Multiple sequence alignment - TraesCS2D01G373100

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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 TraesCS2D01G373100 chr2D 100.000 5412 0 0 1 5412 476841789 476836378 0.000000e+00 9995.0
1 TraesCS2D01G373100 chr2D 88.182 330 36 1 1105 1431 477264777 477264448 1.830000e-104 390.0
2 TraesCS2D01G373100 chr2D 89.251 307 33 0 1125 1431 477394144 477394450 8.500000e-103 385.0
3 TraesCS2D01G373100 chr2B 95.724 1871 57 10 2751 4606 557991760 557993622 0.000000e+00 2990.0
4 TraesCS2D01G373100 chr2B 92.193 1947 83 27 764 2671 557989847 557991763 0.000000e+00 2689.0
5 TraesCS2D01G373100 chr2B 89.423 312 33 0 1120 1431 559193249 559192938 1.410000e-105 394.0
6 TraesCS2D01G373100 chr2B 88.350 309 36 0 1123 1431 559416240 559416548 6.620000e-99 372.0
7 TraesCS2D01G373100 chr2B 85.494 324 47 0 1108 1431 559306322 559306645 6.710000e-89 339.0
8 TraesCS2D01G373100 chr2B 76.818 220 36 10 547 754 445189758 445189542 5.730000e-20 110.0
9 TraesCS2D01G373100 chr2A 96.569 1749 39 7 2751 4479 619203825 619202078 0.000000e+00 2878.0
10 TraesCS2D01G373100 chr2A 91.713 893 24 13 774 1626 619207007 619206125 0.000000e+00 1194.0
11 TraesCS2D01G373100 chr2A 89.431 738 35 14 1939 2671 619204521 619203822 0.000000e+00 891.0
12 TraesCS2D01G373100 chr2A 91.295 471 33 5 1 466 207971302 207971769 2.130000e-178 636.0
13 TraesCS2D01G373100 chr2A 89.815 324 32 1 1108 1431 619628323 619628001 1.080000e-111 414.0
14 TraesCS2D01G373100 chr2A 88.673 309 35 0 1123 1431 619765225 619765533 1.420000e-100 377.0
15 TraesCS2D01G373100 chr2A 85.172 290 36 5 472 758 207972374 207972659 1.910000e-74 291.0
16 TraesCS2D01G373100 chr2A 85.496 262 26 5 472 728 207971950 207972204 4.160000e-66 263.0
17 TraesCS2D01G373100 chr2A 71.324 816 217 14 3576 4381 758882611 758883419 1.540000e-45 195.0
18 TraesCS2D01G373100 chr2A 96.000 50 1 1 1859 1908 619204567 619204519 4.490000e-11 80.5
19 TraesCS2D01G373100 chr6A 85.269 706 76 13 4635 5332 324931048 324930363 0.000000e+00 702.0
20 TraesCS2D01G373100 chr1B 95.476 420 19 0 4913 5332 660656928 660656509 0.000000e+00 671.0
21 TraesCS2D01G373100 chr1B 89.032 310 12 8 4606 4893 660657813 660657504 1.110000e-96 364.0
22 TraesCS2D01G373100 chr1B 93.204 103 7 0 2667 2769 37590671 37590773 9.390000e-33 152.0
23 TraesCS2D01G373100 chr4A 85.983 478 46 10 1 467 58347570 58348037 4.870000e-135 492.0
24 TraesCS2D01G373100 chr4A 96.970 99 2 1 2661 2758 632934365 632934463 1.210000e-36 165.0
25 TraesCS2D01G373100 chr4A 80.337 178 28 6 172 347 543749454 543749626 1.580000e-25 128.0
26 TraesCS2D01G373100 chr5B 85.172 290 38 5 472 758 197184891 197185178 5.300000e-75 292.0
27 TraesCS2D01G373100 chr5B 85.106 141 14 4 508 641 332359252 332359392 2.630000e-28 137.0
28 TraesCS2D01G373100 chr4D 79.397 398 45 12 11 401 131273304 131272937 4.190000e-61 246.0
29 TraesCS2D01G373100 chr4D 80.678 295 48 6 473 758 131271192 131270898 2.540000e-53 220.0
30 TraesCS2D01G373100 chr4D 77.778 261 39 18 133 383 53229549 53229298 5.650000e-30 143.0
31 TraesCS2D01G373100 chr4D 78.000 150 20 11 123 268 505997682 505997542 1.250000e-11 82.4
32 TraesCS2D01G373100 chr4D 97.222 36 1 0 435 470 131271410 131271375 1.630000e-05 62.1
33 TraesCS2D01G373100 chr1D 81.667 240 42 2 525 762 453600959 453600720 1.190000e-46 198.0
34 TraesCS2D01G373100 chr6D 79.221 308 43 18 56 352 447511927 447512224 1.540000e-45 195.0
35 TraesCS2D01G373100 chr5A 78.571 322 47 18 31 341 55176903 55176593 5.530000e-45 193.0
36 TraesCS2D01G373100 chr5D 78.328 323 44 20 31 341 65950217 65949909 9.260000e-43 185.0
37 TraesCS2D01G373100 chrUn 96.970 99 2 1 2661 2758 335557741 335557643 1.210000e-36 165.0
38 TraesCS2D01G373100 chr3B 96.970 99 2 1 2661 2758 752216565 752216467 1.210000e-36 165.0
39 TraesCS2D01G373100 chr3B 93.269 104 7 0 2653 2756 188484178 188484075 2.610000e-33 154.0
40 TraesCS2D01G373100 chr4B 96.842 95 3 0 2660 2754 29271931 29271837 5.610000e-35 159.0
41 TraesCS2D01G373100 chr4B 87.395 119 15 0 643 761 562635706 562635588 2.630000e-28 137.0
42 TraesCS2D01G373100 chr4B 82.313 147 26 0 612 758 587753378 587753524 1.580000e-25 128.0
43 TraesCS2D01G373100 chr1A 95.960 99 3 1 2661 2758 555691446 555691348 5.610000e-35 159.0
44 TraesCS2D01G373100 chr7D 96.809 94 3 0 2665 2758 37655957 37655864 2.020000e-34 158.0
45 TraesCS2D01G373100 chr7D 79.116 249 37 9 524 761 399423242 399422998 2.020000e-34 158.0
46 TraesCS2D01G373100 chr7A 96.809 94 3 0 2663 2756 80994076 80994169 2.020000e-34 158.0


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 TraesCS2D01G373100 chr2D 476836378 476841789 5411 True 9995.000000 9995 100.00000 1 5412 1 chr2D.!!$R1 5411
1 TraesCS2D01G373100 chr2B 557989847 557993622 3775 False 2839.500000 2990 93.95850 764 4606 2 chr2B.!!$F3 3842
2 TraesCS2D01G373100 chr2A 619202078 619207007 4929 True 1260.875000 2878 93.42825 774 4479 4 chr2A.!!$R2 3705
3 TraesCS2D01G373100 chr2A 207971302 207972659 1357 False 396.666667 636 87.32100 1 758 3 chr2A.!!$F3 757
4 TraesCS2D01G373100 chr6A 324930363 324931048 685 True 702.000000 702 85.26900 4635 5332 1 chr6A.!!$R1 697
5 TraesCS2D01G373100 chr1B 660656509 660657813 1304 True 517.500000 671 92.25400 4606 5332 2 chr1B.!!$R1 726

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
885 1071 0.183014 TAAACCCCCGCAACAGAACA 59.817 50.000 0.0 0.00 0.00 3.18 F
2210 3853 0.169451 GTTTGAAATACCGGCCCACG 59.831 55.000 0.0 0.00 43.80 4.94 F
2880 4524 1.071699 TGGTTCTACACTGCTGGGAAC 59.928 52.381 0.0 6.22 35.39 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2480 4123 0.237498 GCGACCGCTTTAGCAAAACT 59.763 50.0 7.19 0.0 42.21 2.66 R
3112 4764 0.687920 TTATGCCCCACGACAAGACA 59.312 50.0 0.00 0.0 0.00 3.41 R
4775 6454 0.660488 TGTGCTGCGTTGGTTACTTG 59.340 50.0 0.00 0.0 0.00 3.16 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
114 115 7.831753 TGAGGTGAACACTTTTTGAAACATAA 58.168 30.769 4.96 0.00 0.00 1.90
386 392 6.530913 TCTTATATGAACGCTCATTTCTGC 57.469 37.500 6.63 0.00 39.36 4.26
398 404 7.382110 ACGCTCATTTCTGCTCTTATATACAT 58.618 34.615 0.00 0.00 0.00 2.29
433 439 4.755266 ATACTCGTTACCAGCCTTCATT 57.245 40.909 0.00 0.00 0.00 2.57
436 442 1.006832 CGTTACCAGCCTTCATTCCG 58.993 55.000 0.00 0.00 0.00 4.30
476 657 0.443869 GCGAGTGCGATGTCAATGTT 59.556 50.000 0.00 0.00 40.82 2.71
486 667 6.582295 GTGCGATGTCAATGTTTACTTTCATT 59.418 34.615 0.00 0.00 35.08 2.57
488 669 7.748683 TGCGATGTCAATGTTTACTTTCATTAC 59.251 33.333 0.00 0.00 33.69 1.89
585 771 1.813753 GCCAGCGCAATTCGTCCTA 60.814 57.895 11.47 0.00 41.07 2.94
593 779 2.675844 CGCAATTCGTCCTAATGTCCAA 59.324 45.455 0.00 0.00 0.00 3.53
606 792 1.303317 GTCCAACCAGCCCGTCAAT 60.303 57.895 0.00 0.00 0.00 2.57
607 793 1.303236 TCCAACCAGCCCGTCAATG 60.303 57.895 0.00 0.00 0.00 2.82
608 794 2.342650 CCAACCAGCCCGTCAATGG 61.343 63.158 0.00 0.00 40.10 3.16
613 799 1.450312 CAGCCCGTCAATGGTCCTC 60.450 63.158 0.00 0.00 0.00 3.71
643 829 4.569162 TCAGCGTATACCAGTTAAACATGC 59.431 41.667 0.00 0.00 0.00 4.06
645 831 4.809426 AGCGTATACCAGTTAAACATGCTC 59.191 41.667 0.00 0.00 0.00 4.26
691 877 5.814705 TCAAAAATTTCGGTGTGCTGATTTT 59.185 32.000 0.00 0.00 0.00 1.82
694 880 2.791383 TTCGGTGTGCTGATTTTTGG 57.209 45.000 0.00 0.00 0.00 3.28
699 885 3.328505 GGTGTGCTGATTTTTGGGATTG 58.671 45.455 0.00 0.00 0.00 2.67
703 889 3.434299 GTGCTGATTTTTGGGATTGCAAG 59.566 43.478 4.94 0.00 0.00 4.01
709 895 6.229733 TGATTTTTGGGATTGCAAGTTTAGG 58.770 36.000 4.94 0.00 0.00 2.69
710 896 4.615588 TTTTGGGATTGCAAGTTTAGGG 57.384 40.909 4.94 0.00 0.00 3.53
713 899 3.161866 TGGGATTGCAAGTTTAGGGTTC 58.838 45.455 4.94 0.00 0.00 3.62
714 900 2.163613 GGGATTGCAAGTTTAGGGTTCG 59.836 50.000 4.94 0.00 0.00 3.95
715 901 3.078837 GGATTGCAAGTTTAGGGTTCGA 58.921 45.455 4.94 0.00 0.00 3.71
728 914 3.259902 AGGGTTCGATTTAGCTTTCGTC 58.740 45.455 11.56 7.55 36.74 4.20
729 915 3.056035 AGGGTTCGATTTAGCTTTCGTCT 60.056 43.478 11.56 5.17 36.74 4.18
731 917 5.048507 GGGTTCGATTTAGCTTTCGTCTAT 58.951 41.667 11.56 0.00 36.74 1.98
732 918 6.040166 AGGGTTCGATTTAGCTTTCGTCTATA 59.960 38.462 11.56 0.00 36.74 1.31
733 919 6.698766 GGGTTCGATTTAGCTTTCGTCTATAA 59.301 38.462 11.56 0.00 36.74 0.98
761 947 5.622346 AGGTTTATTTTGGACTTTTGCCA 57.378 34.783 0.00 0.00 0.00 4.92
762 948 5.610398 AGGTTTATTTTGGACTTTTGCCAG 58.390 37.500 0.00 0.00 36.64 4.85
817 1003 1.736586 CATCGGAGTCCTCTTCCGG 59.263 63.158 13.07 0.00 46.03 5.14
840 1026 1.402107 AAAAGGCAGGGCACAGTTGG 61.402 55.000 0.00 0.00 0.00 3.77
842 1028 2.983725 AAGGCAGGGCACAGTTGGAC 62.984 60.000 0.00 0.00 0.00 4.02
885 1071 0.183014 TAAACCCCCGCAACAGAACA 59.817 50.000 0.00 0.00 0.00 3.18
894 1080 1.014352 GCAACAGAACAGAACACGGT 58.986 50.000 0.00 0.00 0.00 4.83
1350 1555 1.195115 TCGAGAAGATGGGGTTCCTG 58.805 55.000 0.00 0.00 0.00 3.86
1469 1675 1.848932 GCCCGTCGTTTGTTCCTTCC 61.849 60.000 0.00 0.00 0.00 3.46
1470 1676 0.533308 CCCGTCGTTTGTTCCTTCCA 60.533 55.000 0.00 0.00 0.00 3.53
1471 1677 1.519408 CCGTCGTTTGTTCCTTCCAT 58.481 50.000 0.00 0.00 0.00 3.41
1472 1678 2.613474 CCCGTCGTTTGTTCCTTCCATA 60.613 50.000 0.00 0.00 0.00 2.74
1649 1973 4.397417 AGATGAATTTTGGCTCTTCTTCCG 59.603 41.667 0.00 0.00 0.00 4.30
1666 1991 6.428083 TCTTCCGGTGCCAATAATAGATTA 57.572 37.500 0.00 0.00 0.00 1.75
1676 2001 5.629435 GCCAATAATAGATTAAGGTTTGCGC 59.371 40.000 0.00 0.00 0.00 6.09
1759 2085 8.665685 GGAATAACGATCCACAATATAACATCC 58.334 37.037 0.00 0.00 36.92 3.51
1807 2145 1.075542 TAAAGAACCATGAGCGTGCG 58.924 50.000 0.00 0.00 0.00 5.34
1842 2180 4.466370 ACACTTATGCCAAGTACTAGCAGA 59.534 41.667 21.11 15.99 40.40 4.26
1876 3508 4.330074 CAGCGACACTTATTTTAGGTCAGG 59.670 45.833 0.00 0.00 0.00 3.86
1937 3569 4.320788 GCTCTTCCTGACACCAAGAAAATG 60.321 45.833 0.00 0.00 0.00 2.32
2039 3678 9.209175 CCCACAAAATAATCATCTACTAGTAGC 57.791 37.037 22.87 0.00 33.32 3.58
2090 3729 6.818644 CCAGCGTTTATATTATGCTAGACCAT 59.181 38.462 0.00 0.00 36.15 3.55
2151 3794 5.446143 TGATTTAGTTTGGTCGTTGCATT 57.554 34.783 0.00 0.00 0.00 3.56
2204 3847 7.083875 ACTGTCAATATGTTTGAAATACCGG 57.916 36.000 0.00 0.00 0.00 5.28
2210 3853 0.169451 GTTTGAAATACCGGCCCACG 59.831 55.000 0.00 0.00 43.80 4.94
2497 4140 3.349488 AACAGTTTTGCTAAAGCGGTC 57.651 42.857 0.00 0.00 45.83 4.79
2655 4299 4.201990 CCTTTCTATCCATCTTGCTGTTGC 60.202 45.833 0.00 0.00 40.20 4.17
2668 4312 8.781196 CATCTTGCTGTTGCTTCTATAATATGT 58.219 33.333 0.00 0.00 40.48 2.29
2670 4314 9.261180 TCTTGCTGTTGCTTCTATAATATGTAC 57.739 33.333 0.00 0.00 40.48 2.90
2671 4315 9.265901 CTTGCTGTTGCTTCTATAATATGTACT 57.734 33.333 0.00 0.00 40.48 2.73
2672 4316 8.818141 TGCTGTTGCTTCTATAATATGTACTC 57.182 34.615 0.00 0.00 40.48 2.59
2673 4317 7.872993 TGCTGTTGCTTCTATAATATGTACTCC 59.127 37.037 0.00 0.00 40.48 3.85
2674 4318 7.332182 GCTGTTGCTTCTATAATATGTACTCCC 59.668 40.741 0.00 0.00 36.03 4.30
2675 4319 8.492415 TGTTGCTTCTATAATATGTACTCCCT 57.508 34.615 0.00 0.00 0.00 4.20
2676 4320 8.585881 TGTTGCTTCTATAATATGTACTCCCTC 58.414 37.037 0.00 0.00 0.00 4.30
2677 4321 8.808092 GTTGCTTCTATAATATGTACTCCCTCT 58.192 37.037 0.00 0.00 0.00 3.69
2678 4322 8.354711 TGCTTCTATAATATGTACTCCCTCTG 57.645 38.462 0.00 0.00 0.00 3.35
2679 4323 7.950684 TGCTTCTATAATATGTACTCCCTCTGT 59.049 37.037 0.00 0.00 0.00 3.41
2680 4324 9.463902 GCTTCTATAATATGTACTCCCTCTGTA 57.536 37.037 0.00 0.00 0.00 2.74
2695 4339 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2696 4340 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2697 4341 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2698 4342 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2699 4343 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2715 4359 8.828688 AAGAGCGTTTAGACAACTAAAATAGT 57.171 30.769 0.00 0.00 45.97 2.12
2716 4360 8.240883 AGAGCGTTTAGACAACTAAAATAGTG 57.759 34.615 0.00 0.00 45.97 2.74
2717 4361 8.086522 AGAGCGTTTAGACAACTAAAATAGTGA 58.913 33.333 0.00 0.00 45.97 3.41
2718 4362 8.773404 AGCGTTTAGACAACTAAAATAGTGAT 57.227 30.769 0.00 0.00 45.97 3.06
2719 4363 8.870879 AGCGTTTAGACAACTAAAATAGTGATC 58.129 33.333 0.00 0.00 45.97 2.92
2720 4364 8.870879 GCGTTTAGACAACTAAAATAGTGATCT 58.129 33.333 0.00 8.18 45.97 2.75
2747 4391 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
2748 4392 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
2749 4393 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
2750 4394 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
2880 4524 1.071699 TGGTTCTACACTGCTGGGAAC 59.928 52.381 0.00 6.22 35.39 3.62
2961 4613 5.059161 GCATCATCTTGGTCAGCTACAATA 58.941 41.667 0.00 0.00 0.00 1.90
3112 4764 8.207545 GTCAATGTATCTCTTCTAATTGGAGGT 58.792 37.037 0.89 0.00 0.00 3.85
3225 4877 1.278127 GCAGGCTTACAGGGTACTTGA 59.722 52.381 5.17 0.00 0.00 3.02
3227 4879 2.301870 CAGGCTTACAGGGTACTTGACA 59.698 50.000 5.17 0.00 0.00 3.58
3231 4884 5.249852 AGGCTTACAGGGTACTTGACATTTA 59.750 40.000 5.17 0.00 0.00 1.40
3258 4911 0.301388 GCTGCCACGTTTTGCTTTTG 59.699 50.000 0.00 0.00 0.00 2.44
3374 5033 4.837860 TCCTGAAGGTATTTGGCAAAACAT 59.162 37.500 17.70 11.03 36.34 2.71
3397 5056 4.995124 TGAAGGCTTTCTACGAGATGTAC 58.005 43.478 10.19 0.00 34.31 2.90
3440 5099 3.256136 ACTTCCTGTCTCTAACAACGGAG 59.744 47.826 0.00 0.00 37.45 4.63
3553 5212 3.218453 TGGGGGTTATGTCATTATTGCG 58.782 45.455 0.00 0.00 0.00 4.85
3802 5461 3.439825 TCATGATGAACATTGTGGGAACG 59.560 43.478 0.00 0.00 37.07 3.95
4015 5674 1.825191 CAACATGGCGATCCTGGGG 60.825 63.158 0.00 0.00 0.00 4.96
4114 5773 1.071385 CTCCTGAAAGACTGTGTGCCT 59.929 52.381 0.00 0.00 34.07 4.75
4133 5792 1.959226 GCGAAGGTGGCGAAGTTCA 60.959 57.895 3.32 0.00 0.00 3.18
4463 6124 6.073980 TGTTTTGTTATGAAGTCGAGTAGTGC 60.074 38.462 0.00 0.00 0.00 4.40
4468 6129 1.743958 TGAAGTCGAGTAGTGCTAGCC 59.256 52.381 13.29 3.49 0.00 3.93
4486 6147 6.605995 TGCTAGCCTGTCTAAATAGTGTTAGA 59.394 38.462 13.29 0.00 37.69 2.10
4545 6212 7.989741 AGCATAATCAGTGTGTAAAGATAGCTT 59.010 33.333 0.00 0.00 35.37 3.74
4546 6213 8.066595 GCATAATCAGTGTGTAAAGATAGCTTG 58.933 37.037 0.00 0.00 33.79 4.01
4548 6215 7.602517 AATCAGTGTGTAAAGATAGCTTGTC 57.397 36.000 0.00 0.00 33.79 3.18
4549 6216 5.479306 TCAGTGTGTAAAGATAGCTTGTCC 58.521 41.667 0.00 0.00 33.79 4.02
4550 6217 5.011635 TCAGTGTGTAAAGATAGCTTGTCCA 59.988 40.000 0.00 0.00 33.79 4.02
4551 6218 5.349817 CAGTGTGTAAAGATAGCTTGTCCAG 59.650 44.000 0.00 0.00 33.79 3.86
4552 6219 4.631813 GTGTGTAAAGATAGCTTGTCCAGG 59.368 45.833 0.00 0.00 33.79 4.45
4553 6220 4.192317 GTGTAAAGATAGCTTGTCCAGGG 58.808 47.826 0.00 0.00 33.79 4.45
4554 6221 3.844211 TGTAAAGATAGCTTGTCCAGGGT 59.156 43.478 0.00 0.00 33.79 4.34
4555 6222 5.027460 TGTAAAGATAGCTTGTCCAGGGTA 58.973 41.667 0.00 0.00 33.79 3.69
4569 6236 7.174107 TGTCCAGGGTACTATGTAAAGTAAC 57.826 40.000 0.00 0.00 38.68 2.50
4588 6255 9.833917 AAAGTAACTTCTTAGTTTGCTTCTACT 57.166 29.630 0.00 0.00 41.85 2.57
4589 6256 9.478768 AAGTAACTTCTTAGTTTGCTTCTACTC 57.521 33.333 0.00 0.00 41.85 2.59
4590 6257 8.089597 AGTAACTTCTTAGTTTGCTTCTACTCC 58.910 37.037 0.00 0.00 41.85 3.85
4600 6267 3.838565 TGCTTCTACTCCTATCTCCTGG 58.161 50.000 0.00 0.00 0.00 4.45
4625 6292 2.338620 GGCTTTTCAACACCCGGC 59.661 61.111 0.00 0.00 0.00 6.13
4627 6294 2.050442 CTTTTCAACACCCGGCGC 60.050 61.111 0.00 0.00 0.00 6.53
4628 6295 2.829003 TTTTCAACACCCGGCGCA 60.829 55.556 10.83 0.00 0.00 6.09
4653 6331 2.894387 GGAGCTGCTCGCATGGAC 60.894 66.667 22.25 3.95 42.61 4.02
4830 6511 3.025978 CAATCTCTGTCTCTCTCCAGCT 58.974 50.000 0.00 0.00 0.00 4.24
4986 7237 2.029649 AGATGCTGTTTTCAATGCGCTT 60.030 40.909 9.73 0.00 0.00 4.68
5078 7329 5.009854 ACTGTCTCCAAAACAAATGGTTG 57.990 39.130 0.00 0.00 40.35 3.77
5080 7331 3.130633 GTCTCCAAAACAAATGGTTGCC 58.869 45.455 0.00 0.00 40.35 4.52
5185 7436 3.244596 CCTGCTAATTAGACCTAAGGCCC 60.245 52.174 16.85 0.00 0.00 5.80
5193 7444 2.119495 AGACCTAAGGCCCAGTACATG 58.881 52.381 0.00 0.00 0.00 3.21
5198 7449 2.513897 GGCCCAGTACATGTCGCC 60.514 66.667 0.00 3.25 35.83 5.54
5218 7469 3.620719 GCCTGTCAGATGAGTCAAATGGA 60.621 47.826 0.00 0.00 0.00 3.41
5254 7505 0.380378 TTGTTTGCAACTCGTCAGGC 59.620 50.000 0.00 0.00 0.00 4.85
5261 7512 3.245668 AACTCGTCAGGCCCTGCAG 62.246 63.158 5.66 6.78 0.00 4.41
5281 7532 4.025061 GCAGGAATCTCGATGTGATTCAAG 60.025 45.833 20.89 15.21 46.81 3.02
5332 7583 1.356938 GTGCTACTACACCTTTCCGC 58.643 55.000 0.00 0.00 34.35 5.54
5333 7584 1.067071 GTGCTACTACACCTTTCCGCT 60.067 52.381 0.00 0.00 34.35 5.52
5334 7585 1.621814 TGCTACTACACCTTTCCGCTT 59.378 47.619 0.00 0.00 0.00 4.68
5335 7586 2.038033 TGCTACTACACCTTTCCGCTTT 59.962 45.455 0.00 0.00 0.00 3.51
5336 7587 3.072211 GCTACTACACCTTTCCGCTTTT 58.928 45.455 0.00 0.00 0.00 2.27
5337 7588 3.501062 GCTACTACACCTTTCCGCTTTTT 59.499 43.478 0.00 0.00 0.00 1.94
5338 7589 4.378149 GCTACTACACCTTTCCGCTTTTTC 60.378 45.833 0.00 0.00 0.00 2.29
5339 7590 3.816994 ACTACACCTTTCCGCTTTTTCT 58.183 40.909 0.00 0.00 0.00 2.52
5340 7591 3.564225 ACTACACCTTTCCGCTTTTTCTG 59.436 43.478 0.00 0.00 0.00 3.02
5341 7592 1.067060 ACACCTTTCCGCTTTTTCTGC 59.933 47.619 0.00 0.00 0.00 4.26
5342 7593 1.338020 CACCTTTCCGCTTTTTCTGCT 59.662 47.619 0.00 0.00 0.00 4.24
5343 7594 2.031870 ACCTTTCCGCTTTTTCTGCTT 58.968 42.857 0.00 0.00 0.00 3.91
5344 7595 2.430694 ACCTTTCCGCTTTTTCTGCTTT 59.569 40.909 0.00 0.00 0.00 3.51
5345 7596 3.118775 ACCTTTCCGCTTTTTCTGCTTTT 60.119 39.130 0.00 0.00 0.00 2.27
5346 7597 3.871006 CCTTTCCGCTTTTTCTGCTTTTT 59.129 39.130 0.00 0.00 0.00 1.94
5347 7598 5.047188 CCTTTCCGCTTTTTCTGCTTTTTA 58.953 37.500 0.00 0.00 0.00 1.52
5348 7599 5.522097 CCTTTCCGCTTTTTCTGCTTTTTAA 59.478 36.000 0.00 0.00 0.00 1.52
5349 7600 6.202762 CCTTTCCGCTTTTTCTGCTTTTTAAT 59.797 34.615 0.00 0.00 0.00 1.40
5350 7601 7.383843 CCTTTCCGCTTTTTCTGCTTTTTAATA 59.616 33.333 0.00 0.00 0.00 0.98
5351 7602 7.631915 TTCCGCTTTTTCTGCTTTTTAATAC 57.368 32.000 0.00 0.00 0.00 1.89
5352 7603 6.977213 TCCGCTTTTTCTGCTTTTTAATACT 58.023 32.000 0.00 0.00 0.00 2.12
5353 7604 7.081976 TCCGCTTTTTCTGCTTTTTAATACTC 58.918 34.615 0.00 0.00 0.00 2.59
5354 7605 6.308041 CCGCTTTTTCTGCTTTTTAATACTCC 59.692 38.462 0.00 0.00 0.00 3.85
5355 7606 6.861055 CGCTTTTTCTGCTTTTTAATACTCCA 59.139 34.615 0.00 0.00 0.00 3.86
5356 7607 7.381139 CGCTTTTTCTGCTTTTTAATACTCCAA 59.619 33.333 0.00 0.00 0.00 3.53
5357 7608 9.040939 GCTTTTTCTGCTTTTTAATACTCCAAA 57.959 29.630 0.00 0.00 0.00 3.28
5362 7613 9.691362 TTCTGCTTTTTAATACTCCAAATTGTC 57.309 29.630 0.00 0.00 0.00 3.18
5363 7614 8.303876 TCTGCTTTTTAATACTCCAAATTGTCC 58.696 33.333 0.00 0.00 0.00 4.02
5364 7615 8.189119 TGCTTTTTAATACTCCAAATTGTCCT 57.811 30.769 0.00 0.00 0.00 3.85
5365 7616 9.303116 TGCTTTTTAATACTCCAAATTGTCCTA 57.697 29.630 0.00 0.00 0.00 2.94
5370 7621 6.715347 AATACTCCAAATTGTCCTATTGGC 57.285 37.500 0.00 0.00 42.65 4.52
5371 7622 4.322057 ACTCCAAATTGTCCTATTGGCT 57.678 40.909 0.00 0.00 42.65 4.75
5372 7623 5.450818 ACTCCAAATTGTCCTATTGGCTA 57.549 39.130 0.00 0.00 42.65 3.93
5373 7624 6.018433 ACTCCAAATTGTCCTATTGGCTAT 57.982 37.500 0.00 0.00 42.65 2.97
5374 7625 5.829924 ACTCCAAATTGTCCTATTGGCTATG 59.170 40.000 0.00 0.00 42.65 2.23
5375 7626 4.584325 TCCAAATTGTCCTATTGGCTATGC 59.416 41.667 0.00 0.00 42.65 3.14
5393 7644 8.202745 GGCTATGCCTCTTTCATAATGTATAC 57.797 38.462 0.73 0.00 46.69 1.47
5394 7645 8.043710 GGCTATGCCTCTTTCATAATGTATACT 58.956 37.037 4.17 0.00 46.69 2.12
5395 7646 9.092876 GCTATGCCTCTTTCATAATGTATACTC 57.907 37.037 4.17 0.00 0.00 2.59
5396 7647 9.593134 CTATGCCTCTTTCATAATGTATACTCC 57.407 37.037 4.17 0.00 0.00 3.85
5397 7648 7.373617 TGCCTCTTTCATAATGTATACTCCA 57.626 36.000 4.17 0.00 0.00 3.86
5398 7649 7.801104 TGCCTCTTTCATAATGTATACTCCAA 58.199 34.615 4.17 0.00 0.00 3.53
5399 7650 8.439971 TGCCTCTTTCATAATGTATACTCCAAT 58.560 33.333 4.17 0.00 0.00 3.16
5400 7651 9.289782 GCCTCTTTCATAATGTATACTCCAATT 57.710 33.333 4.17 0.00 0.00 2.32
5408 7659 9.948964 CATAATGTATACTCCAATTCCAGATCA 57.051 33.333 4.17 0.00 0.00 2.92
5410 7661 8.859236 AATGTATACTCCAATTCCAGATCATG 57.141 34.615 4.17 0.00 0.00 3.07
5411 7662 7.379059 TGTATACTCCAATTCCAGATCATGT 57.621 36.000 4.17 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 8.457261 CCTCAAAATGGATTGTGTTTTCAAAAA 58.543 29.630 0.00 0.00 30.13 1.94
84 85 7.593875 TTCAAAAAGTGTTCACCTCAAAATG 57.406 32.000 0.00 0.00 0.00 2.32
85 86 7.659390 TGTTTCAAAAAGTGTTCACCTCAAAAT 59.341 29.630 0.00 0.00 0.00 1.82
342 348 7.211573 TAAGAAAACCTTTCGGGAATTTTTCC 58.788 34.615 10.31 0.00 41.41 3.13
353 359 6.772078 AGCGTTCATATAAGAAAACCTTTCG 58.228 36.000 0.00 0.00 36.34 3.46
398 404 7.132213 GGTAACGAGTATATTTAGCGTGTACA 58.868 38.462 0.00 0.00 35.16 2.90
433 439 1.686325 GCCTCACCTAGCCAATCGGA 61.686 60.000 0.00 0.00 0.00 4.55
541 727 4.436448 GCAGTTGCTCGCACGCTC 62.436 66.667 0.00 0.00 38.21 5.03
585 771 1.303317 GACGGGCTGGTTGGACATT 60.303 57.895 0.00 0.00 0.00 2.71
593 779 2.351276 GACCATTGACGGGCTGGT 59.649 61.111 0.00 0.00 45.80 4.00
606 792 3.680786 CTGACGTGGCGAGGACCA 61.681 66.667 0.00 0.00 37.38 4.02
624 810 6.238103 CCTTGAGCATGTTTAACTGGTATACG 60.238 42.308 0.00 0.00 0.00 3.06
626 812 6.717289 ACCTTGAGCATGTTTAACTGGTATA 58.283 36.000 0.00 0.00 0.00 1.47
659 845 4.343814 ACACCGAAATTTTTGATCCTGGTT 59.656 37.500 0.00 0.00 0.00 3.67
663 849 3.573967 AGCACACCGAAATTTTTGATCCT 59.426 39.130 0.00 0.00 0.00 3.24
665 851 4.545610 TCAGCACACCGAAATTTTTGATC 58.454 39.130 0.00 0.00 0.00 2.92
674 860 2.223923 CCCAAAAATCAGCACACCGAAA 60.224 45.455 0.00 0.00 0.00 3.46
675 861 1.339610 CCCAAAAATCAGCACACCGAA 59.660 47.619 0.00 0.00 0.00 4.30
676 862 0.958091 CCCAAAAATCAGCACACCGA 59.042 50.000 0.00 0.00 0.00 4.69
677 863 0.958091 TCCCAAAAATCAGCACACCG 59.042 50.000 0.00 0.00 0.00 4.94
691 877 3.252554 ACCCTAAACTTGCAATCCCAA 57.747 42.857 0.00 0.00 0.00 4.12
694 880 3.078837 TCGAACCCTAAACTTGCAATCC 58.921 45.455 0.00 0.00 0.00 3.01
699 885 4.395231 AGCTAAATCGAACCCTAAACTTGC 59.605 41.667 0.00 0.00 0.00 4.01
703 889 5.121298 ACGAAAGCTAAATCGAACCCTAAAC 59.879 40.000 19.45 0.00 41.43 2.01
709 895 7.689953 TTATAGACGAAAGCTAAATCGAACC 57.310 36.000 19.45 10.14 41.43 3.62
737 923 6.418946 TGGCAAAAGTCCAAAATAAACCTTT 58.581 32.000 0.00 0.00 0.00 3.11
738 924 5.995446 TGGCAAAAGTCCAAAATAAACCTT 58.005 33.333 0.00 0.00 0.00 3.50
739 925 5.130311 ACTGGCAAAAGTCCAAAATAAACCT 59.870 36.000 0.00 0.00 32.41 3.50
740 926 5.364778 ACTGGCAAAAGTCCAAAATAAACC 58.635 37.500 0.00 0.00 32.41 3.27
741 927 6.918892 AACTGGCAAAAGTCCAAAATAAAC 57.081 33.333 0.00 0.00 32.41 2.01
742 928 7.607991 TCAAAACTGGCAAAAGTCCAAAATAAA 59.392 29.630 0.00 0.00 32.41 1.40
743 929 7.106239 TCAAAACTGGCAAAAGTCCAAAATAA 58.894 30.769 0.00 0.00 32.41 1.40
745 931 5.495640 TCAAAACTGGCAAAAGTCCAAAAT 58.504 33.333 0.00 0.00 32.41 1.82
746 932 4.899502 TCAAAACTGGCAAAAGTCCAAAA 58.100 34.783 0.00 0.00 32.41 2.44
747 933 4.543590 TCAAAACTGGCAAAAGTCCAAA 57.456 36.364 0.00 0.00 32.41 3.28
750 936 3.132111 TCCTTCAAAACTGGCAAAAGTCC 59.868 43.478 0.00 0.00 0.00 3.85
751 937 4.363138 CTCCTTCAAAACTGGCAAAAGTC 58.637 43.478 0.00 0.00 0.00 3.01
752 938 3.132824 CCTCCTTCAAAACTGGCAAAAGT 59.867 43.478 0.00 0.00 0.00 2.66
753 939 3.721035 CCTCCTTCAAAACTGGCAAAAG 58.279 45.455 0.00 0.00 0.00 2.27
755 941 1.412343 GCCTCCTTCAAAACTGGCAAA 59.588 47.619 0.00 0.00 40.04 3.68
756 942 1.039856 GCCTCCTTCAAAACTGGCAA 58.960 50.000 0.00 0.00 40.04 4.52
757 943 0.827507 GGCCTCCTTCAAAACTGGCA 60.828 55.000 0.00 0.00 41.86 4.92
758 944 1.866853 CGGCCTCCTTCAAAACTGGC 61.867 60.000 0.00 0.00 39.61 4.85
759 945 0.537371 ACGGCCTCCTTCAAAACTGG 60.537 55.000 0.00 0.00 0.00 4.00
761 947 0.537371 CCACGGCCTCCTTCAAAACT 60.537 55.000 0.00 0.00 0.00 2.66
762 948 1.524008 CCCACGGCCTCCTTCAAAAC 61.524 60.000 0.00 0.00 0.00 2.43
840 1026 3.682999 GCCTTCCTATTGGAACTGGAGTC 60.683 52.174 15.46 0.00 46.57 3.36
842 1028 2.422093 GGCCTTCCTATTGGAACTGGAG 60.422 54.545 15.46 2.44 46.57 3.86
885 1071 2.029073 CAGCCGTGACCGTGTTCT 59.971 61.111 0.00 0.00 0.00 3.01
894 1080 2.355445 GATCTCGATGCCAGCCGTGA 62.355 60.000 0.00 0.00 33.75 4.35
951 1137 2.124653 TGTTTGCGGTTCCACGGT 60.125 55.556 0.00 0.00 0.00 4.83
1337 1542 0.622665 CTGCTTCAGGAACCCCATCT 59.377 55.000 0.00 0.00 33.88 2.90
1350 1555 3.793144 CGCGTGAAGGGCTGCTTC 61.793 66.667 0.00 0.00 0.00 3.86
1494 1700 0.952497 ACAGCAGACGCACCAATCTG 60.952 55.000 0.00 0.00 44.37 2.90
1649 1973 6.923508 GCAAACCTTAATCTATTATTGGCACC 59.076 38.462 0.00 0.00 0.00 5.01
1727 2052 5.379732 TTGTGGATCGTTATTCCAAAACC 57.620 39.130 0.00 0.00 44.62 3.27
1759 2085 1.318576 AAAGAAAACTGGCCGGAGTG 58.681 50.000 21.41 0.00 0.00 3.51
1807 2145 2.587956 CATAAGTGTGCATGTGTGTGC 58.412 47.619 0.00 0.00 45.25 4.57
1842 2180 7.907214 AATAAGTGTCGCTGATTTAGAAACT 57.093 32.000 0.00 0.00 34.18 2.66
1905 3537 2.700371 TGTCAGGAAGAGCAGTCAGAAA 59.300 45.455 0.00 0.00 0.00 2.52
1908 3540 1.337635 GGTGTCAGGAAGAGCAGTCAG 60.338 57.143 0.00 0.00 0.00 3.51
1910 3542 0.681733 TGGTGTCAGGAAGAGCAGTC 59.318 55.000 0.00 0.00 0.00 3.51
1937 3569 3.802722 TGCGCAATGGCAAAATTAAAC 57.197 38.095 8.16 0.00 40.59 2.01
2039 3678 9.294030 GGAAAACAAGTGCATTGAATTAGATAG 57.706 33.333 13.53 0.00 41.83 2.08
2090 3729 7.440856 GGAAGAGCATAAAACAAAATTCAACCA 59.559 33.333 0.00 0.00 0.00 3.67
2171 3814 9.624697 TTCAAACATATTGACAGTAGCAATTTC 57.375 29.630 0.00 0.00 37.22 2.17
2223 3866 5.796424 AATATTGAATCAGAACATGGCCC 57.204 39.130 0.00 0.00 0.00 5.80
2252 3895 2.355209 GCCAAACCCACCTGTTCAAAAA 60.355 45.455 0.00 0.00 0.00 1.94
2253 3896 1.208293 GCCAAACCCACCTGTTCAAAA 59.792 47.619 0.00 0.00 0.00 2.44
2479 4122 1.950472 CGACCGCTTTAGCAAAACTG 58.050 50.000 2.29 0.00 42.21 3.16
2480 4123 0.237498 GCGACCGCTTTAGCAAAACT 59.763 50.000 7.19 0.00 42.21 2.66
2481 4124 0.728129 GGCGACCGCTTTAGCAAAAC 60.728 55.000 14.25 0.00 42.21 2.43
2482 4125 1.167155 TGGCGACCGCTTTAGCAAAA 61.167 50.000 14.25 0.00 42.21 2.44
2485 4128 2.031314 TTGGCGACCGCTTTAGCA 59.969 55.556 14.25 0.41 42.21 3.49
2488 4131 1.669760 CCAGTTGGCGACCGCTTTA 60.670 57.895 14.25 0.00 41.60 1.85
2489 4132 2.951475 TTCCAGTTGGCGACCGCTTT 62.951 55.000 14.25 0.00 41.60 3.51
2490 4133 2.748058 ATTCCAGTTGGCGACCGCTT 62.748 55.000 14.25 0.00 41.60 4.68
2491 4134 1.895020 TATTCCAGTTGGCGACCGCT 61.895 55.000 14.25 0.00 41.60 5.52
2669 4313 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2670 4314 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2671 4315 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2672 4316 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2673 4317 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2689 4333 9.918630 ACTATTTTAGTTGTCTAAACGCTCTTA 57.081 29.630 0.74 0.00 43.20 2.10
2690 4334 8.709646 CACTATTTTAGTTGTCTAAACGCTCTT 58.290 33.333 0.74 0.00 43.20 2.85
2691 4335 8.086522 TCACTATTTTAGTTGTCTAAACGCTCT 58.913 33.333 0.74 0.00 43.20 4.09
2692 4336 8.236084 TCACTATTTTAGTTGTCTAAACGCTC 57.764 34.615 0.74 0.00 43.20 5.03
2693 4337 8.773404 ATCACTATTTTAGTTGTCTAAACGCT 57.227 30.769 0.74 0.00 43.20 5.07
2694 4338 8.870879 AGATCACTATTTTAGTTGTCTAAACGC 58.129 33.333 0.00 0.00 43.20 4.84
2721 4365 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
2722 4366 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
2723 4367 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
2724 4368 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
2725 4369 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
2726 4370 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2727 4371 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
2728 4372 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
2729 4373 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
2730 4374 8.995027 TTGTACTCCCTCCGTAAACTAATATA 57.005 34.615 0.00 0.00 0.00 0.86
2731 4375 7.562821 ACTTGTACTCCCTCCGTAAACTAATAT 59.437 37.037 0.00 0.00 0.00 1.28
2732 4376 6.891908 ACTTGTACTCCCTCCGTAAACTAATA 59.108 38.462 0.00 0.00 0.00 0.98
2733 4377 5.718607 ACTTGTACTCCCTCCGTAAACTAAT 59.281 40.000 0.00 0.00 0.00 1.73
2734 4378 5.079643 ACTTGTACTCCCTCCGTAAACTAA 58.920 41.667 0.00 0.00 0.00 2.24
2735 4379 4.666512 ACTTGTACTCCCTCCGTAAACTA 58.333 43.478 0.00 0.00 0.00 2.24
2736 4380 3.504375 ACTTGTACTCCCTCCGTAAACT 58.496 45.455 0.00 0.00 0.00 2.66
2737 4381 3.256631 TGACTTGTACTCCCTCCGTAAAC 59.743 47.826 0.00 0.00 0.00 2.01
2738 4382 3.256631 GTGACTTGTACTCCCTCCGTAAA 59.743 47.826 0.00 0.00 0.00 2.01
2739 4383 2.821969 GTGACTTGTACTCCCTCCGTAA 59.178 50.000 0.00 0.00 0.00 3.18
2740 4384 2.224843 TGTGACTTGTACTCCCTCCGTA 60.225 50.000 0.00 0.00 0.00 4.02
2741 4385 1.254954 GTGACTTGTACTCCCTCCGT 58.745 55.000 0.00 0.00 0.00 4.69
2742 4386 1.254026 TGTGACTTGTACTCCCTCCG 58.746 55.000 0.00 0.00 0.00 4.63
2743 4387 2.897969 TCTTGTGACTTGTACTCCCTCC 59.102 50.000 0.00 0.00 0.00 4.30
2744 4388 4.039366 ACTTCTTGTGACTTGTACTCCCTC 59.961 45.833 0.00 0.00 0.00 4.30
2745 4389 3.967987 ACTTCTTGTGACTTGTACTCCCT 59.032 43.478 0.00 0.00 0.00 4.20
2746 4390 4.338379 ACTTCTTGTGACTTGTACTCCC 57.662 45.455 0.00 0.00 0.00 4.30
2747 4391 7.116519 GTCAATACTTCTTGTGACTTGTACTCC 59.883 40.741 0.00 0.00 37.88 3.85
2748 4392 7.868415 AGTCAATACTTCTTGTGACTTGTACTC 59.132 37.037 0.00 0.00 46.57 2.59
2749 4393 7.653713 CAGTCAATACTTCTTGTGACTTGTACT 59.346 37.037 2.51 0.00 46.57 2.73
2750 4394 7.652105 TCAGTCAATACTTCTTGTGACTTGTAC 59.348 37.037 2.51 0.00 46.57 2.90
3103 4755 2.494059 CACGACAAGACACCTCCAATT 58.506 47.619 0.00 0.00 0.00 2.32
3112 4764 0.687920 TTATGCCCCACGACAAGACA 59.312 50.000 0.00 0.00 0.00 3.41
3225 4877 1.073763 TGGCAGCCTGTGTCTAAATGT 59.926 47.619 14.15 0.00 0.00 2.71
3227 4879 1.826385 GTGGCAGCCTGTGTCTAAAT 58.174 50.000 14.15 0.00 0.00 1.40
3231 4884 2.608970 AAACGTGGCAGCCTGTGTCT 62.609 55.000 14.15 0.00 0.00 3.41
3258 4911 5.611796 TCTCAACAGTTACATGTGATTGC 57.388 39.130 9.11 0.00 32.52 3.56
3262 4915 9.990360 TTATTAGTTCTCAACAGTTACATGTGA 57.010 29.630 9.11 0.00 32.52 3.58
3295 4948 2.351726 GGTTATGAACACCTGCGATGTC 59.648 50.000 0.00 0.00 0.00 3.06
3374 5033 4.537135 ACATCTCGTAGAAAGCCTTCAA 57.463 40.909 0.00 0.00 34.09 2.69
3397 5056 6.734104 AGTGATTTCGATTTCTTCTCCTTG 57.266 37.500 0.00 0.00 0.00 3.61
3456 5115 4.202398 TGTCATCAAAAGACTCAGCTTCCT 60.202 41.667 0.00 0.00 36.94 3.36
3553 5212 3.694889 GCAACCAGTCGTTATTGCC 57.305 52.632 0.00 0.00 41.25 4.52
3802 5461 1.654954 CTTGCATCAGGTCAGCAGCC 61.655 60.000 0.00 0.00 39.72 4.85
3979 5638 1.877637 TGCGGTACATGATGGCATAC 58.122 50.000 0.00 0.00 32.27 2.39
4015 5674 3.310860 AACCGACAGGCCATCGACC 62.311 63.158 26.10 0.00 42.25 4.79
4114 5773 1.959226 GAACTTCGCCACCTTCGCA 60.959 57.895 0.00 0.00 0.00 5.10
4133 5792 3.640407 CGCCATGGGGATCGGGAT 61.640 66.667 23.98 0.00 35.59 3.85
4209 5868 3.313526 CCATTCCCAGCAAAAGAGTATCG 59.686 47.826 0.00 0.00 42.67 2.92
4282 5941 4.467084 ATCCCGTCGCCGCACATT 62.467 61.111 0.00 0.00 0.00 2.71
4528 6195 5.482908 CTGGACAAGCTATCTTTACACACT 58.517 41.667 0.00 0.00 0.00 3.55
4545 6212 6.955851 AGTTACTTTACATAGTACCCTGGACA 59.044 38.462 0.00 0.00 30.62 4.02
4546 6213 7.415592 AGTTACTTTACATAGTACCCTGGAC 57.584 40.000 0.00 0.00 30.62 4.02
4548 6215 8.075761 AGAAGTTACTTTACATAGTACCCTGG 57.924 38.462 0.00 0.00 30.62 4.45
4569 6236 8.691797 AGATAGGAGTAGAAGCAAACTAAGAAG 58.308 37.037 0.00 0.00 0.00 2.85
4587 6254 2.623889 CGGTTACACCAGGAGATAGGAG 59.376 54.545 0.00 0.00 38.47 3.69
4588 6255 2.662866 CGGTTACACCAGGAGATAGGA 58.337 52.381 0.00 0.00 38.47 2.94
4589 6256 1.687123 CCGGTTACACCAGGAGATAGG 59.313 57.143 0.00 0.00 38.47 2.57
4590 6257 1.068741 GCCGGTTACACCAGGAGATAG 59.931 57.143 1.90 0.00 38.47 2.08
4600 6267 2.542205 GGTGTTGAAAAGCCGGTTACAC 60.542 50.000 11.59 11.59 35.04 2.90
4653 6331 2.740981 GCACAATCTCTCAGACTTGTGG 59.259 50.000 19.86 8.10 40.26 4.17
4775 6454 0.660488 TGTGCTGCGTTGGTTACTTG 59.340 50.000 0.00 0.00 0.00 3.16
4777 6456 1.156736 GATGTGCTGCGTTGGTTACT 58.843 50.000 0.00 0.00 0.00 2.24
4898 6592 2.029288 CCGCGCACTGTTCATCTGT 61.029 57.895 8.75 0.00 0.00 3.41
4986 7237 4.955335 TCCTCTTGATAAAGGTGGGACTA 58.045 43.478 0.00 0.00 34.12 2.59
5185 7436 1.202348 TCTGACAGGCGACATGTACTG 59.798 52.381 18.06 18.06 37.01 2.74
5193 7444 0.528017 TGACTCATCTGACAGGCGAC 59.472 55.000 1.81 0.00 0.00 5.19
5218 7469 1.768870 ACAACAGGGTGCTTAGTGAGT 59.231 47.619 0.00 0.00 0.00 3.41
5254 7505 0.467384 ACATCGAGATTCCTGCAGGG 59.533 55.000 32.23 15.25 35.41 4.45
5261 7512 3.812053 CCCTTGAATCACATCGAGATTCC 59.188 47.826 18.12 6.13 46.78 3.01
5281 7532 1.285078 GGCACCCCATTATCCTATCCC 59.715 57.143 0.00 0.00 0.00 3.85
5336 7587 9.691362 GACAATTTGGAGTATTAAAAAGCAGAA 57.309 29.630 0.78 0.00 0.00 3.02
5337 7588 8.303876 GGACAATTTGGAGTATTAAAAAGCAGA 58.696 33.333 0.78 0.00 0.00 4.26
5338 7589 8.306761 AGGACAATTTGGAGTATTAAAAAGCAG 58.693 33.333 0.78 0.00 0.00 4.24
5339 7590 8.189119 AGGACAATTTGGAGTATTAAAAAGCA 57.811 30.769 0.78 0.00 0.00 3.91
5344 7595 8.691797 GCCAATAGGACAATTTGGAGTATTAAA 58.308 33.333 5.15 0.00 42.02 1.52
5345 7596 8.058847 AGCCAATAGGACAATTTGGAGTATTAA 58.941 33.333 5.15 0.00 42.02 1.40
5346 7597 7.582719 AGCCAATAGGACAATTTGGAGTATTA 58.417 34.615 5.15 0.00 42.02 0.98
5347 7598 6.435164 AGCCAATAGGACAATTTGGAGTATT 58.565 36.000 5.15 0.00 42.02 1.89
5348 7599 6.018433 AGCCAATAGGACAATTTGGAGTAT 57.982 37.500 5.15 0.00 42.02 2.12
5349 7600 5.450818 AGCCAATAGGACAATTTGGAGTA 57.549 39.130 5.15 0.00 42.02 2.59
5350 7601 4.322057 AGCCAATAGGACAATTTGGAGT 57.678 40.909 5.15 0.00 42.02 3.85
5351 7602 5.278660 GCATAGCCAATAGGACAATTTGGAG 60.279 44.000 5.15 0.00 42.02 3.86
5352 7603 4.584325 GCATAGCCAATAGGACAATTTGGA 59.416 41.667 5.15 0.00 42.02 3.53
5353 7604 4.874970 GCATAGCCAATAGGACAATTTGG 58.125 43.478 0.78 0.00 42.28 3.28
5369 7620 9.092876 GAGTATACATTATGAAAGAGGCATAGC 57.907 37.037 5.50 0.00 30.61 2.97
5370 7621 9.593134 GGAGTATACATTATGAAAGAGGCATAG 57.407 37.037 5.50 0.00 30.61 2.23
5371 7622 9.100197 TGGAGTATACATTATGAAAGAGGCATA 57.900 33.333 5.50 0.00 0.00 3.14
5372 7623 7.977818 TGGAGTATACATTATGAAAGAGGCAT 58.022 34.615 5.50 0.00 0.00 4.40
5373 7624 7.373617 TGGAGTATACATTATGAAAGAGGCA 57.626 36.000 5.50 0.00 0.00 4.75
5374 7625 8.854614 ATTGGAGTATACATTATGAAAGAGGC 57.145 34.615 5.50 0.00 0.00 4.70
5382 7633 9.948964 TGATCTGGAATTGGAGTATACATTATG 57.051 33.333 5.50 0.00 0.00 1.90
5384 7635 9.948964 CATGATCTGGAATTGGAGTATACATTA 57.051 33.333 5.50 0.00 0.00 1.90
5385 7636 8.443176 ACATGATCTGGAATTGGAGTATACATT 58.557 33.333 5.50 0.00 0.00 2.71
5386 7637 7.982252 ACATGATCTGGAATTGGAGTATACAT 58.018 34.615 5.50 0.00 0.00 2.29
5387 7638 7.379059 ACATGATCTGGAATTGGAGTATACA 57.621 36.000 5.50 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.