Multiple sequence alignment - TraesCS2B01G326200

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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 TraesCS2B01G326200 chr2B 100.000 5846 0 0 1 5846 465830640 465824795 0.000000e+00 10796.0
1 TraesCS2B01G326200 chr2B 94.872 897 46 0 4950 5846 504485536 504484640 0.000000e+00 1402.0
2 TraesCS2B01G326200 chr2B 86.275 51 7 0 4558 4608 492793464 492793414 8.180000e-04 56.5
3 TraesCS2B01G326200 chr2D 87.967 2701 112 70 49 2658 394123826 394121248 0.000000e+00 2990.0
4 TraesCS2B01G326200 chr2D 97.132 1290 30 4 3633 4916 394120326 394119038 0.000000e+00 2170.0
5 TraesCS2B01G326200 chr2D 94.091 897 52 1 4950 5846 557271364 557270469 0.000000e+00 1362.0
6 TraesCS2B01G326200 chr2D 90.398 729 37 12 2736 3456 394121106 394120403 0.000000e+00 928.0
7 TraesCS2B01G326200 chr2A 87.078 2012 121 66 49 2000 532090703 532088771 0.000000e+00 2146.0
8 TraesCS2B01G326200 chr2A 95.665 1338 37 9 3598 4916 532087209 532085874 0.000000e+00 2130.0
9 TraesCS2B01G326200 chr2A 91.938 1352 51 20 2198 3528 532088532 532087218 0.000000e+00 1840.0
10 TraesCS2B01G326200 chr2A 96.210 897 34 0 4950 5846 16877681 16878577 0.000000e+00 1469.0
11 TraesCS2B01G326200 chr2A 94.444 36 2 0 4558 4593 569905938 569905973 8.180000e-04 56.5
12 TraesCS2B01G326200 chr1A 95.875 897 36 1 4950 5846 257989261 257990156 0.000000e+00 1450.0
13 TraesCS2B01G326200 chr4A 95.541 897 40 0 4950 5846 619153187 619152291 0.000000e+00 1435.0
14 TraesCS2B01G326200 chr4A 80.754 769 125 17 3853 4611 533261361 533262116 3.930000e-161 579.0
15 TraesCS2B01G326200 chr4A 92.070 227 18 0 1333 1559 533258397 533258623 2.630000e-83 320.0
16 TraesCS2B01G326200 chr4A 94.737 38 0 2 1484 1520 709275503 709275467 2.280000e-04 58.4
17 TraesCS2B01G326200 chr4A 94.737 38 0 2 1484 1520 709421835 709421799 2.280000e-04 58.4
18 TraesCS2B01G326200 chr7A 95.429 897 41 0 4950 5846 70110285 70109389 0.000000e+00 1430.0
19 TraesCS2B01G326200 chr6A 93.088 897 58 1 4950 5846 48051551 48052443 0.000000e+00 1310.0
20 TraesCS2B01G326200 chr5A 91.648 898 73 2 4950 5846 400568282 400569178 0.000000e+00 1242.0
21 TraesCS2B01G326200 chr3D 94.051 790 47 0 4950 5739 330222483 330223272 0.000000e+00 1199.0
22 TraesCS2B01G326200 chr4D 80.605 794 135 13 3853 4638 63044408 63043626 3.900000e-166 595.0
23 TraesCS2B01G326200 chr4D 91.630 227 19 0 1333 1559 63047294 63047068 1.220000e-81 315.0
24 TraesCS2B01G326200 chr4B 81.030 738 130 7 3909 4638 93409084 93408349 3.930000e-161 579.0
25 TraesCS2B01G326200 chr4B 91.189 227 20 0 1333 1559 93412245 93412019 5.690000e-80 309.0
26 TraesCS2B01G326200 chrUn 85.893 319 43 2 4321 4638 478813213 478812896 7.260000e-89 339.0
27 TraesCS2B01G326200 chrUn 94.737 38 0 2 1484 1520 346600436 346600472 2.280000e-04 58.4
28 TraesCS2B01G326200 chr7D 94.595 37 2 0 1484 1520 25291563 25291527 2.280000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G326200 chr2B 465824795 465830640 5845 True 10796.000000 10796 100.000000 1 5846 1 chr2B.!!$R1 5845
1 TraesCS2B01G326200 chr2B 504484640 504485536 896 True 1402.000000 1402 94.872000 4950 5846 1 chr2B.!!$R3 896
2 TraesCS2B01G326200 chr2D 394119038 394123826 4788 True 2029.333333 2990 91.832333 49 4916 3 chr2D.!!$R2 4867
3 TraesCS2B01G326200 chr2D 557270469 557271364 895 True 1362.000000 1362 94.091000 4950 5846 1 chr2D.!!$R1 896
4 TraesCS2B01G326200 chr2A 532085874 532090703 4829 True 2038.666667 2146 91.560333 49 4916 3 chr2A.!!$R1 4867
5 TraesCS2B01G326200 chr2A 16877681 16878577 896 False 1469.000000 1469 96.210000 4950 5846 1 chr2A.!!$F1 896
6 TraesCS2B01G326200 chr1A 257989261 257990156 895 False 1450.000000 1450 95.875000 4950 5846 1 chr1A.!!$F1 896
7 TraesCS2B01G326200 chr4A 619152291 619153187 896 True 1435.000000 1435 95.541000 4950 5846 1 chr4A.!!$R1 896
8 TraesCS2B01G326200 chr4A 533258397 533262116 3719 False 449.500000 579 86.412000 1333 4611 2 chr4A.!!$F1 3278
9 TraesCS2B01G326200 chr7A 70109389 70110285 896 True 1430.000000 1430 95.429000 4950 5846 1 chr7A.!!$R1 896
10 TraesCS2B01G326200 chr6A 48051551 48052443 892 False 1310.000000 1310 93.088000 4950 5846 1 chr6A.!!$F1 896
11 TraesCS2B01G326200 chr5A 400568282 400569178 896 False 1242.000000 1242 91.648000 4950 5846 1 chr5A.!!$F1 896
12 TraesCS2B01G326200 chr3D 330222483 330223272 789 False 1199.000000 1199 94.051000 4950 5739 1 chr3D.!!$F1 789
13 TraesCS2B01G326200 chr4D 63043626 63047294 3668 True 455.000000 595 86.117500 1333 4638 2 chr4D.!!$R1 3305
14 TraesCS2B01G326200 chr4B 93408349 93412245 3896 True 444.000000 579 86.109500 1333 4638 2 chr4B.!!$R1 3305

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
20 21 0.392193 AGCACGCCAAGAATCAGGAG 60.392 55.0 0.00 0.0 0.00 3.69 F
1633 1715 0.107945 GGAAGGAGTGGCTAGCAGTG 60.108 60.0 18.24 0.0 0.00 3.66 F
1861 2143 0.470456 ATGGCCGGGGACTAACGATA 60.470 55.0 2.18 0.0 0.00 2.92 F
3317 3841 0.239082 ACGTGTGCTGATGTGCAATG 59.761 50.0 0.00 0.0 45.12 2.82 F
3860 5945 0.036164 ACCATGCACGCAGGTTCTTA 59.964 50.0 2.75 0.0 29.58 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 2094 0.544120 TTGAATTCAACCTGGCCCCC 60.544 55.0 16.91 0.00 0.00 5.40 R
3288 3809 0.110509 CAGCACACGTGATTCAGCAC 60.111 55.0 25.01 1.86 35.46 4.40 R
3677 5457 0.181350 CAGGATTGGTAGGGCAGACC 59.819 60.0 0.27 0.27 40.67 3.85 R
4670 6770 0.107606 CCTCTGCTGCAATCTGAGCT 60.108 55.0 3.02 0.00 36.11 4.09 R
4940 7046 0.302890 GACGATGCTCTTGGCGATTG 59.697 55.0 0.00 0.00 45.43 2.67 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
18 19 1.798735 CAGCACGCCAAGAATCAGG 59.201 57.895 0.00 0.00 0.00 3.86
19 20 0.674581 CAGCACGCCAAGAATCAGGA 60.675 55.000 0.00 0.00 0.00 3.86
20 21 0.392193 AGCACGCCAAGAATCAGGAG 60.392 55.000 0.00 0.00 0.00 3.69
21 22 1.372087 GCACGCCAAGAATCAGGAGG 61.372 60.000 0.00 0.00 0.00 4.30
22 23 1.078143 ACGCCAAGAATCAGGAGGC 60.078 57.895 0.00 0.00 41.86 4.70
23 24 1.078214 CGCCAAGAATCAGGAGGCA 60.078 57.895 0.00 0.00 45.47 4.75
24 25 0.465097 CGCCAAGAATCAGGAGGCAT 60.465 55.000 0.00 0.00 45.47 4.40
25 26 1.202687 CGCCAAGAATCAGGAGGCATA 60.203 52.381 0.00 0.00 45.47 3.14
26 27 2.551721 CGCCAAGAATCAGGAGGCATAT 60.552 50.000 0.00 0.00 45.47 1.78
27 28 3.080319 GCCAAGAATCAGGAGGCATATC 58.920 50.000 0.00 0.00 44.59 1.63
28 29 3.244840 GCCAAGAATCAGGAGGCATATCT 60.245 47.826 0.00 0.00 44.59 1.98
29 30 4.019860 GCCAAGAATCAGGAGGCATATCTA 60.020 45.833 0.00 0.00 44.59 1.98
30 31 5.339035 GCCAAGAATCAGGAGGCATATCTAT 60.339 44.000 0.00 0.00 44.59 1.98
31 32 6.347696 CCAAGAATCAGGAGGCATATCTATC 58.652 44.000 0.00 0.00 0.00 2.08
32 33 6.156602 CCAAGAATCAGGAGGCATATCTATCT 59.843 42.308 0.00 0.00 0.00 1.98
33 34 7.344093 CCAAGAATCAGGAGGCATATCTATCTA 59.656 40.741 0.00 0.00 0.00 1.98
34 35 8.926374 CAAGAATCAGGAGGCATATCTATCTAT 58.074 37.037 0.00 0.00 0.00 1.98
35 36 8.710749 AGAATCAGGAGGCATATCTATCTATC 57.289 38.462 0.00 0.00 0.00 2.08
36 37 8.513658 AGAATCAGGAGGCATATCTATCTATCT 58.486 37.037 0.00 0.00 0.00 1.98
37 38 9.806448 GAATCAGGAGGCATATCTATCTATCTA 57.194 37.037 0.00 0.00 0.00 1.98
39 40 9.979897 ATCAGGAGGCATATCTATCTATCTATC 57.020 37.037 0.00 0.00 0.00 2.08
40 41 9.181462 TCAGGAGGCATATCTATCTATCTATCT 57.819 37.037 0.00 0.00 0.00 1.98
123 139 6.304356 TCTATATTGTAGCATGCAACTTGC 57.696 37.500 21.98 6.82 45.30 4.01
146 162 6.970043 TGCGGTGCAAAATCTGTTAAATATAC 59.030 34.615 0.00 0.00 34.76 1.47
147 163 7.148154 TGCGGTGCAAAATCTGTTAAATATACT 60.148 33.333 0.00 0.00 34.76 2.12
164 180 8.980481 AAATATACTTCCACTCCGAATCATTT 57.020 30.769 0.00 0.00 0.00 2.32
165 181 8.608844 AATATACTTCCACTCCGAATCATTTC 57.391 34.615 0.00 0.00 0.00 2.17
166 182 3.610911 ACTTCCACTCCGAATCATTTCC 58.389 45.455 0.00 0.00 0.00 3.13
167 183 3.264450 ACTTCCACTCCGAATCATTTCCT 59.736 43.478 0.00 0.00 0.00 3.36
168 184 4.263506 ACTTCCACTCCGAATCATTTCCTT 60.264 41.667 0.00 0.00 0.00 3.36
172 188 5.130311 TCCACTCCGAATCATTTCCTTCATA 59.870 40.000 0.00 0.00 0.00 2.15
175 191 7.210174 CACTCCGAATCATTTCCTTCATAGTA 58.790 38.462 0.00 0.00 0.00 1.82
354 392 4.293626 GTGTCGTGTGCACCGTGC 62.294 66.667 16.93 16.93 45.29 5.34
414 452 8.511126 ACATCAATTCCACTATATTTTAGGGGT 58.489 33.333 2.81 0.00 39.15 4.95
431 471 3.974642 AGGGGTCATCAAGTAGTTATCCC 59.025 47.826 0.00 0.00 0.00 3.85
496 540 7.442364 TCACTGATAAGTCTTCCAGAAAAACAG 59.558 37.037 17.09 0.00 0.00 3.16
501 545 9.670719 GATAAGTCTTCCAGAAAAACAGAAAAG 57.329 33.333 0.00 0.00 0.00 2.27
518 562 8.779354 ACAGAAAAGAACTCACCAATATAGAC 57.221 34.615 0.00 0.00 0.00 2.59
528 572 7.042335 ACTCACCAATATAGACAAAGCAGTAC 58.958 38.462 0.00 0.00 0.00 2.73
529 573 7.093289 ACTCACCAATATAGACAAAGCAGTACT 60.093 37.037 0.00 0.00 0.00 2.73
530 574 8.301252 TCACCAATATAGACAAAGCAGTACTA 57.699 34.615 0.00 0.00 0.00 1.82
531 575 8.195436 TCACCAATATAGACAAAGCAGTACTAC 58.805 37.037 0.00 0.00 0.00 2.73
565 609 4.513406 ACTTGGGTCAGGAAACAACTTA 57.487 40.909 0.00 0.00 0.00 2.24
566 610 5.061721 ACTTGGGTCAGGAAACAACTTAT 57.938 39.130 0.00 0.00 0.00 1.73
567 611 6.195600 ACTTGGGTCAGGAAACAACTTATA 57.804 37.500 0.00 0.00 0.00 0.98
568 612 6.790319 ACTTGGGTCAGGAAACAACTTATAT 58.210 36.000 0.00 0.00 0.00 0.86
571 615 7.743116 TGGGTCAGGAAACAACTTATATCTA 57.257 36.000 0.00 0.00 0.00 1.98
646 691 0.398318 GTTGACCTGGAAGCTGACCT 59.602 55.000 0.00 0.00 0.00 3.85
654 699 0.957888 GGAAGCTGACCTCTGGTTGC 60.958 60.000 1.83 1.45 35.25 4.17
677 722 3.883830 TTTCCAGCAAAGCAGAACAAA 57.116 38.095 0.00 0.00 0.00 2.83
678 723 3.883830 TTCCAGCAAAGCAGAACAAAA 57.116 38.095 0.00 0.00 0.00 2.44
680 725 3.520569 TCCAGCAAAGCAGAACAAAAAC 58.479 40.909 0.00 0.00 0.00 2.43
681 726 3.056250 TCCAGCAAAGCAGAACAAAAACA 60.056 39.130 0.00 0.00 0.00 2.83
682 727 3.062504 CCAGCAAAGCAGAACAAAAACAC 59.937 43.478 0.00 0.00 0.00 3.32
715 768 2.095567 CCCAACAATTCGAGCAAGTCAG 60.096 50.000 0.00 0.00 0.00 3.51
732 785 6.404708 CAAGTCAGTCCATATCCATATCCAG 58.595 44.000 0.00 0.00 0.00 3.86
849 911 2.125147 TGCGCTGCCACTATGGAC 60.125 61.111 9.73 0.00 40.96 4.02
855 917 1.276421 GCTGCCACTATGGACCGATAT 59.724 52.381 0.00 0.00 40.96 1.63
873 935 2.204748 TCGACCCCGAAATTCCGAT 58.795 52.632 0.00 0.00 42.51 4.18
881 943 2.747446 CCCGAAATTCCGATGTGAAAGT 59.253 45.455 0.00 0.00 0.00 2.66
928 990 1.635663 GGCATTCGTCCGTCCACAAG 61.636 60.000 0.00 0.00 0.00 3.16
929 991 0.669318 GCATTCGTCCGTCCACAAGA 60.669 55.000 0.00 0.00 0.00 3.02
930 992 1.350193 CATTCGTCCGTCCACAAGAG 58.650 55.000 0.00 0.00 0.00 2.85
932 994 0.596577 TTCGTCCGTCCACAAGAGAG 59.403 55.000 0.00 0.00 0.00 3.20
933 995 1.213013 CGTCCGTCCACAAGAGAGG 59.787 63.158 0.00 0.00 0.00 3.69
934 996 1.592223 GTCCGTCCACAAGAGAGGG 59.408 63.158 0.00 0.00 40.01 4.30
935 997 2.266055 CCGTCCACAAGAGAGGGC 59.734 66.667 0.00 0.00 32.94 5.19
938 1000 1.298014 GTCCACAAGAGAGGGCAGG 59.702 63.158 0.00 0.00 29.69 4.85
939 1001 2.045536 CCACAAGAGAGGGCAGGC 60.046 66.667 0.00 0.00 0.00 4.85
940 1002 2.435586 CACAAGAGAGGGCAGGCG 60.436 66.667 0.00 0.00 0.00 5.52
1021 1086 0.669318 TTACCTACGCAGCACAGCAC 60.669 55.000 0.00 0.00 0.00 4.40
1049 1116 2.736719 GCAGAGCTCGTCATTCAGCTAA 60.737 50.000 8.37 0.00 46.31 3.09
1051 1118 3.305629 CAGAGCTCGTCATTCAGCTAAAC 59.694 47.826 8.37 0.00 46.31 2.01
1064 1131 2.649331 GCTAAACTAGCGGTGACTGA 57.351 50.000 0.00 0.00 42.62 3.41
1134 1201 0.247460 CATGGACGTTGAGAGCTCCA 59.753 55.000 10.93 5.38 37.22 3.86
1228 1295 2.540515 CGTCTTCGTCCTAGGTACGTA 58.459 52.381 23.88 17.47 41.08 3.57
1255 1324 7.407393 ACTCCTACCTACATCAAGTTAGTTC 57.593 40.000 0.00 0.00 0.00 3.01
1274 1343 2.493035 TCGTTATACGGACGAGCCATA 58.507 47.619 0.00 0.00 43.79 2.74
1285 1354 1.759445 ACGAGCCATAGAGCAATGTCT 59.241 47.619 0.00 0.00 34.23 3.41
1286 1355 2.959030 ACGAGCCATAGAGCAATGTCTA 59.041 45.455 0.00 0.00 33.52 2.59
1287 1356 3.576118 ACGAGCCATAGAGCAATGTCTAT 59.424 43.478 0.00 1.38 39.87 1.98
1288 1357 4.039730 ACGAGCCATAGAGCAATGTCTATT 59.960 41.667 0.00 0.00 37.62 1.73
1289 1358 4.388165 CGAGCCATAGAGCAATGTCTATTG 59.612 45.833 0.00 0.00 45.17 1.90
1290 1359 5.301835 AGCCATAGAGCAATGTCTATTGT 57.698 39.130 0.00 0.00 44.41 2.71
1291 1360 5.303971 AGCCATAGAGCAATGTCTATTGTC 58.696 41.667 0.00 0.00 44.41 3.18
1292 1361 5.071519 AGCCATAGAGCAATGTCTATTGTCT 59.928 40.000 0.00 0.00 44.41 3.41
1301 1370 7.743749 AGCAATGTCTATTGTCTATCCAATCT 58.256 34.615 0.00 0.00 44.41 2.40
1318 1387 4.889856 TATGGCGCGCGTGCTGAT 62.890 61.111 39.35 31.42 39.65 2.90
1565 1641 3.480342 GAGCTCTCGGTACTCCTCA 57.520 57.895 6.43 0.00 0.00 3.86
1567 1643 0.621609 AGCTCTCGGTACTCCTCACT 59.378 55.000 0.00 0.00 0.00 3.41
1568 1644 1.838715 AGCTCTCGGTACTCCTCACTA 59.161 52.381 0.00 0.00 0.00 2.74
1632 1714 0.252467 AGGAAGGAGTGGCTAGCAGT 60.252 55.000 18.24 5.63 0.00 4.40
1633 1715 0.107945 GGAAGGAGTGGCTAGCAGTG 60.108 60.000 18.24 0.00 0.00 3.66
1635 1717 0.610687 AAGGAGTGGCTAGCAGTGAC 59.389 55.000 18.24 7.16 0.00 3.67
1636 1718 1.219393 GGAGTGGCTAGCAGTGACC 59.781 63.158 18.24 9.06 0.00 4.02
1718 1996 4.142687 CGTGTGAGAGTGTTTTTCCTTTGT 60.143 41.667 0.00 0.00 0.00 2.83
1812 2094 1.512230 CATGCATGGACCCGGTTTG 59.488 57.895 19.40 0.00 0.00 2.93
1855 2137 3.479203 CAGCATGGCCGGGGACTA 61.479 66.667 2.18 0.00 0.00 2.59
1857 2139 2.516225 GCATGGCCGGGGACTAAC 60.516 66.667 2.18 0.00 0.00 2.34
1861 2143 0.470456 ATGGCCGGGGACTAACGATA 60.470 55.000 2.18 0.00 0.00 2.92
1862 2144 0.470456 TGGCCGGGGACTAACGATAT 60.470 55.000 2.18 0.00 0.00 1.63
1864 2146 0.963962 GCCGGGGACTAACGATATGA 59.036 55.000 2.18 0.00 0.00 2.15
1865 2147 1.549170 GCCGGGGACTAACGATATGAT 59.451 52.381 2.18 0.00 0.00 2.45
1866 2148 2.756760 GCCGGGGACTAACGATATGATA 59.243 50.000 2.18 0.00 0.00 2.15
1867 2149 3.194116 GCCGGGGACTAACGATATGATAA 59.806 47.826 2.18 0.00 0.00 1.75
1868 2150 4.142004 GCCGGGGACTAACGATATGATAAT 60.142 45.833 2.18 0.00 0.00 1.28
1869 2151 5.589192 CCGGGGACTAACGATATGATAATC 58.411 45.833 0.00 0.00 0.00 1.75
1870 2152 5.126545 CCGGGGACTAACGATATGATAATCA 59.873 44.000 0.00 0.00 0.00 2.57
1874 2156 8.883731 GGGGACTAACGATATGATAATCATTTG 58.116 37.037 0.00 0.00 38.26 2.32
1918 2204 1.346395 AGAACTACACACGCCAATGGA 59.654 47.619 2.05 0.00 0.00 3.41
1937 2223 7.811713 CCAATGGAAATTTGTTTGTTGTTGTTT 59.188 29.630 0.00 0.00 0.00 2.83
1939 2225 8.739649 ATGGAAATTTGTTTGTTGTTGTTTTG 57.260 26.923 0.00 0.00 0.00 2.44
2000 2286 5.120363 GTGCTAGTGTTACTTGCCTACTTTC 59.880 44.000 11.66 0.00 44.40 2.62
2001 2287 5.221561 TGCTAGTGTTACTTGCCTACTTTCA 60.222 40.000 11.66 0.00 44.40 2.69
2021 2327 5.344743 TCAACTATCCTAGGCACTTCTTG 57.655 43.478 2.96 1.01 41.75 3.02
2037 2343 7.054855 CACTTCTTGCTTTTACTAGTAGCAG 57.945 40.000 16.28 11.13 44.80 4.24
2041 2347 6.755206 TCTTGCTTTTACTAGTAGCAGACAA 58.245 36.000 16.28 14.56 44.80 3.18
2043 2349 4.921515 TGCTTTTACTAGTAGCAGACAACG 59.078 41.667 13.61 0.00 39.79 4.10
2057 2363 4.913345 GCAGACAACGTTTGTAATTTACCC 59.087 41.667 0.00 0.00 45.52 3.69
2064 2370 7.920151 ACAACGTTTGTAATTTACCCTAAAACC 59.080 33.333 0.00 0.00 43.27 3.27
2068 2374 7.380536 GTTTGTAATTTACCCTAAAACCCTGG 58.619 38.462 4.17 0.00 0.00 4.45
2072 2378 7.956881 TGTAATTTACCCTAAAACCCTGGATTT 59.043 33.333 4.17 0.00 0.00 2.17
2073 2379 9.478238 GTAATTTACCCTAAAACCCTGGATTTA 57.522 33.333 0.00 0.00 0.00 1.40
2074 2380 8.975925 AATTTACCCTAAAACCCTGGATTTAA 57.024 30.769 0.00 0.00 0.00 1.52
2075 2381 7.779754 TTTACCCTAAAACCCTGGATTTAAC 57.220 36.000 0.00 0.00 0.00 2.01
2076 2382 5.342361 ACCCTAAAACCCTGGATTTAACA 57.658 39.130 0.00 0.00 0.00 2.41
2077 2383 5.330233 ACCCTAAAACCCTGGATTTAACAG 58.670 41.667 0.00 0.00 35.74 3.16
2078 2384 5.075344 ACCCTAAAACCCTGGATTTAACAGA 59.925 40.000 0.00 0.00 38.20 3.41
2082 2388 9.250246 CCTAAAACCCTGGATTTAACAGAAATA 57.750 33.333 0.00 0.00 38.20 1.40
2169 2538 9.744468 ATAAAATCGGAAATAGTATGTTTTGCC 57.256 29.630 0.00 0.00 0.00 4.52
2172 2541 4.638421 TCGGAAATAGTATGTTTTGCCTGG 59.362 41.667 0.00 0.00 0.00 4.45
2174 2543 5.299279 CGGAAATAGTATGTTTTGCCTGGAT 59.701 40.000 0.00 0.00 0.00 3.41
2176 2545 7.555965 GGAAATAGTATGTTTTGCCTGGATTT 58.444 34.615 0.00 0.00 0.00 2.17
2177 2546 8.040727 GGAAATAGTATGTTTTGCCTGGATTTT 58.959 33.333 0.00 0.00 0.00 1.82
2180 2557 9.869757 AATAGTATGTTTTGCCTGGATTTTTAC 57.130 29.630 0.00 0.00 0.00 2.01
2185 2562 6.744112 TGTTTTGCCTGGATTTTTACTAGTG 58.256 36.000 5.39 0.00 0.00 2.74
2195 2581 8.282455 TGGATTTTTACTAGTGTGTTTTGTCA 57.718 30.769 5.39 0.00 0.00 3.58
2196 2582 8.740906 TGGATTTTTACTAGTGTGTTTTGTCAA 58.259 29.630 5.39 0.00 0.00 3.18
2711 3202 4.625742 ACTCAATGATTGTAAAGACGGACG 59.374 41.667 4.93 0.00 0.00 4.79
2716 3207 3.491639 TGATTGTAAAGACGGACGTGTTG 59.508 43.478 8.01 0.00 31.81 3.33
2723 3214 3.587797 AGACGGACGTGTTGATTGTAT 57.412 42.857 0.53 0.00 0.00 2.29
2724 3215 3.921677 AGACGGACGTGTTGATTGTATT 58.078 40.909 0.53 0.00 0.00 1.89
2725 3216 4.312443 AGACGGACGTGTTGATTGTATTT 58.688 39.130 0.53 0.00 0.00 1.40
2778 3288 4.574013 ACTTTGCGCATTCAAAAATTGGAA 59.426 33.333 12.75 0.00 35.75 3.53
2787 3297 6.634035 GCATTCAAAAATTGGAAGAAGTTTGC 59.366 34.615 0.00 0.00 0.00 3.68
2875 3386 8.893219 AAATCCTTTTCAGAAATTTCCAAGAC 57.107 30.769 14.61 0.00 0.00 3.01
2936 3447 8.311395 TGATCTGATCACATTACTATATCCCC 57.689 38.462 16.06 0.00 33.59 4.81
2957 3468 4.536888 CCCCCTCTAGCTAGTACTCTATGA 59.463 50.000 20.10 0.00 0.00 2.15
3021 3532 4.439289 CGTCATCATTCAGTCAGTCAGCTA 60.439 45.833 0.00 0.00 0.00 3.32
3059 3570 4.335315 TCACCTTGTCACATTCAACAGTTC 59.665 41.667 0.00 0.00 0.00 3.01
3061 3572 5.527214 CACCTTGTCACATTCAACAGTTCTA 59.473 40.000 0.00 0.00 0.00 2.10
3062 3573 5.760253 ACCTTGTCACATTCAACAGTTCTAG 59.240 40.000 0.00 0.00 0.00 2.43
3086 3597 4.927267 TTTGGGGCCATATGATAGGTAG 57.073 45.455 4.39 0.00 0.00 3.18
3087 3598 3.577968 TGGGGCCATATGATAGGTAGT 57.422 47.619 4.39 0.00 0.00 2.73
3088 3599 4.703101 TGGGGCCATATGATAGGTAGTA 57.297 45.455 4.39 0.00 0.00 1.82
3140 3653 6.774673 TCAGATCTAGTCAGATACACCTAGG 58.225 44.000 7.41 7.41 41.78 3.02
3141 3654 5.943416 CAGATCTAGTCAGATACACCTAGGG 59.057 48.000 14.81 4.64 41.78 3.53
3142 3655 5.852807 AGATCTAGTCAGATACACCTAGGGA 59.147 44.000 14.81 0.00 41.78 4.20
3143 3656 5.988865 TCTAGTCAGATACACCTAGGGAA 57.011 43.478 14.81 0.00 0.00 3.97
3144 3657 5.942961 TCTAGTCAGATACACCTAGGGAAG 58.057 45.833 14.81 5.12 0.00 3.46
3232 3750 3.929610 GACTGTTAGGATGTCAGTTCTGC 59.070 47.826 0.00 0.00 41.58 4.26
3234 3752 2.299013 TGTTAGGATGTCAGTTCTGCGT 59.701 45.455 0.00 0.00 0.00 5.24
3288 3809 3.308053 CAGAACTGACTGCGGATTATGTG 59.692 47.826 0.00 0.00 0.00 3.21
3317 3841 0.239082 ACGTGTGCTGATGTGCAATG 59.761 50.000 0.00 0.00 45.12 2.82
3428 4512 8.694394 GCTGTTTTTGTCAAATGAGATTAAGAC 58.306 33.333 0.00 0.00 0.00 3.01
3451 4535 7.231317 AGACCATTTTGACACAGAAATGTACAT 59.769 33.333 1.41 1.41 40.11 2.29
3458 4542 5.240623 TGACACAGAAATGTACATTTGGACC 59.759 40.000 32.90 20.25 40.77 4.46
3461 4545 6.016276 ACACAGAAATGTACATTTGGACCTTC 60.016 38.462 32.90 19.08 40.77 3.46
3462 4546 6.016360 CACAGAAATGTACATTTGGACCTTCA 60.016 38.462 32.90 0.00 40.77 3.02
3466 4607 8.090214 AGAAATGTACATTTGGACCTTCATTTG 58.910 33.333 32.90 0.00 40.77 2.32
3467 4608 6.916360 ATGTACATTTGGACCTTCATTTGT 57.084 33.333 1.41 0.00 0.00 2.83
3468 4609 6.723298 TGTACATTTGGACCTTCATTTGTT 57.277 33.333 0.00 0.00 0.00 2.83
3469 4610 7.118496 TGTACATTTGGACCTTCATTTGTTT 57.882 32.000 0.00 0.00 0.00 2.83
3470 4611 8.239038 TGTACATTTGGACCTTCATTTGTTTA 57.761 30.769 0.00 0.00 0.00 2.01
3471 4612 8.865090 TGTACATTTGGACCTTCATTTGTTTAT 58.135 29.630 0.00 0.00 0.00 1.40
3475 4616 8.711457 CATTTGGACCTTCATTTGTTTATTGTC 58.289 33.333 0.00 0.00 0.00 3.18
3488 4629 9.912634 ATTTGTTTATTGTCAACCAAGATACAG 57.087 29.630 0.00 0.00 37.46 2.74
3542 4873 3.920231 ATTTGCAGCTGATCCTGACTA 57.080 42.857 20.43 0.00 34.77 2.59
3559 4959 5.468540 TGACTAACTTGTAGTGACATGCT 57.531 39.130 0.00 0.00 34.86 3.79
3560 4960 6.350194 CCTGACTAACTTGTAGTGACATGCTA 60.350 42.308 0.00 0.00 34.86 3.49
3562 4962 6.208797 TGACTAACTTGTAGTGACATGCTAGT 59.791 38.462 0.00 6.71 41.61 2.57
3563 4963 7.392393 TGACTAACTTGTAGTGACATGCTAGTA 59.608 37.037 0.00 0.00 40.22 1.82
3564 4964 8.118976 ACTAACTTGTAGTGACATGCTAGTAA 57.881 34.615 0.00 0.00 39.23 2.24
3585 4985 4.978083 AAAAATATGCTGCAGAGTCCTG 57.022 40.909 20.43 0.00 43.22 3.86
3596 4996 2.149578 CAGAGTCCTGCTGTTTCCTTG 58.850 52.381 0.00 0.00 33.07 3.61
3663 5443 1.289380 GTGTTCGTCGCCTCCTTCT 59.711 57.895 0.00 0.00 0.00 2.85
3677 5457 1.905215 TCCTTCTCCAAGAGGAAGCAG 59.095 52.381 0.00 0.00 45.19 4.24
3847 5645 1.270274 TGACATGCTGTGAAACCATGC 59.730 47.619 0.00 0.00 39.24 4.06
3860 5945 0.036164 ACCATGCACGCAGGTTCTTA 59.964 50.000 2.75 0.00 29.58 2.10
4548 6648 3.263503 CTCGGCGACAACGACCTCA 62.264 63.158 4.99 0.00 45.81 3.86
4670 6770 1.632965 ATGGCTCTGATGCTGCCTCA 61.633 55.000 7.39 7.39 46.23 3.86
4728 6831 3.387374 CAGCTGAAGACCTACATGGAGAT 59.613 47.826 8.42 0.00 39.71 2.75
4916 7022 9.088512 AGCATAGTCTTCAGTAAACTTATTTCG 57.911 33.333 0.00 0.00 0.00 3.46
4918 7024 6.723131 AGTCTTCAGTAAACTTATTTCGCC 57.277 37.500 0.00 0.00 0.00 5.54
4919 7025 6.228258 AGTCTTCAGTAAACTTATTTCGCCA 58.772 36.000 0.00 0.00 0.00 5.69
4920 7026 6.879458 AGTCTTCAGTAAACTTATTTCGCCAT 59.121 34.615 0.00 0.00 0.00 4.40
4921 7027 6.961554 GTCTTCAGTAAACTTATTTCGCCATG 59.038 38.462 0.00 0.00 0.00 3.66
4922 7028 6.876789 TCTTCAGTAAACTTATTTCGCCATGA 59.123 34.615 0.00 0.00 0.00 3.07
4923 7029 7.552687 TCTTCAGTAAACTTATTTCGCCATGAT 59.447 33.333 0.00 0.00 0.00 2.45
4924 7030 7.246674 TCAGTAAACTTATTTCGCCATGATC 57.753 36.000 0.00 0.00 0.00 2.92
4925 7031 6.821160 TCAGTAAACTTATTTCGCCATGATCA 59.179 34.615 0.00 0.00 0.00 2.92
4926 7032 7.498900 TCAGTAAACTTATTTCGCCATGATCAT 59.501 33.333 1.18 1.18 0.00 2.45
4927 7033 7.800380 CAGTAAACTTATTTCGCCATGATCATC 59.200 37.037 4.86 0.00 0.00 2.92
4928 7034 4.997905 ACTTATTTCGCCATGATCATCG 57.002 40.909 4.86 7.86 0.00 3.84
4929 7035 3.187227 ACTTATTTCGCCATGATCATCGC 59.813 43.478 14.60 14.60 0.00 4.58
4930 7036 0.514255 ATTTCGCCATGATCATCGCG 59.486 50.000 33.23 33.23 47.00 5.87
4934 7040 1.864862 GCCATGATCATCGCGAAGG 59.135 57.895 15.24 9.12 0.00 3.46
4935 7041 0.882042 GCCATGATCATCGCGAAGGT 60.882 55.000 15.24 4.12 0.00 3.50
4936 7042 0.863799 CCATGATCATCGCGAAGGTG 59.136 55.000 15.24 7.51 0.00 4.00
4937 7043 0.863799 CATGATCATCGCGAAGGTGG 59.136 55.000 15.24 0.32 0.00 4.61
4938 7044 0.465705 ATGATCATCGCGAAGGTGGT 59.534 50.000 15.24 2.33 0.00 4.16
4939 7045 1.107945 TGATCATCGCGAAGGTGGTA 58.892 50.000 15.24 0.00 0.00 3.25
4940 7046 1.202371 TGATCATCGCGAAGGTGGTAC 60.202 52.381 15.24 3.36 0.00 3.34
4941 7047 0.821517 ATCATCGCGAAGGTGGTACA 59.178 50.000 15.24 0.00 0.00 2.90
4942 7048 0.604073 TCATCGCGAAGGTGGTACAA 59.396 50.000 15.24 0.00 44.16 2.41
4943 7049 1.206132 TCATCGCGAAGGTGGTACAAT 59.794 47.619 15.24 0.00 44.16 2.71
4944 7050 1.593006 CATCGCGAAGGTGGTACAATC 59.407 52.381 15.24 0.00 44.16 2.67
4945 7051 0.457166 TCGCGAAGGTGGTACAATCG 60.457 55.000 6.20 0.00 44.16 3.34
4947 7053 2.380081 CGAAGGTGGTACAATCGCC 58.620 57.895 0.00 0.00 44.16 5.54
4948 7054 0.390603 CGAAGGTGGTACAATCGCCA 60.391 55.000 0.00 0.00 44.16 5.69
5054 7160 2.283529 ACATGTCCGCCCTCGTCTT 61.284 57.895 0.00 0.00 0.00 3.01
5123 7229 8.567948 CAACTTCATGTATGTTAGAAACCTTGT 58.432 33.333 0.00 0.00 0.00 3.16
5167 7273 3.626930 ACTCGCTCTCTCCTATTCAAGT 58.373 45.455 0.00 0.00 0.00 3.16
5240 7346 1.601419 CTACGGAGGCGAGGTTTCCA 61.601 60.000 0.00 0.00 0.00 3.53
5251 7357 3.559655 GCGAGGTTTCCAAAGCAAATTTT 59.440 39.130 4.19 0.00 38.79 1.82
5344 7450 0.184451 CAAGCATGGCCAGGGACTAT 59.816 55.000 20.75 0.00 36.02 2.12
5392 7498 6.599244 CCTCCTTTTTGTGATAGCTATTGACA 59.401 38.462 7.87 11.05 0.00 3.58
5465 7571 2.367512 AGGGAGAGGGGTCATGGC 60.368 66.667 0.00 0.00 0.00 4.40
5478 7584 2.094659 CATGGCGCGAACGTCTCTT 61.095 57.895 12.10 0.00 46.43 2.85
5511 7617 2.258013 GGCTGTGTTTGTAGCGCCA 61.258 57.895 2.29 0.00 40.78 5.69
5537 7643 0.898320 AGAGATGTGGACAACCTCGG 59.102 55.000 0.00 0.00 37.04 4.63
5650 7757 2.672996 GCCACATCACGCAAGGGT 60.673 61.111 0.00 0.00 45.20 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.674581 TCCTGATTCTTGGCGTGCTG 60.675 55.000 0.00 0.00 0.00 4.41
1 2 0.392193 CTCCTGATTCTTGGCGTGCT 60.392 55.000 0.00 0.00 0.00 4.40
2 3 1.372087 CCTCCTGATTCTTGGCGTGC 61.372 60.000 0.00 0.00 0.00 5.34
3 4 1.372087 GCCTCCTGATTCTTGGCGTG 61.372 60.000 0.00 0.00 33.96 5.34
4 5 1.078143 GCCTCCTGATTCTTGGCGT 60.078 57.895 0.00 0.00 33.96 5.68
5 6 0.465097 ATGCCTCCTGATTCTTGGCG 60.465 55.000 0.00 0.00 45.90 5.69
6 7 2.645838 TATGCCTCCTGATTCTTGGC 57.354 50.000 0.00 0.00 43.49 4.52
7 8 4.637387 AGATATGCCTCCTGATTCTTGG 57.363 45.455 0.00 0.00 0.00 3.61
8 9 7.185318 AGATAGATATGCCTCCTGATTCTTG 57.815 40.000 0.00 0.00 0.00 3.02
9 10 9.146586 GATAGATAGATATGCCTCCTGATTCTT 57.853 37.037 0.00 0.00 0.00 2.52
10 11 8.513658 AGATAGATAGATATGCCTCCTGATTCT 58.486 37.037 0.00 0.00 0.00 2.40
11 12 8.710749 AGATAGATAGATATGCCTCCTGATTC 57.289 38.462 0.00 0.00 0.00 2.52
13 14 9.979897 GATAGATAGATAGATATGCCTCCTGAT 57.020 37.037 0.00 0.00 0.00 2.90
14 15 9.181462 AGATAGATAGATAGATATGCCTCCTGA 57.819 37.037 0.00 0.00 0.00 3.86
123 139 9.221775 GAAGTATATTTAACAGATTTTGCACCG 57.778 33.333 0.00 0.00 0.00 4.94
146 162 3.878778 AGGAAATGATTCGGAGTGGAAG 58.121 45.455 0.00 0.00 36.36 3.46
147 163 4.261801 GAAGGAAATGATTCGGAGTGGAA 58.738 43.478 0.00 0.00 36.36 3.53
151 167 6.240549 ACTATGAAGGAAATGATTCGGAGT 57.759 37.500 0.00 0.00 36.36 3.85
152 168 7.437748 AGTACTATGAAGGAAATGATTCGGAG 58.562 38.462 0.00 0.00 36.36 4.63
164 180 4.079970 CGGATGCCTAGTACTATGAAGGA 58.920 47.826 12.77 0.78 0.00 3.36
165 181 4.079970 TCGGATGCCTAGTACTATGAAGG 58.920 47.826 9.15 7.16 0.00 3.46
166 182 5.650266 AGATCGGATGCCTAGTACTATGAAG 59.350 44.000 9.15 0.00 0.00 3.02
167 183 5.416013 CAGATCGGATGCCTAGTACTATGAA 59.584 44.000 9.15 0.00 0.00 2.57
168 184 4.944317 CAGATCGGATGCCTAGTACTATGA 59.056 45.833 9.15 0.00 0.00 2.15
172 188 1.889829 GCAGATCGGATGCCTAGTACT 59.110 52.381 0.00 0.00 37.73 2.73
175 191 0.678395 CAGCAGATCGGATGCCTAGT 59.322 55.000 0.00 0.00 44.97 2.57
414 452 3.949754 ACGACGGGATAACTACTTGATGA 59.050 43.478 0.00 0.00 0.00 2.92
431 471 1.711060 AAAACCACAGCCACACGACG 61.711 55.000 0.00 0.00 0.00 5.12
501 545 6.595716 ACTGCTTTGTCTATATTGGTGAGTTC 59.404 38.462 0.00 0.00 0.00 3.01
518 562 5.714047 TGACTGAGATGTAGTACTGCTTTG 58.286 41.667 12.42 1.82 0.00 2.77
528 572 5.308825 ACCCAAGTTTTGACTGAGATGTAG 58.691 41.667 0.00 0.00 0.00 2.74
529 573 5.163248 TGACCCAAGTTTTGACTGAGATGTA 60.163 40.000 0.00 0.00 0.00 2.29
530 574 4.137543 GACCCAAGTTTTGACTGAGATGT 58.862 43.478 0.00 0.00 0.00 3.06
531 575 4.136796 TGACCCAAGTTTTGACTGAGATG 58.863 43.478 0.00 0.00 0.00 2.90
565 609 8.046708 AGCAGAGACGTTCAGATAGATAGATAT 58.953 37.037 0.00 0.00 0.00 1.63
566 610 7.390823 AGCAGAGACGTTCAGATAGATAGATA 58.609 38.462 0.00 0.00 0.00 1.98
567 611 6.237901 AGCAGAGACGTTCAGATAGATAGAT 58.762 40.000 0.00 0.00 0.00 1.98
568 612 5.616270 AGCAGAGACGTTCAGATAGATAGA 58.384 41.667 0.00 0.00 0.00 1.98
571 615 4.642437 TGAAGCAGAGACGTTCAGATAGAT 59.358 41.667 0.00 0.00 0.00 1.98
654 699 2.030893 TGTTCTGCTTTGCTGGAAATCG 60.031 45.455 0.00 0.00 0.00 3.34
677 722 0.827507 GGGCAGGTCCATGTGTGTTT 60.828 55.000 0.00 0.00 36.21 2.83
678 723 1.228552 GGGCAGGTCCATGTGTGTT 60.229 57.895 0.00 0.00 36.21 3.32
680 725 1.228521 TTGGGCAGGTCCATGTGTG 60.229 57.895 0.00 0.00 36.58 3.82
681 726 1.228552 GTTGGGCAGGTCCATGTGT 60.229 57.895 0.00 0.00 36.58 3.72
682 727 0.827089 TTGTTGGGCAGGTCCATGTG 60.827 55.000 0.00 0.00 36.58 3.21
715 768 3.430929 GGCGTCTGGATATGGATATGGAC 60.431 52.174 0.00 0.00 0.00 4.02
732 785 0.306840 CACATGCATCAGATGGCGTC 59.693 55.000 12.54 0.00 0.00 5.19
759 812 4.678743 GGGAGGGCCAAAAGGCGT 62.679 66.667 6.18 0.00 43.60 5.68
849 911 2.334838 GAATTTCGGGGTCGATATCGG 58.665 52.381 24.12 8.50 45.51 4.18
855 917 0.179094 CATCGGAATTTCGGGGTCGA 60.179 55.000 6.24 1.42 44.44 4.20
881 943 1.679944 GCATTGAGCTAGTGGCCTTCA 60.680 52.381 3.32 0.00 43.05 3.02
928 990 3.844090 GACTCCGCCTGCCCTCTC 61.844 72.222 0.00 0.00 0.00 3.20
929 991 3.991924 ATGACTCCGCCTGCCCTCT 62.992 63.158 0.00 0.00 0.00 3.69
930 992 3.453070 GATGACTCCGCCTGCCCTC 62.453 68.421 0.00 0.00 0.00 4.30
932 994 4.899239 CGATGACTCCGCCTGCCC 62.899 72.222 0.00 0.00 0.00 5.36
940 1002 2.887568 CAGCACGGCGATGACTCC 60.888 66.667 16.62 0.00 0.00 3.85
1038 1105 8.985866 CAGTCACCGCTAGTTTAGCTGAATGA 62.986 46.154 16.25 8.25 46.17 2.57
1049 1116 0.603569 CCAGTCAGTCACCGCTAGTT 59.396 55.000 0.00 0.00 0.00 2.24
1051 1118 1.153745 GCCAGTCAGTCACCGCTAG 60.154 63.158 0.00 0.00 0.00 3.42
1064 1131 4.731612 CTCGTGCTCGCAGCCAGT 62.732 66.667 2.69 0.00 41.51 4.00
1084 1151 0.899720 TCAACCGGGTTAGGTAGCAG 59.100 55.000 12.95 0.00 45.21 4.24
1134 1201 4.148825 GGAGACCTCATGCGCCGT 62.149 66.667 4.18 0.00 0.00 5.68
1228 1295 7.641249 ACTAACTTGATGTAGGTAGGAGTACT 58.359 38.462 0.00 0.00 39.31 2.73
1255 1324 2.481568 TCTATGGCTCGTCCGTATAACG 59.518 50.000 0.00 0.00 42.11 3.18
1266 1335 2.522836 AGACATTGCTCTATGGCTCG 57.477 50.000 0.00 0.00 39.77 5.03
1271 1340 8.309656 TGGATAGACAATAGACATTGCTCTATG 58.690 37.037 17.46 0.00 44.62 2.23
1274 1343 6.737720 TGGATAGACAATAGACATTGCTCT 57.262 37.500 0.00 3.52 44.62 4.09
1301 1370 4.889856 ATCAGCACGCGCGCCATA 62.890 61.111 32.58 12.61 45.49 2.74
1318 1387 0.607217 CTGCACATCAGCCTCACCAA 60.607 55.000 0.00 0.00 35.78 3.67
1441 1517 1.227853 GCCCACGAAGTTGGTCACT 60.228 57.895 0.00 0.00 46.15 3.41
1565 1641 9.540538 AGTATATAGATTGTGAGGAAGCATAGT 57.459 33.333 0.00 0.00 0.00 2.12
1567 1643 8.972127 GGAGTATATAGATTGTGAGGAAGCATA 58.028 37.037 0.00 0.00 0.00 3.14
1568 1644 7.677745 AGGAGTATATAGATTGTGAGGAAGCAT 59.322 37.037 0.00 0.00 0.00 3.79
1718 1996 0.677288 AACAGTCAATCGGTCGGTCA 59.323 50.000 0.00 0.00 0.00 4.02
1812 2094 0.544120 TTGAATTCAACCTGGCCCCC 60.544 55.000 16.91 0.00 0.00 5.40
1847 2129 6.203808 TGATTATCATATCGTTAGTCCCCG 57.796 41.667 0.00 0.00 0.00 5.73
1848 2130 8.883731 CAAATGATTATCATATCGTTAGTCCCC 58.116 37.037 8.23 0.00 35.76 4.81
1849 2131 9.436957 ACAAATGATTATCATATCGTTAGTCCC 57.563 33.333 8.23 0.00 35.76 4.46
1879 2161 5.923684 AGTTCTAGTCGCTTTTCTTTCAGAG 59.076 40.000 0.00 0.00 0.00 3.35
1896 2178 2.930040 CCATTGGCGTGTGTAGTTCTAG 59.070 50.000 0.00 0.00 0.00 2.43
1899 2181 1.803334 TCCATTGGCGTGTGTAGTTC 58.197 50.000 0.00 0.00 0.00 3.01
1918 2204 6.450545 CCCCAAAACAACAACAAACAAATTT 58.549 32.000 0.00 0.00 0.00 1.82
1937 2223 1.074926 TTTTCAGGCAAGCCCCCAA 60.075 52.632 7.62 0.00 36.58 4.12
1939 2225 1.406860 TTGTTTTCAGGCAAGCCCCC 61.407 55.000 7.62 0.00 36.58 5.40
2021 2327 4.922103 ACGTTGTCTGCTACTAGTAAAAGC 59.078 41.667 8.87 8.87 36.77 3.51
2032 2338 6.073112 GGGTAAATTACAAACGTTGTCTGCTA 60.073 38.462 0.00 0.00 44.12 3.49
2034 2340 4.913345 GGGTAAATTACAAACGTTGTCTGC 59.087 41.667 0.00 0.00 44.12 4.26
2035 2341 6.308371 AGGGTAAATTACAAACGTTGTCTG 57.692 37.500 0.00 0.00 44.12 3.51
2037 2343 8.957028 GTTTTAGGGTAAATTACAAACGTTGTC 58.043 33.333 0.00 0.00 44.12 3.18
2041 2347 6.777091 AGGGTTTTAGGGTAAATTACAAACGT 59.223 34.615 5.45 0.00 0.00 3.99
2043 2349 7.233144 TCCAGGGTTTTAGGGTAAATTACAAAC 59.767 37.037 5.45 6.83 0.00 2.93
2146 2515 7.257722 CAGGCAAAACATACTATTTCCGATTT 58.742 34.615 0.00 0.00 0.00 2.17
2158 2527 8.520351 ACTAGTAAAAATCCAGGCAAAACATAC 58.480 33.333 0.00 0.00 0.00 2.39
2161 2530 6.322712 ACACTAGTAAAAATCCAGGCAAAACA 59.677 34.615 0.00 0.00 0.00 2.83
2162 2531 6.640907 CACACTAGTAAAAATCCAGGCAAAAC 59.359 38.462 0.00 0.00 0.00 2.43
2163 2532 6.322712 ACACACTAGTAAAAATCCAGGCAAAA 59.677 34.615 0.00 0.00 0.00 2.44
2164 2533 5.830991 ACACACTAGTAAAAATCCAGGCAAA 59.169 36.000 0.00 0.00 0.00 3.68
2166 2535 4.980573 ACACACTAGTAAAAATCCAGGCA 58.019 39.130 0.00 0.00 0.00 4.75
2167 2536 5.959618 AACACACTAGTAAAAATCCAGGC 57.040 39.130 0.00 0.00 0.00 4.85
2168 2537 7.712797 ACAAAACACACTAGTAAAAATCCAGG 58.287 34.615 0.00 0.00 0.00 4.45
2169 2538 8.402472 TGACAAAACACACTAGTAAAAATCCAG 58.598 33.333 0.00 0.00 0.00 3.86
2172 2541 9.562583 TGTTGACAAAACACACTAGTAAAAATC 57.437 29.630 0.00 0.00 0.00 2.17
2174 2543 8.024285 CCTGTTGACAAAACACACTAGTAAAAA 58.976 33.333 0.00 0.00 0.00 1.94
2176 2545 6.094325 CCCTGTTGACAAAACACACTAGTAAA 59.906 38.462 0.00 0.00 0.00 2.01
2177 2546 5.587043 CCCTGTTGACAAAACACACTAGTAA 59.413 40.000 0.00 0.00 0.00 2.24
2180 2557 3.243068 GCCCTGTTGACAAAACACACTAG 60.243 47.826 0.00 0.00 0.00 2.57
2185 2562 2.165437 TGAAGCCCTGTTGACAAAACAC 59.835 45.455 0.00 0.00 0.00 3.32
2195 2581 3.838317 TGACAGTAGTATGAAGCCCTGTT 59.162 43.478 0.00 0.00 33.60 3.16
2196 2582 3.441101 TGACAGTAGTATGAAGCCCTGT 58.559 45.455 0.00 0.00 35.97 4.00
2778 3288 2.632987 ACCTAACGGTGCAAACTTCT 57.367 45.000 0.00 0.00 43.51 2.85
2787 3297 1.674817 CCTGCCACTAACCTAACGGTG 60.675 57.143 0.00 0.00 44.73 4.94
2901 3412 7.698506 AATGTGATCAGATCATTTGTCTTGT 57.301 32.000 16.37 0.00 42.04 3.16
2936 3447 8.764558 TCTAATCATAGAGTACTAGCTAGAGGG 58.235 40.741 27.45 1.58 33.17 4.30
2990 3501 6.929049 ACTGACTGAATGATGACGAAACTAAA 59.071 34.615 0.00 0.00 0.00 1.85
3059 3570 6.125029 CCTATCATATGGCCCCAAATTCTAG 58.875 44.000 0.00 0.00 0.00 2.43
3061 3572 4.358006 ACCTATCATATGGCCCCAAATTCT 59.642 41.667 0.00 0.00 0.00 2.40
3062 3573 4.677182 ACCTATCATATGGCCCCAAATTC 58.323 43.478 0.00 0.00 0.00 2.17
3086 3597 9.274065 GCAAGCAAATATGTAAACTACTTGTAC 57.726 33.333 0.00 0.00 35.56 2.90
3087 3598 8.455682 GGCAAGCAAATATGTAAACTACTTGTA 58.544 33.333 0.00 0.00 35.56 2.41
3088 3599 7.312899 GGCAAGCAAATATGTAAACTACTTGT 58.687 34.615 0.00 0.00 35.56 3.16
3140 3653 2.605366 GAGCACATCGTTTCTAGCTTCC 59.395 50.000 0.00 0.00 31.61 3.46
3141 3654 3.516615 AGAGCACATCGTTTCTAGCTTC 58.483 45.455 0.00 0.00 31.61 3.86
3142 3655 3.194542 AGAGAGCACATCGTTTCTAGCTT 59.805 43.478 0.00 0.00 31.61 3.74
3143 3656 2.757868 AGAGAGCACATCGTTTCTAGCT 59.242 45.455 0.00 0.00 34.61 3.32
3144 3657 2.857152 CAGAGAGCACATCGTTTCTAGC 59.143 50.000 0.00 0.00 0.00 3.42
3232 3750 0.881118 ACCAAAACCATAGCTGCACG 59.119 50.000 1.02 0.00 0.00 5.34
3234 3752 1.075374 AGGACCAAAACCATAGCTGCA 59.925 47.619 1.02 0.00 0.00 4.41
3240 3758 3.737559 ATCAGCAGGACCAAAACCATA 57.262 42.857 0.00 0.00 0.00 2.74
3241 3759 2.610438 ATCAGCAGGACCAAAACCAT 57.390 45.000 0.00 0.00 0.00 3.55
3242 3760 3.153919 GTTATCAGCAGGACCAAAACCA 58.846 45.455 0.00 0.00 0.00 3.67
3288 3809 0.110509 CAGCACACGTGATTCAGCAC 60.111 55.000 25.01 1.86 35.46 4.40
3428 4512 8.489559 CAAATGTACATTTCTGTGTCAAAATGG 58.510 33.333 27.12 10.14 43.78 3.16
3451 4535 7.786030 TGACAATAAACAAATGAAGGTCCAAA 58.214 30.769 0.00 0.00 0.00 3.28
3458 4542 8.870160 TCTTGGTTGACAATAAACAAATGAAG 57.130 30.769 0.00 0.00 36.86 3.02
3461 4545 9.689976 TGTATCTTGGTTGACAATAAACAAATG 57.310 29.630 0.00 0.00 36.86 2.32
3462 4546 9.912634 CTGTATCTTGGTTGACAATAAACAAAT 57.087 29.630 0.00 0.00 36.86 2.32
3466 4607 7.326063 GCAACTGTATCTTGGTTGACAATAAAC 59.674 37.037 8.88 0.00 41.71 2.01
3467 4608 7.367285 GCAACTGTATCTTGGTTGACAATAAA 58.633 34.615 8.88 0.00 41.71 1.40
3468 4609 6.348132 CGCAACTGTATCTTGGTTGACAATAA 60.348 38.462 8.88 0.00 41.71 1.40
3469 4610 5.121611 CGCAACTGTATCTTGGTTGACAATA 59.878 40.000 8.88 0.00 41.71 1.90
3470 4611 4.083324 CGCAACTGTATCTTGGTTGACAAT 60.083 41.667 8.88 0.00 41.71 2.71
3471 4612 3.249799 CGCAACTGTATCTTGGTTGACAA 59.750 43.478 8.88 0.00 41.71 3.18
3475 4616 2.095768 CCACGCAACTGTATCTTGGTTG 60.096 50.000 0.00 0.00 41.96 3.77
3502 4646 8.638685 GCAAATAGCAAATCTGATGTAAATGT 57.361 30.769 0.00 0.00 44.79 2.71
3542 4873 8.671384 TTTTTACTAGCATGTCACTACAAGTT 57.329 30.769 0.00 0.00 39.58 2.66
3564 4964 4.978083 CAGGACTCTGCAGCATATTTTT 57.022 40.909 9.47 0.00 33.86 1.94
3578 4978 2.550830 TCAAGGAAACAGCAGGACTC 57.449 50.000 0.00 0.00 0.00 3.36
3579 4979 3.117888 TCTTTCAAGGAAACAGCAGGACT 60.118 43.478 0.00 0.00 0.00 3.85
3580 4980 3.214328 TCTTTCAAGGAAACAGCAGGAC 58.786 45.455 0.00 0.00 0.00 3.85
3581 4981 3.576078 TCTTTCAAGGAAACAGCAGGA 57.424 42.857 0.00 0.00 0.00 3.86
3585 4985 7.595311 TTTTTCTTTCTTTCAAGGAAACAGC 57.405 32.000 0.00 0.00 31.97 4.40
3611 5346 1.003545 CAGTTCGCACCAACTTGTCAG 60.004 52.381 0.00 0.00 34.17 3.51
3612 5347 1.013596 CAGTTCGCACCAACTTGTCA 58.986 50.000 0.00 0.00 34.17 3.58
3613 5348 0.317020 GCAGTTCGCACCAACTTGTC 60.317 55.000 0.00 0.00 41.79 3.18
3614 5349 0.748005 AGCAGTTCGCACCAACTTGT 60.748 50.000 0.00 0.00 46.13 3.16
3615 5350 1.225855 TAGCAGTTCGCACCAACTTG 58.774 50.000 0.00 0.00 46.13 3.16
3622 5359 2.095768 TGCAGAATTTAGCAGTTCGCAC 60.096 45.455 2.07 0.00 46.13 5.34
3657 5437 1.905215 CTGCTTCCTCTTGGAGAAGGA 59.095 52.381 0.00 0.00 44.24 3.36
3663 5443 0.979665 CAGACCTGCTTCCTCTTGGA 59.020 55.000 0.00 0.00 41.36 3.53
3677 5457 0.181350 CAGGATTGGTAGGGCAGACC 59.819 60.000 0.27 0.27 40.67 3.85
3847 5645 2.069273 CCTTGTCTAAGAACCTGCGTG 58.931 52.381 0.00 0.00 35.92 5.34
3860 5945 2.356313 CTGACGCACGCCTTGTCT 60.356 61.111 0.00 0.00 33.81 3.41
4154 6245 1.986575 GCTTCATGAAGGGCACGAGC 61.987 60.000 31.41 15.47 38.80 5.03
4548 6648 1.456287 GGTCCAGCCTGTCCTTGTT 59.544 57.895 0.00 0.00 0.00 2.83
4670 6770 0.107606 CCTCTGCTGCAATCTGAGCT 60.108 55.000 3.02 0.00 36.11 4.09
4773 6876 3.525199 AGCACTTCTTTCCCCATCACTAT 59.475 43.478 0.00 0.00 0.00 2.12
4916 7022 0.882042 ACCTTCGCGATGATCATGGC 60.882 55.000 27.34 27.34 38.86 4.40
4918 7024 0.863799 CCACCTTCGCGATGATCATG 59.136 55.000 22.25 13.82 0.00 3.07
4919 7025 0.465705 ACCACCTTCGCGATGATCAT 59.534 50.000 22.25 8.25 0.00 2.45
4920 7026 1.107945 TACCACCTTCGCGATGATCA 58.892 50.000 22.25 0.00 0.00 2.92
4921 7027 1.202371 TGTACCACCTTCGCGATGATC 60.202 52.381 22.25 6.86 0.00 2.92
4922 7028 0.821517 TGTACCACCTTCGCGATGAT 59.178 50.000 22.25 2.80 0.00 2.45
4923 7029 0.604073 TTGTACCACCTTCGCGATGA 59.396 50.000 22.25 1.48 0.00 2.92
4924 7030 1.593006 GATTGTACCACCTTCGCGATG 59.407 52.381 10.88 13.11 0.00 3.84
4925 7031 1.801395 CGATTGTACCACCTTCGCGAT 60.801 52.381 10.88 0.00 0.00 4.58
4926 7032 0.457166 CGATTGTACCACCTTCGCGA 60.457 55.000 3.71 3.71 0.00 5.87
4927 7033 1.995991 CGATTGTACCACCTTCGCG 59.004 57.895 0.00 0.00 0.00 5.87
4928 7034 1.713830 GCGATTGTACCACCTTCGC 59.286 57.895 0.00 0.00 46.70 4.70
4929 7035 0.390603 TGGCGATTGTACCACCTTCG 60.391 55.000 0.00 0.00 0.00 3.79
4930 7036 1.737793 CTTGGCGATTGTACCACCTTC 59.262 52.381 0.00 0.00 35.10 3.46
4931 7037 1.349688 TCTTGGCGATTGTACCACCTT 59.650 47.619 0.00 0.00 35.10 3.50
4932 7038 0.981183 TCTTGGCGATTGTACCACCT 59.019 50.000 0.00 0.00 35.10 4.00
4933 7039 1.369625 CTCTTGGCGATTGTACCACC 58.630 55.000 0.00 0.00 35.10 4.61
4934 7040 0.727398 GCTCTTGGCGATTGTACCAC 59.273 55.000 0.00 0.00 35.10 4.16
4935 7041 0.323302 TGCTCTTGGCGATTGTACCA 59.677 50.000 0.00 0.00 45.43 3.25
4936 7042 1.599542 GATGCTCTTGGCGATTGTACC 59.400 52.381 0.00 0.00 45.43 3.34
4937 7043 1.258982 CGATGCTCTTGGCGATTGTAC 59.741 52.381 0.00 0.00 45.43 2.90
4938 7044 1.134818 ACGATGCTCTTGGCGATTGTA 60.135 47.619 0.00 0.00 45.43 2.41
4939 7045 0.391661 ACGATGCTCTTGGCGATTGT 60.392 50.000 0.00 0.00 45.43 2.71
4940 7046 0.302890 GACGATGCTCTTGGCGATTG 59.697 55.000 0.00 0.00 45.43 2.67
4941 7047 1.148157 CGACGATGCTCTTGGCGATT 61.148 55.000 0.00 0.00 43.03 3.34
4942 7048 1.589993 CGACGATGCTCTTGGCGAT 60.590 57.895 0.00 0.00 43.03 4.58
4943 7049 2.202610 CGACGATGCTCTTGGCGA 60.203 61.111 0.00 0.00 43.03 5.54
4944 7050 2.202610 TCGACGATGCTCTTGGCG 60.203 61.111 0.00 0.00 45.43 5.69
4945 7051 0.737715 AAGTCGACGATGCTCTTGGC 60.738 55.000 10.46 0.00 42.22 4.52
4946 7052 1.714794 AAAGTCGACGATGCTCTTGG 58.285 50.000 10.46 0.00 0.00 3.61
4947 7053 2.854777 CCTAAAGTCGACGATGCTCTTG 59.145 50.000 10.46 0.00 0.00 3.02
4948 7054 2.735762 GCCTAAAGTCGACGATGCTCTT 60.736 50.000 10.46 0.00 0.00 2.85
4980 7086 2.636647 TCTTGGCGATTGCATGGATA 57.363 45.000 7.38 0.00 45.35 2.59
5089 7195 4.245660 ACATACATGAAGTTGTCGTGGAG 58.754 43.478 0.00 0.00 46.12 3.86
5167 7273 0.611618 AATGCCTTGCGGATGTCCAA 60.612 50.000 0.00 0.00 35.14 3.53
5240 7346 5.467735 GCAATCCACTCTCAAAATTTGCTTT 59.532 36.000 0.00 0.00 0.00 3.51
5251 7357 1.219124 GAGCCGCAATCCACTCTCA 59.781 57.895 0.00 0.00 0.00 3.27
5392 7498 5.475719 CACATCAAGGATTTGCTTCAATGT 58.524 37.500 4.50 4.50 34.21 2.71
5434 7540 0.905357 CTCCCTCGGACCTTGTGAAT 59.095 55.000 0.00 0.00 0.00 2.57
5472 7578 2.156504 CGCATCATCCGCATAAAGAGAC 59.843 50.000 0.00 0.00 0.00 3.36
5478 7584 1.071299 AGCCGCATCATCCGCATAA 59.929 52.632 0.00 0.00 0.00 1.90
5511 7617 5.388654 AGGTTGTCCACATCTCTTTTGATT 58.611 37.500 0.00 0.00 35.89 2.57
5537 7643 1.250840 AAAACCTCGCAGAATGGCCC 61.251 55.000 0.00 0.00 35.86 5.80
5650 7757 0.324943 GAAGCCCTGACAGCCAGTAA 59.675 55.000 0.00 0.00 41.33 2.24


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

AutoCloner maintained by Alex Coulton.