Multiple sequence alignment - TraesCS7B01G079300

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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 TraesCS7B01G079300 chr7B 100.000 3232 0 0 1 3232 89543935 89540704 0.000000e+00 5969.0
1 TraesCS7B01G079300 chr7B 81.192 1393 226 31 992 2368 89561042 89559670 0.000000e+00 1088.0
2 TraesCS7B01G079300 chr7B 82.234 940 144 19 1463 2388 89656871 89655941 0.000000e+00 789.0
3 TraesCS7B01G079300 chr7B 89.041 365 38 2 988 1352 89657523 89657161 4.920000e-123 451.0
4 TraesCS7B01G079300 chr7B 83.140 172 23 5 2855 3021 546543288 546543458 5.580000e-33 152.0
5 TraesCS7B01G079300 chr7B 83.140 172 23 5 2855 3021 546631970 546632140 5.580000e-33 152.0
6 TraesCS7B01G079300 chr7B 93.827 81 4 1 3146 3225 735283685 735283765 1.570000e-23 121.0
7 TraesCS7B01G079300 chr7D 91.618 2052 139 17 593 2633 127683432 127681403 0.000000e+00 2806.0
8 TraesCS7B01G079300 chr7D 91.072 1781 147 8 1330 3106 127650559 127648787 0.000000e+00 2398.0
9 TraesCS7B01G079300 chr7D 92.297 753 46 4 593 1342 127652288 127651545 0.000000e+00 1059.0
10 TraesCS7B01G079300 chr7D 81.508 968 151 21 1440 2388 127737154 127736196 0.000000e+00 771.0
11 TraesCS7B01G079300 chr7D 81.760 943 151 17 1458 2388 127753006 127752073 0.000000e+00 769.0
12 TraesCS7B01G079300 chr7D 81.693 945 153 15 1458 2388 127765510 127764572 0.000000e+00 769.0
13 TraesCS7B01G079300 chr7D 81.350 874 141 19 992 1858 127700365 127699507 0.000000e+00 691.0
14 TraesCS7B01G079300 chr7D 88.828 367 40 1 992 1358 127753626 127753261 1.770000e-122 449.0
15 TraesCS7B01G079300 chr7D 88.140 371 42 2 988 1358 127766143 127765775 1.060000e-119 440.0
16 TraesCS7B01G079300 chr7D 83.420 386 47 4 119 487 127683859 127683474 3.090000e-90 342.0
17 TraesCS7B01G079300 chr7D 86.628 172 17 6 2855 3021 431326013 431326183 5.510000e-43 185.0
18 TraesCS7B01G079300 chr7D 93.590 78 5 0 3147 3224 597702270 597702193 2.040000e-22 117.0
19 TraesCS7B01G079300 chr7D 100.000 48 0 0 639 686 127671514 127671467 4.440000e-14 89.8
20 TraesCS7B01G079300 chr7D 94.444 54 2 1 3138 3191 500900626 500900678 7.430000e-12 82.4
21 TraesCS7B01G079300 chr7A 89.663 1780 165 12 1379 3147 128405647 128403876 0.000000e+00 2250.0
22 TraesCS7B01G079300 chr7A 91.879 825 37 9 580 1383 128406538 128405723 0.000000e+00 1125.0
23 TraesCS7B01G079300 chr7A 88.251 366 41 2 988 1353 128511408 128511045 1.380000e-118 436.0
24 TraesCS7B01G079300 chr4D 83.740 123 20 0 3021 3143 330362601 330362479 2.040000e-22 117.0
25 TraesCS7B01G079300 chr4D 97.872 47 0 1 3145 3191 418528823 418528868 2.670000e-11 80.5
26 TraesCS7B01G079300 chr2A 83.594 128 18 2 3021 3145 481414917 481414790 2.040000e-22 117.0
27 TraesCS7B01G079300 chr6D 82.812 128 18 4 3021 3145 117432411 117432537 9.480000e-21 111.0
28 TraesCS7B01G079300 chr1A 84.034 119 16 3 3021 3139 151266952 151267067 9.480000e-21 111.0
29 TraesCS7B01G079300 chr5D 82.400 125 22 0 3021 3145 169687028 169687152 3.410000e-20 110.0
30 TraesCS7B01G079300 chr5D 94.643 56 1 2 3136 3191 548209717 548209664 5.750000e-13 86.1
31 TraesCS7B01G079300 chr5B 83.333 120 19 1 3021 3139 313857520 313857639 3.410000e-20 110.0
32 TraesCS7B01G079300 chr5B 88.608 79 9 0 3146 3224 571632552 571632474 2.650000e-16 97.1
33 TraesCS7B01G079300 chr1B 82.540 126 21 1 3021 3145 459288559 459288684 3.410000e-20 110.0
34 TraesCS7B01G079300 chr6A 90.541 74 7 0 3146 3219 169200713 169200640 7.380000e-17 99.0
35 TraesCS7B01G079300 chr5A 90.541 74 7 0 3146 3219 433496600 433496527 7.380000e-17 99.0
36 TraesCS7B01G079300 chrUn 94.000 50 2 1 3136 3184 470912923 470912972 1.240000e-09 75.0


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 TraesCS7B01G079300 chr7B 89540704 89543935 3231 True 5969.0 5969 100.0000 1 3232 1 chr7B.!!$R1 3231
1 TraesCS7B01G079300 chr7B 89559670 89561042 1372 True 1088.0 1088 81.1920 992 2368 1 chr7B.!!$R2 1376
2 TraesCS7B01G079300 chr7B 89655941 89657523 1582 True 620.0 789 85.6375 988 2388 2 chr7B.!!$R3 1400
3 TraesCS7B01G079300 chr7D 127648787 127652288 3501 True 1728.5 2398 91.6845 593 3106 2 chr7D.!!$R5 2513
4 TraesCS7B01G079300 chr7D 127681403 127683859 2456 True 1574.0 2806 87.5190 119 2633 2 chr7D.!!$R6 2514
5 TraesCS7B01G079300 chr7D 127736196 127737154 958 True 771.0 771 81.5080 1440 2388 1 chr7D.!!$R3 948
6 TraesCS7B01G079300 chr7D 127699507 127700365 858 True 691.0 691 81.3500 992 1858 1 chr7D.!!$R2 866
7 TraesCS7B01G079300 chr7D 127752073 127753626 1553 True 609.0 769 85.2940 992 2388 2 chr7D.!!$R7 1396
8 TraesCS7B01G079300 chr7D 127764572 127766143 1571 True 604.5 769 84.9165 988 2388 2 chr7D.!!$R8 1400
9 TraesCS7B01G079300 chr7A 128403876 128406538 2662 True 1687.5 2250 90.7710 580 3147 2 chr7A.!!$R2 2567

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
30 31 0.044855 AGGGTTGTAGGGAGGCAGAT 59.955 55.0 0.0 0.0 0.0 2.90 F
31 32 0.181350 GGGTTGTAGGGAGGCAGATG 59.819 60.0 0.0 0.0 0.0 2.90 F
107 108 0.182537 CACACCCTTTCCCACACAGA 59.817 55.0 0.0 0.0 0.0 3.41 F
111 112 0.320771 CCCTTTCCCACACAGAGTCG 60.321 60.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1498 2813 1.136305 GGTATCTGCTTGTCGGTGCTA 59.864 52.381 0.0 0.0 0.00 3.49 R
1951 3268 1.526887 CGGTGGGGTATCTGCATGT 59.473 57.895 0.0 0.0 0.00 3.21 R
1973 3290 1.924731 AGGCTTTCCTAAAGGGCAAC 58.075 50.000 0.0 0.0 42.06 4.17 R
2642 3978 0.028505 CGCTACCGCTACGTATGTGT 59.971 55.000 0.0 0.0 0.00 3.72 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 3.779271 GAAGTAGTCGAGGGTTGTAGG 57.221 52.381 0.00 0.00 0.00 3.18
22 23 2.140839 AGTAGTCGAGGGTTGTAGGG 57.859 55.000 0.00 0.00 0.00 3.53
23 24 1.637553 AGTAGTCGAGGGTTGTAGGGA 59.362 52.381 0.00 0.00 0.00 4.20
24 25 2.022934 GTAGTCGAGGGTTGTAGGGAG 58.977 57.143 0.00 0.00 0.00 4.30
25 26 0.324460 AGTCGAGGGTTGTAGGGAGG 60.324 60.000 0.00 0.00 0.00 4.30
26 27 1.684734 TCGAGGGTTGTAGGGAGGC 60.685 63.158 0.00 0.00 0.00 4.70
27 28 1.987855 CGAGGGTTGTAGGGAGGCA 60.988 63.158 0.00 0.00 0.00 4.75
28 29 1.908483 GAGGGTTGTAGGGAGGCAG 59.092 63.158 0.00 0.00 0.00 4.85
29 30 0.617820 GAGGGTTGTAGGGAGGCAGA 60.618 60.000 0.00 0.00 0.00 4.26
30 31 0.044855 AGGGTTGTAGGGAGGCAGAT 59.955 55.000 0.00 0.00 0.00 2.90
31 32 0.181350 GGGTTGTAGGGAGGCAGATG 59.819 60.000 0.00 0.00 0.00 2.90
32 33 0.912486 GGTTGTAGGGAGGCAGATGT 59.088 55.000 0.00 0.00 0.00 3.06
33 34 1.407437 GGTTGTAGGGAGGCAGATGTG 60.407 57.143 0.00 0.00 0.00 3.21
34 35 0.911769 TTGTAGGGAGGCAGATGTGG 59.088 55.000 0.00 0.00 0.00 4.17
42 43 2.672996 GCAGATGTGGCCAACGGT 60.673 61.111 7.24 0.00 0.00 4.83
43 44 2.268076 GCAGATGTGGCCAACGGTT 61.268 57.895 7.24 0.00 0.00 4.44
44 45 1.875963 CAGATGTGGCCAACGGTTC 59.124 57.895 7.24 0.00 0.00 3.62
45 46 0.888736 CAGATGTGGCCAACGGTTCA 60.889 55.000 7.24 0.00 0.00 3.18
46 47 0.606401 AGATGTGGCCAACGGTTCAG 60.606 55.000 7.24 0.00 0.00 3.02
47 48 2.200170 GATGTGGCCAACGGTTCAGC 62.200 60.000 7.24 0.00 0.00 4.26
48 49 3.670377 GTGGCCAACGGTTCAGCC 61.670 66.667 19.71 19.71 45.96 4.85
49 50 3.884774 TGGCCAACGGTTCAGCCT 61.885 61.111 24.29 0.00 45.94 4.58
50 51 2.597510 GGCCAACGGTTCAGCCTT 60.598 61.111 19.39 0.00 42.34 4.35
51 52 1.302993 GGCCAACGGTTCAGCCTTA 60.303 57.895 19.39 0.00 42.34 2.69
52 53 1.583495 GGCCAACGGTTCAGCCTTAC 61.583 60.000 19.39 0.00 42.34 2.34
53 54 1.908066 GCCAACGGTTCAGCCTTACG 61.908 60.000 0.00 0.00 34.25 3.18
54 55 0.320073 CCAACGGTTCAGCCTTACGA 60.320 55.000 0.00 0.00 34.25 3.43
55 56 1.674817 CCAACGGTTCAGCCTTACGAT 60.675 52.381 0.00 0.00 34.25 3.73
56 57 1.393539 CAACGGTTCAGCCTTACGATG 59.606 52.381 0.00 0.00 34.25 3.84
57 58 0.606604 ACGGTTCAGCCTTACGATGT 59.393 50.000 0.00 0.00 34.25 3.06
58 59 0.999406 CGGTTCAGCCTTACGATGTG 59.001 55.000 0.00 0.00 34.25 3.21
59 60 1.671850 CGGTTCAGCCTTACGATGTGT 60.672 52.381 0.00 0.00 34.25 3.72
60 61 1.732259 GGTTCAGCCTTACGATGTGTG 59.268 52.381 0.00 0.00 0.00 3.82
61 62 2.413837 GTTCAGCCTTACGATGTGTGT 58.586 47.619 0.00 0.00 0.00 3.72
62 63 2.806244 GTTCAGCCTTACGATGTGTGTT 59.194 45.455 0.00 0.00 0.00 3.32
63 64 3.945981 TCAGCCTTACGATGTGTGTTA 57.054 42.857 0.00 0.00 0.00 2.41
64 65 4.465632 TCAGCCTTACGATGTGTGTTAT 57.534 40.909 0.00 0.00 0.00 1.89
65 66 4.430007 TCAGCCTTACGATGTGTGTTATC 58.570 43.478 0.00 0.00 0.00 1.75
66 67 3.555956 CAGCCTTACGATGTGTGTTATCC 59.444 47.826 0.00 0.00 0.00 2.59
67 68 3.451178 AGCCTTACGATGTGTGTTATCCT 59.549 43.478 0.00 0.00 0.00 3.24
68 69 4.081087 AGCCTTACGATGTGTGTTATCCTT 60.081 41.667 0.00 0.00 0.00 3.36
69 70 5.128171 AGCCTTACGATGTGTGTTATCCTTA 59.872 40.000 0.00 0.00 0.00 2.69
70 71 5.813672 GCCTTACGATGTGTGTTATCCTTAA 59.186 40.000 0.00 0.00 0.00 1.85
71 72 6.238022 GCCTTACGATGTGTGTTATCCTTAAC 60.238 42.308 0.00 0.00 38.56 2.01
72 73 6.257193 CCTTACGATGTGTGTTATCCTTAACC 59.743 42.308 0.00 0.00 37.49 2.85
73 74 4.510571 ACGATGTGTGTTATCCTTAACCC 58.489 43.478 0.00 0.00 37.49 4.11
74 75 4.020039 ACGATGTGTGTTATCCTTAACCCA 60.020 41.667 0.00 0.00 37.49 4.51
75 76 4.331717 CGATGTGTGTTATCCTTAACCCAC 59.668 45.833 5.03 5.03 43.12 4.61
77 78 4.391155 TGTGTGTTATCCTTAACCCACAC 58.609 43.478 12.41 12.41 45.59 3.82
78 79 4.141459 TGTGTGTTATCCTTAACCCACACA 60.141 41.667 16.72 16.72 45.59 3.72
79 80 4.454504 GTGTGTTATCCTTAACCCACACAG 59.545 45.833 13.96 0.00 42.66 3.66
80 81 4.348461 TGTGTTATCCTTAACCCACACAGA 59.652 41.667 0.00 0.00 37.49 3.41
81 82 4.935808 GTGTTATCCTTAACCCACACAGAG 59.064 45.833 0.00 0.00 37.49 3.35
82 83 4.595781 TGTTATCCTTAACCCACACAGAGT 59.404 41.667 0.00 0.00 37.49 3.24
83 84 5.781306 TGTTATCCTTAACCCACACAGAGTA 59.219 40.000 0.00 0.00 37.49 2.59
84 85 6.070995 TGTTATCCTTAACCCACACAGAGTAG 60.071 42.308 0.00 0.00 37.49 2.57
85 86 3.853207 TCCTTAACCCACACAGAGTAGT 58.147 45.455 0.00 0.00 0.00 2.73
86 87 3.576982 TCCTTAACCCACACAGAGTAGTG 59.423 47.826 0.00 0.00 44.93 2.74
91 92 3.986970 CACACAGAGTAGTGGCACA 57.013 52.632 21.41 2.83 43.72 4.57
102 103 2.197324 TGGCACACCCTTTCCCAC 59.803 61.111 0.00 0.00 33.59 4.61
103 104 2.197324 GGCACACCCTTTCCCACA 59.803 61.111 0.00 0.00 0.00 4.17
104 105 2.200337 GGCACACCCTTTCCCACAC 61.200 63.158 0.00 0.00 0.00 3.82
105 106 1.454847 GCACACCCTTTCCCACACA 60.455 57.895 0.00 0.00 0.00 3.72
106 107 1.455383 GCACACCCTTTCCCACACAG 61.455 60.000 0.00 0.00 0.00 3.66
107 108 0.182537 CACACCCTTTCCCACACAGA 59.817 55.000 0.00 0.00 0.00 3.41
108 109 0.474184 ACACCCTTTCCCACACAGAG 59.526 55.000 0.00 0.00 0.00 3.35
109 110 0.474184 CACCCTTTCCCACACAGAGT 59.526 55.000 0.00 0.00 0.00 3.24
110 111 0.765510 ACCCTTTCCCACACAGAGTC 59.234 55.000 0.00 0.00 0.00 3.36
111 112 0.320771 CCCTTTCCCACACAGAGTCG 60.321 60.000 0.00 0.00 0.00 4.18
112 113 0.679505 CCTTTCCCACACAGAGTCGA 59.320 55.000 0.00 0.00 0.00 4.20
113 114 1.337260 CCTTTCCCACACAGAGTCGAG 60.337 57.143 0.00 0.00 0.00 4.04
114 115 0.679505 TTTCCCACACAGAGTCGAGG 59.320 55.000 0.00 0.00 0.00 4.63
115 116 1.185618 TTCCCACACAGAGTCGAGGG 61.186 60.000 0.00 0.00 37.65 4.30
116 117 1.908793 CCCACACAGAGTCGAGGGT 60.909 63.158 0.00 0.00 0.00 4.34
117 118 1.472662 CCCACACAGAGTCGAGGGTT 61.473 60.000 0.00 0.00 0.00 4.11
126 127 1.520787 GTCGAGGGTTGTATGGGCG 60.521 63.158 0.00 0.00 0.00 6.13
132 133 2.511600 GTTGTATGGGCGCGCTCT 60.512 61.111 33.56 19.80 0.00 4.09
133 134 1.227147 GTTGTATGGGCGCGCTCTA 60.227 57.895 33.56 19.84 0.00 2.43
134 135 0.808453 GTTGTATGGGCGCGCTCTAA 60.808 55.000 33.56 17.56 0.00 2.10
137 138 0.808453 GTATGGGCGCGCTCTAACAA 60.808 55.000 33.56 12.24 0.00 2.83
177 178 1.523758 CGTGCATATAGGGAAAGGGC 58.476 55.000 0.00 0.00 0.00 5.19
216 217 4.804608 CCATTAATTGGCGATGTTCGTA 57.195 40.909 0.00 0.00 42.81 3.43
226 227 2.474032 GCGATGTTCGTAGTGAAAAGGC 60.474 50.000 0.00 0.00 42.81 4.35
233 234 1.670326 GTAGTGAAAAGGCGTTTGCG 58.330 50.000 4.95 0.00 44.10 4.85
245 246 0.387112 CGTTTGCGGCATTGACACAT 60.387 50.000 2.28 0.00 0.00 3.21
248 249 1.525718 TTGCGGCATTGACACATGCT 61.526 50.000 2.28 0.00 42.95 3.79
290 291 1.736645 AACGCCGTTGACCGATCAG 60.737 57.895 0.00 0.00 39.56 2.90
330 331 1.222115 GCCTGAAACGTCGCTTCTGT 61.222 55.000 9.58 0.00 0.00 3.41
331 332 1.933500 GCCTGAAACGTCGCTTCTGTA 60.934 52.381 9.58 0.00 0.00 2.74
333 334 2.390938 CTGAAACGTCGCTTCTGTACA 58.609 47.619 9.58 0.00 0.00 2.90
334 335 2.390938 TGAAACGTCGCTTCTGTACAG 58.609 47.619 17.17 17.17 0.00 2.74
349 350 1.195442 TACAGGCGGTTGTGGATGGA 61.195 55.000 0.00 0.00 32.56 3.41
350 351 1.303236 CAGGCGGTTGTGGATGGAA 60.303 57.895 0.00 0.00 0.00 3.53
352 353 0.893727 AGGCGGTTGTGGATGGAAAC 60.894 55.000 0.00 0.00 0.00 2.78
393 394 5.393461 CCACAACCTTGAAATATGAAGGCTC 60.393 44.000 0.00 0.00 42.32 4.70
394 395 4.396166 ACAACCTTGAAATATGAAGGCTCG 59.604 41.667 0.00 0.00 42.32 5.03
410 411 0.803117 CTCGCGAGCCCGATATAGAA 59.197 55.000 25.07 0.00 36.54 2.10
415 433 1.699343 GAGCCCGATATAGAACACGC 58.301 55.000 0.00 0.00 0.00 5.34
424 442 4.500837 CGATATAGAACACGCTCCATATGC 59.499 45.833 0.00 0.00 0.00 3.14
445 463 6.791887 TGCATATAACAATTCTGCTAGAGC 57.208 37.500 0.00 0.00 42.50 4.09
449 467 3.319137 AACAATTCTGCTAGAGCGTCA 57.681 42.857 0.00 0.00 45.83 4.35
457 475 3.118629 TCTGCTAGAGCGTCATTTTGGAT 60.119 43.478 0.00 0.00 45.83 3.41
522 540 9.680315 AGATATCAACAGTTATTAAGTACTCGC 57.320 33.333 5.32 0.00 0.00 5.03
523 541 9.680315 GATATCAACAGTTATTAAGTACTCGCT 57.320 33.333 0.00 0.00 0.00 4.93
525 543 7.807687 TCAACAGTTATTAAGTACTCGCTTC 57.192 36.000 0.00 0.00 0.00 3.86
526 544 6.525628 TCAACAGTTATTAAGTACTCGCTTCG 59.474 38.462 0.00 0.00 0.00 3.79
527 545 5.947443 ACAGTTATTAAGTACTCGCTTCGT 58.053 37.500 0.00 0.00 0.00 3.85
528 546 6.026513 ACAGTTATTAAGTACTCGCTTCGTC 58.973 40.000 0.00 0.00 0.00 4.20
529 547 5.454877 CAGTTATTAAGTACTCGCTTCGTCC 59.545 44.000 0.00 0.00 0.00 4.79
530 548 2.927553 TTAAGTACTCGCTTCGTCCC 57.072 50.000 0.00 0.00 0.00 4.46
531 549 1.825090 TAAGTACTCGCTTCGTCCCA 58.175 50.000 0.00 0.00 0.00 4.37
532 550 1.183549 AAGTACTCGCTTCGTCCCAT 58.816 50.000 0.00 0.00 0.00 4.00
533 551 2.048444 AGTACTCGCTTCGTCCCATA 57.952 50.000 0.00 0.00 0.00 2.74
534 552 2.372264 AGTACTCGCTTCGTCCCATAA 58.628 47.619 0.00 0.00 0.00 1.90
535 553 2.957006 AGTACTCGCTTCGTCCCATAAT 59.043 45.455 0.00 0.00 0.00 1.28
536 554 2.225068 ACTCGCTTCGTCCCATAATG 57.775 50.000 0.00 0.00 0.00 1.90
537 555 1.480954 ACTCGCTTCGTCCCATAATGT 59.519 47.619 0.00 0.00 0.00 2.71
538 556 2.691526 ACTCGCTTCGTCCCATAATGTA 59.308 45.455 0.00 0.00 0.00 2.29
539 557 3.243434 ACTCGCTTCGTCCCATAATGTAG 60.243 47.826 0.00 0.00 0.00 2.74
540 558 2.691526 TCGCTTCGTCCCATAATGTAGT 59.308 45.455 0.00 0.00 0.00 2.73
541 559 2.794910 CGCTTCGTCCCATAATGTAGTG 59.205 50.000 0.00 0.00 0.00 2.74
542 560 3.737047 CGCTTCGTCCCATAATGTAGTGT 60.737 47.826 0.00 0.00 0.00 3.55
543 561 4.189231 GCTTCGTCCCATAATGTAGTGTT 58.811 43.478 0.00 0.00 0.00 3.32
544 562 5.353938 GCTTCGTCCCATAATGTAGTGTTA 58.646 41.667 0.00 0.00 0.00 2.41
545 563 5.813672 GCTTCGTCCCATAATGTAGTGTTAA 59.186 40.000 0.00 0.00 0.00 2.01
546 564 6.018994 GCTTCGTCCCATAATGTAGTGTTAAG 60.019 42.308 0.00 0.00 0.00 1.85
547 565 6.778834 TCGTCCCATAATGTAGTGTTAAGA 57.221 37.500 0.00 0.00 0.00 2.10
548 566 7.172868 TCGTCCCATAATGTAGTGTTAAGAA 57.827 36.000 0.00 0.00 0.00 2.52
549 567 7.613585 TCGTCCCATAATGTAGTGTTAAGAAA 58.386 34.615 0.00 0.00 0.00 2.52
550 568 7.762615 TCGTCCCATAATGTAGTGTTAAGAAAG 59.237 37.037 0.00 0.00 0.00 2.62
551 569 7.548075 CGTCCCATAATGTAGTGTTAAGAAAGT 59.452 37.037 0.00 0.00 0.00 2.66
552 570 8.880750 GTCCCATAATGTAGTGTTAAGAAAGTC 58.119 37.037 0.00 0.00 0.00 3.01
553 571 8.822805 TCCCATAATGTAGTGTTAAGAAAGTCT 58.177 33.333 0.00 0.00 0.00 3.24
554 572 9.449719 CCCATAATGTAGTGTTAAGAAAGTCTT 57.550 33.333 0.00 0.00 40.35 3.01
587 605 7.675062 AGAATGGAGAAGTAGCTATTGTATGG 58.325 38.462 0.00 0.00 0.00 2.74
610 628 2.608261 CCCGCTAGAGTTGCTATAGTGC 60.608 54.545 0.84 0.00 35.33 4.40
677 698 5.924356 TGAATGGACAGAAGAACTTGTACA 58.076 37.500 0.00 0.00 0.00 2.90
678 699 6.533730 TGAATGGACAGAAGAACTTGTACAT 58.466 36.000 0.00 0.00 34.84 2.29
679 700 7.676004 TGAATGGACAGAAGAACTTGTACATA 58.324 34.615 0.00 0.00 33.44 2.29
680 701 8.154203 TGAATGGACAGAAGAACTTGTACATAA 58.846 33.333 0.00 0.00 33.44 1.90
681 702 8.918202 AATGGACAGAAGAACTTGTACATAAA 57.082 30.769 0.00 0.00 33.44 1.40
682 703 7.962964 TGGACAGAAGAACTTGTACATAAAG 57.037 36.000 0.00 0.00 0.00 1.85
716 737 5.240623 TGACGTTCTTTTCTTGCCATTATGT 59.759 36.000 0.00 0.00 0.00 2.29
862 886 3.700538 TGAAAGCAAGGACCATAGCATT 58.299 40.909 0.00 0.00 0.00 3.56
981 1021 0.842613 CTGTCGATCGAAGCACATCG 59.157 55.000 21.31 0.00 42.72 3.84
1248 1288 3.300934 CTGGACGCAGCAGCAGGTA 62.301 63.158 0.82 0.00 42.27 3.08
1341 2378 1.228154 AAGGGTCTCCACAAACGGC 60.228 57.895 0.00 0.00 34.83 5.68
1432 2600 8.697846 TCCTGTGATTTATTTTACGTCACTAG 57.302 34.615 0.00 0.00 39.78 2.57
1700 3017 6.602406 AGCAGTTCATGAAAGATAGCTCAAAT 59.398 34.615 10.35 0.00 0.00 2.32
1714 3031 3.055819 AGCTCAAATGACCGTACTGACAT 60.056 43.478 0.00 0.00 0.00 3.06
1751 3068 0.320771 AGAACCGATGTCGCTTTGCT 60.321 50.000 0.00 0.00 38.18 3.91
1862 3179 3.195610 TCGACTCTAATCCACATGTGCTT 59.804 43.478 20.81 16.82 0.00 3.91
1968 3285 0.546122 TCACATGCAGATACCCCACC 59.454 55.000 0.00 0.00 0.00 4.61
1973 3290 2.505982 CAGATACCCCACCGGCTG 59.494 66.667 0.00 0.00 33.26 4.85
1991 3308 1.546029 CTGTTGCCCTTTAGGAAAGCC 59.454 52.381 0.00 0.00 31.67 4.35
2082 3399 8.664669 TGGTTATACTGATCTCATTGCCTATA 57.335 34.615 0.00 0.00 0.00 1.31
2156 3480 2.027561 CCCCTTGAACAAGTATGACCGA 60.028 50.000 12.54 0.00 36.72 4.69
2159 3483 4.503910 CCTTGAACAAGTATGACCGATCA 58.496 43.478 12.54 0.00 36.61 2.92
2496 3832 9.982651 GAGATATGTGGTTGTAGTATGTAATGT 57.017 33.333 0.00 0.00 0.00 2.71
2585 3921 4.637534 CCATCCATATTCATCGGGATTGAC 59.362 45.833 0.00 0.00 38.05 3.18
2679 4015 0.108615 CGACACCACTAGGGCTTCTG 60.109 60.000 0.00 0.00 42.05 3.02
2683 4019 1.134280 CACCACTAGGGCTTCTGGATG 60.134 57.143 2.03 0.00 42.05 3.51
2690 4026 3.827505 GGCTTCTGGATGCCCATAA 57.172 52.632 14.24 0.00 43.54 1.90
2704 4040 3.072330 TGCCCATAATTCTTCCATCGCTA 59.928 43.478 0.00 0.00 0.00 4.26
2713 4049 4.166187 TCTTCCATCGCTAGATCAATCG 57.834 45.455 0.00 0.00 34.23 3.34
2751 4089 6.544931 TGATGCATTGCTTAGCTAGAAATCTT 59.455 34.615 10.49 0.00 28.86 2.40
2762 4100 5.033522 AGCTAGAAATCTTGTTAGGTCCCT 58.966 41.667 0.00 0.00 0.00 4.20
2763 4101 5.489278 AGCTAGAAATCTTGTTAGGTCCCTT 59.511 40.000 0.00 0.00 0.00 3.95
2772 4110 7.598759 TCTTGTTAGGTCCCTTTAGCTATAG 57.401 40.000 4.35 4.35 30.06 1.31
2783 4121 9.469097 GTCCCTTTAGCTATAGATCTTCTCATA 57.531 37.037 12.28 0.00 0.00 2.15
2798 4136 2.602257 TCATATTGTGAGGAGGCACG 57.398 50.000 0.00 0.00 41.63 5.34
2800 4138 0.469917 ATATTGTGAGGAGGCACGGG 59.530 55.000 0.00 0.00 41.63 5.28
2821 4159 2.231215 CGGAGGGTCAAATAGCTCAG 57.769 55.000 0.00 0.00 0.00 3.35
2837 4175 4.097418 AGCTCAGTGGACTTAAGTACCAT 58.903 43.478 21.85 7.77 36.09 3.55
2846 4184 5.550403 TGGACTTAAGTACCATTTTCTCCCT 59.450 40.000 15.42 0.00 0.00 4.20
2860 4198 4.392921 TTCTCCCTTCACGAATCATCTC 57.607 45.455 0.00 0.00 0.00 2.75
2862 4200 1.202417 TCCCTTCACGAATCATCTCGC 60.202 52.381 0.00 0.00 42.69 5.03
2868 4206 3.206964 TCACGAATCATCTCGCTCTAGT 58.793 45.455 0.00 0.00 42.69 2.57
2877 4215 3.766676 TCTCGCTCTAGTGCAGTTAAG 57.233 47.619 16.44 0.00 0.00 1.85
2882 4220 2.612972 GCTCTAGTGCAGTTAAGCCACA 60.613 50.000 11.82 0.00 0.00 4.17
2890 4228 4.002982 TGCAGTTAAGCCACAAGATAGTG 58.997 43.478 0.00 0.00 39.21 2.74
2897 4235 1.645034 CCACAAGATAGTGCACGAGG 58.355 55.000 12.01 0.00 38.18 4.63
2912 4250 3.126831 CACGAGGCTCTGATACCAATTC 58.873 50.000 13.50 0.00 0.00 2.17
2920 4258 6.894103 AGGCTCTGATACCAATTCAAAAGATT 59.106 34.615 0.39 0.00 0.00 2.40
2936 4274 5.885449 AAAGATTGAGATGGACCTAGAGG 57.115 43.478 0.00 0.00 42.17 3.69
2937 4275 6.352565 CAAAAGATTGAGATGGACCTAGAGGT 60.353 42.308 0.00 0.00 44.81 3.85
2953 4291 7.229581 CCTAGAGGTGGTGAATAGGTATAAC 57.770 44.000 0.00 0.00 0.00 1.89
3031 4371 4.446371 CCTAACAATTGCTACTCCCTCTG 58.554 47.826 5.05 0.00 0.00 3.35
3040 4380 0.614979 TACTCCCTCTGTCCCAGTGC 60.615 60.000 0.00 0.00 32.61 4.40
3053 4393 3.758554 GTCCCAGTGCATAAGTCACATTT 59.241 43.478 0.00 0.00 36.93 2.32
3055 4395 3.758023 CCCAGTGCATAAGTCACATTTGA 59.242 43.478 0.00 0.00 36.93 2.69
3081 4421 1.978455 AACACGACCTGGGTGCAAGA 61.978 55.000 0.00 0.00 38.98 3.02
3083 4423 1.071471 ACGACCTGGGTGCAAGAAG 59.929 57.895 0.00 0.00 0.00 2.85
3088 4428 1.180029 CCTGGGTGCAAGAAGATTGG 58.820 55.000 0.00 0.00 0.00 3.16
3106 4446 3.260269 TGGAGGAGAAGGAGAAACTGA 57.740 47.619 0.00 0.00 0.00 3.41
3108 4448 4.171234 TGGAGGAGAAGGAGAAACTGAAT 58.829 43.478 0.00 0.00 0.00 2.57
3109 4449 4.599241 TGGAGGAGAAGGAGAAACTGAATT 59.401 41.667 0.00 0.00 0.00 2.17
3120 4460 5.066913 AGAAACTGAATTGGTCCTCCTTT 57.933 39.130 0.00 0.00 34.23 3.11
3121 4461 5.073428 AGAAACTGAATTGGTCCTCCTTTC 58.927 41.667 0.00 0.00 34.23 2.62
3125 4465 5.397360 ACTGAATTGGTCCTCCTTTCAATT 58.603 37.500 0.00 0.00 40.96 2.32
3130 4470 5.722021 TTGGTCCTCCTTTCAATTAAAGC 57.278 39.130 0.00 0.00 42.85 3.51
3131 4471 4.086457 TGGTCCTCCTTTCAATTAAAGCC 58.914 43.478 0.00 0.00 42.85 4.35
3133 4473 4.344978 GTCCTCCTTTCAATTAAAGCCCT 58.655 43.478 0.00 0.00 42.85 5.19
3134 4474 4.158579 GTCCTCCTTTCAATTAAAGCCCTG 59.841 45.833 0.00 0.00 42.85 4.45
3139 4479 7.124147 CCTCCTTTCAATTAAAGCCCTGATTTA 59.876 37.037 0.00 0.00 42.85 1.40
3151 4491 7.922699 AAGCCCTGATTTATCTCTTACTAGT 57.077 36.000 0.00 0.00 0.00 2.57
3152 4492 9.435570 AAAGCCCTGATTTATCTCTTACTAGTA 57.564 33.333 0.00 0.00 0.00 1.82
3153 4493 8.644374 AGCCCTGATTTATCTCTTACTAGTAG 57.356 38.462 2.23 0.00 0.00 2.57
3154 4494 8.449625 AGCCCTGATTTATCTCTTACTAGTAGA 58.550 37.037 3.59 0.00 0.00 2.59
3155 4495 9.080097 GCCCTGATTTATCTCTTACTAGTAGAA 57.920 37.037 3.59 0.00 0.00 2.10
3160 4500 9.863845 GATTTATCTCTTACTAGTAGAATGCCC 57.136 37.037 3.59 0.00 0.00 5.36
3161 4501 5.968528 ATCTCTTACTAGTAGAATGCCCG 57.031 43.478 3.59 0.00 0.00 6.13
3162 4502 4.789807 TCTCTTACTAGTAGAATGCCCGT 58.210 43.478 3.59 0.00 0.00 5.28
3163 4503 4.579340 TCTCTTACTAGTAGAATGCCCGTG 59.421 45.833 3.59 0.00 0.00 4.94
3164 4504 3.067742 TCTTACTAGTAGAATGCCCGTGC 59.932 47.826 3.59 0.00 38.26 5.34
3165 4505 0.102481 ACTAGTAGAATGCCCGTGCG 59.898 55.000 3.59 0.00 41.78 5.34
3166 4506 0.102481 CTAGTAGAATGCCCGTGCGT 59.898 55.000 0.00 0.00 41.78 5.24
3168 4508 1.019278 AGTAGAATGCCCGTGCGTTG 61.019 55.000 0.86 0.00 46.55 4.10
3169 4509 2.395360 TAGAATGCCCGTGCGTTGC 61.395 57.895 0.86 0.00 46.55 4.17
3170 4510 4.776647 GAATGCCCGTGCGTTGCC 62.777 66.667 0.86 0.00 46.55 4.52
3188 4528 3.793797 GCCACGGGCTAACAAAATTAT 57.206 42.857 7.58 0.00 46.69 1.28
3189 4529 4.904253 GCCACGGGCTAACAAAATTATA 57.096 40.909 7.58 0.00 46.69 0.98
3190 4530 5.447624 GCCACGGGCTAACAAAATTATAT 57.552 39.130 7.58 0.00 46.69 0.86
3191 4531 6.563222 GCCACGGGCTAACAAAATTATATA 57.437 37.500 7.58 0.00 46.69 0.86
3192 4532 7.153217 GCCACGGGCTAACAAAATTATATAT 57.847 36.000 7.58 0.00 46.69 0.86
3193 4533 7.027161 GCCACGGGCTAACAAAATTATATATG 58.973 38.462 7.58 0.00 46.69 1.78
3194 4534 7.094549 GCCACGGGCTAACAAAATTATATATGA 60.095 37.037 7.58 0.00 46.69 2.15
3195 4535 8.788806 CCACGGGCTAACAAAATTATATATGAA 58.211 33.333 0.00 0.00 0.00 2.57
3196 4536 9.825972 CACGGGCTAACAAAATTATATATGAAG 57.174 33.333 0.00 0.00 0.00 3.02
3197 4537 9.787435 ACGGGCTAACAAAATTATATATGAAGA 57.213 29.630 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.042162 TCCCTACAACCCTCGACTACTT 59.958 50.000 0.00 0.00 0.00 2.24
3 4 1.637553 TCCCTACAACCCTCGACTACT 59.362 52.381 0.00 0.00 0.00 2.57
7 8 1.957765 GCCTCCCTACAACCCTCGAC 61.958 65.000 0.00 0.00 0.00 4.20
8 9 1.684734 GCCTCCCTACAACCCTCGA 60.685 63.158 0.00 0.00 0.00 4.04
9 10 1.961180 CTGCCTCCCTACAACCCTCG 61.961 65.000 0.00 0.00 0.00 4.63
10 11 0.617820 TCTGCCTCCCTACAACCCTC 60.618 60.000 0.00 0.00 0.00 4.30
11 12 0.044855 ATCTGCCTCCCTACAACCCT 59.955 55.000 0.00 0.00 0.00 4.34
12 13 0.181350 CATCTGCCTCCCTACAACCC 59.819 60.000 0.00 0.00 0.00 4.11
13 14 0.912486 ACATCTGCCTCCCTACAACC 59.088 55.000 0.00 0.00 0.00 3.77
14 15 1.407437 CCACATCTGCCTCCCTACAAC 60.407 57.143 0.00 0.00 0.00 3.32
15 16 0.911769 CCACATCTGCCTCCCTACAA 59.088 55.000 0.00 0.00 0.00 2.41
16 17 1.626356 GCCACATCTGCCTCCCTACA 61.626 60.000 0.00 0.00 0.00 2.74
17 18 1.147153 GCCACATCTGCCTCCCTAC 59.853 63.158 0.00 0.00 0.00 3.18
18 19 2.072487 GGCCACATCTGCCTCCCTA 61.072 63.158 0.00 0.00 45.70 3.53
19 20 3.415087 GGCCACATCTGCCTCCCT 61.415 66.667 0.00 0.00 45.70 4.20
25 26 2.200170 GAACCGTTGGCCACATCTGC 62.200 60.000 3.88 0.00 0.00 4.26
26 27 0.888736 TGAACCGTTGGCCACATCTG 60.889 55.000 3.88 0.00 0.00 2.90
27 28 0.606401 CTGAACCGTTGGCCACATCT 60.606 55.000 3.88 0.00 0.00 2.90
28 29 1.875963 CTGAACCGTTGGCCACATC 59.124 57.895 3.88 0.00 0.00 3.06
29 30 2.268076 GCTGAACCGTTGGCCACAT 61.268 57.895 3.88 0.00 0.00 3.21
30 31 2.904866 GCTGAACCGTTGGCCACA 60.905 61.111 3.88 0.00 0.00 4.17
31 32 3.670377 GGCTGAACCGTTGGCCAC 61.670 66.667 3.88 0.00 43.59 5.01
32 33 2.058125 TAAGGCTGAACCGTTGGCCA 62.058 55.000 20.40 0.00 46.23 5.36
33 34 1.302993 TAAGGCTGAACCGTTGGCC 60.303 57.895 13.93 13.93 46.52 5.36
34 35 1.873863 GTAAGGCTGAACCGTTGGC 59.126 57.895 0.00 0.00 46.52 4.52
35 36 0.320073 TCGTAAGGCTGAACCGTTGG 60.320 55.000 0.00 0.00 46.52 3.77
36 37 1.393539 CATCGTAAGGCTGAACCGTTG 59.606 52.381 0.00 0.00 46.52 4.10
37 38 1.001633 ACATCGTAAGGCTGAACCGTT 59.998 47.619 0.00 0.00 46.52 4.44
38 39 0.606604 ACATCGTAAGGCTGAACCGT 59.393 50.000 0.00 0.00 46.52 4.83
39 40 0.999406 CACATCGTAAGGCTGAACCG 59.001 55.000 0.00 0.00 46.52 4.44
40 41 1.732259 CACACATCGTAAGGCTGAACC 59.268 52.381 0.00 0.00 39.61 3.62
41 42 2.413837 ACACACATCGTAAGGCTGAAC 58.586 47.619 0.00 0.00 38.47 3.18
42 43 2.831685 ACACACATCGTAAGGCTGAA 57.168 45.000 0.00 0.00 38.47 3.02
43 44 2.831685 AACACACATCGTAAGGCTGA 57.168 45.000 0.00 0.00 38.47 4.26
44 45 3.555956 GGATAACACACATCGTAAGGCTG 59.444 47.826 0.00 0.00 38.47 4.85
45 46 3.451178 AGGATAACACACATCGTAAGGCT 59.549 43.478 0.00 0.00 38.47 4.58
46 47 3.793559 AGGATAACACACATCGTAAGGC 58.206 45.455 0.00 0.00 38.47 4.35
47 48 6.257193 GGTTAAGGATAACACACATCGTAAGG 59.743 42.308 1.65 0.00 42.66 2.69
48 49 6.257193 GGGTTAAGGATAACACACATCGTAAG 59.743 42.308 1.65 0.00 43.58 2.34
49 50 6.108015 GGGTTAAGGATAACACACATCGTAA 58.892 40.000 1.65 0.00 43.58 3.18
50 51 5.187381 TGGGTTAAGGATAACACACATCGTA 59.813 40.000 0.00 0.00 45.92 3.43
51 52 4.020039 TGGGTTAAGGATAACACACATCGT 60.020 41.667 0.00 0.00 45.92 3.73
52 53 4.509616 TGGGTTAAGGATAACACACATCG 58.490 43.478 0.00 0.00 45.92 3.84
58 59 4.901868 TCTGTGTGGGTTAAGGATAACAC 58.098 43.478 0.00 0.00 44.24 3.32
59 60 4.595781 ACTCTGTGTGGGTTAAGGATAACA 59.404 41.667 1.65 0.00 42.66 2.41
60 61 5.161943 ACTCTGTGTGGGTTAAGGATAAC 57.838 43.478 0.00 0.00 40.60 1.89
61 62 6.021030 ACTACTCTGTGTGGGTTAAGGATAA 58.979 40.000 0.00 0.00 0.00 1.75
62 63 5.421056 CACTACTCTGTGTGGGTTAAGGATA 59.579 44.000 0.00 0.00 33.61 2.59
63 64 4.223032 CACTACTCTGTGTGGGTTAAGGAT 59.777 45.833 0.00 0.00 33.61 3.24
64 65 3.576982 CACTACTCTGTGTGGGTTAAGGA 59.423 47.826 0.00 0.00 33.61 3.36
65 66 3.926616 CACTACTCTGTGTGGGTTAAGG 58.073 50.000 0.00 0.00 33.61 2.69
73 74 1.502231 GTGTGCCACTACTCTGTGTG 58.498 55.000 0.00 0.00 36.30 3.82
74 75 0.393077 GGTGTGCCACTACTCTGTGT 59.607 55.000 0.00 0.00 36.30 3.72
75 76 0.320771 GGGTGTGCCACTACTCTGTG 60.321 60.000 0.00 0.00 37.66 3.66
76 77 0.471971 AGGGTGTGCCACTACTCTGT 60.472 55.000 0.00 0.00 34.40 3.41
77 78 0.687354 AAGGGTGTGCCACTACTCTG 59.313 55.000 0.00 0.00 34.40 3.35
78 79 1.348036 GAAAGGGTGTGCCACTACTCT 59.652 52.381 0.00 0.00 34.40 3.24
79 80 1.610886 GGAAAGGGTGTGCCACTACTC 60.611 57.143 0.00 0.00 34.40 2.59
80 81 0.400594 GGAAAGGGTGTGCCACTACT 59.599 55.000 0.00 2.54 34.40 2.57
81 82 0.608308 GGGAAAGGGTGTGCCACTAC 60.608 60.000 0.00 0.00 34.40 2.73
82 83 1.063070 TGGGAAAGGGTGTGCCACTA 61.063 55.000 0.00 0.00 34.40 2.74
83 84 2.391130 TGGGAAAGGGTGTGCCACT 61.391 57.895 0.00 0.00 34.40 4.00
84 85 2.197324 TGGGAAAGGGTGTGCCAC 59.803 61.111 0.00 0.00 36.17 5.01
85 86 2.197324 GTGGGAAAGGGTGTGCCA 59.803 61.111 0.00 0.00 36.17 4.92
86 87 2.197324 TGTGGGAAAGGGTGTGCC 59.803 61.111 0.00 0.00 0.00 5.01
87 88 1.454847 TGTGTGGGAAAGGGTGTGC 60.455 57.895 0.00 0.00 0.00 4.57
88 89 0.182537 TCTGTGTGGGAAAGGGTGTG 59.817 55.000 0.00 0.00 0.00 3.82
89 90 0.474184 CTCTGTGTGGGAAAGGGTGT 59.526 55.000 0.00 0.00 0.00 4.16
90 91 0.474184 ACTCTGTGTGGGAAAGGGTG 59.526 55.000 0.00 0.00 0.00 4.61
91 92 0.765510 GACTCTGTGTGGGAAAGGGT 59.234 55.000 0.00 0.00 0.00 4.34
92 93 0.320771 CGACTCTGTGTGGGAAAGGG 60.321 60.000 0.00 0.00 0.00 3.95
93 94 0.679505 TCGACTCTGTGTGGGAAAGG 59.320 55.000 0.00 0.00 0.00 3.11
94 95 1.337260 CCTCGACTCTGTGTGGGAAAG 60.337 57.143 0.00 0.00 0.00 2.62
95 96 0.679505 CCTCGACTCTGTGTGGGAAA 59.320 55.000 0.00 0.00 0.00 3.13
96 97 1.185618 CCCTCGACTCTGTGTGGGAA 61.186 60.000 0.00 0.00 36.90 3.97
97 98 1.606601 CCCTCGACTCTGTGTGGGA 60.607 63.158 0.00 0.00 36.90 4.37
98 99 1.472662 AACCCTCGACTCTGTGTGGG 61.473 60.000 0.77 0.77 40.37 4.61
99 100 0.319900 CAACCCTCGACTCTGTGTGG 60.320 60.000 0.00 0.00 0.00 4.17
100 101 0.389391 ACAACCCTCGACTCTGTGTG 59.611 55.000 0.00 0.00 0.00 3.82
101 102 1.991121 TACAACCCTCGACTCTGTGT 58.009 50.000 0.00 0.00 0.00 3.72
102 103 2.417379 CCATACAACCCTCGACTCTGTG 60.417 54.545 0.00 0.00 0.00 3.66
103 104 1.825474 CCATACAACCCTCGACTCTGT 59.175 52.381 0.00 0.00 0.00 3.41
104 105 1.137086 CCCATACAACCCTCGACTCTG 59.863 57.143 0.00 0.00 0.00 3.35
105 106 1.486211 CCCATACAACCCTCGACTCT 58.514 55.000 0.00 0.00 0.00 3.24
106 107 0.179081 GCCCATACAACCCTCGACTC 60.179 60.000 0.00 0.00 0.00 3.36
107 108 1.905512 GCCCATACAACCCTCGACT 59.094 57.895 0.00 0.00 0.00 4.18
108 109 1.520787 CGCCCATACAACCCTCGAC 60.521 63.158 0.00 0.00 0.00 4.20
109 110 2.897207 CGCCCATACAACCCTCGA 59.103 61.111 0.00 0.00 0.00 4.04
110 111 2.895372 GCGCCCATACAACCCTCG 60.895 66.667 0.00 0.00 0.00 4.63
111 112 2.895372 CGCGCCCATACAACCCTC 60.895 66.667 0.00 0.00 0.00 4.30
114 115 2.638330 TAGAGCGCGCCCATACAACC 62.638 60.000 30.33 5.74 0.00 3.77
115 116 0.808453 TTAGAGCGCGCCCATACAAC 60.808 55.000 30.33 9.09 0.00 3.32
116 117 0.808453 GTTAGAGCGCGCCCATACAA 60.808 55.000 30.33 10.74 0.00 2.41
117 118 1.227147 GTTAGAGCGCGCCCATACA 60.227 57.895 30.33 4.04 0.00 2.29
137 138 2.779755 GGAAAATCCGCCCCATTTTT 57.220 45.000 0.00 0.00 34.30 1.94
185 186 0.315869 CAATTAATGGCCGTCGTCGC 60.316 55.000 0.00 0.00 35.54 5.19
186 187 0.303493 CCAATTAATGGCCGTCGTCG 59.697 55.000 0.00 0.00 43.80 5.12
208 209 2.762745 ACGCCTTTTCACTACGAACAT 58.237 42.857 0.00 0.00 31.73 2.71
216 217 1.358759 CCGCAAACGCCTTTTCACT 59.641 52.632 0.00 0.00 38.22 3.41
226 227 0.387112 ATGTGTCAATGCCGCAAACG 60.387 50.000 0.00 0.00 39.67 3.60
245 246 2.203195 ACACTTGCCGCTTCAGCA 60.203 55.556 0.00 0.00 42.21 4.41
258 259 3.561429 CGTTGGCATACGCACACT 58.439 55.556 8.75 0.00 41.24 3.55
266 267 3.568686 GTCAACGGCGTTGGCATA 58.431 55.556 41.93 26.12 45.99 3.14
270 271 2.736682 GATCGGTCAACGGCGTTGG 61.737 63.158 41.58 29.63 42.99 3.77
277 278 3.071459 GCACGCTGATCGGTCAACG 62.071 63.158 19.24 19.24 46.45 4.10
299 300 1.838073 TTTCAGGCCGACCTCTTCCC 61.838 60.000 0.00 0.00 46.34 3.97
307 308 3.774702 GCGACGTTTCAGGCCGAC 61.775 66.667 0.00 0.00 0.00 4.79
310 311 1.668151 AGAAGCGACGTTTCAGGCC 60.668 57.895 23.58 0.00 0.00 5.19
311 312 1.222115 ACAGAAGCGACGTTTCAGGC 61.222 55.000 23.58 0.38 0.00 4.85
330 331 1.195442 TCCATCCACAACCGCCTGTA 61.195 55.000 0.00 0.00 0.00 2.74
331 332 2.034066 CCATCCACAACCGCCTGT 59.966 61.111 0.00 0.00 0.00 4.00
333 334 0.893727 GTTTCCATCCACAACCGCCT 60.894 55.000 0.00 0.00 0.00 5.52
334 335 1.175983 TGTTTCCATCCACAACCGCC 61.176 55.000 0.00 0.00 0.00 6.13
349 350 7.106439 TGTGGACATTGTTATGAAGTTGTTT 57.894 32.000 0.00 0.00 35.65 2.83
350 351 6.707440 TGTGGACATTGTTATGAAGTTGTT 57.293 33.333 0.00 0.00 35.65 2.83
352 353 5.920273 GGTTGTGGACATTGTTATGAAGTTG 59.080 40.000 0.00 0.00 35.65 3.16
362 363 6.493115 TCATATTTCAAGGTTGTGGACATTGT 59.507 34.615 3.90 0.00 46.98 2.71
366 367 5.476599 CCTTCATATTTCAAGGTTGTGGACA 59.523 40.000 0.00 0.00 35.34 4.02
393 394 0.240145 TGTTCTATATCGGGCTCGCG 59.760 55.000 0.00 0.00 36.13 5.87
394 395 1.699343 GTGTTCTATATCGGGCTCGC 58.301 55.000 0.00 0.00 36.13 5.03
399 400 1.611977 TGGAGCGTGTTCTATATCGGG 59.388 52.381 0.00 0.00 0.00 5.14
400 401 3.577649 ATGGAGCGTGTTCTATATCGG 57.422 47.619 0.00 0.00 0.00 4.18
407 408 2.627515 ATGCATATGGAGCGTGTTCT 57.372 45.000 0.00 0.00 33.85 3.01
408 409 5.408299 TGTTATATGCATATGGAGCGTGTTC 59.592 40.000 26.21 4.98 32.61 3.18
410 411 4.893608 TGTTATATGCATATGGAGCGTGT 58.106 39.130 26.21 2.92 32.61 4.49
415 433 8.277490 AGCAGAATTGTTATATGCATATGGAG 57.723 34.615 26.21 8.88 39.34 3.86
424 442 6.642540 TGACGCTCTAGCAGAATTGTTATATG 59.357 38.462 2.44 0.00 42.21 1.78
496 514 9.680315 GCGAGTACTTAATAACTGTTGATATCT 57.320 33.333 2.69 0.00 0.00 1.98
500 518 7.220300 CGAAGCGAGTACTTAATAACTGTTGAT 59.780 37.037 2.69 0.00 0.00 2.57
501 519 6.525628 CGAAGCGAGTACTTAATAACTGTTGA 59.474 38.462 2.69 0.00 0.00 3.18
502 520 6.307318 ACGAAGCGAGTACTTAATAACTGTTG 59.693 38.462 2.69 0.00 0.00 3.33
503 521 6.385033 ACGAAGCGAGTACTTAATAACTGTT 58.615 36.000 0.00 0.00 0.00 3.16
504 522 5.947443 ACGAAGCGAGTACTTAATAACTGT 58.053 37.500 0.00 0.00 0.00 3.55
505 523 5.454877 GGACGAAGCGAGTACTTAATAACTG 59.545 44.000 0.00 0.00 0.00 3.16
506 524 5.449725 GGGACGAAGCGAGTACTTAATAACT 60.450 44.000 0.00 0.00 0.00 2.24
508 526 4.398988 TGGGACGAAGCGAGTACTTAATAA 59.601 41.667 0.00 0.00 0.00 1.40
509 527 3.947196 TGGGACGAAGCGAGTACTTAATA 59.053 43.478 0.00 0.00 0.00 0.98
510 528 2.756760 TGGGACGAAGCGAGTACTTAAT 59.243 45.455 0.00 0.00 0.00 1.40
511 529 2.161855 TGGGACGAAGCGAGTACTTAA 58.838 47.619 0.00 0.00 0.00 1.85
513 531 1.183549 ATGGGACGAAGCGAGTACTT 58.816 50.000 0.00 0.00 0.00 2.24
514 532 2.048444 TATGGGACGAAGCGAGTACT 57.952 50.000 0.00 0.00 0.00 2.73
516 534 2.691526 ACATTATGGGACGAAGCGAGTA 59.308 45.455 0.00 0.00 0.00 2.59
517 535 1.480954 ACATTATGGGACGAAGCGAGT 59.519 47.619 0.00 0.00 0.00 4.18
518 536 2.225068 ACATTATGGGACGAAGCGAG 57.775 50.000 0.00 0.00 0.00 5.03
519 537 2.691526 ACTACATTATGGGACGAAGCGA 59.308 45.455 0.00 0.00 0.00 4.93
520 538 2.794910 CACTACATTATGGGACGAAGCG 59.205 50.000 0.00 0.00 0.00 4.68
522 540 7.262772 TCTTAACACTACATTATGGGACGAAG 58.737 38.462 0.00 0.00 0.00 3.79
523 541 7.172868 TCTTAACACTACATTATGGGACGAA 57.827 36.000 0.00 0.00 0.00 3.85
524 542 6.778834 TCTTAACACTACATTATGGGACGA 57.221 37.500 0.00 0.00 0.00 4.20
525 543 7.548075 ACTTTCTTAACACTACATTATGGGACG 59.452 37.037 0.00 0.00 0.00 4.79
526 544 8.788325 ACTTTCTTAACACTACATTATGGGAC 57.212 34.615 0.00 0.00 0.00 4.46
527 545 8.822805 AGACTTTCTTAACACTACATTATGGGA 58.177 33.333 0.00 0.00 0.00 4.37
528 546 9.449719 AAGACTTTCTTAACACTACATTATGGG 57.550 33.333 0.00 0.00 34.42 4.00
561 579 8.807118 CCATACAATAGCTACTTCTCCATTCTA 58.193 37.037 0.00 0.00 0.00 2.10
562 580 7.675062 CCATACAATAGCTACTTCTCCATTCT 58.325 38.462 0.00 0.00 0.00 2.40
563 581 6.370166 GCCATACAATAGCTACTTCTCCATTC 59.630 42.308 0.00 0.00 0.00 2.67
564 582 6.234177 GCCATACAATAGCTACTTCTCCATT 58.766 40.000 0.00 0.00 0.00 3.16
565 583 5.280215 GGCCATACAATAGCTACTTCTCCAT 60.280 44.000 0.00 0.00 0.00 3.41
566 584 4.040461 GGCCATACAATAGCTACTTCTCCA 59.960 45.833 0.00 0.00 0.00 3.86
567 585 4.563786 GGGCCATACAATAGCTACTTCTCC 60.564 50.000 4.39 0.00 0.00 3.71
568 586 4.563786 GGGGCCATACAATAGCTACTTCTC 60.564 50.000 4.39 0.00 0.00 2.87
569 587 3.328050 GGGGCCATACAATAGCTACTTCT 59.672 47.826 4.39 0.00 0.00 2.85
570 588 3.676093 GGGGCCATACAATAGCTACTTC 58.324 50.000 4.39 0.00 0.00 3.01
571 589 2.038557 CGGGGCCATACAATAGCTACTT 59.961 50.000 4.39 0.00 0.00 2.24
572 590 1.623811 CGGGGCCATACAATAGCTACT 59.376 52.381 4.39 0.00 0.00 2.57
573 591 1.944430 GCGGGGCCATACAATAGCTAC 60.944 57.143 4.39 0.00 0.00 3.58
574 592 0.323629 GCGGGGCCATACAATAGCTA 59.676 55.000 4.39 0.00 0.00 3.32
575 593 1.073199 GCGGGGCCATACAATAGCT 59.927 57.895 4.39 0.00 0.00 3.32
576 594 0.323629 TAGCGGGGCCATACAATAGC 59.676 55.000 4.39 0.00 0.00 2.97
577 595 1.899814 TCTAGCGGGGCCATACAATAG 59.100 52.381 4.39 0.00 0.00 1.73
578 596 1.899814 CTCTAGCGGGGCCATACAATA 59.100 52.381 4.39 0.00 0.00 1.90
579 597 0.687354 CTCTAGCGGGGCCATACAAT 59.313 55.000 4.39 0.00 0.00 2.71
580 598 0.689745 ACTCTAGCGGGGCCATACAA 60.690 55.000 4.39 0.00 0.00 2.41
581 599 0.689745 AACTCTAGCGGGGCCATACA 60.690 55.000 4.39 0.00 0.00 2.29
582 600 0.249911 CAACTCTAGCGGGGCCATAC 60.250 60.000 4.39 0.00 0.00 2.39
583 601 2.040009 GCAACTCTAGCGGGGCCATA 62.040 60.000 4.39 0.00 0.00 2.74
584 602 2.911143 CAACTCTAGCGGGGCCAT 59.089 61.111 4.39 0.00 0.00 4.40
585 603 4.096003 GCAACTCTAGCGGGGCCA 62.096 66.667 4.39 0.00 0.00 5.36
586 604 1.759459 ATAGCAACTCTAGCGGGGCC 61.759 60.000 0.00 0.00 37.01 5.80
587 605 0.966920 TATAGCAACTCTAGCGGGGC 59.033 55.000 0.00 0.00 37.01 5.80
682 703 9.474249 GCAAGAAAAGAACGTCATACTTTATAC 57.526 33.333 0.00 0.00 34.18 1.47
716 737 3.094572 AGGCTAGAACCTAAAGCGTGTA 58.905 45.455 0.00 0.00 38.67 2.90
807 831 5.416083 GCGGGGTCTTAATAAAGCAAAATT 58.584 37.500 0.00 0.00 32.36 1.82
814 838 2.092592 AGGTGGCGGGGTCTTAATAAAG 60.093 50.000 0.00 0.00 0.00 1.85
981 1021 2.027625 CTTGTCTCGACCGGTTGCC 61.028 63.158 17.75 7.89 0.00 4.52
1341 2378 8.918658 CACAAAATGTCATGAATTCCTAACTTG 58.081 33.333 2.27 3.67 0.00 3.16
1422 2579 2.028748 GGAGCCCAAAACTAGTGACGTA 60.029 50.000 0.00 0.00 0.00 3.57
1432 2600 3.319122 CCATATAAGCAGGAGCCCAAAAC 59.681 47.826 0.00 0.00 43.56 2.43
1498 2813 1.136305 GGTATCTGCTTGTCGGTGCTA 59.864 52.381 0.00 0.00 0.00 3.49
1700 3017 3.093814 ACCATACATGTCAGTACGGTCA 58.906 45.455 0.00 0.00 35.84 4.02
1714 3031 1.960040 CTCGAGGCTGCCACCATACA 61.960 60.000 22.65 0.00 0.00 2.29
1742 3059 1.597854 CACCTCCACAGCAAAGCGA 60.598 57.895 0.00 0.00 0.00 4.93
1751 3068 3.493176 CGATAGCATCAATCACCTCCACA 60.493 47.826 0.00 0.00 0.00 4.17
1862 3179 6.614694 AGTTGTTGTATCATGTAGGTACCA 57.385 37.500 15.94 0.00 0.00 3.25
1951 3268 1.526887 CGGTGGGGTATCTGCATGT 59.473 57.895 0.00 0.00 0.00 3.21
1973 3290 1.924731 AGGCTTTCCTAAAGGGCAAC 58.075 50.000 0.00 0.00 42.06 4.17
2046 3363 7.982252 AGATCAGTATAACCATCAATCACCAT 58.018 34.615 0.00 0.00 0.00 3.55
2082 3399 3.259625 GGATTAGCGAGAAATAGCCTCCT 59.740 47.826 0.00 0.00 0.00 3.69
2096 3420 4.380531 TCTTAGGCAAATCTGGATTAGCG 58.619 43.478 0.00 0.00 0.00 4.26
2156 3480 1.899814 TCCTGCGTGTAGAAGGTTGAT 59.100 47.619 0.00 0.00 46.52 2.57
2159 3483 1.207329 GGATCCTGCGTGTAGAAGGTT 59.793 52.381 3.84 0.00 46.52 3.50
2341 3674 5.163550 GGCATTACAGGGGAAGACAATAAAC 60.164 44.000 0.00 0.00 0.00 2.01
2350 3686 7.004086 TCTATATTTTGGCATTACAGGGGAAG 58.996 38.462 0.00 0.00 0.00 3.46
2466 3802 6.546403 ACATACTACAACCACATATCTCTCGT 59.454 38.462 0.00 0.00 0.00 4.18
2496 3832 5.830912 ACAATTTGAATGAGTGAGCGAAAA 58.169 33.333 2.79 0.00 0.00 2.29
2639 3975 2.853662 GCTACCGCTACGTATGTGTCTG 60.854 54.545 0.00 0.00 0.00 3.51
2641 3977 1.751552 GCTACCGCTACGTATGTGTC 58.248 55.000 0.00 0.00 0.00 3.67
2642 3978 0.028505 CGCTACCGCTACGTATGTGT 59.971 55.000 0.00 0.00 0.00 3.72
2646 3982 0.305922 GTGTCGCTACCGCTACGTAT 59.694 55.000 0.00 0.00 34.81 3.06
2648 3984 2.482374 GTGTCGCTACCGCTACGT 59.518 61.111 0.00 0.00 34.81 3.57
2679 4015 3.441572 CGATGGAAGAATTATGGGCATCC 59.558 47.826 0.00 0.00 0.00 3.51
2683 4019 2.508526 AGCGATGGAAGAATTATGGGC 58.491 47.619 0.00 0.00 0.00 5.36
2690 4026 5.167121 CGATTGATCTAGCGATGGAAGAAT 58.833 41.667 9.19 0.00 0.00 2.40
2704 4040 7.439157 TCAATGTTCAAGAAACGATTGATCT 57.561 32.000 0.00 0.00 41.02 2.75
2713 4049 5.407387 AGCAATGCATCAATGTTCAAGAAAC 59.593 36.000 8.35 0.00 38.43 2.78
2751 4089 7.536625 AGATCTATAGCTAAAGGGACCTAACA 58.463 38.462 0.00 0.00 0.00 2.41
2783 4121 2.671070 CCCGTGCCTCCTCACAAT 59.329 61.111 0.00 0.00 36.80 2.71
2798 4136 1.148498 CTATTTGACCCTCCGGCCC 59.852 63.158 0.00 0.00 0.00 5.80
2800 4138 0.533085 GAGCTATTTGACCCTCCGGC 60.533 60.000 0.00 0.00 0.00 6.13
2803 4141 2.420687 CCACTGAGCTATTTGACCCTCC 60.421 54.545 0.00 0.00 0.00 4.30
2804 4142 2.501723 TCCACTGAGCTATTTGACCCTC 59.498 50.000 0.00 0.00 0.00 4.30
2805 4143 2.237392 GTCCACTGAGCTATTTGACCCT 59.763 50.000 0.00 0.00 0.00 4.34
2821 4159 5.646793 GGGAGAAAATGGTACTTAAGTCCAC 59.353 44.000 21.57 12.67 33.91 4.02
2837 4175 5.165961 AGATGATTCGTGAAGGGAGAAAA 57.834 39.130 0.00 0.00 0.00 2.29
2846 4184 3.628032 ACTAGAGCGAGATGATTCGTGAA 59.372 43.478 0.00 0.00 42.38 3.18
2860 4198 1.281899 GGCTTAACTGCACTAGAGCG 58.718 55.000 7.68 5.25 37.31 5.03
2862 4200 3.319137 TGTGGCTTAACTGCACTAGAG 57.681 47.619 0.00 0.00 34.04 2.43
2868 4206 4.002982 CACTATCTTGTGGCTTAACTGCA 58.997 43.478 0.00 0.00 34.56 4.41
2877 4215 1.002366 CTCGTGCACTATCTTGTGGC 58.998 55.000 16.19 0.00 38.31 5.01
2882 4220 1.135915 CAGAGCCTCGTGCACTATCTT 59.864 52.381 16.19 0.00 44.83 2.40
2890 4228 0.175760 TTGGTATCAGAGCCTCGTGC 59.824 55.000 0.00 0.00 41.71 5.34
2897 4235 7.765307 TCAATCTTTTGAATTGGTATCAGAGC 58.235 34.615 0.00 0.00 38.90 4.09
2912 4250 6.054295 CCTCTAGGTCCATCTCAATCTTTTG 58.946 44.000 0.00 0.00 0.00 2.44
2967 4305 9.289303 CGCACTTTCATAAAATTGCTAATAAGT 57.711 29.630 2.56 0.00 44.49 2.24
2968 4306 8.745837 CCGCACTTTCATAAAATTGCTAATAAG 58.254 33.333 2.56 0.00 44.49 1.73
2992 4332 5.547465 TGTTAGGCTCACATTTATATCCCG 58.453 41.667 0.00 0.00 0.00 5.14
2993 4333 8.299570 CAATTGTTAGGCTCACATTTATATCCC 58.700 37.037 1.78 0.00 0.00 3.85
3031 4371 2.472695 TGTGACTTATGCACTGGGAC 57.527 50.000 0.00 0.00 37.18 4.46
3040 4380 5.375417 TGCACCTTCAAATGTGACTTATG 57.625 39.130 2.81 0.00 34.37 1.90
3053 4393 0.813610 CAGGTCGTGTTGCACCTTCA 60.814 55.000 0.00 0.00 41.41 3.02
3055 4395 1.525995 CCAGGTCGTGTTGCACCTT 60.526 57.895 0.00 0.00 41.41 3.50
3081 4421 4.849235 AGTTTCTCCTTCTCCTCCAATCTT 59.151 41.667 0.00 0.00 0.00 2.40
3083 4423 4.223923 TCAGTTTCTCCTTCTCCTCCAATC 59.776 45.833 0.00 0.00 0.00 2.67
3088 4428 4.940654 CCAATTCAGTTTCTCCTTCTCCTC 59.059 45.833 0.00 0.00 0.00 3.71
3106 4446 6.295859 GGCTTTAATTGAAAGGAGGACCAATT 60.296 38.462 0.00 0.00 44.21 2.32
3108 4448 4.526650 GGCTTTAATTGAAAGGAGGACCAA 59.473 41.667 0.00 0.00 44.21 3.67
3109 4449 4.086457 GGCTTTAATTGAAAGGAGGACCA 58.914 43.478 0.00 0.00 44.21 4.02
3125 4465 9.435570 ACTAGTAAGAGATAAATCAGGGCTTTA 57.564 33.333 0.00 0.00 0.00 1.85
3134 4474 9.863845 GGGCATTCTACTAGTAAGAGATAAATC 57.136 37.037 3.76 0.00 0.00 2.17
3139 4479 5.241949 CACGGGCATTCTACTAGTAAGAGAT 59.758 44.000 3.76 0.00 0.00 2.75
3147 4487 0.102481 ACGCACGGGCATTCTACTAG 59.898 55.000 11.77 0.00 41.24 2.57
3148 4488 0.533491 AACGCACGGGCATTCTACTA 59.467 50.000 11.77 0.00 41.24 1.82
3149 4489 1.019278 CAACGCACGGGCATTCTACT 61.019 55.000 11.77 0.00 41.24 2.57
3150 4490 1.423845 CAACGCACGGGCATTCTAC 59.576 57.895 11.77 0.00 41.24 2.59
3151 4491 2.395360 GCAACGCACGGGCATTCTA 61.395 57.895 11.77 0.00 41.24 2.10
3152 4492 3.737172 GCAACGCACGGGCATTCT 61.737 61.111 11.77 0.00 41.24 2.40
3153 4493 4.776647 GGCAACGCACGGGCATTC 62.777 66.667 11.77 0.00 41.24 2.67
3169 4509 8.330466 TCATATATAATTTTGTTAGCCCGTGG 57.670 34.615 0.00 0.00 0.00 4.94
3170 4510 9.825972 CTTCATATATAATTTTGTTAGCCCGTG 57.174 33.333 0.00 0.00 0.00 4.94
3171 4511 9.787435 TCTTCATATATAATTTTGTTAGCCCGT 57.213 29.630 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.