Multiple sequence alignment - TraesCS6A01G248100

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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 TraesCS6A01G248100 chr6A 100.000 2834 0 0 1 2834 460630338 460633171 0.000000e+00 5234
1 TraesCS6A01G248100 chr6D 93.284 2025 68 27 482 2478 323043720 323045704 0.000000e+00 2924
2 TraesCS6A01G248100 chr6D 93.987 449 21 3 1 446 323013002 323013447 0.000000e+00 675
3 TraesCS6A01G248100 chr6B 93.220 1711 51 19 748 2411 500523666 500521974 0.000000e+00 2457
4 TraesCS6A01G248100 chr6B 93.914 723 29 6 1 718 500526781 500526069 0.000000e+00 1077
5 TraesCS6A01G248100 chr2D 82.594 293 32 9 2557 2833 16007053 16007342 1.010000e-59 241
6 TraesCS6A01G248100 chr1B 82.168 286 32 5 2568 2834 262916057 262916342 7.900000e-56 228
7 TraesCS6A01G248100 chr1B 82.510 263 34 6 2568 2819 180405519 180405258 1.320000e-53 220
8 TraesCS6A01G248100 chr1B 79.720 286 29 11 2568 2833 464485336 464485060 2.240000e-41 180
9 TraesCS6A01G248100 chr5B 81.419 296 36 10 2554 2834 280385476 280385767 1.020000e-54 224
10 TraesCS6A01G248100 chr4A 80.822 292 34 8 2565 2834 372315292 372315583 2.860000e-50 209
11 TraesCS6A01G248100 chr3D 80.156 257 40 5 2588 2833 18896337 18896081 6.240000e-42 182
12 TraesCS6A01G248100 chr3D 82.456 171 24 6 2667 2833 173394160 173393992 8.180000e-31 145
13 TraesCS6A01G248100 chr5D 78.598 271 43 7 2565 2825 169972898 169973163 6.280000e-37 165


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 TraesCS6A01G248100 chr6A 460630338 460633171 2833 False 5234 5234 100.000 1 2834 1 chr6A.!!$F1 2833
1 TraesCS6A01G248100 chr6D 323043720 323045704 1984 False 2924 2924 93.284 482 2478 1 chr6D.!!$F2 1996
2 TraesCS6A01G248100 chr6B 500521974 500526781 4807 True 1767 2457 93.567 1 2411 2 chr6B.!!$R1 2410

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
690 696 0.033366 GGTCCACCACAAATTGCACC 59.967 55.0 0.0 0.0 35.64 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 4411 0.038166 CCAAGTGCAGGGTGGTACAT 59.962 55.0 0.0 0.0 44.52 2.29 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
105 106 1.082104 CGTGGCCTCGCTTTTTGAC 60.082 57.895 15.08 0.00 0.00 3.18
130 131 1.194495 CGATTTGCCGTCCTACGTAC 58.806 55.000 0.00 0.00 40.58 3.67
162 163 0.394625 TGCATAGCAAGAGCATGGCA 60.395 50.000 0.00 0.00 45.49 4.92
200 201 1.035932 TACGAGAGCCTGCCTACACC 61.036 60.000 0.00 0.00 0.00 4.16
201 202 2.904131 GAGAGCCTGCCTACACCC 59.096 66.667 0.00 0.00 0.00 4.61
202 203 1.687493 GAGAGCCTGCCTACACCCT 60.687 63.158 0.00 0.00 0.00 4.34
203 204 0.397254 GAGAGCCTGCCTACACCCTA 60.397 60.000 0.00 0.00 0.00 3.53
204 205 0.397816 AGAGCCTGCCTACACCCTAG 60.398 60.000 0.00 0.00 0.00 3.02
205 206 0.688087 GAGCCTGCCTACACCCTAGT 60.688 60.000 0.00 0.00 0.00 2.57
208 209 1.963372 GCCTGCCTACACCCTAGTACA 60.963 57.143 0.00 0.00 0.00 2.90
209 210 2.679082 CCTGCCTACACCCTAGTACAT 58.321 52.381 0.00 0.00 0.00 2.29
211 212 3.069729 CCTGCCTACACCCTAGTACATTC 59.930 52.174 0.00 0.00 0.00 2.67
212 213 2.691526 TGCCTACACCCTAGTACATTCG 59.308 50.000 0.00 0.00 0.00 3.34
269 275 1.396301 CTCTTCTTGCTCGATGCCAAC 59.604 52.381 4.73 0.00 42.00 3.77
317 323 5.969423 AGTATTTCAAAAGATGCATGGGTG 58.031 37.500 2.46 0.00 0.00 4.61
334 340 1.067776 GGTGGACTTCCGTGTGAGTAG 60.068 57.143 0.00 0.00 39.43 2.57
335 341 1.612463 GTGGACTTCCGTGTGAGTAGT 59.388 52.381 0.00 0.00 39.43 2.73
336 342 2.816087 GTGGACTTCCGTGTGAGTAGTA 59.184 50.000 0.00 0.00 39.43 1.82
343 349 2.876091 CCGTGTGAGTAGTACATGGTG 58.124 52.381 2.52 0.00 45.75 4.17
385 391 4.893795 ACTTTATTATTGACTTGCGTCGC 58.106 39.130 11.10 11.10 43.21 5.19
387 393 5.064707 ACTTTATTATTGACTTGCGTCGCAT 59.935 36.000 22.41 6.94 43.21 4.73
398 404 1.259316 GCGTCGCATTTAAAGGCAAG 58.741 50.000 23.09 14.34 34.99 4.01
400 406 2.477863 GCGTCGCATTTAAAGGCAAGAT 60.478 45.455 23.09 0.00 34.99 2.40
412 418 2.550978 AGGCAAGATGTATGTACGTGC 58.449 47.619 0.00 0.00 0.00 5.34
438 444 5.296748 CATTTCGGTTTTCCAAAGGACAAT 58.703 37.500 0.00 0.00 40.70 2.71
450 456 2.732412 AGGACAATATGGATCGAGCG 57.268 50.000 0.00 0.00 0.00 5.03
480 486 1.879380 TGTACAACATGCTGGCTGAAC 59.121 47.619 0.45 0.00 0.00 3.18
498 504 0.532862 ACAGCTGAAGGACCAACACG 60.533 55.000 23.35 0.00 0.00 4.49
540 546 0.911769 CCATAACTCCACAGGCCTGA 59.088 55.000 39.19 16.40 0.00 3.86
541 547 1.134280 CCATAACTCCACAGGCCTGAG 60.134 57.143 39.19 30.44 0.00 3.35
542 548 1.556911 CATAACTCCACAGGCCTGAGT 59.443 52.381 39.19 27.57 40.94 3.41
543 549 2.544768 AACTCCACAGGCCTGAGTT 58.455 52.632 39.19 31.18 42.80 3.01
544 550 0.398318 AACTCCACAGGCCTGAGTTC 59.602 55.000 39.19 0.00 43.87 3.01
545 551 0.764369 ACTCCACAGGCCTGAGTTCA 60.764 55.000 39.19 15.62 35.93 3.18
690 696 0.033366 GGTCCACCACAAATTGCACC 59.967 55.000 0.00 0.00 35.64 5.01
691 697 1.039856 GTCCACCACAAATTGCACCT 58.960 50.000 0.00 0.00 0.00 4.00
809 3191 3.200593 GCAGCATCTCCACCTGCG 61.201 66.667 0.00 0.00 41.99 5.18
922 3313 2.032681 GCCACCACCCTCACTCAC 59.967 66.667 0.00 0.00 0.00 3.51
1086 3477 4.349503 TGCAAGTCCATGGCGGCT 62.350 61.111 11.43 1.92 33.14 5.52
1089 3480 2.045926 AAGTCCATGGCGGCTGAC 60.046 61.111 11.43 13.96 33.14 3.51
1125 3528 1.151668 CAAAGAAGTCGCACCTCCTG 58.848 55.000 0.00 0.00 0.00 3.86
1350 3753 2.419297 GCAGGTGGTCGAGATCATCTTT 60.419 50.000 0.00 0.00 28.49 2.52
1848 4251 5.072040 AGCTGTAAATAAACAATGCCCAC 57.928 39.130 0.00 0.00 0.00 4.61
1856 4259 2.200373 AACAATGCCCACTCCAGTAC 57.800 50.000 0.00 0.00 0.00 2.73
1929 4344 4.613167 GCTCTGCATGCATATAGTTCTTGC 60.613 45.833 22.97 7.36 36.91 4.01
1958 4373 0.866061 GTCGATCCGATCACACACCG 60.866 60.000 9.07 0.00 38.42 4.94
1962 4377 0.895530 ATCCGATCACACACCGAGTT 59.104 50.000 0.00 0.00 0.00 3.01
1968 4383 1.961277 CACACACCGAGTTGGAGCC 60.961 63.158 2.42 0.00 42.00 4.70
1994 4409 2.486592 GCGGTTTAAGGCATGTACAGTT 59.513 45.455 0.33 0.00 0.00 3.16
1996 4411 3.749088 CGGTTTAAGGCATGTACAGTTGA 59.251 43.478 0.33 0.00 0.00 3.18
1997 4412 4.394920 CGGTTTAAGGCATGTACAGTTGAT 59.605 41.667 0.33 0.00 0.00 2.57
2048 4463 1.003545 GCTGTACTGTGCAAGTGTGTG 60.004 52.381 10.59 0.00 40.26 3.82
2058 4473 0.093535 CAAGTGTGTGTATGCTCGCG 59.906 55.000 0.00 0.00 0.00 5.87
2180 4598 0.320771 TGAGGCTTTCGTCTTGAGGC 60.321 55.000 0.00 0.00 36.33 4.70
2226 4659 1.478137 GTCGCATCGTATCAGTGTCC 58.522 55.000 0.00 0.00 0.00 4.02
2245 4678 2.811317 CAGAAGGGAGCGCGTGTC 60.811 66.667 8.43 4.85 0.00 3.67
2246 4679 2.992114 AGAAGGGAGCGCGTGTCT 60.992 61.111 8.43 0.00 0.00 3.41
2247 4680 2.811317 GAAGGGAGCGCGTGTCTG 60.811 66.667 8.43 0.00 0.00 3.51
2248 4681 4.379243 AAGGGAGCGCGTGTCTGG 62.379 66.667 8.43 0.00 0.00 3.86
2406 4839 2.416747 TCAATTCAGGCGTCTCTGTTG 58.583 47.619 0.00 0.00 36.25 3.33
2443 4876 4.152964 CGCTCCTGCCTGCAGCTA 62.153 66.667 13.63 3.24 44.23 3.32
2478 4911 2.765807 ATGGAGCAGCGGCCTACT 60.766 61.111 4.82 0.00 42.56 2.57
2479 4912 1.457643 ATGGAGCAGCGGCCTACTA 60.458 57.895 4.82 0.00 42.56 1.82
2480 4913 1.749334 ATGGAGCAGCGGCCTACTAC 61.749 60.000 4.82 0.00 42.56 2.73
2481 4914 2.026301 GAGCAGCGGCCTACTACG 59.974 66.667 4.82 0.00 42.56 3.51
2482 4915 2.439701 AGCAGCGGCCTACTACGA 60.440 61.111 4.82 0.00 42.56 3.43
2483 4916 2.026301 GCAGCGGCCTACTACGAG 59.974 66.667 0.00 0.00 0.00 4.18
2484 4917 2.478890 GCAGCGGCCTACTACGAGA 61.479 63.158 0.00 0.00 0.00 4.04
2485 4918 2.001361 GCAGCGGCCTACTACGAGAA 62.001 60.000 0.00 0.00 0.00 2.87
2486 4919 0.248539 CAGCGGCCTACTACGAGAAC 60.249 60.000 0.00 0.00 0.00 3.01
2487 4920 1.298190 GCGGCCTACTACGAGAACG 60.298 63.158 0.00 0.00 45.75 3.95
2488 4921 1.354506 CGGCCTACTACGAGAACGG 59.645 63.158 0.00 0.00 44.46 4.44
2489 4922 1.065436 GGCCTACTACGAGAACGGC 59.935 63.158 0.00 0.00 44.46 5.68
2490 4923 1.382692 GGCCTACTACGAGAACGGCT 61.383 60.000 0.00 0.00 44.46 5.52
2491 4924 0.455005 GCCTACTACGAGAACGGCTT 59.545 55.000 0.00 0.00 44.46 4.35
2492 4925 1.135170 GCCTACTACGAGAACGGCTTT 60.135 52.381 0.00 0.00 44.46 3.51
2493 4926 2.673326 GCCTACTACGAGAACGGCTTTT 60.673 50.000 0.00 0.00 44.46 2.27
2494 4927 3.177487 CCTACTACGAGAACGGCTTTTC 58.823 50.000 0.00 0.00 44.46 2.29
2495 4928 2.806608 ACTACGAGAACGGCTTTTCA 57.193 45.000 0.00 0.00 44.46 2.69
2496 4929 3.314541 ACTACGAGAACGGCTTTTCAT 57.685 42.857 0.00 0.00 44.46 2.57
2497 4930 2.993899 ACTACGAGAACGGCTTTTCATG 59.006 45.455 0.00 0.00 44.46 3.07
2498 4931 0.517316 ACGAGAACGGCTTTTCATGC 59.483 50.000 0.00 0.00 44.46 4.06
2499 4932 0.179189 CGAGAACGGCTTTTCATGCC 60.179 55.000 0.00 0.00 46.42 4.40
2505 4938 3.820595 GGCTTTTCATGCCTTGGTC 57.179 52.632 0.00 0.00 46.38 4.02
2506 4939 0.968405 GGCTTTTCATGCCTTGGTCA 59.032 50.000 0.00 0.00 46.38 4.02
2507 4940 1.337167 GGCTTTTCATGCCTTGGTCAC 60.337 52.381 0.00 0.00 46.38 3.67
2508 4941 1.666888 GCTTTTCATGCCTTGGTCACG 60.667 52.381 0.00 0.00 0.00 4.35
2509 4942 0.958091 TTTTCATGCCTTGGTCACGG 59.042 50.000 0.00 0.00 0.00 4.94
2510 4943 0.179004 TTTCATGCCTTGGTCACGGT 60.179 50.000 0.00 0.00 0.00 4.83
2511 4944 0.687920 TTCATGCCTTGGTCACGGTA 59.312 50.000 0.00 0.00 0.00 4.02
2512 4945 0.687920 TCATGCCTTGGTCACGGTAA 59.312 50.000 0.00 0.00 0.00 2.85
2513 4946 1.086696 CATGCCTTGGTCACGGTAAG 58.913 55.000 0.00 0.00 0.00 2.34
2514 4947 0.981183 ATGCCTTGGTCACGGTAAGA 59.019 50.000 0.00 0.00 0.00 2.10
2515 4948 0.320374 TGCCTTGGTCACGGTAAGAG 59.680 55.000 0.00 0.00 0.00 2.85
2516 4949 1.019805 GCCTTGGTCACGGTAAGAGC 61.020 60.000 0.00 0.00 0.00 4.09
2517 4950 0.320374 CCTTGGTCACGGTAAGAGCA 59.680 55.000 0.00 0.00 41.27 4.26
2518 4951 1.066143 CCTTGGTCACGGTAAGAGCAT 60.066 52.381 1.86 0.00 42.35 3.79
2519 4952 2.271800 CTTGGTCACGGTAAGAGCATC 58.728 52.381 1.86 0.00 42.35 3.91
2532 4965 4.976996 GCATCTAGCCGACCTAGC 57.023 61.111 5.51 0.00 42.73 3.42
2533 4966 2.346597 GCATCTAGCCGACCTAGCT 58.653 57.895 0.00 0.00 42.73 3.32
2534 4967 1.535833 GCATCTAGCCGACCTAGCTA 58.464 55.000 0.00 0.00 42.73 3.32
2535 4968 2.096248 GCATCTAGCCGACCTAGCTAT 58.904 52.381 0.00 0.00 42.73 2.97
2536 4969 2.494073 GCATCTAGCCGACCTAGCTATT 59.506 50.000 0.00 0.00 42.73 1.73
2537 4970 3.428316 GCATCTAGCCGACCTAGCTATTC 60.428 52.174 0.00 0.00 42.73 1.75
2538 4971 2.792878 TCTAGCCGACCTAGCTATTCC 58.207 52.381 0.00 0.00 42.73 3.01
2539 4972 1.469308 CTAGCCGACCTAGCTATTCCG 59.531 57.143 0.00 0.00 41.79 4.30
2540 4973 1.179814 AGCCGACCTAGCTATTCCGG 61.180 60.000 18.01 18.01 39.29 5.14
2541 4974 1.289380 CCGACCTAGCTATTCCGGC 59.711 63.158 12.70 0.00 0.00 6.13
2542 4975 1.289380 CGACCTAGCTATTCCGGCC 59.711 63.158 0.00 0.00 0.00 6.13
2543 4976 1.672320 GACCTAGCTATTCCGGCCC 59.328 63.158 0.00 0.00 0.00 5.80
2544 4977 1.828461 GACCTAGCTATTCCGGCCCC 61.828 65.000 0.00 0.00 0.00 5.80
2545 4978 2.657237 CTAGCTATTCCGGCCCCG 59.343 66.667 0.00 0.00 39.44 5.73
2546 4979 2.123164 TAGCTATTCCGGCCCCGT 60.123 61.111 5.93 0.00 37.81 5.28
2547 4980 2.436087 CTAGCTATTCCGGCCCCGTG 62.436 65.000 5.93 0.00 37.81 4.94
2548 4981 4.171103 GCTATTCCGGCCCCGTGT 62.171 66.667 5.93 0.00 37.81 4.49
2549 4982 2.203015 CTATTCCGGCCCCGTGTG 60.203 66.667 5.93 0.00 37.81 3.82
2550 4983 2.684294 TATTCCGGCCCCGTGTGA 60.684 61.111 5.93 0.00 37.81 3.58
2551 4984 2.918230 CTATTCCGGCCCCGTGTGAC 62.918 65.000 5.93 0.00 37.81 3.67
2553 4986 4.682334 TCCGGCCCCGTGTGACTA 62.682 66.667 5.93 0.00 37.81 2.59
2554 4987 3.697747 CCGGCCCCGTGTGACTAA 61.698 66.667 5.93 0.00 37.81 2.24
2555 4988 2.344500 CGGCCCCGTGTGACTAAA 59.656 61.111 0.00 0.00 34.35 1.85
2556 4989 1.301874 CGGCCCCGTGTGACTAAAA 60.302 57.895 0.00 0.00 34.35 1.52
2557 4990 0.885596 CGGCCCCGTGTGACTAAAAA 60.886 55.000 0.00 0.00 34.35 1.94
2581 5014 7.740519 AAAAATATGAACAACGCTAATGCTC 57.259 32.000 0.00 0.00 36.97 4.26
2582 5015 6.435430 AAATATGAACAACGCTAATGCTCA 57.565 33.333 0.00 0.00 36.97 4.26
2583 5016 6.624352 AATATGAACAACGCTAATGCTCAT 57.376 33.333 0.00 0.00 34.75 2.90
2584 5017 7.728847 AATATGAACAACGCTAATGCTCATA 57.271 32.000 8.06 8.06 36.48 2.15
2585 5018 4.857871 TGAACAACGCTAATGCTCATAC 57.142 40.909 0.00 0.00 36.97 2.39
2586 5019 4.249661 TGAACAACGCTAATGCTCATACA 58.750 39.130 0.00 0.00 36.97 2.29
2587 5020 4.875536 TGAACAACGCTAATGCTCATACAT 59.124 37.500 0.00 0.00 36.97 2.29
2588 5021 4.801147 ACAACGCTAATGCTCATACATG 57.199 40.909 0.00 0.00 36.97 3.21
2589 5022 4.191544 ACAACGCTAATGCTCATACATGT 58.808 39.130 2.69 2.69 36.97 3.21
2590 5023 4.034394 ACAACGCTAATGCTCATACATGTG 59.966 41.667 9.11 0.00 36.97 3.21
2591 5024 3.133691 ACGCTAATGCTCATACATGTGG 58.866 45.455 9.11 0.25 36.97 4.17
2592 5025 3.133691 CGCTAATGCTCATACATGTGGT 58.866 45.455 9.11 0.00 36.97 4.16
2593 5026 3.059393 CGCTAATGCTCATACATGTGGTG 60.059 47.826 9.11 7.66 36.97 4.17
2594 5027 4.129380 GCTAATGCTCATACATGTGGTGA 58.871 43.478 9.11 11.66 36.03 4.02
2595 5028 4.212847 GCTAATGCTCATACATGTGGTGAG 59.787 45.833 26.38 26.38 41.69 3.51
2596 5029 4.492494 AATGCTCATACATGTGGTGAGA 57.508 40.909 31.14 21.51 41.38 3.27
2597 5030 3.531934 TGCTCATACATGTGGTGAGAG 57.468 47.619 31.14 20.75 41.38 3.20
2598 5031 2.208431 GCTCATACATGTGGTGAGAGC 58.792 52.381 31.14 24.53 44.62 4.09
2599 5032 2.467838 CTCATACATGTGGTGAGAGCG 58.532 52.381 26.52 9.95 41.38 5.03
2600 5033 2.099405 TCATACATGTGGTGAGAGCGA 58.901 47.619 9.11 0.00 0.00 4.93
2601 5034 2.695147 TCATACATGTGGTGAGAGCGAT 59.305 45.455 9.11 0.00 0.00 4.58
2602 5035 3.888930 TCATACATGTGGTGAGAGCGATA 59.111 43.478 9.11 0.00 0.00 2.92
2603 5036 4.524328 TCATACATGTGGTGAGAGCGATAT 59.476 41.667 9.11 0.00 0.00 1.63
2604 5037 3.377346 ACATGTGGTGAGAGCGATATC 57.623 47.619 0.00 0.00 0.00 1.63
2605 5038 2.036475 ACATGTGGTGAGAGCGATATCC 59.964 50.000 0.00 0.00 0.00 2.59
2606 5039 0.668535 TGTGGTGAGAGCGATATCCG 59.331 55.000 0.00 0.00 42.21 4.18
2615 5048 2.415843 CGATATCCGCCCACACGT 59.584 61.111 0.00 0.00 0.00 4.49
2616 5049 1.227147 CGATATCCGCCCACACGTT 60.227 57.895 0.00 0.00 0.00 3.99
2617 5050 0.808453 CGATATCCGCCCACACGTTT 60.808 55.000 0.00 0.00 0.00 3.60
2618 5051 1.375551 GATATCCGCCCACACGTTTT 58.624 50.000 0.00 0.00 0.00 2.43
2619 5052 2.553086 GATATCCGCCCACACGTTTTA 58.447 47.619 0.00 0.00 0.00 1.52
2620 5053 2.695127 TATCCGCCCACACGTTTTAT 57.305 45.000 0.00 0.00 0.00 1.40
2621 5054 2.695127 ATCCGCCCACACGTTTTATA 57.305 45.000 0.00 0.00 0.00 0.98
2622 5055 2.469274 TCCGCCCACACGTTTTATAA 57.531 45.000 0.00 0.00 0.00 0.98
2623 5056 2.075338 TCCGCCCACACGTTTTATAAC 58.925 47.619 0.00 0.00 0.00 1.89
2624 5057 1.805345 CCGCCCACACGTTTTATAACA 59.195 47.619 0.00 0.00 33.75 2.41
2625 5058 2.413108 CCGCCCACACGTTTTATAACAC 60.413 50.000 0.00 0.00 33.75 3.32
2626 5059 2.223611 CGCCCACACGTTTTATAACACA 59.776 45.455 2.87 0.00 33.75 3.72
2627 5060 3.665848 CGCCCACACGTTTTATAACACAG 60.666 47.826 2.87 0.00 33.75 3.66
2628 5061 3.499157 GCCCACACGTTTTATAACACAGA 59.501 43.478 2.87 0.00 33.75 3.41
2629 5062 4.612033 GCCCACACGTTTTATAACACAGAC 60.612 45.833 2.87 0.00 33.75 3.51
2630 5063 4.753107 CCCACACGTTTTATAACACAGACT 59.247 41.667 2.87 0.00 33.75 3.24
2631 5064 5.333798 CCCACACGTTTTATAACACAGACTG 60.334 44.000 0.00 0.00 33.75 3.51
2632 5065 5.137403 CACACGTTTTATAACACAGACTGC 58.863 41.667 1.25 0.00 33.75 4.40
2633 5066 4.084745 ACACGTTTTATAACACAGACTGCG 60.085 41.667 1.25 0.00 33.75 5.18
2634 5067 4.053295 ACGTTTTATAACACAGACTGCGT 58.947 39.130 1.25 0.00 33.75 5.24
2635 5068 4.149396 ACGTTTTATAACACAGACTGCGTC 59.851 41.667 1.25 1.15 33.75 5.19
2636 5069 4.149221 CGTTTTATAACACAGACTGCGTCA 59.851 41.667 1.25 0.00 32.71 4.35
2637 5070 5.163992 CGTTTTATAACACAGACTGCGTCAT 60.164 40.000 1.25 0.00 32.71 3.06
2638 5071 5.778161 TTTATAACACAGACTGCGTCATG 57.222 39.130 1.25 10.03 34.60 3.07
2639 5072 2.812358 TAACACAGACTGCGTCATGT 57.188 45.000 1.25 10.52 36.28 3.21
2640 5073 1.502231 AACACAGACTGCGTCATGTC 58.498 50.000 1.25 0.00 34.58 3.06
2641 5074 0.389025 ACACAGACTGCGTCATGTCA 59.611 50.000 1.25 0.00 31.60 3.58
2642 5075 0.786581 CACAGACTGCGTCATGTCAC 59.213 55.000 1.25 0.00 34.60 3.67
2643 5076 0.319900 ACAGACTGCGTCATGTCACC 60.320 55.000 1.25 0.00 34.60 4.02
2644 5077 1.080501 AGACTGCGTCATGTCACCG 60.081 57.895 10.52 0.00 34.60 4.94
2648 5081 4.102561 GCGTCATGTCACCGCATA 57.897 55.556 13.80 0.00 46.26 3.14
2649 5082 2.605094 GCGTCATGTCACCGCATAT 58.395 52.632 13.80 0.00 46.26 1.78
2650 5083 1.778334 GCGTCATGTCACCGCATATA 58.222 50.000 13.80 0.00 46.26 0.86
2651 5084 2.337583 GCGTCATGTCACCGCATATAT 58.662 47.619 13.80 0.00 46.26 0.86
2652 5085 3.507786 GCGTCATGTCACCGCATATATA 58.492 45.455 13.80 0.00 46.26 0.86
2653 5086 3.303495 GCGTCATGTCACCGCATATATAC 59.697 47.826 13.80 0.00 46.26 1.47
2654 5087 4.481463 CGTCATGTCACCGCATATATACA 58.519 43.478 0.00 0.00 0.00 2.29
2655 5088 5.102313 CGTCATGTCACCGCATATATACAT 58.898 41.667 0.00 0.00 0.00 2.29
2656 5089 5.004726 CGTCATGTCACCGCATATATACATG 59.995 44.000 14.11 14.11 43.41 3.21
2657 5090 5.869344 GTCATGTCACCGCATATATACATGT 59.131 40.000 17.51 2.69 42.88 3.21
2658 5091 5.868801 TCATGTCACCGCATATATACATGTG 59.131 40.000 17.51 9.02 42.88 3.21
2659 5092 5.461032 TGTCACCGCATATATACATGTGA 57.539 39.130 9.11 0.00 38.44 3.58
2660 5093 5.469479 TGTCACCGCATATATACATGTGAG 58.531 41.667 9.11 0.00 38.44 3.51
2661 5094 5.242838 TGTCACCGCATATATACATGTGAGA 59.757 40.000 9.11 1.57 38.44 3.27
2662 5095 6.156519 GTCACCGCATATATACATGTGAGAA 58.843 40.000 9.11 0.00 38.44 2.87
2663 5096 6.813649 GTCACCGCATATATACATGTGAGAAT 59.186 38.462 9.11 0.00 38.44 2.40
2664 5097 7.973944 GTCACCGCATATATACATGTGAGAATA 59.026 37.037 9.11 0.00 38.44 1.75
2665 5098 8.695456 TCACCGCATATATACATGTGAGAATAT 58.305 33.333 9.11 6.36 38.44 1.28
2666 5099 9.317936 CACCGCATATATACATGTGAGAATATT 57.682 33.333 9.11 0.00 38.44 1.28
2667 5100 9.890629 ACCGCATATATACATGTGAGAATATTT 57.109 29.630 9.11 0.00 38.44 1.40
2720 5153 8.922058 AAATGAAAAATCTGATTGAAGATCCG 57.078 30.769 3.22 0.00 35.83 4.18
2721 5154 7.636150 ATGAAAAATCTGATTGAAGATCCGT 57.364 32.000 3.22 0.00 35.83 4.69
2722 5155 7.452880 TGAAAAATCTGATTGAAGATCCGTT 57.547 32.000 3.22 0.00 35.83 4.44
2723 5156 7.885297 TGAAAAATCTGATTGAAGATCCGTTT 58.115 30.769 3.22 0.00 35.83 3.60
2724 5157 8.359642 TGAAAAATCTGATTGAAGATCCGTTTT 58.640 29.630 3.22 0.00 35.83 2.43
2725 5158 9.196552 GAAAAATCTGATTGAAGATCCGTTTTT 57.803 29.630 3.22 0.00 35.83 1.94
2726 5159 8.748380 AAAATCTGATTGAAGATCCGTTTTTC 57.252 30.769 3.22 0.00 35.83 2.29
2727 5160 5.880054 TCTGATTGAAGATCCGTTTTTCC 57.120 39.130 0.00 0.00 0.00 3.13
2728 5161 5.560724 TCTGATTGAAGATCCGTTTTTCCT 58.439 37.500 0.00 0.00 0.00 3.36
2729 5162 5.643777 TCTGATTGAAGATCCGTTTTTCCTC 59.356 40.000 0.00 0.00 0.00 3.71
2730 5163 4.391830 TGATTGAAGATCCGTTTTTCCTCG 59.608 41.667 0.00 0.00 0.00 4.63
2731 5164 3.396260 TGAAGATCCGTTTTTCCTCGT 57.604 42.857 0.00 0.00 0.00 4.18
2732 5165 3.064207 TGAAGATCCGTTTTTCCTCGTG 58.936 45.455 0.00 0.00 0.00 4.35
2733 5166 3.243941 TGAAGATCCGTTTTTCCTCGTGA 60.244 43.478 0.00 0.00 0.00 4.35
2734 5167 2.685100 AGATCCGTTTTTCCTCGTGAC 58.315 47.619 0.00 0.00 0.00 3.67
2735 5168 2.036733 AGATCCGTTTTTCCTCGTGACA 59.963 45.455 0.00 0.00 0.00 3.58
2736 5169 2.312722 TCCGTTTTTCCTCGTGACAA 57.687 45.000 0.00 0.00 0.00 3.18
2737 5170 2.206750 TCCGTTTTTCCTCGTGACAAG 58.793 47.619 0.00 0.00 0.00 3.16
2738 5171 2.159071 TCCGTTTTTCCTCGTGACAAGA 60.159 45.455 0.00 0.00 0.00 3.02
2739 5172 2.806244 CCGTTTTTCCTCGTGACAAGAT 59.194 45.455 0.00 0.00 0.00 2.40
2740 5173 3.120649 CCGTTTTTCCTCGTGACAAGATC 60.121 47.826 0.00 0.00 0.00 2.75
2741 5174 3.741344 CGTTTTTCCTCGTGACAAGATCT 59.259 43.478 0.00 0.00 0.00 2.75
2742 5175 4.211374 CGTTTTTCCTCGTGACAAGATCTT 59.789 41.667 0.88 0.88 0.00 2.40
2743 5176 5.612709 CGTTTTTCCTCGTGACAAGATCTTC 60.613 44.000 4.57 0.00 0.00 2.87
2744 5177 2.921634 TCCTCGTGACAAGATCTTCG 57.078 50.000 4.57 6.47 0.00 3.79
2745 5178 2.433436 TCCTCGTGACAAGATCTTCGA 58.567 47.619 4.57 10.61 34.83 3.71
2746 5179 2.817844 TCCTCGTGACAAGATCTTCGAA 59.182 45.455 15.29 0.00 35.33 3.71
2747 5180 3.254903 TCCTCGTGACAAGATCTTCGAAA 59.745 43.478 15.29 6.66 35.33 3.46
2748 5181 3.365220 CCTCGTGACAAGATCTTCGAAAC 59.635 47.826 15.29 7.44 35.33 2.78
2749 5182 4.230657 CTCGTGACAAGATCTTCGAAACT 58.769 43.478 15.29 0.00 35.33 2.66
2750 5183 5.366829 TCGTGACAAGATCTTCGAAACTA 57.633 39.130 12.92 0.00 33.77 2.24
2751 5184 5.391449 TCGTGACAAGATCTTCGAAACTAG 58.609 41.667 12.92 0.02 33.77 2.57
2752 5185 5.180680 TCGTGACAAGATCTTCGAAACTAGA 59.819 40.000 12.92 0.00 33.77 2.43
2753 5186 6.030849 CGTGACAAGATCTTCGAAACTAGAT 58.969 40.000 4.57 0.00 33.92 1.98
2754 5187 6.195613 CGTGACAAGATCTTCGAAACTAGATC 59.804 42.308 14.39 14.39 44.54 2.75
2816 5249 8.681486 AAAGTTGCTATGTCTATTGCATATGA 57.319 30.769 6.97 0.00 42.90 2.15
2817 5250 8.681486 AAGTTGCTATGTCTATTGCATATGAA 57.319 30.769 6.97 0.00 42.90 2.57
2818 5251 8.859236 AGTTGCTATGTCTATTGCATATGAAT 57.141 30.769 6.97 6.30 42.90 2.57
2819 5252 9.293404 AGTTGCTATGTCTATTGCATATGAATT 57.707 29.630 6.97 0.00 42.90 2.17
2820 5253 9.338291 GTTGCTATGTCTATTGCATATGAATTG 57.662 33.333 6.97 5.20 42.90 2.32
2821 5254 7.532571 TGCTATGTCTATTGCATATGAATTGC 58.467 34.615 6.97 0.00 39.53 3.56
2822 5255 6.971184 GCTATGTCTATTGCATATGAATTGCC 59.029 38.462 6.97 0.00 39.39 4.52
2823 5256 6.904463 ATGTCTATTGCATATGAATTGCCA 57.096 33.333 6.97 1.96 39.39 4.92
2824 5257 6.904463 TGTCTATTGCATATGAATTGCCAT 57.096 33.333 6.97 0.00 39.39 4.40
2825 5258 7.999450 TGTCTATTGCATATGAATTGCCATA 57.001 32.000 6.97 0.00 39.39 2.74
2826 5259 8.047413 TGTCTATTGCATATGAATTGCCATAG 57.953 34.615 6.97 3.66 42.67 2.23
2827 5260 7.666804 TGTCTATTGCATATGAATTGCCATAGT 59.333 33.333 6.97 0.00 42.27 2.12
2828 5261 7.966753 GTCTATTGCATATGAATTGCCATAGTG 59.033 37.037 6.97 2.19 42.27 2.74
2829 5262 6.659745 ATTGCATATGAATTGCCATAGTGT 57.340 33.333 6.97 0.00 39.39 3.55
2830 5263 6.468333 TTGCATATGAATTGCCATAGTGTT 57.532 33.333 6.97 0.00 39.39 3.32
2831 5264 6.468333 TGCATATGAATTGCCATAGTGTTT 57.532 33.333 6.97 0.00 39.39 2.83
2832 5265 7.579761 TGCATATGAATTGCCATAGTGTTTA 57.420 32.000 6.97 0.00 39.39 2.01
2833 5266 8.180706 TGCATATGAATTGCCATAGTGTTTAT 57.819 30.769 6.97 0.00 39.39 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 0.673644 AGGACGGCAAATCGGACAAG 60.674 55.000 0.00 0.00 0.00 3.16
130 131 2.097661 CTATGCACGCATGGACGCTG 62.098 60.000 14.70 0.00 37.12 5.18
200 201 6.907748 CGTCATATGCTATCGAATGTACTAGG 59.092 42.308 0.00 0.00 0.00 3.02
201 202 6.412362 GCGTCATATGCTATCGAATGTACTAG 59.588 42.308 0.00 0.00 0.00 2.57
202 203 6.093633 AGCGTCATATGCTATCGAATGTACTA 59.906 38.462 0.00 0.00 38.98 1.82
203 204 5.096169 GCGTCATATGCTATCGAATGTACT 58.904 41.667 0.00 0.00 0.00 2.73
204 205 5.096169 AGCGTCATATGCTATCGAATGTAC 58.904 41.667 0.00 0.00 38.98 2.90
205 206 5.310720 AGCGTCATATGCTATCGAATGTA 57.689 39.130 0.00 0.00 38.98 2.29
208 209 5.065704 AGAAGCGTCATATGCTATCGAAT 57.934 39.130 1.61 0.00 40.06 3.34
209 210 4.216472 AGAGAAGCGTCATATGCTATCGAA 59.784 41.667 1.61 0.00 40.06 3.71
211 212 3.850837 CAGAGAAGCGTCATATGCTATCG 59.149 47.826 1.61 1.91 40.06 2.92
212 213 4.804108 ACAGAGAAGCGTCATATGCTATC 58.196 43.478 1.61 0.00 40.06 2.08
294 300 5.105228 CCACCCATGCATCTTTTGAAATACT 60.105 40.000 0.00 0.00 0.00 2.12
334 340 1.081094 GGCAACGTACCACCATGTAC 58.919 55.000 2.74 0.00 38.16 2.90
335 341 3.536548 GGCAACGTACCACCATGTA 57.463 52.632 2.74 0.00 0.00 2.29
336 342 4.390048 GGCAACGTACCACCATGT 57.610 55.556 2.74 0.00 0.00 3.21
385 391 7.639850 CACGTACATACATCTTGCCTTTAAATG 59.360 37.037 0.00 0.00 0.00 2.32
387 393 6.402766 GCACGTACATACATCTTGCCTTTAAA 60.403 38.462 0.00 0.00 0.00 1.52
398 404 2.543777 ATGGGGCACGTACATACATC 57.456 50.000 0.00 0.00 0.00 3.06
400 406 2.634600 GAAATGGGGCACGTACATACA 58.365 47.619 0.00 0.00 0.00 2.29
412 418 2.289382 CCTTTGGAAAACCGAAATGGGG 60.289 50.000 0.00 0.00 44.64 4.96
438 444 1.681486 TTGGTGGCGCTCGATCCATA 61.681 55.000 7.64 0.00 34.47 2.74
450 456 2.736192 GCATGTTGTACAATTTGGTGGC 59.264 45.455 12.26 5.71 0.00 5.01
480 486 0.249868 TCGTGTTGGTCCTTCAGCTG 60.250 55.000 7.63 7.63 0.00 4.24
498 504 5.743872 GGTGTTGTTTGTGAACTCTTTGATC 59.256 40.000 0.00 0.00 36.70 2.92
540 546 0.604578 GCCATGCATGTTGGTGAACT 59.395 50.000 24.58 0.00 36.57 3.01
541 547 0.604578 AGCCATGCATGTTGGTGAAC 59.395 50.000 24.58 4.40 36.57 3.18
542 548 0.604073 CAGCCATGCATGTTGGTGAA 59.396 50.000 24.58 0.00 36.57 3.18
543 549 2.268999 CAGCCATGCATGTTGGTGA 58.731 52.632 24.58 0.00 36.57 4.02
544 550 4.902308 CAGCCATGCATGTTGGTG 57.098 55.556 24.58 20.35 36.57 4.17
691 697 0.178932 ACTGGCACTACTCCACTGGA 60.179 55.000 0.00 0.00 0.00 3.86
1350 3753 0.391395 GAGGAGACCACGACGAGAGA 60.391 60.000 0.00 0.00 0.00 3.10
1797 4200 1.817099 GAGGAAGCATGGGAGCACG 60.817 63.158 0.00 0.00 36.85 5.34
1848 4251 3.082579 GCGGCAGAGGGTACTGGAG 62.083 68.421 0.00 0.00 38.22 3.86
1856 4259 2.839486 TCAATATTAGCGGCAGAGGG 57.161 50.000 1.45 0.00 0.00 4.30
1901 4304 6.817641 AGAACTATATGCATGCAGAGCTAATC 59.182 38.462 26.69 17.04 0.00 1.75
1904 4307 5.735285 AGAACTATATGCATGCAGAGCTA 57.265 39.130 26.69 13.74 0.00 3.32
1906 4309 4.613167 GCAAGAACTATATGCATGCAGAGC 60.613 45.833 26.69 14.26 39.81 4.09
1907 4310 4.755629 AGCAAGAACTATATGCATGCAGAG 59.244 41.667 26.69 22.74 42.45 3.35
1908 4311 4.711399 AGCAAGAACTATATGCATGCAGA 58.289 39.130 26.69 22.88 42.45 4.26
1929 4344 0.956633 TCGGATCGACGGGGATTTAG 59.043 55.000 0.00 0.00 0.00 1.85
1958 4373 3.782042 CGCTAACGGCTCCAACTC 58.218 61.111 0.00 0.00 39.13 3.01
1968 4383 1.735571 ACATGCCTTAAACCGCTAACG 59.264 47.619 0.00 0.00 39.67 3.18
1994 4409 1.064003 AAGTGCAGGGTGGTACATCA 58.936 50.000 0.00 0.00 44.52 3.07
1996 4411 0.038166 CCAAGTGCAGGGTGGTACAT 59.962 55.000 0.00 0.00 44.52 2.29
1997 4412 1.349542 ACCAAGTGCAGGGTGGTACA 61.350 55.000 12.98 0.00 43.90 2.90
2102 4517 2.029380 GGAATAAACCAACCACAGTGCC 60.029 50.000 0.00 0.00 0.00 5.01
2180 4598 2.228822 CCGTTCCATTCCCTTTGTCTTG 59.771 50.000 0.00 0.00 0.00 3.02
2226 4659 2.507992 CACGCGCTCCCTTCTGAG 60.508 66.667 5.73 0.00 35.40 3.35
2245 4678 1.609783 GTCCCATTCCCAGTCCCAG 59.390 63.158 0.00 0.00 0.00 4.45
2246 4679 2.297895 CGTCCCATTCCCAGTCCCA 61.298 63.158 0.00 0.00 0.00 4.37
2247 4680 2.590092 CGTCCCATTCCCAGTCCC 59.410 66.667 0.00 0.00 0.00 4.46
2248 4681 2.124695 GCGTCCCATTCCCAGTCC 60.125 66.667 0.00 0.00 0.00 3.85
2249 4682 2.124695 GGCGTCCCATTCCCAGTC 60.125 66.667 0.00 0.00 0.00 3.51
2250 4683 4.096003 CGGCGTCCCATTCCCAGT 62.096 66.667 0.00 0.00 0.00 4.00
2406 4839 0.818296 AGTAGAGACATCACGTGGCC 59.182 55.000 17.00 0.00 36.01 5.36
2478 4911 1.730064 GCATGAAAAGCCGTTCTCGTA 59.270 47.619 0.00 0.00 35.01 3.43
2479 4912 0.517316 GCATGAAAAGCCGTTCTCGT 59.483 50.000 0.00 0.00 35.01 4.18
2480 4913 0.179189 GGCATGAAAAGCCGTTCTCG 60.179 55.000 0.00 0.00 43.15 4.04
2481 4914 3.702478 GGCATGAAAAGCCGTTCTC 57.298 52.632 0.00 0.00 43.15 2.87
2488 4921 1.666888 CGTGACCAAGGCATGAAAAGC 60.667 52.381 0.00 0.00 0.00 3.51
2489 4922 1.068333 CCGTGACCAAGGCATGAAAAG 60.068 52.381 0.00 0.00 0.00 2.27
2490 4923 0.958091 CCGTGACCAAGGCATGAAAA 59.042 50.000 0.00 0.00 0.00 2.29
2491 4924 0.179004 ACCGTGACCAAGGCATGAAA 60.179 50.000 0.00 0.00 32.98 2.69
2492 4925 0.687920 TACCGTGACCAAGGCATGAA 59.312 50.000 0.00 0.00 32.98 2.57
2493 4926 0.687920 TTACCGTGACCAAGGCATGA 59.312 50.000 0.00 0.00 32.98 3.07
2494 4927 1.086696 CTTACCGTGACCAAGGCATG 58.913 55.000 1.90 0.00 32.98 4.06
2495 4928 0.981183 TCTTACCGTGACCAAGGCAT 59.019 50.000 1.90 0.00 32.98 4.40
2496 4929 0.320374 CTCTTACCGTGACCAAGGCA 59.680 55.000 1.90 0.00 32.98 4.75
2497 4930 1.019805 GCTCTTACCGTGACCAAGGC 61.020 60.000 1.90 0.00 32.98 4.35
2498 4931 0.320374 TGCTCTTACCGTGACCAAGG 59.680 55.000 0.44 0.44 35.99 3.61
2499 4932 2.093973 AGATGCTCTTACCGTGACCAAG 60.094 50.000 0.00 0.00 0.00 3.61
2500 4933 1.899814 AGATGCTCTTACCGTGACCAA 59.100 47.619 0.00 0.00 0.00 3.67
2501 4934 1.557099 AGATGCTCTTACCGTGACCA 58.443 50.000 0.00 0.00 0.00 4.02
2502 4935 2.544069 GCTAGATGCTCTTACCGTGACC 60.544 54.545 0.00 0.00 38.95 4.02
2503 4936 2.544069 GGCTAGATGCTCTTACCGTGAC 60.544 54.545 0.00 0.00 42.39 3.67
2504 4937 1.681793 GGCTAGATGCTCTTACCGTGA 59.318 52.381 0.00 0.00 42.39 4.35
2505 4938 1.600663 CGGCTAGATGCTCTTACCGTG 60.601 57.143 0.00 0.00 38.29 4.94
2506 4939 0.669077 CGGCTAGATGCTCTTACCGT 59.331 55.000 0.00 0.00 38.29 4.83
2507 4940 0.952280 TCGGCTAGATGCTCTTACCG 59.048 55.000 14.64 14.64 41.92 4.02
2508 4941 1.000052 GGTCGGCTAGATGCTCTTACC 60.000 57.143 0.00 0.00 42.39 2.85
2509 4942 1.957877 AGGTCGGCTAGATGCTCTTAC 59.042 52.381 0.00 0.00 42.39 2.34
2510 4943 2.366640 AGGTCGGCTAGATGCTCTTA 57.633 50.000 0.00 0.00 42.39 2.10
2511 4944 2.235016 CTAGGTCGGCTAGATGCTCTT 58.765 52.381 0.00 0.00 42.39 2.85
2512 4945 1.904287 CTAGGTCGGCTAGATGCTCT 58.096 55.000 0.00 0.00 42.39 4.09
2513 4946 0.242555 GCTAGGTCGGCTAGATGCTC 59.757 60.000 0.00 0.00 42.39 4.26
2514 4947 0.178975 AGCTAGGTCGGCTAGATGCT 60.179 55.000 0.00 0.00 42.39 3.79
2515 4948 1.535833 TAGCTAGGTCGGCTAGATGC 58.464 55.000 0.00 0.00 40.74 3.91
2516 4949 3.129638 GGAATAGCTAGGTCGGCTAGATG 59.870 52.174 0.00 0.00 44.05 2.90
2517 4950 3.358118 GGAATAGCTAGGTCGGCTAGAT 58.642 50.000 0.00 0.00 44.05 1.98
2518 4951 2.792878 GGAATAGCTAGGTCGGCTAGA 58.207 52.381 0.00 0.00 44.05 2.43
2519 4952 1.469308 CGGAATAGCTAGGTCGGCTAG 59.531 57.143 0.00 0.00 44.05 3.42
2520 4953 1.531423 CGGAATAGCTAGGTCGGCTA 58.469 55.000 0.00 0.00 44.76 3.93
2521 4954 1.179814 CCGGAATAGCTAGGTCGGCT 61.180 60.000 15.25 0.00 43.02 5.52
2522 4955 1.289380 CCGGAATAGCTAGGTCGGC 59.711 63.158 15.25 0.00 0.00 5.54
2523 4956 1.289380 GCCGGAATAGCTAGGTCGG 59.711 63.158 20.31 20.31 40.33 4.79
2524 4957 1.289380 GGCCGGAATAGCTAGGTCG 59.711 63.158 5.05 2.65 0.00 4.79
2525 4958 1.672320 GGGCCGGAATAGCTAGGTC 59.328 63.158 5.05 0.00 0.00 3.85
2526 4959 1.842010 GGGGCCGGAATAGCTAGGT 60.842 63.158 5.05 0.00 0.00 3.08
2527 4960 2.943978 CGGGGCCGGAATAGCTAGG 61.944 68.421 5.05 0.00 35.56 3.02
2528 4961 2.207924 ACGGGGCCGGAATAGCTAG 61.208 63.158 18.95 0.00 44.69 3.42
2529 4962 2.123164 ACGGGGCCGGAATAGCTA 60.123 61.111 18.95 0.00 44.69 3.32
2530 4963 3.861797 CACGGGGCCGGAATAGCT 61.862 66.667 18.95 0.00 44.69 3.32
2531 4964 4.171103 ACACGGGGCCGGAATAGC 62.171 66.667 18.95 0.00 44.69 2.97
2532 4965 2.203015 CACACGGGGCCGGAATAG 60.203 66.667 18.95 7.03 44.69 1.73
2533 4966 2.684294 TCACACGGGGCCGGAATA 60.684 61.111 18.95 0.00 44.69 1.75
2534 4967 4.404098 GTCACACGGGGCCGGAAT 62.404 66.667 18.95 1.96 44.69 3.01
2536 4969 4.682334 TAGTCACACGGGGCCGGA 62.682 66.667 18.95 0.00 44.69 5.14
2537 4970 2.734948 TTTTAGTCACACGGGGCCGG 62.735 60.000 9.88 9.88 44.69 6.13
2538 4971 0.885596 TTTTTAGTCACACGGGGCCG 60.886 55.000 0.00 0.00 46.03 6.13
2539 4972 3.024431 TTTTTAGTCACACGGGGCC 57.976 52.632 0.00 0.00 0.00 5.80
2559 4992 8.070171 GTATGAGCATTAGCGTTGTTCATATTT 58.930 33.333 18.46 4.21 44.03 1.40
2560 4993 7.226523 TGTATGAGCATTAGCGTTGTTCATATT 59.773 33.333 18.46 4.45 44.03 1.28
2561 4994 6.705825 TGTATGAGCATTAGCGTTGTTCATAT 59.294 34.615 18.46 4.95 44.03 1.78
2572 5005 4.129380 TCACCACATGTATGAGCATTAGC 58.871 43.478 0.00 0.00 42.56 3.09
2573 5006 5.604565 TCTCACCACATGTATGAGCATTAG 58.395 41.667 24.75 9.65 39.80 1.73
2574 5007 5.604565 CTCTCACCACATGTATGAGCATTA 58.395 41.667 24.75 13.01 39.80 1.90
2575 5008 4.449131 CTCTCACCACATGTATGAGCATT 58.551 43.478 24.75 0.00 39.80 3.56
2576 5009 3.743584 GCTCTCACCACATGTATGAGCAT 60.744 47.826 24.75 0.00 41.83 3.79
2577 5010 2.419159 GCTCTCACCACATGTATGAGCA 60.419 50.000 24.75 16.43 41.83 4.26
2578 5011 2.208431 GCTCTCACCACATGTATGAGC 58.792 52.381 24.75 20.39 39.80 4.26
2579 5012 2.099756 TCGCTCTCACCACATGTATGAG 59.900 50.000 24.04 24.04 41.06 2.90
2580 5013 2.099405 TCGCTCTCACCACATGTATGA 58.901 47.619 0.00 4.86 0.00 2.15
2581 5014 2.584492 TCGCTCTCACCACATGTATG 57.416 50.000 0.00 0.00 0.00 2.39
2582 5015 4.081972 GGATATCGCTCTCACCACATGTAT 60.082 45.833 0.00 0.00 0.00 2.29
2583 5016 3.255888 GGATATCGCTCTCACCACATGTA 59.744 47.826 0.00 0.00 0.00 2.29
2584 5017 2.036475 GGATATCGCTCTCACCACATGT 59.964 50.000 0.00 0.00 0.00 3.21
2585 5018 2.681706 GGATATCGCTCTCACCACATG 58.318 52.381 0.00 0.00 0.00 3.21
2586 5019 1.270826 CGGATATCGCTCTCACCACAT 59.729 52.381 0.00 0.00 0.00 3.21
2587 5020 0.668535 CGGATATCGCTCTCACCACA 59.331 55.000 0.00 0.00 0.00 4.17
2588 5021 3.481009 CGGATATCGCTCTCACCAC 57.519 57.895 0.00 0.00 0.00 4.16
2598 5031 0.808453 AAACGTGTGGGCGGATATCG 60.808 55.000 0.00 0.00 42.76 2.92
2599 5032 1.375551 AAAACGTGTGGGCGGATATC 58.624 50.000 0.00 0.00 35.98 1.63
2600 5033 2.695127 TAAAACGTGTGGGCGGATAT 57.305 45.000 0.00 0.00 35.98 1.63
2601 5034 2.695127 ATAAAACGTGTGGGCGGATA 57.305 45.000 0.00 0.00 35.98 2.59
2602 5035 2.679336 GTTATAAAACGTGTGGGCGGAT 59.321 45.455 0.00 0.00 35.98 4.18
2603 5036 2.075338 GTTATAAAACGTGTGGGCGGA 58.925 47.619 0.00 0.00 35.98 5.54
2604 5037 1.805345 TGTTATAAAACGTGTGGGCGG 59.195 47.619 0.00 0.00 38.53 6.13
2605 5038 2.223611 TGTGTTATAAAACGTGTGGGCG 59.776 45.455 1.35 0.00 38.53 6.13
2606 5039 3.499157 TCTGTGTTATAAAACGTGTGGGC 59.501 43.478 1.35 0.00 38.53 5.36
2607 5040 4.753107 AGTCTGTGTTATAAAACGTGTGGG 59.247 41.667 1.35 0.00 38.53 4.61
2608 5041 5.675970 CAGTCTGTGTTATAAAACGTGTGG 58.324 41.667 1.35 0.00 38.53 4.17
2609 5042 5.137403 GCAGTCTGTGTTATAAAACGTGTG 58.863 41.667 0.93 0.00 38.53 3.82
2610 5043 4.084745 CGCAGTCTGTGTTATAAAACGTGT 60.085 41.667 5.17 0.00 38.53 4.49
2611 5044 4.084745 ACGCAGTCTGTGTTATAAAACGTG 60.085 41.667 13.36 0.00 37.97 4.49
2612 5045 4.053295 ACGCAGTCTGTGTTATAAAACGT 58.947 39.130 13.36 1.39 37.97 3.99
2613 5046 4.640805 ACGCAGTCTGTGTTATAAAACG 57.359 40.909 13.36 0.76 37.97 3.60
2632 5065 4.481463 TGTATATATGCGGTGACATGACG 58.519 43.478 0.00 0.00 0.00 4.35
2633 5066 5.869344 ACATGTATATATGCGGTGACATGAC 59.131 40.000 22.24 0.00 44.37 3.06
2634 5067 5.868801 CACATGTATATATGCGGTGACATGA 59.131 40.000 22.24 0.00 44.37 3.07
2635 5068 5.868801 TCACATGTATATATGCGGTGACATG 59.131 40.000 17.90 17.44 46.09 3.21
2636 5069 6.036577 TCACATGTATATATGCGGTGACAT 57.963 37.500 17.90 7.18 29.52 3.06
2637 5070 5.242838 TCTCACATGTATATATGCGGTGACA 59.757 40.000 17.90 9.99 30.66 3.58
2638 5071 5.709966 TCTCACATGTATATATGCGGTGAC 58.290 41.667 17.90 0.51 30.66 3.67
2639 5072 5.975693 TCTCACATGTATATATGCGGTGA 57.024 39.130 19.52 19.52 32.06 4.02
2640 5073 8.877808 ATATTCTCACATGTATATATGCGGTG 57.122 34.615 9.21 14.93 0.00 4.94
2641 5074 9.890629 AAATATTCTCACATGTATATATGCGGT 57.109 29.630 9.21 0.00 0.00 5.68
2695 5128 8.526147 ACGGATCTTCAATCAGATTTTTCATTT 58.474 29.630 0.00 0.00 33.36 2.32
2696 5129 8.059798 ACGGATCTTCAATCAGATTTTTCATT 57.940 30.769 0.00 0.00 33.36 2.57
2697 5130 7.636150 ACGGATCTTCAATCAGATTTTTCAT 57.364 32.000 0.00 0.00 33.36 2.57
2698 5131 7.452880 AACGGATCTTCAATCAGATTTTTCA 57.547 32.000 0.00 0.00 33.36 2.69
2699 5132 8.748380 AAAACGGATCTTCAATCAGATTTTTC 57.252 30.769 0.00 0.00 33.36 2.29
2700 5133 9.196552 GAAAAACGGATCTTCAATCAGATTTTT 57.803 29.630 0.00 0.00 33.36 1.94
2701 5134 7.814587 GGAAAAACGGATCTTCAATCAGATTTT 59.185 33.333 0.00 6.08 33.36 1.82
2702 5135 7.177392 AGGAAAAACGGATCTTCAATCAGATTT 59.823 33.333 0.00 0.00 33.36 2.17
2703 5136 6.660949 AGGAAAAACGGATCTTCAATCAGATT 59.339 34.615 0.00 0.00 33.36 2.40
2704 5137 6.183347 AGGAAAAACGGATCTTCAATCAGAT 58.817 36.000 0.00 0.00 36.12 2.90
2705 5138 5.560724 AGGAAAAACGGATCTTCAATCAGA 58.439 37.500 0.00 0.00 0.00 3.27
2706 5139 5.446473 CGAGGAAAAACGGATCTTCAATCAG 60.446 44.000 0.00 0.00 0.00 2.90
2707 5140 4.391830 CGAGGAAAAACGGATCTTCAATCA 59.608 41.667 0.00 0.00 0.00 2.57
2708 5141 4.392138 ACGAGGAAAAACGGATCTTCAATC 59.608 41.667 0.00 0.00 0.00 2.67
2709 5142 4.154195 CACGAGGAAAAACGGATCTTCAAT 59.846 41.667 0.00 0.00 0.00 2.57
2710 5143 3.496884 CACGAGGAAAAACGGATCTTCAA 59.503 43.478 0.00 0.00 0.00 2.69
2711 5144 3.064207 CACGAGGAAAAACGGATCTTCA 58.936 45.455 0.00 0.00 0.00 3.02
2712 5145 3.123116 GTCACGAGGAAAAACGGATCTTC 59.877 47.826 0.00 0.00 0.00 2.87
2713 5146 3.064931 GTCACGAGGAAAAACGGATCTT 58.935 45.455 0.00 0.00 0.00 2.40
2714 5147 2.036733 TGTCACGAGGAAAAACGGATCT 59.963 45.455 0.00 0.00 0.00 2.75
2715 5148 2.409975 TGTCACGAGGAAAAACGGATC 58.590 47.619 0.00 0.00 0.00 3.36
2716 5149 2.536761 TGTCACGAGGAAAAACGGAT 57.463 45.000 0.00 0.00 0.00 4.18
2717 5150 2.159071 TCTTGTCACGAGGAAAAACGGA 60.159 45.455 0.00 0.00 0.00 4.69
2718 5151 2.206750 TCTTGTCACGAGGAAAAACGG 58.793 47.619 0.00 0.00 0.00 4.44
2719 5152 3.741344 AGATCTTGTCACGAGGAAAAACG 59.259 43.478 0.00 0.00 0.00 3.60
2720 5153 5.612709 CGAAGATCTTGTCACGAGGAAAAAC 60.613 44.000 14.00 0.00 33.16 2.43
2721 5154 4.447724 CGAAGATCTTGTCACGAGGAAAAA 59.552 41.667 14.00 0.00 33.16 1.94
2722 5155 3.987868 CGAAGATCTTGTCACGAGGAAAA 59.012 43.478 14.00 0.00 33.16 2.29
2723 5156 3.254903 TCGAAGATCTTGTCACGAGGAAA 59.745 43.478 14.00 0.00 34.71 3.13
2724 5157 2.817844 TCGAAGATCTTGTCACGAGGAA 59.182 45.455 14.00 0.00 34.71 3.36
2725 5158 2.433436 TCGAAGATCTTGTCACGAGGA 58.567 47.619 14.00 0.00 34.71 3.71
2726 5159 2.921634 TCGAAGATCTTGTCACGAGG 57.078 50.000 14.00 0.00 34.71 4.63
2727 5160 4.230657 AGTTTCGAAGATCTTGTCACGAG 58.769 43.478 14.00 0.00 38.42 4.18
2728 5161 4.238761 AGTTTCGAAGATCTTGTCACGA 57.761 40.909 14.00 12.59 36.61 4.35
2729 5162 5.391449 TCTAGTTTCGAAGATCTTGTCACG 58.609 41.667 14.00 10.28 35.04 4.35
2730 5163 7.444558 GATCTAGTTTCGAAGATCTTGTCAC 57.555 40.000 14.00 4.26 43.14 3.67
2790 5223 9.123902 TCATATGCAATAGACATAGCAACTTTT 57.876 29.630 0.00 0.00 40.76 2.27
2791 5224 8.681486 TCATATGCAATAGACATAGCAACTTT 57.319 30.769 0.00 0.00 40.76 2.66
2792 5225 8.681486 TTCATATGCAATAGACATAGCAACTT 57.319 30.769 0.00 0.00 40.76 2.66
2793 5226 8.859236 ATTCATATGCAATAGACATAGCAACT 57.141 30.769 0.00 0.00 40.76 3.16
2794 5227 9.338291 CAATTCATATGCAATAGACATAGCAAC 57.662 33.333 0.00 0.00 40.76 4.17
2795 5228 8.024865 GCAATTCATATGCAATAGACATAGCAA 58.975 33.333 0.00 0.00 43.29 3.91
2796 5229 7.362315 GGCAATTCATATGCAATAGACATAGCA 60.362 37.037 0.00 0.00 45.60 3.49
2797 5230 6.971184 GGCAATTCATATGCAATAGACATAGC 59.029 38.462 0.00 0.00 45.60 2.97
2798 5231 8.047413 TGGCAATTCATATGCAATAGACATAG 57.953 34.615 0.00 0.00 45.60 2.23
2799 5232 7.999450 TGGCAATTCATATGCAATAGACATA 57.001 32.000 0.00 0.00 45.60 2.29
2800 5233 6.904463 TGGCAATTCATATGCAATAGACAT 57.096 33.333 0.00 0.00 45.60 3.06
2801 5234 6.904463 ATGGCAATTCATATGCAATAGACA 57.096 33.333 0.00 0.00 45.60 3.41
2805 5238 7.764141 ACACTATGGCAATTCATATGCAATA 57.236 32.000 0.00 0.00 45.60 1.90
2806 5239 6.659745 ACACTATGGCAATTCATATGCAAT 57.340 33.333 0.00 0.00 45.60 3.56
2807 5240 6.468333 AACACTATGGCAATTCATATGCAA 57.532 33.333 0.00 0.00 45.60 4.08
2808 5241 6.468333 AAACACTATGGCAATTCATATGCA 57.532 33.333 0.00 0.00 45.60 3.96


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

AutoCloner maintained by Alex Coulton.