Multiple sequence alignment - TraesCS3D01G407900

Loading Multiple Alignment...

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 TraesCS3D01G407900 chr3D 100.000 5569 0 0 1 5569 521315002 521320570 0.000000e+00 10285.0
1 TraesCS3D01G407900 chr3A 94.009 2704 90 32 260 2934 656718490 656721150 0.000000e+00 4030.0
2 TraesCS3D01G407900 chr3A 95.109 1145 46 6 3915 5050 656722043 656723186 0.000000e+00 1796.0
3 TraesCS3D01G407900 chr3A 93.590 858 28 8 3078 3930 656721190 656722025 0.000000e+00 1254.0
4 TraesCS3D01G407900 chr3A 92.529 174 6 2 5142 5311 656723302 656723472 5.570000e-60 243.0
5 TraesCS3D01G407900 chr3A 86.854 213 20 4 5362 5566 656723961 656724173 1.210000e-56 231.0
6 TraesCS3D01G407900 chr3A 96.078 51 2 0 5307 5357 656723496 656723546 3.580000e-12 84.2
7 TraesCS3D01G407900 chr3B 91.487 2972 114 51 29 2957 687062087 687064962 0.000000e+00 3958.0
8 TraesCS3D01G407900 chr3B 95.787 1994 55 14 3078 5057 687064981 687066959 0.000000e+00 3190.0
9 TraesCS3D01G407900 chr3B 88.152 211 22 2 5307 5515 687067423 687067632 1.200000e-61 248.0
10 TraesCS3D01G407900 chr3B 97.391 115 3 0 2962 3076 555505272 555505158 4.400000e-46 196.0
11 TraesCS3D01G407900 chr3B 96.939 98 3 0 5140 5237 687066985 687067082 1.240000e-36 165.0
12 TraesCS3D01G407900 chr3B 87.719 57 3 1 5259 5311 687067319 687067375 4.660000e-06 63.9
13 TraesCS3D01G407900 chr5B 87.662 308 19 7 1123 1418 308798995 308799295 1.920000e-89 340.0
14 TraesCS3D01G407900 chr5B 94.581 203 11 0 1520 1722 308799329 308799531 1.160000e-81 315.0
15 TraesCS3D01G407900 chr5B 97.222 36 1 0 1467 1502 308799296 308799331 1.680000e-05 62.1
16 TraesCS3D01G407900 chr4A 97.458 118 3 0 2959 3076 655254128 655254245 9.460000e-48 202.0
17 TraesCS3D01G407900 chrUn 95.238 126 6 0 2951 3076 45254531 45254656 3.400000e-47 200.0
18 TraesCS3D01G407900 chr7D 96.610 118 4 0 2959 3076 94439081 94439198 4.400000e-46 196.0
19 TraesCS3D01G407900 chr6D 96.610 118 4 0 2959 3076 69785491 69785374 4.400000e-46 196.0
20 TraesCS3D01G407900 chr5D 96.610 118 4 0 2959 3076 104624788 104624905 4.400000e-46 196.0
21 TraesCS3D01G407900 chr5D 96.610 118 4 0 2959 3076 254008448 254008331 4.400000e-46 196.0
22 TraesCS3D01G407900 chr5D 97.059 34 1 0 1388 1421 490497753 490497786 2.170000e-04 58.4
23 TraesCS3D01G407900 chr4B 96.610 118 4 0 2959 3076 63754001 63753884 4.400000e-46 196.0
24 TraesCS3D01G407900 chr1D 96.610 118 4 0 2959 3076 396286963 396286846 4.400000e-46 196.0
25 TraesCS3D01G407900 chr6B 94.118 34 2 0 5524 5557 28039156 28039123 1.000000e-02 52.8
26 TraesCS3D01G407900 chr2A 94.118 34 2 0 5524 5557 244299858 244299825 1.000000e-02 52.8


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 TraesCS3D01G407900 chr3D 521315002 521320570 5568 False 10285.000000 10285 100.000000 1 5569 1 chr3D.!!$F1 5568
1 TraesCS3D01G407900 chr3A 656718490 656724173 5683 False 1273.033333 4030 93.028167 260 5566 6 chr3A.!!$F1 5306
2 TraesCS3D01G407900 chr3B 687062087 687067632 5545 False 1524.980000 3958 92.016800 29 5515 5 chr3B.!!$F1 5486
3 TraesCS3D01G407900 chr5B 308798995 308799531 536 False 239.033333 340 93.155000 1123 1722 3 chr5B.!!$F1 599

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
297 301 0.035152 TCTGTTTCGCCTGATGCCAT 60.035 50.0 0.00 0.0 36.24 4.40 F
312 316 0.530288 GCCATGCGGTACCACAAAAT 59.470 50.0 13.54 0.0 33.28 1.82 F
2015 2072 0.106708 GCTTGCCCATCGATCCAGTA 59.893 55.0 0.00 0.0 0.00 2.74 F
2451 2514 1.230324 GCTTCGAGTTCAAACAGCCT 58.770 50.0 0.00 0.0 0.00 4.58 F
2971 3039 0.395312 TGTTCAACTCCCTCCGTTCC 59.605 55.0 0.00 0.0 0.00 3.62 F
3752 3827 0.593128 CAAGAGGAACTTTGGTGCGG 59.407 55.0 0.00 0.0 41.55 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2053 0.106708 TACTGGATCGATGGGCAAGC 59.893 55.000 0.54 0.0 0.00 4.01 R
2237 2300 1.228429 TTGCCCTTCCGTTCTTGGG 60.228 57.895 0.00 0.0 42.41 4.12 R
2953 3021 0.685660 AGGAACGGAGGGAGTTGAAC 59.314 55.000 0.00 0.0 31.14 3.18 R
3656 3728 1.008538 GGCAGCCAAACAAGACACG 60.009 57.895 6.55 0.0 0.00 4.49 R
4114 4226 1.521457 ATGCAGATGCGGTACACGG 60.521 57.895 0.00 0.0 45.83 4.94 R
5542 6411 1.127343 GGGTGGCTAGCTCTCATCTT 58.873 55.000 15.72 0.0 0.00 2.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.432186 GCTGCCAAAGTCCGTTGT 58.568 55.556 0.00 0.00 0.00 3.32
19 20 1.569493 CTGCCAAAGTCCGTTGTCG 59.431 57.895 0.00 0.00 0.00 4.35
20 21 1.153329 TGCCAAAGTCCGTTGTCGT 60.153 52.632 0.00 0.00 35.01 4.34
23 24 1.425412 CCAAAGTCCGTTGTCGTAGG 58.575 55.000 0.00 0.00 35.01 3.18
25 26 0.390124 AAAGTCCGTTGTCGTAGGCA 59.610 50.000 0.00 0.00 45.30 4.75
33 34 2.678786 TGTCGTAGGCATTCCCAGT 58.321 52.632 0.00 0.00 36.97 4.00
34 35 0.249120 TGTCGTAGGCATTCCCAGTG 59.751 55.000 0.00 0.00 36.97 3.66
35 36 1.090052 GTCGTAGGCATTCCCAGTGC 61.090 60.000 0.00 0.00 41.78 4.40
40 41 3.512516 GCATTCCCAGTGCCGAGC 61.513 66.667 0.00 0.00 36.61 5.03
41 42 2.825836 CATTCCCAGTGCCGAGCC 60.826 66.667 0.00 0.00 0.00 4.70
42 43 3.329889 ATTCCCAGTGCCGAGCCA 61.330 61.111 0.00 0.00 0.00 4.75
43 44 3.628646 ATTCCCAGTGCCGAGCCAC 62.629 63.158 0.00 0.00 35.98 5.01
106 107 2.436646 CCACGCGCCTTCATTCCT 60.437 61.111 5.73 0.00 0.00 3.36
110 111 2.464459 CGCGCCTTCATTCCTGTCC 61.464 63.158 0.00 0.00 0.00 4.02
112 113 2.464459 CGCCTTCATTCCTGTCCGC 61.464 63.158 0.00 0.00 0.00 5.54
133 134 2.666098 GCCTCCGTGTACCCATGGT 61.666 63.158 11.73 1.30 46.27 3.55
141 142 0.321210 TGTACCCATGGTGAGTTGCG 60.321 55.000 11.73 0.00 36.19 4.85
143 144 0.398696 TACCCATGGTGAGTTGCGTT 59.601 50.000 11.73 0.00 36.19 4.84
147 148 1.334960 CCATGGTGAGTTGCGTTGTTC 60.335 52.381 2.57 0.00 0.00 3.18
193 195 8.519799 TGTAATCTAGCTTTTGATTTTAGGGG 57.480 34.615 12.34 0.00 35.01 4.79
207 211 5.476091 TTTTAGGGGGTTGTGCTATTTTG 57.524 39.130 0.00 0.00 0.00 2.44
210 214 3.697166 AGGGGGTTGTGCTATTTTGTAG 58.303 45.455 0.00 0.00 0.00 2.74
221 225 3.621715 GCTATTTTGTAGGGACCTTGTCG 59.378 47.826 0.00 0.00 32.65 4.35
249 253 4.353777 TCAACTAGTGAATAGTGGGCTCT 58.646 43.478 0.00 0.00 44.26 4.09
252 256 2.254152 AGTGAATAGTGGGCTCTCCA 57.746 50.000 0.00 0.00 44.79 3.86
261 265 1.117749 TGGGCTCTCCATCTCATCGG 61.118 60.000 0.00 0.00 41.46 4.18
270 274 6.091986 GCTCTCCATCTCATCGGAATAATTTC 59.908 42.308 0.00 0.00 0.00 2.17
271 275 7.066307 TCTCCATCTCATCGGAATAATTTCA 57.934 36.000 0.00 0.00 33.23 2.69
274 278 6.202762 TCCATCTCATCGGAATAATTTCAACG 59.797 38.462 0.00 0.00 33.23 4.10
297 301 0.035152 TCTGTTTCGCCTGATGCCAT 60.035 50.000 0.00 0.00 36.24 4.40
311 315 0.823769 TGCCATGCGGTACCACAAAA 60.824 50.000 13.54 0.00 33.28 2.44
312 316 0.530288 GCCATGCGGTACCACAAAAT 59.470 50.000 13.54 0.00 33.28 1.82
313 317 1.067213 GCCATGCGGTACCACAAAATT 60.067 47.619 13.54 0.00 33.28 1.82
314 318 2.874849 CCATGCGGTACCACAAAATTC 58.125 47.619 13.54 0.00 0.00 2.17
315 319 2.230025 CCATGCGGTACCACAAAATTCA 59.770 45.455 13.54 0.00 0.00 2.57
319 323 4.950050 TGCGGTACCACAAAATTCATTTT 58.050 34.783 13.54 0.00 40.37 1.82
320 324 6.085555 TGCGGTACCACAAAATTCATTTTA 57.914 33.333 13.54 0.00 37.86 1.52
324 328 6.459923 GGTACCACAAAATTCATTTTAGGCA 58.540 36.000 7.15 2.06 37.86 4.75
343 347 2.914838 GCAAGCCGTATACTGTTTTTGC 59.085 45.455 13.13 13.13 33.83 3.68
345 349 4.541779 CAAGCCGTATACTGTTTTTGCAA 58.458 39.130 0.00 0.00 0.00 4.08
378 385 5.002464 TGCGGTATAACCTAGAGTTGTTC 57.998 43.478 6.81 0.07 39.67 3.18
382 389 6.183360 GCGGTATAACCTAGAGTTGTTCAAAC 60.183 42.308 6.81 0.00 39.67 2.93
385 392 9.933723 GGTATAACCTAGAGTTGTTCAAACTTA 57.066 33.333 6.81 0.00 39.67 2.24
446 453 5.163364 GGGATTGATCTTTACAGCAGAGAGA 60.163 44.000 0.00 0.00 0.00 3.10
531 540 4.572389 ACACAAGAGCTGTAACAAACTCTG 59.428 41.667 0.00 1.23 39.40 3.35
684 697 4.150454 CGCTCTCCCTCCCTCCCT 62.150 72.222 0.00 0.00 0.00 4.20
685 698 2.123033 GCTCTCCCTCCCTCCCTC 60.123 72.222 0.00 0.00 0.00 4.30
686 699 2.612251 CTCTCCCTCCCTCCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
687 700 3.036959 TCTCCCTCCCTCCCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
726 739 1.404047 CCAAATAAAAGCCCACCTGCG 60.404 52.381 0.00 0.00 36.02 5.18
802 815 3.728373 CCCCAGCCCCAGGTACAC 61.728 72.222 0.00 0.00 0.00 2.90
803 816 2.610859 CCCAGCCCCAGGTACACT 60.611 66.667 0.00 0.00 0.00 3.55
804 817 2.670148 CCCAGCCCCAGGTACACTC 61.670 68.421 0.00 0.00 0.00 3.51
805 818 2.670148 CCAGCCCCAGGTACACTCC 61.670 68.421 0.00 0.00 0.00 3.85
809 822 2.058595 CCCCAGGTACACTCCTCCG 61.059 68.421 0.00 0.00 35.37 4.63
839 855 0.973632 TCCACCGCTAAGCAAGAAGA 59.026 50.000 0.00 0.00 0.00 2.87
922 941 4.389576 GCGGTTTGCAGCCACGAG 62.390 66.667 9.58 0.00 45.45 4.18
1083 1114 0.536460 AAAACATTCTGGACGCCGGT 60.536 50.000 1.90 0.00 0.00 5.28
1437 1480 1.212751 GGCCACCGTGCATTTCTTC 59.787 57.895 0.00 0.00 0.00 2.87
1447 1490 0.741221 GCATTTCTTCGACCTCCGCT 60.741 55.000 0.00 0.00 38.37 5.52
1509 1552 4.694233 CAGCAGTGCCGCCTCAGT 62.694 66.667 12.58 0.00 0.00 3.41
1701 1744 3.203412 CCGGACGTCTCCCTCTCG 61.203 72.222 16.46 8.30 31.93 4.04
2015 2072 0.106708 GCTTGCCCATCGATCCAGTA 59.893 55.000 0.00 0.00 0.00 2.74
2289 2352 3.555518 GAAGAAAGCCACAATTGTCGTC 58.444 45.455 8.48 0.60 0.00 4.20
2451 2514 1.230324 GCTTCGAGTTCAAACAGCCT 58.770 50.000 0.00 0.00 0.00 4.58
2480 2543 4.012895 CGACAGCAACGCCACCAC 62.013 66.667 0.00 0.00 0.00 4.16
2481 2544 3.660111 GACAGCAACGCCACCACC 61.660 66.667 0.00 0.00 0.00 4.61
2647 2710 6.912951 ACTAGTACTATATTTCATGGGCGT 57.087 37.500 2.33 0.00 0.00 5.68
2648 2711 9.170734 CTACTAGTACTATATTTCATGGGCGTA 57.829 37.037 2.33 0.00 0.00 4.42
2649 2712 8.591114 ACTAGTACTATATTTCATGGGCGTAT 57.409 34.615 2.33 0.00 0.00 3.06
2650 2713 8.467598 ACTAGTACTATATTTCATGGGCGTATG 58.532 37.037 2.33 0.00 0.00 2.39
2651 2714 6.106673 AGTACTATATTTCATGGGCGTATGC 58.893 40.000 0.00 0.00 41.71 3.14
2652 2715 5.165961 ACTATATTTCATGGGCGTATGCT 57.834 39.130 6.92 0.00 42.25 3.79
2659 2722 2.002586 CATGGGCGTATGCTATGCTAC 58.997 52.381 6.92 0.00 42.25 3.58
2868 2936 4.080356 CCCATAGATTTCAAGTGAGTCCCA 60.080 45.833 0.00 0.00 0.00 4.37
2934 3002 1.398451 CCACGAACACACGCTCAATTC 60.398 52.381 0.00 0.00 36.70 2.17
2943 3011 4.024893 ACACACGCTCAATTCACAACTTAG 60.025 41.667 0.00 0.00 0.00 2.18
2951 3019 9.559958 CGCTCAATTCACAACTTAGAATAAAAT 57.440 29.630 0.00 0.00 33.58 1.82
2964 3032 9.588096 ACTTAGAATAAAATTGTTCAACTCCCT 57.412 29.630 5.60 0.00 31.61 4.20
2966 3034 7.468141 AGAATAAAATTGTTCAACTCCCTCC 57.532 36.000 5.60 0.00 31.61 4.30
2967 3035 5.897377 ATAAAATTGTTCAACTCCCTCCG 57.103 39.130 0.00 0.00 0.00 4.63
2968 3036 2.951229 AATTGTTCAACTCCCTCCGT 57.049 45.000 0.00 0.00 0.00 4.69
2969 3037 2.951229 ATTGTTCAACTCCCTCCGTT 57.049 45.000 0.00 0.00 0.00 4.44
2970 3038 2.249844 TTGTTCAACTCCCTCCGTTC 57.750 50.000 0.00 0.00 0.00 3.95
2971 3039 0.395312 TGTTCAACTCCCTCCGTTCC 59.605 55.000 0.00 0.00 0.00 3.62
2972 3040 0.685660 GTTCAACTCCCTCCGTTCCT 59.314 55.000 0.00 0.00 0.00 3.36
2973 3041 1.897802 GTTCAACTCCCTCCGTTCCTA 59.102 52.381 0.00 0.00 0.00 2.94
2974 3042 2.301009 GTTCAACTCCCTCCGTTCCTAA 59.699 50.000 0.00 0.00 0.00 2.69
2975 3043 2.612000 TCAACTCCCTCCGTTCCTAAA 58.388 47.619 0.00 0.00 0.00 1.85
2976 3044 3.178865 TCAACTCCCTCCGTTCCTAAAT 58.821 45.455 0.00 0.00 0.00 1.40
2977 3045 4.355549 TCAACTCCCTCCGTTCCTAAATA 58.644 43.478 0.00 0.00 0.00 1.40
2978 3046 4.966805 TCAACTCCCTCCGTTCCTAAATAT 59.033 41.667 0.00 0.00 0.00 1.28
2979 3047 6.138263 TCAACTCCCTCCGTTCCTAAATATA 58.862 40.000 0.00 0.00 0.00 0.86
2980 3048 6.612456 TCAACTCCCTCCGTTCCTAAATATAA 59.388 38.462 0.00 0.00 0.00 0.98
2981 3049 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2982 3050 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2983 3051 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2984 3052 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2985 3053 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2986 3054 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2987 3055 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
2988 3056 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
3004 3072 7.118496 AGTCTTTGTAGAGATTCCACTATGG 57.882 40.000 0.00 0.00 39.43 2.74
3005 3073 6.897966 AGTCTTTGTAGAGATTCCACTATGGA 59.102 38.462 0.00 0.00 46.61 3.41
3016 3084 4.442401 TCCACTATGGACTACATACGGA 57.558 45.455 0.00 0.00 42.67 4.69
3017 3085 4.395625 TCCACTATGGACTACATACGGAG 58.604 47.826 0.00 0.00 42.67 4.63
3018 3086 3.057456 CCACTATGGACTACATACGGAGC 60.057 52.174 0.00 0.00 40.96 4.70
3019 3087 3.568430 CACTATGGACTACATACGGAGCA 59.432 47.826 0.00 0.00 41.03 4.26
3020 3088 4.037565 CACTATGGACTACATACGGAGCAA 59.962 45.833 0.00 0.00 41.03 3.91
3021 3089 4.647853 ACTATGGACTACATACGGAGCAAA 59.352 41.667 0.00 0.00 41.03 3.68
3022 3090 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
3023 3091 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
3024 3092 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
3025 3093 3.560068 GGACTACATACGGAGCAAAATGG 59.440 47.826 0.00 0.00 0.00 3.16
3026 3094 4.439057 GACTACATACGGAGCAAAATGGA 58.561 43.478 0.00 0.00 0.00 3.41
3027 3095 5.036117 ACTACATACGGAGCAAAATGGAT 57.964 39.130 0.00 0.00 0.00 3.41
3028 3096 4.816385 ACTACATACGGAGCAAAATGGATG 59.184 41.667 0.00 0.00 0.00 3.51
3029 3097 3.884895 ACATACGGAGCAAAATGGATGA 58.115 40.909 0.00 0.00 0.00 2.92
3030 3098 4.269183 ACATACGGAGCAAAATGGATGAA 58.731 39.130 0.00 0.00 0.00 2.57
3031 3099 4.889409 ACATACGGAGCAAAATGGATGAAT 59.111 37.500 0.00 0.00 0.00 2.57
3032 3100 5.360714 ACATACGGAGCAAAATGGATGAATT 59.639 36.000 0.00 0.00 0.00 2.17
3033 3101 4.806640 ACGGAGCAAAATGGATGAATTT 57.193 36.364 0.00 0.00 0.00 1.82
3034 3102 5.913137 ACGGAGCAAAATGGATGAATTTA 57.087 34.783 0.00 0.00 0.00 1.40
3035 3103 5.650543 ACGGAGCAAAATGGATGAATTTAC 58.349 37.500 0.00 0.00 0.00 2.01
3036 3104 5.184864 ACGGAGCAAAATGGATGAATTTACA 59.815 36.000 0.00 0.00 0.00 2.41
3037 3105 5.516339 CGGAGCAAAATGGATGAATTTACAC 59.484 40.000 0.00 0.00 0.00 2.90
3038 3106 6.625740 CGGAGCAAAATGGATGAATTTACACT 60.626 38.462 0.00 0.00 0.00 3.55
3039 3107 6.753744 GGAGCAAAATGGATGAATTTACACTC 59.246 38.462 0.00 0.00 0.00 3.51
3040 3108 7.363268 GGAGCAAAATGGATGAATTTACACTCT 60.363 37.037 0.00 0.00 30.86 3.24
3041 3109 8.579850 AGCAAAATGGATGAATTTACACTCTA 57.420 30.769 0.00 0.00 0.00 2.43
3042 3110 9.023962 AGCAAAATGGATGAATTTACACTCTAA 57.976 29.630 0.00 0.00 0.00 2.10
3043 3111 9.638239 GCAAAATGGATGAATTTACACTCTAAA 57.362 29.630 0.00 0.00 0.00 1.85
3047 3115 9.807649 AATGGATGAATTTACACTCTAAAATGC 57.192 29.630 0.00 0.00 0.00 3.56
3048 3116 8.347004 TGGATGAATTTACACTCTAAAATGCA 57.653 30.769 0.00 0.00 35.58 3.96
3049 3117 8.970020 TGGATGAATTTACACTCTAAAATGCAT 58.030 29.630 0.00 0.00 41.83 3.96
3060 3128 9.265901 ACACTCTAAAATGCATCTACATACATC 57.734 33.333 0.00 0.00 0.00 3.06
3061 3129 8.715998 CACTCTAAAATGCATCTACATACATCC 58.284 37.037 0.00 0.00 0.00 3.51
3062 3130 8.432013 ACTCTAAAATGCATCTACATACATCCA 58.568 33.333 0.00 0.00 0.00 3.41
3063 3131 9.445878 CTCTAAAATGCATCTACATACATCCAT 57.554 33.333 0.00 0.00 0.00 3.41
3068 3136 8.502105 AATGCATCTACATACATCCATATGTG 57.498 34.615 0.00 0.00 45.99 3.21
3069 3137 6.408869 TGCATCTACATACATCCATATGTGG 58.591 40.000 1.19 1.19 45.99 4.17
3070 3138 6.013466 TGCATCTACATACATCCATATGTGGT 60.013 38.462 8.51 0.00 45.99 4.16
3071 3139 6.881065 GCATCTACATACATCCATATGTGGTT 59.119 38.462 8.51 0.00 45.99 3.67
3072 3140 7.065085 GCATCTACATACATCCATATGTGGTTC 59.935 40.741 8.51 0.00 45.99 3.62
3073 3141 7.610580 TCTACATACATCCATATGTGGTTCA 57.389 36.000 8.51 0.00 45.99 3.18
3074 3142 8.206126 TCTACATACATCCATATGTGGTTCAT 57.794 34.615 8.51 0.00 45.99 2.57
3075 3143 9.320295 TCTACATACATCCATATGTGGTTCATA 57.680 33.333 8.51 0.00 45.99 2.15
3076 3144 9.942850 CTACATACATCCATATGTGGTTCATAA 57.057 33.333 8.51 0.00 45.99 1.90
3080 3148 7.333528 ACATCCATATGTGGTTCATAACAAC 57.666 36.000 8.51 0.00 44.79 3.32
3286 3354 5.247862 CCCAAATGGAAAAGAAATTGGAGG 58.752 41.667 0.00 0.00 39.69 4.30
3395 3463 2.616842 TGTTCGCCTGTCTTTCTTTTCC 59.383 45.455 0.00 0.00 0.00 3.13
3433 3501 1.162505 CTAGGATCCTCCTCCCTCCA 58.837 60.000 20.22 0.00 45.66 3.86
3473 3545 2.677875 CTTTGCACAGCCCTCCCC 60.678 66.667 0.00 0.00 0.00 4.81
3474 3546 3.185203 TTTGCACAGCCCTCCCCT 61.185 61.111 0.00 0.00 0.00 4.79
3478 3550 4.748798 CACAGCCCTCCCCTCCCT 62.749 72.222 0.00 0.00 0.00 4.20
3479 3551 4.748798 ACAGCCCTCCCCTCCCTG 62.749 72.222 0.00 0.00 0.00 4.45
3656 3728 6.144563 GGCTAATTTCAAGCACACTTTCTTTC 59.855 38.462 1.35 0.00 41.93 2.62
3745 3820 2.893489 GCCCAATGACAAGAGGAACTTT 59.107 45.455 0.00 0.00 41.55 2.66
3747 3822 3.256631 CCCAATGACAAGAGGAACTTTGG 59.743 47.826 0.00 0.00 41.55 3.28
3748 3823 3.891366 CCAATGACAAGAGGAACTTTGGT 59.109 43.478 0.00 0.00 41.55 3.67
3749 3824 4.261741 CCAATGACAAGAGGAACTTTGGTG 60.262 45.833 0.00 0.00 41.55 4.17
3750 3825 2.297701 TGACAAGAGGAACTTTGGTGC 58.702 47.619 0.00 0.00 41.55 5.01
3751 3826 1.264288 GACAAGAGGAACTTTGGTGCG 59.736 52.381 0.00 0.00 41.55 5.34
3752 3827 0.593128 CAAGAGGAACTTTGGTGCGG 59.407 55.000 0.00 0.00 41.55 5.69
3832 3908 5.248380 AGCTTTTGACCTCTCCAACTAAT 57.752 39.130 0.00 0.00 0.00 1.73
3837 3913 6.546428 TTTGACCTCTCCAACTAATCTAGG 57.454 41.667 0.00 0.00 0.00 3.02
3838 3914 5.467668 TGACCTCTCCAACTAATCTAGGA 57.532 43.478 0.00 0.00 0.00 2.94
3840 3916 5.044030 TGACCTCTCCAACTAATCTAGGAGT 60.044 44.000 7.16 0.00 46.09 3.85
3841 3917 6.159928 TGACCTCTCCAACTAATCTAGGAGTA 59.840 42.308 7.16 0.00 46.09 2.59
3842 3918 7.147105 TGACCTCTCCAACTAATCTAGGAGTAT 60.147 40.741 7.16 0.00 46.09 2.12
3872 3948 1.502163 GCGCTTGCTCGGCAGATTAT 61.502 55.000 0.00 0.00 40.61 1.28
3873 3949 0.940126 CGCTTGCTCGGCAGATTATT 59.060 50.000 0.00 0.00 40.61 1.40
3874 3950 1.331756 CGCTTGCTCGGCAGATTATTT 59.668 47.619 0.00 0.00 40.61 1.40
3875 3951 2.543848 CGCTTGCTCGGCAGATTATTTA 59.456 45.455 0.00 0.00 40.61 1.40
3876 3952 3.187227 CGCTTGCTCGGCAGATTATTTAT 59.813 43.478 0.00 0.00 40.61 1.40
3918 3997 8.499162 GCACTAGCTATAAATTAATCACTGGTG 58.501 37.037 0.00 0.00 38.11 4.17
3941 4053 7.230222 GTGTTCTATCTTCAAATGAACGTCTG 58.770 38.462 0.00 0.00 39.61 3.51
4114 4226 2.809601 CGTGCAGGTACGTGCTCC 60.810 66.667 33.17 24.08 44.32 4.70
4292 4407 2.939261 CGAGTACCTGCCCGTGGTT 61.939 63.158 0.00 0.00 38.88 3.67
4373 4488 3.214845 ATACCGTCGCCGTCCTCC 61.215 66.667 0.00 0.00 0.00 4.30
4792 4917 3.894782 TTGATGTGTGTGGTTTCGATG 57.105 42.857 0.00 0.00 0.00 3.84
4891 5016 9.366216 GTTCTTGTGGTTTTTAGATTTGAAGTT 57.634 29.630 0.00 0.00 0.00 2.66
4967 5096 4.206088 GCGTTCTTTCGTTCGTTACATTT 58.794 39.130 0.00 0.00 0.00 2.32
5000 5129 6.636666 TTTATGTACTCCGAATTTCGACAC 57.363 37.500 19.91 11.41 43.74 3.67
5035 5165 8.592809 GGTAATGATAGGTTTGATCAGATCTCT 58.407 37.037 11.83 0.00 36.77 3.10
5037 5167 8.495160 AATGATAGGTTTGATCAGATCTCTCT 57.505 34.615 11.83 6.65 36.77 3.10
5038 5168 7.523293 TGATAGGTTTGATCAGATCTCTCTC 57.477 40.000 11.83 0.34 0.00 3.20
5039 5169 7.296856 TGATAGGTTTGATCAGATCTCTCTCT 58.703 38.462 11.83 5.75 0.00 3.10
5040 5170 7.448161 TGATAGGTTTGATCAGATCTCTCTCTC 59.552 40.741 11.83 6.90 0.00 3.20
5041 5171 5.769835 AGGTTTGATCAGATCTCTCTCTCT 58.230 41.667 11.83 0.00 0.00 3.10
5042 5172 5.829924 AGGTTTGATCAGATCTCTCTCTCTC 59.170 44.000 11.83 0.00 0.00 3.20
5043 5173 5.829924 GGTTTGATCAGATCTCTCTCTCTCT 59.170 44.000 11.83 0.00 0.00 3.10
5044 5174 6.016777 GGTTTGATCAGATCTCTCTCTCTCTC 60.017 46.154 11.83 0.00 0.00 3.20
5045 5175 6.505048 TTGATCAGATCTCTCTCTCTCTCT 57.495 41.667 11.83 0.00 0.00 3.10
5046 5176 6.106648 TGATCAGATCTCTCTCTCTCTCTC 57.893 45.833 11.83 0.00 0.00 3.20
5047 5177 5.842874 TGATCAGATCTCTCTCTCTCTCTCT 59.157 44.000 11.83 0.00 0.00 3.10
5048 5178 5.798125 TCAGATCTCTCTCTCTCTCTCTC 57.202 47.826 0.00 0.00 0.00 3.20
5049 5179 5.462240 TCAGATCTCTCTCTCTCTCTCTCT 58.538 45.833 0.00 0.00 0.00 3.10
5050 5180 5.538053 TCAGATCTCTCTCTCTCTCTCTCTC 59.462 48.000 0.00 0.00 0.00 3.20
5051 5181 5.539574 CAGATCTCTCTCTCTCTCTCTCTCT 59.460 48.000 0.00 0.00 0.00 3.10
5052 5182 5.774690 AGATCTCTCTCTCTCTCTCTCTCTC 59.225 48.000 0.00 0.00 0.00 3.20
5053 5183 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
5054 5184 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5055 5185 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5056 5186 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5057 5187 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5058 5188 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5059 5189 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5060 5190 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5061 5191 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5062 5192 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5063 5193 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5064 5194 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5075 5205 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
5078 5208 3.378512 TCTCTCTCTCTCTCTCTCAGCT 58.621 50.000 0.00 0.00 0.00 4.24
5090 5220 4.528206 TCTCTCTCAGCTGAATTACCAACA 59.472 41.667 18.85 0.00 0.00 3.33
5093 5223 4.318332 TCTCAGCTGAATTACCAACACTG 58.682 43.478 18.85 0.98 0.00 3.66
5119 5251 3.576550 TCCATTTTGTTTACTTGGCCCTC 59.423 43.478 0.00 0.00 0.00 4.30
5254 5434 1.871080 AGCTCACTTGGACTTTGTCG 58.129 50.000 0.00 0.00 32.65 4.35
5260 5655 0.514691 CTTGGACTTTGTCGAGCAGC 59.485 55.000 0.00 0.00 32.65 5.25
5268 5663 2.159819 TTGTCGAGCAGCAGGTCCTC 62.160 60.000 2.47 0.00 39.06 3.71
5311 5710 7.816513 GTCCTAAACCTCGAAGTAGTTGTTTAT 59.183 37.037 4.89 0.00 30.48 1.40
5312 5711 7.816031 TCCTAAACCTCGAAGTAGTTGTTTATG 59.184 37.037 4.89 3.62 30.48 1.90
5313 5712 5.857822 AACCTCGAAGTAGTTGTTTATGC 57.142 39.130 0.00 0.00 0.00 3.14
5394 6255 4.158394 GCATGCCTCTACCTTCAAAAATCA 59.842 41.667 6.36 0.00 0.00 2.57
5397 6258 6.084326 TGCCTCTACCTTCAAAAATCAAAC 57.916 37.500 0.00 0.00 0.00 2.93
5474 6335 9.918630 ACCATTTGATTAATGAAACAGAAAGAG 57.081 29.630 1.99 0.00 45.35 2.85
5517 6380 7.759465 TCTTTGTGTAAAACCAAATGACGTAA 58.241 30.769 0.00 0.00 0.00 3.18
5518 6381 8.242053 TCTTTGTGTAAAACCAAATGACGTAAA 58.758 29.630 0.00 0.00 0.00 2.01
5525 6394 7.514573 AAAACCAAATGACGTAAAACTTGAC 57.485 32.000 0.00 0.00 0.00 3.18
5528 6397 6.859017 ACCAAATGACGTAAAACTTGACTTT 58.141 32.000 0.00 0.00 0.00 2.66
5562 6431 0.762461 AGATGAGAGCTAGCCACCCC 60.762 60.000 12.13 2.29 0.00 4.95
5566 6435 1.690985 AGAGCTAGCCACCCCCTTC 60.691 63.158 12.13 0.00 0.00 3.46
5567 6436 1.995626 GAGCTAGCCACCCCCTTCA 60.996 63.158 12.13 0.00 0.00 3.02
5568 6437 1.541368 AGCTAGCCACCCCCTTCAA 60.541 57.895 12.13 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.282875 GACAACGGACTTTGGCAGC 59.717 57.895 0.00 0.00 34.29 5.25
2 3 0.104487 TACGACAACGGACTTTGGCA 59.896 50.000 0.00 0.00 44.46 4.92
3 4 0.788391 CTACGACAACGGACTTTGGC 59.212 55.000 0.00 0.00 44.46 4.52
4 5 1.425412 CCTACGACAACGGACTTTGG 58.575 55.000 0.00 0.00 44.46 3.28
6 7 0.390124 TGCCTACGACAACGGACTTT 59.610 50.000 0.00 0.00 44.46 2.66
7 8 0.606604 ATGCCTACGACAACGGACTT 59.393 50.000 0.00 0.00 44.46 3.01
8 9 0.606604 AATGCCTACGACAACGGACT 59.393 50.000 0.00 0.00 44.46 3.85
9 10 0.997196 GAATGCCTACGACAACGGAC 59.003 55.000 0.00 0.00 44.46 4.79
10 11 0.108520 GGAATGCCTACGACAACGGA 60.109 55.000 0.00 0.00 44.46 4.69
11 12 1.087771 GGGAATGCCTACGACAACGG 61.088 60.000 0.00 0.00 44.46 4.44
12 13 0.390603 TGGGAATGCCTACGACAACG 60.391 55.000 0.00 0.00 45.75 4.10
14 15 0.981183 ACTGGGAATGCCTACGACAA 59.019 50.000 0.00 0.00 0.00 3.18
15 16 0.249120 CACTGGGAATGCCTACGACA 59.751 55.000 0.00 0.00 0.00 4.35
16 17 1.090052 GCACTGGGAATGCCTACGAC 61.090 60.000 0.00 0.00 37.08 4.34
17 18 1.220749 GCACTGGGAATGCCTACGA 59.779 57.895 0.00 0.00 37.08 3.43
23 24 3.512516 GCTCGGCACTGGGAATGC 61.513 66.667 0.00 0.00 42.62 3.56
25 26 3.329889 TGGCTCGGCACTGGGAAT 61.330 61.111 0.00 0.00 0.00 3.01
26 27 4.329545 GTGGCTCGGCACTGGGAA 62.330 66.667 15.37 0.00 0.00 3.97
60 61 2.866028 CTCTGGAGCAAAGCGCAC 59.134 61.111 11.47 0.00 46.13 5.34
91 92 1.741770 GACAGGAATGAAGGCGCGT 60.742 57.895 8.43 0.00 0.00 6.01
92 93 2.464459 GGACAGGAATGAAGGCGCG 61.464 63.158 0.00 0.00 0.00 6.86
93 94 2.464459 CGGACAGGAATGAAGGCGC 61.464 63.158 0.00 0.00 0.00 6.53
94 95 2.464459 GCGGACAGGAATGAAGGCG 61.464 63.158 0.00 0.00 0.00 5.52
95 96 2.464459 CGCGGACAGGAATGAAGGC 61.464 63.158 0.00 0.00 0.00 4.35
96 97 2.464459 GCGCGGACAGGAATGAAGG 61.464 63.158 8.83 0.00 0.00 3.46
97 98 2.802667 CGCGCGGACAGGAATGAAG 61.803 63.158 24.84 0.00 0.00 3.02
98 99 2.813474 CGCGCGGACAGGAATGAA 60.813 61.111 24.84 0.00 0.00 2.57
118 119 0.543410 ACTCACCATGGGTACACGGA 60.543 55.000 18.09 0.96 32.55 4.69
120 121 1.438651 CAACTCACCATGGGTACACG 58.561 55.000 18.09 0.48 32.11 4.49
125 126 1.150536 AACGCAACTCACCATGGGT 59.849 52.632 18.09 0.75 43.55 4.51
127 128 0.667993 AACAACGCAACTCACCATGG 59.332 50.000 11.19 11.19 0.00 3.66
133 134 0.179094 ACCTCGAACAACGCAACTCA 60.179 50.000 0.00 0.00 42.26 3.41
158 159 8.594550 TCAAAAGCTAGATTACAACTAGTTCCT 58.405 33.333 4.77 0.00 39.36 3.36
166 168 9.788960 CCCTAAAATCAAAAGCTAGATTACAAC 57.211 33.333 8.77 0.00 33.58 3.32
193 195 3.442625 GGTCCCTACAAAATAGCACAACC 59.557 47.826 0.00 0.00 0.00 3.77
207 211 4.824289 TGAATTTACGACAAGGTCCCTAC 58.176 43.478 0.00 0.00 0.00 3.18
210 214 4.070009 AGTTGAATTTACGACAAGGTCCC 58.930 43.478 0.00 0.00 0.00 4.46
244 248 1.043816 TTCCGATGAGATGGAGAGCC 58.956 55.000 0.00 0.00 35.26 4.70
246 250 7.157347 TGAAATTATTCCGATGAGATGGAGAG 58.843 38.462 0.00 0.00 35.26 3.20
249 253 6.202762 CGTTGAAATTATTCCGATGAGATGGA 59.797 38.462 0.00 0.00 34.49 3.41
252 256 5.470098 CCCGTTGAAATTATTCCGATGAGAT 59.530 40.000 0.00 0.00 34.49 2.75
256 260 5.470098 AGATCCCGTTGAAATTATTCCGATG 59.530 40.000 0.00 0.00 34.49 3.84
261 265 6.687105 CGAAACAGATCCCGTTGAAATTATTC 59.313 38.462 0.00 0.00 36.04 1.75
270 274 0.673644 AGGCGAAACAGATCCCGTTG 60.674 55.000 0.00 0.00 0.00 4.10
271 275 0.673644 CAGGCGAAACAGATCCCGTT 60.674 55.000 0.00 0.00 0.00 4.44
274 278 1.303309 CATCAGGCGAAACAGATCCC 58.697 55.000 0.00 0.00 0.00 3.85
297 301 4.592485 AAATGAATTTTGTGGTACCGCA 57.408 36.364 24.25 24.25 34.35 5.69
311 315 6.017109 CAGTATACGGCTTGCCTAAAATGAAT 60.017 38.462 10.12 0.00 0.00 2.57
312 316 5.295787 CAGTATACGGCTTGCCTAAAATGAA 59.704 40.000 10.12 0.00 0.00 2.57
313 317 4.814234 CAGTATACGGCTTGCCTAAAATGA 59.186 41.667 10.12 0.00 0.00 2.57
314 318 4.574828 ACAGTATACGGCTTGCCTAAAATG 59.425 41.667 10.12 4.92 0.00 2.32
315 319 4.777463 ACAGTATACGGCTTGCCTAAAAT 58.223 39.130 10.12 1.00 0.00 1.82
319 323 3.899052 AAACAGTATACGGCTTGCCTA 57.101 42.857 10.12 2.19 0.00 3.93
320 324 2.781681 AAACAGTATACGGCTTGCCT 57.218 45.000 10.12 0.00 0.00 4.75
324 328 4.517453 TCTTGCAAAAACAGTATACGGCTT 59.483 37.500 0.00 0.00 0.00 4.35
343 347 2.323939 TACCGCAAAAACGCATCTTG 57.676 45.000 0.00 0.00 0.00 3.02
345 349 3.181504 GGTTATACCGCAAAAACGCATCT 60.182 43.478 0.00 0.00 0.00 2.90
392 399 6.200878 AGGGGAAAATGTAAAAGACTCTCA 57.799 37.500 0.00 0.00 0.00 3.27
425 432 7.794041 AGAATCTCTCTGCTGTAAAGATCAAT 58.206 34.615 0.00 0.00 31.12 2.57
431 438 7.319646 ACTGTAAGAATCTCTCTGCTGTAAAG 58.680 38.462 0.00 0.00 37.43 1.85
531 540 0.250901 CGGGGACATGGATGATTCCC 60.251 60.000 8.07 8.07 41.83 3.97
684 697 1.151413 AGTCTACAGGAACAAGGGGGA 59.849 52.381 0.00 0.00 0.00 4.81
685 698 1.657804 AGTCTACAGGAACAAGGGGG 58.342 55.000 0.00 0.00 0.00 5.40
686 699 2.027100 GGAAGTCTACAGGAACAAGGGG 60.027 54.545 0.00 0.00 0.00 4.79
687 700 2.637872 TGGAAGTCTACAGGAACAAGGG 59.362 50.000 0.00 0.00 0.00 3.95
726 739 0.879090 AATGGTCGCGGGAAAAGAAC 59.121 50.000 6.13 0.00 0.00 3.01
801 814 4.974438 TGGGTTGGGCGGAGGAGT 62.974 66.667 0.00 0.00 0.00 3.85
802 815 4.101448 CTGGGTTGGGCGGAGGAG 62.101 72.222 0.00 0.00 0.00 3.69
803 816 4.974438 ACTGGGTTGGGCGGAGGA 62.974 66.667 0.00 0.00 0.00 3.71
804 817 4.410400 GACTGGGTTGGGCGGAGG 62.410 72.222 0.00 0.00 0.00 4.30
805 818 4.410400 GGACTGGGTTGGGCGGAG 62.410 72.222 0.00 0.00 0.00 4.63
825 841 1.005340 CTGGCTCTTCTTGCTTAGCG 58.995 55.000 0.00 0.00 35.79 4.26
922 941 3.629398 ACATTCTTGGGATTGATTCTCGC 59.371 43.478 0.00 0.00 0.00 5.03
930 949 7.228308 GGAAGATCTAGAACATTCTTGGGATTG 59.772 40.741 10.37 0.00 38.70 2.67
969 991 3.126879 CGAATTGGAGCAGCGGCA 61.127 61.111 12.44 0.00 44.61 5.69
1083 1114 2.851194 ACTAGGGTAGTACTCCTGAGCA 59.149 50.000 12.37 0.00 37.23 4.26
1196 1227 3.936203 GCATGGGCATGGGCATGG 61.936 66.667 0.00 0.00 43.71 3.66
1197 1228 3.936203 GGCATGGGCATGGGCATG 61.936 66.667 0.00 0.00 43.71 4.06
1201 1232 3.238497 CATGGGCATGGGCATGGG 61.238 66.667 0.00 0.00 43.71 4.00
1740 1783 2.264794 CGAGAAGGGTTCGGTGGG 59.735 66.667 0.00 0.00 34.56 4.61
1924 1980 0.863538 CGCGTGAACTCGAGGATGAG 60.864 60.000 18.41 6.26 41.86 2.90
1996 2053 0.106708 TACTGGATCGATGGGCAAGC 59.893 55.000 0.54 0.00 0.00 4.01
2015 2072 6.091577 TGCAATTCACATATTTTAGTCGACGT 59.908 34.615 10.46 1.19 0.00 4.34
2237 2300 1.228429 TTGCCCTTCCGTTCTTGGG 60.228 57.895 0.00 0.00 42.41 4.12
2464 2527 3.660111 GGTGGTGGCGTTGCTGTC 61.660 66.667 0.00 0.00 0.00 3.51
2647 2710 6.260714 CCTTCACACAATTGTAGCATAGCATA 59.739 38.462 11.53 0.00 33.30 3.14
2648 2711 5.066893 CCTTCACACAATTGTAGCATAGCAT 59.933 40.000 11.53 0.00 33.30 3.79
2649 2712 4.395854 CCTTCACACAATTGTAGCATAGCA 59.604 41.667 11.53 0.00 33.30 3.49
2650 2713 4.635765 TCCTTCACACAATTGTAGCATAGC 59.364 41.667 11.53 0.00 33.30 2.97
2651 2714 6.932356 ATCCTTCACACAATTGTAGCATAG 57.068 37.500 11.53 5.49 33.30 2.23
2652 2715 7.537715 CAAATCCTTCACACAATTGTAGCATA 58.462 34.615 11.53 0.00 33.30 3.14
2659 2722 4.261578 AGGCAAATCCTTCACACAATTG 57.738 40.909 3.24 3.24 44.75 2.32
2868 2936 4.264253 TGAATGCAGCAGCTTATAGTTGT 58.736 39.130 0.00 0.00 42.74 3.32
2943 3011 6.072119 ACGGAGGGAGTTGAACAATTTTATTC 60.072 38.462 0.00 0.00 0.00 1.75
2951 3019 1.202722 GGAACGGAGGGAGTTGAACAA 60.203 52.381 0.00 0.00 31.14 2.83
2953 3021 0.685660 AGGAACGGAGGGAGTTGAAC 59.314 55.000 0.00 0.00 31.14 3.18
2954 3022 2.314071 TAGGAACGGAGGGAGTTGAA 57.686 50.000 0.00 0.00 31.14 2.69
2956 3024 3.629142 ATTTAGGAACGGAGGGAGTTG 57.371 47.619 0.00 0.00 31.14 3.16
2957 3025 6.614496 ACTTATATTTAGGAACGGAGGGAGTT 59.386 38.462 0.00 0.00 34.07 3.01
2958 3026 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
2959 3027 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2960 3028 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2961 3029 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2962 3030 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
2963 3031 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
2978 3046 8.696374 CCATAGTGGAATCTCTACAAAGACTTA 58.304 37.037 0.00 0.00 40.96 2.24
2979 3047 7.400339 TCCATAGTGGAATCTCTACAAAGACTT 59.600 37.037 0.00 0.00 45.00 3.01
2980 3048 6.897966 TCCATAGTGGAATCTCTACAAAGACT 59.102 38.462 0.00 0.00 45.00 3.24
2981 3049 7.113658 TCCATAGTGGAATCTCTACAAAGAC 57.886 40.000 0.00 0.00 45.00 3.01
2995 3063 4.395625 CTCCGTATGTAGTCCATAGTGGA 58.604 47.826 0.00 0.00 45.98 4.02
2996 3064 3.057456 GCTCCGTATGTAGTCCATAGTGG 60.057 52.174 0.00 0.00 36.71 4.00
2997 3065 3.568430 TGCTCCGTATGTAGTCCATAGTG 59.432 47.826 0.00 0.00 36.71 2.74
2998 3066 3.828921 TGCTCCGTATGTAGTCCATAGT 58.171 45.455 0.00 0.00 36.71 2.12
2999 3067 4.848562 TTGCTCCGTATGTAGTCCATAG 57.151 45.455 0.00 0.00 36.71 2.23
3000 3068 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
3001 3069 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
3002 3070 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
3003 3071 3.560068 CCATTTTGCTCCGTATGTAGTCC 59.440 47.826 0.00 0.00 0.00 3.85
3004 3072 4.439057 TCCATTTTGCTCCGTATGTAGTC 58.561 43.478 0.00 0.00 0.00 2.59
3005 3073 4.481368 TCCATTTTGCTCCGTATGTAGT 57.519 40.909 0.00 0.00 0.00 2.73
3006 3074 5.056480 TCATCCATTTTGCTCCGTATGTAG 58.944 41.667 0.00 0.00 0.00 2.74
3007 3075 5.029807 TCATCCATTTTGCTCCGTATGTA 57.970 39.130 0.00 0.00 0.00 2.29
3008 3076 3.884895 TCATCCATTTTGCTCCGTATGT 58.115 40.909 0.00 0.00 0.00 2.29
3009 3077 4.898829 TTCATCCATTTTGCTCCGTATG 57.101 40.909 0.00 0.00 0.00 2.39
3010 3078 6.469782 AAATTCATCCATTTTGCTCCGTAT 57.530 33.333 0.00 0.00 0.00 3.06
3011 3079 5.913137 AAATTCATCCATTTTGCTCCGTA 57.087 34.783 0.00 0.00 0.00 4.02
3012 3080 4.806640 AAATTCATCCATTTTGCTCCGT 57.193 36.364 0.00 0.00 0.00 4.69
3013 3081 5.516339 GTGTAAATTCATCCATTTTGCTCCG 59.484 40.000 0.00 0.00 0.00 4.63
3014 3082 6.633856 AGTGTAAATTCATCCATTTTGCTCC 58.366 36.000 0.00 0.00 0.00 4.70
3015 3083 7.542025 AGAGTGTAAATTCATCCATTTTGCTC 58.458 34.615 0.00 0.00 0.00 4.26
3016 3084 7.472334 AGAGTGTAAATTCATCCATTTTGCT 57.528 32.000 0.00 0.00 0.00 3.91
3017 3085 9.638239 TTTAGAGTGTAAATTCATCCATTTTGC 57.362 29.630 0.00 0.00 0.00 3.68
3021 3089 9.807649 GCATTTTAGAGTGTAAATTCATCCATT 57.192 29.630 0.00 0.00 0.00 3.16
3022 3090 8.970020 TGCATTTTAGAGTGTAAATTCATCCAT 58.030 29.630 0.00 0.00 0.00 3.41
3023 3091 8.347004 TGCATTTTAGAGTGTAAATTCATCCA 57.653 30.769 0.00 0.00 0.00 3.41
3024 3092 9.455847 GATGCATTTTAGAGTGTAAATTCATCC 57.544 33.333 0.00 0.00 37.89 3.51
3034 3102 9.265901 GATGTATGTAGATGCATTTTAGAGTGT 57.734 33.333 0.00 0.00 35.26 3.55
3035 3103 8.715998 GGATGTATGTAGATGCATTTTAGAGTG 58.284 37.037 0.00 0.00 35.26 3.51
3036 3104 8.432013 TGGATGTATGTAGATGCATTTTAGAGT 58.568 33.333 0.00 0.00 35.26 3.24
3037 3105 8.837788 TGGATGTATGTAGATGCATTTTAGAG 57.162 34.615 0.00 0.00 35.26 2.43
3041 3109 9.524496 ACATATGGATGTATGTAGATGCATTTT 57.476 29.630 7.80 0.00 44.77 1.82
3042 3110 8.953313 CACATATGGATGTATGTAGATGCATTT 58.047 33.333 7.80 0.00 44.82 2.32
3043 3111 8.502105 CACATATGGATGTATGTAGATGCATT 57.498 34.615 7.80 0.00 44.82 3.56
3061 3129 6.599244 ACCTCAGTTGTTATGAACCACATATG 59.401 38.462 0.00 0.00 40.56 1.78
3062 3130 6.721318 ACCTCAGTTGTTATGAACCACATAT 58.279 36.000 0.00 0.00 40.56 1.78
3063 3131 6.121776 ACCTCAGTTGTTATGAACCACATA 57.878 37.500 0.00 0.00 40.07 2.29
3064 3132 4.985538 ACCTCAGTTGTTATGAACCACAT 58.014 39.130 0.00 0.00 42.39 3.21
3065 3133 4.431416 ACCTCAGTTGTTATGAACCACA 57.569 40.909 0.00 0.00 30.00 4.17
3066 3134 5.790593 TCTACCTCAGTTGTTATGAACCAC 58.209 41.667 0.00 0.00 0.00 4.16
3067 3135 6.428083 TTCTACCTCAGTTGTTATGAACCA 57.572 37.500 0.00 0.00 0.00 3.67
3068 3136 7.739498 TTTTCTACCTCAGTTGTTATGAACC 57.261 36.000 0.00 0.00 0.00 3.62
3069 3137 9.612620 CATTTTTCTACCTCAGTTGTTATGAAC 57.387 33.333 0.00 0.00 0.00 3.18
3070 3138 9.349713 ACATTTTTCTACCTCAGTTGTTATGAA 57.650 29.630 0.00 0.00 0.00 2.57
3071 3139 8.783093 CACATTTTTCTACCTCAGTTGTTATGA 58.217 33.333 0.00 0.00 0.00 2.15
3072 3140 8.023128 CCACATTTTTCTACCTCAGTTGTTATG 58.977 37.037 0.00 0.00 0.00 1.90
3073 3141 7.942341 TCCACATTTTTCTACCTCAGTTGTTAT 59.058 33.333 0.00 0.00 0.00 1.89
3074 3142 7.284074 TCCACATTTTTCTACCTCAGTTGTTA 58.716 34.615 0.00 0.00 0.00 2.41
3075 3143 6.126409 TCCACATTTTTCTACCTCAGTTGTT 58.874 36.000 0.00 0.00 0.00 2.83
3076 3144 5.690865 TCCACATTTTTCTACCTCAGTTGT 58.309 37.500 0.00 0.00 0.00 3.32
3080 3148 3.691609 GCCTCCACATTTTTCTACCTCAG 59.308 47.826 0.00 0.00 0.00 3.35
3286 3354 1.644786 CGAAAAGGATCCGGTGCCAC 61.645 60.000 15.85 0.00 0.00 5.01
3625 3697 2.979813 GTGCTTGAAATTAGCCAACACG 59.020 45.455 0.00 0.00 37.85 4.49
3656 3728 1.008538 GGCAGCCAAACAAGACACG 60.009 57.895 6.55 0.00 0.00 4.49
3704 3778 1.815003 CACTGATGGCAGGTCTTTTCC 59.185 52.381 0.00 0.00 46.60 3.13
3745 3820 3.723097 TTTGGGCAGAACCGCACCA 62.723 57.895 0.00 0.00 40.62 4.17
3747 3822 2.644992 CTTTGGGCAGAACCGCAC 59.355 61.111 0.00 0.00 40.62 5.34
3748 3823 3.294493 GCTTTGGGCAGAACCGCA 61.294 61.111 0.00 0.00 40.62 5.69
3749 3824 4.056125 GGCTTTGGGCAGAACCGC 62.056 66.667 0.00 0.00 44.01 5.68
3750 3825 2.597217 TGGCTTTGGGCAGAACCG 60.597 61.111 0.00 0.00 43.20 4.44
3832 3908 7.166851 AGCGCTACACTATTTATACTCCTAGA 58.833 38.462 8.99 0.00 0.00 2.43
3837 3913 6.142122 GCAAGCGCTACACTATTTATACTC 57.858 41.667 12.05 0.00 34.30 2.59
3855 3931 4.756084 ATAAATAATCTGCCGAGCAAGC 57.244 40.909 0.35 0.00 38.41 4.01
3862 3938 6.391227 AACCTTGGAATAAATAATCTGCCG 57.609 37.500 0.00 0.00 0.00 5.69
3873 3949 8.708021 GCTAGTGCTACCAAAACCTTGGAATAA 61.708 40.741 10.80 0.00 44.50 1.40
3874 3950 7.300429 GCTAGTGCTACCAAAACCTTGGAATA 61.300 42.308 10.80 0.00 44.50 1.75
3875 3951 6.555152 GCTAGTGCTACCAAAACCTTGGAAT 61.555 44.000 10.80 0.00 44.50 3.01
3876 3952 5.285697 GCTAGTGCTACCAAAACCTTGGAA 61.286 45.833 10.80 0.00 44.50 3.53
3893 3972 9.547753 ACACCAGTGATTAATTTATAGCTAGTG 57.452 33.333 4.48 0.00 0.00 2.74
3918 3997 7.582435 TCAGACGTTCATTTGAAGATAGAAC 57.418 36.000 0.00 0.00 34.27 3.01
3921 4000 9.831737 AAAATTCAGACGTTCATTTGAAGATAG 57.168 29.630 0.00 0.00 34.27 2.08
3941 4053 2.096119 GCTGCATGCCACAACAAAATTC 60.096 45.455 16.68 0.00 35.15 2.17
4110 4222 2.585247 GATGCGGTACACGGGAGC 60.585 66.667 0.00 0.00 44.51 4.70
4114 4226 1.521457 ATGCAGATGCGGTACACGG 60.521 57.895 0.00 0.00 45.83 4.94
4137 4249 3.756117 AGGTGAACCTTGTCAAGATTCC 58.244 45.455 15.80 8.05 46.09 3.01
4463 4578 3.632080 TCGGCGTGGGTGGACATT 61.632 61.111 6.85 0.00 0.00 2.71
4509 4627 3.640000 ACCGTCGTCGTCGTCGTT 61.640 61.111 17.80 3.70 44.09 3.85
4553 4671 3.080319 CTATACCTAGTCGGTGTAGCCC 58.920 54.545 4.92 0.00 46.30 5.19
4792 4917 4.439974 GCGATGATGATGATACCTCTCTCC 60.440 50.000 0.00 0.00 0.00 3.71
4981 5110 2.353011 GGGTGTCGAAATTCGGAGTACA 60.353 50.000 15.76 9.36 40.88 2.90
5000 5129 4.982241 ACCTATCATTACCATCACAGGG 57.018 45.455 0.00 0.00 0.00 4.45
5035 5165 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5037 5167 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5038 5168 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5039 5169 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5040 5170 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5041 5171 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5042 5172 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5043 5173 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5044 5174 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5045 5175 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5046 5176 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5047 5177 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5048 5178 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5049 5179 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5050 5180 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5051 5181 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
5052 5182 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
5053 5183 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
5054 5184 4.501229 GCTGAGAGAGAGAGAGAGAGAGAG 60.501 54.167 0.00 0.00 0.00 3.20
5055 5185 3.386078 GCTGAGAGAGAGAGAGAGAGAGA 59.614 52.174 0.00 0.00 0.00 3.10
5056 5186 3.387374 AGCTGAGAGAGAGAGAGAGAGAG 59.613 52.174 0.00 0.00 0.00 3.20
5057 5187 3.133542 CAGCTGAGAGAGAGAGAGAGAGA 59.866 52.174 8.42 0.00 0.00 3.10
5058 5188 3.133542 TCAGCTGAGAGAGAGAGAGAGAG 59.866 52.174 13.74 0.00 0.00 3.20
5059 5189 3.106827 TCAGCTGAGAGAGAGAGAGAGA 58.893 50.000 13.74 0.00 0.00 3.10
5060 5190 3.548745 TCAGCTGAGAGAGAGAGAGAG 57.451 52.381 13.74 0.00 0.00 3.20
5061 5191 3.998913 TTCAGCTGAGAGAGAGAGAGA 57.001 47.619 17.43 0.00 0.00 3.10
5062 5192 5.009010 GGTAATTCAGCTGAGAGAGAGAGAG 59.991 48.000 17.43 0.00 0.00 3.20
5063 5193 4.887071 GGTAATTCAGCTGAGAGAGAGAGA 59.113 45.833 17.43 0.00 0.00 3.10
5064 5194 4.644234 TGGTAATTCAGCTGAGAGAGAGAG 59.356 45.833 17.43 0.00 0.00 3.20
5090 5220 6.345298 CCAAGTAAACAAAATGGAAACCAGT 58.655 36.000 0.00 0.00 36.75 4.00
5093 5223 4.513692 GGCCAAGTAAACAAAATGGAAACC 59.486 41.667 0.00 0.00 32.82 3.27
5094 5224 4.513692 GGGCCAAGTAAACAAAATGGAAAC 59.486 41.667 4.39 0.00 32.82 2.78
5119 5251 6.819649 ACATTAAGGGAACATGAATGCAAATG 59.180 34.615 0.00 0.00 32.36 2.32
5254 5434 2.093235 AGTATTTGAGGACCTGCTGCTC 60.093 50.000 0.00 0.00 37.85 4.26
5260 5655 4.808414 TCAGTGAGTATTTGAGGACCTG 57.192 45.455 0.00 0.00 0.00 4.00
5268 5663 4.494091 AGGACCCATCAGTGAGTATTTG 57.506 45.455 0.00 0.00 0.00 2.32
5350 5801 9.449719 GCATGCCCTATTATTTAGTACTACAAT 57.550 33.333 6.36 8.44 0.00 2.71
5371 6232 4.158394 TGATTTTTGAAGGTAGAGGCATGC 59.842 41.667 9.90 9.90 0.00 4.06
5426 6287 8.645814 TGGTGTAGAAGTTAGATGAGACTTTA 57.354 34.615 0.00 0.00 36.31 1.85
5485 6348 9.405587 CATTTGGTTTTACACAAAGATTCGTAT 57.594 29.630 0.00 0.00 39.63 3.06
5498 6361 8.242053 TCAAGTTTTACGTCATTTGGTTTTACA 58.758 29.630 0.00 0.00 0.00 2.41
5518 6381 9.956720 CTTGATGAGAAATAACAAAGTCAAGTT 57.043 29.630 0.00 0.00 36.77 2.66
5542 6411 1.127343 GGGTGGCTAGCTCTCATCTT 58.873 55.000 15.72 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.