Multiple sequence alignment - TraesCS4D01G295500

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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 TraesCS4D01G295500 chr4D 100.000 4820 0 0 1 4820 465364349 465359530 0.000000e+00 8901.0
1 TraesCS4D01G295500 chr4D 85.714 70 8 1 640 709 380260370 380260437 6.690000e-09 73.1
2 TraesCS4D01G295500 chr4A 87.369 2486 161 62 2 2383 5064445 5066881 0.000000e+00 2710.0
3 TraesCS4D01G295500 chr4A 94.655 1422 55 13 2574 3980 5066878 5068293 0.000000e+00 2185.0
4 TraesCS4D01G295500 chr4A 83.744 406 21 13 4257 4643 5069767 5070146 4.620000e-90 342.0
5 TraesCS4D01G295500 chr4A 86.391 169 8 5 4651 4818 5070419 5070573 2.310000e-38 171.0
6 TraesCS4D01G295500 chr4B 94.941 1601 51 19 2503 4080 582117287 582115694 0.000000e+00 2481.0
7 TraesCS4D01G295500 chr4B 91.912 1187 56 13 1316 2471 582118465 582117288 0.000000e+00 1624.0
8 TraesCS4D01G295500 chr4B 82.979 752 88 25 11 749 582119749 582119025 1.130000e-180 643.0
9 TraesCS4D01G295500 chr4B 85.740 554 20 13 4299 4818 582115048 582114520 9.190000e-147 531.0
10 TraesCS4D01G295500 chr5B 89.983 589 26 21 984 1547 664904580 664904000 0.000000e+00 730.0
11 TraesCS4D01G295500 chr5B 85.841 113 12 4 636 748 313310133 313310025 3.050000e-22 117.0
12 TraesCS4D01G295500 chr5B 97.143 35 0 1 634 667 700207344 700207378 1.870000e-04 58.4
13 TraesCS4D01G295500 chr7A 80.339 295 45 7 1937 2221 574083738 574083447 1.360000e-50 211.0
14 TraesCS4D01G295500 chr5D 81.771 192 26 8 551 735 463186277 463186466 8.360000e-33 152.0
15 TraesCS4D01G295500 chr7B 77.734 256 44 8 1937 2181 534818040 534817787 1.400000e-30 145.0
16 TraesCS4D01G295500 chr7B 85.542 83 8 3 642 724 734350118 734350196 3.090000e-12 84.2
17 TraesCS4D01G295500 chr6B 80.342 117 17 5 2372 2483 518390191 518390076 3.090000e-12 84.2
18 TraesCS4D01G295500 chr2A 100.000 33 0 0 274 306 12609343 12609311 1.450000e-05 62.1
19 TraesCS4D01G295500 chr2A 79.775 89 12 6 638 724 52262033 52262117 5.210000e-05 60.2
20 TraesCS4D01G295500 chr2A 100.000 28 0 0 277 304 78902452 78902479 9.000000e-03 52.8
21 TraesCS4D01G295500 chr2D 85.965 57 4 3 638 692 50942154 50942208 1.870000e-04 58.4
22 TraesCS4D01G295500 chr7D 100.000 30 0 0 275 304 236645961 236645932 6.740000e-04 56.5
23 TraesCS4D01G295500 chr2B 96.970 33 1 0 636 668 374256693 374256661 6.740000e-04 56.5
24 TraesCS4D01G295500 chr6A 100.000 28 0 0 276 303 579797792 579797765 9.000000e-03 52.8
25 TraesCS4D01G295500 chr1D 100.000 28 0 0 273 300 11885011 11885038 9.000000e-03 52.8


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 TraesCS4D01G295500 chr4D 465359530 465364349 4819 True 8901.00 8901 100.00000 1 4820 1 chr4D.!!$R1 4819
1 TraesCS4D01G295500 chr4A 5064445 5070573 6128 False 1352.00 2710 88.03975 2 4818 4 chr4A.!!$F1 4816
2 TraesCS4D01G295500 chr4B 582114520 582119749 5229 True 1319.75 2481 88.89300 11 4818 4 chr4B.!!$R1 4807
3 TraesCS4D01G295500 chr5B 664904000 664904580 580 True 730.00 730 89.98300 984 1547 1 chr5B.!!$R2 563

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
816 854 0.104120 CTGACTCGACCACAACCACA 59.896 55.0 0.00 0.0 0.00 4.17 F
862 901 0.167689 CTTCTTCTTGCGGCAGAAGC 59.832 55.0 24.68 0.0 46.60 3.86 F
1631 1727 0.242017 ATGGCTTGTTCTTTGCGAGC 59.758 50.0 0.00 0.0 41.41 5.03 F
2492 2599 0.030235 GTTGGTCGGGCAAACTTGAC 59.970 55.0 0.00 0.0 34.70 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 2580 0.030235 GTCAAGTTTGCCCGACCAAC 59.970 55.0 0.0 0.0 0.00 3.77 R
2477 2584 0.958822 ATTGGTCAAGTTTGCCCGAC 59.041 50.0 0.0 0.0 0.00 4.79 R
2929 3041 0.107831 TGCTGCCACTTCGGTAACTT 59.892 50.0 0.0 0.0 36.97 2.66 R
4435 6054 0.105593 GGCGATGAAGGAGATGCTGA 59.894 55.0 0.0 0.0 0.00 4.26 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
29 30 3.179443 GGAAATGTCCGCTCTATCACA 57.821 47.619 0.00 0.00 33.05 3.58
32 33 4.576463 GGAAATGTCCGCTCTATCACAAAT 59.424 41.667 0.00 0.00 33.05 2.32
64 65 4.039730 GGCTATCAGGTCAAATCTAGAGCA 59.960 45.833 0.00 0.00 36.03 4.26
102 103 1.820519 TCAAATGCATTGAGAGCCCAC 59.179 47.619 13.82 0.00 43.08 4.61
138 139 7.611467 TGTTGTCAGATTATCCATTTAGCAGTT 59.389 33.333 0.00 0.00 0.00 3.16
188 192 7.965107 CACTTGTTTCATGCTATTCTCCTAAAC 59.035 37.037 0.00 0.00 0.00 2.01
189 193 7.665559 ACTTGTTTCATGCTATTCTCCTAAACA 59.334 33.333 0.00 0.00 34.72 2.83
198 202 7.483307 TGCTATTCTCCTAAACAAATGAATGC 58.517 34.615 0.00 0.00 0.00 3.56
199 203 7.122501 TGCTATTCTCCTAAACAAATGAATGCA 59.877 33.333 0.00 0.00 32.04 3.96
201 205 5.314923 TCTCCTAAACAAATGAATGCAGC 57.685 39.130 0.00 0.00 0.00 5.25
202 206 4.158394 TCTCCTAAACAAATGAATGCAGCC 59.842 41.667 0.00 0.00 0.00 4.85
203 207 3.119531 TCCTAAACAAATGAATGCAGCCG 60.120 43.478 0.00 0.00 0.00 5.52
204 208 3.119531 CCTAAACAAATGAATGCAGCCGA 60.120 43.478 0.00 0.00 0.00 5.54
218 222 0.835941 AGCCGAGATGCTGGATCTTT 59.164 50.000 13.10 0.00 41.91 2.52
220 224 1.495878 CCGAGATGCTGGATCTTTCG 58.504 55.000 13.10 12.43 41.91 3.46
221 225 1.495878 CGAGATGCTGGATCTTTCGG 58.504 55.000 13.10 0.48 41.91 4.30
222 226 1.224965 GAGATGCTGGATCTTTCGGC 58.775 55.000 13.10 0.00 41.91 5.54
251 255 4.884164 AGTTGTGCTGCTAAGTCTTCTTTT 59.116 37.500 0.00 0.00 35.36 2.27
254 258 3.977579 GTGCTGCTAAGTCTTCTTTTTGC 59.022 43.478 0.00 0.00 35.36 3.68
255 259 3.631686 TGCTGCTAAGTCTTCTTTTTGCA 59.368 39.130 0.00 0.00 35.36 4.08
260 264 7.289587 TGCTAAGTCTTCTTTTTGCAAAAAC 57.710 32.000 28.85 20.74 34.46 2.43
295 299 2.096596 GAGCATCTCCAACAGCAGC 58.903 57.895 0.00 0.00 0.00 5.25
330 334 6.759272 AGCGTATGACATATTTAGGACATGT 58.241 36.000 0.00 0.00 35.65 3.21
353 357 1.751437 GGCAAAAATCGGCCTCTAGT 58.249 50.000 0.00 0.00 46.74 2.57
355 359 2.872858 GGCAAAAATCGGCCTCTAGTAG 59.127 50.000 0.00 0.00 46.74 2.57
373 377 4.871822 AGTAGCTGCCCAATCCTAAAAAT 58.128 39.130 0.00 0.00 0.00 1.82
374 378 4.889995 AGTAGCTGCCCAATCCTAAAAATC 59.110 41.667 0.00 0.00 0.00 2.17
376 380 3.956848 AGCTGCCCAATCCTAAAAATCTC 59.043 43.478 0.00 0.00 0.00 2.75
381 385 4.469586 GCCCAATCCTAAAAATCTCCCAAA 59.530 41.667 0.00 0.00 0.00 3.28
382 386 5.045942 GCCCAATCCTAAAAATCTCCCAAAA 60.046 40.000 0.00 0.00 0.00 2.44
383 387 6.521598 GCCCAATCCTAAAAATCTCCCAAAAA 60.522 38.462 0.00 0.00 0.00 1.94
384 388 6.878923 CCCAATCCTAAAAATCTCCCAAAAAC 59.121 38.462 0.00 0.00 0.00 2.43
434 438 3.564264 TCATGCAGCAAATATAGGGCAA 58.436 40.909 0.00 0.00 34.64 4.52
439 443 3.411446 CAGCAAATATAGGGCAATCGGA 58.589 45.455 0.00 0.00 0.00 4.55
454 458 2.044946 GGACGGCTGCCCAGAAAT 60.045 61.111 14.12 0.00 0.00 2.17
498 502 4.011517 GTGGCCGGAAACCCTCGA 62.012 66.667 5.05 0.00 0.00 4.04
500 504 2.745100 GGCCGGAAACCCTCGAAC 60.745 66.667 5.05 0.00 0.00 3.95
503 507 2.046604 CGGAAACCCTCGAACCCC 60.047 66.667 0.00 0.00 0.00 4.95
531 535 4.830765 GGTAGCCGCACGCCATGA 62.831 66.667 0.00 0.00 38.78 3.07
606 611 6.241645 GTCCTATTTTAGGCAGCTATTGGAT 58.758 40.000 0.00 0.00 45.82 3.41
635 641 5.163281 TGCCCTATTTCATGCAAAAACAT 57.837 34.783 0.00 0.00 0.00 2.71
636 642 5.558818 TGCCCTATTTCATGCAAAAACATT 58.441 33.333 0.00 0.00 0.00 2.71
714 726 6.961359 AAAAGCGTTTTTATGCCCTTAATC 57.039 33.333 8.32 0.00 34.81 1.75
774 807 1.354368 TGAATTCCACTTCCACTCCCC 59.646 52.381 2.27 0.00 0.00 4.81
798 836 0.394625 GCGAGACAGAGGTAGGGTCT 60.395 60.000 0.00 0.00 44.12 3.85
813 851 3.196613 GTCTGACTCGACCACAACC 57.803 57.895 0.00 0.00 0.00 3.77
814 852 0.387929 GTCTGACTCGACCACAACCA 59.612 55.000 0.00 0.00 0.00 3.67
815 853 0.387929 TCTGACTCGACCACAACCAC 59.612 55.000 0.00 0.00 0.00 4.16
816 854 0.104120 CTGACTCGACCACAACCACA 59.896 55.000 0.00 0.00 0.00 4.17
817 855 0.537653 TGACTCGACCACAACCACAA 59.462 50.000 0.00 0.00 0.00 3.33
862 901 0.167689 CTTCTTCTTGCGGCAGAAGC 59.832 55.000 24.68 0.00 46.60 3.86
874 913 1.307097 GCAGAAGCCAGAGCCATAAG 58.693 55.000 0.00 0.00 41.25 1.73
880 919 1.156645 GCCAGAGCCATAAGACGCAG 61.157 60.000 0.00 0.00 0.00 5.18
939 996 4.954118 ACCCGCCCACCAGAGACA 62.954 66.667 0.00 0.00 0.00 3.41
953 1010 2.807045 GACACAGAGCAGGCGACG 60.807 66.667 0.00 0.00 0.00 5.12
1138 1201 3.158676 CCCCTAGTAGTAGATCTGTGGC 58.841 54.545 5.18 0.00 0.00 5.01
1381 1448 0.247537 CGCGCCCGATTTGTTTACTC 60.248 55.000 0.00 0.00 36.29 2.59
1391 1458 6.040878 CCGATTTGTTTACTCTCGATACCTT 58.959 40.000 0.00 0.00 0.00 3.50
1616 1712 1.512926 AGATAACGGCGATGAATGGC 58.487 50.000 16.62 0.00 0.00 4.40
1631 1727 0.242017 ATGGCTTGTTCTTTGCGAGC 59.758 50.000 0.00 0.00 41.41 5.03
1672 1769 2.020720 TGTGTGTGTTAGCTTTGGTGG 58.979 47.619 0.00 0.00 0.00 4.61
1679 1776 4.404073 TGTGTTAGCTTTGGTGGTTTGATT 59.596 37.500 0.00 0.00 0.00 2.57
1687 1784 6.599638 AGCTTTGGTGGTTTGATTATCTCTAC 59.400 38.462 0.00 0.00 0.00 2.59
1725 1822 7.410174 TGATACTTTGGAAATAGACCACCATT 58.590 34.615 0.00 0.00 37.13 3.16
1749 1846 9.772973 ATTATACTGTGACTGTCTGTGTTTTAA 57.227 29.630 9.51 7.07 0.00 1.52
1976 2073 1.136419 GCGCAGATAATGTGATGCTCG 60.136 52.381 0.30 0.00 42.31 5.03
2031 2128 9.599866 TTCTGTATTGGATTGTAGTAATCTGTG 57.400 33.333 0.00 0.00 0.00 3.66
2086 2183 6.441274 CATTTTACATGTGTCATGATAGGCC 58.559 40.000 9.11 0.00 0.00 5.19
2087 2184 2.645838 ACATGTGTCATGATAGGCCC 57.354 50.000 15.25 0.00 0.00 5.80
2089 2186 0.250467 ATGTGTCATGATAGGCCCGC 60.250 55.000 0.00 0.00 0.00 6.13
2195 2292 7.953493 AGAATGGGACTTAAGGTTATTTTCCAA 59.047 33.333 7.53 0.00 0.00 3.53
2270 2369 2.029918 GGAGGGCTTTGCTAGTTGTTTG 60.030 50.000 0.00 0.00 0.00 2.93
2288 2387 4.273969 TGTTTGTATTTTGGACGAGACACC 59.726 41.667 0.00 0.00 0.00 4.16
2338 2441 6.593268 ACTCTGTTCTAACTTCTACCCTTC 57.407 41.667 0.00 0.00 0.00 3.46
2406 2513 2.165845 CCTCCTTACCCACTGTAGTTCG 59.834 54.545 0.00 0.00 0.00 3.95
2413 2520 3.332034 ACCCACTGTAGTTCGTAATTGC 58.668 45.455 0.00 0.00 0.00 3.56
2477 2584 9.683069 CAAAATTTTGGCTAGCTATATAGTTGG 57.317 33.333 21.00 8.44 34.59 3.77
2478 2585 8.996651 AAATTTTGGCTAGCTATATAGTTGGT 57.003 30.769 15.72 0.00 0.00 3.67
2479 2586 8.622948 AATTTTGGCTAGCTATATAGTTGGTC 57.377 34.615 15.72 9.35 0.00 4.02
2480 2587 5.386958 TTGGCTAGCTATATAGTTGGTCG 57.613 43.478 15.72 0.00 0.00 4.79
2481 2588 3.762288 TGGCTAGCTATATAGTTGGTCGG 59.238 47.826 15.72 0.00 0.00 4.79
2482 2589 3.130693 GGCTAGCTATATAGTTGGTCGGG 59.869 52.174 15.72 0.00 0.00 5.14
2483 2590 3.429135 GCTAGCTATATAGTTGGTCGGGC 60.429 52.174 7.70 2.43 0.00 6.13
2484 2591 2.605257 AGCTATATAGTTGGTCGGGCA 58.395 47.619 11.38 0.00 0.00 5.36
2485 2592 2.969950 AGCTATATAGTTGGTCGGGCAA 59.030 45.455 11.38 0.00 0.00 4.52
2486 2593 3.389983 AGCTATATAGTTGGTCGGGCAAA 59.610 43.478 11.38 0.00 0.00 3.68
2487 2594 3.497262 GCTATATAGTTGGTCGGGCAAAC 59.503 47.826 11.38 0.00 0.00 2.93
2488 2595 3.926058 ATATAGTTGGTCGGGCAAACT 57.074 42.857 7.63 7.63 43.45 2.66
2489 2596 2.579410 ATAGTTGGTCGGGCAAACTT 57.421 45.000 7.82 0.00 38.13 2.66
2490 2597 1.600023 TAGTTGGTCGGGCAAACTTG 58.400 50.000 7.82 0.00 38.13 3.16
2491 2598 0.106918 AGTTGGTCGGGCAAACTTGA 60.107 50.000 0.00 0.00 38.13 3.02
2492 2599 0.030235 GTTGGTCGGGCAAACTTGAC 59.970 55.000 0.00 0.00 34.70 3.18
2501 2608 2.959516 GGCAAACTTGACCAATTAGCC 58.040 47.619 0.00 0.00 0.00 3.93
2510 2617 3.772387 TGACCAATTAGCCATTGAACCA 58.228 40.909 7.63 1.23 44.78 3.67
2533 2640 6.071728 CCACAGCTTCTTCTTTTGGACAATAT 60.072 38.462 0.00 0.00 0.00 1.28
2534 2641 7.121168 CCACAGCTTCTTCTTTTGGACAATATA 59.879 37.037 0.00 0.00 0.00 0.86
2600 2707 2.674852 CGCAGTGTTGTAGCATCAGATT 59.325 45.455 0.00 0.00 0.00 2.40
2610 2717 2.719739 AGCATCAGATTTCACCCACTG 58.280 47.619 0.00 0.00 0.00 3.66
2614 2721 0.967380 CAGATTTCACCCACTGCCCC 60.967 60.000 0.00 0.00 0.00 5.80
2717 2825 6.016555 TGCTAGTGTGATATGATTAGGGCTA 58.983 40.000 0.00 0.00 0.00 3.93
2772 2880 6.417258 TCATTCCTTCTGCTGTTCATTGATA 58.583 36.000 0.00 0.00 0.00 2.15
2776 2884 5.591472 TCCTTCTGCTGTTCATTGATATTGG 59.409 40.000 0.00 0.00 0.00 3.16
2899 3011 9.283768 CTGTGGATGTATTAGCAAAATGGTATA 57.716 33.333 0.00 0.00 29.73 1.47
2929 3041 9.695155 CCTTATCCTTATCCAAGTTCCTTTTTA 57.305 33.333 0.00 0.00 0.00 1.52
3045 3157 2.990998 ACCCCTTGGTGTTGGTTAGTAT 59.009 45.455 0.00 0.00 45.58 2.12
3087 3199 9.634163 TGTTAGTACTATGATGTTGTAGTGTTG 57.366 33.333 2.79 0.00 33.48 3.33
3282 3403 2.265367 TCCTCAATTCTACACCCAGCA 58.735 47.619 0.00 0.00 0.00 4.41
3303 3424 5.977731 GCAAAATGCTTAACCTTTGTCTTG 58.022 37.500 0.00 0.00 40.96 3.02
3313 3434 8.347035 GCTTAACCTTTGTCTTGTTATGTGTAA 58.653 33.333 0.00 0.00 0.00 2.41
3331 3452 5.329493 GTGTAACAAACCACTGACAAGTTC 58.671 41.667 0.00 0.00 32.39 3.01
3452 3575 4.697352 ACTGTTCAGGTAAATGCACATCTC 59.303 41.667 4.82 0.00 0.00 2.75
3483 3610 2.016905 ACACAGGCTCTGAACTAGGT 57.983 50.000 8.91 0.00 35.18 3.08
3484 3611 1.896465 ACACAGGCTCTGAACTAGGTC 59.104 52.381 0.00 0.00 35.18 3.85
3519 3647 4.701765 TGAAGCTGATTCATTCCTAGCTC 58.298 43.478 3.91 0.00 43.09 4.09
3525 3653 5.782047 CTGATTCATTCCTAGCTCGAAGAT 58.218 41.667 0.00 0.00 33.89 2.40
3542 3670 9.214953 GCTCGAAGATATATTTTGTGTTCTTTG 57.785 33.333 0.00 0.00 33.89 2.77
3552 3680 9.777297 ATATTTTGTGTTCTTTGCTTTTGGTAT 57.223 25.926 0.00 0.00 0.00 2.73
3553 3681 7.913674 TTTTGTGTTCTTTGCTTTTGGTATT 57.086 28.000 0.00 0.00 0.00 1.89
3693 3825 9.962759 CAAGTTAAATTTTCTATTCTGCAATGC 57.037 29.630 0.00 0.00 0.00 3.56
3721 3855 9.693739 TGGTGTTTATATCAATACCTTGTGATT 57.306 29.630 14.45 0.00 38.45 2.57
3832 3970 0.102120 CGACTGAGCCATGAGTCTCC 59.898 60.000 9.77 0.00 37.12 3.71
3844 3982 2.250924 TGAGTCTCCAGCTGTCAATGA 58.749 47.619 13.81 0.89 0.00 2.57
3916 4054 7.484007 GTGAATCATTTCATGTGTAGCAAGAAG 59.516 37.037 0.00 0.00 43.49 2.85
3920 4058 4.350368 TTCATGTGTAGCAAGAAGGACA 57.650 40.909 0.00 0.00 30.86 4.02
4002 4140 4.870123 TTAATTTGATGTTGCTGGCAGT 57.130 36.364 17.16 0.00 0.00 4.40
4006 4144 0.824595 TGATGTTGCTGGCAGTTGCT 60.825 50.000 17.16 0.00 41.70 3.91
4081 4221 4.084589 CGCATTTTTGAGGTTAAGTTTGGC 60.085 41.667 0.00 0.00 0.00 4.52
4092 4232 7.015682 TGAGGTTAAGTTTGGCCATCAATTTAA 59.984 33.333 6.09 9.93 34.98 1.52
4097 4237 5.304778 AGTTTGGCCATCAATTTAACCAAC 58.695 37.500 6.09 2.96 36.93 3.77
4132 4272 8.190122 TGTTATGGTTTTGCAATGCTTATAGAG 58.810 33.333 6.82 0.00 0.00 2.43
4167 4767 6.376864 ACAACCTGCAAATATACAAGTGCATA 59.623 34.615 0.00 0.00 45.34 3.14
4182 4782 7.086376 ACAAGTGCATATAAAAAGACAAGCAG 58.914 34.615 0.00 0.00 0.00 4.24
4183 4783 6.824305 AGTGCATATAAAAAGACAAGCAGT 57.176 33.333 0.00 0.00 0.00 4.40
4191 4791 1.805869 AAGACAAGCAGTAGCAGCAG 58.194 50.000 0.00 0.00 45.49 4.24
4193 4793 1.345741 AGACAAGCAGTAGCAGCAGAA 59.654 47.619 0.00 0.00 45.49 3.02
4195 4795 2.549754 GACAAGCAGTAGCAGCAGAAAA 59.450 45.455 0.00 0.00 45.49 2.29
4196 4796 2.291741 ACAAGCAGTAGCAGCAGAAAAC 59.708 45.455 0.00 0.00 45.49 2.43
4197 4797 2.551459 CAAGCAGTAGCAGCAGAAAACT 59.449 45.455 0.00 0.00 45.49 2.66
4199 4799 3.330267 AGCAGTAGCAGCAGAAAACTAC 58.670 45.455 0.00 0.00 45.49 2.73
4200 4800 3.007398 AGCAGTAGCAGCAGAAAACTACT 59.993 43.478 0.00 0.00 44.67 2.57
4201 4801 3.369451 GCAGTAGCAGCAGAAAACTACTC 59.631 47.826 0.00 0.00 42.56 2.59
4203 4803 3.506455 AGTAGCAGCAGAAAACTACTCGA 59.494 43.478 0.00 0.00 41.00 4.04
4205 4805 3.728845 AGCAGCAGAAAACTACTCGAAA 58.271 40.909 0.00 0.00 0.00 3.46
4222 4848 5.107453 ACTCGAAAGAAACTTGCAGTAATCG 60.107 40.000 0.00 0.00 41.32 3.34
4223 4849 4.151689 TCGAAAGAAACTTGCAGTAATCGG 59.848 41.667 0.00 0.00 37.03 4.18
4264 5864 1.153939 CTCCACGGCGACAAGAGAG 60.154 63.158 16.62 6.07 0.00 3.20
4281 5881 4.880426 GGCATCTCCCTCCCCCGA 62.880 72.222 0.00 0.00 0.00 5.14
4284 5884 3.752167 ATCTCCCTCCCCCGACGT 61.752 66.667 0.00 0.00 0.00 4.34
4285 5885 3.735251 ATCTCCCTCCCCCGACGTC 62.735 68.421 5.18 5.18 0.00 4.34
4306 5910 2.764314 GCGAGCCGGTGATTGCAAT 61.764 57.895 12.83 12.83 37.24 3.56
4307 5911 1.802636 CGAGCCGGTGATTGCAATT 59.197 52.632 14.33 0.00 0.00 2.32
4326 5930 4.782019 ATTACACACGGCATGAACAATT 57.218 36.364 0.00 0.00 0.00 2.32
4335 5939 6.205853 ACACGGCATGAACAATTCTTACTTAA 59.794 34.615 0.00 0.00 0.00 1.85
4339 5943 7.852945 CGGCATGAACAATTCTTACTTAAGATC 59.147 37.037 10.09 0.00 41.52 2.75
4340 5944 8.897752 GGCATGAACAATTCTTACTTAAGATCT 58.102 33.333 10.09 0.00 41.52 2.75
4369 5973 3.181477 TGAAACTGCCATCCAAGTTGTTG 60.181 43.478 1.45 0.00 0.00 3.33
4370 5974 2.071778 ACTGCCATCCAAGTTGTTGT 57.928 45.000 1.45 0.00 30.95 3.32
4371 5975 2.387757 ACTGCCATCCAAGTTGTTGTT 58.612 42.857 1.45 0.00 30.95 2.83
4400 6004 7.429920 GCAAGAAAACAACTGAATAAACGTACA 59.570 33.333 0.00 0.00 0.00 2.90
4432 6040 0.389025 AAAAGAAACTTGCAGGGGCG 59.611 50.000 0.00 0.00 45.35 6.13
4435 6054 1.678970 GAAACTTGCAGGGGCGGAT 60.679 57.895 0.00 0.00 45.35 4.18
4457 6076 0.105593 GCATCTCCTTCATCGCCTCA 59.894 55.000 0.00 0.00 0.00 3.86
4470 6089 2.727103 GCCTCAGCGGATCTACTCT 58.273 57.895 0.00 0.00 33.16 3.24
4471 6090 1.898902 GCCTCAGCGGATCTACTCTA 58.101 55.000 0.00 0.00 33.16 2.43
4472 6091 1.538075 GCCTCAGCGGATCTACTCTAC 59.462 57.143 0.00 0.00 33.16 2.59
4473 6092 2.156098 CCTCAGCGGATCTACTCTACC 58.844 57.143 0.00 0.00 33.16 3.18
4474 6093 2.156098 CTCAGCGGATCTACTCTACCC 58.844 57.143 0.00 0.00 0.00 3.69
4546 6165 2.299013 TGAAGAAGCACATCGTAGGTGT 59.701 45.455 0.00 0.00 38.51 4.16
4760 6645 2.425592 CAGACCCGCACCTTGTGA 59.574 61.111 0.00 0.00 35.23 3.58
4761 6646 1.961277 CAGACCCGCACCTTGTGAC 60.961 63.158 0.00 0.00 35.23 3.67
4762 6647 3.041940 GACCCGCACCTTGTGACG 61.042 66.667 0.00 1.77 35.23 4.35
4764 6649 4.988598 CCCGCACCTTGTGACGCT 62.989 66.667 0.00 0.00 35.23 5.07
4765 6650 3.414700 CCGCACCTTGTGACGCTC 61.415 66.667 0.00 0.00 35.23 5.03
4766 6651 3.414700 CGCACCTTGTGACGCTCC 61.415 66.667 0.00 0.00 35.23 4.70
4767 6652 3.050275 GCACCTTGTGACGCTCCC 61.050 66.667 0.00 0.00 35.23 4.30
4768 6653 2.358737 CACCTTGTGACGCTCCCC 60.359 66.667 0.00 0.00 35.23 4.81
4769 6654 2.526873 ACCTTGTGACGCTCCCCT 60.527 61.111 0.00 0.00 0.00 4.79
4770 6655 2.147387 ACCTTGTGACGCTCCCCTT 61.147 57.895 0.00 0.00 0.00 3.95
4771 6656 1.672356 CCTTGTGACGCTCCCCTTG 60.672 63.158 0.00 0.00 0.00 3.61
4772 6657 1.071471 CTTGTGACGCTCCCCTTGT 59.929 57.895 0.00 0.00 0.00 3.16
4773 6658 1.227823 TTGTGACGCTCCCCTTGTG 60.228 57.895 0.00 0.00 0.00 3.33
4774 6659 1.691195 TTGTGACGCTCCCCTTGTGA 61.691 55.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.132648 TGACCTGATAGCCCTAATCACATTT 59.867 40.000 0.00 0.00 0.00 2.32
32 33 3.653164 TGACCTGATAGCCCTAATCACA 58.347 45.455 0.00 0.00 0.00 3.58
78 79 1.796617 GCTCTCAATGCATTTGACGCC 60.797 52.381 9.83 0.00 39.44 5.68
102 103 2.472695 TCTGACAACAAATCCCCGAG 57.527 50.000 0.00 0.00 0.00 4.63
114 115 7.067372 CCAACTGCTAAATGGATAATCTGACAA 59.933 37.037 0.00 0.00 36.27 3.18
155 156 6.683974 ATAGCATGAAACAAGTGGTGATAC 57.316 37.500 0.00 0.00 0.00 2.24
156 157 7.112122 AGAATAGCATGAAACAAGTGGTGATA 58.888 34.615 0.00 0.00 0.00 2.15
157 158 5.948162 AGAATAGCATGAAACAAGTGGTGAT 59.052 36.000 0.00 0.00 0.00 3.06
161 162 4.946157 AGGAGAATAGCATGAAACAAGTGG 59.054 41.667 0.00 0.00 0.00 4.00
188 192 2.727777 CATCTCGGCTGCATTCATTTG 58.272 47.619 0.50 0.00 0.00 2.32
189 193 1.066605 GCATCTCGGCTGCATTCATTT 59.933 47.619 0.50 0.00 39.46 2.32
201 205 1.495878 CGAAAGATCCAGCATCTCGG 58.504 55.000 0.00 0.00 41.47 4.63
202 206 1.495878 CCGAAAGATCCAGCATCTCG 58.504 55.000 0.00 0.00 41.47 4.04
203 207 1.224965 GCCGAAAGATCCAGCATCTC 58.775 55.000 0.00 0.00 41.47 2.75
204 208 0.543277 TGCCGAAAGATCCAGCATCT 59.457 50.000 0.00 0.00 44.56 2.90
229 233 4.820284 AAAGAAGACTTAGCAGCACAAC 57.180 40.909 0.00 0.00 35.05 3.32
231 235 4.498009 GCAAAAAGAAGACTTAGCAGCACA 60.498 41.667 0.00 0.00 35.05 4.57
232 236 3.977579 GCAAAAAGAAGACTTAGCAGCAC 59.022 43.478 0.00 0.00 35.05 4.40
237 241 7.289587 TGTTTTTGCAAAAAGAAGACTTAGC 57.710 32.000 32.09 18.67 38.44 3.09
245 249 9.609950 CTTCATTTCTTGTTTTTGCAAAAAGAA 57.390 25.926 32.58 32.58 38.37 2.52
251 255 5.184711 AGCCTTCATTTCTTGTTTTTGCAA 58.815 33.333 0.00 0.00 0.00 4.08
254 258 7.095899 GCTCTTAGCCTTCATTTCTTGTTTTTG 60.096 37.037 0.00 0.00 34.48 2.44
255 259 6.925718 GCTCTTAGCCTTCATTTCTTGTTTTT 59.074 34.615 0.00 0.00 34.48 1.94
260 264 5.589452 AGATGCTCTTAGCCTTCATTTCTTG 59.411 40.000 0.00 0.00 41.51 3.02
305 309 7.812669 CACATGTCCTAAATATGTCATACGCTA 59.187 37.037 0.00 0.00 37.59 4.26
306 310 6.646653 CACATGTCCTAAATATGTCATACGCT 59.353 38.462 0.00 0.00 37.59 5.07
309 313 7.604164 CCCTCACATGTCCTAAATATGTCATAC 59.396 40.741 0.00 0.00 37.59 2.39
310 314 7.679783 CCCTCACATGTCCTAAATATGTCATA 58.320 38.462 0.00 0.00 37.59 2.15
316 320 5.387113 TTGCCCTCACATGTCCTAAATAT 57.613 39.130 0.00 0.00 0.00 1.28
325 329 1.545582 CCGATTTTTGCCCTCACATGT 59.454 47.619 0.00 0.00 0.00 3.21
330 334 3.693411 GGCCGATTTTTGCCCTCA 58.307 55.556 0.00 0.00 41.97 3.86
350 354 5.444744 TTTTTAGGATTGGGCAGCTACTA 57.555 39.130 0.00 0.00 0.00 1.82
352 356 4.889995 AGATTTTTAGGATTGGGCAGCTAC 59.110 41.667 0.00 0.00 0.00 3.58
353 357 5.129368 AGATTTTTAGGATTGGGCAGCTA 57.871 39.130 0.00 0.00 0.00 3.32
355 359 3.068732 GGAGATTTTTAGGATTGGGCAGC 59.931 47.826 0.00 0.00 0.00 5.25
407 411 4.457949 CCTATATTTGCTGCATGATGAGCA 59.542 41.667 1.84 13.10 43.47 4.26
412 416 3.770046 TGCCCTATATTTGCTGCATGAT 58.230 40.909 1.84 3.68 0.00 2.45
415 419 3.192001 CGATTGCCCTATATTTGCTGCAT 59.808 43.478 1.84 0.00 0.00 3.96
439 443 3.064324 GCATTTCTGGGCAGCCGT 61.064 61.111 5.00 0.00 0.00 5.68
454 458 4.002506 TTCGGAAGCAGCCTCGCA 62.003 61.111 0.00 0.00 0.00 5.10
480 484 4.323477 CGAGGGTTTCCGGCCACA 62.323 66.667 2.24 0.00 38.33 4.17
516 520 4.830765 GGTCATGGCGTGCGGCTA 62.831 66.667 18.31 6.27 42.94 3.93
606 611 3.831333 TGCATGAAATAGGGCAAAACTGA 59.169 39.130 0.00 0.00 32.54 3.41
693 705 5.914898 AGATTAAGGGCATAAAAACGCTT 57.085 34.783 0.00 0.00 41.37 4.68
694 706 5.914898 AAGATTAAGGGCATAAAAACGCT 57.085 34.783 0.00 0.00 0.00 5.07
747 759 3.760684 GTGGAAGTGGAATTCAGAGCATT 59.239 43.478 7.93 0.00 0.00 3.56
798 836 0.537653 TTGTGGTTGTGGTCGAGTCA 59.462 50.000 0.00 0.00 0.00 3.41
811 849 2.424302 CGTTCGGGGACTTGTGGT 59.576 61.111 0.00 0.00 0.00 4.16
812 850 2.358247 CCGTTCGGGGACTTGTGG 60.358 66.667 3.04 0.00 0.00 4.17
862 901 1.156645 GCTGCGTCTTATGGCTCTGG 61.157 60.000 0.00 0.00 0.00 3.86
866 905 2.202932 CCGCTGCGTCTTATGGCT 60.203 61.111 21.59 0.00 0.00 4.75
891 930 3.674050 GACCTCGGCTGGGGGACTA 62.674 68.421 18.05 0.00 0.00 2.59
928 985 0.037512 CTGCTCTGTGTCTCTGGTGG 60.038 60.000 0.00 0.00 0.00 4.61
931 988 1.079266 GCCTGCTCTGTGTCTCTGG 60.079 63.158 0.00 0.00 0.00 3.86
964 1027 3.492311 GATCTCGCCGGAGCTGGAC 62.492 68.421 5.05 0.00 40.26 4.02
1114 1177 5.074115 CCACAGATCTACTACTAGGGGAAG 58.926 50.000 0.00 0.00 0.00 3.46
1115 1178 4.691935 GCCACAGATCTACTACTAGGGGAA 60.692 50.000 0.00 0.00 0.00 3.97
1116 1179 3.181431 GCCACAGATCTACTACTAGGGGA 60.181 52.174 0.00 0.00 0.00 4.81
1121 1184 2.228059 GCCGCCACAGATCTACTACTA 58.772 52.381 0.00 0.00 0.00 1.82
1122 1185 1.033574 GCCGCCACAGATCTACTACT 58.966 55.000 0.00 0.00 0.00 2.57
1123 1186 0.317938 CGCCGCCACAGATCTACTAC 60.318 60.000 0.00 0.00 0.00 2.73
1306 1369 3.532155 GAGCTGGGATCGAGCGGT 61.532 66.667 9.12 0.00 41.61 5.68
1309 1372 1.886777 GCAAGAGCTGGGATCGAGC 60.887 63.158 7.17 7.17 37.91 5.03
1310 1373 1.591059 CGCAAGAGCTGGGATCGAG 60.591 63.158 0.00 0.00 40.40 4.04
1344 1411 0.787787 CGGTCGAATTCGCAAGTTCA 59.212 50.000 22.90 0.67 39.60 3.18
1418 1512 0.518636 CTGCAACCAGAACCACATCG 59.481 55.000 0.00 0.00 41.77 3.84
1616 1712 2.481568 TCATCAGCTCGCAAAGAACAAG 59.518 45.455 0.00 0.00 0.00 3.16
1631 1727 5.347635 CACAAAAGCAAACATCCATCATCAG 59.652 40.000 0.00 0.00 0.00 2.90
1703 1800 9.841295 GTATAATGGTGGTCTATTTCCAAAGTA 57.159 33.333 0.00 0.00 36.68 2.24
1725 1822 8.418662 AGTTAAAACACAGACAGTCACAGTATA 58.581 33.333 2.66 0.00 0.00 1.47
1749 1846 4.952460 TCGGTACTAAAAGAAAGCACAGT 58.048 39.130 0.00 0.00 0.00 3.55
1805 1902 5.428496 AAAACACATCCATCATCGCTATG 57.572 39.130 0.00 0.00 0.00 2.23
1809 1906 4.361451 AGAAAAACACATCCATCATCGC 57.639 40.909 0.00 0.00 0.00 4.58
1949 2046 5.521372 GCATCACATTATCTGCGCTCATATA 59.479 40.000 9.73 0.00 0.00 0.86
2031 2128 3.325293 TGACCATCAGCTCTCAGAAAC 57.675 47.619 0.00 0.00 0.00 2.78
2035 2132 3.374367 CACATTTGACCATCAGCTCTCAG 59.626 47.826 0.00 0.00 0.00 3.35
2086 2183 2.472488 GCAAGAATGAAAACTGTTGCGG 59.528 45.455 0.00 0.00 31.82 5.69
2087 2184 3.114809 TGCAAGAATGAAAACTGTTGCG 58.885 40.909 0.00 0.00 42.53 4.85
2089 2186 4.935702 TCCTGCAAGAATGAAAACTGTTG 58.064 39.130 0.00 0.00 34.07 3.33
2195 2292 3.067742 GGCAAGAGCAAGCAATATGACAT 59.932 43.478 0.00 0.00 44.61 3.06
2270 2369 3.000727 CCAGGTGTCTCGTCCAAAATAC 58.999 50.000 0.00 0.00 0.00 1.89
2338 2441 7.307337 GGCTGTCAAACAAATACCAGATTTTTG 60.307 37.037 0.00 0.00 36.62 2.44
2406 2513 5.414454 TGAGTTGGTCACTATTGGCAATTAC 59.586 40.000 19.21 11.28 35.01 1.89
2431 2538 1.268625 GGTCAAGGTTTTACTTGCCCG 59.731 52.381 0.00 0.00 45.72 6.13
2468 2575 3.926058 AGTTTGCCCGACCAACTATAT 57.074 42.857 0.00 0.00 0.00 0.86
2471 2578 1.141254 TCAAGTTTGCCCGACCAACTA 59.859 47.619 0.00 0.00 0.00 2.24
2472 2579 0.106918 TCAAGTTTGCCCGACCAACT 60.107 50.000 0.00 0.00 0.00 3.16
2473 2580 0.030235 GTCAAGTTTGCCCGACCAAC 59.970 55.000 0.00 0.00 0.00 3.77
2474 2581 1.104577 GGTCAAGTTTGCCCGACCAA 61.105 55.000 0.00 0.00 45.96 3.67
2475 2582 1.527380 GGTCAAGTTTGCCCGACCA 60.527 57.895 0.00 0.00 45.96 4.02
2476 2583 1.104577 TTGGTCAAGTTTGCCCGACC 61.105 55.000 0.00 0.00 46.69 4.79
2477 2584 0.958822 ATTGGTCAAGTTTGCCCGAC 59.041 50.000 0.00 0.00 0.00 4.79
2478 2585 1.698506 AATTGGTCAAGTTTGCCCGA 58.301 45.000 0.00 0.00 0.00 5.14
2479 2586 2.671070 GCTAATTGGTCAAGTTTGCCCG 60.671 50.000 0.00 0.00 0.00 6.13
2480 2587 2.353704 GGCTAATTGGTCAAGTTTGCCC 60.354 50.000 12.97 0.00 33.78 5.36
2481 2588 2.298729 TGGCTAATTGGTCAAGTTTGCC 59.701 45.455 15.42 15.42 37.34 4.52
2482 2589 3.658757 TGGCTAATTGGTCAAGTTTGC 57.341 42.857 0.00 0.00 0.00 3.68
2483 2590 5.782047 TCAATGGCTAATTGGTCAAGTTTG 58.218 37.500 0.00 1.07 45.00 2.93
2484 2591 6.223120 GTTCAATGGCTAATTGGTCAAGTTT 58.777 36.000 0.00 0.00 45.00 2.66
2485 2592 5.279456 GGTTCAATGGCTAATTGGTCAAGTT 60.279 40.000 0.00 0.00 45.00 2.66
2486 2593 4.220602 GGTTCAATGGCTAATTGGTCAAGT 59.779 41.667 0.00 0.00 45.00 3.16
2487 2594 4.220382 TGGTTCAATGGCTAATTGGTCAAG 59.780 41.667 0.00 0.00 45.00 3.02
2488 2595 4.021544 GTGGTTCAATGGCTAATTGGTCAA 60.022 41.667 0.00 0.00 45.00 3.18
2489 2596 3.509575 GTGGTTCAATGGCTAATTGGTCA 59.490 43.478 0.00 0.00 45.00 4.02
2490 2597 3.509575 TGTGGTTCAATGGCTAATTGGTC 59.490 43.478 11.21 0.00 45.00 4.02
2491 2598 3.505386 TGTGGTTCAATGGCTAATTGGT 58.495 40.909 11.21 0.00 45.00 3.67
2492 2599 3.676873 GCTGTGGTTCAATGGCTAATTGG 60.677 47.826 11.21 0.00 45.00 3.16
2493 2600 3.194116 AGCTGTGGTTCAATGGCTAATTG 59.806 43.478 6.38 6.38 46.10 2.32
2494 2601 3.434309 AGCTGTGGTTCAATGGCTAATT 58.566 40.909 0.00 0.00 0.00 1.40
2495 2602 3.091633 AGCTGTGGTTCAATGGCTAAT 57.908 42.857 0.00 0.00 0.00 1.73
2496 2603 2.584835 AGCTGTGGTTCAATGGCTAA 57.415 45.000 0.00 0.00 0.00 3.09
2497 2604 2.040278 AGAAGCTGTGGTTCAATGGCTA 59.960 45.455 11.27 0.00 41.76 3.93
2498 2605 1.202976 AGAAGCTGTGGTTCAATGGCT 60.203 47.619 11.27 0.00 41.76 4.75
2499 2606 1.251251 AGAAGCTGTGGTTCAATGGC 58.749 50.000 11.27 0.00 41.76 4.40
2500 2607 3.152341 AGAAGAAGCTGTGGTTCAATGG 58.848 45.455 11.27 0.00 41.76 3.16
2501 2608 4.843220 AAGAAGAAGCTGTGGTTCAATG 57.157 40.909 11.27 0.00 41.76 2.82
2510 2617 7.337942 CCTATATTGTCCAAAAGAAGAAGCTGT 59.662 37.037 0.00 0.00 0.00 4.40
2533 2640 4.351407 TGTGTGGTTTCTTATGGTTCCCTA 59.649 41.667 0.00 0.00 0.00 3.53
2534 2641 3.139397 TGTGTGGTTTCTTATGGTTCCCT 59.861 43.478 0.00 0.00 0.00 4.20
2545 2652 7.791029 AGGACAAATTTAATTGTGTGGTTTCT 58.209 30.769 0.00 0.00 43.31 2.52
2551 2658 8.815141 TTGATGAGGACAAATTTAATTGTGTG 57.185 30.769 0.00 0.00 43.31 3.82
2600 2707 1.360393 AAGAAGGGGCAGTGGGTGAA 61.360 55.000 0.00 0.00 0.00 3.18
2610 2717 1.202940 ACTGACAAGGAAAGAAGGGGC 60.203 52.381 0.00 0.00 0.00 5.80
2614 2721 8.954950 ATATATCACACTGACAAGGAAAGAAG 57.045 34.615 0.00 0.00 0.00 2.85
2717 2825 7.862675 AGTAAATACAGTAATCTGAAGGCCTT 58.137 34.615 20.65 20.65 43.76 4.35
2899 3011 6.217693 AGGAACTTGGATAAGGATAAGGTGTT 59.782 38.462 0.00 0.00 38.26 3.32
2929 3041 0.107831 TGCTGCCACTTCGGTAACTT 59.892 50.000 0.00 0.00 36.97 2.66
3135 3248 1.956477 ACCATGGCAACTGAAGAACAC 59.044 47.619 13.04 0.00 37.61 3.32
3246 3360 8.159447 AGAATTGAGGAATAATATAGTGCAGCA 58.841 33.333 0.00 0.00 0.00 4.41
3282 3403 9.260002 CATAACAAGACAAAGGTTAAGCATTTT 57.740 29.630 7.52 0.00 31.49 1.82
3303 3424 6.366315 TGTCAGTGGTTTGTTACACATAAC 57.634 37.500 0.00 0.00 41.07 1.89
3313 3434 5.722021 AAAAGAACTTGTCAGTGGTTTGT 57.278 34.783 0.00 0.00 31.60 2.83
3513 3641 9.469807 AGAACACAAAATATATCTTCGAGCTAG 57.530 33.333 0.00 0.00 0.00 3.42
3519 3647 9.559958 AAGCAAAGAACACAAAATATATCTTCG 57.440 29.630 0.00 0.00 0.00 3.79
3552 3680 9.494271 GAGCACATGATAAATATTAGTGGAGAA 57.506 33.333 0.00 0.00 0.00 2.87
3553 3681 8.874156 AGAGCACATGATAAATATTAGTGGAGA 58.126 33.333 0.00 0.00 0.00 3.71
3693 3825 7.279090 TCACAAGGTATTGATATAAACACCACG 59.721 37.037 2.99 0.00 38.83 4.94
3721 3855 2.203139 CACAACACCGACCTGCCA 60.203 61.111 0.00 0.00 0.00 4.92
3760 3894 0.110678 TCCTCTGTCGTGAGTGACCT 59.889 55.000 0.00 0.00 38.11 3.85
3822 3956 2.756840 TTGACAGCTGGAGACTCATG 57.243 50.000 19.93 0.14 0.00 3.07
3832 3970 5.048504 ACAGTTTATGGTTCATTGACAGCTG 60.049 40.000 13.48 13.48 0.00 4.24
3916 4054 1.451028 GCAGAGTGGATGCCTGTCC 60.451 63.158 0.00 0.00 37.73 4.02
4002 4140 2.777832 AAAACAGCCCAAACAAGCAA 57.222 40.000 0.00 0.00 0.00 3.91
4006 4144 4.339814 AGACGATAAAAACAGCCCAAACAA 59.660 37.500 0.00 0.00 0.00 2.83
4081 4221 8.859156 CAGTTATTTCGTTGGTTAAATTGATGG 58.141 33.333 0.00 0.00 0.00 3.51
4092 4232 6.887626 AACCATAACAGTTATTTCGTTGGT 57.112 33.333 2.77 5.73 0.00 3.67
4097 4237 7.630470 TTGCAAAACCATAACAGTTATTTCG 57.370 32.000 2.77 0.00 0.00 3.46
4132 4272 4.963276 TTTGCAGGTTGTATGTAGATGC 57.037 40.909 0.00 0.00 0.00 3.91
4134 4274 9.845740 TTGTATATTTGCAGGTTGTATGTAGAT 57.154 29.630 0.00 0.00 0.00 1.98
4135 4275 9.325198 CTTGTATATTTGCAGGTTGTATGTAGA 57.675 33.333 0.00 0.00 0.00 2.59
4138 4278 7.628366 GCACTTGTATATTTGCAGGTTGTATGT 60.628 37.037 0.00 0.00 34.97 2.29
4139 4279 6.692681 GCACTTGTATATTTGCAGGTTGTATG 59.307 38.462 0.00 0.00 34.97 2.39
4167 4767 4.761739 TGCTGCTACTGCTTGTCTTTTTAT 59.238 37.500 0.00 0.00 40.48 1.40
4182 4782 3.834610 TCGAGTAGTTTTCTGCTGCTAC 58.165 45.455 0.00 0.00 42.66 3.58
4183 4783 4.514781 TTCGAGTAGTTTTCTGCTGCTA 57.485 40.909 0.00 0.00 42.66 3.49
4191 4791 6.483687 TGCAAGTTTCTTTCGAGTAGTTTTC 58.516 36.000 0.00 0.00 0.00 2.29
4193 4793 6.049263 CTGCAAGTTTCTTTCGAGTAGTTT 57.951 37.500 0.00 0.00 0.00 2.66
4222 4848 2.760385 CTCCGGGGAGTGGAGTCC 60.760 72.222 0.00 0.73 46.49 3.85
4252 4894 0.529555 GAGATGCCTCTCTTGTCGCC 60.530 60.000 11.38 0.00 43.92 5.54
4253 4895 0.529555 GGAGATGCCTCTCTTGTCGC 60.530 60.000 17.16 0.00 46.11 5.19
4264 5864 4.880426 TCGGGGGAGGGAGATGCC 62.880 72.222 0.00 0.00 0.00 4.40
4306 5910 3.818210 AGAATTGTTCATGCCGTGTGTAA 59.182 39.130 0.00 0.00 0.00 2.41
4307 5911 3.407698 AGAATTGTTCATGCCGTGTGTA 58.592 40.909 0.00 0.00 0.00 2.90
4335 5939 6.407525 GGATGGCAGTTTCAACTAGTAGATCT 60.408 42.308 3.59 0.00 37.08 2.75
4339 5943 4.832248 TGGATGGCAGTTTCAACTAGTAG 58.168 43.478 0.00 0.00 37.08 2.57
4340 5944 4.901197 TGGATGGCAGTTTCAACTAGTA 57.099 40.909 0.00 0.00 37.08 1.82
4341 5945 3.788227 TGGATGGCAGTTTCAACTAGT 57.212 42.857 0.00 0.00 37.08 2.57
4342 5946 4.074970 ACTTGGATGGCAGTTTCAACTAG 58.925 43.478 0.00 0.00 37.08 2.57
4343 5947 4.098914 ACTTGGATGGCAGTTTCAACTA 57.901 40.909 0.00 0.00 37.08 2.24
4369 5973 9.261318 GTTTATTCAGTTGTTTTCTTGCAAAAC 57.739 29.630 0.00 2.86 39.78 2.43
4370 5974 8.165428 CGTTTATTCAGTTGTTTTCTTGCAAAA 58.835 29.630 0.00 0.00 0.00 2.44
4371 5975 7.329717 ACGTTTATTCAGTTGTTTTCTTGCAAA 59.670 29.630 0.00 0.00 0.00 3.68
4400 6004 3.694566 AGTTTCTTTTGAGTCGTTGGCTT 59.305 39.130 0.00 0.00 0.00 4.35
4432 6040 2.686235 CGATGAAGGAGATGCTGATCC 58.314 52.381 0.00 0.00 35.71 3.36
4435 6054 0.105593 GGCGATGAAGGAGATGCTGA 59.894 55.000 0.00 0.00 0.00 4.26
4457 6076 1.479021 GGTGGGTAGAGTAGATCCGCT 60.479 57.143 0.00 0.00 0.00 5.52
4517 6136 0.033504 TGTGCTTCTTCACCTCGACC 59.966 55.000 0.00 0.00 36.17 4.79
4608 6227 0.603569 TGGACGACTTTGAGAGGCTC 59.396 55.000 6.34 6.34 0.00 4.70
4760 6645 2.383245 CTGTGTCACAAGGGGAGCGT 62.383 60.000 7.18 0.00 0.00 5.07
4761 6646 1.669115 CTGTGTCACAAGGGGAGCG 60.669 63.158 7.18 0.00 0.00 5.03
4762 6647 1.968540 GCTGTGTCACAAGGGGAGC 60.969 63.158 7.18 2.00 0.00 4.70
4763 6648 1.302832 GGCTGTGTCACAAGGGGAG 60.303 63.158 7.18 0.00 0.00 4.30
4764 6649 1.768684 GAGGCTGTGTCACAAGGGGA 61.769 60.000 7.18 0.00 0.00 4.81
4765 6650 1.302832 GAGGCTGTGTCACAAGGGG 60.303 63.158 7.18 0.00 0.00 4.79
4766 6651 0.321122 GAGAGGCTGTGTCACAAGGG 60.321 60.000 7.18 0.00 0.00 3.95
4767 6652 0.321122 GGAGAGGCTGTGTCACAAGG 60.321 60.000 7.18 0.00 0.00 3.61
4768 6653 0.668706 CGGAGAGGCTGTGTCACAAG 60.669 60.000 7.18 2.89 0.00 3.16
4769 6654 1.367471 CGGAGAGGCTGTGTCACAA 59.633 57.895 7.18 0.00 0.00 3.33
4770 6655 3.051210 CGGAGAGGCTGTGTCACA 58.949 61.111 5.36 5.36 0.00 3.58
4771 6656 2.433318 GCGGAGAGGCTGTGTCAC 60.433 66.667 0.00 0.00 0.00 3.67
4772 6657 3.695606 GGCGGAGAGGCTGTGTCA 61.696 66.667 0.00 0.00 42.90 3.58
4773 6658 4.459089 GGGCGGAGAGGCTGTGTC 62.459 72.222 0.00 0.00 45.89 3.67


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

AutoCloner maintained by Alex Coulton.