Multiple sequence alignment - TraesCS7A01G213700

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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 TraesCS7A01G213700 chr7A 100.000 2618 0 0 1 2618 177345456 177342839 0.000000e+00 4835
1 TraesCS7A01G213700 chr7D 89.225 1717 101 32 355 2030 175662547 175660874 0.000000e+00 2069
2 TraesCS7A01G213700 chr7D 92.810 306 21 1 68 373 175662936 175662632 2.390000e-120 442
3 TraesCS7A01G213700 chr7D 91.958 286 19 3 2184 2465 175660870 175660585 5.250000e-107 398
4 TraesCS7A01G213700 chr7B 86.998 1246 81 32 475 1667 141009291 141008074 0.000000e+00 1328
5 TraesCS7A01G213700 chr7B 92.534 442 26 5 2184 2618 141007671 141007230 6.150000e-176 627
6 TraesCS7A01G213700 chr7B 89.744 390 28 7 1649 2030 141008060 141007675 3.030000e-134 488
7 TraesCS7A01G213700 chr7B 88.889 117 6 5 2074 2189 113525947 113525837 1.260000e-28 137
8 TraesCS7A01G213700 chr5A 84.293 1025 112 18 707 1705 436336907 436337908 0.000000e+00 955
9 TraesCS7A01G213700 chr5A 83.652 1046 101 35 701 1717 436352914 436353918 0.000000e+00 920
10 TraesCS7A01G213700 chr5A 90.112 445 32 6 2184 2618 436622948 436623390 3.780000e-158 568
11 TraesCS7A01G213700 chr5A 90.736 421 36 2 1263 1680 436328994 436328574 2.280000e-155 558
12 TraesCS7A01G213700 chr5A 88.791 455 45 5 1198 1647 436357168 436357621 1.060000e-153 553
13 TraesCS7A01G213700 chr5A 83.893 447 46 12 725 1166 436329417 436328992 1.130000e-108 403
14 TraesCS7A01G213700 chr5A 91.544 272 17 3 1768 2034 436622668 436622938 1.140000e-98 370
15 TraesCS7A01G213700 chr5D 84.631 989 107 19 707 1680 335060592 335061550 0.000000e+00 942
16 TraesCS7A01G213700 chr5D 82.234 985 111 36 707 1680 335083816 335084747 0.000000e+00 791
17 TraesCS7A01G213700 chr5D 91.216 444 28 6 2184 2618 335133430 335133871 6.240000e-166 593
18 TraesCS7A01G213700 chr5D 90.315 444 33 2 1268 1701 334990597 334990154 8.130000e-160 573
19 TraesCS7A01G213700 chr5D 88.745 462 40 7 707 1166 334970043 334969592 2.940000e-154 555
20 TraesCS7A01G213700 chr5D 85.965 513 43 15 655 1166 335121133 335121617 2.990000e-144 521
21 TraesCS7A01G213700 chr5D 82.625 518 40 21 655 1166 335087015 335087488 1.870000e-111 412
22 TraesCS7A01G213700 chr5D 81.203 532 44 31 655 1165 334991097 334990601 6.840000e-101 377
23 TraesCS7A01G213700 chr5D 91.111 270 16 4 1768 2032 335133150 335133416 2.480000e-95 359
24 TraesCS7A01G213700 chr5D 81.183 372 51 8 75 439 335086360 335086719 5.520000e-72 281
25 TraesCS7A01G213700 chr5D 84.766 256 34 3 1768 2018 335220553 335220808 4.330000e-63 252
26 TraesCS7A01G213700 chr5D 88.618 123 9 4 2068 2189 238777671 238777789 7.550000e-31 145
27 TraesCS7A01G213700 chr5D 89.655 116 7 4 2074 2188 6364211 6364100 2.720000e-30 143
28 TraesCS7A01G213700 chr5D 86.992 123 10 5 2068 2189 52264421 52264538 1.630000e-27 134
29 TraesCS7A01G213700 chr5B 89.616 443 34 8 2184 2616 392139069 392139509 1.060000e-153 553
30 TraesCS7A01G213700 chr5B 87.158 475 40 7 655 1127 392118547 392119002 1.070000e-143 520
31 TraesCS7A01G213700 chr5B 84.231 520 54 14 655 1166 391826804 391826305 5.070000e-132 481
32 TraesCS7A01G213700 chr5B 91.111 270 16 4 1768 2032 392138789 392139055 2.480000e-95 359
33 TraesCS7A01G213700 chr5B 81.760 466 45 22 707 1167 391866562 391866992 1.150000e-93 353
34 TraesCS7A01G213700 chr6B 90.517 116 3 6 2074 2187 698335364 698335255 2.100000e-31 147
35 TraesCS7A01G213700 chr3A 88.710 124 9 4 2068 2190 59443558 59443677 2.100000e-31 147
36 TraesCS7A01G213700 chr2A 89.076 119 8 4 2072 2189 19268373 19268259 2.720000e-30 143
37 TraesCS7A01G213700 chr6A 88.430 121 9 4 2074 2193 19179054 19178938 9.770000e-30 141
38 TraesCS7A01G213700 chrUn 88.793 116 7 5 2074 2188 29260086 29259976 1.260000e-28 137


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 TraesCS7A01G213700 chr7A 177342839 177345456 2617 True 4835.000000 4835 100.000000 1 2618 1 chr7A.!!$R1 2617
1 TraesCS7A01G213700 chr7D 175660585 175662936 2351 True 969.666667 2069 91.331000 68 2465 3 chr7D.!!$R1 2397
2 TraesCS7A01G213700 chr7B 141007230 141009291 2061 True 814.333333 1328 89.758667 475 2618 3 chr7B.!!$R2 2143
3 TraesCS7A01G213700 chr5A 436336907 436337908 1001 False 955.000000 955 84.293000 707 1705 1 chr5A.!!$F1 998
4 TraesCS7A01G213700 chr5A 436352914 436357621 4707 False 736.500000 920 86.221500 701 1717 2 chr5A.!!$F2 1016
5 TraesCS7A01G213700 chr5A 436328574 436329417 843 True 480.500000 558 87.314500 725 1680 2 chr5A.!!$R1 955
6 TraesCS7A01G213700 chr5A 436622668 436623390 722 False 469.000000 568 90.828000 1768 2618 2 chr5A.!!$F3 850
7 TraesCS7A01G213700 chr5D 335060592 335061550 958 False 942.000000 942 84.631000 707 1680 1 chr5D.!!$F3 973
8 TraesCS7A01G213700 chr5D 335083816 335087488 3672 False 494.666667 791 82.014000 75 1680 3 chr5D.!!$F6 1605
9 TraesCS7A01G213700 chr5D 335133150 335133871 721 False 476.000000 593 91.163500 1768 2618 2 chr5D.!!$F7 850
10 TraesCS7A01G213700 chr5D 334990154 334991097 943 True 475.000000 573 85.759000 655 1701 2 chr5D.!!$R3 1046
11 TraesCS7A01G213700 chr5B 392138789 392139509 720 False 456.000000 553 90.363500 1768 2616 2 chr5B.!!$F3 848

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
301 302 0.043334 AGGATAGGCACAGGTGGAGT 59.957 55.0 1.1 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 4283 0.03101 ACTAGAGCTTGGGGGTAGGG 60.031 60.0 0.0 0.0 0.0 3.53 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
18 19 4.424711 GGAGCAACATGGGGCCGA 62.425 66.667 0.00 0.00 0.00 5.54
19 20 2.825836 GAGCAACATGGGGCCGAG 60.826 66.667 0.00 0.00 0.00 4.63
20 21 3.329542 GAGCAACATGGGGCCGAGA 62.330 63.158 0.00 0.00 0.00 4.04
21 22 2.124151 GCAACATGGGGCCGAGAT 60.124 61.111 0.00 0.00 0.00 2.75
22 23 1.754234 GCAACATGGGGCCGAGATT 60.754 57.895 0.00 0.00 0.00 2.40
23 24 2.008268 GCAACATGGGGCCGAGATTG 62.008 60.000 9.39 9.39 0.00 2.67
24 25 1.076777 AACATGGGGCCGAGATTGG 60.077 57.895 0.00 0.00 0.00 3.16
25 26 1.570857 AACATGGGGCCGAGATTGGA 61.571 55.000 0.00 0.00 0.00 3.53
26 27 1.227102 CATGGGGCCGAGATTGGAA 59.773 57.895 0.00 0.00 0.00 3.53
27 28 0.178981 CATGGGGCCGAGATTGGAAT 60.179 55.000 0.00 0.00 0.00 3.01
28 29 0.178981 ATGGGGCCGAGATTGGAATG 60.179 55.000 0.00 0.00 0.00 2.67
29 30 1.529244 GGGGCCGAGATTGGAATGG 60.529 63.158 0.00 0.00 0.00 3.16
30 31 1.529244 GGGCCGAGATTGGAATGGG 60.529 63.158 0.00 0.00 0.00 4.00
31 32 1.227383 GGCCGAGATTGGAATGGGT 59.773 57.895 0.00 0.00 0.00 4.51
32 33 0.819666 GGCCGAGATTGGAATGGGTC 60.820 60.000 0.00 0.00 0.00 4.46
33 34 0.107214 GCCGAGATTGGAATGGGTCA 60.107 55.000 0.00 0.00 0.00 4.02
34 35 1.959042 CCGAGATTGGAATGGGTCAG 58.041 55.000 0.00 0.00 0.00 3.51
35 36 1.486310 CCGAGATTGGAATGGGTCAGA 59.514 52.381 0.00 0.00 0.00 3.27
36 37 2.105477 CCGAGATTGGAATGGGTCAGAT 59.895 50.000 0.00 0.00 0.00 2.90
37 38 3.434167 CCGAGATTGGAATGGGTCAGATT 60.434 47.826 0.00 0.00 0.00 2.40
38 39 3.812053 CGAGATTGGAATGGGTCAGATTC 59.188 47.826 0.00 0.00 0.00 2.52
39 40 4.684214 CGAGATTGGAATGGGTCAGATTCA 60.684 45.833 0.00 0.00 32.34 2.57
40 41 5.383476 GAGATTGGAATGGGTCAGATTCAT 58.617 41.667 0.00 0.00 32.34 2.57
41 42 5.774179 AGATTGGAATGGGTCAGATTCATT 58.226 37.500 0.00 2.05 32.34 2.57
42 43 5.832060 AGATTGGAATGGGTCAGATTCATTC 59.168 40.000 15.15 15.15 43.37 2.67
43 44 4.868172 TGGAATGGGTCAGATTCATTCT 57.132 40.909 19.49 0.00 43.52 2.40
44 45 5.974156 TGGAATGGGTCAGATTCATTCTA 57.026 39.130 19.49 14.68 43.52 2.10
45 46 6.520021 TGGAATGGGTCAGATTCATTCTAT 57.480 37.500 19.49 0.00 43.52 1.98
46 47 6.301486 TGGAATGGGTCAGATTCATTCTATG 58.699 40.000 19.49 0.00 43.52 2.23
47 48 5.182760 GGAATGGGTCAGATTCATTCTATGC 59.817 44.000 19.49 7.32 43.52 3.14
48 49 4.776435 TGGGTCAGATTCATTCTATGCA 57.224 40.909 0.00 0.00 31.77 3.96
49 50 5.314718 TGGGTCAGATTCATTCTATGCAT 57.685 39.130 3.79 3.79 31.77 3.96
50 51 5.698104 TGGGTCAGATTCATTCTATGCATT 58.302 37.500 3.54 0.00 31.77 3.56
51 52 5.766670 TGGGTCAGATTCATTCTATGCATTC 59.233 40.000 3.54 0.00 31.77 2.67
52 53 6.002704 GGGTCAGATTCATTCTATGCATTCT 58.997 40.000 3.54 0.00 31.77 2.40
53 54 6.489361 GGGTCAGATTCATTCTATGCATTCTT 59.511 38.462 3.54 0.00 31.77 2.52
54 55 7.361127 GGTCAGATTCATTCTATGCATTCTTG 58.639 38.462 3.54 0.00 31.77 3.02
55 56 7.228108 GGTCAGATTCATTCTATGCATTCTTGA 59.772 37.037 3.54 0.70 31.77 3.02
56 57 8.618677 GTCAGATTCATTCTATGCATTCTTGAA 58.381 33.333 3.54 10.15 31.77 2.69
57 58 9.181061 TCAGATTCATTCTATGCATTCTTGAAA 57.819 29.630 3.54 0.00 31.77 2.69
58 59 9.452065 CAGATTCATTCTATGCATTCTTGAAAG 57.548 33.333 3.54 2.81 31.77 2.62
59 60 9.404848 AGATTCATTCTATGCATTCTTGAAAGA 57.595 29.630 3.54 5.08 30.96 2.52
60 61 9.448294 GATTCATTCTATGCATTCTTGAAAGAC 57.552 33.333 3.54 3.54 34.13 3.01
61 62 7.926674 TCATTCTATGCATTCTTGAAAGACA 57.073 32.000 3.54 0.00 34.13 3.41
62 63 8.515695 TCATTCTATGCATTCTTGAAAGACAT 57.484 30.769 3.54 0.00 34.13 3.06
63 64 8.963725 TCATTCTATGCATTCTTGAAAGACATT 58.036 29.630 3.54 0.00 34.13 2.71
64 65 9.582431 CATTCTATGCATTCTTGAAAGACATTT 57.418 29.630 3.54 0.00 34.13 2.32
65 66 8.975410 TTCTATGCATTCTTGAAAGACATTTG 57.025 30.769 3.54 0.00 34.13 2.32
66 67 8.339344 TCTATGCATTCTTGAAAGACATTTGA 57.661 30.769 3.54 0.00 34.13 2.69
67 68 8.239314 TCTATGCATTCTTGAAAGACATTTGAC 58.761 33.333 3.54 0.00 34.13 3.18
68 69 6.395426 TGCATTCTTGAAAGACATTTGACT 57.605 33.333 0.00 0.00 34.13 3.41
69 70 6.808829 TGCATTCTTGAAAGACATTTGACTT 58.191 32.000 0.00 0.00 34.13 3.01
70 71 6.919662 TGCATTCTTGAAAGACATTTGACTTC 59.080 34.615 0.00 0.00 34.13 3.01
71 72 6.919662 GCATTCTTGAAAGACATTTGACTTCA 59.080 34.615 0.00 0.00 34.13 3.02
72 73 7.114529 GCATTCTTGAAAGACATTTGACTTCAG 59.885 37.037 0.00 0.00 34.13 3.02
73 74 7.630242 TTCTTGAAAGACATTTGACTTCAGT 57.370 32.000 0.00 0.00 34.13 3.41
154 155 2.287668 GGACCTATCCGACGTCATTCAG 60.288 54.545 17.16 6.80 34.48 3.02
166 167 5.221891 ACGTCATTCAGTTGATATGTTGC 57.778 39.130 0.00 0.00 0.00 4.17
197 198 2.885135 TTGGACGGGTGTCTAGTCTA 57.115 50.000 0.00 0.00 44.83 2.59
249 250 5.686159 GAGGATCCAAAAGATGCATAGTG 57.314 43.478 15.82 0.00 45.38 2.74
252 253 7.632160 AGGATCCAAAAGATGCATAGTGGCA 62.632 44.000 15.82 0.00 45.38 4.92
274 275 1.079503 GGCGACTGAGGTGTTTGATC 58.920 55.000 0.00 0.00 0.00 2.92
301 302 0.043334 AGGATAGGCACAGGTGGAGT 59.957 55.000 1.10 0.00 0.00 3.85
331 332 2.791567 CGAGACTACAGACTGTGCATC 58.208 52.381 18.58 11.99 0.00 3.91
353 354 3.134458 GTCTTCAACACCTTGAGACCAG 58.866 50.000 0.00 0.00 37.70 4.00
359 463 3.214696 ACACCTTGAGACCAGAAAAGG 57.785 47.619 0.00 0.00 44.00 3.11
379 483 7.953158 AAAGGTGATCAATACTGTGATATCG 57.047 36.000 0.00 0.00 38.38 2.92
511 615 5.969435 GCAAGAATAAAGTTTACATACCCGC 59.031 40.000 0.00 0.00 0.00 6.13
538 645 4.935352 AAAAGTTTACATGCTGCCTTCA 57.065 36.364 0.00 0.00 0.00 3.02
626 746 1.349234 TGACGTGAATCACATGCTCG 58.651 50.000 14.24 0.59 38.94 5.03
627 747 1.336795 TGACGTGAATCACATGCTCGT 60.337 47.619 14.24 4.09 38.94 4.18
628 748 1.726791 GACGTGAATCACATGCTCGTT 59.273 47.619 14.24 0.00 38.94 3.85
630 750 1.726248 CGTGAATCACATGCTCGTTCA 59.274 47.619 14.24 0.00 33.40 3.18
631 751 2.157474 CGTGAATCACATGCTCGTTCAA 59.843 45.455 14.24 0.00 33.40 2.69
633 753 4.032786 CGTGAATCACATGCTCGTTCAATA 59.967 41.667 14.24 0.00 33.40 1.90
634 754 5.496387 GTGAATCACATGCTCGTTCAATAG 58.504 41.667 8.74 0.00 34.08 1.73
635 755 5.291858 GTGAATCACATGCTCGTTCAATAGA 59.708 40.000 8.74 0.00 34.08 1.98
636 756 5.521372 TGAATCACATGCTCGTTCAATAGAG 59.479 40.000 0.00 0.00 37.54 2.43
640 760 4.393062 CACATGCTCGTTCAATAGAGGTTT 59.607 41.667 0.00 0.00 35.19 3.27
641 761 5.003804 ACATGCTCGTTCAATAGAGGTTTT 58.996 37.500 0.00 0.00 35.19 2.43
674 811 2.262423 ACTTCTCTGTCTGTTTGGCC 57.738 50.000 0.00 0.00 0.00 5.36
849 1013 1.429463 CGGAGCACGGCCTATAAATC 58.571 55.000 0.00 0.00 39.42 2.17
856 1020 1.289109 CGGCCTATAAATCGTGCCCG 61.289 60.000 0.00 0.00 38.92 6.13
905 1087 1.019805 TCGGCGACACAACAACAACA 61.020 50.000 4.99 0.00 0.00 3.33
906 1088 0.179187 CGGCGACACAACAACAACAA 60.179 50.000 0.00 0.00 0.00 2.83
947 1140 3.308438 GCAATCATCTTTGCCTGTTGT 57.692 42.857 0.00 0.00 44.94 3.32
951 1144 3.423539 TCATCTTTGCCTGTTGTAGCT 57.576 42.857 0.00 0.00 0.00 3.32
1127 1354 2.126307 CGTCGTCAGGGCACAGAG 60.126 66.667 0.00 0.00 0.00 3.35
1185 1420 2.093869 GGTACGTACTCCCAAAGCATGA 60.094 50.000 24.07 0.00 0.00 3.07
1190 1425 2.592102 ACTCCCAAAGCATGACATGT 57.408 45.000 16.62 0.00 0.00 3.21
1230 1490 1.517257 CGTTGCTAGACTCAGCCCG 60.517 63.158 0.00 0.00 41.04 6.13
1232 1492 3.019003 TTGCTAGACTCAGCCCGGC 62.019 63.158 0.00 0.00 41.04 6.13
1461 1724 4.961511 GTGCTGTCCGTGGCGTCA 62.962 66.667 0.00 0.00 0.00 4.35
1614 1877 2.677003 CGCGCCCTTCATCAACGTT 61.677 57.895 0.00 0.00 0.00 3.99
1660 1941 5.449041 CCGGATAACACGTGTACTTAGCTAA 60.449 44.000 23.69 5.94 0.00 3.09
1667 1948 5.884792 ACACGTGTACTTAGCTAATAGGACT 59.115 40.000 21.98 0.00 0.00 3.85
1733 2057 6.762702 TTAAAGACGGTTCACCTTTCTTTT 57.237 33.333 19.82 10.04 41.86 2.27
1811 2344 4.194640 ACATGGATTGGAGATCGAAACAG 58.805 43.478 0.00 0.00 0.00 3.16
1814 2347 4.253685 TGGATTGGAGATCGAAACAGTTC 58.746 43.478 0.00 0.00 0.00 3.01
1912 2564 3.375642 GTTGCTTCAACTCCTCTTTTGC 58.624 45.455 2.71 0.00 40.73 3.68
1952 3453 6.431198 TTTCTACAAAAAGAAGCACGAGTT 57.569 33.333 0.00 0.00 36.85 3.01
1961 3462 5.405331 AAGAAGCACGAGTTAACAAAGAC 57.595 39.130 8.61 0.00 0.00 3.01
1987 3592 4.383850 AGACAATGAGAATCGACCAGAG 57.616 45.455 0.00 0.00 38.61 3.35
1988 3593 3.131933 AGACAATGAGAATCGACCAGAGG 59.868 47.826 0.00 0.00 38.61 3.69
1989 3594 3.099905 ACAATGAGAATCGACCAGAGGA 58.900 45.455 0.00 0.00 38.61 3.71
2025 3796 3.633986 GAGGAAAATAGTGAGGCCCAATG 59.366 47.826 0.00 0.00 0.00 2.82
2030 4272 1.965414 TAGTGAGGCCCAATGAGGAA 58.035 50.000 0.00 0.00 41.22 3.36
2032 4274 1.428912 AGTGAGGCCCAATGAGGAAAA 59.571 47.619 0.00 0.00 41.22 2.29
2033 4275 2.043526 AGTGAGGCCCAATGAGGAAAAT 59.956 45.455 0.00 0.00 41.22 1.82
2034 4276 3.269381 AGTGAGGCCCAATGAGGAAAATA 59.731 43.478 0.00 0.00 41.22 1.40
2035 4277 3.633986 GTGAGGCCCAATGAGGAAAATAG 59.366 47.826 0.00 0.00 41.22 1.73
2036 4278 3.269381 TGAGGCCCAATGAGGAAAATAGT 59.731 43.478 0.00 0.00 41.22 2.12
2037 4279 3.633986 GAGGCCCAATGAGGAAAATAGTG 59.366 47.826 0.00 0.00 41.22 2.74
2038 4280 3.269381 AGGCCCAATGAGGAAAATAGTGA 59.731 43.478 0.00 0.00 41.22 3.41
2039 4281 3.633986 GGCCCAATGAGGAAAATAGTGAG 59.366 47.826 0.00 0.00 41.22 3.51
2040 4282 4.273318 GCCCAATGAGGAAAATAGTGAGT 58.727 43.478 0.00 0.00 41.22 3.41
2041 4283 4.336713 GCCCAATGAGGAAAATAGTGAGTC 59.663 45.833 0.00 0.00 41.22 3.36
2042 4284 4.884164 CCCAATGAGGAAAATAGTGAGTCC 59.116 45.833 0.00 0.00 41.22 3.85
2043 4285 4.884164 CCAATGAGGAAAATAGTGAGTCCC 59.116 45.833 0.00 0.00 41.22 4.46
2044 4286 5.339530 CCAATGAGGAAAATAGTGAGTCCCT 60.340 44.000 0.00 0.00 41.22 4.20
2045 4287 6.126768 CCAATGAGGAAAATAGTGAGTCCCTA 60.127 42.308 0.00 0.00 41.22 3.53
2046 4288 5.934402 TGAGGAAAATAGTGAGTCCCTAC 57.066 43.478 0.00 0.00 0.00 3.18
2047 4289 4.715297 TGAGGAAAATAGTGAGTCCCTACC 59.285 45.833 0.00 0.00 0.00 3.18
2048 4290 4.038633 AGGAAAATAGTGAGTCCCTACCC 58.961 47.826 0.00 0.00 0.00 3.69
2049 4291 3.136077 GGAAAATAGTGAGTCCCTACCCC 59.864 52.174 0.00 0.00 0.00 4.95
2050 4292 2.491312 AATAGTGAGTCCCTACCCCC 57.509 55.000 0.00 0.00 0.00 5.40
2051 4293 1.326055 ATAGTGAGTCCCTACCCCCA 58.674 55.000 0.00 0.00 0.00 4.96
2052 4294 1.095130 TAGTGAGTCCCTACCCCCAA 58.905 55.000 0.00 0.00 0.00 4.12
2053 4295 0.252742 AGTGAGTCCCTACCCCCAAG 60.253 60.000 0.00 0.00 0.00 3.61
2054 4296 1.615424 TGAGTCCCTACCCCCAAGC 60.615 63.158 0.00 0.00 0.00 4.01
2055 4297 1.307084 GAGTCCCTACCCCCAAGCT 60.307 63.158 0.00 0.00 0.00 3.74
2056 4298 1.307084 AGTCCCTACCCCCAAGCTC 60.307 63.158 0.00 0.00 0.00 4.09
2057 4299 1.307084 GTCCCTACCCCCAAGCTCT 60.307 63.158 0.00 0.00 0.00 4.09
2058 4300 0.031414 GTCCCTACCCCCAAGCTCTA 60.031 60.000 0.00 0.00 0.00 2.43
2059 4301 0.264955 TCCCTACCCCCAAGCTCTAG 59.735 60.000 0.00 0.00 0.00 2.43
2060 4302 0.031010 CCCTACCCCCAAGCTCTAGT 60.031 60.000 0.00 0.00 0.00 2.57
2061 4303 1.625508 CCCTACCCCCAAGCTCTAGTT 60.626 57.143 0.00 0.00 0.00 2.24
2062 4304 2.197465 CCTACCCCCAAGCTCTAGTTT 58.803 52.381 0.00 0.00 0.00 2.66
2063 4305 3.381335 CCTACCCCCAAGCTCTAGTTTA 58.619 50.000 0.00 0.00 0.00 2.01
2064 4306 3.974642 CCTACCCCCAAGCTCTAGTTTAT 59.025 47.826 0.00 0.00 0.00 1.40
2065 4307 4.412528 CCTACCCCCAAGCTCTAGTTTATT 59.587 45.833 0.00 0.00 0.00 1.40
2066 4308 4.236527 ACCCCCAAGCTCTAGTTTATTG 57.763 45.455 0.00 0.00 0.00 1.90
2067 4309 3.053619 ACCCCCAAGCTCTAGTTTATTGG 60.054 47.826 10.07 10.07 40.10 3.16
2068 4310 3.202151 CCCCCAAGCTCTAGTTTATTGGA 59.798 47.826 15.59 0.00 42.46 3.53
2069 4311 4.141158 CCCCCAAGCTCTAGTTTATTGGAT 60.141 45.833 15.59 0.00 42.46 3.41
2070 4312 5.066593 CCCCAAGCTCTAGTTTATTGGATC 58.933 45.833 15.59 0.00 42.46 3.36
2071 4313 5.397899 CCCCAAGCTCTAGTTTATTGGATCA 60.398 44.000 15.59 0.00 42.46 2.92
2072 4314 6.122277 CCCAAGCTCTAGTTTATTGGATCAA 58.878 40.000 15.59 0.00 42.46 2.57
2073 4315 6.038714 CCCAAGCTCTAGTTTATTGGATCAAC 59.961 42.308 15.59 0.00 42.46 3.18
2074 4316 6.038714 CCAAGCTCTAGTTTATTGGATCAACC 59.961 42.308 11.05 0.00 42.46 3.77
2075 4317 5.360591 AGCTCTAGTTTATTGGATCAACCG 58.639 41.667 0.00 0.00 42.61 4.44
2076 4318 5.128827 AGCTCTAGTTTATTGGATCAACCGA 59.871 40.000 0.00 0.00 42.61 4.69
2077 4319 5.463724 GCTCTAGTTTATTGGATCAACCGAG 59.536 44.000 0.00 1.10 42.61 4.63
2078 4320 6.683110 GCTCTAGTTTATTGGATCAACCGAGA 60.683 42.308 11.04 5.24 42.61 4.04
2079 4321 7.177832 TCTAGTTTATTGGATCAACCGAGAA 57.822 36.000 0.00 0.00 42.61 2.87
2080 4322 7.792032 TCTAGTTTATTGGATCAACCGAGAAT 58.208 34.615 0.00 0.00 42.61 2.40
2081 4323 6.683974 AGTTTATTGGATCAACCGAGAATG 57.316 37.500 0.00 0.00 42.61 2.67
2082 4324 6.180472 AGTTTATTGGATCAACCGAGAATGT 58.820 36.000 0.00 0.00 42.61 2.71
2083 4325 6.659242 AGTTTATTGGATCAACCGAGAATGTT 59.341 34.615 0.00 0.00 42.61 2.71
2084 4326 7.827236 AGTTTATTGGATCAACCGAGAATGTTA 59.173 33.333 0.00 0.00 42.61 2.41
2085 4327 7.786178 TTATTGGATCAACCGAGAATGTTAG 57.214 36.000 0.00 0.00 42.61 2.34
2086 4328 4.137116 TGGATCAACCGAGAATGTTAGG 57.863 45.455 0.00 0.00 42.61 2.69
2087 4329 3.517901 TGGATCAACCGAGAATGTTAGGT 59.482 43.478 0.00 0.00 42.61 3.08
2088 4330 4.019681 TGGATCAACCGAGAATGTTAGGTT 60.020 41.667 0.00 0.00 46.76 3.50
2089 4331 4.941873 GGATCAACCGAGAATGTTAGGTTT 59.058 41.667 0.00 0.00 43.72 3.27
2090 4332 5.414765 GGATCAACCGAGAATGTTAGGTTTT 59.585 40.000 0.00 0.00 43.72 2.43
2091 4333 6.072119 GGATCAACCGAGAATGTTAGGTTTTT 60.072 38.462 0.00 0.00 43.72 1.94
2092 4334 6.067263 TCAACCGAGAATGTTAGGTTTTTG 57.933 37.500 0.00 0.00 43.72 2.44
2093 4335 5.009210 TCAACCGAGAATGTTAGGTTTTTGG 59.991 40.000 0.00 0.00 43.72 3.28
2094 4336 3.824443 ACCGAGAATGTTAGGTTTTTGGG 59.176 43.478 0.00 0.00 32.17 4.12
2095 4337 3.192633 CCGAGAATGTTAGGTTTTTGGGG 59.807 47.826 0.00 0.00 0.00 4.96
2096 4338 3.192633 CGAGAATGTTAGGTTTTTGGGGG 59.807 47.826 0.00 0.00 0.00 5.40
2097 4339 4.157246 GAGAATGTTAGGTTTTTGGGGGT 58.843 43.478 0.00 0.00 0.00 4.95
2098 4340 4.157246 AGAATGTTAGGTTTTTGGGGGTC 58.843 43.478 0.00 0.00 0.00 4.46
2099 4341 2.385135 TGTTAGGTTTTTGGGGGTCC 57.615 50.000 0.00 0.00 0.00 4.46
2100 4342 1.574339 TGTTAGGTTTTTGGGGGTCCA 59.426 47.619 0.00 0.00 42.25 4.02
2101 4343 2.244695 GTTAGGTTTTTGGGGGTCCAG 58.755 52.381 0.00 0.00 45.04 3.86
2102 4344 1.536644 TAGGTTTTTGGGGGTCCAGT 58.463 50.000 0.00 0.00 45.04 4.00
2103 4345 0.639943 AGGTTTTTGGGGGTCCAGTT 59.360 50.000 0.00 0.00 45.04 3.16
2104 4346 1.009060 AGGTTTTTGGGGGTCCAGTTT 59.991 47.619 0.00 0.00 45.04 2.66
2105 4347 1.841277 GGTTTTTGGGGGTCCAGTTTT 59.159 47.619 0.00 0.00 45.04 2.43
2106 4348 2.158871 GGTTTTTGGGGGTCCAGTTTTC 60.159 50.000 0.00 0.00 45.04 2.29
2107 4349 1.796017 TTTTGGGGGTCCAGTTTTCC 58.204 50.000 0.00 0.00 45.04 3.13
2108 4350 0.938192 TTTGGGGGTCCAGTTTTCCT 59.062 50.000 0.00 0.00 45.04 3.36
2109 4351 0.938192 TTGGGGGTCCAGTTTTCCTT 59.062 50.000 0.00 0.00 45.04 3.36
2110 4352 1.835895 TGGGGGTCCAGTTTTCCTTA 58.164 50.000 0.00 0.00 38.32 2.69
2111 4353 2.364190 TGGGGGTCCAGTTTTCCTTAT 58.636 47.619 0.00 0.00 38.32 1.73
2112 4354 3.543661 TGGGGGTCCAGTTTTCCTTATA 58.456 45.455 0.00 0.00 38.32 0.98
2113 4355 3.924072 TGGGGGTCCAGTTTTCCTTATAA 59.076 43.478 0.00 0.00 38.32 0.98
2114 4356 4.357399 TGGGGGTCCAGTTTTCCTTATAAA 59.643 41.667 0.00 0.00 38.32 1.40
2115 4357 4.708421 GGGGGTCCAGTTTTCCTTATAAAC 59.292 45.833 0.00 0.00 36.08 2.01
2116 4358 5.517833 GGGGGTCCAGTTTTCCTTATAAACT 60.518 44.000 0.00 0.00 44.38 2.66
2124 4366 7.520451 AGTTTTCCTTATAAACTGGACCAAC 57.480 36.000 0.00 0.42 42.54 3.77
2125 4367 7.295340 AGTTTTCCTTATAAACTGGACCAACT 58.705 34.615 0.00 8.73 42.54 3.16
2126 4368 7.447545 AGTTTTCCTTATAAACTGGACCAACTC 59.552 37.037 0.00 0.00 42.54 3.01
2127 4369 6.697641 TTCCTTATAAACTGGACCAACTCT 57.302 37.500 0.00 0.00 0.00 3.24
2128 4370 6.295719 TCCTTATAAACTGGACCAACTCTC 57.704 41.667 0.00 0.00 0.00 3.20
2129 4371 6.023603 TCCTTATAAACTGGACCAACTCTCT 58.976 40.000 0.00 0.00 0.00 3.10
2130 4372 6.500751 TCCTTATAAACTGGACCAACTCTCTT 59.499 38.462 0.00 0.00 0.00 2.85
2131 4373 6.819146 CCTTATAAACTGGACCAACTCTCTTC 59.181 42.308 0.00 0.00 0.00 2.87
2132 4374 7.310734 CCTTATAAACTGGACCAACTCTCTTCT 60.311 40.741 0.00 0.00 0.00 2.85
2133 4375 4.779993 AAACTGGACCAACTCTCTTCTT 57.220 40.909 0.00 0.00 0.00 2.52
2134 4376 4.344359 AACTGGACCAACTCTCTTCTTC 57.656 45.455 0.00 0.00 0.00 2.87
2135 4377 3.582164 ACTGGACCAACTCTCTTCTTCT 58.418 45.455 0.00 0.00 0.00 2.85
2136 4378 3.970640 ACTGGACCAACTCTCTTCTTCTT 59.029 43.478 0.00 0.00 0.00 2.52
2137 4379 5.148502 ACTGGACCAACTCTCTTCTTCTTA 58.851 41.667 0.00 0.00 0.00 2.10
2138 4380 5.602978 ACTGGACCAACTCTCTTCTTCTTAA 59.397 40.000 0.00 0.00 0.00 1.85
2139 4381 6.271159 ACTGGACCAACTCTCTTCTTCTTAAT 59.729 38.462 0.00 0.00 0.00 1.40
2140 4382 6.467677 TGGACCAACTCTCTTCTTCTTAATG 58.532 40.000 0.00 0.00 0.00 1.90
2141 4383 6.270000 TGGACCAACTCTCTTCTTCTTAATGA 59.730 38.462 0.00 0.00 0.00 2.57
2142 4384 7.162082 GGACCAACTCTCTTCTTCTTAATGAA 58.838 38.462 0.00 0.00 0.00 2.57
2143 4385 7.661847 GGACCAACTCTCTTCTTCTTAATGAAA 59.338 37.037 0.00 0.00 33.79 2.69
2144 4386 9.225436 GACCAACTCTCTTCTTCTTAATGAAAT 57.775 33.333 0.00 0.00 33.79 2.17
2145 4387 9.007901 ACCAACTCTCTTCTTCTTAATGAAATG 57.992 33.333 0.00 0.00 33.79 2.32
2146 4388 7.967303 CCAACTCTCTTCTTCTTAATGAAATGC 59.033 37.037 0.00 0.00 33.79 3.56
2147 4389 8.509690 CAACTCTCTTCTTCTTAATGAAATGCA 58.490 33.333 0.00 0.00 33.79 3.96
2148 4390 8.266392 ACTCTCTTCTTCTTAATGAAATGCAG 57.734 34.615 0.00 0.00 33.79 4.41
2149 4391 7.336427 ACTCTCTTCTTCTTAATGAAATGCAGG 59.664 37.037 0.00 0.00 33.79 4.85
2150 4392 7.397221 TCTCTTCTTCTTAATGAAATGCAGGA 58.603 34.615 0.00 0.00 33.79 3.86
2151 4393 7.884877 TCTCTTCTTCTTAATGAAATGCAGGAA 59.115 33.333 0.00 0.00 33.79 3.36
2152 4394 7.820648 TCTTCTTCTTAATGAAATGCAGGAAC 58.179 34.615 0.00 0.00 33.79 3.62
2153 4395 6.515272 TCTTCTTAATGAAATGCAGGAACC 57.485 37.500 0.00 0.00 33.79 3.62
2154 4396 5.418840 TCTTCTTAATGAAATGCAGGAACCC 59.581 40.000 0.00 0.00 33.79 4.11
2155 4397 4.023291 TCTTAATGAAATGCAGGAACCCC 58.977 43.478 0.00 0.00 0.00 4.95
2156 4398 1.571955 AATGAAATGCAGGAACCCCC 58.428 50.000 0.00 0.00 0.00 5.40
2175 4417 3.062466 GCCCCCGCAAGAGGTTTC 61.062 66.667 0.00 0.00 43.02 2.78
2176 4418 2.757077 CCCCCGCAAGAGGTTTCT 59.243 61.111 0.00 0.00 43.02 2.52
2178 4420 1.741770 CCCCGCAAGAGGTTTCTCG 60.742 63.158 0.00 0.00 44.47 4.04
2180 4422 0.320421 CCCGCAAGAGGTTTCTCGAA 60.320 55.000 0.00 0.00 44.47 3.71
2186 4428 4.260620 CGCAAGAGGTTTCTCGAAAAGAAA 60.261 41.667 0.00 0.00 45.80 2.52
2230 4472 2.169561 GGAGGAAAGTGGGCTAGAAGAG 59.830 54.545 0.00 0.00 0.00 2.85
2311 4911 0.958822 GGTCAATGCCGTTTTCAGGT 59.041 50.000 0.00 0.00 0.00 4.00
2318 4918 4.657436 ATGCCGTTTTCAGGTGTAAAAA 57.343 36.364 0.00 0.00 0.00 1.94
2320 4920 5.769484 TGCCGTTTTCAGGTGTAAAAATA 57.231 34.783 0.00 0.00 0.00 1.40
2395 5119 3.119459 TGTTATCTCAGCGAACTCACCTC 60.119 47.826 0.00 0.00 0.00 3.85
2423 5147 8.860088 GCTAATATGTTCAACCCTGGAAATTAT 58.140 33.333 0.00 0.00 0.00 1.28
2587 5819 2.941480 AGGCAAGCTCATCTAATTGGG 58.059 47.619 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.424711 TCGGCCCCATGTTGCTCC 62.425 66.667 0.00 0.00 0.00 4.70
2 3 2.615227 ATCTCGGCCCCATGTTGCTC 62.615 60.000 0.00 0.00 0.00 4.26
3 4 2.215451 AATCTCGGCCCCATGTTGCT 62.215 55.000 0.00 0.00 0.00 3.91
4 5 1.754234 AATCTCGGCCCCATGTTGC 60.754 57.895 0.00 0.00 0.00 4.17
5 6 1.386525 CCAATCTCGGCCCCATGTTG 61.387 60.000 0.00 0.00 0.00 3.33
6 7 1.076777 CCAATCTCGGCCCCATGTT 60.077 57.895 0.00 0.00 0.00 2.71
7 8 1.570857 TTCCAATCTCGGCCCCATGT 61.571 55.000 0.00 0.00 0.00 3.21
8 9 0.178981 ATTCCAATCTCGGCCCCATG 60.179 55.000 0.00 0.00 0.00 3.66
9 10 0.178981 CATTCCAATCTCGGCCCCAT 60.179 55.000 0.00 0.00 0.00 4.00
10 11 1.227102 CATTCCAATCTCGGCCCCA 59.773 57.895 0.00 0.00 0.00 4.96
11 12 1.529244 CCATTCCAATCTCGGCCCC 60.529 63.158 0.00 0.00 0.00 5.80
12 13 1.529244 CCCATTCCAATCTCGGCCC 60.529 63.158 0.00 0.00 0.00 5.80
13 14 0.819666 GACCCATTCCAATCTCGGCC 60.820 60.000 0.00 0.00 0.00 6.13
14 15 0.107214 TGACCCATTCCAATCTCGGC 60.107 55.000 0.00 0.00 0.00 5.54
15 16 1.486310 TCTGACCCATTCCAATCTCGG 59.514 52.381 0.00 0.00 0.00 4.63
16 17 2.988010 TCTGACCCATTCCAATCTCG 57.012 50.000 0.00 0.00 0.00 4.04
17 18 4.785301 TGAATCTGACCCATTCCAATCTC 58.215 43.478 0.00 0.00 30.30 2.75
18 19 4.868172 TGAATCTGACCCATTCCAATCT 57.132 40.909 0.00 0.00 30.30 2.40
19 20 5.832060 AGAATGAATCTGACCCATTCCAATC 59.168 40.000 20.73 6.17 44.21 2.67
20 21 5.774179 AGAATGAATCTGACCCATTCCAAT 58.226 37.500 20.73 8.27 44.21 3.16
21 22 5.197224 AGAATGAATCTGACCCATTCCAA 57.803 39.130 20.73 0.00 44.21 3.53
22 23 4.868172 AGAATGAATCTGACCCATTCCA 57.132 40.909 20.73 0.00 44.21 3.53
23 24 5.182760 GCATAGAATGAATCTGACCCATTCC 59.817 44.000 20.73 9.37 44.21 3.01
24 25 5.766670 TGCATAGAATGAATCTGACCCATTC 59.233 40.000 18.49 18.49 43.76 2.67
25 26 5.698104 TGCATAGAATGAATCTGACCCATT 58.302 37.500 6.18 6.18 39.30 3.16
26 27 5.314718 TGCATAGAATGAATCTGACCCAT 57.685 39.130 0.00 0.00 39.30 4.00
27 28 4.776435 TGCATAGAATGAATCTGACCCA 57.224 40.909 0.00 0.00 39.30 4.51
28 29 6.002704 AGAATGCATAGAATGAATCTGACCC 58.997 40.000 0.00 0.00 39.30 4.46
29 30 7.228108 TCAAGAATGCATAGAATGAATCTGACC 59.772 37.037 0.00 0.00 39.30 4.02
30 31 8.151141 TCAAGAATGCATAGAATGAATCTGAC 57.849 34.615 0.00 0.00 39.30 3.51
31 32 8.741603 TTCAAGAATGCATAGAATGAATCTGA 57.258 30.769 0.00 0.00 39.30 3.27
32 33 9.452065 CTTTCAAGAATGCATAGAATGAATCTG 57.548 33.333 0.00 0.40 39.30 2.90
33 34 9.404848 TCTTTCAAGAATGCATAGAATGAATCT 57.595 29.630 0.00 0.00 35.63 2.40
34 35 9.448294 GTCTTTCAAGAATGCATAGAATGAATC 57.552 33.333 0.00 0.00 36.68 2.52
35 36 8.963725 TGTCTTTCAAGAATGCATAGAATGAAT 58.036 29.630 0.00 0.00 36.68 2.57
36 37 8.339344 TGTCTTTCAAGAATGCATAGAATGAA 57.661 30.769 0.00 6.34 36.68 2.57
37 38 7.926674 TGTCTTTCAAGAATGCATAGAATGA 57.073 32.000 0.00 7.46 36.68 2.57
38 39 9.582431 AAATGTCTTTCAAGAATGCATAGAATG 57.418 29.630 0.00 5.34 36.68 2.67
39 40 9.582431 CAAATGTCTTTCAAGAATGCATAGAAT 57.418 29.630 0.00 0.00 36.68 2.40
40 41 8.795513 TCAAATGTCTTTCAAGAATGCATAGAA 58.204 29.630 0.00 0.00 36.68 2.10
41 42 8.239314 GTCAAATGTCTTTCAAGAATGCATAGA 58.761 33.333 0.00 0.00 36.68 1.98
42 43 8.242053 AGTCAAATGTCTTTCAAGAATGCATAG 58.758 33.333 0.00 0.00 36.68 2.23
43 44 8.114331 AGTCAAATGTCTTTCAAGAATGCATA 57.886 30.769 0.00 0.00 36.68 3.14
44 45 6.989659 AGTCAAATGTCTTTCAAGAATGCAT 58.010 32.000 0.00 0.00 36.68 3.96
45 46 6.395426 AGTCAAATGTCTTTCAAGAATGCA 57.605 33.333 0.00 0.00 36.68 3.96
46 47 6.919662 TGAAGTCAAATGTCTTTCAAGAATGC 59.080 34.615 0.00 0.00 36.68 3.56
47 48 8.133627 ACTGAAGTCAAATGTCTTTCAAGAATG 58.866 33.333 0.00 0.00 36.68 2.67
48 49 8.230472 ACTGAAGTCAAATGTCTTTCAAGAAT 57.770 30.769 0.00 0.00 36.68 2.40
49 50 7.630242 ACTGAAGTCAAATGTCTTTCAAGAA 57.370 32.000 0.00 0.00 36.68 2.52
50 51 7.336679 TCAACTGAAGTCAAATGTCTTTCAAGA 59.663 33.333 0.00 0.00 0.00 3.02
51 52 7.475015 TCAACTGAAGTCAAATGTCTTTCAAG 58.525 34.615 0.00 0.00 0.00 3.02
52 53 7.389803 TCAACTGAAGTCAAATGTCTTTCAA 57.610 32.000 0.00 0.00 0.00 2.69
53 54 7.572523 ATCAACTGAAGTCAAATGTCTTTCA 57.427 32.000 0.00 0.00 0.00 2.69
54 55 9.552114 CATATCAACTGAAGTCAAATGTCTTTC 57.448 33.333 0.00 0.00 0.00 2.62
55 56 8.517878 CCATATCAACTGAAGTCAAATGTCTTT 58.482 33.333 0.00 0.00 0.00 2.52
56 57 7.121759 CCCATATCAACTGAAGTCAAATGTCTT 59.878 37.037 0.00 0.00 0.00 3.01
57 58 6.600822 CCCATATCAACTGAAGTCAAATGTCT 59.399 38.462 0.00 0.00 0.00 3.41
58 59 6.599244 TCCCATATCAACTGAAGTCAAATGTC 59.401 38.462 0.00 0.00 0.00 3.06
59 60 6.375455 GTCCCATATCAACTGAAGTCAAATGT 59.625 38.462 0.00 0.00 0.00 2.71
60 61 6.375174 TGTCCCATATCAACTGAAGTCAAATG 59.625 38.462 0.00 0.00 0.00 2.32
61 62 6.484288 TGTCCCATATCAACTGAAGTCAAAT 58.516 36.000 0.00 0.00 0.00 2.32
62 63 5.875224 TGTCCCATATCAACTGAAGTCAAA 58.125 37.500 0.00 0.00 0.00 2.69
63 64 5.497464 TGTCCCATATCAACTGAAGTCAA 57.503 39.130 0.00 0.00 0.00 3.18
64 65 5.698741 ATGTCCCATATCAACTGAAGTCA 57.301 39.130 0.00 0.00 0.00 3.41
65 66 6.599244 TCAAATGTCCCATATCAACTGAAGTC 59.401 38.462 0.00 0.00 0.00 3.01
66 67 6.484288 TCAAATGTCCCATATCAACTGAAGT 58.516 36.000 0.00 0.00 0.00 3.01
67 68 7.395190 TTCAAATGTCCCATATCAACTGAAG 57.605 36.000 0.00 0.00 0.00 3.02
68 69 7.669304 TCTTTCAAATGTCCCATATCAACTGAA 59.331 33.333 0.00 0.00 0.00 3.02
69 70 7.121168 GTCTTTCAAATGTCCCATATCAACTGA 59.879 37.037 0.00 0.00 0.00 3.41
70 71 7.094248 TGTCTTTCAAATGTCCCATATCAACTG 60.094 37.037 0.00 0.00 0.00 3.16
71 72 6.947733 TGTCTTTCAAATGTCCCATATCAACT 59.052 34.615 0.00 0.00 0.00 3.16
72 73 7.156876 TGTCTTTCAAATGTCCCATATCAAC 57.843 36.000 0.00 0.00 0.00 3.18
73 74 7.577426 GCTTGTCTTTCAAATGTCCCATATCAA 60.577 37.037 0.00 0.00 35.48 2.57
90 91 3.056607 AGCACACTTTGTTGCTTGTCTTT 60.057 39.130 0.00 0.00 33.29 2.52
97 98 4.136796 TCATAGAAGCACACTTTGTTGCT 58.863 39.130 0.00 0.00 36.70 3.91
132 133 1.000496 GAATGACGTCGGATAGGTCCC 60.000 57.143 11.62 0.00 41.37 4.46
137 138 4.028852 TCAACTGAATGACGTCGGATAG 57.971 45.455 11.62 9.33 0.00 2.08
143 144 5.063944 AGCAACATATCAACTGAATGACGTC 59.936 40.000 9.11 9.11 30.82 4.34
154 155 9.177304 CAATCATCAATGTAGCAACATATCAAC 57.823 33.333 0.00 0.00 45.79 3.18
166 167 3.561310 CACCCGTCCAATCATCAATGTAG 59.439 47.826 0.00 0.00 0.00 2.74
197 198 2.073816 CCACCGTCGCTTTTACATTCT 58.926 47.619 0.00 0.00 0.00 2.40
234 235 3.428452 CCACTGCCACTATGCATCTTTTG 60.428 47.826 0.19 0.00 41.16 2.44
242 243 2.125147 TCGCCACTGCCACTATGC 60.125 61.111 0.00 0.00 0.00 3.14
252 253 0.532862 CAAACACCTCAGTCGCCACT 60.533 55.000 0.00 0.00 0.00 4.00
293 294 2.360350 CAATGCGCCACTCCACCT 60.360 61.111 4.18 0.00 0.00 4.00
316 317 2.929531 AGACGATGCACAGTCTGTAG 57.070 50.000 20.91 1.79 45.03 2.74
318 319 1.341209 TGAAGACGATGCACAGTCTGT 59.659 47.619 21.89 13.95 45.91 3.41
331 332 2.135933 GGTCTCAAGGTGTTGAAGACG 58.864 52.381 0.00 0.00 42.27 4.18
353 354 8.491152 CGATATCACAGTATTGATCACCTTTTC 58.509 37.037 3.12 0.00 37.42 2.29
359 463 9.425893 CAAAAACGATATCACAGTATTGATCAC 57.574 33.333 3.12 0.00 37.42 3.06
392 496 2.003672 CCGGACAAATCGTTAGGCG 58.996 57.895 0.00 0.00 43.01 5.52
394 498 0.391927 TGGCCGGACAAATCGTTAGG 60.392 55.000 8.12 0.00 0.00 2.69
399 503 3.875838 TTTTTGGCCGGACAAATCG 57.124 47.368 35.19 0.00 39.80 3.34
422 526 9.628500 AGTTTTCTTTAACAAGACCATTAGAGT 57.372 29.630 0.00 0.00 38.86 3.24
467 571 6.322712 TCTTGCTGGTAAAATGGTAACTGTTT 59.677 34.615 0.00 0.00 37.61 2.83
468 572 5.830991 TCTTGCTGGTAAAATGGTAACTGTT 59.169 36.000 0.00 0.00 37.61 3.16
486 590 6.183360 GCGGGTATGTAAACTTTATTCTTGCT 60.183 38.462 0.00 0.00 0.00 3.91
640 760 7.614192 AGACAGAGAAGTTACCAAAAGGAAAAA 59.386 33.333 0.00 0.00 0.00 1.94
641 761 7.067008 CAGACAGAGAAGTTACCAAAAGGAAAA 59.933 37.037 0.00 0.00 0.00 2.29
643 763 6.055588 CAGACAGAGAAGTTACCAAAAGGAA 58.944 40.000 0.00 0.00 0.00 3.36
644 764 5.130477 ACAGACAGAGAAGTTACCAAAAGGA 59.870 40.000 0.00 0.00 0.00 3.36
645 765 5.368989 ACAGACAGAGAAGTTACCAAAAGG 58.631 41.667 0.00 0.00 0.00 3.11
646 766 6.927294 AACAGACAGAGAAGTTACCAAAAG 57.073 37.500 0.00 0.00 0.00 2.27
647 767 6.094881 CCAAACAGACAGAGAAGTTACCAAAA 59.905 38.462 0.00 0.00 0.00 2.44
653 790 3.391296 AGGCCAAACAGACAGAGAAGTTA 59.609 43.478 5.01 0.00 0.00 2.24
700 844 3.760035 CGGACGTGGAGGTGGAGG 61.760 72.222 0.00 0.00 0.00 4.30
701 845 4.436998 GCGGACGTGGAGGTGGAG 62.437 72.222 0.00 0.00 0.00 3.86
856 1020 4.125703 CTGATGTATTGTTCAGGGAGAGC 58.874 47.826 0.00 0.00 36.53 4.09
998 1215 2.475466 GCCATCACAGTCGCCATGG 61.475 63.158 7.63 7.63 39.15 3.66
999 1216 2.475466 GGCCATCACAGTCGCCATG 61.475 63.158 0.00 0.00 41.25 3.66
1152 1379 3.732212 AGTACGTACCTTGGGTTTGTTC 58.268 45.455 21.80 0.00 37.09 3.18
1190 1425 1.535226 CGCCGTGCTGCTTATACAGTA 60.535 52.381 0.00 0.00 39.96 2.74
1215 1456 3.461773 GCCGGGCTGAGTCTAGCA 61.462 66.667 12.87 0.00 45.46 3.49
1230 1490 1.680338 AATATCAGAAACCTGCCGCC 58.320 50.000 0.00 0.00 0.00 6.13
1232 1492 2.684881 AGCAAATATCAGAAACCTGCCG 59.315 45.455 0.00 0.00 0.00 5.69
1660 1941 8.888419 AGGATGATCATCATTTACAAGTCCTAT 58.112 33.333 31.49 0.00 37.20 2.57
1667 1948 9.208022 GAATACGAGGATGATCATCATTTACAA 57.792 33.333 31.49 13.86 37.20 2.41
1733 2057 3.994392 GCCACAAAGAATACGAGTGAGAA 59.006 43.478 0.00 0.00 32.14 2.87
1782 2106 3.808466 TCTCCAATCCATGTCTTCTCG 57.192 47.619 0.00 0.00 0.00 4.04
1961 3462 5.410924 TGGTCGATTCTCATTGTCTAACAG 58.589 41.667 0.00 0.00 0.00 3.16
1987 3592 5.982890 TTTCCTCATTCATTCCACTTTCC 57.017 39.130 0.00 0.00 0.00 3.13
1988 3593 8.743714 ACTATTTTCCTCATTCATTCCACTTTC 58.256 33.333 0.00 0.00 0.00 2.62
1989 3594 8.526147 CACTATTTTCCTCATTCATTCCACTTT 58.474 33.333 0.00 0.00 0.00 2.66
2025 3796 4.101274 GGGTAGGGACTCACTATTTTCCTC 59.899 50.000 0.00 0.00 41.75 3.71
2030 4272 2.046729 TGGGGGTAGGGACTCACTATTT 59.953 50.000 0.00 0.00 41.75 1.40
2032 4274 1.326055 TGGGGGTAGGGACTCACTAT 58.674 55.000 0.00 0.00 41.75 2.12
2033 4275 1.007963 CTTGGGGGTAGGGACTCACTA 59.992 57.143 0.00 0.00 41.75 2.74
2034 4276 0.252742 CTTGGGGGTAGGGACTCACT 60.253 60.000 0.00 0.00 41.75 3.41
2035 4277 1.911702 GCTTGGGGGTAGGGACTCAC 61.912 65.000 0.00 0.00 41.75 3.51
2036 4278 1.615424 GCTTGGGGGTAGGGACTCA 60.615 63.158 0.00 0.00 41.75 3.41
2037 4279 1.307084 AGCTTGGGGGTAGGGACTC 60.307 63.158 0.00 0.00 41.75 3.36
2038 4280 1.307084 GAGCTTGGGGGTAGGGACT 60.307 63.158 0.00 0.00 46.37 3.85
2039 4281 0.031414 TAGAGCTTGGGGGTAGGGAC 60.031 60.000 0.00 0.00 0.00 4.46
2040 4282 0.264955 CTAGAGCTTGGGGGTAGGGA 59.735 60.000 0.00 0.00 0.00 4.20
2041 4283 0.031010 ACTAGAGCTTGGGGGTAGGG 60.031 60.000 0.00 0.00 0.00 3.53
2042 4284 1.880941 AACTAGAGCTTGGGGGTAGG 58.119 55.000 0.00 0.00 0.00 3.18
2043 4285 5.368989 CAATAAACTAGAGCTTGGGGGTAG 58.631 45.833 0.00 0.00 0.00 3.18
2044 4286 4.165372 CCAATAAACTAGAGCTTGGGGGTA 59.835 45.833 0.00 0.00 34.12 3.69
2045 4287 3.053619 CCAATAAACTAGAGCTTGGGGGT 60.054 47.826 0.00 0.00 34.12 4.95
2046 4288 3.202151 TCCAATAAACTAGAGCTTGGGGG 59.798 47.826 0.00 0.00 37.53 5.40
2047 4289 4.503714 TCCAATAAACTAGAGCTTGGGG 57.496 45.455 0.00 0.00 37.53 4.96
2048 4290 5.684704 TGATCCAATAAACTAGAGCTTGGG 58.315 41.667 0.00 0.00 37.53 4.12
2049 4291 6.038714 GGTTGATCCAATAAACTAGAGCTTGG 59.961 42.308 0.00 4.41 38.14 3.61
2050 4292 6.238211 CGGTTGATCCAATAAACTAGAGCTTG 60.238 42.308 0.00 0.00 35.57 4.01
2051 4293 5.817816 CGGTTGATCCAATAAACTAGAGCTT 59.182 40.000 0.00 0.00 35.57 3.74
2052 4294 5.128827 TCGGTTGATCCAATAAACTAGAGCT 59.871 40.000 0.00 0.00 35.57 4.09
2053 4295 5.357257 TCGGTTGATCCAATAAACTAGAGC 58.643 41.667 0.00 0.00 35.57 4.09
2054 4296 6.806751 TCTCGGTTGATCCAATAAACTAGAG 58.193 40.000 0.00 2.25 33.61 2.43
2055 4297 6.785337 TCTCGGTTGATCCAATAAACTAGA 57.215 37.500 0.00 0.00 35.57 2.43
2056 4298 7.495934 ACATTCTCGGTTGATCCAATAAACTAG 59.504 37.037 0.00 0.00 35.57 2.57
2057 4299 7.335627 ACATTCTCGGTTGATCCAATAAACTA 58.664 34.615 0.00 0.00 35.57 2.24
2058 4300 6.180472 ACATTCTCGGTTGATCCAATAAACT 58.820 36.000 0.00 0.00 35.57 2.66
2059 4301 6.436843 ACATTCTCGGTTGATCCAATAAAC 57.563 37.500 0.00 0.00 35.57 2.01
2060 4302 7.282224 CCTAACATTCTCGGTTGATCCAATAAA 59.718 37.037 0.00 0.00 35.57 1.40
2061 4303 6.765989 CCTAACATTCTCGGTTGATCCAATAA 59.234 38.462 0.00 0.00 35.57 1.40
2062 4304 6.126883 ACCTAACATTCTCGGTTGATCCAATA 60.127 38.462 0.00 0.00 35.57 1.90
2063 4305 5.126067 CCTAACATTCTCGGTTGATCCAAT 58.874 41.667 0.00 0.00 35.57 3.16
2064 4306 4.019681 ACCTAACATTCTCGGTTGATCCAA 60.020 41.667 0.00 0.00 35.57 3.53
2065 4307 3.517901 ACCTAACATTCTCGGTTGATCCA 59.482 43.478 0.00 0.00 35.57 3.41
2066 4308 4.138487 ACCTAACATTCTCGGTTGATCC 57.862 45.455 0.00 0.00 0.00 3.36
2067 4309 6.496338 AAAACCTAACATTCTCGGTTGATC 57.504 37.500 0.00 0.00 39.53 2.92
2068 4310 6.294508 CCAAAAACCTAACATTCTCGGTTGAT 60.295 38.462 0.00 0.00 39.53 2.57
2069 4311 5.009210 CCAAAAACCTAACATTCTCGGTTGA 59.991 40.000 0.00 0.00 39.53 3.18
2070 4312 5.219633 CCAAAAACCTAACATTCTCGGTTG 58.780 41.667 0.00 0.00 39.53 3.77
2071 4313 4.279922 CCCAAAAACCTAACATTCTCGGTT 59.720 41.667 0.00 0.00 41.25 4.44
2072 4314 3.824443 CCCAAAAACCTAACATTCTCGGT 59.176 43.478 0.00 0.00 0.00 4.69
2073 4315 3.192633 CCCCAAAAACCTAACATTCTCGG 59.807 47.826 0.00 0.00 0.00 4.63
2074 4316 3.192633 CCCCCAAAAACCTAACATTCTCG 59.807 47.826 0.00 0.00 0.00 4.04
2075 4317 4.157246 ACCCCCAAAAACCTAACATTCTC 58.843 43.478 0.00 0.00 0.00 2.87
2076 4318 4.157246 GACCCCCAAAAACCTAACATTCT 58.843 43.478 0.00 0.00 0.00 2.40
2077 4319 3.259876 GGACCCCCAAAAACCTAACATTC 59.740 47.826 0.00 0.00 0.00 2.67
2078 4320 3.244582 GGACCCCCAAAAACCTAACATT 58.755 45.455 0.00 0.00 0.00 2.71
2079 4321 2.180308 TGGACCCCCAAAAACCTAACAT 59.820 45.455 0.00 0.00 40.09 2.71
2080 4322 1.574339 TGGACCCCCAAAAACCTAACA 59.426 47.619 0.00 0.00 40.09 2.41
2081 4323 2.244695 CTGGACCCCCAAAAACCTAAC 58.755 52.381 0.00 0.00 42.98 2.34
2082 4324 1.860906 ACTGGACCCCCAAAAACCTAA 59.139 47.619 0.00 0.00 42.98 2.69
2083 4325 1.536644 ACTGGACCCCCAAAAACCTA 58.463 50.000 0.00 0.00 42.98 3.08
2084 4326 0.639943 AACTGGACCCCCAAAAACCT 59.360 50.000 0.00 0.00 42.98 3.50
2085 4327 1.502690 AAACTGGACCCCCAAAAACC 58.497 50.000 0.00 0.00 42.98 3.27
2086 4328 2.158871 GGAAAACTGGACCCCCAAAAAC 60.159 50.000 0.00 0.00 42.98 2.43
2087 4329 2.120312 GGAAAACTGGACCCCCAAAAA 58.880 47.619 0.00 0.00 42.98 1.94
2088 4330 1.292546 AGGAAAACTGGACCCCCAAAA 59.707 47.619 0.00 0.00 42.98 2.44
2089 4331 0.938192 AGGAAAACTGGACCCCCAAA 59.062 50.000 0.00 0.00 42.98 3.28
2090 4332 0.938192 AAGGAAAACTGGACCCCCAA 59.062 50.000 0.00 0.00 42.98 4.12
2091 4333 1.835895 TAAGGAAAACTGGACCCCCA 58.164 50.000 0.00 0.00 40.95 4.96
2092 4334 4.596354 TTATAAGGAAAACTGGACCCCC 57.404 45.455 0.00 0.00 0.00 5.40
2093 4335 5.577100 AGTTTATAAGGAAAACTGGACCCC 58.423 41.667 0.69 0.00 43.66 4.95
2100 4342 7.295340 AGTTGGTCCAGTTTATAAGGAAAACT 58.705 34.615 11.84 11.84 45.64 2.66
2101 4343 7.447545 AGAGTTGGTCCAGTTTATAAGGAAAAC 59.552 37.037 0.00 9.15 37.14 2.43
2102 4344 7.523415 AGAGTTGGTCCAGTTTATAAGGAAAA 58.477 34.615 0.00 0.00 32.30 2.29
2103 4345 7.017254 AGAGAGTTGGTCCAGTTTATAAGGAAA 59.983 37.037 0.00 0.00 32.30 3.13
2104 4346 6.500751 AGAGAGTTGGTCCAGTTTATAAGGAA 59.499 38.462 0.00 0.00 32.30 3.36
2105 4347 6.023603 AGAGAGTTGGTCCAGTTTATAAGGA 58.976 40.000 0.00 0.00 0.00 3.36
2106 4348 6.301169 AGAGAGTTGGTCCAGTTTATAAGG 57.699 41.667 0.00 0.00 0.00 2.69
2107 4349 7.616313 AGAAGAGAGTTGGTCCAGTTTATAAG 58.384 38.462 0.00 0.00 0.00 1.73
2108 4350 7.554959 AGAAGAGAGTTGGTCCAGTTTATAA 57.445 36.000 0.00 0.00 0.00 0.98
2109 4351 7.455008 AGAAGAAGAGAGTTGGTCCAGTTTATA 59.545 37.037 0.00 0.00 0.00 0.98
2110 4352 6.271159 AGAAGAAGAGAGTTGGTCCAGTTTAT 59.729 38.462 0.00 0.00 0.00 1.40
2111 4353 5.602978 AGAAGAAGAGAGTTGGTCCAGTTTA 59.397 40.000 0.00 0.00 0.00 2.01
2112 4354 4.410555 AGAAGAAGAGAGTTGGTCCAGTTT 59.589 41.667 0.00 0.00 0.00 2.66
2113 4355 3.970640 AGAAGAAGAGAGTTGGTCCAGTT 59.029 43.478 0.00 0.00 0.00 3.16
2114 4356 3.582164 AGAAGAAGAGAGTTGGTCCAGT 58.418 45.455 0.00 0.00 0.00 4.00
2115 4357 4.615588 AAGAAGAAGAGAGTTGGTCCAG 57.384 45.455 0.00 0.00 0.00 3.86
2116 4358 6.270000 TCATTAAGAAGAAGAGAGTTGGTCCA 59.730 38.462 0.00 0.00 0.00 4.02
2117 4359 6.702329 TCATTAAGAAGAAGAGAGTTGGTCC 58.298 40.000 0.00 0.00 0.00 4.46
2118 4360 8.608844 TTTCATTAAGAAGAAGAGAGTTGGTC 57.391 34.615 0.00 0.00 37.57 4.02
2119 4361 9.007901 CATTTCATTAAGAAGAAGAGAGTTGGT 57.992 33.333 0.00 0.00 37.57 3.67
2120 4362 7.967303 GCATTTCATTAAGAAGAAGAGAGTTGG 59.033 37.037 0.00 0.00 37.57 3.77
2121 4363 8.509690 TGCATTTCATTAAGAAGAAGAGAGTTG 58.490 33.333 0.00 0.00 37.57 3.16
2122 4364 8.627208 TGCATTTCATTAAGAAGAAGAGAGTT 57.373 30.769 0.00 0.00 37.57 3.01
2123 4365 7.336427 CCTGCATTTCATTAAGAAGAAGAGAGT 59.664 37.037 0.00 0.00 37.57 3.24
2124 4366 7.551974 TCCTGCATTTCATTAAGAAGAAGAGAG 59.448 37.037 0.00 0.00 37.57 3.20
2125 4367 7.397221 TCCTGCATTTCATTAAGAAGAAGAGA 58.603 34.615 0.00 0.00 37.57 3.10
2126 4368 7.621428 TCCTGCATTTCATTAAGAAGAAGAG 57.379 36.000 0.00 0.00 37.57 2.85
2127 4369 7.094205 GGTTCCTGCATTTCATTAAGAAGAAGA 60.094 37.037 0.00 0.00 37.57 2.87
2128 4370 7.031975 GGTTCCTGCATTTCATTAAGAAGAAG 58.968 38.462 0.00 0.00 37.57 2.85
2129 4371 6.071391 GGGTTCCTGCATTTCATTAAGAAGAA 60.071 38.462 0.00 0.00 37.57 2.52
2130 4372 5.418840 GGGTTCCTGCATTTCATTAAGAAGA 59.581 40.000 0.00 0.00 37.57 2.87
2131 4373 5.394553 GGGGTTCCTGCATTTCATTAAGAAG 60.395 44.000 0.00 0.00 37.57 2.85
2132 4374 4.466015 GGGGTTCCTGCATTTCATTAAGAA 59.534 41.667 0.00 0.00 0.00 2.52
2133 4375 4.023291 GGGGTTCCTGCATTTCATTAAGA 58.977 43.478 0.00 0.00 0.00 2.10
2134 4376 3.132824 GGGGGTTCCTGCATTTCATTAAG 59.867 47.826 0.00 0.00 0.00 1.85
2135 4377 3.103742 GGGGGTTCCTGCATTTCATTAA 58.896 45.455 0.00 0.00 0.00 1.40
2136 4378 2.314549 AGGGGGTTCCTGCATTTCATTA 59.685 45.455 0.00 0.00 46.07 1.90
2137 4379 1.079323 AGGGGGTTCCTGCATTTCATT 59.921 47.619 0.00 0.00 46.07 2.57
2138 4380 0.712380 AGGGGGTTCCTGCATTTCAT 59.288 50.000 0.00 0.00 46.07 2.57
2139 4381 2.172900 AGGGGGTTCCTGCATTTCA 58.827 52.632 0.00 0.00 46.07 2.69
2156 4398 3.868200 AAACCTCTTGCGGGGGCAG 62.868 63.158 0.00 0.00 0.00 4.85
2157 4399 3.860930 GAAACCTCTTGCGGGGGCA 62.861 63.158 0.00 0.00 0.00 5.36
2158 4400 3.062466 GAAACCTCTTGCGGGGGC 61.062 66.667 0.00 0.00 0.00 5.80
2159 4401 1.377333 GAGAAACCTCTTGCGGGGG 60.377 63.158 0.00 0.00 29.54 5.40
2160 4402 1.741770 CGAGAAACCTCTTGCGGGG 60.742 63.158 0.00 0.00 29.54 5.73
2186 4428 3.133721 TGGCCTGCTTGTTGTGTATTTTT 59.866 39.130 3.32 0.00 0.00 1.94
2230 4472 7.817962 TCAGATACTACTTCTAAACTGGTTTGC 59.182 37.037 8.73 0.00 34.23 3.68
2311 4911 7.367285 CACTTGCAGGCTAGTTTATTTTTACA 58.633 34.615 5.64 0.00 30.18 2.41
2318 4918 4.010349 GTTCCACTTGCAGGCTAGTTTAT 58.990 43.478 5.64 0.00 30.18 1.40
2320 4920 2.158608 AGTTCCACTTGCAGGCTAGTTT 60.159 45.455 5.64 0.00 30.18 2.66
2395 5119 4.780815 TCCAGGGTTGAACATATTAGCTG 58.219 43.478 0.00 0.00 0.00 4.24
2498 5222 6.424812 GCAGCCAGTCAAATAAAATGAGTTTT 59.575 34.615 0.00 0.00 40.48 2.43
2554 5278 1.754803 GCTTGCCTTTGGGGGTATAAC 59.245 52.381 0.00 0.00 35.12 1.89
2587 5819 5.091431 GCAGTTTAGAGATGCACAATGAAC 58.909 41.667 0.00 0.00 39.75 3.18


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

AutoCloner maintained by Alex Coulton.