Multiple sequence alignment - TraesCS6A01G038700

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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 TraesCS6A01G038700 chr6A 100.000 2730 0 0 1 2730 19332052 19329323 0.000000e+00 5042
1 TraesCS6A01G038700 chr6A 92.797 236 16 1 2492 2727 447513309 447513075 9.360000e-90 340
2 TraesCS6A01G038700 chr6A 90.377 239 20 2 2492 2730 457141875 457142110 7.340000e-81 311
3 TraesCS6A01G038700 chr6A 89.958 239 23 1 2492 2730 134042079 134041842 9.500000e-80 307
4 TraesCS6A01G038700 chr6B 90.847 1912 148 15 1 1891 33323079 33324984 0.000000e+00 2536
5 TraesCS6A01G038700 chr6B 83.478 230 26 10 2253 2475 16457809 16457585 1.280000e-48 204
6 TraesCS6A01G038700 chr6B 83.117 231 29 9 2250 2476 251554961 251554737 4.610000e-48 202
7 TraesCS6A01G038700 chr6B 83.117 231 28 11 2250 2476 251554179 251553956 1.660000e-47 200
8 TraesCS6A01G038700 chr6B 79.646 226 32 8 1 212 33314635 33314860 1.690000e-32 150
9 TraesCS6A01G038700 chr6D 89.906 1922 141 34 1 1897 19320064 19321957 0.000000e+00 2425
10 TraesCS6A01G038700 chr6D 90.734 572 42 8 1914 2480 19322204 19322769 0.000000e+00 752
11 TraesCS6A01G038700 chr3A 93.333 240 13 3 2492 2730 395860363 395860600 4.330000e-93 351
12 TraesCS6A01G038700 chr5A 92.083 240 14 5 2492 2730 665210059 665209824 1.570000e-87 333
13 TraesCS6A01G038700 chr2A 91.561 237 18 2 2492 2728 541984020 541984254 2.620000e-85 326
14 TraesCS6A01G038700 chr2A 90.377 239 19 3 2492 2730 602886655 602886421 7.340000e-81 311
15 TraesCS6A01G038700 chr1A 91.213 239 19 2 2492 2730 138078449 138078685 9.430000e-85 324
16 TraesCS6A01G038700 chr4B 89.121 239 24 2 2492 2730 525946813 525946577 2.060000e-76 296
17 TraesCS6A01G038700 chr4B 84.211 228 31 5 2250 2476 434654443 434654220 1.650000e-52 217
18 TraesCS6A01G038700 chr2B 86.161 224 27 4 2255 2476 94222678 94222899 3.510000e-59 239
19 TraesCS6A01G038700 chr7B 84.416 231 27 9 2250 2476 380855231 380855006 4.580000e-53 219
20 TraesCS6A01G038700 chr2D 83.193 238 35 5 2242 2476 26348640 26348875 2.130000e-51 213
21 TraesCS6A01G038700 chr3B 84.234 222 25 10 2250 2466 829532086 829532302 9.910000e-50 207


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 TraesCS6A01G038700 chr6A 19329323 19332052 2729 True 5042.0 5042 100.000 1 2730 1 chr6A.!!$R1 2729
1 TraesCS6A01G038700 chr6B 33323079 33324984 1905 False 2536.0 2536 90.847 1 1891 1 chr6B.!!$F2 1890
2 TraesCS6A01G038700 chr6B 251553956 251554961 1005 True 201.0 202 83.117 2250 2476 2 chr6B.!!$R2 226
3 TraesCS6A01G038700 chr6D 19320064 19322769 2705 False 1588.5 2425 90.320 1 2480 2 chr6D.!!$F1 2479

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
488 506 0.031994 CACGGGTTTTCAAGGCAAGG 59.968 55.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 1881 0.17691 TGTATCGCATCCCTCGCAAA 59.823 50.0 0.0 0.0 0.0 3.68 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
151 166 3.715628 TGCTCTTGAAGGCTTGAAAAC 57.284 42.857 3.46 0.00 0.00 2.43
158 173 2.915137 GGCTTGAAAACGGGGCCA 60.915 61.111 4.39 0.00 42.08 5.36
197 212 1.607801 CTCCGGCCTGTCATGACTCA 61.608 60.000 25.55 6.62 0.00 3.41
213 228 6.373495 TCATGACTCATGAGATCCACTTTTTG 59.627 38.462 29.27 15.76 44.60 2.44
230 245 4.744795 TTTTGTGGGCATGTAAAAGTGT 57.255 36.364 0.00 0.00 0.00 3.55
252 267 8.316214 AGTGTTGCAAGGAAATTCATTTATGAT 58.684 29.630 0.00 0.00 36.56 2.45
286 301 8.084073 AGAAAATGACCATAATGTTGTGAAGTG 58.916 33.333 0.00 0.00 0.00 3.16
331 346 4.193826 ACATGATACAACGAAGTGAGCT 57.806 40.909 0.00 0.00 45.00 4.09
343 358 1.526917 GTGAGCTTGCACCACCAGT 60.527 57.895 0.00 0.00 32.68 4.00
356 371 1.207089 CCACCAGTCACCATACGTCAT 59.793 52.381 0.00 0.00 0.00 3.06
366 381 3.374988 CACCATACGTCATCTTGCACAAT 59.625 43.478 0.00 0.00 0.00 2.71
374 389 4.571984 CGTCATCTTGCACAATGGATAGAA 59.428 41.667 7.46 0.00 0.00 2.10
406 424 6.038997 TCTTTGGTTCCTCTCTTTAGTAGC 57.961 41.667 0.00 0.00 0.00 3.58
408 426 5.662674 TTGGTTCCTCTCTTTAGTAGCTC 57.337 43.478 0.00 0.00 0.00 4.09
414 432 5.326069 TCCTCTCTTTAGTAGCTCAGTTGT 58.674 41.667 0.00 0.00 0.00 3.32
435 453 4.943705 TGTCTTCACCTAGCATTTCCATTC 59.056 41.667 0.00 0.00 0.00 2.67
441 459 2.091111 CCTAGCATTTCCATTCCCCCTT 60.091 50.000 0.00 0.00 0.00 3.95
471 489 0.529119 CGGTAGCCAATCGTACCCAC 60.529 60.000 0.00 0.00 36.12 4.61
488 506 0.031994 CACGGGTTTTCAAGGCAAGG 59.968 55.000 0.00 0.00 0.00 3.61
505 523 2.173669 GGACCATGCACCGACATCG 61.174 63.158 0.00 0.00 39.44 3.84
512 530 1.851658 TGCACCGACATCGATATGTG 58.148 50.000 2.09 4.60 46.49 3.21
563 581 1.398390 CCGATACCTCAAAGCAACAGC 59.602 52.381 0.00 0.00 0.00 4.40
641 659 3.624861 CACTTCCACTGGCTGTTGATATC 59.375 47.826 0.00 0.00 0.00 1.63
644 662 2.092968 TCCACTGGCTGTTGATATCCAC 60.093 50.000 0.00 0.00 0.00 4.02
711 729 2.093306 TCCGTGCATCCTTGTACTTG 57.907 50.000 0.00 0.00 36.43 3.16
736 754 9.743057 TGAATTCAAATTACCCATAATTTAGCG 57.257 29.630 5.45 0.00 45.28 4.26
770 788 3.256704 TCCCATAGGAAGGAGTTTGTGT 58.743 45.455 0.00 0.00 40.08 3.72
835 860 1.183030 CCAGTCGTCACCACCTACCA 61.183 60.000 0.00 0.00 0.00 3.25
848 873 4.207165 CCACCTACCATTCTTATTGGGTG 58.793 47.826 0.00 0.00 41.57 4.61
851 876 4.079958 ACCTACCATTCTTATTGGGTGTCC 60.080 45.833 0.00 0.00 38.64 4.02
899 924 1.475213 GCCCGTTTATAGCTCTTGCCT 60.475 52.381 0.00 0.00 40.80 4.75
931 956 1.078848 CCCAACTTGGAGAGAGGCG 60.079 63.158 9.61 0.00 40.96 5.52
984 1009 2.260869 CCCACGGCAACTCTTGGTG 61.261 63.158 0.00 0.00 0.00 4.17
1003 1028 4.052229 CTCGCCCTTCACCGACGT 62.052 66.667 0.00 0.00 0.00 4.34
1242 1273 2.591429 CCACAGTCAGCGGCACAA 60.591 61.111 1.45 0.00 0.00 3.33
1615 1646 1.150536 GGAGAAACAGGTGTGGGCA 59.849 57.895 0.00 0.00 0.00 5.36
1624 1655 1.826487 GGTGTGGGCAAGTTTCCGT 60.826 57.895 0.00 0.00 0.00 4.69
1649 1680 2.509561 GCTTCGGGAGAACCTCGC 60.510 66.667 0.00 0.00 45.39 5.03
1650 1681 2.184579 CTTCGGGAGAACCTCGCC 59.815 66.667 5.61 0.00 45.39 5.54
1757 1789 6.328641 ACTCAGTATGTACCGATAATGGAC 57.671 41.667 0.00 0.00 37.40 4.02
1835 1867 6.732147 AAAAAGAGTTTTCCTGTGCGATACAC 60.732 38.462 0.00 0.00 40.13 2.90
1902 1934 9.769677 AACTAGAGGAATACATATATACCTGCA 57.230 33.333 0.00 0.00 0.00 4.41
2018 2280 2.491675 ACTGATTTCCCCCGTTTCTC 57.508 50.000 0.00 0.00 0.00 2.87
2031 2293 4.379499 CCCCGTTTCTCAAAAACTGATAGC 60.379 45.833 0.00 0.00 32.14 2.97
2074 2336 9.415544 ACAATTATTTCACTCATTTCAGAAAGC 57.584 29.630 1.28 0.00 33.96 3.51
2162 2424 4.263506 ACACTGATGTAAAAGGCCTTAGCT 60.264 41.667 20.84 9.18 37.26 3.32
2163 2425 4.333926 CACTGATGTAAAAGGCCTTAGCTC 59.666 45.833 20.84 11.85 39.73 4.09
2164 2426 3.879892 CTGATGTAAAAGGCCTTAGCTCC 59.120 47.826 20.84 7.54 39.73 4.70
2168 2430 0.332972 AAAAGGCCTTAGCTCCCTGG 59.667 55.000 20.84 0.00 39.73 4.45
2169 2431 0.846870 AAAGGCCTTAGCTCCCTGGT 60.847 55.000 20.84 0.00 39.73 4.00
2170 2432 0.846870 AAGGCCTTAGCTCCCTGGTT 60.847 55.000 18.87 0.00 39.73 3.67
2171 2433 0.044244 AGGCCTTAGCTCCCTGGTTA 59.956 55.000 0.00 0.00 39.73 2.85
2172 2434 1.141185 GGCCTTAGCTCCCTGGTTAT 58.859 55.000 0.00 0.00 39.73 1.89
2173 2435 2.090153 AGGCCTTAGCTCCCTGGTTATA 60.090 50.000 0.00 0.00 39.73 0.98
2174 2436 2.913617 GGCCTTAGCTCCCTGGTTATAT 59.086 50.000 0.00 0.00 39.73 0.86
2177 2442 3.519913 CCTTAGCTCCCTGGTTATATCCC 59.480 52.174 0.00 0.00 0.00 3.85
2196 2461 2.706190 CCCTGGTTAGATCCCTGGTTAG 59.294 54.545 10.24 0.00 38.93 2.34
2215 2480 5.194432 GTTAGATCCCTTTTCTTCCCCTTC 58.806 45.833 0.00 0.00 0.00 3.46
2218 2483 3.005529 TCCCTTTTCTTCCCCTTCTCT 57.994 47.619 0.00 0.00 0.00 3.10
2237 2502 5.366460 TCTCTCTTATATATAGCCGGTCCG 58.634 45.833 3.60 3.60 0.00 4.79
2301 2566 9.116054 CATTTTTGTTTGTGTTTTTCCTTCTTG 57.884 29.630 0.00 0.00 0.00 3.02
2424 2689 7.264947 ACATTCGGGAAATCATAAAATGTTCC 58.735 34.615 0.00 0.00 33.39 3.62
2441 2709 7.790823 AATGTTCCTGATTTCAACAAAAAGG 57.209 32.000 0.00 0.00 33.84 3.11
2447 2715 6.379703 TCCTGATTTCAACAAAAAGGTCTCAA 59.620 34.615 0.00 0.00 33.74 3.02
2488 2756 3.274067 AAAAAGCATCGCGTCCCC 58.726 55.556 5.77 0.00 0.00 4.81
2489 2757 2.686816 AAAAAGCATCGCGTCCCCG 61.687 57.895 5.77 0.00 37.07 5.73
2501 2769 4.649705 TCCCCGGCCTCCTGTCAA 62.650 66.667 0.00 0.00 0.00 3.18
2502 2770 4.101448 CCCCGGCCTCCTGTCAAG 62.101 72.222 0.00 0.00 0.00 3.02
2503 2771 3.003173 CCCGGCCTCCTGTCAAGA 61.003 66.667 0.00 0.00 0.00 3.02
2504 2772 2.266055 CCGGCCTCCTGTCAAGAC 59.734 66.667 0.00 0.00 0.00 3.01
2505 2773 2.125912 CGGCCTCCTGTCAAGACG 60.126 66.667 0.00 0.00 0.00 4.18
2506 2774 2.266055 GGCCTCCTGTCAAGACGG 59.734 66.667 0.00 2.01 37.44 4.79
2507 2775 2.584391 GGCCTCCTGTCAAGACGGT 61.584 63.158 8.14 0.00 35.97 4.83
2508 2776 1.079750 GCCTCCTGTCAAGACGGTC 60.080 63.158 8.14 0.00 35.97 4.79
2509 2777 1.592223 CCTCCTGTCAAGACGGTCC 59.408 63.158 4.14 0.00 35.97 4.46
2510 2778 1.213013 CTCCTGTCAAGACGGTCCG 59.787 63.158 10.48 10.48 35.97 4.79
2511 2779 1.228337 TCCTGTCAAGACGGTCCGA 60.228 57.895 20.51 0.00 35.97 4.55
2512 2780 0.824595 TCCTGTCAAGACGGTCCGAA 60.825 55.000 20.51 0.00 35.97 4.30
2513 2781 0.666577 CCTGTCAAGACGGTCCGAAC 60.667 60.000 20.51 11.53 35.97 3.95
2514 2782 0.666577 CTGTCAAGACGGTCCGAACC 60.667 60.000 20.51 6.63 42.66 3.62
2515 2783 1.111116 TGTCAAGACGGTCCGAACCT 61.111 55.000 20.51 8.96 44.04 3.50
2516 2784 0.666577 GTCAAGACGGTCCGAACCTG 60.667 60.000 20.51 11.31 44.04 4.00
2517 2785 1.374252 CAAGACGGTCCGAACCTGG 60.374 63.158 20.51 5.71 44.04 4.45
2518 2786 2.580601 AAGACGGTCCGAACCTGGG 61.581 63.158 20.51 0.00 44.04 4.45
2519 2787 3.308705 GACGGTCCGAACCTGGGT 61.309 66.667 20.51 0.00 44.04 4.51
2520 2788 1.978617 GACGGTCCGAACCTGGGTA 60.979 63.158 20.51 0.00 44.04 3.69
2521 2789 1.533753 ACGGTCCGAACCTGGGTAA 60.534 57.895 20.51 0.00 44.04 2.85
2522 2790 1.120795 ACGGTCCGAACCTGGGTAAA 61.121 55.000 20.51 0.00 44.04 2.01
2523 2791 0.035176 CGGTCCGAACCTGGGTAAAA 59.965 55.000 4.91 0.00 44.04 1.52
2524 2792 1.527034 GGTCCGAACCTGGGTAAAAC 58.473 55.000 0.00 0.00 42.80 2.43
2525 2793 1.202794 GGTCCGAACCTGGGTAAAACA 60.203 52.381 0.00 0.00 42.80 2.83
2526 2794 2.553685 GGTCCGAACCTGGGTAAAACAT 60.554 50.000 0.00 0.00 42.80 2.71
2527 2795 2.745821 GTCCGAACCTGGGTAAAACATC 59.254 50.000 0.00 0.00 0.00 3.06
2528 2796 2.372504 TCCGAACCTGGGTAAAACATCA 59.627 45.455 0.00 0.00 0.00 3.07
2529 2797 3.009695 TCCGAACCTGGGTAAAACATCAT 59.990 43.478 0.00 0.00 0.00 2.45
2530 2798 3.128589 CCGAACCTGGGTAAAACATCATG 59.871 47.826 0.00 0.00 0.00 3.07
2531 2799 3.756434 CGAACCTGGGTAAAACATCATGT 59.244 43.478 0.00 0.00 0.00 3.21
2532 2800 4.142687 CGAACCTGGGTAAAACATCATGTC 60.143 45.833 0.00 0.00 0.00 3.06
2533 2801 3.697166 ACCTGGGTAAAACATCATGTCC 58.303 45.455 0.00 0.00 0.00 4.02
2534 2802 3.023832 CCTGGGTAAAACATCATGTCCC 58.976 50.000 5.46 5.46 32.84 4.46
2535 2803 3.023832 CTGGGTAAAACATCATGTCCCC 58.976 50.000 9.34 8.37 31.60 4.81
2536 2804 2.652348 TGGGTAAAACATCATGTCCCCT 59.348 45.455 9.34 0.00 31.60 4.79
2537 2805 3.023832 GGGTAAAACATCATGTCCCCTG 58.976 50.000 1.32 0.00 27.57 4.45
2538 2806 2.427095 GGTAAAACATCATGTCCCCTGC 59.573 50.000 0.00 0.00 0.00 4.85
2539 2807 1.560505 AAAACATCATGTCCCCTGCC 58.439 50.000 0.00 0.00 0.00 4.85
2540 2808 0.706433 AAACATCATGTCCCCTGCCT 59.294 50.000 0.00 0.00 0.00 4.75
2541 2809 0.257039 AACATCATGTCCCCTGCCTC 59.743 55.000 0.00 0.00 0.00 4.70
2542 2810 1.150081 CATCATGTCCCCTGCCTCC 59.850 63.158 0.00 0.00 0.00 4.30
2543 2811 1.005289 ATCATGTCCCCTGCCTCCT 59.995 57.895 0.00 0.00 0.00 3.69
2544 2812 0.268869 ATCATGTCCCCTGCCTCCTA 59.731 55.000 0.00 0.00 0.00 2.94
2545 2813 0.268869 TCATGTCCCCTGCCTCCTAT 59.731 55.000 0.00 0.00 0.00 2.57
2546 2814 1.143813 CATGTCCCCTGCCTCCTATT 58.856 55.000 0.00 0.00 0.00 1.73
2547 2815 2.090210 TCATGTCCCCTGCCTCCTATTA 60.090 50.000 0.00 0.00 0.00 0.98
2548 2816 1.802553 TGTCCCCTGCCTCCTATTAC 58.197 55.000 0.00 0.00 0.00 1.89
2549 2817 1.057471 GTCCCCTGCCTCCTATTACC 58.943 60.000 0.00 0.00 0.00 2.85
2550 2818 0.645496 TCCCCTGCCTCCTATTACCA 59.355 55.000 0.00 0.00 0.00 3.25
2551 2819 1.225694 TCCCCTGCCTCCTATTACCAT 59.774 52.381 0.00 0.00 0.00 3.55
2552 2820 1.630878 CCCCTGCCTCCTATTACCATC 59.369 57.143 0.00 0.00 0.00 3.51
2553 2821 1.276421 CCCTGCCTCCTATTACCATCG 59.724 57.143 0.00 0.00 0.00 3.84
2554 2822 2.248248 CCTGCCTCCTATTACCATCGA 58.752 52.381 0.00 0.00 0.00 3.59
2555 2823 2.834549 CCTGCCTCCTATTACCATCGAT 59.165 50.000 0.00 0.00 0.00 3.59
2556 2824 3.118956 CCTGCCTCCTATTACCATCGATC 60.119 52.174 0.00 0.00 0.00 3.69
2557 2825 2.832129 TGCCTCCTATTACCATCGATCC 59.168 50.000 0.00 0.00 0.00 3.36
2558 2826 3.100671 GCCTCCTATTACCATCGATCCT 58.899 50.000 0.00 0.00 0.00 3.24
2559 2827 4.264217 TGCCTCCTATTACCATCGATCCTA 60.264 45.833 0.00 0.00 0.00 2.94
2560 2828 4.339814 GCCTCCTATTACCATCGATCCTAG 59.660 50.000 0.00 0.00 0.00 3.02
2561 2829 5.756918 CCTCCTATTACCATCGATCCTAGA 58.243 45.833 0.00 0.00 0.00 2.43
2562 2830 5.591067 CCTCCTATTACCATCGATCCTAGAC 59.409 48.000 0.00 0.00 0.00 2.59
2563 2831 5.183969 TCCTATTACCATCGATCCTAGACG 58.816 45.833 0.00 0.00 0.00 4.18
2564 2832 3.851976 ATTACCATCGATCCTAGACGC 57.148 47.619 0.00 0.00 0.00 5.19
2565 2833 2.265589 TACCATCGATCCTAGACGCA 57.734 50.000 0.00 0.00 0.00 5.24
2566 2834 0.669077 ACCATCGATCCTAGACGCAC 59.331 55.000 0.00 0.00 0.00 5.34
2567 2835 0.668535 CCATCGATCCTAGACGCACA 59.331 55.000 0.00 0.00 0.00 4.57
2568 2836 1.335415 CCATCGATCCTAGACGCACAG 60.335 57.143 0.00 0.00 0.00 3.66
2569 2837 1.335182 CATCGATCCTAGACGCACAGT 59.665 52.381 0.00 0.00 0.00 3.55
2570 2838 1.460504 TCGATCCTAGACGCACAGTT 58.539 50.000 0.00 0.00 0.00 3.16
2571 2839 1.400846 TCGATCCTAGACGCACAGTTC 59.599 52.381 0.00 0.00 0.00 3.01
2572 2840 1.828832 GATCCTAGACGCACAGTTCG 58.171 55.000 0.00 0.00 0.00 3.95
2573 2841 0.456221 ATCCTAGACGCACAGTTCGG 59.544 55.000 0.00 0.00 0.00 4.30
2574 2842 1.153823 CCTAGACGCACAGTTCGGG 60.154 63.158 0.00 0.00 0.00 5.14
2575 2843 1.592400 CCTAGACGCACAGTTCGGGA 61.592 60.000 0.00 0.00 0.00 5.14
2576 2844 0.456312 CTAGACGCACAGTTCGGGAC 60.456 60.000 0.00 0.00 0.00 4.46
2577 2845 1.870055 TAGACGCACAGTTCGGGACC 61.870 60.000 0.00 0.00 0.00 4.46
2578 2846 4.309950 ACGCACAGTTCGGGACCC 62.310 66.667 0.00 0.00 0.00 4.46
2580 2848 4.717313 GCACAGTTCGGGACCCCC 62.717 72.222 4.46 0.00 41.09 5.40
2581 2849 2.928396 CACAGTTCGGGACCCCCT 60.928 66.667 4.46 0.00 42.67 4.79
2582 2850 1.611261 CACAGTTCGGGACCCCCTA 60.611 63.158 4.46 0.00 42.67 3.53
2583 2851 1.611556 ACAGTTCGGGACCCCCTAC 60.612 63.158 4.46 0.29 42.67 3.18
2584 2852 2.040114 AGTTCGGGACCCCCTACC 59.960 66.667 4.46 0.00 42.67 3.18
2585 2853 3.085947 GTTCGGGACCCCCTACCC 61.086 72.222 4.46 0.00 42.67 3.69
2586 2854 4.419900 TTCGGGACCCCCTACCCC 62.420 72.222 4.46 0.00 42.67 4.95
2589 2857 3.702623 GGGACCCCCTACCCCAGA 61.703 72.222 0.00 0.00 41.34 3.86
2590 2858 2.710064 GGACCCCCTACCCCAGAT 59.290 66.667 0.00 0.00 0.00 2.90
2591 2859 1.461655 GGACCCCCTACCCCAGATC 60.462 68.421 0.00 0.00 0.00 2.75
2592 2860 1.461655 GACCCCCTACCCCAGATCC 60.462 68.421 0.00 0.00 0.00 3.36
2593 2861 2.526873 CCCCCTACCCCAGATCCG 60.527 72.222 0.00 0.00 0.00 4.18
2594 2862 2.285868 CCCCTACCCCAGATCCGT 59.714 66.667 0.00 0.00 0.00 4.69
2595 2863 1.837499 CCCCTACCCCAGATCCGTC 60.837 68.421 0.00 0.00 0.00 4.79
2596 2864 2.201022 CCCTACCCCAGATCCGTCG 61.201 68.421 0.00 0.00 0.00 5.12
2597 2865 2.201022 CCTACCCCAGATCCGTCGG 61.201 68.421 4.39 4.39 0.00 4.79
2598 2866 1.455217 CTACCCCAGATCCGTCGGT 60.455 63.158 11.88 0.00 0.00 4.69
2599 2867 1.000739 TACCCCAGATCCGTCGGTT 59.999 57.895 11.88 2.07 0.00 4.44
2600 2868 0.615544 TACCCCAGATCCGTCGGTTT 60.616 55.000 11.88 0.00 0.00 3.27
2601 2869 1.298667 CCCCAGATCCGTCGGTTTT 59.701 57.895 11.88 0.00 0.00 2.43
2602 2870 1.024579 CCCCAGATCCGTCGGTTTTG 61.025 60.000 11.88 8.49 0.00 2.44
2603 2871 0.036765 CCCAGATCCGTCGGTTTTGA 60.037 55.000 11.88 0.00 0.00 2.69
2604 2872 1.076332 CCAGATCCGTCGGTTTTGAC 58.924 55.000 11.88 0.00 35.49 3.18
2605 2873 1.606994 CCAGATCCGTCGGTTTTGACA 60.607 52.381 11.88 0.00 38.84 3.58
2606 2874 1.459592 CAGATCCGTCGGTTTTGACAC 59.540 52.381 11.88 0.00 38.84 3.67
2607 2875 0.794473 GATCCGTCGGTTTTGACACC 59.206 55.000 11.88 0.00 38.84 4.16
2615 2883 0.942252 GGTTTTGACACCGACACTCC 59.058 55.000 0.00 0.00 0.00 3.85
2616 2884 0.942252 GTTTTGACACCGACACTCCC 59.058 55.000 0.00 0.00 0.00 4.30
2617 2885 0.179040 TTTTGACACCGACACTCCCC 60.179 55.000 0.00 0.00 0.00 4.81
2618 2886 2.047213 TTTGACACCGACACTCCCCC 62.047 60.000 0.00 0.00 0.00 5.40
2619 2887 2.603776 GACACCGACACTCCCCCT 60.604 66.667 0.00 0.00 0.00 4.79
2620 2888 2.603776 ACACCGACACTCCCCCTC 60.604 66.667 0.00 0.00 0.00 4.30
2621 2889 3.391382 CACCGACACTCCCCCTCC 61.391 72.222 0.00 0.00 0.00 4.30
2622 2890 3.923645 ACCGACACTCCCCCTCCA 61.924 66.667 0.00 0.00 0.00 3.86
2623 2891 3.391382 CCGACACTCCCCCTCCAC 61.391 72.222 0.00 0.00 0.00 4.02
2624 2892 3.391382 CGACACTCCCCCTCCACC 61.391 72.222 0.00 0.00 0.00 4.61
2625 2893 2.203938 GACACTCCCCCTCCACCA 60.204 66.667 0.00 0.00 0.00 4.17
2626 2894 1.846124 GACACTCCCCCTCCACCAA 60.846 63.158 0.00 0.00 0.00 3.67
2627 2895 2.125766 GACACTCCCCCTCCACCAAC 62.126 65.000 0.00 0.00 0.00 3.77
2628 2896 2.153401 CACTCCCCCTCCACCAACA 61.153 63.158 0.00 0.00 0.00 3.33
2629 2897 1.386772 ACTCCCCCTCCACCAACAA 60.387 57.895 0.00 0.00 0.00 2.83
2630 2898 1.380302 CTCCCCCTCCACCAACAAG 59.620 63.158 0.00 0.00 0.00 3.16
2631 2899 2.283173 CCCCCTCCACCAACAAGC 60.283 66.667 0.00 0.00 0.00 4.01
2632 2900 2.520458 CCCCTCCACCAACAAGCA 59.480 61.111 0.00 0.00 0.00 3.91
2633 2901 1.077265 CCCCTCCACCAACAAGCAT 59.923 57.895 0.00 0.00 0.00 3.79
2634 2902 0.967380 CCCCTCCACCAACAAGCATC 60.967 60.000 0.00 0.00 0.00 3.91
2635 2903 0.251297 CCCTCCACCAACAAGCATCA 60.251 55.000 0.00 0.00 0.00 3.07
2636 2904 1.619654 CCTCCACCAACAAGCATCAA 58.380 50.000 0.00 0.00 0.00 2.57
2637 2905 2.173519 CCTCCACCAACAAGCATCAAT 58.826 47.619 0.00 0.00 0.00 2.57
2638 2906 2.165030 CCTCCACCAACAAGCATCAATC 59.835 50.000 0.00 0.00 0.00 2.67
2639 2907 2.165030 CTCCACCAACAAGCATCAATCC 59.835 50.000 0.00 0.00 0.00 3.01
2640 2908 1.894466 CCACCAACAAGCATCAATCCA 59.106 47.619 0.00 0.00 0.00 3.41
2641 2909 2.498481 CCACCAACAAGCATCAATCCAT 59.502 45.455 0.00 0.00 0.00 3.41
2642 2910 3.517602 CACCAACAAGCATCAATCCATG 58.482 45.455 0.00 0.00 0.00 3.66
2643 2911 2.498481 ACCAACAAGCATCAATCCATGG 59.502 45.455 4.97 4.97 0.00 3.66
2644 2912 2.159014 CCAACAAGCATCAATCCATGGG 60.159 50.000 13.02 0.00 0.00 4.00
2645 2913 2.498481 CAACAAGCATCAATCCATGGGT 59.502 45.455 13.02 0.00 0.00 4.51
2646 2914 2.823959 ACAAGCATCAATCCATGGGTT 58.176 42.857 13.02 8.57 0.00 4.11
2647 2915 2.498481 ACAAGCATCAATCCATGGGTTG 59.502 45.455 28.93 28.93 0.00 3.77
2648 2916 1.117150 AGCATCAATCCATGGGTTGC 58.883 50.000 29.78 20.83 33.08 4.17
2649 2917 1.117150 GCATCAATCCATGGGTTGCT 58.883 50.000 29.78 19.87 31.42 3.91
2650 2918 1.068127 GCATCAATCCATGGGTTGCTC 59.932 52.381 29.78 17.63 31.42 4.26
2651 2919 1.335810 CATCAATCCATGGGTTGCTCG 59.664 52.381 29.78 17.32 0.00 5.03
2652 2920 0.617935 TCAATCCATGGGTTGCTCGA 59.382 50.000 29.78 12.44 0.00 4.04
2653 2921 1.004161 TCAATCCATGGGTTGCTCGAA 59.996 47.619 29.78 12.06 0.00 3.71
2654 2922 1.818060 CAATCCATGGGTTGCTCGAAA 59.182 47.619 24.46 0.00 0.00 3.46
2655 2923 1.463674 ATCCATGGGTTGCTCGAAAC 58.536 50.000 13.02 0.00 0.00 2.78
2656 2924 0.109532 TCCATGGGTTGCTCGAAACA 59.890 50.000 13.02 0.00 0.00 2.83
2657 2925 0.958091 CCATGGGTTGCTCGAAACAA 59.042 50.000 2.85 0.00 0.00 2.83
2658 2926 1.335872 CCATGGGTTGCTCGAAACAAC 60.336 52.381 18.21 18.21 45.30 3.32
2659 2927 0.591170 ATGGGTTGCTCGAAACAACG 59.409 50.000 19.20 0.00 46.65 4.10
2660 2928 0.462225 TGGGTTGCTCGAAACAACGA 60.462 50.000 19.20 9.71 46.65 3.85
2667 2935 2.895039 TCGAAACAACGAGTGCCTC 58.105 52.632 0.00 0.00 37.37 4.70
2668 2936 0.599204 TCGAAACAACGAGTGCCTCC 60.599 55.000 0.00 0.00 37.37 4.30
2669 2937 0.878523 CGAAACAACGAGTGCCTCCA 60.879 55.000 0.00 0.00 35.09 3.86
2670 2938 1.305201 GAAACAACGAGTGCCTCCAA 58.695 50.000 0.00 0.00 0.00 3.53
2671 2939 1.880027 GAAACAACGAGTGCCTCCAAT 59.120 47.619 0.00 0.00 0.00 3.16
2672 2940 1.981256 AACAACGAGTGCCTCCAATT 58.019 45.000 0.00 0.00 0.00 2.32
2673 2941 2.851263 ACAACGAGTGCCTCCAATTA 57.149 45.000 0.00 0.00 0.00 1.40
2674 2942 3.134574 ACAACGAGTGCCTCCAATTAA 57.865 42.857 0.00 0.00 0.00 1.40
2675 2943 2.812011 ACAACGAGTGCCTCCAATTAAC 59.188 45.455 0.00 0.00 0.00 2.01
2676 2944 2.811431 CAACGAGTGCCTCCAATTAACA 59.189 45.455 0.00 0.00 0.00 2.41
2677 2945 3.134574 ACGAGTGCCTCCAATTAACAA 57.865 42.857 0.00 0.00 0.00 2.83
2678 2946 3.074412 ACGAGTGCCTCCAATTAACAAG 58.926 45.455 0.00 0.00 0.00 3.16
2679 2947 3.244422 ACGAGTGCCTCCAATTAACAAGA 60.244 43.478 0.00 0.00 0.00 3.02
2680 2948 3.372206 CGAGTGCCTCCAATTAACAAGAG 59.628 47.826 0.00 0.00 0.00 2.85
2681 2949 4.327680 GAGTGCCTCCAATTAACAAGAGT 58.672 43.478 0.00 0.00 0.00 3.24
2682 2950 4.327680 AGTGCCTCCAATTAACAAGAGTC 58.672 43.478 0.00 0.00 0.00 3.36
2683 2951 3.440522 GTGCCTCCAATTAACAAGAGTCC 59.559 47.826 0.00 0.00 0.00 3.85
2684 2952 3.017442 GCCTCCAATTAACAAGAGTCCC 58.983 50.000 0.00 0.00 0.00 4.46
2685 2953 3.561313 GCCTCCAATTAACAAGAGTCCCA 60.561 47.826 0.00 0.00 0.00 4.37
2686 2954 4.265073 CCTCCAATTAACAAGAGTCCCAG 58.735 47.826 0.00 0.00 0.00 4.45
2687 2955 4.265073 CTCCAATTAACAAGAGTCCCAGG 58.735 47.826 0.00 0.00 0.00 4.45
2688 2956 3.010138 TCCAATTAACAAGAGTCCCAGGG 59.990 47.826 0.00 0.00 0.00 4.45
2689 2957 3.356290 CAATTAACAAGAGTCCCAGGGG 58.644 50.000 5.33 0.92 0.00 4.79
2690 2958 1.368374 TTAACAAGAGTCCCAGGGGG 58.632 55.000 5.33 0.00 46.11 5.40
2702 2970 2.080654 CCAGGGGGAGTTTTGTTTGA 57.919 50.000 0.00 0.00 35.59 2.69
2703 2971 2.393646 CCAGGGGGAGTTTTGTTTGAA 58.606 47.619 0.00 0.00 35.59 2.69
2704 2972 2.769095 CCAGGGGGAGTTTTGTTTGAAA 59.231 45.455 0.00 0.00 35.59 2.69
2705 2973 3.390967 CCAGGGGGAGTTTTGTTTGAAAT 59.609 43.478 0.00 0.00 35.59 2.17
2706 2974 4.141505 CCAGGGGGAGTTTTGTTTGAAATT 60.142 41.667 0.00 0.00 35.59 1.82
2707 2975 5.071115 CCAGGGGGAGTTTTGTTTGAAATTA 59.929 40.000 0.00 0.00 35.59 1.40
2708 2976 6.239858 CCAGGGGGAGTTTTGTTTGAAATTAT 60.240 38.462 0.00 0.00 35.59 1.28
2709 2977 7.223584 CAGGGGGAGTTTTGTTTGAAATTATT 58.776 34.615 0.00 0.00 0.00 1.40
2710 2978 7.719193 CAGGGGGAGTTTTGTTTGAAATTATTT 59.281 33.333 0.00 0.00 0.00 1.40
2711 2979 8.278639 AGGGGGAGTTTTGTTTGAAATTATTTT 58.721 29.630 0.00 0.00 0.00 1.82
2712 2980 8.349245 GGGGGAGTTTTGTTTGAAATTATTTTG 58.651 33.333 0.00 0.00 0.00 2.44
2713 2981 9.114952 GGGGAGTTTTGTTTGAAATTATTTTGA 57.885 29.630 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.916397 GCTTATAACACAGTATACAAACATGAC 57.084 33.333 5.50 0.00 0.00 3.06
151 166 2.884639 CCATTACTTTTCTATGGCCCCG 59.115 50.000 0.00 0.00 33.08 5.73
213 228 2.223923 TGCAACACTTTTACATGCCCAC 60.224 45.455 0.00 0.00 36.20 4.61
230 245 9.893634 AATCATCATAAATGAATTTCCTTGCAA 57.106 25.926 0.00 0.00 40.69 4.08
261 276 8.081633 TCACTTCACAACATTATGGTCATTTTC 58.918 33.333 0.00 0.00 0.00 2.29
269 284 6.969366 TGTTCTTCACTTCACAACATTATGG 58.031 36.000 0.00 0.00 0.00 2.74
286 301 9.378551 TGTATAGTAAATGTCACCATGTTCTTC 57.621 33.333 0.00 0.00 0.00 2.87
331 346 0.767998 TATGGTGACTGGTGGTGCAA 59.232 50.000 0.00 0.00 0.00 4.08
343 358 2.028567 TGTGCAAGATGACGTATGGTGA 60.029 45.455 0.00 0.00 0.00 4.02
356 371 5.824624 GGAGATTTCTATCCATTGTGCAAGA 59.175 40.000 0.00 0.00 35.54 3.02
366 381 5.492524 ACCAAAGAAGGGAGATTTCTATCCA 59.507 40.000 0.00 0.00 37.33 3.41
374 389 3.919554 AGAGGAACCAAAGAAGGGAGATT 59.080 43.478 0.00 0.00 0.00 2.40
406 424 3.667497 TGCTAGGTGAAGACAACTGAG 57.333 47.619 0.00 0.00 44.46 3.35
408 426 4.154918 GGAAATGCTAGGTGAAGACAACTG 59.845 45.833 0.00 0.00 44.46 3.16
414 432 4.526970 GGAATGGAAATGCTAGGTGAAGA 58.473 43.478 0.00 0.00 0.00 2.87
435 453 3.646736 ACCGATTTCTTCTTAAGGGGG 57.353 47.619 1.85 0.00 0.00 5.40
441 459 5.047847 CGATTGGCTACCGATTTCTTCTTA 58.952 41.667 0.00 0.00 0.00 2.10
471 489 0.313987 GTCCTTGCCTTGAAAACCCG 59.686 55.000 0.00 0.00 0.00 5.28
488 506 0.530650 ATCGATGTCGGTGCATGGTC 60.531 55.000 0.00 0.00 40.29 4.02
512 530 1.152963 ATCCCACCCGCACTATTGC 60.153 57.895 0.00 0.00 46.21 3.56
526 544 2.514824 GAAGCTCACGGCCATCCC 60.515 66.667 2.24 0.00 43.05 3.85
537 555 2.205911 GCTTTGAGGTATCGGAAGCTC 58.794 52.381 9.35 9.35 40.91 4.09
641 659 4.403137 CGCAACATGCACCCGTGG 62.403 66.667 2.99 0.00 45.36 4.94
644 662 4.101790 GGTCGCAACATGCACCCG 62.102 66.667 2.99 0.00 45.36 5.28
661 679 5.981088 ATAGATCTGATCACAGGTAGCAG 57.019 43.478 19.12 0.00 43.60 4.24
694 712 4.154015 TGAATTCAAGTACAAGGATGCACG 59.846 41.667 5.45 0.00 0.00 5.34
711 729 9.744468 ACGCTAAATTATGGGTAATTTGAATTC 57.256 29.630 13.55 0.00 45.45 2.17
760 778 6.265876 TCCCCTGTAAAAATTACACAAACTCC 59.734 38.462 0.00 0.00 0.00 3.85
796 818 3.063485 GGCGGTGCATGTTACAAAATTT 58.937 40.909 0.00 0.00 0.00 1.82
797 819 2.036475 TGGCGGTGCATGTTACAAAATT 59.964 40.909 0.00 0.00 0.00 1.82
798 820 1.615883 TGGCGGTGCATGTTACAAAAT 59.384 42.857 0.00 0.00 0.00 1.82
835 860 4.600062 GTCCAAGGACACCCAATAAGAAT 58.400 43.478 14.19 0.00 44.02 2.40
848 873 0.966875 TGCCATGCATGTCCAAGGAC 60.967 55.000 24.58 12.30 38.47 3.85
851 876 0.892755 AACTGCCATGCATGTCCAAG 59.107 50.000 24.58 17.06 38.13 3.61
984 1009 2.126031 GTCGGTGAAGGGCGAGAC 60.126 66.667 0.00 0.00 0.00 3.36
1003 1028 6.419484 TGACTCCTGAGAACAACAATTAGA 57.581 37.500 0.22 0.00 0.00 2.10
1213 1244 2.262603 CTGTGGCTGTAGCTGCGA 59.737 61.111 0.00 0.00 41.70 5.10
1450 1481 4.753662 AGCCGGCTCCCTCGTACA 62.754 66.667 27.08 0.00 0.00 2.90
1459 1490 4.863925 GAGCGTCTGAGCCGGCTC 62.864 72.222 43.07 43.07 44.24 4.70
1531 1562 1.006102 CGTCCTGCCGAACTTGAGT 60.006 57.895 0.00 0.00 0.00 3.41
1582 1613 2.030027 TCTCCAGCTCCTTTTCCTCA 57.970 50.000 0.00 0.00 0.00 3.86
1642 1673 3.449227 TCGAGATGCGGCGAGGTT 61.449 61.111 12.98 0.00 41.33 3.50
1649 1680 1.979469 GATATCGTTGTCGAGATGCGG 59.021 52.381 2.63 0.00 45.89 5.69
1650 1681 2.650608 TGATATCGTTGTCGAGATGCG 58.349 47.619 2.63 0.00 45.89 4.73
1757 1789 2.073816 GACGTTACAATGAGTGGTGGG 58.926 52.381 0.00 0.00 0.00 4.61
1849 1881 0.176910 TGTATCGCATCCCTCGCAAA 59.823 50.000 0.00 0.00 0.00 3.68
2010 2272 4.084013 ACGCTATCAGTTTTTGAGAAACGG 60.084 41.667 0.00 0.00 39.68 4.44
2018 2280 9.599322 GAATATATTCCACGCTATCAGTTTTTG 57.401 33.333 13.62 0.00 0.00 2.44
2052 2314 8.394971 TCAGCTTTCTGAAATGAGTGAAATAA 57.605 30.769 2.88 0.00 45.69 1.40
2149 2411 0.332972 CCAGGGAGCTAAGGCCTTTT 59.667 55.000 26.08 10.07 39.73 2.27
2162 2424 3.448277 AACCAGGGATATAACCAGGGA 57.552 47.619 13.13 0.00 33.10 4.20
2163 2425 4.499472 TCTAACCAGGGATATAACCAGGG 58.501 47.826 12.44 9.66 33.10 4.45
2164 2426 5.189934 GGATCTAACCAGGGATATAACCAGG 59.810 48.000 0.99 4.98 34.36 4.45
2168 2430 5.189934 CCAGGGATCTAACCAGGGATATAAC 59.810 48.000 0.00 0.00 0.00 1.89
2169 2431 5.162648 ACCAGGGATCTAACCAGGGATATAA 60.163 44.000 3.54 0.00 33.10 0.98
2170 2432 4.363217 ACCAGGGATCTAACCAGGGATATA 59.637 45.833 3.54 0.00 33.10 0.86
2171 2433 3.146833 ACCAGGGATCTAACCAGGGATAT 59.853 47.826 3.54 0.00 33.10 1.63
2172 2434 2.527057 ACCAGGGATCTAACCAGGGATA 59.473 50.000 3.54 0.00 33.10 2.59
2173 2435 1.298382 ACCAGGGATCTAACCAGGGAT 59.702 52.381 3.54 0.00 33.10 3.85
2174 2436 0.722676 ACCAGGGATCTAACCAGGGA 59.277 55.000 3.54 0.00 33.10 4.20
2177 2442 4.284746 GGATCTAACCAGGGATCTAACCAG 59.715 50.000 4.66 0.00 38.56 4.00
2196 2461 3.525609 AGAGAAGGGGAAGAAAAGGGATC 59.474 47.826 0.00 0.00 0.00 3.36
2215 2480 4.023878 GCGGACCGGCTATATATAAGAGAG 60.024 50.000 17.22 0.00 0.00 3.20
2218 2483 3.379372 GTGCGGACCGGCTATATATAAGA 59.621 47.826 17.22 0.00 0.00 2.10
2286 2551 8.490355 CAGATTAATTGCAAGAAGGAAAAACAC 58.510 33.333 4.94 0.00 0.00 3.32
2366 2631 9.657419 AATTCACAAACATTTTATGATTCCTCC 57.343 29.630 0.00 0.00 0.00 4.30
2424 2689 8.652810 ATTTGAGACCTTTTTGTTGAAATCAG 57.347 30.769 0.00 0.00 0.00 2.90
2484 2752 4.649705 TTGACAGGAGGCCGGGGA 62.650 66.667 2.18 0.00 0.00 4.81
2485 2753 4.101448 CTTGACAGGAGGCCGGGG 62.101 72.222 2.18 0.00 0.00 5.73
2486 2754 3.003173 TCTTGACAGGAGGCCGGG 61.003 66.667 2.18 0.00 0.00 5.73
2487 2755 2.266055 GTCTTGACAGGAGGCCGG 59.734 66.667 0.00 0.00 0.00 6.13
2488 2756 2.125912 CGTCTTGACAGGAGGCCG 60.126 66.667 0.00 0.00 0.00 6.13
2489 2757 2.266055 CCGTCTTGACAGGAGGCC 59.734 66.667 0.00 0.00 0.00 5.19
2490 2758 1.079750 GACCGTCTTGACAGGAGGC 60.080 63.158 14.86 0.00 0.00 4.70
2491 2759 1.592223 GGACCGTCTTGACAGGAGG 59.408 63.158 14.86 0.55 0.00 4.30
2492 2760 1.213013 CGGACCGTCTTGACAGGAG 59.787 63.158 5.48 5.85 0.00 3.69
2493 2761 0.824595 TTCGGACCGTCTTGACAGGA 60.825 55.000 14.79 0.00 0.00 3.86
2494 2762 0.666577 GTTCGGACCGTCTTGACAGG 60.667 60.000 14.79 5.97 0.00 4.00
2495 2763 0.666577 GGTTCGGACCGTCTTGACAG 60.667 60.000 14.79 0.00 35.91 3.51
2496 2764 1.364901 GGTTCGGACCGTCTTGACA 59.635 57.895 14.79 0.00 35.91 3.58
2497 2765 4.256813 GGTTCGGACCGTCTTGAC 57.743 61.111 14.79 6.22 35.91 3.18
2505 2773 1.202794 TGTTTTACCCAGGTTCGGACC 60.203 52.381 4.03 4.03 46.92 4.46
2506 2774 2.259266 TGTTTTACCCAGGTTCGGAC 57.741 50.000 0.00 0.00 0.00 4.79
2507 2775 2.372504 TGATGTTTTACCCAGGTTCGGA 59.627 45.455 0.00 0.00 0.00 4.55
2508 2776 2.785562 TGATGTTTTACCCAGGTTCGG 58.214 47.619 0.00 0.00 0.00 4.30
2509 2777 3.756434 ACATGATGTTTTACCCAGGTTCG 59.244 43.478 0.00 0.00 0.00 3.95
2510 2778 4.157840 GGACATGATGTTTTACCCAGGTTC 59.842 45.833 0.00 0.00 0.00 3.62
2511 2779 4.086457 GGACATGATGTTTTACCCAGGTT 58.914 43.478 0.00 0.00 0.00 3.50
2512 2780 3.563479 GGGACATGATGTTTTACCCAGGT 60.563 47.826 13.50 0.00 32.58 4.00
2513 2781 3.023832 GGGACATGATGTTTTACCCAGG 58.976 50.000 13.50 0.00 32.58 4.45
2514 2782 3.023832 GGGGACATGATGTTTTACCCAG 58.976 50.000 18.42 0.00 33.62 4.45
2515 2783 2.652348 AGGGGACATGATGTTTTACCCA 59.348 45.455 21.94 0.00 33.62 4.51
2516 2784 3.023832 CAGGGGACATGATGTTTTACCC 58.976 50.000 16.01 16.01 31.78 3.69
2517 2785 2.427095 GCAGGGGACATGATGTTTTACC 59.573 50.000 0.00 0.00 0.00 2.85
2518 2786 2.427095 GGCAGGGGACATGATGTTTTAC 59.573 50.000 0.00 0.00 0.00 2.01
2519 2787 2.311542 AGGCAGGGGACATGATGTTTTA 59.688 45.455 0.00 0.00 0.00 1.52
2520 2788 1.077663 AGGCAGGGGACATGATGTTTT 59.922 47.619 0.00 0.00 0.00 2.43
2521 2789 0.706433 AGGCAGGGGACATGATGTTT 59.294 50.000 0.00 0.00 0.00 2.83
2522 2790 0.257039 GAGGCAGGGGACATGATGTT 59.743 55.000 0.00 0.00 0.00 2.71
2523 2791 1.639635 GGAGGCAGGGGACATGATGT 61.640 60.000 0.00 0.00 0.00 3.06
2524 2792 1.150081 GGAGGCAGGGGACATGATG 59.850 63.158 0.00 0.00 0.00 3.07
2525 2793 0.268869 TAGGAGGCAGGGGACATGAT 59.731 55.000 0.00 0.00 0.00 2.45
2526 2794 0.268869 ATAGGAGGCAGGGGACATGA 59.731 55.000 0.00 0.00 0.00 3.07
2527 2795 1.143813 AATAGGAGGCAGGGGACATG 58.856 55.000 0.00 0.00 0.00 3.21
2528 2796 2.339769 GTAATAGGAGGCAGGGGACAT 58.660 52.381 0.00 0.00 0.00 3.06
2529 2797 1.694693 GGTAATAGGAGGCAGGGGACA 60.695 57.143 0.00 0.00 0.00 4.02
2530 2798 1.057471 GGTAATAGGAGGCAGGGGAC 58.943 60.000 0.00 0.00 0.00 4.46
2531 2799 0.645496 TGGTAATAGGAGGCAGGGGA 59.355 55.000 0.00 0.00 0.00 4.81
2532 2800 1.630878 GATGGTAATAGGAGGCAGGGG 59.369 57.143 0.00 0.00 0.00 4.79
2533 2801 1.276421 CGATGGTAATAGGAGGCAGGG 59.724 57.143 0.00 0.00 0.00 4.45
2534 2802 2.248248 TCGATGGTAATAGGAGGCAGG 58.752 52.381 0.00 0.00 0.00 4.85
2535 2803 3.118956 GGATCGATGGTAATAGGAGGCAG 60.119 52.174 0.54 0.00 0.00 4.85
2536 2804 2.832129 GGATCGATGGTAATAGGAGGCA 59.168 50.000 0.54 0.00 0.00 4.75
2537 2805 3.100671 AGGATCGATGGTAATAGGAGGC 58.899 50.000 0.54 0.00 0.00 4.70
2538 2806 5.591067 GTCTAGGATCGATGGTAATAGGAGG 59.409 48.000 0.54 0.00 0.00 4.30
2539 2807 5.294799 CGTCTAGGATCGATGGTAATAGGAG 59.705 48.000 0.54 0.00 0.00 3.69
2540 2808 5.183969 CGTCTAGGATCGATGGTAATAGGA 58.816 45.833 0.54 0.00 0.00 2.94
2541 2809 4.201930 GCGTCTAGGATCGATGGTAATAGG 60.202 50.000 0.54 0.00 0.00 2.57
2542 2810 4.395231 TGCGTCTAGGATCGATGGTAATAG 59.605 45.833 0.54 0.00 0.00 1.73
2543 2811 4.155462 GTGCGTCTAGGATCGATGGTAATA 59.845 45.833 0.54 0.00 0.00 0.98
2544 2812 3.057456 GTGCGTCTAGGATCGATGGTAAT 60.057 47.826 0.54 0.00 0.00 1.89
2545 2813 2.292569 GTGCGTCTAGGATCGATGGTAA 59.707 50.000 0.54 0.00 0.00 2.85
2546 2814 1.878088 GTGCGTCTAGGATCGATGGTA 59.122 52.381 0.54 0.00 0.00 3.25
2547 2815 0.669077 GTGCGTCTAGGATCGATGGT 59.331 55.000 0.54 0.00 0.00 3.55
2548 2816 0.668535 TGTGCGTCTAGGATCGATGG 59.331 55.000 0.54 0.00 0.00 3.51
2549 2817 1.335182 ACTGTGCGTCTAGGATCGATG 59.665 52.381 0.54 0.00 0.00 3.84
2550 2818 1.681538 ACTGTGCGTCTAGGATCGAT 58.318 50.000 0.00 0.00 0.00 3.59
2551 2819 1.400846 GAACTGTGCGTCTAGGATCGA 59.599 52.381 0.00 0.00 0.00 3.59
2552 2820 1.828832 GAACTGTGCGTCTAGGATCG 58.171 55.000 0.00 0.00 0.00 3.69
2553 2821 1.534175 CCGAACTGTGCGTCTAGGATC 60.534 57.143 7.51 0.00 0.00 3.36
2554 2822 0.456221 CCGAACTGTGCGTCTAGGAT 59.544 55.000 7.51 0.00 0.00 3.24
2555 2823 1.592400 CCCGAACTGTGCGTCTAGGA 61.592 60.000 7.51 0.00 0.00 2.94
2556 2824 1.153823 CCCGAACTGTGCGTCTAGG 60.154 63.158 7.51 0.00 0.00 3.02
2557 2825 0.456312 GTCCCGAACTGTGCGTCTAG 60.456 60.000 7.51 0.00 0.00 2.43
2558 2826 1.582968 GTCCCGAACTGTGCGTCTA 59.417 57.895 7.51 0.00 0.00 2.59
2559 2827 2.338984 GTCCCGAACTGTGCGTCT 59.661 61.111 7.51 0.00 0.00 4.18
2560 2828 2.737376 GGTCCCGAACTGTGCGTC 60.737 66.667 7.51 0.00 0.00 5.19
2561 2829 4.309950 GGGTCCCGAACTGTGCGT 62.310 66.667 7.51 0.00 0.00 5.24
2563 2831 4.717313 GGGGGTCCCGAACTGTGC 62.717 72.222 0.48 0.00 36.85 4.57
2572 2840 2.985567 GATCTGGGGTAGGGGGTCCC 62.986 70.000 0.00 0.00 45.90 4.46
2573 2841 1.461655 GATCTGGGGTAGGGGGTCC 60.462 68.421 0.00 0.00 0.00 4.46
2574 2842 1.461655 GGATCTGGGGTAGGGGGTC 60.462 68.421 0.00 0.00 0.00 4.46
2575 2843 2.710064 GGATCTGGGGTAGGGGGT 59.290 66.667 0.00 0.00 0.00 4.95
2576 2844 2.526873 CGGATCTGGGGTAGGGGG 60.527 72.222 0.00 0.00 0.00 5.40
2577 2845 1.837499 GACGGATCTGGGGTAGGGG 60.837 68.421 6.47 0.00 0.00 4.79
2578 2846 2.201022 CGACGGATCTGGGGTAGGG 61.201 68.421 6.47 0.00 0.00 3.53
2579 2847 2.201022 CCGACGGATCTGGGGTAGG 61.201 68.421 8.64 0.00 0.00 3.18
2580 2848 1.041447 AACCGACGGATCTGGGGTAG 61.041 60.000 23.38 0.03 0.00 3.18
2581 2849 0.615544 AAACCGACGGATCTGGGGTA 60.616 55.000 23.38 0.00 0.00 3.69
2582 2850 1.486145 AAAACCGACGGATCTGGGGT 61.486 55.000 23.38 12.43 0.00 4.95
2583 2851 1.024579 CAAAACCGACGGATCTGGGG 61.025 60.000 23.38 9.28 0.00 4.96
2584 2852 0.036765 TCAAAACCGACGGATCTGGG 60.037 55.000 23.38 4.83 0.00 4.45
2585 2853 1.076332 GTCAAAACCGACGGATCTGG 58.924 55.000 23.38 5.95 0.00 3.86
2586 2854 1.459592 GTGTCAAAACCGACGGATCTG 59.540 52.381 23.38 13.62 38.84 2.90
2587 2855 1.607251 GGTGTCAAAACCGACGGATCT 60.607 52.381 23.38 0.95 38.84 2.75
2588 2856 0.794473 GGTGTCAAAACCGACGGATC 59.206 55.000 23.38 0.00 38.84 3.36
2589 2857 2.922779 GGTGTCAAAACCGACGGAT 58.077 52.632 23.38 5.64 38.84 4.18
2590 2858 4.442018 GGTGTCAAAACCGACGGA 57.558 55.556 23.38 0.00 38.84 4.69
2596 2864 0.942252 GGAGTGTCGGTGTCAAAACC 59.058 55.000 0.00 0.00 36.82 3.27
2597 2865 0.942252 GGGAGTGTCGGTGTCAAAAC 59.058 55.000 0.00 0.00 0.00 2.43
2598 2866 0.179040 GGGGAGTGTCGGTGTCAAAA 60.179 55.000 0.00 0.00 0.00 2.44
2599 2867 1.448497 GGGGAGTGTCGGTGTCAAA 59.552 57.895 0.00 0.00 0.00 2.69
2600 2868 2.513259 GGGGGAGTGTCGGTGTCAA 61.513 63.158 0.00 0.00 0.00 3.18
2601 2869 2.920912 GGGGGAGTGTCGGTGTCA 60.921 66.667 0.00 0.00 0.00 3.58
2602 2870 2.603776 AGGGGGAGTGTCGGTGTC 60.604 66.667 0.00 0.00 0.00 3.67
2603 2871 2.603776 GAGGGGGAGTGTCGGTGT 60.604 66.667 0.00 0.00 0.00 4.16
2604 2872 3.391382 GGAGGGGGAGTGTCGGTG 61.391 72.222 0.00 0.00 0.00 4.94
2605 2873 3.923645 TGGAGGGGGAGTGTCGGT 61.924 66.667 0.00 0.00 0.00 4.69
2606 2874 3.391382 GTGGAGGGGGAGTGTCGG 61.391 72.222 0.00 0.00 0.00 4.79
2607 2875 3.391382 GGTGGAGGGGGAGTGTCG 61.391 72.222 0.00 0.00 0.00 4.35
2608 2876 1.846124 TTGGTGGAGGGGGAGTGTC 60.846 63.158 0.00 0.00 0.00 3.67
2609 2877 2.154074 GTTGGTGGAGGGGGAGTGT 61.154 63.158 0.00 0.00 0.00 3.55
2610 2878 1.715019 TTGTTGGTGGAGGGGGAGTG 61.715 60.000 0.00 0.00 0.00 3.51
2611 2879 1.386772 TTGTTGGTGGAGGGGGAGT 60.387 57.895 0.00 0.00 0.00 3.85
2612 2880 1.380302 CTTGTTGGTGGAGGGGGAG 59.620 63.158 0.00 0.00 0.00 4.30
2613 2881 2.840753 GCTTGTTGGTGGAGGGGGA 61.841 63.158 0.00 0.00 0.00 4.81
2614 2882 2.283173 GCTTGTTGGTGGAGGGGG 60.283 66.667 0.00 0.00 0.00 5.40
2615 2883 0.967380 GATGCTTGTTGGTGGAGGGG 60.967 60.000 0.00 0.00 0.00 4.79
2616 2884 0.251297 TGATGCTTGTTGGTGGAGGG 60.251 55.000 0.00 0.00 0.00 4.30
2617 2885 1.619654 TTGATGCTTGTTGGTGGAGG 58.380 50.000 0.00 0.00 0.00 4.30
2618 2886 2.165030 GGATTGATGCTTGTTGGTGGAG 59.835 50.000 0.00 0.00 0.00 3.86
2619 2887 2.170166 GGATTGATGCTTGTTGGTGGA 58.830 47.619 0.00 0.00 0.00 4.02
2620 2888 1.894466 TGGATTGATGCTTGTTGGTGG 59.106 47.619 0.00 0.00 0.00 4.61
2621 2889 3.517602 CATGGATTGATGCTTGTTGGTG 58.482 45.455 0.00 0.00 0.00 4.17
2622 2890 2.498481 CCATGGATTGATGCTTGTTGGT 59.502 45.455 5.56 0.00 0.00 3.67
2623 2891 2.159014 CCCATGGATTGATGCTTGTTGG 60.159 50.000 15.22 0.00 0.00 3.77
2624 2892 2.498481 ACCCATGGATTGATGCTTGTTG 59.502 45.455 15.22 0.00 0.00 3.33
2625 2893 2.823959 ACCCATGGATTGATGCTTGTT 58.176 42.857 15.22 0.00 0.00 2.83
2626 2894 2.498481 CAACCCATGGATTGATGCTTGT 59.502 45.455 14.35 0.00 0.00 3.16
2627 2895 2.740580 GCAACCCATGGATTGATGCTTG 60.741 50.000 24.00 8.28 0.00 4.01
2628 2896 1.483415 GCAACCCATGGATTGATGCTT 59.517 47.619 24.00 0.00 0.00 3.91
2629 2897 1.117150 GCAACCCATGGATTGATGCT 58.883 50.000 24.00 0.00 0.00 3.79
2630 2898 1.068127 GAGCAACCCATGGATTGATGC 59.932 52.381 24.00 17.06 32.66 3.91
2631 2899 1.335810 CGAGCAACCCATGGATTGATG 59.664 52.381 24.00 7.55 0.00 3.07
2632 2900 1.212688 TCGAGCAACCCATGGATTGAT 59.787 47.619 24.00 17.69 0.00 2.57
2633 2901 0.617935 TCGAGCAACCCATGGATTGA 59.382 50.000 24.00 0.00 0.00 2.57
2634 2902 1.462616 TTCGAGCAACCCATGGATTG 58.537 50.000 15.24 15.24 0.00 2.67
2635 2903 1.818674 GTTTCGAGCAACCCATGGATT 59.181 47.619 15.22 0.00 0.00 3.01
2636 2904 1.271871 TGTTTCGAGCAACCCATGGAT 60.272 47.619 15.22 0.00 0.00 3.41
2637 2905 0.109532 TGTTTCGAGCAACCCATGGA 59.890 50.000 15.22 0.00 0.00 3.41
2638 2906 0.958091 TTGTTTCGAGCAACCCATGG 59.042 50.000 4.14 4.14 0.00 3.66
2639 2907 1.662876 CGTTGTTTCGAGCAACCCATG 60.663 52.381 21.27 9.68 42.12 3.66
2640 2908 0.591170 CGTTGTTTCGAGCAACCCAT 59.409 50.000 21.27 0.00 42.12 4.00
2641 2909 0.462225 TCGTTGTTTCGAGCAACCCA 60.462 50.000 21.27 10.98 42.12 4.51
2642 2910 2.313267 TCGTTGTTTCGAGCAACCC 58.687 52.632 21.27 6.08 42.12 4.11
2661 2929 3.440522 GGACTCTTGTTAATTGGAGGCAC 59.559 47.826 8.79 0.00 35.70 5.01
2662 2930 3.561313 GGGACTCTTGTTAATTGGAGGCA 60.561 47.826 8.79 0.00 35.70 4.75
2663 2931 3.017442 GGGACTCTTGTTAATTGGAGGC 58.983 50.000 0.00 0.00 33.44 4.70
2664 2932 4.265073 CTGGGACTCTTGTTAATTGGAGG 58.735 47.826 0.00 0.00 0.00 4.30
2665 2933 4.265073 CCTGGGACTCTTGTTAATTGGAG 58.735 47.826 0.00 0.00 0.00 3.86
2666 2934 3.010138 CCCTGGGACTCTTGTTAATTGGA 59.990 47.826 7.01 0.00 0.00 3.53
2667 2935 3.356290 CCCTGGGACTCTTGTTAATTGG 58.644 50.000 7.01 0.00 0.00 3.16
2668 2936 3.356290 CCCCTGGGACTCTTGTTAATTG 58.644 50.000 16.20 0.00 37.50 2.32
2669 2937 3.739401 CCCCTGGGACTCTTGTTAATT 57.261 47.619 16.20 0.00 37.50 1.40
2670 2938 2.498443 TCCCCCTGGGACTCTTGTTAAT 60.498 50.000 16.20 0.00 46.17 1.40
2671 2939 1.132332 TCCCCCTGGGACTCTTGTTAA 60.132 52.381 16.20 0.00 46.17 2.01
2672 2940 0.494551 TCCCCCTGGGACTCTTGTTA 59.505 55.000 16.20 0.00 46.17 2.41
2673 2941 0.842467 CTCCCCCTGGGACTCTTGTT 60.842 60.000 16.20 0.00 46.17 2.83
2674 2942 1.229658 CTCCCCCTGGGACTCTTGT 60.230 63.158 16.20 0.00 46.17 3.16
2675 2943 0.842467 AACTCCCCCTGGGACTCTTG 60.842 60.000 16.20 0.00 46.17 3.02
2676 2944 0.103876 AAACTCCCCCTGGGACTCTT 60.104 55.000 16.20 0.00 46.17 2.85
2677 2945 0.103876 AAAACTCCCCCTGGGACTCT 60.104 55.000 16.20 0.00 46.17 3.24
2678 2946 0.038310 CAAAACTCCCCCTGGGACTC 59.962 60.000 16.20 0.00 46.17 3.36
2679 2947 0.701310 ACAAAACTCCCCCTGGGACT 60.701 55.000 16.20 0.00 46.17 3.85
2680 2948 0.187606 AACAAAACTCCCCCTGGGAC 59.812 55.000 16.20 0.00 46.17 4.46
2682 2950 1.047801 CAAACAAAACTCCCCCTGGG 58.952 55.000 5.50 5.50 46.11 4.45
2683 2951 2.080654 TCAAACAAAACTCCCCCTGG 57.919 50.000 0.00 0.00 0.00 4.45
2684 2952 4.687901 ATTTCAAACAAAACTCCCCCTG 57.312 40.909 0.00 0.00 0.00 4.45
2685 2953 7.387265 AATAATTTCAAACAAAACTCCCCCT 57.613 32.000 0.00 0.00 0.00 4.79
2686 2954 8.349245 CAAAATAATTTCAAACAAAACTCCCCC 58.651 33.333 0.00 0.00 0.00 5.40
2687 2955 9.114952 TCAAAATAATTTCAAACAAAACTCCCC 57.885 29.630 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.