Multiple sequence alignment - TraesCS6D01G096000

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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 TraesCS6D01G096000 chr6D 100.000 4091 0 0 1 4091 60169384 60165294 0.000000e+00 7555.0
1 TraesCS6D01G096000 chr6D 90.123 243 21 2 2284 2523 60167005 60166763 3.070000e-81 313.0
2 TraesCS6D01G096000 chr6D 90.123 243 21 2 2380 2622 60167101 60166862 3.070000e-81 313.0
3 TraesCS6D01G096000 chr6B 92.452 2186 87 28 618 2771 134000817 133998678 0.000000e+00 3051.0
4 TraesCS6D01G096000 chr6B 92.967 583 29 7 2801 3376 133998600 133998023 0.000000e+00 839.0
5 TraesCS6D01G096000 chr6B 84.637 358 48 5 2172 2527 133999169 133998817 2.340000e-92 350.0
6 TraesCS6D01G096000 chr6B 89.494 257 24 2 2366 2622 133999170 133998917 5.100000e-84 322.0
7 TraesCS6D01G096000 chr6B 89.604 202 16 3 3519 3716 133997856 133997656 6.790000e-63 252.0
8 TraesCS6D01G096000 chr6B 82.781 302 20 18 3800 4091 133997644 133997365 1.470000e-59 241.0
9 TraesCS6D01G096000 chr6B 92.517 147 7 4 79 221 134001970 134001824 1.490000e-49 207.0
10 TraesCS6D01G096000 chr6B 89.441 161 14 3 2462 2622 133999170 133999013 2.490000e-47 200.0
11 TraesCS6D01G096000 chr6A 87.886 2559 137 82 79 2512 76639986 76637476 0.000000e+00 2848.0
12 TraesCS6D01G096000 chr6A 86.100 1554 106 50 2578 4091 76637233 76635750 0.000000e+00 1572.0
13 TraesCS6D01G096000 chr6A 85.714 336 33 7 2284 2607 76637812 76637480 1.410000e-89 340.0
14 TraesCS6D01G096000 chr6A 91.925 161 10 3 2462 2622 76637718 76637561 5.320000e-54 222.0
15 TraesCS6D01G096000 chr7A 84.795 1026 142 14 1103 2122 606331017 606330000 0.000000e+00 1018.0
16 TraesCS6D01G096000 chr7A 89.826 688 37 9 2446 3130 678952466 678951809 0.000000e+00 852.0
17 TraesCS6D01G096000 chr7B 84.834 1022 140 15 1108 2122 562409355 562408342 0.000000e+00 1014.0
18 TraesCS6D01G096000 chr7D 84.706 1020 145 11 1108 2122 525774481 525773468 0.000000e+00 1009.0
19 TraesCS6D01G096000 chr7D 76.667 270 54 9 1108 1373 525989184 525988920 1.530000e-29 141.0
20 TraesCS6D01G096000 chr5A 90.631 555 25 7 2423 2974 48475716 48475186 0.000000e+00 712.0
21 TraesCS6D01G096000 chr5A 90.270 555 27 7 2423 2974 534075528 534076058 0.000000e+00 701.0
22 TraesCS6D01G096000 chr1D 79.197 971 165 34 1129 2079 119010761 119009808 1.240000e-179 640.0
23 TraesCS6D01G096000 chr1B 78.991 971 167 33 1129 2079 181218236 181217283 2.680000e-176 628.0
24 TraesCS6D01G096000 chr1B 93.846 65 4 0 1 65 649338752 649338816 9.360000e-17 99.0
25 TraesCS6D01G096000 chr1A 78.408 1005 172 39 1129 2108 131521549 131520565 2.700000e-171 612.0
26 TraesCS6D01G096000 chr3A 78.668 736 130 25 1132 1857 384319976 384320694 8.010000e-127 464.0
27 TraesCS6D01G096000 chr5D 93.220 59 4 0 7 65 244636668 244636610 2.030000e-13 87.9
28 TraesCS6D01G096000 chr2B 88.136 59 6 1 6 63 526382875 526382933 7.340000e-08 69.4


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 TraesCS6D01G096000 chr6D 60165294 60169384 4090 True 2727.00 7555 93.415333 1 4091 3 chr6D.!!$R1 4090
1 TraesCS6D01G096000 chr6B 133997365 134001970 4605 True 682.75 3051 89.236625 79 4091 8 chr6B.!!$R1 4012
2 TraesCS6D01G096000 chr6A 76635750 76639986 4236 True 1245.50 2848 87.906250 79 4091 4 chr6A.!!$R1 4012
3 TraesCS6D01G096000 chr7A 606330000 606331017 1017 True 1018.00 1018 84.795000 1103 2122 1 chr7A.!!$R1 1019
4 TraesCS6D01G096000 chr7A 678951809 678952466 657 True 852.00 852 89.826000 2446 3130 1 chr7A.!!$R2 684
5 TraesCS6D01G096000 chr7B 562408342 562409355 1013 True 1014.00 1014 84.834000 1108 2122 1 chr7B.!!$R1 1014
6 TraesCS6D01G096000 chr7D 525773468 525774481 1013 True 1009.00 1009 84.706000 1108 2122 1 chr7D.!!$R1 1014
7 TraesCS6D01G096000 chr5A 48475186 48475716 530 True 712.00 712 90.631000 2423 2974 1 chr5A.!!$R1 551
8 TraesCS6D01G096000 chr5A 534075528 534076058 530 False 701.00 701 90.270000 2423 2974 1 chr5A.!!$F1 551
9 TraesCS6D01G096000 chr1D 119009808 119010761 953 True 640.00 640 79.197000 1129 2079 1 chr1D.!!$R1 950
10 TraesCS6D01G096000 chr1B 181217283 181218236 953 True 628.00 628 78.991000 1129 2079 1 chr1B.!!$R1 950
11 TraesCS6D01G096000 chr1A 131520565 131521549 984 True 612.00 612 78.408000 1129 2108 1 chr1A.!!$R1 979
12 TraesCS6D01G096000 chr3A 384319976 384320694 718 False 464.00 464 78.668000 1132 1857 1 chr3A.!!$F1 725

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
62 63 0.103937 GCGCCTGTTAGAGATGCTCT 59.896 55.0 0.0 2.22 43.83 4.09 F
793 1553 0.448197 CTCTCGTTCGTAGCAGCTCA 59.552 55.0 0.0 0.00 0.00 4.26 F
2334 3158 0.179100 CATACCACTCGCCACCTCAG 60.179 60.0 0.0 0.00 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2295 3119 2.843545 GGGGTGGTGGAGCTTGAA 59.156 61.111 0.0 0.0 0.0 2.69 R
2647 3843 0.393537 GAAGGAGACGGGTACGAGGA 60.394 60.000 0.0 0.0 44.6 3.71 R
3803 5144 0.107081 CCCCCACGACAAGTACAACA 59.893 55.000 0.0 0.0 0.0 3.33 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
17 18 2.621000 GATAGGCGCGCGTCAAAG 59.379 61.111 37.48 5.04 0.00 2.77
18 19 3.492980 GATAGGCGCGCGTCAAAGC 62.493 63.158 37.48 22.94 0.00 3.51
22 23 4.666532 GCGCGCGTCAAAGCAGTT 62.667 61.111 32.35 0.00 36.85 3.16
23 24 2.052237 CGCGCGTCAAAGCAGTTT 60.052 55.556 24.19 0.00 36.85 2.66
24 25 1.654137 CGCGCGTCAAAGCAGTTTT 60.654 52.632 24.19 0.00 36.85 2.43
25 26 1.199852 CGCGCGTCAAAGCAGTTTTT 61.200 50.000 24.19 0.00 36.85 1.94
26 27 1.749153 GCGCGTCAAAGCAGTTTTTA 58.251 45.000 8.43 0.00 36.85 1.52
27 28 1.708680 GCGCGTCAAAGCAGTTTTTAG 59.291 47.619 8.43 0.00 36.85 1.85
28 29 2.853281 GCGCGTCAAAGCAGTTTTTAGT 60.853 45.455 8.43 0.00 36.85 2.24
29 30 2.713976 CGCGTCAAAGCAGTTTTTAGTG 59.286 45.455 0.00 0.00 36.85 2.74
30 31 2.467673 GCGTCAAAGCAGTTTTTAGTGC 59.532 45.455 0.00 0.00 40.17 4.40
31 32 2.713976 CGTCAAAGCAGTTTTTAGTGCG 59.286 45.455 0.00 0.00 44.78 5.34
32 33 2.467673 GTCAAAGCAGTTTTTAGTGCGC 59.532 45.455 0.00 0.00 44.78 6.09
33 34 1.447938 CAAAGCAGTTTTTAGTGCGCG 59.552 47.619 0.00 0.00 44.78 6.86
34 35 0.941542 AAGCAGTTTTTAGTGCGCGA 59.058 45.000 12.10 0.00 44.78 5.87
35 36 0.234884 AGCAGTTTTTAGTGCGCGAC 59.765 50.000 12.10 5.29 44.78 5.19
36 37 1.052768 GCAGTTTTTAGTGCGCGACG 61.053 55.000 12.10 0.00 0.00 5.12
54 55 2.126228 CGTTCGGCGCCTGTTAGA 60.126 61.111 26.68 11.29 0.00 2.10
55 56 2.158959 CGTTCGGCGCCTGTTAGAG 61.159 63.158 26.68 6.92 0.00 2.43
56 57 1.214589 GTTCGGCGCCTGTTAGAGA 59.785 57.895 26.68 9.61 0.00 3.10
57 58 0.179108 GTTCGGCGCCTGTTAGAGAT 60.179 55.000 26.68 0.00 0.00 2.75
58 59 0.179111 TTCGGCGCCTGTTAGAGATG 60.179 55.000 26.68 4.37 0.00 2.90
59 60 2.240500 CGGCGCCTGTTAGAGATGC 61.241 63.158 26.68 0.00 0.00 3.91
60 61 1.144936 GGCGCCTGTTAGAGATGCT 59.855 57.895 22.15 0.00 0.00 3.79
61 62 0.878086 GGCGCCTGTTAGAGATGCTC 60.878 60.000 22.15 0.00 0.00 4.26
62 63 0.103937 GCGCCTGTTAGAGATGCTCT 59.896 55.000 0.00 2.22 43.83 4.09
63 64 1.472376 GCGCCTGTTAGAGATGCTCTT 60.472 52.381 0.00 0.00 41.50 2.85
64 65 2.223829 GCGCCTGTTAGAGATGCTCTTA 60.224 50.000 0.00 0.00 41.50 2.10
65 66 3.738281 GCGCCTGTTAGAGATGCTCTTAA 60.738 47.826 0.00 0.00 41.50 1.85
66 67 4.047822 CGCCTGTTAGAGATGCTCTTAAG 58.952 47.826 1.88 0.00 41.50 1.85
67 68 4.202060 CGCCTGTTAGAGATGCTCTTAAGA 60.202 45.833 4.81 4.81 41.50 2.10
68 69 5.288804 GCCTGTTAGAGATGCTCTTAAGAG 58.711 45.833 25.42 25.42 41.50 2.85
69 70 5.163457 GCCTGTTAGAGATGCTCTTAAGAGT 60.163 44.000 28.72 13.88 43.85 3.24
70 71 6.629291 GCCTGTTAGAGATGCTCTTAAGAGTT 60.629 42.308 28.72 18.84 43.85 3.01
71 72 6.978080 CCTGTTAGAGATGCTCTTAAGAGTTC 59.022 42.308 28.72 24.36 43.85 3.01
72 73 6.868622 TGTTAGAGATGCTCTTAAGAGTTCC 58.131 40.000 28.72 18.70 43.85 3.62
73 74 6.437477 TGTTAGAGATGCTCTTAAGAGTTCCA 59.563 38.462 28.72 20.16 43.85 3.53
74 75 7.124901 TGTTAGAGATGCTCTTAAGAGTTCCAT 59.875 37.037 28.72 23.24 43.85 3.41
75 76 5.916318 AGAGATGCTCTTAAGAGTTCCATG 58.084 41.667 28.72 7.67 43.85 3.66
76 77 4.450053 AGATGCTCTTAAGAGTTCCATGC 58.550 43.478 28.72 16.64 43.85 4.06
77 78 2.621338 TGCTCTTAAGAGTTCCATGCG 58.379 47.619 28.72 6.32 43.85 4.73
116 117 0.458669 GGTGGCCAGCAATCAATCAG 59.541 55.000 29.70 0.00 0.00 2.90
146 158 3.681835 GACCGGTGTCGCCAGAGT 61.682 66.667 14.63 0.00 36.97 3.24
256 288 4.814294 GCCGGCCGTGGAGTGTAG 62.814 72.222 26.12 6.10 0.00 2.74
257 289 4.143333 CCGGCCGTGGAGTGTAGG 62.143 72.222 26.12 0.00 0.00 3.18
258 290 3.379445 CGGCCGTGGAGTGTAGGT 61.379 66.667 19.50 0.00 0.00 3.08
259 291 2.939261 CGGCCGTGGAGTGTAGGTT 61.939 63.158 19.50 0.00 0.00 3.50
260 292 1.373812 GGCCGTGGAGTGTAGGTTT 59.626 57.895 0.00 0.00 0.00 3.27
272 977 7.553044 GTGGAGTGTAGGTTTATGAGCTAAATT 59.447 37.037 0.00 0.00 39.86 1.82
273 978 8.764558 TGGAGTGTAGGTTTATGAGCTAAATTA 58.235 33.333 0.00 0.00 39.86 1.40
274 979 9.262358 GGAGTGTAGGTTTATGAGCTAAATTAG 57.738 37.037 0.00 0.00 39.86 1.73
298 1003 5.023533 AGTACTAGTAATGCATGTGGTGG 57.976 43.478 3.61 0.00 0.00 4.61
304 1009 1.097232 AATGCATGTGGTGGTGATCG 58.903 50.000 0.00 0.00 0.00 3.69
365 1085 3.753842 TGAAACGCTGGAATTTATTCGC 58.246 40.909 0.00 0.00 37.67 4.70
381 1101 1.815421 CGCTGGGACGATTCTTGGG 60.815 63.158 0.00 0.00 34.06 4.12
383 1103 1.452108 CTGGGACGATTCTTGGGGC 60.452 63.158 0.00 0.00 0.00 5.80
384 1104 2.124278 GGGACGATTCTTGGGGCC 60.124 66.667 0.00 0.00 0.00 5.80
385 1105 2.674754 GGACGATTCTTGGGGCCA 59.325 61.111 4.39 0.00 0.00 5.36
386 1106 1.001393 GGACGATTCTTGGGGCCAA 60.001 57.895 4.39 0.00 0.00 4.52
424 1147 1.066002 CTCGCATGTAAAATGCCTGGG 59.934 52.381 4.82 0.00 41.71 4.45
465 1188 3.438781 ACGTTTGCTGTGAAGTTCTTCAA 59.561 39.130 15.44 6.93 32.04 2.69
466 1189 4.096382 ACGTTTGCTGTGAAGTTCTTCAAT 59.904 37.500 15.44 0.00 32.04 2.57
467 1190 4.672413 CGTTTGCTGTGAAGTTCTTCAATC 59.328 41.667 15.44 6.54 32.04 2.67
468 1191 5.581605 GTTTGCTGTGAAGTTCTTCAATCA 58.418 37.500 15.44 10.17 32.04 2.57
477 1200 9.467258 TGTGAAGTTCTTCAATCAAAATGAATC 57.533 29.630 15.44 1.70 36.30 2.52
478 1201 9.467258 GTGAAGTTCTTCAATCAAAATGAATCA 57.533 29.630 15.44 0.00 36.30 2.57
497 1222 4.459390 TCAAAATAGGTCGAATCGTCCA 57.541 40.909 19.82 7.46 37.51 4.02
517 1242 2.664568 CAGCGAAAAATCAGTGGCATTG 59.335 45.455 3.22 3.22 0.00 2.82
548 1274 1.406180 CTTGGCCATCGCATGAATCAA 59.594 47.619 6.09 0.00 36.38 2.57
552 1278 2.351447 GGCCATCGCATGAATCAATCAG 60.351 50.000 0.00 0.00 42.53 2.90
555 1281 1.311859 TCGCATGAATCAATCAGCCC 58.688 50.000 0.00 0.00 42.53 5.19
585 1311 1.009335 CGCGAATGGTCATGGCATG 60.009 57.895 21.42 21.42 0.00 4.06
598 1324 2.738139 GCATGGCCCGTTTGCAAC 60.738 61.111 0.00 0.00 36.40 4.17
611 1337 3.139077 GTTTGCAACCTATCTATCCCCG 58.861 50.000 0.00 0.00 0.00 5.73
613 1339 1.968493 TGCAACCTATCTATCCCCGTC 59.032 52.381 0.00 0.00 0.00 4.79
614 1340 1.968493 GCAACCTATCTATCCCCGTCA 59.032 52.381 0.00 0.00 0.00 4.35
615 1341 2.288886 GCAACCTATCTATCCCCGTCAC 60.289 54.545 0.00 0.00 0.00 3.67
616 1342 1.906990 ACCTATCTATCCCCGTCACG 58.093 55.000 0.00 0.00 0.00 4.35
628 1354 2.390599 CGTCACGTCCCCATGCAAG 61.391 63.158 0.00 0.00 0.00 4.01
636 1362 2.493278 CGTCCCCATGCAAGAGAAAAAT 59.507 45.455 0.00 0.00 0.00 1.82
651 1377 5.536538 AGAGAAAAATGAAAGGAGGGTGAAC 59.463 40.000 0.00 0.00 0.00 3.18
709 1460 1.448013 CTTTCCTTCCTCGCCGACC 60.448 63.158 0.00 0.00 0.00 4.79
713 1464 4.831307 CTTCCTCGCCGACCGACG 62.831 72.222 0.00 0.00 41.89 5.12
765 1521 2.617225 CGTCGTCGCAGCATCATG 59.383 61.111 0.00 0.00 0.00 3.07
766 1522 2.863853 CGTCGTCGCAGCATCATGG 61.864 63.158 0.00 0.00 0.00 3.66
767 1523 1.811266 GTCGTCGCAGCATCATGGT 60.811 57.895 0.00 0.00 0.00 3.55
793 1553 0.448197 CTCTCGTTCGTAGCAGCTCA 59.552 55.000 0.00 0.00 0.00 4.26
794 1554 0.448197 TCTCGTTCGTAGCAGCTCAG 59.552 55.000 0.00 0.00 0.00 3.35
795 1555 1.136872 CTCGTTCGTAGCAGCTCAGC 61.137 60.000 0.00 0.00 0.00 4.26
797 1557 1.136872 CGTTCGTAGCAGCTCAGCTC 61.137 60.000 0.00 0.00 45.26 4.09
798 1558 1.136872 GTTCGTAGCAGCTCAGCTCG 61.137 60.000 0.00 0.00 45.26 5.03
799 1559 2.874010 TTCGTAGCAGCTCAGCTCGC 62.874 60.000 11.81 11.81 45.26 5.03
800 1560 2.584694 GTAGCAGCTCAGCTCGCC 60.585 66.667 15.04 0.00 45.26 5.54
801 1561 3.842923 TAGCAGCTCAGCTCGCCC 61.843 66.667 15.04 0.00 45.26 6.13
825 1585 2.037527 GTGACCCCTCCCTCTCGT 59.962 66.667 0.00 0.00 0.00 4.18
967 1746 1.336125 GCTTGCATCCAGCTACATTCC 59.664 52.381 1.51 0.00 45.94 3.01
968 1747 2.928334 CTTGCATCCAGCTACATTCCT 58.072 47.619 0.00 0.00 45.94 3.36
982 1761 6.041523 AGCTACATTCCTCATTCTTCCTAGAC 59.958 42.308 0.00 0.00 0.00 2.59
993 1772 2.828520 TCTTCCTAGACCACAGCTCAAG 59.171 50.000 0.00 0.00 0.00 3.02
994 1773 0.898320 TCCTAGACCACAGCTCAAGC 59.102 55.000 0.00 0.00 42.49 4.01
2043 2855 3.727258 TGGAACTGCATCCCCGGG 61.727 66.667 15.80 15.80 38.82 5.73
2139 2951 1.079336 GTTCCAGGCGTACACTCCC 60.079 63.158 0.00 0.00 0.00 4.30
2223 3038 2.283676 ACCACTCCGTCGTCCCAT 60.284 61.111 0.00 0.00 0.00 4.00
2329 3153 1.518572 CCGTCATACCACTCGCCAC 60.519 63.158 0.00 0.00 0.00 5.01
2330 3154 1.518572 CGTCATACCACTCGCCACC 60.519 63.158 0.00 0.00 0.00 4.61
2331 3155 1.898154 GTCATACCACTCGCCACCT 59.102 57.895 0.00 0.00 0.00 4.00
2332 3156 0.179108 GTCATACCACTCGCCACCTC 60.179 60.000 0.00 0.00 0.00 3.85
2333 3157 0.613572 TCATACCACTCGCCACCTCA 60.614 55.000 0.00 0.00 0.00 3.86
2334 3158 0.179100 CATACCACTCGCCACCTCAG 60.179 60.000 0.00 0.00 0.00 3.35
2335 3159 1.330655 ATACCACTCGCCACCTCAGG 61.331 60.000 0.00 0.00 0.00 3.86
2336 3160 4.087892 CCACTCGCCACCTCAGGG 62.088 72.222 0.00 0.00 38.88 4.45
2337 3161 2.997315 CACTCGCCACCTCAGGGA 60.997 66.667 0.00 0.00 36.25 4.20
2338 3162 2.039624 ACTCGCCACCTCAGGGAT 59.960 61.111 0.00 0.00 36.25 3.85
2339 3163 2.060980 ACTCGCCACCTCAGGGATC 61.061 63.158 0.00 0.00 36.25 3.36
2340 3164 2.764128 TCGCCACCTCAGGGATCC 60.764 66.667 1.92 1.92 36.25 3.36
2341 3165 3.083349 CGCCACCTCAGGGATCCA 61.083 66.667 15.23 0.00 36.25 3.41
2342 3166 2.592308 GCCACCTCAGGGATCCAC 59.408 66.667 15.23 2.86 36.25 4.02
2343 3167 3.049080 GCCACCTCAGGGATCCACC 62.049 68.421 15.23 0.00 36.25 4.61
2344 3168 1.616327 CCACCTCAGGGATCCACCA 60.616 63.158 15.23 0.00 41.20 4.17
2345 3169 1.604378 CACCTCAGGGATCCACCAC 59.396 63.158 15.23 0.00 41.20 4.16
2346 3170 1.990060 ACCTCAGGGATCCACCACG 60.990 63.158 15.23 0.00 41.20 4.94
2347 3171 2.187946 CTCAGGGATCCACCACGC 59.812 66.667 15.23 0.00 41.20 5.34
2348 3172 3.391665 CTCAGGGATCCACCACGCC 62.392 68.421 15.23 0.00 41.20 5.68
2349 3173 3.716195 CAGGGATCCACCACGCCA 61.716 66.667 15.23 0.00 41.20 5.69
2350 3174 2.692368 AGGGATCCACCACGCCAT 60.692 61.111 15.23 0.00 41.20 4.40
2351 3175 2.203209 GGGATCCACCACGCCATC 60.203 66.667 15.23 0.00 41.20 3.51
2352 3176 2.588877 GGATCCACCACGCCATCG 60.589 66.667 6.95 0.00 42.43 3.84
2353 3177 3.272334 GATCCACCACGCCATCGC 61.272 66.667 0.00 0.00 39.84 4.58
2354 3178 4.856801 ATCCACCACGCCATCGCC 62.857 66.667 0.00 0.00 39.84 5.54
2370 3194 2.669569 CCACCAGGCTCAACCACG 60.670 66.667 0.00 0.00 43.14 4.94
2371 3195 3.357079 CACCAGGCTCAACCACGC 61.357 66.667 0.00 0.00 43.14 5.34
2372 3196 4.643387 ACCAGGCTCAACCACGCC 62.643 66.667 0.00 0.00 46.65 5.68
2392 3216 4.137872 CGTACCCGACGCCACCAT 62.138 66.667 0.00 0.00 46.27 3.55
2393 3217 2.202837 GTACCCGACGCCACCATC 60.203 66.667 0.00 0.00 0.00 3.51
2394 3218 3.463585 TACCCGACGCCACCATCC 61.464 66.667 0.00 0.00 0.00 3.51
2396 3220 4.838152 CCCGACGCCACCATCCAG 62.838 72.222 0.00 0.00 0.00 3.86
2398 3222 4.457496 CGACGCCACCATCCAGCT 62.457 66.667 0.00 0.00 0.00 4.24
2399 3223 2.512515 GACGCCACCATCCAGCTC 60.513 66.667 0.00 0.00 0.00 4.09
2400 3224 4.101448 ACGCCACCATCCAGCTCC 62.101 66.667 0.00 0.00 0.00 4.70
2401 3225 4.100084 CGCCACCATCCAGCTCCA 62.100 66.667 0.00 0.00 0.00 3.86
2402 3226 2.124403 GCCACCATCCAGCTCCAG 60.124 66.667 0.00 0.00 0.00 3.86
2403 3227 2.124403 CCACCATCCAGCTCCAGC 60.124 66.667 0.00 0.00 42.49 4.85
2404 3228 2.672908 CACCATCCAGCTCCAGCA 59.327 61.111 0.48 0.00 45.16 4.41
2405 3229 1.748122 CACCATCCAGCTCCAGCAC 60.748 63.158 0.48 0.00 45.16 4.40
2406 3230 2.124403 CCATCCAGCTCCAGCACC 60.124 66.667 0.48 0.00 45.16 5.01
2407 3231 2.124403 CATCCAGCTCCAGCACCC 60.124 66.667 0.48 0.00 45.16 4.61
2408 3232 3.415087 ATCCAGCTCCAGCACCCC 61.415 66.667 0.48 0.00 45.16 4.95
2411 3235 4.767255 CAGCTCCAGCACCCCGTC 62.767 72.222 0.48 0.00 45.16 4.79
2413 3237 4.101448 GCTCCAGCACCCCGTCAT 62.101 66.667 0.00 0.00 41.59 3.06
2414 3238 2.731571 GCTCCAGCACCCCGTCATA 61.732 63.158 0.00 0.00 41.59 2.15
2415 3239 1.144057 CTCCAGCACCCCGTCATAC 59.856 63.158 0.00 0.00 0.00 2.39
2416 3240 2.189521 CCAGCACCCCGTCATACC 59.810 66.667 0.00 0.00 0.00 2.73
2417 3241 2.665089 CCAGCACCCCGTCATACCA 61.665 63.158 0.00 0.00 0.00 3.25
2418 3242 1.449601 CAGCACCCCGTCATACCAC 60.450 63.158 0.00 0.00 0.00 4.16
2419 3243 1.612442 AGCACCCCGTCATACCACT 60.612 57.895 0.00 0.00 0.00 4.00
2420 3244 1.153429 GCACCCCGTCATACCACTC 60.153 63.158 0.00 0.00 0.00 3.51
2421 3245 1.141019 CACCCCGTCATACCACTCG 59.859 63.158 0.00 0.00 0.00 4.18
2544 3464 1.697754 GGGATCCACCACCCCATCT 60.698 63.158 15.23 0.00 40.19 2.90
2548 3468 0.552367 ATCCACCACCCCATCTCCAA 60.552 55.000 0.00 0.00 0.00 3.53
2736 3932 4.681978 GCCGACAAGCCAGACGGT 62.682 66.667 15.68 0.00 46.08 4.83
2932 4179 3.744719 CCTCGCCGTCGTCAGGAA 61.745 66.667 0.00 0.00 33.05 3.36
3142 4402 1.000506 CACCGCCGCCAGTATAATACT 59.999 52.381 0.00 0.00 40.28 2.12
3166 4430 2.202932 CGCGCTCTGCCATTACCT 60.203 61.111 5.56 0.00 42.08 3.08
3295 4574 5.727630 AGGCCCTCCTATGTATTCTTTCTA 58.272 41.667 0.00 0.00 42.06 2.10
3351 4630 1.065854 GTGTAACCTCTGAGCCTGCAT 60.066 52.381 0.00 0.00 0.00 3.96
3354 4633 0.035630 AACCTCTGAGCCTGCATCAC 60.036 55.000 0.00 0.00 0.00 3.06
3369 4648 2.613595 GCATCACGATAATGAGTGGCAA 59.386 45.455 0.00 0.00 38.77 4.52
3371 4650 2.267426 TCACGATAATGAGTGGCAACG 58.733 47.619 0.00 0.00 38.77 4.10
3374 4653 2.094182 ACGATAATGAGTGGCAACGTCT 60.094 45.455 0.00 0.00 42.51 4.18
3375 4654 3.129813 ACGATAATGAGTGGCAACGTCTA 59.870 43.478 0.00 0.00 42.51 2.59
3376 4655 4.109766 CGATAATGAGTGGCAACGTCTAA 58.890 43.478 0.00 0.00 42.51 2.10
3377 4656 4.565166 CGATAATGAGTGGCAACGTCTAAA 59.435 41.667 0.00 0.00 42.51 1.85
3380 4659 2.907634 TGAGTGGCAACGTCTAAAACA 58.092 42.857 0.00 0.00 42.51 2.83
3381 4660 3.472652 TGAGTGGCAACGTCTAAAACAT 58.527 40.909 0.00 0.00 42.51 2.71
3383 4662 2.478894 AGTGGCAACGTCTAAAACATCG 59.521 45.455 0.00 0.00 42.51 3.84
3384 4663 1.195900 TGGCAACGTCTAAAACATCGC 59.804 47.619 0.00 0.00 42.51 4.58
3385 4664 1.195900 GGCAACGTCTAAAACATCGCA 59.804 47.619 0.00 0.00 0.00 5.10
3386 4665 2.495939 GCAACGTCTAAAACATCGCAG 58.504 47.619 0.00 0.00 0.00 5.18
3388 4667 3.181520 GCAACGTCTAAAACATCGCAGAT 60.182 43.478 0.00 0.00 45.12 2.90
3389 4668 4.569029 CAACGTCTAAAACATCGCAGATC 58.431 43.478 0.00 0.00 45.12 2.75
3390 4669 4.111375 ACGTCTAAAACATCGCAGATCT 57.889 40.909 0.00 0.00 45.12 2.75
3391 4670 4.495422 ACGTCTAAAACATCGCAGATCTT 58.505 39.130 0.00 0.00 45.12 2.40
3392 4671 5.647589 ACGTCTAAAACATCGCAGATCTTA 58.352 37.500 0.00 0.00 45.12 2.10
3393 4672 6.273825 ACGTCTAAAACATCGCAGATCTTAT 58.726 36.000 0.00 0.00 45.12 1.73
3402 4687 9.710900 AAACATCGCAGATCTTATTGATACATA 57.289 29.630 0.00 0.00 45.12 2.29
3421 4753 5.872635 ACATAATGATCAAAAGTGTGCTCG 58.127 37.500 0.00 0.00 0.00 5.03
3424 4756 1.792367 TGATCAAAAGTGTGCTCGTCG 59.208 47.619 0.00 0.00 0.00 5.12
3434 4766 1.605232 TGTGCTCGTCGTAACTCTGAA 59.395 47.619 0.00 0.00 0.00 3.02
3435 4767 1.977412 GTGCTCGTCGTAACTCTGAAC 59.023 52.381 0.00 0.00 0.00 3.18
3436 4768 1.878088 TGCTCGTCGTAACTCTGAACT 59.122 47.619 0.00 0.00 0.00 3.01
3437 4769 2.243407 GCTCGTCGTAACTCTGAACTG 58.757 52.381 0.00 0.00 0.00 3.16
3438 4770 2.095869 GCTCGTCGTAACTCTGAACTGA 60.096 50.000 0.00 0.00 0.00 3.41
3441 4773 2.650765 CGTCGTAACTCTGAACTGAACG 59.349 50.000 0.00 0.00 0.00 3.95
3442 4774 3.625938 GTCGTAACTCTGAACTGAACGT 58.374 45.455 0.00 0.00 0.00 3.99
3487 4824 2.429069 GAAACGCAGCGGCCAAAG 60.429 61.111 21.15 0.00 36.38 2.77
3489 4826 2.400896 GAAACGCAGCGGCCAAAGAA 62.401 55.000 21.15 0.00 36.38 2.52
3493 4830 2.126734 CAGCGGCCAAAGAAAGCG 60.127 61.111 2.24 0.00 0.00 4.68
3503 4840 3.129871 CCAAAGAAAGCGGCAATGAAAA 58.870 40.909 1.45 0.00 0.00 2.29
3509 4846 0.517316 AGCGGCAATGAAAACGAGAC 59.483 50.000 1.45 0.00 0.00 3.36
3527 4864 0.394352 ACGGAGAATGTTGGGCATCC 60.394 55.000 0.00 0.00 36.67 3.51
3546 4884 4.213564 TCCATTGCTCTTTCTTCTCCTC 57.786 45.455 0.00 0.00 0.00 3.71
3552 4890 3.258228 GCTCTTTCTTCTCCTCCTTTCG 58.742 50.000 0.00 0.00 0.00 3.46
3595 4933 5.277731 GCAAAAGAGGAATCGGATCAAGATC 60.278 44.000 1.40 1.40 37.11 2.75
3599 4937 5.609423 AGAGGAATCGGATCAAGATCAAAG 58.391 41.667 11.78 3.42 39.54 2.77
3700 5041 2.104729 CATGGCATTTTCCCGGCG 59.895 61.111 0.00 0.00 0.00 6.46
3741 5082 5.361571 TGCTGCAATAAATCAGACATCCATT 59.638 36.000 0.00 0.00 32.26 3.16
3742 5083 5.919141 GCTGCAATAAATCAGACATCCATTC 59.081 40.000 0.00 0.00 32.26 2.67
3743 5084 6.395426 TGCAATAAATCAGACATCCATTCC 57.605 37.500 0.00 0.00 0.00 3.01
3744 5085 5.008911 TGCAATAAATCAGACATCCATTCCG 59.991 40.000 0.00 0.00 0.00 4.30
3750 5091 0.460311 AGACATCCATTCCGTCCGTC 59.540 55.000 0.00 0.00 0.00 4.79
3753 5094 2.056223 ATCCATTCCGTCCGTCCGT 61.056 57.895 0.00 0.00 0.00 4.69
3786 5127 1.000274 GCATCCACCACCTTGTTGTTC 60.000 52.381 0.00 0.00 0.00 3.18
3787 5128 2.586425 CATCCACCACCTTGTTGTTCT 58.414 47.619 0.00 0.00 0.00 3.01
3788 5129 2.818751 TCCACCACCTTGTTGTTCTT 57.181 45.000 0.00 0.00 0.00 2.52
3789 5130 2.374184 TCCACCACCTTGTTGTTCTTG 58.626 47.619 0.00 0.00 0.00 3.02
3790 5131 1.408702 CCACCACCTTGTTGTTCTTGG 59.591 52.381 0.00 0.00 0.00 3.61
3791 5132 2.374184 CACCACCTTGTTGTTCTTGGA 58.626 47.619 0.00 0.00 0.00 3.53
3792 5133 2.358898 CACCACCTTGTTGTTCTTGGAG 59.641 50.000 0.00 0.00 0.00 3.86
3793 5134 2.025321 ACCACCTTGTTGTTCTTGGAGT 60.025 45.455 0.00 0.00 0.00 3.85
3794 5135 3.023832 CCACCTTGTTGTTCTTGGAGTT 58.976 45.455 0.00 0.00 0.00 3.01
3795 5136 3.181487 CCACCTTGTTGTTCTTGGAGTTG 60.181 47.826 0.00 0.00 0.00 3.16
3796 5137 3.443681 CACCTTGTTGTTCTTGGAGTTGT 59.556 43.478 0.00 0.00 0.00 3.32
3797 5138 4.082245 CACCTTGTTGTTCTTGGAGTTGTT 60.082 41.667 0.00 0.00 0.00 2.83
3798 5139 4.526650 ACCTTGTTGTTCTTGGAGTTGTTT 59.473 37.500 0.00 0.00 0.00 2.83
3799 5140 5.011635 ACCTTGTTGTTCTTGGAGTTGTTTT 59.988 36.000 0.00 0.00 0.00 2.43
3800 5141 5.931724 CCTTGTTGTTCTTGGAGTTGTTTTT 59.068 36.000 0.00 0.00 0.00 1.94
3801 5142 6.128580 CCTTGTTGTTCTTGGAGTTGTTTTTG 60.129 38.462 0.00 0.00 0.00 2.44
3802 5143 5.848406 TGTTGTTCTTGGAGTTGTTTTTGT 58.152 33.333 0.00 0.00 0.00 2.83
3803 5144 6.284459 TGTTGTTCTTGGAGTTGTTTTTGTT 58.716 32.000 0.00 0.00 0.00 2.83
3804 5145 6.201806 TGTTGTTCTTGGAGTTGTTTTTGTTG 59.798 34.615 0.00 0.00 0.00 3.33
3805 5146 5.848406 TGTTCTTGGAGTTGTTTTTGTTGT 58.152 33.333 0.00 0.00 0.00 3.32
3806 5147 6.284459 TGTTCTTGGAGTTGTTTTTGTTGTT 58.716 32.000 0.00 0.00 0.00 2.83
3826 5174 0.901580 GTACTTGTCGTGGGGGAGGA 60.902 60.000 0.00 0.00 0.00 3.71
3837 5185 1.392534 GGGGAGGAGGAAGAGGACA 59.607 63.158 0.00 0.00 0.00 4.02
3872 5222 2.124736 CATGGGCATTCCGTCCGT 60.125 61.111 0.00 0.00 45.31 4.69
4008 5369 1.669115 GTGCCGATCGATCCATGGG 60.669 63.158 18.66 15.11 0.00 4.00
4009 5370 1.836604 TGCCGATCGATCCATGGGA 60.837 57.895 18.66 13.21 35.55 4.37
4010 5371 1.194121 TGCCGATCGATCCATGGGAT 61.194 55.000 18.66 6.81 46.28 3.85
4020 5381 2.516930 CATGGGATCCACACCGGC 60.517 66.667 15.23 0.00 35.80 6.13
4023 5384 4.530857 GGGATCCACACCGGCGAG 62.531 72.222 15.23 2.48 33.14 5.03
4025 5386 4.530857 GATCCACACCGGCGAGGG 62.531 72.222 9.30 1.41 46.96 4.30
4035 5396 3.462678 GGCGAGGGTGGAGGAGAC 61.463 72.222 0.00 0.00 0.00 3.36
4036 5397 2.680352 GCGAGGGTGGAGGAGACA 60.680 66.667 0.00 0.00 0.00 3.41
4037 5398 2.716017 GCGAGGGTGGAGGAGACAG 61.716 68.421 0.00 0.00 0.00 3.51
4061 5422 3.474034 GCGAGCGCTCACTGTGAC 61.474 66.667 34.69 12.24 38.26 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.564027 GCTTTGACGCGCGCCTAT 61.564 61.111 32.58 10.83 0.00 2.57
7 8 1.708680 CTAAAAACTGCTTTGACGCGC 59.291 47.619 5.73 0.00 0.00 6.86
8 9 2.713976 CACTAAAAACTGCTTTGACGCG 59.286 45.455 3.53 3.53 0.00 6.01
9 10 2.467673 GCACTAAAAACTGCTTTGACGC 59.532 45.455 0.00 0.00 0.00 5.19
10 11 2.713976 CGCACTAAAAACTGCTTTGACG 59.286 45.455 0.00 0.00 0.00 4.35
11 12 2.467673 GCGCACTAAAAACTGCTTTGAC 59.532 45.455 0.30 0.00 0.00 3.18
12 13 2.726633 GCGCACTAAAAACTGCTTTGA 58.273 42.857 0.30 0.00 0.00 2.69
13 14 1.447938 CGCGCACTAAAAACTGCTTTG 59.552 47.619 8.75 0.00 0.00 2.77
14 15 1.332375 TCGCGCACTAAAAACTGCTTT 59.668 42.857 8.75 0.00 0.00 3.51
15 16 0.941542 TCGCGCACTAAAAACTGCTT 59.058 45.000 8.75 0.00 0.00 3.91
16 17 0.234884 GTCGCGCACTAAAAACTGCT 59.765 50.000 8.75 0.00 0.00 4.24
17 18 1.052768 CGTCGCGCACTAAAAACTGC 61.053 55.000 8.75 0.00 0.00 4.40
18 19 2.968179 CGTCGCGCACTAAAAACTG 58.032 52.632 8.75 0.00 0.00 3.16
38 39 0.179108 ATCTCTAACAGGCGCCGAAC 60.179 55.000 23.20 0.00 0.00 3.95
39 40 0.179111 CATCTCTAACAGGCGCCGAA 60.179 55.000 23.20 6.85 0.00 4.30
40 41 1.437573 CATCTCTAACAGGCGCCGA 59.562 57.895 23.20 10.93 0.00 5.54
41 42 2.240500 GCATCTCTAACAGGCGCCG 61.241 63.158 23.20 18.60 0.00 6.46
42 43 0.878086 GAGCATCTCTAACAGGCGCC 60.878 60.000 21.89 21.89 0.00 6.53
43 44 2.599216 GAGCATCTCTAACAGGCGC 58.401 57.895 0.00 0.00 0.00 6.53
55 56 3.247173 CGCATGGAACTCTTAAGAGCATC 59.753 47.826 28.64 24.88 45.79 3.91
56 57 3.201290 CGCATGGAACTCTTAAGAGCAT 58.799 45.455 28.64 20.99 45.79 3.79
57 58 2.028112 ACGCATGGAACTCTTAAGAGCA 60.028 45.455 28.64 19.83 45.79 4.26
58 59 2.349886 CACGCATGGAACTCTTAAGAGC 59.650 50.000 28.64 15.35 45.79 4.09
59 60 5.449812 ATGCACGCATGGAACTCTTAAGAG 61.450 45.833 27.41 27.41 40.43 2.85
60 61 2.289382 TGCACGCATGGAACTCTTAAGA 60.289 45.455 4.81 4.81 0.00 2.10
61 62 2.076100 TGCACGCATGGAACTCTTAAG 58.924 47.619 0.00 0.00 0.00 1.85
62 63 2.177394 TGCACGCATGGAACTCTTAA 57.823 45.000 0.00 0.00 0.00 1.85
63 64 2.401583 ATGCACGCATGGAACTCTTA 57.598 45.000 3.17 0.00 35.03 2.10
64 65 3.254629 ATGCACGCATGGAACTCTT 57.745 47.368 3.17 0.00 35.03 2.85
75 76 3.454574 CAACACATGCATGCACGC 58.545 55.556 25.37 0.00 0.00 5.34
116 117 2.027469 ACACCGGTCCTAGTCCAAAATC 60.027 50.000 2.59 0.00 0.00 2.17
146 158 2.876550 AGCACGTACGCTCTCATACATA 59.123 45.455 16.72 0.00 37.91 2.29
272 977 7.013942 CCACCACATGCATTACTAGTACTACTA 59.986 40.741 0.91 0.00 0.00 1.82
273 978 6.183360 CCACCACATGCATTACTAGTACTACT 60.183 42.308 0.91 0.00 0.00 2.57
274 979 5.983720 CCACCACATGCATTACTAGTACTAC 59.016 44.000 0.91 0.00 0.00 2.73
287 992 2.039974 GCGATCACCACCACATGCA 61.040 57.895 0.00 0.00 0.00 3.96
298 1003 1.080995 GCTCAGTCACCAGCGATCAC 61.081 60.000 0.00 0.00 0.00 3.06
304 1009 5.220931 CCATTAATTTAGCTCAGTCACCAGC 60.221 44.000 0.00 0.00 35.73 4.85
365 1085 1.452108 GCCCCAAGAATCGTCCCAG 60.452 63.158 0.00 0.00 0.00 4.45
383 1103 4.596585 ACGGGCCAGGTTGGTTGG 62.597 66.667 8.08 0.00 40.46 3.77
384 1104 2.983592 GACGGGCCAGGTTGGTTG 60.984 66.667 8.08 0.00 40.46 3.77
385 1105 4.636435 CGACGGGCCAGGTTGGTT 62.636 66.667 8.08 0.00 40.46 3.67
409 1132 2.091541 CGTGACCCAGGCATTTTACAT 58.908 47.619 0.00 0.00 0.00 2.29
466 1189 9.787532 GATTCGACCTATTTTGATTCATTTTGA 57.212 29.630 0.00 0.00 0.00 2.69
467 1190 8.736742 CGATTCGACCTATTTTGATTCATTTTG 58.263 33.333 0.00 0.00 0.00 2.44
468 1191 8.458843 ACGATTCGACCTATTTTGATTCATTTT 58.541 29.630 13.95 0.00 0.00 1.82
477 1200 3.001330 GCTGGACGATTCGACCTATTTTG 59.999 47.826 24.04 11.00 41.68 2.44
478 1201 3.195661 GCTGGACGATTCGACCTATTTT 58.804 45.455 24.04 0.00 41.68 1.82
497 1222 2.297033 ACAATGCCACTGATTTTTCGCT 59.703 40.909 0.00 0.00 0.00 4.93
517 1242 2.476185 CGATGGCCAAGTTCGAATTCAC 60.476 50.000 20.14 0.00 34.92 3.18
548 1274 3.842923 CTGCGTCTCCGGGCTGAT 61.843 66.667 0.00 0.00 33.68 2.90
592 1318 2.367567 GACGGGGATAGATAGGTTGCAA 59.632 50.000 0.00 0.00 0.00 4.08
598 1324 1.811359 GACGTGACGGGGATAGATAGG 59.189 57.143 10.66 0.00 0.00 2.57
614 1340 0.400213 TTTCTCTTGCATGGGGACGT 59.600 50.000 0.00 0.00 0.00 4.34
615 1341 1.533625 TTTTCTCTTGCATGGGGACG 58.466 50.000 0.00 0.00 0.00 4.79
616 1342 3.511146 TCATTTTTCTCTTGCATGGGGAC 59.489 43.478 0.00 0.00 0.00 4.46
628 1354 5.562890 CGTTCACCCTCCTTTCATTTTTCTC 60.563 44.000 0.00 0.00 0.00 2.87
636 1362 3.284793 TTTTCGTTCACCCTCCTTTCA 57.715 42.857 0.00 0.00 0.00 2.69
651 1377 3.573491 GGGCTCCGCGGATTTTCG 61.573 66.667 31.19 18.06 0.00 3.46
765 1521 1.803519 CGAACGAGAGAGCAGCACC 60.804 63.158 0.00 0.00 0.00 5.01
766 1522 0.168348 TACGAACGAGAGAGCAGCAC 59.832 55.000 0.14 0.00 0.00 4.40
767 1523 0.448197 CTACGAACGAGAGAGCAGCA 59.552 55.000 0.14 0.00 0.00 4.41
800 1560 4.489771 GAGGGGTCACATGGGCGG 62.490 72.222 0.00 0.00 0.00 6.13
801 1561 4.489771 GGAGGGGTCACATGGGCG 62.490 72.222 0.00 0.00 0.00 6.13
802 1562 4.129148 GGGAGGGGTCACATGGGC 62.129 72.222 0.00 0.00 0.00 5.36
967 1746 3.450457 AGCTGTGGTCTAGGAAGAATGAG 59.550 47.826 0.00 0.00 32.16 2.90
968 1747 3.445008 AGCTGTGGTCTAGGAAGAATGA 58.555 45.455 0.00 0.00 32.16 2.57
982 1761 0.896940 ATGGTTGGCTTGAGCTGTGG 60.897 55.000 0.00 0.00 41.70 4.17
993 1772 3.585990 CGCCGGATCATGGTTGGC 61.586 66.667 5.05 12.02 42.29 4.52
994 1773 3.585990 GCGCCGGATCATGGTTGG 61.586 66.667 5.05 0.00 0.00 3.77
2295 3119 2.843545 GGGGTGGTGGAGCTTGAA 59.156 61.111 0.00 0.00 0.00 2.69
2329 3153 2.903357 CGTGGTGGATCCCTGAGG 59.097 66.667 9.90 0.00 34.77 3.86
2330 3154 2.187946 GCGTGGTGGATCCCTGAG 59.812 66.667 9.90 0.00 34.77 3.35
2331 3155 3.399181 GGCGTGGTGGATCCCTGA 61.399 66.667 9.90 0.00 34.77 3.86
2332 3156 2.947938 GATGGCGTGGTGGATCCCTG 62.948 65.000 9.90 0.00 34.77 4.45
2333 3157 2.692368 ATGGCGTGGTGGATCCCT 60.692 61.111 9.90 0.00 34.77 4.20
2334 3158 2.203209 GATGGCGTGGTGGATCCC 60.203 66.667 9.90 0.00 34.77 3.85
2335 3159 2.588877 CGATGGCGTGGTGGATCC 60.589 66.667 4.20 4.20 0.00 3.36
2336 3160 3.272334 GCGATGGCGTGGTGGATC 61.272 66.667 0.00 0.00 40.36 3.36
2337 3161 4.856801 GGCGATGGCGTGGTGGAT 62.857 66.667 0.00 0.00 41.24 3.41
2353 3177 2.669569 CGTGGTTGAGCCTGGTGG 60.670 66.667 0.00 0.00 38.35 4.61
2354 3178 3.357079 GCGTGGTTGAGCCTGGTG 61.357 66.667 0.00 0.00 38.35 4.17
2376 3200 2.202837 GATGGTGGCGTCGGGTAC 60.203 66.667 0.00 0.00 0.00 3.34
2377 3201 3.463585 GGATGGTGGCGTCGGGTA 61.464 66.667 0.00 0.00 0.00 3.69
2379 3203 4.838152 CTGGATGGTGGCGTCGGG 62.838 72.222 0.00 0.00 0.00 5.14
2381 3205 4.457496 AGCTGGATGGTGGCGTCG 62.457 66.667 0.00 0.00 0.00 5.12
2382 3206 2.512515 GAGCTGGATGGTGGCGTC 60.513 66.667 0.00 0.00 0.00 5.19
2383 3207 4.101448 GGAGCTGGATGGTGGCGT 62.101 66.667 0.00 0.00 0.00 5.68
2384 3208 4.100084 TGGAGCTGGATGGTGGCG 62.100 66.667 0.00 0.00 0.00 5.69
2385 3209 2.124403 CTGGAGCTGGATGGTGGC 60.124 66.667 0.00 0.00 0.00 5.01
2386 3210 2.124403 GCTGGAGCTGGATGGTGG 60.124 66.667 0.00 0.00 38.21 4.61
2387 3211 1.748122 GTGCTGGAGCTGGATGGTG 60.748 63.158 0.00 0.00 42.66 4.17
2388 3212 2.673523 GTGCTGGAGCTGGATGGT 59.326 61.111 0.00 0.00 42.66 3.55
2389 3213 2.124403 GGTGCTGGAGCTGGATGG 60.124 66.667 0.00 0.00 42.66 3.51
2390 3214 2.124403 GGGTGCTGGAGCTGGATG 60.124 66.667 0.00 0.00 42.66 3.51
2391 3215 3.415087 GGGGTGCTGGAGCTGGAT 61.415 66.667 0.00 0.00 42.66 3.41
2394 3218 4.767255 GACGGGGTGCTGGAGCTG 62.767 72.222 0.00 0.00 42.66 4.24
2396 3220 2.731571 TATGACGGGGTGCTGGAGC 61.732 63.158 0.00 0.00 42.50 4.70
2397 3221 1.144057 GTATGACGGGGTGCTGGAG 59.856 63.158 0.00 0.00 0.00 3.86
2398 3222 2.363975 GGTATGACGGGGTGCTGGA 61.364 63.158 0.00 0.00 0.00 3.86
2399 3223 2.189521 GGTATGACGGGGTGCTGG 59.810 66.667 0.00 0.00 0.00 4.85
2400 3224 1.449601 GTGGTATGACGGGGTGCTG 60.450 63.158 0.00 0.00 0.00 4.41
2401 3225 1.612442 AGTGGTATGACGGGGTGCT 60.612 57.895 0.00 0.00 0.00 4.40
2402 3226 1.153429 GAGTGGTATGACGGGGTGC 60.153 63.158 0.00 0.00 0.00 5.01
2403 3227 1.141019 CGAGTGGTATGACGGGGTG 59.859 63.158 0.00 0.00 0.00 4.61
2404 3228 2.718073 GCGAGTGGTATGACGGGGT 61.718 63.158 0.00 0.00 0.00 4.95
2405 3229 2.106332 GCGAGTGGTATGACGGGG 59.894 66.667 0.00 0.00 0.00 5.73
2406 3230 2.106332 GGCGAGTGGTATGACGGG 59.894 66.667 0.00 0.00 0.00 5.28
2407 3231 2.278596 CGGCGAGTGGTATGACGG 60.279 66.667 0.00 0.00 0.00 4.79
2408 3232 2.954868 GCGGCGAGTGGTATGACG 60.955 66.667 12.98 0.00 0.00 4.35
2409 3233 2.585247 GGCGGCGAGTGGTATGAC 60.585 66.667 12.98 0.00 0.00 3.06
2410 3234 3.845259 GGGCGGCGAGTGGTATGA 61.845 66.667 12.98 0.00 0.00 2.15
2411 3235 4.910585 GGGGCGGCGAGTGGTATG 62.911 72.222 12.98 0.00 0.00 2.39
2544 3464 4.373116 GTCGAGCCCTGCGTTGGA 62.373 66.667 0.00 0.00 0.00 3.53
2647 3843 0.393537 GAAGGAGACGGGTACGAGGA 60.394 60.000 0.00 0.00 44.60 3.71
2648 3844 1.712977 CGAAGGAGACGGGTACGAGG 61.713 65.000 0.00 0.00 44.60 4.63
2649 3845 1.023513 ACGAAGGAGACGGGTACGAG 61.024 60.000 0.00 0.00 44.60 4.18
2928 4175 1.890510 GGACGGCGTTGTTGTTCCT 60.891 57.895 16.19 0.00 0.00 3.36
2932 4179 3.266376 CGTGGACGGCGTTGTTGT 61.266 61.111 16.19 0.00 35.37 3.32
3142 4402 4.742201 GGCAGAGCGCGAGGTGAA 62.742 66.667 12.10 0.00 45.11 3.18
3179 4443 5.713861 AGAGATGAAAAGAAATCCAAGGTGG 59.286 40.000 0.00 0.00 39.43 4.61
3180 4444 6.830873 AGAGATGAAAAGAAATCCAAGGTG 57.169 37.500 0.00 0.00 0.00 4.00
3181 4445 7.237255 AGAAGAGATGAAAAGAAATCCAAGGT 58.763 34.615 0.00 0.00 0.00 3.50
3184 4448 8.930846 AGAAGAAGAGATGAAAAGAAATCCAA 57.069 30.769 0.00 0.00 0.00 3.53
3185 4449 8.930846 AAGAAGAAGAGATGAAAAGAAATCCA 57.069 30.769 0.00 0.00 0.00 3.41
3186 4450 9.838975 GAAAGAAGAAGAGATGAAAAGAAATCC 57.161 33.333 0.00 0.00 0.00 3.01
3295 4574 0.991355 TAAATCCGGGCATCCAGGGT 60.991 55.000 0.00 0.00 0.00 4.34
3337 4616 1.521010 CGTGATGCAGGCTCAGAGG 60.521 63.158 0.00 0.00 0.00 3.69
3340 4619 2.229675 TTATCGTGATGCAGGCTCAG 57.770 50.000 0.00 0.00 0.00 3.35
3351 4630 2.267426 CGTTGCCACTCATTATCGTGA 58.733 47.619 0.00 0.00 33.04 4.35
3354 4633 2.540515 AGACGTTGCCACTCATTATCG 58.459 47.619 0.00 0.00 0.00 2.92
3369 4648 4.111375 AGATCTGCGATGTTTTAGACGT 57.889 40.909 0.00 0.00 0.00 4.34
3371 4650 8.131455 TCAATAAGATCTGCGATGTTTTAGAC 57.869 34.615 0.00 0.00 0.00 2.59
3374 4653 9.541143 TGTATCAATAAGATCTGCGATGTTTTA 57.459 29.630 0.00 0.00 38.19 1.52
3375 4654 8.437360 TGTATCAATAAGATCTGCGATGTTTT 57.563 30.769 0.00 0.00 38.19 2.43
3376 4655 8.613060 ATGTATCAATAAGATCTGCGATGTTT 57.387 30.769 0.00 0.54 38.19 2.83
3377 4656 9.710900 TTATGTATCAATAAGATCTGCGATGTT 57.289 29.630 0.00 6.28 38.19 2.71
3392 4671 9.740239 GCACACTTTTGATCATTATGTATCAAT 57.260 29.630 15.36 4.67 40.71 2.57
3393 4672 8.959548 AGCACACTTTTGATCATTATGTATCAA 58.040 29.630 12.54 12.54 39.66 2.57
3402 4687 3.120546 CGACGAGCACACTTTTGATCATT 60.121 43.478 0.00 0.00 31.01 2.57
3417 4749 2.095869 TCAGTTCAGAGTTACGACGAGC 60.096 50.000 0.00 0.00 0.00 5.03
3421 4753 3.421231 CACGTTCAGTTCAGAGTTACGAC 59.579 47.826 0.00 0.00 0.00 4.34
3424 4756 3.057734 CCCACGTTCAGTTCAGAGTTAC 58.942 50.000 0.00 0.00 0.00 2.50
3434 4766 3.399330 CAGTAATCAACCCACGTTCAGT 58.601 45.455 0.00 0.00 0.00 3.41
3435 4767 2.742053 CCAGTAATCAACCCACGTTCAG 59.258 50.000 0.00 0.00 0.00 3.02
3436 4768 2.105134 ACCAGTAATCAACCCACGTTCA 59.895 45.455 0.00 0.00 0.00 3.18
3437 4769 2.774687 ACCAGTAATCAACCCACGTTC 58.225 47.619 0.00 0.00 0.00 3.95
3438 4770 2.943036 ACCAGTAATCAACCCACGTT 57.057 45.000 0.00 0.00 0.00 3.99
3441 4773 3.773119 TCCTCTACCAGTAATCAACCCAC 59.227 47.826 0.00 0.00 0.00 4.61
3442 4774 4.030913 CTCCTCTACCAGTAATCAACCCA 58.969 47.826 0.00 0.00 0.00 4.51
3487 4824 1.978782 CTCGTTTTCATTGCCGCTTTC 59.021 47.619 0.00 0.00 0.00 2.62
3489 4826 1.069227 GTCTCGTTTTCATTGCCGCTT 60.069 47.619 0.00 0.00 0.00 4.68
3493 4830 1.128692 CTCCGTCTCGTTTTCATTGCC 59.871 52.381 0.00 0.00 0.00 4.52
3503 4840 0.246635 CCCAACATTCTCCGTCTCGT 59.753 55.000 0.00 0.00 0.00 4.18
3509 4846 0.394216 TGGATGCCCAACATTCTCCG 60.394 55.000 0.00 0.00 39.84 4.63
3527 4864 4.219264 AGGAGGAGAAGAAAGAGCAATG 57.781 45.455 0.00 0.00 0.00 2.82
3562 4900 3.804193 CTCTTTTGCGCGGGGAGC 61.804 66.667 8.83 0.00 43.95 4.70
3595 4933 1.438710 CTCGAAACGCCGCACTTTG 60.439 57.895 0.00 0.00 0.00 2.77
3725 5066 4.703897 GGACGGAATGGATGTCTGATTTA 58.296 43.478 0.00 0.00 33.21 1.40
3786 5127 6.866248 AGTACAACAACAAAAACAACTCCAAG 59.134 34.615 0.00 0.00 0.00 3.61
3787 5128 6.750148 AGTACAACAACAAAAACAACTCCAA 58.250 32.000 0.00 0.00 0.00 3.53
3788 5129 6.334102 AGTACAACAACAAAAACAACTCCA 57.666 33.333 0.00 0.00 0.00 3.86
3789 5130 6.643360 ACAAGTACAACAACAAAAACAACTCC 59.357 34.615 0.00 0.00 0.00 3.85
3790 5131 7.408921 CGACAAGTACAACAACAAAAACAACTC 60.409 37.037 0.00 0.00 0.00 3.01
3791 5132 6.361214 CGACAAGTACAACAACAAAAACAACT 59.639 34.615 0.00 0.00 0.00 3.16
3792 5133 6.142639 ACGACAAGTACAACAACAAAAACAAC 59.857 34.615 0.00 0.00 0.00 3.32
3793 5134 6.142480 CACGACAAGTACAACAACAAAAACAA 59.858 34.615 0.00 0.00 0.00 2.83
3794 5135 5.625721 CACGACAAGTACAACAACAAAAACA 59.374 36.000 0.00 0.00 0.00 2.83
3795 5136 5.059955 CCACGACAAGTACAACAACAAAAAC 59.940 40.000 0.00 0.00 0.00 2.43
3796 5137 5.154932 CCACGACAAGTACAACAACAAAAA 58.845 37.500 0.00 0.00 0.00 1.94
3797 5138 4.379603 CCCACGACAAGTACAACAACAAAA 60.380 41.667 0.00 0.00 0.00 2.44
3798 5139 3.127203 CCCACGACAAGTACAACAACAAA 59.873 43.478 0.00 0.00 0.00 2.83
3799 5140 2.678836 CCCACGACAAGTACAACAACAA 59.321 45.455 0.00 0.00 0.00 2.83
3800 5141 2.281517 CCCACGACAAGTACAACAACA 58.718 47.619 0.00 0.00 0.00 3.33
3801 5142 1.600485 CCCCACGACAAGTACAACAAC 59.400 52.381 0.00 0.00 0.00 3.32
3802 5143 1.475392 CCCCCACGACAAGTACAACAA 60.475 52.381 0.00 0.00 0.00 2.83
3803 5144 0.107081 CCCCCACGACAAGTACAACA 59.893 55.000 0.00 0.00 0.00 3.33
3804 5145 0.393820 TCCCCCACGACAAGTACAAC 59.606 55.000 0.00 0.00 0.00 3.32
3805 5146 0.682852 CTCCCCCACGACAAGTACAA 59.317 55.000 0.00 0.00 0.00 2.41
3806 5147 1.189524 CCTCCCCCACGACAAGTACA 61.190 60.000 0.00 0.00 0.00 2.90
3826 5174 1.613836 ACGTACGTTGTCCTCTTCCT 58.386 50.000 16.72 0.00 0.00 3.36
3837 5185 1.715993 TGCATGCATGTACGTACGTT 58.284 45.000 27.92 5.61 0.00 3.99
3865 5215 2.186903 CCCTCCATGAACGGACGG 59.813 66.667 0.00 0.00 0.00 4.79
3866 5216 2.511600 GCCCTCCATGAACGGACG 60.512 66.667 0.00 0.00 0.00 4.79
3867 5217 2.124695 GGCCCTCCATGAACGGAC 60.125 66.667 0.00 0.00 0.00 4.79
3868 5218 3.407967 GGGCCCTCCATGAACGGA 61.408 66.667 17.04 0.00 35.00 4.69
3869 5219 4.856801 CGGGCCCTCCATGAACGG 62.857 72.222 22.43 0.00 34.36 4.44
3909 5259 4.830765 TGCCGTCTACCCATGCGC 62.831 66.667 0.00 0.00 0.00 6.09
4008 5369 4.530857 CCCTCGCCGGTGTGGATC 62.531 72.222 32.43 0.00 42.00 3.36
4020 5381 2.055042 CCTGTCTCCTCCACCCTCG 61.055 68.421 0.00 0.00 0.00 4.63
4023 5384 2.363172 GCTCCTGTCTCCTCCACCC 61.363 68.421 0.00 0.00 0.00 4.61
4024 5385 2.716017 CGCTCCTGTCTCCTCCACC 61.716 68.421 0.00 0.00 0.00 4.61
4025 5386 1.662438 CTCGCTCCTGTCTCCTCCAC 61.662 65.000 0.00 0.00 0.00 4.02
4026 5387 1.379176 CTCGCTCCTGTCTCCTCCA 60.379 63.158 0.00 0.00 0.00 3.86
4027 5388 2.781158 GCTCGCTCCTGTCTCCTCC 61.781 68.421 0.00 0.00 0.00 4.30
4029 5390 3.137459 CGCTCGCTCCTGTCTCCT 61.137 66.667 0.00 0.00 0.00 3.69
4031 5392 2.407210 CTCGCTCGCTCCTGTCTC 59.593 66.667 0.00 0.00 0.00 3.36
4032 5393 3.821055 GCTCGCTCGCTCCTGTCT 61.821 66.667 0.00 0.00 0.00 3.41
4061 5422 2.435586 CAGCCACTTCCTCGCCAG 60.436 66.667 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.