Multiple sequence alignment - TraesCS2A01G404600

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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 TraesCS2A01G404600 chr2A 100.000 4974 0 0 2166 7139 660220683 660225656 0.000000e+00 9186.0
1 TraesCS2A01G404600 chr2A 100.000 2065 0 0 1 2065 660218518 660220582 0.000000e+00 3814.0
2 TraesCS2A01G404600 chr2A 94.205 880 46 4 2166 3040 673305117 673304238 0.000000e+00 1338.0
3 TraesCS2A01G404600 chr2A 93.695 571 24 5 1507 2065 673309580 673309010 0.000000e+00 845.0
4 TraesCS2A01G404600 chr2A 99.177 243 0 2 2803 3044 660220016 660220257 3.060000e-118 436.0
5 TraesCS2A01G404600 chr2A 99.177 243 0 2 1499 1740 660221320 660221561 3.060000e-118 436.0
6 TraesCS2A01G404600 chr2A 84.516 310 48 0 5657 5966 16475414 16475105 2.500000e-79 307.0
7 TraesCS2A01G404600 chr2A 89.441 161 16 1 3719 3879 16478002 16477843 1.210000e-47 202.0
8 TraesCS2A01G404600 chr2A 97.222 36 1 0 997 1032 16479348 16479313 2.150000e-05 62.1
9 TraesCS2A01G404600 chr2D 91.182 2030 106 29 4762 6732 516369677 516371692 0.000000e+00 2689.0
10 TraesCS2A01G404600 chr2D 90.263 1520 83 27 17 1507 516366374 516367857 0.000000e+00 1927.0
11 TraesCS2A01G404600 chr2D 90.837 884 59 13 3891 4762 516368657 516369530 0.000000e+00 1164.0
12 TraesCS2A01G404600 chr2D 86.667 420 26 8 6729 7139 516374202 516374600 8.500000e-119 438.0
13 TraesCS2A01G404600 chr2D 90.354 311 16 9 3041 3345 516367852 516368154 5.190000e-106 396.0
14 TraesCS2A01G404600 chr2D 95.215 209 5 3 3692 3899 516368428 516368632 6.910000e-85 326.0
15 TraesCS2A01G404600 chr2D 84.543 317 47 1 5657 5973 14105285 14104971 5.380000e-81 313.0
16 TraesCS2A01G404600 chr2D 83.898 236 23 7 3360 3589 516368142 516368368 2.020000e-50 211.0
17 TraesCS2A01G404600 chr2D 89.809 157 15 1 3723 3879 14106349 14106194 4.370000e-47 200.0
18 TraesCS2A01G404600 chr2D 76.018 221 43 9 4932 5150 570106962 570106750 9.790000e-19 106.0
19 TraesCS2A01G404600 chr2D 97.222 36 1 0 997 1032 14107629 14107594 2.150000e-05 62.1
20 TraesCS2A01G404600 chr2B 90.664 1778 131 24 4405 6178 607952128 607953874 0.000000e+00 2331.0
21 TraesCS2A01G404600 chr2B 87.275 1556 89 50 1 1507 607949317 607950812 0.000000e+00 1676.0
22 TraesCS2A01G404600 chr2B 92.794 791 42 10 6358 7139 607954116 607954900 0.000000e+00 1131.0
23 TraesCS2A01G404600 chr2B 86.867 731 46 27 3676 4369 607951414 607952131 0.000000e+00 773.0
24 TraesCS2A01G404600 chr2B 91.148 305 10 6 3041 3345 607950807 607951094 1.440000e-106 398.0
25 TraesCS2A01G404600 chr2B 83.067 313 53 0 5657 5969 25672937 25672625 1.170000e-72 285.0
26 TraesCS2A01G404600 chr2B 92.063 189 7 4 3360 3545 607951082 607951265 7.100000e-65 259.0
27 TraesCS2A01G404600 chr2B 89.241 158 16 1 3716 3872 25687536 25687379 5.650000e-46 196.0
28 TraesCS2A01G404600 chr2B 84.466 206 24 7 6168 6371 607953898 607954097 5.650000e-46 196.0
29 TraesCS2A01G404600 chr2B 97.222 36 1 0 997 1032 25689002 25688967 2.150000e-05 62.1
30 TraesCS2A01G404600 chr1B 99.773 880 2 0 2166 3045 487491678 487490799 0.000000e+00 1615.0
31 TraesCS2A01G404600 chr1B 100.000 562 0 0 1504 2065 487495763 487495202 0.000000e+00 1038.0
32 TraesCS2A01G404600 chr1B 99.582 239 0 1 1499 1737 487491041 487490804 1.100000e-117 435.0
33 TraesCS2A01G404600 chr1B 99.580 238 0 1 2807 3044 487495763 487495527 3.960000e-117 433.0
34 TraesCS2A01G404600 chr7B 97.035 877 23 2 2166 3040 694496697 694497572 0.000000e+00 1472.0
35 TraesCS2A01G404600 chr7B 96.435 561 18 1 1507 2065 694521313 694520753 0.000000e+00 924.0
36 TraesCS2A01G404600 chr7B 97.095 241 3 3 1499 1737 694497334 694497572 3.100000e-108 403.0
37 TraesCS2A01G404600 chr7B 97.835 231 3 1 2810 3038 694521313 694521083 1.440000e-106 398.0
38 TraesCS2A01G404600 chr7B 80.165 242 38 9 5539 5775 565577309 565577545 9.520000e-39 172.0
39 TraesCS2A01G404600 chrUn 100.000 591 0 0 2166 2756 299451295 299450705 0.000000e+00 1092.0
40 TraesCS2A01G404600 chrUn 100.000 562 0 0 1504 2065 299455380 299454819 0.000000e+00 1038.0
41 TraesCS2A01G404600 chrUn 99.580 238 0 1 2807 3044 299455380 299455144 3.960000e-117 433.0
42 TraesCS2A01G404600 chrUn 83.444 151 25 0 3724 3874 92745522 92745372 2.680000e-29 141.0
43 TraesCS2A01G404600 chr3B 98.344 604 10 0 2166 2769 2421579 2422182 0.000000e+00 1061.0
44 TraesCS2A01G404600 chr3B 97.865 562 10 1 1506 2065 2417494 2418055 0.000000e+00 970.0
45 TraesCS2A01G404600 chr3B 97.059 238 4 2 2809 3044 2417494 2417730 1.440000e-106 398.0
46 TraesCS2A01G404600 chr3B 85.870 92 11 2 3042 3132 820905569 820905479 5.890000e-16 97.1
47 TraesCS2A01G404600 chr6B 86.788 386 45 5 5538 5920 490255652 490256034 6.620000e-115 425.0
48 TraesCS2A01G404600 chr6D 85.401 411 54 5 5524 5931 330157621 330157214 8.560000e-114 422.0
49 TraesCS2A01G404600 chr6A 85.158 411 55 5 5524 5931 469432340 469431933 3.980000e-112 416.0
50 TraesCS2A01G404600 chr5A 97.046 237 5 1 2806 3040 6176695 6176459 1.440000e-106 398.0
51 TraesCS2A01G404600 chr5A 96.667 240 5 2 1504 1740 6176695 6176456 5.190000e-106 396.0
52 TraesCS2A01G404600 chr7A 79.424 243 38 11 5539 5775 608359403 608359639 2.060000e-35 161.0
53 TraesCS2A01G404600 chr7A 83.444 151 25 0 3724 3874 724136320 724136170 2.680000e-29 141.0
54 TraesCS2A01G404600 chr7D 79.012 243 39 11 5539 5775 528080135 528080371 9.590000e-34 156.0
55 TraesCS2A01G404600 chr7D 78.146 151 31 2 2323 2472 631468187 631468336 2.120000e-15 95.3
56 TraesCS2A01G404600 chr3A 72.008 493 122 12 2329 2813 717682368 717682852 1.620000e-26 132.0
57 TraesCS2A01G404600 chr3A 85.870 92 11 2 3042 3132 743379846 743379756 5.890000e-16 97.1
58 TraesCS2A01G404600 chr3D 85.870 92 11 2 3042 3132 609741172 609741082 5.890000e-16 97.1
59 TraesCS2A01G404600 chr4D 100.000 29 0 0 5534 5562 116270927 116270955 4.000000e-03 54.7


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 TraesCS2A01G404600 chr2A 660218518 660225656 7138 False 4478.666667 9186 99.725667 1 7139 3 chr2A.!!$F2 7138
1 TraesCS2A01G404600 chr2A 673304238 673309580 5342 True 1091.500000 1338 93.950000 1507 3040 2 chr2A.!!$R2 1533
2 TraesCS2A01G404600 chr2D 516366374 516374600 8226 False 1021.571429 2689 89.773714 17 7139 7 chr2D.!!$F1 7122
3 TraesCS2A01G404600 chr2B 607949317 607954900 5583 False 966.285714 2331 89.325286 1 7139 7 chr2B.!!$F1 7138
4 TraesCS2A01G404600 chr1B 487490799 487491678 879 True 1025.000000 1615 99.677500 1499 3045 2 chr1B.!!$R1 1546
5 TraesCS2A01G404600 chr1B 487495202 487495763 561 True 735.500000 1038 99.790000 1504 3044 2 chr1B.!!$R2 1540
6 TraesCS2A01G404600 chr7B 694496697 694497572 875 False 937.500000 1472 97.065000 1499 3040 2 chr7B.!!$F2 1541
7 TraesCS2A01G404600 chr7B 694520753 694521313 560 True 661.000000 924 97.135000 1507 3038 2 chr7B.!!$R1 1531
8 TraesCS2A01G404600 chrUn 299450705 299455380 4675 True 854.333333 1092 99.860000 1504 3044 3 chrUn.!!$R2 1540
9 TraesCS2A01G404600 chr3B 2417494 2422182 4688 False 809.666667 1061 97.756000 1506 3044 3 chr3B.!!$F1 1538

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
929 970 0.107214 AGACTCTCTCGAGCTGGAGG 60.107 60.0 23.58 14.97 41.09 4.30 F
930 971 0.107410 GACTCTCTCGAGCTGGAGGA 60.107 60.0 23.58 17.87 41.09 3.71 F
932 973 0.107214 CTCTCTCGAGCTGGAGGAGT 60.107 60.0 23.58 0.00 34.74 3.85 F
937 978 0.180642 TCGAGCTGGAGGAGTACGAT 59.819 55.0 0.00 0.00 0.00 3.73 F
2756 6683 0.246635 TCCTCTACAGCGTTCTTGGC 59.753 55.0 0.00 0.00 0.00 4.52 F
3190 7123 0.107831 TACCACCAGCTCAACCACAC 59.892 55.0 0.00 0.00 0.00 3.82 F
3639 7630 0.391927 TTTTGCCGCGGTATAGCTGT 60.392 50.0 28.70 0.00 34.40 4.40 F
4189 8224 0.690077 GGACGGTGATTAGGACCCCT 60.690 60.0 0.00 0.00 37.71 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2833 6763 0.898320 ATGCAGTCGTTGAGTAGCCT 59.102 50.000 0.00 0.0 0.00 4.58 R
2920 6850 1.282248 GATACACACGCACGCACACT 61.282 55.000 0.00 0.0 0.00 3.55 R
2929 6859 3.119459 TGAGGAGAAGAAGATACACACGC 60.119 47.826 0.00 0.0 0.00 5.34 R
3045 6977 1.201647 GGTTCATGGTCTTCTCGTCGA 59.798 52.381 0.00 0.0 0.00 4.20 R
3642 7633 0.029834 CAAATAGCGGCACCATGCTC 59.970 55.000 1.45 0.0 44.28 4.26 R
4129 8152 0.542702 CATGCCCAGGTCCCAGTTTT 60.543 55.000 0.00 0.0 0.00 2.43 R
5468 9665 0.379316 GTGTGGAACTTCGCCGTTTT 59.621 50.000 0.00 0.0 38.04 2.43 R
6219 10450 0.035630 CCAGGAGAAGCCCAAGACAG 60.036 60.000 0.00 0.0 37.37 3.51 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
84 89 0.744281 CACGGGCAAACCTGAAAAGT 59.256 50.000 0.00 0.00 46.41 2.66
85 90 0.744281 ACGGGCAAACCTGAAAAGTG 59.256 50.000 0.00 0.00 46.41 3.16
86 91 1.028905 CGGGCAAACCTGAAAAGTGA 58.971 50.000 0.00 0.00 46.41 3.41
87 92 1.407258 CGGGCAAACCTGAAAAGTGAA 59.593 47.619 0.00 0.00 46.41 3.18
89 94 3.677424 CGGGCAAACCTGAAAAGTGAAAA 60.677 43.478 0.00 0.00 46.41 2.29
154 159 2.676121 CCGGCTTCCATGTGGCAA 60.676 61.111 0.00 0.00 34.44 4.52
215 220 3.435186 GCTGGCCGCTTGGAGTTC 61.435 66.667 11.61 0.00 35.14 3.01
230 242 2.118076 TTCCCAGCCCAGCCTTTG 59.882 61.111 0.00 0.00 0.00 2.77
271 283 2.096980 TGTAGATGTCGCCTAACAGTCG 59.903 50.000 0.00 0.00 31.50 4.18
322 335 2.257676 GGACTGACCGGACACGTC 59.742 66.667 9.46 16.87 38.78 4.34
446 469 2.048127 GCAGACAGTGACCGGACC 60.048 66.667 9.46 0.00 0.00 4.46
449 472 2.048127 GACAGTGACCGGACCTGC 60.048 66.667 9.46 4.99 0.00 4.85
489 512 2.758130 GAGATCACTTTCCTCCTCCCT 58.242 52.381 0.00 0.00 0.00 4.20
490 513 2.698274 GAGATCACTTTCCTCCTCCCTC 59.302 54.545 0.00 0.00 0.00 4.30
491 514 1.410882 GATCACTTTCCTCCTCCCTCG 59.589 57.143 0.00 0.00 0.00 4.63
492 515 1.219393 CACTTTCCTCCTCCCTCGC 59.781 63.158 0.00 0.00 0.00 5.03
493 516 1.229209 ACTTTCCTCCTCCCTCGCA 60.229 57.895 0.00 0.00 0.00 5.10
495 518 0.391793 CTTTCCTCCTCCCTCGCAAC 60.392 60.000 0.00 0.00 0.00 4.17
496 519 0.836400 TTTCCTCCTCCCTCGCAACT 60.836 55.000 0.00 0.00 0.00 3.16
498 521 1.078848 CCTCCTCCCTCGCAACTTG 60.079 63.158 0.00 0.00 0.00 3.16
502 525 4.697756 TCCCTCGCAACTTGCCCG 62.698 66.667 8.20 0.00 41.12 6.13
504 527 4.697756 CCTCGCAACTTGCCCGGA 62.698 66.667 0.73 0.00 41.12 5.14
505 528 2.668212 CTCGCAACTTGCCCGGAA 60.668 61.111 0.73 0.00 41.12 4.30
506 529 2.668212 TCGCAACTTGCCCGGAAG 60.668 61.111 0.73 1.18 41.12 3.46
602 635 0.375803 CCAACGTAAACGCATAGGCC 59.624 55.000 0.00 0.00 44.43 5.19
656 689 7.904977 CAGAATCGAACCAAAACACATATACAG 59.095 37.037 0.00 0.00 0.00 2.74
661 697 7.116662 TCGAACCAAAACACATATACAGTACAC 59.883 37.037 0.00 0.00 0.00 2.90
706 742 3.036577 CACCTGCACTGCACCTTG 58.963 61.111 0.00 0.00 33.79 3.61
742 778 1.337118 GGCACAAACAAAGATCCCCA 58.663 50.000 0.00 0.00 0.00 4.96
929 970 0.107214 AGACTCTCTCGAGCTGGAGG 60.107 60.000 23.58 14.97 41.09 4.30
930 971 0.107410 GACTCTCTCGAGCTGGAGGA 60.107 60.000 23.58 17.87 41.09 3.71
932 973 0.107214 CTCTCTCGAGCTGGAGGAGT 60.107 60.000 23.58 0.00 34.74 3.85
933 974 1.140052 CTCTCTCGAGCTGGAGGAGTA 59.860 57.143 23.58 5.40 34.74 2.59
934 975 1.134340 TCTCTCGAGCTGGAGGAGTAC 60.134 57.143 23.58 0.00 34.74 2.73
935 976 0.462225 TCTCGAGCTGGAGGAGTACG 60.462 60.000 23.58 2.60 34.74 3.67
936 977 0.462225 CTCGAGCTGGAGGAGTACGA 60.462 60.000 17.37 3.11 33.11 3.43
937 978 0.180642 TCGAGCTGGAGGAGTACGAT 59.819 55.000 0.00 0.00 0.00 3.73
949 990 5.226194 AGGAGTACGATTACGATCCTACT 57.774 43.478 0.00 0.00 42.94 2.57
961 1002 3.128852 GATCCTACTGAGCGGAGAGTA 57.871 52.381 0.00 0.00 31.82 2.59
963 1004 2.920524 TCCTACTGAGCGGAGAGTAAG 58.079 52.381 0.00 0.00 0.00 2.34
977 1018 1.028330 AGTAAGCCGTCGATCCGTCA 61.028 55.000 0.00 0.00 0.00 4.35
1032 1082 4.214327 GGCTCCGAGGAAGCCGAG 62.214 72.222 13.88 0.00 39.06 4.63
1052 1102 4.785453 GGAGGCCGTCAAGCAGGG 62.785 72.222 0.00 0.00 0.00 4.45
1089 1142 4.082523 CACGGACATGGACGCCCT 62.083 66.667 10.64 0.00 0.00 5.19
1168 1239 0.919981 CTCAGATTCGCTTCGCTCAC 59.080 55.000 0.00 0.00 0.00 3.51
1209 1280 2.351418 TCGCTAATTTCCTGTTCGCATG 59.649 45.455 0.00 0.00 0.00 4.06
1232 1303 4.817063 CGATTGCAAGCCGCGGTG 62.817 66.667 28.70 19.45 46.97 4.94
2756 6683 0.246635 TCCTCTACAGCGTTCTTGGC 59.753 55.000 0.00 0.00 0.00 4.52
2833 6763 5.416639 TGTTAGACTGAATACCGCTTCTACA 59.583 40.000 0.00 0.00 0.00 2.74
2836 6766 2.159085 ACTGAATACCGCTTCTACAGGC 60.159 50.000 0.00 0.00 0.00 4.85
2879 6809 3.725459 CAGCATGCAACGTCGGCA 61.725 61.111 21.98 15.93 46.66 5.69
2929 6859 1.577468 TTGGTTACAGAGTGTGCGTG 58.423 50.000 0.00 0.00 0.00 5.34
3011 6941 6.037172 GGATGAATACAACACGCTGATTACTT 59.963 38.462 0.00 0.00 0.00 2.24
3040 6972 9.750125 TCTATGCACACTAAATACATTCTACAG 57.250 33.333 0.00 0.00 0.00 2.74
3041 6973 9.534565 CTATGCACACTAAATACATTCTACAGT 57.465 33.333 0.00 0.00 0.00 3.55
3042 6974 7.595311 TGCACACTAAATACATTCTACAGTG 57.405 36.000 0.00 0.00 38.26 3.66
3043 6975 6.593770 TGCACACTAAATACATTCTACAGTGG 59.406 38.462 0.00 0.00 36.97 4.00
3044 6976 6.037172 GCACACTAAATACATTCTACAGTGGG 59.963 42.308 0.00 0.00 38.64 4.61
3045 6977 7.103641 CACACTAAATACATTCTACAGTGGGT 58.896 38.462 0.00 0.00 36.97 4.51
3154 7086 1.019278 AAGAATGGCAGGTACGCACG 61.019 55.000 0.00 0.00 0.00 5.34
3155 7087 3.095898 GAATGGCAGGTACGCACGC 62.096 63.158 0.00 0.00 0.00 5.34
3156 7088 3.892740 AATGGCAGGTACGCACGCA 62.893 57.895 0.00 0.00 0.00 5.24
3190 7123 0.107831 TACCACCAGCTCAACCACAC 59.892 55.000 0.00 0.00 0.00 3.82
3208 7141 2.717485 CCATCGCCATTGAAGCCG 59.283 61.111 0.00 0.00 0.00 5.52
3210 7143 3.211963 ATCGCCATTGAAGCCGGC 61.212 61.111 21.89 21.89 42.64 6.13
3225 7158 4.867599 GGCCGGGTCGTTAGCTCG 62.868 72.222 2.18 0.00 0.00 5.03
3229 7162 1.372087 CCGGGTCGTTAGCTCGTAGT 61.372 60.000 0.00 0.00 0.00 2.73
3230 7163 1.290203 CGGGTCGTTAGCTCGTAGTA 58.710 55.000 0.00 0.00 0.00 1.82
3231 7164 1.260033 CGGGTCGTTAGCTCGTAGTAG 59.740 57.143 0.00 0.00 0.00 2.57
3275 7208 1.772063 CGATCCGGCGGTCCATTTTC 61.772 60.000 27.32 11.04 0.00 2.29
3298 7234 0.684153 ACAATCCGGCCCAGAAATGG 60.684 55.000 0.00 0.00 0.00 3.16
3326 7262 3.680458 GGATATGCCGCTAAAACTAGCTC 59.320 47.826 0.00 0.00 40.75 4.09
3342 7278 2.832672 GCTCGAGCTTACAAAATGGG 57.167 50.000 29.88 0.00 38.21 4.00
3343 7279 2.084546 GCTCGAGCTTACAAAATGGGT 58.915 47.619 29.88 0.00 38.21 4.51
3344 7280 2.488153 GCTCGAGCTTACAAAATGGGTT 59.512 45.455 29.88 0.00 38.21 4.11
3345 7281 3.057526 GCTCGAGCTTACAAAATGGGTTT 60.058 43.478 29.88 0.00 38.21 3.27
3346 7282 4.558697 GCTCGAGCTTACAAAATGGGTTTT 60.559 41.667 29.88 0.00 36.70 2.43
3347 7283 5.523438 TCGAGCTTACAAAATGGGTTTTT 57.477 34.783 0.00 0.00 38.05 1.94
3494 7433 7.688478 TCATACATTTGTATACACTGTACGC 57.312 36.000 21.28 0.00 39.06 4.42
3527 7469 1.338107 CTGGAGTACTGACCACACCA 58.662 55.000 0.00 0.00 35.66 4.17
3545 7487 4.336993 ACACCACACGTGACACATAAATTT 59.663 37.500 25.01 0.00 46.20 1.82
3546 7488 5.163602 ACACCACACGTGACACATAAATTTT 60.164 36.000 25.01 0.00 46.20 1.82
3547 7489 6.038382 ACACCACACGTGACACATAAATTTTA 59.962 34.615 25.01 0.00 46.20 1.52
3548 7490 6.577055 CACCACACGTGACACATAAATTTTAG 59.423 38.462 25.01 0.00 46.20 1.85
3549 7491 6.261381 ACCACACGTGACACATAAATTTTAGT 59.739 34.615 25.01 0.00 0.00 2.24
3550 7492 7.136119 CCACACGTGACACATAAATTTTAGTT 58.864 34.615 25.01 0.00 0.00 2.24
3551 7493 7.112844 CCACACGTGACACATAAATTTTAGTTG 59.887 37.037 25.01 2.74 0.00 3.16
3552 7494 6.635239 ACACGTGACACATAAATTTTAGTTGC 59.365 34.615 25.01 0.00 0.00 4.17
3553 7495 6.634837 CACGTGACACATAAATTTTAGTTGCA 59.365 34.615 10.90 0.00 0.00 4.08
3554 7496 6.855914 ACGTGACACATAAATTTTAGTTGCAG 59.144 34.615 6.37 0.00 0.00 4.41
3555 7497 6.183359 CGTGACACATAAATTTTAGTTGCAGC 60.183 38.462 6.37 0.00 0.00 5.25
3556 7498 6.640499 GTGACACATAAATTTTAGTTGCAGCA 59.360 34.615 2.55 0.00 0.00 4.41
3578 7534 2.112297 TTGGTGCCGTTCTGGTCC 59.888 61.111 0.00 0.00 41.21 4.46
3579 7535 3.485346 TTGGTGCCGTTCTGGTCCC 62.485 63.158 0.00 0.00 41.21 4.46
3580 7536 3.948719 GGTGCCGTTCTGGTCCCA 61.949 66.667 0.00 0.00 41.21 4.37
3583 7539 0.893727 GTGCCGTTCTGGTCCCATTT 60.894 55.000 0.00 0.00 41.21 2.32
3586 7542 1.739067 CCGTTCTGGTCCCATTTCTC 58.261 55.000 0.00 0.00 0.00 2.87
3598 7589 1.070108 CCATTTCTCGCGCAGATCATG 60.070 52.381 8.75 13.39 0.00 3.07
3624 7615 3.629858 GCTAGGCCGAGCAATTTTG 57.370 52.632 30.47 0.00 42.36 2.44
3636 7627 1.753956 CAATTTTGCCGCGGTATAGC 58.246 50.000 28.70 12.57 0.00 2.97
3637 7628 1.333619 CAATTTTGCCGCGGTATAGCT 59.666 47.619 28.70 6.02 34.40 3.32
3638 7629 0.944386 ATTTTGCCGCGGTATAGCTG 59.056 50.000 28.70 0.00 34.40 4.24
3639 7630 0.391927 TTTTGCCGCGGTATAGCTGT 60.392 50.000 28.70 0.00 34.40 4.40
3640 7631 0.391927 TTTGCCGCGGTATAGCTGTT 60.392 50.000 28.70 0.00 34.40 3.16
3641 7632 0.391927 TTGCCGCGGTATAGCTGTTT 60.392 50.000 28.70 0.00 34.40 2.83
3642 7633 1.087202 TGCCGCGGTATAGCTGTTTG 61.087 55.000 28.70 0.00 34.40 2.93
3643 7634 0.808453 GCCGCGGTATAGCTGTTTGA 60.808 55.000 28.70 0.00 34.40 2.69
3644 7635 1.209128 CCGCGGTATAGCTGTTTGAG 58.791 55.000 19.50 0.00 34.40 3.02
3653 7644 1.080298 GCTGTTTGAGCATGGTGCC 60.080 57.895 0.00 0.00 46.52 5.01
3657 7648 1.002746 TTTGAGCATGGTGCCGCTA 60.003 52.632 0.00 0.00 46.52 4.26
3662 7653 1.066257 GCATGGTGCCGCTATTTGG 59.934 57.895 0.00 0.00 37.42 3.28
3675 7666 2.484264 GCTATTTGGCATAACCCGCTAG 59.516 50.000 0.00 0.00 37.83 3.42
3676 7667 1.318576 ATTTGGCATAACCCGCTAGC 58.681 50.000 4.06 4.06 37.83 3.42
3679 7670 1.348064 TGGCATAACCCGCTAGCTAT 58.652 50.000 13.93 0.47 37.83 2.97
3680 7671 1.697432 TGGCATAACCCGCTAGCTATT 59.303 47.619 13.93 6.68 37.83 1.73
3681 7672 2.105821 TGGCATAACCCGCTAGCTATTT 59.894 45.455 13.93 5.05 37.83 1.40
3682 7673 3.325425 TGGCATAACCCGCTAGCTATTTA 59.675 43.478 13.93 7.15 37.83 1.40
3683 7674 4.202377 TGGCATAACCCGCTAGCTATTTAA 60.202 41.667 13.93 0.00 37.83 1.52
3685 7676 5.239963 GGCATAACCCGCTAGCTATTTAAAA 59.760 40.000 13.93 0.00 0.00 1.52
3686 7677 6.140786 GCATAACCCGCTAGCTATTTAAAAC 58.859 40.000 13.93 0.00 0.00 2.43
3687 7678 6.017357 GCATAACCCGCTAGCTATTTAAAACT 60.017 38.462 13.93 0.00 0.00 2.66
3688 7679 7.172019 GCATAACCCGCTAGCTATTTAAAACTA 59.828 37.037 13.93 0.00 0.00 2.24
3689 7680 6.915544 AACCCGCTAGCTATTTAAAACTAC 57.084 37.500 13.93 0.00 0.00 2.73
3690 7681 5.045872 ACCCGCTAGCTATTTAAAACTACG 58.954 41.667 13.93 2.77 0.00 3.51
3721 7712 2.767445 GGCGCGGGGTGGTAATTTC 61.767 63.158 8.83 0.00 0.00 2.17
3870 7861 2.630580 ACCACCTCTTCAGAAGTGAGTC 59.369 50.000 12.93 0.00 38.44 3.36
3871 7862 2.028567 CCACCTCTTCAGAAGTGAGTCC 60.029 54.545 12.93 0.00 38.44 3.85
3872 7863 2.896685 CACCTCTTCAGAAGTGAGTCCT 59.103 50.000 12.93 0.00 38.44 3.85
3873 7864 3.056891 CACCTCTTCAGAAGTGAGTCCTC 60.057 52.174 12.93 0.00 38.44 3.71
3981 8004 1.197721 CTGACAACGATCTTGGGTTGC 59.802 52.381 10.11 5.42 45.62 4.17
4040 8063 5.699839 ACTCGCAAAAGCCAAATAAACTAG 58.300 37.500 0.00 0.00 0.00 2.57
4082 8105 6.051074 TGTCATCATCAAACTGCTAGTATGG 58.949 40.000 0.00 0.00 0.00 2.74
4088 8111 7.217200 TCATCAAACTGCTAGTATGGGATTAC 58.783 38.462 0.00 0.00 0.00 1.89
4098 8121 6.042208 GCTAGTATGGGATTACTTCCTCAGTT 59.958 42.308 0.00 0.00 44.75 3.16
4125 8148 4.384846 CCAACCGATAGTATAACGACATGC 59.615 45.833 0.00 0.00 39.36 4.06
4129 8152 4.986034 CCGATAGTATAACGACATGCCAAA 59.014 41.667 0.00 0.00 39.36 3.28
4189 8224 0.690077 GGACGGTGATTAGGACCCCT 60.690 60.000 0.00 0.00 37.71 4.79
4194 8229 1.696314 TGATTAGGACCCCTGGGCC 60.696 63.158 7.39 3.95 39.32 5.80
4196 8231 1.697754 ATTAGGACCCCTGGGCCAG 60.698 63.158 27.04 27.04 39.32 4.85
4233 8268 1.473857 CGGTTTGTATCGTACGCCCG 61.474 60.000 11.24 8.91 32.38 6.13
4247 8282 3.953775 CCCGGAGCCCACTTGTGT 61.954 66.667 0.73 0.00 0.00 3.72
4326 8365 8.966155 TGAAAGAGTTTTCCCCCTAAATAAAT 57.034 30.769 0.00 0.00 41.62 1.40
4327 8366 9.387397 TGAAAGAGTTTTCCCCCTAAATAAATT 57.613 29.630 0.00 0.00 41.62 1.82
4335 8374 9.831682 TTTTCCCCCTAAATAAATTGAAGTACT 57.168 29.630 0.00 0.00 0.00 2.73
4376 8415 8.831715 ACAATCAATTTAATCTTGTTGGGAAC 57.168 30.769 12.58 0.00 0.00 3.62
4541 8581 4.993584 CCTATGAGTTACAAGCATGCTAGG 59.006 45.833 23.00 18.61 0.00 3.02
4617 8657 6.889722 AGGATATTTTGTCTCCATCCGAAAAA 59.110 34.615 0.00 0.00 40.13 1.94
4679 8720 4.640364 TGGATTTCAAAGCCCAACAATTC 58.360 39.130 0.92 0.00 35.65 2.17
4771 8959 7.148356 CCGATTACTTTGAGTACCCCTAAAAAC 60.148 40.741 0.00 0.00 28.93 2.43
4790 8978 7.582667 AAAAACACCTATTACTTTGAGCACT 57.417 32.000 0.00 0.00 0.00 4.40
4796 8984 5.412904 ACCTATTACTTTGAGCACTTGAAGC 59.587 40.000 0.00 0.00 0.00 3.86
4865 9057 5.163457 CCTTAAAATGGGTGTAAATGCGGAT 60.163 40.000 0.00 0.00 0.00 4.18
4898 9090 2.949447 AGCTCAAATTCACCCTTGTGT 58.051 42.857 0.00 0.00 43.26 3.72
4911 9103 3.569701 ACCCTTGTGTGCAATAAAGTCAG 59.430 43.478 0.00 0.00 33.65 3.51
4918 9110 9.462174 CTTGTGTGCAATAAAGTCAGAAAATAA 57.538 29.630 0.00 0.00 33.65 1.40
4919 9111 9.979578 TTGTGTGCAATAAAGTCAGAAAATAAT 57.020 25.926 0.00 0.00 0.00 1.28
5192 9389 3.004419 TGCTCGTAGTGGTAGCATATGAC 59.996 47.826 6.97 0.00 41.15 3.06
5200 9397 3.057876 GTGGTAGCATATGACCTCGAGAG 60.058 52.174 15.71 6.69 36.62 3.20
5217 9414 6.192234 TCGAGAGTAGAAGGACATTGTTAC 57.808 41.667 0.00 0.00 0.00 2.50
5281 9478 6.572153 TGATGAAATTAACATGCATTTCGC 57.428 33.333 15.56 12.23 40.77 4.70
5283 9480 3.856521 TGAAATTAACATGCATTTCGCGG 59.143 39.130 6.13 0.00 46.97 6.46
5468 9665 4.440880 CTCTTCCATTGCAACAAACCAAA 58.559 39.130 0.00 0.00 0.00 3.28
5486 9683 1.096416 AAAAACGGCGAAGTTCCACA 58.904 45.000 16.62 0.00 32.43 4.17
5500 9697 2.279935 TCCACACGCCAAACCTAATT 57.720 45.000 0.00 0.00 0.00 1.40
5502 9699 2.294791 TCCACACGCCAAACCTAATTTG 59.705 45.455 0.00 0.00 46.32 2.32
5507 9704 5.007682 ACACGCCAAACCTAATTTGTATCT 58.992 37.500 0.00 0.00 45.45 1.98
5682 9879 0.520404 ACGTGAAGAGCGACGTGTAT 59.480 50.000 0.00 0.00 46.60 2.29
5931 10128 1.153489 CTCCATGGCAGAGGTCGTG 60.153 63.158 6.96 0.00 35.37 4.35
5935 10132 1.977009 ATGGCAGAGGTCGTGACGA 60.977 57.895 2.39 2.39 0.00 4.20
6141 10338 2.105128 CCTCGGGTGAGATGACGC 59.895 66.667 0.00 0.00 45.57 5.19
6219 10450 1.877576 CTTTTCGGCCCAGCTTTCCC 61.878 60.000 0.00 0.00 0.00 3.97
6246 10477 2.035442 GCTTCTCCTGGGCACGTTC 61.035 63.158 0.00 0.00 0.00 3.95
6290 10531 1.366319 AGTGAGGCAGGTCTGGAATT 58.634 50.000 0.00 0.00 0.00 2.17
6291 10532 1.280421 AGTGAGGCAGGTCTGGAATTC 59.720 52.381 0.00 0.00 0.00 2.17
6443 10733 1.556911 TGATGCTCCCTTCTCCTTGAC 59.443 52.381 0.00 0.00 0.00 3.18
6483 10773 2.022764 TGATGCACCCTCATTGTACG 57.977 50.000 0.00 0.00 0.00 3.67
6498 10788 5.974751 TCATTGTACGAAAGCAAACCTTTTC 59.025 36.000 0.00 0.00 43.64 2.29
6499 10789 5.570234 TTGTACGAAAGCAAACCTTTTCT 57.430 34.783 0.00 0.00 43.64 2.52
6657 10968 7.633281 GCTGATTGAATTTAATTTGAATGCACG 59.367 33.333 0.00 0.00 0.00 5.34
6720 11035 5.530915 TGGCTAGTGTATATCCAAACAATGC 59.469 40.000 0.00 0.00 0.00 3.56
6759 13587 2.094659 ATGTGCGCGCTGTCTGTAC 61.095 57.895 33.29 20.12 0.00 2.90
6830 13666 1.652563 CGTGCATGCATGATGGGAG 59.347 57.895 31.95 10.28 35.09 4.30
6872 13709 0.328258 AAGAAGCCGGCTACCATGTT 59.672 50.000 33.07 16.43 0.00 2.71
6890 13727 1.037493 TTCTGTAGCACACTGACCGT 58.963 50.000 0.00 0.00 35.10 4.83
6966 13803 0.392998 CCCACCTCTGAACATTCCCG 60.393 60.000 0.00 0.00 0.00 5.14
7034 13875 1.503542 CCATGCAACTTGGTCTCGC 59.496 57.895 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 89 0.730265 GACCTGCACGTGTGTTTTCA 59.270 50.000 18.38 4.22 0.00 2.69
85 90 0.315869 CGACCTGCACGTGTGTTTTC 60.316 55.000 18.38 6.81 0.00 2.29
86 91 1.719117 CGACCTGCACGTGTGTTTT 59.281 52.632 18.38 0.00 0.00 2.43
87 92 2.819552 GCGACCTGCACGTGTGTTT 61.820 57.895 18.38 0.00 45.45 2.83
230 242 0.737715 CGACTACACAAGGCAGAGGC 60.738 60.000 0.00 0.00 40.13 4.70
271 283 4.410743 GTGCTGCGCTTTGCTCCC 62.411 66.667 9.73 0.04 46.63 4.30
294 306 0.108019 GGTCAGTCCGGAAACAGGTT 59.892 55.000 5.23 0.00 0.00 3.50
364 377 1.440893 CTGCCCTGACAGAGATCGG 59.559 63.158 3.32 0.00 40.25 4.18
449 472 0.955919 GGGGAGAAGCTGACAAACGG 60.956 60.000 0.00 0.00 0.00 4.44
489 512 2.668212 CTTCCGGGCAAGTTGCGA 60.668 61.111 21.11 10.53 46.21 5.10
490 513 4.404654 GCTTCCGGGCAAGTTGCG 62.405 66.667 21.11 8.66 46.21 4.85
491 514 4.056125 GGCTTCCGGGCAAGTTGC 62.056 66.667 19.87 19.87 44.08 4.17
492 515 3.737172 CGGCTTCCGGGCAAGTTG 61.737 66.667 0.00 0.00 44.15 3.16
512 535 3.106407 GTGTCTGCTCGACGTGCC 61.106 66.667 18.25 4.78 45.87 5.01
587 620 2.353269 TGAAATGGCCTATGCGTTTACG 59.647 45.455 3.32 0.00 43.27 3.18
656 689 1.374252 CCCCGTGTCAGCTGTGTAC 60.374 63.158 14.67 10.24 0.00 2.90
688 724 2.908940 AAGGTGCAGTGCAGGTGC 60.909 61.111 20.42 13.08 40.08 5.01
689 725 0.534877 TACAAGGTGCAGTGCAGGTG 60.535 55.000 20.42 18.28 40.08 4.00
690 726 0.182537 TTACAAGGTGCAGTGCAGGT 59.817 50.000 20.42 16.29 40.08 4.00
691 727 0.593128 GTTACAAGGTGCAGTGCAGG 59.407 55.000 20.42 11.08 40.08 4.85
886 927 4.208686 CTGGCTACGGCGGGAGAC 62.209 72.222 13.24 11.22 39.81 3.36
932 973 3.431233 CGCTCAGTAGGATCGTAATCGTA 59.569 47.826 0.00 0.00 38.33 3.43
933 974 2.223611 CGCTCAGTAGGATCGTAATCGT 59.776 50.000 0.00 0.00 38.33 3.73
934 975 2.412977 CCGCTCAGTAGGATCGTAATCG 60.413 54.545 0.00 0.00 33.44 3.34
935 976 2.812591 TCCGCTCAGTAGGATCGTAATC 59.187 50.000 0.00 0.00 33.44 1.75
936 977 2.814919 CTCCGCTCAGTAGGATCGTAAT 59.185 50.000 0.00 0.00 35.75 1.89
937 978 2.158856 TCTCCGCTCAGTAGGATCGTAA 60.159 50.000 0.00 0.00 35.75 3.18
949 990 3.197614 CGGCTTACTCTCCGCTCA 58.802 61.111 0.00 0.00 39.14 4.26
961 1002 1.153823 CTTGACGGATCGACGGCTT 60.154 57.895 2.77 0.00 43.79 4.35
963 1004 3.255379 GCTTGACGGATCGACGGC 61.255 66.667 0.00 0.00 43.68 5.68
977 1018 0.536006 AGCTCAACCGCAGAAAGCTT 60.536 50.000 0.00 0.00 40.26 3.74
988 1029 0.039618 TTCCCCATGGAAGCTCAACC 59.960 55.000 15.22 0.00 45.88 3.77
1032 1082 4.329545 TGCTTGACGGCCTCCACC 62.330 66.667 0.00 0.00 0.00 4.61
1089 1142 1.001633 GGAGAAGTGGCGTTACCTTGA 59.998 52.381 0.00 0.00 40.22 3.02
1162 1233 2.697425 CGCGGAATTGAGTGAGCG 59.303 61.111 0.00 0.00 41.56 5.03
1168 1239 1.741401 TGAGCCACGCGGAATTGAG 60.741 57.895 12.47 0.00 0.00 3.02
1209 1280 1.010350 CGGCTTGCAATCGCTGATC 60.010 57.895 12.91 0.00 39.64 2.92
1290 1361 1.226802 CTGCTCATGGACGACGAGG 60.227 63.158 0.00 0.00 0.00 4.63
2756 6683 0.951040 GGTGAGACTGTTGCGGAAGG 60.951 60.000 0.00 0.00 0.00 3.46
2808 6738 4.745649 AGAAGCGGTATTCAGTCTAACAC 58.254 43.478 0.00 0.00 0.00 3.32
2816 6746 2.101582 AGCCTGTAGAAGCGGTATTCAG 59.898 50.000 0.00 0.00 0.00 3.02
2833 6763 0.898320 ATGCAGTCGTTGAGTAGCCT 59.102 50.000 0.00 0.00 0.00 4.58
2836 6766 4.036852 TGGATAGATGCAGTCGTTGAGTAG 59.963 45.833 0.00 0.00 0.00 2.57
2864 6794 2.502510 CTTGCCGACGTTGCATGC 60.503 61.111 11.82 11.82 38.76 4.06
2920 6850 1.282248 GATACACACGCACGCACACT 61.282 55.000 0.00 0.00 0.00 3.55
2929 6859 3.119459 TGAGGAGAAGAAGATACACACGC 60.119 47.826 0.00 0.00 0.00 5.34
3040 6972 1.212229 GGTCTTCTCGTCGACCCAC 59.788 63.158 10.58 0.00 43.05 4.61
3041 6973 3.677527 GGTCTTCTCGTCGACCCA 58.322 61.111 10.58 0.00 43.05 4.51
3044 6976 2.251893 GTTCATGGTCTTCTCGTCGAC 58.748 52.381 5.18 5.18 0.00 4.20
3045 6977 1.201647 GGTTCATGGTCTTCTCGTCGA 59.798 52.381 0.00 0.00 0.00 4.20
3155 7087 4.063967 TAGGTGGAGTGGCGCGTG 62.064 66.667 8.43 0.00 0.00 5.34
3156 7088 4.065281 GTAGGTGGAGTGGCGCGT 62.065 66.667 8.43 0.00 0.00 6.01
3157 7089 4.814294 GGTAGGTGGAGTGGCGCG 62.814 72.222 0.00 0.00 0.00 6.86
3158 7090 3.702048 TGGTAGGTGGAGTGGCGC 61.702 66.667 0.00 0.00 0.00 6.53
3160 7092 2.185310 CTGGTGGTAGGTGGAGTGGC 62.185 65.000 0.00 0.00 0.00 5.01
3161 7093 1.983224 CTGGTGGTAGGTGGAGTGG 59.017 63.158 0.00 0.00 0.00 4.00
3190 7123 3.122850 GGCTTCAATGGCGATGGG 58.877 61.111 0.00 0.00 0.00 4.00
3208 7141 4.867599 CGAGCTAACGACCCGGCC 62.868 72.222 0.00 0.00 35.09 6.13
3210 7143 1.354506 CTACGAGCTAACGACCCGG 59.645 63.158 1.33 0.00 37.03 5.73
3211 7144 1.260033 CTACTACGAGCTAACGACCCG 59.740 57.143 1.33 0.00 37.03 5.28
3212 7145 2.543430 CTCTACTACGAGCTAACGACCC 59.457 54.545 1.33 0.00 37.03 4.46
3213 7146 3.452474 TCTCTACTACGAGCTAACGACC 58.548 50.000 1.33 0.00 37.03 4.79
3225 7158 5.573669 CGCCTTTCTTTCACTTCTCTACTAC 59.426 44.000 0.00 0.00 0.00 2.73
3229 7162 3.326747 GCGCCTTTCTTTCACTTCTCTA 58.673 45.455 0.00 0.00 0.00 2.43
3230 7163 2.147150 GCGCCTTTCTTTCACTTCTCT 58.853 47.619 0.00 0.00 0.00 3.10
3231 7164 1.136224 CGCGCCTTTCTTTCACTTCTC 60.136 52.381 0.00 0.00 0.00 2.87
3260 7193 0.958382 TCAAGAAAATGGACCGCCGG 60.958 55.000 0.00 0.00 36.79 6.13
3262 7195 1.243902 TGTCAAGAAAATGGACCGCC 58.756 50.000 0.00 0.00 0.00 6.13
3275 7208 0.322456 TTCTGGGCCGGATTGTCAAG 60.322 55.000 17.51 0.00 0.00 3.02
3298 7234 0.243907 TTAGCGGCATATCCTCTCGC 59.756 55.000 1.45 0.00 45.72 5.03
3348 7284 9.557061 GGTAACCAATTTTGTACCCATTTAAAA 57.443 29.630 0.00 0.00 31.53 1.52
3349 7285 7.871463 CGGTAACCAATTTTGTACCCATTTAAA 59.129 33.333 0.00 0.00 33.77 1.52
3350 7286 7.376615 CGGTAACCAATTTTGTACCCATTTAA 58.623 34.615 0.00 0.00 33.77 1.52
3351 7287 6.071503 CCGGTAACCAATTTTGTACCCATTTA 60.072 38.462 0.00 0.00 33.77 1.40
3352 7288 5.279556 CCGGTAACCAATTTTGTACCCATTT 60.280 40.000 0.00 0.00 33.77 2.32
3353 7289 4.221041 CCGGTAACCAATTTTGTACCCATT 59.779 41.667 0.00 0.00 33.77 3.16
3354 7290 3.764972 CCGGTAACCAATTTTGTACCCAT 59.235 43.478 0.00 0.00 33.77 4.00
3355 7291 3.155501 CCGGTAACCAATTTTGTACCCA 58.844 45.455 0.00 0.00 33.77 4.51
3356 7292 2.094597 GCCGGTAACCAATTTTGTACCC 60.095 50.000 1.90 0.00 33.77 3.69
3357 7293 2.557490 TGCCGGTAACCAATTTTGTACC 59.443 45.455 1.90 0.00 33.95 3.34
3358 7294 3.567530 GTGCCGGTAACCAATTTTGTAC 58.432 45.455 1.90 0.00 0.00 2.90
3359 7295 2.557490 GGTGCCGGTAACCAATTTTGTA 59.443 45.455 20.02 0.00 37.65 2.41
3360 7296 1.341852 GGTGCCGGTAACCAATTTTGT 59.658 47.619 20.02 0.00 37.65 2.83
3361 7297 1.341531 TGGTGCCGGTAACCAATTTTG 59.658 47.619 23.92 0.00 44.72 2.44
3362 7298 1.705873 TGGTGCCGGTAACCAATTTT 58.294 45.000 23.92 0.00 44.72 1.82
3363 7299 3.441241 TGGTGCCGGTAACCAATTT 57.559 47.368 23.92 0.00 44.72 1.82
3404 7340 1.669115 CCGTGTGGAACTGGCTCAG 60.669 63.158 1.16 1.16 38.04 3.35
3405 7341 2.425592 CCGTGTGGAACTGGCTCA 59.574 61.111 0.00 0.00 38.04 4.26
3438 7374 2.660064 ATGGTCTGACCGTCTGGCC 61.660 63.158 21.15 19.35 42.58 5.36
3439 7375 2.982130 ATGGTCTGACCGTCTGGC 59.018 61.111 21.15 3.68 42.58 4.85
3494 7433 4.929808 AGTACTCCAGCGAATTAACAACTG 59.070 41.667 0.00 0.00 0.00 3.16
3527 7469 6.635239 GCAACTAAAATTTATGTGTCACGTGT 59.365 34.615 16.51 0.00 0.00 4.49
3545 7487 1.317613 CCAACCTGTGCTGCAACTAA 58.682 50.000 2.77 0.00 0.00 2.24
3546 7488 0.182537 ACCAACCTGTGCTGCAACTA 59.817 50.000 2.77 0.00 0.00 2.24
3547 7489 1.076777 ACCAACCTGTGCTGCAACT 60.077 52.632 2.77 0.00 0.00 3.16
3548 7490 1.066257 CACCAACCTGTGCTGCAAC 59.934 57.895 2.77 0.00 0.00 4.17
3549 7491 3.524014 CACCAACCTGTGCTGCAA 58.476 55.556 2.77 0.00 0.00 4.08
3555 7497 1.525995 AGAACGGCACCAACCTGTG 60.526 57.895 0.00 0.00 39.29 3.66
3556 7498 1.525995 CAGAACGGCACCAACCTGT 60.526 57.895 0.00 0.00 0.00 4.00
3571 7527 1.218047 CGCGAGAAATGGGACCAGA 59.782 57.895 0.00 0.00 0.00 3.86
3578 7534 1.070108 CATGATCTGCGCGAGAAATGG 60.070 52.381 12.10 0.00 33.12 3.16
3579 7535 1.070108 CCATGATCTGCGCGAGAAATG 60.070 52.381 12.10 16.22 33.12 2.32
3580 7536 1.224075 CCATGATCTGCGCGAGAAAT 58.776 50.000 12.10 5.87 33.12 2.17
3583 7539 1.066422 GACCATGATCTGCGCGAGA 59.934 57.895 12.10 10.76 34.25 4.04
3586 7542 3.316821 CAGACCATGATCTGCGCG 58.683 61.111 3.54 0.00 39.77 6.86
3598 7589 3.438017 CTCGGCCTAGCAGCAGACC 62.438 68.421 0.00 0.00 33.29 3.85
3618 7609 1.333619 CAGCTATACCGCGGCAAAATT 59.666 47.619 28.58 7.06 34.40 1.82
3619 7610 0.944386 CAGCTATACCGCGGCAAAAT 59.056 50.000 28.58 16.22 34.40 1.82
3624 7615 0.808453 TCAAACAGCTATACCGCGGC 60.808 55.000 28.58 11.19 34.40 6.53
3625 7616 1.209128 CTCAAACAGCTATACCGCGG 58.791 55.000 26.86 26.86 34.40 6.46
3626 7617 0.577269 GCTCAAACAGCTATACCGCG 59.423 55.000 0.00 0.00 45.83 6.46
3636 7627 1.210931 CGGCACCATGCTCAAACAG 59.789 57.895 0.13 0.00 44.28 3.16
3637 7628 2.918345 GCGGCACCATGCTCAAACA 61.918 57.895 0.13 0.00 44.28 2.83
3638 7629 1.305219 TAGCGGCACCATGCTCAAAC 61.305 55.000 1.45 0.00 44.28 2.93
3639 7630 0.394216 ATAGCGGCACCATGCTCAAA 60.394 50.000 1.45 0.00 44.28 2.69
3640 7631 0.394216 AATAGCGGCACCATGCTCAA 60.394 50.000 1.45 0.00 44.28 3.02
3641 7632 0.394216 AAATAGCGGCACCATGCTCA 60.394 50.000 1.45 0.00 44.28 4.26
3642 7633 0.029834 CAAATAGCGGCACCATGCTC 59.970 55.000 1.45 0.00 44.28 4.26
3643 7634 1.386525 CCAAATAGCGGCACCATGCT 61.387 55.000 1.45 0.00 44.28 3.79
3644 7635 1.066257 CCAAATAGCGGCACCATGC 59.934 57.895 1.45 0.00 44.08 4.06
3653 7644 0.040425 GCGGGTTATGCCAAATAGCG 60.040 55.000 0.00 0.00 39.65 4.26
3657 7648 1.133792 AGCTAGCGGGTTATGCCAAAT 60.134 47.619 9.55 0.00 39.65 2.32
3662 7653 5.934935 TTTAAATAGCTAGCGGGTTATGC 57.065 39.130 9.55 0.00 0.00 3.14
3667 7658 5.045872 CGTAGTTTTAAATAGCTAGCGGGT 58.954 41.667 9.55 0.00 0.00 5.28
3675 7666 7.095899 CGGGTTAGATCCGTAGTTTTAAATAGC 60.096 40.741 0.00 0.00 42.33 2.97
3676 7667 8.290663 CGGGTTAGATCCGTAGTTTTAAATAG 57.709 38.462 0.00 0.00 42.33 1.73
3690 7681 2.588034 GCGCCACGGGTTAGATCC 60.588 66.667 0.00 0.00 0.00 3.36
3704 7695 1.310216 AAGAAATTACCACCCCGCGC 61.310 55.000 0.00 0.00 0.00 6.86
3711 7702 2.225491 TCGCACTGCAAGAAATTACCAC 59.775 45.455 1.11 0.00 37.43 4.16
3714 7705 2.484264 ACCTCGCACTGCAAGAAATTAC 59.516 45.455 1.11 0.00 37.43 1.89
3715 7706 2.483877 CACCTCGCACTGCAAGAAATTA 59.516 45.455 1.11 0.00 37.43 1.40
3717 7708 0.877071 CACCTCGCACTGCAAGAAAT 59.123 50.000 1.11 0.00 37.43 2.17
3721 7712 0.882042 AGTTCACCTCGCACTGCAAG 60.882 55.000 1.11 0.00 42.29 4.01
3870 7861 0.404040 AGCGATAGGAGAGGAGGAGG 59.596 60.000 0.00 0.00 0.00 4.30
3871 7862 1.533625 CAGCGATAGGAGAGGAGGAG 58.466 60.000 0.00 0.00 0.00 3.69
3872 7863 0.538516 GCAGCGATAGGAGAGGAGGA 60.539 60.000 0.00 0.00 0.00 3.71
3873 7864 0.825425 TGCAGCGATAGGAGAGGAGG 60.825 60.000 0.00 0.00 0.00 4.30
3936 7959 1.673033 GGTCAACCCAGTCGACATCAG 60.673 57.143 19.50 5.85 0.00 2.90
3981 8004 4.360563 CCATCACACTTAGTTAGCGTAGG 58.639 47.826 0.00 0.00 0.00 3.18
4040 8063 2.749621 GACAATCACATCACCTTCACCC 59.250 50.000 0.00 0.00 0.00 4.61
4082 8105 3.559171 TGGCACAACTGAGGAAGTAATCC 60.559 47.826 0.00 0.00 42.59 3.01
4098 8121 3.380954 TCGTTATACTATCGGTTGGCACA 59.619 43.478 0.00 0.00 0.00 4.57
4129 8152 0.542702 CATGCCCAGGTCCCAGTTTT 60.543 55.000 0.00 0.00 0.00 2.43
4206 8241 1.219935 GATACAAACCGGACGGCCT 59.780 57.895 9.46 0.00 39.32 5.19
4233 8268 2.561478 TTTAGACACAAGTGGGCTCC 57.439 50.000 5.08 0.00 34.19 4.70
4376 8415 9.981114 ATGTCCAACTTTAATCCTGTTTTAAAG 57.019 29.630 12.14 12.14 45.61 1.85
4399 8438 5.772393 TCTTTGATGGTACCCAAGTATGT 57.228 39.130 10.07 0.00 36.95 2.29
4430 8469 9.549078 TTGTACAGACAATATCACAAGTAAACA 57.451 29.630 0.00 0.00 40.72 2.83
4535 8575 7.456269 TCTTTAATTTCCCAATTTTCCCTAGCA 59.544 33.333 0.00 0.00 34.29 3.49
4541 8581 8.669946 TGTGTTCTTTAATTTCCCAATTTTCC 57.330 30.769 0.00 0.00 34.29 3.13
4679 8720 1.271871 TGGGCCTGTATTGTCCACAAG 60.272 52.381 4.53 0.00 39.47 3.16
4736 8777 8.772036 GTACTCAAAGTAATCGGTAGGCCGTT 62.772 46.154 0.00 3.19 44.44 4.44
4747 8788 8.509690 GTGTTTTTAGGGGTACTCAAAGTAATC 58.490 37.037 0.00 0.00 31.62 1.75
4771 8959 6.621596 GCTTCAAGTGCTCAAAGTAATAGGTG 60.622 42.308 0.00 0.00 0.00 4.00
4865 9057 7.773690 GGTGAATTTGAGCTTATAAACTCCCTA 59.226 37.037 12.28 0.34 31.65 3.53
5039 9234 9.462174 CACAACAAAAATGAGCTCTACAAAATA 57.538 29.630 16.19 0.00 0.00 1.40
5053 9248 7.547370 TGGTCTAGGAAAAACACAACAAAAATG 59.453 33.333 0.00 0.00 0.00 2.32
5162 9358 3.572604 ACCACTACGAGCAGTAAACTC 57.427 47.619 0.00 0.00 34.45 3.01
5164 9361 3.177487 GCTACCACTACGAGCAGTAAAC 58.823 50.000 0.00 0.00 36.20 2.01
5172 9369 3.821600 AGGTCATATGCTACCACTACGAG 59.178 47.826 14.30 0.00 38.30 4.18
5175 9372 3.819337 TCGAGGTCATATGCTACCACTAC 59.181 47.826 14.30 0.00 38.30 2.73
5180 9377 3.150767 ACTCTCGAGGTCATATGCTACC 58.849 50.000 13.56 5.60 35.91 3.18
5181 9378 5.239351 TCTACTCTCGAGGTCATATGCTAC 58.761 45.833 13.56 0.00 0.00 3.58
5192 9389 3.697045 ACAATGTCCTTCTACTCTCGAGG 59.303 47.826 13.56 5.96 0.00 4.63
5251 9448 8.867112 ATGCATGTTAATTTCATCATCTTGAC 57.133 30.769 0.00 0.00 0.00 3.18
5252 9449 9.878667 AAATGCATGTTAATTTCATCATCTTGA 57.121 25.926 0.00 0.00 0.00 3.02
5281 9478 2.436646 ATCCGCCTTCTGCAACCG 60.437 61.111 0.00 0.00 41.33 4.44
5283 9480 0.674895 ACAGATCCGCCTTCTGCAAC 60.675 55.000 7.22 0.00 43.57 4.17
5369 9566 1.444553 GTGCTTCTCCGACGAGTGG 60.445 63.158 0.00 0.00 37.40 4.00
5440 9637 0.597568 TTGCAATGGAAGAGGCGTTG 59.402 50.000 0.00 0.00 0.00 4.10
5441 9638 0.598065 GTTGCAATGGAAGAGGCGTT 59.402 50.000 0.59 0.00 0.00 4.84
5443 9640 0.597568 TTGTTGCAATGGAAGAGGCG 59.402 50.000 0.59 0.00 0.00 5.52
5444 9641 2.407090 GTTTGTTGCAATGGAAGAGGC 58.593 47.619 0.59 0.00 0.00 4.70
5445 9642 2.364970 TGGTTTGTTGCAATGGAAGAGG 59.635 45.455 0.59 0.00 0.00 3.69
5447 9644 4.478206 TTTGGTTTGTTGCAATGGAAGA 57.522 36.364 0.59 0.00 0.00 2.87
5448 9645 5.557891 TTTTTGGTTTGTTGCAATGGAAG 57.442 34.783 0.59 0.00 0.00 3.46
5468 9665 0.379316 GTGTGGAACTTCGCCGTTTT 59.621 50.000 0.00 0.00 38.04 2.43
5500 9697 3.555966 TGATGAGGAGAGCGAGATACAA 58.444 45.455 0.00 0.00 0.00 2.41
5502 9699 3.755905 TGATGATGAGGAGAGCGAGATAC 59.244 47.826 0.00 0.00 0.00 2.24
5507 9704 1.000618 GCATGATGATGAGGAGAGCGA 59.999 52.381 0.00 0.00 0.00 4.93
5931 10128 1.448922 CGATCTCCTCCAGGGTCGTC 61.449 65.000 0.00 0.00 36.25 4.20
5935 10132 1.456705 GCTCGATCTCCTCCAGGGT 60.457 63.158 0.00 0.00 36.25 4.34
6058 10255 4.694233 CGACTGCTGCTGGTGCCT 62.694 66.667 11.29 0.00 38.71 4.75
6141 10338 4.834453 CAGCTCGCTCTGGGCCAG 62.834 72.222 28.01 28.01 37.74 4.85
6219 10450 0.035630 CCAGGAGAAGCCCAAGACAG 60.036 60.000 0.00 0.00 37.37 3.51
6246 10477 4.235731 GGTGGGCCGAAAGTATGG 57.764 61.111 0.00 0.00 0.00 2.74
6290 10531 5.879763 TCTCCAACATTTTCTCCATCTTGA 58.120 37.500 0.00 0.00 0.00 3.02
6291 10532 5.942236 TCTCTCCAACATTTTCTCCATCTTG 59.058 40.000 0.00 0.00 0.00 3.02
6388 10678 3.495100 CGCCCTCCAAGAGCAATTAGTAT 60.495 47.826 0.00 0.00 0.00 2.12
6414 10704 2.134789 AGGGAGCATCATTCCAACAC 57.865 50.000 0.00 0.00 36.40 3.32
6443 10733 6.757897 TCAATTAGTTTTGCAGATACTGGG 57.242 37.500 7.47 0.00 31.21 4.45
6498 10788 6.338146 ACCCGGAAAAAGAAAGAAAGAAAAG 58.662 36.000 0.73 0.00 0.00 2.27
6499 10789 6.288941 ACCCGGAAAAAGAAAGAAAGAAAA 57.711 33.333 0.73 0.00 0.00 2.29
6517 10807 8.848474 ATACATCAAAATCTAAGATAACCCGG 57.152 34.615 0.00 0.00 0.00 5.73
6568 10874 9.599866 CCACATCATCTAATCTACAACAAGTAA 57.400 33.333 0.00 0.00 30.92 2.24
6585 10891 2.739932 CGTTCAGGACCTCCACATCATC 60.740 54.545 0.00 0.00 38.89 2.92
6657 10968 4.025401 CACCGAACAGGCGCAACC 62.025 66.667 10.83 0.00 46.52 3.77
6720 11035 7.462331 GCACATGTACGTACAGTAATAACAGTG 60.462 40.741 30.15 21.35 39.92 3.66
6759 13587 0.809385 TGGAGCGACCTAACGAGAAG 59.191 55.000 0.00 0.00 39.86 2.85
6816 13644 2.651455 ACTTGACTCCCATCATGCATG 58.349 47.619 21.07 21.07 0.00 4.06
6817 13645 3.285484 GAACTTGACTCCCATCATGCAT 58.715 45.455 0.00 0.00 0.00 3.96
6818 13646 2.715046 GAACTTGACTCCCATCATGCA 58.285 47.619 0.00 0.00 0.00 3.96
6819 13647 1.667724 CGAACTTGACTCCCATCATGC 59.332 52.381 0.00 0.00 0.00 4.06
6830 13666 0.806492 GCGGGGAGATCGAACTTGAC 60.806 60.000 0.00 0.00 0.00 3.18
6863 13700 3.928992 CAGTGTGCTACAGAACATGGTAG 59.071 47.826 0.00 0.00 35.73 3.18
6864 13701 3.576550 TCAGTGTGCTACAGAACATGGTA 59.423 43.478 0.00 0.00 35.73 3.25
6872 13709 0.596577 GACGGTCAGTGTGCTACAGA 59.403 55.000 2.62 0.00 0.00 3.41
6890 13727 9.558396 AAAAATTCAATGAAGCTGTAAATTGGA 57.442 25.926 1.10 3.74 32.17 3.53
6947 13784 0.392998 CGGGAATGTTCAGAGGTGGG 60.393 60.000 0.00 0.00 0.00 4.61
6966 13803 1.693083 GCACATTCGCGTGTAGGGAC 61.693 60.000 5.77 0.00 41.78 4.46


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

AutoCloner maintained by Alex Coulton.