Multiple sequence alignment - TraesCS1B01G306500

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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 TraesCS1B01G306500 chr1B 100.000 2687 0 0 1 2687 529707394 529710080 0.000000e+00 4963
1 TraesCS1B01G306500 chr1B 100.000 264 0 0 3028 3291 529710421 529710684 3.820000e-134 488
2 TraesCS1B01G306500 chr1D 91.791 2083 76 29 606 2646 392945538 392943509 0.000000e+00 2811
3 TraesCS1B01G306500 chr1D 88.889 441 27 8 2 423 392946150 392945713 1.050000e-144 523
4 TraesCS1B01G306500 chr1D 91.176 136 4 3 427 562 392945662 392945535 9.380000e-41 178
5 TraesCS1B01G306500 chr1D 88.372 86 7 3 3028 3112 399158878 399158961 2.090000e-17 100
6 TraesCS1B01G306500 chr1A 93.062 1326 49 21 1050 2352 492275330 492276635 0.000000e+00 1899
7 TraesCS1B01G306500 chr1A 83.234 334 41 7 1 319 492274453 492274786 3.210000e-75 292
8 TraesCS1B01G306500 chr1A 88.235 136 8 5 427 562 492274951 492275078 4.400000e-34 156
9 TraesCS1B01G306500 chr1A 88.710 124 11 2 2523 2646 492276747 492276867 7.360000e-32 148
10 TraesCS1B01G306500 chr3D 83.835 266 38 5 3028 3291 15422312 15422574 7.050000e-62 248
11 TraesCS1B01G306500 chr3D 90.155 193 15 3 3101 3291 578899680 578899870 7.050000e-62 248
12 TraesCS1B01G306500 chr3D 82.784 273 29 12 3028 3287 583474169 583474436 9.190000e-56 228
13 TraesCS1B01G306500 chr3D 81.181 271 37 9 3028 3291 403482915 403483178 4.300000e-49 206
14 TraesCS1B01G306500 chr5B 84.170 259 26 8 3046 3291 320443788 320444044 1.530000e-58 237
15 TraesCS1B01G306500 chr3A 82.437 279 30 11 3028 3291 633048563 633048289 3.300000e-55 226
16 TraesCS1B01G306500 chr6B 89.773 176 17 1 3117 3291 578906814 578906989 1.190000e-54 224
17 TraesCS1B01G306500 chr6B 81.588 277 33 10 3031 3291 508935479 508935753 2.570000e-51 213
18 TraesCS1B01G306500 chr2A 90.323 155 13 2 3138 3291 34294004 34293851 5.570000e-48 202
19 TraesCS1B01G306500 chr6D 80.460 261 33 8 3028 3272 431286671 431286413 2.020000e-42 183


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 TraesCS1B01G306500 chr1B 529707394 529710684 3290 False 2725.500000 4963 100.000000 1 3291 2 chr1B.!!$F1 3290
1 TraesCS1B01G306500 chr1D 392943509 392946150 2641 True 1170.666667 2811 90.618667 2 2646 3 chr1D.!!$R1 2644
2 TraesCS1B01G306500 chr1A 492274453 492276867 2414 False 623.750000 1899 88.310250 1 2646 4 chr1A.!!$F1 2645

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
36 39 0.033504 AATGAAGCCGTCTCACGTGT 59.966 50.0 16.51 0.00 40.58 4.49 F
830 1049 0.107017 GGCATAGTGAGCACACCCAT 60.107 55.0 10.88 2.07 46.99 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 2208 0.386113 TGGCCTGCCGTAAAACAAAC 59.614 50.0 3.32 0.0 39.42 2.93 R
2656 2932 0.391597 CCAACGCCGATGGGTATAGT 59.608 55.0 5.36 0.0 36.50 2.12 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
36 39 0.033504 AATGAAGCCGTCTCACGTGT 59.966 50.000 16.51 0.00 40.58 4.49
38 41 1.299926 GAAGCCGTCTCACGTGTGT 60.300 57.895 16.51 0.00 40.58 3.72
95 108 8.450578 TGAAAAGATTGACTGCTAAAAGAGAA 57.549 30.769 0.00 0.00 0.00 2.87
98 111 7.903995 AAGATTGACTGCTAAAAGAGAAGAG 57.096 36.000 0.00 0.00 33.83 2.85
99 112 7.238486 AGATTGACTGCTAAAAGAGAAGAGA 57.762 36.000 0.00 0.00 33.83 3.10
101 114 7.765360 AGATTGACTGCTAAAAGAGAAGAGATG 59.235 37.037 0.00 0.00 33.83 2.90
102 115 6.596309 TGACTGCTAAAAGAGAAGAGATGA 57.404 37.500 0.00 0.00 33.83 2.92
103 116 6.997655 TGACTGCTAAAAGAGAAGAGATGAA 58.002 36.000 0.00 0.00 33.83 2.57
104 117 6.870965 TGACTGCTAAAAGAGAAGAGATGAAC 59.129 38.462 0.00 0.00 33.83 3.18
105 118 7.003402 ACTGCTAAAAGAGAAGAGATGAACT 57.997 36.000 0.00 0.00 33.83 3.01
106 119 7.449247 ACTGCTAAAAGAGAAGAGATGAACTT 58.551 34.615 0.00 0.00 33.83 2.66
107 120 7.602265 ACTGCTAAAAGAGAAGAGATGAACTTC 59.398 37.037 0.00 0.00 42.53 3.01
114 130 3.589988 GAAGAGATGAACTTCTCGGCAA 58.410 45.455 10.52 0.00 45.56 4.52
136 152 1.202687 TGATGTCATCGGCCCTTCATC 60.203 52.381 8.29 5.70 34.28 2.92
169 185 3.053896 GAAAACGTCGGGGCCAGG 61.054 66.667 4.39 0.00 0.00 4.45
197 213 1.228894 ACTCCCCTTCTCTGCGACA 60.229 57.895 0.00 0.00 0.00 4.35
211 227 1.273606 TGCGACAGGAAGAGAAGAAGG 59.726 52.381 0.00 0.00 0.00 3.46
217 233 0.393673 GGAAGAGAAGAAGGCCCTGC 60.394 60.000 0.00 0.00 0.00 4.85
260 276 4.436852 CGACACTATAACAACATGCCAACC 60.437 45.833 0.00 0.00 0.00 3.77
270 286 4.053295 CAACATGCCAACCTTTTCTTGAG 58.947 43.478 0.00 0.00 0.00 3.02
277 293 3.571401 CCAACCTTTTCTTGAGAGTGCAT 59.429 43.478 0.00 0.00 0.00 3.96
279 295 4.090761 ACCTTTTCTTGAGAGTGCATGA 57.909 40.909 0.00 0.00 0.00 3.07
292 308 2.501128 CATGAGACCACCGCCGAT 59.499 61.111 0.00 0.00 0.00 4.18
386 410 1.308998 GCTAACATTAGGTGGCGCAT 58.691 50.000 10.83 0.00 0.00 4.73
464 568 1.801025 GCCCCGTCAAAAACAACACAG 60.801 52.381 0.00 0.00 0.00 3.66
558 759 4.223700 TGAGCTGTCTGATTAAGTCATGGT 59.776 41.667 0.00 0.00 35.97 3.55
559 760 5.171339 AGCTGTCTGATTAAGTCATGGTT 57.829 39.130 0.00 0.00 35.97 3.67
560 761 6.070824 TGAGCTGTCTGATTAAGTCATGGTTA 60.071 38.462 0.00 0.00 35.97 2.85
561 762 6.893583 AGCTGTCTGATTAAGTCATGGTTAT 58.106 36.000 0.00 0.00 35.97 1.89
562 763 7.341805 AGCTGTCTGATTAAGTCATGGTTATT 58.658 34.615 0.00 0.00 35.97 1.40
563 764 8.486210 AGCTGTCTGATTAAGTCATGGTTATTA 58.514 33.333 0.00 0.00 35.97 0.98
564 765 9.277783 GCTGTCTGATTAAGTCATGGTTATTAT 57.722 33.333 0.00 0.00 35.97 1.28
566 767 9.559732 TGTCTGATTAAGTCATGGTTATTATGG 57.440 33.333 0.00 0.00 35.97 2.74
567 768 8.507249 GTCTGATTAAGTCATGGTTATTATGGC 58.493 37.037 0.00 0.00 35.97 4.40
568 769 8.217111 TCTGATTAAGTCATGGTTATTATGGCA 58.783 33.333 0.00 0.00 35.97 4.92
569 770 8.759481 TGATTAAGTCATGGTTATTATGGCAA 57.241 30.769 0.00 0.00 32.71 4.52
570 771 9.365906 TGATTAAGTCATGGTTATTATGGCAAT 57.634 29.630 0.00 0.00 32.71 3.56
826 1045 2.670635 CTCGGCATAGTGAGCACAC 58.329 57.895 6.11 6.11 46.24 3.82
827 1046 0.807667 CTCGGCATAGTGAGCACACC 60.808 60.000 10.88 0.00 46.99 4.16
828 1047 1.815421 CGGCATAGTGAGCACACCC 60.815 63.158 10.88 4.09 46.99 4.61
829 1048 1.299648 GGCATAGTGAGCACACCCA 59.700 57.895 10.88 0.00 46.99 4.51
830 1049 0.107017 GGCATAGTGAGCACACCCAT 60.107 55.000 10.88 2.07 46.99 4.00
831 1050 1.303309 GCATAGTGAGCACACCCATC 58.697 55.000 10.88 0.00 46.99 3.51
832 1051 1.134280 GCATAGTGAGCACACCCATCT 60.134 52.381 10.88 0.00 46.99 2.90
833 1052 2.831333 CATAGTGAGCACACCCATCTC 58.169 52.381 10.88 0.00 46.99 2.75
834 1053 1.937191 TAGTGAGCACACCCATCTCA 58.063 50.000 10.88 0.00 46.99 3.27
877 1096 3.830192 CCCAGGCTCAAATGGCGC 61.830 66.667 0.00 0.00 35.10 6.53
887 1106 0.179000 CAAATGGCGCCTCTCCTACT 59.821 55.000 29.70 0.00 0.00 2.57
900 1119 4.325501 CCTCTCCTACTCCTACAAGAACCT 60.326 50.000 0.00 0.00 0.00 3.50
906 1125 3.323775 ACTCCTACAAGAACCTTCCCAA 58.676 45.455 0.00 0.00 0.00 4.12
912 1131 5.304357 CCTACAAGAACCTTCCCAACAAAAT 59.696 40.000 0.00 0.00 0.00 1.82
917 1136 2.588620 ACCTTCCCAACAAAATACGCA 58.411 42.857 0.00 0.00 0.00 5.24
924 1143 0.242286 AACAAAATACGCATGCGCCA 59.758 45.000 38.15 26.81 44.19 5.69
927 1146 0.179140 AAAATACGCATGCGCCAAGG 60.179 50.000 38.15 13.30 44.19 3.61
949 1168 4.731612 CTCTGCCGCACTCGCACT 62.732 66.667 0.00 0.00 38.40 4.40
950 1169 4.724602 TCTGCCGCACTCGCACTC 62.725 66.667 0.00 0.00 38.40 3.51
976 1195 3.880846 CCGCCGAGCCATCTTTGC 61.881 66.667 0.00 0.00 0.00 3.68
987 1206 3.631227 AGCCATCTTTGCTCTTTCATAGC 59.369 43.478 0.00 0.00 40.50 2.97
1628 1854 0.586802 GTCAGCACGGTTCCTTCAAC 59.413 55.000 0.00 0.00 0.00 3.18
1700 1926 2.726760 GGTGTCGCATCGTATCTGATTC 59.273 50.000 0.00 0.00 0.00 2.52
1701 1927 3.372060 GTGTCGCATCGTATCTGATTCA 58.628 45.455 0.00 0.00 0.00 2.57
1711 1937 3.496130 CGTATCTGATTCACTGATTGGCC 59.504 47.826 0.00 0.00 38.03 5.36
1746 1978 2.856000 AAGGTGCTGGAGCTGGGT 60.856 61.111 0.54 0.00 42.66 4.51
1752 1984 2.033141 CTGGAGCTGGGTGTGGTG 59.967 66.667 0.00 0.00 0.00 4.17
1910 2147 2.479275 GAGCACACCGTAGTTTCTTTCC 59.521 50.000 0.00 0.00 0.00 3.13
1911 2148 1.193874 GCACACCGTAGTTTCTTTCCG 59.806 52.381 0.00 0.00 0.00 4.30
1918 2157 1.123756 GTAGTTTCTTTCCGCGTGTCG 59.876 52.381 4.92 0.00 38.08 4.35
1922 2161 0.242825 TTCTTTCCGCGTGTCGATCT 59.757 50.000 4.92 0.00 41.67 2.75
1977 2220 3.490800 AAGTAACCGTGCGTTTGTTTT 57.509 38.095 0.00 0.00 35.79 2.43
2363 2615 0.032678 AGGCAATCGATCAGTAGCCG 59.967 55.000 15.42 0.00 46.34 5.52
2368 2620 3.181510 GCAATCGATCAGTAGCCGTTTTT 60.182 43.478 0.00 0.00 0.00 1.94
2400 2652 4.503296 GGAGCTCAAAGTTTGGAGTACAGA 60.503 45.833 17.19 0.00 33.66 3.41
2450 2702 2.670414 GCTAGCACACACTGATTCAGAC 59.330 50.000 20.33 2.79 35.18 3.51
2462 2714 3.894257 TTCAGACGCTGAACAGAGG 57.106 52.632 15.33 0.00 44.27 3.69
2463 2715 1.328279 TTCAGACGCTGAACAGAGGA 58.672 50.000 15.33 0.00 44.27 3.71
2464 2716 0.884514 TCAGACGCTGAACAGAGGAG 59.115 55.000 5.97 0.00 37.57 3.69
2465 2717 0.735632 CAGACGCTGAACAGAGGAGC 60.736 60.000 5.97 0.00 32.44 4.70
2466 2718 1.446966 GACGCTGAACAGAGGAGCC 60.447 63.158 5.97 0.00 32.25 4.70
2481 2733 2.279120 GCCGAGCGGAGTCTCATG 60.279 66.667 13.94 0.00 37.50 3.07
2498 2750 0.040425 ATGGCGTTCGTTGTTGCTTC 60.040 50.000 0.00 0.00 0.00 3.86
2504 2756 0.303493 TTCGTTGTTGCTTCGCTGAC 59.697 50.000 0.00 0.00 0.00 3.51
2596 2868 6.159988 CCCTCGAATATAATCCAGTTGTCTC 58.840 44.000 0.00 0.00 0.00 3.36
2610 2882 5.067153 CCAGTTGTCTCTAGATACTGTCAGG 59.933 48.000 17.04 7.69 37.62 3.86
2611 2883 5.883115 CAGTTGTCTCTAGATACTGTCAGGA 59.117 44.000 9.43 0.00 36.09 3.86
2612 2884 6.038161 CAGTTGTCTCTAGATACTGTCAGGAG 59.962 46.154 9.43 0.24 36.09 3.69
2620 2892 5.654901 AGATACTGTCAGGAGATAGGTGA 57.345 43.478 4.53 0.00 37.31 4.02
2624 2896 8.228206 AGATACTGTCAGGAGATAGGTGAAATA 58.772 37.037 4.53 0.00 37.31 1.40
2630 2906 7.502895 TGTCAGGAGATAGGTGAAATAGAGTAC 59.497 40.741 0.00 0.00 0.00 2.73
2646 2922 1.173913 GTACTGCTTCCCCGCAAAAT 58.826 50.000 0.00 0.00 39.80 1.82
2647 2923 2.026636 AGTACTGCTTCCCCGCAAAATA 60.027 45.455 0.00 0.00 39.80 1.40
2648 2924 1.917872 ACTGCTTCCCCGCAAAATAA 58.082 45.000 0.00 0.00 39.80 1.40
2649 2925 1.818674 ACTGCTTCCCCGCAAAATAAG 59.181 47.619 0.00 0.00 39.80 1.73
2650 2926 2.091541 CTGCTTCCCCGCAAAATAAGA 58.908 47.619 0.00 0.00 39.80 2.10
2651 2927 2.091541 TGCTTCCCCGCAAAATAAGAG 58.908 47.619 0.00 0.00 36.89 2.85
2652 2928 2.092323 GCTTCCCCGCAAAATAAGAGT 58.908 47.619 0.00 0.00 0.00 3.24
2653 2929 3.275999 GCTTCCCCGCAAAATAAGAGTA 58.724 45.455 0.00 0.00 0.00 2.59
2654 2930 3.692593 GCTTCCCCGCAAAATAAGAGTAA 59.307 43.478 0.00 0.00 0.00 2.24
2655 2931 4.338400 GCTTCCCCGCAAAATAAGAGTAAT 59.662 41.667 0.00 0.00 0.00 1.89
2656 2932 5.529800 GCTTCCCCGCAAAATAAGAGTAATA 59.470 40.000 0.00 0.00 0.00 0.98
2657 2933 6.512903 GCTTCCCCGCAAAATAAGAGTAATAC 60.513 42.308 0.00 0.00 0.00 1.89
2658 2934 6.243216 TCCCCGCAAAATAAGAGTAATACT 57.757 37.500 0.00 0.00 0.00 2.12
2659 2935 7.364149 TCCCCGCAAAATAAGAGTAATACTA 57.636 36.000 0.00 0.00 0.00 1.82
2660 2936 7.970102 TCCCCGCAAAATAAGAGTAATACTAT 58.030 34.615 0.00 0.00 0.00 2.12
2661 2937 9.092338 TCCCCGCAAAATAAGAGTAATACTATA 57.908 33.333 0.00 0.00 0.00 1.31
2662 2938 9.148104 CCCCGCAAAATAAGAGTAATACTATAC 57.852 37.037 0.00 0.00 0.00 1.47
2663 2939 9.148104 CCCGCAAAATAAGAGTAATACTATACC 57.852 37.037 0.00 0.00 0.00 2.73
2664 2940 9.148104 CCGCAAAATAAGAGTAATACTATACCC 57.852 37.037 0.00 0.00 0.00 3.69
2665 2941 9.701098 CGCAAAATAAGAGTAATACTATACCCA 57.299 33.333 0.00 0.00 0.00 4.51
2670 2946 6.527057 AAGAGTAATACTATACCCATCGGC 57.473 41.667 0.00 0.00 0.00 5.54
2671 2947 4.639310 AGAGTAATACTATACCCATCGGCG 59.361 45.833 0.00 0.00 0.00 6.46
2672 2948 4.338879 AGTAATACTATACCCATCGGCGT 58.661 43.478 6.85 0.00 0.00 5.68
2673 2949 4.768968 AGTAATACTATACCCATCGGCGTT 59.231 41.667 6.85 0.00 0.00 4.84
2674 2950 3.587797 ATACTATACCCATCGGCGTTG 57.412 47.619 6.85 9.17 0.00 4.10
2675 2951 0.391597 ACTATACCCATCGGCGTTGG 59.608 55.000 26.16 26.16 0.00 3.77
2680 2956 4.856801 CCATCGGCGTTGGGGGAG 62.857 72.222 25.58 3.26 0.00 4.30
2684 2960 4.090588 CGGCGTTGGGGGAGCTTA 62.091 66.667 0.00 0.00 0.00 3.09
2685 2961 2.124695 GGCGTTGGGGGAGCTTAG 60.125 66.667 0.00 0.00 0.00 2.18
2686 2962 2.666098 GGCGTTGGGGGAGCTTAGA 61.666 63.158 0.00 0.00 0.00 2.10
3045 3321 3.706287 GAACCGGCGGTATTTTTGG 57.294 52.632 34.37 1.54 33.12 3.28
3046 3322 0.457166 GAACCGGCGGTATTTTTGGC 60.457 55.000 34.37 10.34 33.12 4.52
3048 3324 2.871828 CGGCGGTATTTTTGGCGT 59.128 55.556 0.00 0.00 45.26 5.68
3049 3325 1.513160 CGGCGGTATTTTTGGCGTG 60.513 57.895 0.00 0.00 45.26 5.34
3050 3326 1.153920 GGCGGTATTTTTGGCGTGG 60.154 57.895 0.00 0.00 0.00 4.94
3051 3327 1.153920 GCGGTATTTTTGGCGTGGG 60.154 57.895 0.00 0.00 0.00 4.61
3052 3328 1.509004 CGGTATTTTTGGCGTGGGG 59.491 57.895 0.00 0.00 0.00 4.96
3053 3329 1.894512 GGTATTTTTGGCGTGGGGG 59.105 57.895 0.00 0.00 0.00 5.40
3054 3330 1.216977 GTATTTTTGGCGTGGGGGC 59.783 57.895 0.00 0.00 42.69 5.80
3055 3331 2.344203 TATTTTTGGCGTGGGGGCG 61.344 57.895 0.00 0.00 46.04 6.13
3056 3332 2.766306 TATTTTTGGCGTGGGGGCGA 62.766 55.000 0.00 0.00 46.04 5.54
3057 3333 4.669809 TTTTGGCGTGGGGGCGAT 62.670 61.111 0.00 0.00 46.04 4.58
3064 3340 4.851179 GTGGGGGCGATCGGGTTC 62.851 72.222 18.30 0.00 0.00 3.62
3067 3343 2.841044 GGGGCGATCGGGTTCCTA 60.841 66.667 18.30 0.00 0.00 2.94
3068 3344 2.735237 GGGCGATCGGGTTCCTAG 59.265 66.667 18.30 0.00 0.00 3.02
3069 3345 2.029221 GGCGATCGGGTTCCTAGC 59.971 66.667 18.30 0.00 0.00 3.42
3070 3346 2.029221 GCGATCGGGTTCCTAGCC 59.971 66.667 18.30 0.00 38.61 3.93
3076 3352 4.832608 GGGTTCCTAGCCGCCGTG 62.833 72.222 0.00 0.00 31.15 4.94
3094 3370 4.475444 CCCAGGTCGCCCCCTAGA 62.475 72.222 0.00 0.00 32.08 2.43
3095 3371 2.122813 CCAGGTCGCCCCCTAGAT 60.123 66.667 0.00 0.00 32.08 1.98
3096 3372 2.511452 CCAGGTCGCCCCCTAGATG 61.511 68.421 0.00 0.00 32.08 2.90
3097 3373 2.844839 AGGTCGCCCCCTAGATGC 60.845 66.667 0.00 0.00 31.31 3.91
3098 3374 3.942439 GGTCGCCCCCTAGATGCC 61.942 72.222 0.00 0.00 0.00 4.40
3099 3375 3.942439 GTCGCCCCCTAGATGCCC 61.942 72.222 0.00 0.00 0.00 5.36
3100 3376 4.172232 TCGCCCCCTAGATGCCCT 62.172 66.667 0.00 0.00 0.00 5.19
3101 3377 3.171388 CGCCCCCTAGATGCCCTT 61.171 66.667 0.00 0.00 0.00 3.95
3102 3378 2.757124 CGCCCCCTAGATGCCCTTT 61.757 63.158 0.00 0.00 0.00 3.11
3103 3379 1.620818 GCCCCCTAGATGCCCTTTT 59.379 57.895 0.00 0.00 0.00 2.27
3104 3380 0.756815 GCCCCCTAGATGCCCTTTTG 60.757 60.000 0.00 0.00 0.00 2.44
3105 3381 0.926293 CCCCCTAGATGCCCTTTTGA 59.074 55.000 0.00 0.00 0.00 2.69
3106 3382 1.287739 CCCCCTAGATGCCCTTTTGAA 59.712 52.381 0.00 0.00 0.00 2.69
3107 3383 2.292192 CCCCCTAGATGCCCTTTTGAAA 60.292 50.000 0.00 0.00 0.00 2.69
3108 3384 3.440127 CCCCTAGATGCCCTTTTGAAAA 58.560 45.455 0.00 0.00 0.00 2.29
3109 3385 3.195610 CCCCTAGATGCCCTTTTGAAAAC 59.804 47.826 0.00 0.00 0.00 2.43
3110 3386 3.831911 CCCTAGATGCCCTTTTGAAAACA 59.168 43.478 0.00 0.00 0.00 2.83
3111 3387 4.467438 CCCTAGATGCCCTTTTGAAAACAT 59.533 41.667 0.00 0.00 0.00 2.71
3112 3388 5.656416 CCCTAGATGCCCTTTTGAAAACATA 59.344 40.000 0.00 0.00 0.00 2.29
3113 3389 6.405842 CCCTAGATGCCCTTTTGAAAACATAC 60.406 42.308 0.00 0.00 0.00 2.39
3114 3390 6.378280 CCTAGATGCCCTTTTGAAAACATACT 59.622 38.462 0.00 0.00 0.00 2.12
3115 3391 6.670695 AGATGCCCTTTTGAAAACATACTT 57.329 33.333 0.00 0.00 0.00 2.24
3116 3392 6.458210 AGATGCCCTTTTGAAAACATACTTG 58.542 36.000 0.00 0.00 0.00 3.16
3117 3393 4.954875 TGCCCTTTTGAAAACATACTTGG 58.045 39.130 0.00 0.00 0.00 3.61
3118 3394 3.745975 GCCCTTTTGAAAACATACTTGGC 59.254 43.478 0.00 0.00 0.00 4.52
3119 3395 4.314961 CCCTTTTGAAAACATACTTGGCC 58.685 43.478 0.00 0.00 0.00 5.36
3120 3396 4.202305 CCCTTTTGAAAACATACTTGGCCA 60.202 41.667 0.00 0.00 0.00 5.36
3121 3397 4.990426 CCTTTTGAAAACATACTTGGCCAG 59.010 41.667 5.11 2.72 0.00 4.85
3122 3398 5.221422 CCTTTTGAAAACATACTTGGCCAGA 60.221 40.000 5.11 0.00 0.00 3.86
3123 3399 5.860941 TTTGAAAACATACTTGGCCAGAA 57.139 34.783 5.11 0.00 0.00 3.02
3124 3400 6.418057 TTTGAAAACATACTTGGCCAGAAT 57.582 33.333 5.11 0.00 0.00 2.40
3125 3401 6.418057 TTGAAAACATACTTGGCCAGAATT 57.582 33.333 5.11 0.00 0.00 2.17
3126 3402 6.024552 TGAAAACATACTTGGCCAGAATTC 57.975 37.500 5.11 0.00 0.00 2.17
3127 3403 4.701956 AAACATACTTGGCCAGAATTCG 57.298 40.909 5.11 0.00 0.00 3.34
3128 3404 3.350219 ACATACTTGGCCAGAATTCGT 57.650 42.857 5.11 0.00 0.00 3.85
3129 3405 3.270877 ACATACTTGGCCAGAATTCGTC 58.729 45.455 5.11 0.00 0.00 4.20
3130 3406 3.270027 CATACTTGGCCAGAATTCGTCA 58.730 45.455 5.11 0.00 0.00 4.35
3131 3407 2.270352 ACTTGGCCAGAATTCGTCAA 57.730 45.000 5.11 0.10 0.00 3.18
3132 3408 2.582052 ACTTGGCCAGAATTCGTCAAA 58.418 42.857 5.11 0.00 0.00 2.69
3133 3409 2.293399 ACTTGGCCAGAATTCGTCAAAC 59.707 45.455 5.11 0.00 0.00 2.93
3134 3410 1.974265 TGGCCAGAATTCGTCAAACA 58.026 45.000 0.00 0.00 0.00 2.83
3135 3411 1.606668 TGGCCAGAATTCGTCAAACAC 59.393 47.619 0.00 0.00 0.00 3.32
3148 3424 4.500703 GTCAAACACGACATAGATTCGG 57.499 45.455 0.00 0.00 40.92 4.30
3149 3425 2.927477 TCAAACACGACATAGATTCGGC 59.073 45.455 0.00 0.00 40.92 5.54
3150 3426 1.556564 AACACGACATAGATTCGGCG 58.443 50.000 0.00 0.00 40.92 6.46
3151 3427 0.736636 ACACGACATAGATTCGGCGA 59.263 50.000 4.99 4.99 40.92 5.54
3152 3428 1.337071 ACACGACATAGATTCGGCGAT 59.663 47.619 11.76 0.10 40.92 4.58
3153 3429 2.551032 ACACGACATAGATTCGGCGATA 59.449 45.455 11.76 0.00 40.92 2.92
3154 3430 3.164358 CACGACATAGATTCGGCGATAG 58.836 50.000 11.76 0.00 40.92 2.08
3155 3431 2.812591 ACGACATAGATTCGGCGATAGT 59.187 45.455 11.76 3.18 40.92 2.12
3156 3432 3.999001 ACGACATAGATTCGGCGATAGTA 59.001 43.478 11.76 2.49 40.92 1.82
3157 3433 4.093115 ACGACATAGATTCGGCGATAGTAG 59.907 45.833 11.76 6.46 40.92 2.57
3158 3434 4.494362 CGACATAGATTCGGCGATAGTAGG 60.494 50.000 11.76 6.72 39.35 3.18
3159 3435 3.128938 ACATAGATTCGGCGATAGTAGGC 59.871 47.826 11.76 0.00 39.35 3.93
3165 3441 3.654178 GGCGATAGTAGGCGTTTCA 57.346 52.632 0.00 0.00 39.35 2.69
3166 3442 1.206523 GGCGATAGTAGGCGTTTCAC 58.793 55.000 0.00 0.00 39.35 3.18
3167 3443 1.470285 GGCGATAGTAGGCGTTTCACA 60.470 52.381 0.00 0.00 39.35 3.58
3168 3444 1.852895 GCGATAGTAGGCGTTTCACAG 59.147 52.381 0.00 0.00 39.35 3.66
3169 3445 2.734492 GCGATAGTAGGCGTTTCACAGT 60.734 50.000 0.00 0.00 39.35 3.55
3170 3446 3.106672 CGATAGTAGGCGTTTCACAGTC 58.893 50.000 0.00 0.00 0.00 3.51
3171 3447 3.181499 CGATAGTAGGCGTTTCACAGTCT 60.181 47.826 0.00 0.00 0.00 3.24
3172 3448 4.674623 CGATAGTAGGCGTTTCACAGTCTT 60.675 45.833 0.00 0.00 0.00 3.01
3173 3449 3.470645 AGTAGGCGTTTCACAGTCTTT 57.529 42.857 0.00 0.00 0.00 2.52
3174 3450 3.805207 AGTAGGCGTTTCACAGTCTTTT 58.195 40.909 0.00 0.00 0.00 2.27
3175 3451 4.196971 AGTAGGCGTTTCACAGTCTTTTT 58.803 39.130 0.00 0.00 0.00 1.94
3176 3452 3.420839 AGGCGTTTCACAGTCTTTTTG 57.579 42.857 0.00 0.00 0.00 2.44
3177 3453 1.852280 GGCGTTTCACAGTCTTTTTGC 59.148 47.619 0.00 0.00 0.00 3.68
3178 3454 2.525055 GCGTTTCACAGTCTTTTTGCA 58.475 42.857 0.00 0.00 0.00 4.08
3179 3455 3.115554 GCGTTTCACAGTCTTTTTGCAT 58.884 40.909 0.00 0.00 0.00 3.96
3180 3456 4.286910 GCGTTTCACAGTCTTTTTGCATA 58.713 39.130 0.00 0.00 0.00 3.14
3181 3457 4.917415 GCGTTTCACAGTCTTTTTGCATAT 59.083 37.500 0.00 0.00 0.00 1.78
3182 3458 5.402270 GCGTTTCACAGTCTTTTTGCATATT 59.598 36.000 0.00 0.00 0.00 1.28
3183 3459 6.614162 GCGTTTCACAGTCTTTTTGCATATTG 60.614 38.462 0.00 0.00 0.00 1.90
3184 3460 6.636447 CGTTTCACAGTCTTTTTGCATATTGA 59.364 34.615 0.00 0.00 0.00 2.57
3185 3461 7.167302 CGTTTCACAGTCTTTTTGCATATTGAA 59.833 33.333 0.00 0.00 0.00 2.69
3186 3462 8.816144 GTTTCACAGTCTTTTTGCATATTGAAA 58.184 29.630 0.00 0.00 0.00 2.69
3187 3463 8.939201 TTCACAGTCTTTTTGCATATTGAAAA 57.061 26.923 0.00 0.00 0.00 2.29
3188 3464 8.351495 TCACAGTCTTTTTGCATATTGAAAAC 57.649 30.769 0.00 0.00 0.00 2.43
3189 3465 7.978414 TCACAGTCTTTTTGCATATTGAAAACA 59.022 29.630 0.00 0.00 0.00 2.83
3190 3466 8.767085 CACAGTCTTTTTGCATATTGAAAACAT 58.233 29.630 0.00 0.00 0.00 2.71
3191 3467 9.979578 ACAGTCTTTTTGCATATTGAAAACATA 57.020 25.926 0.00 0.00 0.00 2.29
3227 3503 2.962089 AAAAACTGTTGCTGCTGCG 58.038 47.368 11.21 0.00 43.34 5.18
3228 3504 1.147557 AAAAACTGTTGCTGCTGCGC 61.148 50.000 11.21 0.00 43.34 6.09
3229 3505 2.959220 AAAACTGTTGCTGCTGCGCC 62.959 55.000 4.18 4.34 43.34 6.53
3230 3506 4.943252 ACTGTTGCTGCTGCGCCT 62.943 61.111 4.18 0.00 43.34 5.52
3231 3507 2.743538 CTGTTGCTGCTGCGCCTA 60.744 61.111 4.18 0.00 43.34 3.93
3232 3508 3.031964 CTGTTGCTGCTGCGCCTAC 62.032 63.158 4.18 6.98 43.34 3.18
3233 3509 3.049674 GTTGCTGCTGCGCCTACA 61.050 61.111 4.18 0.00 43.34 2.74
3234 3510 2.743538 TTGCTGCTGCGCCTACAG 60.744 61.111 4.18 11.12 43.34 2.74
3235 3511 4.765449 TGCTGCTGCGCCTACAGG 62.765 66.667 19.12 0.00 43.34 4.00
3247 3523 1.726853 CCTACAGGCCGAAGAACTTG 58.273 55.000 0.00 0.00 0.00 3.16
3248 3524 1.079503 CTACAGGCCGAAGAACTTGC 58.920 55.000 0.00 0.00 0.00 4.01
3249 3525 0.685097 TACAGGCCGAAGAACTTGCT 59.315 50.000 0.00 0.00 0.00 3.91
3250 3526 0.886490 ACAGGCCGAAGAACTTGCTG 60.886 55.000 0.00 0.00 0.00 4.41
3251 3527 0.603707 CAGGCCGAAGAACTTGCTGA 60.604 55.000 0.00 0.00 0.00 4.26
3252 3528 0.108585 AGGCCGAAGAACTTGCTGAA 59.891 50.000 0.00 0.00 0.00 3.02
3253 3529 0.519077 GGCCGAAGAACTTGCTGAAG 59.481 55.000 0.00 0.00 35.07 3.02
3254 3530 0.519077 GCCGAAGAACTTGCTGAAGG 59.481 55.000 0.00 0.00 32.95 3.46
3255 3531 0.519077 CCGAAGAACTTGCTGAAGGC 59.481 55.000 0.00 0.00 42.22 4.35
3266 3542 0.864455 GCTGAAGGCATCATAGTCGC 59.136 55.000 0.00 0.00 41.35 5.19
3267 3543 1.506493 CTGAAGGCATCATAGTCGCC 58.494 55.000 0.00 0.00 46.62 5.54
3270 3546 2.029666 GGCATCATAGTCGCCGCT 59.970 61.111 0.00 0.00 35.79 5.52
3271 3547 2.313172 GGCATCATAGTCGCCGCTG 61.313 63.158 0.00 0.00 35.79 5.18
3272 3548 1.592669 GCATCATAGTCGCCGCTGT 60.593 57.895 0.00 0.00 0.00 4.40
3273 3549 1.552348 GCATCATAGTCGCCGCTGTC 61.552 60.000 0.00 0.00 0.00 3.51
3274 3550 1.008424 ATCATAGTCGCCGCTGTCG 60.008 57.895 0.00 0.00 0.00 4.35
3275 3551 1.725557 ATCATAGTCGCCGCTGTCGT 61.726 55.000 0.00 0.00 0.00 4.34
3276 3552 1.939785 CATAGTCGCCGCTGTCGTC 60.940 63.158 0.00 0.00 0.00 4.20
3277 3553 3.450559 ATAGTCGCCGCTGTCGTCG 62.451 63.158 0.00 0.00 38.53 5.12
3283 3559 4.477975 CCGCTGTCGTCGTCCTCC 62.478 72.222 0.00 0.00 0.00 4.30
3284 3560 3.432588 CGCTGTCGTCGTCCTCCT 61.433 66.667 0.00 0.00 0.00 3.69
3285 3561 2.963371 GCTGTCGTCGTCCTCCTT 59.037 61.111 0.00 0.00 0.00 3.36
3286 3562 1.153997 GCTGTCGTCGTCCTCCTTC 60.154 63.158 0.00 0.00 0.00 3.46
3287 3563 1.587933 GCTGTCGTCGTCCTCCTTCT 61.588 60.000 0.00 0.00 0.00 2.85
3288 3564 0.448593 CTGTCGTCGTCCTCCTTCTC 59.551 60.000 0.00 0.00 0.00 2.87
3289 3565 0.959372 TGTCGTCGTCCTCCTTCTCC 60.959 60.000 0.00 0.00 0.00 3.71
3290 3566 0.677414 GTCGTCGTCCTCCTTCTCCT 60.677 60.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 108 3.685139 TTTGCCGAGAAGTTCATCTCT 57.315 42.857 5.50 0.00 43.00 3.10
98 111 4.095483 ACATCATTTGCCGAGAAGTTCATC 59.905 41.667 5.50 0.00 0.00 2.92
99 112 4.012374 ACATCATTTGCCGAGAAGTTCAT 58.988 39.130 5.50 0.00 0.00 2.57
101 114 3.436704 TGACATCATTTGCCGAGAAGTTC 59.563 43.478 0.00 0.00 0.00 3.01
102 115 3.411446 TGACATCATTTGCCGAGAAGTT 58.589 40.909 0.00 0.00 0.00 2.66
103 116 3.057969 TGACATCATTTGCCGAGAAGT 57.942 42.857 0.00 0.00 0.00 3.01
104 117 3.302935 CGATGACATCATTTGCCGAGAAG 60.303 47.826 15.58 0.00 36.57 2.85
105 118 2.609002 CGATGACATCATTTGCCGAGAA 59.391 45.455 15.58 0.00 36.57 2.87
106 119 2.204237 CGATGACATCATTTGCCGAGA 58.796 47.619 15.58 0.00 36.57 4.04
107 120 1.262417 CCGATGACATCATTTGCCGAG 59.738 52.381 15.58 0.00 36.57 4.63
114 130 1.212688 TGAAGGGCCGATGACATCATT 59.787 47.619 15.58 2.10 36.57 2.57
136 152 3.121126 CGTTTTCAGTAACGTGTAGCCAG 60.121 47.826 0.00 0.00 44.28 4.85
197 213 1.284313 CAGGGCCTTCTTCTCTTCCT 58.716 55.000 1.32 0.00 0.00 3.36
211 227 1.000171 CTCAAGAAAACAAGGCAGGGC 60.000 52.381 0.00 0.00 0.00 5.19
217 233 2.290641 CGACACCCTCAAGAAAACAAGG 59.709 50.000 0.00 0.00 0.00 3.61
260 276 4.153835 GGTCTCATGCACTCTCAAGAAAAG 59.846 45.833 0.00 0.00 0.00 2.27
270 286 2.103042 GCGGTGGTCTCATGCACTC 61.103 63.158 0.00 0.00 0.00 3.51
277 293 2.420568 GGTATCGGCGGTGGTCTCA 61.421 63.158 7.21 0.00 0.00 3.27
279 295 3.524606 CGGTATCGGCGGTGGTCT 61.525 66.667 7.21 0.00 0.00 3.85
292 308 1.838112 ACTCCACCATAACGTCGGTA 58.162 50.000 4.15 0.00 32.98 4.02
349 373 3.685139 AGCCGTGCTTATATAGTGCAT 57.315 42.857 13.23 0.00 33.89 3.96
359 383 3.527533 CACCTAATGTTAGCCGTGCTTA 58.472 45.455 3.71 0.00 40.44 3.09
424 481 3.365565 GGCAACAACTAACCATAACCACG 60.366 47.826 0.00 0.00 0.00 4.94
464 568 5.404968 CAGCTACTACTTATGAGCATCTTGC 59.595 44.000 0.00 0.00 45.46 4.01
508 612 5.067936 TGCTCTAGGTTCATCTTAGCACTAC 59.932 44.000 0.00 0.00 32.97 2.73
509 613 5.201243 TGCTCTAGGTTCATCTTAGCACTA 58.799 41.667 0.00 0.00 32.97 2.74
510 614 4.026744 TGCTCTAGGTTCATCTTAGCACT 58.973 43.478 0.00 0.00 32.97 4.40
511 615 4.392921 TGCTCTAGGTTCATCTTAGCAC 57.607 45.455 0.00 0.00 32.97 4.40
512 616 4.406972 ACATGCTCTAGGTTCATCTTAGCA 59.593 41.667 0.00 0.00 38.23 3.49
513 617 4.749099 CACATGCTCTAGGTTCATCTTAGC 59.251 45.833 0.00 0.00 0.00 3.09
514 618 6.154203 TCACATGCTCTAGGTTCATCTTAG 57.846 41.667 0.00 0.00 0.00 2.18
594 795 9.612066 CTAACCATTGCCATAATAACCATTTTT 57.388 29.630 0.00 0.00 0.00 1.94
595 796 8.767436 ACTAACCATTGCCATAATAACCATTTT 58.233 29.630 0.00 0.00 0.00 1.82
596 797 8.317776 ACTAACCATTGCCATAATAACCATTT 57.682 30.769 0.00 0.00 0.00 2.32
597 798 7.255451 CGACTAACCATTGCCATAATAACCATT 60.255 37.037 0.00 0.00 0.00 3.16
598 799 6.206634 CGACTAACCATTGCCATAATAACCAT 59.793 38.462 0.00 0.00 0.00 3.55
599 800 5.529430 CGACTAACCATTGCCATAATAACCA 59.471 40.000 0.00 0.00 0.00 3.67
600 801 5.529800 ACGACTAACCATTGCCATAATAACC 59.470 40.000 0.00 0.00 0.00 2.85
601 802 6.613755 ACGACTAACCATTGCCATAATAAC 57.386 37.500 0.00 0.00 0.00 1.89
602 803 6.600032 ACAACGACTAACCATTGCCATAATAA 59.400 34.615 0.00 0.00 0.00 1.40
603 804 6.116806 ACAACGACTAACCATTGCCATAATA 58.883 36.000 0.00 0.00 0.00 0.98
604 805 4.947388 ACAACGACTAACCATTGCCATAAT 59.053 37.500 0.00 0.00 0.00 1.28
696 901 6.311935 GCCGAATATAACTACCAATAATGCGA 59.688 38.462 0.00 0.00 0.00 5.10
755 974 1.504359 TCGGTTTGGACGTTTGCTAG 58.496 50.000 0.00 0.00 0.00 3.42
811 1030 0.107017 ATGGGTGTGCTCACTATGCC 60.107 55.000 17.68 11.08 43.41 4.40
827 1046 0.533755 GCGGTTCCCAGATGAGATGG 60.534 60.000 0.00 0.00 37.58 3.51
828 1047 0.533755 GGCGGTTCCCAGATGAGATG 60.534 60.000 0.00 0.00 0.00 2.90
829 1048 1.832912 GGCGGTTCCCAGATGAGAT 59.167 57.895 0.00 0.00 0.00 2.75
830 1049 2.721167 CGGCGGTTCCCAGATGAGA 61.721 63.158 0.00 0.00 0.00 3.27
831 1050 2.202932 CGGCGGTTCCCAGATGAG 60.203 66.667 0.00 0.00 0.00 2.90
832 1051 4.467084 GCGGCGGTTCCCAGATGA 62.467 66.667 9.78 0.00 0.00 2.92
833 1052 4.473520 AGCGGCGGTTCCCAGATG 62.474 66.667 5.44 0.00 0.00 2.90
834 1053 4.162690 GAGCGGCGGTTCCCAGAT 62.163 66.667 14.71 0.00 0.00 2.90
858 1077 3.464494 GCCATTTGAGCCTGGGCC 61.464 66.667 8.11 0.00 43.17 5.80
859 1078 3.830192 CGCCATTTGAGCCTGGGC 61.830 66.667 3.00 3.00 41.20 5.36
877 1096 3.955551 GGTTCTTGTAGGAGTAGGAGAGG 59.044 52.174 0.00 0.00 0.00 3.69
879 1098 4.949966 AGGTTCTTGTAGGAGTAGGAGA 57.050 45.455 0.00 0.00 0.00 3.71
887 1106 3.050089 TGTTGGGAAGGTTCTTGTAGGA 58.950 45.455 0.00 0.00 0.00 2.94
900 1119 2.669670 CGCATGCGTATTTTGTTGGGAA 60.670 45.455 31.33 0.00 34.35 3.97
906 1125 0.242286 TTGGCGCATGCGTATTTTGT 59.758 45.000 37.54 0.00 44.10 2.83
917 1136 3.064324 GAGGTTGCCTTGGCGCAT 61.064 61.111 10.83 0.15 38.87 4.73
954 1173 4.899239 GATGGCTCGGCGGTGGAG 62.899 72.222 7.21 0.00 34.62 3.86
967 1186 4.275443 GGAGCTATGAAAGAGCAAAGATGG 59.725 45.833 0.00 0.00 42.69 3.51
968 1187 4.025061 CGGAGCTATGAAAGAGCAAAGATG 60.025 45.833 0.00 0.00 42.69 2.90
970 1189 3.525537 CGGAGCTATGAAAGAGCAAAGA 58.474 45.455 0.00 0.00 42.69 2.52
1234 1456 1.378250 GGAAGAGGTCCGTCTCCGA 60.378 63.158 0.00 0.00 36.40 4.55
1494 1716 1.820581 GGATTCCGGGTCGTCATGA 59.179 57.895 0.00 0.00 0.00 3.07
1643 1869 6.347402 GCAACGCTCTGTTTTGTTTCTATCTA 60.347 38.462 0.00 0.00 39.29 1.98
1700 1926 2.034066 ACCACCGGCCAATCAGTG 59.966 61.111 0.00 1.50 0.00 3.66
1701 1927 2.351276 GACCACCGGCCAATCAGT 59.649 61.111 0.00 0.00 0.00 3.41
1711 1937 1.440938 TTCGCAACAAAGGACCACCG 61.441 55.000 0.00 0.00 41.83 4.94
1752 1984 0.596083 CGATGATGAGCGAGTGGACC 60.596 60.000 0.00 0.00 30.60 4.46
1910 2147 2.202479 TCAGCAGATCGACACGCG 60.202 61.111 3.53 3.53 42.69 6.01
1911 2148 1.136872 GTCTCAGCAGATCGACACGC 61.137 60.000 0.00 0.00 0.00 5.34
1918 2157 1.596727 GCATTTCGGTCTCAGCAGATC 59.403 52.381 0.00 0.00 0.00 2.75
1922 2161 0.674581 CAGGCATTTCGGTCTCAGCA 60.675 55.000 0.00 0.00 0.00 4.41
1969 2208 0.386113 TGGCCTGCCGTAAAACAAAC 59.614 50.000 3.32 0.00 39.42 2.93
1970 2209 1.067821 CTTGGCCTGCCGTAAAACAAA 59.932 47.619 3.32 0.00 39.42 2.83
1977 2220 2.349755 GGAACTTGGCCTGCCGTA 59.650 61.111 3.32 0.00 39.42 4.02
2297 2540 3.662078 TCAGAAGGTGATCATCTCCCAT 58.338 45.455 9.43 0.00 30.62 4.00
2363 2615 2.884639 TGAGCTCCAGCCTAACAAAAAC 59.115 45.455 12.15 0.00 43.38 2.43
2368 2620 1.699634 ACTTTGAGCTCCAGCCTAACA 59.300 47.619 12.15 0.00 43.38 2.41
2400 2652 3.881713 GCCTTGTATTCCATGGTCCCTTT 60.882 47.826 12.58 0.00 39.89 3.11
2450 2702 2.507992 CGGCTCCTCTGTTCAGCG 60.508 66.667 0.00 0.00 33.66 5.18
2462 2714 2.485795 ATGAGACTCCGCTCGGCTC 61.486 63.158 2.96 5.57 37.73 4.70
2463 2715 2.441164 ATGAGACTCCGCTCGGCT 60.441 61.111 2.96 0.00 37.73 5.52
2464 2716 2.279120 CATGAGACTCCGCTCGGC 60.279 66.667 2.96 0.00 37.73 5.54
2465 2717 2.415010 CCATGAGACTCCGCTCGG 59.585 66.667 1.14 1.14 37.73 4.63
2466 2718 2.279120 GCCATGAGACTCCGCTCG 60.279 66.667 0.00 0.00 37.73 5.03
2481 2733 1.721133 CGAAGCAACAACGAACGCC 60.721 57.895 0.00 0.00 0.00 5.68
2596 2868 6.774673 TCACCTATCTCCTGACAGTATCTAG 58.225 44.000 0.93 0.00 0.00 2.43
2602 2874 6.436027 TCTATTTCACCTATCTCCTGACAGT 58.564 40.000 0.93 0.00 0.00 3.55
2605 2877 6.969993 ACTCTATTTCACCTATCTCCTGAC 57.030 41.667 0.00 0.00 0.00 3.51
2610 2882 7.519032 AGCAGTACTCTATTTCACCTATCTC 57.481 40.000 0.00 0.00 0.00 2.75
2611 2883 7.014808 GGAAGCAGTACTCTATTTCACCTATCT 59.985 40.741 0.00 0.00 0.00 1.98
2612 2884 7.149307 GGAAGCAGTACTCTATTTCACCTATC 58.851 42.308 0.00 0.00 0.00 2.08
2620 2892 2.158943 GCGGGGAAGCAGTACTCTATTT 60.159 50.000 0.00 0.00 37.05 1.40
2624 2896 1.609501 TGCGGGGAAGCAGTACTCT 60.610 57.895 0.00 0.00 42.92 3.24
2646 2922 6.317140 CGCCGATGGGTATAGTATTACTCTTA 59.683 42.308 0.00 0.00 34.97 2.10
2647 2923 5.125097 CGCCGATGGGTATAGTATTACTCTT 59.875 44.000 0.00 0.00 34.97 2.85
2648 2924 4.639310 CGCCGATGGGTATAGTATTACTCT 59.361 45.833 0.00 0.00 34.97 3.24
2649 2925 4.397417 ACGCCGATGGGTATAGTATTACTC 59.603 45.833 0.00 0.00 35.62 2.59
2650 2926 4.338879 ACGCCGATGGGTATAGTATTACT 58.661 43.478 1.30 1.30 35.62 2.24
2651 2927 4.708726 ACGCCGATGGGTATAGTATTAC 57.291 45.455 0.00 0.00 35.62 1.89
2652 2928 4.082081 CCAACGCCGATGGGTATAGTATTA 60.082 45.833 5.36 0.00 36.50 0.98
2653 2929 3.306502 CCAACGCCGATGGGTATAGTATT 60.307 47.826 5.36 0.00 36.50 1.89
2654 2930 2.232941 CCAACGCCGATGGGTATAGTAT 59.767 50.000 5.36 0.00 36.50 2.12
2655 2931 1.614903 CCAACGCCGATGGGTATAGTA 59.385 52.381 5.36 0.00 36.50 1.82
2656 2932 0.391597 CCAACGCCGATGGGTATAGT 59.608 55.000 5.36 0.00 36.50 2.12
2657 2933 3.210857 CCAACGCCGATGGGTATAG 57.789 57.895 5.36 0.00 36.50 1.31
2663 2939 4.856801 CTCCCCCAACGCCGATGG 62.857 72.222 6.40 6.40 37.71 3.51
2667 2943 4.090588 TAAGCTCCCCCAACGCCG 62.091 66.667 0.00 0.00 0.00 6.46
2668 2944 2.124695 CTAAGCTCCCCCAACGCC 60.125 66.667 0.00 0.00 0.00 5.68
2669 2945 2.987125 TCTAAGCTCCCCCAACGC 59.013 61.111 0.00 0.00 0.00 4.84
3027 3303 0.457166 GCCAAAAATACCGCCGGTTC 60.457 55.000 16.82 0.00 37.09 3.62
3028 3304 1.587568 GCCAAAAATACCGCCGGTT 59.412 52.632 16.82 0.00 37.09 4.44
3029 3305 2.692766 CGCCAAAAATACCGCCGGT 61.693 57.895 15.63 15.63 40.16 5.28
3030 3306 2.101380 CGCCAAAAATACCGCCGG 59.899 61.111 0.00 0.00 0.00 6.13
3031 3307 1.513160 CACGCCAAAAATACCGCCG 60.513 57.895 0.00 0.00 0.00 6.46
3032 3308 1.153920 CCACGCCAAAAATACCGCC 60.154 57.895 0.00 0.00 0.00 6.13
3033 3309 1.153920 CCCACGCCAAAAATACCGC 60.154 57.895 0.00 0.00 0.00 5.68
3034 3310 1.509004 CCCCACGCCAAAAATACCG 59.491 57.895 0.00 0.00 0.00 4.02
3035 3311 1.894512 CCCCCACGCCAAAAATACC 59.105 57.895 0.00 0.00 0.00 2.73
3036 3312 1.216977 GCCCCCACGCCAAAAATAC 59.783 57.895 0.00 0.00 0.00 1.89
3037 3313 2.344203 CGCCCCCACGCCAAAAATA 61.344 57.895 0.00 0.00 0.00 1.40
3038 3314 3.690280 CGCCCCCACGCCAAAAAT 61.690 61.111 0.00 0.00 0.00 1.82
3039 3315 4.896829 TCGCCCCCACGCCAAAAA 62.897 61.111 0.00 0.00 0.00 1.94
3040 3316 4.669809 ATCGCCCCCACGCCAAAA 62.670 61.111 0.00 0.00 0.00 2.44
3047 3323 4.851179 GAACCCGATCGCCCCCAC 62.851 72.222 10.32 0.00 0.00 4.61
3050 3326 2.841044 TAGGAACCCGATCGCCCC 60.841 66.667 10.32 7.36 0.00 5.80
3051 3327 2.735237 CTAGGAACCCGATCGCCC 59.265 66.667 10.32 7.72 0.00 6.13
3052 3328 2.029221 GCTAGGAACCCGATCGCC 59.971 66.667 10.32 5.40 0.00 5.54
3053 3329 2.029221 GGCTAGGAACCCGATCGC 59.971 66.667 10.32 0.00 0.00 4.58
3059 3335 4.832608 CACGGCGGCTAGGAACCC 62.833 72.222 13.24 0.00 0.00 4.11
3082 3358 3.942439 GGGCATCTAGGGGGCGAC 61.942 72.222 0.00 0.00 0.00 5.19
3083 3359 3.714078 AAGGGCATCTAGGGGGCGA 62.714 63.158 0.00 0.00 0.00 5.54
3084 3360 2.284515 AAAAGGGCATCTAGGGGGCG 62.285 60.000 0.00 0.00 0.00 6.13
3085 3361 0.756815 CAAAAGGGCATCTAGGGGGC 60.757 60.000 0.00 0.00 0.00 5.80
3086 3362 0.926293 TCAAAAGGGCATCTAGGGGG 59.074 55.000 0.00 0.00 0.00 5.40
3087 3363 2.826674 TTCAAAAGGGCATCTAGGGG 57.173 50.000 0.00 0.00 0.00 4.79
3088 3364 3.831911 TGTTTTCAAAAGGGCATCTAGGG 59.168 43.478 0.00 0.00 0.00 3.53
3089 3365 5.665916 ATGTTTTCAAAAGGGCATCTAGG 57.334 39.130 0.00 0.00 0.00 3.02
3090 3366 7.396540 AGTATGTTTTCAAAAGGGCATCTAG 57.603 36.000 0.00 0.00 0.00 2.43
3091 3367 7.309744 CCAAGTATGTTTTCAAAAGGGCATCTA 60.310 37.037 0.00 0.00 0.00 1.98
3092 3368 6.458210 CAAGTATGTTTTCAAAAGGGCATCT 58.542 36.000 0.00 0.00 0.00 2.90
3093 3369 5.639082 CCAAGTATGTTTTCAAAAGGGCATC 59.361 40.000 0.00 0.00 0.00 3.91
3094 3370 5.550290 CCAAGTATGTTTTCAAAAGGGCAT 58.450 37.500 0.00 0.00 0.00 4.40
3095 3371 4.742138 GCCAAGTATGTTTTCAAAAGGGCA 60.742 41.667 0.00 0.00 35.10 5.36
3096 3372 3.745975 GCCAAGTATGTTTTCAAAAGGGC 59.254 43.478 0.00 0.00 0.00 5.19
3097 3373 4.202305 TGGCCAAGTATGTTTTCAAAAGGG 60.202 41.667 0.61 0.00 0.00 3.95
3098 3374 4.954875 TGGCCAAGTATGTTTTCAAAAGG 58.045 39.130 0.61 0.00 0.00 3.11
3099 3375 5.841810 TCTGGCCAAGTATGTTTTCAAAAG 58.158 37.500 7.01 0.00 0.00 2.27
3100 3376 5.860941 TCTGGCCAAGTATGTTTTCAAAA 57.139 34.783 7.01 0.00 0.00 2.44
3101 3377 5.860941 TTCTGGCCAAGTATGTTTTCAAA 57.139 34.783 7.01 0.00 0.00 2.69
3102 3378 6.418057 AATTCTGGCCAAGTATGTTTTCAA 57.582 33.333 7.01 0.00 0.00 2.69
3103 3379 5.335583 CGAATTCTGGCCAAGTATGTTTTCA 60.336 40.000 7.01 0.00 0.00 2.69
3104 3380 5.095490 CGAATTCTGGCCAAGTATGTTTTC 58.905 41.667 7.01 2.24 0.00 2.29
3105 3381 4.522789 ACGAATTCTGGCCAAGTATGTTTT 59.477 37.500 7.01 0.00 0.00 2.43
3106 3382 4.079253 ACGAATTCTGGCCAAGTATGTTT 58.921 39.130 7.01 0.00 0.00 2.83
3107 3383 3.686016 ACGAATTCTGGCCAAGTATGTT 58.314 40.909 7.01 0.00 0.00 2.71
3108 3384 3.270877 GACGAATTCTGGCCAAGTATGT 58.729 45.455 7.01 0.77 0.00 2.29
3109 3385 3.270027 TGACGAATTCTGGCCAAGTATG 58.730 45.455 7.01 0.00 0.00 2.39
3110 3386 3.627395 TGACGAATTCTGGCCAAGTAT 57.373 42.857 7.01 0.00 0.00 2.12
3111 3387 3.410631 TTGACGAATTCTGGCCAAGTA 57.589 42.857 7.01 0.00 0.00 2.24
3112 3388 2.270352 TTGACGAATTCTGGCCAAGT 57.730 45.000 7.01 0.00 0.00 3.16
3113 3389 2.293122 TGTTTGACGAATTCTGGCCAAG 59.707 45.455 7.01 0.66 0.00 3.61
3114 3390 2.034053 GTGTTTGACGAATTCTGGCCAA 59.966 45.455 7.01 0.00 0.00 4.52
3115 3391 1.606668 GTGTTTGACGAATTCTGGCCA 59.393 47.619 4.71 4.71 0.00 5.36
3116 3392 2.331809 GTGTTTGACGAATTCTGGCC 57.668 50.000 3.52 0.00 0.00 5.36
3127 3403 3.241995 GCCGAATCTATGTCGTGTTTGAC 60.242 47.826 0.00 0.00 36.77 3.18
3128 3404 2.927477 GCCGAATCTATGTCGTGTTTGA 59.073 45.455 0.00 0.00 36.77 2.69
3129 3405 2.285026 CGCCGAATCTATGTCGTGTTTG 60.285 50.000 0.00 0.00 36.77 2.93
3130 3406 1.924524 CGCCGAATCTATGTCGTGTTT 59.075 47.619 0.00 0.00 36.77 2.83
3131 3407 1.133598 TCGCCGAATCTATGTCGTGTT 59.866 47.619 0.00 0.00 36.77 3.32
3132 3408 0.736636 TCGCCGAATCTATGTCGTGT 59.263 50.000 0.00 0.00 36.77 4.49
3133 3409 2.051879 ATCGCCGAATCTATGTCGTG 57.948 50.000 0.00 0.00 36.77 4.35
3134 3410 2.812591 ACTATCGCCGAATCTATGTCGT 59.187 45.455 0.00 0.00 36.77 4.34
3135 3411 3.473093 ACTATCGCCGAATCTATGTCG 57.527 47.619 0.00 0.00 38.24 4.35
3136 3412 4.731193 GCCTACTATCGCCGAATCTATGTC 60.731 50.000 0.00 0.00 0.00 3.06
3137 3413 3.128938 GCCTACTATCGCCGAATCTATGT 59.871 47.826 0.00 0.00 0.00 2.29
3138 3414 3.696898 GCCTACTATCGCCGAATCTATG 58.303 50.000 0.00 0.00 0.00 2.23
3139 3415 2.355132 CGCCTACTATCGCCGAATCTAT 59.645 50.000 0.00 0.00 0.00 1.98
3140 3416 1.736126 CGCCTACTATCGCCGAATCTA 59.264 52.381 0.00 0.00 0.00 1.98
3141 3417 0.522180 CGCCTACTATCGCCGAATCT 59.478 55.000 0.00 0.00 0.00 2.40
3142 3418 0.240411 ACGCCTACTATCGCCGAATC 59.760 55.000 0.00 0.00 0.00 2.52
3143 3419 0.672342 AACGCCTACTATCGCCGAAT 59.328 50.000 0.00 0.00 0.00 3.34
3144 3420 0.457035 AAACGCCTACTATCGCCGAA 59.543 50.000 0.00 0.00 0.00 4.30
3145 3421 0.029834 GAAACGCCTACTATCGCCGA 59.970 55.000 0.00 0.00 0.00 5.54
3146 3422 0.248743 TGAAACGCCTACTATCGCCG 60.249 55.000 0.00 0.00 0.00 6.46
3147 3423 1.206523 GTGAAACGCCTACTATCGCC 58.793 55.000 0.00 0.00 0.00 5.54
3148 3424 1.852895 CTGTGAAACGCCTACTATCGC 59.147 52.381 0.00 0.00 42.39 4.58
3149 3425 3.106672 GACTGTGAAACGCCTACTATCG 58.893 50.000 0.00 0.00 42.39 2.92
3150 3426 4.373348 AGACTGTGAAACGCCTACTATC 57.627 45.455 0.00 0.00 42.39 2.08
3151 3427 4.803098 AAGACTGTGAAACGCCTACTAT 57.197 40.909 0.00 0.00 42.39 2.12
3152 3428 4.595762 AAAGACTGTGAAACGCCTACTA 57.404 40.909 0.00 0.00 42.39 1.82
3153 3429 3.470645 AAAGACTGTGAAACGCCTACT 57.529 42.857 0.00 0.00 42.39 2.57
3154 3430 4.279659 CAAAAAGACTGTGAAACGCCTAC 58.720 43.478 0.00 0.00 42.39 3.18
3155 3431 3.242936 GCAAAAAGACTGTGAAACGCCTA 60.243 43.478 0.00 0.00 42.39 3.93
3156 3432 2.479560 GCAAAAAGACTGTGAAACGCCT 60.480 45.455 0.00 0.00 42.39 5.52
3157 3433 1.852280 GCAAAAAGACTGTGAAACGCC 59.148 47.619 0.00 0.00 42.39 5.68
3158 3434 2.525055 TGCAAAAAGACTGTGAAACGC 58.475 42.857 0.00 0.00 42.39 4.84
3159 3435 6.636447 TCAATATGCAAAAAGACTGTGAAACG 59.364 34.615 0.00 0.00 42.39 3.60
3160 3436 7.928908 TCAATATGCAAAAAGACTGTGAAAC 57.071 32.000 0.00 0.00 37.35 2.78
3161 3437 8.939201 TTTCAATATGCAAAAAGACTGTGAAA 57.061 26.923 0.00 0.00 0.00 2.69
3162 3438 8.816144 GTTTTCAATATGCAAAAAGACTGTGAA 58.184 29.630 0.00 0.00 0.00 3.18
3163 3439 7.978414 TGTTTTCAATATGCAAAAAGACTGTGA 59.022 29.630 0.00 0.00 0.00 3.58
3164 3440 8.129161 TGTTTTCAATATGCAAAAAGACTGTG 57.871 30.769 0.00 0.00 0.00 3.66
3165 3441 8.891671 ATGTTTTCAATATGCAAAAAGACTGT 57.108 26.923 0.00 0.00 0.00 3.55
3209 3485 2.962089 CGCAGCAGCAACAGTTTTT 58.038 47.368 0.82 0.00 42.27 1.94
3210 3486 4.715983 CGCAGCAGCAACAGTTTT 57.284 50.000 0.82 0.00 42.27 2.43
3228 3504 1.726853 CAAGTTCTTCGGCCTGTAGG 58.273 55.000 0.00 0.00 38.53 3.18
3229 3505 1.079503 GCAAGTTCTTCGGCCTGTAG 58.920 55.000 0.00 0.00 0.00 2.74
3230 3506 0.685097 AGCAAGTTCTTCGGCCTGTA 59.315 50.000 0.00 0.00 0.00 2.74
3231 3507 0.886490 CAGCAAGTTCTTCGGCCTGT 60.886 55.000 0.00 0.00 0.00 4.00
3232 3508 0.603707 TCAGCAAGTTCTTCGGCCTG 60.604 55.000 0.00 0.00 0.00 4.85
3233 3509 0.108585 TTCAGCAAGTTCTTCGGCCT 59.891 50.000 0.00 0.00 0.00 5.19
3234 3510 0.519077 CTTCAGCAAGTTCTTCGGCC 59.481 55.000 0.00 0.00 0.00 6.13
3235 3511 0.519077 CCTTCAGCAAGTTCTTCGGC 59.481 55.000 0.00 0.00 0.00 5.54
3236 3512 0.519077 GCCTTCAGCAAGTTCTTCGG 59.481 55.000 0.00 0.00 42.97 4.30
3247 3523 0.864455 GCGACTATGATGCCTTCAGC 59.136 55.000 0.00 0.00 37.89 4.26
3248 3524 1.506493 GGCGACTATGATGCCTTCAG 58.494 55.000 0.00 0.00 45.40 3.02
3249 3525 0.249447 CGGCGACTATGATGCCTTCA 60.249 55.000 0.00 0.00 46.67 3.02
3250 3526 1.560860 GCGGCGACTATGATGCCTTC 61.561 60.000 12.98 0.00 46.67 3.46
3251 3527 1.595382 GCGGCGACTATGATGCCTT 60.595 57.895 12.98 0.00 46.67 4.35
3252 3528 2.029666 GCGGCGACTATGATGCCT 59.970 61.111 12.98 0.00 46.67 4.75
3253 3529 2.029666 AGCGGCGACTATGATGCC 59.970 61.111 12.98 0.00 45.39 4.40
3254 3530 1.552348 GACAGCGGCGACTATGATGC 61.552 60.000 12.98 0.00 0.00 3.91
3255 3531 1.271446 CGACAGCGGCGACTATGATG 61.271 60.000 12.98 0.00 0.00 3.07
3256 3532 1.008424 CGACAGCGGCGACTATGAT 60.008 57.895 12.98 0.00 0.00 2.45
3257 3533 2.319011 GACGACAGCGGCGACTATGA 62.319 60.000 12.98 0.00 43.17 2.15
3258 3534 1.939785 GACGACAGCGGCGACTATG 60.940 63.158 12.98 5.63 43.17 2.23
3259 3535 2.408022 GACGACAGCGGCGACTAT 59.592 61.111 12.98 0.00 43.17 2.12
3266 3542 4.477975 GGAGGACGACGACAGCGG 62.478 72.222 0.00 0.00 43.17 5.52
3267 3543 2.852431 GAAGGAGGACGACGACAGCG 62.852 65.000 0.00 0.00 44.79 5.18
3268 3544 1.153997 GAAGGAGGACGACGACAGC 60.154 63.158 0.00 0.00 0.00 4.40
3269 3545 0.448593 GAGAAGGAGGACGACGACAG 59.551 60.000 0.00 0.00 0.00 3.51
3270 3546 0.959372 GGAGAAGGAGGACGACGACA 60.959 60.000 0.00 0.00 0.00 4.35
3271 3547 0.677414 AGGAGAAGGAGGACGACGAC 60.677 60.000 0.00 0.00 0.00 4.34
3272 3548 1.684035 AGGAGAAGGAGGACGACGA 59.316 57.895 0.00 0.00 0.00 4.20
3273 3549 4.322689 AGGAGAAGGAGGACGACG 57.677 61.111 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.