Multiple sequence alignment - TraesCS6B01G361000

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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 TraesCS6B01G361000 chr6B 100.000 4093 0 0 1 4093 632847768 632851860 0.000000e+00 7559.0
1 TraesCS6B01G361000 chr6B 97.384 344 8 1 3655 3998 632876867 632877209 5.900000e-163 584.0
2 TraesCS6B01G361000 chr6B 78.384 458 70 22 3655 4093 67417933 67417486 1.880000e-68 270.0
3 TraesCS6B01G361000 chr6D 93.621 2618 115 21 828 3410 419837155 419839755 0.000000e+00 3862.0
4 TraesCS6B01G361000 chr6D 86.757 740 61 16 45 780 419773748 419774454 0.000000e+00 789.0
5 TraesCS6B01G361000 chr6D 100.000 33 0 0 1579 1611 419837956 419837988 1.230000e-05 62.1
6 TraesCS6B01G361000 chr6A 93.856 1481 61 13 1613 3089 562930752 562932206 0.000000e+00 2204.0
7 TraesCS6B01G361000 chr6A 91.310 794 39 7 845 1612 562929996 562930785 0.000000e+00 1057.0
8 TraesCS6B01G361000 chr6A 80.102 784 91 33 48 780 562929138 562929907 1.300000e-144 523.0
9 TraesCS6B01G361000 chr6A 86.018 329 32 7 3327 3654 562933000 562933315 1.410000e-89 340.0
10 TraesCS6B01G361000 chr6A 82.081 173 20 9 3688 3855 88598644 88598478 1.980000e-28 137.0
11 TraesCS6B01G361000 chr6A 92.982 57 4 0 3264 3320 562932672 562932728 2.620000e-12 84.2
12 TraesCS6B01G361000 chr2B 90.000 440 41 3 3655 4093 438433353 438432916 2.140000e-157 566.0
13 TraesCS6B01G361000 chr2B 91.765 340 26 2 3655 3994 438428292 438427955 4.790000e-129 472.0
14 TraesCS6B01G361000 chr2B 93.023 215 14 1 3655 3869 477004469 477004682 3.070000e-81 313.0
15 TraesCS6B01G361000 chr2B 94.059 202 12 0 3654 3855 477003628 477003829 1.430000e-79 307.0
16 TraesCS6B01G361000 chr5B 83.848 421 56 12 3678 4093 106787206 106786793 1.380000e-104 390.0
17 TraesCS6B01G361000 chr5B 87.597 258 25 5 3841 4093 112539608 112539863 4.000000e-75 292.0
18 TraesCS6B01G361000 chr5B 80.909 330 45 15 3676 3995 112552646 112552967 1.140000e-60 244.0
19 TraesCS6B01G361000 chr2A 79.156 403 60 21 3699 4088 492388850 492388459 1.460000e-64 257.0
20 TraesCS6B01G361000 chr2A 89.773 88 9 0 4001 4088 87666590 87666503 3.340000e-21 113.0
21 TraesCS6B01G361000 chr5A 74.118 425 86 22 3676 4087 23806781 23807194 1.970000e-33 154.0
22 TraesCS6B01G361000 chr1A 78.070 228 40 7 3650 3869 482835359 482835584 7.140000e-28 135.0
23 TraesCS6B01G361000 chr7D 86.777 121 14 2 3974 4093 556185588 556185707 2.570000e-27 134.0
24 TraesCS6B01G361000 chr4B 85.484 62 5 3 3997 4057 193997011 193997069 1.230000e-05 62.1


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 TraesCS6B01G361000 chr6B 632847768 632851860 4092 False 7559.00 7559 100.0000 1 4093 1 chr6B.!!$F1 4092
1 TraesCS6B01G361000 chr6D 419837155 419839755 2600 False 1962.05 3862 96.8105 828 3410 2 chr6D.!!$F2 2582
2 TraesCS6B01G361000 chr6D 419773748 419774454 706 False 789.00 789 86.7570 45 780 1 chr6D.!!$F1 735
3 TraesCS6B01G361000 chr6A 562929138 562933315 4177 False 841.64 2204 88.8536 48 3654 5 chr6A.!!$F1 3606
4 TraesCS6B01G361000 chr2B 477003628 477004682 1054 False 310.00 313 93.5410 3654 3869 2 chr2B.!!$F1 215


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
622 652 0.032615 AGCACCACCTTCACCCAAAA 60.033 50.0 0.0 0.0 0.00 2.44 F
1494 1664 0.102300 TGCGATATGACGACAGTGGG 59.898 55.0 0.0 0.0 35.09 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2559 2740 0.173708 GACCTGACTGATCGGTGGTC 59.826 60.0 22.00 22.00 36.14 4.02 R
3098 3282 0.041839 GGCTAATGCGCAACATCGAG 60.042 55.0 17.11 6.69 38.34 4.04 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
34 35 7.552050 TCATTAAAAAGATGAATGGGGTTGT 57.448 32.000 0.00 0.00 32.52 3.32
35 36 7.385267 TCATTAAAAAGATGAATGGGGTTGTG 58.615 34.615 0.00 0.00 32.52 3.33
36 37 4.622260 AAAAAGATGAATGGGGTTGTGG 57.378 40.909 0.00 0.00 0.00 4.17
37 38 2.236489 AAGATGAATGGGGTTGTGGG 57.764 50.000 0.00 0.00 0.00 4.61
38 39 0.336048 AGATGAATGGGGTTGTGGGG 59.664 55.000 0.00 0.00 0.00 4.96
39 40 0.334676 GATGAATGGGGTTGTGGGGA 59.665 55.000 0.00 0.00 0.00 4.81
40 41 1.018031 ATGAATGGGGTTGTGGGGAT 58.982 50.000 0.00 0.00 0.00 3.85
41 42 1.687492 TGAATGGGGTTGTGGGGATA 58.313 50.000 0.00 0.00 0.00 2.59
42 43 2.003830 TGAATGGGGTTGTGGGGATAA 58.996 47.619 0.00 0.00 0.00 1.75
43 44 2.383683 TGAATGGGGTTGTGGGGATAAA 59.616 45.455 0.00 0.00 0.00 1.40
44 45 2.846665 ATGGGGTTGTGGGGATAAAG 57.153 50.000 0.00 0.00 0.00 1.85
45 46 1.761711 TGGGGTTGTGGGGATAAAGA 58.238 50.000 0.00 0.00 0.00 2.52
46 47 2.074579 TGGGGTTGTGGGGATAAAGAA 58.925 47.619 0.00 0.00 0.00 2.52
74 75 5.324409 TCTTTGTTGCCTAATCACCATTCT 58.676 37.500 0.00 0.00 0.00 2.40
271 288 9.330063 GTGAATAATATCTTCATGGTCAGACAA 57.670 33.333 2.17 0.00 35.26 3.18
347 364 1.680860 GGCCAATTTAGCTACCACGGT 60.681 52.381 0.00 0.00 0.00 4.83
363 380 6.091718 ACCACGGTAGCAAAATAAATGTTT 57.908 33.333 0.00 0.00 0.00 2.83
385 403 0.247185 TCATGACTGCAGCATCGACA 59.753 50.000 15.27 5.27 0.00 4.35
423 441 5.879777 TCATACGTGATGGATGAACAACAAT 59.120 36.000 0.00 0.00 36.08 2.71
484 502 7.588143 TTTTACAACAAACATGTTCAAGTGG 57.412 32.000 12.39 10.97 32.27 4.00
571 590 7.171848 GGTGTTCCAAAAACTTAACAAACAACT 59.828 33.333 0.00 0.00 33.92 3.16
602 621 9.950680 CGGAGCACATATTTTATTTTCTTACAT 57.049 29.630 0.00 0.00 0.00 2.29
618 648 0.328258 ACATAGCACCACCTTCACCC 59.672 55.000 0.00 0.00 0.00 4.61
622 652 0.032615 AGCACCACCTTCACCCAAAA 60.033 50.000 0.00 0.00 0.00 2.44
639 686 9.784531 TCACCCAAAATTATAAGAATGCAAAAA 57.215 25.926 0.00 0.00 0.00 1.94
712 793 8.411991 TTTTTAGGGGTTATTGTTTACTCAGG 57.588 34.615 0.00 0.00 0.00 3.86
713 794 6.707273 TTAGGGGTTATTGTTTACTCAGGT 57.293 37.500 0.00 0.00 0.00 4.00
714 795 4.918588 AGGGGTTATTGTTTACTCAGGTG 58.081 43.478 0.00 0.00 0.00 4.00
715 796 3.442625 GGGGTTATTGTTTACTCAGGTGC 59.557 47.826 0.00 0.00 0.00 5.01
780 861 0.754217 GCCATCAGCCCATCACACAT 60.754 55.000 0.00 0.00 34.35 3.21
781 862 1.771565 CCATCAGCCCATCACACATT 58.228 50.000 0.00 0.00 0.00 2.71
782 863 2.104967 CCATCAGCCCATCACACATTT 58.895 47.619 0.00 0.00 0.00 2.32
783 864 2.100252 CCATCAGCCCATCACACATTTC 59.900 50.000 0.00 0.00 0.00 2.17
784 865 2.885135 TCAGCCCATCACACATTTCT 57.115 45.000 0.00 0.00 0.00 2.52
785 866 2.715046 TCAGCCCATCACACATTTCTC 58.285 47.619 0.00 0.00 0.00 2.87
786 867 2.040145 TCAGCCCATCACACATTTCTCA 59.960 45.455 0.00 0.00 0.00 3.27
787 868 2.821378 CAGCCCATCACACATTTCTCAA 59.179 45.455 0.00 0.00 0.00 3.02
788 869 3.256383 CAGCCCATCACACATTTCTCAAA 59.744 43.478 0.00 0.00 0.00 2.69
789 870 3.896888 AGCCCATCACACATTTCTCAAAA 59.103 39.130 0.00 0.00 0.00 2.44
790 871 4.344679 AGCCCATCACACATTTCTCAAAAA 59.655 37.500 0.00 0.00 0.00 1.94
996 1147 1.373059 GGAGATTCCCAGATCGGCC 59.627 63.158 0.00 0.00 0.00 6.13
1208 1359 0.390735 ACCATCGCCGTCAAGGTAAC 60.391 55.000 0.00 0.00 43.70 2.50
1210 1361 0.108329 CATCGCCGTCAAGGTAACCT 60.108 55.000 0.00 0.00 43.70 3.50
1215 1366 1.202615 GCCGTCAAGGTAACCTATCCC 60.203 57.143 0.00 0.00 43.70 3.85
1216 1367 2.395619 CCGTCAAGGTAACCTATCCCT 58.604 52.381 0.00 0.00 31.13 4.20
1217 1368 2.102588 CCGTCAAGGTAACCTATCCCTG 59.897 54.545 0.00 0.00 31.13 4.45
1218 1369 2.483188 CGTCAAGGTAACCTATCCCTGC 60.483 54.545 0.00 0.00 31.13 4.85
1225 1379 1.639635 AACCTATCCCTGCCTGCCTG 61.640 60.000 0.00 0.00 0.00 4.85
1236 1390 3.449227 CTGCCTGCCCGTCTCGTA 61.449 66.667 0.00 0.00 0.00 3.43
1317 1484 3.853831 TCAAGTTGATTACGCGGTAGA 57.146 42.857 12.47 0.00 0.00 2.59
1321 1488 5.062934 TCAAGTTGATTACGCGGTAGATTTG 59.937 40.000 12.47 5.66 0.00 2.32
1324 1494 2.605818 TGATTACGCGGTAGATTTGTGC 59.394 45.455 12.47 0.00 0.00 4.57
1330 1500 0.457166 CGGTAGATTTGTGCGTCGGA 60.457 55.000 0.00 0.00 0.00 4.55
1336 1506 1.541310 ATTTGTGCGTCGGAGGGAGA 61.541 55.000 0.00 0.00 0.00 3.71
1340 1510 3.760035 GCGTCGGAGGGAGAAGCA 61.760 66.667 0.00 0.00 41.52 3.91
1343 1513 1.878656 CGTCGGAGGGAGAAGCAGTT 61.879 60.000 0.00 0.00 0.00 3.16
1366 1536 1.152830 GGTCCTGGTTTTGCTGGGA 59.847 57.895 0.00 0.00 0.00 4.37
1367 1537 0.895559 GGTCCTGGTTTTGCTGGGAG 60.896 60.000 0.00 0.00 0.00 4.30
1395 1565 1.103398 GCCGCAGCACCCAGATTTAT 61.103 55.000 0.00 0.00 39.53 1.40
1409 1579 7.124147 CACCCAGATTTATGGTTAATTGGAACT 59.876 37.037 0.00 0.00 38.81 3.01
1492 1662 1.908065 TGTGCGATATGACGACAGTG 58.092 50.000 0.00 0.00 35.09 3.66
1494 1664 0.102300 TGCGATATGACGACAGTGGG 59.898 55.000 0.00 0.00 35.09 4.61
1633 1803 6.593268 ATGGTCTGATGAGATCACTAGATG 57.407 41.667 0.00 0.00 42.33 2.90
1683 1853 4.527038 TCGGTGATTCCTTCTGTCTAAAGT 59.473 41.667 0.00 0.00 0.00 2.66
1757 1927 1.212616 GATTCGGCTCACAGGATTCG 58.787 55.000 0.00 0.00 0.00 3.34
1774 1944 5.946377 AGGATTCGGAATTTGCTTTTCTACT 59.054 36.000 4.47 0.00 0.00 2.57
1780 1950 6.932400 TCGGAATTTGCTTTTCTACTGACTTA 59.068 34.615 0.00 0.00 0.00 2.24
1829 2001 4.076394 AGGCGCAAAAGGTGACTAATAAA 58.924 39.130 10.83 0.00 45.83 1.40
2038 2210 9.398170 CCATTGTTTGTCACTATAACTGAAAAG 57.602 33.333 0.00 0.00 0.00 2.27
2259 2431 7.362802 GGAATTAGTCCTATAGTCCAACTGT 57.637 40.000 0.00 0.00 43.98 3.55
2405 2585 4.501229 GGTCAATTTGCATTCACAACCTCA 60.501 41.667 0.00 0.00 0.00 3.86
2462 2642 2.544721 AGTGCAGAGAAAGGATCAGGA 58.455 47.619 0.00 0.00 0.00 3.86
2465 2645 2.235650 TGCAGAGAAAGGATCAGGAGTG 59.764 50.000 0.00 0.00 0.00 3.51
2579 2760 1.258445 ACCACCGATCAGTCAGGTCC 61.258 60.000 0.00 0.00 35.85 4.46
2642 2823 9.887629 AATTGTGTGCAATATGAATATTTTCCA 57.112 25.926 0.00 0.00 43.89 3.53
2810 2991 9.581099 CTTTTAACTTTCTAAAGCTTTTGGTGA 57.419 29.630 18.47 8.22 39.63 4.02
2840 3021 3.311596 GCGTCCGCTAGAAAATGGTTAAT 59.688 43.478 4.10 0.00 38.26 1.40
3015 3199 2.993008 AGCATCATGTCGCTGGGT 59.007 55.556 10.23 0.00 37.02 4.51
3089 3273 7.192852 TCAGGAAAAAGAAGCTCATCTAGAT 57.807 36.000 0.00 0.00 0.00 1.98
3096 3280 5.482163 AGAAGCTCATCTAGATTAAGCCC 57.518 43.478 23.90 18.41 32.82 5.19
3098 3282 2.028567 AGCTCATCTAGATTAAGCCCGC 60.029 50.000 23.90 9.21 33.43 6.13
3133 3317 1.620822 AGCCCAGATTGTTGTTCACC 58.379 50.000 0.00 0.00 0.00 4.02
3180 3621 5.568685 TTCTTCATGTTTGGTTCGAACAA 57.431 34.783 28.24 16.48 40.54 2.83
3217 3658 6.039941 GGAGAACTCATAGCATGTACTGTACT 59.960 42.308 17.98 1.53 0.00 2.73
3255 3696 7.337184 TGATCCATTTTAGCCGTGTTGTATTAA 59.663 33.333 0.00 0.00 0.00 1.40
3256 3697 7.633193 TCCATTTTAGCCGTGTTGTATTAAT 57.367 32.000 0.00 0.00 0.00 1.40
3258 3699 7.337184 TCCATTTTAGCCGTGTTGTATTAATGA 59.663 33.333 0.00 0.00 0.00 2.57
3320 3801 8.450578 TGTCCATCTTTTGTATCATTGATACC 57.549 34.615 26.38 13.77 42.81 2.73
3352 4098 1.323271 ATGATGACCAGTCGGCGACT 61.323 55.000 34.91 34.91 44.44 4.18
3405 4151 5.107337 GCGTACTGGTACCTCTTTAACAAAC 60.107 44.000 14.36 0.00 32.61 2.93
3424 4170 5.880332 ACAAACTGTATTAATCGGTGATGCT 59.120 36.000 0.00 0.00 0.00 3.79
3427 4173 4.811024 ACTGTATTAATCGGTGATGCTGTG 59.189 41.667 0.00 0.00 0.00 3.66
3493 4239 4.598062 GGCCAAATACGAGTAAGCATTTC 58.402 43.478 0.00 0.00 0.00 2.17
3495 4241 5.266242 GCCAAATACGAGTAAGCATTTCAG 58.734 41.667 0.00 0.00 0.00 3.02
3538 4285 5.469373 TCTTGTTATTCGCATGATGTCAC 57.531 39.130 0.00 0.00 0.00 3.67
3540 4287 3.872696 TGTTATTCGCATGATGTCACCT 58.127 40.909 0.00 0.00 0.00 4.00
3561 4308 7.546667 TCACCTTGTACGTTTATGGTAATCTTC 59.453 37.037 0.00 0.00 0.00 2.87
3601 4348 2.717580 TGCTTCATTCTGCTTGCTTG 57.282 45.000 0.00 0.00 0.00 4.01
3606 4353 4.795308 GCTTCATTCTGCTTGCTTGTTTCT 60.795 41.667 0.00 0.00 0.00 2.52
3608 4355 5.618056 TCATTCTGCTTGCTTGTTTCTAG 57.382 39.130 0.00 0.00 0.00 2.43
3636 4383 1.371183 CTTTCCGACTCCACAGGCA 59.629 57.895 0.00 0.00 0.00 4.75
3647 4394 4.985538 ACTCCACAGGCAAAGATAAGAAA 58.014 39.130 0.00 0.00 0.00 2.52
3648 4395 5.574188 ACTCCACAGGCAAAGATAAGAAAT 58.426 37.500 0.00 0.00 0.00 2.17
3649 4396 5.416952 ACTCCACAGGCAAAGATAAGAAATG 59.583 40.000 0.00 0.00 0.00 2.32
3650 4397 5.324409 TCCACAGGCAAAGATAAGAAATGT 58.676 37.500 0.00 0.00 0.00 2.71
3651 4398 5.183713 TCCACAGGCAAAGATAAGAAATGTG 59.816 40.000 0.00 0.00 36.23 3.21
3652 4399 5.183713 CCACAGGCAAAGATAAGAAATGTGA 59.816 40.000 0.00 0.00 38.16 3.58
3667 4414 3.680786 TGAGTGTCAGCGTCCCCG 61.681 66.667 0.00 0.00 37.07 5.73
3723 4470 4.193334 TCGCAGGACTCGCCGATG 62.193 66.667 0.00 0.00 43.43 3.84
3816 4563 1.111116 TACCCGCAGCGCCTACTTAT 61.111 55.000 10.07 0.00 0.00 1.73
3820 4567 1.825285 CGCAGCGCCTACTTATGCAG 61.825 60.000 14.68 5.07 36.70 4.41
3829 4576 0.529773 TACTTATGCAGCCTTCCGCG 60.530 55.000 0.00 0.00 44.76 6.46
3861 4608 1.211212 CATCCAGTGGATCAGAAGGCA 59.789 52.381 22.36 0.00 40.98 4.75
3862 4609 0.615331 TCCAGTGGATCAGAAGGCAC 59.385 55.000 8.12 0.00 0.00 5.01
3864 4611 0.742281 CAGTGGATCAGAAGGCACGG 60.742 60.000 0.00 0.00 0.00 4.94
3865 4612 2.109126 GTGGATCAGAAGGCACGGC 61.109 63.158 0.00 0.00 0.00 5.68
3867 4614 2.892425 GATCAGAAGGCACGGCGG 60.892 66.667 13.24 0.66 0.00 6.13
3882 4629 4.109675 CGGCACCGATCCCCCTTT 62.110 66.667 2.01 0.00 42.83 3.11
3883 4630 2.124278 GGCACCGATCCCCCTTTC 60.124 66.667 0.00 0.00 0.00 2.62
3884 4631 2.124278 GCACCGATCCCCCTTTCC 60.124 66.667 0.00 0.00 0.00 3.13
3885 4632 2.595655 CACCGATCCCCCTTTCCC 59.404 66.667 0.00 0.00 0.00 3.97
3886 4633 2.694992 ACCGATCCCCCTTTCCCC 60.695 66.667 0.00 0.00 0.00 4.81
3887 4634 2.368329 CCGATCCCCCTTTCCCCT 60.368 66.667 0.00 0.00 0.00 4.79
3888 4635 2.452937 CCGATCCCCCTTTCCCCTC 61.453 68.421 0.00 0.00 0.00 4.30
3889 4636 1.384643 CGATCCCCCTTTCCCCTCT 60.385 63.158 0.00 0.00 0.00 3.69
3890 4637 1.411651 CGATCCCCCTTTCCCCTCTC 61.412 65.000 0.00 0.00 0.00 3.20
3891 4638 1.384643 ATCCCCCTTTCCCCTCTCG 60.385 63.158 0.00 0.00 0.00 4.04
3892 4639 3.798511 CCCCCTTTCCCCTCTCGC 61.799 72.222 0.00 0.00 0.00 5.03
3893 4640 2.689034 CCCCTTTCCCCTCTCGCT 60.689 66.667 0.00 0.00 0.00 4.93
3908 4655 2.025155 CTCGCTCAAGAACCCTAGCTA 58.975 52.381 0.00 0.00 32.73 3.32
3911 4658 1.831736 GCTCAAGAACCCTAGCTACCA 59.168 52.381 0.00 0.00 32.18 3.25
3913 4660 3.118223 GCTCAAGAACCCTAGCTACCAAT 60.118 47.826 0.00 0.00 32.18 3.16
3914 4661 4.698575 CTCAAGAACCCTAGCTACCAATC 58.301 47.826 0.00 0.00 0.00 2.67
3915 4662 3.454812 TCAAGAACCCTAGCTACCAATCC 59.545 47.826 0.00 0.00 0.00 3.01
3916 4663 2.409570 AGAACCCTAGCTACCAATCCC 58.590 52.381 0.00 0.00 0.00 3.85
3917 4664 1.420514 GAACCCTAGCTACCAATCCCC 59.579 57.143 0.00 0.00 0.00 4.81
3928 4727 2.718563 ACCAATCCCCAATTCGTGTAC 58.281 47.619 0.00 0.00 0.00 2.90
3929 4728 2.307686 ACCAATCCCCAATTCGTGTACT 59.692 45.455 0.00 0.00 0.00 2.73
3931 4730 3.370527 CCAATCCCCAATTCGTGTACTCT 60.371 47.826 0.00 0.00 0.00 3.24
3932 4731 3.821421 ATCCCCAATTCGTGTACTCTC 57.179 47.619 0.00 0.00 0.00 3.20
3933 4732 2.816411 TCCCCAATTCGTGTACTCTCT 58.184 47.619 0.00 0.00 0.00 3.10
3934 4733 2.496070 TCCCCAATTCGTGTACTCTCTG 59.504 50.000 0.00 0.00 0.00 3.35
3935 4734 2.233922 CCCCAATTCGTGTACTCTCTGT 59.766 50.000 0.00 0.00 0.00 3.41
3937 4736 4.081862 CCCCAATTCGTGTACTCTCTGTAA 60.082 45.833 0.00 0.00 32.25 2.41
3940 4739 5.573282 CCAATTCGTGTACTCTCTGTAACTG 59.427 44.000 0.00 0.00 32.25 3.16
3941 4740 6.379386 CAATTCGTGTACTCTCTGTAACTGA 58.621 40.000 0.00 0.00 32.25 3.41
3946 4745 6.206048 TCGTGTACTCTCTGTAACTGATTGAA 59.794 38.462 0.00 0.00 32.25 2.69
3947 4746 6.305877 CGTGTACTCTCTGTAACTGATTGAAC 59.694 42.308 0.00 0.00 32.25 3.18
3948 4747 6.586844 GTGTACTCTCTGTAACTGATTGAACC 59.413 42.308 0.00 0.00 32.25 3.62
3949 4748 6.493802 TGTACTCTCTGTAACTGATTGAACCT 59.506 38.462 0.00 0.00 32.25 3.50
3951 4750 6.226787 ACTCTCTGTAACTGATTGAACCTTG 58.773 40.000 0.00 0.00 0.00 3.61
3952 4751 6.042093 ACTCTCTGTAACTGATTGAACCTTGA 59.958 38.462 0.00 0.00 0.00 3.02
3953 4752 7.009179 TCTCTGTAACTGATTGAACCTTGAT 57.991 36.000 0.00 0.00 0.00 2.57
3954 4753 8.134202 TCTCTGTAACTGATTGAACCTTGATA 57.866 34.615 0.00 0.00 0.00 2.15
3955 4754 8.593679 TCTCTGTAACTGATTGAACCTTGATAA 58.406 33.333 0.00 0.00 0.00 1.75
3956 4755 9.388506 CTCTGTAACTGATTGAACCTTGATAAT 57.611 33.333 0.00 0.00 0.00 1.28
3957 4756 9.383519 TCTGTAACTGATTGAACCTTGATAATC 57.616 33.333 0.00 0.00 0.00 1.75
3958 4757 8.506168 TGTAACTGATTGAACCTTGATAATCC 57.494 34.615 0.00 0.00 0.00 3.01
3959 4758 8.328758 TGTAACTGATTGAACCTTGATAATCCT 58.671 33.333 0.00 0.00 0.00 3.24
3960 4759 7.872113 AACTGATTGAACCTTGATAATCCTC 57.128 36.000 0.00 0.00 0.00 3.71
3961 4760 6.360618 ACTGATTGAACCTTGATAATCCTCC 58.639 40.000 0.00 0.00 0.00 4.30
3962 4761 6.159398 ACTGATTGAACCTTGATAATCCTCCT 59.841 38.462 0.00 0.00 0.00 3.69
3963 4762 6.973642 TGATTGAACCTTGATAATCCTCCTT 58.026 36.000 0.00 0.00 0.00 3.36
3964 4763 7.056635 TGATTGAACCTTGATAATCCTCCTTC 58.943 38.462 0.00 0.00 0.00 3.46
3965 4764 6.642733 TTGAACCTTGATAATCCTCCTTCT 57.357 37.500 0.00 0.00 0.00 2.85
3966 4765 5.994250 TGAACCTTGATAATCCTCCTTCTG 58.006 41.667 0.00 0.00 0.00 3.02
3967 4766 4.429854 ACCTTGATAATCCTCCTTCTGC 57.570 45.455 0.00 0.00 0.00 4.26
3968 4767 4.043596 ACCTTGATAATCCTCCTTCTGCT 58.956 43.478 0.00 0.00 0.00 4.24
3969 4768 5.219739 ACCTTGATAATCCTCCTTCTGCTA 58.780 41.667 0.00 0.00 0.00 3.49
3970 4769 5.848921 ACCTTGATAATCCTCCTTCTGCTAT 59.151 40.000 0.00 0.00 0.00 2.97
3971 4770 7.019388 ACCTTGATAATCCTCCTTCTGCTATA 58.981 38.462 0.00 0.00 0.00 1.31
3972 4771 7.038658 ACCTTGATAATCCTCCTTCTGCTATAC 60.039 40.741 0.00 0.00 0.00 1.47
3973 4772 7.038729 CCTTGATAATCCTCCTTCTGCTATACA 60.039 40.741 0.00 0.00 0.00 2.29
3974 4773 7.855784 TGATAATCCTCCTTCTGCTATACAA 57.144 36.000 0.00 0.00 0.00 2.41
3978 4777 3.574396 TCCTCCTTCTGCTATACAATCCG 59.426 47.826 0.00 0.00 0.00 4.18
3983 4782 4.499183 CTTCTGCTATACAATCCGATCCC 58.501 47.826 0.00 0.00 0.00 3.85
3985 4784 3.511540 TCTGCTATACAATCCGATCCCTG 59.488 47.826 0.00 0.00 0.00 4.45
3987 4786 2.234908 GCTATACAATCCGATCCCTGCT 59.765 50.000 0.00 0.00 0.00 4.24
4005 4804 3.086282 TGCTCTTACACGTGGTATCAGA 58.914 45.455 21.57 11.60 0.00 3.27
4006 4805 3.128764 TGCTCTTACACGTGGTATCAGAG 59.871 47.826 21.57 20.15 38.87 3.35
4007 4806 3.377485 GCTCTTACACGTGGTATCAGAGA 59.623 47.826 24.22 14.33 38.44 3.10
4008 4807 4.731193 GCTCTTACACGTGGTATCAGAGAC 60.731 50.000 24.22 16.07 38.44 3.36
4009 4808 3.693085 TCTTACACGTGGTATCAGAGACC 59.307 47.826 21.57 7.34 37.49 3.85
4010 4809 1.919240 ACACGTGGTATCAGAGACCA 58.081 50.000 21.57 13.23 44.86 4.02
4015 4814 2.919772 TGGTATCAGAGACCACTCCA 57.080 50.000 13.23 0.00 42.15 3.86
4016 4815 2.457598 TGGTATCAGAGACCACTCCAC 58.542 52.381 13.23 0.00 42.15 4.02
4018 4817 2.624557 GGTATCAGAGACCACTCCACCT 60.625 54.545 9.53 0.00 43.53 4.00
4019 4818 1.859302 ATCAGAGACCACTCCACCTC 58.141 55.000 0.00 0.00 43.53 3.85
4020 4819 0.251832 TCAGAGACCACTCCACCTCC 60.252 60.000 0.00 0.00 43.53 4.30
4023 4822 0.545548 GAGACCACTCCACCTCCCTT 60.546 60.000 0.00 0.00 37.19 3.95
4024 4823 0.545548 AGACCACTCCACCTCCCTTC 60.546 60.000 0.00 0.00 0.00 3.46
4025 4824 0.545548 GACCACTCCACCTCCCTTCT 60.546 60.000 0.00 0.00 0.00 2.85
4026 4825 0.104409 ACCACTCCACCTCCCTTCTT 60.104 55.000 0.00 0.00 0.00 2.52
4027 4826 0.615850 CCACTCCACCTCCCTTCTTC 59.384 60.000 0.00 0.00 0.00 2.87
4028 4827 1.650528 CACTCCACCTCCCTTCTTCT 58.349 55.000 0.00 0.00 0.00 2.85
4029 4828 1.552792 CACTCCACCTCCCTTCTTCTC 59.447 57.143 0.00 0.00 0.00 2.87
4030 4829 1.199615 CTCCACCTCCCTTCTTCTCC 58.800 60.000 0.00 0.00 0.00 3.71
4031 4830 0.614979 TCCACCTCCCTTCTTCTCCG 60.615 60.000 0.00 0.00 0.00 4.63
4032 4831 1.219393 CACCTCCCTTCTTCTCCGC 59.781 63.158 0.00 0.00 0.00 5.54
4033 4832 1.990614 ACCTCCCTTCTTCTCCGCC 60.991 63.158 0.00 0.00 0.00 6.13
4035 4834 1.219393 CTCCCTTCTTCTCCGCCAC 59.781 63.158 0.00 0.00 0.00 5.01
4036 4835 1.229209 TCCCTTCTTCTCCGCCACT 60.229 57.895 0.00 0.00 0.00 4.00
4037 4836 1.219393 CCCTTCTTCTCCGCCACTC 59.781 63.158 0.00 0.00 0.00 3.51
4038 4837 1.261238 CCCTTCTTCTCCGCCACTCT 61.261 60.000 0.00 0.00 0.00 3.24
4039 4838 0.108424 CCTTCTTCTCCGCCACTCTG 60.108 60.000 0.00 0.00 0.00 3.35
4049 4848 3.909662 CCACTCTGGCCCAAATCG 58.090 61.111 0.00 0.00 0.00 3.34
4050 4849 1.002134 CCACTCTGGCCCAAATCGT 60.002 57.895 0.00 0.00 0.00 3.73
4051 4850 1.026718 CCACTCTGGCCCAAATCGTC 61.027 60.000 0.00 0.00 0.00 4.20
4053 4852 1.218047 CTCTGGCCCAAATCGTCGA 59.782 57.895 0.00 0.00 0.00 4.20
4054 4853 0.807667 CTCTGGCCCAAATCGTCGAG 60.808 60.000 0.00 0.00 0.00 4.04
4055 4854 1.218047 CTGGCCCAAATCGTCGAGA 59.782 57.895 0.00 0.00 0.00 4.04
4056 4855 1.079405 TGGCCCAAATCGTCGAGAC 60.079 57.895 0.00 0.00 0.00 3.36
4057 4856 1.218316 GGCCCAAATCGTCGAGACT 59.782 57.895 0.00 0.00 0.00 3.24
4060 4859 0.525668 CCCAAATCGTCGAGACTCGG 60.526 60.000 23.92 9.72 40.88 4.63
4061 4860 1.140407 CCAAATCGTCGAGACTCGGC 61.140 60.000 23.92 21.73 41.75 5.54
4091 4890 4.624293 CGAGATCGCAGCTGGTAG 57.376 61.111 17.12 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.669887 CCCCATTCATCTTTTTAATGAATCAAA 57.330 29.630 8.06 0.00 46.03 2.69
5 6 8.824783 ACCCCATTCATCTTTTTAATGAATCAA 58.175 29.630 8.06 0.00 46.03 2.57
6 7 8.378115 ACCCCATTCATCTTTTTAATGAATCA 57.622 30.769 8.06 0.00 46.03 2.57
7 8 9.101655 CAACCCCATTCATCTTTTTAATGAATC 57.898 33.333 8.06 0.00 46.03 2.52
9 10 7.877097 CACAACCCCATTCATCTTTTTAATGAA 59.123 33.333 1.43 1.43 44.72 2.57
10 11 7.385267 CACAACCCCATTCATCTTTTTAATGA 58.615 34.615 0.00 0.00 33.38 2.57
11 12 6.594937 CCACAACCCCATTCATCTTTTTAATG 59.405 38.462 0.00 0.00 0.00 1.90
12 13 6.296374 CCCACAACCCCATTCATCTTTTTAAT 60.296 38.462 0.00 0.00 0.00 1.40
13 14 5.012561 CCCACAACCCCATTCATCTTTTTAA 59.987 40.000 0.00 0.00 0.00 1.52
14 15 4.530161 CCCACAACCCCATTCATCTTTTTA 59.470 41.667 0.00 0.00 0.00 1.52
15 16 3.327464 CCCACAACCCCATTCATCTTTTT 59.673 43.478 0.00 0.00 0.00 1.94
16 17 2.905736 CCCACAACCCCATTCATCTTTT 59.094 45.455 0.00 0.00 0.00 2.27
17 18 2.539302 CCCACAACCCCATTCATCTTT 58.461 47.619 0.00 0.00 0.00 2.52
18 19 1.273211 CCCCACAACCCCATTCATCTT 60.273 52.381 0.00 0.00 0.00 2.40
19 20 0.336048 CCCCACAACCCCATTCATCT 59.664 55.000 0.00 0.00 0.00 2.90
20 21 0.334676 TCCCCACAACCCCATTCATC 59.665 55.000 0.00 0.00 0.00 2.92
21 22 1.018031 ATCCCCACAACCCCATTCAT 58.982 50.000 0.00 0.00 0.00 2.57
22 23 1.687492 TATCCCCACAACCCCATTCA 58.313 50.000 0.00 0.00 0.00 2.57
23 24 2.838637 TTATCCCCACAACCCCATTC 57.161 50.000 0.00 0.00 0.00 2.67
24 25 2.657459 TCTTTATCCCCACAACCCCATT 59.343 45.455 0.00 0.00 0.00 3.16
25 26 2.293246 TCTTTATCCCCACAACCCCAT 58.707 47.619 0.00 0.00 0.00 4.00
26 27 1.761711 TCTTTATCCCCACAACCCCA 58.238 50.000 0.00 0.00 0.00 4.96
27 28 2.911552 TTCTTTATCCCCACAACCCC 57.088 50.000 0.00 0.00 0.00 4.95
28 29 7.699878 AGATATATTCTTTATCCCCACAACCC 58.300 38.462 0.00 0.00 0.00 4.11
43 44 9.289782 GGTGATTAGGCAACAAAGATATATTCT 57.710 33.333 0.00 0.00 41.41 2.40
44 45 9.066892 TGGTGATTAGGCAACAAAGATATATTC 57.933 33.333 0.00 0.00 41.41 1.75
45 46 8.995027 TGGTGATTAGGCAACAAAGATATATT 57.005 30.769 0.00 0.00 41.41 1.28
46 47 9.592196 AATGGTGATTAGGCAACAAAGATATAT 57.408 29.630 0.00 0.00 39.23 0.86
60 61 5.483685 TCCGGAATAGAATGGTGATTAGG 57.516 43.478 0.00 0.00 0.00 2.69
119 120 5.965033 TGGAAGCATTTAAGAGAGAGGAT 57.035 39.130 0.00 0.00 0.00 3.24
240 257 9.423061 TGACCATGAAGATATTATTCACATACG 57.577 33.333 0.00 0.00 39.36 3.06
363 380 2.160219 GTCGATGCTGCAGTCATGAAAA 59.840 45.455 22.74 7.44 0.00 2.29
371 389 0.742281 GGTGATGTCGATGCTGCAGT 60.742 55.000 16.64 0.00 0.00 4.40
385 403 2.497675 ACGTATGACTCAAGCTGGTGAT 59.502 45.455 0.00 0.00 0.00 3.06
510 528 6.370718 TCAGAGTGTCATGAATGTCATTTCAG 59.629 38.462 0.00 0.00 38.90 3.02
567 586 8.687824 ATAAAATATGTGCTCCGAAAAAGTTG 57.312 30.769 0.00 0.00 0.00 3.16
571 590 9.921637 AGAAAATAAAATATGTGCTCCGAAAAA 57.078 25.926 0.00 0.00 0.00 1.94
602 621 0.847373 TTTGGGTGAAGGTGGTGCTA 59.153 50.000 0.00 0.00 0.00 3.49
701 782 0.679505 AGCTCGCACCTGAGTAAACA 59.320 50.000 0.00 0.00 38.28 2.83
702 783 2.649331 TAGCTCGCACCTGAGTAAAC 57.351 50.000 0.00 0.00 38.28 2.01
703 784 3.671008 TTTAGCTCGCACCTGAGTAAA 57.329 42.857 0.00 0.00 38.28 2.01
704 785 3.006537 AGTTTTAGCTCGCACCTGAGTAA 59.993 43.478 0.00 0.00 38.28 2.24
705 786 2.561419 AGTTTTAGCTCGCACCTGAGTA 59.439 45.455 0.00 0.00 38.28 2.59
706 787 1.344763 AGTTTTAGCTCGCACCTGAGT 59.655 47.619 0.00 0.00 38.28 3.41
707 788 1.996191 GAGTTTTAGCTCGCACCTGAG 59.004 52.381 0.00 0.00 39.05 3.35
708 789 1.337823 GGAGTTTTAGCTCGCACCTGA 60.338 52.381 0.00 0.00 36.41 3.86
709 790 1.079503 GGAGTTTTAGCTCGCACCTG 58.920 55.000 0.00 0.00 36.41 4.00
710 791 0.036294 GGGAGTTTTAGCTCGCACCT 60.036 55.000 0.00 0.00 44.62 4.00
711 792 0.036294 AGGGAGTTTTAGCTCGCACC 60.036 55.000 11.95 0.00 46.71 5.01
712 793 1.079503 CAGGGAGTTTTAGCTCGCAC 58.920 55.000 11.95 0.00 46.71 5.34
713 794 0.685097 ACAGGGAGTTTTAGCTCGCA 59.315 50.000 11.95 0.00 46.71 5.10
714 795 1.360820 GACAGGGAGTTTTAGCTCGC 58.639 55.000 0.00 3.04 45.29 5.03
715 796 1.405661 GGGACAGGGAGTTTTAGCTCG 60.406 57.143 0.00 0.00 36.41 5.03
794 875 2.228822 GTCGTGTGATGGGCTGATTTTT 59.771 45.455 0.00 0.00 0.00 1.94
795 876 1.812571 GTCGTGTGATGGGCTGATTTT 59.187 47.619 0.00 0.00 0.00 1.82
796 877 1.453155 GTCGTGTGATGGGCTGATTT 58.547 50.000 0.00 0.00 0.00 2.17
797 878 0.392998 GGTCGTGTGATGGGCTGATT 60.393 55.000 0.00 0.00 0.00 2.57
798 879 1.221840 GGTCGTGTGATGGGCTGAT 59.778 57.895 0.00 0.00 0.00 2.90
799 880 2.171209 CTGGTCGTGTGATGGGCTGA 62.171 60.000 0.00 0.00 0.00 4.26
800 881 1.742880 CTGGTCGTGTGATGGGCTG 60.743 63.158 0.00 0.00 0.00 4.85
801 882 1.913262 TCTGGTCGTGTGATGGGCT 60.913 57.895 0.00 0.00 0.00 5.19
802 883 1.741770 GTCTGGTCGTGTGATGGGC 60.742 63.158 0.00 0.00 0.00 5.36
803 884 1.135083 GTAGTCTGGTCGTGTGATGGG 60.135 57.143 0.00 0.00 0.00 4.00
804 885 1.819288 AGTAGTCTGGTCGTGTGATGG 59.181 52.381 0.00 0.00 0.00 3.51
805 886 3.057526 TGAAGTAGTCTGGTCGTGTGATG 60.058 47.826 0.00 0.00 0.00 3.07
806 887 3.057456 GTGAAGTAGTCTGGTCGTGTGAT 60.057 47.826 0.00 0.00 0.00 3.06
807 888 2.292569 GTGAAGTAGTCTGGTCGTGTGA 59.707 50.000 0.00 0.00 0.00 3.58
808 889 2.293677 AGTGAAGTAGTCTGGTCGTGTG 59.706 50.000 0.00 0.00 0.00 3.82
809 890 2.584236 AGTGAAGTAGTCTGGTCGTGT 58.416 47.619 0.00 0.00 0.00 4.49
810 891 3.309388 CAAGTGAAGTAGTCTGGTCGTG 58.691 50.000 0.00 0.00 0.00 4.35
811 892 2.288273 GCAAGTGAAGTAGTCTGGTCGT 60.288 50.000 0.00 0.00 0.00 4.34
812 893 2.288213 TGCAAGTGAAGTAGTCTGGTCG 60.288 50.000 0.00 0.00 0.00 4.79
813 894 3.060602 GTGCAAGTGAAGTAGTCTGGTC 58.939 50.000 0.00 0.00 0.00 4.02
1208 1359 2.834688 CAGGCAGGCAGGGATAGG 59.165 66.667 0.00 0.00 0.00 2.57
1210 1361 3.492353 GGCAGGCAGGCAGGGATA 61.492 66.667 0.00 0.00 43.51 2.59
1225 1379 0.310232 GTATGGAGTACGAGACGGGC 59.690 60.000 0.00 0.00 0.00 6.13
1236 1390 7.040062 GCACAGTAGAATCTATCTGTATGGAGT 60.040 40.741 18.21 0.98 39.30 3.85
1317 1484 1.079127 CTCCCTCCGACGCACAAAT 60.079 57.895 0.00 0.00 0.00 2.32
1321 1488 2.182030 CTTCTCCCTCCGACGCAC 59.818 66.667 0.00 0.00 0.00 5.34
1324 1494 1.878656 AACTGCTTCTCCCTCCGACG 61.879 60.000 0.00 0.00 0.00 5.12
1330 1500 2.835156 GACCTCTAAACTGCTTCTCCCT 59.165 50.000 0.00 0.00 0.00 4.20
1336 1506 2.339769 ACCAGGACCTCTAAACTGCTT 58.660 47.619 0.00 0.00 0.00 3.91
1340 1510 3.138468 AGCAAAACCAGGACCTCTAAACT 59.862 43.478 0.00 0.00 0.00 2.66
1343 1513 2.224769 CCAGCAAAACCAGGACCTCTAA 60.225 50.000 0.00 0.00 0.00 2.10
1386 1556 7.341769 TCCAGTTCCAATTAACCATAAATCTGG 59.658 37.037 0.00 0.00 42.35 3.86
1395 1565 3.806949 AGCTCCAGTTCCAATTAACCA 57.193 42.857 0.00 0.00 0.00 3.67
1409 1579 3.429410 CGACATCATTCACACTAGCTCCA 60.429 47.826 0.00 0.00 0.00 3.86
1492 1662 8.547173 AGATATTCTAGAACCATCATTCATCCC 58.453 37.037 22.07 2.84 0.00 3.85
1494 1664 9.381033 CCAGATATTCTAGAACCATCATTCATC 57.619 37.037 22.07 9.79 0.00 2.92
1548 1718 1.665161 CGCGTCACCGACTTAAAGAGT 60.665 52.381 0.00 0.00 42.70 3.24
1683 1853 2.584835 CTGGAAGGAAACCACCATGA 57.415 50.000 0.00 0.00 33.53 3.07
1757 1927 9.914131 AAATAAGTCAGTAGAAAAGCAAATTCC 57.086 29.630 0.00 0.00 0.00 3.01
1780 1950 9.312904 CACACCCATGGGATCTTATAAATAAAT 57.687 33.333 38.07 5.59 38.96 1.40
1812 1982 8.586273 CGATGCATTTTTATTAGTCACCTTTTG 58.414 33.333 0.00 0.00 0.00 2.44
2200 2372 2.892215 TGCAAATTGTCTTGATGAGGCA 59.108 40.909 0.00 0.00 38.47 4.75
2201 2373 3.057033 ACTGCAAATTGTCTTGATGAGGC 60.057 43.478 0.00 0.00 0.00 4.70
2257 2429 5.299028 TCAAGCAAATTCTTAAGCTCACACA 59.701 36.000 0.00 0.00 36.07 3.72
2259 2431 6.579666 ATCAAGCAAATTCTTAAGCTCACA 57.420 33.333 0.00 0.00 36.07 3.58
2426 2606 4.651045 TCTGCACTATCTATCCAGAAGCAA 59.349 41.667 0.00 0.00 33.50 3.91
2462 2642 8.352942 GTTTTCCAATCAAGATTTACAGACACT 58.647 33.333 0.00 0.00 0.00 3.55
2465 2645 7.809806 CCAGTTTTCCAATCAAGATTTACAGAC 59.190 37.037 0.00 0.00 0.00 3.51
2559 2740 0.173708 GACCTGACTGATCGGTGGTC 59.826 60.000 22.00 22.00 36.14 4.02
2640 2821 0.464036 TAGTTCTACGCCCTGCATGG 59.536 55.000 3.22 3.22 0.00 3.66
2642 2823 1.683917 CTCTAGTTCTACGCCCTGCAT 59.316 52.381 0.00 0.00 0.00 3.96
2840 3021 8.154203 TCATGTCAAGTTATTTCAGGACAAGTA 58.846 33.333 0.00 0.00 38.58 2.24
2882 3065 4.201871 CCAACTTAAAGTCTTGCACGACAA 60.202 41.667 23.55 9.71 36.38 3.18
3015 3199 0.809636 CTGACACCACAACGCAGACA 60.810 55.000 0.00 0.00 0.00 3.41
3024 3208 1.832883 ACTGCAAAACTGACACCACA 58.167 45.000 0.00 0.00 0.00 4.17
3089 3273 1.366111 GCAACATCGAGCGGGCTTAA 61.366 55.000 0.00 0.00 0.00 1.85
3098 3282 0.041839 GGCTAATGCGCAACATCGAG 60.042 55.000 17.11 6.69 38.34 4.04
3148 3589 8.664669 AACCAAACATGAAGAAATAACCCTAT 57.335 30.769 0.00 0.00 0.00 2.57
3152 3593 6.674066 TCGAACCAAACATGAAGAAATAACC 58.326 36.000 0.00 0.00 0.00 2.85
3180 3621 2.826128 TGAGTTCTCCACTAGCGTGAAT 59.174 45.455 0.00 0.00 43.97 2.57
3217 3658 8.196771 GGCTAAAATGGATCATTGTTACATTGA 58.803 33.333 11.55 11.55 34.04 2.57
3255 3696 6.380079 AGAAAGAACACTCCAACCTATCAT 57.620 37.500 0.00 0.00 0.00 2.45
3256 3697 5.825593 AGAAAGAACACTCCAACCTATCA 57.174 39.130 0.00 0.00 0.00 2.15
3258 3699 7.741554 AGATAGAAAGAACACTCCAACCTAT 57.258 36.000 0.00 0.00 0.00 2.57
3260 3701 6.043243 TGAAGATAGAAAGAACACTCCAACCT 59.957 38.462 0.00 0.00 0.00 3.50
3320 3801 2.295909 GGTCATCATCGAGAGGAAGGAG 59.704 54.545 0.00 0.00 39.01 3.69
3352 4098 1.013596 CGCGGCTTACATTCCAATCA 58.986 50.000 0.00 0.00 0.00 2.57
3405 4151 5.049828 TCACAGCATCACCGATTAATACAG 58.950 41.667 0.00 0.00 0.00 2.74
3424 4170 6.054941 TGATTTCTTTACAAGAGTGCTCACA 58.945 36.000 2.63 0.00 39.03 3.58
3427 4173 7.608308 ATCTGATTTCTTTACAAGAGTGCTC 57.392 36.000 0.00 0.00 39.03 4.26
3435 4181 5.477984 AGCCAGCAATCTGATTTCTTTACAA 59.522 36.000 0.00 0.00 42.95 2.41
3509 4256 8.623903 ACATCATGCGAATAACAAGATAACAAT 58.376 29.630 0.00 0.00 0.00 2.71
3511 4258 7.279758 TGACATCATGCGAATAACAAGATAACA 59.720 33.333 0.00 0.00 0.00 2.41
3512 4259 7.584123 GTGACATCATGCGAATAACAAGATAAC 59.416 37.037 0.00 0.00 0.00 1.89
3513 4260 7.254761 GGTGACATCATGCGAATAACAAGATAA 60.255 37.037 0.00 0.00 0.00 1.75
3514 4261 6.202762 GGTGACATCATGCGAATAACAAGATA 59.797 38.462 0.00 0.00 0.00 1.98
3515 4262 5.008019 GGTGACATCATGCGAATAACAAGAT 59.992 40.000 0.00 0.00 0.00 2.40
3516 4263 4.332543 GGTGACATCATGCGAATAACAAGA 59.667 41.667 0.00 0.00 0.00 3.02
3517 4264 4.333649 AGGTGACATCATGCGAATAACAAG 59.666 41.667 0.00 0.00 0.00 3.16
3518 4265 4.260985 AGGTGACATCATGCGAATAACAA 58.739 39.130 0.00 0.00 0.00 2.83
3519 4266 3.872696 AGGTGACATCATGCGAATAACA 58.127 40.909 0.00 0.00 0.00 2.41
3520 4267 4.094887 ACAAGGTGACATCATGCGAATAAC 59.905 41.667 0.00 0.00 0.00 1.89
3527 4274 2.346803 ACGTACAAGGTGACATCATGC 58.653 47.619 0.00 0.00 0.00 4.06
3533 4280 4.339872 ACCATAAACGTACAAGGTGACA 57.660 40.909 0.00 0.00 0.00 3.58
3538 4285 7.046033 AGGAAGATTACCATAAACGTACAAGG 58.954 38.462 0.00 0.00 0.00 3.61
3540 4287 7.844009 AGAGGAAGATTACCATAAACGTACAA 58.156 34.615 0.00 0.00 0.00 2.41
3571 4318 5.412594 AGCAGAATGAAGCAAACGAAGATAA 59.587 36.000 0.00 0.00 39.69 1.75
3578 4325 1.717645 GCAAGCAGAATGAAGCAAACG 59.282 47.619 0.00 0.00 39.69 3.60
3584 4331 4.868067 AGAAACAAGCAAGCAGAATGAAG 58.132 39.130 0.00 0.00 39.69 3.02
3601 4348 4.142881 CGGAAAGCAAGGTTAGCTAGAAAC 60.143 45.833 0.00 0.00 42.53 2.78
3606 4353 2.565834 AGTCGGAAAGCAAGGTTAGCTA 59.434 45.455 0.00 0.00 42.53 3.32
3608 4355 1.732809 GAGTCGGAAAGCAAGGTTAGC 59.267 52.381 0.00 0.00 0.00 3.09
3636 4383 6.128445 CGCTGACACTCACATTTCTTATCTTT 60.128 38.462 0.00 0.00 0.00 2.52
3647 4394 1.293498 GGGACGCTGACACTCACAT 59.707 57.895 0.00 0.00 0.00 3.21
3648 4395 2.734591 GGGACGCTGACACTCACA 59.265 61.111 0.00 0.00 0.00 3.58
3649 4396 2.048127 GGGGACGCTGACACTCAC 60.048 66.667 0.00 0.00 0.00 3.51
3740 4487 4.475135 GGTTGGGCCTCCGAGCTC 62.475 72.222 4.53 2.73 40.83 4.09
3841 4588 1.211212 TGCCTTCTGATCCACTGGATG 59.789 52.381 15.78 2.24 43.27 3.51
3865 4612 4.109675 AAAGGGGGATCGGTGCCG 62.110 66.667 0.00 3.94 36.54 5.69
3867 4614 2.124278 GGAAAGGGGGATCGGTGC 60.124 66.667 0.00 0.00 0.00 5.01
3868 4615 2.595655 GGGAAAGGGGGATCGGTG 59.404 66.667 0.00 0.00 0.00 4.94
3869 4616 2.694992 GGGGAAAGGGGGATCGGT 60.695 66.667 0.00 0.00 0.00 4.69
3870 4617 2.368329 AGGGGAAAGGGGGATCGG 60.368 66.667 0.00 0.00 0.00 4.18
3871 4618 1.384643 AGAGGGGAAAGGGGGATCG 60.385 63.158 0.00 0.00 0.00 3.69
3872 4619 1.411651 CGAGAGGGGAAAGGGGGATC 61.412 65.000 0.00 0.00 0.00 3.36
3873 4620 1.384643 CGAGAGGGGAAAGGGGGAT 60.385 63.158 0.00 0.00 0.00 3.85
3874 4621 2.040606 CGAGAGGGGAAAGGGGGA 59.959 66.667 0.00 0.00 0.00 4.81
3875 4622 3.798511 GCGAGAGGGGAAAGGGGG 61.799 72.222 0.00 0.00 0.00 5.40
3876 4623 2.689034 AGCGAGAGGGGAAAGGGG 60.689 66.667 0.00 0.00 0.00 4.79
3877 4624 1.553690 TTGAGCGAGAGGGGAAAGGG 61.554 60.000 0.00 0.00 0.00 3.95
3878 4625 0.107945 CTTGAGCGAGAGGGGAAAGG 60.108 60.000 0.00 0.00 0.00 3.11
3879 4626 0.898320 TCTTGAGCGAGAGGGGAAAG 59.102 55.000 0.00 0.00 0.00 2.62
3880 4627 1.002087 GTTCTTGAGCGAGAGGGGAAA 59.998 52.381 0.00 0.00 0.00 3.13
3881 4628 0.608640 GTTCTTGAGCGAGAGGGGAA 59.391 55.000 0.00 0.00 0.00 3.97
3882 4629 1.258445 GGTTCTTGAGCGAGAGGGGA 61.258 60.000 0.00 0.00 0.00 4.81
3883 4630 1.219393 GGTTCTTGAGCGAGAGGGG 59.781 63.158 0.00 0.00 0.00 4.79
3884 4631 1.219393 GGGTTCTTGAGCGAGAGGG 59.781 63.158 0.00 0.00 0.00 4.30
3885 4632 1.407258 CTAGGGTTCTTGAGCGAGAGG 59.593 57.143 0.00 0.00 0.00 3.69
3886 4633 1.202359 GCTAGGGTTCTTGAGCGAGAG 60.202 57.143 0.00 0.00 0.00 3.20
3887 4634 0.818296 GCTAGGGTTCTTGAGCGAGA 59.182 55.000 0.00 0.00 0.00 4.04
3888 4635 0.820871 AGCTAGGGTTCTTGAGCGAG 59.179 55.000 0.00 0.00 39.96 5.03
3889 4636 1.749634 GTAGCTAGGGTTCTTGAGCGA 59.250 52.381 0.00 0.00 39.96 4.93
3890 4637 1.202428 GGTAGCTAGGGTTCTTGAGCG 60.202 57.143 0.00 0.00 39.96 5.03
3891 4638 1.831736 TGGTAGCTAGGGTTCTTGAGC 59.168 52.381 0.00 0.00 35.07 4.26
3892 4639 4.443598 GGATTGGTAGCTAGGGTTCTTGAG 60.444 50.000 0.00 0.00 0.00 3.02
3893 4640 3.454812 GGATTGGTAGCTAGGGTTCTTGA 59.545 47.826 0.00 0.00 0.00 3.02
3908 4655 2.307686 AGTACACGAATTGGGGATTGGT 59.692 45.455 0.00 0.00 37.18 3.67
3911 4658 3.775316 AGAGAGTACACGAATTGGGGATT 59.225 43.478 0.00 0.00 0.00 3.01
3913 4660 2.496070 CAGAGAGTACACGAATTGGGGA 59.504 50.000 0.00 0.00 0.00 4.81
3914 4661 2.233922 ACAGAGAGTACACGAATTGGGG 59.766 50.000 0.00 0.00 0.00 4.96
3915 4662 3.594603 ACAGAGAGTACACGAATTGGG 57.405 47.619 0.00 0.00 0.00 4.12
3916 4663 5.573282 CAGTTACAGAGAGTACACGAATTGG 59.427 44.000 0.00 0.00 30.91 3.16
3917 4664 6.379386 TCAGTTACAGAGAGTACACGAATTG 58.621 40.000 0.00 0.00 30.91 2.32
3928 4727 6.459066 TCAAGGTTCAATCAGTTACAGAGAG 58.541 40.000 0.00 0.00 0.00 3.20
3929 4728 6.419484 TCAAGGTTCAATCAGTTACAGAGA 57.581 37.500 0.00 0.00 0.00 3.10
3931 4730 9.383519 GATTATCAAGGTTCAATCAGTTACAGA 57.616 33.333 0.00 0.00 0.00 3.41
3932 4731 8.616076 GGATTATCAAGGTTCAATCAGTTACAG 58.384 37.037 0.00 0.00 0.00 2.74
3933 4732 8.328758 AGGATTATCAAGGTTCAATCAGTTACA 58.671 33.333 0.00 0.00 0.00 2.41
3934 4733 8.738645 AGGATTATCAAGGTTCAATCAGTTAC 57.261 34.615 0.00 0.00 0.00 2.50
3935 4734 7.993183 GGAGGATTATCAAGGTTCAATCAGTTA 59.007 37.037 0.00 0.00 0.00 2.24
3937 4736 6.159398 AGGAGGATTATCAAGGTTCAATCAGT 59.841 38.462 0.00 0.00 0.00 3.41
3940 4739 7.228308 CAGAAGGAGGATTATCAAGGTTCAATC 59.772 40.741 0.00 0.00 0.00 2.67
3941 4740 7.059156 CAGAAGGAGGATTATCAAGGTTCAAT 58.941 38.462 0.00 0.00 0.00 2.57
3946 4745 4.043596 AGCAGAAGGAGGATTATCAAGGT 58.956 43.478 0.00 0.00 0.00 3.50
3947 4746 4.703379 AGCAGAAGGAGGATTATCAAGG 57.297 45.455 0.00 0.00 0.00 3.61
3948 4747 7.901029 TGTATAGCAGAAGGAGGATTATCAAG 58.099 38.462 0.00 0.00 0.00 3.02
3949 4748 7.855784 TGTATAGCAGAAGGAGGATTATCAA 57.144 36.000 0.00 0.00 0.00 2.57
3951 4750 7.984617 GGATTGTATAGCAGAAGGAGGATTATC 59.015 40.741 0.00 0.00 0.00 1.75
3952 4751 7.364232 CGGATTGTATAGCAGAAGGAGGATTAT 60.364 40.741 0.00 0.00 0.00 1.28
3953 4752 6.071334 CGGATTGTATAGCAGAAGGAGGATTA 60.071 42.308 0.00 0.00 0.00 1.75
3954 4753 5.279708 CGGATTGTATAGCAGAAGGAGGATT 60.280 44.000 0.00 0.00 0.00 3.01
3955 4754 4.221703 CGGATTGTATAGCAGAAGGAGGAT 59.778 45.833 0.00 0.00 0.00 3.24
3956 4755 3.574396 CGGATTGTATAGCAGAAGGAGGA 59.426 47.826 0.00 0.00 0.00 3.71
3957 4756 3.574396 TCGGATTGTATAGCAGAAGGAGG 59.426 47.826 0.00 0.00 0.00 4.30
3958 4757 4.855715 TCGGATTGTATAGCAGAAGGAG 57.144 45.455 0.00 0.00 0.00 3.69
3959 4758 4.220821 GGATCGGATTGTATAGCAGAAGGA 59.779 45.833 0.00 0.00 0.00 3.36
3960 4759 4.499183 GGATCGGATTGTATAGCAGAAGG 58.501 47.826 0.00 0.00 0.00 3.46
3961 4760 4.221703 AGGGATCGGATTGTATAGCAGAAG 59.778 45.833 0.00 0.00 0.00 2.85
3962 4761 4.021104 CAGGGATCGGATTGTATAGCAGAA 60.021 45.833 0.00 0.00 0.00 3.02
3963 4762 3.511540 CAGGGATCGGATTGTATAGCAGA 59.488 47.826 0.00 0.00 0.00 4.26
3964 4763 3.854666 CAGGGATCGGATTGTATAGCAG 58.145 50.000 0.00 0.00 0.00 4.24
3965 4764 2.028112 GCAGGGATCGGATTGTATAGCA 60.028 50.000 0.00 0.00 0.00 3.49
3966 4765 2.234908 AGCAGGGATCGGATTGTATAGC 59.765 50.000 0.00 0.00 0.00 2.97
3967 4766 3.766591 AGAGCAGGGATCGGATTGTATAG 59.233 47.826 0.00 0.00 0.00 1.31
3968 4767 3.779444 AGAGCAGGGATCGGATTGTATA 58.221 45.455 0.00 0.00 0.00 1.47
3969 4768 2.614259 AGAGCAGGGATCGGATTGTAT 58.386 47.619 0.00 0.00 0.00 2.29
3970 4769 2.088104 AGAGCAGGGATCGGATTGTA 57.912 50.000 0.00 0.00 0.00 2.41
3971 4770 1.207791 AAGAGCAGGGATCGGATTGT 58.792 50.000 0.00 0.00 0.00 2.71
3972 4771 2.103094 TGTAAGAGCAGGGATCGGATTG 59.897 50.000 0.00 0.00 0.00 2.67
3973 4772 2.103263 GTGTAAGAGCAGGGATCGGATT 59.897 50.000 0.00 0.00 0.00 3.01
3974 4773 1.689273 GTGTAAGAGCAGGGATCGGAT 59.311 52.381 0.00 0.00 0.00 4.18
3978 4777 1.471676 CCACGTGTAAGAGCAGGGATC 60.472 57.143 15.65 0.00 0.00 3.36
3983 4782 3.128764 TCTGATACCACGTGTAAGAGCAG 59.871 47.826 15.65 13.73 31.94 4.24
3985 4784 3.377485 TCTCTGATACCACGTGTAAGAGC 59.623 47.826 15.65 0.00 35.62 4.09
3987 4786 3.693085 GGTCTCTGATACCACGTGTAAGA 59.307 47.826 15.65 8.48 36.96 2.10
4005 4804 0.545548 GAAGGGAGGTGGAGTGGTCT 60.546 60.000 0.00 0.00 0.00 3.85
4006 4805 0.545548 AGAAGGGAGGTGGAGTGGTC 60.546 60.000 0.00 0.00 0.00 4.02
4007 4806 0.104409 AAGAAGGGAGGTGGAGTGGT 60.104 55.000 0.00 0.00 0.00 4.16
4008 4807 0.615850 GAAGAAGGGAGGTGGAGTGG 59.384 60.000 0.00 0.00 0.00 4.00
4009 4808 1.552792 GAGAAGAAGGGAGGTGGAGTG 59.447 57.143 0.00 0.00 0.00 3.51
4010 4809 1.553651 GGAGAAGAAGGGAGGTGGAGT 60.554 57.143 0.00 0.00 0.00 3.85
4011 4810 1.199615 GGAGAAGAAGGGAGGTGGAG 58.800 60.000 0.00 0.00 0.00 3.86
4012 4811 0.614979 CGGAGAAGAAGGGAGGTGGA 60.615 60.000 0.00 0.00 0.00 4.02
4013 4812 1.901085 CGGAGAAGAAGGGAGGTGG 59.099 63.158 0.00 0.00 0.00 4.61
4014 4813 1.219393 GCGGAGAAGAAGGGAGGTG 59.781 63.158 0.00 0.00 0.00 4.00
4015 4814 1.990614 GGCGGAGAAGAAGGGAGGT 60.991 63.158 0.00 0.00 0.00 3.85
4016 4815 1.990060 TGGCGGAGAAGAAGGGAGG 60.990 63.158 0.00 0.00 0.00 4.30
4018 4817 1.229209 AGTGGCGGAGAAGAAGGGA 60.229 57.895 0.00 0.00 0.00 4.20
4019 4818 1.219393 GAGTGGCGGAGAAGAAGGG 59.781 63.158 0.00 0.00 0.00 3.95
4020 4819 0.108424 CAGAGTGGCGGAGAAGAAGG 60.108 60.000 0.00 0.00 0.00 3.46
4023 4822 3.700109 CCAGAGTGGCGGAGAAGA 58.300 61.111 0.00 0.00 0.00 2.87
4032 4831 1.002134 ACGATTTGGGCCAGAGTGG 60.002 57.895 6.23 0.71 41.55 4.00
4033 4832 1.361668 CGACGATTTGGGCCAGAGTG 61.362 60.000 6.23 1.13 0.00 3.51
4035 4834 0.807667 CTCGACGATTTGGGCCAGAG 60.808 60.000 6.23 4.14 0.00 3.35
4036 4835 1.218047 CTCGACGATTTGGGCCAGA 59.782 57.895 6.23 1.42 0.00 3.86
4037 4836 1.084370 GTCTCGACGATTTGGGCCAG 61.084 60.000 6.23 0.00 0.00 4.85
4038 4837 1.079405 GTCTCGACGATTTGGGCCA 60.079 57.895 0.00 0.00 0.00 5.36
4039 4838 0.806492 GAGTCTCGACGATTTGGGCC 60.806 60.000 0.00 0.00 36.20 5.80
4042 4841 1.140407 GCCGAGTCTCGACGATTTGG 61.140 60.000 23.74 5.24 43.74 3.28
4044 4843 4.787999 GCCGAGTCTCGACGATTT 57.212 55.556 23.74 0.00 43.74 2.17
4063 4862 2.951745 GATCTCGCCTGTCGCACG 60.952 66.667 0.00 0.00 37.30 5.34
4074 4873 1.659954 GCTACCAGCTGCGATCTCG 60.660 63.158 8.66 0.00 38.45 4.04
4075 4874 4.334837 GCTACCAGCTGCGATCTC 57.665 61.111 8.66 0.00 38.45 2.75



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

AutoCloner maintained by Alex Coulton.