Multiple sequence alignment - TraesCS2B01G325100

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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 TraesCS2B01G325100 chr2B 100.000 8566 0 0 1 8566 464681415 464672850 0.000000e+00 15819.0
1 TraesCS2B01G325100 chr2B 93.701 127 3 4 1612 1734 464679683 464679558 1.470000e-42 185.0
2 TraesCS2B01G325100 chr2B 93.701 127 3 4 1733 1858 464679804 464679682 1.470000e-42 185.0
3 TraesCS2B01G325100 chr2D 94.633 3615 102 31 768 4360 392694797 392691253 0.000000e+00 5517.0
4 TraesCS2B01G325100 chr2D 94.840 1880 55 11 6228 8074 392689012 392687142 0.000000e+00 2896.0
5 TraesCS2B01G325100 chr2D 94.676 1653 75 11 4359 6003 392691159 392689512 0.000000e+00 2553.0
6 TraesCS2B01G325100 chr2D 86.785 734 65 17 6 714 392695531 392694805 0.000000e+00 789.0
7 TraesCS2B01G325100 chr2D 93.906 361 22 0 8206 8566 646798387 646798747 5.850000e-151 545.0
8 TraesCS2B01G325100 chr2D 88.667 300 15 6 5946 6235 392689534 392689244 1.770000e-91 348.0
9 TraesCS2B01G325100 chr2D 93.706 143 7 2 8067 8208 392687108 392686967 6.740000e-51 213.0
10 TraesCS2B01G325100 chr2D 95.161 124 4 2 1612 1734 392693841 392693719 2.440000e-45 195.0
11 TraesCS2B01G325100 chr2D 92.063 126 5 4 1733 1858 392693960 392693840 1.140000e-38 172.0
12 TraesCS2B01G325100 chr2A 95.543 3388 103 21 2613 5981 530749995 530746637 0.000000e+00 5376.0
13 TraesCS2B01G325100 chr2A 94.966 1927 81 9 5946 7863 530746634 530744715 0.000000e+00 3007.0
14 TraesCS2B01G325100 chr2A 92.375 1036 45 13 728 1734 530751736 530750706 0.000000e+00 1445.0
15 TraesCS2B01G325100 chr2A 96.973 859 19 4 1729 2587 530750832 530749981 0.000000e+00 1435.0
16 TraesCS2B01G325100 chr2A 90.637 502 38 5 214 713 530753473 530752979 0.000000e+00 658.0
17 TraesCS2B01G325100 chr2A 88.489 139 12 1 6 144 530753970 530753836 1.910000e-36 165.0
18 TraesCS2B01G325100 chr5D 95.798 357 15 0 8210 8566 353959041 353958685 2.070000e-160 577.0
19 TraesCS2B01G325100 chr5D 85.185 54 4 3 4791 4841 272352084 272352136 1.600000e-02 52.8
20 TraesCS2B01G325100 chr1D 94.915 354 18 0 8213 8566 481927285 481926932 9.720000e-154 555.0
21 TraesCS2B01G325100 chr4D 94.633 354 19 0 8213 8566 460659864 460660217 4.520000e-152 549.0
22 TraesCS2B01G325100 chr4D 94.633 354 19 0 8213 8566 460661129 460661482 4.520000e-152 549.0
23 TraesCS2B01G325100 chr4D 94.633 354 19 0 8213 8566 460665781 460666134 4.520000e-152 549.0
24 TraesCS2B01G325100 chr4D 94.633 354 19 0 8213 8566 460668303 460668656 4.520000e-152 549.0
25 TraesCS2B01G325100 chr3B 93.906 361 22 0 8206 8566 200831818 200831458 5.850000e-151 545.0
26 TraesCS2B01G325100 chr3B 93.906 361 22 0 8206 8566 200856727 200856367 5.850000e-151 545.0
27 TraesCS2B01G325100 chr4B 87.912 91 3 6 4760 4842 580533817 580533727 5.470000e-17 100.0
28 TraesCS2B01G325100 chr7A 83.529 85 6 3 4750 4826 227742191 227742107 1.190000e-08 73.1
29 TraesCS2B01G325100 chr3D 91.111 45 4 0 4790 4834 239898914 239898870 2.580000e-05 62.1
30 TraesCS2B01G325100 chr7B 92.683 41 3 0 4800 4840 443309437 443309397 9.290000e-05 60.2


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 TraesCS2B01G325100 chr2B 464672850 464681415 8565 True 5396.333333 15819 95.800667 1 8566 3 chr2B.!!$R1 8565
1 TraesCS2B01G325100 chr2D 392686967 392695531 8564 True 1585.375000 5517 92.566375 6 8208 8 chr2D.!!$R1 8202
2 TraesCS2B01G325100 chr2A 530744715 530753970 9255 True 2014.333333 5376 93.163833 6 7863 6 chr2A.!!$R1 7857
3 TraesCS2B01G325100 chr4D 460659864 460661482 1618 False 549.000000 549 94.633000 8213 8566 2 chr4D.!!$F1 353
4 TraesCS2B01G325100 chr4D 460665781 460668656 2875 False 549.000000 549 94.633000 8213 8566 2 chr4D.!!$F2 353

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
420 719 0.179004 TGCCCTTTCGTGTGTTCCAT 60.179 50.000 0.00 0.00 0.00 3.41 F
1414 2969 0.109365 CACTCGACTCTGAGCTGTGG 60.109 60.000 4.19 0.00 39.68 4.17 F
1417 2972 1.000283 CTCGACTCTGAGCTGTGGTTT 60.000 52.381 4.19 0.00 0.00 3.27 F
2221 3781 1.134367 TCGATGGTAAAGGTGAGCTCG 59.866 52.381 9.64 0.00 0.00 5.03 F
2981 4543 1.499913 ATGATGACCCAGGCACCACA 61.500 55.000 0.00 0.00 0.00 4.17 F
4438 6105 0.250166 GCACAAGTGGTACTCCCGTT 60.250 55.000 2.00 0.00 35.15 4.44 F
4949 6624 0.171903 CATGTTGCAGCTACTTGCCC 59.828 55.000 8.50 0.00 43.43 5.36 F
5707 7383 1.176619 TTCTCACTGGACGCGGAGAA 61.177 55.000 12.47 14.75 42.36 2.87 F
5987 7669 1.484240 CATCTGGTGACTCCTCTTCCC 59.516 57.143 0.00 0.00 37.07 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 3879 0.915872 ACCTCCATGACTCATGCCCA 60.916 55.000 12.92 0.0 40.20 5.36 R
2756 4316 0.037326 CAGGTAGAGCCTCAAACGCA 60.037 55.000 0.00 0.0 46.96 5.24 R
3120 4682 0.403271 AAGATCCAGTTGCTGCCACT 59.597 50.000 0.00 0.0 0.00 4.00 R
3494 5056 0.167470 CATCAACGAAGGCTGCACAG 59.833 55.000 0.50 0.0 0.00 3.66 R
4949 6624 0.749649 CTGGGTTCCTCATCTCCTCG 59.250 60.000 0.00 0.0 0.00 4.63 R
5722 7398 0.038599 TCTGTTGCCAGCATCACCAT 59.961 50.000 0.00 0.0 38.66 3.55 R
6161 7887 0.319555 CGCACTCGGTTTCCTCTCAA 60.320 55.000 0.00 0.0 0.00 3.02 R
6954 8942 1.134075 CTGCGAGCACTGCATCAAC 59.866 57.895 3.30 0.0 42.32 3.18 R
7926 9921 0.110912 GCGCGCTAAGATTCATGCTC 60.111 55.000 26.67 0.0 0.00 4.26 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
25 26 4.160626 GGTGAGCACTACAAGAGGAGTAAT 59.839 45.833 0.16 0.00 0.00 1.89
40 41 0.589729 GTAATGATGCACTTGCCGCG 60.590 55.000 0.00 0.00 41.18 6.46
87 88 0.957362 AGAGCAAAGGAGCAGCAAAC 59.043 50.000 0.00 0.00 36.85 2.93
91 92 1.000060 GCAAAGGAGCAGCAAACATGA 60.000 47.619 0.00 0.00 0.00 3.07
92 93 2.546373 GCAAAGGAGCAGCAAACATGAA 60.546 45.455 0.00 0.00 0.00 2.57
93 94 3.314553 CAAAGGAGCAGCAAACATGAAG 58.685 45.455 0.00 0.00 0.00 3.02
94 95 2.283145 AGGAGCAGCAAACATGAAGT 57.717 45.000 0.00 0.00 0.00 3.01
103 104 5.093457 CAGCAAACATGAAGTAAGATGCAG 58.907 41.667 0.00 0.00 35.11 4.41
118 122 9.703892 AGTAAGATGCAGATATAATCTCAACAC 57.296 33.333 0.00 0.00 37.58 3.32
126 130 7.465916 GCAGATATAATCTCAACACGCAAAAGA 60.466 37.037 0.00 0.00 37.58 2.52
128 132 8.768955 AGATATAATCTCAACACGCAAAAGATC 58.231 33.333 0.00 0.00 33.42 2.75
134 138 1.244019 ACACGCAAAAGATCAGGGCC 61.244 55.000 0.00 0.00 0.00 5.80
136 140 2.491621 GCAAAAGATCAGGGCCGC 59.508 61.111 0.00 0.00 0.00 6.53
160 422 7.096803 CGCGTAATACACTTGACATTTGTTTTT 60.097 33.333 0.00 0.00 0.00 1.94
161 423 7.995998 GCGTAATACACTTGACATTTGTTTTTG 59.004 33.333 0.00 0.00 0.00 2.44
169 431 6.091169 ACTTGACATTTGTTTTTGACTTGCAG 59.909 34.615 0.00 0.00 0.00 4.41
180 442 4.389890 TTGACTTGCAGCATTTTCAGTT 57.610 36.364 0.00 0.00 0.00 3.16
182 444 3.130869 TGACTTGCAGCATTTTCAGTTGT 59.869 39.130 0.00 0.00 0.00 3.32
190 464 4.688879 CAGCATTTTCAGTTGTTGATGCAT 59.311 37.500 0.00 0.00 40.28 3.96
192 466 4.449743 GCATTTTCAGTTGTTGATGCATGT 59.550 37.500 2.46 0.00 38.57 3.21
198 472 4.877823 TCAGTTGTTGATGCATGTATCTCC 59.122 41.667 22.15 13.71 0.00 3.71
201 475 3.812262 TGTTGATGCATGTATCTCCCTG 58.188 45.455 22.15 0.00 0.00 4.45
223 520 7.148120 CCCTGGCATAAATATATTCAGCTTCTG 60.148 40.741 13.20 0.00 0.00 3.02
241 538 6.595716 AGCTTCTGTGGTCAAAATATCTGTAC 59.404 38.462 0.00 0.00 0.00 2.90
245 542 6.756542 TCTGTGGTCAAAATATCTGTACATCG 59.243 38.462 0.00 0.00 0.00 3.84
250 547 7.438160 TGGTCAAAATATCTGTACATCGACATC 59.562 37.037 0.00 0.00 0.00 3.06
264 561 1.136141 CGACATCTGACAAGCAAGCAC 60.136 52.381 0.00 0.00 0.00 4.40
268 565 1.586422 TCTGACAAGCAAGCACACTC 58.414 50.000 0.00 0.00 0.00 3.51
309 606 6.370186 TTCTGCTATGCATAATCAGGAGAT 57.630 37.500 24.15 0.00 38.13 2.75
323 620 5.604758 TCAGGAGATGAGAGGTTAATGTG 57.395 43.478 0.00 0.00 32.77 3.21
328 625 3.776969 AGATGAGAGGTTAATGTGAGCCA 59.223 43.478 0.00 0.00 0.00 4.75
382 681 3.018423 AGAGAAAAACCTTGGCACAGT 57.982 42.857 0.00 0.00 42.39 3.55
420 719 0.179004 TGCCCTTTCGTGTGTTCCAT 60.179 50.000 0.00 0.00 0.00 3.41
425 724 3.058501 CCCTTTCGTGTGTTCCATTGTAC 60.059 47.826 0.00 0.00 0.00 2.90
462 761 6.992063 AATGACTCAAGCTGGTAGTTATTG 57.008 37.500 10.63 0.00 30.82 1.90
503 802 6.695429 TCAGAGATATTGAGATGGTGTATGC 58.305 40.000 0.00 0.00 0.00 3.14
510 809 2.092429 TGAGATGGTGTATGCCCTTTCC 60.092 50.000 0.00 0.00 0.00 3.13
573 872 8.599624 AGTTTTCATGATCCTTATTCCATGTT 57.400 30.769 0.00 0.00 38.00 2.71
602 901 2.223363 CGTCAGTCGTCTATGTCAGCAT 60.223 50.000 0.00 0.00 35.63 3.79
607 906 3.566322 AGTCGTCTATGTCAGCATACTCC 59.434 47.826 0.00 0.00 36.58 3.85
610 909 1.613925 TCTATGTCAGCATACTCCGCC 59.386 52.381 0.00 0.00 36.58 6.13
615 914 1.221840 CAGCATACTCCGCCAACCT 59.778 57.895 0.00 0.00 0.00 3.50
637 936 1.713932 GTGCGCGGAAAATGAACTTTC 59.286 47.619 8.83 0.00 35.04 2.62
685 984 9.311916 CAAGGTGTTTGTGAAAATTAGATCAAA 57.688 29.630 0.00 0.00 31.92 2.69
860 2391 0.182775 AAAGTGCGGAGTGAAACCCT 59.817 50.000 0.00 0.00 37.80 4.34
894 2430 4.207955 ACGAGTGGATAGATGTTGCTCTA 58.792 43.478 0.00 0.00 32.49 2.43
898 2434 4.586841 AGTGGATAGATGTTGCTCTACCTC 59.413 45.833 0.00 0.00 30.77 3.85
1297 2843 2.046217 GAGGGACCGCCTTGTTCC 60.046 66.667 0.00 0.00 33.67 3.62
1392 2947 2.597713 GCAAGCGGCCAAAGTTTGC 61.598 57.895 13.24 13.24 45.46 3.68
1399 2954 1.661509 GCCAAAGTTTGCGGCACTC 60.662 57.895 10.25 0.00 45.52 3.51
1405 2960 1.664965 GTTTGCGGCACTCGACTCT 60.665 57.895 0.05 0.00 42.43 3.24
1413 2968 0.732196 GCACTCGACTCTGAGCTGTG 60.732 60.000 4.19 9.52 39.68 3.66
1414 2969 0.109365 CACTCGACTCTGAGCTGTGG 60.109 60.000 4.19 0.00 39.68 4.17
1417 2972 1.000283 CTCGACTCTGAGCTGTGGTTT 60.000 52.381 4.19 0.00 0.00 3.27
1506 3061 1.336131 TTGTATTTGCAGCAAGGGCA 58.664 45.000 8.12 5.78 44.61 5.36
1526 3086 4.132336 GCACATGATAGCTTGAGATTGGA 58.868 43.478 0.00 0.00 0.00 3.53
1536 3096 5.075493 AGCTTGAGATTGGAAATTGTCAGT 58.925 37.500 0.00 0.00 0.00 3.41
1682 3242 7.201884 CCCATTTTGATATTCTTGTGAGCATCT 60.202 37.037 0.00 0.00 34.92 2.90
1683 3243 8.195436 CCATTTTGATATTCTTGTGAGCATCTT 58.805 33.333 0.00 0.00 34.92 2.40
1684 3244 9.234384 CATTTTGATATTCTTGTGAGCATCTTC 57.766 33.333 0.00 0.00 34.92 2.87
1689 3249 3.777106 TCTTGTGAGCATCTTCCTTGT 57.223 42.857 0.00 0.00 34.92 3.16
1699 3259 8.730680 GTGAGCATCTTCCTTGTTCTTATTTTA 58.269 33.333 0.00 0.00 34.92 1.52
1700 3260 8.730680 TGAGCATCTTCCTTGTTCTTATTTTAC 58.269 33.333 0.00 0.00 34.92 2.01
1701 3261 8.635765 AGCATCTTCCTTGTTCTTATTTTACA 57.364 30.769 0.00 0.00 0.00 2.41
1702 3262 9.247861 AGCATCTTCCTTGTTCTTATTTTACAT 57.752 29.630 0.00 0.00 0.00 2.29
1778 3338 5.181748 TGTTAATTTGCTTTGGTTTGCACT 58.818 33.333 0.00 0.00 39.05 4.40
1806 3366 6.932356 TTGATATTCTTGTGAGCATCTTCC 57.068 37.500 0.00 0.00 34.92 3.46
1807 3367 6.244552 TGATATTCTTGTGAGCATCTTCCT 57.755 37.500 0.00 0.00 34.92 3.36
1808 3368 6.286758 TGATATTCTTGTGAGCATCTTCCTC 58.713 40.000 0.00 0.00 34.92 3.71
1998 3558 9.612066 TTTATCTCTTTGTTTTTCCTGCATTTT 57.388 25.926 0.00 0.00 0.00 1.82
2129 3689 2.485426 TGCGAAATTCTGCTTCCTCTTG 59.515 45.455 10.12 0.00 0.00 3.02
2197 3757 3.603965 TGGTGGTTGGTTTATCAGGTT 57.396 42.857 0.00 0.00 0.00 3.50
2221 3781 1.134367 TCGATGGTAAAGGTGAGCTCG 59.866 52.381 9.64 0.00 0.00 5.03
2302 3862 3.019564 GTTCCTCAGAATGACCCATTGG 58.980 50.000 0.00 0.00 42.56 3.16
2319 3879 7.186268 ACCCATTGGTGTACCTTTGTATAATT 58.814 34.615 1.20 0.00 45.58 1.40
2358 3918 8.852135 TGGAGGTAAAATTATTGAGTCGTTTTT 58.148 29.630 0.00 0.00 0.00 1.94
2555 4115 4.919677 GGCACCAAATTTCGTTAAATGG 57.080 40.909 0.00 0.00 35.46 3.16
2594 4154 5.126061 CCTTTCTGCATGGCTTAGTATGTTT 59.874 40.000 0.00 0.00 0.00 2.83
2595 4155 5.818136 TTCTGCATGGCTTAGTATGTTTC 57.182 39.130 0.00 0.00 0.00 2.78
2596 4156 5.102953 TCTGCATGGCTTAGTATGTTTCT 57.897 39.130 0.00 0.00 0.00 2.52
2597 4157 4.877823 TCTGCATGGCTTAGTATGTTTCTG 59.122 41.667 0.00 0.00 0.00 3.02
2598 4158 3.378112 TGCATGGCTTAGTATGTTTCTGC 59.622 43.478 0.00 0.00 0.00 4.26
2599 4159 3.378112 GCATGGCTTAGTATGTTTCTGCA 59.622 43.478 0.00 0.00 0.00 4.41
2600 4160 4.037208 GCATGGCTTAGTATGTTTCTGCAT 59.963 41.667 0.00 0.00 0.00 3.96
2601 4161 5.516996 CATGGCTTAGTATGTTTCTGCATG 58.483 41.667 0.00 0.00 0.00 4.06
2602 4162 3.947196 TGGCTTAGTATGTTTCTGCATGG 59.053 43.478 0.00 0.00 0.00 3.66
2603 4163 3.243201 GGCTTAGTATGTTTCTGCATGGC 60.243 47.826 0.00 0.00 0.00 4.40
2604 4164 3.629398 GCTTAGTATGTTTCTGCATGGCT 59.371 43.478 0.00 0.00 0.00 4.75
2605 4165 4.096984 GCTTAGTATGTTTCTGCATGGCTT 59.903 41.667 0.00 0.00 0.00 4.35
2606 4166 5.296780 GCTTAGTATGTTTCTGCATGGCTTA 59.703 40.000 0.00 0.00 0.00 3.09
2607 4167 6.512415 GCTTAGTATGTTTCTGCATGGCTTAG 60.512 42.308 0.00 0.00 0.00 2.18
2608 4168 4.848357 AGTATGTTTCTGCATGGCTTAGT 58.152 39.130 0.00 0.00 0.00 2.24
2609 4169 5.989477 AGTATGTTTCTGCATGGCTTAGTA 58.011 37.500 0.00 0.00 0.00 1.82
2610 4170 6.595682 AGTATGTTTCTGCATGGCTTAGTAT 58.404 36.000 0.00 0.00 0.00 2.12
2611 4171 5.762825 ATGTTTCTGCATGGCTTAGTATG 57.237 39.130 0.00 0.00 0.00 2.39
2612 4172 4.588899 TGTTTCTGCATGGCTTAGTATGT 58.411 39.130 0.00 0.00 0.00 2.29
2613 4173 5.009631 TGTTTCTGCATGGCTTAGTATGTT 58.990 37.500 0.00 0.00 0.00 2.71
2614 4174 5.476599 TGTTTCTGCATGGCTTAGTATGTTT 59.523 36.000 0.00 0.00 0.00 2.83
2684 4244 5.982890 ATACACTTTGCTGTTGCCTTTAT 57.017 34.783 0.00 0.00 38.71 1.40
2708 4268 1.556564 TTTCTCGTATAGCTGCGTGC 58.443 50.000 0.00 0.00 43.29 5.34
2756 4316 1.592223 GTGTCTCTAGCCTTGCCGT 59.408 57.895 0.00 0.00 0.00 5.68
2887 4449 5.321102 ACATGACCAACATTTACTTGCCTA 58.679 37.500 0.00 0.00 37.07 3.93
2903 4465 2.090719 TGCCTACCTAGTGCCTATTCCT 60.091 50.000 0.00 0.00 0.00 3.36
2981 4543 1.499913 ATGATGACCCAGGCACCACA 61.500 55.000 0.00 0.00 0.00 4.17
3087 4649 2.043939 AGGACCAAGGAAAAATACCCCC 59.956 50.000 0.00 0.00 0.00 5.40
3120 4682 5.368145 ACTGTTGATGTTTCAGCTACTGAA 58.632 37.500 5.94 5.94 46.93 3.02
3628 5190 6.465084 AGGGTGATACTGAACAAGTAAGTTC 58.535 40.000 0.00 0.00 44.57 3.01
3799 5365 9.937175 GCACATTTATCTACTCAAATTTAGGAC 57.063 33.333 0.00 0.00 0.00 3.85
3864 5430 9.243637 TGTTGTAATATTCTTTTTGTCAGTTGC 57.756 29.630 0.00 0.00 0.00 4.17
3881 5447 3.565482 AGTTGCTTCCATGTGTGTACAAG 59.435 43.478 0.00 0.00 40.84 3.16
3896 5462 8.556194 TGTGTGTACAAGTGAACTAAATTGATC 58.444 33.333 0.00 0.00 32.88 2.92
3918 5484 6.553953 TCCTGATTATGCTGTACAGGTAAA 57.446 37.500 23.95 3.69 45.50 2.01
4244 5811 2.176273 GCTGGCTATCTGCACACCG 61.176 63.158 0.00 0.00 45.15 4.94
4326 5895 3.653836 TGGCTAGGTCCTTTCCTGTTTTA 59.346 43.478 0.00 0.00 38.41 1.52
4438 6105 0.250166 GCACAAGTGGTACTCCCGTT 60.250 55.000 2.00 0.00 35.15 4.44
4455 6122 3.495453 CCCGTTTGTAGAGGGTTTCTTCA 60.495 47.826 0.00 0.00 40.27 3.02
4476 6143 9.636789 TCTTCATGTATTCATTTTCTGGATGAT 57.363 29.630 0.00 0.00 33.82 2.45
4526 6193 9.760660 CTAACATAAACACTTTGATTAGCAGAC 57.239 33.333 0.00 0.00 0.00 3.51
4530 6197 6.560253 AAACACTTTGATTAGCAGACGAAT 57.440 33.333 0.00 0.00 0.00 3.34
4707 6375 1.024579 GGTGGTCGTACTGGCATTGG 61.025 60.000 0.00 0.00 0.00 3.16
4758 6426 4.870991 GTGCCAGTTTCAGTAATACTCTCC 59.129 45.833 0.00 0.00 0.00 3.71
4770 6438 0.978907 TACTCTCCCCGTCCCAAAAC 59.021 55.000 0.00 0.00 0.00 2.43
4789 6459 8.076178 CCCAAAACAAGTCTCAACTTTATACTG 58.924 37.037 0.00 0.00 43.28 2.74
4852 6526 8.800332 GGACGGAGGTAGTATGAAATTATTCTA 58.200 37.037 0.00 0.00 36.48 2.10
4949 6624 0.171903 CATGTTGCAGCTACTTGCCC 59.828 55.000 8.50 0.00 43.43 5.36
5126 6801 4.214971 GCAACTGGAGGATATGCTGTAATG 59.785 45.833 0.00 0.00 34.29 1.90
5294 6969 9.525409 AACTGTACCAATCTATGAACGTAATAC 57.475 33.333 0.00 0.00 0.00 1.89
5301 6976 7.171508 CCAATCTATGAACGTAATACTGTGCAT 59.828 37.037 11.51 11.51 38.01 3.96
5319 6994 7.093112 ACTGTGCATATCTTCTCTAACCTTCTT 60.093 37.037 0.00 0.00 0.00 2.52
5320 6995 8.306313 TGTGCATATCTTCTCTAACCTTCTTA 57.694 34.615 0.00 0.00 0.00 2.10
5370 7045 2.593725 CATGGGCGCATCTCCTGG 60.594 66.667 14.18 0.00 0.00 4.45
5558 7233 6.806388 TCAATACCTTTTTCCCGTCTAAAC 57.194 37.500 0.00 0.00 0.00 2.01
5640 7315 8.035394 CAGTAATAGTAGAGAAGAAAGTGGCAA 58.965 37.037 0.00 0.00 0.00 4.52
5707 7383 1.176619 TTCTCACTGGACGCGGAGAA 61.177 55.000 12.47 14.75 42.36 2.87
5755 7431 3.129502 CAGACACGGGCATGCTGG 61.130 66.667 18.92 12.15 0.00 4.85
5777 7456 4.241555 GGCCATGGACGCCGAGAT 62.242 66.667 18.40 0.00 36.47 2.75
5806 7485 2.279918 ACGAGGTGACGTGGTTGC 60.280 61.111 0.00 0.00 44.84 4.17
5971 7650 4.552365 CCCGTGGCGCCATCATCT 62.552 66.667 35.23 0.00 0.00 2.90
5987 7669 1.484240 CATCTGGTGACTCCTCTTCCC 59.516 57.143 0.00 0.00 37.07 3.97
6039 7762 3.333381 TCCATCTCCTTGAATTTCCACCA 59.667 43.478 0.00 0.00 0.00 4.17
6161 7887 3.008485 AGCGAACAAAGGAAAGAGAGGAT 59.992 43.478 0.00 0.00 0.00 3.24
6162 7888 3.753797 GCGAACAAAGGAAAGAGAGGATT 59.246 43.478 0.00 0.00 0.00 3.01
6310 8276 6.106673 AGGGAGTATTGAACATTTAGTGTCG 58.893 40.000 0.00 0.00 41.14 4.35
6392 8378 8.989653 TGTTTTTAGTTCTTTTTGTACCCTTG 57.010 30.769 0.00 0.00 0.00 3.61
6426 8412 8.792830 TTGTTCTATAAATGCCTATCATAGCC 57.207 34.615 0.00 0.00 34.33 3.93
6431 8417 1.666365 ATGCCTATCATAGCCTGCCT 58.334 50.000 0.00 0.00 32.59 4.75
6456 8442 5.660460 GTGCTCCTATTTTTGGGGTTATTG 58.340 41.667 0.00 0.00 0.00 1.90
6488 8475 6.548321 ACTTGGTAGGTGATGGAAATTGTTA 58.452 36.000 0.00 0.00 0.00 2.41
6503 8490 9.709495 TGGAAATTGTTAAGGAGATTTGAATTG 57.291 29.630 0.00 0.00 0.00 2.32
6551 8538 7.276438 CCCTGAATCAGCTTTTATTTTTGCTAC 59.724 37.037 4.40 0.00 34.10 3.58
6559 8546 7.327032 CAGCTTTTATTTTTGCTACAAGACTCC 59.673 37.037 0.00 0.00 34.10 3.85
6796 8783 9.586435 AAATTTAGATTTATGCCACTACAAAGC 57.414 29.630 0.00 0.00 33.78 3.51
6833 8821 3.959535 ATGCCACTGGTGTTTTAATGG 57.040 42.857 0.00 0.00 0.00 3.16
6954 8942 4.337274 TGCTTATTCTGACATGGCATCTTG 59.663 41.667 0.00 0.00 0.00 3.02
7067 9055 7.010460 TCAGCTCACATGTTAACTTTATGATCG 59.990 37.037 7.22 0.00 0.00 3.69
7101 9089 5.012046 TGCTTCTCTTTCACTTGGATGTCTA 59.988 40.000 0.00 0.00 0.00 2.59
7253 9241 1.831736 AGTAGCATCTGTTAACCGGCT 59.168 47.619 0.00 9.03 35.50 5.52
7254 9242 1.933853 GTAGCATCTGTTAACCGGCTG 59.066 52.381 0.00 7.53 33.10 4.85
7382 9370 0.179163 GTTGCGACCATGCCTAAAGC 60.179 55.000 0.00 0.00 44.14 3.51
7532 9520 9.722056 GTTCATATCACCTCAATTTTGATACAC 57.278 33.333 0.00 0.00 35.56 2.90
7539 9527 6.638063 CACCTCAATTTTGATACACTGTGTTG 59.362 38.462 19.73 8.59 36.46 3.33
7656 9644 2.552315 GCTTTCGGATCTTTTGTGGTCA 59.448 45.455 0.00 0.00 0.00 4.02
7762 9750 2.818921 TGAAATAACAAGGCCTGCCAT 58.181 42.857 5.69 0.00 38.92 4.40
7812 9806 6.670695 AAACAAAGGGAAATGCTATTCAGT 57.329 33.333 4.78 0.00 0.00 3.41
7877 9871 3.562182 ACCGAGAAACAAAGGGAAATGT 58.438 40.909 0.00 0.00 0.00 2.71
7922 9917 3.689649 GTGATTTCCAGCAAACTACGGAT 59.310 43.478 0.00 0.00 0.00 4.18
7923 9918 4.156008 GTGATTTCCAGCAAACTACGGATT 59.844 41.667 0.00 0.00 0.00 3.01
7924 9919 4.764823 TGATTTCCAGCAAACTACGGATTT 59.235 37.500 0.00 0.00 0.00 2.17
7925 9920 5.242838 TGATTTCCAGCAAACTACGGATTTT 59.757 36.000 0.00 0.00 0.00 1.82
7926 9921 4.497473 TTCCAGCAAACTACGGATTTTG 57.503 40.909 6.11 6.11 36.06 2.44
7927 9922 3.745799 TCCAGCAAACTACGGATTTTGA 58.254 40.909 14.18 0.00 35.13 2.69
7939 9943 7.047891 ACTACGGATTTTGAGCATGAATCTTA 58.952 34.615 0.00 0.00 0.00 2.10
7948 9952 1.724018 GCATGAATCTTAGCGCGCATC 60.724 52.381 35.10 19.80 0.00 3.91
8017 10021 1.139947 GTCGCTCAGACTAGCCACC 59.860 63.158 0.00 0.00 46.13 4.61
8018 10022 1.000771 TCGCTCAGACTAGCCACCT 60.001 57.895 0.00 0.00 39.43 4.00
8019 10023 0.612174 TCGCTCAGACTAGCCACCTT 60.612 55.000 0.00 0.00 39.43 3.50
8023 10027 1.153549 CAGACTAGCCACCTTCGCC 60.154 63.158 0.00 0.00 0.00 5.54
8045 10049 4.324991 GGAGTTGCCGTCCCCGTT 62.325 66.667 0.00 0.00 0.00 4.44
8061 10065 2.589442 TTGCCCAACCACGACGTC 60.589 61.111 5.18 5.18 0.00 4.34
8064 10068 2.109387 CCCAACCACGACGTCCAA 59.891 61.111 10.58 0.00 0.00 3.53
8073 10119 0.037605 ACGACGTCCAAATCCCTGTC 60.038 55.000 10.58 0.00 0.00 3.51
8093 10139 2.046892 CAAGGAGCACCCGTCCTG 60.047 66.667 0.00 0.00 44.17 3.86
8106 10152 4.776322 TCCTGCCCGCCATCGTTG 62.776 66.667 0.00 0.00 0.00 4.10
8111 10157 3.508840 CCCGCCATCGTTGAAGCC 61.509 66.667 0.00 0.00 0.00 4.35
8113 10159 4.520846 CGCCATCGTTGAAGCCGC 62.521 66.667 0.00 0.00 0.00 6.53
8127 10173 4.446413 CCGCCCCCGTGTCTACAC 62.446 72.222 3.08 3.08 43.15 2.90
8223 10270 3.056891 ACATTCATTAAGGGCGTGTTTGG 60.057 43.478 0.00 0.00 0.00 3.28
8232 10279 2.653766 CGTGTTTGGTTGCCGTGC 60.654 61.111 0.00 0.00 0.00 5.34
8241 10288 1.735198 GTTGCCGTGCGCTACAGTA 60.735 57.895 9.73 0.00 42.09 2.74
8262 12831 1.745087 CCCGCATTGCATACACTTCTT 59.255 47.619 9.69 0.00 0.00 2.52
8275 12844 1.142870 CACTTCTTCACCCAACCTGGA 59.857 52.381 0.00 0.00 40.96 3.86
8326 12895 1.219646 CATGTTGTTTGGTTGCCTGC 58.780 50.000 0.00 0.00 0.00 4.85
8330 12899 0.106335 TTGTTTGGTTGCCTGCATGG 59.894 50.000 0.00 0.00 39.35 3.66
8339 12908 2.044252 CCTGCATGGCCTCTTGCT 60.044 61.111 21.17 0.00 42.44 3.91
8367 12936 0.396435 CAGAACCACACTGCCTGGTA 59.604 55.000 0.00 0.00 41.45 3.25
8377 12946 1.203050 ACTGCCTGGTATTTGGTTGCT 60.203 47.619 0.00 0.00 0.00 3.91
8421 12990 4.040936 AGGCATGGTGTTTGGTTGTATA 57.959 40.909 0.00 0.00 0.00 1.47
8466 13035 2.270352 TTGGCTAGTTGGTGAGGTTG 57.730 50.000 0.00 0.00 0.00 3.77
8492 13061 2.029288 ACTTCGGCAGCACACATCG 61.029 57.895 0.00 0.00 0.00 3.84
8514 13083 6.448852 TCGTAAGCACAACAGAGTATAAACA 58.551 36.000 0.00 0.00 37.18 2.83
8534 13103 6.857777 AACAGAGCATCAACTAGCATAATC 57.142 37.500 0.00 0.00 37.82 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.108615 CCTCTTGTAGTGCTCACCGG 60.109 60.000 0.00 0.00 0.00 5.28
1 2 0.888619 TCCTCTTGTAGTGCTCACCG 59.111 55.000 0.00 0.00 0.00 4.94
2 3 1.896465 ACTCCTCTTGTAGTGCTCACC 59.104 52.381 0.00 0.00 0.00 4.02
3 4 4.785511 TTACTCCTCTTGTAGTGCTCAC 57.214 45.455 0.00 0.00 0.00 3.51
4 5 5.016831 TCATTACTCCTCTTGTAGTGCTCA 58.983 41.667 0.00 0.00 30.83 4.26
40 41 0.179124 CCAGTGCTCGTTCTCTAGCC 60.179 60.000 0.00 0.00 37.97 3.93
73 74 2.961062 ACTTCATGTTTGCTGCTCCTTT 59.039 40.909 0.00 0.00 0.00 3.11
92 93 9.703892 GTGTTGAGATTATATCTGCATCTTACT 57.296 33.333 0.00 0.00 40.38 2.24
93 94 8.642885 CGTGTTGAGATTATATCTGCATCTTAC 58.357 37.037 0.00 0.00 40.38 2.34
94 95 7.329471 GCGTGTTGAGATTATATCTGCATCTTA 59.671 37.037 0.00 0.00 40.38 2.10
103 104 8.551205 TGATCTTTTGCGTGTTGAGATTATATC 58.449 33.333 0.00 0.00 0.00 1.63
118 122 2.793946 CGGCCCTGATCTTTTGCG 59.206 61.111 0.00 0.00 0.00 4.85
126 130 0.249741 GTGTATTACGCGGCCCTGAT 60.250 55.000 12.47 0.00 0.00 2.90
128 132 0.461339 AAGTGTATTACGCGGCCCTG 60.461 55.000 12.47 0.00 33.01 4.45
134 138 4.953269 ACAAATGTCAAGTGTATTACGCG 58.047 39.130 3.53 3.53 33.01 6.01
136 140 9.227490 TCAAAAACAAATGTCAAGTGTATTACG 57.773 29.630 0.00 0.00 0.00 3.18
160 422 3.130869 ACAACTGAAAATGCTGCAAGTCA 59.869 39.130 6.36 9.56 35.30 3.41
161 423 3.709987 ACAACTGAAAATGCTGCAAGTC 58.290 40.909 6.36 5.03 35.30 3.01
169 431 4.449743 ACATGCATCAACAACTGAAAATGC 59.550 37.500 0.00 0.00 37.85 3.56
180 442 3.434024 CCAGGGAGATACATGCATCAACA 60.434 47.826 8.63 0.00 0.00 3.33
182 444 2.487805 GCCAGGGAGATACATGCATCAA 60.488 50.000 8.63 0.00 0.00 2.57
190 464 9.056799 TGAATATATTTATGCCAGGGAGATACA 57.943 33.333 0.00 0.00 0.00 2.29
192 466 8.213679 GCTGAATATATTTATGCCAGGGAGATA 58.786 37.037 11.16 0.00 0.00 1.98
198 472 7.392673 ACAGAAGCTGAATATATTTATGCCAGG 59.607 37.037 11.16 0.00 35.18 4.45
201 475 7.175641 ACCACAGAAGCTGAATATATTTATGCC 59.824 37.037 0.00 0.00 35.18 4.40
223 520 6.533723 TGTCGATGTACAGATATTTTGACCAC 59.466 38.462 0.33 0.00 0.00 4.16
241 538 2.222976 GCTTGCTTGTCAGATGTCGATG 60.223 50.000 0.00 0.00 0.00 3.84
245 542 1.875514 TGTGCTTGCTTGTCAGATGTC 59.124 47.619 0.00 0.00 0.00 3.06
250 547 1.263484 CTGAGTGTGCTTGCTTGTCAG 59.737 52.381 0.00 0.00 0.00 3.51
264 561 4.198028 TGGTCATTCTGATGTCTGAGTG 57.802 45.455 6.20 6.20 34.77 3.51
309 606 4.574674 ATTGGCTCACATTAACCTCTCA 57.425 40.909 0.00 0.00 0.00 3.27
369 668 1.529244 GCCTGACTGTGCCAAGGTT 60.529 57.895 0.00 0.00 0.00 3.50
382 681 0.622136 ACAGATTGCCATCAGCCTGA 59.378 50.000 0.00 0.00 42.71 3.86
425 724 8.194104 AGCTTGAGTCATTACATAGTTACAGAG 58.806 37.037 0.00 0.00 0.00 3.35
462 761 2.069273 CTGATTCAACACCGACCAGTC 58.931 52.381 0.00 0.00 0.00 3.51
540 839 9.710900 AATAAGGATCATGAAAACTTGGAAAAC 57.289 29.630 15.87 0.00 0.00 2.43
573 872 2.388310 AGACGACTGACGAGATCTGA 57.612 50.000 0.00 0.00 45.77 3.27
602 901 3.065306 CACCAGGTTGGCGGAGTA 58.935 61.111 0.00 0.00 42.67 2.59
610 909 2.141122 ATTTTCCGCGCACCAGGTTG 62.141 55.000 8.75 0.00 0.00 3.77
615 914 1.169661 AGTTCATTTTCCGCGCACCA 61.170 50.000 8.75 0.00 0.00 4.17
637 936 7.167968 CCTTGCAAAAATGATATTGATACACCG 59.832 37.037 0.00 0.00 0.00 4.94
715 1014 4.217550 GCTGAGCAGGTTTTGGTTGTAATA 59.782 41.667 0.00 0.00 37.72 0.98
716 1015 3.005791 GCTGAGCAGGTTTTGGTTGTAAT 59.994 43.478 0.00 0.00 37.72 1.89
717 1016 2.360801 GCTGAGCAGGTTTTGGTTGTAA 59.639 45.455 0.00 0.00 37.72 2.41
718 1017 1.953686 GCTGAGCAGGTTTTGGTTGTA 59.046 47.619 0.00 0.00 37.72 2.41
720 1019 1.000938 GAGCTGAGCAGGTTTTGGTTG 60.001 52.381 7.39 0.00 39.57 3.77
721 1020 1.322442 GAGCTGAGCAGGTTTTGGTT 58.678 50.000 7.39 0.00 39.57 3.67
722 1021 0.183492 TGAGCTGAGCAGGTTTTGGT 59.817 50.000 7.39 0.00 39.57 3.67
724 1023 1.888215 TCTGAGCTGAGCAGGTTTTG 58.112 50.000 7.39 0.00 39.57 2.44
725 1024 2.645838 TTCTGAGCTGAGCAGGTTTT 57.354 45.000 7.39 0.00 39.57 2.43
726 1025 2.645838 TTTCTGAGCTGAGCAGGTTT 57.354 45.000 7.39 0.00 39.57 3.27
860 2391 3.945981 TCCACTCGTACAATACAAGCA 57.054 42.857 0.00 0.00 0.00 3.91
894 2430 4.691238 TGTAGTAACATAACAGGGGAGGT 58.309 43.478 0.00 0.00 0.00 3.85
898 2434 3.454812 AGGCTGTAGTAACATAACAGGGG 59.545 47.826 4.09 0.00 40.76 4.79
941 2477 0.389166 CTCTCTCGCCTTTCGCTGTT 60.389 55.000 0.00 0.00 38.27 3.16
1308 2854 2.118683 CCAAACACAGCACAATTCACG 58.881 47.619 0.00 0.00 0.00 4.35
1392 2947 2.202544 GCTCAGAGTCGAGTGCCG 60.203 66.667 0.00 0.00 35.33 5.69
1399 2954 1.795286 GAAAACCACAGCTCAGAGTCG 59.205 52.381 0.00 0.00 0.00 4.18
1405 2960 1.581934 CTCACGAAAACCACAGCTCA 58.418 50.000 0.00 0.00 0.00 4.26
1413 2968 2.930682 GTGGATCTAGCTCACGAAAACC 59.069 50.000 0.00 0.00 0.00 3.27
1476 3031 5.709631 TGCTGCAAATACAAATAGGAGAACA 59.290 36.000 0.00 0.00 0.00 3.18
1506 3061 7.341256 ACAATTTCCAATCTCAAGCTATCATGT 59.659 33.333 0.00 0.00 0.00 3.21
1526 3086 5.710099 ACACGGATGGATAAACTGACAATTT 59.290 36.000 0.00 0.00 0.00 1.82
1536 3096 3.767131 TGTCAGAGACACGGATGGATAAA 59.233 43.478 0.00 0.00 37.67 1.40
1630 3190 6.763135 TGCAAACCAAAGCAAATTAACATACA 59.237 30.769 0.00 0.00 37.90 2.29
1778 3338 8.515695 AGATGCTCACAAGAATATCAAAATGA 57.484 30.769 0.00 0.00 0.00 2.57
1998 3558 5.947663 TGGGAAGGTAAATTTGAGAACAGA 58.052 37.500 0.00 0.00 0.00 3.41
2197 3757 3.260884 AGCTCACCTTTACCATCGAAGAA 59.739 43.478 0.00 0.00 43.58 2.52
2221 3781 5.523369 AGTGCAGAAACAAAGAATAACTGC 58.477 37.500 0.00 0.00 45.92 4.40
2302 3862 6.320164 TCATGCCCAATTATACAAAGGTACAC 59.680 38.462 0.00 0.00 30.94 2.90
2319 3879 0.915872 ACCTCCATGACTCATGCCCA 60.916 55.000 12.92 0.00 40.20 5.36
2358 3918 2.944129 AGGTTAAGCAGGTTCAAGCAA 58.056 42.857 7.52 0.00 0.00 3.91
2456 4016 2.961741 TGGCCATCAAAGTAAAGCACAA 59.038 40.909 0.00 0.00 0.00 3.33
2534 4094 4.311606 ACCATTTAACGAAATTTGGTGCC 58.688 39.130 6.60 0.00 34.37 5.01
2594 4154 4.877823 CAGAAACATACTAAGCCATGCAGA 59.122 41.667 0.00 0.00 0.00 4.26
2595 4155 4.497006 GCAGAAACATACTAAGCCATGCAG 60.497 45.833 0.00 0.00 0.00 4.41
2596 4156 3.378112 GCAGAAACATACTAAGCCATGCA 59.622 43.478 0.00 0.00 0.00 3.96
2597 4157 3.378112 TGCAGAAACATACTAAGCCATGC 59.622 43.478 0.00 0.00 0.00 4.06
2598 4158 5.506815 CCATGCAGAAACATACTAAGCCATG 60.507 44.000 0.00 0.00 0.00 3.66
2599 4159 4.581824 CCATGCAGAAACATACTAAGCCAT 59.418 41.667 0.00 0.00 0.00 4.40
2600 4160 3.947196 CCATGCAGAAACATACTAAGCCA 59.053 43.478 0.00 0.00 0.00 4.75
2601 4161 3.243201 GCCATGCAGAAACATACTAAGCC 60.243 47.826 0.00 0.00 0.00 4.35
2602 4162 3.629398 AGCCATGCAGAAACATACTAAGC 59.371 43.478 0.00 0.00 0.00 3.09
2603 4163 5.824904 AAGCCATGCAGAAACATACTAAG 57.175 39.130 0.00 0.00 0.00 2.18
2604 4164 7.393234 ACTTAAAGCCATGCAGAAACATACTAA 59.607 33.333 0.00 0.00 0.00 2.24
2605 4165 6.884295 ACTTAAAGCCATGCAGAAACATACTA 59.116 34.615 0.00 0.00 0.00 1.82
2606 4166 5.711976 ACTTAAAGCCATGCAGAAACATACT 59.288 36.000 0.00 0.00 0.00 2.12
2607 4167 5.954335 ACTTAAAGCCATGCAGAAACATAC 58.046 37.500 0.00 0.00 0.00 2.39
2608 4168 7.695480 TTACTTAAAGCCATGCAGAAACATA 57.305 32.000 0.00 0.00 0.00 2.29
2609 4169 6.588719 TTACTTAAAGCCATGCAGAAACAT 57.411 33.333 0.00 0.00 0.00 2.71
2610 4170 6.588719 ATTACTTAAAGCCATGCAGAAACA 57.411 33.333 0.00 0.00 0.00 2.83
2611 4171 7.090173 TGAATTACTTAAAGCCATGCAGAAAC 58.910 34.615 0.00 0.00 0.00 2.78
2612 4172 7.225784 TGAATTACTTAAAGCCATGCAGAAA 57.774 32.000 0.00 0.00 0.00 2.52
2613 4173 6.832520 TGAATTACTTAAAGCCATGCAGAA 57.167 33.333 0.00 0.00 0.00 3.02
2614 4174 6.832520 TTGAATTACTTAAAGCCATGCAGA 57.167 33.333 0.00 0.00 0.00 4.26
2684 4244 3.317149 ACGCAGCTATACGAGAAATACCA 59.683 43.478 9.63 0.00 0.00 3.25
2756 4316 0.037326 CAGGTAGAGCCTCAAACGCA 60.037 55.000 0.00 0.00 46.96 5.24
3087 4649 3.441496 ACATCAACAGTTGCACCTTTG 57.559 42.857 8.58 2.38 0.00 2.77
3120 4682 0.403271 AAGATCCAGTTGCTGCCACT 59.597 50.000 0.00 0.00 0.00 4.00
3238 4800 4.524802 TGGCACATAGAAGATCCCATTT 57.475 40.909 0.00 0.00 0.00 2.32
3494 5056 0.167470 CATCAACGAAGGCTGCACAG 59.833 55.000 0.50 0.00 0.00 3.66
3628 5190 4.455606 CCTATTACCAAGCTTCTGAAGGG 58.544 47.826 18.38 13.28 0.00 3.95
3684 5247 5.484715 TGTAGGAACCTTTAAGAACCATCG 58.515 41.667 0.00 0.00 0.00 3.84
3864 5430 4.816385 AGTTCACTTGTACACACATGGAAG 59.184 41.667 0.00 0.00 34.84 3.46
3881 5447 8.844244 AGCATAATCAGGATCAATTTAGTTCAC 58.156 33.333 0.00 0.00 0.00 3.18
3918 5484 9.142014 GTATCAATAGATAGCATAGGTCCTGAT 57.858 37.037 0.00 0.00 37.41 2.90
4244 5811 4.925646 TGCTACATGCGACATGATAGATTC 59.074 41.667 21.37 10.16 46.63 2.52
4326 5895 1.196104 ATTTGGGCCACAAGCAGCAT 61.196 50.000 5.23 0.00 46.50 3.79
4438 6105 7.685481 TGAATACATGAAGAAACCCTCTACAA 58.315 34.615 0.00 0.00 32.46 2.41
4455 6122 8.222637 TCCTCATCATCCAGAAAATGAATACAT 58.777 33.333 0.00 0.00 36.75 2.29
4504 6171 7.060600 TCGTCTGCTAATCAAAGTGTTTATG 57.939 36.000 0.00 0.00 0.00 1.90
4512 6179 9.941664 AATGAATTATTCGTCTGCTAATCAAAG 57.058 29.630 0.00 0.00 0.00 2.77
4553 6220 7.173907 CCACCTATAGATTGATGCCAACTAAAG 59.826 40.741 0.00 0.00 34.72 1.85
4667 6335 3.276857 CTCACTAAGCCATGATTGCAGT 58.723 45.455 0.00 0.00 0.00 4.40
4668 6336 2.617308 CCTCACTAAGCCATGATTGCAG 59.383 50.000 0.00 0.00 0.00 4.41
4672 6340 2.578021 ACCACCTCACTAAGCCATGATT 59.422 45.455 0.00 0.00 0.00 2.57
4732 6400 3.994392 AGTATTACTGAAACTGGCACACG 59.006 43.478 0.00 0.00 0.00 4.49
4758 6426 1.235724 GAGACTTGTTTTGGGACGGG 58.764 55.000 0.00 0.00 0.00 5.28
4817 6491 4.914177 ACTACCTCCGTCCCAAAATAAA 57.086 40.909 0.00 0.00 0.00 1.40
4949 6624 0.749649 CTGGGTTCCTCATCTCCTCG 59.250 60.000 0.00 0.00 0.00 4.63
5055 6730 3.256879 TCGCTGCAAAATAAATTCCCACA 59.743 39.130 0.00 0.00 0.00 4.17
5126 6801 7.802251 CAGATAAGCAGTGCTAAGAATAATTGC 59.198 37.037 20.09 0.00 38.25 3.56
5206 6881 2.018644 GCAACATCATGGGTCATCGGT 61.019 52.381 0.00 0.00 0.00 4.69
5294 6969 6.815089 AGAAGGTTAGAGAAGATATGCACAG 58.185 40.000 0.00 0.00 0.00 3.66
5320 6995 8.988546 TGTTAATAGCCACAACAATGGTATAT 57.011 30.769 0.00 0.00 42.28 0.86
5370 7045 1.608590 CCATGCGGTTATCCCATTGAC 59.391 52.381 0.00 0.00 0.00 3.18
5640 7315 2.738521 CTAGCCGCAACAGCACGT 60.739 61.111 0.00 0.00 0.00 4.49
5722 7398 0.038599 TCTGTTGCCAGCATCACCAT 59.961 50.000 0.00 0.00 38.66 3.55
5772 7451 2.100631 GTCCACAACCGGCATCTCG 61.101 63.158 0.00 0.00 0.00 4.04
5777 7456 4.308458 CCTCGTCCACAACCGGCA 62.308 66.667 0.00 0.00 0.00 5.69
5820 7499 1.763770 CTGCCTCCCAACCTCAAGT 59.236 57.895 0.00 0.00 0.00 3.16
5970 7649 1.893786 CGGGAAGAGGAGTCACCAG 59.106 63.158 0.00 0.00 42.04 4.00
5971 7650 2.283529 GCGGGAAGAGGAGTCACCA 61.284 63.158 0.00 0.00 42.04 4.17
6039 7762 4.096003 CGGGATTGGACCAGCGGT 62.096 66.667 0.00 0.00 39.44 5.68
6134 7860 5.794894 TCTCTTTCCTTTGTTCGCTCTATT 58.205 37.500 0.00 0.00 0.00 1.73
6161 7887 0.319555 CGCACTCGGTTTCCTCTCAA 60.320 55.000 0.00 0.00 0.00 3.02
6162 7888 1.289066 CGCACTCGGTTTCCTCTCA 59.711 57.895 0.00 0.00 0.00 3.27
6260 8226 1.005924 CCCCAATCTAGTGCCCAAAGT 59.994 52.381 0.00 0.00 0.00 2.66
6261 8227 1.284785 TCCCCAATCTAGTGCCCAAAG 59.715 52.381 0.00 0.00 0.00 2.77
6262 8228 1.377690 TCCCCAATCTAGTGCCCAAA 58.622 50.000 0.00 0.00 0.00 3.28
6264 8230 0.623723 GTTCCCCAATCTAGTGCCCA 59.376 55.000 0.00 0.00 0.00 5.36
6265 8231 0.623723 TGTTCCCCAATCTAGTGCCC 59.376 55.000 0.00 0.00 0.00 5.36
6266 8232 1.559682 TCTGTTCCCCAATCTAGTGCC 59.440 52.381 0.00 0.00 0.00 5.01
6349 8315 0.816421 CATGGGAGCATGCATCGACA 60.816 55.000 21.98 15.59 0.00 4.35
6431 8417 1.353022 ACCCCAAAAATAGGAGCACGA 59.647 47.619 0.00 0.00 0.00 4.35
6456 8442 5.773680 TCCATCACCTACCAAGTAGTATAGC 59.226 44.000 1.40 0.00 34.62 2.97
6488 8475 5.712152 AAACTCGCAATTCAAATCTCCTT 57.288 34.783 0.00 0.00 0.00 3.36
6503 8490 4.201599 GGAAGAATGAAGTCGTAAACTCGC 60.202 45.833 0.00 0.00 37.17 5.03
6551 8538 9.846248 AATTCGAAATCAAATTTAGGAGTCTTG 57.154 29.630 0.00 0.00 31.47 3.02
6580 8567 8.969260 AGCTTCAGAATTCACATGTAATCATA 57.031 30.769 8.44 0.00 32.47 2.15
6625 8612 1.699083 TCTGGAGTCATGCCAACTTGA 59.301 47.619 0.00 0.00 34.44 3.02
6833 8821 2.044946 GGTCCAGGTCCCACATGC 60.045 66.667 0.00 0.00 0.00 4.06
6954 8942 1.134075 CTGCGAGCACTGCATCAAC 59.866 57.895 3.30 0.00 42.32 3.18
7067 9055 4.024472 GTGAAAGAGAAGCAAGGTGAGTTC 60.024 45.833 0.00 0.00 0.00 3.01
7101 9089 4.719026 AACATCCATGACCTAGCATCAT 57.281 40.909 0.00 2.65 37.27 2.45
7253 9241 3.648067 ACATGAAGTTCCTCTGTTCCTCA 59.352 43.478 0.00 0.00 0.00 3.86
7254 9242 3.999663 CACATGAAGTTCCTCTGTTCCTC 59.000 47.826 0.00 0.00 0.00 3.71
7382 9370 5.140747 ACTTTGCTACTTCACTACTCTGG 57.859 43.478 0.00 0.00 0.00 3.86
7539 9527 3.936453 ACATTTTCATGCATTGTCATGGC 59.064 39.130 16.02 0.00 42.96 4.40
7770 9764 9.573133 CTTTGTTTTTCAGTTATGCCTAATAGG 57.427 33.333 0.99 0.99 38.80 2.57
7812 9806 2.289547 GCAGGCTAAAAACTGACGTCAA 59.710 45.455 20.49 2.14 36.86 3.18
7877 9871 6.092122 CACCTAAAATGACGTCAGCTGAATAA 59.908 38.462 24.41 3.03 0.00 1.40
7922 9917 3.485711 CGCGCTAAGATTCATGCTCAAAA 60.486 43.478 5.56 0.00 0.00 2.44
7923 9918 2.030823 CGCGCTAAGATTCATGCTCAAA 59.969 45.455 5.56 0.00 0.00 2.69
7924 9919 1.594397 CGCGCTAAGATTCATGCTCAA 59.406 47.619 5.56 0.00 0.00 3.02
7925 9920 1.211743 CGCGCTAAGATTCATGCTCA 58.788 50.000 5.56 0.00 0.00 4.26
7926 9921 0.110912 GCGCGCTAAGATTCATGCTC 60.111 55.000 26.67 0.00 0.00 4.26
7927 9922 0.811219 TGCGCGCTAAGATTCATGCT 60.811 50.000 33.29 0.00 0.00 3.79
7948 9952 3.390135 TCAAAGTTAAGAGTGGCAGACG 58.610 45.455 0.00 0.00 0.00 4.18
8018 10022 1.302511 GGCAACTCCTTCAGGCGAA 60.303 57.895 0.00 0.00 34.44 4.70
8019 10023 2.347490 GGCAACTCCTTCAGGCGA 59.653 61.111 0.00 0.00 34.44 5.54
8023 10027 1.376037 GGGACGGCAACTCCTTCAG 60.376 63.158 0.00 0.00 34.96 3.02
8045 10049 4.612412 GGACGTCGTGGTTGGGCA 62.612 66.667 9.92 0.00 0.00 5.36
8048 10052 0.515564 GATTTGGACGTCGTGGTTGG 59.484 55.000 9.92 0.00 0.00 3.77
8061 10065 1.003118 TCCTTGTCGACAGGGATTTGG 59.997 52.381 37.38 21.46 45.65 3.28
8073 10119 2.432628 GACGGGTGCTCCTTGTCG 60.433 66.667 12.62 7.17 32.72 4.35
8093 10139 4.179579 GCTTCAACGATGGCGGGC 62.180 66.667 0.00 0.00 43.17 6.13
8127 10173 0.100146 GCGTCGGGACCTTGTAGTAG 59.900 60.000 0.00 0.00 0.00 2.57
8208 10255 0.386113 GCAACCAAACACGCCCTTAA 59.614 50.000 0.00 0.00 0.00 1.85
8209 10256 1.457009 GGCAACCAAACACGCCCTTA 61.457 55.000 0.00 0.00 38.67 2.69
8210 10257 2.791868 GGCAACCAAACACGCCCTT 61.792 57.895 0.00 0.00 38.67 3.95
8211 10258 3.223589 GGCAACCAAACACGCCCT 61.224 61.111 0.00 0.00 38.67 5.19
8232 10279 1.762222 GCAATGCGGGTACTGTAGCG 61.762 60.000 10.55 7.50 36.83 4.26
8241 10288 1.094785 GAAGTGTATGCAATGCGGGT 58.905 50.000 0.00 0.00 0.00 5.28
8262 12831 1.294041 TGCATATCCAGGTTGGGTGA 58.706 50.000 0.00 0.00 38.32 4.02
8301 12870 3.305950 GGCAACCAAACAACATGCAGATA 60.306 43.478 0.00 0.00 38.73 1.98
8326 12895 0.179111 CATGCAAGCAAGAGGCCATG 60.179 55.000 5.01 1.50 46.50 3.66
8330 12899 2.890371 CCCATGCAAGCAAGAGGC 59.110 61.111 0.00 0.00 45.30 4.70
8367 12936 4.309099 CACTAACATGCAAGCAACCAAAT 58.691 39.130 0.00 0.00 0.00 2.32
8377 12946 2.625790 GGGTTTGTCCACTAACATGCAA 59.374 45.455 0.00 0.00 38.11 4.08
8421 12990 1.973816 TACCACACACCAGGCGTTGT 61.974 55.000 0.00 0.00 0.00 3.32
8492 13061 7.412020 GCTCTGTTTATACTCTGTTGTGCTTAC 60.412 40.741 0.00 0.00 0.00 2.34
8514 13083 5.306419 TCTGGATTATGCTAGTTGATGCTCT 59.694 40.000 0.00 0.00 0.00 4.09
8534 13103 5.537300 AGTGTGGTACTGCTTATATCTGG 57.463 43.478 0.00 0.00 38.49 3.86


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

AutoCloner maintained by Alex Coulton.