Multiple sequence alignment - TraesCS3D01G488000

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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 TraesCS3D01G488000 chr3D 100.000 2868 0 0 1 2868 583010639 583007772 0.000000e+00 5297
1 TraesCS3D01G488000 chr3D 89.603 731 58 9 1582 2304 582991192 582990472 0.000000e+00 913
2 TraesCS3D01G488000 chr3D 82.521 1087 128 38 827 1870 582909769 582908702 0.000000e+00 898
3 TraesCS3D01G488000 chr3D 81.072 1194 139 56 956 2073 583001426 583000244 0.000000e+00 872
4 TraesCS3D01G488000 chr3D 82.136 1030 122 38 827 1813 582922191 582921181 0.000000e+00 826
5 TraesCS3D01G488000 chr3D 89.465 598 56 5 992 1584 582991823 582991228 0.000000e+00 749
6 TraesCS3D01G488000 chr3D 90.971 443 31 4 2435 2868 582990447 582990005 3.180000e-164 588
7 TraesCS3D01G488000 chr3D 80.485 743 79 38 1384 2075 582934968 582934241 2.550000e-140 508
8 TraesCS3D01G488000 chr3B 89.745 2038 140 25 106 2095 779805864 779803848 0.000000e+00 2543
9 TraesCS3D01G488000 chr3B 87.734 2030 158 37 106 2087 779963860 779961874 0.000000e+00 2285
10 TraesCS3D01G488000 chr3B 91.601 1643 122 7 314 1944 780133509 780131871 0.000000e+00 2255
11 TraesCS3D01G488000 chr3B 93.304 1150 59 7 811 1943 780048996 780047848 0.000000e+00 1681
12 TraesCS3D01G488000 chr3B 88.047 1188 108 18 923 2095 780081218 780080050 0.000000e+00 1376
13 TraesCS3D01G488000 chr3B 83.988 968 112 28 976 1904 779646077 779645114 0.000000e+00 889
14 TraesCS3D01G488000 chr3B 89.418 567 41 8 232 785 780081842 780081282 0.000000e+00 697
15 TraesCS3D01G488000 chr3B 91.422 443 33 3 2431 2868 780246844 780246402 1.140000e-168 603
16 TraesCS3D01G488000 chr3B 85.904 603 33 14 1534 2095 780247594 780247003 1.900000e-166 595
17 TraesCS3D01G488000 chr3B 90.541 444 36 5 2431 2868 780131519 780131076 1.480000e-162 582
18 TraesCS3D01G488000 chr3B 90.367 436 36 5 107 540 780050194 780049763 4.150000e-158 568
19 TraesCS3D01G488000 chr3B 88.767 454 43 6 2423 2868 780079871 780079418 1.500000e-152 549
20 TraesCS3D01G488000 chr3B 88.496 452 46 4 2423 2868 780047503 780047052 2.510000e-150 542
21 TraesCS3D01G488000 chr3B 87.805 451 50 3 2423 2868 779930290 779929840 9.100000e-145 523
22 TraesCS3D01G488000 chr3B 88.009 442 49 2 2431 2868 779803660 779803219 1.180000e-143 520
23 TraesCS3D01G488000 chr3B 88.810 420 42 3 2453 2868 779987039 779986621 7.090000e-141 510
24 TraesCS3D01G488000 chr3B 89.722 360 35 2 2501 2858 779818022 779817663 2.600000e-125 459
25 TraesCS3D01G488000 chr3B 86.544 327 36 5 515 835 780061550 780061226 1.260000e-93 353
26 TraesCS3D01G488000 chr3B 91.358 162 12 2 610 770 780049161 780049001 1.340000e-53 220
27 TraesCS3D01G488000 chrUn 91.543 473 31 3 314 780 41703586 41704055 0.000000e+00 643
28 TraesCS3D01G488000 chrUn 90.598 117 11 0 2303 2419 22143591 22143707 3.830000e-34 156
29 TraesCS3D01G488000 chr4B 90.756 119 11 0 2302 2420 663766212 663766094 2.960000e-35 159
30 TraesCS3D01G488000 chr5B 90.678 118 11 0 2302 2419 173271476 173271593 1.060000e-34 158
31 TraesCS3D01G488000 chr7D 89.916 119 12 0 2303 2421 610248281 610248163 1.380000e-33 154
32 TraesCS3D01G488000 chr6A 89.431 123 12 1 2298 2420 27336539 27336418 1.380000e-33 154
33 TraesCS3D01G488000 chr2D 89.831 118 12 0 2302 2419 531675857 531675974 4.950000e-33 152
34 TraesCS3D01G488000 chr6D 89.256 121 12 1 2303 2422 108860765 108860645 1.780000e-32 150
35 TraesCS3D01G488000 chr6D 83.333 156 23 2 2269 2421 147675533 147675688 1.070000e-29 141
36 TraesCS3D01G488000 chr1B 88.618 123 14 0 2298 2420 426475884 426475762 1.780000e-32 150


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 TraesCS3D01G488000 chr3D 583007772 583010639 2867 True 5297.00 5297 100.00000 1 2868 1 chr3D.!!$R5 2867
1 TraesCS3D01G488000 chr3D 582908702 582909769 1067 True 898.00 898 82.52100 827 1870 1 chr3D.!!$R1 1043
2 TraesCS3D01G488000 chr3D 583000244 583001426 1182 True 872.00 872 81.07200 956 2073 1 chr3D.!!$R4 1117
3 TraesCS3D01G488000 chr3D 582921181 582922191 1010 True 826.00 826 82.13600 827 1813 1 chr3D.!!$R2 986
4 TraesCS3D01G488000 chr3D 582990005 582991823 1818 True 750.00 913 90.01300 992 2868 3 chr3D.!!$R6 1876
5 TraesCS3D01G488000 chr3D 582934241 582934968 727 True 508.00 508 80.48500 1384 2075 1 chr3D.!!$R3 691
6 TraesCS3D01G488000 chr3B 779961874 779963860 1986 True 2285.00 2285 87.73400 106 2087 1 chr3B.!!$R4 1981
7 TraesCS3D01G488000 chr3B 779803219 779805864 2645 True 1531.50 2543 88.87700 106 2868 2 chr3B.!!$R7 2762
8 TraesCS3D01G488000 chr3B 780131076 780133509 2433 True 1418.50 2255 91.07100 314 2868 2 chr3B.!!$R10 2554
9 TraesCS3D01G488000 chr3B 779645114 779646077 963 True 889.00 889 83.98800 976 1904 1 chr3B.!!$R1 928
10 TraesCS3D01G488000 chr3B 780079418 780081842 2424 True 874.00 1376 88.74400 232 2868 3 chr3B.!!$R9 2636
11 TraesCS3D01G488000 chr3B 780047052 780050194 3142 True 752.75 1681 90.88125 107 2868 4 chr3B.!!$R8 2761
12 TraesCS3D01G488000 chr3B 780246402 780247594 1192 True 599.00 603 88.66300 1534 2868 2 chr3B.!!$R11 1334

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 0.099082 GGAGTTACGTCTCGCCTCTG 59.901 60.0 0.0 0.0 35.52 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2890 0.097325 GTGACGTGACACCGCAAAAA 59.903 50.0 0.0 0.0 35.07 1.94 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 4.846779 AAAAAGGTTGCTCGCAATCTAA 57.153 36.364 16.91 0.00 45.60 2.10
49 50 5.391312 AAAAAGGTTGCTCGCAATCTAAT 57.609 34.783 16.91 7.43 45.60 1.73
50 51 4.622701 AAAGGTTGCTCGCAATCTAATC 57.377 40.909 16.91 0.00 45.60 1.75
51 52 2.205074 AGGTTGCTCGCAATCTAATCG 58.795 47.619 15.25 0.00 44.63 3.34
52 53 1.333258 GGTTGCTCGCAATCTAATCGC 60.333 52.381 7.67 0.00 38.28 4.58
53 54 0.937304 TTGCTCGCAATCTAATCGCC 59.063 50.000 0.00 0.00 0.00 5.54
54 55 0.880278 TGCTCGCAATCTAATCGCCC 60.880 55.000 0.00 0.00 0.00 6.13
55 56 1.891060 GCTCGCAATCTAATCGCCCG 61.891 60.000 0.00 0.00 0.00 6.13
56 57 0.318699 CTCGCAATCTAATCGCCCGA 60.319 55.000 0.00 0.00 0.00 5.14
57 58 0.318699 TCGCAATCTAATCGCCCGAG 60.319 55.000 0.00 0.00 0.00 4.63
58 59 0.318699 CGCAATCTAATCGCCCGAGA 60.319 55.000 0.00 0.00 0.00 4.04
59 60 1.423395 GCAATCTAATCGCCCGAGAG 58.577 55.000 0.00 0.00 0.00 3.20
60 61 1.423395 CAATCTAATCGCCCGAGAGC 58.577 55.000 0.00 0.00 0.00 4.09
61 62 1.000283 CAATCTAATCGCCCGAGAGCT 60.000 52.381 0.00 0.00 0.00 4.09
62 63 2.201921 ATCTAATCGCCCGAGAGCTA 57.798 50.000 0.00 0.00 0.00 3.32
63 64 2.201921 TCTAATCGCCCGAGAGCTAT 57.798 50.000 0.00 0.00 0.00 2.97
64 65 3.345508 TCTAATCGCCCGAGAGCTATA 57.654 47.619 0.00 0.00 0.00 1.31
65 66 3.887352 TCTAATCGCCCGAGAGCTATAT 58.113 45.455 0.00 0.00 0.00 0.86
66 67 5.032327 TCTAATCGCCCGAGAGCTATATA 57.968 43.478 0.00 0.00 0.00 0.86
67 68 5.622180 TCTAATCGCCCGAGAGCTATATAT 58.378 41.667 0.00 0.00 0.00 0.86
68 69 4.576216 AATCGCCCGAGAGCTATATATG 57.424 45.455 0.00 0.00 0.00 1.78
69 70 3.000684 TCGCCCGAGAGCTATATATGT 57.999 47.619 0.00 0.00 0.00 2.29
70 71 2.943690 TCGCCCGAGAGCTATATATGTC 59.056 50.000 0.00 0.00 0.00 3.06
71 72 2.946329 CGCCCGAGAGCTATATATGTCT 59.054 50.000 0.00 0.00 0.00 3.41
72 73 3.242903 CGCCCGAGAGCTATATATGTCTG 60.243 52.174 0.00 0.00 0.00 3.51
73 74 3.697045 GCCCGAGAGCTATATATGTCTGT 59.303 47.826 0.00 0.00 0.00 3.41
74 75 4.158764 GCCCGAGAGCTATATATGTCTGTT 59.841 45.833 0.00 0.00 0.00 3.16
75 76 5.645624 CCCGAGAGCTATATATGTCTGTTG 58.354 45.833 0.00 0.00 0.00 3.33
76 77 5.098893 CCGAGAGCTATATATGTCTGTTGC 58.901 45.833 0.00 0.00 0.00 4.17
77 78 4.790651 CGAGAGCTATATATGTCTGTTGCG 59.209 45.833 0.00 0.00 0.00 4.85
78 79 5.390991 CGAGAGCTATATATGTCTGTTGCGA 60.391 44.000 0.00 0.00 0.00 5.10
79 80 5.948588 AGAGCTATATATGTCTGTTGCGAG 58.051 41.667 0.00 0.00 0.00 5.03
80 81 5.065704 AGCTATATATGTCTGTTGCGAGG 57.934 43.478 0.00 0.00 0.00 4.63
81 82 3.614616 GCTATATATGTCTGTTGCGAGGC 59.385 47.826 0.00 0.00 0.00 4.70
82 83 2.134201 TATATGTCTGTTGCGAGGCG 57.866 50.000 0.00 0.00 0.00 5.52
83 84 0.530650 ATATGTCTGTTGCGAGGCGG 60.531 55.000 0.00 0.00 0.00 6.13
84 85 1.600511 TATGTCTGTTGCGAGGCGGA 61.601 55.000 0.00 0.00 0.00 5.54
85 86 2.811317 GTCTGTTGCGAGGCGGAG 60.811 66.667 0.00 0.00 0.00 4.63
86 87 3.303135 TCTGTTGCGAGGCGGAGT 61.303 61.111 0.00 0.00 0.00 3.85
87 88 2.357517 CTGTTGCGAGGCGGAGTT 60.358 61.111 0.00 0.00 0.00 3.01
88 89 1.080093 CTGTTGCGAGGCGGAGTTA 60.080 57.895 0.00 0.00 0.00 2.24
89 90 1.352156 CTGTTGCGAGGCGGAGTTAC 61.352 60.000 0.00 0.00 0.00 2.50
90 91 2.126228 TTGCGAGGCGGAGTTACG 60.126 61.111 0.00 0.00 0.00 3.18
91 92 2.922950 TTGCGAGGCGGAGTTACGT 61.923 57.895 0.00 0.00 35.98 3.57
92 93 2.578981 GCGAGGCGGAGTTACGTC 60.579 66.667 0.00 0.00 39.08 4.34
96 97 2.578981 GGCGGAGTTACGTCTCGC 60.579 66.667 0.00 1.46 35.22 5.03
97 98 2.578981 GCGGAGTTACGTCTCGCC 60.579 66.667 0.00 0.00 35.52 5.54
98 99 3.048941 GCGGAGTTACGTCTCGCCT 62.049 63.158 0.00 0.00 35.52 5.52
99 100 1.062206 CGGAGTTACGTCTCGCCTC 59.938 63.158 0.00 0.00 35.52 4.70
100 101 1.367599 CGGAGTTACGTCTCGCCTCT 61.368 60.000 0.00 0.00 35.52 3.69
101 102 0.099082 GGAGTTACGTCTCGCCTCTG 59.901 60.000 0.00 0.00 35.52 3.35
102 103 1.085091 GAGTTACGTCTCGCCTCTGA 58.915 55.000 0.00 0.00 0.00 3.27
103 104 0.803740 AGTTACGTCTCGCCTCTGAC 59.196 55.000 0.00 0.00 0.00 3.51
109 110 4.056125 CTCGCCTCTGACGCCACA 62.056 66.667 0.00 0.00 0.00 4.17
114 115 1.845809 GCCTCTGACGCCACAGTTTG 61.846 60.000 0.00 0.00 38.79 2.93
207 210 7.954447 TCTTTTTCGTTGTATGTTTTGTTTGG 58.046 30.769 0.00 0.00 0.00 3.28
212 215 7.050281 TCGTTGTATGTTTTGTTTGGTTTTG 57.950 32.000 0.00 0.00 0.00 2.44
250 254 7.575332 TTCTCGGTTTTTGTTTCTTTCTTTG 57.425 32.000 0.00 0.00 0.00 2.77
286 290 6.849588 TTTCTTCGGTTTTTACTAGGACAC 57.150 37.500 0.00 0.00 0.00 3.67
346 357 4.840005 GTACGGCTCCCTGCAGGC 62.840 72.222 28.39 16.03 45.15 4.85
371 382 1.827344 CATGGCTAGGACTCACTGTGA 59.173 52.381 10.50 10.50 0.00 3.58
408 419 3.795688 CCCATATAATCAGGGTGCAGT 57.204 47.619 0.00 0.00 37.81 4.40
424 435 1.354040 CAGTGATGCCTCGACTTGAC 58.646 55.000 0.00 0.00 0.00 3.18
449 460 6.258507 CGCTTGCACCATTGATGCTATATATA 59.741 38.462 4.29 0.00 43.77 0.86
450 461 7.201635 CGCTTGCACCATTGATGCTATATATAA 60.202 37.037 4.29 0.00 43.77 0.98
480 491 2.106683 CGAGGATGCGTGGGGAAAC 61.107 63.158 0.00 0.00 0.00 2.78
673 1223 8.455903 AATTTAGCATGATATACAAGTGCTGT 57.544 30.769 8.29 0.00 42.47 4.40
680 1230 0.677731 ATACAAGTGCTGTGCCGCAT 60.678 50.000 0.00 0.00 42.62 4.73
875 1432 2.093341 GGAGAACCTACAAATACCGGCA 60.093 50.000 0.00 0.00 0.00 5.69
962 1530 2.588620 GCTAGCTAGCTACCTTCTCCA 58.411 52.381 33.71 0.00 45.62 3.86
1191 1761 4.595538 TCCGACGCTGTTGCCGTT 62.596 61.111 0.00 0.00 35.36 4.44
1192 1762 2.735478 CCGACGCTGTTGCCGTTA 60.735 61.111 0.00 0.00 35.36 3.18
1224 1794 4.052229 AACGCCGTCCTCGAGTGG 62.052 66.667 12.31 11.19 39.71 4.00
1242 1812 4.335647 CTCCGCAACCAGGTGCCT 62.336 66.667 1.31 0.00 41.73 4.75
1311 1881 4.215742 CGCATCGACCCGGGCTTA 62.216 66.667 24.08 5.95 0.00 3.09
1368 1938 2.805353 CACTTCCTCGACGGTGCG 60.805 66.667 0.00 0.00 0.00 5.34
1512 2088 3.689649 GCCGTTCTATGTTCATCACCTTT 59.310 43.478 0.00 0.00 0.00 3.11
1571 2149 6.804770 TGAGTACTTCAGAGAGTAAGTGTC 57.195 41.667 0.00 0.00 36.62 3.67
1771 2418 1.734137 GGAGGCGATCGTGAAGCTA 59.266 57.895 17.81 0.00 0.00 3.32
1808 2455 1.410517 GGCTCGTCAAGATCTCCATCA 59.589 52.381 0.00 0.00 0.00 3.07
1893 2540 7.161404 TCGAGGAATCCATATAATCCTTGTTG 58.839 38.462 0.61 0.00 42.28 3.33
1908 2569 2.671130 TGTTGCGTCTATGCTCATGA 57.329 45.000 0.00 0.00 35.36 3.07
2015 2764 7.502226 TCTGCTTGAGATTGGAAGAAAAAGTTA 59.498 33.333 0.00 0.00 0.00 2.24
2037 2800 9.000486 AGTTAGTTGCTCTTAATTTTGTACTCC 58.000 33.333 0.00 0.00 0.00 3.85
2038 2801 8.780249 GTTAGTTGCTCTTAATTTTGTACTCCA 58.220 33.333 0.00 0.00 0.00 3.86
2039 2802 7.203255 AGTTGCTCTTAATTTTGTACTCCAC 57.797 36.000 0.00 0.00 0.00 4.02
2040 2803 6.998673 AGTTGCTCTTAATTTTGTACTCCACT 59.001 34.615 0.00 0.00 0.00 4.00
2045 2808 8.451748 GCTCTTAATTTTGTACTCCACTAAAGG 58.548 37.037 0.00 0.00 35.74 3.11
2086 2879 0.173708 CCTAGCTCCTTCGTGTCACC 59.826 60.000 0.00 0.00 0.00 4.02
2087 2880 0.179161 CTAGCTCCTTCGTGTCACCG 60.179 60.000 0.00 0.00 0.00 4.94
2088 2881 0.892358 TAGCTCCTTCGTGTCACCGT 60.892 55.000 0.00 0.00 0.00 4.83
2089 2882 0.892358 AGCTCCTTCGTGTCACCGTA 60.892 55.000 0.00 0.00 0.00 4.02
2090 2883 0.038892 GCTCCTTCGTGTCACCGTAA 60.039 55.000 0.00 0.00 0.00 3.18
2091 2884 1.694639 CTCCTTCGTGTCACCGTAAC 58.305 55.000 0.00 0.00 0.00 2.50
2092 2885 0.314935 TCCTTCGTGTCACCGTAACC 59.685 55.000 0.00 0.00 0.00 2.85
2093 2886 0.316204 CCTTCGTGTCACCGTAACCT 59.684 55.000 0.00 0.00 0.00 3.50
2094 2887 1.269936 CCTTCGTGTCACCGTAACCTT 60.270 52.381 0.00 0.00 0.00 3.50
2095 2888 2.476821 CTTCGTGTCACCGTAACCTTT 58.523 47.619 0.00 0.00 0.00 3.11
2096 2889 2.600470 TCGTGTCACCGTAACCTTTT 57.400 45.000 0.00 0.00 0.00 2.27
2097 2890 2.903798 TCGTGTCACCGTAACCTTTTT 58.096 42.857 0.00 0.00 0.00 1.94
2115 2908 2.467962 TTTTTGCGGTGTCACGTCA 58.532 47.368 0.00 0.00 35.98 4.35
2116 2909 0.097325 TTTTTGCGGTGTCACGTCAC 59.903 50.000 0.00 0.00 37.57 3.67
2154 2947 1.697284 TCACATCATCGCCTAGCTCT 58.303 50.000 0.00 0.00 0.00 4.09
2175 2969 1.161563 TCGCGTCACCAAAACCCTTC 61.162 55.000 5.77 0.00 0.00 3.46
2180 2974 3.677700 GCGTCACCAAAACCCTTCTTTTT 60.678 43.478 0.00 0.00 0.00 1.94
2202 2996 1.665735 GCGATGTTGCGTCACCAAAAT 60.666 47.619 0.00 0.00 0.00 1.82
2208 3002 3.129462 TGTTGCGTCACCAAAATCTTGAA 59.871 39.130 0.00 0.00 34.14 2.69
2234 3028 6.127758 GGGCAAAAGTTCTTGGTTTTGATTTT 60.128 34.615 10.85 0.00 43.42 1.82
2295 3089 0.534203 ACACAACGGTCACCCATGTC 60.534 55.000 0.00 0.00 30.24 3.06
2304 3098 0.668096 TCACCCATGTCGCAACGTAC 60.668 55.000 0.00 0.00 0.00 3.67
2305 3099 1.375013 ACCCATGTCGCAACGTACC 60.375 57.895 0.00 0.00 0.00 3.34
2306 3100 2.104253 CCCATGTCGCAACGTACCC 61.104 63.158 0.00 0.00 0.00 3.69
2309 3103 3.652539 ATGTCGCAACGTACCCCCG 62.653 63.158 0.00 0.00 0.00 5.73
2318 3112 3.384532 GTACCCCCGCCGTCTGAA 61.385 66.667 0.00 0.00 0.00 3.02
2319 3113 2.604079 TACCCCCGCCGTCTGAAA 60.604 61.111 0.00 0.00 0.00 2.69
2320 3114 2.215625 TACCCCCGCCGTCTGAAAA 61.216 57.895 0.00 0.00 0.00 2.29
2321 3115 1.555477 TACCCCCGCCGTCTGAAAAT 61.555 55.000 0.00 0.00 0.00 1.82
2322 3116 1.222387 CCCCCGCCGTCTGAAAATA 59.778 57.895 0.00 0.00 0.00 1.40
2324 3118 0.107848 CCCCGCCGTCTGAAAATACT 60.108 55.000 0.00 0.00 0.00 2.12
2325 3119 1.677820 CCCCGCCGTCTGAAAATACTT 60.678 52.381 0.00 0.00 0.00 2.24
2326 3120 2.419021 CCCCGCCGTCTGAAAATACTTA 60.419 50.000 0.00 0.00 0.00 2.24
2327 3121 3.463944 CCCGCCGTCTGAAAATACTTAT 58.536 45.455 0.00 0.00 0.00 1.73
2328 3122 3.875134 CCCGCCGTCTGAAAATACTTATT 59.125 43.478 0.00 0.00 0.00 1.40
2329 3123 4.260620 CCCGCCGTCTGAAAATACTTATTG 60.261 45.833 0.00 0.00 0.00 1.90
2330 3124 4.260620 CCGCCGTCTGAAAATACTTATTGG 60.261 45.833 0.00 0.00 0.00 3.16
2331 3125 4.569162 CGCCGTCTGAAAATACTTATTGGA 59.431 41.667 0.00 0.00 0.00 3.53
2332 3126 5.064198 CGCCGTCTGAAAATACTTATTGGAA 59.936 40.000 0.00 0.00 0.00 3.53
2333 3127 6.402766 CGCCGTCTGAAAATACTTATTGGAAA 60.403 38.462 0.00 0.00 0.00 3.13
2334 3128 7.309920 GCCGTCTGAAAATACTTATTGGAAAA 58.690 34.615 0.00 0.00 0.00 2.29
2335 3129 7.810759 GCCGTCTGAAAATACTTATTGGAAAAA 59.189 33.333 0.00 0.00 0.00 1.94
2336 3130 9.855021 CCGTCTGAAAATACTTATTGGAAAAAT 57.145 29.630 0.00 0.00 0.00 1.82
2352 3146 8.894768 TTGGAAAAATGAATAAAAACGGATGT 57.105 26.923 0.00 0.00 0.00 3.06
2353 3147 9.982651 TTGGAAAAATGAATAAAAACGGATGTA 57.017 25.926 0.00 0.00 0.00 2.29
2394 3188 8.908903 ACATCTAGATATATCCATTTCTCCGAC 58.091 37.037 4.54 0.00 0.00 4.79
2395 3189 8.907885 CATCTAGATATATCCATTTCTCCGACA 58.092 37.037 4.54 0.00 0.00 4.35
2396 3190 8.879427 TCTAGATATATCCATTTCTCCGACAA 57.121 34.615 9.18 0.00 0.00 3.18
2397 3191 8.961634 TCTAGATATATCCATTTCTCCGACAAG 58.038 37.037 9.18 0.00 0.00 3.16
2398 3192 7.546250 AGATATATCCATTTCTCCGACAAGT 57.454 36.000 9.18 0.00 0.00 3.16
2399 3193 8.651589 AGATATATCCATTTCTCCGACAAGTA 57.348 34.615 9.18 0.00 0.00 2.24
2400 3194 9.261035 AGATATATCCATTTCTCCGACAAGTAT 57.739 33.333 9.18 0.00 0.00 2.12
2401 3195 9.877178 GATATATCCATTTCTCCGACAAGTATT 57.123 33.333 0.81 0.00 0.00 1.89
2403 3197 6.927294 ATCCATTTCTCCGACAAGTATTTC 57.073 37.500 0.00 0.00 0.00 2.17
2404 3198 5.183228 TCCATTTCTCCGACAAGTATTTCC 58.817 41.667 0.00 0.00 0.00 3.13
2405 3199 4.034048 CCATTTCTCCGACAAGTATTTCCG 59.966 45.833 0.00 0.00 0.00 4.30
2406 3200 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
2407 3201 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
2408 3202 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
2409 3203 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
2410 3204 1.135315 CCGACAAGTATTTCCGGACGA 60.135 52.381 1.83 0.00 42.49 4.20
2411 3205 2.598589 CGACAAGTATTTCCGGACGAA 58.401 47.619 1.83 0.00 0.00 3.85
2412 3206 2.597305 CGACAAGTATTTCCGGACGAAG 59.403 50.000 1.83 0.00 0.00 3.79
2413 3207 2.928116 GACAAGTATTTCCGGACGAAGG 59.072 50.000 1.83 0.00 0.00 3.46
2414 3208 2.277084 CAAGTATTTCCGGACGAAGGG 58.723 52.381 1.83 0.00 0.00 3.95
2415 3209 1.856629 AGTATTTCCGGACGAAGGGA 58.143 50.000 1.83 0.00 0.00 4.20
2416 3210 1.755380 AGTATTTCCGGACGAAGGGAG 59.245 52.381 1.83 0.00 33.01 4.30
2417 3211 1.479730 GTATTTCCGGACGAAGGGAGT 59.520 52.381 1.83 0.00 33.01 3.85
2418 3212 1.856629 ATTTCCGGACGAAGGGAGTA 58.143 50.000 1.83 0.00 33.01 2.59
2419 3213 1.856629 TTTCCGGACGAAGGGAGTAT 58.143 50.000 1.83 0.00 33.01 2.12
2420 3214 2.734755 TTCCGGACGAAGGGAGTATA 57.265 50.000 1.83 0.00 33.01 1.47
2421 3215 2.734755 TCCGGACGAAGGGAGTATAA 57.265 50.000 0.00 0.00 0.00 0.98
2422 3216 2.301346 TCCGGACGAAGGGAGTATAAC 58.699 52.381 0.00 0.00 0.00 1.89
2423 3217 1.339291 CCGGACGAAGGGAGTATAACC 59.661 57.143 0.00 0.00 0.00 2.85
2439 3233 2.286425 CCCTCCATCCCCCACTGT 60.286 66.667 0.00 0.00 0.00 3.55
2441 3235 1.616327 CCTCCATCCCCCACTGTCA 60.616 63.158 0.00 0.00 0.00 3.58
2488 3282 2.990967 ATGCACCTTGCCCAACCG 60.991 61.111 0.00 0.00 44.23 4.44
2532 3330 9.436957 GAGTCCATCTCAACTTTACTTTAATCA 57.563 33.333 0.00 0.00 42.34 2.57
2693 3495 5.067283 ACATTTGCCGTTGTCTAAATATCCC 59.933 40.000 0.00 0.00 0.00 3.85
2706 3508 9.901172 TGTCTAAATATCCCTTAGTTTCTTTCC 57.099 33.333 0.00 0.00 0.00 3.13
2823 3629 3.478857 TTTAGCCACATACATACCCCG 57.521 47.619 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.846779 TTAGATTGCGAGCAACCTTTTT 57.153 36.364 11.65 0.00 38.88 1.94
28 29 4.437390 CGATTAGATTGCGAGCAACCTTTT 60.437 41.667 11.65 0.00 38.88 2.27
29 30 3.063997 CGATTAGATTGCGAGCAACCTTT 59.936 43.478 11.65 0.00 38.88 3.11
30 31 2.609459 CGATTAGATTGCGAGCAACCTT 59.391 45.455 11.65 4.48 38.88 3.50
31 32 2.205074 CGATTAGATTGCGAGCAACCT 58.795 47.619 13.05 11.39 38.88 3.50
32 33 1.333258 GCGATTAGATTGCGAGCAACC 60.333 52.381 13.05 2.90 38.88 3.77
33 34 1.333258 GGCGATTAGATTGCGAGCAAC 60.333 52.381 13.05 7.36 40.69 4.17
34 35 0.937304 GGCGATTAGATTGCGAGCAA 59.063 50.000 13.16 13.16 40.69 3.91
35 36 0.880278 GGGCGATTAGATTGCGAGCA 60.880 55.000 0.00 0.00 40.69 4.26
36 37 1.862806 GGGCGATTAGATTGCGAGC 59.137 57.895 0.00 0.00 40.69 5.03
37 38 0.318699 TCGGGCGATTAGATTGCGAG 60.319 55.000 0.00 0.00 40.69 5.03
38 39 0.318699 CTCGGGCGATTAGATTGCGA 60.319 55.000 0.00 0.00 40.69 5.10
39 40 0.318699 TCTCGGGCGATTAGATTGCG 60.319 55.000 0.00 0.00 40.69 4.85
40 41 1.423395 CTCTCGGGCGATTAGATTGC 58.577 55.000 0.00 0.00 39.00 3.56
41 42 1.000283 AGCTCTCGGGCGATTAGATTG 60.000 52.381 0.00 0.00 37.29 2.67
42 43 1.333177 AGCTCTCGGGCGATTAGATT 58.667 50.000 0.00 0.00 37.29 2.40
43 44 2.201921 TAGCTCTCGGGCGATTAGAT 57.798 50.000 0.00 0.00 37.29 1.98
44 45 2.201921 ATAGCTCTCGGGCGATTAGA 57.798 50.000 0.00 0.00 37.29 2.10
45 46 5.239744 ACATATATAGCTCTCGGGCGATTAG 59.760 44.000 0.00 0.00 37.29 1.73
46 47 5.131067 ACATATATAGCTCTCGGGCGATTA 58.869 41.667 0.00 0.00 37.29 1.75
47 48 3.954904 ACATATATAGCTCTCGGGCGATT 59.045 43.478 0.00 0.00 37.29 3.34
48 49 3.556999 ACATATATAGCTCTCGGGCGAT 58.443 45.455 0.00 0.00 37.29 4.58
49 50 2.943690 GACATATATAGCTCTCGGGCGA 59.056 50.000 0.00 0.00 37.29 5.54
50 51 2.946329 AGACATATATAGCTCTCGGGCG 59.054 50.000 0.00 0.00 37.29 6.13
51 52 3.697045 ACAGACATATATAGCTCTCGGGC 59.303 47.826 0.00 0.00 0.00 6.13
52 53 5.645624 CAACAGACATATATAGCTCTCGGG 58.354 45.833 0.00 0.00 0.00 5.14
53 54 5.098893 GCAACAGACATATATAGCTCTCGG 58.901 45.833 0.00 0.00 0.00 4.63
54 55 4.790651 CGCAACAGACATATATAGCTCTCG 59.209 45.833 0.00 0.00 0.00 4.04
55 56 5.944013 TCGCAACAGACATATATAGCTCTC 58.056 41.667 0.00 0.00 0.00 3.20
56 57 5.105957 CCTCGCAACAGACATATATAGCTCT 60.106 44.000 0.00 0.00 0.00 4.09
57 58 5.098893 CCTCGCAACAGACATATATAGCTC 58.901 45.833 0.00 0.00 0.00 4.09
58 59 4.619394 GCCTCGCAACAGACATATATAGCT 60.619 45.833 0.00 0.00 0.00 3.32
59 60 3.614616 GCCTCGCAACAGACATATATAGC 59.385 47.826 0.00 0.00 0.00 2.97
60 61 3.854240 CGCCTCGCAACAGACATATATAG 59.146 47.826 0.00 0.00 0.00 1.31
61 62 3.366985 CCGCCTCGCAACAGACATATATA 60.367 47.826 0.00 0.00 0.00 0.86
62 63 2.610479 CCGCCTCGCAACAGACATATAT 60.610 50.000 0.00 0.00 0.00 0.86
63 64 1.269569 CCGCCTCGCAACAGACATATA 60.270 52.381 0.00 0.00 0.00 0.86
64 65 0.530650 CCGCCTCGCAACAGACATAT 60.531 55.000 0.00 0.00 0.00 1.78
65 66 1.153647 CCGCCTCGCAACAGACATA 60.154 57.895 0.00 0.00 0.00 2.29
66 67 2.434884 CCGCCTCGCAACAGACAT 60.435 61.111 0.00 0.00 0.00 3.06
67 68 3.573772 CTCCGCCTCGCAACAGACA 62.574 63.158 0.00 0.00 0.00 3.41
68 69 2.811317 CTCCGCCTCGCAACAGAC 60.811 66.667 0.00 0.00 0.00 3.51
69 70 1.529152 TAACTCCGCCTCGCAACAGA 61.529 55.000 0.00 0.00 0.00 3.41
70 71 1.080093 TAACTCCGCCTCGCAACAG 60.080 57.895 0.00 0.00 0.00 3.16
71 72 1.373748 GTAACTCCGCCTCGCAACA 60.374 57.895 0.00 0.00 0.00 3.33
72 73 2.442188 CGTAACTCCGCCTCGCAAC 61.442 63.158 0.00 0.00 0.00 4.17
73 74 2.126228 CGTAACTCCGCCTCGCAA 60.126 61.111 0.00 0.00 0.00 4.85
74 75 3.332493 GACGTAACTCCGCCTCGCA 62.332 63.158 0.00 0.00 0.00 5.10
75 76 2.578981 GACGTAACTCCGCCTCGC 60.579 66.667 0.00 0.00 0.00 5.03
76 77 1.062206 GAGACGTAACTCCGCCTCG 59.938 63.158 0.00 0.00 27.98 4.63
77 78 1.062206 CGAGACGTAACTCCGCCTC 59.938 63.158 0.00 0.00 34.50 4.70
78 79 3.048941 GCGAGACGTAACTCCGCCT 62.049 63.158 0.00 0.00 33.75 5.52
79 80 2.578981 GCGAGACGTAACTCCGCC 60.579 66.667 0.00 0.00 33.75 6.13
80 81 2.578981 GGCGAGACGTAACTCCGC 60.579 66.667 9.85 9.85 36.51 5.54
81 82 1.062206 GAGGCGAGACGTAACTCCG 59.938 63.158 0.00 0.00 33.83 4.63
82 83 0.099082 CAGAGGCGAGACGTAACTCC 59.901 60.000 0.00 0.00 33.83 3.85
83 84 1.085091 TCAGAGGCGAGACGTAACTC 58.915 55.000 0.00 0.00 0.00 3.01
84 85 0.803740 GTCAGAGGCGAGACGTAACT 59.196 55.000 0.00 0.00 0.00 2.24
85 86 3.309453 GTCAGAGGCGAGACGTAAC 57.691 57.895 0.00 0.00 0.00 2.50
90 91 3.749064 TGGCGTCAGAGGCGAGAC 61.749 66.667 8.97 0.00 39.82 3.36
91 92 3.749064 GTGGCGTCAGAGGCGAGA 61.749 66.667 8.97 0.00 39.82 4.04
92 93 3.978723 CTGTGGCGTCAGAGGCGAG 62.979 68.421 6.22 1.67 39.82 5.03
93 94 4.056125 CTGTGGCGTCAGAGGCGA 62.056 66.667 6.22 2.14 39.82 5.54
94 95 3.865929 AACTGTGGCGTCAGAGGCG 62.866 63.158 19.20 0.00 38.46 5.52
95 96 1.598130 AAACTGTGGCGTCAGAGGC 60.598 57.895 19.20 6.55 38.46 4.70
96 97 1.230635 CCAAACTGTGGCGTCAGAGG 61.231 60.000 19.20 0.36 41.72 3.69
97 98 2.238353 CCAAACTGTGGCGTCAGAG 58.762 57.895 13.30 13.30 41.72 3.35
98 99 4.454948 CCAAACTGTGGCGTCAGA 57.545 55.556 14.65 0.00 41.72 3.27
183 185 7.734554 ACCAAACAAAACATACAACGAAAAAG 58.265 30.769 0.00 0.00 0.00 2.27
184 186 7.653767 ACCAAACAAAACATACAACGAAAAA 57.346 28.000 0.00 0.00 0.00 1.94
224 228 7.812309 AAGAAAGAAACAAAAACCGAGAAAG 57.188 32.000 0.00 0.00 0.00 2.62
237 241 7.672240 ACCAGTAAAAACCAAAGAAAGAAACA 58.328 30.769 0.00 0.00 0.00 2.83
250 254 5.252969 ACCGAAGAAAACCAGTAAAAACC 57.747 39.130 0.00 0.00 0.00 3.27
260 264 6.260714 TGTCCTAGTAAAAACCGAAGAAAACC 59.739 38.462 0.00 0.00 0.00 3.27
286 290 6.757897 TTAGCTTGGTTTCACATCCTTATG 57.242 37.500 0.00 0.00 39.17 1.90
371 382 1.079127 GGTGTGACTATGTGCCGCT 60.079 57.895 0.00 0.00 0.00 5.52
408 419 4.889427 CGTCAAGTCGAGGCATCA 57.111 55.556 0.00 0.00 0.00 3.07
424 435 0.734309 TAGCATCAATGGTGCAAGCG 59.266 50.000 21.46 0.00 44.87 4.68
449 460 1.210478 CATCCTCGACCCACAATCCTT 59.790 52.381 0.00 0.00 0.00 3.36
450 461 0.833287 CATCCTCGACCCACAATCCT 59.167 55.000 0.00 0.00 0.00 3.24
480 491 2.223829 CCACTTCCACCATCTAGCTACG 60.224 54.545 0.00 0.00 0.00 3.51
603 1023 8.758829 ACTGGTTAATGTTATACTCATCAGTGA 58.241 33.333 0.00 0.00 33.62 3.41
655 1205 3.059393 CGGCACAGCACTTGTATATCATG 60.059 47.826 0.00 0.00 38.16 3.07
657 1207 2.549926 CGGCACAGCACTTGTATATCA 58.450 47.619 0.00 0.00 38.16 2.15
673 1223 2.173758 TAACCACTTCGGATGCGGCA 62.174 55.000 4.58 4.58 38.63 5.69
680 1230 3.071479 GTCATTGCTTAACCACTTCGGA 58.929 45.455 0.00 0.00 38.63 4.55
875 1432 1.645391 TGATGGGTCAATGGGGAATGT 59.355 47.619 0.00 0.00 0.00 2.71
1174 1744 2.495366 ATAACGGCAACAGCGTCGGA 62.495 55.000 0.00 0.00 0.00 4.55
1252 1822 1.301558 CAGAGATGAGCGGGATGGC 60.302 63.158 0.00 0.00 0.00 4.40
1311 1881 1.299976 GTCCTGGTGGAAGGCGAAT 59.700 57.895 0.00 0.00 45.18 3.34
1347 1917 3.691342 CCGTCGAGGAAGTGGGCA 61.691 66.667 6.70 0.00 45.00 5.36
1368 1938 3.049912 GTCATTGAAAACGAACTTGCCC 58.950 45.455 0.00 0.00 0.00 5.36
1408 1978 0.178921 AGCCCAGTCTCAGACTTCCA 60.179 55.000 3.92 0.00 41.37 3.53
1771 2418 1.220206 CCTCTCGCCATTGAGCACT 59.780 57.895 0.00 0.00 35.90 4.40
1808 2455 1.680735 GAGCCAGATCTGACGATGTCT 59.319 52.381 24.62 8.14 33.15 3.41
1893 2540 2.266554 GGCTATCATGAGCATAGACGC 58.733 52.381 8.97 0.00 44.76 5.19
1908 2569 7.761981 ATCCATAATTGGTAGATCTGGCTAT 57.238 36.000 5.18 0.00 44.06 2.97
1936 2597 7.803189 ACAAATCTTATTTGAAGTTGTACGCTG 59.197 33.333 16.94 0.00 31.15 5.18
1972 2709 9.165035 CTCAAGCAGATCTTTCTTTCTCTTATT 57.835 33.333 0.00 0.00 31.27 1.40
1973 2710 8.538701 TCTCAAGCAGATCTTTCTTTCTCTTAT 58.461 33.333 0.00 0.00 31.27 1.73
1978 2715 6.374894 CCAATCTCAAGCAGATCTTTCTTTCT 59.625 38.462 0.00 0.00 41.47 2.52
2015 2764 6.998673 AGTGGAGTACAAAATTAAGAGCAACT 59.001 34.615 0.00 0.00 0.00 3.16
2030 2784 5.836024 AATGGTTCCTTTAGTGGAGTACA 57.164 39.130 0.00 0.00 37.43 2.90
2036 2799 5.476599 TGTGATCAAATGGTTCCTTTAGTGG 59.523 40.000 0.00 0.00 0.00 4.00
2037 2800 6.573664 TGTGATCAAATGGTTCCTTTAGTG 57.426 37.500 0.00 0.00 0.00 2.74
2038 2801 6.947733 TGATGTGATCAAATGGTTCCTTTAGT 59.052 34.615 2.15 0.00 36.11 2.24
2039 2802 7.395190 TGATGTGATCAAATGGTTCCTTTAG 57.605 36.000 2.15 0.00 36.11 1.85
2040 2803 7.201723 CGATGATGTGATCAAATGGTTCCTTTA 60.202 37.037 2.15 0.00 43.50 1.85
2045 2808 4.285292 GCGATGATGTGATCAAATGGTTC 58.715 43.478 2.15 0.00 43.50 3.62
2097 2890 0.097325 GTGACGTGACACCGCAAAAA 59.903 50.000 0.00 0.00 35.07 1.94
2098 2891 1.716760 GTGACGTGACACCGCAAAA 59.283 52.632 0.00 0.00 35.07 2.44
2099 2892 3.401095 GTGACGTGACACCGCAAA 58.599 55.556 0.00 0.00 35.07 3.68
2105 2898 1.375551 AGGTTTTGGTGACGTGACAC 58.624 50.000 7.63 2.92 39.70 3.67
2106 2899 1.740585 CAAGGTTTTGGTGACGTGACA 59.259 47.619 7.63 0.00 0.00 3.58
2107 2900 2.011222 TCAAGGTTTTGGTGACGTGAC 58.989 47.619 0.00 0.00 34.97 3.67
2108 2901 2.011222 GTCAAGGTTTTGGTGACGTGA 58.989 47.619 0.00 0.00 32.98 4.35
2109 2902 2.468532 GTCAAGGTTTTGGTGACGTG 57.531 50.000 0.00 0.00 32.98 4.49
2112 2905 0.666374 CCCGTCAAGGTTTTGGTGAC 59.334 55.000 0.00 0.00 38.62 3.67
2113 2906 1.104577 GCCCGTCAAGGTTTTGGTGA 61.105 55.000 0.00 0.00 38.74 4.02
2114 2907 1.362355 GCCCGTCAAGGTTTTGGTG 59.638 57.895 0.00 0.00 38.74 4.17
2115 2908 2.190841 CGCCCGTCAAGGTTTTGGT 61.191 57.895 0.00 0.00 38.74 3.67
2116 2909 1.241315 ATCGCCCGTCAAGGTTTTGG 61.241 55.000 0.00 0.00 38.74 3.28
2154 2947 0.748729 AGGGTTTTGGTGACGCGAAA 60.749 50.000 15.93 0.00 35.38 3.46
2180 2974 1.440145 TTGGTGACGCAACATCGCAA 61.440 50.000 0.00 0.00 28.36 4.85
2183 2977 2.095768 AGATTTTGGTGACGCAACATCG 60.096 45.455 0.00 0.00 28.36 3.84
2184 2978 3.559238 AGATTTTGGTGACGCAACATC 57.441 42.857 0.00 5.40 28.36 3.06
2185 2979 3.317711 TCAAGATTTTGGTGACGCAACAT 59.682 39.130 0.00 0.00 34.97 2.71
2189 2983 2.293122 CCTTCAAGATTTTGGTGACGCA 59.707 45.455 0.00 0.00 34.97 5.24
2202 2996 3.384467 CCAAGAACTTTTGCCCTTCAAGA 59.616 43.478 0.00 0.00 35.84 3.02
2208 3002 3.517500 TCAAAACCAAGAACTTTTGCCCT 59.482 39.130 0.00 0.00 37.31 5.19
2234 3028 2.029200 TGGTCCGACATGCGTAGTTTAA 60.029 45.455 0.00 0.00 38.67 1.52
2265 3059 5.294060 GGTGACCGTTGTGTAAAAGTTAAGA 59.706 40.000 0.00 0.00 0.00 2.10
2304 3098 1.093496 GTATTTTCAGACGGCGGGGG 61.093 60.000 13.24 0.00 0.00 5.40
2305 3099 0.107848 AGTATTTTCAGACGGCGGGG 60.108 55.000 13.24 0.00 0.00 5.73
2306 3100 1.734163 AAGTATTTTCAGACGGCGGG 58.266 50.000 13.24 0.00 0.00 6.13
2309 3103 6.431198 TTCCAATAAGTATTTTCAGACGGC 57.569 37.500 0.00 0.00 0.00 5.68
2310 3104 9.855021 ATTTTTCCAATAAGTATTTTCAGACGG 57.145 29.630 0.00 0.00 0.00 4.79
2326 3120 9.500785 ACATCCGTTTTTATTCATTTTTCCAAT 57.499 25.926 0.00 0.00 0.00 3.16
2327 3121 8.894768 ACATCCGTTTTTATTCATTTTTCCAA 57.105 26.923 0.00 0.00 0.00 3.53
2368 3162 8.908903 GTCGGAGAAATGGATATATCTAGATGT 58.091 37.037 15.79 11.37 39.69 3.06
2369 3163 8.907885 TGTCGGAGAAATGGATATATCTAGATG 58.092 37.037 15.79 0.00 39.69 2.90
2370 3164 9.480861 TTGTCGGAGAAATGGATATATCTAGAT 57.519 33.333 10.73 10.73 39.69 1.98
2371 3165 8.879427 TTGTCGGAGAAATGGATATATCTAGA 57.121 34.615 12.42 0.00 39.69 2.43
2372 3166 8.744652 ACTTGTCGGAGAAATGGATATATCTAG 58.255 37.037 12.42 0.00 39.69 2.43
2373 3167 8.651589 ACTTGTCGGAGAAATGGATATATCTA 57.348 34.615 12.42 6.97 39.69 1.98
2374 3168 7.546250 ACTTGTCGGAGAAATGGATATATCT 57.454 36.000 12.42 0.00 39.69 1.98
2375 3169 9.877178 AATACTTGTCGGAGAAATGGATATATC 57.123 33.333 3.96 3.96 39.69 1.63
2377 3171 9.706691 GAAATACTTGTCGGAGAAATGGATATA 57.293 33.333 0.00 0.00 39.69 0.86
2378 3172 7.661847 GGAAATACTTGTCGGAGAAATGGATAT 59.338 37.037 0.00 0.00 39.69 1.63
2379 3173 6.990349 GGAAATACTTGTCGGAGAAATGGATA 59.010 38.462 0.00 0.00 39.69 2.59
2380 3174 5.823045 GGAAATACTTGTCGGAGAAATGGAT 59.177 40.000 0.00 0.00 39.69 3.41
2381 3175 5.183228 GGAAATACTTGTCGGAGAAATGGA 58.817 41.667 0.00 0.00 39.69 3.41
2382 3176 4.034048 CGGAAATACTTGTCGGAGAAATGG 59.966 45.833 0.00 0.00 39.69 3.16
2383 3177 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
2384 3178 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
2385 3179 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
2386 3180 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
2387 3181 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
2388 3182 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
2389 3183 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
2390 3184 1.135315 TCGTCCGGAAATACTTGTCGG 60.135 52.381 5.23 0.00 41.80 4.79
2391 3185 2.267188 TCGTCCGGAAATACTTGTCG 57.733 50.000 5.23 1.58 0.00 4.35
2392 3186 2.928116 CCTTCGTCCGGAAATACTTGTC 59.072 50.000 5.23 0.00 33.34 3.18
2393 3187 2.354403 CCCTTCGTCCGGAAATACTTGT 60.354 50.000 5.23 0.00 33.34 3.16
2394 3188 2.093869 TCCCTTCGTCCGGAAATACTTG 60.094 50.000 5.23 0.00 33.34 3.16
2395 3189 2.167900 CTCCCTTCGTCCGGAAATACTT 59.832 50.000 5.23 0.00 33.34 2.24
2396 3190 1.755380 CTCCCTTCGTCCGGAAATACT 59.245 52.381 5.23 0.00 33.34 2.12
2397 3191 1.479730 ACTCCCTTCGTCCGGAAATAC 59.520 52.381 5.23 0.00 33.34 1.89
2398 3192 1.856629 ACTCCCTTCGTCCGGAAATA 58.143 50.000 5.23 0.00 33.34 1.40
2399 3193 1.856629 TACTCCCTTCGTCCGGAAAT 58.143 50.000 5.23 0.00 33.34 2.17
2400 3194 1.856629 ATACTCCCTTCGTCCGGAAA 58.143 50.000 5.23 0.00 33.34 3.13
2401 3195 2.689983 GTTATACTCCCTTCGTCCGGAA 59.310 50.000 5.23 0.00 0.00 4.30
2402 3196 2.301346 GTTATACTCCCTTCGTCCGGA 58.699 52.381 0.00 0.00 0.00 5.14
2403 3197 1.339291 GGTTATACTCCCTTCGTCCGG 59.661 57.143 0.00 0.00 0.00 5.14
2404 3198 1.339291 GGGTTATACTCCCTTCGTCCG 59.661 57.143 5.24 0.00 41.58 4.79
2414 3208 2.267192 GGGGGATGGAGGGTTATACTC 58.733 57.143 0.00 0.00 0.00 2.59
2415 3209 1.588583 TGGGGGATGGAGGGTTATACT 59.411 52.381 0.00 0.00 0.00 2.12
2416 3210 1.703513 GTGGGGGATGGAGGGTTATAC 59.296 57.143 0.00 0.00 0.00 1.47
2417 3211 1.588583 AGTGGGGGATGGAGGGTTATA 59.411 52.381 0.00 0.00 0.00 0.98
2418 3212 0.350541 AGTGGGGGATGGAGGGTTAT 59.649 55.000 0.00 0.00 0.00 1.89
2419 3213 0.623324 CAGTGGGGGATGGAGGGTTA 60.623 60.000 0.00 0.00 0.00 2.85
2420 3214 1.930656 CAGTGGGGGATGGAGGGTT 60.931 63.158 0.00 0.00 0.00 4.11
2421 3215 2.286425 CAGTGGGGGATGGAGGGT 60.286 66.667 0.00 0.00 0.00 4.34
2422 3216 2.286425 ACAGTGGGGGATGGAGGG 60.286 66.667 0.00 0.00 0.00 4.30
2423 3217 0.990282 ATGACAGTGGGGGATGGAGG 60.990 60.000 0.00 0.00 0.00 4.30
2424 3218 0.182061 CATGACAGTGGGGGATGGAG 59.818 60.000 0.00 0.00 0.00 3.86
2425 3219 0.549902 ACATGACAGTGGGGGATGGA 60.550 55.000 0.00 0.00 0.00 3.41
2426 3220 0.332632 AACATGACAGTGGGGGATGG 59.667 55.000 0.00 0.00 0.00 3.51
2427 3221 1.283029 AGAACATGACAGTGGGGGATG 59.717 52.381 0.00 0.00 0.00 3.51
2428 3222 1.283029 CAGAACATGACAGTGGGGGAT 59.717 52.381 0.00 0.00 0.00 3.85
2429 3223 0.692476 CAGAACATGACAGTGGGGGA 59.308 55.000 0.00 0.00 0.00 4.81
2439 3233 6.127925 GCTCATGTCCAAATAACAGAACATGA 60.128 38.462 13.48 13.48 39.90 3.07
2441 3235 5.711506 TGCTCATGTCCAAATAACAGAACAT 59.288 36.000 0.00 0.00 0.00 2.71
2488 3282 1.475403 TCGGAGAATCAGAGGACCAC 58.525 55.000 0.00 0.00 33.37 4.16
2572 3374 1.340308 CCCAATGAGGTGTCATGAGCA 60.340 52.381 0.00 0.00 43.04 4.26
2575 3377 1.065199 GCTCCCAATGAGGTGTCATGA 60.065 52.381 0.00 0.00 43.04 3.07
2624 3426 3.722728 GCAAGCTTAATTAGGCATGCT 57.277 42.857 30.74 14.51 45.48 3.79
2663 3465 4.385358 AGACAACGGCAAATGTTTCTTT 57.615 36.364 0.00 0.00 0.00 2.52
2788 3593 7.716799 TGTGGCTAAATCCAATAGTCAAAAT 57.283 32.000 0.00 0.00 36.80 1.82
2804 3610 1.071071 GCGGGGTATGTATGTGGCTAA 59.929 52.381 0.00 0.00 0.00 3.09
2805 3611 0.682852 GCGGGGTATGTATGTGGCTA 59.317 55.000 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.