Multiple sequence alignment - TraesCS7B01G079900

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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 TraesCS7B01G079900 chr7B 100.000 9616 0 0 1 9616 89892562 89882947 0.000000e+00 17758.0
1 TraesCS7B01G079900 chr7B 96.609 2035 67 2 6956 8988 89919746 89917712 0.000000e+00 3374.0
2 TraesCS7B01G079900 chr7B 90.914 2036 140 20 6873 8895 89788820 89786817 0.000000e+00 2693.0
3 TraesCS7B01G079900 chr7B 89.052 1224 63 31 181 1359 89790002 89788805 0.000000e+00 1452.0
4 TraesCS7B01G079900 chr7B 95.785 783 33 0 7851 8633 89912294 89911512 0.000000e+00 1264.0
5 TraesCS7B01G079900 chr7B 94.565 552 19 5 8982 9532 89907876 89907335 0.000000e+00 843.0
6 TraesCS7B01G079900 chr7B 98.370 368 6 0 8632 8999 89909228 89908861 0.000000e+00 647.0
7 TraesCS7B01G079900 chr7B 79.892 741 78 42 439 1130 89920845 89920127 2.430000e-130 477.0
8 TraesCS7B01G079900 chr7B 94.413 179 7 1 1177 1355 89919995 89919820 1.230000e-68 272.0
9 TraesCS7B01G079900 chr7B 83.505 291 24 7 9017 9286 89786808 89786521 5.770000e-62 250.0
10 TraesCS7B01G079900 chr7B 92.958 142 8 2 12 152 89863950 89863810 1.270000e-48 206.0
11 TraesCS7B01G079900 chr7B 100.000 29 0 0 1242 1270 487218466 487218494 5.000000e-03 54.7
12 TraesCS7B01G079900 chr7B 100.000 28 0 0 1 28 89863953 89863926 1.700000e-02 52.8
13 TraesCS7B01G079900 chr6A 93.335 4306 273 10 2228 6531 186485510 186489803 0.000000e+00 6349.0
14 TraesCS7B01G079900 chr6A 96.900 3613 110 2 3244 6855 555211068 555207457 0.000000e+00 6050.0
15 TraesCS7B01G079900 chr6A 97.028 1245 37 0 1368 2612 549174148 549172904 0.000000e+00 2095.0
16 TraesCS7B01G079900 chr6A 77.941 1360 243 30 7290 8616 537874866 537876201 0.000000e+00 797.0
17 TraesCS7B01G079900 chr6A 89.243 251 27 0 6963 7213 537874504 537874754 2.020000e-81 315.0
18 TraesCS7B01G079900 chr1A 96.924 3771 112 3 3080 6848 15128888 15125120 0.000000e+00 6318.0
19 TraesCS7B01G079900 chr1A 96.766 3772 120 2 3080 6849 15085030 15081259 0.000000e+00 6288.0
20 TraesCS7B01G079900 chr1A 96.156 3772 116 6 3080 6849 15041611 15037867 0.000000e+00 6135.0
21 TraesCS7B01G079900 chr1A 97.090 1718 50 0 1368 3085 15052269 15050552 0.000000e+00 2896.0
22 TraesCS7B01G079900 chr1A 96.740 1718 56 0 1368 3085 15139879 15138162 0.000000e+00 2863.0
23 TraesCS7B01G079900 chr1A 96.740 1718 55 1 1368 3085 15095646 15093930 0.000000e+00 2861.0
24 TraesCS7B01G079900 chr4A 92.767 4217 302 3 2636 6851 694704886 694709100 0.000000e+00 6095.0
25 TraesCS7B01G079900 chr4A 92.507 4217 314 2 2636 6851 694690895 694695110 0.000000e+00 6035.0
26 TraesCS7B01G079900 chr4A 90.661 2752 214 21 1370 4113 670925032 670922316 0.000000e+00 3618.0
27 TraesCS7B01G079900 chr4A 91.431 1272 106 3 1369 2638 694687418 694688688 0.000000e+00 1742.0
28 TraesCS7B01G079900 chr4A 90.881 1272 113 3 1369 2638 694701402 694702672 0.000000e+00 1703.0
29 TraesCS7B01G079900 chr4A 97.143 35 1 0 8909 8943 593681705 593681739 1.040000e-04 60.2
30 TraesCS7B01G079900 chr2B 92.719 3516 253 3 3341 6855 677870181 677866668 0.000000e+00 5072.0
31 TraesCS7B01G079900 chr2B 90.426 94 7 1 9525 9616 398570360 398570267 1.310000e-23 122.0
32 TraesCS7B01G079900 chr3A 97.081 2878 79 1 3973 6850 719685929 719688801 0.000000e+00 4844.0
33 TraesCS7B01G079900 chr3A 93.173 2666 173 6 2473 5136 657480219 657477561 0.000000e+00 3906.0
34 TraesCS7B01G079900 chr3A 93.779 1061 65 1 1417 2476 657518958 657517898 0.000000e+00 1592.0
35 TraesCS7B01G079900 chr1B 92.910 2680 181 6 2552 5230 327867582 327864911 0.000000e+00 3888.0
36 TraesCS7B01G079900 chr1B 92.103 1051 80 2 1369 2418 327891634 327890586 0.000000e+00 1478.0
37 TraesCS7B01G079900 chr1B 85.455 55 4 4 7453 7505 39588963 39588911 5.000000e-03 54.7
38 TraesCS7B01G079900 chr7D 93.326 1933 101 15 6956 8873 128480307 128478388 0.000000e+00 2830.0
39 TraesCS7B01G079900 chr7D 91.585 1937 135 17 6956 8868 128748125 128746193 0.000000e+00 2649.0
40 TraesCS7B01G079900 chr7D 91.523 1628 103 20 7257 8865 128143317 128141706 0.000000e+00 2209.0
41 TraesCS7B01G079900 chr7D 89.295 1121 75 17 37 1130 128145632 128144530 0.000000e+00 1363.0
42 TraesCS7B01G079900 chr7D 89.058 1115 79 19 37 1130 128481761 128480669 0.000000e+00 1343.0
43 TraesCS7B01G079900 chr7D 85.481 489 52 15 8401 8880 128472157 128471679 8.680000e-135 492.0
44 TraesCS7B01G079900 chr7D 79.809 733 78 45 439 1130 128749203 128748500 4.070000e-128 470.0
45 TraesCS7B01G079900 chr7D 84.306 497 56 13 8397 8880 128745605 128745118 5.260000e-127 466.0
46 TraesCS7B01G079900 chr7D 95.896 268 11 0 6956 7223 128143778 128143511 1.480000e-117 435.0
47 TraesCS7B01G079900 chr7D 90.000 240 10 6 1127 1355 128144478 128144242 2.030000e-76 298.0
48 TraesCS7B01G079900 chr7D 89.256 242 9 10 1128 1355 128748439 128748201 4.390000e-73 287.0
49 TraesCS7B01G079900 chr7D 88.066 243 15 5 1124 1355 128480622 128480383 9.510000e-70 276.0
50 TraesCS7B01G079900 chr7D 89.091 110 11 1 9203 9312 128743998 128743890 1.680000e-27 135.0
51 TraesCS7B01G079900 chr7D 94.737 38 2 0 67 104 128782226 128782189 1.040000e-04 60.2
52 TraesCS7B01G079900 chr7D 100.000 29 0 0 1242 1270 463965316 463965288 5.000000e-03 54.7
53 TraesCS7B01G079900 chr7A 89.463 2031 160 29 6877 8873 128776234 128774224 0.000000e+00 2516.0
54 TraesCS7B01G079900 chr7A 83.830 470 41 18 680 1130 128776961 128776508 1.930000e-111 414.0
55 TraesCS7B01G079900 chr7A 87.903 248 11 11 1128 1359 128776467 128776223 3.420000e-69 274.0
56 TraesCS7B01G079900 chr7A 83.913 230 30 7 8868 9094 467590124 467590349 7.560000e-51 213.0
57 TraesCS7B01G079900 chr7A 83.843 229 30 7 8869 9094 467585434 467585658 2.720000e-50 211.0
58 TraesCS7B01G079900 chr7A 100.000 29 0 0 1242 1270 536121612 536121640 5.000000e-03 54.7
59 TraesCS7B01G079900 chr6B 79.424 1458 244 33 6963 8385 585327725 585329161 0.000000e+00 979.0
60 TraesCS7B01G079900 chr6B 73.684 1273 266 59 7365 8606 585246824 585248058 1.920000e-116 431.0
61 TraesCS7B01G079900 chr6B 95.349 86 2 1 9533 9616 101624766 101624681 1.680000e-27 135.0
62 TraesCS7B01G079900 chr6B 94.186 86 3 1 9533 9616 498018246 498018161 7.840000e-26 130.0
63 TraesCS7B01G079900 chr6B 92.308 91 5 1 9528 9616 345961390 345961480 2.820000e-25 128.0
64 TraesCS7B01G079900 chr6D 79.588 1117 198 14 7290 8385 391694491 391695598 0.000000e+00 773.0
65 TraesCS7B01G079900 chr6D 90.837 251 20 1 6963 7213 391694136 391694383 5.570000e-87 333.0
66 TraesCS7B01G079900 chr6D 83.333 252 42 0 6962 7213 391687690 391687941 5.810000e-57 233.0
67 TraesCS7B01G079900 chr3D 79.941 339 49 14 8868 9190 385391522 385391857 2.090000e-56 231.0
68 TraesCS7B01G079900 chr3D 94.186 86 3 1 9533 9616 153137727 153137812 7.840000e-26 130.0
69 TraesCS7B01G079900 chr5D 84.716 229 30 5 8868 9094 487527148 487527373 3.490000e-54 224.0
70 TraesCS7B01G079900 chr5D 87.356 87 6 3 9432 9518 442126291 442126210 2.860000e-15 95.3
71 TraesCS7B01G079900 chr4D 83.750 240 31 8 8858 9094 482347914 482348148 4.520000e-53 220.0
72 TraesCS7B01G079900 chr3B 95.238 84 2 1 9535 9616 461594167 461594084 2.180000e-26 132.0
73 TraesCS7B01G079900 chr3B 94.186 86 3 1 9533 9616 482710220 482710305 7.840000e-26 130.0
74 TraesCS7B01G079900 chr2A 94.118 85 3 1 9534 9616 430063919 430063835 2.820000e-25 128.0
75 TraesCS7B01G079900 chr2D 88.776 98 9 1 9521 9616 286954775 286954872 1.700000e-22 119.0
76 TraesCS7B01G079900 chrUn 93.243 74 5 0 8870 8943 330519483 330519556 1.020000e-19 110.0
77 TraesCS7B01G079900 chrUn 93.023 43 3 0 281 323 30105160 30105118 8.060000e-06 63.9


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 TraesCS7B01G079900 chr7B 89882947 89892562 9615 True 17758.000000 17758 100.000000 1 9616 1 chr7B.!!$R1 9615
1 TraesCS7B01G079900 chr7B 89786521 89790002 3481 True 1465.000000 2693 87.823667 181 9286 3 chr7B.!!$R2 9105
2 TraesCS7B01G079900 chr7B 89917712 89920845 3133 True 1374.333333 3374 90.304667 439 8988 3 chr7B.!!$R5 8549
3 TraesCS7B01G079900 chr7B 89907335 89912294 4959 True 918.000000 1264 96.240000 7851 9532 3 chr7B.!!$R4 1681
4 TraesCS7B01G079900 chr6A 186485510 186489803 4293 False 6349.000000 6349 93.335000 2228 6531 1 chr6A.!!$F1 4303
5 TraesCS7B01G079900 chr6A 555207457 555211068 3611 True 6050.000000 6050 96.900000 3244 6855 1 chr6A.!!$R2 3611
6 TraesCS7B01G079900 chr6A 549172904 549174148 1244 True 2095.000000 2095 97.028000 1368 2612 1 chr6A.!!$R1 1244
7 TraesCS7B01G079900 chr6A 537874504 537876201 1697 False 556.000000 797 83.592000 6963 8616 2 chr6A.!!$F2 1653
8 TraesCS7B01G079900 chr1A 15125120 15128888 3768 True 6318.000000 6318 96.924000 3080 6848 1 chr1A.!!$R5 3768
9 TraesCS7B01G079900 chr1A 15081259 15085030 3771 True 6288.000000 6288 96.766000 3080 6849 1 chr1A.!!$R3 3769
10 TraesCS7B01G079900 chr1A 15037867 15041611 3744 True 6135.000000 6135 96.156000 3080 6849 1 chr1A.!!$R1 3769
11 TraesCS7B01G079900 chr1A 15050552 15052269 1717 True 2896.000000 2896 97.090000 1368 3085 1 chr1A.!!$R2 1717
12 TraesCS7B01G079900 chr1A 15138162 15139879 1717 True 2863.000000 2863 96.740000 1368 3085 1 chr1A.!!$R6 1717
13 TraesCS7B01G079900 chr1A 15093930 15095646 1716 True 2861.000000 2861 96.740000 1368 3085 1 chr1A.!!$R4 1717
14 TraesCS7B01G079900 chr4A 694701402 694709100 7698 False 3899.000000 6095 91.824000 1369 6851 2 chr4A.!!$F3 5482
15 TraesCS7B01G079900 chr4A 694687418 694695110 7692 False 3888.500000 6035 91.969000 1369 6851 2 chr4A.!!$F2 5482
16 TraesCS7B01G079900 chr4A 670922316 670925032 2716 True 3618.000000 3618 90.661000 1370 4113 1 chr4A.!!$R1 2743
17 TraesCS7B01G079900 chr2B 677866668 677870181 3513 True 5072.000000 5072 92.719000 3341 6855 1 chr2B.!!$R2 3514
18 TraesCS7B01G079900 chr3A 719685929 719688801 2872 False 4844.000000 4844 97.081000 3973 6850 1 chr3A.!!$F1 2877
19 TraesCS7B01G079900 chr3A 657477561 657480219 2658 True 3906.000000 3906 93.173000 2473 5136 1 chr3A.!!$R1 2663
20 TraesCS7B01G079900 chr3A 657517898 657518958 1060 True 1592.000000 1592 93.779000 1417 2476 1 chr3A.!!$R2 1059
21 TraesCS7B01G079900 chr1B 327864911 327867582 2671 True 3888.000000 3888 92.910000 2552 5230 1 chr1B.!!$R2 2678
22 TraesCS7B01G079900 chr1B 327890586 327891634 1048 True 1478.000000 1478 92.103000 1369 2418 1 chr1B.!!$R3 1049
23 TraesCS7B01G079900 chr7D 128478388 128481761 3373 True 1483.000000 2830 90.150000 37 8873 3 chr7D.!!$R5 8836
24 TraesCS7B01G079900 chr7D 128141706 128145632 3926 True 1076.250000 2209 91.678500 37 8865 4 chr7D.!!$R4 8828
25 TraesCS7B01G079900 chr7D 128743890 128749203 5313 True 801.400000 2649 86.809400 439 9312 5 chr7D.!!$R6 8873
26 TraesCS7B01G079900 chr7A 128774224 128776961 2737 True 1068.000000 2516 87.065333 680 8873 3 chr7A.!!$R1 8193
27 TraesCS7B01G079900 chr6B 585327725 585329161 1436 False 979.000000 979 79.424000 6963 8385 1 chr6B.!!$F3 1422
28 TraesCS7B01G079900 chr6B 585246824 585248058 1234 False 431.000000 431 73.684000 7365 8606 1 chr6B.!!$F2 1241
29 TraesCS7B01G079900 chr6D 391694136 391695598 1462 False 553.000000 773 85.212500 6963 8385 2 chr6D.!!$F2 1422

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
482 495 1.039856 ACCGCATGTTCCAAAAGCTT 58.960 45.000 0.00 0.00 0.00 3.74 F
1209 1427 0.528470 AGGAGAGCAACTACACGAGC 59.472 55.000 0.00 0.00 0.00 5.03 F
2425 2648 0.983467 TGTCTAAGGAGGCATGCACA 59.017 50.000 21.36 9.61 30.32 4.57 F
2623 2846 1.197721 GTTGACTTGAGCAATGGGTCG 59.802 52.381 0.00 0.00 44.47 4.79 F
3815 6701 0.899720 GGTCGGATGGTACTTGGTGA 59.100 55.000 0.00 0.00 0.00 4.02 F
4915 7815 0.308993 GAGGTGCAGCAACAAGTGTC 59.691 55.000 19.63 0.00 0.00 3.67 F
6301 9203 0.674534 GTACAGGAGGCTCCATACGG 59.325 60.000 33.86 19.25 39.61 4.02 F
6593 9495 2.126346 GCGTTGGCAGCATTGACC 60.126 61.111 1.39 0.00 39.62 4.02 F
7141 10437 0.176219 CAATCCATGGCGCCATTGTT 59.824 50.000 38.86 27.65 33.90 2.83 F
7599 11071 0.107017 ATGATCGCCCCAGGTCAAAG 60.107 55.000 0.00 0.00 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2406 2629 0.983467 TGTGCATGCCTCCTTAGACA 59.017 50.000 16.68 7.20 0.00 3.41 R
2623 2846 1.153549 GGCCGCCGATCTATCATCC 60.154 63.158 0.00 0.00 0.00 3.51 R
3580 6463 0.820871 ATCAGCCAACTCCTCTCGTC 59.179 55.000 0.00 0.00 0.00 4.20 R
4030 6916 1.412343 GCTGGAAAAACCTTGCTGGAA 59.588 47.619 3.40 0.00 39.71 3.53 R
5293 8195 1.499438 TGTCCGGACTATCCAGGAGAT 59.501 52.381 33.39 0.00 38.96 2.75 R
6889 9791 0.603439 TTTCCAGTAAACGGCCGACC 60.603 55.000 35.90 15.85 0.00 4.79 R
7141 10437 0.619255 TTCCGAGCTTGGGGTGGATA 60.619 55.000 20.46 0.00 0.00 2.59 R
7453 10925 0.968901 TGATCCGGAGCAGGTACGTT 60.969 55.000 20.59 0.00 0.00 3.99 R
8136 11650 1.542187 GCCGTACTCCACCACCTTCT 61.542 60.000 0.00 0.00 0.00 2.85 R
9564 18372 0.037303 AGGGTCGTGAAGTCGTAGGA 59.963 55.000 0.00 0.00 0.00 2.94 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
247 248 5.647225 AGCTTCCTCATTTCTGCTAAAGAAG 59.353 40.000 0.00 0.00 45.64 2.85
279 280 9.403583 ACAAAGTGGTCAAAATTCTACTTTCTA 57.596 29.630 4.13 0.00 41.12 2.10
343 346 3.131933 ACATACTGGCTGAGATGAGTGAC 59.868 47.826 14.37 0.00 0.00 3.67
482 495 1.039856 ACCGCATGTTCCAAAAGCTT 58.960 45.000 0.00 0.00 0.00 3.74
494 508 6.429385 TGTTCCAAAAGCTTGTGTTGATTTTT 59.571 30.769 15.53 0.00 0.00 1.94
655 711 2.042686 TCAGGGATAACTGCATGCAC 57.957 50.000 18.46 6.48 38.36 4.57
727 795 8.700994 GCTTTCTAGCGATTATATTTGACAAC 57.299 34.615 0.00 0.00 37.71 3.32
754 831 3.631145 ATCATATGAAACCATGCACGC 57.369 42.857 9.99 0.00 0.00 5.34
757 836 2.303208 TATGAAACCATGCACGCGCG 62.303 55.000 30.96 30.96 42.97 6.86
779 861 3.822192 CATCGTCGACCGGGCTCA 61.822 66.667 5.33 0.00 37.11 4.26
797 893 1.995626 AATCCTGTCACCCTCCCCG 60.996 63.158 0.00 0.00 0.00 5.73
799 895 3.706373 CCTGTCACCCTCCCCGTG 61.706 72.222 0.00 0.00 0.00 4.94
835 933 1.577328 CGTGCGTCTGCTTGGGATTT 61.577 55.000 0.00 0.00 43.34 2.17
842 940 2.686915 GTCTGCTTGGGATTTCCATCAG 59.313 50.000 7.21 7.21 46.52 2.90
942 1060 3.306019 GCTAGCTAGCTTCTTGATCTCCC 60.306 52.174 33.71 4.16 45.62 4.30
978 1096 2.493973 GAGCAGAGCTCGGTGAGG 59.506 66.667 15.48 0.54 45.85 3.86
1024 1142 2.479219 GGTATAGCTAAGATACCGGCGC 60.479 54.545 0.00 0.00 39.52 6.53
1048 1166 0.825840 TTGGTTACTTGGGGCAGTGC 60.826 55.000 6.55 6.55 0.00 4.40
1051 1169 1.064685 GGTTACTTGGGGCAGTGCTAT 60.065 52.381 16.11 0.00 0.00 2.97
1101 1219 1.079819 CGCCAAGACTCGTCACCAT 60.080 57.895 0.00 0.00 0.00 3.55
1155 1359 3.690628 TGTACACATGCCATCTCAACATG 59.309 43.478 0.00 0.00 45.28 3.21
1165 1372 5.355071 TGCCATCTCAACATGTCATAAACTC 59.645 40.000 0.00 0.00 0.00 3.01
1168 1375 6.183360 CCATCTCAACATGTCATAAACTCACC 60.183 42.308 0.00 0.00 0.00 4.02
1169 1376 4.929211 TCTCAACATGTCATAAACTCACCG 59.071 41.667 0.00 0.00 0.00 4.94
1174 1392 5.245531 ACATGTCATAAACTCACCGTCATT 58.754 37.500 0.00 0.00 0.00 2.57
1175 1393 5.705441 ACATGTCATAAACTCACCGTCATTT 59.295 36.000 0.00 0.00 0.00 2.32
1207 1425 4.705507 AGATTAAGGAGAGCAACTACACGA 59.294 41.667 0.00 0.00 0.00 4.35
1208 1426 4.436242 TTAAGGAGAGCAACTACACGAG 57.564 45.455 0.00 0.00 0.00 4.18
1209 1427 0.528470 AGGAGAGCAACTACACGAGC 59.472 55.000 0.00 0.00 0.00 5.03
1354 1572 6.295719 CCATCCACTGGTAAGTTAGTTAGT 57.704 41.667 0.00 0.00 40.49 2.24
1355 1573 6.338937 CCATCCACTGGTAAGTTAGTTAGTC 58.661 44.000 0.00 0.00 40.49 2.59
1356 1574 6.154706 CCATCCACTGGTAAGTTAGTTAGTCT 59.845 42.308 0.00 0.00 40.49 3.24
1357 1575 6.585695 TCCACTGGTAAGTTAGTTAGTCTG 57.414 41.667 0.00 0.00 32.98 3.51
1358 1576 5.479375 TCCACTGGTAAGTTAGTTAGTCTGG 59.521 44.000 0.00 0.00 32.98 3.86
1359 1577 5.245526 CCACTGGTAAGTTAGTTAGTCTGGT 59.754 44.000 0.00 0.00 32.98 4.00
1360 1578 6.239515 CCACTGGTAAGTTAGTTAGTCTGGTT 60.240 42.308 0.00 0.00 32.98 3.67
1361 1579 7.215085 CACTGGTAAGTTAGTTAGTCTGGTTT 58.785 38.462 0.00 0.00 32.98 3.27
1362 1580 7.384387 CACTGGTAAGTTAGTTAGTCTGGTTTC 59.616 40.741 0.00 0.00 32.98 2.78
1363 1581 6.762333 TGGTAAGTTAGTTAGTCTGGTTTCC 58.238 40.000 0.00 0.00 0.00 3.13
1364 1582 6.169094 GGTAAGTTAGTTAGTCTGGTTTCCC 58.831 44.000 0.00 0.00 0.00 3.97
1365 1583 6.013898 GGTAAGTTAGTTAGTCTGGTTTCCCT 60.014 42.308 0.00 0.00 0.00 4.20
1366 1584 7.179160 GGTAAGTTAGTTAGTCTGGTTTCCCTA 59.821 40.741 0.00 0.00 0.00 3.53
1600 1819 3.254166 GTGATGTGCTGGAACAACTCAAT 59.746 43.478 0.00 0.00 38.70 2.57
1959 2182 5.133322 TCTGGCTCCAAATTCATAAGATCCT 59.867 40.000 0.00 0.00 0.00 3.24
2275 2498 2.561956 GCTCTATGCGGACGGCCTA 61.562 63.158 5.33 0.00 42.61 3.93
2425 2648 0.983467 TGTCTAAGGAGGCATGCACA 59.017 50.000 21.36 9.61 30.32 4.57
2470 2693 3.356529 AGGAAAAGACTCGCATTGGAT 57.643 42.857 0.00 0.00 0.00 3.41
2623 2846 1.197721 GTTGACTTGAGCAATGGGTCG 59.802 52.381 0.00 0.00 44.47 4.79
2923 5805 3.159472 ACTGTGTTGGATTCATGTGCAT 58.841 40.909 0.00 0.00 0.00 3.96
3199 6081 1.201429 ATGGGACTTGGGCTTCTCGT 61.201 55.000 0.00 0.00 0.00 4.18
3360 6242 1.539388 CATAGTCCGCTTTTGGTGCAA 59.461 47.619 0.00 0.00 0.00 4.08
3580 6463 5.509771 TGTGACACATGAAATTGAGAAACG 58.490 37.500 3.56 0.00 0.00 3.60
3783 6669 3.302480 GCGTGCACGAAGGAACTATATTG 60.302 47.826 41.19 8.15 43.02 1.90
3815 6701 0.899720 GGTCGGATGGTACTTGGTGA 59.100 55.000 0.00 0.00 0.00 4.02
3923 6809 2.494059 CTTGAAGGAGTTCTGCCGAAA 58.506 47.619 0.00 0.00 33.38 3.46
4367 7267 8.510243 AGTGCATTCATCACATACAAAATCTA 57.490 30.769 0.00 0.00 36.93 1.98
4516 7416 5.178996 GGATTATGACATGTGTGAGATCAGC 59.821 44.000 1.15 0.00 0.00 4.26
4540 7440 8.892723 AGCACGATATTCTGTCAAATTTAATGA 58.107 29.630 0.00 0.00 0.00 2.57
4865 7765 5.241506 CCTTTTCTCTGGAAACTGTAATGCA 59.758 40.000 0.00 0.00 40.63 3.96
4915 7815 0.308993 GAGGTGCAGCAACAAGTGTC 59.691 55.000 19.63 0.00 0.00 3.67
5068 7968 2.915604 AGATCCTCATCAAGGTTGTGGT 59.084 45.455 0.00 0.00 46.32 4.16
5087 7987 7.953005 TGTGGTACAATCAATTCCAACATAT 57.047 32.000 0.00 0.00 44.16 1.78
5114 8014 1.070786 TGTGTTCCGACTTCCTGCC 59.929 57.895 0.00 0.00 0.00 4.85
5117 8017 1.118965 TGTTCCGACTTCCTGCCTCA 61.119 55.000 0.00 0.00 0.00 3.86
5412 8314 1.092348 GGCGGTGTGGAAAGGTATTC 58.908 55.000 0.00 0.00 0.00 1.75
5664 8566 5.507637 TGAAGATTCGTACTTCTCCTAGGT 58.492 41.667 9.08 0.00 42.63 3.08
5682 8584 6.328934 TCCTAGGTATGTGCAGGATTTCATTA 59.671 38.462 9.08 0.00 32.20 1.90
5690 8592 3.823873 TGCAGGATTTCATTACGTGGTTT 59.176 39.130 0.00 0.00 0.00 3.27
5980 8882 5.557576 AGCTTCCATGCTCTTGTATCATA 57.442 39.130 0.00 0.00 39.34 2.15
6301 9203 0.674534 GTACAGGAGGCTCCATACGG 59.325 60.000 33.86 19.25 39.61 4.02
6503 9405 2.334946 GGAAGCGGAACTGCATGCA 61.335 57.895 21.29 21.29 37.31 3.96
6593 9495 2.126346 GCGTTGGCAGCATTGACC 60.126 61.111 1.39 0.00 39.62 4.02
6597 9499 3.203086 TTGGCAGCATTGACCGGGA 62.203 57.895 6.32 0.00 0.00 5.14
6660 9562 6.436738 AGATCAAGCATCATATGGAGACTT 57.563 37.500 2.13 0.00 33.29 3.01
6742 9644 6.441093 TTTGTATAGTCGTACGGAGTTCAT 57.559 37.500 16.52 3.54 37.78 2.57
6743 9645 5.663795 TGTATAGTCGTACGGAGTTCATC 57.336 43.478 16.52 0.91 37.78 2.92
6939 9843 4.142988 CCGCTAAACTTAATTTCTGACGCA 60.143 41.667 0.00 0.00 0.00 5.24
6941 9845 6.021596 CGCTAAACTTAATTTCTGACGCAAT 58.978 36.000 0.00 0.00 0.00 3.56
7141 10437 0.176219 CAATCCATGGCGCCATTGTT 59.824 50.000 38.86 27.65 33.90 2.83
7253 10694 9.624373 CTTCCATCCATGCTTATAATAAGCTAT 57.376 33.333 1.08 0.00 43.38 2.97
7498 10970 2.593956 GGGGCTCTCCAACGACCTT 61.594 63.158 0.00 0.00 37.22 3.50
7511 10983 1.623973 CGACCTTTTCTTCGGCGTCC 61.624 60.000 6.85 0.00 0.00 4.79
7536 11008 2.420043 CAACCTCACCGTGGTCGT 59.580 61.111 0.00 0.00 36.69 4.34
7599 11071 0.107017 ATGATCGCCCCAGGTCAAAG 60.107 55.000 0.00 0.00 0.00 2.77
7686 11185 1.452145 GCAACACACCCCGACATTGT 61.452 55.000 0.00 0.00 0.00 2.71
8269 11783 3.621558 GAGAGGGTTCGGGAATTTTGAT 58.378 45.455 0.00 0.00 0.00 2.57
8330 11844 2.203640 ACCAGAGCACGGTCTCCA 60.204 61.111 0.00 0.00 33.66 3.86
8340 11854 1.002134 CGGTCTCCATGCCCAAAGT 60.002 57.895 0.00 0.00 0.00 2.66
8451 11967 3.242870 GGAGCGAATTAATCAAGTGCCAG 60.243 47.826 0.00 0.00 0.00 4.85
8469 11985 4.515191 TGCCAGTCTCTAATGTTTTGTGTC 59.485 41.667 0.00 0.00 0.00 3.67
8628 12148 6.533730 CCTACCTGCTAAATAATCCACATGA 58.466 40.000 0.00 0.00 0.00 3.07
8655 14460 2.224079 GGCGGACATATGCAGTACAATG 59.776 50.000 1.58 0.00 0.00 2.82
9041 16806 1.418342 GGCGCGTTCGAATAGCTTGA 61.418 55.000 20.82 0.00 38.10 3.02
9044 16809 1.852280 CGCGTTCGAATAGCTTGATCA 59.148 47.619 20.82 0.00 38.10 2.92
9138 16922 8.400947 CAAAATACTCTCTCTCTCTCTCTCTTG 58.599 40.741 0.00 0.00 0.00 3.02
9139 16923 6.814954 ATACTCTCTCTCTCTCTCTCTTGT 57.185 41.667 0.00 0.00 0.00 3.16
9140 16924 4.836825 ACTCTCTCTCTCTCTCTCTTGTG 58.163 47.826 0.00 0.00 0.00 3.33
9283 18090 6.759827 GCATCATGGAGTTCAAGCAATAATTT 59.240 34.615 0.00 0.00 0.00 1.82
9294 18101 8.783093 GTTCAAGCAATAATTTTAAAAGGGCTT 58.217 29.630 15.53 15.53 39.42 4.35
9308 18115 6.976934 AAAAGGGCTTGTCATTTTCTCTAA 57.023 33.333 0.00 0.00 0.00 2.10
9343 18150 0.535102 ACACCCCTTTGAAGAGCGTG 60.535 55.000 0.00 0.00 0.00 5.34
9344 18151 0.535102 CACCCCTTTGAAGAGCGTGT 60.535 55.000 0.00 0.00 0.00 4.49
9345 18152 0.250338 ACCCCTTTGAAGAGCGTGTC 60.250 55.000 0.00 0.00 0.00 3.67
9346 18153 0.955919 CCCCTTTGAAGAGCGTGTCC 60.956 60.000 0.00 0.00 0.00 4.02
9347 18154 0.035458 CCCTTTGAAGAGCGTGTCCT 59.965 55.000 0.00 0.00 0.00 3.85
9348 18155 1.543429 CCCTTTGAAGAGCGTGTCCTT 60.543 52.381 0.00 0.00 0.00 3.36
9349 18156 2.222027 CCTTTGAAGAGCGTGTCCTTT 58.778 47.619 0.00 0.00 0.00 3.11
9443 18250 0.830023 GGGGGCTGTTTGGTTGCTAA 60.830 55.000 0.00 0.00 0.00 3.09
9532 18340 0.598065 AGCGTTTTTCCCTCACATGC 59.402 50.000 0.00 0.00 0.00 4.06
9533 18341 0.313672 GCGTTTTTCCCTCACATGCA 59.686 50.000 0.00 0.00 0.00 3.96
9534 18342 1.269517 GCGTTTTTCCCTCACATGCAA 60.270 47.619 0.00 0.00 0.00 4.08
9535 18343 2.664916 CGTTTTTCCCTCACATGCAAG 58.335 47.619 0.00 0.00 0.00 4.01
9536 18344 2.607771 CGTTTTTCCCTCACATGCAAGG 60.608 50.000 6.94 6.94 0.00 3.61
9537 18345 2.365293 GTTTTTCCCTCACATGCAAGGT 59.635 45.455 11.84 0.00 0.00 3.50
9538 18346 3.517296 TTTTCCCTCACATGCAAGGTA 57.483 42.857 11.84 0.00 0.00 3.08
9539 18347 2.787473 TTCCCTCACATGCAAGGTAG 57.213 50.000 11.84 0.00 0.00 3.18
9540 18348 1.656587 TCCCTCACATGCAAGGTAGT 58.343 50.000 11.84 0.00 0.00 2.73
9541 18349 1.555075 TCCCTCACATGCAAGGTAGTC 59.445 52.381 11.84 0.00 0.00 2.59
9542 18350 1.278985 CCCTCACATGCAAGGTAGTCA 59.721 52.381 11.84 0.00 0.00 3.41
9543 18351 2.625737 CCTCACATGCAAGGTAGTCAG 58.374 52.381 5.92 0.00 0.00 3.51
9544 18352 2.234661 CCTCACATGCAAGGTAGTCAGA 59.765 50.000 5.92 0.00 0.00 3.27
9545 18353 3.306989 CCTCACATGCAAGGTAGTCAGAA 60.307 47.826 5.92 0.00 0.00 3.02
9546 18354 4.511527 CTCACATGCAAGGTAGTCAGAAT 58.488 43.478 0.00 0.00 0.00 2.40
9547 18355 4.507710 TCACATGCAAGGTAGTCAGAATC 58.492 43.478 0.00 0.00 0.00 2.52
9548 18356 3.624861 CACATGCAAGGTAGTCAGAATCC 59.375 47.826 0.00 0.00 0.00 3.01
9549 18357 3.209410 CATGCAAGGTAGTCAGAATCCC 58.791 50.000 0.00 0.00 0.00 3.85
9550 18358 1.207089 TGCAAGGTAGTCAGAATCCCG 59.793 52.381 0.00 0.00 0.00 5.14
9551 18359 1.480954 GCAAGGTAGTCAGAATCCCGA 59.519 52.381 0.00 0.00 0.00 5.14
9552 18360 2.738964 GCAAGGTAGTCAGAATCCCGAC 60.739 54.545 0.00 0.00 0.00 4.79
9553 18361 1.777941 AGGTAGTCAGAATCCCGACC 58.222 55.000 0.00 0.00 32.33 4.79
9554 18362 0.751452 GGTAGTCAGAATCCCGACCC 59.249 60.000 0.00 0.00 32.33 4.46
9555 18363 0.384669 GTAGTCAGAATCCCGACCCG 59.615 60.000 0.00 0.00 32.33 5.28
9556 18364 0.256752 TAGTCAGAATCCCGACCCGA 59.743 55.000 0.00 0.00 32.33 5.14
9557 18365 1.141234 GTCAGAATCCCGACCCGAC 59.859 63.158 0.00 0.00 0.00 4.79
9558 18366 1.000019 TCAGAATCCCGACCCGACT 60.000 57.895 0.00 0.00 0.00 4.18
9559 18367 0.613853 TCAGAATCCCGACCCGACTT 60.614 55.000 0.00 0.00 0.00 3.01
9560 18368 0.179108 CAGAATCCCGACCCGACTTC 60.179 60.000 0.00 0.00 0.00 3.01
9561 18369 1.226888 GAATCCCGACCCGACTTCG 60.227 63.158 0.00 0.00 39.44 3.79
9562 18370 1.660560 GAATCCCGACCCGACTTCGA 61.661 60.000 0.00 0.00 43.02 3.71
9563 18371 1.252904 AATCCCGACCCGACTTCGAA 61.253 55.000 0.00 0.00 43.02 3.71
9564 18372 1.041447 ATCCCGACCCGACTTCGAAT 61.041 55.000 0.00 0.00 43.02 3.34
9565 18373 1.226888 CCCGACCCGACTTCGAATC 60.227 63.158 0.00 0.00 43.02 2.52
9566 18374 1.226888 CCGACCCGACTTCGAATCC 60.227 63.158 0.00 0.00 43.02 3.01
9567 18375 1.664321 CCGACCCGACTTCGAATCCT 61.664 60.000 0.00 0.00 43.02 3.24
9568 18376 1.019673 CGACCCGACTTCGAATCCTA 58.980 55.000 0.00 0.00 43.02 2.94
9569 18377 1.268437 CGACCCGACTTCGAATCCTAC 60.268 57.143 0.00 0.00 43.02 3.18
9570 18378 0.737219 ACCCGACTTCGAATCCTACG 59.263 55.000 0.00 0.76 43.02 3.51
9571 18379 1.019673 CCCGACTTCGAATCCTACGA 58.980 55.000 0.00 0.00 43.02 3.43
9572 18380 1.268437 CCCGACTTCGAATCCTACGAC 60.268 57.143 0.00 0.00 43.02 4.34
9573 18381 1.669779 CCGACTTCGAATCCTACGACT 59.330 52.381 0.00 0.00 43.02 4.18
9574 18382 2.097142 CCGACTTCGAATCCTACGACTT 59.903 50.000 0.00 0.00 43.02 3.01
9575 18383 3.352652 CGACTTCGAATCCTACGACTTC 58.647 50.000 0.00 0.00 43.02 3.01
9576 18384 3.181513 CGACTTCGAATCCTACGACTTCA 60.182 47.826 0.00 0.00 43.02 3.02
9577 18385 4.094090 ACTTCGAATCCTACGACTTCAC 57.906 45.455 0.00 0.00 39.46 3.18
9578 18386 2.819422 TCGAATCCTACGACTTCACG 57.181 50.000 0.00 0.00 34.85 4.35
9579 18387 2.349590 TCGAATCCTACGACTTCACGA 58.650 47.619 0.00 0.00 34.85 4.35
9580 18388 2.094894 TCGAATCCTACGACTTCACGAC 59.905 50.000 0.00 0.00 34.85 4.34
9581 18389 2.790468 CGAATCCTACGACTTCACGACC 60.790 54.545 0.00 0.00 37.03 4.79
9582 18390 1.101331 ATCCTACGACTTCACGACCC 58.899 55.000 0.00 0.00 37.03 4.46
9583 18391 0.037303 TCCTACGACTTCACGACCCT 59.963 55.000 0.00 0.00 37.03 4.34
9584 18392 1.278985 TCCTACGACTTCACGACCCTA 59.721 52.381 0.00 0.00 37.03 3.53
9585 18393 1.399791 CCTACGACTTCACGACCCTAC 59.600 57.143 0.00 0.00 37.03 3.18
9586 18394 1.061711 CTACGACTTCACGACCCTACG 59.938 57.143 0.00 0.00 37.03 3.51
9587 18395 0.603707 ACGACTTCACGACCCTACGA 60.604 55.000 0.00 0.00 37.03 3.43
9588 18396 0.518636 CGACTTCACGACCCTACGAA 59.481 55.000 0.00 0.00 37.03 3.85
9589 18397 1.069022 CGACTTCACGACCCTACGAAA 60.069 52.381 0.00 0.00 37.03 3.46
9590 18398 2.593257 GACTTCACGACCCTACGAAAG 58.407 52.381 0.00 0.00 36.51 2.62
9591 18399 1.336609 ACTTCACGACCCTACGAAAGC 60.337 52.381 0.00 0.00 35.17 3.51
9592 18400 0.675083 TTCACGACCCTACGAAAGCA 59.325 50.000 0.00 0.00 37.03 3.91
9593 18401 0.892755 TCACGACCCTACGAAAGCAT 59.107 50.000 0.00 0.00 37.03 3.79
9594 18402 0.999406 CACGACCCTACGAAAGCATG 59.001 55.000 0.00 0.00 37.03 4.06
9595 18403 0.606604 ACGACCCTACGAAAGCATGT 59.393 50.000 0.00 0.00 37.03 3.21
9596 18404 1.278238 CGACCCTACGAAAGCATGTC 58.722 55.000 0.00 0.00 35.09 3.06
9605 18413 2.927553 GAAAGCATGTCGAGCCAAAT 57.072 45.000 0.00 0.00 0.00 2.32
9606 18414 2.790387 GAAAGCATGTCGAGCCAAATC 58.210 47.619 0.00 0.00 0.00 2.17
9607 18415 1.098050 AAGCATGTCGAGCCAAATCC 58.902 50.000 0.00 0.00 0.00 3.01
9608 18416 0.749454 AGCATGTCGAGCCAAATCCC 60.749 55.000 0.00 0.00 0.00 3.85
9609 18417 1.031571 GCATGTCGAGCCAAATCCCA 61.032 55.000 0.00 0.00 0.00 4.37
9610 18418 0.734889 CATGTCGAGCCAAATCCCAC 59.265 55.000 0.00 0.00 0.00 4.61
9611 18419 0.620556 ATGTCGAGCCAAATCCCACT 59.379 50.000 0.00 0.00 0.00 4.00
9612 18420 1.271856 TGTCGAGCCAAATCCCACTA 58.728 50.000 0.00 0.00 0.00 2.74
9613 18421 1.837439 TGTCGAGCCAAATCCCACTAT 59.163 47.619 0.00 0.00 0.00 2.12
9614 18422 2.213499 GTCGAGCCAAATCCCACTATG 58.787 52.381 0.00 0.00 0.00 2.23
9615 18423 2.115427 TCGAGCCAAATCCCACTATGA 58.885 47.619 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.656323 ACCACCATTGAATCTACTAATCTACTA 57.344 33.333 0.00 0.00 0.00 1.82
27 28 8.554490 ACCACCATTGAATCTACTAATCTACT 57.446 34.615 0.00 0.00 0.00 2.57
28 29 7.873505 GGACCACCATTGAATCTACTAATCTAC 59.126 40.741 0.00 0.00 35.97 2.59
29 30 7.789831 AGGACCACCATTGAATCTACTAATCTA 59.210 37.037 0.00 0.00 38.94 1.98
30 31 6.617371 AGGACCACCATTGAATCTACTAATCT 59.383 38.462 0.00 0.00 38.94 2.40
31 32 6.831976 AGGACCACCATTGAATCTACTAATC 58.168 40.000 0.00 0.00 38.94 1.75
32 33 6.831664 AGGACCACCATTGAATCTACTAAT 57.168 37.500 0.00 0.00 38.94 1.73
33 34 7.743116 TTAGGACCACCATTGAATCTACTAA 57.257 36.000 0.00 0.00 38.94 2.24
34 35 7.743116 TTTAGGACCACCATTGAATCTACTA 57.257 36.000 0.00 0.00 38.94 1.82
35 36 6.636454 TTTAGGACCACCATTGAATCTACT 57.364 37.500 0.00 0.00 38.94 2.57
39 40 7.410120 AATCTTTTAGGACCACCATTGAATC 57.590 36.000 0.00 0.00 38.94 2.52
247 248 3.502191 TTTTGACCACTTTGTGTCAGC 57.498 42.857 0.00 0.00 30.31 4.26
249 250 5.913137 AGAATTTTGACCACTTTGTGTCA 57.087 34.783 0.00 0.00 0.00 3.58
494 508 9.719279 ACACGTACTTTTTCGAAAATTAATCAA 57.281 25.926 23.05 6.47 0.00 2.57
655 711 0.853224 GACGACGTGAAATGCATGCG 60.853 55.000 14.09 5.83 36.99 4.73
710 776 9.107367 GATTAGCTTGTTGTCAAATATAATCGC 57.893 33.333 0.00 0.00 31.18 4.58
727 795 6.639686 GTGCATGGTTTCATATGATTAGCTTG 59.360 38.462 6.17 14.86 31.33 4.01
779 861 1.995626 CGGGGAGGGTGACAGGATT 60.996 63.158 0.00 0.00 0.00 3.01
797 893 4.743644 GCACGAGGTATTTATAGGTCACAC 59.256 45.833 0.00 0.00 0.00 3.82
799 895 3.979495 CGCACGAGGTATTTATAGGTCAC 59.021 47.826 0.00 0.00 0.00 3.67
835 933 1.288188 TGGAATGGACTGCTGATGGA 58.712 50.000 0.00 0.00 0.00 3.41
842 940 0.034186 TGTGGGATGGAATGGACTGC 60.034 55.000 0.00 0.00 0.00 4.40
891 993 3.846590 CACGCACGCTAGCTGCTG 61.847 66.667 26.00 22.18 40.11 4.41
942 1060 3.103911 GCTCGACCGTGAACCGTG 61.104 66.667 0.00 0.00 33.66 4.94
1024 1142 0.603065 GCCCCAAGTAACCAAAGCAG 59.397 55.000 0.00 0.00 0.00 4.24
1048 1166 0.460311 ACGGAAACTCCCAGCGATAG 59.540 55.000 0.00 0.00 31.13 2.08
1051 1169 0.245539 CTAACGGAAACTCCCAGCGA 59.754 55.000 0.00 0.00 31.13 4.93
1151 1355 4.265904 TGACGGTGAGTTTATGACATGT 57.734 40.909 0.00 0.00 0.00 3.21
1155 1359 9.620660 AAAATAAAATGACGGTGAGTTTATGAC 57.379 29.630 12.42 0.00 0.00 3.06
1165 1372 6.949578 AATCTGCAAAATAAAATGACGGTG 57.050 33.333 0.00 0.00 0.00 4.94
1168 1375 8.909708 TCCTTAATCTGCAAAATAAAATGACG 57.090 30.769 0.00 0.00 0.00 4.35
1174 1392 7.701539 TGCTCTCCTTAATCTGCAAAATAAA 57.298 32.000 0.00 0.00 0.00 1.40
1175 1393 7.394359 AGTTGCTCTCCTTAATCTGCAAAATAA 59.606 33.333 0.00 0.00 41.14 1.40
1209 1427 1.221293 CCTCTCCTTGCAGAGCCTG 59.779 63.158 0.00 0.00 38.98 4.85
1396 1614 1.613925 CGGAATCGCCAGAGAGGATAA 59.386 52.381 0.00 0.00 41.22 1.75
1600 1819 6.875948 TCATCAAATTCTTCGTCTTCCAAA 57.124 33.333 0.00 0.00 0.00 3.28
1776 1995 1.275291 CAAAGAGCTTCGGACCTACCA 59.725 52.381 0.00 0.00 38.90 3.25
1959 2182 3.478857 TTTTCTTACAGAACGCCTCCA 57.521 42.857 0.00 0.00 33.26 3.86
2275 2498 4.821532 ATCATGGGAAGGAGGCTTATTT 57.178 40.909 0.00 0.00 0.00 1.40
2406 2629 0.983467 TGTGCATGCCTCCTTAGACA 59.017 50.000 16.68 7.20 0.00 3.41
2437 2660 2.840038 TCTTTTCCTAGCAGCAGGATCA 59.160 45.455 12.69 3.02 44.26 2.92
2623 2846 1.153549 GGCCGCCGATCTATCATCC 60.154 63.158 0.00 0.00 0.00 3.51
2923 5805 2.345876 CACTCGCACATCAATGTACCA 58.654 47.619 0.00 0.00 39.39 3.25
3199 6081 9.253832 ACCATTGTCATATGTAAAAGGAAATCA 57.746 29.630 16.14 0.00 0.00 2.57
3580 6463 0.820871 ATCAGCCAACTCCTCTCGTC 59.179 55.000 0.00 0.00 0.00 4.20
3783 6669 1.880340 CCGACCATCGCAGCTTCTC 60.880 63.158 0.00 0.00 38.82 2.87
3815 6701 2.780414 TCCATGTCAGAAGGGGATGAT 58.220 47.619 0.00 0.00 0.00 2.45
3923 6809 4.960938 TGTTGTTCATAGCTTCAGACACT 58.039 39.130 0.00 0.00 0.00 3.55
3955 6841 2.269940 CCTCCTCCTCAGAAAAAGGGA 58.730 52.381 0.00 0.00 34.46 4.20
4030 6916 1.412343 GCTGGAAAAACCTTGCTGGAA 59.588 47.619 3.40 0.00 39.71 3.53
4034 6920 1.975660 TACGCTGGAAAAACCTTGCT 58.024 45.000 0.00 0.00 39.86 3.91
4367 7267 4.685628 CACGCAGCAATATTGTTTCCTTTT 59.314 37.500 16.61 0.00 0.00 2.27
4397 7297 2.037641 GGCCTTGGACAAATCAAGCTTT 59.962 45.455 0.00 0.00 40.00 3.51
4540 7440 7.520451 GGTGTAAAAACCTCCAATAACTTCT 57.480 36.000 0.00 0.00 37.24 2.85
4865 7765 4.598036 ATTGATTTCCTCCACCACTGAT 57.402 40.909 0.00 0.00 0.00 2.90
4915 7815 4.794169 CAAACCGAGGTATTTTGGTTCAG 58.206 43.478 0.00 0.00 42.74 3.02
5087 7987 4.304110 GAAGTCGGAACACACTCATAACA 58.696 43.478 0.00 0.00 0.00 2.41
5114 8014 9.761504 ATCTTTATAAGATCATCACACACTGAG 57.238 33.333 0.00 0.00 44.79 3.35
5269 8171 4.756630 CCTGCTTGGCCAACAAAC 57.243 55.556 16.05 5.06 38.91 2.93
5293 8195 1.499438 TGTCCGGACTATCCAGGAGAT 59.501 52.381 33.39 0.00 38.96 2.75
5412 8314 5.466728 TCTTCAAAAGATCAAGTCCGTGAAG 59.533 40.000 0.00 0.00 39.01 3.02
5664 8566 4.574421 CCACGTAATGAAATCCTGCACATA 59.426 41.667 0.00 0.00 0.00 2.29
5682 8584 2.943033 CACTCTTTTCAGGAAACCACGT 59.057 45.455 0.00 0.00 0.00 4.49
5690 8592 4.503714 AAAGTGTCCACTCTTTTCAGGA 57.496 40.909 0.00 0.00 41.58 3.86
5750 8652 5.476614 GAGGAACTTAAGTGTACCGAATGT 58.523 41.667 9.34 0.00 41.55 2.71
5834 8736 8.081517 TCCAAGCCATAATCTTCATTTTCAAT 57.918 30.769 0.00 0.00 0.00 2.57
5980 8882 4.404394 TCCAAATTCTGCTTGCATGATCAT 59.596 37.500 1.18 1.18 0.00 2.45
6057 8959 4.460263 ACATTTAACAGCCAGTCTTGTCA 58.540 39.130 0.00 0.00 0.00 3.58
6062 8964 4.022849 GCAAGAACATTTAACAGCCAGTCT 60.023 41.667 0.00 0.00 0.00 3.24
6194 9096 4.994282 TGTAACTCTGGAGGTAGTCTGAA 58.006 43.478 2.58 0.00 29.99 3.02
6301 9203 4.821589 CGCTCGGCCTGGGAACTC 62.822 72.222 0.00 0.00 0.00 3.01
6593 9495 2.038033 TGACCTGGTTAAACTCTTCCCG 59.962 50.000 0.00 0.00 0.00 5.14
6597 9499 4.439253 AAGCTGACCTGGTTAAACTCTT 57.561 40.909 0.00 0.00 0.00 2.85
6660 9562 5.423610 TGATTTTTGAAGGAACAAACTCCCA 59.576 36.000 0.00 0.00 39.08 4.37
6742 9644 1.123077 CCCTAGCCATACAGCAGTGA 58.877 55.000 0.00 0.00 34.23 3.41
6743 9645 1.069823 CTCCCTAGCCATACAGCAGTG 59.930 57.143 0.00 0.00 34.23 3.66
6869 9771 4.711399 ACCGCCAGACTAACTAACTTTTT 58.289 39.130 0.00 0.00 0.00 1.94
6870 9772 4.313282 GACCGCCAGACTAACTAACTTTT 58.687 43.478 0.00 0.00 0.00 2.27
6871 9773 3.613432 CGACCGCCAGACTAACTAACTTT 60.613 47.826 0.00 0.00 0.00 2.66
6872 9774 2.094854 CGACCGCCAGACTAACTAACTT 60.095 50.000 0.00 0.00 0.00 2.66
6873 9775 1.471684 CGACCGCCAGACTAACTAACT 59.528 52.381 0.00 0.00 0.00 2.24
6874 9776 1.468736 CCGACCGCCAGACTAACTAAC 60.469 57.143 0.00 0.00 0.00 2.34
6875 9777 0.813184 CCGACCGCCAGACTAACTAA 59.187 55.000 0.00 0.00 0.00 2.24
6876 9778 1.660560 GCCGACCGCCAGACTAACTA 61.661 60.000 0.00 0.00 0.00 2.24
6877 9779 3.003113 GCCGACCGCCAGACTAACT 62.003 63.158 0.00 0.00 0.00 2.24
6878 9780 2.508663 GCCGACCGCCAGACTAAC 60.509 66.667 0.00 0.00 0.00 2.34
6889 9791 0.603439 TTTCCAGTAAACGGCCGACC 60.603 55.000 35.90 15.85 0.00 4.79
6890 9792 1.445871 ATTTCCAGTAAACGGCCGAC 58.554 50.000 35.90 20.61 0.00 4.79
6901 9803 4.497291 TTAGCGGATGGTTATTTCCAGT 57.503 40.909 0.00 0.00 41.05 4.00
6941 9845 8.564509 TGCCTGTGTACACGTACATATATATA 57.435 34.615 20.61 0.00 46.36 0.86
6946 10242 4.368315 CATGCCTGTGTACACGTACATAT 58.632 43.478 20.61 7.78 46.36 1.78
6952 10248 0.602638 CACCATGCCTGTGTACACGT 60.603 55.000 20.61 7.96 0.00 4.49
7141 10437 0.619255 TTCCGAGCTTGGGGTGGATA 60.619 55.000 20.46 0.00 0.00 2.59
7253 10694 6.641723 TCGAACATATCAAGTTAACGACAACA 59.358 34.615 0.00 0.00 0.00 3.33
7396 10868 2.741092 GAGCACGGGAACAGGTCA 59.259 61.111 0.00 0.00 34.00 4.02
7453 10925 0.968901 TGATCCGGAGCAGGTACGTT 60.969 55.000 20.59 0.00 0.00 3.99
7536 11008 2.598099 TGTAGTGGCCGTCGGTGA 60.598 61.111 13.94 0.00 0.00 4.02
7599 11071 3.918220 CGAGAAGCGCGTCCATGC 61.918 66.667 19.90 6.40 0.00 4.06
7686 11185 2.477176 GCGGTGCTGTTGTTGACCA 61.477 57.895 0.00 0.00 0.00 4.02
8136 11650 1.542187 GCCGTACTCCACCACCTTCT 61.542 60.000 0.00 0.00 0.00 2.85
8269 11783 3.706373 GCCGGGTCCTTCTGCTCA 61.706 66.667 2.18 0.00 0.00 4.26
8451 11967 5.237344 AGCACAGACACAAAACATTAGAGAC 59.763 40.000 0.00 0.00 0.00 3.36
8628 12148 2.760092 ACTGCATATGTCCGCCATTTTT 59.240 40.909 4.29 0.00 34.86 1.94
8988 15751 4.699735 CCTTACCACACACAAAGCATCATA 59.300 41.667 0.00 0.00 0.00 2.15
8990 15753 2.884012 CCTTACCACACACAAAGCATCA 59.116 45.455 0.00 0.00 0.00 3.07
9029 16794 3.133691 GTGCCATGATCAAGCTATTCGA 58.866 45.455 18.64 0.00 0.00 3.71
9041 16806 4.858850 TGATCCTAAGTTTGTGCCATGAT 58.141 39.130 0.00 0.00 0.00 2.45
9044 16809 6.014327 ACAAAATGATCCTAAGTTTGTGCCAT 60.014 34.615 8.69 0.00 40.06 4.40
9138 16922 2.536728 CGATGAACACACACACACACAC 60.537 50.000 0.00 0.00 0.00 3.82
9139 16923 1.663135 CGATGAACACACACACACACA 59.337 47.619 0.00 0.00 0.00 3.72
9140 16924 1.663643 ACGATGAACACACACACACAC 59.336 47.619 0.00 0.00 0.00 3.82
9283 18090 6.976934 AGAGAAAATGACAAGCCCTTTTAA 57.023 33.333 0.00 0.00 0.00 1.52
9315 18122 2.972348 TCAAAGGGGTGTAGAGAGTGT 58.028 47.619 0.00 0.00 0.00 3.55
9343 18150 7.147602 TGCCTAGAACTTATTAGGGTAAAGGAC 60.148 40.741 0.00 0.00 37.50 3.85
9344 18151 6.904654 TGCCTAGAACTTATTAGGGTAAAGGA 59.095 38.462 0.00 0.00 37.50 3.36
9345 18152 7.133133 TGCCTAGAACTTATTAGGGTAAAGG 57.867 40.000 0.00 0.00 37.50 3.11
9346 18153 8.652290 AGATGCCTAGAACTTATTAGGGTAAAG 58.348 37.037 0.00 0.00 37.50 1.85
9347 18154 8.429641 CAGATGCCTAGAACTTATTAGGGTAAA 58.570 37.037 0.00 0.00 37.50 2.01
9348 18155 7.567622 ACAGATGCCTAGAACTTATTAGGGTAA 59.432 37.037 0.00 0.00 37.50 2.85
9349 18156 7.073854 ACAGATGCCTAGAACTTATTAGGGTA 58.926 38.462 0.00 0.00 37.50 3.69
9390 18197 5.231702 TGGTCAATACGGGACTTACTTTT 57.768 39.130 0.00 0.00 35.61 2.27
9391 18198 4.895668 TGGTCAATACGGGACTTACTTT 57.104 40.909 0.00 0.00 35.61 2.66
9443 18250 1.475751 CCAGGCAAATATCGCTCAGGT 60.476 52.381 0.00 0.00 0.00 4.00
9532 18340 2.159085 GGTCGGGATTCTGACTACCTTG 60.159 54.545 12.86 0.00 45.99 3.61
9533 18341 2.108970 GGTCGGGATTCTGACTACCTT 58.891 52.381 12.86 0.00 45.99 3.50
9534 18342 1.688627 GGGTCGGGATTCTGACTACCT 60.689 57.143 12.86 0.00 45.99 3.08
9535 18343 0.751452 GGGTCGGGATTCTGACTACC 59.249 60.000 12.86 2.83 45.99 3.18
9536 18344 0.384669 CGGGTCGGGATTCTGACTAC 59.615 60.000 12.86 5.65 45.99 2.73
9537 18345 0.256752 TCGGGTCGGGATTCTGACTA 59.743 55.000 12.86 0.00 45.99 2.59
9538 18346 1.000019 TCGGGTCGGGATTCTGACT 60.000 57.895 12.86 0.00 45.99 3.41
9539 18347 1.141234 GTCGGGTCGGGATTCTGAC 59.859 63.158 4.13 4.13 46.01 3.51
9540 18348 0.613853 AAGTCGGGTCGGGATTCTGA 60.614 55.000 0.00 0.00 0.00 3.27
9541 18349 0.179108 GAAGTCGGGTCGGGATTCTG 60.179 60.000 0.00 0.00 0.00 3.02
9542 18350 1.664321 CGAAGTCGGGTCGGGATTCT 61.664 60.000 0.00 0.00 34.85 2.40
9543 18351 1.226888 CGAAGTCGGGTCGGGATTC 60.227 63.158 0.00 0.00 34.85 2.52
9544 18352 1.252904 TTCGAAGTCGGGTCGGGATT 61.253 55.000 0.00 0.00 39.01 3.01
9545 18353 1.041447 ATTCGAAGTCGGGTCGGGAT 61.041 55.000 3.35 0.00 39.01 3.85
9546 18354 1.660560 GATTCGAAGTCGGGTCGGGA 61.661 60.000 3.35 0.00 39.01 5.14
9547 18355 1.226888 GATTCGAAGTCGGGTCGGG 60.227 63.158 3.35 0.00 39.01 5.14
9548 18356 1.226888 GGATTCGAAGTCGGGTCGG 60.227 63.158 3.35 0.00 39.01 4.79
9549 18357 1.019673 TAGGATTCGAAGTCGGGTCG 58.980 55.000 3.35 0.00 40.29 4.79
9550 18358 1.268437 CGTAGGATTCGAAGTCGGGTC 60.268 57.143 3.35 0.00 40.29 4.46
9551 18359 0.737219 CGTAGGATTCGAAGTCGGGT 59.263 55.000 3.35 0.00 40.29 5.28
9552 18360 1.019673 TCGTAGGATTCGAAGTCGGG 58.980 55.000 3.35 0.00 40.29 5.14
9553 18361 1.669779 AGTCGTAGGATTCGAAGTCGG 59.330 52.381 3.35 0.00 39.01 4.79
9554 18362 3.181513 TGAAGTCGTAGGATTCGAAGTCG 60.182 47.826 3.35 4.18 39.01 4.18
9555 18363 4.097012 GTGAAGTCGTAGGATTCGAAGTC 58.903 47.826 3.35 1.66 39.01 3.01
9556 18364 3.425892 CGTGAAGTCGTAGGATTCGAAGT 60.426 47.826 3.35 0.00 39.01 3.01
9557 18365 3.099362 CGTGAAGTCGTAGGATTCGAAG 58.901 50.000 3.35 0.00 39.01 3.79
9558 18366 2.743664 TCGTGAAGTCGTAGGATTCGAA 59.256 45.455 0.00 0.00 39.01 3.71
9559 18367 2.094894 GTCGTGAAGTCGTAGGATTCGA 59.905 50.000 0.00 0.00 34.91 3.71
9560 18368 2.438583 GTCGTGAAGTCGTAGGATTCG 58.561 52.381 0.00 0.00 0.00 3.34
9561 18369 2.479219 GGGTCGTGAAGTCGTAGGATTC 60.479 54.545 0.00 0.00 0.00 2.52
9562 18370 1.475682 GGGTCGTGAAGTCGTAGGATT 59.524 52.381 0.00 0.00 0.00 3.01
9563 18371 1.101331 GGGTCGTGAAGTCGTAGGAT 58.899 55.000 0.00 0.00 0.00 3.24
9564 18372 0.037303 AGGGTCGTGAAGTCGTAGGA 59.963 55.000 0.00 0.00 0.00 2.94
9565 18373 1.399791 GTAGGGTCGTGAAGTCGTAGG 59.600 57.143 0.00 0.00 0.00 3.18
9566 18374 1.061711 CGTAGGGTCGTGAAGTCGTAG 59.938 57.143 0.00 0.00 0.00 3.51
9567 18375 1.078709 CGTAGGGTCGTGAAGTCGTA 58.921 55.000 0.00 0.00 0.00 3.43
9568 18376 0.603707 TCGTAGGGTCGTGAAGTCGT 60.604 55.000 0.00 0.00 0.00 4.34
9569 18377 0.518636 TTCGTAGGGTCGTGAAGTCG 59.481 55.000 0.00 0.00 0.00 4.18
9570 18378 2.593257 CTTTCGTAGGGTCGTGAAGTC 58.407 52.381 0.00 0.00 0.00 3.01
9571 18379 1.336609 GCTTTCGTAGGGTCGTGAAGT 60.337 52.381 0.00 0.00 32.53 3.01
9572 18380 1.336517 TGCTTTCGTAGGGTCGTGAAG 60.337 52.381 0.00 0.00 0.00 3.02
9573 18381 0.675083 TGCTTTCGTAGGGTCGTGAA 59.325 50.000 0.00 0.00 0.00 3.18
9574 18382 0.892755 ATGCTTTCGTAGGGTCGTGA 59.107 50.000 0.00 0.00 0.00 4.35
9575 18383 0.999406 CATGCTTTCGTAGGGTCGTG 59.001 55.000 0.00 0.00 0.00 4.35
9576 18384 0.606604 ACATGCTTTCGTAGGGTCGT 59.393 50.000 0.00 0.00 0.00 4.34
9577 18385 1.278238 GACATGCTTTCGTAGGGTCG 58.722 55.000 0.00 0.00 0.00 4.79
9578 18386 1.135199 TCGACATGCTTTCGTAGGGTC 60.135 52.381 4.38 0.00 37.73 4.46
9579 18387 0.892755 TCGACATGCTTTCGTAGGGT 59.107 50.000 4.38 0.00 37.73 4.34
9580 18388 1.560923 CTCGACATGCTTTCGTAGGG 58.439 55.000 4.38 0.00 37.73 3.53
9581 18389 0.924090 GCTCGACATGCTTTCGTAGG 59.076 55.000 4.38 0.00 37.73 3.18
9582 18390 0.924090 GGCTCGACATGCTTTCGTAG 59.076 55.000 4.38 2.92 37.73 3.51
9583 18391 0.245266 TGGCTCGACATGCTTTCGTA 59.755 50.000 4.38 0.00 37.73 3.43
9584 18392 0.602638 TTGGCTCGACATGCTTTCGT 60.603 50.000 4.38 0.00 37.73 3.85
9585 18393 0.516877 TTTGGCTCGACATGCTTTCG 59.483 50.000 0.00 0.00 37.85 3.46
9586 18394 2.478539 GGATTTGGCTCGACATGCTTTC 60.479 50.000 0.00 0.00 0.00 2.62
9587 18395 1.474077 GGATTTGGCTCGACATGCTTT 59.526 47.619 0.00 0.00 0.00 3.51
9588 18396 1.098050 GGATTTGGCTCGACATGCTT 58.902 50.000 0.00 0.00 0.00 3.91
9589 18397 0.749454 GGGATTTGGCTCGACATGCT 60.749 55.000 0.00 0.00 0.00 3.79
9590 18398 1.031571 TGGGATTTGGCTCGACATGC 61.032 55.000 0.00 0.00 0.00 4.06
9591 18399 0.734889 GTGGGATTTGGCTCGACATG 59.265 55.000 0.00 0.00 0.00 3.21
9592 18400 0.620556 AGTGGGATTTGGCTCGACAT 59.379 50.000 0.00 0.00 0.00 3.06
9593 18401 1.271856 TAGTGGGATTTGGCTCGACA 58.728 50.000 0.00 0.00 0.00 4.35
9594 18402 2.158957 TCATAGTGGGATTTGGCTCGAC 60.159 50.000 0.00 0.00 0.00 4.20
9595 18403 2.115427 TCATAGTGGGATTTGGCTCGA 58.885 47.619 0.00 0.00 0.00 4.04
9596 18404 2.620251 TCATAGTGGGATTTGGCTCG 57.380 50.000 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.