Multiple sequence alignment - TraesCS4D01G227500

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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 TraesCS4D01G227500 chr4D 100.000 3829 0 0 1 3829 386829999 386833827 0.000000e+00 7071.0
1 TraesCS4D01G227500 chr4B 91.408 3061 126 55 6 2997 474377407 474380399 0.000000e+00 4069.0
2 TraesCS4D01G227500 chr4B 90.282 638 26 19 3216 3829 474380433 474381058 0.000000e+00 802.0
3 TraesCS4D01G227500 chr4B 99.329 149 1 0 2998 3146 60366712 60366860 1.750000e-68 270.0
4 TraesCS4D01G227500 chr4B 74.341 569 97 31 1295 1828 494692231 494691677 3.020000e-46 196.0
5 TraesCS4D01G227500 chr4B 97.959 49 0 1 3143 3190 474380384 474380432 2.450000e-12 84.2
6 TraesCS4D01G227500 chr4A 89.457 3073 136 53 5 2997 68140294 68143258 0.000000e+00 3707.0
7 TraesCS4D01G227500 chr4A 85.877 701 50 23 3143 3826 68143243 68143911 0.000000e+00 701.0
8 TraesCS4D01G227500 chr2D 82.182 724 93 26 1150 1846 131777776 131777062 1.180000e-164 590.0
9 TraesCS4D01G227500 chr2D 100.000 28 0 0 2720 2747 131776486 131776459 7.000000e-03 52.8
10 TraesCS4D01G227500 chr2B 82.019 723 96 25 1150 1846 186311856 186312570 5.510000e-163 584.0
11 TraesCS4D01G227500 chr2B 87.018 285 35 2 1563 1846 185776816 185776533 1.720000e-83 320.0
12 TraesCS4D01G227500 chr2B 100.000 28 0 0 2720 2747 185775988 185775961 7.000000e-03 52.8
13 TraesCS4D01G227500 chr2B 96.774 31 1 0 2717 2747 186313105 186313135 7.000000e-03 52.8
14 TraesCS4D01G227500 chr2A 81.302 722 103 27 1150 1846 138827332 138826618 1.200000e-154 556.0
15 TraesCS4D01G227500 chr2A 100.000 154 0 0 2995 3148 5680322 5680475 6.260000e-73 285.0
16 TraesCS4D01G227500 chr2A 100.000 28 0 0 2720 2747 138826121 138826094 7.000000e-03 52.8
17 TraesCS4D01G227500 chr5B 77.530 672 112 28 1167 1829 512212665 512213306 6.040000e-98 368.0
18 TraesCS4D01G227500 chr5B 100.000 153 0 0 2996 3148 234875998 234875846 2.250000e-72 283.0
19 TraesCS4D01G227500 chr5B 74.118 680 121 36 1200 1829 656925821 656926495 2.980000e-56 230.0
20 TraesCS4D01G227500 chr5D 77.434 678 108 32 1167 1829 424033304 424033951 2.810000e-96 363.0
21 TraesCS4D01G227500 chr5D 76.061 660 119 25 1200 1829 520910025 520910675 1.340000e-79 307.0
22 TraesCS4D01G227500 chr5A 77.198 671 116 25 1167 1829 537626132 537626773 1.310000e-94 357.0
23 TraesCS4D01G227500 chr5A 100.000 152 0 0 2997 3148 689253229 689253380 8.100000e-72 281.0
24 TraesCS4D01G227500 chr5A 75.112 671 121 29 1200 1829 649441485 649442150 4.870000e-69 272.0
25 TraesCS4D01G227500 chr6A 98.802 167 2 0 2991 3157 550731856 550732022 8.040000e-77 298.0
26 TraesCS4D01G227500 chr6D 100.000 155 0 0 2994 3148 408219821 408219975 1.740000e-73 287.0
27 TraesCS4D01G227500 chr7A 98.734 158 1 1 2992 3148 565750360 565750517 2.910000e-71 279.0
28 TraesCS4D01G227500 chr7A 72.014 561 110 33 1294 1829 631365246 631365784 5.190000e-24 122.0
29 TraesCS4D01G227500 chr3B 99.351 154 1 0 2996 3149 53136962 53137115 2.910000e-71 279.0
30 TraesCS4D01G227500 chr1B 100.000 151 0 0 2998 3148 144729960 144729810 2.910000e-71 279.0
31 TraesCS4D01G227500 chr7D 72.321 560 107 36 1295 1829 547458020 547457484 8.630000e-27 132.0
32 TraesCS4D01G227500 chr7B 71.429 560 115 34 1294 1829 590500947 590500409 5.230000e-19 106.0


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 TraesCS4D01G227500 chr4D 386829999 386833827 3828 False 7071.000000 7071 100.000000 1 3829 1 chr4D.!!$F1 3828
1 TraesCS4D01G227500 chr4B 474377407 474381058 3651 False 1651.733333 4069 93.216333 6 3829 3 chr4B.!!$F2 3823
2 TraesCS4D01G227500 chr4A 68140294 68143911 3617 False 2204.000000 3707 87.667000 5 3826 2 chr4A.!!$F1 3821
3 TraesCS4D01G227500 chr2D 131776459 131777776 1317 True 321.400000 590 91.091000 1150 2747 2 chr2D.!!$R1 1597
4 TraesCS4D01G227500 chr2B 186311856 186313135 1279 False 318.400000 584 89.396500 1150 2747 2 chr2B.!!$F1 1597
5 TraesCS4D01G227500 chr2A 138826094 138827332 1238 True 304.400000 556 90.651000 1150 2747 2 chr2A.!!$R1 1597
6 TraesCS4D01G227500 chr5B 512212665 512213306 641 False 368.000000 368 77.530000 1167 1829 1 chr5B.!!$F1 662
7 TraesCS4D01G227500 chr5B 656925821 656926495 674 False 230.000000 230 74.118000 1200 1829 1 chr5B.!!$F2 629
8 TraesCS4D01G227500 chr5D 424033304 424033951 647 False 363.000000 363 77.434000 1167 1829 1 chr5D.!!$F1 662
9 TraesCS4D01G227500 chr5D 520910025 520910675 650 False 307.000000 307 76.061000 1200 1829 1 chr5D.!!$F2 629
10 TraesCS4D01G227500 chr5A 537626132 537626773 641 False 357.000000 357 77.198000 1167 1829 1 chr5A.!!$F1 662
11 TraesCS4D01G227500 chr5A 649441485 649442150 665 False 272.000000 272 75.112000 1200 1829 1 chr5A.!!$F2 629

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
816 839 0.106419 CCTAGGCCGAGACTTCTCCT 60.106 60.0 15.38 0.0 39.79 3.69 F
978 1019 0.107831 GTGACCACCAGCACTAACCA 59.892 55.0 0.00 0.0 32.44 3.67 F
2031 2172 0.030638 CTTTGGTTGGTGCCTGAACG 59.969 55.0 0.00 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 2153 0.030638 CGTTCAGGCACCAACCAAAG 59.969 55.0 0.00 0.0 0.0 2.77 R
2107 2249 0.107831 TCACTGTCCCCTTCCGTTTG 59.892 55.0 0.00 0.0 0.0 2.93 R
3128 3513 0.525455 CAGCGCTGCTATACACACGA 60.525 55.0 26.68 0.0 36.4 4.35 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
27 28 7.358830 CCATTCAGTTTTCAGTCTTCTCTTTC 58.641 38.462 0.00 0.00 0.00 2.62
39 40 6.648310 CAGTCTTCTCTTTCTGCACTGAATTA 59.352 38.462 0.00 0.00 33.10 1.40
40 41 7.172190 CAGTCTTCTCTTTCTGCACTGAATTAA 59.828 37.037 0.00 0.00 33.10 1.40
41 42 7.716998 AGTCTTCTCTTTCTGCACTGAATTAAA 59.283 33.333 0.00 0.00 0.00 1.52
108 109 1.683917 ACCGAGATATGACAGTCCAGC 59.316 52.381 0.00 0.00 0.00 4.85
214 218 6.226787 TCTTCAGTTTTCCATCTCTCTCAAC 58.773 40.000 0.00 0.00 0.00 3.18
232 236 3.058983 TCAACACATTTACTGCTCGCTTG 60.059 43.478 0.00 0.00 0.00 4.01
330 345 4.059511 TGCATTCAGCCAACAAGATTTTG 58.940 39.130 0.00 0.00 44.83 2.44
465 483 1.334869 CTGCCAAAAGATACGGCCATC 59.665 52.381 2.24 0.00 45.63 3.51
466 484 1.340502 TGCCAAAAGATACGGCCATCA 60.341 47.619 2.24 0.00 45.63 3.07
494 512 3.116959 ACCAAACCCCGATACAATCCTA 58.883 45.455 0.00 0.00 0.00 2.94
495 513 3.720002 ACCAAACCCCGATACAATCCTAT 59.280 43.478 0.00 0.00 0.00 2.57
498 516 4.635699 AACCCCGATACAATCCTATTCC 57.364 45.455 0.00 0.00 0.00 3.01
499 517 3.870559 ACCCCGATACAATCCTATTCCT 58.129 45.455 0.00 0.00 0.00 3.36
504 522 5.344066 CCGATACAATCCTATTCCTGATCG 58.656 45.833 0.00 0.00 34.83 3.69
516 534 3.371102 TCCTGATCGATCGTGGAAATC 57.629 47.619 27.19 10.65 32.00 2.17
521 539 0.454196 TCGATCGTGGAAATCGCAGA 59.546 50.000 15.94 0.00 44.32 4.26
601 619 2.626743 CTGAATCCAATCAAGCCCCATC 59.373 50.000 0.00 0.00 0.00 3.51
645 663 4.766373 TGAAAGCATGATAAAAGCTGGTCA 59.234 37.500 0.00 0.00 38.86 4.02
646 664 4.978083 AAGCATGATAAAAGCTGGTCAG 57.022 40.909 0.00 0.00 38.86 3.51
647 665 3.285484 AGCATGATAAAAGCTGGTCAGG 58.715 45.455 0.00 0.00 37.20 3.86
648 666 3.019564 GCATGATAAAAGCTGGTCAGGT 58.980 45.455 0.00 0.00 41.53 4.00
649 667 3.065925 GCATGATAAAAGCTGGTCAGGTC 59.934 47.826 0.00 0.00 38.35 3.85
668 686 1.078759 CAGTGAACGGCCGCTCTTAG 61.079 60.000 28.58 12.43 0.00 2.18
734 752 3.325753 GCTCCCTGCACCTCTGGT 61.326 66.667 0.00 0.00 42.31 4.00
749 767 1.958902 CTGGTCTCTGCCTCTGCCTC 61.959 65.000 0.00 0.00 36.33 4.70
750 768 1.685421 GGTCTCTGCCTCTGCCTCT 60.685 63.158 0.00 0.00 36.33 3.69
751 769 1.516892 GTCTCTGCCTCTGCCTCTG 59.483 63.158 0.00 0.00 36.33 3.35
752 770 2.187424 CTCTGCCTCTGCCTCTGC 59.813 66.667 0.00 0.00 36.33 4.26
753 771 3.388703 CTCTGCCTCTGCCTCTGCC 62.389 68.421 0.00 0.00 36.33 4.85
754 772 3.400928 CTGCCTCTGCCTCTGCCT 61.401 66.667 0.00 0.00 36.33 4.75
757 775 2.901813 CCTCTGCCTCTGCCTCTG 59.098 66.667 0.00 0.00 36.33 3.35
815 838 0.106619 TCCTAGGCCGAGACTTCTCC 60.107 60.000 15.38 0.00 39.79 3.71
816 839 0.106419 CCTAGGCCGAGACTTCTCCT 60.106 60.000 15.38 0.00 39.79 3.69
817 840 1.314730 CTAGGCCGAGACTTCTCCTC 58.685 60.000 7.14 0.00 39.79 3.71
973 1014 1.003580 CCATTAGTGACCACCAGCACT 59.996 52.381 0.00 0.00 46.31 4.40
978 1019 0.107831 GTGACCACCAGCACTAACCA 59.892 55.000 0.00 0.00 32.44 3.67
1008 1054 5.484715 CATTGCTTCAAGAACATGGGAATT 58.515 37.500 0.00 0.00 0.00 2.17
1020 1066 5.473066 ACATGGGAATTCAAAGAGTTTGG 57.527 39.130 7.93 0.00 40.98 3.28
1044 1090 0.804364 TCCTTGCGCTGCTTTGTATG 59.196 50.000 9.73 0.00 0.00 2.39
1076 1122 3.364764 GGTAATTCGATCGTCGTAGAGGG 60.365 52.174 15.94 0.00 43.36 4.30
1078 1124 1.293924 TTCGATCGTCGTAGAGGGAC 58.706 55.000 15.94 0.00 43.36 4.46
1092 1138 1.807814 AGGGACTCTGTGTTGGAAGT 58.192 50.000 0.00 0.00 0.00 3.01
1094 1140 3.314693 AGGGACTCTGTGTTGGAAGTTA 58.685 45.455 0.00 0.00 0.00 2.24
1095 1141 3.714798 AGGGACTCTGTGTTGGAAGTTAA 59.285 43.478 0.00 0.00 0.00 2.01
1096 1142 4.065789 GGGACTCTGTGTTGGAAGTTAAG 58.934 47.826 0.00 0.00 0.00 1.85
1097 1143 4.444449 GGGACTCTGTGTTGGAAGTTAAGT 60.444 45.833 0.00 0.00 0.00 2.24
1098 1144 5.123936 GGACTCTGTGTTGGAAGTTAAGTT 58.876 41.667 0.00 0.00 0.00 2.66
1100 1146 5.497474 ACTCTGTGTTGGAAGTTAAGTTGT 58.503 37.500 0.00 0.00 0.00 3.32
1101 1147 6.646267 ACTCTGTGTTGGAAGTTAAGTTGTA 58.354 36.000 0.00 0.00 0.00 2.41
1103 1149 6.053005 TCTGTGTTGGAAGTTAAGTTGTAGG 58.947 40.000 0.00 0.00 0.00 3.18
1104 1150 5.991861 TGTGTTGGAAGTTAAGTTGTAGGA 58.008 37.500 0.00 0.00 0.00 2.94
1105 1151 6.053005 TGTGTTGGAAGTTAAGTTGTAGGAG 58.947 40.000 0.00 0.00 0.00 3.69
1145 1198 5.885881 ACATCGTATTTGTGTTGTGTTTGT 58.114 33.333 0.00 0.00 0.00 2.83
1854 1970 0.120377 ACCCCAAGGTCCATACTCCA 59.880 55.000 0.00 0.00 46.45 3.86
1855 1971 1.275002 ACCCCAAGGTCCATACTCCAT 60.275 52.381 0.00 0.00 46.45 3.41
1856 1972 1.143684 CCCCAAGGTCCATACTCCATG 59.856 57.143 0.00 0.00 0.00 3.66
1858 1974 1.477558 CCAAGGTCCATACTCCATGCC 60.478 57.143 0.00 0.00 32.84 4.40
1859 1975 0.846693 AAGGTCCATACTCCATGCCC 59.153 55.000 0.00 0.00 32.84 5.36
1860 1976 0.327480 AGGTCCATACTCCATGCCCA 60.327 55.000 0.00 0.00 32.84 5.36
1863 1979 0.623031 TCCATACTCCATGCCCACCA 60.623 55.000 0.00 0.00 32.84 4.17
1864 1980 0.466189 CCATACTCCATGCCCACCAC 60.466 60.000 0.00 0.00 32.84 4.16
1884 2017 0.243636 GCGCCTTAACCACTGCATTT 59.756 50.000 0.00 0.00 0.00 2.32
1885 2018 1.470890 GCGCCTTAACCACTGCATTTA 59.529 47.619 0.00 0.00 0.00 1.40
1886 2019 2.731027 GCGCCTTAACCACTGCATTTAC 60.731 50.000 0.00 0.00 0.00 2.01
1902 2038 7.439655 ACTGCATTTACTAATCACTAGCTAAGC 59.560 37.037 0.00 0.00 0.00 3.09
2031 2172 0.030638 CTTTGGTTGGTGCCTGAACG 59.969 55.000 0.00 0.00 0.00 3.95
2107 2249 0.032952 TCCGATATGCCGTGCTTACC 59.967 55.000 0.00 0.00 0.00 2.85
2163 2311 5.596772 TGGAAGATGATGCATTGTGATGATT 59.403 36.000 0.00 0.00 35.16 2.57
2172 2320 4.877823 TGCATTGTGATGATTAGTCTGGAC 59.122 41.667 0.00 0.00 35.16 4.02
2173 2321 5.121811 GCATTGTGATGATTAGTCTGGACT 58.878 41.667 8.36 8.36 39.22 3.85
2174 2322 5.007430 GCATTGTGATGATTAGTCTGGACTG 59.993 44.000 12.87 0.00 37.57 3.51
2175 2323 4.743057 TGTGATGATTAGTCTGGACTGG 57.257 45.455 12.87 0.00 42.52 4.00
2176 2324 4.352893 TGTGATGATTAGTCTGGACTGGA 58.647 43.478 12.87 2.93 42.52 3.86
2268 2446 1.152546 GGTTTGACCCCTGTGGCTT 60.153 57.895 0.00 0.00 37.83 4.35
2277 2455 2.091555 ACCCCTGTGGCTTTCACTTTTA 60.092 45.455 0.00 0.00 46.20 1.52
2278 2456 2.296190 CCCCTGTGGCTTTCACTTTTAC 59.704 50.000 0.00 0.00 46.20 2.01
2279 2457 3.222603 CCCTGTGGCTTTCACTTTTACT 58.777 45.455 0.00 0.00 46.20 2.24
2306 2485 1.601903 GGTTTGCACATCAACGTCAGA 59.398 47.619 0.00 0.00 33.73 3.27
2318 2506 2.955402 GTCAGACGTCGGAGCAGT 59.045 61.111 18.96 0.00 0.00 4.40
2346 2534 5.471456 GGGCAGTCATATTCTTATCTTGTGG 59.529 44.000 0.00 0.00 0.00 4.17
2356 2544 6.419484 TTCTTATCTTGTGGTGAAGTCAGA 57.581 37.500 0.00 0.00 0.00 3.27
2495 2683 7.928307 TTATGTTTCTCCTGATCCTCTTTTG 57.072 36.000 0.00 0.00 0.00 2.44
2529 2719 0.028505 GCGTGCATTCATTCGAGCAT 59.971 50.000 0.00 0.00 39.43 3.79
2530 2720 1.532505 GCGTGCATTCATTCGAGCATT 60.533 47.619 0.00 0.00 39.43 3.56
2535 2725 2.852143 GCATTCATTCGAGCATTCACCG 60.852 50.000 0.00 0.00 0.00 4.94
2561 2751 3.515630 GAGCATCTGATCGTGAACTCAA 58.484 45.455 12.69 0.00 0.00 3.02
2997 3382 4.148645 GGCGCTCGCGGAAAGAAC 62.149 66.667 13.56 0.00 43.06 3.01
2998 3383 4.485208 GCGCTCGCGGAAAGAACG 62.485 66.667 13.56 0.97 40.19 3.95
2999 3384 2.803670 CGCTCGCGGAAAGAACGA 60.804 61.111 6.13 0.00 35.56 3.85
3000 3385 2.369629 CGCTCGCGGAAAGAACGAA 61.370 57.895 6.13 0.00 35.07 3.85
3001 3386 1.857364 GCTCGCGGAAAGAACGAAA 59.143 52.632 6.13 0.00 35.07 3.46
3002 3387 0.450645 GCTCGCGGAAAGAACGAAAC 60.451 55.000 6.13 0.00 35.07 2.78
3003 3388 1.137513 CTCGCGGAAAGAACGAAACT 58.862 50.000 6.13 0.00 35.07 2.66
3004 3389 0.856641 TCGCGGAAAGAACGAAACTG 59.143 50.000 6.13 0.00 31.97 3.16
3005 3390 0.721483 CGCGGAAAGAACGAAACTGC 60.721 55.000 0.00 0.00 0.00 4.40
3006 3391 0.586802 GCGGAAAGAACGAAACTGCT 59.413 50.000 0.00 0.00 0.00 4.24
3007 3392 1.796459 GCGGAAAGAACGAAACTGCTA 59.204 47.619 0.00 0.00 0.00 3.49
3008 3393 2.411160 GCGGAAAGAACGAAACTGCTAC 60.411 50.000 0.00 0.00 0.00 3.58
3009 3394 2.160013 CGGAAAGAACGAAACTGCTACG 60.160 50.000 0.00 0.00 0.00 3.51
3010 3395 2.798847 GGAAAGAACGAAACTGCTACGT 59.201 45.455 0.00 0.00 41.97 3.57
3011 3396 3.983344 GGAAAGAACGAAACTGCTACGTA 59.017 43.478 0.00 0.00 39.31 3.57
3012 3397 4.089636 GGAAAGAACGAAACTGCTACGTAG 59.910 45.833 18.47 18.47 39.31 3.51
3013 3398 4.494350 AAGAACGAAACTGCTACGTAGA 57.506 40.909 26.53 10.25 39.31 2.59
3014 3399 3.819537 AGAACGAAACTGCTACGTAGAC 58.180 45.455 26.53 16.83 39.31 2.59
3015 3400 2.238245 ACGAAACTGCTACGTAGACG 57.762 50.000 26.53 19.42 46.33 4.18
3016 3401 1.800586 ACGAAACTGCTACGTAGACGA 59.199 47.619 26.53 7.89 43.02 4.20
3017 3402 2.417933 ACGAAACTGCTACGTAGACGAT 59.582 45.455 26.53 7.56 43.02 3.73
3018 3403 2.776765 CGAAACTGCTACGTAGACGATG 59.223 50.000 26.53 11.89 43.02 3.84
3019 3404 2.190325 AACTGCTACGTAGACGATGC 57.810 50.000 26.53 10.90 43.02 3.91
3020 3405 1.092348 ACTGCTACGTAGACGATGCA 58.908 50.000 26.53 14.96 43.54 3.96
3021 3406 1.676529 ACTGCTACGTAGACGATGCAT 59.323 47.619 26.53 0.00 44.15 3.96
3022 3407 2.047040 CTGCTACGTAGACGATGCATG 58.953 52.381 26.53 6.96 44.15 4.06
3023 3408 1.404035 TGCTACGTAGACGATGCATGT 59.596 47.619 26.53 2.18 42.12 3.21
3024 3409 1.781429 GCTACGTAGACGATGCATGTG 59.219 52.381 26.53 0.00 43.02 3.21
3025 3410 2.794981 GCTACGTAGACGATGCATGTGT 60.795 50.000 26.53 1.53 43.02 3.72
3026 3411 1.629013 ACGTAGACGATGCATGTGTG 58.371 50.000 2.46 0.00 43.02 3.82
3027 3412 0.298707 CGTAGACGATGCATGTGTGC 59.701 55.000 2.46 4.29 46.44 4.57
3041 3426 4.148230 GTGCACGACACTAGGACG 57.852 61.111 0.00 0.00 46.41 4.79
3042 3427 1.577922 GTGCACGACACTAGGACGA 59.422 57.895 0.00 0.00 46.41 4.20
3043 3428 0.728466 GTGCACGACACTAGGACGAC 60.728 60.000 0.00 0.00 46.41 4.34
3044 3429 1.511464 GCACGACACTAGGACGACG 60.511 63.158 11.20 0.00 0.00 5.12
3045 3430 1.134075 CACGACACTAGGACGACGG 59.866 63.158 0.00 0.00 0.00 4.79
3046 3431 2.037136 ACGACACTAGGACGACGGG 61.037 63.158 0.00 0.00 0.00 5.28
3047 3432 2.488820 GACACTAGGACGACGGGC 59.511 66.667 0.00 0.00 0.00 6.13
3048 3433 2.282674 ACACTAGGACGACGGGCA 60.283 61.111 0.00 0.00 0.00 5.36
3049 3434 2.267681 GACACTAGGACGACGGGCAG 62.268 65.000 0.00 0.00 0.00 4.85
3050 3435 2.035312 ACTAGGACGACGGGCAGT 59.965 61.111 0.00 0.00 0.00 4.40
3051 3436 2.045131 ACTAGGACGACGGGCAGTC 61.045 63.158 7.78 7.78 46.16 3.51
3062 3447 4.479993 GGCAGTCCAGCCGCTGAT 62.480 66.667 22.35 4.46 46.12 2.90
3063 3448 2.501128 GCAGTCCAGCCGCTGATA 59.499 61.111 22.35 6.62 34.87 2.15
3064 3449 1.070445 GCAGTCCAGCCGCTGATAT 59.930 57.895 22.35 3.72 34.87 1.63
3065 3450 1.226686 GCAGTCCAGCCGCTGATATG 61.227 60.000 22.35 16.13 34.87 1.78
3066 3451 1.070445 AGTCCAGCCGCTGATATGC 59.930 57.895 22.35 6.71 32.44 3.14
3076 3461 2.376808 GCTGATATGCGCTGGATAGT 57.623 50.000 9.73 0.00 0.00 2.12
3077 3462 3.510388 GCTGATATGCGCTGGATAGTA 57.490 47.619 9.73 0.00 0.00 1.82
3078 3463 4.052159 GCTGATATGCGCTGGATAGTAT 57.948 45.455 9.73 0.00 0.00 2.12
3079 3464 3.801050 GCTGATATGCGCTGGATAGTATG 59.199 47.826 9.73 0.00 0.00 2.39
3080 3465 3.785486 TGATATGCGCTGGATAGTATGC 58.215 45.455 9.73 0.00 0.00 3.14
3081 3466 3.195396 TGATATGCGCTGGATAGTATGCA 59.805 43.478 9.73 4.13 34.75 3.96
3082 3467 2.775911 ATGCGCTGGATAGTATGCAT 57.224 45.000 9.73 3.79 35.81 3.96
3083 3468 1.799544 TGCGCTGGATAGTATGCATG 58.200 50.000 10.16 2.65 0.00 4.06
3084 3469 1.081892 GCGCTGGATAGTATGCATGG 58.918 55.000 10.16 1.78 0.00 3.66
3085 3470 1.338105 GCGCTGGATAGTATGCATGGA 60.338 52.381 10.16 0.00 0.00 3.41
3086 3471 2.341257 CGCTGGATAGTATGCATGGAC 58.659 52.381 10.16 0.00 0.00 4.02
3087 3472 2.341257 GCTGGATAGTATGCATGGACG 58.659 52.381 10.16 0.00 0.00 4.79
3088 3473 2.932622 GCTGGATAGTATGCATGGACGG 60.933 54.545 10.16 0.11 0.00 4.79
3089 3474 1.001974 TGGATAGTATGCATGGACGGC 59.998 52.381 10.16 0.00 0.00 5.68
3090 3475 1.276421 GGATAGTATGCATGGACGGCT 59.724 52.381 10.16 0.66 0.00 5.52
3091 3476 2.289694 GGATAGTATGCATGGACGGCTT 60.290 50.000 10.16 0.00 0.00 4.35
3092 3477 2.238942 TAGTATGCATGGACGGCTTG 57.761 50.000 10.16 0.00 0.00 4.01
3093 3478 0.541392 AGTATGCATGGACGGCTTGA 59.459 50.000 10.16 0.00 0.00 3.02
3094 3479 1.141657 AGTATGCATGGACGGCTTGAT 59.858 47.619 10.16 0.00 0.00 2.57
3095 3480 2.368548 AGTATGCATGGACGGCTTGATA 59.631 45.455 10.16 0.00 0.00 2.15
3096 3481 2.574006 ATGCATGGACGGCTTGATAT 57.426 45.000 0.00 0.00 0.00 1.63
3097 3482 1.596603 TGCATGGACGGCTTGATATG 58.403 50.000 0.00 0.00 0.00 1.78
3098 3483 1.134128 TGCATGGACGGCTTGATATGT 60.134 47.619 0.00 0.00 0.00 2.29
3099 3484 1.265095 GCATGGACGGCTTGATATGTG 59.735 52.381 0.00 0.00 0.00 3.21
3100 3485 1.265095 CATGGACGGCTTGATATGTGC 59.735 52.381 0.00 0.00 0.00 4.57
3101 3486 0.541392 TGGACGGCTTGATATGTGCT 59.459 50.000 0.00 0.00 0.00 4.40
3102 3487 0.940126 GGACGGCTTGATATGTGCTG 59.060 55.000 0.00 0.00 38.86 4.41
3103 3488 3.861341 ACGGCTTGATATGTGCTGT 57.139 47.368 0.00 0.00 40.94 4.40
3104 3489 1.656652 ACGGCTTGATATGTGCTGTC 58.343 50.000 0.00 0.00 41.84 3.51
3105 3490 0.578683 CGGCTTGATATGTGCTGTCG 59.421 55.000 0.00 0.00 0.00 4.35
3106 3491 1.656652 GGCTTGATATGTGCTGTCGT 58.343 50.000 0.00 0.00 0.00 4.34
3107 3492 1.328680 GGCTTGATATGTGCTGTCGTG 59.671 52.381 0.00 0.00 0.00 4.35
3108 3493 1.267732 GCTTGATATGTGCTGTCGTGC 60.268 52.381 0.00 0.00 0.00 5.34
3109 3494 2.001872 CTTGATATGTGCTGTCGTGCA 58.998 47.619 0.00 0.00 41.05 4.57
3120 3505 4.379143 TCGTGCACGAGTCGTCCG 62.379 66.667 36.40 17.53 44.22 4.79
3122 3507 4.994201 GTGCACGAGTCGTCCGCA 62.994 66.667 22.41 22.41 38.32 5.69
3123 3508 4.994201 TGCACGAGTCGTCCGCAC 62.994 66.667 22.41 8.85 38.32 5.34
3140 3525 3.597162 CGGCGTCGTGTGTATAGC 58.403 61.111 0.00 0.00 0.00 2.97
3141 3526 1.226463 CGGCGTCGTGTGTATAGCA 60.226 57.895 0.00 0.00 0.00 3.49
3142 3527 1.200474 CGGCGTCGTGTGTATAGCAG 61.200 60.000 0.00 0.00 0.00 4.24
3143 3528 1.480219 GGCGTCGTGTGTATAGCAGC 61.480 60.000 0.00 0.00 0.00 5.25
3144 3529 1.798368 GCGTCGTGTGTATAGCAGCG 61.798 60.000 0.00 0.00 0.00 5.18
3145 3530 1.798368 CGTCGTGTGTATAGCAGCGC 61.798 60.000 0.00 0.00 0.00 5.92
3146 3531 0.525668 GTCGTGTGTATAGCAGCGCT 60.526 55.000 2.64 2.64 43.41 5.92
3147 3532 0.525455 TCGTGTGTATAGCAGCGCTG 60.525 55.000 32.83 32.83 40.10 5.18
3242 3627 6.295462 CCATTGTAAAATCCATCCATCCATCC 60.295 42.308 0.00 0.00 0.00 3.51
3243 3628 5.400552 TGTAAAATCCATCCATCCATCCA 57.599 39.130 0.00 0.00 0.00 3.41
3245 3630 6.012113 TGTAAAATCCATCCATCCATCCATC 58.988 40.000 0.00 0.00 0.00 3.51
3247 3632 5.349738 AAATCCATCCATCCATCCATCTT 57.650 39.130 0.00 0.00 0.00 2.40
3248 3633 5.349738 AATCCATCCATCCATCCATCTTT 57.650 39.130 0.00 0.00 0.00 2.52
3249 3634 4.819702 TCCATCCATCCATCCATCTTTT 57.180 40.909 0.00 0.00 0.00 2.27
3250 3635 5.146868 TCCATCCATCCATCCATCTTTTT 57.853 39.130 0.00 0.00 0.00 1.94
3251 3636 5.142639 TCCATCCATCCATCCATCTTTTTC 58.857 41.667 0.00 0.00 0.00 2.29
3252 3637 4.897076 CCATCCATCCATCCATCTTTTTCA 59.103 41.667 0.00 0.00 0.00 2.69
3259 3644 7.310237 CCATCCATCCATCTTTTTCAGTTTTCT 60.310 37.037 0.00 0.00 0.00 2.52
3263 3648 8.768019 CCATCCATCTTTTTCAGTTTTCTTTTC 58.232 33.333 0.00 0.00 0.00 2.29
3392 3815 2.427232 TTGTATATACGCACTCGCCC 57.573 50.000 8.33 0.00 39.84 6.13
3441 3881 4.441634 GGCGAACACACTATAACCTGATCT 60.442 45.833 0.00 0.00 0.00 2.75
3445 3885 6.363626 CGAACACACTATAACCTGATCTATGC 59.636 42.308 0.00 0.00 0.00 3.14
3446 3886 6.731292 ACACACTATAACCTGATCTATGCA 57.269 37.500 0.00 0.00 0.00 3.96
3483 3923 1.516892 CTCTCAGCTGTCAGAGGCC 59.483 63.158 19.92 0.00 33.69 5.19
3508 3948 2.998670 CCTGGTCAAGCTATGATATGCG 59.001 50.000 0.00 0.00 40.97 4.73
3612 4053 1.402968 AGTGTCACAGTGCTTTGCTTG 59.597 47.619 5.62 0.00 0.00 4.01
3624 4065 4.268939 TGCTTGCCGCACTGTTGC 62.269 61.111 0.00 0.00 45.47 4.17
3637 4078 2.034124 ACTGTTGCTGTGGCTGATTTT 58.966 42.857 0.00 0.00 39.59 1.82
3647 4088 3.509575 TGTGGCTGATTTTCCATAACCAC 59.490 43.478 0.00 0.00 45.16 4.16
3648 4089 3.509575 GTGGCTGATTTTCCATAACCACA 59.490 43.478 0.00 0.00 44.50 4.17
3761 4206 0.575859 CTCGCAGCTGATGATTGACG 59.424 55.000 20.43 8.92 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.759183 AGAGAAGACTGAAAACTGAATGGC 59.241 41.667 0.00 0.00 0.00 4.40
2 3 6.874288 AAGAGAAGACTGAAAACTGAATGG 57.126 37.500 0.00 0.00 0.00 3.16
5 6 6.037610 GCAGAAAGAGAAGACTGAAAACTGAA 59.962 38.462 0.00 0.00 32.90 3.02
7 8 5.295292 TGCAGAAAGAGAAGACTGAAAACTG 59.705 40.000 0.00 0.00 32.90 3.16
8 9 5.295540 GTGCAGAAAGAGAAGACTGAAAACT 59.704 40.000 0.00 0.00 32.90 2.66
9 10 5.295540 AGTGCAGAAAGAGAAGACTGAAAAC 59.704 40.000 0.00 0.00 32.90 2.43
27 28 7.420800 AGAGTCAAGTTTTTAATTCAGTGCAG 58.579 34.615 0.00 0.00 0.00 4.41
39 40 6.238593 GCTGATGTGAAGAGAGTCAAGTTTTT 60.239 38.462 0.00 0.00 0.00 1.94
40 41 5.238214 GCTGATGTGAAGAGAGTCAAGTTTT 59.762 40.000 0.00 0.00 0.00 2.43
41 42 4.754114 GCTGATGTGAAGAGAGTCAAGTTT 59.246 41.667 0.00 0.00 0.00 2.66
108 109 2.032894 CGTACTGTGTGCTTCAGGTTTG 60.033 50.000 0.00 0.00 37.25 2.93
214 218 2.995939 TCTCAAGCGAGCAGTAAATGTG 59.004 45.455 0.00 0.00 39.30 3.21
232 236 1.333791 CCGGTTGTTGCTTCGTTTCTC 60.334 52.381 0.00 0.00 0.00 2.87
330 345 1.004745 TGGAATGGAGGAACCTTGCTC 59.995 52.381 0.00 0.00 43.91 4.26
465 483 2.855514 CGGGGTTTGGTGCTTGGTG 61.856 63.158 0.00 0.00 0.00 4.17
466 484 2.366153 ATCGGGGTTTGGTGCTTGGT 62.366 55.000 0.00 0.00 0.00 3.67
494 512 3.819564 TTTCCACGATCGATCAGGAAT 57.180 42.857 32.82 11.87 39.12 3.01
495 513 3.717707 GATTTCCACGATCGATCAGGAA 58.282 45.455 30.65 30.65 38.24 3.36
498 516 1.453524 GCGATTTCCACGATCGATCAG 59.546 52.381 24.34 18.31 46.93 2.90
499 517 1.202359 TGCGATTTCCACGATCGATCA 60.202 47.619 24.34 4.78 46.93 2.92
504 522 2.209838 TCTCTGCGATTTCCACGATC 57.790 50.000 0.00 0.00 0.00 3.69
516 534 2.029838 AGGGCTAATTGTTCTCTGCG 57.970 50.000 0.00 0.00 0.00 5.18
521 539 4.141914 CGAAGGTCTAGGGCTAATTGTTCT 60.142 45.833 0.00 0.00 0.00 3.01
601 619 5.054477 TCACTTTACTGAAGAAAGAACGGG 58.946 41.667 2.31 0.00 38.77 5.28
645 663 4.681978 GCGGCCGTTCACTGACCT 62.682 66.667 28.70 0.00 0.00 3.85
646 664 4.681978 AGCGGCCGTTCACTGACC 62.682 66.667 28.70 6.22 0.00 4.02
647 665 3.112709 GAGCGGCCGTTCACTGAC 61.113 66.667 33.62 12.02 0.00 3.51
648 666 1.529152 TAAGAGCGGCCGTTCACTGA 61.529 55.000 38.03 20.09 0.00 3.41
649 667 1.078759 CTAAGAGCGGCCGTTCACTG 61.079 60.000 38.03 24.27 0.00 3.66
668 686 2.026636 TCCATGGCCGTATTTATAGCCC 60.027 50.000 6.96 0.00 45.14 5.19
734 752 2.357575 GCAGAGGCAGAGGCAGAGA 61.358 63.158 0.00 0.00 43.71 3.10
749 767 3.237746 TCAGGATTAGGATCAGAGGCAG 58.762 50.000 0.00 0.00 33.77 4.85
750 768 3.334910 TCAGGATTAGGATCAGAGGCA 57.665 47.619 0.00 0.00 33.77 4.75
751 769 5.022787 ACTATCAGGATTAGGATCAGAGGC 58.977 45.833 0.00 0.00 33.77 4.70
752 770 7.552050 AAACTATCAGGATTAGGATCAGAGG 57.448 40.000 0.00 0.00 33.77 3.69
754 772 9.040259 CCATAAACTATCAGGATTAGGATCAGA 57.960 37.037 0.00 0.00 33.77 3.27
757 775 8.043710 CACCCATAAACTATCAGGATTAGGATC 58.956 40.741 0.00 0.00 0.00 3.36
815 838 3.181448 GGAGACAGTAGAGGGAGGTAGAG 60.181 56.522 0.00 0.00 0.00 2.43
816 839 2.778850 GGAGACAGTAGAGGGAGGTAGA 59.221 54.545 0.00 0.00 0.00 2.59
817 840 2.158579 GGGAGACAGTAGAGGGAGGTAG 60.159 59.091 0.00 0.00 0.00 3.18
973 1014 2.086869 GAAGCAATGCAGCTCTGGTTA 58.913 47.619 8.35 0.00 45.89 2.85
978 1019 2.195741 TCTTGAAGCAATGCAGCTCT 57.804 45.000 8.35 0.00 45.89 4.09
1008 1054 1.766496 AGGACGACCCAAACTCTTTGA 59.234 47.619 0.00 0.00 43.26 2.69
1044 1090 2.961526 TCGAATTACCTCTCAGGCAC 57.038 50.000 0.00 0.00 39.63 5.01
1076 1122 5.585047 ACAACTTAACTTCCAACACAGAGTC 59.415 40.000 0.00 0.00 0.00 3.36
1078 1124 6.202954 CCTACAACTTAACTTCCAACACAGAG 59.797 42.308 0.00 0.00 0.00 3.35
1081 1127 5.991861 TCCTACAACTTAACTTCCAACACA 58.008 37.500 0.00 0.00 0.00 3.72
1082 1128 6.285990 TCTCCTACAACTTAACTTCCAACAC 58.714 40.000 0.00 0.00 0.00 3.32
1083 1129 6.488769 TCTCCTACAACTTAACTTCCAACA 57.511 37.500 0.00 0.00 0.00 3.33
1084 1130 7.159372 TCATCTCCTACAACTTAACTTCCAAC 58.841 38.462 0.00 0.00 0.00 3.77
1085 1131 7.311092 TCATCTCCTACAACTTAACTTCCAA 57.689 36.000 0.00 0.00 0.00 3.53
1086 1132 6.928348 TCATCTCCTACAACTTAACTTCCA 57.072 37.500 0.00 0.00 0.00 3.53
1089 1135 7.044798 GCTCATCATCTCCTACAACTTAACTT 58.955 38.462 0.00 0.00 0.00 2.66
1090 1136 6.382570 AGCTCATCATCTCCTACAACTTAACT 59.617 38.462 0.00 0.00 0.00 2.24
1092 1138 6.381133 TCAGCTCATCATCTCCTACAACTTAA 59.619 38.462 0.00 0.00 0.00 1.85
1094 1140 4.713814 TCAGCTCATCATCTCCTACAACTT 59.286 41.667 0.00 0.00 0.00 2.66
1095 1141 4.285020 TCAGCTCATCATCTCCTACAACT 58.715 43.478 0.00 0.00 0.00 3.16
1096 1142 4.662468 TCAGCTCATCATCTCCTACAAC 57.338 45.455 0.00 0.00 0.00 3.32
1097 1143 5.883685 ATTCAGCTCATCATCTCCTACAA 57.116 39.130 0.00 0.00 0.00 2.41
1098 1144 5.364735 TCAATTCAGCTCATCATCTCCTACA 59.635 40.000 0.00 0.00 0.00 2.74
1100 1146 5.364735 TGTCAATTCAGCTCATCATCTCCTA 59.635 40.000 0.00 0.00 0.00 2.94
1101 1147 4.163649 TGTCAATTCAGCTCATCATCTCCT 59.836 41.667 0.00 0.00 0.00 3.69
1103 1149 5.107414 CGATGTCAATTCAGCTCATCATCTC 60.107 44.000 9.26 0.00 35.91 2.75
1104 1150 4.750598 CGATGTCAATTCAGCTCATCATCT 59.249 41.667 9.26 0.00 35.91 2.90
1105 1151 4.510711 ACGATGTCAATTCAGCTCATCATC 59.489 41.667 9.26 0.00 35.91 2.92
1145 1198 1.455849 CTCCACCCTCTGCACCAAA 59.544 57.895 0.00 0.00 0.00 3.28
1858 1974 3.428282 GGTTAAGGCGCGTGGTGG 61.428 66.667 8.43 0.00 0.00 4.61
1859 1975 2.666862 TGGTTAAGGCGCGTGGTG 60.667 61.111 8.43 0.00 0.00 4.17
1860 1976 2.667199 GTGGTTAAGGCGCGTGGT 60.667 61.111 8.43 0.00 0.00 4.16
1863 1979 3.047877 GCAGTGGTTAAGGCGCGT 61.048 61.111 8.43 0.00 0.00 6.01
1864 1980 1.922135 AATGCAGTGGTTAAGGCGCG 61.922 55.000 0.00 0.00 0.00 6.86
1884 2017 5.598830 AGCAAGGCTTAGCTAGTGATTAGTA 59.401 40.000 18.37 0.00 39.78 1.82
1885 2018 4.407296 AGCAAGGCTTAGCTAGTGATTAGT 59.593 41.667 18.37 0.00 39.78 2.24
1886 2019 4.954875 AGCAAGGCTTAGCTAGTGATTAG 58.045 43.478 18.37 0.00 39.78 1.73
2012 2153 0.030638 CGTTCAGGCACCAACCAAAG 59.969 55.000 0.00 0.00 0.00 2.77
2013 2154 0.394488 TCGTTCAGGCACCAACCAAA 60.394 50.000 0.00 0.00 0.00 3.28
2014 2155 0.179004 ATCGTTCAGGCACCAACCAA 60.179 50.000 0.00 0.00 0.00 3.67
2015 2156 0.888736 CATCGTTCAGGCACCAACCA 60.889 55.000 0.00 0.00 0.00 3.67
2016 2157 1.586154 CCATCGTTCAGGCACCAACC 61.586 60.000 0.00 0.00 0.00 3.77
2107 2249 0.107831 TCACTGTCCCCTTCCGTTTG 59.892 55.000 0.00 0.00 0.00 2.93
2163 2311 3.820195 TGGTAACTCCAGTCCAGACTA 57.180 47.619 0.00 0.00 41.93 2.59
2173 2321 6.446451 ACCCACTAATATACTGGTAACTCCA 58.554 40.000 0.00 0.00 45.01 3.86
2174 2322 6.990908 ACCCACTAATATACTGGTAACTCC 57.009 41.667 0.00 0.00 37.61 3.85
2175 2323 8.703378 ACTACCCACTAATATACTGGTAACTC 57.297 38.462 0.00 0.00 37.61 3.01
2176 2324 9.804977 CTACTACCCACTAATATACTGGTAACT 57.195 37.037 0.00 0.00 37.61 2.24
2268 2446 1.202557 ACCGACGGCAGTAAAAGTGAA 60.203 47.619 15.39 0.00 0.00 3.18
2277 2455 3.276846 GTGCAAACCGACGGCAGT 61.277 61.111 15.39 0.00 38.38 4.40
2278 2456 2.513065 GATGTGCAAACCGACGGCAG 62.513 60.000 15.39 5.04 38.38 4.85
2279 2457 2.593148 ATGTGCAAACCGACGGCA 60.593 55.556 15.39 2.64 34.70 5.69
2306 2485 4.363990 CCTGCACTGCTCCGACGT 62.364 66.667 1.98 0.00 0.00 4.34
2318 2506 4.349048 AGATAAGAATATGACTGCCCTGCA 59.651 41.667 0.00 0.00 36.92 4.41
2346 2534 4.402793 TGGCCTAGTCTATTCTGACTTCAC 59.597 45.833 3.32 0.00 44.01 3.18
2356 2544 7.571919 CCATCATTCATATGGCCTAGTCTATT 58.428 38.462 3.32 0.00 37.67 1.73
2462 2650 4.019411 TCAGGAGAAACATAATCCAGCACA 60.019 41.667 0.00 0.00 35.45 4.57
2529 2719 0.321564 CAGATGCTCCAACCGGTGAA 60.322 55.000 8.52 0.00 0.00 3.18
2530 2720 1.191489 TCAGATGCTCCAACCGGTGA 61.191 55.000 8.52 0.00 0.00 4.02
2535 2725 1.134699 TCACGATCAGATGCTCCAACC 60.135 52.381 0.00 0.00 0.00 3.77
2561 2751 3.749088 TGCACACGAAAAGAATAACGGAT 59.251 39.130 0.00 0.00 0.00 4.18
2770 3124 4.626081 CCGGGATCATGGCCGTCC 62.626 72.222 0.00 0.50 0.00 4.79
2997 3382 2.515641 TCGTCTACGTAGCAGTTTCG 57.484 50.000 18.00 13.56 40.80 3.46
2998 3383 2.530700 GCATCGTCTACGTAGCAGTTTC 59.469 50.000 18.00 2.28 40.80 2.78
2999 3384 2.094906 TGCATCGTCTACGTAGCAGTTT 60.095 45.455 18.00 4.18 41.87 2.66
3000 3385 1.471287 TGCATCGTCTACGTAGCAGTT 59.529 47.619 18.00 6.34 41.87 3.16
3001 3386 1.092348 TGCATCGTCTACGTAGCAGT 58.908 50.000 18.00 1.05 41.87 4.40
3002 3387 2.047040 CATGCATCGTCTACGTAGCAG 58.953 52.381 18.00 13.32 46.24 4.24
3003 3388 1.404035 ACATGCATCGTCTACGTAGCA 59.596 47.619 18.00 20.22 46.71 3.49
3004 3389 1.781429 CACATGCATCGTCTACGTAGC 59.219 52.381 18.00 11.68 40.80 3.58
3005 3390 2.783832 CACACATGCATCGTCTACGTAG 59.216 50.000 16.73 16.73 40.80 3.51
3006 3391 2.792749 CACACATGCATCGTCTACGTA 58.207 47.619 0.00 0.00 40.80 3.57
3007 3392 1.629013 CACACATGCATCGTCTACGT 58.371 50.000 0.00 0.00 40.80 3.57
3025 3410 1.577922 GTCGTCCTAGTGTCGTGCA 59.422 57.895 0.00 0.00 0.00 4.57
3026 3411 1.511464 CGTCGTCCTAGTGTCGTGC 60.511 63.158 0.00 0.00 0.00 5.34
3027 3412 1.134075 CCGTCGTCCTAGTGTCGTG 59.866 63.158 0.00 0.00 0.00 4.35
3028 3413 2.037136 CCCGTCGTCCTAGTGTCGT 61.037 63.158 0.00 0.00 0.00 4.34
3029 3414 2.789917 CCCGTCGTCCTAGTGTCG 59.210 66.667 0.00 0.00 0.00 4.35
3030 3415 2.267681 CTGCCCGTCGTCCTAGTGTC 62.268 65.000 0.00 0.00 0.00 3.67
3031 3416 2.282674 TGCCCGTCGTCCTAGTGT 60.283 61.111 0.00 0.00 0.00 3.55
3032 3417 2.267681 GACTGCCCGTCGTCCTAGTG 62.268 65.000 0.00 0.00 32.04 2.74
3033 3418 2.035312 ACTGCCCGTCGTCCTAGT 59.965 61.111 0.00 0.00 0.00 2.57
3034 3419 2.772691 GGACTGCCCGTCGTCCTAG 61.773 68.421 0.00 0.00 44.90 3.02
3035 3420 2.753043 GGACTGCCCGTCGTCCTA 60.753 66.667 0.00 0.00 44.90 2.94
3047 3432 1.226686 GCATATCAGCGGCTGGACTG 61.227 60.000 28.18 21.52 35.15 3.51
3048 3433 1.070445 GCATATCAGCGGCTGGACT 59.930 57.895 28.18 16.05 31.51 3.85
3049 3434 3.647824 GCATATCAGCGGCTGGAC 58.352 61.111 28.18 10.79 31.51 4.02
3057 3442 2.376808 ACTATCCAGCGCATATCAGC 57.623 50.000 11.47 0.00 0.00 4.26
3058 3443 3.801050 GCATACTATCCAGCGCATATCAG 59.199 47.826 11.47 3.23 0.00 2.90
3059 3444 3.195396 TGCATACTATCCAGCGCATATCA 59.805 43.478 11.47 0.00 0.00 2.15
3060 3445 3.785486 TGCATACTATCCAGCGCATATC 58.215 45.455 11.47 0.00 0.00 1.63
3061 3446 3.893326 TGCATACTATCCAGCGCATAT 57.107 42.857 11.47 1.79 0.00 1.78
3062 3447 3.524541 CATGCATACTATCCAGCGCATA 58.475 45.455 11.47 0.00 35.09 3.14
3063 3448 2.353323 CATGCATACTATCCAGCGCAT 58.647 47.619 11.47 0.00 36.45 4.73
3064 3449 1.608801 CCATGCATACTATCCAGCGCA 60.609 52.381 11.47 0.00 31.62 6.09
3065 3450 1.081892 CCATGCATACTATCCAGCGC 58.918 55.000 0.00 0.00 0.00 5.92
3066 3451 2.341257 GTCCATGCATACTATCCAGCG 58.659 52.381 0.00 0.00 0.00 5.18
3067 3452 2.341257 CGTCCATGCATACTATCCAGC 58.659 52.381 0.00 0.00 0.00 4.85
3068 3453 2.932622 GCCGTCCATGCATACTATCCAG 60.933 54.545 0.00 0.00 0.00 3.86
3069 3454 1.001974 GCCGTCCATGCATACTATCCA 59.998 52.381 0.00 0.00 0.00 3.41
3070 3455 1.276421 AGCCGTCCATGCATACTATCC 59.724 52.381 0.00 0.00 0.00 2.59
3071 3456 2.738846 CAAGCCGTCCATGCATACTATC 59.261 50.000 0.00 0.00 0.00 2.08
3072 3457 2.368548 TCAAGCCGTCCATGCATACTAT 59.631 45.455 0.00 0.00 0.00 2.12
3073 3458 1.760029 TCAAGCCGTCCATGCATACTA 59.240 47.619 0.00 0.00 0.00 1.82
3074 3459 0.541392 TCAAGCCGTCCATGCATACT 59.459 50.000 0.00 0.00 0.00 2.12
3075 3460 1.597742 ATCAAGCCGTCCATGCATAC 58.402 50.000 0.00 0.00 0.00 2.39
3076 3461 3.244526 ACATATCAAGCCGTCCATGCATA 60.245 43.478 0.00 0.00 0.00 3.14
3077 3462 2.156917 CATATCAAGCCGTCCATGCAT 58.843 47.619 0.00 0.00 0.00 3.96
3078 3463 1.134128 ACATATCAAGCCGTCCATGCA 60.134 47.619 0.00 0.00 0.00 3.96
3079 3464 1.265095 CACATATCAAGCCGTCCATGC 59.735 52.381 0.00 0.00 0.00 4.06
3080 3465 1.265095 GCACATATCAAGCCGTCCATG 59.735 52.381 0.00 0.00 0.00 3.66
3081 3466 1.141657 AGCACATATCAAGCCGTCCAT 59.858 47.619 0.00 0.00 0.00 3.41
3082 3467 0.541392 AGCACATATCAAGCCGTCCA 59.459 50.000 0.00 0.00 0.00 4.02
3083 3468 0.940126 CAGCACATATCAAGCCGTCC 59.060 55.000 0.00 0.00 0.00 4.79
3084 3469 1.594862 GACAGCACATATCAAGCCGTC 59.405 52.381 0.00 0.00 0.00 4.79
3085 3470 1.656652 GACAGCACATATCAAGCCGT 58.343 50.000 0.00 0.00 0.00 5.68
3086 3471 0.578683 CGACAGCACATATCAAGCCG 59.421 55.000 0.00 0.00 0.00 5.52
3087 3472 1.328680 CACGACAGCACATATCAAGCC 59.671 52.381 0.00 0.00 0.00 4.35
3088 3473 1.267732 GCACGACAGCACATATCAAGC 60.268 52.381 0.00 0.00 0.00 4.01
3089 3474 2.001872 TGCACGACAGCACATATCAAG 58.998 47.619 0.00 0.00 40.11 3.02
3090 3475 2.091852 TGCACGACAGCACATATCAA 57.908 45.000 0.00 0.00 40.11 2.57
3091 3476 3.830679 TGCACGACAGCACATATCA 57.169 47.368 0.00 0.00 40.11 2.15
3098 3483 2.354656 GACTCGTGCACGACAGCA 60.355 61.111 36.40 17.35 44.22 4.41
3099 3484 3.461982 CGACTCGTGCACGACAGC 61.462 66.667 36.40 25.10 44.22 4.40
3100 3485 2.051256 ACGACTCGTGCACGACAG 60.051 61.111 36.40 28.78 44.22 3.51
3101 3486 2.051614 GACGACTCGTGCACGACA 60.052 61.111 36.40 18.91 44.22 4.35
3102 3487 2.799916 GGACGACTCGTGCACGAC 60.800 66.667 36.40 26.07 46.80 4.34
3123 3508 1.200474 CTGCTATACACACGACGCCG 61.200 60.000 0.00 0.00 42.50 6.46
3124 3509 1.480219 GCTGCTATACACACGACGCC 61.480 60.000 0.00 0.00 0.00 5.68
3125 3510 1.798368 CGCTGCTATACACACGACGC 61.798 60.000 0.00 0.00 0.00 5.19
3126 3511 1.798368 GCGCTGCTATACACACGACG 61.798 60.000 0.00 0.00 0.00 5.12
3127 3512 0.525668 AGCGCTGCTATACACACGAC 60.526 55.000 10.39 0.00 36.99 4.34
3128 3513 0.525455 CAGCGCTGCTATACACACGA 60.525 55.000 26.68 0.00 36.40 4.35
3129 3514 1.920051 CAGCGCTGCTATACACACG 59.080 57.895 26.68 0.00 36.40 4.49
3140 3525 1.226211 CATTCTTTCCGCAGCGCTG 60.226 57.895 32.83 32.83 0.00 5.18
3141 3526 2.401766 CCATTCTTTCCGCAGCGCT 61.402 57.895 10.07 2.64 0.00 5.92
3142 3527 2.100991 CCATTCTTTCCGCAGCGC 59.899 61.111 10.07 0.00 0.00 5.92
3143 3528 2.793946 CCCATTCTTTCCGCAGCG 59.206 61.111 8.18 8.18 0.00 5.18
3144 3529 2.491621 GCCCATTCTTTCCGCAGC 59.508 61.111 0.00 0.00 0.00 5.25
3145 3530 2.764314 CGGCCCATTCTTTCCGCAG 61.764 63.158 0.00 0.00 35.20 5.18
3146 3531 2.749839 CGGCCCATTCTTTCCGCA 60.750 61.111 0.00 0.00 35.20 5.69
3147 3532 2.340328 AACGGCCCATTCTTTCCGC 61.340 57.895 0.00 0.00 45.23 5.54
3148 3533 1.241315 ACAACGGCCCATTCTTTCCG 61.241 55.000 0.00 0.00 46.61 4.30
3149 3534 0.966179 AACAACGGCCCATTCTTTCC 59.034 50.000 0.00 0.00 0.00 3.13
3150 3535 1.611491 TCAACAACGGCCCATTCTTTC 59.389 47.619 0.00 0.00 0.00 2.62
3151 3536 1.698506 TCAACAACGGCCCATTCTTT 58.301 45.000 0.00 0.00 0.00 2.52
3152 3537 1.545582 CATCAACAACGGCCCATTCTT 59.454 47.619 0.00 0.00 0.00 2.52
3153 3538 1.176527 CATCAACAACGGCCCATTCT 58.823 50.000 0.00 0.00 0.00 2.40
3154 3539 0.887933 ACATCAACAACGGCCCATTC 59.112 50.000 0.00 0.00 0.00 2.67
3155 3540 0.602562 CACATCAACAACGGCCCATT 59.397 50.000 0.00 0.00 0.00 3.16
3156 3541 1.876497 GCACATCAACAACGGCCCAT 61.876 55.000 0.00 0.00 0.00 4.00
3247 3632 9.353999 GCAAACTAGAGAAAAGAAAACTGAAAA 57.646 29.630 0.00 0.00 0.00 2.29
3248 3633 8.519526 TGCAAACTAGAGAAAAGAAAACTGAAA 58.480 29.630 0.00 0.00 0.00 2.69
3249 3634 7.968405 GTGCAAACTAGAGAAAAGAAAACTGAA 59.032 33.333 0.00 0.00 0.00 3.02
3250 3635 7.472543 GTGCAAACTAGAGAAAAGAAAACTGA 58.527 34.615 0.00 0.00 0.00 3.41
3251 3636 6.412072 CGTGCAAACTAGAGAAAAGAAAACTG 59.588 38.462 0.00 0.00 0.00 3.16
3252 3637 6.458342 CCGTGCAAACTAGAGAAAAGAAAACT 60.458 38.462 0.00 0.00 0.00 2.66
3259 3644 2.548057 CAGCCGTGCAAACTAGAGAAAA 59.452 45.455 0.00 0.00 0.00 2.29
3263 3648 0.792640 CACAGCCGTGCAAACTAGAG 59.207 55.000 0.00 0.00 36.06 2.43
3345 3767 3.130160 CTCTTCTTGGGCAGCGGC 61.130 66.667 0.00 0.00 40.13 6.53
3349 3771 4.282957 TCATAGATAGCTCTTCTTGGGCAG 59.717 45.833 4.58 0.00 32.66 4.85
3350 3772 4.226384 TCATAGATAGCTCTTCTTGGGCA 58.774 43.478 4.58 0.00 32.66 5.36
3351 3773 4.881019 TCATAGATAGCTCTTCTTGGGC 57.119 45.455 4.58 0.00 32.66 5.36
3352 3774 6.767456 ACAATCATAGATAGCTCTTCTTGGG 58.233 40.000 4.58 0.00 32.66 4.12
3392 3815 2.356818 GATCGGCCGGAGAACTGGAG 62.357 65.000 27.83 0.00 44.87 3.86
3426 3849 6.753180 AGTGTGCATAGATCAGGTTATAGTG 58.247 40.000 0.00 0.00 0.00 2.74
3441 3881 5.067674 GCAAATCCCAGAATAAGTGTGCATA 59.932 40.000 0.00 0.00 0.00 3.14
3445 3885 4.946157 AGAGCAAATCCCAGAATAAGTGTG 59.054 41.667 0.00 0.00 0.00 3.82
3446 3886 5.184892 AGAGCAAATCCCAGAATAAGTGT 57.815 39.130 0.00 0.00 0.00 3.55
3483 3923 5.278169 GCATATCATAGCTTGACCAGGTTTG 60.278 44.000 0.00 0.00 37.11 2.93
3508 3948 0.855995 GAGCCTAATCTTCGCTTCGC 59.144 55.000 0.00 0.00 31.61 4.70
3624 4065 3.763360 TGGTTATGGAAAATCAGCCACAG 59.237 43.478 0.00 0.00 36.92 3.66
3628 4069 4.799564 TTGTGGTTATGGAAAATCAGCC 57.200 40.909 0.00 0.00 0.00 4.85
3637 4078 3.392947 TCTGACTGGTTTGTGGTTATGGA 59.607 43.478 0.00 0.00 0.00 3.41
3647 4088 1.808945 GCCACATCTCTGACTGGTTTG 59.191 52.381 0.00 0.00 0.00 2.93
3648 4089 1.421268 TGCCACATCTCTGACTGGTTT 59.579 47.619 0.00 0.00 0.00 3.27
3761 4206 5.182001 TCTTCCTTTTAGCTGTTGATTGAGC 59.818 40.000 0.00 0.00 35.28 4.26


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

AutoCloner maintained by Alex Coulton.