Multiple sequence alignment - TraesCS4A01G227700

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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 TraesCS4A01G227700 chr4A 100.000 3319 0 0 1 3319 535874014 535870696 0.000000e+00 6130
1 TraesCS4A01G227700 chr4A 97.983 2975 26 7 348 3319 35615015 35612072 0.000000e+00 5131
2 TraesCS4A01G227700 chr7B 99.058 2972 25 1 348 3319 446152841 446155809 0.000000e+00 5330
3 TraesCS4A01G227700 chr7B 98.754 2969 23 2 348 3316 245984002 245986956 0.000000e+00 5265
4 TraesCS4A01G227700 chr7B 98.250 2972 43 2 348 3319 582235322 582238284 0.000000e+00 5192
5 TraesCS4A01G227700 chr7B 98.150 2973 36 4 348 3319 156960754 156963708 0.000000e+00 5168
6 TraesCS4A01G227700 chr7B 99.137 2780 21 1 540 3319 446171847 446174623 0.000000e+00 4998
7 TraesCS4A01G227700 chr5B 98.856 2973 25 1 347 3319 513600267 513603230 0.000000e+00 5293
8 TraesCS4A01G227700 chr5B 96.995 1564 27 10 331 1893 321476072 321474528 0.000000e+00 2610
9 TraesCS4A01G227700 chr2B 98.126 2988 30 7 342 3319 49092670 49095641 0.000000e+00 5184
10 TraesCS4A01G227700 chr2B 98.016 2974 34 4 346 3319 338772767 338769819 0.000000e+00 5142
11 TraesCS4A01G227700 chr2A 98.149 2972 43 4 348 3319 568410549 568407590 0.000000e+00 5173
12 TraesCS4A01G227700 chr4B 97.914 2972 46 3 348 3319 15939349 15936394 0.000000e+00 5131
13 TraesCS4A01G227700 chr4B 94.857 350 12 4 1 348 89405844 89405499 2.910000e-150 542
14 TraesCS4A01G227700 chr3B 93.125 480 27 6 348 824 215616245 215615769 0.000000e+00 699
15 TraesCS4A01G227700 chr6B 92.067 479 28 7 346 824 48489773 48489305 0.000000e+00 665
16 TraesCS4A01G227700 chr4D 95.089 224 8 2 125 348 61129048 61129268 1.890000e-92 350
17 TraesCS4A01G227700 chr4D 95.804 143 4 1 1 141 61128889 61129031 2.580000e-56 230


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 TraesCS4A01G227700 chr4A 535870696 535874014 3318 True 6130 6130 100.000 1 3319 1 chr4A.!!$R2 3318
1 TraesCS4A01G227700 chr4A 35612072 35615015 2943 True 5131 5131 97.983 348 3319 1 chr4A.!!$R1 2971
2 TraesCS4A01G227700 chr7B 446152841 446155809 2968 False 5330 5330 99.058 348 3319 1 chr7B.!!$F3 2971
3 TraesCS4A01G227700 chr7B 245984002 245986956 2954 False 5265 5265 98.754 348 3316 1 chr7B.!!$F2 2968
4 TraesCS4A01G227700 chr7B 582235322 582238284 2962 False 5192 5192 98.250 348 3319 1 chr7B.!!$F5 2971
5 TraesCS4A01G227700 chr7B 156960754 156963708 2954 False 5168 5168 98.150 348 3319 1 chr7B.!!$F1 2971
6 TraesCS4A01G227700 chr7B 446171847 446174623 2776 False 4998 4998 99.137 540 3319 1 chr7B.!!$F4 2779
7 TraesCS4A01G227700 chr5B 513600267 513603230 2963 False 5293 5293 98.856 347 3319 1 chr5B.!!$F1 2972
8 TraesCS4A01G227700 chr5B 321474528 321476072 1544 True 2610 2610 96.995 331 1893 1 chr5B.!!$R1 1562
9 TraesCS4A01G227700 chr2B 49092670 49095641 2971 False 5184 5184 98.126 342 3319 1 chr2B.!!$F1 2977
10 TraesCS4A01G227700 chr2B 338769819 338772767 2948 True 5142 5142 98.016 346 3319 1 chr2B.!!$R1 2973
11 TraesCS4A01G227700 chr2A 568407590 568410549 2959 True 5173 5173 98.149 348 3319 1 chr2A.!!$R1 2971
12 TraesCS4A01G227700 chr4B 15936394 15939349 2955 True 5131 5131 97.914 348 3319 1 chr4B.!!$R1 2971

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
74 75 0.035056 GAGGGTGGGAGGTTGACATG 60.035 60.0 0.00 0.0 0.00 3.21 F
130 131 0.108138 CTTCCCAGCGAACGGAATCT 60.108 55.0 0.00 0.0 37.52 2.40 F
338 339 0.240945 GGGCCACATTCGTTTGACTG 59.759 55.0 4.39 0.0 0.00 3.51 F
867 922 0.322277 CATCAAGCTGTGCCTCCTGT 60.322 55.0 0.00 0.0 0.00 4.00 F
1531 1589 1.309499 CGACTTCCTCACTCGCCTCT 61.309 60.0 0.00 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1081 1136 1.062488 ACAGGGAAGGCCAACTCAGT 61.062 55.000 5.01 0.00 35.15 3.41 R
1605 1663 1.358402 CTCCTCAGATCGCACCTCG 59.642 63.158 0.00 0.00 40.15 4.63 R
2163 2221 0.672401 GAACATGAGAAACGGCGGGA 60.672 55.000 13.24 0.00 0.00 5.14 R
2166 2224 2.004583 TAGGAACATGAGAAACGGCG 57.995 50.000 4.80 4.80 0.00 6.46 R
2405 2463 2.203922 TGGTGGAGGTGGCAGCTA 60.204 61.111 20.63 1.41 0.00 3.32 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
24 25 6.530019 TTCAGCATGTTATACTCTCTGTCA 57.470 37.500 0.00 0.00 37.40 3.58
25 26 6.721704 TCAGCATGTTATACTCTCTGTCAT 57.278 37.500 0.00 0.00 37.40 3.06
26 27 7.823745 TCAGCATGTTATACTCTCTGTCATA 57.176 36.000 0.00 0.00 37.40 2.15
27 28 7.880105 TCAGCATGTTATACTCTCTGTCATAG 58.120 38.462 0.00 0.00 37.40 2.23
28 29 7.040132 TCAGCATGTTATACTCTCTGTCATAGG 60.040 40.741 0.00 0.00 37.40 2.57
29 30 7.007116 AGCATGTTATACTCTCTGTCATAGGA 58.993 38.462 0.00 0.00 0.00 2.94
30 31 7.176515 AGCATGTTATACTCTCTGTCATAGGAG 59.823 40.741 0.00 0.00 32.91 3.69
31 32 7.040062 GCATGTTATACTCTCTGTCATAGGAGT 60.040 40.741 0.00 0.00 39.08 3.85
32 33 8.855110 CATGTTATACTCTCTGTCATAGGAGTT 58.145 37.037 0.00 0.00 37.76 3.01
33 34 8.824756 TGTTATACTCTCTGTCATAGGAGTTT 57.175 34.615 0.00 0.00 37.76 2.66
34 35 9.256228 TGTTATACTCTCTGTCATAGGAGTTTT 57.744 33.333 0.00 0.00 37.76 2.43
35 36 9.522804 GTTATACTCTCTGTCATAGGAGTTTTG 57.477 37.037 0.00 0.00 37.76 2.44
36 37 7.726033 ATACTCTCTGTCATAGGAGTTTTGT 57.274 36.000 0.00 0.00 37.76 2.83
37 38 6.426646 ACTCTCTGTCATAGGAGTTTTGTT 57.573 37.500 0.00 0.00 35.01 2.83
38 39 6.831976 ACTCTCTGTCATAGGAGTTTTGTTT 58.168 36.000 0.00 0.00 35.01 2.83
39 40 7.283329 ACTCTCTGTCATAGGAGTTTTGTTTT 58.717 34.615 0.00 0.00 35.01 2.43
40 41 7.227512 ACTCTCTGTCATAGGAGTTTTGTTTTG 59.772 37.037 0.00 0.00 35.01 2.44
41 42 7.054124 TCTCTGTCATAGGAGTTTTGTTTTGT 58.946 34.615 0.00 0.00 0.00 2.83
42 43 7.012327 TCTCTGTCATAGGAGTTTTGTTTTGTG 59.988 37.037 0.00 0.00 0.00 3.33
43 44 5.587289 TGTCATAGGAGTTTTGTTTTGTGC 58.413 37.500 0.00 0.00 0.00 4.57
44 45 5.359576 TGTCATAGGAGTTTTGTTTTGTGCT 59.640 36.000 0.00 0.00 0.00 4.40
45 46 6.544197 TGTCATAGGAGTTTTGTTTTGTGCTA 59.456 34.615 0.00 0.00 0.00 3.49
46 47 6.856426 GTCATAGGAGTTTTGTTTTGTGCTAC 59.144 38.462 0.00 0.00 0.00 3.58
47 48 6.544197 TCATAGGAGTTTTGTTTTGTGCTACA 59.456 34.615 0.00 0.00 0.00 2.74
48 49 5.248870 AGGAGTTTTGTTTTGTGCTACAG 57.751 39.130 0.00 0.00 0.00 2.74
49 50 4.705023 AGGAGTTTTGTTTTGTGCTACAGT 59.295 37.500 0.00 0.00 0.00 3.55
50 51 5.185056 AGGAGTTTTGTTTTGTGCTACAGTT 59.815 36.000 0.00 0.00 0.00 3.16
51 52 6.376018 AGGAGTTTTGTTTTGTGCTACAGTTA 59.624 34.615 0.00 0.00 0.00 2.24
52 53 6.471198 GGAGTTTTGTTTTGTGCTACAGTTAC 59.529 38.462 0.00 0.00 0.00 2.50
53 54 6.915349 AGTTTTGTTTTGTGCTACAGTTACA 58.085 32.000 0.00 0.00 0.00 2.41
54 55 7.027161 AGTTTTGTTTTGTGCTACAGTTACAG 58.973 34.615 0.00 0.00 0.00 2.74
55 56 5.493133 TTGTTTTGTGCTACAGTTACAGG 57.507 39.130 0.00 0.00 0.00 4.00
56 57 4.771903 TGTTTTGTGCTACAGTTACAGGA 58.228 39.130 0.00 0.00 0.00 3.86
57 58 4.814234 TGTTTTGTGCTACAGTTACAGGAG 59.186 41.667 0.00 0.00 0.00 3.69
58 59 3.678056 TTGTGCTACAGTTACAGGAGG 57.322 47.619 0.00 0.00 0.00 4.30
59 60 1.899814 TGTGCTACAGTTACAGGAGGG 59.100 52.381 0.00 0.00 0.00 4.30
60 61 1.900486 GTGCTACAGTTACAGGAGGGT 59.100 52.381 0.00 0.00 0.00 4.34
61 62 1.899814 TGCTACAGTTACAGGAGGGTG 59.100 52.381 0.00 0.00 0.00 4.61
62 63 1.207329 GCTACAGTTACAGGAGGGTGG 59.793 57.143 0.00 0.00 0.00 4.61
63 64 1.831736 CTACAGTTACAGGAGGGTGGG 59.168 57.143 0.00 0.00 0.00 4.61
64 65 0.192566 ACAGTTACAGGAGGGTGGGA 59.807 55.000 0.00 0.00 0.00 4.37
65 66 0.905357 CAGTTACAGGAGGGTGGGAG 59.095 60.000 0.00 0.00 0.00 4.30
66 67 0.252742 AGTTACAGGAGGGTGGGAGG 60.253 60.000 0.00 0.00 0.00 4.30
67 68 0.546988 GTTACAGGAGGGTGGGAGGT 60.547 60.000 0.00 0.00 0.00 3.85
68 69 0.195096 TTACAGGAGGGTGGGAGGTT 59.805 55.000 0.00 0.00 0.00 3.50
69 70 0.546747 TACAGGAGGGTGGGAGGTTG 60.547 60.000 0.00 0.00 0.00 3.77
70 71 1.538876 CAGGAGGGTGGGAGGTTGA 60.539 63.158 0.00 0.00 0.00 3.18
71 72 1.539124 AGGAGGGTGGGAGGTTGAC 60.539 63.158 0.00 0.00 0.00 3.18
72 73 1.846124 GGAGGGTGGGAGGTTGACA 60.846 63.158 0.00 0.00 0.00 3.58
73 74 1.208165 GGAGGGTGGGAGGTTGACAT 61.208 60.000 0.00 0.00 0.00 3.06
74 75 0.035056 GAGGGTGGGAGGTTGACATG 60.035 60.000 0.00 0.00 0.00 3.21
75 76 0.475632 AGGGTGGGAGGTTGACATGA 60.476 55.000 0.00 0.00 0.00 3.07
76 77 0.322546 GGGTGGGAGGTTGACATGAC 60.323 60.000 0.00 0.00 0.00 3.06
77 78 0.400213 GGTGGGAGGTTGACATGACA 59.600 55.000 0.00 0.00 0.00 3.58
78 79 1.004745 GGTGGGAGGTTGACATGACAT 59.995 52.381 0.00 0.00 0.00 3.06
79 80 2.555227 GGTGGGAGGTTGACATGACATT 60.555 50.000 0.00 0.00 0.00 2.71
80 81 3.308117 GGTGGGAGGTTGACATGACATTA 60.308 47.826 0.00 0.00 0.00 1.90
81 82 4.331968 GTGGGAGGTTGACATGACATTAA 58.668 43.478 0.00 0.00 0.00 1.40
82 83 4.396166 GTGGGAGGTTGACATGACATTAAG 59.604 45.833 0.00 0.00 0.00 1.85
83 84 4.288366 TGGGAGGTTGACATGACATTAAGA 59.712 41.667 0.00 0.00 0.00 2.10
84 85 5.222027 TGGGAGGTTGACATGACATTAAGAA 60.222 40.000 0.00 0.00 0.00 2.52
85 86 5.355350 GGGAGGTTGACATGACATTAAGAAG 59.645 44.000 0.00 0.00 0.00 2.85
86 87 5.940470 GGAGGTTGACATGACATTAAGAAGT 59.060 40.000 0.00 0.00 0.00 3.01
87 88 6.431234 GGAGGTTGACATGACATTAAGAAGTT 59.569 38.462 0.00 0.00 0.00 2.66
88 89 7.040409 GGAGGTTGACATGACATTAAGAAGTTT 60.040 37.037 0.00 0.00 0.00 2.66
89 90 7.651808 AGGTTGACATGACATTAAGAAGTTTG 58.348 34.615 0.00 0.00 0.00 2.93
90 91 7.285401 AGGTTGACATGACATTAAGAAGTTTGT 59.715 33.333 0.00 0.00 0.00 2.83
91 92 8.564574 GGTTGACATGACATTAAGAAGTTTGTA 58.435 33.333 0.00 0.00 0.00 2.41
92 93 9.599322 GTTGACATGACATTAAGAAGTTTGTAG 57.401 33.333 0.00 0.00 0.00 2.74
93 94 8.322906 TGACATGACATTAAGAAGTTTGTAGG 57.677 34.615 0.00 0.00 0.00 3.18
94 95 7.094805 TGACATGACATTAAGAAGTTTGTAGGC 60.095 37.037 0.00 0.00 0.00 3.93
95 96 6.714810 ACATGACATTAAGAAGTTTGTAGGCA 59.285 34.615 0.00 0.00 0.00 4.75
96 97 6.801539 TGACATTAAGAAGTTTGTAGGCAG 57.198 37.500 0.00 0.00 0.00 4.85
97 98 5.705441 TGACATTAAGAAGTTTGTAGGCAGG 59.295 40.000 0.00 0.00 0.00 4.85
98 99 5.010282 ACATTAAGAAGTTTGTAGGCAGGG 58.990 41.667 0.00 0.00 0.00 4.45
99 100 1.911057 AAGAAGTTTGTAGGCAGGGC 58.089 50.000 0.00 0.00 0.00 5.19
111 112 2.967270 GCAGGGCCATGATTATCCC 58.033 57.895 24.18 0.00 39.05 3.85
113 114 1.203100 GCAGGGCCATGATTATCCCTT 60.203 52.381 24.18 0.00 46.52 3.95
114 115 2.800250 CAGGGCCATGATTATCCCTTC 58.200 52.381 13.35 0.00 46.52 3.46
115 116 1.713078 AGGGCCATGATTATCCCTTCC 59.287 52.381 6.18 0.00 46.52 3.46
116 117 1.272704 GGGCCATGATTATCCCTTCCC 60.273 57.143 4.39 0.00 35.87 3.97
117 118 1.428912 GGCCATGATTATCCCTTCCCA 59.571 52.381 0.00 0.00 0.00 4.37
118 119 2.556114 GGCCATGATTATCCCTTCCCAG 60.556 54.545 0.00 0.00 0.00 4.45
119 120 2.800250 CCATGATTATCCCTTCCCAGC 58.200 52.381 0.00 0.00 0.00 4.85
120 121 2.430465 CATGATTATCCCTTCCCAGCG 58.570 52.381 0.00 0.00 0.00 5.18
121 122 1.801242 TGATTATCCCTTCCCAGCGA 58.199 50.000 0.00 0.00 0.00 4.93
122 123 2.123589 TGATTATCCCTTCCCAGCGAA 58.876 47.619 0.00 0.00 0.00 4.70
123 124 2.158813 TGATTATCCCTTCCCAGCGAAC 60.159 50.000 0.00 0.00 0.00 3.95
124 125 0.177141 TTATCCCTTCCCAGCGAACG 59.823 55.000 0.00 0.00 0.00 3.95
125 126 1.682451 TATCCCTTCCCAGCGAACGG 61.682 60.000 0.00 0.00 0.00 4.44
126 127 3.702048 CCCTTCCCAGCGAACGGA 61.702 66.667 0.00 0.00 30.41 4.69
127 128 2.345991 CCTTCCCAGCGAACGGAA 59.654 61.111 0.00 0.00 36.69 4.30
128 129 1.078426 CCTTCCCAGCGAACGGAAT 60.078 57.895 0.00 0.00 37.52 3.01
129 130 1.090052 CCTTCCCAGCGAACGGAATC 61.090 60.000 0.00 0.00 37.52 2.52
130 131 0.108138 CTTCCCAGCGAACGGAATCT 60.108 55.000 0.00 0.00 37.52 2.40
131 132 0.323629 TTCCCAGCGAACGGAATCTT 59.676 50.000 0.00 0.00 33.14 2.40
132 133 1.187974 TCCCAGCGAACGGAATCTTA 58.812 50.000 0.00 0.00 0.00 2.10
133 134 1.136305 TCCCAGCGAACGGAATCTTAG 59.864 52.381 0.00 0.00 0.00 2.18
134 135 1.134788 CCCAGCGAACGGAATCTTAGT 60.135 52.381 0.00 0.00 0.00 2.24
135 136 2.100252 CCCAGCGAACGGAATCTTAGTA 59.900 50.000 0.00 0.00 0.00 1.82
136 137 3.114065 CCAGCGAACGGAATCTTAGTAC 58.886 50.000 0.00 0.00 0.00 2.73
137 138 3.428452 CCAGCGAACGGAATCTTAGTACA 60.428 47.826 0.00 0.00 0.00 2.90
138 139 3.791887 CAGCGAACGGAATCTTAGTACAG 59.208 47.826 0.00 0.00 0.00 2.74
139 140 3.693085 AGCGAACGGAATCTTAGTACAGA 59.307 43.478 0.00 0.00 0.00 3.41
140 141 4.338682 AGCGAACGGAATCTTAGTACAGAT 59.661 41.667 0.00 0.00 34.78 2.90
141 142 5.530171 AGCGAACGGAATCTTAGTACAGATA 59.470 40.000 0.00 0.00 32.84 1.98
142 143 5.624491 GCGAACGGAATCTTAGTACAGATAC 59.376 44.000 0.00 0.00 32.84 2.24
143 144 6.141462 CGAACGGAATCTTAGTACAGATACC 58.859 44.000 0.00 0.00 32.84 2.73
144 145 6.017275 CGAACGGAATCTTAGTACAGATACCT 60.017 42.308 0.00 0.00 32.84 3.08
145 146 6.636562 ACGGAATCTTAGTACAGATACCTG 57.363 41.667 0.00 0.00 45.76 4.00
146 147 5.535406 ACGGAATCTTAGTACAGATACCTGG 59.465 44.000 0.00 0.00 44.60 4.45
147 148 5.565045 CGGAATCTTAGTACAGATACCTGGC 60.565 48.000 0.00 0.00 44.60 4.85
148 149 5.304614 GGAATCTTAGTACAGATACCTGGCA 59.695 44.000 0.00 0.00 44.60 4.92
149 150 6.183360 GGAATCTTAGTACAGATACCTGGCAA 60.183 42.308 0.00 0.00 44.60 4.52
150 151 6.808321 ATCTTAGTACAGATACCTGGCAAA 57.192 37.500 0.00 0.00 44.60 3.68
151 152 6.614694 TCTTAGTACAGATACCTGGCAAAA 57.385 37.500 0.00 0.00 44.60 2.44
152 153 6.640518 TCTTAGTACAGATACCTGGCAAAAG 58.359 40.000 0.00 0.00 44.60 2.27
153 154 4.910458 AGTACAGATACCTGGCAAAAGT 57.090 40.909 0.00 0.00 44.60 2.66
154 155 7.398047 TCTTAGTACAGATACCTGGCAAAAGTA 59.602 37.037 0.00 0.00 44.60 2.24
155 156 5.731591 AGTACAGATACCTGGCAAAAGTAC 58.268 41.667 0.00 9.82 44.60 2.73
156 157 4.910458 ACAGATACCTGGCAAAAGTACT 57.090 40.909 0.00 0.00 44.60 2.73
157 158 5.242795 ACAGATACCTGGCAAAAGTACTT 57.757 39.130 1.12 1.12 44.60 2.24
158 159 5.246307 ACAGATACCTGGCAAAAGTACTTC 58.754 41.667 8.95 0.00 44.60 3.01
159 160 5.221843 ACAGATACCTGGCAAAAGTACTTCA 60.222 40.000 8.95 1.50 44.60 3.02
160 161 5.352569 CAGATACCTGGCAAAAGTACTTCAG 59.647 44.000 8.95 11.33 36.77 3.02
161 162 3.577805 ACCTGGCAAAAGTACTTCAGT 57.422 42.857 8.95 0.94 0.00 3.41
162 163 3.214328 ACCTGGCAAAAGTACTTCAGTG 58.786 45.455 8.95 8.82 0.00 3.66
163 164 2.030805 CCTGGCAAAAGTACTTCAGTGC 60.031 50.000 21.79 21.79 0.00 4.40
164 165 2.706555 GGCAAAAGTACTTCAGTGCC 57.293 50.000 28.23 28.23 44.23 5.01
165 166 2.230660 GGCAAAAGTACTTCAGTGCCT 58.769 47.619 31.48 8.71 46.42 4.75
166 167 3.408634 GGCAAAAGTACTTCAGTGCCTA 58.591 45.455 31.48 0.00 46.42 3.93
167 168 4.010349 GGCAAAAGTACTTCAGTGCCTAT 58.990 43.478 31.48 7.50 46.42 2.57
168 169 4.459337 GGCAAAAGTACTTCAGTGCCTATT 59.541 41.667 31.48 12.07 46.42 1.73
169 170 5.048013 GGCAAAAGTACTTCAGTGCCTATTT 60.048 40.000 31.48 11.50 46.42 1.40
170 171 5.858581 GCAAAAGTACTTCAGTGCCTATTTG 59.141 40.000 20.31 13.31 0.00 2.32
171 172 6.381801 CAAAAGTACTTCAGTGCCTATTTGG 58.618 40.000 8.95 0.00 39.35 3.28
183 184 3.998913 CCTATTTGGCAAATTTGGGGT 57.001 42.857 28.56 7.93 32.38 4.95
184 185 3.608796 CCTATTTGGCAAATTTGGGGTG 58.391 45.455 28.56 11.27 32.38 4.61
185 186 3.008923 CCTATTTGGCAAATTTGGGGTGT 59.991 43.478 28.56 6.47 32.38 4.16
186 187 3.591695 ATTTGGCAAATTTGGGGTGTT 57.408 38.095 19.39 0.00 0.00 3.32
187 188 4.713792 ATTTGGCAAATTTGGGGTGTTA 57.286 36.364 19.39 0.00 0.00 2.41
188 189 3.477210 TTGGCAAATTTGGGGTGTTAC 57.523 42.857 19.47 0.35 0.00 2.50
189 190 2.683768 TGGCAAATTTGGGGTGTTACT 58.316 42.857 19.47 0.00 0.00 2.24
190 191 3.845860 TGGCAAATTTGGGGTGTTACTA 58.154 40.909 19.47 0.00 0.00 1.82
191 192 3.829601 TGGCAAATTTGGGGTGTTACTAG 59.170 43.478 19.47 0.00 0.00 2.57
192 193 4.083565 GGCAAATTTGGGGTGTTACTAGA 58.916 43.478 19.47 0.00 0.00 2.43
193 194 4.082408 GGCAAATTTGGGGTGTTACTAGAC 60.082 45.833 19.47 0.00 0.00 2.59
194 195 4.379082 GCAAATTTGGGGTGTTACTAGACG 60.379 45.833 19.47 0.00 0.00 4.18
195 196 4.628963 AATTTGGGGTGTTACTAGACGT 57.371 40.909 0.00 0.00 0.00 4.34
196 197 4.628963 ATTTGGGGTGTTACTAGACGTT 57.371 40.909 0.00 0.00 0.00 3.99
197 198 3.389925 TTGGGGTGTTACTAGACGTTG 57.610 47.619 0.00 0.00 0.00 4.10
198 199 2.596346 TGGGGTGTTACTAGACGTTGA 58.404 47.619 0.00 0.00 0.00 3.18
199 200 2.559668 TGGGGTGTTACTAGACGTTGAG 59.440 50.000 0.00 0.00 0.00 3.02
200 201 2.094338 GGGGTGTTACTAGACGTTGAGG 60.094 54.545 0.00 0.00 0.00 3.86
201 202 2.821969 GGGTGTTACTAGACGTTGAGGA 59.178 50.000 0.00 0.00 0.00 3.71
202 203 3.256631 GGGTGTTACTAGACGTTGAGGAA 59.743 47.826 0.00 0.00 0.00 3.36
203 204 4.262164 GGGTGTTACTAGACGTTGAGGAAA 60.262 45.833 0.00 0.00 0.00 3.13
204 205 4.922103 GGTGTTACTAGACGTTGAGGAAAG 59.078 45.833 0.00 0.00 0.00 2.62
205 206 5.278660 GGTGTTACTAGACGTTGAGGAAAGA 60.279 44.000 0.00 0.00 0.00 2.52
206 207 5.857517 GTGTTACTAGACGTTGAGGAAAGAG 59.142 44.000 0.00 0.00 0.00 2.85
207 208 5.533903 TGTTACTAGACGTTGAGGAAAGAGT 59.466 40.000 0.00 0.00 0.00 3.24
208 209 6.712095 TGTTACTAGACGTTGAGGAAAGAGTA 59.288 38.462 0.00 0.00 0.00 2.59
209 210 5.625921 ACTAGACGTTGAGGAAAGAGTAC 57.374 43.478 0.00 0.00 0.00 2.73
210 211 5.315348 ACTAGACGTTGAGGAAAGAGTACT 58.685 41.667 0.00 0.00 0.00 2.73
211 212 6.471146 ACTAGACGTTGAGGAAAGAGTACTA 58.529 40.000 0.00 0.00 0.00 1.82
212 213 5.883503 AGACGTTGAGGAAAGAGTACTAG 57.116 43.478 0.00 0.00 0.00 2.57
213 214 5.558818 AGACGTTGAGGAAAGAGTACTAGA 58.441 41.667 0.00 0.00 0.00 2.43
214 215 6.002704 AGACGTTGAGGAAAGAGTACTAGAA 58.997 40.000 0.00 0.00 0.00 2.10
215 216 6.660094 AGACGTTGAGGAAAGAGTACTAGAAT 59.340 38.462 0.00 0.00 0.00 2.40
216 217 7.177041 AGACGTTGAGGAAAGAGTACTAGAATT 59.823 37.037 0.00 0.00 0.00 2.17
217 218 7.314393 ACGTTGAGGAAAGAGTACTAGAATTC 58.686 38.462 0.00 0.00 0.00 2.17
218 219 7.177041 ACGTTGAGGAAAGAGTACTAGAATTCT 59.823 37.037 13.56 13.56 0.00 2.40
219 220 8.675504 CGTTGAGGAAAGAGTACTAGAATTCTA 58.324 37.037 14.42 14.42 0.00 2.10
284 285 9.912634 ACAACAAATGTGATAAAATAGAACAGG 57.087 29.630 0.00 0.00 41.93 4.00
303 304 9.225436 AGAACAGGATTAATTTCTGAAGTTCTC 57.775 33.333 19.85 1.53 33.19 2.87
304 305 7.602517 ACAGGATTAATTTCTGAAGTTCTCG 57.397 36.000 19.85 0.00 33.19 4.04
305 306 6.595716 ACAGGATTAATTTCTGAAGTTCTCGG 59.404 38.462 19.85 0.00 33.19 4.63
306 307 6.818644 CAGGATTAATTTCTGAAGTTCTCGGA 59.181 38.462 11.91 0.00 37.69 4.55
307 308 7.334421 CAGGATTAATTTCTGAAGTTCTCGGAA 59.666 37.037 11.91 3.82 45.90 4.30
311 312 3.830744 TTCTGAAGTTCTCGGAAACCA 57.169 42.857 4.17 0.00 44.84 3.67
312 313 4.351874 TTCTGAAGTTCTCGGAAACCAT 57.648 40.909 4.17 0.00 44.84 3.55
313 314 4.351874 TCTGAAGTTCTCGGAAACCATT 57.648 40.909 4.17 0.00 36.44 3.16
314 315 4.315803 TCTGAAGTTCTCGGAAACCATTC 58.684 43.478 4.17 0.00 36.44 2.67
315 316 4.065088 CTGAAGTTCTCGGAAACCATTCA 58.935 43.478 4.17 0.00 37.29 2.57
316 317 4.651778 TGAAGTTCTCGGAAACCATTCAT 58.348 39.130 4.17 0.00 37.29 2.57
317 318 4.455533 TGAAGTTCTCGGAAACCATTCATG 59.544 41.667 4.17 0.00 37.29 3.07
318 319 2.749621 AGTTCTCGGAAACCATTCATGC 59.250 45.455 0.00 0.00 37.29 4.06
319 320 1.368641 TCTCGGAAACCATTCATGCG 58.631 50.000 0.00 0.00 37.29 4.73
320 321 0.378257 CTCGGAAACCATTCATGCGG 59.622 55.000 0.00 0.00 37.29 5.69
321 322 1.029408 TCGGAAACCATTCATGCGGG 61.029 55.000 0.00 0.00 37.29 6.13
322 323 1.141665 GGAAACCATTCATGCGGGC 59.858 57.895 0.00 0.00 37.29 6.13
323 324 1.141665 GAAACCATTCATGCGGGCC 59.858 57.895 0.00 0.00 35.54 5.80
324 325 1.603236 GAAACCATTCATGCGGGCCA 61.603 55.000 4.39 0.00 35.54 5.36
325 326 1.887344 AAACCATTCATGCGGGCCAC 61.887 55.000 4.39 0.00 0.00 5.01
326 327 2.755064 CCATTCATGCGGGCCACA 60.755 61.111 4.39 0.00 0.00 4.17
327 328 2.129146 CCATTCATGCGGGCCACAT 61.129 57.895 4.39 1.64 0.00 3.21
328 329 1.678598 CCATTCATGCGGGCCACATT 61.679 55.000 3.81 0.00 0.00 2.71
329 330 0.249155 CATTCATGCGGGCCACATTC 60.249 55.000 3.81 0.00 0.00 2.67
330 331 1.727511 ATTCATGCGGGCCACATTCG 61.728 55.000 3.81 0.00 0.00 3.34
331 332 3.133464 CATGCGGGCCACATTCGT 61.133 61.111 3.81 0.00 0.00 3.85
332 333 2.361104 ATGCGGGCCACATTCGTT 60.361 55.556 4.39 0.00 0.00 3.85
333 334 1.976474 ATGCGGGCCACATTCGTTT 60.976 52.632 4.39 0.00 0.00 3.60
334 335 2.126502 GCGGGCCACATTCGTTTG 60.127 61.111 4.39 0.00 0.00 2.93
335 336 2.622011 GCGGGCCACATTCGTTTGA 61.622 57.895 4.39 0.00 0.00 2.69
336 337 1.209127 CGGGCCACATTCGTTTGAC 59.791 57.895 4.39 0.00 0.00 3.18
337 338 1.234615 CGGGCCACATTCGTTTGACT 61.235 55.000 4.39 0.00 0.00 3.41
338 339 0.240945 GGGCCACATTCGTTTGACTG 59.759 55.000 4.39 0.00 0.00 3.51
339 340 0.951558 GGCCACATTCGTTTGACTGT 59.048 50.000 0.00 0.00 38.41 3.55
340 341 1.336755 GGCCACATTCGTTTGACTGTT 59.663 47.619 0.00 0.00 36.00 3.16
344 345 3.790820 CCACATTCGTTTGACTGTTTGTG 59.209 43.478 0.00 0.00 36.00 3.33
867 922 0.322277 CATCAAGCTGTGCCTCCTGT 60.322 55.000 0.00 0.00 0.00 4.00
1081 1136 2.853542 TGCTGCCCACTCCTCCAA 60.854 61.111 0.00 0.00 0.00 3.53
1214 1270 3.201290 GGACAAATGATGATGCTCGAGT 58.799 45.455 15.13 0.00 0.00 4.18
1531 1589 1.309499 CGACTTCCTCACTCGCCTCT 61.309 60.000 0.00 0.00 0.00 3.69
2163 2221 5.588648 TCTTTCCACGTCTTCTTTTCATGTT 59.411 36.000 0.00 0.00 0.00 2.71
2166 2224 3.058224 CCACGTCTTCTTTTCATGTTCCC 60.058 47.826 0.00 0.00 0.00 3.97
2292 2350 0.393537 ATCGTCGTACGGGGACTCTT 60.394 55.000 16.52 0.00 42.81 2.85
2405 2463 1.693606 CATCACCACCCCTTTTGCTTT 59.306 47.619 0.00 0.00 0.00 3.51
2493 2551 3.189495 GCTTGTCTTCTTTGGTTAGGAGC 59.811 47.826 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.935167 TGACAGAGAGTATAACATGCTGAAA 58.065 36.000 0.00 0.00 0.00 2.69
3 4 7.040132 TCCTATGACAGAGAGTATAACATGCTG 60.040 40.741 0.00 0.00 0.00 4.41
4 5 7.007116 TCCTATGACAGAGAGTATAACATGCT 58.993 38.462 0.00 0.00 0.00 3.79
5 6 7.040062 ACTCCTATGACAGAGAGTATAACATGC 60.040 40.741 0.00 0.00 34.75 4.06
6 7 8.402798 ACTCCTATGACAGAGAGTATAACATG 57.597 38.462 0.00 0.00 34.75 3.21
7 8 9.427821 AAACTCCTATGACAGAGAGTATAACAT 57.572 33.333 0.00 0.00 35.17 2.71
14 15 6.426646 AACAAAACTCCTATGACAGAGAGT 57.573 37.500 0.00 0.00 36.76 3.24
15 16 7.227512 ACAAAACAAAACTCCTATGACAGAGAG 59.772 37.037 0.00 0.00 34.13 3.20
17 18 7.134815 CACAAAACAAAACTCCTATGACAGAG 58.865 38.462 0.00 0.00 36.16 3.35
18 19 6.459573 GCACAAAACAAAACTCCTATGACAGA 60.460 38.462 0.00 0.00 0.00 3.41
19 20 5.687285 GCACAAAACAAAACTCCTATGACAG 59.313 40.000 0.00 0.00 0.00 3.51
20 21 5.359576 AGCACAAAACAAAACTCCTATGACA 59.640 36.000 0.00 0.00 0.00 3.58
21 22 5.831997 AGCACAAAACAAAACTCCTATGAC 58.168 37.500 0.00 0.00 0.00 3.06
22 23 6.544197 TGTAGCACAAAACAAAACTCCTATGA 59.456 34.615 0.00 0.00 0.00 2.15
23 24 6.734137 TGTAGCACAAAACAAAACTCCTATG 58.266 36.000 0.00 0.00 0.00 2.23
24 25 6.546034 ACTGTAGCACAAAACAAAACTCCTAT 59.454 34.615 0.00 0.00 0.00 2.57
25 26 5.883673 ACTGTAGCACAAAACAAAACTCCTA 59.116 36.000 0.00 0.00 0.00 2.94
26 27 4.705023 ACTGTAGCACAAAACAAAACTCCT 59.295 37.500 0.00 0.00 0.00 3.69
27 28 4.993905 ACTGTAGCACAAAACAAAACTCC 58.006 39.130 0.00 0.00 0.00 3.85
28 29 7.024768 TGTAACTGTAGCACAAAACAAAACTC 58.975 34.615 0.00 0.00 0.00 3.01
29 30 6.915349 TGTAACTGTAGCACAAAACAAAACT 58.085 32.000 0.00 0.00 0.00 2.66
30 31 6.252655 CCTGTAACTGTAGCACAAAACAAAAC 59.747 38.462 0.00 0.00 0.00 2.43
31 32 6.151312 TCCTGTAACTGTAGCACAAAACAAAA 59.849 34.615 0.00 0.00 0.00 2.44
32 33 5.648526 TCCTGTAACTGTAGCACAAAACAAA 59.351 36.000 0.00 0.00 0.00 2.83
33 34 5.186942 TCCTGTAACTGTAGCACAAAACAA 58.813 37.500 0.00 0.00 0.00 2.83
34 35 4.771903 TCCTGTAACTGTAGCACAAAACA 58.228 39.130 0.00 0.00 0.00 2.83
35 36 4.213482 CCTCCTGTAACTGTAGCACAAAAC 59.787 45.833 0.00 0.00 0.00 2.43
36 37 4.385825 CCTCCTGTAACTGTAGCACAAAA 58.614 43.478 0.00 0.00 0.00 2.44
37 38 3.244422 CCCTCCTGTAACTGTAGCACAAA 60.244 47.826 0.00 0.00 0.00 2.83
38 39 2.301870 CCCTCCTGTAACTGTAGCACAA 59.698 50.000 0.00 0.00 0.00 3.33
39 40 1.899814 CCCTCCTGTAACTGTAGCACA 59.100 52.381 0.00 0.00 0.00 4.57
40 41 1.900486 ACCCTCCTGTAACTGTAGCAC 59.100 52.381 0.00 0.00 0.00 4.40
41 42 1.899814 CACCCTCCTGTAACTGTAGCA 59.100 52.381 0.00 0.00 0.00 3.49
42 43 1.207329 CCACCCTCCTGTAACTGTAGC 59.793 57.143 0.00 0.00 0.00 3.58
43 44 1.831736 CCCACCCTCCTGTAACTGTAG 59.168 57.143 0.00 0.00 0.00 2.74
44 45 1.433985 TCCCACCCTCCTGTAACTGTA 59.566 52.381 0.00 0.00 0.00 2.74
45 46 0.192566 TCCCACCCTCCTGTAACTGT 59.807 55.000 0.00 0.00 0.00 3.55
46 47 0.905357 CTCCCACCCTCCTGTAACTG 59.095 60.000 0.00 0.00 0.00 3.16
47 48 0.252742 CCTCCCACCCTCCTGTAACT 60.253 60.000 0.00 0.00 0.00 2.24
48 49 0.546988 ACCTCCCACCCTCCTGTAAC 60.547 60.000 0.00 0.00 0.00 2.50
49 50 0.195096 AACCTCCCACCCTCCTGTAA 59.805 55.000 0.00 0.00 0.00 2.41
50 51 0.546747 CAACCTCCCACCCTCCTGTA 60.547 60.000 0.00 0.00 0.00 2.74
51 52 1.847968 CAACCTCCCACCCTCCTGT 60.848 63.158 0.00 0.00 0.00 4.00
52 53 1.538876 TCAACCTCCCACCCTCCTG 60.539 63.158 0.00 0.00 0.00 3.86
53 54 1.539124 GTCAACCTCCCACCCTCCT 60.539 63.158 0.00 0.00 0.00 3.69
54 55 1.208165 ATGTCAACCTCCCACCCTCC 61.208 60.000 0.00 0.00 0.00 4.30
55 56 0.035056 CATGTCAACCTCCCACCCTC 60.035 60.000 0.00 0.00 0.00 4.30
56 57 0.475632 TCATGTCAACCTCCCACCCT 60.476 55.000 0.00 0.00 0.00 4.34
57 58 0.322546 GTCATGTCAACCTCCCACCC 60.323 60.000 0.00 0.00 0.00 4.61
58 59 0.400213 TGTCATGTCAACCTCCCACC 59.600 55.000 0.00 0.00 0.00 4.61
59 60 2.496899 ATGTCATGTCAACCTCCCAC 57.503 50.000 0.00 0.00 0.00 4.61
60 61 4.288366 TCTTAATGTCATGTCAACCTCCCA 59.712 41.667 0.00 0.00 0.00 4.37
61 62 4.843728 TCTTAATGTCATGTCAACCTCCC 58.156 43.478 0.00 0.00 0.00 4.30
62 63 5.940470 ACTTCTTAATGTCATGTCAACCTCC 59.060 40.000 0.00 0.00 0.00 4.30
63 64 7.440523 AACTTCTTAATGTCATGTCAACCTC 57.559 36.000 0.00 0.00 0.00 3.85
64 65 7.285401 ACAAACTTCTTAATGTCATGTCAACCT 59.715 33.333 0.00 0.00 0.00 3.50
65 66 7.425606 ACAAACTTCTTAATGTCATGTCAACC 58.574 34.615 0.00 0.00 0.00 3.77
66 67 9.599322 CTACAAACTTCTTAATGTCATGTCAAC 57.401 33.333 0.00 0.00 0.00 3.18
67 68 8.783093 CCTACAAACTTCTTAATGTCATGTCAA 58.217 33.333 0.00 0.00 0.00 3.18
68 69 7.094805 GCCTACAAACTTCTTAATGTCATGTCA 60.095 37.037 0.00 0.00 0.00 3.58
69 70 7.094805 TGCCTACAAACTTCTTAATGTCATGTC 60.095 37.037 0.00 0.00 0.00 3.06
70 71 6.714810 TGCCTACAAACTTCTTAATGTCATGT 59.285 34.615 0.00 0.00 0.00 3.21
71 72 7.144722 TGCCTACAAACTTCTTAATGTCATG 57.855 36.000 0.00 0.00 0.00 3.07
72 73 6.375455 CCTGCCTACAAACTTCTTAATGTCAT 59.625 38.462 0.00 0.00 0.00 3.06
73 74 5.705441 CCTGCCTACAAACTTCTTAATGTCA 59.295 40.000 0.00 0.00 0.00 3.58
74 75 5.123979 CCCTGCCTACAAACTTCTTAATGTC 59.876 44.000 0.00 0.00 0.00 3.06
75 76 5.010282 CCCTGCCTACAAACTTCTTAATGT 58.990 41.667 0.00 0.00 0.00 2.71
76 77 4.142381 GCCCTGCCTACAAACTTCTTAATG 60.142 45.833 0.00 0.00 0.00 1.90
77 78 4.017126 GCCCTGCCTACAAACTTCTTAAT 58.983 43.478 0.00 0.00 0.00 1.40
78 79 3.418047 GCCCTGCCTACAAACTTCTTAA 58.582 45.455 0.00 0.00 0.00 1.85
79 80 2.290705 GGCCCTGCCTACAAACTTCTTA 60.291 50.000 0.00 0.00 46.69 2.10
80 81 1.547901 GGCCCTGCCTACAAACTTCTT 60.548 52.381 0.00 0.00 46.69 2.52
81 82 0.038310 GGCCCTGCCTACAAACTTCT 59.962 55.000 0.00 0.00 46.69 2.85
82 83 2.568003 GGCCCTGCCTACAAACTTC 58.432 57.895 0.00 0.00 46.69 3.01
83 84 4.843624 GGCCCTGCCTACAAACTT 57.156 55.556 0.00 0.00 46.69 2.66
93 94 2.967270 GGGATAATCATGGCCCTGC 58.033 57.895 0.00 0.00 37.59 4.85
96 97 1.272704 GGGAAGGGATAATCATGGCCC 60.273 57.143 0.00 0.00 41.00 5.80
97 98 1.428912 TGGGAAGGGATAATCATGGCC 59.571 52.381 0.00 0.00 0.00 5.36
98 99 2.800250 CTGGGAAGGGATAATCATGGC 58.200 52.381 0.00 0.00 0.00 4.40
99 100 2.800250 GCTGGGAAGGGATAATCATGG 58.200 52.381 0.00 0.00 0.00 3.66
100 101 2.038952 TCGCTGGGAAGGGATAATCATG 59.961 50.000 0.00 0.00 0.00 3.07
101 102 2.338809 TCGCTGGGAAGGGATAATCAT 58.661 47.619 0.00 0.00 0.00 2.45
102 103 1.801242 TCGCTGGGAAGGGATAATCA 58.199 50.000 0.00 0.00 0.00 2.57
103 104 2.495084 GTTCGCTGGGAAGGGATAATC 58.505 52.381 7.46 0.00 34.69 1.75
104 105 1.202651 CGTTCGCTGGGAAGGGATAAT 60.203 52.381 16.48 0.00 36.98 1.28
105 106 0.177141 CGTTCGCTGGGAAGGGATAA 59.823 55.000 16.48 0.00 36.98 1.75
106 107 1.820581 CGTTCGCTGGGAAGGGATA 59.179 57.895 16.48 0.00 36.98 2.59
107 108 2.584608 CGTTCGCTGGGAAGGGAT 59.415 61.111 16.48 0.00 36.98 3.85
110 111 1.078426 ATTCCGTTCGCTGGGAAGG 60.078 57.895 17.10 17.10 44.93 3.46
111 112 0.108138 AGATTCCGTTCGCTGGGAAG 60.108 55.000 7.46 2.75 44.93 3.46
112 113 0.323629 AAGATTCCGTTCGCTGGGAA 59.676 50.000 2.72 2.72 45.72 3.97
113 114 1.136305 CTAAGATTCCGTTCGCTGGGA 59.864 52.381 0.00 0.00 0.00 4.37
114 115 1.134788 ACTAAGATTCCGTTCGCTGGG 60.135 52.381 0.00 0.00 0.00 4.45
115 116 2.295253 ACTAAGATTCCGTTCGCTGG 57.705 50.000 0.00 0.00 0.00 4.85
116 117 3.766151 TGTACTAAGATTCCGTTCGCTG 58.234 45.455 0.00 0.00 0.00 5.18
117 118 3.693085 TCTGTACTAAGATTCCGTTCGCT 59.307 43.478 0.00 0.00 0.00 4.93
118 119 4.025015 TCTGTACTAAGATTCCGTTCGC 57.975 45.455 0.00 0.00 0.00 4.70
119 120 6.017275 AGGTATCTGTACTAAGATTCCGTTCG 60.017 42.308 11.06 0.00 44.61 3.95
120 121 7.140048 CAGGTATCTGTACTAAGATTCCGTTC 58.860 42.308 11.06 0.00 44.61 3.95
121 122 6.040616 CCAGGTATCTGTACTAAGATTCCGTT 59.959 42.308 1.52 0.00 44.61 4.44
122 123 5.535406 CCAGGTATCTGTACTAAGATTCCGT 59.465 44.000 1.52 1.66 44.61 4.69
123 124 5.565045 GCCAGGTATCTGTACTAAGATTCCG 60.565 48.000 1.52 7.76 44.61 4.30
124 125 5.304614 TGCCAGGTATCTGTACTAAGATTCC 59.695 44.000 1.52 9.58 41.87 3.01
125 126 6.406692 TGCCAGGTATCTGTACTAAGATTC 57.593 41.667 1.52 0.00 39.31 2.52
126 127 6.808321 TTGCCAGGTATCTGTACTAAGATT 57.192 37.500 1.52 0.00 39.31 2.40
127 128 6.808321 TTTGCCAGGTATCTGTACTAAGAT 57.192 37.500 1.52 0.00 39.31 2.40
128 129 6.212791 ACTTTTGCCAGGTATCTGTACTAAGA 59.787 38.462 1.52 0.00 39.31 2.10
129 130 6.407202 ACTTTTGCCAGGTATCTGTACTAAG 58.593 40.000 1.52 3.41 39.31 2.18
130 131 6.368779 ACTTTTGCCAGGTATCTGTACTAA 57.631 37.500 1.52 0.00 39.31 2.24
131 132 6.666546 AGTACTTTTGCCAGGTATCTGTACTA 59.333 38.462 1.52 0.00 39.31 1.82
132 133 4.910458 ACTTTTGCCAGGTATCTGTACT 57.090 40.909 1.52 0.00 39.31 2.73
133 134 5.731591 AGTACTTTTGCCAGGTATCTGTAC 58.268 41.667 1.52 0.00 39.31 2.90
134 135 6.014070 TGAAGTACTTTTGCCAGGTATCTGTA 60.014 38.462 10.02 0.00 39.31 2.74
135 136 4.910458 AGTACTTTTGCCAGGTATCTGT 57.090 40.909 1.52 0.00 39.31 3.41
136 137 5.245531 TGAAGTACTTTTGCCAGGTATCTG 58.754 41.667 10.02 0.00 40.59 2.90
137 138 5.013183 ACTGAAGTACTTTTGCCAGGTATCT 59.987 40.000 20.21 2.98 0.00 1.98
138 139 5.122396 CACTGAAGTACTTTTGCCAGGTATC 59.878 44.000 20.21 2.40 0.00 2.24
139 140 5.003804 CACTGAAGTACTTTTGCCAGGTAT 58.996 41.667 20.21 3.53 0.00 2.73
140 141 4.385825 CACTGAAGTACTTTTGCCAGGTA 58.614 43.478 20.21 0.00 0.00 3.08
141 142 3.214328 CACTGAAGTACTTTTGCCAGGT 58.786 45.455 20.21 8.30 0.00 4.00
142 143 2.030805 GCACTGAAGTACTTTTGCCAGG 60.031 50.000 20.21 12.92 0.00 4.45
143 144 3.273919 GCACTGAAGTACTTTTGCCAG 57.726 47.619 19.60 18.12 0.00 4.85
145 146 2.706555 GGCACTGAAGTACTTTTGCC 57.293 50.000 27.56 27.56 42.57 4.52
146 147 5.629079 AATAGGCACTGAAGTACTTTTGC 57.371 39.130 21.09 21.09 41.52 3.68
147 148 6.381801 CCAAATAGGCACTGAAGTACTTTTG 58.618 40.000 10.02 8.75 41.52 2.44
148 149 6.575162 CCAAATAGGCACTGAAGTACTTTT 57.425 37.500 10.02 0.00 41.52 2.27
163 164 3.008923 ACACCCCAAATTTGCCAAATAGG 59.991 43.478 12.92 8.59 41.84 2.57
164 165 4.284829 ACACCCCAAATTTGCCAAATAG 57.715 40.909 12.92 0.00 0.00 1.73
165 166 4.713792 AACACCCCAAATTTGCCAAATA 57.286 36.364 12.92 0.00 0.00 1.40
166 167 3.591695 AACACCCCAAATTTGCCAAAT 57.408 38.095 12.92 0.00 0.00 2.32
167 168 3.456277 AGTAACACCCCAAATTTGCCAAA 59.544 39.130 12.92 0.00 0.00 3.28
168 169 3.041946 AGTAACACCCCAAATTTGCCAA 58.958 40.909 12.92 0.00 0.00 4.52
169 170 2.683768 AGTAACACCCCAAATTTGCCA 58.316 42.857 12.92 0.00 0.00 4.92
170 171 4.082408 GTCTAGTAACACCCCAAATTTGCC 60.082 45.833 12.92 0.00 0.00 4.52
171 172 4.379082 CGTCTAGTAACACCCCAAATTTGC 60.379 45.833 12.92 0.00 0.00 3.68
172 173 4.758165 ACGTCTAGTAACACCCCAAATTTG 59.242 41.667 11.40 11.40 0.00 2.32
173 174 4.976864 ACGTCTAGTAACACCCCAAATTT 58.023 39.130 0.00 0.00 0.00 1.82
174 175 4.628963 ACGTCTAGTAACACCCCAAATT 57.371 40.909 0.00 0.00 0.00 1.82
175 176 4.040706 TCAACGTCTAGTAACACCCCAAAT 59.959 41.667 0.00 0.00 0.00 2.32
176 177 3.387374 TCAACGTCTAGTAACACCCCAAA 59.613 43.478 0.00 0.00 0.00 3.28
177 178 2.964464 TCAACGTCTAGTAACACCCCAA 59.036 45.455 0.00 0.00 0.00 4.12
178 179 2.559668 CTCAACGTCTAGTAACACCCCA 59.440 50.000 0.00 0.00 0.00 4.96
179 180 2.094338 CCTCAACGTCTAGTAACACCCC 60.094 54.545 0.00 0.00 0.00 4.95
180 181 2.821969 TCCTCAACGTCTAGTAACACCC 59.178 50.000 0.00 0.00 0.00 4.61
181 182 4.510038 TTCCTCAACGTCTAGTAACACC 57.490 45.455 0.00 0.00 0.00 4.16
182 183 5.766222 TCTTTCCTCAACGTCTAGTAACAC 58.234 41.667 0.00 0.00 0.00 3.32
183 184 5.533903 ACTCTTTCCTCAACGTCTAGTAACA 59.466 40.000 0.00 0.00 0.00 2.41
184 185 6.011476 ACTCTTTCCTCAACGTCTAGTAAC 57.989 41.667 0.00 0.00 0.00 2.50
185 186 6.939163 AGTACTCTTTCCTCAACGTCTAGTAA 59.061 38.462 0.00 0.00 0.00 2.24
186 187 6.471146 AGTACTCTTTCCTCAACGTCTAGTA 58.529 40.000 0.00 0.00 0.00 1.82
187 188 5.315348 AGTACTCTTTCCTCAACGTCTAGT 58.685 41.667 0.00 0.00 0.00 2.57
188 189 5.883503 AGTACTCTTTCCTCAACGTCTAG 57.116 43.478 0.00 0.00 0.00 2.43
189 190 6.705302 TCTAGTACTCTTTCCTCAACGTCTA 58.295 40.000 0.00 0.00 0.00 2.59
190 191 5.558818 TCTAGTACTCTTTCCTCAACGTCT 58.441 41.667 0.00 0.00 0.00 4.18
191 192 5.876612 TCTAGTACTCTTTCCTCAACGTC 57.123 43.478 0.00 0.00 0.00 4.34
192 193 6.837471 ATTCTAGTACTCTTTCCTCAACGT 57.163 37.500 0.00 0.00 0.00 3.99
193 194 7.540299 AGAATTCTAGTACTCTTTCCTCAACG 58.460 38.462 6.06 0.00 0.00 4.10
224 225 8.648693 ACTCTACACTTGTAGGAAAGTTATTGT 58.351 33.333 14.94 0.00 46.01 2.71
225 226 9.490379 AACTCTACACTTGTAGGAAAGTTATTG 57.510 33.333 14.94 0.00 46.01 1.90
258 259 9.912634 CCTGTTCTATTTTATCACATTTGTTGT 57.087 29.630 0.00 0.00 39.91 3.32
277 278 9.225436 GAGAACTTCAGAAATTAATCCTGTTCT 57.775 33.333 14.81 14.81 41.68 3.01
278 279 8.171840 CGAGAACTTCAGAAATTAATCCTGTTC 58.828 37.037 13.98 11.45 0.00 3.18
279 280 7.119846 CCGAGAACTTCAGAAATTAATCCTGTT 59.880 37.037 13.98 5.38 0.00 3.16
280 281 6.595716 CCGAGAACTTCAGAAATTAATCCTGT 59.404 38.462 13.98 0.47 0.00 4.00
281 282 6.818644 TCCGAGAACTTCAGAAATTAATCCTG 59.181 38.462 10.10 10.10 0.00 3.86
282 283 6.947464 TCCGAGAACTTCAGAAATTAATCCT 58.053 36.000 0.00 0.00 0.00 3.24
283 284 7.611213 TTCCGAGAACTTCAGAAATTAATCC 57.389 36.000 0.00 0.00 0.00 3.01
284 285 7.963465 GGTTTCCGAGAACTTCAGAAATTAATC 59.037 37.037 0.00 0.00 35.32 1.75
285 286 7.447238 TGGTTTCCGAGAACTTCAGAAATTAAT 59.553 33.333 5.47 0.00 35.32 1.40
286 287 6.768861 TGGTTTCCGAGAACTTCAGAAATTAA 59.231 34.615 5.47 0.00 35.32 1.40
287 288 6.292923 TGGTTTCCGAGAACTTCAGAAATTA 58.707 36.000 5.47 0.00 35.32 1.40
288 289 5.130350 TGGTTTCCGAGAACTTCAGAAATT 58.870 37.500 5.47 0.00 35.32 1.82
289 290 4.714632 TGGTTTCCGAGAACTTCAGAAAT 58.285 39.130 5.47 0.00 35.32 2.17
290 291 4.145365 TGGTTTCCGAGAACTTCAGAAA 57.855 40.909 0.00 0.00 31.41 2.52
291 292 3.830744 TGGTTTCCGAGAACTTCAGAA 57.169 42.857 0.00 0.00 0.00 3.02
292 293 4.202315 TGAATGGTTTCCGAGAACTTCAGA 60.202 41.667 0.00 0.00 0.00 3.27
293 294 4.065088 TGAATGGTTTCCGAGAACTTCAG 58.935 43.478 0.00 0.00 0.00 3.02
294 295 4.079980 TGAATGGTTTCCGAGAACTTCA 57.920 40.909 0.00 0.00 0.00 3.02
295 296 4.672801 GCATGAATGGTTTCCGAGAACTTC 60.673 45.833 0.00 0.00 0.00 3.01
296 297 3.191371 GCATGAATGGTTTCCGAGAACTT 59.809 43.478 0.00 0.00 0.00 2.66
297 298 2.749621 GCATGAATGGTTTCCGAGAACT 59.250 45.455 0.00 0.00 0.00 3.01
298 299 2.476185 CGCATGAATGGTTTCCGAGAAC 60.476 50.000 0.00 0.00 0.00 3.01
299 300 1.737236 CGCATGAATGGTTTCCGAGAA 59.263 47.619 0.00 0.00 0.00 2.87
300 301 1.368641 CGCATGAATGGTTTCCGAGA 58.631 50.000 0.00 0.00 0.00 4.04
301 302 0.378257 CCGCATGAATGGTTTCCGAG 59.622 55.000 0.00 0.00 0.00 4.63
302 303 1.029408 CCCGCATGAATGGTTTCCGA 61.029 55.000 0.00 0.00 0.00 4.55
303 304 1.433064 CCCGCATGAATGGTTTCCG 59.567 57.895 0.00 0.00 0.00 4.30
304 305 1.141665 GCCCGCATGAATGGTTTCC 59.858 57.895 0.00 0.00 0.00 3.13
305 306 1.141665 GGCCCGCATGAATGGTTTC 59.858 57.895 0.00 0.00 0.00 2.78
306 307 1.608918 TGGCCCGCATGAATGGTTT 60.609 52.632 0.00 0.00 0.00 3.27
307 308 2.037049 TGGCCCGCATGAATGGTT 59.963 55.556 0.00 0.00 0.00 3.67
308 309 2.755469 GTGGCCCGCATGAATGGT 60.755 61.111 0.00 0.00 0.00 3.55
309 310 1.678598 AATGTGGCCCGCATGAATGG 61.679 55.000 11.22 0.00 34.63 3.16
310 311 0.249155 GAATGTGGCCCGCATGAATG 60.249 55.000 11.22 0.00 34.63 2.67
311 312 1.727511 CGAATGTGGCCCGCATGAAT 61.728 55.000 11.22 0.00 34.63 2.57
312 313 2.405805 CGAATGTGGCCCGCATGAA 61.406 57.895 11.22 0.00 34.63 2.57
313 314 2.823593 CGAATGTGGCCCGCATGA 60.824 61.111 11.22 0.00 34.63 3.07
314 315 2.211619 AAACGAATGTGGCCCGCATG 62.212 55.000 11.22 1.53 34.63 4.06
315 316 1.976474 AAACGAATGTGGCCCGCAT 60.976 52.632 3.32 3.32 36.02 4.73
316 317 2.596046 AAACGAATGTGGCCCGCA 60.596 55.556 0.00 0.00 0.00 5.69
317 318 2.126502 CAAACGAATGTGGCCCGC 60.127 61.111 0.00 0.00 0.00 6.13
318 319 1.209127 GTCAAACGAATGTGGCCCG 59.791 57.895 0.00 0.00 0.00 6.13
319 320 0.240945 CAGTCAAACGAATGTGGCCC 59.759 55.000 0.00 0.00 0.00 5.80
320 321 0.951558 ACAGTCAAACGAATGTGGCC 59.048 50.000 0.00 0.00 40.05 5.36
321 322 2.774439 AACAGTCAAACGAATGTGGC 57.226 45.000 0.00 0.00 40.63 5.01
322 323 3.790820 CACAAACAGTCAAACGAATGTGG 59.209 43.478 0.00 0.00 40.63 4.17
323 324 4.262743 CACACAAACAGTCAAACGAATGTG 59.737 41.667 0.00 0.00 40.63 3.21
324 325 4.083003 ACACACAAACAGTCAAACGAATGT 60.083 37.500 0.00 0.00 43.18 2.71
325 326 4.262743 CACACACAAACAGTCAAACGAATG 59.737 41.667 0.00 0.00 34.68 2.67
326 327 4.083003 ACACACACAAACAGTCAAACGAAT 60.083 37.500 0.00 0.00 0.00 3.34
327 328 3.251245 ACACACACAAACAGTCAAACGAA 59.749 39.130 0.00 0.00 0.00 3.85
328 329 2.809119 ACACACACAAACAGTCAAACGA 59.191 40.909 0.00 0.00 0.00 3.85
329 330 3.196007 ACACACACAAACAGTCAAACG 57.804 42.857 0.00 0.00 0.00 3.60
330 331 5.933790 TCTAACACACACAAACAGTCAAAC 58.066 37.500 0.00 0.00 0.00 2.93
331 332 6.017026 TGTTCTAACACACACAAACAGTCAAA 60.017 34.615 0.00 0.00 33.17 2.69
332 333 5.470437 TGTTCTAACACACACAAACAGTCAA 59.530 36.000 0.00 0.00 33.17 3.18
333 334 4.998033 TGTTCTAACACACACAAACAGTCA 59.002 37.500 0.00 0.00 33.17 3.41
334 335 5.447279 CCTGTTCTAACACACACAAACAGTC 60.447 44.000 10.95 0.00 41.09 3.51
335 336 4.394920 CCTGTTCTAACACACACAAACAGT 59.605 41.667 10.95 0.00 41.09 3.55
336 337 4.201910 CCCTGTTCTAACACACACAAACAG 60.202 45.833 6.16 6.16 41.89 3.16
337 338 3.692101 CCCTGTTCTAACACACACAAACA 59.308 43.478 0.00 0.00 34.70 2.83
338 339 3.692593 ACCCTGTTCTAACACACACAAAC 59.307 43.478 0.00 0.00 34.70 2.93
339 340 3.958018 ACCCTGTTCTAACACACACAAA 58.042 40.909 0.00 0.00 34.70 2.83
340 341 3.637911 ACCCTGTTCTAACACACACAA 57.362 42.857 0.00 0.00 34.70 3.33
344 345 2.032924 GCACAACCCTGTTCTAACACAC 59.967 50.000 0.00 0.00 34.70 3.82
443 444 7.879677 TGTTATGAAGTGAGCCTATATTCCATG 59.120 37.037 0.00 0.00 0.00 3.66
712 761 0.896923 CAGAGAAGAGGAGCAGCAGT 59.103 55.000 0.00 0.00 0.00 4.40
867 922 0.179059 TCGTTGAAGACCAGCAGCAA 60.179 50.000 0.00 0.00 0.00 3.91
1081 1136 1.062488 ACAGGGAAGGCCAACTCAGT 61.062 55.000 5.01 0.00 35.15 3.41
1214 1270 4.528206 TGCTGTTCACCAAGATAGAAGAGA 59.472 41.667 0.00 0.00 35.40 3.10
1531 1589 4.069232 CTGCTCGAACTCCGGCCA 62.069 66.667 2.24 0.00 39.14 5.36
1605 1663 1.358402 CTCCTCAGATCGCACCTCG 59.642 63.158 0.00 0.00 40.15 4.63
2163 2221 0.672401 GAACATGAGAAACGGCGGGA 60.672 55.000 13.24 0.00 0.00 5.14
2166 2224 2.004583 TAGGAACATGAGAAACGGCG 57.995 50.000 4.80 4.80 0.00 6.46
2405 2463 2.203922 TGGTGGAGGTGGCAGCTA 60.204 61.111 20.63 1.41 0.00 3.32
2493 2551 3.066900 CAGATACAGACCCTAGAACACCG 59.933 52.174 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.