Multiple sequence alignment - TraesCS1A01G386000

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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 TraesCS1A01G386000 chr1A 100.000 3131 0 0 1 3131 555524163 555521033 0.000000e+00 5782.0
1 TraesCS1A01G386000 chr1A 87.490 1311 134 15 1044 2331 555485005 555483702 0.000000e+00 1485.0
2 TraesCS1A01G386000 chr1A 86.699 1233 132 13 951 2165 555533446 555534664 0.000000e+00 1339.0
3 TraesCS1A01G386000 chr1D 94.783 2645 78 21 1 2623 463327432 463324826 0.000000e+00 4065.0
4 TraesCS1A01G386000 chr1D 87.615 1308 133 14 1044 2328 463283148 463281847 0.000000e+00 1491.0
5 TraesCS1A01G386000 chr1D 87.251 1255 128 12 949 2185 463341299 463342539 0.000000e+00 1402.0
6 TraesCS1A01G386000 chr1D 93.210 324 21 1 2809 3131 354529342 354529665 2.830000e-130 475.0
7 TraesCS1A01G386000 chr1D 92.632 190 7 2 2618 2806 463324127 463323944 1.850000e-67 267.0
8 TraesCS1A01G386000 chr1B 94.838 1879 65 9 651 2516 638822293 638820434 0.000000e+00 2904.0
9 TraesCS1A01G386000 chr1B 87.891 1280 123 15 1050 2307 638783788 638782519 0.000000e+00 1476.0
10 TraesCS1A01G386000 chr1B 85.613 1404 157 24 949 2323 638881982 638883369 0.000000e+00 1432.0
11 TraesCS1A01G386000 chr1B 92.424 330 23 2 2804 3131 268797597 268797926 1.310000e-128 470.0
12 TraesCS1A01G386000 chr1B 86.182 275 18 10 1 273 638822553 638822297 2.380000e-71 279.0
13 TraesCS1A01G386000 chr1B 91.954 87 5 2 2509 2595 638819786 638819702 1.530000e-23 121.0
14 TraesCS1A01G386000 chr1B 88.889 54 3 3 412 464 174123364 174123313 2.610000e-06 63.9
15 TraesCS1A01G386000 chr3D 77.812 978 183 23 1053 2012 371870640 371869679 9.740000e-160 573.0
16 TraesCS1A01G386000 chr3D 92.945 326 21 2 2808 3131 577823880 577823555 1.020000e-129 473.0
17 TraesCS1A01G386000 chr5D 93.519 324 21 0 2808 3131 280309288 280308965 1.690000e-132 483.0
18 TraesCS1A01G386000 chr5D 92.705 329 22 2 2805 3131 372333754 372334082 1.020000e-129 473.0
19 TraesCS1A01G386000 chr7D 93.252 326 20 2 2808 3131 555002392 555002717 2.180000e-131 479.0
20 TraesCS1A01G386000 chr6D 93.231 325 21 1 2808 3131 53763983 53763659 7.860000e-131 477.0
21 TraesCS1A01G386000 chr6D 93.231 325 21 1 2808 3131 316415187 316414863 7.860000e-131 477.0
22 TraesCS1A01G386000 chr6D 88.172 93 8 3 297 387 361225151 361225242 1.190000e-19 108.0
23 TraesCS1A01G386000 chr7A 92.727 330 23 1 2803 3131 60722804 60723133 2.830000e-130 475.0
24 TraesCS1A01G386000 chr6B 89.000 100 8 3 294 391 502296872 502296774 1.530000e-23 121.0
25 TraesCS1A01G386000 chr3A 89.474 95 7 3 296 388 9747481 9747574 1.970000e-22 117.0
26 TraesCS1A01G386000 chr2B 87.379 103 10 3 295 395 657105186 657105085 7.100000e-22 115.0
27 TraesCS1A01G386000 chr2B 90.741 54 3 2 412 464 575477993 575477941 1.560000e-08 71.3
28 TraesCS1A01G386000 chr7B 86.667 105 11 3 293 395 75889903 75890006 2.550000e-21 113.0
29 TraesCS1A01G386000 chr6A 87.000 100 10 3 291 388 458226474 458226572 3.300000e-20 110.0
30 TraesCS1A01G386000 chr6A 88.172 93 8 3 297 387 502335244 502335335 1.190000e-19 108.0
31 TraesCS1A01G386000 chr4B 77.157 197 34 9 416 605 328750631 328750823 1.540000e-18 104.0
32 TraesCS1A01G386000 chr2A 85.437 103 11 4 292 391 692661033 692660932 1.540000e-18 104.0


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 TraesCS1A01G386000 chr1A 555521033 555524163 3130 True 5782.000000 5782 100.000000 1 3131 1 chr1A.!!$R2 3130
1 TraesCS1A01G386000 chr1A 555483702 555485005 1303 True 1485.000000 1485 87.490000 1044 2331 1 chr1A.!!$R1 1287
2 TraesCS1A01G386000 chr1A 555533446 555534664 1218 False 1339.000000 1339 86.699000 951 2165 1 chr1A.!!$F1 1214
3 TraesCS1A01G386000 chr1D 463323944 463327432 3488 True 2166.000000 4065 93.707500 1 2806 2 chr1D.!!$R2 2805
4 TraesCS1A01G386000 chr1D 463281847 463283148 1301 True 1491.000000 1491 87.615000 1044 2328 1 chr1D.!!$R1 1284
5 TraesCS1A01G386000 chr1D 463341299 463342539 1240 False 1402.000000 1402 87.251000 949 2185 1 chr1D.!!$F2 1236
6 TraesCS1A01G386000 chr1B 638782519 638783788 1269 True 1476.000000 1476 87.891000 1050 2307 1 chr1B.!!$R2 1257
7 TraesCS1A01G386000 chr1B 638881982 638883369 1387 False 1432.000000 1432 85.613000 949 2323 1 chr1B.!!$F2 1374
8 TraesCS1A01G386000 chr1B 638819702 638822553 2851 True 1101.333333 2904 90.991333 1 2595 3 chr1B.!!$R3 2594
9 TraesCS1A01G386000 chr3D 371869679 371870640 961 True 573.000000 573 77.812000 1053 2012 1 chr3D.!!$R1 959

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
133 146 0.591659 CATGCATGATTGAGCCGAGG 59.408 55.000 22.59 0.0 0.00 4.63 F
1197 1233 2.029666 GTCACGCTGGTGCAGTCT 59.970 61.111 0.00 0.0 44.03 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1305 1.369091 GGCGCGAGAACCACATGAAT 61.369 55.0 12.10 0.0 0.0 2.57 R
2957 4406 0.034186 TCTGCGCCCCTTCATCAATT 60.034 50.0 4.18 0.0 0.0 2.32 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
39 40 8.616076 CAAGTCTCTTTAGTTGAACACTTCATT 58.384 33.333 0.00 0.00 39.84 2.57
40 41 8.738645 AGTCTCTTTAGTTGAACACTTCATTT 57.261 30.769 0.00 0.00 39.84 2.32
41 42 9.178758 AGTCTCTTTAGTTGAACACTTCATTTT 57.821 29.630 0.00 0.00 39.84 1.82
42 43 9.439537 GTCTCTTTAGTTGAACACTTCATTTTC 57.560 33.333 0.00 0.00 39.84 2.29
43 44 9.396022 TCTCTTTAGTTGAACACTTCATTTTCT 57.604 29.630 0.00 0.00 39.84 2.52
46 47 9.237846 CTTTAGTTGAACACTTCATTTTCTTCC 57.762 33.333 0.00 0.00 39.84 3.46
47 48 6.149129 AGTTGAACACTTCATTTTCTTCCC 57.851 37.500 0.00 0.00 39.84 3.97
48 49 5.893824 AGTTGAACACTTCATTTTCTTCCCT 59.106 36.000 0.00 0.00 39.84 4.20
92 105 4.783903 GTGCCAACACACACACAC 57.216 55.556 0.00 0.00 46.61 3.82
133 146 0.591659 CATGCATGATTGAGCCGAGG 59.408 55.000 22.59 0.00 0.00 4.63
149 162 4.838986 AGCCGAGGTATGATAAGTACCATT 59.161 41.667 5.25 0.00 43.26 3.16
295 312 9.874205 ATATTTTGAAACATATGTTGGGTTCTG 57.126 29.630 21.46 0.00 38.44 3.02
312 329 6.449041 TGGGTTCTGGTTTAATAGTCCCTAAT 59.551 38.462 0.00 0.00 33.67 1.73
313 330 7.628505 TGGGTTCTGGTTTAATAGTCCCTAATA 59.371 37.037 0.00 0.00 33.67 0.98
436 454 6.470278 ACATACTACCTTTGTCCTGGTTTAC 58.530 40.000 0.00 0.00 37.74 2.01
619 639 9.645128 AATGGTCAAAATATGATCCAGAATACA 57.355 29.630 0.00 0.00 40.31 2.29
627 647 9.512588 AAATATGATCCAGAATACAATGAGGAC 57.487 33.333 0.00 0.00 0.00 3.85
671 691 6.370994 GGTATCCACATTCAGAGATATGCTTG 59.629 42.308 0.00 0.00 0.00 4.01
687 707 9.529823 AGATATGCTTGGATTCATAATGAATGT 57.470 29.630 0.00 0.00 46.20 2.71
1197 1233 2.029666 GTCACGCTGGTGCAGTCT 59.970 61.111 0.00 0.00 44.03 3.24
1359 1395 1.079819 GCTCTTCGCCTACAGCACA 60.080 57.895 0.00 0.00 44.04 4.57
1449 1485 4.077184 GTCATCGTCCGCCACCCA 62.077 66.667 0.00 0.00 0.00 4.51
1473 1509 0.041312 CCTTCAACAACCTCAACGCG 60.041 55.000 3.53 3.53 0.00 6.01
2179 2249 1.141645 GTACGCACGAACCATGTGAA 58.858 50.000 0.00 0.00 39.73 3.18
2271 2362 2.182825 GCATTAGGTGTAGACGTGTCG 58.817 52.381 0.00 0.00 34.09 4.35
2323 2414 3.996150 ACAGCTCACAAAATGACAAGG 57.004 42.857 0.00 0.00 32.37 3.61
2367 2458 3.206150 TGCCTTGTGAGTTTCTCTTCAC 58.794 45.455 0.00 0.00 0.00 3.18
2378 2469 3.306917 TTCTCTTCACGGTTATTCGCA 57.693 42.857 0.00 0.00 0.00 5.10
2379 2470 3.306917 TCTCTTCACGGTTATTCGCAA 57.693 42.857 0.00 0.00 0.00 4.85
2486 2577 4.406648 TGTAGTACCATCAAGGCATCAG 57.593 45.455 0.00 0.00 43.14 2.90
2610 3354 6.094048 GTGGGCGTATGCATTTGATATTATCT 59.906 38.462 3.54 0.00 45.35 1.98
2720 4169 3.694538 GCCCAAGCCCGCATTGTT 61.695 61.111 0.00 0.00 0.00 2.83
2721 4170 2.347322 GCCCAAGCCCGCATTGTTA 61.347 57.895 0.00 0.00 0.00 2.41
2722 4171 1.510844 CCCAAGCCCGCATTGTTAC 59.489 57.895 0.00 0.00 0.00 2.50
2723 4172 0.965363 CCCAAGCCCGCATTGTTACT 60.965 55.000 0.00 0.00 0.00 2.24
2724 4173 0.171007 CCAAGCCCGCATTGTTACTG 59.829 55.000 0.00 0.00 0.00 2.74
2725 4174 0.456653 CAAGCCCGCATTGTTACTGC 60.457 55.000 0.00 0.00 36.26 4.40
2758 4207 4.558898 CGAGTAGCAAAGGAACACACTAGT 60.559 45.833 0.00 0.00 0.00 2.57
2764 4213 6.631962 AGCAAAGGAACACACTAGTACTATC 58.368 40.000 2.33 0.00 0.00 2.08
2772 4221 4.335874 ACACACTAGTACTATCTGAAGCGG 59.664 45.833 2.33 0.00 0.00 5.52
2806 4255 2.554893 TCCATTTGTTTCCAACGCTACC 59.445 45.455 0.00 0.00 0.00 3.18
2807 4256 2.556622 CCATTTGTTTCCAACGCTACCT 59.443 45.455 0.00 0.00 0.00 3.08
2808 4257 3.005367 CCATTTGTTTCCAACGCTACCTT 59.995 43.478 0.00 0.00 0.00 3.50
2809 4258 4.500716 CCATTTGTTTCCAACGCTACCTTT 60.501 41.667 0.00 0.00 0.00 3.11
2810 4259 4.722361 TTTGTTTCCAACGCTACCTTTT 57.278 36.364 0.00 0.00 0.00 2.27
2811 4260 4.722361 TTGTTTCCAACGCTACCTTTTT 57.278 36.364 0.00 0.00 0.00 1.94
2840 4289 2.510664 GAGAATGACTCCGGCCTCT 58.489 57.895 0.00 0.00 39.53 3.69
2841 4290 0.103937 GAGAATGACTCCGGCCTCTG 59.896 60.000 0.00 0.00 39.53 3.35
2842 4291 1.522580 GAATGACTCCGGCCTCTGC 60.523 63.158 0.00 0.00 0.00 4.26
2843 4292 2.244117 GAATGACTCCGGCCTCTGCA 62.244 60.000 0.00 0.00 40.13 4.41
2844 4293 1.630126 AATGACTCCGGCCTCTGCAT 61.630 55.000 0.00 0.00 40.13 3.96
2845 4294 2.037620 ATGACTCCGGCCTCTGCATC 62.038 60.000 0.00 0.00 40.13 3.91
2846 4295 2.364842 ACTCCGGCCTCTGCATCT 60.365 61.111 0.00 0.00 40.13 2.90
2847 4296 2.108566 CTCCGGCCTCTGCATCTG 59.891 66.667 0.00 0.00 40.13 2.90
2848 4297 3.457625 CTCCGGCCTCTGCATCTGG 62.458 68.421 0.00 0.00 40.13 3.86
2849 4298 4.559063 CCGGCCTCTGCATCTGGG 62.559 72.222 0.00 0.00 40.13 4.45
2852 4301 4.166888 GCCTCTGCATCTGGGCGA 62.167 66.667 0.00 0.00 37.47 5.54
2853 4302 2.827423 CCTCTGCATCTGGGCGAT 59.173 61.111 0.00 0.00 36.28 4.58
2860 4309 3.310727 CATCTGGGCGATGCATACA 57.689 52.632 0.00 0.00 42.75 2.29
2861 4310 1.596603 CATCTGGGCGATGCATACAA 58.403 50.000 0.00 0.00 42.75 2.41
2862 4311 1.265095 CATCTGGGCGATGCATACAAC 59.735 52.381 0.00 0.00 42.75 3.32
2863 4312 0.463654 TCTGGGCGATGCATACAACC 60.464 55.000 0.00 0.30 0.00 3.77
2864 4313 0.747644 CTGGGCGATGCATACAACCA 60.748 55.000 0.00 5.45 0.00 3.67
2865 4314 1.029408 TGGGCGATGCATACAACCAC 61.029 55.000 0.00 0.00 0.00 4.16
2866 4315 0.748005 GGGCGATGCATACAACCACT 60.748 55.000 0.00 0.00 0.00 4.00
2867 4316 1.094785 GGCGATGCATACAACCACTT 58.905 50.000 0.00 0.00 0.00 3.16
2868 4317 1.472480 GGCGATGCATACAACCACTTT 59.528 47.619 0.00 0.00 0.00 2.66
2869 4318 2.680841 GGCGATGCATACAACCACTTTA 59.319 45.455 0.00 0.00 0.00 1.85
2870 4319 3.315191 GGCGATGCATACAACCACTTTAT 59.685 43.478 0.00 0.00 0.00 1.40
2871 4320 4.202010 GGCGATGCATACAACCACTTTATT 60.202 41.667 0.00 0.00 0.00 1.40
2872 4321 5.008217 GGCGATGCATACAACCACTTTATTA 59.992 40.000 0.00 0.00 0.00 0.98
2873 4322 6.459024 GGCGATGCATACAACCACTTTATTAA 60.459 38.462 0.00 0.00 0.00 1.40
2874 4323 7.138736 GCGATGCATACAACCACTTTATTAAT 58.861 34.615 0.00 0.00 0.00 1.40
2875 4324 7.647715 GCGATGCATACAACCACTTTATTAATT 59.352 33.333 0.00 0.00 0.00 1.40
2920 4369 8.535690 AAGTCATACAACAGTAAGACTAAAGC 57.464 34.615 12.21 0.00 42.62 3.51
2921 4370 7.097834 AGTCATACAACAGTAAGACTAAAGCC 58.902 38.462 10.67 0.00 42.02 4.35
2922 4371 6.034683 GTCATACAACAGTAAGACTAAAGCCG 59.965 42.308 4.35 0.00 34.99 5.52
2923 4372 3.064931 ACAACAGTAAGACTAAAGCCGC 58.935 45.455 0.00 0.00 0.00 6.53
2924 4373 3.244112 ACAACAGTAAGACTAAAGCCGCT 60.244 43.478 0.00 0.00 0.00 5.52
2925 4374 2.960819 ACAGTAAGACTAAAGCCGCTG 58.039 47.619 0.00 0.00 0.00 5.18
2926 4375 2.299297 ACAGTAAGACTAAAGCCGCTGT 59.701 45.455 0.00 0.00 0.00 4.40
2927 4376 2.924290 CAGTAAGACTAAAGCCGCTGTC 59.076 50.000 0.00 0.00 0.00 3.51
2928 4377 2.826725 AGTAAGACTAAAGCCGCTGTCT 59.173 45.455 6.12 6.12 40.95 3.41
2929 4378 4.015084 AGTAAGACTAAAGCCGCTGTCTA 58.985 43.478 11.20 0.53 38.63 2.59
2930 4379 3.955650 AAGACTAAAGCCGCTGTCTAA 57.044 42.857 11.20 0.00 38.63 2.10
2931 4380 3.512033 AGACTAAAGCCGCTGTCTAAG 57.488 47.619 9.52 0.00 37.92 2.18
2944 4393 4.120646 CTGTCTAAGCAACAAACTGTCG 57.879 45.455 0.00 0.00 0.00 4.35
2945 4394 2.869801 TGTCTAAGCAACAAACTGTCGG 59.130 45.455 0.00 0.00 0.00 4.79
2946 4395 2.870411 GTCTAAGCAACAAACTGTCGGT 59.130 45.455 0.00 0.00 0.00 4.69
2947 4396 4.053295 GTCTAAGCAACAAACTGTCGGTA 58.947 43.478 0.00 0.00 0.00 4.02
2948 4397 4.053295 TCTAAGCAACAAACTGTCGGTAC 58.947 43.478 0.00 0.00 0.00 3.34
2949 4398 2.319136 AGCAACAAACTGTCGGTACA 57.681 45.000 0.00 0.00 0.00 2.90
2950 4399 2.846193 AGCAACAAACTGTCGGTACAT 58.154 42.857 0.00 0.00 34.37 2.29
2951 4400 2.806244 AGCAACAAACTGTCGGTACATC 59.194 45.455 0.00 0.00 34.37 3.06
2952 4401 2.806244 GCAACAAACTGTCGGTACATCT 59.194 45.455 0.00 0.00 34.37 2.90
2953 4402 3.991773 GCAACAAACTGTCGGTACATCTA 59.008 43.478 0.00 0.00 34.37 1.98
2954 4403 4.630069 GCAACAAACTGTCGGTACATCTAT 59.370 41.667 0.00 0.00 34.37 1.98
2955 4404 5.220416 GCAACAAACTGTCGGTACATCTATC 60.220 44.000 0.00 0.00 34.37 2.08
2956 4405 5.007385 ACAAACTGTCGGTACATCTATCC 57.993 43.478 0.00 0.00 34.37 2.59
2957 4406 4.464951 ACAAACTGTCGGTACATCTATCCA 59.535 41.667 0.00 0.00 34.37 3.41
2958 4407 5.046878 ACAAACTGTCGGTACATCTATCCAA 60.047 40.000 0.00 0.00 34.37 3.53
2959 4408 5.871396 AACTGTCGGTACATCTATCCAAT 57.129 39.130 0.00 0.00 34.37 3.16
2960 4409 5.871396 ACTGTCGGTACATCTATCCAATT 57.129 39.130 0.00 0.00 34.37 2.32
2961 4410 5.601662 ACTGTCGGTACATCTATCCAATTG 58.398 41.667 0.00 0.00 34.37 2.32
2962 4411 5.362717 ACTGTCGGTACATCTATCCAATTGA 59.637 40.000 7.12 0.00 34.37 2.57
2963 4412 6.042093 ACTGTCGGTACATCTATCCAATTGAT 59.958 38.462 7.12 1.44 34.37 2.57
2964 4413 6.223120 TGTCGGTACATCTATCCAATTGATG 58.777 40.000 7.12 4.78 44.47 3.07
2965 4414 6.041523 TGTCGGTACATCTATCCAATTGATGA 59.958 38.462 7.12 0.00 42.54 2.92
2966 4415 6.929049 GTCGGTACATCTATCCAATTGATGAA 59.071 38.462 7.12 0.00 42.54 2.57
2967 4416 7.116948 GTCGGTACATCTATCCAATTGATGAAG 59.883 40.741 7.12 0.00 42.54 3.02
2968 4417 6.369890 CGGTACATCTATCCAATTGATGAAGG 59.630 42.308 7.12 0.00 42.54 3.46
2969 4418 6.656693 GGTACATCTATCCAATTGATGAAGGG 59.343 42.308 7.12 0.00 42.54 3.95
2970 4419 5.638133 ACATCTATCCAATTGATGAAGGGG 58.362 41.667 7.12 0.00 42.54 4.79
2971 4420 4.104383 TCTATCCAATTGATGAAGGGGC 57.896 45.455 7.12 0.00 34.76 5.80
2972 4421 1.696063 ATCCAATTGATGAAGGGGCG 58.304 50.000 7.12 0.00 30.54 6.13
2973 4422 1.037030 TCCAATTGATGAAGGGGCGC 61.037 55.000 7.12 0.00 0.00 6.53
2974 4423 1.321805 CCAATTGATGAAGGGGCGCA 61.322 55.000 10.83 0.00 0.00 6.09
2975 4424 0.101759 CAATTGATGAAGGGGCGCAG 59.898 55.000 10.83 0.00 0.00 5.18
2976 4425 0.034186 AATTGATGAAGGGGCGCAGA 60.034 50.000 10.83 0.00 0.00 4.26
2977 4426 0.184451 ATTGATGAAGGGGCGCAGAT 59.816 50.000 10.83 0.00 0.00 2.90
2978 4427 0.836606 TTGATGAAGGGGCGCAGATA 59.163 50.000 10.83 0.00 0.00 1.98
2979 4428 0.394192 TGATGAAGGGGCGCAGATAG 59.606 55.000 10.83 0.00 0.00 2.08
2980 4429 0.394565 GATGAAGGGGCGCAGATAGT 59.605 55.000 10.83 0.00 0.00 2.12
2981 4430 0.394565 ATGAAGGGGCGCAGATAGTC 59.605 55.000 10.83 0.00 0.00 2.59
2982 4431 0.687757 TGAAGGGGCGCAGATAGTCT 60.688 55.000 10.83 0.00 0.00 3.24
2983 4432 0.249657 GAAGGGGCGCAGATAGTCTG 60.250 60.000 10.83 2.65 46.90 3.51
2984 4433 1.690219 AAGGGGCGCAGATAGTCTGG 61.690 60.000 10.83 1.19 44.43 3.86
2985 4434 2.134287 GGGGCGCAGATAGTCTGGA 61.134 63.158 10.83 0.00 44.43 3.86
2986 4435 1.476007 GGGGCGCAGATAGTCTGGAT 61.476 60.000 10.83 0.00 44.43 3.41
2987 4436 0.037790 GGGCGCAGATAGTCTGGATC 60.038 60.000 10.83 0.00 44.43 3.36
2988 4437 0.965439 GGCGCAGATAGTCTGGATCT 59.035 55.000 10.83 0.00 44.43 2.75
2989 4438 2.163509 GGCGCAGATAGTCTGGATCTA 58.836 52.381 10.83 0.00 44.43 1.98
2990 4439 2.558795 GGCGCAGATAGTCTGGATCTAA 59.441 50.000 10.83 0.00 44.43 2.10
2991 4440 3.194542 GGCGCAGATAGTCTGGATCTAAT 59.805 47.826 10.83 0.00 44.43 1.73
2992 4441 4.399618 GGCGCAGATAGTCTGGATCTAATA 59.600 45.833 10.83 0.00 44.43 0.98
2993 4442 5.336744 GCGCAGATAGTCTGGATCTAATAC 58.663 45.833 0.30 0.00 44.43 1.89
2994 4443 5.677598 GCGCAGATAGTCTGGATCTAATACC 60.678 48.000 0.30 0.00 44.43 2.73
2995 4444 5.416013 CGCAGATAGTCTGGATCTAATACCA 59.584 44.000 8.85 0.00 44.43 3.25
2996 4445 6.071896 CGCAGATAGTCTGGATCTAATACCAA 60.072 42.308 8.85 0.00 44.43 3.67
2997 4446 7.523873 CGCAGATAGTCTGGATCTAATACCAAA 60.524 40.741 8.85 0.00 44.43 3.28
2998 4447 7.600752 GCAGATAGTCTGGATCTAATACCAAAC 59.399 40.741 8.85 0.00 44.43 2.93
2999 4448 8.642432 CAGATAGTCTGGATCTAATACCAAACA 58.358 37.037 0.00 0.00 40.71 2.83
3000 4449 8.865090 AGATAGTCTGGATCTAATACCAAACAG 58.135 37.037 0.00 0.00 35.67 3.16
3001 4450 8.783660 ATAGTCTGGATCTAATACCAAACAGA 57.216 34.615 0.00 0.00 35.67 3.41
3003 4452 6.867519 TCTGGATCTAATACCAAACAGACA 57.132 37.500 0.00 0.00 35.67 3.41
3004 4453 7.437713 TCTGGATCTAATACCAAACAGACAT 57.562 36.000 0.00 0.00 35.67 3.06
3005 4454 7.500992 TCTGGATCTAATACCAAACAGACATC 58.499 38.462 0.00 0.00 35.67 3.06
3006 4455 6.280643 TGGATCTAATACCAAACAGACATCG 58.719 40.000 0.00 0.00 32.93 3.84
3007 4456 6.127168 TGGATCTAATACCAAACAGACATCGT 60.127 38.462 0.00 0.00 32.93 3.73
3008 4457 7.068962 TGGATCTAATACCAAACAGACATCGTA 59.931 37.037 0.00 0.00 32.93 3.43
3009 4458 7.595502 GGATCTAATACCAAACAGACATCGTAG 59.404 40.741 0.00 0.00 0.00 3.51
3010 4459 6.270815 TCTAATACCAAACAGACATCGTAGC 58.729 40.000 0.00 0.00 0.00 3.58
3011 4460 2.094762 ACCAAACAGACATCGTAGCC 57.905 50.000 0.00 0.00 0.00 3.93
3012 4461 1.346395 ACCAAACAGACATCGTAGCCA 59.654 47.619 0.00 0.00 0.00 4.75
3013 4462 2.224426 ACCAAACAGACATCGTAGCCAA 60.224 45.455 0.00 0.00 0.00 4.52
3014 4463 2.416547 CCAAACAGACATCGTAGCCAAG 59.583 50.000 0.00 0.00 0.00 3.61
3015 4464 1.726853 AACAGACATCGTAGCCAAGC 58.273 50.000 0.00 0.00 0.00 4.01
3016 4465 0.108138 ACAGACATCGTAGCCAAGCC 60.108 55.000 0.00 0.00 0.00 4.35
3017 4466 0.176680 CAGACATCGTAGCCAAGCCT 59.823 55.000 0.00 0.00 0.00 4.58
3018 4467 1.409064 CAGACATCGTAGCCAAGCCTA 59.591 52.381 0.00 0.00 0.00 3.93
3019 4468 2.108168 AGACATCGTAGCCAAGCCTAA 58.892 47.619 0.00 0.00 0.00 2.69
3020 4469 2.159085 AGACATCGTAGCCAAGCCTAAC 60.159 50.000 0.00 0.00 0.00 2.34
3021 4470 1.553248 ACATCGTAGCCAAGCCTAACA 59.447 47.619 0.00 0.00 0.00 2.41
3022 4471 2.170607 ACATCGTAGCCAAGCCTAACAT 59.829 45.455 0.00 0.00 0.00 2.71
3023 4472 2.596904 TCGTAGCCAAGCCTAACATC 57.403 50.000 0.00 0.00 0.00 3.06
3024 4473 2.108168 TCGTAGCCAAGCCTAACATCT 58.892 47.619 0.00 0.00 0.00 2.90
3025 4474 3.293337 TCGTAGCCAAGCCTAACATCTA 58.707 45.455 0.00 0.00 0.00 1.98
3026 4475 3.702548 TCGTAGCCAAGCCTAACATCTAA 59.297 43.478 0.00 0.00 0.00 2.10
3027 4476 4.051922 CGTAGCCAAGCCTAACATCTAAG 58.948 47.826 0.00 0.00 0.00 2.18
3028 4477 4.202121 CGTAGCCAAGCCTAACATCTAAGA 60.202 45.833 0.00 0.00 0.00 2.10
3029 4478 4.143986 AGCCAAGCCTAACATCTAAGAC 57.856 45.455 0.00 0.00 0.00 3.01
3030 4479 3.118223 AGCCAAGCCTAACATCTAAGACC 60.118 47.826 0.00 0.00 0.00 3.85
3031 4480 3.118223 GCCAAGCCTAACATCTAAGACCT 60.118 47.826 0.00 0.00 0.00 3.85
3032 4481 4.446371 CCAAGCCTAACATCTAAGACCTG 58.554 47.826 0.00 0.00 0.00 4.00
3033 4482 4.162320 CCAAGCCTAACATCTAAGACCTGA 59.838 45.833 0.00 0.00 0.00 3.86
3034 4483 5.355596 CAAGCCTAACATCTAAGACCTGAG 58.644 45.833 0.00 0.00 0.00 3.35
3035 4484 4.873010 AGCCTAACATCTAAGACCTGAGA 58.127 43.478 0.00 0.00 0.00 3.27
3036 4485 4.647399 AGCCTAACATCTAAGACCTGAGAC 59.353 45.833 0.00 0.00 0.00 3.36
3037 4486 4.402793 GCCTAACATCTAAGACCTGAGACA 59.597 45.833 0.00 0.00 0.00 3.41
3038 4487 5.680151 GCCTAACATCTAAGACCTGAGACAC 60.680 48.000 0.00 0.00 0.00 3.67
3039 4488 4.810191 AACATCTAAGACCTGAGACACC 57.190 45.455 0.00 0.00 0.00 4.16
3040 4489 3.779444 ACATCTAAGACCTGAGACACCA 58.221 45.455 0.00 0.00 0.00 4.17
3041 4490 4.160329 ACATCTAAGACCTGAGACACCAA 58.840 43.478 0.00 0.00 0.00 3.67
3042 4491 4.021016 ACATCTAAGACCTGAGACACCAAC 60.021 45.833 0.00 0.00 0.00 3.77
3043 4492 2.897969 TCTAAGACCTGAGACACCAACC 59.102 50.000 0.00 0.00 0.00 3.77
3044 4493 1.807814 AAGACCTGAGACACCAACCT 58.192 50.000 0.00 0.00 0.00 3.50
3045 4494 2.696526 AGACCTGAGACACCAACCTA 57.303 50.000 0.00 0.00 0.00 3.08
3046 4495 2.530701 AGACCTGAGACACCAACCTAG 58.469 52.381 0.00 0.00 0.00 3.02
3047 4496 0.977395 ACCTGAGACACCAACCTAGC 59.023 55.000 0.00 0.00 0.00 3.42
3048 4497 0.250513 CCTGAGACACCAACCTAGCC 59.749 60.000 0.00 0.00 0.00 3.93
3049 4498 0.976641 CTGAGACACCAACCTAGCCA 59.023 55.000 0.00 0.00 0.00 4.75
3050 4499 0.685097 TGAGACACCAACCTAGCCAC 59.315 55.000 0.00 0.00 0.00 5.01
3051 4500 0.977395 GAGACACCAACCTAGCCACT 59.023 55.000 0.00 0.00 0.00 4.00
3052 4501 1.348036 GAGACACCAACCTAGCCACTT 59.652 52.381 0.00 0.00 0.00 3.16
3053 4502 1.072331 AGACACCAACCTAGCCACTTG 59.928 52.381 0.00 0.00 0.00 3.16
3054 4503 1.071699 GACACCAACCTAGCCACTTGA 59.928 52.381 0.00 0.00 0.00 3.02
3055 4504 1.705186 ACACCAACCTAGCCACTTGAT 59.295 47.619 0.00 0.00 0.00 2.57
3056 4505 2.086869 CACCAACCTAGCCACTTGATG 58.913 52.381 0.00 0.00 0.00 3.07
3065 4514 2.386864 CCACTTGATGGGTCTGGGA 58.613 57.895 0.00 0.00 45.95 4.37
3066 4515 0.035056 CCACTTGATGGGTCTGGGAC 60.035 60.000 0.00 0.00 45.95 4.46
3067 4516 0.692476 CACTTGATGGGTCTGGGACA 59.308 55.000 0.14 0.00 33.68 4.02
3068 4517 0.693049 ACTTGATGGGTCTGGGACAC 59.307 55.000 0.14 0.00 36.36 3.67
3072 4521 3.236391 TGGGTCTGGGACACACAC 58.764 61.111 0.00 0.00 41.38 3.82
3073 4522 1.383943 TGGGTCTGGGACACACACT 60.384 57.895 0.00 0.00 41.38 3.55
3074 4523 1.071471 GGGTCTGGGACACACACTG 59.929 63.158 0.14 0.00 35.79 3.66
3075 4524 1.071471 GGTCTGGGACACACACTGG 59.929 63.158 0.14 0.00 33.68 4.00
3076 4525 1.696097 GGTCTGGGACACACACTGGT 61.696 60.000 0.14 0.00 33.68 4.00
3077 4526 0.249911 GTCTGGGACACACACTGGTC 60.250 60.000 0.00 0.00 32.09 4.02
3080 4529 2.030562 GGACACACACTGGTCCGG 59.969 66.667 0.00 0.00 43.67 5.14
3081 4530 2.665185 GACACACACTGGTCCGGC 60.665 66.667 0.00 0.00 0.00 6.13
3082 4531 4.602259 ACACACACTGGTCCGGCG 62.602 66.667 0.00 0.00 0.00 6.46
3083 4532 4.602259 CACACACTGGTCCGGCGT 62.602 66.667 6.01 0.00 0.00 5.68
3084 4533 4.602259 ACACACTGGTCCGGCGTG 62.602 66.667 15.97 15.97 34.92 5.34
3089 4538 4.379243 CTGGTCCGGCGTGCTCTT 62.379 66.667 6.01 0.00 0.00 2.85
3090 4539 2.992689 TGGTCCGGCGTGCTCTTA 60.993 61.111 6.01 0.00 0.00 2.10
3091 4540 2.202756 GGTCCGGCGTGCTCTTAG 60.203 66.667 6.01 0.00 0.00 2.18
3092 4541 2.707849 GGTCCGGCGTGCTCTTAGA 61.708 63.158 6.01 0.00 0.00 2.10
3093 4542 1.226717 GTCCGGCGTGCTCTTAGAG 60.227 63.158 6.01 4.63 0.00 2.43
3094 4543 2.105128 CCGGCGTGCTCTTAGAGG 59.895 66.667 11.54 0.00 0.00 3.69
3095 4544 2.583593 CGGCGTGCTCTTAGAGGC 60.584 66.667 11.54 5.94 0.00 4.70
3096 4545 2.202946 GGCGTGCTCTTAGAGGCC 60.203 66.667 11.54 11.34 30.17 5.19
3097 4546 2.583593 GCGTGCTCTTAGAGGCCG 60.584 66.667 11.54 9.72 0.00 6.13
3098 4547 2.583593 CGTGCTCTTAGAGGCCGC 60.584 66.667 11.54 0.00 0.00 6.53
3099 4548 2.202946 GTGCTCTTAGAGGCCGCC 60.203 66.667 11.54 0.00 0.00 6.13
3100 4549 3.838271 TGCTCTTAGAGGCCGCCG 61.838 66.667 11.54 0.00 0.00 6.46
3118 4567 4.954970 CCACCAACTGCCACCGCT 62.955 66.667 0.00 0.00 35.36 5.52
3119 4568 3.357079 CACCAACTGCCACCGCTC 61.357 66.667 0.00 0.00 35.36 5.03
3120 4569 4.643387 ACCAACTGCCACCGCTCC 62.643 66.667 0.00 0.00 35.36 4.70
3121 4570 4.641645 CCAACTGCCACCGCTCCA 62.642 66.667 0.00 0.00 35.36 3.86
3122 4571 2.360350 CAACTGCCACCGCTCCAT 60.360 61.111 0.00 0.00 35.36 3.41
3123 4572 2.045926 AACTGCCACCGCTCCATC 60.046 61.111 0.00 0.00 35.36 3.51
3124 4573 2.596851 AACTGCCACCGCTCCATCT 61.597 57.895 0.00 0.00 35.36 2.90
3125 4574 2.129555 AACTGCCACCGCTCCATCTT 62.130 55.000 0.00 0.00 35.36 2.40
3126 4575 1.377725 CTGCCACCGCTCCATCTTT 60.378 57.895 0.00 0.00 35.36 2.52
3127 4576 0.107703 CTGCCACCGCTCCATCTTTA 60.108 55.000 0.00 0.00 35.36 1.85
3128 4577 0.107703 TGCCACCGCTCCATCTTTAG 60.108 55.000 0.00 0.00 35.36 1.85
3129 4578 0.178068 GCCACCGCTCCATCTTTAGA 59.822 55.000 0.00 0.00 0.00 2.10
3130 4579 1.406887 GCCACCGCTCCATCTTTAGAA 60.407 52.381 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 5.249622 ACCAAACAAAAGGAAAGGGAAGAAA 59.750 36.000 0.00 0.00 0.00 2.52
40 41 4.780554 ACCAAACAAAAGGAAAGGGAAGAA 59.219 37.500 0.00 0.00 0.00 2.52
41 42 4.358214 ACCAAACAAAAGGAAAGGGAAGA 58.642 39.130 0.00 0.00 0.00 2.87
42 43 4.753516 ACCAAACAAAAGGAAAGGGAAG 57.246 40.909 0.00 0.00 0.00 3.46
43 44 4.837972 CAACCAAACAAAAGGAAAGGGAA 58.162 39.130 0.00 0.00 0.00 3.97
44 45 3.369997 GCAACCAAACAAAAGGAAAGGGA 60.370 43.478 0.00 0.00 0.00 4.20
45 46 2.942376 GCAACCAAACAAAAGGAAAGGG 59.058 45.455 0.00 0.00 0.00 3.95
46 47 3.373748 GTGCAACCAAACAAAAGGAAAGG 59.626 43.478 0.00 0.00 0.00 3.11
47 48 4.252878 AGTGCAACCAAACAAAAGGAAAG 58.747 39.130 0.00 0.00 37.80 2.62
48 49 4.278975 AGTGCAACCAAACAAAAGGAAA 57.721 36.364 0.00 0.00 37.80 3.13
89 102 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
90 103 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
91 104 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
92 105 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
248 265 8.631480 AATATATACCCCTCCGTTTCAAAATC 57.369 34.615 0.00 0.00 0.00 2.17
285 302 4.703575 GGGACTATTAAACCAGAACCCAAC 59.296 45.833 0.00 0.00 34.54 3.77
436 454 6.062258 TGACCCAAAATCTTTAGGGACTAG 57.938 41.667 2.90 0.00 44.25 2.57
478 498 6.075762 TGGCATGCATTACTATTTTGCTAG 57.924 37.500 21.36 0.00 37.28 3.42
607 627 7.296628 ACTAGTCCTCATTGTATTCTGGATC 57.703 40.000 0.00 0.00 0.00 3.36
609 629 8.603898 TTTACTAGTCCTCATTGTATTCTGGA 57.396 34.615 0.00 0.00 0.00 3.86
619 639 6.276847 CGCTTCTGATTTACTAGTCCTCATT 58.723 40.000 0.00 0.00 0.00 2.57
627 647 4.657436 ACCTCCGCTTCTGATTTACTAG 57.343 45.455 0.00 0.00 0.00 2.57
655 675 9.976776 ATTATGAATCCAAGCATATCTCTGAAT 57.023 29.630 0.00 0.00 0.00 2.57
687 707 6.638168 CGAGTAGATACGGATGTATTCGTA 57.362 41.667 18.12 7.77 41.37 3.43
1212 1248 4.619227 AACACGGCGACCACCAGG 62.619 66.667 16.62 0.00 42.21 4.45
1269 1305 1.369091 GGCGCGAGAACCACATGAAT 61.369 55.000 12.10 0.00 0.00 2.57
1359 1395 4.148825 GACACCGGCAGGAGCGAT 62.149 66.667 10.86 0.00 43.41 4.58
1449 1485 3.279434 GTTGAGGTTGTTGAAGGTGAGT 58.721 45.455 0.00 0.00 0.00 3.41
2271 2362 5.505173 ACATTGCCTAATAGATGCAACAC 57.495 39.130 6.18 0.00 46.60 3.32
2316 2407 2.885135 ACAAGCATCCATCCTTGTCA 57.115 45.000 0.56 0.00 46.22 3.58
2323 2414 1.404583 GCCACCAAACAAGCATCCATC 60.405 52.381 0.00 0.00 0.00 3.51
2391 2482 5.566627 GCTCTGCTAAACTCTGAAGAGAACT 60.567 44.000 14.20 0.96 44.74 3.01
2460 2551 6.765989 TGATGCCTTGATGGTACTACATTAAC 59.234 38.462 0.00 0.00 38.35 2.01
2486 2577 1.480545 ACCAAAAACACAAGTCCCTGC 59.519 47.619 0.00 0.00 0.00 4.85
2610 3354 3.075884 GTGGGCGAACTGTTAATACCAA 58.924 45.455 0.00 0.00 0.00 3.67
2661 4110 1.270625 CGAGCAACCTTCCTACCAACA 60.271 52.381 0.00 0.00 0.00 3.33
2662 4111 1.439679 CGAGCAACCTTCCTACCAAC 58.560 55.000 0.00 0.00 0.00 3.77
2666 4115 2.269172 GTTAGCGAGCAACCTTCCTAC 58.731 52.381 0.00 0.00 0.00 3.18
2720 4169 5.548406 TGCTACTCGATATCACTAGCAGTA 58.452 41.667 16.52 3.88 35.91 2.74
2721 4170 4.390264 TGCTACTCGATATCACTAGCAGT 58.610 43.478 16.52 6.04 35.91 4.40
2722 4171 5.363979 TTGCTACTCGATATCACTAGCAG 57.636 43.478 18.36 8.44 40.57 4.24
2723 4172 5.278512 CCTTTGCTACTCGATATCACTAGCA 60.279 44.000 16.52 16.52 38.40 3.49
2724 4173 5.048643 TCCTTTGCTACTCGATATCACTAGC 60.049 44.000 13.02 13.02 0.00 3.42
2725 4174 6.561737 TCCTTTGCTACTCGATATCACTAG 57.438 41.667 3.12 0.00 0.00 2.57
2758 4207 1.333931 CGTCTGCCGCTTCAGATAGTA 59.666 52.381 7.82 0.00 44.04 1.82
2772 4221 1.135859 CAAATGGACTTGAGCGTCTGC 60.136 52.381 0.00 0.00 43.24 4.26
2822 4271 0.103937 CAGAGGCCGGAGTCATTCTC 59.896 60.000 5.05 0.00 42.07 2.87
2823 4272 1.965754 GCAGAGGCCGGAGTCATTCT 61.966 60.000 5.05 0.00 0.00 2.40
2824 4273 1.522580 GCAGAGGCCGGAGTCATTC 60.523 63.158 5.05 0.00 0.00 2.67
2825 4274 1.630126 ATGCAGAGGCCGGAGTCATT 61.630 55.000 5.05 0.00 40.13 2.57
2826 4275 2.037620 GATGCAGAGGCCGGAGTCAT 62.038 60.000 5.05 0.00 40.13 3.06
2827 4276 2.685017 ATGCAGAGGCCGGAGTCA 60.685 61.111 5.05 0.00 40.13 3.41
2828 4277 2.107953 GATGCAGAGGCCGGAGTC 59.892 66.667 5.05 0.00 40.13 3.36
2829 4278 2.364842 AGATGCAGAGGCCGGAGT 60.365 61.111 5.05 0.00 40.13 3.85
2830 4279 2.108566 CAGATGCAGAGGCCGGAG 59.891 66.667 5.05 0.00 40.13 4.63
2831 4280 3.473647 CCAGATGCAGAGGCCGGA 61.474 66.667 5.05 0.00 40.13 5.14
2832 4281 4.559063 CCCAGATGCAGAGGCCGG 62.559 72.222 0.00 0.00 40.13 6.13
2835 4284 3.472943 ATCGCCCAGATGCAGAGGC 62.473 63.158 8.59 8.59 42.18 4.70
2836 4285 2.827423 ATCGCCCAGATGCAGAGG 59.173 61.111 0.00 0.00 38.36 3.69
2843 4292 1.597742 GTTGTATGCATCGCCCAGAT 58.402 50.000 0.19 0.00 41.01 2.90
2844 4293 0.463654 GGTTGTATGCATCGCCCAGA 60.464 55.000 0.19 0.00 0.00 3.86
2845 4294 0.747644 TGGTTGTATGCATCGCCCAG 60.748 55.000 0.19 0.00 0.00 4.45
2846 4295 1.029408 GTGGTTGTATGCATCGCCCA 61.029 55.000 0.19 2.59 0.00 5.36
2847 4296 0.748005 AGTGGTTGTATGCATCGCCC 60.748 55.000 0.19 0.00 0.00 6.13
2848 4297 1.094785 AAGTGGTTGTATGCATCGCC 58.905 50.000 0.19 1.97 0.00 5.54
2849 4298 2.919666 AAAGTGGTTGTATGCATCGC 57.080 45.000 0.19 0.00 0.00 4.58
2897 4346 6.034683 CGGCTTTAGTCTTACTGTTGTATGAC 59.965 42.308 11.70 11.70 45.97 3.06
2898 4347 6.097356 CGGCTTTAGTCTTACTGTTGTATGA 58.903 40.000 0.00 0.00 32.61 2.15
2899 4348 5.220416 GCGGCTTTAGTCTTACTGTTGTATG 60.220 44.000 0.00 0.00 0.00 2.39
2900 4349 4.868734 GCGGCTTTAGTCTTACTGTTGTAT 59.131 41.667 0.00 0.00 0.00 2.29
2901 4350 4.021719 AGCGGCTTTAGTCTTACTGTTGTA 60.022 41.667 0.00 0.00 0.00 2.41
2902 4351 3.064931 GCGGCTTTAGTCTTACTGTTGT 58.935 45.455 0.00 0.00 0.00 3.32
2903 4352 3.123621 CAGCGGCTTTAGTCTTACTGTTG 59.876 47.826 0.00 0.00 0.00 3.33
2904 4353 3.244112 ACAGCGGCTTTAGTCTTACTGTT 60.244 43.478 0.00 0.00 33.56 3.16
2905 4354 2.299297 ACAGCGGCTTTAGTCTTACTGT 59.701 45.455 0.00 0.00 32.54 3.55
2906 4355 2.924290 GACAGCGGCTTTAGTCTTACTG 59.076 50.000 0.00 0.00 0.00 2.74
2907 4356 2.826725 AGACAGCGGCTTTAGTCTTACT 59.173 45.455 13.83 0.00 38.08 2.24
2908 4357 3.233684 AGACAGCGGCTTTAGTCTTAC 57.766 47.619 13.83 0.00 38.08 2.34
2909 4358 4.677250 GCTTAGACAGCGGCTTTAGTCTTA 60.677 45.833 21.74 14.33 41.27 2.10
2910 4359 3.851098 CTTAGACAGCGGCTTTAGTCTT 58.149 45.455 21.74 10.00 41.27 3.01
2911 4360 2.417515 GCTTAGACAGCGGCTTTAGTCT 60.418 50.000 20.74 20.74 43.25 3.24
2912 4361 1.927838 GCTTAGACAGCGGCTTTAGTC 59.072 52.381 0.00 5.21 39.29 2.59
2913 4362 2.011540 GCTTAGACAGCGGCTTTAGT 57.988 50.000 0.00 0.00 39.29 2.24
2923 4372 3.059597 CCGACAGTTTGTTGCTTAGACAG 60.060 47.826 0.00 0.00 30.35 3.51
2924 4373 2.869801 CCGACAGTTTGTTGCTTAGACA 59.130 45.455 0.00 0.00 30.35 3.41
2925 4374 2.870411 ACCGACAGTTTGTTGCTTAGAC 59.130 45.455 0.00 0.00 30.35 2.59
2926 4375 3.188159 ACCGACAGTTTGTTGCTTAGA 57.812 42.857 0.00 0.00 30.35 2.10
2927 4376 3.805422 TGTACCGACAGTTTGTTGCTTAG 59.195 43.478 0.00 0.00 30.35 2.18
2928 4377 3.794717 TGTACCGACAGTTTGTTGCTTA 58.205 40.909 0.00 0.00 30.35 3.09
2929 4378 2.634600 TGTACCGACAGTTTGTTGCTT 58.365 42.857 0.00 0.00 30.35 3.91
2930 4379 2.319136 TGTACCGACAGTTTGTTGCT 57.681 45.000 0.00 0.00 30.35 3.91
2931 4380 2.806244 AGATGTACCGACAGTTTGTTGC 59.194 45.455 0.00 0.00 39.50 4.17
2932 4381 5.291128 GGATAGATGTACCGACAGTTTGTTG 59.709 44.000 0.00 0.00 39.50 3.33
2933 4382 5.046878 TGGATAGATGTACCGACAGTTTGTT 60.047 40.000 0.00 0.00 39.50 2.83
2934 4383 4.464951 TGGATAGATGTACCGACAGTTTGT 59.535 41.667 0.00 0.00 39.50 2.83
2935 4384 5.006153 TGGATAGATGTACCGACAGTTTG 57.994 43.478 0.00 0.00 39.50 2.93
2936 4385 5.670792 TTGGATAGATGTACCGACAGTTT 57.329 39.130 0.00 0.00 39.50 2.66
2937 4386 5.871396 ATTGGATAGATGTACCGACAGTT 57.129 39.130 0.00 0.00 39.50 3.16
2938 4387 5.362717 TCAATTGGATAGATGTACCGACAGT 59.637 40.000 5.42 0.00 39.50 3.55
2939 4388 5.842907 TCAATTGGATAGATGTACCGACAG 58.157 41.667 5.42 0.00 39.50 3.51
2940 4389 5.862678 TCAATTGGATAGATGTACCGACA 57.137 39.130 5.42 0.00 40.72 4.35
2941 4390 6.455647 TCATCAATTGGATAGATGTACCGAC 58.544 40.000 5.42 0.00 39.96 4.79
2942 4391 6.664428 TCATCAATTGGATAGATGTACCGA 57.336 37.500 5.42 0.00 39.96 4.69
2943 4392 6.369890 CCTTCATCAATTGGATAGATGTACCG 59.630 42.308 5.42 0.00 39.96 4.02
2944 4393 6.656693 CCCTTCATCAATTGGATAGATGTACC 59.343 42.308 5.42 0.00 39.96 3.34
2945 4394 6.656693 CCCCTTCATCAATTGGATAGATGTAC 59.343 42.308 5.42 0.00 39.96 2.90
2946 4395 6.748045 GCCCCTTCATCAATTGGATAGATGTA 60.748 42.308 5.42 0.00 39.96 2.29
2947 4396 5.638133 CCCCTTCATCAATTGGATAGATGT 58.362 41.667 5.42 0.00 39.96 3.06
2948 4397 4.461781 GCCCCTTCATCAATTGGATAGATG 59.538 45.833 5.42 1.69 40.29 2.90
2949 4398 4.670765 GCCCCTTCATCAATTGGATAGAT 58.329 43.478 5.42 0.00 33.95 1.98
2950 4399 3.496692 CGCCCCTTCATCAATTGGATAGA 60.497 47.826 5.42 0.00 33.95 1.98
2951 4400 2.816087 CGCCCCTTCATCAATTGGATAG 59.184 50.000 5.42 0.00 33.95 2.08
2952 4401 2.862541 CGCCCCTTCATCAATTGGATA 58.137 47.619 5.42 0.00 33.95 2.59
2953 4402 1.696063 CGCCCCTTCATCAATTGGAT 58.304 50.000 5.42 0.00 36.39 3.41
2954 4403 1.037030 GCGCCCCTTCATCAATTGGA 61.037 55.000 5.42 0.00 0.00 3.53
2955 4404 1.321805 TGCGCCCCTTCATCAATTGG 61.322 55.000 4.18 0.00 0.00 3.16
2956 4405 0.101759 CTGCGCCCCTTCATCAATTG 59.898 55.000 4.18 0.00 0.00 2.32
2957 4406 0.034186 TCTGCGCCCCTTCATCAATT 60.034 50.000 4.18 0.00 0.00 2.32
2958 4407 0.184451 ATCTGCGCCCCTTCATCAAT 59.816 50.000 4.18 0.00 0.00 2.57
2959 4408 0.836606 TATCTGCGCCCCTTCATCAA 59.163 50.000 4.18 0.00 0.00 2.57
2960 4409 0.394192 CTATCTGCGCCCCTTCATCA 59.606 55.000 4.18 0.00 0.00 3.07
2961 4410 0.394565 ACTATCTGCGCCCCTTCATC 59.605 55.000 4.18 0.00 0.00 2.92
2962 4411 0.394565 GACTATCTGCGCCCCTTCAT 59.605 55.000 4.18 0.00 0.00 2.57
2963 4412 0.687757 AGACTATCTGCGCCCCTTCA 60.688 55.000 4.18 0.00 0.00 3.02
2964 4413 0.249657 CAGACTATCTGCGCCCCTTC 60.250 60.000 4.18 0.00 37.72 3.46
2965 4414 1.690219 CCAGACTATCTGCGCCCCTT 61.690 60.000 4.18 0.00 42.98 3.95
2966 4415 2.136878 CCAGACTATCTGCGCCCCT 61.137 63.158 4.18 0.00 42.98 4.79
2967 4416 1.476007 ATCCAGACTATCTGCGCCCC 61.476 60.000 4.18 0.00 42.98 5.80
2968 4417 0.037790 GATCCAGACTATCTGCGCCC 60.038 60.000 4.18 0.00 42.98 6.13
2969 4418 0.965439 AGATCCAGACTATCTGCGCC 59.035 55.000 4.18 0.00 42.98 6.53
2970 4419 3.924918 TTAGATCCAGACTATCTGCGC 57.075 47.619 0.00 0.00 42.98 6.09
2971 4420 5.416013 TGGTATTAGATCCAGACTATCTGCG 59.584 44.000 0.02 0.00 42.98 5.18
2972 4421 6.842437 TGGTATTAGATCCAGACTATCTGC 57.158 41.667 0.02 0.00 42.98 4.26
2973 4422 8.642432 TGTTTGGTATTAGATCCAGACTATCTG 58.358 37.037 0.00 0.00 43.91 2.90
2974 4423 8.783660 TGTTTGGTATTAGATCCAGACTATCT 57.216 34.615 0.00 0.00 38.89 1.98
2975 4424 8.861086 TCTGTTTGGTATTAGATCCAGACTATC 58.139 37.037 0.00 0.00 38.89 2.08
2976 4425 8.643324 GTCTGTTTGGTATTAGATCCAGACTAT 58.357 37.037 11.72 0.00 42.51 2.12
2977 4426 7.618117 TGTCTGTTTGGTATTAGATCCAGACTA 59.382 37.037 16.85 6.37 44.78 2.59
2978 4427 6.440647 TGTCTGTTTGGTATTAGATCCAGACT 59.559 38.462 16.85 0.00 44.78 3.24
2979 4428 6.640518 TGTCTGTTTGGTATTAGATCCAGAC 58.359 40.000 11.96 11.96 44.76 3.51
2980 4429 6.867519 TGTCTGTTTGGTATTAGATCCAGA 57.132 37.500 0.00 0.00 35.05 3.86
2981 4430 6.422100 CGATGTCTGTTTGGTATTAGATCCAG 59.578 42.308 0.00 0.00 35.05 3.86
2982 4431 6.127168 ACGATGTCTGTTTGGTATTAGATCCA 60.127 38.462 0.00 0.00 0.00 3.41
2983 4432 6.281405 ACGATGTCTGTTTGGTATTAGATCC 58.719 40.000 0.00 0.00 0.00 3.36
2984 4433 7.115095 GCTACGATGTCTGTTTGGTATTAGATC 59.885 40.741 0.00 0.00 0.00 2.75
2985 4434 6.924060 GCTACGATGTCTGTTTGGTATTAGAT 59.076 38.462 0.00 0.00 0.00 1.98
2986 4435 6.270815 GCTACGATGTCTGTTTGGTATTAGA 58.729 40.000 0.00 0.00 0.00 2.10
2987 4436 5.462398 GGCTACGATGTCTGTTTGGTATTAG 59.538 44.000 0.00 0.00 0.00 1.73
2988 4437 5.105269 TGGCTACGATGTCTGTTTGGTATTA 60.105 40.000 0.00 0.00 0.00 0.98
2989 4438 4.189231 GGCTACGATGTCTGTTTGGTATT 58.811 43.478 0.00 0.00 0.00 1.89
2990 4439 3.196901 TGGCTACGATGTCTGTTTGGTAT 59.803 43.478 0.00 0.00 0.00 2.73
2991 4440 2.563620 TGGCTACGATGTCTGTTTGGTA 59.436 45.455 0.00 0.00 0.00 3.25
2992 4441 1.346395 TGGCTACGATGTCTGTTTGGT 59.654 47.619 0.00 0.00 0.00 3.67
2993 4442 2.093306 TGGCTACGATGTCTGTTTGG 57.907 50.000 0.00 0.00 0.00 3.28
2994 4443 2.159653 GCTTGGCTACGATGTCTGTTTG 60.160 50.000 0.00 0.00 0.00 2.93
2995 4444 2.076863 GCTTGGCTACGATGTCTGTTT 58.923 47.619 0.00 0.00 0.00 2.83
2996 4445 1.676014 GGCTTGGCTACGATGTCTGTT 60.676 52.381 0.00 0.00 0.00 3.16
2997 4446 0.108138 GGCTTGGCTACGATGTCTGT 60.108 55.000 0.00 0.00 0.00 3.41
2998 4447 0.176680 AGGCTTGGCTACGATGTCTG 59.823 55.000 0.00 0.00 0.00 3.51
2999 4448 1.776662 TAGGCTTGGCTACGATGTCT 58.223 50.000 0.00 0.00 0.00 3.41
3000 4449 2.202566 GTTAGGCTTGGCTACGATGTC 58.797 52.381 3.32 0.00 0.00 3.06
3001 4450 1.553248 TGTTAGGCTTGGCTACGATGT 59.447 47.619 3.32 0.00 0.00 3.06
3002 4451 2.309528 TGTTAGGCTTGGCTACGATG 57.690 50.000 3.32 0.00 0.00 3.84
3003 4452 2.700897 AGATGTTAGGCTTGGCTACGAT 59.299 45.455 3.32 0.00 0.00 3.73
3004 4453 2.108168 AGATGTTAGGCTTGGCTACGA 58.892 47.619 3.32 0.00 0.00 3.43
3005 4454 2.604046 AGATGTTAGGCTTGGCTACG 57.396 50.000 3.32 0.00 0.00 3.51
3006 4455 5.051153 GTCTTAGATGTTAGGCTTGGCTAC 58.949 45.833 3.32 1.23 0.00 3.58
3007 4456 4.101119 GGTCTTAGATGTTAGGCTTGGCTA 59.899 45.833 0.00 0.00 0.00 3.93
3008 4457 3.118223 GGTCTTAGATGTTAGGCTTGGCT 60.118 47.826 0.00 1.64 0.00 4.75
3009 4458 3.118223 AGGTCTTAGATGTTAGGCTTGGC 60.118 47.826 0.00 0.00 0.00 4.52
3010 4459 4.162320 TCAGGTCTTAGATGTTAGGCTTGG 59.838 45.833 0.00 0.00 0.00 3.61
3011 4460 5.127845 TCTCAGGTCTTAGATGTTAGGCTTG 59.872 44.000 0.00 0.00 0.00 4.01
3012 4461 5.128008 GTCTCAGGTCTTAGATGTTAGGCTT 59.872 44.000 0.00 0.00 0.00 4.35
3013 4462 4.647399 GTCTCAGGTCTTAGATGTTAGGCT 59.353 45.833 0.00 0.00 0.00 4.58
3014 4463 4.402793 TGTCTCAGGTCTTAGATGTTAGGC 59.597 45.833 0.00 0.00 0.00 3.93
3015 4464 5.163499 GGTGTCTCAGGTCTTAGATGTTAGG 60.163 48.000 0.00 0.00 0.00 2.69
3016 4465 5.419155 TGGTGTCTCAGGTCTTAGATGTTAG 59.581 44.000 0.00 0.00 0.00 2.34
3017 4466 5.330233 TGGTGTCTCAGGTCTTAGATGTTA 58.670 41.667 0.00 0.00 0.00 2.41
3018 4467 4.160329 TGGTGTCTCAGGTCTTAGATGTT 58.840 43.478 0.00 0.00 0.00 2.71
3019 4468 3.779444 TGGTGTCTCAGGTCTTAGATGT 58.221 45.455 0.00 0.00 0.00 3.06
3020 4469 4.499183 GTTGGTGTCTCAGGTCTTAGATG 58.501 47.826 0.00 0.00 0.00 2.90
3021 4470 3.515901 GGTTGGTGTCTCAGGTCTTAGAT 59.484 47.826 0.00 0.00 0.00 1.98
3022 4471 2.897969 GGTTGGTGTCTCAGGTCTTAGA 59.102 50.000 0.00 0.00 0.00 2.10
3023 4472 2.900546 AGGTTGGTGTCTCAGGTCTTAG 59.099 50.000 0.00 0.00 0.00 2.18
3024 4473 2.972348 AGGTTGGTGTCTCAGGTCTTA 58.028 47.619 0.00 0.00 0.00 2.10
3025 4474 1.807814 AGGTTGGTGTCTCAGGTCTT 58.192 50.000 0.00 0.00 0.00 3.01
3026 4475 2.530701 CTAGGTTGGTGTCTCAGGTCT 58.469 52.381 0.00 0.00 0.00 3.85
3027 4476 1.066787 GCTAGGTTGGTGTCTCAGGTC 60.067 57.143 0.00 0.00 0.00 3.85
3028 4477 0.977395 GCTAGGTTGGTGTCTCAGGT 59.023 55.000 0.00 0.00 0.00 4.00
3029 4478 0.250513 GGCTAGGTTGGTGTCTCAGG 59.749 60.000 0.00 0.00 0.00 3.86
3030 4479 0.976641 TGGCTAGGTTGGTGTCTCAG 59.023 55.000 0.00 0.00 0.00 3.35
3031 4480 0.685097 GTGGCTAGGTTGGTGTCTCA 59.315 55.000 0.00 0.00 0.00 3.27
3032 4481 0.977395 AGTGGCTAGGTTGGTGTCTC 59.023 55.000 0.00 0.00 0.00 3.36
3033 4482 1.072331 CAAGTGGCTAGGTTGGTGTCT 59.928 52.381 0.00 0.00 0.00 3.41
3034 4483 1.071699 TCAAGTGGCTAGGTTGGTGTC 59.928 52.381 0.00 0.00 0.00 3.67
3035 4484 1.136828 TCAAGTGGCTAGGTTGGTGT 58.863 50.000 0.00 0.00 0.00 4.16
3036 4485 2.086869 CATCAAGTGGCTAGGTTGGTG 58.913 52.381 0.00 0.00 0.00 4.17
3037 4486 1.004745 CCATCAAGTGGCTAGGTTGGT 59.995 52.381 0.00 0.00 42.12 3.67
3038 4487 1.755179 CCATCAAGTGGCTAGGTTGG 58.245 55.000 0.00 0.00 42.12 3.77
3048 4497 0.692476 TGTCCCAGACCCATCAAGTG 59.308 55.000 0.00 0.00 0.00 3.16
3049 4498 0.693049 GTGTCCCAGACCCATCAAGT 59.307 55.000 0.00 0.00 0.00 3.16
3050 4499 0.692476 TGTGTCCCAGACCCATCAAG 59.308 55.000 0.00 0.00 0.00 3.02
3051 4500 0.400213 GTGTGTCCCAGACCCATCAA 59.600 55.000 0.00 0.00 0.00 2.57
3052 4501 0.766288 TGTGTGTCCCAGACCCATCA 60.766 55.000 0.00 0.00 0.00 3.07
3053 4502 0.321653 GTGTGTGTCCCAGACCCATC 60.322 60.000 0.00 0.00 31.28 3.51
3054 4503 0.768221 AGTGTGTGTCCCAGACCCAT 60.768 55.000 0.00 0.00 38.07 4.00
3055 4504 1.383943 AGTGTGTGTCCCAGACCCA 60.384 57.895 0.00 0.00 38.07 4.51
3056 4505 1.071471 CAGTGTGTGTCCCAGACCC 59.929 63.158 0.00 0.00 38.07 4.46
3057 4506 1.071471 CCAGTGTGTGTCCCAGACC 59.929 63.158 0.00 0.00 38.07 3.85
3058 4507 0.249911 GACCAGTGTGTGTCCCAGAC 60.250 60.000 0.00 0.00 37.60 3.51
3059 4508 1.407656 GGACCAGTGTGTGTCCCAGA 61.408 60.000 5.91 0.00 44.32 3.86
3060 4509 1.071471 GGACCAGTGTGTGTCCCAG 59.929 63.158 5.91 0.00 44.32 4.45
3061 4510 2.802724 CGGACCAGTGTGTGTCCCA 61.803 63.158 10.42 0.00 46.78 4.37
3062 4511 2.030562 CGGACCAGTGTGTGTCCC 59.969 66.667 10.42 0.00 46.78 4.46
3063 4512 2.030562 CCGGACCAGTGTGTGTCC 59.969 66.667 0.00 6.91 46.15 4.02
3064 4513 2.665185 GCCGGACCAGTGTGTGTC 60.665 66.667 5.05 0.00 0.00 3.67
3065 4514 4.602259 CGCCGGACCAGTGTGTGT 62.602 66.667 5.05 0.00 0.00 3.72
3066 4515 4.602259 ACGCCGGACCAGTGTGTG 62.602 66.667 5.05 0.00 0.00 3.82
3067 4516 4.602259 CACGCCGGACCAGTGTGT 62.602 66.667 5.05 0.13 40.14 3.72
3072 4521 2.890847 CTAAGAGCACGCCGGACCAG 62.891 65.000 5.05 0.00 0.00 4.00
3073 4522 2.992689 TAAGAGCACGCCGGACCA 60.993 61.111 5.05 0.00 0.00 4.02
3074 4523 2.202756 CTAAGAGCACGCCGGACC 60.203 66.667 5.05 0.00 0.00 4.46
3075 4524 1.226717 CTCTAAGAGCACGCCGGAC 60.227 63.158 5.05 0.00 0.00 4.79
3076 4525 2.415608 CCTCTAAGAGCACGCCGGA 61.416 63.158 5.05 0.00 0.00 5.14
3077 4526 2.105128 CCTCTAAGAGCACGCCGG 59.895 66.667 0.00 0.00 0.00 6.13
3078 4527 2.583593 GCCTCTAAGAGCACGCCG 60.584 66.667 0.00 0.00 0.00 6.46
3079 4528 2.202946 GGCCTCTAAGAGCACGCC 60.203 66.667 0.00 0.00 30.17 5.68
3080 4529 2.583593 CGGCCTCTAAGAGCACGC 60.584 66.667 0.00 0.00 0.00 5.34
3081 4530 2.583593 GCGGCCTCTAAGAGCACG 60.584 66.667 0.00 0.00 33.07 5.34
3082 4531 2.202946 GGCGGCCTCTAAGAGCAC 60.203 66.667 12.87 0.00 0.00 4.40
3083 4532 3.838271 CGGCGGCCTCTAAGAGCA 61.838 66.667 18.34 0.00 0.00 4.26
3101 4550 4.954970 AGCGGTGGCAGTTGGTGG 62.955 66.667 0.00 0.00 43.41 4.61
3102 4551 3.357079 GAGCGGTGGCAGTTGGTG 61.357 66.667 0.00 0.00 43.41 4.17
3103 4552 4.643387 GGAGCGGTGGCAGTTGGT 62.643 66.667 0.00 0.00 43.41 3.67
3104 4553 3.925630 ATGGAGCGGTGGCAGTTGG 62.926 63.158 0.00 0.00 43.41 3.77
3105 4554 2.360350 ATGGAGCGGTGGCAGTTG 60.360 61.111 0.00 0.00 43.41 3.16
3106 4555 2.045926 GATGGAGCGGTGGCAGTT 60.046 61.111 0.00 0.00 43.41 3.16
3107 4556 2.129555 AAAGATGGAGCGGTGGCAGT 62.130 55.000 0.00 0.00 43.41 4.40
3108 4557 0.107703 TAAAGATGGAGCGGTGGCAG 60.108 55.000 0.00 0.00 43.41 4.85
3109 4558 0.107703 CTAAAGATGGAGCGGTGGCA 60.108 55.000 0.00 0.00 43.41 4.92
3110 4559 0.178068 TCTAAAGATGGAGCGGTGGC 59.822 55.000 0.00 0.00 40.37 5.01
3111 4560 2.691409 TTCTAAAGATGGAGCGGTGG 57.309 50.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.