Multiple sequence alignment - TraesCS4D01G013600

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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 TraesCS4D01G013600 chr4D 100.000 4704 0 0 1 4704 6421842 6426545 0.000000e+00 8687.0
1 TraesCS4D01G013600 chr4B 90.148 1959 127 34 2018 3917 11657829 11655878 0.000000e+00 2488.0
2 TraesCS4D01G013600 chr4B 86.808 1463 120 44 96 1523 11660106 11658682 0.000000e+00 1565.0
3 TraesCS4D01G013600 chr4B 87.199 539 32 14 1535 2041 11658373 11657840 3.160000e-161 579.0
4 TraesCS4D01G013600 chr4B 79.763 761 89 23 3993 4695 11662724 11663477 4.230000e-135 492.0
5 TraesCS4D01G013600 chr4B 87.433 374 32 8 3971 4329 11561193 11560820 2.620000e-112 416.0
6 TraesCS4D01G013600 chr4B 88.146 329 18 8 3638 3950 11665539 11665862 5.750000e-99 372.0
7 TraesCS4D01G013600 chr4B 92.121 165 13 0 3461 3625 11665330 11665494 2.830000e-57 233.0
8 TraesCS4D01G013600 chr4B 84.513 226 23 7 4478 4695 11655094 11654873 3.690000e-51 213.0
9 TraesCS4D01G013600 chr4B 94.574 129 7 0 3999 4127 11665860 11665988 2.870000e-47 200.0
10 TraesCS4D01G013600 chr4B 92.453 53 0 3 4052 4101 11655820 11655769 6.530000e-09 73.1
11 TraesCS4D01G013600 chr4A 92.386 1668 79 18 2321 3950 597014418 597016075 0.000000e+00 2333.0
12 TraesCS4D01G013600 chr4A 88.619 1731 121 30 544 2235 597012629 597014322 0.000000e+00 2036.0
13 TraesCS4D01G013600 chr4A 85.353 553 45 21 1 535 597006103 597006637 1.490000e-149 540.0
14 TraesCS4D01G013600 chr4A 86.944 337 32 9 3999 4330 597016073 597016402 7.440000e-98 368.0
15 TraesCS4D01G013600 chr4A 92.500 40 3 0 503 542 60016199 60016238 1.830000e-04 58.4
16 TraesCS4D01G013600 chr5A 79.519 1040 186 20 2583 3610 613700664 613701688 0.000000e+00 715.0
17 TraesCS4D01G013600 chr5A 88.136 59 5 2 2443 2501 44879316 44879372 8.450000e-08 69.4
18 TraesCS4D01G013600 chr5D 79.271 1042 185 24 2583 3610 491527753 491528777 0.000000e+00 699.0
19 TraesCS4D01G013600 chr5D 90.385 52 3 2 2450 2499 556882646 556882697 3.040000e-07 67.6
20 TraesCS4D01G013600 chr5D 89.362 47 5 0 2443 2489 55904913 55904959 5.080000e-05 60.2
21 TraesCS4D01G013600 chr5B 78.958 1036 197 15 2584 3610 606301625 606302648 0.000000e+00 686.0
22 TraesCS4D01G013600 chr3A 76.085 1037 201 39 2599 3610 724515618 724516632 9.090000e-137 497.0
23 TraesCS4D01G013600 chr3A 90.385 52 4 1 2443 2493 43633718 43633769 3.040000e-07 67.6
24 TraesCS4D01G013600 chr3A 90.385 52 4 1 2443 2493 44216816 44216867 3.040000e-07 67.6
25 TraesCS4D01G013600 chr3D 75.984 991 200 32 2643 3611 593236195 593237169 1.180000e-130 477.0
26 TraesCS4D01G013600 chr3B 75.678 1032 207 37 2599 3605 795839894 795840906 4.260000e-130 475.0
27 TraesCS4D01G013600 chr1A 70.291 515 134 14 2856 3362 539756836 539757339 8.390000e-13 86.1
28 TraesCS4D01G013600 chr2D 93.182 44 3 0 510 553 128455589 128455546 1.090000e-06 65.8
29 TraesCS4D01G013600 chr2D 91.111 45 4 0 501 545 416856716 416856672 1.410000e-05 62.1
30 TraesCS4D01G013600 chrUn 91.304 46 4 0 2444 2489 79655570 79655525 3.930000e-06 63.9
31 TraesCS4D01G013600 chr1D 91.304 46 4 0 501 546 313208276 313208321 3.930000e-06 63.9
32 TraesCS4D01G013600 chr1B 91.304 46 4 0 501 546 423584003 423584048 3.930000e-06 63.9
33 TraesCS4D01G013600 chr7D 92.857 42 3 0 501 542 575581206 575581247 1.410000e-05 62.1
34 TraesCS4D01G013600 chr7D 87.500 48 6 0 2443 2490 5431619 5431666 6.580000e-04 56.5
35 TraesCS4D01G013600 chr2A 94.872 39 2 0 515 553 135475008 135474970 1.410000e-05 62.1


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 TraesCS4D01G013600 chr4D 6421842 6426545 4703 False 8687.00 8687 100.000000 1 4704 1 chr4D.!!$F1 4703
1 TraesCS4D01G013600 chr4B 11654873 11660106 5233 True 983.62 2488 88.224200 96 4695 5 chr4B.!!$R2 4599
2 TraesCS4D01G013600 chr4B 11662724 11665988 3264 False 324.25 492 88.651000 3461 4695 4 chr4B.!!$F1 1234
3 TraesCS4D01G013600 chr4A 597012629 597016402 3773 False 1579.00 2333 89.316333 544 4330 3 chr4A.!!$F3 3786
4 TraesCS4D01G013600 chr4A 597006103 597006637 534 False 540.00 540 85.353000 1 535 1 chr4A.!!$F2 534
5 TraesCS4D01G013600 chr5A 613700664 613701688 1024 False 715.00 715 79.519000 2583 3610 1 chr5A.!!$F2 1027
6 TraesCS4D01G013600 chr5D 491527753 491528777 1024 False 699.00 699 79.271000 2583 3610 1 chr5D.!!$F2 1027
7 TraesCS4D01G013600 chr5B 606301625 606302648 1023 False 686.00 686 78.958000 2584 3610 1 chr5B.!!$F1 1026
8 TraesCS4D01G013600 chr3A 724515618 724516632 1014 False 497.00 497 76.085000 2599 3610 1 chr3A.!!$F3 1011
9 TraesCS4D01G013600 chr3D 593236195 593237169 974 False 477.00 477 75.984000 2643 3611 1 chr3D.!!$F1 968
10 TraesCS4D01G013600 chr3B 795839894 795840906 1012 False 475.00 475 75.678000 2599 3605 1 chr3B.!!$F1 1006

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
793 849 0.186873 GCACCTCCCCATCATCCAAT 59.813 55.000 0.00 0.00 0.00 3.16 F
1749 2131 0.035317 TTGAGTCAGAAGCATGCGGT 59.965 50.000 13.01 4.02 0.00 5.68 F
2420 2926 1.063321 TGTTAGTGTTGCTTGTGTGCG 59.937 47.619 0.00 0.00 35.36 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 2845 0.102844 AAATTTCCCGGCATGATGCG 59.897 50.000 11.75 6.80 46.21 4.73 R
2573 3116 1.074423 CATATCTGCAGGCAGGGGG 59.926 63.158 20.19 5.32 43.75 5.40 R
3842 4440 0.622738 ATGGGCTCCTGTCCTGTGAT 60.623 55.000 0.00 0.00 39.11 3.06 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
41 42 4.176752 GCACCGTGATCCCCTCCC 62.177 72.222 1.65 0.00 0.00 4.30
42 43 3.480133 CACCGTGATCCCCTCCCC 61.480 72.222 0.00 0.00 0.00 4.81
104 106 2.672996 GGGCTCGGCAAAGAAGCA 60.673 61.111 0.00 0.00 35.83 3.91
115 117 3.056322 GGCAAAGAAGCATGGAGTTTCAT 60.056 43.478 0.00 0.00 39.64 2.57
116 118 4.562143 GGCAAAGAAGCATGGAGTTTCATT 60.562 41.667 0.00 0.00 39.64 2.57
126 128 7.542025 AGCATGGAGTTTCATTATCTTTTGAC 58.458 34.615 0.00 0.00 0.00 3.18
127 129 7.177216 AGCATGGAGTTTCATTATCTTTTGACA 59.823 33.333 0.00 0.00 0.00 3.58
138 140 1.487142 TCTTTTGACAGTGGAACCCGA 59.513 47.619 0.00 0.00 37.80 5.14
139 141 1.602377 CTTTTGACAGTGGAACCCGAC 59.398 52.381 0.00 0.00 37.80 4.79
159 161 4.386711 GACCTTTTTATCGGACCCTATGG 58.613 47.826 0.00 0.00 37.80 2.74
178 180 8.000780 CCTATGGGAAAAGAATAGGAACTTTG 57.999 38.462 2.38 0.00 43.85 2.77
180 182 5.144100 TGGGAAAAGAATAGGAACTTTGCA 58.856 37.500 0.00 0.00 41.75 4.08
240 242 3.063997 GCGTTGACATTCAAGTAGGATGG 59.936 47.826 0.00 0.00 37.00 3.51
328 341 5.689383 ATCTGAAGAGAGATTCGCTAGTC 57.311 43.478 0.00 0.00 31.52 2.59
329 342 4.518249 TCTGAAGAGAGATTCGCTAGTCA 58.482 43.478 0.00 0.00 31.52 3.41
333 346 6.634805 TGAAGAGAGATTCGCTAGTCAAAAT 58.365 36.000 0.00 0.00 31.52 1.82
365 378 0.586802 GTTGGTTCTCAAGGCACGAC 59.413 55.000 0.00 0.00 35.80 4.34
366 379 0.878523 TTGGTTCTCAAGGCACGACG 60.879 55.000 0.00 0.00 0.00 5.12
367 380 1.006571 GGTTCTCAAGGCACGACGA 60.007 57.895 0.00 0.00 0.00 4.20
379 392 1.593793 GCACGACGAACAAACTTGGAC 60.594 52.381 0.00 0.00 0.00 4.02
389 402 2.491693 ACAAACTTGGACAACACACTGG 59.508 45.455 0.00 0.00 0.00 4.00
391 404 3.297134 AACTTGGACAACACACTGGAT 57.703 42.857 0.00 0.00 0.00 3.41
420 438 3.780624 ACACCAGTGTTGACCTGAC 57.219 52.632 0.00 0.00 41.83 3.51
421 439 0.908910 ACACCAGTGTTGACCTGACA 59.091 50.000 0.00 0.00 41.83 3.58
463 487 2.366266 ACTGCCAACTTTGTTGATGCAT 59.634 40.909 0.00 0.00 0.00 3.96
465 489 3.132160 TGCCAACTTTGTTGATGCATTG 58.868 40.909 11.47 0.00 0.00 2.82
466 490 2.096119 GCCAACTTTGTTGATGCATTGC 60.096 45.455 11.47 0.46 0.00 3.56
467 491 3.395639 CCAACTTTGTTGATGCATTGCT 58.604 40.909 10.49 0.00 0.00 3.91
468 492 3.430895 CCAACTTTGTTGATGCATTGCTC 59.569 43.478 10.49 5.76 0.00 4.26
469 493 4.304110 CAACTTTGTTGATGCATTGCTCT 58.696 39.130 10.49 0.00 0.00 4.09
546 580 7.544622 AGTGTCGCTGATCTAGTACAATTTTA 58.455 34.615 0.00 0.00 0.00 1.52
616 652 2.680312 TGTAGAGCTAGCTGCCTTTG 57.320 50.000 24.99 0.00 44.23 2.77
745 795 3.604667 CAAAAGCAGCCACCGCCA 61.605 61.111 0.00 0.00 34.57 5.69
746 796 3.605664 AAAAGCAGCCACCGCCAC 61.606 61.111 0.00 0.00 34.57 5.01
793 849 0.186873 GCACCTCCCCATCATCCAAT 59.813 55.000 0.00 0.00 0.00 3.16
812 868 1.676678 TTCGCATCCCTTCTCCTCCG 61.677 60.000 0.00 0.00 0.00 4.63
864 927 4.609691 AATCCGCGTTAAATTCGTGAAT 57.390 36.364 4.92 0.00 40.55 2.57
867 930 3.432592 TCCGCGTTAAATTCGTGAATTCA 59.567 39.130 3.38 3.38 39.88 2.57
869 932 4.791163 CCGCGTTAAATTCGTGAATTCATT 59.209 37.500 12.12 3.96 39.88 2.57
871 934 6.161578 CGCGTTAAATTCGTGAATTCATTTG 58.838 36.000 12.12 5.26 39.88 2.32
873 936 6.161578 CGTTAAATTCGTGAATTCATTTGCG 58.838 36.000 12.12 10.46 39.88 4.85
875 938 5.499268 AAATTCGTGAATTCATTTGCGTG 57.501 34.783 12.12 0.00 39.88 5.34
878 941 1.685302 GTGAATTCATTTGCGTGCGT 58.315 45.000 12.12 0.00 0.00 5.24
881 944 1.008361 AATTCATTTGCGTGCGTGCC 61.008 50.000 0.00 0.00 0.00 5.01
929 1002 1.078918 CTGGTGCTTGCTCCGATCA 60.079 57.895 8.83 0.00 0.00 2.92
975 1048 3.964875 GCGTGGTTGTGTGGCTGG 61.965 66.667 0.00 0.00 0.00 4.85
982 1055 0.250727 GTTGTGTGGCTGGGAGCTTA 60.251 55.000 0.00 0.00 41.99 3.09
989 1062 1.661498 GGCTGGGAGCTTAGCTTTGC 61.661 60.000 8.58 10.22 41.99 3.68
995 1068 1.543358 GGAGCTTAGCTTTGCTGCTTT 59.457 47.619 19.47 0.00 42.92 3.51
998 1071 2.030451 AGCTTAGCTTTGCTGCTTTGAC 60.030 45.455 0.00 0.00 43.74 3.18
1248 1321 2.282783 GGTGGCCATCCCCAACAAC 61.283 63.158 9.72 0.00 42.31 3.32
1343 1416 3.487202 CGGCGTCAACATCCGGTG 61.487 66.667 0.00 1.37 39.52 4.94
1344 1417 2.047655 GGCGTCAACATCCGGTGA 60.048 61.111 0.00 0.00 0.00 4.02
1345 1418 2.100631 GGCGTCAACATCCGGTGAG 61.101 63.158 0.00 0.00 0.00 3.51
1374 1447 2.507058 CCACTCCTCCTCAATCCATGAA 59.493 50.000 0.00 0.00 37.67 2.57
1376 1449 3.199508 CACTCCTCCTCAATCCATGAACT 59.800 47.826 0.00 0.00 37.67 3.01
1377 1450 4.406972 CACTCCTCCTCAATCCATGAACTA 59.593 45.833 0.00 0.00 37.67 2.24
1378 1451 5.071519 CACTCCTCCTCAATCCATGAACTAT 59.928 44.000 0.00 0.00 37.67 2.12
1381 1454 6.624297 TCCTCCTCAATCCATGAACTATCTA 58.376 40.000 0.00 0.00 37.67 1.98
1383 1456 7.179872 TCCTCCTCAATCCATGAACTATCTATG 59.820 40.741 0.00 0.00 37.67 2.23
1384 1457 7.179872 CCTCCTCAATCCATGAACTATCTATGA 59.820 40.741 0.00 0.00 37.67 2.15
1385 1458 8.676397 TCCTCAATCCATGAACTATCTATGAT 57.324 34.615 0.00 0.00 37.67 2.45
1427 1500 3.496875 CTCGGATGCCCTCTCTGCG 62.497 68.421 0.00 0.00 0.00 5.18
1429 1502 2.202987 GGATGCCCTCTCTGCGTG 60.203 66.667 0.00 0.00 0.00 5.34
1502 1583 5.873179 TTGCAGTTTTAATTACTCCCTCG 57.127 39.130 0.00 0.00 0.00 4.63
1507 1645 6.294342 GCAGTTTTAATTACTCCCTCGGTTTT 60.294 38.462 0.00 0.00 0.00 2.43
1526 1664 7.172019 TCGGTTTTAAAATAGGTGTCTCAACTC 59.828 37.037 3.52 0.00 31.86 3.01
1530 1908 8.603242 TTTAAAATAGGTGTCTCAACTCTGTC 57.397 34.615 0.00 0.00 31.86 3.51
1560 1938 6.971527 TGAGACACTTGTTTTAAGACGAAA 57.028 33.333 0.00 0.00 0.00 3.46
1676 2058 6.403333 TCTTGATTTGTGTACAACGATAGC 57.597 37.500 0.00 0.00 42.67 2.97
1689 2071 8.192110 TGTACAACGATAGCACTATTTATGTCA 58.808 33.333 0.00 0.00 42.67 3.58
1737 2119 3.458118 TCCTCTTCCAAAACCTTGAGTCA 59.542 43.478 0.00 0.00 34.14 3.41
1749 2131 0.035317 TTGAGTCAGAAGCATGCGGT 59.965 50.000 13.01 4.02 0.00 5.68
1776 2170 3.331150 ACCGTTTGATAATTCACAGCGA 58.669 40.909 0.00 0.00 0.00 4.93
1847 2255 2.100989 GTCCCTACCTGACTCGTTCAT 58.899 52.381 0.00 0.00 32.17 2.57
1965 2378 1.303561 GTCCTGCCCAGTTGATGCA 60.304 57.895 0.00 0.00 0.00 3.96
1976 2389 3.438087 CCAGTTGATGCACGAAGAATCTT 59.562 43.478 0.00 0.00 0.00 2.40
1990 2403 5.613358 AAGAATCTTACTTTCGGCACTTG 57.387 39.130 0.00 0.00 0.00 3.16
2023 2436 8.715088 GCTAACTTGTTCTTCGGTAGAAAATTA 58.285 33.333 0.00 0.00 44.25 1.40
2081 2535 4.196826 GATCTGTCACGCGCACGC 62.197 66.667 5.73 4.64 45.53 5.34
2140 2594 4.028993 TCTTGTCGCCTAAAAGGGAATT 57.971 40.909 0.00 0.00 35.37 2.17
2141 2595 3.756434 TCTTGTCGCCTAAAAGGGAATTG 59.244 43.478 0.00 0.00 35.37 2.32
2194 2651 4.222124 TCTGATTTAAGTGGCCCTTCTC 57.778 45.455 9.46 6.86 34.46 2.87
2232 2689 4.105057 ACCCACCAAGTCCTTAACACATTA 59.895 41.667 0.00 0.00 0.00 1.90
2239 2729 9.802039 ACCAAGTCCTTAACACATTATTTTCTA 57.198 29.630 0.00 0.00 0.00 2.10
2275 2767 4.782019 ACTGTTCAGTGCAAAGTTTTGA 57.218 36.364 8.70 0.00 40.55 2.69
2277 2769 5.163513 ACTGTTCAGTGCAAAGTTTTGAAG 58.836 37.500 8.70 0.00 40.55 3.02
2278 2770 5.048083 ACTGTTCAGTGCAAAGTTTTGAAGA 60.048 36.000 8.70 0.54 40.55 2.87
2280 2772 5.633182 TGTTCAGTGCAAAGTTTTGAAGAAC 59.367 36.000 8.70 13.55 40.55 3.01
2281 2773 5.643379 TCAGTGCAAAGTTTTGAAGAACT 57.357 34.783 8.70 3.61 41.44 3.01
2282 2774 6.751514 TCAGTGCAAAGTTTTGAAGAACTA 57.248 33.333 8.70 0.00 38.86 2.24
2283 2775 7.151999 TCAGTGCAAAGTTTTGAAGAACTAA 57.848 32.000 8.70 0.00 38.86 2.24
2313 2818 5.584251 GGTGATCAGTTGGAGAAGAATCTTC 59.416 44.000 14.77 14.77 35.54 2.87
2314 2819 6.169094 GTGATCAGTTGGAGAAGAATCTTCA 58.831 40.000 23.20 2.40 39.53 3.02
2336 2841 1.208535 ACATCATGCAATTTGCCCTGG 59.791 47.619 18.27 7.16 44.23 4.45
2340 2845 4.100084 GCAATTTGCCCTGGCCCC 62.100 66.667 10.34 0.00 37.42 5.80
2356 2861 2.828095 CCGCATCATGCCGGGAAA 60.828 61.111 0.00 0.00 41.12 3.13
2397 2903 3.006967 AGCCGTCACAACTGAAACTATCT 59.993 43.478 0.00 0.00 0.00 1.98
2420 2926 1.063321 TGTTAGTGTTGCTTGTGTGCG 59.937 47.619 0.00 0.00 35.36 5.34
2463 3003 2.030946 GTGTCCGCTTGATGCTACATTC 59.969 50.000 0.25 0.00 37.48 2.67
2526 3069 7.099266 TCATCTGGGTTAATAACAGCATTTG 57.901 36.000 5.45 0.00 32.42 2.32
2573 3116 9.630098 CATGGTATGAAAACTAATTATGCATCC 57.370 33.333 0.19 0.00 0.00 3.51
2881 3424 0.395311 TCTACCCGTACCTCAGCCTG 60.395 60.000 0.00 0.00 0.00 4.85
2905 3448 1.210931 CAACGACGACTTCCCGCTA 59.789 57.895 0.00 0.00 0.00 4.26
3010 3556 4.700365 CTCGTGTCGGCGCTCACA 62.700 66.667 25.13 16.32 34.66 3.58
3402 3951 3.184683 GAGCAAGCTCGCGGACAG 61.185 66.667 6.13 0.00 36.85 3.51
3502 4051 1.144057 CGCCTCCTACGCCTTCAAT 59.856 57.895 0.00 0.00 0.00 2.57
3667 4248 4.373116 TTGACGACGGCCCTGCTC 62.373 66.667 0.00 0.00 0.00 4.26
3705 4286 1.283347 ATGGTGACCATGCTCTGAGT 58.717 50.000 17.79 0.00 43.39 3.41
3749 4335 4.942483 GTGCTAGTTAGTAGTGACTGGAGA 59.058 45.833 9.66 0.00 36.28 3.71
3761 4354 6.919775 AGTGACTGGAGAAGTTAACTACAT 57.080 37.500 8.92 0.00 40.07 2.29
3766 4359 7.232737 TGACTGGAGAAGTTAACTACATGAAGA 59.767 37.037 8.92 0.00 40.07 2.87
3842 4440 8.650714 CGTGTTACGCTACTGTAGTATATATGA 58.349 37.037 15.71 0.00 33.65 2.15
3847 4445 8.788325 ACGCTACTGTAGTATATATGATCACA 57.212 34.615 15.71 0.00 0.00 3.58
3848 4446 8.884726 ACGCTACTGTAGTATATATGATCACAG 58.115 37.037 15.71 13.00 38.26 3.66
3849 4447 8.338986 CGCTACTGTAGTATATATGATCACAGG 58.661 40.741 15.71 6.84 36.97 4.00
3899 4500 8.161425 TCCAAGGGTTTATTTAGATGTATAGCC 58.839 37.037 0.00 0.00 0.00 3.93
3950 4551 2.470257 CGTTGTCTTCCTTGTGTCGTAC 59.530 50.000 0.00 0.00 0.00 3.67
3951 4552 3.714391 GTTGTCTTCCTTGTGTCGTACT 58.286 45.455 0.00 0.00 0.00 2.73
3952 4553 3.637998 TGTCTTCCTTGTGTCGTACTC 57.362 47.619 0.00 0.00 0.00 2.59
3953 4554 3.220110 TGTCTTCCTTGTGTCGTACTCT 58.780 45.455 0.00 0.00 0.00 3.24
3954 4555 3.252701 TGTCTTCCTTGTGTCGTACTCTC 59.747 47.826 0.00 0.00 0.00 3.20
3955 4556 3.502979 GTCTTCCTTGTGTCGTACTCTCT 59.497 47.826 0.00 0.00 0.00 3.10
3956 4557 3.752222 TCTTCCTTGTGTCGTACTCTCTC 59.248 47.826 0.00 0.00 0.00 3.20
3957 4558 2.434428 TCCTTGTGTCGTACTCTCTCC 58.566 52.381 0.00 0.00 0.00 3.71
3958 4559 2.160205 CCTTGTGTCGTACTCTCTCCA 58.840 52.381 0.00 0.00 0.00 3.86
3959 4560 2.755655 CCTTGTGTCGTACTCTCTCCAT 59.244 50.000 0.00 0.00 0.00 3.41
3960 4561 3.181495 CCTTGTGTCGTACTCTCTCCATC 60.181 52.174 0.00 0.00 0.00 3.51
3961 4562 2.366533 TGTGTCGTACTCTCTCCATCC 58.633 52.381 0.00 0.00 0.00 3.51
3962 4563 1.677052 GTGTCGTACTCTCTCCATCCC 59.323 57.143 0.00 0.00 0.00 3.85
3963 4564 1.283905 TGTCGTACTCTCTCCATCCCA 59.716 52.381 0.00 0.00 0.00 4.37
3964 4565 2.291346 TGTCGTACTCTCTCCATCCCAA 60.291 50.000 0.00 0.00 0.00 4.12
3965 4566 2.758979 GTCGTACTCTCTCCATCCCAAA 59.241 50.000 0.00 0.00 0.00 3.28
3966 4567 3.385111 GTCGTACTCTCTCCATCCCAAAT 59.615 47.826 0.00 0.00 0.00 2.32
3967 4568 4.583489 GTCGTACTCTCTCCATCCCAAATA 59.417 45.833 0.00 0.00 0.00 1.40
3968 4569 5.068723 GTCGTACTCTCTCCATCCCAAATAA 59.931 44.000 0.00 0.00 0.00 1.40
3969 4570 5.302059 TCGTACTCTCTCCATCCCAAATAAG 59.698 44.000 0.00 0.00 0.00 1.73
3970 4571 5.069251 CGTACTCTCTCCATCCCAAATAAGT 59.931 44.000 0.00 0.00 0.00 2.24
3971 4572 6.407074 CGTACTCTCTCCATCCCAAATAAGTT 60.407 42.308 0.00 0.00 0.00 2.66
3972 4573 5.749462 ACTCTCTCCATCCCAAATAAGTTG 58.251 41.667 0.00 0.00 36.94 3.16
3973 4574 5.488919 ACTCTCTCCATCCCAAATAAGTTGA 59.511 40.000 0.00 0.00 39.87 3.18
3974 4575 5.994250 TCTCTCCATCCCAAATAAGTTGAG 58.006 41.667 0.00 0.00 39.87 3.02
3975 4576 5.488919 TCTCTCCATCCCAAATAAGTTGAGT 59.511 40.000 0.00 0.00 39.87 3.41
3976 4577 6.672218 TCTCTCCATCCCAAATAAGTTGAGTA 59.328 38.462 0.00 0.00 39.87 2.59
3977 4578 7.182026 TCTCTCCATCCCAAATAAGTTGAGTAA 59.818 37.037 0.00 0.00 39.87 2.24
3978 4579 7.110155 TCTCCATCCCAAATAAGTTGAGTAAC 58.890 38.462 0.00 0.00 39.87 2.50
3994 4595 9.420551 AGTTGAGTAACTTATTTTAGAACGGAG 57.579 33.333 0.00 0.00 44.57 4.63
3995 4596 8.654215 GTTGAGTAACTTATTTTAGAACGGAGG 58.346 37.037 0.00 0.00 33.94 4.30
3996 4597 8.125978 TGAGTAACTTATTTTAGAACGGAGGA 57.874 34.615 0.00 0.00 0.00 3.71
3997 4598 8.587608 TGAGTAACTTATTTTAGAACGGAGGAA 58.412 33.333 0.00 0.00 0.00 3.36
4018 4619 5.453480 GGAAGTATATCTTTGAGGGCGAGTT 60.453 44.000 0.00 0.00 36.40 3.01
4112 4721 3.776969 TGGAGCATATGAAGGTGAACTCT 59.223 43.478 6.97 0.00 0.00 3.24
4151 4760 1.303309 GCTCGTCTCCATGGATTTGG 58.697 55.000 16.63 3.29 38.18 3.28
4186 4795 5.905480 CTTTCAGCCAAAGCGTTTTTATT 57.095 34.783 0.00 0.00 46.67 1.40
4187 4796 5.649602 TTTCAGCCAAAGCGTTTTTATTG 57.350 34.783 0.00 0.00 46.67 1.90
4188 4797 3.648009 TCAGCCAAAGCGTTTTTATTGG 58.352 40.909 0.00 0.00 46.67 3.16
4189 4798 2.736192 CAGCCAAAGCGTTTTTATTGGG 59.264 45.455 0.00 0.00 46.67 4.12
4190 4799 2.073056 GCCAAAGCGTTTTTATTGGGG 58.927 47.619 0.00 0.00 42.05 4.96
4191 4800 2.694213 CCAAAGCGTTTTTATTGGGGG 58.306 47.619 0.00 0.00 38.89 5.40
4192 4801 2.037902 CCAAAGCGTTTTTATTGGGGGT 59.962 45.455 0.00 0.00 38.89 4.95
4193 4802 3.495276 CCAAAGCGTTTTTATTGGGGGTT 60.495 43.478 0.00 0.00 38.89 4.11
4194 4803 3.671008 AAGCGTTTTTATTGGGGGTTC 57.329 42.857 0.00 0.00 0.00 3.62
4195 4804 1.542472 AGCGTTTTTATTGGGGGTTCG 59.458 47.619 0.00 0.00 0.00 3.95
4196 4805 1.270274 GCGTTTTTATTGGGGGTTCGT 59.730 47.619 0.00 0.00 0.00 3.85
4197 4806 2.288334 GCGTTTTTATTGGGGGTTCGTT 60.288 45.455 0.00 0.00 0.00 3.85
4198 4807 3.799574 GCGTTTTTATTGGGGGTTCGTTT 60.800 43.478 0.00 0.00 0.00 3.60
4202 4811 0.036448 TATTGGGGGTTCGTTTGCGA 59.964 50.000 0.00 0.00 46.36 5.10
4229 5173 4.512944 GCAAGTATGGACTATGTGGTCATG 59.487 45.833 0.00 0.00 37.91 3.07
4230 5174 5.674525 CAAGTATGGACTATGTGGTCATGT 58.325 41.667 0.00 0.00 37.91 3.21
4232 5176 6.313519 AGTATGGACTATGTGGTCATGTTT 57.686 37.500 0.00 0.00 37.91 2.83
4233 5177 6.115446 AGTATGGACTATGTGGTCATGTTTG 58.885 40.000 0.00 0.00 37.91 2.93
4234 5178 4.365514 TGGACTATGTGGTCATGTTTGT 57.634 40.909 0.00 0.00 37.91 2.83
4236 5180 4.202409 TGGACTATGTGGTCATGTTTGTCA 60.202 41.667 0.00 0.00 37.91 3.58
4277 5234 4.069304 TGGGTTTCATGTTTTCCGAGTAG 58.931 43.478 0.00 0.00 0.00 2.57
4278 5235 4.070009 GGGTTTCATGTTTTCCGAGTAGT 58.930 43.478 0.00 0.00 0.00 2.73
4279 5236 4.153655 GGGTTTCATGTTTTCCGAGTAGTC 59.846 45.833 0.00 0.00 0.00 2.59
4280 5237 4.995487 GGTTTCATGTTTTCCGAGTAGTCT 59.005 41.667 0.00 0.00 0.00 3.24
4281 5238 5.107065 GGTTTCATGTTTTCCGAGTAGTCTG 60.107 44.000 0.00 0.00 0.00 3.51
4294 5252 4.870426 CGAGTAGTCTGCATATGGTTTGTT 59.130 41.667 4.56 0.00 0.00 2.83
4339 5297 4.672413 CAGTTTTGCAAAATCTCAGTCGAC 59.328 41.667 26.24 7.70 0.00 4.20
4342 5300 1.800586 TGCAAAATCTCAGTCGACTGC 59.199 47.619 35.48 24.06 43.46 4.40
4355 5313 2.592194 TCGACTGCGACTTGTTCATAC 58.408 47.619 0.00 0.00 42.51 2.39
4356 5314 2.030628 TCGACTGCGACTTGTTCATACA 60.031 45.455 0.00 0.00 42.51 2.29
4357 5315 2.923655 CGACTGCGACTTGTTCATACAT 59.076 45.455 0.00 0.00 40.82 2.29
4358 5316 3.367932 CGACTGCGACTTGTTCATACATT 59.632 43.478 0.00 0.00 40.82 2.71
4359 5317 4.561213 CGACTGCGACTTGTTCATACATTA 59.439 41.667 0.00 0.00 40.82 1.90
4360 5318 5.061684 CGACTGCGACTTGTTCATACATTAA 59.938 40.000 0.00 0.00 40.82 1.40
4361 5319 6.408858 ACTGCGACTTGTTCATACATTAAG 57.591 37.500 0.00 0.00 33.44 1.85
4362 5320 6.163476 ACTGCGACTTGTTCATACATTAAGA 58.837 36.000 0.00 0.00 33.44 2.10
4363 5321 6.818644 ACTGCGACTTGTTCATACATTAAGAT 59.181 34.615 0.00 0.00 33.44 2.40
4365 5323 6.019881 TGCGACTTGTTCATACATTAAGATCG 60.020 38.462 0.00 0.00 33.44 3.69
4366 5324 6.019801 GCGACTTGTTCATACATTAAGATCGT 60.020 38.462 0.00 0.00 33.44 3.73
4367 5325 7.330318 CGACTTGTTCATACATTAAGATCGTG 58.670 38.462 0.00 0.00 33.44 4.35
4368 5326 7.009265 CGACTTGTTCATACATTAAGATCGTGT 59.991 37.037 0.00 0.00 33.44 4.49
4369 5327 9.297586 GACTTGTTCATACATTAAGATCGTGTA 57.702 33.333 0.00 0.00 33.44 2.90
4370 5328 9.647797 ACTTGTTCATACATTAAGATCGTGTAA 57.352 29.630 7.17 0.00 33.44 2.41
4421 5379 9.979578 TTTTCTTTCATACACATTATTGCACTT 57.020 25.926 0.00 0.00 0.00 3.16
4422 5380 8.969121 TTCTTTCATACACATTATTGCACTTG 57.031 30.769 0.00 0.00 0.00 3.16
4423 5381 8.334263 TCTTTCATACACATTATTGCACTTGA 57.666 30.769 0.00 0.00 0.00 3.02
4424 5382 8.236586 TCTTTCATACACATTATTGCACTTGAC 58.763 33.333 0.00 0.00 0.00 3.18
4425 5383 7.686438 TTCATACACATTATTGCACTTGACT 57.314 32.000 0.00 0.00 0.00 3.41
4426 5384 7.075674 TCATACACATTATTGCACTTGACTG 57.924 36.000 0.00 0.00 0.00 3.51
4427 5385 6.878389 TCATACACATTATTGCACTTGACTGA 59.122 34.615 0.00 0.00 0.00 3.41
4428 5386 5.618056 ACACATTATTGCACTTGACTGAG 57.382 39.130 0.00 0.00 0.00 3.35
4429 5387 5.308014 ACACATTATTGCACTTGACTGAGA 58.692 37.500 0.00 0.00 0.00 3.27
4430 5388 5.942236 ACACATTATTGCACTTGACTGAGAT 59.058 36.000 0.00 0.00 0.00 2.75
4431 5389 6.432162 ACACATTATTGCACTTGACTGAGATT 59.568 34.615 0.00 0.00 0.00 2.40
4432 5390 7.040201 ACACATTATTGCACTTGACTGAGATTT 60.040 33.333 0.00 0.00 0.00 2.17
4436 5394 6.585695 ATTGCACTTGACTGAGATTTGATT 57.414 33.333 0.00 0.00 0.00 2.57
4441 5399 7.095060 TGCACTTGACTGAGATTTGATTAAGTC 60.095 37.037 0.00 0.00 35.66 3.01
4473 5431 8.827677 CAACTAAAAACTAGGCACATCCTATAC 58.172 37.037 0.00 0.00 45.99 1.47
4474 5432 7.506971 ACTAAAAACTAGGCACATCCTATACC 58.493 38.462 0.00 0.00 45.99 2.73
4504 5485 0.105224 TCGAAGAGGCCACGTTTGAA 59.895 50.000 5.01 0.00 0.00 2.69
4510 5491 1.008538 GGCCACGTTTGAAGCACAG 60.009 57.895 0.00 0.00 0.00 3.66
4513 5494 1.641140 CACGTTTGAAGCACAGCGA 59.359 52.632 13.13 0.00 34.62 4.93
4514 5495 0.383491 CACGTTTGAAGCACAGCGAG 60.383 55.000 13.13 5.57 34.62 5.03
4515 5496 0.810031 ACGTTTGAAGCACAGCGAGT 60.810 50.000 13.13 0.00 34.62 4.18
4516 5497 1.136690 CGTTTGAAGCACAGCGAGTA 58.863 50.000 0.00 0.00 33.22 2.59
4517 5498 1.125021 CGTTTGAAGCACAGCGAGTAG 59.875 52.381 0.00 0.00 33.22 2.57
4518 5499 2.404215 GTTTGAAGCACAGCGAGTAGA 58.596 47.619 0.00 0.00 0.00 2.59
4519 5500 2.800544 GTTTGAAGCACAGCGAGTAGAA 59.199 45.455 0.00 0.00 0.00 2.10
4539 5527 4.698304 AGAACAACTTCCAAGAACAACGAA 59.302 37.500 0.00 0.00 0.00 3.85
4546 5534 2.981805 TCCAAGAACAACGAACGATACG 59.018 45.455 0.14 0.00 0.00 3.06
4547 5535 2.471749 CCAAGAACAACGAACGATACGC 60.472 50.000 0.14 0.00 0.00 4.42
4552 5540 1.384409 ACAACGAACGATACGCTTTCG 59.616 47.619 12.59 12.59 42.20 3.46
4565 5553 1.385999 GCTTTCGTGTTGCTTTCGTC 58.614 50.000 0.00 0.00 0.00 4.20
4572 5560 3.399770 TTGCTTTCGTCGCCGTCG 61.400 61.111 0.00 0.00 35.01 5.12
4573 5561 3.827551 TTGCTTTCGTCGCCGTCGA 62.828 57.895 1.66 1.66 43.28 4.20
4584 5572 2.485582 CCGTCGATGTCTGTCGCT 59.514 61.111 3.52 0.00 41.22 4.93
4592 5580 4.452733 GTCTGTCGCTTCCCCCGG 62.453 72.222 0.00 0.00 0.00 5.73
4595 5583 3.006728 TGTCGCTTCCCCCGGAAT 61.007 61.111 0.73 0.00 41.23 3.01
4626 5614 2.279717 GCTCGCTCATGCCGATCA 60.280 61.111 8.40 0.00 35.36 2.92
4627 5615 1.884464 GCTCGCTCATGCCGATCAA 60.884 57.895 8.40 0.00 35.36 2.57
4637 5625 3.056536 TCATGCCGATCAATAGGAGTAGC 60.057 47.826 0.00 0.00 0.00 3.58
4638 5626 2.316108 TGCCGATCAATAGGAGTAGCA 58.684 47.619 0.00 0.00 0.00 3.49
4645 5633 5.278512 CGATCAATAGGAGTAGCACAGCTAA 60.279 44.000 0.00 0.00 43.07 3.09
4646 5634 5.521906 TCAATAGGAGTAGCACAGCTAAG 57.478 43.478 0.00 0.00 43.07 2.18
4657 5645 1.726791 CACAGCTAAGCCAACGTGTAG 59.273 52.381 0.00 0.00 0.00 2.74
4669 5657 0.669318 ACGTGTAGACATGGCGTTGG 60.669 55.000 6.81 0.00 37.19 3.77
4670 5658 1.794222 GTGTAGACATGGCGTTGGC 59.206 57.895 0.00 0.00 38.90 4.52
4688 5676 2.196925 CCATCTCCGACGGCTAGCT 61.197 63.158 15.72 0.00 0.00 3.32
4700 5688 4.135153 CTAGCTGCGAGGCACGGT 62.135 66.667 6.44 0.00 42.83 4.83
4701 5689 4.435436 TAGCTGCGAGGCACGGTG 62.435 66.667 6.44 3.15 42.83 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.460305 ATGGATCCACCTCCCCTCG 60.460 63.158 18.99 0.00 39.86 4.63
74 75 1.453669 GAGCCCATGGATCCACCTC 59.546 63.158 18.99 15.90 39.86 3.85
76 77 2.111878 CGAGCCCATGGATCCACC 59.888 66.667 18.99 6.00 34.17 4.61
104 106 8.517878 CACTGTCAAAAGATAATGAAACTCCAT 58.482 33.333 0.00 0.00 0.00 3.41
115 117 4.069304 CGGGTTCCACTGTCAAAAGATAA 58.931 43.478 0.00 0.00 0.00 1.75
116 118 3.325425 TCGGGTTCCACTGTCAAAAGATA 59.675 43.478 0.00 0.00 0.00 1.98
126 128 1.687563 AAAAAGGTCGGGTTCCACTG 58.312 50.000 0.00 0.00 0.00 3.66
127 129 3.682696 GATAAAAAGGTCGGGTTCCACT 58.317 45.455 0.00 0.00 0.00 4.00
138 140 3.137728 CCCATAGGGTCCGATAAAAAGGT 59.862 47.826 0.00 0.00 38.25 3.50
139 141 3.393278 TCCCATAGGGTCCGATAAAAAGG 59.607 47.826 1.36 0.00 44.74 3.11
151 153 5.736616 AGTTCCTATTCTTTTCCCATAGGGT 59.263 40.000 1.36 0.00 44.74 4.34
154 156 7.122650 TGCAAAGTTCCTATTCTTTTCCCATAG 59.877 37.037 0.00 0.00 32.52 2.23
159 161 5.578336 GCATGCAAAGTTCCTATTCTTTTCC 59.422 40.000 14.21 0.00 32.52 3.13
160 162 6.393171 AGCATGCAAAGTTCCTATTCTTTTC 58.607 36.000 21.98 0.00 32.52 2.29
162 164 5.990120 AGCATGCAAAGTTCCTATTCTTT 57.010 34.783 21.98 0.00 34.74 2.52
165 167 4.427312 CCAAGCATGCAAAGTTCCTATTC 58.573 43.478 21.98 0.00 0.00 1.75
174 176 0.388907 CCGAACCCAAGCATGCAAAG 60.389 55.000 21.98 8.78 0.00 2.77
177 179 2.130821 TACCCGAACCCAAGCATGCA 62.131 55.000 21.98 0.00 0.00 3.96
178 180 1.377987 TACCCGAACCCAAGCATGC 60.378 57.895 10.51 10.51 0.00 4.06
180 182 0.402504 TTGTACCCGAACCCAAGCAT 59.597 50.000 0.00 0.00 0.00 3.79
240 242 2.005971 ATTAAGAACAGGACGCCGTC 57.994 50.000 9.15 9.15 0.00 4.79
328 341 7.651704 AGAACCAACTCAACCGAAATAATTTTG 59.348 33.333 0.00 0.00 0.00 2.44
329 342 7.722363 AGAACCAACTCAACCGAAATAATTTT 58.278 30.769 0.00 0.00 0.00 1.82
333 346 5.369833 TGAGAACCAACTCAACCGAAATAA 58.630 37.500 0.00 0.00 42.79 1.40
365 378 3.119990 AGTGTGTTGTCCAAGTTTGTTCG 60.120 43.478 0.00 0.00 0.00 3.95
366 379 4.165779 CAGTGTGTTGTCCAAGTTTGTTC 58.834 43.478 0.00 0.00 0.00 3.18
367 380 3.056891 CCAGTGTGTTGTCCAAGTTTGTT 60.057 43.478 0.00 0.00 0.00 2.83
379 392 1.610038 ACATGTGCATCCAGTGTGTTG 59.390 47.619 0.00 0.00 0.00 3.33
389 402 3.253188 ACACTGGTGTTAACATGTGCATC 59.747 43.478 25.38 9.39 41.83 3.91
391 404 2.649190 ACACTGGTGTTAACATGTGCA 58.351 42.857 25.38 0.00 41.83 4.57
463 487 3.118519 TCTCTGCAAGCATCATAGAGCAA 60.119 43.478 0.00 0.00 35.89 3.91
465 489 3.109044 TCTCTGCAAGCATCATAGAGC 57.891 47.619 0.00 0.00 35.89 4.09
466 490 4.633175 ACATCTCTGCAAGCATCATAGAG 58.367 43.478 0.00 0.00 36.96 2.43
467 491 4.684484 ACATCTCTGCAAGCATCATAGA 57.316 40.909 0.00 0.00 0.00 1.98
468 492 4.930405 CCTACATCTCTGCAAGCATCATAG 59.070 45.833 0.00 0.00 0.00 2.23
469 493 4.346127 ACCTACATCTCTGCAAGCATCATA 59.654 41.667 0.00 0.00 0.00 2.15
546 580 5.105716 ACAATAGATCAGCGACACTTACACT 60.106 40.000 0.00 0.00 0.00 3.55
616 652 3.134127 GCCGGTGATGGTGAAGGC 61.134 66.667 1.90 0.00 37.61 4.35
745 795 7.148306 ACGATTTGATTATTTTTCTAGTGCGGT 60.148 33.333 0.00 0.00 0.00 5.68
746 796 7.186804 ACGATTTGATTATTTTTCTAGTGCGG 58.813 34.615 0.00 0.00 0.00 5.69
747 797 8.601243 AACGATTTGATTATTTTTCTAGTGCG 57.399 30.769 0.00 0.00 0.00 5.34
748 798 8.725046 CGAACGATTTGATTATTTTTCTAGTGC 58.275 33.333 0.00 0.00 0.00 4.40
749 799 8.725046 GCGAACGATTTGATTATTTTTCTAGTG 58.275 33.333 0.00 0.00 0.00 2.74
793 849 1.676678 CGGAGGAGAAGGGATGCGAA 61.677 60.000 0.00 0.00 0.00 4.70
812 868 2.491621 GGGGACGTACGTGTAGGC 59.508 66.667 28.16 10.76 0.00 3.93
864 927 2.050533 GGCACGCACGCAAATGAA 60.051 55.556 0.00 0.00 0.00 2.57
867 930 2.669569 AGAGGCACGCACGCAAAT 60.670 55.556 0.00 0.00 0.00 2.32
869 932 4.908687 ACAGAGGCACGCACGCAA 62.909 61.111 0.00 0.00 0.00 4.85
873 936 2.588877 ACACACAGAGGCACGCAC 60.589 61.111 0.00 0.00 0.00 5.34
875 938 3.349006 CCACACACAGAGGCACGC 61.349 66.667 0.00 0.00 0.00 5.34
881 944 1.233019 CTTTGAGGCCACACACAGAG 58.767 55.000 5.01 0.00 0.00 3.35
929 1002 1.000955 ACGCAGGAAGAGTTCACGAAT 59.999 47.619 0.00 0.00 0.00 3.34
959 1032 3.286751 CCCAGCCACACAACCACG 61.287 66.667 0.00 0.00 0.00 4.94
960 1033 1.898574 CTCCCAGCCACACAACCAC 60.899 63.158 0.00 0.00 0.00 4.16
961 1034 2.515398 CTCCCAGCCACACAACCA 59.485 61.111 0.00 0.00 0.00 3.67
962 1035 2.983725 AAGCTCCCAGCCACACAACC 62.984 60.000 0.00 0.00 43.77 3.77
975 1048 1.172175 AAGCAGCAAAGCTAAGCTCC 58.828 50.000 9.66 1.62 45.89 4.70
989 1062 2.703798 CCCGCCATGGTCAAAGCAG 61.704 63.158 14.67 0.00 35.15 4.24
1025 1098 3.745803 GCAGCAGAAGCACCAGCC 61.746 66.667 0.00 0.00 45.49 4.85
1343 1416 1.326951 GGAGGAGTGGAGGTGCTCTC 61.327 65.000 0.00 0.00 41.71 3.20
1344 1417 1.305718 GGAGGAGTGGAGGTGCTCT 60.306 63.158 0.00 0.00 33.16 4.09
1345 1418 1.305718 AGGAGGAGTGGAGGTGCTC 60.306 63.158 0.00 0.00 0.00 4.26
1374 1447 6.578238 CGAGGAGGAAGAGGATCATAGATAGT 60.578 46.154 0.00 0.00 37.82 2.12
1376 1449 5.489278 TCGAGGAGGAAGAGGATCATAGATA 59.511 44.000 0.00 0.00 37.82 1.98
1377 1450 4.290985 TCGAGGAGGAAGAGGATCATAGAT 59.709 45.833 0.00 0.00 37.82 1.98
1378 1451 3.653352 TCGAGGAGGAAGAGGATCATAGA 59.347 47.826 0.00 0.00 37.82 1.98
1381 1454 3.541242 ATCGAGGAGGAAGAGGATCAT 57.459 47.619 0.00 0.00 37.82 2.45
1383 1456 3.226777 TGAATCGAGGAGGAAGAGGATC 58.773 50.000 0.00 0.00 0.00 3.36
1384 1457 3.117322 TCTGAATCGAGGAGGAAGAGGAT 60.117 47.826 0.00 0.00 0.00 3.24
1385 1458 2.242452 TCTGAATCGAGGAGGAAGAGGA 59.758 50.000 0.00 0.00 0.00 3.71
1427 1500 3.715628 ACAGGCATGAAAACAGAACAC 57.284 42.857 4.84 0.00 0.00 3.32
1429 1502 4.305989 TGAACAGGCATGAAAACAGAAC 57.694 40.909 4.84 0.00 0.00 3.01
1502 1583 8.290325 CAGAGTTGAGACACCTATTTTAAAACC 58.710 37.037 1.97 0.00 0.00 3.27
1507 1645 6.269077 TGGACAGAGTTGAGACACCTATTTTA 59.731 38.462 0.00 0.00 0.00 1.52
1514 1652 1.964223 TCTGGACAGAGTTGAGACACC 59.036 52.381 0.00 0.00 32.82 4.16
1526 1664 3.181471 ACAAGTGTCTCAACTCTGGACAG 60.181 47.826 0.00 0.00 40.06 3.51
1530 1908 6.538742 TCTTAAAACAAGTGTCTCAACTCTGG 59.461 38.462 0.00 0.00 29.93 3.86
1714 2096 4.104738 TGACTCAAGGTTTTGGAAGAGGAT 59.895 41.667 0.00 0.00 34.97 3.24
1737 2119 0.598065 GTTTTGGACCGCATGCTTCT 59.402 50.000 17.13 0.00 0.00 2.85
1749 2131 6.392625 TGTGAATTATCAAACGGTTTTGGA 57.607 33.333 2.79 0.00 42.23 3.53
1776 2170 5.428783 ACCTATGGTGAGTATTTTAGGCACT 59.571 40.000 0.00 0.00 37.12 4.40
1847 2255 2.653726 TGCTGACAAGAAAGCTTCCAA 58.346 42.857 0.00 0.00 40.21 3.53
1965 2378 3.678548 GTGCCGAAAGTAAGATTCTTCGT 59.321 43.478 1.27 0.00 0.00 3.85
1976 2389 3.682858 GCAGATAACAAGTGCCGAAAGTA 59.317 43.478 0.00 0.00 0.00 2.24
1990 2403 5.638234 ACCGAAGAACAAGTTAGCAGATAAC 59.362 40.000 0.00 0.00 43.58 1.89
2080 2534 2.203153 ACGTGGGTTCACTGGTGC 60.203 61.111 0.00 0.00 41.53 5.01
2081 2535 1.891919 CCACGTGGGTTCACTGGTG 60.892 63.158 27.57 0.00 41.53 4.17
2082 2536 2.067605 TCCACGTGGGTTCACTGGT 61.068 57.895 33.40 0.00 41.53 4.00
2101 2555 3.482156 AGAATTCAGTGGGATGATCGG 57.518 47.619 8.44 0.00 0.00 4.18
2164 2621 4.397417 GCCACTTAAATCAGATCAAGTGCT 59.603 41.667 21.95 0.00 44.12 4.40
2194 2651 4.814294 GGTGTCTAGTGGGCGCCG 62.814 72.222 22.54 6.07 0.00 6.46
2232 2689 5.070313 AGTTTGTGCCCATGTTGTAGAAAAT 59.930 36.000 0.00 0.00 0.00 1.82
2239 2729 1.484038 ACAGTTTGTGCCCATGTTGT 58.516 45.000 0.00 0.00 0.00 3.32
2298 2803 5.868454 TGATGTGTGAAGATTCTTCTCCAA 58.132 37.500 23.29 12.93 0.00 3.53
2302 2807 5.250982 TGCATGATGTGTGAAGATTCTTCT 58.749 37.500 23.29 6.42 0.00 2.85
2303 2808 5.556355 TGCATGATGTGTGAAGATTCTTC 57.444 39.130 17.76 17.76 0.00 2.87
2340 2845 0.102844 AAATTTCCCGGCATGATGCG 59.897 50.000 11.75 6.80 46.21 4.73
2342 2847 2.965572 ACAAATTTCCCGGCATGATG 57.034 45.000 0.00 0.00 0.00 3.07
2351 2856 1.069358 TCACCCGCAAACAAATTTCCC 59.931 47.619 0.00 0.00 0.00 3.97
2353 2858 3.453424 AGTTCACCCGCAAACAAATTTC 58.547 40.909 0.00 0.00 0.00 2.17
2356 2861 2.030274 GCTAGTTCACCCGCAAACAAAT 60.030 45.455 0.00 0.00 0.00 2.32
2382 2887 8.204836 ACACTAACAGAAGATAGTTTCAGTTGT 58.795 33.333 6.75 2.14 37.37 3.32
2397 2903 3.181501 GCACACAAGCAACACTAACAGAA 60.182 43.478 0.00 0.00 0.00 3.02
2420 2926 1.020437 GGCCTCTGCATAGCAAAGAC 58.980 55.000 0.00 0.00 38.41 3.01
2573 3116 1.074423 CATATCTGCAGGCAGGGGG 59.926 63.158 20.19 5.32 43.75 5.40
2579 3122 1.097547 ACGGCAACATATCTGCAGGC 61.098 55.000 15.13 7.11 41.78 4.85
2881 3424 1.339946 GGAAGTCGTCGTTGCCGTAC 61.340 60.000 0.00 0.00 35.01 3.67
3151 3697 2.925706 TACTGGTTGGGCCGCAGA 60.926 61.111 0.00 0.00 41.21 4.26
3262 3808 4.715523 GCGTACTTGGGCTGGCCA 62.716 66.667 20.19 20.19 37.98 5.36
3502 4051 1.679311 CTGCACCTGGAAGTAGGCA 59.321 57.895 0.00 0.00 41.75 4.75
3634 4186 2.674380 AAGAGTACCGTCGGCCGT 60.674 61.111 27.15 8.36 33.66 5.68
3705 4286 2.407090 CGCATAGCAATCAGATTCGGA 58.593 47.619 0.00 0.00 0.00 4.55
3749 4335 8.254508 CCTCTAGCTTCTTCATGTAGTTAACTT 58.745 37.037 14.49 0.00 0.00 2.66
3761 4354 4.833380 AGTGTGTAACCTCTAGCTTCTTCA 59.167 41.667 0.00 0.00 34.36 3.02
3766 4359 4.957684 ACAAGTGTGTAACCTCTAGCTT 57.042 40.909 0.00 0.00 35.72 3.74
3842 4440 0.622738 ATGGGCTCCTGTCCTGTGAT 60.623 55.000 0.00 0.00 39.11 3.06
3843 4441 1.229625 ATGGGCTCCTGTCCTGTGA 60.230 57.895 0.00 0.00 39.11 3.58
3844 4442 1.077930 CATGGGCTCCTGTCCTGTG 60.078 63.158 0.00 0.00 39.11 3.66
3845 4443 2.304056 CCATGGGCTCCTGTCCTGT 61.304 63.158 2.85 0.00 39.11 4.00
3846 4444 1.997311 TCCATGGGCTCCTGTCCTG 60.997 63.158 13.02 0.00 39.11 3.86
3847 4445 1.997874 GTCCATGGGCTCCTGTCCT 60.998 63.158 9.76 0.00 39.11 3.85
3848 4446 2.592308 GTCCATGGGCTCCTGTCC 59.408 66.667 9.76 0.00 38.74 4.02
3849 4447 1.977293 GAGGTCCATGGGCTCCTGTC 61.977 65.000 17.62 0.00 30.09 3.51
3899 4500 4.454847 ACATCAGTGTGCTCAATCTTTCTG 59.545 41.667 0.00 0.00 37.14 3.02
3926 4527 2.546778 GACACAAGGAAGACAACGACA 58.453 47.619 0.00 0.00 0.00 4.35
3950 4551 5.994250 TCAACTTATTTGGGATGGAGAGAG 58.006 41.667 0.00 0.00 35.69 3.20
3951 4552 5.488919 ACTCAACTTATTTGGGATGGAGAGA 59.511 40.000 0.00 0.00 38.03 3.10
3952 4553 5.749462 ACTCAACTTATTTGGGATGGAGAG 58.251 41.667 0.00 0.00 38.03 3.20
3953 4554 5.779241 ACTCAACTTATTTGGGATGGAGA 57.221 39.130 0.00 0.00 38.03 3.71
3954 4555 7.112779 AGTTACTCAACTTATTTGGGATGGAG 58.887 38.462 0.00 0.00 42.51 3.86
3955 4556 7.027874 AGTTACTCAACTTATTTGGGATGGA 57.972 36.000 0.00 0.00 42.51 3.41
3969 4570 8.654215 CCTCCGTTCTAAAATAAGTTACTCAAC 58.346 37.037 0.00 0.00 34.67 3.18
3970 4571 8.587608 TCCTCCGTTCTAAAATAAGTTACTCAA 58.412 33.333 0.00 0.00 0.00 3.02
3971 4572 8.125978 TCCTCCGTTCTAAAATAAGTTACTCA 57.874 34.615 0.00 0.00 0.00 3.41
3972 4573 8.992835 TTCCTCCGTTCTAAAATAAGTTACTC 57.007 34.615 0.00 0.00 0.00 2.59
3973 4574 8.591940 ACTTCCTCCGTTCTAAAATAAGTTACT 58.408 33.333 0.00 0.00 0.00 2.24
3974 4575 8.768957 ACTTCCTCCGTTCTAAAATAAGTTAC 57.231 34.615 0.00 0.00 0.00 2.50
3982 4583 9.595823 CAAAGATATACTTCCTCCGTTCTAAAA 57.404 33.333 0.00 0.00 37.93 1.52
3983 4584 8.974238 TCAAAGATATACTTCCTCCGTTCTAAA 58.026 33.333 0.00 0.00 37.93 1.85
3984 4585 8.529424 TCAAAGATATACTTCCTCCGTTCTAA 57.471 34.615 0.00 0.00 37.93 2.10
3985 4586 7.230913 CCTCAAAGATATACTTCCTCCGTTCTA 59.769 40.741 0.00 0.00 37.93 2.10
3986 4587 6.041069 CCTCAAAGATATACTTCCTCCGTTCT 59.959 42.308 0.00 0.00 37.93 3.01
3987 4588 6.217294 CCTCAAAGATATACTTCCTCCGTTC 58.783 44.000 0.00 0.00 37.93 3.95
3988 4589 5.070580 CCCTCAAAGATATACTTCCTCCGTT 59.929 44.000 0.00 0.00 37.93 4.44
3989 4590 4.589374 CCCTCAAAGATATACTTCCTCCGT 59.411 45.833 0.00 0.00 37.93 4.69
3990 4591 4.561734 GCCCTCAAAGATATACTTCCTCCG 60.562 50.000 0.00 0.00 37.93 4.63
3991 4592 4.561734 CGCCCTCAAAGATATACTTCCTCC 60.562 50.000 0.00 0.00 37.93 4.30
3992 4593 4.281182 TCGCCCTCAAAGATATACTTCCTC 59.719 45.833 0.00 0.00 37.93 3.71
3993 4594 4.223953 TCGCCCTCAAAGATATACTTCCT 58.776 43.478 0.00 0.00 37.93 3.36
3994 4595 4.039366 ACTCGCCCTCAAAGATATACTTCC 59.961 45.833 0.00 0.00 37.93 3.46
3995 4596 5.203060 ACTCGCCCTCAAAGATATACTTC 57.797 43.478 0.00 0.00 37.93 3.01
3996 4597 5.615925 AACTCGCCCTCAAAGATATACTT 57.384 39.130 0.00 0.00 40.98 2.24
3997 4598 5.615925 AAACTCGCCCTCAAAGATATACT 57.384 39.130 0.00 0.00 0.00 2.12
4018 4619 1.447140 GCCACGAGCACGGTGATAA 60.447 57.895 13.29 0.00 44.46 1.75
4173 4782 3.553302 CGAACCCCCAATAAAAACGCTTT 60.553 43.478 0.00 0.00 0.00 3.51
4183 4792 2.557451 CGCAAACGAACCCCCAATA 58.443 52.632 0.00 0.00 43.93 1.90
4184 4793 3.361174 CGCAAACGAACCCCCAAT 58.639 55.556 0.00 0.00 43.93 3.16
4202 4811 4.080356 ACCACATAGTCCATACTTGCACAT 60.080 41.667 0.00 0.00 37.15 3.21
4206 5149 4.137116 TGACCACATAGTCCATACTTGC 57.863 45.455 0.00 0.00 37.15 4.01
4229 5173 4.035017 CCACACGATCAACTTTGACAAAC 58.965 43.478 0.00 0.00 40.49 2.93
4230 5174 3.692101 ACCACACGATCAACTTTGACAAA 59.308 39.130 0.00 0.00 40.49 2.83
4232 5176 2.869801 GACCACACGATCAACTTTGACA 59.130 45.455 0.00 0.00 40.49 3.58
4233 5177 2.869801 TGACCACACGATCAACTTTGAC 59.130 45.455 0.00 0.00 40.49 3.18
4234 5178 3.186702 TGACCACACGATCAACTTTGA 57.813 42.857 0.00 0.00 42.14 2.69
4236 5180 2.813754 CCATGACCACACGATCAACTTT 59.186 45.455 0.00 0.00 0.00 2.66
4270 5227 3.735237 AACCATATGCAGACTACTCGG 57.265 47.619 0.00 0.00 0.00 4.63
4277 5234 5.314923 ACATCAACAAACCATATGCAGAC 57.685 39.130 0.00 0.00 0.00 3.51
4278 5235 5.981088 AACATCAACAAACCATATGCAGA 57.019 34.783 0.00 0.00 0.00 4.26
4279 5236 6.309494 CAGAAACATCAACAAACCATATGCAG 59.691 38.462 0.00 0.00 0.00 4.41
4280 5237 6.157904 CAGAAACATCAACAAACCATATGCA 58.842 36.000 0.00 0.00 0.00 3.96
4281 5238 6.158598 ACAGAAACATCAACAAACCATATGC 58.841 36.000 0.00 0.00 0.00 3.14
4320 5278 3.303990 GCAGTCGACTGAGATTTTGCAAA 60.304 43.478 42.03 8.05 46.59 3.68
4325 5283 2.724977 TCGCAGTCGACTGAGATTTT 57.275 45.000 42.03 6.81 45.52 1.82
4339 5297 6.647212 TCTTAATGTATGAACAAGTCGCAG 57.353 37.500 0.00 0.00 39.58 5.18
4342 5300 7.009265 ACACGATCTTAATGTATGAACAAGTCG 59.991 37.037 0.00 0.00 39.58 4.18
4395 5353 9.979578 AAGTGCAATAATGTGTATGAAAGAAAA 57.020 25.926 0.00 0.00 0.00 2.29
4396 5354 9.409312 CAAGTGCAATAATGTGTATGAAAGAAA 57.591 29.630 0.00 0.00 0.00 2.52
4397 5355 8.791675 TCAAGTGCAATAATGTGTATGAAAGAA 58.208 29.630 0.00 0.00 0.00 2.52
4398 5356 8.236586 GTCAAGTGCAATAATGTGTATGAAAGA 58.763 33.333 0.00 0.00 0.00 2.52
4399 5357 8.239314 AGTCAAGTGCAATAATGTGTATGAAAG 58.761 33.333 0.00 0.00 0.00 2.62
4400 5358 8.022550 CAGTCAAGTGCAATAATGTGTATGAAA 58.977 33.333 0.00 0.00 0.00 2.69
4401 5359 7.390162 TCAGTCAAGTGCAATAATGTGTATGAA 59.610 33.333 0.00 0.00 0.00 2.57
4402 5360 6.878389 TCAGTCAAGTGCAATAATGTGTATGA 59.122 34.615 0.00 0.00 0.00 2.15
4403 5361 7.064966 TCTCAGTCAAGTGCAATAATGTGTATG 59.935 37.037 0.00 0.00 0.00 2.39
4404 5362 7.105588 TCTCAGTCAAGTGCAATAATGTGTAT 58.894 34.615 0.00 0.00 0.00 2.29
4405 5363 6.463360 TCTCAGTCAAGTGCAATAATGTGTA 58.537 36.000 0.00 0.00 0.00 2.90
4406 5364 5.308014 TCTCAGTCAAGTGCAATAATGTGT 58.692 37.500 0.00 0.00 0.00 3.72
4407 5365 5.868043 TCTCAGTCAAGTGCAATAATGTG 57.132 39.130 0.00 0.00 0.00 3.21
4408 5366 7.175467 TCAAATCTCAGTCAAGTGCAATAATGT 59.825 33.333 0.00 0.00 0.00 2.71
4409 5367 7.532571 TCAAATCTCAGTCAAGTGCAATAATG 58.467 34.615 0.00 0.00 0.00 1.90
4410 5368 7.692460 TCAAATCTCAGTCAAGTGCAATAAT 57.308 32.000 0.00 0.00 0.00 1.28
4411 5369 7.692460 ATCAAATCTCAGTCAAGTGCAATAA 57.308 32.000 0.00 0.00 0.00 1.40
4412 5370 7.692460 AATCAAATCTCAGTCAAGTGCAATA 57.308 32.000 0.00 0.00 0.00 1.90
4413 5371 6.585695 AATCAAATCTCAGTCAAGTGCAAT 57.414 33.333 0.00 0.00 0.00 3.56
4414 5372 7.229306 ACTTAATCAAATCTCAGTCAAGTGCAA 59.771 33.333 0.00 0.00 0.00 4.08
4415 5373 6.712095 ACTTAATCAAATCTCAGTCAAGTGCA 59.288 34.615 0.00 0.00 0.00 4.57
4416 5374 7.118971 AGACTTAATCAAATCTCAGTCAAGTGC 59.881 37.037 0.00 0.00 34.33 4.40
4417 5375 8.545229 AGACTTAATCAAATCTCAGTCAAGTG 57.455 34.615 0.00 0.00 34.33 3.16
4421 5379 9.862371 GACTTAGACTTAATCAAATCTCAGTCA 57.138 33.333 8.75 0.00 40.11 3.41
4422 5380 9.862371 TGACTTAGACTTAATCAAATCTCAGTC 57.138 33.333 7.26 7.26 40.49 3.51
4436 5394 9.702494 GCCTAGTTTTTAGTTGACTTAGACTTA 57.298 33.333 0.00 0.00 0.00 2.24
4441 5399 7.724305 TGTGCCTAGTTTTTAGTTGACTTAG 57.276 36.000 0.00 0.00 0.00 2.18
4461 5419 4.261801 ACACAGTTTGGTATAGGATGTGC 58.738 43.478 0.00 0.00 40.05 4.57
4473 5431 2.408050 CCTCTTCGAGACACAGTTTGG 58.592 52.381 0.00 0.00 0.00 3.28
4474 5432 1.795286 GCCTCTTCGAGACACAGTTTG 59.205 52.381 0.00 0.00 0.00 2.93
4504 5485 1.341531 AGTTGTTCTACTCGCTGTGCT 59.658 47.619 0.00 0.00 0.00 4.40
4510 5491 3.650139 TCTTGGAAGTTGTTCTACTCGC 58.350 45.455 0.00 0.00 32.72 5.03
4513 5494 5.293569 CGTTGTTCTTGGAAGTTGTTCTACT 59.706 40.000 0.00 0.00 32.72 2.57
4514 5495 5.292589 TCGTTGTTCTTGGAAGTTGTTCTAC 59.707 40.000 0.00 0.00 32.72 2.59
4515 5496 5.421277 TCGTTGTTCTTGGAAGTTGTTCTA 58.579 37.500 0.00 0.00 32.72 2.10
4516 5497 4.258543 TCGTTGTTCTTGGAAGTTGTTCT 58.741 39.130 0.00 0.00 32.72 3.01
4517 5498 4.609691 TCGTTGTTCTTGGAAGTTGTTC 57.390 40.909 0.00 0.00 0.00 3.18
4518 5499 4.670735 CGTTCGTTGTTCTTGGAAGTTGTT 60.671 41.667 0.00 0.00 0.00 2.83
4519 5500 3.181514 CGTTCGTTGTTCTTGGAAGTTGT 60.182 43.478 0.00 0.00 0.00 3.32
4546 5534 1.385999 GACGAAAGCAACACGAAAGC 58.614 50.000 0.00 0.00 0.00 3.51
4547 5535 1.647748 CGACGAAAGCAACACGAAAG 58.352 50.000 0.00 0.00 0.00 2.62
4565 5553 2.944557 CGACAGACATCGACGGCG 60.945 66.667 2.87 2.87 45.13 6.46
4572 5560 1.153349 GGGGGAAGCGACAGACATC 60.153 63.158 0.00 0.00 0.00 3.06
4573 5561 2.990479 GGGGGAAGCGACAGACAT 59.010 61.111 0.00 0.00 0.00 3.06
4574 5562 3.691342 CGGGGGAAGCGACAGACA 61.691 66.667 0.00 0.00 0.00 3.41
4578 5566 3.006728 ATTCCGGGGGAAGCGACA 61.007 61.111 0.00 0.00 45.48 4.35
4584 5572 1.003112 CACGTTCATTCCGGGGGAA 60.003 57.895 0.00 0.00 46.39 3.97
4592 5580 1.996191 GAGCTCTGGACACGTTCATTC 59.004 52.381 6.43 0.00 0.00 2.67
4595 5583 1.285950 CGAGCTCTGGACACGTTCA 59.714 57.895 12.85 0.00 0.00 3.18
4626 5614 3.070302 GGCTTAGCTGTGCTACTCCTATT 59.930 47.826 3.59 0.00 41.12 1.73
4627 5615 2.630580 GGCTTAGCTGTGCTACTCCTAT 59.369 50.000 3.59 0.00 41.12 2.57
4637 5625 1.726791 CTACACGTTGGCTTAGCTGTG 59.273 52.381 3.59 10.44 0.00 3.66
4638 5626 1.616865 TCTACACGTTGGCTTAGCTGT 59.383 47.619 3.59 2.60 0.00 4.40
4645 5633 0.673644 GCCATGTCTACACGTTGGCT 60.674 55.000 16.09 0.00 45.03 4.75
4646 5634 1.794222 GCCATGTCTACACGTTGGC 59.206 57.895 9.24 9.24 43.39 4.52
4672 5660 2.851071 GCAGCTAGCCGTCGGAGAT 61.851 63.158 17.49 0.00 36.34 2.75


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

AutoCloner maintained by Alex Coulton.