Multiple sequence alignment - TraesCS1A01G341400

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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 TraesCS1A01G341400 chr1A 100.000 4118 0 0 1 4118 531046365 531050482 0.000000e+00 7605.0
1 TraesCS1A01G341400 chr1A 88.034 117 14 0 2136 2252 531008852 531008968 5.550000e-29 139.0
2 TraesCS1A01G341400 chr1D 88.246 2816 176 70 804 3534 432701964 432704709 0.000000e+00 3223.0
3 TraesCS1A01G341400 chr1D 87.983 466 43 5 3654 4117 432705217 432705671 4.680000e-149 538.0
4 TraesCS1A01G341400 chr1D 88.421 95 8 2 3646 3737 455504976 455505070 1.210000e-20 111.0
5 TraesCS1A01G341400 chr1D 91.803 61 5 0 3647 3707 37205515 37205575 7.330000e-13 86.1
6 TraesCS1A01G341400 chr1B 89.588 2478 165 51 804 3235 584102588 584105018 0.000000e+00 3061.0
7 TraesCS1A01G341400 chr1B 98.885 807 7 2 1 807 167951480 167950676 0.000000e+00 1439.0
8 TraesCS1A01G341400 chr1B 94.000 100 5 1 2992 3091 427472252 427472154 2.560000e-32 150.0
9 TraesCS1A01G341400 chr5A 98.755 803 8 2 1 803 400069491 400068691 0.000000e+00 1426.0
10 TraesCS1A01G341400 chr5A 98.630 803 9 2 1 803 521677435 521678235 0.000000e+00 1421.0
11 TraesCS1A01G341400 chr5A 98.630 803 9 2 1 803 687717644 687716844 0.000000e+00 1421.0
12 TraesCS1A01G341400 chr5A 94.792 96 4 1 2993 3088 97230020 97229926 9.220000e-32 148.0
13 TraesCS1A01G341400 chr5A 81.560 141 16 8 3642 3779 309020699 309020566 1.570000e-19 108.0
14 TraesCS1A01G341400 chr5A 77.778 162 30 3 3551 3707 580921617 580921457 1.220000e-15 95.3
15 TraesCS1A01G341400 chr5A 83.908 87 9 2 3646 3729 546988021 546988105 1.230000e-10 78.7
16 TraesCS1A01G341400 chr7A 98.630 803 9 2 1 803 708293952 708293152 0.000000e+00 1421.0
17 TraesCS1A01G341400 chr5B 98.630 803 8 3 1 803 158896316 158897115 0.000000e+00 1419.0
18 TraesCS1A01G341400 chr7B 98.389 807 10 3 1 807 74088652 74089455 0.000000e+00 1415.0
19 TraesCS1A01G341400 chr3B 98.506 803 10 2 1 803 706353196 706353996 0.000000e+00 1415.0
20 TraesCS1A01G341400 chr3B 98.030 812 14 2 1 812 706326299 706325490 0.000000e+00 1410.0
21 TraesCS1A01G341400 chr3B 93.069 101 3 3 2992 3088 826657615 826657715 1.190000e-30 145.0
22 TraesCS1A01G341400 chr3B 78.392 199 20 16 3551 3732 712095571 712095763 1.570000e-19 108.0
23 TraesCS1A01G341400 chr2A 93.269 104 5 2 2992 3093 24307482 24307379 7.130000e-33 152.0
24 TraesCS1A01G341400 chr7D 91.667 108 7 2 2981 3088 590446674 590446779 9.220000e-32 148.0
25 TraesCS1A01G341400 chr3A 94.681 94 2 2 2994 3087 655646674 655646764 4.290000e-30 143.0
26 TraesCS1A01G341400 chr2D 96.512 86 2 1 3009 3093 22506708 22506623 1.540000e-29 141.0
27 TraesCS1A01G341400 chr2D 87.059 85 11 0 3718 3802 44693077 44692993 3.390000e-16 97.1
28 TraesCS1A01G341400 chr6A 82.313 147 20 3 3551 3692 189920469 189920324 5.590000e-24 122.0
29 TraesCS1A01G341400 chr3D 91.304 69 5 1 3640 3707 566554069 566554001 4.380000e-15 93.5
30 TraesCS1A01G341400 chr2B 93.443 61 3 1 3647 3707 595924989 595925048 5.670000e-14 89.8


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 TraesCS1A01G341400 chr1A 531046365 531050482 4117 False 7605.0 7605 100.0000 1 4118 1 chr1A.!!$F2 4117
1 TraesCS1A01G341400 chr1D 432701964 432705671 3707 False 1880.5 3223 88.1145 804 4117 2 chr1D.!!$F3 3313
2 TraesCS1A01G341400 chr1B 584102588 584105018 2430 False 3061.0 3061 89.5880 804 3235 1 chr1B.!!$F1 2431
3 TraesCS1A01G341400 chr1B 167950676 167951480 804 True 1439.0 1439 98.8850 1 807 1 chr1B.!!$R1 806
4 TraesCS1A01G341400 chr5A 400068691 400069491 800 True 1426.0 1426 98.7550 1 803 1 chr5A.!!$R3 802
5 TraesCS1A01G341400 chr5A 521677435 521678235 800 False 1421.0 1421 98.6300 1 803 1 chr5A.!!$F1 802
6 TraesCS1A01G341400 chr5A 687716844 687717644 800 True 1421.0 1421 98.6300 1 803 1 chr5A.!!$R5 802
7 TraesCS1A01G341400 chr7A 708293152 708293952 800 True 1421.0 1421 98.6300 1 803 1 chr7A.!!$R1 802
8 TraesCS1A01G341400 chr5B 158896316 158897115 799 False 1419.0 1419 98.6300 1 803 1 chr5B.!!$F1 802
9 TraesCS1A01G341400 chr7B 74088652 74089455 803 False 1415.0 1415 98.3890 1 807 1 chr7B.!!$F1 806
10 TraesCS1A01G341400 chr3B 706353196 706353996 800 False 1415.0 1415 98.5060 1 803 1 chr3B.!!$F1 802
11 TraesCS1A01G341400 chr3B 706325490 706326299 809 True 1410.0 1410 98.0300 1 812 1 chr3B.!!$R1 811

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
779 781 0.249322 CGGGTTCTTATCGACGCCAT 60.249 55.0 0.0 0.0 0.00 4.40 F
1152 1161 0.039437 ACTGACATCGACGTTTCGCT 60.039 50.0 0.0 0.0 45.46 4.93 F
2183 2217 0.318699 GCATCTACACGCTGCCGATA 60.319 55.0 0.0 0.0 38.29 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 1846 0.176680 ACATAGCTGCGGTTCAGAGG 59.823 55.0 0.00 0.0 45.72 3.69 R
2945 3012 0.178992 CTTGGTTCCTCACAGGCCAA 60.179 55.0 5.01 0.0 35.85 4.52 R
3908 4389 0.034670 ACTTTCAGCATGCCTCTCCC 60.035 55.0 15.66 0.0 34.76 4.30 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
115 116 0.584876 GGCAACTGTCGTTACACACC 59.415 55.000 0.00 0.00 0.00 4.16
116 117 1.578583 GCAACTGTCGTTACACACCT 58.421 50.000 0.00 0.00 0.00 4.00
434 435 1.323271 TGATCGTGTCTGGAGGGCTC 61.323 60.000 0.00 0.00 0.00 4.70
475 476 2.484602 GATGGGAAGGGTTAGGGTGTA 58.515 52.381 0.00 0.00 0.00 2.90
681 683 4.572571 GGGGTTGCCACACACCGA 62.573 66.667 0.00 0.00 27.79 4.69
779 781 0.249322 CGGGTTCTTATCGACGCCAT 60.249 55.000 0.00 0.00 0.00 4.40
807 809 1.471287 GCAGTTATTCGGACCCCAAAC 59.529 52.381 0.00 0.00 0.00 2.93
812 814 4.132336 GTTATTCGGACCCCAAACCTATC 58.868 47.826 0.00 0.00 0.00 2.08
813 815 1.659022 TTCGGACCCCAAACCTATCA 58.341 50.000 0.00 0.00 0.00 2.15
846 848 2.159435 ACAACAAAGCTGAACAACCGTC 60.159 45.455 0.00 0.00 0.00 4.79
881 883 1.935327 CTGAGACCGGTCGTTCCTCC 61.935 65.000 28.26 12.80 34.09 4.30
912 914 4.349682 CCGGTAGGTAGGTGCTGA 57.650 61.111 0.00 0.00 0.00 4.26
913 915 2.116383 CCGGTAGGTAGGTGCTGAG 58.884 63.158 0.00 0.00 0.00 3.35
914 916 1.437986 CGGTAGGTAGGTGCTGAGC 59.562 63.158 0.00 0.00 0.00 4.26
962 971 4.426313 GCGCCCTGGCCCTAGTTT 62.426 66.667 0.00 0.00 37.98 2.66
979 988 2.779742 TTTCAATGGCCCCACCCTCG 62.780 60.000 0.00 0.00 37.83 4.63
1008 1017 2.882876 CGTCCGTTCGGAGTCCAT 59.117 61.111 14.40 0.00 34.60 3.41
1009 1018 1.226603 CGTCCGTTCGGAGTCCATC 60.227 63.158 14.40 1.06 34.60 3.51
1010 1019 1.654954 CGTCCGTTCGGAGTCCATCT 61.655 60.000 14.40 0.00 34.60 2.90
1099 1108 2.973899 GCTCTGCCTTCTCGGTCA 59.026 61.111 0.00 0.00 34.25 4.02
1143 1152 3.916172 GCGTTGTAGTTAACTGACATCGA 59.084 43.478 28.76 13.30 38.12 3.59
1144 1153 4.201466 GCGTTGTAGTTAACTGACATCGAC 60.201 45.833 28.76 22.03 38.12 4.20
1152 1161 0.039437 ACTGACATCGACGTTTCGCT 60.039 50.000 0.00 0.00 45.46 4.93
1160 1169 1.710339 GACGTTTCGCTCTGATGCC 59.290 57.895 0.00 0.00 0.00 4.40
1171 1180 1.524355 CTCTGATGCCTTAATCGTGCG 59.476 52.381 0.00 0.00 0.00 5.34
1321 1330 2.368011 GGAGGAAGAAGGGTCGGGG 61.368 68.421 0.00 0.00 0.00 5.73
1360 1369 3.992317 GGGCTCGCCGAGATACCC 61.992 72.222 20.05 15.30 37.79 3.69
1441 1453 0.321653 CTCACAAGGTACACTGCCCC 60.322 60.000 0.00 0.00 0.00 5.80
1475 1487 1.069227 CGCCGTGTCAGATGATCGATA 60.069 52.381 0.00 0.00 0.00 2.92
1479 1491 3.251004 CCGTGTCAGATGATCGATACTCA 59.749 47.826 0.00 0.00 0.00 3.41
1489 1501 0.518195 TCGATACTCAACACGCGTGA 59.482 50.000 42.94 21.98 0.00 4.35
1514 1526 6.842437 TCAGAAGTTCAGACTAAGCTATGT 57.158 37.500 5.50 0.00 34.21 2.29
1539 1551 9.595823 GTATAAAAATGGTGTGAACTAGAGCTA 57.404 33.333 0.00 0.00 0.00 3.32
1540 1552 6.803154 AAAAATGGTGTGAACTAGAGCTAC 57.197 37.500 0.00 0.00 0.00 3.58
1562 1581 1.387420 TGTCTTGTGTATAAACGCGCG 59.613 47.619 30.96 30.96 39.05 6.86
1588 1607 3.385755 GCATGCAGGAATGGGTCTATTTT 59.614 43.478 14.21 0.00 0.00 1.82
1595 1614 5.065218 CAGGAATGGGTCTATTTTCTGAACG 59.935 44.000 0.00 0.00 30.30 3.95
1596 1615 5.045869 AGGAATGGGTCTATTTTCTGAACGA 60.046 40.000 0.00 0.00 0.00 3.85
1600 1619 4.041198 TGGGTCTATTTTCTGAACGAAGGT 59.959 41.667 0.00 0.00 32.21 3.50
1660 1679 1.134491 GGACTAACCAATCCACTCCGG 60.134 57.143 0.00 0.00 38.79 5.14
1690 1709 4.755266 TGCTCAAGGTAATAGAGGGTTC 57.245 45.455 0.00 0.00 0.00 3.62
1692 1711 4.162320 TGCTCAAGGTAATAGAGGGTTCTG 59.838 45.833 0.00 0.00 34.79 3.02
1750 1775 2.157738 GAGATTTGGAGCTTGCACAGT 58.842 47.619 0.00 0.00 0.00 3.55
1762 1787 1.639722 TGCACAGTAGCAGGTAAGGA 58.360 50.000 0.00 0.00 40.11 3.36
1787 1812 3.870955 ACGCAGTGGTCAGAGGAA 58.129 55.556 0.00 0.00 42.51 3.36
1797 1822 1.829222 GGTCAGAGGAACCATCGGTAA 59.171 52.381 0.00 0.00 33.12 2.85
1821 1846 0.740868 TAAGCATGCACCGTCAGAGC 60.741 55.000 21.98 0.00 0.00 4.09
1837 1862 1.949847 GAGCCTCTGAACCGCAGCTA 61.950 60.000 0.00 0.00 44.52 3.32
1866 1900 7.827236 TGGTAACATTACAAGATCCTAACCTTG 59.173 37.037 4.27 0.00 46.17 3.61
1899 1933 0.905357 ACCGGAGCAGTTAAGCAGAT 59.095 50.000 9.46 0.00 36.85 2.90
1904 1938 2.799412 GGAGCAGTTAAGCAGATCATCG 59.201 50.000 0.00 0.00 36.85 3.84
1909 1943 4.509230 GCAGTTAAGCAGATCATCGATTCA 59.491 41.667 0.00 0.00 0.00 2.57
1957 1991 2.661537 CTGCGCGACCAAGACACA 60.662 61.111 12.10 0.00 0.00 3.72
2004 2038 0.538057 CCATCCCATCCCATGTTCGG 60.538 60.000 0.00 0.00 0.00 4.30
2005 2039 1.151450 ATCCCATCCCATGTTCGGC 59.849 57.895 0.00 0.00 0.00 5.54
2006 2040 2.357593 ATCCCATCCCATGTTCGGCC 62.358 60.000 0.00 0.00 0.00 6.13
2066 2100 3.119955 GCGGACTACTGATTTGGGTTTTC 60.120 47.826 0.00 0.00 0.00 2.29
2100 2134 1.474677 CGCTGGATTTCAGGATCAGCT 60.475 52.381 11.07 0.00 43.54 4.24
2172 2206 2.501128 GCTCCGGCTGCATCTACA 59.499 61.111 13.20 0.00 35.22 2.74
2173 2207 1.884926 GCTCCGGCTGCATCTACAC 60.885 63.158 13.20 0.00 35.22 2.90
2183 2217 0.318699 GCATCTACACGCTGCCGATA 60.319 55.000 0.00 0.00 38.29 2.92
2186 2220 1.100510 TCTACACGCTGCCGATACTT 58.899 50.000 0.00 0.00 38.29 2.24
2213 2247 3.681835 GTGGCCGTCCTGTCGTCT 61.682 66.667 0.00 0.00 0.00 4.18
2216 2250 3.681835 GCCGTCCTGTCGTCTGGT 61.682 66.667 5.57 0.00 34.80 4.00
2223 2257 1.613925 TCCTGTCGTCTGGTCTGAAAG 59.386 52.381 5.57 0.00 34.80 2.62
2301 2344 0.814457 AGACTGGACTCTGACGATGC 59.186 55.000 0.00 0.00 0.00 3.91
2302 2345 0.528017 GACTGGACTCTGACGATGCA 59.472 55.000 0.00 0.00 0.00 3.96
2303 2346 1.135915 GACTGGACTCTGACGATGCAT 59.864 52.381 0.00 0.00 0.00 3.96
2304 2347 1.134877 ACTGGACTCTGACGATGCATG 60.135 52.381 2.46 0.00 0.00 4.06
2371 2414 1.331138 CTACTTCGTCGGCTCAGGTAG 59.669 57.143 0.00 0.00 0.00 3.18
2390 2433 1.216178 GGCGCAAATGCAACCTCAT 59.784 52.632 10.83 0.00 42.21 2.90
2397 2440 1.760192 AATGCAACCTCATCTCAGCC 58.240 50.000 0.00 0.00 0.00 4.85
2399 2442 1.817099 GCAACCTCATCTCAGCCCG 60.817 63.158 0.00 0.00 0.00 6.13
2413 2456 2.112198 GCCCGATGAAATCACGCCA 61.112 57.895 0.00 0.00 45.97 5.69
2416 2459 1.472552 CCCGATGAAATCACGCCACTA 60.473 52.381 0.00 0.00 45.97 2.74
2423 2466 4.793071 TGAAATCACGCCACTAAAATGTG 58.207 39.130 0.00 0.00 37.66 3.21
2424 2467 4.277174 TGAAATCACGCCACTAAAATGTGT 59.723 37.500 0.00 0.00 36.30 3.72
2436 2482 6.803320 CCACTAAAATGTGTAGCTGAATGTTG 59.197 38.462 0.00 0.00 36.30 3.33
2437 2483 7.362662 CACTAAAATGTGTAGCTGAATGTTGT 58.637 34.615 0.00 0.00 33.61 3.32
2438 2484 7.862372 CACTAAAATGTGTAGCTGAATGTTGTT 59.138 33.333 0.00 0.00 33.61 2.83
2439 2485 7.862372 ACTAAAATGTGTAGCTGAATGTTGTTG 59.138 33.333 0.00 0.00 0.00 3.33
2440 2486 6.389830 AAATGTGTAGCTGAATGTTGTTGA 57.610 33.333 0.00 0.00 0.00 3.18
2441 2487 6.579666 AATGTGTAGCTGAATGTTGTTGAT 57.420 33.333 0.00 0.00 0.00 2.57
2445 2491 1.881973 AGCTGAATGTTGTTGATGCGT 59.118 42.857 0.00 0.00 0.00 5.24
2447 2493 3.120199 AGCTGAATGTTGTTGATGCGTAC 60.120 43.478 0.00 0.00 0.00 3.67
2448 2494 3.407252 CTGAATGTTGTTGATGCGTACG 58.593 45.455 11.84 11.84 0.00 3.67
2449 2495 2.803386 TGAATGTTGTTGATGCGTACGT 59.197 40.909 17.90 0.00 0.00 3.57
2450 2496 2.873170 ATGTTGTTGATGCGTACGTG 57.127 45.000 17.90 0.00 0.00 4.49
2795 2853 1.140852 TCGTATTCTGCCATGGAAGGG 59.859 52.381 20.43 4.79 43.76 3.95
2797 2855 2.104111 CGTATTCTGCCATGGAAGGGTA 59.896 50.000 20.43 10.08 42.11 3.69
2798 2856 3.244561 CGTATTCTGCCATGGAAGGGTAT 60.245 47.826 20.43 12.90 42.11 2.73
2799 2857 4.020573 CGTATTCTGCCATGGAAGGGTATA 60.021 45.833 20.43 11.97 42.11 1.47
2809 2867 6.378661 CATGGAAGGGTATAAGATCATGGA 57.621 41.667 0.00 0.00 0.00 3.41
2817 2876 5.181748 GGTATAAGATCATGGAGGTGATGC 58.818 45.833 0.00 0.00 38.88 3.91
2819 2878 6.155221 GGTATAAGATCATGGAGGTGATGCTA 59.845 42.308 0.00 0.00 38.88 3.49
2826 2885 2.470990 TGGAGGTGATGCTAGTGATGT 58.529 47.619 0.00 0.00 0.00 3.06
2928 2988 3.911365 CGTATGAGCGACATTCTGATCTC 59.089 47.826 4.93 0.00 40.07 2.75
2945 3012 0.323178 CTCATGAAGGTTGGCTGGCT 60.323 55.000 2.00 0.00 0.00 4.75
2948 3015 0.901580 ATGAAGGTTGGCTGGCTTGG 60.902 55.000 2.00 0.00 0.00 3.61
2949 3016 2.919328 AAGGTTGGCTGGCTTGGC 60.919 61.111 2.00 0.00 0.00 4.52
2962 3029 1.455849 CTTGGCCTGTGAGGAACCA 59.544 57.895 3.32 0.00 37.67 3.67
2969 3036 1.630369 CCTGTGAGGAACCAAGGATGA 59.370 52.381 0.00 0.00 37.67 2.92
3112 3200 7.493320 TGGTGAGCCGTAAATAATTAGTAGTTG 59.507 37.037 0.00 0.00 37.67 3.16
3117 3205 9.317936 AGCCGTAAATAATTAGTAGTTGGTTAC 57.682 33.333 0.00 0.00 0.00 2.50
3208 3300 3.092081 GCGGTTGCTTTGACATCAC 57.908 52.632 0.00 0.00 38.39 3.06
3220 3312 3.953712 TGACATCACGGTGTTATCAGT 57.046 42.857 8.17 0.00 31.16 3.41
3221 3313 4.265904 TGACATCACGGTGTTATCAGTT 57.734 40.909 8.17 0.00 31.16 3.16
3225 3317 5.997385 ACATCACGGTGTTATCAGTTTTTC 58.003 37.500 8.17 0.00 0.00 2.29
3299 3391 6.311445 AGTCAGAAGAAATACACATAGTTGCG 59.689 38.462 0.00 0.00 0.00 4.85
3308 3400 9.341899 GAAATACACATAGTTGCGAAAGAAATT 57.658 29.630 0.00 0.00 0.00 1.82
3371 3463 1.766496 AGACAGAAAACGGAGTGGGAA 59.234 47.619 0.00 0.00 45.00 3.97
3372 3464 2.171870 AGACAGAAAACGGAGTGGGAAA 59.828 45.455 0.00 0.00 45.00 3.13
3386 3478 3.456277 AGTGGGAAACTGACTGAAGAAGT 59.544 43.478 0.00 0.00 43.85 3.01
3411 3504 0.096976 CAAAATGGAGCGGCTACACG 59.903 55.000 18.90 2.61 0.00 4.49
3422 3515 1.063027 CGGCTACACGTCAGTCGATTA 59.937 52.381 13.92 0.00 43.67 1.75
3469 3562 6.849811 CGATTTTCATCTTTCAATCTCCATCG 59.150 38.462 0.00 0.00 0.00 3.84
3472 3565 6.426980 TTCATCTTTCAATCTCCATCGTTG 57.573 37.500 0.00 0.00 0.00 4.10
3498 3591 2.582052 TGATCAAACGCCCAGAACTTT 58.418 42.857 0.00 0.00 0.00 2.66
3511 3604 5.560724 CCCAGAACTTTATCTTCAACCTCA 58.439 41.667 0.00 0.00 0.00 3.86
3513 3606 6.490040 CCCAGAACTTTATCTTCAACCTCAAA 59.510 38.462 0.00 0.00 0.00 2.69
3516 3609 8.624776 CAGAACTTTATCTTCAACCTCAAACTT 58.375 33.333 0.00 0.00 0.00 2.66
3517 3610 8.624776 AGAACTTTATCTTCAACCTCAAACTTG 58.375 33.333 0.00 0.00 0.00 3.16
3534 3627 2.107953 GATCTGTCCTGAGCCGCC 59.892 66.667 0.00 0.00 0.00 6.13
3535 3628 3.781770 GATCTGTCCTGAGCCGCCG 62.782 68.421 0.00 0.00 0.00 6.46
3551 3644 4.462280 CGGCCTAACCACCGGTCC 62.462 72.222 2.59 0.00 45.74 4.46
3552 3645 4.105553 GGCCTAACCACCGGTCCC 62.106 72.222 2.59 0.00 38.86 4.46
3553 3646 4.105553 GCCTAACCACCGGTCCCC 62.106 72.222 2.59 0.00 33.12 4.81
3554 3647 2.608368 CCTAACCACCGGTCCCCA 60.608 66.667 2.59 0.00 33.12 4.96
3555 3648 2.666812 CTAACCACCGGTCCCCAC 59.333 66.667 2.59 0.00 33.12 4.61
3556 3649 2.929477 TAACCACCGGTCCCCACC 60.929 66.667 2.59 0.00 39.69 4.61
3566 3659 4.273262 TCCCCACCCTCCCCGAAA 62.273 66.667 0.00 0.00 0.00 3.46
3567 3660 4.043100 CCCCACCCTCCCCGAAAC 62.043 72.222 0.00 0.00 0.00 2.78
3568 3661 4.043100 CCCACCCTCCCCGAAACC 62.043 72.222 0.00 0.00 0.00 3.27
3569 3662 3.253838 CCACCCTCCCCGAAACCA 61.254 66.667 0.00 0.00 0.00 3.67
3570 3663 2.033602 CACCCTCCCCGAAACCAC 59.966 66.667 0.00 0.00 0.00 4.16
3571 3664 3.254617 ACCCTCCCCGAAACCACC 61.255 66.667 0.00 0.00 0.00 4.61
3572 3665 4.043100 CCCTCCCCGAAACCACCC 62.043 72.222 0.00 0.00 0.00 4.61
3573 3666 4.043100 CCTCCCCGAAACCACCCC 62.043 72.222 0.00 0.00 0.00 4.95
3574 3667 2.933834 CTCCCCGAAACCACCCCT 60.934 66.667 0.00 0.00 0.00 4.79
3575 3668 1.614226 CTCCCCGAAACCACCCCTA 60.614 63.158 0.00 0.00 0.00 3.53
3576 3669 1.907222 CTCCCCGAAACCACCCCTAC 61.907 65.000 0.00 0.00 0.00 3.18
3577 3670 2.672908 CCCGAAACCACCCCTACC 59.327 66.667 0.00 0.00 0.00 3.18
3578 3671 2.266689 CCGAAACCACCCCTACCG 59.733 66.667 0.00 0.00 0.00 4.02
3579 3672 2.586293 CCGAAACCACCCCTACCGT 61.586 63.158 0.00 0.00 0.00 4.83
3580 3673 1.372307 CGAAACCACCCCTACCGTT 59.628 57.895 0.00 0.00 0.00 4.44
3581 3674 0.952010 CGAAACCACCCCTACCGTTG 60.952 60.000 0.00 0.00 0.00 4.10
3582 3675 0.607217 GAAACCACCCCTACCGTTGG 60.607 60.000 0.00 0.00 0.00 3.77
3583 3676 1.354942 AAACCACCCCTACCGTTGGT 61.355 55.000 0.00 0.00 40.16 3.67
3584 3677 1.771783 AACCACCCCTACCGTTGGTC 61.772 60.000 0.00 0.00 37.09 4.02
3585 3678 1.916777 CCACCCCTACCGTTGGTCT 60.917 63.158 0.00 0.00 37.09 3.85
3586 3679 1.486145 CCACCCCTACCGTTGGTCTT 61.486 60.000 0.00 0.00 37.09 3.01
3587 3680 0.036671 CACCCCTACCGTTGGTCTTC 60.037 60.000 0.00 0.00 37.09 2.87
3588 3681 1.196766 ACCCCTACCGTTGGTCTTCC 61.197 60.000 0.00 0.00 37.09 3.46
3589 3682 1.217244 CCCTACCGTTGGTCTTCCG 59.783 63.158 0.00 0.00 37.09 4.30
3590 3683 1.447314 CCTACCGTTGGTCTTCCGC 60.447 63.158 0.00 0.00 37.09 5.54
3591 3684 1.447314 CTACCGTTGGTCTTCCGCC 60.447 63.158 0.00 0.00 37.09 6.13
3592 3685 3.285523 TACCGTTGGTCTTCCGCCG 62.286 63.158 0.00 0.00 37.09 6.46
3609 3702 3.890926 GCCCCTGGCCATACCTCC 61.891 72.222 5.51 0.00 44.06 4.30
3610 3703 3.178611 CCCCTGGCCATACCTCCC 61.179 72.222 5.51 0.00 40.22 4.30
3611 3704 3.178611 CCCTGGCCATACCTCCCC 61.179 72.222 5.51 0.00 40.22 4.81
3612 3705 3.178611 CCTGGCCATACCTCCCCC 61.179 72.222 5.51 0.00 40.22 5.40
3613 3706 2.039405 CTGGCCATACCTCCCCCT 60.039 66.667 5.51 0.00 40.22 4.79
3614 3707 1.697754 CTGGCCATACCTCCCCCTT 60.698 63.158 5.51 0.00 40.22 3.95
3615 3708 1.999634 CTGGCCATACCTCCCCCTTG 62.000 65.000 5.51 0.00 40.22 3.61
3616 3709 2.195956 GCCATACCTCCCCCTTGC 59.804 66.667 0.00 0.00 0.00 4.01
3617 3710 2.510906 CCATACCTCCCCCTTGCG 59.489 66.667 0.00 0.00 0.00 4.85
3618 3711 2.203209 CATACCTCCCCCTTGCGC 60.203 66.667 0.00 0.00 0.00 6.09
3619 3712 3.489513 ATACCTCCCCCTTGCGCC 61.490 66.667 4.18 0.00 0.00 6.53
3626 3719 2.983592 CCCCTTGCGCCGAGTTTT 60.984 61.111 4.18 0.00 0.00 2.43
3627 3720 2.561037 CCCCTTGCGCCGAGTTTTT 61.561 57.895 4.18 0.00 0.00 1.94
3650 4107 0.323725 CTAGCAAAGCCCCACACCAT 60.324 55.000 0.00 0.00 0.00 3.55
3652 4109 1.907807 GCAAAGCCCCACACCATCA 60.908 57.895 0.00 0.00 0.00 3.07
3661 4142 2.121506 ACACCATCACCCCCACCT 60.122 61.111 0.00 0.00 0.00 4.00
3683 4164 8.368668 CACCTTAAACCCTAAGATAGATACTGG 58.631 40.741 0.00 0.00 0.00 4.00
3684 4165 7.513091 ACCTTAAACCCTAAGATAGATACTGGG 59.487 40.741 0.00 0.00 39.06 4.45
3685 4166 7.038231 CCTTAAACCCTAAGATAGATACTGGGG 60.038 44.444 0.00 0.00 37.56 4.96
3686 4167 5.435545 AACCCTAAGATAGATACTGGGGT 57.564 43.478 0.00 0.00 42.04 4.95
3687 4168 6.556644 AACCCTAAGATAGATACTGGGGTA 57.443 41.667 0.00 0.00 40.64 3.69
3688 4169 6.155247 ACCCTAAGATAGATACTGGGGTAG 57.845 45.833 0.00 0.00 40.16 3.18
3689 4170 4.957327 CCCTAAGATAGATACTGGGGTAGC 59.043 50.000 0.00 0.00 34.85 3.58
3690 4171 4.957327 CCTAAGATAGATACTGGGGTAGCC 59.043 50.000 1.07 1.07 35.17 3.93
3691 4172 4.768807 AAGATAGATACTGGGGTAGCCT 57.231 45.455 11.48 0.00 35.17 4.58
3693 4174 3.926671 AGATAGATACTGGGGTAGCCTCT 59.073 47.826 11.48 7.86 35.17 3.69
3694 4175 2.687003 AGATACTGGGGTAGCCTCTC 57.313 55.000 11.48 1.31 35.17 3.20
3695 4176 1.148236 AGATACTGGGGTAGCCTCTCC 59.852 57.143 11.48 0.00 35.17 3.71
3696 4177 0.178958 ATACTGGGGTAGCCTCTCCG 60.179 60.000 11.48 0.00 0.00 4.63
3697 4178 2.294170 TACTGGGGTAGCCTCTCCGG 62.294 65.000 11.48 0.00 0.00 5.14
3736 4217 0.324943 TTTCTTCCTTCCCTCTGGCG 59.675 55.000 0.00 0.00 0.00 5.69
3759 4240 5.008118 CGCCTCATTTCTTCTAGGGAAAATC 59.992 44.000 13.03 4.20 36.47 2.17
3773 4254 3.128764 GGGAAAATCGACTGACCCAAATC 59.871 47.826 12.66 0.00 37.50 2.17
3774 4255 3.181510 GGAAAATCGACTGACCCAAATCG 60.182 47.826 0.00 0.00 35.91 3.34
3778 4259 1.136305 TCGACTGACCCAAATCGGATC 59.864 52.381 0.00 0.00 36.56 3.36
3784 4265 1.943340 GACCCAAATCGGATCTTCAGC 59.057 52.381 0.00 0.00 36.56 4.26
3791 4272 0.820226 TCGGATCTTCAGCTGACTGG 59.180 55.000 18.03 9.95 44.59 4.00
3834 4315 6.870965 CCAATATATCTAACAGCTGACACCTC 59.129 42.308 23.35 0.00 0.00 3.85
3836 4317 0.888619 TCTAACAGCTGACACCTCGG 59.111 55.000 23.35 1.61 0.00 4.63
3841 4322 4.803426 GCTGACACCTCGGGAGCG 62.803 72.222 0.00 0.00 0.00 5.03
3843 4324 2.362503 TGACACCTCGGGAGCGAT 60.363 61.111 0.00 0.00 0.00 4.58
3848 4329 4.271816 CCTCGGGAGCGATCCACG 62.272 72.222 23.22 21.39 45.66 4.94
3863 4344 1.229975 CCACGACAGCACATGCAGAA 61.230 55.000 6.64 0.00 45.16 3.02
3908 4389 4.468095 GGAAATGATATTCCGTTGGTCG 57.532 45.455 0.00 0.00 39.54 4.79
3923 4404 2.364186 TCGGGAGAGGCATGCTGA 60.364 61.111 18.92 1.83 0.00 4.26
3939 4420 4.277515 TGCTGAAAGTGCTAGAATCACT 57.722 40.909 0.00 0.00 45.83 3.41
3942 4423 4.874966 GCTGAAAGTGCTAGAATCACTGAT 59.125 41.667 0.00 0.00 43.36 2.90
3945 4426 5.046376 TGAAAGTGCTAGAATCACTGATGGA 60.046 40.000 0.00 0.00 43.36 3.41
3968 4449 9.159254 TGGATATGTTAGATCTAGTTGTGGATT 57.841 33.333 2.02 0.00 0.00 3.01
3996 4477 5.184711 TGCACATACATTCTGCTTGATGTA 58.815 37.500 8.37 8.37 34.51 2.29
4010 4491 6.759272 TGCTTGATGTATAGGATGGTTAGAC 58.241 40.000 0.00 0.00 0.00 2.59
4011 4492 5.864474 GCTTGATGTATAGGATGGTTAGACG 59.136 44.000 0.00 0.00 0.00 4.18
4013 4494 6.819397 TGATGTATAGGATGGTTAGACGAG 57.181 41.667 0.00 0.00 0.00 4.18
4038 4519 1.471684 GTCGTCCATACTCTTCGTGGT 59.528 52.381 0.00 0.00 34.61 4.16
4049 4530 3.572682 ACTCTTCGTGGTTGATGACACTA 59.427 43.478 0.00 0.00 35.51 2.74
4057 4538 2.679837 GGTTGATGACACTATGCCACAG 59.320 50.000 0.00 0.00 0.00 3.66
4066 4547 1.806542 ACTATGCCACAGCGACAAAAG 59.193 47.619 0.00 0.00 44.31 2.27
4069 4550 0.380378 TGCCACAGCGACAAAAGAAC 59.620 50.000 0.00 0.00 44.31 3.01
4070 4551 0.663153 GCCACAGCGACAAAAGAACT 59.337 50.000 0.00 0.00 0.00 3.01
4072 4553 2.719798 CCACAGCGACAAAAGAACTTG 58.280 47.619 0.00 0.00 0.00 3.16
4112 4593 1.057636 TCGATCGACGTTGTCTTTGC 58.942 50.000 15.15 0.00 43.13 3.68
4117 4598 3.021269 TCGACGTTGTCTTTGCTATGT 57.979 42.857 1.96 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
434 435 4.473520 AGCCGCCCACTCCAATCG 62.474 66.667 0.00 0.00 0.00 3.34
475 476 4.699522 GCGCTCCGACCCCAAACT 62.700 66.667 0.00 0.00 0.00 2.66
779 781 1.545136 TCCGAATAACTGCCACACGTA 59.455 47.619 0.00 0.00 0.00 3.57
827 829 2.354821 GAGACGGTTGTTCAGCTTTGTT 59.645 45.455 0.00 0.00 0.00 2.83
864 866 1.935327 CTGGAGGAACGACCGGTCTC 61.935 65.000 30.92 22.16 44.74 3.36
881 883 4.101448 CCGGTCCCAAGGCTCCTG 62.101 72.222 0.00 0.00 0.00 3.86
947 950 0.033109 ATTGAAACTAGGGCCAGGGC 60.033 55.000 6.18 3.77 41.06 5.19
956 964 1.474330 GGTGGGGCCATTGAAACTAG 58.526 55.000 4.39 0.00 37.17 2.57
962 971 3.727258 CGAGGGTGGGGCCATTGA 61.727 66.667 4.39 0.00 39.65 2.57
992 1001 1.386533 TAGATGGACTCCGAACGGAC 58.613 55.000 12.04 3.74 39.76 4.79
994 1003 2.226912 GAGATAGATGGACTCCGAACGG 59.773 54.545 6.94 6.94 0.00 4.44
1000 1009 2.227865 GTGCGAGAGATAGATGGACTCC 59.772 54.545 0.00 0.00 0.00 3.85
1002 1011 1.876799 CGTGCGAGAGATAGATGGACT 59.123 52.381 0.00 0.00 0.00 3.85
1003 1012 1.664588 GCGTGCGAGAGATAGATGGAC 60.665 57.143 0.00 0.00 0.00 4.02
1004 1013 0.593618 GCGTGCGAGAGATAGATGGA 59.406 55.000 0.00 0.00 0.00 3.41
1005 1014 0.595588 AGCGTGCGAGAGATAGATGG 59.404 55.000 0.00 0.00 0.00 3.51
1006 1015 2.315011 GAAGCGTGCGAGAGATAGATG 58.685 52.381 0.00 0.00 0.00 2.90
1008 1017 0.663688 GGAAGCGTGCGAGAGATAGA 59.336 55.000 0.00 0.00 0.00 1.98
1009 1018 0.665835 AGGAAGCGTGCGAGAGATAG 59.334 55.000 0.00 0.00 0.00 2.08
1010 1019 0.663688 GAGGAAGCGTGCGAGAGATA 59.336 55.000 0.00 0.00 0.00 1.98
1143 1152 0.320771 AAGGCATCAGAGCGAAACGT 60.321 50.000 0.00 0.00 34.64 3.99
1144 1153 1.640428 TAAGGCATCAGAGCGAAACG 58.360 50.000 0.00 0.00 34.64 3.60
1152 1161 1.134818 ACGCACGATTAAGGCATCAGA 60.135 47.619 0.00 0.00 0.00 3.27
1160 1169 0.790207 ACTGCACACGCACGATTAAG 59.210 50.000 0.00 0.00 45.36 1.85
1171 1180 2.956987 GCCATGGACACTGCACAC 59.043 61.111 18.40 0.00 0.00 3.82
1270 1279 0.677731 CCGTGATGTCCTGCACCAAT 60.678 55.000 0.00 0.00 0.00 3.16
1273 1282 2.034879 CACCGTGATGTCCTGCACC 61.035 63.158 0.00 0.00 0.00 5.01
1408 1420 4.704833 TGAGAGTTGGCCGGCAGC 62.705 66.667 30.85 17.28 42.60 5.25
1457 1469 3.251004 TGAGTATCGATCATCTGACACGG 59.749 47.826 0.00 0.00 38.61 4.94
1475 1487 1.139989 CTGAATCACGCGTGTTGAGT 58.860 50.000 35.74 18.74 0.00 3.41
1479 1491 1.865865 ACTTCTGAATCACGCGTGTT 58.134 45.000 35.74 27.83 0.00 3.32
1489 1501 7.846066 ACATAGCTTAGTCTGAACTTCTGAAT 58.154 34.615 0.00 4.37 36.92 2.57
1514 1526 9.595823 GTAGCTCTAGTTCACACCATTTTTATA 57.404 33.333 0.00 0.00 0.00 0.98
1536 1548 5.490213 GCGTTTATACACAAGACATGTAGC 58.510 41.667 0.00 0.00 41.46 3.58
1539 1551 3.181524 GCGCGTTTATACACAAGACATGT 60.182 43.478 8.43 0.00 45.34 3.21
1540 1552 3.342269 GCGCGTTTATACACAAGACATG 58.658 45.455 8.43 0.00 0.00 3.21
1562 1581 4.918129 CCATTCCTGCATGCGCGC 62.918 66.667 27.26 27.26 42.97 6.86
1588 1607 3.374367 CGATCTGACTACCTTCGTTCAGA 59.626 47.826 2.80 2.80 38.38 3.27
1595 1614 3.280295 TGACCTCGATCTGACTACCTTC 58.720 50.000 0.00 0.00 0.00 3.46
1596 1615 3.367646 TGACCTCGATCTGACTACCTT 57.632 47.619 0.00 0.00 0.00 3.50
1600 1619 4.840271 TGTAGTTGACCTCGATCTGACTA 58.160 43.478 0.00 0.00 0.00 2.59
1635 1654 4.224370 GGAGTGGATTGGTTAGTCCAGTTA 59.776 45.833 3.48 0.00 45.75 2.24
1660 1679 6.291377 TCTATTACCTTGAGCAATGGTGATC 58.709 40.000 11.88 0.00 40.73 2.92
1750 1775 2.236395 GTGAAGCCTTCCTTACCTGCTA 59.764 50.000 1.21 0.00 32.78 3.49
1787 1812 1.275856 TGCTTACCGTTTACCGATGGT 59.724 47.619 0.00 0.00 41.67 3.55
1821 1846 0.176680 ACATAGCTGCGGTTCAGAGG 59.823 55.000 0.00 0.00 45.72 3.69
1837 1862 7.773690 GGTTAGGATCTTGTAATGTTACCACAT 59.226 37.037 0.00 0.00 46.34 3.21
1866 1900 0.608035 TCCGGTTCCTGTGATTTGGC 60.608 55.000 0.00 0.00 0.00 4.52
1899 1933 1.947456 AGTCGTCGGATGAATCGATGA 59.053 47.619 0.00 4.56 46.30 2.92
1904 1938 3.247173 ACGTAGTAGTCGTCGGATGAATC 59.753 47.826 3.10 0.00 41.94 2.52
1957 1991 4.812626 CCACTCTACAACTTTGTTACCGTT 59.187 41.667 0.00 0.00 42.35 4.44
2004 2038 4.891727 ATCGATCACACCGGCGGC 62.892 66.667 28.71 7.46 0.00 6.53
2005 2039 2.629050 AAGATCGATCACACCGGCGG 62.629 60.000 27.06 27.06 0.00 6.13
2006 2040 1.226974 AAGATCGATCACACCGGCG 60.227 57.895 26.47 0.00 0.00 6.46
2167 2201 1.100510 AAGTATCGGCAGCGTGTAGA 58.899 50.000 0.00 0.00 0.00 2.59
2168 2202 1.200483 CAAGTATCGGCAGCGTGTAG 58.800 55.000 0.00 0.00 0.00 2.74
2172 2206 2.186903 CCCAAGTATCGGCAGCGT 59.813 61.111 0.00 0.00 0.00 5.07
2173 2207 2.588877 CCCCAAGTATCGGCAGCG 60.589 66.667 0.00 0.00 0.00 5.18
2183 2217 2.430367 GCCACGTTCTCCCCAAGT 59.570 61.111 0.00 0.00 0.00 3.16
2213 2247 1.971357 GTCCTCACCTCTTTCAGACCA 59.029 52.381 0.00 0.00 0.00 4.02
2216 2250 3.769844 GGTATGTCCTCACCTCTTTCAGA 59.230 47.826 0.00 0.00 0.00 3.27
2235 2269 2.353704 CGTGGCTGAATGTTGAGAGGTA 60.354 50.000 0.00 0.00 0.00 3.08
2242 2285 0.442310 CGTACCGTGGCTGAATGTTG 59.558 55.000 0.00 0.00 0.00 3.33
2301 2344 3.136123 CTTCACGCCCTGCCCATG 61.136 66.667 0.00 0.00 0.00 3.66
2302 2345 4.431131 CCTTCACGCCCTGCCCAT 62.431 66.667 0.00 0.00 0.00 4.00
2371 2414 2.125952 GAGGTTGCATTTGCGCCC 60.126 61.111 4.18 7.13 45.83 6.13
2390 2433 1.471501 CGTGATTTCATCGGGCTGAGA 60.472 52.381 1.04 0.00 0.00 3.27
2397 2440 1.934589 TAGTGGCGTGATTTCATCGG 58.065 50.000 0.00 0.00 0.00 4.18
2399 2442 5.512788 CACATTTTAGTGGCGTGATTTCATC 59.487 40.000 0.00 0.00 35.88 2.92
2413 2456 7.510549 ACAACATTCAGCTACACATTTTAGT 57.489 32.000 0.00 0.00 0.00 2.24
2416 2459 6.804677 TCAACAACATTCAGCTACACATTTT 58.195 32.000 0.00 0.00 0.00 1.82
2423 2466 3.120199 ACGCATCAACAACATTCAGCTAC 60.120 43.478 0.00 0.00 0.00 3.58
2424 2467 3.073678 ACGCATCAACAACATTCAGCTA 58.926 40.909 0.00 0.00 0.00 3.32
2445 2491 2.183300 GGATGGCTGCGTCACGTA 59.817 61.111 0.00 0.00 0.00 3.57
2447 2493 3.190849 CAGGATGGCTGCGTCACG 61.191 66.667 0.00 0.00 0.00 4.35
2795 2853 6.047511 AGCATCACCTCCATGATCTTATAC 57.952 41.667 0.00 0.00 37.20 1.47
2797 2855 5.784390 ACTAGCATCACCTCCATGATCTTAT 59.216 40.000 0.00 0.00 37.20 1.73
2798 2856 5.011431 CACTAGCATCACCTCCATGATCTTA 59.989 44.000 0.00 0.00 37.20 2.10
2799 2857 3.972638 ACTAGCATCACCTCCATGATCTT 59.027 43.478 0.00 0.00 37.20 2.40
2809 2867 2.093288 CCACACATCACTAGCATCACCT 60.093 50.000 0.00 0.00 0.00 4.00
2817 2876 2.941064 CAATCCTGCCACACATCACTAG 59.059 50.000 0.00 0.00 0.00 2.57
2819 2878 1.074405 ACAATCCTGCCACACATCACT 59.926 47.619 0.00 0.00 0.00 3.41
2826 2885 0.251297 CCCTCAACAATCCTGCCACA 60.251 55.000 0.00 0.00 0.00 4.17
2928 2988 0.245539 CAAGCCAGCCAACCTTCATG 59.754 55.000 0.00 0.00 0.00 3.07
2945 3012 0.178992 CTTGGTTCCTCACAGGCCAA 60.179 55.000 5.01 0.00 35.85 4.52
2948 3015 0.329596 ATCCTTGGTTCCTCACAGGC 59.670 55.000 0.00 0.00 34.61 4.85
2949 3016 1.630369 TCATCCTTGGTTCCTCACAGG 59.370 52.381 0.00 0.00 36.46 4.00
2950 3017 3.077359 GTTCATCCTTGGTTCCTCACAG 58.923 50.000 0.00 0.00 0.00 3.66
2951 3018 2.441375 TGTTCATCCTTGGTTCCTCACA 59.559 45.455 0.00 0.00 0.00 3.58
2952 3019 3.140325 TGTTCATCCTTGGTTCCTCAC 57.860 47.619 0.00 0.00 0.00 3.51
2962 3029 5.624159 TCACAGTCAGAAATGTTCATCCTT 58.376 37.500 0.00 0.00 0.00 3.36
2969 3036 2.508526 GCCCTCACAGTCAGAAATGTT 58.491 47.619 0.00 0.00 0.00 2.71
3000 3067 1.202245 CGGTGGGCGATTTTTGGTATG 60.202 52.381 0.00 0.00 0.00 2.39
3004 3071 1.080839 CACGGTGGGCGATTTTTGG 60.081 57.895 0.00 0.00 0.00 3.28
3112 3200 2.415512 GCATCGGAAAGTCACAGTAACC 59.584 50.000 0.00 0.00 0.00 2.85
3117 3205 1.391485 CTTCGCATCGGAAAGTCACAG 59.609 52.381 0.00 0.00 0.00 3.66
3123 3211 1.078759 ACGCTCTTCGCATCGGAAAG 61.079 55.000 0.00 0.00 43.23 2.62
3208 3300 9.840427 ATCATAAAAGAAAAACTGATAACACCG 57.160 29.630 0.00 0.00 0.00 4.94
3220 3312 5.738693 CGCGATGCTCATCATAAAAGAAAAA 59.261 36.000 0.00 0.00 37.69 1.94
3221 3313 5.163764 ACGCGATGCTCATCATAAAAGAAAA 60.164 36.000 15.93 0.00 37.69 2.29
3225 3317 3.001634 ACACGCGATGCTCATCATAAAAG 59.998 43.478 15.93 0.00 37.69 2.27
3299 3391 5.278808 GGTGTCCACCCTTGTAATTTCTTTC 60.279 44.000 5.08 0.00 45.68 2.62
3386 3478 0.316841 GCCGCTCCATTTTGGTTTGA 59.683 50.000 0.00 0.00 39.03 2.69
3429 3522 7.886446 AGATGAAAATCGACTAACCCCTTAAAA 59.114 33.333 0.00 0.00 0.00 1.52
3440 3533 8.040727 TGGAGATTGAAAGATGAAAATCGACTA 58.959 33.333 0.00 0.00 34.84 2.59
3469 3562 2.159379 GGGCGTTTGATCAAGATCCAAC 60.159 50.000 8.41 13.92 39.01 3.77
3472 3565 1.672881 CTGGGCGTTTGATCAAGATCC 59.327 52.381 8.41 10.20 37.02 3.36
3483 3576 4.394729 TGAAGATAAAGTTCTGGGCGTTT 58.605 39.130 0.00 0.00 0.00 3.60
3487 3580 4.336280 AGGTTGAAGATAAAGTTCTGGGC 58.664 43.478 0.00 0.00 0.00 5.36
3498 3591 7.453393 ACAGATCAAGTTTGAGGTTGAAGATA 58.547 34.615 0.00 0.00 41.08 1.98
3511 3604 2.613977 CGGCTCAGGACAGATCAAGTTT 60.614 50.000 0.00 0.00 0.00 2.66
3513 3606 0.534412 CGGCTCAGGACAGATCAAGT 59.466 55.000 0.00 0.00 0.00 3.16
3516 3609 2.725312 GGCGGCTCAGGACAGATCA 61.725 63.158 0.00 0.00 0.00 2.92
3517 3610 2.107953 GGCGGCTCAGGACAGATC 59.892 66.667 0.00 0.00 0.00 2.75
3534 3627 4.462280 GGACCGGTGGTTAGGCCG 62.462 72.222 14.63 0.00 46.80 6.13
3535 3628 4.105553 GGGACCGGTGGTTAGGCC 62.106 72.222 14.63 4.34 35.25 5.19
3536 3629 4.105553 GGGGACCGGTGGTTAGGC 62.106 72.222 14.63 0.00 40.86 3.93
3549 3642 4.273262 TTTCGGGGAGGGTGGGGA 62.273 66.667 0.00 0.00 0.00 4.81
3550 3643 4.043100 GTTTCGGGGAGGGTGGGG 62.043 72.222 0.00 0.00 0.00 4.96
3551 3644 4.043100 GGTTTCGGGGAGGGTGGG 62.043 72.222 0.00 0.00 0.00 4.61
3552 3645 3.253838 TGGTTTCGGGGAGGGTGG 61.254 66.667 0.00 0.00 0.00 4.61
3553 3646 2.033602 GTGGTTTCGGGGAGGGTG 59.966 66.667 0.00 0.00 0.00 4.61
3554 3647 3.254617 GGTGGTTTCGGGGAGGGT 61.255 66.667 0.00 0.00 0.00 4.34
3555 3648 4.043100 GGGTGGTTTCGGGGAGGG 62.043 72.222 0.00 0.00 0.00 4.30
3556 3649 4.043100 GGGGTGGTTTCGGGGAGG 62.043 72.222 0.00 0.00 0.00 4.30
3557 3650 1.614226 TAGGGGTGGTTTCGGGGAG 60.614 63.158 0.00 0.00 0.00 4.30
3558 3651 1.919816 GTAGGGGTGGTTTCGGGGA 60.920 63.158 0.00 0.00 0.00 4.81
3559 3652 2.672908 GTAGGGGTGGTTTCGGGG 59.327 66.667 0.00 0.00 0.00 5.73
3560 3653 2.672908 GGTAGGGGTGGTTTCGGG 59.327 66.667 0.00 0.00 0.00 5.14
3561 3654 2.115734 AACGGTAGGGGTGGTTTCGG 62.116 60.000 0.00 0.00 0.00 4.30
3562 3655 0.952010 CAACGGTAGGGGTGGTTTCG 60.952 60.000 0.00 0.00 0.00 3.46
3563 3656 0.607217 CCAACGGTAGGGGTGGTTTC 60.607 60.000 0.00 0.00 0.00 2.78
3564 3657 1.354942 ACCAACGGTAGGGGTGGTTT 61.355 55.000 0.00 0.00 32.11 3.27
3565 3658 1.771336 ACCAACGGTAGGGGTGGTT 60.771 57.895 0.00 0.00 32.11 3.67
3566 3659 2.122279 ACCAACGGTAGGGGTGGT 60.122 61.111 0.00 0.00 32.11 4.16
3567 3660 1.486145 AAGACCAACGGTAGGGGTGG 61.486 60.000 4.08 0.00 35.25 4.61
3568 3661 0.036671 GAAGACCAACGGTAGGGGTG 60.037 60.000 4.08 0.00 35.25 4.61
3569 3662 1.196766 GGAAGACCAACGGTAGGGGT 61.197 60.000 4.10 1.81 35.25 4.95
3570 3663 1.600638 GGAAGACCAACGGTAGGGG 59.399 63.158 4.10 0.00 35.25 4.79
3571 3664 1.217244 CGGAAGACCAACGGTAGGG 59.783 63.158 0.00 0.00 35.25 3.53
3572 3665 1.447314 GCGGAAGACCAACGGTAGG 60.447 63.158 0.00 0.00 35.25 3.18
3573 3666 1.447314 GGCGGAAGACCAACGGTAG 60.447 63.158 0.00 0.00 35.25 3.18
3574 3667 2.658422 GGCGGAAGACCAACGGTA 59.342 61.111 0.00 0.00 35.25 4.02
3575 3668 4.675029 CGGCGGAAGACCAACGGT 62.675 66.667 0.00 0.00 39.44 4.83
3593 3686 3.178611 GGGAGGTATGGCCAGGGG 61.179 72.222 13.05 0.00 40.61 4.79
3594 3687 3.178611 GGGGAGGTATGGCCAGGG 61.179 72.222 13.05 0.00 40.61 4.45
3595 3688 3.178611 GGGGGAGGTATGGCCAGG 61.179 72.222 13.05 0.00 40.61 4.45
3596 3689 1.697754 AAGGGGGAGGTATGGCCAG 60.698 63.158 13.05 0.00 40.61 4.85
3597 3690 2.006415 CAAGGGGGAGGTATGGCCA 61.006 63.158 8.56 8.56 40.61 5.36
3598 3691 2.927056 CAAGGGGGAGGTATGGCC 59.073 66.667 0.00 0.00 37.58 5.36
3599 3692 2.195956 GCAAGGGGGAGGTATGGC 59.804 66.667 0.00 0.00 0.00 4.40
3600 3693 2.510906 CGCAAGGGGGAGGTATGG 59.489 66.667 0.00 0.00 0.00 2.74
3601 3694 2.203209 GCGCAAGGGGGAGGTATG 60.203 66.667 0.30 0.00 38.28 2.39
3602 3695 3.489513 GGCGCAAGGGGGAGGTAT 61.490 66.667 10.83 0.00 38.28 2.73
3609 3702 2.561037 AAAAACTCGGCGCAAGGGG 61.561 57.895 10.83 0.00 38.28 4.79
3610 3703 3.039134 AAAAACTCGGCGCAAGGG 58.961 55.556 10.83 4.81 38.28 3.95
3624 3717 2.890945 GTGGGGCTTTGCTAGAGAAAAA 59.109 45.455 0.00 0.00 0.00 1.94
3625 3718 2.158534 TGTGGGGCTTTGCTAGAGAAAA 60.159 45.455 0.00 0.00 0.00 2.29
3626 3719 1.423541 TGTGGGGCTTTGCTAGAGAAA 59.576 47.619 0.00 0.00 0.00 2.52
3627 3720 1.064003 TGTGGGGCTTTGCTAGAGAA 58.936 50.000 0.00 0.00 0.00 2.87
3628 3721 0.324943 GTGTGGGGCTTTGCTAGAGA 59.675 55.000 0.00 0.00 0.00 3.10
3629 3722 0.678048 GGTGTGGGGCTTTGCTAGAG 60.678 60.000 0.00 0.00 0.00 2.43
3630 3723 1.378762 GGTGTGGGGCTTTGCTAGA 59.621 57.895 0.00 0.00 0.00 2.43
3631 3724 0.323725 ATGGTGTGGGGCTTTGCTAG 60.324 55.000 0.00 0.00 0.00 3.42
3632 3725 0.323360 GATGGTGTGGGGCTTTGCTA 60.323 55.000 0.00 0.00 0.00 3.49
3633 3726 1.607467 GATGGTGTGGGGCTTTGCT 60.607 57.895 0.00 0.00 0.00 3.91
3636 4093 1.228862 GGTGATGGTGTGGGGCTTT 60.229 57.895 0.00 0.00 0.00 3.51
3650 4107 0.403750 AGGGTTTAAGGTGGGGGTGA 60.404 55.000 0.00 0.00 0.00 4.02
3652 4109 1.997791 CTTAGGGTTTAAGGTGGGGGT 59.002 52.381 0.00 0.00 0.00 4.95
3661 4142 7.375890 ACCCCAGTATCTATCTTAGGGTTTAA 58.624 38.462 0.00 0.00 44.14 1.52
3716 4197 1.271379 CGCCAGAGGGAAGGAAGAAAA 60.271 52.381 0.00 0.00 35.59 2.29
3736 4217 5.008118 CGATTTTCCCTAGAAGAAATGAGGC 59.992 44.000 8.25 0.00 33.45 4.70
3759 4240 3.760693 ATCCGATTTGGGTCAGTCG 57.239 52.632 0.00 0.00 38.76 4.18
3773 4254 0.820226 TCCAGTCAGCTGAAGATCCG 59.180 55.000 20.19 3.12 45.28 4.18
3774 4255 1.830477 ACTCCAGTCAGCTGAAGATCC 59.170 52.381 20.19 5.47 45.28 3.36
3778 4259 2.999355 GCTAAACTCCAGTCAGCTGAAG 59.001 50.000 20.19 14.79 45.28 3.02
3813 4294 4.519350 CCGAGGTGTCAGCTGTTAGATATA 59.481 45.833 14.67 0.00 0.00 0.86
3820 4301 1.821061 CTCCCGAGGTGTCAGCTGTT 61.821 60.000 14.67 0.00 0.00 3.16
3821 4302 2.203640 TCCCGAGGTGTCAGCTGT 60.204 61.111 14.67 0.00 0.00 4.40
3823 4304 3.386237 GCTCCCGAGGTGTCAGCT 61.386 66.667 3.69 3.69 0.00 4.24
3834 4315 3.758088 CTGTCGTGGATCGCTCCCG 62.758 68.421 2.20 6.36 41.29 5.14
3836 4317 2.583593 GCTGTCGTGGATCGCTCC 60.584 66.667 0.00 0.00 42.45 4.70
3841 4322 1.020861 TGCATGTGCTGTCGTGGATC 61.021 55.000 6.55 0.00 42.66 3.36
3843 4324 1.668793 CTGCATGTGCTGTCGTGGA 60.669 57.895 6.55 0.00 42.66 4.02
3863 4344 6.322201 CCCTAATAAGGTTCTTGATGTGCATT 59.678 38.462 0.00 0.00 41.89 3.56
3900 4381 3.019003 ATGCCTCTCCCGACCAACG 62.019 63.158 0.00 0.00 42.18 4.10
3908 4389 0.034670 ACTTTCAGCATGCCTCTCCC 60.035 55.000 15.66 0.00 34.76 4.30
3910 4391 0.450983 GCACTTTCAGCATGCCTCTC 59.549 55.000 15.66 0.00 34.76 3.20
3923 4404 5.426689 TCCATCAGTGATTCTAGCACTTT 57.573 39.130 1.86 0.00 43.67 2.66
3939 4420 8.588472 CCACAACTAGATCTAACATATCCATCA 58.412 37.037 3.57 0.00 0.00 3.07
3942 4423 8.727100 ATCCACAACTAGATCTAACATATCCA 57.273 34.615 3.57 0.00 0.00 3.41
3971 4452 5.126545 ACATCAAGCAGAATGTATGTGCATT 59.873 36.000 0.00 0.00 41.28 3.56
3982 4463 6.445451 ACCATCCTATACATCAAGCAGAAT 57.555 37.500 0.00 0.00 0.00 2.40
3985 4466 6.870965 GTCTAACCATCCTATACATCAAGCAG 59.129 42.308 0.00 0.00 0.00 4.24
3991 4472 6.207025 ACACTCGTCTAACCATCCTATACATC 59.793 42.308 0.00 0.00 0.00 3.06
3996 4477 3.564644 CGACACTCGTCTAACCATCCTAT 59.435 47.826 0.00 0.00 40.23 2.57
4010 4491 0.725686 AGTATGGACGACGACACTCG 59.274 55.000 0.00 0.00 46.93 4.18
4011 4492 2.008329 AGAGTATGGACGACGACACTC 58.992 52.381 0.00 5.05 34.07 3.51
4013 4494 2.783333 GAAGAGTATGGACGACGACAC 58.217 52.381 0.00 0.00 0.00 3.67
4019 4500 1.830279 ACCACGAAGAGTATGGACGA 58.170 50.000 0.00 0.00 36.94 4.20
4038 4519 2.358957 GCTGTGGCATAGTGTCATCAA 58.641 47.619 13.02 0.00 33.03 2.57
4049 4530 1.001378 GTTCTTTTGTCGCTGTGGCAT 60.001 47.619 0.00 0.00 38.60 4.40
4057 4538 2.922335 GCATCCCAAGTTCTTTTGTCGC 60.922 50.000 0.00 0.00 0.00 5.19
4066 4547 3.905249 GGGTCGCATCCCAAGTTC 58.095 61.111 8.16 0.00 46.30 3.01
4083 4564 2.251040 ACGTCGATCGAACATTGACAG 58.749 47.619 21.31 5.44 42.86 3.51


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

AutoCloner maintained by Alex Coulton.