Multiple sequence alignment - TraesCS1A01G142400

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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 TraesCS1A01G142400 chr1A 100.000 4120 0 0 1 4120 243163917 243159798 0.000000e+00 7609
1 TraesCS1A01G142400 chr1A 95.266 169 8 0 1 169 322177353 322177185 6.790000e-68 268
2 TraesCS1A01G142400 chr1D 93.652 2426 63 33 171 2555 194928216 194925841 0.000000e+00 3542
3 TraesCS1A01G142400 chr1D 92.786 804 38 9 2561 3360 194925786 194924999 0.000000e+00 1146
4 TraesCS1A01G142400 chr1D 92.319 690 43 3 3431 4120 194920009 194919330 0.000000e+00 972
5 TraesCS1A01G142400 chr1D 82.123 179 27 5 3643 3818 383256882 383257058 9.230000e-32 148
6 TraesCS1A01G142400 chr1B 98.595 1210 17 0 1042 2251 270792726 270793935 0.000000e+00 2141
7 TraesCS1A01G142400 chr1B 93.091 854 48 8 2561 3411 270794709 270795554 0.000000e+00 1240
8 TraesCS1A01G142400 chr1B 88.351 867 41 21 177 1027 270791844 270792666 0.000000e+00 987
9 TraesCS1A01G142400 chr1B 91.367 278 13 4 2283 2555 270794381 270794652 1.810000e-98 370
10 TraesCS1A01G142400 chr4B 78.453 1564 261 49 1046 2542 602450600 602449046 0.000000e+00 952
11 TraesCS1A01G142400 chr4B 98.101 158 3 0 2 159 34046380 34046537 4.060000e-70 276
12 TraesCS1A01G142400 chr4A 80.540 1259 182 42 1046 2250 684271355 684270106 0.000000e+00 909
13 TraesCS1A01G142400 chr4A 95.808 167 7 0 1 167 466938090 466938256 1.890000e-68 270
14 TraesCS1A01G142400 chr4D 80.498 1246 181 37 1062 2249 477508642 477507401 0.000000e+00 898
15 TraesCS1A01G142400 chr6D 83.526 692 101 9 3431 4120 165401890 165401210 5.810000e-178 634
16 TraesCS1A01G142400 chr6D 82.764 615 100 6 1069 1680 463549412 463548801 1.010000e-150 544
17 TraesCS1A01G142400 chr6B 83.362 589 94 4 1064 1650 706910965 706911551 3.620000e-150 542
18 TraesCS1A01G142400 chr6B 95.783 166 7 0 1 166 114057195 114057030 6.790000e-68 268
19 TraesCS1A01G142400 chr6A 83.562 584 90 6 1069 1649 610203852 610204432 3.620000e-150 542
20 TraesCS1A01G142400 chr2D 81.069 692 118 5 3431 4120 194061044 194060364 1.300000e-149 540
21 TraesCS1A01G142400 chr5A 80.651 553 99 6 1067 1615 688973634 688974182 4.920000e-114 422
22 TraesCS1A01G142400 chr5A 95.732 164 7 0 1 164 332643731 332643894 8.780000e-67 265
23 TraesCS1A01G142400 chr5A 80.233 172 30 3 2720 2889 688975461 688975630 4.320000e-25 126
24 TraesCS1A01G142400 chr3A 95.906 171 5 2 1 170 89152743 89152574 4.060000e-70 276
25 TraesCS1A01G142400 chr3B 96.914 162 5 0 1 162 117922555 117922394 5.250000e-69 272
26 TraesCS1A01G142400 chr3B 93.258 178 12 0 1 178 669714010 669713833 3.160000e-66 263
27 TraesCS1A01G142400 chr2A 95.783 166 7 0 1 166 478761516 478761351 6.790000e-68 268
28 TraesCS1A01G142400 chr2B 81.224 245 42 4 3408 3652 550219351 550219591 1.170000e-45 195


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 TraesCS1A01G142400 chr1A 243159798 243163917 4119 True 7609.0 7609 100.000 1 4120 1 chr1A.!!$R1 4119
1 TraesCS1A01G142400 chr1D 194924999 194928216 3217 True 2344.0 3542 93.219 171 3360 2 chr1D.!!$R2 3189
2 TraesCS1A01G142400 chr1D 194919330 194920009 679 True 972.0 972 92.319 3431 4120 1 chr1D.!!$R1 689
3 TraesCS1A01G142400 chr1B 270791844 270795554 3710 False 1184.5 2141 92.851 177 3411 4 chr1B.!!$F1 3234
4 TraesCS1A01G142400 chr4B 602449046 602450600 1554 True 952.0 952 78.453 1046 2542 1 chr4B.!!$R1 1496
5 TraesCS1A01G142400 chr4A 684270106 684271355 1249 True 909.0 909 80.540 1046 2250 1 chr4A.!!$R1 1204
6 TraesCS1A01G142400 chr4D 477507401 477508642 1241 True 898.0 898 80.498 1062 2249 1 chr4D.!!$R1 1187
7 TraesCS1A01G142400 chr6D 165401210 165401890 680 True 634.0 634 83.526 3431 4120 1 chr6D.!!$R1 689
8 TraesCS1A01G142400 chr6D 463548801 463549412 611 True 544.0 544 82.764 1069 1680 1 chr6D.!!$R2 611
9 TraesCS1A01G142400 chr6B 706910965 706911551 586 False 542.0 542 83.362 1064 1650 1 chr6B.!!$F1 586
10 TraesCS1A01G142400 chr6A 610203852 610204432 580 False 542.0 542 83.562 1069 1649 1 chr6A.!!$F1 580
11 TraesCS1A01G142400 chr2D 194060364 194061044 680 True 540.0 540 81.069 3431 4120 1 chr2D.!!$R1 689
12 TraesCS1A01G142400 chr5A 688973634 688975630 1996 False 274.0 422 80.442 1067 2889 2 chr5A.!!$F2 1822

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
787 804 0.246635 AGTGGCGTAGTTGCGAGATT 59.753 50.000 0.0 0.0 35.06 2.40 F
1449 1515 0.038166 GTTCATCCTCAAGGTGGCCA 59.962 55.000 0.0 0.0 36.34 5.36 F
1814 1919 0.866061 CCGACTACATGAACGAGCCG 60.866 60.000 0.0 0.0 0.00 5.52 F
2986 4137 1.192534 GCAACACGTAAGCAGACAGAC 59.807 52.381 0.0 0.0 45.62 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2599 3649 0.618458 TTAGTGCACCTGGTCATCCC 59.382 55.0 14.63 0.00 0.00 3.85 R
2949 4100 0.032815 TGCACTACTGCTGCAACGTA 59.967 50.0 3.02 2.62 44.57 3.57 R
3009 4160 0.036483 AATTGCCCCATTTTCACGGC 60.036 50.0 0.00 0.00 41.99 5.68 R
4054 5211 0.896019 ACCCTCCGCCTATCAGATCG 60.896 60.0 0.00 0.00 0.00 3.69 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
43 44 9.706691 TTATCTTTCTAGACATTTCAAACGACT 57.293 29.630 0.00 0.00 31.99 4.18
45 46 8.516811 TCTTTCTAGACATTTCAAACGACTAC 57.483 34.615 0.00 0.00 0.00 2.73
46 47 8.358148 TCTTTCTAGACATTTCAAACGACTACT 58.642 33.333 0.00 0.00 0.00 2.57
47 48 9.622004 CTTTCTAGACATTTCAAACGACTACTA 57.378 33.333 0.00 0.00 0.00 1.82
48 49 8.961294 TTCTAGACATTTCAAACGACTACTAC 57.039 34.615 0.00 0.00 0.00 2.73
49 50 8.102800 TCTAGACATTTCAAACGACTACTACA 57.897 34.615 0.00 0.00 0.00 2.74
50 51 8.737175 TCTAGACATTTCAAACGACTACTACAT 58.263 33.333 0.00 0.00 0.00 2.29
51 52 9.999009 CTAGACATTTCAAACGACTACTACATA 57.001 33.333 0.00 0.00 0.00 2.29
52 53 8.684973 AGACATTTCAAACGACTACTACATAC 57.315 34.615 0.00 0.00 0.00 2.39
53 54 7.484007 AGACATTTCAAACGACTACTACATACG 59.516 37.037 0.00 0.00 0.00 3.06
54 55 6.529125 ACATTTCAAACGACTACTACATACGG 59.471 38.462 0.00 0.00 0.00 4.02
55 56 5.878332 TTCAAACGACTACTACATACGGA 57.122 39.130 0.00 0.00 0.00 4.69
56 57 6.441093 TTCAAACGACTACTACATACGGAT 57.559 37.500 0.00 0.00 0.00 4.18
57 58 5.813717 TCAAACGACTACTACATACGGATG 58.186 41.667 5.94 5.94 39.16 3.51
59 60 6.538381 TCAAACGACTACTACATACGGATGTA 59.462 38.462 19.32 19.32 44.77 2.29
60 61 7.227314 TCAAACGACTACTACATACGGATGTAT 59.773 37.037 20.64 13.02 45.42 2.29
97 98 5.931441 AAGTGTAGATTCACTCACTTTGC 57.069 39.130 12.16 0.00 46.25 3.68
98 99 5.220710 AGTGTAGATTCACTCACTTTGCT 57.779 39.130 0.00 0.00 44.07 3.91
99 100 5.233988 AGTGTAGATTCACTCACTTTGCTC 58.766 41.667 0.00 0.00 44.07 4.26
100 101 4.390297 GTGTAGATTCACTCACTTTGCTCC 59.610 45.833 0.00 0.00 35.68 4.70
101 102 2.693069 AGATTCACTCACTTTGCTCCG 58.307 47.619 0.00 0.00 0.00 4.63
102 103 2.037772 AGATTCACTCACTTTGCTCCGT 59.962 45.455 0.00 0.00 0.00 4.69
103 104 3.258372 AGATTCACTCACTTTGCTCCGTA 59.742 43.478 0.00 0.00 0.00 4.02
104 105 3.678056 TTCACTCACTTTGCTCCGTAT 57.322 42.857 0.00 0.00 0.00 3.06
105 106 2.959516 TCACTCACTTTGCTCCGTATG 58.040 47.619 0.00 0.00 0.00 2.39
106 107 2.299013 TCACTCACTTTGCTCCGTATGT 59.701 45.455 0.00 0.00 0.00 2.29
107 108 3.508402 TCACTCACTTTGCTCCGTATGTA 59.492 43.478 0.00 0.00 0.00 2.29
108 109 3.859961 CACTCACTTTGCTCCGTATGTAG 59.140 47.826 0.00 0.00 0.00 2.74
109 110 3.510360 ACTCACTTTGCTCCGTATGTAGT 59.490 43.478 0.00 0.00 0.00 2.73
110 111 4.106029 TCACTTTGCTCCGTATGTAGTC 57.894 45.455 0.00 0.00 0.00 2.59
111 112 3.508402 TCACTTTGCTCCGTATGTAGTCA 59.492 43.478 0.00 0.00 0.00 3.41
112 113 3.612860 CACTTTGCTCCGTATGTAGTCAC 59.387 47.826 0.00 0.00 0.00 3.67
113 114 3.510360 ACTTTGCTCCGTATGTAGTCACT 59.490 43.478 0.00 0.00 0.00 3.41
114 115 4.021368 ACTTTGCTCCGTATGTAGTCACTT 60.021 41.667 0.00 0.00 0.00 3.16
115 116 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
116 117 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
117 118 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
118 119 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
119 120 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
120 121 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
121 122 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
122 123 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
123 124 6.367695 TCCGTATGTAGTCACTTGTTGAAATG 59.632 38.462 0.00 0.00 35.39 2.32
124 125 6.015504 CGTATGTAGTCACTTGTTGAAATGC 58.984 40.000 0.00 0.00 35.39 3.56
125 126 4.829064 TGTAGTCACTTGTTGAAATGCC 57.171 40.909 0.00 0.00 35.39 4.40
126 127 4.460263 TGTAGTCACTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 35.39 4.75
127 128 5.616270 TGTAGTCACTTGTTGAAATGCCTA 58.384 37.500 0.00 0.00 35.39 3.93
128 129 5.700832 TGTAGTCACTTGTTGAAATGCCTAG 59.299 40.000 0.00 0.00 35.39 3.02
129 130 4.973168 AGTCACTTGTTGAAATGCCTAGA 58.027 39.130 0.00 0.00 35.39 2.43
130 131 5.376625 AGTCACTTGTTGAAATGCCTAGAA 58.623 37.500 0.00 0.00 35.39 2.10
131 132 5.827797 AGTCACTTGTTGAAATGCCTAGAAA 59.172 36.000 0.00 0.00 35.39 2.52
132 133 6.016777 AGTCACTTGTTGAAATGCCTAGAAAG 60.017 38.462 0.00 0.00 35.39 2.62
133 134 6.017109 GTCACTTGTTGAAATGCCTAGAAAGA 60.017 38.462 0.00 0.00 35.39 2.52
134 135 6.017109 TCACTTGTTGAAATGCCTAGAAAGAC 60.017 38.462 0.00 0.00 0.00 3.01
135 136 5.827797 ACTTGTTGAAATGCCTAGAAAGACA 59.172 36.000 0.00 0.00 0.00 3.41
136 137 6.321181 ACTTGTTGAAATGCCTAGAAAGACAA 59.679 34.615 0.00 0.00 0.00 3.18
137 138 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
138 139 5.827797 TGTTGAAATGCCTAGAAAGACAAGT 59.172 36.000 0.00 0.00 0.00 3.16
139 140 6.995686 TGTTGAAATGCCTAGAAAGACAAGTA 59.004 34.615 0.00 0.00 0.00 2.24
140 141 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
141 142 8.515414 GTTGAAATGCCTAGAAAGACAAGTATT 58.485 33.333 0.00 0.00 0.00 1.89
142 143 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
143 144 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
145 146 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
146 147 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
147 148 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
148 149 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
149 150 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
150 151 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
151 152 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
152 153 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
153 154 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
154 155 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
155 156 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
156 157 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
157 158 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
158 159 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
159 160 5.713807 AGTATTTAGGAACGGAGGGAGTAT 58.286 41.667 0.00 0.00 0.00 2.12
160 161 6.141790 AGTATTTAGGAACGGAGGGAGTATT 58.858 40.000 0.00 0.00 0.00 1.89
161 162 5.970501 ATTTAGGAACGGAGGGAGTATTT 57.029 39.130 0.00 0.00 0.00 1.40
162 163 5.349061 TTTAGGAACGGAGGGAGTATTTC 57.651 43.478 0.00 0.00 0.00 2.17
163 164 3.117552 AGGAACGGAGGGAGTATTTCT 57.882 47.619 0.00 0.00 0.00 2.52
164 165 3.451890 AGGAACGGAGGGAGTATTTCTT 58.548 45.455 0.00 0.00 0.00 2.52
165 166 4.617593 AGGAACGGAGGGAGTATTTCTTA 58.382 43.478 0.00 0.00 0.00 2.10
166 167 5.028131 AGGAACGGAGGGAGTATTTCTTAA 58.972 41.667 0.00 0.00 0.00 1.85
167 168 5.105023 AGGAACGGAGGGAGTATTTCTTAAC 60.105 44.000 0.00 0.00 0.00 2.01
168 169 5.337813 GGAACGGAGGGAGTATTTCTTAACA 60.338 44.000 0.00 0.00 0.00 2.41
169 170 5.340439 ACGGAGGGAGTATTTCTTAACAG 57.660 43.478 0.00 0.00 0.00 3.16
170 171 5.021458 ACGGAGGGAGTATTTCTTAACAGA 58.979 41.667 0.00 0.00 0.00 3.41
171 172 5.127356 ACGGAGGGAGTATTTCTTAACAGAG 59.873 44.000 0.00 0.00 0.00 3.35
172 173 5.452077 CGGAGGGAGTATTTCTTAACAGAGG 60.452 48.000 0.00 0.00 0.00 3.69
173 174 5.163290 GGAGGGAGTATTTCTTAACAGAGGG 60.163 48.000 0.00 0.00 0.00 4.30
174 175 5.600749 AGGGAGTATTTCTTAACAGAGGGA 58.399 41.667 0.00 0.00 0.00 4.20
175 176 6.030082 AGGGAGTATTTCTTAACAGAGGGAA 58.970 40.000 0.00 0.00 0.00 3.97
280 281 1.522130 ACCGCCCGCGTTAAATAGG 60.522 57.895 4.92 0.00 37.81 2.57
284 285 2.248835 CCCGCGTTAAATAGGCCGG 61.249 63.158 4.92 0.00 34.15 6.13
352 360 3.558099 CTGCCACTCGTCAGTCGCA 62.558 63.158 0.00 0.00 43.66 5.10
644 660 1.003116 CTCTAAACCGATGCATGCTGC 60.003 52.381 20.33 9.71 45.29 5.25
645 661 1.019673 CTAAACCGATGCATGCTGCT 58.980 50.000 20.33 3.26 45.31 4.24
646 662 2.158971 TCTAAACCGATGCATGCTGCTA 60.159 45.455 20.33 0.00 45.31 3.49
647 663 1.019673 AAACCGATGCATGCTGCTAG 58.980 50.000 20.33 6.51 45.31 3.42
688 704 0.320374 ACGGCCGATCAAACTTCAGA 59.680 50.000 35.90 0.00 0.00 3.27
689 705 0.721718 CGGCCGATCAAACTTCAGAC 59.278 55.000 24.07 0.00 0.00 3.51
690 706 1.808411 GGCCGATCAAACTTCAGACA 58.192 50.000 0.00 0.00 0.00 3.41
691 707 1.734465 GGCCGATCAAACTTCAGACAG 59.266 52.381 0.00 0.00 0.00 3.51
718 734 0.926628 GTTTGTTTTCCCGTCGTGCG 60.927 55.000 0.00 0.00 40.95 5.34
739 755 2.820037 GACCACCTTAGCCGCTGC 60.820 66.667 2.16 0.00 37.95 5.25
740 756 4.760047 ACCACCTTAGCCGCTGCG 62.760 66.667 16.34 16.34 44.33 5.18
772 789 3.567164 AGCAGTTTGAGTGATTTCAGTGG 59.433 43.478 0.00 0.00 0.00 4.00
781 798 1.804151 TGATTTCAGTGGCGTAGTTGC 59.196 47.619 0.00 0.00 0.00 4.17
787 804 0.246635 AGTGGCGTAGTTGCGAGATT 59.753 50.000 0.00 0.00 35.06 2.40
788 805 1.475280 AGTGGCGTAGTTGCGAGATTA 59.525 47.619 0.00 0.00 35.06 1.75
814 831 5.550232 TCTTCAAATCATGATTGACCACG 57.450 39.130 21.39 8.60 38.03 4.94
886 907 4.098196 GGGACTCTCCTACACTATTGACAC 59.902 50.000 0.00 0.00 36.57 3.67
910 931 3.013921 AGTTTCTGTTTCTTTGCACCGA 58.986 40.909 0.00 0.00 0.00 4.69
962 983 1.003233 ACTCATTCTGACCGGAAACCC 59.997 52.381 9.46 0.00 0.00 4.11
991 1012 0.251354 ATTGTCGCTGGCTGATCAGT 59.749 50.000 23.38 0.00 37.12 3.41
1039 1078 6.048073 TCTTCTTCTTCACAACAATTGTCG 57.952 37.500 12.39 2.57 43.23 4.35
1449 1515 0.038166 GTTCATCCTCAAGGTGGCCA 59.962 55.000 0.00 0.00 36.34 5.36
1616 1682 1.153168 CTTCCCGGCCATGATCGTT 60.153 57.895 2.24 0.00 0.00 3.85
1706 1808 4.785453 CAAGAGTCGGCTGGGGGC 62.785 72.222 0.00 0.00 40.90 5.80
1814 1919 0.866061 CCGACTACATGAACGAGCCG 60.866 60.000 0.00 0.00 0.00 5.52
2281 2907 9.703892 TCTGAAAATCTGACAGTTTTTCAAAAA 57.296 25.926 33.29 25.01 45.53 1.94
2502 3144 2.742053 GCTTCTTGCCGTTGTGATTCTA 59.258 45.455 0.00 0.00 35.15 2.10
2550 3196 3.999046 TCCAACCGGTAACTCTTTCTTC 58.001 45.455 8.00 0.00 0.00 2.87
2555 3201 2.614734 CCGGTAACTCTTTCTTCCCCAC 60.615 54.545 0.00 0.00 0.00 4.61
2556 3202 2.614734 CGGTAACTCTTTCTTCCCCACC 60.615 54.545 0.00 0.00 0.00 4.61
2559 3205 2.118403 ACTCTTTCTTCCCCACCTGA 57.882 50.000 0.00 0.00 0.00 3.86
2567 3587 6.663523 TCTTTCTTCCCCACCTGAATAATTTC 59.336 38.462 0.00 0.00 0.00 2.17
2596 3646 9.818796 GTTAGACTTGAGAAAAATCTTGTGATC 57.181 33.333 0.00 0.00 31.51 2.92
2597 3647 9.784531 TTAGACTTGAGAAAAATCTTGTGATCT 57.215 29.630 0.00 0.00 31.51 2.75
2599 3649 8.566260 AGACTTGAGAAAAATCTTGTGATCTTG 58.434 33.333 0.00 0.00 31.51 3.02
2619 3669 1.407437 GGGATGACCAGGTGCACTAAG 60.407 57.143 17.98 7.86 39.85 2.18
2952 4103 3.779271 GGAACAACTCCTACTCCTACG 57.221 52.381 0.00 0.00 41.61 3.51
2953 4104 3.087781 GGAACAACTCCTACTCCTACGT 58.912 50.000 0.00 0.00 41.61 3.57
2954 4105 3.509184 GGAACAACTCCTACTCCTACGTT 59.491 47.826 0.00 0.00 41.61 3.99
2985 4136 1.202475 TGCAACACGTAAGCAGACAGA 60.202 47.619 4.83 0.00 45.62 3.41
2986 4137 1.192534 GCAACACGTAAGCAGACAGAC 59.807 52.381 0.00 0.00 45.62 3.51
2987 4138 2.469826 CAACACGTAAGCAGACAGACA 58.530 47.619 0.00 0.00 45.62 3.41
2988 4139 2.423926 ACACGTAAGCAGACAGACAG 57.576 50.000 0.00 0.00 45.62 3.51
2993 4144 2.342179 GTAAGCAGACAGACAGCTTCC 58.658 52.381 5.82 0.00 45.73 3.46
3024 4176 2.573340 CAGCCGTGAAAATGGGGC 59.427 61.111 0.00 0.00 45.91 5.80
3046 4200 6.293462 GGGCAATTTACCTGATTATCGTCTTC 60.293 42.308 0.00 0.00 0.00 2.87
3084 4238 3.949047 GCCCGAAATTAGGCGCGG 61.949 66.667 8.83 0.00 39.87 6.46
3128 4282 2.939460 AAGCAAATAATGGGCGTGTC 57.061 45.000 0.00 0.00 0.00 3.67
3148 4302 4.096833 TGTCTTGTACGTGTGTTGTACTCT 59.903 41.667 0.00 0.00 42.09 3.24
3149 4303 5.296531 TGTCTTGTACGTGTGTTGTACTCTA 59.703 40.000 0.00 0.00 42.09 2.43
3150 4304 5.622856 GTCTTGTACGTGTGTTGTACTCTAC 59.377 44.000 0.00 0.00 42.09 2.59
3152 4306 3.559655 TGTACGTGTGTTGTACTCTACGT 59.440 43.478 0.00 18.47 45.29 3.57
3153 4307 4.747605 TGTACGTGTGTTGTACTCTACGTA 59.252 41.667 0.00 17.30 43.43 3.57
3154 4308 4.395581 ACGTGTGTTGTACTCTACGTAG 57.604 45.455 16.73 16.73 42.14 3.51
3155 4309 4.058124 ACGTGTGTTGTACTCTACGTAGA 58.942 43.478 23.34 23.34 42.14 2.59
3396 4550 4.366267 AGAAGTGGGATTGATGTAGGTCT 58.634 43.478 0.00 0.00 0.00 3.85
3399 4553 5.878406 AGTGGGATTGATGTAGGTCTTAG 57.122 43.478 0.00 0.00 0.00 2.18
3405 4559 7.400339 TGGGATTGATGTAGGTCTTAGATATCC 59.600 40.741 0.00 0.00 0.00 2.59
3424 4578 9.956720 AGATATCCTTTTTATGAAGAAAATGCG 57.043 29.630 0.00 0.00 0.00 4.73
3425 4579 9.950680 GATATCCTTTTTATGAAGAAAATGCGA 57.049 29.630 0.00 0.00 0.00 5.10
3428 4582 8.464770 TCCTTTTTATGAAGAAAATGCGATTG 57.535 30.769 0.00 0.00 0.00 2.67
3429 4583 8.303156 TCCTTTTTATGAAGAAAATGCGATTGA 58.697 29.630 0.00 0.00 0.00 2.57
3466 4620 5.705609 AAAGCCATACGAAAACAGTCAAT 57.294 34.783 0.00 0.00 0.00 2.57
3473 4627 4.483476 ACGAAAACAGTCAATAACCAGC 57.517 40.909 0.00 0.00 0.00 4.85
3474 4628 3.880490 ACGAAAACAGTCAATAACCAGCA 59.120 39.130 0.00 0.00 0.00 4.41
3478 4632 6.291585 CGAAAACAGTCAATAACCAGCAAAAC 60.292 38.462 0.00 0.00 0.00 2.43
3484 4638 3.900601 TCAATAACCAGCAAAACCCACAT 59.099 39.130 0.00 0.00 0.00 3.21
3494 4649 3.843999 CAAAACCCACATAAACCATCCG 58.156 45.455 0.00 0.00 0.00 4.18
3519 4674 2.898612 TCATACGAACCACCCAACACTA 59.101 45.455 0.00 0.00 0.00 2.74
3531 4686 5.127491 CACCCAACACTAGGTAACAAAAGA 58.873 41.667 0.00 0.00 41.41 2.52
3548 4704 3.375782 AAGAAGGCAACAATTCAGTGC 57.624 42.857 0.00 0.00 41.41 4.40
3583 4739 0.323360 ACAACATAAGGGGCACGCAT 60.323 50.000 0.00 0.00 46.88 4.73
3598 4754 3.195002 CATGCCACCACCTACGCG 61.195 66.667 3.53 3.53 0.00 6.01
3623 4779 3.550437 AAAGATCCAAGCAGCTACGAT 57.450 42.857 0.00 0.00 0.00 3.73
3642 4798 0.179059 TGAAGCACAAGCAGACGGAA 60.179 50.000 0.00 0.00 45.49 4.30
3664 4820 1.552337 AGACATCAGATTGGCAGACGT 59.448 47.619 0.00 0.00 0.00 4.34
3695 4851 3.018856 GTTGATCAACATCTCCATGCCA 58.981 45.455 29.43 0.00 40.84 4.92
3700 4856 2.026075 TCAACATCTCCATGCCATCACA 60.026 45.455 0.00 0.00 32.57 3.58
3706 4862 0.255604 TCCATGCCATCACAATCCGT 59.744 50.000 0.00 0.00 0.00 4.69
3719 4875 4.624024 TCACAATCCGTCGATTTAGTCAAC 59.376 41.667 0.00 0.00 36.54 3.18
3720 4876 3.611113 ACAATCCGTCGATTTAGTCAACG 59.389 43.478 0.00 0.00 36.54 4.10
3725 4881 4.325204 TCCGTCGATTTAGTCAACGATTTG 59.675 41.667 0.00 0.00 37.14 2.32
3868 5025 4.228210 AGTCCAAAATAATCTCCTGGAGCA 59.772 41.667 19.08 8.43 36.86 4.26
3950 5107 2.335316 TGTACCAGGAACCAACACAC 57.665 50.000 0.00 0.00 0.00 3.82
4054 5211 0.960861 CCAGGCCCGTTCCTTTTCTC 60.961 60.000 0.00 0.00 33.25 2.87
4063 5220 4.202121 CCCGTTCCTTTTCTCGATCTGATA 60.202 45.833 0.00 0.00 0.00 2.15
4114 5271 3.134262 TGCCAGAGGAAGATCTTGATCTG 59.866 47.826 26.02 26.02 34.25 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.706691 AGTCGTTTGAAATGTCTAGAAAGATAA 57.293 29.630 0.00 0.00 33.30 1.75
19 20 9.141400 GTAGTCGTTTGAAATGTCTAGAAAGAT 57.859 33.333 4.71 0.00 33.30 2.40
20 21 8.358148 AGTAGTCGTTTGAAATGTCTAGAAAGA 58.642 33.333 4.71 0.00 0.00 2.52
21 22 8.522178 AGTAGTCGTTTGAAATGTCTAGAAAG 57.478 34.615 4.71 0.00 0.00 2.62
22 23 9.403110 GTAGTAGTCGTTTGAAATGTCTAGAAA 57.597 33.333 4.71 0.00 0.00 2.52
23 24 8.570488 TGTAGTAGTCGTTTGAAATGTCTAGAA 58.430 33.333 4.71 0.00 0.00 2.10
24 25 8.102800 TGTAGTAGTCGTTTGAAATGTCTAGA 57.897 34.615 4.71 0.00 0.00 2.43
25 26 8.912787 ATGTAGTAGTCGTTTGAAATGTCTAG 57.087 34.615 4.71 0.00 0.00 2.43
26 27 9.778993 GTATGTAGTAGTCGTTTGAAATGTCTA 57.221 33.333 0.98 0.98 0.00 2.59
27 28 7.484007 CGTATGTAGTAGTCGTTTGAAATGTCT 59.516 37.037 2.73 2.73 0.00 3.41
28 29 7.253552 CCGTATGTAGTAGTCGTTTGAAATGTC 60.254 40.741 0.00 0.00 0.00 3.06
29 30 6.529125 CCGTATGTAGTAGTCGTTTGAAATGT 59.471 38.462 0.00 0.00 0.00 2.71
30 31 6.748658 TCCGTATGTAGTAGTCGTTTGAAATG 59.251 38.462 0.00 0.00 0.00 2.32
31 32 6.855836 TCCGTATGTAGTAGTCGTTTGAAAT 58.144 36.000 0.00 0.00 0.00 2.17
32 33 6.252967 TCCGTATGTAGTAGTCGTTTGAAA 57.747 37.500 0.00 0.00 0.00 2.69
33 34 5.878332 TCCGTATGTAGTAGTCGTTTGAA 57.122 39.130 0.00 0.00 0.00 2.69
34 35 5.355071 ACATCCGTATGTAGTAGTCGTTTGA 59.645 40.000 0.00 0.00 44.66 2.69
35 36 5.575957 ACATCCGTATGTAGTAGTCGTTTG 58.424 41.667 0.00 0.00 44.66 2.93
36 37 5.824904 ACATCCGTATGTAGTAGTCGTTT 57.175 39.130 0.00 0.00 44.66 3.60
77 78 4.390297 GGAGCAAAGTGAGTGAATCTACAC 59.610 45.833 0.00 0.00 40.60 2.90
78 79 4.569943 GGAGCAAAGTGAGTGAATCTACA 58.430 43.478 0.00 0.00 0.00 2.74
79 80 3.614616 CGGAGCAAAGTGAGTGAATCTAC 59.385 47.826 0.00 0.00 0.00 2.59
80 81 3.258372 ACGGAGCAAAGTGAGTGAATCTA 59.742 43.478 0.00 0.00 0.00 1.98
81 82 2.037772 ACGGAGCAAAGTGAGTGAATCT 59.962 45.455 0.00 0.00 0.00 2.40
82 83 2.417719 ACGGAGCAAAGTGAGTGAATC 58.582 47.619 0.00 0.00 0.00 2.52
83 84 2.550830 ACGGAGCAAAGTGAGTGAAT 57.449 45.000 0.00 0.00 0.00 2.57
84 85 3.244078 ACATACGGAGCAAAGTGAGTGAA 60.244 43.478 0.00 0.00 0.00 3.18
85 86 2.299013 ACATACGGAGCAAAGTGAGTGA 59.701 45.455 0.00 0.00 0.00 3.41
86 87 2.688507 ACATACGGAGCAAAGTGAGTG 58.311 47.619 0.00 0.00 0.00 3.51
87 88 3.510360 ACTACATACGGAGCAAAGTGAGT 59.490 43.478 0.00 0.00 0.00 3.41
88 89 4.106197 GACTACATACGGAGCAAAGTGAG 58.894 47.826 0.00 0.00 0.00 3.51
89 90 3.508402 TGACTACATACGGAGCAAAGTGA 59.492 43.478 0.00 0.00 0.00 3.41
90 91 3.612860 GTGACTACATACGGAGCAAAGTG 59.387 47.826 0.00 0.00 0.00 3.16
91 92 3.510360 AGTGACTACATACGGAGCAAAGT 59.490 43.478 0.00 0.00 0.00 2.66
92 93 4.111375 AGTGACTACATACGGAGCAAAG 57.889 45.455 0.00 0.00 0.00 2.77
93 94 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
94 95 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
95 96 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
96 97 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
97 98 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
98 99 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
99 100 6.534059 CATTTCAACAAGTGACTACATACGG 58.466 40.000 0.00 0.00 35.39 4.02
100 101 6.015504 GCATTTCAACAAGTGACTACATACG 58.984 40.000 0.00 0.00 35.39 3.06
101 102 6.149474 AGGCATTTCAACAAGTGACTACATAC 59.851 38.462 0.00 0.00 35.84 2.39
102 103 6.237901 AGGCATTTCAACAAGTGACTACATA 58.762 36.000 0.00 0.00 35.84 2.29
103 104 5.072741 AGGCATTTCAACAAGTGACTACAT 58.927 37.500 0.00 0.00 35.84 2.29
104 105 4.460263 AGGCATTTCAACAAGTGACTACA 58.540 39.130 0.00 0.00 35.84 2.74
105 106 5.932303 TCTAGGCATTTCAACAAGTGACTAC 59.068 40.000 0.00 0.00 38.51 2.73
106 107 6.109156 TCTAGGCATTTCAACAAGTGACTA 57.891 37.500 0.00 0.00 38.51 2.59
107 108 4.973168 TCTAGGCATTTCAACAAGTGACT 58.027 39.130 0.00 0.00 40.60 3.41
108 109 5.689383 TTCTAGGCATTTCAACAAGTGAC 57.311 39.130 0.00 0.00 35.39 3.67
109 110 6.017109 GTCTTTCTAGGCATTTCAACAAGTGA 60.017 38.462 0.00 0.00 0.00 3.41
110 111 6.145535 GTCTTTCTAGGCATTTCAACAAGTG 58.854 40.000 0.00 0.00 0.00 3.16
111 112 5.827797 TGTCTTTCTAGGCATTTCAACAAGT 59.172 36.000 0.00 0.00 29.10 3.16
112 113 6.317789 TGTCTTTCTAGGCATTTCAACAAG 57.682 37.500 0.00 0.00 29.10 3.16
113 114 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
114 115 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
115 116 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
116 117 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
117 118 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
119 120 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
120 121 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
121 122 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
122 123 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
123 124 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
124 125 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
125 126 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
126 127 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
127 128 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
128 129 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
129 130 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
130 131 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
131 132 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
132 133 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
133 134 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
134 135 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
135 136 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
136 137 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
137 138 6.416631 AATACTCCCTCCGTTCCTAAATAC 57.583 41.667 0.00 0.00 0.00 1.89
138 139 6.842807 AGAAATACTCCCTCCGTTCCTAAATA 59.157 38.462 0.00 0.00 0.00 1.40
139 140 5.666265 AGAAATACTCCCTCCGTTCCTAAAT 59.334 40.000 0.00 0.00 0.00 1.40
140 141 5.028131 AGAAATACTCCCTCCGTTCCTAAA 58.972 41.667 0.00 0.00 0.00 1.85
141 142 4.617593 AGAAATACTCCCTCCGTTCCTAA 58.382 43.478 0.00 0.00 0.00 2.69
142 143 4.261411 AGAAATACTCCCTCCGTTCCTA 57.739 45.455 0.00 0.00 0.00 2.94
143 144 3.117552 AGAAATACTCCCTCCGTTCCT 57.882 47.619 0.00 0.00 0.00 3.36
144 145 3.908643 AAGAAATACTCCCTCCGTTCC 57.091 47.619 0.00 0.00 0.00 3.62
145 146 5.727434 TGTTAAGAAATACTCCCTCCGTTC 58.273 41.667 0.00 0.00 0.00 3.95
146 147 5.482878 TCTGTTAAGAAATACTCCCTCCGTT 59.517 40.000 0.00 0.00 0.00 4.44
147 148 5.021458 TCTGTTAAGAAATACTCCCTCCGT 58.979 41.667 0.00 0.00 0.00 4.69
148 149 5.452077 CCTCTGTTAAGAAATACTCCCTCCG 60.452 48.000 0.00 0.00 30.03 4.63
149 150 5.163290 CCCTCTGTTAAGAAATACTCCCTCC 60.163 48.000 0.00 0.00 30.03 4.30
150 151 5.661759 TCCCTCTGTTAAGAAATACTCCCTC 59.338 44.000 0.00 0.00 30.03 4.30
151 152 5.600749 TCCCTCTGTTAAGAAATACTCCCT 58.399 41.667 0.00 0.00 30.03 4.20
152 153 5.952347 TCCCTCTGTTAAGAAATACTCCC 57.048 43.478 0.00 0.00 30.03 4.30
166 167 8.097662 GCAAGCTTAGTATTATATTCCCTCTGT 58.902 37.037 0.00 0.00 0.00 3.41
167 168 8.317679 AGCAAGCTTAGTATTATATTCCCTCTG 58.682 37.037 0.00 0.00 0.00 3.35
168 169 8.442660 AGCAAGCTTAGTATTATATTCCCTCT 57.557 34.615 0.00 0.00 0.00 3.69
169 170 8.536175 AGAGCAAGCTTAGTATTATATTCCCTC 58.464 37.037 0.00 0.00 0.00 4.30
170 171 8.442660 AGAGCAAGCTTAGTATTATATTCCCT 57.557 34.615 0.00 0.00 0.00 4.20
171 172 8.940952 CAAGAGCAAGCTTAGTATTATATTCCC 58.059 37.037 0.00 0.00 0.00 3.97
172 173 8.447053 GCAAGAGCAAGCTTAGTATTATATTCC 58.553 37.037 0.00 0.00 41.58 3.01
173 174 8.447053 GGCAAGAGCAAGCTTAGTATTATATTC 58.553 37.037 0.00 0.00 44.61 1.75
174 175 7.391833 GGGCAAGAGCAAGCTTAGTATTATATT 59.608 37.037 0.00 0.00 44.61 1.28
175 176 6.881602 GGGCAAGAGCAAGCTTAGTATTATAT 59.118 38.462 0.00 0.00 44.61 0.86
280 281 2.202756 CGAGTGCTTAGGACCGGC 60.203 66.667 0.00 0.00 0.00 6.13
284 285 1.255667 TGGGACCGAGTGCTTAGGAC 61.256 60.000 0.00 0.00 0.00 3.85
352 360 0.325765 GGAGTAGGAGCAGGGACCTT 60.326 60.000 0.00 0.00 37.68 3.50
561 577 2.033448 TTGCTAAGGTGCCACCGG 59.967 61.111 8.52 0.00 44.90 5.28
563 579 4.002797 CCTTGCTAAGGTGCCACC 57.997 61.111 5.50 5.50 43.95 4.61
599 615 1.373497 CACGGAGGTCAGTCAGCAC 60.373 63.158 0.00 0.00 0.00 4.40
644 660 0.878416 CGCTCTGGGTAGCTAGCTAG 59.122 60.000 24.78 25.50 40.49 3.42
645 661 1.173444 GCGCTCTGGGTAGCTAGCTA 61.173 60.000 20.67 20.67 40.49 3.32
646 662 2.494530 GCGCTCTGGGTAGCTAGCT 61.495 63.158 23.12 23.12 40.49 3.32
647 663 2.028337 GCGCTCTGGGTAGCTAGC 59.972 66.667 14.67 14.67 40.49 3.42
690 706 4.018490 ACGGGAAAACAAACAGGTAAACT 58.982 39.130 0.00 0.00 0.00 2.66
691 707 4.353737 GACGGGAAAACAAACAGGTAAAC 58.646 43.478 0.00 0.00 0.00 2.01
751 767 3.854784 GCCACTGAAATCACTCAAACTGC 60.855 47.826 0.00 0.00 0.00 4.40
772 789 6.362551 TGAAGATTATAATCTCGCAACTACGC 59.637 38.462 24.75 8.03 44.67 4.42
788 805 8.347771 CGTGGTCAATCATGATTTGAAGATTAT 58.652 33.333 18.41 0.00 38.03 1.28
812 829 0.657840 GTGCAGAAAAGACACAGCGT 59.342 50.000 0.00 0.00 34.43 5.07
814 831 1.401552 TGTGTGCAGAAAAGACACAGC 59.598 47.619 0.00 0.00 43.83 4.40
886 907 2.531508 GTGCAAAGAAACAGAAACTGCG 59.468 45.455 0.00 0.00 34.37 5.18
910 931 4.284490 TGCTTAGATTAGATCCTGCGGAAT 59.716 41.667 0.00 0.00 34.34 3.01
962 983 1.064505 CCAGCGACAATAATGCCAGTG 59.935 52.381 0.00 0.00 0.00 3.66
991 1012 2.874648 ATTCAGCCGATGGAGCGCAA 62.875 55.000 11.47 0.00 34.64 4.85
1034 1073 1.065764 CGCCATCTCCGATCGACAA 59.934 57.895 18.66 0.75 0.00 3.18
1039 1078 0.943359 CTCAAGCGCCATCTCCGATC 60.943 60.000 2.29 0.00 0.00 3.69
1616 1682 1.072173 CAGGTGTTGGTGATGACTCCA 59.928 52.381 0.00 0.00 37.81 3.86
1706 1808 3.041940 GCCACAACGACGTCCTGG 61.042 66.667 10.58 16.16 0.00 4.45
2296 2922 4.035558 TGATCCGAATTAGCAGCATGTTTC 59.964 41.667 0.00 0.00 39.31 2.78
2502 3144 5.596836 TTGAGGCAACATTTGAAAGAACT 57.403 34.783 0.00 0.00 41.41 3.01
2550 3196 6.889722 TCTAACAAGAAATTATTCAGGTGGGG 59.110 38.462 0.00 0.00 38.06 4.96
2567 3587 9.443283 CACAAGATTTTTCTCAAGTCTAACAAG 57.557 33.333 0.00 0.00 0.00 3.16
2596 3646 0.962356 GTGCACCTGGTCATCCCAAG 60.962 60.000 5.22 0.00 44.65 3.61
2597 3647 1.074775 GTGCACCTGGTCATCCCAA 59.925 57.895 5.22 0.00 44.65 4.12
2599 3649 0.618458 TTAGTGCACCTGGTCATCCC 59.382 55.000 14.63 0.00 0.00 3.85
2613 3663 5.985530 TGATTCCGAGATAACATGCTTAGTG 59.014 40.000 0.00 0.00 0.00 2.74
2619 3669 6.017605 ACAAAGATGATTCCGAGATAACATGC 60.018 38.462 0.00 0.00 0.00 4.06
2630 3680 4.618489 GCACTGAAAACAAAGATGATTCCG 59.382 41.667 0.00 0.00 0.00 4.30
2700 3851 0.687354 AGGCTTTCTTCTCCGAAGCA 59.313 50.000 9.21 0.00 0.00 3.91
2946 4097 1.067846 CACTACTGCTGCAACGTAGGA 60.068 52.381 24.22 2.92 35.97 2.94
2947 4098 1.350193 CACTACTGCTGCAACGTAGG 58.650 55.000 24.22 14.20 35.97 3.18
2948 4099 0.716108 GCACTACTGCTGCAACGTAG 59.284 55.000 20.92 20.92 40.63 3.51
2949 4100 0.032815 TGCACTACTGCTGCAACGTA 59.967 50.000 3.02 2.62 44.57 3.57
2950 4101 1.227527 TGCACTACTGCTGCAACGT 60.228 52.632 3.02 1.37 44.57 3.99
2951 4102 3.641492 TGCACTACTGCTGCAACG 58.359 55.556 3.02 0.00 44.57 4.10
2954 4105 1.498043 CGTGTTGCACTACTGCTGCA 61.498 55.000 0.88 0.88 44.57 4.41
2993 4144 0.379669 CGGCTGCTTCCTTGCTTATG 59.620 55.000 0.00 0.00 0.00 1.90
3009 4160 0.036483 AATTGCCCCATTTTCACGGC 60.036 50.000 0.00 0.00 41.99 5.68
3024 4176 9.529325 TGTAGAAGACGATAATCAGGTAAATTG 57.471 33.333 0.00 0.00 0.00 2.32
3046 4200 4.031426 GGCGAGAAGTTTACACGAATGTAG 59.969 45.833 0.00 0.00 42.29 2.74
3128 4282 4.610122 CGTAGAGTACAACACACGTACAAG 59.390 45.833 0.00 0.00 41.40 3.16
3148 4302 6.535150 CGACCGGGTAATCTTATATCTACGTA 59.465 42.308 6.32 0.00 0.00 3.57
3149 4303 5.352569 CGACCGGGTAATCTTATATCTACGT 59.647 44.000 6.32 0.00 0.00 3.57
3150 4304 5.582269 TCGACCGGGTAATCTTATATCTACG 59.418 44.000 6.32 0.00 0.00 3.51
3152 4306 5.582269 CGTCGACCGGGTAATCTTATATCTA 59.418 44.000 10.58 0.00 0.00 1.98
3153 4307 4.394300 CGTCGACCGGGTAATCTTATATCT 59.606 45.833 10.58 0.00 0.00 1.98
3154 4308 4.656041 CGTCGACCGGGTAATCTTATATC 58.344 47.826 10.58 0.00 0.00 1.63
3155 4309 3.119708 GCGTCGACCGGGTAATCTTATAT 60.120 47.826 10.58 0.00 36.94 0.86
3190 4344 1.657094 CTTTCGAATACAACGGACGGG 59.343 52.381 0.00 0.00 0.00 5.28
3318 4472 6.374333 AGTGTTGAAATATATTGACCGCACTT 59.626 34.615 0.00 0.00 0.00 3.16
3399 4553 9.950680 TCGCATTTTCTTCATAAAAAGGATATC 57.049 29.630 0.00 0.00 31.01 1.63
3405 4559 8.375465 GGTCAATCGCATTTTCTTCATAAAAAG 58.625 33.333 0.00 0.00 32.42 2.27
3411 4565 3.689161 TCGGTCAATCGCATTTTCTTCAT 59.311 39.130 0.00 0.00 0.00 2.57
3412 4566 3.070748 TCGGTCAATCGCATTTTCTTCA 58.929 40.909 0.00 0.00 0.00 3.02
3413 4567 3.125316 AGTCGGTCAATCGCATTTTCTTC 59.875 43.478 0.00 0.00 0.00 2.87
3414 4568 3.074412 AGTCGGTCAATCGCATTTTCTT 58.926 40.909 0.00 0.00 0.00 2.52
3415 4569 2.699954 AGTCGGTCAATCGCATTTTCT 58.300 42.857 0.00 0.00 0.00 2.52
3416 4570 3.471495 AAGTCGGTCAATCGCATTTTC 57.529 42.857 0.00 0.00 0.00 2.29
3417 4571 3.915437 AAAGTCGGTCAATCGCATTTT 57.085 38.095 0.00 0.00 0.00 1.82
3418 4572 6.671614 TTATAAAGTCGGTCAATCGCATTT 57.328 33.333 0.00 0.00 0.00 2.32
3419 4573 6.671614 TTTATAAAGTCGGTCAATCGCATT 57.328 33.333 0.00 0.00 0.00 3.56
3420 4574 6.861065 ATTTATAAAGTCGGTCAATCGCAT 57.139 33.333 3.94 0.00 0.00 4.73
3421 4575 7.773864 TTATTTATAAAGTCGGTCAATCGCA 57.226 32.000 3.94 0.00 0.00 5.10
3422 4576 7.320560 GCTTTATTTATAAAGTCGGTCAATCGC 59.679 37.037 18.51 2.98 46.78 4.58
3423 4577 7.797123 GGCTTTATTTATAAAGTCGGTCAATCG 59.203 37.037 18.51 0.00 46.78 3.34
3457 4611 4.202212 GGGTTTTGCTGGTTATTGACTGTT 60.202 41.667 0.00 0.00 0.00 3.16
3459 4613 3.320541 TGGGTTTTGCTGGTTATTGACTG 59.679 43.478 0.00 0.00 0.00 3.51
3466 4620 4.039366 GGTTTATGTGGGTTTTGCTGGTTA 59.961 41.667 0.00 0.00 0.00 2.85
3473 4627 3.367910 CCGGATGGTTTATGTGGGTTTTG 60.368 47.826 0.00 0.00 0.00 2.44
3474 4628 2.829120 CCGGATGGTTTATGTGGGTTTT 59.171 45.455 0.00 0.00 0.00 2.43
3478 4632 1.211949 ACTCCGGATGGTTTATGTGGG 59.788 52.381 3.57 0.00 36.30 4.61
3484 4638 3.289836 TCGTATGACTCCGGATGGTTTA 58.710 45.455 3.57 0.00 36.30 2.01
3494 4649 0.899720 TGGGTGGTTCGTATGACTCC 59.100 55.000 0.00 0.00 0.00 3.85
3519 4674 5.869649 ATTGTTGCCTTCTTTTGTTACCT 57.130 34.783 0.00 0.00 0.00 3.08
3531 4686 1.069049 GTGGCACTGAATTGTTGCCTT 59.931 47.619 11.13 0.00 45.20 4.35
3548 4704 1.733402 TTGTTTTCAGGCCTGCGTGG 61.733 55.000 28.91 3.92 39.35 4.94
3559 4715 2.294791 CGTGCCCCTTATGTTGTTTTCA 59.705 45.455 0.00 0.00 0.00 2.69
3598 4754 1.271656 AGCTGCTTGGATCTTTTGTGC 59.728 47.619 0.00 0.00 0.00 4.57
3623 4779 0.179059 TTCCGTCTGCTTGTGCTTCA 60.179 50.000 0.00 0.00 40.48 3.02
3642 4798 2.159128 CGTCTGCCAATCTGATGTCTCT 60.159 50.000 0.00 0.00 0.00 3.10
3695 4851 5.006153 TGACTAAATCGACGGATTGTGAT 57.994 39.130 0.00 0.00 41.99 3.06
3706 4862 4.688879 AGTGCAAATCGTTGACTAAATCGA 59.311 37.500 0.00 0.00 36.83 3.59
3760 4916 9.162764 GTGTTTTCCTTAATAAGTCTGCTGATA 57.837 33.333 0.00 0.00 0.00 2.15
3777 4934 8.721133 AAATTTACTATTCAGGGTGTTTTCCT 57.279 30.769 0.00 0.00 34.39 3.36
3806 4963 2.453638 GGCGCTTTGGACTACTCGC 61.454 63.158 7.64 0.00 41.55 5.03
3837 4994 6.068853 AGGAGATTATTTTGGACTGGATTGGA 60.069 38.462 0.00 0.00 0.00 3.53
3950 5107 1.378378 GGCCAATTTGGTTTGGGGG 59.622 57.895 16.62 0.00 45.25 5.40
4054 5211 0.896019 ACCCTCCGCCTATCAGATCG 60.896 60.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.