Multiple sequence alignment - TraesCS7D01G023100

Loading Multiple Alignment...

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 TraesCS7D01G023100 chr7D 100.000 2465 0 0 1 2465 10809420 10811884 0.000000e+00 4553.0
1 TraesCS7D01G023100 chr7D 80.682 264 49 2 1277 1540 9165802 9165541 1.160000e-48 204.0
2 TraesCS7D01G023100 chr7D 91.176 68 2 1 614 677 10595427 10595360 3.380000e-14 89.8
3 TraesCS7D01G023100 chr7D 96.970 33 0 1 2310 2342 10812365 10812334 1.000000e-03 54.7
4 TraesCS7D01G023100 chr4A 91.142 858 44 13 940 1791 727746355 727745524 0.000000e+00 1134.0
5 TraesCS7D01G023100 chr4A 85.891 404 44 8 1202 1593 727841924 727841522 3.790000e-113 418.0
6 TraesCS7D01G023100 chr4A 75.424 708 154 13 1027 1720 729308217 729307516 2.360000e-85 326.0
7 TraesCS7D01G023100 chr4A 92.432 185 14 0 576 760 727755139 727754955 5.230000e-67 265.0
8 TraesCS7D01G023100 chr4A 87.288 236 24 6 1202 1431 728129692 728129927 5.230000e-67 265.0
9 TraesCS7D01G023100 chr4A 92.258 155 7 2 301 450 727755365 727755211 5.340000e-52 215.0
10 TraesCS7D01G023100 chr4A 94.231 104 4 1 816 917 727754958 727754855 9.130000e-35 158.0
11 TraesCS7D01G023100 chr7A 87.097 806 47 16 625 1394 10004188 10004972 0.000000e+00 859.0
12 TraesCS7D01G023100 chr7A 90.704 398 22 8 149 536 10003476 10003868 1.310000e-142 516.0
13 TraesCS7D01G023100 chr7A 78.010 764 106 36 1028 1740 10017105 10017857 8.150000e-115 424.0
14 TraesCS7D01G023100 chr7A 80.466 558 80 16 999 1528 9997202 9997758 1.370000e-107 399.0
15 TraesCS7D01G023100 chr7A 81.023 469 45 29 1000 1431 9720315 9719854 1.410000e-87 333.0
16 TraesCS7D01G023100 chr7A 83.777 376 29 6 258 601 10033525 10033900 6.570000e-86 327.0
17 TraesCS7D01G023100 chr7A 84.918 305 23 7 772 1061 10034123 10034419 1.120000e-73 287.0
18 TraesCS7D01G023100 chr7A 78.481 237 43 7 1793 2027 432991828 432991598 5.490000e-32 148.0
19 TraesCS7D01G023100 chr7A 82.812 128 20 2 1795 1922 607796739 607796614 2.000000e-21 113.0
20 TraesCS7D01G023100 chr7A 85.057 87 7 3 614 695 9720660 9720575 1.570000e-12 84.2
21 TraesCS7D01G023100 chr5A 80.579 484 69 16 1792 2273 469657428 469656968 1.400000e-92 350.0
22 TraesCS7D01G023100 chr5A 83.088 136 13 1 2340 2465 469656957 469656822 5.570000e-22 115.0
23 TraesCS7D01G023100 chr6D 80.636 346 51 4 1854 2190 13691008 13690670 1.130000e-63 254.0
24 TraesCS7D01G023100 chr4B 83.478 230 29 8 1792 2018 423891148 423890925 3.210000e-49 206.0
25 TraesCS7D01G023100 chr2D 81.609 261 33 13 1770 2027 449558723 449558971 4.160000e-48 202.0
26 TraesCS7D01G023100 chr3B 82.653 196 32 2 1790 1985 83333163 83333356 3.260000e-39 172.0
27 TraesCS7D01G023100 chr6B 91.209 91 8 0 1 91 364904314 364904224 9.260000e-25 124.0
28 TraesCS7D01G023100 chr6B 91.549 71 6 0 8 78 610827544 610827474 5.610000e-17 99.0
29 TraesCS7D01G023100 chr4D 83.898 118 16 2 1812 1928 259779341 259779456 2.590000e-20 110.0
30 TraesCS7D01G023100 chr1D 88.889 90 9 1 1 89 435259134 435259045 2.590000e-20 110.0
31 TraesCS7D01G023100 chr3A 82.443 131 11 8 2345 2465 547342543 547342415 1.210000e-18 104.0


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 TraesCS7D01G023100 chr7D 10809420 10811884 2464 False 4553.000000 4553 100.000000 1 2465 1 chr7D.!!$F1 2464
1 TraesCS7D01G023100 chr4A 727745524 727746355 831 True 1134.000000 1134 91.142000 940 1791 1 chr4A.!!$R1 851
2 TraesCS7D01G023100 chr4A 729307516 729308217 701 True 326.000000 326 75.424000 1027 1720 1 chr4A.!!$R3 693
3 TraesCS7D01G023100 chr4A 727754855 727755365 510 True 212.666667 265 92.973667 301 917 3 chr4A.!!$R4 616
4 TraesCS7D01G023100 chr7A 10003476 10004972 1496 False 687.500000 859 88.900500 149 1394 2 chr7A.!!$F3 1245
5 TraesCS7D01G023100 chr7A 10017105 10017857 752 False 424.000000 424 78.010000 1028 1740 1 chr7A.!!$F2 712
6 TraesCS7D01G023100 chr7A 9997202 9997758 556 False 399.000000 399 80.466000 999 1528 1 chr7A.!!$F1 529
7 TraesCS7D01G023100 chr7A 10033525 10034419 894 False 307.000000 327 84.347500 258 1061 2 chr7A.!!$F4 803
8 TraesCS7D01G023100 chr7A 9719854 9720660 806 True 208.600000 333 83.040000 614 1431 2 chr7A.!!$R3 817
9 TraesCS7D01G023100 chr5A 469656822 469657428 606 True 232.500000 350 81.833500 1792 2465 2 chr5A.!!$R1 673

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
101 102 0.248949 GGAGCCTTACGTAAGCCGAG 60.249 60.0 26.57 15.48 45.62 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1926 2563 0.178958 TAACCGGCCCAACAACCAAT 60.179 50.0 0.0 0.0 0.0 3.16 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
21 22 3.383620 TTCCATGCAAAAATCAAGCGT 57.616 38.095 0.00 0.00 0.00 5.07
22 23 2.674954 TCCATGCAAAAATCAAGCGTG 58.325 42.857 0.00 0.00 43.14 5.34
24 25 1.127213 CATGCAAAAATCAAGCGTGGC 59.873 47.619 0.00 0.00 40.60 5.01
25 26 0.599728 TGCAAAAATCAAGCGTGGCC 60.600 50.000 0.00 0.00 0.00 5.36
26 27 1.616872 GCAAAAATCAAGCGTGGCCG 61.617 55.000 0.00 0.00 37.07 6.13
27 28 1.008361 CAAAAATCAAGCGTGGCCGG 61.008 55.000 0.00 0.00 33.68 6.13
29 30 2.141122 AAAATCAAGCGTGGCCGGTG 62.141 55.000 1.90 0.00 45.47 4.94
30 31 3.842925 AATCAAGCGTGGCCGGTGT 62.843 57.895 1.90 0.00 45.47 4.16
31 32 3.842925 ATCAAGCGTGGCCGGTGTT 62.843 57.895 1.90 0.00 45.47 3.32
32 33 2.457743 ATCAAGCGTGGCCGGTGTTA 62.458 55.000 1.90 0.00 45.47 2.41
33 34 2.038269 CAAGCGTGGCCGGTGTTAT 61.038 57.895 1.90 0.00 45.47 1.89
34 35 0.741574 CAAGCGTGGCCGGTGTTATA 60.742 55.000 1.90 0.00 45.47 0.98
35 36 0.741927 AAGCGTGGCCGGTGTTATAC 60.742 55.000 1.90 0.00 45.47 1.47
36 37 1.448189 GCGTGGCCGGTGTTATACA 60.448 57.895 1.90 0.00 33.68 2.29
81 82 6.702723 TGTATACAAATACACCGATACCAAGC 59.297 38.462 2.20 0.00 42.40 4.01
82 83 2.933906 ACAAATACACCGATACCAAGCG 59.066 45.455 0.00 0.00 0.00 4.68
98 99 4.414732 CGGAGCCTTACGTAAGCC 57.585 61.111 26.57 20.93 45.62 4.35
99 100 1.588139 CGGAGCCTTACGTAAGCCG 60.588 63.158 27.10 27.10 45.62 5.52
100 101 1.811860 GGAGCCTTACGTAAGCCGA 59.188 57.895 26.57 0.00 45.62 5.54
101 102 0.248949 GGAGCCTTACGTAAGCCGAG 60.249 60.000 26.57 15.48 45.62 4.63
102 103 0.455005 GAGCCTTACGTAAGCCGAGT 59.545 55.000 26.57 10.48 45.62 4.18
103 104 1.672881 GAGCCTTACGTAAGCCGAGTA 59.327 52.381 26.57 0.00 45.62 2.59
104 105 1.403323 AGCCTTACGTAAGCCGAGTAC 59.597 52.381 26.57 10.92 45.62 2.73
105 106 1.133025 GCCTTACGTAAGCCGAGTACA 59.867 52.381 26.57 0.00 45.62 2.90
106 107 2.790387 CCTTACGTAAGCCGAGTACAC 58.210 52.381 26.57 0.00 45.62 2.90
107 108 2.434761 CTTACGTAAGCCGAGTACACG 58.565 52.381 21.57 5.66 45.62 4.49
108 109 1.720805 TACGTAAGCCGAGTACACGA 58.279 50.000 14.54 0.00 45.62 4.35
109 110 1.089920 ACGTAAGCCGAGTACACGAT 58.910 50.000 14.54 2.94 45.62 3.73
110 111 2.279741 ACGTAAGCCGAGTACACGATA 58.720 47.619 14.54 2.02 45.62 2.92
111 112 2.677836 ACGTAAGCCGAGTACACGATAA 59.322 45.455 14.54 0.00 45.62 1.75
112 113 3.313526 ACGTAAGCCGAGTACACGATAAT 59.686 43.478 14.54 0.56 45.62 1.28
113 114 4.511454 ACGTAAGCCGAGTACACGATAATA 59.489 41.667 14.54 0.00 45.62 0.98
114 115 5.007626 ACGTAAGCCGAGTACACGATAATAA 59.992 40.000 14.54 0.00 45.62 1.40
115 116 6.082338 CGTAAGCCGAGTACACGATAATAAT 58.918 40.000 14.54 0.00 39.56 1.28
116 117 6.580041 CGTAAGCCGAGTACACGATAATAATT 59.420 38.462 14.54 1.39 39.56 1.40
117 118 7.113965 CGTAAGCCGAGTACACGATAATAATTT 59.886 37.037 14.54 0.25 39.56 1.82
118 119 9.398170 GTAAGCCGAGTACACGATAATAATTTA 57.602 33.333 14.54 0.00 35.09 1.40
119 120 7.864307 AGCCGAGTACACGATAATAATTTAC 57.136 36.000 14.54 0.00 35.09 2.01
120 121 7.428020 AGCCGAGTACACGATAATAATTTACA 58.572 34.615 14.54 0.00 35.09 2.41
121 122 7.380602 AGCCGAGTACACGATAATAATTTACAC 59.619 37.037 14.54 0.00 35.09 2.90
122 123 7.380602 GCCGAGTACACGATAATAATTTACACT 59.619 37.037 14.54 0.00 35.09 3.55
123 124 8.899776 CCGAGTACACGATAATAATTTACACTC 58.100 37.037 14.54 0.00 35.09 3.51
124 125 8.616425 CGAGTACACGATAATAATTTACACTCG 58.384 37.037 6.90 0.00 42.75 4.18
125 126 8.792831 AGTACACGATAATAATTTACACTCGG 57.207 34.615 0.00 0.00 0.00 4.63
126 127 6.520792 ACACGATAATAATTTACACTCGGC 57.479 37.500 0.00 0.00 0.00 5.54
127 128 6.278363 ACACGATAATAATTTACACTCGGCT 58.722 36.000 0.00 0.00 0.00 5.52
128 129 6.759827 ACACGATAATAATTTACACTCGGCTT 59.240 34.615 0.00 0.00 0.00 4.35
129 130 7.922278 ACACGATAATAATTTACACTCGGCTTA 59.078 33.333 0.00 0.00 0.00 3.09
130 131 8.922676 CACGATAATAATTTACACTCGGCTTAT 58.077 33.333 0.00 0.00 0.00 1.73
131 132 8.922676 ACGATAATAATTTACACTCGGCTTATG 58.077 33.333 0.00 0.00 0.00 1.90
132 133 8.922676 CGATAATAATTTACACTCGGCTTATGT 58.077 33.333 0.00 0.00 0.00 2.29
134 135 9.772973 ATAATAATTTACACTCGGCTTATGTCA 57.227 29.630 0.00 0.00 0.00 3.58
135 136 7.715265 ATAATTTACACTCGGCTTATGTCAG 57.285 36.000 0.00 0.00 0.00 3.51
136 137 2.579207 TACACTCGGCTTATGTCAGC 57.421 50.000 0.00 0.00 39.28 4.26
137 138 0.608130 ACACTCGGCTTATGTCAGCA 59.392 50.000 0.00 0.00 42.10 4.41
138 139 1.001974 ACACTCGGCTTATGTCAGCAA 59.998 47.619 0.00 0.00 42.10 3.91
139 140 1.394917 CACTCGGCTTATGTCAGCAAC 59.605 52.381 0.00 0.00 42.10 4.17
140 141 1.001974 ACTCGGCTTATGTCAGCAACA 59.998 47.619 0.00 0.00 42.10 3.33
142 143 3.118775 ACTCGGCTTATGTCAGCAACATA 60.119 43.478 7.62 7.62 46.95 2.29
199 200 3.378427 GGCAGGACTTTGCTTATACTTGG 59.622 47.826 0.00 0.00 43.57 3.61
204 205 7.254932 GCAGGACTTTGCTTATACTTGGATAAG 60.255 40.741 7.96 7.96 40.81 1.73
223 224 0.948678 GCCTAGTGTTGTTTTGCCGA 59.051 50.000 0.00 0.00 0.00 5.54
257 258 4.219070 ACACTTACATAAGCCGAGTACACA 59.781 41.667 0.00 0.00 36.79 3.72
317 318 3.581755 TCCTGTAGTGAAACGCATACAC 58.418 45.455 0.00 0.00 45.86 2.90
370 384 2.380660 GACAAGATCGAGATCGTGCTC 58.619 52.381 22.47 16.57 46.50 4.26
382 396 3.558411 GTGCTCTGATGCGTCGGC 61.558 66.667 10.09 10.15 40.52 5.54
562 595 1.294780 CACACCTGACCTGCCTCTC 59.705 63.158 0.00 0.00 0.00 3.20
571 604 3.465403 CTGCCTCTCCCTGTCCCG 61.465 72.222 0.00 0.00 0.00 5.14
651 942 4.452114 TCAATCATTCGCCATTAATCTCCG 59.548 41.667 0.00 0.00 0.00 4.63
760 1178 6.822170 TCTGTGTCTGTCGATTGTAGTACTAT 59.178 38.462 5.75 0.00 0.00 2.12
762 1180 8.496707 TGTGTCTGTCGATTGTAGTACTATAA 57.503 34.615 13.66 13.66 0.00 0.98
763 1181 8.610035 TGTGTCTGTCGATTGTAGTACTATAAG 58.390 37.037 16.01 5.52 0.00 1.73
764 1182 8.610896 GTGTCTGTCGATTGTAGTACTATAAGT 58.389 37.037 16.01 6.24 0.00 2.24
765 1183 9.822185 TGTCTGTCGATTGTAGTACTATAAGTA 57.178 33.333 16.01 3.45 0.00 2.24
807 1230 3.912907 CCCCGCCCTGTAGCTACG 61.913 72.222 18.74 12.95 0.00 3.51
856 1282 2.438800 TCTTCTCCTACCTCCTTCCG 57.561 55.000 0.00 0.00 0.00 4.30
961 1461 4.935885 AGACTGCAAAAGAAATCGCTAG 57.064 40.909 0.00 0.00 0.00 3.42
980 1480 2.777094 AGCTTTCTGCCTCACTTCTTC 58.223 47.619 0.00 0.00 44.23 2.87
981 1481 2.371510 AGCTTTCTGCCTCACTTCTTCT 59.628 45.455 0.00 0.00 44.23 2.85
982 1482 3.580458 AGCTTTCTGCCTCACTTCTTCTA 59.420 43.478 0.00 0.00 44.23 2.10
983 1483 3.932089 GCTTTCTGCCTCACTTCTTCTAG 59.068 47.826 0.00 0.00 35.15 2.43
1146 1674 2.492090 CCGAGCCTCACCTTCGAG 59.508 66.667 0.00 0.00 36.49 4.04
1200 1775 0.610232 GTCACCATGGCCTTGAGCTT 60.610 55.000 19.85 0.00 43.05 3.74
1444 2039 3.721706 CGCCCTTCCTCCTGCCTT 61.722 66.667 0.00 0.00 0.00 4.35
1446 2041 1.910580 CGCCCTTCCTCCTGCCTTTA 61.911 60.000 0.00 0.00 0.00 1.85
1448 2043 1.477740 GCCCTTCCTCCTGCCTTTATC 60.478 57.143 0.00 0.00 0.00 1.75
1449 2044 1.202698 CCCTTCCTCCTGCCTTTATCG 60.203 57.143 0.00 0.00 0.00 2.92
1450 2045 1.587547 CTTCCTCCTGCCTTTATCGC 58.412 55.000 0.00 0.00 0.00 4.58
1451 2046 1.139853 CTTCCTCCTGCCTTTATCGCT 59.860 52.381 0.00 0.00 0.00 4.93
1452 2047 0.753262 TCCTCCTGCCTTTATCGCTC 59.247 55.000 0.00 0.00 0.00 5.03
1453 2048 0.250081 CCTCCTGCCTTTATCGCTCC 60.250 60.000 0.00 0.00 0.00 4.70
1454 2049 0.250081 CTCCTGCCTTTATCGCTCCC 60.250 60.000 0.00 0.00 0.00 4.30
1455 2050 1.595382 CCTGCCTTTATCGCTCCCG 60.595 63.158 0.00 0.00 0.00 5.14
1456 2051 1.144057 CTGCCTTTATCGCTCCCGT 59.856 57.895 0.00 0.00 35.54 5.28
1487 2115 1.588667 CGCTGGGTGTTGTTTGCAC 60.589 57.895 0.00 0.00 36.22 4.57
1504 2132 2.125552 CAATCCGGCGACTGCAGA 60.126 61.111 23.35 0.00 45.35 4.26
1581 2217 1.786937 AATCAACCCAACCACAGCAA 58.213 45.000 0.00 0.00 0.00 3.91
1616 2252 1.082756 CGCGGTGAGCTGTTGAAAC 60.083 57.895 0.00 0.00 45.59 2.78
1629 2265 4.783242 CTGTTGAAACATTTTCCGATCGT 58.217 39.130 15.09 0.00 38.41 3.73
1759 2396 7.086376 CACCAAGAAGAAAAAGTGGACATATG 58.914 38.462 0.00 0.00 33.39 1.78
1774 2411 8.370940 AGTGGACATATGTACATCAGGAAATAG 58.629 37.037 23.47 0.00 41.59 1.73
1807 2444 7.604164 TGAAGTAGATCACTGTTCAAGAATTCC 59.396 37.037 0.65 0.00 37.63 3.01
1810 2447 5.495640 AGATCACTGTTCAAGAATTCCTCC 58.504 41.667 0.65 0.00 0.00 4.30
1816 2453 6.540189 CACTGTTCAAGAATTCCTCCGATTAT 59.460 38.462 0.65 0.00 0.00 1.28
1819 2456 6.257849 TGTTCAAGAATTCCTCCGATTATTCG 59.742 38.462 0.65 0.02 45.08 3.34
1830 2467 3.891056 CGATTATTCGGTTAAAGGGCC 57.109 47.619 0.00 0.00 41.74 5.80
1831 2468 3.207778 CGATTATTCGGTTAAAGGGCCA 58.792 45.455 6.18 0.00 41.74 5.36
1832 2469 3.628487 CGATTATTCGGTTAAAGGGCCAA 59.372 43.478 6.18 0.00 41.74 4.52
1833 2470 4.277423 CGATTATTCGGTTAAAGGGCCAAT 59.723 41.667 6.18 0.00 41.74 3.16
1847 2484 2.548480 GGGCCAATGTTAATCGCTACTC 59.452 50.000 4.39 0.00 0.00 2.59
1848 2485 3.202906 GGCCAATGTTAATCGCTACTCA 58.797 45.455 0.00 0.00 0.00 3.41
1851 2488 5.120830 GGCCAATGTTAATCGCTACTCATAG 59.879 44.000 0.00 0.00 0.00 2.23
1852 2489 5.120830 GCCAATGTTAATCGCTACTCATAGG 59.879 44.000 0.00 0.00 0.00 2.57
1857 2494 0.969894 ATCGCTACTCATAGGGTGGC 59.030 55.000 0.00 0.00 41.15 5.01
1863 2500 1.043673 ACTCATAGGGTGGCCGACTC 61.044 60.000 0.00 0.00 0.00 3.36
1865 2502 2.043248 ATAGGGTGGCCGACTCGT 60.043 61.111 0.00 0.00 0.00 4.18
1878 2515 4.500375 GGCCGACTCGTATAACACCTATTT 60.500 45.833 0.00 0.00 0.00 1.40
1882 2519 5.394613 CGACTCGTATAACACCTATTTGTCG 59.605 44.000 0.00 0.00 36.87 4.35
1893 2530 4.060205 ACCTATTTGTCGCGTTAACTTGT 58.940 39.130 5.77 0.00 0.00 3.16
1906 2543 4.152759 CGTTAACTTGTCAGGCCGATTAAA 59.847 41.667 3.71 0.00 0.00 1.52
1907 2544 5.163794 CGTTAACTTGTCAGGCCGATTAAAT 60.164 40.000 3.71 0.00 0.00 1.40
1908 2545 4.701956 AACTTGTCAGGCCGATTAAATG 57.298 40.909 0.00 0.00 0.00 2.32
1909 2546 3.016736 ACTTGTCAGGCCGATTAAATGG 58.983 45.455 0.00 0.00 0.00 3.16
1920 2557 5.108385 CCGATTAAATGGCATGTTAGACC 57.892 43.478 0.00 0.00 0.00 3.85
1921 2558 4.319477 CCGATTAAATGGCATGTTAGACCG 60.319 45.833 0.00 6.88 0.00 4.79
1922 2559 4.272504 CGATTAAATGGCATGTTAGACCGT 59.727 41.667 0.00 0.00 0.00 4.83
1924 2561 2.779755 AATGGCATGTTAGACCGTCA 57.220 45.000 0.00 0.00 0.00 4.35
1925 2562 2.779755 ATGGCATGTTAGACCGTCAA 57.220 45.000 0.00 0.00 0.00 3.18
1926 2563 2.552599 TGGCATGTTAGACCGTCAAA 57.447 45.000 0.40 0.00 0.00 2.69
1927 2564 3.066291 TGGCATGTTAGACCGTCAAAT 57.934 42.857 0.40 0.00 0.00 2.32
1928 2565 3.417101 TGGCATGTTAGACCGTCAAATT 58.583 40.909 0.40 0.00 0.00 1.82
1929 2566 3.190327 TGGCATGTTAGACCGTCAAATTG 59.810 43.478 0.40 0.00 0.00 2.32
1930 2567 3.427503 GGCATGTTAGACCGTCAAATTGG 60.428 47.826 0.40 0.00 0.00 3.16
1935 2572 4.641094 TGTTAGACCGTCAAATTGGTTGTT 59.359 37.500 0.40 0.00 38.99 2.83
1936 2573 3.708563 AGACCGTCAAATTGGTTGTTG 57.291 42.857 0.40 0.00 38.99 3.33
1942 2579 0.602372 CAAATTGGTTGTTGGGCCGG 60.602 55.000 0.00 0.00 32.08 6.13
1960 2597 0.324275 GGTTAATCCTTGCTGGCCCA 60.324 55.000 0.00 0.00 35.26 5.36
1967 2604 1.077005 TCCTTGCTGGCCCATTAACTT 59.923 47.619 0.00 0.00 35.26 2.66
1970 2607 2.008242 TGCTGGCCCATTAACTTGTT 57.992 45.000 0.00 0.00 0.00 2.83
1986 2623 0.608640 TGTTGGCAAACAAAACCCGT 59.391 45.000 3.53 0.00 43.32 5.28
1996 2633 3.114668 ACAAAACCCGTTTATTTGGCC 57.885 42.857 0.00 0.00 38.14 5.36
2005 2642 2.449464 GTTTATTTGGCCCGTAACCCT 58.551 47.619 0.00 0.00 0.00 4.34
2006 2643 2.423446 TTATTTGGCCCGTAACCCTC 57.577 50.000 0.00 0.00 0.00 4.30
2009 2646 4.660611 TGGCCCGTAACCCTCCCA 62.661 66.667 0.00 0.00 0.00 4.37
2011 2648 2.686106 GCCCGTAACCCTCCCAGA 60.686 66.667 0.00 0.00 0.00 3.86
2013 2650 1.305887 CCCGTAACCCTCCCAGACT 60.306 63.158 0.00 0.00 0.00 3.24
2014 2651 1.328430 CCCGTAACCCTCCCAGACTC 61.328 65.000 0.00 0.00 0.00 3.36
2015 2652 1.328430 CCGTAACCCTCCCAGACTCC 61.328 65.000 0.00 0.00 0.00 3.85
2016 2653 1.328430 CGTAACCCTCCCAGACTCCC 61.328 65.000 0.00 0.00 0.00 4.30
2017 2654 0.252558 GTAACCCTCCCAGACTCCCA 60.253 60.000 0.00 0.00 0.00 4.37
2018 2655 0.042731 TAACCCTCCCAGACTCCCAG 59.957 60.000 0.00 0.00 0.00 4.45
2019 2656 2.049792 AACCCTCCCAGACTCCCAGT 62.050 60.000 0.00 0.00 0.00 4.00
2020 2657 1.687493 CCCTCCCAGACTCCCAGTC 60.687 68.421 0.00 0.00 45.38 3.51
2021 2658 1.687493 CCTCCCAGACTCCCAGTCC 60.687 68.421 0.00 0.00 46.18 3.85
2041 2678 1.896465 CCCTCCCTCTCCTAAATAGCG 59.104 57.143 0.00 0.00 0.00 4.26
2044 2681 3.492337 CTCCCTCTCCTAAATAGCGAGT 58.508 50.000 0.00 0.00 0.00 4.18
2049 2686 5.068723 CCCTCTCCTAAATAGCGAGTGTTTA 59.931 44.000 0.00 0.00 0.00 2.01
2053 2690 3.808174 CCTAAATAGCGAGTGTTTAGCCC 59.192 47.826 8.21 0.00 38.11 5.19
2092 2729 1.271934 CTCCTCATGTCCTAGATGGCG 59.728 57.143 0.00 0.00 35.26 5.69
2096 2733 0.250038 CATGTCCTAGATGGCGTGGG 60.250 60.000 0.00 0.00 35.26 4.61
2111 2748 4.432741 GGGCAGGTCCTCCTTGGC 62.433 72.222 0.00 0.00 43.07 4.52
2114 2751 4.020617 CAGGTCCTCCTTGGCGCA 62.021 66.667 10.83 0.00 43.07 6.09
2116 2753 2.514824 GGTCCTCCTTGGCGCATC 60.515 66.667 10.83 0.00 35.26 3.91
2120 2757 2.125552 CTCCTTGGCGCATCGTCA 60.126 61.111 10.83 0.00 40.58 4.35
2133 2770 0.688087 ATCGTCACTTCCCCTCCTCC 60.688 60.000 0.00 0.00 0.00 4.30
2139 2776 1.394151 CTTCCCCTCCTCCCTCTGT 59.606 63.158 0.00 0.00 0.00 3.41
2140 2777 0.980231 CTTCCCCTCCTCCCTCTGTG 60.980 65.000 0.00 0.00 0.00 3.66
2157 2794 0.391793 GTGTGCTGCTACTTCCCCTC 60.392 60.000 0.00 0.00 0.00 4.30
2159 2796 1.081092 TGCTGCTACTTCCCCTCCT 59.919 57.895 0.00 0.00 0.00 3.69
2166 2803 2.894864 GCTACTTCCCCTCCTCCTTTCT 60.895 54.545 0.00 0.00 0.00 2.52
2171 2808 0.547712 CCCCTCCTCCTTTCTGACCA 60.548 60.000 0.00 0.00 0.00 4.02
2172 2809 1.589414 CCCTCCTCCTTTCTGACCAT 58.411 55.000 0.00 0.00 0.00 3.55
2177 2814 1.065126 CCTCCTTTCTGACCATCCACC 60.065 57.143 0.00 0.00 0.00 4.61
2178 2815 1.912043 CTCCTTTCTGACCATCCACCT 59.088 52.381 0.00 0.00 0.00 4.00
2179 2816 1.909302 TCCTTTCTGACCATCCACCTC 59.091 52.381 0.00 0.00 0.00 3.85
2180 2817 1.065126 CCTTTCTGACCATCCACCTCC 60.065 57.143 0.00 0.00 0.00 4.30
2181 2818 0.613260 TTTCTGACCATCCACCTCCG 59.387 55.000 0.00 0.00 0.00 4.63
2182 2819 1.264749 TTCTGACCATCCACCTCCGG 61.265 60.000 0.00 0.00 0.00 5.14
2183 2820 3.391665 CTGACCATCCACCTCCGGC 62.392 68.421 0.00 0.00 0.00 6.13
2185 2822 2.933287 ACCATCCACCTCCGGCAA 60.933 61.111 0.00 0.00 0.00 4.52
2186 2823 2.438434 CCATCCACCTCCGGCAAC 60.438 66.667 0.00 0.00 0.00 4.17
2187 2824 2.671070 CATCCACCTCCGGCAACT 59.329 61.111 0.00 0.00 0.00 3.16
2188 2825 1.746615 CATCCACCTCCGGCAACTG 60.747 63.158 0.00 0.00 0.00 3.16
2189 2826 1.918293 ATCCACCTCCGGCAACTGA 60.918 57.895 0.00 0.00 0.00 3.41
2190 2827 2.185310 ATCCACCTCCGGCAACTGAC 62.185 60.000 0.00 0.00 0.00 3.51
2231 2868 1.071385 ACTGCTGACACCTTCCTTCTG 59.929 52.381 0.00 0.00 0.00 3.02
2232 2869 1.071385 CTGCTGACACCTTCCTTCTGT 59.929 52.381 0.00 0.00 0.00 3.41
2235 2872 0.836606 TGACACCTTCCTTCTGTGCA 59.163 50.000 0.00 0.00 33.30 4.57
2241 2878 1.159285 CTTCCTTCTGTGCATCGCAA 58.841 50.000 0.00 0.00 41.47 4.85
2244 2881 0.027194 CCTTCTGTGCATCGCAATCG 59.973 55.000 0.00 0.00 41.47 3.34
2266 2903 1.039785 CAGCCACCATCTCTCGGAGA 61.040 60.000 7.60 7.60 43.20 3.71
2276 2913 3.401033 TCTCTCGGAGATGCAACAAAA 57.599 42.857 8.39 0.00 33.35 2.44
2277 2914 3.738982 TCTCTCGGAGATGCAACAAAAA 58.261 40.909 8.39 0.00 33.35 1.94
2293 2930 3.465307 AAAAATGTTTCGACGCCGG 57.535 47.368 0.00 0.00 36.24 6.13
2294 2931 0.039888 AAAAATGTTTCGACGCCGGG 60.040 50.000 2.18 0.00 36.24 5.73
2295 2932 1.858372 AAAATGTTTCGACGCCGGGG 61.858 55.000 18.33 18.33 36.24 5.73
2296 2933 2.734948 AAATGTTTCGACGCCGGGGA 62.735 55.000 27.23 0.00 36.24 4.81
2297 2934 3.945304 ATGTTTCGACGCCGGGGAC 62.945 63.158 27.23 18.65 36.24 4.46
2323 2960 3.369381 CGGAGCATGTCTTGGTAGG 57.631 57.895 0.00 0.00 35.82 3.18
2324 2961 0.537188 CGGAGCATGTCTTGGTAGGT 59.463 55.000 0.00 0.00 35.82 3.08
2325 2962 1.754803 CGGAGCATGTCTTGGTAGGTA 59.245 52.381 0.00 0.00 35.82 3.08
2326 2963 2.365617 CGGAGCATGTCTTGGTAGGTAT 59.634 50.000 0.00 0.00 35.82 2.73
2327 2964 3.733337 GGAGCATGTCTTGGTAGGTATG 58.267 50.000 0.00 0.00 35.82 2.39
2328 2965 3.134458 GAGCATGTCTTGGTAGGTATGC 58.866 50.000 0.00 0.00 39.38 3.14
2329 2966 1.867233 GCATGTCTTGGTAGGTATGCG 59.133 52.381 0.00 0.00 34.17 4.73
2330 2967 2.483876 CATGTCTTGGTAGGTATGCGG 58.516 52.381 0.00 0.00 0.00 5.69
2331 2968 0.177141 TGTCTTGGTAGGTATGCGGC 59.823 55.000 0.00 0.00 0.00 6.53
2332 2969 0.177141 GTCTTGGTAGGTATGCGGCA 59.823 55.000 4.58 4.58 0.00 5.69
2333 2970 0.906066 TCTTGGTAGGTATGCGGCAA 59.094 50.000 6.82 0.00 0.00 4.52
2334 2971 1.134521 TCTTGGTAGGTATGCGGCAAG 60.135 52.381 6.82 0.00 0.00 4.01
2386 3023 6.991485 ACATGTTTGTTGATGATTTTCGAC 57.009 33.333 0.00 0.00 29.55 4.20
2387 3024 6.502652 ACATGTTTGTTGATGATTTTCGACA 58.497 32.000 0.00 0.00 38.07 4.35
2422 3069 7.017498 TGTTTGTTGTTGTATACATGTTCGT 57.983 32.000 2.30 0.00 36.44 3.85
2423 3070 6.907748 TGTTTGTTGTTGTATACATGTTCGTG 59.092 34.615 2.30 0.00 36.44 4.35
2424 3071 5.599359 TGTTGTTGTATACATGTTCGTGG 57.401 39.130 2.30 0.00 36.44 4.94
2426 3073 5.177881 TGTTGTTGTATACATGTTCGTGGTC 59.822 40.000 2.30 0.00 36.44 4.02
2431 3078 7.276878 TGTTGTATACATGTTCGTGGTCTATTG 59.723 37.037 2.30 0.00 0.00 1.90
2449 3096 3.715628 TTGAGAAAAGAAAGCAGTGCC 57.284 42.857 12.58 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.493877 CACGCTTGATTTTTGCATGGAAA 59.506 39.130 8.47 8.47 0.00 3.13
2 3 2.609984 CCACGCTTGATTTTTGCATGGA 60.610 45.455 0.00 0.00 41.86 3.41
3 4 1.727880 CCACGCTTGATTTTTGCATGG 59.272 47.619 0.00 0.00 33.80 3.66
4 5 1.127213 GCCACGCTTGATTTTTGCATG 59.873 47.619 0.00 0.00 0.00 4.06
5 6 1.431496 GCCACGCTTGATTTTTGCAT 58.569 45.000 0.00 0.00 0.00 3.96
6 7 0.599728 GGCCACGCTTGATTTTTGCA 60.600 50.000 0.00 0.00 0.00 4.08
7 8 1.616872 CGGCCACGCTTGATTTTTGC 61.617 55.000 2.24 0.00 0.00 3.68
8 9 1.008361 CCGGCCACGCTTGATTTTTG 61.008 55.000 2.24 0.00 39.22 2.44
9 10 1.288752 CCGGCCACGCTTGATTTTT 59.711 52.632 2.24 0.00 39.22 1.94
10 11 1.901464 ACCGGCCACGCTTGATTTT 60.901 52.632 0.00 0.00 39.22 1.82
11 12 2.282180 ACCGGCCACGCTTGATTT 60.282 55.556 0.00 0.00 39.22 2.17
12 13 3.055719 CACCGGCCACGCTTGATT 61.056 61.111 0.00 0.00 39.22 2.57
13 14 2.457743 TAACACCGGCCACGCTTGAT 62.458 55.000 0.00 0.00 39.22 2.57
14 15 2.457743 ATAACACCGGCCACGCTTGA 62.458 55.000 0.00 0.00 39.22 3.02
15 16 0.741574 TATAACACCGGCCACGCTTG 60.742 55.000 0.00 0.00 39.22 4.01
16 17 0.741927 GTATAACACCGGCCACGCTT 60.742 55.000 0.00 0.00 39.22 4.68
17 18 1.153509 GTATAACACCGGCCACGCT 60.154 57.895 0.00 0.00 39.22 5.07
18 19 1.448189 TGTATAACACCGGCCACGC 60.448 57.895 0.00 0.00 39.22 5.34
19 20 2.375981 GTGTATAACACCGGCCACG 58.624 57.895 0.00 0.00 43.05 4.94
51 52 8.086522 GGTATCGGTGTATTTGTATACATCTGT 58.913 37.037 6.36 0.00 46.09 3.41
52 53 8.085909 TGGTATCGGTGTATTTGTATACATCTG 58.914 37.037 6.36 0.00 46.09 2.90
53 54 8.185506 TGGTATCGGTGTATTTGTATACATCT 57.814 34.615 6.36 0.00 46.09 2.90
54 55 8.821147 TTGGTATCGGTGTATTTGTATACATC 57.179 34.615 6.36 0.68 46.09 3.06
55 56 7.386848 GCTTGGTATCGGTGTATTTGTATACAT 59.613 37.037 6.36 0.00 46.09 2.29
56 57 6.702723 GCTTGGTATCGGTGTATTTGTATACA 59.297 38.462 0.08 0.08 43.28 2.29
57 58 6.129009 CGCTTGGTATCGGTGTATTTGTATAC 60.129 42.308 0.00 0.00 37.68 1.47
58 59 5.921976 CGCTTGGTATCGGTGTATTTGTATA 59.078 40.000 0.00 0.00 0.00 1.47
59 60 4.748102 CGCTTGGTATCGGTGTATTTGTAT 59.252 41.667 0.00 0.00 0.00 2.29
60 61 4.114073 CGCTTGGTATCGGTGTATTTGTA 58.886 43.478 0.00 0.00 0.00 2.41
61 62 2.933906 CGCTTGGTATCGGTGTATTTGT 59.066 45.455 0.00 0.00 0.00 2.83
62 63 2.286833 CCGCTTGGTATCGGTGTATTTG 59.713 50.000 0.00 0.00 40.72 2.32
63 64 2.168936 TCCGCTTGGTATCGGTGTATTT 59.831 45.455 0.47 0.00 45.44 1.40
64 65 1.758280 TCCGCTTGGTATCGGTGTATT 59.242 47.619 0.47 0.00 45.44 1.89
65 66 1.340248 CTCCGCTTGGTATCGGTGTAT 59.660 52.381 0.47 0.00 45.44 2.29
66 67 0.742505 CTCCGCTTGGTATCGGTGTA 59.257 55.000 0.47 0.00 45.44 2.90
67 68 1.515954 CTCCGCTTGGTATCGGTGT 59.484 57.895 0.47 0.00 45.44 4.16
68 69 1.883084 GCTCCGCTTGGTATCGGTG 60.883 63.158 0.47 0.00 45.44 4.94
69 70 2.499685 GCTCCGCTTGGTATCGGT 59.500 61.111 0.47 0.00 45.44 4.69
70 71 2.280186 GGCTCCGCTTGGTATCGG 60.280 66.667 0.00 0.00 46.52 4.18
71 72 0.387929 TAAGGCTCCGCTTGGTATCG 59.612 55.000 0.00 0.00 0.00 2.92
72 73 1.867166 GTAAGGCTCCGCTTGGTATC 58.133 55.000 0.00 0.00 0.00 2.24
73 74 0.104304 CGTAAGGCTCCGCTTGGTAT 59.896 55.000 0.00 0.00 0.00 2.73
74 75 1.252904 ACGTAAGGCTCCGCTTGGTA 61.253 55.000 6.46 0.00 46.39 3.25
75 76 1.252904 TACGTAAGGCTCCGCTTGGT 61.253 55.000 6.46 0.00 46.39 3.67
76 77 0.108520 TTACGTAAGGCTCCGCTTGG 60.109 55.000 3.29 0.00 46.39 3.61
77 78 1.278238 CTTACGTAAGGCTCCGCTTG 58.722 55.000 24.73 0.00 46.39 4.01
78 79 0.459759 GCTTACGTAAGGCTCCGCTT 60.460 55.000 30.94 0.00 46.39 4.68
79 80 1.141234 GCTTACGTAAGGCTCCGCT 59.859 57.895 30.94 0.00 46.39 5.52
80 81 3.702253 GCTTACGTAAGGCTCCGC 58.298 61.111 30.94 16.41 46.39 5.54
86 87 2.789092 CGTGTACTCGGCTTACGTAAGG 60.789 54.545 30.94 19.11 44.69 2.69
87 88 2.094258 TCGTGTACTCGGCTTACGTAAG 59.906 50.000 27.37 27.37 44.69 2.34
88 89 2.073056 TCGTGTACTCGGCTTACGTAA 58.927 47.619 16.50 7.94 44.69 3.18
89 90 1.720805 TCGTGTACTCGGCTTACGTA 58.279 50.000 16.50 0.00 44.69 3.57
90 91 1.089920 ATCGTGTACTCGGCTTACGT 58.910 50.000 16.50 0.00 44.69 3.57
91 92 3.323729 TTATCGTGTACTCGGCTTACG 57.676 47.619 16.50 5.48 46.11 3.18
92 93 7.864307 AATTATTATCGTGTACTCGGCTTAC 57.136 36.000 16.50 0.00 0.00 2.34
93 94 9.398170 GTAAATTATTATCGTGTACTCGGCTTA 57.602 33.333 16.50 4.87 0.00 3.09
94 95 7.922278 TGTAAATTATTATCGTGTACTCGGCTT 59.078 33.333 16.50 5.73 0.00 4.35
95 96 7.380602 GTGTAAATTATTATCGTGTACTCGGCT 59.619 37.037 16.50 7.78 0.00 5.52
96 97 7.380602 AGTGTAAATTATTATCGTGTACTCGGC 59.619 37.037 16.50 0.00 0.00 5.54
97 98 8.792831 AGTGTAAATTATTATCGTGTACTCGG 57.207 34.615 16.50 0.00 0.00 4.63
98 99 8.616425 CGAGTGTAAATTATTATCGTGTACTCG 58.384 37.037 10.97 10.97 43.94 4.18
99 100 8.899776 CCGAGTGTAAATTATTATCGTGTACTC 58.100 37.037 0.00 0.00 0.00 2.59
100 101 7.380602 GCCGAGTGTAAATTATTATCGTGTACT 59.619 37.037 0.00 0.00 0.00 2.73
101 102 7.380602 AGCCGAGTGTAAATTATTATCGTGTAC 59.619 37.037 0.00 0.00 0.00 2.90
102 103 7.428020 AGCCGAGTGTAAATTATTATCGTGTA 58.572 34.615 0.00 0.00 0.00 2.90
103 104 6.278363 AGCCGAGTGTAAATTATTATCGTGT 58.722 36.000 0.00 0.00 0.00 4.49
104 105 6.764877 AGCCGAGTGTAAATTATTATCGTG 57.235 37.500 0.00 0.00 0.00 4.35
105 106 8.922676 CATAAGCCGAGTGTAAATTATTATCGT 58.077 33.333 0.00 0.00 0.00 3.73
106 107 8.922676 ACATAAGCCGAGTGTAAATTATTATCG 58.077 33.333 0.00 0.00 0.00 2.92
108 109 9.772973 TGACATAAGCCGAGTGTAAATTATTAT 57.227 29.630 0.00 0.00 0.00 1.28
109 110 9.256477 CTGACATAAGCCGAGTGTAAATTATTA 57.744 33.333 0.00 0.00 0.00 0.98
110 111 7.254795 GCTGACATAAGCCGAGTGTAAATTATT 60.255 37.037 0.00 0.00 37.20 1.40
111 112 6.202954 GCTGACATAAGCCGAGTGTAAATTAT 59.797 38.462 0.00 0.00 37.20 1.28
112 113 5.522460 GCTGACATAAGCCGAGTGTAAATTA 59.478 40.000 0.00 0.00 37.20 1.40
113 114 4.332819 GCTGACATAAGCCGAGTGTAAATT 59.667 41.667 0.00 0.00 37.20 1.82
114 115 3.871594 GCTGACATAAGCCGAGTGTAAAT 59.128 43.478 0.00 0.00 37.20 1.40
115 116 3.259064 GCTGACATAAGCCGAGTGTAAA 58.741 45.455 0.00 0.00 37.20 2.01
116 117 2.232696 TGCTGACATAAGCCGAGTGTAA 59.767 45.455 0.00 0.00 42.83 2.41
117 118 1.822371 TGCTGACATAAGCCGAGTGTA 59.178 47.619 0.00 0.00 42.83 2.90
118 119 0.608130 TGCTGACATAAGCCGAGTGT 59.392 50.000 0.00 0.00 42.83 3.55
119 120 1.394917 GTTGCTGACATAAGCCGAGTG 59.605 52.381 0.00 0.00 42.83 3.51
120 121 1.001974 TGTTGCTGACATAAGCCGAGT 59.998 47.619 0.00 0.00 42.83 4.18
121 122 1.725641 TGTTGCTGACATAAGCCGAG 58.274 50.000 0.00 0.00 42.83 4.63
122 123 2.401583 ATGTTGCTGACATAAGCCGA 57.598 45.000 4.74 0.00 47.00 5.54
128 129 3.118775 ACTCGGCTTATGTTGCTGACATA 60.119 43.478 8.74 8.74 47.00 2.29
130 131 1.001974 ACTCGGCTTATGTTGCTGACA 59.998 47.619 0.00 0.00 40.45 3.58
131 132 1.726853 ACTCGGCTTATGTTGCTGAC 58.273 50.000 0.00 0.00 40.45 3.51
132 133 2.028112 AGAACTCGGCTTATGTTGCTGA 60.028 45.455 0.00 0.00 42.74 4.26
133 134 2.350522 AGAACTCGGCTTATGTTGCTG 58.649 47.619 0.00 0.00 38.10 4.41
134 135 2.770164 AGAACTCGGCTTATGTTGCT 57.230 45.000 0.00 0.00 0.00 3.91
135 136 3.831715 AAAGAACTCGGCTTATGTTGC 57.168 42.857 0.00 0.00 0.00 4.17
136 137 6.422776 ACATAAAGAACTCGGCTTATGTTG 57.577 37.500 0.00 0.00 0.00 3.33
137 138 7.201617 GCTTACATAAAGAACTCGGCTTATGTT 60.202 37.037 10.56 0.00 37.38 2.71
138 139 6.258068 GCTTACATAAAGAACTCGGCTTATGT 59.742 38.462 10.24 10.24 37.38 2.29
139 140 6.292919 GGCTTACATAAAGAACTCGGCTTATG 60.293 42.308 0.00 0.00 37.38 1.90
140 141 5.758784 GGCTTACATAAAGAACTCGGCTTAT 59.241 40.000 0.00 0.00 37.38 1.73
141 142 5.114081 GGCTTACATAAAGAACTCGGCTTA 58.886 41.667 0.00 0.00 37.38 3.09
142 143 3.939592 GGCTTACATAAAGAACTCGGCTT 59.060 43.478 0.00 0.00 37.38 4.35
143 144 3.532542 GGCTTACATAAAGAACTCGGCT 58.467 45.455 0.00 0.00 37.38 5.52
144 145 2.284417 CGGCTTACATAAAGAACTCGGC 59.716 50.000 0.00 0.00 37.38 5.54
145 146 3.777478 TCGGCTTACATAAAGAACTCGG 58.223 45.455 0.00 0.00 37.38 4.63
146 147 4.265556 CACTCGGCTTACATAAAGAACTCG 59.734 45.833 0.00 0.00 37.38 4.18
147 148 5.169295 ACACTCGGCTTACATAAAGAACTC 58.831 41.667 0.00 0.00 37.38 3.01
176 177 4.009675 CAAGTATAAGCAAAGTCCTGCCA 58.990 43.478 0.00 0.00 43.73 4.92
178 179 4.261801 TCCAAGTATAAGCAAAGTCCTGC 58.738 43.478 0.00 0.00 42.97 4.85
179 180 8.147642 CTTATCCAAGTATAAGCAAAGTCCTG 57.852 38.462 0.00 0.00 33.81 3.86
199 200 4.671766 CGGCAAAACAACACTAGGCTTATC 60.672 45.833 0.00 0.00 0.00 1.75
204 205 0.948678 TCGGCAAAACAACACTAGGC 59.051 50.000 0.00 0.00 0.00 3.93
205 206 4.000988 AGTATCGGCAAAACAACACTAGG 58.999 43.478 0.00 0.00 0.00 3.02
207 208 4.633175 TGAGTATCGGCAAAACAACACTA 58.367 39.130 0.00 0.00 38.61 2.74
257 258 7.413328 GCCGACTTAAACCGAGTGTAAATTATT 60.413 37.037 0.00 0.00 0.00 1.40
277 278 2.228822 GGAAAATCACATGTTGCCGACT 59.771 45.455 0.00 0.00 0.00 4.18
317 318 3.435671 ACATGCATGCATCTCGTGATATG 59.564 43.478 30.07 18.29 35.62 1.78
370 384 1.953138 GGATCAGCCGACGCATCAG 60.953 63.158 0.00 0.00 37.52 2.90
382 396 0.543277 TGTTAGCTGGCTGGGATCAG 59.457 55.000 5.25 0.00 43.64 2.90
562 595 3.771160 CGGGAACTCGGGACAGGG 61.771 72.222 0.00 0.00 0.00 4.45
571 604 2.028484 TGCGTGTGTCGGGAACTC 59.972 61.111 0.00 0.00 40.26 3.01
596 629 0.175073 GGTAGGGTGTGTGTCGATCC 59.825 60.000 0.00 0.00 0.00 3.36
601 634 1.666872 GTGCGGTAGGGTGTGTGTC 60.667 63.158 0.00 0.00 0.00 3.67
651 942 0.575390 CAAGGTTGTGTGTCGACGAC 59.425 55.000 20.97 20.97 0.00 4.34
760 1178 4.337555 GGATGGCGACTGAAGTAGTACTTA 59.662 45.833 15.52 4.22 38.80 2.24
762 1180 2.688958 GGATGGCGACTGAAGTAGTACT 59.311 50.000 0.00 0.00 40.53 2.73
763 1181 2.688958 AGGATGGCGACTGAAGTAGTAC 59.311 50.000 0.00 0.00 40.53 2.73
764 1182 2.688446 CAGGATGGCGACTGAAGTAGTA 59.312 50.000 0.00 0.00 40.53 1.82
765 1183 1.478510 CAGGATGGCGACTGAAGTAGT 59.521 52.381 0.00 0.00 44.02 2.73
766 1184 1.804372 GCAGGATGGCGACTGAAGTAG 60.804 57.143 7.02 0.00 36.86 2.57
807 1230 4.657436 ATCAAGCAGCTAGTGGTAGTAC 57.343 45.455 0.00 0.00 35.15 2.73
856 1282 4.411136 GCTAGAGAGCTTGCGGTC 57.589 61.111 0.00 0.00 45.98 4.79
961 1461 2.777094 AGAAGAAGTGAGGCAGAAAGC 58.223 47.619 0.00 0.00 44.65 3.51
980 1480 6.226787 CCCATTAATCAACTGAGGTAGCTAG 58.773 44.000 0.00 0.00 0.00 3.42
981 1481 5.071788 CCCCATTAATCAACTGAGGTAGCTA 59.928 44.000 0.00 0.00 0.00 3.32
982 1482 4.141390 CCCCATTAATCAACTGAGGTAGCT 60.141 45.833 0.00 0.00 0.00 3.32
983 1483 4.137543 CCCCATTAATCAACTGAGGTAGC 58.862 47.826 0.00 0.00 0.00 3.58
1127 1655 4.821589 CGAAGGTGAGGCTCGGGC 62.822 72.222 10.42 0.00 37.82 6.13
1342 1929 2.359850 GCGGTGGAAGATGTGCCA 60.360 61.111 0.00 0.00 0.00 4.92
1443 2038 1.063006 CGACGACGGGAGCGATAAA 59.937 57.895 0.00 0.00 35.72 1.40
1444 2039 2.108514 ACGACGACGGGAGCGATAA 61.109 57.895 12.58 0.00 44.46 1.75
1446 2041 4.175489 CACGACGACGGGAGCGAT 62.175 66.667 12.58 0.00 46.86 4.58
1455 2050 3.735029 AGCGGGAGTCACGACGAC 61.735 66.667 21.32 0.00 45.77 4.34
1456 2051 3.733960 CAGCGGGAGTCACGACGA 61.734 66.667 21.32 0.00 36.20 4.20
1487 2115 1.699656 CTTCTGCAGTCGCCGGATTG 61.700 60.000 14.67 0.00 37.32 2.67
1598 2234 1.082756 GTTTCAACAGCTCACCGCG 60.083 57.895 0.00 0.00 45.59 6.46
1616 2252 1.583054 GAGGGGACGATCGGAAAATG 58.417 55.000 20.98 0.00 0.00 2.32
1645 2281 4.641989 CCTGGGGTCTTTATTGTGAGAATG 59.358 45.833 0.00 0.00 0.00 2.67
1746 2383 6.560003 TCCTGATGTACATATGTCCACTTT 57.440 37.500 12.68 0.00 0.00 2.66
1774 2411 8.932945 TGAACAGTGATCTACTTCATGTAATC 57.067 34.615 0.00 0.00 37.60 1.75
1779 2416 7.895975 TTCTTGAACAGTGATCTACTTCATG 57.104 36.000 0.00 0.00 37.60 3.07
1816 2453 2.296073 ACATTGGCCCTTTAACCGAA 57.704 45.000 0.00 0.00 0.00 4.30
1819 2456 4.678622 CGATTAACATTGGCCCTTTAACC 58.321 43.478 0.00 0.00 0.00 2.85
1820 2457 4.109766 GCGATTAACATTGGCCCTTTAAC 58.890 43.478 0.00 0.00 0.00 2.01
1825 2462 2.172717 AGTAGCGATTAACATTGGCCCT 59.827 45.455 0.00 0.00 0.00 5.19
1826 2463 2.548480 GAGTAGCGATTAACATTGGCCC 59.452 50.000 0.00 0.00 0.00 5.80
1828 2465 5.120830 CCTATGAGTAGCGATTAACATTGGC 59.879 44.000 0.00 0.00 0.00 4.52
1830 2467 6.146184 CACCCTATGAGTAGCGATTAACATTG 59.854 42.308 0.00 0.00 0.00 2.82
1831 2468 6.223852 CACCCTATGAGTAGCGATTAACATT 58.776 40.000 0.00 0.00 0.00 2.71
1832 2469 5.279506 CCACCCTATGAGTAGCGATTAACAT 60.280 44.000 0.00 0.00 0.00 2.71
1833 2470 4.038763 CCACCCTATGAGTAGCGATTAACA 59.961 45.833 0.00 0.00 0.00 2.41
1847 2484 1.105167 TACGAGTCGGCCACCCTATG 61.105 60.000 18.30 0.00 0.00 2.23
1848 2485 0.178970 ATACGAGTCGGCCACCCTAT 60.179 55.000 18.30 0.54 0.00 2.57
1851 2488 0.249197 GTTATACGAGTCGGCCACCC 60.249 60.000 18.30 0.00 0.00 4.61
1852 2489 0.457035 TGTTATACGAGTCGGCCACC 59.543 55.000 18.30 2.24 0.00 4.61
1857 2494 5.585390 ACAAATAGGTGTTATACGAGTCGG 58.415 41.667 18.30 0.00 0.00 4.79
1863 2500 3.792956 ACGCGACAAATAGGTGTTATACG 59.207 43.478 15.93 0.00 0.00 3.06
1865 2502 7.035004 AGTTAACGCGACAAATAGGTGTTATA 58.965 34.615 15.93 0.00 36.76 0.98
1878 2515 1.493772 CCTGACAAGTTAACGCGACA 58.506 50.000 15.93 0.00 0.00 4.35
1882 2519 0.947180 TCGGCCTGACAAGTTAACGC 60.947 55.000 0.00 0.00 0.00 4.84
1906 2543 2.779755 TTGACGGTCTAACATGCCAT 57.220 45.000 9.88 0.00 0.00 4.40
1907 2544 2.552599 TTTGACGGTCTAACATGCCA 57.447 45.000 9.88 0.00 0.00 4.92
1908 2545 3.427503 CCAATTTGACGGTCTAACATGCC 60.428 47.826 9.88 0.00 0.00 4.40
1909 2546 3.190535 ACCAATTTGACGGTCTAACATGC 59.809 43.478 9.88 0.00 0.00 4.06
1910 2547 5.153513 CAACCAATTTGACGGTCTAACATG 58.846 41.667 9.88 10.40 37.39 3.21
1911 2548 4.825085 ACAACCAATTTGACGGTCTAACAT 59.175 37.500 9.88 0.00 38.73 2.71
1912 2549 4.200874 ACAACCAATTTGACGGTCTAACA 58.799 39.130 9.88 0.00 38.73 2.41
1913 2550 4.823790 ACAACCAATTTGACGGTCTAAC 57.176 40.909 9.88 0.00 38.73 2.34
1914 2551 4.036971 CCAACAACCAATTTGACGGTCTAA 59.963 41.667 9.88 8.59 38.73 2.10
1915 2552 3.566322 CCAACAACCAATTTGACGGTCTA 59.434 43.478 9.88 0.00 38.73 2.59
1916 2553 2.360801 CCAACAACCAATTTGACGGTCT 59.639 45.455 9.88 0.00 38.73 3.85
1917 2554 2.544903 CCCAACAACCAATTTGACGGTC 60.545 50.000 0.00 0.00 38.73 4.79
1918 2555 1.410882 CCCAACAACCAATTTGACGGT 59.589 47.619 0.00 0.00 38.73 4.83
1919 2556 1.871822 GCCCAACAACCAATTTGACGG 60.872 52.381 0.00 0.00 38.73 4.79
1920 2557 1.496934 GCCCAACAACCAATTTGACG 58.503 50.000 0.00 0.00 38.73 4.35
1921 2558 1.871822 CGGCCCAACAACCAATTTGAC 60.872 52.381 0.00 0.00 38.73 3.18
1922 2559 0.390860 CGGCCCAACAACCAATTTGA 59.609 50.000 0.00 0.00 38.73 2.69
1924 2561 1.051556 ACCGGCCCAACAACCAATTT 61.052 50.000 0.00 0.00 0.00 1.82
1925 2562 1.051556 AACCGGCCCAACAACCAATT 61.052 50.000 0.00 0.00 0.00 2.32
1926 2563 0.178958 TAACCGGCCCAACAACCAAT 60.179 50.000 0.00 0.00 0.00 3.16
1927 2564 0.396695 TTAACCGGCCCAACAACCAA 60.397 50.000 0.00 0.00 0.00 3.67
1928 2565 0.178958 ATTAACCGGCCCAACAACCA 60.179 50.000 0.00 0.00 0.00 3.67
1929 2566 0.528924 GATTAACCGGCCCAACAACC 59.471 55.000 0.00 0.00 0.00 3.77
1930 2567 0.528924 GGATTAACCGGCCCAACAAC 59.471 55.000 0.00 0.00 0.00 3.32
1935 2572 1.379309 GCAAGGATTAACCGGCCCA 60.379 57.895 0.00 0.00 44.74 5.36
1936 2573 1.076995 AGCAAGGATTAACCGGCCC 60.077 57.895 0.00 0.00 44.74 5.80
1942 2579 1.780503 ATGGGCCAGCAAGGATTAAC 58.219 50.000 13.78 0.00 41.22 2.01
1967 2604 0.608640 ACGGGTTTTGTTTGCCAACA 59.391 45.000 0.00 0.00 41.39 3.33
1970 2607 3.821421 ATAAACGGGTTTTGTTTGCCA 57.179 38.095 1.70 0.00 39.69 4.92
1981 2618 0.327591 TACGGGCCAAATAAACGGGT 59.672 50.000 4.39 0.00 0.00 5.28
1984 2621 1.132834 GGGTTACGGGCCAAATAAACG 59.867 52.381 4.39 0.00 0.00 3.60
1986 2623 2.621147 GGAGGGTTACGGGCCAAATAAA 60.621 50.000 4.39 0.00 0.00 1.40
1996 2633 1.328430 GGAGTCTGGGAGGGTTACGG 61.328 65.000 0.00 0.00 0.00 4.02
2005 2642 2.450243 GGGACTGGGAGTCTGGGA 59.550 66.667 3.85 0.00 44.46 4.37
2006 2643 2.689034 GGGGACTGGGAGTCTGGG 60.689 72.222 3.85 0.00 44.46 4.45
2009 2646 2.781406 GGAGGGGACTGGGAGTCT 59.219 66.667 3.85 0.00 44.46 3.24
2011 2648 2.876858 AGGGAGGGGACTGGGAGT 60.877 66.667 0.00 0.00 44.43 3.85
2013 2650 2.540910 AGAGGGAGGGGACTGGGA 60.541 66.667 0.00 0.00 44.43 4.37
2014 2651 2.041405 GAGAGGGAGGGGACTGGG 60.041 72.222 0.00 0.00 44.43 4.45
2015 2652 1.297409 TAGGAGAGGGAGGGGACTGG 61.297 65.000 0.00 0.00 44.43 4.00
2016 2653 0.637195 TTAGGAGAGGGAGGGGACTG 59.363 60.000 0.00 0.00 44.43 3.51
2018 2655 2.498473 ATTTAGGAGAGGGAGGGGAC 57.502 55.000 0.00 0.00 0.00 4.46
2019 2656 2.158143 GCTATTTAGGAGAGGGAGGGGA 60.158 54.545 0.00 0.00 0.00 4.81
2020 2657 2.261729 GCTATTTAGGAGAGGGAGGGG 58.738 57.143 0.00 0.00 0.00 4.79
2021 2658 1.896465 CGCTATTTAGGAGAGGGAGGG 59.104 57.143 0.00 0.00 0.00 4.30
2041 2678 0.542333 GGGAGGAGGGCTAAACACTC 59.458 60.000 0.00 0.00 0.00 3.51
2044 2681 2.666098 GCGGGAGGAGGGCTAAACA 61.666 63.158 0.00 0.00 0.00 2.83
2053 2690 1.152567 ATGAGAGGAGCGGGAGGAG 60.153 63.158 0.00 0.00 0.00 3.69
2104 2741 2.434185 GTGACGATGCGCCAAGGA 60.434 61.111 4.18 0.00 0.00 3.36
2106 2743 1.421485 GAAGTGACGATGCGCCAAG 59.579 57.895 4.18 0.00 0.00 3.61
2111 2748 1.519455 GAGGGGAAGTGACGATGCG 60.519 63.158 0.00 0.00 0.00 4.73
2113 2750 0.461961 GAGGAGGGGAAGTGACGATG 59.538 60.000 0.00 0.00 0.00 3.84
2114 2751 0.688087 GGAGGAGGGGAAGTGACGAT 60.688 60.000 0.00 0.00 0.00 3.73
2116 2753 2.359967 GGGAGGAGGGGAAGTGACG 61.360 68.421 0.00 0.00 0.00 4.35
2120 2757 1.394151 CAGAGGGAGGAGGGGAAGT 59.606 63.158 0.00 0.00 0.00 3.01
2133 2770 1.674221 GGAAGTAGCAGCACACAGAGG 60.674 57.143 0.00 0.00 0.00 3.69
2139 2776 1.553690 GGAGGGGAAGTAGCAGCACA 61.554 60.000 0.00 0.00 0.00 4.57
2140 2777 1.222113 GGAGGGGAAGTAGCAGCAC 59.778 63.158 0.00 0.00 0.00 4.40
2157 2794 1.065126 GGTGGATGGTCAGAAAGGAGG 60.065 57.143 0.00 0.00 0.00 4.30
2159 2796 1.909302 GAGGTGGATGGTCAGAAAGGA 59.091 52.381 0.00 0.00 0.00 3.36
2178 2815 4.595538 AACGCGTCAGTTGCCGGA 62.596 61.111 14.44 0.00 32.39 5.14
2179 2816 4.072088 GAACGCGTCAGTTGCCGG 62.072 66.667 14.44 0.00 34.00 6.13
2180 2817 3.334751 TGAACGCGTCAGTTGCCG 61.335 61.111 14.44 0.00 34.00 5.69
2211 2848 1.071385 CAGAAGGAAGGTGTCAGCAGT 59.929 52.381 4.59 0.00 0.00 4.40
2216 2853 0.836606 TGCACAGAAGGAAGGTGTCA 59.163 50.000 0.00 0.00 35.05 3.58
2217 2854 2.079925 GATGCACAGAAGGAAGGTGTC 58.920 52.381 0.00 0.00 35.05 3.67
2241 2878 4.166888 AGATGGTGGCTGCGCGAT 62.167 61.111 12.10 0.00 0.00 4.58
2244 2881 2.894387 GAGAGATGGTGGCTGCGC 60.894 66.667 0.00 0.00 0.00 6.09
2248 2885 0.105760 ATCTCCGAGAGATGGTGGCT 60.106 55.000 13.53 0.00 46.21 4.75
2276 2913 1.577421 CCCGGCGTCGAAACATTTT 59.423 52.632 12.93 0.00 39.00 1.82
2277 2914 2.329614 CCCCGGCGTCGAAACATTT 61.330 57.895 12.93 0.00 39.00 2.32
2278 2915 2.744709 CCCCGGCGTCGAAACATT 60.745 61.111 12.93 0.00 39.00 2.71
2280 2917 4.668118 GTCCCCGGCGTCGAAACA 62.668 66.667 12.93 0.00 39.00 2.83
2295 2932 4.194720 ATGCTCCGCCTCGTCGTC 62.195 66.667 0.00 0.00 0.00 4.20
2296 2933 4.498520 CATGCTCCGCCTCGTCGT 62.499 66.667 0.00 0.00 0.00 4.34
2297 2934 4.498520 ACATGCTCCGCCTCGTCG 62.499 66.667 0.00 0.00 0.00 5.12
2298 2935 2.564553 AAGACATGCTCCGCCTCGTC 62.565 60.000 0.00 0.00 0.00 4.20
2299 2936 2.650116 AAGACATGCTCCGCCTCGT 61.650 57.895 0.00 0.00 0.00 4.18
2300 2937 2.169789 CAAGACATGCTCCGCCTCG 61.170 63.158 0.00 0.00 0.00 4.63
2301 2938 1.817099 CCAAGACATGCTCCGCCTC 60.817 63.158 0.00 0.00 0.00 4.70
2302 2939 1.264749 TACCAAGACATGCTCCGCCT 61.265 55.000 0.00 0.00 0.00 5.52
2303 2940 0.811616 CTACCAAGACATGCTCCGCC 60.812 60.000 0.00 0.00 0.00 6.13
2304 2941 0.811616 CCTACCAAGACATGCTCCGC 60.812 60.000 0.00 0.00 0.00 5.54
2305 2942 0.537188 ACCTACCAAGACATGCTCCG 59.463 55.000 0.00 0.00 0.00 4.63
2306 2943 3.733337 CATACCTACCAAGACATGCTCC 58.267 50.000 0.00 0.00 0.00 4.70
2307 2944 3.134458 GCATACCTACCAAGACATGCTC 58.866 50.000 0.00 0.00 37.05 4.26
2308 2945 2.483714 CGCATACCTACCAAGACATGCT 60.484 50.000 0.00 0.00 37.47 3.79
2309 2946 1.867233 CGCATACCTACCAAGACATGC 59.133 52.381 0.00 0.00 36.84 4.06
2310 2947 2.483876 CCGCATACCTACCAAGACATG 58.516 52.381 0.00 0.00 0.00 3.21
2311 2948 1.202651 GCCGCATACCTACCAAGACAT 60.203 52.381 0.00 0.00 0.00 3.06
2312 2949 0.177141 GCCGCATACCTACCAAGACA 59.823 55.000 0.00 0.00 0.00 3.41
2313 2950 0.177141 TGCCGCATACCTACCAAGAC 59.823 55.000 0.00 0.00 0.00 3.01
2314 2951 0.906066 TTGCCGCATACCTACCAAGA 59.094 50.000 0.00 0.00 0.00 3.02
2315 2952 1.299541 CTTGCCGCATACCTACCAAG 58.700 55.000 0.00 0.00 0.00 3.61
2316 2953 0.746563 GCTTGCCGCATACCTACCAA 60.747 55.000 0.00 0.00 38.92 3.67
2317 2954 1.153249 GCTTGCCGCATACCTACCA 60.153 57.895 0.00 0.00 38.92 3.25
2318 2955 1.153249 TGCTTGCCGCATACCTACC 60.153 57.895 0.00 0.00 45.47 3.18
2319 2956 4.532490 TGCTTGCCGCATACCTAC 57.468 55.556 0.00 0.00 45.47 3.18
2327 2964 4.619140 GCCGATGATGCTTGCCGC 62.619 66.667 0.00 0.00 39.77 6.53
2328 2965 2.268988 TTTGCCGATGATGCTTGCCG 62.269 55.000 0.00 0.00 0.00 5.69
2329 2966 0.108709 TTTTGCCGATGATGCTTGCC 60.109 50.000 0.00 0.00 0.00 4.52
2330 2967 1.712401 TTTTTGCCGATGATGCTTGC 58.288 45.000 0.00 0.00 0.00 4.01
2351 2988 7.213216 TCAACAAACATGTATACAGCAACAT 57.787 32.000 11.91 0.00 36.78 2.71
2352 2989 6.625873 TCAACAAACATGTATACAGCAACA 57.374 33.333 11.91 0.00 0.00 3.33
2387 3024 4.837860 ACAACAACAAACATCCATATGGGT 59.162 37.500 21.78 12.51 37.43 4.51
2422 3069 6.205464 CACTGCTTTCTTTTCTCAATAGACCA 59.795 38.462 0.00 0.00 0.00 4.02
2423 3070 6.606768 CACTGCTTTCTTTTCTCAATAGACC 58.393 40.000 0.00 0.00 0.00 3.85
2424 3071 6.082984 GCACTGCTTTCTTTTCTCAATAGAC 58.917 40.000 0.00 0.00 0.00 2.59
2426 3073 5.048504 TGGCACTGCTTTCTTTTCTCAATAG 60.049 40.000 0.00 0.00 0.00 1.73
2431 3078 3.930634 ATGGCACTGCTTTCTTTTCTC 57.069 42.857 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.