Multiple sequence alignment - TraesCS7A01G291500

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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 TraesCS7A01G291500 chr7A 100.000 7401 0 0 1 7401 355696645 355689245 0.000000e+00 13668.0
1 TraesCS7A01G291500 chr7A 96.491 114 2 2 6822 6934 355689769 355689657 3.530000e-43 187.0
2 TraesCS7A01G291500 chr7A 96.491 114 2 2 6877 6989 355689824 355689712 3.530000e-43 187.0
3 TraesCS7A01G291500 chr7A 96.610 59 2 0 6822 6880 355689715 355689657 1.700000e-16 99.0
4 TraesCS7A01G291500 chr7A 96.610 59 2 0 6931 6989 355689824 355689766 1.700000e-16 99.0
5 TraesCS7A01G291500 chr7B 96.548 6866 171 26 6 6838 350449326 350456158 0.000000e+00 11306.0
6 TraesCS7A01G291500 chr7B 91.304 253 13 3 6978 7222 350456172 350456423 3.310000e-88 337.0
7 TraesCS7A01G291500 chr7B 89.474 190 16 2 7216 7401 350456671 350456860 3.450000e-58 237.0
8 TraesCS7A01G291500 chr7B 98.969 97 0 1 7091 7187 350456499 350456594 9.870000e-39 172.0
9 TraesCS7A01G291500 chr7B 95.745 47 2 0 6938 6984 131939978 131940024 7.960000e-10 76.8
10 TraesCS7A01G291500 chr7B 88.136 59 5 2 6927 6984 744201277 744201334 1.330000e-07 69.4
11 TraesCS7A01G291500 chr7D 98.159 6354 83 10 511 6838 302028964 302022619 0.000000e+00 11055.0
12 TraesCS7A01G291500 chr7D 92.677 396 28 1 1 396 302036479 302036085 3.000000e-158 569.0
13 TraesCS7A01G291500 chr7D 84.890 364 26 16 6989 7345 302022540 302022199 2.560000e-89 340.0
14 TraesCS7A01G291500 chr7D 96.078 51 1 1 6834 6883 234809080 234809130 1.710000e-11 82.4
15 TraesCS7A01G291500 chr7D 90.164 61 3 2 6835 6892 140290175 140290235 7.960000e-10 76.8
16 TraesCS7A01G291500 chr7D 94.118 51 1 2 6889 6937 234809080 234809130 7.960000e-10 76.8
17 TraesCS7A01G291500 chr7D 88.525 61 3 3 6890 6946 140290175 140290235 3.700000e-08 71.3
18 TraesCS7A01G291500 chr7D 92.157 51 3 1 6984 7034 302022599 302022550 3.700000e-08 71.3
19 TraesCS7A01G291500 chr7D 88.333 60 3 4 6889 6944 6576305 6576364 1.330000e-07 69.4
20 TraesCS7A01G291500 chrUn 100.000 418 0 0 4289 4706 477001134 477000717 0.000000e+00 773.0
21 TraesCS7A01G291500 chrUn 92.453 53 4 0 6823 6875 339555047 339555099 7.960000e-10 76.8
22 TraesCS7A01G291500 chr3A 85.124 363 38 8 1952 2306 525288914 525288560 2.540000e-94 357.0
23 TraesCS7A01G291500 chr3A 90.909 55 2 3 6822 6875 586583627 586583679 3.700000e-08 71.3
24 TraesCS7A01G291500 chr1B 80.130 463 44 10 2154 2571 550914086 550914545 1.210000e-77 302.0
25 TraesCS7A01G291500 chr1B 89.933 149 15 0 1761 1909 550911890 550912038 7.580000e-45 193.0
26 TraesCS7A01G291500 chr1B 94.231 52 3 0 6824 6875 10962884 10962833 6.160000e-11 80.5
27 TraesCS7A01G291500 chr1B 94.595 37 2 0 15 51 60797498 60797534 2.880000e-04 58.4
28 TraesCS7A01G291500 chr5B 96.000 50 2 0 6935 6984 375129357 375129308 1.710000e-11 82.4
29 TraesCS7A01G291500 chr5B 100.000 43 0 0 6942 6984 528505198 528505156 6.160000e-11 80.5
30 TraesCS7A01G291500 chr5B 90.741 54 5 0 6822 6875 61384278 61384331 1.030000e-08 73.1
31 TraesCS7A01G291500 chr5B 100.000 28 0 0 24 51 504597162 504597189 1.300000e-02 52.8
32 TraesCS7A01G291500 chr4B 83.146 89 11 3 6826 6910 454040510 454040422 2.210000e-10 78.7
33 TraesCS7A01G291500 chr4B 81.111 90 12 4 6880 6964 454040511 454040422 4.790000e-07 67.6
34 TraesCS7A01G291500 chr4B 100.000 33 0 0 23 55 19747086 19747054 2.230000e-05 62.1
35 TraesCS7A01G291500 chr5D 88.235 68 3 5 6831 6893 183640966 183640899 7.960000e-10 76.8
36 TraesCS7A01G291500 chr5D 86.765 68 3 6 6886 6947 183640966 183640899 3.700000e-08 71.3
37 TraesCS7A01G291500 chr5D 95.349 43 1 1 6888 6929 10354928 10354970 4.790000e-07 67.6
38 TraesCS7A01G291500 chr5D 91.667 48 4 0 6828 6875 514202121 514202074 4.790000e-07 67.6
39 TraesCS7A01G291500 chr3B 95.745 47 2 0 6938 6984 822768207 822768161 7.960000e-10 76.8
40 TraesCS7A01G291500 chr3B 93.878 49 3 0 6936 6984 224471751 224471703 2.860000e-09 75.0
41 TraesCS7A01G291500 chr3B 86.567 67 5 3 24 88 29598897 29598961 3.700000e-08 71.3
42 TraesCS7A01G291500 chr3B 92.157 51 3 1 6825 6875 488122836 488122787 3.700000e-08 71.3
43 TraesCS7A01G291500 chr6A 85.333 75 7 4 6823 6893 611411305 611411231 2.860000e-09 75.0
44 TraesCS7A01G291500 chr6A 83.544 79 9 3 6833 6907 490991469 490991391 3.700000e-08 71.3
45 TraesCS7A01G291500 chr6A 84.000 75 7 4 6888 6957 490991469 490991395 4.790000e-07 67.6
46 TraesCS7A01G291500 chr6A 82.895 76 7 6 6878 6947 611411306 611411231 6.200000e-06 63.9
47 TraesCS7A01G291500 chr6A 100.000 30 0 0 24 53 182322059 182322088 1.000000e-03 56.5
48 TraesCS7A01G291500 chr2D 87.692 65 4 4 6920 6984 76750487 76750427 1.030000e-08 73.1
49 TraesCS7A01G291500 chr6B 89.655 58 1 5 6819 6875 599053373 599053426 1.330000e-07 69.4
50 TraesCS7A01G291500 chr1A 100.000 32 0 0 23 54 19817989 19817958 8.020000e-05 60.2
51 TraesCS7A01G291500 chr2B 100.000 29 0 0 24 52 604158058 604158030 4.000000e-03 54.7
52 TraesCS7A01G291500 chr4A 100.000 28 0 0 24 51 520683023 520683050 1.300000e-02 52.8
53 TraesCS7A01G291500 chr3D 100.000 28 0 0 24 51 47604206 47604179 1.300000e-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 TraesCS7A01G291500 chr7A 355689245 355696645 7400 True 13668.0 13668 100.000000 1 7401 1 chr7A.!!$R1 7400
1 TraesCS7A01G291500 chr7B 350449326 350456860 7534 False 3013.0 11306 94.073750 6 7401 4 chr7B.!!$F3 7395
2 TraesCS7A01G291500 chr7D 302022199 302028964 6765 True 3822.1 11055 91.735333 511 7345 3 chr7D.!!$R2 6834
3 TraesCS7A01G291500 chr1B 550911890 550914545 2655 False 247.5 302 85.031500 1761 2571 2 chr1B.!!$F2 810

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
491 494 0.109913 GGGGGCCTAATAAACCCGAG 59.890 60.000 0.84 0.0 45.27 4.63 F
493 496 1.134228 GGGCCTAATAAACCCGAGGA 58.866 55.000 0.84 0.0 32.92 3.71 F
1165 1183 1.157870 CGGTGACCACGCTGTTTCTT 61.158 55.000 1.11 0.0 0.00 2.52 F
2796 4723 0.610174 TGAATGCTCGAAGTCAGCCT 59.390 50.000 0.00 0.0 35.89 4.58 F
4075 6002 0.662619 TGCGTTGACAAGAAAGCTGG 59.337 50.000 0.00 0.0 32.27 4.85 F
4892 6819 0.967380 CTGAAAGGGGTGGTGATGGC 60.967 60.000 0.00 0.0 0.00 4.40 F
5616 7548 1.141053 GTGTTCCCCAGTTGACAGAGT 59.859 52.381 0.00 0.0 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 1382 1.662629 CATAGAGAACCACAGCAAGCG 59.337 52.381 0.00 0.00 0.00 4.68 R
1441 1462 2.105821 TGAACACCCTTGGTACCAGAAG 59.894 50.000 15.65 10.68 32.11 2.85 R
3028 4955 2.350134 CCTCCAGAGCAGCTGCAA 59.650 61.111 38.24 17.65 43.50 4.08 R
4717 6644 0.035317 ACTTGACCATGAGCGCTTCA 59.965 50.000 13.26 8.23 40.85 3.02 R
5623 7555 0.250770 GTTCTCTGGACAACCCACCC 60.251 60.000 0.00 0.00 40.82 4.61 R
6389 8324 0.320374 AGTCCTCGTCAAAATCGCCA 59.680 50.000 0.00 0.00 0.00 5.69 R
6774 8715 0.395311 AAGTGATGCCAGGATGCAGG 60.395 55.000 0.00 0.00 45.93 4.85 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
30 31 9.326413 CATGTTTCGACTTTTTATATACTCCCT 57.674 33.333 0.00 0.00 0.00 4.20
36 37 6.016443 CGACTTTTTATATACTCCCTCCGTCT 60.016 42.308 0.00 0.00 0.00 4.18
97 98 4.307259 TCTTATTAGGCCCCTCTGTTGAT 58.693 43.478 0.00 0.00 0.00 2.57
99 100 1.213296 TTAGGCCCCTCTGTTGATCC 58.787 55.000 0.00 0.00 0.00 3.36
132 133 4.575885 AGTAAGTGCGCTCCATTTCTTTA 58.424 39.130 9.73 0.00 0.00 1.85
144 145 5.858381 TCCATTTCTTTATCGATCTCCCAG 58.142 41.667 0.00 0.00 0.00 4.45
147 148 2.964209 TCTTTATCGATCTCCCAGGCT 58.036 47.619 0.00 0.00 0.00 4.58
165 166 1.530646 GCTACGGTTCGTCTTACGGAG 60.531 57.143 0.00 0.00 42.81 4.63
167 168 4.068302 GGTTCGTCTTACGGAGCG 57.932 61.111 0.00 0.00 37.88 5.03
183 184 0.740737 AGCGCAATCAATTACCAGCC 59.259 50.000 11.47 0.00 0.00 4.85
184 185 0.455410 GCGCAATCAATTACCAGCCA 59.545 50.000 0.30 0.00 0.00 4.75
186 187 2.481795 GCGCAATCAATTACCAGCCATT 60.482 45.455 0.30 0.00 0.00 3.16
187 188 3.117794 CGCAATCAATTACCAGCCATTG 58.882 45.455 0.00 0.00 0.00 2.82
213 214 7.182761 GCATGTAGAAACTGATGTACATTGAC 58.817 38.462 10.30 0.00 34.57 3.18
226 227 7.337689 TGATGTACATTGACCGTACTAGTACTT 59.662 37.037 26.36 15.58 39.96 2.24
238 239 6.215845 CGTACTAGTACTTCTCCTAGTCTCC 58.784 48.000 26.36 0.00 42.14 3.71
261 262 1.063649 CAGCCAGTGCATGCGATTC 59.936 57.895 14.09 3.60 41.13 2.52
338 341 2.950172 GCGCCTTGTTCGAAAGCGA 61.950 57.895 26.93 6.45 46.33 4.93
364 367 5.552178 AGAAAACTAACTGAGCCTAGGTTG 58.448 41.667 11.31 0.00 0.00 3.77
414 417 3.845775 CAGTAAATCACGCATGAAAACCG 59.154 43.478 0.00 0.00 38.69 4.44
415 418 3.749088 AGTAAATCACGCATGAAAACCGA 59.251 39.130 0.00 0.00 38.69 4.69
417 420 3.634568 AATCACGCATGAAAACCGAAA 57.365 38.095 0.00 0.00 38.69 3.46
488 491 1.690209 GGTTGGGGGCCTAATAAACCC 60.690 57.143 0.84 2.81 43.44 4.11
490 493 0.623911 TGGGGGCCTAATAAACCCGA 60.624 55.000 0.84 0.00 45.27 5.14
491 494 0.109913 GGGGGCCTAATAAACCCGAG 59.890 60.000 0.84 0.00 45.27 4.63
492 495 0.109913 GGGGCCTAATAAACCCGAGG 59.890 60.000 0.84 0.00 45.27 4.63
493 496 1.134228 GGGCCTAATAAACCCGAGGA 58.866 55.000 0.84 0.00 32.92 3.71
494 497 1.491754 GGGCCTAATAAACCCGAGGAA 59.508 52.381 0.84 0.00 32.92 3.36
499 505 5.455755 GGCCTAATAAACCCGAGGAAGTATT 60.456 44.000 0.00 0.00 0.00 1.89
501 507 6.017357 GCCTAATAAACCCGAGGAAGTATTTG 60.017 42.308 0.00 0.00 0.00 2.32
513 519 7.383687 CGAGGAAGTATTTGTTATATAGCCCA 58.616 38.462 0.00 0.00 0.00 5.36
690 706 2.890961 GGCGGCGAAGTAGAAGGC 60.891 66.667 12.98 0.00 0.00 4.35
699 715 3.800604 GCGAAGTAGAAGGCCCAATAGAG 60.801 52.174 0.00 0.00 0.00 2.43
797 813 3.033764 GTTTCGTCGCGTGCCTGA 61.034 61.111 5.77 0.00 0.00 3.86
1029 1047 5.733620 AGTCTGGAACAAAAGGTATACGA 57.266 39.130 0.00 0.00 38.70 3.43
1165 1183 1.157870 CGGTGACCACGCTGTTTCTT 61.158 55.000 1.11 0.00 0.00 2.52
1217 1235 1.597797 ATGTTCTCGCCGTTCGGGTA 61.598 55.000 13.16 0.00 40.26 3.69
1364 1382 5.878406 TTCCTCATCTTTCAGATCTACCC 57.122 43.478 0.00 0.00 31.32 3.69
1424 1445 4.041567 TGAAAGGATGAAGGCAGTTGACTA 59.958 41.667 0.00 0.00 29.55 2.59
1441 1462 3.321111 TGACTAGACTTGTGGTGGTCTTC 59.679 47.826 0.00 0.00 42.06 2.87
1614 1635 7.728847 AACTCAATGTTTTCCTTAATTTGGC 57.271 32.000 0.00 0.00 34.84 4.52
1680 1701 1.822990 CAGTGGCATTGCTGAGGAATT 59.177 47.619 8.82 0.00 34.87 2.17
1744 1765 6.253727 GTGGACTGTCACACTATTATTCTTCG 59.746 42.308 10.38 0.00 37.57 3.79
2642 4569 3.119602 GCATTTCATCATATGGCGAGCAT 60.120 43.478 2.13 0.00 0.00 3.79
2664 4591 4.901868 TCGCAAGGTTAAAACACTAGGAT 58.098 39.130 0.00 0.00 38.47 3.24
2796 4723 0.610174 TGAATGCTCGAAGTCAGCCT 59.390 50.000 0.00 0.00 35.89 4.58
2950 4877 2.492088 GGCCTTTGTTTCCCACTACATC 59.508 50.000 0.00 0.00 0.00 3.06
3060 4987 3.451178 TCTGGAGGGTAATACTGCACTTC 59.549 47.826 0.00 0.00 32.68 3.01
3089 5016 4.252073 TGTTGAGCAATGCAAACAAAACT 58.748 34.783 19.47 0.00 35.54 2.66
3139 5066 6.038271 GCTAAATCTTCGGATGTTACCATGTT 59.962 38.462 0.00 0.00 34.49 2.71
3414 5341 3.681897 GTCAACAGTTGCTGAGGTCATAG 59.318 47.826 8.58 0.00 35.18 2.23
3684 5611 6.430000 AGACTTGAGTTCTCTGTCTCTTACTC 59.570 42.308 16.46 0.00 33.31 2.59
3698 5625 4.021456 TCTCTTACTCAGGAACATTTCGCA 60.021 41.667 0.00 0.00 0.00 5.10
3938 5865 2.289002 GAGCGATGATAAACTTGGGCAG 59.711 50.000 0.00 0.00 0.00 4.85
4075 6002 0.662619 TGCGTTGACAAGAAAGCTGG 59.337 50.000 0.00 0.00 32.27 4.85
4287 6214 3.262660 TCATGGTCTCAATTCAGAGTGCT 59.737 43.478 0.00 0.00 36.97 4.40
4706 6633 5.709164 CAGGAAGGAAGATTGTGATGTTTCT 59.291 40.000 0.00 0.00 0.00 2.52
4709 6636 5.511386 AGGAAGATTGTGATGTTTCTCCT 57.489 39.130 0.00 0.00 0.00 3.69
4717 6644 5.233083 TGTGATGTTTCTCCTGTCTCATT 57.767 39.130 0.00 0.00 0.00 2.57
4892 6819 0.967380 CTGAAAGGGGTGGTGATGGC 60.967 60.000 0.00 0.00 0.00 4.40
5240 7172 3.983741 ACTAATGCCGCATACTCTCTTC 58.016 45.455 6.22 0.00 0.00 2.87
5241 7173 3.639094 ACTAATGCCGCATACTCTCTTCT 59.361 43.478 6.22 0.00 0.00 2.85
5242 7174 3.550437 AATGCCGCATACTCTCTTCTT 57.450 42.857 6.22 0.00 0.00 2.52
5333 7265 1.890979 GGTGGAGCATCTCGGCATG 60.891 63.158 0.00 0.00 35.83 4.06
5548 7480 4.396166 GCAGCAAATACAAGTACCATGTCT 59.604 41.667 5.26 0.00 32.27 3.41
5616 7548 1.141053 GTGTTCCCCAGTTGACAGAGT 59.859 52.381 0.00 0.00 0.00 3.24
5623 7555 2.498167 CCAGTTGACAGAGTTGGAAGG 58.502 52.381 0.00 0.00 0.00 3.46
5624 7556 2.498167 CAGTTGACAGAGTTGGAAGGG 58.502 52.381 0.00 0.00 0.00 3.95
5722 7654 3.157881 TGGTCGATATGGTCCTCAGATC 58.842 50.000 3.00 0.00 39.88 2.75
6015 7947 4.127171 GTTATGCGTGGTAGTCCATCAAT 58.873 43.478 0.00 0.00 46.20 2.57
6348 8283 6.065976 TGGAGATAAACTTCATCCACACAT 57.934 37.500 0.00 0.00 35.16 3.21
6356 8291 4.084287 ACTTCATCCACACATTTCTGCAT 58.916 39.130 0.00 0.00 0.00 3.96
6389 8324 1.303643 CCGCAAAGAGGAAGCCCTT 60.304 57.895 0.00 0.00 44.53 3.95
6540 8475 5.652452 AGTCATTACTATTTGCCAAAGGGAC 59.348 40.000 0.00 0.00 32.84 4.46
6728 8669 8.804912 TTTGCAATCTTATTTAATGGGCATTT 57.195 26.923 0.00 0.00 32.50 2.32
6755 8696 7.180229 TCCCTGTATGAGATTCACTTAAACAGA 59.820 37.037 0.00 0.00 35.57 3.41
6778 8719 4.380841 TCAATCATTTGAAGCATCCTGC 57.619 40.909 0.00 0.00 38.90 4.85
6779 8720 3.764972 TCAATCATTTGAAGCATCCTGCA 59.235 39.130 1.52 0.00 40.40 4.41
6780 8721 4.404394 TCAATCATTTGAAGCATCCTGCAT 59.596 37.500 1.52 0.00 40.40 3.96
6781 8722 4.745125 CAATCATTTGAAGCATCCTGCATC 59.255 41.667 1.52 0.00 41.06 3.91
6839 8788 7.427214 ACTGTCAGTTCTCTTAAGTTGTACTC 58.573 38.462 0.00 0.00 0.00 2.59
6840 8789 6.746120 TGTCAGTTCTCTTAAGTTGTACTCC 58.254 40.000 1.63 1.55 0.00 3.85
6841 8790 6.157904 GTCAGTTCTCTTAAGTTGTACTCCC 58.842 44.000 1.63 0.00 0.00 4.30
6842 8791 6.015265 GTCAGTTCTCTTAAGTTGTACTCCCT 60.015 42.308 1.63 0.00 0.00 4.20
6844 8793 5.481122 AGTTCTCTTAAGTTGTACTCCCTCC 59.519 44.000 1.63 0.00 0.00 4.30
6846 8795 3.762823 CTCTTAAGTTGTACTCCCTCCGT 59.237 47.826 1.63 0.00 0.00 4.69
6847 8796 4.154942 TCTTAAGTTGTACTCCCTCCGTT 58.845 43.478 1.63 0.00 0.00 4.44
6848 8797 4.219288 TCTTAAGTTGTACTCCCTCCGTTC 59.781 45.833 1.63 0.00 0.00 3.95
6849 8798 1.264295 AGTTGTACTCCCTCCGTTCC 58.736 55.000 0.00 0.00 0.00 3.62
6850 8799 0.971386 GTTGTACTCCCTCCGTTCCA 59.029 55.000 0.00 0.00 0.00 3.53
6851 8800 1.345415 GTTGTACTCCCTCCGTTCCAA 59.655 52.381 0.00 0.00 0.00 3.53
6852 8801 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
6853 8802 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
6854 8803 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
6855 8804 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
6856 8805 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
6857 8806 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
6858 8807 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
6859 8808 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
6860 8809 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
6861 8810 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
6862 8811 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
6863 8812 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
6864 8813 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
6865 8814 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
6866 8815 4.644685 CCGTTCCAAAATAGATGACCCAAT 59.355 41.667 0.00 0.00 0.00 3.16
6867 8816 5.127031 CCGTTCCAAAATAGATGACCCAATT 59.873 40.000 0.00 0.00 0.00 2.32
6868 8817 6.350949 CCGTTCCAAAATAGATGACCCAATTT 60.351 38.462 0.00 0.00 0.00 1.82
6869 8818 7.096551 CGTTCCAAAATAGATGACCCAATTTT 58.903 34.615 0.00 0.00 33.07 1.82
6870 8819 8.247562 CGTTCCAAAATAGATGACCCAATTTTA 58.752 33.333 0.00 0.00 31.97 1.52
6877 8826 9.847224 AAATAGATGACCCAATTTTATACTCGT 57.153 29.630 0.00 0.00 0.00 4.18
6878 8827 9.847224 AATAGATGACCCAATTTTATACTCGTT 57.153 29.630 0.00 0.00 0.00 3.85
6879 8828 9.847224 ATAGATGACCCAATTTTATACTCGTTT 57.153 29.630 0.00 0.00 0.00 3.60
6880 8829 8.575649 AGATGACCCAATTTTATACTCGTTTT 57.424 30.769 0.00 0.00 0.00 2.43
6881 8830 8.674607 AGATGACCCAATTTTATACTCGTTTTC 58.325 33.333 0.00 0.00 0.00 2.29
6882 8831 7.989416 TGACCCAATTTTATACTCGTTTTCT 57.011 32.000 0.00 0.00 0.00 2.52
6883 8832 8.398878 TGACCCAATTTTATACTCGTTTTCTT 57.601 30.769 0.00 0.00 0.00 2.52
6884 8833 9.504708 TGACCCAATTTTATACTCGTTTTCTTA 57.495 29.630 0.00 0.00 0.00 2.10
6895 8844 8.754230 ATACTCGTTTTCTTAAGTTGTACTCC 57.246 34.615 1.63 0.00 0.00 3.85
6896 8845 5.987953 ACTCGTTTTCTTAAGTTGTACTCCC 59.012 40.000 1.63 0.00 0.00 4.30
6897 8846 6.165700 TCGTTTTCTTAAGTTGTACTCCCT 57.834 37.500 1.63 0.00 0.00 4.20
6898 8847 6.218746 TCGTTTTCTTAAGTTGTACTCCCTC 58.781 40.000 1.63 0.00 0.00 4.30
6899 8848 5.407691 CGTTTTCTTAAGTTGTACTCCCTCC 59.592 44.000 1.63 0.00 0.00 4.30
6900 8849 4.796038 TTCTTAAGTTGTACTCCCTCCG 57.204 45.455 1.63 0.00 0.00 4.63
6901 8850 3.771216 TCTTAAGTTGTACTCCCTCCGT 58.229 45.455 1.63 0.00 0.00 4.69
6902 8851 4.154942 TCTTAAGTTGTACTCCCTCCGTT 58.845 43.478 1.63 0.00 0.00 4.44
6903 8852 4.219288 TCTTAAGTTGTACTCCCTCCGTTC 59.781 45.833 1.63 0.00 0.00 3.95
6904 8853 1.264295 AGTTGTACTCCCTCCGTTCC 58.736 55.000 0.00 0.00 0.00 3.62
6905 8854 0.971386 GTTGTACTCCCTCCGTTCCA 59.029 55.000 0.00 0.00 0.00 3.53
6906 8855 1.345415 GTTGTACTCCCTCCGTTCCAA 59.655 52.381 0.00 0.00 0.00 3.53
6907 8856 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
6908 8857 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
6909 8858 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
6910 8859 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
6911 8860 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
6912 8861 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
6913 8862 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
6914 8863 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
6915 8864 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
6916 8865 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
6917 8866 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
6918 8867 4.513442 CTCCGTTCCAAAATAGATGACCA 58.487 43.478 0.00 0.00 0.00 4.02
6919 8868 4.912586 TCCGTTCCAAAATAGATGACCAA 58.087 39.130 0.00 0.00 0.00 3.67
6920 8869 5.505780 TCCGTTCCAAAATAGATGACCAAT 58.494 37.500 0.00 0.00 0.00 3.16
6921 8870 5.949354 TCCGTTCCAAAATAGATGACCAATT 59.051 36.000 0.00 0.00 0.00 2.32
6922 8871 6.435904 TCCGTTCCAAAATAGATGACCAATTT 59.564 34.615 0.00 0.00 0.00 1.82
6923 8872 7.039363 TCCGTTCCAAAATAGATGACCAATTTT 60.039 33.333 0.00 0.00 34.09 1.82
6924 8873 8.247562 CCGTTCCAAAATAGATGACCAATTTTA 58.752 33.333 0.00 0.00 32.89 1.52
6925 8874 9.801873 CGTTCCAAAATAGATGACCAATTTTAT 57.198 29.630 0.00 0.00 32.89 1.40
6936 8885 9.449719 AGATGACCAATTTTATACTCGTTTTCT 57.550 29.630 0.00 0.00 0.00 2.52
6949 8898 8.754230 ATACTCGTTTTCTTAAGTTGTACTCC 57.246 34.615 1.63 0.00 0.00 3.85
6950 8899 5.987953 ACTCGTTTTCTTAAGTTGTACTCCC 59.012 40.000 1.63 0.00 0.00 4.30
6951 8900 6.165700 TCGTTTTCTTAAGTTGTACTCCCT 57.834 37.500 1.63 0.00 0.00 4.20
6952 8901 6.218746 TCGTTTTCTTAAGTTGTACTCCCTC 58.781 40.000 1.63 0.00 0.00 4.30
6953 8902 5.407691 CGTTTTCTTAAGTTGTACTCCCTCC 59.592 44.000 1.63 0.00 0.00 4.30
6954 8903 4.796038 TTCTTAAGTTGTACTCCCTCCG 57.204 45.455 1.63 0.00 0.00 4.63
6955 8904 3.771216 TCTTAAGTTGTACTCCCTCCGT 58.229 45.455 1.63 0.00 0.00 4.69
6956 8905 4.154942 TCTTAAGTTGTACTCCCTCCGTT 58.845 43.478 1.63 0.00 0.00 4.44
6957 8906 4.590222 TCTTAAGTTGTACTCCCTCCGTTT 59.410 41.667 1.63 0.00 0.00 3.60
6958 8907 3.397849 AAGTTGTACTCCCTCCGTTTC 57.602 47.619 0.00 0.00 0.00 2.78
6959 8908 2.322658 AGTTGTACTCCCTCCGTTTCA 58.677 47.619 0.00 0.00 0.00 2.69
6960 8909 2.701951 AGTTGTACTCCCTCCGTTTCAA 59.298 45.455 0.00 0.00 0.00 2.69
6961 8910 3.135167 AGTTGTACTCCCTCCGTTTCAAA 59.865 43.478 0.00 0.00 0.00 2.69
6962 8911 3.842007 TGTACTCCCTCCGTTTCAAAA 57.158 42.857 0.00 0.00 0.00 2.44
6963 8912 4.360951 TGTACTCCCTCCGTTTCAAAAT 57.639 40.909 0.00 0.00 0.00 1.82
6964 8913 5.486735 TGTACTCCCTCCGTTTCAAAATA 57.513 39.130 0.00 0.00 0.00 1.40
6965 8914 5.484715 TGTACTCCCTCCGTTTCAAAATAG 58.515 41.667 0.00 0.00 0.00 1.73
6966 8915 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
6967 8916 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
6968 8917 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
6969 8918 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
6970 8919 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
6971 8920 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
6972 8921 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
6973 8922 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
6974 8923 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
6975 8924 5.949354 TCCGTTTCAAAATAGATGACCCAAT 59.051 36.000 0.00 0.00 0.00 3.16
6976 8925 6.435904 TCCGTTTCAAAATAGATGACCCAATT 59.564 34.615 0.00 0.00 0.00 2.32
6977 8926 7.039363 TCCGTTTCAAAATAGATGACCCAATTT 60.039 33.333 0.00 0.00 0.00 1.82
6978 8927 7.602265 CCGTTTCAAAATAGATGACCCAATTTT 59.398 33.333 0.00 0.00 33.07 1.82
6979 8928 9.632807 CGTTTCAAAATAGATGACCCAATTTTA 57.367 29.630 0.00 0.00 31.97 1.52
7070 9080 5.212194 CACATGTTAAGTACAAACTGTGGC 58.788 41.667 20.65 0.00 40.89 5.01
7078 9088 5.642163 AGTACAAACTGTGGCAGATGGCA 62.642 47.826 4.78 4.78 40.64 4.92
7104 9114 1.233019 CATCTCACGATTGCCATCCC 58.767 55.000 0.00 0.00 0.00 3.85
7114 9124 1.361204 TTGCCATCCCTCAACAGAGA 58.639 50.000 0.00 0.00 0.00 3.10
7263 9538 1.621317 TCCTCACGTTGCTGTCCAATA 59.379 47.619 0.00 0.00 35.55 1.90
7280 9556 3.494626 CCAATATCGTACATGTGACTGGC 59.505 47.826 9.11 0.00 0.00 4.85
7345 9624 6.542370 GGTAAGGATTAACTACATGCATGTGT 59.458 38.462 36.72 28.32 35.92 3.72
7347 9626 6.683974 AGGATTAACTACATGCATGTGTTC 57.316 37.500 36.72 24.35 41.89 3.18
7372 9651 7.496920 TCATGTCATTCCACTGTATTTCATCTC 59.503 37.037 0.00 0.00 0.00 2.75
7373 9652 6.710278 TGTCATTCCACTGTATTTCATCTCA 58.290 36.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.123830 AGTATATAAAAAGTCGAAACATGCGC 58.876 34.615 0.00 0.00 0.00 6.09
2 3 7.792508 GGAGTATATAAAAAGTCGAAACATGCG 59.207 37.037 0.00 0.00 0.00 4.73
3 4 8.068380 GGGAGTATATAAAAAGTCGAAACATGC 58.932 37.037 0.00 0.00 0.00 4.06
4 5 9.326413 AGGGAGTATATAAAAAGTCGAAACATG 57.674 33.333 0.00 0.00 0.00 3.21
5 6 9.543783 GAGGGAGTATATAAAAAGTCGAAACAT 57.456 33.333 0.00 0.00 0.00 2.71
6 7 7.983484 GGAGGGAGTATATAAAAAGTCGAAACA 59.017 37.037 0.00 0.00 0.00 2.83
7 8 7.168804 CGGAGGGAGTATATAAAAAGTCGAAAC 59.831 40.741 0.00 0.00 0.00 2.78
8 9 7.147846 ACGGAGGGAGTATATAAAAAGTCGAAA 60.148 37.037 0.00 0.00 0.00 3.46
9 10 6.322201 ACGGAGGGAGTATATAAAAAGTCGAA 59.678 38.462 0.00 0.00 0.00 3.71
10 11 5.829924 ACGGAGGGAGTATATAAAAAGTCGA 59.170 40.000 0.00 0.00 0.00 4.20
11 12 6.016443 AGACGGAGGGAGTATATAAAAAGTCG 60.016 42.308 0.00 0.00 0.00 4.18
12 13 7.146648 CAGACGGAGGGAGTATATAAAAAGTC 58.853 42.308 0.00 0.00 0.00 3.01
13 14 6.041751 CCAGACGGAGGGAGTATATAAAAAGT 59.958 42.308 0.00 0.00 0.00 2.66
14 15 6.456501 CCAGACGGAGGGAGTATATAAAAAG 58.543 44.000 0.00 0.00 0.00 2.27
15 16 6.415206 CCAGACGGAGGGAGTATATAAAAA 57.585 41.667 0.00 0.00 0.00 1.94
30 31 0.034863 GCCCAATAAACCCAGACGGA 60.035 55.000 0.00 0.00 34.64 4.69
36 37 1.304547 CACGGGCCCAATAAACCCA 60.305 57.895 24.92 0.00 44.49 4.51
70 71 0.105142 AGGGGCCTAATAAGAGCGGA 60.105 55.000 0.84 0.00 0.00 5.54
78 79 2.979678 GGATCAACAGAGGGGCCTAATA 59.020 50.000 0.84 0.00 0.00 0.98
97 98 0.109723 ACTTACTTTTGGCAGCCGGA 59.890 50.000 5.05 0.00 0.00 5.14
99 100 0.387239 GCACTTACTTTTGGCAGCCG 60.387 55.000 7.03 0.00 0.00 5.52
132 133 0.896019 CCGTAGCCTGGGAGATCGAT 60.896 60.000 0.00 0.00 0.00 3.59
144 145 0.524180 CCGTAAGACGAACCGTAGCC 60.524 60.000 0.00 0.00 46.05 3.93
147 148 0.447801 GCTCCGTAAGACGAACCGTA 59.552 55.000 0.00 0.00 46.05 4.02
165 166 0.455410 TGGCTGGTAATTGATTGCGC 59.545 50.000 0.00 0.00 0.00 6.09
167 168 3.460103 CCAATGGCTGGTAATTGATTGC 58.540 45.455 0.00 0.00 40.78 3.56
183 184 5.571784 ACATCAGTTTCTACATGCCAATG 57.428 39.130 0.00 0.00 39.89 2.82
184 185 6.179756 TGTACATCAGTTTCTACATGCCAAT 58.820 36.000 0.00 0.00 0.00 3.16
186 187 5.159273 TGTACATCAGTTTCTACATGCCA 57.841 39.130 0.00 0.00 0.00 4.92
187 188 6.316140 TCAATGTACATCAGTTTCTACATGCC 59.684 38.462 9.23 0.00 0.00 4.40
188 189 7.182761 GTCAATGTACATCAGTTTCTACATGC 58.817 38.462 9.23 0.00 0.00 4.06
190 191 6.535150 CGGTCAATGTACATCAGTTTCTACAT 59.465 38.462 9.23 0.00 0.00 2.29
191 192 5.867174 CGGTCAATGTACATCAGTTTCTACA 59.133 40.000 9.23 0.00 0.00 2.74
193 194 6.032956 ACGGTCAATGTACATCAGTTTCTA 57.967 37.500 9.23 0.00 0.00 2.10
196 197 5.790593 AGTACGGTCAATGTACATCAGTTT 58.209 37.500 9.23 0.00 43.61 2.66
197 198 5.401531 AGTACGGTCAATGTACATCAGTT 57.598 39.130 9.23 0.00 43.61 3.16
198 199 5.651139 ACTAGTACGGTCAATGTACATCAGT 59.349 40.000 9.23 6.45 43.61 3.41
226 227 0.260230 CTGGCTGGGAGACTAGGAGA 59.740 60.000 0.00 0.00 39.75 3.71
238 239 3.449227 CATGCACTGGCTGGCTGG 61.449 66.667 12.46 3.50 41.91 4.85
261 262 7.654568 TGCATGCCTAATGAAAAGATGATTAG 58.345 34.615 16.68 0.00 38.72 1.73
319 322 2.126850 GCTTTCGAACAAGGCGCC 60.127 61.111 21.89 21.89 0.00 6.53
338 341 5.071923 ACCTAGGCTCAGTTAGTTTTCTTGT 59.928 40.000 9.30 0.00 0.00 3.16
341 344 5.552178 CAACCTAGGCTCAGTTAGTTTTCT 58.448 41.667 9.30 0.00 0.00 2.52
451 454 6.493458 CCCCCAACCAAAATATAGGTATCAAG 59.507 42.308 0.00 0.00 37.07 3.02
461 464 3.786213 TTAGGCCCCCAACCAAAATAT 57.214 42.857 0.00 0.00 0.00 1.28
463 466 2.659264 ATTAGGCCCCCAACCAAAAT 57.341 45.000 0.00 0.00 0.00 1.82
471 474 0.623911 TCGGGTTTATTAGGCCCCCA 60.624 55.000 11.10 0.00 39.22 4.96
472 475 0.109913 CTCGGGTTTATTAGGCCCCC 59.890 60.000 0.00 0.00 39.22 5.40
488 491 7.383687 TGGGCTATATAACAAATACTTCCTCG 58.616 38.462 0.00 0.00 0.00 4.63
490 493 7.660208 CGTTGGGCTATATAACAAATACTTCCT 59.340 37.037 0.00 0.00 0.00 3.36
491 494 7.443272 ACGTTGGGCTATATAACAAATACTTCC 59.557 37.037 0.00 0.00 0.00 3.46
492 495 8.374327 ACGTTGGGCTATATAACAAATACTTC 57.626 34.615 0.00 0.00 0.00 3.01
493 496 7.443272 GGACGTTGGGCTATATAACAAATACTT 59.557 37.037 0.00 0.00 0.00 2.24
494 497 6.932960 GGACGTTGGGCTATATAACAAATACT 59.067 38.462 0.00 0.00 0.00 2.12
499 505 4.444536 GTGGACGTTGGGCTATATAACAA 58.555 43.478 0.00 0.00 0.00 2.83
501 507 3.070590 AGGTGGACGTTGGGCTATATAAC 59.929 47.826 0.00 0.00 0.00 1.89
690 706 2.768527 TGCTCCAGACTTCTCTATTGGG 59.231 50.000 0.00 0.00 0.00 4.12
699 715 1.739562 CACGGCTGCTCCAGACTTC 60.740 63.158 0.00 0.00 37.36 3.01
801 817 2.278330 CCTTTTCACCCTGCCTGCC 61.278 63.158 0.00 0.00 0.00 4.85
802 818 2.278330 CCCTTTTCACCCTGCCTGC 61.278 63.158 0.00 0.00 0.00 4.85
803 819 0.895559 GACCCTTTTCACCCTGCCTG 60.896 60.000 0.00 0.00 0.00 4.85
804 820 1.460699 GACCCTTTTCACCCTGCCT 59.539 57.895 0.00 0.00 0.00 4.75
1029 1047 8.616799 AGTGAGATTTCTAAGATCTAGGGTTT 57.383 34.615 0.00 0.00 34.13 3.27
1217 1235 3.706594 TCCTCGGACAAAGCAGATCTAAT 59.293 43.478 0.00 0.00 0.00 1.73
1364 1382 1.662629 CATAGAGAACCACAGCAAGCG 59.337 52.381 0.00 0.00 0.00 4.68
1424 1445 3.041946 AGAAGAAGACCACCACAAGTCT 58.958 45.455 0.00 0.00 45.18 3.24
1441 1462 2.105821 TGAACACCCTTGGTACCAGAAG 59.894 50.000 15.65 10.68 32.11 2.85
1614 1635 2.554032 ACTTCCTTGAACCAAATCAGCG 59.446 45.455 0.00 0.00 0.00 5.18
2324 4246 3.767711 TCTTGAGCCACTTCTAGACTCA 58.232 45.455 6.02 6.02 35.67 3.41
2637 4564 3.058224 AGTGTTTTAACCTTGCGATGCTC 60.058 43.478 0.00 0.00 0.00 4.26
2642 4569 4.339872 TCCTAGTGTTTTAACCTTGCGA 57.660 40.909 0.00 0.00 0.00 5.10
2664 4591 2.957680 TCTTTTCTTCCATGTGCTTGCA 59.042 40.909 0.00 0.00 0.00 4.08
2950 4877 3.132646 AGGAGCAGACTCAGAGCTATTTG 59.867 47.826 0.00 0.00 45.42 2.32
3028 4955 2.350134 CCTCCAGAGCAGCTGCAA 59.650 61.111 38.24 17.65 43.50 4.08
3060 4987 5.006844 TGTTTGCATTGCTCAACAAAGAATG 59.993 36.000 18.75 0.00 42.86 2.67
3139 5066 4.261801 GCCTGGATTGCTTGAGTTAGTTA 58.738 43.478 0.00 0.00 0.00 2.24
3414 5341 8.840867 GTGAATTTTATCAACAGAATGACGAAC 58.159 33.333 0.00 0.00 39.69 3.95
3489 5416 4.018141 AGGATGAAATGAACCATCACCTGA 60.018 41.667 0.00 0.00 40.55 3.86
3684 5611 4.997062 GCAGCAAATGCGAAATGTTCCTG 61.997 47.826 0.00 0.00 46.99 3.86
3698 5625 4.060205 GTTTCTCCACATTTGCAGCAAAT 58.940 39.130 25.07 25.07 43.71 2.32
3938 5865 4.305769 CAGATATGCTCTGTAGTGAAGCC 58.694 47.826 0.00 0.00 45.42 4.35
4075 6002 4.272991 GGTCTGAATCATTGTCTGCATCTC 59.727 45.833 0.00 0.00 0.00 2.75
4287 6214 6.070824 TCCATGTCAGTATCTGCTTGTTTAGA 60.071 38.462 0.00 0.00 0.00 2.10
4706 6633 0.610174 AGCGCTTCAATGAGACAGGA 59.390 50.000 2.64 0.00 0.00 3.86
4709 6636 2.004733 CATGAGCGCTTCAATGAGACA 58.995 47.619 13.26 0.78 39.77 3.41
4717 6644 0.035317 ACTTGACCATGAGCGCTTCA 59.965 50.000 13.26 8.23 40.85 3.02
4892 6819 7.683578 TGATATTCAATGGATCCTCACCTAAG 58.316 38.462 14.23 0.00 0.00 2.18
5240 7172 6.239396 AGCCATCATCAGATCTGGATTAAAG 58.761 40.000 22.42 7.79 30.20 1.85
5241 7173 6.196918 AGCCATCATCAGATCTGGATTAAA 57.803 37.500 22.42 2.26 30.20 1.52
5242 7174 5.837770 AGCCATCATCAGATCTGGATTAA 57.162 39.130 22.42 3.04 30.20 1.40
5317 7249 0.462581 GAACATGCCGAGATGCTCCA 60.463 55.000 0.00 0.00 0.00 3.86
5333 7265 1.200020 CCCTCGGATGTTTGCTTGAAC 59.800 52.381 0.00 0.00 0.00 3.18
5548 7480 7.680730 AGCTACTTTTGTTTCTCATCCTTCTA 58.319 34.615 0.00 0.00 0.00 2.10
5616 7548 1.539665 GACAACCCACCCCTTCCAA 59.460 57.895 0.00 0.00 0.00 3.53
5623 7555 0.250770 GTTCTCTGGACAACCCACCC 60.251 60.000 0.00 0.00 40.82 4.61
5624 7556 0.250770 GGTTCTCTGGACAACCCACC 60.251 60.000 0.00 0.00 40.82 4.61
5722 7654 6.490566 TCATCAATGGCATGATCTTTATCG 57.509 37.500 0.00 0.00 37.96 2.92
6015 7947 9.739276 AATCATGTTGAGAGTAAGTGGAATTTA 57.261 29.630 0.00 0.00 0.00 1.40
6348 8283 2.573009 TCAGGTGATCTGGATGCAGAAA 59.427 45.455 21.52 9.83 43.53 2.52
6356 8291 1.191489 TGCGGTTCAGGTGATCTGGA 61.191 55.000 0.00 0.00 43.53 3.86
6389 8324 0.320374 AGTCCTCGTCAAAATCGCCA 59.680 50.000 0.00 0.00 0.00 5.69
6540 8475 3.325870 TCTTATGTGGCTTGAACAGACG 58.674 45.455 0.00 0.00 29.50 4.18
6728 8669 7.685481 TGTTTAAGTGAATCTCATACAGGGAA 58.315 34.615 0.00 0.00 0.00 3.97
6774 8715 0.395311 AAGTGATGCCAGGATGCAGG 60.395 55.000 0.00 0.00 45.93 4.85
6775 8716 1.022735 GAAGTGATGCCAGGATGCAG 58.977 55.000 0.00 0.00 45.93 4.41
6776 8717 0.622136 AGAAGTGATGCCAGGATGCA 59.378 50.000 0.00 0.00 46.94 3.96
6777 8718 1.022735 CAGAAGTGATGCCAGGATGC 58.977 55.000 0.00 0.00 31.97 3.91
6778 8719 2.286872 GACAGAAGTGATGCCAGGATG 58.713 52.381 0.00 0.00 0.00 3.51
6779 8720 1.911357 TGACAGAAGTGATGCCAGGAT 59.089 47.619 0.00 0.00 0.00 3.24
6780 8721 1.351076 TGACAGAAGTGATGCCAGGA 58.649 50.000 0.00 0.00 0.00 3.86
6781 8722 2.414994 ATGACAGAAGTGATGCCAGG 57.585 50.000 0.00 0.00 0.00 4.45
6828 8777 2.827921 GGAACGGAGGGAGTACAACTTA 59.172 50.000 0.00 0.00 0.00 2.24
6830 8779 1.264295 GGAACGGAGGGAGTACAACT 58.736 55.000 0.00 0.00 0.00 3.16
6831 8780 0.971386 TGGAACGGAGGGAGTACAAC 59.029 55.000 0.00 0.00 0.00 3.32
6833 8782 1.719529 TTTGGAACGGAGGGAGTACA 58.280 50.000 0.00 0.00 0.00 2.90
6834 8783 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
6835 8784 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
6836 8785 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
6837 8786 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
6839 8788 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
6840 8789 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
6841 8790 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
6842 8791 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
6844 8793 5.835113 ATTGGGTCATCTATTTTGGAACG 57.165 39.130 0.00 0.00 0.00 3.95
6851 8800 9.847224 ACGAGTATAAAATTGGGTCATCTATTT 57.153 29.630 0.00 0.00 0.00 1.40
6852 8801 9.847224 AACGAGTATAAAATTGGGTCATCTATT 57.153 29.630 0.00 0.00 0.00 1.73
6853 8802 9.847224 AAACGAGTATAAAATTGGGTCATCTAT 57.153 29.630 0.00 0.00 0.00 1.98
6854 8803 9.675464 AAAACGAGTATAAAATTGGGTCATCTA 57.325 29.630 0.00 0.00 0.00 1.98
6855 8804 8.575649 AAAACGAGTATAAAATTGGGTCATCT 57.424 30.769 0.00 0.00 0.00 2.90
6856 8805 8.674607 AGAAAACGAGTATAAAATTGGGTCATC 58.325 33.333 0.00 0.00 0.00 2.92
6857 8806 8.575649 AGAAAACGAGTATAAAATTGGGTCAT 57.424 30.769 0.00 0.00 0.00 3.06
6858 8807 7.989416 AGAAAACGAGTATAAAATTGGGTCA 57.011 32.000 0.00 0.00 0.00 4.02
6869 8818 9.846248 GGAGTACAACTTAAGAAAACGAGTATA 57.154 33.333 10.09 0.00 0.00 1.47
6870 8819 7.816513 GGGAGTACAACTTAAGAAAACGAGTAT 59.183 37.037 10.09 0.00 0.00 2.12
6871 8820 7.014615 AGGGAGTACAACTTAAGAAAACGAGTA 59.985 37.037 10.09 0.00 0.00 2.59
6872 8821 5.987953 GGGAGTACAACTTAAGAAAACGAGT 59.012 40.000 10.09 0.00 0.00 4.18
6873 8822 6.221659 AGGGAGTACAACTTAAGAAAACGAG 58.778 40.000 10.09 0.00 0.00 4.18
6874 8823 6.165700 AGGGAGTACAACTTAAGAAAACGA 57.834 37.500 10.09 0.00 0.00 3.85
6875 8824 5.407691 GGAGGGAGTACAACTTAAGAAAACG 59.592 44.000 10.09 0.00 0.00 3.60
6876 8825 5.407691 CGGAGGGAGTACAACTTAAGAAAAC 59.592 44.000 10.09 2.01 0.00 2.43
6877 8826 5.070847 ACGGAGGGAGTACAACTTAAGAAAA 59.929 40.000 10.09 0.00 0.00 2.29
6878 8827 4.590222 ACGGAGGGAGTACAACTTAAGAAA 59.410 41.667 10.09 0.00 0.00 2.52
6879 8828 4.154942 ACGGAGGGAGTACAACTTAAGAA 58.845 43.478 10.09 0.00 0.00 2.52
6880 8829 3.771216 ACGGAGGGAGTACAACTTAAGA 58.229 45.455 10.09 0.00 0.00 2.10
6881 8830 4.492611 GAACGGAGGGAGTACAACTTAAG 58.507 47.826 0.00 0.00 0.00 1.85
6882 8831 3.259123 GGAACGGAGGGAGTACAACTTAA 59.741 47.826 0.00 0.00 0.00 1.85
6883 8832 2.827921 GGAACGGAGGGAGTACAACTTA 59.172 50.000 0.00 0.00 0.00 2.24
6884 8833 1.622312 GGAACGGAGGGAGTACAACTT 59.378 52.381 0.00 0.00 0.00 2.66
6885 8834 1.264295 GGAACGGAGGGAGTACAACT 58.736 55.000 0.00 0.00 0.00 3.16
6886 8835 0.971386 TGGAACGGAGGGAGTACAAC 59.029 55.000 0.00 0.00 0.00 3.32
6887 8836 1.719529 TTGGAACGGAGGGAGTACAA 58.280 50.000 0.00 0.00 0.00 2.41
6888 8837 1.719529 TTTGGAACGGAGGGAGTACA 58.280 50.000 0.00 0.00 0.00 2.90
6889 8838 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
6890 8839 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
6891 8840 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
6892 8841 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
6893 8842 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
6894 8843 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
6895 8844 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
6896 8845 4.513442 TGGTCATCTATTTTGGAACGGAG 58.487 43.478 0.00 0.00 0.00 4.63
6897 8846 4.561500 TGGTCATCTATTTTGGAACGGA 57.438 40.909 0.00 0.00 0.00 4.69
6898 8847 5.835113 ATTGGTCATCTATTTTGGAACGG 57.165 39.130 0.00 0.00 0.00 4.44
6899 8848 9.801873 ATAAAATTGGTCATCTATTTTGGAACG 57.198 29.630 0.81 0.00 34.39 3.95
6910 8859 9.449719 AGAAAACGAGTATAAAATTGGTCATCT 57.550 29.630 0.00 0.00 0.00 2.90
6923 8872 9.846248 GGAGTACAACTTAAGAAAACGAGTATA 57.154 33.333 10.09 0.00 0.00 1.47
6924 8873 7.816513 GGGAGTACAACTTAAGAAAACGAGTAT 59.183 37.037 10.09 0.00 0.00 2.12
6925 8874 7.014615 AGGGAGTACAACTTAAGAAAACGAGTA 59.985 37.037 10.09 0.00 0.00 2.59
6926 8875 5.987953 GGGAGTACAACTTAAGAAAACGAGT 59.012 40.000 10.09 0.00 0.00 4.18
6927 8876 6.221659 AGGGAGTACAACTTAAGAAAACGAG 58.778 40.000 10.09 0.00 0.00 4.18
6928 8877 6.165700 AGGGAGTACAACTTAAGAAAACGA 57.834 37.500 10.09 0.00 0.00 3.85
6929 8878 5.407691 GGAGGGAGTACAACTTAAGAAAACG 59.592 44.000 10.09 0.00 0.00 3.60
6930 8879 5.407691 CGGAGGGAGTACAACTTAAGAAAAC 59.592 44.000 10.09 2.01 0.00 2.43
6931 8880 5.070847 ACGGAGGGAGTACAACTTAAGAAAA 59.929 40.000 10.09 0.00 0.00 2.29
6932 8881 4.590222 ACGGAGGGAGTACAACTTAAGAAA 59.410 41.667 10.09 0.00 0.00 2.52
6933 8882 4.154942 ACGGAGGGAGTACAACTTAAGAA 58.845 43.478 10.09 0.00 0.00 2.52
6934 8883 3.771216 ACGGAGGGAGTACAACTTAAGA 58.229 45.455 10.09 0.00 0.00 2.10
6935 8884 4.532314 AACGGAGGGAGTACAACTTAAG 57.468 45.455 0.00 0.00 0.00 1.85
6936 8885 4.344679 TGAAACGGAGGGAGTACAACTTAA 59.655 41.667 0.00 0.00 0.00 1.85
6937 8886 3.896888 TGAAACGGAGGGAGTACAACTTA 59.103 43.478 0.00 0.00 0.00 2.24
6938 8887 2.701951 TGAAACGGAGGGAGTACAACTT 59.298 45.455 0.00 0.00 0.00 2.66
6939 8888 2.322658 TGAAACGGAGGGAGTACAACT 58.677 47.619 0.00 0.00 0.00 3.16
6940 8889 2.825861 TGAAACGGAGGGAGTACAAC 57.174 50.000 0.00 0.00 0.00 3.32
6941 8890 3.842007 TTTGAAACGGAGGGAGTACAA 57.158 42.857 0.00 0.00 0.00 2.41
6942 8891 3.842007 TTTTGAAACGGAGGGAGTACA 57.158 42.857 0.00 0.00 0.00 2.90
6943 8892 5.727434 TCTATTTTGAAACGGAGGGAGTAC 58.273 41.667 0.00 0.00 0.00 2.73
6944 8893 6.155565 TCATCTATTTTGAAACGGAGGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
6945 8894 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
6946 8895 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
6947 8896 5.183228 GTCATCTATTTTGAAACGGAGGGA 58.817 41.667 0.00 0.00 0.00 4.20
6948 8897 4.335594 GGTCATCTATTTTGAAACGGAGGG 59.664 45.833 0.00 0.00 0.00 4.30
6949 8898 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
6950 8899 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
6951 8900 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
6952 8901 5.637006 TTGGGTCATCTATTTTGAAACGG 57.363 39.130 0.00 0.00 0.00 4.44
6953 8902 8.532977 AAAATTGGGTCATCTATTTTGAAACG 57.467 30.769 0.00 0.00 31.14 3.60
6960 8909 9.847224 ACGAGTATAAAATTGGGTCATCTATTT 57.153 29.630 0.00 0.00 0.00 1.40
6961 8910 9.847224 AACGAGTATAAAATTGGGTCATCTATT 57.153 29.630 0.00 0.00 0.00 1.73
6962 8911 9.847224 AAACGAGTATAAAATTGGGTCATCTAT 57.153 29.630 0.00 0.00 0.00 1.98
6963 8912 9.104965 CAAACGAGTATAAAATTGGGTCATCTA 57.895 33.333 0.00 0.00 0.00 1.98
6964 8913 7.827236 TCAAACGAGTATAAAATTGGGTCATCT 59.173 33.333 0.00 0.00 0.00 2.90
6965 8914 7.908601 GTCAAACGAGTATAAAATTGGGTCATC 59.091 37.037 0.00 0.00 0.00 2.92
6966 8915 7.392113 TGTCAAACGAGTATAAAATTGGGTCAT 59.608 33.333 0.00 0.00 0.00 3.06
6967 8916 6.711194 TGTCAAACGAGTATAAAATTGGGTCA 59.289 34.615 0.00 0.00 0.00 4.02
6968 8917 7.019418 GTGTCAAACGAGTATAAAATTGGGTC 58.981 38.462 0.00 0.00 0.00 4.46
6969 8918 6.487331 TGTGTCAAACGAGTATAAAATTGGGT 59.513 34.615 0.00 0.00 0.00 4.51
6970 8919 6.904498 TGTGTCAAACGAGTATAAAATTGGG 58.096 36.000 0.00 0.00 0.00 4.12
6976 8925 8.178964 GCCAAATATGTGTCAAACGAGTATAAA 58.821 33.333 0.00 0.00 0.00 1.40
6977 8926 7.201661 GGCCAAATATGTGTCAAACGAGTATAA 60.202 37.037 0.00 0.00 0.00 0.98
6978 8927 6.259167 GGCCAAATATGTGTCAAACGAGTATA 59.741 38.462 0.00 0.00 0.00 1.47
6979 8928 5.065988 GGCCAAATATGTGTCAAACGAGTAT 59.934 40.000 0.00 0.00 0.00 2.12
6980 8929 4.393680 GGCCAAATATGTGTCAAACGAGTA 59.606 41.667 0.00 0.00 0.00 2.59
6981 8930 3.190535 GGCCAAATATGTGTCAAACGAGT 59.809 43.478 0.00 0.00 0.00 4.18
6982 8931 3.190327 TGGCCAAATATGTGTCAAACGAG 59.810 43.478 0.61 0.00 0.00 4.18
7035 9045 4.404073 ACTTAACATGTGGTTTTCCTTGCA 59.596 37.500 0.00 0.00 40.96 4.08
7044 9054 6.183360 CCACAGTTTGTACTTAACATGTGGTT 60.183 38.462 27.21 0.00 42.27 3.67
7070 9080 3.126514 GTGAGATGTGAGTTTGCCATCTG 59.873 47.826 6.14 0.00 43.94 2.90
7104 9114 1.085091 GTGCATGGCTCTCTGTTGAG 58.915 55.000 0.00 0.00 41.51 3.02
7114 9124 2.154462 GTGAACTAACTGTGCATGGCT 58.846 47.619 0.00 0.00 36.45 4.75
7243 9514 0.396435 ATTGGACAGCAACGTGAGGA 59.604 50.000 0.00 0.00 0.00 3.71
7263 9538 1.134699 CCTGCCAGTCACATGTACGAT 60.135 52.381 0.00 0.00 0.00 3.73
7280 9556 1.736645 CACTACCACGCGGTTCCTG 60.737 63.158 12.47 0.00 46.31 3.86
7345 9624 7.830697 AGATGAAATACAGTGGAATGACATGAA 59.169 33.333 0.00 0.00 0.00 2.57
7347 9626 7.281549 TGAGATGAAATACAGTGGAATGACATG 59.718 37.037 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.