Multiple sequence alignment - TraesCS2B01G616700

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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 TraesCS2B01G616700 chr2B 100.000 3272 0 0 1 3272 793788018 793784747 0.000000e+00 6043.0
1 TraesCS2B01G616700 chr2B 98.039 51 1 0 2716 2766 596102604 596102654 4.500000e-14 89.8
2 TraesCS2B01G616700 chrUn 94.625 2586 88 20 1 2565 124825353 124827908 0.000000e+00 3958.0
3 TraesCS2B01G616700 chrUn 92.333 900 61 4 1373 2271 124710433 124709541 0.000000e+00 1273.0
4 TraesCS2B01G616700 chrUn 96.154 52 2 0 2715 2766 7817107 7817158 5.820000e-13 86.1
5 TraesCS2B01G616700 chr2D 93.481 1396 62 12 1182 2565 635760412 635759034 0.000000e+00 2047.0
6 TraesCS2B01G616700 chr2D 87.340 624 69 8 7 628 635761542 635760927 0.000000e+00 706.0
7 TraesCS2B01G616700 chr2D 81.621 691 62 29 569 1222 635760956 635760294 2.250000e-141 512.0
8 TraesCS2B01G616700 chr2D 78.418 607 86 27 7 577 316659188 316658591 1.440000e-93 353.0
9 TraesCS2B01G616700 chr2D 87.500 240 16 6 1819 2058 635938036 635938261 6.960000e-67 265.0
10 TraesCS2B01G616700 chr2D 95.597 159 7 0 2098 2256 635938257 635938415 4.190000e-64 255.0
11 TraesCS2B01G616700 chr2D 78.495 186 35 3 1514 1698 560991574 560991755 2.060000e-22 117.0
12 TraesCS2B01G616700 chr3D 79.873 631 89 18 1 596 438564542 438565169 8.390000e-116 427.0
13 TraesCS2B01G616700 chr3D 79.066 578 91 16 7 561 495274643 495275213 1.430000e-98 370.0
14 TraesCS2B01G616700 chr3D 78.502 614 85 26 1 577 339841274 339841877 3.100000e-95 359.0
15 TraesCS2B01G616700 chr4B 79.576 519 77 15 9 503 639153865 639153352 8.690000e-91 344.0
16 TraesCS2B01G616700 chr5D 82.630 403 48 18 171 566 369564048 369563661 1.450000e-88 337.0
17 TraesCS2B01G616700 chr5D 85.946 185 24 2 376 559 337167599 337167782 2.580000e-46 196.0
18 TraesCS2B01G616700 chr7B 77.905 611 85 26 7 577 643324947 643325547 5.230000e-88 335.0
19 TraesCS2B01G616700 chr7B 77.123 577 78 24 1 544 322492655 322493210 5.340000e-73 285.0
20 TraesCS2B01G616700 chr7B 81.006 179 28 5 388 565 730271983 730271810 1.580000e-28 137.0
21 TraesCS2B01G616700 chr7B 77.957 186 37 4 1564 1747 505451271 505451088 2.670000e-21 113.0
22 TraesCS2B01G616700 chr7B 93.333 60 3 1 2710 2769 524227532 524227474 1.620000e-13 87.9
23 TraesCS2B01G616700 chr7A 79.957 469 74 11 114 567 131854693 131855156 8.750000e-86 327.0
24 TraesCS2B01G616700 chr7A 80.000 155 29 2 1564 1717 515199730 515199883 2.670000e-21 113.0
25 TraesCS2B01G616700 chr4D 82.776 389 26 13 2768 3123 145941965 145941585 3.170000e-80 309.0
26 TraesCS2B01G616700 chr4D 81.333 150 3 8 2579 2717 145942092 145941957 7.470000e-17 99.0
27 TraesCS2B01G616700 chr4D 93.023 43 2 1 1468 1510 394358134 394358175 9.800000e-06 62.1
28 TraesCS2B01G616700 chr4D 96.970 33 1 0 1478 1510 498949335 498949367 4.560000e-04 56.5
29 TraesCS2B01G616700 chr4A 76.268 611 110 19 1 584 737207399 737206797 3.190000e-75 292.0
30 TraesCS2B01G616700 chr4A 83.568 213 29 6 9 221 672407071 672407277 9.260000e-46 195.0
31 TraesCS2B01G616700 chr4A 94.545 55 3 0 2715 2769 674557239 674557185 5.820000e-13 86.1
32 TraesCS2B01G616700 chr4A 93.023 43 2 1 1468 1510 75461773 75461814 9.800000e-06 62.1
33 TraesCS2B01G616700 chr1D 78.395 486 69 19 2 454 192415931 192415449 1.920000e-72 283.0
34 TraesCS2B01G616700 chr1D 77.251 211 40 7 1478 1684 81726190 81726396 2.060000e-22 117.0
35 TraesCS2B01G616700 chr1D 81.301 123 19 4 1593 1713 62936182 62936302 2.690000e-16 97.1
36 TraesCS2B01G616700 chr1D 96.296 54 2 0 2716 2769 15320798 15320745 4.500000e-14 89.8
37 TraesCS2B01G616700 chr2A 75.209 597 98 39 9 577 56868120 56868694 1.520000e-58 237.0
38 TraesCS2B01G616700 chr6D 81.029 311 42 10 7 305 386429815 386429510 7.060000e-57 231.0
39 TraesCS2B01G616700 chr3B 82.558 258 38 6 109 364 646736371 646736119 1.530000e-53 220.0
40 TraesCS2B01G616700 chr3B 96.296 54 2 0 2716 2769 132957493 132957440 4.500000e-14 89.8
41 TraesCS2B01G616700 chr5B 83.260 227 33 5 371 593 502031616 502031391 1.540000e-48 204.0
42 TraesCS2B01G616700 chr7D 74.773 551 73 39 1 526 363052907 363053416 1.550000e-43 187.0
43 TraesCS2B01G616700 chr3A 86.364 154 18 3 428 579 730924505 730924353 7.260000e-37 165.0
44 TraesCS2B01G616700 chr1A 81.928 166 27 3 432 595 589687870 589688034 1.580000e-28 137.0
45 TraesCS2B01G616700 chr1A 77.021 235 39 10 1465 1693 360009646 360009871 1.590000e-23 121.0
46 TraesCS2B01G616700 chr1A 81.301 123 19 4 1593 1713 61341573 61341693 2.690000e-16 97.1
47 TraesCS2B01G616700 chr1B 80.986 142 23 4 1593 1732 100631445 100631584 3.450000e-20 110.0
48 TraesCS2B01G616700 chr1B 76.168 214 43 8 1478 1687 136312560 136312769 4.470000e-19 106.0
49 TraesCS2B01G616700 chr1B 94.643 56 3 0 2714 2769 60193654 60193599 1.620000e-13 87.9
50 TraesCS2B01G616700 chr1B 96.154 52 2 0 2715 2766 638094552 638094603 5.820000e-13 86.1
51 TraesCS2B01G616700 chr1B 96.154 52 2 0 2715 2766 638121104 638121155 5.820000e-13 86.1


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 TraesCS2B01G616700 chr2B 793784747 793788018 3271 True 6043.000000 6043 100.000000 1 3272 1 chr2B.!!$R1 3271
1 TraesCS2B01G616700 chrUn 124825353 124827908 2555 False 3958.000000 3958 94.625000 1 2565 1 chrUn.!!$F2 2564
2 TraesCS2B01G616700 chrUn 124709541 124710433 892 True 1273.000000 1273 92.333000 1373 2271 1 chrUn.!!$R1 898
3 TraesCS2B01G616700 chr2D 635759034 635761542 2508 True 1088.333333 2047 87.480667 7 2565 3 chr2D.!!$R2 2558
4 TraesCS2B01G616700 chr2D 316658591 316659188 597 True 353.000000 353 78.418000 7 577 1 chr2D.!!$R1 570
5 TraesCS2B01G616700 chr3D 438564542 438565169 627 False 427.000000 427 79.873000 1 596 1 chr3D.!!$F2 595
6 TraesCS2B01G616700 chr3D 495274643 495275213 570 False 370.000000 370 79.066000 7 561 1 chr3D.!!$F3 554
7 TraesCS2B01G616700 chr3D 339841274 339841877 603 False 359.000000 359 78.502000 1 577 1 chr3D.!!$F1 576
8 TraesCS2B01G616700 chr4B 639153352 639153865 513 True 344.000000 344 79.576000 9 503 1 chr4B.!!$R1 494
9 TraesCS2B01G616700 chr7B 643324947 643325547 600 False 335.000000 335 77.905000 7 577 1 chr7B.!!$F2 570
10 TraesCS2B01G616700 chr7B 322492655 322493210 555 False 285.000000 285 77.123000 1 544 1 chr7B.!!$F1 543
11 TraesCS2B01G616700 chr4D 145941585 145942092 507 True 204.000000 309 82.054500 2579 3123 2 chr4D.!!$R1 544
12 TraesCS2B01G616700 chr4A 737206797 737207399 602 True 292.000000 292 76.268000 1 584 1 chr4A.!!$R2 583
13 TraesCS2B01G616700 chr2A 56868120 56868694 574 False 237.000000 237 75.209000 9 577 1 chr2A.!!$F1 568

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
107 120 0.043940 AACATGCTCCTCCTCCTCCT 59.956 55.0 0.0 0.0 0.0 3.69 F
1126 1251 0.108424 CGCACAAGGAAGAGGAGGAG 60.108 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1167 1292 0.326618 CTCCTCCATACCCACCACCT 60.327 60.0 0.0 0.0 0.00 4.00 R
2682 2842 0.107654 GTTGGGTCATCTCTTCCCGG 60.108 60.0 0.0 0.0 43.75 5.73 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
67 79 2.450476 CCTATTGCAGCTGAACCCTTT 58.550 47.619 20.43 0.00 0.00 3.11
106 119 0.467804 GAACATGCTCCTCCTCCTCC 59.532 60.000 0.00 0.00 0.00 4.30
107 120 0.043940 AACATGCTCCTCCTCCTCCT 59.956 55.000 0.00 0.00 0.00 3.69
108 121 0.398381 ACATGCTCCTCCTCCTCCTC 60.398 60.000 0.00 0.00 0.00 3.71
121 134 1.047002 CCTCCTCTCCGCATCTTCAT 58.953 55.000 0.00 0.00 0.00 2.57
367 429 1.464376 GGAGAAGCGGGATGGATCGA 61.464 60.000 0.00 0.00 0.00 3.59
474 536 8.470657 AAAGATGGAAGAAGAATAAATAGGGC 57.529 34.615 0.00 0.00 0.00 5.19
579 643 1.003580 GCTCCCCACATTTGTCTCTGA 59.996 52.381 0.00 0.00 0.00 3.27
587 651 4.503817 CCACATTTGTCTCTGACTTGAGGA 60.504 45.833 0.00 0.00 34.98 3.71
599 663 6.298361 TCTGACTTGAGGATGAAAACATGAA 58.702 36.000 0.00 0.00 0.00 2.57
638 732 1.153329 AAAACGTGTCTGGACCGCA 60.153 52.632 0.00 0.00 0.00 5.69
653 747 3.097728 GCACCGCGGATCGATACG 61.098 66.667 35.90 25.76 41.67 3.06
695 804 3.341263 TGTCTGGACAGCGTAGTCT 57.659 52.632 8.82 0.00 38.57 3.24
696 805 1.617322 TGTCTGGACAGCGTAGTCTT 58.383 50.000 8.82 0.00 38.57 3.01
697 806 1.269723 TGTCTGGACAGCGTAGTCTTG 59.730 52.381 8.82 3.68 38.57 3.02
698 807 0.888619 TCTGGACAGCGTAGTCTTGG 59.111 55.000 8.82 1.78 38.57 3.61
699 808 0.603569 CTGGACAGCGTAGTCTTGGT 59.396 55.000 8.82 0.00 38.57 3.67
700 809 0.317160 TGGACAGCGTAGTCTTGGTG 59.683 55.000 8.82 3.27 38.57 4.17
701 810 0.389948 GGACAGCGTAGTCTTGGTGG 60.390 60.000 8.82 0.00 38.57 4.61
702 811 0.317479 GACAGCGTAGTCTTGGTGGT 59.683 55.000 8.33 0.00 37.89 4.16
830 945 7.201173 CGCACATGCATGTTTGAATATTATACG 60.201 37.037 29.48 13.74 39.39 3.06
831 946 7.591057 GCACATGCATGTTTGAATATTATACGT 59.409 33.333 29.48 0.00 39.39 3.57
919 1044 3.995048 CAGATCCATGGATTCATCTGTCG 59.005 47.826 27.93 6.60 34.60 4.35
973 1098 3.009033 CAGTACCCATCTCAAACCTCCAA 59.991 47.826 0.00 0.00 0.00 3.53
974 1099 2.586648 ACCCATCTCAAACCTCCAAC 57.413 50.000 0.00 0.00 0.00 3.77
975 1100 1.075536 ACCCATCTCAAACCTCCAACC 59.924 52.381 0.00 0.00 0.00 3.77
976 1101 1.355720 CCCATCTCAAACCTCCAACCT 59.644 52.381 0.00 0.00 0.00 3.50
977 1102 2.225117 CCCATCTCAAACCTCCAACCTT 60.225 50.000 0.00 0.00 0.00 3.50
1074 1199 4.874977 GCCCTAGCGTCCGTGCTC 62.875 72.222 0.00 0.00 45.87 4.26
1124 1249 1.078848 CCGCACAAGGAAGAGGAGG 60.079 63.158 0.00 0.00 0.00 4.30
1125 1250 1.544825 CCGCACAAGGAAGAGGAGGA 61.545 60.000 0.00 0.00 0.00 3.71
1126 1251 0.108424 CGCACAAGGAAGAGGAGGAG 60.108 60.000 0.00 0.00 0.00 3.69
1167 1292 1.507140 GAGGATATGGTGGTGGTGGA 58.493 55.000 0.00 0.00 0.00 4.02
1213 1341 0.545787 AGGATACGGTGGTGGTGGAA 60.546 55.000 0.00 0.00 46.39 3.53
1332 1466 0.470341 GTGACTATCAAGGGGGAGGC 59.530 60.000 0.00 0.00 0.00 4.70
2151 2285 2.485479 GGAGACGGCCATGTATGTGAAT 60.485 50.000 2.24 0.00 0.00 2.57
2259 2393 1.005748 CGTCAGGCTCAACTGCAGA 60.006 57.895 23.35 0.00 38.36 4.26
2282 2416 1.745320 CTCAACTAGCCCGCCCGTAT 61.745 60.000 0.00 0.00 0.00 3.06
2283 2417 0.467844 TCAACTAGCCCGCCCGTATA 60.468 55.000 0.00 0.00 0.00 1.47
2285 2419 0.606604 AACTAGCCCGCCCGTATATG 59.393 55.000 0.00 0.00 0.00 1.78
2292 2426 4.217510 AGCCCGCCCGTATATGTATATAA 58.782 43.478 0.00 0.00 0.00 0.98
2359 2502 6.715264 GGCCAATGTAATAATAAGCCTACACT 59.285 38.462 0.00 0.00 36.22 3.55
2360 2503 7.881232 GGCCAATGTAATAATAAGCCTACACTA 59.119 37.037 0.00 0.00 36.22 2.74
2361 2504 8.718734 GCCAATGTAATAATAAGCCTACACTAC 58.281 37.037 0.00 0.00 0.00 2.73
2367 2510 9.387123 GTAATAATAAGCCTACACTACACGTAC 57.613 37.037 0.00 0.00 0.00 3.67
2368 2511 2.907910 AAGCCTACACTACACGTACG 57.092 50.000 15.01 15.01 0.00 3.67
2386 2529 2.821546 ACGTATGCATGCGTACTCATT 58.178 42.857 36.18 20.43 46.84 2.57
2387 2530 2.539688 ACGTATGCATGCGTACTCATTG 59.460 45.455 36.18 25.56 46.84 2.82
2412 2555 4.155310 GCATGTAAAAACGTGCTAGGTT 57.845 40.909 13.95 0.00 46.07 3.50
2465 2608 6.667370 TGCATAATGTGTACACTTGAACTTG 58.333 36.000 25.60 14.47 0.00 3.16
2517 2660 2.037251 CGGACTTGTCAAAGGAGGAGAA 59.963 50.000 3.08 0.00 37.76 2.87
2518 2661 3.403968 GGACTTGTCAAAGGAGGAGAAC 58.596 50.000 3.08 0.00 37.76 3.01
2519 2662 3.181454 GGACTTGTCAAAGGAGGAGAACA 60.181 47.826 3.08 0.00 37.76 3.18
2574 2723 8.923609 ATCTTTGATCATGCATATAGAGTACG 57.076 34.615 0.00 0.00 0.00 3.67
2575 2724 7.886338 TCTTTGATCATGCATATAGAGTACGT 58.114 34.615 0.00 0.00 0.00 3.57
2576 2725 8.360390 TCTTTGATCATGCATATAGAGTACGTT 58.640 33.333 0.00 0.00 0.00 3.99
2577 2726 7.873739 TTGATCATGCATATAGAGTACGTTG 57.126 36.000 0.00 0.00 0.00 4.10
2616 2765 9.810545 TCATCGAGACATTAACACAAACATATA 57.189 29.630 0.00 0.00 0.00 0.86
2632 2792 8.543774 ACAAACATATAGAGGAGACTGAAATGT 58.456 33.333 0.00 0.00 44.43 2.71
2633 2793 8.824781 CAAACATATAGAGGAGACTGAAATGTG 58.175 37.037 0.00 0.00 44.43 3.21
2655 2815 1.757118 GGCAAGGATTTTAAGGGAGCC 59.243 52.381 0.00 0.00 0.00 4.70
2656 2816 2.456577 GCAAGGATTTTAAGGGAGCCA 58.543 47.619 0.00 0.00 0.00 4.75
2657 2817 3.033909 GCAAGGATTTTAAGGGAGCCAT 58.966 45.455 0.00 0.00 0.00 4.40
2658 2818 3.181472 GCAAGGATTTTAAGGGAGCCATG 60.181 47.826 0.00 0.00 0.00 3.66
2659 2819 2.670939 AGGATTTTAAGGGAGCCATGC 58.329 47.619 0.00 0.00 0.00 4.06
2660 2820 2.024080 AGGATTTTAAGGGAGCCATGCA 60.024 45.455 0.00 0.00 0.00 3.96
2661 2821 2.967887 GGATTTTAAGGGAGCCATGCAT 59.032 45.455 0.00 0.00 0.00 3.96
2662 2822 4.140947 AGGATTTTAAGGGAGCCATGCATA 60.141 41.667 0.00 0.00 0.00 3.14
2663 2823 4.774200 GGATTTTAAGGGAGCCATGCATAT 59.226 41.667 0.00 0.00 0.00 1.78
2664 2824 5.337009 GGATTTTAAGGGAGCCATGCATATG 60.337 44.000 0.00 0.00 0.00 1.78
2682 2842 2.723746 CATGCATGGGCTAACGGC 59.276 61.111 19.40 0.00 41.91 5.68
2699 2859 2.367202 GCCGGGAAGAGATGACCCA 61.367 63.158 2.18 0.00 43.40 4.51
2717 2877 2.224917 CCCAACCTAGCCTAAACACCAA 60.225 50.000 0.00 0.00 0.00 3.67
2718 2878 3.492337 CCAACCTAGCCTAAACACCAAA 58.508 45.455 0.00 0.00 0.00 3.28
2719 2879 3.892588 CCAACCTAGCCTAAACACCAAAA 59.107 43.478 0.00 0.00 0.00 2.44
2720 2880 4.342665 CCAACCTAGCCTAAACACCAAAAA 59.657 41.667 0.00 0.00 0.00 1.94
2721 2881 5.011635 CCAACCTAGCCTAAACACCAAAAAT 59.988 40.000 0.00 0.00 0.00 1.82
2722 2882 5.722021 ACCTAGCCTAAACACCAAAAATG 57.278 39.130 0.00 0.00 0.00 2.32
2723 2883 4.021456 ACCTAGCCTAAACACCAAAAATGC 60.021 41.667 0.00 0.00 0.00 3.56
2724 2884 4.220602 CCTAGCCTAAACACCAAAAATGCT 59.779 41.667 0.00 0.00 0.00 3.79
2725 2885 5.417580 CCTAGCCTAAACACCAAAAATGCTA 59.582 40.000 0.00 0.00 0.00 3.49
2726 2886 5.391312 AGCCTAAACACCAAAAATGCTAG 57.609 39.130 0.00 0.00 0.00 3.42
2727 2887 5.076873 AGCCTAAACACCAAAAATGCTAGA 58.923 37.500 0.00 0.00 0.00 2.43
2728 2888 5.048013 AGCCTAAACACCAAAAATGCTAGAC 60.048 40.000 0.00 0.00 0.00 2.59
2729 2889 5.390613 CCTAAACACCAAAAATGCTAGACG 58.609 41.667 0.00 0.00 0.00 4.18
2730 2890 4.911514 AAACACCAAAAATGCTAGACGT 57.088 36.364 0.00 0.00 0.00 4.34
2731 2891 6.148150 CCTAAACACCAAAAATGCTAGACGTA 59.852 38.462 0.00 0.00 0.00 3.57
2732 2892 5.352643 AACACCAAAAATGCTAGACGTAC 57.647 39.130 0.00 0.00 0.00 3.67
2733 2893 4.382291 ACACCAAAAATGCTAGACGTACA 58.618 39.130 0.00 0.00 0.00 2.90
2734 2894 4.817464 ACACCAAAAATGCTAGACGTACAA 59.183 37.500 0.00 0.00 0.00 2.41
2735 2895 5.297278 ACACCAAAAATGCTAGACGTACAAA 59.703 36.000 0.00 0.00 0.00 2.83
2736 2896 6.183360 ACACCAAAAATGCTAGACGTACAAAA 60.183 34.615 0.00 0.00 0.00 2.44
2737 2897 6.359617 CACCAAAAATGCTAGACGTACAAAAG 59.640 38.462 0.00 0.00 0.00 2.27
2738 2898 6.261381 ACCAAAAATGCTAGACGTACAAAAGA 59.739 34.615 0.00 0.00 0.00 2.52
2739 2899 7.040686 ACCAAAAATGCTAGACGTACAAAAGAT 60.041 33.333 0.00 0.00 0.00 2.40
2740 2900 7.807907 CCAAAAATGCTAGACGTACAAAAGATT 59.192 33.333 0.00 0.00 0.00 2.40
2741 2901 9.820229 CAAAAATGCTAGACGTACAAAAGATTA 57.180 29.630 0.00 0.00 0.00 1.75
2742 2902 9.821662 AAAAATGCTAGACGTACAAAAGATTAC 57.178 29.630 0.00 0.00 0.00 1.89
2743 2903 8.542497 AAATGCTAGACGTACAAAAGATTACA 57.458 30.769 0.00 0.00 0.00 2.41
2744 2904 8.718102 AATGCTAGACGTACAAAAGATTACAT 57.282 30.769 0.00 0.00 0.00 2.29
2745 2905 7.520119 TGCTAGACGTACAAAAGATTACATG 57.480 36.000 0.00 0.00 0.00 3.21
2746 2906 7.317390 TGCTAGACGTACAAAAGATTACATGA 58.683 34.615 0.00 0.00 0.00 3.07
2747 2907 7.979537 TGCTAGACGTACAAAAGATTACATGAT 59.020 33.333 0.00 0.00 0.00 2.45
2748 2908 8.818057 GCTAGACGTACAAAAGATTACATGATT 58.182 33.333 0.00 0.00 0.00 2.57
2756 2916 8.986477 ACAAAAGATTACATGATTTTACAGGC 57.014 30.769 0.00 0.00 0.00 4.85
2757 2917 8.806146 ACAAAAGATTACATGATTTTACAGGCT 58.194 29.630 0.00 0.00 0.00 4.58
2758 2918 9.294030 CAAAAGATTACATGATTTTACAGGCTC 57.706 33.333 0.00 0.00 0.00 4.70
2759 2919 8.814038 AAAGATTACATGATTTTACAGGCTCT 57.186 30.769 0.00 0.00 0.00 4.09
2760 2920 8.814038 AAGATTACATGATTTTACAGGCTCTT 57.186 30.769 0.00 0.00 0.00 2.85
2761 2921 8.814038 AGATTACATGATTTTACAGGCTCTTT 57.186 30.769 0.00 0.00 0.00 2.52
2762 2922 9.247861 AGATTACATGATTTTACAGGCTCTTTT 57.752 29.630 0.00 0.00 0.00 2.27
2763 2923 9.508567 GATTACATGATTTTACAGGCTCTTTTC 57.491 33.333 0.00 0.00 0.00 2.29
2764 2924 6.899393 ACATGATTTTACAGGCTCTTTTCA 57.101 33.333 0.00 0.00 0.00 2.69
2765 2925 7.472334 ACATGATTTTACAGGCTCTTTTCAT 57.528 32.000 0.00 0.00 0.00 2.57
2766 2926 8.579850 ACATGATTTTACAGGCTCTTTTCATA 57.420 30.769 0.00 0.00 0.00 2.15
2767 2927 9.193806 ACATGATTTTACAGGCTCTTTTCATAT 57.806 29.630 0.00 0.00 0.00 1.78
2774 2934 6.759497 ACAGGCTCTTTTCATATAAACACC 57.241 37.500 0.00 0.00 0.00 4.16
2775 2935 6.245408 ACAGGCTCTTTTCATATAAACACCA 58.755 36.000 0.00 0.00 0.00 4.17
2780 2940 7.067494 GGCTCTTTTCATATAAACACCATGAGT 59.933 37.037 0.00 0.00 30.77 3.41
2838 2998 3.798337 CACAAAGAGTTGCCATGTTTGTC 59.202 43.478 5.61 0.00 38.87 3.18
2851 3011 0.668401 GTTTGTCATGCAGCTTGCCC 60.668 55.000 3.32 0.00 44.23 5.36
2873 3033 1.523758 GTGATGCCCAAGACGAACTT 58.476 50.000 0.00 0.00 39.70 2.66
2874 3034 1.464997 GTGATGCCCAAGACGAACTTC 59.535 52.381 0.00 0.00 36.61 3.01
2875 3035 1.071542 TGATGCCCAAGACGAACTTCA 59.928 47.619 0.00 0.00 36.61 3.02
2878 3038 2.972625 TGCCCAAGACGAACTTCATAG 58.027 47.619 0.00 0.00 36.61 2.23
2882 3042 2.280628 CAAGACGAACTTCATAGGCCC 58.719 52.381 0.00 0.00 36.61 5.80
2883 3043 1.867363 AGACGAACTTCATAGGCCCT 58.133 50.000 0.00 0.00 0.00 5.19
2895 3079 4.556697 TCATAGGCCCTCAGAATCACTTA 58.443 43.478 0.00 0.00 0.00 2.24
2896 3080 5.158141 TCATAGGCCCTCAGAATCACTTAT 58.842 41.667 0.00 0.00 0.00 1.73
2997 3190 4.899239 GCGGATGGCCACTCCTCG 62.899 72.222 23.52 17.08 34.80 4.63
3032 3225 0.666577 GACACCACTCGTTTCTCCGG 60.667 60.000 0.00 0.00 0.00 5.14
3066 3259 0.539986 TACCTCCAACTCCAATCCGC 59.460 55.000 0.00 0.00 0.00 5.54
3071 3264 0.179000 CCAACTCCAATCCGCTAGCT 59.821 55.000 13.93 0.00 0.00 3.32
3072 3265 1.412710 CCAACTCCAATCCGCTAGCTA 59.587 52.381 13.93 0.56 0.00 3.32
3073 3266 2.546795 CCAACTCCAATCCGCTAGCTAG 60.547 54.545 16.84 16.84 0.00 3.42
3076 3269 1.373497 CCAATCCGCTAGCTAGCCG 60.373 63.158 34.27 28.64 46.34 5.52
3077 3270 2.024319 CAATCCGCTAGCTAGCCGC 61.024 63.158 34.27 15.80 46.34 6.53
3078 3271 3.227792 AATCCGCTAGCTAGCCGCC 62.228 63.158 34.27 12.39 46.34 6.13
3081 3274 4.654412 CGCTAGCTAGCCGCCCTG 62.654 72.222 34.27 18.71 46.34 4.45
3086 3279 2.921853 TAGCTAGCCGCCCTGCTACA 62.922 60.000 12.13 0.00 42.75 2.74
3107 3300 9.026074 GCTACAGACATCAGTATTCTTCTTTAC 57.974 37.037 0.00 0.00 0.00 2.01
3119 3312 4.468095 TCTTCTTTACAGTTTCGCAAGC 57.532 40.909 0.00 0.00 37.18 4.01
3123 3316 2.748461 TTACAGTTTCGCAAGCACAC 57.252 45.000 0.00 0.00 37.18 3.82
3124 3317 0.579630 TACAGTTTCGCAAGCACACG 59.420 50.000 0.00 0.00 37.18 4.49
3125 3318 1.351707 CAGTTTCGCAAGCACACGT 59.648 52.632 0.00 0.00 37.18 4.49
3126 3319 0.248054 CAGTTTCGCAAGCACACGTT 60.248 50.000 0.00 0.00 37.18 3.99
3127 3320 0.248054 AGTTTCGCAAGCACACGTTG 60.248 50.000 0.00 0.00 37.18 4.10
3128 3321 1.063327 TTTCGCAAGCACACGTTGG 59.937 52.632 0.00 0.00 37.18 3.77
3129 3322 2.928313 TTTCGCAAGCACACGTTGGC 62.928 55.000 0.00 0.00 37.18 4.52
3130 3323 4.980903 CGCAAGCACACGTTGGCC 62.981 66.667 0.00 0.00 0.00 5.36
3131 3324 4.980903 GCAAGCACACGTTGGCCG 62.981 66.667 0.00 0.00 44.03 6.13
3132 3325 4.980903 CAAGCACACGTTGGCCGC 62.981 66.667 0.00 0.00 41.42 6.53
3147 3340 4.827087 CGCTCGCTGGGCATCAGT 62.827 66.667 7.89 0.00 45.08 3.41
3151 3344 2.046988 CGCTGGGCATCAGTGTCA 60.047 61.111 10.51 0.00 46.05 3.58
3152 3345 2.393768 CGCTGGGCATCAGTGTCAC 61.394 63.158 10.51 0.00 46.05 3.67
3153 3346 2.393768 GCTGGGCATCAGTGTCACG 61.394 63.158 7.89 0.00 45.08 4.35
3154 3347 1.742880 CTGGGCATCAGTGTCACGG 60.743 63.158 0.00 0.00 38.64 4.94
3155 3348 2.436646 GGGCATCAGTGTCACGGG 60.437 66.667 3.17 0.00 0.00 5.28
3156 3349 2.436646 GGCATCAGTGTCACGGGG 60.437 66.667 3.17 0.00 0.00 5.73
3157 3350 2.436646 GCATCAGTGTCACGGGGG 60.437 66.667 3.17 0.00 0.00 5.40
3158 3351 3.068881 CATCAGTGTCACGGGGGT 58.931 61.111 3.17 0.00 0.00 4.95
3159 3352 1.375908 CATCAGTGTCACGGGGGTG 60.376 63.158 3.17 0.00 0.00 4.61
3160 3353 2.592993 ATCAGTGTCACGGGGGTGG 61.593 63.158 3.17 0.00 0.00 4.61
3186 3379 2.002505 CCTCCAGGAGGTGATATCGT 57.997 55.000 26.30 0.00 44.25 3.73
3187 3380 1.615883 CCTCCAGGAGGTGATATCGTG 59.384 57.143 26.30 0.00 44.25 4.35
3191 3384 3.309961 CAGGAGGTGATATCGTGGATG 57.690 52.381 0.00 0.00 0.00 3.51
3192 3385 2.028658 CAGGAGGTGATATCGTGGATGG 60.029 54.545 0.00 0.00 0.00 3.51
3193 3386 2.158310 AGGAGGTGATATCGTGGATGGA 60.158 50.000 0.00 0.00 0.00 3.41
3194 3387 2.232452 GGAGGTGATATCGTGGATGGAG 59.768 54.545 0.00 0.00 0.00 3.86
3195 3388 2.232452 GAGGTGATATCGTGGATGGAGG 59.768 54.545 0.00 0.00 0.00 4.30
3196 3389 1.338200 GGTGATATCGTGGATGGAGGC 60.338 57.143 0.00 0.00 0.00 4.70
3197 3390 1.620819 GTGATATCGTGGATGGAGGCT 59.379 52.381 0.00 0.00 0.00 4.58
3198 3391 2.037772 GTGATATCGTGGATGGAGGCTT 59.962 50.000 0.00 0.00 0.00 4.35
3199 3392 2.300152 TGATATCGTGGATGGAGGCTTC 59.700 50.000 0.00 0.00 0.00 3.86
3200 3393 2.088104 TATCGTGGATGGAGGCTTCT 57.912 50.000 0.00 0.00 0.00 2.85
3201 3394 0.755686 ATCGTGGATGGAGGCTTCTC 59.244 55.000 0.00 0.00 36.81 2.87
3202 3395 0.614697 TCGTGGATGGAGGCTTCTCA 60.615 55.000 0.00 0.00 39.23 3.27
3203 3396 0.460987 CGTGGATGGAGGCTTCTCAC 60.461 60.000 0.00 0.00 39.23 3.51
3204 3397 0.615331 GTGGATGGAGGCTTCTCACA 59.385 55.000 0.00 0.00 39.23 3.58
3205 3398 1.211457 GTGGATGGAGGCTTCTCACAT 59.789 52.381 0.00 0.00 39.23 3.21
3206 3399 1.211212 TGGATGGAGGCTTCTCACATG 59.789 52.381 0.00 0.00 39.23 3.21
3207 3400 1.476471 GGATGGAGGCTTCTCACATGG 60.476 57.143 0.00 0.00 39.23 3.66
3208 3401 0.106819 ATGGAGGCTTCTCACATGGC 60.107 55.000 0.00 0.00 39.23 4.40
3209 3402 1.817099 GGAGGCTTCTCACATGGCG 60.817 63.158 0.00 0.00 39.23 5.69
3210 3403 1.817099 GAGGCTTCTCACATGGCGG 60.817 63.158 0.00 0.00 37.47 6.13
3211 3404 3.512516 GGCTTCTCACATGGCGGC 61.513 66.667 0.00 0.00 0.00 6.53
3212 3405 3.869272 GCTTCTCACATGGCGGCG 61.869 66.667 0.51 0.51 0.00 6.46
3213 3406 3.197790 CTTCTCACATGGCGGCGG 61.198 66.667 9.78 0.99 0.00 6.13
3217 3410 4.168291 TCACATGGCGGCGGCATA 62.168 61.111 41.87 27.72 47.00 3.14
3218 3411 2.979676 CACATGGCGGCGGCATAT 60.980 61.111 41.87 33.06 47.00 1.78
3219 3412 2.979676 ACATGGCGGCGGCATATG 60.980 61.111 41.87 34.70 47.00 1.78
3220 3413 2.979676 CATGGCGGCGGCATATGT 60.980 61.111 41.87 23.91 47.00 2.29
3221 3414 2.979676 ATGGCGGCGGCATATGTG 60.980 61.111 41.92 0.00 46.84 3.21
3229 3422 2.516930 GGCATATGTGGCGCCAGT 60.517 61.111 33.73 24.18 45.52 4.00
3230 3423 2.120909 GGCATATGTGGCGCCAGTT 61.121 57.895 33.73 22.77 45.52 3.16
3231 3424 1.064621 GCATATGTGGCGCCAGTTG 59.935 57.895 33.73 24.21 0.00 3.16
3232 3425 1.375853 GCATATGTGGCGCCAGTTGA 61.376 55.000 33.73 16.42 0.00 3.18
3233 3426 1.093972 CATATGTGGCGCCAGTTGAA 58.906 50.000 33.73 14.56 0.00 2.69
3234 3427 1.472082 CATATGTGGCGCCAGTTGAAA 59.528 47.619 33.73 12.96 0.00 2.69
3235 3428 1.164411 TATGTGGCGCCAGTTGAAAG 58.836 50.000 33.73 0.00 0.00 2.62
3236 3429 1.526575 ATGTGGCGCCAGTTGAAAGG 61.527 55.000 33.73 0.00 0.00 3.11
3243 3436 2.428834 CCAGTTGAAAGGCTTGGCA 58.571 52.632 0.00 0.00 0.00 4.92
3244 3437 0.032540 CCAGTTGAAAGGCTTGGCAC 59.967 55.000 0.00 0.00 0.00 5.01
3245 3438 0.032540 CAGTTGAAAGGCTTGGCACC 59.967 55.000 0.00 0.00 0.00 5.01
3246 3439 1.007387 GTTGAAAGGCTTGGCACCG 60.007 57.895 0.00 0.00 0.00 4.94
3247 3440 2.199652 TTGAAAGGCTTGGCACCGG 61.200 57.895 0.00 0.00 0.00 5.28
3248 3441 2.597510 GAAAGGCTTGGCACCGGT 60.598 61.111 0.00 0.00 0.00 5.28
3249 3442 2.123468 AAAGGCTTGGCACCGGTT 60.123 55.556 2.97 0.00 0.00 4.44
3250 3443 1.744320 GAAAGGCTTGGCACCGGTTT 61.744 55.000 2.97 0.00 0.00 3.27
3251 3444 2.026945 AAAGGCTTGGCACCGGTTTG 62.027 55.000 2.97 0.00 0.00 2.93
3252 3445 3.989787 GGCTTGGCACCGGTTTGG 61.990 66.667 2.97 0.00 46.41 3.28
3253 3446 3.989787 GCTTGGCACCGGTTTGGG 61.990 66.667 2.97 0.00 44.64 4.12
3254 3447 2.203422 CTTGGCACCGGTTTGGGA 60.203 61.111 2.97 0.00 44.64 4.37
3255 3448 1.606313 CTTGGCACCGGTTTGGGAT 60.606 57.895 2.97 0.00 44.64 3.85
3256 3449 1.595093 CTTGGCACCGGTTTGGGATC 61.595 60.000 2.97 0.00 44.64 3.36
3257 3450 3.131478 GGCACCGGTTTGGGATCG 61.131 66.667 2.97 0.00 44.64 3.69
3261 3454 2.189521 CCGGTTTGGGATCGGGAG 59.810 66.667 0.00 0.00 40.07 4.30
3262 3455 2.363975 CCGGTTTGGGATCGGGAGA 61.364 63.158 0.00 0.00 46.90 3.71
3263 3456 1.144057 CGGTTTGGGATCGGGAGAG 59.856 63.158 0.00 0.00 45.48 3.20
3264 3457 1.153147 GGTTTGGGATCGGGAGAGC 60.153 63.158 0.00 0.00 45.48 4.09
3265 3458 1.627297 GGTTTGGGATCGGGAGAGCT 61.627 60.000 0.00 0.00 46.30 4.09
3266 3459 0.462759 GTTTGGGATCGGGAGAGCTG 60.463 60.000 0.00 0.00 46.30 4.24
3267 3460 1.626356 TTTGGGATCGGGAGAGCTGG 61.626 60.000 0.00 0.00 46.30 4.85
3268 3461 2.444895 GGGATCGGGAGAGCTGGT 60.445 66.667 0.00 0.00 46.30 4.00
3269 3462 1.152525 GGGATCGGGAGAGCTGGTA 60.153 63.158 0.00 0.00 46.30 3.25
3270 3463 1.182385 GGGATCGGGAGAGCTGGTAG 61.182 65.000 0.00 0.00 46.30 3.18
3271 3464 0.178987 GGATCGGGAGAGCTGGTAGA 60.179 60.000 0.00 0.00 46.30 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 79 2.569853 TCTCAATTTCAAGGGCTCGGTA 59.430 45.455 0.00 0.00 0.00 4.02
106 119 1.539929 GGTCCATGAAGATGCGGAGAG 60.540 57.143 0.00 0.00 0.00 3.20
107 120 0.465705 GGTCCATGAAGATGCGGAGA 59.534 55.000 0.00 0.00 0.00 3.71
108 121 0.178767 TGGTCCATGAAGATGCGGAG 59.821 55.000 0.00 0.00 0.00 4.63
121 134 1.282738 AGTGATGATGCATGTGGTCCA 59.717 47.619 2.46 0.00 0.00 4.02
474 536 3.746949 GACCCTGCGCCTCCATCTG 62.747 68.421 4.18 0.00 0.00 2.90
549 612 1.603739 GTGGGGAGCTTTGTGGGAC 60.604 63.158 0.00 0.00 0.00 4.46
579 643 7.232127 AGACAATTCATGTTTTCATCCTCAAGT 59.768 33.333 0.00 0.00 44.12 3.16
587 651 4.380867 GCCGGAGACAATTCATGTTTTCAT 60.381 41.667 5.05 0.00 44.12 2.57
599 663 3.366396 TCTCTCTTAAGCCGGAGACAAT 58.634 45.455 5.05 0.00 35.17 2.71
638 732 2.944429 CTCGTATCGATCCGCGGT 59.056 61.111 27.15 12.96 41.33 5.68
691 800 0.468226 TCTCGCAAACCACCAAGACT 59.532 50.000 0.00 0.00 0.00 3.24
692 801 1.197721 CATCTCGCAAACCACCAAGAC 59.802 52.381 0.00 0.00 0.00 3.01
693 802 1.522668 CATCTCGCAAACCACCAAGA 58.477 50.000 0.00 0.00 0.00 3.02
694 803 0.109597 GCATCTCGCAAACCACCAAG 60.110 55.000 0.00 0.00 41.79 3.61
695 804 0.537143 AGCATCTCGCAAACCACCAA 60.537 50.000 0.00 0.00 46.13 3.67
696 805 0.955428 GAGCATCTCGCAAACCACCA 60.955 55.000 0.00 0.00 46.13 4.17
697 806 1.796796 GAGCATCTCGCAAACCACC 59.203 57.895 0.00 0.00 46.13 4.61
830 945 1.936547 GCATGCAGCTTGGAGTAGTAC 59.063 52.381 14.21 0.00 41.15 2.73
831 946 1.134401 GGCATGCAGCTTGGAGTAGTA 60.134 52.381 21.36 0.00 44.79 1.82
832 947 0.393537 GGCATGCAGCTTGGAGTAGT 60.394 55.000 21.36 0.00 44.79 2.73
833 948 0.393402 TGGCATGCAGCTTGGAGTAG 60.393 55.000 21.36 0.00 44.79 2.57
835 950 1.000019 ATGGCATGCAGCTTGGAGT 60.000 52.632 21.36 0.00 44.79 3.85
837 952 1.035385 CAGATGGCATGCAGCTTGGA 61.035 55.000 21.36 0.00 44.79 3.53
838 953 1.035385 TCAGATGGCATGCAGCTTGG 61.035 55.000 21.36 4.08 44.79 3.61
839 954 0.100682 GTCAGATGGCATGCAGCTTG 59.899 55.000 21.36 12.13 44.79 4.01
973 1098 7.092623 TGTGGTTTAGATGGATATGTGTAAGGT 60.093 37.037 0.00 0.00 0.00 3.50
974 1099 7.279615 TGTGGTTTAGATGGATATGTGTAAGG 58.720 38.462 0.00 0.00 0.00 2.69
975 1100 8.731275 TTGTGGTTTAGATGGATATGTGTAAG 57.269 34.615 0.00 0.00 0.00 2.34
976 1101 9.119418 CATTGTGGTTTAGATGGATATGTGTAA 57.881 33.333 0.00 0.00 0.00 2.41
977 1102 7.719193 CCATTGTGGTTTAGATGGATATGTGTA 59.281 37.037 0.00 0.00 41.20 2.90
1124 1249 4.208686 CGCCACCGTAGCCTCCTC 62.209 72.222 0.00 0.00 0.00 3.71
1167 1292 0.326618 CTCCTCCATACCCACCACCT 60.327 60.000 0.00 0.00 0.00 4.00
1213 1341 5.043732 CACTATATCCTCCTCCTCCATACCT 60.044 48.000 0.00 0.00 0.00 3.08
1255 1386 1.068948 TATCCTCCTCCTCCTCCTCG 58.931 60.000 0.00 0.00 0.00 4.63
1603 1737 2.579787 GACGGCGTCGATGACCTG 60.580 66.667 25.42 8.23 40.11 4.00
2151 2285 4.373116 GGGCTGTCGGCGAACTGA 62.373 66.667 12.92 0.00 42.94 3.41
2283 2417 8.962884 TCTTGCATGCCGATATTTATATACAT 57.037 30.769 16.68 0.00 0.00 2.29
2292 2426 5.348724 CGTACTTATCTTGCATGCCGATATT 59.651 40.000 20.71 15.30 0.00 1.28
2359 2502 1.202166 ACGCATGCATACGTACGTGTA 60.202 47.619 30.25 14.76 41.48 2.90
2360 2503 0.457166 ACGCATGCATACGTACGTGT 60.457 50.000 30.25 21.74 41.48 4.49
2361 2504 1.468895 TACGCATGCATACGTACGTG 58.531 50.000 30.25 15.95 43.35 4.49
2367 2510 2.660094 GCAATGAGTACGCATGCATACG 60.660 50.000 17.39 17.65 0.00 3.06
2368 2511 2.287644 TGCAATGAGTACGCATGCATAC 59.712 45.455 22.59 15.87 31.89 2.39
2386 2529 2.057316 GCACGTTTTTACATGCATGCA 58.943 42.857 26.53 25.04 38.00 3.96
2387 2530 2.327568 AGCACGTTTTTACATGCATGC 58.672 42.857 26.53 11.82 40.63 4.06
2412 2555 0.474079 TACTGGGGTTGCACCTACCA 60.474 55.000 8.29 3.53 38.64 3.25
2436 2579 7.075674 TCAAGTGTACACATTATGCATCAAG 57.924 36.000 27.06 0.00 0.00 3.02
2565 2714 5.706369 ACTCACTCTGTTCAACGTACTCTAT 59.294 40.000 0.00 0.00 0.00 1.98
2566 2715 5.061853 ACTCACTCTGTTCAACGTACTCTA 58.938 41.667 0.00 0.00 0.00 2.43
2567 2716 3.884091 ACTCACTCTGTTCAACGTACTCT 59.116 43.478 0.00 0.00 0.00 3.24
2568 2717 4.226113 ACTCACTCTGTTCAACGTACTC 57.774 45.455 0.00 0.00 0.00 2.59
2569 2718 4.608951 GAACTCACTCTGTTCAACGTACT 58.391 43.478 0.00 0.00 42.22 2.73
2570 2719 4.950654 GAACTCACTCTGTTCAACGTAC 57.049 45.455 0.00 0.00 42.22 3.67
2577 2726 4.162812 GTCTCGATGAACTCACTCTGTTC 58.837 47.826 0.00 0.00 42.77 3.18
2616 2765 2.235898 GCCTCACATTTCAGTCTCCTCT 59.764 50.000 0.00 0.00 0.00 3.69
2632 2792 3.877735 GCTCCCTTAAAATCCTTGCCTCA 60.878 47.826 0.00 0.00 0.00 3.86
2633 2793 2.690497 GCTCCCTTAAAATCCTTGCCTC 59.310 50.000 0.00 0.00 0.00 4.70
2659 2819 2.414957 CGTTAGCCCATGCATGCATATG 60.415 50.000 31.73 24.61 41.13 1.78
2660 2820 1.814394 CGTTAGCCCATGCATGCATAT 59.186 47.619 31.73 19.57 41.13 1.78
2661 2821 1.237533 CGTTAGCCCATGCATGCATA 58.762 50.000 31.73 14.35 41.13 3.14
2662 2822 1.457823 CCGTTAGCCCATGCATGCAT 61.458 55.000 27.46 27.46 41.13 3.96
2663 2823 2.120282 CCGTTAGCCCATGCATGCA 61.120 57.895 25.04 25.04 41.13 3.96
2664 2824 2.723746 CCGTTAGCCCATGCATGC 59.276 61.111 21.69 11.82 41.13 4.06
2682 2842 0.107654 GTTGGGTCATCTCTTCCCGG 60.108 60.000 0.00 0.00 43.75 5.73
2683 2843 0.107654 GGTTGGGTCATCTCTTCCCG 60.108 60.000 0.00 0.00 43.75 5.14
2684 2844 1.290134 AGGTTGGGTCATCTCTTCCC 58.710 55.000 0.00 0.00 41.41 3.97
2685 2845 2.158885 GCTAGGTTGGGTCATCTCTTCC 60.159 54.545 0.00 0.00 0.00 3.46
2686 2846 2.158885 GGCTAGGTTGGGTCATCTCTTC 60.159 54.545 0.00 0.00 0.00 2.87
2687 2847 1.840635 GGCTAGGTTGGGTCATCTCTT 59.159 52.381 0.00 0.00 0.00 2.85
2699 2859 5.510690 GCATTTTTGGTGTTTAGGCTAGGTT 60.511 40.000 0.00 0.00 0.00 3.50
2717 2877 8.995220 TGTAATCTTTTGTACGTCTAGCATTTT 58.005 29.630 0.00 0.00 0.00 1.82
2718 2878 8.542497 TGTAATCTTTTGTACGTCTAGCATTT 57.458 30.769 0.00 0.00 0.00 2.32
2719 2879 8.604035 CATGTAATCTTTTGTACGTCTAGCATT 58.396 33.333 0.00 0.00 0.00 3.56
2720 2880 7.979537 TCATGTAATCTTTTGTACGTCTAGCAT 59.020 33.333 0.00 0.00 0.00 3.79
2721 2881 7.317390 TCATGTAATCTTTTGTACGTCTAGCA 58.683 34.615 0.00 0.00 0.00 3.49
2722 2882 7.751047 TCATGTAATCTTTTGTACGTCTAGC 57.249 36.000 0.00 0.00 0.00 3.42
2731 2891 8.806146 AGCCTGTAAAATCATGTAATCTTTTGT 58.194 29.630 0.00 0.00 0.00 2.83
2732 2892 9.294030 GAGCCTGTAAAATCATGTAATCTTTTG 57.706 33.333 0.00 0.00 0.00 2.44
2733 2893 9.247861 AGAGCCTGTAAAATCATGTAATCTTTT 57.752 29.630 0.00 0.00 0.00 2.27
2734 2894 8.814038 AGAGCCTGTAAAATCATGTAATCTTT 57.186 30.769 0.00 0.00 0.00 2.52
2735 2895 8.814038 AAGAGCCTGTAAAATCATGTAATCTT 57.186 30.769 0.00 0.00 0.00 2.40
2736 2896 8.814038 AAAGAGCCTGTAAAATCATGTAATCT 57.186 30.769 0.00 0.00 0.00 2.40
2737 2897 9.508567 GAAAAGAGCCTGTAAAATCATGTAATC 57.491 33.333 0.00 0.00 0.00 1.75
2738 2898 9.023962 TGAAAAGAGCCTGTAAAATCATGTAAT 57.976 29.630 0.00 0.00 0.00 1.89
2739 2899 8.402798 TGAAAAGAGCCTGTAAAATCATGTAA 57.597 30.769 0.00 0.00 0.00 2.41
2740 2900 7.994425 TGAAAAGAGCCTGTAAAATCATGTA 57.006 32.000 0.00 0.00 0.00 2.29
2741 2901 6.899393 TGAAAAGAGCCTGTAAAATCATGT 57.101 33.333 0.00 0.00 0.00 3.21
2748 2908 8.736244 GGTGTTTATATGAAAAGAGCCTGTAAA 58.264 33.333 0.00 0.00 0.00 2.01
2749 2909 7.885922 TGGTGTTTATATGAAAAGAGCCTGTAA 59.114 33.333 0.00 0.00 31.25 2.41
2750 2910 7.398829 TGGTGTTTATATGAAAAGAGCCTGTA 58.601 34.615 0.00 0.00 31.25 2.74
2751 2911 6.245408 TGGTGTTTATATGAAAAGAGCCTGT 58.755 36.000 0.00 0.00 31.25 4.00
2752 2912 6.757897 TGGTGTTTATATGAAAAGAGCCTG 57.242 37.500 0.00 0.00 31.25 4.85
2753 2913 7.118723 TCATGGTGTTTATATGAAAAGAGCCT 58.881 34.615 0.00 0.00 31.25 4.58
2754 2914 7.067494 ACTCATGGTGTTTATATGAAAAGAGCC 59.933 37.037 0.00 0.00 31.25 4.70
2755 2915 7.989826 ACTCATGGTGTTTATATGAAAAGAGC 58.010 34.615 0.00 0.00 32.49 4.09
2766 2926 9.793259 TTTCTCTTTCTTACTCATGGTGTTTAT 57.207 29.630 0.00 0.00 0.00 1.40
2767 2927 9.621629 TTTTCTCTTTCTTACTCATGGTGTTTA 57.378 29.630 0.00 0.00 0.00 2.01
2768 2928 8.519799 TTTTCTCTTTCTTACTCATGGTGTTT 57.480 30.769 0.00 0.00 0.00 2.83
2769 2929 8.697507 ATTTTCTCTTTCTTACTCATGGTGTT 57.302 30.769 0.00 0.00 0.00 3.32
2770 2930 9.442047 CTATTTTCTCTTTCTTACTCATGGTGT 57.558 33.333 0.00 0.00 0.00 4.16
2771 2931 9.658799 TCTATTTTCTCTTTCTTACTCATGGTG 57.341 33.333 0.00 0.00 0.00 4.17
2772 2932 9.883142 CTCTATTTTCTCTTTCTTACTCATGGT 57.117 33.333 0.00 0.00 0.00 3.55
2775 2935 9.796120 CGTCTCTATTTTCTCTTTCTTACTCAT 57.204 33.333 0.00 0.00 0.00 2.90
2780 2940 8.037382 TCGTCGTCTCTATTTTCTCTTTCTTA 57.963 34.615 0.00 0.00 0.00 2.10
2782 2942 6.497785 TCGTCGTCTCTATTTTCTCTTTCT 57.502 37.500 0.00 0.00 0.00 2.52
2784 2944 7.273815 GTCATTCGTCGTCTCTATTTTCTCTTT 59.726 37.037 0.00 0.00 0.00 2.52
2787 2947 5.169915 CGTCATTCGTCGTCTCTATTTTCTC 59.830 44.000 0.00 0.00 34.52 2.87
2851 3011 3.853330 CGTCTTGGGCATCACGCG 61.853 66.667 3.53 3.53 43.84 6.01
2854 3014 1.464997 GAAGTTCGTCTTGGGCATCAC 59.535 52.381 1.01 0.00 36.40 3.06
2857 3017 2.496899 ATGAAGTTCGTCTTGGGCAT 57.503 45.000 0.00 0.00 36.40 4.40
2862 3022 2.093447 AGGGCCTATGAAGTTCGTCTTG 60.093 50.000 2.82 0.00 36.40 3.02
2873 3033 3.051940 AGTGATTCTGAGGGCCTATGA 57.948 47.619 5.73 4.71 0.00 2.15
2874 3034 3.853355 AAGTGATTCTGAGGGCCTATG 57.147 47.619 5.73 1.76 0.00 2.23
2875 3035 4.534103 GGATAAGTGATTCTGAGGGCCTAT 59.466 45.833 5.73 0.00 0.00 2.57
2878 3038 2.708325 AGGATAAGTGATTCTGAGGGCC 59.292 50.000 0.00 0.00 0.00 5.80
2882 3042 5.566429 CGGATGGAGGATAAGTGATTCTGAG 60.566 48.000 0.00 0.00 0.00 3.35
2883 3043 4.281941 CGGATGGAGGATAAGTGATTCTGA 59.718 45.833 0.00 0.00 0.00 3.27
2895 3079 3.133014 CACGAGCGGATGGAGGAT 58.867 61.111 0.00 0.00 0.00 3.24
2896 3080 3.838271 GCACGAGCGGATGGAGGA 61.838 66.667 0.00 0.00 0.00 3.71
2922 3106 1.799994 TGAATCGCATGGCATATGACG 59.200 47.619 6.97 2.25 0.00 4.35
2924 3108 2.553602 GGTTGAATCGCATGGCATATGA 59.446 45.455 6.97 0.92 0.00 2.15
2927 3111 0.943673 CGGTTGAATCGCATGGCATA 59.056 50.000 0.00 0.00 0.00 3.14
2957 3150 4.029287 GGGACCTCTAAATCGCGC 57.971 61.111 0.00 0.00 0.00 6.86
3016 3209 1.664306 GACCGGAGAAACGAGTGGT 59.336 57.895 9.46 0.00 35.47 4.16
3021 3214 1.669440 CAAGGGACCGGAGAAACGA 59.331 57.895 9.46 0.00 35.47 3.85
3032 3225 0.900421 AGGTACGGTAAGCAAGGGAC 59.100 55.000 0.00 0.00 0.00 4.46
3046 3239 1.742750 GCGGATTGGAGTTGGAGGTAC 60.743 57.143 0.00 0.00 0.00 3.34
3066 3259 1.903890 TAGCAGGGCGGCTAGCTAG 60.904 63.158 24.05 16.84 43.70 3.42
3071 3264 2.043349 TCTGTAGCAGGGCGGCTA 60.043 61.111 9.56 5.52 43.70 3.93
3073 3266 3.391665 ATGTCTGTAGCAGGGCGGC 62.392 63.158 0.00 0.00 31.51 6.53
3076 3269 0.539051 ACTGATGTCTGTAGCAGGGC 59.461 55.000 0.00 0.00 38.35 5.19
3077 3270 4.343526 AGAATACTGATGTCTGTAGCAGGG 59.656 45.833 0.00 0.00 38.35 4.45
3078 3271 5.528043 AGAATACTGATGTCTGTAGCAGG 57.472 43.478 0.00 0.00 38.35 4.85
3079 3272 6.804677 AGAAGAATACTGATGTCTGTAGCAG 58.195 40.000 6.06 0.00 39.84 4.24
3080 3273 6.782082 AGAAGAATACTGATGTCTGTAGCA 57.218 37.500 6.06 0.00 34.54 3.49
3081 3274 9.026074 GTAAAGAAGAATACTGATGTCTGTAGC 57.974 37.037 6.06 2.01 34.54 3.58
3107 3300 0.248054 AACGTGTGCTTGCGAAACTG 60.248 50.000 0.00 0.00 0.00 3.16
3130 3323 4.827087 ACTGATGCCCAGCGAGCG 62.827 66.667 3.43 0.00 46.81 5.03
3131 3324 3.200593 CACTGATGCCCAGCGAGC 61.201 66.667 3.43 0.00 46.81 5.03
3132 3325 1.812922 GACACTGATGCCCAGCGAG 60.813 63.158 3.43 0.00 46.81 5.03
3133 3326 2.265739 GACACTGATGCCCAGCGA 59.734 61.111 3.43 0.00 46.81 4.93
3134 3327 2.046988 TGACACTGATGCCCAGCG 60.047 61.111 3.43 0.00 46.81 5.18
3135 3328 2.393768 CGTGACACTGATGCCCAGC 61.394 63.158 3.68 0.00 46.81 4.85
3137 3330 2.347114 CCGTGACACTGATGCCCA 59.653 61.111 3.68 0.00 0.00 5.36
3138 3331 2.436646 CCCGTGACACTGATGCCC 60.437 66.667 3.68 0.00 0.00 5.36
3139 3332 2.436646 CCCCGTGACACTGATGCC 60.437 66.667 3.68 0.00 0.00 4.40
3140 3333 2.436646 CCCCCGTGACACTGATGC 60.437 66.667 3.68 0.00 0.00 3.91
3141 3334 1.375908 CACCCCCGTGACACTGATG 60.376 63.158 3.68 0.00 43.14 3.07
3142 3335 2.592993 CCACCCCCGTGACACTGAT 61.593 63.158 3.68 0.00 43.14 2.90
3143 3336 3.238497 CCACCCCCGTGACACTGA 61.238 66.667 3.68 0.00 43.14 3.41
3168 3361 1.615883 CCACGATATCACCTCCTGGAG 59.384 57.143 17.02 17.02 37.04 3.86
3169 3362 1.216930 TCCACGATATCACCTCCTGGA 59.783 52.381 3.12 0.00 37.04 3.86
3170 3363 1.704641 TCCACGATATCACCTCCTGG 58.295 55.000 3.12 0.00 39.83 4.45
3171 3364 2.028658 CCATCCACGATATCACCTCCTG 60.029 54.545 3.12 0.00 0.00 3.86
3172 3365 2.158310 TCCATCCACGATATCACCTCCT 60.158 50.000 3.12 0.00 0.00 3.69
3173 3366 2.232452 CTCCATCCACGATATCACCTCC 59.768 54.545 3.12 0.00 0.00 4.30
3174 3367 2.232452 CCTCCATCCACGATATCACCTC 59.768 54.545 3.12 0.00 0.00 3.85
3175 3368 2.251818 CCTCCATCCACGATATCACCT 58.748 52.381 3.12 0.00 0.00 4.00
3176 3369 1.338200 GCCTCCATCCACGATATCACC 60.338 57.143 3.12 0.00 0.00 4.02
3177 3370 1.620819 AGCCTCCATCCACGATATCAC 59.379 52.381 3.12 0.00 0.00 3.06
3178 3371 2.015456 AGCCTCCATCCACGATATCA 57.985 50.000 3.12 0.00 0.00 2.15
3179 3372 2.564947 AGAAGCCTCCATCCACGATATC 59.435 50.000 0.00 0.00 0.00 1.63
3180 3373 2.564947 GAGAAGCCTCCATCCACGATAT 59.435 50.000 0.00 0.00 33.30 1.63
3181 3374 1.964223 GAGAAGCCTCCATCCACGATA 59.036 52.381 0.00 0.00 33.30 2.92
3182 3375 0.755686 GAGAAGCCTCCATCCACGAT 59.244 55.000 0.00 0.00 33.30 3.73
3183 3376 0.614697 TGAGAAGCCTCCATCCACGA 60.615 55.000 0.00 0.00 38.66 4.35
3184 3377 0.460987 GTGAGAAGCCTCCATCCACG 60.461 60.000 0.00 0.00 38.66 4.94
3185 3378 0.615331 TGTGAGAAGCCTCCATCCAC 59.385 55.000 0.00 0.00 38.66 4.02
3186 3379 1.211212 CATGTGAGAAGCCTCCATCCA 59.789 52.381 0.00 0.00 38.66 3.41
3187 3380 1.476471 CCATGTGAGAAGCCTCCATCC 60.476 57.143 0.00 0.00 38.66 3.51
3188 3381 1.964552 CCATGTGAGAAGCCTCCATC 58.035 55.000 0.00 0.00 38.66 3.51
3189 3382 0.106819 GCCATGTGAGAAGCCTCCAT 60.107 55.000 0.00 0.00 38.66 3.41
3190 3383 1.300963 GCCATGTGAGAAGCCTCCA 59.699 57.895 0.00 0.00 38.66 3.86
3191 3384 1.817099 CGCCATGTGAGAAGCCTCC 60.817 63.158 0.00 0.00 38.66 4.30
3192 3385 1.817099 CCGCCATGTGAGAAGCCTC 60.817 63.158 0.00 0.00 39.86 4.70
3193 3386 2.270205 CCGCCATGTGAGAAGCCT 59.730 61.111 0.00 0.00 0.00 4.58
3194 3387 3.512516 GCCGCCATGTGAGAAGCC 61.513 66.667 0.00 0.00 0.00 4.35
3195 3388 3.869272 CGCCGCCATGTGAGAAGC 61.869 66.667 0.00 0.00 0.00 3.86
3196 3389 3.197790 CCGCCGCCATGTGAGAAG 61.198 66.667 0.00 0.00 0.00 2.85
3200 3393 3.474486 ATATGCCGCCGCCATGTGA 62.474 57.895 0.00 0.00 0.00 3.58
3201 3394 2.979676 ATATGCCGCCGCCATGTG 60.980 61.111 0.00 0.00 0.00 3.21
3202 3395 2.979676 CATATGCCGCCGCCATGT 60.980 61.111 0.00 0.00 0.00 3.21
3203 3396 2.979676 ACATATGCCGCCGCCATG 60.980 61.111 1.58 7.03 34.29 3.66
3204 3397 2.979676 CACATATGCCGCCGCCAT 60.980 61.111 1.58 0.00 0.00 4.40
3213 3406 1.064621 CAACTGGCGCCACATATGC 59.935 57.895 29.03 0.00 0.00 3.14
3214 3407 1.093972 TTCAACTGGCGCCACATATG 58.906 50.000 29.03 20.89 0.00 1.78
3215 3408 1.745087 CTTTCAACTGGCGCCACATAT 59.255 47.619 29.03 8.67 0.00 1.78
3216 3409 1.164411 CTTTCAACTGGCGCCACATA 58.836 50.000 29.03 8.64 0.00 2.29
3217 3410 1.526575 CCTTTCAACTGGCGCCACAT 61.527 55.000 29.03 14.72 0.00 3.21
3218 3411 2.192861 CCTTTCAACTGGCGCCACA 61.193 57.895 29.03 5.41 0.00 4.17
3219 3412 2.644992 CCTTTCAACTGGCGCCAC 59.355 61.111 29.03 0.00 0.00 5.01
3220 3413 3.294493 GCCTTTCAACTGGCGCCA 61.294 61.111 30.59 30.59 39.71 5.69
3225 3418 0.032540 GTGCCAAGCCTTTCAACTGG 59.967 55.000 0.00 0.00 0.00 4.00
3226 3419 0.032540 GGTGCCAAGCCTTTCAACTG 59.967 55.000 0.00 0.00 0.00 3.16
3227 3420 1.455383 CGGTGCCAAGCCTTTCAACT 61.455 55.000 0.00 0.00 0.00 3.16
3228 3421 1.007387 CGGTGCCAAGCCTTTCAAC 60.007 57.895 0.00 0.00 0.00 3.18
3229 3422 2.199652 CCGGTGCCAAGCCTTTCAA 61.200 57.895 0.00 0.00 0.00 2.69
3230 3423 2.597217 CCGGTGCCAAGCCTTTCA 60.597 61.111 0.00 0.00 0.00 2.69
3231 3424 1.744320 AAACCGGTGCCAAGCCTTTC 61.744 55.000 8.52 0.00 0.00 2.62
3232 3425 1.760480 AAACCGGTGCCAAGCCTTT 60.760 52.632 8.52 0.00 0.00 3.11
3233 3426 2.123468 AAACCGGTGCCAAGCCTT 60.123 55.556 8.52 0.00 0.00 4.35
3234 3427 2.912025 CAAACCGGTGCCAAGCCT 60.912 61.111 8.52 0.00 0.00 4.58
3235 3428 3.989787 CCAAACCGGTGCCAAGCC 61.990 66.667 8.52 0.00 0.00 4.35
3236 3429 3.989787 CCCAAACCGGTGCCAAGC 61.990 66.667 8.52 0.00 0.00 4.01
3237 3430 1.595093 GATCCCAAACCGGTGCCAAG 61.595 60.000 8.52 0.00 0.00 3.61
3238 3431 1.605165 GATCCCAAACCGGTGCCAA 60.605 57.895 8.52 0.00 0.00 4.52
3239 3432 2.034999 GATCCCAAACCGGTGCCA 59.965 61.111 8.52 0.00 0.00 4.92
3240 3433 3.131478 CGATCCCAAACCGGTGCC 61.131 66.667 8.52 0.00 0.00 5.01
3241 3434 3.131478 CCGATCCCAAACCGGTGC 61.131 66.667 8.52 0.00 38.55 5.01
3242 3435 2.437716 CCCGATCCCAAACCGGTG 60.438 66.667 8.52 0.00 41.53 4.94
3243 3436 2.608368 TCCCGATCCCAAACCGGT 60.608 61.111 0.00 0.00 41.53 5.28
3244 3437 2.189521 CTCCCGATCCCAAACCGG 59.810 66.667 0.00 0.00 42.64 5.28
3245 3438 1.144057 CTCTCCCGATCCCAAACCG 59.856 63.158 0.00 0.00 0.00 4.44
3246 3439 1.153147 GCTCTCCCGATCCCAAACC 60.153 63.158 0.00 0.00 0.00 3.27
3247 3440 0.462759 CAGCTCTCCCGATCCCAAAC 60.463 60.000 0.00 0.00 0.00 2.93
3248 3441 1.626356 CCAGCTCTCCCGATCCCAAA 61.626 60.000 0.00 0.00 0.00 3.28
3249 3442 2.066393 CCAGCTCTCCCGATCCCAA 61.066 63.158 0.00 0.00 0.00 4.12
3250 3443 1.944896 TACCAGCTCTCCCGATCCCA 61.945 60.000 0.00 0.00 0.00 4.37
3251 3444 1.152525 TACCAGCTCTCCCGATCCC 60.153 63.158 0.00 0.00 0.00 3.85
3252 3445 0.178987 TCTACCAGCTCTCCCGATCC 60.179 60.000 0.00 0.00 0.00 3.36
3253 3446 3.423344 TCTACCAGCTCTCCCGATC 57.577 57.895 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.