Multiple sequence alignment - TraesCS5A01G301600

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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 TraesCS5A01G301600 chr5A 100.000 3587 0 0 1 3587 510462797 510466383 0.000000e+00 6625.0
1 TraesCS5A01G301600 chr5A 89.744 585 48 8 2995 3572 702710758 702710179 0.000000e+00 737.0
2 TraesCS5A01G301600 chr5A 77.047 806 144 22 1687 2463 487325551 487326344 3.310000e-115 425.0
3 TraesCS5A01G301600 chr5A 81.911 293 27 21 1105 1384 510464180 510463901 1.300000e-54 224.0
4 TraesCS5A01G301600 chr5D 91.581 1746 84 42 1001 2714 402977001 402975287 0.000000e+00 2351.0
5 TraesCS5A01G301600 chr5D 89.113 744 43 12 2877 3583 402975286 402974544 0.000000e+00 891.0
6 TraesCS5A01G301600 chr5D 89.226 659 52 12 1 650 402978099 402977451 0.000000e+00 806.0
7 TraesCS5A01G301600 chr5D 84.698 281 26 13 1106 1384 402976616 402976881 7.640000e-67 265.0
8 TraesCS5A01G301600 chr5D 86.782 174 21 2 2713 2885 189021914 189021742 3.650000e-45 193.0
9 TraesCS5A01G301600 chr5D 89.655 145 10 3 876 1016 402977156 402977013 2.850000e-41 180.0
10 TraesCS5A01G301600 chr5B 92.210 1502 70 26 1224 2713 482418695 482417229 0.000000e+00 2082.0
11 TraesCS5A01G301600 chr5B 88.180 643 54 8 3 626 482421549 482420910 0.000000e+00 747.0
12 TraesCS5A01G301600 chr5B 83.830 470 43 13 842 1284 482420667 482420204 1.990000e-112 416.0
13 TraesCS5A01G301600 chr5B 94.898 98 1 3 1297 1390 482420291 482420388 2.230000e-32 150.0
14 TraesCS5A01G301600 chr5B 91.358 81 3 2 665 745 471409268 471409344 1.360000e-19 108.0
15 TraesCS5A01G301600 chr5B 90.909 77 5 2 671 745 12295629 12295553 6.340000e-18 102.0
16 TraesCS5A01G301600 chr3D 90.365 602 47 7 2992 3587 441438985 441438389 0.000000e+00 780.0
17 TraesCS5A01G301600 chr3D 93.590 78 3 2 671 746 169888139 169888216 8.140000e-22 115.0
18 TraesCS5A01G301600 chr4B 87.969 640 58 9 2954 3583 132295849 132296479 0.000000e+00 737.0
19 TraesCS5A01G301600 chr4B 89.052 612 35 11 2995 3583 438602207 438601605 0.000000e+00 730.0
20 TraesCS5A01G301600 chr4B 85.574 610 58 12 2997 3587 28919078 28919676 2.370000e-171 612.0
21 TraesCS5A01G301600 chr4B 86.747 166 21 1 2713 2878 636168456 636168620 2.200000e-42 183.0
22 TraesCS5A01G301600 chr4B 83.799 179 27 2 2713 2890 570345797 570345974 6.160000e-38 169.0
23 TraesCS5A01G301600 chr4B 88.372 86 8 2 673 757 142056811 142056895 6.340000e-18 102.0
24 TraesCS5A01G301600 chr6B 88.833 600 44 15 2995 3587 702282176 702281593 0.000000e+00 715.0
25 TraesCS5A01G301600 chr6B 80.989 647 60 31 2997 3587 57123956 57123317 4.220000e-124 455.0
26 TraesCS5A01G301600 chr6B 98.810 84 1 0 1105 1188 473067441 473067524 2.230000e-32 150.0
27 TraesCS5A01G301600 chr6B 97.674 86 2 0 1301 1386 473067524 473067439 8.020000e-32 148.0
28 TraesCS5A01G301600 chr6B 79.310 145 22 8 3432 3573 41415320 41415459 1.060000e-15 95.3
29 TraesCS5A01G301600 chr1B 90.851 470 39 4 3121 3587 221325569 221325101 8.450000e-176 627.0
30 TraesCS5A01G301600 chr1B 90.000 470 43 4 3121 3587 221305591 221305123 3.960000e-169 604.0
31 TraesCS5A01G301600 chr2B 85.927 604 58 16 2997 3576 800573328 800573928 1.410000e-173 619.0
32 TraesCS5A01G301600 chr2B 85.927 604 58 16 2997 3576 800585102 800585702 1.410000e-173 619.0
33 TraesCS5A01G301600 chr2B 82.766 470 45 12 3150 3587 407214404 407213939 1.560000e-103 387.0
34 TraesCS5A01G301600 chr2B 78.076 447 37 35 3146 3587 170992694 170992304 3.600000e-55 226.0
35 TraesCS5A01G301600 chr2B 86.869 99 7 5 665 759 762916463 762916559 4.900000e-19 106.0
36 TraesCS5A01G301600 chr3B 81.593 364 35 9 3255 3587 33498436 33498798 4.560000e-69 272.0
37 TraesCS5A01G301600 chr2D 88.166 169 19 1 2710 2878 161648028 161647861 2.180000e-47 200.0
38 TraesCS5A01G301600 chr6D 86.826 167 20 2 2713 2878 373362720 373362885 6.120000e-43 185.0
39 TraesCS5A01G301600 chr6D 98.810 84 1 0 1105 1188 306137314 306137397 2.230000e-32 150.0
40 TraesCS5A01G301600 chr6D 97.619 84 2 0 1301 1384 306137397 306137314 1.040000e-30 145.0
41 TraesCS5A01G301600 chr4A 85.795 176 23 2 2709 2883 428284288 428284114 6.120000e-43 185.0
42 TraesCS5A01G301600 chr7D 85.714 168 23 1 2711 2878 37292853 37293019 3.680000e-40 176.0
43 TraesCS5A01G301600 chr7D 97.701 87 1 1 1297 1383 252062991 252063076 8.020000e-32 148.0
44 TraesCS5A01G301600 chr7D 97.590 83 2 0 1106 1188 252063076 252062994 3.730000e-30 143.0
45 TraesCS5A01G301600 chr1A 85.294 170 24 1 2712 2881 284146822 284146654 1.320000e-39 174.0
46 TraesCS5A01G301600 chr1A 89.286 84 7 2 663 746 440885268 440885349 1.760000e-18 104.0
47 TraesCS5A01G301600 chrUn 84.884 172 25 1 2712 2883 96037724 96037894 4.760000e-39 172.0
48 TraesCS5A01G301600 chr2A 78.571 308 33 11 3304 3583 59586295 59585993 4.760000e-39 172.0
49 TraesCS5A01G301600 chr2A 89.655 87 6 3 658 744 754039002 754039085 1.360000e-19 108.0
50 TraesCS5A01G301600 chr7B 100.000 84 0 0 1302 1385 228827641 228827724 4.800000e-34 156.0
51 TraesCS5A01G301600 chr7A 97.727 88 0 2 1106 1191 269102218 269102305 2.230000e-32 150.0
52 TraesCS5A01G301600 chr6A 98.795 83 1 0 1105 1187 441499326 441499408 8.020000e-32 148.0
53 TraesCS5A01G301600 chr6A 90.476 84 2 4 664 742 91911534 91911616 4.900000e-19 106.0
54 TraesCS5A01G301600 chr1D 90.476 84 2 3 664 742 433017536 433017454 4.900000e-19 106.0
55 TraesCS5A01G301600 chr4D 97.778 45 1 0 2997 3041 7101597 7101641 1.070000e-10 78.7


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 TraesCS5A01G301600 chr5A 510462797 510466383 3586 False 6625.000000 6625 100.000000 1 3587 1 chr5A.!!$F2 3586
1 TraesCS5A01G301600 chr5A 702710179 702710758 579 True 737.000000 737 89.744000 2995 3572 1 chr5A.!!$R2 577
2 TraesCS5A01G301600 chr5A 487325551 487326344 793 False 425.000000 425 77.047000 1687 2463 1 chr5A.!!$F1 776
3 TraesCS5A01G301600 chr5D 402974544 402978099 3555 True 1057.000000 2351 89.893750 1 3583 4 chr5D.!!$R2 3582
4 TraesCS5A01G301600 chr5B 482417229 482421549 4320 True 1081.666667 2082 88.073333 3 2713 3 chr5B.!!$R2 2710
5 TraesCS5A01G301600 chr3D 441438389 441438985 596 True 780.000000 780 90.365000 2992 3587 1 chr3D.!!$R1 595
6 TraesCS5A01G301600 chr4B 132295849 132296479 630 False 737.000000 737 87.969000 2954 3583 1 chr4B.!!$F2 629
7 TraesCS5A01G301600 chr4B 438601605 438602207 602 True 730.000000 730 89.052000 2995 3583 1 chr4B.!!$R1 588
8 TraesCS5A01G301600 chr4B 28919078 28919676 598 False 612.000000 612 85.574000 2997 3587 1 chr4B.!!$F1 590
9 TraesCS5A01G301600 chr6B 702281593 702282176 583 True 715.000000 715 88.833000 2995 3587 1 chr6B.!!$R3 592
10 TraesCS5A01G301600 chr6B 57123317 57123956 639 True 455.000000 455 80.989000 2997 3587 1 chr6B.!!$R1 590
11 TraesCS5A01G301600 chr2B 800573328 800573928 600 False 619.000000 619 85.927000 2997 3576 1 chr2B.!!$F2 579
12 TraesCS5A01G301600 chr2B 800585102 800585702 600 False 619.000000 619 85.927000 2997 3576 1 chr2B.!!$F3 579

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
150 158 0.107459 GCTTGGGAGGAGCTACAAGG 60.107 60.0 0.00 0.0 40.37 3.61 F
1574 3486 0.922111 CACAAACCGAACGTGAACGC 60.922 55.0 2.11 0.0 44.43 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 3577 0.163788 GACCGCTGTGTCGAACATTG 59.836 55.0 0.0 0.0 38.39 2.82 R
2973 4931 0.313672 GCACAAAAACAGGCGATCCA 59.686 50.0 0.0 0.0 33.74 3.41 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
25 26 2.821366 CGAGAGCATGTGGCCCAC 60.821 66.667 7.01 7.01 46.50 4.61
26 27 2.673523 GAGAGCATGTGGCCCACT 59.326 61.111 16.23 0.00 46.50 4.00
93 94 2.158928 AGAGCTCTCCTATTGCAAGCAG 60.159 50.000 11.45 4.53 35.42 4.24
111 115 2.860628 GCGTTCTGCATACGAGGCG 61.861 63.158 21.35 9.83 45.45 5.52
121 125 1.464376 ATACGAGGCGCCACATAGCT 61.464 55.000 31.54 5.22 0.00 3.32
150 158 0.107459 GCTTGGGAGGAGCTACAAGG 60.107 60.000 0.00 0.00 40.37 3.61
158 166 1.840635 AGGAGCTACAAGGGGACATTC 59.159 52.381 0.00 0.00 0.00 2.67
163 171 1.561542 CTACAAGGGGACATTCCTGCT 59.438 52.381 0.00 0.00 36.57 4.24
166 174 1.064166 CAAGGGGACATTCCTGCTGAT 60.064 52.381 0.00 0.00 36.57 2.90
171 179 1.476471 GGACATTCCTGCTGATGAGGG 60.476 57.143 0.00 0.00 32.53 4.30
191 199 4.651503 AGGGAACACATGAGATACTAGTGG 59.348 45.833 5.39 0.00 34.65 4.00
478 497 4.875536 GGGTTAATGTTTTGGGCATCAATC 59.124 41.667 0.00 0.00 34.98 2.67
529 556 1.148236 TGGGGAGTTTAGTTTTGGGGG 59.852 52.381 0.00 0.00 0.00 5.40
530 557 1.148446 GGGGAGTTTAGTTTTGGGGGT 59.852 52.381 0.00 0.00 0.00 4.95
532 559 2.425247 GGGAGTTTAGTTTTGGGGGTGT 60.425 50.000 0.00 0.00 0.00 4.16
533 560 2.889045 GGAGTTTAGTTTTGGGGGTGTC 59.111 50.000 0.00 0.00 0.00 3.67
534 561 3.558033 GAGTTTAGTTTTGGGGGTGTCA 58.442 45.455 0.00 0.00 0.00 3.58
535 562 4.149598 GAGTTTAGTTTTGGGGGTGTCAT 58.850 43.478 0.00 0.00 0.00 3.06
539 566 5.538849 TTAGTTTTGGGGGTGTCATTTTC 57.461 39.130 0.00 0.00 0.00 2.29
546 573 3.245300 TGGGGGTGTCATTTTCGGAATTA 60.245 43.478 0.00 0.00 0.00 1.40
572 599 7.335422 AGTTTTTGGCTATGAGTAGAGTTGATG 59.665 37.037 0.00 0.00 0.00 3.07
586 613 1.741706 GTTGATGTGAGGTGCTCCATG 59.258 52.381 7.70 0.00 35.89 3.66
615 642 3.250280 GGAAACAAGGGAGAAACTCGAAC 59.750 47.826 0.00 0.00 0.00 3.95
616 643 3.553828 AACAAGGGAGAAACTCGAACA 57.446 42.857 0.00 0.00 0.00 3.18
623 650 2.092838 GGAGAAACTCGAACATTGAGCG 59.907 50.000 0.00 0.00 36.94 5.03
625 652 2.731976 AGAAACTCGAACATTGAGCGAC 59.268 45.455 0.00 0.00 36.94 5.19
626 653 2.440539 AACTCGAACATTGAGCGACT 57.559 45.000 0.00 0.00 36.94 4.18
629 656 3.909430 ACTCGAACATTGAGCGACTTTA 58.091 40.909 0.00 0.00 36.94 1.85
631 658 4.386049 ACTCGAACATTGAGCGACTTTAAG 59.614 41.667 0.00 0.00 36.94 1.85
632 659 3.122948 TCGAACATTGAGCGACTTTAAGC 59.877 43.478 0.00 0.00 0.00 3.09
639 826 7.210174 ACATTGAGCGACTTTAAGCATAGATA 58.790 34.615 0.00 0.00 35.48 1.98
642 829 6.569780 TGAGCGACTTTAAGCATAGATAACA 58.430 36.000 0.00 0.00 35.48 2.41
680 867 5.211973 TGAGCTTAATCATGTACTCCCTCT 58.788 41.667 0.00 0.00 0.00 3.69
683 870 6.136857 AGCTTAATCATGTACTCCCTCTGTA 58.863 40.000 0.00 0.00 0.00 2.74
684 871 6.611642 AGCTTAATCATGTACTCCCTCTGTAA 59.388 38.462 0.00 0.00 0.00 2.41
685 872 7.125811 AGCTTAATCATGTACTCCCTCTGTAAA 59.874 37.037 0.00 0.00 0.00 2.01
686 873 7.439655 GCTTAATCATGTACTCCCTCTGTAAAG 59.560 40.741 0.00 0.00 0.00 1.85
699 886 9.757227 CTCCCTCTGTAAAGAAATATAAGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
701 888 9.892130 CCCTCTGTAAAGAAATATAAGAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
717 904 7.588143 AAGAGTGTTTGATCTGATCTAAACG 57.412 36.000 24.13 0.00 35.24 3.60
718 905 5.578727 AGAGTGTTTGATCTGATCTAAACGC 59.421 40.000 28.19 28.19 38.95 4.84
719 906 5.482908 AGTGTTTGATCTGATCTAAACGCT 58.517 37.500 30.06 30.06 41.11 5.07
720 907 5.578727 AGTGTTTGATCTGATCTAAACGCTC 59.421 40.000 30.06 22.75 41.53 5.03
721 908 5.578727 GTGTTTGATCTGATCTAAACGCTCT 59.421 40.000 28.16 0.00 37.55 4.09
722 909 6.091441 GTGTTTGATCTGATCTAAACGCTCTT 59.909 38.462 28.16 0.00 37.55 2.85
763 1043 4.324267 AGTATTCACCAAAGGAGAAACGG 58.676 43.478 0.21 0.00 36.05 4.44
769 1049 4.941263 TCACCAAAGGAGAAACGGATATTG 59.059 41.667 0.00 0.00 0.00 1.90
776 1056 5.605534 AGGAGAAACGGATATTGTCATGAG 58.394 41.667 0.00 0.00 0.00 2.90
799 1079 1.342174 CCCAAATCAAGCACTTGCAGT 59.658 47.619 5.49 0.00 45.16 4.40
819 1104 2.489938 AGGCTTGTCTAATGCGGAAA 57.510 45.000 0.00 0.00 0.00 3.13
822 1107 2.415491 GGCTTGTCTAATGCGGAAAACC 60.415 50.000 0.00 0.00 0.00 3.27
823 1108 2.227865 GCTTGTCTAATGCGGAAAACCA 59.772 45.455 0.00 0.00 0.00 3.67
824 1109 3.119495 GCTTGTCTAATGCGGAAAACCAT 60.119 43.478 0.00 0.00 0.00 3.55
844 1129 4.744631 CCATGTTAACTTTTGTTGACCAGC 59.255 41.667 7.22 0.00 44.99 4.85
850 1135 1.136695 CTTTTGTTGACCAGCAAGGCA 59.863 47.619 0.01 0.00 43.14 4.75
851 1136 1.189752 TTTGTTGACCAGCAAGGCAA 58.810 45.000 0.01 0.00 43.14 4.52
856 1141 1.484038 TGACCAGCAAGGCAAAGTTT 58.516 45.000 0.00 0.00 43.14 2.66
871 1156 4.703093 GCAAAGTTTACTTGCTACCCCATA 59.297 41.667 0.00 0.00 36.12 2.74
872 1157 5.392703 GCAAAGTTTACTTGCTACCCCATAC 60.393 44.000 0.00 0.00 36.12 2.39
874 1159 3.847780 AGTTTACTTGCTACCCCATACCA 59.152 43.478 0.00 0.00 0.00 3.25
899 1185 6.992063 AAACCAAGATAGTGTAGATGCTTG 57.008 37.500 0.00 0.00 34.18 4.01
951 1237 3.890756 TCATGATAATTGTGCATGTCCCC 59.109 43.478 13.27 0.00 40.12 4.81
957 1243 2.307496 TTGTGCATGTCCCCAAGATT 57.693 45.000 0.00 0.00 0.00 2.40
962 1248 3.701040 GTGCATGTCCCCAAGATTTGTAT 59.299 43.478 0.00 0.00 0.00 2.29
975 1261 7.717875 CCCAAGATTTGTATCCGAGGTTTATAA 59.282 37.037 0.00 0.00 0.00 0.98
1075 1394 9.935682 ATTCATAATAAGTTCATAAGTGTTGCG 57.064 29.630 0.00 0.00 0.00 4.85
1076 1395 7.915508 TCATAATAAGTTCATAAGTGTTGCGG 58.084 34.615 0.00 0.00 0.00 5.69
1184 1527 3.330126 ACCACTGAGCTATAAGGGCTA 57.670 47.619 0.00 0.00 40.40 3.93
1190 1534 5.049129 CACTGAGCTATAAGGGCTATTTTGC 60.049 44.000 0.00 0.00 40.40 3.68
1194 1538 7.461749 TGAGCTATAAGGGCTATTTTGCTTAT 58.538 34.615 0.00 0.00 40.40 1.73
1195 1539 7.944554 TGAGCTATAAGGGCTATTTTGCTTATT 59.055 33.333 0.00 0.00 40.40 1.40
1288 3191 7.987268 TTAATGTAAGAGAAGACGTATGCAG 57.013 36.000 0.00 0.00 0.00 4.41
1289 3192 3.770666 TGTAAGAGAAGACGTATGCAGC 58.229 45.455 0.00 0.00 0.00 5.25
1290 3193 3.444034 TGTAAGAGAAGACGTATGCAGCT 59.556 43.478 0.00 0.00 0.00 4.24
1291 3194 4.638865 TGTAAGAGAAGACGTATGCAGCTA 59.361 41.667 0.00 0.00 0.00 3.32
1292 3195 3.701532 AGAGAAGACGTATGCAGCTAC 57.298 47.619 0.00 0.00 0.00 3.58
1295 3198 4.098654 AGAGAAGACGTATGCAGCTACAAT 59.901 41.667 0.00 0.00 0.00 2.71
1296 3199 5.299531 AGAGAAGACGTATGCAGCTACAATA 59.700 40.000 0.00 0.00 0.00 1.90
1431 3343 7.998753 ATACTCCCTACTTTATTTTCGAACG 57.001 36.000 0.00 0.00 0.00 3.95
1432 3344 5.173664 ACTCCCTACTTTATTTTCGAACGG 58.826 41.667 0.00 0.00 0.00 4.44
1433 3345 5.047092 ACTCCCTACTTTATTTTCGAACGGA 60.047 40.000 0.00 0.00 0.00 4.69
1434 3346 5.413499 TCCCTACTTTATTTTCGAACGGAG 58.587 41.667 0.00 0.00 0.00 4.63
1435 3347 4.569564 CCCTACTTTATTTTCGAACGGAGG 59.430 45.833 0.00 0.00 0.00 4.30
1436 3348 4.569564 CCTACTTTATTTTCGAACGGAGGG 59.430 45.833 0.00 0.00 0.00 4.30
1437 3349 4.276058 ACTTTATTTTCGAACGGAGGGA 57.724 40.909 0.00 0.00 0.00 4.20
1438 3350 4.251268 ACTTTATTTTCGAACGGAGGGAG 58.749 43.478 0.00 0.00 0.00 4.30
1439 3351 3.967332 TTATTTTCGAACGGAGGGAGT 57.033 42.857 0.00 0.00 0.00 3.85
1440 3352 5.047092 ACTTTATTTTCGAACGGAGGGAGTA 60.047 40.000 0.00 0.00 0.00 2.59
1465 3377 7.641760 ACAAATTTCGTACCGTAATCAAACTT 58.358 30.769 0.00 0.00 0.00 2.66
1468 3380 8.496872 AATTTCGTACCGTAATCAAACTTTTG 57.503 30.769 0.00 0.00 39.48 2.44
1469 3381 6.601741 TTCGTACCGTAATCAAACTTTTGT 57.398 33.333 1.75 0.00 39.18 2.83
1470 3382 6.214205 TCGTACCGTAATCAAACTTTTGTC 57.786 37.500 1.75 0.00 39.18 3.18
1471 3383 5.752472 TCGTACCGTAATCAAACTTTTGTCA 59.248 36.000 1.75 0.00 39.18 3.58
1569 3481 3.102985 TGGCACAAACCGAACGTG 58.897 55.556 0.00 0.00 31.92 4.49
1574 3486 0.922111 CACAAACCGAACGTGAACGC 60.922 55.000 2.11 0.00 44.43 4.84
1672 3590 2.527671 CGGAGCAATGTTCGACACA 58.472 52.632 3.49 3.49 40.71 3.72
1778 3696 4.443266 GCCGCGTGAAGCTCCTCT 62.443 66.667 4.92 0.00 45.59 3.69
2048 3977 3.506096 CGTACCCGCTCGAGCTCA 61.506 66.667 32.88 13.65 39.32 4.26
2500 4444 4.499183 CTTACGACCAGATGAAGCTTCTT 58.501 43.478 26.09 20.33 0.00 2.52
2511 4456 2.033299 TGAAGCTTCTTTTGAACTGCCG 59.967 45.455 26.09 0.00 32.14 5.69
2517 4462 4.572571 TTTGAACTGCCGGCCGGT 62.573 61.111 42.53 25.81 37.65 5.28
2628 4573 2.914797 AATCGTCGAGCGCGTAGTGG 62.915 60.000 10.30 0.00 41.07 4.00
2715 4660 9.796180 AGAATTTCTGACTACTCCGTATATACT 57.204 33.333 11.05 0.00 0.00 2.12
2717 4662 7.976135 TTTCTGACTACTCCGTATATACTCC 57.024 40.000 11.05 0.00 0.00 3.85
2718 4663 6.047511 TCTGACTACTCCGTATATACTCCC 57.952 45.833 11.05 0.00 0.00 4.30
2719 4664 5.784390 TCTGACTACTCCGTATATACTCCCT 59.216 44.000 11.05 0.00 0.00 4.20
2720 4665 6.047511 TGACTACTCCGTATATACTCCCTC 57.952 45.833 11.05 0.00 0.00 4.30
2721 4666 5.046014 TGACTACTCCGTATATACTCCCTCC 60.046 48.000 11.05 0.00 0.00 4.30
2722 4667 3.735720 ACTCCGTATATACTCCCTCCC 57.264 52.381 11.05 0.00 0.00 4.30
2723 4668 3.267259 ACTCCGTATATACTCCCTCCCT 58.733 50.000 11.05 0.00 0.00 4.20
2724 4669 3.661654 ACTCCGTATATACTCCCTCCCTT 59.338 47.826 11.05 0.00 0.00 3.95
2725 4670 4.017808 CTCCGTATATACTCCCTCCCTTG 58.982 52.174 11.05 0.00 0.00 3.61
2726 4671 2.496470 CCGTATATACTCCCTCCCTTGC 59.504 54.545 11.05 0.00 0.00 4.01
2727 4672 3.432378 CGTATATACTCCCTCCCTTGCT 58.568 50.000 11.05 0.00 0.00 3.91
2728 4673 4.569228 CCGTATATACTCCCTCCCTTGCTA 60.569 50.000 11.05 0.00 0.00 3.49
2729 4674 5.014858 CGTATATACTCCCTCCCTTGCTAA 58.985 45.833 11.05 0.00 0.00 3.09
2730 4675 5.479375 CGTATATACTCCCTCCCTTGCTAAA 59.521 44.000 11.05 0.00 0.00 1.85
2731 4676 6.154706 CGTATATACTCCCTCCCTTGCTAAAT 59.845 42.308 11.05 0.00 0.00 1.40
2732 4677 7.341256 CGTATATACTCCCTCCCTTGCTAAATA 59.659 40.741 11.05 0.00 0.00 1.40
2733 4678 9.214962 GTATATACTCCCTCCCTTGCTAAATAT 57.785 37.037 5.58 0.00 0.00 1.28
2735 4680 9.799223 ATATACTCCCTCCCTTGCTAAATATAA 57.201 33.333 0.00 0.00 0.00 0.98
2736 4681 6.441088 ACTCCCTCCCTTGCTAAATATAAG 57.559 41.667 0.00 0.00 0.00 1.73
2737 4682 5.911766 ACTCCCTCCCTTGCTAAATATAAGT 59.088 40.000 0.00 0.00 0.00 2.24
2738 4683 6.043358 ACTCCCTCCCTTGCTAAATATAAGTC 59.957 42.308 0.00 0.00 0.00 3.01
2739 4684 6.151049 TCCCTCCCTTGCTAAATATAAGTCT 58.849 40.000 0.00 0.00 0.00 3.24
2740 4685 6.619852 TCCCTCCCTTGCTAAATATAAGTCTT 59.380 38.462 0.00 0.00 0.00 3.01
2741 4686 7.128883 TCCCTCCCTTGCTAAATATAAGTCTTT 59.871 37.037 0.00 0.00 0.00 2.52
2742 4687 7.780271 CCCTCCCTTGCTAAATATAAGTCTTTT 59.220 37.037 0.00 0.00 0.00 2.27
2743 4688 9.190317 CCTCCCTTGCTAAATATAAGTCTTTTT 57.810 33.333 0.00 0.00 0.00 1.94
2781 4726 9.970395 ACAAATGACCATATACATAGCAAAATG 57.030 29.630 0.00 0.00 0.00 2.32
2786 4731 9.571816 TGACCATATACATAGCAAAATGAATGA 57.428 29.630 1.26 0.00 0.00 2.57
2795 4740 9.182214 ACATAGCAAAATGAATGAATCTACACT 57.818 29.630 1.26 0.00 0.00 3.55
2796 4741 9.661187 CATAGCAAAATGAATGAATCTACACTC 57.339 33.333 0.00 0.00 0.00 3.51
2797 4742 7.934855 AGCAAAATGAATGAATCTACACTCT 57.065 32.000 0.00 0.00 0.00 3.24
2799 4744 9.453572 AGCAAAATGAATGAATCTACACTCTAA 57.546 29.630 0.00 0.00 0.00 2.10
2884 4829 7.893124 TTAAGAACGAAGGGAGTATATCTGT 57.107 36.000 0.00 0.00 0.00 3.41
2915 4860 8.970020 TGCAATCTCATAAATGTTTGGATAGTT 58.030 29.630 0.00 0.00 0.00 2.24
2924 4869 3.142951 TGTTTGGATAGTTCAACCACCG 58.857 45.455 0.00 0.00 33.20 4.94
2927 4872 1.276989 TGGATAGTTCAACCACCGTCC 59.723 52.381 0.00 0.00 0.00 4.79
2973 4931 2.217429 AAAAATCTTTTGCGGCGTGT 57.783 40.000 9.37 0.00 0.00 4.49
2990 4948 1.336755 GTGTGGATCGCCTGTTTTTGT 59.663 47.619 0.00 0.00 34.31 2.83
3069 5033 2.945984 GCGCTAAACTGCAGTGCA 59.054 55.556 22.49 18.58 46.40 4.57
3199 5223 9.645128 TTCATTCCACAATATCATCTAACCAAT 57.355 29.630 0.00 0.00 0.00 3.16
3292 5321 1.813786 CTCGTCTTCGTCCTCCTCTTT 59.186 52.381 0.00 0.00 38.33 2.52
3313 5343 5.620738 TTCTCCGATTCATCTTCCTCATT 57.379 39.130 0.00 0.00 0.00 2.57
3353 5383 1.016130 CCTCTTCATTGTCGCACGCT 61.016 55.000 0.00 0.00 0.00 5.07
3477 5518 3.329497 ATGCCTCCCATGAGAGACA 57.671 52.632 5.69 0.00 41.42 3.41
3583 5633 3.866582 GCCGCCCATGGTAGCTCT 61.867 66.667 11.73 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.609131 GTGTTGCTAGTGGGCCACAT 60.609 55.000 36.28 23.37 39.43 3.21
42 43 1.966493 CTTTATTGTGCGGCGCTCGT 61.966 55.000 33.26 22.41 41.72 4.18
53 54 4.680975 GCTCTCTTACGAGGCCTTTATTGT 60.681 45.833 6.77 3.64 37.86 2.71
93 94 2.860628 CGCCTCGTATGCAGAACGC 61.861 63.158 17.08 5.24 40.12 4.84
97 98 3.457263 TGGCGCCTCGTATGCAGA 61.457 61.111 29.70 0.00 0.00 4.26
99 100 2.022240 TATGTGGCGCCTCGTATGCA 62.022 55.000 29.70 14.43 0.00 3.96
102 106 1.006102 GCTATGTGGCGCCTCGTAT 60.006 57.895 29.70 16.60 0.00 3.06
111 115 0.807667 CTGGTCGTGAGCTATGTGGC 60.808 60.000 0.39 0.00 0.00 5.01
121 125 2.525629 TCCCAAGCCTGGTCGTGA 60.526 61.111 0.00 0.00 41.72 4.35
150 158 1.476471 CCTCATCAGCAGGAATGTCCC 60.476 57.143 0.00 0.00 37.19 4.46
158 166 0.325933 TGTGTTCCCTCATCAGCAGG 59.674 55.000 0.00 0.00 0.00 4.85
163 171 4.964897 AGTATCTCATGTGTTCCCTCATCA 59.035 41.667 0.00 0.00 0.00 3.07
166 174 5.360999 CACTAGTATCTCATGTGTTCCCTCA 59.639 44.000 0.00 0.00 0.00 3.86
171 179 4.045104 CGCCACTAGTATCTCATGTGTTC 58.955 47.826 0.00 0.00 0.00 3.18
191 199 1.290203 TCGATGAAATCTTCAGCCGC 58.710 50.000 0.00 0.00 42.82 6.53
275 284 4.574674 AAGTCAAGCCTTCATACCATGA 57.425 40.909 0.00 0.00 37.55 3.07
366 382 6.184789 TCCAACTTCATAATTCAAGGTACCC 58.815 40.000 8.74 0.00 0.00 3.69
367 383 7.393515 ACTTCCAACTTCATAATTCAAGGTACC 59.606 37.037 2.73 2.73 0.00 3.34
478 497 1.196104 TACGGGGAGGGTGGTTTCTG 61.196 60.000 0.00 0.00 0.00 3.02
518 545 3.570550 CGAAAATGACACCCCCAAAACTA 59.429 43.478 0.00 0.00 0.00 2.24
529 556 7.568679 GCCAAAAACTAATTCCGAAAATGACAC 60.569 37.037 0.00 0.00 0.00 3.67
530 557 6.422400 GCCAAAAACTAATTCCGAAAATGACA 59.578 34.615 0.00 0.00 0.00 3.58
532 559 6.754193 AGCCAAAAACTAATTCCGAAAATGA 58.246 32.000 0.00 0.00 0.00 2.57
533 560 8.594687 CATAGCCAAAAACTAATTCCGAAAATG 58.405 33.333 0.00 0.00 0.00 2.32
534 561 8.527810 TCATAGCCAAAAACTAATTCCGAAAAT 58.472 29.630 0.00 0.00 0.00 1.82
535 562 7.887381 TCATAGCCAAAAACTAATTCCGAAAA 58.113 30.769 0.00 0.00 0.00 2.29
539 566 6.436843 ACTCATAGCCAAAAACTAATTCCG 57.563 37.500 0.00 0.00 0.00 4.30
546 573 6.769512 TCAACTCTACTCATAGCCAAAAACT 58.230 36.000 0.00 0.00 0.00 2.66
572 599 0.036732 TCCAACATGGAGCACCTCAC 59.963 55.000 0.71 0.00 42.67 3.51
586 613 3.154827 TCTCCCTTGTTTCCATCCAAC 57.845 47.619 0.00 0.00 0.00 3.77
615 642 5.973651 TCTATGCTTAAAGTCGCTCAATG 57.026 39.130 0.00 0.00 0.00 2.82
616 643 7.710907 TGTTATCTATGCTTAAAGTCGCTCAAT 59.289 33.333 0.00 0.00 0.00 2.57
623 650 7.384115 TGCGGTATGTTATCTATGCTTAAAGTC 59.616 37.037 0.00 0.00 0.00 3.01
625 652 7.652300 TGCGGTATGTTATCTATGCTTAAAG 57.348 36.000 0.00 0.00 0.00 1.85
626 653 8.028540 CATGCGGTATGTTATCTATGCTTAAA 57.971 34.615 0.00 0.00 31.92 1.52
642 829 4.342862 AAGCTCATCTAACATGCGGTAT 57.657 40.909 0.00 0.00 0.00 2.73
693 880 6.091441 GCGTTTAGATCAGATCAAACACTCTT 59.909 38.462 23.69 4.62 33.70 2.85
694 881 5.578727 GCGTTTAGATCAGATCAAACACTCT 59.421 40.000 23.69 5.61 33.70 3.24
696 883 5.482908 AGCGTTTAGATCAGATCAAACACT 58.517 37.500 23.69 19.86 33.70 3.55
697 884 5.578727 AGAGCGTTTAGATCAGATCAAACAC 59.421 40.000 23.69 18.69 37.82 3.32
699 886 6.654793 AAGAGCGTTTAGATCAGATCAAAC 57.345 37.500 13.14 16.81 37.82 2.93
714 901 9.930693 CCCTCTATAAAGAAATATAAGAGCGTT 57.069 33.333 0.00 0.00 0.00 4.84
729 1009 7.934120 CCTTTGGTGAATACTCCCTCTATAAAG 59.066 40.741 0.00 0.00 0.00 1.85
730 1010 7.626084 TCCTTTGGTGAATACTCCCTCTATAAA 59.374 37.037 0.00 0.00 0.00 1.40
731 1011 7.136885 TCCTTTGGTGAATACTCCCTCTATAA 58.863 38.462 0.00 0.00 0.00 0.98
732 1012 6.689561 TCCTTTGGTGAATACTCCCTCTATA 58.310 40.000 0.00 0.00 0.00 1.31
734 1014 4.955335 TCCTTTGGTGAATACTCCCTCTA 58.045 43.478 0.00 0.00 0.00 2.43
763 1043 7.572523 TGATTTGGGTTCTCATGACAATATC 57.427 36.000 0.00 2.30 0.00 1.63
769 1049 3.507233 TGCTTGATTTGGGTTCTCATGAC 59.493 43.478 0.00 0.00 0.00 3.06
776 1056 2.224018 TGCAAGTGCTTGATTTGGGTTC 60.224 45.455 15.31 0.00 42.93 3.62
799 1079 3.620427 TTTCCGCATTAGACAAGCCTA 57.380 42.857 0.00 0.00 0.00 3.93
819 1104 6.287589 TGGTCAACAAAAGTTAACATGGTT 57.712 33.333 8.61 3.52 0.00 3.67
822 1107 5.347342 TGCTGGTCAACAAAAGTTAACATG 58.653 37.500 8.61 6.46 0.00 3.21
823 1108 5.590530 TGCTGGTCAACAAAAGTTAACAT 57.409 34.783 8.61 0.00 0.00 2.71
824 1109 5.392767 TTGCTGGTCAACAAAAGTTAACA 57.607 34.783 8.61 0.00 0.00 2.41
844 1129 4.546570 GGTAGCAAGTAAACTTTGCCTTG 58.453 43.478 6.36 9.68 37.84 3.61
850 1135 5.222171 TGGTATGGGGTAGCAAGTAAACTTT 60.222 40.000 0.00 0.00 37.83 2.66
851 1136 4.290196 TGGTATGGGGTAGCAAGTAAACTT 59.710 41.667 0.00 0.00 37.83 2.66
862 1147 4.668636 TCTTGGTTTTTGGTATGGGGTAG 58.331 43.478 0.00 0.00 0.00 3.18
871 1156 6.151144 GCATCTACACTATCTTGGTTTTTGGT 59.849 38.462 0.00 0.00 0.00 3.67
872 1157 6.375455 AGCATCTACACTATCTTGGTTTTTGG 59.625 38.462 0.00 0.00 0.00 3.28
874 1159 7.665559 TCAAGCATCTACACTATCTTGGTTTTT 59.334 33.333 0.00 0.00 33.68 1.94
899 1185 9.710900 ATTTTTCCAGAATCTATTGGTTGTTTC 57.289 29.630 0.00 0.00 35.89 2.78
932 1218 3.378861 TGGGGACATGCACAATTATCA 57.621 42.857 0.00 0.00 33.40 2.15
945 1231 2.841266 TCGGATACAAATCTTGGGGACA 59.159 45.455 0.00 0.00 39.83 4.02
957 1243 7.227910 GGCAAGATTTATAAACCTCGGATACAA 59.772 37.037 0.00 0.00 0.00 2.41
962 1248 5.105567 TGGCAAGATTTATAAACCTCGGA 57.894 39.130 0.00 0.00 0.00 4.55
975 1261 7.669427 TGATCAAACATAAACTTGGCAAGATT 58.331 30.769 32.50 27.59 0.00 2.40
1074 1393 4.581824 TGCTACTACCTAAATACTCCACCG 59.418 45.833 0.00 0.00 0.00 4.94
1075 1394 6.127253 TGTTGCTACTACCTAAATACTCCACC 60.127 42.308 0.00 0.00 0.00 4.61
1076 1395 6.870769 TGTTGCTACTACCTAAATACTCCAC 58.129 40.000 0.00 0.00 0.00 4.02
1110 1453 2.512515 GATCCTGCGTGAGGGCAC 60.513 66.667 3.14 0.00 43.06 5.01
1220 1564 8.953313 TCAGTAGAAGATGACGTTGATAACTAA 58.047 33.333 0.00 0.00 0.00 2.24
1221 1565 8.502105 TCAGTAGAAGATGACGTTGATAACTA 57.498 34.615 0.00 0.00 0.00 2.24
1224 1568 9.087424 CAATTCAGTAGAAGATGACGTTGATAA 57.913 33.333 0.00 0.00 37.14 1.75
1269 3172 4.035278 AGCTGCATACGTCTTCTCTTAC 57.965 45.455 1.02 0.00 0.00 2.34
1271 3174 3.444034 TGTAGCTGCATACGTCTTCTCTT 59.556 43.478 0.00 0.00 0.00 2.85
1275 3178 5.518847 TGTTATTGTAGCTGCATACGTCTTC 59.481 40.000 4.98 0.00 0.00 2.87
1277 3180 5.006153 TGTTATTGTAGCTGCATACGTCT 57.994 39.130 4.98 0.00 0.00 4.18
1278 3181 5.712217 TTGTTATTGTAGCTGCATACGTC 57.288 39.130 4.98 0.00 0.00 4.34
1284 3187 4.545610 GCTGTTTTGTTATTGTAGCTGCA 58.454 39.130 0.00 0.00 0.00 4.41
1285 3188 3.920412 GGCTGTTTTGTTATTGTAGCTGC 59.080 43.478 0.00 0.00 0.00 5.25
1286 3189 4.218417 AGGGCTGTTTTGTTATTGTAGCTG 59.782 41.667 0.00 0.00 0.00 4.24
1288 3191 4.783764 AGGGCTGTTTTGTTATTGTAGC 57.216 40.909 0.00 0.00 0.00 3.58
1289 3192 8.129211 GCTATAAGGGCTGTTTTGTTATTGTAG 58.871 37.037 0.00 0.00 0.00 2.74
1290 3193 7.832187 AGCTATAAGGGCTGTTTTGTTATTGTA 59.168 33.333 0.00 0.00 38.73 2.41
1291 3194 6.663523 AGCTATAAGGGCTGTTTTGTTATTGT 59.336 34.615 0.00 0.00 38.73 2.71
1292 3195 7.100458 AGCTATAAGGGCTGTTTTGTTATTG 57.900 36.000 0.00 0.00 38.73 1.90
1295 3198 5.811190 TGAGCTATAAGGGCTGTTTTGTTA 58.189 37.500 0.00 0.00 40.40 2.41
1296 3199 4.662278 TGAGCTATAAGGGCTGTTTTGTT 58.338 39.130 0.00 0.00 40.40 2.83
1412 3324 4.569564 CCTCCGTTCGAAAATAAAGTAGGG 59.430 45.833 0.00 0.00 0.00 3.53
1416 3328 4.251268 CTCCCTCCGTTCGAAAATAAAGT 58.749 43.478 0.00 0.00 0.00 2.66
1417 3329 4.251268 ACTCCCTCCGTTCGAAAATAAAG 58.749 43.478 0.00 0.00 0.00 1.85
1418 3330 4.276058 ACTCCCTCCGTTCGAAAATAAA 57.724 40.909 0.00 0.00 0.00 1.40
1421 3333 2.564062 TGTACTCCCTCCGTTCGAAAAT 59.436 45.455 0.00 0.00 0.00 1.82
1426 3338 2.667473 ATTTGTACTCCCTCCGTTCG 57.333 50.000 0.00 0.00 0.00 3.95
1427 3339 3.370061 CGAAATTTGTACTCCCTCCGTTC 59.630 47.826 0.00 0.00 0.00 3.95
1431 3343 4.186926 GGTACGAAATTTGTACTCCCTCC 58.813 47.826 19.53 2.45 41.47 4.30
1465 3377 5.124776 AGTTCATCACGACCTTTTTGACAAA 59.875 36.000 0.00 0.00 0.00 2.83
1468 3380 4.511826 AGAGTTCATCACGACCTTTTTGAC 59.488 41.667 0.00 0.00 0.00 3.18
1469 3381 4.511454 CAGAGTTCATCACGACCTTTTTGA 59.489 41.667 0.00 0.00 0.00 2.69
1470 3382 4.511454 TCAGAGTTCATCACGACCTTTTTG 59.489 41.667 0.00 0.00 0.00 2.44
1471 3383 4.703897 TCAGAGTTCATCACGACCTTTTT 58.296 39.130 0.00 0.00 0.00 1.94
1511 3423 2.591148 CGTACGTGTAGATCGTTTGGTG 59.409 50.000 7.22 0.00 41.72 4.17
1556 3468 1.349282 GCGTTCACGTTCGGTTTGT 59.651 52.632 0.62 0.00 42.22 2.83
1574 3486 1.669115 CTCCTGGACCAGCAACGTG 60.669 63.158 16.72 1.24 0.00 4.49
1659 3577 0.163788 GACCGCTGTGTCGAACATTG 59.836 55.000 0.00 0.00 38.39 2.82
2475 4419 1.560923 CTTCATCTGGTCGTAAGCCG 58.439 55.000 0.00 0.00 36.50 5.52
2500 4444 4.572571 ACCGGCCGGCAGTTCAAA 62.573 61.111 43.58 0.00 39.32 2.69
2628 4573 7.122550 CCTACGTCGTACTACTATTTCACTTC 58.877 42.308 0.00 0.00 0.00 3.01
2714 4659 6.271159 AGACTTATATTTAGCAAGGGAGGGAG 59.729 42.308 0.00 0.00 0.00 4.30
2715 4660 6.151049 AGACTTATATTTAGCAAGGGAGGGA 58.849 40.000 0.00 0.00 0.00 4.20
2716 4661 6.441088 AGACTTATATTTAGCAAGGGAGGG 57.559 41.667 0.00 0.00 0.00 4.30
2717 4662 8.753497 AAAAGACTTATATTTAGCAAGGGAGG 57.247 34.615 0.00 0.00 0.00 4.30
2755 4700 9.970395 CATTTTGCTATGTATATGGTCATTTGT 57.030 29.630 0.00 0.00 0.00 2.83
2760 4705 9.571816 TCATTCATTTTGCTATGTATATGGTCA 57.428 29.630 0.00 0.00 0.00 4.02
2769 4714 9.182214 AGTGTAGATTCATTCATTTTGCTATGT 57.818 29.630 0.00 0.00 0.00 2.29
2770 4715 9.661187 GAGTGTAGATTCATTCATTTTGCTATG 57.339 33.333 0.00 0.00 0.00 2.23
2771 4716 9.624373 AGAGTGTAGATTCATTCATTTTGCTAT 57.376 29.630 0.00 0.00 0.00 2.97
2773 4718 7.934855 AGAGTGTAGATTCATTCATTTTGCT 57.065 32.000 0.00 0.00 0.00 3.91
2858 4803 8.925338 ACAGATATACTCCCTTCGTTCTTAAAT 58.075 33.333 0.00 0.00 0.00 1.40
2859 4804 8.302515 ACAGATATACTCCCTTCGTTCTTAAA 57.697 34.615 0.00 0.00 0.00 1.52
2860 4805 7.893124 ACAGATATACTCCCTTCGTTCTTAA 57.107 36.000 0.00 0.00 0.00 1.85
2861 4806 9.584008 AATACAGATATACTCCCTTCGTTCTTA 57.416 33.333 0.00 0.00 0.00 2.10
2862 4807 8.480133 AATACAGATATACTCCCTTCGTTCTT 57.520 34.615 0.00 0.00 0.00 2.52
2863 4808 8.480133 AAATACAGATATACTCCCTTCGTTCT 57.520 34.615 0.00 0.00 0.00 3.01
2864 4809 8.979574 CAAAATACAGATATACTCCCTTCGTTC 58.020 37.037 0.00 0.00 0.00 3.95
2865 4810 7.441458 GCAAAATACAGATATACTCCCTTCGTT 59.559 37.037 0.00 0.00 0.00 3.85
2866 4811 6.929606 GCAAAATACAGATATACTCCCTTCGT 59.070 38.462 0.00 0.00 0.00 3.85
2867 4812 6.929049 TGCAAAATACAGATATACTCCCTTCG 59.071 38.462 0.00 0.00 0.00 3.79
2868 4813 8.677148 TTGCAAAATACAGATATACTCCCTTC 57.323 34.615 0.00 0.00 0.00 3.46
2869 4814 9.289782 GATTGCAAAATACAGATATACTCCCTT 57.710 33.333 1.71 0.00 0.00 3.95
2870 4815 8.664079 AGATTGCAAAATACAGATATACTCCCT 58.336 33.333 1.71 0.00 0.00 4.20
2871 4816 8.854614 AGATTGCAAAATACAGATATACTCCC 57.145 34.615 1.71 0.00 0.00 4.30
2872 4817 9.494271 TGAGATTGCAAAATACAGATATACTCC 57.506 33.333 1.71 0.00 0.00 3.85
2915 4860 2.927580 GCTCTCGGACGGTGGTTGA 61.928 63.158 0.00 0.00 0.00 3.18
2924 4869 0.532573 TGTTGGAGATGCTCTCGGAC 59.467 55.000 6.97 8.08 44.28 4.79
2927 4872 0.809241 GGCTGTTGGAGATGCTCTCG 60.809 60.000 6.97 0.00 44.28 4.04
2959 4917 1.573829 GATCCACACGCCGCAAAAGA 61.574 55.000 0.00 0.00 0.00 2.52
2971 4929 1.336440 CACAAAAACAGGCGATCCACA 59.664 47.619 0.00 0.00 33.74 4.17
2973 4931 0.313672 GCACAAAAACAGGCGATCCA 59.686 50.000 0.00 0.00 33.74 3.41
3044 5007 1.076533 GCAGTTTAGCGCGTCTGCTA 61.077 55.000 27.60 9.99 45.14 3.49
3077 5043 1.006086 CAACATATGACAAGCGCCGA 58.994 50.000 10.38 0.00 0.00 5.54
3134 5126 7.704472 TGTCATGAACTTGTTTGGTTTATGTTC 59.296 33.333 0.00 0.00 39.79 3.18
3140 5132 9.097257 CTTTTATGTCATGAACTTGTTTGGTTT 57.903 29.630 0.00 0.00 0.00 3.27
3185 5209 9.402320 TCGGATTTTGAAATTGGTTAGATGATA 57.598 29.630 0.00 0.00 0.00 2.15
3192 5216 6.315091 TCGTTCGGATTTTGAAATTGGTTA 57.685 33.333 0.00 0.00 0.00 2.85
3199 5223 5.487153 TGAACTTCGTTCGGATTTTGAAA 57.513 34.783 2.71 0.00 44.55 2.69
3226 5250 3.119316 TGCCATTCGTTTGTGTGAACTTT 60.119 39.130 0.00 0.00 0.00 2.66
3292 5321 4.651045 TGAATGAGGAAGATGAATCGGAGA 59.349 41.667 0.00 0.00 45.75 3.71
3313 5343 4.528596 AGGAGAAGGAAGAATCGTCTTTGA 59.471 41.667 0.00 0.00 44.42 2.69
3353 5383 1.808891 CGAGCTCCACATGATGATGCA 60.809 52.381 8.47 0.00 32.14 3.96
3450 5491 3.415087 GGGAGGCATGGGAGCACT 61.415 66.667 0.00 0.00 35.83 4.40
3477 5518 2.173519 CATGGGAGGCATGAGTTTTGT 58.826 47.619 0.00 0.00 32.09 2.83


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

AutoCloner maintained by Alex Coulton.