Multiple sequence alignment - TraesCS5A01G198400

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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 TraesCS5A01G198400 chr5A 100.000 4566 0 0 1 4566 402904342 402908907 0.000000e+00 8432.0
1 TraesCS5A01G198400 chr5A 80.576 278 50 4 4270 4544 679743558 679743282 1.290000e-50 211.0
2 TraesCS5A01G198400 chr5B 94.343 2298 90 15 317 2594 354782290 354784567 0.000000e+00 3487.0
3 TraesCS5A01G198400 chr5B 93.766 1171 48 10 2737 3895 354784586 354785743 0.000000e+00 1735.0
4 TraesCS5A01G198400 chr5B 88.218 331 31 7 1 329 354781516 354781840 5.540000e-104 388.0
5 TraesCS5A01G198400 chr5B 82.692 312 40 7 4267 4565 447559956 447560266 9.740000e-67 265.0
6 TraesCS5A01G198400 chr5B 81.737 334 45 8 4247 4565 696434436 696434768 9.740000e-67 265.0
7 TraesCS5A01G198400 chr5D 93.248 2355 90 20 311 2616 309675059 309677393 0.000000e+00 3404.0
8 TraesCS5A01G198400 chr5D 93.610 1252 39 14 2722 3966 309677454 309678671 0.000000e+00 1831.0
9 TraesCS5A01G198400 chr5D 96.009 426 17 0 4141 4566 309678674 309679099 0.000000e+00 693.0
10 TraesCS5A01G198400 chr5D 92.121 165 13 0 3969 4133 151671712 151671548 2.750000e-57 233.0
11 TraesCS5A01G198400 chrUn 85.285 1230 131 28 605 1787 31777638 31778864 0.000000e+00 1223.0
12 TraesCS5A01G198400 chrUn 90.460 587 54 1 1203 1787 31805400 31805986 0.000000e+00 773.0
13 TraesCS5A01G198400 chrUn 91.909 309 23 1 1203 1509 276916181 276916489 9.070000e-117 431.0
14 TraesCS5A01G198400 chrUn 91.909 309 23 1 1203 1509 276923611 276923919 9.070000e-117 431.0
15 TraesCS5A01G198400 chrUn 93.293 164 11 0 3977 4140 42175681 42175518 4.560000e-60 243.0
16 TraesCS5A01G198400 chrUn 84.483 232 23 5 765 983 31805105 31805336 2.770000e-52 217.0
17 TraesCS5A01G198400 chrUn 84.483 232 23 5 765 983 276915886 276916117 2.770000e-52 217.0
18 TraesCS5A01G198400 chrUn 84.483 232 23 5 765 983 276923316 276923547 2.770000e-52 217.0
19 TraesCS5A01G198400 chr2B 88.672 1024 84 19 779 1787 775126571 775127577 0.000000e+00 1219.0
20 TraesCS5A01G198400 chr2B 81.737 334 45 8 4247 4565 209817998 209818330 9.740000e-67 265.0
21 TraesCS5A01G198400 chr2B 76.113 247 38 9 4271 4497 52687787 52687542 4.830000e-20 110.0
22 TraesCS5A01G198400 chr2A 85.838 579 50 16 765 1334 759853885 759853330 1.830000e-163 586.0
23 TraesCS5A01G198400 chr2A 87.607 234 29 0 1561 1794 759853150 759852917 5.820000e-69 272.0
24 TraesCS5A01G198400 chr2A 92.169 166 13 0 3969 4134 189020834 189020999 7.640000e-58 235.0
25 TraesCS5A01G198400 chr2D 86.910 466 39 7 1349 1794 631896245 631896708 1.900000e-138 503.0
26 TraesCS5A01G198400 chr2D 93.373 166 11 0 3968 4133 314044087 314043922 3.530000e-61 246.0
27 TraesCS5A01G198400 chr2D 88.235 68 8 0 4267 4334 4277349 4277416 1.050000e-11 82.4
28 TraesCS5A01G198400 chr6B 82.036 334 44 9 4247 4565 339351230 339351562 2.090000e-68 270.0
29 TraesCS5A01G198400 chr1B 83.013 312 40 5 4267 4565 671525896 671526207 2.090000e-68 270.0
30 TraesCS5A01G198400 chr3B 82.445 319 40 8 4247 4550 642888375 642888692 9.740000e-67 265.0
31 TraesCS5A01G198400 chr3A 93.252 163 11 0 3971 4133 744958437 744958275 1.640000e-59 241.0
32 TraesCS5A01G198400 chr3A 93.252 163 11 0 3971 4133 745031363 745031201 1.640000e-59 241.0
33 TraesCS5A01G198400 chr3A 93.252 163 11 0 3971 4133 745098274 745098112 1.640000e-59 241.0
34 TraesCS5A01G198400 chr7B 81.311 305 46 9 4249 4545 658025969 658026270 2.120000e-58 237.0
35 TraesCS5A01G198400 chr4B 90.698 172 16 0 3965 4136 596398136 596398307 3.550000e-56 230.0
36 TraesCS5A01G198400 chr4B 96.970 33 1 0 3358 3390 500253402 500253370 6.380000e-04 56.5
37 TraesCS5A01G198400 chr4A 88.649 185 20 1 3950 4133 729702054 729701870 1.650000e-54 224.0
38 TraesCS5A01G198400 chr4A 79.851 134 18 7 3266 3390 60926364 60926231 6.290000e-14 89.8
39 TraesCS5A01G198400 chr4A 87.500 48 6 0 3342 3389 180397967 180398014 6.380000e-04 56.5
40 TraesCS5A01G198400 chr7A 75.191 262 45 6 4256 4497 689538617 689538356 6.250000e-19 106.0
41 TraesCS5A01G198400 chr7A 76.224 143 28 4 4383 4520 617576459 617576318 2.280000e-08 71.3
42 TraesCS5A01G198400 chr4D 78.358 134 20 6 3266 3390 403396604 403396471 1.360000e-10 78.7
43 TraesCS5A01G198400 chr4D 91.111 45 4 0 3354 3398 301299465 301299421 1.370000e-05 62.1
44 TraesCS5A01G198400 chr3D 82.418 91 15 1 4252 4342 415176795 415176706 1.360000e-10 78.7
45 TraesCS5A01G198400 chr6D 91.111 45 3 1 1513 1557 14076816 14076859 4.930000e-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 TraesCS5A01G198400 chr5A 402904342 402908907 4565 False 8432 8432 100.0000 1 4566 1 chr5A.!!$F1 4565
1 TraesCS5A01G198400 chr5B 354781516 354785743 4227 False 1870 3487 92.1090 1 3895 3 chr5B.!!$F3 3894
2 TraesCS5A01G198400 chr5D 309675059 309679099 4040 False 1976 3404 94.2890 311 4566 3 chr5D.!!$F1 4255
3 TraesCS5A01G198400 chrUn 31777638 31778864 1226 False 1223 1223 85.2850 605 1787 1 chrUn.!!$F1 1182
4 TraesCS5A01G198400 chrUn 31805105 31805986 881 False 495 773 87.4715 765 1787 2 chrUn.!!$F2 1022
5 TraesCS5A01G198400 chrUn 276915886 276916489 603 False 324 431 88.1960 765 1509 2 chrUn.!!$F3 744
6 TraesCS5A01G198400 chrUn 276923316 276923919 603 False 324 431 88.1960 765 1509 2 chrUn.!!$F4 744
7 TraesCS5A01G198400 chr2B 775126571 775127577 1006 False 1219 1219 88.6720 779 1787 1 chr2B.!!$F2 1008
8 TraesCS5A01G198400 chr2A 759852917 759853885 968 True 429 586 86.7225 765 1794 2 chr2A.!!$R1 1029

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
553 1022 0.165944 GGTCATTTTCCACGACGCAG 59.834 55.0 0.00 0.0 0.00 5.18 F
838 1352 0.597377 GCACACCGGCCTTTGAAAAG 60.597 55.0 0.00 0.0 35.79 2.27 F
1902 2523 0.486879 TGGGAAAGAAGGCCATGGTT 59.513 50.0 14.67 0.0 0.00 3.67 F
2678 3312 0.033601 TTTTGCGGGGGCAGACATAT 60.034 50.0 0.00 0.0 0.00 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2523 0.107643 TGTCGAACATGTCCTTGCCA 59.892 50.0 0.0 0.0 0.00 4.92 R
2659 3293 0.033601 ATATGTCTGCCCCCGCAAAA 60.034 50.0 0.0 0.0 46.66 2.44 R
2717 3351 0.698238 ACTAGCCACAAGATTGCCCA 59.302 50.0 0.0 0.0 0.00 5.36 R
4220 4873 0.319900 CAGGTGACAGACGTTGGAGG 60.320 60.0 0.0 0.0 0.00 4.30 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
29 30 1.004918 CTGGGACGTCACAACCCTC 60.005 63.158 22.91 0.00 43.59 4.30
34 35 2.738521 CGTCACAACCCTCTGCCG 60.739 66.667 0.00 0.00 0.00 5.69
56 58 1.294780 CTAGCGCATCCCCATCTCC 59.705 63.158 11.47 0.00 0.00 3.71
85 87 1.338136 ATGACTCGGTTGCCCCTAGG 61.338 60.000 0.06 0.06 30.16 3.02
133 135 1.137825 CGCCTCGGTCTTCAGTCTC 59.862 63.158 0.00 0.00 0.00 3.36
134 136 1.137825 GCCTCGGTCTTCAGTCTCG 59.862 63.158 0.00 0.00 0.00 4.04
135 137 1.587933 GCCTCGGTCTTCAGTCTCGT 61.588 60.000 0.00 0.00 0.00 4.18
136 138 0.169230 CCTCGGTCTTCAGTCTCGTG 59.831 60.000 0.00 0.00 0.00 4.35
144 146 1.318785 CTTCAGTCTCGTGCGAAATCG 59.681 52.381 0.00 0.00 43.27 3.34
149 151 0.519961 TCTCGTGCGAAATCGACTGA 59.480 50.000 7.06 0.00 43.02 3.41
170 173 0.794605 GCGAGCGAAATTTGAGGCAC 60.795 55.000 0.00 0.00 0.00 5.01
175 178 3.356290 AGCGAAATTTGAGGCACCTAAT 58.644 40.909 0.00 0.00 0.00 1.73
179 182 6.096846 AGCGAAATTTGAGGCACCTAATATTT 59.903 34.615 0.00 2.96 0.00 1.40
181 184 7.591426 GCGAAATTTGAGGCACCTAATATTTAG 59.409 37.037 0.00 4.75 0.00 1.85
190 193 6.033966 GGCACCTAATATTTAGCAAACACAC 58.966 40.000 0.00 0.00 0.00 3.82
209 212 2.030540 CACTTTTGCAGATGTCACCTGG 60.031 50.000 0.00 0.00 32.51 4.45
210 213 1.542915 CTTTTGCAGATGTCACCTGGG 59.457 52.381 0.00 0.00 32.51 4.45
231 234 1.475280 CGAACCCTAGACATCGGAACA 59.525 52.381 0.00 0.00 0.00 3.18
287 290 5.935789 TGTTATATATAAGACTTTGGCGGGC 59.064 40.000 5.39 0.00 0.00 6.13
291 294 0.672401 TAAGACTTTGGCGGGCGAAG 60.672 55.000 25.24 25.24 0.00 3.79
300 303 2.095252 GCGGGCGAAGAGAGTGAAC 61.095 63.158 0.00 0.00 0.00 3.18
306 309 2.545952 GGCGAAGAGAGTGAACAAGACA 60.546 50.000 0.00 0.00 0.00 3.41
307 310 2.473235 GCGAAGAGAGTGAACAAGACAC 59.527 50.000 0.00 0.00 38.38 3.67
309 312 4.556898 GCGAAGAGAGTGAACAAGACACTA 60.557 45.833 0.00 0.00 46.57 2.74
329 794 7.236529 ACACTAAAGCCCATGATATGATGAAT 58.763 34.615 3.45 0.00 0.00 2.57
336 801 5.620654 GCCCATGATATGATGAATTTCCACG 60.621 44.000 3.45 0.00 0.00 4.94
338 803 5.106038 CCATGATATGATGAATTTCCACGGG 60.106 44.000 3.45 0.00 0.00 5.28
351 816 1.959226 CACGGGTGCTTACTTGCGT 60.959 57.895 0.00 0.00 35.36 5.24
506 974 1.474677 CCATGGCAAAAGCACCAACAA 60.475 47.619 0.00 0.00 39.96 2.83
507 975 1.598601 CATGGCAAAAGCACCAACAAC 59.401 47.619 0.00 0.00 39.96 3.32
508 976 0.610174 TGGCAAAAGCACCAACAACA 59.390 45.000 0.00 0.00 31.46 3.33
553 1022 0.165944 GGTCATTTTCCACGACGCAG 59.834 55.000 0.00 0.00 0.00 5.18
556 1025 1.599518 ATTTTCCACGACGCAGGCA 60.600 52.632 0.00 0.00 0.00 4.75
557 1026 1.169661 ATTTTCCACGACGCAGGCAA 61.170 50.000 0.00 0.00 0.00 4.52
574 1043 5.625197 GCAGGCAAAATACCAAGTCATCATT 60.625 40.000 0.00 0.00 0.00 2.57
578 1047 6.038356 GCAAAATACCAAGTCATCATTCCAG 58.962 40.000 0.00 0.00 0.00 3.86
587 1078 2.097142 GTCATCATTCCAGCAACAGCTC 59.903 50.000 0.00 0.00 36.19 4.09
588 1079 2.089201 CATCATTCCAGCAACAGCTCA 58.911 47.619 0.00 0.00 36.19 4.26
598 1089 1.605710 GCAACAGCTCAAGACACATGT 59.394 47.619 0.00 0.00 0.00 3.21
599 1090 2.603892 GCAACAGCTCAAGACACATGTG 60.604 50.000 24.25 24.25 0.00 3.21
616 1107 4.826733 ACATGTGTTCCAAATTAGCACTGA 59.173 37.500 0.00 0.00 0.00 3.41
640 1131 6.397272 AGTCAAATGAGATCTCTGTTCAGTC 58.603 40.000 22.95 11.41 0.00 3.51
838 1352 0.597377 GCACACCGGCCTTTGAAAAG 60.597 55.000 0.00 0.00 35.79 2.27
846 1360 1.275471 GCCTTTGAAAAGTTCGCCGC 61.275 55.000 2.33 0.00 34.20 6.53
862 1376 2.256461 GCCTTTGTCCGCTTGCAG 59.744 61.111 0.00 0.00 0.00 4.41
960 1504 0.825410 CAGAGCTCTCAGTCCAGCAT 59.175 55.000 14.96 0.00 38.18 3.79
1594 2209 2.474612 AACGCCAACGACAACCACC 61.475 57.895 0.00 0.00 43.93 4.61
1683 2298 0.759346 CCGGACCTATCCCCAAGAAG 59.241 60.000 0.00 0.00 42.83 2.85
1709 2324 2.483745 CTTCCGCGACGACAGCTA 59.516 61.111 8.23 0.00 0.00 3.32
1787 2408 4.276642 GGGGAGAGCAAATCAAAGAAGAT 58.723 43.478 0.00 0.00 0.00 2.40
1887 2508 0.693049 GGAAGAGGAACAAGCTGGGA 59.307 55.000 0.00 0.00 0.00 4.37
1902 2523 0.486879 TGGGAAAGAAGGCCATGGTT 59.513 50.000 14.67 0.00 0.00 3.67
2363 2984 3.052082 CAACGGCAGCCTCCACAG 61.052 66.667 10.54 0.00 0.00 3.66
2405 3030 4.261656 CCTTCGCTCCTCTCGTTACAATAT 60.262 45.833 0.00 0.00 0.00 1.28
2408 3033 6.570672 TCGCTCCTCTCGTTACAATATAAT 57.429 37.500 0.00 0.00 0.00 1.28
2412 3037 7.145985 GCTCCTCTCGTTACAATATAATGTCA 58.854 38.462 0.00 0.00 34.75 3.58
2436 3062 7.763528 TCAGAGAAGAGAAAATACAATCTGCTC 59.236 37.037 1.46 1.46 42.57 4.26
2478 3107 6.339587 ACAAGAAAGTTTCAACACTTGGAA 57.660 33.333 17.65 0.00 39.09 3.53
2618 3252 5.613358 GAATTCACCAATTCGAAGTGACT 57.387 39.130 25.91 13.80 40.10 3.41
2619 3253 6.002062 GAATTCACCAATTCGAAGTGACTT 57.998 37.500 25.91 20.32 40.10 3.01
2620 3254 7.129109 GAATTCACCAATTCGAAGTGACTTA 57.871 36.000 25.91 8.87 40.10 2.24
2622 3256 7.687941 ATTCACCAATTCGAAGTGACTTATT 57.312 32.000 25.91 4.41 40.10 1.40
2623 3257 7.504924 TTCACCAATTCGAAGTGACTTATTT 57.495 32.000 25.91 0.00 40.10 1.40
2624 3258 7.129109 TCACCAATTCGAAGTGACTTATTTC 57.871 36.000 25.91 0.00 35.67 2.17
2626 3260 7.444183 TCACCAATTCGAAGTGACTTATTTCTT 59.556 33.333 25.91 0.00 35.67 2.52
2627 3261 7.535258 CACCAATTCGAAGTGACTTATTTCTTG 59.465 37.037 25.91 9.38 33.21 3.02
2628 3262 7.228706 ACCAATTCGAAGTGACTTATTTCTTGT 59.771 33.333 25.91 8.32 0.00 3.16
2629 3263 8.717821 CCAATTCGAAGTGACTTATTTCTTGTA 58.282 33.333 25.91 0.00 0.00 2.41
2632 3266 7.827819 TCGAAGTGACTTATTTCTTGTATGG 57.172 36.000 0.00 0.00 0.00 2.74
2635 3269 8.883731 CGAAGTGACTTATTTCTTGTATGGAAT 58.116 33.333 0.00 0.00 0.00 3.01
2636 3270 9.994432 GAAGTGACTTATTTCTTGTATGGAATG 57.006 33.333 0.00 0.00 0.00 2.67
2637 3271 7.989826 AGTGACTTATTTCTTGTATGGAATGC 58.010 34.615 0.00 0.00 0.00 3.56
2638 3272 7.611467 AGTGACTTATTTCTTGTATGGAATGCA 59.389 33.333 0.00 0.00 37.07 3.96
2640 3274 7.828717 TGACTTATTTCTTGTATGGAATGCAGA 59.171 33.333 0.00 0.00 40.90 4.26
2641 3275 7.989826 ACTTATTTCTTGTATGGAATGCAGAC 58.010 34.615 0.00 0.00 40.90 3.51
2643 3277 8.523915 TTATTTCTTGTATGGAATGCAGACAT 57.476 30.769 2.57 0.00 40.90 3.06
2644 3278 9.625747 TTATTTCTTGTATGGAATGCAGACATA 57.374 29.630 2.57 0.00 40.90 2.29
2645 3279 8.701908 ATTTCTTGTATGGAATGCAGACATAT 57.298 30.769 2.57 0.00 40.90 1.78
2647 3281 9.797642 TTTCTTGTATGGAATGCAGACATATAT 57.202 29.630 2.57 0.00 40.90 0.86
2649 3283 9.875691 TCTTGTATGGAATGCAGACATATATAC 57.124 33.333 2.57 5.21 40.90 1.47
2652 3286 8.815912 TGTATGGAATGCAGACATATATACAGT 58.184 33.333 0.00 0.00 32.63 3.55
2655 3289 8.978874 TGGAATGCAGACATATATACAGTTTT 57.021 30.769 0.00 0.00 34.62 2.43
2656 3290 9.056005 TGGAATGCAGACATATATACAGTTTTC 57.944 33.333 0.00 0.00 34.62 2.29
2676 3310 1.532794 TTTTTGCGGGGGCAGACAT 60.533 52.632 0.00 0.00 0.00 3.06
2677 3311 0.251386 TTTTTGCGGGGGCAGACATA 60.251 50.000 0.00 0.00 0.00 2.29
2678 3312 0.033601 TTTTGCGGGGGCAGACATAT 60.034 50.000 0.00 0.00 0.00 1.78
2679 3313 0.840617 TTTGCGGGGGCAGACATATA 59.159 50.000 0.00 0.00 0.00 0.86
2680 3314 1.064003 TTGCGGGGGCAGACATATAT 58.936 50.000 0.00 0.00 0.00 0.86
2681 3315 1.945580 TGCGGGGGCAGACATATATA 58.054 50.000 0.00 0.00 0.00 0.86
2682 3316 2.477245 TGCGGGGGCAGACATATATAT 58.523 47.619 0.00 0.00 0.00 0.86
2683 3317 3.648739 TGCGGGGGCAGACATATATATA 58.351 45.455 0.00 0.00 0.00 0.86
2684 3318 3.641436 TGCGGGGGCAGACATATATATAG 59.359 47.826 0.00 0.00 0.00 1.31
2685 3319 3.641906 GCGGGGGCAGACATATATATAGT 59.358 47.826 0.00 0.00 0.00 2.12
2686 3320 4.101119 GCGGGGGCAGACATATATATAGTT 59.899 45.833 0.00 0.00 0.00 2.24
2687 3321 5.601662 CGGGGGCAGACATATATATAGTTG 58.398 45.833 0.00 0.00 0.00 3.16
2688 3322 5.362717 CGGGGGCAGACATATATATAGTTGA 59.637 44.000 0.00 0.00 0.00 3.18
2689 3323 6.461648 CGGGGGCAGACATATATATAGTTGAG 60.462 46.154 0.00 0.00 0.00 3.02
2690 3324 6.384305 GGGGGCAGACATATATATAGTTGAGT 59.616 42.308 0.00 0.00 0.00 3.41
2691 3325 7.092846 GGGGGCAGACATATATATAGTTGAGTT 60.093 40.741 0.00 0.00 0.00 3.01
2692 3326 7.766278 GGGGCAGACATATATATAGTTGAGTTG 59.234 40.741 0.00 0.00 0.00 3.16
2693 3327 8.314751 GGGCAGACATATATATAGTTGAGTTGT 58.685 37.037 0.00 0.00 0.00 3.32
2735 3369 2.062971 ATGGGCAATCTTGTGGCTAG 57.937 50.000 0.00 0.00 43.37 3.42
2803 3437 6.155827 GCTAACACATGCCAACTTTTATGAA 58.844 36.000 0.00 0.00 0.00 2.57
2841 3475 9.443283 GATAAACATTTCCTGATTCTTTCATCG 57.557 33.333 0.00 0.00 32.72 3.84
2921 3561 3.777478 TCCGAGCGAAGAAAATAACGAT 58.223 40.909 0.00 0.00 0.00 3.73
2933 3573 8.480643 AAGAAAATAACGATGTTCTTCTCGAT 57.519 30.769 0.00 0.00 43.45 3.59
2937 3577 8.425577 AAATAACGATGTTCTTCTCGATGATT 57.574 30.769 0.00 0.00 38.24 2.57
3004 3644 1.634757 CGCGCCTTCACATTGCTACA 61.635 55.000 0.00 0.00 0.00 2.74
3097 3737 0.464735 CGTCCTCCTCCATCGACTCT 60.465 60.000 0.00 0.00 0.00 3.24
3582 4222 1.070786 GACAGGAGCACCGAACCAA 59.929 57.895 0.00 0.00 41.83 3.67
3684 4324 7.087895 AGATCATATTCATCACACTCCCATT 57.912 36.000 0.00 0.00 0.00 3.16
3704 4344 6.209391 CCCATTTTGTACTTTCCTTCACTCAT 59.791 38.462 0.00 0.00 0.00 2.90
3705 4345 7.393234 CCCATTTTGTACTTTCCTTCACTCATA 59.607 37.037 0.00 0.00 0.00 2.15
3706 4346 8.960591 CCATTTTGTACTTTCCTTCACTCATAT 58.039 33.333 0.00 0.00 0.00 1.78
3712 4352 9.653287 TGTACTTTCCTTCACTCATATAAACTG 57.347 33.333 0.00 0.00 0.00 3.16
3713 4353 9.654663 GTACTTTCCTTCACTCATATAAACTGT 57.345 33.333 0.00 0.00 0.00 3.55
3714 4354 8.553459 ACTTTCCTTCACTCATATAAACTGTG 57.447 34.615 0.00 0.00 0.00 3.66
3715 4355 8.157476 ACTTTCCTTCACTCATATAAACTGTGT 58.843 33.333 0.00 0.00 0.00 3.72
3779 4428 3.564511 GATACCAACATTGCACACACAC 58.435 45.455 0.00 0.00 0.00 3.82
3859 4508 5.837437 ACTCGCTCTTATCTGATTGTAAGG 58.163 41.667 0.00 0.00 0.00 2.69
3863 4512 6.535150 TCGCTCTTATCTGATTGTAAGGTTTG 59.465 38.462 0.00 0.00 0.00 2.93
3877 4526 4.753516 AAGGTTTGGCTAGCAAACTTTT 57.246 36.364 26.95 21.54 38.21 2.27
3878 4527 4.753516 AGGTTTGGCTAGCAAACTTTTT 57.246 36.364 26.95 15.75 41.01 1.94
3890 4539 7.438160 GCTAGCAAACTTTTTGTAACCAAAGAT 59.562 33.333 10.63 0.00 41.37 2.40
3916 4565 1.568612 ATTGACGGTGAGCGTGCTTG 61.569 55.000 16.53 0.00 0.00 4.01
3956 4609 0.951558 TTTGAGAAACCGGCTGAAGC 59.048 50.000 0.00 0.00 41.14 3.86
3966 4619 0.947244 CGGCTGAAGCACTGTCTTTT 59.053 50.000 4.43 0.00 44.36 2.27
3968 4621 1.949525 GGCTGAAGCACTGTCTTTTCA 59.050 47.619 4.43 0.00 44.36 2.69
3969 4622 2.555757 GGCTGAAGCACTGTCTTTTCAT 59.444 45.455 4.43 0.00 44.36 2.57
3970 4623 3.753272 GGCTGAAGCACTGTCTTTTCATA 59.247 43.478 4.43 0.00 44.36 2.15
3971 4624 4.397417 GGCTGAAGCACTGTCTTTTCATAT 59.603 41.667 4.43 0.00 44.36 1.78
3972 4625 5.586243 GGCTGAAGCACTGTCTTTTCATATA 59.414 40.000 4.43 0.00 44.36 0.86
3973 4626 6.457528 GGCTGAAGCACTGTCTTTTCATATAC 60.458 42.308 4.43 0.00 44.36 1.47
3974 4627 6.314896 GCTGAAGCACTGTCTTTTCATATACT 59.685 38.462 0.00 0.00 41.59 2.12
3975 4628 7.465245 GCTGAAGCACTGTCTTTTCATATACTC 60.465 40.741 0.00 0.00 41.59 2.59
3976 4629 6.818644 TGAAGCACTGTCTTTTCATATACTCC 59.181 38.462 0.00 0.00 0.00 3.85
3977 4630 5.675538 AGCACTGTCTTTTCATATACTCCC 58.324 41.667 0.00 0.00 0.00 4.30
3978 4631 5.426833 AGCACTGTCTTTTCATATACTCCCT 59.573 40.000 0.00 0.00 0.00 4.20
3979 4632 5.755861 GCACTGTCTTTTCATATACTCCCTC 59.244 44.000 0.00 0.00 0.00 4.30
3980 4633 6.284459 CACTGTCTTTTCATATACTCCCTCC 58.716 44.000 0.00 0.00 0.00 4.30
3981 4634 5.964477 ACTGTCTTTTCATATACTCCCTCCA 59.036 40.000 0.00 0.00 0.00 3.86
3982 4635 6.617371 ACTGTCTTTTCATATACTCCCTCCAT 59.383 38.462 0.00 0.00 0.00 3.41
3983 4636 7.127955 ACTGTCTTTTCATATACTCCCTCCATT 59.872 37.037 0.00 0.00 0.00 3.16
3984 4637 7.509546 TGTCTTTTCATATACTCCCTCCATTC 58.490 38.462 0.00 0.00 0.00 2.67
3985 4638 6.937465 GTCTTTTCATATACTCCCTCCATTCC 59.063 42.308 0.00 0.00 0.00 3.01
3986 4639 6.851836 TCTTTTCATATACTCCCTCCATTCCT 59.148 38.462 0.00 0.00 0.00 3.36
3987 4640 8.016652 TCTTTTCATATACTCCCTCCATTCCTA 58.983 37.037 0.00 0.00 0.00 2.94
3988 4641 8.575736 TTTTCATATACTCCCTCCATTCCTAA 57.424 34.615 0.00 0.00 0.00 2.69
3989 4642 8.575736 TTTCATATACTCCCTCCATTCCTAAA 57.424 34.615 0.00 0.00 0.00 1.85
3990 4643 8.757307 TTCATATACTCCCTCCATTCCTAAAT 57.243 34.615 0.00 0.00 0.00 1.40
3991 4644 9.852784 TTCATATACTCCCTCCATTCCTAAATA 57.147 33.333 0.00 0.00 0.00 1.40
3996 4649 9.860393 ATACTCCCTCCATTCCTAAATATAAGT 57.140 33.333 0.00 0.00 0.00 2.24
3997 4650 8.208575 ACTCCCTCCATTCCTAAATATAAGTC 57.791 38.462 0.00 0.00 0.00 3.01
3998 4651 8.019652 ACTCCCTCCATTCCTAAATATAAGTCT 58.980 37.037 0.00 0.00 0.00 3.24
3999 4652 8.814448 TCCCTCCATTCCTAAATATAAGTCTT 57.186 34.615 0.00 0.00 0.00 3.01
4000 4653 9.237706 TCCCTCCATTCCTAAATATAAGTCTTT 57.762 33.333 0.00 0.00 0.00 2.52
4019 4672 8.749026 AGTCTTTATAGAGATTTCACTACGGA 57.251 34.615 0.00 0.00 0.00 4.69
4020 4673 8.623030 AGTCTTTATAGAGATTTCACTACGGAC 58.377 37.037 0.00 0.00 0.00 4.79
4021 4674 7.861872 GTCTTTATAGAGATTTCACTACGGACC 59.138 40.741 0.00 0.00 0.00 4.46
4022 4675 7.558807 TCTTTATAGAGATTTCACTACGGACCA 59.441 37.037 0.00 0.00 0.00 4.02
4023 4676 3.870633 AGAGATTTCACTACGGACCAC 57.129 47.619 0.00 0.00 0.00 4.16
4024 4677 3.162666 AGAGATTTCACTACGGACCACA 58.837 45.455 0.00 0.00 0.00 4.17
4025 4678 3.769844 AGAGATTTCACTACGGACCACAT 59.230 43.478 0.00 0.00 0.00 3.21
4026 4679 4.954202 AGAGATTTCACTACGGACCACATA 59.046 41.667 0.00 0.00 0.00 2.29
4027 4680 5.007385 AGATTTCACTACGGACCACATAC 57.993 43.478 0.00 0.00 0.00 2.39
4028 4681 4.464951 AGATTTCACTACGGACCACATACA 59.535 41.667 0.00 0.00 0.00 2.29
4029 4682 4.811969 TTTCACTACGGACCACATACAT 57.188 40.909 0.00 0.00 0.00 2.29
4030 4683 5.918426 TTTCACTACGGACCACATACATA 57.082 39.130 0.00 0.00 0.00 2.29
4031 4684 6.474140 TTTCACTACGGACCACATACATAT 57.526 37.500 0.00 0.00 0.00 1.78
4032 4685 5.447624 TCACTACGGACCACATACATATG 57.552 43.478 0.00 0.00 39.55 1.78
4034 4687 6.063404 TCACTACGGACCACATACATATGTA 58.937 40.000 17.65 17.65 44.57 2.29
4035 4688 6.717997 TCACTACGGACCACATACATATGTAT 59.282 38.462 20.49 20.49 44.57 2.29
4036 4689 7.027760 CACTACGGACCACATACATATGTATC 58.972 42.308 22.81 13.56 44.57 2.24
4037 4690 6.946583 ACTACGGACCACATACATATGTATCT 59.053 38.462 22.81 11.12 44.57 1.98
4038 4691 8.105197 ACTACGGACCACATACATATGTATCTA 58.895 37.037 22.81 1.91 44.57 1.98
4039 4692 7.956328 ACGGACCACATACATATGTATCTAT 57.044 36.000 22.81 10.72 44.57 1.98
4041 4694 9.642343 ACGGACCACATACATATGTATCTATAT 57.358 33.333 22.81 9.81 44.57 0.86
4042 4695 9.899226 CGGACCACATACATATGTATCTATATG 57.101 37.037 22.81 16.45 44.57 1.78
4043 4696 9.698309 GGACCACATACATATGTATCTATATGC 57.302 37.037 22.81 10.95 44.57 3.14
4075 4728 9.678260 AGAGTATAGATTCACTCATTTTGCTTT 57.322 29.630 4.70 0.00 42.99 3.51
4076 4729 9.713740 GAGTATAGATTCACTCATTTTGCTTTG 57.286 33.333 0.00 0.00 40.74 2.77
4077 4730 9.236006 AGTATAGATTCACTCATTTTGCTTTGT 57.764 29.630 0.00 0.00 0.00 2.83
4081 4734 7.889469 AGATTCACTCATTTTGCTTTGTATGT 58.111 30.769 0.00 0.00 0.00 2.29
4082 4735 7.811236 AGATTCACTCATTTTGCTTTGTATGTG 59.189 33.333 0.00 0.00 0.00 3.21
4083 4736 5.771469 TCACTCATTTTGCTTTGTATGTGG 58.229 37.500 0.00 0.00 0.00 4.17
4084 4737 5.301551 TCACTCATTTTGCTTTGTATGTGGT 59.698 36.000 0.00 0.00 0.00 4.16
4085 4738 5.630680 CACTCATTTTGCTTTGTATGTGGTC 59.369 40.000 0.00 0.00 0.00 4.02
4086 4739 5.132897 TCATTTTGCTTTGTATGTGGTCC 57.867 39.130 0.00 0.00 0.00 4.46
4087 4740 4.586421 TCATTTTGCTTTGTATGTGGTCCA 59.414 37.500 0.00 0.00 0.00 4.02
4088 4741 5.245751 TCATTTTGCTTTGTATGTGGTCCAT 59.754 36.000 0.00 0.00 37.58 3.41
4089 4742 4.517952 TTTGCTTTGTATGTGGTCCATG 57.482 40.909 0.00 0.00 34.86 3.66
4090 4743 2.445427 TGCTTTGTATGTGGTCCATGG 58.555 47.619 4.97 4.97 34.86 3.66
4091 4744 2.224992 TGCTTTGTATGTGGTCCATGGT 60.225 45.455 12.58 0.00 34.86 3.55
4092 4745 2.164219 GCTTTGTATGTGGTCCATGGTG 59.836 50.000 12.58 0.00 34.86 4.17
4093 4746 2.505650 TTGTATGTGGTCCATGGTGG 57.494 50.000 12.58 0.00 39.43 4.61
4094 4747 1.662686 TGTATGTGGTCCATGGTGGA 58.337 50.000 12.58 0.00 45.98 4.02
4131 4784 9.453830 AGACTTATATTTAGAAATGGAGGGAGT 57.546 33.333 0.00 0.00 0.00 3.85
4137 4790 7.996758 ATTTAGAAATGGAGGGAGTAGAAGA 57.003 36.000 0.00 0.00 0.00 2.87
4138 4791 7.996758 TTTAGAAATGGAGGGAGTAGAAGAT 57.003 36.000 0.00 0.00 0.00 2.40
4139 4792 9.676129 ATTTAGAAATGGAGGGAGTAGAAGATA 57.324 33.333 0.00 0.00 0.00 1.98
4165 4818 1.957695 GCCAGCCTTTGCACAAAGC 60.958 57.895 16.04 11.87 44.76 3.51
4175 4828 2.480555 CACAAAGCATCGCCGGTC 59.519 61.111 1.90 0.00 0.00 4.79
4220 4873 2.618312 GATGAACCCCTTGCGCATGC 62.618 60.000 12.75 7.91 43.20 4.06
4369 5022 1.027357 CCATTGAAAGATCTGGCCGG 58.973 55.000 4.71 4.71 0.00 6.13
4427 5080 2.348888 ACCCCCGCACGACTAAGAG 61.349 63.158 0.00 0.00 0.00 2.85
4503 5156 2.851805 TCTTCCAGATGTCGTCGATG 57.148 50.000 0.00 0.00 0.00 3.84
4504 5157 2.092323 TCTTCCAGATGTCGTCGATGT 58.908 47.619 4.21 0.00 0.00 3.06
4529 5182 2.133553 CACTATCTGCATCCGCTTCTG 58.866 52.381 0.00 0.00 39.64 3.02
4530 5183 1.069823 ACTATCTGCATCCGCTTCTGG 59.930 52.381 0.00 0.00 39.64 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.050275 GCGGCAGAGGGTTGTGAC 61.050 66.667 0.00 0.00 0.00 3.67
34 35 2.794820 GATGGGGATGCGCTAGGAGC 62.795 65.000 9.73 0.00 38.02 4.70
56 58 2.278206 CGAGTCATGACCTCGCCG 60.278 66.667 24.46 16.41 33.86 6.46
115 117 1.137825 GAGACTGAAGACCGAGGCG 59.862 63.158 0.00 0.00 0.00 5.52
130 132 0.519961 TCAGTCGATTTCGCACGAGA 59.480 50.000 0.00 0.00 39.16 4.04
133 135 1.337150 CGTCAGTCGATTTCGCACG 59.663 57.895 0.00 0.00 42.86 5.34
134 136 1.057361 GCGTCAGTCGATTTCGCAC 59.943 57.895 17.59 0.00 45.01 5.34
135 137 2.433334 CGCGTCAGTCGATTTCGCA 61.433 57.895 20.56 0.00 45.77 5.10
136 138 2.056087 CTCGCGTCAGTCGATTTCGC 62.056 60.000 5.77 14.18 42.86 4.70
144 146 0.438830 AAATTTCGCTCGCGTCAGTC 59.561 50.000 5.77 0.00 40.74 3.51
149 151 1.787847 CCTCAAATTTCGCTCGCGT 59.212 52.632 5.77 0.00 40.74 6.01
190 193 1.542915 CCCAGGTGACATCTGCAAAAG 59.457 52.381 10.43 0.00 0.00 2.27
196 199 1.021390 GTTCGCCCAGGTGACATCTG 61.021 60.000 8.88 8.88 34.07 2.90
209 212 1.067582 CCGATGTCTAGGGTTCGCC 59.932 63.158 0.00 0.00 0.00 5.54
210 213 0.458669 TTCCGATGTCTAGGGTTCGC 59.541 55.000 0.00 0.00 0.00 4.70
231 234 5.508200 TTTGAGTACTTGTGCGGAATTTT 57.492 34.783 0.00 0.00 0.00 1.82
239 242 9.463443 ACAAAAAGAATATTTGAGTACTTGTGC 57.537 29.630 0.00 0.00 39.56 4.57
269 272 1.414919 TCGCCCGCCAAAGTCTTATAT 59.585 47.619 0.00 0.00 0.00 0.86
270 273 0.825410 TCGCCCGCCAAAGTCTTATA 59.175 50.000 0.00 0.00 0.00 0.98
280 283 4.069232 CACTCTCTTCGCCCGCCA 62.069 66.667 0.00 0.00 0.00 5.69
281 284 3.296709 TTCACTCTCTTCGCCCGCC 62.297 63.158 0.00 0.00 0.00 6.13
287 290 3.971150 AGTGTCTTGTTCACTCTCTTCG 58.029 45.455 0.00 0.00 41.52 3.79
291 294 4.449405 GGCTTTAGTGTCTTGTTCACTCTC 59.551 45.833 1.82 0.00 43.76 3.20
300 303 6.057533 TCATATCATGGGCTTTAGTGTCTTG 58.942 40.000 0.00 0.00 0.00 3.02
306 309 8.716674 AAATTCATCATATCATGGGCTTTAGT 57.283 30.769 0.00 0.00 0.00 2.24
307 310 8.248945 GGAAATTCATCATATCATGGGCTTTAG 58.751 37.037 0.00 0.00 0.00 1.85
309 312 6.555738 TGGAAATTCATCATATCATGGGCTTT 59.444 34.615 0.00 0.00 0.00 3.51
329 794 1.600023 CAAGTAAGCACCCGTGGAAA 58.400 50.000 0.00 0.00 0.00 3.13
351 816 5.656416 CAGAATTTTACAATAGCAGGGGGAA 59.344 40.000 0.00 0.00 0.00 3.97
400 868 7.490402 GCTAATTACAGTTACATCTTACGTGGT 59.510 37.037 0.00 0.00 0.00 4.16
401 869 7.305820 CGCTAATTACAGTTACATCTTACGTGG 60.306 40.741 0.00 0.00 0.00 4.94
402 870 7.430211 TCGCTAATTACAGTTACATCTTACGTG 59.570 37.037 0.00 0.00 0.00 4.49
403 871 7.475015 TCGCTAATTACAGTTACATCTTACGT 58.525 34.615 0.00 0.00 0.00 3.57
404 872 7.903452 TCGCTAATTACAGTTACATCTTACG 57.097 36.000 0.00 0.00 0.00 3.18
405 873 9.512435 TCTTCGCTAATTACAGTTACATCTTAC 57.488 33.333 0.00 0.00 0.00 2.34
407 875 8.997621 TTCTTCGCTAATTACAGTTACATCTT 57.002 30.769 0.00 0.00 0.00 2.40
408 876 7.222999 GCTTCTTCGCTAATTACAGTTACATCT 59.777 37.037 0.00 0.00 0.00 2.90
409 877 7.010183 TGCTTCTTCGCTAATTACAGTTACATC 59.990 37.037 0.00 0.00 0.00 3.06
410 878 6.816640 TGCTTCTTCGCTAATTACAGTTACAT 59.183 34.615 0.00 0.00 0.00 2.29
411 879 6.160684 TGCTTCTTCGCTAATTACAGTTACA 58.839 36.000 0.00 0.00 0.00 2.41
412 880 6.642683 TGCTTCTTCGCTAATTACAGTTAC 57.357 37.500 0.00 0.00 0.00 2.50
413 881 6.647481 TGTTGCTTCTTCGCTAATTACAGTTA 59.353 34.615 0.00 0.00 0.00 2.24
414 882 5.468746 TGTTGCTTCTTCGCTAATTACAGTT 59.531 36.000 0.00 0.00 0.00 3.16
553 1022 5.105392 TGGAATGATGACTTGGTATTTTGCC 60.105 40.000 0.00 0.00 0.00 4.52
556 1025 5.716228 TGCTGGAATGATGACTTGGTATTTT 59.284 36.000 0.00 0.00 0.00 1.82
557 1026 5.263599 TGCTGGAATGATGACTTGGTATTT 58.736 37.500 0.00 0.00 0.00 1.40
578 1047 1.605710 ACATGTGTCTTGAGCTGTTGC 59.394 47.619 0.00 0.00 40.05 4.17
587 1078 5.630680 GCTAATTTGGAACACATGTGTCTTG 59.369 40.000 30.64 14.06 44.13 3.02
588 1079 5.301551 TGCTAATTTGGAACACATGTGTCTT 59.698 36.000 30.64 17.25 44.13 3.01
598 1089 4.713553 TGACTCAGTGCTAATTTGGAACA 58.286 39.130 0.00 0.00 0.00 3.18
599 1090 5.689383 TTGACTCAGTGCTAATTTGGAAC 57.311 39.130 0.00 0.00 0.00 3.62
616 1107 6.357579 ACTGAACAGAGATCTCATTTGACT 57.642 37.500 24.39 7.36 0.00 3.41
640 1131 1.679032 GGGAATCTCTCCGTTTGGTGG 60.679 57.143 0.00 0.00 46.51 4.61
838 1352 4.084888 CGGACAAAGGCGGCGAAC 62.085 66.667 12.98 1.56 0.00 3.95
960 1504 1.229082 AGCTCACTGAACCCCGGTA 60.229 57.895 0.00 0.00 31.91 4.02
1302 1875 3.068064 TCGATGGTGCCGCTGAGA 61.068 61.111 0.00 0.00 0.00 3.27
1476 2070 1.376466 GAGCTTCCTGAGGTTGCCA 59.624 57.895 12.98 0.00 35.91 4.92
1553 2168 4.884257 TTATGAGGCCGCGGACGC 62.884 66.667 33.48 31.42 38.22 5.19
1594 2209 0.329261 TCAGGAATGGTGCCTTGGAG 59.671 55.000 0.00 0.00 32.12 3.86
1787 2408 1.412710 GGTACATGAGGATCCTTCGCA 59.587 52.381 17.42 10.08 0.00 5.10
1902 2523 0.107643 TGTCGAACATGTCCTTGCCA 59.892 50.000 0.00 0.00 0.00 4.92
2363 2984 1.069258 GGCATACCGTGGAGTAGCC 59.931 63.158 0.00 0.00 32.90 3.93
2408 3033 7.332926 GCAGATTGTATTTTCTCTTCTCTGACA 59.667 37.037 0.00 0.00 31.49 3.58
2412 3037 7.047271 GGAGCAGATTGTATTTTCTCTTCTCT 58.953 38.462 0.00 0.00 0.00 3.10
2422 3048 5.255687 TGTGATGTGGAGCAGATTGTATTT 58.744 37.500 0.00 0.00 0.00 1.40
2436 3062 7.381766 TCTTGTTTGAATCTATGTGATGTGG 57.618 36.000 0.00 0.00 35.21 4.17
2514 3144 6.197468 GTGAACGGATCTAATCTCTTCTTTCG 59.803 42.308 0.00 0.00 0.00 3.46
2529 3163 3.181465 ACCATACATCCAGTGAACGGATC 60.181 47.826 0.00 0.00 41.48 3.36
2616 3250 7.611467 TGTCTGCATTCCATACAAGAAATAAGT 59.389 33.333 0.00 0.00 28.81 2.24
2617 3251 7.988737 TGTCTGCATTCCATACAAGAAATAAG 58.011 34.615 0.00 0.00 28.81 1.73
2618 3252 7.936496 TGTCTGCATTCCATACAAGAAATAA 57.064 32.000 0.00 0.00 28.81 1.40
2619 3253 9.797642 ATATGTCTGCATTCCATACAAGAAATA 57.202 29.630 0.00 0.00 34.69 1.40
2620 3254 8.701908 ATATGTCTGCATTCCATACAAGAAAT 57.298 30.769 0.00 0.00 34.69 2.17
2623 3257 9.875691 GTATATATGTCTGCATTCCATACAAGA 57.124 33.333 0.00 0.00 34.69 3.02
2624 3258 9.657419 TGTATATATGTCTGCATTCCATACAAG 57.343 33.333 0.00 0.00 34.69 3.16
2626 3260 8.815912 ACTGTATATATGTCTGCATTCCATACA 58.184 33.333 0.00 0.00 35.37 2.29
2627 3261 9.658799 AACTGTATATATGTCTGCATTCCATAC 57.341 33.333 0.00 0.00 36.58 2.39
2629 3263 9.578576 AAAACTGTATATATGTCTGCATTCCAT 57.421 29.630 0.00 0.00 36.58 3.41
2630 3264 8.978874 AAAACTGTATATATGTCTGCATTCCA 57.021 30.769 0.00 0.00 36.58 3.53
2631 3265 9.277783 AGAAAACTGTATATATGTCTGCATTCC 57.722 33.333 0.00 0.00 36.58 3.01
2659 3293 0.033601 ATATGTCTGCCCCCGCAAAA 60.034 50.000 0.00 0.00 46.66 2.44
2660 3294 0.840617 TATATGTCTGCCCCCGCAAA 59.159 50.000 0.00 0.00 46.66 3.68
2662 3296 1.945580 TATATATGTCTGCCCCCGCA 58.054 50.000 0.00 0.00 44.78 5.69
2663 3297 3.641906 ACTATATATATGTCTGCCCCCGC 59.358 47.826 5.44 0.00 0.00 6.13
2664 3298 5.362717 TCAACTATATATATGTCTGCCCCCG 59.637 44.000 5.44 0.00 0.00 5.73
2665 3299 6.384305 ACTCAACTATATATATGTCTGCCCCC 59.616 42.308 5.44 0.00 0.00 5.40
2666 3300 7.425224 ACTCAACTATATATATGTCTGCCCC 57.575 40.000 5.44 0.00 0.00 5.80
2667 3301 8.314751 ACAACTCAACTATATATATGTCTGCCC 58.685 37.037 5.44 0.00 0.00 5.36
2697 3331 9.812347 TTGCCCATATGATATTCTCTAATTTGT 57.188 29.630 3.65 0.00 0.00 2.83
2702 3336 9.676861 CAAGATTGCCCATATGATATTCTCTAA 57.323 33.333 3.65 0.00 0.00 2.10
2703 3337 8.829746 ACAAGATTGCCCATATGATATTCTCTA 58.170 33.333 3.65 0.00 0.00 2.43
2704 3338 7.610692 CACAAGATTGCCCATATGATATTCTCT 59.389 37.037 3.65 0.00 0.00 3.10
2705 3339 7.148120 CCACAAGATTGCCCATATGATATTCTC 60.148 40.741 3.65 0.00 0.00 2.87
2706 3340 6.662234 CCACAAGATTGCCCATATGATATTCT 59.338 38.462 3.65 0.00 0.00 2.40
2707 3341 6.626623 GCCACAAGATTGCCCATATGATATTC 60.627 42.308 3.65 0.00 0.00 1.75
2708 3342 5.186409 GCCACAAGATTGCCCATATGATATT 59.814 40.000 3.65 0.00 0.00 1.28
2709 3343 4.708421 GCCACAAGATTGCCCATATGATAT 59.292 41.667 3.65 0.00 0.00 1.63
2710 3344 4.081406 GCCACAAGATTGCCCATATGATA 58.919 43.478 3.65 0.00 0.00 2.15
2711 3345 2.895404 GCCACAAGATTGCCCATATGAT 59.105 45.455 3.65 0.00 0.00 2.45
2712 3346 2.091720 AGCCACAAGATTGCCCATATGA 60.092 45.455 3.65 0.00 0.00 2.15
2713 3347 2.313317 AGCCACAAGATTGCCCATATG 58.687 47.619 0.00 0.00 0.00 1.78
2714 3348 2.761786 AGCCACAAGATTGCCCATAT 57.238 45.000 0.00 0.00 0.00 1.78
2715 3349 2.509548 ACTAGCCACAAGATTGCCCATA 59.490 45.455 0.00 0.00 0.00 2.74
2716 3350 1.285962 ACTAGCCACAAGATTGCCCAT 59.714 47.619 0.00 0.00 0.00 4.00
2717 3351 0.698238 ACTAGCCACAAGATTGCCCA 59.302 50.000 0.00 0.00 0.00 5.36
2718 3352 1.474077 CAACTAGCCACAAGATTGCCC 59.526 52.381 0.00 0.00 0.00 5.36
2719 3353 1.135286 GCAACTAGCCACAAGATTGCC 60.135 52.381 0.00 0.00 37.14 4.52
2720 3354 2.268730 GCAACTAGCCACAAGATTGC 57.731 50.000 0.00 0.00 37.23 3.56
2735 3369 2.460757 AAAATGTGCATGAGGGCAAC 57.539 45.000 0.00 0.00 46.93 4.17
2823 3457 4.071423 TGCACGATGAAAGAATCAGGAAA 58.929 39.130 0.00 0.00 42.53 3.13
2838 3472 7.849804 AATCTTACAAGAACTAATGCACGAT 57.150 32.000 0.00 0.00 38.77 3.73
2839 3473 8.817100 CATAATCTTACAAGAACTAATGCACGA 58.183 33.333 0.00 0.00 38.77 4.35
2841 3475 8.616076 AGCATAATCTTACAAGAACTAATGCAC 58.384 33.333 20.81 5.62 39.51 4.57
2870 3505 7.220300 ACATTTTACTACGAACTAATGCTCGAG 59.780 37.037 8.45 8.45 38.43 4.04
2921 3561 6.037500 CCTGCAAATAATCATCGAGAAGAACA 59.962 38.462 0.00 0.00 0.00 3.18
2933 3573 7.544804 TCTCTATAGAGCCTGCAAATAATCA 57.455 36.000 22.81 0.00 41.80 2.57
3130 3770 1.150536 GTTGGTGGACTTGAGGGCA 59.849 57.895 0.00 0.00 0.00 5.36
3340 3980 1.517832 GATCACCGAGGTCACCCAG 59.482 63.158 0.00 0.00 0.00 4.45
3582 4222 1.748493 GAGAACTCTCAGACTGCCGAT 59.252 52.381 0.00 0.00 42.42 4.18
3664 4304 7.104043 ACAAAATGGGAGTGTGATGAATATG 57.896 36.000 0.00 0.00 0.00 1.78
3704 4344 7.754851 TCTCTGTAGTCACACACAGTTTATA 57.245 36.000 8.87 0.00 42.28 0.98
3705 4345 6.650427 TCTCTGTAGTCACACACAGTTTAT 57.350 37.500 8.87 0.00 42.28 1.40
3706 4346 6.096423 AGTTCTCTGTAGTCACACACAGTTTA 59.904 38.462 8.87 0.00 42.28 2.01
3707 4347 5.105310 AGTTCTCTGTAGTCACACACAGTTT 60.105 40.000 8.87 0.00 42.28 2.66
3708 4348 4.402793 AGTTCTCTGTAGTCACACACAGTT 59.597 41.667 8.87 0.00 42.28 3.16
3709 4349 3.954904 AGTTCTCTGTAGTCACACACAGT 59.045 43.478 8.87 0.00 42.28 3.55
3710 4350 4.277174 AGAGTTCTCTGTAGTCACACACAG 59.723 45.833 1.23 3.67 42.88 3.66
3711 4351 4.207955 AGAGTTCTCTGTAGTCACACACA 58.792 43.478 1.23 0.00 0.00 3.72
3712 4352 4.839668 AGAGTTCTCTGTAGTCACACAC 57.160 45.455 1.23 0.00 0.00 3.82
3713 4353 5.622180 ACTAGAGTTCTCTGTAGTCACACA 58.378 41.667 12.00 0.00 44.06 3.72
3725 4365 8.760103 ACGGAAAAATTAAGACTAGAGTTCTC 57.240 34.615 0.00 0.00 0.00 2.87
3753 4394 5.067674 GTGTGTGCAATGTTGGTATCCATAT 59.932 40.000 0.00 0.00 31.53 1.78
3757 4398 2.556189 TGTGTGTGCAATGTTGGTATCC 59.444 45.455 0.00 0.00 0.00 2.59
3765 4406 1.818060 ACAACTGTGTGTGTGCAATGT 59.182 42.857 0.00 0.00 36.31 2.71
3863 4512 4.939271 TGGTTACAAAAAGTTTGCTAGCC 58.061 39.130 13.29 0.00 0.00 3.93
3878 4527 9.537192 CCGTCAATAGTATTATCTTTGGTTACA 57.463 33.333 0.00 0.00 0.00 2.41
3935 4588 2.605580 GCTTCAGCCGGTTTCTCAAAAG 60.606 50.000 1.90 0.00 34.31 2.27
3956 4609 6.127054 TGGAGGGAGTATATGAAAAGACAGTG 60.127 42.308 0.00 0.00 0.00 3.66
3970 4623 9.860393 ACTTATATTTAGGAATGGAGGGAGTAT 57.140 33.333 0.00 0.00 0.00 2.12
3971 4624 9.322769 GACTTATATTTAGGAATGGAGGGAGTA 57.677 37.037 0.00 0.00 0.00 2.59
3972 4625 8.019652 AGACTTATATTTAGGAATGGAGGGAGT 58.980 37.037 0.00 0.00 0.00 3.85
3973 4626 8.442660 AGACTTATATTTAGGAATGGAGGGAG 57.557 38.462 0.00 0.00 0.00 4.30
3974 4627 8.814448 AAGACTTATATTTAGGAATGGAGGGA 57.186 34.615 0.00 0.00 0.00 4.20
3993 4646 9.186837 TCCGTAGTGAAATCTCTATAAAGACTT 57.813 33.333 0.00 0.00 0.00 3.01
3994 4647 8.623030 GTCCGTAGTGAAATCTCTATAAAGACT 58.377 37.037 0.00 0.00 0.00 3.24
3995 4648 7.861872 GGTCCGTAGTGAAATCTCTATAAAGAC 59.138 40.741 0.00 0.00 0.00 3.01
3996 4649 7.558807 TGGTCCGTAGTGAAATCTCTATAAAGA 59.441 37.037 0.00 0.00 0.00 2.52
3997 4650 7.648510 GTGGTCCGTAGTGAAATCTCTATAAAG 59.351 40.741 0.00 0.00 0.00 1.85
3998 4651 7.123098 TGTGGTCCGTAGTGAAATCTCTATAAA 59.877 37.037 0.00 0.00 0.00 1.40
3999 4652 6.604396 TGTGGTCCGTAGTGAAATCTCTATAA 59.396 38.462 0.00 0.00 0.00 0.98
4000 4653 6.124340 TGTGGTCCGTAGTGAAATCTCTATA 58.876 40.000 0.00 0.00 0.00 1.31
4001 4654 4.954202 TGTGGTCCGTAGTGAAATCTCTAT 59.046 41.667 0.00 0.00 0.00 1.98
4002 4655 4.338012 TGTGGTCCGTAGTGAAATCTCTA 58.662 43.478 0.00 0.00 0.00 2.43
4003 4656 3.162666 TGTGGTCCGTAGTGAAATCTCT 58.837 45.455 0.00 0.00 0.00 3.10
4004 4657 3.587797 TGTGGTCCGTAGTGAAATCTC 57.412 47.619 0.00 0.00 0.00 2.75
4005 4658 4.464951 TGTATGTGGTCCGTAGTGAAATCT 59.535 41.667 0.00 0.00 0.00 2.40
4006 4659 4.751060 TGTATGTGGTCCGTAGTGAAATC 58.249 43.478 0.00 0.00 0.00 2.17
4007 4660 4.811969 TGTATGTGGTCCGTAGTGAAAT 57.188 40.909 0.00 0.00 0.00 2.17
4008 4661 4.811969 ATGTATGTGGTCCGTAGTGAAA 57.188 40.909 0.00 0.00 0.00 2.69
4009 4662 5.361571 ACATATGTATGTGGTCCGTAGTGAA 59.638 40.000 6.56 0.00 44.66 3.18
4010 4663 4.891168 ACATATGTATGTGGTCCGTAGTGA 59.109 41.667 6.56 0.00 44.66 3.41
4011 4664 5.196341 ACATATGTATGTGGTCCGTAGTG 57.804 43.478 6.56 0.00 44.66 2.74
4012 4665 6.946583 AGATACATATGTATGTGGTCCGTAGT 59.053 38.462 28.82 4.95 45.77 2.73
4013 4666 7.392494 AGATACATATGTATGTGGTCCGTAG 57.608 40.000 28.82 0.00 45.77 3.51
4015 4668 7.956328 ATAGATACATATGTATGTGGTCCGT 57.044 36.000 28.82 6.34 45.77 4.69
4016 4669 9.899226 CATATAGATACATATGTATGTGGTCCG 57.101 37.037 28.82 12.72 45.77 4.79
4017 4670 9.698309 GCATATAGATACATATGTATGTGGTCC 57.302 37.037 28.82 15.22 45.77 4.46
4049 4702 9.678260 AAAGCAAAATGAGTGAATCTATACTCT 57.322 29.630 0.00 0.00 42.86 3.24
4050 4703 9.713740 CAAAGCAAAATGAGTGAATCTATACTC 57.286 33.333 0.00 0.00 42.77 2.59
4051 4704 9.236006 ACAAAGCAAAATGAGTGAATCTATACT 57.764 29.630 0.00 0.00 0.00 2.12
4055 4708 9.013229 ACATACAAAGCAAAATGAGTGAATCTA 57.987 29.630 0.00 0.00 0.00 1.98
4056 4709 7.811236 CACATACAAAGCAAAATGAGTGAATCT 59.189 33.333 0.00 0.00 0.00 2.40
4057 4710 7.062605 CCACATACAAAGCAAAATGAGTGAATC 59.937 37.037 0.00 0.00 0.00 2.52
4058 4711 6.869913 CCACATACAAAGCAAAATGAGTGAAT 59.130 34.615 0.00 0.00 0.00 2.57
4059 4712 6.183360 ACCACATACAAAGCAAAATGAGTGAA 60.183 34.615 0.00 0.00 0.00 3.18
4060 4713 5.301551 ACCACATACAAAGCAAAATGAGTGA 59.698 36.000 0.00 0.00 0.00 3.41
4061 4714 5.531634 ACCACATACAAAGCAAAATGAGTG 58.468 37.500 0.00 0.00 0.00 3.51
4062 4715 5.278957 GGACCACATACAAAGCAAAATGAGT 60.279 40.000 0.00 0.00 0.00 3.41
4063 4716 5.163513 GGACCACATACAAAGCAAAATGAG 58.836 41.667 0.00 0.00 0.00 2.90
4064 4717 4.586421 TGGACCACATACAAAGCAAAATGA 59.414 37.500 0.00 0.00 0.00 2.57
4065 4718 4.880759 TGGACCACATACAAAGCAAAATG 58.119 39.130 0.00 0.00 0.00 2.32
4066 4719 5.481105 CATGGACCACATACAAAGCAAAAT 58.519 37.500 0.00 0.00 37.84 1.82
4067 4720 4.262377 CCATGGACCACATACAAAGCAAAA 60.262 41.667 5.56 0.00 37.84 2.44
4068 4721 3.257873 CCATGGACCACATACAAAGCAAA 59.742 43.478 5.56 0.00 37.84 3.68
4069 4722 2.824936 CCATGGACCACATACAAAGCAA 59.175 45.455 5.56 0.00 37.84 3.91
4070 4723 2.224992 ACCATGGACCACATACAAAGCA 60.225 45.455 21.47 0.00 37.84 3.91
4071 4724 2.164219 CACCATGGACCACATACAAAGC 59.836 50.000 21.47 0.00 37.84 3.51
4072 4725 2.754552 CCACCATGGACCACATACAAAG 59.245 50.000 21.47 0.00 40.96 2.77
4073 4726 2.376855 TCCACCATGGACCACATACAAA 59.623 45.455 21.47 0.00 42.67 2.83
4074 4727 1.988846 TCCACCATGGACCACATACAA 59.011 47.619 21.47 0.00 42.67 2.41
4075 4728 1.662686 TCCACCATGGACCACATACA 58.337 50.000 21.47 0.00 42.67 2.29
4105 4758 9.453830 ACTCCCTCCATTTCTAAATATAAGTCT 57.546 33.333 0.00 0.00 0.00 3.24
4111 4764 9.676129 TCTTCTACTCCCTCCATTTCTAAATAT 57.324 33.333 0.00 0.00 0.00 1.28
4112 4765 9.676129 ATCTTCTACTCCCTCCATTTCTAAATA 57.324 33.333 0.00 0.00 0.00 1.40
4113 4766 7.996758 TCTTCTACTCCCTCCATTTCTAAAT 57.003 36.000 0.00 0.00 0.00 1.40
4114 4767 7.996758 ATCTTCTACTCCCTCCATTTCTAAA 57.003 36.000 0.00 0.00 0.00 1.85
4115 4768 8.925338 GTTATCTTCTACTCCCTCCATTTCTAA 58.075 37.037 0.00 0.00 0.00 2.10
4116 4769 8.065627 TGTTATCTTCTACTCCCTCCATTTCTA 58.934 37.037 0.00 0.00 0.00 2.10
4117 4770 6.903534 TGTTATCTTCTACTCCCTCCATTTCT 59.096 38.462 0.00 0.00 0.00 2.52
4118 4771 7.125792 TGTTATCTTCTACTCCCTCCATTTC 57.874 40.000 0.00 0.00 0.00 2.17
4119 4772 7.510675 TTGTTATCTTCTACTCCCTCCATTT 57.489 36.000 0.00 0.00 0.00 2.32
4120 4773 7.510675 TTTGTTATCTTCTACTCCCTCCATT 57.489 36.000 0.00 0.00 0.00 3.16
4121 4774 7.510675 TTTTGTTATCTTCTACTCCCTCCAT 57.489 36.000 0.00 0.00 0.00 3.41
4122 4775 6.945636 TTTTGTTATCTTCTACTCCCTCCA 57.054 37.500 0.00 0.00 0.00 3.86
4123 4776 6.261158 GCATTTTGTTATCTTCTACTCCCTCC 59.739 42.308 0.00 0.00 0.00 4.30
4124 4777 6.261158 GGCATTTTGTTATCTTCTACTCCCTC 59.739 42.308 0.00 0.00 0.00 4.30
4125 4778 6.122964 GGCATTTTGTTATCTTCTACTCCCT 58.877 40.000 0.00 0.00 0.00 4.20
4126 4779 5.885912 TGGCATTTTGTTATCTTCTACTCCC 59.114 40.000 0.00 0.00 0.00 4.30
4127 4780 6.458888 GCTGGCATTTTGTTATCTTCTACTCC 60.459 42.308 0.00 0.00 0.00 3.85
4128 4781 6.458888 GGCTGGCATTTTGTTATCTTCTACTC 60.459 42.308 0.00 0.00 0.00 2.59
4129 4782 5.358160 GGCTGGCATTTTGTTATCTTCTACT 59.642 40.000 0.00 0.00 0.00 2.57
4130 4783 5.358160 AGGCTGGCATTTTGTTATCTTCTAC 59.642 40.000 3.38 0.00 0.00 2.59
4131 4784 5.509498 AGGCTGGCATTTTGTTATCTTCTA 58.491 37.500 3.38 0.00 0.00 2.10
4132 4785 4.347607 AGGCTGGCATTTTGTTATCTTCT 58.652 39.130 3.38 0.00 0.00 2.85
4133 4786 4.725790 AGGCTGGCATTTTGTTATCTTC 57.274 40.909 3.38 0.00 0.00 2.87
4134 4787 5.240121 CAAAGGCTGGCATTTTGTTATCTT 58.760 37.500 3.38 0.00 0.00 2.40
4135 4788 4.824289 CAAAGGCTGGCATTTTGTTATCT 58.176 39.130 3.38 0.00 0.00 1.98
4136 4789 3.371898 GCAAAGGCTGGCATTTTGTTATC 59.628 43.478 14.44 0.00 34.98 1.75
4137 4790 3.244491 TGCAAAGGCTGGCATTTTGTTAT 60.244 39.130 9.76 0.00 41.91 1.89
4138 4791 2.103771 TGCAAAGGCTGGCATTTTGTTA 59.896 40.909 9.76 5.06 41.91 2.41
4139 4792 1.134159 TGCAAAGGCTGGCATTTTGTT 60.134 42.857 9.76 0.00 41.91 2.83
4188 4841 7.201902 GCAAGGGGTTCATCAATATTGATTGTA 60.202 37.037 25.16 12.92 45.13 2.41
4220 4873 0.319900 CAGGTGACAGACGTTGGAGG 60.320 60.000 0.00 0.00 0.00 4.30
4260 4913 3.009033 TGAAGAGGTGATTCGTCCCATTT 59.991 43.478 0.00 0.00 0.00 2.32
4265 4918 1.405661 GGGTGAAGAGGTGATTCGTCC 60.406 57.143 0.00 0.00 0.00 4.79
4269 4922 1.740718 GCTCGGGTGAAGAGGTGATTC 60.741 57.143 0.00 0.00 36.31 2.52
4325 4978 7.039574 GGCCTTTGGTAAATTACTTTGAAGGTA 60.040 37.037 18.49 0.00 0.00 3.08
4337 4990 6.432403 TCTTTCAATGGCCTTTGGTAAATT 57.568 33.333 26.26 3.34 0.00 1.82
4386 5039 0.387202 AGATCTGGAGTTCGATGGCG 59.613 55.000 0.00 0.00 39.35 5.69
4427 5080 1.664873 GTATGGTTTCCTTCTCCGGC 58.335 55.000 0.00 0.00 0.00 6.13
4503 5156 2.608261 GCGGATGCAGATAGTGGTCTAC 60.608 54.545 0.00 0.00 42.15 2.59
4504 5157 1.613925 GCGGATGCAGATAGTGGTCTA 59.386 52.381 0.00 0.00 42.15 2.59
4529 5182 0.617820 TGGAGCTTGGGAGGTAGTCC 60.618 60.000 0.00 0.00 46.10 3.85
4530 5183 0.537653 GTGGAGCTTGGGAGGTAGTC 59.462 60.000 0.00 0.00 32.79 2.59


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

AutoCloner maintained by Alex Coulton.