Multiple sequence alignment - TraesCS1D01G328100

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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 TraesCS1D01G328100 chr1D 100.000 3208 0 0 1 3208 420001241 419998034 0.000000e+00 5925.0
1 TraesCS1D01G328100 chr1D 93.579 732 21 4 2502 3208 23325216 23325946 0.000000e+00 1068.0
2 TraesCS1D01G328100 chr1D 80.139 433 82 4 14 444 371094923 371095353 1.440000e-83 320.0
3 TraesCS1D01G328100 chr1B 93.911 1084 46 6 1256 2335 566983494 566982427 0.000000e+00 1618.0
4 TraesCS1D01G328100 chr1B 88.450 684 54 11 1 667 566986324 566985649 0.000000e+00 802.0
5 TraesCS1D01G328100 chr1B 87.978 366 24 6 910 1262 566983893 566983535 6.400000e-112 414.0
6 TraesCS1D01G328100 chr1B 95.556 90 3 1 656 745 566984686 566984598 3.340000e-30 143.0
7 TraesCS1D01G328100 chr1B 81.548 168 10 8 743 909 566984324 566984177 5.620000e-23 119.0
8 TraesCS1D01G328100 chr1A 89.333 750 38 11 2499 3208 7525152 7524405 0.000000e+00 904.0
9 TraesCS1D01G328100 chr1A 87.812 640 67 6 102 734 516592690 516592055 0.000000e+00 739.0
10 TraesCS1D01G328100 chr1A 83.011 465 50 13 2667 3108 32189607 32189149 8.340000e-106 394.0
11 TraesCS1D01G328100 chr1A 82.578 419 69 4 14 432 539318494 539318080 1.820000e-97 366.0
12 TraesCS1D01G328100 chr1A 81.596 451 71 6 1 450 262943471 262943032 2.350000e-96 363.0
13 TraesCS1D01G328100 chr1A 78.899 436 82 9 14 447 537823681 537823254 1.460000e-73 287.0
14 TraesCS1D01G328100 chr3D 83.295 880 128 5 1319 2184 536143457 536144331 0.000000e+00 793.0
15 TraesCS1D01G328100 chr3D 82.474 388 53 12 1286 1670 535650917 535650542 3.090000e-85 326.0
16 TraesCS1D01G328100 chr3D 81.633 392 56 14 1291 1677 536243978 536244358 8.640000e-81 311.0
17 TraesCS1D01G328100 chr3D 79.427 384 58 18 1293 1670 535644740 535644372 5.310000e-63 252.0
18 TraesCS1D01G328100 chr3D 81.928 166 27 3 1018 1183 535651180 535651018 1.550000e-28 137.0
19 TraesCS1D01G328100 chr3D 74.352 347 77 9 1327 1670 536210970 536211307 1.550000e-28 137.0
20 TraesCS1D01G328100 chr3D 91.525 59 4 1 2938 2996 477020794 477020851 2.650000e-11 80.5
21 TraesCS1D01G328100 chr3B 82.880 882 128 9 1319 2184 708362176 708361302 0.000000e+00 771.0
22 TraesCS1D01G328100 chr3B 79.023 839 144 23 1296 2127 708311150 708310337 2.180000e-151 545.0
23 TraesCS1D01G328100 chr3B 82.338 385 49 17 1291 1670 707128692 707128322 1.860000e-82 316.0
24 TraesCS1D01G328100 chr3B 87.387 111 14 0 1018 1128 707128965 707128855 9.340000e-26 128.0
25 TraesCS1D01G328100 chr3A 81.880 883 139 8 1319 2184 671678548 671677670 0.000000e+00 725.0
26 TraesCS1D01G328100 chr3A 78.690 840 148 21 1296 2127 671661150 671660334 6.090000e-147 531.0
27 TraesCS1D01G328100 chr3A 82.916 439 60 8 5 431 393879468 393879033 6.490000e-102 381.0
28 TraesCS1D01G328100 chr3A 80.156 514 68 19 2499 2993 449506827 449507325 1.420000e-93 353.0
29 TraesCS1D01G328100 chr3A 82.078 385 50 17 1291 1670 670834597 670834227 8.640000e-81 311.0
30 TraesCS1D01G328100 chr3A 81.330 391 57 14 1291 1677 671722949 671723327 1.450000e-78 303.0
31 TraesCS1D01G328100 chr3A 89.394 66 7 0 1563 1628 671659391 671659326 2.050000e-12 84.2
32 TraesCS1D01G328100 chr5A 85.085 704 52 21 2507 3206 41711059 41711713 0.000000e+00 669.0
33 TraesCS1D01G328100 chr5A 82.335 651 71 11 2499 3109 546386862 546387508 2.830000e-145 525.0
34 TraesCS1D01G328100 chr2A 83.614 653 65 9 2494 3109 734772733 734772086 2.780000e-160 575.0
35 TraesCS1D01G328100 chr2A 78.072 415 81 7 14 422 718467376 718466966 1.480000e-63 254.0
36 TraesCS1D01G328100 chr7A 82.867 607 69 17 2531 3109 307378428 307379027 2.210000e-141 512.0
37 TraesCS1D01G328100 chr7A 82.598 408 45 10 2609 3000 493654480 493654083 1.430000e-88 337.0
38 TraesCS1D01G328100 chr7B 84.354 441 56 7 14 443 104298769 104298331 1.380000e-113 420.0
39 TraesCS1D01G328100 chr7B 81.714 350 46 11 2645 2992 460564172 460563839 3.150000e-70 276.0
40 TraesCS1D01G328100 chr7B 82.353 153 20 4 2957 3108 601319170 601319024 3.360000e-25 126.0
41 TraesCS1D01G328100 chr5D 84.419 430 55 6 14 432 536239961 536239533 2.300000e-111 412.0
42 TraesCS1D01G328100 chr5D 97.872 47 1 0 2946 2992 557498072 557498026 7.380000e-12 82.4
43 TraesCS1D01G328100 chr2D 80.925 519 63 22 2496 2991 499118133 499118638 8.400000e-101 377.0
44 TraesCS1D01G328100 chr4B 84.770 348 37 5 2660 2994 107963539 107963883 5.130000e-88 335.0
45 TraesCS1D01G328100 chr2B 77.103 642 89 30 2495 3108 382236830 382236219 5.160000e-83 318.0
46 TraesCS1D01G328100 chr2B 78.571 434 79 10 18 443 67910741 67910314 1.130000e-69 274.0
47 TraesCS1D01G328100 chr2B 84.971 173 23 3 2937 3108 161152474 161152644 4.250000e-39 172.0
48 TraesCS1D01G328100 chr4D 80.057 351 66 3 84 434 455915022 455914676 1.140000e-64 257.0
49 TraesCS1D01G328100 chr4A 89.583 96 8 2 2962 3056 379462987 379463081 1.560000e-23 121.0


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 TraesCS1D01G328100 chr1D 419998034 420001241 3207 True 5925.0 5925 100.0000 1 3208 1 chr1D.!!$R1 3207
1 TraesCS1D01G328100 chr1D 23325216 23325946 730 False 1068.0 1068 93.5790 2502 3208 1 chr1D.!!$F1 706
2 TraesCS1D01G328100 chr1B 566982427 566986324 3897 True 619.2 1618 89.4886 1 2335 5 chr1B.!!$R1 2334
3 TraesCS1D01G328100 chr1A 7524405 7525152 747 True 904.0 904 89.3330 2499 3208 1 chr1A.!!$R1 709
4 TraesCS1D01G328100 chr1A 516592055 516592690 635 True 739.0 739 87.8120 102 734 1 chr1A.!!$R4 632
5 TraesCS1D01G328100 chr3D 536143457 536144331 874 False 793.0 793 83.2950 1319 2184 1 chr3D.!!$F2 865
6 TraesCS1D01G328100 chr3D 535650542 535651180 638 True 231.5 326 82.2010 1018 1670 2 chr3D.!!$R2 652
7 TraesCS1D01G328100 chr3B 708361302 708362176 874 True 771.0 771 82.8800 1319 2184 1 chr3B.!!$R2 865
8 TraesCS1D01G328100 chr3B 708310337 708311150 813 True 545.0 545 79.0230 1296 2127 1 chr3B.!!$R1 831
9 TraesCS1D01G328100 chr3B 707128322 707128965 643 True 222.0 316 84.8625 1018 1670 2 chr3B.!!$R3 652
10 TraesCS1D01G328100 chr3A 671677670 671678548 878 True 725.0 725 81.8800 1319 2184 1 chr3A.!!$R3 865
11 TraesCS1D01G328100 chr3A 671659326 671661150 1824 True 307.6 531 84.0420 1296 2127 2 chr3A.!!$R4 831
12 TraesCS1D01G328100 chr5A 41711059 41711713 654 False 669.0 669 85.0850 2507 3206 1 chr5A.!!$F1 699
13 TraesCS1D01G328100 chr5A 546386862 546387508 646 False 525.0 525 82.3350 2499 3109 1 chr5A.!!$F2 610
14 TraesCS1D01G328100 chr2A 734772086 734772733 647 True 575.0 575 83.6140 2494 3109 1 chr2A.!!$R2 615
15 TraesCS1D01G328100 chr7A 307378428 307379027 599 False 512.0 512 82.8670 2531 3109 1 chr7A.!!$F1 578
16 TraesCS1D01G328100 chr2D 499118133 499118638 505 False 377.0 377 80.9250 2496 2991 1 chr2D.!!$F1 495
17 TraesCS1D01G328100 chr2B 382236219 382236830 611 True 318.0 318 77.1030 2495 3108 1 chr2B.!!$R2 613

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
978 2534 0.105039 GCTACCATCAACGAGGGGAG 59.895 60.0 2.46 2.46 46.22 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 3998 0.106519 GCTAGGACATGGCCCAACAT 60.107 55.0 16.13 0.0 0.0 2.71 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 6.585702 CGACAGCTATCTGAAGATGGAATAAG 59.414 42.308 7.77 0.00 42.95 1.73
34 35 7.602265 GCTATCTGAAGATGGAATAAGGTTCTC 59.398 40.741 7.77 0.00 35.34 2.87
37 38 4.166144 TGAAGATGGAATAAGGTTCTCCCC 59.834 45.833 0.00 0.00 0.00 4.81
39 40 0.544697 TGGAATAAGGTTCTCCCCGC 59.455 55.000 0.00 0.00 0.00 6.13
51 52 2.758737 CCCCGCCTAGTCTCCGTT 60.759 66.667 0.00 0.00 0.00 4.44
52 53 2.783288 CCCCGCCTAGTCTCCGTTC 61.783 68.421 0.00 0.00 0.00 3.95
53 54 2.783288 CCCGCCTAGTCTCCGTTCC 61.783 68.421 0.00 0.00 0.00 3.62
55 56 2.404995 CGCCTAGTCTCCGTTCCGT 61.405 63.158 0.00 0.00 0.00 4.69
58 59 0.886563 CCTAGTCTCCGTTCCGTTGT 59.113 55.000 0.00 0.00 0.00 3.32
87 88 0.250858 CATTGTCAGTGGGCCTGTGA 60.251 55.000 4.53 4.50 42.19 3.58
132 133 2.214376 TTGGTGGATTTGCTCGGATT 57.786 45.000 0.00 0.00 0.00 3.01
139 140 2.177173 GATTTGCTCGGATTTTGTCGC 58.823 47.619 0.00 0.00 0.00 5.19
154 155 1.268692 TGTCGCAGTTCGTCTACGTTT 60.269 47.619 0.00 0.00 40.80 3.60
164 165 3.772932 TCGTCTACGTTTGTGTGTCTTT 58.227 40.909 0.00 0.00 40.80 2.52
249 250 1.637553 CCTATGGGGCCTTAGCATGAT 59.362 52.381 0.84 0.00 42.56 2.45
251 252 0.113776 ATGGGGCCTTAGCATGATGG 59.886 55.000 0.84 0.00 42.56 3.51
257 258 2.305009 GCCTTAGCATGATGGCTTCTT 58.695 47.619 5.12 0.00 42.71 2.52
259 260 3.548770 CCTTAGCATGATGGCTTCTTGA 58.451 45.455 17.10 0.00 42.71 3.02
260 261 3.314635 CCTTAGCATGATGGCTTCTTGAC 59.685 47.826 17.10 10.01 42.71 3.18
357 362 9.386010 GTATTCATCGATAGGTAGTCTACAGAT 57.614 37.037 12.08 4.23 31.74 2.90
360 365 8.363761 TCATCGATAGGTAGTCTACAGATCTA 57.636 38.462 12.08 4.60 30.24 1.98
364 369 9.697990 TCGATAGGTAGTCTACAGATCTAGATA 57.302 37.037 4.89 0.00 0.00 1.98
465 470 9.617975 CAAATGTTAGTCATCTTTCTCTTTTCC 57.382 33.333 0.00 0.00 35.48 3.13
583 599 7.141100 ACGAAAACAATCTTATAACCCACTG 57.859 36.000 0.00 0.00 0.00 3.66
636 655 1.425412 ATAGACACCGCACACGTTTC 58.575 50.000 0.00 0.00 37.70 2.78
748 2020 0.535335 TCAGAGGGGTTCATACGTGC 59.465 55.000 0.00 0.00 0.00 5.34
753 2025 1.702491 GGGGTTCATACGTGCTTCGC 61.702 60.000 0.00 0.00 44.19 4.70
799 2071 5.936686 ATTTGCATCTGGATCGAGTAATG 57.063 39.130 4.53 3.67 0.00 1.90
800 2072 3.391506 TGCATCTGGATCGAGTAATGG 57.608 47.619 4.53 0.00 0.00 3.16
802 2074 3.387699 TGCATCTGGATCGAGTAATGGAA 59.612 43.478 4.53 0.00 0.00 3.53
803 2075 4.040829 TGCATCTGGATCGAGTAATGGAAT 59.959 41.667 4.53 0.00 0.00 3.01
804 2076 4.999950 GCATCTGGATCGAGTAATGGAATT 59.000 41.667 4.53 0.00 41.28 2.17
805 2077 5.106791 GCATCTGGATCGAGTAATGGAATTG 60.107 44.000 4.53 0.00 36.99 2.32
806 2078 4.380531 TCTGGATCGAGTAATGGAATTGC 58.619 43.478 4.53 0.00 39.39 3.56
807 2079 4.129380 CTGGATCGAGTAATGGAATTGCA 58.871 43.478 0.79 0.79 41.74 4.08
808 2080 3.876914 TGGATCGAGTAATGGAATTGCAC 59.123 43.478 0.12 0.00 41.74 4.57
809 2081 3.876914 GGATCGAGTAATGGAATTGCACA 59.123 43.478 0.12 0.00 41.74 4.57
810 2082 4.516698 GGATCGAGTAATGGAATTGCACAT 59.483 41.667 0.12 0.00 41.74 3.21
811 2083 4.880886 TCGAGTAATGGAATTGCACATG 57.119 40.909 0.12 0.00 41.74 3.21
813 2085 4.940654 TCGAGTAATGGAATTGCACATGAA 59.059 37.500 0.12 0.00 41.74 2.57
814 2086 5.030295 CGAGTAATGGAATTGCACATGAAC 58.970 41.667 0.12 0.00 41.74 3.18
815 2087 4.985413 AGTAATGGAATTGCACATGAACG 58.015 39.130 0.12 0.00 41.74 3.95
816 2088 2.282701 ATGGAATTGCACATGAACGC 57.717 45.000 0.12 0.00 0.00 4.84
817 2089 0.957362 TGGAATTGCACATGAACGCA 59.043 45.000 0.00 2.00 36.05 5.24
818 2090 1.335780 TGGAATTGCACATGAACGCAC 60.336 47.619 0.00 0.00 38.00 5.34
819 2091 1.068333 GGAATTGCACATGAACGCACT 60.068 47.619 0.00 0.00 38.00 4.40
820 2092 2.607771 GGAATTGCACATGAACGCACTT 60.608 45.455 0.00 5.80 38.00 3.16
821 2093 2.054687 ATTGCACATGAACGCACTTG 57.945 45.000 0.00 0.00 38.00 3.16
822 2094 0.594540 TTGCACATGAACGCACTTGC 60.595 50.000 0.00 0.00 38.00 4.01
823 2095 1.008652 GCACATGAACGCACTTGCA 60.009 52.632 0.00 0.00 42.21 4.08
824 2096 0.387622 GCACATGAACGCACTTGCAT 60.388 50.000 0.00 0.00 42.21 3.96
825 2097 1.609932 CACATGAACGCACTTGCATC 58.390 50.000 0.00 0.00 42.21 3.91
826 2098 0.523072 ACATGAACGCACTTGCATCC 59.477 50.000 0.00 0.00 42.21 3.51
827 2099 0.179156 CATGAACGCACTTGCATCCC 60.179 55.000 1.48 0.00 42.21 3.85
828 2100 1.315257 ATGAACGCACTTGCATCCCC 61.315 55.000 1.48 0.00 42.21 4.81
829 2101 1.971167 GAACGCACTTGCATCCCCA 60.971 57.895 1.48 0.00 42.21 4.96
830 2102 1.926511 GAACGCACTTGCATCCCCAG 61.927 60.000 1.48 0.00 42.21 4.45
831 2103 2.360350 CGCACTTGCATCCCCAGT 60.360 61.111 1.48 0.00 42.21 4.00
832 2104 2.693762 CGCACTTGCATCCCCAGTG 61.694 63.158 10.51 10.51 42.21 3.66
833 2105 2.345760 GCACTTGCATCCCCAGTGG 61.346 63.158 15.40 0.63 41.59 4.00
874 2146 1.590525 CGGCCATGAATGCACATGC 60.591 57.895 10.95 0.00 44.11 4.06
888 2160 0.604578 ACATGCACATGGAGGTTTGC 59.395 50.000 14.73 0.00 42.91 3.68
897 2169 1.522668 TGGAGGTTTGCGATTCACTG 58.477 50.000 0.00 0.00 0.00 3.66
903 2175 0.874390 TTTGCGATTCACTGGCTCAC 59.126 50.000 0.00 0.00 0.00 3.51
906 2178 0.445436 GCGATTCACTGGCTCACTTG 59.555 55.000 0.00 0.00 0.00 3.16
924 2480 0.829990 TGGGAAGCTGCATGACGATA 59.170 50.000 1.02 0.00 0.00 2.92
927 2483 2.402305 GGAAGCTGCATGACGATAGAG 58.598 52.381 1.02 0.00 41.38 2.43
949 2505 8.214721 AGAGTAGCATTTTATTTTGCCTCTAC 57.785 34.615 0.00 0.00 36.42 2.59
956 2512 6.484818 TTTTATTTTGCCTCTACGTACCAC 57.515 37.500 0.00 0.00 0.00 4.16
957 2513 3.975168 ATTTTGCCTCTACGTACCACT 57.025 42.857 0.00 0.00 0.00 4.00
958 2514 6.528537 TTATTTTGCCTCTACGTACCACTA 57.471 37.500 0.00 0.00 0.00 2.74
959 2515 4.445452 TTTTGCCTCTACGTACCACTAG 57.555 45.455 0.00 0.00 0.00 2.57
972 2528 2.453521 ACCACTAGCTACCATCAACGA 58.546 47.619 0.00 0.00 0.00 3.85
974 2530 2.223829 CCACTAGCTACCATCAACGAGG 60.224 54.545 0.00 0.00 0.00 4.63
975 2531 2.032620 ACTAGCTACCATCAACGAGGG 58.967 52.381 0.00 0.00 39.63 4.30
976 2532 1.341531 CTAGCTACCATCAACGAGGGG 59.658 57.143 0.00 0.00 37.87 4.79
977 2533 0.325296 AGCTACCATCAACGAGGGGA 60.325 55.000 0.00 0.00 37.87 4.81
978 2534 0.105039 GCTACCATCAACGAGGGGAG 59.895 60.000 2.46 2.46 46.22 4.30
979 2535 0.753262 CTACCATCAACGAGGGGAGG 59.247 60.000 0.00 0.00 40.44 4.30
980 2536 0.689745 TACCATCAACGAGGGGAGGG 60.690 60.000 0.00 0.00 37.87 4.30
981 2537 1.995626 CCATCAACGAGGGGAGGGT 60.996 63.158 0.00 0.00 30.64 4.34
982 2538 1.221840 CATCAACGAGGGGAGGGTG 59.778 63.158 0.00 0.00 0.00 4.61
983 2539 1.995626 ATCAACGAGGGGAGGGTGG 60.996 63.158 0.00 0.00 0.00 4.61
984 2540 4.410400 CAACGAGGGGAGGGTGGC 62.410 72.222 0.00 0.00 0.00 5.01
1006 2578 4.545706 GGGCGATCGACATGGGCA 62.546 66.667 24.83 0.00 35.24 5.36
1041 2613 1.982395 CAGGGTCAGCCACTCGGTA 60.982 63.158 0.00 0.00 36.17 4.02
1194 2766 0.106819 GCCATGCCAACCTCATCTCT 60.107 55.000 0.00 0.00 0.00 3.10
1221 2799 2.951642 TGGTTCAGCTCAAGAAAAGGTG 59.048 45.455 0.00 0.00 42.26 4.00
1227 2805 3.003480 AGCTCAAGAAAAGGTGCGTATC 58.997 45.455 0.00 0.00 0.00 2.24
1228 2806 2.742053 GCTCAAGAAAAGGTGCGTATCA 59.258 45.455 0.00 0.00 0.00 2.15
1230 2808 4.142600 GCTCAAGAAAAGGTGCGTATCAAT 60.143 41.667 0.00 0.00 0.00 2.57
1233 2811 5.935206 TCAAGAAAAGGTGCGTATCAATGTA 59.065 36.000 0.00 0.00 0.00 2.29
1234 2812 6.597672 TCAAGAAAAGGTGCGTATCAATGTAT 59.402 34.615 0.00 0.00 0.00 2.29
1235 2813 6.363577 AGAAAAGGTGCGTATCAATGTATG 57.636 37.500 0.00 0.00 0.00 2.39
1237 2815 5.484173 AAAGGTGCGTATCAATGTATGTG 57.516 39.130 0.00 0.00 0.00 3.21
1238 2816 2.872245 AGGTGCGTATCAATGTATGTGC 59.128 45.455 0.00 0.00 0.00 4.57
1239 2817 2.611751 GGTGCGTATCAATGTATGTGCA 59.388 45.455 0.00 0.00 0.00 4.57
1271 2896 7.008628 GTGTTACTTAATTTGCATGCTCATGTC 59.991 37.037 20.33 4.95 40.80 3.06
1967 3615 2.432628 CAGTTCCTCGACACGGCC 60.433 66.667 0.00 0.00 0.00 6.13
2054 3702 3.984193 CTGCTTCGGCCTGGGGAAG 62.984 68.421 12.36 12.36 41.96 3.46
2100 3748 0.034896 CCGGCAGTGGAACAACTACT 59.965 55.000 0.00 0.00 44.16 2.57
2136 3784 0.915364 GGAGAGGAGGAATGCCAAGT 59.085 55.000 0.00 0.00 36.29 3.16
2232 3892 2.586079 CGGCGCGTGATTCTGGAT 60.586 61.111 8.43 0.00 0.00 3.41
2255 3915 2.348620 TGCTGAGGCATCGCTTGT 59.651 55.556 14.27 0.00 44.28 3.16
2256 3916 1.596408 TGCTGAGGCATCGCTTGTA 59.404 52.632 14.27 0.00 44.28 2.41
2257 3917 0.460811 TGCTGAGGCATCGCTTGTAG 60.461 55.000 14.27 0.00 44.28 2.74
2258 3918 0.460987 GCTGAGGCATCGCTTGTAGT 60.461 55.000 7.72 0.00 38.54 2.73
2259 3919 1.202417 GCTGAGGCATCGCTTGTAGTA 60.202 52.381 7.72 0.00 38.54 1.82
2260 3920 2.464865 CTGAGGCATCGCTTGTAGTAC 58.535 52.381 0.00 0.00 0.00 2.73
2261 3921 1.822371 TGAGGCATCGCTTGTAGTACA 59.178 47.619 0.00 0.00 0.00 2.90
2302 3962 7.591426 GTCTCGTTCAGAAATAACAGCAAAAAT 59.409 33.333 0.00 0.00 30.72 1.82
2335 3995 4.156455 AGGGCAACATAATGATCGAACT 57.844 40.909 0.00 0.00 39.74 3.01
2336 3996 5.290493 AGGGCAACATAATGATCGAACTA 57.710 39.130 0.00 0.00 39.74 2.24
2337 3997 5.057149 AGGGCAACATAATGATCGAACTAC 58.943 41.667 0.00 0.00 39.74 2.73
2338 3998 4.814234 GGGCAACATAATGATCGAACTACA 59.186 41.667 0.00 0.00 39.74 2.74
2339 3999 5.470098 GGGCAACATAATGATCGAACTACAT 59.530 40.000 0.00 0.00 39.74 2.29
2340 4000 6.365839 GGCAACATAATGATCGAACTACATG 58.634 40.000 0.00 0.00 0.00 3.21
2341 4001 6.017934 GGCAACATAATGATCGAACTACATGT 60.018 38.462 2.69 2.69 0.00 3.21
2342 4002 7.409697 GCAACATAATGATCGAACTACATGTT 58.590 34.615 2.30 10.48 42.38 2.71
2343 4003 8.757817 CAACATAATGATCGAACTACATGTTG 57.242 34.615 20.98 20.98 42.94 3.33
2344 4004 7.482654 ACATAATGATCGAACTACATGTTGG 57.517 36.000 2.30 0.00 39.30 3.77
2345 4005 6.483307 ACATAATGATCGAACTACATGTTGGG 59.517 38.462 2.30 0.00 39.30 4.12
2346 4006 2.627945 TGATCGAACTACATGTTGGGC 58.372 47.619 2.30 0.00 39.30 5.36
2347 4007 1.940613 GATCGAACTACATGTTGGGCC 59.059 52.381 2.30 0.00 39.30 5.80
2348 4008 0.687920 TCGAACTACATGTTGGGCCA 59.312 50.000 0.00 0.00 39.30 5.36
2349 4009 1.280710 TCGAACTACATGTTGGGCCAT 59.719 47.619 7.26 0.00 39.30 4.40
2350 4010 1.401552 CGAACTACATGTTGGGCCATG 59.598 52.381 7.26 5.37 46.14 3.66
2354 4014 4.770540 CATGTTGGGCCATGTCCT 57.229 55.556 7.26 0.00 37.91 3.85
2355 4015 3.901087 CATGTTGGGCCATGTCCTA 57.099 52.632 7.26 0.00 37.91 2.94
2356 4016 1.683943 CATGTTGGGCCATGTCCTAG 58.316 55.000 7.26 0.00 37.91 3.02
2357 4017 0.106519 ATGTTGGGCCATGTCCTAGC 60.107 55.000 7.26 0.00 0.00 3.42
2358 4018 1.207488 TGTTGGGCCATGTCCTAGCT 61.207 55.000 7.26 0.00 0.00 3.32
2359 4019 0.749454 GTTGGGCCATGTCCTAGCTG 60.749 60.000 7.26 0.00 0.00 4.24
2360 4020 0.913934 TTGGGCCATGTCCTAGCTGA 60.914 55.000 7.26 0.00 0.00 4.26
2361 4021 0.913934 TGGGCCATGTCCTAGCTGAA 60.914 55.000 0.00 0.00 0.00 3.02
2362 4022 0.255890 GGGCCATGTCCTAGCTGAAA 59.744 55.000 4.39 0.00 0.00 2.69
2363 4023 1.673168 GGCCATGTCCTAGCTGAAAG 58.327 55.000 0.00 0.00 0.00 2.62
2381 4041 3.963622 GCAGATCGCTCAGTTGTTG 57.036 52.632 2.84 0.00 37.77 3.33
2382 4042 0.179205 GCAGATCGCTCAGTTGTTGC 60.179 55.000 2.84 0.00 37.77 4.17
2383 4043 1.150827 CAGATCGCTCAGTTGTTGCA 58.849 50.000 0.00 0.00 0.00 4.08
2384 4044 1.736126 CAGATCGCTCAGTTGTTGCAT 59.264 47.619 0.00 0.00 0.00 3.96
2385 4045 2.161012 CAGATCGCTCAGTTGTTGCATT 59.839 45.455 0.00 0.00 0.00 3.56
2386 4046 2.417933 AGATCGCTCAGTTGTTGCATTC 59.582 45.455 0.00 0.00 0.00 2.67
2387 4047 0.874390 TCGCTCAGTTGTTGCATTCC 59.126 50.000 0.00 0.00 0.00 3.01
2388 4048 0.877071 CGCTCAGTTGTTGCATTCCT 59.123 50.000 0.00 0.00 0.00 3.36
2389 4049 1.267806 CGCTCAGTTGTTGCATTCCTT 59.732 47.619 0.00 0.00 0.00 3.36
2390 4050 2.287788 CGCTCAGTTGTTGCATTCCTTT 60.288 45.455 0.00 0.00 0.00 3.11
2391 4051 3.311966 GCTCAGTTGTTGCATTCCTTTC 58.688 45.455 0.00 0.00 0.00 2.62
2392 4052 3.005155 GCTCAGTTGTTGCATTCCTTTCT 59.995 43.478 0.00 0.00 0.00 2.52
2393 4053 4.500375 GCTCAGTTGTTGCATTCCTTTCTT 60.500 41.667 0.00 0.00 0.00 2.52
2394 4054 5.594926 CTCAGTTGTTGCATTCCTTTCTTT 58.405 37.500 0.00 0.00 0.00 2.52
2395 4055 5.976458 TCAGTTGTTGCATTCCTTTCTTTT 58.024 33.333 0.00 0.00 0.00 2.27
2396 4056 6.405538 TCAGTTGTTGCATTCCTTTCTTTTT 58.594 32.000 0.00 0.00 0.00 1.94
2418 4078 7.775397 TTTTATAACCTACTGATAACACGCC 57.225 36.000 0.00 0.00 0.00 5.68
2419 4079 6.468333 TTATAACCTACTGATAACACGCCA 57.532 37.500 0.00 0.00 0.00 5.69
2420 4080 2.961526 ACCTACTGATAACACGCCAG 57.038 50.000 0.00 0.00 0.00 4.85
2421 4081 1.134788 ACCTACTGATAACACGCCAGC 60.135 52.381 0.00 0.00 0.00 4.85
2422 4082 1.571919 CTACTGATAACACGCCAGCC 58.428 55.000 0.00 0.00 0.00 4.85
2423 4083 1.137086 CTACTGATAACACGCCAGCCT 59.863 52.381 0.00 0.00 0.00 4.58
2424 4084 0.108138 ACTGATAACACGCCAGCCTC 60.108 55.000 0.00 0.00 0.00 4.70
2425 4085 0.811616 CTGATAACACGCCAGCCTCC 60.812 60.000 0.00 0.00 0.00 4.30
2426 4086 1.523938 GATAACACGCCAGCCTCCC 60.524 63.158 0.00 0.00 0.00 4.30
2427 4087 2.942648 GATAACACGCCAGCCTCCCC 62.943 65.000 0.00 0.00 0.00 4.81
2429 4089 2.808761 TAACACGCCAGCCTCCCCTA 62.809 60.000 0.00 0.00 0.00 3.53
2430 4090 3.399181 CACGCCAGCCTCCCCTAA 61.399 66.667 0.00 0.00 0.00 2.69
2431 4091 2.609610 ACGCCAGCCTCCCCTAAA 60.610 61.111 0.00 0.00 0.00 1.85
2432 4092 2.228480 ACGCCAGCCTCCCCTAAAA 61.228 57.895 0.00 0.00 0.00 1.52
2433 4093 1.001393 CGCCAGCCTCCCCTAAAAA 60.001 57.895 0.00 0.00 0.00 1.94
2450 4110 1.445871 AAAAGGATAACACGTCGGCC 58.554 50.000 0.00 0.00 0.00 6.13
2451 4111 0.611714 AAAGGATAACACGTCGGCCT 59.388 50.000 0.00 0.00 0.00 5.19
2452 4112 1.477553 AAGGATAACACGTCGGCCTA 58.522 50.000 0.00 0.00 0.00 3.93
2453 4113 1.030457 AGGATAACACGTCGGCCTAG 58.970 55.000 0.00 0.00 0.00 3.02
2454 4114 0.596859 GGATAACACGTCGGCCTAGC 60.597 60.000 0.00 0.00 0.00 3.42
2455 4115 0.384669 GATAACACGTCGGCCTAGCT 59.615 55.000 0.00 0.00 0.00 3.32
2456 4116 1.605710 GATAACACGTCGGCCTAGCTA 59.394 52.381 0.00 0.00 0.00 3.32
2457 4117 0.734889 TAACACGTCGGCCTAGCTAC 59.265 55.000 0.00 0.00 0.00 3.58
2458 4118 1.246056 AACACGTCGGCCTAGCTACA 61.246 55.000 0.00 0.00 0.00 2.74
2459 4119 1.226603 CACGTCGGCCTAGCTACAC 60.227 63.158 0.00 0.00 0.00 2.90
2460 4120 1.378250 ACGTCGGCCTAGCTACACT 60.378 57.895 0.00 0.00 0.00 3.55
2461 4121 0.107508 ACGTCGGCCTAGCTACACTA 60.108 55.000 0.00 0.00 0.00 2.74
2462 4122 1.019673 CGTCGGCCTAGCTACACTAA 58.980 55.000 0.00 0.00 0.00 2.24
2463 4123 1.402968 CGTCGGCCTAGCTACACTAAA 59.597 52.381 0.00 0.00 0.00 1.85
2464 4124 2.541178 CGTCGGCCTAGCTACACTAAAG 60.541 54.545 0.00 0.00 0.00 1.85
2465 4125 2.686915 GTCGGCCTAGCTACACTAAAGA 59.313 50.000 0.00 0.00 0.00 2.52
2466 4126 3.129988 GTCGGCCTAGCTACACTAAAGAA 59.870 47.826 0.00 0.00 0.00 2.52
2467 4127 3.765511 TCGGCCTAGCTACACTAAAGAAA 59.234 43.478 0.00 0.00 0.00 2.52
2468 4128 4.404715 TCGGCCTAGCTACACTAAAGAAAT 59.595 41.667 0.00 0.00 0.00 2.17
2469 4129 5.105064 TCGGCCTAGCTACACTAAAGAAATT 60.105 40.000 0.00 0.00 0.00 1.82
2470 4130 5.585047 CGGCCTAGCTACACTAAAGAAATTT 59.415 40.000 0.00 0.00 0.00 1.82
2471 4131 6.238130 CGGCCTAGCTACACTAAAGAAATTTC 60.238 42.308 10.33 10.33 0.00 2.17
2472 4132 6.824196 GGCCTAGCTACACTAAAGAAATTTCT 59.176 38.462 15.11 15.11 39.74 2.52
2485 4145 5.690997 AGAAATTTCTTTCCGGAGTCAAC 57.309 39.130 15.11 0.00 41.46 3.18
2486 4146 4.519350 AGAAATTTCTTTCCGGAGTCAACC 59.481 41.667 15.11 0.00 41.46 3.77
2487 4147 2.265589 TTTCTTTCCGGAGTCAACCC 57.734 50.000 3.34 0.00 0.00 4.11
2488 4148 1.133363 TTCTTTCCGGAGTCAACCCA 58.867 50.000 3.34 0.00 0.00 4.51
2489 4149 1.358152 TCTTTCCGGAGTCAACCCAT 58.642 50.000 3.34 0.00 0.00 4.00
2490 4150 1.702957 TCTTTCCGGAGTCAACCCATT 59.297 47.619 3.34 0.00 0.00 3.16
2491 4151 2.107552 TCTTTCCGGAGTCAACCCATTT 59.892 45.455 3.34 0.00 0.00 2.32
2492 4152 3.328343 TCTTTCCGGAGTCAACCCATTTA 59.672 43.478 3.34 0.00 0.00 1.40
2592 4283 0.662619 CGCTGACTTTTCTTGCCACA 59.337 50.000 0.00 0.00 0.00 4.17
2597 4288 2.024414 GACTTTTCTTGCCACACTGGT 58.976 47.619 0.00 0.00 40.46 4.00
2918 4750 0.182775 AGGGCGGTTGACAAGAGTTT 59.817 50.000 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.292120 AGAACCTTATTCCATCTTCAGATAGCT 59.708 37.037 0.00 0.00 32.63 3.32
11 12 6.183361 GGGAGAACCTTATTCCATCTTCAGAT 60.183 42.308 0.00 0.00 35.85 2.90
12 13 5.131142 GGGAGAACCTTATTCCATCTTCAGA 59.869 44.000 0.00 0.00 35.85 3.27
13 14 5.372373 GGGAGAACCTTATTCCATCTTCAG 58.628 45.833 0.00 0.00 35.85 3.02
28 29 1.381463 AGACTAGGCGGGGAGAACC 60.381 63.158 0.00 0.00 39.11 3.62
34 35 2.758737 AACGGAGACTAGGCGGGG 60.759 66.667 0.00 0.00 0.00 5.73
75 76 2.078665 ACACCTTCACAGGCCCACT 61.079 57.895 0.00 0.00 45.56 4.00
139 140 2.855963 ACACACAAACGTAGACGAACTG 59.144 45.455 9.41 5.33 43.02 3.16
154 155 4.698201 TGATCCAACCTAAAGACACACA 57.302 40.909 0.00 0.00 0.00 3.72
249 250 4.149598 TGTAGTAGACAGTCAAGAAGCCA 58.850 43.478 2.66 0.00 32.86 4.75
251 252 5.529791 TGTTGTAGTAGACAGTCAAGAAGC 58.470 41.667 2.66 0.00 39.88 3.86
257 258 7.101054 ACAAAACTTGTTGTAGTAGACAGTCA 58.899 34.615 2.66 0.00 42.22 3.41
259 260 6.537660 GGACAAAACTTGTTGTAGTAGACAGT 59.462 38.462 0.00 0.00 45.52 3.55
260 261 6.292168 CGGACAAAACTTGTTGTAGTAGACAG 60.292 42.308 0.00 0.00 45.52 3.51
384 389 3.980646 TCATGGCAGTACAACAAACAC 57.019 42.857 0.00 0.00 0.00 3.32
439 444 9.617975 GGAAAAGAGAAAGATGACTAACATTTG 57.382 33.333 0.00 0.00 39.56 2.32
519 525 7.155328 TGTAGAGGAGAGAGACAATGAAAAAC 58.845 38.462 0.00 0.00 0.00 2.43
522 528 7.487822 AATGTAGAGGAGAGAGACAATGAAA 57.512 36.000 0.00 0.00 0.00 2.69
583 599 8.804688 AGAGATCGAGCAAGTACAATATTAAC 57.195 34.615 2.38 0.00 0.00 2.01
590 606 5.638596 TGTTAGAGATCGAGCAAGTACAA 57.361 39.130 2.38 0.00 0.00 2.41
636 655 2.653702 GATCGATGGAGCTCCGGG 59.346 66.667 27.43 18.28 39.43 5.73
703 1699 2.603560 GCCCATTCTTTTACGTCTCTCG 59.396 50.000 0.00 0.00 46.00 4.04
753 2025 2.800881 TATCGTATCTGCTGCCACAG 57.199 50.000 0.00 0.00 39.12 3.66
799 2071 1.068333 AGTGCGTTCATGTGCAATTCC 60.068 47.619 10.67 1.21 43.75 3.01
800 2072 2.336554 AGTGCGTTCATGTGCAATTC 57.663 45.000 10.67 1.49 43.75 2.17
802 2074 1.931709 GCAAGTGCGTTCATGTGCAAT 60.932 47.619 10.67 7.77 43.75 3.56
803 2075 0.594540 GCAAGTGCGTTCATGTGCAA 60.595 50.000 10.67 0.00 43.75 4.08
804 2076 1.008652 GCAAGTGCGTTCATGTGCA 60.009 52.632 6.05 6.05 39.13 4.57
805 2077 0.387622 ATGCAAGTGCGTTCATGTGC 60.388 50.000 0.00 0.00 45.83 4.57
806 2078 1.609932 GATGCAAGTGCGTTCATGTG 58.390 50.000 0.00 0.00 45.83 3.21
807 2079 0.523072 GGATGCAAGTGCGTTCATGT 59.477 50.000 0.00 0.00 45.83 3.21
808 2080 0.179156 GGGATGCAAGTGCGTTCATG 60.179 55.000 6.14 0.00 45.83 3.07
809 2081 1.315257 GGGGATGCAAGTGCGTTCAT 61.315 55.000 6.14 0.00 45.83 2.57
810 2082 1.971167 GGGGATGCAAGTGCGTTCA 60.971 57.895 6.14 0.00 45.83 3.18
811 2083 1.926511 CTGGGGATGCAAGTGCGTTC 61.927 60.000 0.00 0.00 45.83 3.95
813 2085 2.360350 CTGGGGATGCAAGTGCGT 60.360 61.111 0.00 0.00 45.83 5.24
814 2086 2.360350 ACTGGGGATGCAAGTGCG 60.360 61.111 0.00 0.00 45.83 5.34
815 2087 2.345760 CCACTGGGGATGCAAGTGC 61.346 63.158 9.54 0.00 39.99 4.40
816 2088 1.379916 TCCACTGGGGATGCAAGTG 59.620 57.895 8.26 8.26 42.15 3.16
817 2089 3.920817 TCCACTGGGGATGCAAGT 58.079 55.556 0.00 0.00 42.15 3.16
824 2096 0.401395 AGGTGAAAGTCCACTGGGGA 60.401 55.000 0.00 0.00 45.89 4.81
825 2097 0.036875 GAGGTGAAAGTCCACTGGGG 59.963 60.000 0.00 0.00 37.24 4.96
826 2098 1.059913 AGAGGTGAAAGTCCACTGGG 58.940 55.000 0.00 0.00 37.24 4.45
827 2099 2.370189 AGAAGAGGTGAAAGTCCACTGG 59.630 50.000 0.00 0.00 37.24 4.00
828 2100 3.760580 AGAAGAGGTGAAAGTCCACTG 57.239 47.619 0.00 0.00 37.24 3.66
829 2101 3.711704 TGAAGAAGAGGTGAAAGTCCACT 59.288 43.478 0.00 0.00 37.24 4.00
830 2102 4.061596 CTGAAGAAGAGGTGAAAGTCCAC 58.938 47.826 0.00 0.00 36.37 4.02
831 2103 3.711704 ACTGAAGAAGAGGTGAAAGTCCA 59.288 43.478 0.00 0.00 0.00 4.02
832 2104 4.311606 GACTGAAGAAGAGGTGAAAGTCC 58.688 47.826 0.00 0.00 0.00 3.85
833 2105 3.984633 CGACTGAAGAAGAGGTGAAAGTC 59.015 47.826 0.00 0.00 0.00 3.01
838 2110 0.241213 CGCGACTGAAGAAGAGGTGA 59.759 55.000 0.00 0.00 0.00 4.02
874 2146 1.811965 TGAATCGCAAACCTCCATGTG 59.188 47.619 0.00 0.00 0.00 3.21
875 2147 1.812571 GTGAATCGCAAACCTCCATGT 59.187 47.619 0.00 0.00 0.00 3.21
876 2148 2.086869 AGTGAATCGCAAACCTCCATG 58.913 47.619 0.00 0.00 0.00 3.66
877 2149 2.086869 CAGTGAATCGCAAACCTCCAT 58.913 47.619 0.00 0.00 0.00 3.41
878 2150 1.522668 CAGTGAATCGCAAACCTCCA 58.477 50.000 0.00 0.00 0.00 3.86
879 2151 0.804989 CCAGTGAATCGCAAACCTCC 59.195 55.000 0.00 0.00 0.00 4.30
888 2160 1.081892 CCAAGTGAGCCAGTGAATCG 58.918 55.000 0.00 0.00 0.00 3.34
897 2169 2.338785 GCAGCTTCCCAAGTGAGCC 61.339 63.158 0.00 0.00 37.11 4.70
903 2175 0.674581 TCGTCATGCAGCTTCCCAAG 60.675 55.000 0.00 0.00 0.00 3.61
906 2178 1.069204 TCTATCGTCATGCAGCTTCCC 59.931 52.381 0.00 0.00 0.00 3.97
924 2480 7.011482 CGTAGAGGCAAAATAAAATGCTACTCT 59.989 37.037 10.07 10.07 41.20 3.24
927 2483 6.782150 ACGTAGAGGCAAAATAAAATGCTAC 58.218 36.000 0.00 0.00 42.20 3.58
942 2498 1.677942 AGCTAGTGGTACGTAGAGGC 58.322 55.000 0.00 0.00 0.00 4.70
949 2505 3.703420 GTTGATGGTAGCTAGTGGTACG 58.297 50.000 0.00 0.00 45.22 3.67
956 2512 1.341531 CCCCTCGTTGATGGTAGCTAG 59.658 57.143 0.00 0.00 0.00 3.42
957 2513 1.063492 TCCCCTCGTTGATGGTAGCTA 60.063 52.381 0.00 0.00 0.00 3.32
958 2514 0.325296 TCCCCTCGTTGATGGTAGCT 60.325 55.000 0.00 0.00 0.00 3.32
959 2515 0.105039 CTCCCCTCGTTGATGGTAGC 59.895 60.000 0.00 0.00 0.00 3.58
984 2540 1.884464 CATGTCGATCGCCCAGTGG 60.884 63.158 11.09 0.63 0.00 4.00
985 2541 1.884464 CCATGTCGATCGCCCAGTG 60.884 63.158 11.09 9.35 0.00 3.66
988 2544 4.545706 GCCCATGTCGATCGCCCA 62.546 66.667 11.09 10.01 0.00 5.36
1194 2766 4.890158 TTCTTGAGCTGAACCATGAGTA 57.110 40.909 0.00 0.00 0.00 2.59
1221 2799 3.846023 GCACTGCACATACATTGATACGC 60.846 47.826 0.00 0.00 0.00 4.42
1227 2805 2.227149 ACACTGCACTGCACATACATTG 59.773 45.455 0.00 0.00 33.79 2.82
1228 2806 2.507484 ACACTGCACTGCACATACATT 58.493 42.857 0.00 0.00 33.79 2.71
1230 2808 1.965935 AACACTGCACTGCACATACA 58.034 45.000 0.00 0.00 33.79 2.29
1233 2811 2.260844 AGTAACACTGCACTGCACAT 57.739 45.000 0.00 0.00 33.79 3.21
1234 2812 2.036958 AAGTAACACTGCACTGCACA 57.963 45.000 0.00 0.00 33.79 4.57
1235 2813 4.749245 ATTAAGTAACACTGCACTGCAC 57.251 40.909 0.00 0.00 33.79 4.57
1237 2815 4.382754 GCAAATTAAGTAACACTGCACTGC 59.617 41.667 0.00 0.00 0.00 4.40
1238 2816 5.518812 TGCAAATTAAGTAACACTGCACTG 58.481 37.500 0.00 0.00 33.65 3.66
1239 2817 5.766150 TGCAAATTAAGTAACACTGCACT 57.234 34.783 0.00 0.00 33.65 4.40
1271 2896 1.908065 CATGCATGCATGTGAGTGTG 58.092 50.000 40.30 22.47 46.20 3.82
1300 2941 3.797353 GCCCCGGGAATGCTCTCA 61.797 66.667 26.32 0.00 0.00 3.27
1445 3086 2.125552 TTGAGGAGGTGCGCGATG 60.126 61.111 12.10 0.00 0.00 3.84
1819 3464 2.797278 ATCATCTCCACCGTCCGCC 61.797 63.158 0.00 0.00 0.00 6.13
1871 3516 3.075005 GCCTGCTCGTGGTCCCTA 61.075 66.667 0.00 0.00 0.00 3.53
2030 3678 3.003173 AGGCCGAAGCAGCAGGTA 61.003 61.111 0.00 0.00 42.56 3.08
2050 3698 2.545731 GGAGATCGCTCAACTTCTTCC 58.454 52.381 0.00 0.00 43.14 3.46
2054 3702 0.528684 CCCGGAGATCGCTCAACTTC 60.529 60.000 0.73 0.00 43.14 3.01
2082 3730 1.429463 GAGTAGTTGTTCCACTGCCG 58.571 55.000 0.00 0.00 30.04 5.69
2093 3741 1.421410 GCGTCATGGCCGAGTAGTTG 61.421 60.000 9.44 0.00 0.00 3.16
2216 3876 1.295792 TAAATCCAGAATCACGCGCC 58.704 50.000 5.73 0.00 0.00 6.53
2274 3934 4.447724 TGCTGTTATTTCTGAACGAGACAC 59.552 41.667 0.00 0.00 0.00 3.67
2321 3981 6.566564 GCCCAACATGTAGTTCGATCATTATG 60.567 42.308 0.00 0.42 38.74 1.90
2326 3986 2.627945 GCCCAACATGTAGTTCGATCA 58.372 47.619 0.00 0.00 38.74 2.92
2338 3998 0.106519 GCTAGGACATGGCCCAACAT 60.107 55.000 16.13 0.00 0.00 2.71
2339 3999 1.207488 AGCTAGGACATGGCCCAACA 61.207 55.000 16.13 0.00 35.62 3.33
2340 4000 0.749454 CAGCTAGGACATGGCCCAAC 60.749 60.000 16.13 3.11 35.62 3.77
2341 4001 0.913934 TCAGCTAGGACATGGCCCAA 60.914 55.000 16.13 1.07 35.62 4.12
2342 4002 0.913934 TTCAGCTAGGACATGGCCCA 60.914 55.000 16.13 0.00 35.62 5.36
2343 4003 0.255890 TTTCAGCTAGGACATGGCCC 59.744 55.000 16.13 6.08 35.62 5.80
2344 4004 1.673168 CTTTCAGCTAGGACATGGCC 58.327 55.000 10.65 10.65 35.62 5.36
2345 4005 1.020437 GCTTTCAGCTAGGACATGGC 58.980 55.000 0.00 0.00 38.45 4.40
2346 4006 2.093288 TCTGCTTTCAGCTAGGACATGG 60.093 50.000 0.00 0.00 42.97 3.66
2347 4007 3.257469 TCTGCTTTCAGCTAGGACATG 57.743 47.619 0.00 0.00 42.97 3.21
2348 4008 3.492309 CGATCTGCTTTCAGCTAGGACAT 60.492 47.826 0.00 0.00 42.97 3.06
2349 4009 2.159184 CGATCTGCTTTCAGCTAGGACA 60.159 50.000 0.00 0.00 42.97 4.02
2350 4010 2.468831 CGATCTGCTTTCAGCTAGGAC 58.531 52.381 0.00 0.00 42.97 3.85
2351 4011 1.202463 GCGATCTGCTTTCAGCTAGGA 60.202 52.381 0.00 0.00 42.97 2.94
2352 4012 1.216122 GCGATCTGCTTTCAGCTAGG 58.784 55.000 0.00 0.00 42.97 3.02
2363 4023 0.179205 GCAACAACTGAGCGATCTGC 60.179 55.000 7.52 0.78 46.98 4.26
2364 4024 1.150827 TGCAACAACTGAGCGATCTG 58.849 50.000 5.98 5.98 0.00 2.90
2365 4025 2.105006 ATGCAACAACTGAGCGATCT 57.895 45.000 0.90 0.00 0.00 2.75
2366 4026 2.476854 GGAATGCAACAACTGAGCGATC 60.477 50.000 0.00 0.00 0.00 3.69
2367 4027 1.470098 GGAATGCAACAACTGAGCGAT 59.530 47.619 0.00 0.00 0.00 4.58
2368 4028 0.874390 GGAATGCAACAACTGAGCGA 59.126 50.000 0.00 0.00 0.00 4.93
2369 4029 0.877071 AGGAATGCAACAACTGAGCG 59.123 50.000 0.00 0.00 0.00 5.03
2370 4030 3.005155 AGAAAGGAATGCAACAACTGAGC 59.995 43.478 0.00 0.00 0.00 4.26
2371 4031 4.843220 AGAAAGGAATGCAACAACTGAG 57.157 40.909 0.00 0.00 0.00 3.35
2372 4032 5.596836 AAAGAAAGGAATGCAACAACTGA 57.403 34.783 0.00 0.00 0.00 3.41
2373 4033 6.667007 AAAAAGAAAGGAATGCAACAACTG 57.333 33.333 0.00 0.00 0.00 3.16
2393 4053 7.823310 TGGCGTGTTATCAGTAGGTTATAAAAA 59.177 33.333 0.00 0.00 0.00 1.94
2394 4054 7.329499 TGGCGTGTTATCAGTAGGTTATAAAA 58.671 34.615 0.00 0.00 0.00 1.52
2395 4055 6.876155 TGGCGTGTTATCAGTAGGTTATAAA 58.124 36.000 0.00 0.00 0.00 1.40
2396 4056 6.468333 TGGCGTGTTATCAGTAGGTTATAA 57.532 37.500 0.00 0.00 0.00 0.98
2397 4057 5.508489 GCTGGCGTGTTATCAGTAGGTTATA 60.508 44.000 0.00 0.00 0.00 0.98
2398 4058 4.739735 GCTGGCGTGTTATCAGTAGGTTAT 60.740 45.833 0.00 0.00 0.00 1.89
2399 4059 3.429822 GCTGGCGTGTTATCAGTAGGTTA 60.430 47.826 0.00 0.00 0.00 2.85
2400 4060 2.677037 GCTGGCGTGTTATCAGTAGGTT 60.677 50.000 0.00 0.00 0.00 3.50
2401 4061 1.134788 GCTGGCGTGTTATCAGTAGGT 60.135 52.381 0.00 0.00 0.00 3.08
2402 4062 1.571919 GCTGGCGTGTTATCAGTAGG 58.428 55.000 0.00 0.00 0.00 3.18
2403 4063 1.137086 AGGCTGGCGTGTTATCAGTAG 59.863 52.381 0.00 0.00 0.00 2.57
2404 4064 1.136305 GAGGCTGGCGTGTTATCAGTA 59.864 52.381 0.00 0.00 0.00 2.74
2405 4065 0.108138 GAGGCTGGCGTGTTATCAGT 60.108 55.000 0.00 0.00 0.00 3.41
2406 4066 0.811616 GGAGGCTGGCGTGTTATCAG 60.812 60.000 0.00 0.00 0.00 2.90
2407 4067 1.220749 GGAGGCTGGCGTGTTATCA 59.779 57.895 0.00 0.00 0.00 2.15
2408 4068 1.523938 GGGAGGCTGGCGTGTTATC 60.524 63.158 0.00 0.00 0.00 1.75
2409 4069 2.590092 GGGAGGCTGGCGTGTTAT 59.410 61.111 0.00 0.00 0.00 1.89
2410 4070 2.808761 TAGGGGAGGCTGGCGTGTTA 62.809 60.000 0.00 0.00 0.00 2.41
2412 4072 4.715130 TAGGGGAGGCTGGCGTGT 62.715 66.667 0.00 0.00 0.00 4.49
2413 4073 2.478335 TTTTAGGGGAGGCTGGCGTG 62.478 60.000 0.00 0.00 0.00 5.34
2414 4074 1.785353 TTTTTAGGGGAGGCTGGCGT 61.785 55.000 0.00 0.00 0.00 5.68
2415 4075 1.001393 TTTTTAGGGGAGGCTGGCG 60.001 57.895 0.00 0.00 0.00 5.69
2430 4090 1.808343 GGCCGACGTGTTATCCTTTTT 59.192 47.619 0.00 0.00 0.00 1.94
2431 4091 1.002773 AGGCCGACGTGTTATCCTTTT 59.997 47.619 0.00 0.00 0.00 2.27
2432 4092 0.611714 AGGCCGACGTGTTATCCTTT 59.388 50.000 0.00 0.00 0.00 3.11
2433 4093 1.407979 CTAGGCCGACGTGTTATCCTT 59.592 52.381 0.00 0.00 0.00 3.36
2434 4094 1.030457 CTAGGCCGACGTGTTATCCT 58.970 55.000 0.00 0.00 0.00 3.24
2435 4095 0.596859 GCTAGGCCGACGTGTTATCC 60.597 60.000 0.00 0.00 0.00 2.59
2436 4096 0.384669 AGCTAGGCCGACGTGTTATC 59.615 55.000 0.00 0.00 0.00 1.75
2437 4097 1.336125 GTAGCTAGGCCGACGTGTTAT 59.664 52.381 0.00 0.00 0.00 1.89
2438 4098 0.734889 GTAGCTAGGCCGACGTGTTA 59.265 55.000 0.00 0.00 0.00 2.41
2439 4099 1.246056 TGTAGCTAGGCCGACGTGTT 61.246 55.000 0.00 0.00 0.00 3.32
2440 4100 1.676635 TGTAGCTAGGCCGACGTGT 60.677 57.895 0.00 0.00 0.00 4.49
2441 4101 1.226603 GTGTAGCTAGGCCGACGTG 60.227 63.158 0.00 0.00 0.00 4.49
2442 4102 0.107508 TAGTGTAGCTAGGCCGACGT 60.108 55.000 0.00 0.00 0.00 4.34
2443 4103 1.019673 TTAGTGTAGCTAGGCCGACG 58.980 55.000 0.00 0.00 0.00 5.12
2444 4104 2.686915 TCTTTAGTGTAGCTAGGCCGAC 59.313 50.000 0.00 0.00 0.00 4.79
2445 4105 3.008835 TCTTTAGTGTAGCTAGGCCGA 57.991 47.619 0.00 0.00 0.00 5.54
2446 4106 3.795623 TTCTTTAGTGTAGCTAGGCCG 57.204 47.619 0.00 0.00 0.00 6.13
2447 4107 6.824196 AGAAATTTCTTTAGTGTAGCTAGGCC 59.176 38.462 15.11 0.00 32.55 5.19
2448 4108 7.851387 AGAAATTTCTTTAGTGTAGCTAGGC 57.149 36.000 15.11 0.00 32.55 3.93
2463 4123 4.519350 GGTTGACTCCGGAAAGAAATTTCT 59.481 41.667 15.11 15.11 39.74 2.52
2464 4124 4.321008 GGGTTGACTCCGGAAAGAAATTTC 60.321 45.833 5.23 10.33 0.00 2.17
2465 4125 3.572682 GGGTTGACTCCGGAAAGAAATTT 59.427 43.478 5.23 0.00 0.00 1.82
2466 4126 3.154710 GGGTTGACTCCGGAAAGAAATT 58.845 45.455 5.23 0.00 0.00 1.82
2467 4127 2.107552 TGGGTTGACTCCGGAAAGAAAT 59.892 45.455 5.23 0.00 0.00 2.17
2468 4128 1.491332 TGGGTTGACTCCGGAAAGAAA 59.509 47.619 5.23 0.00 0.00 2.52
2469 4129 1.133363 TGGGTTGACTCCGGAAAGAA 58.867 50.000 5.23 0.00 0.00 2.52
2470 4130 1.358152 ATGGGTTGACTCCGGAAAGA 58.642 50.000 5.23 0.00 0.00 2.52
2471 4131 2.200373 AATGGGTTGACTCCGGAAAG 57.800 50.000 5.23 0.00 0.00 2.62
2472 4132 2.668144 AAATGGGTTGACTCCGGAAA 57.332 45.000 5.23 0.00 0.00 3.13
2473 4133 5.640158 ATATAAATGGGTTGACTCCGGAA 57.360 39.130 5.23 0.00 0.00 4.30
2474 4134 5.640158 AATATAAATGGGTTGACTCCGGA 57.360 39.130 2.93 2.93 0.00 5.14
2475 4135 5.009610 CCAAATATAAATGGGTTGACTCCGG 59.990 44.000 0.00 0.00 32.87 5.14
2476 4136 6.072112 CCAAATATAAATGGGTTGACTCCG 57.928 41.667 0.26 0.00 32.87 4.63
2529 4190 4.612412 AGCGTGACCGGCCGAAAA 62.612 61.111 30.73 8.32 33.68 2.29
2579 4269 1.536709 GCACCAGTGTGGCAAGAAAAG 60.537 52.381 0.00 0.00 42.67 2.27
2597 4288 3.884774 AGTTTGCCTGGGACCGCA 61.885 61.111 0.00 0.00 0.00 5.69
2744 4536 1.503542 CAGCCGGATGCAACACTTC 59.496 57.895 6.84 0.00 44.83 3.01
2918 4750 1.621317 TCACATCGGTACTTCCAGCAA 59.379 47.619 0.00 0.00 35.57 3.91


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

AutoCloner maintained by Alex Coulton.