Multiple sequence alignment - TraesCS4A01G136800

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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 TraesCS4A01G136800 chr4A 100.000 2631 0 0 494 3124 192629735 192627105 0.000000e+00 4859.0
1 TraesCS4A01G136800 chr4A 100.000 228 0 0 1 228 192630228 192630001 3.730000e-114 422.0
2 TraesCS4A01G136800 chr4D 90.356 1462 49 26 1207 2597 296725844 296727284 0.000000e+00 1834.0
3 TraesCS4A01G136800 chr4D 88.486 469 23 9 778 1215 296725353 296725821 3.550000e-149 538.0
4 TraesCS4A01G136800 chr4D 95.208 313 6 4 2615 2921 296727271 296727580 1.300000e-133 486.0
5 TraesCS4A01G136800 chr4D 85.081 248 21 7 519 764 296721497 296721730 4.030000e-59 239.0
6 TraesCS4A01G136800 chr4D 89.655 87 2 3 1444 1530 352127882 352127803 1.530000e-18 104.0
7 TraesCS4A01G136800 chr4D 82.407 108 13 4 1 103 28245074 28245180 4.290000e-14 89.8
8 TraesCS4A01G136800 chr4D 81.081 111 18 3 1 108 99347065 99347175 5.550000e-13 86.1
9 TraesCS4A01G136800 chr4D 100.000 41 0 0 2936 2976 296727642 296727682 3.340000e-10 76.8
10 TraesCS4A01G136800 chr4B 87.337 1453 52 56 1535 2936 366926420 366927791 0.000000e+00 1543.0
11 TraesCS4A01G136800 chr4B 86.948 521 30 10 719 1217 366925569 366926073 4.550000e-153 551.0
12 TraesCS4A01G136800 chr4B 95.455 220 6 1 1209 1428 366926096 366926311 6.410000e-92 348.0
13 TraesCS4A01G136800 chr4B 88.060 67 8 0 42 108 42932251 42932317 2.580000e-11 80.5
14 TraesCS4A01G136800 chr7A 98.013 151 3 0 2974 3124 139052204 139052054 2.390000e-66 263.0
15 TraesCS4A01G136800 chr7A 98.013 151 3 0 2974 3124 291622579 291622429 2.390000e-66 263.0
16 TraesCS4A01G136800 chr7A 97.351 151 4 0 2974 3124 9210710 9210560 1.110000e-64 257.0
17 TraesCS4A01G136800 chr7A 100.000 29 0 0 772 800 215323182 215323154 2.000000e-03 54.7
18 TraesCS4A01G136800 chr7B 97.368 152 4 0 2973 3124 608379611 608379460 3.090000e-65 259.0
19 TraesCS4A01G136800 chr6A 96.753 154 5 0 2971 3124 510214465 510214618 1.110000e-64 257.0
20 TraesCS4A01G136800 chr6A 90.361 83 1 3 1444 1526 93285778 93285703 5.510000e-18 102.0
21 TraesCS4A01G136800 chr6A 85.333 75 10 1 34 108 617087816 617087743 3.340000e-10 76.8
22 TraesCS4A01G136800 chr2A 95.652 161 6 1 2965 3124 477947466 477947306 1.110000e-64 257.0
23 TraesCS4A01G136800 chr1B 96.753 154 5 0 2971 3124 297475510 297475663 1.110000e-64 257.0
24 TraesCS4A01G136800 chr1B 88.235 51 5 1 770 820 652280369 652280418 3.360000e-05 60.2
25 TraesCS4A01G136800 chr1A 97.351 151 4 0 2974 3124 358543553 358543403 1.110000e-64 257.0
26 TraesCS4A01G136800 chr6B 94.578 166 6 3 2959 3122 427030551 427030715 1.440000e-63 254.0
27 TraesCS4A01G136800 chr6B 91.463 82 0 3 1444 1525 13827600 13827526 4.260000e-19 106.0
28 TraesCS4A01G136800 chr5A 91.566 83 0 3 1443 1525 3296086 3296161 1.180000e-19 108.0
29 TraesCS4A01G136800 chr5A 91.463 82 0 3 1444 1525 450750718 450750792 4.260000e-19 106.0
30 TraesCS4A01G136800 chr5A 87.671 73 8 1 41 112 521774905 521774977 2.000000e-12 84.2
31 TraesCS4A01G136800 chr5A 81.013 79 10 3 746 819 673779552 673779630 1.210000e-04 58.4
32 TraesCS4A01G136800 chrUn 91.463 82 0 3 1444 1525 37403316 37403242 4.260000e-19 106.0
33 TraesCS4A01G136800 chr2D 90.476 84 1 3 1443 1526 529010254 529010330 1.530000e-18 104.0
34 TraesCS4A01G136800 chr5D 90.361 83 1 3 1443 1525 6375606 6375531 5.510000e-18 102.0
35 TraesCS4A01G136800 chr6D 86.813 91 6 2 7 91 255521138 255521228 2.560000e-16 97.1
36 TraesCS4A01G136800 chr3D 81.897 116 17 3 1 112 166489998 166489883 9.220000e-16 95.3
37 TraesCS4A01G136800 chr3A 88.235 68 8 0 41 108 712383280 712383347 7.180000e-12 82.4
38 TraesCS4A01G136800 chr3B 86.765 68 9 0 41 108 719093952 719093885 3.340000e-10 76.8
39 TraesCS4A01G136800 chr7D 84.932 73 7 4 1 69 564528839 564528911 1.550000e-08 71.3
40 TraesCS4A01G136800 chr1D 80.952 84 8 5 722 805 483133062 483132987 3.360000e-05 60.2


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 TraesCS4A01G136800 chr4A 192627105 192630228 3123 True 2640.50 4859 100.000000 1 3124 2 chr4A.!!$R1 3123
1 TraesCS4A01G136800 chr4D 296721497 296727682 6185 False 634.76 1834 91.826200 519 2976 5 chr4D.!!$F3 2457
2 TraesCS4A01G136800 chr4B 366925569 366927791 2222 False 814.00 1543 89.913333 719 2936 3 chr4B.!!$F2 2217

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
563 564 0.179073 AAACATGAGAGCGCGGCTAT 60.179 50.0 8.83 2.23 39.88 2.97 F
910 4525 0.319555 CTCGCCTTTCTCGGTGTTCA 60.320 55.0 0.00 0.00 36.01 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 5774 0.037326 TGCTCATCCACGTTCTCCAC 60.037 55.0 0.00 0.00 0.00 4.02 R
2729 6522 0.773644 ATCTTGAGGGTTGCACACCT 59.226 50.0 8.06 8.06 46.38 4.00 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
37 38 5.368256 GTCAAGATGACAGCTTCAAATGT 57.632 39.130 2.21 0.00 46.22 2.71
38 39 6.486253 GTCAAGATGACAGCTTCAAATGTA 57.514 37.500 2.21 0.00 46.22 2.29
39 40 6.310197 GTCAAGATGACAGCTTCAAATGTAC 58.690 40.000 2.21 0.00 46.22 2.90
40 41 5.120674 TCAAGATGACAGCTTCAAATGTACG 59.879 40.000 2.21 0.00 37.92 3.67
41 42 4.569943 AGATGACAGCTTCAAATGTACGT 58.430 39.130 0.00 0.00 37.92 3.57
42 43 5.720202 AGATGACAGCTTCAAATGTACGTA 58.280 37.500 0.00 0.00 37.92 3.57
43 44 6.341316 AGATGACAGCTTCAAATGTACGTAT 58.659 36.000 0.00 0.00 37.92 3.06
44 45 6.818644 AGATGACAGCTTCAAATGTACGTATT 59.181 34.615 0.00 0.00 37.92 1.89
45 46 7.979537 AGATGACAGCTTCAAATGTACGTATTA 59.020 33.333 0.00 0.00 37.92 0.98
46 47 7.285783 TGACAGCTTCAAATGTACGTATTAC 57.714 36.000 0.00 0.00 0.00 1.89
47 48 7.094631 TGACAGCTTCAAATGTACGTATTACT 58.905 34.615 0.00 0.00 0.00 2.24
48 49 7.601130 TGACAGCTTCAAATGTACGTATTACTT 59.399 33.333 0.00 0.00 0.00 2.24
49 50 8.319143 ACAGCTTCAAATGTACGTATTACTTT 57.681 30.769 0.00 0.00 31.04 2.66
50 51 8.227791 ACAGCTTCAAATGTACGTATTACTTTG 58.772 33.333 0.00 7.09 33.99 2.77
51 52 8.227791 CAGCTTCAAATGTACGTATTACTTTGT 58.772 33.333 0.00 0.00 34.16 2.83
52 53 9.426837 AGCTTCAAATGTACGTATTACTTTGTA 57.573 29.630 0.00 0.97 34.16 2.41
56 57 9.709495 TCAAATGTACGTATTACTTTGTAAGGT 57.291 29.630 0.00 0.00 34.16 3.50
87 88 9.701098 ATGAATAATTAGTAAAATGGCTGCATG 57.299 29.630 0.50 0.00 0.00 4.06
88 89 7.652909 TGAATAATTAGTAAAATGGCTGCATGC 59.347 33.333 11.82 11.82 41.94 4.06
89 90 5.341872 AATTAGTAAAATGGCTGCATGCA 57.658 34.783 21.29 21.29 45.15 3.96
90 91 5.540400 ATTAGTAAAATGGCTGCATGCAT 57.460 34.783 22.97 6.91 45.15 3.96
91 92 3.899052 AGTAAAATGGCTGCATGCATT 57.101 38.095 22.97 13.89 45.15 3.56
92 93 4.210724 AGTAAAATGGCTGCATGCATTT 57.789 36.364 22.97 19.69 45.15 2.32
93 94 4.581868 AGTAAAATGGCTGCATGCATTTT 58.418 34.783 24.98 24.98 45.15 1.82
94 95 4.632688 AGTAAAATGGCTGCATGCATTTTC 59.367 37.500 25.24 17.91 45.15 2.29
95 96 2.032680 AATGGCTGCATGCATTTTCC 57.967 45.000 22.97 19.03 45.15 3.13
96 97 0.906066 ATGGCTGCATGCATTTTCCA 59.094 45.000 22.97 23.56 45.15 3.53
97 98 0.248012 TGGCTGCATGCATTTTCCAG 59.752 50.000 22.97 8.76 45.15 3.86
98 99 0.533491 GGCTGCATGCATTTTCCAGA 59.467 50.000 22.97 0.00 45.15 3.86
99 100 1.138266 GGCTGCATGCATTTTCCAGAT 59.862 47.619 22.97 0.00 45.15 2.90
100 101 2.201732 GCTGCATGCATTTTCCAGATG 58.798 47.619 22.97 6.35 42.31 2.90
106 107 2.288961 GCATTTTCCAGATGCAGTGG 57.711 50.000 11.04 11.04 46.96 4.00
107 108 1.738030 GCATTTTCCAGATGCAGTGGC 60.738 52.381 12.24 0.00 46.96 5.01
129 130 6.311055 GCAGAGCCAGGAAATTAAGATTAG 57.689 41.667 0.00 0.00 0.00 1.73
130 131 5.240403 GCAGAGCCAGGAAATTAAGATTAGG 59.760 44.000 0.00 0.00 0.00 2.69
131 132 5.767168 CAGAGCCAGGAAATTAAGATTAGGG 59.233 44.000 0.00 0.00 0.00 3.53
132 133 5.672194 AGAGCCAGGAAATTAAGATTAGGGA 59.328 40.000 0.00 0.00 0.00 4.20
133 134 5.946486 AGCCAGGAAATTAAGATTAGGGAG 58.054 41.667 0.00 0.00 0.00 4.30
134 135 5.073428 GCCAGGAAATTAAGATTAGGGAGG 58.927 45.833 0.00 0.00 0.00 4.30
135 136 5.073428 CCAGGAAATTAAGATTAGGGAGGC 58.927 45.833 0.00 0.00 0.00 4.70
136 137 5.163045 CCAGGAAATTAAGATTAGGGAGGCT 60.163 44.000 0.00 0.00 0.00 4.58
137 138 6.044404 CCAGGAAATTAAGATTAGGGAGGCTA 59.956 42.308 0.00 0.00 0.00 3.93
138 139 7.421382 CCAGGAAATTAAGATTAGGGAGGCTAA 60.421 40.741 0.00 0.00 0.00 3.09
139 140 7.998964 CAGGAAATTAAGATTAGGGAGGCTAAA 59.001 37.037 0.00 0.00 0.00 1.85
140 141 8.737633 AGGAAATTAAGATTAGGGAGGCTAAAT 58.262 33.333 0.00 0.00 0.00 1.40
141 142 8.797438 GGAAATTAAGATTAGGGAGGCTAAATG 58.203 37.037 0.00 0.00 0.00 2.32
142 143 9.574516 GAAATTAAGATTAGGGAGGCTAAATGA 57.425 33.333 0.00 0.00 0.00 2.57
143 144 8.926092 AATTAAGATTAGGGAGGCTAAATGAC 57.074 34.615 0.00 0.00 0.00 3.06
144 145 5.975988 AAGATTAGGGAGGCTAAATGACA 57.024 39.130 0.00 0.00 0.00 3.58
145 146 5.297569 AGATTAGGGAGGCTAAATGACAC 57.702 43.478 0.00 0.00 0.00 3.67
146 147 4.721776 AGATTAGGGAGGCTAAATGACACA 59.278 41.667 0.00 0.00 0.00 3.72
147 148 4.919774 TTAGGGAGGCTAAATGACACAA 57.080 40.909 0.00 0.00 0.00 3.33
148 149 3.356529 AGGGAGGCTAAATGACACAAG 57.643 47.619 0.00 0.00 0.00 3.16
149 150 2.912956 AGGGAGGCTAAATGACACAAGA 59.087 45.455 0.00 0.00 0.00 3.02
150 151 3.525199 AGGGAGGCTAAATGACACAAGAT 59.475 43.478 0.00 0.00 0.00 2.40
151 152 4.018050 AGGGAGGCTAAATGACACAAGATT 60.018 41.667 0.00 0.00 0.00 2.40
152 153 4.706962 GGGAGGCTAAATGACACAAGATTT 59.293 41.667 0.00 0.00 0.00 2.17
153 154 5.185828 GGGAGGCTAAATGACACAAGATTTT 59.814 40.000 0.00 0.00 0.00 1.82
154 155 6.095377 GGAGGCTAAATGACACAAGATTTTG 58.905 40.000 0.00 0.00 40.24 2.44
155 156 6.071952 GGAGGCTAAATGACACAAGATTTTGA 60.072 38.462 2.48 0.00 37.73 2.69
156 157 7.363268 GGAGGCTAAATGACACAAGATTTTGAT 60.363 37.037 2.48 0.00 37.73 2.57
157 158 7.899973 AGGCTAAATGACACAAGATTTTGATT 58.100 30.769 2.48 0.00 37.73 2.57
158 159 7.816031 AGGCTAAATGACACAAGATTTTGATTG 59.184 33.333 2.48 0.00 37.73 2.67
159 160 7.063780 GGCTAAATGACACAAGATTTTGATTGG 59.936 37.037 2.48 0.00 37.73 3.16
160 161 7.814107 GCTAAATGACACAAGATTTTGATTGGA 59.186 33.333 2.48 0.00 37.73 3.53
161 162 9.350357 CTAAATGACACAAGATTTTGATTGGAG 57.650 33.333 2.48 0.00 37.73 3.86
162 163 5.710513 TGACACAAGATTTTGATTGGAGG 57.289 39.130 2.48 0.00 37.73 4.30
163 164 4.523943 TGACACAAGATTTTGATTGGAGGG 59.476 41.667 2.48 0.00 37.73 4.30
164 165 3.834231 ACACAAGATTTTGATTGGAGGGG 59.166 43.478 2.48 0.00 37.73 4.79
165 166 2.833943 ACAAGATTTTGATTGGAGGGGC 59.166 45.455 2.48 0.00 37.73 5.80
166 167 2.165357 AGATTTTGATTGGAGGGGCC 57.835 50.000 0.00 0.00 37.10 5.80
167 168 4.388703 CAAGATTTTGATTGGAGGGGCCA 61.389 47.826 4.39 0.00 39.88 5.36
179 180 5.941146 TGGAGGGGCCAAACTATATTTAT 57.059 39.130 4.39 0.00 45.87 1.40
180 181 5.640147 TGGAGGGGCCAAACTATATTTATG 58.360 41.667 4.39 0.00 45.87 1.90
181 182 4.462834 GGAGGGGCCAAACTATATTTATGC 59.537 45.833 4.39 0.00 36.34 3.14
182 183 5.073437 AGGGGCCAAACTATATTTATGCA 57.927 39.130 4.39 0.00 0.00 3.96
183 184 5.654370 AGGGGCCAAACTATATTTATGCAT 58.346 37.500 4.39 3.79 0.00 3.96
184 185 5.481473 AGGGGCCAAACTATATTTATGCATG 59.519 40.000 10.16 0.00 0.00 4.06
185 186 5.245977 GGGGCCAAACTATATTTATGCATGT 59.754 40.000 10.16 0.00 0.00 3.21
186 187 6.158598 GGGCCAAACTATATTTATGCATGTG 58.841 40.000 10.16 0.00 0.00 3.21
187 188 6.239289 GGGCCAAACTATATTTATGCATGTGT 60.239 38.462 10.16 0.00 0.00 3.72
188 189 6.863126 GGCCAAACTATATTTATGCATGTGTC 59.137 38.462 10.16 0.00 0.00 3.67
189 190 7.255590 GGCCAAACTATATTTATGCATGTGTCT 60.256 37.037 10.16 0.00 0.00 3.41
190 191 8.137437 GCCAAACTATATTTATGCATGTGTCTT 58.863 33.333 10.16 0.00 0.00 3.01
217 218 9.466497 TTTTCCTAATTTCTGCACTATTCATCT 57.534 29.630 0.00 0.00 0.00 2.90
218 219 9.466497 TTTCCTAATTTCTGCACTATTCATCTT 57.534 29.630 0.00 0.00 0.00 2.40
219 220 8.668510 TCCTAATTTCTGCACTATTCATCTTC 57.331 34.615 0.00 0.00 0.00 2.87
220 221 8.267183 TCCTAATTTCTGCACTATTCATCTTCA 58.733 33.333 0.00 0.00 0.00 3.02
221 222 8.896744 CCTAATTTCTGCACTATTCATCTTCAA 58.103 33.333 0.00 0.00 0.00 2.69
223 224 8.976986 AATTTCTGCACTATTCATCTTCAAAC 57.023 30.769 0.00 0.00 0.00 2.93
224 225 7.750229 TTTCTGCACTATTCATCTTCAAACT 57.250 32.000 0.00 0.00 0.00 2.66
225 226 8.846943 TTTCTGCACTATTCATCTTCAAACTA 57.153 30.769 0.00 0.00 0.00 2.24
226 227 9.453572 TTTCTGCACTATTCATCTTCAAACTAT 57.546 29.630 0.00 0.00 0.00 2.12
535 536 8.920509 ACACTTTTTAGCGTTTTAATGAAACT 57.079 26.923 0.00 0.00 44.37 2.66
556 557 4.083643 ACTGAACATGAAAACATGAGAGCG 60.084 41.667 15.53 4.34 36.48 5.03
560 561 1.226128 GAAAACATGAGAGCGCGGC 60.226 57.895 8.83 0.00 0.00 6.53
561 562 1.639298 GAAAACATGAGAGCGCGGCT 61.639 55.000 8.83 5.31 43.88 5.52
562 563 0.391130 AAAACATGAGAGCGCGGCTA 60.391 50.000 8.83 0.00 39.88 3.93
563 564 0.179073 AAACATGAGAGCGCGGCTAT 60.179 50.000 8.83 2.23 39.88 2.97
564 565 0.598680 AACATGAGAGCGCGGCTATC 60.599 55.000 8.83 12.96 45.72 2.08
584 585 3.937814 TCGTGAGATGGCTACATGTTTT 58.062 40.909 2.30 0.00 37.47 2.43
585 586 4.323417 TCGTGAGATGGCTACATGTTTTT 58.677 39.130 2.30 0.00 37.47 1.94
599 600 9.937175 GCTACATGTTTTTGATATTACTTCCTC 57.063 33.333 2.30 0.00 0.00 3.71
602 603 6.431198 TGTTTTTGATATTACTTCCTCCGC 57.569 37.500 0.00 0.00 0.00 5.54
603 604 5.355910 TGTTTTTGATATTACTTCCTCCGCC 59.644 40.000 0.00 0.00 0.00 6.13
645 647 6.928348 TGATTTTATATTCTAGGCGGAGGA 57.072 37.500 0.00 0.00 0.00 3.71
663 665 7.435305 GCGGAGGAAGTATTAAGTAAGAGAAT 58.565 38.462 0.00 0.00 0.00 2.40
664 666 7.927092 GCGGAGGAAGTATTAAGTAAGAGAATT 59.073 37.037 0.00 0.00 0.00 2.17
665 667 9.250624 CGGAGGAAGTATTAAGTAAGAGAATTG 57.749 37.037 0.00 0.00 0.00 2.32
764 766 8.202137 TGTGTCTAGATATGTTTTAGGGTTAGC 58.798 37.037 0.00 0.00 0.00 3.09
776 778 7.767198 TGTTTTAGGGTTAGCTACATGTGTATC 59.233 37.037 9.11 0.00 0.00 2.24
877 4492 9.747898 GGATACCACTATATAGATATGGAGAGG 57.252 40.741 19.65 3.15 0.00 3.69
910 4525 0.319555 CTCGCCTTTCTCGGTGTTCA 60.320 55.000 0.00 0.00 36.01 3.18
939 4571 2.849294 AGCCACAAACTCTCTCTTCC 57.151 50.000 0.00 0.00 0.00 3.46
940 4572 2.334023 AGCCACAAACTCTCTCTTCCT 58.666 47.619 0.00 0.00 0.00 3.36
960 4594 2.003658 CTCTGCTGTCTCTCTCGCCC 62.004 65.000 0.00 0.00 0.00 6.13
969 4603 2.065906 CTCTCTCGCCCCGCTTCTAC 62.066 65.000 0.00 0.00 0.00 2.59
1166 4808 7.334421 ACATATGTATATGCCTTTTTCGCCTAG 59.666 37.037 6.56 0.00 42.98 3.02
1188 4834 1.089920 GCTGGTTGTGCGATCTTCAT 58.910 50.000 0.00 0.00 0.00 2.57
1203 4849 2.967887 TCTTCATCATGCCTGCTAGCTA 59.032 45.455 17.23 1.31 0.00 3.32
1204 4850 3.006644 TCTTCATCATGCCTGCTAGCTAG 59.993 47.826 16.84 16.84 0.00 3.42
1221 4898 2.616510 GCTAGCTCTTTCTTTCTGGGCA 60.617 50.000 7.70 0.00 0.00 5.36
1244 4921 8.345565 GGCAACTTAATTAAGTAGATGGATGTG 58.654 37.037 26.94 19.19 45.17 3.21
1379 5056 2.029518 CGTGCAGCAGACAGACCA 59.970 61.111 0.00 0.00 0.00 4.02
1432 5109 8.826710 TGCTTGATTTGTTTCTTATATACTCCG 58.173 33.333 0.00 0.00 0.00 4.63
1442 5119 8.854117 GTTTCTTATATACTCCGTAAAGAGGGA 58.146 37.037 0.00 0.00 38.26 4.20
1455 5149 9.425248 TCCGTAAAGAGGGAGTAAAGAAATATA 57.575 33.333 0.00 0.00 34.63 0.86
1500 5197 9.654663 AAAAAGTAGTGATCTAAACGCTCTTAT 57.345 29.630 0.00 0.00 0.00 1.73
1578 5297 6.434028 CAGGGAGATTTGGATTGAAACAGTAA 59.566 38.462 0.00 0.00 0.00 2.24
1579 5298 7.123247 CAGGGAGATTTGGATTGAAACAGTAAT 59.877 37.037 0.00 0.00 0.00 1.89
1581 5300 8.406297 GGGAGATTTGGATTGAAACAGTAATAC 58.594 37.037 0.00 0.00 0.00 1.89
1582 5301 8.956426 GGAGATTTGGATTGAAACAGTAATACA 58.044 33.333 0.00 0.00 0.00 2.29
1583 5302 9.774742 GAGATTTGGATTGAAACAGTAATACAC 57.225 33.333 0.00 0.00 27.25 2.90
1773 5511 1.467920 GGCTTCTGGTTTCCATCCTG 58.532 55.000 0.00 0.00 30.82 3.86
1882 5622 5.969423 AGGTAACAACAAGCTAATACGCTA 58.031 37.500 0.00 0.00 38.21 4.26
1894 5634 8.984764 CAAGCTAATACGCTATGTACCAAAATA 58.015 33.333 0.00 0.00 39.86 1.40
1895 5635 9.720769 AAGCTAATACGCTATGTACCAAAATAT 57.279 29.630 0.00 0.00 39.86 1.28
1963 5703 4.887655 ACGGACTGACCAAAAGAAGAAAAT 59.112 37.500 0.00 0.00 38.90 1.82
2180 5920 6.291377 ACCGTCAAGCATCTCAATAACATAT 58.709 36.000 0.00 0.00 0.00 1.78
2181 5921 7.441836 ACCGTCAAGCATCTCAATAACATATA 58.558 34.615 0.00 0.00 0.00 0.86
2182 5922 7.600375 ACCGTCAAGCATCTCAATAACATATAG 59.400 37.037 0.00 0.00 0.00 1.31
2211 5951 7.509546 TGGTTAATCTGGTCTATTGATTCTCC 58.490 38.462 0.00 0.00 33.24 3.71
2220 5960 6.103353 TGGTCTATTGATTCTCCCTCTCTCTA 59.897 42.308 0.00 0.00 0.00 2.43
2222 5962 8.333235 GGTCTATTGATTCTCCCTCTCTCTATA 58.667 40.741 0.00 0.00 0.00 1.31
2248 6013 9.756571 ATATATCATATATCTCCCTACCGTTCC 57.243 37.037 0.00 0.00 0.00 3.62
2249 6014 5.531753 TCATATATCTCCCTACCGTTCCT 57.468 43.478 0.00 0.00 0.00 3.36
2250 6015 5.900437 TCATATATCTCCCTACCGTTCCTT 58.100 41.667 0.00 0.00 0.00 3.36
2251 6016 5.950549 TCATATATCTCCCTACCGTTCCTTC 59.049 44.000 0.00 0.00 0.00 3.46
2254 6019 1.078324 TCTCCCTACCGTTCCTTCCTT 59.922 52.381 0.00 0.00 0.00 3.36
2255 6020 1.207329 CTCCCTACCGTTCCTTCCTTG 59.793 57.143 0.00 0.00 0.00 3.61
2256 6021 0.981943 CCCTACCGTTCCTTCCTTGT 59.018 55.000 0.00 0.00 0.00 3.16
2257 6022 1.350019 CCCTACCGTTCCTTCCTTGTT 59.650 52.381 0.00 0.00 0.00 2.83
2258 6023 2.614734 CCCTACCGTTCCTTCCTTGTTC 60.615 54.545 0.00 0.00 0.00 3.18
2259 6024 2.334838 CTACCGTTCCTTCCTTGTTCG 58.665 52.381 0.00 0.00 0.00 3.95
2260 6025 0.466963 ACCGTTCCTTCCTTGTTCGT 59.533 50.000 0.00 0.00 0.00 3.85
2261 6026 1.145803 CCGTTCCTTCCTTGTTCGTC 58.854 55.000 0.00 0.00 0.00 4.20
2262 6027 1.270147 CCGTTCCTTCCTTGTTCGTCT 60.270 52.381 0.00 0.00 0.00 4.18
2263 6028 2.029649 CCGTTCCTTCCTTGTTCGTCTA 60.030 50.000 0.00 0.00 0.00 2.59
2272 6037 2.259618 CTTGTTCGTCTACCGGTGATG 58.740 52.381 19.93 17.34 37.11 3.07
2286 6051 3.072211 CGGTGATGGATGAATGATGAGG 58.928 50.000 0.00 0.00 0.00 3.86
2299 6064 2.666317 TGATGAGGTGCCTATTCTCGA 58.334 47.619 0.00 0.00 0.00 4.04
2358 6123 3.841643 GGCATAATATGACCAAGCATGC 58.158 45.455 10.51 10.51 37.23 4.06
2359 6124 3.256383 GGCATAATATGACCAAGCATGCA 59.744 43.478 21.98 0.00 39.17 3.96
2360 6125 4.081862 GGCATAATATGACCAAGCATGCAT 60.082 41.667 21.98 4.57 39.17 3.96
2433 6198 2.968675 GCTAAGAGCTAAACGGTTGGA 58.031 47.619 0.00 0.00 38.45 3.53
2597 6377 7.123247 AGTTGTTGCATGGATAATAAAGCTCTT 59.877 33.333 0.00 0.00 0.00 2.85
2598 6378 8.405531 GTTGTTGCATGGATAATAAAGCTCTTA 58.594 33.333 0.00 0.00 0.00 2.10
2599 6379 8.696043 TGTTGCATGGATAATAAAGCTCTTAT 57.304 30.769 0.00 0.00 0.00 1.73
2600 6380 8.786898 TGTTGCATGGATAATAAAGCTCTTATC 58.213 33.333 12.11 12.11 34.85 1.75
2605 6385 6.295719 GGATAATAAAGCTCTTATCCGGGA 57.704 41.667 19.10 0.00 41.94 5.14
2606 6386 6.708285 GGATAATAAAGCTCTTATCCGGGAA 58.292 40.000 19.10 0.00 41.94 3.97
2607 6387 7.166167 GGATAATAAAGCTCTTATCCGGGAAA 58.834 38.462 19.10 0.00 41.94 3.13
2608 6388 7.664318 GGATAATAAAGCTCTTATCCGGGAAAA 59.336 37.037 19.10 0.00 41.94 2.29
2609 6389 8.990163 ATAATAAAGCTCTTATCCGGGAAAAA 57.010 30.769 0.00 0.00 0.00 1.94
2729 6522 9.118300 GTAGGAGTAGAATAGTAAGCAACAGTA 57.882 37.037 0.00 0.00 0.00 2.74
2736 6529 2.767505 AGTAAGCAACAGTAGGTGTGC 58.232 47.619 0.00 0.00 40.26 4.57
2737 6530 2.104111 AGTAAGCAACAGTAGGTGTGCA 59.896 45.455 0.00 0.00 40.26 4.57
2738 6531 2.051334 AAGCAACAGTAGGTGTGCAA 57.949 45.000 0.00 0.00 40.26 4.08
2739 6532 1.308998 AGCAACAGTAGGTGTGCAAC 58.691 50.000 0.00 0.00 40.26 4.17
2749 6543 2.489938 GGTGTGCAACCCTCAAGATA 57.510 50.000 6.76 0.00 44.02 1.98
2793 6587 1.770294 AAGGCGAGGTTCCAAAAACA 58.230 45.000 0.00 0.00 0.00 2.83
2889 6690 3.772619 GCCAAGGCAACGATAGGTA 57.227 52.632 6.14 0.00 46.39 3.08
2890 6691 1.583054 GCCAAGGCAACGATAGGTAG 58.417 55.000 6.14 0.00 46.39 3.18
2976 6828 2.027561 TCTTGGTGCGTTGGCTAATACT 60.028 45.455 0.00 0.00 40.82 2.12
2977 6829 2.018542 TGGTGCGTTGGCTAATACTC 57.981 50.000 0.00 0.00 40.82 2.59
2978 6830 1.296727 GGTGCGTTGGCTAATACTCC 58.703 55.000 0.00 0.00 40.82 3.85
2979 6831 1.296727 GTGCGTTGGCTAATACTCCC 58.703 55.000 0.00 0.00 40.82 4.30
2980 6832 1.134491 GTGCGTTGGCTAATACTCCCT 60.134 52.381 0.00 0.00 40.82 4.20
2981 6833 1.138266 TGCGTTGGCTAATACTCCCTC 59.862 52.381 0.00 0.00 40.82 4.30
2982 6834 1.540580 GCGTTGGCTAATACTCCCTCC 60.541 57.143 0.00 0.00 35.83 4.30
2983 6835 1.269621 CGTTGGCTAATACTCCCTCCG 60.270 57.143 0.00 0.00 0.00 4.63
2984 6836 1.070289 GTTGGCTAATACTCCCTCCGG 59.930 57.143 0.00 0.00 0.00 5.14
2985 6837 0.263765 TGGCTAATACTCCCTCCGGT 59.736 55.000 0.00 0.00 0.00 5.28
2986 6838 0.967662 GGCTAATACTCCCTCCGGTC 59.032 60.000 0.00 0.00 0.00 4.79
2987 6839 1.480869 GGCTAATACTCCCTCCGGTCT 60.481 57.143 0.00 0.00 0.00 3.85
2988 6840 2.317973 GCTAATACTCCCTCCGGTCTT 58.682 52.381 0.00 0.00 0.00 3.01
2989 6841 2.699321 GCTAATACTCCCTCCGGTCTTT 59.301 50.000 0.00 0.00 0.00 2.52
2990 6842 3.134262 GCTAATACTCCCTCCGGTCTTTT 59.866 47.826 0.00 0.00 0.00 2.27
2991 6843 4.383880 GCTAATACTCCCTCCGGTCTTTTT 60.384 45.833 0.00 0.00 0.00 1.94
3013 6865 6.509418 TTTACTCTACACATTGGATTTGCC 57.491 37.500 0.00 0.00 37.10 4.52
3014 6866 3.009723 ACTCTACACATTGGATTTGCCG 58.990 45.455 0.00 0.00 40.66 5.69
3015 6867 3.270027 CTCTACACATTGGATTTGCCGA 58.730 45.455 0.00 0.00 40.66 5.54
3016 6868 3.680490 TCTACACATTGGATTTGCCGAA 58.320 40.909 0.00 0.00 40.66 4.30
3017 6869 4.075682 TCTACACATTGGATTTGCCGAAA 58.924 39.130 0.00 0.00 40.66 3.46
3018 6870 3.302365 ACACATTGGATTTGCCGAAAG 57.698 42.857 0.00 0.00 40.66 2.62
3019 6871 2.627699 ACACATTGGATTTGCCGAAAGT 59.372 40.909 0.00 0.00 40.66 2.66
3020 6872 3.244976 CACATTGGATTTGCCGAAAGTC 58.755 45.455 0.00 0.00 40.66 3.01
3021 6873 2.890311 ACATTGGATTTGCCGAAAGTCA 59.110 40.909 0.00 0.00 40.66 3.41
3022 6874 3.320541 ACATTGGATTTGCCGAAAGTCAA 59.679 39.130 0.00 0.00 40.66 3.18
3023 6875 4.202202 ACATTGGATTTGCCGAAAGTCAAA 60.202 37.500 0.00 0.00 40.66 2.69
3024 6876 3.363341 TGGATTTGCCGAAAGTCAAAC 57.637 42.857 0.00 0.00 40.66 2.93
3025 6877 2.955660 TGGATTTGCCGAAAGTCAAACT 59.044 40.909 0.00 0.00 40.66 2.66
3026 6878 3.383185 TGGATTTGCCGAAAGTCAAACTT 59.617 39.130 0.00 0.00 38.90 2.66
3027 6879 4.142049 TGGATTTGCCGAAAGTCAAACTTT 60.142 37.500 4.82 4.82 41.99 2.66
3028 6880 6.190408 TGGATTTGCCGAAAGTCAAACTTTG 61.190 40.000 9.65 0.00 42.50 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.120674 CGTACATTTGAAGCTGTCATCTTGA 59.879 40.000 0.00 0.00 35.70 3.02
17 18 5.106948 ACGTACATTTGAAGCTGTCATCTTG 60.107 40.000 0.00 0.00 35.70 3.02
18 19 4.997395 ACGTACATTTGAAGCTGTCATCTT 59.003 37.500 0.00 0.00 35.70 2.40
19 20 4.569943 ACGTACATTTGAAGCTGTCATCT 58.430 39.130 0.00 0.00 35.70 2.90
20 21 4.928661 ACGTACATTTGAAGCTGTCATC 57.071 40.909 0.00 0.00 35.70 2.92
21 22 6.985188 AATACGTACATTTGAAGCTGTCAT 57.015 33.333 0.00 0.00 35.70 3.06
22 23 7.094631 AGTAATACGTACATTTGAAGCTGTCA 58.905 34.615 0.00 0.00 34.88 3.58
23 24 7.521509 AGTAATACGTACATTTGAAGCTGTC 57.478 36.000 0.00 0.00 34.88 3.51
24 25 7.900782 AAGTAATACGTACATTTGAAGCTGT 57.099 32.000 0.00 0.00 34.88 4.40
25 26 8.227791 ACAAAGTAATACGTACATTTGAAGCTG 58.772 33.333 21.04 6.21 35.99 4.24
26 27 8.319143 ACAAAGTAATACGTACATTTGAAGCT 57.681 30.769 21.04 0.00 35.99 3.74
30 31 9.709495 ACCTTACAAAGTAATACGTACATTTGA 57.291 29.630 21.04 9.28 35.99 2.69
61 62 9.701098 CATGCAGCCATTTTACTAATTATTCAT 57.299 29.630 0.00 0.00 0.00 2.57
62 63 7.652909 GCATGCAGCCATTTTACTAATTATTCA 59.347 33.333 14.21 0.00 37.23 2.57
63 64 7.652909 TGCATGCAGCCATTTTACTAATTATTC 59.347 33.333 18.46 0.00 44.83 1.75
64 65 7.499292 TGCATGCAGCCATTTTACTAATTATT 58.501 30.769 18.46 0.00 44.83 1.40
65 66 7.053316 TGCATGCAGCCATTTTACTAATTAT 57.947 32.000 18.46 0.00 44.83 1.28
66 67 6.462552 TGCATGCAGCCATTTTACTAATTA 57.537 33.333 18.46 0.00 44.83 1.40
67 68 5.341872 TGCATGCAGCCATTTTACTAATT 57.658 34.783 18.46 0.00 44.83 1.40
68 69 5.540400 ATGCATGCAGCCATTTTACTAAT 57.460 34.783 26.69 0.11 44.83 1.73
69 70 5.341872 AATGCATGCAGCCATTTTACTAA 57.658 34.783 26.69 0.00 44.83 2.24
70 71 5.341872 AAATGCATGCAGCCATTTTACTA 57.658 34.783 26.69 0.00 44.83 1.82
71 72 3.899052 AATGCATGCAGCCATTTTACT 57.101 38.095 26.69 1.43 44.83 2.24
72 73 4.201841 GGAAAATGCATGCAGCCATTTTAC 60.202 41.667 26.71 24.95 44.83 2.01
73 74 3.940221 GGAAAATGCATGCAGCCATTTTA 59.060 39.130 26.71 0.00 44.83 1.52
74 75 2.750712 GGAAAATGCATGCAGCCATTTT 59.249 40.909 26.87 26.87 44.83 1.82
75 76 2.290387 TGGAAAATGCATGCAGCCATTT 60.290 40.909 26.69 21.44 44.83 2.32
76 77 1.279558 TGGAAAATGCATGCAGCCATT 59.720 42.857 26.69 16.75 44.83 3.16
77 78 0.906066 TGGAAAATGCATGCAGCCAT 59.094 45.000 26.69 11.94 44.83 4.40
78 79 0.248012 CTGGAAAATGCATGCAGCCA 59.752 50.000 26.69 25.06 44.83 4.75
79 80 0.533491 TCTGGAAAATGCATGCAGCC 59.467 50.000 26.69 22.19 44.83 4.85
80 81 2.201732 CATCTGGAAAATGCATGCAGC 58.798 47.619 26.69 14.37 45.96 5.25
81 82 2.201732 GCATCTGGAAAATGCATGCAG 58.798 47.619 26.69 10.51 46.93 4.41
82 83 2.303163 GCATCTGGAAAATGCATGCA 57.697 45.000 25.04 25.04 46.93 3.96
88 89 1.546923 TGCCACTGCATCTGGAAAATG 59.453 47.619 13.60 0.00 44.23 2.32
89 90 1.927487 TGCCACTGCATCTGGAAAAT 58.073 45.000 13.60 0.00 44.23 1.82
90 91 3.435846 TGCCACTGCATCTGGAAAA 57.564 47.368 13.60 0.00 44.23 2.29
106 107 5.240403 CCTAATCTTAATTTCCTGGCTCTGC 59.760 44.000 0.00 0.00 0.00 4.26
107 108 5.767168 CCCTAATCTTAATTTCCTGGCTCTG 59.233 44.000 0.00 0.00 0.00 3.35
108 109 5.672194 TCCCTAATCTTAATTTCCTGGCTCT 59.328 40.000 0.00 0.00 0.00 4.09
109 110 5.941788 TCCCTAATCTTAATTTCCTGGCTC 58.058 41.667 0.00 0.00 0.00 4.70
110 111 5.163045 CCTCCCTAATCTTAATTTCCTGGCT 60.163 44.000 0.00 0.00 0.00 4.75
111 112 5.073428 CCTCCCTAATCTTAATTTCCTGGC 58.927 45.833 0.00 0.00 0.00 4.85
112 113 5.073428 GCCTCCCTAATCTTAATTTCCTGG 58.927 45.833 0.00 0.00 0.00 4.45
113 114 5.946486 AGCCTCCCTAATCTTAATTTCCTG 58.054 41.667 0.00 0.00 0.00 3.86
114 115 7.707467 TTAGCCTCCCTAATCTTAATTTCCT 57.293 36.000 0.00 0.00 31.17 3.36
115 116 8.797438 CATTTAGCCTCCCTAATCTTAATTTCC 58.203 37.037 0.00 0.00 36.00 3.13
116 117 9.574516 TCATTTAGCCTCCCTAATCTTAATTTC 57.425 33.333 0.00 0.00 36.00 2.17
117 118 9.355916 GTCATTTAGCCTCCCTAATCTTAATTT 57.644 33.333 0.00 0.00 36.00 1.82
118 119 8.502738 TGTCATTTAGCCTCCCTAATCTTAATT 58.497 33.333 0.00 0.00 36.00 1.40
119 120 7.939588 GTGTCATTTAGCCTCCCTAATCTTAAT 59.060 37.037 0.00 0.00 36.00 1.40
120 121 7.092623 TGTGTCATTTAGCCTCCCTAATCTTAA 60.093 37.037 0.00 0.00 36.00 1.85
121 122 6.385759 TGTGTCATTTAGCCTCCCTAATCTTA 59.614 38.462 0.00 0.00 36.00 2.10
122 123 5.191722 TGTGTCATTTAGCCTCCCTAATCTT 59.808 40.000 0.00 0.00 36.00 2.40
123 124 4.721776 TGTGTCATTTAGCCTCCCTAATCT 59.278 41.667 0.00 0.00 36.00 2.40
124 125 5.036117 TGTGTCATTTAGCCTCCCTAATC 57.964 43.478 0.00 0.00 36.00 1.75
125 126 5.191722 TCTTGTGTCATTTAGCCTCCCTAAT 59.808 40.000 0.00 0.00 36.00 1.73
126 127 4.534500 TCTTGTGTCATTTAGCCTCCCTAA 59.466 41.667 0.00 0.00 34.27 2.69
127 128 4.101114 TCTTGTGTCATTTAGCCTCCCTA 58.899 43.478 0.00 0.00 0.00 3.53
128 129 2.912956 TCTTGTGTCATTTAGCCTCCCT 59.087 45.455 0.00 0.00 0.00 4.20
129 130 3.350219 TCTTGTGTCATTTAGCCTCCC 57.650 47.619 0.00 0.00 0.00 4.30
130 131 5.904362 AAATCTTGTGTCATTTAGCCTCC 57.096 39.130 0.00 0.00 0.00 4.30
131 132 6.913170 TCAAAATCTTGTGTCATTTAGCCTC 58.087 36.000 0.00 0.00 33.94 4.70
132 133 6.899393 TCAAAATCTTGTGTCATTTAGCCT 57.101 33.333 0.00 0.00 33.94 4.58
133 134 7.063780 CCAATCAAAATCTTGTGTCATTTAGCC 59.936 37.037 0.00 0.00 33.94 3.93
134 135 7.814107 TCCAATCAAAATCTTGTGTCATTTAGC 59.186 33.333 0.00 0.00 33.94 3.09
135 136 9.350357 CTCCAATCAAAATCTTGTGTCATTTAG 57.650 33.333 0.00 0.00 33.94 1.85
136 137 8.306038 CCTCCAATCAAAATCTTGTGTCATTTA 58.694 33.333 0.00 0.00 33.94 1.40
137 138 7.156673 CCTCCAATCAAAATCTTGTGTCATTT 58.843 34.615 0.00 0.00 33.94 2.32
138 139 6.295462 CCCTCCAATCAAAATCTTGTGTCATT 60.295 38.462 0.00 0.00 33.94 2.57
139 140 5.186409 CCCTCCAATCAAAATCTTGTGTCAT 59.814 40.000 0.00 0.00 33.94 3.06
140 141 4.523943 CCCTCCAATCAAAATCTTGTGTCA 59.476 41.667 0.00 0.00 33.94 3.58
141 142 4.082026 CCCCTCCAATCAAAATCTTGTGTC 60.082 45.833 0.00 0.00 33.94 3.67
142 143 3.834231 CCCCTCCAATCAAAATCTTGTGT 59.166 43.478 0.00 0.00 33.94 3.72
143 144 3.368739 GCCCCTCCAATCAAAATCTTGTG 60.369 47.826 0.00 0.00 33.94 3.33
144 145 2.833943 GCCCCTCCAATCAAAATCTTGT 59.166 45.455 0.00 0.00 33.94 3.16
145 146 2.169144 GGCCCCTCCAATCAAAATCTTG 59.831 50.000 0.00 0.00 34.01 3.02
146 147 2.225598 TGGCCCCTCCAATCAAAATCTT 60.226 45.455 0.00 0.00 43.21 2.40
147 148 1.362237 TGGCCCCTCCAATCAAAATCT 59.638 47.619 0.00 0.00 43.21 2.40
148 149 1.864669 TGGCCCCTCCAATCAAAATC 58.135 50.000 0.00 0.00 43.21 2.17
157 158 5.640147 CATAAATATAGTTTGGCCCCTCCA 58.360 41.667 0.00 0.00 44.85 3.86
158 159 4.462834 GCATAAATATAGTTTGGCCCCTCC 59.537 45.833 0.00 0.00 0.00 4.30
159 160 5.076873 TGCATAAATATAGTTTGGCCCCTC 58.923 41.667 0.00 0.00 0.00 4.30
160 161 5.073437 TGCATAAATATAGTTTGGCCCCT 57.927 39.130 0.00 0.00 0.00 4.79
161 162 5.245977 ACATGCATAAATATAGTTTGGCCCC 59.754 40.000 0.00 0.00 0.00 5.80
162 163 6.158598 CACATGCATAAATATAGTTTGGCCC 58.841 40.000 0.00 0.00 0.00 5.80
163 164 6.748132 ACACATGCATAAATATAGTTTGGCC 58.252 36.000 0.00 0.00 0.00 5.36
164 165 7.651808 AGACACATGCATAAATATAGTTTGGC 58.348 34.615 0.00 0.00 0.00 4.52
191 192 9.466497 AGATGAATAGTGCAGAAATTAGGAAAA 57.534 29.630 0.00 0.00 0.00 2.29
192 193 9.466497 AAGATGAATAGTGCAGAAATTAGGAAA 57.534 29.630 0.00 0.00 0.00 3.13
193 194 9.113838 GAAGATGAATAGTGCAGAAATTAGGAA 57.886 33.333 0.00 0.00 0.00 3.36
194 195 8.267183 TGAAGATGAATAGTGCAGAAATTAGGA 58.733 33.333 0.00 0.00 0.00 2.94
195 196 8.442632 TGAAGATGAATAGTGCAGAAATTAGG 57.557 34.615 0.00 0.00 0.00 2.69
198 199 8.800332 AGTTTGAAGATGAATAGTGCAGAAATT 58.200 29.630 0.00 0.00 0.00 1.82
199 200 8.345724 AGTTTGAAGATGAATAGTGCAGAAAT 57.654 30.769 0.00 0.00 0.00 2.17
200 201 7.750229 AGTTTGAAGATGAATAGTGCAGAAA 57.250 32.000 0.00 0.00 0.00 2.52
556 557 2.024319 GCCATCTCACGATAGCCGC 61.024 63.158 0.00 0.00 43.32 6.53
560 561 4.511617 ACATGTAGCCATCTCACGATAG 57.488 45.455 0.00 0.00 46.19 2.08
561 562 4.937201 AACATGTAGCCATCTCACGATA 57.063 40.909 0.00 0.00 0.00 2.92
562 563 3.827008 AACATGTAGCCATCTCACGAT 57.173 42.857 0.00 0.00 0.00 3.73
563 564 3.610040 AAACATGTAGCCATCTCACGA 57.390 42.857 0.00 0.00 0.00 4.35
564 565 4.154015 TCAAAAACATGTAGCCATCTCACG 59.846 41.667 0.00 0.00 0.00 4.35
565 566 5.627499 TCAAAAACATGTAGCCATCTCAC 57.373 39.130 0.00 0.00 0.00 3.51
566 567 8.523915 AATATCAAAAACATGTAGCCATCTCA 57.476 30.769 0.00 0.00 0.00 3.27
567 568 9.884465 GTAATATCAAAAACATGTAGCCATCTC 57.116 33.333 0.00 0.00 0.00 2.75
584 585 3.071023 CAGGGCGGAGGAAGTAATATCAA 59.929 47.826 0.00 0.00 0.00 2.57
585 586 2.632996 CAGGGCGGAGGAAGTAATATCA 59.367 50.000 0.00 0.00 0.00 2.15
596 597 2.872038 GCAAGATATTACAGGGCGGAGG 60.872 54.545 0.00 0.00 0.00 4.30
599 600 2.254546 TGCAAGATATTACAGGGCGG 57.745 50.000 0.00 0.00 0.00 6.13
600 601 4.630894 TTTTGCAAGATATTACAGGGCG 57.369 40.909 0.00 0.00 0.00 6.13
602 603 9.603921 AAAATCATTTTGCAAGATATTACAGGG 57.396 29.630 1.59 0.00 0.00 4.45
633 634 4.801164 ACTTAATACTTCCTCCGCCTAGA 58.199 43.478 0.00 0.00 0.00 2.43
748 750 7.626390 ACACATGTAGCTAACCCTAAAACATA 58.374 34.615 0.00 0.00 0.00 2.29
807 4418 9.620259 GACCTTCTGATTTCCATATTTACTTCT 57.380 33.333 0.00 0.00 0.00 2.85
824 4439 1.687563 TCACTCACGTGACCTTCTGA 58.312 50.000 15.76 7.50 44.85 3.27
877 4492 2.498726 CGAGAAGGCTGGAGCTCC 59.501 66.667 26.78 26.78 41.70 4.70
925 4540 3.511146 AGCAGAGAGGAAGAGAGAGTTTG 59.489 47.826 0.00 0.00 0.00 2.93
928 4543 2.041620 ACAGCAGAGAGGAAGAGAGAGT 59.958 50.000 0.00 0.00 0.00 3.24
939 4571 0.378257 GCGAGAGAGACAGCAGAGAG 59.622 60.000 0.00 0.00 0.00 3.20
940 4572 1.029408 GGCGAGAGAGACAGCAGAGA 61.029 60.000 0.00 0.00 0.00 3.10
960 4594 1.482593 ACAATCTCCCAGTAGAAGCGG 59.517 52.381 0.00 0.00 0.00 5.52
969 4603 2.110967 CCGCAGCACAATCTCCCAG 61.111 63.158 0.00 0.00 0.00 4.45
1166 4808 0.674895 AAGATCGCACAACCAGCTCC 60.675 55.000 0.00 0.00 0.00 4.70
1203 4849 2.158549 AGTTGCCCAGAAAGAAAGAGCT 60.159 45.455 0.00 0.00 0.00 4.09
1204 4850 2.234143 AGTTGCCCAGAAAGAAAGAGC 58.766 47.619 0.00 0.00 0.00 4.09
1205 4851 6.581171 ATTAAGTTGCCCAGAAAGAAAGAG 57.419 37.500 0.00 0.00 0.00 2.85
1244 4921 4.175489 CAGCTGCAGCCACGCATC 62.175 66.667 34.39 5.26 42.06 3.91
1364 5041 0.831711 TAGGTGGTCTGTCTGCTGCA 60.832 55.000 0.88 0.88 0.00 4.41
1429 5106 6.616237 ATTTCTTTACTCCCTCTTTACGGA 57.384 37.500 0.00 0.00 0.00 4.69
1501 5198 9.862149 TTTTACTCCCTCTGTAAAGAAAGAAAT 57.138 29.630 0.00 0.00 39.85 2.17
1502 5199 9.338622 CTTTTACTCCCTCTGTAAAGAAAGAAA 57.661 33.333 0.00 0.00 39.85 2.52
1504 5201 8.258850 TCTTTTACTCCCTCTGTAAAGAAAGA 57.741 34.615 0.00 0.00 39.85 2.52
1505 5202 8.151596 ACTCTTTTACTCCCTCTGTAAAGAAAG 58.848 37.037 0.00 0.00 39.85 2.62
1773 5511 1.446272 CAACTCGTCGAAGGCCTCC 60.446 63.158 5.23 0.00 0.00 4.30
1894 5634 7.820578 AGACGTTTCTGTAGGCTAGTTATAT 57.179 36.000 0.00 0.00 0.00 0.86
1895 5635 7.636150 AAGACGTTTCTGTAGGCTAGTTATA 57.364 36.000 0.00 0.00 29.98 0.98
1935 5675 4.819105 TCTTTTGGTCAGTCCGTATCAT 57.181 40.909 0.00 0.00 39.52 2.45
1936 5676 4.282449 TCTTCTTTTGGTCAGTCCGTATCA 59.718 41.667 0.00 0.00 39.52 2.15
1978 5718 9.624373 GGAAATCATCATCTGGCTTACATATAT 57.376 33.333 0.00 0.00 0.00 0.86
1985 5725 5.131642 AGAGTGGAAATCATCATCTGGCTTA 59.868 40.000 0.00 0.00 30.01 3.09
1992 5732 8.039538 TGCATAGATAGAGTGGAAATCATCATC 58.960 37.037 0.00 0.00 30.01 2.92
2034 5774 0.037326 TGCTCATCCACGTTCTCCAC 60.037 55.000 0.00 0.00 0.00 4.02
2222 5962 9.756571 GGAACGGTAGGGAGATATATGATATAT 57.243 37.037 4.69 4.69 0.00 0.86
2224 5964 7.827787 AGGAACGGTAGGGAGATATATGATAT 58.172 38.462 0.00 0.00 0.00 1.63
2226 5966 6.093617 AGGAACGGTAGGGAGATATATGAT 57.906 41.667 0.00 0.00 0.00 2.45
2258 6023 1.029681 TCATCCATCACCGGTAGACG 58.970 55.000 6.87 0.00 43.80 4.18
2259 6024 3.069586 TCATTCATCCATCACCGGTAGAC 59.930 47.826 6.87 0.00 0.00 2.59
2260 6025 3.304829 TCATTCATCCATCACCGGTAGA 58.695 45.455 6.87 8.11 0.00 2.59
2261 6026 3.751479 TCATTCATCCATCACCGGTAG 57.249 47.619 6.87 1.53 0.00 3.18
2262 6027 3.645687 TCATCATTCATCCATCACCGGTA 59.354 43.478 6.87 0.00 0.00 4.02
2263 6028 2.439135 TCATCATTCATCCATCACCGGT 59.561 45.455 0.00 0.00 0.00 5.28
2272 6037 2.653234 AGGCACCTCATCATTCATCC 57.347 50.000 0.00 0.00 0.00 3.51
2286 6051 4.485024 TTACTCGATCGAGAATAGGCAC 57.515 45.455 42.97 0.00 44.53 5.01
2299 6064 7.042456 GCATCATGACTAACAACATTACTCGAT 60.042 37.037 0.00 0.00 0.00 3.59
2352 6117 2.561419 GGCCTTAATCATGATGCATGCT 59.439 45.455 20.33 4.11 41.18 3.79
2358 6123 6.835819 ATGATCAAGGCCTTAATCATGATG 57.164 37.500 34.37 15.06 37.44 3.07
2433 6198 1.814394 TGATACGTACGACACAAGGCT 59.186 47.619 24.41 0.00 0.00 4.58
2480 6260 1.065491 GGTGGACATGTACATCCTGCA 60.065 52.381 15.33 8.24 35.86 4.41
2729 6522 0.773644 ATCTTGAGGGTTGCACACCT 59.226 50.000 8.06 8.06 46.38 4.00
2736 6529 9.846248 CTTTTATTCAAACTATCTTGAGGGTTG 57.154 33.333 0.00 0.00 36.69 3.77
2737 6530 9.807921 TCTTTTATTCAAACTATCTTGAGGGTT 57.192 29.630 0.00 0.00 36.69 4.11
2738 6531 9.454859 CTCTTTTATTCAAACTATCTTGAGGGT 57.545 33.333 0.00 0.00 36.69 4.34
2739 6532 8.897752 CCTCTTTTATTCAAACTATCTTGAGGG 58.102 37.037 0.00 0.00 36.69 4.30
2740 6533 9.672673 TCCTCTTTTATTCAAACTATCTTGAGG 57.327 33.333 0.00 0.00 36.69 3.86
2744 6537 9.467796 CCCTTCCTCTTTTATTCAAACTATCTT 57.532 33.333 0.00 0.00 0.00 2.40
2749 6543 5.393866 TGCCCTTCCTCTTTTATTCAAACT 58.606 37.500 0.00 0.00 0.00 2.66
2793 6587 1.552337 TCTCATTCGCTGCTTTCCTCT 59.448 47.619 0.00 0.00 0.00 3.69
2889 6690 2.363147 GCCGACCTCACCCTCTCT 60.363 66.667 0.00 0.00 0.00 3.10
2890 6691 3.462678 GGCCGACCTCACCCTCTC 61.463 72.222 0.00 0.00 0.00 3.20
2988 6840 7.375053 GGCAAATCCAATGTGTAGAGTAAAAA 58.625 34.615 0.00 0.00 34.01 1.94
2989 6841 6.348950 CGGCAAATCCAATGTGTAGAGTAAAA 60.349 38.462 0.00 0.00 34.01 1.52
2990 6842 5.123186 CGGCAAATCCAATGTGTAGAGTAAA 59.877 40.000 0.00 0.00 34.01 2.01
2991 6843 4.634004 CGGCAAATCCAATGTGTAGAGTAA 59.366 41.667 0.00 0.00 34.01 2.24
2992 6844 4.081365 TCGGCAAATCCAATGTGTAGAGTA 60.081 41.667 0.00 0.00 34.01 2.59
2993 6845 3.009723 CGGCAAATCCAATGTGTAGAGT 58.990 45.455 0.00 0.00 34.01 3.24
2994 6846 3.270027 TCGGCAAATCCAATGTGTAGAG 58.730 45.455 0.00 0.00 34.01 2.43
2995 6847 3.342377 TCGGCAAATCCAATGTGTAGA 57.658 42.857 0.00 0.00 34.01 2.59
2996 6848 4.082787 ACTTTCGGCAAATCCAATGTGTAG 60.083 41.667 0.00 0.00 34.01 2.74
2997 6849 3.823873 ACTTTCGGCAAATCCAATGTGTA 59.176 39.130 0.00 0.00 34.01 2.90
2998 6850 2.627699 ACTTTCGGCAAATCCAATGTGT 59.372 40.909 0.00 0.00 34.01 3.72
2999 6851 3.244976 GACTTTCGGCAAATCCAATGTG 58.755 45.455 0.00 0.00 34.01 3.21
3000 6852 2.890311 TGACTTTCGGCAAATCCAATGT 59.110 40.909 0.00 0.00 34.01 2.71
3001 6853 3.574284 TGACTTTCGGCAAATCCAATG 57.426 42.857 0.00 0.00 34.01 2.82
3002 6854 4.039124 AGTTTGACTTTCGGCAAATCCAAT 59.961 37.500 0.00 0.00 36.51 3.16
3003 6855 3.383185 AGTTTGACTTTCGGCAAATCCAA 59.617 39.130 0.00 0.00 36.51 3.53
3004 6856 2.955660 AGTTTGACTTTCGGCAAATCCA 59.044 40.909 0.00 0.00 36.51 3.41
3005 6857 3.643159 AGTTTGACTTTCGGCAAATCC 57.357 42.857 0.00 0.00 36.51 3.01
3006 6858 4.318050 GCAAAGTTTGACTTTCGGCAAATC 60.318 41.667 19.82 0.00 44.47 2.17
3007 6859 3.555547 GCAAAGTTTGACTTTCGGCAAAT 59.444 39.130 19.82 0.00 44.47 2.32
3008 6860 2.926838 GCAAAGTTTGACTTTCGGCAAA 59.073 40.909 19.82 0.00 44.47 3.68
3009 6861 2.165437 AGCAAAGTTTGACTTTCGGCAA 59.835 40.909 19.82 0.00 44.47 4.52
3010 6862 1.748493 AGCAAAGTTTGACTTTCGGCA 59.252 42.857 19.82 0.00 44.47 5.69
3011 6863 2.492019 AGCAAAGTTTGACTTTCGGC 57.508 45.000 19.82 5.65 44.47 5.54
3012 6864 5.169836 ACTTAGCAAAGTTTGACTTTCGG 57.830 39.130 19.82 8.79 44.47 4.30


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

AutoCloner maintained by Alex Coulton.