Multiple sequence alignment - TraesCS2A01G353200

Loading Multiple Alignment...

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 TraesCS2A01G353200 chr2A 100.000 3863 0 0 1 3863 593647369 593651231 0.000000e+00 7134.0
1 TraesCS2A01G353200 chr2B 91.700 2976 133 43 387 3318 529255156 529258061 0.000000e+00 4023.0
2 TraesCS2A01G353200 chr2B 91.471 340 22 4 45 383 529254769 529255102 9.780000e-126 460.0
3 TraesCS2A01G353200 chr2B 93.210 162 10 1 3703 3863 784739830 784739991 1.790000e-58 237.0
4 TraesCS2A01G353200 chr2B 80.531 113 21 1 501 612 116043935 116043823 6.880000e-13 86.1
5 TraesCS2A01G353200 chr2D 96.176 1412 40 11 1906 3310 449070726 449069322 0.000000e+00 2296.0
6 TraesCS2A01G353200 chr2D 92.221 1504 76 18 390 1868 449072334 449070847 0.000000e+00 2091.0
7 TraesCS2A01G353200 chr2D 90.179 336 28 2 45 379 449072715 449072384 2.130000e-117 433.0
8 TraesCS2A01G353200 chr2D 100.000 38 0 0 3333 3370 49185782 49185745 1.930000e-08 71.3
9 TraesCS2A01G353200 chr3D 86.525 705 43 25 915 1577 391258506 391259200 0.000000e+00 728.0
10 TraesCS2A01G353200 chr5A 93.333 165 10 1 3700 3863 43542993 43543157 3.860000e-60 243.0
11 TraesCS2A01G353200 chr5A 93.865 163 7 3 3702 3863 239402923 239403083 3.860000e-60 243.0
12 TraesCS2A01G353200 chr1A 94.872 156 7 1 3703 3857 367028019 367028174 3.860000e-60 243.0
13 TraesCS2A01G353200 chr1A 92.727 165 10 2 3700 3863 23018242 23018079 1.790000e-58 237.0
14 TraesCS2A01G353200 chr7A 92.547 161 12 0 3703 3863 100550881 100550721 8.350000e-57 231.0
15 TraesCS2A01G353200 chr7A 90.062 161 11 5 3707 3863 553044829 553044988 1.820000e-48 204.0
16 TraesCS2A01G353200 chr4A 92.405 158 9 2 3701 3857 25794495 25794650 5.020000e-54 222.0
17 TraesCS2A01G353200 chr6D 91.954 87 7 0 637 723 18905686 18905772 5.240000e-24 122.0
18 TraesCS2A01G353200 chr6D 100.000 38 0 0 3333 3370 78352771 78352734 1.930000e-08 71.3
19 TraesCS2A01G353200 chr6B 85.915 71 6 2 3333 3400 351345737 351345806 5.350000e-09 73.1
20 TraesCS2A01G353200 chr6B 100.000 37 0 0 3333 3369 174971075 174971111 6.930000e-08 69.4
21 TraesCS2A01G353200 chr5B 89.655 58 5 1 3333 3389 170597874 170597817 5.350000e-09 73.1
22 TraesCS2A01G353200 chr3B 95.455 44 2 0 3327 3370 74812183 74812140 1.930000e-08 71.3
23 TraesCS2A01G353200 chr7D 100.000 37 0 0 3333 3369 290544895 290544859 6.930000e-08 69.4
24 TraesCS2A01G353200 chr1D 97.500 40 1 0 3330 3369 85644469 85644508 6.930000e-08 69.4
25 TraesCS2A01G353200 chr3A 88.889 54 5 1 3811 3863 691673686 691673739 8.960000e-07 65.8
26 TraesCS2A01G353200 chr4D 90.698 43 4 0 3327 3369 134117544 134117586 1.500000e-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 TraesCS2A01G353200 chr2A 593647369 593651231 3862 False 7134.000000 7134 100.000000 1 3863 1 chr2A.!!$F1 3862
1 TraesCS2A01G353200 chr2B 529254769 529258061 3292 False 2241.500000 4023 91.585500 45 3318 2 chr2B.!!$F2 3273
2 TraesCS2A01G353200 chr2D 449069322 449072715 3393 True 1606.666667 2296 92.858667 45 3310 3 chr2D.!!$R2 3265
3 TraesCS2A01G353200 chr3D 391258506 391259200 694 False 728.000000 728 86.525000 915 1577 1 chr3D.!!$F1 662

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
496 548 0.745845 CCCTTGCTCAATCCGACCTG 60.746 60.0 0.00 0.0 0.00 4.00 F
1155 1248 0.390340 CTAGTTCCAAGCTCGCAGCA 60.390 55.0 10.16 0.0 45.56 4.41 F
1613 1734 0.452987 CTGGTGTGGAATGGCGATTG 59.547 55.0 0.00 0.0 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 2192 1.303806 CCAAGTAAACCCCACCCCG 60.304 63.158 0.0 0.0 0.00 5.73 R
2796 3009 1.216710 CTCCTCGCTGTCACTTCCC 59.783 63.158 0.0 0.0 0.00 3.97 R
3014 3230 2.301009 ACACCTAAACCTCCAGTTACCG 59.699 50.000 0.0 0.0 37.88 4.02 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
20 21 3.433513 GCACGAGTTAGGGTACTAAGG 57.566 52.381 0.00 0.00 39.73 2.69
21 22 2.480932 GCACGAGTTAGGGTACTAAGGC 60.481 54.545 0.00 0.00 39.73 4.35
22 23 2.756760 CACGAGTTAGGGTACTAAGGCA 59.243 50.000 0.00 0.00 39.73 4.75
23 24 2.757314 ACGAGTTAGGGTACTAAGGCAC 59.243 50.000 0.00 0.00 39.73 5.01
25 26 3.066481 CGAGTTAGGGTACTAAGGCACTC 59.934 52.174 0.00 0.00 38.49 3.51
26 27 4.021916 GAGTTAGGGTACTAAGGCACTCA 58.978 47.826 0.00 0.00 38.49 3.41
27 28 4.621769 AGTTAGGGTACTAAGGCACTCAT 58.378 43.478 0.00 0.00 38.49 2.90
28 29 4.406003 AGTTAGGGTACTAAGGCACTCATG 59.594 45.833 0.00 0.00 38.49 3.07
29 30 2.834113 AGGGTACTAAGGCACTCATGT 58.166 47.619 0.00 0.00 38.49 3.21
30 31 2.766828 AGGGTACTAAGGCACTCATGTC 59.233 50.000 0.00 0.00 38.49 3.06
31 32 2.766828 GGGTACTAAGGCACTCATGTCT 59.233 50.000 0.00 0.00 44.96 3.41
39 40 4.457834 AGGCACTCATGTCTTAGTACAC 57.542 45.455 0.00 0.00 37.58 2.90
40 41 3.195825 AGGCACTCATGTCTTAGTACACC 59.804 47.826 0.00 0.00 37.58 4.16
41 42 3.056107 GGCACTCATGTCTTAGTACACCA 60.056 47.826 0.00 0.00 30.75 4.17
42 43 4.562757 GGCACTCATGTCTTAGTACACCAA 60.563 45.833 0.00 0.00 30.75 3.67
43 44 4.389077 GCACTCATGTCTTAGTACACCAAC 59.611 45.833 0.00 0.00 30.75 3.77
55 56 4.394729 AGTACACCAACAACCTTGTATGG 58.605 43.478 13.45 13.45 41.31 2.74
63 64 5.106157 CCAACAACCTTGTATGGATCTTCAC 60.106 44.000 11.14 0.00 41.31 3.18
92 93 4.604490 TCCTGGGAACTTAATTTGTAGGGT 59.396 41.667 0.00 0.00 0.00 4.34
149 150 7.821652 TCAACAACAACTTCACATTAAAGTCA 58.178 30.769 0.00 0.00 35.96 3.41
154 155 5.995282 ACAACTTCACATTAAAGTCATCGGA 59.005 36.000 0.00 0.00 35.96 4.55
194 196 3.040147 GAGGTGATCCAACGAACTCAA 57.960 47.619 0.00 0.00 35.89 3.02
223 225 2.289257 GGGTTGGGTGAGTGTGTAGTAC 60.289 54.545 0.00 0.00 0.00 2.73
302 304 4.020128 ACCTCCTTGACCATTAGAACTGAC 60.020 45.833 0.00 0.00 0.00 3.51
304 306 5.513094 CCTCCTTGACCATTAGAACTGACAA 60.513 44.000 0.00 0.00 0.00 3.18
383 385 1.608025 GCTCACACCACGATCCTCAAA 60.608 52.381 0.00 0.00 0.00 2.69
388 440 2.038426 ACACCACGATCCTCAAATGTCA 59.962 45.455 0.00 0.00 0.00 3.58
411 463 8.687301 GTCAACCAACAAACTTTAATTCATACG 58.313 33.333 0.00 0.00 0.00 3.06
441 493 4.084849 TGTTTTCTTTTGTTGCAACACACG 60.085 37.500 31.17 21.99 38.92 4.49
455 507 5.179555 TGCAACACACGTACATTTATGCTAA 59.820 36.000 0.00 0.00 32.74 3.09
492 544 2.125147 CGCCCTTGCTCAATCCGA 60.125 61.111 0.00 0.00 34.43 4.55
495 547 1.604378 CCCTTGCTCAATCCGACCT 59.396 57.895 0.00 0.00 0.00 3.85
496 548 0.745845 CCCTTGCTCAATCCGACCTG 60.746 60.000 0.00 0.00 0.00 4.00
497 549 0.745845 CCTTGCTCAATCCGACCTGG 60.746 60.000 0.00 0.00 40.09 4.45
506 558 3.072476 TCAATCCGACCTGGGGAAATATC 59.928 47.826 0.00 0.00 37.07 1.63
518 570 4.079500 TGGGGAAATATCATGTGCTACCAA 60.080 41.667 0.00 0.00 0.00 3.67
551 603 1.515954 CGTGATACGGGCTCTTGGT 59.484 57.895 0.00 0.00 38.08 3.67
562 615 2.093341 GGGCTCTTGGTAACGTTGGATA 60.093 50.000 11.99 0.00 42.51 2.59
580 633 3.007398 GGATATCAGATCAAACGGCTCCT 59.993 47.826 4.83 0.00 0.00 3.69
581 634 4.220821 GGATATCAGATCAAACGGCTCCTA 59.779 45.833 4.83 0.00 0.00 2.94
582 635 5.105146 GGATATCAGATCAAACGGCTCCTAT 60.105 44.000 4.83 0.00 0.00 2.57
653 707 2.572290 GTGCAGGTACAACAACTCCTT 58.428 47.619 0.00 0.00 0.00 3.36
655 709 4.324267 GTGCAGGTACAACAACTCCTTAT 58.676 43.478 0.00 0.00 0.00 1.73
683 737 1.137086 CGGATCTGAGATCCAACGGTT 59.863 52.381 33.76 0.00 38.08 4.44
832 907 2.286502 GGAGGCCTTCCTTCCCCT 60.287 66.667 6.77 0.00 44.46 4.79
833 908 1.931180 GGAGGCCTTCCTTCCCCTT 60.931 63.158 6.77 0.00 44.46 3.95
834 909 1.610327 GAGGCCTTCCTTCCCCTTC 59.390 63.158 6.77 0.00 44.46 3.46
835 910 1.927569 GAGGCCTTCCTTCCCCTTCC 61.928 65.000 6.77 0.00 44.46 3.46
836 911 2.684104 GCCTTCCTTCCCCTTCCC 59.316 66.667 0.00 0.00 0.00 3.97
837 912 2.997584 GCCTTCCTTCCCCTTCCCC 61.998 68.421 0.00 0.00 0.00 4.81
864 939 2.360165 TCTCCTTTACCTTATCGGCGTC 59.640 50.000 6.85 0.00 35.61 5.19
910 985 3.396502 CGCACGCGTCGTACCAAA 61.397 61.111 9.86 0.00 38.32 3.28
982 1063 1.882352 GCACGGTTCCAATCTGGTTCT 60.882 52.381 0.00 0.00 39.03 3.01
1153 1246 0.460987 CCCTAGTTCCAAGCTCGCAG 60.461 60.000 0.00 0.00 0.00 5.18
1154 1247 1.086634 CCTAGTTCCAAGCTCGCAGC 61.087 60.000 0.00 0.47 42.84 5.25
1155 1248 0.390340 CTAGTTCCAAGCTCGCAGCA 60.390 55.000 10.16 0.00 45.56 4.41
1162 1255 1.302366 CAAGCTCGCAGCAATCCATA 58.698 50.000 10.16 0.00 45.56 2.74
1175 1268 4.941325 CAATCCATATCTGATTGCTCCG 57.059 45.455 10.16 0.00 41.69 4.63
1191 1287 2.189521 CGCCCGCAAACCCTATCT 59.810 61.111 0.00 0.00 0.00 1.98
1240 1336 3.438087 TCTTGCTGCTTGTAGATGCTTTC 59.562 43.478 0.00 0.00 0.00 2.62
1244 1341 4.279169 TGCTGCTTGTAGATGCTTTCTTTT 59.721 37.500 0.00 0.00 35.79 2.27
1252 1349 7.581213 TGTAGATGCTTTCTTTTCCTTTTGA 57.419 32.000 0.00 0.00 35.79 2.69
1253 1350 8.181904 TGTAGATGCTTTCTTTTCCTTTTGAT 57.818 30.769 0.00 0.00 35.79 2.57
1254 1351 8.084073 TGTAGATGCTTTCTTTTCCTTTTGATG 58.916 33.333 0.00 0.00 35.79 3.07
1423 1524 2.046120 GCTTGCTCTCTGCTGGCT 60.046 61.111 0.00 0.00 43.37 4.75
1448 1550 5.682943 TGTTGGTGGATTTAGTTTCTTCG 57.317 39.130 0.00 0.00 0.00 3.79
1613 1734 0.452987 CTGGTGTGGAATGGCGATTG 59.547 55.000 0.00 0.00 0.00 2.67
1632 1753 7.394872 GCGATTGACTTTATAGTGCATATAGC 58.605 38.462 0.00 0.00 45.96 2.97
1720 1841 3.252284 CTGTGCCACCCAGGGTCT 61.252 66.667 8.79 0.00 38.09 3.85
1733 1854 1.001282 AGGGTCTAGTCGTCCTTCCT 58.999 55.000 0.00 0.00 0.00 3.36
1790 1912 4.333926 GGTTTGCCATCAGACATTAGACTC 59.666 45.833 0.00 0.00 34.09 3.36
1798 1920 3.377485 TCAGACATTAGACTCGTGCTACC 59.623 47.826 0.00 0.00 0.00 3.18
1821 1943 6.205270 ACCGTAAAAGGTAGTACAACCATTTG 59.795 38.462 2.06 0.00 43.89 2.32
1858 1980 1.888215 ATTGCAGCCATCCACGATAG 58.112 50.000 0.00 0.00 46.19 2.08
1893 2015 7.012704 GCTTCAGAAGTCTAATGATGCCATTTA 59.987 37.037 11.94 0.00 42.56 1.40
1899 2021 6.426587 AGTCTAATGATGCCATTTACTTGGT 58.573 36.000 0.00 0.00 42.56 3.67
1902 2024 8.034804 GTCTAATGATGCCATTTACTTGGTTTT 58.965 33.333 0.00 0.00 42.56 2.43
1904 2026 5.798125 TGATGCCATTTACTTGGTTTTCA 57.202 34.783 0.00 0.00 39.11 2.69
1985 2191 1.760613 TCAACCTAGGTCCGCATTAGG 59.239 52.381 16.64 1.18 39.86 2.69
1986 2192 0.468648 AACCTAGGTCCGCATTAGGC 59.531 55.000 16.64 0.00 37.97 3.93
2060 2267 6.766467 ACATGGTTATTGGCTTACTAGTTAGC 59.234 38.462 22.63 22.63 34.76 3.09
2064 2273 7.124599 TGGTTATTGGCTTACTAGTTAGCACTA 59.875 37.037 29.23 16.52 37.00 2.74
2065 2274 8.148999 GGTTATTGGCTTACTAGTTAGCACTAT 58.851 37.037 29.23 21.89 37.00 2.12
2107 2318 7.956420 TTTGTACTTATAAGGTCACTGTGTG 57.044 36.000 16.73 0.00 34.45 3.82
2179 2390 2.203470 GTCCCCTATAGGACGAGGAG 57.797 60.000 21.07 1.09 46.57 3.69
2367 2578 6.834168 ATGTTTGTTACATTTAGGTCCCAG 57.166 37.500 0.00 0.00 45.19 4.45
2517 2730 9.762933 AATACAAATGTAATAATTGGCCACATC 57.237 29.630 3.88 0.00 33.76 3.06
2796 3009 2.203056 TCCCGATCCAAGCATGCG 60.203 61.111 13.01 0.00 0.00 4.73
2899 3112 2.614987 GCCCAATACCAATTTGCTTGCA 60.615 45.455 0.00 0.00 33.20 4.08
3120 3336 8.758829 TGTACTTGATGGATAGTGACAGTATTT 58.241 33.333 4.29 0.00 0.00 1.40
3345 3564 7.719871 ATACACATGTTCTACCTCTGTAACT 57.280 36.000 0.00 0.00 0.00 2.24
3346 3565 8.818622 ATACACATGTTCTACCTCTGTAACTA 57.181 34.615 0.00 0.00 0.00 2.24
3347 3566 7.534723 ACACATGTTCTACCTCTGTAACTAA 57.465 36.000 0.00 0.00 0.00 2.24
3348 3567 7.959175 ACACATGTTCTACCTCTGTAACTAAA 58.041 34.615 0.00 0.00 0.00 1.85
3349 3568 8.594550 ACACATGTTCTACCTCTGTAACTAAAT 58.405 33.333 0.00 0.00 0.00 1.40
3376 3595 6.455360 AGATGTTTTTGCAGTTTCTCTTCA 57.545 33.333 0.00 0.00 0.00 3.02
3377 3596 6.501781 AGATGTTTTTGCAGTTTCTCTTCAG 58.498 36.000 0.00 0.00 0.00 3.02
3378 3597 5.643379 TGTTTTTGCAGTTTCTCTTCAGT 57.357 34.783 0.00 0.00 0.00 3.41
3379 3598 6.751514 TGTTTTTGCAGTTTCTCTTCAGTA 57.248 33.333 0.00 0.00 0.00 2.74
3380 3599 7.151999 TGTTTTTGCAGTTTCTCTTCAGTAA 57.848 32.000 0.00 0.00 0.00 2.24
3381 3600 7.027161 TGTTTTTGCAGTTTCTCTTCAGTAAC 58.973 34.615 0.00 0.00 31.62 2.50
3382 3601 7.094377 TGTTTTTGCAGTTTCTCTTCAGTAACT 60.094 33.333 0.00 0.00 40.02 2.24
3383 3602 8.395633 GTTTTTGCAGTTTCTCTTCAGTAACTA 58.604 33.333 0.00 0.00 37.98 2.24
3384 3603 8.500753 TTTTGCAGTTTCTCTTCAGTAACTAA 57.499 30.769 0.00 0.00 37.98 2.24
3385 3604 8.500753 TTTGCAGTTTCTCTTCAGTAACTAAA 57.499 30.769 0.00 0.00 37.98 1.85
3386 3605 8.677148 TTGCAGTTTCTCTTCAGTAACTAAAT 57.323 30.769 0.00 0.00 37.98 1.40
3387 3606 9.772973 TTGCAGTTTCTCTTCAGTAACTAAATA 57.227 29.630 0.00 0.00 37.98 1.40
3388 3607 9.944376 TGCAGTTTCTCTTCAGTAACTAAATAT 57.056 29.630 0.00 0.00 37.98 1.28
3437 3656 8.994429 TTTTAAGACTTTTGCAGTTCATTTGA 57.006 26.923 0.00 0.00 35.01 2.69
3438 3657 8.994429 TTTAAGACTTTTGCAGTTCATTTGAA 57.006 26.923 0.00 0.00 35.01 2.69
3509 3728 8.991783 AATGAATCTGATGATACTGATTTGGT 57.008 30.769 0.00 0.00 38.11 3.67
3515 3734 9.857656 ATCTGATGATACTGATTTGGTATTTGT 57.142 29.630 0.00 0.00 31.03 2.83
3516 3735 9.112725 TCTGATGATACTGATTTGGTATTTGTG 57.887 33.333 0.00 0.00 31.03 3.33
3517 3736 8.224389 TGATGATACTGATTTGGTATTTGTGG 57.776 34.615 0.00 0.00 31.03 4.17
3518 3737 8.052141 TGATGATACTGATTTGGTATTTGTGGA 58.948 33.333 0.00 0.00 31.03 4.02
3519 3738 9.071276 GATGATACTGATTTGGTATTTGTGGAT 57.929 33.333 0.00 0.00 31.03 3.41
3521 3740 9.913310 TGATACTGATTTGGTATTTGTGGATAA 57.087 29.630 0.00 0.00 31.03 1.75
3524 3743 8.650143 ACTGATTTGGTATTTGTGGATAAACT 57.350 30.769 0.00 0.00 0.00 2.66
3525 3744 9.088987 ACTGATTTGGTATTTGTGGATAAACTT 57.911 29.630 0.00 0.00 0.00 2.66
3526 3745 9.357652 CTGATTTGGTATTTGTGGATAAACTTG 57.642 33.333 0.00 0.00 0.00 3.16
3527 3746 8.310382 TGATTTGGTATTTGTGGATAAACTTGG 58.690 33.333 0.00 0.00 0.00 3.61
3528 3747 7.604657 TTTGGTATTTGTGGATAAACTTGGT 57.395 32.000 0.00 0.00 0.00 3.67
3529 3748 6.827586 TGGTATTTGTGGATAAACTTGGTC 57.172 37.500 0.00 0.00 0.00 4.02
3530 3749 6.307776 TGGTATTTGTGGATAAACTTGGTCA 58.692 36.000 0.00 0.00 0.00 4.02
3531 3750 6.778069 TGGTATTTGTGGATAAACTTGGTCAA 59.222 34.615 0.00 0.00 0.00 3.18
3532 3751 7.287927 TGGTATTTGTGGATAAACTTGGTCAAA 59.712 33.333 0.00 0.00 0.00 2.69
3533 3752 8.311109 GGTATTTGTGGATAAACTTGGTCAAAT 58.689 33.333 0.00 0.00 37.75 2.32
3534 3753 9.705290 GTATTTGTGGATAAACTTGGTCAAATT 57.295 29.630 0.00 0.00 36.28 1.82
3535 3754 8.831715 ATTTGTGGATAAACTTGGTCAAATTC 57.168 30.769 0.00 0.00 32.73 2.17
3536 3755 6.968263 TGTGGATAAACTTGGTCAAATTCA 57.032 33.333 0.00 0.00 0.00 2.57
3537 3756 6.980593 TGTGGATAAACTTGGTCAAATTCAG 58.019 36.000 0.00 0.00 0.00 3.02
3538 3757 6.549364 TGTGGATAAACTTGGTCAAATTCAGT 59.451 34.615 0.00 0.00 0.00 3.41
3539 3758 6.863126 GTGGATAAACTTGGTCAAATTCAGTG 59.137 38.462 0.00 0.00 0.00 3.66
3540 3759 6.549364 TGGATAAACTTGGTCAAATTCAGTGT 59.451 34.615 0.00 0.00 0.00 3.55
3541 3760 7.721842 TGGATAAACTTGGTCAAATTCAGTGTA 59.278 33.333 0.00 0.00 0.00 2.90
3542 3761 8.237267 GGATAAACTTGGTCAAATTCAGTGTAG 58.763 37.037 0.00 0.00 0.00 2.74
3543 3762 8.691661 ATAAACTTGGTCAAATTCAGTGTAGT 57.308 30.769 0.00 0.00 0.00 2.73
3544 3763 9.787435 ATAAACTTGGTCAAATTCAGTGTAGTA 57.213 29.630 0.00 0.00 0.00 1.82
3545 3764 8.691661 AAACTTGGTCAAATTCAGTGTAGTAT 57.308 30.769 0.00 0.00 0.00 2.12
3546 3765 7.672983 ACTTGGTCAAATTCAGTGTAGTATG 57.327 36.000 0.00 0.00 0.00 2.39
3547 3766 7.450074 ACTTGGTCAAATTCAGTGTAGTATGA 58.550 34.615 0.00 0.00 0.00 2.15
3548 3767 7.387948 ACTTGGTCAAATTCAGTGTAGTATGAC 59.612 37.037 0.00 0.00 36.18 3.06
3549 3768 6.764379 TGGTCAAATTCAGTGTAGTATGACA 58.236 36.000 15.32 0.00 38.09 3.58
3550 3769 7.394016 TGGTCAAATTCAGTGTAGTATGACAT 58.606 34.615 15.32 0.00 38.09 3.06
3551 3770 7.882791 TGGTCAAATTCAGTGTAGTATGACATT 59.117 33.333 15.32 0.00 38.09 2.71
3552 3771 9.378551 GGTCAAATTCAGTGTAGTATGACATTA 57.621 33.333 15.32 0.00 38.09 1.90
3595 3814 5.588240 GGTATTACCTTGCTAACAATTGGC 58.412 41.667 10.83 4.28 34.73 4.52
3596 3815 5.126384 GGTATTACCTTGCTAACAATTGGCA 59.874 40.000 10.83 7.08 45.81 4.92
3603 3822 4.019792 TGCTAACAATTGGCAGAGAAGA 57.980 40.909 10.83 0.00 42.49 2.87
3604 3823 4.397420 TGCTAACAATTGGCAGAGAAGAA 58.603 39.130 10.83 0.00 42.49 2.52
3605 3824 4.826733 TGCTAACAATTGGCAGAGAAGAAA 59.173 37.500 10.83 0.00 42.49 2.52
3606 3825 5.301551 TGCTAACAATTGGCAGAGAAGAAAA 59.698 36.000 10.83 0.00 42.49 2.29
3607 3826 6.183360 TGCTAACAATTGGCAGAGAAGAAAAA 60.183 34.615 10.83 0.00 42.49 1.94
3642 3861 9.763465 CATCCTTGCAAATGAACAAAATTTATC 57.237 29.630 5.34 0.00 0.00 1.75
3643 3862 9.729281 ATCCTTGCAAATGAACAAAATTTATCT 57.271 25.926 0.00 0.00 0.00 1.98
3644 3863 9.558396 TCCTTGCAAATGAACAAAATTTATCTT 57.442 25.926 0.00 0.00 0.00 2.40
3648 3867 8.782144 TGCAAATGAACAAAATTTATCTTTCCC 58.218 29.630 0.00 0.00 0.00 3.97
3649 3868 7.956943 GCAAATGAACAAAATTTATCTTTCCCG 59.043 33.333 0.00 0.00 0.00 5.14
3650 3869 8.442384 CAAATGAACAAAATTTATCTTTCCCGG 58.558 33.333 0.00 0.00 0.00 5.73
3651 3870 6.658188 TGAACAAAATTTATCTTTCCCGGT 57.342 33.333 0.00 0.00 0.00 5.28
3652 3871 6.451393 TGAACAAAATTTATCTTTCCCGGTG 58.549 36.000 0.00 0.00 0.00 4.94
3653 3872 6.265649 TGAACAAAATTTATCTTTCCCGGTGA 59.734 34.615 0.00 0.00 0.00 4.02
3654 3873 6.850752 ACAAAATTTATCTTTCCCGGTGAT 57.149 33.333 0.00 1.19 0.00 3.06
3655 3874 7.239763 ACAAAATTTATCTTTCCCGGTGATT 57.760 32.000 0.00 0.00 0.00 2.57
3656 3875 7.676004 ACAAAATTTATCTTTCCCGGTGATTT 58.324 30.769 0.00 0.00 0.00 2.17
3657 3876 8.154203 ACAAAATTTATCTTTCCCGGTGATTTT 58.846 29.630 0.00 0.00 0.00 1.82
3658 3877 8.998377 CAAAATTTATCTTTCCCGGTGATTTTT 58.002 29.630 0.00 0.94 0.00 1.94
3704 3923 4.962836 GGCACACTGGCACTGGCT 62.963 66.667 3.97 0.00 43.14 4.75
3705 3924 2.032528 GCACACTGGCACTGGCTA 59.967 61.111 3.97 0.00 40.87 3.93
3706 3925 1.600636 GCACACTGGCACTGGCTAA 60.601 57.895 3.97 0.00 40.87 3.09
3707 3926 0.962356 GCACACTGGCACTGGCTAAT 60.962 55.000 3.97 0.00 40.87 1.73
3708 3927 1.538047 CACACTGGCACTGGCTAATT 58.462 50.000 3.97 0.00 40.87 1.40
3709 3928 1.888512 CACACTGGCACTGGCTAATTT 59.111 47.619 3.97 0.00 40.87 1.82
3710 3929 2.297033 CACACTGGCACTGGCTAATTTT 59.703 45.455 3.97 0.00 40.87 1.82
3711 3930 2.965147 ACACTGGCACTGGCTAATTTTT 59.035 40.909 3.97 0.00 40.87 1.94
3793 4012 9.945904 TTTTTAAAAATATTAACCAATCGGCCT 57.054 25.926 9.31 0.00 34.57 5.19
3796 4015 7.891498 AAAAATATTAACCAATCGGCCTACT 57.109 32.000 0.00 0.00 34.57 2.57
3797 4016 6.877611 AAATATTAACCAATCGGCCTACTG 57.122 37.500 0.00 0.00 34.57 2.74
3798 4017 2.032680 TTAACCAATCGGCCTACTGC 57.967 50.000 0.00 0.00 40.16 4.40
3799 4018 1.200519 TAACCAATCGGCCTACTGCT 58.799 50.000 0.00 0.00 40.92 4.24
3807 4026 3.997672 GGCCTACTGCTGATCGATT 57.002 52.632 0.00 0.00 40.92 3.34
3808 4027 1.506493 GGCCTACTGCTGATCGATTG 58.494 55.000 0.00 0.00 40.92 2.67
3809 4028 1.506493 GCCTACTGCTGATCGATTGG 58.494 55.000 0.00 0.00 36.87 3.16
3810 4029 1.069204 GCCTACTGCTGATCGATTGGA 59.931 52.381 0.00 0.00 36.87 3.53
3811 4030 2.748605 CCTACTGCTGATCGATTGGAC 58.251 52.381 0.00 0.00 0.00 4.02
3812 4031 2.546795 CCTACTGCTGATCGATTGGACC 60.547 54.545 0.00 0.00 0.00 4.46
3813 4032 0.179000 ACTGCTGATCGATTGGACCC 59.821 55.000 0.00 0.00 0.00 4.46
3814 4033 0.178767 CTGCTGATCGATTGGACCCA 59.821 55.000 0.00 0.00 0.00 4.51
3815 4034 0.178767 TGCTGATCGATTGGACCCAG 59.821 55.000 0.00 2.05 33.92 4.45
3816 4035 0.179000 GCTGATCGATTGGACCCAGT 59.821 55.000 0.00 0.00 33.55 4.00
3817 4036 1.808133 GCTGATCGATTGGACCCAGTC 60.808 57.143 0.00 1.87 33.55 3.51
3821 4040 2.124695 GATTGGACCCAGTCGGCC 60.125 66.667 0.00 0.00 32.65 6.13
3822 4041 2.610859 ATTGGACCCAGTCGGCCT 60.611 61.111 0.00 0.00 32.65 5.19
3823 4042 2.876368 GATTGGACCCAGTCGGCCTG 62.876 65.000 0.00 0.00 41.15 4.85
3826 4045 4.767255 GACCCAGTCGGCCTGCTG 62.767 72.222 14.32 14.32 40.06 4.41
3837 4056 3.515286 CCTGCTGCTGGCCGATTG 61.515 66.667 12.79 0.00 40.92 2.67
3838 4057 3.515286 CTGCTGCTGGCCGATTGG 61.515 66.667 0.00 0.00 40.92 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.480932 GCCTTAGTACCCTAACTCGTGC 60.481 54.545 0.00 0.00 0.00 5.34
1 2 2.756760 TGCCTTAGTACCCTAACTCGTG 59.243 50.000 0.00 0.00 0.00 4.35
2 3 2.757314 GTGCCTTAGTACCCTAACTCGT 59.243 50.000 0.00 0.00 0.00 4.18
3 4 3.022406 AGTGCCTTAGTACCCTAACTCG 58.978 50.000 0.00 0.00 0.00 4.18
4 5 4.021916 TGAGTGCCTTAGTACCCTAACTC 58.978 47.826 0.00 0.00 31.93 3.01
5 6 4.057063 TGAGTGCCTTAGTACCCTAACT 57.943 45.455 0.00 0.00 0.00 2.24
6 7 4.161754 ACATGAGTGCCTTAGTACCCTAAC 59.838 45.833 0.00 0.00 0.00 2.34
7 8 4.359105 ACATGAGTGCCTTAGTACCCTAA 58.641 43.478 0.00 0.00 0.00 2.69
8 9 3.958798 GACATGAGTGCCTTAGTACCCTA 59.041 47.826 0.00 0.00 0.00 3.53
9 10 2.766828 GACATGAGTGCCTTAGTACCCT 59.233 50.000 0.00 0.00 0.00 4.34
10 11 2.766828 AGACATGAGTGCCTTAGTACCC 59.233 50.000 0.00 0.00 0.00 3.69
11 12 4.473477 AAGACATGAGTGCCTTAGTACC 57.527 45.455 0.00 0.00 0.00 3.34
16 17 5.105473 GGTGTACTAAGACATGAGTGCCTTA 60.105 44.000 0.00 0.00 30.30 2.69
17 18 4.322801 GGTGTACTAAGACATGAGTGCCTT 60.323 45.833 0.00 0.00 32.51 4.35
18 19 3.195825 GGTGTACTAAGACATGAGTGCCT 59.804 47.826 0.00 0.00 0.00 4.75
19 20 3.056107 TGGTGTACTAAGACATGAGTGCC 60.056 47.826 0.00 0.00 0.00 5.01
20 21 4.188247 TGGTGTACTAAGACATGAGTGC 57.812 45.455 0.00 0.00 0.00 4.40
21 22 5.538118 TGTTGGTGTACTAAGACATGAGTG 58.462 41.667 0.00 0.00 0.00 3.51
22 23 5.801531 TGTTGGTGTACTAAGACATGAGT 57.198 39.130 0.00 0.00 0.00 3.41
23 24 5.408604 GGTTGTTGGTGTACTAAGACATGAG 59.591 44.000 0.00 0.00 0.00 2.90
24 25 5.071250 AGGTTGTTGGTGTACTAAGACATGA 59.929 40.000 0.00 0.00 0.00 3.07
25 26 5.305585 AGGTTGTTGGTGTACTAAGACATG 58.694 41.667 0.00 0.00 0.00 3.21
26 27 5.562298 AGGTTGTTGGTGTACTAAGACAT 57.438 39.130 0.00 0.00 0.00 3.06
27 28 5.120399 CAAGGTTGTTGGTGTACTAAGACA 58.880 41.667 0.00 0.00 0.00 3.41
28 29 5.121105 ACAAGGTTGTTGGTGTACTAAGAC 58.879 41.667 0.00 0.00 38.47 3.01
29 30 5.362105 ACAAGGTTGTTGGTGTACTAAGA 57.638 39.130 0.00 0.00 38.47 2.10
30 31 6.148811 CCATACAAGGTTGTTGGTGTACTAAG 59.851 42.308 0.00 0.00 42.35 2.18
31 32 5.998981 CCATACAAGGTTGTTGGTGTACTAA 59.001 40.000 0.00 0.00 42.35 2.24
32 33 5.307456 TCCATACAAGGTTGTTGGTGTACTA 59.693 40.000 16.74 2.72 42.35 1.82
33 34 4.103469 TCCATACAAGGTTGTTGGTGTACT 59.897 41.667 16.74 0.00 42.35 2.73
34 35 4.391155 TCCATACAAGGTTGTTGGTGTAC 58.609 43.478 16.74 0.00 42.35 2.90
35 36 4.708576 TCCATACAAGGTTGTTGGTGTA 57.291 40.909 16.74 0.00 42.35 2.90
36 37 3.586470 TCCATACAAGGTTGTTGGTGT 57.414 42.857 16.74 0.00 42.35 4.16
37 38 4.335416 AGATCCATACAAGGTTGTTGGTG 58.665 43.478 16.74 8.64 42.35 4.17
38 39 4.657814 AGATCCATACAAGGTTGTTGGT 57.342 40.909 16.74 9.37 42.35 3.67
39 40 5.009631 TGAAGATCCATACAAGGTTGTTGG 58.990 41.667 0.00 8.72 42.35 3.77
40 41 5.473162 TGTGAAGATCCATACAAGGTTGTTG 59.527 40.000 0.00 0.30 42.35 3.33
41 42 5.630121 TGTGAAGATCCATACAAGGTTGTT 58.370 37.500 0.00 0.00 42.35 2.83
42 43 5.221925 ACTGTGAAGATCCATACAAGGTTGT 60.222 40.000 0.24 0.24 44.86 3.32
43 44 5.122869 CACTGTGAAGATCCATACAAGGTTG 59.877 44.000 0.32 0.00 0.00 3.77
55 56 2.768527 TCCCAGGATCACTGTGAAGATC 59.231 50.000 15.31 7.91 46.06 2.75
123 124 8.465999 TGACTTTAATGTGAAGTTGTTGTTGAT 58.534 29.630 0.00 0.00 37.46 2.57
143 144 0.613853 TCCTCCCGTCCGATGACTTT 60.614 55.000 0.00 0.00 39.47 2.66
149 150 1.455959 CCTCTTCCTCCCGTCCGAT 60.456 63.158 0.00 0.00 0.00 4.18
154 155 2.364961 CTCCCCTCTTCCTCCCGT 59.635 66.667 0.00 0.00 0.00 5.28
194 196 2.698797 CACTCACCCAACCCGATATAGT 59.301 50.000 0.00 0.00 0.00 2.12
223 225 0.302890 GCATGAGATCGGAGCAAACG 59.697 55.000 0.00 0.00 0.00 3.60
277 279 3.910627 AGTTCTAATGGTCAAGGAGGTGT 59.089 43.478 0.00 0.00 0.00 4.16
320 322 8.129496 ACCCGAGTAAATTAATTTGGTTGAAT 57.871 30.769 21.19 2.38 0.00 2.57
344 346 3.873952 GAGCTCAAGACATGGGTTATGAC 59.126 47.826 9.40 0.00 39.21 3.06
388 440 9.458374 CTTCGTATGAATTAAAGTTTGTTGGTT 57.542 29.630 0.00 0.00 32.61 3.67
411 463 8.439286 TGTTGCAACAAAAGAAAACATTACTTC 58.561 29.630 29.36 0.00 35.67 3.01
415 467 7.513968 GTGTGTTGCAACAAAAGAAAACATTA 58.486 30.769 32.61 2.99 41.21 1.90
455 507 5.239525 GGGCGCATCTCTTCTTTGTTTATAT 59.760 40.000 10.83 0.00 0.00 0.86
492 544 2.515429 AGCACATGATATTTCCCCAGGT 59.485 45.455 0.00 0.00 0.00 4.00
495 547 3.461458 TGGTAGCACATGATATTTCCCCA 59.539 43.478 0.00 0.00 0.00 4.96
496 548 4.098914 TGGTAGCACATGATATTTCCCC 57.901 45.455 0.00 0.00 0.00 4.81
497 549 4.024048 CGTTGGTAGCACATGATATTTCCC 60.024 45.833 0.00 0.00 0.00 3.97
506 558 3.071479 ACCTAAACGTTGGTAGCACATG 58.929 45.455 8.47 0.00 34.36 3.21
518 570 4.496341 CGTATCACGGTATCACCTAAACGT 60.496 45.833 0.00 0.00 38.08 3.99
551 603 5.751509 CCGTTTGATCTGATATCCAACGTTA 59.248 40.000 17.55 0.00 42.13 3.18
562 615 3.643320 TCATAGGAGCCGTTTGATCTGAT 59.357 43.478 0.00 0.00 0.00 2.90
615 669 4.229096 TGCACGCAATTTCAAGATTCTTC 58.771 39.130 0.00 0.00 0.00 2.87
620 674 1.888512 ACCTGCACGCAATTTCAAGAT 59.111 42.857 0.00 0.00 0.00 2.40
653 707 3.067684 TCTCAGATCCGACGGCATATA 57.932 47.619 9.66 0.00 0.00 0.86
655 709 1.813178 GATCTCAGATCCGACGGCATA 59.187 52.381 9.66 0.00 0.00 3.14
683 737 1.758936 ACCATGATACGGACGTCTGA 58.241 50.000 30.55 14.40 0.00 3.27
832 907 2.850568 GGTAAAGGAGAAGATGGGGGAA 59.149 50.000 0.00 0.00 0.00 3.97
833 908 2.047296 AGGTAAAGGAGAAGATGGGGGA 59.953 50.000 0.00 0.00 0.00 4.81
834 909 2.493091 AGGTAAAGGAGAAGATGGGGG 58.507 52.381 0.00 0.00 0.00 5.40
835 910 5.511545 CGATAAGGTAAAGGAGAAGATGGGG 60.512 48.000 0.00 0.00 0.00 4.96
836 911 5.511545 CCGATAAGGTAAAGGAGAAGATGGG 60.512 48.000 0.00 0.00 34.51 4.00
837 912 5.542779 CCGATAAGGTAAAGGAGAAGATGG 58.457 45.833 0.00 0.00 34.51 3.51
864 939 0.033366 TATGACGGGTGATGGCGATG 59.967 55.000 0.00 0.00 0.00 3.84
910 985 2.149521 TCCCTTTTTCCTCCCTCCTT 57.850 50.000 0.00 0.00 0.00 3.36
964 1045 1.337823 CGAGAACCAGATTGGAACCGT 60.338 52.381 1.40 0.00 40.96 4.83
982 1063 4.161295 CCTCGATTGCTGGGCCGA 62.161 66.667 0.00 0.00 0.00 5.54
1175 1268 0.756903 TCTAGATAGGGTTTGCGGGC 59.243 55.000 0.00 0.00 0.00 6.13
1191 1287 1.826921 GGACGTCCCGGCAGATCTA 60.827 63.158 24.75 0.00 36.10 1.98
1240 1336 5.018809 TCCCCTCATCATCAAAAGGAAAAG 58.981 41.667 0.00 0.00 0.00 2.27
1244 1341 3.192944 AGTCCCCTCATCATCAAAAGGA 58.807 45.455 0.00 0.00 0.00 3.36
1252 1349 5.424252 TCGTTAGTAAAAGTCCCCTCATCAT 59.576 40.000 0.00 0.00 0.00 2.45
1253 1350 4.773674 TCGTTAGTAAAAGTCCCCTCATCA 59.226 41.667 0.00 0.00 0.00 3.07
1254 1351 5.334724 TCGTTAGTAAAAGTCCCCTCATC 57.665 43.478 0.00 0.00 0.00 2.92
1423 1524 6.975772 CGAAGAAACTAAATCCACCAACAAAA 59.024 34.615 0.00 0.00 0.00 2.44
1448 1550 4.660789 ATCATGGCCAAAATTACAGAGC 57.339 40.909 10.96 0.00 0.00 4.09
1720 1841 2.561419 CAAACCAGAGGAAGGACGACTA 59.439 50.000 0.00 0.00 0.00 2.59
1733 1854 2.092429 ACTCAAAGGTCAGCAAACCAGA 60.092 45.455 9.87 4.38 42.12 3.86
1798 1920 7.193377 ACAAATGGTTGTACTACCTTTTACG 57.807 36.000 27.53 21.56 46.33 3.18
1821 1943 2.128771 ATAATGGGTGTGCCACTGAC 57.871 50.000 0.00 0.00 34.40 3.51
1835 1957 1.948834 TCGTGGATGGCTGCAATAATG 59.051 47.619 0.50 0.00 0.00 1.90
1836 1958 2.346766 TCGTGGATGGCTGCAATAAT 57.653 45.000 0.50 0.00 0.00 1.28
1858 1980 8.251721 TCATTAGACTTCTGAAGCTAGGTAAAC 58.748 37.037 17.00 0.00 0.00 2.01
1893 2015 6.208599 TCAAAGAGAACAAGTGAAAACCAAGT 59.791 34.615 0.00 0.00 0.00 3.16
1902 2024 8.846943 TGCTATTTATCAAAGAGAACAAGTGA 57.153 30.769 0.00 0.00 31.51 3.41
1904 2026 9.289782 AGTTGCTATTTATCAAAGAGAACAAGT 57.710 29.630 0.00 0.00 31.51 3.16
1985 2191 1.974875 CAAGTAAACCCCACCCCGC 60.975 63.158 0.00 0.00 0.00 6.13
1986 2192 1.303806 CCAAGTAAACCCCACCCCG 60.304 63.158 0.00 0.00 0.00 5.73
1994 2200 5.989168 ACAATAAAGCTTTGCCAAGTAAACC 59.011 36.000 22.02 0.00 31.86 3.27
2060 2267 3.591196 GGCTGAGCCTGATCTATAGTG 57.409 52.381 17.96 0.00 46.69 2.74
2147 2358 5.485353 CCTATAGGGGACAAGAGCATCATTA 59.515 44.000 11.33 0.00 37.82 1.90
2179 2390 2.167487 CTCCACCTCACCTCTCTTTAGC 59.833 54.545 0.00 0.00 0.00 3.09
2350 2561 5.188359 TCACCTACTGGGACCTAAATGTAAC 59.812 44.000 0.00 0.00 38.76 2.50
2393 2605 3.213506 TGTCAGAAACTCAACACATGGG 58.786 45.455 0.00 0.00 34.78 4.00
2517 2730 7.227116 ACTTTTTGGTGTTTTCCATTCATCATG 59.773 33.333 0.00 0.00 37.33 3.07
2796 3009 1.216710 CTCCTCGCTGTCACTTCCC 59.783 63.158 0.00 0.00 0.00 3.97
2899 3112 6.484643 CGATTCAAAATGATATGACCTCAGGT 59.515 38.462 0.00 0.00 39.44 4.00
2996 3212 4.813296 ACCGAACATTCTGTTGAGAAAC 57.187 40.909 0.00 0.00 41.28 2.78
2997 3213 6.018262 CAGTTACCGAACATTCTGTTGAGAAA 60.018 38.462 0.00 0.00 41.28 2.52
2998 3214 5.465390 CAGTTACCGAACATTCTGTTGAGAA 59.535 40.000 0.00 0.00 41.28 2.87
3014 3230 2.301009 ACACCTAAACCTCCAGTTACCG 59.699 50.000 0.00 0.00 37.88 4.02
3319 3538 9.422681 AGTTACAGAGGTAGAACATGTGTATAT 57.577 33.333 0.00 0.00 38.20 0.86
3320 3539 8.818622 AGTTACAGAGGTAGAACATGTGTATA 57.181 34.615 0.00 0.00 38.20 1.47
3321 3540 7.719871 AGTTACAGAGGTAGAACATGTGTAT 57.280 36.000 0.00 0.00 38.20 2.29
3322 3541 8.640063 TTAGTTACAGAGGTAGAACATGTGTA 57.360 34.615 0.00 0.00 37.55 2.90
3323 3542 7.534723 TTAGTTACAGAGGTAGAACATGTGT 57.465 36.000 0.00 0.32 39.66 3.72
3350 3569 8.632679 TGAAGAGAAACTGCAAAAACATCTTAT 58.367 29.630 0.00 0.00 29.99 1.73
3351 3570 7.995289 TGAAGAGAAACTGCAAAAACATCTTA 58.005 30.769 0.00 0.00 29.99 2.10
3352 3571 6.866480 TGAAGAGAAACTGCAAAAACATCTT 58.134 32.000 0.00 0.00 29.99 2.40
3353 3572 6.096001 ACTGAAGAGAAACTGCAAAAACATCT 59.904 34.615 0.00 0.00 33.16 2.90
3354 3573 6.268566 ACTGAAGAGAAACTGCAAAAACATC 58.731 36.000 0.00 0.00 33.16 3.06
3355 3574 6.212888 ACTGAAGAGAAACTGCAAAAACAT 57.787 33.333 0.00 0.00 33.16 2.71
3356 3575 5.643379 ACTGAAGAGAAACTGCAAAAACA 57.357 34.783 0.00 0.00 33.16 2.83
3357 3576 7.251281 AGTTACTGAAGAGAAACTGCAAAAAC 58.749 34.615 0.00 0.00 33.16 2.43
3358 3577 7.391148 AGTTACTGAAGAGAAACTGCAAAAA 57.609 32.000 0.00 0.00 33.16 1.94
3359 3578 8.500753 TTAGTTACTGAAGAGAAACTGCAAAA 57.499 30.769 0.00 0.00 33.16 2.44
3360 3579 8.500753 TTTAGTTACTGAAGAGAAACTGCAAA 57.499 30.769 0.00 0.00 33.16 3.68
3361 3580 8.677148 ATTTAGTTACTGAAGAGAAACTGCAA 57.323 30.769 0.00 0.00 33.16 4.08
3362 3581 9.944376 ATATTTAGTTACTGAAGAGAAACTGCA 57.056 29.630 0.00 0.00 34.23 4.41
3411 3630 9.429359 TCAAATGAACTGCAAAAGTCTTAAAAA 57.571 25.926 0.00 0.00 38.56 1.94
3412 3631 8.994429 TCAAATGAACTGCAAAAGTCTTAAAA 57.006 26.923 0.00 0.00 38.56 1.52
3413 3632 8.994429 TTCAAATGAACTGCAAAAGTCTTAAA 57.006 26.923 0.00 0.00 38.56 1.52
3484 3703 8.991783 ACCAAATCAGTATCATCAGATTCATT 57.008 30.769 0.00 0.00 35.67 2.57
3489 3708 9.857656 ACAAATACCAAATCAGTATCATCAGAT 57.142 29.630 0.00 0.00 38.29 2.90
3490 3709 9.112725 CACAAATACCAAATCAGTATCATCAGA 57.887 33.333 0.00 0.00 30.10 3.27
3491 3710 8.347771 CCACAAATACCAAATCAGTATCATCAG 58.652 37.037 0.00 0.00 30.10 2.90
3492 3711 8.052141 TCCACAAATACCAAATCAGTATCATCA 58.948 33.333 0.00 0.00 30.10 3.07
3493 3712 8.450578 TCCACAAATACCAAATCAGTATCATC 57.549 34.615 0.00 0.00 30.10 2.92
3495 3714 9.913310 TTATCCACAAATACCAAATCAGTATCA 57.087 29.630 0.00 0.00 30.10 2.15
3498 3717 9.747898 AGTTTATCCACAAATACCAAATCAGTA 57.252 29.630 0.00 0.00 0.00 2.74
3499 3718 8.650143 AGTTTATCCACAAATACCAAATCAGT 57.350 30.769 0.00 0.00 0.00 3.41
3500 3719 9.357652 CAAGTTTATCCACAAATACCAAATCAG 57.642 33.333 0.00 0.00 0.00 2.90
3501 3720 8.310382 CCAAGTTTATCCACAAATACCAAATCA 58.690 33.333 0.00 0.00 0.00 2.57
3502 3721 8.311109 ACCAAGTTTATCCACAAATACCAAATC 58.689 33.333 0.00 0.00 0.00 2.17
3503 3722 8.201242 ACCAAGTTTATCCACAAATACCAAAT 57.799 30.769 0.00 0.00 0.00 2.32
3504 3723 7.287927 TGACCAAGTTTATCCACAAATACCAAA 59.712 33.333 0.00 0.00 0.00 3.28
3505 3724 6.778069 TGACCAAGTTTATCCACAAATACCAA 59.222 34.615 0.00 0.00 0.00 3.67
3506 3725 6.307776 TGACCAAGTTTATCCACAAATACCA 58.692 36.000 0.00 0.00 0.00 3.25
3507 3726 6.827586 TGACCAAGTTTATCCACAAATACC 57.172 37.500 0.00 0.00 0.00 2.73
3508 3727 9.705290 AATTTGACCAAGTTTATCCACAAATAC 57.295 29.630 0.00 0.00 36.27 1.89
3509 3728 9.921637 GAATTTGACCAAGTTTATCCACAAATA 57.078 29.630 0.00 0.00 36.27 1.40
3510 3729 8.428063 TGAATTTGACCAAGTTTATCCACAAAT 58.572 29.630 0.00 0.00 38.00 2.32
3511 3730 7.786030 TGAATTTGACCAAGTTTATCCACAAA 58.214 30.769 0.00 0.00 0.00 2.83
3512 3731 7.069331 ACTGAATTTGACCAAGTTTATCCACAA 59.931 33.333 0.00 0.00 0.00 3.33
3513 3732 6.549364 ACTGAATTTGACCAAGTTTATCCACA 59.451 34.615 0.00 0.00 0.00 4.17
3514 3733 6.863126 CACTGAATTTGACCAAGTTTATCCAC 59.137 38.462 0.00 0.00 0.00 4.02
3515 3734 6.549364 ACACTGAATTTGACCAAGTTTATCCA 59.451 34.615 0.00 0.00 0.00 3.41
3516 3735 6.981722 ACACTGAATTTGACCAAGTTTATCC 58.018 36.000 0.00 0.00 0.00 2.59
3517 3736 8.784043 ACTACACTGAATTTGACCAAGTTTATC 58.216 33.333 0.00 0.00 0.00 1.75
3518 3737 8.691661 ACTACACTGAATTTGACCAAGTTTAT 57.308 30.769 0.00 0.00 0.00 1.40
3519 3738 9.787435 ATACTACACTGAATTTGACCAAGTTTA 57.213 29.630 0.00 0.00 0.00 2.01
3520 3739 8.567948 CATACTACACTGAATTTGACCAAGTTT 58.432 33.333 0.00 0.00 0.00 2.66
3521 3740 7.936847 TCATACTACACTGAATTTGACCAAGTT 59.063 33.333 0.00 0.00 0.00 2.66
3522 3741 7.387948 GTCATACTACACTGAATTTGACCAAGT 59.612 37.037 0.00 0.00 0.00 3.16
3523 3742 7.387673 TGTCATACTACACTGAATTTGACCAAG 59.612 37.037 0.00 0.00 33.12 3.61
3524 3743 7.220740 TGTCATACTACACTGAATTTGACCAA 58.779 34.615 0.00 0.00 33.12 3.67
3525 3744 6.764379 TGTCATACTACACTGAATTTGACCA 58.236 36.000 0.00 0.00 33.12 4.02
3526 3745 7.849804 ATGTCATACTACACTGAATTTGACC 57.150 36.000 0.00 0.00 33.12 4.02
3572 3791 5.126384 TGCCAATTGTTAGCAAGGTAATACC 59.874 40.000 0.07 0.07 38.10 2.73
3573 3792 6.094881 TCTGCCAATTGTTAGCAAGGTAATAC 59.905 38.462 4.43 0.00 38.10 1.89
3574 3793 6.184068 TCTGCCAATTGTTAGCAAGGTAATA 58.816 36.000 4.43 0.00 38.10 0.98
3575 3794 5.016173 TCTGCCAATTGTTAGCAAGGTAAT 58.984 37.500 4.43 0.00 38.10 1.89
3576 3795 4.402829 TCTGCCAATTGTTAGCAAGGTAA 58.597 39.130 4.43 0.00 38.10 2.85
3577 3796 4.009675 CTCTGCCAATTGTTAGCAAGGTA 58.990 43.478 4.43 0.00 38.10 3.08
3578 3797 2.821969 CTCTGCCAATTGTTAGCAAGGT 59.178 45.455 4.43 0.00 38.10 3.50
3579 3798 3.084039 TCTCTGCCAATTGTTAGCAAGG 58.916 45.455 4.43 3.38 38.10 3.61
3580 3799 4.456911 TCTTCTCTGCCAATTGTTAGCAAG 59.543 41.667 4.43 7.56 38.10 4.01
3581 3800 4.397420 TCTTCTCTGCCAATTGTTAGCAA 58.603 39.130 4.43 0.00 35.79 3.91
3582 3801 4.019792 TCTTCTCTGCCAATTGTTAGCA 57.980 40.909 4.43 6.21 34.79 3.49
3583 3802 5.376854 TTTCTTCTCTGCCAATTGTTAGC 57.623 39.130 4.43 1.34 0.00 3.09
3616 3835 9.763465 GATAAATTTTGTTCATTTGCAAGGATG 57.237 29.630 0.00 1.62 0.00 3.51
3617 3836 9.729281 AGATAAATTTTGTTCATTTGCAAGGAT 57.271 25.926 0.00 0.00 0.00 3.24
3618 3837 9.558396 AAGATAAATTTTGTTCATTTGCAAGGA 57.442 25.926 0.00 0.00 0.00 3.36
3622 3841 8.782144 GGGAAAGATAAATTTTGTTCATTTGCA 58.218 29.630 0.00 0.00 0.00 4.08
3623 3842 7.956943 CGGGAAAGATAAATTTTGTTCATTTGC 59.043 33.333 0.00 0.00 0.00 3.68
3624 3843 8.442384 CCGGGAAAGATAAATTTTGTTCATTTG 58.558 33.333 0.00 0.00 0.00 2.32
3625 3844 8.154203 ACCGGGAAAGATAAATTTTGTTCATTT 58.846 29.630 6.32 0.00 0.00 2.32
3626 3845 7.602265 CACCGGGAAAGATAAATTTTGTTCATT 59.398 33.333 6.32 0.00 0.00 2.57
3627 3846 7.039363 TCACCGGGAAAGATAAATTTTGTTCAT 60.039 33.333 6.32 0.00 0.00 2.57
3628 3847 6.265649 TCACCGGGAAAGATAAATTTTGTTCA 59.734 34.615 6.32 0.00 0.00 3.18
3629 3848 6.683715 TCACCGGGAAAGATAAATTTTGTTC 58.316 36.000 6.32 0.00 0.00 3.18
3630 3849 6.658188 TCACCGGGAAAGATAAATTTTGTT 57.342 33.333 6.32 0.00 0.00 2.83
3631 3850 6.850752 ATCACCGGGAAAGATAAATTTTGT 57.149 33.333 6.32 0.00 0.00 2.83
3632 3851 8.546597 AAAATCACCGGGAAAGATAAATTTTG 57.453 30.769 6.32 0.00 0.00 2.44
3678 3897 2.659063 CCAGTGTGCCATCGGGAGA 61.659 63.158 0.00 0.00 46.90 3.71
3679 3898 2.124983 CCAGTGTGCCATCGGGAG 60.125 66.667 0.00 0.00 35.59 4.30
3680 3899 4.408821 GCCAGTGTGCCATCGGGA 62.409 66.667 0.00 0.00 35.59 5.14
3681 3900 4.720902 TGCCAGTGTGCCATCGGG 62.721 66.667 1.78 0.00 37.18 5.14
3682 3901 3.434319 GTGCCAGTGTGCCATCGG 61.434 66.667 1.78 0.00 0.00 4.18
3683 3902 2.359107 AGTGCCAGTGTGCCATCG 60.359 61.111 1.78 0.00 0.00 3.84
3684 3903 2.338015 CCAGTGCCAGTGTGCCATC 61.338 63.158 0.00 0.00 0.00 3.51
3685 3904 2.282674 CCAGTGCCAGTGTGCCAT 60.283 61.111 0.00 0.00 0.00 4.40
3687 3906 3.551496 TAGCCAGTGCCAGTGTGCC 62.551 63.158 8.72 0.00 38.69 5.01
3688 3907 0.962356 ATTAGCCAGTGCCAGTGTGC 60.962 55.000 0.00 2.13 38.69 4.57
3689 3908 1.538047 AATTAGCCAGTGCCAGTGTG 58.462 50.000 0.00 0.00 38.69 3.82
3690 3909 2.292828 AAATTAGCCAGTGCCAGTGT 57.707 45.000 0.00 0.00 38.69 3.55
3691 3910 3.665745 AAAAATTAGCCAGTGCCAGTG 57.334 42.857 0.00 0.00 38.69 3.66
3767 3986 9.945904 AGGCCGATTGGTTAATATTTTTAAAAA 57.054 25.926 15.38 15.38 37.67 1.94
3770 3989 9.411189 AGTAGGCCGATTGGTTAATATTTTTAA 57.589 29.630 0.00 0.00 37.67 1.52
3771 3990 8.842280 CAGTAGGCCGATTGGTTAATATTTTTA 58.158 33.333 0.00 0.00 37.67 1.52
3772 3991 7.683463 GCAGTAGGCCGATTGGTTAATATTTTT 60.683 37.037 10.31 0.00 37.67 1.94
3773 3992 6.238925 GCAGTAGGCCGATTGGTTAATATTTT 60.239 38.462 10.31 0.00 37.67 1.82
3774 3993 5.240844 GCAGTAGGCCGATTGGTTAATATTT 59.759 40.000 10.31 0.00 37.67 1.40
3775 3994 4.760204 GCAGTAGGCCGATTGGTTAATATT 59.240 41.667 10.31 0.00 37.67 1.28
3776 3995 4.041691 AGCAGTAGGCCGATTGGTTAATAT 59.958 41.667 7.24 0.00 46.50 1.28
3777 3996 3.389983 AGCAGTAGGCCGATTGGTTAATA 59.610 43.478 7.24 0.00 46.50 0.98
3778 3997 2.172717 AGCAGTAGGCCGATTGGTTAAT 59.827 45.455 7.24 0.00 46.50 1.40
3779 3998 1.557832 AGCAGTAGGCCGATTGGTTAA 59.442 47.619 7.24 0.00 46.50 2.01
3780 3999 1.134521 CAGCAGTAGGCCGATTGGTTA 60.135 52.381 10.30 0.00 46.50 2.85
3781 4000 0.392998 CAGCAGTAGGCCGATTGGTT 60.393 55.000 10.30 0.00 46.50 3.67
3782 4001 1.221840 CAGCAGTAGGCCGATTGGT 59.778 57.895 7.24 7.24 46.50 3.67
3783 4002 0.107456 ATCAGCAGTAGGCCGATTGG 59.893 55.000 10.31 0.00 46.50 3.16
3784 4003 1.506493 GATCAGCAGTAGGCCGATTG 58.494 55.000 3.87 3.87 46.50 2.67
3785 4004 0.032678 CGATCAGCAGTAGGCCGATT 59.967 55.000 0.00 0.00 46.50 3.34
3786 4005 0.823769 TCGATCAGCAGTAGGCCGAT 60.824 55.000 0.00 0.00 46.50 4.18
3787 4006 0.823769 ATCGATCAGCAGTAGGCCGA 60.824 55.000 0.00 0.00 46.50 5.54
3788 4007 0.032678 AATCGATCAGCAGTAGGCCG 59.967 55.000 0.00 0.00 46.50 6.13
3789 4008 1.506493 CAATCGATCAGCAGTAGGCC 58.494 55.000 0.00 0.00 46.50 5.19
3790 4009 1.069204 TCCAATCGATCAGCAGTAGGC 59.931 52.381 0.00 0.00 45.30 3.93
3791 4010 2.546795 GGTCCAATCGATCAGCAGTAGG 60.547 54.545 0.00 0.00 0.00 3.18
3792 4011 2.546795 GGGTCCAATCGATCAGCAGTAG 60.547 54.545 0.00 0.00 0.00 2.57
3793 4012 1.412710 GGGTCCAATCGATCAGCAGTA 59.587 52.381 0.00 0.00 0.00 2.74
3794 4013 0.179000 GGGTCCAATCGATCAGCAGT 59.821 55.000 0.00 0.00 0.00 4.40
3795 4014 0.178767 TGGGTCCAATCGATCAGCAG 59.821 55.000 0.00 0.00 0.00 4.24
3796 4015 0.178767 CTGGGTCCAATCGATCAGCA 59.821 55.000 0.00 0.00 0.00 4.41
3797 4016 0.179000 ACTGGGTCCAATCGATCAGC 59.821 55.000 0.00 0.00 31.59 4.26
3798 4017 1.536922 CGACTGGGTCCAATCGATCAG 60.537 57.143 14.67 3.01 46.70 2.90
3799 4018 0.459899 CGACTGGGTCCAATCGATCA 59.540 55.000 14.67 0.00 46.70 2.92
3800 4019 0.249489 CCGACTGGGTCCAATCGATC 60.249 60.000 20.38 0.00 46.70 3.69
3801 4020 1.823295 CCGACTGGGTCCAATCGAT 59.177 57.895 20.38 0.00 46.70 3.59
3802 4021 3.014085 GCCGACTGGGTCCAATCGA 62.014 63.158 20.38 0.00 46.70 3.59
3803 4022 2.511600 GCCGACTGGGTCCAATCG 60.512 66.667 13.12 13.12 43.95 3.34
3804 4023 2.124695 GGCCGACTGGGTCCAATC 60.125 66.667 0.00 0.00 38.44 2.67
3805 4024 2.610859 AGGCCGACTGGGTCCAAT 60.611 61.111 0.00 0.00 43.46 3.16
3806 4025 3.636231 CAGGCCGACTGGGTCCAA 61.636 66.667 0.00 0.00 43.46 3.53
3820 4039 3.515286 CAATCGGCCAGCAGCAGG 61.515 66.667 2.24 0.00 46.50 4.85
3821 4040 3.515286 CCAATCGGCCAGCAGCAG 61.515 66.667 2.24 0.00 46.50 4.24


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

AutoCloner maintained by Alex Coulton.