Multiple sequence alignment - TraesCS3A01G188000

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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 TraesCS3A01G188000 chr3A 100.000 9277 0 0 1 9277 227407327 227416603 0.000000e+00 17132.0
1 TraesCS3A01G188000 chr3D 95.341 4937 150 40 1 4933 181572544 181567684 0.000000e+00 7769.0
2 TraesCS3A01G188000 chr3D 95.768 3403 97 21 5059 8458 181567686 181564328 0.000000e+00 5443.0
3 TraesCS3A01G188000 chr3D 85.897 858 76 21 8458 9275 181564170 181563318 0.000000e+00 872.0
4 TraesCS3A01G188000 chr3D 94.017 117 7 0 6361 6477 422517670 422517786 2.660000e-40 178.0
5 TraesCS3A01G188000 chr3D 88.372 86 10 0 8633 8718 611068363 611068278 4.580000e-18 104.0
6 TraesCS3A01G188000 chr3B 95.512 4144 158 22 805 4933 259858832 259854702 0.000000e+00 6597.0
7 TraesCS3A01G188000 chr3B 93.481 3835 155 39 5059 8851 259854704 259850923 0.000000e+00 5609.0
8 TraesCS3A01G188000 chr3B 96.260 722 22 2 1 722 259859868 259859152 0.000000e+00 1179.0
9 TraesCS3A01G188000 chr3B 88.443 424 37 6 8863 9275 259850864 259850442 1.390000e-137 501.0
10 TraesCS3A01G188000 chr3B 95.302 149 4 3 4930 5077 797566757 797566611 5.600000e-57 233.0
11 TraesCS3A01G188000 chr5D 95.775 426 11 3 170 594 35981667 35981248 0.000000e+00 680.0
12 TraesCS3A01G188000 chr5D 95.000 120 6 0 6361 6480 468170593 468170474 1.230000e-43 189.0
13 TraesCS3A01G188000 chr5D 92.105 38 2 1 9238 9275 258193064 258193028 1.700000e-02 52.8
14 TraesCS3A01G188000 chr5A 79.972 709 107 26 8486 9170 552743081 552742384 3.010000e-134 490.0
15 TraesCS3A01G188000 chr4D 77.959 735 103 33 8486 9173 337088748 337088026 1.120000e-108 405.0
16 TraesCS3A01G188000 chr4A 83.178 321 40 8 8864 9173 135676613 135676930 1.970000e-71 281.0
17 TraesCS3A01G188000 chr4A 92.969 128 7 2 4934 5061 647203704 647203579 1.590000e-42 185.0
18 TraesCS3A01G188000 chr4A 94.167 120 7 0 6361 6480 475420648 475420529 5.720000e-42 183.0
19 TraesCS3A01G188000 chr5B 85.217 230 29 5 8942 9169 278852744 278852518 2.010000e-56 231.0
20 TraesCS3A01G188000 chr5B 95.000 120 6 0 6361 6480 574956569 574956450 1.230000e-43 189.0
21 TraesCS3A01G188000 chr5B 81.633 196 33 3 8596 8790 278863041 278862848 9.640000e-35 159.0
22 TraesCS3A01G188000 chr1B 93.960 149 6 3 4930 5077 53316467 53316613 1.210000e-53 222.0
23 TraesCS3A01G188000 chr1B 84.536 194 25 5 8977 9167 662489453 662489644 4.420000e-43 187.0
24 TraesCS3A01G188000 chr4B 79.153 307 54 9 8486 8785 416248068 416247765 4.390000e-48 204.0
25 TraesCS3A01G188000 chr4B 96.341 82 3 0 4930 5011 309244077 309244158 1.620000e-27 135.0
26 TraesCS3A01G188000 chr4B 100.000 28 0 0 9248 9275 408258672 408258699 1.700000e-02 52.8
27 TraesCS3A01G188000 chr2D 96.639 119 4 0 4934 5052 259327387 259327269 2.040000e-46 198.0
28 TraesCS3A01G188000 chr2D 84.211 152 13 6 6326 6477 203042789 203042929 4.520000e-28 137.0
29 TraesCS3A01G188000 chr2D 94.444 36 1 1 9238 9273 362615539 362615505 5.000000e-03 54.7
30 TraesCS3A01G188000 chr7A 92.424 132 7 2 4930 5061 40545467 40545595 1.590000e-42 185.0
31 TraesCS3A01G188000 chr7A 86.184 152 19 1 6329 6480 654795234 654795085 7.450000e-36 163.0
32 TraesCS3A01G188000 chr7A 85.417 96 12 2 8630 8725 115311546 115311453 2.130000e-16 99.0
33 TraesCS3A01G188000 chr7B 94.167 120 7 0 6361 6480 639088012 639087893 5.720000e-42 183.0
34 TraesCS3A01G188000 chr7B 82.979 94 12 3 8632 8725 68655818 68655729 2.150000e-11 82.4
35 TraesCS3A01G188000 chr6B 93.333 120 8 0 6361 6480 337237279 337237160 2.660000e-40 178.0
36 TraesCS3A01G188000 chr2A 87.919 149 10 4 6329 6477 231352802 231352942 1.600000e-37 169.0
37 TraesCS3A01G188000 chr2A 75.566 221 50 3 8486 8703 771551602 771551821 1.270000e-18 106.0
38 TraesCS3A01G188000 chr1D 88.889 81 1 1 6329 6409 194462652 194462724 9.920000e-15 93.5
39 TraesCS3A01G188000 chr6A 85.185 81 11 1 1748 1827 351827532 351827612 2.150000e-11 82.4


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 TraesCS3A01G188000 chr3A 227407327 227416603 9276 False 17132.000000 17132 100.000000 1 9277 1 chr3A.!!$F1 9276
1 TraesCS3A01G188000 chr3D 181563318 181572544 9226 True 4694.666667 7769 92.335333 1 9275 3 chr3D.!!$R2 9274
2 TraesCS3A01G188000 chr3B 259850442 259859868 9426 True 3471.500000 6597 93.424000 1 9275 4 chr3B.!!$R2 9274
3 TraesCS3A01G188000 chr5A 552742384 552743081 697 True 490.000000 490 79.972000 8486 9170 1 chr5A.!!$R1 684
4 TraesCS3A01G188000 chr4D 337088026 337088748 722 True 405.000000 405 77.959000 8486 9173 1 chr4D.!!$R1 687

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
79 80 0.546747 CTTACCCCCTCCCACAGACA 60.547 60.000 0.00 0.00 0.00 3.41 F
203 204 0.610232 AAGTGATGACAAGCAGGGCC 60.610 55.000 0.00 0.00 0.00 5.80 F
877 1116 1.137872 ACCTCCTCTTGCTTATGCTCG 59.862 52.381 1.96 0.00 40.48 5.03 F
920 1159 1.273886 AGCTTCCAGACTTCGTCTTCC 59.726 52.381 0.00 0.00 41.37 3.46 F
1458 1697 1.649664 CTCCTCATGAGCTTCCAACG 58.350 55.000 17.76 1.09 33.47 4.10 F
3210 3482 0.629596 TCAGGGGGTCGAGTAGATGT 59.370 55.000 0.00 0.00 0.00 3.06 F
3213 3485 0.751452 GGGGGTCGAGTAGATGTTCC 59.249 60.000 0.00 0.00 0.00 3.62 F
3764 4037 0.779997 AAATGCAAGACCAGGGACCT 59.220 50.000 0.00 0.00 0.00 3.85 F
4935 5211 3.490439 TGACTGAGGTCATCAAAGCAA 57.510 42.857 0.00 0.00 46.19 3.91 F
6343 6621 0.038166 GGGAGCCTTGTGACCATGAA 59.962 55.000 0.00 0.00 0.00 2.57 F
6437 6715 0.179001 CCAAACTGGTCGGACCCTTT 60.179 55.000 23.81 17.15 37.50 3.11 F
7584 7871 0.255890 AGTACCATTTCAGCCCGCAT 59.744 50.000 0.00 0.00 0.00 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1224 1463 0.250510 TTGTGCAGGTGCCGTTGATA 60.251 50.000 0.00 0.00 41.18 2.15 R
1348 1587 1.738365 CGACTCTGACATCCTTGCCAG 60.738 57.143 0.00 0.00 34.89 4.85 R
2447 2690 0.625849 ATGGCAGGGGTCTTACAAGG 59.374 55.000 0.00 0.00 0.00 3.61 R
2701 2945 2.243221 ACAAGGAAGCATTAGGGCAGAT 59.757 45.455 0.00 0.00 35.83 2.90 R
3225 3497 3.055385 GGCCTTTATACCTGTGACTCACA 60.055 47.826 11.44 11.44 42.45 3.58 R
4381 4654 3.904136 AGCGAGTTCACCTTTGAAATG 57.096 42.857 0.00 0.00 43.52 2.32 R
4986 5262 4.341235 AGCGATACACTTATCCACTTAGCA 59.659 41.667 0.00 0.00 31.70 3.49 R
4998 5274 4.342862 AGCCAATCATAGCGATACACTT 57.657 40.909 0.00 0.00 32.51 3.16 R
6360 6638 0.034896 GGCTGTTTCCAGGACTCGAA 59.965 55.000 0.00 0.00 39.22 3.71 R
7584 7871 0.686441 CTACCCACTCCCATCCGTCA 60.686 60.000 0.00 0.00 0.00 4.35 R
7590 7877 1.330655 CGTGCTCTACCCACTCCCAT 61.331 60.000 0.00 0.00 0.00 4.00 R
9187 9731 0.179156 CCGTGAACAGATGCATTGCC 60.179 55.000 6.12 0.00 0.00 4.52 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
37 38 7.040409 AGGAGTAATTTAAACAGCAAGTCAAGG 60.040 37.037 0.00 0.00 0.00 3.61
67 68 0.816421 ACACACGTTGCACTTACCCC 60.816 55.000 0.00 0.00 0.00 4.95
68 69 1.228033 ACACGTTGCACTTACCCCC 60.228 57.895 0.00 0.00 0.00 5.40
79 80 0.546747 CTTACCCCCTCCCACAGACA 60.547 60.000 0.00 0.00 0.00 3.41
128 129 5.205565 GTCTCTTCTTTTGCGACGAAAATT 58.794 37.500 0.89 0.00 0.00 1.82
203 204 0.610232 AAGTGATGACAAGCAGGGCC 60.610 55.000 0.00 0.00 0.00 5.80
316 317 5.475719 CAAGTTGCAAATGGACATCTGAAT 58.524 37.500 0.00 0.00 0.00 2.57
615 617 9.760077 ATAGTTTATCGAGGAATTAACAACGAT 57.240 29.630 0.00 0.00 41.86 3.73
641 643 5.295045 GGTGAGAAAGTTACAGACGGAAAAA 59.705 40.000 0.00 0.00 0.00 1.94
732 734 3.119291 GTTGATAGCTCACACCGAGATG 58.881 50.000 0.00 0.00 45.45 2.90
746 748 3.196901 ACCGAGATGCCAACAGTAATACA 59.803 43.478 0.00 0.00 0.00 2.29
876 1115 2.998316 ACCTCCTCTTGCTTATGCTC 57.002 50.000 1.96 0.00 40.48 4.26
877 1116 1.137872 ACCTCCTCTTGCTTATGCTCG 59.862 52.381 1.96 0.00 40.48 5.03
903 1142 3.721793 GGCTCATGATGCCTTAGCT 57.278 52.632 21.85 0.00 46.38 3.32
920 1159 1.273886 AGCTTCCAGACTTCGTCTTCC 59.726 52.381 0.00 0.00 41.37 3.46
997 1236 4.275196 TCGACACCAAGGATAAGATCTACG 59.725 45.833 0.00 0.00 0.00 3.51
998 1237 4.275196 CGACACCAAGGATAAGATCTACGA 59.725 45.833 0.00 0.00 0.00 3.43
999 1238 5.561145 CGACACCAAGGATAAGATCTACGAG 60.561 48.000 0.00 0.00 0.00 4.18
1042 1281 4.732285 TGCAGATTTCTCTCGTGTTTTC 57.268 40.909 0.00 0.00 0.00 2.29
1152 1391 3.675698 CGGAGTTTAAGCAGAAGACAGAC 59.324 47.826 0.00 0.00 0.00 3.51
1224 1463 3.245016 TGCCTTTCAATCTCATGTCCTGT 60.245 43.478 0.00 0.00 0.00 4.00
1348 1587 3.891977 GCCCATAAGGAAAAGAATCTCCC 59.108 47.826 0.00 0.00 38.24 4.30
1380 1619 2.257676 GAGTCGTCCGTGTGGGTC 59.742 66.667 0.00 0.00 37.00 4.46
1389 1628 2.281761 GTGTGGGTCACAGGGCAG 60.282 66.667 0.53 0.00 45.43 4.85
1392 1631 3.640407 TGGGTCACAGGGCAGAGC 61.640 66.667 0.00 0.00 0.00 4.09
1458 1697 1.649664 CTCCTCATGAGCTTCCAACG 58.350 55.000 17.76 1.09 33.47 4.10
1609 1848 8.862085 AGACTTAGGGTTATAATCTTCTACAGC 58.138 37.037 0.00 0.00 0.00 4.40
1659 1898 2.097825 GCAAAGATCACCCTTGCATCT 58.902 47.619 13.66 0.00 0.00 2.90
1746 1985 4.451900 AGGTGATACTTTATGCCCGAAAG 58.548 43.478 0.00 0.00 39.38 2.62
2003 2243 8.015185 AGTGACTTTAGTACAACCAGAACTTA 57.985 34.615 0.00 0.00 0.00 2.24
2037 2278 5.594725 AGAAAAGACAGCGGAGATAGTCATA 59.405 40.000 0.00 0.00 33.56 2.15
2088 2329 9.382244 GAAGTCAAACAGAAATGTATGTAACAC 57.618 33.333 0.00 0.00 42.09 3.32
2125 2366 5.825679 TGCATACCCAATGTTATAACTGGAC 59.174 40.000 20.27 8.60 37.93 4.02
2142 2383 6.590234 ACTGGACCAATGAAGGAAATTAAC 57.410 37.500 0.00 0.00 0.00 2.01
2158 2399 6.352823 GGAAATTAACTCCTGCTAGGTAAGGT 60.353 42.308 0.00 0.00 36.53 3.50
2170 2411 9.185680 CCTGCTAGGTAAGGTTAAAATAATGTT 57.814 33.333 0.00 0.00 0.00 2.71
2421 2663 5.425577 TTGCAAACAAATTAGTCGCTGTA 57.574 34.783 0.00 0.00 31.21 2.74
2447 2690 3.804786 TTCAGTTTTCGGTTTTTCCCC 57.195 42.857 0.00 0.00 0.00 4.81
2458 2701 2.895404 GGTTTTTCCCCCTTGTAAGACC 59.105 50.000 0.00 0.00 0.00 3.85
2504 2747 8.415950 TTCTAATACTGCCCATTCAAGAAAAA 57.584 30.769 0.00 0.00 0.00 1.94
2634 2878 6.030548 TGAACAACATTTCACAAACCTTGA 57.969 33.333 0.00 0.00 30.29 3.02
2701 2945 7.870954 GTCGTATCACATAATGGAAGGTGAATA 59.129 37.037 0.00 0.00 42.83 1.75
2705 2949 8.859236 ATCACATAATGGAAGGTGAATATCTG 57.141 34.615 0.00 0.00 42.83 2.90
2914 3158 4.008330 CTCAACTTCATCCTCTTGCATGT 58.992 43.478 0.00 0.00 0.00 3.21
2976 3220 3.819564 AGAAACCCACCAAAAGCTTTC 57.180 42.857 13.10 0.00 0.00 2.62
2996 3240 8.796475 AGCTTTCACATATGACTATTTGTTGTT 58.204 29.630 10.38 0.00 33.38 2.83
3016 3260 8.511321 TGTTGTTGCTGACTTAAAATATAGTGG 58.489 33.333 0.00 0.00 0.00 4.00
3208 3480 0.927767 ACTCAGGGGGTCGAGTAGAT 59.072 55.000 0.00 0.00 40.67 1.98
3209 3481 1.323412 CTCAGGGGGTCGAGTAGATG 58.677 60.000 0.00 0.00 0.00 2.90
3210 3482 0.629596 TCAGGGGGTCGAGTAGATGT 59.370 55.000 0.00 0.00 0.00 3.06
3211 3483 1.006758 TCAGGGGGTCGAGTAGATGTT 59.993 52.381 0.00 0.00 0.00 2.71
3212 3484 1.409427 CAGGGGGTCGAGTAGATGTTC 59.591 57.143 0.00 0.00 0.00 3.18
3213 3485 0.751452 GGGGGTCGAGTAGATGTTCC 59.249 60.000 0.00 0.00 0.00 3.62
3214 3486 1.688627 GGGGGTCGAGTAGATGTTCCT 60.689 57.143 0.00 0.00 0.00 3.36
3215 3487 2.423947 GGGGGTCGAGTAGATGTTCCTA 60.424 54.545 0.00 0.00 0.00 2.94
3216 3488 3.498334 GGGGTCGAGTAGATGTTCCTAT 58.502 50.000 0.00 0.00 0.00 2.57
3217 3489 3.896272 GGGGTCGAGTAGATGTTCCTATT 59.104 47.826 0.00 0.00 0.00 1.73
3218 3490 5.075493 GGGGTCGAGTAGATGTTCCTATTA 58.925 45.833 0.00 0.00 0.00 0.98
3219 3491 5.715753 GGGGTCGAGTAGATGTTCCTATTAT 59.284 44.000 0.00 0.00 0.00 1.28
3220 3492 6.888632 GGGGTCGAGTAGATGTTCCTATTATA 59.111 42.308 0.00 0.00 0.00 0.98
3221 3493 7.395489 GGGGTCGAGTAGATGTTCCTATTATAA 59.605 40.741 0.00 0.00 0.00 0.98
3222 3494 8.968969 GGGTCGAGTAGATGTTCCTATTATAAT 58.031 37.037 2.97 2.97 0.00 1.28
3254 3526 4.781087 TCACAGGTATAAAGGCCTACTGTT 59.219 41.667 5.16 0.00 33.07 3.16
3255 3527 4.876107 CACAGGTATAAAGGCCTACTGTTG 59.124 45.833 5.16 1.65 33.07 3.33
3365 3637 7.828717 TGATGTGTGTTCCATCATTAGTTATGT 59.171 33.333 0.00 0.00 42.73 2.29
3366 3638 9.325198 GATGTGTGTTCCATCATTAGTTATGTA 57.675 33.333 0.00 0.00 38.82 2.29
3541 3814 5.178438 TGCCAACAGTGTTTTTGAAGTTTTC 59.822 36.000 5.57 0.00 0.00 2.29
3657 3930 5.185454 TCACTACTACCATGGCTTCAAATG 58.815 41.667 13.04 2.78 0.00 2.32
3680 3953 6.563422 TGAAATAATGGTTGAATGCTACTGC 58.437 36.000 0.00 0.00 40.20 4.40
3764 4037 0.779997 AAATGCAAGACCAGGGACCT 59.220 50.000 0.00 0.00 0.00 3.85
3881 4154 4.310769 AGATTTGTTCGGTGAAGTCTCAG 58.689 43.478 0.00 0.00 30.14 3.35
3999 4272 8.964476 ATCTCAGTCGTTCCATTAAACATAAT 57.036 30.769 0.00 0.00 0.00 1.28
4454 4727 7.092891 TGTGTTCCTGATAACTATGATGGTTCT 60.093 37.037 0.00 0.00 0.00 3.01
4513 4786 6.205853 ACACAGTTGAACAGAAACTAACAACA 59.794 34.615 0.00 0.00 39.62 3.33
4514 4787 7.081349 CACAGTTGAACAGAAACTAACAACAA 58.919 34.615 0.00 0.00 39.62 2.83
4515 4788 7.271223 CACAGTTGAACAGAAACTAACAACAAG 59.729 37.037 0.00 0.00 39.62 3.16
4516 4789 6.251376 CAGTTGAACAGAAACTAACAACAAGC 59.749 38.462 0.00 0.00 39.62 4.01
4517 4790 6.151144 AGTTGAACAGAAACTAACAACAAGCT 59.849 34.615 0.00 0.00 39.62 3.74
4592 4868 9.838339 AGTTTGCTAGCTATTGTAGTATGATTT 57.162 29.630 17.23 0.00 0.00 2.17
4616 4892 4.767000 TCATGTCTATGACCCTAGGGAT 57.233 45.455 35.38 20.35 38.37 3.85
4935 5211 3.490439 TGACTGAGGTCATCAAAGCAA 57.510 42.857 0.00 0.00 46.19 3.91
4936 5212 4.025040 TGACTGAGGTCATCAAAGCAAT 57.975 40.909 0.00 0.00 46.19 3.56
4937 5213 3.754850 TGACTGAGGTCATCAAAGCAATG 59.245 43.478 0.00 0.00 46.19 2.82
4938 5214 3.755378 GACTGAGGTCATCAAAGCAATGT 59.245 43.478 0.00 0.00 41.75 2.71
4939 5215 4.910195 ACTGAGGTCATCAAAGCAATGTA 58.090 39.130 0.00 0.00 37.52 2.29
4940 5216 5.503927 ACTGAGGTCATCAAAGCAATGTAT 58.496 37.500 0.00 0.00 37.52 2.29
4941 5217 6.653020 ACTGAGGTCATCAAAGCAATGTATA 58.347 36.000 0.00 0.00 37.52 1.47
4942 5218 7.285566 ACTGAGGTCATCAAAGCAATGTATAT 58.714 34.615 0.00 0.00 37.52 0.86
4943 5219 8.432013 ACTGAGGTCATCAAAGCAATGTATATA 58.568 33.333 0.00 0.00 37.52 0.86
4944 5220 8.837788 TGAGGTCATCAAAGCAATGTATATAG 57.162 34.615 0.00 0.00 34.02 1.31
4945 5221 7.388776 TGAGGTCATCAAAGCAATGTATATAGC 59.611 37.037 0.00 0.00 34.02 2.97
4946 5222 7.456725 AGGTCATCAAAGCAATGTATATAGCT 58.543 34.615 0.00 0.00 39.37 3.32
4947 5223 8.597167 AGGTCATCAAAGCAATGTATATAGCTA 58.403 33.333 0.00 0.00 36.07 3.32
4948 5224 8.877779 GGTCATCAAAGCAATGTATATAGCTAG 58.122 37.037 0.00 0.00 36.07 3.42
4949 5225 9.429359 GTCATCAAAGCAATGTATATAGCTAGT 57.571 33.333 0.00 0.00 36.07 2.57
4952 5228 8.988064 TCAAAGCAATGTATATAGCTAGTAGC 57.012 34.615 14.62 14.62 42.84 3.58
4967 5243 6.670077 GCTAGTAGCTTTCATTACTTGCTT 57.330 37.500 15.16 0.00 41.88 3.91
4968 5244 6.481984 GCTAGTAGCTTTCATTACTTGCTTG 58.518 40.000 15.16 0.00 41.88 4.01
4969 5245 6.313905 GCTAGTAGCTTTCATTACTTGCTTGA 59.686 38.462 15.16 0.00 41.88 3.02
4970 5246 7.011857 GCTAGTAGCTTTCATTACTTGCTTGAT 59.988 37.037 15.16 0.00 41.88 2.57
4971 5247 9.534565 CTAGTAGCTTTCATTACTTGCTTGATA 57.465 33.333 0.00 0.00 35.47 2.15
4972 5248 8.792830 AGTAGCTTTCATTACTTGCTTGATAA 57.207 30.769 0.00 0.00 35.47 1.75
4973 5249 9.231297 AGTAGCTTTCATTACTTGCTTGATAAA 57.769 29.630 0.00 0.00 35.47 1.40
4974 5250 9.495754 GTAGCTTTCATTACTTGCTTGATAAAG 57.504 33.333 0.00 0.00 35.47 1.85
4975 5251 7.031975 AGCTTTCATTACTTGCTTGATAAAGC 58.968 34.615 7.97 7.97 45.67 3.51
4976 5252 7.031975 GCTTTCATTACTTGCTTGATAAAGCT 58.968 34.615 16.00 0.00 45.66 3.74
4977 5253 7.543520 GCTTTCATTACTTGCTTGATAAAGCTT 59.456 33.333 16.00 0.00 45.66 3.74
4978 5254 9.415544 CTTTCATTACTTGCTTGATAAAGCTTT 57.584 29.630 17.30 17.30 45.66 3.51
4989 5265 9.874205 TGCTTGATAAAGCTTTAATAAATTGCT 57.126 25.926 22.13 3.04 45.66 3.91
5007 5283 7.715265 AATTGCTAAGTGGATAAGTGTATCG 57.285 36.000 0.00 0.00 37.58 2.92
5008 5284 4.617959 TGCTAAGTGGATAAGTGTATCGC 58.382 43.478 0.00 0.00 37.58 4.58
5009 5285 4.341235 TGCTAAGTGGATAAGTGTATCGCT 59.659 41.667 0.00 0.00 37.58 4.93
5010 5286 5.533528 TGCTAAGTGGATAAGTGTATCGCTA 59.466 40.000 0.00 0.00 37.58 4.26
5011 5287 6.208797 TGCTAAGTGGATAAGTGTATCGCTAT 59.791 38.462 0.00 0.00 37.58 2.97
5012 5288 6.528423 GCTAAGTGGATAAGTGTATCGCTATG 59.472 42.308 0.00 0.00 37.58 2.23
5013 5289 6.650427 AAGTGGATAAGTGTATCGCTATGA 57.350 37.500 0.00 0.00 37.58 2.15
5014 5290 6.842437 AGTGGATAAGTGTATCGCTATGAT 57.158 37.500 0.00 0.00 37.58 2.45
5015 5291 7.233389 AGTGGATAAGTGTATCGCTATGATT 57.767 36.000 0.00 0.00 37.58 2.57
5016 5292 7.093354 AGTGGATAAGTGTATCGCTATGATTG 58.907 38.462 0.00 0.00 37.58 2.67
5017 5293 6.311445 GTGGATAAGTGTATCGCTATGATTGG 59.689 42.308 0.00 0.00 37.58 3.16
5018 5294 5.292101 GGATAAGTGTATCGCTATGATTGGC 59.708 44.000 0.00 0.00 37.58 4.52
5019 5295 4.342862 AAGTGTATCGCTATGATTGGCT 57.657 40.909 0.00 0.00 38.57 4.75
5020 5296 5.468540 AAGTGTATCGCTATGATTGGCTA 57.531 39.130 0.00 0.00 38.57 3.93
5021 5297 5.667539 AGTGTATCGCTATGATTGGCTAT 57.332 39.130 0.00 0.00 38.57 2.97
5022 5298 6.775594 AGTGTATCGCTATGATTGGCTATA 57.224 37.500 0.00 0.00 38.57 1.31
5023 5299 7.170393 AGTGTATCGCTATGATTGGCTATAA 57.830 36.000 0.00 0.00 38.57 0.98
5024 5300 7.261325 AGTGTATCGCTATGATTGGCTATAAG 58.739 38.462 0.00 0.00 38.57 1.73
5025 5301 7.036220 GTGTATCGCTATGATTGGCTATAAGT 58.964 38.462 0.00 0.00 38.57 2.24
5026 5302 7.221067 GTGTATCGCTATGATTGGCTATAAGTC 59.779 40.741 0.00 0.00 38.57 3.01
5027 5303 5.984695 TCGCTATGATTGGCTATAAGTCT 57.015 39.130 0.00 0.00 0.00 3.24
5028 5304 5.955488 TCGCTATGATTGGCTATAAGTCTC 58.045 41.667 0.00 0.00 0.00 3.36
5029 5305 5.476945 TCGCTATGATTGGCTATAAGTCTCA 59.523 40.000 0.00 0.00 0.00 3.27
5030 5306 5.804473 CGCTATGATTGGCTATAAGTCTCAG 59.196 44.000 0.00 0.00 0.00 3.35
5031 5307 6.349694 CGCTATGATTGGCTATAAGTCTCAGA 60.350 42.308 0.00 0.00 0.00 3.27
5032 5308 7.382110 GCTATGATTGGCTATAAGTCTCAGAA 58.618 38.462 0.00 0.00 0.00 3.02
5033 5309 8.040132 GCTATGATTGGCTATAAGTCTCAGAAT 58.960 37.037 0.00 0.00 0.00 2.40
5034 5310 9.941325 CTATGATTGGCTATAAGTCTCAGAATT 57.059 33.333 0.00 0.00 0.00 2.17
5035 5311 8.845413 ATGATTGGCTATAAGTCTCAGAATTC 57.155 34.615 0.00 0.00 0.00 2.17
5036 5312 7.795047 TGATTGGCTATAAGTCTCAGAATTCA 58.205 34.615 8.44 0.00 0.00 2.57
5037 5313 8.267183 TGATTGGCTATAAGTCTCAGAATTCAA 58.733 33.333 8.44 0.00 0.00 2.69
5038 5314 8.674263 ATTGGCTATAAGTCTCAGAATTCAAG 57.326 34.615 8.44 4.93 0.00 3.02
5039 5315 7.187824 TGGCTATAAGTCTCAGAATTCAAGT 57.812 36.000 8.44 0.00 0.00 3.16
5040 5316 7.624549 TGGCTATAAGTCTCAGAATTCAAGTT 58.375 34.615 8.44 2.45 0.00 2.66
5041 5317 8.758829 TGGCTATAAGTCTCAGAATTCAAGTTA 58.241 33.333 8.44 4.46 0.00 2.24
5042 5318 9.036671 GGCTATAAGTCTCAGAATTCAAGTTAC 57.963 37.037 8.44 0.72 0.00 2.50
5043 5319 9.587772 GCTATAAGTCTCAGAATTCAAGTTACA 57.412 33.333 8.44 0.00 0.00 2.41
5048 5324 8.994429 AGTCTCAGAATTCAAGTTACACTATG 57.006 34.615 8.44 0.00 0.00 2.23
5049 5325 7.547370 AGTCTCAGAATTCAAGTTACACTATGC 59.453 37.037 8.44 0.00 0.00 3.14
5050 5326 7.547370 GTCTCAGAATTCAAGTTACACTATGCT 59.453 37.037 8.44 0.00 0.00 3.79
5051 5327 7.547019 TCTCAGAATTCAAGTTACACTATGCTG 59.453 37.037 8.44 0.00 0.00 4.41
5052 5328 6.595326 TCAGAATTCAAGTTACACTATGCTGG 59.405 38.462 8.44 0.00 0.00 4.85
5053 5329 6.595326 CAGAATTCAAGTTACACTATGCTGGA 59.405 38.462 8.44 0.00 0.00 3.86
5054 5330 7.119699 CAGAATTCAAGTTACACTATGCTGGAA 59.880 37.037 8.44 0.00 0.00 3.53
5055 5331 7.665559 AGAATTCAAGTTACACTATGCTGGAAA 59.334 33.333 8.44 0.00 0.00 3.13
5056 5332 7.759489 ATTCAAGTTACACTATGCTGGAAAA 57.241 32.000 0.00 0.00 0.00 2.29
5057 5333 6.554334 TCAAGTTACACTATGCTGGAAAAC 57.446 37.500 0.00 0.00 0.00 2.43
5058 5334 6.058833 TCAAGTTACACTATGCTGGAAAACA 58.941 36.000 0.00 0.00 0.00 2.83
5059 5335 6.544197 TCAAGTTACACTATGCTGGAAAACAA 59.456 34.615 0.00 0.00 0.00 2.83
5249 5525 1.858091 CCGCACTCAGGTCATGATAC 58.142 55.000 0.00 0.00 37.28 2.24
5380 5657 8.607459 CGATTCAATTCTTACTACAGCAATTCT 58.393 33.333 0.00 0.00 0.00 2.40
5603 5881 1.570857 TTACCTGGCATGGGAGGTGG 61.571 60.000 5.68 0.00 42.80 4.61
5997 6275 6.318648 TGGAATATCTAAACAGCAATGGTGTC 59.681 38.462 18.81 2.76 43.73 3.67
6093 6371 3.599343 TGTCGATCTTCATGGGAACTTG 58.401 45.455 0.00 0.00 36.86 3.16
6343 6621 0.038166 GGGAGCCTTGTGACCATGAA 59.962 55.000 0.00 0.00 0.00 2.57
6359 6637 2.743636 TGAAGTCATGGGTTCGAGTC 57.256 50.000 0.00 0.00 0.00 3.36
6360 6638 2.248248 TGAAGTCATGGGTTCGAGTCT 58.752 47.619 0.00 0.00 0.00 3.24
6361 6639 2.632996 TGAAGTCATGGGTTCGAGTCTT 59.367 45.455 0.00 0.00 0.00 3.01
6405 6683 3.092301 GCAGAAATGTAGGGAAAGGCTT 58.908 45.455 0.00 0.00 0.00 4.35
6407 6685 4.335416 CAGAAATGTAGGGAAAGGCTTCA 58.665 43.478 0.00 0.00 32.75 3.02
6423 6701 4.280929 AGGCTTCATACAAAAGACCCAAAC 59.719 41.667 0.00 0.00 31.72 2.93
6437 6715 0.179001 CCAAACTGGTCGGACCCTTT 60.179 55.000 23.81 17.15 37.50 3.11
6447 6725 3.725032 GACCCTTTCCCGGACCCC 61.725 72.222 0.73 0.00 0.00 4.95
6579 6859 5.240121 CACCTTTATGAGCAAAAGCCATTT 58.760 37.500 0.00 0.00 33.48 2.32
6601 6881 3.748645 TTTGCTATCCCCTGCCTAAAA 57.251 42.857 0.00 0.00 0.00 1.52
6669 6949 7.994425 TGACCAATGAGCAATAGTTTTTCTA 57.006 32.000 0.00 0.00 0.00 2.10
6740 7022 7.158697 TGTATACGAAGCATGCATTAACCTAT 58.841 34.615 21.98 7.34 0.00 2.57
6741 7023 8.308207 TGTATACGAAGCATGCATTAACCTATA 58.692 33.333 21.98 6.43 0.00 1.31
6749 7031 7.911651 AGCATGCATTAACCTATAGAGTACAT 58.088 34.615 21.98 0.00 0.00 2.29
6837 7119 3.120786 GCATCACAAGAAATGCAGCAAAC 60.121 43.478 0.00 0.00 45.97 2.93
6862 7144 9.401058 ACCACTCTTTCTTCATATCCTTTAATG 57.599 33.333 0.00 0.00 0.00 1.90
6882 7164 6.893020 AATGTTCCAGAGGATAGGTAGTTT 57.107 37.500 0.00 0.00 0.00 2.66
6887 7169 8.287350 TGTTCCAGAGGATAGGTAGTTTATAGT 58.713 37.037 0.00 0.00 0.00 2.12
6945 7229 7.038659 TGGCCAATGCAATAGTTTTAATACAC 58.961 34.615 0.61 0.00 40.13 2.90
6946 7230 7.038659 GGCCAATGCAATAGTTTTAATACACA 58.961 34.615 0.00 0.00 40.13 3.72
6947 7231 7.710475 GGCCAATGCAATAGTTTTAATACACAT 59.290 33.333 0.00 0.00 40.13 3.21
7010 7294 6.892658 TTAACTACAGGTGCAATCATGTTT 57.107 33.333 0.00 0.00 34.27 2.83
7016 7300 4.981674 ACAGGTGCAATCATGTTTAAAACG 59.018 37.500 0.00 0.00 0.00 3.60
7097 7381 3.971305 TGTTCTTCCCTCCTTCACACTAA 59.029 43.478 0.00 0.00 0.00 2.24
7098 7382 4.410883 TGTTCTTCCCTCCTTCACACTAAA 59.589 41.667 0.00 0.00 0.00 1.85
7103 7389 3.073946 TCCCTCCTTCACACTAAAAAGGG 59.926 47.826 0.00 0.00 43.01 3.95
7107 7393 3.464080 TCCTTCACACTAAAAAGGGGGAA 59.536 43.478 0.00 0.00 40.03 3.97
7112 7398 4.010349 CACACTAAAAAGGGGGAAGCTAG 58.990 47.826 0.00 0.00 0.00 3.42
7115 7401 2.604912 AAAAAGGGGGAAGCTAGTGG 57.395 50.000 0.00 0.00 0.00 4.00
7121 7407 1.420514 GGGGGAAGCTAGTGGTTATCC 59.579 57.143 0.00 0.00 33.64 2.59
7171 7457 3.479489 TCAAATGTGCTCTGCTCTCAAA 58.521 40.909 0.00 0.00 0.00 2.69
7179 7465 6.230472 TGTGCTCTGCTCTCAAAATAGTTTA 58.770 36.000 0.00 0.00 0.00 2.01
7186 7472 9.640963 TCTGCTCTCAAAATAGTTTAAGAGTAC 57.359 33.333 15.40 2.98 36.14 2.73
7250 7537 4.617253 TTGTCCTTAAGCTGCTTGACTA 57.383 40.909 24.35 16.08 0.00 2.59
7332 7619 4.416738 GACTGCCACAGCCCTCCC 62.417 72.222 0.00 0.00 38.69 4.30
7542 7829 2.037641 CACCGGCTCCATCTTCATGATA 59.962 50.000 0.00 0.00 33.36 2.15
7551 7838 4.081807 TCCATCTTCATGATATCCGAGCAG 60.082 45.833 0.00 0.00 33.36 4.24
7584 7871 0.255890 AGTACCATTTCAGCCCGCAT 59.744 50.000 0.00 0.00 0.00 4.73
7887 8174 1.045911 AAAAGGTCAGCCCCGCAAAA 61.046 50.000 0.00 0.00 34.57 2.44
7953 8249 3.440228 GTCCTCTTCGCTTGCTACTTAG 58.560 50.000 0.00 0.00 0.00 2.18
7994 8291 2.599848 GCTAATGACGCCTACGCAATTG 60.600 50.000 0.00 0.00 45.53 2.32
8054 8351 2.504244 GACGCGGTGGTCTTCGAG 60.504 66.667 12.47 0.00 34.09 4.04
8090 8387 0.961019 TAAGCAACAAGGCAAGGCTG 59.039 50.000 0.00 0.00 34.56 4.85
8146 8443 2.084546 GAATGCTTACCGGAGCTTTGT 58.915 47.619 17.66 0.00 43.11 2.83
8435 8732 6.574350 AGCTAGCTATGTACACCTTGTTAAG 58.426 40.000 17.69 0.00 0.00 1.85
8446 8743 5.891451 ACACCTTGTTAAGAAAAACAGAGC 58.109 37.500 0.00 0.00 40.29 4.09
8458 8755 6.641474 AGAAAAACAGAGCCTACCTATGTAC 58.359 40.000 0.00 0.00 44.80 2.90
8459 8756 6.212791 AGAAAAACAGAGCCTACCTATGTACA 59.787 38.462 0.00 0.00 44.80 2.90
8465 8920 5.470777 CAGAGCCTACCTATGTACAGTAGTC 59.529 48.000 15.68 6.80 33.18 2.59
8467 8922 6.558014 AGAGCCTACCTATGTACAGTAGTCTA 59.442 42.308 15.68 0.00 33.18 2.59
8518 8973 0.912487 TCCTGTAAACCGGGCCATCT 60.912 55.000 6.32 0.00 39.73 2.90
8539 8994 7.062138 CCATCTGACAAAATAACCGTTGATTTG 59.938 37.037 16.14 16.14 37.10 2.32
8547 9002 0.250124 ACCGTTGATTTGCAGGACGA 60.250 50.000 9.80 0.00 33.65 4.20
8562 9017 3.125316 CAGGACGAAGACTAATTTGCCAC 59.875 47.826 0.00 0.00 0.00 5.01
8566 9021 2.706890 GAAGACTAATTTGCCACCCGA 58.293 47.619 0.00 0.00 0.00 5.14
8574 9029 1.698506 TTTGCCACCCGAAACAGATT 58.301 45.000 0.00 0.00 0.00 2.40
8580 9035 3.000727 CCACCCGAAACAGATTCAGTAC 58.999 50.000 0.00 0.00 37.96 2.73
8587 9043 6.102663 CCGAAACAGATTCAGTACATTCTCT 58.897 40.000 0.00 0.00 37.96 3.10
8618 9077 4.965283 TTTAAGGGATCCTCCAAACCAT 57.035 40.909 12.58 0.00 38.64 3.55
8653 9114 9.958180 TTTTCATATCTACAGGATTTGAACTCA 57.042 29.630 9.68 0.00 45.23 3.41
8733 9194 0.325933 CATGGTCTTCCCTGAGCACA 59.674 55.000 0.00 0.00 45.40 4.57
8745 9207 1.374758 GAGCACAACCTCACCGGAG 60.375 63.158 9.46 0.00 41.02 4.63
8757 9219 3.842923 CCGGAGTGCCTCGATGCT 61.843 66.667 13.93 0.00 0.00 3.79
8853 9360 4.514577 GCTAGCTTCTGCCGCCGA 62.515 66.667 7.70 0.00 40.80 5.54
8874 9398 2.581354 CGCTACTGCCTGCTCCTT 59.419 61.111 0.00 0.00 35.36 3.36
9006 9539 7.342026 GGAAGATGGACCCAATTGTAATTTAGT 59.658 37.037 4.43 0.00 0.00 2.24
9013 9546 4.439563 CCCAATTGTAATTTAGTGGGCGTC 60.440 45.833 4.43 0.00 0.00 5.19
9174 9718 5.046304 TCTGCTAGAAATGTTCTTAGGCAGT 60.046 40.000 23.40 0.00 45.53 4.40
9187 9731 4.614673 GCAGTTGACGCCAAACAG 57.385 55.556 0.00 0.00 33.49 3.16
9241 9786 1.613925 CCACGGACATGGATACGAGAT 59.386 52.381 0.00 0.00 43.02 2.75
9243 9788 2.554462 CACGGACATGGATACGAGATCT 59.446 50.000 0.00 0.00 42.51 2.75
9246 9791 3.441922 CGGACATGGATACGAGATCTGAT 59.558 47.826 0.00 0.00 42.51 2.90
9275 9820 7.071321 AGGTAAGGAGTCAGGTATAAATCTTGG 59.929 40.741 0.00 0.00 0.00 3.61
9276 9821 7.070821 GGTAAGGAGTCAGGTATAAATCTTGGA 59.929 40.741 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.719633 ACTTGCTGTTTAAATTACTCCTTCTGA 59.280 33.333 0.00 0.00 0.00 3.27
37 38 3.036084 CGTGTGTCCTGCGTCACC 61.036 66.667 0.00 0.00 34.14 4.02
47 48 0.584876 GGGTAAGTGCAACGTGTGTC 59.415 55.000 0.00 0.00 45.86 3.67
67 68 4.559862 AACTTCTTATGTCTGTGGGAGG 57.440 45.455 0.00 0.00 0.00 4.30
68 69 5.582665 GCTAAACTTCTTATGTCTGTGGGAG 59.417 44.000 0.00 0.00 0.00 4.30
105 106 3.854286 TTTCGTCGCAAAAGAAGAGAC 57.146 42.857 0.00 0.00 30.91 3.36
128 129 1.825474 CCCTGAGAAGGTCTCGCTAAA 59.175 52.381 1.07 0.00 46.25 1.85
316 317 3.007506 TGAAGTCGATGGTTGCTTAGGAA 59.992 43.478 0.00 0.00 0.00 3.36
383 384 9.425248 TTCTATTCAATTGGATGGAATAAAGCT 57.575 29.630 18.79 0.00 34.23 3.74
421 423 7.164230 TGTTTCTATTGGACAAGTTTTGTGT 57.836 32.000 0.00 0.00 45.52 3.72
603 605 5.768164 ACTTTCTCACCCATCGTTGTTAATT 59.232 36.000 0.00 0.00 0.00 1.40
612 614 3.927142 GTCTGTAACTTTCTCACCCATCG 59.073 47.826 0.00 0.00 0.00 3.84
615 617 2.036733 CCGTCTGTAACTTTCTCACCCA 59.963 50.000 0.00 0.00 0.00 4.51
641 643 7.226523 GTGGTTTGCTTTCCTTTTCAATAATGT 59.773 33.333 0.00 0.00 0.00 2.71
732 734 2.640184 GGGAGGTGTATTACTGTTGGC 58.360 52.381 0.00 0.00 0.00 4.52
783 786 3.561725 GGAAGCACATAAGGTATGCAGTC 59.438 47.826 0.00 0.00 41.97 3.51
840 1079 3.319405 GGAGGTATCATGAGCTTCTTCGA 59.681 47.826 0.09 0.00 0.00 3.71
843 1082 4.555689 AGAGGAGGTATCATGAGCTTCTT 58.444 43.478 0.09 0.00 32.74 2.52
876 1115 3.549299 GCATCATGAGCCTTTTATCCG 57.451 47.619 0.09 0.00 0.00 4.18
920 1159 4.292178 GCCTCTGCGATCCTCGGG 62.292 72.222 0.00 0.00 40.84 5.14
933 1172 0.242555 GTCCTCTATAGCTGCGCCTC 59.757 60.000 4.18 0.00 0.00 4.70
977 1216 5.446860 TCTCGTAGATCTTATCCTTGGTGT 58.553 41.667 0.00 0.00 33.89 4.16
1042 1281 6.128553 ACGATAAGACATGCTACAAAACACAG 60.129 38.462 0.00 0.00 0.00 3.66
1152 1391 3.412386 CTCCTGGTACTCCCAAAACTTG 58.588 50.000 0.00 0.00 44.65 3.16
1224 1463 0.250510 TTGTGCAGGTGCCGTTGATA 60.251 50.000 0.00 0.00 41.18 2.15
1320 1559 2.919602 TCTTTTCCTTATGGGCAGGACT 59.080 45.455 0.00 0.00 40.37 3.85
1348 1587 1.738365 CGACTCTGACATCCTTGCCAG 60.738 57.143 0.00 0.00 34.89 4.85
1380 1619 2.202987 GATCCGCTCTGCCCTGTG 60.203 66.667 0.00 0.00 0.00 3.66
1386 1625 3.056962 TCTCATAGATTGATCCGCTCTGC 60.057 47.826 0.00 0.00 32.72 4.26
1389 1628 3.509575 ACCTCTCATAGATTGATCCGCTC 59.490 47.826 0.00 0.00 32.72 5.03
1392 1631 5.468592 CAGAACCTCTCATAGATTGATCCG 58.531 45.833 0.00 0.00 32.72 4.18
1458 1697 3.518068 GTTGCATACCCAGCCGCC 61.518 66.667 0.00 0.00 0.00 6.13
2003 2243 3.059597 CGCTGTCTTTTCTCAACATCGTT 60.060 43.478 0.00 0.00 30.39 3.85
2037 2278 7.841729 TCTCCTGTATATTTTCCTTCACTCTCT 59.158 37.037 0.00 0.00 0.00 3.10
2088 2329 3.270877 GGGTATGCAACTAGTGTTCCTG 58.729 50.000 0.00 0.00 33.52 3.86
2125 2366 5.420104 AGCAGGAGTTAATTTCCTTCATTGG 59.580 40.000 8.37 0.17 42.40 3.16
2142 2383 9.057089 CATTATTTTAACCTTACCTAGCAGGAG 57.943 37.037 8.91 0.00 37.67 3.69
2421 2663 5.350365 GGAAAAACCGAAAACTGAAAAGCTT 59.650 36.000 0.00 0.00 0.00 3.74
2447 2690 0.625849 ATGGCAGGGGTCTTACAAGG 59.374 55.000 0.00 0.00 0.00 3.61
2504 2747 8.115490 AGTGAAAGCATAATAGCAACTTCTTT 57.885 30.769 0.00 0.00 36.85 2.52
2634 2878 4.775236 AGCTTGACTTTGTGTCTTCTCTT 58.225 39.130 0.00 0.00 45.54 2.85
2701 2945 2.243221 ACAAGGAAGCATTAGGGCAGAT 59.757 45.455 0.00 0.00 35.83 2.90
2976 3220 7.482743 GTCAGCAACAACAAATAGTCATATGTG 59.517 37.037 1.90 0.00 33.41 3.21
2996 3240 9.851686 ATTGATCCACTATATTTTAAGTCAGCA 57.148 29.630 0.00 0.00 0.00 4.41
3220 3492 7.499232 GCCTTTATACCTGTGACTCACAATATT 59.501 37.037 12.92 2.32 44.08 1.28
3221 3493 6.992715 GCCTTTATACCTGTGACTCACAATAT 59.007 38.462 12.92 14.34 44.08 1.28
3222 3494 6.346096 GCCTTTATACCTGTGACTCACAATA 58.654 40.000 12.92 8.83 44.08 1.90
3223 3495 5.186198 GCCTTTATACCTGTGACTCACAAT 58.814 41.667 12.92 6.69 44.08 2.71
3224 3496 4.564821 GGCCTTTATACCTGTGACTCACAA 60.565 45.833 12.92 0.00 44.08 3.33
3225 3497 3.055385 GGCCTTTATACCTGTGACTCACA 60.055 47.826 11.44 11.44 42.45 3.58
3226 3498 3.197983 AGGCCTTTATACCTGTGACTCAC 59.802 47.826 0.00 1.86 34.07 3.51
3227 3499 3.450904 AGGCCTTTATACCTGTGACTCA 58.549 45.455 0.00 0.00 34.07 3.41
3228 3500 4.650131 AGTAGGCCTTTATACCTGTGACTC 59.350 45.833 12.58 0.00 36.77 3.36
3229 3501 4.406003 CAGTAGGCCTTTATACCTGTGACT 59.594 45.833 12.58 0.00 36.77 3.41
3541 3814 2.875933 TCAGTTAACCAAACCTTCTGCG 59.124 45.455 0.88 0.00 39.03 5.18
3657 3930 6.694411 CAGCAGTAGCATTCAACCATTATTTC 59.306 38.462 0.00 0.00 45.49 2.17
3680 3953 1.766494 TGGCAATTCCACCTATGCAG 58.234 50.000 0.00 0.00 40.72 4.41
3764 4037 6.993308 TGCTAAACATACCTTACTGTGAACAA 59.007 34.615 0.00 0.00 0.00 2.83
3881 4154 5.294552 GTCATTGACCAGTATAGGAGCAAAC 59.705 44.000 5.44 0.00 33.07 2.93
4342 4615 5.184287 GGGTAATGTTGCCTTGTTAGCTTTA 59.816 40.000 0.00 0.00 33.03 1.85
4381 4654 3.904136 AGCGAGTTCACCTTTGAAATG 57.096 42.857 0.00 0.00 43.52 2.32
4454 4727 7.283580 ACTTGTTGCACTGTTATGGTTAACTTA 59.716 33.333 5.42 0.00 38.81 2.24
4944 5220 6.313905 TCAAGCAAGTAATGAAAGCTACTAGC 59.686 38.462 0.00 0.00 42.84 3.42
4945 5221 7.834068 TCAAGCAAGTAATGAAAGCTACTAG 57.166 36.000 0.00 0.00 34.66 2.57
4946 5222 9.884636 TTATCAAGCAAGTAATGAAAGCTACTA 57.115 29.630 0.00 0.00 34.66 1.82
4947 5223 8.792830 TTATCAAGCAAGTAATGAAAGCTACT 57.207 30.769 0.00 0.00 34.66 2.57
4948 5224 9.495754 CTTTATCAAGCAAGTAATGAAAGCTAC 57.504 33.333 0.00 0.00 34.66 3.58
4981 5257 9.256477 CGATACACTTATCCACTTAGCAATTTA 57.744 33.333 0.00 0.00 31.70 1.40
4982 5258 7.254795 GCGATACACTTATCCACTTAGCAATTT 60.255 37.037 0.00 0.00 31.70 1.82
4983 5259 6.202954 GCGATACACTTATCCACTTAGCAATT 59.797 38.462 0.00 0.00 31.70 2.32
4984 5260 5.696724 GCGATACACTTATCCACTTAGCAAT 59.303 40.000 0.00 0.00 31.70 3.56
4985 5261 5.047847 GCGATACACTTATCCACTTAGCAA 58.952 41.667 0.00 0.00 31.70 3.91
4986 5262 4.341235 AGCGATACACTTATCCACTTAGCA 59.659 41.667 0.00 0.00 31.70 3.49
4987 5263 4.872664 AGCGATACACTTATCCACTTAGC 58.127 43.478 0.00 0.00 31.70 3.09
4988 5264 7.817641 TCATAGCGATACACTTATCCACTTAG 58.182 38.462 0.00 0.00 31.70 2.18
4989 5265 7.754851 TCATAGCGATACACTTATCCACTTA 57.245 36.000 0.00 0.00 31.70 2.24
4990 5266 6.650427 TCATAGCGATACACTTATCCACTT 57.350 37.500 0.00 0.00 31.70 3.16
4991 5267 6.842437 ATCATAGCGATACACTTATCCACT 57.158 37.500 0.00 0.00 31.70 4.00
4992 5268 6.311445 CCAATCATAGCGATACACTTATCCAC 59.689 42.308 0.00 0.00 32.51 4.02
4993 5269 6.398095 CCAATCATAGCGATACACTTATCCA 58.602 40.000 0.00 0.00 32.51 3.41
4994 5270 5.292101 GCCAATCATAGCGATACACTTATCC 59.708 44.000 0.00 0.00 32.51 2.59
4995 5271 6.102663 AGCCAATCATAGCGATACACTTATC 58.897 40.000 0.00 0.00 32.51 1.75
4996 5272 6.042638 AGCCAATCATAGCGATACACTTAT 57.957 37.500 0.00 0.00 32.51 1.73
4997 5273 5.468540 AGCCAATCATAGCGATACACTTA 57.531 39.130 0.00 0.00 32.51 2.24
4998 5274 4.342862 AGCCAATCATAGCGATACACTT 57.657 40.909 0.00 0.00 32.51 3.16
4999 5275 5.667539 ATAGCCAATCATAGCGATACACT 57.332 39.130 0.00 0.00 32.51 3.55
5000 5276 7.036220 ACTTATAGCCAATCATAGCGATACAC 58.964 38.462 0.00 0.00 32.51 2.90
5001 5277 7.122799 AGACTTATAGCCAATCATAGCGATACA 59.877 37.037 0.00 0.00 32.51 2.29
5002 5278 7.484975 AGACTTATAGCCAATCATAGCGATAC 58.515 38.462 0.00 0.00 32.51 2.24
5003 5279 7.339466 TGAGACTTATAGCCAATCATAGCGATA 59.661 37.037 0.00 0.00 32.51 2.92
5004 5280 6.153510 TGAGACTTATAGCCAATCATAGCGAT 59.846 38.462 0.00 0.00 35.12 4.58
5005 5281 5.476945 TGAGACTTATAGCCAATCATAGCGA 59.523 40.000 0.00 0.00 0.00 4.93
5006 5282 5.714047 TGAGACTTATAGCCAATCATAGCG 58.286 41.667 0.00 0.00 0.00 4.26
5007 5283 6.929625 TCTGAGACTTATAGCCAATCATAGC 58.070 40.000 0.00 0.00 0.00 2.97
5008 5284 9.941325 AATTCTGAGACTTATAGCCAATCATAG 57.059 33.333 0.00 0.00 0.00 2.23
5009 5285 9.935241 GAATTCTGAGACTTATAGCCAATCATA 57.065 33.333 0.00 0.00 0.00 2.15
5010 5286 8.435187 TGAATTCTGAGACTTATAGCCAATCAT 58.565 33.333 7.05 0.00 0.00 2.45
5011 5287 7.795047 TGAATTCTGAGACTTATAGCCAATCA 58.205 34.615 7.05 0.00 0.00 2.57
5012 5288 8.668510 TTGAATTCTGAGACTTATAGCCAATC 57.331 34.615 7.05 0.00 0.00 2.67
5013 5289 8.270744 ACTTGAATTCTGAGACTTATAGCCAAT 58.729 33.333 7.05 0.00 0.00 3.16
5014 5290 7.624549 ACTTGAATTCTGAGACTTATAGCCAA 58.375 34.615 7.05 0.00 0.00 4.52
5015 5291 7.187824 ACTTGAATTCTGAGACTTATAGCCA 57.812 36.000 7.05 0.00 0.00 4.75
5016 5292 9.036671 GTAACTTGAATTCTGAGACTTATAGCC 57.963 37.037 7.05 0.00 0.00 3.93
5017 5293 9.587772 TGTAACTTGAATTCTGAGACTTATAGC 57.412 33.333 7.05 0.00 0.00 2.97
5038 5314 6.554334 TCTTGTTTTCCAGCATAGTGTAAC 57.446 37.500 0.00 0.00 0.00 2.50
5039 5315 6.939730 TCATCTTGTTTTCCAGCATAGTGTAA 59.060 34.615 0.00 0.00 0.00 2.41
5040 5316 6.472016 TCATCTTGTTTTCCAGCATAGTGTA 58.528 36.000 0.00 0.00 0.00 2.90
5041 5317 5.316167 TCATCTTGTTTTCCAGCATAGTGT 58.684 37.500 0.00 0.00 0.00 3.55
5042 5318 5.885230 TCATCTTGTTTTCCAGCATAGTG 57.115 39.130 0.00 0.00 0.00 2.74
5043 5319 7.472334 AATTCATCTTGTTTTCCAGCATAGT 57.528 32.000 0.00 0.00 0.00 2.12
5044 5320 8.030692 TCAAATTCATCTTGTTTTCCAGCATAG 58.969 33.333 0.00 0.00 0.00 2.23
5045 5321 7.894708 TCAAATTCATCTTGTTTTCCAGCATA 58.105 30.769 0.00 0.00 0.00 3.14
5046 5322 6.761312 TCAAATTCATCTTGTTTTCCAGCAT 58.239 32.000 0.00 0.00 0.00 3.79
5047 5323 6.159299 TCAAATTCATCTTGTTTTCCAGCA 57.841 33.333 0.00 0.00 0.00 4.41
5048 5324 6.146673 CCTTCAAATTCATCTTGTTTTCCAGC 59.853 38.462 0.00 0.00 0.00 4.85
5049 5325 7.436118 TCCTTCAAATTCATCTTGTTTTCCAG 58.564 34.615 0.00 0.00 0.00 3.86
5050 5326 7.358770 TCCTTCAAATTCATCTTGTTTTCCA 57.641 32.000 0.00 0.00 0.00 3.53
5051 5327 7.928167 AGTTCCTTCAAATTCATCTTGTTTTCC 59.072 33.333 0.00 0.00 0.00 3.13
5052 5328 8.877808 AGTTCCTTCAAATTCATCTTGTTTTC 57.122 30.769 0.00 0.00 0.00 2.29
5053 5329 9.317936 GAAGTTCCTTCAAATTCATCTTGTTTT 57.682 29.630 0.00 0.00 38.67 2.43
5054 5330 8.477256 TGAAGTTCCTTCAAATTCATCTTGTTT 58.523 29.630 4.27 0.00 45.84 2.83
5055 5331 8.010733 TGAAGTTCCTTCAAATTCATCTTGTT 57.989 30.769 4.27 0.00 45.84 2.83
5056 5332 7.587037 TGAAGTTCCTTCAAATTCATCTTGT 57.413 32.000 4.27 0.00 45.84 3.16
5119 5395 7.094805 TGGTTCATTTTTATCTTTCGACTCCAG 60.095 37.037 0.00 0.00 0.00 3.86
5603 5881 4.647424 TGTTGACTTGGACCAAAATGAC 57.353 40.909 8.59 6.03 0.00 3.06
5997 6275 3.758755 TCATGTCTTAGCCATAGCCAG 57.241 47.619 0.00 0.00 41.25 4.85
6093 6371 7.224753 TCGTCACCATTTCTTTCTCTAATATGC 59.775 37.037 0.00 0.00 0.00 3.14
6310 6588 2.989571 AGGCTCCCCTTCCATAATAAGG 59.010 50.000 0.00 0.00 38.74 2.69
6354 6632 1.166129 TTCCAGGACTCGAAGACTCG 58.834 55.000 0.00 0.00 46.87 4.18
6355 6633 2.296471 TGTTTCCAGGACTCGAAGACTC 59.704 50.000 0.00 0.00 0.00 3.36
6356 6634 2.297597 CTGTTTCCAGGACTCGAAGACT 59.702 50.000 0.00 0.00 34.90 3.24
6357 6635 2.678324 CTGTTTCCAGGACTCGAAGAC 58.322 52.381 0.00 0.00 34.90 3.01
6358 6636 1.000955 GCTGTTTCCAGGACTCGAAGA 59.999 52.381 0.00 0.00 39.22 2.87
6359 6637 1.433534 GCTGTTTCCAGGACTCGAAG 58.566 55.000 0.00 0.00 39.22 3.79
6360 6638 0.034896 GGCTGTTTCCAGGACTCGAA 59.965 55.000 0.00 0.00 39.22 3.71
6361 6639 0.832135 AGGCTGTTTCCAGGACTCGA 60.832 55.000 0.00 0.00 39.22 4.04
6384 6662 2.728007 AGCCTTTCCCTACATTTCTGC 58.272 47.619 0.00 0.00 0.00 4.26
6405 6683 4.798882 ACCAGTTTGGGTCTTTTGTATGA 58.201 39.130 0.00 0.00 43.37 2.15
6550 6830 0.734309 TGCTCATAAAGGTGCATGCG 59.266 50.000 14.09 0.00 0.00 4.73
6579 6859 3.748645 TTAGGCAGGGGATAGCAAAAA 57.251 42.857 0.00 0.00 0.00 1.94
6584 6864 2.555448 GGGATTTTAGGCAGGGGATAGC 60.555 54.545 0.00 0.00 0.00 2.97
6585 6865 2.290323 CGGGATTTTAGGCAGGGGATAG 60.290 54.545 0.00 0.00 0.00 2.08
6590 6870 2.186826 CGCGGGATTTTAGGCAGGG 61.187 63.158 0.00 0.00 0.00 4.45
6597 6877 2.960384 TGAGGAGATACGCGGGATTTTA 59.040 45.455 12.47 0.00 0.00 1.52
6601 6881 1.410004 TTTGAGGAGATACGCGGGAT 58.590 50.000 12.47 2.56 0.00 3.85
6679 6959 9.574458 CTTGAGTAGAAGATTCGTAATTTCTCA 57.426 33.333 0.00 0.00 32.54 3.27
6689 6969 9.703892 ATGGAATTATCTTGAGTAGAAGATTCG 57.296 33.333 0.00 0.00 41.82 3.34
6749 7031 9.537852 TCCTACCTGTGAATTCTTAACTACTTA 57.462 33.333 7.05 0.00 0.00 2.24
6768 7050 6.240060 CCAGTTCTCTAGCTATACTCCTACCT 60.240 46.154 0.00 0.00 0.00 3.08
6770 7052 6.771573 TCCAGTTCTCTAGCTATACTCCTAC 58.228 44.000 0.00 0.00 0.00 3.18
6837 7119 9.401058 ACATTAAAGGATATGAAGAAAGAGTGG 57.599 33.333 0.00 0.00 0.00 4.00
6862 7144 8.709272 ACTATAAACTACCTATCCTCTGGAAC 57.291 38.462 0.00 0.00 34.34 3.62
6887 7169 7.012327 CCAAGTAATTGCGGAAAGATCAATCTA 59.988 37.037 0.00 0.00 35.76 1.98
6945 7229 7.649370 ACACTTTTGAGATATCGCTGATATG 57.351 36.000 13.40 4.08 35.64 1.78
6946 7230 9.764363 TTAACACTTTTGAGATATCGCTGATAT 57.236 29.630 8.00 9.76 37.87 1.63
6947 7231 9.249457 CTTAACACTTTTGAGATATCGCTGATA 57.751 33.333 8.00 1.68 0.00 2.15
7010 7294 9.872757 CTAAATTTGTTAGAAGCTCACGTTTTA 57.127 29.630 0.00 0.00 0.00 1.52
7016 7300 7.435068 TGTCCTAAATTTGTTAGAAGCTCAC 57.565 36.000 0.00 0.00 0.00 3.51
7097 7381 1.456919 ACCACTAGCTTCCCCCTTTT 58.543 50.000 0.00 0.00 0.00 2.27
7098 7382 1.456919 AACCACTAGCTTCCCCCTTT 58.543 50.000 0.00 0.00 0.00 3.11
7103 7389 4.505324 AAAGGATAACCACTAGCTTCCC 57.495 45.455 0.00 0.00 38.94 3.97
7131 7417 4.852134 TGAATGATGGTGTTGTTTGAGG 57.148 40.909 0.00 0.00 0.00 3.86
7332 7619 3.303329 CGATGAATGCAACCTTGGTATCG 60.303 47.826 0.00 5.02 0.00 2.92
7406 7693 6.971726 TTCTGTTATACTGGTACATCCGAT 57.028 37.500 0.00 0.00 38.20 4.18
7509 7796 3.151022 CCGGTGAGGGAGAGAGGC 61.151 72.222 0.00 0.00 35.97 4.70
7584 7871 0.686441 CTACCCACTCCCATCCGTCA 60.686 60.000 0.00 0.00 0.00 4.35
7590 7877 1.330655 CGTGCTCTACCCACTCCCAT 61.331 60.000 0.00 0.00 0.00 4.00
7887 8174 3.168528 AGGGTGCCGAGGTGTTGT 61.169 61.111 0.00 0.00 0.00 3.32
7953 8249 2.799562 GCGACCCCGTACCAATTACTAC 60.800 54.545 0.00 0.00 38.24 2.73
8090 8387 3.036084 CCTGCACACACGACCGTC 61.036 66.667 0.00 0.00 0.00 4.79
8435 8732 6.403878 TGTACATAGGTAGGCTCTGTTTTTC 58.596 40.000 0.00 0.00 0.00 2.29
8446 8743 9.386010 GATCATAGACTACTGTACATAGGTAGG 57.614 40.741 19.34 11.01 37.73 3.18
8458 8755 9.429359 ACAAGAAAACTTGATCATAGACTACTG 57.571 33.333 15.32 0.00 37.72 2.74
8459 8756 9.429359 CACAAGAAAACTTGATCATAGACTACT 57.571 33.333 15.32 0.00 37.72 2.57
8465 8920 7.759465 AGATGCACAAGAAAACTTGATCATAG 58.241 34.615 15.32 0.00 37.72 2.23
8467 8922 6.433404 AGAGATGCACAAGAAAACTTGATCAT 59.567 34.615 15.32 15.17 37.72 2.45
8518 8973 5.592054 TGCAAATCAACGGTTATTTTGTCA 58.408 33.333 19.93 16.69 31.56 3.58
8539 8994 2.096013 GGCAAATTAGTCTTCGTCCTGC 59.904 50.000 0.00 0.00 0.00 4.85
8547 9002 2.871096 TCGGGTGGCAAATTAGTCTT 57.129 45.000 0.00 0.00 0.00 3.01
8562 9017 5.178797 AGAATGTACTGAATCTGTTTCGGG 58.821 41.667 11.00 2.33 43.85 5.14
8649 9110 3.880490 TGCAGGTTCGTGTAAAAATGAGT 59.120 39.130 0.00 0.00 0.00 3.41
8653 9114 5.411781 TGTTTTGCAGGTTCGTGTAAAAAT 58.588 33.333 17.53 0.00 41.66 1.82
8733 9194 2.526873 AGGCACTCCGGTGAGGTT 60.527 61.111 11.17 0.00 45.61 3.50
8853 9360 3.302347 GAGCAGGCAGTAGCGGTGT 62.302 63.158 0.00 0.00 43.41 4.16
8861 9368 2.433446 CCACAAGGAGCAGGCAGT 59.567 61.111 0.00 0.00 36.89 4.40
8918 9442 1.378382 ATGGCCAACACGCTATGCA 60.378 52.632 10.96 0.00 0.00 3.96
9027 9570 1.960417 TGGTCTCGACAAATTGCACA 58.040 45.000 0.00 0.00 0.00 4.57
9028 9571 2.483877 TCATGGTCTCGACAAATTGCAC 59.516 45.455 0.00 0.00 0.00 4.57
9029 9572 2.777094 TCATGGTCTCGACAAATTGCA 58.223 42.857 0.00 0.00 0.00 4.08
9030 9573 3.829886 TTCATGGTCTCGACAAATTGC 57.170 42.857 0.00 0.00 0.00 3.56
9031 9574 8.400947 AGAATATTTCATGGTCTCGACAAATTG 58.599 33.333 0.00 0.00 0.00 2.32
9033 9576 8.511604 AAGAATATTTCATGGTCTCGACAAAT 57.488 30.769 0.00 0.04 0.00 2.32
9187 9731 0.179156 CCGTGAACAGATGCATTGCC 60.179 55.000 6.12 0.00 0.00 4.52
9241 9786 5.590818 ACCTGACTCCTTACCTTTATCAGA 58.409 41.667 0.00 0.00 35.22 3.27
9243 9788 9.496710 TTTATACCTGACTCCTTACCTTTATCA 57.503 33.333 0.00 0.00 0.00 2.15
9246 9791 9.725206 AGATTTATACCTGACTCCTTACCTTTA 57.275 33.333 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.