Multiple sequence alignment - TraesCS1A01G120700

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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 TraesCS1A01G120700 chr1A 100.000 2397 0 0 2079 4475 133161516 133159120 0.000000e+00 4427.0
1 TraesCS1A01G120700 chr1A 100.000 1846 0 0 1 1846 133163594 133161749 0.000000e+00 3410.0
2 TraesCS1A01G120700 chr1A 87.343 1035 128 3 33 1066 391706368 391705336 0.000000e+00 1182.0
3 TraesCS1A01G120700 chr1A 91.667 48 2 2 1 48 548319428 548319383 1.040000e-06 65.8
4 TraesCS1A01G120700 chr1D 96.293 1214 30 12 2481 3692 121318294 121317094 0.000000e+00 1978.0
5 TraesCS1A01G120700 chr1D 93.391 696 46 0 3780 4475 121316767 121316072 0.000000e+00 1031.0
6 TraesCS1A01G120700 chr1D 89.728 662 58 7 1171 1825 121395788 121395130 0.000000e+00 837.0
7 TraesCS1A01G120700 chr1D 90.547 402 37 1 2079 2479 121394807 121394406 8.520000e-147 531.0
8 TraesCS1A01G120700 chr1D 85.500 400 48 3 1390 1779 142668504 142668105 4.170000e-110 409.0
9 TraesCS1A01G120700 chr1D 81.190 420 63 6 1370 1773 167156404 167156823 1.550000e-84 324.0
10 TraesCS1A01G120700 chr1D 82.500 200 29 6 2285 2480 433402093 433402290 2.140000e-38 171.0
11 TraesCS1A01G120700 chr1D 88.660 97 6 3 3691 3782 121317013 121316917 3.660000e-21 113.0
12 TraesCS1A01G120700 chr1D 100.000 39 0 0 1 39 465526977 465527015 6.210000e-09 73.1
13 TraesCS1A01G120700 chr1B 93.383 1330 50 23 2482 3782 185077521 185076201 0.000000e+00 1934.0
14 TraesCS1A01G120700 chr1B 87.714 700 73 7 3780 4475 185075790 185075100 0.000000e+00 804.0
15 TraesCS1A01G120700 chr1B 85.504 407 48 8 2079 2479 185078024 185077623 8.960000e-112 414.0
16 TraesCS1A01G120700 chr1B 81.006 179 33 1 3784 3962 584136205 584136382 1.680000e-29 141.0
17 TraesCS1A01G120700 chr1B 82.927 123 17 4 2331 2451 594003169 594003289 1.700000e-19 108.0
18 TraesCS1A01G120700 chr6D 89.168 1034 107 3 33 1066 348672804 348671776 0.000000e+00 1284.0
19 TraesCS1A01G120700 chr6D 82.785 395 59 4 1374 1760 332325376 332324983 1.190000e-90 344.0
20 TraesCS1A01G120700 chr6D 91.026 78 6 1 1559 1636 322884005 322883929 2.200000e-18 104.0
21 TraesCS1A01G120700 chr6D 89.744 78 7 1 1559 1636 158368455 158368379 1.020000e-16 99.0
22 TraesCS1A01G120700 chr6D 89.474 76 7 1 1559 1633 376812540 376812465 1.330000e-15 95.3
23 TraesCS1A01G120700 chr6D 86.047 86 8 4 1551 1636 441211173 441211092 6.170000e-14 89.8
24 TraesCS1A01G120700 chr2D 88.058 1030 121 2 33 1062 364829744 364828717 0.000000e+00 1219.0
25 TraesCS1A01G120700 chr2D 87.379 1030 127 3 33 1062 364672271 364671245 0.000000e+00 1179.0
26 TraesCS1A01G120700 chr2D 83.777 413 53 5 1374 1773 278681492 278681903 3.270000e-101 379.0
27 TraesCS1A01G120700 chr2D 85.577 104 6 6 3681 3776 592648590 592648488 2.850000e-17 100.0
28 TraesCS1A01G120700 chr7D 87.923 1035 121 4 33 1066 107807588 107806557 0.000000e+00 1216.0
29 TraesCS1A01G120700 chr7D 88.091 1016 118 3 33 1047 107810068 107809055 0.000000e+00 1203.0
30 TraesCS1A01G120700 chr7D 87.306 1032 128 3 32 1062 351687505 351686476 0.000000e+00 1177.0
31 TraesCS1A01G120700 chr5D 87.585 1031 123 5 33 1062 16150243 16149217 0.000000e+00 1190.0
32 TraesCS1A01G120700 chr5D 87.488 1031 126 3 34 1063 18517490 18518518 0.000000e+00 1186.0
33 TraesCS1A01G120700 chr5D 83.293 413 54 5 1374 1773 320757421 320757831 2.540000e-97 366.0
34 TraesCS1A01G120700 chr5D 87.037 108 8 5 3681 3782 443898271 443898164 2.830000e-22 117.0
35 TraesCS1A01G120700 chr5D 97.619 42 1 0 1 42 502656279 502656320 6.210000e-09 73.1
36 TraesCS1A01G120700 chr4D 83.971 418 53 4 1373 1776 87657831 87657414 5.430000e-104 388.0
37 TraesCS1A01G120700 chr4D 83.453 417 55 5 1373 1776 253720461 253720046 4.230000e-100 375.0
38 TraesCS1A01G120700 chr4D 83.412 422 51 6 1373 1776 303596553 303596133 1.520000e-99 374.0
39 TraesCS1A01G120700 chr4D 83.014 418 57 5 1373 1776 170022642 170022225 2.540000e-97 366.0
40 TraesCS1A01G120700 chr4D 80.825 412 62 8 1379 1776 227814197 227813789 1.560000e-79 307.0
41 TraesCS1A01G120700 chr4D 82.716 162 27 1 1416 1576 332105803 332105642 4.670000e-30 143.0
42 TraesCS1A01G120700 chr4D 87.850 107 10 2 3679 3782 301526025 301525919 6.080000e-24 122.0
43 TraesCS1A01G120700 chr4D 78.125 160 26 6 1378 1536 82231582 82231733 4.770000e-15 93.5
44 TraesCS1A01G120700 chr4D 78.723 141 24 4 1378 1518 484773289 484773155 6.170000e-14 89.8
45 TraesCS1A01G120700 chr4D 82.292 96 9 5 1682 1770 298899822 298899916 4.800000e-10 76.8
46 TraesCS1A01G120700 chr3D 83.933 417 53 5 1370 1773 278634879 278635294 1.950000e-103 387.0
47 TraesCS1A01G120700 chr3D 82.734 417 57 5 1370 1773 338427674 338428088 1.530000e-94 357.0
48 TraesCS1A01G120700 chr3D 83.212 137 20 3 2332 2467 276915268 276915402 6.080000e-24 122.0
49 TraesCS1A01G120700 chr3D 86.111 108 9 4 3681 3782 615079967 615079860 1.320000e-20 111.0
50 TraesCS1A01G120700 chr3D 84.762 105 11 5 3681 3780 64764484 64764588 2.850000e-17 100.0
51 TraesCS1A01G120700 chr3D 95.349 43 0 2 1 43 546709211 546709251 2.890000e-07 67.6
52 TraesCS1A01G120700 chr5B 83.933 417 50 6 1371 1773 225393447 225393860 2.530000e-102 383.0
53 TraesCS1A01G120700 chr5B 81.208 149 21 4 2305 2451 327053560 327053703 3.660000e-21 113.0
54 TraesCS1A01G120700 chr5A 83.376 391 59 5 1370 1757 266014401 266014788 1.530000e-94 357.0
55 TraesCS1A01G120700 chr5A 82.759 174 27 3 3842 4014 503790451 503790280 7.750000e-33 152.0
56 TraesCS1A01G120700 chr5A 96.875 32 1 0 3651 3682 510218205 510218174 2.000000e-03 54.7
57 TraesCS1A01G120700 chr4B 82.308 390 61 6 1374 1760 210167502 210167118 9.280000e-87 331.0
58 TraesCS1A01G120700 chr4B 82.243 107 11 6 3681 3781 666801506 666801610 7.980000e-13 86.1
59 TraesCS1A01G120700 chrUn 82.915 199 30 4 2286 2480 344351329 344351527 4.600000e-40 176.0
60 TraesCS1A01G120700 chrUn 77.885 208 37 7 3825 4027 31098633 31098836 2.190000e-23 121.0
61 TraesCS1A01G120700 chr7B 83.163 196 29 4 2289 2480 684931896 684931701 4.600000e-40 176.0
62 TraesCS1A01G120700 chr7B 97.500 40 0 1 3 42 741292046 741292084 2.890000e-07 67.6
63 TraesCS1A01G120700 chr6A 83.240 179 26 2 3853 4030 29203949 29203774 1.290000e-35 161.0
64 TraesCS1A01G120700 chr6A 90.741 54 4 1 1 53 63210447 63210500 2.230000e-08 71.3
65 TraesCS1A01G120700 chr2A 83.051 177 24 5 3841 4014 720375227 720375400 5.990000e-34 156.0
66 TraesCS1A01G120700 chr3B 78.947 228 45 3 3806 4031 583372275 583372049 7.750000e-33 152.0
67 TraesCS1A01G120700 chr3B 76.389 216 47 2 3796 4011 564955134 564955345 3.660000e-21 113.0
68 TraesCS1A01G120700 chr2B 85.455 110 10 2 3681 3784 474614489 474614380 4.730000e-20 110.0
69 TraesCS1A01G120700 chr2B 84.259 108 15 2 2331 2437 28430861 28430755 2.200000e-18 104.0
70 TraesCS1A01G120700 chr7A 80.583 103 11 5 3681 3782 169387684 169387778 2.230000e-08 71.3
71 TraesCS1A01G120700 chr7A 97.561 41 1 0 1 41 610448714 610448754 2.230000e-08 71.3
72 TraesCS1A01G120700 chr4A 97.561 41 1 0 1 41 579437815 579437855 2.230000e-08 71.3
73 TraesCS1A01G120700 chr6B 91.667 48 2 2 4 50 213152525 213152571 1.040000e-06 65.8
74 TraesCS1A01G120700 chr3A 79.412 102 10 5 3681 3782 722502924 722503014 1.340000e-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 TraesCS1A01G120700 chr1A 133159120 133163594 4474 True 3918.500000 4427 100.000000 1 4475 2 chr1A.!!$R3 4474
1 TraesCS1A01G120700 chr1A 391705336 391706368 1032 True 1182.000000 1182 87.343000 33 1066 1 chr1A.!!$R1 1033
2 TraesCS1A01G120700 chr1D 121316072 121318294 2222 True 1040.666667 1978 92.781333 2481 4475 3 chr1D.!!$R2 1994
3 TraesCS1A01G120700 chr1D 121394406 121395788 1382 True 684.000000 837 90.137500 1171 2479 2 chr1D.!!$R3 1308
4 TraesCS1A01G120700 chr1B 185075100 185078024 2924 True 1050.666667 1934 88.867000 2079 4475 3 chr1B.!!$R1 2396
5 TraesCS1A01G120700 chr6D 348671776 348672804 1028 True 1284.000000 1284 89.168000 33 1066 1 chr6D.!!$R4 1033
6 TraesCS1A01G120700 chr2D 364828717 364829744 1027 True 1219.000000 1219 88.058000 33 1062 1 chr2D.!!$R2 1029
7 TraesCS1A01G120700 chr2D 364671245 364672271 1026 True 1179.000000 1179 87.379000 33 1062 1 chr2D.!!$R1 1029
8 TraesCS1A01G120700 chr7D 107806557 107810068 3511 True 1209.500000 1216 88.007000 33 1066 2 chr7D.!!$R2 1033
9 TraesCS1A01G120700 chr7D 351686476 351687505 1029 True 1177.000000 1177 87.306000 32 1062 1 chr7D.!!$R1 1030
10 TraesCS1A01G120700 chr5D 16149217 16150243 1026 True 1190.000000 1190 87.585000 33 1062 1 chr5D.!!$R1 1029
11 TraesCS1A01G120700 chr5D 18517490 18518518 1028 False 1186.000000 1186 87.488000 34 1063 1 chr5D.!!$F1 1029

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
590 593 0.034477 CCGCTACCCCAACCAAAGAT 60.034 55.0 0.0 0.0 0.00 2.40 F
998 3483 0.037605 GAAACGACCCAGATCACCGT 60.038 55.0 0.0 0.0 34.74 4.83 F
1693 4179 0.037326 CCACCAGCAGCGAGTAAGAA 60.037 55.0 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 3926 0.034670 CAGAAGAAAGGGGCTGGAGG 60.035 60.0 0.0 0.0 0.00 4.30 R
1818 4310 0.835971 AACCCCATTGACCCAAAGGC 60.836 55.0 0.0 0.0 31.72 4.35 R
3475 6148 0.679640 CACGCAATCCCAGCCCTTAA 60.680 55.0 0.0 0.0 0.00 1.85 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
30 31 7.455058 TCATCTAGATGAGTTCTAGGTACTCC 58.545 42.308 27.93 8.04 44.99 3.85
31 32 6.657541 CATCTAGATGAGTTCTAGGTACTCCC 59.342 46.154 25.78 12.05 44.99 4.30
103 104 1.817520 CACACGCACACACCCAAGA 60.818 57.895 0.00 0.00 0.00 3.02
118 119 2.705658 CCCAAGACAGGATACATAGGCA 59.294 50.000 0.00 0.00 41.41 4.75
149 150 3.936461 TCAATACCACCCCTAGCACTAT 58.064 45.455 0.00 0.00 0.00 2.12
240 243 1.072159 GCTCCAAGCCGATGCCTAT 59.928 57.895 0.00 0.00 38.69 2.57
287 290 2.045340 CCGCCCGACCCAAGAATT 60.045 61.111 0.00 0.00 0.00 2.17
298 301 4.323562 CGACCCAAGAATTAGAGTTTCCCT 60.324 45.833 0.00 0.00 0.00 4.20
314 317 1.079819 CCTCGGAGCAACACGACAT 60.080 57.895 0.00 0.00 35.04 3.06
320 323 1.428448 GAGCAACACGACATGCAGTA 58.572 50.000 12.12 0.00 44.95 2.74
389 392 2.361438 GGTCCGTCCGAAGATAGAACAT 59.639 50.000 0.00 0.00 0.00 2.71
420 423 1.540363 CGGCTAATATTCACCGCCACT 60.540 52.381 14.10 0.00 40.72 4.00
424 427 3.815401 GCTAATATTCACCGCCACTGAAT 59.185 43.478 0.00 0.00 40.64 2.57
433 436 0.603707 CGCCACTGAATGTCACACCT 60.604 55.000 0.00 0.00 0.00 4.00
514 517 3.315142 ATGAGCACCGCGACACCAT 62.315 57.895 8.23 1.08 0.00 3.55
525 528 2.858476 ACACCATCACCAGGGCCA 60.858 61.111 6.18 0.00 0.00 5.36
526 529 2.215451 GACACCATCACCAGGGCCAT 62.215 60.000 6.18 0.00 0.00 4.40
546 549 2.687200 CCCCGACATCCAGGACCA 60.687 66.667 0.00 0.00 0.00 4.02
568 571 3.626924 GCCACCTCACCCGTCACT 61.627 66.667 0.00 0.00 0.00 3.41
590 593 0.034477 CCGCTACCCCAACCAAAGAT 60.034 55.000 0.00 0.00 0.00 2.40
591 594 1.094785 CGCTACCCCAACCAAAGATG 58.905 55.000 0.00 0.00 0.00 2.90
628 632 1.280998 GCCTTTCACACCCCTAAGCTA 59.719 52.381 0.00 0.00 0.00 3.32
642 646 1.120530 AAGCTATCCCCAACGTCGAT 58.879 50.000 0.00 0.00 0.00 3.59
677 681 1.176527 CAAAACTGGCCACCATCGAT 58.823 50.000 0.00 0.00 30.82 3.59
680 800 1.561769 AACTGGCCACCATCGATCCA 61.562 55.000 0.00 0.00 30.82 3.41
734 1955 3.482783 GCCAGACGCGAGACAAGC 61.483 66.667 15.93 3.73 0.00 4.01
741 1962 2.343758 GCGAGACAAGCCAGGTCA 59.656 61.111 0.00 0.00 37.74 4.02
749 1970 3.214190 AAGCCAGGTCATGCTGCCA 62.214 57.895 0.00 0.00 38.00 4.92
826 3252 4.373116 GTGCGGGACAAGCTCGGA 62.373 66.667 0.00 0.00 42.02 4.55
895 3380 1.831736 CAACCCTCCGATGAAGGTAGT 59.168 52.381 0.00 0.00 34.05 2.73
906 3391 0.458025 GAAGGTAGTGCCCGAACGAG 60.458 60.000 0.00 0.00 38.26 4.18
908 3393 2.643232 GGTAGTGCCCGAACGAGGT 61.643 63.158 0.00 0.00 0.00 3.85
909 3394 1.315257 GGTAGTGCCCGAACGAGGTA 61.315 60.000 0.00 0.00 0.00 3.08
912 3397 0.896940 AGTGCCCGAACGAGGTAGAA 60.897 55.000 0.00 0.00 0.00 2.10
941 3426 1.215647 GGTCGACAAGGACGCTCAT 59.784 57.895 18.91 0.00 37.82 2.90
972 3457 2.657237 CCGAAGAAGTCCAGCCGT 59.343 61.111 0.00 0.00 0.00 5.68
975 3460 1.289380 GAAGAAGTCCAGCCGTCGT 59.711 57.895 0.00 0.00 0.00 4.34
998 3483 0.037605 GAAACGACCCAGATCACCGT 60.038 55.000 0.00 0.00 34.74 4.83
1067 3552 4.115199 GGGCAGCCCCGAGTCATT 62.115 66.667 21.62 0.00 42.67 2.57
1068 3553 2.044946 GGCAGCCCCGAGTCATTT 60.045 61.111 0.00 0.00 0.00 2.32
1069 3554 1.678970 GGCAGCCCCGAGTCATTTT 60.679 57.895 0.00 0.00 0.00 1.82
1070 3555 1.508088 GCAGCCCCGAGTCATTTTG 59.492 57.895 0.00 0.00 0.00 2.44
1071 3556 1.244019 GCAGCCCCGAGTCATTTTGT 61.244 55.000 0.00 0.00 0.00 2.83
1072 3557 0.804989 CAGCCCCGAGTCATTTTGTC 59.195 55.000 0.00 0.00 0.00 3.18
1073 3558 0.673644 AGCCCCGAGTCATTTTGTCG 60.674 55.000 0.00 0.00 0.00 4.35
1080 3565 4.563524 CGAGTCATTTTGTCGGAACTAC 57.436 45.455 0.00 0.00 0.00 2.73
1081 3566 3.367025 CGAGTCATTTTGTCGGAACTACC 59.633 47.826 0.00 0.00 0.00 3.18
1092 3577 2.298411 GGAACTACCGCCGTATCAAA 57.702 50.000 0.00 0.00 0.00 2.69
1093 3578 2.620242 GGAACTACCGCCGTATCAAAA 58.380 47.619 0.00 0.00 0.00 2.44
1094 3579 3.002102 GGAACTACCGCCGTATCAAAAA 58.998 45.455 0.00 0.00 0.00 1.94
1095 3580 3.063045 GGAACTACCGCCGTATCAAAAAG 59.937 47.826 0.00 0.00 0.00 2.27
1096 3581 2.004733 ACTACCGCCGTATCAAAAAGC 58.995 47.619 0.00 0.00 0.00 3.51
1097 3582 1.329599 CTACCGCCGTATCAAAAAGCC 59.670 52.381 0.00 0.00 0.00 4.35
1098 3583 0.322187 ACCGCCGTATCAAAAAGCCT 60.322 50.000 0.00 0.00 0.00 4.58
1099 3584 0.098728 CCGCCGTATCAAAAAGCCTG 59.901 55.000 0.00 0.00 0.00 4.85
1100 3585 0.098728 CGCCGTATCAAAAAGCCTGG 59.901 55.000 0.00 0.00 0.00 4.45
1101 3586 0.179137 GCCGTATCAAAAAGCCTGGC 60.179 55.000 11.65 11.65 0.00 4.85
1102 3587 1.173043 CCGTATCAAAAAGCCTGGCA 58.827 50.000 22.65 0.00 0.00 4.92
1103 3588 1.135402 CCGTATCAAAAAGCCTGGCAC 60.135 52.381 22.65 6.45 0.00 5.01
1104 3589 1.465689 CGTATCAAAAAGCCTGGCACG 60.466 52.381 22.65 15.02 0.00 5.34
1105 3590 1.135402 GTATCAAAAAGCCTGGCACGG 60.135 52.381 22.65 5.50 0.00 4.94
1106 3591 0.539438 ATCAAAAAGCCTGGCACGGA 60.539 50.000 22.65 10.90 36.31 4.69
1107 3592 1.007387 CAAAAAGCCTGGCACGGAC 60.007 57.895 22.65 0.00 36.31 4.79
1108 3593 1.454847 AAAAAGCCTGGCACGGACA 60.455 52.632 22.65 0.00 36.31 4.02
1109 3594 1.455383 AAAAAGCCTGGCACGGACAG 61.455 55.000 22.65 0.13 38.64 3.51
1110 3595 2.624674 AAAAGCCTGGCACGGACAGT 62.625 55.000 22.65 0.00 36.87 3.55
1111 3596 2.624674 AAAGCCTGGCACGGACAGTT 62.625 55.000 22.65 0.00 36.87 3.16
1112 3597 2.594592 GCCTGGCACGGACAGTTT 60.595 61.111 15.17 0.00 36.87 2.66
1113 3598 2.908073 GCCTGGCACGGACAGTTTG 61.908 63.158 15.17 0.00 36.87 2.93
1114 3599 1.227823 CCTGGCACGGACAGTTTGA 60.228 57.895 6.09 0.00 36.87 2.69
1115 3600 0.817634 CCTGGCACGGACAGTTTGAA 60.818 55.000 6.09 0.00 36.87 2.69
1116 3601 0.307760 CTGGCACGGACAGTTTGAAC 59.692 55.000 0.00 0.00 33.29 3.18
1117 3602 0.107410 TGGCACGGACAGTTTGAACT 60.107 50.000 0.00 0.00 40.60 3.01
1118 3603 1.021968 GGCACGGACAGTTTGAACTT 58.978 50.000 0.00 0.00 37.08 2.66
1119 3604 1.268539 GGCACGGACAGTTTGAACTTG 60.269 52.381 0.00 0.00 37.08 3.16
1120 3605 1.268539 GCACGGACAGTTTGAACTTGG 60.269 52.381 0.00 0.00 37.08 3.61
1121 3606 1.021968 ACGGACAGTTTGAACTTGGC 58.978 50.000 0.00 0.00 37.08 4.52
1122 3607 1.308998 CGGACAGTTTGAACTTGGCT 58.691 50.000 0.00 0.00 37.08 4.75
1123 3608 1.264288 CGGACAGTTTGAACTTGGCTC 59.736 52.381 0.00 0.00 37.08 4.70
1124 3609 1.264288 GGACAGTTTGAACTTGGCTCG 59.736 52.381 0.00 0.00 37.08 5.03
1125 3610 1.264288 GACAGTTTGAACTTGGCTCGG 59.736 52.381 0.00 0.00 37.08 4.63
1126 3611 0.040067 CAGTTTGAACTTGGCTCGGC 60.040 55.000 0.00 0.00 37.08 5.54
1127 3612 0.179018 AGTTTGAACTTGGCTCGGCT 60.179 50.000 0.00 0.00 35.21 5.52
1128 3613 0.238553 GTTTGAACTTGGCTCGGCTC 59.761 55.000 0.00 0.00 0.00 4.70
1129 3614 1.227999 TTTGAACTTGGCTCGGCTCG 61.228 55.000 0.00 0.00 0.00 5.03
1130 3615 2.048127 GAACTTGGCTCGGCTCGT 60.048 61.111 0.00 0.00 0.00 4.18
1131 3616 1.668151 GAACTTGGCTCGGCTCGTT 60.668 57.895 0.00 0.00 0.00 3.85
1132 3617 1.627550 GAACTTGGCTCGGCTCGTTC 61.628 60.000 8.66 8.66 0.00 3.95
1133 3618 2.048222 CTTGGCTCGGCTCGTTCA 60.048 61.111 0.00 0.00 0.00 3.18
1134 3619 2.357034 TTGGCTCGGCTCGTTCAC 60.357 61.111 0.00 0.00 0.00 3.18
1135 3620 4.717629 TGGCTCGGCTCGTTCACG 62.718 66.667 0.00 0.00 41.45 4.35
1145 3630 2.774587 TCGTTCACGAAAGACGACG 58.225 52.632 0.00 0.00 46.30 5.12
1146 3631 1.125266 CGTTCACGAAAGACGACGC 59.875 57.895 0.00 0.00 45.77 5.19
1147 3632 1.125266 GTTCACGAAAGACGACGCG 59.875 57.895 3.53 3.53 45.77 6.01
1148 3633 2.641783 TTCACGAAAGACGACGCGC 61.642 57.895 5.73 0.00 45.77 6.86
1149 3634 4.449161 CACGAAAGACGACGCGCG 62.449 66.667 30.96 30.96 45.77 6.86
1158 3643 2.767059 CGACGCGCGTTTGTGTAT 59.233 55.556 38.03 11.66 31.57 2.29
1159 3644 1.574147 CGACGCGCGTTTGTGTATG 60.574 57.895 38.03 14.87 31.57 2.39
1160 3645 1.857426 GACGCGCGTTTGTGTATGC 60.857 57.895 38.03 17.01 31.57 3.14
1165 3650 2.429213 CGCGTTTGTGTATGCGTATT 57.571 45.000 0.00 0.00 45.78 1.89
1166 3651 2.350616 CGCGTTTGTGTATGCGTATTC 58.649 47.619 0.00 0.00 45.78 1.75
1167 3652 2.222618 CGCGTTTGTGTATGCGTATTCA 60.223 45.455 0.00 0.00 45.78 2.57
1168 3653 3.342269 GCGTTTGTGTATGCGTATTCAG 58.658 45.455 0.00 0.00 0.00 3.02
1169 3654 3.181524 GCGTTTGTGTATGCGTATTCAGT 60.182 43.478 0.00 0.00 0.00 3.41
1189 3674 4.034626 CAGTACCGTCACAAACATGTTCAA 59.965 41.667 12.39 0.00 0.00 2.69
1281 3766 3.074094 ACATCTGATATGGAGCAAGGCAT 59.926 43.478 0.00 0.00 0.00 4.40
1283 3768 4.980339 TCTGATATGGAGCAAGGCATAA 57.020 40.909 0.00 0.00 0.00 1.90
1380 3865 2.102588 GACCACTATACCACGGCTCATT 59.897 50.000 0.00 0.00 0.00 2.57
1381 3866 2.158957 ACCACTATACCACGGCTCATTG 60.159 50.000 0.00 0.00 0.00 2.82
1402 3887 9.337396 TCATTGTCATTCACCCACTATATTAAC 57.663 33.333 0.00 0.00 0.00 2.01
1405 3890 8.958119 TGTCATTCACCCACTATATTAACTTC 57.042 34.615 0.00 0.00 0.00 3.01
1408 3893 8.768397 TCATTCACCCACTATATTAACTTCAGT 58.232 33.333 0.00 0.00 0.00 3.41
1411 3896 6.099269 TCACCCACTATATTAACTTCAGTCCC 59.901 42.308 0.00 0.00 0.00 4.46
1415 3900 6.214399 CACTATATTAACTTCAGTCCCGGTC 58.786 44.000 0.00 0.00 0.00 4.79
1445 3931 3.309296 GACCCATAGTCATTCTCCTCCA 58.691 50.000 0.00 0.00 45.55 3.86
1446 3932 3.312890 ACCCATAGTCATTCTCCTCCAG 58.687 50.000 0.00 0.00 0.00 3.86
1448 3934 2.038295 CCATAGTCATTCTCCTCCAGCC 59.962 54.545 0.00 0.00 0.00 4.85
1449 3935 1.794714 TAGTCATTCTCCTCCAGCCC 58.205 55.000 0.00 0.00 0.00 5.19
1462 3948 0.401738 CCAGCCCCTTTCTTCTGTCA 59.598 55.000 0.00 0.00 0.00 3.58
1463 3949 1.612726 CCAGCCCCTTTCTTCTGTCAG 60.613 57.143 0.00 0.00 0.00 3.51
1471 3957 2.533266 TTCTTCTGTCAGCACCACTC 57.467 50.000 0.00 0.00 0.00 3.51
1474 3960 0.836606 TTCTGTCAGCACCACTCCAA 59.163 50.000 0.00 0.00 0.00 3.53
1488 3974 1.967066 ACTCCAATCATAGCCTCCTCG 59.033 52.381 0.00 0.00 0.00 4.63
1489 3975 0.681733 TCCAATCATAGCCTCCTCGC 59.318 55.000 0.00 0.00 0.00 5.03
1490 3976 0.668706 CCAATCATAGCCTCCTCGCG 60.669 60.000 0.00 0.00 0.00 5.87
1516 4002 2.541233 AGCTCTCTGGGATGTACTGT 57.459 50.000 0.00 0.00 0.00 3.55
1518 4004 2.103373 GCTCTCTGGGATGTACTGTCA 58.897 52.381 0.00 0.00 0.00 3.58
1521 4007 2.179427 CTCTGGGATGTACTGTCACCA 58.821 52.381 0.00 2.48 0.00 4.17
1524 4010 2.167281 CTGGGATGTACTGTCACCAGAG 59.833 54.545 19.49 3.27 46.38 3.35
1540 4026 1.998315 CAGAGCAGACGAAGGACATTG 59.002 52.381 0.00 0.00 0.00 2.82
1542 4028 0.322975 AGCAGACGAAGGACATTGCT 59.677 50.000 0.00 0.00 37.09 3.91
1553 4039 0.463474 GACATTGCTGGCTCCTCTCC 60.463 60.000 0.00 0.00 0.00 3.71
1596 4082 0.457853 GACGTATTGTCGCAGGAGCA 60.458 55.000 0.00 0.00 42.27 4.26
1617 4103 2.586357 GAAGGACATCGCCGGCTC 60.586 66.667 26.68 15.25 0.00 4.70
1650 4136 4.429212 TCCGTCGCCATGACCACG 62.429 66.667 0.00 0.00 45.23 4.94
1652 4138 2.431771 CGTCGCCATGACCACGAA 60.432 61.111 0.00 0.00 45.23 3.85
1658 4144 3.499737 CATGACCACGAAGCCGGC 61.500 66.667 21.89 21.89 40.78 6.13
1693 4179 0.037326 CCACCAGCAGCGAGTAAGAA 60.037 55.000 0.00 0.00 0.00 2.52
1709 4195 6.163135 AGTAAGAATAGTGCATGGTAGGTC 57.837 41.667 0.00 0.00 0.00 3.85
1719 4205 3.142838 GGTAGGTCACCGCCGCTA 61.143 66.667 0.00 0.00 37.63 4.26
1780 4266 4.080015 AGCTTGGTGGGCTAAATATGTGTA 60.080 41.667 0.00 0.00 38.36 2.90
1785 4271 7.726033 TGGTGGGCTAAATATGTGTATTTTT 57.274 32.000 0.00 0.00 40.21 1.94
1796 4282 9.669887 AAATATGTGTATTTTTGTTGATGGCAT 57.330 25.926 0.00 0.00 37.24 4.40
1800 4286 8.893219 TGTGTATTTTTGTTGATGGCATTTAA 57.107 26.923 0.00 0.00 0.00 1.52
1825 4317 1.402787 ACAGTGAAACAGGCCTTTGG 58.597 50.000 0.00 0.00 41.43 3.28
1826 4318 0.675633 CAGTGAAACAGGCCTTTGGG 59.324 55.000 0.00 0.00 41.43 4.12
1827 4319 0.261696 AGTGAAACAGGCCTTTGGGT 59.738 50.000 0.00 0.00 41.43 4.51
1828 4320 0.673985 GTGAAACAGGCCTTTGGGTC 59.326 55.000 0.00 0.00 36.32 4.46
1829 4321 0.260230 TGAAACAGGCCTTTGGGTCA 59.740 50.000 0.00 0.00 40.27 4.02
1830 4322 1.342474 TGAAACAGGCCTTTGGGTCAA 60.342 47.619 0.00 0.00 40.27 3.18
1831 4323 1.970640 GAAACAGGCCTTTGGGTCAAT 59.029 47.619 0.00 0.00 40.27 2.57
1832 4324 1.341080 AACAGGCCTTTGGGTCAATG 58.659 50.000 0.00 0.00 40.27 2.82
1833 4325 0.542702 ACAGGCCTTTGGGTCAATGG 60.543 55.000 0.00 7.84 40.27 3.16
1834 4326 1.079073 AGGCCTTTGGGTCAATGGG 59.921 57.895 0.00 5.63 40.27 4.00
1835 4327 1.989508 GGCCTTTGGGTCAATGGGG 60.990 63.158 12.45 3.71 38.56 4.96
1836 4328 1.229177 GCCTTTGGGTCAATGGGGT 60.229 57.895 12.45 0.00 38.56 4.95
1837 4329 0.835971 GCCTTTGGGTCAATGGGGTT 60.836 55.000 12.45 0.00 38.56 4.11
1838 4330 1.266178 CCTTTGGGTCAATGGGGTTC 58.734 55.000 5.08 0.00 35.75 3.62
1839 4331 1.482177 CCTTTGGGTCAATGGGGTTCA 60.482 52.381 5.08 0.00 35.75 3.18
1840 4332 1.618343 CTTTGGGTCAATGGGGTTCAC 59.382 52.381 0.00 0.00 0.00 3.18
1841 4333 0.178947 TTGGGTCAATGGGGTTCACC 60.179 55.000 0.00 0.00 39.11 4.02
2096 4657 1.761174 GCTGGGAACAACCTCCTGA 59.239 57.895 0.00 0.00 42.06 3.86
2137 4698 1.648302 CCCTCCTCCATGGCATCCAA 61.648 60.000 6.96 0.00 36.95 3.53
2187 4748 8.637986 ACATTGGTCTGTAAAATCTTAGCAAAA 58.362 29.630 0.00 0.00 0.00 2.44
2199 4760 7.566858 AATCTTAGCAAAATTTTGTACGCAG 57.433 32.000 27.13 17.30 40.24 5.18
2214 4775 7.835634 TTGTACGCAGTCATCATAATTTACA 57.164 32.000 0.00 0.00 43.93 2.41
2313 4877 8.995220 ACTTTTTACTATGCGTGTAAGATTTGA 58.005 29.630 0.00 0.00 32.43 2.69
2315 4879 6.897259 TTACTATGCGTGTAAGATTTGACC 57.103 37.500 0.00 0.00 0.00 4.02
2484 5050 8.868522 AAGATGGTCAAACTTTATGAATGAGA 57.131 30.769 0.00 0.00 0.00 3.27
2485 5051 8.868522 AGATGGTCAAACTTTATGAATGAGAA 57.131 30.769 0.00 0.00 0.00 2.87
2486 5052 9.300681 AGATGGTCAAACTTTATGAATGAGAAA 57.699 29.630 0.00 0.00 0.00 2.52
2487 5053 9.912634 GATGGTCAAACTTTATGAATGAGAAAA 57.087 29.630 0.00 0.00 0.00 2.29
2488 5054 9.918630 ATGGTCAAACTTTATGAATGAGAAAAG 57.081 29.630 0.00 0.00 35.54 2.27
2510 5174 9.551734 AAAAGAAATCAAAGATGGAAGGAAAAG 57.448 29.630 0.00 0.00 0.00 2.27
2525 5189 6.724441 GGAAGGAAAAGAAATAAGGAAAGGGA 59.276 38.462 0.00 0.00 0.00 4.20
2563 5227 2.867975 GGACGAAGGAAAGTTGAAACGA 59.132 45.455 0.00 0.00 0.00 3.85
2663 5327 6.800892 GGCGTTAACATGCTATCTACTACTAC 59.199 42.308 6.39 0.00 35.00 2.73
3351 6024 2.335712 GGGCAAGAAAGACCCTGCG 61.336 63.158 0.00 0.00 40.75 5.18
3475 6148 0.460311 CGTCGCAGGACTTCCCTAAT 59.540 55.000 0.00 0.00 45.60 1.73
3782 6562 5.874810 TGAGTCACTTAGATGTGCAATAACC 59.125 40.000 0.00 0.00 37.81 2.85
3823 7016 3.928727 TTGTAGTCCACCTAACGACAG 57.071 47.619 0.00 0.00 34.46 3.51
3876 7069 2.764128 GTCATCGCCCCTCCCTCA 60.764 66.667 0.00 0.00 0.00 3.86
3893 7086 2.892852 CCTCAATGGAGTCAGGCAAAAA 59.107 45.455 0.00 0.00 39.64 1.94
3905 7098 7.341445 AGTCAGGCAAAAATTGTTGTAGTAA 57.659 32.000 10.07 0.00 0.00 2.24
3949 7142 2.849942 AGGCATCATATAACAAGCGCA 58.150 42.857 11.47 0.00 0.00 6.09
3989 7182 6.353323 TCGAGATGAAGAGAAGTGTAGATCT 58.647 40.000 0.00 0.00 0.00 2.75
4021 7214 5.007234 CCAACTTGAAGACACACGAACATAA 59.993 40.000 0.00 0.00 0.00 1.90
4101 7294 7.862372 CACGTCAAATGAATATTTTCCCTATGG 59.138 37.037 0.00 0.00 34.34 2.74
4146 7339 9.985730 TGCATTTGAGAACTAATTTTGAGATTT 57.014 25.926 0.00 0.00 0.00 2.17
4180 7373 8.938906 ACGTTTTTGTCAAGTTTTCTTAGAGTA 58.061 29.630 0.00 0.00 38.17 2.59
4271 7473 9.906660 GATTCCATTTACTTTGTTACACATCAA 57.093 29.630 0.00 0.00 0.00 2.57
4373 7575 1.133945 TGCTGTCAGGTGGTTGCTTTA 60.134 47.619 1.14 0.00 0.00 1.85
4460 7662 4.563061 TCATGTCAAGCTCATCGATATGG 58.437 43.478 0.00 0.00 33.61 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 3.009695 ACCGGGTTATTGGTGATCTTTGA 59.990 43.478 6.32 0.00 37.02 2.69
103 104 3.005897 CGCTTAGTGCCTATGTATCCTGT 59.994 47.826 0.00 0.00 38.78 4.00
118 119 2.561569 GGTGGTATTGATGCGCTTAGT 58.438 47.619 9.73 0.00 0.00 2.24
121 122 0.751643 GGGGTGGTATTGATGCGCTT 60.752 55.000 9.73 0.55 0.00 4.68
132 133 4.673968 CTCATATAGTGCTAGGGGTGGTA 58.326 47.826 0.00 0.00 0.00 3.25
165 168 2.604174 GCGTGTTCACGGTTGAGGG 61.604 63.158 23.27 0.00 31.71 4.30
230 233 3.367087 CGTAACCTTCCTATAGGCATCGG 60.367 52.174 14.50 12.70 38.99 4.18
233 236 4.038883 GTGTCGTAACCTTCCTATAGGCAT 59.961 45.833 14.50 0.90 38.99 4.40
240 243 2.198827 TCGGTGTCGTAACCTTCCTA 57.801 50.000 7.51 0.00 38.14 2.94
284 287 2.838202 TGCTCCGAGGGAAACTCTAATT 59.162 45.455 0.00 0.00 44.33 1.40
287 290 1.549170 GTTGCTCCGAGGGAAACTCTA 59.451 52.381 0.00 0.00 44.33 2.43
298 301 2.027073 GCATGTCGTGTTGCTCCGA 61.027 57.895 0.00 0.00 35.95 4.55
314 317 2.126071 GTCGCGGCTCTTACTGCA 60.126 61.111 1.90 0.00 42.32 4.41
389 392 3.655615 ATATTAGCCGGGGTGAAAACA 57.344 42.857 9.43 0.00 0.00 2.83
420 423 2.552155 GGTAGCCAAGGTGTGACATTCA 60.552 50.000 0.00 0.00 0.00 2.57
424 427 0.107831 GTGGTAGCCAAGGTGTGACA 59.892 55.000 0.00 0.00 34.18 3.58
525 528 3.550431 CCTGGATGTCGGGGCGAT 61.550 66.667 0.00 0.00 38.42 4.58
526 529 4.770362 TCCTGGATGTCGGGGCGA 62.770 66.667 0.00 0.00 42.31 5.54
546 549 4.082523 CGGGTGAGGTGGCGTCAT 62.083 66.667 0.00 0.00 31.03 3.06
564 567 1.534476 TTGGGGTAGCGGTGAGTGA 60.534 57.895 0.00 0.00 0.00 3.41
568 571 1.706995 TTTGGTTGGGGTAGCGGTGA 61.707 55.000 0.00 0.00 0.00 4.02
590 593 1.758592 CGGTTCCTTTCCACTCCCA 59.241 57.895 0.00 0.00 0.00 4.37
591 594 1.674651 GCGGTTCCTTTCCACTCCC 60.675 63.158 0.00 0.00 0.00 4.30
592 595 1.674651 GGCGGTTCCTTTCCACTCC 60.675 63.158 0.00 0.00 0.00 3.85
628 632 0.688418 TGGGTATCGACGTTGGGGAT 60.688 55.000 2.20 0.59 0.00 3.85
642 646 1.572689 TTTGGCCGGCCTATTGGGTA 61.573 55.000 43.34 20.74 37.43 3.69
722 842 3.575351 GACCTGGCTTGTCTCGCGT 62.575 63.158 5.77 0.00 0.00 6.01
749 1970 4.462417 CGAACTCGTCTCGCGCCT 62.462 66.667 0.00 0.00 41.07 5.52
810 3236 4.373116 GTCCGAGCTTGTCCCGCA 62.373 66.667 0.00 0.00 0.00 5.69
837 3321 4.794439 CATCGCCCGTCTCGTGCA 62.794 66.667 0.00 0.00 29.43 4.57
895 3380 0.245539 CTTTCTACCTCGTTCGGGCA 59.754 55.000 0.00 0.00 0.00 5.36
906 3391 3.129988 TCGACCTTCGATTCCTTTCTACC 59.870 47.826 0.00 0.00 44.82 3.18
934 3419 0.169230 GTCTGTCTGTCGATGAGCGT 59.831 55.000 0.00 0.00 41.80 5.07
941 3426 2.183858 CTTCGGCGTCTGTCTGTCGA 62.184 60.000 6.85 0.00 0.00 4.20
992 3477 4.028490 GGTGGCCCATGACGGTGA 62.028 66.667 0.00 0.00 0.00 4.02
998 3483 4.343323 CGTGGTGGTGGCCCATGA 62.343 66.667 0.00 0.00 44.35 3.07
1073 3558 2.298411 TTTGATACGGCGGTAGTTCC 57.702 50.000 13.24 0.78 30.81 3.62
1074 3559 3.484721 GCTTTTTGATACGGCGGTAGTTC 60.485 47.826 13.24 4.46 30.81 3.01
1075 3560 2.417586 GCTTTTTGATACGGCGGTAGTT 59.582 45.455 13.24 0.00 30.81 2.24
1076 3561 2.004733 GCTTTTTGATACGGCGGTAGT 58.995 47.619 13.24 0.00 30.81 2.73
1077 3562 1.329599 GGCTTTTTGATACGGCGGTAG 59.670 52.381 13.24 0.00 30.81 3.18
1078 3563 1.065998 AGGCTTTTTGATACGGCGGTA 60.066 47.619 13.24 6.59 0.00 4.02
1079 3564 0.322187 AGGCTTTTTGATACGGCGGT 60.322 50.000 13.24 1.39 0.00 5.68
1080 3565 0.098728 CAGGCTTTTTGATACGGCGG 59.901 55.000 13.24 0.00 0.00 6.13
1081 3566 0.098728 CCAGGCTTTTTGATACGGCG 59.901 55.000 4.80 4.80 0.00 6.46
1082 3567 0.179137 GCCAGGCTTTTTGATACGGC 60.179 55.000 3.29 0.00 0.00 5.68
1083 3568 1.135402 GTGCCAGGCTTTTTGATACGG 60.135 52.381 14.15 0.00 0.00 4.02
1084 3569 1.465689 CGTGCCAGGCTTTTTGATACG 60.466 52.381 14.15 7.67 0.00 3.06
1085 3570 1.135402 CCGTGCCAGGCTTTTTGATAC 60.135 52.381 14.15 0.00 0.00 2.24
1086 3571 1.173043 CCGTGCCAGGCTTTTTGATA 58.827 50.000 14.15 0.00 0.00 2.15
1087 3572 0.539438 TCCGTGCCAGGCTTTTTGAT 60.539 50.000 14.15 0.00 0.00 2.57
1088 3573 1.152860 TCCGTGCCAGGCTTTTTGA 60.153 52.632 14.15 0.00 0.00 2.69
1089 3574 1.007387 GTCCGTGCCAGGCTTTTTG 60.007 57.895 14.15 0.00 0.00 2.44
1090 3575 1.454847 TGTCCGTGCCAGGCTTTTT 60.455 52.632 14.15 0.00 0.00 1.94
1091 3576 1.898574 CTGTCCGTGCCAGGCTTTT 60.899 57.895 14.15 0.00 0.00 2.27
1092 3577 2.281761 CTGTCCGTGCCAGGCTTT 60.282 61.111 14.15 0.00 0.00 3.51
1093 3578 2.624674 AAACTGTCCGTGCCAGGCTT 62.625 55.000 14.15 0.00 34.16 4.35
1094 3579 3.120086 AAACTGTCCGTGCCAGGCT 62.120 57.895 14.15 0.00 34.16 4.58
1095 3580 2.594592 AAACTGTCCGTGCCAGGC 60.595 61.111 3.66 3.66 34.16 4.85
1096 3581 0.817634 TTCAAACTGTCCGTGCCAGG 60.818 55.000 0.00 0.00 34.16 4.45
1097 3582 0.307760 GTTCAAACTGTCCGTGCCAG 59.692 55.000 0.00 0.00 36.01 4.85
1098 3583 0.107410 AGTTCAAACTGTCCGTGCCA 60.107 50.000 0.00 0.00 37.98 4.92
1099 3584 1.021968 AAGTTCAAACTGTCCGTGCC 58.978 50.000 0.00 0.00 39.66 5.01
1100 3585 1.268539 CCAAGTTCAAACTGTCCGTGC 60.269 52.381 0.00 0.00 39.66 5.34
1101 3586 1.268539 GCCAAGTTCAAACTGTCCGTG 60.269 52.381 0.00 0.00 39.66 4.94
1102 3587 1.021968 GCCAAGTTCAAACTGTCCGT 58.978 50.000 0.00 0.00 39.66 4.69
1103 3588 1.264288 GAGCCAAGTTCAAACTGTCCG 59.736 52.381 0.00 0.00 39.66 4.79
1104 3589 1.264288 CGAGCCAAGTTCAAACTGTCC 59.736 52.381 0.00 0.00 39.66 4.02
1105 3590 1.264288 CCGAGCCAAGTTCAAACTGTC 59.736 52.381 0.00 0.00 39.66 3.51
1106 3591 1.308998 CCGAGCCAAGTTCAAACTGT 58.691 50.000 0.00 0.00 39.66 3.55
1107 3592 0.040067 GCCGAGCCAAGTTCAAACTG 60.040 55.000 0.00 0.00 39.66 3.16
1108 3593 0.179018 AGCCGAGCCAAGTTCAAACT 60.179 50.000 0.00 0.00 42.04 2.66
1109 3594 0.238553 GAGCCGAGCCAAGTTCAAAC 59.761 55.000 0.00 0.00 0.00 2.93
1110 3595 1.227999 CGAGCCGAGCCAAGTTCAAA 61.228 55.000 0.00 0.00 0.00 2.69
1111 3596 1.667830 CGAGCCGAGCCAAGTTCAA 60.668 57.895 0.00 0.00 0.00 2.69
1112 3597 2.048222 CGAGCCGAGCCAAGTTCA 60.048 61.111 0.00 0.00 0.00 3.18
1113 3598 1.627550 GAACGAGCCGAGCCAAGTTC 61.628 60.000 1.50 10.39 32.90 3.01
1114 3599 1.668151 GAACGAGCCGAGCCAAGTT 60.668 57.895 1.50 0.00 0.00 2.66
1115 3600 2.048127 GAACGAGCCGAGCCAAGT 60.048 61.111 1.50 0.00 0.00 3.16
1116 3601 2.048222 TGAACGAGCCGAGCCAAG 60.048 61.111 1.50 0.00 0.00 3.61
1117 3602 2.357034 GTGAACGAGCCGAGCCAA 60.357 61.111 1.50 0.00 0.00 4.52
1118 3603 4.717629 CGTGAACGAGCCGAGCCA 62.718 66.667 0.00 0.00 43.02 4.75
1119 3604 4.415332 TCGTGAACGAGCCGAGCC 62.415 66.667 0.50 0.00 44.22 4.70
1128 3613 1.125266 GCGTCGTCTTTCGTGAACG 59.875 57.895 0.00 0.00 39.24 3.95
1129 3614 1.125266 CGCGTCGTCTTTCGTGAAC 59.875 57.895 0.00 0.00 39.45 3.18
1130 3615 2.641783 GCGCGTCGTCTTTCGTGAA 61.642 57.895 8.43 0.00 39.45 3.18
1131 3616 3.095278 GCGCGTCGTCTTTCGTGA 61.095 61.111 8.43 0.00 39.45 4.35
1132 3617 4.449161 CGCGCGTCGTCTTTCGTG 62.449 66.667 24.19 0.00 40.80 4.35
1141 3626 1.574147 CATACACAAACGCGCGTCG 60.574 57.895 37.77 30.53 45.38 5.12
1142 3627 1.857426 GCATACACAAACGCGCGTC 60.857 57.895 37.77 16.63 0.00 5.19
1143 3628 2.172419 GCATACACAAACGCGCGT 59.828 55.556 32.73 32.73 0.00 6.01
1144 3629 2.932050 CGCATACACAAACGCGCG 60.932 61.111 30.96 30.96 41.38 6.86
1147 3632 3.181524 ACTGAATACGCATACACAAACGC 60.182 43.478 0.00 0.00 0.00 4.84
1148 3633 4.577687 ACTGAATACGCATACACAAACG 57.422 40.909 0.00 0.00 0.00 3.60
1149 3634 5.499652 CGGTACTGAATACGCATACACAAAC 60.500 44.000 0.00 0.00 34.22 2.93
1150 3635 4.563580 CGGTACTGAATACGCATACACAAA 59.436 41.667 0.00 0.00 34.22 2.83
1151 3636 4.106909 CGGTACTGAATACGCATACACAA 58.893 43.478 0.00 0.00 34.22 3.33
1152 3637 3.129113 ACGGTACTGAATACGCATACACA 59.871 43.478 9.17 0.00 34.22 3.72
1153 3638 3.699067 ACGGTACTGAATACGCATACAC 58.301 45.455 9.17 0.00 34.22 2.90
1154 3639 3.377798 TGACGGTACTGAATACGCATACA 59.622 43.478 9.17 0.00 34.22 2.29
1155 3640 3.727723 GTGACGGTACTGAATACGCATAC 59.272 47.826 9.17 0.00 34.22 2.39
1156 3641 3.377798 TGTGACGGTACTGAATACGCATA 59.622 43.478 9.17 0.00 34.22 3.14
1157 3642 2.164827 TGTGACGGTACTGAATACGCAT 59.835 45.455 9.17 0.00 34.22 4.73
1158 3643 1.540707 TGTGACGGTACTGAATACGCA 59.459 47.619 9.17 6.86 34.22 5.24
1159 3644 2.267188 TGTGACGGTACTGAATACGC 57.733 50.000 9.17 4.45 34.22 4.42
1160 3645 3.982701 TGTTTGTGACGGTACTGAATACG 59.017 43.478 9.17 0.00 34.22 3.06
1161 3646 5.407387 ACATGTTTGTGACGGTACTGAATAC 59.593 40.000 9.17 4.89 33.85 1.89
1162 3647 5.543714 ACATGTTTGTGACGGTACTGAATA 58.456 37.500 9.17 0.00 33.85 1.75
1163 3648 4.385825 ACATGTTTGTGACGGTACTGAAT 58.614 39.130 9.17 0.00 33.85 2.57
1164 3649 3.799366 ACATGTTTGTGACGGTACTGAA 58.201 40.909 9.17 0.00 33.85 3.02
1165 3650 3.462483 ACATGTTTGTGACGGTACTGA 57.538 42.857 9.17 0.00 33.85 3.41
1166 3651 3.558006 TGAACATGTTTGTGACGGTACTG 59.442 43.478 13.36 0.00 35.83 2.74
1167 3652 3.799366 TGAACATGTTTGTGACGGTACT 58.201 40.909 13.36 0.00 35.83 2.73
1168 3653 4.523813 CTTGAACATGTTTGTGACGGTAC 58.476 43.478 13.36 0.00 35.83 3.34
1169 3654 3.002862 GCTTGAACATGTTTGTGACGGTA 59.997 43.478 13.36 0.00 35.83 4.02
1189 3674 4.760047 GGCGGACCGTGTGATGCT 62.760 66.667 16.73 0.00 0.00 3.79
1281 3766 4.519350 TGTTGTGCCGTATCAAATGGTTTA 59.481 37.500 0.00 0.00 36.53 2.01
1283 3768 2.887783 TGTTGTGCCGTATCAAATGGTT 59.112 40.909 0.00 0.00 36.53 3.67
1368 3853 1.271325 TGAATGACAATGAGCCGTGGT 60.271 47.619 0.00 0.00 0.00 4.16
1371 3856 1.453155 GGTGAATGACAATGAGCCGT 58.547 50.000 0.00 0.00 0.00 5.68
1380 3865 8.544622 TGAAGTTAATATAGTGGGTGAATGACA 58.455 33.333 0.00 0.00 0.00 3.58
1381 3866 8.958119 TGAAGTTAATATAGTGGGTGAATGAC 57.042 34.615 0.00 0.00 0.00 3.06
1402 3887 0.824109 TGCTATGACCGGGACTGAAG 59.176 55.000 6.32 0.00 0.00 3.02
1405 3890 0.179100 CTGTGCTATGACCGGGACTG 60.179 60.000 6.32 0.00 0.00 3.51
1408 3893 1.327690 GGTCTGTGCTATGACCGGGA 61.328 60.000 6.32 0.00 42.51 5.14
1415 3900 4.613925 ATGACTATGGGTCTGTGCTATG 57.386 45.455 0.00 0.00 44.74 2.23
1430 3916 1.692762 GGGGCTGGAGGAGAATGACTA 60.693 57.143 0.00 0.00 0.00 2.59
1438 3924 0.254462 GAAGAAAGGGGCTGGAGGAG 59.746 60.000 0.00 0.00 0.00 3.69
1440 3926 0.034670 CAGAAGAAAGGGGCTGGAGG 60.035 60.000 0.00 0.00 0.00 4.30
1441 3927 0.695347 ACAGAAGAAAGGGGCTGGAG 59.305 55.000 0.00 0.00 32.82 3.86
1444 3930 1.818642 CTGACAGAAGAAAGGGGCTG 58.181 55.000 0.00 0.00 34.65 4.85
1445 3931 0.037447 GCTGACAGAAGAAAGGGGCT 59.963 55.000 6.65 0.00 0.00 5.19
1446 3932 0.250901 TGCTGACAGAAGAAAGGGGC 60.251 55.000 6.65 0.00 0.00 5.80
1448 3934 1.202806 TGGTGCTGACAGAAGAAAGGG 60.203 52.381 6.65 0.00 0.00 3.95
1449 3935 1.876156 GTGGTGCTGACAGAAGAAAGG 59.124 52.381 6.65 0.00 0.00 3.11
1462 3948 1.133976 GGCTATGATTGGAGTGGTGCT 60.134 52.381 0.00 0.00 0.00 4.40
1463 3949 1.133976 AGGCTATGATTGGAGTGGTGC 60.134 52.381 0.00 0.00 0.00 5.01
1471 3957 0.668706 CGCGAGGAGGCTATGATTGG 60.669 60.000 0.00 0.00 0.00 3.16
1474 3960 1.872197 GAGCGCGAGGAGGCTATGAT 61.872 60.000 12.10 0.00 40.16 2.45
1516 4002 0.539669 TCCTTCGTCTGCTCTGGTGA 60.540 55.000 0.00 0.00 0.00 4.02
1518 4004 0.827925 TGTCCTTCGTCTGCTCTGGT 60.828 55.000 0.00 0.00 0.00 4.00
1521 4007 1.674221 GCAATGTCCTTCGTCTGCTCT 60.674 52.381 0.00 0.00 0.00 4.09
1524 4010 0.445436 CAGCAATGTCCTTCGTCTGC 59.555 55.000 0.00 0.00 0.00 4.26
1571 4057 2.333926 CTGCGACAATACGTCCAAGAA 58.666 47.619 0.00 0.00 42.07 2.52
1596 4082 2.490217 CGGCGATGTCCTTCGTCT 59.510 61.111 0.00 0.00 41.43 4.18
1630 4116 2.105128 GGTCATGGCGACGGAGAG 59.895 66.667 0.00 0.00 46.42 3.20
1635 4121 2.431771 TTCGTGGTCATGGCGACG 60.432 61.111 26.26 26.26 46.42 5.12
1638 4124 3.499737 GGCTTCGTGGTCATGGCG 61.500 66.667 0.00 0.00 0.00 5.69
1643 4129 4.980805 GTGCCGGCTTCGTGGTCA 62.981 66.667 29.70 0.00 0.00 4.02
1676 4162 2.761208 ACTATTCTTACTCGCTGCTGGT 59.239 45.455 0.00 0.00 0.00 4.00
1679 4165 2.166459 TGCACTATTCTTACTCGCTGCT 59.834 45.455 0.00 0.00 0.00 4.24
1683 4169 3.458189 ACCATGCACTATTCTTACTCGC 58.542 45.455 0.00 0.00 0.00 5.03
1685 4171 6.163135 ACCTACCATGCACTATTCTTACTC 57.837 41.667 0.00 0.00 0.00 2.59
1709 4195 4.910585 GGGACCATAGCGGCGGTG 62.911 72.222 23.33 7.68 39.03 4.94
1719 4205 1.384191 GTGGCCTTTCTGGGACCAT 59.616 57.895 3.32 0.00 35.91 3.55
1817 4309 1.989508 CCCCATTGACCCAAAGGCC 60.990 63.158 0.00 0.00 31.72 5.19
1818 4310 0.835971 AACCCCATTGACCCAAAGGC 60.836 55.000 0.00 0.00 31.72 4.35
2088 4649 2.233922 ACAAATTCGATCGTCAGGAGGT 59.766 45.455 15.94 3.63 0.00 3.85
2117 4678 2.081161 GGATGCCATGGAGGAGGGT 61.081 63.158 18.40 0.00 41.22 4.34
2137 4698 6.875972 AATAGGACCTTAATATCTGGCGAT 57.124 37.500 0.00 0.00 0.00 4.58
2151 4712 7.504926 TTTACAGACCAATGTAATAGGACCT 57.495 36.000 0.00 0.00 43.30 3.85
2187 4748 9.716507 GTAAATTATGATGACTGCGTACAAAAT 57.283 29.630 0.00 0.00 0.00 1.82
2279 4843 6.097356 CACGCATAGTAAAAAGTACCAGAGA 58.903 40.000 0.00 0.00 0.00 3.10
2287 4851 8.995220 TCAAATCTTACACGCATAGTAAAAAGT 58.005 29.630 0.00 0.00 31.66 2.66
2313 4877 6.316890 TCAAACTTAACAAAGCTTACTTCGGT 59.683 34.615 0.00 0.00 34.05 4.69
2315 4879 6.631636 GGTCAAACTTAACAAAGCTTACTTCG 59.368 38.462 0.00 0.00 34.05 3.79
2479 5045 8.529476 CCTTCCATCTTTGATTTCTTTTCTCAT 58.471 33.333 0.00 0.00 0.00 2.90
2480 5046 7.725397 TCCTTCCATCTTTGATTTCTTTTCTCA 59.275 33.333 0.00 0.00 0.00 3.27
2481 5047 8.115490 TCCTTCCATCTTTGATTTCTTTTCTC 57.885 34.615 0.00 0.00 0.00 2.87
2482 5048 8.482852 TTCCTTCCATCTTTGATTTCTTTTCT 57.517 30.769 0.00 0.00 0.00 2.52
2483 5049 9.546428 TTTTCCTTCCATCTTTGATTTCTTTTC 57.454 29.630 0.00 0.00 0.00 2.29
2484 5050 9.551734 CTTTTCCTTCCATCTTTGATTTCTTTT 57.448 29.630 0.00 0.00 0.00 2.27
2485 5051 8.927411 TCTTTTCCTTCCATCTTTGATTTCTTT 58.073 29.630 0.00 0.00 0.00 2.52
2486 5052 8.482852 TCTTTTCCTTCCATCTTTGATTTCTT 57.517 30.769 0.00 0.00 0.00 2.52
2487 5053 8.482852 TTCTTTTCCTTCCATCTTTGATTTCT 57.517 30.769 0.00 0.00 0.00 2.52
2488 5054 9.716531 ATTTCTTTTCCTTCCATCTTTGATTTC 57.283 29.630 0.00 0.00 0.00 2.17
2510 5174 5.087391 AGACGTCTCCCTTTCCTTATTTC 57.913 43.478 13.58 0.00 0.00 2.17
2525 5189 2.678836 CGTCCAATCTCTGTAGACGTCT 59.321 50.000 23.66 23.66 43.89 4.18
3080 5753 1.153745 CAGTCGTCTAGGCAGTGGC 60.154 63.158 9.02 9.02 40.13 5.01
3475 6148 0.679640 CACGCAATCCCAGCCCTTAA 60.680 55.000 0.00 0.00 0.00 1.85
3597 6285 8.526147 AGGAAATCCACATTAGAAAACTGAATG 58.474 33.333 1.67 0.00 38.89 2.67
3803 6996 2.029649 GCTGTCGTTAGGTGGACTACAA 60.030 50.000 0.00 0.00 34.31 2.41
3823 7016 2.285488 GGCTCAATTTAGTGCTCGTAGC 59.715 50.000 0.58 0.58 42.82 3.58
3876 7069 4.961438 ACAATTTTTGCCTGACTCCATT 57.039 36.364 0.00 0.00 0.00 3.16
3893 7086 3.078837 CCCGGCTGTTTACTACAACAAT 58.921 45.455 0.00 0.00 36.22 2.71
3905 7098 2.342648 GACGACTTCCCGGCTGTT 59.657 61.111 0.00 0.00 34.11 3.16
3949 7142 4.271696 TCTCGATGATTGTTGTTCTGGT 57.728 40.909 0.00 0.00 0.00 4.00
3989 7182 5.239306 GTGTGTCTTCAAGTTGGATCATTCA 59.761 40.000 2.34 0.00 0.00 2.57
4101 7294 7.516198 AATGCATAGACATAAAAGGTGGATC 57.484 36.000 0.00 0.00 0.00 3.36
4155 7348 9.422196 CTACTCTAAGAAAACTTGACAAAAACG 57.578 33.333 0.00 0.00 0.00 3.60
4271 7473 6.038356 CGTTCCCTATTTAGTTGTCGTGTAT 58.962 40.000 0.00 0.00 0.00 2.29
4276 7478 3.518590 AGCGTTCCCTATTTAGTTGTCG 58.481 45.455 0.00 0.00 0.00 4.35
4355 7557 3.411446 TGATAAAGCAACCACCTGACAG 58.589 45.455 0.00 0.00 0.00 3.51
4397 7599 4.706035 ACATCAACAAACAACAATGGCAT 58.294 34.783 0.00 0.00 0.00 4.40
4399 7601 5.695816 ACATACATCAACAAACAACAATGGC 59.304 36.000 0.00 0.00 0.00 4.40
4445 7647 4.993584 GTGTTGATCCATATCGATGAGCTT 59.006 41.667 8.54 0.00 34.73 3.74


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

AutoCloner maintained by Alex Coulton.