Multiple sequence alignment - TraesCS2B01G434300

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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 TraesCS2B01G434300 chr2B 100.000 2828 0 0 1 2828 624356768 624353941 0.000000e+00 5223
1 TraesCS2B01G434300 chr2D 92.321 1719 73 24 142 1830 527294933 527293244 0.000000e+00 2388
2 TraesCS2B01G434300 chr2D 94.199 362 15 3 2472 2828 527292647 527292287 5.330000e-152 547
3 TraesCS2B01G434300 chr2D 90.808 359 17 7 1923 2267 527293210 527292854 1.530000e-127 466
4 TraesCS2B01G434300 chr2A 92.000 1325 76 18 585 1889 672293169 672291855 0.000000e+00 1832
5 TraesCS2B01G434300 chr2A 88.473 347 25 11 142 484 672293579 672293244 3.390000e-109 405
6 TraesCS2B01G434300 chr2A 86.761 355 26 12 1931 2267 672291850 672291499 2.660000e-100 375
7 TraesCS2B01G434300 chr2A 83.123 397 29 15 2470 2828 672291278 672290882 7.550000e-86 327
8 TraesCS2B01G434300 chr6D 89.575 259 27 0 1285 1543 326540360 326540618 2.100000e-86 329
9 TraesCS2B01G434300 chr6D 85.714 266 35 2 1285 1550 326760711 326760973 7.720000e-71 278
10 TraesCS2B01G434300 chr6B 89.575 259 27 0 1285 1543 495806711 495806453 2.100000e-86 329
11 TraesCS2B01G434300 chr6B 86.090 266 34 2 1285 1550 495543773 495543511 1.660000e-72 283
12 TraesCS2B01G434300 chr6A 89.575 259 27 0 1285 1543 465231917 465232175 2.100000e-86 329
13 TraesCS2B01G434300 chr6A 88.211 246 29 0 1285 1530 465389787 465390032 7.660000e-76 294
14 TraesCS2B01G434300 chr1A 85.606 264 33 4 1283 1542 388849402 388849664 3.590000e-69 272


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 TraesCS2B01G434300 chr2B 624353941 624356768 2827 True 5223.000000 5223 100.000000 1 2828 1 chr2B.!!$R1 2827
1 TraesCS2B01G434300 chr2D 527292287 527294933 2646 True 1133.666667 2388 92.442667 142 2828 3 chr2D.!!$R1 2686
2 TraesCS2B01G434300 chr2A 672290882 672293579 2697 True 734.750000 1832 87.589250 142 2828 4 chr2A.!!$R1 2686

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
95 96 0.034767 TAGTCTCCCGTCGATGGTGT 60.035 55.0 22.05 4.57 0.0 4.16 F
96 97 0.034767 AGTCTCCCGTCGATGGTGTA 60.035 55.0 22.05 6.67 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1098 1168 0.252239 TCTTGGGGAGCTCTAGCACA 60.252 55.000 14.64 0.83 45.16 4.57 R
2061 2138 1.225704 CCAGGGAAGTCCATCCTGC 59.774 63.158 0.00 0.00 44.87 4.85 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
26 27 9.909644 ATATTAACAGGAATACATAGTCGTCAC 57.090 33.333 0.00 0.00 0.00 3.67
27 28 4.650754 ACAGGAATACATAGTCGTCACC 57.349 45.455 0.00 0.00 0.00 4.02
28 29 3.066342 ACAGGAATACATAGTCGTCACCG 59.934 47.826 0.00 0.00 0.00 4.94
29 30 2.621998 AGGAATACATAGTCGTCACCGG 59.378 50.000 0.00 0.00 33.95 5.28
30 31 2.360165 GGAATACATAGTCGTCACCGGT 59.640 50.000 0.00 0.00 33.95 5.28
31 32 3.565482 GGAATACATAGTCGTCACCGGTA 59.435 47.826 6.87 0.00 33.95 4.02
32 33 4.036734 GGAATACATAGTCGTCACCGGTAA 59.963 45.833 6.87 0.00 33.95 2.85
33 34 5.278660 GGAATACATAGTCGTCACCGGTAAT 60.279 44.000 6.87 0.00 33.95 1.89
34 35 5.779529 ATACATAGTCGTCACCGGTAATT 57.220 39.130 6.87 0.00 33.95 1.40
35 36 4.460948 ACATAGTCGTCACCGGTAATTT 57.539 40.909 6.87 0.00 33.95 1.82
36 37 4.824289 ACATAGTCGTCACCGGTAATTTT 58.176 39.130 6.87 0.00 33.95 1.82
37 38 4.628333 ACATAGTCGTCACCGGTAATTTTG 59.372 41.667 6.87 0.40 33.95 2.44
38 39 2.419667 AGTCGTCACCGGTAATTTTGG 58.580 47.619 6.87 0.00 33.95 3.28
39 40 2.145536 GTCGTCACCGGTAATTTTGGT 58.854 47.619 6.87 0.00 36.10 3.67
40 41 2.549329 GTCGTCACCGGTAATTTTGGTT 59.451 45.455 6.87 0.00 32.48 3.67
41 42 3.745458 GTCGTCACCGGTAATTTTGGTTA 59.255 43.478 6.87 0.00 32.48 2.85
42 43 3.745458 TCGTCACCGGTAATTTTGGTTAC 59.255 43.478 6.87 0.00 32.48 2.50
43 44 3.497640 CGTCACCGGTAATTTTGGTTACA 59.502 43.478 6.87 0.00 36.51 2.41
44 45 4.154556 CGTCACCGGTAATTTTGGTTACAT 59.845 41.667 6.87 0.00 36.51 2.29
45 46 5.633927 GTCACCGGTAATTTTGGTTACATC 58.366 41.667 6.87 0.00 36.51 3.06
46 47 5.413523 GTCACCGGTAATTTTGGTTACATCT 59.586 40.000 6.87 0.00 36.51 2.90
47 48 6.594937 GTCACCGGTAATTTTGGTTACATCTA 59.405 38.462 6.87 0.00 36.51 1.98
48 49 7.119553 GTCACCGGTAATTTTGGTTACATCTAA 59.880 37.037 6.87 0.00 36.51 2.10
49 50 7.119553 TCACCGGTAATTTTGGTTACATCTAAC 59.880 37.037 6.87 0.00 36.51 2.34
50 51 6.092533 ACCGGTAATTTTGGTTACATCTAACG 59.907 38.462 4.49 0.00 36.51 3.18
51 52 6.457257 CCGGTAATTTTGGTTACATCTAACGG 60.457 42.308 0.00 0.00 36.51 4.44
52 53 6.457257 CGGTAATTTTGGTTACATCTAACGGG 60.457 42.308 0.00 0.00 36.51 5.28
53 54 4.976224 ATTTTGGTTACATCTAACGGGC 57.024 40.909 0.00 0.00 34.10 6.13
54 55 3.420300 TTTGGTTACATCTAACGGGCA 57.580 42.857 0.00 0.00 34.10 5.36
55 56 3.420300 TTGGTTACATCTAACGGGCAA 57.580 42.857 0.00 0.00 34.10 4.52
56 57 3.420300 TGGTTACATCTAACGGGCAAA 57.580 42.857 0.00 0.00 34.10 3.68
57 58 3.752665 TGGTTACATCTAACGGGCAAAA 58.247 40.909 0.00 0.00 34.10 2.44
58 59 4.337145 TGGTTACATCTAACGGGCAAAAT 58.663 39.130 0.00 0.00 34.10 1.82
59 60 5.498393 TGGTTACATCTAACGGGCAAAATA 58.502 37.500 0.00 0.00 34.10 1.40
60 61 5.944599 TGGTTACATCTAACGGGCAAAATAA 59.055 36.000 0.00 0.00 34.10 1.40
61 62 6.094325 TGGTTACATCTAACGGGCAAAATAAG 59.906 38.462 0.00 0.00 34.10 1.73
62 63 6.094464 GGTTACATCTAACGGGCAAAATAAGT 59.906 38.462 0.00 0.00 34.10 2.24
63 64 7.362315 GGTTACATCTAACGGGCAAAATAAGTT 60.362 37.037 0.00 0.00 34.10 2.66
64 65 5.949735 ACATCTAACGGGCAAAATAAGTTG 58.050 37.500 0.00 0.00 0.00 3.16
65 66 5.105917 ACATCTAACGGGCAAAATAAGTTGG 60.106 40.000 0.00 0.00 0.00 3.77
66 67 4.400120 TCTAACGGGCAAAATAAGTTGGT 58.600 39.130 0.00 0.00 0.00 3.67
67 68 5.558818 TCTAACGGGCAAAATAAGTTGGTA 58.441 37.500 0.00 0.00 0.00 3.25
68 69 4.508461 AACGGGCAAAATAAGTTGGTAC 57.492 40.909 0.00 0.00 0.00 3.34
69 70 3.488363 ACGGGCAAAATAAGTTGGTACA 58.512 40.909 0.00 0.00 0.00 2.90
70 71 3.504520 ACGGGCAAAATAAGTTGGTACAG 59.495 43.478 0.00 0.00 42.39 2.74
71 72 3.119637 CGGGCAAAATAAGTTGGTACAGG 60.120 47.826 0.00 0.00 42.39 4.00
72 73 3.194755 GGGCAAAATAAGTTGGTACAGGG 59.805 47.826 0.00 0.00 42.39 4.45
73 74 3.194755 GGCAAAATAAGTTGGTACAGGGG 59.805 47.826 0.00 0.00 42.39 4.79
74 75 3.830178 GCAAAATAAGTTGGTACAGGGGT 59.170 43.478 0.00 0.00 42.39 4.95
75 76 4.282449 GCAAAATAAGTTGGTACAGGGGTT 59.718 41.667 0.00 0.00 42.39 4.11
76 77 5.221561 GCAAAATAAGTTGGTACAGGGGTTT 60.222 40.000 0.00 0.00 42.39 3.27
77 78 6.015265 GCAAAATAAGTTGGTACAGGGGTTTA 60.015 38.462 0.00 0.00 42.39 2.01
78 79 7.599171 CAAAATAAGTTGGTACAGGGGTTTAG 58.401 38.462 0.00 0.00 42.39 1.85
79 80 6.458630 AATAAGTTGGTACAGGGGTTTAGT 57.541 37.500 0.00 0.00 42.39 2.24
80 81 4.362470 AAGTTGGTACAGGGGTTTAGTC 57.638 45.455 0.00 0.00 42.39 2.59
81 82 3.595021 AGTTGGTACAGGGGTTTAGTCT 58.405 45.455 0.00 0.00 42.39 3.24
82 83 3.581770 AGTTGGTACAGGGGTTTAGTCTC 59.418 47.826 0.00 0.00 42.39 3.36
83 84 2.543635 TGGTACAGGGGTTTAGTCTCC 58.456 52.381 0.00 0.00 0.00 3.71
84 85 1.836166 GGTACAGGGGTTTAGTCTCCC 59.164 57.143 0.00 0.00 42.73 4.30
85 86 1.479730 GTACAGGGGTTTAGTCTCCCG 59.520 57.143 0.00 0.00 45.13 5.14
86 87 0.178912 ACAGGGGTTTAGTCTCCCGT 60.179 55.000 0.00 0.00 45.13 5.28
87 88 0.535797 CAGGGGTTTAGTCTCCCGTC 59.464 60.000 0.00 0.00 45.13 4.79
88 89 0.969409 AGGGGTTTAGTCTCCCGTCG 60.969 60.000 0.00 0.00 45.13 5.12
89 90 0.967380 GGGGTTTAGTCTCCCGTCGA 60.967 60.000 0.00 0.00 44.27 4.20
90 91 1.109609 GGGTTTAGTCTCCCGTCGAT 58.890 55.000 0.00 0.00 33.97 3.59
91 92 1.202382 GGGTTTAGTCTCCCGTCGATG 60.202 57.143 0.00 0.00 33.97 3.84
92 93 1.202382 GGTTTAGTCTCCCGTCGATGG 60.202 57.143 17.27 17.27 0.00 3.51
93 94 1.475682 GTTTAGTCTCCCGTCGATGGT 59.524 52.381 22.05 5.96 0.00 3.55
94 95 1.100510 TTAGTCTCCCGTCGATGGTG 58.899 55.000 22.05 14.13 0.00 4.17
95 96 0.034767 TAGTCTCCCGTCGATGGTGT 60.035 55.000 22.05 4.57 0.00 4.16
96 97 0.034767 AGTCTCCCGTCGATGGTGTA 60.035 55.000 22.05 6.67 0.00 2.90
97 98 1.030457 GTCTCCCGTCGATGGTGTAT 58.970 55.000 22.05 0.00 0.00 2.29
98 99 1.029681 TCTCCCGTCGATGGTGTATG 58.970 55.000 22.05 6.72 0.00 2.39
99 100 1.029681 CTCCCGTCGATGGTGTATGA 58.970 55.000 22.05 10.68 0.00 2.15
100 101 1.613925 CTCCCGTCGATGGTGTATGAT 59.386 52.381 22.05 0.00 0.00 2.45
101 102 2.035961 CTCCCGTCGATGGTGTATGATT 59.964 50.000 22.05 0.00 0.00 2.57
102 103 2.035449 TCCCGTCGATGGTGTATGATTC 59.965 50.000 22.05 0.00 0.00 2.52
103 104 2.035961 CCCGTCGATGGTGTATGATTCT 59.964 50.000 22.05 0.00 0.00 2.40
104 105 3.052745 CCGTCGATGGTGTATGATTCTG 58.947 50.000 15.98 0.00 0.00 3.02
105 106 3.490933 CCGTCGATGGTGTATGATTCTGT 60.491 47.826 15.98 0.00 0.00 3.41
106 107 3.487207 CGTCGATGGTGTATGATTCTGTG 59.513 47.826 0.00 0.00 0.00 3.66
107 108 3.804325 GTCGATGGTGTATGATTCTGTGG 59.196 47.826 0.00 0.00 0.00 4.17
108 109 3.450817 TCGATGGTGTATGATTCTGTGGT 59.549 43.478 0.00 0.00 0.00 4.16
109 110 4.647399 TCGATGGTGTATGATTCTGTGGTA 59.353 41.667 0.00 0.00 0.00 3.25
110 111 4.984785 CGATGGTGTATGATTCTGTGGTAG 59.015 45.833 0.00 0.00 0.00 3.18
111 112 5.451937 CGATGGTGTATGATTCTGTGGTAGT 60.452 44.000 0.00 0.00 0.00 2.73
112 113 5.084818 TGGTGTATGATTCTGTGGTAGTG 57.915 43.478 0.00 0.00 0.00 2.74
113 114 4.530553 TGGTGTATGATTCTGTGGTAGTGT 59.469 41.667 0.00 0.00 0.00 3.55
114 115 5.717654 TGGTGTATGATTCTGTGGTAGTGTA 59.282 40.000 0.00 0.00 0.00 2.90
115 116 6.211785 TGGTGTATGATTCTGTGGTAGTGTAA 59.788 38.462 0.00 0.00 0.00 2.41
116 117 7.101054 GGTGTATGATTCTGTGGTAGTGTAAA 58.899 38.462 0.00 0.00 0.00 2.01
117 118 7.064253 GGTGTATGATTCTGTGGTAGTGTAAAC 59.936 40.741 0.00 0.00 0.00 2.01
118 119 7.817962 GTGTATGATTCTGTGGTAGTGTAAACT 59.182 37.037 0.00 0.00 0.00 2.66
119 120 8.033038 TGTATGATTCTGTGGTAGTGTAAACTC 58.967 37.037 0.00 0.00 0.00 3.01
120 121 6.665992 TGATTCTGTGGTAGTGTAAACTCT 57.334 37.500 0.00 0.00 0.00 3.24
121 122 7.770366 TGATTCTGTGGTAGTGTAAACTCTA 57.230 36.000 0.00 0.00 0.00 2.43
122 123 8.362464 TGATTCTGTGGTAGTGTAAACTCTAT 57.638 34.615 0.00 0.00 0.00 1.98
123 124 8.812972 TGATTCTGTGGTAGTGTAAACTCTATT 58.187 33.333 0.00 0.00 0.00 1.73
124 125 9.654663 GATTCTGTGGTAGTGTAAACTCTATTT 57.345 33.333 0.00 0.00 0.00 1.40
125 126 8.827177 TTCTGTGGTAGTGTAAACTCTATTTG 57.173 34.615 0.00 0.00 0.00 2.32
126 127 7.959175 TCTGTGGTAGTGTAAACTCTATTTGT 58.041 34.615 0.00 0.00 0.00 2.83
127 128 8.426489 TCTGTGGTAGTGTAAACTCTATTTGTT 58.574 33.333 0.00 0.00 0.00 2.83
128 129 8.597662 TGTGGTAGTGTAAACTCTATTTGTTC 57.402 34.615 0.00 0.00 0.00 3.18
129 130 7.658575 TGTGGTAGTGTAAACTCTATTTGTTCC 59.341 37.037 0.00 0.00 0.00 3.62
130 131 7.118825 GTGGTAGTGTAAACTCTATTTGTTCCC 59.881 40.741 0.00 0.00 0.00 3.97
131 132 7.016858 TGGTAGTGTAAACTCTATTTGTTCCCT 59.983 37.037 0.00 0.00 0.00 4.20
132 133 7.881751 GGTAGTGTAAACTCTATTTGTTCCCTT 59.118 37.037 0.00 0.00 0.00 3.95
133 134 9.933723 GTAGTGTAAACTCTATTTGTTCCCTTA 57.066 33.333 0.00 0.00 0.00 2.69
135 136 9.856162 AGTGTAAACTCTATTTGTTCCCTTAAA 57.144 29.630 0.00 0.00 0.00 1.52
207 208 5.705441 GGAACACATCATGGTAGAGTTTTGA 59.295 40.000 0.00 0.00 0.00 2.69
209 210 7.094205 GGAACACATCATGGTAGAGTTTTGATT 60.094 37.037 0.00 0.00 0.00 2.57
210 211 7.149569 ACACATCATGGTAGAGTTTTGATTG 57.850 36.000 0.00 0.00 0.00 2.67
222 223 7.145932 AGAGTTTTGATTGTTAGGATTTCCG 57.854 36.000 0.00 0.00 42.08 4.30
225 226 8.575649 AGTTTTGATTGTTAGGATTTCCGTAT 57.424 30.769 0.00 0.00 42.08 3.06
247 248 9.627395 CGTATAAGATCTCAATTAGTTTCCGAT 57.373 33.333 0.00 0.00 0.00 4.18
250 251 5.859495 AGATCTCAATTAGTTTCCGATCCC 58.141 41.667 0.00 0.00 0.00 3.85
251 252 5.604650 AGATCTCAATTAGTTTCCGATCCCT 59.395 40.000 0.00 0.00 0.00 4.20
252 253 6.782988 AGATCTCAATTAGTTTCCGATCCCTA 59.217 38.462 0.00 0.00 0.00 3.53
253 254 6.406692 TCTCAATTAGTTTCCGATCCCTAG 57.593 41.667 0.00 0.00 0.00 3.02
254 255 6.134055 TCTCAATTAGTTTCCGATCCCTAGA 58.866 40.000 0.00 0.00 0.00 2.43
255 256 6.782988 TCTCAATTAGTTTCCGATCCCTAGAT 59.217 38.462 0.00 0.00 34.57 1.98
256 257 7.290248 TCTCAATTAGTTTCCGATCCCTAGATT 59.710 37.037 0.00 0.00 30.90 2.40
257 258 7.442656 TCAATTAGTTTCCGATCCCTAGATTC 58.557 38.462 0.00 0.00 30.90 2.52
258 259 5.803237 TTAGTTTCCGATCCCTAGATTCC 57.197 43.478 0.00 0.00 30.90 3.01
259 260 3.930035 AGTTTCCGATCCCTAGATTCCT 58.070 45.455 0.00 0.00 30.90 3.36
260 261 3.643792 AGTTTCCGATCCCTAGATTCCTG 59.356 47.826 0.00 0.00 30.90 3.86
261 262 2.310779 TCCGATCCCTAGATTCCTGG 57.689 55.000 0.00 0.00 30.90 4.45
276 277 2.612746 TGGCCTCAACCCTACCCC 60.613 66.667 3.32 0.00 0.00 4.95
290 295 1.544691 CTACCCCGGATATCACCTTCG 59.455 57.143 0.73 0.00 0.00 3.79
299 304 4.380973 CGGATATCACCTTCGTGCTATCAT 60.381 45.833 4.83 0.00 44.51 2.45
341 346 1.134220 GCTCCGATGAACCCCAATACA 60.134 52.381 0.00 0.00 0.00 2.29
347 352 2.595750 TGAACCCCAATACAACCCAG 57.404 50.000 0.00 0.00 0.00 4.45
353 358 2.041081 CCCCAATACAACCCAGTCTGAA 59.959 50.000 0.00 0.00 0.00 3.02
363 368 0.926155 CCAGTCTGAACGATGATGCG 59.074 55.000 0.00 0.00 37.29 4.73
389 394 1.301677 GAGGAGAACAAGCTTGCCGG 61.302 60.000 26.27 0.00 0.00 6.13
410 415 4.495349 CGGAGCAGAATCTACAAGCAAATG 60.495 45.833 0.00 0.00 0.00 2.32
414 419 4.156556 GCAGAATCTACAAGCAAATGGTGA 59.843 41.667 0.00 0.00 0.00 4.02
465 470 1.259609 ACTGGCATTGGTTCACATGG 58.740 50.000 0.00 0.00 0.00 3.66
499 532 8.877864 TGGTTAGTAATTCCATTCTGTTGAAT 57.122 30.769 0.00 0.00 43.10 2.57
500 533 9.967451 TGGTTAGTAATTCCATTCTGTTGAATA 57.033 29.630 0.00 0.00 40.61 1.75
533 568 8.181573 AGTTGATTGTAGCATGGTTTAAATACG 58.818 33.333 1.12 0.00 0.00 3.06
547 582 3.329929 AAATACGGTTCAGTGACCTCC 57.670 47.619 0.00 0.00 37.56 4.30
674 710 9.875691 TTTCCTACTTGCATGCATATATACTAG 57.124 33.333 23.37 15.40 0.00 2.57
675 711 8.595362 TCCTACTTGCATGCATATATACTAGT 57.405 34.615 23.37 20.33 0.00 2.57
676 712 9.695155 TCCTACTTGCATGCATATATACTAGTA 57.305 33.333 23.37 20.36 0.00 1.82
677 713 9.737427 CCTACTTGCATGCATATATACTAGTAC 57.263 37.037 23.37 0.00 0.00 2.73
698 734 8.276252 AGTACTACTTCTCTTTGCAAAAACAA 57.724 30.769 13.84 4.93 0.00 2.83
801 842 8.160765 TCAATCCTCACTTCACCTTGTTTATTA 58.839 33.333 0.00 0.00 0.00 0.98
804 845 8.754991 TCCTCACTTCACCTTGTTTATTAAAA 57.245 30.769 0.00 0.00 0.00 1.52
856 924 7.224949 ACGTTGAAAAAGAAAGGAAAACAAACA 59.775 29.630 0.00 0.00 0.00 2.83
882 950 0.679640 TTTACTCAATGGCCCCAGCG 60.680 55.000 0.00 0.00 41.24 5.18
905 973 1.581447 GCCAAAGAAGAAGCCACCG 59.419 57.895 0.00 0.00 0.00 4.94
938 1006 1.098712 CGAAGGCGCTCTCTACTCCT 61.099 60.000 7.64 0.00 0.00 3.69
989 1059 1.691434 CTACAGGCCTTCAGATCCCTC 59.309 57.143 0.00 0.00 0.00 4.30
993 1063 1.295292 AGGCCTTCAGATCCCTCCTAA 59.705 52.381 0.00 0.00 0.00 2.69
1098 1168 4.316823 TCCTCCCTCGCCACCAGT 62.317 66.667 0.00 0.00 0.00 4.00
1143 1213 1.901464 GCCCAAGCACCCGAAGAAA 60.901 57.895 0.00 0.00 39.53 2.52
1240 1310 2.355837 GCAGCACCGACGAAGACA 60.356 61.111 0.00 0.00 0.00 3.41
1344 1417 2.036731 TGGGTGTCCGAGATCCGT 59.963 61.111 0.00 0.00 36.31 4.69
1725 1801 2.476199 CTTCTTCTGGACCTGAGGGAT 58.524 52.381 2.38 0.00 36.25 3.85
1782 1858 3.885521 GCCGAGGAGTACGACGGG 61.886 72.222 18.58 10.19 41.55 5.28
1803 1879 4.254709 TGCTGCGTTGGGCTCAGT 62.255 61.111 0.00 0.00 44.05 3.41
1840 1916 5.187186 TGGGCCGAGTAGGAATATATTCTTC 59.813 44.000 21.80 14.12 45.00 2.87
1842 1918 6.334202 GGCCGAGTAGGAATATATTCTTCAG 58.666 44.000 21.80 10.67 45.00 3.02
1844 1920 7.379750 GCCGAGTAGGAATATATTCTTCAGTT 58.620 38.462 21.80 6.47 45.00 3.16
1889 1965 7.759886 TGAATTGCTTTGCTAGTGTACTAGTAG 59.240 37.037 17.65 13.72 45.85 2.57
1890 1966 6.585695 TTGCTTTGCTAGTGTACTAGTAGT 57.414 37.500 17.65 8.14 45.85 2.73
1891 1967 7.692460 TTGCTTTGCTAGTGTACTAGTAGTA 57.308 36.000 17.65 5.90 45.85 1.82
1892 1968 7.876936 TGCTTTGCTAGTGTACTAGTAGTAT 57.123 36.000 13.09 0.62 45.85 2.12
1893 1969 7.704271 TGCTTTGCTAGTGTACTAGTAGTATG 58.296 38.462 13.09 5.92 45.85 2.39
1894 1970 7.140048 GCTTTGCTAGTGTACTAGTAGTATGG 58.860 42.308 13.09 1.44 45.85 2.74
1895 1971 6.630444 TTGCTAGTGTACTAGTAGTATGGC 57.370 41.667 13.09 11.08 45.85 4.40
1896 1972 5.687780 TGCTAGTGTACTAGTAGTATGGCA 58.312 41.667 13.09 13.30 45.85 4.92
1897 1973 6.124340 TGCTAGTGTACTAGTAGTATGGCAA 58.876 40.000 13.09 1.11 45.85 4.52
1898 1974 6.262496 TGCTAGTGTACTAGTAGTATGGCAAG 59.738 42.308 13.09 8.66 45.85 4.01
1899 1975 6.294065 GCTAGTGTACTAGTAGTATGGCAAGG 60.294 46.154 13.09 3.26 45.85 3.61
1900 1976 5.516984 AGTGTACTAGTAGTATGGCAAGGT 58.483 41.667 13.09 0.00 32.65 3.50
1901 1977 5.956563 AGTGTACTAGTAGTATGGCAAGGTT 59.043 40.000 13.09 0.00 32.65 3.50
1902 1978 6.040878 GTGTACTAGTAGTATGGCAAGGTTG 58.959 44.000 13.09 0.00 32.65 3.77
1903 1979 4.755266 ACTAGTAGTATGGCAAGGTTGG 57.245 45.455 0.00 0.00 0.00 3.77
2061 2138 2.867975 CAACAAAAGAAGCTTTGCCAGG 59.132 45.455 0.00 0.00 39.46 4.45
2064 2141 0.677842 AAAGAAGCTTTGCCAGGCAG 59.322 50.000 15.50 5.13 40.61 4.85
2090 2167 3.181443 GGACTTCCCTGGAAAAGAAGACA 60.181 47.826 14.74 0.00 39.50 3.41
2115 2192 6.376018 ACAGGTTTACTCTACAAGTTTGCAAA 59.624 34.615 8.05 8.05 39.55 3.68
2171 2258 3.987954 ATGGTGGGCCGCCGTTTAG 62.988 63.158 29.85 0.00 36.72 1.85
2182 2272 2.384203 CCGTTTAGTGGCAGCTAGC 58.616 57.895 6.62 6.62 44.65 3.42
2212 2303 3.323729 ACTCGATGCGTTGCAATTATG 57.676 42.857 0.59 0.00 43.62 1.90
2216 2307 4.480541 TCGATGCGTTGCAATTATGTTTT 58.519 34.783 0.59 0.00 43.62 2.43
2217 2308 4.323070 TCGATGCGTTGCAATTATGTTTTG 59.677 37.500 0.59 0.00 43.62 2.44
2219 2310 4.963237 TGCGTTGCAATTATGTTTTGTC 57.037 36.364 0.59 0.00 34.76 3.18
2220 2311 4.363138 TGCGTTGCAATTATGTTTTGTCA 58.637 34.783 0.59 0.00 34.76 3.58
2221 2312 4.443725 TGCGTTGCAATTATGTTTTGTCAG 59.556 37.500 0.59 0.00 34.76 3.51
2226 2319 7.253917 CGTTGCAATTATGTTTTGTCAGTTTGA 60.254 33.333 0.59 0.00 0.00 2.69
2243 2336 9.276590 GTCAGTTTGATGATATTCATATGGTGA 57.723 33.333 2.13 0.00 37.20 4.02
2254 2347 0.479815 ATATGGTGATGGCCTGGTGG 59.520 55.000 3.32 0.00 0.00 4.61
2281 2409 2.356382 CGGCCGGATTTATACAAGCAAA 59.644 45.455 20.10 0.00 0.00 3.68
2284 2412 5.356426 GGCCGGATTTATACAAGCAAAAAT 58.644 37.500 5.05 0.00 0.00 1.82
2286 2414 6.981559 GGCCGGATTTATACAAGCAAAAATAA 59.018 34.615 5.05 0.00 0.00 1.40
2287 2415 7.492994 GGCCGGATTTATACAAGCAAAAATAAA 59.507 33.333 5.05 0.00 0.00 1.40
2366 2512 2.606272 GTGTTAGCGTGTTATACTGCCC 59.394 50.000 0.00 0.00 31.95 5.36
2373 2519 2.481449 CGTGTTATACTGCCCCACTCTC 60.481 54.545 0.00 0.00 0.00 3.20
2381 2528 2.596851 GCCCCACTCTCCAGCAGAA 61.597 63.158 0.00 0.00 0.00 3.02
2416 2563 5.321927 ACGAACAAACTCCCTAATTTCCAT 58.678 37.500 0.00 0.00 0.00 3.41
2432 2579 9.255304 CTAATTTCCATAGAGCTCTGACTTTAC 57.745 37.037 26.78 0.00 0.00 2.01
2433 2580 6.859112 TTTCCATAGAGCTCTGACTTTACT 57.141 37.500 26.78 0.00 0.00 2.24
2434 2581 6.458232 TTCCATAGAGCTCTGACTTTACTC 57.542 41.667 26.78 0.00 0.00 2.59
2435 2582 5.761205 TCCATAGAGCTCTGACTTTACTCT 58.239 41.667 26.78 0.00 40.65 3.24
2436 2583 6.191315 TCCATAGAGCTCTGACTTTACTCTT 58.809 40.000 26.78 0.00 38.59 2.85
2437 2584 7.347252 TCCATAGAGCTCTGACTTTACTCTTA 58.653 38.462 26.78 1.05 38.59 2.10
2438 2585 7.283580 TCCATAGAGCTCTGACTTTACTCTTAC 59.716 40.741 26.78 0.00 38.59 2.34
2439 2586 7.284489 CCATAGAGCTCTGACTTTACTCTTACT 59.716 40.741 26.78 0.00 38.59 2.24
2440 2587 6.753107 AGAGCTCTGACTTTACTCTTACTC 57.247 41.667 17.42 0.00 34.06 2.59
2441 2588 6.481643 AGAGCTCTGACTTTACTCTTACTCT 58.518 40.000 17.42 0.00 34.06 3.24
2442 2589 6.946009 AGAGCTCTGACTTTACTCTTACTCTT 59.054 38.462 17.42 0.00 34.06 2.85
2443 2590 6.919721 AGCTCTGACTTTACTCTTACTCTTG 58.080 40.000 0.00 0.00 0.00 3.02
2444 2591 5.575218 GCTCTGACTTTACTCTTACTCTTGC 59.425 44.000 0.00 0.00 0.00 4.01
2445 2592 6.571537 GCTCTGACTTTACTCTTACTCTTGCT 60.572 42.308 0.00 0.00 0.00 3.91
2446 2593 6.682746 TCTGACTTTACTCTTACTCTTGCTG 58.317 40.000 0.00 0.00 0.00 4.41
2447 2594 5.230942 TGACTTTACTCTTACTCTTGCTGC 58.769 41.667 0.00 0.00 0.00 5.25
2448 2595 5.011125 TGACTTTACTCTTACTCTTGCTGCT 59.989 40.000 0.00 0.00 0.00 4.24
2449 2596 5.859495 ACTTTACTCTTACTCTTGCTGCTT 58.141 37.500 0.00 0.00 0.00 3.91
2450 2597 6.292150 ACTTTACTCTTACTCTTGCTGCTTT 58.708 36.000 0.00 0.00 0.00 3.51
2451 2598 6.768381 ACTTTACTCTTACTCTTGCTGCTTTT 59.232 34.615 0.00 0.00 0.00 2.27
2452 2599 7.283354 ACTTTACTCTTACTCTTGCTGCTTTTT 59.717 33.333 0.00 0.00 0.00 1.94
2493 2640 0.734253 CTTGCTGCTCTTACGTCGCT 60.734 55.000 0.00 0.00 0.00 4.93
2526 2673 4.508763 GGATCTCTAGAAATACGGAGGGGA 60.509 50.000 0.00 0.00 0.00 4.81
2584 2742 6.143919 GCCTTTTAATTACATGCGGCTTATTC 59.856 38.462 0.00 0.00 33.68 1.75
2741 2918 4.251103 AGGGTCAAAGAAAGTTCCAACT 57.749 40.909 0.00 0.00 42.04 3.16
2782 2959 1.454111 TCTCCTAGCAGCGGAGGTC 60.454 63.158 14.51 0.00 46.43 3.85
2795 2984 1.136446 CGGAGGTCAGTTAAAAACGCG 60.136 52.381 3.53 3.53 36.23 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.909644 GTGACGACTATGTATTCCTGTTAATAT 57.090 33.333 0.00 0.00 0.00 1.28
1 2 8.355169 GGTGACGACTATGTATTCCTGTTAATA 58.645 37.037 0.00 0.00 0.00 0.98
2 3 7.208080 GGTGACGACTATGTATTCCTGTTAAT 58.792 38.462 0.00 0.00 0.00 1.40
3 4 6.567050 GGTGACGACTATGTATTCCTGTTAA 58.433 40.000 0.00 0.00 0.00 2.01
4 5 6.140303 GGTGACGACTATGTATTCCTGTTA 57.860 41.667 0.00 0.00 0.00 2.41
5 6 5.007385 GGTGACGACTATGTATTCCTGTT 57.993 43.478 0.00 0.00 0.00 3.16
6 7 4.650754 GGTGACGACTATGTATTCCTGT 57.349 45.455 0.00 0.00 0.00 4.00
22 23 5.413523 AGATGTAACCAAAATTACCGGTGAC 59.586 40.000 19.93 0.00 35.05 3.67
23 24 5.562635 AGATGTAACCAAAATTACCGGTGA 58.437 37.500 19.93 10.28 34.67 4.02
24 25 5.890424 AGATGTAACCAAAATTACCGGTG 57.110 39.130 19.93 0.00 34.67 4.94
25 26 6.092533 CGTTAGATGTAACCAAAATTACCGGT 59.907 38.462 13.98 13.98 35.96 5.28
26 27 6.457257 CCGTTAGATGTAACCAAAATTACCGG 60.457 42.308 0.00 0.00 35.96 5.28
27 28 6.457257 CCCGTTAGATGTAACCAAAATTACCG 60.457 42.308 7.14 0.00 35.96 4.02
28 29 6.678655 GCCCGTTAGATGTAACCAAAATTACC 60.679 42.308 7.14 0.00 35.96 2.85
29 30 6.127952 TGCCCGTTAGATGTAACCAAAATTAC 60.128 38.462 7.14 0.00 35.96 1.89
30 31 5.944599 TGCCCGTTAGATGTAACCAAAATTA 59.055 36.000 7.14 0.00 35.96 1.40
31 32 4.767928 TGCCCGTTAGATGTAACCAAAATT 59.232 37.500 7.14 0.00 35.96 1.82
32 33 4.337145 TGCCCGTTAGATGTAACCAAAAT 58.663 39.130 7.14 0.00 35.96 1.82
33 34 3.752665 TGCCCGTTAGATGTAACCAAAA 58.247 40.909 7.14 0.00 35.96 2.44
34 35 3.420300 TGCCCGTTAGATGTAACCAAA 57.580 42.857 7.14 0.00 35.96 3.28
35 36 3.420300 TTGCCCGTTAGATGTAACCAA 57.580 42.857 7.14 3.58 35.96 3.67
36 37 3.420300 TTTGCCCGTTAGATGTAACCA 57.580 42.857 7.14 0.00 35.96 3.67
37 38 4.976224 ATTTTGCCCGTTAGATGTAACC 57.024 40.909 7.14 0.00 35.96 2.85
38 39 7.080353 ACTTATTTTGCCCGTTAGATGTAAC 57.920 36.000 2.68 2.68 36.00 2.50
39 40 7.362229 CCAACTTATTTTGCCCGTTAGATGTAA 60.362 37.037 0.00 0.00 0.00 2.41
40 41 6.094325 CCAACTTATTTTGCCCGTTAGATGTA 59.906 38.462 0.00 0.00 0.00 2.29
41 42 5.105917 CCAACTTATTTTGCCCGTTAGATGT 60.106 40.000 0.00 0.00 0.00 3.06
42 43 5.105917 ACCAACTTATTTTGCCCGTTAGATG 60.106 40.000 0.00 0.00 0.00 2.90
43 44 5.014202 ACCAACTTATTTTGCCCGTTAGAT 58.986 37.500 0.00 0.00 0.00 1.98
44 45 4.400120 ACCAACTTATTTTGCCCGTTAGA 58.600 39.130 0.00 0.00 0.00 2.10
45 46 4.776795 ACCAACTTATTTTGCCCGTTAG 57.223 40.909 0.00 0.00 0.00 2.34
46 47 5.068636 TGTACCAACTTATTTTGCCCGTTA 58.931 37.500 0.00 0.00 0.00 3.18
47 48 3.890147 TGTACCAACTTATTTTGCCCGTT 59.110 39.130 0.00 0.00 0.00 4.44
48 49 3.488363 TGTACCAACTTATTTTGCCCGT 58.512 40.909 0.00 0.00 0.00 5.28
49 50 3.119637 CCTGTACCAACTTATTTTGCCCG 60.120 47.826 0.00 0.00 0.00 6.13
50 51 3.194755 CCCTGTACCAACTTATTTTGCCC 59.805 47.826 0.00 0.00 0.00 5.36
51 52 3.194755 CCCCTGTACCAACTTATTTTGCC 59.805 47.826 0.00 0.00 0.00 4.52
52 53 3.830178 ACCCCTGTACCAACTTATTTTGC 59.170 43.478 0.00 0.00 0.00 3.68
53 54 6.413783 AAACCCCTGTACCAACTTATTTTG 57.586 37.500 0.00 0.00 0.00 2.44
54 55 7.299896 ACTAAACCCCTGTACCAACTTATTTT 58.700 34.615 0.00 0.00 0.00 1.82
55 56 6.855667 ACTAAACCCCTGTACCAACTTATTT 58.144 36.000 0.00 0.00 0.00 1.40
56 57 6.273965 AGACTAAACCCCTGTACCAACTTATT 59.726 38.462 0.00 0.00 0.00 1.40
57 58 5.789054 AGACTAAACCCCTGTACCAACTTAT 59.211 40.000 0.00 0.00 0.00 1.73
58 59 5.157395 AGACTAAACCCCTGTACCAACTTA 58.843 41.667 0.00 0.00 0.00 2.24
59 60 3.978672 AGACTAAACCCCTGTACCAACTT 59.021 43.478 0.00 0.00 0.00 2.66
60 61 3.581770 GAGACTAAACCCCTGTACCAACT 59.418 47.826 0.00 0.00 0.00 3.16
61 62 3.307269 GGAGACTAAACCCCTGTACCAAC 60.307 52.174 0.00 0.00 0.00 3.77
62 63 2.908351 GGAGACTAAACCCCTGTACCAA 59.092 50.000 0.00 0.00 0.00 3.67
63 64 2.543635 GGAGACTAAACCCCTGTACCA 58.456 52.381 0.00 0.00 0.00 3.25
64 65 1.836166 GGGAGACTAAACCCCTGTACC 59.164 57.143 0.00 0.00 40.19 3.34
65 66 1.479730 CGGGAGACTAAACCCCTGTAC 59.520 57.143 0.00 0.00 42.86 2.90
66 67 1.077663 ACGGGAGACTAAACCCCTGTA 59.922 52.381 0.00 0.00 42.86 2.74
67 68 0.178912 ACGGGAGACTAAACCCCTGT 60.179 55.000 0.00 0.00 42.86 4.00
68 69 0.535797 GACGGGAGACTAAACCCCTG 59.464 60.000 0.00 0.00 42.86 4.45
69 70 0.969409 CGACGGGAGACTAAACCCCT 60.969 60.000 0.00 0.00 42.86 4.79
70 71 0.967380 TCGACGGGAGACTAAACCCC 60.967 60.000 0.00 0.00 42.86 4.95
71 72 1.109609 ATCGACGGGAGACTAAACCC 58.890 55.000 0.00 0.00 42.43 4.11
72 73 1.202382 CCATCGACGGGAGACTAAACC 60.202 57.143 0.00 0.00 0.00 3.27
73 74 1.475682 ACCATCGACGGGAGACTAAAC 59.524 52.381 11.67 0.00 0.00 2.01
74 75 1.475280 CACCATCGACGGGAGACTAAA 59.525 52.381 11.67 0.00 0.00 1.85
75 76 1.100510 CACCATCGACGGGAGACTAA 58.899 55.000 11.67 0.00 0.00 2.24
76 77 0.034767 ACACCATCGACGGGAGACTA 60.035 55.000 11.67 0.00 0.00 2.59
77 78 0.034767 TACACCATCGACGGGAGACT 60.035 55.000 11.67 0.00 0.00 3.24
78 79 1.030457 ATACACCATCGACGGGAGAC 58.970 55.000 11.67 0.00 0.00 3.36
79 80 1.029681 CATACACCATCGACGGGAGA 58.970 55.000 11.67 0.00 0.00 3.71
80 81 1.029681 TCATACACCATCGACGGGAG 58.970 55.000 11.67 6.42 0.00 4.30
81 82 1.699730 ATCATACACCATCGACGGGA 58.300 50.000 11.67 0.00 0.00 5.14
82 83 2.035961 AGAATCATACACCATCGACGGG 59.964 50.000 1.13 2.48 0.00 5.28
83 84 3.052745 CAGAATCATACACCATCGACGG 58.947 50.000 0.00 0.00 0.00 4.79
84 85 3.487207 CACAGAATCATACACCATCGACG 59.513 47.826 0.00 0.00 0.00 5.12
85 86 3.804325 CCACAGAATCATACACCATCGAC 59.196 47.826 0.00 0.00 0.00 4.20
86 87 3.450817 ACCACAGAATCATACACCATCGA 59.549 43.478 0.00 0.00 0.00 3.59
87 88 3.797039 ACCACAGAATCATACACCATCG 58.203 45.455 0.00 0.00 0.00 3.84
88 89 5.755375 CACTACCACAGAATCATACACCATC 59.245 44.000 0.00 0.00 0.00 3.51
89 90 5.189736 ACACTACCACAGAATCATACACCAT 59.810 40.000 0.00 0.00 0.00 3.55
90 91 4.530553 ACACTACCACAGAATCATACACCA 59.469 41.667 0.00 0.00 0.00 4.17
91 92 5.086104 ACACTACCACAGAATCATACACC 57.914 43.478 0.00 0.00 0.00 4.16
92 93 7.817962 AGTTTACACTACCACAGAATCATACAC 59.182 37.037 0.00 0.00 0.00 2.90
93 94 7.903145 AGTTTACACTACCACAGAATCATACA 58.097 34.615 0.00 0.00 0.00 2.29
94 95 8.251721 AGAGTTTACACTACCACAGAATCATAC 58.748 37.037 0.00 0.00 31.22 2.39
95 96 8.362464 AGAGTTTACACTACCACAGAATCATA 57.638 34.615 0.00 0.00 31.22 2.15
96 97 7.246171 AGAGTTTACACTACCACAGAATCAT 57.754 36.000 0.00 0.00 31.22 2.45
97 98 6.665992 AGAGTTTACACTACCACAGAATCA 57.334 37.500 0.00 0.00 31.22 2.57
98 99 9.654663 AAATAGAGTTTACACTACCACAGAATC 57.345 33.333 0.00 0.00 31.22 2.52
99 100 9.436957 CAAATAGAGTTTACACTACCACAGAAT 57.563 33.333 0.00 0.00 31.22 2.40
100 101 8.426489 ACAAATAGAGTTTACACTACCACAGAA 58.574 33.333 0.00 0.00 31.22 3.02
101 102 7.959175 ACAAATAGAGTTTACACTACCACAGA 58.041 34.615 0.00 0.00 31.22 3.41
102 103 8.603242 AACAAATAGAGTTTACACTACCACAG 57.397 34.615 0.00 0.00 31.22 3.66
103 104 7.658575 GGAACAAATAGAGTTTACACTACCACA 59.341 37.037 0.00 0.00 31.22 4.17
104 105 7.118825 GGGAACAAATAGAGTTTACACTACCAC 59.881 40.741 0.00 0.00 31.22 4.16
105 106 7.016858 AGGGAACAAATAGAGTTTACACTACCA 59.983 37.037 0.00 0.00 31.22 3.25
106 107 7.392418 AGGGAACAAATAGAGTTTACACTACC 58.608 38.462 0.00 0.00 31.22 3.18
107 108 8.843885 AAGGGAACAAATAGAGTTTACACTAC 57.156 34.615 0.00 0.00 31.22 2.73
109 110 9.856162 TTTAAGGGAACAAATAGAGTTTACACT 57.144 29.630 0.00 0.00 35.17 3.55
169 170 9.219603 CATGATGTGTTCCTTTAAAAGTCTCTA 57.780 33.333 0.00 0.00 0.00 2.43
173 174 6.981722 ACCATGATGTGTTCCTTTAAAAGTC 58.018 36.000 0.00 0.00 0.00 3.01
174 175 6.976934 ACCATGATGTGTTCCTTTAAAAGT 57.023 33.333 0.00 0.00 0.00 2.66
175 176 8.335532 TCTACCATGATGTGTTCCTTTAAAAG 57.664 34.615 0.00 0.00 0.00 2.27
178 179 7.016153 ACTCTACCATGATGTGTTCCTTTAA 57.984 36.000 0.00 0.00 0.00 1.52
181 182 5.505181 AACTCTACCATGATGTGTTCCTT 57.495 39.130 0.00 0.00 0.00 3.36
183 184 5.705441 TCAAAACTCTACCATGATGTGTTCC 59.295 40.000 0.00 0.00 0.00 3.62
184 185 6.801539 TCAAAACTCTACCATGATGTGTTC 57.198 37.500 0.00 0.00 0.00 3.18
185 186 7.231317 ACAATCAAAACTCTACCATGATGTGTT 59.769 33.333 0.00 0.00 31.49 3.32
186 187 6.716628 ACAATCAAAACTCTACCATGATGTGT 59.283 34.615 0.00 0.00 31.49 3.72
187 188 7.149569 ACAATCAAAACTCTACCATGATGTG 57.850 36.000 0.00 0.00 31.49 3.21
188 189 7.765695 AACAATCAAAACTCTACCATGATGT 57.234 32.000 0.00 0.00 31.49 3.06
189 190 8.400947 CCTAACAATCAAAACTCTACCATGATG 58.599 37.037 0.00 0.00 31.49 3.07
207 208 9.930693 GAGATCTTATACGGAAATCCTAACAAT 57.069 33.333 0.00 0.00 0.00 2.71
209 210 8.473358 TGAGATCTTATACGGAAATCCTAACA 57.527 34.615 0.00 0.00 0.00 2.41
210 211 9.930693 ATTGAGATCTTATACGGAAATCCTAAC 57.069 33.333 0.00 0.00 0.00 2.34
225 226 7.290248 AGGGATCGGAAACTAATTGAGATCTTA 59.710 37.037 0.00 0.00 33.97 2.10
247 248 0.642156 TGAGGCCAGGAATCTAGGGA 59.358 55.000 5.01 0.00 0.00 4.20
248 249 1.141858 GTTGAGGCCAGGAATCTAGGG 59.858 57.143 5.01 0.00 0.00 3.53
250 251 1.141858 GGGTTGAGGCCAGGAATCTAG 59.858 57.143 5.01 0.00 0.00 2.43
251 252 1.213296 GGGTTGAGGCCAGGAATCTA 58.787 55.000 5.01 0.00 0.00 1.98
252 253 0.551131 AGGGTTGAGGCCAGGAATCT 60.551 55.000 5.01 0.00 0.00 2.40
253 254 1.134068 GTAGGGTTGAGGCCAGGAATC 60.134 57.143 5.01 0.00 0.00 2.52
254 255 0.919710 GTAGGGTTGAGGCCAGGAAT 59.080 55.000 5.01 0.00 0.00 3.01
255 256 1.205460 GGTAGGGTTGAGGCCAGGAA 61.205 60.000 5.01 0.00 0.00 3.36
256 257 1.615424 GGTAGGGTTGAGGCCAGGA 60.615 63.158 5.01 0.00 0.00 3.86
257 258 2.680370 GGGTAGGGTTGAGGCCAGG 61.680 68.421 5.01 0.00 0.00 4.45
258 259 2.680370 GGGGTAGGGTTGAGGCCAG 61.680 68.421 5.01 0.00 0.00 4.85
259 260 2.612746 GGGGTAGGGTTGAGGCCA 60.613 66.667 5.01 0.00 0.00 5.36
260 261 3.793888 CGGGGTAGGGTTGAGGCC 61.794 72.222 0.00 0.00 0.00 5.19
261 262 3.793888 CCGGGGTAGGGTTGAGGC 61.794 72.222 0.00 0.00 0.00 4.70
299 304 4.959839 GCCCCCTTAAACTTGATTGGATAA 59.040 41.667 0.00 0.00 0.00 1.75
341 346 2.936993 GCATCATCGTTCAGACTGGGTT 60.937 50.000 1.81 0.00 0.00 4.11
347 352 1.154205 CCCCGCATCATCGTTCAGAC 61.154 60.000 0.00 0.00 0.00 3.51
353 358 3.550431 CCTCCCCCGCATCATCGT 61.550 66.667 0.00 0.00 0.00 3.73
363 368 1.916206 GCTTGTTCTCCTCCTCCCCC 61.916 65.000 0.00 0.00 0.00 5.40
389 394 4.397417 ACCATTTGCTTGTAGATTCTGCTC 59.603 41.667 3.38 0.00 0.00 4.26
410 415 5.584649 TCTGATTCGGATTTATTGTGTCACC 59.415 40.000 0.00 0.00 0.00 4.02
414 419 5.063438 CACGTCTGATTCGGATTTATTGTGT 59.937 40.000 0.00 0.00 0.00 3.72
499 532 7.116075 ACCATGCTACAATCAACTGGTTTATA 58.884 34.615 0.00 0.00 31.69 0.98
500 533 5.951747 ACCATGCTACAATCAACTGGTTTAT 59.048 36.000 0.00 0.00 31.69 1.40
533 568 2.586648 AAATGGGAGGTCACTGAACC 57.413 50.000 0.00 0.00 39.80 3.62
547 582 6.649973 TGCAGTCAATTGGTCAATTAAAATGG 59.350 34.615 5.42 0.00 38.84 3.16
673 709 7.859325 TGTTTTTGCAAAGAGAAGTAGTACT 57.141 32.000 12.41 0.00 0.00 2.73
676 712 9.683069 CATATTGTTTTTGCAAAGAGAAGTAGT 57.317 29.630 15.86 4.19 31.63 2.73
677 713 9.897744 TCATATTGTTTTTGCAAAGAGAAGTAG 57.102 29.630 15.86 9.05 31.63 2.57
812 853 8.821147 TTCAACGTGTTAGTACTATTCACAAT 57.179 30.769 24.85 16.05 0.00 2.71
813 854 8.645730 TTTCAACGTGTTAGTACTATTCACAA 57.354 30.769 24.85 15.50 0.00 3.33
814 855 8.645730 TTTTCAACGTGTTAGTACTATTCACA 57.354 30.769 24.85 16.15 0.00 3.58
856 924 2.029380 GGGCCATTGAGTAAAGCGTTTT 60.029 45.455 4.39 2.00 0.00 2.43
882 950 1.271597 TGGCTTCTTCTTTGGCCTCTC 60.272 52.381 3.32 0.00 44.36 3.20
905 973 2.740452 GCCTTCGGCCGTATATATAGC 58.260 52.381 27.15 13.69 44.06 2.97
938 1006 1.371183 CAAGAAGCGTGGGGACTGA 59.629 57.895 0.00 0.00 0.00 3.41
1014 1084 2.601367 GTGGTGGGTGCATGGCTT 60.601 61.111 0.00 0.00 0.00 4.35
1098 1168 0.252239 TCTTGGGGAGCTCTAGCACA 60.252 55.000 14.64 0.83 45.16 4.57
1193 1263 4.717629 CGTCTCCTCGTGCGCCAA 62.718 66.667 4.18 0.00 0.00 4.52
1200 1270 2.403378 GCTGCTCTCGTCTCCTCGT 61.403 63.158 0.00 0.00 0.00 4.18
1323 1396 1.481871 GGATCTCGGACACCCACTTA 58.518 55.000 0.00 0.00 0.00 2.24
1344 1417 2.738521 GACTTCTTGCGCGGCTCA 60.739 61.111 8.83 0.00 0.00 4.26
1725 1801 3.706373 GGCGACCAGAAGAGCCCA 61.706 66.667 0.00 0.00 43.54 5.36
1803 1879 2.596851 GGCCCACAAGAGAGGCTCA 61.597 63.158 18.26 0.00 46.31 4.26
1840 1916 2.225727 GAGCCCAGAACGGTAAAAACTG 59.774 50.000 0.00 0.00 0.00 3.16
1842 1918 2.223745 TGAGCCCAGAACGGTAAAAAC 58.776 47.619 0.00 0.00 0.00 2.43
1844 1920 2.039216 TCATGAGCCCAGAACGGTAAAA 59.961 45.455 0.00 0.00 0.00 1.52
1889 1965 4.529109 TTTTTAGCCAACCTTGCCATAC 57.471 40.909 0.00 0.00 0.00 2.39
1909 1985 9.528489 TCTTTTATCCTTGCCATACTACTTTTT 57.472 29.630 0.00 0.00 0.00 1.94
1910 1986 9.700831 ATCTTTTATCCTTGCCATACTACTTTT 57.299 29.630 0.00 0.00 0.00 2.27
1911 1987 9.700831 AATCTTTTATCCTTGCCATACTACTTT 57.299 29.630 0.00 0.00 0.00 2.66
1912 1988 9.700831 AAATCTTTTATCCTTGCCATACTACTT 57.299 29.630 0.00 0.00 0.00 2.24
1916 1992 9.125026 CACTAAATCTTTTATCCTTGCCATACT 57.875 33.333 0.00 0.00 0.00 2.12
1917 1993 8.352942 CCACTAAATCTTTTATCCTTGCCATAC 58.647 37.037 0.00 0.00 0.00 2.39
1918 1994 8.058847 ACCACTAAATCTTTTATCCTTGCCATA 58.941 33.333 0.00 0.00 0.00 2.74
1919 1995 6.897413 ACCACTAAATCTTTTATCCTTGCCAT 59.103 34.615 0.00 0.00 0.00 4.40
1920 1996 6.252995 ACCACTAAATCTTTTATCCTTGCCA 58.747 36.000 0.00 0.00 0.00 4.92
1921 1997 6.775594 ACCACTAAATCTTTTATCCTTGCC 57.224 37.500 0.00 0.00 0.00 4.52
1922 1998 7.067008 TGCTACCACTAAATCTTTTATCCTTGC 59.933 37.037 0.00 0.00 0.00 4.01
1923 1999 8.506168 TGCTACCACTAAATCTTTTATCCTTG 57.494 34.615 0.00 0.00 0.00 3.61
1924 2000 8.329502 ACTGCTACCACTAAATCTTTTATCCTT 58.670 33.333 0.00 0.00 0.00 3.36
1925 2001 7.862675 ACTGCTACCACTAAATCTTTTATCCT 58.137 34.615 0.00 0.00 0.00 3.24
1926 2002 9.262358 CTACTGCTACCACTAAATCTTTTATCC 57.738 37.037 0.00 0.00 0.00 2.59
1927 2003 8.766151 GCTACTGCTACCACTAAATCTTTTATC 58.234 37.037 0.00 0.00 36.03 1.75
1928 2004 8.265055 TGCTACTGCTACCACTAAATCTTTTAT 58.735 33.333 0.00 0.00 40.48 1.40
1929 2005 7.548075 GTGCTACTGCTACCACTAAATCTTTTA 59.452 37.037 0.00 0.00 40.48 1.52
2061 2138 1.225704 CCAGGGAAGTCCATCCTGC 59.774 63.158 0.00 0.00 44.87 4.85
2064 2141 2.308866 TCTTTTCCAGGGAAGTCCATCC 59.691 50.000 0.42 0.00 38.24 3.51
2090 2167 5.433526 TGCAAACTTGTAGAGTAAACCTGT 58.566 37.500 0.00 0.00 37.72 4.00
2115 2192 5.884232 TCAACTGAGCAATCATCTAAAGCAT 59.116 36.000 0.00 0.00 0.00 3.79
2171 2258 4.636206 AGTTAATTAACTGCTAGCTGCCAC 59.364 41.667 26.30 7.61 44.30 5.01
2175 2262 6.563010 GCATCGAGTTAATTAACTGCTAGCTG 60.563 42.308 30.66 20.25 45.84 4.24
2182 2272 4.723862 GCAACGCATCGAGTTAATTAACTG 59.276 41.667 30.66 22.13 45.84 3.16
2190 2280 4.331443 ACATAATTGCAACGCATCGAGTTA 59.669 37.500 0.00 0.00 38.76 2.24
2192 2282 2.677836 ACATAATTGCAACGCATCGAGT 59.322 40.909 0.00 0.00 38.76 4.18
2216 2307 9.059260 CACCATATGAATATCATCAAACTGACA 57.941 33.333 3.65 0.00 38.26 3.58
2217 2308 9.276590 TCACCATATGAATATCATCAAACTGAC 57.723 33.333 3.65 0.00 38.26 3.51
2220 2311 9.239551 CCATCACCATATGAATATCATCAAACT 57.760 33.333 3.65 0.00 41.93 2.66
2221 2312 7.972277 GCCATCACCATATGAATATCATCAAAC 59.028 37.037 3.65 0.00 41.93 2.93
2226 2319 6.127101 CAGGCCATCACCATATGAATATCAT 58.873 40.000 5.01 0.00 41.93 2.45
2256 2349 0.250124 TGTATAAATCCGGCCGGCAG 60.250 55.000 39.89 25.71 34.68 4.85
2286 2414 8.439172 TGAAATCAGGAAGGAATTTGGATTTTT 58.561 29.630 0.00 0.00 34.65 1.94
2287 2415 7.879677 GTGAAATCAGGAAGGAATTTGGATTTT 59.120 33.333 0.00 0.00 34.65 1.82
2291 2419 5.392995 TGTGAAATCAGGAAGGAATTTGGA 58.607 37.500 0.00 0.00 0.00 3.53
2293 2421 6.144402 CGTTTGTGAAATCAGGAAGGAATTTG 59.856 38.462 0.00 0.00 0.00 2.32
2294 2422 6.040391 TCGTTTGTGAAATCAGGAAGGAATTT 59.960 34.615 0.00 0.00 0.00 1.82
2296 2424 5.070001 TCGTTTGTGAAATCAGGAAGGAAT 58.930 37.500 0.00 0.00 0.00 3.01
2303 2446 4.290155 CCAAACTCGTTTGTGAAATCAGG 58.710 43.478 18.12 0.05 46.19 3.86
2330 2473 4.327680 GCTAACACAAGAGTCCATTCCTT 58.672 43.478 0.00 0.00 0.00 3.36
2366 2512 0.673022 GCACTTCTGCTGGAGAGTGG 60.673 60.000 20.90 10.62 40.63 4.00
2373 2519 3.632189 GTTAAAAGTGCACTTCTGCTGG 58.368 45.455 31.20 0.00 44.57 4.85
2381 2528 5.305139 AGTTTGTTCGTTAAAAGTGCACT 57.695 34.783 15.25 15.25 0.00 4.40
2416 2563 7.626390 AGAGTAAGAGTAAAGTCAGAGCTCTA 58.374 38.462 17.75 2.18 35.72 2.43
2458 2605 4.619973 CAGCAAGAGTAACCATGCAAAAA 58.380 39.130 0.00 0.00 41.18 1.94
2459 2606 3.552684 GCAGCAAGAGTAACCATGCAAAA 60.553 43.478 0.00 0.00 41.18 2.44
2460 2607 2.030007 GCAGCAAGAGTAACCATGCAAA 60.030 45.455 0.00 0.00 41.18 3.68
2461 2608 1.541147 GCAGCAAGAGTAACCATGCAA 59.459 47.619 0.00 0.00 41.18 4.08
2462 2609 1.167851 GCAGCAAGAGTAACCATGCA 58.832 50.000 0.00 0.00 41.18 3.96
2463 2610 1.399791 GAGCAGCAAGAGTAACCATGC 59.600 52.381 0.00 0.00 39.06 4.06
2464 2611 2.983229 AGAGCAGCAAGAGTAACCATG 58.017 47.619 0.00 0.00 0.00 3.66
2465 2612 3.710209 AAGAGCAGCAAGAGTAACCAT 57.290 42.857 0.00 0.00 0.00 3.55
2466 2613 3.614150 CGTAAGAGCAGCAAGAGTAACCA 60.614 47.826 0.00 0.00 43.02 3.67
2467 2614 2.924290 CGTAAGAGCAGCAAGAGTAACC 59.076 50.000 0.00 0.00 43.02 2.85
2468 2615 3.576648 ACGTAAGAGCAGCAAGAGTAAC 58.423 45.455 0.00 0.00 43.62 2.50
2526 2673 9.780186 GGCATTGGAGTACTAGTATAAGATTTT 57.220 33.333 5.75 0.00 0.00 1.82
2572 2730 1.672881 GAGCAGTTGAATAAGCCGCAT 59.327 47.619 0.00 0.00 0.00 4.73
2584 2742 1.000955 ACTTCACCTACGGAGCAGTTG 59.999 52.381 0.00 0.00 0.00 3.16
2711 2888 4.829492 ACTTTCTTTGACCCTTCCATCTTG 59.171 41.667 0.00 0.00 0.00 3.02
2712 2889 5.066913 ACTTTCTTTGACCCTTCCATCTT 57.933 39.130 0.00 0.00 0.00 2.40
2723 2900 5.504830 GCTCAGAGTTGGAACTTTCTTTGAC 60.505 44.000 0.00 0.00 39.88 3.18
2741 2918 0.462581 GGGAATGATGTGCGCTCAGA 60.463 55.000 17.93 7.32 0.00 3.27
2782 2959 2.392933 TGGCTTCGCGTTTTTAACTG 57.607 45.000 5.77 0.00 0.00 3.16
2795 2984 5.363005 TCCTAACCTAGTAGTCATTGGCTTC 59.637 44.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.