Multiple sequence alignment - TraesCS1A01G390100

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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 TraesCS1A01G390100 chr1A 100.000 4469 0 0 1 4469 557916567 557912099 0.000000e+00 8253.0
1 TraesCS1A01G390100 chr1A 97.007 1203 32 4 1495 2696 550300397 550301596 0.000000e+00 2019.0
2 TraesCS1A01G390100 chr1A 95.923 1202 47 2 1495 2696 321899566 321900765 0.000000e+00 1947.0
3 TraesCS1A01G390100 chr5A 96.090 1202 44 3 1495 2696 564430632 564429434 0.000000e+00 1956.0
4 TraesCS1A01G390100 chr5A 99.462 186 1 0 4284 4469 639917581 639917396 5.540000e-89 339.0
5 TraesCS1A01G390100 chr1B 93.825 1247 67 6 3043 4284 642172700 642171459 0.000000e+00 1868.0
6 TraesCS1A01G390100 chr1B 91.455 1182 91 6 3108 4284 642200909 642199733 0.000000e+00 1615.0
7 TraesCS1A01G390100 chr1B 93.367 603 37 3 1494 2096 49344013 49344612 0.000000e+00 889.0
8 TraesCS1A01G390100 chr1B 98.261 345 6 0 983 1327 642173899 642173555 4.940000e-169 604.0
9 TraesCS1A01G390100 chr1B 94.250 400 10 7 927 1316 642176824 642176428 2.300000e-167 599.0
10 TraesCS1A01G390100 chr1B 97.904 334 5 2 983 1316 642201659 642201328 1.080000e-160 577.0
11 TraesCS1A01G390100 chr1B 89.440 464 32 12 533 990 642174775 642174323 1.800000e-158 569.0
12 TraesCS1A01G390100 chr1B 89.440 464 32 12 533 990 642202535 642202083 1.800000e-158 569.0
13 TraesCS1A01G390100 chr1B 93.931 346 20 1 194 538 642175330 642174985 5.120000e-144 521.0
14 TraesCS1A01G390100 chr1B 93.931 346 20 1 194 538 642203090 642202745 5.120000e-144 521.0
15 TraesCS1A01G390100 chr1B 100.000 187 0 0 4283 4469 584618010 584617824 3.310000e-91 346.0
16 TraesCS1A01G390100 chr1B 92.531 241 14 3 2457 2696 36275843 36275606 4.280000e-90 342.0
17 TraesCS1A01G390100 chr1B 93.289 149 9 1 2696 2844 642173465 642173318 7.530000e-53 219.0
18 TraesCS1A01G390100 chr1B 89.286 112 6 4 1384 1494 642173562 642173456 7.800000e-28 135.0
19 TraesCS1A01G390100 chr1D 93.986 1164 67 2 3124 4284 465444977 465443814 0.000000e+00 1759.0
20 TraesCS1A01G390100 chr1D 90.702 1183 101 3 3108 4284 465409804 465408625 0.000000e+00 1567.0
21 TraesCS1A01G390100 chr1D 89.236 576 24 12 1 538 465447642 465447067 0.000000e+00 686.0
22 TraesCS1A01G390100 chr1D 83.482 672 73 26 811 1470 465410727 465410082 3.850000e-165 592.0
23 TraesCS1A01G390100 chr1D 81.842 749 84 24 607 1328 465446709 465445986 2.320000e-162 582.0
24 TraesCS1A01G390100 chr1D 96.800 125 4 0 2334 2458 12065706 12065582 4.530000e-50 209.0
25 TraesCS1A01G390100 chr1D 94.030 134 5 1 2325 2458 462735674 462735544 2.730000e-47 200.0
26 TraesCS1A01G390100 chr3B 95.643 964 40 2 1495 2458 809150336 809151297 0.000000e+00 1546.0
27 TraesCS1A01G390100 chr3B 93.220 472 31 1 1494 1965 794286120 794285650 0.000000e+00 693.0
28 TraesCS1A01G390100 chr3B 95.044 343 15 2 1494 1836 33953822 33954162 5.090000e-149 538.0
29 TraesCS1A01G390100 chr3B 94.191 241 12 2 2457 2696 617377232 617377471 2.540000e-97 366.0
30 TraesCS1A01G390100 chr3B 93.852 244 13 2 2457 2699 809151331 809151573 2.540000e-97 366.0
31 TraesCS1A01G390100 chr3B 93.220 236 14 2 2465 2699 487555519 487555285 3.310000e-91 346.0
32 TraesCS1A01G390100 chr5B 92.715 604 42 2 1494 2096 507760506 507761108 0.000000e+00 870.0
33 TraesCS1A01G390100 chr5B 93.160 307 20 1 2019 2325 526767601 526767906 2.450000e-122 449.0
34 TraesCS1A01G390100 chr5B 100.000 186 0 0 4284 4469 370090074 370089889 1.190000e-90 344.0
35 TraesCS1A01G390100 chr5B 99.462 186 1 0 4284 4469 377196460 377196645 5.540000e-89 339.0
36 TraesCS1A01G390100 chr5B 74.091 220 49 8 1060 1275 711244862 711244647 2.860000e-12 84.2
37 TraesCS1A01G390100 chr2B 95.754 471 19 1 1495 1965 788847383 788846914 0.000000e+00 758.0
38 TraesCS1A01G390100 chr2B 93.485 307 19 1 2019 2325 638416384 638416689 5.270000e-124 455.0
39 TraesCS1A01G390100 chr2B 91.531 307 25 1 2019 2325 638408253 638408558 5.340000e-114 422.0
40 TraesCS1A01G390100 chr2B 93.469 245 13 2 2457 2700 788844959 788844717 1.180000e-95 361.0
41 TraesCS1A01G390100 chr2B 99.462 186 1 0 4284 4469 335201776 335201591 5.540000e-89 339.0
42 TraesCS1A01G390100 chr2A 75.445 1124 251 19 3173 4282 737316453 737315341 1.420000e-144 523.0
43 TraesCS1A01G390100 chr3D 74.560 967 212 26 3293 4242 571563295 571562346 4.190000e-105 392.0
44 TraesCS1A01G390100 chr3D 95.902 122 5 0 2334 2455 64758806 64758927 9.810000e-47 198.0
45 TraesCS1A01G390100 chr7A 89.384 292 29 2 2034 2325 336000440 336000151 2.540000e-97 366.0
46 TraesCS1A01G390100 chr7A 88.014 292 32 3 2034 2325 336291799 336291511 4.280000e-90 342.0
47 TraesCS1A01G390100 chr6B 100.000 189 0 0 4281 4469 481458013 481457825 2.560000e-92 350.0
48 TraesCS1A01G390100 chr6B 100.000 185 0 0 4285 4469 466679252 466679068 4.280000e-90 342.0
49 TraesCS1A01G390100 chr4A 89.416 274 27 2 1759 2032 344446778 344447049 1.190000e-90 344.0
50 TraesCS1A01G390100 chr2D 92.245 245 15 3 2454 2696 164280666 164280908 1.190000e-90 344.0
51 TraesCS1A01G390100 chr4B 100.000 185 0 0 4285 4469 404406851 404406667 4.280000e-90 342.0
52 TraesCS1A01G390100 chr3A 98.438 192 2 1 4279 4469 634550457 634550648 1.990000e-88 337.0
53 TraesCS1A01G390100 chr7B 94.776 134 7 0 2325 2458 580167758 580167625 4.530000e-50 209.0
54 TraesCS1A01G390100 chr6D 96.000 125 5 0 2334 2458 380441798 380441922 2.110000e-48 204.0


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 TraesCS1A01G390100 chr1A 557912099 557916567 4468 True 8253.0 8253 100.000000 1 4469 1 chr1A.!!$R1 4468
1 TraesCS1A01G390100 chr1A 550300397 550301596 1199 False 2019.0 2019 97.007000 1495 2696 1 chr1A.!!$F2 1201
2 TraesCS1A01G390100 chr1A 321899566 321900765 1199 False 1947.0 1947 95.923000 1495 2696 1 chr1A.!!$F1 1201
3 TraesCS1A01G390100 chr5A 564429434 564430632 1198 True 1956.0 1956 96.090000 1495 2696 1 chr5A.!!$R1 1201
4 TraesCS1A01G390100 chr1B 49344013 49344612 599 False 889.0 889 93.367000 1494 2096 1 chr1B.!!$F1 602
5 TraesCS1A01G390100 chr1B 642199733 642203090 3357 True 820.5 1615 93.182500 194 4284 4 chr1B.!!$R4 4090
6 TraesCS1A01G390100 chr1B 642171459 642176824 5365 True 645.0 1868 93.183143 194 4284 7 chr1B.!!$R3 4090
7 TraesCS1A01G390100 chr1D 465408625 465410727 2102 True 1079.5 1567 87.092000 811 4284 2 chr1D.!!$R3 3473
8 TraesCS1A01G390100 chr1D 465443814 465447642 3828 True 1009.0 1759 88.354667 1 4284 3 chr1D.!!$R4 4283
9 TraesCS1A01G390100 chr3B 809150336 809151573 1237 False 956.0 1546 94.747500 1495 2699 2 chr3B.!!$F3 1204
10 TraesCS1A01G390100 chr5B 507760506 507761108 602 False 870.0 870 92.715000 1494 2096 1 chr5B.!!$F2 602
11 TraesCS1A01G390100 chr2B 788844717 788847383 2666 True 559.5 758 94.611500 1495 2700 2 chr2B.!!$R2 1205
12 TraesCS1A01G390100 chr2A 737315341 737316453 1112 True 523.0 523 75.445000 3173 4282 1 chr2A.!!$R1 1109
13 TraesCS1A01G390100 chr3D 571562346 571563295 949 True 392.0 392 74.560000 3293 4242 1 chr3D.!!$R1 949

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
845 2484 0.179020 CAAGAGTGGGTGGCTTGTGA 60.179 55.0 0.00 0.0 35.49 3.58 F
1394 3491 0.173708 ACTTTCCCGAGTCTCGCATC 59.826 55.0 17.02 0.0 38.82 3.91 F
2876 7699 0.042581 TGCCATGAGGTGAGGGAGTA 59.957 55.0 0.00 0.0 37.19 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2541 6889 0.035739 GAGGGCGTTTCCAACAGGTA 59.964 55.000 0.0 0.0 36.21 3.08 R
3188 8095 1.148273 TGAGGCATGGTAATCCGCC 59.852 57.895 0.0 0.0 39.49 6.13 R
4344 9272 0.102300 GTTGGGTGCTGTTGTTGGTC 59.898 55.000 0.0 0.0 0.00 4.02 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
91 94 4.564769 CGGATCTAGAAAAGAGAAGCACAC 59.435 45.833 0.00 0.00 37.74 3.82
92 95 5.482908 GGATCTAGAAAAGAGAAGCACACA 58.517 41.667 0.00 0.00 37.74 3.72
94 97 6.597280 GGATCTAGAAAAGAGAAGCACACATT 59.403 38.462 0.00 0.00 37.74 2.71
95 98 7.120432 GGATCTAGAAAAGAGAAGCACACATTT 59.880 37.037 0.00 0.00 37.74 2.32
96 99 9.155975 GATCTAGAAAAGAGAAGCACACATTTA 57.844 33.333 0.00 0.00 37.74 1.40
97 100 8.539770 TCTAGAAAAGAGAAGCACACATTTAG 57.460 34.615 0.00 0.00 0.00 1.85
99 102 4.773323 AAAGAGAAGCACACATTTAGCC 57.227 40.909 0.00 0.00 0.00 3.93
101 104 2.307098 AGAGAAGCACACATTTAGCCCT 59.693 45.455 0.00 0.00 0.00 5.19
127 155 2.203480 ACATGCGTTGGGCCACTT 60.203 55.556 5.23 0.00 42.61 3.16
199 1501 4.519350 TCGCTCTAGTACAATGGATCGAAT 59.481 41.667 0.00 0.00 27.61 3.34
201 1503 5.562890 CGCTCTAGTACAATGGATCGAATGA 60.563 44.000 0.00 0.00 0.00 2.57
233 1535 3.763897 GGCCGCCATATAGGAAATTCAAT 59.236 43.478 3.91 0.00 41.22 2.57
236 1538 5.648092 GCCGCCATATAGGAAATTCAATACT 59.352 40.000 0.00 0.00 41.22 2.12
491 1804 2.915869 ACTCCCTCTCCAAACCATACA 58.084 47.619 0.00 0.00 0.00 2.29
493 1806 4.631234 ACTCCCTCTCCAAACCATACATA 58.369 43.478 0.00 0.00 0.00 2.29
520 1833 9.944663 TTCTTAATTGTTGTGTATGAAACTGAC 57.055 29.630 0.00 0.00 0.00 3.51
524 1837 1.803334 TGTGTATGAAACTGACCCGC 58.197 50.000 0.00 0.00 0.00 6.13
543 2093 3.546020 CCGCTACCTAACATTCATTTGCG 60.546 47.826 0.00 0.00 39.46 4.85
559 2109 4.034258 CGCACCTGCACTGGCTTG 62.034 66.667 0.00 0.00 42.21 4.01
690 2301 5.416639 AGGAAAACACGAACTTTACTGGTTT 59.583 36.000 0.00 0.00 0.00 3.27
693 2304 3.208594 ACACGAACTTTACTGGTTTCCC 58.791 45.455 0.00 0.00 0.00 3.97
715 2336 2.039405 GCTGCTCCACTGCTTCTGG 61.039 63.158 0.00 0.00 39.94 3.86
778 2400 3.003763 AGTCCTCCCGCACCTTCC 61.004 66.667 0.00 0.00 0.00 3.46
779 2401 3.003763 GTCCTCCCGCACCTTCCT 61.004 66.667 0.00 0.00 0.00 3.36
786 2408 1.139095 CCGCACCTTCCTCGTAGTC 59.861 63.158 0.00 0.00 0.00 2.59
788 2410 1.881602 GCACCTTCCTCGTAGTCGT 59.118 57.895 0.00 0.00 38.33 4.34
845 2484 0.179020 CAAGAGTGGGTGGCTTGTGA 60.179 55.000 0.00 0.00 35.49 3.58
881 2520 3.414700 GTCCTGACGCGCCAACAG 61.415 66.667 5.73 10.98 0.00 3.16
892 2531 4.379243 CCAACAGCCGCGTCTCCT 62.379 66.667 4.92 0.00 0.00 3.69
923 2562 1.507141 CGTGCCCTCAAGGACACAAC 61.507 60.000 14.70 0.00 40.59 3.32
926 2565 1.507141 GCCCTCAAGGACACAACACG 61.507 60.000 0.00 0.00 38.24 4.49
927 2566 1.507141 CCCTCAAGGACACAACACGC 61.507 60.000 0.00 0.00 38.24 5.34
941 2584 4.929808 CACAACACGCTCTTCCTTACTTAT 59.070 41.667 0.00 0.00 0.00 1.73
990 3068 1.056660 TTGTTGTGGGAGAGAGGGAC 58.943 55.000 0.00 0.00 0.00 4.46
992 3070 1.280457 GTTGTGGGAGAGAGGGACAT 58.720 55.000 0.00 0.00 0.00 3.06
1055 3133 2.332654 GGAAACAAGTCGCGGGCAT 61.333 57.895 6.13 0.00 0.00 4.40
1330 3410 4.057406 CTCACTTATTGAGCTCTCCAGG 57.943 50.000 16.19 5.26 45.51 4.45
1332 3412 3.449018 TCACTTATTGAGCTCTCCAGGTC 59.551 47.826 16.19 0.00 45.94 3.85
1340 3420 3.530535 GAGCTCTCCAGGTCAAAAGATC 58.469 50.000 6.43 0.00 45.20 2.75
1348 3428 4.508662 CCAGGTCAAAAGATCTGGTCTAC 58.491 47.826 15.06 0.00 45.90 2.59
1349 3429 4.020218 CCAGGTCAAAAGATCTGGTCTACA 60.020 45.833 15.06 0.00 45.90 2.74
1362 3459 5.376625 TCTGGTCTACAAGCAAGTGATTTT 58.623 37.500 0.00 0.00 34.32 1.82
1369 3466 5.280654 ACAAGCAAGTGATTTTTGTGGAT 57.719 34.783 0.00 0.00 31.34 3.41
1391 3488 2.358939 TTTACTTTCCCGAGTCTCGC 57.641 50.000 17.02 0.00 38.82 5.03
1392 3489 1.250328 TTACTTTCCCGAGTCTCGCA 58.750 50.000 17.02 2.34 38.82 5.10
1393 3490 1.471119 TACTTTCCCGAGTCTCGCAT 58.529 50.000 17.02 0.75 38.82 4.73
1394 3491 0.173708 ACTTTCCCGAGTCTCGCATC 59.826 55.000 17.02 0.00 38.82 3.91
1397 3494 1.758936 TTCCCGAGTCTCGCATCTTA 58.241 50.000 17.02 0.00 38.82 2.10
1409 3935 9.944663 GAGTCTCGCATCTTATAGGATTATTAG 57.055 37.037 0.00 0.00 0.00 1.73
1412 3938 8.687242 TCTCGCATCTTATAGGATTATTAGTGG 58.313 37.037 0.00 0.00 0.00 4.00
1413 3939 8.589701 TCGCATCTTATAGGATTATTAGTGGA 57.410 34.615 0.00 0.00 0.00 4.02
1414 3940 9.201989 TCGCATCTTATAGGATTATTAGTGGAT 57.798 33.333 0.00 0.00 0.00 3.41
1527 4071 1.414866 AAACCACCACATTTGGGGCC 61.415 55.000 2.32 0.00 46.42 5.80
1545 4089 3.026694 GGCCTATCTTGCAGAAAACCAT 58.973 45.455 0.00 0.00 0.00 3.55
1669 4214 1.889530 GCCGGACTGTAAGGAGCTGT 61.890 60.000 5.05 0.00 39.30 4.40
1717 4262 8.398743 ACCTCCCTGGATCTTATAAAAGAAAAA 58.601 33.333 0.00 0.00 41.19 1.94
1775 4324 2.052690 CCTCTCGCCGGGAAGAAGA 61.053 63.158 2.18 0.00 0.00 2.87
2541 6889 2.831526 GTGTGTGATTATTTTGGGCCCT 59.168 45.455 25.70 4.56 0.00 5.19
2548 6896 3.837399 TTATTTTGGGCCCTACCTGTT 57.163 42.857 25.70 3.82 39.10 3.16
2696 7044 3.319122 GGTGGTTTCTTGCAATTCACTCT 59.681 43.478 0.00 0.00 0.00 3.24
2700 7048 7.147976 GTGGTTTCTTGCAATTCACTCTATTT 58.852 34.615 0.00 0.00 0.00 1.40
2701 7049 7.327032 GTGGTTTCTTGCAATTCACTCTATTTC 59.673 37.037 0.00 0.00 0.00 2.17
2702 7050 7.231317 TGGTTTCTTGCAATTCACTCTATTTCT 59.769 33.333 0.00 0.00 0.00 2.52
2703 7051 7.752686 GGTTTCTTGCAATTCACTCTATTTCTC 59.247 37.037 0.00 0.00 0.00 2.87
2704 7052 6.992063 TCTTGCAATTCACTCTATTTCTCC 57.008 37.500 0.00 0.00 0.00 3.71
2705 7053 6.475504 TCTTGCAATTCACTCTATTTCTCCA 58.524 36.000 0.00 0.00 0.00 3.86
2706 7054 7.114754 TCTTGCAATTCACTCTATTTCTCCAT 58.885 34.615 0.00 0.00 0.00 3.41
2707 7055 7.613022 TCTTGCAATTCACTCTATTTCTCCATT 59.387 33.333 0.00 0.00 0.00 3.16
2708 7056 7.707624 TGCAATTCACTCTATTTCTCCATTT 57.292 32.000 0.00 0.00 0.00 2.32
2709 7057 7.541162 TGCAATTCACTCTATTTCTCCATTTG 58.459 34.615 0.00 0.00 0.00 2.32
2710 7058 6.474751 GCAATTCACTCTATTTCTCCATTTGC 59.525 38.462 0.00 0.00 0.00 3.68
2711 7059 7.630082 GCAATTCACTCTATTTCTCCATTTGCT 60.630 37.037 0.00 0.00 32.66 3.91
2712 7060 6.992063 TTCACTCTATTTCTCCATTTGCTC 57.008 37.500 0.00 0.00 0.00 4.26
2763 7112 2.416972 GCAGAGTATTTTCCGACGTCCT 60.417 50.000 10.58 0.00 0.00 3.85
2771 7120 2.825861 TTCCGACGTCCTTAAAGCTT 57.174 45.000 10.58 0.00 0.00 3.74
2805 7158 9.391006 ACTATTAAGTTCAATTTATCTTCGCCA 57.609 29.630 0.00 0.00 29.00 5.69
2820 7173 2.577700 TCGCCAAGTTCTTTTGCCTTA 58.422 42.857 0.00 0.00 0.00 2.69
2834 7187 1.834896 TGCCTTAATGCTTCGTAGGGA 59.165 47.619 4.32 0.00 0.00 4.20
2846 7649 4.567159 GCTTCGTAGGGATTCACTAAACTG 59.433 45.833 0.00 0.00 0.00 3.16
2876 7699 0.042581 TGCCATGAGGTGAGGGAGTA 59.957 55.000 0.00 0.00 37.19 2.59
2886 7709 4.168101 AGGTGAGGGAGTAAAGTGATTGA 58.832 43.478 0.00 0.00 0.00 2.57
2895 7718 8.383175 AGGGAGTAAAGTGATTGAAGACATTAA 58.617 33.333 0.00 0.00 0.00 1.40
2948 7771 8.810652 TCAAATTGTAGCAAATTTCAGTTACC 57.189 30.769 0.00 0.00 37.59 2.85
2959 7782 9.129209 GCAAATTTCAGTTACCTCAGAAATAAC 57.871 33.333 0.00 0.00 39.14 1.89
2991 7814 1.764134 TGTATACACCATCCCCCGTTC 59.236 52.381 0.08 0.00 0.00 3.95
3002 7825 5.012768 ACCATCCCCCGTTCAATAATACTAG 59.987 44.000 0.00 0.00 0.00 2.57
3035 7912 6.877611 TGGAACTTCCATCTTTAACTTCAC 57.122 37.500 6.39 0.00 42.67 3.18
3036 7913 6.361433 TGGAACTTCCATCTTTAACTTCACA 58.639 36.000 6.39 0.00 42.67 3.58
3037 7914 6.486657 TGGAACTTCCATCTTTAACTTCACAG 59.513 38.462 6.39 0.00 42.67 3.66
3038 7915 6.710744 GGAACTTCCATCTTTAACTTCACAGA 59.289 38.462 2.62 0.00 36.28 3.41
3039 7916 7.095017 GGAACTTCCATCTTTAACTTCACAGAG 60.095 40.741 2.62 0.00 36.28 3.35
3040 7917 7.067496 ACTTCCATCTTTAACTTCACAGAGA 57.933 36.000 0.00 0.00 0.00 3.10
3041 7918 7.684529 ACTTCCATCTTTAACTTCACAGAGAT 58.315 34.615 0.00 0.00 0.00 2.75
3045 7922 8.324306 TCCATCTTTAACTTCACAGAGATGAAT 58.676 33.333 11.54 0.00 41.71 2.57
3188 8095 4.009675 TCCTGGAACAATCAAATTCTCCG 58.990 43.478 0.00 0.00 38.70 4.63
3385 8298 7.257199 GGAGGGATATGGAGAAGGACAAAATAT 60.257 40.741 0.00 0.00 0.00 1.28
3439 8352 8.418662 ACGCTAGAGAAGATATATCTATCGTCT 58.581 37.037 15.64 13.86 46.04 4.18
3459 8372 2.676471 ATTGTCGGGCTTGGTGGC 60.676 61.111 0.00 0.00 40.96 5.01
3495 8411 4.217118 ACATTGGCTGAATCAGTCTTTGTC 59.783 41.667 16.35 0.00 36.97 3.18
3496 8412 2.783135 TGGCTGAATCAGTCTTTGTCC 58.217 47.619 16.35 5.24 36.97 4.02
3497 8413 2.373169 TGGCTGAATCAGTCTTTGTCCT 59.627 45.455 16.35 0.00 36.97 3.85
3516 8432 4.220602 GTCCTAGACAAAATGGCCAACAAT 59.779 41.667 10.96 0.00 32.09 2.71
3519 8435 5.997129 CCTAGACAAAATGGCCAACAATTTT 59.003 36.000 10.96 9.50 29.91 1.82
3783 8699 3.242248 GCAGAGTTATTGTAACTACGCGG 59.758 47.826 12.47 0.00 0.00 6.46
3792 8708 1.728425 GTAACTACGCGGAACCAAAGG 59.272 52.381 12.47 0.00 0.00 3.11
3810 8729 7.938140 CCAAAGGGTAGTGAATAAAATGAGA 57.062 36.000 0.00 0.00 0.00 3.27
3879 8798 6.992123 ACTCTGATCAAATCAACTTGTGTGTA 59.008 34.615 0.00 0.00 39.11 2.90
4257 9185 4.371624 TGGATACATTCATGGGGATGAC 57.628 45.455 10.31 3.77 46.17 3.06
4258 9186 3.721050 TGGATACATTCATGGGGATGACA 59.279 43.478 10.31 0.00 46.17 3.58
4323 9251 5.624344 CGAGAGCCCGACTTTATAGATAA 57.376 43.478 0.00 0.00 0.00 1.75
4324 9252 6.010294 CGAGAGCCCGACTTTATAGATAAA 57.990 41.667 0.00 0.00 0.00 1.40
4346 9274 3.393089 CCACCAGGCAGAGTATATGAC 57.607 52.381 0.00 0.00 0.00 3.06
4347 9275 2.037772 CCACCAGGCAGAGTATATGACC 59.962 54.545 0.00 0.00 0.00 4.02
4348 9276 2.700371 CACCAGGCAGAGTATATGACCA 59.300 50.000 0.00 0.00 0.00 4.02
4349 9277 3.134623 CACCAGGCAGAGTATATGACCAA 59.865 47.826 0.00 0.00 0.00 3.67
4350 9278 3.134804 ACCAGGCAGAGTATATGACCAAC 59.865 47.826 0.00 0.00 0.00 3.77
4351 9279 3.134623 CCAGGCAGAGTATATGACCAACA 59.865 47.826 0.00 0.00 0.00 3.33
4352 9280 4.384098 CCAGGCAGAGTATATGACCAACAA 60.384 45.833 0.00 0.00 0.00 2.83
4353 9281 4.572389 CAGGCAGAGTATATGACCAACAAC 59.428 45.833 0.00 0.00 0.00 3.32
4354 9282 4.225042 AGGCAGAGTATATGACCAACAACA 59.775 41.667 0.00 0.00 0.00 3.33
4355 9283 4.572389 GGCAGAGTATATGACCAACAACAG 59.428 45.833 0.00 0.00 0.00 3.16
4356 9284 4.034510 GCAGAGTATATGACCAACAACAGC 59.965 45.833 0.00 0.00 0.00 4.40
4357 9285 5.178061 CAGAGTATATGACCAACAACAGCA 58.822 41.667 0.00 0.00 0.00 4.41
4358 9286 5.063944 CAGAGTATATGACCAACAACAGCAC 59.936 44.000 0.00 0.00 0.00 4.40
4359 9287 4.261801 AGTATATGACCAACAACAGCACC 58.738 43.478 0.00 0.00 0.00 5.01
4360 9288 1.904287 TATGACCAACAACAGCACCC 58.096 50.000 0.00 0.00 0.00 4.61
4361 9289 0.106268 ATGACCAACAACAGCACCCA 60.106 50.000 0.00 0.00 0.00 4.51
4362 9290 0.323816 TGACCAACAACAGCACCCAA 60.324 50.000 0.00 0.00 0.00 4.12
4363 9291 0.102300 GACCAACAACAGCACCCAAC 59.898 55.000 0.00 0.00 0.00 3.77
4364 9292 0.613292 ACCAACAACAGCACCCAACA 60.613 50.000 0.00 0.00 0.00 3.33
4365 9293 0.534412 CCAACAACAGCACCCAACAA 59.466 50.000 0.00 0.00 0.00 2.83
4366 9294 1.066573 CCAACAACAGCACCCAACAAA 60.067 47.619 0.00 0.00 0.00 2.83
4367 9295 2.270047 CAACAACAGCACCCAACAAAG 58.730 47.619 0.00 0.00 0.00 2.77
4368 9296 1.555967 ACAACAGCACCCAACAAAGT 58.444 45.000 0.00 0.00 0.00 2.66
4369 9297 2.729194 ACAACAGCACCCAACAAAGTA 58.271 42.857 0.00 0.00 0.00 2.24
4370 9298 3.295973 ACAACAGCACCCAACAAAGTAT 58.704 40.909 0.00 0.00 0.00 2.12
4371 9299 3.317993 ACAACAGCACCCAACAAAGTATC 59.682 43.478 0.00 0.00 0.00 2.24
4372 9300 3.222173 ACAGCACCCAACAAAGTATCA 57.778 42.857 0.00 0.00 0.00 2.15
4373 9301 2.884639 ACAGCACCCAACAAAGTATCAC 59.115 45.455 0.00 0.00 0.00 3.06
4374 9302 2.095768 CAGCACCCAACAAAGTATCACG 60.096 50.000 0.00 0.00 0.00 4.35
4375 9303 1.401018 GCACCCAACAAAGTATCACGC 60.401 52.381 0.00 0.00 0.00 5.34
4376 9304 1.136085 CACCCAACAAAGTATCACGCG 60.136 52.381 3.53 3.53 0.00 6.01
4377 9305 0.179200 CCCAACAAAGTATCACGCGC 60.179 55.000 5.73 0.00 0.00 6.86
4378 9306 0.515127 CCAACAAAGTATCACGCGCA 59.485 50.000 5.73 0.00 0.00 6.09
4379 9307 1.464023 CCAACAAAGTATCACGCGCAG 60.464 52.381 5.73 2.42 0.00 5.18
4380 9308 1.459209 CAACAAAGTATCACGCGCAGA 59.541 47.619 5.73 4.85 0.00 4.26
4381 9309 1.790755 ACAAAGTATCACGCGCAGAA 58.209 45.000 5.73 0.00 0.00 3.02
4382 9310 1.726791 ACAAAGTATCACGCGCAGAAG 59.273 47.619 5.73 0.00 0.00 2.85
4383 9311 1.992667 CAAAGTATCACGCGCAGAAGA 59.007 47.619 5.73 0.00 0.00 2.87
4384 9312 2.586258 AAGTATCACGCGCAGAAGAT 57.414 45.000 5.73 7.15 0.00 2.40
4385 9313 3.710326 AAGTATCACGCGCAGAAGATA 57.290 42.857 5.73 6.11 0.00 1.98
4386 9314 3.710326 AGTATCACGCGCAGAAGATAA 57.290 42.857 5.73 0.00 0.00 1.75
4387 9315 4.041740 AGTATCACGCGCAGAAGATAAA 57.958 40.909 5.73 0.00 0.00 1.40
4388 9316 4.045104 AGTATCACGCGCAGAAGATAAAG 58.955 43.478 5.73 0.00 0.00 1.85
4389 9317 2.363788 TCACGCGCAGAAGATAAAGT 57.636 45.000 5.73 0.00 0.00 2.66
4390 9318 3.497297 TCACGCGCAGAAGATAAAGTA 57.503 42.857 5.73 0.00 0.00 2.24
4391 9319 4.041740 TCACGCGCAGAAGATAAAGTAT 57.958 40.909 5.73 0.00 0.00 2.12
4392 9320 4.042398 TCACGCGCAGAAGATAAAGTATC 58.958 43.478 5.73 0.00 35.41 2.24
4393 9321 3.796717 CACGCGCAGAAGATAAAGTATCA 59.203 43.478 5.73 0.00 37.65 2.15
4394 9322 4.445718 CACGCGCAGAAGATAAAGTATCAT 59.554 41.667 5.73 0.00 37.65 2.45
4395 9323 5.050490 ACGCGCAGAAGATAAAGTATCATT 58.950 37.500 5.73 0.00 37.65 2.57
4396 9324 6.143919 CACGCGCAGAAGATAAAGTATCATTA 59.856 38.462 5.73 0.00 37.65 1.90
4397 9325 6.144080 ACGCGCAGAAGATAAAGTATCATTAC 59.856 38.462 5.73 0.00 37.65 1.89
4398 9326 6.143919 CGCGCAGAAGATAAAGTATCATTACA 59.856 38.462 8.75 0.00 37.65 2.41
4399 9327 7.306574 CGCGCAGAAGATAAAGTATCATTACAA 60.307 37.037 8.75 0.00 37.65 2.41
4400 9328 8.006590 GCGCAGAAGATAAAGTATCATTACAAG 58.993 37.037 0.30 0.00 37.65 3.16
4401 9329 8.491152 CGCAGAAGATAAAGTATCATTACAAGG 58.509 37.037 0.00 0.00 37.65 3.61
4402 9330 8.286097 GCAGAAGATAAAGTATCATTACAAGGC 58.714 37.037 0.00 0.00 37.65 4.35
4403 9331 8.778358 CAGAAGATAAAGTATCATTACAAGGCC 58.222 37.037 0.00 0.00 37.65 5.19
4404 9332 8.494433 AGAAGATAAAGTATCATTACAAGGCCA 58.506 33.333 5.01 0.00 37.65 5.36
4405 9333 8.682936 AAGATAAAGTATCATTACAAGGCCAG 57.317 34.615 5.01 0.00 37.65 4.85
4406 9334 6.712547 AGATAAAGTATCATTACAAGGCCAGC 59.287 38.462 5.01 0.00 37.65 4.85
4407 9335 2.838736 AGTATCATTACAAGGCCAGCG 58.161 47.619 5.01 0.00 0.00 5.18
4408 9336 1.873591 GTATCATTACAAGGCCAGCGG 59.126 52.381 5.01 0.00 0.00 5.52
4418 9346 3.211963 GCCAGCGGCCTTACATGG 61.212 66.667 0.00 2.55 44.06 3.66
4426 9354 3.501396 CCTTACATGGCACGCAGG 58.499 61.111 0.00 0.00 0.00 4.85
4427 9355 2.764314 CCTTACATGGCACGCAGGC 61.764 63.158 0.00 0.00 44.50 4.85
4436 9364 2.359850 CACGCAGGCCAGCCTAAA 60.360 61.111 15.33 0.00 46.28 1.85
4437 9365 2.359975 ACGCAGGCCAGCCTAAAC 60.360 61.111 15.33 3.21 46.28 2.01
4438 9366 3.134127 CGCAGGCCAGCCTAAACC 61.134 66.667 15.33 0.00 46.28 3.27
4439 9367 2.035626 GCAGGCCAGCCTAAACCA 59.964 61.111 11.67 0.00 46.28 3.67
4440 9368 2.048603 GCAGGCCAGCCTAAACCAG 61.049 63.158 11.67 0.00 46.28 4.00
4441 9369 1.685224 CAGGCCAGCCTAAACCAGA 59.315 57.895 11.67 0.00 46.28 3.86
4442 9370 0.678048 CAGGCCAGCCTAAACCAGAC 60.678 60.000 11.67 0.00 46.28 3.51
4443 9371 1.133809 AGGCCAGCCTAAACCAGACA 61.134 55.000 10.11 0.00 46.14 3.41
4444 9372 0.960861 GGCCAGCCTAAACCAGACAC 60.961 60.000 0.00 0.00 0.00 3.67
4445 9373 0.960861 GCCAGCCTAAACCAGACACC 60.961 60.000 0.00 0.00 0.00 4.16
4446 9374 0.400213 CCAGCCTAAACCAGACACCA 59.600 55.000 0.00 0.00 0.00 4.17
4447 9375 1.202879 CCAGCCTAAACCAGACACCAA 60.203 52.381 0.00 0.00 0.00 3.67
4448 9376 2.582052 CAGCCTAAACCAGACACCAAA 58.418 47.619 0.00 0.00 0.00 3.28
4449 9377 2.955660 CAGCCTAAACCAGACACCAAAA 59.044 45.455 0.00 0.00 0.00 2.44
4450 9378 3.004734 CAGCCTAAACCAGACACCAAAAG 59.995 47.826 0.00 0.00 0.00 2.27
4451 9379 3.117663 AGCCTAAACCAGACACCAAAAGA 60.118 43.478 0.00 0.00 0.00 2.52
4452 9380 3.253432 GCCTAAACCAGACACCAAAAGAG 59.747 47.826 0.00 0.00 0.00 2.85
4453 9381 3.253432 CCTAAACCAGACACCAAAAGAGC 59.747 47.826 0.00 0.00 0.00 4.09
4454 9382 2.435372 AACCAGACACCAAAAGAGCA 57.565 45.000 0.00 0.00 0.00 4.26
4455 9383 2.664402 ACCAGACACCAAAAGAGCAT 57.336 45.000 0.00 0.00 0.00 3.79
4456 9384 2.949447 ACCAGACACCAAAAGAGCATT 58.051 42.857 0.00 0.00 0.00 3.56
4457 9385 2.887152 ACCAGACACCAAAAGAGCATTC 59.113 45.455 0.00 0.00 0.00 2.67
4458 9386 2.886523 CCAGACACCAAAAGAGCATTCA 59.113 45.455 0.00 0.00 0.00 2.57
4459 9387 3.057736 CCAGACACCAAAAGAGCATTCAG 60.058 47.826 0.00 0.00 0.00 3.02
4460 9388 3.057736 CAGACACCAAAAGAGCATTCAGG 60.058 47.826 0.00 0.00 0.00 3.86
4461 9389 3.149196 GACACCAAAAGAGCATTCAGGA 58.851 45.455 0.00 0.00 0.00 3.86
4462 9390 3.565307 ACACCAAAAGAGCATTCAGGAA 58.435 40.909 0.00 0.00 0.00 3.36
4463 9391 3.571401 ACACCAAAAGAGCATTCAGGAAG 59.429 43.478 0.00 0.00 0.00 3.46
4464 9392 2.560105 ACCAAAAGAGCATTCAGGAAGC 59.440 45.455 0.00 0.00 0.00 3.86
4465 9393 2.094338 CCAAAAGAGCATTCAGGAAGCC 60.094 50.000 0.00 0.00 0.00 4.35
4466 9394 1.457346 AAAGAGCATTCAGGAAGCCG 58.543 50.000 0.00 0.00 0.00 5.52
4467 9395 0.326264 AAGAGCATTCAGGAAGCCGT 59.674 50.000 0.00 0.00 0.00 5.68
4468 9396 0.107945 AGAGCATTCAGGAAGCCGTC 60.108 55.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.028993 TGTGATCAGGTTTTCCCTTACC 57.971 45.455 0.00 0.00 42.73 2.85
22 24 7.067496 TCTTGAACCTTAGAGTCTGAATTGT 57.933 36.000 1.86 0.00 0.00 2.71
111 139 2.259204 CAAGTGGCCCAACGCATG 59.741 61.111 0.00 0.00 40.31 4.06
148 176 2.481441 AGAATGCAGGGTCATACTCCA 58.519 47.619 0.00 0.00 0.00 3.86
233 1535 3.005554 CGGACCGAACTCTTCTACAGTA 58.994 50.000 8.64 0.00 0.00 2.74
236 1538 0.524862 GCGGACCGAACTCTTCTACA 59.475 55.000 20.50 0.00 0.00 2.74
354 1656 2.838202 ACTGGTACCGATGGAATTCAGT 59.162 45.455 7.57 0.00 0.00 3.41
355 1657 3.198068 CACTGGTACCGATGGAATTCAG 58.802 50.000 7.57 0.00 0.00 3.02
419 1723 0.546507 TGTGTGATGCAGGAGGGGTA 60.547 55.000 0.00 0.00 0.00 3.69
508 1821 2.167900 AGGTAGCGGGTCAGTTTCATAC 59.832 50.000 0.00 0.00 0.00 2.39
520 1833 3.243068 GCAAATGAATGTTAGGTAGCGGG 60.243 47.826 0.00 0.00 0.00 6.13
524 1837 4.342772 GTGCGCAAATGAATGTTAGGTAG 58.657 43.478 14.00 0.00 0.00 3.18
543 2093 1.930908 GATCAAGCCAGTGCAGGTGC 61.931 60.000 0.00 0.00 41.13 5.01
559 2109 2.095364 CAGAAACAACAGGCAGCTGATC 60.095 50.000 20.43 8.76 0.00 2.92
690 2301 2.530151 AGTGGAGCAGCTTGGGGA 60.530 61.111 0.00 0.00 0.00 4.81
693 2304 1.602888 AAGCAGTGGAGCAGCTTGG 60.603 57.895 0.00 0.00 46.14 3.61
715 2336 3.507009 CCCTCCTCGACGACCGAC 61.507 72.222 0.00 0.00 43.23 4.79
730 2351 2.137528 GGCAGTCTAGCTCCTCCCC 61.138 68.421 0.00 0.00 34.17 4.81
778 2400 9.499585 TCTTCTTTTATTATTGACGACTACGAG 57.500 33.333 0.00 0.00 42.66 4.18
779 2401 9.844790 TTCTTCTTTTATTATTGACGACTACGA 57.155 29.630 0.00 0.00 42.66 3.43
786 2408 9.676899 CTCGTCTTTCTTCTTTTATTATTGACG 57.323 33.333 0.00 0.00 42.12 4.35
813 2440 5.023452 ACCCACTCTTGTTTTCTTTTTCCT 58.977 37.500 0.00 0.00 0.00 3.36
845 2484 4.748798 CTGGGACTGGGAGGGGCT 62.749 72.222 0.00 0.00 0.00 5.19
923 2562 5.298276 AGAGAGATAAGTAAGGAAGAGCGTG 59.702 44.000 0.00 0.00 0.00 5.34
926 2565 6.096282 ACACAGAGAGATAAGTAAGGAAGAGC 59.904 42.308 0.00 0.00 0.00 4.09
927 2566 7.639113 ACACAGAGAGATAAGTAAGGAAGAG 57.361 40.000 0.00 0.00 0.00 2.85
963 2606 3.322541 TCTCTCCCACAACAATGTCGTTA 59.677 43.478 0.00 0.00 37.82 3.18
990 3068 1.964891 CCCGCTCATGCCAGCTATG 60.965 63.158 5.02 0.00 37.25 2.23
992 3070 2.593468 GAACCCGCTCATGCCAGCTA 62.593 60.000 5.02 0.00 37.25 3.32
1055 3133 3.611674 TGGCGAGTTCACCGAGCA 61.612 61.111 0.00 0.00 0.00 4.26
1328 3408 5.799213 CTTGTAGACCAGATCTTTTGACCT 58.201 41.667 0.00 0.00 39.04 3.85
1330 3410 4.997395 TGCTTGTAGACCAGATCTTTTGAC 59.003 41.667 0.00 0.00 39.04 3.18
1332 3412 5.471456 ACTTGCTTGTAGACCAGATCTTTTG 59.529 40.000 0.00 0.00 39.04 2.44
1333 3413 5.471456 CACTTGCTTGTAGACCAGATCTTTT 59.529 40.000 0.00 0.00 39.04 2.27
1336 3416 3.834813 TCACTTGCTTGTAGACCAGATCT 59.165 43.478 0.00 0.00 41.95 2.75
1338 3418 4.833478 ATCACTTGCTTGTAGACCAGAT 57.167 40.909 0.00 0.00 0.00 2.90
1340 3420 5.695851 AAAATCACTTGCTTGTAGACCAG 57.304 39.130 0.00 0.00 0.00 4.00
1348 3428 6.607735 AAATCCACAAAAATCACTTGCTTG 57.392 33.333 0.00 0.00 0.00 4.01
1349 3429 7.628769 AAAAATCCACAAAAATCACTTGCTT 57.371 28.000 0.00 0.00 0.00 3.91
1375 3472 0.173708 GATGCGAGACTCGGGAAAGT 59.826 55.000 25.31 0.00 40.84 2.66
1376 3473 0.457851 AGATGCGAGACTCGGGAAAG 59.542 55.000 25.31 0.00 40.84 2.62
1377 3474 0.895530 AAGATGCGAGACTCGGGAAA 59.104 50.000 25.31 0.00 40.84 3.13
1383 3480 9.944663 CTAATAATCCTATAAGATGCGAGACTC 57.055 37.037 0.00 0.00 0.00 3.36
1386 3483 8.687242 CCACTAATAATCCTATAAGATGCGAGA 58.313 37.037 0.00 0.00 0.00 4.04
1387 3484 8.687242 TCCACTAATAATCCTATAAGATGCGAG 58.313 37.037 0.00 0.00 0.00 5.03
1388 3485 8.589701 TCCACTAATAATCCTATAAGATGCGA 57.410 34.615 0.00 0.00 0.00 5.10
1397 3494 8.384693 TGAGCATCATCCACTAATAATCCTAT 57.615 34.615 0.00 0.00 42.56 2.57
1478 4021 7.970614 GCAATTCACTCGGAGAAATAAGAAAAT 59.029 33.333 12.86 0.00 34.09 1.82
1527 4071 5.496133 CCAGATGGTTTTCTGCAAGATAG 57.504 43.478 0.00 0.00 46.36 2.08
1545 4089 2.984562 TGCAAATGATTAGCGACCAGA 58.015 42.857 0.00 0.00 0.00 3.86
1669 4214 7.675062 AGGTATATGTCAATTTGTTGCCAAAA 58.325 30.769 0.00 0.00 43.43 2.44
2012 4561 2.596338 TCTGCGTCGTCCTCACCA 60.596 61.111 0.00 0.00 0.00 4.17
2058 4607 1.752694 GAGAGAGCAGAGGACCGCT 60.753 63.158 0.00 0.00 42.42 5.52
2073 4622 1.153765 CCGCTGCTTCATGTCGAGA 60.154 57.895 0.00 0.00 0.00 4.04
2204 4753 4.430765 CGCCGCCACCTAGTTCGT 62.431 66.667 0.00 0.00 0.00 3.85
2331 4880 3.414193 CCATGGCCTCCTGCTCCA 61.414 66.667 3.32 0.00 40.92 3.86
2500 6847 7.446013 CACACACAGACCCCTAGTAAATTTTAA 59.554 37.037 0.00 0.00 0.00 1.52
2507 6855 3.247948 TCACACACAGACCCCTAGTAA 57.752 47.619 0.00 0.00 0.00 2.24
2541 6889 0.035739 GAGGGCGTTTCCAACAGGTA 59.964 55.000 0.00 0.00 36.21 3.08
2548 6896 2.281208 CGGTTGAGGGCGTTTCCA 60.281 61.111 0.00 0.00 36.21 3.53
2598 6946 2.222953 CCACCGCGTATTCAGTAAAAGC 60.223 50.000 4.92 0.00 0.00 3.51
2696 7044 7.063308 GCAAAATTTCGAGCAAATGGAGAAATA 59.937 33.333 0.00 0.00 39.65 1.40
2700 7048 4.236935 GCAAAATTTCGAGCAAATGGAGA 58.763 39.130 0.00 0.00 34.69 3.71
2701 7049 3.989167 TGCAAAATTTCGAGCAAATGGAG 59.011 39.130 9.60 0.00 34.69 3.86
2702 7050 3.987547 TGCAAAATTTCGAGCAAATGGA 58.012 36.364 9.60 0.00 34.69 3.41
2703 7051 4.932268 ATGCAAAATTTCGAGCAAATGG 57.068 36.364 14.31 0.00 40.76 3.16
2704 7052 6.595794 AGAAATGCAAAATTTCGAGCAAATG 58.404 32.000 14.31 0.00 41.49 2.32
2705 7053 6.424509 TGAGAAATGCAAAATTTCGAGCAAAT 59.575 30.769 14.31 8.21 41.49 2.32
2706 7054 5.752472 TGAGAAATGCAAAATTTCGAGCAAA 59.248 32.000 14.31 0.00 41.49 3.68
2707 7055 5.288015 TGAGAAATGCAAAATTTCGAGCAA 58.712 33.333 14.31 2.54 41.49 3.91
2708 7056 4.869215 TGAGAAATGCAAAATTTCGAGCA 58.131 34.783 13.15 13.15 41.49 4.26
2709 7057 5.005107 GGATGAGAAATGCAAAATTTCGAGC 59.995 40.000 5.79 0.00 41.49 5.03
2710 7058 6.034256 GTGGATGAGAAATGCAAAATTTCGAG 59.966 38.462 5.79 0.00 41.49 4.04
2711 7059 5.863397 GTGGATGAGAAATGCAAAATTTCGA 59.137 36.000 5.79 0.00 41.49 3.71
2712 7060 5.062558 GGTGGATGAGAAATGCAAAATTTCG 59.937 40.000 5.79 0.00 41.49 3.46
2763 7112 9.998106 AACTTAATAGTCACTCTGAAGCTTTAA 57.002 29.630 0.00 0.00 31.99 1.52
2805 7158 5.221244 ACGAAGCATTAAGGCAAAAGAACTT 60.221 36.000 15.35 0.00 35.83 2.66
2820 7173 3.914426 AGTGAATCCCTACGAAGCATT 57.086 42.857 0.00 0.00 0.00 3.56
2834 7187 8.034804 GGCATAAACAATTCCAGTTTAGTGAAT 58.965 33.333 0.00 0.00 42.63 2.57
2846 7649 4.402155 TCACCTCATGGCATAAACAATTCC 59.598 41.667 0.00 0.00 36.63 3.01
2886 7709 7.730364 ACACTTGACGAAGATTTAATGTCTT 57.270 32.000 0.00 3.94 38.57 3.01
2895 7718 3.485463 TCCCAACACTTGACGAAGATT 57.515 42.857 0.00 0.00 32.98 2.40
2902 7725 7.681939 TTGATAACTTATCCCAACACTTGAC 57.318 36.000 6.37 0.00 34.26 3.18
2948 7771 8.525290 ACAAATAGGGATTGGTTATTTCTGAG 57.475 34.615 0.00 0.00 32.02 3.35
2959 7782 6.659242 GGATGGTGTATACAAATAGGGATTGG 59.341 42.308 7.25 0.00 32.02 3.16
3014 7891 7.657761 TCTCTGTGAAGTTAAAGATGGAAGTTC 59.342 37.037 0.00 0.00 36.13 3.01
3027 7904 8.102676 TCCATTGAATTCATCTCTGTGAAGTTA 58.897 33.333 9.40 0.00 41.05 2.24
3029 7906 6.479006 TCCATTGAATTCATCTCTGTGAAGT 58.521 36.000 9.40 0.00 41.05 3.01
3030 7907 6.997239 TCCATTGAATTCATCTCTGTGAAG 57.003 37.500 9.40 0.00 41.05 3.02
3031 7908 6.944290 AGTTCCATTGAATTCATCTCTGTGAA 59.056 34.615 9.40 7.84 41.88 3.18
3032 7909 6.479006 AGTTCCATTGAATTCATCTCTGTGA 58.521 36.000 9.40 0.00 31.98 3.58
3033 7910 6.754702 AGTTCCATTGAATTCATCTCTGTG 57.245 37.500 9.40 2.39 31.98 3.66
3034 7911 7.173722 AGAAGTTCCATTGAATTCATCTCTGT 58.826 34.615 9.40 0.00 31.98 3.41
3035 7912 7.627298 AGAAGTTCCATTGAATTCATCTCTG 57.373 36.000 9.40 5.10 31.98 3.35
3036 7913 8.647256 AAAGAAGTTCCATTGAATTCATCTCT 57.353 30.769 9.40 0.33 31.98 3.10
3038 7915 9.525826 ACTAAAGAAGTTCCATTGAATTCATCT 57.474 29.630 9.40 3.57 33.35 2.90
3040 7917 9.918630 CAACTAAAGAAGTTCCATTGAATTCAT 57.081 29.630 9.40 0.00 45.64 2.57
3041 7918 9.130661 TCAACTAAAGAAGTTCCATTGAATTCA 57.869 29.630 3.38 3.38 45.64 2.57
3045 7922 8.746052 TTCTCAACTAAAGAAGTTCCATTGAA 57.254 30.769 0.00 0.00 45.64 2.69
3092 7969 9.593565 AGACACATCTCTTTATGACTCCATATA 57.406 33.333 0.00 0.00 35.38 0.86
3188 8095 1.148273 TGAGGCATGGTAATCCGCC 59.852 57.895 0.00 0.00 39.49 6.13
3241 8148 1.915983 CCTGGCCCTCCTTTCCTAC 59.084 63.158 0.00 0.00 0.00 3.18
3385 8298 3.055167 TCATAGTTTAGCAGCAGCCTGAA 60.055 43.478 0.00 0.00 41.77 3.02
3423 8336 7.170151 CCGACAATCGAGACGATAGATATATCT 59.830 40.741 18.99 18.99 46.30 1.98
3439 8352 1.375396 CACCAAGCCCGACAATCGA 60.375 57.895 0.00 0.00 43.74 3.59
3459 8372 2.505819 AGCCAATGTTGACTACCCTAGG 59.494 50.000 0.06 0.06 0.00 3.02
3466 8379 4.910195 ACTGATTCAGCCAATGTTGACTA 58.090 39.130 13.64 0.00 34.37 2.59
3495 8411 4.806640 ATTGTTGGCCATTTTGTCTAGG 57.193 40.909 6.09 0.00 0.00 3.02
3496 8412 6.705381 TCAAAATTGTTGGCCATTTTGTCTAG 59.295 34.615 28.63 13.09 41.84 2.43
3497 8413 6.586344 TCAAAATTGTTGGCCATTTTGTCTA 58.414 32.000 28.63 15.61 41.84 2.59
3516 8432 0.250727 CCCAGGCTCGGACTTCAAAA 60.251 55.000 0.00 0.00 0.00 2.44
3519 8435 2.203788 ACCCAGGCTCGGACTTCA 60.204 61.111 4.75 0.00 0.00 3.02
3639 8555 6.982724 CAGCAAGTTCCTTTTTGAGATTTTCT 59.017 34.615 0.00 0.00 0.00 2.52
3783 8699 8.117813 TCATTTTATTCACTACCCTTTGGTTC 57.882 34.615 0.00 0.00 44.75 3.62
3792 8708 5.878669 ACCGGTTCTCATTTTATTCACTACC 59.121 40.000 0.00 0.00 0.00 3.18
3825 8744 4.055360 CGGGACAAATTTTCCTTTGGTTC 58.945 43.478 14.86 0.00 39.83 3.62
3879 8798 6.065976 TCCCAACAGTCATCAGTTGATAAT 57.934 37.500 6.85 0.00 46.01 1.28
4083 9002 2.564947 GTCCTTGTGATCTCTGTGACCT 59.435 50.000 0.00 0.00 0.00 3.85
4300 9228 1.607628 TCTATAAAGTCGGGCTCTCGC 59.392 52.381 0.00 0.00 0.00 5.03
4301 9229 5.624344 TTATCTATAAAGTCGGGCTCTCG 57.376 43.478 0.00 0.00 0.00 4.04
4302 9230 5.865013 GCTTTATCTATAAAGTCGGGCTCTC 59.135 44.000 18.85 1.69 46.78 3.20
4303 9231 5.279556 GGCTTTATCTATAAAGTCGGGCTCT 60.280 44.000 18.85 0.00 46.78 4.09
4304 9232 4.930405 GGCTTTATCTATAAAGTCGGGCTC 59.070 45.833 18.85 5.41 46.78 4.70
4305 9233 4.895961 GGCTTTATCTATAAAGTCGGGCT 58.104 43.478 18.85 0.00 46.78 5.19
4326 9254 2.037772 GGTCATATACTCTGCCTGGTGG 59.962 54.545 0.00 0.00 0.00 4.61
4327 9255 2.700371 TGGTCATATACTCTGCCTGGTG 59.300 50.000 0.00 0.00 0.00 4.17
4328 9256 3.046283 TGGTCATATACTCTGCCTGGT 57.954 47.619 0.00 0.00 0.00 4.00
4329 9257 3.134623 TGTTGGTCATATACTCTGCCTGG 59.865 47.826 0.00 0.00 0.00 4.45
4330 9258 4.406648 TGTTGGTCATATACTCTGCCTG 57.593 45.455 0.00 0.00 0.00 4.85
4331 9259 4.225042 TGTTGTTGGTCATATACTCTGCCT 59.775 41.667 0.00 0.00 0.00 4.75
4332 9260 4.513442 TGTTGTTGGTCATATACTCTGCC 58.487 43.478 0.00 0.00 0.00 4.85
4333 9261 4.034510 GCTGTTGTTGGTCATATACTCTGC 59.965 45.833 0.00 0.00 0.00 4.26
4334 9262 5.063944 GTGCTGTTGTTGGTCATATACTCTG 59.936 44.000 0.00 0.00 0.00 3.35
4335 9263 5.178797 GTGCTGTTGTTGGTCATATACTCT 58.821 41.667 0.00 0.00 0.00 3.24
4336 9264 4.332819 GGTGCTGTTGTTGGTCATATACTC 59.667 45.833 0.00 0.00 0.00 2.59
4337 9265 4.261801 GGTGCTGTTGTTGGTCATATACT 58.738 43.478 0.00 0.00 0.00 2.12
4338 9266 3.377172 GGGTGCTGTTGTTGGTCATATAC 59.623 47.826 0.00 0.00 0.00 1.47
4339 9267 3.009584 TGGGTGCTGTTGTTGGTCATATA 59.990 43.478 0.00 0.00 0.00 0.86
4340 9268 2.224992 TGGGTGCTGTTGTTGGTCATAT 60.225 45.455 0.00 0.00 0.00 1.78
4341 9269 1.143889 TGGGTGCTGTTGTTGGTCATA 59.856 47.619 0.00 0.00 0.00 2.15
4342 9270 0.106268 TGGGTGCTGTTGTTGGTCAT 60.106 50.000 0.00 0.00 0.00 3.06
4343 9271 0.323816 TTGGGTGCTGTTGTTGGTCA 60.324 50.000 0.00 0.00 0.00 4.02
4344 9272 0.102300 GTTGGGTGCTGTTGTTGGTC 59.898 55.000 0.00 0.00 0.00 4.02
4345 9273 0.613292 TGTTGGGTGCTGTTGTTGGT 60.613 50.000 0.00 0.00 0.00 3.67
4346 9274 0.534412 TTGTTGGGTGCTGTTGTTGG 59.466 50.000 0.00 0.00 0.00 3.77
4347 9275 2.270047 CTTTGTTGGGTGCTGTTGTTG 58.730 47.619 0.00 0.00 0.00 3.33
4348 9276 1.899142 ACTTTGTTGGGTGCTGTTGTT 59.101 42.857 0.00 0.00 0.00 2.83
4349 9277 1.555967 ACTTTGTTGGGTGCTGTTGT 58.444 45.000 0.00 0.00 0.00 3.32
4350 9278 3.317711 TGATACTTTGTTGGGTGCTGTTG 59.682 43.478 0.00 0.00 0.00 3.33
4351 9279 3.317993 GTGATACTTTGTTGGGTGCTGTT 59.682 43.478 0.00 0.00 0.00 3.16
4352 9280 2.884639 GTGATACTTTGTTGGGTGCTGT 59.115 45.455 0.00 0.00 0.00 4.40
4353 9281 2.095768 CGTGATACTTTGTTGGGTGCTG 60.096 50.000 0.00 0.00 0.00 4.41
4354 9282 2.151202 CGTGATACTTTGTTGGGTGCT 58.849 47.619 0.00 0.00 0.00 4.40
4355 9283 1.401018 GCGTGATACTTTGTTGGGTGC 60.401 52.381 0.00 0.00 0.00 5.01
4356 9284 1.136085 CGCGTGATACTTTGTTGGGTG 60.136 52.381 0.00 0.00 0.00 4.61
4357 9285 1.153353 CGCGTGATACTTTGTTGGGT 58.847 50.000 0.00 0.00 0.00 4.51
4358 9286 0.179200 GCGCGTGATACTTTGTTGGG 60.179 55.000 8.43 0.00 0.00 4.12
4359 9287 0.515127 TGCGCGTGATACTTTGTTGG 59.485 50.000 8.43 0.00 0.00 3.77
4360 9288 1.459209 TCTGCGCGTGATACTTTGTTG 59.541 47.619 8.43 0.00 0.00 3.33
4361 9289 1.790755 TCTGCGCGTGATACTTTGTT 58.209 45.000 8.43 0.00 0.00 2.83
4362 9290 1.726791 CTTCTGCGCGTGATACTTTGT 59.273 47.619 8.43 0.00 0.00 2.83
4363 9291 1.992667 TCTTCTGCGCGTGATACTTTG 59.007 47.619 8.43 0.00 0.00 2.77
4364 9292 2.363788 TCTTCTGCGCGTGATACTTT 57.636 45.000 8.43 0.00 0.00 2.66
4365 9293 2.586258 ATCTTCTGCGCGTGATACTT 57.414 45.000 8.43 0.00 0.00 2.24
4366 9294 3.710326 TTATCTTCTGCGCGTGATACT 57.290 42.857 8.43 0.00 0.00 2.12
4367 9295 3.797256 ACTTTATCTTCTGCGCGTGATAC 59.203 43.478 8.43 0.00 0.00 2.24
4368 9296 4.041740 ACTTTATCTTCTGCGCGTGATA 57.958 40.909 8.43 5.20 0.00 2.15
4369 9297 2.893637 ACTTTATCTTCTGCGCGTGAT 58.106 42.857 8.43 6.21 0.00 3.06
4370 9298 2.363788 ACTTTATCTTCTGCGCGTGA 57.636 45.000 8.43 3.59 0.00 4.35
4371 9299 3.796717 TGATACTTTATCTTCTGCGCGTG 59.203 43.478 8.43 0.68 36.17 5.34
4372 9300 4.041740 TGATACTTTATCTTCTGCGCGT 57.958 40.909 8.43 0.00 36.17 6.01
4373 9301 5.582439 AATGATACTTTATCTTCTGCGCG 57.418 39.130 0.00 0.00 36.17 6.86
4374 9302 7.408132 TGTAATGATACTTTATCTTCTGCGC 57.592 36.000 0.00 0.00 36.17 6.09
4375 9303 8.491152 CCTTGTAATGATACTTTATCTTCTGCG 58.509 37.037 0.00 0.00 36.17 5.18
4376 9304 8.286097 GCCTTGTAATGATACTTTATCTTCTGC 58.714 37.037 0.00 0.00 36.17 4.26
4377 9305 8.778358 GGCCTTGTAATGATACTTTATCTTCTG 58.222 37.037 0.00 0.00 36.17 3.02
4378 9306 8.494433 TGGCCTTGTAATGATACTTTATCTTCT 58.506 33.333 3.32 0.00 36.17 2.85
4379 9307 8.677148 TGGCCTTGTAATGATACTTTATCTTC 57.323 34.615 3.32 0.00 36.17 2.87
4380 9308 7.229506 GCTGGCCTTGTAATGATACTTTATCTT 59.770 37.037 3.32 0.00 36.17 2.40
4381 9309 6.712547 GCTGGCCTTGTAATGATACTTTATCT 59.287 38.462 3.32 0.00 36.17 1.98
4382 9310 6.347725 CGCTGGCCTTGTAATGATACTTTATC 60.348 42.308 3.32 0.00 35.74 1.75
4383 9311 5.470098 CGCTGGCCTTGTAATGATACTTTAT 59.530 40.000 3.32 0.00 32.98 1.40
4384 9312 4.814234 CGCTGGCCTTGTAATGATACTTTA 59.186 41.667 3.32 0.00 32.98 1.85
4385 9313 3.627577 CGCTGGCCTTGTAATGATACTTT 59.372 43.478 3.32 0.00 32.98 2.66
4386 9314 3.206150 CGCTGGCCTTGTAATGATACTT 58.794 45.455 3.32 0.00 32.98 2.24
4387 9315 2.485479 CCGCTGGCCTTGTAATGATACT 60.485 50.000 3.32 0.00 32.98 2.12
4388 9316 1.873591 CCGCTGGCCTTGTAATGATAC 59.126 52.381 3.32 0.00 0.00 2.24
4389 9317 1.813862 GCCGCTGGCCTTGTAATGATA 60.814 52.381 3.32 0.00 44.06 2.15
4390 9318 1.103398 GCCGCTGGCCTTGTAATGAT 61.103 55.000 3.32 0.00 44.06 2.45
4391 9319 1.748879 GCCGCTGGCCTTGTAATGA 60.749 57.895 3.32 0.00 44.06 2.57
4392 9320 2.800736 GCCGCTGGCCTTGTAATG 59.199 61.111 3.32 0.00 44.06 1.90
4409 9337 2.764314 GCCTGCGTGCCATGTAAGG 61.764 63.158 4.04 4.04 0.00 2.69
4410 9338 2.793946 GCCTGCGTGCCATGTAAG 59.206 61.111 0.00 0.00 0.00 2.34
4425 9353 0.960861 GTGTCTGGTTTAGGCTGGCC 60.961 60.000 3.00 3.00 0.00 5.36
4426 9354 0.960861 GGTGTCTGGTTTAGGCTGGC 60.961 60.000 0.00 0.00 0.00 4.85
4427 9355 0.400213 TGGTGTCTGGTTTAGGCTGG 59.600 55.000 0.00 0.00 0.00 4.85
4428 9356 2.270352 TTGGTGTCTGGTTTAGGCTG 57.730 50.000 0.00 0.00 0.00 4.85
4429 9357 3.117663 TCTTTTGGTGTCTGGTTTAGGCT 60.118 43.478 0.00 0.00 0.00 4.58
4430 9358 3.219281 TCTTTTGGTGTCTGGTTTAGGC 58.781 45.455 0.00 0.00 0.00 3.93
4431 9359 3.253432 GCTCTTTTGGTGTCTGGTTTAGG 59.747 47.826 0.00 0.00 0.00 2.69
4432 9360 3.882888 TGCTCTTTTGGTGTCTGGTTTAG 59.117 43.478 0.00 0.00 0.00 1.85
4433 9361 3.892284 TGCTCTTTTGGTGTCTGGTTTA 58.108 40.909 0.00 0.00 0.00 2.01
4434 9362 2.733956 TGCTCTTTTGGTGTCTGGTTT 58.266 42.857 0.00 0.00 0.00 3.27
4435 9363 2.435372 TGCTCTTTTGGTGTCTGGTT 57.565 45.000 0.00 0.00 0.00 3.67
4436 9364 2.664402 ATGCTCTTTTGGTGTCTGGT 57.336 45.000 0.00 0.00 0.00 4.00
4437 9365 2.886523 TGAATGCTCTTTTGGTGTCTGG 59.113 45.455 0.00 0.00 0.00 3.86
4438 9366 3.057736 CCTGAATGCTCTTTTGGTGTCTG 60.058 47.826 0.00 0.00 0.00 3.51
4439 9367 3.152341 CCTGAATGCTCTTTTGGTGTCT 58.848 45.455 0.00 0.00 0.00 3.41
4440 9368 3.149196 TCCTGAATGCTCTTTTGGTGTC 58.851 45.455 0.00 0.00 0.00 3.67
4441 9369 3.228188 TCCTGAATGCTCTTTTGGTGT 57.772 42.857 0.00 0.00 0.00 4.16
4442 9370 3.613432 GCTTCCTGAATGCTCTTTTGGTG 60.613 47.826 0.00 0.00 0.00 4.17
4443 9371 2.560105 GCTTCCTGAATGCTCTTTTGGT 59.440 45.455 0.00 0.00 0.00 3.67
4444 9372 2.094338 GGCTTCCTGAATGCTCTTTTGG 60.094 50.000 0.00 0.00 0.00 3.28
4445 9373 2.415090 CGGCTTCCTGAATGCTCTTTTG 60.415 50.000 0.00 0.00 0.00 2.44
4446 9374 1.815003 CGGCTTCCTGAATGCTCTTTT 59.185 47.619 0.00 0.00 0.00 2.27
4447 9375 1.271597 ACGGCTTCCTGAATGCTCTTT 60.272 47.619 0.00 0.00 0.00 2.52
4448 9376 0.326264 ACGGCTTCCTGAATGCTCTT 59.674 50.000 0.00 0.00 0.00 2.85
4449 9377 0.107945 GACGGCTTCCTGAATGCTCT 60.108 55.000 0.00 0.00 0.00 4.09
4450 9378 2.388347 GACGGCTTCCTGAATGCTC 58.612 57.895 0.00 0.00 0.00 4.26
4451 9379 4.625800 GACGGCTTCCTGAATGCT 57.374 55.556 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.