Multiple sequence alignment - TraesCS3B01G504000

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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 TraesCS3B01G504000 chr3B 100.000 5720 0 0 1 5720 748450799 748456518 0.000000e+00 10563
1 TraesCS3B01G504000 chr3B 94.892 3113 141 13 242 3345 748411437 748414540 0.000000e+00 4852
2 TraesCS3B01G504000 chr3B 81.004 2511 370 63 2311 4769 748614575 748617030 0.000000e+00 1895
3 TraesCS3B01G504000 chr3B 79.925 2386 386 59 2421 4769 747834479 747836808 0.000000e+00 1666
4 TraesCS3B01G504000 chr3B 79.883 2386 389 59 2421 4770 747822003 747824333 0.000000e+00 1663
5 TraesCS3B01G504000 chr3B 79.874 2385 389 59 2421 4769 747851006 747853335 0.000000e+00 1661
6 TraesCS3B01G504000 chr3B 84.108 1441 212 15 3339 4769 748414604 748416037 0.000000e+00 1376
7 TraesCS3B01G504000 chr3B 90.491 326 25 4 4777 5100 748617009 748617330 5.300000e-115 425
8 TraesCS3B01G504000 chr3B 74.474 1046 225 25 275 1297 747832436 747833462 1.150000e-111 414
9 TraesCS3B01G504000 chr3B 74.403 1047 224 26 275 1297 747848963 747849989 5.330000e-110 409
10 TraesCS3B01G504000 chr3B 99.015 203 2 0 5518 5720 726480327 726480125 1.170000e-96 364
11 TraesCS3B01G504000 chr3B 96.891 193 5 1 1 193 748411246 748411437 7.150000e-84 322
12 TraesCS3B01G504000 chr3B 83.276 293 43 3 1 288 748611493 748611784 1.220000e-66 265
13 TraesCS3B01G504000 chr3A 94.828 4776 196 17 1 4765 697274570 697279305 0.000000e+00 7404
14 TraesCS3B01G504000 chr3A 81.415 2502 369 58 2311 4769 697373524 697375972 0.000000e+00 1956
15 TraesCS3B01G504000 chr3A 80.856 2382 377 54 2428 4769 697261216 697263558 0.000000e+00 1799
16 TraesCS3B01G504000 chr3A 93.182 396 11 3 4814 5193 697279306 697279701 8.320000e-158 568
17 TraesCS3B01G504000 chr3A 91.104 326 25 3 4777 5100 697375951 697376274 6.800000e-119 438
18 TraesCS3B01G504000 chr3A 91.824 318 19 3 5203 5518 697280129 697280441 2.450000e-118 436
19 TraesCS3B01G504000 chr3A 98.537 205 2 1 5517 5720 670849941 670850145 1.520000e-95 361
20 TraesCS3B01G504000 chr3A 83.891 329 48 2 2 325 697370589 697370917 5.570000e-80 309
21 TraesCS3B01G504000 chr3A 87.234 188 23 1 1254 1440 697372017 697372204 4.490000e-51 213
22 TraesCS3B01G504000 chr3D 93.063 1355 90 2 3416 4769 561444124 561445475 0.000000e+00 1978
23 TraesCS3B01G504000 chr3D 80.366 2292 359 63 2421 4665 561155270 561157517 0.000000e+00 1655
24 TraesCS3B01G504000 chr3D 80.950 2126 337 46 2569 4665 561171805 561173891 0.000000e+00 1620
25 TraesCS3B01G504000 chr3D 80.435 2162 349 41 2633 4769 561375381 561377493 0.000000e+00 1581
26 TraesCS3B01G504000 chr3D 75.261 1055 216 27 268 1297 561373138 561374172 1.450000e-125 460
27 TraesCS3B01G504000 chr3D 91.104 326 25 3 4777 5100 561445454 561445777 6.800000e-119 438
28 TraesCS3B01G504000 chr3D 86.932 176 17 3 5342 5515 561445854 561446025 5.850000e-45 193
29 TraesCS3B01G504000 chr3D 98.333 60 1 0 1 60 561437370 561437429 7.840000e-19 106
30 TraesCS3B01G504000 chr6D 77.862 1057 191 27 860 1892 120648720 120649757 2.930000e-172 616
31 TraesCS3B01G504000 chr6D 76.701 485 86 17 2211 2673 120650000 120650479 1.590000e-60 244
32 TraesCS3B01G504000 chr6B 75.910 1071 211 31 869 1922 212628987 212627947 6.610000e-139 505
33 TraesCS3B01G504000 chr6B 98.529 204 3 0 5517 5720 527576875 527577078 1.520000e-95 361
34 TraesCS3B01G504000 chr6B 75.992 504 88 19 2211 2692 212627681 212627189 4.460000e-56 230
35 TraesCS3B01G504000 chrUn 74.665 1046 222 29 275 1297 354097505 354096480 1.910000e-114 424
36 TraesCS3B01G504000 chrUn 74.474 1046 225 25 275 1297 354040161 354041187 1.150000e-111 414
37 TraesCS3B01G504000 chrUn 98.529 204 3 0 5517 5720 449434577 449434374 1.520000e-95 361
38 TraesCS3B01G504000 chrUn 77.064 545 110 11 755 1297 354241824 354242355 3.350000e-77 300
39 TraesCS3B01G504000 chr5B 98.113 212 3 1 5510 5720 646248220 646248009 9.050000e-98 368
40 TraesCS3B01G504000 chr4B 99.020 204 2 0 5517 5720 661203957 661204160 3.260000e-97 366
41 TraesCS3B01G504000 chr4A 99.015 203 2 0 5518 5720 602731296 602731498 1.170000e-96 364
42 TraesCS3B01G504000 chr7B 98.522 203 3 0 5518 5720 744908612 744908410 5.450000e-95 359
43 TraesCS3B01G504000 chr5A 97.596 208 4 1 5513 5720 341950736 341950530 7.050000e-94 355


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 TraesCS3B01G504000 chr3B 748450799 748456518 5719 False 10563.000000 10563 100.000000 1 5720 1 chr3B.!!$F2 5719
1 TraesCS3B01G504000 chr3B 748411246 748416037 4791 False 2183.333333 4852 91.963667 1 4769 3 chr3B.!!$F5 4768
2 TraesCS3B01G504000 chr3B 747822003 747824333 2330 False 1663.000000 1663 79.883000 2421 4770 1 chr3B.!!$F1 2349
3 TraesCS3B01G504000 chr3B 747832436 747836808 4372 False 1040.000000 1666 77.199500 275 4769 2 chr3B.!!$F3 4494
4 TraesCS3B01G504000 chr3B 747848963 747853335 4372 False 1035.000000 1661 77.138500 275 4769 2 chr3B.!!$F4 4494
5 TraesCS3B01G504000 chr3B 748611493 748617330 5837 False 861.666667 1895 84.923667 1 5100 3 chr3B.!!$F6 5099
6 TraesCS3B01G504000 chr3A 697274570 697280441 5871 False 2802.666667 7404 93.278000 1 5518 3 chr3A.!!$F3 5517
7 TraesCS3B01G504000 chr3A 697261216 697263558 2342 False 1799.000000 1799 80.856000 2428 4769 1 chr3A.!!$F2 2341
8 TraesCS3B01G504000 chr3A 697370589 697376274 5685 False 729.000000 1956 85.911000 2 5100 4 chr3A.!!$F4 5098
9 TraesCS3B01G504000 chr3D 561155270 561157517 2247 False 1655.000000 1655 80.366000 2421 4665 1 chr3D.!!$F1 2244
10 TraesCS3B01G504000 chr3D 561171805 561173891 2086 False 1620.000000 1620 80.950000 2569 4665 1 chr3D.!!$F2 2096
11 TraesCS3B01G504000 chr3D 561373138 561377493 4355 False 1020.500000 1581 77.848000 268 4769 2 chr3D.!!$F4 4501
12 TraesCS3B01G504000 chr3D 561444124 561446025 1901 False 869.666667 1978 90.366333 3416 5515 3 chr3D.!!$F5 2099
13 TraesCS3B01G504000 chr6D 120648720 120650479 1759 False 430.000000 616 77.281500 860 2673 2 chr6D.!!$F1 1813
14 TraesCS3B01G504000 chr6B 212627189 212628987 1798 True 367.500000 505 75.951000 869 2692 2 chr6B.!!$R1 1823
15 TraesCS3B01G504000 chrUn 354096480 354097505 1025 True 424.000000 424 74.665000 275 1297 1 chrUn.!!$R1 1022
16 TraesCS3B01G504000 chrUn 354040161 354041187 1026 False 414.000000 414 74.474000 275 1297 1 chrUn.!!$F1 1022
17 TraesCS3B01G504000 chrUn 354241824 354242355 531 False 300.000000 300 77.064000 755 1297 1 chrUn.!!$F2 542

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
513 677 0.390998 TCTTGATGCGACAATGCCGA 60.391 50.000 0.00 0.00 0.00 5.54 F
956 1144 3.613559 AGGGTTCTAATGGATGGGCTAT 58.386 45.455 0.00 0.00 0.00 2.97 F
1408 1643 1.482182 TGCTAGTGATACACAGCCCAG 59.518 52.381 16.72 4.61 37.55 4.45 F
1917 2638 2.548480 GCAGGTGGTGTAAACAAGAGAC 59.452 50.000 0.00 0.00 0.00 3.36 F
3421 4585 0.179070 TAGTGCGTCACTGGTTGCAA 60.179 50.000 18.70 0.00 45.01 4.08 F
4498 5686 0.464036 TCAGACTCAAACAGGCACGT 59.536 50.000 0.00 0.00 28.45 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 1643 0.392998 ATCACCACAATCACCGGAGC 60.393 55.000 9.46 0.0 0.00 4.70 R
1917 2638 3.124128 GCTCATGTGGCATGTGTATATCG 59.876 47.826 8.68 0.0 0.00 2.92 R
3035 4122 1.211949 CGGCCATAGAAAAGAAGGGGA 59.788 52.381 2.24 0.0 0.00 4.81 R
3855 5039 0.033504 TCGAGTCCACAAACTCAGGC 59.966 55.000 5.04 0.0 44.88 4.85 R
4679 5867 0.108138 CTCGACGGCCTCCAAGATTT 60.108 55.000 0.00 0.0 0.00 2.17 R
5566 7209 0.036388 AGCGTGGATCGGATTGTTGT 60.036 50.000 0.00 0.0 40.26 3.32 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
207 212 6.951971 AGACTGCAGATTACCTTGTTTATCT 58.048 36.000 23.35 4.19 0.00 1.98
244 251 6.584185 TCATCAAGTTGTACTGCACTAGTA 57.416 37.500 2.11 0.00 40.89 1.82
409 570 3.257375 TCGTTCCTAGAAAGCTAGCACAA 59.743 43.478 18.83 0.00 42.29 3.33
513 677 0.390998 TCTTGATGCGACAATGCCGA 60.391 50.000 0.00 0.00 0.00 5.54
652 816 6.622833 TGTAATTCATGTGATAGTGCATGG 57.377 37.500 0.00 0.00 41.83 3.66
729 894 8.798859 ATTGATTCATGTCTGCTTAACTAAGT 57.201 30.769 0.00 0.00 35.75 2.24
956 1144 3.613559 AGGGTTCTAATGGATGGGCTAT 58.386 45.455 0.00 0.00 0.00 2.97
1099 1287 6.791887 TTTTTGTTCTTTGTGTTTGCATCA 57.208 29.167 0.00 0.00 0.00 3.07
1392 1627 4.122046 CTCAAATGGTGATGACGATGCTA 58.878 43.478 0.00 0.00 35.07 3.49
1408 1643 1.482182 TGCTAGTGATACACAGCCCAG 59.518 52.381 16.72 4.61 37.55 4.45
1420 1655 2.825836 GCCCAGCTCCGGTGATTG 60.826 66.667 7.92 4.67 32.22 2.67
1677 1929 9.877222 TGTAAGAGTTAATATAGGATGTGAGGA 57.123 33.333 0.00 0.00 0.00 3.71
1771 2023 4.858935 TGTTGTGTTGCTTGCTTCTAATC 58.141 39.130 0.00 0.00 0.00 1.75
1917 2638 2.548480 GCAGGTGGTGTAAACAAGAGAC 59.452 50.000 0.00 0.00 0.00 3.36
2030 2751 2.673368 GTGTAAAATCGGACTGAGCAGG 59.327 50.000 2.20 0.00 0.00 4.85
2336 3349 9.765795 GAAGATTAACATATACCTGTTAGCTGT 57.234 33.333 0.00 0.00 41.32 4.40
2663 3722 8.107399 TCCTGTAGATACATACATTTACCTCG 57.893 38.462 0.00 0.00 35.21 4.63
2684 3743 3.488678 CGTCATCCATCGATCTGTCTTTG 59.511 47.826 0.00 0.00 0.00 2.77
2814 3879 5.876357 TGCACCTTTAGTTTATTCCAGTCT 58.124 37.500 0.00 0.00 0.00 3.24
2818 3892 7.278203 GCACCTTTAGTTTATTCCAGTCTAGAC 59.722 40.741 15.41 15.41 0.00 2.59
2873 3951 3.362295 CGTAAAATGATGTGCATTCGGG 58.638 45.455 0.00 0.00 46.25 5.14
3055 4145 1.211949 TCCCCTTCTTTTCTATGGCCG 59.788 52.381 0.00 0.00 0.00 6.13
3080 4170 7.518848 CGCATATGTGTTTCTATGCAGTTGTAT 60.519 37.037 8.16 0.00 46.79 2.29
3216 4308 4.934602 CAGAGAAGGACAAGAAGATCAACC 59.065 45.833 0.00 0.00 0.00 3.77
3225 4317 6.539103 GGACAAGAAGATCAACCCATTAGTAC 59.461 42.308 0.00 0.00 0.00 2.73
3248 4340 6.633856 ACATATGGGCTTTTCTGAAAATGAC 58.366 36.000 15.30 11.49 0.00 3.06
3280 4372 6.524734 TGGCTATTACAAGATGTGGTATGAG 58.475 40.000 0.00 0.00 0.00 2.90
3337 4429 3.118665 CCATTGGAAAAGGCACCTTATGG 60.119 47.826 11.83 11.83 34.84 2.74
3350 4514 8.219660 AGGCACCTTATGGTATATATTTCTGT 57.780 34.615 0.00 0.00 46.60 3.41
3374 4538 7.284489 TGTGTAAATTTTCCTAGGTATGGATGC 59.716 37.037 9.08 0.00 33.09 3.91
3421 4585 0.179070 TAGTGCGTCACTGGTTGCAA 60.179 50.000 18.70 0.00 45.01 4.08
3504 4678 9.080915 GGAAAATGCTTGATCTCTTTGATTTAC 57.919 33.333 0.00 0.00 35.14 2.01
3571 4748 7.609097 ATGAATAGATGCTCTGACTCCTTTA 57.391 36.000 0.00 0.00 0.00 1.85
3855 5039 5.181009 TCAAGTTCTCTGTATGGCATTCAG 58.819 41.667 23.49 23.49 0.00 3.02
3966 5150 1.349026 CTTCCTCTGCCTCCAAAGACA 59.651 52.381 0.00 0.00 0.00 3.41
4148 5335 7.458409 AAGATATCATCAAACAGTGCAAAGT 57.542 32.000 5.32 0.00 0.00 2.66
4179 5366 6.837312 TCTTGTCTGGATAGGAAAGAACAAA 58.163 36.000 0.00 0.00 0.00 2.83
4398 5585 1.488393 GGAGGAGAGGTAGCTTTGCAT 59.512 52.381 6.74 0.00 0.00 3.96
4407 5594 2.024414 GTAGCTTTGCATAGGTTGGGG 58.976 52.381 14.05 0.00 0.00 4.96
4447 5634 7.012327 CAGTGGTTTCTGTTGAGATAGACAAAA 59.988 37.037 0.00 0.00 0.00 2.44
4498 5686 0.464036 TCAGACTCAAACAGGCACGT 59.536 50.000 0.00 0.00 28.45 4.49
4669 5857 5.147162 GCAAGGAATCTGTTTTGTTCTACG 58.853 41.667 0.00 0.00 0.00 3.51
4679 5867 4.141756 TGTTTTGTTCTACGAGTACCCCAA 60.142 41.667 0.00 0.00 0.00 4.12
4696 5884 0.447801 CAAAATCTTGGAGGCCGTCG 59.552 55.000 0.00 0.00 0.00 5.12
4773 5961 8.520119 TTTAATGCTTTATATCTAGGAGGGGT 57.480 34.615 0.00 0.00 0.00 4.95
4774 5962 8.520119 TTAATGCTTTATATCTAGGAGGGGTT 57.480 34.615 0.00 0.00 0.00 4.11
4775 5963 7.408013 AATGCTTTATATCTAGGAGGGGTTT 57.592 36.000 0.00 0.00 0.00 3.27
4776 5964 8.520119 AATGCTTTATATCTAGGAGGGGTTTA 57.480 34.615 0.00 0.00 0.00 2.01
4777 5965 8.701643 ATGCTTTATATCTAGGAGGGGTTTAT 57.298 34.615 0.00 0.00 0.00 1.40
4778 5966 8.520119 TGCTTTATATCTAGGAGGGGTTTATT 57.480 34.615 0.00 0.00 0.00 1.40
4779 5967 8.955794 TGCTTTATATCTAGGAGGGGTTTATTT 58.044 33.333 0.00 0.00 0.00 1.40
4785 5973 6.841781 TCTAGGAGGGGTTTATTTAATGCT 57.158 37.500 0.00 0.00 0.00 3.79
4786 5974 7.220890 TCTAGGAGGGGTTTATTTAATGCTT 57.779 36.000 0.00 0.00 0.00 3.91
4787 5975 7.648770 TCTAGGAGGGGTTTATTTAATGCTTT 58.351 34.615 0.00 0.00 0.00 3.51
4788 5976 8.783903 TCTAGGAGGGGTTTATTTAATGCTTTA 58.216 33.333 0.00 0.00 0.00 1.85
4789 5977 9.588096 CTAGGAGGGGTTTATTTAATGCTTTAT 57.412 33.333 0.00 0.00 0.00 1.40
4791 5979 9.363401 AGGAGGGGTTTATTTAATGCTTTATAC 57.637 33.333 0.00 0.00 0.00 1.47
4792 5980 8.582437 GGAGGGGTTTATTTAATGCTTTATACC 58.418 37.037 0.00 0.00 0.00 2.73
4793 5981 9.363401 GAGGGGTTTATTTAATGCTTTATACCT 57.637 33.333 0.00 0.00 0.00 3.08
4802 5990 9.965902 ATTTAATGCTTTATACCTAGGAGGATG 57.034 33.333 17.98 2.01 37.67 3.51
4803 5991 8.506196 TTAATGCTTTATACCTAGGAGGATGT 57.494 34.615 17.98 0.00 37.67 3.06
4804 5992 9.610104 TTAATGCTTTATACCTAGGAGGATGTA 57.390 33.333 17.98 0.00 37.67 2.29
4805 5993 7.726033 ATGCTTTATACCTAGGAGGATGTAG 57.274 40.000 17.98 8.37 37.67 2.74
4806 5994 5.480772 TGCTTTATACCTAGGAGGATGTAGC 59.519 44.000 17.98 16.40 37.67 3.58
4811 5999 3.847081 ACCTAGGAGGATGTAGCCTTAC 58.153 50.000 17.98 0.00 37.67 2.34
4812 6000 2.820787 CCTAGGAGGATGTAGCCTTACG 59.179 54.545 1.05 0.00 37.67 3.18
4837 6025 7.097047 CGTGTGTTTAAACATTGAGTTGATGTC 60.097 37.037 23.11 6.99 41.19 3.06
5015 6210 7.690952 ACATTTAGTTTTACGCATTCCCTTA 57.309 32.000 0.00 0.00 0.00 2.69
5108 6312 7.859377 CCAACAGAATTTGTACATATGAGCATC 59.141 37.037 10.38 3.10 39.73 3.91
5137 6341 1.614903 CTGGTTGCTCCAAATTCTGCA 59.385 47.619 3.15 0.00 46.59 4.41
5141 6345 2.420628 TGCTCCAAATTCTGCAAACG 57.579 45.000 0.00 0.00 32.12 3.60
5185 6389 2.879103 TCACTCAGATTTGTTCCCCC 57.121 50.000 0.00 0.00 0.00 5.40
5193 6397 2.171003 GATTTGTTCCCCCAGAGTTGG 58.829 52.381 0.00 0.00 44.60 3.77
5196 6400 0.184933 TGTTCCCCCAGAGTTGGTTG 59.815 55.000 0.00 0.00 43.40 3.77
5197 6401 0.185175 GTTCCCCCAGAGTTGGTTGT 59.815 55.000 0.00 0.00 43.40 3.32
5198 6402 0.930726 TTCCCCCAGAGTTGGTTGTT 59.069 50.000 0.00 0.00 43.40 2.83
5199 6403 0.476771 TCCCCCAGAGTTGGTTGTTC 59.523 55.000 0.00 0.00 43.40 3.18
5200 6404 0.184933 CCCCCAGAGTTGGTTGTTCA 59.815 55.000 0.00 0.00 43.40 3.18
5201 6405 1.203050 CCCCCAGAGTTGGTTGTTCAT 60.203 52.381 0.00 0.00 43.40 2.57
5212 6834 5.643777 AGTTGGTTGTTCATATACTCACTGC 59.356 40.000 0.00 0.00 0.00 4.40
5303 6925 9.545105 TTTGATTTATTTGCAAACATGTCTCTT 57.455 25.926 15.41 0.00 0.00 2.85
5345 6985 5.107133 GCGTAGAGGTAGCAGAATAAACAA 58.893 41.667 0.00 0.00 0.00 2.83
5426 7069 4.201753 CGGAGTTTCTGTTGCTGACATATG 60.202 45.833 0.00 0.00 37.69 1.78
5430 7073 5.641209 AGTTTCTGTTGCTGACATATGTCTC 59.359 40.000 30.67 23.06 44.99 3.36
5446 7089 1.335496 GTCTCGGAGACTACATCCAGC 59.665 57.143 26.79 0.50 41.88 4.85
5454 7097 1.257750 ACTACATCCAGCGGCAGTCA 61.258 55.000 1.45 0.00 0.00 3.41
5477 7120 3.689649 AGGATTTAAGACGCGCAAATTCT 59.310 39.130 5.73 6.67 0.00 2.40
5518 7161 8.506437 CACTGTAATGTTCTGCATTTTCTCTTA 58.494 33.333 0.00 0.00 44.82 2.10
5519 7162 8.507249 ACTGTAATGTTCTGCATTTTCTCTTAC 58.493 33.333 0.00 0.00 44.82 2.34
5520 7163 7.816640 TGTAATGTTCTGCATTTTCTCTTACC 58.183 34.615 0.00 0.00 44.82 2.85
5521 7164 5.551760 ATGTTCTGCATTTTCTCTTACCG 57.448 39.130 0.00 0.00 33.14 4.02
5522 7165 4.637276 TGTTCTGCATTTTCTCTTACCGA 58.363 39.130 0.00 0.00 0.00 4.69
5523 7166 5.060506 TGTTCTGCATTTTCTCTTACCGAA 58.939 37.500 0.00 0.00 0.00 4.30
5524 7167 5.529430 TGTTCTGCATTTTCTCTTACCGAAA 59.471 36.000 0.00 0.00 0.00 3.46
5525 7168 6.206634 TGTTCTGCATTTTCTCTTACCGAAAT 59.793 34.615 0.00 0.00 31.17 2.17
5526 7169 7.389330 TGTTCTGCATTTTCTCTTACCGAAATA 59.611 33.333 0.00 0.00 31.17 1.40
5527 7170 7.539712 TCTGCATTTTCTCTTACCGAAATAG 57.460 36.000 0.00 0.00 31.17 1.73
5528 7171 6.538742 TCTGCATTTTCTCTTACCGAAATAGG 59.461 38.462 0.00 0.00 31.17 2.57
5529 7172 5.065988 TGCATTTTCTCTTACCGAAATAGGC 59.934 40.000 0.00 0.00 31.17 3.93
5530 7173 5.297029 GCATTTTCTCTTACCGAAATAGGCT 59.703 40.000 0.00 0.00 31.17 4.58
5531 7174 6.183360 GCATTTTCTCTTACCGAAATAGGCTT 60.183 38.462 0.00 0.00 31.17 4.35
5532 7175 7.012044 GCATTTTCTCTTACCGAAATAGGCTTA 59.988 37.037 0.00 0.00 31.17 3.09
5533 7176 7.838771 TTTTCTCTTACCGAAATAGGCTTAC 57.161 36.000 0.00 0.00 31.17 2.34
5534 7177 5.179045 TCTCTTACCGAAATAGGCTTACG 57.821 43.478 0.00 0.00 33.69 3.18
5535 7178 3.709987 TCTTACCGAAATAGGCTTACGC 58.290 45.455 0.00 0.00 33.69 4.42
5546 7189 3.527434 GCTTACGCCCCGCTATATT 57.473 52.632 0.00 0.00 0.00 1.28
5547 7190 1.076332 GCTTACGCCCCGCTATATTG 58.924 55.000 0.00 0.00 0.00 1.90
5548 7191 1.337447 GCTTACGCCCCGCTATATTGA 60.337 52.381 0.00 0.00 0.00 2.57
5549 7192 2.677037 GCTTACGCCCCGCTATATTGAT 60.677 50.000 0.00 0.00 0.00 2.57
5550 7193 3.429822 GCTTACGCCCCGCTATATTGATA 60.430 47.826 0.00 0.00 0.00 2.15
5551 7194 4.739735 GCTTACGCCCCGCTATATTGATAT 60.740 45.833 0.00 0.00 0.00 1.63
5552 7195 5.508489 GCTTACGCCCCGCTATATTGATATA 60.508 44.000 0.00 0.00 0.00 0.86
5553 7196 4.585955 ACGCCCCGCTATATTGATATAG 57.414 45.455 11.86 11.86 43.16 1.31
5564 7207 5.755409 ATATTGATATAGCAACCACCCGA 57.245 39.130 5.38 0.00 0.00 5.14
5565 7208 3.916359 TTGATATAGCAACCACCCGAA 57.084 42.857 0.00 0.00 0.00 4.30
5566 7209 3.916359 TGATATAGCAACCACCCGAAA 57.084 42.857 0.00 0.00 0.00 3.46
5567 7210 3.537580 TGATATAGCAACCACCCGAAAC 58.462 45.455 0.00 0.00 0.00 2.78
5568 7211 3.055021 TGATATAGCAACCACCCGAAACA 60.055 43.478 0.00 0.00 0.00 2.83
5569 7212 2.279935 ATAGCAACCACCCGAAACAA 57.720 45.000 0.00 0.00 0.00 2.83
5570 7213 1.310904 TAGCAACCACCCGAAACAAC 58.689 50.000 0.00 0.00 0.00 3.32
5571 7214 0.681564 AGCAACCACCCGAAACAACA 60.682 50.000 0.00 0.00 0.00 3.33
5572 7215 0.173708 GCAACCACCCGAAACAACAA 59.826 50.000 0.00 0.00 0.00 2.83
5573 7216 1.202475 GCAACCACCCGAAACAACAAT 60.202 47.619 0.00 0.00 0.00 2.71
5574 7217 2.738135 CAACCACCCGAAACAACAATC 58.262 47.619 0.00 0.00 0.00 2.67
5575 7218 1.324383 ACCACCCGAAACAACAATCC 58.676 50.000 0.00 0.00 0.00 3.01
5576 7219 0.239879 CCACCCGAAACAACAATCCG 59.760 55.000 0.00 0.00 0.00 4.18
5577 7220 1.231221 CACCCGAAACAACAATCCGA 58.769 50.000 0.00 0.00 0.00 4.55
5578 7221 1.810151 CACCCGAAACAACAATCCGAT 59.190 47.619 0.00 0.00 0.00 4.18
5579 7222 2.081462 ACCCGAAACAACAATCCGATC 58.919 47.619 0.00 0.00 0.00 3.69
5580 7223 1.400494 CCCGAAACAACAATCCGATCC 59.600 52.381 0.00 0.00 0.00 3.36
5581 7224 2.080693 CCGAAACAACAATCCGATCCA 58.919 47.619 0.00 0.00 0.00 3.41
5582 7225 2.159572 CCGAAACAACAATCCGATCCAC 60.160 50.000 0.00 0.00 0.00 4.02
5583 7226 2.473868 CGAAACAACAATCCGATCCACG 60.474 50.000 0.00 0.00 42.18 4.94
5584 7227 0.802494 AACAACAATCCGATCCACGC 59.198 50.000 0.00 0.00 41.07 5.34
5585 7228 0.036388 ACAACAATCCGATCCACGCT 60.036 50.000 0.00 0.00 41.07 5.07
5586 7229 0.652592 CAACAATCCGATCCACGCTC 59.347 55.000 0.00 0.00 41.07 5.03
5587 7230 0.806102 AACAATCCGATCCACGCTCG 60.806 55.000 0.00 0.00 41.07 5.03
5592 7235 4.812476 CGATCCACGCTCGGGCAA 62.812 66.667 8.62 0.00 38.60 4.52
5593 7236 2.435938 GATCCACGCTCGGGCAAA 60.436 61.111 8.62 0.00 38.60 3.68
5594 7237 2.746277 ATCCACGCTCGGGCAAAC 60.746 61.111 8.62 0.00 38.60 2.93
5595 7238 3.545124 ATCCACGCTCGGGCAAACA 62.545 57.895 8.62 0.00 38.60 2.83
5596 7239 3.726517 CCACGCTCGGGCAAACAG 61.727 66.667 8.62 0.00 38.60 3.16
5597 7240 4.389576 CACGCTCGGGCAAACAGC 62.390 66.667 8.62 0.00 44.65 4.40
5606 7249 3.604400 GCAAACAGCACAAGCACG 58.396 55.556 0.00 0.00 45.49 5.34
5607 7250 2.579574 GCAAACAGCACAAGCACGC 61.580 57.895 0.00 0.00 45.49 5.34
5608 7251 1.945662 CAAACAGCACAAGCACGCC 60.946 57.895 0.00 0.00 45.49 5.68
5609 7252 3.137637 AAACAGCACAAGCACGCCC 62.138 57.895 0.00 0.00 45.49 6.13
5610 7253 4.873810 ACAGCACAAGCACGCCCA 62.874 61.111 0.00 0.00 45.49 5.36
5611 7254 3.594775 CAGCACAAGCACGCCCAA 61.595 61.111 0.00 0.00 45.49 4.12
5612 7255 2.832661 AGCACAAGCACGCCCAAA 60.833 55.556 0.00 0.00 45.49 3.28
5613 7256 2.105930 GCACAAGCACGCCCAAAA 59.894 55.556 0.00 0.00 41.58 2.44
5614 7257 1.950630 GCACAAGCACGCCCAAAAG 60.951 57.895 0.00 0.00 41.58 2.27
5615 7258 1.732917 CACAAGCACGCCCAAAAGA 59.267 52.632 0.00 0.00 0.00 2.52
5616 7259 0.102120 CACAAGCACGCCCAAAAGAA 59.898 50.000 0.00 0.00 0.00 2.52
5617 7260 0.820871 ACAAGCACGCCCAAAAGAAA 59.179 45.000 0.00 0.00 0.00 2.52
5618 7261 1.412343 ACAAGCACGCCCAAAAGAAAT 59.588 42.857 0.00 0.00 0.00 2.17
5619 7262 2.625790 ACAAGCACGCCCAAAAGAAATA 59.374 40.909 0.00 0.00 0.00 1.40
5620 7263 3.068873 ACAAGCACGCCCAAAAGAAATAA 59.931 39.130 0.00 0.00 0.00 1.40
5621 7264 3.297830 AGCACGCCCAAAAGAAATAAC 57.702 42.857 0.00 0.00 0.00 1.89
5622 7265 2.625790 AGCACGCCCAAAAGAAATAACA 59.374 40.909 0.00 0.00 0.00 2.41
5623 7266 3.068873 AGCACGCCCAAAAGAAATAACAA 59.931 39.130 0.00 0.00 0.00 2.83
5624 7267 3.428534 GCACGCCCAAAAGAAATAACAAG 59.571 43.478 0.00 0.00 0.00 3.16
5625 7268 4.794655 GCACGCCCAAAAGAAATAACAAGA 60.795 41.667 0.00 0.00 0.00 3.02
5626 7269 4.917415 CACGCCCAAAAGAAATAACAAGAG 59.083 41.667 0.00 0.00 0.00 2.85
5627 7270 4.825085 ACGCCCAAAAGAAATAACAAGAGA 59.175 37.500 0.00 0.00 0.00 3.10
5628 7271 5.300792 ACGCCCAAAAGAAATAACAAGAGAA 59.699 36.000 0.00 0.00 0.00 2.87
5629 7272 6.183360 ACGCCCAAAAGAAATAACAAGAGAAA 60.183 34.615 0.00 0.00 0.00 2.52
5630 7273 6.699642 CGCCCAAAAGAAATAACAAGAGAAAA 59.300 34.615 0.00 0.00 0.00 2.29
5631 7274 7.384932 CGCCCAAAAGAAATAACAAGAGAAAAT 59.615 33.333 0.00 0.00 0.00 1.82
5632 7275 9.705290 GCCCAAAAGAAATAACAAGAGAAAATA 57.295 29.630 0.00 0.00 0.00 1.40
5645 7288 9.905171 AACAAGAGAAAATAAGAGAAGAAATGC 57.095 29.630 0.00 0.00 0.00 3.56
5646 7289 8.518702 ACAAGAGAAAATAAGAGAAGAAATGCC 58.481 33.333 0.00 0.00 0.00 4.40
5647 7290 8.517878 CAAGAGAAAATAAGAGAAGAAATGCCA 58.482 33.333 0.00 0.00 0.00 4.92
5648 7291 8.641498 AGAGAAAATAAGAGAAGAAATGCCAA 57.359 30.769 0.00 0.00 0.00 4.52
5649 7292 8.518702 AGAGAAAATAAGAGAAGAAATGCCAAC 58.481 33.333 0.00 0.00 0.00 3.77
5650 7293 8.181904 AGAAAATAAGAGAAGAAATGCCAACA 57.818 30.769 0.00 0.00 0.00 3.33
5651 7294 8.641541 AGAAAATAAGAGAAGAAATGCCAACAA 58.358 29.630 0.00 0.00 0.00 2.83
5652 7295 8.593492 AAAATAAGAGAAGAAATGCCAACAAC 57.407 30.769 0.00 0.00 0.00 3.32
5653 7296 3.904136 AGAGAAGAAATGCCAACAACG 57.096 42.857 0.00 0.00 0.00 4.10
5654 7297 2.030805 AGAGAAGAAATGCCAACAACGC 60.031 45.455 0.00 0.00 0.00 4.84
5655 7298 1.000274 AGAAGAAATGCCAACAACGCC 60.000 47.619 0.00 0.00 0.00 5.68
5656 7299 0.318614 AAGAAATGCCAACAACGCCG 60.319 50.000 0.00 0.00 0.00 6.46
5657 7300 1.732683 GAAATGCCAACAACGCCGG 60.733 57.895 0.00 0.00 0.00 6.13
5658 7301 2.136196 GAAATGCCAACAACGCCGGA 62.136 55.000 5.05 0.00 0.00 5.14
5659 7302 1.531739 AAATGCCAACAACGCCGGAT 61.532 50.000 5.05 0.00 0.00 4.18
5660 7303 1.933115 AATGCCAACAACGCCGGATC 61.933 55.000 5.05 0.00 0.00 3.36
5661 7304 4.160635 GCCAACAACGCCGGATCG 62.161 66.667 5.05 1.69 0.00 3.69
5662 7305 2.433491 CCAACAACGCCGGATCGA 60.433 61.111 5.05 0.00 0.00 3.59
5663 7306 2.736682 CCAACAACGCCGGATCGAC 61.737 63.158 5.05 0.00 0.00 4.20
5664 7307 2.807895 AACAACGCCGGATCGACG 60.808 61.111 5.05 0.00 38.88 5.12
5665 7308 3.271706 AACAACGCCGGATCGACGA 62.272 57.895 5.05 0.00 36.09 4.20
5666 7309 2.505337 CAACGCCGGATCGACGAA 60.505 61.111 5.05 0.00 36.09 3.85
5667 7310 2.089936 CAACGCCGGATCGACGAAA 61.090 57.895 5.05 0.00 36.09 3.46
5668 7311 1.804326 AACGCCGGATCGACGAAAG 60.804 57.895 5.05 0.00 36.09 2.62
5669 7312 3.617538 CGCCGGATCGACGAAAGC 61.618 66.667 5.05 1.60 34.16 3.51
5670 7313 2.202756 GCCGGATCGACGAAAGCT 60.203 61.111 5.05 0.00 35.47 3.74
5671 7314 1.065273 GCCGGATCGACGAAAGCTA 59.935 57.895 5.05 0.00 35.47 3.32
5672 7315 1.207377 GCCGGATCGACGAAAGCTAC 61.207 60.000 5.05 0.00 35.47 3.58
5673 7316 0.928908 CCGGATCGACGAAAGCTACG 60.929 60.000 0.00 10.86 35.47 3.51
5674 7317 0.928908 CGGATCGACGAAAGCTACGG 60.929 60.000 15.59 0.00 35.47 4.02
5675 7318 1.207377 GGATCGACGAAAGCTACGGC 61.207 60.000 15.59 12.37 39.06 5.68
5676 7319 0.524816 GATCGACGAAAGCTACGGCA 60.525 55.000 17.02 6.74 38.84 5.69
5677 7320 0.801067 ATCGACGAAAGCTACGGCAC 60.801 55.000 17.02 8.00 38.84 5.01
5678 7321 1.731613 CGACGAAAGCTACGGCACA 60.732 57.895 17.02 0.00 38.84 4.57
5679 7322 1.779683 GACGAAAGCTACGGCACAC 59.220 57.895 13.07 0.00 41.70 3.82
5680 7323 1.623973 GACGAAAGCTACGGCACACC 61.624 60.000 13.07 0.00 41.70 4.16
5690 7333 4.147322 GGCACACCGCGATCGTTG 62.147 66.667 17.81 13.64 43.84 4.10
5691 7334 4.794241 GCACACCGCGATCGTTGC 62.794 66.667 17.81 13.35 30.80 4.17
5701 7344 4.690719 ATCGTTGCGCCCACCGAA 62.691 61.111 4.18 0.00 39.34 4.30
5704 7347 2.746277 GTTGCGCCCACCGAAGAT 60.746 61.111 4.18 0.00 40.02 2.40
5705 7348 1.448893 GTTGCGCCCACCGAAGATA 60.449 57.895 4.18 0.00 40.02 1.98
5706 7349 1.022451 GTTGCGCCCACCGAAGATAA 61.022 55.000 4.18 0.00 40.02 1.75
5707 7350 1.022451 TTGCGCCCACCGAAGATAAC 61.022 55.000 4.18 0.00 40.02 1.89
5708 7351 2.178235 GCGCCCACCGAAGATAACC 61.178 63.158 0.00 0.00 40.02 2.85
5709 7352 1.219664 CGCCCACCGAAGATAACCA 59.780 57.895 0.00 0.00 40.02 3.67
5710 7353 1.087771 CGCCCACCGAAGATAACCAC 61.088 60.000 0.00 0.00 40.02 4.16
5711 7354 0.746923 GCCCACCGAAGATAACCACC 60.747 60.000 0.00 0.00 0.00 4.61
5712 7355 0.616371 CCCACCGAAGATAACCACCA 59.384 55.000 0.00 0.00 0.00 4.17
5713 7356 1.677820 CCCACCGAAGATAACCACCAC 60.678 57.143 0.00 0.00 0.00 4.16
5714 7357 1.355971 CACCGAAGATAACCACCACG 58.644 55.000 0.00 0.00 0.00 4.94
5715 7358 0.390735 ACCGAAGATAACCACCACGC 60.391 55.000 0.00 0.00 0.00 5.34
5716 7359 0.108329 CCGAAGATAACCACCACGCT 60.108 55.000 0.00 0.00 0.00 5.07
5717 7360 1.278238 CGAAGATAACCACCACGCTC 58.722 55.000 0.00 0.00 0.00 5.03
5718 7361 1.653151 GAAGATAACCACCACGCTCC 58.347 55.000 0.00 0.00 0.00 4.70
5719 7362 0.981183 AAGATAACCACCACGCTCCA 59.019 50.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.655372 TCCAGTGTGTCATCATGGGA 58.345 50.000 0.00 0.00 0.00 4.37
207 212 4.018490 ACTTGATGATGCTTGCACCAATA 58.982 39.130 0.00 0.00 0.00 1.90
330 338 2.509243 TGGCTATTTTATGGGAGGGGT 58.491 47.619 0.00 0.00 0.00 4.95
389 548 5.643777 TGAATTGTGCTAGCTTTCTAGGAAC 59.356 40.000 17.23 2.58 43.45 3.62
584 748 3.871594 AGCGTGAAACCAGTATAGCAATC 59.128 43.478 0.00 0.00 0.00 2.67
729 894 4.846040 TCATGATCATCACAATCACACCA 58.154 39.130 4.86 0.00 36.04 4.17
956 1144 2.443203 TAGATGGCGCTTCCCCGA 60.443 61.111 7.64 0.00 0.00 5.14
1081 1269 5.284079 ACAGATGATGCAAACACAAAGAAC 58.716 37.500 0.00 0.00 0.00 3.01
1099 1287 4.080863 ACCAAAAGCCTCGATTAGACAGAT 60.081 41.667 0.00 0.00 0.00 2.90
1392 1627 0.539051 GAGCTGGGCTGTGTATCACT 59.461 55.000 0.00 0.00 39.88 3.41
1408 1643 0.392998 ATCACCACAATCACCGGAGC 60.393 55.000 9.46 0.00 0.00 4.70
1420 1655 5.282055 TGAATCATCTACCTCATCACCAC 57.718 43.478 0.00 0.00 0.00 4.16
1677 1929 3.431766 GGCATTGGTCTAACGGTAGTCAT 60.432 47.826 7.50 0.00 0.00 3.06
1917 2638 3.124128 GCTCATGTGGCATGTGTATATCG 59.876 47.826 8.68 0.00 0.00 2.92
2030 2751 7.552459 AGCTTATACTTCTTCTGAACTCTTCC 58.448 38.462 0.00 0.00 0.00 3.46
2149 2884 5.001232 TCCTTTGATTCTACGGAAAAGTGG 58.999 41.667 0.00 0.00 34.90 4.00
2336 3349 5.640147 AGGTATTGACACCCTCATTTTTCA 58.360 37.500 0.00 0.00 39.62 2.69
2604 3654 5.200483 GTGTTCCCATCCATCCTATTTCAA 58.800 41.667 0.00 0.00 0.00 2.69
2640 3695 8.565416 TGACGAGGTAAATGTATGTATCTACAG 58.435 37.037 0.00 0.00 39.92 2.74
2663 3722 4.505922 GTCAAAGACAGATCGATGGATGAC 59.494 45.833 0.54 4.18 30.31 3.06
2814 3879 7.067421 ACCTACACTAGCAATATGAAGGTCTA 58.933 38.462 0.00 0.00 28.80 2.59
2818 3892 7.291411 ACTACCTACACTAGCAATATGAAGG 57.709 40.000 0.00 0.00 0.00 3.46
3035 4122 1.211949 CGGCCATAGAAAAGAAGGGGA 59.788 52.381 2.24 0.00 0.00 4.81
3080 4170 8.339714 CAACTAAGTGAACGTTGATAAGGAAAA 58.660 33.333 5.00 0.00 40.19 2.29
3216 4308 6.998074 TCAGAAAAGCCCATATGTACTAATGG 59.002 38.462 16.06 16.06 42.02 3.16
3225 4317 5.745294 CGTCATTTTCAGAAAAGCCCATATG 59.255 40.000 13.71 5.79 33.22 1.78
3248 4340 6.798476 CACATCTTGTAATAGCCATATTTGCG 59.202 38.462 0.00 0.00 33.58 4.85
3350 4514 7.502226 CAGCATCCATACCTAGGAAAATTTACA 59.498 37.037 17.98 0.00 38.93 2.41
3374 4538 6.420306 CGAATCAACCAATACAGAGAGATCAG 59.580 42.308 0.00 0.00 0.00 2.90
3504 4678 5.633830 ATTGCAGTGTCCTTACATCAAAG 57.366 39.130 0.00 0.00 38.08 2.77
3571 4748 8.964772 CATCAATCTTATTTTCTTTGTCCCTCT 58.035 33.333 0.00 0.00 0.00 3.69
3855 5039 0.033504 TCGAGTCCACAAACTCAGGC 59.966 55.000 5.04 0.00 44.88 4.85
3966 5150 2.158755 CCGAGGGAATGCCTCAAGTATT 60.159 50.000 20.67 0.00 34.28 1.89
4148 5335 6.867519 TTCCTATCCAGACAAGATTGTACA 57.132 37.500 0.00 0.00 42.43 2.90
4179 5366 1.076192 AGGCTCCAATGCAGCAACT 59.924 52.632 0.00 0.00 38.77 3.16
4236 5423 0.616395 TGATGGCGAGTCCCCTTGTA 60.616 55.000 0.00 0.00 0.00 2.41
4398 5585 2.126882 CTCATGTGGATCCCCAACCTA 58.873 52.381 9.90 0.00 45.59 3.08
4447 5634 5.351405 ACCCCTGAAAATCCTCTTACTAGT 58.649 41.667 0.00 0.00 0.00 2.57
4498 5686 6.370433 TTTCACGTCATCAAACTCAATCAA 57.630 33.333 0.00 0.00 0.00 2.57
4679 5867 0.108138 CTCGACGGCCTCCAAGATTT 60.108 55.000 0.00 0.00 0.00 2.17
4696 5884 1.068885 CATCCTCGACATAGCGTCCTC 60.069 57.143 0.00 0.00 42.07 3.71
4701 5889 1.401670 GGCTACATCCTCGACATAGCG 60.402 57.143 0.00 0.00 39.33 4.26
4708 5896 5.773176 TGTAATGATTAGGCTACATCCTCGA 59.227 40.000 0.00 0.00 37.66 4.04
4776 5964 9.965902 CATCCTCCTAGGTATAAAGCATTAAAT 57.034 33.333 9.08 0.00 36.53 1.40
4777 5965 8.945193 ACATCCTCCTAGGTATAAAGCATTAAA 58.055 33.333 9.08 0.00 36.53 1.52
4778 5966 8.506196 ACATCCTCCTAGGTATAAAGCATTAA 57.494 34.615 9.08 0.00 36.53 1.40
4779 5967 9.256228 CTACATCCTCCTAGGTATAAAGCATTA 57.744 37.037 9.08 0.00 36.53 1.90
4780 5968 7.310734 GCTACATCCTCCTAGGTATAAAGCATT 60.311 40.741 9.08 0.00 36.53 3.56
4781 5969 6.155393 GCTACATCCTCCTAGGTATAAAGCAT 59.845 42.308 9.08 0.00 36.53 3.79
4782 5970 5.480772 GCTACATCCTCCTAGGTATAAAGCA 59.519 44.000 9.08 0.00 36.53 3.91
4783 5971 5.105269 GGCTACATCCTCCTAGGTATAAAGC 60.105 48.000 9.08 10.11 36.53 3.51
4784 5972 6.257586 AGGCTACATCCTCCTAGGTATAAAG 58.742 44.000 9.08 0.00 36.53 1.85
4785 5973 6.228977 AGGCTACATCCTCCTAGGTATAAA 57.771 41.667 9.08 0.00 36.53 1.40
4786 5974 5.880279 AGGCTACATCCTCCTAGGTATAA 57.120 43.478 9.08 0.00 36.53 0.98
4787 5975 5.880279 AAGGCTACATCCTCCTAGGTATA 57.120 43.478 9.08 0.00 36.53 1.47
4788 5976 4.768807 AAGGCTACATCCTCCTAGGTAT 57.231 45.455 9.08 0.00 36.53 2.73
4789 5977 4.506271 CGTAAGGCTACATCCTCCTAGGTA 60.506 50.000 9.08 0.00 36.53 3.08
4790 5978 3.751245 CGTAAGGCTACATCCTCCTAGGT 60.751 52.174 9.08 0.00 36.53 3.08
4791 5979 2.820787 CGTAAGGCTACATCCTCCTAGG 59.179 54.545 0.82 0.82 34.82 3.02
4792 5980 3.253677 CACGTAAGGCTACATCCTCCTAG 59.746 52.174 0.00 0.00 46.39 3.02
4793 5981 3.220110 CACGTAAGGCTACATCCTCCTA 58.780 50.000 0.00 0.00 46.39 2.94
4794 5982 2.032620 CACGTAAGGCTACATCCTCCT 58.967 52.381 0.00 0.00 46.39 3.69
4795 5983 1.755380 ACACGTAAGGCTACATCCTCC 59.245 52.381 0.00 0.00 46.39 4.30
4796 5984 2.165845 ACACACGTAAGGCTACATCCTC 59.834 50.000 0.00 0.00 46.39 3.71
4797 5985 2.176889 ACACACGTAAGGCTACATCCT 58.823 47.619 0.00 0.00 46.39 3.24
4798 5986 2.667473 ACACACGTAAGGCTACATCC 57.333 50.000 0.00 0.00 46.39 3.51
4799 5987 6.073657 TGTTTAAACACACGTAAGGCTACATC 60.074 38.462 17.01 0.00 36.09 3.06
4800 5988 5.759273 TGTTTAAACACACGTAAGGCTACAT 59.241 36.000 17.01 0.00 36.09 2.29
4801 5989 5.114780 TGTTTAAACACACGTAAGGCTACA 58.885 37.500 17.01 0.00 36.09 2.74
4802 5990 5.655893 TGTTTAAACACACGTAAGGCTAC 57.344 39.130 17.01 0.00 36.09 3.58
4803 5991 6.482641 TCAATGTTTAAACACACGTAAGGCTA 59.517 34.615 22.78 0.00 42.51 3.93
4804 5992 5.297278 TCAATGTTTAAACACACGTAAGGCT 59.703 36.000 22.78 0.63 42.51 4.58
4805 5993 5.512473 TCAATGTTTAAACACACGTAAGGC 58.488 37.500 22.78 0.00 42.51 4.35
4806 5994 6.721321 ACTCAATGTTTAAACACACGTAAGG 58.279 36.000 22.78 10.23 42.51 2.69
4811 5999 6.690957 ACATCAACTCAATGTTTAAACACACG 59.309 34.615 22.78 13.81 42.51 4.49
4812 6000 7.097047 CGACATCAACTCAATGTTTAAACACAC 60.097 37.037 22.78 0.00 42.51 3.82
4837 6025 6.151144 ACATTTCTCTCAAATAAAACCCCTCG 59.849 38.462 0.00 0.00 0.00 4.63
5185 6389 7.063898 CAGTGAGTATATGAACAACCAACTCTG 59.936 40.741 0.00 0.00 34.41 3.35
5193 6397 6.968131 TGAAGCAGTGAGTATATGAACAAC 57.032 37.500 0.00 0.00 0.00 3.32
5196 6400 7.928706 ACCTAATGAAGCAGTGAGTATATGAAC 59.071 37.037 0.00 0.00 0.00 3.18
5197 6401 8.023021 ACCTAATGAAGCAGTGAGTATATGAA 57.977 34.615 0.00 0.00 0.00 2.57
5198 6402 7.287696 TGACCTAATGAAGCAGTGAGTATATGA 59.712 37.037 0.00 0.00 0.00 2.15
5199 6403 7.436933 TGACCTAATGAAGCAGTGAGTATATG 58.563 38.462 0.00 0.00 0.00 1.78
5200 6404 7.507277 TCTGACCTAATGAAGCAGTGAGTATAT 59.493 37.037 0.00 0.00 0.00 0.86
5201 6405 6.833933 TCTGACCTAATGAAGCAGTGAGTATA 59.166 38.462 0.00 0.00 0.00 1.47
5212 6834 3.937706 CACAAGCCTCTGACCTAATGAAG 59.062 47.826 0.00 0.00 0.00 3.02
5316 6938 2.159421 TCTGCTACCTCTACGCGAAAAG 60.159 50.000 15.93 7.38 0.00 2.27
5317 6939 1.814394 TCTGCTACCTCTACGCGAAAA 59.186 47.619 15.93 0.00 0.00 2.29
5318 6940 1.456296 TCTGCTACCTCTACGCGAAA 58.544 50.000 15.93 0.00 0.00 3.46
5319 6941 1.456296 TTCTGCTACCTCTACGCGAA 58.544 50.000 15.93 0.00 0.00 4.70
5320 6942 1.676746 ATTCTGCTACCTCTACGCGA 58.323 50.000 15.93 0.00 0.00 5.87
5345 6985 7.201461 GCGTATGCAGAAATGATGAAAACAATT 60.201 33.333 0.89 0.00 42.15 2.32
5426 7069 1.335496 GCTGGATGTAGTCTCCGAGAC 59.665 57.143 19.26 19.26 45.38 3.36
5430 7073 1.360551 CCGCTGGATGTAGTCTCCG 59.639 63.158 0.00 0.00 35.41 4.63
5446 7089 2.348666 CGTCTTAAATCCTTGACTGCCG 59.651 50.000 0.00 0.00 0.00 5.69
5454 7097 4.156008 AGAATTTGCGCGTCTTAAATCCTT 59.844 37.500 8.43 0.00 0.00 3.36
5477 7120 2.551270 ACAGTGGAGATAGGAAAGCCA 58.449 47.619 0.00 0.00 36.29 4.75
5529 7172 2.736144 TCAATATAGCGGGGCGTAAG 57.264 50.000 0.00 0.00 43.44 2.34
5530 7173 6.080648 CTATATCAATATAGCGGGGCGTAA 57.919 41.667 4.53 0.00 36.77 3.18
5531 7174 5.700722 CTATATCAATATAGCGGGGCGTA 57.299 43.478 4.53 0.00 36.77 4.42
5532 7175 4.585955 CTATATCAATATAGCGGGGCGT 57.414 45.455 4.53 0.00 36.77 5.68
5540 7183 6.873997 TCGGGTGGTTGCTATATCAATATAG 58.126 40.000 11.20 11.20 43.16 1.31
5541 7184 6.860790 TCGGGTGGTTGCTATATCAATATA 57.139 37.500 0.00 0.00 0.00 0.86
5542 7185 5.755409 TCGGGTGGTTGCTATATCAATAT 57.245 39.130 0.00 0.00 0.00 1.28
5543 7186 5.554437 TTCGGGTGGTTGCTATATCAATA 57.446 39.130 0.00 0.00 0.00 1.90
5544 7187 4.431416 TTCGGGTGGTTGCTATATCAAT 57.569 40.909 0.00 0.00 0.00 2.57
5545 7188 3.916359 TTCGGGTGGTTGCTATATCAA 57.084 42.857 0.00 0.00 0.00 2.57
5546 7189 3.055021 TGTTTCGGGTGGTTGCTATATCA 60.055 43.478 0.00 0.00 0.00 2.15
5547 7190 3.537580 TGTTTCGGGTGGTTGCTATATC 58.462 45.455 0.00 0.00 0.00 1.63
5548 7191 3.637911 TGTTTCGGGTGGTTGCTATAT 57.362 42.857 0.00 0.00 0.00 0.86
5549 7192 3.075884 GTTGTTTCGGGTGGTTGCTATA 58.924 45.455 0.00 0.00 0.00 1.31
5550 7193 1.883926 GTTGTTTCGGGTGGTTGCTAT 59.116 47.619 0.00 0.00 0.00 2.97
5551 7194 1.310904 GTTGTTTCGGGTGGTTGCTA 58.689 50.000 0.00 0.00 0.00 3.49
5552 7195 0.681564 TGTTGTTTCGGGTGGTTGCT 60.682 50.000 0.00 0.00 0.00 3.91
5553 7196 0.173708 TTGTTGTTTCGGGTGGTTGC 59.826 50.000 0.00 0.00 0.00 4.17
5554 7197 2.544903 GGATTGTTGTTTCGGGTGGTTG 60.545 50.000 0.00 0.00 0.00 3.77
5555 7198 1.684450 GGATTGTTGTTTCGGGTGGTT 59.316 47.619 0.00 0.00 0.00 3.67
5556 7199 1.324383 GGATTGTTGTTTCGGGTGGT 58.676 50.000 0.00 0.00 0.00 4.16
5557 7200 0.239879 CGGATTGTTGTTTCGGGTGG 59.760 55.000 0.00 0.00 0.00 4.61
5558 7201 1.231221 TCGGATTGTTGTTTCGGGTG 58.769 50.000 0.00 0.00 0.00 4.61
5559 7202 2.081462 GATCGGATTGTTGTTTCGGGT 58.919 47.619 0.00 0.00 0.00 5.28
5560 7203 1.400494 GGATCGGATTGTTGTTTCGGG 59.600 52.381 0.00 0.00 0.00 5.14
5561 7204 2.080693 TGGATCGGATTGTTGTTTCGG 58.919 47.619 0.00 0.00 0.00 4.30
5562 7205 2.473868 CGTGGATCGGATTGTTGTTTCG 60.474 50.000 0.00 0.00 35.71 3.46
5563 7206 2.727916 GCGTGGATCGGATTGTTGTTTC 60.728 50.000 0.00 0.00 40.26 2.78
5564 7207 1.199097 GCGTGGATCGGATTGTTGTTT 59.801 47.619 0.00 0.00 40.26 2.83
5565 7208 0.802494 GCGTGGATCGGATTGTTGTT 59.198 50.000 0.00 0.00 40.26 2.83
5566 7209 0.036388 AGCGTGGATCGGATTGTTGT 60.036 50.000 0.00 0.00 40.26 3.32
5567 7210 0.652592 GAGCGTGGATCGGATTGTTG 59.347 55.000 0.00 0.00 40.26 3.33
5568 7211 0.806102 CGAGCGTGGATCGGATTGTT 60.806 55.000 0.00 0.00 37.82 2.83
5569 7212 1.226974 CGAGCGTGGATCGGATTGT 60.227 57.895 0.00 0.00 37.82 2.71
5570 7213 3.617824 CGAGCGTGGATCGGATTG 58.382 61.111 0.00 0.00 37.82 2.67
5575 7218 4.812476 TTGCCCGAGCGTGGATCG 62.812 66.667 0.00 0.00 44.31 3.69
5576 7219 2.435938 TTTGCCCGAGCGTGGATC 60.436 61.111 0.00 0.00 44.31 3.36
5577 7220 2.746277 GTTTGCCCGAGCGTGGAT 60.746 61.111 0.00 0.00 44.31 3.41
5578 7221 4.243008 TGTTTGCCCGAGCGTGGA 62.243 61.111 0.00 0.00 44.31 4.02
5579 7222 3.726517 CTGTTTGCCCGAGCGTGG 61.727 66.667 0.00 0.00 44.31 4.94
5580 7223 4.389576 GCTGTTTGCCCGAGCGTG 62.390 66.667 0.00 0.00 44.31 5.34
5581 7224 4.927782 TGCTGTTTGCCCGAGCGT 62.928 61.111 0.00 0.00 44.31 5.07
5582 7225 4.389576 GTGCTGTTTGCCCGAGCG 62.390 66.667 0.00 0.00 44.31 5.03
5583 7226 2.737932 CTTGTGCTGTTTGCCCGAGC 62.738 60.000 0.00 0.00 42.00 5.03
5584 7227 1.283793 CTTGTGCTGTTTGCCCGAG 59.716 57.895 0.00 0.00 42.00 4.63
5585 7228 2.844451 GCTTGTGCTGTTTGCCCGA 61.844 57.895 0.00 0.00 42.00 5.14
5586 7229 2.355009 GCTTGTGCTGTTTGCCCG 60.355 61.111 0.00 0.00 42.00 6.13
5587 7230 1.592400 GTGCTTGTGCTGTTTGCCC 60.592 57.895 0.00 0.00 42.00 5.36
5588 7231 1.945662 CGTGCTTGTGCTGTTTGCC 60.946 57.895 0.00 0.00 42.00 4.52
5589 7232 2.579574 GCGTGCTTGTGCTGTTTGC 61.580 57.895 0.00 0.00 40.48 3.68
5590 7233 1.945662 GGCGTGCTTGTGCTGTTTG 60.946 57.895 0.00 0.00 40.48 2.93
5591 7234 2.412937 GGCGTGCTTGTGCTGTTT 59.587 55.556 0.00 0.00 40.48 2.83
5592 7235 3.595758 GGGCGTGCTTGTGCTGTT 61.596 61.111 0.00 0.00 40.48 3.16
5593 7236 4.873810 TGGGCGTGCTTGTGCTGT 62.874 61.111 0.00 0.00 40.48 4.40
5594 7237 2.625973 TTTTGGGCGTGCTTGTGCTG 62.626 55.000 0.00 0.00 40.48 4.41
5595 7238 2.354074 CTTTTGGGCGTGCTTGTGCT 62.354 55.000 0.00 0.00 40.48 4.40
5596 7239 1.950630 CTTTTGGGCGTGCTTGTGC 60.951 57.895 0.00 0.00 40.20 4.57
5597 7240 0.102120 TTCTTTTGGGCGTGCTTGTG 59.898 50.000 0.00 0.00 0.00 3.33
5598 7241 0.820871 TTTCTTTTGGGCGTGCTTGT 59.179 45.000 0.00 0.00 0.00 3.16
5599 7242 2.153366 ATTTCTTTTGGGCGTGCTTG 57.847 45.000 0.00 0.00 0.00 4.01
5600 7243 3.068873 TGTTATTTCTTTTGGGCGTGCTT 59.931 39.130 0.00 0.00 0.00 3.91
5601 7244 2.625790 TGTTATTTCTTTTGGGCGTGCT 59.374 40.909 0.00 0.00 0.00 4.40
5602 7245 3.019933 TGTTATTTCTTTTGGGCGTGC 57.980 42.857 0.00 0.00 0.00 5.34
5603 7246 4.865776 TCTTGTTATTTCTTTTGGGCGTG 58.134 39.130 0.00 0.00 0.00 5.34
5604 7247 4.825085 TCTCTTGTTATTTCTTTTGGGCGT 59.175 37.500 0.00 0.00 0.00 5.68
5605 7248 5.371115 TCTCTTGTTATTTCTTTTGGGCG 57.629 39.130 0.00 0.00 0.00 6.13
5606 7249 8.607441 ATTTTCTCTTGTTATTTCTTTTGGGC 57.393 30.769 0.00 0.00 0.00 5.36
5619 7262 9.905171 GCATTTCTTCTCTTATTTTCTCTTGTT 57.095 29.630 0.00 0.00 0.00 2.83
5620 7263 8.518702 GGCATTTCTTCTCTTATTTTCTCTTGT 58.481 33.333 0.00 0.00 0.00 3.16
5621 7264 8.517878 TGGCATTTCTTCTCTTATTTTCTCTTG 58.482 33.333 0.00 0.00 0.00 3.02
5622 7265 8.641498 TGGCATTTCTTCTCTTATTTTCTCTT 57.359 30.769 0.00 0.00 0.00 2.85
5623 7266 8.518702 GTTGGCATTTCTTCTCTTATTTTCTCT 58.481 33.333 0.00 0.00 0.00 3.10
5624 7267 8.299570 TGTTGGCATTTCTTCTCTTATTTTCTC 58.700 33.333 0.00 0.00 0.00 2.87
5625 7268 8.181904 TGTTGGCATTTCTTCTCTTATTTTCT 57.818 30.769 0.00 0.00 0.00 2.52
5626 7269 8.703336 GTTGTTGGCATTTCTTCTCTTATTTTC 58.297 33.333 0.00 0.00 0.00 2.29
5627 7270 7.382218 CGTTGTTGGCATTTCTTCTCTTATTTT 59.618 33.333 0.00 0.00 0.00 1.82
5628 7271 6.863126 CGTTGTTGGCATTTCTTCTCTTATTT 59.137 34.615 0.00 0.00 0.00 1.40
5629 7272 6.381801 CGTTGTTGGCATTTCTTCTCTTATT 58.618 36.000 0.00 0.00 0.00 1.40
5630 7273 5.619981 GCGTTGTTGGCATTTCTTCTCTTAT 60.620 40.000 0.00 0.00 0.00 1.73
5631 7274 4.320202 GCGTTGTTGGCATTTCTTCTCTTA 60.320 41.667 0.00 0.00 0.00 2.10
5632 7275 3.550842 GCGTTGTTGGCATTTCTTCTCTT 60.551 43.478 0.00 0.00 0.00 2.85
5633 7276 2.030805 GCGTTGTTGGCATTTCTTCTCT 60.031 45.455 0.00 0.00 0.00 3.10
5634 7277 2.319472 GCGTTGTTGGCATTTCTTCTC 58.681 47.619 0.00 0.00 0.00 2.87
5635 7278 1.000274 GGCGTTGTTGGCATTTCTTCT 60.000 47.619 0.00 0.00 0.00 2.85
5636 7279 1.418373 GGCGTTGTTGGCATTTCTTC 58.582 50.000 0.00 0.00 0.00 2.87
5637 7280 0.318614 CGGCGTTGTTGGCATTTCTT 60.319 50.000 0.00 0.00 0.00 2.52
5638 7281 1.285641 CGGCGTTGTTGGCATTTCT 59.714 52.632 0.00 0.00 0.00 2.52
5639 7282 1.732683 CCGGCGTTGTTGGCATTTC 60.733 57.895 6.01 0.00 0.00 2.17
5640 7283 1.531739 ATCCGGCGTTGTTGGCATTT 61.532 50.000 6.01 0.00 0.00 2.32
5641 7284 1.933115 GATCCGGCGTTGTTGGCATT 61.933 55.000 6.01 0.00 0.00 3.56
5642 7285 2.361104 ATCCGGCGTTGTTGGCAT 60.361 55.556 6.01 0.00 0.00 4.40
5643 7286 3.053291 GATCCGGCGTTGTTGGCA 61.053 61.111 6.01 0.00 0.00 4.92
5644 7287 4.160635 CGATCCGGCGTTGTTGGC 62.161 66.667 6.01 0.00 0.00 4.52
5645 7288 2.433491 TCGATCCGGCGTTGTTGG 60.433 61.111 6.01 0.00 0.00 3.77
5646 7289 2.776072 GTCGATCCGGCGTTGTTG 59.224 61.111 6.01 0.00 0.00 3.33
5653 7296 1.065273 TAGCTTTCGTCGATCCGGC 59.935 57.895 0.00 0.00 0.00 6.13
5654 7297 0.928908 CGTAGCTTTCGTCGATCCGG 60.929 60.000 0.00 0.00 0.00 5.14
5655 7298 0.928908 CCGTAGCTTTCGTCGATCCG 60.929 60.000 0.00 0.00 0.00 4.18
5656 7299 1.207377 GCCGTAGCTTTCGTCGATCC 61.207 60.000 0.00 0.00 35.50 3.36
5657 7300 0.524816 TGCCGTAGCTTTCGTCGATC 60.525 55.000 0.00 0.00 40.80 3.69
5658 7301 0.801067 GTGCCGTAGCTTTCGTCGAT 60.801 55.000 0.00 0.00 40.80 3.59
5659 7302 1.443194 GTGCCGTAGCTTTCGTCGA 60.443 57.895 0.00 0.00 40.80 4.20
5660 7303 1.731613 TGTGCCGTAGCTTTCGTCG 60.732 57.895 0.00 0.00 40.80 5.12
5661 7304 1.623973 GGTGTGCCGTAGCTTTCGTC 61.624 60.000 0.00 0.00 40.80 4.20
5662 7305 1.666872 GGTGTGCCGTAGCTTTCGT 60.667 57.895 0.00 0.00 40.80 3.85
5663 7306 3.165498 GGTGTGCCGTAGCTTTCG 58.835 61.111 0.00 0.00 40.80 3.46
5684 7327 4.690719 TTCGGTGGGCGCAACGAT 62.691 61.111 39.05 0.00 44.22 3.73
5687 7330 1.022451 TTATCTTCGGTGGGCGCAAC 61.022 55.000 10.83 9.11 0.00 4.17
5688 7331 1.022451 GTTATCTTCGGTGGGCGCAA 61.022 55.000 10.83 0.00 0.00 4.85
5689 7332 1.448893 GTTATCTTCGGTGGGCGCA 60.449 57.895 10.83 0.00 0.00 6.09
5690 7333 2.178235 GGTTATCTTCGGTGGGCGC 61.178 63.158 0.00 0.00 0.00 6.53
5691 7334 1.087771 GTGGTTATCTTCGGTGGGCG 61.088 60.000 0.00 0.00 0.00 6.13
5692 7335 0.746923 GGTGGTTATCTTCGGTGGGC 60.747 60.000 0.00 0.00 0.00 5.36
5693 7336 0.616371 TGGTGGTTATCTTCGGTGGG 59.384 55.000 0.00 0.00 0.00 4.61
5694 7337 1.734163 GTGGTGGTTATCTTCGGTGG 58.266 55.000 0.00 0.00 0.00 4.61
5695 7338 1.355971 CGTGGTGGTTATCTTCGGTG 58.644 55.000 0.00 0.00 0.00 4.94
5696 7339 0.390735 GCGTGGTGGTTATCTTCGGT 60.391 55.000 0.00 0.00 0.00 4.69
5697 7340 0.108329 AGCGTGGTGGTTATCTTCGG 60.108 55.000 0.00 0.00 0.00 4.30
5698 7341 1.278238 GAGCGTGGTGGTTATCTTCG 58.722 55.000 0.00 0.00 0.00 3.79
5699 7342 1.066430 TGGAGCGTGGTGGTTATCTTC 60.066 52.381 0.00 0.00 0.00 2.87
5700 7343 0.981183 TGGAGCGTGGTGGTTATCTT 59.019 50.000 0.00 0.00 0.00 2.40
5701 7344 2.678786 TGGAGCGTGGTGGTTATCT 58.321 52.632 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.