Multiple sequence alignment - TraesCS4A01G420200

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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 TraesCS4A01G420200 chr4A 100.000 4163 0 0 1 4163 690939246 690935084 0.000000e+00 7688.0
1 TraesCS4A01G420200 chr4A 87.927 1201 75 31 403 1560 690690034 690688861 0.000000e+00 1351.0
2 TraesCS4A01G420200 chr4A 86.626 1159 86 18 2105 3233 690880414 690879295 0.000000e+00 1218.0
3 TraesCS4A01G420200 chr4A 87.578 966 78 29 982 1936 690881577 690880643 0.000000e+00 1081.0
4 TraesCS4A01G420200 chr4A 87.565 965 63 26 719 1672 691166227 691167145 0.000000e+00 1064.0
5 TraesCS4A01G420200 chr4A 89.488 723 53 17 966 1672 690887006 690886291 0.000000e+00 893.0
6 TraesCS4A01G420200 chr4A 86.529 824 81 15 2429 3233 690885093 690884281 0.000000e+00 880.0
7 TraesCS4A01G420200 chr4A 85.784 816 97 6 2382 3184 691168531 691169340 0.000000e+00 846.0
8 TraesCS4A01G420200 chr4A 81.494 924 97 47 992 1886 691246753 691247631 0.000000e+00 691.0
9 TraesCS4A01G420200 chr4A 81.358 869 105 28 2385 3233 691325139 691325970 0.000000e+00 654.0
10 TraesCS4A01G420200 chr4A 83.041 684 59 34 1204 1864 691150812 691151461 6.040000e-158 568.0
11 TraesCS4A01G420200 chr4A 85.714 532 58 15 95 613 691149893 691150419 2.830000e-151 545.0
12 TraesCS4A01G420200 chr4A 81.965 682 66 31 34 667 690882591 690881919 3.690000e-145 525.0
13 TraesCS4A01G420200 chr4A 89.851 335 19 3 4 323 690690469 690690135 2.320000e-112 416.0
14 TraesCS4A01G420200 chr4A 89.591 269 10 4 1670 1936 691167303 691167555 4.010000e-85 326.0
15 TraesCS4A01G420200 chr4A 87.372 293 19 5 34 323 690732544 690732267 1.870000e-83 320.0
16 TraesCS4A01G420200 chr4A 82.680 306 35 11 370 663 690732192 690731893 5.340000e-64 255.0
17 TraesCS4A01G420200 chr4A 93.939 165 10 0 367 531 691165741 691165905 2.480000e-62 250.0
18 TraesCS4A01G420200 chr4A 92.169 166 11 1 373 536 690887871 690887706 2.500000e-57 233.0
19 TraesCS4A01G420200 chr4A 89.385 179 10 3 676 848 690881789 690881614 2.520000e-52 217.0
20 TraesCS4A01G420200 chr4A 90.476 168 9 4 4000 4163 691155039 691155203 9.060000e-52 215.0
21 TraesCS4A01G420200 chr4A 85.308 211 21 7 666 873 691150412 691150615 4.220000e-50 209.0
22 TraesCS4A01G420200 chr4A 93.939 99 6 0 1670 1768 690886133 690886035 2.590000e-32 150.0
23 TraesCS4A01G420200 chr4A 93.617 94 5 1 1786 1879 690688716 690688624 5.610000e-29 139.0
24 TraesCS4A01G420200 chr4A 87.342 79 10 0 382 460 690882145 690882067 1.590000e-14 91.6
25 TraesCS4A01G420200 chr4A 94.000 50 3 0 3998 4047 690673042 690672993 4.460000e-10 76.8
26 TraesCS4A01G420200 chr4A 100.000 41 0 0 4000 4040 691170424 691170464 4.460000e-10 76.8
27 TraesCS4A01G420200 chr4A 100.000 31 0 0 531 561 691165920 691165950 1.620000e-04 58.4
28 TraesCS4A01G420200 chr4A 100.000 29 0 0 3943 3971 480535 480563 2.000000e-03 54.7
29 TraesCS4A01G420200 chr7D 86.559 1421 130 20 2105 3482 34446347 34447749 0.000000e+00 1509.0
30 TraesCS4A01G420200 chr7D 86.180 1288 92 48 678 1936 34444661 34445891 0.000000e+00 1314.0
31 TraesCS4A01G420200 chr7D 86.393 1242 79 48 681 1886 34077492 34076305 0.000000e+00 1275.0
32 TraesCS4A01G420200 chr7D 88.558 1075 73 25 681 1735 34152013 34150969 0.000000e+00 1258.0
33 TraesCS4A01G420200 chr7D 86.305 847 82 14 2407 3233 34074589 34073757 0.000000e+00 891.0
34 TraesCS4A01G420200 chr7D 82.882 923 73 30 997 1884 33754618 33755490 0.000000e+00 750.0
35 TraesCS4A01G420200 chr7D 81.325 830 109 21 2387 3191 34010950 34010142 2.110000e-177 632.0
36 TraesCS4A01G420200 chr7D 84.992 593 47 20 3576 4163 34146955 34146400 7.810000e-157 564.0
37 TraesCS4A01G420200 chr7D 86.717 527 36 15 39 533 34443991 34444515 4.700000e-154 555.0
38 TraesCS4A01G420200 chr7D 86.192 478 53 10 2888 3359 34149534 34149064 4.800000e-139 505.0
39 TraesCS4A01G420200 chr7D 84.952 525 44 14 2358 2864 34150026 34149519 2.230000e-137 499.0
40 TraesCS4A01G420200 chr7D 91.554 296 19 1 34 323 34078393 34078098 1.800000e-108 403.0
41 TraesCS4A01G420200 chr7D 94.378 249 7 3 75 323 34168930 34168689 3.930000e-100 375.0
42 TraesCS4A01G420200 chr7D 88.433 268 5 7 370 613 34078011 34077746 2.430000e-77 300.0
43 TraesCS4A01G420200 chr7D 83.680 337 20 10 370 675 34168598 34168266 6.810000e-73 285.0
44 TraesCS4A01G420200 chr7D 93.605 172 7 1 1769 1936 34150967 34150796 1.920000e-63 254.0
45 TraesCS4A01G420200 chr7D 80.460 261 14 13 386 613 34152421 34152165 9.260000e-37 165.0
46 TraesCS4A01G420200 chr7D 91.000 100 8 1 760 859 33754330 33754428 2.610000e-27 134.0
47 TraesCS4A01G420200 chr7D 94.000 50 2 1 675 724 34167839 34167791 1.610000e-09 75.0
48 TraesCS4A01G420200 chr7A 83.844 848 100 17 2407 3233 34518220 34517389 0.000000e+00 773.0
49 TraesCS4A01G420200 chr7A 82.604 914 76 38 1000 1875 34106557 34105689 0.000000e+00 730.0
50 TraesCS4A01G420200 chr7A 86.003 643 51 24 1260 1886 34519357 34518738 0.000000e+00 652.0
51 TraesCS4A01G420200 chr7A 85.741 526 38 20 676 1191 34519950 34519452 4.770000e-144 521.0
52 TraesCS4A01G420200 chr7A 95.595 227 8 2 98 323 34520621 34520396 3.060000e-96 363.0
53 TraesCS4A01G420200 chr7A 89.615 260 9 9 370 611 34520381 34520122 8.690000e-82 315.0
54 TraesCS4A01G420200 chr7A 85.263 285 27 10 40 323 34119507 34119237 3.170000e-71 279.0
55 TraesCS4A01G420200 chr7A 92.405 79 6 0 382 460 34520273 34520195 3.400000e-21 113.0
56 TraesCS4A01G420200 chr2B 92.228 193 13 1 1941 2131 569130986 569130794 5.300000e-69 272.0
57 TraesCS4A01G420200 chr4D 91.282 195 15 1 1939 2131 470124416 470124610 8.870000e-67 265.0
58 TraesCS4A01G420200 chr3B 90.674 193 17 1 1940 2131 518618200 518618392 5.340000e-64 255.0
59 TraesCS4A01G420200 chr7B 90.625 192 16 2 1942 2131 554524154 554524345 1.920000e-63 254.0
60 TraesCS4A01G420200 chr7B 89.055 201 19 2 1934 2131 88283918 88283718 3.210000e-61 246.0
61 TraesCS4A01G420200 chr3D 91.005 189 15 1 1945 2131 254079389 254079201 1.920000e-63 254.0
62 TraesCS4A01G420200 chr5B 90.155 193 18 1 1940 2131 262824401 262824593 2.480000e-62 250.0
63 TraesCS4A01G420200 chr4B 89.899 198 14 2 1936 2131 450686720 450686913 2.480000e-62 250.0
64 TraesCS4A01G420200 chr2D 90.526 190 16 1 1944 2131 82890011 82889822 2.480000e-62 250.0
65 TraesCS4A01G420200 chr2A 100.000 28 0 0 3944 3971 350359367 350359394 8.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G420200 chr4A 690935084 690939246 4162 True 7688.000000 7688 100.000000 1 4163 1 chr4A.!!$R2 4162
1 TraesCS4A01G420200 chr4A 691246753 691247631 878 False 691.000000 691 81.494000 992 1886 1 chr4A.!!$F2 894
2 TraesCS4A01G420200 chr4A 691325139 691325970 831 False 654.000000 654 81.358000 2385 3233 1 chr4A.!!$F3 848
3 TraesCS4A01G420200 chr4A 690688624 690690469 1845 True 635.333333 1351 90.465000 4 1879 3 chr4A.!!$R3 1875
4 TraesCS4A01G420200 chr4A 690879295 690887871 8576 True 587.622222 1218 88.335667 34 3233 9 chr4A.!!$R5 3199
5 TraesCS4A01G420200 chr4A 691165741 691170464 4723 False 436.866667 1064 92.813167 367 4040 6 chr4A.!!$F5 3673
6 TraesCS4A01G420200 chr4A 691149893 691155203 5310 False 384.250000 568 86.134750 95 4163 4 chr4A.!!$F4 4068
7 TraesCS4A01G420200 chr4A 690731893 690732544 651 True 287.500000 320 85.026000 34 663 2 chr4A.!!$R4 629
8 TraesCS4A01G420200 chr7D 34443991 34447749 3758 False 1126.000000 1509 86.485333 39 3482 3 chr7D.!!$F2 3443
9 TraesCS4A01G420200 chr7D 34073757 34078393 4636 True 717.250000 1275 88.171250 34 3233 4 chr7D.!!$R2 3199
10 TraesCS4A01G420200 chr7D 34010142 34010950 808 True 632.000000 632 81.325000 2387 3191 1 chr7D.!!$R1 804
11 TraesCS4A01G420200 chr7D 34146400 34152421 6021 True 540.833333 1258 86.459833 386 4163 6 chr7D.!!$R3 3777
12 TraesCS4A01G420200 chr7D 33754330 33755490 1160 False 442.000000 750 86.941000 760 1884 2 chr7D.!!$F1 1124
13 TraesCS4A01G420200 chr7D 34167791 34168930 1139 True 245.000000 375 90.686000 75 724 3 chr7D.!!$R4 649
14 TraesCS4A01G420200 chr7A 34105689 34106557 868 True 730.000000 730 82.604000 1000 1875 1 chr7A.!!$R1 875
15 TraesCS4A01G420200 chr7A 34517389 34520621 3232 True 456.166667 773 88.867167 98 3233 6 chr7A.!!$R3 3135

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
975 6929 0.104855 AGTGATCGCTGTGTGTGTGT 59.895 50.0 8.28 0.00 0.00 3.72 F
1152 7113 0.104304 ACGTCGACCTCAACAAGCTT 59.896 50.0 10.58 0.00 0.00 3.74 F
2018 9343 0.392336 TTGGTGCTCAATTGGTTGGC 59.608 50.0 5.42 6.19 35.99 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2122 9771 0.251916 TCGGTAATGGAGGTTGGCTG 59.748 55.0 0.0 0.0 0.00 4.85 R
2271 10210 0.321298 TTTCGCTGCAAGGTACTCCC 60.321 55.0 0.0 0.0 38.49 4.30 R
3783 14576 0.033504 AACTCGCCGAATGTGACACT 59.966 50.0 7.2 0.0 0.00 3.55 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
46 5294 9.197694 CAATTAATCAGGTCACAGCTATAGTAC 57.802 37.037 0.84 0.00 0.00 2.73
50 5298 2.959707 AGGTCACAGCTATAGTACAGCC 59.040 50.000 0.00 0.00 39.99 4.85
157 5405 3.846588 TCTAGTCTCCATCCTGGCTTTTT 59.153 43.478 0.00 0.00 37.47 1.94
168 5416 2.553028 CCTGGCTTTTTGCTCCTGTAGA 60.553 50.000 0.00 0.00 42.39 2.59
297 5555 6.429385 AGAAGTCAAGAAAGCTGTTCCATTAG 59.571 38.462 0.00 0.00 0.00 1.73
330 5652 0.112412 TCTTCCCTCCAACCAAAGGC 59.888 55.000 0.00 0.00 0.00 4.35
346 5668 0.675633 AGGCGAGCAATGCAACTTTT 59.324 45.000 8.35 0.00 0.00 2.27
348 5670 1.985684 GGCGAGCAATGCAACTTTTAC 59.014 47.619 8.35 0.00 0.00 2.01
349 5671 2.351738 GGCGAGCAATGCAACTTTTACT 60.352 45.455 8.35 0.00 0.00 2.24
350 5672 3.119990 GGCGAGCAATGCAACTTTTACTA 60.120 43.478 8.35 0.00 0.00 1.82
351 5673 3.846335 GCGAGCAATGCAACTTTTACTAC 59.154 43.478 8.35 0.00 0.00 2.73
354 5676 5.629079 AGCAATGCAACTTTTACTACTCC 57.371 39.130 8.35 0.00 0.00 3.85
355 5677 4.154195 AGCAATGCAACTTTTACTACTCCG 59.846 41.667 8.35 0.00 0.00 4.63
356 5678 4.083484 GCAATGCAACTTTTACTACTCCGT 60.083 41.667 0.00 0.00 0.00 4.69
357 5679 5.618561 CAATGCAACTTTTACTACTCCGTC 58.381 41.667 0.00 0.00 0.00 4.79
358 5680 4.325028 TGCAACTTTTACTACTCCGTCA 57.675 40.909 0.00 0.00 0.00 4.35
359 5681 4.890088 TGCAACTTTTACTACTCCGTCAT 58.110 39.130 0.00 0.00 0.00 3.06
360 5682 4.688879 TGCAACTTTTACTACTCCGTCATG 59.311 41.667 0.00 0.00 0.00 3.07
361 5683 4.435651 GCAACTTTTACTACTCCGTCATGC 60.436 45.833 0.00 0.00 0.00 4.06
363 5685 3.192001 ACTTTTACTACTCCGTCATGCGA 59.808 43.478 10.48 0.00 44.77 5.10
364 5686 4.142227 ACTTTTACTACTCCGTCATGCGAT 60.142 41.667 10.48 0.39 44.77 4.58
365 5687 3.620929 TTACTACTCCGTCATGCGATC 57.379 47.619 10.48 0.00 44.77 3.69
476 5816 5.506317 GCACACATCTTTTACTTTCTGCAGT 60.506 40.000 14.67 0.00 0.00 4.40
524 5899 2.096909 GTCAACCGTGAACATGAACGAG 60.097 50.000 17.57 11.80 42.32 4.18
533 5908 4.619336 GTGAACATGAACGAGAAGAGAGAC 59.381 45.833 0.00 0.00 0.00 3.36
561 5951 1.831389 CGACCGTTCCTGTTGCTGTG 61.831 60.000 0.00 0.00 0.00 3.66
626 6050 1.601162 GCCATGCATGCTGATTTACCG 60.601 52.381 21.69 4.60 0.00 4.02
632 6060 0.814010 ATGCTGATTTACCGGGCGAC 60.814 55.000 6.32 0.00 0.00 5.19
705 6598 0.401395 TCCCTCTCAAGGTTGGTGGT 60.401 55.000 0.00 0.00 41.59 4.16
716 6609 1.278413 GGTTGGTGGTACTTCTCCTCC 59.722 57.143 0.00 0.00 38.61 4.30
975 6929 0.104855 AGTGATCGCTGTGTGTGTGT 59.895 50.000 8.28 0.00 0.00 3.72
976 6930 0.233074 GTGATCGCTGTGTGTGTGTG 59.767 55.000 0.00 0.00 0.00 3.82
979 6933 0.389025 ATCGCTGTGTGTGTGTGAGA 59.611 50.000 0.00 0.00 0.00 3.27
980 6934 0.249031 TCGCTGTGTGTGTGTGAGAG 60.249 55.000 0.00 0.00 0.00 3.20
981 6935 0.249031 CGCTGTGTGTGTGTGAGAGA 60.249 55.000 0.00 0.00 0.00 3.10
1152 7113 0.104304 ACGTCGACCTCAACAAGCTT 59.896 50.000 10.58 0.00 0.00 3.74
1238 7230 0.524414 TGCACAATGCTAGCTTGCAG 59.476 50.000 26.13 16.67 46.71 4.41
1363 7364 2.105821 CCACAAGGACAAGAAGTACCCA 59.894 50.000 0.00 0.00 36.89 4.51
1414 7415 2.843545 GGGTTCTGGAAGGCCACA 59.156 61.111 5.01 0.00 39.92 4.17
1428 7429 4.722700 CACAGGCCGGGACAAGGG 62.723 72.222 8.08 0.00 0.00 3.95
1519 7532 0.603707 CACACGGCCACAAGTCTGAT 60.604 55.000 2.24 0.00 0.00 2.90
1685 7921 4.245660 ACTACTGTAGTACGTTGCGACTA 58.754 43.478 18.42 0.00 37.23 2.59
1889 8348 3.871485 TGATGCAATGGGTTAATTTGCC 58.129 40.909 0.00 0.00 43.91 4.52
1912 8376 2.229784 GTGGGAGCTGTGATTTCCTTTG 59.770 50.000 0.00 0.00 0.00 2.77
1937 9262 2.125673 CGGCGTCACGGAAAGGAT 60.126 61.111 0.00 0.00 0.00 3.24
1939 9264 1.143969 CGGCGTCACGGAAAGGATAC 61.144 60.000 0.00 0.00 0.00 2.24
1960 9285 5.161943 ACTAAGAGCCTAATTGGTTTCGT 57.838 39.130 0.00 0.00 38.35 3.85
1961 9286 4.935808 ACTAAGAGCCTAATTGGTTTCGTG 59.064 41.667 0.00 0.00 38.35 4.35
1968 9293 5.883673 AGCCTAATTGGTTTCGTGCTAATAA 59.116 36.000 0.00 0.00 38.35 1.40
1969 9294 6.546034 AGCCTAATTGGTTTCGTGCTAATAAT 59.454 34.615 0.00 0.00 38.35 1.28
1971 9296 7.167468 GCCTAATTGGTTTCGTGCTAATAATTG 59.833 37.037 0.00 0.00 38.35 2.32
1972 9297 7.647715 CCTAATTGGTTTCGTGCTAATAATTGG 59.352 37.037 0.00 0.00 0.00 3.16
2001 9326 5.463061 CCAATTGTTGGCAAGTCTAAGTTTG 59.537 40.000 0.00 0.00 45.17 2.93
2002 9327 4.647424 TTGTTGGCAAGTCTAAGTTTGG 57.353 40.909 0.00 0.00 0.00 3.28
2011 9336 5.507985 GCAAGTCTAAGTTTGGTGCTCAATT 60.508 40.000 0.00 0.00 34.98 2.32
2013 9338 4.520492 AGTCTAAGTTTGGTGCTCAATTGG 59.480 41.667 5.42 0.00 34.98 3.16
2018 9343 0.392336 TTGGTGCTCAATTGGTTGGC 59.608 50.000 5.42 6.19 35.99 4.52
2023 9348 2.754552 GTGCTCAATTGGTTGGCTATCA 59.245 45.455 5.42 0.00 35.99 2.15
2024 9349 3.193267 GTGCTCAATTGGTTGGCTATCAA 59.807 43.478 5.42 0.00 35.99 2.57
2032 9357 7.427989 AATTGGTTGGCTATCAATTGATTCT 57.572 32.000 25.26 5.76 38.97 2.40
2037 9362 3.638160 TGGCTATCAATTGATTCTTGCCC 59.362 43.478 29.82 20.60 36.06 5.36
2038 9363 3.638160 GGCTATCAATTGATTCTTGCCCA 59.362 43.478 25.26 4.79 36.05 5.36
2040 9365 4.500375 GCTATCAATTGATTCTTGCCCACC 60.500 45.833 25.26 0.00 36.05 4.61
2041 9366 3.173953 TCAATTGATTCTTGCCCACCT 57.826 42.857 3.38 0.00 0.00 4.00
2042 9367 3.091545 TCAATTGATTCTTGCCCACCTC 58.908 45.455 3.38 0.00 0.00 3.85
2044 9369 2.496899 TTGATTCTTGCCCACCTCTC 57.503 50.000 0.00 0.00 0.00 3.20
2045 9370 1.361204 TGATTCTTGCCCACCTCTCA 58.639 50.000 0.00 0.00 0.00 3.27
2047 9372 2.108075 TGATTCTTGCCCACCTCTCAAA 59.892 45.455 0.00 0.00 0.00 2.69
2050 9375 2.586425 TCTTGCCCACCTCTCAAAAAG 58.414 47.619 0.00 0.00 0.00 2.27
2051 9376 2.091885 TCTTGCCCACCTCTCAAAAAGT 60.092 45.455 0.00 0.00 0.00 2.66
2052 9377 2.452600 TGCCCACCTCTCAAAAAGTT 57.547 45.000 0.00 0.00 0.00 2.66
2054 9379 4.112634 TGCCCACCTCTCAAAAAGTTAT 57.887 40.909 0.00 0.00 0.00 1.89
2057 9382 4.522789 GCCCACCTCTCAAAAAGTTATCAA 59.477 41.667 0.00 0.00 0.00 2.57
2060 9385 7.670364 CCCACCTCTCAAAAAGTTATCAATTT 58.330 34.615 0.00 0.00 0.00 1.82
2061 9386 8.150296 CCCACCTCTCAAAAAGTTATCAATTTT 58.850 33.333 0.00 0.00 0.00 1.82
2073 9398 9.786105 AAAGTTATCAATTTTTGGCAACTTTTG 57.214 25.926 17.49 4.21 43.86 2.44
2074 9399 7.929159 AGTTATCAATTTTTGGCAACTTTTGG 58.071 30.769 0.00 0.00 33.97 3.28
2076 9401 6.772360 ATCAATTTTTGGCAACTTTTGGTT 57.228 29.167 0.00 0.00 38.93 3.67
2079 9404 6.865205 TCAATTTTTGGCAACTTTTGGTTTTG 59.135 30.769 0.00 0.00 35.74 2.44
2097 9746 4.662468 TTTGCCAAATGTTAGCTTGTCA 57.338 36.364 0.00 0.00 0.00 3.58
2106 9755 7.201548 CCAAATGTTAGCTTGTCAAATATTGGC 60.202 37.037 0.00 0.00 35.37 4.52
2107 9756 5.973899 TGTTAGCTTGTCAAATATTGGCA 57.026 34.783 0.00 0.00 44.76 4.92
2253 10192 5.414789 TGAGATCCATCGACAAACCTTTA 57.585 39.130 0.00 0.00 0.00 1.85
2271 10210 1.103803 TAGAGCTGGCTTCGGTAGTG 58.896 55.000 0.00 0.00 0.00 2.74
2282 10254 1.843368 TCGGTAGTGGGAGTACCTTG 58.157 55.000 0.00 0.00 41.09 3.61
2363 10531 7.984391 TCACATGTAATTAAGCACATCGATTT 58.016 30.769 0.00 0.00 33.12 2.17
2419 10659 3.149981 TGTAAATGAATTGGCGGTGTCA 58.850 40.909 0.00 0.00 0.00 3.58
2421 10661 3.508744 AAATGAATTGGCGGTGTCATC 57.491 42.857 0.00 0.00 30.45 2.92
2709 10985 2.230992 GCTCGATCACATCCTCAGCTAT 59.769 50.000 0.00 0.00 0.00 2.97
2794 11076 1.021390 GCTGGACCACCTGATCAACG 61.021 60.000 0.00 0.00 37.31 4.10
2959 11241 1.140804 GAGCTCAACGGCCTCTCTC 59.859 63.158 9.40 0.00 0.00 3.20
2964 11246 2.203788 AACGGCCTCTCTCACCCA 60.204 61.111 0.00 0.00 0.00 4.51
2976 11258 3.055719 CACCCAGCGTCGGCAAAT 61.056 61.111 0.00 0.00 43.41 2.32
3042 11327 4.051167 TCCTACTCCGGCGGTGGA 62.051 66.667 29.03 24.71 36.37 4.02
3130 11416 2.884087 ATCGCTACACGCCGACTTGG 62.884 60.000 0.00 0.00 43.23 3.61
3159 11445 2.478894 CTGTTTTAACGCTGTCGGATGT 59.521 45.455 0.00 0.00 40.69 3.06
3171 11457 1.044611 TCGGATGTTGACACTGTCCA 58.955 50.000 6.72 0.00 31.97 4.02
3284 11631 5.016051 ACGAGATGCAGAGTGAATATGTT 57.984 39.130 0.00 0.00 0.00 2.71
3361 11951 2.765502 AGGAGGTCCTATCCAAAGACC 58.234 52.381 0.00 0.03 46.48 3.85
3435 12349 2.624316 ACTTTGCTGCAATGATGACG 57.376 45.000 28.20 9.92 0.00 4.35
3441 12355 1.268386 GCTGCAATGATGACGATGTGG 60.268 52.381 0.00 0.00 0.00 4.17
3469 12757 1.839424 CTCTTTGGACCATGGGTTCC 58.161 55.000 18.09 15.44 35.25 3.62
3492 12780 5.292834 CCAAACAGTAGCTATGTGTCATCTG 59.707 44.000 11.07 7.07 0.00 2.90
3495 12783 5.414360 ACAGTAGCTATGTGTCATCTGTTG 58.586 41.667 0.00 0.00 32.15 3.33
3498 12786 7.147828 ACAGTAGCTATGTGTCATCTGTTGTAT 60.148 37.037 0.00 0.00 32.15 2.29
3499 12787 7.168804 CAGTAGCTATGTGTCATCTGTTGTATG 59.831 40.741 0.00 0.00 0.00 2.39
3509 12797 5.633601 GTCATCTGTTGTATGTCGTTCTTCA 59.366 40.000 0.00 0.00 0.00 3.02
3515 12803 7.328493 TCTGTTGTATGTCGTTCTTCAATACAG 59.672 37.037 0.00 0.00 0.00 2.74
3517 12805 7.328493 TGTTGTATGTCGTTCTTCAATACAGAG 59.672 37.037 0.00 0.00 0.00 3.35
3540 12840 9.761504 AGAGATGTCTAACATTATTGTGATCAG 57.238 33.333 0.00 0.00 39.27 2.90
3545 12845 9.283768 TGTCTAACATTATTGTGATCAGTTTGT 57.716 29.630 0.00 0.00 35.83 2.83
3561 12861 6.887368 TCAGTTTGTTGTAATTCTCGATGTG 58.113 36.000 0.00 0.00 0.00 3.21
3565 12865 7.643764 AGTTTGTTGTAATTCTCGATGTGTTTG 59.356 33.333 0.00 0.00 0.00 2.93
3566 12866 6.612247 TGTTGTAATTCTCGATGTGTTTGT 57.388 33.333 0.00 0.00 0.00 2.83
3567 12867 6.655062 TGTTGTAATTCTCGATGTGTTTGTC 58.345 36.000 0.00 0.00 0.00 3.18
3568 12868 5.856126 TGTAATTCTCGATGTGTTTGTCC 57.144 39.130 0.00 0.00 0.00 4.02
3570 12870 5.637810 TGTAATTCTCGATGTGTTTGTCCTC 59.362 40.000 0.00 0.00 0.00 3.71
3571 12871 2.347697 TCTCGATGTGTTTGTCCTCG 57.652 50.000 0.00 0.00 0.00 4.63
3573 12873 1.721389 CTCGATGTGTTTGTCCTCGTG 59.279 52.381 0.00 0.00 0.00 4.35
3575 12875 1.192312 CGATGTGTTTGTCCTCGTGTG 59.808 52.381 0.00 0.00 0.00 3.82
3577 12877 2.613026 TGTGTTTGTCCTCGTGTGAT 57.387 45.000 0.00 0.00 0.00 3.06
3578 12878 2.209273 TGTGTTTGTCCTCGTGTGATG 58.791 47.619 0.00 0.00 0.00 3.07
3580 12880 2.221055 GTGTTTGTCCTCGTGTGATGAC 59.779 50.000 0.00 0.00 39.41 3.06
3583 12883 0.541998 TGTCCTCGTGTGATGACCCT 60.542 55.000 0.00 0.00 38.54 4.34
3591 14384 1.531149 GTGTGATGACCCTTTGACACG 59.469 52.381 0.00 0.00 0.00 4.49
3595 14388 0.320421 ATGACCCTTTGACACGGACG 60.320 55.000 0.00 0.00 0.00 4.79
3596 14389 1.666872 GACCCTTTGACACGGACGG 60.667 63.158 0.00 0.00 0.00 4.79
3622 14415 1.746991 GCCCTGGCACTCAGCTTAC 60.747 63.158 2.58 0.00 44.79 2.34
3701 14494 5.802451 GGCTACTACTTTTTACTCGGTGTAC 59.198 44.000 0.00 0.00 0.00 2.90
3705 14498 5.772169 ACTACTTTTTACTCGGTGTACCTCT 59.228 40.000 0.00 0.00 0.00 3.69
3713 14506 1.289109 CGGTGTACCTCTTTGCCGTG 61.289 60.000 0.00 0.00 35.11 4.94
3716 14509 0.319211 TGTACCTCTTTGCCGTGTCG 60.319 55.000 0.00 0.00 0.00 4.35
3725 14518 3.185594 TCTTTGCCGTGTCGATAACAAAG 59.814 43.478 19.05 19.05 43.23 2.77
3729 14522 2.929592 GCCGTGTCGATAACAAAGACCT 60.930 50.000 0.00 0.00 40.31 3.85
3730 14523 2.666508 CCGTGTCGATAACAAAGACCTG 59.333 50.000 0.00 0.00 40.31 4.00
3733 14526 2.037902 TGTCGATAACAAAGACCTGCCA 59.962 45.455 0.00 0.00 34.03 4.92
3735 14528 1.737793 CGATAACAAAGACCTGCCACC 59.262 52.381 0.00 0.00 0.00 4.61
3736 14529 2.615493 CGATAACAAAGACCTGCCACCT 60.615 50.000 0.00 0.00 0.00 4.00
3745 14538 3.384168 AGACCTGCCACCTATGTTCATA 58.616 45.455 0.00 0.00 0.00 2.15
3746 14539 3.780294 AGACCTGCCACCTATGTTCATAA 59.220 43.478 0.00 0.00 0.00 1.90
3761 14554 9.698309 CTATGTTCATAAACTGTCTGGGTATAG 57.302 37.037 0.00 0.00 36.30 1.31
3765 14558 5.606749 TCATAAACTGTCTGGGTATAGGCAT 59.393 40.000 0.00 0.00 30.88 4.40
3777 14570 2.775911 ATAGGCATAGTGCGCATCAT 57.224 45.000 15.91 7.18 46.21 2.45
3779 14572 0.107268 AGGCATAGTGCGCATCATCA 59.893 50.000 15.91 0.00 46.21 3.07
3781 14574 0.236711 GCATAGTGCGCATCATCACC 59.763 55.000 15.91 0.00 31.71 4.02
3782 14575 0.509929 CATAGTGCGCATCATCACCG 59.490 55.000 15.91 0.00 33.90 4.94
3783 14576 0.389025 ATAGTGCGCATCATCACCGA 59.611 50.000 15.91 0.00 33.90 4.69
3804 14597 1.132640 GTCACATTCGGCGAGTTGC 59.867 57.895 10.46 0.00 45.38 4.17
3846 14639 1.003355 CCGAGTGGATTGCACACCT 60.003 57.895 11.08 0.00 39.63 4.00
3885 14678 3.049206 CTGTTGTGTTAATTTGCCGGTG 58.951 45.455 1.90 0.00 0.00 4.94
3890 14683 3.252215 TGTGTTAATTTGCCGGTGAGAAG 59.748 43.478 1.90 0.00 0.00 2.85
3902 14695 2.613977 CGGTGAGAAGGCATGAGAGTTT 60.614 50.000 0.00 0.00 0.00 2.66
3947 14740 9.234384 CGAGTTCTGTCGATATTAAATTGTACT 57.766 33.333 0.00 0.00 42.85 2.73
3950 14743 9.530633 GTTCTGTCGATATTAAATTGTACTCCT 57.469 33.333 0.00 0.00 0.00 3.69
3953 14746 8.570096 TGTCGATATTAAATTGTACTCCTTCG 57.430 34.615 0.00 0.00 0.00 3.79
3961 14754 9.729281 ATTAAATTGTACTCCTTCGGTAAAGAA 57.271 29.630 0.00 0.00 37.12 2.52
3971 14764 8.979534 ACTCCTTCGGTAAAGAAATATAAGAGT 58.020 33.333 0.00 0.00 37.12 3.24
3991 14784 8.608844 AAGAGTGTTCTTACATTCCTTTACAG 57.391 34.615 0.00 0.00 41.82 2.74
4042 14835 6.223852 TCTATCTTCGCTTGTTTCTGAAACT 58.776 36.000 27.75 11.51 41.90 2.66
4053 14850 8.186821 GCTTGTTTCTGAAACTAGATATTGCAT 58.813 33.333 33.41 0.00 43.74 3.96
4066 14863 8.760735 ACTAGATATTGCATAGCTGATGATCTT 58.239 33.333 0.00 0.00 37.82 2.40
4067 14864 7.851387 AGATATTGCATAGCTGATGATCTTG 57.149 36.000 0.00 0.00 37.82 3.02
4105 14902 3.007398 CACCAGCAGAGAGGTTTTCTACT 59.993 47.826 0.00 0.00 35.87 2.57
4107 14904 4.221041 ACCAGCAGAGAGGTTTTCTACTAC 59.779 45.833 0.00 0.00 35.87 2.73
4108 14905 4.220821 CCAGCAGAGAGGTTTTCTACTACA 59.779 45.833 0.00 0.00 35.87 2.74
4109 14906 5.164954 CAGCAGAGAGGTTTTCTACTACAC 58.835 45.833 0.00 0.00 35.87 2.90
4114 14911 5.780793 AGAGAGGTTTTCTACTACACACCAT 59.219 40.000 0.00 0.00 35.87 3.55
4130 14927 3.243873 ACACCATATCAGGTAGCACATCG 60.244 47.826 0.00 0.00 40.77 3.84
4139 14936 4.629634 TCAGGTAGCACATCGTTAAACATG 59.370 41.667 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.921896 ACCAAGGCTGCAGATGGTAT 59.078 50.000 27.73 12.14 44.11 2.73
2 3 3.174313 ACCAAGGCTGCAGATGGT 58.826 55.556 25.06 25.06 41.25 3.55
14 15 5.392380 GCTGTGACCTGATTAATTGACCAAG 60.392 44.000 0.00 0.00 0.00 3.61
46 5294 4.397103 TGCTGTCTTTGATATTTCAGGCTG 59.603 41.667 8.58 8.58 32.27 4.85
50 5298 4.495349 CGGCTGCTGTCTTTGATATTTCAG 60.495 45.833 0.00 0.00 32.27 3.02
64 5312 1.598130 GGAGAACAACGGCTGCTGT 60.598 57.895 8.62 8.62 0.00 4.40
157 5405 1.279271 GCTTTTCCCTCTACAGGAGCA 59.721 52.381 0.00 0.00 43.65 4.26
168 5416 1.734655 TCTGTCTCCTGCTTTTCCCT 58.265 50.000 0.00 0.00 0.00 4.20
330 5652 5.283060 AGTAGTAAAAGTTGCATTGCTCG 57.717 39.130 10.49 0.00 0.00 5.03
349 5671 7.482156 AGGTACTAGATCGCATGACGGAGTA 62.482 48.000 0.00 4.21 38.04 2.59
350 5672 6.793837 AGGTACTAGATCGCATGACGGAGT 62.794 50.000 0.00 5.06 41.75 3.85
351 5673 2.095668 GGTACTAGATCGCATGACGGAG 60.096 54.545 0.00 0.00 43.89 4.63
354 5676 3.243101 ACAAGGTACTAGATCGCATGACG 60.243 47.826 0.00 0.00 38.49 4.35
355 5677 4.045104 CACAAGGTACTAGATCGCATGAC 58.955 47.826 0.00 0.00 38.49 3.06
356 5678 3.068165 CCACAAGGTACTAGATCGCATGA 59.932 47.826 0.00 0.00 38.49 3.07
357 5679 3.068165 TCCACAAGGTACTAGATCGCATG 59.932 47.826 0.00 0.00 38.49 4.06
358 5680 3.296854 TCCACAAGGTACTAGATCGCAT 58.703 45.455 0.00 0.00 38.49 4.73
359 5681 2.730382 TCCACAAGGTACTAGATCGCA 58.270 47.619 0.00 0.00 38.49 5.10
360 5682 3.130693 AGTTCCACAAGGTACTAGATCGC 59.869 47.826 0.00 0.00 42.95 4.58
361 5683 4.985538 AGTTCCACAAGGTACTAGATCG 57.014 45.455 0.00 0.00 42.95 3.69
363 5685 6.875972 ATCAAGTTCCACAAGGTACTAGAT 57.124 37.500 0.00 0.00 43.85 1.98
364 5686 6.681729 AATCAAGTTCCACAAGGTACTAGA 57.318 37.500 0.00 0.00 43.85 2.43
365 5687 6.371825 GGAAATCAAGTTCCACAAGGTACTAG 59.628 42.308 4.43 0.00 43.85 2.57
524 5899 4.109050 GGTCGATCAATGTGTCTCTCTTC 58.891 47.826 0.00 0.00 0.00 2.87
533 5908 1.660607 CAGGAACGGTCGATCAATGTG 59.339 52.381 0.00 0.00 0.00 3.21
561 5951 1.738099 AGCACCGTCGATCAGCAAC 60.738 57.895 0.00 0.00 0.00 4.17
616 6040 3.700961 CGTCGCCCGGTAAATCAG 58.299 61.111 0.00 0.00 0.00 2.90
639 6073 0.460987 GAACTGATCCCCTCTGCGTG 60.461 60.000 0.00 0.00 0.00 5.34
705 6598 1.815003 GTTCGTTCGGGAGGAGAAGTA 59.185 52.381 0.00 0.00 0.00 2.24
716 6609 3.500982 TGGATTAGTTACGTTCGTTCGG 58.499 45.455 2.62 0.00 34.94 4.30
781 6682 1.269517 GCAAGGAAACAATGGCAACGA 60.270 47.619 0.00 0.00 42.51 3.85
975 6929 2.370349 GACGGGTGAATCTCTCTCTCA 58.630 52.381 0.00 0.00 0.00 3.27
976 6930 1.332375 CGACGGGTGAATCTCTCTCTC 59.668 57.143 0.00 0.00 0.00 3.20
979 6933 1.096416 GTCGACGGGTGAATCTCTCT 58.904 55.000 0.00 0.00 0.00 3.10
980 6934 0.100861 GGTCGACGGGTGAATCTCTC 59.899 60.000 9.92 0.00 0.00 3.20
981 6935 0.611062 TGGTCGACGGGTGAATCTCT 60.611 55.000 9.92 0.00 0.00 3.10
1122 7083 2.360225 TCGACGTCGGGGATGACA 60.360 61.111 35.05 12.79 38.84 3.58
1152 7113 0.256752 CTTGGATGTCCCATGGCTCA 59.743 55.000 6.09 7.91 46.10 4.26
1238 7230 3.814005 ATGAACCCATGAGTACGTACC 57.186 47.619 21.80 13.64 0.00 3.34
1312 7313 3.864686 CAATCGTTCTGCGGGCCG 61.865 66.667 24.35 24.35 41.72 6.13
1327 7328 0.840617 TGTGGCTGAACAGGTACCAA 59.159 50.000 15.94 0.00 30.82 3.67
1519 7532 1.470805 CGGTACTCGTGCATGATCCAA 60.471 52.381 9.53 0.00 0.00 3.53
1763 8026 7.642978 CCACGTGTACATACATAGAAAGAGTAC 59.357 40.741 15.65 0.00 38.63 2.73
1766 8029 5.459107 GCCACGTGTACATACATAGAAAGAG 59.541 44.000 15.65 0.00 38.63 2.85
1767 8030 5.105675 TGCCACGTGTACATACATAGAAAGA 60.106 40.000 15.65 0.00 38.63 2.52
1889 8348 1.004044 AGGAAATCACAGCTCCCACTG 59.996 52.381 0.00 0.00 43.59 3.66
1937 9262 6.103997 CACGAAACCAATTAGGCTCTTAGTA 58.896 40.000 0.00 0.00 43.14 1.82
1939 9264 4.201822 GCACGAAACCAATTAGGCTCTTAG 60.202 45.833 0.00 0.00 43.14 2.18
1947 9272 7.167468 GCCAATTATTAGCACGAAACCAATTAG 59.833 37.037 0.00 0.00 0.00 1.73
1948 9273 6.975772 GCCAATTATTAGCACGAAACCAATTA 59.024 34.615 0.00 0.00 0.00 1.40
1955 9280 4.358851 GCATGCCAATTATTAGCACGAAA 58.641 39.130 6.36 0.00 39.77 3.46
1957 9282 2.293122 GGCATGCCAATTATTAGCACGA 59.707 45.455 32.08 0.00 39.77 4.35
1979 9304 5.128663 ACCAAACTTAGACTTGCCAACAATT 59.871 36.000 0.00 0.00 34.61 2.32
1981 9306 4.020543 ACCAAACTTAGACTTGCCAACAA 58.979 39.130 0.00 0.00 0.00 2.83
1983 9308 3.795488 GCACCAAACTTAGACTTGCCAAC 60.795 47.826 0.00 0.00 0.00 3.77
1986 9311 2.226674 GAGCACCAAACTTAGACTTGCC 59.773 50.000 0.00 0.00 0.00 4.52
1987 9312 2.878406 TGAGCACCAAACTTAGACTTGC 59.122 45.455 0.00 0.00 0.00 4.01
1988 9313 5.695851 ATTGAGCACCAAACTTAGACTTG 57.304 39.130 0.00 0.00 38.43 3.16
1990 9315 4.520492 CCAATTGAGCACCAAACTTAGACT 59.480 41.667 7.12 0.00 38.43 3.24
1992 9317 4.469657 ACCAATTGAGCACCAAACTTAGA 58.530 39.130 7.12 0.00 38.43 2.10
1993 9318 4.853924 ACCAATTGAGCACCAAACTTAG 57.146 40.909 7.12 0.00 38.43 2.18
1994 9319 4.202202 CCAACCAATTGAGCACCAAACTTA 60.202 41.667 7.12 0.00 38.15 2.24
1996 9321 2.102925 CCAACCAATTGAGCACCAAACT 59.897 45.455 7.12 0.00 38.15 2.66
2001 9326 1.544724 TAGCCAACCAATTGAGCACC 58.455 50.000 7.12 0.00 38.15 5.01
2002 9327 2.754552 TGATAGCCAACCAATTGAGCAC 59.245 45.455 7.12 1.97 38.15 4.40
2011 9336 5.394443 GCAAGAATCAATTGATAGCCAACCA 60.394 40.000 21.00 0.00 37.63 3.67
2013 9338 5.045872 GGCAAGAATCAATTGATAGCCAAC 58.954 41.667 29.78 17.37 37.81 3.77
2018 9343 4.891756 AGGTGGGCAAGAATCAATTGATAG 59.108 41.667 21.00 12.26 33.73 2.08
2023 9348 3.245371 TGAGAGGTGGGCAAGAATCAATT 60.245 43.478 0.00 0.00 0.00 2.32
2024 9349 2.309755 TGAGAGGTGGGCAAGAATCAAT 59.690 45.455 0.00 0.00 0.00 2.57
2027 9352 2.496899 TTGAGAGGTGGGCAAGAATC 57.503 50.000 0.00 0.00 0.00 2.52
2028 9353 2.978156 TTTGAGAGGTGGGCAAGAAT 57.022 45.000 0.00 0.00 0.00 2.40
2032 9357 2.452600 ACTTTTTGAGAGGTGGGCAA 57.547 45.000 0.00 0.00 0.00 4.52
2044 9369 9.786105 AAGTTGCCAAAAATTGATAACTTTTTG 57.214 25.926 10.17 10.17 45.38 2.44
2047 9372 9.786105 CAAAAGTTGCCAAAAATTGATAACTTT 57.214 25.926 19.69 19.69 46.26 2.66
2050 9375 7.702386 ACCAAAAGTTGCCAAAAATTGATAAC 58.298 30.769 0.00 0.00 0.00 1.89
2051 9376 7.872113 ACCAAAAGTTGCCAAAAATTGATAA 57.128 28.000 0.00 0.00 0.00 1.75
2052 9377 7.872113 AACCAAAAGTTGCCAAAAATTGATA 57.128 28.000 0.00 0.00 37.29 2.15
2054 9379 6.581171 AAACCAAAAGTTGCCAAAAATTGA 57.419 29.167 0.00 0.00 39.19 2.57
2057 9382 5.167121 GCAAAACCAAAAGTTGCCAAAAAT 58.833 33.333 0.00 0.00 41.41 1.82
2060 9385 3.839051 GCAAAACCAAAAGTTGCCAAA 57.161 38.095 0.00 0.00 41.41 3.28
2072 9397 9.886657 TTGACAAGCTAACATTTGGCAAAACCA 62.887 37.037 17.70 2.03 46.29 3.67
2073 9398 4.126437 ACAAGCTAACATTTGGCAAAACC 58.874 39.130 17.70 2.25 39.92 3.27
2074 9399 4.808364 TGACAAGCTAACATTTGGCAAAAC 59.192 37.500 17.70 2.92 39.27 2.43
2076 9401 4.662468 TGACAAGCTAACATTTGGCAAA 57.338 36.364 16.01 16.01 39.27 3.68
2079 9404 7.201548 CCAATATTTGACAAGCTAACATTTGGC 60.202 37.037 0.00 0.00 37.42 4.52
2081 9406 7.331440 TGCCAATATTTGACAAGCTAACATTTG 59.669 33.333 0.00 0.00 0.00 2.32
2087 9412 5.811613 GCATTGCCAATATTTGACAAGCTAA 59.188 36.000 0.00 0.00 36.48 3.09
2088 9413 5.350633 GCATTGCCAATATTTGACAAGCTA 58.649 37.500 0.00 0.00 36.48 3.32
2089 9414 4.186159 GCATTGCCAATATTTGACAAGCT 58.814 39.130 0.00 0.00 36.48 3.74
2090 9415 4.525411 GCATTGCCAATATTTGACAAGC 57.475 40.909 0.00 0.00 36.48 4.01
2113 9762 0.752658 GAGGTTGGCTGCCAAAGTTT 59.247 50.000 33.75 19.42 45.73 2.66
2114 9763 1.115326 GGAGGTTGGCTGCCAAAGTT 61.115 55.000 33.75 21.80 45.73 2.66
2115 9764 1.531602 GGAGGTTGGCTGCCAAAGT 60.532 57.895 33.75 23.70 45.73 2.66
2116 9765 0.901580 ATGGAGGTTGGCTGCCAAAG 60.902 55.000 33.75 0.00 45.73 2.77
2121 9770 1.376609 CGGTAATGGAGGTTGGCTGC 61.377 60.000 0.00 0.00 0.00 5.25
2122 9771 0.251916 TCGGTAATGGAGGTTGGCTG 59.748 55.000 0.00 0.00 0.00 4.85
2123 9772 0.541863 CTCGGTAATGGAGGTTGGCT 59.458 55.000 0.00 0.00 0.00 4.75
2124 9773 1.095807 GCTCGGTAATGGAGGTTGGC 61.096 60.000 0.00 0.00 32.10 4.52
2125 9774 0.810031 CGCTCGGTAATGGAGGTTGG 60.810 60.000 0.00 0.00 32.10 3.77
2194 10104 3.138304 GCATGTACGCCCTTTATCATGA 58.862 45.455 0.00 0.00 35.98 3.07
2195 10105 2.877786 TGCATGTACGCCCTTTATCATG 59.122 45.455 0.00 0.00 36.68 3.07
2196 10106 3.207265 TGCATGTACGCCCTTTATCAT 57.793 42.857 0.00 0.00 0.00 2.45
2197 10107 2.700722 TGCATGTACGCCCTTTATCA 57.299 45.000 0.00 0.00 0.00 2.15
2253 10192 1.608717 CCACTACCGAAGCCAGCTCT 61.609 60.000 0.00 0.00 0.00 4.09
2271 10210 0.321298 TTTCGCTGCAAGGTACTCCC 60.321 55.000 0.00 0.00 38.49 4.30
2282 10254 1.052287 CGGTGTTGAATTTTCGCTGC 58.948 50.000 0.00 0.00 0.00 5.25
2340 10489 9.109393 AGTAAATCGATGTGCTTAATTACATGT 57.891 29.630 2.69 2.69 37.63 3.21
2356 10505 6.237861 GCTACAAAGAGCGAAAGTAAATCGAT 60.238 38.462 0.00 0.00 42.76 3.59
2419 10659 2.159184 CCTGCGCATATCATACGGAGAT 60.159 50.000 12.24 0.00 46.54 2.75
2421 10661 1.067565 ACCTGCGCATATCATACGGAG 60.068 52.381 12.24 0.00 43.74 4.63
2694 10970 2.568956 GCCCATATAGCTGAGGATGTGA 59.431 50.000 0.00 0.00 0.00 3.58
2709 10985 2.828868 GTGGATGAGCGGCCCATA 59.171 61.111 0.00 0.00 31.94 2.74
2823 11105 4.806247 AGCTTCATGAACTTATCGTACTGC 59.194 41.667 3.38 1.94 0.00 4.40
2824 11106 5.460419 GGAGCTTCATGAACTTATCGTACTG 59.540 44.000 3.38 0.00 0.00 2.74
2825 11107 5.452077 GGGAGCTTCATGAACTTATCGTACT 60.452 44.000 3.38 0.00 0.00 2.73
2832 11114 2.354704 CGGTGGGAGCTTCATGAACTTA 60.355 50.000 3.38 0.00 0.00 2.24
2959 11241 1.743623 TATTTGCCGACGCTGGGTG 60.744 57.895 0.70 0.00 35.36 4.61
2964 11246 3.776656 GTCGTATTTGCCGACGCT 58.223 55.556 0.00 0.00 44.29 5.07
2973 11255 4.945246 AGGACATGCTATTCGTCGTATTT 58.055 39.130 0.00 0.00 0.00 1.40
2976 11258 3.878699 TGTAGGACATGCTATTCGTCGTA 59.121 43.478 0.00 0.00 0.00 3.43
2986 11268 1.068083 CGGCGATGTAGGACATGCT 59.932 57.895 0.00 0.00 39.27 3.79
3042 11327 1.885163 CGGAGGAAGCGTGTAGGGTT 61.885 60.000 0.00 0.00 0.00 4.11
3045 11330 1.139095 GACGGAGGAAGCGTGTAGG 59.861 63.158 0.00 0.00 0.00 3.18
3072 11357 4.293648 CACAGGTCACCGTCGCCA 62.294 66.667 0.00 0.00 0.00 5.69
3130 11416 3.120442 ACAGCGTTAAAACAGGTTATCGC 60.120 43.478 10.76 10.76 45.73 4.58
3159 11445 0.257328 TTGGGCTTGGACAGTGTCAA 59.743 50.000 24.20 11.33 33.68 3.18
3220 11519 1.658596 TGTAGTGCGTGCGATTGAATC 59.341 47.619 0.00 0.00 0.00 2.52
3255 11556 5.175090 TCACTCTGCATCTCGTTATGTAG 57.825 43.478 10.09 10.09 39.95 2.74
3319 11905 9.722317 CTCCTCCATCCTAGGTTATTTATCTAT 57.278 37.037 9.08 0.00 35.48 1.98
3335 11921 1.150135 TGGATAGGACCTCCTCCATCC 59.850 57.143 17.84 14.95 44.77 3.51
3435 12349 3.209410 CAAAGAGCACTATCCCCACATC 58.791 50.000 0.00 0.00 0.00 3.06
3441 12355 1.559682 TGGTCCAAAGAGCACTATCCC 59.440 52.381 0.00 0.00 45.34 3.85
3469 12757 5.871524 ACAGATGACACATAGCTACTGTTTG 59.128 40.000 0.00 0.00 34.42 2.93
3492 12780 7.541091 TCTCTGTATTGAAGAACGACATACAAC 59.459 37.037 0.00 0.00 0.00 3.32
3495 12783 7.702772 ACATCTCTGTATTGAAGAACGACATAC 59.297 37.037 0.00 0.00 32.49 2.39
3498 12786 6.025749 ACATCTCTGTATTGAAGAACGACA 57.974 37.500 0.00 0.00 32.49 4.35
3499 12787 6.326375 AGACATCTCTGTATTGAAGAACGAC 58.674 40.000 0.00 0.00 35.14 4.34
3515 12803 9.539825 ACTGATCACAATAATGTTAGACATCTC 57.460 33.333 0.00 0.00 37.97 2.75
3540 12840 7.431084 ACAAACACATCGAGAATTACAACAAAC 59.569 33.333 0.00 0.00 0.00 2.93
3545 12845 5.995282 AGGACAAACACATCGAGAATTACAA 59.005 36.000 0.00 0.00 0.00 2.41
3566 12866 1.001974 CAAAGGGTCATCACACGAGGA 59.998 52.381 0.00 0.00 0.00 3.71
3567 12867 1.001974 TCAAAGGGTCATCACACGAGG 59.998 52.381 0.00 0.00 0.00 4.63
3568 12868 2.069273 GTCAAAGGGTCATCACACGAG 58.931 52.381 0.00 0.00 0.00 4.18
3570 12870 1.531149 GTGTCAAAGGGTCATCACACG 59.469 52.381 0.00 0.00 0.00 4.49
3571 12871 1.531149 CGTGTCAAAGGGTCATCACAC 59.469 52.381 0.00 0.00 0.00 3.82
3573 12873 1.156736 CCGTGTCAAAGGGTCATCAC 58.843 55.000 0.00 0.00 0.00 3.06
3575 12875 1.439679 GTCCGTGTCAAAGGGTCATC 58.560 55.000 0.00 0.00 35.20 2.92
3577 12877 1.068417 CGTCCGTGTCAAAGGGTCA 59.932 57.895 0.00 0.00 35.20 4.02
3578 12878 1.666872 CCGTCCGTGTCAAAGGGTC 60.667 63.158 0.00 0.00 35.20 4.46
3580 12880 0.949105 CTTCCGTCCGTGTCAAAGGG 60.949 60.000 0.00 0.00 34.94 3.95
3583 12883 1.595929 GGCTTCCGTCCGTGTCAAA 60.596 57.895 0.00 0.00 0.00 2.69
3603 14396 1.920325 TAAGCTGAGTGCCAGGGCT 60.920 57.895 12.19 0.00 43.13 5.19
3616 14409 0.033781 TTAACGGCGGTGTGTAAGCT 59.966 50.000 8.19 0.00 0.00 3.74
3622 14415 2.547305 CACGTTAACGGCGGTGTG 59.453 61.111 29.81 15.14 44.95 3.82
3665 14458 4.831674 AGTAGTAGCCCACGGTAAAAAT 57.168 40.909 0.00 0.00 0.00 1.82
3671 14464 3.580022 AGTAAAAAGTAGTAGCCCACGGT 59.420 43.478 0.00 0.00 0.00 4.83
3672 14465 4.179298 GAGTAAAAAGTAGTAGCCCACGG 58.821 47.826 0.00 0.00 0.00 4.94
3701 14494 1.659098 GTTATCGACACGGCAAAGAGG 59.341 52.381 0.00 0.00 0.00 3.69
3705 14498 3.059461 GTCTTTGTTATCGACACGGCAAA 60.059 43.478 0.00 0.00 38.18 3.68
3713 14506 2.415512 GTGGCAGGTCTTTGTTATCGAC 59.584 50.000 0.00 0.00 0.00 4.20
3716 14509 3.073274 AGGTGGCAGGTCTTTGTTATC 57.927 47.619 0.00 0.00 0.00 1.75
3725 14518 2.717639 ATGAACATAGGTGGCAGGTC 57.282 50.000 0.00 0.00 0.00 3.85
3729 14522 4.917385 ACAGTTTATGAACATAGGTGGCA 58.083 39.130 2.93 0.00 38.26 4.92
3730 14523 5.065218 CAGACAGTTTATGAACATAGGTGGC 59.935 44.000 2.93 0.00 38.26 5.01
3733 14526 5.250774 ACCCAGACAGTTTATGAACATAGGT 59.749 40.000 2.93 0.00 38.26 3.08
3735 14528 9.698309 CTATACCCAGACAGTTTATGAACATAG 57.302 37.037 2.93 0.00 38.26 2.23
3736 14529 8.647796 CCTATACCCAGACAGTTTATGAACATA 58.352 37.037 2.93 0.00 38.26 2.29
3745 14538 4.969359 ACTATGCCTATACCCAGACAGTTT 59.031 41.667 0.00 0.00 0.00 2.66
3746 14539 4.345257 CACTATGCCTATACCCAGACAGTT 59.655 45.833 0.00 0.00 0.00 3.16
3761 14554 0.236711 GTGATGATGCGCACTATGCC 59.763 55.000 14.90 0.20 41.12 4.40
3765 14558 0.249031 CTCGGTGATGATGCGCACTA 60.249 55.000 14.90 4.69 35.43 2.74
3777 14570 0.038618 CCGAATGTGACACTCGGTGA 60.039 55.000 25.41 0.00 45.62 4.02
3779 14572 4.988065 CCGAATGTGACACTCGGT 57.012 55.556 25.41 0.00 45.62 4.69
3781 14574 1.406219 CTCGCCGAATGTGACACTCG 61.406 60.000 9.70 9.70 0.00 4.18
3782 14575 0.388649 ACTCGCCGAATGTGACACTC 60.389 55.000 7.20 0.00 0.00 3.51
3783 14576 0.033504 AACTCGCCGAATGTGACACT 59.966 50.000 7.20 0.00 0.00 3.55
3804 14597 2.972625 TGAGTAATTTCACCTCGGCAG 58.027 47.619 0.00 0.00 0.00 4.85
3846 14639 7.284489 ACACAACAGGAAAAAGCTTATAAGACA 59.716 33.333 16.85 0.00 0.00 3.41
3885 14678 4.759183 AGAACAAAACTCTCATGCCTTCTC 59.241 41.667 0.00 0.00 0.00 2.87
3913 14706 0.179187 CGACAGAACTCGCGTCTCAT 60.179 55.000 5.77 0.00 0.00 2.90
3971 14764 6.271391 TCCCTCTGTAAAGGAATGTAAGAACA 59.729 38.462 0.00 0.00 38.87 3.18
3975 14768 6.301169 ACTCCCTCTGTAAAGGAATGTAAG 57.699 41.667 0.00 0.00 38.87 2.34
3979 14772 9.495572 GATTATTACTCCCTCTGTAAAGGAATG 57.504 37.037 0.00 0.00 38.87 2.67
3983 14776 9.984190 GTAAGATTATTACTCCCTCTGTAAAGG 57.016 37.037 0.00 0.00 34.20 3.11
3991 14784 8.032451 GCTCATGAGTAAGATTATTACTCCCTC 58.968 40.741 23.38 5.37 46.27 4.30
4042 14835 7.985752 CCAAGATCATCAGCTATGCAATATCTA 59.014 37.037 0.00 0.00 35.38 1.98
4053 14850 1.202568 CGGCACCAAGATCATCAGCTA 60.203 52.381 0.00 0.00 0.00 3.32
4105 14902 4.027437 TGTGCTACCTGATATGGTGTGTA 58.973 43.478 0.00 0.00 41.05 2.90
4107 14904 3.541996 TGTGCTACCTGATATGGTGTG 57.458 47.619 0.00 0.00 41.05 3.82
4108 14905 3.243873 CGATGTGCTACCTGATATGGTGT 60.244 47.826 0.00 0.00 41.05 4.16
4109 14906 3.243873 ACGATGTGCTACCTGATATGGTG 60.244 47.826 0.00 0.00 41.05 4.17
4114 14911 5.968254 TGTTTAACGATGTGCTACCTGATA 58.032 37.500 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.