Multiple sequence alignment - TraesCS7A01G391100

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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 TraesCS7A01G391100 chr7A 100.000 8643 0 0 1 8643 567373615 567382257 0.000000e+00 15961.0
1 TraesCS7A01G391100 chr7A 90.428 2173 152 27 5507 7650 567006855 567009000 0.000000e+00 2809.0
2 TraesCS7A01G391100 chr7A 86.150 917 70 26 1884 2751 567003413 567004321 0.000000e+00 937.0
3 TraesCS7A01G391100 chr7A 88.415 751 56 10 3418 4168 567004946 567005665 0.000000e+00 876.0
4 TraesCS7A01G391100 chr7A 84.435 938 91 32 4203 5122 567005724 567006624 0.000000e+00 872.0
5 TraesCS7A01G391100 chr7A 93.450 458 29 1 2760 3216 567004413 567004870 0.000000e+00 678.0
6 TraesCS7A01G391100 chr7A 85.106 470 50 16 1430 1884 567002786 567003250 6.110000e-126 462.0
7 TraesCS7A01G391100 chr7A 89.730 185 11 2 5175 5353 567006604 567006786 6.750000e-56 230.0
8 TraesCS7A01G391100 chr7B 93.957 4799 181 34 3268 7992 529671382 529676145 0.000000e+00 7155.0
9 TraesCS7A01G391100 chr7B 92.836 1368 72 9 1922 3270 529669946 529671306 0.000000e+00 1960.0
10 TraesCS7A01G391100 chr7B 91.925 805 47 11 1084 1884 529668992 529669782 0.000000e+00 1110.0
11 TraesCS7A01G391100 chr7B 86.871 1013 54 21 73 1051 529668028 529668995 0.000000e+00 1061.0
12 TraesCS7A01G391100 chr7B 90.850 612 35 6 7990 8599 529676302 529676894 0.000000e+00 800.0
13 TraesCS7A01G391100 chr7B 93.878 49 3 0 5129 5177 461473735 461473687 3.350000e-09 75.0
14 TraesCS7A01G391100 chr7D 93.802 4324 176 48 3730 7992 500890744 500895036 0.000000e+00 6416.0
15 TraesCS7A01G391100 chr7D 90.116 2236 162 36 5479 7682 500823975 500826183 0.000000e+00 2850.0
16 TraesCS7A01G391100 chr7D 89.916 1428 70 29 497 1884 500887267 500888660 0.000000e+00 1772.0
17 TraesCS7A01G391100 chr7D 93.340 961 47 4 2761 3720 500889753 500890697 0.000000e+00 1404.0
18 TraesCS7A01G391100 chr7D 90.311 867 52 8 1908 2748 500888779 500889639 0.000000e+00 1107.0
19 TraesCS7A01G391100 chr7D 86.392 970 77 32 4171 5122 500822824 500823756 0.000000e+00 1009.0
20 TraesCS7A01G391100 chr7D 85.932 917 72 27 1884 2751 500820507 500821415 0.000000e+00 926.0
21 TraesCS7A01G391100 chr7D 88.682 751 58 9 3418 4168 500822058 500822781 0.000000e+00 891.0
22 TraesCS7A01G391100 chr7D 89.465 617 38 9 7990 8599 500895267 500895863 0.000000e+00 754.0
23 TraesCS7A01G391100 chr7D 92.779 457 32 1 2761 3216 500821526 500821982 0.000000e+00 660.0
24 TraesCS7A01G391100 chr7D 89.140 442 23 9 71 499 500886446 500886875 2.140000e-145 527.0
25 TraesCS7A01G391100 chr7D 87.339 466 45 8 1431 1884 500819881 500820344 9.940000e-144 521.0
26 TraesCS7A01G391100 chr7D 90.270 185 10 2 5175 5353 500823736 500823918 1.450000e-57 235.0
27 TraesCS7A01G391100 chr7D 97.368 38 0 1 5141 5177 445118592 445118555 7.240000e-06 63.9
28 TraesCS7A01G391100 chrUn 89.857 2238 163 38 5479 7682 86625770 86627977 0.000000e+00 2817.0
29 TraesCS7A01G391100 chrUn 86.834 1352 104 39 1431 2751 86621927 86623235 0.000000e+00 1443.0
30 TraesCS7A01G391100 chrUn 85.155 970 89 33 4171 5122 86624619 86625551 0.000000e+00 942.0
31 TraesCS7A01G391100 chrUn 88.313 753 65 9 3418 4168 86623845 86624576 0.000000e+00 881.0
32 TraesCS7A01G391100 chrUn 94.737 361 19 0 2856 3216 86623409 86623769 5.860000e-156 562.0
33 TraesCS7A01G391100 chrUn 90.270 185 10 2 5175 5353 86625531 86625713 1.450000e-57 235.0
34 TraesCS7A01G391100 chr3D 79.612 206 38 4 7170 7373 323333822 323334025 2.510000e-30 145.0
35 TraesCS7A01G391100 chr3B 83.007 153 26 0 7221 7373 395852531 395852379 1.170000e-28 139.0
36 TraesCS7A01G391100 chr3A 83.007 153 26 0 7221 7373 399573945 399573793 1.170000e-28 139.0
37 TraesCS7A01G391100 chr4B 90.385 52 3 2 5128 5177 497553609 497553558 5.600000e-07 67.6
38 TraesCS7A01G391100 chr4A 90.385 52 3 2 5128 5177 59483684 59483633 5.600000e-07 67.6
39 TraesCS7A01G391100 chr5D 90.385 52 2 3 5129 5177 453818816 453818765 2.010000e-06 65.8
40 TraesCS7A01G391100 chr5A 90.385 52 2 3 5129 5177 572843254 572843203 2.010000e-06 65.8
41 TraesCS7A01G391100 chr6A 89.796 49 3 2 5128 5174 223554297 223554249 2.610000e-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 TraesCS7A01G391100 chr7A 567373615 567382257 8642 False 15961.000000 15961 100.000000 1 8643 1 chr7A.!!$F1 8642
1 TraesCS7A01G391100 chr7A 567002786 567009000 6214 False 980.571429 2809 88.244857 1430 7650 7 chr7A.!!$F2 6220
2 TraesCS7A01G391100 chr7B 529668028 529676894 8866 False 2417.200000 7155 91.287800 73 8599 5 chr7B.!!$F1 8526
3 TraesCS7A01G391100 chr7D 500886446 500895863 9417 False 1996.666667 6416 90.995667 71 8599 6 chr7D.!!$F2 8528
4 TraesCS7A01G391100 chr7D 500819881 500826183 6302 False 1013.142857 2850 88.787143 1431 7682 7 chr7D.!!$F1 6251
5 TraesCS7A01G391100 chrUn 86621927 86627977 6050 False 1146.666667 2817 89.194333 1431 7682 6 chrUn.!!$F1 6251

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
983 1438 0.043334 TCTTTCTGGGAGGAGGAGGG 59.957 60.000 0.00 0.00 0.00 4.30 F
1362 1823 1.375268 GTGGCTCTCACTCACCTGC 60.375 63.158 0.00 0.00 42.86 4.85 F
2013 2670 1.623311 TCTGATGTCCGGTGTTCATGT 59.377 47.619 0.00 0.00 0.00 3.21 F
3581 4490 0.034059 CTTTCGACAGGAGCCAGTGT 59.966 55.000 0.00 0.00 0.00 3.55 F
4577 5598 0.608130 TTCAGTACGCCATGAGTGCT 59.392 50.000 0.00 0.00 34.95 4.40 F
5059 6085 0.106469 TGGCTCTATCTCTGCGGTCT 60.106 55.000 0.00 0.00 0.00 3.85 F
6036 7101 0.040058 TACCTGGAGTGAACGGCCTA 59.960 55.000 0.00 0.00 0.00 3.93 F
6674 7790 0.255890 TGACTAATGGAAGGCCTGCC 59.744 55.000 24.95 24.95 34.31 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2646 0.321671 AACACCGGACATCAGACCAG 59.678 55.000 9.46 0.00 0.00 4.00 R
3111 3939 0.662619 CAAGCACATGTTCACGTGGT 59.337 50.000 17.00 1.64 45.23 4.16 R
3970 4942 0.238553 GCTTGAAGAAGACCGGCAAC 59.761 55.000 0.00 0.00 0.00 4.17 R
4953 5979 0.611618 ATTTCCCCAACGCTGCATGA 60.612 50.000 0.00 0.00 0.00 3.07 R
6036 7101 1.480137 CTCTTCCTCTGCTCCGTTGAT 59.520 52.381 0.00 0.00 0.00 2.57 R
6667 7783 0.610174 TCGATCATATCAGGCAGGCC 59.390 55.000 0.97 0.97 0.00 5.19 R
7600 8719 2.169352 CACCTTGATGGAGAGACCGAAT 59.831 50.000 0.00 0.00 42.61 3.34 R
8610 10017 0.105964 AGCAGAACGTAGGCACACAA 59.894 50.000 8.44 0.00 0.00 3.33 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
22 23 3.963383 CGGAATCCGTTGATAAAAGGG 57.037 47.619 14.46 0.00 42.73 3.95
23 24 2.616842 CGGAATCCGTTGATAAAAGGGG 59.383 50.000 14.46 0.00 42.73 4.79
24 25 3.683281 CGGAATCCGTTGATAAAAGGGGA 60.683 47.826 14.46 0.00 42.73 4.81
25 26 4.274978 GGAATCCGTTGATAAAAGGGGAA 58.725 43.478 0.00 0.00 0.00 3.97
26 27 4.097437 GGAATCCGTTGATAAAAGGGGAAC 59.903 45.833 0.00 0.00 0.00 3.62
27 28 4.586306 ATCCGTTGATAAAAGGGGAACT 57.414 40.909 0.00 0.00 0.00 3.01
28 29 5.703730 ATCCGTTGATAAAAGGGGAACTA 57.296 39.130 0.00 0.00 0.00 2.24
29 30 5.502089 TCCGTTGATAAAAGGGGAACTAA 57.498 39.130 0.00 0.00 0.00 2.24
30 31 5.878627 TCCGTTGATAAAAGGGGAACTAAA 58.121 37.500 0.00 0.00 0.00 1.85
31 32 5.706833 TCCGTTGATAAAAGGGGAACTAAAC 59.293 40.000 0.00 0.00 0.00 2.01
32 33 5.474189 CCGTTGATAAAAGGGGAACTAAACA 59.526 40.000 0.00 0.00 0.00 2.83
33 34 6.152154 CCGTTGATAAAAGGGGAACTAAACAT 59.848 38.462 0.00 0.00 0.00 2.71
34 35 7.027161 CGTTGATAAAAGGGGAACTAAACATG 58.973 38.462 0.00 0.00 0.00 3.21
35 36 7.320399 GTTGATAAAAGGGGAACTAAACATGG 58.680 38.462 0.00 0.00 0.00 3.66
36 37 5.420739 TGATAAAAGGGGAACTAAACATGGC 59.579 40.000 0.00 0.00 0.00 4.40
37 38 2.231716 AAGGGGAACTAAACATGGCC 57.768 50.000 0.00 0.00 0.00 5.36
38 39 1.382914 AGGGGAACTAAACATGGCCT 58.617 50.000 3.32 0.00 0.00 5.19
39 40 1.716503 AGGGGAACTAAACATGGCCTT 59.283 47.619 3.32 0.00 0.00 4.35
40 41 2.923629 AGGGGAACTAAACATGGCCTTA 59.076 45.455 3.32 0.00 0.00 2.69
41 42 3.053619 AGGGGAACTAAACATGGCCTTAG 60.054 47.826 3.32 6.10 0.00 2.18
42 43 3.053917 GGGGAACTAAACATGGCCTTAGA 60.054 47.826 14.62 0.00 0.00 2.10
43 44 4.200092 GGGAACTAAACATGGCCTTAGAG 58.800 47.826 14.62 3.08 0.00 2.43
44 45 4.080526 GGGAACTAAACATGGCCTTAGAGA 60.081 45.833 14.62 0.00 0.00 3.10
45 46 5.398012 GGGAACTAAACATGGCCTTAGAGAT 60.398 44.000 14.62 2.86 0.00 2.75
46 47 5.529060 GGAACTAAACATGGCCTTAGAGATG 59.471 44.000 14.62 6.71 0.00 2.90
47 48 4.455606 ACTAAACATGGCCTTAGAGATGC 58.544 43.478 14.62 0.00 0.00 3.91
48 49 3.370840 AAACATGGCCTTAGAGATGCA 57.629 42.857 3.32 0.00 0.00 3.96
49 50 2.338577 ACATGGCCTTAGAGATGCAC 57.661 50.000 3.32 0.00 0.00 4.57
50 51 1.561076 ACATGGCCTTAGAGATGCACA 59.439 47.619 3.32 0.00 0.00 4.57
51 52 2.174210 ACATGGCCTTAGAGATGCACAT 59.826 45.455 3.32 0.00 0.00 3.21
52 53 2.627515 TGGCCTTAGAGATGCACATC 57.372 50.000 3.32 2.28 38.09 3.06
66 67 7.670009 AGATGCACATCTCTAAAATATCTGC 57.330 36.000 7.34 0.00 44.37 4.26
67 68 7.451732 AGATGCACATCTCTAAAATATCTGCT 58.548 34.615 7.34 0.00 44.37 4.24
68 69 8.591940 AGATGCACATCTCTAAAATATCTGCTA 58.408 33.333 7.34 0.00 44.37 3.49
69 70 8.774890 ATGCACATCTCTAAAATATCTGCTAG 57.225 34.615 0.00 0.00 0.00 3.42
78 79 7.835822 TCTAAAATATCTGCTAGAGATGCTCC 58.164 38.462 12.34 0.00 41.86 4.70
81 82 1.603456 TCTGCTAGAGATGCTCCTCG 58.397 55.000 0.00 0.00 38.19 4.63
94 95 4.238761 TGCTCCTCGGATAGAATAAACG 57.761 45.455 0.00 0.00 0.00 3.60
107 108 0.437295 ATAAACGAAGTCACGTGCGC 59.563 50.000 11.67 0.00 45.00 6.09
123 124 3.607987 GCGCGTACGTGCTAGCAG 61.608 66.667 38.55 14.64 46.85 4.24
332 337 1.554042 CGGGACAACGACCAGTTTCG 61.554 60.000 0.00 0.00 42.02 3.46
412 425 2.742372 ACGAGCAGCCGCGAAAAT 60.742 55.556 8.23 0.00 45.49 1.82
414 427 2.100991 GAGCAGCCGCGAAAATGG 59.899 61.111 8.23 0.00 45.49 3.16
426 440 3.119495 CGCGAAAATGGGAAAGGAAAGAT 60.119 43.478 0.00 0.00 0.00 2.40
437 451 1.831580 AGGAAAGATGACTTGCAGCC 58.168 50.000 0.00 0.00 36.39 4.85
438 452 1.074405 AGGAAAGATGACTTGCAGCCA 59.926 47.619 0.00 0.00 36.39 4.75
439 453 1.200948 GGAAAGATGACTTGCAGCCAC 59.799 52.381 0.00 0.00 36.39 5.01
440 454 1.881973 GAAAGATGACTTGCAGCCACA 59.118 47.619 0.00 0.00 36.39 4.17
441 455 1.531423 AAGATGACTTGCAGCCACAG 58.469 50.000 0.00 0.00 34.80 3.66
445 459 0.603707 TGACTTGCAGCCACAGTAGC 60.604 55.000 0.00 0.00 0.00 3.58
510 918 1.625818 AGAGAAGTTGGCACCCACTAG 59.374 52.381 0.00 0.00 30.78 2.57
571 979 3.863407 GGATTCCTCTCCCACACAC 57.137 57.895 0.00 0.00 0.00 3.82
572 980 0.984230 GGATTCCTCTCCCACACACA 59.016 55.000 0.00 0.00 0.00 3.72
573 981 1.339151 GGATTCCTCTCCCACACACAC 60.339 57.143 0.00 0.00 0.00 3.82
609 1024 1.269517 GCATTCCGGTTTTCAACTGCA 60.270 47.619 0.00 0.00 36.43 4.41
682 1105 2.820037 CCGCCTTTCTTCCTCCGC 60.820 66.667 0.00 0.00 0.00 5.54
711 1134 0.976073 GGTGGGCCACTACTAGAGCA 60.976 60.000 33.87 0.00 34.40 4.26
731 1158 0.256752 CAGGATCCATTGCACCCTCA 59.743 55.000 15.82 0.00 0.00 3.86
772 1214 2.225791 GAATTGAAACCCCCGCTGCC 62.226 60.000 0.00 0.00 0.00 4.85
824 1266 0.397254 AGCCCGCCCGCTATATATCT 60.397 55.000 0.00 0.00 37.32 1.98
957 1407 0.604073 TGCACGAACCTTGATCCGTA 59.396 50.000 0.00 0.00 33.62 4.02
958 1408 1.278238 GCACGAACCTTGATCCGTAG 58.722 55.000 0.00 0.00 33.62 3.51
980 1435 2.260822 CACTTCTTTCTGGGAGGAGGA 58.739 52.381 0.00 0.00 0.00 3.71
983 1438 0.043334 TCTTTCTGGGAGGAGGAGGG 59.957 60.000 0.00 0.00 0.00 4.30
984 1439 0.043334 CTTTCTGGGAGGAGGAGGGA 59.957 60.000 0.00 0.00 0.00 4.20
985 1440 0.043334 TTTCTGGGAGGAGGAGGGAG 59.957 60.000 0.00 0.00 0.00 4.30
986 1441 2.445654 CTGGGAGGAGGAGGGAGC 60.446 72.222 0.00 0.00 0.00 4.70
987 1442 2.955246 TGGGAGGAGGAGGGAGCT 60.955 66.667 0.00 0.00 0.00 4.09
988 1443 2.123033 GGGAGGAGGAGGGAGCTC 60.123 72.222 4.71 4.71 0.00 4.09
989 1444 2.520741 GGAGGAGGAGGGAGCTCG 60.521 72.222 7.83 0.00 0.00 5.03
990 1445 3.223589 GAGGAGGAGGGAGCTCGC 61.224 72.222 22.44 22.44 0.00 5.03
1105 1560 4.808238 GGGCGTCGTCGTCGAGTC 62.808 72.222 15.85 1.57 46.96 3.36
1149 1604 2.494445 CTCATGTGGGCGTCGCTA 59.506 61.111 18.11 3.77 0.00 4.26
1284 1745 2.357034 TTGCTCGACCGGCTTGTC 60.357 61.111 0.00 0.00 0.00 3.18
1357 1818 1.527433 CGACAGGTGGCTCTCACTCA 61.527 60.000 0.00 0.00 45.38 3.41
1362 1823 1.375268 GTGGCTCTCACTCACCTGC 60.375 63.158 0.00 0.00 42.86 4.85
1417 1878 5.516059 TCTCTTTCTACTGTCCTCACCTA 57.484 43.478 0.00 0.00 0.00 3.08
1418 1879 6.080969 TCTCTTTCTACTGTCCTCACCTAT 57.919 41.667 0.00 0.00 0.00 2.57
1419 1880 7.209340 TCTCTTTCTACTGTCCTCACCTATA 57.791 40.000 0.00 0.00 0.00 1.31
1421 1882 8.282982 TCTCTTTCTACTGTCCTCACCTATATT 58.717 37.037 0.00 0.00 0.00 1.28
1422 1883 8.840200 TCTTTCTACTGTCCTCACCTATATTT 57.160 34.615 0.00 0.00 0.00 1.40
1423 1884 8.696374 TCTTTCTACTGTCCTCACCTATATTTG 58.304 37.037 0.00 0.00 0.00 2.32
1424 1885 6.406692 TCTACTGTCCTCACCTATATTTGC 57.593 41.667 0.00 0.00 0.00 3.68
1425 1886 6.136857 TCTACTGTCCTCACCTATATTTGCT 58.863 40.000 0.00 0.00 0.00 3.91
1426 1887 7.295340 TCTACTGTCCTCACCTATATTTGCTA 58.705 38.462 0.00 0.00 0.00 3.49
1557 2031 3.075134 GGGATGCTGAATTTCTCCCCTAT 59.925 47.826 9.36 0.00 39.80 2.57
1559 2033 5.143369 GGATGCTGAATTTCTCCCCTATTT 58.857 41.667 0.00 0.00 0.00 1.40
1712 2186 2.494059 GTACTGCCAAGAGTGCTGAAA 58.506 47.619 0.00 0.00 0.00 2.69
1763 2244 2.507484 TGTTCTTCAAGCCTGACCATG 58.493 47.619 0.00 0.00 0.00 3.66
1902 2551 7.159372 AGAGGTACTGTTTATGTTGTTGTAGG 58.841 38.462 0.00 0.00 41.55 3.18
1938 2595 3.876914 TCAAACATTCTTCAGCACTCGTT 59.123 39.130 0.00 0.00 0.00 3.85
1961 2618 7.472543 GTTGATTTTCTGTATTTATGCCGTCT 58.527 34.615 0.00 0.00 0.00 4.18
1963 2620 7.693952 TGATTTTCTGTATTTATGCCGTCTTC 58.306 34.615 0.00 0.00 0.00 2.87
1966 2623 8.958119 TTTTCTGTATTTATGCCGTCTTCTAT 57.042 30.769 0.00 0.00 0.00 1.98
1967 2624 7.946655 TTCTGTATTTATGCCGTCTTCTATG 57.053 36.000 0.00 0.00 0.00 2.23
1979 2636 6.821160 TGCCGTCTTCTATGAACATATTTCAA 59.179 34.615 4.99 0.00 31.55 2.69
1989 2646 6.709145 TGAACATATTTCAATTGCACTTGC 57.291 33.333 11.69 0.00 42.50 4.01
2013 2670 1.623311 TCTGATGTCCGGTGTTCATGT 59.377 47.619 0.00 0.00 0.00 3.21
2074 2731 2.829120 AGGGAAGACTACACTGCTTCTC 59.171 50.000 0.00 0.00 38.99 2.87
2133 2810 5.536554 AATCAACTTGACTGATTACAGCG 57.463 39.130 0.00 0.00 46.95 5.18
2144 2821 6.650807 TGACTGATTACAGCGATCTTTCTTTT 59.349 34.615 0.00 0.00 46.95 2.27
2183 2865 7.660208 AGGAAACTTACTTTTGTGTGATACGAT 59.340 33.333 0.00 0.00 37.44 3.73
2184 2866 8.928733 GGAAACTTACTTTTGTGTGATACGATA 58.071 33.333 0.00 0.00 0.00 2.92
2193 2875 9.702726 CTTTTGTGTGATACGATATAAACCAAG 57.297 33.333 0.00 0.00 0.00 3.61
2211 2893 3.888930 CCAAGCAGGTTTCAGGAAAAGTA 59.111 43.478 0.00 0.00 31.33 2.24
2377 3060 4.759693 ACGGTGAGCTCAAAATTAATCACA 59.240 37.500 20.19 0.00 38.99 3.58
2378 3061 5.088739 CGGTGAGCTCAAAATTAATCACAC 58.911 41.667 20.19 1.00 38.99 3.82
2537 3221 2.555547 GGCAATATCAGTGGGCGGC 61.556 63.158 0.00 0.00 0.00 6.53
2580 3264 4.501571 CCGATTACATCCTCAAGGTACTGG 60.502 50.000 0.00 0.00 40.86 4.00
2593 3303 4.447138 AGGTACTGGATCCAACAACAAA 57.553 40.909 17.00 0.00 37.18 2.83
2616 3326 4.432712 ACCTTGTTCTTCAATGTGCAAAC 58.567 39.130 0.00 0.00 34.53 2.93
2617 3327 4.160252 ACCTTGTTCTTCAATGTGCAAACT 59.840 37.500 0.00 0.00 34.53 2.66
3111 3939 4.632327 TGGTCACATTGTGTATCAAGGA 57.368 40.909 16.06 0.00 39.79 3.36
3162 3990 1.358787 TCCATGGGCTTCAAATGTCCT 59.641 47.619 13.02 0.00 0.00 3.85
3207 4035 5.835113 TTTTGCAAGAAGTAAGTCAGCTT 57.165 34.783 0.00 0.00 38.66 3.74
3216 4044 8.721478 CAAGAAGTAAGTCAGCTTAAATGCTTA 58.279 33.333 0.00 0.00 41.98 3.09
3340 4246 8.833231 TTGACTTAGGACAAATCTAGAACTTG 57.167 34.615 13.67 13.67 0.00 3.16
3408 4317 7.843490 TGATGTTTAGTTACTAACATCAGCC 57.157 36.000 26.79 14.67 38.25 4.85
3409 4318 6.821665 TGATGTTTAGTTACTAACATCAGCCC 59.178 38.462 26.79 14.46 38.25 5.19
3448 4357 4.005650 GTGACATCAAGGAAAGATCAGCA 58.994 43.478 0.00 0.00 0.00 4.41
3473 4382 0.834687 ACTGGGCAAGGAGTAACCGA 60.835 55.000 0.00 0.00 44.74 4.69
3581 4490 0.034059 CTTTCGACAGGAGCCAGTGT 59.966 55.000 0.00 0.00 0.00 3.55
3596 4505 1.344438 CAGTGTCACCCTGCTTCACTA 59.656 52.381 0.00 0.00 37.27 2.74
3605 4514 1.272490 CCTGCTTCACTAACGACCTCA 59.728 52.381 0.00 0.00 0.00 3.86
3660 4569 2.107953 GCATCGAGAGGGAGTGGC 59.892 66.667 0.00 0.00 0.00 5.01
3752 4712 4.209538 TCCCATTTCAGTTCAGGCATATG 58.790 43.478 0.00 0.00 0.00 1.78
3760 4720 5.988287 TCAGTTCAGGCATATGTTCATACA 58.012 37.500 4.29 0.00 38.95 2.29
3798 4770 9.342308 GATTGATGAACTAATGGAAATACCTGA 57.658 33.333 0.00 0.00 39.86 3.86
3970 4942 2.099756 GCTAGCTTTGGCCACCATAAAG 59.900 50.000 3.88 7.45 39.73 1.85
4135 5107 2.386661 CAGATGTTGGAAGGTACGCT 57.613 50.000 0.00 0.00 0.00 5.07
4151 5123 7.807977 AGGTACGCTTCAAATATCAATCATT 57.192 32.000 0.00 0.00 0.00 2.57
4219 5230 3.359033 TCCTACAAGTAGCACGTACCAT 58.641 45.455 1.69 0.00 31.06 3.55
4232 5243 7.658179 AGCACGTACCATTATTAATCATCTG 57.342 36.000 0.00 0.00 0.00 2.90
4252 5263 2.429971 TGGTTGTTTTCTTGCATGCAGA 59.570 40.909 21.50 16.91 0.00 4.26
4360 5371 2.223923 GGTTGTTGCAAATACACTGGCA 60.224 45.455 0.00 0.00 0.00 4.92
4438 5449 4.104383 TGCTCCTCTTCTGGAACAAAAT 57.896 40.909 0.00 0.00 38.70 1.82
4439 5450 5.241403 TGCTCCTCTTCTGGAACAAAATA 57.759 39.130 0.00 0.00 38.70 1.40
4444 5455 8.739972 GCTCCTCTTCTGGAACAAAATAAATAA 58.260 33.333 0.00 0.00 38.70 1.40
4577 5598 0.608130 TTCAGTACGCCATGAGTGCT 59.392 50.000 0.00 0.00 34.95 4.40
4831 5853 1.139058 GCACTCCTGGGATACGTCATT 59.861 52.381 0.00 0.00 37.60 2.57
4921 5947 7.171508 TGGAATTTTGCAATGCGTATTTTGTTA 59.828 29.630 0.00 0.00 0.00 2.41
4940 5966 5.858381 TGTTAAAGCACTTGATCTGAGACT 58.142 37.500 0.00 0.00 0.00 3.24
4948 5974 7.041107 AGCACTTGATCTGAGACTATTTCTTC 58.959 38.462 0.00 0.00 33.22 2.87
5001 6027 5.124457 GCAAATTCTTTCAGAGGATGCACTA 59.876 40.000 0.00 0.00 31.97 2.74
5025 6051 2.158842 GGAGAAGCATGCCAGTATCACT 60.159 50.000 15.66 2.31 0.00 3.41
5057 6083 0.965439 GATGGCTCTATCTCTGCGGT 59.035 55.000 0.00 0.00 0.00 5.68
5058 6084 0.965439 ATGGCTCTATCTCTGCGGTC 59.035 55.000 0.00 0.00 0.00 4.79
5059 6085 0.106469 TGGCTCTATCTCTGCGGTCT 60.106 55.000 0.00 0.00 0.00 3.85
5070 6096 1.608717 CTGCGGTCTCAGGTAAGGCT 61.609 60.000 0.00 0.00 0.00 4.58
5182 6208 1.473497 ATGCACACAGCCATGGCAAA 61.473 50.000 37.18 14.91 44.83 3.68
5198 6224 3.245586 TGGCAAAATGTCATCTAAGGGGT 60.246 43.478 0.00 0.00 0.00 4.95
5361 6393 0.885196 GCGGTAATGCCCTTCAACAA 59.115 50.000 0.00 0.00 0.00 2.83
5432 6465 0.937304 TCTGCGCACTGAAACTCAAC 59.063 50.000 5.66 0.00 0.00 3.18
5497 6561 6.554334 TCCAACTAATTAACTTGCTGACAC 57.446 37.500 0.00 0.00 0.00 3.67
5505 6569 7.713764 AATTAACTTGCTGACACAAAAATCC 57.286 32.000 0.00 0.00 0.00 3.01
5656 6720 1.430632 GCTGATGGATGTGTTGGCG 59.569 57.895 0.00 0.00 0.00 5.69
5819 6883 0.678395 CTACTCCGCATGGCTCAGAT 59.322 55.000 0.00 0.00 34.14 2.90
6036 7101 0.040058 TACCTGGAGTGAACGGCCTA 59.960 55.000 0.00 0.00 0.00 3.93
6063 7128 1.220477 GCAGAGGAAGAGGCTGACC 59.780 63.158 0.00 0.00 0.00 4.02
6439 7544 7.068226 TCCTCCTTTTCAAGTTCTTTTTAGGTG 59.932 37.037 0.00 0.00 0.00 4.00
6452 7557 4.597404 TTTTAGGTGTTGCATTGCATGA 57.403 36.364 12.95 0.00 38.76 3.07
6470 7575 5.576774 TGCATGACTTTGAGTGATAGTAACG 59.423 40.000 0.00 0.00 0.00 3.18
6670 7786 3.584733 AGGATTGACTAATGGAAGGCC 57.415 47.619 0.00 0.00 0.00 5.19
6671 7787 3.126453 AGGATTGACTAATGGAAGGCCT 58.874 45.455 0.00 0.00 34.31 5.19
6672 7788 3.117738 AGGATTGACTAATGGAAGGCCTG 60.118 47.826 5.69 0.00 34.31 4.85
6673 7789 2.128771 TTGACTAATGGAAGGCCTGC 57.871 50.000 5.69 2.81 34.31 4.85
6674 7790 0.255890 TGACTAATGGAAGGCCTGCC 59.744 55.000 24.95 24.95 34.31 4.85
6685 7801 0.612229 AGGCCTGCCTGATATGATCG 59.388 55.000 10.51 0.00 46.22 3.69
6686 7802 0.610174 GGCCTGCCTGATATGATCGA 59.390 55.000 0.00 0.00 0.00 3.59
6687 7803 1.674221 GGCCTGCCTGATATGATCGAC 60.674 57.143 0.00 0.00 0.00 4.20
6688 7804 1.988063 CCTGCCTGATATGATCGACG 58.012 55.000 0.00 0.00 0.00 5.12
6689 7805 1.403382 CCTGCCTGATATGATCGACGG 60.403 57.143 0.00 0.00 0.00 4.79
6690 7806 1.541588 CTGCCTGATATGATCGACGGA 59.458 52.381 0.00 0.00 0.00 4.69
6691 7807 1.269723 TGCCTGATATGATCGACGGAC 59.730 52.381 0.00 0.00 0.00 4.79
6693 7809 2.094494 GCCTGATATGATCGACGGACAT 60.094 50.000 11.07 11.07 0.00 3.06
6714 7831 8.250332 GGACATTGACAAACAATATGTGGTATT 58.750 33.333 0.00 0.00 46.01 1.89
7435 8554 2.927856 TGCCCGGTGTCATGGACT 60.928 61.111 0.00 0.00 33.15 3.85
7561 8680 2.915659 TTCCTGGGTGTCGTCGCT 60.916 61.111 0.00 0.00 0.00 4.93
7600 8719 2.355837 GTCCTGTTCGCTGTCGCA 60.356 61.111 0.00 0.00 35.30 5.10
7686 8809 1.611491 GGACCAACGGCTCAATTTCAA 59.389 47.619 0.00 0.00 0.00 2.69
7697 8820 1.885887 TCAATTTCAACCAGCCGGAAG 59.114 47.619 5.05 0.00 35.59 3.46
7732 8858 6.073980 CGCATGTGTTTGTAGTTTGTACTAGT 60.074 38.462 0.00 0.00 37.53 2.57
7733 8859 7.115236 CGCATGTGTTTGTAGTTTGTACTAGTA 59.885 37.037 0.00 0.00 37.53 1.82
7734 8860 8.433126 GCATGTGTTTGTAGTTTGTACTAGTAG 58.567 37.037 1.87 0.00 37.53 2.57
7802 8928 5.627499 TTTCTCTCGGTTCCATTGATTTG 57.373 39.130 0.00 0.00 0.00 2.32
8068 9464 7.591006 AAATAAAGCTCAATTGCACAATCAG 57.409 32.000 0.00 0.00 34.99 2.90
8093 9489 8.367156 AGTGTGGAATTTAAACACAATGCTTAT 58.633 29.630 16.68 0.00 45.53 1.73
8094 9490 9.632807 GTGTGGAATTTAAACACAATGCTTATA 57.367 29.630 10.65 0.00 45.53 0.98
8134 9532 8.647796 AGATAGACGGAAATAACAATACATGGA 58.352 33.333 0.00 0.00 0.00 3.41
8162 9560 9.528018 ACAAAAGTGTACCAAATCAATAGTTTG 57.472 29.630 0.00 0.00 35.72 2.93
8206 9604 0.526524 TTTTCGCAGTTGTTTGCCGG 60.527 50.000 0.00 0.00 41.01 6.13
8216 9614 2.857748 GTTGTTTGCCGGTGAAGAAAAG 59.142 45.455 1.90 0.00 0.00 2.27
8236 9634 4.246712 AGGACCCTTCATCGTCTACTTA 57.753 45.455 0.00 0.00 0.00 2.24
8241 9639 6.433404 GGACCCTTCATCGTCTACTTATATGA 59.567 42.308 0.00 0.00 0.00 2.15
8244 9642 9.702253 ACCCTTCATCGTCTACTTATATGATAT 57.298 33.333 0.00 0.00 0.00 1.63
8279 9677 7.940178 TGATATGAAAATGCATCAATTGAGC 57.060 32.000 14.54 16.44 0.00 4.26
8574 9978 0.661780 GTGCGTGCGAGCTCTATAGG 60.662 60.000 12.85 4.78 38.13 2.57
8599 10006 0.898326 AGTTCGGGCCCAAATTGGAC 60.898 55.000 24.92 10.03 40.96 4.02
8600 10007 0.898326 GTTCGGGCCCAAATTGGACT 60.898 55.000 24.92 0.00 40.96 3.85
8601 10008 0.178947 TTCGGGCCCAAATTGGACTT 60.179 50.000 24.92 0.00 40.96 3.01
8602 10009 0.610785 TCGGGCCCAAATTGGACTTC 60.611 55.000 24.92 0.00 40.96 3.01
8603 10010 1.604147 CGGGCCCAAATTGGACTTCC 61.604 60.000 24.92 8.57 40.96 3.46
8604 10011 0.252239 GGGCCCAAATTGGACTTCCT 60.252 55.000 19.95 0.00 40.96 3.36
8605 10012 1.186200 GGCCCAAATTGGACTTCCTC 58.814 55.000 14.62 0.00 40.96 3.71
8606 10013 0.811281 GCCCAAATTGGACTTCCTCG 59.189 55.000 14.62 0.00 40.96 4.63
8607 10014 1.463674 CCCAAATTGGACTTCCTCGG 58.536 55.000 14.62 0.00 40.96 4.63
8608 10015 0.811281 CCAAATTGGACTTCCTCGGC 59.189 55.000 6.04 0.00 40.96 5.54
8609 10016 0.811281 CAAATTGGACTTCCTCGGCC 59.189 55.000 0.00 0.00 36.82 6.13
8610 10017 0.698818 AAATTGGACTTCCTCGGCCT 59.301 50.000 0.00 0.00 36.82 5.19
8611 10018 0.698818 AATTGGACTTCCTCGGCCTT 59.301 50.000 0.00 0.00 36.82 4.35
8612 10019 0.035056 ATTGGACTTCCTCGGCCTTG 60.035 55.000 0.00 0.00 36.82 3.61
8613 10020 1.415672 TTGGACTTCCTCGGCCTTGT 61.416 55.000 0.00 0.00 36.82 3.16
8614 10021 1.376037 GGACTTCCTCGGCCTTGTG 60.376 63.158 0.00 0.00 0.00 3.33
8615 10022 1.371558 GACTTCCTCGGCCTTGTGT 59.628 57.895 0.00 0.00 0.00 3.72
8616 10023 0.951040 GACTTCCTCGGCCTTGTGTG 60.951 60.000 0.00 0.00 0.00 3.82
8617 10024 2.281484 TTCCTCGGCCTTGTGTGC 60.281 61.111 0.00 0.00 0.00 4.57
8618 10025 3.842925 TTCCTCGGCCTTGTGTGCC 62.843 63.158 0.00 0.00 45.70 5.01
8623 10030 2.032071 GGCCTTGTGTGCCTACGT 59.968 61.111 0.00 0.00 45.70 3.57
8624 10031 1.599797 GGCCTTGTGTGCCTACGTT 60.600 57.895 0.00 0.00 45.70 3.99
8625 10032 1.574702 GGCCTTGTGTGCCTACGTTC 61.575 60.000 0.00 0.00 45.70 3.95
8626 10033 0.602905 GCCTTGTGTGCCTACGTTCT 60.603 55.000 0.00 0.00 0.00 3.01
8627 10034 1.148310 CCTTGTGTGCCTACGTTCTG 58.852 55.000 0.00 0.00 0.00 3.02
8628 10035 0.512952 CTTGTGTGCCTACGTTCTGC 59.487 55.000 0.00 0.00 0.00 4.26
8629 10036 0.105964 TTGTGTGCCTACGTTCTGCT 59.894 50.000 0.00 0.00 0.00 4.24
8630 10037 0.599991 TGTGTGCCTACGTTCTGCTG 60.600 55.000 0.00 0.00 0.00 4.41
8631 10038 1.005037 TGTGCCTACGTTCTGCTGG 60.005 57.895 0.00 0.00 0.00 4.85
8632 10039 1.292223 GTGCCTACGTTCTGCTGGA 59.708 57.895 0.00 0.00 0.00 3.86
8633 10040 1.014564 GTGCCTACGTTCTGCTGGAC 61.015 60.000 0.00 0.00 0.00 4.02
8634 10041 1.185618 TGCCTACGTTCTGCTGGACT 61.186 55.000 0.00 0.00 0.00 3.85
8635 10042 0.737715 GCCTACGTTCTGCTGGACTG 60.738 60.000 0.00 0.00 0.00 3.51
8636 10043 0.737715 CCTACGTTCTGCTGGACTGC 60.738 60.000 0.00 0.00 0.00 4.40
8637 10044 1.073216 CTACGTTCTGCTGGACTGCG 61.073 60.000 0.00 0.00 35.36 5.18
8638 10045 3.782244 CGTTCTGCTGGACTGCGC 61.782 66.667 0.00 0.00 35.36 6.09
8639 10046 3.426568 GTTCTGCTGGACTGCGCC 61.427 66.667 4.18 0.00 35.36 6.53
8640 10047 4.704833 TTCTGCTGGACTGCGCCC 62.705 66.667 4.18 0.00 35.36 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.893521 TCCCCTTTTATCAACGGATTCC 58.106 45.455 0.00 0.00 34.89 3.01
4 5 4.948004 AGTTCCCCTTTTATCAACGGATTC 59.052 41.667 0.00 0.00 34.89 2.52
5 6 4.930696 AGTTCCCCTTTTATCAACGGATT 58.069 39.130 0.00 0.00 34.89 3.01
6 7 4.586306 AGTTCCCCTTTTATCAACGGAT 57.414 40.909 0.00 0.00 37.55 4.18
7 8 5.502089 TTAGTTCCCCTTTTATCAACGGA 57.498 39.130 0.00 0.00 0.00 4.69
8 9 5.474189 TGTTTAGTTCCCCTTTTATCAACGG 59.526 40.000 0.00 0.00 0.00 4.44
9 10 6.563222 TGTTTAGTTCCCCTTTTATCAACG 57.437 37.500 0.00 0.00 0.00 4.10
10 11 7.320399 CCATGTTTAGTTCCCCTTTTATCAAC 58.680 38.462 0.00 0.00 0.00 3.18
11 12 6.071051 GCCATGTTTAGTTCCCCTTTTATCAA 60.071 38.462 0.00 0.00 0.00 2.57
12 13 5.420739 GCCATGTTTAGTTCCCCTTTTATCA 59.579 40.000 0.00 0.00 0.00 2.15
13 14 5.163447 GGCCATGTTTAGTTCCCCTTTTATC 60.163 44.000 0.00 0.00 0.00 1.75
14 15 4.714802 GGCCATGTTTAGTTCCCCTTTTAT 59.285 41.667 0.00 0.00 0.00 1.40
15 16 4.090819 GGCCATGTTTAGTTCCCCTTTTA 58.909 43.478 0.00 0.00 0.00 1.52
16 17 2.903784 GGCCATGTTTAGTTCCCCTTTT 59.096 45.455 0.00 0.00 0.00 2.27
17 18 2.111792 AGGCCATGTTTAGTTCCCCTTT 59.888 45.455 5.01 0.00 0.00 3.11
18 19 1.716503 AGGCCATGTTTAGTTCCCCTT 59.283 47.619 5.01 0.00 0.00 3.95
19 20 1.382914 AGGCCATGTTTAGTTCCCCT 58.617 50.000 5.01 0.00 0.00 4.79
20 21 2.231716 AAGGCCATGTTTAGTTCCCC 57.768 50.000 5.01 0.00 0.00 4.81
21 22 4.080526 TCTCTAAGGCCATGTTTAGTTCCC 60.081 45.833 5.01 0.00 0.00 3.97
22 23 5.099042 TCTCTAAGGCCATGTTTAGTTCC 57.901 43.478 5.01 0.00 0.00 3.62
23 24 5.008118 GCATCTCTAAGGCCATGTTTAGTTC 59.992 44.000 5.01 0.00 0.00 3.01
24 25 4.884164 GCATCTCTAAGGCCATGTTTAGTT 59.116 41.667 5.01 0.00 0.00 2.24
25 26 4.080356 TGCATCTCTAAGGCCATGTTTAGT 60.080 41.667 5.01 0.00 0.00 2.24
26 27 4.274459 GTGCATCTCTAAGGCCATGTTTAG 59.726 45.833 5.01 4.12 0.00 1.85
27 28 4.199310 GTGCATCTCTAAGGCCATGTTTA 58.801 43.478 5.01 0.00 0.00 2.01
28 29 3.019564 GTGCATCTCTAAGGCCATGTTT 58.980 45.455 5.01 0.00 0.00 2.83
29 30 2.025981 TGTGCATCTCTAAGGCCATGTT 60.026 45.455 5.01 0.00 0.00 2.71
30 31 1.561076 TGTGCATCTCTAAGGCCATGT 59.439 47.619 5.01 0.00 0.00 3.21
31 32 2.336945 TGTGCATCTCTAAGGCCATG 57.663 50.000 5.01 0.00 0.00 3.66
32 33 2.709934 AGATGTGCATCTCTAAGGCCAT 59.290 45.455 5.01 0.00 44.37 4.40
33 34 2.121948 AGATGTGCATCTCTAAGGCCA 58.878 47.619 5.01 0.00 44.37 5.36
34 35 2.926778 AGATGTGCATCTCTAAGGCC 57.073 50.000 8.74 0.00 44.37 5.19
43 44 7.670009 AGCAGATATTTTAGAGATGTGCATC 57.330 36.000 2.75 4.12 41.11 3.91
44 45 8.591940 TCTAGCAGATATTTTAGAGATGTGCAT 58.408 33.333 2.75 0.00 41.11 3.96
45 46 7.955918 TCTAGCAGATATTTTAGAGATGTGCA 58.044 34.615 2.75 0.00 41.11 4.57
46 47 8.303156 TCTCTAGCAGATATTTTAGAGATGTGC 58.697 37.037 6.09 0.00 41.75 4.57
52 53 7.975616 GGAGCATCTCTAGCAGATATTTTAGAG 59.024 40.741 4.89 1.87 40.20 2.43
53 54 7.673504 AGGAGCATCTCTAGCAGATATTTTAGA 59.326 37.037 4.89 0.00 40.20 2.10
54 55 7.839907 AGGAGCATCTCTAGCAGATATTTTAG 58.160 38.462 4.89 0.00 40.20 1.85
55 56 7.362487 CGAGGAGCATCTCTAGCAGATATTTTA 60.362 40.741 4.89 0.00 40.20 1.52
56 57 6.572119 CGAGGAGCATCTCTAGCAGATATTTT 60.572 42.308 4.89 0.00 40.20 1.82
57 58 5.105797 CGAGGAGCATCTCTAGCAGATATTT 60.106 44.000 4.89 0.00 40.20 1.40
58 59 4.398988 CGAGGAGCATCTCTAGCAGATATT 59.601 45.833 4.89 0.00 40.20 1.28
59 60 3.947196 CGAGGAGCATCTCTAGCAGATAT 59.053 47.826 4.89 0.00 40.20 1.63
60 61 3.342719 CGAGGAGCATCTCTAGCAGATA 58.657 50.000 4.89 0.00 40.20 1.98
61 62 2.161855 CGAGGAGCATCTCTAGCAGAT 58.838 52.381 5.09 0.44 43.33 2.90
62 63 1.603456 CGAGGAGCATCTCTAGCAGA 58.397 55.000 5.09 0.00 34.78 4.26
63 64 0.597568 CCGAGGAGCATCTCTAGCAG 59.402 60.000 5.09 0.00 33.73 4.24
64 65 0.183731 TCCGAGGAGCATCTCTAGCA 59.816 55.000 5.09 0.00 33.73 3.49
65 66 1.544724 ATCCGAGGAGCATCTCTAGC 58.455 55.000 0.00 0.00 33.73 3.42
66 67 4.214986 TCTATCCGAGGAGCATCTCTAG 57.785 50.000 0.00 0.00 33.73 2.43
67 68 4.642466 TTCTATCCGAGGAGCATCTCTA 57.358 45.455 0.00 0.00 33.73 2.43
68 69 3.517296 TTCTATCCGAGGAGCATCTCT 57.483 47.619 0.00 0.00 33.73 3.10
69 70 5.906113 TTATTCTATCCGAGGAGCATCTC 57.094 43.478 0.00 0.00 33.73 2.75
78 79 5.395778 CGTGACTTCGTTTATTCTATCCGAG 59.604 44.000 0.00 0.00 0.00 4.63
81 82 5.276254 GCACGTGACTTCGTTTATTCTATCC 60.276 44.000 22.23 0.00 42.27 2.59
107 108 0.316772 ATACTGCTAGCACGTACGCG 60.317 55.000 14.93 3.53 44.93 6.01
114 115 1.866063 GCCGACTGATACTGCTAGCAC 60.866 57.143 14.93 4.53 0.00 4.40
123 124 0.374758 TACACGACGCCGACTGATAC 59.625 55.000 0.00 0.00 39.50 2.24
275 280 0.110147 CTTCTCGTTGAGACTCGCGT 60.110 55.000 5.77 0.00 38.51 6.01
332 337 5.135330 GTCTTACGTGGAAAATCAACGAAC 58.865 41.667 13.77 3.54 0.00 3.95
412 425 3.157087 GCAAGTCATCTTTCCTTTCCCA 58.843 45.455 0.00 0.00 0.00 4.37
414 427 3.366781 GCTGCAAGTCATCTTTCCTTTCC 60.367 47.826 0.00 0.00 35.30 3.13
437 451 4.154375 TGAGACGTTCTAGAAGCTACTGTG 59.846 45.833 5.12 0.00 0.00 3.66
438 452 4.325119 TGAGACGTTCTAGAAGCTACTGT 58.675 43.478 5.12 0.00 0.00 3.55
439 453 4.393680 ACTGAGACGTTCTAGAAGCTACTG 59.606 45.833 5.12 4.19 0.00 2.74
440 454 4.581868 ACTGAGACGTTCTAGAAGCTACT 58.418 43.478 5.12 3.47 0.00 2.57
441 455 4.632688 AGACTGAGACGTTCTAGAAGCTAC 59.367 45.833 5.12 0.00 0.00 3.58
445 459 4.258543 AGGAGACTGAGACGTTCTAGAAG 58.741 47.826 5.12 3.05 41.13 2.85
510 918 6.211515 TGCTTTTTGAGATCTCTTGCTTTTC 58.788 36.000 22.95 6.83 0.00 2.29
570 978 1.822186 GGACACACTTTGGCCGTGT 60.822 57.895 12.49 12.49 46.56 4.49
571 979 3.030652 GGACACACTTTGGCCGTG 58.969 61.111 7.63 7.63 46.56 4.94
587 995 3.101019 GTTGAAAACCGGAATGCGG 57.899 52.632 12.68 12.68 42.21 5.69
643 1066 2.687805 GCTTCCGGACGAAAAGGGC 61.688 63.158 12.95 0.00 0.00 5.19
644 1067 0.605589 AAGCTTCCGGACGAAAAGGG 60.606 55.000 12.95 0.00 0.00 3.95
645 1068 0.796927 GAAGCTTCCGGACGAAAAGG 59.203 55.000 15.97 0.00 0.00 3.11
646 1069 0.796927 GGAAGCTTCCGGACGAAAAG 59.203 55.000 29.09 3.66 37.65 2.27
647 1070 2.922779 GGAAGCTTCCGGACGAAAA 58.077 52.632 29.09 0.00 37.65 2.29
648 1071 4.687464 GGAAGCTTCCGGACGAAA 57.313 55.556 29.09 0.00 37.65 3.46
705 1128 1.839354 TGCAATGGATCCTGTGCTCTA 59.161 47.619 28.96 14.68 37.87 2.43
711 1134 0.257039 GAGGGTGCAATGGATCCTGT 59.743 55.000 12.44 0.00 0.00 4.00
751 1193 0.897863 CAGCGGGGGTTTCAATTCCA 60.898 55.000 0.00 0.00 0.00 3.53
812 1254 3.738281 CGGGGCAAGAAGATATATAGCGG 60.738 52.174 0.00 0.00 0.00 5.52
813 1255 3.448686 CGGGGCAAGAAGATATATAGCG 58.551 50.000 0.00 0.00 0.00 4.26
957 1407 2.903135 CTCCTCCCAGAAAGAAGTGTCT 59.097 50.000 0.00 0.00 34.72 3.41
958 1408 2.027653 CCTCCTCCCAGAAAGAAGTGTC 60.028 54.545 0.00 0.00 0.00 3.67
1322 1783 1.285578 GTCGATTCTCTGCTTGAGCC 58.714 55.000 0.00 0.00 42.38 4.70
1335 1796 0.247736 GTGAGAGCCACCTGTCGATT 59.752 55.000 0.00 0.00 39.86 3.34
1357 1818 0.321475 GAAGAGCAGAGCAAGCAGGT 60.321 55.000 0.00 0.00 0.00 4.00
1362 1823 1.066716 AGCAGAGAAGAGCAGAGCAAG 60.067 52.381 0.00 0.00 0.00 4.01
1557 2031 6.712998 TCGATCCCAACTCTGAAACAAATAAA 59.287 34.615 0.00 0.00 0.00 1.40
1559 2033 5.642063 GTCGATCCCAACTCTGAAACAAATA 59.358 40.000 0.00 0.00 0.00 1.40
1763 2244 0.746659 AAGGCAGGCACAAACAGAAC 59.253 50.000 0.00 0.00 0.00 3.01
1902 2551 5.979517 AGAATGTTTGACAGCAAAGTAAAGC 59.020 36.000 0.00 0.00 44.12 3.51
1938 2595 7.552687 AGAAGACGGCATAAATACAGAAAATCA 59.447 33.333 0.00 0.00 0.00 2.57
1963 2620 8.537223 GCAAGTGCAATTGAAATATGTTCATAG 58.463 33.333 29.48 0.00 41.59 2.23
1966 2623 6.366604 CAGCAAGTGCAATTGAAATATGTTCA 59.633 34.615 29.48 0.00 45.16 3.18
1967 2624 6.183360 CCAGCAAGTGCAATTGAAATATGTTC 60.183 38.462 29.48 8.94 45.16 3.18
1979 2636 1.816835 CATCAGACCAGCAAGTGCAAT 59.183 47.619 6.00 0.00 45.16 3.56
1989 2646 0.321671 AACACCGGACATCAGACCAG 59.678 55.000 9.46 0.00 0.00 4.00
2074 2731 0.804989 CTAGTTTCCCTGCCAAAGCG 59.195 55.000 0.00 0.00 44.31 4.68
2144 2821 8.575649 AAGTAAGTTTCCTTGAACTTCAGAAA 57.424 30.769 6.30 3.27 44.30 2.52
2147 2824 8.244113 ACAAAAGTAAGTTTCCTTGAACTTCAG 58.756 33.333 6.30 0.00 44.30 3.02
2156 2833 7.496591 TCGTATCACACAAAAGTAAGTTTCCTT 59.503 33.333 0.00 0.00 34.56 3.36
2189 2871 2.695147 ACTTTTCCTGAAACCTGCTTGG 59.305 45.455 0.00 0.00 42.93 3.61
2190 2872 5.163561 TGTTACTTTTCCTGAAACCTGCTTG 60.164 40.000 0.00 0.00 0.00 4.01
2193 2875 4.911514 TGTTACTTTTCCTGAAACCTGC 57.088 40.909 0.00 0.00 0.00 4.85
2211 2893 4.288398 TCATTCCATGCCCATTGTATGTT 58.712 39.130 0.00 0.00 35.49 2.71
2316 2998 1.224039 GCATCTGGCTGAGAAGGCT 59.776 57.895 0.00 0.00 40.25 4.58
2394 3078 5.587844 GCACACAATTATGAAGTGAGAGGAT 59.412 40.000 0.00 0.00 37.90 3.24
2406 3090 9.791820 TTCATCAGAAATTAGCACACAATTATG 57.208 29.630 0.00 0.00 0.00 1.90
2465 3149 4.202441 TGATATTTGCAGCTTTCTCCCTC 58.798 43.478 0.00 0.00 0.00 4.30
2537 3221 5.793817 TCGGTGATGATATTTGTATCCTGG 58.206 41.667 0.00 0.00 0.00 4.45
2616 3326 6.073548 GGTTCAACATAACAGTCAGTCAGAAG 60.074 42.308 0.00 0.00 0.00 2.85
2617 3327 5.758296 GGTTCAACATAACAGTCAGTCAGAA 59.242 40.000 0.00 0.00 0.00 3.02
2867 3695 5.104982 TCAGAAAAATTCAAGCAACCAAGGT 60.105 36.000 0.00 0.00 0.00 3.50
3111 3939 0.662619 CAAGCACATGTTCACGTGGT 59.337 50.000 17.00 1.64 45.23 4.16
3286 4191 7.611213 ATTTAAGTTTGACCGAGTTCATAGG 57.389 36.000 0.00 0.00 0.00 2.57
3291 4196 7.430992 AACCTATTTAAGTTTGACCGAGTTC 57.569 36.000 0.00 0.00 0.00 3.01
3340 4246 5.136105 ACTCCATCCATTCCAAATTAGCTC 58.864 41.667 0.00 0.00 0.00 4.09
3408 4317 9.226606 TGATGTCACCTATAAGTTTTACAAAGG 57.773 33.333 0.00 0.00 0.00 3.11
3448 4357 4.332828 GTTACTCCTTGCCCAGTATTGTT 58.667 43.478 0.00 0.00 0.00 2.83
3473 4382 4.028131 TGACTGGGACGTATTGGTATCTT 58.972 43.478 0.00 0.00 0.00 2.40
3547 4456 1.608717 GAAAGGGCGAGAGAGCTCCA 61.609 60.000 10.93 0.00 38.69 3.86
3581 4490 1.000506 GTCGTTAGTGAAGCAGGGTGA 59.999 52.381 0.00 0.00 0.00 4.02
3596 4505 0.318107 CACCGTACGTTGAGGTCGTT 60.318 55.000 15.21 0.00 41.72 3.85
3605 4514 1.959226 CTTGCTGGCACCGTACGTT 60.959 57.895 15.21 0.00 0.00 3.99
3660 4569 7.318141 ACAAACATATTCCTTTTCATGAGCAG 58.682 34.615 0.00 0.00 0.00 4.24
3715 4624 7.673926 ACTGAAATGGGAGGCTAAAGAAAATTA 59.326 33.333 0.00 0.00 0.00 1.40
3717 4626 6.019108 ACTGAAATGGGAGGCTAAAGAAAAT 58.981 36.000 0.00 0.00 0.00 1.82
3718 4627 5.393866 ACTGAAATGGGAGGCTAAAGAAAA 58.606 37.500 0.00 0.00 0.00 2.29
3722 4631 4.335416 TGAACTGAAATGGGAGGCTAAAG 58.665 43.478 0.00 0.00 0.00 1.85
3786 4758 5.310331 TGCAGATGGATATCAGGTATTTCCA 59.690 40.000 4.83 0.00 46.03 3.53
3787 4759 5.809001 TGCAGATGGATATCAGGTATTTCC 58.191 41.667 4.83 0.00 36.51 3.13
3798 4770 2.709934 ACCAGAAGCTGCAGATGGATAT 59.290 45.455 25.35 3.93 34.99 1.63
3970 4942 0.238553 GCTTGAAGAAGACCGGCAAC 59.761 55.000 0.00 0.00 0.00 4.17
4036 5008 5.890985 AGATATCGGTATCTTGAGGATCCAG 59.109 44.000 15.82 2.47 43.53 3.86
4135 5107 7.064847 GCCACAGCAAAATGATTGATATTTGAA 59.935 33.333 0.00 0.00 39.53 2.69
4219 5230 9.638239 GCAAGAAAACAACCAGATGATTAATAA 57.362 29.630 0.00 0.00 0.00 1.40
4232 5243 2.796593 GTCTGCATGCAAGAAAACAACC 59.203 45.455 22.88 4.28 0.00 3.77
4473 5484 7.914346 GCAAATATGAAAATCCTGTCTCTGAAG 59.086 37.037 0.00 0.00 0.00 3.02
4577 5598 4.693566 CCAAGGAACTCGTTTACAGCAATA 59.306 41.667 0.00 0.00 38.49 1.90
4831 5853 3.476552 GGTGAAGAGGATGTTGAACACA 58.523 45.455 0.00 0.00 40.71 3.72
4921 5947 7.393216 AGAAATAGTCTCAGATCAAGTGCTTT 58.607 34.615 0.00 0.00 0.00 3.51
4940 5966 6.925610 ACGCTGCATGATTTAGAAGAAATA 57.074 33.333 0.00 0.00 0.00 1.40
4948 5974 1.066002 CCCCAACGCTGCATGATTTAG 59.934 52.381 0.00 0.00 0.00 1.85
4953 5979 0.611618 ATTTCCCCAACGCTGCATGA 60.612 50.000 0.00 0.00 0.00 3.07
5001 6027 3.054139 TGATACTGGCATGCTTCTCCTTT 60.054 43.478 18.92 0.00 0.00 3.11
5025 6051 1.377202 GCCATCAGGAGTTTCGCCA 60.377 57.895 0.00 0.00 36.89 5.69
5057 6083 2.497675 CTGCAAGTAGCCTTACCTGAGA 59.502 50.000 0.00 0.00 44.83 3.27
5058 6084 2.898705 CTGCAAGTAGCCTTACCTGAG 58.101 52.381 0.00 0.00 44.83 3.35
5081 6107 4.191033 TGTTCATTCATGTCCCAATTGC 57.809 40.909 0.00 0.00 0.00 3.56
5082 6108 5.113383 CCATGTTCATTCATGTCCCAATTG 58.887 41.667 0.00 0.00 42.29 2.32
5083 6109 4.778958 ACCATGTTCATTCATGTCCCAATT 59.221 37.500 0.00 0.00 42.29 2.32
5125 6151 3.876550 GCCGGGGTTTATCTCCTTTTCTT 60.877 47.826 2.18 0.00 33.68 2.52
5126 6152 2.356844 GCCGGGGTTTATCTCCTTTTCT 60.357 50.000 2.18 0.00 33.68 2.52
5127 6153 2.022195 GCCGGGGTTTATCTCCTTTTC 58.978 52.381 2.18 0.00 33.68 2.29
5128 6154 1.341679 GGCCGGGGTTTATCTCCTTTT 60.342 52.381 2.18 0.00 33.68 2.27
5157 6183 1.317431 ATGGCTGTGTGCATCGCAAT 61.317 50.000 0.00 0.00 41.47 3.56
5182 6208 5.520748 AGTTTGACCCCTTAGATGACATT 57.479 39.130 0.00 0.00 0.00 2.71
5198 6224 7.311092 TGTTCCCTACATAAGAGAAGTTTGA 57.689 36.000 0.00 0.00 0.00 2.69
5361 6393 3.181407 ACCATTGAAGGGAGTTGGGAAAT 60.181 43.478 1.57 0.00 0.00 2.17
5407 6440 2.744202 AGTTTCAGTGCGCAGATTAAGG 59.256 45.455 12.22 0.00 0.00 2.69
5656 6720 2.993853 CCTCCAGTCTTCCTGCCC 59.006 66.667 0.00 0.00 40.06 5.36
5835 6899 4.070009 ACATACCTTTCTTGTTTCCGACC 58.930 43.478 0.00 0.00 0.00 4.79
6036 7101 1.480137 CTCTTCCTCTGCTCCGTTGAT 59.520 52.381 0.00 0.00 0.00 2.57
6063 7128 2.507102 ACAAGCTCGACCGCGATG 60.507 61.111 8.23 0.00 46.80 3.84
6259 7324 9.558396 AACATGCATGAAAAAGGAAATTTCTAA 57.442 25.926 32.75 0.00 37.60 2.10
6439 7544 3.427528 CACTCAAAGTCATGCAATGCAAC 59.572 43.478 13.45 7.01 46.21 4.17
6452 7557 6.874134 AGCAAATCGTTACTATCACTCAAAGT 59.126 34.615 0.00 0.00 0.00 2.66
6470 7575 6.202188 CCTGATAAAATTGATGCCAGCAAATC 59.798 38.462 0.00 0.00 0.00 2.17
6659 7775 1.225373 ATCAGGCAGGCCTTCCATTA 58.775 50.000 24.31 8.49 45.70 1.90
6667 7783 0.610174 TCGATCATATCAGGCAGGCC 59.390 55.000 0.97 0.97 0.00 5.19
6668 7784 1.719600 GTCGATCATATCAGGCAGGC 58.280 55.000 0.00 0.00 0.00 4.85
6669 7785 1.403382 CCGTCGATCATATCAGGCAGG 60.403 57.143 0.00 0.00 0.00 4.85
6670 7786 1.541588 TCCGTCGATCATATCAGGCAG 59.458 52.381 0.00 0.00 0.00 4.85
6671 7787 1.269723 GTCCGTCGATCATATCAGGCA 59.730 52.381 0.00 0.00 0.00 4.75
6672 7788 1.269723 TGTCCGTCGATCATATCAGGC 59.730 52.381 0.00 0.00 0.00 4.85
6673 7789 3.857549 ATGTCCGTCGATCATATCAGG 57.142 47.619 0.00 0.00 0.00 3.86
6674 7790 4.618912 GTCAATGTCCGTCGATCATATCAG 59.381 45.833 0.00 0.00 0.00 2.90
6675 7791 4.037446 TGTCAATGTCCGTCGATCATATCA 59.963 41.667 0.00 0.00 0.00 2.15
6677 7793 4.584327 TGTCAATGTCCGTCGATCATAT 57.416 40.909 0.00 0.00 0.00 1.78
6679 7795 2.959507 TGTCAATGTCCGTCGATCAT 57.040 45.000 0.00 0.00 0.00 2.45
6680 7796 2.734276 TTGTCAATGTCCGTCGATCA 57.266 45.000 0.00 0.00 0.00 2.92
6681 7797 2.734606 TGTTTGTCAATGTCCGTCGATC 59.265 45.455 0.00 0.00 0.00 3.69
6682 7798 2.761559 TGTTTGTCAATGTCCGTCGAT 58.238 42.857 0.00 0.00 0.00 3.59
6683 7799 2.226602 TGTTTGTCAATGTCCGTCGA 57.773 45.000 0.00 0.00 0.00 4.20
6684 7800 3.536158 ATTGTTTGTCAATGTCCGTCG 57.464 42.857 0.00 0.00 44.06 5.12
6685 7801 5.794945 CACATATTGTTTGTCAATGTCCGTC 59.205 40.000 3.73 0.00 45.14 4.79
6686 7802 5.335583 CCACATATTGTTTGTCAATGTCCGT 60.336 40.000 3.73 0.00 45.14 4.69
6687 7803 5.094812 CCACATATTGTTTGTCAATGTCCG 58.905 41.667 3.73 0.00 45.14 4.79
6688 7804 6.024552 ACCACATATTGTTTGTCAATGTCC 57.975 37.500 3.73 0.00 45.14 4.02
6689 7805 9.638239 AAATACCACATATTGTTTGTCAATGTC 57.362 29.630 3.73 0.00 45.14 3.06
6714 7831 6.095440 GCTCTGGTTTCTCCTGCAAAATATAA 59.905 38.462 0.00 0.00 37.07 0.98
7087 8206 2.279517 GCTGAGTACATCCCGGCG 60.280 66.667 0.00 0.00 0.00 6.46
7163 8282 2.580276 GATCACCCCGTACGCCAA 59.420 61.111 10.49 0.00 0.00 4.52
7384 8503 2.436646 CTCCACCACACGGGCATC 60.437 66.667 0.00 0.00 42.05 3.91
7435 8554 3.075005 GCCACCAGCCCGTAGAGA 61.075 66.667 0.00 0.00 34.35 3.10
7561 8680 3.509137 GAACCCGGCAGTGACGACA 62.509 63.158 22.85 0.00 35.20 4.35
7600 8719 2.169352 CACCTTGATGGAGAGACCGAAT 59.831 50.000 0.00 0.00 42.61 3.34
7686 8809 2.436646 CATTCGCTTCCGGCTGGT 60.437 61.111 12.43 0.00 39.13 4.00
8068 9464 6.843069 AAGCATTGTGTTTAAATTCCACAC 57.157 33.333 9.05 5.28 38.71 3.82
8127 9525 8.871629 ATTTGGTACACTTTTGTATCCATGTA 57.128 30.769 0.00 0.00 38.42 2.29
8128 9526 7.450014 TGATTTGGTACACTTTTGTATCCATGT 59.550 33.333 0.00 0.00 38.42 3.21
8157 9555 4.278419 GCACAGATGAAGTAAACCCAAACT 59.722 41.667 0.00 0.00 0.00 2.66
8162 9560 3.010420 GAGGCACAGATGAAGTAAACCC 58.990 50.000 0.00 0.00 0.00 4.11
8163 9561 3.010420 GGAGGCACAGATGAAGTAAACC 58.990 50.000 0.00 0.00 0.00 3.27
8164 9562 3.010420 GGGAGGCACAGATGAAGTAAAC 58.990 50.000 0.00 0.00 0.00 2.01
8165 9563 2.642311 TGGGAGGCACAGATGAAGTAAA 59.358 45.455 0.00 0.00 0.00 2.01
8166 9564 2.265367 TGGGAGGCACAGATGAAGTAA 58.735 47.619 0.00 0.00 0.00 2.24
8167 9565 1.951209 TGGGAGGCACAGATGAAGTA 58.049 50.000 0.00 0.00 0.00 2.24
8168 9566 1.293062 ATGGGAGGCACAGATGAAGT 58.707 50.000 0.00 0.00 0.00 3.01
8169 9567 2.431954 AATGGGAGGCACAGATGAAG 57.568 50.000 0.00 0.00 0.00 3.02
8206 9604 3.437049 CGATGAAGGGTCCTTTTCTTCAC 59.563 47.826 9.65 5.03 46.17 3.18
8216 9614 6.433404 TCATATAAGTAGACGATGAAGGGTCC 59.567 42.308 0.00 0.00 33.66 4.46
8244 9642 9.839817 ATGCATTTTCATATCAATTCCATTTCA 57.160 25.926 0.00 0.00 0.00 2.69
8279 9677 4.804608 TTGAAATGTACCGTGTGTTGAG 57.195 40.909 0.00 0.00 0.00 3.02
8599 10006 2.328099 GCACACAAGGCCGAGGAAG 61.328 63.158 0.00 0.00 0.00 3.46
8600 10007 2.281484 GCACACAAGGCCGAGGAA 60.281 61.111 0.00 0.00 0.00 3.36
8601 10008 4.329545 GGCACACAAGGCCGAGGA 62.330 66.667 0.00 0.00 42.39 3.71
8607 10014 0.602905 AGAACGTAGGCACACAAGGC 60.603 55.000 0.00 0.00 0.00 4.35
8608 10015 1.148310 CAGAACGTAGGCACACAAGG 58.852 55.000 0.00 0.00 0.00 3.61
8609 10016 0.512952 GCAGAACGTAGGCACACAAG 59.487 55.000 0.00 0.00 0.00 3.16
8610 10017 0.105964 AGCAGAACGTAGGCACACAA 59.894 50.000 8.44 0.00 0.00 3.33
8611 10018 0.599991 CAGCAGAACGTAGGCACACA 60.600 55.000 8.44 0.00 0.00 3.72
8612 10019 1.291877 CCAGCAGAACGTAGGCACAC 61.292 60.000 8.44 0.00 0.00 3.82
8613 10020 1.005037 CCAGCAGAACGTAGGCACA 60.005 57.895 8.44 0.00 0.00 4.57
8614 10021 1.014564 GTCCAGCAGAACGTAGGCAC 61.015 60.000 8.44 0.00 0.00 5.01
8615 10022 1.185618 AGTCCAGCAGAACGTAGGCA 61.186 55.000 8.44 0.00 0.00 4.75
8616 10023 0.737715 CAGTCCAGCAGAACGTAGGC 60.738 60.000 0.00 0.00 0.00 3.93
8617 10024 0.737715 GCAGTCCAGCAGAACGTAGG 60.738 60.000 0.00 0.00 0.00 3.18
8618 10025 1.073216 CGCAGTCCAGCAGAACGTAG 61.073 60.000 0.00 0.00 0.00 3.51
8619 10026 1.080772 CGCAGTCCAGCAGAACGTA 60.081 57.895 0.00 0.00 0.00 3.57
8620 10027 2.356313 CGCAGTCCAGCAGAACGT 60.356 61.111 0.00 0.00 0.00 3.99
8621 10028 3.782244 GCGCAGTCCAGCAGAACG 61.782 66.667 0.30 0.00 0.00 3.95
8622 10029 3.426568 GGCGCAGTCCAGCAGAAC 61.427 66.667 10.83 0.00 34.54 3.01


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

AutoCloner maintained by Alex Coulton.