Multiple sequence alignment - TraesCS5B01G542200

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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 TraesCS5B01G542200 chr5B 100.000 3242 0 0 408 3649 696164638 696167879 0.000000e+00 5987.0
1 TraesCS5B01G542200 chr5B 89.067 375 37 4 3085 3456 57511297 57511670 2.570000e-126 462.0
2 TraesCS5B01G542200 chr5B 88.800 375 38 4 3085 3456 57511838 57512211 1.190000e-124 457.0
3 TraesCS5B01G542200 chr5B 91.561 237 20 0 1183 1419 696154640 696154876 9.770000e-86 327.0
4 TraesCS5B01G542200 chr5B 100.000 89 0 0 1 89 696164231 696164319 8.110000e-37 165.0
5 TraesCS5B01G542200 chr5B 85.714 119 17 0 1980 2098 689670338 689670456 3.830000e-25 126.0
6 TraesCS5B01G542200 chr5B 91.139 79 6 1 3548 3625 212190229 212190151 4.980000e-19 106.0
7 TraesCS5B01G542200 chr5D 91.220 1606 100 22 1489 3069 554520839 554519250 0.000000e+00 2146.0
8 TraesCS5B01G542200 chr5D 92.494 413 28 2 408 819 554521887 554521477 4.060000e-164 588.0
9 TraesCS5B01G542200 chr5D 96.721 305 10 0 1149 1453 554521148 554520844 3.250000e-140 508.0
10 TraesCS5B01G542200 chr5D 88.800 375 38 4 3085 3456 6249989 6250362 1.190000e-124 457.0
11 TraesCS5B01G542200 chr5D 88.800 375 38 4 3085 3456 459215187 459215560 1.190000e-124 457.0
12 TraesCS5B01G542200 chr5D 83.932 473 51 19 955 1419 554577459 554577004 2.600000e-116 429.0
13 TraesCS5B01G542200 chr5D 89.623 318 16 6 863 1163 554521483 554521166 4.420000e-104 388.0
14 TraesCS5B01G542200 chr5D 88.608 79 8 1 3548 3625 201519613 201519535 1.080000e-15 95.3
15 TraesCS5B01G542200 chr5D 95.652 46 1 1 1451 1495 430065270 430065225 5.050000e-09 73.1
16 TraesCS5B01G542200 chr4A 91.160 1595 107 25 1489 3069 614015107 614016681 0.000000e+00 2134.0
17 TraesCS5B01G542200 chr4A 91.589 1070 50 15 414 1453 614014043 614015102 0.000000e+00 1441.0
18 TraesCS5B01G542200 chr4A 83.628 452 42 22 982 1419 614004472 614004905 2.640000e-106 396.0
19 TraesCS5B01G542200 chr5A 89.067 375 37 4 3085 3456 559028663 559029036 2.570000e-126 462.0
20 TraesCS5B01G542200 chr5A 97.436 39 1 0 1452 1490 473323662 473323624 2.350000e-07 67.6
21 TraesCS5B01G542200 chr3A 89.067 375 37 4 3085 3456 593309808 593309435 2.570000e-126 462.0
22 TraesCS5B01G542200 chr3A 88.372 86 6 3 1018 1099 647499722 647499637 2.320000e-17 100.0
23 TraesCS5B01G542200 chr3A 90.141 71 7 0 1018 1088 647510182 647510112 3.880000e-15 93.5
24 TraesCS5B01G542200 chr1A 89.067 375 37 4 3085 3456 554485308 554484935 2.570000e-126 462.0
25 TraesCS5B01G542200 chr1A 89.062 64 5 1 1449 1512 591297212 591297273 1.090000e-10 78.7
26 TraesCS5B01G542200 chr1A 95.556 45 1 1 1452 1495 396427707 396427663 1.820000e-08 71.3
27 TraesCS5B01G542200 chr1A 87.500 56 1 3 1463 1512 482962063 482962118 3.940000e-05 60.2
28 TraesCS5B01G542200 chr1A 88.235 51 0 3 1462 1506 482962854 482962904 5.090000e-04 56.5
29 TraesCS5B01G542200 chr1D 88.800 375 38 4 3085 3456 180382964 180383337 1.190000e-124 457.0
30 TraesCS5B01G542200 chr1D 88.889 72 8 0 1018 1089 462298737 462298808 5.020000e-14 89.8
31 TraesCS5B01G542200 chr4D 87.755 392 43 5 3085 3472 19904006 19903616 1.540000e-123 453.0
32 TraesCS5B01G542200 chr4D 83.656 465 50 20 999 1452 477089481 477089032 7.290000e-112 414.0
33 TraesCS5B01G542200 chr4D 90.800 250 19 4 1587 1833 477088943 477088695 7.550000e-87 331.0
34 TraesCS5B01G542200 chr4D 78.041 296 46 14 1976 2258 477088336 477088047 6.270000e-38 169.0
35 TraesCS5B01G542200 chr2D 83.019 424 50 16 999 1418 593223963 593224368 7.450000e-97 364.0
36 TraesCS5B01G542200 chr2A 81.604 424 54 17 1001 1418 728021712 728022117 2.720000e-86 329.0
37 TraesCS5B01G542200 chr2A 83.673 245 33 7 2416 2655 728028546 728028788 1.320000e-54 224.0
38 TraesCS5B01G542200 chr2B 80.886 429 52 15 1001 1418 719496495 719496904 9.840000e-81 311.0
39 TraesCS5B01G542200 chr2B 83.265 245 37 4 2415 2655 719516741 719516985 4.740000e-54 222.0
40 TraesCS5B01G542200 chr3D 88.372 86 6 3 1018 1099 511444272 511444187 2.320000e-17 100.0
41 TraesCS5B01G542200 chr3B 88.372 86 6 3 1018 1099 673098168 673098083 2.320000e-17 100.0
42 TraesCS5B01G542200 chr3B 85.870 92 13 0 998 1089 673106511 673106420 8.340000e-17 99.0
43 TraesCS5B01G542200 chr7D 90.196 51 5 0 1451 1501 519273451 519273401 2.350000e-07 67.6
44 TraesCS5B01G542200 chr4B 95.122 41 0 2 1449 1488 651148397 651148358 3.040000e-06 63.9
45 TraesCS5B01G542200 chr4B 97.222 36 1 0 3548 3583 545019817 545019852 1.090000e-05 62.1
46 TraesCS5B01G542200 chr7B 81.818 77 9 2 1452 1523 601256804 601256880 3.940000e-05 60.2


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 TraesCS5B01G542200 chr5B 696164231 696167879 3648 False 3076.000000 5987 100.000000 1 3649 2 chr5B.!!$F4 3648
1 TraesCS5B01G542200 chr5B 57511297 57512211 914 False 459.500000 462 88.933500 3085 3456 2 chr5B.!!$F3 371
2 TraesCS5B01G542200 chr5D 554519250 554521887 2637 True 907.500000 2146 92.514500 408 3069 4 chr5D.!!$R4 2661
3 TraesCS5B01G542200 chr4A 614014043 614016681 2638 False 1787.500000 2134 91.374500 414 3069 2 chr4A.!!$F2 2655
4 TraesCS5B01G542200 chr4D 477088047 477089481 1434 True 304.666667 414 84.165667 999 2258 3 chr4D.!!$R2 1259

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
75 76 0.109532 TGAAAGCCACGGTCATTGGA 59.890 50.0 0.00 0.00 36.02 3.53 F
687 690 0.447801 GTTAATGGTGTCGCCTGCAG 59.552 55.0 6.78 6.78 38.35 4.41 F
1463 1543 0.530744 TGCCATGTACTCACTCCGTC 59.469 55.0 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1020 1053 0.105453 GGCTCCACATCTCCTCCCTA 60.105 60.0 0.0 0.0 0.00 3.53 R
1708 1797 0.173708 CGTGTAGGAGAAGAGGGTGC 59.826 60.0 0.0 0.0 0.00 5.01 R
3045 3381 0.250166 ACCTTTGGCGTGTGTAGGTC 60.250 55.0 0.0 0.0 34.15 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.405769 GTGAGAATTATCACTTAGAGCTTTGC 58.594 38.462 22.82 0.00 45.03 3.68
26 27 6.540189 TGAGAATTATCACTTAGAGCTTTGCC 59.460 38.462 0.00 0.00 0.00 4.52
27 28 6.657875 AGAATTATCACTTAGAGCTTTGCCT 58.342 36.000 0.00 0.00 0.00 4.75
28 29 6.765512 AGAATTATCACTTAGAGCTTTGCCTC 59.234 38.462 0.00 0.00 0.00 4.70
29 30 2.770164 TCACTTAGAGCTTTGCCTCC 57.230 50.000 0.00 0.00 32.17 4.30
30 31 1.977854 TCACTTAGAGCTTTGCCTCCA 59.022 47.619 0.00 0.00 32.17 3.86
31 32 2.371841 TCACTTAGAGCTTTGCCTCCAA 59.628 45.455 0.00 0.00 32.17 3.53
32 33 2.746362 CACTTAGAGCTTTGCCTCCAAG 59.254 50.000 0.00 0.00 36.86 3.61
33 34 2.639839 ACTTAGAGCTTTGCCTCCAAGA 59.360 45.455 4.76 0.00 35.18 3.02
34 35 3.265479 ACTTAGAGCTTTGCCTCCAAGAT 59.735 43.478 4.76 0.00 35.18 2.40
35 36 4.471386 ACTTAGAGCTTTGCCTCCAAGATA 59.529 41.667 4.76 0.00 35.18 1.98
36 37 5.045578 ACTTAGAGCTTTGCCTCCAAGATAA 60.046 40.000 4.76 0.00 35.18 1.75
37 38 3.883669 AGAGCTTTGCCTCCAAGATAAG 58.116 45.455 0.00 0.00 32.17 1.73
38 39 2.357323 GAGCTTTGCCTCCAAGATAAGC 59.643 50.000 0.00 0.00 33.39 3.09
39 40 2.094675 GCTTTGCCTCCAAGATAAGCA 58.905 47.619 0.00 0.00 33.42 3.91
40 41 2.098770 GCTTTGCCTCCAAGATAAGCAG 59.901 50.000 0.00 0.00 33.42 4.24
41 42 3.350833 CTTTGCCTCCAAGATAAGCAGT 58.649 45.455 0.00 0.00 34.45 4.40
42 43 2.408271 TGCCTCCAAGATAAGCAGTG 57.592 50.000 0.00 0.00 0.00 3.66
43 44 1.020437 GCCTCCAAGATAAGCAGTGC 58.980 55.000 7.13 7.13 0.00 4.40
44 45 1.673168 CCTCCAAGATAAGCAGTGCC 58.327 55.000 12.58 0.00 0.00 5.01
45 46 1.293924 CTCCAAGATAAGCAGTGCCG 58.706 55.000 12.58 0.00 0.00 5.69
46 47 0.901827 TCCAAGATAAGCAGTGCCGA 59.098 50.000 12.58 0.00 0.00 5.54
47 48 1.486310 TCCAAGATAAGCAGTGCCGAT 59.514 47.619 12.58 5.14 0.00 4.18
48 49 1.600957 CCAAGATAAGCAGTGCCGATG 59.399 52.381 12.58 2.87 0.00 3.84
49 50 2.554142 CAAGATAAGCAGTGCCGATGA 58.446 47.619 12.58 0.00 0.00 2.92
50 51 3.136763 CAAGATAAGCAGTGCCGATGAT 58.863 45.455 12.58 0.00 0.00 2.45
51 52 2.763933 AGATAAGCAGTGCCGATGATG 58.236 47.619 12.58 0.00 0.00 3.07
52 53 2.103771 AGATAAGCAGTGCCGATGATGT 59.896 45.455 12.58 0.00 0.00 3.06
53 54 3.321968 AGATAAGCAGTGCCGATGATGTA 59.678 43.478 12.58 0.00 0.00 2.29
54 55 1.945387 AAGCAGTGCCGATGATGTAG 58.055 50.000 12.58 0.00 0.00 2.74
55 56 1.114627 AGCAGTGCCGATGATGTAGA 58.885 50.000 12.58 0.00 0.00 2.59
56 57 1.690893 AGCAGTGCCGATGATGTAGAT 59.309 47.619 12.58 0.00 0.00 1.98
57 58 1.797046 GCAGTGCCGATGATGTAGATG 59.203 52.381 2.85 0.00 0.00 2.90
58 59 2.546584 GCAGTGCCGATGATGTAGATGA 60.547 50.000 2.85 0.00 0.00 2.92
59 60 3.721035 CAGTGCCGATGATGTAGATGAA 58.279 45.455 0.00 0.00 0.00 2.57
60 61 4.122046 CAGTGCCGATGATGTAGATGAAA 58.878 43.478 0.00 0.00 0.00 2.69
61 62 4.210746 CAGTGCCGATGATGTAGATGAAAG 59.789 45.833 0.00 0.00 0.00 2.62
62 63 3.059325 GTGCCGATGATGTAGATGAAAGC 60.059 47.826 0.00 0.00 0.00 3.51
63 64 2.481952 GCCGATGATGTAGATGAAAGCC 59.518 50.000 0.00 0.00 0.00 4.35
64 65 3.732212 CCGATGATGTAGATGAAAGCCA 58.268 45.455 0.00 0.00 0.00 4.75
65 66 3.496130 CCGATGATGTAGATGAAAGCCAC 59.504 47.826 0.00 0.00 0.00 5.01
66 67 3.183172 CGATGATGTAGATGAAAGCCACG 59.817 47.826 0.00 0.00 0.00 4.94
67 68 2.905075 TGATGTAGATGAAAGCCACGG 58.095 47.619 0.00 0.00 0.00 4.94
68 69 2.236146 TGATGTAGATGAAAGCCACGGT 59.764 45.455 0.00 0.00 0.00 4.83
69 70 2.380084 TGTAGATGAAAGCCACGGTC 57.620 50.000 0.00 0.00 0.00 4.79
70 71 1.621317 TGTAGATGAAAGCCACGGTCA 59.379 47.619 0.00 0.00 0.00 4.02
71 72 2.236146 TGTAGATGAAAGCCACGGTCAT 59.764 45.455 0.00 0.00 34.71 3.06
72 73 2.496899 AGATGAAAGCCACGGTCATT 57.503 45.000 0.00 0.00 32.18 2.57
73 74 2.086869 AGATGAAAGCCACGGTCATTG 58.913 47.619 0.00 0.00 32.18 2.82
74 75 1.133025 GATGAAAGCCACGGTCATTGG 59.867 52.381 0.00 0.00 37.17 3.16
75 76 0.109532 TGAAAGCCACGGTCATTGGA 59.890 50.000 0.00 0.00 36.02 3.53
76 77 1.243902 GAAAGCCACGGTCATTGGAA 58.756 50.000 0.00 0.00 36.02 3.53
77 78 1.818674 GAAAGCCACGGTCATTGGAAT 59.181 47.619 0.00 0.00 36.02 3.01
78 79 2.799126 AAGCCACGGTCATTGGAATA 57.201 45.000 0.00 0.00 36.02 1.75
79 80 2.332063 AGCCACGGTCATTGGAATAG 57.668 50.000 0.00 0.00 36.02 1.73
80 81 1.134098 AGCCACGGTCATTGGAATAGG 60.134 52.381 0.00 0.00 36.02 2.57
81 82 1.408266 GCCACGGTCATTGGAATAGGT 60.408 52.381 0.00 0.00 36.02 3.08
82 83 2.288666 CCACGGTCATTGGAATAGGTG 58.711 52.381 0.00 0.00 36.02 4.00
83 84 2.093181 CCACGGTCATTGGAATAGGTGA 60.093 50.000 0.00 0.00 36.02 4.02
84 85 2.936498 CACGGTCATTGGAATAGGTGAC 59.064 50.000 0.00 0.00 40.07 3.67
88 89 3.950397 GTCATTGGAATAGGTGACCACA 58.050 45.455 3.63 0.00 35.98 4.17
446 447 1.376037 GTCGTGAGCTCCTTTGGGG 60.376 63.158 12.15 0.00 0.00 4.96
653 654 2.218953 TCACTGTTGGTTCGTCACTC 57.781 50.000 0.00 0.00 0.00 3.51
654 655 1.202486 TCACTGTTGGTTCGTCACTCC 60.202 52.381 0.00 0.00 0.00 3.85
659 660 0.827089 TTGGTTCGTCACTCCCCGTA 60.827 55.000 0.00 0.00 0.00 4.02
660 661 0.827089 TGGTTCGTCACTCCCCGTAA 60.827 55.000 0.00 0.00 0.00 3.18
677 680 9.595823 CTCCCCGTAAATATATAGTTAATGGTG 57.404 37.037 15.69 8.88 0.00 4.17
687 690 0.447801 GTTAATGGTGTCGCCTGCAG 59.552 55.000 6.78 6.78 38.35 4.41
697 700 2.749441 GCCTGCAGAGCTGGTTCC 60.749 66.667 17.39 0.00 46.96 3.62
707 710 2.464459 GCTGGTTCCTCATTCGGCG 61.464 63.158 0.00 0.00 0.00 6.46
762 765 1.522676 CGTAGCGGCATGTCACAATAG 59.477 52.381 1.45 0.00 0.00 1.73
800 803 1.452145 TTGGCCAGAAGCGGTGAAAC 61.452 55.000 5.11 0.00 45.17 2.78
815 818 2.710377 TGAAACACATTCATCCTCGGG 58.290 47.619 0.00 0.00 43.08 5.14
825 828 1.443407 ATCCTCGGGATGCACGAAG 59.557 57.895 4.81 0.00 41.43 3.79
826 829 2.650813 ATCCTCGGGATGCACGAAGC 62.651 60.000 4.81 0.00 41.43 3.86
839 853 2.410469 GAAGCGGCCATGTCATGC 59.590 61.111 7.35 3.29 0.00 4.06
849 863 3.923782 ATGTCATGCGTGCCTGCCA 62.924 57.895 0.00 0.00 0.00 4.92
896 910 7.066887 TGACAGCTTAATTTGTTGAGTTCTTGA 59.933 33.333 0.00 0.00 0.00 3.02
975 1008 3.466836 ACAGTTCACTCATTTGAGCGAA 58.533 40.909 7.48 7.15 45.79 4.70
996 1029 2.525381 CAGAGCTAGGGGCCGGAT 60.525 66.667 5.05 0.00 43.05 4.18
1046 1079 3.785859 GATGTGGAGCCTGGCCGA 61.786 66.667 16.57 1.08 0.00 5.54
1111 1152 7.388776 GGTATATCATATGTTCACACATGCACT 59.611 37.037 1.90 0.00 43.92 4.40
1143 1184 6.870965 TCTCTTCTGCTCTTCATTCTACAAAC 59.129 38.462 0.00 0.00 0.00 2.93
1343 1416 1.541588 TCTCTGTCTGTGATGTGTCCG 59.458 52.381 0.00 0.00 0.00 4.79
1453 1533 5.637006 TGGAAGTTAAACATGCCATGTAC 57.363 39.130 11.38 5.93 44.07 2.90
1457 1537 5.880054 AGTTAAACATGCCATGTACTCAC 57.120 39.130 11.38 6.06 44.07 3.51
1458 1538 5.560724 AGTTAAACATGCCATGTACTCACT 58.439 37.500 11.38 8.19 44.07 3.41
1462 1542 1.134699 CATGCCATGTACTCACTCCGT 60.135 52.381 0.00 0.00 0.00 4.69
1463 1543 0.530744 TGCCATGTACTCACTCCGTC 59.469 55.000 0.00 0.00 0.00 4.79
1464 1544 0.818296 GCCATGTACTCACTCCGTCT 59.182 55.000 0.00 0.00 0.00 4.18
1466 1546 2.092323 CCATGTACTCACTCCGTCTCA 58.908 52.381 0.00 0.00 0.00 3.27
1467 1547 2.690497 CCATGTACTCACTCCGTCTCAT 59.310 50.000 0.00 0.00 0.00 2.90
1468 1548 3.883489 CCATGTACTCACTCCGTCTCATA 59.117 47.826 0.00 0.00 0.00 2.15
1469 1549 4.338400 CCATGTACTCACTCCGTCTCATAA 59.662 45.833 0.00 0.00 0.00 1.90
1472 1552 7.094162 CCATGTACTCACTCCGTCTCATAATAT 60.094 40.741 0.00 0.00 0.00 1.28
1474 1554 8.913487 TGTACTCACTCCGTCTCATAATATAA 57.087 34.615 0.00 0.00 0.00 0.98
1475 1555 9.000486 TGTACTCACTCCGTCTCATAATATAAG 58.000 37.037 0.00 0.00 0.00 1.73
1476 1556 9.217278 GTACTCACTCCGTCTCATAATATAAGA 57.783 37.037 0.00 0.00 0.00 2.10
1477 1557 8.871629 ACTCACTCCGTCTCATAATATAAGAT 57.128 34.615 0.00 0.00 0.00 2.40
1478 1558 8.952278 ACTCACTCCGTCTCATAATATAAGATC 58.048 37.037 0.00 0.00 0.00 2.75
1480 1560 7.606839 TCACTCCGTCTCATAATATAAGATCGT 59.393 37.037 0.00 0.00 0.00 3.73
1481 1561 8.237949 CACTCCGTCTCATAATATAAGATCGTT 58.762 37.037 0.00 0.00 0.00 3.85
1482 1562 8.794553 ACTCCGTCTCATAATATAAGATCGTTT 58.205 33.333 0.00 0.00 0.00 3.60
1483 1563 9.627395 CTCCGTCTCATAATATAAGATCGTTTT 57.373 33.333 0.00 0.00 0.00 2.43
1484 1564 9.406828 TCCGTCTCATAATATAAGATCGTTTTG 57.593 33.333 0.00 0.00 0.00 2.44
1485 1565 8.162880 CCGTCTCATAATATAAGATCGTTTTGC 58.837 37.037 0.00 0.00 0.00 3.68
1506 1595 7.739022 TTGCAAGCAAAACGATCTTATATTG 57.261 32.000 4.79 0.00 32.44 1.90
1509 1598 6.197096 GCAAGCAAAACGATCTTATATTGTGG 59.803 38.462 0.00 0.00 0.00 4.17
1512 1601 6.772716 AGCAAAACGATCTTATATTGTGGGAT 59.227 34.615 0.00 0.00 0.00 3.85
1513 1602 7.285401 AGCAAAACGATCTTATATTGTGGGATT 59.715 33.333 0.00 0.00 0.00 3.01
1518 1607 6.270000 ACGATCTTATATTGTGGGATTGAGGA 59.730 38.462 0.00 0.00 0.00 3.71
1527 1616 6.442541 TTGTGGGATTGAGGAAGTAAGTTA 57.557 37.500 0.00 0.00 0.00 2.24
1551 1640 1.896339 TTTGATGCCTCAACGCGACG 61.896 55.000 15.93 2.43 41.05 5.12
1708 1797 2.169789 CCATCTCAGCCAACTCGCG 61.170 63.158 0.00 0.00 0.00 5.87
1888 2191 7.579589 TTGTTTGTGTCATCTGAACAAAAAG 57.420 32.000 15.61 0.00 43.32 2.27
1901 2204 1.001815 ACAAAAAGGCGTCCATCGTTG 60.002 47.619 0.00 0.00 42.13 4.10
1911 2214 4.271533 GGCGTCCATCGTTGTATGAATTTA 59.728 41.667 0.00 0.00 42.13 1.40
1912 2215 5.220700 GGCGTCCATCGTTGTATGAATTTAA 60.221 40.000 0.00 0.00 42.13 1.52
2038 2347 4.717313 GAGTGGGGCCCCGACAAC 62.717 72.222 36.00 27.25 39.42 3.32
2271 2591 4.683832 TCTCTTAATAGACCGAAGCAAGC 58.316 43.478 0.00 0.00 0.00 4.01
2287 2607 4.725758 GCGCTAGCACTGTTTTCG 57.274 55.556 16.45 0.00 44.35 3.46
2293 2613 2.030946 GCTAGCACTGTTTTCGCTATGG 59.969 50.000 10.63 0.00 37.60 2.74
2318 2638 5.649602 CAAGATTAAGAGCTTGTCGGATC 57.350 43.478 0.00 0.00 42.76 3.36
2335 2656 6.030849 GTCGGATCGATATTCCAATCACTAG 58.969 44.000 0.00 0.00 38.42 2.57
2340 2661 8.037758 GGATCGATATTCCAATCACTAGTTCAT 58.962 37.037 0.00 0.00 33.21 2.57
2372 2693 8.970859 AAAATCTGTATAGCATAGCTTGTTCT 57.029 30.769 0.00 0.00 40.44 3.01
2373 2694 8.600449 AAATCTGTATAGCATAGCTTGTTCTC 57.400 34.615 0.00 0.00 40.44 2.87
2384 2705 6.183360 GCATAGCTTGTTCTCTCTAGTCTCTT 60.183 42.308 0.00 0.00 0.00 2.85
2405 2726 5.476945 TCTTCAACCAAGAAATTAGAAGCCC 59.523 40.000 0.00 0.00 38.26 5.19
2406 2727 4.998051 TCAACCAAGAAATTAGAAGCCCT 58.002 39.130 0.00 0.00 0.00 5.19
2435 2757 4.536065 TCAAACTGCTAGCAATTTTCACG 58.464 39.130 20.76 10.39 0.00 4.35
2437 2759 4.568152 AACTGCTAGCAATTTTCACGTT 57.432 36.364 19.86 13.30 0.00 3.99
2706 3038 9.390795 CTCTTGATTTCTTGGAAAATATATGCG 57.609 33.333 0.00 0.00 0.00 4.73
2723 3055 0.461961 GCGTAGGAGAGTGGAGCAAT 59.538 55.000 0.00 0.00 0.00 3.56
2762 3094 9.563748 ACTAAGTAAGTTATGCCAACTAACAAA 57.436 29.630 1.58 0.00 33.35 2.83
2778 3110 4.829872 AACAAATGGCATCATTGTGGAT 57.170 36.364 16.07 1.18 42.29 3.41
2798 3130 0.179004 ACCTTGGCACATTTCACGGA 60.179 50.000 0.00 0.00 39.30 4.69
2804 3136 0.310543 GCACATTTCACGGAACAGCA 59.689 50.000 0.00 0.00 0.00 4.41
2882 3215 6.127647 GCTTGTTTTGTATGAAGATGGATGGA 60.128 38.462 0.00 0.00 0.00 3.41
2899 3232 5.964477 TGGATGGAGGACTACTATTCAGTTT 59.036 40.000 0.00 0.00 36.14 2.66
3045 3381 1.229428 CCAATGTACGGGCAGCATAG 58.771 55.000 0.00 0.00 0.00 2.23
3056 3392 1.560923 GCAGCATAGACCTACACACG 58.439 55.000 0.00 0.00 0.00 4.49
3069 3405 0.951558 ACACACGCCAAAGGTTGATC 59.048 50.000 0.00 0.00 0.00 2.92
3070 3406 0.240945 CACACGCCAAAGGTTGATCC 59.759 55.000 0.00 0.00 0.00 3.36
3082 3418 3.615155 AGGTTGATCCTCAGCTTAAAGC 58.385 45.455 0.00 0.00 44.42 3.51
3083 3419 2.685388 GGTTGATCCTCAGCTTAAAGCC 59.315 50.000 0.00 0.00 43.77 4.35
3109 3445 4.147321 TCAAAAGGATTTCTGCTTGCTCT 58.853 39.130 0.00 0.00 37.28 4.09
3120 3456 2.415857 CTGCTTGCTCTGTGAATGTCTC 59.584 50.000 0.00 0.00 0.00 3.36
3121 3457 2.224354 TGCTTGCTCTGTGAATGTCTCA 60.224 45.455 0.00 0.00 0.00 3.27
3150 3486 9.336462 AGAAGATATGATATCCTGGAATTGAGT 57.664 33.333 8.76 0.00 0.00 3.41
3175 3511 9.934190 GTTTTAACATCTTTTAGGTGTTTACGA 57.066 29.630 10.29 0.00 37.30 3.43
3186 3522 5.871396 AGGTGTTTACGATACTCATCCAT 57.129 39.130 0.00 0.00 0.00 3.41
3223 3559 7.228706 ACCTGTTCAATTTCTAACGAATCAAGT 59.771 33.333 0.00 0.00 0.00 3.16
3233 3569 9.720769 TTTCTAACGAATCAAGTTATCCTCTTT 57.279 29.630 0.00 0.00 34.10 2.52
3252 3588 8.323567 TCCTCTTTTTCCGGTATAAATAGTTGT 58.676 33.333 0.00 0.00 0.00 3.32
3266 3602 8.910351 ATAAATAGTTGTTATCTGCTCTTCCC 57.090 34.615 0.00 0.00 0.00 3.97
3319 3656 4.405358 GCAATTCCCTTAATCATCAACCCA 59.595 41.667 0.00 0.00 0.00 4.51
3327 3664 3.899052 AATCATCAACCCATTGCCAAG 57.101 42.857 0.00 0.00 35.63 3.61
3331 3668 1.327303 TCAACCCATTGCCAAGTGAC 58.673 50.000 0.00 0.00 35.63 3.67
3333 3670 2.107378 TCAACCCATTGCCAAGTGACTA 59.893 45.455 0.00 0.00 35.63 2.59
3336 3673 2.041620 ACCCATTGCCAAGTGACTATGT 59.958 45.455 0.00 0.00 0.00 2.29
3358 3696 3.764434 TCTTGTTTATCGAGAGCAGAGGT 59.236 43.478 0.00 0.00 33.12 3.85
3372 3710 2.035066 GCAGAGGTGAATTGTGCAAAGT 59.965 45.455 0.00 0.00 34.18 2.66
3378 3716 4.044426 GGTGAATTGTGCAAAGTCTTGTC 58.956 43.478 0.00 0.00 34.79 3.18
3384 3722 3.609853 TGTGCAAAGTCTTGTCACTCTT 58.390 40.909 14.71 0.00 38.89 2.85
3385 3723 3.374988 TGTGCAAAGTCTTGTCACTCTTG 59.625 43.478 14.71 0.00 38.89 3.02
3386 3724 3.375299 GTGCAAAGTCTTGTCACTCTTGT 59.625 43.478 9.16 0.00 36.98 3.16
3401 3739 6.551385 CACTCTTGTGAATTGAGCTAGTTT 57.449 37.500 0.00 0.00 46.55 2.66
3416 3754 7.188834 TGAGCTAGTTTCAATTATGATTTGCG 58.811 34.615 0.00 0.00 34.96 4.85
3420 3759 5.104374 AGTTTCAATTATGATTTGCGGCTG 58.896 37.500 0.00 0.00 34.96 4.85
3430 3769 0.248990 TTTGCGGCTGCTTGTTTCAG 60.249 50.000 20.27 0.00 43.34 3.02
3450 3789 3.988459 GCTTTAATTTGAGCCGCGA 57.012 47.368 8.23 0.00 32.80 5.87
3456 3795 1.017387 AATTTGAGCCGCGAATCCTC 58.983 50.000 8.23 8.37 30.07 3.71
3457 3796 0.107703 ATTTGAGCCGCGAATCCTCA 60.108 50.000 8.23 11.07 34.07 3.86
3458 3797 0.321210 TTTGAGCCGCGAATCCTCAA 60.321 50.000 19.78 19.78 42.12 3.02
3460 3799 2.509336 AGCCGCGAATCCTCAACG 60.509 61.111 8.23 0.00 0.00 4.10
3461 3800 2.508439 GCCGCGAATCCTCAACGA 60.508 61.111 8.23 0.00 0.00 3.85
3462 3801 2.098233 GCCGCGAATCCTCAACGAA 61.098 57.895 8.23 0.00 0.00 3.85
3465 3804 1.463528 CCGCGAATCCTCAACGAAAAC 60.464 52.381 8.23 0.00 0.00 2.43
3466 3805 1.193650 CGCGAATCCTCAACGAAAACA 59.806 47.619 0.00 0.00 0.00 2.83
3467 3806 2.159707 CGCGAATCCTCAACGAAAACAT 60.160 45.455 0.00 0.00 0.00 2.71
3468 3807 3.061563 CGCGAATCCTCAACGAAAACATA 59.938 43.478 0.00 0.00 0.00 2.29
3471 3810 6.027749 GCGAATCCTCAACGAAAACATAAAT 58.972 36.000 0.00 0.00 0.00 1.40
3472 3811 6.021468 GCGAATCCTCAACGAAAACATAAATG 60.021 38.462 0.00 0.00 0.00 2.32
3473 3812 6.468956 CGAATCCTCAACGAAAACATAAATGG 59.531 38.462 0.00 0.00 0.00 3.16
3474 3813 7.461182 AATCCTCAACGAAAACATAAATGGA 57.539 32.000 0.00 0.00 0.00 3.41
3475 3814 6.885952 TCCTCAACGAAAACATAAATGGAA 57.114 33.333 0.00 0.00 0.00 3.53
3476 3815 7.461182 TCCTCAACGAAAACATAAATGGAAT 57.539 32.000 0.00 0.00 0.00 3.01
3477 3816 7.535139 TCCTCAACGAAAACATAAATGGAATC 58.465 34.615 0.00 0.00 0.00 2.52
3478 3817 7.393234 TCCTCAACGAAAACATAAATGGAATCT 59.607 33.333 0.00 0.00 0.00 2.40
3482 3821 8.798153 CAACGAAAACATAAATGGAATCTAAGC 58.202 33.333 0.00 0.00 0.00 3.09
3518 3857 7.188468 TCAAAATGTTATTTTCAGCAAAGCC 57.812 32.000 0.00 0.00 0.00 4.35
3519 3858 6.765036 TCAAAATGTTATTTTCAGCAAAGCCA 59.235 30.769 0.00 0.00 0.00 4.75
3520 3859 7.444792 TCAAAATGTTATTTTCAGCAAAGCCAT 59.555 29.630 0.00 0.00 0.00 4.40
3522 3861 7.748691 AATGTTATTTTCAGCAAAGCCATTT 57.251 28.000 0.00 0.00 0.00 2.32
3535 3878 6.534793 AGCAAAGCCATTTAATTTATCAACGG 59.465 34.615 0.00 0.00 0.00 4.44
3538 3881 8.716909 CAAAGCCATTTAATTTATCAACGGTTT 58.283 29.630 0.00 0.00 0.00 3.27
3539 3882 9.930693 AAAGCCATTTAATTTATCAACGGTTTA 57.069 25.926 0.00 0.00 0.00 2.01
3540 3883 8.920509 AGCCATTTAATTTATCAACGGTTTAC 57.079 30.769 0.00 0.00 0.00 2.01
3541 3884 8.745590 AGCCATTTAATTTATCAACGGTTTACT 58.254 29.630 0.00 0.00 0.00 2.24
3565 3908 8.241367 ACTAGAAAGTAAATGGCAAATAAACGG 58.759 33.333 0.00 0.00 32.84 4.44
3566 3909 5.867174 AGAAAGTAAATGGCAAATAAACGGC 59.133 36.000 0.00 0.00 0.00 5.68
3567 3910 3.765026 AGTAAATGGCAAATAAACGGCG 58.235 40.909 4.80 4.80 0.00 6.46
3568 3911 2.734276 AAATGGCAAATAAACGGCGT 57.266 40.000 6.77 6.77 0.00 5.68
3569 3912 2.271821 AATGGCAAATAAACGGCGTC 57.728 45.000 15.17 0.00 0.00 5.19
3570 3913 0.454196 ATGGCAAATAAACGGCGTCC 59.546 50.000 15.17 9.07 0.00 4.79
3581 3924 4.719369 GGCGTCCGCAAGTCTCGT 62.719 66.667 14.19 0.00 44.11 4.18
3583 3926 2.308039 GCGTCCGCAAGTCTCGTTT 61.308 57.895 6.82 0.00 41.49 3.60
3585 3928 0.982673 CGTCCGCAAGTCTCGTTTAG 59.017 55.000 0.00 0.00 0.00 1.85
3586 3929 1.665161 CGTCCGCAAGTCTCGTTTAGT 60.665 52.381 0.00 0.00 0.00 2.24
3587 3930 2.401351 GTCCGCAAGTCTCGTTTAGTT 58.599 47.619 0.00 0.00 0.00 2.24
3588 3931 3.568538 GTCCGCAAGTCTCGTTTAGTTA 58.431 45.455 0.00 0.00 0.00 2.24
3589 3932 3.607209 GTCCGCAAGTCTCGTTTAGTTAG 59.393 47.826 0.00 0.00 0.00 2.34
3590 3933 2.344741 CCGCAAGTCTCGTTTAGTTAGC 59.655 50.000 0.00 0.00 0.00 3.09
3591 3934 3.243336 CGCAAGTCTCGTTTAGTTAGCT 58.757 45.455 0.00 0.00 0.00 3.32
3592 3935 3.673809 CGCAAGTCTCGTTTAGTTAGCTT 59.326 43.478 0.00 0.00 0.00 3.74
3593 3936 4.150098 CGCAAGTCTCGTTTAGTTAGCTTT 59.850 41.667 0.00 0.00 0.00 3.51
3594 3937 5.344128 CGCAAGTCTCGTTTAGTTAGCTTTA 59.656 40.000 0.00 0.00 0.00 1.85
3595 3938 6.129009 CGCAAGTCTCGTTTAGTTAGCTTTAA 60.129 38.462 0.00 0.00 0.00 1.52
3596 3939 7.008278 GCAAGTCTCGTTTAGTTAGCTTTAAC 58.992 38.462 0.00 0.00 0.00 2.01
3598 3941 9.403110 CAAGTCTCGTTTAGTTAGCTTTAACTA 57.597 33.333 5.19 5.19 40.43 2.24
3600 3943 9.786105 AGTCTCGTTTAGTTAGCTTTAACTATC 57.214 33.333 9.40 6.16 40.82 2.08
3601 3944 9.786105 GTCTCGTTTAGTTAGCTTTAACTATCT 57.214 33.333 9.40 0.00 40.82 1.98
3603 3946 9.235537 CTCGTTTAGTTAGCTTTAACTATCTCC 57.764 37.037 9.40 0.00 40.82 3.71
3604 3947 8.742777 TCGTTTAGTTAGCTTTAACTATCTCCA 58.257 33.333 9.40 0.00 40.82 3.86
3620 4001 4.672587 TCTCCATAGTTCATTTCCTCCG 57.327 45.455 0.00 0.00 0.00 4.63
3622 4003 4.714802 TCTCCATAGTTCATTTCCTCCGAA 59.285 41.667 0.00 0.00 0.00 4.30
3625 4006 6.423182 TCCATAGTTCATTTCCTCCGAAAAT 58.577 36.000 0.00 0.00 41.25 1.82
3627 4008 8.050325 TCCATAGTTCATTTCCTCCGAAAATAA 58.950 33.333 0.00 0.00 41.25 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.405769 GCAAAGCTCTAAGTGATAATTCTCAC 58.594 38.462 14.42 14.42 44.78 3.51
1 2 6.540189 GGCAAAGCTCTAAGTGATAATTCTCA 59.460 38.462 0.00 0.00 0.00 3.27
2 3 6.765512 AGGCAAAGCTCTAAGTGATAATTCTC 59.234 38.462 0.00 0.00 0.00 2.87
3 4 6.657875 AGGCAAAGCTCTAAGTGATAATTCT 58.342 36.000 0.00 0.00 0.00 2.40
4 5 6.017523 GGAGGCAAAGCTCTAAGTGATAATTC 60.018 42.308 0.00 0.00 0.00 2.17
5 6 5.825151 GGAGGCAAAGCTCTAAGTGATAATT 59.175 40.000 0.00 0.00 0.00 1.40
6 7 5.104360 TGGAGGCAAAGCTCTAAGTGATAAT 60.104 40.000 0.00 0.00 0.00 1.28
7 8 4.225042 TGGAGGCAAAGCTCTAAGTGATAA 59.775 41.667 0.00 0.00 0.00 1.75
8 9 3.774766 TGGAGGCAAAGCTCTAAGTGATA 59.225 43.478 0.00 0.00 0.00 2.15
9 10 2.573462 TGGAGGCAAAGCTCTAAGTGAT 59.427 45.455 0.00 0.00 0.00 3.06
10 11 1.977854 TGGAGGCAAAGCTCTAAGTGA 59.022 47.619 0.00 0.00 0.00 3.41
11 12 2.479566 TGGAGGCAAAGCTCTAAGTG 57.520 50.000 0.00 0.00 0.00 3.16
12 13 2.639839 TCTTGGAGGCAAAGCTCTAAGT 59.360 45.455 11.60 0.00 38.66 2.24
13 14 3.340814 TCTTGGAGGCAAAGCTCTAAG 57.659 47.619 7.27 7.27 38.83 2.18
14 15 5.431765 CTTATCTTGGAGGCAAAGCTCTAA 58.568 41.667 0.00 0.00 0.00 2.10
15 16 4.684485 GCTTATCTTGGAGGCAAAGCTCTA 60.684 45.833 0.00 0.00 37.08 2.43
16 17 3.883669 CTTATCTTGGAGGCAAAGCTCT 58.116 45.455 0.00 0.00 0.00 4.09
17 18 2.357323 GCTTATCTTGGAGGCAAAGCTC 59.643 50.000 0.00 0.00 37.08 4.09
18 19 2.291153 TGCTTATCTTGGAGGCAAAGCT 60.291 45.455 6.44 0.00 39.93 3.74
19 20 2.094675 TGCTTATCTTGGAGGCAAAGC 58.905 47.619 0.00 0.00 39.73 3.51
20 21 3.128242 CACTGCTTATCTTGGAGGCAAAG 59.872 47.826 0.00 0.00 32.43 2.77
21 22 3.084039 CACTGCTTATCTTGGAGGCAAA 58.916 45.455 0.00 0.00 32.43 3.68
22 23 2.715046 CACTGCTTATCTTGGAGGCAA 58.285 47.619 0.00 0.00 32.43 4.52
23 24 1.679944 GCACTGCTTATCTTGGAGGCA 60.680 52.381 0.00 0.00 0.00 4.75
24 25 1.020437 GCACTGCTTATCTTGGAGGC 58.980 55.000 0.00 0.00 0.00 4.70
25 26 1.673168 GGCACTGCTTATCTTGGAGG 58.327 55.000 0.00 0.00 0.00 4.30
26 27 1.134699 TCGGCACTGCTTATCTTGGAG 60.135 52.381 0.00 0.00 0.00 3.86
27 28 0.901827 TCGGCACTGCTTATCTTGGA 59.098 50.000 0.00 0.00 0.00 3.53
28 29 1.600957 CATCGGCACTGCTTATCTTGG 59.399 52.381 0.00 0.00 0.00 3.61
29 30 2.554142 TCATCGGCACTGCTTATCTTG 58.446 47.619 0.00 0.00 0.00 3.02
30 31 2.988010 TCATCGGCACTGCTTATCTT 57.012 45.000 0.00 0.00 0.00 2.40
31 32 2.103771 ACATCATCGGCACTGCTTATCT 59.896 45.455 0.00 0.00 0.00 1.98
32 33 2.487934 ACATCATCGGCACTGCTTATC 58.512 47.619 0.00 0.00 0.00 1.75
33 34 2.627515 ACATCATCGGCACTGCTTAT 57.372 45.000 0.00 0.00 0.00 1.73
34 35 2.693074 TCTACATCATCGGCACTGCTTA 59.307 45.455 0.00 0.00 0.00 3.09
35 36 1.482182 TCTACATCATCGGCACTGCTT 59.518 47.619 0.00 0.00 0.00 3.91
36 37 1.114627 TCTACATCATCGGCACTGCT 58.885 50.000 0.00 0.00 0.00 4.24
37 38 1.797046 CATCTACATCATCGGCACTGC 59.203 52.381 0.00 0.00 0.00 4.40
38 39 3.375782 TCATCTACATCATCGGCACTG 57.624 47.619 0.00 0.00 0.00 3.66
39 40 4.375272 CTTTCATCTACATCATCGGCACT 58.625 43.478 0.00 0.00 0.00 4.40
40 41 3.059325 GCTTTCATCTACATCATCGGCAC 60.059 47.826 0.00 0.00 0.00 5.01
41 42 3.133691 GCTTTCATCTACATCATCGGCA 58.866 45.455 0.00 0.00 0.00 5.69
42 43 2.481952 GGCTTTCATCTACATCATCGGC 59.518 50.000 0.00 0.00 0.00 5.54
43 44 3.496130 GTGGCTTTCATCTACATCATCGG 59.504 47.826 0.00 0.00 0.00 4.18
44 45 3.183172 CGTGGCTTTCATCTACATCATCG 59.817 47.826 0.00 0.00 0.00 3.84
45 46 3.496130 CCGTGGCTTTCATCTACATCATC 59.504 47.826 0.00 0.00 0.00 2.92
46 47 3.118261 ACCGTGGCTTTCATCTACATCAT 60.118 43.478 0.00 0.00 0.00 2.45
47 48 2.236146 ACCGTGGCTTTCATCTACATCA 59.764 45.455 0.00 0.00 0.00 3.07
48 49 2.866762 GACCGTGGCTTTCATCTACATC 59.133 50.000 0.00 0.00 0.00 3.06
49 50 2.236146 TGACCGTGGCTTTCATCTACAT 59.764 45.455 0.00 0.00 0.00 2.29
50 51 1.621317 TGACCGTGGCTTTCATCTACA 59.379 47.619 0.00 0.00 0.00 2.74
51 52 2.380084 TGACCGTGGCTTTCATCTAC 57.620 50.000 0.00 0.00 0.00 2.59
52 53 3.270027 CAATGACCGTGGCTTTCATCTA 58.730 45.455 0.00 0.00 0.00 1.98
53 54 2.086869 CAATGACCGTGGCTTTCATCT 58.913 47.619 0.00 0.00 0.00 2.90
54 55 1.133025 CCAATGACCGTGGCTTTCATC 59.867 52.381 0.00 0.00 0.00 2.92
55 56 1.176527 CCAATGACCGTGGCTTTCAT 58.823 50.000 0.00 0.00 0.00 2.57
56 57 0.109532 TCCAATGACCGTGGCTTTCA 59.890 50.000 0.00 0.00 35.99 2.69
57 58 1.243902 TTCCAATGACCGTGGCTTTC 58.756 50.000 0.00 0.00 35.99 2.62
58 59 1.923356 ATTCCAATGACCGTGGCTTT 58.077 45.000 0.00 0.00 35.99 3.51
59 60 2.643551 CTATTCCAATGACCGTGGCTT 58.356 47.619 0.00 0.00 35.99 4.35
60 61 1.134098 CCTATTCCAATGACCGTGGCT 60.134 52.381 0.00 0.00 35.99 4.75
61 62 1.308998 CCTATTCCAATGACCGTGGC 58.691 55.000 0.00 0.00 35.99 5.01
62 63 2.093181 TCACCTATTCCAATGACCGTGG 60.093 50.000 0.00 0.00 37.51 4.94
63 64 2.936498 GTCACCTATTCCAATGACCGTG 59.064 50.000 0.00 0.00 36.31 4.94
64 65 3.261981 GTCACCTATTCCAATGACCGT 57.738 47.619 0.00 0.00 36.31 4.83
67 68 3.950397 TGTGGTCACCTATTCCAATGAC 58.050 45.455 0.00 0.00 40.62 3.06
431 432 2.361737 GGCCCCAAAGGAGCTCAC 60.362 66.667 17.19 5.01 38.24 3.51
446 447 2.747446 TGTTTCCGAGCTTTATTGAGGC 59.253 45.455 0.00 0.00 0.00 4.70
653 654 9.374838 GACACCATTAACTATATATTTACGGGG 57.625 37.037 7.63 7.63 0.00 5.73
654 655 9.079833 CGACACCATTAACTATATATTTACGGG 57.920 37.037 10.14 8.66 0.00 5.28
659 660 7.119262 GCAGGCGACACCATTAACTATATATTT 59.881 37.037 0.00 0.00 43.14 1.40
660 661 6.594159 GCAGGCGACACCATTAACTATATATT 59.406 38.462 0.00 0.00 43.14 1.28
677 680 3.890936 AACCAGCTCTGCAGGCGAC 62.891 63.158 15.13 0.80 38.85 5.19
687 690 1.092345 GCCGAATGAGGAACCAGCTC 61.092 60.000 0.00 0.00 0.00 4.09
697 700 6.706055 AACATTGTATATACGCCGAATGAG 57.294 37.500 21.52 5.58 0.00 2.90
810 813 3.257561 CGCTTCGTGCATCCCGAG 61.258 66.667 0.00 0.00 43.06 4.63
815 818 3.204827 ATGGCCGCTTCGTGCATC 61.205 61.111 0.00 0.00 43.06 3.91
825 828 4.541482 CACGCATGACATGGCCGC 62.541 66.667 17.03 0.00 0.00 6.53
826 829 4.541482 GCACGCATGACATGGCCG 62.541 66.667 17.03 14.36 0.00 6.13
827 830 4.197498 GGCACGCATGACATGGCC 62.197 66.667 17.03 16.24 32.03 5.36
839 853 2.513204 CTGGAGATGGCAGGCACG 60.513 66.667 0.00 0.00 0.00 5.34
896 910 3.570212 AGGAACCCAAGGCACGCT 61.570 61.111 0.00 0.00 0.00 5.07
975 1008 2.760385 GGCCCCTAGCTCTGTCGT 60.760 66.667 0.00 0.00 43.05 4.34
996 1029 1.078637 GCAGTCAGCAGCCATCTCA 60.079 57.895 0.00 0.00 44.79 3.27
1020 1053 0.105453 GGCTCCACATCTCCTCCCTA 60.105 60.000 0.00 0.00 0.00 3.53
1111 1152 1.863325 AGAGCAGAAGAGAGGCATGA 58.137 50.000 0.00 0.00 0.00 3.07
1119 1160 6.183360 CGTTTGTAGAATGAAGAGCAGAAGAG 60.183 42.308 0.00 0.00 0.00 2.85
1143 1184 6.807230 ACATGTAAAGAAGACTACTAACTGCG 59.193 38.462 0.00 0.00 0.00 5.18
1343 1416 1.255667 TTCTCCCTGTCGGCACCTAC 61.256 60.000 0.00 0.00 0.00 3.18
1457 1537 9.627395 AAAACGATCTTATATTATGAGACGGAG 57.373 33.333 16.71 7.18 0.00 4.63
1458 1538 9.406828 CAAAACGATCTTATATTATGAGACGGA 57.593 33.333 16.71 0.00 0.00 4.69
1463 1543 9.322776 GCTTGCAAAACGATCTTATATTATGAG 57.677 33.333 0.00 0.00 0.00 2.90
1464 1544 8.835439 TGCTTGCAAAACGATCTTATATTATGA 58.165 29.630 0.00 0.00 0.00 2.15
1467 1547 9.847706 TTTTGCTTGCAAAACGATCTTATATTA 57.152 25.926 24.07 3.09 0.00 0.98
1468 1548 8.647226 GTTTTGCTTGCAAAACGATCTTATATT 58.353 29.630 33.28 0.00 42.63 1.28
1469 1549 8.173321 GTTTTGCTTGCAAAACGATCTTATAT 57.827 30.769 33.28 0.00 42.63 0.86
1472 1552 5.881637 GTTTTGCTTGCAAAACGATCTTA 57.118 34.783 33.28 12.50 42.63 2.10
1480 1560 8.646356 CAATATAAGATCGTTTTGCTTGCAAAA 58.354 29.630 24.07 24.07 0.00 2.44
1481 1561 7.812191 ACAATATAAGATCGTTTTGCTTGCAAA 59.188 29.630 15.66 15.66 0.00 3.68
1482 1562 7.273164 CACAATATAAGATCGTTTTGCTTGCAA 59.727 33.333 3.70 3.70 0.00 4.08
1483 1563 6.746822 CACAATATAAGATCGTTTTGCTTGCA 59.253 34.615 0.00 0.00 0.00 4.08
1484 1564 6.197096 CCACAATATAAGATCGTTTTGCTTGC 59.803 38.462 0.00 0.00 0.00 4.01
1485 1565 6.692681 CCCACAATATAAGATCGTTTTGCTTG 59.307 38.462 0.00 0.00 0.00 4.01
1487 1567 6.119536 TCCCACAATATAAGATCGTTTTGCT 58.880 36.000 0.00 0.00 0.00 3.91
1527 1616 4.152402 GTCGCGTTGAGGCATCAAATATAT 59.848 41.667 16.43 0.00 46.75 0.86
1660 1749 1.073763 TCCAAGTTGGTGGTCATCAGG 59.926 52.381 21.35 0.00 39.03 3.86
1708 1797 0.173708 CGTGTAGGAGAAGAGGGTGC 59.826 60.000 0.00 0.00 0.00 5.01
1878 2181 1.265635 CGATGGACGCCTTTTTGTTCA 59.734 47.619 0.00 0.00 34.51 3.18
1879 2182 1.265905 ACGATGGACGCCTTTTTGTTC 59.734 47.619 0.00 0.00 46.94 3.18
1888 2191 1.647346 TTCATACAACGATGGACGCC 58.353 50.000 0.00 0.00 46.94 5.68
2181 2499 6.995511 TTTCCTTCCCAATATAAAGTGACG 57.004 37.500 0.00 0.00 0.00 4.35
2225 2545 8.362639 AGATGGCTATTTTGGTGCAAATAATAG 58.637 33.333 12.64 12.64 33.19 1.73
2271 2591 1.346365 TAGCGAAAACAGTGCTAGCG 58.654 50.000 10.77 0.00 40.06 4.26
2278 2598 4.890088 TCTTGTACCATAGCGAAAACAGT 58.110 39.130 0.00 0.00 0.00 3.55
2287 2607 7.183580 CAAGCTCTTAATCTTGTACCATAGC 57.816 40.000 0.00 0.00 36.01 2.97
2318 2638 7.116948 GTCCATGAACTAGTGATTGGAATATCG 59.883 40.741 17.77 0.00 35.19 2.92
2372 2693 6.978674 TTTCTTGGTTGAAGAGACTAGAGA 57.021 37.500 0.00 0.00 41.86 3.10
2373 2694 9.364989 CTAATTTCTTGGTTGAAGAGACTAGAG 57.635 37.037 0.00 0.00 41.86 2.43
2384 2705 4.998051 AGGGCTTCTAATTTCTTGGTTGA 58.002 39.130 0.00 0.00 0.00 3.18
2412 2733 4.614284 CGTGAAAATTGCTAGCAGTTTGAG 59.386 41.667 31.29 20.60 36.29 3.02
2492 2815 4.904241 AGTGCTCTTGCTTCATAAACTCT 58.096 39.130 0.00 0.00 40.48 3.24
2689 3021 7.015292 ACTCTCCTACGCATATATTTTCCAAGA 59.985 37.037 0.00 0.00 0.00 3.02
2701 3033 1.319541 GCTCCACTCTCCTACGCATA 58.680 55.000 0.00 0.00 0.00 3.14
2706 3038 8.910351 ATTTATTTATTGCTCCACTCTCCTAC 57.090 34.615 0.00 0.00 0.00 3.18
2762 3094 3.889859 AGGTATCCACAATGATGCCAT 57.110 42.857 10.16 0.00 46.48 4.40
2778 3110 1.072489 TCCGTGAAATGTGCCAAGGTA 59.928 47.619 0.00 0.00 34.31 3.08
2798 3130 3.938334 TGCACATTCATACGTATGCTGTT 59.062 39.130 27.15 16.76 34.18 3.16
2804 3136 6.272318 CCCAAATTTGCACATTCATACGTAT 58.728 36.000 12.92 1.14 0.00 3.06
2860 3192 5.887598 CCTCCATCCATCTTCATACAAAACA 59.112 40.000 0.00 0.00 0.00 2.83
2882 3215 7.304497 ACAACTCAAACTGAATAGTAGTCCT 57.696 36.000 0.00 0.00 35.69 3.85
3008 3343 1.584495 GGTGGTTCAATTCGGGCAC 59.416 57.895 0.00 0.00 0.00 5.01
3011 3347 1.204467 CATTGGGTGGTTCAATTCGGG 59.796 52.381 0.00 0.00 33.08 5.14
3045 3381 0.250166 ACCTTTGGCGTGTGTAGGTC 60.250 55.000 0.00 0.00 34.15 3.85
3069 3405 1.004745 TGAAGGGGCTTTAAGCTGAGG 59.995 52.381 16.89 0.00 41.99 3.86
3070 3406 2.496899 TGAAGGGGCTTTAAGCTGAG 57.503 50.000 16.89 0.00 41.99 3.35
3071 3407 2.969821 TTGAAGGGGCTTTAAGCTGA 57.030 45.000 16.89 0.00 41.99 4.26
3072 3408 3.306294 CCTTTTGAAGGGGCTTTAAGCTG 60.306 47.826 16.89 0.00 45.27 4.24
3073 3409 2.899900 CCTTTTGAAGGGGCTTTAAGCT 59.100 45.455 16.89 0.00 45.27 3.74
3074 3410 3.319137 CCTTTTGAAGGGGCTTTAAGC 57.681 47.619 8.66 8.66 45.27 3.09
3100 3436 2.224354 TGAGACATTCACAGAGCAAGCA 60.224 45.455 0.00 0.00 0.00 3.91
3136 3472 8.655935 AAGATGTTAAAACTCAATTCCAGGAT 57.344 30.769 0.00 0.00 0.00 3.24
3155 3491 8.308931 TGAGTATCGTAAACACCTAAAAGATGT 58.691 33.333 0.00 0.00 38.61 3.06
3156 3492 8.697846 TGAGTATCGTAAACACCTAAAAGATG 57.302 34.615 0.00 0.00 38.61 2.90
3233 3569 9.048446 GCAGATAACAACTATTTATACCGGAAA 57.952 33.333 9.46 0.00 0.00 3.13
3250 3586 1.839994 CCAGGGGAAGAGCAGATAACA 59.160 52.381 0.00 0.00 0.00 2.41
3252 3588 1.009552 TCCCAGGGGAAGAGCAGATAA 59.990 52.381 5.33 0.00 42.05 1.75
3266 3602 1.530771 CAGGCAATCCTCTCCCAGG 59.469 63.158 0.00 0.00 41.93 4.45
3290 3627 9.822185 GTTGATGATTAAGGGAATTGCTTAAAT 57.178 29.630 0.00 0.00 0.00 1.40
3311 3648 1.895131 GTCACTTGGCAATGGGTTGAT 59.105 47.619 0.00 0.00 37.53 2.57
3314 3651 2.969821 TAGTCACTTGGCAATGGGTT 57.030 45.000 0.00 0.00 0.00 4.11
3319 3656 4.655963 ACAAGACATAGTCACTTGGCAAT 58.344 39.130 0.00 0.00 43.28 3.56
3327 3664 6.197468 GCTCTCGATAAACAAGACATAGTCAC 59.803 42.308 0.00 0.00 34.60 3.67
3331 3668 6.499172 TCTGCTCTCGATAAACAAGACATAG 58.501 40.000 0.00 0.00 0.00 2.23
3333 3670 5.330455 TCTGCTCTCGATAAACAAGACAT 57.670 39.130 0.00 0.00 0.00 3.06
3336 3673 3.764434 ACCTCTGCTCTCGATAAACAAGA 59.236 43.478 0.00 0.00 0.00 3.02
3358 3696 4.398988 AGTGACAAGACTTTGCACAATTCA 59.601 37.500 15.71 0.00 40.55 2.57
3384 3722 9.230122 TCATAATTGAAACTAGCTCAATTCACA 57.770 29.630 25.49 15.34 45.88 3.58
3401 3739 2.689471 AGCAGCCGCAAATCATAATTGA 59.311 40.909 0.00 0.00 42.27 2.57
3407 3745 0.604578 AACAAGCAGCCGCAAATCAT 59.395 45.000 0.00 0.00 42.27 2.45
3416 3754 1.466851 AAGCCCTGAAACAAGCAGCC 61.467 55.000 0.00 0.00 32.06 4.85
3420 3759 5.296748 TCAAATTAAAGCCCTGAAACAAGC 58.703 37.500 0.00 0.00 0.00 4.01
3450 3789 7.461182 TCCATTTATGTTTTCGTTGAGGATT 57.539 32.000 0.00 0.00 0.00 3.01
3456 3795 8.798153 GCTTAGATTCCATTTATGTTTTCGTTG 58.202 33.333 0.00 0.00 0.00 4.10
3457 3796 8.519526 TGCTTAGATTCCATTTATGTTTTCGTT 58.480 29.630 0.00 0.00 0.00 3.85
3458 3797 8.050778 TGCTTAGATTCCATTTATGTTTTCGT 57.949 30.769 0.00 0.00 0.00 3.85
3492 3831 8.934825 GGCTTTGCTGAAAATAACATTTTGATA 58.065 29.630 1.77 0.00 0.00 2.15
3493 3832 7.444792 TGGCTTTGCTGAAAATAACATTTTGAT 59.555 29.630 1.77 0.00 0.00 2.57
3494 3833 6.765036 TGGCTTTGCTGAAAATAACATTTTGA 59.235 30.769 1.77 0.00 0.00 2.69
3495 3834 6.957150 TGGCTTTGCTGAAAATAACATTTTG 58.043 32.000 1.77 0.00 0.00 2.44
3496 3835 7.748691 ATGGCTTTGCTGAAAATAACATTTT 57.251 28.000 0.00 0.00 0.00 1.82
3497 3836 7.748691 AATGGCTTTGCTGAAAATAACATTT 57.251 28.000 0.00 0.00 28.81 2.32
3498 3837 7.748691 AAATGGCTTTGCTGAAAATAACATT 57.251 28.000 0.00 0.00 31.81 2.71
3499 3838 8.845413 TTAAATGGCTTTGCTGAAAATAACAT 57.155 26.923 0.00 0.00 0.00 2.71
3500 3839 8.845413 ATTAAATGGCTTTGCTGAAAATAACA 57.155 26.923 0.00 0.00 0.00 2.41
3506 3845 9.499479 TTGATAAATTAAATGGCTTTGCTGAAA 57.501 25.926 0.00 0.00 0.00 2.69
3507 3846 8.934825 GTTGATAAATTAAATGGCTTTGCTGAA 58.065 29.630 0.00 0.00 0.00 3.02
3508 3847 7.275341 CGTTGATAAATTAAATGGCTTTGCTGA 59.725 33.333 0.00 0.00 0.00 4.26
3509 3848 7.393327 CGTTGATAAATTAAATGGCTTTGCTG 58.607 34.615 0.00 0.00 0.00 4.41
3512 3851 7.826260 ACCGTTGATAAATTAAATGGCTTTG 57.174 32.000 0.00 0.00 33.96 2.77
3513 3852 8.840833 AAACCGTTGATAAATTAAATGGCTTT 57.159 26.923 0.00 0.00 33.96 3.51
3514 3853 9.361315 GTAAACCGTTGATAAATTAAATGGCTT 57.639 29.630 0.00 0.00 33.96 4.35
3515 3854 8.745590 AGTAAACCGTTGATAAATTAAATGGCT 58.254 29.630 0.00 0.00 33.96 4.75
3539 3882 8.241367 CCGTTTATTTGCCATTTACTTTCTAGT 58.759 33.333 0.00 0.00 38.44 2.57
3540 3883 7.220108 GCCGTTTATTTGCCATTTACTTTCTAG 59.780 37.037 0.00 0.00 0.00 2.43
3541 3884 7.030768 GCCGTTTATTTGCCATTTACTTTCTA 58.969 34.615 0.00 0.00 0.00 2.10
3542 3885 5.867174 GCCGTTTATTTGCCATTTACTTTCT 59.133 36.000 0.00 0.00 0.00 2.52
3543 3886 5.220135 CGCCGTTTATTTGCCATTTACTTTC 60.220 40.000 0.00 0.00 0.00 2.62
3544 3887 4.623595 CGCCGTTTATTTGCCATTTACTTT 59.376 37.500 0.00 0.00 0.00 2.66
3545 3888 4.170256 CGCCGTTTATTTGCCATTTACTT 58.830 39.130 0.00 0.00 0.00 2.24
3547 3890 3.503891 ACGCCGTTTATTTGCCATTTAC 58.496 40.909 0.00 0.00 0.00 2.01
3551 3894 0.454196 GGACGCCGTTTATTTGCCAT 59.546 50.000 0.00 0.00 0.00 4.40
3552 3895 1.877367 GGACGCCGTTTATTTGCCA 59.123 52.632 0.00 0.00 0.00 4.92
3553 3896 1.226184 CGGACGCCGTTTATTTGCC 60.226 57.895 9.69 0.00 42.73 4.52
3565 3908 1.005294 TAAACGAGACTTGCGGACGC 61.005 55.000 10.13 10.13 42.35 5.19
3566 3909 0.982673 CTAAACGAGACTTGCGGACG 59.017 55.000 0.00 0.00 0.00 4.79
3567 3910 2.061740 ACTAAACGAGACTTGCGGAC 57.938 50.000 0.00 0.00 0.00 4.79
3568 3911 2.806608 AACTAAACGAGACTTGCGGA 57.193 45.000 0.00 0.00 0.00 5.54
3569 3912 2.344741 GCTAACTAAACGAGACTTGCGG 59.655 50.000 0.00 0.00 0.00 5.69
3570 3913 3.243336 AGCTAACTAAACGAGACTTGCG 58.757 45.455 0.00 0.00 0.00 4.85
3571 3914 5.593183 AAAGCTAACTAAACGAGACTTGC 57.407 39.130 0.00 0.00 0.00 4.01
3572 3915 8.295569 AGTTAAAGCTAACTAAACGAGACTTG 57.704 34.615 0.00 0.00 44.85 3.16
3595 3938 6.015010 CGGAGGAAATGAACTATGGAGATAGT 60.015 42.308 0.00 0.00 45.75 2.12
3596 3939 6.209589 TCGGAGGAAATGAACTATGGAGATAG 59.790 42.308 0.00 0.00 38.06 2.08
3598 3941 4.901849 TCGGAGGAAATGAACTATGGAGAT 59.098 41.667 0.00 0.00 0.00 2.75
3599 3942 4.286707 TCGGAGGAAATGAACTATGGAGA 58.713 43.478 0.00 0.00 0.00 3.71
3600 3943 4.672587 TCGGAGGAAATGAACTATGGAG 57.327 45.455 0.00 0.00 0.00 3.86
3601 3944 5.429681 TTTCGGAGGAAATGAACTATGGA 57.570 39.130 0.00 0.00 37.24 3.41


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

AutoCloner maintained by Alex Coulton.