Multiple sequence alignment - TraesCS1B01G209700

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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 TraesCS1B01G209700 chr1B 100.000 4490 0 0 1 4490 380471361 380466872 0.000000e+00 8292.0
1 TraesCS1B01G209700 chr1D 90.054 2785 113 56 3 2664 279950892 279948149 0.000000e+00 3458.0
2 TraesCS1B01G209700 chr1D 94.715 1192 42 8 2684 3859 279948159 279946973 0.000000e+00 1832.0
3 TraesCS1B01G209700 chr1D 95.501 489 11 3 4003 4490 279946906 279946428 0.000000e+00 771.0
4 TraesCS1B01G209700 chr1A 91.382 1230 47 28 185 1370 351886883 351885669 0.000000e+00 1629.0
5 TraesCS1B01G209700 chr1A 90.844 972 53 20 2916 3861 351883886 351882925 0.000000e+00 1269.0
6 TraesCS1B01G209700 chr1A 87.918 538 28 14 3968 4490 351882929 351882414 2.310000e-167 599.0
7 TraesCS1B01G209700 chr1A 91.789 341 11 5 1483 1806 351885363 351885023 4.090000e-125 459.0
8 TraesCS1B01G209700 chr1A 85.981 428 35 15 2235 2638 351884581 351884155 6.900000e-118 435.0
9 TraesCS1B01G209700 chr1A 96.761 247 3 2 1854 2096 351884933 351884688 1.500000e-109 407.0
10 TraesCS1B01G209700 chr1A 97.525 202 5 0 2684 2885 351884148 351883947 3.320000e-91 346.0
11 TraesCS1B01G209700 chr1A 90.000 190 19 0 3 192 351887381 351887192 3.470000e-61 246.0
12 TraesCS1B01G209700 chr1A 86.000 100 14 0 3874 3973 307696687 307696786 1.710000e-19 108.0
13 TraesCS1B01G209700 chr5D 85.484 124 17 1 3854 3976 229363500 229363377 1.310000e-25 128.0
14 TraesCS1B01G209700 chr5D 87.037 54 6 1 3866 3919 394008203 394008151 4.850000e-05 60.2
15 TraesCS1B01G209700 chr5D 97.059 34 1 0 3886 3919 433340871 433340838 1.740000e-04 58.4
16 TraesCS1B01G209700 chr7D 85.593 118 16 1 3850 3967 139053161 139053045 6.100000e-24 122.0
17 TraesCS1B01G209700 chr7D 92.308 65 4 1 3908 3971 437643725 437643789 1.720000e-14 91.6
18 TraesCS1B01G209700 chr7D 91.837 49 4 0 3875 3923 437643671 437643719 8.060000e-08 69.4
19 TraesCS1B01G209700 chr5A 93.443 61 4 0 3908 3968 491947110 491947050 1.720000e-14 91.6
20 TraesCS1B01G209700 chr2D 87.097 62 7 1 3858 3919 423208502 423208562 8.060000e-08 69.4
21 TraesCS1B01G209700 chr2B 94.444 36 2 0 3886 3921 667802052 667802087 6.270000e-04 56.5


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 TraesCS1B01G209700 chr1B 380466872 380471361 4489 True 8292.000000 8292 100.000000 1 4490 1 chr1B.!!$R1 4489
1 TraesCS1B01G209700 chr1D 279946428 279950892 4464 True 2020.333333 3458 93.423333 3 4490 3 chr1D.!!$R1 4487
2 TraesCS1B01G209700 chr1A 351882414 351887381 4967 True 673.750000 1629 91.525000 3 4490 8 chr1A.!!$R1 4487

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
837 1172 0.450583 TGCTCGCTACAACTCCTACG 59.549 55.0 0.0 0.0 0.00 3.51 F
1444 1815 0.394352 ACATCGGGTTGCTTGATCCC 60.394 55.0 0.0 0.0 37.98 3.85 F
2193 2870 0.595095 GAGACCCAGCAAAGCACTTG 59.405 55.0 0.0 0.0 38.15 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2187 2864 0.029300 TGCTTTTCGTGCTCAAGTGC 59.971 50.0 0.0 0.0 0.0 4.40 R
2351 3031 0.175073 CACGTAGGCTCTTACCACCC 59.825 60.0 0.0 0.0 0.0 4.61 R
3952 4752 0.036306 CTAAGGCCCTGTTCGGTGTT 59.964 55.0 0.0 0.0 0.0 3.32 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
86 87 3.118992 TGAGATCACCTCGTTTCTCATGG 60.119 47.826 0.00 0.00 44.92 3.66
112 113 3.428797 CATGGCCATCCTTGCGAG 58.571 61.111 17.61 0.00 31.81 5.03
121 122 2.468831 CATCCTTGCGAGAAGTAGAGC 58.531 52.381 1.22 0.00 0.00 4.09
124 125 1.540407 CTTGCGAGAAGTAGAGCGAC 58.460 55.000 0.00 0.00 0.00 5.19
156 157 1.674322 CACCTGTTCGGGCGGAAAT 60.674 57.895 9.21 0.00 36.14 2.17
168 169 2.159379 GGGCGGAAATGAGTTTGATGAC 60.159 50.000 0.00 0.00 0.00 3.06
235 554 4.247380 GAGGCCCTCCTGATGCGG 62.247 72.222 0.00 0.00 44.46 5.69
388 711 1.152383 GCTAAATCTCGCCACCGTCC 61.152 60.000 0.00 0.00 35.54 4.79
461 788 1.442765 CATCGAATTTGCGTGCGTAC 58.557 50.000 0.00 0.00 0.00 3.67
702 1037 3.707189 GGAGGGAAGGGGAGGGGA 61.707 72.222 0.00 0.00 0.00 4.81
821 1156 4.640690 ACTCGGACACCCCCTGCT 62.641 66.667 0.00 0.00 0.00 4.24
836 1171 1.202313 CCTGCTCGCTACAACTCCTAC 60.202 57.143 0.00 0.00 0.00 3.18
837 1172 0.450583 TGCTCGCTACAACTCCTACG 59.549 55.000 0.00 0.00 0.00 3.51
921 1256 7.390718 CCAGTAAAGCAGTAAGTAATTCCACTT 59.609 37.037 0.00 0.00 41.56 3.16
942 1279 3.155167 CCGCCACCTCCCTCTACC 61.155 72.222 0.00 0.00 0.00 3.18
955 1292 2.240162 CTCTACCCCGGCGCTTTCTT 62.240 60.000 7.64 0.00 0.00 2.52
961 1298 3.041940 CGGCGCTTTCTTGGACGT 61.042 61.111 7.64 0.00 0.00 4.34
962 1299 2.861006 GGCGCTTTCTTGGACGTC 59.139 61.111 7.64 7.13 0.00 4.34
963 1300 2.470286 GCGCTTTCTTGGACGTCG 59.530 61.111 9.92 0.00 0.00 5.12
965 1302 2.307309 CGCTTTCTTGGACGTCGCA 61.307 57.895 9.92 6.05 0.00 5.10
967 1304 1.901650 GCTTTCTTGGACGTCGCAGG 61.902 60.000 9.92 9.38 0.00 4.85
968 1305 1.901650 CTTTCTTGGACGTCGCAGGC 61.902 60.000 9.92 0.00 0.00 4.85
991 1337 2.742774 GTACAAGCAAAAGCAACCAGG 58.257 47.619 0.00 0.00 0.00 4.45
992 1338 1.484038 ACAAGCAAAAGCAACCAGGA 58.516 45.000 0.00 0.00 0.00 3.86
993 1339 1.830477 ACAAGCAAAAGCAACCAGGAA 59.170 42.857 0.00 0.00 0.00 3.36
1008 1354 2.036256 GAACCAGCCATGTGCCCT 59.964 61.111 2.95 0.00 42.71 5.19
1405 1775 6.621394 AGAAAGAATCATGGATGGATGGATT 58.379 36.000 0.00 0.00 0.00 3.01
1406 1776 6.720288 AGAAAGAATCATGGATGGATGGATTC 59.280 38.462 0.00 0.00 0.00 2.52
1407 1777 4.586884 AGAATCATGGATGGATGGATTCG 58.413 43.478 0.00 0.00 31.78 3.34
1408 1778 4.287845 AGAATCATGGATGGATGGATTCGA 59.712 41.667 0.00 0.00 31.78 3.71
1409 1779 4.857130 ATCATGGATGGATGGATTCGAT 57.143 40.909 0.00 0.00 0.00 3.59
1410 1780 4.212143 TCATGGATGGATGGATTCGATC 57.788 45.455 0.34 0.34 38.48 3.69
1442 1813 1.398390 GTCACATCGGGTTGCTTGATC 59.602 52.381 0.00 0.00 0.00 2.92
1443 1814 0.734889 CACATCGGGTTGCTTGATCC 59.265 55.000 0.00 0.00 0.00 3.36
1444 1815 0.394352 ACATCGGGTTGCTTGATCCC 60.394 55.000 0.00 0.00 37.98 3.85
1445 1816 1.103398 CATCGGGTTGCTTGATCCCC 61.103 60.000 0.00 0.00 38.09 4.81
1446 1817 1.570857 ATCGGGTTGCTTGATCCCCA 61.571 55.000 3.71 0.00 38.09 4.96
1447 1818 1.076777 CGGGTTGCTTGATCCCCAT 60.077 57.895 3.71 0.00 38.09 4.00
1448 1819 0.684153 CGGGTTGCTTGATCCCCATT 60.684 55.000 3.71 0.00 38.09 3.16
1449 1820 1.114627 GGGTTGCTTGATCCCCATTC 58.885 55.000 0.00 0.00 37.09 2.67
1450 1821 1.342374 GGGTTGCTTGATCCCCATTCT 60.342 52.381 0.00 0.00 37.09 2.40
1451 1822 2.027385 GGTTGCTTGATCCCCATTCTC 58.973 52.381 0.00 0.00 0.00 2.87
1452 1823 2.357569 GGTTGCTTGATCCCCATTCTCT 60.358 50.000 0.00 0.00 0.00 3.10
1463 1834 2.091830 CCCCATTCTCTTCTTTACCCCC 60.092 54.545 0.00 0.00 0.00 5.40
1465 1836 2.289565 CATTCTCTTCTTTACCCCCGC 58.710 52.381 0.00 0.00 0.00 6.13
1466 1837 1.354101 TTCTCTTCTTTACCCCCGCA 58.646 50.000 0.00 0.00 0.00 5.69
1467 1838 1.354101 TCTCTTCTTTACCCCCGCAA 58.646 50.000 0.00 0.00 0.00 4.85
1468 1839 1.278127 TCTCTTCTTTACCCCCGCAAG 59.722 52.381 0.00 0.00 0.00 4.01
1469 1840 1.278127 CTCTTCTTTACCCCCGCAAGA 59.722 52.381 0.00 0.00 43.02 3.02
1470 1841 1.700739 TCTTCTTTACCCCCGCAAGAA 59.299 47.619 0.00 0.00 43.02 2.52
1471 1842 2.307686 TCTTCTTTACCCCCGCAAGAAT 59.692 45.455 0.00 0.00 36.26 2.40
1472 1843 2.413310 TCTTTACCCCCGCAAGAATC 57.587 50.000 0.00 0.00 43.02 2.52
1473 1844 1.913419 TCTTTACCCCCGCAAGAATCT 59.087 47.619 0.00 0.00 43.02 2.40
1474 1845 3.109151 TCTTTACCCCCGCAAGAATCTA 58.891 45.455 0.00 0.00 43.02 1.98
1607 2191 3.066064 CAGCTAGTCGTTGAGCATCTACT 59.934 47.826 7.69 0.00 41.36 2.57
1610 2202 4.555116 GCTAGTCGTTGAGCATCTACTACC 60.555 50.000 0.00 0.00 37.27 3.18
1678 2270 1.329171 ATCTGCTTCCTCTCGCTGCT 61.329 55.000 0.00 0.00 0.00 4.24
1717 2312 2.430465 ACTCCAGTGCAGCATTAACTG 58.570 47.619 0.00 0.44 40.81 3.16
1729 2324 2.352715 GCATTAACTGTGCTCCAAACCC 60.353 50.000 0.00 0.00 39.45 4.11
1826 2438 1.403323 GCTGGTTCTAATCAAGGCTGC 59.597 52.381 0.00 0.00 0.00 5.25
1843 2459 3.736483 CGCCTGCCGCTAATTGAT 58.264 55.556 0.00 0.00 34.21 2.57
1844 2460 2.024918 CGCCTGCCGCTAATTGATT 58.975 52.632 0.00 0.00 34.21 2.57
1846 2462 1.601903 CGCCTGCCGCTAATTGATTAA 59.398 47.619 0.00 0.00 34.21 1.40
1847 2463 2.226437 CGCCTGCCGCTAATTGATTAAT 59.774 45.455 0.00 0.00 34.21 1.40
1848 2464 3.304659 CGCCTGCCGCTAATTGATTAATT 60.305 43.478 0.74 0.74 39.69 1.40
1849 2465 4.083537 CGCCTGCCGCTAATTGATTAATTA 60.084 41.667 2.99 2.99 37.64 1.40
1850 2466 5.391950 CGCCTGCCGCTAATTGATTAATTAT 60.392 40.000 3.38 0.00 37.92 1.28
1851 2467 6.183360 CGCCTGCCGCTAATTGATTAATTATA 60.183 38.462 3.38 0.00 37.92 0.98
1852 2468 7.189512 GCCTGCCGCTAATTGATTAATTATAG 58.810 38.462 3.38 1.82 37.92 1.31
1886 2533 1.681666 CTGATGGTGGTGCAGGAGT 59.318 57.895 0.00 0.00 0.00 3.85
2113 2760 1.224315 CCCATCGCCCACTCATTCA 59.776 57.895 0.00 0.00 0.00 2.57
2188 2865 2.669569 TGCGAGACCCAGCAAAGC 60.670 61.111 0.00 0.00 40.78 3.51
2189 2866 2.669569 GCGAGACCCAGCAAAGCA 60.670 61.111 0.00 0.00 0.00 3.91
2190 2867 2.970974 GCGAGACCCAGCAAAGCAC 61.971 63.158 0.00 0.00 0.00 4.40
2192 2869 0.886490 CGAGACCCAGCAAAGCACTT 60.886 55.000 0.00 0.00 0.00 3.16
2193 2870 0.595095 GAGACCCAGCAAAGCACTTG 59.405 55.000 0.00 0.00 38.15 3.16
2264 2944 4.258702 ACTAGCGAGACAATCTTGTTGT 57.741 40.909 0.00 0.00 42.43 3.32
2351 3031 3.199677 TCTTGGCGTTAATTATCCGTGG 58.800 45.455 6.84 0.00 0.00 4.94
2353 3033 1.232119 GGCGTTAATTATCCGTGGGG 58.768 55.000 6.84 0.00 0.00 4.96
2354 3034 1.475571 GGCGTTAATTATCCGTGGGGT 60.476 52.381 6.84 0.00 33.83 4.95
2355 3035 1.600485 GCGTTAATTATCCGTGGGGTG 59.400 52.381 6.84 0.00 33.83 4.61
2356 3036 2.215196 CGTTAATTATCCGTGGGGTGG 58.785 52.381 0.00 0.00 33.83 4.61
2357 3037 2.420408 CGTTAATTATCCGTGGGGTGGT 60.420 50.000 0.00 0.00 33.83 4.16
2358 3038 3.181467 CGTTAATTATCCGTGGGGTGGTA 60.181 47.826 0.00 0.00 33.83 3.25
2359 3039 4.682859 CGTTAATTATCCGTGGGGTGGTAA 60.683 45.833 0.00 0.00 33.83 2.85
2360 3040 3.570912 AATTATCCGTGGGGTGGTAAG 57.429 47.619 0.00 0.00 33.83 2.34
2361 3041 2.250921 TTATCCGTGGGGTGGTAAGA 57.749 50.000 0.00 0.00 33.83 2.10
2362 3042 1.784358 TATCCGTGGGGTGGTAAGAG 58.216 55.000 0.00 0.00 33.83 2.85
2363 3043 1.623542 ATCCGTGGGGTGGTAAGAGC 61.624 60.000 0.00 0.00 33.83 4.09
2364 3044 2.267961 CGTGGGGTGGTAAGAGCC 59.732 66.667 0.00 0.00 0.00 4.70
2365 3045 2.291043 CGTGGGGTGGTAAGAGCCT 61.291 63.158 0.00 0.00 33.70 4.58
2366 3046 0.974010 CGTGGGGTGGTAAGAGCCTA 60.974 60.000 0.00 0.00 33.70 3.93
2367 3047 0.540454 GTGGGGTGGTAAGAGCCTAC 59.460 60.000 0.00 0.00 37.75 3.18
2368 3048 0.974010 TGGGGTGGTAAGAGCCTACG 60.974 60.000 0.00 0.00 33.70 3.51
2369 3049 0.974525 GGGGTGGTAAGAGCCTACGT 60.975 60.000 0.00 0.00 33.70 3.57
2370 3050 0.175073 GGGTGGTAAGAGCCTACGTG 59.825 60.000 0.00 0.00 0.00 4.49
2371 3051 0.893447 GGTGGTAAGAGCCTACGTGT 59.107 55.000 0.00 0.00 0.00 4.49
2387 3067 1.323534 CGTGTCAATACAAGCGCCTAC 59.676 52.381 2.29 0.00 37.36 3.18
2388 3068 1.323534 GTGTCAATACAAGCGCCTACG 59.676 52.381 2.29 0.00 37.36 3.51
2389 3069 1.067425 TGTCAATACAAGCGCCTACGT 60.067 47.619 2.29 0.00 35.37 3.57
2391 3071 1.067425 TCAATACAAGCGCCTACGTGT 60.067 47.619 2.29 3.51 42.83 4.49
2392 3072 1.323534 CAATACAAGCGCCTACGTGTC 59.676 52.381 2.29 0.00 42.83 3.67
2393 3073 0.528924 ATACAAGCGCCTACGTGTCA 59.471 50.000 2.29 0.00 42.83 3.58
2394 3074 0.314618 TACAAGCGCCTACGTGTCAA 59.685 50.000 2.29 0.00 42.83 3.18
2395 3075 0.531090 ACAAGCGCCTACGTGTCAAA 60.531 50.000 2.29 0.00 42.83 2.69
2515 3243 4.324402 CCGCAAGAAAACAAATACTGATGC 59.676 41.667 0.00 0.00 43.02 3.91
2517 3245 5.164158 CGCAAGAAAACAAATACTGATGCAC 60.164 40.000 0.00 0.00 43.02 4.57
2523 3251 7.880195 AGAAAACAAATACTGATGCACTCTACT 59.120 33.333 0.00 0.00 0.00 2.57
2618 3352 3.252458 AGGTGGACAATCGCACTTTTAAC 59.748 43.478 0.00 0.00 0.00 2.01
2624 3358 4.290155 ACAATCGCACTTTTAACTTGCTG 58.710 39.130 0.00 0.00 33.90 4.41
2638 3372 4.691860 ACTTGCTGCAGCTACTTATTTG 57.308 40.909 36.61 18.89 42.66 2.32
2640 3374 4.520492 ACTTGCTGCAGCTACTTATTTGTT 59.480 37.500 36.61 7.35 42.66 2.83
2641 3375 5.010012 ACTTGCTGCAGCTACTTATTTGTTT 59.990 36.000 36.61 6.03 42.66 2.83
2643 3377 5.460646 TGCTGCAGCTACTTATTTGTTTTC 58.539 37.500 36.61 4.71 42.66 2.29
2648 3382 6.922957 TGCAGCTACTTATTTGTTTTCCTTTG 59.077 34.615 0.00 0.00 0.00 2.77
2649 3383 7.145323 GCAGCTACTTATTTGTTTTCCTTTGA 58.855 34.615 0.00 0.00 0.00 2.69
2650 3384 7.651704 GCAGCTACTTATTTGTTTTCCTTTGAA 59.348 33.333 0.00 0.00 0.00 2.69
2651 3385 8.968242 CAGCTACTTATTTGTTTTCCTTTGAAC 58.032 33.333 0.00 0.00 0.00 3.18
2653 3387 7.114388 GCTACTTATTTGTTTTCCTTTGAACCG 59.886 37.037 0.00 0.00 0.00 4.44
2654 3388 7.102847 ACTTATTTGTTTTCCTTTGAACCGA 57.897 32.000 0.00 0.00 0.00 4.69
2655 3389 7.200455 ACTTATTTGTTTTCCTTTGAACCGAG 58.800 34.615 0.00 0.00 0.00 4.63
2656 3390 5.845391 ATTTGTTTTCCTTTGAACCGAGA 57.155 34.783 0.00 0.00 0.00 4.04
2657 3391 5.646577 TTTGTTTTCCTTTGAACCGAGAA 57.353 34.783 0.00 0.00 0.00 2.87
2658 3392 4.625972 TGTTTTCCTTTGAACCGAGAAC 57.374 40.909 0.00 0.00 0.00 3.01
2659 3393 4.266714 TGTTTTCCTTTGAACCGAGAACT 58.733 39.130 0.00 0.00 0.00 3.01
2660 3394 4.095782 TGTTTTCCTTTGAACCGAGAACTG 59.904 41.667 0.00 0.00 0.00 3.16
2661 3395 2.543777 TCCTTTGAACCGAGAACTGG 57.456 50.000 0.00 0.00 0.00 4.00
2662 3396 1.766496 TCCTTTGAACCGAGAACTGGT 59.234 47.619 0.00 0.00 42.98 4.00
2663 3397 2.143925 CCTTTGAACCGAGAACTGGTC 58.856 52.381 0.00 0.00 39.29 4.02
2664 3398 1.792949 CTTTGAACCGAGAACTGGTCG 59.207 52.381 0.00 0.00 39.29 4.79
2665 3399 0.748450 TTGAACCGAGAACTGGTCGT 59.252 50.000 0.00 0.00 39.29 4.34
2666 3400 0.748450 TGAACCGAGAACTGGTCGTT 59.252 50.000 0.00 0.00 39.29 3.85
2722 3456 3.614092 TCTGAATTCTGATGGGAAGCAC 58.386 45.455 10.68 0.00 0.00 4.40
2737 3471 3.467803 GAAGCACTGTCCTACTTGTTGT 58.532 45.455 0.00 0.00 0.00 3.32
2899 3640 5.554822 TTAGGACACCGCAATTAATTGAC 57.445 39.130 28.33 18.60 40.14 3.18
2901 3642 4.016444 AGGACACCGCAATTAATTGACAT 58.984 39.130 28.33 11.51 40.14 3.06
2903 3644 4.562394 GGACACCGCAATTAATTGACATTG 59.438 41.667 28.33 19.81 40.14 2.82
2904 3645 5.384063 ACACCGCAATTAATTGACATTGA 57.616 34.783 28.33 0.00 40.14 2.57
2909 3650 7.166307 CACCGCAATTAATTGACATTGATAGTG 59.834 37.037 28.33 16.30 40.14 2.74
3121 3897 4.719369 GAGCACGGCGTCCTCGTT 62.719 66.667 16.03 0.00 38.94 3.85
3295 4071 2.248835 GCCAAGGTACACACGCGTT 61.249 57.895 10.22 0.00 0.00 4.84
3304 4080 3.184986 GGTACACACGCGTTAATGAACTT 59.815 43.478 10.22 0.00 33.01 2.66
3305 4081 3.515071 ACACACGCGTTAATGAACTTC 57.485 42.857 10.22 0.00 33.01 3.01
3315 4099 5.059710 GCGTTAATGAACTTCAGCATTTCAC 59.940 40.000 0.00 0.00 36.27 3.18
3332 4116 6.743172 GCATTTCACCTCGAAAATTCTAAGAC 59.257 38.462 0.00 0.00 46.48 3.01
3343 4127 7.824289 TCGAAAATTCTAAGACAATCCAGTGAT 59.176 33.333 0.00 0.00 0.00 3.06
3344 4128 8.454106 CGAAAATTCTAAGACAATCCAGTGATT 58.546 33.333 0.00 0.00 41.96 2.57
3408 4193 0.601311 GCAGTGACGAGCTGAAGGTT 60.601 55.000 0.00 0.00 36.12 3.50
3447 4232 3.879892 AGAACAAGAAGCTGAACAACCTC 59.120 43.478 0.00 0.00 0.00 3.85
3503 4288 7.730332 GGACTTGGATTAGGGATTCCATTATTT 59.270 37.037 4.80 0.00 34.83 1.40
3551 4336 7.347485 AGCTAGGGTTGTATTCTTTATGTACCT 59.653 37.037 0.00 0.00 0.00 3.08
3552 4337 8.645110 GCTAGGGTTGTATTCTTTATGTACCTA 58.355 37.037 0.00 0.00 0.00 3.08
3595 4381 5.755849 TCTCCTGAAAAGGGAAATATGGTC 58.244 41.667 0.00 0.00 31.92 4.02
3653 4442 2.794910 CGCATGTATTCCACTCTTACCG 59.205 50.000 0.00 0.00 0.00 4.02
3734 4526 6.731292 AAAGGGAAAATAAGTCTGCAGTTT 57.269 33.333 14.67 12.01 0.00 2.66
3797 4597 7.382110 TGAACAAATGTCAAAAGTTTCAAGGA 58.618 30.769 0.00 0.00 0.00 3.36
3860 4660 9.890352 TGAAACTGAAACTTTTGAAAAATTTGG 57.110 25.926 1.55 0.00 0.00 3.28
3862 4662 9.891828 AAACTGAAACTTTTGAAAAATTTGGAC 57.108 25.926 1.55 0.00 0.00 4.02
3863 4663 8.039603 ACTGAAACTTTTGAAAAATTTGGACC 57.960 30.769 1.55 0.00 0.00 4.46
3864 4664 7.663493 ACTGAAACTTTTGAAAAATTTGGACCA 59.337 29.630 1.55 0.00 0.00 4.02
3865 4665 8.572855 TGAAACTTTTGAAAAATTTGGACCAT 57.427 26.923 1.55 0.00 0.00 3.55
3866 4666 8.457261 TGAAACTTTTGAAAAATTTGGACCATG 58.543 29.630 1.55 0.00 0.00 3.66
3867 4667 7.936496 AACTTTTGAAAAATTTGGACCATGT 57.064 28.000 0.00 0.00 0.00 3.21
3868 4668 7.936496 ACTTTTGAAAAATTTGGACCATGTT 57.064 28.000 0.00 0.00 0.00 2.71
3869 4669 7.984391 ACTTTTGAAAAATTTGGACCATGTTC 58.016 30.769 0.00 0.00 0.00 3.18
3870 4670 7.609532 ACTTTTGAAAAATTTGGACCATGTTCA 59.390 29.630 0.00 0.00 0.00 3.18
3871 4671 7.551035 TTTGAAAAATTTGGACCATGTTCAG 57.449 32.000 0.00 0.00 0.00 3.02
3872 4672 6.232581 TGAAAAATTTGGACCATGTTCAGT 57.767 33.333 0.00 0.00 0.00 3.41
3873 4673 7.353414 TGAAAAATTTGGACCATGTTCAGTA 57.647 32.000 0.00 0.00 0.00 2.74
3874 4674 7.786030 TGAAAAATTTGGACCATGTTCAGTAA 58.214 30.769 0.00 0.00 0.00 2.24
3875 4675 8.260818 TGAAAAATTTGGACCATGTTCAGTAAA 58.739 29.630 0.00 0.00 0.00 2.01
3876 4676 8.432110 AAAAATTTGGACCATGTTCAGTAAAC 57.568 30.769 0.00 0.00 38.43 2.01
3877 4677 5.722021 ATTTGGACCATGTTCAGTAAACC 57.278 39.130 0.00 0.00 37.03 3.27
3878 4678 3.866703 TGGACCATGTTCAGTAAACCA 57.133 42.857 0.00 0.00 37.03 3.67
3879 4679 3.482436 TGGACCATGTTCAGTAAACCAC 58.518 45.455 0.00 0.00 37.03 4.16
3880 4680 2.817844 GGACCATGTTCAGTAAACCACC 59.182 50.000 0.00 0.00 37.03 4.61
3881 4681 3.482436 GACCATGTTCAGTAAACCACCA 58.518 45.455 0.00 0.00 37.03 4.17
3882 4682 3.886505 GACCATGTTCAGTAAACCACCAA 59.113 43.478 0.00 0.00 37.03 3.67
3883 4683 3.634910 ACCATGTTCAGTAAACCACCAAC 59.365 43.478 0.00 0.00 37.03 3.77
3884 4684 3.634448 CCATGTTCAGTAAACCACCAACA 59.366 43.478 0.00 0.00 37.03 3.33
3885 4685 4.499019 CCATGTTCAGTAAACCACCAACAC 60.499 45.833 0.00 0.00 34.74 3.32
3886 4686 3.018149 TGTTCAGTAAACCACCAACACC 58.982 45.455 0.00 0.00 37.03 4.16
3887 4687 2.351706 TCAGTAAACCACCAACACCC 57.648 50.000 0.00 0.00 0.00 4.61
3888 4688 0.948678 CAGTAAACCACCAACACCCG 59.051 55.000 0.00 0.00 0.00 5.28
3889 4689 0.179012 AGTAAACCACCAACACCCGG 60.179 55.000 0.00 0.00 0.00 5.73
3890 4690 0.179023 GTAAACCACCAACACCCGGA 60.179 55.000 0.73 0.00 0.00 5.14
3891 4691 0.549950 TAAACCACCAACACCCGGAA 59.450 50.000 0.73 0.00 0.00 4.30
3892 4692 0.105913 AAACCACCAACACCCGGAAT 60.106 50.000 0.73 0.00 0.00 3.01
3893 4693 0.538746 AACCACCAACACCCGGAATC 60.539 55.000 0.73 0.00 0.00 2.52
3894 4694 1.378762 CCACCAACACCCGGAATCT 59.621 57.895 0.73 0.00 0.00 2.40
3895 4695 0.960364 CCACCAACACCCGGAATCTG 60.960 60.000 0.73 0.00 0.00 2.90
3896 4696 1.303317 ACCAACACCCGGAATCTGC 60.303 57.895 0.73 0.00 0.00 4.26
3897 4697 2.398554 CCAACACCCGGAATCTGCG 61.399 63.158 0.73 0.00 0.00 5.18
3918 4718 2.747855 CGGGGAAACTGCAGCTCC 60.748 66.667 21.97 21.97 0.00 4.70
3919 4719 2.747855 GGGGAAACTGCAGCTCCG 60.748 66.667 22.76 0.00 0.00 4.63
3920 4720 3.435186 GGGAAACTGCAGCTCCGC 61.435 66.667 22.76 14.93 0.00 5.54
3921 4721 3.435186 GGAAACTGCAGCTCCGCC 61.435 66.667 15.27 4.74 0.00 6.13
3922 4722 2.669569 GAAACTGCAGCTCCGCCA 60.670 61.111 15.27 0.00 0.00 5.69
3923 4723 2.670934 AAACTGCAGCTCCGCCAG 60.671 61.111 15.27 0.00 0.00 4.85
3942 4742 3.691342 TCCGGGAGCGGAGTTGTG 61.691 66.667 0.00 0.00 33.62 3.33
3943 4743 4.760047 CCGGGAGCGGAGTTGTGG 62.760 72.222 0.00 0.00 0.00 4.17
3944 4744 3.691342 CGGGAGCGGAGTTGTGGA 61.691 66.667 0.00 0.00 0.00 4.02
3945 4745 2.266055 GGGAGCGGAGTTGTGGAG 59.734 66.667 0.00 0.00 0.00 3.86
3946 4746 2.435059 GGAGCGGAGTTGTGGAGC 60.435 66.667 0.00 0.00 0.00 4.70
3947 4747 2.811317 GAGCGGAGTTGTGGAGCG 60.811 66.667 0.00 0.00 0.00 5.03
3948 4748 4.379243 AGCGGAGTTGTGGAGCGG 62.379 66.667 0.00 0.00 0.00 5.52
3949 4749 4.373116 GCGGAGTTGTGGAGCGGA 62.373 66.667 0.00 0.00 0.00 5.54
3950 4750 2.125912 CGGAGTTGTGGAGCGGAG 60.126 66.667 0.00 0.00 0.00 4.63
3965 4765 1.966451 GGAGCAACACCGAACAGGG 60.966 63.158 0.00 0.00 46.96 4.45
3966 4766 2.594592 AGCAACACCGAACAGGGC 60.595 61.111 0.00 0.00 46.96 5.19
3983 4783 2.238898 AGGGCCTTAGTGTACATGGTTC 59.761 50.000 0.00 0.00 0.00 3.62
4047 4880 8.707938 TGACAACTACATATTCATCTGACAAG 57.292 34.615 0.00 0.00 0.00 3.16
4073 4906 5.754782 ACCATCCTAAATTGCATACACAGA 58.245 37.500 0.00 0.00 0.00 3.41
4074 4907 6.186957 ACCATCCTAAATTGCATACACAGAA 58.813 36.000 0.00 0.00 0.00 3.02
4075 4908 6.095440 ACCATCCTAAATTGCATACACAGAAC 59.905 38.462 0.00 0.00 0.00 3.01
4076 4909 6.319658 CCATCCTAAATTGCATACACAGAACT 59.680 38.462 0.00 0.00 0.00 3.01
4077 4910 6.985188 TCCTAAATTGCATACACAGAACTC 57.015 37.500 0.00 0.00 0.00 3.01
4078 4911 6.711277 TCCTAAATTGCATACACAGAACTCT 58.289 36.000 0.00 0.00 0.00 3.24
4079 4912 6.818644 TCCTAAATTGCATACACAGAACTCTC 59.181 38.462 0.00 0.00 0.00 3.20
4080 4913 6.595326 CCTAAATTGCATACACAGAACTCTCA 59.405 38.462 0.00 0.00 0.00 3.27
4081 4914 7.281774 CCTAAATTGCATACACAGAACTCTCAT 59.718 37.037 0.00 0.00 0.00 2.90
4120 4953 5.477984 ACTTAACATTCACAGCATCACCATT 59.522 36.000 0.00 0.00 0.00 3.16
4121 4954 4.877378 AACATTCACAGCATCACCATTT 57.123 36.364 0.00 0.00 0.00 2.32
4122 4955 5.981088 AACATTCACAGCATCACCATTTA 57.019 34.783 0.00 0.00 0.00 1.40
4278 5111 0.235926 GCTCCACAGAAAACGACAGC 59.764 55.000 0.00 0.00 0.00 4.40
4312 5145 2.090210 TCCAAGGCACCCATAGATAGGA 60.090 50.000 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 0.743097 GGATGGCCATGCTCTGTTTC 59.257 55.000 28.45 9.30 0.00 2.78
95 96 0.749091 TTCTCGCAAGGATGGCCATG 60.749 55.000 26.56 11.95 35.99 3.66
112 113 1.002251 CGATCCTGGTCGCTCTACTTC 60.002 57.143 5.90 0.00 34.56 3.01
121 122 1.560923 GTGTCATTCGATCCTGGTCG 58.439 55.000 10.97 10.97 42.74 4.79
124 125 1.208052 ACAGGTGTCATTCGATCCTGG 59.792 52.381 12.95 0.00 43.92 4.45
156 157 3.767131 TCTCGTATGGGTCATCAAACTCA 59.233 43.478 0.00 0.00 33.25 3.41
168 169 8.888579 ATACTCTTAACAAAATCTCGTATGGG 57.111 34.615 0.00 0.00 0.00 4.00
388 711 3.423154 GGCGTTGACCTCTTGGCG 61.423 66.667 0.00 0.00 36.63 5.69
461 788 2.406616 CGTCCGCTGGAATTTGGGG 61.407 63.158 0.00 0.00 37.59 4.96
821 1156 1.805254 GGCGTAGGAGTTGTAGCGA 59.195 57.895 0.00 0.00 0.00 4.93
942 1279 3.431725 GTCCAAGAAAGCGCCGGG 61.432 66.667 2.29 0.00 0.00 5.73
951 1288 2.357034 GCCTGCGACGTCCAAGAA 60.357 61.111 10.58 0.00 0.00 2.52
961 1298 2.736995 GCTTGTACGTGCCTGCGA 60.737 61.111 0.00 0.00 35.59 5.10
962 1299 2.111932 TTTGCTTGTACGTGCCTGCG 62.112 55.000 0.00 0.00 37.94 5.18
963 1300 0.030101 TTTTGCTTGTACGTGCCTGC 59.970 50.000 0.00 4.56 0.00 4.85
965 1302 0.310854 GCTTTTGCTTGTACGTGCCT 59.689 50.000 0.00 0.00 43.35 4.75
991 1337 2.036256 AGGGCACATGGCTGGTTC 59.964 61.111 5.33 0.00 44.01 3.62
992 1338 2.283388 CAGGGCACATGGCTGGTT 60.283 61.111 5.33 0.00 44.01 3.67
993 1339 4.371417 CCAGGGCACATGGCTGGT 62.371 66.667 5.33 0.00 44.01 4.00
1370 1740 7.138736 TCCATGATTCTTTCTTGAAACGAAAC 58.861 34.615 0.00 8.76 32.55 2.78
1371 1741 7.270757 TCCATGATTCTTTCTTGAAACGAAA 57.729 32.000 0.00 0.00 32.55 3.46
1372 1742 6.875948 TCCATGATTCTTTCTTGAAACGAA 57.124 33.333 0.00 8.95 32.55 3.85
1373 1743 6.127925 CCATCCATGATTCTTTCTTGAAACGA 60.128 38.462 0.00 0.00 32.55 3.85
1374 1744 6.032094 CCATCCATGATTCTTTCTTGAAACG 58.968 40.000 0.00 0.00 32.55 3.60
1436 1807 5.825151 GGTAAAGAAGAGAATGGGGATCAAG 59.175 44.000 0.00 0.00 0.00 3.02
1442 1813 2.091830 GGGGGTAAAGAAGAGAATGGGG 60.092 54.545 0.00 0.00 0.00 4.96
1443 1814 2.421529 CGGGGGTAAAGAAGAGAATGGG 60.422 54.545 0.00 0.00 0.00 4.00
1444 1815 2.919228 CGGGGGTAAAGAAGAGAATGG 58.081 52.381 0.00 0.00 0.00 3.16
1445 1816 2.289565 GCGGGGGTAAAGAAGAGAATG 58.710 52.381 0.00 0.00 0.00 2.67
1446 1817 1.913419 TGCGGGGGTAAAGAAGAGAAT 59.087 47.619 0.00 0.00 0.00 2.40
1447 1818 1.354101 TGCGGGGGTAAAGAAGAGAA 58.646 50.000 0.00 0.00 0.00 2.87
1448 1819 1.278127 CTTGCGGGGGTAAAGAAGAGA 59.722 52.381 0.00 0.00 0.00 3.10
1449 1820 1.278127 TCTTGCGGGGGTAAAGAAGAG 59.722 52.381 0.00 0.00 0.00 2.85
1450 1821 1.354101 TCTTGCGGGGGTAAAGAAGA 58.646 50.000 0.00 0.00 0.00 2.87
1451 1822 2.194201 TTCTTGCGGGGGTAAAGAAG 57.806 50.000 0.00 0.00 35.54 2.85
1452 1823 2.307686 AGATTCTTGCGGGGGTAAAGAA 59.692 45.455 0.00 0.00 42.41 2.52
1463 1834 5.470368 TCGGGAATAGATTAGATTCTTGCG 58.530 41.667 0.00 0.00 34.36 4.85
1465 1836 6.254589 GCGATCGGGAATAGATTAGATTCTTG 59.745 42.308 18.30 0.00 34.36 3.02
1466 1837 6.334202 GCGATCGGGAATAGATTAGATTCTT 58.666 40.000 18.30 0.00 34.36 2.52
1467 1838 5.163499 GGCGATCGGGAATAGATTAGATTCT 60.163 44.000 18.30 0.00 34.36 2.40
1468 1839 5.044558 GGCGATCGGGAATAGATTAGATTC 58.955 45.833 18.30 0.00 33.34 2.52
1469 1840 4.440250 CGGCGATCGGGAATAGATTAGATT 60.440 45.833 18.30 0.00 34.75 2.40
1470 1841 3.066900 CGGCGATCGGGAATAGATTAGAT 59.933 47.826 18.30 0.00 34.75 1.98
1471 1842 2.422479 CGGCGATCGGGAATAGATTAGA 59.578 50.000 18.30 0.00 34.75 2.10
1472 1843 2.798680 CGGCGATCGGGAATAGATTAG 58.201 52.381 18.30 0.00 34.75 1.73
1473 1844 2.933495 CGGCGATCGGGAATAGATTA 57.067 50.000 18.30 0.00 34.75 1.75
1474 1845 3.814577 CGGCGATCGGGAATAGATT 57.185 52.632 18.30 0.00 34.75 2.40
1607 2191 5.476945 GCCAAGGAGAAAGAAAGAAATGGTA 59.523 40.000 0.00 0.00 0.00 3.25
1610 2202 4.022849 ACGCCAAGGAGAAAGAAAGAAATG 60.023 41.667 0.00 0.00 0.00 2.32
1717 2312 2.991540 GCCAGGGGTTTGGAGCAC 60.992 66.667 0.00 0.00 40.87 4.40
1826 2438 4.083537 TAATTAATCAATTAGCGGCAGGCG 60.084 41.667 13.01 13.01 39.89 5.52
1848 2464 8.753133 CCATCAGCCACTCAGATTAATACTATA 58.247 37.037 0.00 0.00 0.00 1.31
1849 2465 7.236432 ACCATCAGCCACTCAGATTAATACTAT 59.764 37.037 0.00 0.00 0.00 2.12
1850 2466 6.554982 ACCATCAGCCACTCAGATTAATACTA 59.445 38.462 0.00 0.00 0.00 1.82
1851 2467 5.367937 ACCATCAGCCACTCAGATTAATACT 59.632 40.000 0.00 0.00 0.00 2.12
1852 2468 5.468072 CACCATCAGCCACTCAGATTAATAC 59.532 44.000 0.00 0.00 0.00 1.89
1886 2533 0.475632 ACCTCCACCTCCACCATCAA 60.476 55.000 0.00 0.00 0.00 2.57
2105 2752 2.797156 GCTCGCGTATGAATGAATGAGT 59.203 45.455 5.77 0.00 0.00 3.41
2113 2760 4.012554 CGGTGCTCGCGTATGAAT 57.987 55.556 5.77 0.00 0.00 2.57
2186 2863 0.308993 GCTTTTCGTGCTCAAGTGCT 59.691 50.000 0.00 0.00 0.00 4.40
2187 2864 0.029300 TGCTTTTCGTGCTCAAGTGC 59.971 50.000 0.00 0.00 0.00 4.40
2188 2865 1.334419 CCTGCTTTTCGTGCTCAAGTG 60.334 52.381 0.00 0.00 0.00 3.16
2189 2866 0.947244 CCTGCTTTTCGTGCTCAAGT 59.053 50.000 0.00 0.00 0.00 3.16
2190 2867 1.196354 CTCCTGCTTTTCGTGCTCAAG 59.804 52.381 0.00 0.00 0.00 3.02
2192 2869 0.392706 TCTCCTGCTTTTCGTGCTCA 59.607 50.000 0.00 0.00 0.00 4.26
2193 2870 1.074752 CTCTCCTGCTTTTCGTGCTC 58.925 55.000 0.00 0.00 0.00 4.26
2217 2897 2.614481 GGATTCGTAACAGGACAGGCAA 60.614 50.000 0.00 0.00 0.00 4.52
2264 2944 0.181587 TCTTTCCGTGCTGGGTTTCA 59.818 50.000 0.00 0.00 38.76 2.69
2351 3031 0.175073 CACGTAGGCTCTTACCACCC 59.825 60.000 0.00 0.00 0.00 4.61
2353 3033 1.542915 TGACACGTAGGCTCTTACCAC 59.457 52.381 0.00 0.00 0.00 4.16
2354 3034 1.913778 TGACACGTAGGCTCTTACCA 58.086 50.000 0.00 0.00 0.00 3.25
2355 3035 3.521947 ATTGACACGTAGGCTCTTACC 57.478 47.619 0.00 0.00 0.00 2.85
2356 3036 4.990257 TGTATTGACACGTAGGCTCTTAC 58.010 43.478 0.00 0.00 0.00 2.34
2357 3037 5.647589 CTTGTATTGACACGTAGGCTCTTA 58.352 41.667 0.00 0.00 34.48 2.10
2358 3038 4.495422 CTTGTATTGACACGTAGGCTCTT 58.505 43.478 0.00 0.00 34.48 2.85
2359 3039 3.676324 GCTTGTATTGACACGTAGGCTCT 60.676 47.826 0.00 0.00 34.48 4.09
2360 3040 2.603560 GCTTGTATTGACACGTAGGCTC 59.396 50.000 0.00 0.00 34.48 4.70
2361 3041 2.618053 GCTTGTATTGACACGTAGGCT 58.382 47.619 0.00 0.00 34.48 4.58
2362 3042 1.323534 CGCTTGTATTGACACGTAGGC 59.676 52.381 0.00 0.00 34.48 3.93
2363 3043 1.323534 GCGCTTGTATTGACACGTAGG 59.676 52.381 0.00 0.00 34.48 3.18
2364 3044 1.323534 GGCGCTTGTATTGACACGTAG 59.676 52.381 7.64 0.00 34.48 3.51
2365 3045 1.067425 AGGCGCTTGTATTGACACGTA 60.067 47.619 7.64 0.00 34.48 3.57
2366 3046 0.320421 AGGCGCTTGTATTGACACGT 60.320 50.000 7.64 0.00 34.48 4.49
2367 3047 1.323534 GTAGGCGCTTGTATTGACACG 59.676 52.381 7.64 0.00 34.48 4.49
2368 3048 1.323534 CGTAGGCGCTTGTATTGACAC 59.676 52.381 7.64 0.00 34.48 3.67
2369 3049 1.067425 ACGTAGGCGCTTGTATTGACA 60.067 47.619 7.64 0.00 42.83 3.58
2370 3050 1.323534 CACGTAGGCGCTTGTATTGAC 59.676 52.381 7.64 0.00 42.83 3.18
2371 3051 1.067425 ACACGTAGGCGCTTGTATTGA 60.067 47.619 7.64 0.00 42.83 2.57
2387 3067 3.708563 ATTGGGTTTGAGTTTGACACG 57.291 42.857 0.00 0.00 0.00 4.49
2388 3068 5.977129 CACTTATTGGGTTTGAGTTTGACAC 59.023 40.000 0.00 0.00 0.00 3.67
2389 3069 5.068460 CCACTTATTGGGTTTGAGTTTGACA 59.932 40.000 0.00 0.00 42.54 3.58
2391 3071 5.450453 TCCACTTATTGGGTTTGAGTTTGA 58.550 37.500 0.00 0.00 46.92 2.69
2392 3072 5.782893 TCCACTTATTGGGTTTGAGTTTG 57.217 39.130 0.00 0.00 46.92 2.93
2393 3073 6.074648 TCATCCACTTATTGGGTTTGAGTTT 58.925 36.000 0.00 0.00 46.92 2.66
2394 3074 5.640147 TCATCCACTTATTGGGTTTGAGTT 58.360 37.500 0.00 0.00 46.92 3.01
2395 3075 5.014123 TCTCATCCACTTATTGGGTTTGAGT 59.986 40.000 12.69 0.00 46.92 3.41
2515 3243 5.297278 GTGGACTAGGATGTGTAGTAGAGTG 59.703 48.000 0.00 0.00 30.60 3.51
2517 3245 5.297278 GTGTGGACTAGGATGTGTAGTAGAG 59.703 48.000 0.00 0.00 30.60 2.43
2523 3251 4.836175 TCTTTGTGTGGACTAGGATGTGTA 59.164 41.667 0.00 0.00 0.00 2.90
2618 3352 4.691860 ACAAATAAGTAGCTGCAGCAAG 57.308 40.909 38.24 18.58 45.16 4.01
2624 3358 7.145323 TCAAAGGAAAACAAATAAGTAGCTGC 58.855 34.615 0.00 0.00 0.00 5.25
2638 3372 4.497507 CCAGTTCTCGGTTCAAAGGAAAAC 60.498 45.833 0.00 0.00 34.13 2.43
2640 3374 3.211045 CCAGTTCTCGGTTCAAAGGAAA 58.789 45.455 0.00 0.00 34.13 3.13
2641 3375 2.171870 ACCAGTTCTCGGTTCAAAGGAA 59.828 45.455 0.00 0.00 30.53 3.36
2643 3377 2.143925 GACCAGTTCTCGGTTCAAAGG 58.856 52.381 0.00 0.00 36.69 3.11
2648 3382 3.582743 AACGACCAGTTCTCGGTTC 57.417 52.632 0.00 0.00 39.16 3.62
2674 3408 6.127026 ACAGAGGACTAGTTCTCAGTGTTTTT 60.127 38.462 29.14 6.71 30.37 1.94
2675 3409 5.364157 ACAGAGGACTAGTTCTCAGTGTTTT 59.636 40.000 29.14 7.41 30.37 2.43
2676 3410 4.896482 ACAGAGGACTAGTTCTCAGTGTTT 59.104 41.667 29.14 8.10 30.37 2.83
2677 3411 4.475345 ACAGAGGACTAGTTCTCAGTGTT 58.525 43.478 29.14 8.80 30.37 3.32
2678 3412 4.107127 ACAGAGGACTAGTTCTCAGTGT 57.893 45.455 29.14 22.59 30.37 3.55
2679 3413 5.242838 AGAAACAGAGGACTAGTTCTCAGTG 59.757 44.000 29.14 22.01 31.63 3.66
2680 3414 5.242838 CAGAAACAGAGGACTAGTTCTCAGT 59.757 44.000 29.14 24.87 32.37 3.41
2681 3415 5.475220 TCAGAAACAGAGGACTAGTTCTCAG 59.525 44.000 29.14 24.25 30.83 3.35
2682 3416 5.386060 TCAGAAACAGAGGACTAGTTCTCA 58.614 41.667 29.14 6.71 30.83 3.27
2690 3424 5.815233 TCAGAATTCAGAAACAGAGGACT 57.185 39.130 8.44 0.00 0.00 3.85
2722 3456 1.202758 TGGCCACAACAAGTAGGACAG 60.203 52.381 0.00 0.00 33.33 3.51
2737 3471 2.584064 CGCTGTAGTGGATGGCCA 59.416 61.111 8.56 8.56 43.47 5.36
2861 3602 1.336755 CCTAAAGGGTGTGTGTGTTGC 59.663 52.381 0.00 0.00 0.00 4.17
3241 4017 3.731728 GGGGTGAGCATCTGGGCA 61.732 66.667 0.00 0.00 34.92 5.36
3295 4071 5.122239 CGAGGTGAAATGCTGAAGTTCATTA 59.878 40.000 5.91 0.00 44.10 1.90
3304 4080 4.761739 AGAATTTTCGAGGTGAAATGCTGA 59.238 37.500 0.80 0.00 45.62 4.26
3305 4081 5.051891 AGAATTTTCGAGGTGAAATGCTG 57.948 39.130 0.80 0.00 45.62 4.41
3315 4099 6.595716 ACTGGATTGTCTTAGAATTTTCGAGG 59.404 38.462 0.00 0.00 0.00 4.63
3332 4116 5.163622 GGAACACACCATAATCACTGGATTG 60.164 44.000 0.41 0.00 43.47 2.67
3343 4127 5.071250 AGTCAGTTACAGGAACACACCATAA 59.929 40.000 0.00 0.00 40.86 1.90
3344 4128 4.591498 AGTCAGTTACAGGAACACACCATA 59.409 41.667 0.00 0.00 40.86 2.74
3408 4193 2.365617 GTTCTGAATCCTCTGCGGGATA 59.634 50.000 6.18 0.00 44.50 2.59
3447 4232 0.599558 CACTGGCAAACTCCACCATG 59.400 55.000 0.00 0.00 31.79 3.66
3503 4288 3.008157 TGCCCTTGTGAGGTAAACGAATA 59.992 43.478 0.00 0.00 41.85 1.75
3653 4442 2.019984 CTCAAATGCTCTTACCAGCCC 58.980 52.381 0.00 0.00 38.80 5.19
3734 4526 3.201353 TGCTGTACAAGGCAGTAACAA 57.799 42.857 5.73 0.00 36.42 2.83
3783 4583 7.969536 TCTATCTCACTCCTTGAAACTTTTG 57.030 36.000 0.00 0.00 32.21 2.44
3789 4589 8.774546 ACTCATATCTATCTCACTCCTTGAAA 57.225 34.615 0.00 0.00 32.21 2.69
3856 4656 4.339814 GTGGTTTACTGAACATGGTCCAAA 59.660 41.667 8.62 3.33 40.13 3.28
3859 4659 2.817844 GGTGGTTTACTGAACATGGTCC 59.182 50.000 8.62 0.00 40.13 4.46
3860 4660 3.482436 TGGTGGTTTACTGAACATGGTC 58.518 45.455 2.98 2.98 40.13 4.02
3861 4661 3.586470 TGGTGGTTTACTGAACATGGT 57.414 42.857 0.00 0.00 40.13 3.55
3862 4662 3.634448 TGTTGGTGGTTTACTGAACATGG 59.366 43.478 0.00 0.00 40.13 3.66
3863 4663 4.499019 GGTGTTGGTGGTTTACTGAACATG 60.499 45.833 0.00 0.00 40.13 3.21
3864 4664 3.634910 GGTGTTGGTGGTTTACTGAACAT 59.365 43.478 0.00 0.00 40.13 2.71
3865 4665 3.018149 GGTGTTGGTGGTTTACTGAACA 58.982 45.455 0.00 0.00 40.13 3.18
3866 4666 2.359848 GGGTGTTGGTGGTTTACTGAAC 59.640 50.000 0.00 0.00 37.53 3.18
3867 4667 2.657143 GGGTGTTGGTGGTTTACTGAA 58.343 47.619 0.00 0.00 0.00 3.02
3868 4668 1.475392 CGGGTGTTGGTGGTTTACTGA 60.475 52.381 0.00 0.00 0.00 3.41
3869 4669 0.948678 CGGGTGTTGGTGGTTTACTG 59.051 55.000 0.00 0.00 0.00 2.74
3870 4670 0.179012 CCGGGTGTTGGTGGTTTACT 60.179 55.000 0.00 0.00 0.00 2.24
3871 4671 0.179023 TCCGGGTGTTGGTGGTTTAC 60.179 55.000 0.00 0.00 0.00 2.01
3872 4672 0.549950 TTCCGGGTGTTGGTGGTTTA 59.450 50.000 0.00 0.00 0.00 2.01
3873 4673 0.105913 ATTCCGGGTGTTGGTGGTTT 60.106 50.000 0.00 0.00 0.00 3.27
3874 4674 0.538746 GATTCCGGGTGTTGGTGGTT 60.539 55.000 0.00 0.00 0.00 3.67
3875 4675 1.074248 GATTCCGGGTGTTGGTGGT 59.926 57.895 0.00 0.00 0.00 4.16
3876 4676 0.960364 CAGATTCCGGGTGTTGGTGG 60.960 60.000 0.00 0.00 0.00 4.61
3877 4677 1.586154 GCAGATTCCGGGTGTTGGTG 61.586 60.000 0.00 0.00 0.00 4.17
3878 4678 1.303317 GCAGATTCCGGGTGTTGGT 60.303 57.895 0.00 0.00 0.00 3.67
3879 4679 2.398554 CGCAGATTCCGGGTGTTGG 61.399 63.158 0.00 0.00 0.00 3.77
3880 4680 2.398554 CCGCAGATTCCGGGTGTTG 61.399 63.158 0.00 0.00 41.99 3.33
3881 4681 2.046314 CCGCAGATTCCGGGTGTT 60.046 61.111 0.00 0.00 41.99 3.32
3882 4682 3.000819 TCCGCAGATTCCGGGTGT 61.001 61.111 0.00 0.00 45.60 4.16
3883 4683 2.202932 CTCCGCAGATTCCGGGTG 60.203 66.667 0.00 0.00 45.60 4.61
3884 4684 4.162690 GCTCCGCAGATTCCGGGT 62.163 66.667 0.00 0.00 45.60 5.28
3888 4688 4.918201 CCCCGCTCCGCAGATTCC 62.918 72.222 0.00 0.00 0.00 3.01
3889 4689 2.869503 TTTCCCCGCTCCGCAGATTC 62.870 60.000 0.00 0.00 0.00 2.52
3890 4690 2.966732 TTTCCCCGCTCCGCAGATT 61.967 57.895 0.00 0.00 0.00 2.40
3891 4691 3.399181 TTTCCCCGCTCCGCAGAT 61.399 61.111 0.00 0.00 0.00 2.90
3892 4692 4.388499 GTTTCCCCGCTCCGCAGA 62.388 66.667 0.00 0.00 0.00 4.26
3893 4693 4.394712 AGTTTCCCCGCTCCGCAG 62.395 66.667 0.00 0.00 0.00 5.18
3894 4694 4.697756 CAGTTTCCCCGCTCCGCA 62.698 66.667 0.00 0.00 0.00 5.69
3896 4696 4.697756 TGCAGTTTCCCCGCTCCG 62.698 66.667 0.00 0.00 0.00 4.63
3897 4697 2.747855 CTGCAGTTTCCCCGCTCC 60.748 66.667 5.25 0.00 0.00 4.70
3898 4698 3.435186 GCTGCAGTTTCCCCGCTC 61.435 66.667 16.64 0.00 0.00 5.03
3899 4699 3.909086 GAGCTGCAGTTTCCCCGCT 62.909 63.158 16.64 3.74 0.00 5.52
3900 4700 3.435186 GAGCTGCAGTTTCCCCGC 61.435 66.667 16.64 0.00 0.00 6.13
3901 4701 2.747855 GGAGCTGCAGTTTCCCCG 60.748 66.667 21.91 0.00 0.00 5.73
3902 4702 2.747855 CGGAGCTGCAGTTTCCCC 60.748 66.667 24.65 13.31 0.00 4.81
3927 4727 3.649277 CTCCACAACTCCGCTCCCG 62.649 68.421 0.00 0.00 0.00 5.14
3928 4728 2.266055 CTCCACAACTCCGCTCCC 59.734 66.667 0.00 0.00 0.00 4.30
3929 4729 2.435059 GCTCCACAACTCCGCTCC 60.435 66.667 0.00 0.00 0.00 4.70
3930 4730 2.811317 CGCTCCACAACTCCGCTC 60.811 66.667 0.00 0.00 0.00 5.03
3931 4731 4.379243 CCGCTCCACAACTCCGCT 62.379 66.667 0.00 0.00 0.00 5.52
3932 4732 4.373116 TCCGCTCCACAACTCCGC 62.373 66.667 0.00 0.00 0.00 5.54
3933 4733 2.125912 CTCCGCTCCACAACTCCG 60.126 66.667 0.00 0.00 0.00 4.63
3934 4734 2.435059 GCTCCGCTCCACAACTCC 60.435 66.667 0.00 0.00 0.00 3.85
3935 4735 1.301716 TTGCTCCGCTCCACAACTC 60.302 57.895 0.00 0.00 0.00 3.01
3936 4736 1.598130 GTTGCTCCGCTCCACAACT 60.598 57.895 0.00 0.00 39.39 3.16
3937 4737 1.891919 TGTTGCTCCGCTCCACAAC 60.892 57.895 0.00 0.00 42.10 3.32
3938 4738 1.891919 GTGTTGCTCCGCTCCACAA 60.892 57.895 0.00 0.00 32.92 3.33
3939 4739 2.280797 GTGTTGCTCCGCTCCACA 60.281 61.111 0.00 0.00 32.92 4.17
3940 4740 3.050275 GGTGTTGCTCCGCTCCAC 61.050 66.667 0.00 0.00 32.29 4.02
3941 4741 4.680237 CGGTGTTGCTCCGCTCCA 62.680 66.667 0.00 0.00 41.48 3.86
3942 4742 3.876589 TTCGGTGTTGCTCCGCTCC 62.877 63.158 4.94 0.00 46.49 4.70
3943 4743 2.357034 TTCGGTGTTGCTCCGCTC 60.357 61.111 4.94 0.00 46.49 5.03
3944 4744 2.665185 GTTCGGTGTTGCTCCGCT 60.665 61.111 4.94 0.00 46.49 5.52
3945 4745 2.954753 CTGTTCGGTGTTGCTCCGC 61.955 63.158 4.94 0.00 46.49 5.54
3947 4747 1.966451 CCCTGTTCGGTGTTGCTCC 60.966 63.158 0.00 0.00 0.00 4.70
3948 4748 2.617274 GCCCTGTTCGGTGTTGCTC 61.617 63.158 0.00 0.00 0.00 4.26
3949 4749 2.594592 GCCCTGTTCGGTGTTGCT 60.595 61.111 0.00 0.00 0.00 3.91
3950 4750 3.670377 GGCCCTGTTCGGTGTTGC 61.670 66.667 0.00 0.00 0.00 4.17
3951 4751 0.250553 TAAGGCCCTGTTCGGTGTTG 60.251 55.000 0.00 0.00 0.00 3.33
3952 4752 0.036306 CTAAGGCCCTGTTCGGTGTT 59.964 55.000 0.00 0.00 0.00 3.32
3953 4753 1.125711 ACTAAGGCCCTGTTCGGTGT 61.126 55.000 0.00 0.00 0.00 4.16
3954 4754 0.673644 CACTAAGGCCCTGTTCGGTG 60.674 60.000 0.00 0.00 0.00 4.94
3955 4755 1.125711 ACACTAAGGCCCTGTTCGGT 61.126 55.000 0.00 0.00 0.00 4.69
3956 4756 0.899720 TACACTAAGGCCCTGTTCGG 59.100 55.000 0.00 0.00 0.00 4.30
3957 4757 1.274167 TGTACACTAAGGCCCTGTTCG 59.726 52.381 0.00 0.00 0.00 3.95
3958 4758 3.270877 CATGTACACTAAGGCCCTGTTC 58.729 50.000 0.00 0.00 0.00 3.18
3959 4759 2.026262 CCATGTACACTAAGGCCCTGTT 60.026 50.000 0.00 0.00 0.00 3.16
3960 4760 1.559682 CCATGTACACTAAGGCCCTGT 59.440 52.381 0.00 0.00 0.00 4.00
3961 4761 1.559682 ACCATGTACACTAAGGCCCTG 59.440 52.381 0.00 0.00 0.00 4.45
3962 4762 1.966845 ACCATGTACACTAAGGCCCT 58.033 50.000 0.00 0.00 0.00 5.19
3963 4763 2.640184 GAACCATGTACACTAAGGCCC 58.360 52.381 0.00 0.00 0.00 5.80
3964 4764 2.026636 TGGAACCATGTACACTAAGGCC 60.027 50.000 0.00 0.00 0.00 5.19
3965 4765 3.007635 GTGGAACCATGTACACTAAGGC 58.992 50.000 0.00 0.00 0.00 4.35
3966 4766 4.280436 TGTGGAACCATGTACACTAAGG 57.720 45.455 0.00 0.46 34.36 2.69
3983 4783 6.309251 ACTTGTTTATTTGACGTTGTTTGTGG 59.691 34.615 0.00 0.00 0.00 4.17
4047 4880 6.862209 TGTGTATGCAATTTAGGATGGTTTC 58.138 36.000 0.00 0.00 0.00 2.78
4073 4906 3.995199 TGAGCTTTGTCGAATGAGAGTT 58.005 40.909 0.00 0.00 0.00 3.01
4074 4907 3.667497 TGAGCTTTGTCGAATGAGAGT 57.333 42.857 0.00 0.00 0.00 3.24
4075 4908 5.347342 AGTATGAGCTTTGTCGAATGAGAG 58.653 41.667 0.00 0.00 0.00 3.20
4076 4909 5.330455 AGTATGAGCTTTGTCGAATGAGA 57.670 39.130 0.00 0.00 0.00 3.27
4077 4910 7.063426 TGTTAAGTATGAGCTTTGTCGAATGAG 59.937 37.037 0.00 0.00 0.00 2.90
4078 4911 6.871492 TGTTAAGTATGAGCTTTGTCGAATGA 59.129 34.615 0.00 0.00 0.00 2.57
4079 4912 7.060600 TGTTAAGTATGAGCTTTGTCGAATG 57.939 36.000 0.00 0.00 0.00 2.67
4080 4913 7.849804 ATGTTAAGTATGAGCTTTGTCGAAT 57.150 32.000 0.00 0.00 0.00 3.34
4081 4914 7.386573 TGAATGTTAAGTATGAGCTTTGTCGAA 59.613 33.333 0.00 0.00 0.00 3.71
4278 5111 1.202746 GCCTTGGAGCCTAGGATTGAG 60.203 57.143 19.19 5.62 40.55 3.02
4312 5145 2.057922 TCCACTCCCTTTTGCTCTCTT 58.942 47.619 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.