Multiple sequence alignment - TraesCS1A01G160800

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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 TraesCS1A01G160800 chr1A 100.000 4891 0 0 1 4891 289328903 289333793 0.000000e+00 9033.0
1 TraesCS1A01G160800 chr1B 90.180 1833 95 42 885 2652 322398032 322399844 0.000000e+00 2309.0
2 TraesCS1A01G160800 chr1B 94.300 1228 62 7 2765 3989 322400108 322401330 0.000000e+00 1873.0
3 TraesCS1A01G160800 chr1B 86.957 506 44 7 4197 4681 322401660 322402164 2.570000e-152 549.0
4 TraesCS1A01G160800 chr1B 92.308 143 5 3 743 880 322392480 322392621 1.070000e-46 198.0
5 TraesCS1A01G160800 chr1B 90.977 133 12 0 4759 4891 322402514 322402646 3.890000e-41 180.0
6 TraesCS1A01G160800 chr1B 91.346 104 7 2 4055 4156 322401331 322401434 1.840000e-29 141.0
7 TraesCS1A01G160800 chr1B 91.111 45 4 0 4155 4199 322401453 322401497 1.470000e-05 62.1
8 TraesCS1A01G160800 chr1D 93.467 1546 73 14 2765 4294 222901209 222902742 0.000000e+00 2270.0
9 TraesCS1A01G160800 chr1D 92.284 972 46 12 1224 2193 222899588 222900532 0.000000e+00 1352.0
10 TraesCS1A01G160800 chr1D 92.692 520 19 8 670 1185 222898852 222899356 0.000000e+00 732.0
11 TraesCS1A01G160800 chr1D 85.413 617 47 22 2178 2768 222900545 222901144 7.000000e-168 601.0
12 TraesCS1A01G160800 chr5B 95.645 643 18 6 1 633 61079295 61079937 0.000000e+00 1024.0
13 TraesCS1A01G160800 chr5B 73.626 637 129 26 4222 4827 482979266 482978638 4.960000e-50 209.0
14 TraesCS1A01G160800 chr7B 75.253 396 71 21 4214 4592 198943804 198944189 3.920000e-36 163.0
15 TraesCS1A01G160800 chr5D 74.924 327 74 8 4285 4604 23873690 23874015 5.100000e-30 143.0
16 TraesCS1A01G160800 chr4A 75.909 220 42 10 4619 4833 650411301 650411514 8.660000e-18 102.0
17 TraesCS1A01G160800 chr3B 74.468 188 37 10 4617 4799 637341107 637341288 2.440000e-08 71.3
18 TraesCS1A01G160800 chr4D 73.632 201 43 10 4386 4580 25425829 25426025 8.780000e-08 69.4
19 TraesCS1A01G160800 chr3D 93.333 45 3 0 4617 4661 478106452 478106496 3.160000e-07 67.6


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 TraesCS1A01G160800 chr1A 289328903 289333793 4890 False 9033.00 9033 100.000000 1 4891 1 chr1A.!!$F1 4890
1 TraesCS1A01G160800 chr1B 322398032 322402646 4614 False 852.35 2309 90.811833 885 4891 6 chr1B.!!$F2 4006
2 TraesCS1A01G160800 chr1D 222898852 222902742 3890 False 1238.75 2270 90.964000 670 4294 4 chr1D.!!$F1 3624
3 TraesCS1A01G160800 chr5B 61079295 61079937 642 False 1024.00 1024 95.645000 1 633 1 chr5B.!!$F1 632
4 TraesCS1A01G160800 chr5B 482978638 482979266 628 True 209.00 209 73.626000 4222 4827 1 chr5B.!!$R1 605

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
880 895 0.027848 TCAAACCGCCGAACGTTTTC 59.972 50.0 0.46 0.0 33.74 2.29 F
1492 1734 0.108520 TTGAGGTAATGCGACGGGAC 60.109 55.0 0.00 0.0 0.00 4.46 F
2407 2704 0.179043 TTGTCGTGCCCTGCAGTTTA 60.179 50.0 13.81 0.0 40.08 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 2523 0.250338 GCAACTTCAACTCCTCCCGT 60.250 55.0 0.00 0.0 0.00 5.28 R
3120 3585 0.804989 CGCCATTCACAAGAGAACCC 59.195 55.0 0.00 0.0 0.00 4.11 R
3991 4458 0.656785 GCACGTTTACGAACACCCAA 59.343 50.0 9.53 0.0 43.02 4.12 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
28 29 5.407407 TGAAGAGATCAAGTACCAACCTC 57.593 43.478 0.00 0.00 34.30 3.85
111 112 7.262772 CACCGGTGACTAACTCTTTCATTATA 58.737 38.462 31.31 0.00 0.00 0.98
112 113 7.222224 CACCGGTGACTAACTCTTTCATTATAC 59.778 40.741 31.31 0.00 0.00 1.47
113 114 7.123847 ACCGGTGACTAACTCTTTCATTATACT 59.876 37.037 6.12 0.00 0.00 2.12
116 117 9.303537 GGTGACTAACTCTTTCATTATACTGAC 57.696 37.037 0.00 0.00 0.00 3.51
118 119 8.188799 TGACTAACTCTTTCATTATACTGACGG 58.811 37.037 0.00 0.00 0.00 4.79
119 120 8.289939 ACTAACTCTTTCATTATACTGACGGA 57.710 34.615 0.00 0.00 0.00 4.69
141 151 2.747989 GGAGGAAGGTTGGACGAAAATC 59.252 50.000 0.00 0.00 0.00 2.17
187 197 0.251832 AAGAAGAGTGGGAGGAGCGA 60.252 55.000 0.00 0.00 0.00 4.93
250 260 5.554636 CGAGACAAACAAAGTATGATGAGC 58.445 41.667 0.00 0.00 0.00 4.26
286 296 1.001974 TGTTAGAGCTGACCGCATGTT 59.998 47.619 0.00 0.00 42.61 2.71
366 376 6.811665 CGGACTGTCAGACAATTTGTAATCTA 59.188 38.462 6.91 0.00 0.00 1.98
391 401 1.612395 GGCAGAGGAGGACAGGTCTG 61.612 65.000 0.00 0.00 39.60 3.51
456 466 8.992073 ACAAATTTGCAGGAATTTAGATTGAAC 58.008 29.630 18.12 0.00 37.17 3.18
505 515 0.255890 TCATCTTTGTGCTAGGGGGC 59.744 55.000 0.00 0.00 0.00 5.80
506 516 0.034186 CATCTTTGTGCTAGGGGGCA 60.034 55.000 0.00 0.00 40.15 5.36
507 517 0.929244 ATCTTTGTGCTAGGGGGCAT 59.071 50.000 0.00 0.00 44.34 4.40
626 637 1.075536 AGGAGGGCGGTTCTCAAAAAT 59.924 47.619 0.00 0.00 33.18 1.82
629 640 3.699538 GGAGGGCGGTTCTCAAAAATAAT 59.300 43.478 0.00 0.00 33.18 1.28
633 644 7.229907 GGAGGGCGGTTCTCAAAAATAATAATA 59.770 37.037 0.00 0.00 33.18 0.98
634 645 8.706322 AGGGCGGTTCTCAAAAATAATAATAT 57.294 30.769 0.00 0.00 0.00 1.28
635 646 9.802039 AGGGCGGTTCTCAAAAATAATAATATA 57.198 29.630 0.00 0.00 0.00 0.86
651 662 7.510549 AATAATATAGGATTGGTGTGTGTGC 57.489 36.000 0.00 0.00 0.00 4.57
652 663 2.877097 ATAGGATTGGTGTGTGTGCA 57.123 45.000 0.00 0.00 0.00 4.57
653 664 1.890876 TAGGATTGGTGTGTGTGCAC 58.109 50.000 10.75 10.75 45.44 4.57
664 675 2.337583 GTGTGTGCACGTCTATGATGT 58.662 47.619 13.13 0.00 35.75 3.06
691 702 8.398665 GCTCAAGAACTTTCTCTTCTAAAAACA 58.601 33.333 0.00 0.00 36.28 2.83
694 705 9.374960 CAAGAACTTTCTCTTCTAAAAACATCG 57.625 33.333 0.00 0.00 36.28 3.84
735 746 8.292448 TCTCTTCTAAAAACAATGAATGTCAGC 58.708 33.333 0.00 0.00 42.99 4.26
738 749 9.252962 CTTCTAAAAACAATGAATGTCAGCTTT 57.747 29.630 0.00 0.00 42.99 3.51
739 750 8.801715 TCTAAAAACAATGAATGTCAGCTTTC 57.198 30.769 0.00 0.00 42.99 2.62
741 752 7.473027 AAAAACAATGAATGTCAGCTTTCAG 57.527 32.000 4.95 0.00 42.99 3.02
742 753 6.395426 AAACAATGAATGTCAGCTTTCAGA 57.605 33.333 4.95 0.00 42.99 3.27
743 754 6.585695 AACAATGAATGTCAGCTTTCAGAT 57.414 33.333 4.95 0.00 42.99 2.90
832 843 1.952296 GGCCAGCTCAAACCATATCTG 59.048 52.381 0.00 0.00 0.00 2.90
854 865 6.017440 TCTGGAACCACTTTAGAAAAATCACG 60.017 38.462 0.00 0.00 0.00 4.35
855 866 5.009210 TGGAACCACTTTAGAAAAATCACGG 59.991 40.000 0.00 0.00 0.00 4.94
867 878 0.887933 AATCACGGGCACATCAAACC 59.112 50.000 0.00 0.00 0.00 3.27
880 895 0.027848 TCAAACCGCCGAACGTTTTC 59.972 50.000 0.46 0.00 33.74 2.29
881 896 0.931202 CAAACCGCCGAACGTTTTCC 60.931 55.000 0.46 0.00 33.74 3.13
882 897 1.096967 AAACCGCCGAACGTTTTCCT 61.097 50.000 0.46 0.00 41.42 3.36
945 960 3.222354 GACGGAGGAGTGCCACGTT 62.222 63.158 2.95 0.00 45.72 3.99
946 961 2.030562 CGGAGGAGTGCCACGTTT 59.969 61.111 0.00 0.00 36.29 3.60
947 962 2.027625 CGGAGGAGTGCCACGTTTC 61.028 63.158 0.00 0.00 36.29 2.78
948 963 1.371558 GGAGGAGTGCCACGTTTCT 59.628 57.895 0.00 0.00 36.29 2.52
949 964 0.670854 GGAGGAGTGCCACGTTTCTC 60.671 60.000 0.00 0.00 36.29 2.87
950 965 0.318762 GAGGAGTGCCACGTTTCTCT 59.681 55.000 0.00 0.00 36.29 3.10
1063 1094 0.178990 GCCTCCTCTCTCTCCTCTCC 60.179 65.000 0.00 0.00 0.00 3.71
1104 1135 2.903855 CTGCGCCATCATCCACCC 60.904 66.667 4.18 0.00 0.00 4.61
1304 1537 1.514678 CCTCTGCGAGATCGAGGAGG 61.515 65.000 20.79 20.79 45.67 4.30
1305 1538 2.128853 CTCTGCGAGATCGAGGAGGC 62.129 65.000 6.39 0.00 43.02 4.70
1306 1539 3.534970 CTGCGAGATCGAGGAGGCG 62.535 68.421 6.39 0.00 43.02 5.52
1307 1540 4.335584 GCGAGATCGAGGAGGCGG 62.336 72.222 6.39 0.00 43.02 6.13
1308 1541 2.592001 CGAGATCGAGGAGGCGGA 60.592 66.667 0.00 0.00 43.02 5.54
1309 1542 2.899044 CGAGATCGAGGAGGCGGAC 61.899 68.421 0.00 0.00 43.02 4.79
1310 1543 2.899044 GAGATCGAGGAGGCGGACG 61.899 68.421 0.00 0.00 0.00 4.79
1311 1544 4.632458 GATCGAGGAGGCGGACGC 62.632 72.222 8.39 8.39 41.06 5.19
1474 1716 2.223203 CGTCGCTATCAAGTACGGAGTT 60.223 50.000 0.00 0.00 37.78 3.01
1492 1734 0.108520 TTGAGGTAATGCGACGGGAC 60.109 55.000 0.00 0.00 0.00 4.46
1505 1747 0.547553 ACGGGACTACTCCTCTCTCC 59.452 60.000 0.00 0.00 36.68 3.71
1636 1887 8.196802 TGACGATAATAAGGTGTTTGAATGAG 57.803 34.615 0.00 0.00 0.00 2.90
1714 1965 1.421268 ACTGACCTCCAGATGTTTGCA 59.579 47.619 0.00 0.00 45.78 4.08
1735 1986 1.741401 CAAGACGCTGCGGATTCCA 60.741 57.895 26.95 0.00 0.00 3.53
1837 2088 7.231467 AGTATGTTGCTTCCCTTTTTCTTCTA 58.769 34.615 0.00 0.00 0.00 2.10
1934 2185 6.020599 CAGCTTAGTGTTGTGTGTATCGATAC 60.021 42.308 25.48 25.48 0.00 2.24
1937 2188 5.899120 AGTGTTGTGTGTATCGATACTCT 57.101 39.130 30.20 12.61 34.41 3.24
1960 2211 8.217131 TCTAGAATTGTTACTACATCGCTACA 57.783 34.615 0.00 0.00 33.44 2.74
2078 2330 2.503895 AAGTGAAGCTGGAATGGGAG 57.496 50.000 0.00 0.00 0.00 4.30
2099 2351 5.037383 AGTATGGTCTCGTAGTCTCATGA 57.963 43.478 0.00 0.00 0.00 3.07
2102 2354 5.860941 ATGGTCTCGTAGTCTCATGAAAT 57.139 39.130 0.00 0.00 0.00 2.17
2107 2359 6.913673 GGTCTCGTAGTCTCATGAAATAACTC 59.086 42.308 0.00 0.00 0.00 3.01
2116 2368 6.258947 GTCTCATGAAATAACTCCTTAGGCAC 59.741 42.308 0.00 0.00 0.00 5.01
2152 2404 9.355916 AGCCAGAATTATTACCTTATTTTCTCC 57.644 33.333 0.00 0.00 0.00 3.71
2165 2417 6.768381 CCTTATTTTCTCCTAACCATGTCTCC 59.232 42.308 0.00 0.00 0.00 3.71
2243 2523 5.854866 GCATGCTATAAGTCGTATCACGTAA 59.145 40.000 11.37 0.00 43.14 3.18
2245 2525 5.434706 TGCTATAAGTCGTATCACGTAACG 58.565 41.667 10.10 10.10 43.14 3.18
2255 2535 0.599558 TCACGTAACGGGAGGAGTTG 59.400 55.000 0.00 0.00 32.99 3.16
2262 2542 0.250338 ACGGGAGGAGTTGAAGTTGC 60.250 55.000 0.00 0.00 0.00 4.17
2339 2619 6.183360 GGCGGTTACATAACTTCGGAATTTTA 60.183 38.462 0.00 0.00 36.47 1.52
2352 2632 9.319143 ACTTCGGAATTTTAGATTCTGACTATG 57.681 33.333 6.52 2.05 41.54 2.23
2353 2633 9.534565 CTTCGGAATTTTAGATTCTGACTATGA 57.465 33.333 6.52 0.00 41.54 2.15
2354 2634 9.884636 TTCGGAATTTTAGATTCTGACTATGAA 57.115 29.630 6.52 0.00 41.54 2.57
2366 2646 6.505048 TCTGACTATGAATGGTTGGATGAT 57.495 37.500 0.00 0.00 0.00 2.45
2372 2652 9.071276 GACTATGAATGGTTGGATGATTACATT 57.929 33.333 0.00 0.00 36.82 2.71
2401 2698 0.179163 GCTAAATTGTCGTGCCCTGC 60.179 55.000 0.00 0.00 0.00 4.85
2406 2703 0.823356 ATTGTCGTGCCCTGCAGTTT 60.823 50.000 13.81 0.00 40.08 2.66
2407 2704 0.179043 TTGTCGTGCCCTGCAGTTTA 60.179 50.000 13.81 0.00 40.08 2.01
2414 2711 4.104776 CGTGCCCTGCAGTTTATAAATTG 58.895 43.478 13.81 14.56 40.08 2.32
2415 2712 4.380444 CGTGCCCTGCAGTTTATAAATTGT 60.380 41.667 18.56 0.00 40.08 2.71
2478 2775 2.529632 AGGCAGGGAAAATGGAGAAAC 58.470 47.619 0.00 0.00 0.00 2.78
2509 2817 3.665190 ACGAACTCTCAAACCCTCAATC 58.335 45.455 0.00 0.00 0.00 2.67
2523 2831 4.202461 ACCCTCAATCTTCTTGTGCTTACA 60.202 41.667 0.00 0.00 0.00 2.41
2537 2845 2.224646 TGCTTACACATACTGGCCACAA 60.225 45.455 0.00 0.00 0.00 3.33
2559 2867 6.127196 ACAATTTTCTCCTTTGTAACAAGGCA 60.127 34.615 0.00 0.00 36.15 4.75
2570 2878 6.985188 TTGTAACAAGGCATGTAGATTCTC 57.015 37.500 0.00 0.00 42.99 2.87
2585 2893 7.378966 TGTAGATTCTCGTCACTTTCTGAAAT 58.621 34.615 2.88 0.00 0.00 2.17
2611 2919 7.935338 AAGTCAACAAAAATAGCATTCACTG 57.065 32.000 0.00 0.00 0.00 3.66
2616 2924 6.017400 ACAAAAATAGCATTCACTGTGAGG 57.983 37.500 10.77 8.65 0.00 3.86
2617 2925 5.769662 ACAAAAATAGCATTCACTGTGAGGA 59.230 36.000 10.77 0.00 0.00 3.71
2624 2932 3.118629 GCATTCACTGTGAGGATGAGGTA 60.119 47.826 20.95 1.81 0.00 3.08
2635 2943 6.386927 TGTGAGGATGAGGTACTTTTGGATAT 59.613 38.462 0.00 0.00 41.55 1.63
2646 2954 9.760077 AGGTACTTTTGGATATATTTGACTACG 57.240 33.333 0.00 0.00 27.25 3.51
2652 2960 5.538118 TGGATATATTTGACTACGGCAGTG 58.462 41.667 0.00 0.00 37.72 3.66
2654 2962 5.989777 GGATATATTTGACTACGGCAGTGTT 59.010 40.000 0.00 0.00 37.72 3.32
2655 2963 6.482308 GGATATATTTGACTACGGCAGTGTTT 59.518 38.462 0.00 0.00 37.72 2.83
2656 2964 7.012044 GGATATATTTGACTACGGCAGTGTTTT 59.988 37.037 0.00 0.00 37.72 2.43
2657 2965 3.684103 TTTGACTACGGCAGTGTTTTG 57.316 42.857 0.00 0.00 37.72 2.44
2668 2976 4.981806 GCAGTGTTTTGCCCATAATCTA 57.018 40.909 0.00 0.00 38.13 1.98
2669 2977 5.520376 GCAGTGTTTTGCCCATAATCTAT 57.480 39.130 0.00 0.00 38.13 1.98
2670 2978 5.906073 GCAGTGTTTTGCCCATAATCTATT 58.094 37.500 0.00 0.00 38.13 1.73
2671 2979 7.038154 GCAGTGTTTTGCCCATAATCTATTA 57.962 36.000 0.00 0.00 38.13 0.98
2675 3072 9.338622 AGTGTTTTGCCCATAATCTATTACTAC 57.661 33.333 0.00 0.00 0.00 2.73
2681 3078 9.860650 TTGCCCATAATCTATTACTACATGTTT 57.139 29.630 2.30 0.00 0.00 2.83
2720 3117 2.359900 ACTTGGGATCGCAAATGACTC 58.640 47.619 23.57 0.00 0.00 3.36
2721 3118 2.026822 ACTTGGGATCGCAAATGACTCT 60.027 45.455 23.57 0.00 0.00 3.24
2724 3121 2.290260 TGGGATCGCAAATGACTCTTGT 60.290 45.455 10.47 0.00 0.00 3.16
2741 3138 7.041098 TGACTCTTGTTTTCTGCCTTTTAGATC 60.041 37.037 0.00 0.00 0.00 2.75
2761 3158 6.773638 AGATCTTACAACACTTCATGAACCT 58.226 36.000 3.38 0.00 0.00 3.50
2768 3165 6.827727 ACAACACTTCATGAACCTACTACTT 58.172 36.000 3.38 0.00 0.00 2.24
2769 3166 6.706270 ACAACACTTCATGAACCTACTACTTG 59.294 38.462 3.38 1.18 0.00 3.16
2772 3169 6.210784 ACACTTCATGAACCTACTACTTGCTA 59.789 38.462 3.38 0.00 0.00 3.49
2778 3175 5.464168 TGAACCTACTACTTGCTACGTTTC 58.536 41.667 0.00 0.00 0.00 2.78
2780 3177 5.056894 ACCTACTACTTGCTACGTTTCTG 57.943 43.478 0.00 0.00 0.00 3.02
2781 3178 4.522022 ACCTACTACTTGCTACGTTTCTGT 59.478 41.667 0.00 0.00 0.00 3.41
2783 3180 5.572126 CCTACTACTTGCTACGTTTCTGTTC 59.428 44.000 0.00 0.00 0.00 3.18
2784 3181 3.979495 ACTACTTGCTACGTTTCTGTTCG 59.021 43.478 0.00 0.00 0.00 3.95
2786 3183 3.968649 ACTTGCTACGTTTCTGTTCGTA 58.031 40.909 0.00 0.00 40.70 3.43
2787 3184 4.553323 ACTTGCTACGTTTCTGTTCGTAT 58.447 39.130 0.00 0.00 40.76 3.06
2788 3185 4.620184 ACTTGCTACGTTTCTGTTCGTATC 59.380 41.667 0.00 0.00 40.76 2.24
2789 3186 4.163458 TGCTACGTTTCTGTTCGTATCA 57.837 40.909 0.00 0.00 40.76 2.15
2790 3187 4.740268 TGCTACGTTTCTGTTCGTATCAT 58.260 39.130 0.00 0.00 40.76 2.45
2792 3189 6.324042 TGCTACGTTTCTGTTCGTATCATTA 58.676 36.000 0.00 0.00 40.76 1.90
2793 3190 6.252015 TGCTACGTTTCTGTTCGTATCATTAC 59.748 38.462 0.00 0.00 40.76 1.89
2794 3191 6.252015 GCTACGTTTCTGTTCGTATCATTACA 59.748 38.462 0.00 0.00 40.76 2.41
2892 3357 5.698089 GCGTCTTCATGATGATCTATTGGAA 59.302 40.000 13.82 0.00 33.63 3.53
2922 3387 2.014128 CGAACACCAAGACACAAGGTT 58.986 47.619 0.00 0.00 32.15 3.50
2991 3456 2.875296 CCAAAGAGGGATCCAACACAA 58.125 47.619 15.23 0.00 0.00 3.33
3006 3471 2.775890 ACACAAGAAGGCACTGAGATG 58.224 47.619 0.00 0.00 40.86 2.90
3007 3472 1.467734 CACAAGAAGGCACTGAGATGC 59.532 52.381 0.00 0.00 45.34 3.91
3045 3510 4.452114 GGCAAATCAATTTCCTTGGTTGAC 59.548 41.667 0.00 0.00 37.18 3.18
3051 3516 0.882927 TTTCCTTGGTTGACGAGCCG 60.883 55.000 0.00 0.00 0.00 5.52
3120 3585 1.915141 AACCCAGAAGCCAGACAATG 58.085 50.000 0.00 0.00 0.00 2.82
3159 3624 3.221771 CGAGTCTGAGGAGAATGGAGAT 58.778 50.000 0.00 0.00 0.00 2.75
3162 3627 3.037549 GTCTGAGGAGAATGGAGATGGT 58.962 50.000 0.00 0.00 0.00 3.55
3172 3637 0.776810 TGGAGATGGTGAAAGGCCAA 59.223 50.000 5.01 0.00 39.72 4.52
3186 3651 2.595095 CCAATAAGGAGGCGCCCA 59.405 61.111 26.15 3.43 41.22 5.36
3601 4066 2.576191 TGGCTATATCCCATGTAAGCCC 59.424 50.000 8.57 0.00 40.18 5.19
3749 4215 1.547372 GGGTAGAGGCGTTACTTGTCA 59.453 52.381 2.36 0.00 0.00 3.58
3802 4268 4.521256 GCCTTGGGTATTCTTTTGTACACA 59.479 41.667 0.00 0.00 32.69 3.72
3829 4295 8.742125 TTGGAGATAATGTAGGATGAATAGGT 57.258 34.615 0.00 0.00 0.00 3.08
3991 4458 3.969287 TGCAGCTCATTTCTCTACAGT 57.031 42.857 0.00 0.00 0.00 3.55
4021 4488 0.320073 TAAACGTGCTGGTTCGGAGG 60.320 55.000 0.00 0.00 0.00 4.30
4028 4495 1.592223 CTGGTTCGGAGGTCCTGTC 59.408 63.158 0.00 0.00 0.00 3.51
4049 4516 0.465705 GTGATGCGGGAATCTCCTCA 59.534 55.000 0.00 0.00 36.57 3.86
4090 4557 6.815089 TGTGAAGTTCATGCAAAATTAGGTT 58.185 32.000 9.18 0.00 0.00 3.50
4114 4581 7.936950 TGAAAACATTCATAATGCGTTTCAA 57.063 28.000 19.44 10.36 44.51 2.69
4116 4583 8.986847 TGAAAACATTCATAATGCGTTTCAATT 58.013 25.926 19.44 0.00 44.51 2.32
4117 4584 9.810231 GAAAACATTCATAATGCGTTTCAATTT 57.190 25.926 16.65 2.01 41.34 1.82
4188 4727 1.094785 AAAGATACACCGCATGGCAC 58.905 50.000 0.00 0.00 39.70 5.01
4331 5010 0.319728 GAGCAGAGAGACAAGTGGCA 59.680 55.000 0.00 0.00 0.00 4.92
4336 5015 1.342819 AGAGAGACAAGTGGCACTCAC 59.657 52.381 22.31 14.62 42.28 3.51
4349 5031 0.824109 CACTCACCCCGAGCATAGAA 59.176 55.000 0.00 0.00 46.63 2.10
4380 5062 2.509964 ACTAAACCCATCAAGCCTAGGG 59.490 50.000 11.72 0.00 46.96 3.53
4404 5086 2.126071 CGAACCGGCATGACGTCT 60.126 61.111 21.63 5.88 0.00 4.18
4413 5095 2.223595 CGGCATGACGTCTAACATCTCT 60.224 50.000 14.35 0.00 0.00 3.10
4425 5107 5.351740 GTCTAACATCTCTAAAGCCAACACC 59.648 44.000 0.00 0.00 0.00 4.16
4446 5128 2.510238 GACGCAGCGAGGAAGCAT 60.510 61.111 24.65 0.00 40.15 3.79
4487 5171 1.773052 AGTGATGCTATGAGGCACCAT 59.227 47.619 0.00 0.00 45.36 3.55
4495 5179 0.107456 ATGAGGCACCATCATCCGTC 59.893 55.000 0.00 0.00 31.76 4.79
4497 5181 1.690219 GAGGCACCATCATCCGTCCT 61.690 60.000 0.00 0.00 0.00 3.85
4514 5198 3.006537 CGTCCTGAAGAACCAGACCTAAA 59.993 47.826 0.00 0.00 36.29 1.85
4530 5214 2.565391 CCTAAAATTTCCCCCGTTGCTT 59.435 45.455 0.00 0.00 0.00 3.91
4551 5235 7.564793 TGCTTAAAGAGGAGCATAGATAAACA 58.435 34.615 0.00 0.00 43.46 2.83
4566 5250 1.398692 AAACACCATGACAACGCCTT 58.601 45.000 0.00 0.00 0.00 4.35
4674 5379 3.008049 TCAAGGTCCAGAGGTAAGAAAGC 59.992 47.826 0.00 0.00 0.00 3.51
4675 5380 1.909986 AGGTCCAGAGGTAAGAAAGCC 59.090 52.381 0.00 0.00 0.00 4.35
4681 5386 2.501723 CAGAGGTAAGAAAGCCAGCCTA 59.498 50.000 0.00 0.00 0.00 3.93
4703 5408 2.046938 GTCGAGACCACCACCTCAA 58.953 57.895 0.00 0.00 0.00 3.02
4706 5411 0.898320 CGAGACCACCACCTCAAGAT 59.102 55.000 0.00 0.00 0.00 2.40
4712 5418 1.625228 CCACCACCTCAAGATAGGGGA 60.625 57.143 0.00 0.00 43.35 4.81
4749 5455 4.764771 CATGGGGTGGCACCTGGG 62.765 72.222 33.87 18.11 38.64 4.45
4804 5781 3.583054 CATGAAGGTGGACATGGCT 57.417 52.632 0.00 0.00 39.79 4.75
4805 5782 1.100510 CATGAAGGTGGACATGGCTG 58.899 55.000 0.00 0.00 39.79 4.85
4816 5793 3.329889 ATGGCTGGGAAGGCGACA 61.330 61.111 0.00 0.00 37.15 4.35
4817 5794 2.683465 ATGGCTGGGAAGGCGACAT 61.683 57.895 0.00 0.00 37.15 3.06
4833 5810 2.809119 CGACATAGTAGAGAGTGCCGAT 59.191 50.000 0.00 0.00 0.00 4.18
4838 5815 1.753078 TAGAGAGTGCCGATGCCGT 60.753 57.895 0.00 0.00 36.33 5.68
4870 5847 0.324091 AAGCTGAATGGGAAGGCAGG 60.324 55.000 0.00 0.00 0.00 4.85
4873 5850 0.394899 CTGAATGGGAAGGCAGGTCC 60.395 60.000 0.00 0.00 0.00 4.46
4880 5857 3.672295 GAAGGCAGGTCCGAGCTGG 62.672 68.421 25.10 10.26 43.49 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 2.589157 TTAGTCACCGGTGCTGGGG 61.589 63.158 30.25 5.21 0.00 4.96
111 112 0.178929 AACCTTCCTCCTCCGTCAGT 60.179 55.000 0.00 0.00 0.00 3.41
112 113 0.247736 CAACCTTCCTCCTCCGTCAG 59.752 60.000 0.00 0.00 0.00 3.51
113 114 1.192146 CCAACCTTCCTCCTCCGTCA 61.192 60.000 0.00 0.00 0.00 4.35
116 117 1.597461 GTCCAACCTTCCTCCTCCG 59.403 63.158 0.00 0.00 0.00 4.63
118 119 0.974383 TTCGTCCAACCTTCCTCCTC 59.026 55.000 0.00 0.00 0.00 3.71
119 120 1.430992 TTTCGTCCAACCTTCCTCCT 58.569 50.000 0.00 0.00 0.00 3.69
141 151 3.067106 ACAAACTGCTCCGTCAGTATTG 58.933 45.455 14.79 14.79 45.77 1.90
187 197 2.657237 GTCCCGTGCTACTGCTGT 59.343 61.111 0.66 0.66 40.48 4.40
250 260 5.152623 TCTAACACCAAAGGATCAGTCAG 57.847 43.478 0.00 0.00 0.00 3.51
286 296 0.036199 GCCAAAAGCATTGCATCCCA 60.036 50.000 11.91 0.00 42.97 4.37
366 376 0.252881 TGTCCTCCTCTGCCTTCCAT 60.253 55.000 0.00 0.00 0.00 3.41
456 466 7.042658 GGGATATTAGCACTTCTACGAACAAAG 60.043 40.741 0.00 0.00 0.00 2.77
626 637 8.214364 TGCACACACACCAATCCTATATTATTA 58.786 33.333 0.00 0.00 0.00 0.98
629 640 5.820423 GTGCACACACACCAATCCTATATTA 59.180 40.000 13.17 0.00 46.61 0.98
633 644 2.436417 GTGCACACACACCAATCCTAT 58.564 47.619 13.17 0.00 46.61 2.57
634 645 1.890876 GTGCACACACACCAATCCTA 58.109 50.000 13.17 0.00 46.61 2.94
635 646 2.719376 GTGCACACACACCAATCCT 58.281 52.632 13.17 0.00 46.61 3.24
644 655 2.092681 CACATCATAGACGTGCACACAC 59.907 50.000 18.64 7.22 43.76 3.82
645 656 2.336667 CACATCATAGACGTGCACACA 58.663 47.619 18.64 0.00 0.00 3.72
651 662 3.774066 TCTTGAGCACATCATAGACGTG 58.226 45.455 0.00 0.00 37.89 4.49
652 663 4.081972 AGTTCTTGAGCACATCATAGACGT 60.082 41.667 0.00 0.00 37.89 4.34
653 664 4.428209 AGTTCTTGAGCACATCATAGACG 58.572 43.478 0.00 0.00 37.89 4.18
654 665 6.593382 AGAAAGTTCTTGAGCACATCATAGAC 59.407 38.462 0.00 0.00 37.89 2.59
655 666 6.705302 AGAAAGTTCTTGAGCACATCATAGA 58.295 36.000 0.00 0.00 37.89 1.98
656 667 6.817641 AGAGAAAGTTCTTGAGCACATCATAG 59.182 38.462 0.00 0.00 37.89 2.23
657 668 6.705302 AGAGAAAGTTCTTGAGCACATCATA 58.295 36.000 0.00 0.00 37.89 2.15
658 669 5.558818 AGAGAAAGTTCTTGAGCACATCAT 58.441 37.500 0.00 0.00 37.89 2.45
659 670 4.965814 AGAGAAAGTTCTTGAGCACATCA 58.034 39.130 0.00 0.00 37.73 3.07
660 671 5.700373 AGAAGAGAAAGTTCTTGAGCACATC 59.300 40.000 0.00 0.00 37.53 3.06
661 672 5.619220 AGAAGAGAAAGTTCTTGAGCACAT 58.381 37.500 0.00 0.00 37.53 3.21
662 673 5.028549 AGAAGAGAAAGTTCTTGAGCACA 57.971 39.130 0.00 0.00 37.53 4.57
663 674 7.484035 TTTAGAAGAGAAAGTTCTTGAGCAC 57.516 36.000 0.00 0.00 37.53 4.40
664 675 8.398665 GTTTTTAGAAGAGAAAGTTCTTGAGCA 58.601 33.333 0.00 0.00 37.53 4.26
665 676 8.398665 TGTTTTTAGAAGAGAAAGTTCTTGAGC 58.601 33.333 0.00 0.00 37.53 4.26
668 679 9.374960 CGATGTTTTTAGAAGAGAAAGTTCTTG 57.625 33.333 0.00 0.00 37.53 3.02
669 680 8.560374 CCGATGTTTTTAGAAGAGAAAGTTCTT 58.440 33.333 0.00 0.00 40.02 2.52
670 681 7.715686 ACCGATGTTTTTAGAAGAGAAAGTTCT 59.284 33.333 0.00 0.00 41.00 3.01
671 682 7.862648 ACCGATGTTTTTAGAAGAGAAAGTTC 58.137 34.615 0.00 0.00 0.00 3.01
715 726 8.578308 TGAAAGCTGACATTCATTGTTTTTAG 57.422 30.769 0.00 0.00 39.18 1.85
716 727 8.412456 TCTGAAAGCTGACATTCATTGTTTTTA 58.588 29.630 0.00 0.00 39.18 1.52
717 728 7.267128 TCTGAAAGCTGACATTCATTGTTTTT 58.733 30.769 0.00 0.00 39.18 1.94
718 729 6.808829 TCTGAAAGCTGACATTCATTGTTTT 58.191 32.000 0.00 0.00 39.18 2.43
719 730 6.395426 TCTGAAAGCTGACATTCATTGTTT 57.605 33.333 0.00 0.00 39.18 2.83
730 741 3.365767 GCCAAACTGATCTGAAAGCTGAC 60.366 47.826 6.60 0.00 0.00 3.51
735 746 4.589216 TTTGGCCAAACTGATCTGAAAG 57.411 40.909 27.13 0.00 0.00 2.62
738 749 4.155826 CGTATTTTGGCCAAACTGATCTGA 59.844 41.667 30.43 13.76 0.00 3.27
739 750 4.414852 CGTATTTTGGCCAAACTGATCTG 58.585 43.478 30.43 13.02 0.00 2.90
741 752 3.179048 GCGTATTTTGGCCAAACTGATC 58.821 45.455 30.43 17.18 0.00 2.92
742 753 2.560542 TGCGTATTTTGGCCAAACTGAT 59.439 40.909 30.43 22.36 0.00 2.90
743 754 1.957177 TGCGTATTTTGGCCAAACTGA 59.043 42.857 30.43 16.86 0.00 3.41
832 843 5.458015 CCGTGATTTTTCTAAAGTGGTTCC 58.542 41.667 0.00 0.00 0.00 3.62
854 865 4.114997 CGGCGGTTTGATGTGCCC 62.115 66.667 0.00 0.00 44.71 5.36
855 866 2.622011 TTCGGCGGTTTGATGTGCC 61.622 57.895 7.21 0.00 44.09 5.01
880 895 5.418310 TCAGCTCGAAACTTTGTAAAAGG 57.582 39.130 4.86 0.00 0.00 3.11
881 896 6.412072 CAGTTCAGCTCGAAACTTTGTAAAAG 59.588 38.462 0.00 0.00 34.69 2.27
882 897 6.128117 ACAGTTCAGCTCGAAACTTTGTAAAA 60.128 34.615 0.00 0.00 34.69 1.52
944 959 4.451900 ACGCAGGAAAGAGAAAAGAGAAA 58.548 39.130 0.00 0.00 0.00 2.52
945 960 4.058817 GACGCAGGAAAGAGAAAAGAGAA 58.941 43.478 0.00 0.00 0.00 2.87
946 961 3.555168 GGACGCAGGAAAGAGAAAAGAGA 60.555 47.826 0.00 0.00 0.00 3.10
947 962 2.739379 GGACGCAGGAAAGAGAAAAGAG 59.261 50.000 0.00 0.00 0.00 2.85
948 963 2.550208 GGGACGCAGGAAAGAGAAAAGA 60.550 50.000 0.00 0.00 0.00 2.52
949 964 1.807142 GGGACGCAGGAAAGAGAAAAG 59.193 52.381 0.00 0.00 0.00 2.27
950 965 1.544759 GGGGACGCAGGAAAGAGAAAA 60.545 52.381 0.00 0.00 0.00 2.29
1474 1716 0.968901 AGTCCCGTCGCATTACCTCA 60.969 55.000 0.00 0.00 0.00 3.86
1492 1734 1.478654 GCCCTGAGGAGAGAGGAGTAG 60.479 61.905 0.00 0.00 33.47 2.57
1539 1782 5.397899 CCCTCTGGTATTCCAATGTGTATGT 60.398 44.000 0.00 0.00 43.81 2.29
1657 1908 2.356382 CCTCTTGACGTCAGCTACCTAG 59.644 54.545 19.11 11.38 0.00 3.02
1714 1965 1.291877 GAATCCGCAGCGTCTTGTGT 61.292 55.000 15.05 0.00 0.00 3.72
1735 1986 3.746957 GGATGCCTTCCAGGGAGT 58.253 61.111 0.00 0.00 39.79 3.85
1837 2088 6.476378 AGTAGTCACATGTTAATGCCTTTCT 58.524 36.000 0.00 0.00 37.29 2.52
1934 2185 8.343366 TGTAGCGATGTAGTAACAATTCTAGAG 58.657 37.037 0.00 0.00 39.58 2.43
1937 2188 8.464404 ACTTGTAGCGATGTAGTAACAATTCTA 58.536 33.333 0.00 0.00 39.58 2.10
1969 2220 8.270030 ACTCATTTGATCCTGATACAGATTTGA 58.730 33.333 0.00 0.00 32.44 2.69
1975 2226 7.330454 CGGAATACTCATTTGATCCTGATACAG 59.670 40.741 0.00 0.00 0.00 2.74
2051 2302 5.533903 CCATTCCAGCTTCACTTAATGCTAT 59.466 40.000 0.00 0.00 34.10 2.97
2056 2307 4.018050 ACTCCCATTCCAGCTTCACTTAAT 60.018 41.667 0.00 0.00 0.00 1.40
2078 2330 5.752892 TTCATGAGACTACGAGACCATAC 57.247 43.478 0.00 0.00 0.00 2.39
2099 2351 5.416271 TTCGAGTGCCTAAGGAGTTATTT 57.584 39.130 0.00 0.00 0.00 1.40
2102 2354 4.382685 CCATTTCGAGTGCCTAAGGAGTTA 60.383 45.833 0.00 0.00 0.00 2.24
2107 2359 2.555199 CTCCATTTCGAGTGCCTAAGG 58.445 52.381 0.00 0.00 0.00 2.69
2116 2368 6.073003 GGTAATAATTCTGGCTCCATTTCGAG 60.073 42.308 0.00 0.00 0.00 4.04
2152 2404 9.667107 TTAGTTTCATAAAGGAGACATGGTTAG 57.333 33.333 0.00 0.00 0.00 2.34
2226 2506 3.876914 TCCCGTTACGTGATACGACTTAT 59.123 43.478 17.49 0.00 46.05 1.73
2233 2513 2.019984 ACTCCTCCCGTTACGTGATAC 58.980 52.381 3.52 0.00 0.00 2.24
2243 2523 0.250338 GCAACTTCAACTCCTCCCGT 60.250 55.000 0.00 0.00 0.00 5.28
2245 2525 1.609072 GTTGCAACTTCAACTCCTCCC 59.391 52.381 22.36 0.00 42.15 4.30
2255 2535 6.292328 GGCTACTGAAATTTTGTTGCAACTTC 60.292 38.462 28.61 22.23 34.98 3.01
2271 2551 7.438160 CGTCATACAGATAAATTGGCTACTGAA 59.562 37.037 0.00 0.00 0.00 3.02
2292 2572 4.142403 CCAAACTGATTAATGGCACGTCAT 60.142 41.667 0.00 0.00 0.00 3.06
2339 2619 6.566079 TCCAACCATTCATAGTCAGAATCT 57.434 37.500 0.00 0.00 33.64 2.40
2357 2637 9.986833 GCCAAAATAAAAATGTAATCATCCAAC 57.013 29.630 0.00 0.00 32.56 3.77
2358 2638 9.956640 AGCCAAAATAAAAATGTAATCATCCAA 57.043 25.926 0.00 0.00 32.56 3.53
2372 2652 6.146347 GGCACGACAATTTAGCCAAAATAAAA 59.854 34.615 0.00 0.00 44.59 1.52
2393 2690 5.072040 ACAATTTATAAACTGCAGGGCAC 57.928 39.130 19.93 0.00 33.79 5.01
2414 2711 9.109393 TCAGCTTAACTTATGTTCAATATGGAC 57.891 33.333 0.00 0.00 37.59 4.02
2415 2712 9.109393 GTCAGCTTAACTTATGTTCAATATGGA 57.891 33.333 0.00 0.00 37.59 3.41
2427 2724 5.003804 CCTTGGTGTGTCAGCTTAACTTAT 58.996 41.667 0.00 0.00 32.61 1.73
2478 2775 5.444122 GTTTGAGAGTTCGTCAAAATCTGG 58.556 41.667 0.03 0.00 42.13 3.86
2523 2831 3.763897 GGAGAAAATTGTGGCCAGTATGT 59.236 43.478 5.11 0.00 0.00 2.29
2559 2867 6.516739 TCAGAAAGTGACGAGAATCTACAT 57.483 37.500 0.00 0.00 0.00 2.29
2570 2878 7.406553 TGTTGACTTTATTTCAGAAAGTGACG 58.593 34.615 5.55 0.00 45.02 4.35
2585 2893 9.462174 CAGTGAATGCTATTTTTGTTGACTTTA 57.538 29.630 0.00 0.00 0.00 1.85
2599 2907 4.202336 CCTCATCCTCACAGTGAATGCTAT 60.202 45.833 4.41 0.00 0.00 2.97
2611 2919 4.553330 TCCAAAAGTACCTCATCCTCAC 57.447 45.455 0.00 0.00 0.00 3.51
2624 2932 7.051623 TGCCGTAGTCAAATATATCCAAAAGT 58.948 34.615 0.00 0.00 0.00 2.66
2635 2943 4.319911 GCAAAACACTGCCGTAGTCAAATA 60.320 41.667 0.00 0.00 37.60 1.40
2639 2947 0.941542 GCAAAACACTGCCGTAGTCA 59.058 50.000 0.00 0.00 37.60 3.41
2654 2962 9.860650 AACATGTAGTAATAGATTATGGGCAAA 57.139 29.630 0.00 0.00 0.00 3.68
2655 2963 9.860650 AAACATGTAGTAATAGATTATGGGCAA 57.139 29.630 0.00 0.00 0.00 4.52
2656 2964 9.860650 AAAACATGTAGTAATAGATTATGGGCA 57.139 29.630 0.00 0.00 0.00 5.36
2681 3078 8.970020 TCCCAAGTACGTAGAACAGAATATTAA 58.030 33.333 0.00 0.00 0.00 1.40
2691 3088 2.159338 TGCGATCCCAAGTACGTAGAAC 60.159 50.000 0.00 0.00 0.00 3.01
2695 3092 3.119065 TCATTTGCGATCCCAAGTACGTA 60.119 43.478 0.00 0.00 0.00 3.57
2696 3093 2.006888 CATTTGCGATCCCAAGTACGT 58.993 47.619 0.00 0.00 0.00 3.57
2697 3094 2.030457 GTCATTTGCGATCCCAAGTACG 59.970 50.000 0.00 0.00 0.00 3.67
2698 3095 3.270877 AGTCATTTGCGATCCCAAGTAC 58.729 45.455 0.00 0.00 0.00 2.73
2720 3117 8.567948 TGTAAGATCTAAAAGGCAGAAAACAAG 58.432 33.333 0.00 0.00 0.00 3.16
2721 3118 8.458573 TGTAAGATCTAAAAGGCAGAAAACAA 57.541 30.769 0.00 0.00 0.00 2.83
2724 3121 8.349983 GTGTTGTAAGATCTAAAAGGCAGAAAA 58.650 33.333 0.00 0.00 0.00 2.29
2741 3138 8.088981 AGTAGTAGGTTCATGAAGTGTTGTAAG 58.911 37.037 8.80 0.00 0.00 2.34
2761 3158 5.149273 CGAACAGAAACGTAGCAAGTAGTA 58.851 41.667 0.00 0.00 0.00 1.82
2769 3166 5.697848 AATGATACGAACAGAAACGTAGC 57.302 39.130 0.00 0.00 46.58 3.58
2772 3169 7.591006 ATTGTAATGATACGAACAGAAACGT 57.409 32.000 0.00 0.00 44.72 3.99
2844 3309 5.050490 CGTGGAGTACATTCCCTGAAATAG 58.950 45.833 0.00 0.00 36.35 1.73
2892 3357 2.948979 TCTTGGTGTTCGCAAAACTGAT 59.051 40.909 1.21 0.00 0.00 2.90
2980 3445 2.227388 CAGTGCCTTCTTGTGTTGGATC 59.773 50.000 0.00 0.00 0.00 3.36
2982 3447 1.211703 TCAGTGCCTTCTTGTGTTGGA 59.788 47.619 0.00 0.00 0.00 3.53
2985 3450 3.144506 CATCTCAGTGCCTTCTTGTGTT 58.855 45.455 0.00 0.00 0.00 3.32
3000 3465 5.624159 CCTTTTCCATATACTGGCATCTCA 58.376 41.667 0.00 0.00 45.52 3.27
3006 3471 5.068987 TGATTTGCCTTTTCCATATACTGGC 59.931 40.000 0.00 0.00 45.52 4.85
3027 3492 3.191371 GCTCGTCAACCAAGGAAATTGAT 59.809 43.478 0.00 0.00 41.83 2.57
3045 3510 3.978723 CTCTGCAGACCACGGCTCG 62.979 68.421 13.74 0.00 38.02 5.03
3071 3536 2.356382 TCAAACATGAACGTGTTGGGAC 59.644 45.455 12.20 0.00 41.22 4.46
3120 3585 0.804989 CGCCATTCACAAGAGAACCC 59.195 55.000 0.00 0.00 0.00 4.11
3159 3624 2.291540 CCTCCTTATTGGCCTTTCACCA 60.292 50.000 3.32 0.00 35.26 4.17
3162 3627 1.681780 CGCCTCCTTATTGGCCTTTCA 60.682 52.381 3.32 0.00 45.90 2.69
3172 3637 1.037579 GCTTTTGGGCGCCTCCTTAT 61.038 55.000 28.56 0.00 34.39 1.73
3186 3651 1.941812 CAACTCGCCGTCAGCTTTT 59.058 52.632 0.00 0.00 40.39 2.27
3707 4173 4.126437 CGCCACAACATCTCCAACATATA 58.874 43.478 0.00 0.00 0.00 0.86
3708 4174 2.945008 CGCCACAACATCTCCAACATAT 59.055 45.455 0.00 0.00 0.00 1.78
3829 4295 5.622346 TCACACATACAACATATAGCCCA 57.378 39.130 0.00 0.00 0.00 5.36
3989 4456 1.935199 CACGTTTACGAACACCCAACT 59.065 47.619 9.53 0.00 43.02 3.16
3991 4458 0.656785 GCACGTTTACGAACACCCAA 59.343 50.000 9.53 0.00 43.02 4.12
4021 4488 2.509336 CCGCATCACCGACAGGAC 60.509 66.667 0.00 0.00 41.02 3.85
4028 4495 1.595382 GGAGATTCCCGCATCACCG 60.595 63.158 0.00 0.00 0.00 4.94
4049 4516 5.299279 ACTTCACATGAGATGTTCGGTTTTT 59.701 36.000 0.00 0.00 42.70 1.94
4090 4557 7.936950 TTGAAACGCATTATGAATGTTTTCA 57.063 28.000 17.80 17.80 45.57 2.69
4188 4727 5.808540 CCATGCCTTCTCATGTATTTGTTTG 59.191 40.000 0.00 0.00 41.60 2.93
4266 4944 4.938226 TCATGTATTTGTTCGTGCCATGTA 59.062 37.500 0.00 0.00 32.24 2.29
4349 5031 6.315144 GCTTGATGGGTTTAGTTTGTGTTTTT 59.685 34.615 0.00 0.00 0.00 1.94
4404 5086 4.250464 CGGTGTTGGCTTTAGAGATGTTA 58.750 43.478 0.00 0.00 0.00 2.41
4413 5095 0.940519 CGTCGACGGTGTTGGCTTTA 60.941 55.000 29.70 0.00 35.37 1.85
4425 5107 4.753877 TTCCTCGCTGCGTCGACG 62.754 66.667 32.57 32.57 43.27 5.12
4446 5128 2.569853 TCCCCTTTTGAAGACGCTATCA 59.430 45.455 0.00 0.00 0.00 2.15
4487 5171 1.550524 CTGGTTCTTCAGGACGGATGA 59.449 52.381 0.00 0.00 0.00 2.92
4495 5179 6.071896 GGAAATTTTAGGTCTGGTTCTTCAGG 60.072 42.308 0.00 0.00 35.58 3.86
4497 5181 5.773176 GGGAAATTTTAGGTCTGGTTCTTCA 59.227 40.000 0.00 0.00 0.00 3.02
4514 5198 3.502356 TCTTTAAGCAACGGGGGAAATT 58.498 40.909 0.00 0.00 0.00 1.82
4530 5214 7.432148 TGGTGTTTATCTATGCTCCTCTTTA 57.568 36.000 0.00 0.00 0.00 1.85
4550 5234 0.950836 TTGAAGGCGTTGTCATGGTG 59.049 50.000 0.00 0.00 0.00 4.17
4551 5235 1.202758 TCTTGAAGGCGTTGTCATGGT 60.203 47.619 0.00 0.00 0.00 3.55
4566 5250 2.685897 CGGGTGTTGTTTTCCTTCTTGA 59.314 45.455 0.00 0.00 0.00 3.02
4624 5329 1.755179 CAATGGGATTGCTCGGACTT 58.245 50.000 0.00 0.00 32.92 3.01
4692 5397 0.839946 CCCCTATCTTGAGGTGGTGG 59.160 60.000 0.00 0.00 34.45 4.61
4697 5402 0.269173 CCCCTCCCCTATCTTGAGGT 59.731 60.000 0.00 0.00 43.42 3.85
4742 5448 0.821711 TTTTTGAGGACGCCCAGGTG 60.822 55.000 0.00 0.00 33.88 4.00
4804 5781 2.092049 TCTCTACTATGTCGCCTTCCCA 60.092 50.000 0.00 0.00 0.00 4.37
4805 5782 2.554893 CTCTCTACTATGTCGCCTTCCC 59.445 54.545 0.00 0.00 0.00 3.97
4816 5793 1.889829 GGCATCGGCACTCTCTACTAT 59.110 52.381 0.00 0.00 43.71 2.12
4817 5794 1.319541 GGCATCGGCACTCTCTACTA 58.680 55.000 0.00 0.00 43.71 1.82
4848 5825 1.101331 GCCTTCCCATTCAGCTTCTG 58.899 55.000 0.00 0.00 0.00 3.02
4851 5828 0.324091 CCTGCCTTCCCATTCAGCTT 60.324 55.000 0.00 0.00 0.00 3.74
4859 5836 3.003173 CTCGGACCTGCCTTCCCA 61.003 66.667 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.