Multiple sequence alignment - TraesCS3B01G201100

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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 TraesCS3B01G201100 chr3B 100.000 3952 0 0 1 3952 232562374 232566325 0.000000e+00 7299.0
1 TraesCS3B01G201100 chr3B 100.000 1894 0 0 4158 6051 232566531 232568424 0.000000e+00 3498.0
2 TraesCS3B01G201100 chr3B 98.843 951 11 0 3002 3952 785272134 785273084 0.000000e+00 1696.0
3 TraesCS3B01G201100 chr5A 91.829 2056 160 7 866 2918 570228577 570226527 0.000000e+00 2859.0
4 TraesCS3B01G201100 chr5A 90.896 714 58 6 161 871 570229310 570228601 0.000000e+00 952.0
5 TraesCS3B01G201100 chr5A 92.190 589 40 4 5466 6051 570215965 570215380 0.000000e+00 828.0
6 TraesCS3B01G201100 chr5A 94.609 371 20 0 5098 5468 570216366 570215996 5.260000e-160 575.0
7 TraesCS3B01G201100 chr2B 96.033 1689 48 4 4369 6051 11908195 11909870 0.000000e+00 2730.0
8 TraesCS3B01G201100 chr2B 78.494 1009 192 17 992 1984 259685585 259686584 6.610000e-179 638.0
9 TraesCS3B01G201100 chr2B 96.407 334 12 0 2613 2946 11907833 11908166 8.860000e-153 551.0
10 TraesCS3B01G201100 chr2B 75.184 1088 219 43 4377 5446 259687898 259688952 3.300000e-127 466.0
11 TraesCS3B01G201100 chr2B 92.926 311 20 2 87 396 11907518 11907827 9.250000e-123 451.0
12 TraesCS3B01G201100 chr2B 97.917 96 1 1 1 95 11907325 11907420 1.350000e-36 165.0
13 TraesCS3B01G201100 chr2B 93.333 45 3 0 2959 3003 11908164 11908208 3.910000e-07 67.6
14 TraesCS3B01G201100 chr1B 95.807 1407 55 3 1153 2556 662066082 662067487 0.000000e+00 2268.0
15 TraesCS3B01G201100 chr1B 96.085 281 10 1 870 1149 662065202 662065482 1.990000e-124 457.0
16 TraesCS3B01G201100 chr1B 92.593 243 17 1 627 868 662064927 662065169 1.250000e-91 348.0
17 TraesCS3B01G201100 chr3A 98.843 951 11 0 3002 3952 686801147 686800197 0.000000e+00 1696.0
18 TraesCS3B01G201100 chr3A 98.509 939 14 0 3002 3940 27681773 27680835 0.000000e+00 1657.0
19 TraesCS3B01G201100 chr1A 98.741 953 12 0 3000 3952 14611170 14610218 0.000000e+00 1694.0
20 TraesCS3B01G201100 chr1A 98.537 957 13 1 2996 3952 588133509 588132554 0.000000e+00 1688.0
21 TraesCS3B01G201100 chr1A 98.424 952 13 2 3002 3952 587860460 587859510 0.000000e+00 1674.0
22 TraesCS3B01G201100 chr2A 98.528 951 13 1 3002 3952 32519635 32520584 0.000000e+00 1677.0
23 TraesCS3B01G201100 chr2A 98.212 951 17 0 3002 3952 406657006 406657956 0.000000e+00 1663.0
24 TraesCS3B01G201100 chr6B 98.318 951 16 0 3002 3952 13504195 13503245 0.000000e+00 1668.0
25 TraesCS3B01G201100 chr7A 75.912 1781 358 52 982 2713 102055266 102057024 0.000000e+00 846.0
26 TraesCS3B01G201100 chr7A 77.819 1073 209 20 997 2050 675494268 675495330 2.380000e-178 636.0
27 TraesCS3B01G201100 chr7A 76.444 1091 202 40 4371 5443 102057306 102058359 1.920000e-149 540.0
28 TraesCS3B01G201100 chr7A 84.982 273 40 1 5175 5446 675497364 675497636 5.970000e-70 276.0
29 TraesCS3B01G201100 chr7D 74.479 2065 440 62 989 2995 86073182 86071147 0.000000e+00 813.0
30 TraesCS3B01G201100 chrUn 80.745 805 152 2 988 1791 48372808 48372006 5.150000e-175 625.0
31 TraesCS3B01G201100 chrUn 80.693 808 153 2 982 1788 318400779 318401584 5.150000e-175 625.0
32 TraesCS3B01G201100 chr2D 77.622 1068 210 15 997 2044 431392377 431391319 6.660000e-174 621.0
33 TraesCS3B01G201100 chr5B 78.166 458 76 19 4994 5446 126446505 126446943 2.780000e-68 270.0
34 TraesCS3B01G201100 chr5B 76.250 560 89 18 4371 4919 126445608 126446134 2.160000e-64 257.0
35 TraesCS3B01G201100 chr5B 85.039 127 19 0 5681 5807 126447195 126447321 4.920000e-26 130.0


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 TraesCS3B01G201100 chr3B 232562374 232568424 6050 False 5398.500000 7299 100.000000 1 6051 2 chr3B.!!$F2 6050
1 TraesCS3B01G201100 chr3B 785272134 785273084 950 False 1696.000000 1696 98.843000 3002 3952 1 chr3B.!!$F1 950
2 TraesCS3B01G201100 chr5A 570226527 570229310 2783 True 1905.500000 2859 91.362500 161 2918 2 chr5A.!!$R2 2757
3 TraesCS3B01G201100 chr5A 570215380 570216366 986 True 701.500000 828 93.399500 5098 6051 2 chr5A.!!$R1 953
4 TraesCS3B01G201100 chr2B 11907325 11909870 2545 False 792.920000 2730 95.323200 1 6051 5 chr2B.!!$F1 6050
5 TraesCS3B01G201100 chr2B 259685585 259688952 3367 False 552.000000 638 76.839000 992 5446 2 chr2B.!!$F2 4454
6 TraesCS3B01G201100 chr1B 662064927 662067487 2560 False 1024.333333 2268 94.828333 627 2556 3 chr1B.!!$F1 1929
7 TraesCS3B01G201100 chr3A 686800197 686801147 950 True 1696.000000 1696 98.843000 3002 3952 1 chr3A.!!$R2 950
8 TraesCS3B01G201100 chr3A 27680835 27681773 938 True 1657.000000 1657 98.509000 3002 3940 1 chr3A.!!$R1 938
9 TraesCS3B01G201100 chr1A 14610218 14611170 952 True 1694.000000 1694 98.741000 3000 3952 1 chr1A.!!$R1 952
10 TraesCS3B01G201100 chr1A 588132554 588133509 955 True 1688.000000 1688 98.537000 2996 3952 1 chr1A.!!$R3 956
11 TraesCS3B01G201100 chr1A 587859510 587860460 950 True 1674.000000 1674 98.424000 3002 3952 1 chr1A.!!$R2 950
12 TraesCS3B01G201100 chr2A 32519635 32520584 949 False 1677.000000 1677 98.528000 3002 3952 1 chr2A.!!$F1 950
13 TraesCS3B01G201100 chr2A 406657006 406657956 950 False 1663.000000 1663 98.212000 3002 3952 1 chr2A.!!$F2 950
14 TraesCS3B01G201100 chr6B 13503245 13504195 950 True 1668.000000 1668 98.318000 3002 3952 1 chr6B.!!$R1 950
15 TraesCS3B01G201100 chr7A 102055266 102058359 3093 False 693.000000 846 76.178000 982 5443 2 chr7A.!!$F1 4461
16 TraesCS3B01G201100 chr7A 675494268 675497636 3368 False 456.000000 636 81.400500 997 5446 2 chr7A.!!$F2 4449
17 TraesCS3B01G201100 chr7D 86071147 86073182 2035 True 813.000000 813 74.479000 989 2995 1 chr7D.!!$R1 2006
18 TraesCS3B01G201100 chrUn 48372006 48372808 802 True 625.000000 625 80.745000 988 1791 1 chrUn.!!$R1 803
19 TraesCS3B01G201100 chrUn 318400779 318401584 805 False 625.000000 625 80.693000 982 1788 1 chrUn.!!$F1 806
20 TraesCS3B01G201100 chr2D 431391319 431392377 1058 True 621.000000 621 77.622000 997 2044 1 chr2D.!!$R1 1047
21 TraesCS3B01G201100 chr5B 126445608 126447321 1713 False 219.000000 270 79.818333 4371 5807 3 chr5B.!!$F1 1436

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
117 119 0.031314 CTATCGCACGCCTCTGACAT 59.969 55.0 0.0 0.0 0.00 3.06 F
151 153 0.033504 CTCCGCACTTGTACACTGGT 59.966 55.0 0.0 0.0 0.00 4.00 F
1104 1139 0.106519 GTGATGGGGATGGTTCAGGG 60.107 60.0 0.0 0.0 0.00 4.45 F
1691 2405 0.472471 TGGAATTGGGGAGGATACGC 59.528 55.0 0.0 0.0 46.39 4.42 F
2609 3646 0.765510 AGAGGGAAGACACCAACACC 59.234 55.0 0.0 0.0 0.00 4.16 F
4260 5319 0.397957 GAGGAAGGAGGAGGGGAGAC 60.398 65.0 0.0 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 1590 0.173708 CTACTGACGGCTCAACTCCC 59.826 60.000 0.0 0.0 0.00 4.30 R
2121 2852 0.394488 TCCGCACCTGTTGTTTTCCA 60.394 50.000 0.0 0.0 0.00 3.53 R
2199 3214 0.250124 CTGTCGTGGGCTTTGGTGTA 60.250 55.000 0.0 0.0 0.00 2.90 R
2762 3816 1.490910 GATCAAGTAGGGTCAAGGGGG 59.509 57.143 0.0 0.0 0.00 5.40 R
4326 5385 0.252284 TCCAAGACAGACTCCCCTCC 60.252 60.000 0.0 0.0 0.00 4.30 R
5630 7374 0.107214 GGGCAGGCAGTAACTATGCA 60.107 55.000 0.0 0.0 45.68 3.96 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
21 22 2.524394 GGATCCCCGCTGCCTCTA 60.524 66.667 0.00 0.00 0.00 2.43
95 97 1.667724 CGCACATGGAAAGGAAGCTAG 59.332 52.381 0.00 0.00 0.00 3.42
96 98 2.019984 GCACATGGAAAGGAAGCTAGG 58.980 52.381 0.00 0.00 0.00 3.02
99 101 1.213926 CATGGAAAGGAAGCTAGGCCT 59.786 52.381 11.78 11.78 35.61 5.19
100 102 2.263895 TGGAAAGGAAGCTAGGCCTA 57.736 50.000 13.09 13.09 33.20 3.93
101 103 2.776665 TGGAAAGGAAGCTAGGCCTAT 58.223 47.619 14.30 0.00 33.20 2.57
104 106 0.682292 AAGGAAGCTAGGCCTATCGC 59.318 55.000 14.30 14.52 33.20 4.58
105 107 0.470080 AGGAAGCTAGGCCTATCGCA 60.470 55.000 22.24 0.00 40.31 5.10
108 110 2.701163 AAGCTAGGCCTATCGCACGC 62.701 60.000 22.24 16.74 40.31 5.34
109 111 2.049063 CTAGGCCTATCGCACGCC 60.049 66.667 14.30 0.00 43.35 5.68
113 115 2.659897 GCCTATCGCACGCCTCTG 60.660 66.667 0.00 0.00 37.47 3.35
114 116 3.120105 CCTATCGCACGCCTCTGA 58.880 61.111 0.00 0.00 0.00 3.27
115 117 1.299468 CCTATCGCACGCCTCTGAC 60.299 63.158 0.00 0.00 0.00 3.51
116 118 1.433471 CTATCGCACGCCTCTGACA 59.567 57.895 0.00 0.00 0.00 3.58
117 119 0.031314 CTATCGCACGCCTCTGACAT 59.969 55.000 0.00 0.00 0.00 3.06
118 120 0.249031 TATCGCACGCCTCTGACATG 60.249 55.000 0.00 0.00 0.00 3.21
119 121 2.913054 ATCGCACGCCTCTGACATGG 62.913 60.000 0.00 0.00 0.00 3.66
120 122 2.821366 GCACGCCTCTGACATGGG 60.821 66.667 0.00 0.00 0.00 4.00
122 124 4.101448 ACGCCTCTGACATGGGCC 62.101 66.667 0.00 0.00 42.58 5.80
125 127 4.100084 CCTCTGACATGGGCCGCA 62.100 66.667 0.00 0.00 0.00 5.69
126 128 2.821366 CTCTGACATGGGCCGCAC 60.821 66.667 0.00 0.00 0.00 5.34
127 129 3.610619 CTCTGACATGGGCCGCACA 62.611 63.158 0.00 0.00 0.00 4.57
128 130 3.129502 CTGACATGGGCCGCACAG 61.130 66.667 0.00 2.17 0.00 3.66
131 133 4.746309 ACATGGGCCGCACAGCAT 62.746 61.111 0.00 0.00 0.00 3.79
132 134 3.896133 CATGGGCCGCACAGCATC 61.896 66.667 0.00 0.00 0.00 3.91
133 135 4.119363 ATGGGCCGCACAGCATCT 62.119 61.111 0.00 0.00 0.00 2.90
134 136 4.783621 TGGGCCGCACAGCATCTC 62.784 66.667 0.00 0.00 0.00 2.75
139 141 3.857854 CGCACAGCATCTCCGCAC 61.858 66.667 0.00 0.00 0.00 5.34
140 142 2.435586 GCACAGCATCTCCGCACT 60.436 61.111 0.00 0.00 0.00 4.40
141 143 2.037136 GCACAGCATCTCCGCACTT 61.037 57.895 0.00 0.00 0.00 3.16
142 144 1.792301 CACAGCATCTCCGCACTTG 59.208 57.895 0.00 0.00 0.00 3.16
143 145 0.952497 CACAGCATCTCCGCACTTGT 60.952 55.000 0.00 0.00 0.00 3.16
144 146 0.608130 ACAGCATCTCCGCACTTGTA 59.392 50.000 0.00 0.00 0.00 2.41
145 147 1.002366 CAGCATCTCCGCACTTGTAC 58.998 55.000 0.00 0.00 0.00 2.90
146 148 0.608130 AGCATCTCCGCACTTGTACA 59.392 50.000 0.00 0.00 0.00 2.90
147 149 0.721718 GCATCTCCGCACTTGTACAC 59.278 55.000 0.00 0.00 0.00 2.90
148 150 1.673033 GCATCTCCGCACTTGTACACT 60.673 52.381 0.00 0.00 0.00 3.55
149 151 1.995484 CATCTCCGCACTTGTACACTG 59.005 52.381 0.00 0.00 0.00 3.66
150 152 0.317160 TCTCCGCACTTGTACACTGG 59.683 55.000 0.00 0.00 0.00 4.00
151 153 0.033504 CTCCGCACTTGTACACTGGT 59.966 55.000 0.00 0.00 0.00 4.00
152 154 0.249699 TCCGCACTTGTACACTGGTG 60.250 55.000 14.66 14.66 0.00 4.17
153 155 1.227999 CCGCACTTGTACACTGGTGG 61.228 60.000 18.33 12.52 34.19 4.61
154 156 1.227999 CGCACTTGTACACTGGTGGG 61.228 60.000 18.26 18.26 36.59 4.61
155 157 1.515521 GCACTTGTACACTGGTGGGC 61.516 60.000 18.33 7.41 34.19 5.36
156 158 0.108585 CACTTGTACACTGGTGGGCT 59.891 55.000 12.35 0.00 34.19 5.19
157 159 0.108585 ACTTGTACACTGGTGGGCTG 59.891 55.000 0.00 0.00 34.19 4.85
158 160 0.108585 CTTGTACACTGGTGGGCTGT 59.891 55.000 0.00 0.00 34.19 4.40
159 161 1.346395 CTTGTACACTGGTGGGCTGTA 59.654 52.381 0.00 0.00 34.19 2.74
160 162 1.651737 TGTACACTGGTGGGCTGTAT 58.348 50.000 5.70 0.00 34.19 2.29
161 163 1.982226 TGTACACTGGTGGGCTGTATT 59.018 47.619 5.70 0.00 34.19 1.89
162 164 2.373836 TGTACACTGGTGGGCTGTATTT 59.626 45.455 5.70 0.00 34.19 1.40
163 165 2.675658 ACACTGGTGGGCTGTATTTT 57.324 45.000 5.70 0.00 34.19 1.82
164 166 3.799432 ACACTGGTGGGCTGTATTTTA 57.201 42.857 5.70 0.00 34.19 1.52
190 192 1.080705 GTACCAGCGCGAAGACTGT 60.081 57.895 12.10 0.00 31.76 3.55
290 292 5.359009 CAGCATTGACCATGGAAGAACTAAT 59.641 40.000 21.47 5.06 32.81 1.73
325 327 9.158233 TCTATTCAGTTTACCGTTTAATTGAGG 57.842 33.333 0.00 0.00 0.00 3.86
329 331 8.674263 TCAGTTTACCGTTTAATTGAGGTTTA 57.326 30.769 0.00 0.00 38.12 2.01
330 332 9.287373 TCAGTTTACCGTTTAATTGAGGTTTAT 57.713 29.630 0.00 0.00 38.12 1.40
376 378 6.260936 AGGTTAACTGCAATACTATCATGCAC 59.739 38.462 5.42 0.00 44.52 4.57
395 397 3.256631 GCACAATCTGTTCCAAATCCTGT 59.743 43.478 0.00 0.00 0.00 4.00
400 402 0.400213 TGTTCCAAATCCTGTCCGCT 59.600 50.000 0.00 0.00 0.00 5.52
406 408 1.667724 CAAATCCTGTCCGCTCATGAC 59.332 52.381 0.00 0.00 0.00 3.06
439 441 4.925646 GGAACACAAAATCAGCCTCAAATC 59.074 41.667 0.00 0.00 0.00 2.17
445 447 4.811969 AAATCAGCCTCAAATCATGCAA 57.188 36.364 0.00 0.00 0.00 4.08
464 466 3.049206 CAACGAAACACGCCATTCAATT 58.951 40.909 0.00 0.00 46.94 2.32
471 473 2.487762 ACACGCCATTCAATTGGTAGTG 59.512 45.455 5.42 14.86 45.00 2.74
491 493 5.858381 AGTGTGATTACGCAGATCCATAAT 58.142 37.500 3.84 0.00 39.77 1.28
525 527 5.722021 AAACACATTTATGTTGGGAGACC 57.278 39.130 0.00 0.00 45.92 3.85
539 541 2.222027 GGAGACCAGTGAACACTTTGG 58.778 52.381 4.63 7.99 40.20 3.28
553 555 5.705609 ACACTTTGGCATAATCTCGTTTT 57.294 34.783 0.00 0.00 0.00 2.43
593 595 5.633830 AACAGCTAATTCAGTGTCAATGG 57.366 39.130 0.00 0.00 0.00 3.16
602 604 1.206578 GTGTCAATGGTTCACGCGG 59.793 57.895 12.47 0.00 0.00 6.46
603 605 1.227704 TGTCAATGGTTCACGCGGT 60.228 52.632 12.47 0.00 0.00 5.68
620 622 1.377333 GTAGGCCAGGTTCTGTGCC 60.377 63.158 5.01 15.01 43.30 5.01
640 642 1.355210 CGTGGAACAGTTTTGCGCT 59.645 52.632 9.73 0.00 41.80 5.92
643 645 1.065600 GGAACAGTTTTGCGCTGCA 59.934 52.632 9.73 0.00 37.47 4.41
647 649 1.659335 CAGTTTTGCGCTGCACAGG 60.659 57.895 9.73 0.00 38.71 4.00
648 650 2.120909 AGTTTTGCGCTGCACAGGT 61.121 52.632 9.73 0.00 38.71 4.00
655 657 1.595109 CGCTGCACAGGTCTGTTCA 60.595 57.895 0.20 2.16 42.83 3.18
663 665 0.387367 CAGGTCTGTTCACTCGTCCG 60.387 60.000 0.00 0.00 0.00 4.79
670 672 1.881324 TGTTCACTCGTCCGTGATACA 59.119 47.619 5.96 9.36 42.91 2.29
754 756 1.153862 CTCGCTCTGCTTCTTCGCT 60.154 57.895 0.00 0.00 0.00 4.93
843 846 1.494960 GGCAAGGATCACTCTCCTCT 58.505 55.000 0.00 0.00 45.15 3.69
896 930 2.266279 CGGATAGGTACCCCATTCCAT 58.734 52.381 8.74 0.00 35.02 3.41
897 931 2.236395 CGGATAGGTACCCCATTCCATC 59.764 54.545 8.74 0.61 35.02 3.51
1058 1093 6.227522 TGGTTGTCAATCGATTAGAGAACAA 58.772 36.000 29.33 23.49 37.30 2.83
1104 1139 0.106519 GTGATGGGGATGGTTCAGGG 60.107 60.000 0.00 0.00 0.00 4.45
1108 1143 3.346734 GGGATGGTTCAGGGGGCA 61.347 66.667 0.00 0.00 0.00 5.36
1121 1156 2.133641 GGGGCACAACTGGTTTGCT 61.134 57.895 3.61 0.00 39.01 3.91
1240 1420 3.470709 GGATTCGATGGAATGCTTGAGA 58.529 45.455 13.51 0.00 44.76 3.27
1282 1462 7.985184 AGATCAACCTGAAATACAACGCTTATA 59.015 33.333 0.00 0.00 0.00 0.98
1309 1489 6.561737 TGGATAGAGTCGATGTAGATTCAC 57.438 41.667 0.00 0.00 30.44 3.18
1357 1537 6.655003 AGGTGTTATTGAACTATGTGACAAGG 59.345 38.462 0.00 0.00 36.45 3.61
1410 1590 2.797156 CGATTCAACCATAGAAGGCGAG 59.203 50.000 0.00 0.00 32.18 5.03
1427 2061 1.534235 AGGGAGTTGAGCCGTCAGT 60.534 57.895 0.00 0.00 32.98 3.41
1451 2085 1.948104 TGCATTGAGTATACCCGTGC 58.052 50.000 0.00 6.26 0.00 5.34
1594 2308 7.099764 TGTTATTTTTGTTGTTGGTCATGTGT 58.900 30.769 0.00 0.00 0.00 3.72
1691 2405 0.472471 TGGAATTGGGGAGGATACGC 59.528 55.000 0.00 0.00 46.39 4.42
1867 2598 3.497262 CGCACATGCTCACATATGATTCT 59.503 43.478 10.38 0.00 32.09 2.40
1868 2599 4.687483 CGCACATGCTCACATATGATTCTA 59.313 41.667 10.38 0.00 32.09 2.10
1869 2600 5.178067 CGCACATGCTCACATATGATTCTAA 59.822 40.000 10.38 0.00 32.09 2.10
2115 2846 5.989777 AGTACTACATCAAAACACGCTTCTT 59.010 36.000 0.00 0.00 0.00 2.52
2118 2849 5.989777 ACTACATCAAAACACGCTTCTTACT 59.010 36.000 0.00 0.00 0.00 2.24
2120 2851 6.131544 ACATCAAAACACGCTTCTTACTTT 57.868 33.333 0.00 0.00 0.00 2.66
2121 2852 6.560711 ACATCAAAACACGCTTCTTACTTTT 58.439 32.000 0.00 0.00 0.00 2.27
2172 3187 3.454375 CGTGAGAAACCTAAGTGTGTGT 58.546 45.455 0.00 0.00 0.00 3.72
2279 3300 3.211045 GGAATAGCTATGCCAAAACCGA 58.789 45.455 24.17 0.00 31.18 4.69
2358 3379 4.895668 AAAGCCATTGTCCATGTTCATT 57.104 36.364 0.00 0.00 0.00 2.57
2441 3478 1.239968 AACTCGGCGTACTTCTCCGT 61.240 55.000 6.85 0.00 43.86 4.69
2530 3567 6.233434 TCACTTTCACTGACAAGCTAATGAT 58.767 36.000 0.00 0.00 0.00 2.45
2603 3640 3.604582 CATCTTGAAGAGGGAAGACACC 58.395 50.000 0.00 0.00 31.09 4.16
2609 3646 0.765510 AGAGGGAAGACACCAACACC 59.234 55.000 0.00 0.00 0.00 4.16
2752 3806 7.730364 AAAATCATACAAGCGACCTTATAGG 57.270 36.000 0.00 0.00 42.49 2.57
2755 3809 4.280174 TCATACAAGCGACCTTATAGGACC 59.720 45.833 0.00 0.00 37.67 4.46
2762 3816 2.557490 CGACCTTATAGGACCTAGGCAC 59.443 54.545 9.30 1.27 37.67 5.01
2823 3881 1.598130 GCGAACAGCCCTGTGTCTT 60.598 57.895 1.07 0.00 44.13 3.01
2881 3939 4.518970 GTCAGGCACATCAAAGAAAACCTA 59.481 41.667 0.00 0.00 0.00 3.08
2897 3955 1.893137 ACCTACTCACGTGATCAGCAA 59.107 47.619 20.40 0.00 0.00 3.91
2901 3959 1.546029 ACTCACGTGATCAGCAAGCTA 59.454 47.619 20.40 0.00 0.00 3.32
2947 4005 1.699083 TCAGAGCCCACACAATCAGAA 59.301 47.619 0.00 0.00 0.00 3.02
2957 4015 4.525996 CACACAATCAGAACCCCATATCA 58.474 43.478 0.00 0.00 0.00 2.15
2964 4022 4.826616 TCAGAACCCCATATCACAGGATA 58.173 43.478 0.00 0.00 40.17 2.59
2993 4051 7.394359 ACCATAATGGAAATCGCTAGCAATATT 59.606 33.333 16.45 8.24 40.96 1.28
2997 4055 4.211164 TGGAAATCGCTAGCAATATTGTCG 59.789 41.667 16.45 13.95 0.00 4.35
2998 4056 3.795561 AATCGCTAGCAATATTGTCGC 57.204 42.857 16.45 14.29 0.00 5.19
3876 4935 2.273179 CGACGGAGAGGAACCACCA 61.273 63.158 0.00 0.00 42.04 4.17
4174 5233 4.436998 AACGCGCGGAGGAGGAAG 62.437 66.667 35.22 1.83 0.00 3.46
4176 5235 4.560856 CGCGCGGAGGAGGAAGAG 62.561 72.222 24.84 0.00 0.00 2.85
4177 5236 4.882396 GCGCGGAGGAGGAAGAGC 62.882 72.222 8.83 0.00 0.00 4.09
4178 5237 3.452786 CGCGGAGGAGGAAGAGCA 61.453 66.667 0.00 0.00 0.00 4.26
4179 5238 2.498726 GCGGAGGAGGAAGAGCAG 59.501 66.667 0.00 0.00 0.00 4.24
4180 5239 3.087666 GCGGAGGAGGAAGAGCAGG 62.088 68.421 0.00 0.00 0.00 4.85
4181 5240 2.430610 CGGAGGAGGAAGAGCAGGG 61.431 68.421 0.00 0.00 0.00 4.45
4182 5241 2.741055 GGAGGAGGAAGAGCAGGGC 61.741 68.421 0.00 0.00 0.00 5.19
4183 5242 2.690510 AGGAGGAAGAGCAGGGCC 60.691 66.667 0.00 0.00 0.00 5.80
4184 5243 3.803162 GGAGGAAGAGCAGGGCCC 61.803 72.222 16.46 16.46 0.00 5.80
4185 5244 3.803162 GAGGAAGAGCAGGGCCCC 61.803 72.222 21.43 3.37 0.00 5.80
4250 5309 3.532155 CGGCGAGGGAGGAAGGAG 61.532 72.222 0.00 0.00 0.00 3.69
4251 5310 3.157949 GGCGAGGGAGGAAGGAGG 61.158 72.222 0.00 0.00 0.00 4.30
4252 5311 2.042843 GCGAGGGAGGAAGGAGGA 60.043 66.667 0.00 0.00 0.00 3.71
4253 5312 2.131067 GCGAGGGAGGAAGGAGGAG 61.131 68.421 0.00 0.00 0.00 3.69
4254 5313 1.456705 CGAGGGAGGAAGGAGGAGG 60.457 68.421 0.00 0.00 0.00 4.30
4255 5314 1.074850 GAGGGAGGAAGGAGGAGGG 60.075 68.421 0.00 0.00 0.00 4.30
4256 5315 2.040359 GGGAGGAAGGAGGAGGGG 60.040 72.222 0.00 0.00 0.00 4.79
4257 5316 2.647949 GGGAGGAAGGAGGAGGGGA 61.648 68.421 0.00 0.00 0.00 4.81
4258 5317 1.074850 GGAGGAAGGAGGAGGGGAG 60.075 68.421 0.00 0.00 0.00 4.30
4259 5318 1.595058 GGAGGAAGGAGGAGGGGAGA 61.595 65.000 0.00 0.00 0.00 3.71
4260 5319 0.397957 GAGGAAGGAGGAGGGGAGAC 60.398 65.000 0.00 0.00 0.00 3.36
4340 5399 2.365768 GGGGGAGGGGAGTCTGTC 60.366 72.222 0.00 0.00 0.00 3.51
4341 5400 2.781406 GGGGAGGGGAGTCTGTCT 59.219 66.667 0.00 0.00 0.00 3.41
4342 5401 1.081277 GGGGAGGGGAGTCTGTCTT 59.919 63.158 0.00 0.00 0.00 3.01
4343 5402 1.268283 GGGGAGGGGAGTCTGTCTTG 61.268 65.000 0.00 0.00 0.00 3.02
4344 5403 1.268283 GGGAGGGGAGTCTGTCTTGG 61.268 65.000 0.00 0.00 0.00 3.61
4345 5404 0.252284 GGAGGGGAGTCTGTCTTGGA 60.252 60.000 0.00 0.00 0.00 3.53
4346 5405 1.645710 GAGGGGAGTCTGTCTTGGAA 58.354 55.000 0.00 0.00 0.00 3.53
4347 5406 1.978580 GAGGGGAGTCTGTCTTGGAAA 59.021 52.381 0.00 0.00 0.00 3.13
4349 5408 1.003696 GGGGAGTCTGTCTTGGAAAGG 59.996 57.143 0.00 0.00 46.24 3.11
4350 5409 1.700186 GGGAGTCTGTCTTGGAAAGGT 59.300 52.381 0.00 0.00 46.24 3.50
4351 5410 2.551071 GGGAGTCTGTCTTGGAAAGGTG 60.551 54.545 0.00 0.00 46.24 4.00
4352 5411 2.104963 GGAGTCTGTCTTGGAAAGGTGT 59.895 50.000 0.00 0.00 46.24 4.16
4353 5412 3.394719 GAGTCTGTCTTGGAAAGGTGTC 58.605 50.000 0.00 0.00 46.24 3.67
4354 5413 2.771943 AGTCTGTCTTGGAAAGGTGTCA 59.228 45.455 0.00 0.00 46.24 3.58
4355 5414 2.872858 GTCTGTCTTGGAAAGGTGTCAC 59.127 50.000 0.00 0.00 46.24 3.67
4356 5415 2.771943 TCTGTCTTGGAAAGGTGTCACT 59.228 45.455 2.35 0.00 46.24 3.41
4357 5416 2.874701 CTGTCTTGGAAAGGTGTCACTG 59.125 50.000 2.35 0.00 46.24 3.66
4358 5417 2.238646 TGTCTTGGAAAGGTGTCACTGT 59.761 45.455 2.35 0.00 46.24 3.55
4359 5418 2.872858 GTCTTGGAAAGGTGTCACTGTC 59.127 50.000 2.35 0.00 46.24 3.51
4360 5419 1.867233 CTTGGAAAGGTGTCACTGTCG 59.133 52.381 2.35 0.00 41.27 4.35
4361 5420 0.828022 TGGAAAGGTGTCACTGTCGT 59.172 50.000 2.35 0.00 0.00 4.34
4362 5421 1.217882 GGAAAGGTGTCACTGTCGTG 58.782 55.000 2.35 0.00 42.59 4.35
4363 5422 1.472728 GGAAAGGTGTCACTGTCGTGT 60.473 52.381 2.35 0.00 41.89 4.49
4364 5423 1.593006 GAAAGGTGTCACTGTCGTGTG 59.407 52.381 2.35 0.00 41.89 3.82
4365 5424 0.821517 AAGGTGTCACTGTCGTGTGA 59.178 50.000 2.35 5.00 43.72 3.58
4366 5425 1.040646 AGGTGTCACTGTCGTGTGAT 58.959 50.000 2.35 0.00 46.77 3.06
4367 5426 1.000163 AGGTGTCACTGTCGTGTGATC 60.000 52.381 2.35 0.00 46.77 2.92
4368 5427 1.269569 GGTGTCACTGTCGTGTGATCA 60.270 52.381 2.35 0.00 46.77 2.92
4369 5428 2.610479 GGTGTCACTGTCGTGTGATCAT 60.610 50.000 0.00 0.00 46.77 2.45
4375 5434 5.004821 GTCACTGTCGTGTGATCATATTGTC 59.995 44.000 0.00 0.00 46.77 3.18
4465 5524 4.008330 TCGTTTTGTTTGGGTCAACTACA 58.992 39.130 0.00 0.00 0.00 2.74
4644 5703 2.948979 CCATTACCGAGCCAGCAAATTA 59.051 45.455 0.00 0.00 0.00 1.40
4663 5722 8.594687 GCAAATTACATATGTGTCATCAAAACC 58.405 33.333 18.81 0.00 39.77 3.27
4679 5738 6.716934 TCAAAACCACTTTATAGTTTGCCA 57.283 33.333 0.00 0.00 34.12 4.92
4694 5753 4.281688 AGTTTGCCACACTCTAAAATGCAT 59.718 37.500 0.00 0.00 0.00 3.96
4696 5755 5.973899 TTGCCACACTCTAAAATGCATTA 57.026 34.783 13.39 0.00 0.00 1.90
4782 6134 3.057969 TGAAATCCATCGACAGCTTGT 57.942 42.857 0.00 0.00 0.00 3.16
4871 6223 1.938585 ATTCTCGAAGGACACTCCCA 58.061 50.000 0.00 0.00 37.19 4.37
4943 6295 8.159344 TGTTTCACAAAGTTTTCATTTTGGTT 57.841 26.923 2.54 0.00 38.33 3.67
4954 6306 4.599047 TCATTTTGGTTGTGTCCCATTC 57.401 40.909 0.00 0.00 0.00 2.67
4959 6311 0.598065 GGTTGTGTCCCATTCTGCAC 59.402 55.000 0.00 0.00 0.00 4.57
4962 6314 2.741985 TGTCCCATTCTGCACGCG 60.742 61.111 3.53 3.53 0.00 6.01
4972 6324 2.512745 TGCACGCGTTTCACCACT 60.513 55.556 10.22 0.00 0.00 4.00
4974 6326 2.935955 CACGCGTTTCACCACTCC 59.064 61.111 10.22 0.00 0.00 3.85
5004 6680 6.268158 TCCCTTGTGTTATGTGTAGACAACTA 59.732 38.462 0.00 0.00 35.11 2.24
5190 6875 3.932710 CGTTTGTATGCAGTGGTACATCT 59.067 43.478 0.00 0.00 44.52 2.90
5382 7067 3.423539 TCTTTAGCTCATGGCACTGTT 57.576 42.857 8.58 0.00 44.79 3.16
5630 7374 2.520741 CCCAACCCCGCAAACACT 60.521 61.111 0.00 0.00 0.00 3.55
5644 7388 4.083581 CAAACACTGCATAGTTACTGCC 57.916 45.455 4.57 0.00 38.89 4.85
5648 7392 1.303309 CTGCATAGTTACTGCCTGCC 58.697 55.000 11.75 0.00 38.89 4.85
5654 7409 1.549203 AGTTACTGCCTGCCCAAATG 58.451 50.000 0.00 0.00 0.00 2.32
5655 7410 1.075374 AGTTACTGCCTGCCCAAATGA 59.925 47.619 0.00 0.00 0.00 2.57
5659 7414 1.565759 ACTGCCTGCCCAAATGATCTA 59.434 47.619 0.00 0.00 0.00 1.98
5660 7415 1.952296 CTGCCTGCCCAAATGATCTAC 59.048 52.381 0.00 0.00 0.00 2.59
5661 7416 1.565759 TGCCTGCCCAAATGATCTACT 59.434 47.619 0.00 0.00 0.00 2.57
5662 7417 2.777114 TGCCTGCCCAAATGATCTACTA 59.223 45.455 0.00 0.00 0.00 1.82
5663 7418 3.201930 TGCCTGCCCAAATGATCTACTAA 59.798 43.478 0.00 0.00 0.00 2.24
5664 7419 4.207165 GCCTGCCCAAATGATCTACTAAA 58.793 43.478 0.00 0.00 0.00 1.85
5665 7420 4.036852 GCCTGCCCAAATGATCTACTAAAC 59.963 45.833 0.00 0.00 0.00 2.01
5838 7600 4.811024 TGATCGGTCTGCTCATGTAATTTC 59.189 41.667 0.00 0.00 0.00 2.17
5844 7606 6.562270 CGGTCTGCTCATGTAATTTCGATTAC 60.562 42.308 2.58 2.58 37.49 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 98 2.659897 CAGAGGCGTGCGATAGGC 60.660 66.667 0.00 0.00 43.96 3.93
99 101 0.249031 CATGTCAGAGGCGTGCGATA 60.249 55.000 0.00 0.00 0.00 2.92
100 102 1.520120 CATGTCAGAGGCGTGCGAT 60.520 57.895 0.00 0.00 0.00 4.58
101 103 2.125952 CATGTCAGAGGCGTGCGA 60.126 61.111 0.00 0.00 0.00 5.10
104 106 2.821366 GCCCATGTCAGAGGCGTG 60.821 66.667 0.41 0.00 36.84 5.34
108 110 4.100084 TGCGGCCCATGTCAGAGG 62.100 66.667 0.00 0.00 0.00 3.69
109 111 2.821366 GTGCGGCCCATGTCAGAG 60.821 66.667 0.00 0.00 0.00 3.35
110 112 3.610619 CTGTGCGGCCCATGTCAGA 62.611 63.158 0.00 0.00 0.00 3.27
111 113 3.129502 CTGTGCGGCCCATGTCAG 61.130 66.667 0.00 0.00 0.00 3.51
114 116 4.746309 ATGCTGTGCGGCCCATGT 62.746 61.111 0.00 0.00 0.00 3.21
115 117 3.896133 GATGCTGTGCGGCCCATG 61.896 66.667 0.00 0.00 0.00 3.66
116 118 4.119363 AGATGCTGTGCGGCCCAT 62.119 61.111 0.00 0.00 0.00 4.00
117 119 4.783621 GAGATGCTGTGCGGCCCA 62.784 66.667 0.00 0.00 0.00 5.36
122 124 3.857854 GTGCGGAGATGCTGTGCG 61.858 66.667 0.00 0.00 35.36 5.34
123 125 2.037136 AAGTGCGGAGATGCTGTGC 61.037 57.895 0.00 0.00 35.36 4.57
124 126 0.952497 ACAAGTGCGGAGATGCTGTG 60.952 55.000 0.00 0.00 35.36 3.66
125 127 0.608130 TACAAGTGCGGAGATGCTGT 59.392 50.000 0.00 0.00 35.36 4.40
126 128 1.002366 GTACAAGTGCGGAGATGCTG 58.998 55.000 0.00 0.00 35.36 4.41
127 129 0.608130 TGTACAAGTGCGGAGATGCT 59.392 50.000 0.00 0.00 35.36 3.79
128 130 0.721718 GTGTACAAGTGCGGAGATGC 59.278 55.000 0.00 0.00 0.00 3.91
129 131 1.995484 CAGTGTACAAGTGCGGAGATG 59.005 52.381 0.00 0.00 0.00 2.90
130 132 1.066858 CCAGTGTACAAGTGCGGAGAT 60.067 52.381 0.00 0.00 0.00 2.75
131 133 0.317160 CCAGTGTACAAGTGCGGAGA 59.683 55.000 0.00 0.00 0.00 3.71
132 134 0.033504 ACCAGTGTACAAGTGCGGAG 59.966 55.000 0.00 0.00 0.00 4.63
133 135 0.249699 CACCAGTGTACAAGTGCGGA 60.250 55.000 0.00 0.00 0.00 5.54
134 136 1.227999 CCACCAGTGTACAAGTGCGG 61.228 60.000 13.75 7.31 0.00 5.69
135 137 1.227999 CCCACCAGTGTACAAGTGCG 61.228 60.000 13.75 4.86 0.00 5.34
136 138 1.515521 GCCCACCAGTGTACAAGTGC 61.516 60.000 13.75 3.51 0.00 4.40
137 139 0.108585 AGCCCACCAGTGTACAAGTG 59.891 55.000 12.69 12.69 0.00 3.16
138 140 0.108585 CAGCCCACCAGTGTACAAGT 59.891 55.000 0.00 0.00 0.00 3.16
139 141 0.108585 ACAGCCCACCAGTGTACAAG 59.891 55.000 0.00 0.00 0.00 3.16
140 142 1.425694 TACAGCCCACCAGTGTACAA 58.574 50.000 0.00 0.00 0.00 2.41
141 143 1.651737 ATACAGCCCACCAGTGTACA 58.348 50.000 0.00 0.00 29.67 2.90
142 144 2.781681 AATACAGCCCACCAGTGTAC 57.218 50.000 0.00 0.00 29.67 2.90
143 145 3.799432 AAAATACAGCCCACCAGTGTA 57.201 42.857 0.00 0.00 0.00 2.90
144 146 2.675658 AAAATACAGCCCACCAGTGT 57.324 45.000 0.00 0.00 0.00 3.55
145 147 4.336433 CAGATAAAATACAGCCCACCAGTG 59.664 45.833 0.00 0.00 0.00 3.66
146 148 4.526970 CAGATAAAATACAGCCCACCAGT 58.473 43.478 0.00 0.00 0.00 4.00
147 149 3.316308 GCAGATAAAATACAGCCCACCAG 59.684 47.826 0.00 0.00 0.00 4.00
148 150 3.287222 GCAGATAAAATACAGCCCACCA 58.713 45.455 0.00 0.00 0.00 4.17
149 151 3.287222 TGCAGATAAAATACAGCCCACC 58.713 45.455 0.00 0.00 0.00 4.61
150 152 4.339247 ACATGCAGATAAAATACAGCCCAC 59.661 41.667 0.00 0.00 0.00 4.61
151 153 4.535781 ACATGCAGATAAAATACAGCCCA 58.464 39.130 0.00 0.00 0.00 5.36
152 154 5.048713 GGTACATGCAGATAAAATACAGCCC 60.049 44.000 0.00 0.00 0.00 5.19
153 155 5.530915 TGGTACATGCAGATAAAATACAGCC 59.469 40.000 0.00 0.00 0.00 4.85
154 156 6.618287 TGGTACATGCAGATAAAATACAGC 57.382 37.500 0.00 0.00 0.00 4.40
155 157 6.564686 CGCTGGTACATGCAGATAAAATACAG 60.565 42.308 9.44 0.00 38.20 2.74
156 158 5.236263 CGCTGGTACATGCAGATAAAATACA 59.764 40.000 9.44 0.00 38.20 2.29
157 159 5.679906 CGCTGGTACATGCAGATAAAATAC 58.320 41.667 9.44 0.00 38.20 1.89
158 160 4.213270 GCGCTGGTACATGCAGATAAAATA 59.787 41.667 0.00 0.00 39.07 1.40
159 161 3.003689 GCGCTGGTACATGCAGATAAAAT 59.996 43.478 0.00 0.00 39.07 1.82
160 162 2.354510 GCGCTGGTACATGCAGATAAAA 59.645 45.455 0.00 0.00 39.07 1.52
161 163 1.939934 GCGCTGGTACATGCAGATAAA 59.060 47.619 0.00 0.00 39.07 1.40
162 164 1.581934 GCGCTGGTACATGCAGATAA 58.418 50.000 0.00 0.00 39.07 1.75
163 165 0.597377 CGCGCTGGTACATGCAGATA 60.597 55.000 5.56 0.00 39.17 1.98
164 166 1.884464 CGCGCTGGTACATGCAGAT 60.884 57.895 5.56 0.00 39.17 2.90
190 192 4.173256 CACATGATTGTGCTAGTACGTGA 58.827 43.478 6.48 0.00 46.20 4.35
219 221 4.357947 GACGTGGCTCTCCGCACA 62.358 66.667 0.00 0.00 43.01 4.57
259 261 3.443045 GGTCAATGCTGGGCCACG 61.443 66.667 0.00 0.00 0.00 4.94
269 271 6.038356 GCAATTAGTTCTTCCATGGTCAATG 58.962 40.000 12.58 0.00 35.89 2.82
290 292 7.045416 ACGGTAAACTGAATAGATATGTGCAA 58.955 34.615 0.00 0.00 0.00 4.08
305 307 9.902196 AATAAACCTCAATTAAACGGTAAACTG 57.098 29.630 0.00 0.00 0.00 3.16
336 338 6.672147 CAGTTAACCTCTTGATTGTTCCAAG 58.328 40.000 0.88 0.00 41.63 3.61
339 341 4.518970 TGCAGTTAACCTCTTGATTGTTCC 59.481 41.667 0.88 0.00 0.00 3.62
349 351 6.708054 GCATGATAGTATTGCAGTTAACCTCT 59.292 38.462 0.88 0.00 36.40 3.69
376 378 3.127548 CGGACAGGATTTGGAACAGATTG 59.872 47.826 0.00 0.00 42.39 2.67
395 397 1.271325 ACAAATGTGGTCATGAGCGGA 60.271 47.619 19.36 9.07 34.19 5.54
430 432 2.634982 TTCGTTGCATGATTTGAGGC 57.365 45.000 0.00 0.00 0.00 4.70
439 441 0.387112 ATGGCGTGTTTCGTTGCATG 60.387 50.000 0.00 0.00 42.13 4.06
445 447 2.606795 CCAATTGAATGGCGTGTTTCGT 60.607 45.455 7.12 0.00 42.13 3.85
464 466 3.181479 GGATCTGCGTAATCACACTACCA 60.181 47.826 0.00 0.00 0.00 3.25
505 507 4.202567 ACTGGTCTCCCAACATAAATGTGT 60.203 41.667 0.00 0.00 41.27 3.72
513 515 1.774254 TGTTCACTGGTCTCCCAACAT 59.226 47.619 0.00 0.00 41.27 2.71
525 527 5.633830 AGATTATGCCAAAGTGTTCACTG 57.366 39.130 6.22 0.00 0.00 3.66
532 534 4.324402 GCAAAACGAGATTATGCCAAAGTG 59.676 41.667 0.00 0.00 0.00 3.16
533 535 4.485163 GCAAAACGAGATTATGCCAAAGT 58.515 39.130 0.00 0.00 0.00 2.66
539 541 2.825086 ACGGCAAAACGAGATTATGC 57.175 45.000 0.00 0.00 37.61 3.14
578 580 3.304659 GCGTGAACCATTGACACTGAATT 60.305 43.478 0.00 0.00 33.13 2.17
593 595 2.813908 CTGGCCTACCGCGTGAAC 60.814 66.667 3.32 0.00 39.70 3.18
602 604 1.377333 GGCACAGAACCTGGCCTAC 60.377 63.158 3.32 0.00 41.35 3.18
603 605 2.954684 CGGCACAGAACCTGGCCTA 61.955 63.158 3.32 0.00 41.92 3.93
620 622 2.003443 CGCAAAACTGTTCCACGCG 61.003 57.895 3.53 3.53 34.89 6.01
632 634 1.823470 AGACCTGTGCAGCGCAAAA 60.823 52.632 11.47 0.00 41.47 2.44
640 642 0.249447 CGAGTGAACAGACCTGTGCA 60.249 55.000 6.73 6.73 46.37 4.57
647 649 0.309922 TCACGGACGAGTGAACAGAC 59.690 55.000 9.79 0.00 46.81 3.51
648 650 2.710440 TCACGGACGAGTGAACAGA 58.290 52.632 9.79 0.00 46.81 3.41
655 657 2.846039 GTGATGTATCACGGACGAGT 57.154 50.000 9.04 0.00 46.46 4.18
670 672 3.302434 CGTAGTAAATTGCGTGACGTGAT 59.698 43.478 6.91 0.00 0.00 3.06
754 756 1.001393 GGTGGATTTCCCTTCCGCA 60.001 57.895 5.71 0.00 44.03 5.69
804 807 2.693762 CCGCCCAGTAGTTCGACGA 61.694 63.158 0.00 0.00 0.00 4.20
868 871 0.468648 GGTACCTATCCGCTTTGCCT 59.531 55.000 4.06 0.00 0.00 4.75
896 930 1.893062 CAGCAGATCGTGAGTGGGA 59.107 57.895 0.00 0.00 0.00 4.37
897 931 1.812922 GCAGCAGATCGTGAGTGGG 60.813 63.158 0.00 0.00 0.00 4.61
1058 1093 0.537188 ATCTTCGGGCGACTGTTCAT 59.463 50.000 0.00 0.00 38.16 2.57
1104 1139 0.530431 CAAGCAAACCAGTTGTGCCC 60.530 55.000 11.48 0.00 39.63 5.36
1108 1143 3.181476 GGTGATTCAAGCAAACCAGTTGT 60.181 43.478 0.00 0.00 39.63 3.32
1121 1156 3.252215 GGACGTGAAACATGGTGATTCAA 59.748 43.478 0.00 0.00 40.11 2.69
1240 1420 6.837568 AGGTTGATCTTCTGCCATGATTTTAT 59.162 34.615 0.00 0.00 0.00 1.40
1282 1462 9.467796 TGAATCTACATCGACTCTATCCATTAT 57.532 33.333 0.00 0.00 0.00 1.28
1309 1489 5.839262 TGGCGCTCAAGATTTATTATACG 57.161 39.130 7.64 0.00 0.00 3.06
1357 1537 5.750067 GGATGCCAAACACATAATTCATGTC 59.250 40.000 0.00 0.00 44.99 3.06
1410 1590 0.173708 CTACTGACGGCTCAACTCCC 59.826 60.000 0.00 0.00 0.00 4.30
1427 2061 3.386726 ACGGGTATACTCAATGCAAGCTA 59.613 43.478 3.12 0.00 0.00 3.32
1625 2339 3.444742 CAGTGCAGCCCAGAAATCAATTA 59.555 43.478 0.00 0.00 0.00 1.40
1867 2598 5.050227 GCTGCAAATGAAAACAACAGCATTA 60.050 36.000 7.18 0.00 46.28 1.90
1868 2599 4.260866 GCTGCAAATGAAAACAACAGCATT 60.261 37.500 7.18 0.00 46.28 3.56
1869 2600 3.249080 GCTGCAAATGAAAACAACAGCAT 59.751 39.130 7.18 0.00 46.28 3.79
2115 2846 4.675671 CGCACCTGTTGTTTTCCAAAAGTA 60.676 41.667 0.00 0.00 36.76 2.24
2118 2849 2.611518 CGCACCTGTTGTTTTCCAAAA 58.388 42.857 0.00 0.00 34.07 2.44
2120 2851 0.457851 CCGCACCTGTTGTTTTCCAA 59.542 50.000 0.00 0.00 0.00 3.53
2121 2852 0.394488 TCCGCACCTGTTGTTTTCCA 60.394 50.000 0.00 0.00 0.00 3.53
2172 3187 1.860676 CACAAACTTCCTTCGGACGA 58.139 50.000 0.00 0.00 0.00 4.20
2199 3214 0.250124 CTGTCGTGGGCTTTGGTGTA 60.250 55.000 0.00 0.00 0.00 2.90
2279 3300 9.450807 GTATATAATTTGAAAACTCTTGCGCAT 57.549 29.630 12.75 0.00 0.00 4.73
2358 3379 9.209048 AGGTGGTAGTCAAATTGTATGTATCTA 57.791 33.333 0.00 0.00 0.00 1.98
2415 3452 1.211190 GTACGCCGAGTTTCTCCGT 59.789 57.895 0.00 6.39 34.14 4.69
2441 3478 2.046023 CCACGGGCATTCTGCTCA 60.046 61.111 0.00 0.00 46.28 4.26
2603 3640 2.073816 GGAGGTACATTGTCGGTGTTG 58.926 52.381 0.00 0.00 0.00 3.33
2609 3646 1.953559 CCATGGGAGGTACATTGTCG 58.046 55.000 2.85 0.00 0.00 4.35
2740 3794 1.545136 GCCTAGGTCCTATAAGGTCGC 59.455 57.143 11.31 0.00 36.53 5.19
2752 3806 1.615424 TCAAGGGGGTGCCTAGGTC 60.615 63.158 11.31 3.32 0.00 3.85
2755 3809 2.680370 GGGTCAAGGGGGTGCCTAG 61.680 68.421 0.00 0.00 0.00 3.02
2762 3816 1.490910 GATCAAGTAGGGTCAAGGGGG 59.509 57.143 0.00 0.00 0.00 5.40
2814 3872 3.755378 CCATCTCTTTTCCAAGACACAGG 59.245 47.826 0.00 0.00 33.80 4.00
2823 3881 5.819991 AGATAAACTGCCATCTCTTTTCCA 58.180 37.500 0.00 0.00 0.00 3.53
2881 3939 7.806695 ACAATAGCTTGCTGATCACGTGAGT 62.807 44.000 24.41 11.96 39.81 3.41
2897 3955 2.041081 TGGGGTTAGTGCAACAATAGCT 59.959 45.455 0.00 0.00 41.43 3.32
2901 3959 2.672098 TGTTGGGGTTAGTGCAACAAT 58.328 42.857 0.00 0.00 41.43 2.71
2947 4005 3.910627 GGTTCTATCCTGTGATATGGGGT 59.089 47.826 0.00 0.00 33.08 4.95
2957 4015 6.936900 CGATTTCCATTATGGTTCTATCCTGT 59.063 38.462 11.39 0.00 39.03 4.00
2964 4022 4.757149 GCTAGCGATTTCCATTATGGTTCT 59.243 41.667 11.39 3.67 39.03 3.01
2993 4051 2.226912 CCCTTTTTCGGTAAATGCGACA 59.773 45.455 0.00 0.00 0.00 4.35
2997 4055 3.991773 GGAAACCCTTTTTCGGTAAATGC 59.008 43.478 0.00 0.00 31.69 3.56
3735 4794 3.953652 TGGGGAGGAAGGGGAGCA 61.954 66.667 0.00 0.00 0.00 4.26
4157 5216 4.436998 CTTCCTCCTCCGCGCGTT 62.437 66.667 29.95 0.00 0.00 4.84
4159 5218 4.560856 CTCTTCCTCCTCCGCGCG 62.561 72.222 25.67 25.67 0.00 6.86
4160 5219 4.882396 GCTCTTCCTCCTCCGCGC 62.882 72.222 0.00 0.00 0.00 6.86
4161 5220 3.423162 CTGCTCTTCCTCCTCCGCG 62.423 68.421 0.00 0.00 0.00 6.46
4162 5221 2.498726 CTGCTCTTCCTCCTCCGC 59.501 66.667 0.00 0.00 0.00 5.54
4163 5222 2.430610 CCCTGCTCTTCCTCCTCCG 61.431 68.421 0.00 0.00 0.00 4.63
4164 5223 2.741055 GCCCTGCTCTTCCTCCTCC 61.741 68.421 0.00 0.00 0.00 4.30
4165 5224 2.741055 GGCCCTGCTCTTCCTCCTC 61.741 68.421 0.00 0.00 0.00 3.71
4166 5225 2.690510 GGCCCTGCTCTTCCTCCT 60.691 66.667 0.00 0.00 0.00 3.69
4167 5226 3.803162 GGGCCCTGCTCTTCCTCC 61.803 72.222 17.04 0.00 0.00 4.30
4168 5227 3.803162 GGGGCCCTGCTCTTCCTC 61.803 72.222 24.38 0.00 0.00 3.71
4233 5292 3.532155 CTCCTTCCTCCCTCGCCG 61.532 72.222 0.00 0.00 0.00 6.46
4234 5293 3.157949 CCTCCTTCCTCCCTCGCC 61.158 72.222 0.00 0.00 0.00 5.54
4235 5294 2.042843 TCCTCCTTCCTCCCTCGC 60.043 66.667 0.00 0.00 0.00 5.03
4236 5295 1.456705 CCTCCTCCTTCCTCCCTCG 60.457 68.421 0.00 0.00 0.00 4.63
4237 5296 1.074850 CCCTCCTCCTTCCTCCCTC 60.075 68.421 0.00 0.00 0.00 4.30
4238 5297 2.652113 CCCCTCCTCCTTCCTCCCT 61.652 68.421 0.00 0.00 0.00 4.20
4239 5298 2.040359 CCCCTCCTCCTTCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
4240 5299 1.074850 CTCCCCTCCTCCTTCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
4241 5300 0.397957 GTCTCCCCTCCTCCTTCCTC 60.398 65.000 0.00 0.00 0.00 3.71
4242 5301 1.707200 GTCTCCCCTCCTCCTTCCT 59.293 63.158 0.00 0.00 0.00 3.36
4243 5302 1.383386 GGTCTCCCCTCCTCCTTCC 60.383 68.421 0.00 0.00 0.00 3.46
4244 5303 1.758906 CGGTCTCCCCTCCTCCTTC 60.759 68.421 0.00 0.00 0.00 3.46
4245 5304 2.364961 CGGTCTCCCCTCCTCCTT 59.635 66.667 0.00 0.00 0.00 3.36
4246 5305 3.756783 CCGGTCTCCCCTCCTCCT 61.757 72.222 0.00 0.00 0.00 3.69
4247 5306 3.742248 CTCCGGTCTCCCCTCCTCC 62.742 73.684 0.00 0.00 0.00 4.30
4248 5307 2.123640 CTCCGGTCTCCCCTCCTC 60.124 72.222 0.00 0.00 0.00 3.71
4249 5308 3.756783 CCTCCGGTCTCCCCTCCT 61.757 72.222 0.00 0.00 0.00 3.69
4323 5382 2.365768 GACAGACTCCCCTCCCCC 60.366 72.222 0.00 0.00 0.00 5.40
4324 5383 1.081277 AAGACAGACTCCCCTCCCC 59.919 63.158 0.00 0.00 0.00 4.81
4325 5384 1.268283 CCAAGACAGACTCCCCTCCC 61.268 65.000 0.00 0.00 0.00 4.30
4326 5385 0.252284 TCCAAGACAGACTCCCCTCC 60.252 60.000 0.00 0.00 0.00 4.30
4327 5386 1.645710 TTCCAAGACAGACTCCCCTC 58.354 55.000 0.00 0.00 0.00 4.30
4328 5387 1.981495 CTTTCCAAGACAGACTCCCCT 59.019 52.381 0.00 0.00 0.00 4.79
4329 5388 1.003696 CCTTTCCAAGACAGACTCCCC 59.996 57.143 0.00 0.00 0.00 4.81
4330 5389 1.700186 ACCTTTCCAAGACAGACTCCC 59.300 52.381 0.00 0.00 0.00 4.30
4331 5390 2.104963 ACACCTTTCCAAGACAGACTCC 59.895 50.000 0.00 0.00 0.00 3.85
4332 5391 3.181465 TGACACCTTTCCAAGACAGACTC 60.181 47.826 0.00 0.00 0.00 3.36
4333 5392 2.771943 TGACACCTTTCCAAGACAGACT 59.228 45.455 0.00 0.00 0.00 3.24
4334 5393 2.872858 GTGACACCTTTCCAAGACAGAC 59.127 50.000 0.00 0.00 0.00 3.51
4335 5394 2.771943 AGTGACACCTTTCCAAGACAGA 59.228 45.455 0.84 0.00 0.00 3.41
4336 5395 2.874701 CAGTGACACCTTTCCAAGACAG 59.125 50.000 0.84 0.00 0.00 3.51
4337 5396 2.238646 ACAGTGACACCTTTCCAAGACA 59.761 45.455 0.84 0.00 0.00 3.41
4338 5397 2.872858 GACAGTGACACCTTTCCAAGAC 59.127 50.000 0.84 0.00 0.00 3.01
4339 5398 2.483013 CGACAGTGACACCTTTCCAAGA 60.483 50.000 0.84 0.00 0.00 3.02
4340 5399 1.867233 CGACAGTGACACCTTTCCAAG 59.133 52.381 0.84 0.00 0.00 3.61
4341 5400 1.208535 ACGACAGTGACACCTTTCCAA 59.791 47.619 0.84 0.00 0.00 3.53
4342 5401 0.828022 ACGACAGTGACACCTTTCCA 59.172 50.000 0.84 0.00 0.00 3.53
4343 5402 3.680842 ACGACAGTGACACCTTTCC 57.319 52.632 0.84 0.00 0.00 3.13
4354 5413 4.105486 CGACAATATGATCACACGACAGT 58.895 43.478 0.00 0.00 0.00 3.55
4355 5414 3.060940 GCGACAATATGATCACACGACAG 60.061 47.826 0.00 0.00 0.00 3.51
4356 5415 2.857748 GCGACAATATGATCACACGACA 59.142 45.455 0.00 0.00 0.00 4.35
4357 5416 2.857748 TGCGACAATATGATCACACGAC 59.142 45.455 0.00 0.00 0.00 4.34
4358 5417 3.157932 TGCGACAATATGATCACACGA 57.842 42.857 0.00 0.00 0.00 4.35
4359 5418 4.457433 AATGCGACAATATGATCACACG 57.543 40.909 0.00 0.00 0.00 4.49
4360 5419 6.354362 CGTAAAATGCGACAATATGATCACAC 59.646 38.462 0.00 0.00 0.00 3.82
4361 5420 6.256757 TCGTAAAATGCGACAATATGATCACA 59.743 34.615 0.00 0.00 33.09 3.58
4362 5421 6.645705 TCGTAAAATGCGACAATATGATCAC 58.354 36.000 0.00 0.00 33.09 3.06
4363 5422 6.836577 TCGTAAAATGCGACAATATGATCA 57.163 33.333 0.00 0.00 33.09 2.92
4364 5423 7.509797 TCATCGTAAAATGCGACAATATGATC 58.490 34.615 0.00 0.00 41.33 2.92
4365 5424 7.420184 TCATCGTAAAATGCGACAATATGAT 57.580 32.000 0.00 0.00 41.33 2.45
4366 5425 6.836577 TCATCGTAAAATGCGACAATATGA 57.163 33.333 0.00 0.00 41.33 2.15
4367 5426 7.513132 AGATCATCGTAAAATGCGACAATATG 58.487 34.615 0.00 0.00 41.33 1.78
4368 5427 7.658179 AGATCATCGTAAAATGCGACAATAT 57.342 32.000 0.00 0.00 41.33 1.28
4369 5428 7.477144 AAGATCATCGTAAAATGCGACAATA 57.523 32.000 0.00 0.00 41.33 1.90
4375 5434 5.133264 GCTGTAAGATCATCGTAAAATGCG 58.867 41.667 0.00 0.00 34.07 4.73
4465 5524 6.627087 TCAATCTTCAAAGGTACTCCATCT 57.373 37.500 0.00 0.00 38.49 2.90
4644 5703 6.899393 AAGTGGTTTTGATGACACATATGT 57.101 33.333 1.41 1.41 43.71 2.29
4663 5722 7.667043 TTAGAGTGTGGCAAACTATAAAGTG 57.333 36.000 19.76 0.00 35.62 3.16
4679 5738 5.183140 GGTGTGGTAATGCATTTTAGAGTGT 59.817 40.000 18.75 0.00 0.00 3.55
4694 5753 4.308526 TCCTGCAATTATGGTGTGGTAA 57.691 40.909 0.00 0.00 0.00 2.85
4696 5755 2.897271 TCCTGCAATTATGGTGTGGT 57.103 45.000 0.00 0.00 0.00 4.16
4782 6134 4.248174 TGGGTCATTGGATCATTTAGCA 57.752 40.909 0.00 0.00 0.00 3.49
4871 6223 6.947733 TCAACAAATTTCCTCCATATGTGTCT 59.052 34.615 1.24 0.00 0.00 3.41
4954 6306 2.052237 GTGGTGAAACGCGTGCAG 60.052 61.111 14.98 0.00 38.12 4.41
4959 6311 4.072088 GCGGAGTGGTGAAACGCG 62.072 66.667 3.53 3.53 40.84 6.01
4972 6324 1.895020 ATAACACAAGGGAGCGCGGA 61.895 55.000 8.83 0.00 0.00 5.54
4974 6326 1.019278 ACATAACACAAGGGAGCGCG 61.019 55.000 0.00 0.00 0.00 6.86
5004 6680 0.532115 GGGTCAGCATTCGCCAAAAT 59.468 50.000 0.00 0.00 39.83 1.82
5190 6875 1.073444 ACTATCAGGTAGGATCGCCGA 59.927 52.381 0.00 0.00 39.96 5.54
5630 7374 0.107214 GGGCAGGCAGTAACTATGCA 60.107 55.000 0.00 0.00 45.68 3.96
5644 7388 5.066505 GGTGTTTAGTAGATCATTTGGGCAG 59.933 44.000 0.00 0.00 0.00 4.85
5648 7392 5.647658 TGCAGGTGTTTAGTAGATCATTTGG 59.352 40.000 0.00 0.00 0.00 3.28
5654 7409 6.149474 ACACAAATGCAGGTGTTTAGTAGATC 59.851 38.462 13.85 0.00 45.39 2.75
5655 7410 6.003950 ACACAAATGCAGGTGTTTAGTAGAT 58.996 36.000 13.85 0.00 45.39 1.98
5659 7414 4.518970 CCTACACAAATGCAGGTGTTTAGT 59.481 41.667 21.70 11.31 45.39 2.24
5660 7415 4.759693 TCCTACACAAATGCAGGTGTTTAG 59.240 41.667 21.70 17.85 45.39 1.85
5661 7416 4.517453 GTCCTACACAAATGCAGGTGTTTA 59.483 41.667 21.70 11.11 45.39 2.01
5662 7417 3.317993 GTCCTACACAAATGCAGGTGTTT 59.682 43.478 21.70 10.62 45.39 2.83
5663 7418 2.884639 GTCCTACACAAATGCAGGTGTT 59.115 45.455 21.70 10.05 45.39 3.32
5665 7420 2.503331 TGTCCTACACAAATGCAGGTG 58.497 47.619 12.73 12.73 40.04 4.00
5838 7600 9.478019 CAAGTTTGTTCTGCTTATAAGTAATCG 57.522 33.333 13.91 0.00 0.00 3.34
5844 7606 9.209175 AGTCTACAAGTTTGTTCTGCTTATAAG 57.791 33.333 8.20 8.20 42.35 1.73


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

AutoCloner maintained by Alex Coulton.