Multiple sequence alignment - TraesCS1D01G315800

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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 TraesCS1D01G315800 chr1D 100.000 6680 0 0 1 6680 410799235 410792556 0.000000e+00 12336.0
1 TraesCS1D01G315800 chr1A 96.158 2941 91 11 3750 6680 507081462 507078534 0.000000e+00 4785.0
2 TraesCS1D01G315800 chr1A 89.703 1447 105 22 823 2249 507084407 507082985 0.000000e+00 1807.0
3 TraesCS1D01G315800 chr1A 90.949 906 73 8 2294 3194 507082996 507082095 0.000000e+00 1210.0
4 TraesCS1D01G315800 chr1A 91.147 802 57 8 8 802 507085923 507085129 0.000000e+00 1075.0
5 TraesCS1D01G315800 chr1A 93.333 210 14 0 3536 3745 507081755 507081546 1.810000e-80 311.0
6 TraesCS1D01G315800 chr1A 92.857 210 6 5 3332 3534 507082048 507081841 5.070000e-76 296.0
7 TraesCS1D01G315800 chr1B 93.219 2979 147 25 3333 6308 553634557 553631631 0.000000e+00 4331.0
8 TraesCS1D01G315800 chr1B 89.787 1312 89 19 949 2244 553636799 553635517 0.000000e+00 1639.0
9 TraesCS1D01G315800 chr1B 90.447 963 82 9 2294 3249 553635523 553634564 0.000000e+00 1260.0
10 TraesCS1D01G315800 chr1B 92.800 125 8 1 6556 6679 553631543 553631419 5.320000e-41 180.0
11 TraesCS1D01G315800 chr7B 81.398 758 114 15 75 813 379493854 379493105 1.600000e-165 593.0
12 TraesCS1D01G315800 chr7B 91.209 91 3 5 3244 3331 142285350 142285262 1.180000e-22 119.0
13 TraesCS1D01G315800 chr7B 88.571 70 6 1 3276 3343 527038846 527038915 4.290000e-12 84.2
14 TraesCS1D01G315800 chr7D 80.183 767 120 12 75 817 33808370 33809128 4.560000e-151 545.0
15 TraesCS1D01G315800 chr7D 85.714 70 8 1 3276 3343 498714316 498714385 9.290000e-09 73.1
16 TraesCS1D01G315800 chr2B 90.986 355 27 2 5942 6292 234631643 234631290 2.180000e-129 473.0
17 TraesCS1D01G315800 chr2B 96.104 77 3 0 5780 5856 234631727 234631651 7.030000e-25 126.0
18 TraesCS1D01G315800 chr4D 80.000 560 89 19 274 816 357508356 357507803 6.280000e-105 392.0
19 TraesCS1D01G315800 chr5A 93.103 87 6 0 3245 3331 382114855 382114941 1.960000e-25 128.0
20 TraesCS1D01G315800 chr5A 94.737 76 4 0 3255 3330 594323315 594323240 1.180000e-22 119.0
21 TraesCS1D01G315800 chr4A 96.104 77 3 0 3249 3325 662286419 662286495 7.030000e-25 126.0
22 TraesCS1D01G315800 chr4A 92.857 84 6 0 3248 3331 662286502 662286419 9.100000e-24 122.0
23 TraesCS1D01G315800 chr4A 88.776 98 7 3 3236 3331 699896040 699895945 4.230000e-22 117.0
24 TraesCS1D01G315800 chr4A 90.588 85 8 0 3247 3331 697388804 697388888 5.480000e-21 113.0
25 TraesCS1D01G315800 chr6B 92.857 84 6 0 3248 3331 16341348 16341431 9.100000e-24 122.0
26 TraesCS1D01G315800 chr5B 93.671 79 5 0 3253 3331 582392054 582391976 1.180000e-22 119.0
27 TraesCS1D01G315800 chr6D 92.308 52 3 1 6440 6490 155705640 155705691 9.290000e-09 73.1
28 TraesCS1D01G315800 chr2A 97.500 40 1 0 2256 2295 744284069 744284030 1.200000e-07 69.4
29 TraesCS1D01G315800 chr2A 100.000 30 0 0 5890 5919 610175336 610175307 1.000000e-03 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 TraesCS1D01G315800 chr1D 410792556 410799235 6679 True 12336.000000 12336 100.000000 1 6680 1 chr1D.!!$R1 6679
1 TraesCS1D01G315800 chr1A 507078534 507085923 7389 True 1580.666667 4785 92.357833 8 6680 6 chr1A.!!$R1 6672
2 TraesCS1D01G315800 chr1B 553631419 553636799 5380 True 1852.500000 4331 91.563250 949 6679 4 chr1B.!!$R1 5730
3 TraesCS1D01G315800 chr7B 379493105 379493854 749 True 593.000000 593 81.398000 75 813 1 chr7B.!!$R2 738
4 TraesCS1D01G315800 chr7D 33808370 33809128 758 False 545.000000 545 80.183000 75 817 1 chr7D.!!$F1 742
5 TraesCS1D01G315800 chr4D 357507803 357508356 553 True 392.000000 392 80.000000 274 816 1 chr4D.!!$R1 542

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
845 1571 0.107752 ACACGGGTGTACGGTTTGTT 60.108 50.000 1.96 0.00 42.90 2.83 F
847 1573 0.177604 ACGGGTGTACGGTTTGTTGA 59.822 50.000 0.00 0.00 38.39 3.18 F
2291 3037 0.037734 CCCTCCTTTAACTGCCCGTT 59.962 55.000 0.00 0.00 39.64 4.44 F
2325 3071 1.154150 GGCAGTGCTTGTGCGATTC 60.154 57.895 16.11 0.00 42.19 2.52 F
2618 3365 1.293062 AGGTTGATGTCCCAGCATCT 58.707 50.000 7.45 0.00 44.02 2.90 F
3521 4280 0.036875 AGCCGCTCTAGTTTTTGCCT 59.963 50.000 0.00 0.00 0.00 4.75 F
3810 4731 0.108585 TGGAAGGTGCTCCAGTGTTC 59.891 55.000 7.70 1.95 40.71 3.18 F
4162 5091 0.248843 CACCTTCACTCAGAGAGGCC 59.751 60.000 3.79 0.00 33.35 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2272 3018 0.037734 AACGGGCAGTTAAAGGAGGG 59.962 55.000 0.00 0.0 42.14 4.30 R
2356 3102 0.246635 CCCAGTTGGTACACCTCTCG 59.753 60.000 0.00 0.0 39.29 4.04 R
3505 4264 1.128692 CCGAAGGCAAAAACTAGAGCG 59.871 52.381 0.00 0.0 46.14 5.03 R
3521 4280 1.825090 AGCATGCATGTCTTTCCGAA 58.175 45.000 26.79 0.0 0.00 4.30 R
3656 4499 1.888436 CTGACAGCGCCTGGAGGTAA 61.888 60.000 2.29 0.0 35.51 2.85 R
4715 5644 4.703897 AGCAGTTAACGTACATGGCATAT 58.296 39.130 0.00 0.0 0.00 1.78 R
5601 6530 4.037923 GTCAAACCTTCTTTCTGATTGGCA 59.962 41.667 0.00 0.0 0.00 4.92 R
5913 6842 2.222027 GGGGAACTCATTCATTAGCGG 58.778 52.381 0.00 0.0 36.46 5.52 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
26 27 0.179073 AGGGTTTGATGAGATCCGCG 60.179 55.000 0.00 0.00 0.00 6.46
60 61 3.234630 CTTCGCCGTGGGTCTTGGA 62.235 63.158 0.00 0.00 0.00 3.53
69 70 0.253610 TGGGTCTTGGACGTGTGTTT 59.746 50.000 0.00 0.00 32.65 2.83
151 152 3.253955 GCTTTTTGGAGCGAGCGA 58.746 55.556 0.00 0.00 32.23 4.93
207 208 4.711846 ACTATGTTGCAGACCTCTATGTCA 59.288 41.667 0.00 0.00 37.73 3.58
222 223 5.055144 TCTATGTCATTGCATTCTCTCTGC 58.945 41.667 0.00 0.00 40.10 4.26
393 404 4.357699 CAGATCATGCCCGAGCTC 57.642 61.111 2.73 2.73 40.80 4.09
452 463 2.273179 TGGACACGCTAGCGACCTT 61.273 57.895 41.33 21.99 42.83 3.50
459 470 1.542915 ACGCTAGCGACCTTGAGTAAA 59.457 47.619 41.33 0.00 42.83 2.01
460 471 2.029649 ACGCTAGCGACCTTGAGTAAAA 60.030 45.455 41.33 0.00 42.83 1.52
489 502 0.673022 CTCCTGTCAAGTGAGCAGCC 60.673 60.000 0.00 0.00 0.00 4.85
502 515 2.320781 GAGCAGCCAGAGGTTCCTATA 58.679 52.381 0.00 0.00 0.00 1.31
538 556 2.489971 GGGAACCGCGATTTCATGATA 58.510 47.619 8.23 0.00 40.86 2.15
612 630 2.356673 GTCGGTTTTCTCGCCCGT 60.357 61.111 0.00 0.00 42.30 5.28
652 673 1.822371 GTTGAGGGTTGTGGTTGTTGT 59.178 47.619 0.00 0.00 0.00 3.32
653 674 3.018149 GTTGAGGGTTGTGGTTGTTGTA 58.982 45.455 0.00 0.00 0.00 2.41
701 726 1.707239 GCGGTCGTGGTGTTGTTGAA 61.707 55.000 0.00 0.00 0.00 2.69
704 729 1.599419 GGTCGTGGTGTTGTTGAATGC 60.599 52.381 0.00 0.00 0.00 3.56
718 743 7.710044 TGTTGTTGAATGCATTTGTTTGTATCT 59.290 29.630 14.33 0.00 0.00 1.98
778 803 9.454859 AATTCTCTTCTTCCGAATTAATCAACT 57.545 29.630 0.00 0.00 36.06 3.16
804 829 2.286365 TCCTTTTGCCTCCGTTTCAT 57.714 45.000 0.00 0.00 0.00 2.57
844 1570 0.749649 TACACGGGTGTACGGTTTGT 59.250 50.000 0.00 0.00 44.42 2.83
845 1571 0.107752 ACACGGGTGTACGGTTTGTT 60.108 50.000 1.96 0.00 42.90 2.83
847 1573 0.177604 ACGGGTGTACGGTTTGTTGA 59.822 50.000 0.00 0.00 38.39 3.18
849 1575 1.232119 GGGTGTACGGTTTGTTGAGG 58.768 55.000 0.00 0.00 0.00 3.86
850 1576 1.232119 GGTGTACGGTTTGTTGAGGG 58.768 55.000 0.00 0.00 0.00 4.30
851 1577 1.202675 GGTGTACGGTTTGTTGAGGGA 60.203 52.381 0.00 0.00 0.00 4.20
852 1578 2.563702 GTGTACGGTTTGTTGAGGGAA 58.436 47.619 0.00 0.00 0.00 3.97
853 1579 2.944349 GTGTACGGTTTGTTGAGGGAAA 59.056 45.455 0.00 0.00 0.00 3.13
907 1633 0.959553 CCGCACGAGTATACCTGGAT 59.040 55.000 0.00 0.00 0.00 3.41
938 1664 0.834612 TCGTTTGTCCAGTTCCCACT 59.165 50.000 0.00 0.00 0.00 4.00
968 1694 2.032528 CAAAGTCAGCGCAGGGGA 59.967 61.111 11.47 0.00 0.00 4.81
1121 1847 2.813908 CTCAACCCGTACCAGCGC 60.814 66.667 0.00 0.00 0.00 5.92
1135 1861 4.459089 GCGCCTCCCGAGCTTTCT 62.459 66.667 0.00 0.00 40.02 2.52
1263 1989 3.135530 CCTCCGATTCCTCAATTTCCTCT 59.864 47.826 0.00 0.00 0.00 3.69
1301 2027 1.949257 CGTGACCTGCCTTGGTTTC 59.051 57.895 0.00 0.00 41.00 2.78
1498 2227 2.113139 CCCAGCGAGGTTGGTTGT 59.887 61.111 0.00 0.00 31.87 3.32
1510 2240 1.069500 GTTGGTTGTGGTGTATCGTGC 60.069 52.381 0.00 0.00 0.00 5.34
1511 2241 0.394938 TGGTTGTGGTGTATCGTGCT 59.605 50.000 0.00 0.00 0.00 4.40
1512 2242 1.076332 GGTTGTGGTGTATCGTGCTC 58.924 55.000 0.00 0.00 0.00 4.26
1513 2243 1.606994 GGTTGTGGTGTATCGTGCTCA 60.607 52.381 0.00 0.00 0.00 4.26
1519 2249 1.202582 GGTGTATCGTGCTCACTCACT 59.797 52.381 0.00 0.00 34.92 3.41
1548 2278 1.367346 TTGGGGTGATTCTGGTGCTA 58.633 50.000 0.00 0.00 0.00 3.49
1653 2383 0.178961 AGGAACTTTTGCAGGGACCC 60.179 55.000 0.59 0.59 27.25 4.46
1691 2421 9.537192 TGTATACCAGTATTGTAATGTGCTAAC 57.463 33.333 0.00 0.00 0.00 2.34
1697 2427 9.547753 CCAGTATTGTAATGTGCTAACTATTCT 57.452 33.333 0.00 0.00 0.00 2.40
1708 2438 5.582269 GTGCTAACTATTCTCACTTGCATCA 59.418 40.000 0.00 0.00 0.00 3.07
1715 2445 4.335400 TTCTCACTTGCATCACACAGTA 57.665 40.909 0.00 0.00 0.00 2.74
1720 2450 3.364920 CACTTGCATCACACAGTACGTAG 59.635 47.826 0.00 0.00 0.00 3.51
1727 2457 5.455849 GCATCACACAGTACGTAGTCTATTG 59.544 44.000 0.00 0.00 43.93 1.90
1792 2528 8.606040 AAATTGGGTCAATAAATTGTGTCAAG 57.394 30.769 2.80 0.00 38.84 3.02
1793 2529 5.132897 TGGGTCAATAAATTGTGTCAAGC 57.867 39.130 2.80 0.00 38.84 4.01
1798 2534 5.858581 GTCAATAAATTGTGTCAAGCTGTCC 59.141 40.000 2.80 0.00 38.84 4.02
1807 2543 1.672030 CAAGCTGTCCATCGCCACA 60.672 57.895 0.00 0.00 0.00 4.17
1831 2567 4.889832 AGAGCGAAAATTAAGGCAGATG 57.110 40.909 0.00 0.00 0.00 2.90
1851 2587 7.431249 CAGATGCTTAGATTGGTGCATATTTT 58.569 34.615 0.00 0.00 44.80 1.82
1912 2648 3.778075 TGTAAAGGGCTGTAGGATTAGCA 59.222 43.478 0.00 0.00 41.63 3.49
1981 2725 5.072736 TGCACAGAGAATATCCATCCTGAAT 59.927 40.000 0.00 0.00 0.00 2.57
1984 2728 6.649973 CACAGAGAATATCCATCCTGAATGAC 59.350 42.308 0.00 0.00 37.59 3.06
2033 2777 2.658285 TCTTTTCCTGGCATATGCAGG 58.342 47.619 28.07 27.53 44.36 4.85
2053 2797 2.357569 GGCTGAGGAATCAGGGAACATT 60.358 50.000 7.33 0.00 38.14 2.71
2056 2800 4.384647 GCTGAGGAATCAGGGAACATTAGT 60.385 45.833 7.33 0.00 38.14 2.24
2058 2802 4.141937 TGAGGAATCAGGGAACATTAGTCG 60.142 45.833 0.00 0.00 0.00 4.18
2111 2855 2.086869 CTGAGTTACTTGCCATGGTGG 58.913 52.381 14.67 6.41 41.55 4.61
2125 2869 2.534042 TGGTGGGTGTTTCTTTTCCA 57.466 45.000 0.00 0.00 0.00 3.53
2135 2879 5.005299 GGTGTTTCTTTTCCATGTGAAAACG 59.995 40.000 14.39 11.74 45.64 3.60
2140 2884 9.620660 GTTTCTTTTCCATGTGAAAACGTATAT 57.379 29.630 14.39 0.00 45.64 0.86
2146 2890 8.735303 TTCCATGTGAAAACGTATATTTGTTG 57.265 30.769 0.00 0.00 0.00 3.33
2150 2894 8.785101 CATGTGAAAACGTATATTTGTTGCTAC 58.215 33.333 0.00 0.00 0.00 3.58
2185 2929 9.933723 TTTTGTTTACCCAGATTCTAGTACTAC 57.066 33.333 0.00 0.00 0.00 2.73
2187 2931 8.890410 TGTTTACCCAGATTCTAGTACTACTT 57.110 34.615 0.00 0.00 0.00 2.24
2188 2932 8.964772 TGTTTACCCAGATTCTAGTACTACTTC 58.035 37.037 0.00 0.00 0.00 3.01
2189 2933 8.964772 GTTTACCCAGATTCTAGTACTACTTCA 58.035 37.037 0.00 0.00 0.00 3.02
2190 2934 9.710818 TTTACCCAGATTCTAGTACTACTTCAT 57.289 33.333 0.00 0.00 0.00 2.57
2191 2935 7.826918 ACCCAGATTCTAGTACTACTTCATC 57.173 40.000 0.00 0.00 0.00 2.92
2202 2946 4.618920 ACTACTTCATCGGGACTTTTGT 57.381 40.909 0.00 0.00 0.00 2.83
2225 2971 6.646653 TGTCTTGAGCAACATAAACTCTGTAG 59.353 38.462 0.00 0.00 0.00 2.74
2228 2974 8.097038 TCTTGAGCAACATAAACTCTGTAGATT 58.903 33.333 0.00 0.00 0.00 2.40
2231 2977 8.721478 TGAGCAACATAAACTCTGTAGATTTTC 58.279 33.333 1.17 0.00 30.97 2.29
2237 2983 9.268268 ACATAAACTCTGTAGATTTTCGTTTCA 57.732 29.630 1.17 0.00 30.97 2.69
2240 2986 6.170675 ACTCTGTAGATTTTCGTTTCATGC 57.829 37.500 0.00 0.00 0.00 4.06
2241 2987 5.934625 ACTCTGTAGATTTTCGTTTCATGCT 59.065 36.000 0.00 0.00 0.00 3.79
2242 2988 7.097192 ACTCTGTAGATTTTCGTTTCATGCTA 58.903 34.615 0.00 0.00 0.00 3.49
2243 2989 7.766278 ACTCTGTAGATTTTCGTTTCATGCTAT 59.234 33.333 0.00 0.00 0.00 2.97
2244 2990 8.492673 TCTGTAGATTTTCGTTTCATGCTATT 57.507 30.769 0.00 0.00 0.00 1.73
2245 2991 9.594478 TCTGTAGATTTTCGTTTCATGCTATTA 57.406 29.630 0.00 0.00 0.00 0.98
2250 2996 9.353999 AGATTTTCGTTTCATGCTATTAAAACC 57.646 29.630 0.00 0.00 0.00 3.27
2251 2997 7.555639 TTTTCGTTTCATGCTATTAAAACCG 57.444 32.000 0.00 0.00 0.00 4.44
2252 2998 4.654015 TCGTTTCATGCTATTAAAACCGC 58.346 39.130 0.00 0.00 0.00 5.68
2253 2999 4.154375 TCGTTTCATGCTATTAAAACCGCA 59.846 37.500 0.00 0.00 36.75 5.69
2254 3000 4.495472 CGTTTCATGCTATTAAAACCGCAG 59.505 41.667 0.00 0.00 35.66 5.18
2286 3032 3.254470 GAGAGTCCCTCCTTTAACTGC 57.746 52.381 0.00 0.00 35.87 4.40
2287 3033 1.909986 AGAGTCCCTCCTTTAACTGCC 59.090 52.381 0.00 0.00 0.00 4.85
2288 3034 0.992695 AGTCCCTCCTTTAACTGCCC 59.007 55.000 0.00 0.00 0.00 5.36
2289 3035 0.392595 GTCCCTCCTTTAACTGCCCG 60.393 60.000 0.00 0.00 0.00 6.13
2290 3036 0.838987 TCCCTCCTTTAACTGCCCGT 60.839 55.000 0.00 0.00 0.00 5.28
2291 3037 0.037734 CCCTCCTTTAACTGCCCGTT 59.962 55.000 0.00 0.00 39.64 4.44
2292 3038 1.279846 CCCTCCTTTAACTGCCCGTTA 59.720 52.381 0.00 0.00 37.05 3.18
2309 3055 3.746492 CCGTTAGTGCTATAAGAATGGGC 59.254 47.826 0.00 0.00 0.00 5.36
2315 3061 2.173356 TGCTATAAGAATGGGCAGTGCT 59.827 45.455 16.11 0.00 0.00 4.40
2317 3063 3.004106 GCTATAAGAATGGGCAGTGCTTG 59.996 47.826 16.11 0.00 0.00 4.01
2321 3067 2.807631 GAATGGGCAGTGCTTGTGCG 62.808 60.000 16.11 0.00 42.19 5.34
2325 3071 1.154150 GGCAGTGCTTGTGCGATTC 60.154 57.895 16.11 0.00 42.19 2.52
2349 3095 5.801531 TCACTGAAAGGAAGTGCTACTTA 57.198 39.130 2.17 0.00 43.88 2.24
2356 3102 9.303537 CTGAAAGGAAGTGCTACTTAGTAATAC 57.696 37.037 0.00 0.00 38.80 1.89
2359 3105 7.261829 AGGAAGTGCTACTTAGTAATACGAG 57.738 40.000 0.00 0.00 38.80 4.18
2368 3114 6.934048 ACTTAGTAATACGAGAGGTGTACC 57.066 41.667 0.00 0.00 0.00 3.34
2371 3117 5.573337 AGTAATACGAGAGGTGTACCAAC 57.427 43.478 3.56 0.00 38.89 3.77
2383 3129 2.682856 GTGTACCAACTGGGCATACATG 59.317 50.000 0.00 0.00 42.05 3.21
2391 3137 5.450412 CCAACTGGGCATACATGATTACAAC 60.450 44.000 0.00 0.00 0.00 3.32
2395 3141 6.146601 TGGGCATACATGATTACAACAATG 57.853 37.500 0.00 0.00 0.00 2.82
2412 3159 4.599041 ACAATGGAGGCAATAGCTGTTTA 58.401 39.130 0.00 0.00 41.70 2.01
2413 3160 5.016173 ACAATGGAGGCAATAGCTGTTTAA 58.984 37.500 0.00 0.00 41.70 1.52
2415 3162 6.155049 ACAATGGAGGCAATAGCTGTTTAAAT 59.845 34.615 0.00 0.00 41.70 1.40
2417 3164 4.142182 TGGAGGCAATAGCTGTTTAAATGC 60.142 41.667 0.00 0.00 41.70 3.56
2419 3166 5.394553 GGAGGCAATAGCTGTTTAAATGCTT 60.395 40.000 19.01 7.73 41.70 3.91
2425 3172 6.726258 ATAGCTGTTTAAATGCTTTTTGGC 57.274 33.333 19.01 2.23 38.15 4.52
2428 3175 5.589855 AGCTGTTTAAATGCTTTTTGGCTTT 59.410 32.000 11.34 0.00 32.61 3.51
2430 3177 7.281999 AGCTGTTTAAATGCTTTTTGGCTTTAA 59.718 29.630 11.34 0.00 32.61 1.52
2461 3208 7.386299 TGTTCTTTGAGCTCAGAAAGAGTAATC 59.614 37.037 23.34 15.53 46.47 1.75
2467 3214 7.563020 TGAGCTCAGAAAGAGTAATCATGAAT 58.437 34.615 13.74 0.00 46.47 2.57
2508 3255 6.998258 AATCAGAACTGCATTTCTTTTTCG 57.002 33.333 16.01 5.78 33.31 3.46
2591 3338 2.999355 GTCATCTCAGCACCTCAGTTTC 59.001 50.000 0.00 0.00 0.00 2.78
2615 3362 3.420893 CTTTTAGGTTGATGTCCCAGCA 58.579 45.455 0.00 0.00 0.00 4.41
2618 3365 1.293062 AGGTTGATGTCCCAGCATCT 58.707 50.000 7.45 0.00 44.02 2.90
2721 3468 4.201851 CCGATGTAAATCAGAAGCAGGTTG 60.202 45.833 0.00 0.00 0.00 3.77
2764 3511 2.810400 GCCTGCCCTGATTTATAGCGAA 60.810 50.000 0.00 0.00 0.00 4.70
2771 3518 4.991687 CCCTGATTTATAGCGAAGGAAGAC 59.008 45.833 0.00 0.00 0.00 3.01
2806 3553 6.712095 TCAGCCATTATCAGGTTGAATATGAC 59.288 38.462 0.00 0.00 42.36 3.06
2827 3574 2.016905 CCGGATCCTCCCTTGAGTAT 57.983 55.000 10.75 0.00 36.86 2.12
2830 3577 3.258622 CCGGATCCTCCCTTGAGTATAAC 59.741 52.174 10.75 0.00 36.86 1.89
2840 3587 6.889198 TCCCTTGAGTATAACAGGAAGAATG 58.111 40.000 0.00 0.00 0.00 2.67
2881 3628 2.689983 CCCATCAACAATAGCCAAGTCC 59.310 50.000 0.00 0.00 0.00 3.85
2923 3670 3.445008 AGGAGTCTCAGCCTTAACATCA 58.555 45.455 1.47 0.00 0.00 3.07
2946 3693 6.883756 TCAAGTGTAAGGTTCATTATGATGCA 59.116 34.615 0.00 0.00 33.14 3.96
2962 3709 5.112220 TGATGCAGTTTCATTTCACTGAC 57.888 39.130 3.48 0.00 42.74 3.51
2970 3717 5.827797 AGTTTCATTTCACTGACCTTTAGCA 59.172 36.000 0.00 0.00 0.00 3.49
2974 3721 6.946340 TCATTTCACTGACCTTTAGCATCTA 58.054 36.000 0.00 0.00 0.00 1.98
2976 3723 7.550551 TCATTTCACTGACCTTTAGCATCTAAG 59.449 37.037 0.00 0.00 0.00 2.18
2977 3724 6.605471 TTCACTGACCTTTAGCATCTAAGA 57.395 37.500 0.00 0.00 0.00 2.10
2983 3734 7.004555 TGACCTTTAGCATCTAAGAACAAGA 57.995 36.000 0.00 0.00 0.00 3.02
3000 3751 9.899226 AAGAACAAGATGCACTTAGTTTTTATC 57.101 29.630 0.00 0.00 37.03 1.75
3025 3776 6.511282 CGAGTTGATGATCTTGGTCAATGATG 60.511 42.308 0.00 0.00 34.71 3.07
3037 3788 4.951094 TGGTCAATGATGATCAGAATGCAA 59.049 37.500 0.09 0.00 41.75 4.08
3059 3810 2.601763 GACATATCAACGTTCCACCGAC 59.398 50.000 0.00 0.00 0.00 4.79
3060 3811 1.586578 CATATCAACGTTCCACCGACG 59.413 52.381 0.00 0.00 45.46 5.12
3187 3939 8.222637 TCAGTAATAAGCATAGGACCTAGTGTA 58.777 37.037 7.43 0.00 0.00 2.90
3208 3960 7.815068 AGTGTATTTGTAAGTTCAGTCAGCTAG 59.185 37.037 0.00 0.00 0.00 3.42
3260 4013 9.952030 TTGATCAATGTAATACAACCTCTGTAA 57.048 29.630 3.38 0.00 43.75 2.41
3261 4014 9.378551 TGATCAATGTAATACAACCTCTGTAAC 57.621 33.333 0.00 0.00 43.75 2.50
3262 4015 9.601217 GATCAATGTAATACAACCTCTGTAACT 57.399 33.333 0.00 0.00 43.75 2.24
3274 4027 9.798994 ACAACCTCTGTAACTAAATATAAGACG 57.201 33.333 0.00 0.00 36.10 4.18
3275 4028 9.798994 CAACCTCTGTAACTAAATATAAGACGT 57.201 33.333 0.00 0.00 0.00 4.34
3286 4039 9.821662 ACTAAATATAAGACGTTTTTGCAGTTC 57.178 29.630 0.00 0.00 0.00 3.01
3287 4040 9.820229 CTAAATATAAGACGTTTTTGCAGTTCA 57.180 29.630 0.00 0.00 0.00 3.18
3289 4042 9.522804 AAATATAAGACGTTTTTGCAGTTCAAA 57.477 25.926 0.00 0.00 42.50 2.69
3290 4043 9.691362 AATATAAGACGTTTTTGCAGTTCAAAT 57.309 25.926 0.00 0.00 43.53 2.32
3291 4044 9.691362 ATATAAGACGTTTTTGCAGTTCAAATT 57.309 25.926 0.00 0.00 43.53 1.82
3292 4045 5.701029 AGACGTTTTTGCAGTTCAAATTG 57.299 34.783 0.00 0.00 43.53 2.32
3293 4046 5.406649 AGACGTTTTTGCAGTTCAAATTGA 58.593 33.333 0.00 0.00 43.53 2.57
3294 4047 5.866633 AGACGTTTTTGCAGTTCAAATTGAA 59.133 32.000 4.03 4.03 43.53 2.69
3330 4083 9.939424 AGTCTTATATTTAGTTACAGAGGGAGT 57.061 33.333 0.00 0.00 0.00 3.85
3366 4119 9.369904 GTTGAAAACTTGATGCCATTACATATT 57.630 29.630 0.00 0.00 45.32 1.28
3443 4196 3.807622 CGTCCTCACTGAAGCTAAAAACA 59.192 43.478 0.00 0.00 0.00 2.83
3475 4228 5.413833 AGTCTAATTCTGTTTGAGGCATGTG 59.586 40.000 0.00 0.00 0.00 3.21
3507 4266 4.676924 GCTTATTCATTGTCAATTAGCCGC 59.323 41.667 0.00 0.00 32.25 6.53
3516 4275 4.575885 TGTCAATTAGCCGCTCTAGTTTT 58.424 39.130 0.00 0.00 0.00 2.43
3521 4280 0.036875 AGCCGCTCTAGTTTTTGCCT 59.963 50.000 0.00 0.00 0.00 4.75
3523 4282 1.135660 GCCGCTCTAGTTTTTGCCTTC 60.136 52.381 0.00 0.00 0.00 3.46
3534 4293 3.641437 TTTTGCCTTCGGAAAGACATG 57.359 42.857 0.00 0.00 34.14 3.21
3718 4561 3.198635 ACATCCACTGTCTTCCTGGTATG 59.801 47.826 0.00 0.00 29.94 2.39
3770 4691 8.941977 ACATTTATGACGTCAGCTGTTAATAAA 58.058 29.630 24.41 18.96 0.00 1.40
3810 4731 0.108585 TGGAAGGTGCTCCAGTGTTC 59.891 55.000 7.70 1.95 40.71 3.18
3900 4821 3.305720 TCAGGTGAGTTTACTGGTGTCT 58.694 45.455 0.00 0.00 33.19 3.41
3973 4902 3.614092 ACAGCTTGTGATTACATGGGAG 58.386 45.455 0.00 0.00 36.53 4.30
4009 4938 3.011566 TGGAGCAGAAACAAACTGGAA 57.988 42.857 0.00 0.00 36.09 3.53
4011 4940 2.952310 GGAGCAGAAACAAACTGGAACT 59.048 45.455 0.00 0.00 36.09 3.01
4023 4952 5.594317 ACAAACTGGAACTAATTGAGCAAGT 59.406 36.000 0.00 0.00 0.00 3.16
4065 4994 6.449635 TGACAAAAGTGCAGACAGTAAAAT 57.550 33.333 0.00 0.00 0.00 1.82
4079 5008 7.336679 CAGACAGTAAAATGGTGGAATCATGTA 59.663 37.037 0.00 0.00 0.00 2.29
4090 5019 5.948162 GGTGGAATCATGTAGCATGGATAAT 59.052 40.000 8.95 0.00 0.00 1.28
4096 5025 9.828039 GAATCATGTAGCATGGATAATCATAGA 57.172 33.333 8.95 0.00 0.00 1.98
4117 5046 6.120507 AGAAGGTTTGTCTCTAATTCAGCT 57.879 37.500 0.00 0.00 0.00 4.24
4162 5091 0.248843 CACCTTCACTCAGAGAGGCC 59.751 60.000 3.79 0.00 33.35 5.19
4336 5265 5.069648 CACCTCACTTGCTGGAGAATATCTA 59.930 44.000 0.00 0.00 32.87 1.98
4391 5320 5.988310 TTGCAAGATGTCCAATGAAGATT 57.012 34.783 0.00 0.00 0.00 2.40
4394 5323 5.713389 TGCAAGATGTCCAATGAAGATTCTT 59.287 36.000 0.00 0.00 0.00 2.52
4736 5665 6.721571 ATATATGCCATGTACGTTAACTGC 57.278 37.500 3.71 0.00 0.00 4.40
5042 5971 1.687660 ACCACTGTCAAATTGCATGCA 59.312 42.857 18.46 18.46 0.00 3.96
5132 6061 5.007682 GGTGTTTTCCTGCTTCACCTATAA 58.992 41.667 0.00 0.00 43.34 0.98
5210 6139 8.816144 GCAGTCATCTTAGTTTTCTAGATTCTG 58.184 37.037 0.00 0.00 33.61 3.02
5238 6167 2.752903 GCCCAACATACTCGTTTCCATT 59.247 45.455 0.00 0.00 0.00 3.16
5601 6530 5.880887 AGTTTCGGAGTTCTCAAAGTTTCTT 59.119 36.000 2.24 0.00 0.00 2.52
5725 6654 7.659186 CACAAATGGATAGTACTAGTACCCTC 58.341 42.308 25.97 21.44 36.75 4.30
5744 6673 6.071984 ACCCTCAATACATAGGAGTACAGAG 58.928 44.000 0.00 0.00 34.58 3.35
5886 6815 3.084039 CAAGGCCTTCAAAGCATACTCA 58.916 45.455 17.29 0.00 0.00 3.41
5913 6842 0.394899 AGATTGCTAACCAGGCCTGC 60.395 55.000 28.39 16.37 0.00 4.85
5930 6859 2.289002 CCTGCCGCTAATGAATGAGTTC 59.711 50.000 0.00 0.00 34.85 3.01
5931 6860 2.288666 TGCCGCTAATGAATGAGTTCC 58.711 47.619 0.00 0.00 33.26 3.62
5932 6861 1.604278 GCCGCTAATGAATGAGTTCCC 59.396 52.381 0.00 0.00 33.26 3.97
5934 6863 2.222027 CGCTAATGAATGAGTTCCCCC 58.778 52.381 0.00 0.00 33.26 5.40
5999 6928 6.499350 TCCAAGTAGAAGGGTGTTACAATAGT 59.501 38.462 0.00 0.00 0.00 2.12
6003 6932 4.324267 AGAAGGGTGTTACAATAGTGTGC 58.676 43.478 5.98 0.00 38.82 4.57
6046 6975 6.043411 GTGGACATATCTTCAGGAAGTGTAC 58.957 44.000 8.75 7.52 39.38 2.90
6149 7078 3.806316 TTTTTAGCGTCTGCAGTTAGC 57.194 42.857 14.67 16.81 46.23 3.09
6183 7112 9.558648 CATCGACATGTTTTCTGATTCATTTAA 57.441 29.630 0.00 0.00 0.00 1.52
6320 7250 5.730269 CACGAAACAAACGTTATACAGTGT 58.270 37.500 0.00 0.00 42.07 3.55
6321 7251 6.186785 CACGAAACAAACGTTATACAGTGTT 58.813 36.000 0.00 4.46 42.07 3.32
6322 7252 7.336232 CACGAAACAAACGTTATACAGTGTTA 58.664 34.615 12.68 0.00 42.07 2.41
6357 7287 7.213151 GCGAAATAACGTTATACAGTGTTTGTC 59.787 37.037 20.62 7.37 37.12 3.18
6414 7344 5.408604 GTGAACAACACGTCCTCTTATCATT 59.591 40.000 0.00 0.00 39.78 2.57
6460 7390 0.391228 TTCAGTGCCGTAACTGCAGA 59.609 50.000 23.35 0.00 45.93 4.26
6510 7441 0.325933 AGCAGCAGTTAGGCATCACA 59.674 50.000 0.00 0.00 35.83 3.58
6516 7447 0.537188 AGTTAGGCATCACACCTCCG 59.463 55.000 0.00 0.00 38.81 4.63
6543 7474 5.510520 GGGGCATTGAAAACAATGAACAGTA 60.511 40.000 21.74 0.00 43.26 2.74
6547 7478 8.028938 GGCATTGAAAACAATGAACAGTATAGT 58.971 33.333 21.74 0.00 43.26 2.12
6559 7490 7.821595 TGAACAGTATAGTTTGACAATACCG 57.178 36.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.354948 TCTCATCAAACCCTCACATGG 57.645 47.619 0.00 0.00 0.00 3.66
1 2 3.881688 GGATCTCATCAAACCCTCACATG 59.118 47.826 0.00 0.00 0.00 3.21
3 4 2.093500 CGGATCTCATCAAACCCTCACA 60.093 50.000 0.00 0.00 0.00 3.58
4 5 2.555199 CGGATCTCATCAAACCCTCAC 58.445 52.381 0.00 0.00 0.00 3.51
5 6 1.134401 GCGGATCTCATCAAACCCTCA 60.134 52.381 0.00 0.00 0.00 3.86
6 7 1.587547 GCGGATCTCATCAAACCCTC 58.412 55.000 0.00 0.00 0.00 4.30
50 51 0.253610 AAACACACGTCCAAGACCCA 59.746 50.000 0.00 0.00 0.00 4.51
54 55 3.194861 CAGAGAAAACACACGTCCAAGA 58.805 45.455 0.00 0.00 0.00 3.02
55 56 2.286418 GCAGAGAAAACACACGTCCAAG 60.286 50.000 0.00 0.00 0.00 3.61
60 61 1.933853 GACTGCAGAGAAAACACACGT 59.066 47.619 23.35 0.00 0.00 4.49
151 152 4.855298 AGAGTCTACTCAGAGTAGCCTT 57.145 45.455 27.13 16.82 45.93 4.35
207 208 1.434622 CCGCGCAGAGAGAATGCAAT 61.435 55.000 8.75 0.00 44.05 3.56
222 223 4.072088 GAGCAAACACCGACCGCG 62.072 66.667 0.00 0.00 37.24 6.46
300 311 2.521224 GGGGAGGTAGGCGTCGAT 60.521 66.667 0.00 0.00 0.00 3.59
393 404 3.199880 AGACTCAAACACAACTCCCTG 57.800 47.619 0.00 0.00 0.00 4.45
489 502 6.938596 TGCATCATCAATTATAGGAACCTCTG 59.061 38.462 0.00 0.00 0.00 3.35
502 515 4.621274 CGGTTCCCTTTTGCATCATCAATT 60.621 41.667 0.00 0.00 0.00 2.32
538 556 7.548097 ACGACATGACAAAGTGATTACTATCT 58.452 34.615 0.00 0.00 35.69 1.98
554 572 0.944311 AGCCACGTCAACGACATGAC 60.944 55.000 9.88 9.61 44.96 3.06
557 575 0.586319 CAAAGCCACGTCAACGACAT 59.414 50.000 9.88 0.00 43.02 3.06
561 579 2.051345 GCCAAAGCCACGTCAACG 60.051 61.111 0.12 0.12 46.33 4.10
588 606 1.202203 CGAGAAAACCGACAACGACA 58.798 50.000 0.00 0.00 42.66 4.35
612 630 2.224426 ACACTTCTACAATGCGGAACCA 60.224 45.455 0.00 0.00 0.00 3.67
652 673 3.355378 CTCACCAAATGCTCCCAACATA 58.645 45.455 0.00 0.00 0.00 2.29
653 674 2.173519 CTCACCAAATGCTCCCAACAT 58.826 47.619 0.00 0.00 0.00 2.71
683 704 0.941542 ATTCAACAACACCACGACCG 59.058 50.000 0.00 0.00 0.00 4.79
704 729 8.859156 CCGGATAAAAACAGATACAAACAAATG 58.141 33.333 0.00 0.00 0.00 2.32
745 770 3.832490 TCGGAAGAAGAGAATTGTCCAGA 59.168 43.478 0.00 0.00 37.03 3.86
817 842 0.684153 TACACCCGTGTAGCCCTACC 60.684 60.000 3.57 0.00 44.42 3.18
818 843 0.457443 GTACACCCGTGTAGCCCTAC 59.543 60.000 7.93 0.00 45.61 3.18
819 844 1.031571 CGTACACCCGTGTAGCCCTA 61.032 60.000 7.93 0.00 45.61 3.53
820 845 2.345760 CGTACACCCGTGTAGCCCT 61.346 63.158 7.93 0.00 45.61 5.19
821 846 2.182537 CGTACACCCGTGTAGCCC 59.817 66.667 7.93 0.00 45.61 5.19
938 1664 3.675775 GCTGACTTTGTTTGCTGGTTGAA 60.676 43.478 0.00 0.00 0.00 2.69
1032 1758 2.964389 GCCATCGCCGAGAAGCTC 60.964 66.667 0.00 0.00 31.69 4.09
1243 1969 3.134804 GGAGAGGAAATTGAGGAATCGGA 59.865 47.826 0.00 0.00 0.00 4.55
1263 1989 0.596577 CGATTAGGCTCGAATCCGGA 59.403 55.000 6.61 6.61 41.12 5.14
1301 2027 4.078516 GGACCCCGACCTGGAACG 62.079 72.222 0.00 5.88 42.00 3.95
1498 2227 1.067846 GTGAGTGAGCACGATACACCA 60.068 52.381 0.00 0.00 35.47 4.17
1519 2249 3.524789 AGAATCACCCCAATCAGACATGA 59.475 43.478 0.00 0.00 40.50 3.07
1691 2421 4.934001 ACTGTGTGATGCAAGTGAGAATAG 59.066 41.667 0.00 0.00 0.00 1.73
1697 2427 2.223947 ACGTACTGTGTGATGCAAGTGA 60.224 45.455 0.00 0.00 0.00 3.41
1708 2438 5.391736 GCACTCAATAGACTACGTACTGTGT 60.392 44.000 0.00 0.00 0.00 3.72
1763 2499 9.218440 GACACAATTTATTGACCCAATTTCATT 57.782 29.630 9.32 0.00 40.14 2.57
1772 2508 5.163513 CAGCTTGACACAATTTATTGACCC 58.836 41.667 9.32 0.00 40.14 4.46
1773 2509 5.772521 ACAGCTTGACACAATTTATTGACC 58.227 37.500 9.32 0.00 40.14 4.02
1775 2511 5.534278 TGGACAGCTTGACACAATTTATTGA 59.466 36.000 9.32 0.00 40.14 2.57
1779 2515 4.154015 CGATGGACAGCTTGACACAATTTA 59.846 41.667 0.00 0.00 0.00 1.40
1780 2516 3.058016 CGATGGACAGCTTGACACAATTT 60.058 43.478 0.00 0.00 0.00 1.82
1781 2517 2.485426 CGATGGACAGCTTGACACAATT 59.515 45.455 0.00 0.00 0.00 2.32
1782 2518 2.079158 CGATGGACAGCTTGACACAAT 58.921 47.619 0.00 0.00 0.00 2.71
1783 2519 1.511850 CGATGGACAGCTTGACACAA 58.488 50.000 0.00 0.00 0.00 3.33
1784 2520 0.950555 GCGATGGACAGCTTGACACA 60.951 55.000 0.00 0.00 0.00 3.72
1785 2521 1.639298 GGCGATGGACAGCTTGACAC 61.639 60.000 0.00 0.00 0.00 3.67
1792 2528 0.940126 CTTATGTGGCGATGGACAGC 59.060 55.000 0.00 0.00 0.00 4.40
1793 2529 2.477825 CTCTTATGTGGCGATGGACAG 58.522 52.381 0.00 0.00 0.00 3.51
1807 2543 6.514048 GCATCTGCCTTAATTTTCGCTCTTAT 60.514 38.462 0.00 0.00 34.31 1.73
1815 2551 7.650903 CCAATCTAAGCATCTGCCTTAATTTTC 59.349 37.037 0.00 0.00 43.38 2.29
1820 2556 4.883585 CACCAATCTAAGCATCTGCCTTAA 59.116 41.667 0.00 0.00 43.38 1.85
1824 2560 1.336125 GCACCAATCTAAGCATCTGCC 59.664 52.381 0.00 0.00 43.38 4.85
1831 2567 5.754890 CCCAAAAATATGCACCAATCTAAGC 59.245 40.000 0.00 0.00 0.00 3.09
1875 2611 5.505780 CCCTTTACAATACTGTCCCATTGA 58.494 41.667 8.37 0.00 36.96 2.57
1895 2631 2.478872 TCTGCTAATCCTACAGCCCT 57.521 50.000 0.00 0.00 36.95 5.19
1930 2674 7.857734 TCTTCAACACACAGAATTAAGAACA 57.142 32.000 0.00 0.00 0.00 3.18
1933 2677 7.467267 GCAGTTCTTCAACACACAGAATTAAGA 60.467 37.037 0.00 0.00 34.60 2.10
2013 2757 2.658285 CCTGCATATGCCAGGAAAAGA 58.342 47.619 28.27 8.80 39.83 2.52
2033 2777 2.725221 ATGTTCCCTGATTCCTCAGC 57.275 50.000 0.00 0.00 46.39 4.26
2053 2797 2.025155 GCTCCAGAATCTCCACGACTA 58.975 52.381 0.00 0.00 0.00 2.59
2056 2800 1.107114 GAGCTCCAGAATCTCCACGA 58.893 55.000 0.87 0.00 0.00 4.35
2058 2802 0.467804 GGGAGCTCCAGAATCTCCAC 59.532 60.000 33.29 8.80 46.24 4.02
2125 2869 8.726988 AGTAGCAACAAATATACGTTTTCACAT 58.273 29.630 0.00 0.00 0.00 3.21
2181 2925 4.283722 AGACAAAAGTCCCGATGAAGTAGT 59.716 41.667 0.00 0.00 0.00 2.73
2182 2926 4.822026 AGACAAAAGTCCCGATGAAGTAG 58.178 43.478 0.00 0.00 0.00 2.57
2183 2927 4.884668 AGACAAAAGTCCCGATGAAGTA 57.115 40.909 0.00 0.00 0.00 2.24
2184 2928 3.771577 AGACAAAAGTCCCGATGAAGT 57.228 42.857 0.00 0.00 0.00 3.01
2185 2929 4.065088 TCAAGACAAAAGTCCCGATGAAG 58.935 43.478 0.00 0.00 0.00 3.02
2187 2931 3.664107 CTCAAGACAAAAGTCCCGATGA 58.336 45.455 0.00 0.00 0.00 2.92
2188 2932 2.160417 GCTCAAGACAAAAGTCCCGATG 59.840 50.000 0.00 0.00 0.00 3.84
2189 2933 2.224523 TGCTCAAGACAAAAGTCCCGAT 60.225 45.455 0.00 0.00 0.00 4.18
2190 2934 1.140052 TGCTCAAGACAAAAGTCCCGA 59.860 47.619 0.00 0.00 0.00 5.14
2191 2935 1.593196 TGCTCAAGACAAAAGTCCCG 58.407 50.000 0.00 0.00 0.00 5.14
2202 2946 6.993079 TCTACAGAGTTTATGTTGCTCAAGA 58.007 36.000 0.00 0.00 32.02 3.02
2204 2948 8.621532 AAATCTACAGAGTTTATGTTGCTCAA 57.378 30.769 0.00 0.00 32.02 3.02
2209 2953 9.878599 AAACGAAAATCTACAGAGTTTATGTTG 57.121 29.630 16.35 5.38 41.62 3.33
2225 2971 8.311120 CGGTTTTAATAGCATGAAACGAAAATC 58.689 33.333 0.00 0.00 33.86 2.17
2228 2974 5.569823 GCGGTTTTAATAGCATGAAACGAAA 59.430 36.000 0.00 0.00 33.86 3.46
2231 2977 4.407818 TGCGGTTTTAATAGCATGAAACG 58.592 39.130 0.00 0.00 34.39 3.60
2237 2983 2.654863 AGCCTGCGGTTTTAATAGCAT 58.345 42.857 0.00 0.00 39.02 3.79
2238 2984 2.122783 AGCCTGCGGTTTTAATAGCA 57.877 45.000 0.00 0.00 38.03 3.49
2239 2985 4.497507 CCTTTAGCCTGCGGTTTTAATAGC 60.498 45.833 0.00 0.00 0.00 2.97
2240 2986 4.036380 CCCTTTAGCCTGCGGTTTTAATAG 59.964 45.833 0.00 0.00 0.00 1.73
2241 2987 3.949113 CCCTTTAGCCTGCGGTTTTAATA 59.051 43.478 0.00 0.00 0.00 0.98
2242 2988 2.758423 CCCTTTAGCCTGCGGTTTTAAT 59.242 45.455 0.00 0.00 0.00 1.40
2243 2989 2.164338 CCCTTTAGCCTGCGGTTTTAA 58.836 47.619 0.00 0.00 0.00 1.52
2244 2990 1.614850 CCCCTTTAGCCTGCGGTTTTA 60.615 52.381 0.00 0.00 0.00 1.52
2245 2991 0.898326 CCCCTTTAGCCTGCGGTTTT 60.898 55.000 0.00 0.00 0.00 2.43
2246 2992 1.304134 CCCCTTTAGCCTGCGGTTT 60.304 57.895 0.00 0.00 0.00 3.27
2247 2993 2.355115 CCCCTTTAGCCTGCGGTT 59.645 61.111 0.00 0.00 0.00 4.44
2248 2994 3.728373 CCCCCTTTAGCCTGCGGT 61.728 66.667 0.00 0.00 0.00 5.68
2270 3016 0.392595 CGGGCAGTTAAAGGAGGGAC 60.393 60.000 0.00 0.00 0.00 4.46
2271 3017 0.838987 ACGGGCAGTTAAAGGAGGGA 60.839 55.000 0.00 0.00 0.00 4.20
2272 3018 0.037734 AACGGGCAGTTAAAGGAGGG 59.962 55.000 0.00 0.00 42.14 4.30
2273 3019 2.027469 ACTAACGGGCAGTTAAAGGAGG 60.027 50.000 11.28 1.89 43.96 4.30
2274 3020 3.000727 CACTAACGGGCAGTTAAAGGAG 58.999 50.000 11.28 4.00 43.96 3.69
2275 3021 2.872842 GCACTAACGGGCAGTTAAAGGA 60.873 50.000 11.28 0.00 43.96 3.36
2276 3022 1.467342 GCACTAACGGGCAGTTAAAGG 59.533 52.381 11.28 3.20 43.96 3.11
2277 3023 2.423577 AGCACTAACGGGCAGTTAAAG 58.576 47.619 11.28 5.36 43.96 1.85
2278 3024 2.554370 AGCACTAACGGGCAGTTAAA 57.446 45.000 11.28 0.00 43.96 1.52
2279 3025 3.899052 ATAGCACTAACGGGCAGTTAA 57.101 42.857 11.28 0.00 43.96 2.01
2280 3026 4.646040 TCTTATAGCACTAACGGGCAGTTA 59.354 41.667 9.81 9.81 43.86 2.24
2281 3027 3.449737 TCTTATAGCACTAACGGGCAGTT 59.550 43.478 8.34 8.34 46.36 3.16
2282 3028 3.028850 TCTTATAGCACTAACGGGCAGT 58.971 45.455 0.00 0.00 0.00 4.40
2283 3029 3.728076 TCTTATAGCACTAACGGGCAG 57.272 47.619 0.00 0.00 0.00 4.85
2284 3030 4.377021 CATTCTTATAGCACTAACGGGCA 58.623 43.478 0.00 0.00 0.00 5.36
2285 3031 3.746492 CCATTCTTATAGCACTAACGGGC 59.254 47.826 0.00 0.00 0.00 6.13
2286 3032 4.315803 CCCATTCTTATAGCACTAACGGG 58.684 47.826 0.00 0.00 0.00 5.28
2287 3033 3.746492 GCCCATTCTTATAGCACTAACGG 59.254 47.826 0.00 0.00 0.00 4.44
2288 3034 4.377021 TGCCCATTCTTATAGCACTAACG 58.623 43.478 0.00 0.00 0.00 3.18
2289 3035 5.237344 CACTGCCCATTCTTATAGCACTAAC 59.763 44.000 0.00 0.00 0.00 2.34
2290 3036 5.368145 CACTGCCCATTCTTATAGCACTAA 58.632 41.667 0.00 0.00 0.00 2.24
2291 3037 4.743651 GCACTGCCCATTCTTATAGCACTA 60.744 45.833 0.00 0.00 0.00 2.74
2292 3038 3.813443 CACTGCCCATTCTTATAGCACT 58.187 45.455 0.00 0.00 0.00 4.40
2309 3055 1.532437 TGAAGAATCGCACAAGCACTG 59.468 47.619 0.00 0.00 42.27 3.66
2315 3061 3.250762 CCTTTCAGTGAAGAATCGCACAA 59.749 43.478 5.56 0.00 38.58 3.33
2317 3063 3.067106 TCCTTTCAGTGAAGAATCGCAC 58.933 45.455 5.56 1.95 38.58 5.34
2321 3067 4.759183 AGCACTTCCTTTCAGTGAAGAATC 59.241 41.667 5.56 1.19 43.90 2.52
2325 3071 4.636249 AGTAGCACTTCCTTTCAGTGAAG 58.364 43.478 5.56 0.00 43.90 3.02
2349 3095 5.125097 CAGTTGGTACACCTCTCGTATTACT 59.875 44.000 0.00 0.00 39.29 2.24
2356 3102 0.246635 CCCAGTTGGTACACCTCTCG 59.753 60.000 0.00 0.00 39.29 4.04
2359 3105 0.328258 ATGCCCAGTTGGTACACCTC 59.672 55.000 0.00 0.00 39.29 3.85
2368 3114 5.125257 TGTTGTAATCATGTATGCCCAGTTG 59.875 40.000 0.00 0.00 0.00 3.16
2371 3117 5.833406 TTGTTGTAATCATGTATGCCCAG 57.167 39.130 0.00 0.00 0.00 4.45
2383 3129 5.300286 AGCTATTGCCTCCATTGTTGTAATC 59.700 40.000 0.00 0.00 40.80 1.75
2391 3137 5.581126 TTAAACAGCTATTGCCTCCATTG 57.419 39.130 0.00 0.00 40.80 2.82
2395 3141 4.098501 AGCATTTAAACAGCTATTGCCTCC 59.901 41.667 13.61 0.00 40.80 4.30
2412 3159 6.772233 ACATCCTTTAAAGCCAAAAAGCATTT 59.228 30.769 9.86 0.00 42.41 2.32
2413 3160 6.298361 ACATCCTTTAAAGCCAAAAAGCATT 58.702 32.000 9.86 0.00 32.48 3.56
2415 3162 5.289083 ACATCCTTTAAAGCCAAAAAGCA 57.711 34.783 9.86 0.00 32.48 3.91
2417 3164 8.337532 CAAAGAACATCCTTTAAAGCCAAAAAG 58.662 33.333 9.86 0.00 34.85 2.27
2419 3166 7.560368 TCAAAGAACATCCTTTAAAGCCAAAA 58.440 30.769 9.86 0.00 34.85 2.44
2425 3172 7.173907 TCTGAGCTCAAAGAACATCCTTTAAAG 59.826 37.037 18.85 8.32 34.85 1.85
2428 3175 6.114187 TCTGAGCTCAAAGAACATCCTTTA 57.886 37.500 18.85 0.00 34.85 1.85
2430 3177 4.630644 TCTGAGCTCAAAGAACATCCTT 57.369 40.909 18.85 0.00 0.00 3.36
2558 3305 6.430308 GGTGCTGAGATGACAATGAATCATAT 59.570 38.462 0.00 0.00 36.92 1.78
2569 3316 1.637338 ACTGAGGTGCTGAGATGACA 58.363 50.000 0.00 0.00 0.00 3.58
2570 3317 2.758736 AACTGAGGTGCTGAGATGAC 57.241 50.000 0.00 0.00 0.00 3.06
2574 3321 0.687354 GGGAAACTGAGGTGCTGAGA 59.313 55.000 0.00 0.00 0.00 3.27
2591 3338 2.042433 TGGGACATCAACCTAAAAGGGG 59.958 50.000 0.00 0.00 40.58 4.79
2630 3377 9.071276 GAACCATCATATGTTAACAAGGATGAT 57.929 33.333 29.71 27.10 36.00 2.45
2632 3379 8.131100 GTGAACCATCATATGTTAACAAGGATG 58.869 37.037 25.40 25.40 38.01 3.51
2764 3511 3.132467 GGCTGATAACGGTAAGTCTTCCT 59.868 47.826 0.00 0.00 0.00 3.36
2771 3518 5.639506 CCTGATAATGGCTGATAACGGTAAG 59.360 44.000 0.00 0.00 0.00 2.34
2827 3574 6.155221 ACTCAGCATAGACATTCTTCCTGTTA 59.845 38.462 0.00 0.00 0.00 2.41
2830 3577 5.021033 ACTCAGCATAGACATTCTTCCTG 57.979 43.478 0.00 0.00 0.00 3.86
2840 3587 3.516615 GGTCAACAGACTCAGCATAGAC 58.483 50.000 0.00 0.00 32.81 2.59
2881 3628 4.449068 CCTAGTATAGCAATTCTTGTGGCG 59.551 45.833 0.00 0.00 37.37 5.69
2897 3644 5.767670 TGTTAAGGCTGAGACTCCTAGTAT 58.232 41.667 0.00 0.00 31.24 2.12
2923 3670 6.886459 ACTGCATCATAATGAACCTTACACTT 59.114 34.615 0.00 0.00 34.61 3.16
2946 3693 5.827797 TGCTAAAGGTCAGTGAAATGAAACT 59.172 36.000 0.00 0.00 0.00 2.66
2970 3717 8.854614 AAACTAAGTGCATCTTGTTCTTAGAT 57.145 30.769 19.26 9.06 39.56 1.98
2974 3721 9.899226 GATAAAAACTAAGTGCATCTTGTTCTT 57.101 29.630 10.59 1.14 37.56 2.52
2976 3723 8.227791 TCGATAAAAACTAAGTGCATCTTGTTC 58.772 33.333 10.59 3.14 37.56 3.18
2977 3724 8.094798 TCGATAAAAACTAAGTGCATCTTGTT 57.905 30.769 10.59 9.70 37.56 2.83
2983 3734 7.667043 TCAACTCGATAAAAACTAAGTGCAT 57.333 32.000 0.00 0.00 0.00 3.96
3000 3751 4.872124 TCATTGACCAAGATCATCAACTCG 59.128 41.667 0.00 0.00 35.28 4.18
3025 3776 6.018425 ACGTTGATATGTCTTGCATTCTGATC 60.018 38.462 0.00 0.00 38.94 2.92
3037 3788 2.494471 TCGGTGGAACGTTGATATGTCT 59.506 45.455 5.00 0.00 38.12 3.41
3060 3811 4.459089 GAGTCCCCTCGCTGTGGC 62.459 72.222 0.00 0.00 0.00 5.01
3157 3908 7.439108 AGGTCCTATGCTTATTACTGAACTT 57.561 36.000 0.00 0.00 0.00 2.66
3159 3910 7.868415 CACTAGGTCCTATGCTTATTACTGAAC 59.132 40.741 0.00 0.00 0.00 3.18
3167 3918 8.263854 ACAAATACACTAGGTCCTATGCTTAT 57.736 34.615 0.00 0.00 0.00 1.73
3177 3929 8.086522 TGACTGAACTTACAAATACACTAGGTC 58.913 37.037 0.00 0.00 0.00 3.85
3187 3939 7.217200 TGTTCTAGCTGACTGAACTTACAAAT 58.783 34.615 17.82 0.00 40.27 2.32
3249 4002 9.798994 ACGTCTTATATTTAGTTACAGAGGTTG 57.201 33.333 0.00 0.00 0.00 3.77
3260 4013 9.821662 GAACTGCAAAAACGTCTTATATTTAGT 57.178 29.630 0.00 0.00 0.00 2.24
3261 4014 9.820229 TGAACTGCAAAAACGTCTTATATTTAG 57.180 29.630 0.00 0.00 0.00 1.85
3263 4016 9.522804 TTTGAACTGCAAAAACGTCTTATATTT 57.477 25.926 0.00 0.00 43.18 1.40
3304 4057 9.939424 ACTCCCTCTGTAACTAAATATAAGACT 57.061 33.333 0.00 0.00 0.00 3.24
3309 4062 9.931698 TGAAGACTCCCTCTGTAACTAAATATA 57.068 33.333 0.00 0.00 0.00 0.86
3310 4063 8.840200 TGAAGACTCCCTCTGTAACTAAATAT 57.160 34.615 0.00 0.00 0.00 1.28
3311 4064 8.660295 TTGAAGACTCCCTCTGTAACTAAATA 57.340 34.615 0.00 0.00 0.00 1.40
3312 4065 7.554959 TTGAAGACTCCCTCTGTAACTAAAT 57.445 36.000 0.00 0.00 0.00 1.40
3313 4066 6.989155 TTGAAGACTCCCTCTGTAACTAAA 57.011 37.500 0.00 0.00 0.00 1.85
3314 4067 6.325545 TGTTTGAAGACTCCCTCTGTAACTAA 59.674 38.462 0.00 0.00 0.00 2.24
3315 4068 5.836898 TGTTTGAAGACTCCCTCTGTAACTA 59.163 40.000 0.00 0.00 0.00 2.24
3316 4069 4.654262 TGTTTGAAGACTCCCTCTGTAACT 59.346 41.667 0.00 0.00 0.00 2.24
3317 4070 4.957296 TGTTTGAAGACTCCCTCTGTAAC 58.043 43.478 0.00 0.00 0.00 2.50
3318 4071 4.654262 ACTGTTTGAAGACTCCCTCTGTAA 59.346 41.667 0.00 0.00 0.00 2.41
3319 4072 4.223953 ACTGTTTGAAGACTCCCTCTGTA 58.776 43.478 0.00 0.00 0.00 2.74
3320 4073 3.041946 ACTGTTTGAAGACTCCCTCTGT 58.958 45.455 0.00 0.00 0.00 3.41
3321 4074 3.760580 ACTGTTTGAAGACTCCCTCTG 57.239 47.619 0.00 0.00 0.00 3.35
3322 4075 3.711704 TCAACTGTTTGAAGACTCCCTCT 59.288 43.478 0.00 0.00 38.87 3.69
3323 4076 4.073293 TCAACTGTTTGAAGACTCCCTC 57.927 45.455 0.00 0.00 38.87 4.30
3324 4077 4.503714 TTCAACTGTTTGAAGACTCCCT 57.496 40.909 0.00 0.00 45.08 4.20
3443 4196 7.365117 CCTCAAACAGAATTAGACTATCCCTGT 60.365 40.741 0.00 0.00 35.22 4.00
3505 4264 1.128692 CCGAAGGCAAAAACTAGAGCG 59.871 52.381 0.00 0.00 46.14 5.03
3521 4280 1.825090 AGCATGCATGTCTTTCCGAA 58.175 45.000 26.79 0.00 0.00 4.30
3523 4282 3.976793 AATAGCATGCATGTCTTTCCG 57.023 42.857 26.79 0.03 0.00 4.30
3534 4293 9.994432 GACATAATAAAGTGGATAATAGCATGC 57.006 33.333 10.51 10.51 0.00 4.06
3637 4480 1.945662 GCAGTTTGCAACAGCACCG 60.946 57.895 0.00 0.00 44.26 4.94
3652 4495 2.512515 GCGCCTGGAGGTAAGCAG 60.513 66.667 0.00 0.00 37.57 4.24
3656 4499 1.888436 CTGACAGCGCCTGGAGGTAA 61.888 60.000 2.29 0.00 35.51 2.85
3745 4588 9.935682 ATTTATTAACAGCTGACGTCATAAATG 57.064 29.630 23.35 16.57 29.49 2.32
3749 4592 9.982291 GAAAATTTATTAACAGCTGACGTCATA 57.018 29.630 23.35 5.12 0.00 2.15
3750 4593 8.511321 TGAAAATTTATTAACAGCTGACGTCAT 58.489 29.630 23.35 6.25 0.00 3.06
3753 4596 9.691362 ATTTGAAAATTTATTAACAGCTGACGT 57.309 25.926 23.35 7.65 0.00 4.34
3783 4704 2.504175 TGGAGCACCTTCCATACCTTAC 59.496 50.000 0.71 0.00 42.24 2.34
3810 4731 6.072175 TCCCCACAAGACAAGAATTTTTATCG 60.072 38.462 0.00 0.00 0.00 2.92
3924 4853 8.023021 TGCAGATACCTAAGTTCACATATCTT 57.977 34.615 0.00 0.00 29.06 2.40
3940 4869 2.353889 CACAAGCTGTCATGCAGATACC 59.646 50.000 17.76 3.79 43.97 2.73
4023 4952 8.675705 TTTGTCATCAAGTAGTTCATTTGAGA 57.324 30.769 0.00 0.00 36.44 3.27
4065 4994 2.509131 TCCATGCTACATGATTCCACCA 59.491 45.455 9.10 0.00 0.00 4.17
4079 5008 7.293073 ACAAACCTTCTATGATTATCCATGCT 58.707 34.615 0.00 0.00 0.00 3.79
4090 5019 7.766278 GCTGAATTAGAGACAAACCTTCTATGA 59.234 37.037 0.00 0.00 0.00 2.15
4096 5025 8.103305 TCATTAGCTGAATTAGAGACAAACCTT 58.897 33.333 0.00 0.00 0.00 3.50
4113 5042 8.090831 TGCTATACTGATTAAGGTCATTAGCTG 58.909 37.037 0.00 0.00 34.94 4.24
4117 5046 9.944376 GGAATGCTATACTGATTAAGGTCATTA 57.056 33.333 0.00 0.00 0.00 1.90
4162 5091 4.330074 GTGACAAGAACAACCGAGGATATG 59.670 45.833 0.00 0.00 0.00 1.78
4336 5265 7.444299 ACTGCAACAATTTATTTTCTCCATGT 58.556 30.769 0.00 0.00 0.00 3.21
4391 5320 7.765695 AGAATGAAACCTCATGCTTAAAAGA 57.234 32.000 0.00 0.00 44.55 2.52
4656 5585 9.623000 GGAAACTATGGTTCTAAGGCTTATTAA 57.377 33.333 7.54 2.93 34.14 1.40
4715 5644 4.703897 AGCAGTTAACGTACATGGCATAT 58.296 39.130 0.00 0.00 0.00 1.78
4720 5649 9.828852 TTAAAATAAAGCAGTTAACGTACATGG 57.171 29.630 0.00 0.00 0.00 3.66
5042 5971 9.975218 AAAGAATGGGTAATACTGATACAAACT 57.025 29.630 0.00 0.00 0.00 2.66
5601 6530 4.037923 GTCAAACCTTCTTTCTGATTGGCA 59.962 41.667 0.00 0.00 0.00 4.92
5725 6654 6.307776 TCCTCCTCTGTACTCCTATGTATTG 58.692 44.000 0.00 0.00 0.00 1.90
5744 6673 8.178313 TCCTTAGTTTTTCATTCTTTTCCTCC 57.822 34.615 0.00 0.00 0.00 4.30
5886 6815 4.521146 CCTGGTTAGCAATCTCAATCTGT 58.479 43.478 0.00 0.00 0.00 3.41
5913 6842 2.222027 GGGGAACTCATTCATTAGCGG 58.778 52.381 0.00 0.00 36.46 5.52
5999 6928 6.094464 CACTATCTGGAATCAAATTCAGCACA 59.906 38.462 2.42 0.00 41.03 4.57
6046 6975 4.302455 CTGTATTGCTTCCAGTATCCTCG 58.698 47.826 0.00 0.00 0.00 4.63
6149 7078 4.503741 AAAACATGTCGATGGTTTCAGG 57.496 40.909 0.00 0.00 44.72 3.86
6414 7344 2.292569 GTCTTACATCACTATCCGGCGA 59.707 50.000 9.30 0.00 0.00 5.54
6445 7375 1.425428 GCATCTGCAGTTACGGCAC 59.575 57.895 14.67 0.00 41.59 5.01
6456 7386 0.607489 ACTGACCCAACTGCATCTGC 60.607 55.000 0.00 0.00 42.50 4.26
6460 7390 0.473755 TGTCACTGACCCAACTGCAT 59.526 50.000 6.72 0.00 0.00 3.96
6510 7441 1.497309 TTCAATGCCCCTTCGGAGGT 61.497 55.000 9.48 0.00 41.85 3.85
6543 7474 8.483758 AGGATTACTTCGGTATTGTCAAACTAT 58.516 33.333 0.00 0.00 0.00 2.12
6547 7478 7.043565 GGTAGGATTACTTCGGTATTGTCAAA 58.956 38.462 0.00 0.00 0.00 2.69
6549 7480 5.657745 TGGTAGGATTACTTCGGTATTGTCA 59.342 40.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.