Multiple sequence alignment - TraesCS5A01G114300

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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 TraesCS5A01G114300 chr5A 100.000 3059 0 0 1 3059 228886331 228883273 0.000000e+00 5650.0
1 TraesCS5A01G114300 chr5A 87.140 1874 193 14 405 2232 158753813 158751942 0.000000e+00 2082.0
2 TraesCS5A01G114300 chr5A 95.158 475 18 4 2587 3059 228874653 228874182 0.000000e+00 745.0
3 TraesCS5A01G114300 chr5A 94.538 476 23 3 2586 3059 308326056 308325582 0.000000e+00 732.0
4 TraesCS5A01G114300 chr5A 77.854 1165 216 27 275 1408 7966535 7965382 0.000000e+00 684.0
5 TraesCS5A01G114300 chr5A 77.663 1164 220 25 275 1408 7990651 7989498 0.000000e+00 673.0
6 TraesCS5A01G114300 chr5A 77.644 1163 222 24 275 1408 8050302 8049149 0.000000e+00 673.0
7 TraesCS5A01G114300 chr5A 91.858 479 32 6 2583 3059 124868275 124867802 0.000000e+00 662.0
8 TraesCS5A01G114300 chr5A 91.350 474 30 6 2587 3059 124859349 124858886 3.330000e-179 638.0
9 TraesCS5A01G114300 chr5A 90.625 128 11 1 279 405 158754243 158754116 5.250000e-38 169.0
10 TraesCS5A01G114300 chr5D 91.418 2342 141 25 270 2575 191265487 191267804 0.000000e+00 3157.0
11 TraesCS5A01G114300 chr5D 73.782 1129 254 28 265 1362 494186312 494187429 1.020000e-109 407.0
12 TraesCS5A01G114300 chr5D 76.364 770 148 20 616 1362 374626664 374625906 1.720000e-102 383.0
13 TraesCS5A01G114300 chr5D 76.904 394 79 8 995 1380 103642568 103642957 2.390000e-51 213.0
14 TraesCS5A01G114300 chr5D 94.161 137 5 2 1 135 191260504 191260639 4.000000e-49 206.0
15 TraesCS5A01G114300 chr5D 94.186 86 5 0 135 220 191260677 191260762 6.880000e-27 132.0
16 TraesCS5A01G114300 chr5D 100.000 43 0 0 227 269 191265424 191265466 2.530000e-11 80.5
17 TraesCS5A01G114300 chr3D 88.169 2130 200 14 275 2356 87446174 87444049 0.000000e+00 2490.0
18 TraesCS5A01G114300 chr3D 88.455 615 68 3 1744 2356 363507994 363508607 0.000000e+00 739.0
19 TraesCS5A01G114300 chr3D 93.665 221 13 1 2354 2574 322866708 322866489 2.270000e-86 329.0
20 TraesCS5A01G114300 chr3D 83.784 74 11 1 281 353 26082005 26081932 5.470000e-08 69.4
21 TraesCS5A01G114300 chr3D 97.143 35 1 0 285 319 564489839 564489805 3.290000e-05 60.2
22 TraesCS5A01G114300 chr6D 90.612 948 73 9 1411 2356 450810924 450809991 0.000000e+00 1243.0
23 TraesCS5A01G114300 chr6D 87.383 642 57 9 705 1329 450811632 450810998 0.000000e+00 715.0
24 TraesCS5A01G114300 chr6D 80.668 719 134 5 1618 2333 2416180 2415464 1.240000e-153 553.0
25 TraesCS5A01G114300 chr6D 78.539 671 142 2 1687 2356 385943612 385944281 1.010000e-119 440.0
26 TraesCS5A01G114300 chr6D 92.760 221 14 2 2353 2573 307682567 307682349 4.920000e-83 318.0
27 TraesCS5A01G114300 chr6D 92.377 223 16 1 2353 2575 229476837 229476616 1.770000e-82 316.0
28 TraesCS5A01G114300 chr6D 80.228 263 49 3 1099 1359 456549075 456549336 8.650000e-46 195.0
29 TraesCS5A01G114300 chr4D 75.736 2139 443 47 275 2353 57057803 57059925 0.000000e+00 1005.0
30 TraesCS5A01G114300 chr4D 92.793 222 15 1 2353 2574 367711918 367712138 1.370000e-83 320.0
31 TraesCS5A01G114300 chr3A 75.666 2141 450 40 275 2356 729953087 729955215 0.000000e+00 1002.0
32 TraesCS5A01G114300 chr3A 78.584 1144 205 24 1246 2356 54275662 54274526 0.000000e+00 719.0
33 TraesCS5A01G114300 chr3A 93.501 477 25 5 2587 3059 337671437 337671911 0.000000e+00 704.0
34 TraesCS5A01G114300 chrUn 77.637 1659 315 35 747 2356 30446997 30448648 0.000000e+00 957.0
35 TraesCS5A01G114300 chr4B 76.496 1621 321 26 784 2353 28281359 28282970 0.000000e+00 828.0
36 TraesCS5A01G114300 chr3B 85.021 721 81 16 709 1408 473456287 473457001 0.000000e+00 708.0
37 TraesCS5A01G114300 chr3B 88.889 342 33 4 1416 1753 473457033 473457373 1.700000e-112 416.0
38 TraesCS5A01G114300 chr3B 92.683 41 3 0 279 319 806108538 806108578 3.290000e-05 60.2
39 TraesCS5A01G114300 chr7A 77.778 1161 226 19 275 1408 80365291 80366446 0.000000e+00 686.0
40 TraesCS5A01G114300 chr7A 77.444 1166 222 25 275 1408 60631325 60630169 0.000000e+00 658.0
41 TraesCS5A01G114300 chr4A 76.941 1262 256 15 1126 2356 187561661 187560404 0.000000e+00 686.0
42 TraesCS5A01G114300 chr4A 77.105 380 82 3 275 649 187567025 187566646 6.640000e-52 215.0
43 TraesCS5A01G114300 chr2A 91.632 478 35 5 2587 3059 709010136 709009659 0.000000e+00 656.0
44 TraesCS5A01G114300 chr2A 91.195 477 31 9 2593 3059 709007597 709007122 3.330000e-179 638.0
45 TraesCS5A01G114300 chr1A 91.597 476 33 5 2587 3059 191469975 191470446 0.000000e+00 651.0
46 TraesCS5A01G114300 chr1A 93.182 220 14 1 2353 2572 178681976 178681758 3.800000e-84 322.0
47 TraesCS5A01G114300 chr1A 97.826 46 0 1 275 319 387052714 387052759 9.090000e-11 78.7
48 TraesCS5A01G114300 chr6A 91.368 475 36 5 2587 3057 321914904 321915377 0.000000e+00 645.0
49 TraesCS5A01G114300 chr5B 76.557 1156 230 27 284 1408 693175765 693174620 2.030000e-166 595.0
50 TraesCS5A01G114300 chr5B 85.193 466 59 7 950 1408 147421414 147421876 1.280000e-128 470.0
51 TraesCS5A01G114300 chr5B 73.866 1102 257 16 287 1362 522415997 522414901 7.890000e-111 411.0
52 TraesCS5A01G114300 chr5B 75.676 851 177 18 532 1359 421818832 421819675 6.150000e-107 398.0
53 TraesCS5A01G114300 chr5B 92.793 222 14 2 2354 2575 181832019 181832238 1.370000e-83 320.0
54 TraesCS5A01G114300 chr5B 92.308 39 3 0 281 319 625144970 625145008 4.260000e-04 56.5
55 TraesCS5A01G114300 chr5B 92.308 39 3 0 281 319 628726937 628726975 4.260000e-04 56.5
56 TraesCS5A01G114300 chr7B 73.675 1113 259 20 275 1359 481317498 481318604 4.750000e-108 401.0
57 TraesCS5A01G114300 chr7B 93.694 222 12 2 2353 2574 616294342 616294561 6.320000e-87 331.0
58 TraesCS5A01G114300 chr6B 92.793 222 15 1 2353 2574 474743225 474743005 1.370000e-83 320.0
59 TraesCS5A01G114300 chr2D 97.143 35 1 0 285 319 595413312 595413278 3.290000e-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 TraesCS5A01G114300 chr5A 228883273 228886331 3058 True 5650.00 5650 100.0000 1 3059 1 chr5A.!!$R7 3058
1 TraesCS5A01G114300 chr5A 158751942 158754243 2301 True 1125.50 2082 88.8825 279 2232 2 chr5A.!!$R9 1953
2 TraesCS5A01G114300 chr5A 7965382 7966535 1153 True 684.00 684 77.8540 275 1408 1 chr5A.!!$R1 1133
3 TraesCS5A01G114300 chr5A 7989498 7990651 1153 True 673.00 673 77.6630 275 1408 1 chr5A.!!$R2 1133
4 TraesCS5A01G114300 chr5A 8049149 8050302 1153 True 673.00 673 77.6440 275 1408 1 chr5A.!!$R3 1133
5 TraesCS5A01G114300 chr5D 191265424 191267804 2380 False 1618.75 3157 95.7090 227 2575 2 chr5D.!!$F4 2348
6 TraesCS5A01G114300 chr5D 494186312 494187429 1117 False 407.00 407 73.7820 265 1362 1 chr5D.!!$F2 1097
7 TraesCS5A01G114300 chr5D 374625906 374626664 758 True 383.00 383 76.3640 616 1362 1 chr5D.!!$R1 746
8 TraesCS5A01G114300 chr3D 87444049 87446174 2125 True 2490.00 2490 88.1690 275 2356 1 chr3D.!!$R2 2081
9 TraesCS5A01G114300 chr3D 363507994 363508607 613 False 739.00 739 88.4550 1744 2356 1 chr3D.!!$F1 612
10 TraesCS5A01G114300 chr6D 450809991 450811632 1641 True 979.00 1243 88.9975 705 2356 2 chr6D.!!$R4 1651
11 TraesCS5A01G114300 chr6D 2415464 2416180 716 True 553.00 553 80.6680 1618 2333 1 chr6D.!!$R1 715
12 TraesCS5A01G114300 chr6D 385943612 385944281 669 False 440.00 440 78.5390 1687 2356 1 chr6D.!!$F1 669
13 TraesCS5A01G114300 chr4D 57057803 57059925 2122 False 1005.00 1005 75.7360 275 2353 1 chr4D.!!$F1 2078
14 TraesCS5A01G114300 chr3A 729953087 729955215 2128 False 1002.00 1002 75.6660 275 2356 1 chr3A.!!$F2 2081
15 TraesCS5A01G114300 chr3A 54274526 54275662 1136 True 719.00 719 78.5840 1246 2356 1 chr3A.!!$R1 1110
16 TraesCS5A01G114300 chrUn 30446997 30448648 1651 False 957.00 957 77.6370 747 2356 1 chrUn.!!$F1 1609
17 TraesCS5A01G114300 chr4B 28281359 28282970 1611 False 828.00 828 76.4960 784 2353 1 chr4B.!!$F1 1569
18 TraesCS5A01G114300 chr3B 473456287 473457373 1086 False 562.00 708 86.9550 709 1753 2 chr3B.!!$F2 1044
19 TraesCS5A01G114300 chr7A 80365291 80366446 1155 False 686.00 686 77.7780 275 1408 1 chr7A.!!$F1 1133
20 TraesCS5A01G114300 chr7A 60630169 60631325 1156 True 658.00 658 77.4440 275 1408 1 chr7A.!!$R1 1133
21 TraesCS5A01G114300 chr4A 187560404 187561661 1257 True 686.00 686 76.9410 1126 2356 1 chr4A.!!$R1 1230
22 TraesCS5A01G114300 chr2A 709007122 709010136 3014 True 647.00 656 91.4135 2587 3059 2 chr2A.!!$R1 472
23 TraesCS5A01G114300 chr5B 693174620 693175765 1145 True 595.00 595 76.5570 284 1408 1 chr5B.!!$R2 1124
24 TraesCS5A01G114300 chr5B 522414901 522415997 1096 True 411.00 411 73.8660 287 1362 1 chr5B.!!$R1 1075
25 TraesCS5A01G114300 chr5B 421818832 421819675 843 False 398.00 398 75.6760 532 1359 1 chr5B.!!$F3 827
26 TraesCS5A01G114300 chr7B 481317498 481318604 1106 False 401.00 401 73.6750 275 1359 1 chr7B.!!$F1 1084

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
184 185 0.107654 ACTAAGGGCATCTCCAACGC 60.108 55.0 0.0 0.0 36.21 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 2558 0.027194 CGCTGAAGGATGCATCAACG 59.973 55.0 27.25 16.13 0.0 4.1 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.291741 GGCAGCCTATTATGTCACAAGC 59.708 50.000 3.29 0.00 0.00 4.01
22 23 3.209410 GCAGCCTATTATGTCACAAGCT 58.791 45.455 0.00 0.00 0.00 3.74
23 24 4.380531 GCAGCCTATTATGTCACAAGCTA 58.619 43.478 0.00 0.00 0.00 3.32
24 25 4.450419 GCAGCCTATTATGTCACAAGCTAG 59.550 45.833 0.00 0.00 0.00 3.42
25 26 5.605534 CAGCCTATTATGTCACAAGCTAGT 58.394 41.667 0.00 0.00 0.00 2.57
26 27 5.464722 CAGCCTATTATGTCACAAGCTAGTG 59.535 44.000 0.00 0.00 40.85 2.74
27 28 5.363868 AGCCTATTATGTCACAAGCTAGTGA 59.636 40.000 0.00 0.00 45.64 3.41
34 35 2.959516 TCACAAGCTAGTGATTCCGTG 58.040 47.619 0.00 0.00 43.18 4.94
35 36 2.002586 CACAAGCTAGTGATTCCGTGG 58.997 52.381 0.00 0.00 42.05 4.94
36 37 1.623811 ACAAGCTAGTGATTCCGTGGT 59.376 47.619 0.00 0.00 0.00 4.16
37 38 2.002586 CAAGCTAGTGATTCCGTGGTG 58.997 52.381 0.00 0.00 0.00 4.17
38 39 0.108138 AGCTAGTGATTCCGTGGTGC 60.108 55.000 0.00 0.00 0.00 5.01
39 40 0.391130 GCTAGTGATTCCGTGGTGCA 60.391 55.000 0.00 0.00 0.00 4.57
40 41 1.359848 CTAGTGATTCCGTGGTGCAC 58.640 55.000 8.80 8.80 0.00 4.57
41 42 0.973632 TAGTGATTCCGTGGTGCACT 59.026 50.000 17.98 12.80 31.34 4.40
42 43 0.108585 AGTGATTCCGTGGTGCACTT 59.891 50.000 17.98 0.00 31.34 3.16
43 44 0.238289 GTGATTCCGTGGTGCACTTG 59.762 55.000 17.98 6.67 31.34 3.16
44 45 0.179032 TGATTCCGTGGTGCACTTGT 60.179 50.000 17.98 0.00 31.34 3.16
45 46 0.951558 GATTCCGTGGTGCACTTGTT 59.048 50.000 17.98 0.00 31.34 2.83
46 47 1.336755 GATTCCGTGGTGCACTTGTTT 59.663 47.619 17.98 0.00 31.34 2.83
47 48 0.453793 TTCCGTGGTGCACTTGTTTG 59.546 50.000 17.98 1.18 31.34 2.93
48 49 0.678366 TCCGTGGTGCACTTGTTTGT 60.678 50.000 17.98 0.00 31.34 2.83
49 50 0.172352 CCGTGGTGCACTTGTTTGTT 59.828 50.000 17.98 0.00 31.34 2.83
50 51 1.403514 CCGTGGTGCACTTGTTTGTTT 60.404 47.619 17.98 0.00 31.34 2.83
51 52 1.917303 CGTGGTGCACTTGTTTGTTTC 59.083 47.619 17.98 0.00 31.34 2.78
52 53 2.267426 GTGGTGCACTTGTTTGTTTCC 58.733 47.619 17.98 0.00 0.00 3.13
53 54 2.094234 GTGGTGCACTTGTTTGTTTCCT 60.094 45.455 17.98 0.00 0.00 3.36
54 55 2.564947 TGGTGCACTTGTTTGTTTCCTT 59.435 40.909 17.98 0.00 0.00 3.36
55 56 2.929398 GGTGCACTTGTTTGTTTCCTTG 59.071 45.455 17.98 0.00 0.00 3.61
56 57 2.929398 GTGCACTTGTTTGTTTCCTTGG 59.071 45.455 10.32 0.00 0.00 3.61
57 58 2.828520 TGCACTTGTTTGTTTCCTTGGA 59.171 40.909 0.00 0.00 0.00 3.53
58 59 3.259374 TGCACTTGTTTGTTTCCTTGGAA 59.741 39.130 0.00 0.00 0.00 3.53
59 60 4.081198 TGCACTTGTTTGTTTCCTTGGAAT 60.081 37.500 2.65 0.00 0.00 3.01
60 61 4.875536 GCACTTGTTTGTTTCCTTGGAATT 59.124 37.500 2.65 0.00 0.00 2.17
61 62 5.220643 GCACTTGTTTGTTTCCTTGGAATTG 60.221 40.000 2.65 0.00 0.00 2.32
62 63 4.875536 ACTTGTTTGTTTCCTTGGAATTGC 59.124 37.500 2.65 0.00 0.00 3.56
63 64 4.751767 TGTTTGTTTCCTTGGAATTGCT 57.248 36.364 2.65 0.00 0.00 3.91
64 65 4.440880 TGTTTGTTTCCTTGGAATTGCTG 58.559 39.130 2.65 0.00 0.00 4.41
65 66 2.818130 TGTTTCCTTGGAATTGCTGC 57.182 45.000 2.65 0.00 0.00 5.25
66 67 2.037901 TGTTTCCTTGGAATTGCTGCA 58.962 42.857 0.00 0.00 0.00 4.41
67 68 2.224018 TGTTTCCTTGGAATTGCTGCAC 60.224 45.455 0.00 0.00 0.00 4.57
68 69 1.999648 TTCCTTGGAATTGCTGCACT 58.000 45.000 0.00 0.00 0.00 4.40
69 70 2.877097 TCCTTGGAATTGCTGCACTA 57.123 45.000 0.00 0.00 0.00 2.74
70 71 3.370840 TCCTTGGAATTGCTGCACTAT 57.629 42.857 0.00 0.00 0.00 2.12
71 72 3.700538 TCCTTGGAATTGCTGCACTATT 58.299 40.909 0.00 0.00 0.00 1.73
72 73 4.854173 TCCTTGGAATTGCTGCACTATTA 58.146 39.130 0.00 0.00 0.00 0.98
73 74 5.448654 TCCTTGGAATTGCTGCACTATTAT 58.551 37.500 0.00 0.00 0.00 1.28
74 75 5.532406 TCCTTGGAATTGCTGCACTATTATC 59.468 40.000 0.00 0.00 0.00 1.75
75 76 5.300034 CCTTGGAATTGCTGCACTATTATCA 59.700 40.000 0.00 0.63 0.00 2.15
76 77 6.381481 TTGGAATTGCTGCACTATTATCAG 57.619 37.500 0.00 0.00 0.00 2.90
96 97 9.715123 TTATCAGCATATAAATTTGTTCACGTG 57.285 29.630 9.94 9.94 0.00 4.49
97 98 7.139896 TCAGCATATAAATTTGTTCACGTGT 57.860 32.000 16.51 0.00 0.00 4.49
98 99 7.240674 TCAGCATATAAATTTGTTCACGTGTC 58.759 34.615 16.51 10.68 0.00 3.67
99 100 7.020602 CAGCATATAAATTTGTTCACGTGTCA 58.979 34.615 16.51 13.18 0.00 3.58
100 101 7.216881 CAGCATATAAATTTGTTCACGTGTCAG 59.783 37.037 16.51 3.08 0.00 3.51
101 102 7.119116 AGCATATAAATTTGTTCACGTGTCAGA 59.881 33.333 16.51 11.60 0.00 3.27
102 103 7.748683 GCATATAAATTTGTTCACGTGTCAGAA 59.251 33.333 16.51 5.74 0.00 3.02
103 104 9.605955 CATATAAATTTGTTCACGTGTCAGAAA 57.394 29.630 16.51 14.15 0.00 2.52
112 113 9.647797 TTGTTCACGTGTCAGAAATATAATACT 57.352 29.630 16.51 0.00 0.00 2.12
113 114 9.647797 TGTTCACGTGTCAGAAATATAATACTT 57.352 29.630 16.51 0.00 0.00 2.24
136 137 9.449719 ACTTAAGTAAAATCGTGAAGATCCATT 57.550 29.630 6.26 0.00 38.98 3.16
137 138 9.922305 CTTAAGTAAAATCGTGAAGATCCATTC 57.078 33.333 0.00 0.00 38.98 2.67
138 139 6.589830 AGTAAAATCGTGAAGATCCATTCG 57.410 37.500 0.00 0.00 38.98 3.34
139 140 3.951979 AAATCGTGAAGATCCATTCGC 57.048 42.857 0.00 0.00 38.98 4.70
140 141 2.602257 ATCGTGAAGATCCATTCGCA 57.398 45.000 8.46 0.00 39.20 5.10
141 142 2.602257 TCGTGAAGATCCATTCGCAT 57.398 45.000 8.46 0.00 39.20 4.73
142 143 2.905075 TCGTGAAGATCCATTCGCATT 58.095 42.857 8.46 0.00 39.20 3.56
143 144 3.270027 TCGTGAAGATCCATTCGCATTT 58.730 40.909 8.46 0.00 39.20 2.32
144 145 3.309682 TCGTGAAGATCCATTCGCATTTC 59.690 43.478 8.46 0.00 39.20 2.17
145 146 3.546815 CGTGAAGATCCATTCGCATTTCC 60.547 47.826 8.46 0.00 39.20 3.13
146 147 3.378112 GTGAAGATCCATTCGCATTTCCA 59.622 43.478 3.97 0.00 39.09 3.53
147 148 3.378112 TGAAGATCCATTCGCATTTCCAC 59.622 43.478 0.00 0.00 31.52 4.02
148 149 3.287867 AGATCCATTCGCATTTCCACT 57.712 42.857 0.00 0.00 0.00 4.00
149 150 3.624777 AGATCCATTCGCATTTCCACTT 58.375 40.909 0.00 0.00 0.00 3.16
150 151 4.780815 AGATCCATTCGCATTTCCACTTA 58.219 39.130 0.00 0.00 0.00 2.24
151 152 5.192927 AGATCCATTCGCATTTCCACTTAA 58.807 37.500 0.00 0.00 0.00 1.85
152 153 4.695217 TCCATTCGCATTTCCACTTAAC 57.305 40.909 0.00 0.00 0.00 2.01
153 154 4.331968 TCCATTCGCATTTCCACTTAACT 58.668 39.130 0.00 0.00 0.00 2.24
154 155 4.764823 TCCATTCGCATTTCCACTTAACTT 59.235 37.500 0.00 0.00 0.00 2.66
155 156 5.095490 CCATTCGCATTTCCACTTAACTTC 58.905 41.667 0.00 0.00 0.00 3.01
156 157 5.335583 CCATTCGCATTTCCACTTAACTTCA 60.336 40.000 0.00 0.00 0.00 3.02
157 158 5.957842 TTCGCATTTCCACTTAACTTCAT 57.042 34.783 0.00 0.00 0.00 2.57
158 159 5.957842 TCGCATTTCCACTTAACTTCATT 57.042 34.783 0.00 0.00 0.00 2.57
159 160 7.441890 TTCGCATTTCCACTTAACTTCATTA 57.558 32.000 0.00 0.00 0.00 1.90
160 161 7.624360 TCGCATTTCCACTTAACTTCATTAT 57.376 32.000 0.00 0.00 0.00 1.28
161 162 7.693952 TCGCATTTCCACTTAACTTCATTATC 58.306 34.615 0.00 0.00 0.00 1.75
162 163 7.335673 TCGCATTTCCACTTAACTTCATTATCA 59.664 33.333 0.00 0.00 0.00 2.15
163 164 7.641411 CGCATTTCCACTTAACTTCATTATCAG 59.359 37.037 0.00 0.00 0.00 2.90
164 165 8.462016 GCATTTCCACTTAACTTCATTATCAGT 58.538 33.333 0.00 0.00 0.00 3.41
173 174 9.262358 CTTAACTTCATTATCAGTACTAAGGGC 57.738 37.037 0.00 0.00 0.00 5.19
174 175 6.808321 ACTTCATTATCAGTACTAAGGGCA 57.192 37.500 0.00 0.00 0.00 5.36
175 176 7.380423 ACTTCATTATCAGTACTAAGGGCAT 57.620 36.000 0.00 0.00 0.00 4.40
176 177 7.445945 ACTTCATTATCAGTACTAAGGGCATC 58.554 38.462 0.00 0.00 0.00 3.91
177 178 7.291182 ACTTCATTATCAGTACTAAGGGCATCT 59.709 37.037 0.00 0.00 0.00 2.90
178 179 7.233389 TCATTATCAGTACTAAGGGCATCTC 57.767 40.000 0.00 0.00 0.00 2.75
179 180 6.211584 TCATTATCAGTACTAAGGGCATCTCC 59.788 42.308 0.00 0.00 0.00 3.71
180 181 3.398318 TCAGTACTAAGGGCATCTCCA 57.602 47.619 0.00 0.00 36.21 3.86
181 182 3.719871 TCAGTACTAAGGGCATCTCCAA 58.280 45.455 0.00 0.00 36.21 3.53
182 183 3.451178 TCAGTACTAAGGGCATCTCCAAC 59.549 47.826 0.00 0.00 36.21 3.77
183 184 2.431057 AGTACTAAGGGCATCTCCAACG 59.569 50.000 0.00 0.00 36.21 4.10
184 185 0.107654 ACTAAGGGCATCTCCAACGC 60.108 55.000 0.00 0.00 36.21 4.84
185 186 0.179000 CTAAGGGCATCTCCAACGCT 59.821 55.000 0.00 0.00 36.21 5.07
186 187 0.618458 TAAGGGCATCTCCAACGCTT 59.382 50.000 0.00 0.00 39.54 4.68
187 188 0.678048 AAGGGCATCTCCAACGCTTC 60.678 55.000 0.00 0.00 36.21 3.86
188 189 1.377202 GGGCATCTCCAACGCTTCA 60.377 57.895 0.00 0.00 36.21 3.02
189 190 0.960364 GGGCATCTCCAACGCTTCAA 60.960 55.000 0.00 0.00 36.21 2.69
190 191 0.449388 GGCATCTCCAACGCTTCAAG 59.551 55.000 0.00 0.00 34.01 3.02
191 192 1.160137 GCATCTCCAACGCTTCAAGT 58.840 50.000 0.00 0.00 0.00 3.16
192 193 1.537202 GCATCTCCAACGCTTCAAGTT 59.463 47.619 0.00 0.00 0.00 2.66
193 194 2.030805 GCATCTCCAACGCTTCAAGTTT 60.031 45.455 0.00 0.00 0.00 2.66
194 195 3.188460 GCATCTCCAACGCTTCAAGTTTA 59.812 43.478 0.00 0.00 0.00 2.01
195 196 4.142600 GCATCTCCAACGCTTCAAGTTTAT 60.143 41.667 0.00 0.00 0.00 1.40
196 197 5.619981 GCATCTCCAACGCTTCAAGTTTATT 60.620 40.000 0.00 0.00 0.00 1.40
197 198 6.381801 CATCTCCAACGCTTCAAGTTTATTT 58.618 36.000 0.00 0.00 0.00 1.40
198 199 5.997385 TCTCCAACGCTTCAAGTTTATTTC 58.003 37.500 0.00 0.00 0.00 2.17
199 200 5.763204 TCTCCAACGCTTCAAGTTTATTTCT 59.237 36.000 0.00 0.00 0.00 2.52
200 201 6.932400 TCTCCAACGCTTCAAGTTTATTTCTA 59.068 34.615 0.00 0.00 0.00 2.10
201 202 6.894828 TCCAACGCTTCAAGTTTATTTCTAC 58.105 36.000 0.00 0.00 0.00 2.59
202 203 6.708949 TCCAACGCTTCAAGTTTATTTCTACT 59.291 34.615 0.00 0.00 0.00 2.57
203 204 7.015877 CCAACGCTTCAAGTTTATTTCTACTC 58.984 38.462 0.00 0.00 0.00 2.59
204 205 7.307751 CCAACGCTTCAAGTTTATTTCTACTCA 60.308 37.037 0.00 0.00 0.00 3.41
205 206 7.724305 ACGCTTCAAGTTTATTTCTACTCAA 57.276 32.000 0.00 0.00 0.00 3.02
206 207 8.324163 ACGCTTCAAGTTTATTTCTACTCAAT 57.676 30.769 0.00 0.00 0.00 2.57
207 208 8.784043 ACGCTTCAAGTTTATTTCTACTCAATT 58.216 29.630 0.00 0.00 0.00 2.32
339 361 4.657969 TGGGGGTTTCTCAAACAAATGATT 59.342 37.500 1.78 0.00 43.15 2.57
403 729 4.436050 GCAATGTGTCTCTTCGGTTACATG 60.436 45.833 0.00 0.00 0.00 3.21
462 788 6.553852 AGTTATACCCACACGAGGATTAAGAT 59.446 38.462 0.00 0.00 0.00 2.40
507 833 5.833406 TCTGTTTTTGATTTGCACAGAGA 57.167 34.783 0.00 0.00 39.12 3.10
511 837 6.441274 TGTTTTTGATTTGCACAGAGAGATC 58.559 36.000 0.00 0.00 0.00 2.75
555 884 3.338250 TGGGCGGATTGGAAGGCT 61.338 61.111 0.00 0.00 0.00 4.58
593 922 5.873712 AGATGCACCATCGATATCTCATTTC 59.126 40.000 0.00 0.00 44.67 2.17
610 939 2.910688 TTCCTCTTTGCAGACGACTT 57.089 45.000 0.00 0.00 0.00 3.01
649 978 6.380095 AGCAAATGTTCAAAATGCAAACAT 57.620 29.167 7.70 7.70 43.53 2.71
696 1025 2.622942 TGTGAAAGTTCTGGGCAATGTC 59.377 45.455 0.00 0.00 0.00 3.06
782 1113 9.643693 GATGTATGTTGAAATCTGGACATTTTT 57.356 29.630 0.00 0.00 34.76 1.94
788 1119 8.859090 TGTTGAAATCTGGACATTTTTACTGAT 58.141 29.630 0.00 0.00 0.00 2.90
810 1141 7.506114 TGATGCCTTAACGGATAAGTATCTTT 58.494 34.615 14.56 0.00 39.56 2.52
838 1169 2.653543 ACTATGGTAGGGGTGGACAA 57.346 50.000 0.00 0.00 0.00 3.18
939 1270 7.092716 GCAAGGAAAAGAAATATTGCTGAAGA 58.907 34.615 0.00 0.00 39.82 2.87
946 1277 5.809001 AGAAATATTGCTGAAGACTGTGGA 58.191 37.500 0.00 0.00 0.00 4.02
947 1278 5.879223 AGAAATATTGCTGAAGACTGTGGAG 59.121 40.000 0.00 0.00 0.00 3.86
948 1279 5.426689 AATATTGCTGAAGACTGTGGAGA 57.573 39.130 0.00 0.00 0.00 3.71
975 1319 9.820229 TTATGCTTTGTCAGTATTTAAACTTCG 57.180 29.630 0.00 0.00 0.00 3.79
987 1331 2.736144 AAACTTCGCGAGACCATACA 57.264 45.000 9.59 0.00 41.84 2.29
988 1332 2.279582 AACTTCGCGAGACCATACAG 57.720 50.000 9.59 3.47 41.84 2.74
1068 1425 1.673626 GCATTGGTTTGCATGGTGGAG 60.674 52.381 0.00 0.00 42.31 3.86
1133 1490 6.016777 AGACCTTCACAGTTTTAATCTTGCTG 60.017 38.462 0.00 0.00 0.00 4.41
1279 1637 3.230743 ACTTGGCAAGTGTTGTTTCAC 57.769 42.857 30.71 0.00 41.01 3.18
1297 1655 7.251994 TGTTTCACGCATACAAACTTTTAAGT 58.748 30.769 0.00 0.00 42.04 2.24
1340 1698 1.238439 ACGGGCTCACAAATCAACAG 58.762 50.000 0.00 0.00 0.00 3.16
1382 1740 6.575162 TCCTTCTAGCAAATCAAGGAAAAC 57.425 37.500 5.99 0.00 41.22 2.43
1528 1913 6.239120 GGTGATGGAAGATTTTGTATCATGGG 60.239 42.308 0.00 0.00 0.00 4.00
1538 1923 9.533831 AGATTTTGTATCATGGGATTATAACCC 57.466 33.333 13.36 13.36 46.87 4.11
1691 2078 2.814336 CCTGGTAAGGTCAAGCACTTTC 59.186 50.000 0.00 0.00 38.96 2.62
1775 2162 2.535984 GTCACGAGGCAATGTTCGATAG 59.464 50.000 14.16 5.88 39.93 2.08
1815 2202 5.599732 AGATGCACAACATTGCTTGTTTAA 58.400 33.333 0.00 0.00 46.51 1.52
1837 2224 9.720667 TTTAATTGTGAAAGAGCGATGAATATG 57.279 29.630 0.00 0.00 0.00 1.78
1854 2241 1.557269 ATGTGGAGTGAGCTGGGACC 61.557 60.000 0.00 0.00 0.00 4.46
1906 2293 3.284197 CCGGTCGGTATCATTCACC 57.716 57.895 0.55 0.00 0.00 4.02
2028 2424 1.411216 GGTCAAGGGGGAGACGATCTA 60.411 57.143 0.00 0.00 35.63 1.98
2045 2441 3.202829 TCTAACAGCCGAACCAAACTT 57.797 42.857 0.00 0.00 0.00 2.66
2155 2551 2.356535 GCCAATGAGAGGAGTGGTCAAT 60.357 50.000 0.00 0.00 33.45 2.57
2161 2558 7.227512 CCAATGAGAGGAGTGGTCAATATTAAC 59.772 40.741 0.00 0.00 0.00 2.01
2202 2600 1.765314 GGAGACCATGACTGCAGGTAT 59.235 52.381 19.93 8.93 35.36 2.73
2210 2608 1.319541 GACTGCAGGTATAGGAGCGA 58.680 55.000 19.93 0.00 0.00 4.93
2213 2611 3.497332 ACTGCAGGTATAGGAGCGATAA 58.503 45.455 19.93 0.00 0.00 1.75
2229 2627 3.375642 CGATAACACGAGATGAGCATGT 58.624 45.455 0.00 0.00 35.09 3.21
2246 2644 1.514003 TGTCAAGTTTATTGCCGCGA 58.486 45.000 8.23 0.00 0.00 5.87
2329 2727 4.249638 TGGATTTTACCTAGCAGCCAAT 57.750 40.909 0.00 0.00 0.00 3.16
2363 2761 1.888512 ACTTGCACATTGATGACCCAC 59.111 47.619 0.00 0.00 0.00 4.61
2385 2783 6.390721 CACAAGTATAGGGGATCAATCGTAG 58.609 44.000 0.00 0.00 0.00 3.51
2417 2815 4.618920 AAGTAAGAGTGTCGAACCCAAT 57.381 40.909 0.00 0.00 0.00 3.16
2431 2829 0.914644 CCCAATGAGGAGCAGAAGGA 59.085 55.000 0.00 0.00 41.22 3.36
2451 2849 4.116238 GGAAAATGACAAGCGGTTTTCAA 58.884 39.130 18.88 4.53 40.52 2.69
2466 2864 5.174943 CGGTTTTCAACAAGGTAATTTCTGC 59.825 40.000 0.00 0.00 0.00 4.26
2488 2886 2.812011 AGGCACTGAAATTGTCGGTAAC 59.188 45.455 0.00 0.00 44.55 2.50
2490 2888 5.224752 AGGCACTGAAATTGTCGGTAACAA 61.225 41.667 0.00 0.00 44.55 2.83
2502 2900 6.489127 TGTCGGTAACAAATAGTTTGATGG 57.511 37.500 9.21 0.00 43.26 3.51
2507 2905 6.348950 CGGTAACAAATAGTTTGATGGCAAGA 60.349 38.462 9.21 0.00 43.26 3.02
2521 2919 6.563422 TGATGGCAAGATAATTTGTAGCAAC 58.437 36.000 0.00 0.00 0.00 4.17
2522 2920 6.377996 TGATGGCAAGATAATTTGTAGCAACT 59.622 34.615 0.00 0.00 0.00 3.16
2523 2921 7.555914 TGATGGCAAGATAATTTGTAGCAACTA 59.444 33.333 0.00 0.00 0.00 2.24
2524 2922 7.695480 TGGCAAGATAATTTGTAGCAACTAA 57.305 32.000 0.00 0.00 0.00 2.24
2525 2923 8.116651 TGGCAAGATAATTTGTAGCAACTAAA 57.883 30.769 0.00 0.00 0.00 1.85
2526 2924 8.580720 TGGCAAGATAATTTGTAGCAACTAAAA 58.419 29.630 0.00 0.00 0.00 1.52
2527 2925 9.418045 GGCAAGATAATTTGTAGCAACTAAAAA 57.582 29.630 0.00 0.00 29.21 1.94
2575 2973 4.142160 GCAAGGTAGCCCAATCCTTTTTAG 60.142 45.833 0.00 0.00 39.22 1.85
2576 2974 4.251103 AGGTAGCCCAATCCTTTTTAGG 57.749 45.455 0.00 0.00 0.00 2.69
2577 2975 2.693591 GGTAGCCCAATCCTTTTTAGGC 59.306 50.000 0.00 0.00 40.79 3.93
2578 2976 2.928036 AGCCCAATCCTTTTTAGGCT 57.072 45.000 0.00 0.00 45.72 4.58
2579 2977 2.967599 GCCCAATCCTTTTTAGGCTG 57.032 50.000 0.00 0.00 37.42 4.85
2580 2978 1.482182 GCCCAATCCTTTTTAGGCTGG 59.518 52.381 0.00 0.00 37.42 4.85
2581 2979 2.888069 GCCCAATCCTTTTTAGGCTGGA 60.888 50.000 0.00 0.00 37.42 3.86
2582 2980 3.440127 CCCAATCCTTTTTAGGCTGGAA 58.560 45.455 0.00 0.00 35.14 3.53
2583 2981 4.033009 CCCAATCCTTTTTAGGCTGGAAT 58.967 43.478 0.00 0.00 35.14 3.01
2584 2982 4.141869 CCCAATCCTTTTTAGGCTGGAATG 60.142 45.833 0.00 0.00 35.14 2.67
2585 2983 4.141869 CCAATCCTTTTTAGGCTGGAATGG 60.142 45.833 9.73 9.73 41.48 3.16
2618 3016 4.506654 CCGGTGTAATGATGCTACAGTAAC 59.493 45.833 0.00 0.00 30.04 2.50
2621 3019 4.814771 GTGTAATGATGCTACAGTAACCCC 59.185 45.833 0.00 0.00 30.04 4.95
2622 3020 3.577805 AATGATGCTACAGTAACCCCC 57.422 47.619 0.00 0.00 0.00 5.40
2624 3022 0.106149 GATGCTACAGTAACCCCCGG 59.894 60.000 0.00 0.00 0.00 5.73
2638 3036 1.137697 CCCCGGGGTTAAGCTAATCT 58.862 55.000 33.25 0.00 0.00 2.40
2651 3049 9.639601 GGTTAAGCTAATCTTTTTGCTAAACAT 57.360 29.630 0.00 0.00 42.01 2.71
2655 3053 6.587608 AGCTAATCTTTTTGCTAAACATGTGC 59.412 34.615 0.00 0.00 41.23 4.57
2656 3054 6.183360 GCTAATCTTTTTGCTAAACATGTGCC 60.183 38.462 0.00 0.00 31.89 5.01
2659 3057 4.340666 TCTTTTTGCTAAACATGTGCCTGA 59.659 37.500 0.00 0.00 0.00 3.86
2664 3062 4.018490 TGCTAAACATGTGCCTGATCATT 58.982 39.130 0.00 0.00 0.00 2.57
2672 3070 5.530171 ACATGTGCCTGATCATTATTGTCTC 59.470 40.000 0.00 0.00 0.00 3.36
2673 3071 5.363562 TGTGCCTGATCATTATTGTCTCT 57.636 39.130 0.00 0.00 0.00 3.10
2675 3073 5.587443 TGTGCCTGATCATTATTGTCTCTTG 59.413 40.000 0.00 0.00 0.00 3.02
2677 3075 6.094603 GTGCCTGATCATTATTGTCTCTTGTT 59.905 38.462 0.00 0.00 0.00 2.83
2678 3076 6.317140 TGCCTGATCATTATTGTCTCTTGTTC 59.683 38.462 0.00 0.00 0.00 3.18
2679 3077 6.541641 GCCTGATCATTATTGTCTCTTGTTCT 59.458 38.462 0.00 0.00 0.00 3.01
2682 3080 9.985318 CTGATCATTATTGTCTCTTGTTCTTTC 57.015 33.333 0.00 0.00 0.00 2.62
2683 3081 9.506018 TGATCATTATTGTCTCTTGTTCTTTCA 57.494 29.630 0.00 0.00 0.00 2.69
2888 5823 1.202818 GGAGAGAGAGAGGGAGAGAGC 60.203 61.905 0.00 0.00 0.00 4.09
2899 5840 0.174617 GGAGAGAGCAAACTCCTCCG 59.825 60.000 13.35 0.00 43.95 4.63
2917 5858 3.246112 TGGACCGAACCCACCTGG 61.246 66.667 0.00 0.00 41.37 4.45
2940 5881 2.987125 CCCACCTAACCCACTCCG 59.013 66.667 0.00 0.00 0.00 4.63
2977 5918 4.547367 CCCATTCCCCCTCGTCGC 62.547 72.222 0.00 0.00 0.00 5.19
2984 5925 3.391382 CCCCTCGTCGCCTCCTTT 61.391 66.667 0.00 0.00 0.00 3.11
2995 5936 2.577059 CTCCTTTCCCGCGCACTA 59.423 61.111 8.75 0.00 0.00 2.74
3003 5944 4.554363 CCGCGCACTACTCCTCCG 62.554 72.222 8.75 0.00 0.00 4.63
3029 5970 2.051166 GGATAGAGCGCGTCCGTC 60.051 66.667 8.43 5.36 36.67 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.209410 AGCTTGTGACATAATAGGCTGC 58.791 45.455 0.00 0.00 0.00 5.25
15 16 2.002586 CCACGGAATCACTAGCTTGTG 58.997 52.381 20.50 20.50 39.15 3.33
16 17 1.623811 ACCACGGAATCACTAGCTTGT 59.376 47.619 0.00 0.00 0.00 3.16
17 18 2.002586 CACCACGGAATCACTAGCTTG 58.997 52.381 0.00 0.00 0.00 4.01
18 19 1.676014 GCACCACGGAATCACTAGCTT 60.676 52.381 0.00 0.00 0.00 3.74
19 20 0.108138 GCACCACGGAATCACTAGCT 60.108 55.000 0.00 0.00 0.00 3.32
20 21 0.391130 TGCACCACGGAATCACTAGC 60.391 55.000 0.00 0.00 0.00 3.42
21 22 1.066858 AGTGCACCACGGAATCACTAG 60.067 52.381 14.63 0.00 39.64 2.57
22 23 0.973632 AGTGCACCACGGAATCACTA 59.026 50.000 14.63 0.00 39.64 2.74
23 24 0.108585 AAGTGCACCACGGAATCACT 59.891 50.000 14.63 0.00 39.64 3.41
24 25 0.238289 CAAGTGCACCACGGAATCAC 59.762 55.000 14.63 0.00 39.64 3.06
25 26 0.179032 ACAAGTGCACCACGGAATCA 60.179 50.000 14.63 0.00 39.64 2.57
26 27 0.951558 AACAAGTGCACCACGGAATC 59.048 50.000 14.63 0.00 39.64 2.52
27 28 1.066908 CAAACAAGTGCACCACGGAAT 59.933 47.619 14.63 0.00 39.64 3.01
28 29 0.453793 CAAACAAGTGCACCACGGAA 59.546 50.000 14.63 0.00 39.64 4.30
29 30 0.678366 ACAAACAAGTGCACCACGGA 60.678 50.000 14.63 0.00 39.64 4.69
30 31 0.172352 AACAAACAAGTGCACCACGG 59.828 50.000 14.63 3.02 39.64 4.94
31 32 1.917303 GAAACAAACAAGTGCACCACG 59.083 47.619 14.63 4.59 39.64 4.94
32 33 2.094234 AGGAAACAAACAAGTGCACCAC 60.094 45.455 14.63 0.00 34.10 4.16
33 34 2.175202 AGGAAACAAACAAGTGCACCA 58.825 42.857 14.63 0.00 0.00 4.17
34 35 2.929398 CAAGGAAACAAACAAGTGCACC 59.071 45.455 14.63 0.00 0.00 5.01
35 36 2.929398 CCAAGGAAACAAACAAGTGCAC 59.071 45.455 9.40 9.40 0.00 4.57
36 37 2.828520 TCCAAGGAAACAAACAAGTGCA 59.171 40.909 0.00 0.00 0.00 4.57
37 38 3.518634 TCCAAGGAAACAAACAAGTGC 57.481 42.857 0.00 0.00 0.00 4.40
38 39 5.220643 GCAATTCCAAGGAAACAAACAAGTG 60.221 40.000 5.52 0.00 37.69 3.16
39 40 4.875536 GCAATTCCAAGGAAACAAACAAGT 59.124 37.500 5.52 0.00 37.69 3.16
40 41 5.006941 CAGCAATTCCAAGGAAACAAACAAG 59.993 40.000 5.52 0.00 37.69 3.16
41 42 4.874966 CAGCAATTCCAAGGAAACAAACAA 59.125 37.500 5.52 0.00 37.69 2.83
42 43 4.440880 CAGCAATTCCAAGGAAACAAACA 58.559 39.130 5.52 0.00 37.69 2.83
43 44 3.248363 GCAGCAATTCCAAGGAAACAAAC 59.752 43.478 5.52 0.00 37.69 2.93
44 45 3.118482 TGCAGCAATTCCAAGGAAACAAA 60.118 39.130 5.52 0.00 37.69 2.83
45 46 2.433604 TGCAGCAATTCCAAGGAAACAA 59.566 40.909 5.52 0.00 37.69 2.83
46 47 2.037901 TGCAGCAATTCCAAGGAAACA 58.962 42.857 5.52 0.00 37.69 2.83
47 48 2.036346 AGTGCAGCAATTCCAAGGAAAC 59.964 45.455 5.52 0.00 37.69 2.78
48 49 2.318908 AGTGCAGCAATTCCAAGGAAA 58.681 42.857 5.52 0.00 37.69 3.13
49 50 1.999648 AGTGCAGCAATTCCAAGGAA 58.000 45.000 3.67 3.67 38.59 3.36
50 51 2.877097 TAGTGCAGCAATTCCAAGGA 57.123 45.000 0.00 0.00 0.00 3.36
51 52 5.300034 TGATAATAGTGCAGCAATTCCAAGG 59.700 40.000 0.00 0.00 0.00 3.61
52 53 6.381481 TGATAATAGTGCAGCAATTCCAAG 57.619 37.500 0.00 0.00 0.00 3.61
53 54 6.381481 CTGATAATAGTGCAGCAATTCCAA 57.619 37.500 0.00 0.00 0.00 3.53
70 71 9.715123 CACGTGAACAAATTTATATGCTGATAA 57.285 29.630 10.90 0.00 0.00 1.75
71 72 8.888716 ACACGTGAACAAATTTATATGCTGATA 58.111 29.630 25.01 0.00 0.00 2.15
72 73 7.761409 ACACGTGAACAAATTTATATGCTGAT 58.239 30.769 25.01 0.00 0.00 2.90
73 74 7.095017 TGACACGTGAACAAATTTATATGCTGA 60.095 33.333 25.01 0.00 0.00 4.26
74 75 7.020602 TGACACGTGAACAAATTTATATGCTG 58.979 34.615 25.01 0.00 0.00 4.41
75 76 7.119116 TCTGACACGTGAACAAATTTATATGCT 59.881 33.333 25.01 0.00 0.00 3.79
76 77 7.240674 TCTGACACGTGAACAAATTTATATGC 58.759 34.615 25.01 0.00 0.00 3.14
77 78 9.605955 TTTCTGACACGTGAACAAATTTATATG 57.394 29.630 25.01 6.86 0.00 1.78
86 87 9.647797 AGTATTATATTTCTGACACGTGAACAA 57.352 29.630 25.01 7.66 0.00 2.83
87 88 9.647797 AAGTATTATATTTCTGACACGTGAACA 57.352 29.630 25.01 19.44 0.00 3.18
110 111 9.449719 AATGGATCTTCACGATTTTACTTAAGT 57.550 29.630 13.68 13.68 30.84 2.24
111 112 9.922305 GAATGGATCTTCACGATTTTACTTAAG 57.078 33.333 0.00 0.00 30.84 1.85
112 113 8.600625 CGAATGGATCTTCACGATTTTACTTAA 58.399 33.333 0.00 0.00 30.84 1.85
113 114 7.254319 GCGAATGGATCTTCACGATTTTACTTA 60.254 37.037 0.00 0.00 30.84 2.24
114 115 6.456988 GCGAATGGATCTTCACGATTTTACTT 60.457 38.462 0.00 0.00 30.84 2.24
115 116 5.006746 GCGAATGGATCTTCACGATTTTACT 59.993 40.000 0.00 0.00 30.84 2.24
116 117 5.198274 GCGAATGGATCTTCACGATTTTAC 58.802 41.667 0.00 0.00 30.84 2.01
117 118 4.873259 TGCGAATGGATCTTCACGATTTTA 59.127 37.500 0.00 0.00 30.84 1.52
118 119 3.689161 TGCGAATGGATCTTCACGATTTT 59.311 39.130 0.00 0.00 30.84 1.82
119 120 3.270027 TGCGAATGGATCTTCACGATTT 58.730 40.909 0.00 0.00 30.84 2.17
120 121 2.905075 TGCGAATGGATCTTCACGATT 58.095 42.857 0.00 0.00 30.84 3.34
121 122 2.602257 TGCGAATGGATCTTCACGAT 57.398 45.000 0.00 0.00 34.25 3.73
122 123 2.602257 ATGCGAATGGATCTTCACGA 57.398 45.000 0.00 0.00 0.00 4.35
123 124 3.546815 GGAAATGCGAATGGATCTTCACG 60.547 47.826 0.00 0.00 0.00 4.35
124 125 3.378112 TGGAAATGCGAATGGATCTTCAC 59.622 43.478 0.00 0.00 0.00 3.18
125 126 3.378112 GTGGAAATGCGAATGGATCTTCA 59.622 43.478 0.00 0.00 0.00 3.02
126 127 3.629398 AGTGGAAATGCGAATGGATCTTC 59.371 43.478 0.00 0.00 0.00 2.87
127 128 3.624777 AGTGGAAATGCGAATGGATCTT 58.375 40.909 0.00 0.00 0.00 2.40
128 129 3.287867 AGTGGAAATGCGAATGGATCT 57.712 42.857 0.00 0.00 0.00 2.75
129 130 5.066505 AGTTAAGTGGAAATGCGAATGGATC 59.933 40.000 0.00 0.00 0.00 3.36
130 131 4.949856 AGTTAAGTGGAAATGCGAATGGAT 59.050 37.500 0.00 0.00 0.00 3.41
131 132 4.331968 AGTTAAGTGGAAATGCGAATGGA 58.668 39.130 0.00 0.00 0.00 3.41
132 133 4.701956 AGTTAAGTGGAAATGCGAATGG 57.298 40.909 0.00 0.00 0.00 3.16
133 134 5.698832 TGAAGTTAAGTGGAAATGCGAATG 58.301 37.500 0.00 0.00 0.00 2.67
134 135 5.957842 TGAAGTTAAGTGGAAATGCGAAT 57.042 34.783 0.00 0.00 0.00 3.34
135 136 5.957842 ATGAAGTTAAGTGGAAATGCGAA 57.042 34.783 0.00 0.00 0.00 4.70
136 137 5.957842 AATGAAGTTAAGTGGAAATGCGA 57.042 34.783 0.00 0.00 0.00 5.10
137 138 7.471721 TGATAATGAAGTTAAGTGGAAATGCG 58.528 34.615 0.00 0.00 0.00 4.73
138 139 8.462016 ACTGATAATGAAGTTAAGTGGAAATGC 58.538 33.333 0.00 0.00 0.00 3.56
147 148 9.262358 GCCCTTAGTACTGATAATGAAGTTAAG 57.738 37.037 5.39 0.00 0.00 1.85
148 149 8.764558 TGCCCTTAGTACTGATAATGAAGTTAA 58.235 33.333 5.39 0.00 0.00 2.01
149 150 8.313944 TGCCCTTAGTACTGATAATGAAGTTA 57.686 34.615 5.39 0.00 0.00 2.24
150 151 7.195374 TGCCCTTAGTACTGATAATGAAGTT 57.805 36.000 5.39 0.00 0.00 2.66
151 152 6.808321 TGCCCTTAGTACTGATAATGAAGT 57.192 37.500 5.39 0.00 0.00 3.01
152 153 7.675062 AGATGCCCTTAGTACTGATAATGAAG 58.325 38.462 5.39 0.00 0.00 3.02
153 154 7.256332 GGAGATGCCCTTAGTACTGATAATGAA 60.256 40.741 5.39 0.00 0.00 2.57
154 155 6.211584 GGAGATGCCCTTAGTACTGATAATGA 59.788 42.308 5.39 0.00 0.00 2.57
155 156 6.014242 TGGAGATGCCCTTAGTACTGATAATG 60.014 42.308 5.39 0.00 34.97 1.90
156 157 6.084738 TGGAGATGCCCTTAGTACTGATAAT 58.915 40.000 5.39 0.00 34.97 1.28
157 158 5.464069 TGGAGATGCCCTTAGTACTGATAA 58.536 41.667 5.39 0.00 34.97 1.75
158 159 5.074746 TGGAGATGCCCTTAGTACTGATA 57.925 43.478 5.39 0.00 34.97 2.15
159 160 3.928754 TGGAGATGCCCTTAGTACTGAT 58.071 45.455 5.39 0.00 34.97 2.90
160 161 3.398318 TGGAGATGCCCTTAGTACTGA 57.602 47.619 5.39 0.00 34.97 3.41
161 162 3.738281 CGTTGGAGATGCCCTTAGTACTG 60.738 52.174 5.39 0.00 34.97 2.74
162 163 2.431057 CGTTGGAGATGCCCTTAGTACT 59.569 50.000 0.00 0.00 34.97 2.73
163 164 2.822764 CGTTGGAGATGCCCTTAGTAC 58.177 52.381 0.00 0.00 34.97 2.73
164 165 1.138266 GCGTTGGAGATGCCCTTAGTA 59.862 52.381 0.00 0.00 34.03 1.82
165 166 0.107654 GCGTTGGAGATGCCCTTAGT 60.108 55.000 0.00 0.00 34.03 2.24
166 167 0.179000 AGCGTTGGAGATGCCCTTAG 59.821 55.000 0.00 0.00 41.38 2.18
167 168 0.618458 AAGCGTTGGAGATGCCCTTA 59.382 50.000 0.00 0.00 41.38 2.69
168 169 0.678048 GAAGCGTTGGAGATGCCCTT 60.678 55.000 0.00 0.00 41.38 3.95
169 170 1.078143 GAAGCGTTGGAGATGCCCT 60.078 57.895 0.00 0.00 41.38 5.19
170 171 0.960364 TTGAAGCGTTGGAGATGCCC 60.960 55.000 0.00 0.00 41.38 5.36
171 172 0.449388 CTTGAAGCGTTGGAGATGCC 59.551 55.000 0.00 0.00 41.38 4.40
172 173 1.160137 ACTTGAAGCGTTGGAGATGC 58.840 50.000 0.00 0.00 40.73 3.91
173 174 3.904136 AAACTTGAAGCGTTGGAGATG 57.096 42.857 0.00 0.00 0.00 2.90
174 175 6.431234 AGAAATAAACTTGAAGCGTTGGAGAT 59.569 34.615 0.00 0.00 0.00 2.75
175 176 5.763204 AGAAATAAACTTGAAGCGTTGGAGA 59.237 36.000 0.00 0.00 0.00 3.71
176 177 6.002062 AGAAATAAACTTGAAGCGTTGGAG 57.998 37.500 0.00 0.00 0.00 3.86
177 178 6.708949 AGTAGAAATAAACTTGAAGCGTTGGA 59.291 34.615 0.00 0.00 0.00 3.53
178 179 6.899114 AGTAGAAATAAACTTGAAGCGTTGG 58.101 36.000 0.00 0.00 0.00 3.77
179 180 7.572759 TGAGTAGAAATAAACTTGAAGCGTTG 58.427 34.615 0.00 0.00 0.00 4.10
180 181 7.724305 TGAGTAGAAATAAACTTGAAGCGTT 57.276 32.000 0.00 0.00 0.00 4.84
181 182 7.724305 TTGAGTAGAAATAAACTTGAAGCGT 57.276 32.000 0.00 0.00 0.00 5.07
201 202 9.672086 GCTCTTAGTAGTACTGATGTAATTGAG 57.328 37.037 13.29 6.92 0.00 3.02
202 203 9.185680 TGCTCTTAGTAGTACTGATGTAATTGA 57.814 33.333 13.29 0.00 0.00 2.57
203 204 9.973450 ATGCTCTTAGTAGTACTGATGTAATTG 57.027 33.333 13.29 0.00 0.00 2.32
205 206 9.581289 AGATGCTCTTAGTAGTACTGATGTAAT 57.419 33.333 13.29 0.68 0.00 1.89
206 207 8.982091 AGATGCTCTTAGTAGTACTGATGTAA 57.018 34.615 13.29 0.00 0.00 2.41
207 208 7.662258 GGAGATGCTCTTAGTAGTACTGATGTA 59.338 40.741 13.29 1.50 0.00 2.29
208 209 6.488683 GGAGATGCTCTTAGTAGTACTGATGT 59.511 42.308 13.29 0.00 0.00 3.06
209 210 6.488344 TGGAGATGCTCTTAGTAGTACTGATG 59.512 42.308 13.29 3.28 0.00 3.07
210 211 6.606069 TGGAGATGCTCTTAGTAGTACTGAT 58.394 40.000 13.29 0.00 0.00 2.90
211 212 6.002653 TGGAGATGCTCTTAGTAGTACTGA 57.997 41.667 13.29 3.71 0.00 3.41
212 213 6.701145 TTGGAGATGCTCTTAGTAGTACTG 57.299 41.667 13.29 0.00 0.00 2.74
213 214 7.013846 GTCATTGGAGATGCTCTTAGTAGTACT 59.986 40.741 8.14 8.14 0.00 2.73
214 215 7.142680 GTCATTGGAGATGCTCTTAGTAGTAC 58.857 42.308 0.00 0.00 0.00 2.73
215 216 6.833933 TGTCATTGGAGATGCTCTTAGTAGTA 59.166 38.462 0.00 0.00 0.00 1.82
216 217 5.658634 TGTCATTGGAGATGCTCTTAGTAGT 59.341 40.000 0.00 0.00 0.00 2.73
217 218 6.154203 TGTCATTGGAGATGCTCTTAGTAG 57.846 41.667 0.00 0.00 0.00 2.57
218 219 6.737720 ATGTCATTGGAGATGCTCTTAGTA 57.262 37.500 0.00 0.00 0.00 1.82
219 220 5.627182 ATGTCATTGGAGATGCTCTTAGT 57.373 39.130 0.00 0.00 0.00 2.24
220 221 5.931146 GGTATGTCATTGGAGATGCTCTTAG 59.069 44.000 0.00 0.00 31.41 2.18
221 222 5.509670 CGGTATGTCATTGGAGATGCTCTTA 60.510 44.000 0.00 0.00 31.41 2.10
222 223 4.712476 GGTATGTCATTGGAGATGCTCTT 58.288 43.478 0.00 0.00 31.41 2.85
223 224 3.244009 CGGTATGTCATTGGAGATGCTCT 60.244 47.826 0.00 0.00 31.41 4.09
224 225 3.062763 CGGTATGTCATTGGAGATGCTC 58.937 50.000 0.00 0.00 31.41 4.26
225 226 2.808202 GCGGTATGTCATTGGAGATGCT 60.808 50.000 0.00 0.00 31.41 3.79
421 747 7.177041 TGGGTATAACTTCAGCCGTTTTATTTT 59.823 33.333 0.00 0.00 34.99 1.82
424 750 5.587443 GTGGGTATAACTTCAGCCGTTTTAT 59.413 40.000 0.00 0.00 34.99 1.40
433 759 3.446161 TCCTCGTGTGGGTATAACTTCAG 59.554 47.826 0.00 0.00 0.00 3.02
480 806 8.114331 TCTGTGCAAATCAAAAACAGATAGAT 57.886 30.769 0.00 0.00 41.63 1.98
481 807 7.445096 TCTCTGTGCAAATCAAAAACAGATAGA 59.555 33.333 4.44 0.00 44.47 1.98
501 827 8.055279 GCTAATAAGCTAGATGATCTCTCTGT 57.945 38.462 0.00 0.00 45.85 3.41
528 857 1.335810 CAATCCGCCCACATCTTCATG 59.664 52.381 0.00 0.00 35.92 3.07
530 859 0.394216 CCAATCCGCCCACATCTTCA 60.394 55.000 0.00 0.00 0.00 3.02
536 865 2.354729 CCTTCCAATCCGCCCACA 59.645 61.111 0.00 0.00 0.00 4.17
555 884 4.159321 TGGTGCATCTCAACAAACTCAAAA 59.841 37.500 0.00 0.00 39.94 2.44
593 922 0.514691 GCAAGTCGTCTGCAAAGAGG 59.485 55.000 0.00 0.00 0.00 3.69
610 939 9.357652 GAACATTTGCTTTCATAAGAATTAGCA 57.642 29.630 3.55 3.55 42.70 3.49
649 978 1.277273 CATCCACAACTCTCCTCAGCA 59.723 52.381 0.00 0.00 0.00 4.41
727 1057 2.083774 CATGCACACTTGTATTCGGGT 58.916 47.619 0.00 0.00 0.00 5.28
782 1113 5.864418 ACTTATCCGTTAAGGCATCAGTA 57.136 39.130 7.15 0.00 41.46 2.74
788 1119 6.646267 ACAAAGATACTTATCCGTTAAGGCA 58.354 36.000 7.15 0.00 41.46 4.75
838 1169 7.934855 ATAAGATGCTGAAAACATTCACTCT 57.065 32.000 0.00 0.00 0.00 3.24
939 1270 4.910195 TGACAAAGCATAATCTCCACAGT 58.090 39.130 0.00 0.00 0.00 3.55
975 1319 6.700081 TGTTATTATGTTCTGTATGGTCTCGC 59.300 38.462 0.00 0.00 0.00 5.03
987 1331 8.969260 TGCAATCTCATCTGTTATTATGTTCT 57.031 30.769 0.00 0.00 0.00 3.01
988 1332 8.288208 CCTGCAATCTCATCTGTTATTATGTTC 58.712 37.037 0.00 0.00 0.00 3.18
1032 1378 3.431346 CCAATGCATCTTCTTCTCCTCGA 60.431 47.826 0.00 0.00 0.00 4.04
1068 1425 2.622064 ACTCTTCGGGGTGCATAATC 57.378 50.000 0.00 0.00 0.00 1.75
1133 1490 2.546789 ACCAACGCTGTTTTGCTAGTAC 59.453 45.455 0.00 0.00 0.00 2.73
1148 1505 3.435671 GGATTCTGGAGTAAACACCAACG 59.564 47.826 0.93 0.00 36.20 4.10
1193 1550 8.651389 TCTGCCTAGATAGTATTTTGCACTTAT 58.349 33.333 0.00 0.00 0.00 1.73
1279 1637 6.236017 TCCTCACTTAAAAGTTTGTATGCG 57.764 37.500 0.00 0.00 37.08 4.73
1297 1655 2.355197 CACACGCCAAATACATCCTCA 58.645 47.619 0.00 0.00 0.00 3.86
1340 1698 0.685458 AACCCAAGGATCATGCCAGC 60.685 55.000 0.00 0.00 0.00 4.85
1538 1923 3.997021 ACGCACAGTAAATTCTCCAGAAG 59.003 43.478 0.00 0.00 37.48 2.85
1691 2078 3.244700 ACTCCTTTGATCACCTTCCACAG 60.245 47.826 0.00 0.00 0.00 3.66
1775 2162 4.584325 TGCATCTTCAAAACCTATATGGCC 59.416 41.667 0.00 0.00 40.22 5.36
1815 2202 6.238566 CCACATATTCATCGCTCTTTCACAAT 60.239 38.462 0.00 0.00 0.00 2.71
1837 2224 1.768684 TTGGTCCCAGCTCACTCCAC 61.769 60.000 0.00 0.00 0.00 4.02
1854 2241 9.237846 GTACAACTTTCTGAATTTCTTCCTTTG 57.762 33.333 0.00 0.00 0.00 2.77
1896 2283 6.796785 TGAGAGAAGACATGGTGAATGATA 57.203 37.500 0.00 0.00 38.72 2.15
1906 2293 5.425630 TGTTGATCCATGAGAGAAGACATG 58.574 41.667 0.00 0.00 42.12 3.21
2028 2424 4.929819 ATTAAAGTTTGGTTCGGCTGTT 57.070 36.364 0.00 0.00 0.00 3.16
2155 2551 5.007626 GCTGAAGGATGCATCAACGTTAATA 59.992 40.000 27.25 3.69 0.00 0.98
2161 2558 0.027194 CGCTGAAGGATGCATCAACG 59.973 55.000 27.25 16.13 0.00 4.10
2202 2600 3.473625 TCATCTCGTGTTATCGCTCCTA 58.526 45.455 0.00 0.00 0.00 2.94
2210 2608 4.391405 TGACATGCTCATCTCGTGTTAT 57.609 40.909 0.00 0.00 34.15 1.89
2213 2611 2.028658 ACTTGACATGCTCATCTCGTGT 60.029 45.455 0.00 0.00 36.47 4.49
2229 2627 1.463056 CAGTCGCGGCAATAAACTTGA 59.537 47.619 15.58 0.00 0.00 3.02
2347 2745 1.888512 ACTTGTGGGTCATCAATGTGC 59.111 47.619 0.00 0.00 0.00 4.57
2363 2761 6.350277 GGACTACGATTGATCCCCTATACTTG 60.350 46.154 0.00 0.00 0.00 3.16
2385 2783 7.088905 TCGACACTCTTACTTATTGAAAGGAC 58.911 38.462 0.00 0.00 0.00 3.85
2417 2815 3.072915 TGTCATTTTCCTTCTGCTCCTCA 59.927 43.478 0.00 0.00 0.00 3.86
2451 2849 2.558359 GTGCCTGCAGAAATTACCTTGT 59.442 45.455 17.39 0.00 0.00 3.16
2466 2864 1.238439 ACCGACAATTTCAGTGCCTG 58.762 50.000 0.00 0.00 0.00 4.85
2501 2899 8.980143 TTTTAGTTGCTACAAATTATCTTGCC 57.020 30.769 0.13 0.00 0.00 4.52
2526 2924 9.712305 CTGCACCTATTATTACTATTGCTACTT 57.288 33.333 0.00 0.00 0.00 2.24
2527 2925 7.819900 GCTGCACCTATTATTACTATTGCTACT 59.180 37.037 0.00 0.00 0.00 2.57
2528 2926 7.602644 TGCTGCACCTATTATTACTATTGCTAC 59.397 37.037 0.00 0.00 0.00 3.58
2529 2927 7.676004 TGCTGCACCTATTATTACTATTGCTA 58.324 34.615 0.00 0.00 0.00 3.49
2530 2928 6.533730 TGCTGCACCTATTATTACTATTGCT 58.466 36.000 0.00 0.00 0.00 3.91
2531 2929 6.801539 TGCTGCACCTATTATTACTATTGC 57.198 37.500 0.00 0.00 0.00 3.56
2532 2930 7.445402 ACCTTGCTGCACCTATTATTACTATTG 59.555 37.037 0.00 0.00 0.00 1.90
2533 2931 7.518188 ACCTTGCTGCACCTATTATTACTATT 58.482 34.615 0.00 0.00 0.00 1.73
2534 2932 7.079451 ACCTTGCTGCACCTATTATTACTAT 57.921 36.000 0.00 0.00 0.00 2.12
2541 2939 2.158813 GGCTACCTTGCTGCACCTATTA 60.159 50.000 0.00 0.00 0.00 0.98
2618 3016 3.827957 AAGATTAGCTTAACCCCGGGGG 61.828 54.545 42.40 31.11 41.46 5.40
2621 3019 4.676986 GCAAAAAGATTAGCTTAACCCCGG 60.677 45.833 0.00 0.00 35.24 5.73
2622 3020 4.157840 AGCAAAAAGATTAGCTTAACCCCG 59.842 41.667 0.00 0.00 35.24 5.73
2624 3022 8.085909 TGTTTAGCAAAAAGATTAGCTTAACCC 58.914 33.333 11.12 0.00 42.58 4.11
2638 3036 4.662468 TCAGGCACATGTTTAGCAAAAA 57.338 36.364 8.69 0.00 0.00 1.94
2651 3049 5.363562 AGAGACAATAATGATCAGGCACA 57.636 39.130 0.09 0.00 0.00 4.57
2655 3053 8.503458 AAGAACAAGAGACAATAATGATCAGG 57.497 34.615 0.09 0.00 0.00 3.86
2656 3054 9.985318 GAAAGAACAAGAGACAATAATGATCAG 57.015 33.333 0.09 0.00 0.00 2.90
2664 3062 9.130661 TGGAATTTGAAAGAACAAGAGACAATA 57.869 29.630 0.00 0.00 0.00 1.90
2672 3070 8.652810 ATTCAACTGGAATTTGAAAGAACAAG 57.347 30.769 1.90 0.00 43.76 3.16
2715 5648 9.058174 TCATGTTTGAGCAATTTTGAAATTCAT 57.942 25.926 0.00 0.00 36.52 2.57
2728 5661 8.715191 ACATTTTAGTTTTCATGTTTGAGCAA 57.285 26.923 0.00 0.00 32.27 3.91
2768 5701 8.553153 TCACCACCAATATTACCAGAAGAATAA 58.447 33.333 0.00 0.00 0.00 1.40
2867 5802 2.412591 CTCTCTCCCTCTCTCTCTCCT 58.587 57.143 0.00 0.00 0.00 3.69
2880 5815 0.174617 CGGAGGAGTTTGCTCTCTCC 59.825 60.000 15.73 15.73 45.51 3.71
2970 5911 2.184579 GGGAAAGGAGGCGACGAG 59.815 66.667 0.00 0.00 0.00 4.18
2971 5912 3.755628 CGGGAAAGGAGGCGACGA 61.756 66.667 0.00 0.00 0.00 4.20
2977 5918 3.014085 TAGTGCGCGGGAAAGGAGG 62.014 63.158 8.83 0.00 0.00 4.30
2984 5925 3.138798 GAGGAGTAGTGCGCGGGA 61.139 66.667 8.83 0.00 0.00 5.14
3003 5944 2.646143 GCTCTATCCCGCTCGGTC 59.354 66.667 7.59 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.