458 4.155709 TGCCCAAAATTACTGACATTGGA 58.844 39.130 5.05 0.00 42.46 3.53
481 482 1.850377 CAACAAAAGACATTGCCGCA 58.150 45.000 0.00 0.00 33.52 5.69
491 492 3.735591 AGCTACTAACCGCAACAAAAGA 58.264 40.909 0.00 0.00 0.00 2.52
493 494 6.374565 TTTTAGCTACTAACCGCAACAAAA 57.625 33.333 0.00 0.00 0.00 2.44
653 654 8.144862 TGCAGTATTAAATGGGGAAAAGAATT 57.855 30.769 0.00 0.00 0.00 2.17
664 665 7.650890 TGCTGATATGTTGCAGTATTAAATGG 58.349 34.615 0.00 0.00 34.66 3.16
698 699 6.599437 GTGTAGTCTTGTGCGATTGTTAATT 58.401 36.000 0.00 0.00 0.00 1.40
699 700 5.163992 CGTGTAGTCTTGTGCGATTGTTAAT 60.164 40.000 0.00 0.00 0.00 1.40
700 701 4.149221 CGTGTAGTCTTGTGCGATTGTTAA 59.851 41.667 0.00 0.00 0.00 2.01
701 702 3.671459 CGTGTAGTCTTGTGCGATTGTTA 59.329 43.478 0.00 0.00 0.00 2.41
702 703 2.475111 CGTGTAGTCTTGTGCGATTGTT 59.525 45.455 0.00 0.00 0.00 2.83
704 705 2.324860 TCGTGTAGTCTTGTGCGATTG 58.675 47.619 0.00 0.00 0.00 2.67
705 706 2.717580 TCGTGTAGTCTTGTGCGATT 57.282 45.000 0.00 0.00 0.00 3.34
708 1060 4.896562 TTTATTCGTGTAGTCTTGTGCG 57.103 40.909 0.00 0.00 0.00 5.34
768 1135 7.415318 GGTTTTCTCCTTTCCCGATCTAAATTC 60.415 40.741 0.00 0.00 0.00 2.17
891 1264 2.611964 ATTGGTGGTGGGTTTGGGCA 62.612 55.000 0.00 0.00 0.00 5.36
1146 1520 1.668826 AGATGGGGTACTTGAAGCCA 58.331 50.000 0.00 0.00 38.85 4.75
1284 1658 1.153667 GCAGAAGACGAGGCTGAGG 60.154 63.158 0.00 0.00 0.00 3.86
1395 1769 1.412710 ACGGTCATGATGTAGGCGAAT 59.587 47.619 0.00 0.00 0.00 3.34
1660 2036 4.069312 TGAGGGAGTCACCTACCATTTA 57.931 45.455 0.61 0.00 45.27 1.40
1681 2057 1.532868 GACAGCACGCTCAATCAACTT 59.467 47.619 0.00 0.00 0.00 2.66
1722 2098 7.817910 TCATCCCTAAAGTTTTCCCTAGTTA 57.182 36.000 0.00 0.00 0.00 2.24
1723 2099 6.713731 TCATCCCTAAAGTTTTCCCTAGTT 57.286 37.500 0.00 0.00 0.00 2.24
1732 2108 5.264395 CCCAACTCATCATCCCTAAAGTTT 58.736 41.667 0.00 0.00 0.00 2.66
1803 2186 4.287067 TCTCTCCAGACAACTAAATGGCTT 59.713 41.667 0.00 0.00 36.18 4.35
1826 2209 4.320935 GCACACAATTAGTCAACCGGATTT 60.321 41.667 9.46 0.00 0.00 2.17
1846 2229 5.466819 CCCAATGACATATGAATCATGCAC 58.533 41.667 10.38 0.00 35.71 4.57
1887 2270 6.015940 GGCAGAACAATTATATTTCCTCAGGG 60.016 42.308 0.00 0.00 0.00 4.45
1946 2511 4.157246 GGGGTTTTCCTGTAAAGGTCAAT 58.843 43.478 0.00 0.00 40.46 2.57
2043 2644 7.998753 TTCAAGCTATATATCATCAGCATCG 57.001 36.000 7.73 0.00 36.47 3.84
2105 2706 5.172687 TGCCACAACTAACATCATAAGGA 57.827 39.130 0.00 0.00 0.00 3.36
2119 2720 5.102313 GGCTCAACTTAATAATGCCACAAC 58.898 41.667 0.00 0.00 38.79 3.32
2161 2773 5.597806 TGGGAATTACGACAGCTACATAAG 58.402 41.667 0.00 0.00 0.00 1.73
2249 2861 6.758886 ACTAACTACAGAAGATACATGCAAGC 59.241 38.462 0.00 0.00 0.00 4.01
2283 2895 7.236640 TCCAGCTCTCTCATAGACTAGAATAGA 59.763 40.741 0.00 0.00 42.77 1.98
2326 2943 6.164876 TGGTTTGCGCACTAATAGTTAGTTA 58.835 36.000 11.12 0.00 43.70 2.24
2339 2956 2.474735 CCTGTAAATTTGGTTTGCGCAC 59.525 45.455 11.12 0.00 35.45 5.34
2340 2957 2.546795 CCCTGTAAATTTGGTTTGCGCA 60.547 45.455 5.66 5.66 35.45 6.09
2486 3106 9.970553 AGCATCCATTTATAATGTGTCATCTAT 57.029 29.630 0.00 0.00 0.00 1.98
2488 3108 8.162085 AGAGCATCCATTTATAATGTGTCATCT 58.838 33.333 0.00 0.00 33.66 2.90
2502 3122 9.887629 CTCATGAATAGTATAGAGCATCCATTT 57.112 33.333 0.00 0.00 33.66 2.32
2545 3165 7.772757 AGACAAATCCTAGAAGCTTCCTATTTG 59.227 37.037 29.12 29.12 0.00 2.32
2654 3373 9.571810 GCAGAATAGTCAAGAGTCATGATATAG 57.428 37.037 0.00 0.00 0.00 1.31
2661 3380 3.449018 ACGGCAGAATAGTCAAGAGTCAT 59.551 43.478 0.00 0.00 0.00 3.06
3001 7145 6.128580 GCATAAAAGGCCACATGTAAAACAAG 60.129 38.462 5.01 0.00 0.00 3.16
3022 7167 7.068593 CAGGTTAATGGAAGAGATTTTGGCATA 59.931 37.037 0.00 0.00 0.00 3.14
3048 7193 8.825667 TTTTAAATTCAAATCTACAAGGTGGC 57.174 30.769 0.00 0.00 0.00 5.01
3084 7229 7.761704 AGGATCACGAATAATAATTCCAGATCG 59.238 37.037 14.58 0.00 42.63 3.69
3107 7253 7.875554 TGCTGCGTATGTGAATTATATAAAGGA 59.124 33.333 0.00 0.00 0.00 3.36
3111 7257 8.088365 ACTCTGCTGCGTATGTGAATTATATAA 58.912 33.333 0.00 0.00 0.00 0.98
3126 7272 2.969628 AAAGCTATACTCTGCTGCGT 57.030 45.000 0.00 0.00 39.71 5.24
3204 7485 6.378661 AGTAGCCATCTGCATCCATATTTA 57.621 37.500 0.00 0.00 44.83 1.40
3216 7497 6.094603 ACAGCTGAAAAATAAGTAGCCATCTG 59.905 38.462 23.35 0.00 35.05 2.90
3332 7616 2.634600 GTGCCCCACACGAATTATACA 58.365 47.619 0.00 0.00 40.07 2.29
3374 7659 3.836949 ACAAGCTCGCATAACAAAATGG 58.163 40.909 0.00 0.00 0.00 3.16
3387 7672 4.795970 ACTTAACAGTGAAACAAGCTCG 57.204 40.909 0.00 0.00 41.43 5.03
3400 7685 7.033791 ACAATCGTGTATACTCCACTTAACAG 58.966 38.462 4.17 0.00 35.72 3.16
3485 7773 5.891551 ACATTTAGTTATGGGCTTACTTGGG 59.108 40.000 0.00 0.00 0.00 4.12
3517 7805 1.067425 TGCTTTAGGTGTATCACGCGT 60.067 47.619 5.58 5.58 34.83 6.01
3518 7806 1.635844 TGCTTTAGGTGTATCACGCG 58.364 50.000 3.53 3.53 34.83 6.01
3520 7808 6.182634 CGTAAAATGCTTTAGGTGTATCACG 58.817 40.000 0.00 0.00 34.83 4.35
3532 7822 5.705441 TGAAGACAGATCCGTAAAATGCTTT 59.295 36.000 0.00 0.00 0.00 3.51
3543 7833 4.122776 CCCATAGTTTGAAGACAGATCCG 58.877 47.826 0.00 0.00 0.00 4.18
3676 7969 7.507956 TGATCAAAGAGCCAATATGAATTCCAT 59.492 33.333 2.27 0.00 39.25 3.41
3725 8018 5.409520 TCACTCAACAGATGCAGACAAATAC 59.590 40.000 0.00 0.00 0.00 1.89
3758 8051 8.584157 TGCATTATGGTCAAAATAGAACAGTTT 58.416 29.630 0.00 0.00 38.86 2.66
3809 8102 3.509575 AGACAACCTTGTGAGCAAAAACA 59.490 39.130 0.00 0.00 42.43 2.83
3822 8115 5.729974 GTTGAACGAACTAAGACAACCTT 57.270 39.130 0.00 0.00 38.87 3.50
3868 8161 0.537143 TCGCCAAGCCACTCATTTGT 60.537 50.000 0.00 0.00 0.00 2.83
3877 8170 6.348132 CGTGAATATATTAAATCGCCAAGCCA 60.348 38.462 0.00 0.00 0.00 4.75
3882 8175 6.932400 AGGAACGTGAATATATTAAATCGCCA 59.068 34.615 0.00 0.00 0.00 5.69
3884 8177 9.314501 GAAAGGAACGTGAATATATTAAATCGC 57.685 33.333 0.00 0.00 0.00 4.58
3893 8186 5.395990 GGACCTGGAAAGGAACGTGAATATA 60.396 44.000 0.00 0.00 0.00 0.86
3899 8192 0.396811 AGGACCTGGAAAGGAACGTG 59.603 55.000 0.00 0.00 0.00 4.49
3940 8233 2.061773 AGAATTGAGACGACAACTGCG 58.938 47.619 0.00 0.00 32.50 5.18
3964 8257 5.763204 GGTTACAGACACAGGATTCTTGAAA 59.237 40.000 2.39 0.00 0.00 2.69
4051 8344 1.074889 TGGGGAACTTAGGGTTTGCTC 59.925 52.381 0.00 0.00 38.41 4.26
4133 8426 2.070650 GCCCCGGATGTAGTTCCCT 61.071 63.158 0.73 0.00 31.61 4.20
4568 8865 4.096382 ACAGGCAAGAACATTAATTAGCCG 59.904 41.667 0.00 0.00 45.19 5.52
4569 8866 5.582689 ACAGGCAAGAACATTAATTAGCC 57.417 39.130 0.00 0.00 41.08 3.93
4570 8867 6.620678 TCAACAGGCAAGAACATTAATTAGC 58.379 36.000 0.00 0.00 0.00 3.09
4622 8939 1.748122 CCAGGCAGACACAGCATCC 60.748 63.158 0.00 0.00 0.00 3.51
4633 8950 0.242825 CACATTTGCTCACCAGGCAG 59.757 55.000 0.00 0.00 40.90 4.85
4634 8951 0.467844 ACACATTTGCTCACCAGGCA 60.468 50.000 0.00 0.00 37.97 4.75
4635 8952 1.533625 TACACATTTGCTCACCAGGC 58.466 50.000 0.00 0.00 0.00 4.85
4637 8954 4.940046 AGAGATTACACATTTGCTCACCAG 59.060 41.667 0.00 0.00 0.00 4.00
4638 8955 4.910195 AGAGATTACACATTTGCTCACCA 58.090 39.130 0.00 0.00 0.00 4.17
4640 8957 5.871524 TCAGAGAGATTACACATTTGCTCAC 59.128 40.000 0.00 0.00 0.00 3.51
4641 8958 6.041423 TCAGAGAGATTACACATTTGCTCA 57.959 37.500 0.00 0.00 0.00 4.26
4642 8959 6.538021 ACATCAGAGAGATTACACATTTGCTC 59.462 38.462 0.00 0.00 33.72 4.26
4644 8961 6.457934 CCACATCAGAGAGATTACACATTTGC 60.458 42.308 0.00 0.00 33.72 3.68
4645 8962 6.457934 GCCACATCAGAGAGATTACACATTTG 60.458 42.308 0.00 0.00 33.72 2.32
4646 8963 5.587844 GCCACATCAGAGAGATTACACATTT 59.412 40.000 0.00 0.00 33.72 2.32
4654 8971 3.947612 AATGGCCACATCAGAGAGATT 57.052 42.857 8.16 0.00 35.94 2.40
4662 8979 0.038890 TTCCCGAAATGGCCACATCA 59.961 50.000 8.16 0.00 35.94 3.07
4665 8982 1.969064 CGTTCCCGAAATGGCCACA 60.969 57.895 8.16 0.00 35.87 4.17
4666 8983 1.673009 TCGTTCCCGAAATGGCCAC 60.673 57.895 8.16 0.00 40.86 5.01
4667 8984 2.751018 TCGTTCCCGAAATGGCCA 59.249 55.556 8.56 8.56 40.86 5.36
4689 9006 8.830580 CAGAATAGAAGTCTCAAAACACTTGAA 58.169 33.333 0.00 0.00 32.83 2.69
4743 9062 7.855784 TGAATACCTGAGTCATATACATGGT 57.144 36.000 0.00 0.00 33.66 3.55
4785 9104 8.648557 AGAAAGTTTTAGCTTGAAATTTGTCC 57.351 30.769 10.56 0.37 0.00 4.02
4812 9131 0.669619 CTGCATGGAAGTGTGTTGCA 59.330 50.000 0.00 0.00 40.73 4.08
4829 9148 1.860950 CGATATTCTCGCACAACCCTG 59.139 52.381 0.00 0.00 41.14 4.45
4850 9169 1.501292 TGCGATTTGTCATGCACCG 59.499 52.632 0.00 0.00 31.31 4.94
4879 9198 3.838271 CGGCCCGAGCTCTGCTTA 61.838 66.667 20.26 0.00 39.88 3.09
4891 9210 5.066593 AGAGAAAAATCTTGATATCGGCCC 58.933 41.667 0.00 0.00 0.00 5.80
4894 9213 9.098355 TGTGTAAGAGAAAAATCTTGATATCGG 57.902 33.333 0.00 0.00 39.81 4.18
4925 9245 5.064834 GGCTAGTCAAACTGTATTTAGGCAC 59.935 44.000 0.00 0.00 33.83 5.01
4926 9246 5.183228 GGCTAGTCAAACTGTATTTAGGCA 58.817 41.667 0.00 0.00 33.83 4.75
4927 9247 4.270325 CGGCTAGTCAAACTGTATTTAGGC 59.730 45.833 0.00 0.00 0.00 3.93
4928 9248 5.657474 TCGGCTAGTCAAACTGTATTTAGG 58.343 41.667 0.00 0.00 0.00 2.69
4929 9249 7.042658 GGAATCGGCTAGTCAAACTGTATTTAG 60.043 40.741 0.00 0.00 0.00 1.85
4930 9250 6.759827 GGAATCGGCTAGTCAAACTGTATTTA 59.240 38.462 0.00 0.00 0.00 1.40
4931 9251 5.585047 GGAATCGGCTAGTCAAACTGTATTT 59.415 40.000 0.00 0.00 0.00 1.40
4932 9252 5.116882 GGAATCGGCTAGTCAAACTGTATT 58.883 41.667 0.00 0.00 0.00 1.89
4933 9253 4.161565 TGGAATCGGCTAGTCAAACTGTAT 59.838 41.667 0.00 0.00 0.00 2.29
4934 9254 3.512329 TGGAATCGGCTAGTCAAACTGTA 59.488 43.478 0.00 0.00 0.00 2.74
4935 9255 2.301870 TGGAATCGGCTAGTCAAACTGT 59.698 45.455 0.00 0.00 0.00 3.55
4936 9256 2.972625 TGGAATCGGCTAGTCAAACTG 58.027 47.619 0.00 0.00 0.00 3.16
4937 9257 3.695830 TTGGAATCGGCTAGTCAAACT 57.304 42.857 0.00 0.00 0.00 2.66
4938 9258 4.759516 TTTTGGAATCGGCTAGTCAAAC 57.240 40.909 0.00 0.00 0.00 2.93
4939 9259 4.398044 GGATTTTGGAATCGGCTAGTCAAA 59.602 41.667 0.00 0.00 42.12 2.69
4940 9260 3.945285 GGATTTTGGAATCGGCTAGTCAA 59.055 43.478 0.00 0.00 42.12 3.18
4941 9261 3.199946 AGGATTTTGGAATCGGCTAGTCA 59.800 43.478 0.00 0.00 42.12 3.41
4942 9262 3.809905 AGGATTTTGGAATCGGCTAGTC 58.190 45.455 0.00 0.00 42.12 2.59
4943 9263 3.933861 AGGATTTTGGAATCGGCTAGT 57.066 42.857 0.00 0.00 42.12 2.57
4944 9264 5.335191 GCAATAGGATTTTGGAATCGGCTAG 60.335 44.000 0.00 0.00 42.12 3.42
4945 9265 4.518970 GCAATAGGATTTTGGAATCGGCTA 59.481 41.667 0.00 0.00 42.12 3.93
4946 9266 3.319122 GCAATAGGATTTTGGAATCGGCT 59.681 43.478 0.00 0.00 42.12 5.52
4947 9267 3.642705 GCAATAGGATTTTGGAATCGGC 58.357 45.455 0.00 0.00 42.12 5.54
4948 9268 3.315191 ACGCAATAGGATTTTGGAATCGG 59.685 43.478 0.00 0.00 42.12 4.18
4949 9269 4.282068 CACGCAATAGGATTTTGGAATCG 58.718 43.478 0.00 0.00 42.12 3.34
4950 9270 4.044426 GCACGCAATAGGATTTTGGAATC 58.956 43.478 0.00 0.00 40.78 2.52
4951 9271 3.181476 GGCACGCAATAGGATTTTGGAAT 60.181 43.478 0.00 0.00 0.00 3.01
4952 9272 2.165437 GGCACGCAATAGGATTTTGGAA 59.835 45.455 0.00 0.00 0.00 3.53
4953 9273 1.748493 GGCACGCAATAGGATTTTGGA 59.252 47.619 0.00 0.00 0.00 3.53
4954 9274 1.750778 AGGCACGCAATAGGATTTTGG 59.249 47.619 0.00 0.00 0.00 3.28
4955 9275 4.630894 TTAGGCACGCAATAGGATTTTG 57.369 40.909 0.00 0.00 0.00 2.44
4956 9276 5.852282 ATTTAGGCACGCAATAGGATTTT 57.148 34.783 0.00 0.00 0.00 1.82
4957 9277 5.825679 TGTATTTAGGCACGCAATAGGATTT 59.174 36.000 0.00 0.00 0.00 2.17
4958 9278 5.373222 TGTATTTAGGCACGCAATAGGATT 58.627 37.500 0.00 0.00 0.00 3.01
4959 9279 4.968259 TGTATTTAGGCACGCAATAGGAT 58.032 39.130 0.00 0.00 0.00 3.24
4960 9280 4.377021 CTGTATTTAGGCACGCAATAGGA 58.623 43.478 0.00 0.00 0.00 2.94
4961 9281 3.498397 CCTGTATTTAGGCACGCAATAGG 59.502 47.826 0.00 0.00 0.00 2.57
4962 9282 4.377021 TCCTGTATTTAGGCACGCAATAG 58.623 43.478 0.00 0.00 37.76 1.73
4963 9283 4.100344 TCTCCTGTATTTAGGCACGCAATA 59.900 41.667 0.00 0.00 37.76 1.90
4964 9284 3.118408 TCTCCTGTATTTAGGCACGCAAT 60.118 43.478 0.00 0.00 37.76 3.56
4965 9285 2.235155 TCTCCTGTATTTAGGCACGCAA 59.765 45.455 0.00 0.00 37.76 4.85
4966 9286 1.828595 TCTCCTGTATTTAGGCACGCA 59.171 47.619 0.00 0.00 37.76 5.24
4967 9287 2.596904 TCTCCTGTATTTAGGCACGC 57.403 50.000 0.00 0.00 37.76 5.34
4968 9288 5.844004 ACTATTCTCCTGTATTTAGGCACG 58.156 41.667 0.00 0.00 37.76 5.34
4969 9289 8.368668 ACATACTATTCTCCTGTATTTAGGCAC 58.631 37.037 0.00 0.00 37.76 5.01
4970 9290 8.492415 ACATACTATTCTCCTGTATTTAGGCA 57.508 34.615 0.00 0.00 37.76 4.75
4971 9291 9.425577 GAACATACTATTCTCCTGTATTTAGGC 57.574 37.037 0.00 0.00 37.76 3.93
5021 9341 9.631452 CTATTATCGAATGAGATTACTTGAGCA 57.369 33.333 0.00 0.00 32.39 4.26
5022 9342 9.632807 ACTATTATCGAATGAGATTACTTGAGC 57.367 33.333 0.00 0.00 32.39 4.26
5024 9344 9.914131 CCACTATTATCGAATGAGATTACTTGA 57.086 33.333 0.00 0.00 32.39 3.02
5025 9345 9.914131 TCCACTATTATCGAATGAGATTACTTG 57.086 33.333 0.00 0.00 32.39 3.16
5027 9347 9.303116 ACTCCACTATTATCGAATGAGATTACT 57.697 33.333 0.00 0.00 32.39 2.24
5028 9348 9.915629 AACTCCACTATTATCGAATGAGATTAC 57.084 33.333 0.00 0.00 32.39 1.89
5029 9349 9.914131 CAACTCCACTATTATCGAATGAGATTA 57.086 33.333 0.00 0.00 32.39 1.75
5030 9350 8.642432 TCAACTCCACTATTATCGAATGAGATT 58.358 33.333 0.00 0.00 32.39 2.40
5031 9351 8.085296 GTCAACTCCACTATTATCGAATGAGAT 58.915 37.037 0.00 0.00 34.79 2.75
5032 9352 7.426410 GTCAACTCCACTATTATCGAATGAGA 58.574 38.462 0.00 0.00 0.00 3.27
5033 9353 6.642950 GGTCAACTCCACTATTATCGAATGAG 59.357 42.308 0.00 0.00 0.00 2.90
5034 9354 6.462487 GGGTCAACTCCACTATTATCGAATGA 60.462 42.308 0.00 0.00 0.00 2.57
5035 9355 5.696724 GGGTCAACTCCACTATTATCGAATG 59.303 44.000 0.00 0.00 0.00 2.67
5036 9356 5.509163 CGGGTCAACTCCACTATTATCGAAT 60.509 44.000 0.00 0.00 0.00 3.34
5037 9357 4.202080 CGGGTCAACTCCACTATTATCGAA 60.202 45.833 0.00 0.00 0.00 3.71
5038 9358 3.317149 CGGGTCAACTCCACTATTATCGA 59.683 47.826 0.00 0.00 0.00 3.59
5039 9359 3.317149 TCGGGTCAACTCCACTATTATCG 59.683 47.826 0.00 0.00 0.00 2.92
5040 9360 4.931661 TCGGGTCAACTCCACTATTATC 57.068 45.455 0.00 0.00 0.00 1.75
5041 9361 5.888982 AATCGGGTCAACTCCACTATTAT 57.111 39.130 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.