Multiple sequence alignment - TraesCS4D01G201400

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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 TraesCS4D01G201400 chr4D 100.000 4666 0 0 1 4666 348314298 348309633 0.000000e+00 8617.0
1 TraesCS4D01G201400 chr4D 100.000 31 0 0 1362 1392 485141359 485141389 1.810000e-04 58.4
2 TraesCS4D01G201400 chr4A 95.553 2923 95 17 1392 4295 117277900 117280806 0.000000e+00 4645.0
3 TraesCS4D01G201400 chr4A 96.117 515 15 3 793 1302 117277371 117277885 0.000000e+00 835.0
4 TraesCS4D01G201400 chr4B 93.794 1708 63 16 2614 4306 428468207 428466528 0.000000e+00 2527.0
5 TraesCS4D01G201400 chr4B 94.955 1229 47 8 1392 2613 428469466 428468246 0.000000e+00 1912.0
6 TraesCS4D01G201400 chr4B 92.578 741 52 3 3 742 204727136 204727874 0.000000e+00 1061.0
7 TraesCS4D01G201400 chr4B 89.233 743 74 5 3 742 23376514 23375775 0.000000e+00 924.0
8 TraesCS4D01G201400 chr4B 96.086 511 17 2 794 1302 428469990 428469481 0.000000e+00 830.0
9 TraesCS4D01G201400 chr4B 100.000 58 0 0 1300 1357 499912843 499912900 1.780000e-19 108.0
10 TraesCS4D01G201400 chr4B 100.000 58 0 0 1300 1357 525327662 525327719 1.780000e-19 108.0
11 TraesCS4D01G201400 chr4B 100.000 57 0 0 1300 1356 665242047 665242103 6.390000e-19 106.0
12 TraesCS4D01G201400 chr4B 97.222 36 1 0 4305 4340 428466514 428466479 1.400000e-05 62.1
13 TraesCS4D01G201400 chr4B 100.000 31 0 0 1362 1392 253155381 253155411 1.810000e-04 58.4
14 TraesCS4D01G201400 chr6A 91.240 742 62 3 3 742 180593682 180594422 0.000000e+00 1007.0
15 TraesCS4D01G201400 chr5D 88.022 743 87 2 1 742 309782699 309781958 0.000000e+00 878.0
16 TraesCS4D01G201400 chr5D 97.576 330 5 3 4339 4666 213081992 213081664 3.150000e-156 562.0
17 TraesCS4D01G201400 chr5D 96.689 302 8 2 4336 4635 563590334 563590635 6.970000e-138 501.0
18 TraesCS4D01G201400 chr5D 100.000 33 0 0 4634 4666 563590607 563590639 1.400000e-05 62.1
19 TraesCS4D01G201400 chr7B 87.114 745 90 6 1 742 125895391 125894650 0.000000e+00 839.0
20 TraesCS4D01G201400 chr7B 85.734 743 96 9 4 742 587454095 587453359 0.000000e+00 776.0
21 TraesCS4D01G201400 chr7B 85.135 740 108 2 4 742 587237795 587237057 0.000000e+00 756.0
22 TraesCS4D01G201400 chr7B 84.367 742 112 4 4 743 587081271 587080532 0.000000e+00 725.0
23 TraesCS4D01G201400 chr7B 100.000 60 0 0 1300 1359 561852142 561852201 1.370000e-20 111.0
24 TraesCS4D01G201400 chr7B 100.000 58 0 0 1300 1357 453627430 453627373 1.780000e-19 108.0
25 TraesCS4D01G201400 chr7B 100.000 31 0 0 1362 1392 561852039 561852069 1.810000e-04 58.4
26 TraesCS4D01G201400 chrUn 85.101 745 105 6 1 742 38689110 38689851 0.000000e+00 756.0
27 TraesCS4D01G201400 chr2D 98.480 329 4 1 4339 4666 33943006 33943334 3.130000e-161 579.0
28 TraesCS4D01G201400 chr2D 98.413 63 0 1 1300 1362 247111341 247111280 4.940000e-20 110.0
29 TraesCS4D01G201400 chr7D 97.885 331 5 2 4338 4666 276479354 276479024 5.240000e-159 571.0
30 TraesCS4D01G201400 chr7D 94.848 330 7 4 4339 4666 293594436 293594115 1.500000e-139 507.0
31 TraesCS4D01G201400 chr7D 96.441 281 6 4 4339 4617 52630124 52629846 1.180000e-125 460.0
32 TraesCS4D01G201400 chr7D 94.932 296 5 4 4339 4632 293595401 293595114 5.500000e-124 455.0
33 TraesCS4D01G201400 chr7D 98.333 60 1 0 1300 1359 550461541 550461482 6.390000e-19 106.0
34 TraesCS4D01G201400 chr7D 100.000 30 0 0 1363 1392 601441529 601441500 6.520000e-04 56.5
35 TraesCS4D01G201400 chr6D 97.872 329 6 1 4339 4666 263957073 263957401 6.780000e-158 568.0
36 TraesCS4D01G201400 chr1A 94.098 305 11 2 4338 4635 47822404 47822100 1.530000e-124 457.0
37 TraesCS4D01G201400 chr5B 96.825 63 2 0 1300 1362 288167772 288167710 6.390000e-19 106.0
38 TraesCS4D01G201400 chr1D 100.000 57 0 0 1300 1356 49359071 49359127 6.390000e-19 106.0
39 TraesCS4D01G201400 chr6B 89.796 49 1 4 1362 1409 123933561 123933516 5.040000e-05 60.2
40 TraesCS4D01G201400 chr6B 100.000 31 0 0 1362 1392 690433886 690433856 1.810000e-04 58.4
41 TraesCS4D01G201400 chr3B 100.000 31 0 0 1362 1392 58703341 58703371 1.810000e-04 58.4
42 TraesCS4D01G201400 chr3B 100.000 31 0 0 1362 1392 58720855 58720885 1.810000e-04 58.4
43 TraesCS4D01G201400 chr3B 100.000 31 0 0 1362 1392 712102040 712102010 1.810000e-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 TraesCS4D01G201400 chr4D 348309633 348314298 4665 True 8617.000 8617 100.00000 1 4666 1 chr4D.!!$R1 4665
1 TraesCS4D01G201400 chr4A 117277371 117280806 3435 False 2740.000 4645 95.83500 793 4295 2 chr4A.!!$F1 3502
2 TraesCS4D01G201400 chr4B 428466479 428469990 3511 True 1332.775 2527 95.51425 794 4340 4 chr4B.!!$R2 3546
3 TraesCS4D01G201400 chr4B 204727136 204727874 738 False 1061.000 1061 92.57800 3 742 1 chr4B.!!$F1 739
4 TraesCS4D01G201400 chr4B 23375775 23376514 739 True 924.000 924 89.23300 3 742 1 chr4B.!!$R1 739
5 TraesCS4D01G201400 chr6A 180593682 180594422 740 False 1007.000 1007 91.24000 3 742 1 chr6A.!!$F1 739
6 TraesCS4D01G201400 chr5D 309781958 309782699 741 True 878.000 878 88.02200 1 742 1 chr5D.!!$R2 741
7 TraesCS4D01G201400 chr7B 125894650 125895391 741 True 839.000 839 87.11400 1 742 1 chr7B.!!$R1 741
8 TraesCS4D01G201400 chr7B 587453359 587454095 736 True 776.000 776 85.73400 4 742 1 chr7B.!!$R5 738
9 TraesCS4D01G201400 chr7B 587237057 587237795 738 True 756.000 756 85.13500 4 742 1 chr7B.!!$R4 738
10 TraesCS4D01G201400 chr7B 587080532 587081271 739 True 725.000 725 84.36700 4 743 1 chr7B.!!$R3 739
11 TraesCS4D01G201400 chrUn 38689110 38689851 741 False 756.000 756 85.10100 1 742 1 chrUn.!!$F1 741
12 TraesCS4D01G201400 chr7D 293594115 293595401 1286 True 481.000 507 94.89000 4339 4666 2 chr7D.!!$R5 327

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
779 783 0.102481 ACTAACTATGTCGCCAGCGG 59.898 55.000 12.71 0.0 40.25 5.52 F
1307 1316 0.035056 AGGAGTGGCGGAATCAAAGG 60.035 55.000 0.00 0.0 0.00 3.11 F
1359 1368 0.108585 AATCATCCAATCCCCCGACG 59.891 55.000 0.00 0.0 0.00 5.12 F
1373 1382 0.108992 CCGACGGACGAGAAATTGGA 60.109 55.000 8.64 0.0 45.77 3.53 F
2341 2356 0.398696 TTTATCCCATGGGCGCGTAT 59.601 50.000 27.41 16.2 34.68 3.06 F
3023 3077 1.153349 GCTTGAGAGGGTAAGGCGG 60.153 63.158 0.00 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 1906 1.142870 TGGGAAGGACCACTCAGTTTG 59.857 52.381 0.00 0.0 41.20 2.93 R
2167 2182 2.158755 GGTATGGCCTGTTGCAGTAGAT 60.159 50.000 3.32 0.0 43.89 1.98 R
2822 2876 5.047872 ACAGAGCAATTAAACATGACATGCA 60.048 36.000 15.49 0.0 34.89 3.96 R
3196 3253 5.417754 TTGCATTTCTTGGGATTTGCATA 57.582 34.783 0.00 0.0 38.54 3.14 R
3578 3643 0.037326 TGGTTGCATCAGTCCTCGAC 60.037 55.000 0.00 0.0 0.00 4.20 R
4035 4105 0.407528 TTCCCTAGCCCAACAATGCA 59.592 50.000 0.00 0.0 0.00 3.96 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
253 254 1.968017 CCAGAGAAAGCTGCGGCAA 60.968 57.895 21.93 0.00 41.70 4.52
373 374 1.742761 CACTCCGTGGCATCTTTGAT 58.257 50.000 0.00 0.00 0.00 2.57
472 474 1.099689 GCGGCAAGCCAAGGTATTTA 58.900 50.000 12.19 0.00 40.81 1.40
519 521 3.010138 CCAGAAATCCTTTCCACCCTGTA 59.990 47.826 0.00 0.00 40.54 2.74
597 600 0.404040 AACCCGATGCCTCTCCAAAA 59.596 50.000 0.00 0.00 0.00 2.44
610 613 5.256474 CCTCTCCAAAAAGATTTAGGAGCA 58.744 41.667 16.27 8.77 40.21 4.26
743 747 2.755876 TCTCGGTCGCCAGCTCAT 60.756 61.111 0.00 0.00 0.00 2.90
744 748 2.185350 CTCGGTCGCCAGCTCATT 59.815 61.111 0.00 0.00 0.00 2.57
745 749 1.448540 CTCGGTCGCCAGCTCATTT 60.449 57.895 0.00 0.00 0.00 2.32
746 750 0.179111 CTCGGTCGCCAGCTCATTTA 60.179 55.000 0.00 0.00 0.00 1.40
747 751 0.179111 TCGGTCGCCAGCTCATTTAG 60.179 55.000 0.00 0.00 0.00 1.85
748 752 0.179111 CGGTCGCCAGCTCATTTAGA 60.179 55.000 0.00 0.00 0.00 2.10
749 753 1.539065 CGGTCGCCAGCTCATTTAGAT 60.539 52.381 0.00 0.00 0.00 1.98
750 754 2.288213 CGGTCGCCAGCTCATTTAGATA 60.288 50.000 0.00 0.00 0.00 1.98
751 755 3.321497 GGTCGCCAGCTCATTTAGATAG 58.679 50.000 0.00 0.00 0.00 2.08
752 756 2.734079 GTCGCCAGCTCATTTAGATAGC 59.266 50.000 0.00 0.00 36.48 2.97
758 762 2.039613 AGCTCATTTAGATAGCTGGGGC 59.960 50.000 0.00 0.00 44.67 5.80
759 763 2.877708 GCTCATTTAGATAGCTGGGGCC 60.878 54.545 0.00 0.00 39.73 5.80
760 764 2.373169 CTCATTTAGATAGCTGGGGCCA 59.627 50.000 4.39 0.00 39.73 5.36
761 765 2.106511 TCATTTAGATAGCTGGGGCCAC 59.893 50.000 4.39 0.00 39.73 5.01
762 766 1.893315 TTTAGATAGCTGGGGCCACT 58.107 50.000 6.53 1.42 39.73 4.00
763 767 2.787339 TTAGATAGCTGGGGCCACTA 57.213 50.000 6.53 4.05 39.73 2.74
764 768 2.787339 TAGATAGCTGGGGCCACTAA 57.213 50.000 6.53 0.00 39.73 2.24
765 769 1.132500 AGATAGCTGGGGCCACTAAC 58.868 55.000 6.53 2.75 39.73 2.34
766 770 1.132500 GATAGCTGGGGCCACTAACT 58.868 55.000 6.53 2.99 39.73 2.24
767 771 2.090719 AGATAGCTGGGGCCACTAACTA 60.091 50.000 6.53 5.53 39.73 2.24
768 772 2.489528 TAGCTGGGGCCACTAACTAT 57.510 50.000 6.53 0.00 39.73 2.12
769 773 0.839946 AGCTGGGGCCACTAACTATG 59.160 55.000 6.53 0.00 39.73 2.23
770 774 0.546598 GCTGGGGCCACTAACTATGT 59.453 55.000 6.53 0.00 0.00 2.29
771 775 1.475213 GCTGGGGCCACTAACTATGTC 60.475 57.143 6.53 0.00 0.00 3.06
772 776 0.828022 TGGGGCCACTAACTATGTCG 59.172 55.000 6.53 0.00 0.00 4.35
773 777 0.532196 GGGGCCACTAACTATGTCGC 60.532 60.000 4.39 0.00 0.00 5.19
774 778 0.532196 GGGCCACTAACTATGTCGCC 60.532 60.000 4.39 0.00 40.23 5.54
775 779 0.177141 GGCCACTAACTATGTCGCCA 59.823 55.000 0.00 0.00 40.57 5.69
776 780 1.571919 GCCACTAACTATGTCGCCAG 58.428 55.000 0.00 0.00 0.00 4.85
777 781 1.571919 CCACTAACTATGTCGCCAGC 58.428 55.000 0.00 0.00 0.00 4.85
778 782 1.200483 CACTAACTATGTCGCCAGCG 58.800 55.000 5.50 5.50 41.35 5.18
779 783 0.102481 ACTAACTATGTCGCCAGCGG 59.898 55.000 12.71 0.00 40.25 5.52
780 784 0.102481 CTAACTATGTCGCCAGCGGT 59.898 55.000 12.71 0.00 40.25 5.68
781 785 0.179121 TAACTATGTCGCCAGCGGTG 60.179 55.000 12.71 7.86 40.25 4.94
782 786 3.264897 CTATGTCGCCAGCGGTGC 61.265 66.667 12.71 3.97 40.25 5.01
783 787 4.830765 TATGTCGCCAGCGGTGCC 62.831 66.667 12.71 0.00 40.25 5.01
788 792 4.705519 CGCCAGCGGTGCCAAAAG 62.706 66.667 9.63 0.00 35.56 2.27
900 907 1.564207 GGTAAGCCCGTGATACGTTC 58.436 55.000 0.00 0.00 40.58 3.95
927 934 2.881403 GCATGTCAGTGAAACCCATCCT 60.881 50.000 0.00 0.00 37.80 3.24
929 936 1.774254 TGTCAGTGAAACCCATCCTGT 59.226 47.619 0.00 0.00 37.80 4.00
930 937 2.224523 TGTCAGTGAAACCCATCCTGTC 60.225 50.000 0.00 0.00 37.80 3.51
931 938 1.351017 TCAGTGAAACCCATCCTGTCC 59.649 52.381 0.00 0.00 37.80 4.02
932 939 1.352352 CAGTGAAACCCATCCTGTCCT 59.648 52.381 0.00 0.00 37.80 3.85
1081 1090 2.012673 GCTCGATCTCAGTGGCATTTT 58.987 47.619 0.00 0.00 0.00 1.82
1142 1151 2.423898 CCGTAGCGGGATCACAGGT 61.424 63.158 0.00 0.00 44.15 4.00
1302 1311 2.981859 TTAGAAGGAGTGGCGGAATC 57.018 50.000 0.00 0.00 0.00 2.52
1303 1312 1.860641 TAGAAGGAGTGGCGGAATCA 58.139 50.000 0.00 0.00 0.00 2.57
1305 1314 1.351017 AGAAGGAGTGGCGGAATCAAA 59.649 47.619 0.00 0.00 0.00 2.69
1307 1316 0.035056 AGGAGTGGCGGAATCAAAGG 60.035 55.000 0.00 0.00 0.00 3.11
1308 1317 1.032114 GGAGTGGCGGAATCAAAGGG 61.032 60.000 0.00 0.00 0.00 3.95
1309 1318 1.657751 GAGTGGCGGAATCAAAGGGC 61.658 60.000 0.00 0.00 0.00 5.19
1311 1320 1.228706 TGGCGGAATCAAAGGGCAA 60.229 52.632 0.00 0.00 31.59 4.52
1312 1321 0.829602 TGGCGGAATCAAAGGGCAAA 60.830 50.000 0.00 0.00 31.59 3.68
1314 1323 1.471501 GGCGGAATCAAAGGGCAAATC 60.472 52.381 0.00 0.00 0.00 2.17
1315 1324 1.204467 GCGGAATCAAAGGGCAAATCA 59.796 47.619 0.00 0.00 0.00 2.57
1316 1325 2.159057 GCGGAATCAAAGGGCAAATCAT 60.159 45.455 0.00 0.00 0.00 2.45
1317 1326 3.709987 CGGAATCAAAGGGCAAATCATC 58.290 45.455 0.00 0.00 0.00 2.92
1318 1327 3.491447 CGGAATCAAAGGGCAAATCATCC 60.491 47.826 0.00 0.00 0.00 3.51
1319 1328 3.451902 GGAATCAAAGGGCAAATCATCCA 59.548 43.478 0.00 0.00 0.00 3.41
1320 1329 4.080975 GGAATCAAAGGGCAAATCATCCAA 60.081 41.667 0.00 0.00 0.00 3.53
1321 1330 3.959535 TCAAAGGGCAAATCATCCAAC 57.040 42.857 0.00 0.00 0.00 3.77
1322 1331 2.566724 TCAAAGGGCAAATCATCCAACC 59.433 45.455 0.00 0.00 0.00 3.77
1323 1332 1.571955 AAGGGCAAATCATCCAACCC 58.428 50.000 0.00 0.00 37.63 4.11
1324 1333 0.325577 AGGGCAAATCATCCAACCCC 60.326 55.000 0.00 0.00 38.14 4.95
1325 1334 0.325577 GGGCAAATCATCCAACCCCT 60.326 55.000 0.00 0.00 0.00 4.79
1326 1335 1.571955 GGCAAATCATCCAACCCCTT 58.428 50.000 0.00 0.00 0.00 3.95
1327 1336 1.207811 GGCAAATCATCCAACCCCTTG 59.792 52.381 0.00 0.00 0.00 3.61
1328 1337 1.901833 GCAAATCATCCAACCCCTTGT 59.098 47.619 0.00 0.00 0.00 3.16
1329 1338 3.096092 GCAAATCATCCAACCCCTTGTA 58.904 45.455 0.00 0.00 0.00 2.41
1330 1339 3.513515 GCAAATCATCCAACCCCTTGTAA 59.486 43.478 0.00 0.00 0.00 2.41
1331 1340 4.020662 GCAAATCATCCAACCCCTTGTAAA 60.021 41.667 0.00 0.00 0.00 2.01
1332 1341 5.723295 CAAATCATCCAACCCCTTGTAAAG 58.277 41.667 0.00 0.00 45.69 1.85
1333 1342 4.675063 ATCATCCAACCCCTTGTAAAGT 57.325 40.909 0.00 0.00 44.25 2.66
1334 1343 3.761897 TCATCCAACCCCTTGTAAAGTG 58.238 45.455 0.00 0.00 44.25 3.16
1336 1345 1.146152 TCCAACCCCTTGTAAAGTGGG 59.854 52.381 10.35 10.35 46.66 4.61
1340 1349 3.448469 CCCTTGTAAAGTGGGGCAA 57.552 52.632 0.00 0.00 44.25 4.52
1341 1350 1.710816 CCCTTGTAAAGTGGGGCAAA 58.289 50.000 0.00 0.00 44.25 3.68
1342 1351 2.256306 CCCTTGTAAAGTGGGGCAAAT 58.744 47.619 0.00 0.00 44.25 2.32
1343 1352 2.233676 CCCTTGTAAAGTGGGGCAAATC 59.766 50.000 0.00 0.00 44.25 2.17
1344 1353 2.896685 CCTTGTAAAGTGGGGCAAATCA 59.103 45.455 0.00 0.00 44.25 2.57
1345 1354 3.515104 CCTTGTAAAGTGGGGCAAATCAT 59.485 43.478 0.00 0.00 44.25 2.45
1346 1355 4.381932 CCTTGTAAAGTGGGGCAAATCATC 60.382 45.833 0.00 0.00 44.25 2.92
1347 1356 3.096092 TGTAAAGTGGGGCAAATCATCC 58.904 45.455 0.00 0.00 0.00 3.51
1348 1357 2.323999 AAAGTGGGGCAAATCATCCA 57.676 45.000 0.00 0.00 0.00 3.41
1349 1358 2.323999 AAGTGGGGCAAATCATCCAA 57.676 45.000 0.00 0.00 0.00 3.53
1350 1359 2.555732 AGTGGGGCAAATCATCCAAT 57.444 45.000 0.00 0.00 0.00 3.16
1351 1360 2.391678 AGTGGGGCAAATCATCCAATC 58.608 47.619 0.00 0.00 0.00 2.67
1352 1361 1.413812 GTGGGGCAAATCATCCAATCC 59.586 52.381 0.00 0.00 0.00 3.01
1353 1362 1.051008 GGGGCAAATCATCCAATCCC 58.949 55.000 0.00 0.00 0.00 3.85
1354 1363 1.051008 GGGCAAATCATCCAATCCCC 58.949 55.000 0.00 0.00 0.00 4.81
1355 1364 1.051008 GGCAAATCATCCAATCCCCC 58.949 55.000 0.00 0.00 0.00 5.40
1356 1365 0.675633 GCAAATCATCCAATCCCCCG 59.324 55.000 0.00 0.00 0.00 5.73
1357 1366 1.753847 GCAAATCATCCAATCCCCCGA 60.754 52.381 0.00 0.00 0.00 5.14
1358 1367 1.956477 CAAATCATCCAATCCCCCGAC 59.044 52.381 0.00 0.00 0.00 4.79
1359 1368 0.108585 AATCATCCAATCCCCCGACG 59.891 55.000 0.00 0.00 0.00 5.12
1360 1369 1.768684 ATCATCCAATCCCCCGACGG 61.769 60.000 6.99 6.99 0.00 4.79
1361 1370 2.041301 ATCCAATCCCCCGACGGA 60.041 61.111 17.49 0.00 36.02 4.69
1362 1371 2.440817 ATCCAATCCCCCGACGGAC 61.441 63.158 17.49 0.00 33.77 4.79
1363 1372 4.524318 CCAATCCCCCGACGGACG 62.524 72.222 17.49 4.48 42.18 4.79
1364 1373 3.454573 CAATCCCCCGACGGACGA 61.455 66.667 17.49 10.49 45.77 4.20
1365 1374 3.145551 AATCCCCCGACGGACGAG 61.146 66.667 17.49 0.00 45.77 4.18
1366 1375 3.650298 AATCCCCCGACGGACGAGA 62.650 63.158 17.49 6.52 45.77 4.04
1367 1376 3.650298 ATCCCCCGACGGACGAGAA 62.650 63.158 17.49 0.00 45.77 2.87
1368 1377 3.376078 CCCCCGACGGACGAGAAA 61.376 66.667 17.49 0.00 45.77 2.52
1369 1378 2.718073 CCCCCGACGGACGAGAAAT 61.718 63.158 17.49 0.00 45.77 2.17
1370 1379 1.217244 CCCCGACGGACGAGAAATT 59.783 57.895 17.49 0.00 45.77 1.82
1371 1380 1.082117 CCCCGACGGACGAGAAATTG 61.082 60.000 17.49 0.00 45.77 2.32
1372 1381 1.082117 CCCGACGGACGAGAAATTGG 61.082 60.000 17.49 0.00 45.77 3.16
1373 1382 0.108992 CCGACGGACGAGAAATTGGA 60.109 55.000 8.64 0.00 45.77 3.53
1374 1383 1.470979 CCGACGGACGAGAAATTGGAT 60.471 52.381 8.64 0.00 45.77 3.41
1375 1384 1.852895 CGACGGACGAGAAATTGGATC 59.147 52.381 0.00 0.00 45.77 3.36
1376 1385 2.479730 CGACGGACGAGAAATTGGATCT 60.480 50.000 0.00 0.00 45.77 2.75
1377 1386 3.522553 GACGGACGAGAAATTGGATCTT 58.477 45.455 0.00 0.00 0.00 2.40
1378 1387 3.933332 GACGGACGAGAAATTGGATCTTT 59.067 43.478 0.00 0.00 0.00 2.52
1379 1388 4.324267 ACGGACGAGAAATTGGATCTTTT 58.676 39.130 0.00 0.00 0.00 2.27
1380 1389 4.154195 ACGGACGAGAAATTGGATCTTTTG 59.846 41.667 0.00 0.00 0.00 2.44
1381 1390 4.415735 GGACGAGAAATTGGATCTTTTGC 58.584 43.478 0.00 0.00 0.00 3.68
1382 1391 4.415735 GACGAGAAATTGGATCTTTTGCC 58.584 43.478 0.00 0.00 0.00 4.52
1383 1392 3.193479 ACGAGAAATTGGATCTTTTGCCC 59.807 43.478 0.00 0.00 0.00 5.36
1384 1393 3.429410 CGAGAAATTGGATCTTTTGCCCC 60.429 47.826 0.00 0.00 0.00 5.80
1385 1394 3.515104 GAGAAATTGGATCTTTTGCCCCA 59.485 43.478 0.00 0.00 0.00 4.96
1386 1395 3.261643 AGAAATTGGATCTTTTGCCCCAC 59.738 43.478 0.00 0.00 0.00 4.61
1387 1396 2.629017 ATTGGATCTTTTGCCCCACT 57.371 45.000 0.00 0.00 0.00 4.00
1388 1397 2.397044 TTGGATCTTTTGCCCCACTT 57.603 45.000 0.00 0.00 0.00 3.16
1389 1398 2.397044 TGGATCTTTTGCCCCACTTT 57.603 45.000 0.00 0.00 0.00 2.66
1390 1399 3.534357 TGGATCTTTTGCCCCACTTTA 57.466 42.857 0.00 0.00 0.00 1.85
1468 1477 1.432514 TCTGTTGCGAGCATCTGAAC 58.567 50.000 11.51 2.45 0.00 3.18
1786 1798 5.670485 TGTATGTGACTTTCGAGGCATTAT 58.330 37.500 0.00 0.00 0.00 1.28
1824 1837 6.426328 TCTTGTTTCTGCTGAAGAGAAGATTC 59.574 38.462 16.19 0.00 33.43 2.52
1893 1906 9.241317 CATTTGCCTTTCTCATGTACATTATTC 57.759 33.333 5.37 0.00 0.00 1.75
1894 1907 7.936496 TTGCCTTTCTCATGTACATTATTCA 57.064 32.000 5.37 0.00 0.00 2.57
1957 1970 6.992063 ACTGTTTATCTGCTGTTAGATTGG 57.008 37.500 0.00 0.00 38.35 3.16
1968 1981 3.071479 TGTTAGATTGGGTGTTCTTCGC 58.929 45.455 0.00 0.00 0.00 4.70
2001 2014 5.977533 ACTCCACTATCCTATTGATACCCA 58.022 41.667 0.00 0.00 34.76 4.51
2032 2047 6.821665 AGTTGTACACTGTGATTTGTACTGTT 59.178 34.615 15.86 0.00 45.60 3.16
2066 2081 4.737054 AGTTATGCTGTTTTGCACTATGC 58.263 39.130 0.00 0.00 46.33 3.14
2083 2098 6.479001 GCACTATGCGGAATCTTTAGAGTAAA 59.521 38.462 0.00 0.00 31.71 2.01
2084 2099 7.011109 GCACTATGCGGAATCTTTAGAGTAAAA 59.989 37.037 0.00 0.00 31.71 1.52
2166 2181 8.445275 TCATGTTGTACATTTCAGTAACACTT 57.555 30.769 0.00 0.00 36.53 3.16
2167 2182 9.549078 TCATGTTGTACATTTCAGTAACACTTA 57.451 29.630 0.00 0.00 36.53 2.24
2341 2356 0.398696 TTTATCCCATGGGCGCGTAT 59.601 50.000 27.41 16.20 34.68 3.06
2363 2378 6.775594 ATGGTTTATTTTCTGCTCCCTAAC 57.224 37.500 0.00 0.00 0.00 2.34
2382 2397 8.861086 TCCCTAACTCATCTATGTATCTTGTTC 58.139 37.037 0.00 0.00 0.00 3.18
2438 2453 7.389607 AGCGGTTTGTTCTAATGTGTATTACTT 59.610 33.333 0.00 0.00 0.00 2.24
2552 2568 7.055667 TGTTTTGTGGTTAAGGCATGAATAA 57.944 32.000 0.00 0.00 0.00 1.40
2707 2761 2.866156 TCACTTTTCTGTGTTGCTCGAG 59.134 45.455 8.45 8.45 38.90 4.04
2723 2777 3.388308 CTCGAGATGCAGGAAACATAGG 58.612 50.000 6.58 0.00 0.00 2.57
3023 3077 1.153349 GCTTGAGAGGGTAAGGCGG 60.153 63.158 0.00 0.00 0.00 6.13
3196 3253 5.676552 TGGTATGTGTTACAACTGTTGACT 58.323 37.500 26.00 8.12 31.99 3.41
3299 3363 6.536447 TGAGATCCATAATGCAGCTATTGAA 58.464 36.000 0.00 0.00 0.00 2.69
3313 3377 8.023128 TGCAGCTATTGAAATTTTCTAGTTGAC 58.977 33.333 18.27 12.84 0.00 3.18
3396 3460 4.493220 GCTCAAGTTGATGACATAGAACGC 60.493 45.833 5.91 0.00 0.00 4.84
3498 3563 3.817647 GCCAGGATGTGATTAAGTCCATC 59.182 47.826 0.00 0.00 35.51 3.51
3578 3643 0.250553 TGGTGCTGGTAAAGTTCGGG 60.251 55.000 0.00 0.00 0.00 5.14
3648 3713 3.659786 TGTCTGAACAATCCTGTTACCG 58.340 45.455 0.00 0.00 45.98 4.02
3669 3734 3.869246 CGTGCGGGTTATTCAGTAATCTT 59.131 43.478 0.00 0.00 0.00 2.40
3728 3794 5.219739 TCAACCTAGGATCTGAAGCCTATT 58.780 41.667 17.98 0.00 42.54 1.73
3755 3821 5.595885 GCATGTGATAGAGATGTGTACACT 58.404 41.667 25.60 12.04 0.00 3.55
3756 3822 5.689514 GCATGTGATAGAGATGTGTACACTC 59.310 44.000 25.60 19.12 0.00 3.51
3757 3823 5.836821 TGTGATAGAGATGTGTACACTCC 57.163 43.478 25.60 16.74 0.00 3.85
3758 3824 5.261216 TGTGATAGAGATGTGTACACTCCA 58.739 41.667 25.60 7.33 0.00 3.86
3952 4022 6.183360 ACCATGGTTGTATCATTATGTTGCTG 60.183 38.462 13.00 0.00 0.00 4.41
4035 4105 5.768317 ACTGCGTGTTGCTTAAAAATACAT 58.232 33.333 0.00 0.00 46.63 2.29
4049 4119 5.674052 AAAATACATGCATTGTTGGGCTA 57.326 34.783 0.00 0.00 39.87 3.93
4052 4122 0.748450 CATGCATTGTTGGGCTAGGG 59.252 55.000 0.00 0.00 0.00 3.53
4089 4159 8.306761 GTTGTTTCATCTTCCATTTGGTTCTAT 58.693 33.333 0.00 0.00 36.34 1.98
4163 4233 5.517770 GTGGAGAATGCATGCAAAGAAATAC 59.482 40.000 26.68 14.41 39.99 1.89
4164 4234 4.736793 GGAGAATGCATGCAAAGAAATACG 59.263 41.667 26.68 0.00 0.00 3.06
4165 4235 5.314923 AGAATGCATGCAAAGAAATACGT 57.685 34.783 26.68 0.00 0.00 3.57
4166 4236 6.435430 AGAATGCATGCAAAGAAATACGTA 57.565 33.333 26.68 0.00 0.00 3.57
4167 4237 6.258160 AGAATGCATGCAAAGAAATACGTAC 58.742 36.000 26.68 4.01 0.00 3.67
4168 4238 5.818136 ATGCATGCAAAGAAATACGTACT 57.182 34.783 26.68 0.00 0.00 2.73
4169 4239 5.621197 TGCATGCAAAGAAATACGTACTT 57.379 34.783 20.30 0.00 0.00 2.24
4170 4240 6.729391 TGCATGCAAAGAAATACGTACTTA 57.271 33.333 20.30 0.00 0.00 2.24
4224 4299 0.955905 ATGAAACGGAAACAACGGGG 59.044 50.000 0.00 0.00 35.23 5.73
4300 4376 9.109533 GTCAATTTGTTGTTTATTCGACGTAAT 57.890 29.630 0.00 0.00 0.00 1.89
4309 4400 8.916657 TGTTTATTCGACGTAATTTGTTGTAC 57.083 30.769 0.00 0.00 0.00 2.90
4341 4432 1.567504 GCGTGATGGTGCGTATTACT 58.432 50.000 0.00 0.00 0.00 2.24
4418 4511 2.679930 CGAAATGACCAGGTTACCCTCC 60.680 54.545 0.00 0.00 39.89 4.30
4419 4512 2.053747 AATGACCAGGTTACCCTCCA 57.946 50.000 0.00 0.00 39.89 3.86
4420 4513 1.584724 ATGACCAGGTTACCCTCCAG 58.415 55.000 0.00 0.00 39.89 3.86
4421 4514 0.192566 TGACCAGGTTACCCTCCAGT 59.807 55.000 0.00 0.00 39.89 4.00
4422 4515 1.359168 GACCAGGTTACCCTCCAGTT 58.641 55.000 0.00 0.00 39.89 3.16
4423 4516 1.703513 GACCAGGTTACCCTCCAGTTT 59.296 52.381 0.00 0.00 39.89 2.66
4424 4517 2.107726 GACCAGGTTACCCTCCAGTTTT 59.892 50.000 0.00 0.00 39.89 2.43
4469 4562 1.379977 TCGTCTTCCAGATCCGCCT 60.380 57.895 0.00 0.00 0.00 5.52
4617 5674 2.123982 CCATCTTCCTGGGCCAGC 60.124 66.667 28.51 0.00 32.28 4.85
4659 5716 2.765807 AGCAGATCCCCCACCTCG 60.766 66.667 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.069636 GCTTCAAAACAGCTCTGTCGG 60.070 52.381 2.68 0.00 44.13 4.79
201 202 2.036098 CCAGTGGAGGGCAATGCA 59.964 61.111 1.68 0.00 0.00 3.96
253 254 9.553064 AAGACGATCAAAGCTATGAATAAGATT 57.447 29.630 0.00 0.00 32.06 2.40
472 474 1.228552 AGCGGGCACTTTTCCATGT 60.229 52.632 0.00 0.00 0.00 3.21
597 600 5.486526 CTTGTGTCTCTGCTCCTAAATCTT 58.513 41.667 0.00 0.00 0.00 2.40
610 613 4.888326 AGATCTTCAAGCTTGTGTCTCT 57.112 40.909 25.19 18.74 0.00 3.10
743 747 1.893315 AGTGGCCCCAGCTATCTAAA 58.107 50.000 0.00 0.00 39.73 1.85
744 748 2.704065 GTTAGTGGCCCCAGCTATCTAA 59.296 50.000 0.00 0.00 39.73 2.10
745 749 2.090719 AGTTAGTGGCCCCAGCTATCTA 60.091 50.000 0.00 0.00 39.73 1.98
746 750 1.132500 GTTAGTGGCCCCAGCTATCT 58.868 55.000 0.00 0.00 39.73 1.98
747 751 1.132500 AGTTAGTGGCCCCAGCTATC 58.868 55.000 0.00 0.00 39.73 2.08
748 752 2.489528 TAGTTAGTGGCCCCAGCTAT 57.510 50.000 0.00 0.00 39.73 2.97
749 753 2.047061 CATAGTTAGTGGCCCCAGCTA 58.953 52.381 0.00 0.00 39.73 3.32
750 754 0.839946 CATAGTTAGTGGCCCCAGCT 59.160 55.000 0.00 0.00 39.73 4.24
751 755 0.546598 ACATAGTTAGTGGCCCCAGC 59.453 55.000 0.00 0.00 38.76 4.85
752 756 1.202533 CGACATAGTTAGTGGCCCCAG 60.203 57.143 0.00 0.00 0.00 4.45
753 757 0.828022 CGACATAGTTAGTGGCCCCA 59.172 55.000 0.00 0.00 0.00 4.96
754 758 0.532196 GCGACATAGTTAGTGGCCCC 60.532 60.000 0.00 0.00 35.09 5.80
755 759 2.987752 GCGACATAGTTAGTGGCCC 58.012 57.895 0.00 0.00 35.09 5.80
757 761 1.571919 CTGGCGACATAGTTAGTGGC 58.428 55.000 0.00 0.00 41.51 5.01
758 762 1.571919 GCTGGCGACATAGTTAGTGG 58.428 55.000 0.00 0.00 41.51 4.00
759 763 1.200483 CGCTGGCGACATAGTTAGTG 58.800 55.000 9.51 0.00 42.83 2.74
760 764 0.102481 CCGCTGGCGACATAGTTAGT 59.898 55.000 16.79 0.00 42.83 2.24
761 765 0.102481 ACCGCTGGCGACATAGTTAG 59.898 55.000 16.79 0.00 42.83 2.34
762 766 0.179121 CACCGCTGGCGACATAGTTA 60.179 55.000 16.79 0.00 42.83 2.24
763 767 1.447838 CACCGCTGGCGACATAGTT 60.448 57.895 16.79 0.00 42.83 2.24
764 768 2.184322 CACCGCTGGCGACATAGT 59.816 61.111 16.79 2.37 42.83 2.12
765 769 3.264897 GCACCGCTGGCGACATAG 61.265 66.667 16.79 1.72 42.83 2.23
766 770 4.830765 GGCACCGCTGGCGACATA 62.831 66.667 16.79 0.00 42.83 2.29
771 775 4.705519 CTTTTGGCACCGCTGGCG 62.706 66.667 8.08 8.08 46.17 5.69
781 785 2.864343 GCATCAATCTCATGCTTTTGGC 59.136 45.455 0.00 0.00 42.95 4.52
788 792 3.119602 ACACACAAGCATCAATCTCATGC 60.120 43.478 0.00 0.00 46.05 4.06
789 793 4.412207 CACACACAAGCATCAATCTCATG 58.588 43.478 0.00 0.00 0.00 3.07
790 794 3.119602 GCACACACAAGCATCAATCTCAT 60.120 43.478 0.00 0.00 0.00 2.90
791 795 2.227149 GCACACACAAGCATCAATCTCA 59.773 45.455 0.00 0.00 0.00 3.27
900 907 2.744202 GGTTTCACTGACATGCTGTAGG 59.256 50.000 0.00 0.00 0.00 3.18
927 934 1.671850 GGAGAACGATGCGAAAGGACA 60.672 52.381 0.00 0.00 0.00 4.02
929 936 0.108329 GGGAGAACGATGCGAAAGGA 60.108 55.000 0.00 0.00 0.00 3.36
930 937 1.421410 CGGGAGAACGATGCGAAAGG 61.421 60.000 0.00 0.00 35.47 3.11
931 938 0.457853 TCGGGAGAACGATGCGAAAG 60.458 55.000 0.00 0.00 38.06 2.62
932 939 0.038067 TTCGGGAGAACGATGCGAAA 60.038 50.000 0.00 0.00 45.39 3.46
1081 1090 1.758514 GACGAGAGGATGCAGGGGA 60.759 63.158 0.00 0.00 0.00 4.81
1302 1311 2.355007 GGGTTGGATGATTTGCCCTTTG 60.355 50.000 0.00 0.00 33.58 2.77
1303 1312 1.908619 GGGTTGGATGATTTGCCCTTT 59.091 47.619 0.00 0.00 33.58 3.11
1305 1314 0.325577 GGGGTTGGATGATTTGCCCT 60.326 55.000 0.00 0.00 36.46 5.19
1307 1316 1.207811 CAAGGGGTTGGATGATTTGCC 59.792 52.381 0.00 0.00 0.00 4.52
1308 1317 1.901833 ACAAGGGGTTGGATGATTTGC 59.098 47.619 0.00 0.00 0.00 3.68
1309 1318 5.245977 ACTTTACAAGGGGTTGGATGATTTG 59.754 40.000 0.00 0.00 0.00 2.32
1311 1320 4.772100 CACTTTACAAGGGGTTGGATGATT 59.228 41.667 0.00 0.00 0.00 2.57
1312 1321 4.344104 CACTTTACAAGGGGTTGGATGAT 58.656 43.478 0.00 0.00 0.00 2.45
1322 1331 1.710816 TTTGCCCCACTTTACAAGGG 58.289 50.000 0.00 0.00 42.94 3.95
1323 1332 2.896685 TGATTTGCCCCACTTTACAAGG 59.103 45.455 0.00 0.00 0.00 3.61
1324 1333 4.381932 GGATGATTTGCCCCACTTTACAAG 60.382 45.833 0.00 0.00 0.00 3.16
1325 1334 3.513515 GGATGATTTGCCCCACTTTACAA 59.486 43.478 0.00 0.00 0.00 2.41
1326 1335 3.096092 GGATGATTTGCCCCACTTTACA 58.904 45.455 0.00 0.00 0.00 2.41
1327 1336 3.096092 TGGATGATTTGCCCCACTTTAC 58.904 45.455 0.00 0.00 0.00 2.01
1328 1337 3.464720 TGGATGATTTGCCCCACTTTA 57.535 42.857 0.00 0.00 0.00 1.85
1329 1338 2.323999 TGGATGATTTGCCCCACTTT 57.676 45.000 0.00 0.00 0.00 2.66
1330 1339 2.323999 TTGGATGATTTGCCCCACTT 57.676 45.000 0.00 0.00 0.00 3.16
1331 1340 2.391678 GATTGGATGATTTGCCCCACT 58.608 47.619 0.00 0.00 0.00 4.00
1332 1341 1.413812 GGATTGGATGATTTGCCCCAC 59.586 52.381 0.00 0.00 0.00 4.61
1333 1342 1.692121 GGGATTGGATGATTTGCCCCA 60.692 52.381 0.00 0.00 32.98 4.96
1334 1343 1.051008 GGGATTGGATGATTTGCCCC 58.949 55.000 0.00 0.00 0.00 5.80
1335 1344 1.051008 GGGGATTGGATGATTTGCCC 58.949 55.000 0.00 0.00 32.23 5.36
1336 1345 1.051008 GGGGGATTGGATGATTTGCC 58.949 55.000 0.00 0.00 0.00 4.52
1337 1346 0.675633 CGGGGGATTGGATGATTTGC 59.324 55.000 0.00 0.00 0.00 3.68
1338 1347 1.956477 GTCGGGGGATTGGATGATTTG 59.044 52.381 0.00 0.00 0.00 2.32
1339 1348 1.476833 CGTCGGGGGATTGGATGATTT 60.477 52.381 0.00 0.00 0.00 2.17
1340 1349 0.108585 CGTCGGGGGATTGGATGATT 59.891 55.000 0.00 0.00 0.00 2.57
1341 1350 1.754745 CGTCGGGGGATTGGATGAT 59.245 57.895 0.00 0.00 0.00 2.45
1342 1351 2.439960 CCGTCGGGGGATTGGATGA 61.440 63.158 2.34 0.00 0.00 2.92
1343 1352 2.111043 CCGTCGGGGGATTGGATG 59.889 66.667 2.34 0.00 0.00 3.51
1344 1353 2.041301 TCCGTCGGGGGATTGGAT 60.041 61.111 12.29 0.00 36.01 3.41
1345 1354 3.078836 GTCCGTCGGGGGATTGGA 61.079 66.667 12.29 0.00 38.61 3.53
1346 1355 4.524318 CGTCCGTCGGGGGATTGG 62.524 72.222 12.29 0.00 38.61 3.16
1347 1356 3.426117 CTCGTCCGTCGGGGGATTG 62.426 68.421 12.29 0.00 38.61 2.67
1348 1357 3.145551 CTCGTCCGTCGGGGGATT 61.146 66.667 12.29 0.00 38.61 3.01
1349 1358 3.650298 TTCTCGTCCGTCGGGGGAT 62.650 63.158 12.29 0.00 40.91 3.85
1350 1359 3.866379 TTTCTCGTCCGTCGGGGGA 62.866 63.158 12.29 8.16 40.91 4.81
1351 1360 2.234913 AATTTCTCGTCCGTCGGGGG 62.235 60.000 12.29 3.68 40.91 5.40
1352 1361 1.082117 CAATTTCTCGTCCGTCGGGG 61.082 60.000 12.29 4.07 40.91 5.73
1353 1362 1.082117 CCAATTTCTCGTCCGTCGGG 61.082 60.000 12.29 0.00 42.07 5.14
1354 1363 0.108992 TCCAATTTCTCGTCCGTCGG 60.109 55.000 4.39 4.39 40.32 4.79
1355 1364 1.852895 GATCCAATTTCTCGTCCGTCG 59.147 52.381 0.00 0.00 41.41 5.12
1356 1365 3.166489 AGATCCAATTTCTCGTCCGTC 57.834 47.619 0.00 0.00 0.00 4.79
1357 1366 3.611766 AAGATCCAATTTCTCGTCCGT 57.388 42.857 0.00 0.00 0.00 4.69
1358 1367 4.651994 CAAAAGATCCAATTTCTCGTCCG 58.348 43.478 0.00 0.00 0.00 4.79
1359 1368 4.415735 GCAAAAGATCCAATTTCTCGTCC 58.584 43.478 0.00 0.00 0.00 4.79
1360 1369 4.415735 GGCAAAAGATCCAATTTCTCGTC 58.584 43.478 0.00 0.00 0.00 4.20
1361 1370 3.193479 GGGCAAAAGATCCAATTTCTCGT 59.807 43.478 0.00 0.00 0.00 4.18
1362 1371 3.429410 GGGGCAAAAGATCCAATTTCTCG 60.429 47.826 0.00 0.00 0.00 4.04
1363 1372 3.515104 TGGGGCAAAAGATCCAATTTCTC 59.485 43.478 0.00 0.00 0.00 2.87
1364 1373 3.261643 GTGGGGCAAAAGATCCAATTTCT 59.738 43.478 0.00 0.00 0.00 2.52
1365 1374 3.261643 AGTGGGGCAAAAGATCCAATTTC 59.738 43.478 0.00 0.00 0.00 2.17
1366 1375 3.250617 AGTGGGGCAAAAGATCCAATTT 58.749 40.909 0.00 0.00 0.00 1.82
1367 1376 2.906568 AGTGGGGCAAAAGATCCAATT 58.093 42.857 0.00 0.00 0.00 2.32
1368 1377 2.629017 AGTGGGGCAAAAGATCCAAT 57.371 45.000 0.00 0.00 0.00 3.16
1369 1378 2.397044 AAGTGGGGCAAAAGATCCAA 57.603 45.000 0.00 0.00 0.00 3.53
1370 1379 2.397044 AAAGTGGGGCAAAAGATCCA 57.603 45.000 0.00 0.00 0.00 3.41
1371 1380 3.161866 TGTAAAGTGGGGCAAAAGATCC 58.838 45.455 0.00 0.00 0.00 3.36
1372 1381 4.220602 ACATGTAAAGTGGGGCAAAAGATC 59.779 41.667 0.00 0.00 0.00 2.75
1373 1382 4.159557 ACATGTAAAGTGGGGCAAAAGAT 58.840 39.130 0.00 0.00 0.00 2.40
1374 1383 3.571590 ACATGTAAAGTGGGGCAAAAGA 58.428 40.909 0.00 0.00 0.00 2.52
1375 1384 4.522789 ACTACATGTAAAGTGGGGCAAAAG 59.477 41.667 7.06 0.00 0.00 2.27
1376 1385 4.475345 ACTACATGTAAAGTGGGGCAAAA 58.525 39.130 7.06 0.00 0.00 2.44
1377 1386 4.107127 ACTACATGTAAAGTGGGGCAAA 57.893 40.909 7.06 0.00 0.00 3.68
1378 1387 3.799432 ACTACATGTAAAGTGGGGCAA 57.201 42.857 7.06 0.00 0.00 4.52
1379 1388 3.073209 TGAACTACATGTAAAGTGGGGCA 59.927 43.478 7.06 0.00 0.00 5.36
1380 1389 3.681593 TGAACTACATGTAAAGTGGGGC 58.318 45.455 7.06 0.00 0.00 5.80
1381 1390 5.943416 TCAATGAACTACATGTAAAGTGGGG 59.057 40.000 7.06 0.00 39.39 4.96
1382 1391 6.094048 CCTCAATGAACTACATGTAAAGTGGG 59.906 42.308 7.06 3.00 39.39 4.61
1383 1392 6.655003 ACCTCAATGAACTACATGTAAAGTGG 59.345 38.462 7.06 2.80 39.39 4.00
1384 1393 7.672983 ACCTCAATGAACTACATGTAAAGTG 57.327 36.000 7.06 3.33 39.39 3.16
1385 1394 9.383519 CATACCTCAATGAACTACATGTAAAGT 57.616 33.333 7.06 0.82 39.39 2.66
1386 1395 8.830580 CCATACCTCAATGAACTACATGTAAAG 58.169 37.037 7.06 0.11 39.39 1.85
1387 1396 8.325787 ACCATACCTCAATGAACTACATGTAAA 58.674 33.333 7.06 0.00 39.39 2.01
1388 1397 7.768582 CACCATACCTCAATGAACTACATGTAA 59.231 37.037 7.06 0.00 39.39 2.41
1389 1398 7.272244 CACCATACCTCAATGAACTACATGTA 58.728 38.462 5.25 5.25 39.39 2.29
1390 1399 6.115446 CACCATACCTCAATGAACTACATGT 58.885 40.000 2.69 2.69 39.39 3.21
1468 1477 3.207778 TCCAAACGTTTGACACCCTAAG 58.792 45.455 36.20 19.07 40.55 2.18
1800 1813 6.427547 AGAATCTTCTCTTCAGCAGAAACAAG 59.572 38.462 0.00 0.00 32.35 3.16
1824 1837 9.734620 TTTACATCAGTTCAAGAATGTGAAAAG 57.265 29.630 0.00 0.00 39.18 2.27
1893 1906 1.142870 TGGGAAGGACCACTCAGTTTG 59.857 52.381 0.00 0.00 41.20 2.93
1894 1907 1.518367 TGGGAAGGACCACTCAGTTT 58.482 50.000 0.00 0.00 41.20 2.66
1957 1970 1.971695 CCCCCAAGCGAAGAACACC 60.972 63.158 0.00 0.00 0.00 4.16
1968 1981 1.694696 GATAGTGGAGTAGCCCCCAAG 59.305 57.143 0.00 0.00 33.69 3.61
2001 2014 5.730296 AATCACAGTGTACAACTAGCTCT 57.270 39.130 0.00 0.00 36.83 4.09
2066 2081 9.989869 GGAAGAAATTTTACTCTAAAGATTCCG 57.010 33.333 0.00 0.00 30.69 4.30
2084 2099 9.382275 GCAAAATTATTACACCATGGAAGAAAT 57.618 29.630 21.47 13.99 23.82 2.17
2088 2103 8.442384 GTTTGCAAAATTATTACACCATGGAAG 58.558 33.333 21.47 13.13 0.00 3.46
2137 2152 5.314923 ACTGAAATGTACAACATGATGGC 57.685 39.130 7.95 0.86 37.97 4.40
2166 2181 3.071023 GGTATGGCCTGTTGCAGTAGATA 59.929 47.826 3.32 0.00 43.89 1.98
2167 2182 2.158755 GGTATGGCCTGTTGCAGTAGAT 60.159 50.000 3.32 0.00 43.89 1.98
2341 2356 5.887754 AGTTAGGGAGCAGAAAATAAACCA 58.112 37.500 0.00 0.00 0.00 3.67
2438 2453 5.265191 AGACTCCTGAGCATTACTGACTTA 58.735 41.667 0.00 0.00 0.00 2.24
2707 2761 5.189180 AGAAGAACCTATGTTTCCTGCATC 58.811 41.667 0.00 0.00 33.97 3.91
2723 2777 5.585047 ACGCAGGGACATTAATAAGAAGAAC 59.415 40.000 0.00 0.00 0.00 3.01
2822 2876 5.047872 ACAGAGCAATTAAACATGACATGCA 60.048 36.000 15.49 0.00 34.89 3.96
3023 3077 7.011482 ACCAAATGAGATAACGATAAAGAGTGC 59.989 37.037 0.00 0.00 0.00 4.40
3196 3253 5.417754 TTGCATTTCTTGGGATTTGCATA 57.582 34.783 0.00 0.00 38.54 3.14
3313 3377 5.641636 ACCCAAACAGCAAAAACAAAGTAAG 59.358 36.000 0.00 0.00 0.00 2.34
3396 3460 1.512926 AGTTAGTGCCGCACAAGAAG 58.487 50.000 24.97 0.00 36.74 2.85
3458 3522 1.740296 CTAACAAGGACCACCGCCG 60.740 63.158 0.00 0.00 41.83 6.46
3498 3563 2.025981 TGGTGGAATCAGACAAGGATGG 60.026 50.000 0.00 0.00 0.00 3.51
3578 3643 0.037326 TGGTTGCATCAGTCCTCGAC 60.037 55.000 0.00 0.00 0.00 4.20
3648 3713 5.353123 TGAAAGATTACTGAATAACCCGCAC 59.647 40.000 0.00 0.00 0.00 5.34
3669 3734 5.221621 TGACACACACATGATAAGACCTGAA 60.222 40.000 0.00 0.00 0.00 3.02
3728 3794 1.413812 ACATCTCTATCACATGCGCCA 59.586 47.619 4.18 0.00 0.00 5.69
3755 3821 9.081204 CATAATAAATCAGGTTGAATGGATGGA 57.919 33.333 0.00 0.00 0.00 3.41
3756 3822 8.308931 CCATAATAAATCAGGTTGAATGGATGG 58.691 37.037 0.00 0.00 34.57 3.51
3757 3823 8.308931 CCCATAATAAATCAGGTTGAATGGATG 58.691 37.037 0.00 0.00 34.57 3.51
3758 3824 8.012477 ACCCATAATAAATCAGGTTGAATGGAT 58.988 33.333 0.00 0.00 34.57 3.41
3952 4022 6.330278 ACTTTTGGTTTTCTACAGCAACTTC 58.670 36.000 0.00 0.00 31.49 3.01
4035 4105 0.407528 TTCCCTAGCCCAACAATGCA 59.592 50.000 0.00 0.00 0.00 3.96
4049 4119 5.948742 TGAAACAACCTCAAAATTTCCCT 57.051 34.783 0.00 0.00 0.00 4.20
4052 4122 7.710475 TGGAAGATGAAACAACCTCAAAATTTC 59.290 33.333 0.00 0.00 0.00 2.17
4089 4159 6.439375 ACGTTAATGCCCAGGATATCAGTATA 59.561 38.462 4.83 0.00 0.00 1.47
4163 4233 6.607689 TGAGCCAATGAAAAACATAAGTACG 58.392 36.000 0.00 0.00 38.38 3.67
4164 4234 7.593825 ACTGAGCCAATGAAAAACATAAGTAC 58.406 34.615 0.00 0.00 38.38 2.73
4165 4235 7.759489 ACTGAGCCAATGAAAAACATAAGTA 57.241 32.000 0.00 0.00 38.38 2.24
4166 4236 6.655078 ACTGAGCCAATGAAAAACATAAGT 57.345 33.333 0.00 0.00 38.38 2.24
4167 4237 9.294030 GAATACTGAGCCAATGAAAAACATAAG 57.706 33.333 0.00 0.00 38.38 1.73
4168 4238 8.250332 GGAATACTGAGCCAATGAAAAACATAA 58.750 33.333 0.00 0.00 38.38 1.90
4169 4239 7.395772 TGGAATACTGAGCCAATGAAAAACATA 59.604 33.333 0.00 0.00 38.38 2.29
4170 4240 6.211184 TGGAATACTGAGCCAATGAAAAACAT 59.789 34.615 0.00 0.00 41.45 2.71
4224 4299 1.602851 TCGCAGACGCTCCTACTATTC 59.397 52.381 0.00 0.00 39.84 1.75
4267 4343 7.481275 AATAAACAACAAATTGACTTGCCTG 57.519 32.000 0.00 0.00 39.30 4.85
4275 4351 9.666626 AATTACGTCGAATAAACAACAAATTGA 57.333 25.926 0.00 0.00 39.30 2.57
4300 4376 5.507876 CGCGTACTACTATTCGTACAACAAA 59.492 40.000 0.00 0.00 36.63 2.83
4303 4379 4.431389 CACGCGTACTACTATTCGTACAAC 59.569 45.833 13.44 0.00 36.63 3.32
4309 4400 3.223953 CCATCACGCGTACTACTATTCG 58.776 50.000 13.44 0.00 0.00 3.34
4418 4511 5.233988 AGACGAGGAGAGAATTCAAAACTG 58.766 41.667 8.44 0.00 0.00 3.16
4419 4512 5.474825 GAGACGAGGAGAGAATTCAAAACT 58.525 41.667 8.44 0.32 0.00 2.66
4420 4513 4.627900 GGAGACGAGGAGAGAATTCAAAAC 59.372 45.833 8.44 0.00 0.00 2.43
4421 4514 4.283467 TGGAGACGAGGAGAGAATTCAAAA 59.717 41.667 8.44 0.00 0.00 2.44
4422 4515 3.832490 TGGAGACGAGGAGAGAATTCAAA 59.168 43.478 8.44 0.00 0.00 2.69
4423 4516 3.193691 GTGGAGACGAGGAGAGAATTCAA 59.806 47.826 8.44 0.00 0.00 2.69
4424 4517 2.755655 GTGGAGACGAGGAGAGAATTCA 59.244 50.000 8.44 0.00 0.00 2.57
4578 5635 1.419387 GAGGATGGAAGGGGATCTGTG 59.581 57.143 0.00 0.00 0.00 3.66
4617 5674 0.470833 AGGACGATGAGGGGGATCTG 60.471 60.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.