Multiple sequence alignment - TraesCS5A01G541300

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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 TraesCS5A01G541300 chr5A 100.000 3507 0 0 364 3870 698181244 698177738 0.000000e+00 6477.0
1 TraesCS5A01G541300 chr5A 84.042 1059 149 17 1830 2873 698163108 698162055 0.000000e+00 1002.0
2 TraesCS5A01G541300 chr5A 80.773 905 92 49 492 1344 698164402 698163528 1.960000e-177 632.0
3 TraesCS5A01G541300 chr5A 100.000 137 0 0 1 137 698181607 698181471 1.780000e-63 254.0
4 TraesCS5A01G541300 chr5A 83.588 262 22 8 458 718 698186548 698186307 3.890000e-55 226.0
5 TraesCS5A01G541300 chr4D 93.267 2109 81 18 1565 3626 509340271 509338177 0.000000e+00 3051.0
6 TraesCS5A01G541300 chr4D 90.465 1248 53 18 365 1566 509341602 509340375 0.000000e+00 1585.0
7 TraesCS5A01G541300 chr4D 85.033 1049 134 16 1830 2864 509283456 509282417 0.000000e+00 1046.0
8 TraesCS5A01G541300 chr4D 81.779 933 94 36 473 1352 509284740 509283831 0.000000e+00 712.0
9 TraesCS5A01G541300 chr4D 88.043 276 26 6 462 737 509326369 509326101 1.730000e-83 320.0
10 TraesCS5A01G541300 chr4D 88.760 258 27 2 495 752 509288224 509287969 8.070000e-82 315.0
11 TraesCS5A01G541300 chr4D 80.714 420 55 19 3208 3626 509282215 509281821 1.750000e-78 303.0
12 TraesCS5A01G541300 chr4D 89.069 247 17 4 473 718 509355855 509355618 8.130000e-77 298.0
13 TraesCS5A01G541300 chr4B 94.289 1891 78 14 1754 3626 657516552 657518430 0.000000e+00 2867.0
14 TraesCS5A01G541300 chr4B 88.749 1431 75 36 365 1745 657497767 657499161 0.000000e+00 1672.0
15 TraesCS5A01G541300 chr4B 88.641 1435 73 35 365 1745 657514952 657516350 0.000000e+00 1664.0
16 TraesCS5A01G541300 chr4B 84.667 1050 131 21 1837 2869 657527412 657528448 0.000000e+00 1020.0
17 TraesCS5A01G541300 chr4B 94.228 589 23 5 1754 2333 657499363 657499949 0.000000e+00 889.0
18 TraesCS5A01G541300 chr4B 81.881 436 58 16 3199 3626 657528644 657529066 7.960000e-92 348.0
19 TraesCS5A01G541300 chr4B 82.143 392 41 17 933 1296 657509731 657510121 3.760000e-80 309.0
20 TraesCS5A01G541300 chr4B 87.850 214 25 1 933 1145 657526418 657526631 2.310000e-62 250.0
21 TraesCS5A01G541300 chr4B 98.077 52 1 0 1713 1764 657499158 657499209 1.480000e-14 91.6
22 TraesCS5A01G541300 chr4B 98.077 52 1 0 1713 1764 657516347 657516398 1.480000e-14 91.6
23 TraesCS5A01G541300 chrUn 94.312 1301 55 9 2335 3626 343816555 343817845 0.000000e+00 1975.0
24 TraesCS5A01G541300 chrUn 82.262 389 40 17 936 1296 324637534 324637147 3.760000e-80 309.0
25 TraesCS5A01G541300 chrUn 88.152 211 24 1 936 1145 402488101 402487891 2.310000e-62 250.0
26 TraesCS5A01G541300 chr6A 97.189 249 7 0 3622 3870 76520677 76520925 4.620000e-114 422.0
27 TraesCS5A01G541300 chr7A 96.813 251 8 0 3620 3870 5906677 5906427 1.660000e-113 420.0
28 TraesCS5A01G541300 chr6D 97.189 249 5 2 3622 3870 160793770 160794016 1.660000e-113 420.0
29 TraesCS5A01G541300 chr7D 96.787 249 8 0 3622 3870 445784964 445784716 2.150000e-112 416.0
30 TraesCS5A01G541300 chr3A 96.787 249 8 0 3622 3870 161457161 161457409 2.150000e-112 416.0
31 TraesCS5A01G541300 chr2D 96.787 249 8 0 3622 3870 52060282 52060034 2.150000e-112 416.0
32 TraesCS5A01G541300 chr2D 96.414 251 9 0 3620 3870 204112681 204112931 7.740000e-112 414.0
33 TraesCS5A01G541300 chr3D 95.720 257 11 0 3614 3870 586579204 586578948 7.740000e-112 414.0
34 TraesCS5A01G541300 chr3D 95.703 256 9 2 3617 3870 101428506 101428761 1.000000e-110 411.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G541300 chr5A 698177738 698181607 3869 True 3365.500000 6477 100.000000 1 3870 2 chr5A.!!$R3 3869
1 TraesCS5A01G541300 chr5A 698162055 698164402 2347 True 817.000000 1002 82.407500 492 2873 2 chr5A.!!$R2 2381
2 TraesCS5A01G541300 chr4D 509338177 509341602 3425 True 2318.000000 3051 91.866000 365 3626 2 chr4D.!!$R4 3261
3 TraesCS5A01G541300 chr4D 509281821 509288224 6403 True 594.000000 1046 84.071500 473 3626 4 chr4D.!!$R3 3153
4 TraesCS5A01G541300 chr4B 657514952 657518430 3478 False 1540.866667 2867 93.669000 365 3626 3 chr4B.!!$F3 3261
5 TraesCS5A01G541300 chr4B 657497767 657499949 2182 False 884.200000 1672 93.684667 365 2333 3 chr4B.!!$F2 1968
6 TraesCS5A01G541300 chr4B 657526418 657529066 2648 False 539.333333 1020 84.799333 933 3626 3 chr4B.!!$F4 2693
7 TraesCS5A01G541300 chrUn 343816555 343817845 1290 False 1975.000000 1975 94.312000 2335 3626 1 chrUn.!!$F1 1291

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
934 4491 0.032615 ACATCTCTCCTCCTCGGCTT 60.033 55.0 0.0 0.0 0.0 4.35 F
1177 4760 0.392461 GCCAGCCAACTTCGACCATA 60.392 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 6284 0.613260 TGATCTGAGTCCGTTTGGGG 59.387 55.000 0.0 0.0 36.01 4.96 R
2906 7019 1.210478 ACGGGTGGATCAATCAGAAGG 59.790 52.381 0.0 0.0 0.00 3.46 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
26 27 6.759497 AGAAAGATAAACATAGCCACAACC 57.241 37.500 0.00 0.00 0.00 3.77
27 28 5.652452 AGAAAGATAAACATAGCCACAACCC 59.348 40.000 0.00 0.00 0.00 4.11
28 29 3.541632 AGATAAACATAGCCACAACCCG 58.458 45.455 0.00 0.00 0.00 5.28
29 30 1.455248 TAAACATAGCCACAACCCGC 58.545 50.000 0.00 0.00 0.00 6.13
30 31 0.538516 AAACATAGCCACAACCCGCA 60.539 50.000 0.00 0.00 0.00 5.69
31 32 0.960364 AACATAGCCACAACCCGCAG 60.960 55.000 0.00 0.00 0.00 5.18
47 48 2.949451 GCAGGACGAGAAGATCAGAA 57.051 50.000 0.00 0.00 0.00 3.02
48 49 3.451141 GCAGGACGAGAAGATCAGAAT 57.549 47.619 0.00 0.00 0.00 2.40
49 50 4.576216 GCAGGACGAGAAGATCAGAATA 57.424 45.455 0.00 0.00 0.00 1.75
50 51 5.132897 GCAGGACGAGAAGATCAGAATAT 57.867 43.478 0.00 0.00 0.00 1.28
51 52 4.922692 GCAGGACGAGAAGATCAGAATATG 59.077 45.833 0.00 0.00 0.00 1.78
52 53 4.922692 CAGGACGAGAAGATCAGAATATGC 59.077 45.833 0.00 0.00 0.00 3.14
53 54 4.021544 AGGACGAGAAGATCAGAATATGCC 60.022 45.833 0.00 0.00 0.00 4.40
54 55 4.262207 GGACGAGAAGATCAGAATATGCCA 60.262 45.833 0.00 0.00 0.00 4.92
55 56 5.282055 ACGAGAAGATCAGAATATGCCAA 57.718 39.130 0.00 0.00 0.00 4.52
56 57 5.674525 ACGAGAAGATCAGAATATGCCAAA 58.325 37.500 0.00 0.00 0.00 3.28
57 58 5.525378 ACGAGAAGATCAGAATATGCCAAAC 59.475 40.000 0.00 0.00 0.00 2.93
58 59 5.332883 CGAGAAGATCAGAATATGCCAAACG 60.333 44.000 0.00 0.00 0.00 3.60
59 60 5.674525 AGAAGATCAGAATATGCCAAACGA 58.325 37.500 0.00 0.00 0.00 3.85
60 61 6.115446 AGAAGATCAGAATATGCCAAACGAA 58.885 36.000 0.00 0.00 0.00 3.85
61 62 6.599244 AGAAGATCAGAATATGCCAAACGAAA 59.401 34.615 0.00 0.00 0.00 3.46
62 63 6.757897 AGATCAGAATATGCCAAACGAAAA 57.242 33.333 0.00 0.00 0.00 2.29
63 64 7.156876 AGATCAGAATATGCCAAACGAAAAA 57.843 32.000 0.00 0.00 0.00 1.94
119 120 3.157680 CCACCGGTGGTTTCCTCT 58.842 61.111 40.44 0.00 45.53 3.69
120 121 1.454539 CCACCGGTGGTTTCCTCTT 59.545 57.895 40.44 0.00 45.53 2.85
121 122 0.889186 CCACCGGTGGTTTCCTCTTG 60.889 60.000 40.44 15.04 45.53 3.02
122 123 1.228154 ACCGGTGGTTTCCTCTTGC 60.228 57.895 6.12 0.00 27.29 4.01
123 124 1.228124 CCGGTGGTTTCCTCTTGCA 60.228 57.895 0.00 0.00 0.00 4.08
124 125 0.821711 CCGGTGGTTTCCTCTTGCAA 60.822 55.000 0.00 0.00 0.00 4.08
125 126 0.310854 CGGTGGTTTCCTCTTGCAAC 59.689 55.000 0.00 0.00 0.00 4.17
126 127 1.398692 GGTGGTTTCCTCTTGCAACA 58.601 50.000 0.00 0.00 0.00 3.33
127 128 1.338020 GGTGGTTTCCTCTTGCAACAG 59.662 52.381 0.00 0.00 0.00 3.16
128 129 1.032014 TGGTTTCCTCTTGCAACAGC 58.968 50.000 0.00 0.00 0.00 4.40
129 130 0.040067 GGTTTCCTCTTGCAACAGCG 60.040 55.000 0.00 0.00 0.00 5.18
130 131 0.944386 GTTTCCTCTTGCAACAGCGA 59.056 50.000 0.00 0.00 0.00 4.93
131 132 1.069636 GTTTCCTCTTGCAACAGCGAG 60.070 52.381 0.00 0.13 40.48 5.03
132 133 0.603707 TTCCTCTTGCAACAGCGAGG 60.604 55.000 21.03 21.03 43.44 4.63
133 134 2.037136 CCTCTTGCAACAGCGAGGG 61.037 63.158 19.85 1.36 39.55 4.30
134 135 2.032528 TCTTGCAACAGCGAGGGG 59.967 61.111 0.00 0.00 39.73 4.79
135 136 2.281761 CTTGCAACAGCGAGGGGT 60.282 61.111 0.00 0.00 36.35 4.95
136 137 1.898574 CTTGCAACAGCGAGGGGTT 60.899 57.895 0.00 0.00 36.35 4.11
420 421 1.205893 AGTCCTCGCTGGTTCTCATTC 59.794 52.381 0.00 0.00 37.07 2.67
423 424 2.690497 TCCTCGCTGGTTCTCATTCTAG 59.310 50.000 0.00 0.00 37.07 2.43
448 449 6.194235 AGTTTAGTTTCCATGCCCATGATAA 58.806 36.000 9.73 1.69 41.20 1.75
452 453 4.768968 AGTTTCCATGCCCATGATAATAGC 59.231 41.667 9.73 0.00 41.20 2.97
534 547 3.882288 GGCATGGTTTCCATTTTGTTGTT 59.118 39.130 0.00 0.00 42.23 2.83
551 564 1.766496 TGTTTTTGTCTCCCTCGGACT 59.234 47.619 0.00 0.00 35.04 3.85
578 591 6.872920 TGTGTTAGCATCTCCTTTTTGTTTT 58.127 32.000 0.00 0.00 0.00 2.43
579 592 6.756074 TGTGTTAGCATCTCCTTTTTGTTTTG 59.244 34.615 0.00 0.00 0.00 2.44
580 593 6.978080 GTGTTAGCATCTCCTTTTTGTTTTGA 59.022 34.615 0.00 0.00 0.00 2.69
581 594 6.978080 TGTTAGCATCTCCTTTTTGTTTTGAC 59.022 34.615 0.00 0.00 0.00 3.18
583 596 3.182372 GCATCTCCTTTTTGTTTTGACGC 59.818 43.478 0.00 0.00 0.00 5.19
584 597 4.610945 CATCTCCTTTTTGTTTTGACGCT 58.389 39.130 0.00 0.00 0.00 5.07
585 598 4.027572 TCTCCTTTTTGTTTTGACGCTG 57.972 40.909 0.00 0.00 0.00 5.18
586 599 3.692101 TCTCCTTTTTGTTTTGACGCTGA 59.308 39.130 0.00 0.00 0.00 4.26
588 601 2.857748 CCTTTTTGTTTTGACGCTGACC 59.142 45.455 0.00 0.00 0.00 4.02
695 4216 2.890371 GGCTCCTCCGCGTAAGAA 59.110 61.111 4.92 0.00 43.02 2.52
696 4217 1.217244 GGCTCCTCCGCGTAAGAAA 59.783 57.895 4.92 0.00 43.02 2.52
697 4218 0.806492 GGCTCCTCCGCGTAAGAAAG 60.806 60.000 4.92 4.78 43.02 2.62
698 4219 0.172803 GCTCCTCCGCGTAAGAAAGA 59.827 55.000 4.92 0.00 43.02 2.52
754 4275 2.531771 TCCGACCCACTCATTAGTTGA 58.468 47.619 0.00 0.00 31.97 3.18
808 4352 1.881903 TTCTGGCCTGAGAGCTCACG 61.882 60.000 17.77 6.28 35.46 4.35
926 4475 2.925724 TCTTCCTCGACATCTCTCCTC 58.074 52.381 0.00 0.00 0.00 3.71
934 4491 0.032615 ACATCTCTCCTCCTCGGCTT 60.033 55.000 0.00 0.00 0.00 4.35
954 4511 2.666190 CCACGCACCAGACCACAG 60.666 66.667 0.00 0.00 0.00 3.66
1176 4759 1.675641 GCCAGCCAACTTCGACCAT 60.676 57.895 0.00 0.00 0.00 3.55
1177 4760 0.392461 GCCAGCCAACTTCGACCATA 60.392 55.000 0.00 0.00 0.00 2.74
1320 4915 4.261363 GCCCACATCGTAAGTAGTAGTACC 60.261 50.000 4.02 0.00 39.48 3.34
1357 4952 4.545706 TGCCGATGGATGCGTCCC 62.546 66.667 22.40 6.82 44.41 4.46
1358 4953 4.241555 GCCGATGGATGCGTCCCT 62.242 66.667 22.40 12.84 44.41 4.20
1389 4984 6.672218 CCTCCTTAAAAATCCCCACCTAATTT 59.328 38.462 0.00 0.00 0.00 1.82
1401 4996 6.797540 TCCCCACCTAATTTATGTCCATCTAT 59.202 38.462 0.00 0.00 0.00 1.98
1499 5226 9.784680 CTCAATTGTTCTCCTGAAAAAGATATG 57.215 33.333 5.13 0.00 33.39 1.78
1706 5542 6.423001 GTGTTCAATAACTAACCAACTCGACT 59.577 38.462 0.00 0.00 36.51 4.18
1794 5877 9.234827 TCTTTATGGGATCAAGCAATACATATG 57.765 33.333 0.00 0.00 0.00 1.78
1795 5878 5.909621 ATGGGATCAAGCAATACATATGC 57.090 39.130 1.58 0.00 44.15 3.14
1816 5899 3.303990 GCGCTCAATTCTCAACTTGTCAA 60.304 43.478 0.00 0.00 0.00 3.18
1902 5986 1.496060 TACTGGATCGATGCACCCTT 58.504 50.000 16.33 3.42 0.00 3.95
2139 6232 6.995686 TCCTTGTTTAGTTAGTTTGCATCAGA 59.004 34.615 0.00 0.00 0.00 3.27
2150 6243 6.100404 AGTTTGCATCAGAAAATTGCCTAA 57.900 33.333 0.00 0.00 35.51 2.69
2203 6298 0.476771 ATGTTCACCCCAAACGGACT 59.523 50.000 0.00 0.00 0.00 3.85
2216 6311 4.935205 CCAAACGGACTCAGATCACAATTA 59.065 41.667 0.00 0.00 0.00 1.40
2230 6325 9.642312 CAGATCACAATTATTGATGAAGTTACG 57.358 33.333 12.28 0.00 33.70 3.18
2277 6377 3.772572 ACATACATGTACAGGGCTACACA 59.227 43.478 12.79 0.00 39.68 3.72
2333 6434 3.495377 TCGTAGACCAATTGTTTTGGACG 59.505 43.478 11.16 10.21 42.06 4.79
2338 6439 1.202463 CCAATTGTTTTGGACGGTGCA 60.202 47.619 4.43 0.00 42.06 4.57
2347 6448 0.107643 TGGACGGTGCACATCTTTGA 59.892 50.000 20.43 0.00 0.00 2.69
2372 6473 5.712152 AAAAATGCCAGAGGAGTTGTTAG 57.288 39.130 0.00 0.00 0.00 2.34
2384 6485 3.067833 GAGTTGTTAGCTTCCACTGTCC 58.932 50.000 0.00 0.00 0.00 4.02
2386 6491 2.808543 GTTGTTAGCTTCCACTGTCCAG 59.191 50.000 0.00 0.00 0.00 3.86
2480 6588 9.277783 CAATTAGATACTTCATAAACAGGGGAG 57.722 37.037 0.00 0.00 0.00 4.30
2726 6839 1.401552 GGCGCTATGACAAGCAAATCA 59.598 47.619 7.64 0.00 42.91 2.57
2940 7053 0.818040 ACCCGTGAAGCAGTTGTTCC 60.818 55.000 0.00 0.00 0.00 3.62
2993 7106 3.876914 TCGATTGGAGCCATTATGTTGAC 59.123 43.478 0.00 0.00 0.00 3.18
3155 7268 2.783284 GTGACAAGTGCGATTGTTGTTG 59.217 45.455 7.67 0.00 43.32 3.33
3246 7362 9.289303 CCAACTCAAAATTAAATACGAATGAGG 57.711 33.333 0.00 0.00 37.85 3.86
3247 7364 8.798153 CAACTCAAAATTAAATACGAATGAGGC 58.202 33.333 0.00 0.00 37.85 4.70
3294 7412 3.390175 TCTTGAGGACTTCTCTAGGGG 57.610 52.381 0.00 0.00 42.80 4.79
3312 7430 2.510613 GGGTGGAAAACGGATTGAGAA 58.489 47.619 0.00 0.00 0.00 2.87
3317 7440 5.334646 GGTGGAAAACGGATTGAGAAAGTAC 60.335 44.000 0.00 0.00 0.00 2.73
3328 7451 4.801330 TGAGAAAGTACACCATCACGAT 57.199 40.909 0.00 0.00 0.00 3.73
3352 7475 4.035091 TGCCGAACATGTACAATGCTTATC 59.965 41.667 0.00 0.00 0.00 1.75
3425 7548 8.961634 TGCAACCACATGTATATTAAAAAGCTA 58.038 29.630 0.00 0.00 0.00 3.32
3449 7572 5.616270 TGTGTCAGCTAACTAATTTGTGGA 58.384 37.500 0.00 0.00 0.00 4.02
3462 7585 9.975218 AACTAATTTGTGGACTTATCATAGGTT 57.025 29.630 0.00 0.00 0.00 3.50
3539 7662 6.867816 GCATGGAAAACTGTGAACATATCAAA 59.132 34.615 0.00 0.00 40.50 2.69
3540 7663 7.546667 GCATGGAAAACTGTGAACATATCAAAT 59.453 33.333 0.00 0.00 40.50 2.32
3541 7664 9.426837 CATGGAAAACTGTGAACATATCAAATT 57.573 29.630 0.00 0.00 40.50 1.82
3565 7688 5.060662 TCAAGACATCACTACAGCTGTAC 57.939 43.478 22.67 11.01 0.00 2.90
3576 7699 2.893637 ACAGCTGTACATCATCCGAAC 58.106 47.619 20.16 0.00 0.00 3.95
3626 7749 7.921745 GTGTTCCTTATCTAGTTGGATGTACTC 59.078 40.741 0.00 0.00 0.00 2.59
3627 7750 7.069578 TGTTCCTTATCTAGTTGGATGTACTCC 59.930 40.741 0.00 0.00 45.19 3.85
3628 7751 6.075984 TCCTTATCTAGTTGGATGTACTCCC 58.924 44.000 8.36 3.66 44.23 4.30
3629 7752 6.078664 CCTTATCTAGTTGGATGTACTCCCT 58.921 44.000 8.36 3.43 44.23 4.20
3630 7753 6.209788 CCTTATCTAGTTGGATGTACTCCCTC 59.790 46.154 8.36 3.28 44.23 4.30
3631 7754 3.912248 TCTAGTTGGATGTACTCCCTCC 58.088 50.000 8.36 3.94 44.23 4.30
3632 7755 1.486211 AGTTGGATGTACTCCCTCCG 58.514 55.000 8.36 0.00 44.23 4.63
3633 7756 1.192428 GTTGGATGTACTCCCTCCGT 58.808 55.000 8.36 0.00 44.23 4.69
3634 7757 1.553704 GTTGGATGTACTCCCTCCGTT 59.446 52.381 8.36 0.00 44.23 4.44
3635 7758 1.946984 TGGATGTACTCCCTCCGTTT 58.053 50.000 8.36 0.00 44.23 3.60
3636 7759 1.829222 TGGATGTACTCCCTCCGTTTC 59.171 52.381 8.36 0.00 44.23 2.78
3637 7760 2.108970 GGATGTACTCCCTCCGTTTCT 58.891 52.381 0.00 0.00 38.19 2.52
3638 7761 2.500504 GGATGTACTCCCTCCGTTTCTT 59.499 50.000 0.00 0.00 38.19 2.52
3639 7762 3.055312 GGATGTACTCCCTCCGTTTCTTT 60.055 47.826 0.00 0.00 38.19 2.52
3640 7763 4.565028 GGATGTACTCCCTCCGTTTCTTTT 60.565 45.833 0.00 0.00 38.19 2.27
3641 7764 4.426736 TGTACTCCCTCCGTTTCTTTTT 57.573 40.909 0.00 0.00 0.00 1.94
3642 7765 5.549742 TGTACTCCCTCCGTTTCTTTTTA 57.450 39.130 0.00 0.00 0.00 1.52
3643 7766 5.299949 TGTACTCCCTCCGTTTCTTTTTAC 58.700 41.667 0.00 0.00 0.00 2.01
3644 7767 4.701651 ACTCCCTCCGTTTCTTTTTACT 57.298 40.909 0.00 0.00 0.00 2.24
3645 7768 4.639334 ACTCCCTCCGTTTCTTTTTACTC 58.361 43.478 0.00 0.00 0.00 2.59
3646 7769 4.001652 CTCCCTCCGTTTCTTTTTACTCC 58.998 47.826 0.00 0.00 0.00 3.85
3647 7770 2.740447 CCCTCCGTTTCTTTTTACTCCG 59.260 50.000 0.00 0.00 0.00 4.63
3648 7771 2.159037 CCTCCGTTTCTTTTTACTCCGC 59.841 50.000 0.00 0.00 0.00 5.54
3649 7772 2.803956 CTCCGTTTCTTTTTACTCCGCA 59.196 45.455 0.00 0.00 0.00 5.69
3650 7773 3.404899 TCCGTTTCTTTTTACTCCGCAT 58.595 40.909 0.00 0.00 0.00 4.73
3651 7774 4.567971 TCCGTTTCTTTTTACTCCGCATA 58.432 39.130 0.00 0.00 0.00 3.14
3652 7775 5.180271 TCCGTTTCTTTTTACTCCGCATAT 58.820 37.500 0.00 0.00 0.00 1.78
3653 7776 6.339730 TCCGTTTCTTTTTACTCCGCATATA 58.660 36.000 0.00 0.00 0.00 0.86
3654 7777 6.817641 TCCGTTTCTTTTTACTCCGCATATAA 59.182 34.615 0.00 0.00 0.00 0.98
3655 7778 7.010738 TCCGTTTCTTTTTACTCCGCATATAAG 59.989 37.037 0.00 0.00 0.00 1.73
3656 7779 7.010738 CCGTTTCTTTTTACTCCGCATATAAGA 59.989 37.037 0.00 0.00 0.00 2.10
3657 7780 8.548721 CGTTTCTTTTTACTCCGCATATAAGAT 58.451 33.333 0.00 0.00 0.00 2.40
3661 7784 8.836413 TCTTTTTACTCCGCATATAAGATTTGG 58.164 33.333 0.00 0.00 0.00 3.28
3662 7785 8.514330 TTTTTACTCCGCATATAAGATTTGGT 57.486 30.769 0.00 0.00 0.00 3.67
3663 7786 7.724305 TTTACTCCGCATATAAGATTTGGTC 57.276 36.000 0.00 0.00 0.00 4.02
3664 7787 5.290493 ACTCCGCATATAAGATTTGGTCA 57.710 39.130 0.00 0.00 0.00 4.02
3665 7788 5.680619 ACTCCGCATATAAGATTTGGTCAA 58.319 37.500 0.00 0.00 0.00 3.18
3666 7789 6.119536 ACTCCGCATATAAGATTTGGTCAAA 58.880 36.000 0.00 0.00 34.46 2.69
3667 7790 6.260936 ACTCCGCATATAAGATTTGGTCAAAG 59.739 38.462 2.55 0.00 33.32 2.77
3668 7791 6.119536 TCCGCATATAAGATTTGGTCAAAGT 58.880 36.000 2.55 0.00 33.32 2.66
3669 7792 6.260050 TCCGCATATAAGATTTGGTCAAAGTC 59.740 38.462 2.55 1.51 33.32 3.01
3670 7793 6.038161 CCGCATATAAGATTTGGTCAAAGTCA 59.962 38.462 2.55 0.00 33.32 3.41
3671 7794 7.415095 CCGCATATAAGATTTGGTCAAAGTCAA 60.415 37.037 2.55 0.00 33.32 3.18
3672 7795 7.967854 CGCATATAAGATTTGGTCAAAGTCAAA 59.032 33.333 2.55 0.00 37.29 2.69
3673 7796 9.076596 GCATATAAGATTTGGTCAAAGTCAAAC 57.923 33.333 2.55 0.00 35.97 2.93
3676 7799 4.936891 AGATTTGGTCAAAGTCAAACTGC 58.063 39.130 2.55 0.00 35.97 4.40
3677 7800 4.402155 AGATTTGGTCAAAGTCAAACTGCA 59.598 37.500 2.55 0.00 35.97 4.41
3678 7801 3.502191 TTGGTCAAAGTCAAACTGCAC 57.498 42.857 0.00 0.00 0.00 4.57
3679 7802 2.441410 TGGTCAAAGTCAAACTGCACA 58.559 42.857 0.00 0.00 0.00 4.57
3680 7803 2.822561 TGGTCAAAGTCAAACTGCACAA 59.177 40.909 0.00 0.00 0.00 3.33
3681 7804 3.256879 TGGTCAAAGTCAAACTGCACAAA 59.743 39.130 0.00 0.00 0.00 2.83
3682 7805 3.859386 GGTCAAAGTCAAACTGCACAAAG 59.141 43.478 0.00 0.00 0.00 2.77
3683 7806 4.485163 GTCAAAGTCAAACTGCACAAAGT 58.515 39.130 0.00 0.00 0.00 2.66
3684 7807 4.923281 GTCAAAGTCAAACTGCACAAAGTT 59.077 37.500 0.00 0.00 42.21 2.66
3690 7813 3.951775 AAACTGCACAAAGTTTGACCA 57.048 38.095 22.23 15.46 46.16 4.02
3691 7814 3.951775 AACTGCACAAAGTTTGACCAA 57.048 38.095 22.23 4.11 37.05 3.67
3692 7815 3.951775 ACTGCACAAAGTTTGACCAAA 57.048 38.095 22.23 2.48 0.00 3.28
3693 7816 4.470334 ACTGCACAAAGTTTGACCAAAT 57.530 36.364 22.23 6.71 32.36 2.32
3694 7817 4.831107 ACTGCACAAAGTTTGACCAAATT 58.169 34.783 22.23 0.00 32.36 1.82
3695 7818 5.244755 ACTGCACAAAGTTTGACCAAATTT 58.755 33.333 22.23 0.00 32.66 1.82
3696 7819 6.402222 ACTGCACAAAGTTTGACCAAATTTA 58.598 32.000 22.23 0.00 31.37 1.40
3697 7820 7.047271 ACTGCACAAAGTTTGACCAAATTTAT 58.953 30.769 22.23 0.00 31.37 1.40
3698 7821 8.200792 ACTGCACAAAGTTTGACCAAATTTATA 58.799 29.630 22.23 0.00 31.37 0.98
3699 7822 9.206870 CTGCACAAAGTTTGACCAAATTTATAT 57.793 29.630 22.23 0.00 31.37 0.86
3761 7884 8.765488 AATATGAACATACATTTCATGGTCCA 57.235 30.769 7.65 0.00 42.44 4.02
3762 7885 8.945195 ATATGAACATACATTTCATGGTCCAT 57.055 30.769 0.00 0.00 42.44 3.41
3763 7886 6.698008 TGAACATACATTTCATGGTCCATC 57.302 37.500 0.00 0.00 39.01 3.51
3764 7887 6.425735 TGAACATACATTTCATGGTCCATCT 58.574 36.000 0.00 0.00 39.01 2.90
3765 7888 6.319405 TGAACATACATTTCATGGTCCATCTG 59.681 38.462 0.00 0.37 39.01 2.90
3766 7889 6.005066 ACATACATTTCATGGTCCATCTGA 57.995 37.500 0.00 0.00 33.60 3.27
3767 7890 6.607970 ACATACATTTCATGGTCCATCTGAT 58.392 36.000 0.00 0.00 33.60 2.90
3768 7891 7.748677 ACATACATTTCATGGTCCATCTGATA 58.251 34.615 0.00 0.00 33.60 2.15
3769 7892 8.219868 ACATACATTTCATGGTCCATCTGATAA 58.780 33.333 0.00 0.00 33.60 1.75
3770 7893 9.239551 CATACATTTCATGGTCCATCTGATAAT 57.760 33.333 0.00 0.34 33.60 1.28
3773 7896 9.818270 ACATTTCATGGTCCATCTGATAATATT 57.182 29.630 0.00 0.00 33.60 1.28
3835 7958 7.484035 AGTTAGTCAAACTCTACAAAGCTTG 57.516 36.000 0.00 0.00 45.64 4.01
3836 7959 7.272978 AGTTAGTCAAACTCTACAAAGCTTGA 58.727 34.615 0.00 0.00 45.64 3.02
3837 7960 5.993106 AGTCAAACTCTACAAAGCTTGAC 57.007 39.130 0.00 10.63 0.00 3.18
3838 7961 5.675538 AGTCAAACTCTACAAAGCTTGACT 58.324 37.500 13.94 13.94 0.00 3.41
3839 7962 6.116126 AGTCAAACTCTACAAAGCTTGACTT 58.884 36.000 13.94 3.16 41.70 3.01
3850 7973 5.859205 AAAGCTTGACTTTGACCAAATCT 57.141 34.783 0.00 0.00 47.00 2.40
3851 7974 5.859205 AAGCTTGACTTTGACCAAATCTT 57.141 34.783 0.00 0.00 33.71 2.40
3852 7975 6.959639 AAGCTTGACTTTGACCAAATCTTA 57.040 33.333 0.00 0.00 33.71 2.10
3853 7976 7.530426 AAGCTTGACTTTGACCAAATCTTAT 57.470 32.000 0.00 0.00 33.71 1.73
3854 7977 8.635765 AAGCTTGACTTTGACCAAATCTTATA 57.364 30.769 0.00 0.00 33.71 0.98
3855 7978 8.814038 AGCTTGACTTTGACCAAATCTTATAT 57.186 30.769 0.00 0.00 0.00 0.86
3856 7979 8.680903 AGCTTGACTTTGACCAAATCTTATATG 58.319 33.333 0.00 0.00 0.00 1.78
3857 7980 7.433425 GCTTGACTTTGACCAAATCTTATATGC 59.567 37.037 0.00 0.00 0.00 3.14
3858 7981 7.015226 TGACTTTGACCAAATCTTATATGCG 57.985 36.000 0.00 0.00 0.00 4.73
3859 7982 6.821160 TGACTTTGACCAAATCTTATATGCGA 59.179 34.615 0.00 0.00 0.00 5.10
3860 7983 7.335673 TGACTTTGACCAAATCTTATATGCGAA 59.664 33.333 0.00 0.00 0.00 4.70
3861 7984 7.472543 ACTTTGACCAAATCTTATATGCGAAC 58.527 34.615 0.00 0.00 0.00 3.95
3862 7985 7.336931 ACTTTGACCAAATCTTATATGCGAACT 59.663 33.333 0.00 0.00 0.00 3.01
3863 7986 8.725405 TTTGACCAAATCTTATATGCGAACTA 57.275 30.769 0.00 0.00 0.00 2.24
3864 7987 8.725405 TTGACCAAATCTTATATGCGAACTAA 57.275 30.769 0.00 0.00 0.00 2.24
3865 7988 8.725405 TGACCAAATCTTATATGCGAACTAAA 57.275 30.769 0.00 0.00 0.00 1.85
3866 7989 9.168451 TGACCAAATCTTATATGCGAACTAAAA 57.832 29.630 0.00 0.00 0.00 1.52
3867 7990 9.997482 GACCAAATCTTATATGCGAACTAAAAA 57.003 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.152831 GGGTTGTGGCTATGTTTATCTTTCTT 59.847 38.462 0.00 0.00 0.00 2.52
3 4 5.652452 GGGTTGTGGCTATGTTTATCTTTCT 59.348 40.000 0.00 0.00 0.00 2.52
4 5 5.448632 CGGGTTGTGGCTATGTTTATCTTTC 60.449 44.000 0.00 0.00 0.00 2.62
5 6 4.398044 CGGGTTGTGGCTATGTTTATCTTT 59.602 41.667 0.00 0.00 0.00 2.52
6 7 3.945285 CGGGTTGTGGCTATGTTTATCTT 59.055 43.478 0.00 0.00 0.00 2.40
7 8 3.541632 CGGGTTGTGGCTATGTTTATCT 58.458 45.455 0.00 0.00 0.00 1.98
8 9 2.032924 GCGGGTTGTGGCTATGTTTATC 59.967 50.000 0.00 0.00 0.00 1.75
9 10 2.021457 GCGGGTTGTGGCTATGTTTAT 58.979 47.619 0.00 0.00 0.00 1.40
10 11 1.271434 TGCGGGTTGTGGCTATGTTTA 60.271 47.619 0.00 0.00 0.00 2.01
11 12 0.538516 TGCGGGTTGTGGCTATGTTT 60.539 50.000 0.00 0.00 0.00 2.83
12 13 0.960364 CTGCGGGTTGTGGCTATGTT 60.960 55.000 0.00 0.00 0.00 2.71
13 14 1.377202 CTGCGGGTTGTGGCTATGT 60.377 57.895 0.00 0.00 0.00 2.29
14 15 2.114670 CCTGCGGGTTGTGGCTATG 61.115 63.158 2.29 0.00 0.00 2.23
15 16 2.272146 CCTGCGGGTTGTGGCTAT 59.728 61.111 2.29 0.00 0.00 2.97
16 17 2.925706 TCCTGCGGGTTGTGGCTA 60.926 61.111 12.43 0.00 0.00 3.93
17 18 4.643387 GTCCTGCGGGTTGTGGCT 62.643 66.667 12.43 0.00 0.00 4.75
19 20 4.308458 TCGTCCTGCGGGTTGTGG 62.308 66.667 12.43 0.00 41.72 4.17
20 21 2.709125 TTCTCGTCCTGCGGGTTGTG 62.709 60.000 12.43 6.51 42.76 3.33
21 22 2.436087 CTTCTCGTCCTGCGGGTTGT 62.436 60.000 12.43 0.00 42.76 3.32
22 23 1.738099 CTTCTCGTCCTGCGGGTTG 60.738 63.158 12.43 5.42 42.76 3.77
23 24 1.258445 ATCTTCTCGTCCTGCGGGTT 61.258 55.000 12.43 0.00 42.76 4.11
24 25 1.668101 GATCTTCTCGTCCTGCGGGT 61.668 60.000 12.43 0.00 42.76 5.28
25 26 1.066587 GATCTTCTCGTCCTGCGGG 59.933 63.158 4.71 4.71 43.78 6.13
26 27 0.248825 CTGATCTTCTCGTCCTGCGG 60.249 60.000 0.00 0.00 41.72 5.69
27 28 0.735471 TCTGATCTTCTCGTCCTGCG 59.265 55.000 0.00 0.00 43.01 5.18
28 29 2.949451 TTCTGATCTTCTCGTCCTGC 57.051 50.000 0.00 0.00 0.00 4.85
29 30 4.922692 GCATATTCTGATCTTCTCGTCCTG 59.077 45.833 0.00 0.00 0.00 3.86
30 31 4.021544 GGCATATTCTGATCTTCTCGTCCT 60.022 45.833 0.00 0.00 0.00 3.85
31 32 4.241681 GGCATATTCTGATCTTCTCGTCC 58.758 47.826 0.00 0.00 0.00 4.79
32 33 4.876125 TGGCATATTCTGATCTTCTCGTC 58.124 43.478 0.00 0.00 0.00 4.20
33 34 4.944619 TGGCATATTCTGATCTTCTCGT 57.055 40.909 0.00 0.00 0.00 4.18
34 35 5.332883 CGTTTGGCATATTCTGATCTTCTCG 60.333 44.000 0.00 0.00 0.00 4.04
35 36 5.755375 TCGTTTGGCATATTCTGATCTTCTC 59.245 40.000 0.00 0.00 0.00 2.87
36 37 5.674525 TCGTTTGGCATATTCTGATCTTCT 58.325 37.500 0.00 0.00 0.00 2.85
37 38 5.991328 TCGTTTGGCATATTCTGATCTTC 57.009 39.130 0.00 0.00 0.00 2.87
38 39 6.757897 TTTCGTTTGGCATATTCTGATCTT 57.242 33.333 0.00 0.00 0.00 2.40
39 40 6.757897 TTTTCGTTTGGCATATTCTGATCT 57.242 33.333 0.00 0.00 0.00 2.75
61 62 1.478105 GCTTCCGCATCCCATCTTTTT 59.522 47.619 0.00 0.00 35.78 1.94
62 63 1.106285 GCTTCCGCATCCCATCTTTT 58.894 50.000 0.00 0.00 35.78 2.27
63 64 0.034186 TGCTTCCGCATCCCATCTTT 60.034 50.000 0.00 0.00 42.25 2.52
64 65 1.609239 TGCTTCCGCATCCCATCTT 59.391 52.632 0.00 0.00 42.25 2.40
65 66 3.323622 TGCTTCCGCATCCCATCT 58.676 55.556 0.00 0.00 42.25 2.90
103 104 1.515521 GCAAGAGGAAACCACCGGTG 61.516 60.000 28.26 28.26 35.34 4.94
104 105 1.228154 GCAAGAGGAAACCACCGGT 60.228 57.895 0.00 0.00 37.65 5.28
105 106 0.821711 TTGCAAGAGGAAACCACCGG 60.822 55.000 0.00 0.00 34.73 5.28
106 107 0.310854 GTTGCAAGAGGAAACCACCG 59.689 55.000 0.00 0.00 34.73 4.94
107 108 1.338020 CTGTTGCAAGAGGAAACCACC 59.662 52.381 15.62 0.00 0.00 4.61
108 109 1.269257 GCTGTTGCAAGAGGAAACCAC 60.269 52.381 23.56 2.83 39.41 4.16
109 110 1.032014 GCTGTTGCAAGAGGAAACCA 58.968 50.000 23.56 3.98 39.41 3.67
110 111 0.040067 CGCTGTTGCAAGAGGAAACC 60.040 55.000 23.56 6.88 39.64 3.27
111 112 0.944386 TCGCTGTTGCAAGAGGAAAC 59.056 50.000 23.56 7.23 39.64 2.78
112 113 1.229428 CTCGCTGTTGCAAGAGGAAA 58.771 50.000 23.56 0.71 39.64 3.13
113 114 0.603707 CCTCGCTGTTGCAAGAGGAA 60.604 55.000 23.56 5.33 44.41 3.36
114 115 1.004560 CCTCGCTGTTGCAAGAGGA 60.005 57.895 23.56 17.15 44.41 3.71
115 116 2.037136 CCCTCGCTGTTGCAAGAGG 61.037 63.158 23.56 21.83 42.62 3.69
116 117 2.037136 CCCCTCGCTGTTGCAAGAG 61.037 63.158 18.83 18.83 39.64 2.85
117 118 2.032528 CCCCTCGCTGTTGCAAGA 59.967 61.111 0.00 0.00 39.64 3.02
118 119 1.898574 AACCCCTCGCTGTTGCAAG 60.899 57.895 0.00 0.00 39.64 4.01
119 120 2.194597 AACCCCTCGCTGTTGCAA 59.805 55.556 0.00 0.00 39.64 4.08
369 370 2.666098 GCTTAACCGGCCTCCTGGA 61.666 63.158 0.00 0.00 34.57 3.86
420 421 4.843728 TGGGCATGGAAACTAAACTCTAG 58.156 43.478 0.00 0.00 0.00 2.43
423 424 4.016444 TCATGGGCATGGAAACTAAACTC 58.984 43.478 0.00 0.00 39.24 3.01
534 547 3.211045 CAAAAGTCCGAGGGAGACAAAA 58.789 45.455 0.00 0.00 36.68 2.44
551 564 6.872920 ACAAAAAGGAGATGCTAACACAAAA 58.127 32.000 0.00 0.00 0.00 2.44
695 4216 6.111768 CGATCCATCGTTGATTTCTTTCTT 57.888 37.500 0.55 0.00 44.74 2.52
696 4217 5.725110 CGATCCATCGTTGATTTCTTTCT 57.275 39.130 0.55 0.00 44.74 2.52
754 4275 8.239314 CGATATGGCAACTATCAAAATATTGCT 58.761 33.333 8.41 0.00 44.03 3.91
847 4396 3.564264 ACTTGTAGTAGTAGCTAGGGCC 58.436 50.000 0.00 0.00 39.73 5.80
926 4475 4.069232 TGCGTGGAGAAGCCGAGG 62.069 66.667 0.00 0.00 40.66 4.63
934 4491 2.523168 TGGTCTGGTGCGTGGAGA 60.523 61.111 0.00 0.00 0.00 3.71
968 4527 1.202568 GCTCCAAGGTTTGCTTGCTTT 60.203 47.619 0.00 0.00 0.00 3.51
1102 4661 2.328099 GGGCGAAGAACTGGTGCTG 61.328 63.158 0.00 0.00 0.00 4.41
1176 4759 1.003118 GGTGTGGTCCATGTTCTGCTA 59.997 52.381 0.00 0.00 0.00 3.49
1177 4760 0.250901 GGTGTGGTCCATGTTCTGCT 60.251 55.000 0.00 0.00 0.00 4.24
1265 4851 0.463295 CTGCACTAGGTGAGCCATGG 60.463 60.000 7.63 7.63 35.23 3.66
1320 4915 4.795278 GGCAAGAGATGAAACAATTAAGCG 59.205 41.667 0.00 0.00 0.00 4.68
1357 4952 3.701542 GGGATTTTTAAGGAGGAAGCCAG 59.298 47.826 0.00 0.00 29.45 4.85
1358 4953 3.565670 GGGGATTTTTAAGGAGGAAGCCA 60.566 47.826 0.00 0.00 29.45 4.75
1389 4984 8.555896 TTTTGTAGTGGGTATAGATGGACATA 57.444 34.615 0.00 0.00 0.00 2.29
1465 5192 2.094417 GGAGAACAATTGAGCAGCGTAC 59.906 50.000 13.59 0.00 0.00 3.67
1499 5226 4.583871 AGAATATCAAGATCCATTCCCGC 58.416 43.478 0.00 0.00 0.00 6.13
1528 5255 9.326489 ACAAACTCTATATATGCCTCCATAGAA 57.674 33.333 0.00 0.00 37.36 2.10
1706 5542 3.970410 CTTCCCCCAGCTGTGCCA 61.970 66.667 13.81 0.00 0.00 4.92
1794 5877 2.224079 TGACAAGTTGAGAATTGAGCGC 59.776 45.455 10.54 0.00 0.00 5.92
1795 5878 4.472691 TTGACAAGTTGAGAATTGAGCG 57.527 40.909 10.54 0.00 0.00 5.03
1816 5899 8.811017 CATAAAGTGTGGACTCCAGATAGATAT 58.189 37.037 0.00 0.00 32.34 1.63
1951 6037 8.746922 TGCAAAACTAGCTCAAGATAAAATTG 57.253 30.769 0.00 0.00 0.00 2.32
2092 6180 6.608808 AGGATCTTCTTTCCATTTTGTATGGG 59.391 38.462 4.10 0.00 39.60 4.00
2191 6284 0.613260 TGATCTGAGTCCGTTTGGGG 59.387 55.000 0.00 0.00 36.01 4.96
2216 6311 8.974408 GTTTTTAAAAGGCGTAACTTCATCAAT 58.026 29.630 0.14 0.00 0.00 2.57
2372 6473 4.207891 TCTATTTCTGGACAGTGGAAGC 57.792 45.455 0.00 0.00 0.00 3.86
2480 6588 5.472820 AGGGTAGCAGATACGTACTTGATAC 59.527 44.000 20.05 20.05 34.99 2.24
2726 6839 4.810191 AAGCTTTTCTGGACTCGTATCT 57.190 40.909 0.00 0.00 0.00 1.98
2906 7019 1.210478 ACGGGTGGATCAATCAGAAGG 59.790 52.381 0.00 0.00 0.00 3.46
2940 7053 9.199982 TCACTAACCGACTTATTTTACTTTGAG 57.800 33.333 0.00 0.00 0.00 3.02
2993 7106 8.044060 TCTGCTGACCATTTTAAATAGTCAAG 57.956 34.615 16.83 13.13 37.04 3.02
3195 7309 7.415206 GGCGATGACTTAATTCAACTGGTTAAT 60.415 37.037 0.00 0.00 0.00 1.40
3196 7310 6.128117 GGCGATGACTTAATTCAACTGGTTAA 60.128 38.462 0.00 0.00 0.00 2.01
3294 7412 4.830826 ACTTTCTCAATCCGTTTTCCAC 57.169 40.909 0.00 0.00 0.00 4.02
3312 7430 2.356135 GGCAATCGTGATGGTGTACTT 58.644 47.619 0.00 0.00 0.00 2.24
3317 7440 0.096976 GTTCGGCAATCGTGATGGTG 59.903 55.000 0.00 0.00 40.32 4.17
3328 7451 2.158559 AGCATTGTACATGTTCGGCAA 58.841 42.857 2.30 5.53 0.00 4.52
3425 7548 6.149474 GTCCACAAATTAGTTAGCTGACACAT 59.851 38.462 11.65 0.00 0.00 3.21
3462 7585 7.557724 TCATTCGTACACATTGGAGGTATTTA 58.442 34.615 0.00 0.00 0.00 1.40
3539 7662 6.882656 ACAGCTGTAGTGATGTCTTGATAAT 58.117 36.000 20.16 0.00 0.00 1.28
3540 7663 6.286240 ACAGCTGTAGTGATGTCTTGATAA 57.714 37.500 20.16 0.00 0.00 1.75
3541 7664 5.921962 ACAGCTGTAGTGATGTCTTGATA 57.078 39.130 20.16 0.00 0.00 2.15
3542 7665 4.815533 ACAGCTGTAGTGATGTCTTGAT 57.184 40.909 20.16 0.00 0.00 2.57
3543 7666 4.522789 TGTACAGCTGTAGTGATGTCTTGA 59.477 41.667 26.70 0.00 0.00 3.02
3544 7667 4.809673 TGTACAGCTGTAGTGATGTCTTG 58.190 43.478 26.70 0.00 0.00 3.02
3545 7668 5.185828 TGATGTACAGCTGTAGTGATGTCTT 59.814 40.000 26.70 11.02 0.00 3.01
3546 7669 4.706962 TGATGTACAGCTGTAGTGATGTCT 59.293 41.667 26.70 5.61 0.00 3.41
3554 7677 3.990318 TCGGATGATGTACAGCTGTAG 57.010 47.619 26.70 12.41 41.44 2.74
3593 7716 7.942341 TCCAACTAGATAAGGAACACACAATTT 59.058 33.333 0.00 0.00 0.00 1.82
3626 7749 2.740447 CGGAGTAAAAAGAAACGGAGGG 59.260 50.000 0.00 0.00 0.00 4.30
3627 7750 2.159037 GCGGAGTAAAAAGAAACGGAGG 59.841 50.000 0.00 0.00 0.00 4.30
3628 7751 2.803956 TGCGGAGTAAAAAGAAACGGAG 59.196 45.455 0.00 0.00 0.00 4.63
3629 7752 2.836262 TGCGGAGTAAAAAGAAACGGA 58.164 42.857 0.00 0.00 0.00 4.69
3630 7753 3.824414 ATGCGGAGTAAAAAGAAACGG 57.176 42.857 0.00 0.00 0.00 4.44
3631 7754 7.902032 TCTTATATGCGGAGTAAAAAGAAACG 58.098 34.615 0.00 0.00 0.00 3.60
3635 7758 8.836413 CCAAATCTTATATGCGGAGTAAAAAGA 58.164 33.333 0.00 0.00 0.00 2.52
3636 7759 8.621286 ACCAAATCTTATATGCGGAGTAAAAAG 58.379 33.333 0.00 0.00 0.00 2.27
3637 7760 8.514330 ACCAAATCTTATATGCGGAGTAAAAA 57.486 30.769 0.00 0.00 0.00 1.94
3638 7761 7.771361 TGACCAAATCTTATATGCGGAGTAAAA 59.229 33.333 0.00 0.00 0.00 1.52
3639 7762 7.276658 TGACCAAATCTTATATGCGGAGTAAA 58.723 34.615 0.00 0.00 0.00 2.01
3640 7763 6.822442 TGACCAAATCTTATATGCGGAGTAA 58.178 36.000 0.00 0.00 0.00 2.24
3641 7764 6.413783 TGACCAAATCTTATATGCGGAGTA 57.586 37.500 0.00 0.00 0.00 2.59
3642 7765 5.290493 TGACCAAATCTTATATGCGGAGT 57.710 39.130 0.00 0.00 0.00 3.85
3643 7766 6.260936 ACTTTGACCAAATCTTATATGCGGAG 59.739 38.462 0.00 0.00 0.00 4.63
3644 7767 6.119536 ACTTTGACCAAATCTTATATGCGGA 58.880 36.000 0.00 0.00 0.00 5.54
3645 7768 6.038161 TGACTTTGACCAAATCTTATATGCGG 59.962 38.462 0.00 0.00 0.00 5.69
3646 7769 7.015226 TGACTTTGACCAAATCTTATATGCG 57.985 36.000 0.00 0.00 0.00 4.73
3647 7770 9.076596 GTTTGACTTTGACCAAATCTTATATGC 57.923 33.333 0.00 0.00 35.14 3.14
3650 7773 8.296713 GCAGTTTGACTTTGACCAAATCTTATA 58.703 33.333 0.00 0.00 35.14 0.98
3651 7774 7.147976 GCAGTTTGACTTTGACCAAATCTTAT 58.852 34.615 0.00 0.00 35.14 1.73
3652 7775 6.096141 TGCAGTTTGACTTTGACCAAATCTTA 59.904 34.615 0.00 0.00 35.14 2.10
3653 7776 5.105392 TGCAGTTTGACTTTGACCAAATCTT 60.105 36.000 0.00 0.00 35.14 2.40
3654 7777 4.402155 TGCAGTTTGACTTTGACCAAATCT 59.598 37.500 0.00 0.00 35.14 2.40
3655 7778 4.504097 GTGCAGTTTGACTTTGACCAAATC 59.496 41.667 0.00 0.00 35.14 2.17
3656 7779 4.081752 TGTGCAGTTTGACTTTGACCAAAT 60.082 37.500 0.00 0.00 35.14 2.32
3657 7780 3.256879 TGTGCAGTTTGACTTTGACCAAA 59.743 39.130 0.00 0.00 0.00 3.28
3658 7781 2.822561 TGTGCAGTTTGACTTTGACCAA 59.177 40.909 0.00 0.00 0.00 3.67
3659 7782 2.441410 TGTGCAGTTTGACTTTGACCA 58.559 42.857 0.00 0.00 0.00 4.02
3660 7783 3.502191 TTGTGCAGTTTGACTTTGACC 57.498 42.857 0.00 0.00 0.00 4.02
3661 7784 4.485163 ACTTTGTGCAGTTTGACTTTGAC 58.515 39.130 0.00 0.00 0.00 3.18
3662 7785 4.782019 ACTTTGTGCAGTTTGACTTTGA 57.218 36.364 0.00 0.00 0.00 2.69
3663 7786 5.844301 AAACTTTGTGCAGTTTGACTTTG 57.156 34.783 1.37 0.00 43.88 2.77
3670 7793 3.951775 TGGTCAAACTTTGTGCAGTTT 57.048 38.095 1.44 0.00 46.00 2.66
3671 7794 3.951775 TTGGTCAAACTTTGTGCAGTT 57.048 38.095 1.44 0.00 38.74 3.16
3672 7795 3.951775 TTTGGTCAAACTTTGTGCAGT 57.048 38.095 1.44 0.00 0.00 4.40
3673 7796 5.799681 AAATTTGGTCAAACTTTGTGCAG 57.200 34.783 1.44 0.00 32.51 4.41
3735 7858 9.859152 TGGACCATGAAATGTATGTTCATATTA 57.141 29.630 0.00 0.00 44.81 0.98
3736 7859 8.765488 TGGACCATGAAATGTATGTTCATATT 57.235 30.769 0.00 0.00 44.81 1.28
3737 7860 8.945195 ATGGACCATGAAATGTATGTTCATAT 57.055 30.769 6.06 0.00 44.81 1.78
3738 7861 8.219868 AGATGGACCATGAAATGTATGTTCATA 58.780 33.333 12.99 0.00 44.81 2.15
3739 7862 7.013942 CAGATGGACCATGAAATGTATGTTCAT 59.986 37.037 12.99 0.00 44.81 2.57
3740 7863 6.319405 CAGATGGACCATGAAATGTATGTTCA 59.681 38.462 12.99 0.00 44.81 3.18
3741 7864 6.543465 TCAGATGGACCATGAAATGTATGTTC 59.457 38.462 12.99 0.00 44.81 3.18
3742 7865 6.425735 TCAGATGGACCATGAAATGTATGTT 58.574 36.000 12.99 0.00 44.81 2.71
3743 7866 6.005066 TCAGATGGACCATGAAATGTATGT 57.995 37.500 12.99 0.00 44.81 2.29
3744 7867 8.625786 TTATCAGATGGACCATGAAATGTATG 57.374 34.615 12.99 0.00 44.81 2.39
3747 7870 9.818270 AATATTATCAGATGGACCATGAAATGT 57.182 29.630 12.99 4.58 44.81 2.71
3807 7930 9.780186 AGCTTTGTAGAGTTTGACTAACTTTAT 57.220 29.630 3.78 0.00 47.00 1.40
3808 7931 9.609346 AAGCTTTGTAGAGTTTGACTAACTTTA 57.391 29.630 3.78 0.37 47.00 1.85
3809 7932 8.398665 CAAGCTTTGTAGAGTTTGACTAACTTT 58.601 33.333 0.00 1.31 47.00 2.66
3810 7933 7.769044 TCAAGCTTTGTAGAGTTTGACTAACTT 59.231 33.333 0.00 0.00 47.00 2.66
3812 7935 7.478520 TCAAGCTTTGTAGAGTTTGACTAAC 57.521 36.000 0.00 0.00 40.46 2.34
3829 7952 5.859205 AAGATTTGGTCAAAGTCAAGCTT 57.141 34.783 0.00 0.00 39.52 3.74
3830 7953 8.680903 CATATAAGATTTGGTCAAAGTCAAGCT 58.319 33.333 2.55 0.00 33.32 3.74
3831 7954 7.433425 GCATATAAGATTTGGTCAAAGTCAAGC 59.567 37.037 2.55 0.00 33.32 4.01
3832 7955 7.641411 CGCATATAAGATTTGGTCAAAGTCAAG 59.359 37.037 2.55 0.00 33.32 3.02
3833 7956 7.335673 TCGCATATAAGATTTGGTCAAAGTCAA 59.664 33.333 2.55 0.00 33.32 3.18
3834 7957 6.821160 TCGCATATAAGATTTGGTCAAAGTCA 59.179 34.615 2.55 0.00 33.32 3.41
3835 7958 7.246674 TCGCATATAAGATTTGGTCAAAGTC 57.753 36.000 2.55 1.51 33.32 3.01
3836 7959 7.336931 AGTTCGCATATAAGATTTGGTCAAAGT 59.663 33.333 2.55 0.00 33.32 2.66
3837 7960 7.697691 AGTTCGCATATAAGATTTGGTCAAAG 58.302 34.615 2.55 0.00 33.32 2.77
3838 7961 7.624360 AGTTCGCATATAAGATTTGGTCAAA 57.376 32.000 0.00 0.00 34.46 2.69
3839 7962 8.725405 TTAGTTCGCATATAAGATTTGGTCAA 57.275 30.769 0.00 0.00 0.00 3.18
3840 7963 8.725405 TTTAGTTCGCATATAAGATTTGGTCA 57.275 30.769 0.00 0.00 0.00 4.02
3841 7964 9.997482 TTTTTAGTTCGCATATAAGATTTGGTC 57.003 29.630 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.