Multiple sequence alignment - TraesCS3A01G024500

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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 TraesCS3A01G024500 chr3A 100.000 4245 0 0 1 4245 13187518 13191762 0.000000e+00 7840.0
1 TraesCS3A01G024500 chr3D 91.411 1956 111 33 1581 3524 7124065 7122155 0.000000e+00 2628.0
2 TraesCS3A01G024500 chr3D 92.158 1594 79 21 3 1578 7125595 7124030 0.000000e+00 2209.0
3 TraesCS3A01G024500 chr3D 84.115 661 63 25 3555 4191 7122152 7121510 6.070000e-168 601.0
4 TraesCS3A01G024500 chr3D 81.967 122 20 2 410 529 44968408 44968529 7.510000e-18 102.0
5 TraesCS3A01G024500 chr3D 92.157 51 3 1 2346 2396 410521724 410521773 2.120000e-08 71.3
6 TraesCS3A01G024500 chr3B 89.603 1837 108 40 1729 3524 8686497 8684703 0.000000e+00 2257.0
7 TraesCS3A01G024500 chr3B 88.717 709 38 19 719 1409 8687200 8686516 0.000000e+00 828.0
8 TraesCS3A01G024500 chr3B 81.967 122 20 2 410 529 70095811 70095932 7.510000e-18 102.0
9 TraesCS3A01G024500 chr3B 94.872 39 2 0 213 251 799204053 799204015 1.270000e-05 62.1
10 TraesCS3A01G024500 chr1D 87.658 632 60 10 1730 2348 449310170 449310796 0.000000e+00 719.0
11 TraesCS3A01G024500 chr1D 80.843 783 75 39 2398 3158 449310798 449311527 2.890000e-151 545.0
12 TraesCS3A01G024500 chr1D 86.605 433 32 12 991 1416 449309748 449310161 5.000000e-124 455.0
13 TraesCS3A01G024500 chr1D 91.367 139 11 1 1024 1161 449281826 449281964 5.600000e-44 189.0
14 TraesCS3A01G024500 chr1D 80.822 146 17 9 545 688 449309343 449309479 2.090000e-18 104.0
15 TraesCS3A01G024500 chr1D 83.529 85 14 0 2653 2737 449283330 449283414 3.520000e-11 80.5
16 TraesCS3A01G024500 chr1D 97.143 35 1 0 192 226 121314559 121314525 4.580000e-05 60.2
17 TraesCS3A01G024500 chr1A 87.184 632 64 12 1730 2348 544493278 544493905 0.000000e+00 702.0
18 TraesCS3A01G024500 chr1A 83.577 548 41 19 2649 3195 544494162 544494661 6.430000e-128 468.0
19 TraesCS3A01G024500 chr1A 78.715 794 79 52 612 1373 544492500 544493235 8.370000e-122 448.0
20 TraesCS3A01G024500 chr1A 88.722 133 15 0 1024 1156 544487034 544487166 3.400000e-36 163.0
21 TraesCS3A01G024500 chr1A 83.529 85 14 0 2653 2737 544488550 544488634 3.520000e-11 80.5
22 TraesCS3A01G024500 chr1A 92.308 39 0 2 199 237 551305501 551305536 8.000000e-03 52.8
23 TraesCS3A01G024500 chr1B 86.842 608 65 7 1736 2330 614968409 614969014 0.000000e+00 665.0
24 TraesCS3A01G024500 chr1B 79.454 769 68 42 638 1372 614967618 614968330 2.990000e-126 462.0
25 TraesCS3A01G024500 chr1B 93.182 264 16 2 2897 3158 614969491 614969754 1.850000e-103 387.0
26 TraesCS3A01G024500 chr1B 90.000 130 13 0 1024 1153 614942629 614942758 7.300000e-38 169.0
27 TraesCS3A01G024500 chr1B 83.815 173 19 5 2398 2570 614969038 614969201 5.680000e-34 156.0
28 TraesCS3A01G024500 chr1B 84.000 75 12 0 2663 2737 614944200 614944274 5.890000e-09 73.1
29 TraesCS3A01G024500 chr4B 81.496 254 35 11 3569 3814 144728228 144728477 9.310000e-47 198.0
30 TraesCS3A01G024500 chr6A 81.304 230 32 8 3569 3790 116819113 116819339 4.360000e-40 176.0
31 TraesCS3A01G024500 chr2A 79.528 254 39 12 3569 3814 197252840 197252592 7.300000e-38 169.0
32 TraesCS3A01G024500 chr2A 97.059 34 1 0 194 227 740075211 740075178 1.650000e-04 58.4
33 TraesCS3A01G024500 chr5B 84.921 126 16 3 410 533 361110477 361110353 1.600000e-24 124.0
34 TraesCS3A01G024500 chr5B 80.672 119 20 3 413 529 129316192 129316075 5.850000e-14 89.8
35 TraesCS3A01G024500 chr5B 100.000 30 0 0 199 228 520584609 520584580 5.930000e-04 56.5
36 TraesCS3A01G024500 chrUn 82.258 124 16 6 410 529 79187082 79187203 7.510000e-18 102.0
37 TraesCS3A01G024500 chrUn 92.157 51 2 2 2347 2396 15945035 15945084 2.120000e-08 71.3
38 TraesCS3A01G024500 chr6B 80.000 120 22 1 410 529 217168874 217168757 2.100000e-13 87.9
39 TraesCS3A01G024500 chr6B 93.750 48 3 0 2347 2394 719968956 719968909 5.890000e-09 73.1
40 TraesCS3A01G024500 chr6D 80.342 117 18 4 415 529 262522761 262522874 2.720000e-12 84.2
41 TraesCS3A01G024500 chr4A 79.032 124 25 1 411 533 733524856 733524733 2.720000e-12 84.2
42 TraesCS3A01G024500 chr7D 96.000 50 2 0 2347 2396 414373043 414373092 9.780000e-12 82.4
43 TraesCS3A01G024500 chr7A 94.000 50 3 0 2347 2396 47504449 47504400 4.550000e-10 76.8
44 TraesCS3A01G024500 chr5D 93.617 47 3 0 2343 2389 506089364 506089410 2.120000e-08 71.3
45 TraesCS3A01G024500 chr5D 96.970 33 1 0 195 227 352021227 352021259 5.930000e-04 56.5
46 TraesCS3A01G024500 chr5D 100.000 29 0 0 199 227 27468755 27468783 2.000000e-03 54.7
47 TraesCS3A01G024500 chr5A 89.286 56 5 1 2347 2402 654621036 654621090 7.620000e-08 69.4
48 TraesCS3A01G024500 chr2D 100.000 29 0 0 199 227 636609257 636609229 2.000000e-03 54.7


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 TraesCS3A01G024500 chr3A 13187518 13191762 4244 False 7840.000000 7840 100.00000 1 4245 1 chr3A.!!$F1 4244
1 TraesCS3A01G024500 chr3D 7121510 7125595 4085 True 1812.666667 2628 89.22800 3 4191 3 chr3D.!!$R1 4188
2 TraesCS3A01G024500 chr3B 8684703 8687200 2497 True 1542.500000 2257 89.16000 719 3524 2 chr3B.!!$R2 2805
3 TraesCS3A01G024500 chr1D 449309343 449311527 2184 False 455.750000 719 83.98200 545 3158 4 chr1D.!!$F2 2613
4 TraesCS3A01G024500 chr1A 544487034 544494661 7627 False 372.300000 702 84.34540 612 3195 5 chr1A.!!$F2 2583
5 TraesCS3A01G024500 chr1B 614967618 614969754 2136 False 417.500000 665 85.82325 638 3158 4 chr1B.!!$F2 2520

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
438 451 1.171308 GCTTCAGTCACCATGTGCAT 58.829 50.000 0.00 0.00 32.98 3.96 F
1162 6151 0.804544 CCAGGTACGTACGCCATGTG 60.805 60.000 16.72 6.71 0.00 3.21 F
1639 6672 1.068333 TCCTGTACGCGTTTCCTACAC 60.068 52.381 20.78 8.30 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 6938 0.464036 ACTTGGTGCAGTTCTCGTCA 59.536 50.0 0.00 0.0 0.00 4.35 R
2224 7275 1.076533 CCACCTGAAACCGATCGACG 61.077 60.0 18.66 2.8 42.18 5.12 R
3354 8462 0.892755 AACCGCACTGATTCGTCCTA 59.107 50.0 0.00 0.0 0.00 2.94 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
58 59 9.793252 ATGAATTTAGATGTGACATTGCTAAAC 57.207 29.630 16.76 9.43 34.88 2.01
86 87 9.579932 TCATCTAGATGAGACTTAGCAAATCTA 57.420 33.333 27.93 3.35 42.42 1.98
168 170 3.423154 GAGCAGGGTGCCGAAACG 61.423 66.667 0.00 0.00 46.52 3.60
304 311 2.692041 GGTAGCTTGTCCATAGTACGGT 59.308 50.000 0.00 0.00 0.00 4.83
311 318 5.277731 GCTTGTCCATAGTACGGTCTACTAC 60.278 48.000 0.00 0.00 33.41 2.73
438 451 1.171308 GCTTCAGTCACCATGTGCAT 58.829 50.000 0.00 0.00 32.98 3.96
470 483 3.748048 GTCTGTGTCATGTGTTGTAGCAT 59.252 43.478 0.00 0.00 0.00 3.79
536 550 6.823678 CAAGCTTTGCATATTCCTGATTTC 57.176 37.500 0.00 0.00 0.00 2.17
541 555 7.548075 AGCTTTGCATATTCCTGATTTCTTTTG 59.452 33.333 0.00 0.00 0.00 2.44
554 568 8.023128 CCTGATTTCTTTTGTACATGATTCGTT 58.977 33.333 0.00 0.00 0.00 3.85
630 5525 4.226427 TGAAGTTGAATATCCAGCTGCT 57.774 40.909 8.66 0.00 0.00 4.24
795 5706 1.406065 CGAGATGCCTCCACCCTCAT 61.406 60.000 0.00 0.00 36.04 2.90
806 5717 1.827969 CCACCCTCATATCCCGATCTC 59.172 57.143 0.00 0.00 0.00 2.75
811 5722 3.762288 CCCTCATATCCCGATCTCGTTTA 59.238 47.826 0.00 0.00 37.74 2.01
881 5840 1.227556 CCTTTATCCTCCACCGGCG 60.228 63.158 0.00 0.00 0.00 6.46
882 5841 1.520666 CTTTATCCTCCACCGGCGT 59.479 57.895 6.01 0.00 0.00 5.68
951 5925 3.586461 CTGAGAGCAGTGGCAGCGT 62.586 63.158 0.00 0.00 44.61 5.07
952 5926 3.117171 GAGAGCAGTGGCAGCGTG 61.117 66.667 0.00 0.00 44.61 5.34
953 5927 4.694233 AGAGCAGTGGCAGCGTGG 62.694 66.667 0.00 0.00 44.61 4.94
989 5963 2.496817 CTAGCTGACCTCCACGGC 59.503 66.667 0.00 0.00 39.61 5.68
1162 6151 0.804544 CCAGGTACGTACGCCATGTG 60.805 60.000 16.72 6.71 0.00 3.21
1222 6211 1.597461 CCTTCCGTTGACCCTCTCC 59.403 63.158 0.00 0.00 0.00 3.71
1241 6230 3.149196 TCCTTGTTTCTTCATCAGGCAC 58.851 45.455 0.00 0.00 0.00 5.01
1416 6449 2.758423 TGCCACGTCAGTCATAGTACAT 59.242 45.455 0.00 0.00 0.00 2.29
1431 6464 6.546403 TCATAGTACATTCTCTAAAGCCTCGT 59.454 38.462 0.00 0.00 0.00 4.18
1435 6468 4.894784 ACATTCTCTAAAGCCTCGTTTGA 58.105 39.130 0.00 0.00 0.00 2.69
1454 6487 5.845391 TTGATTTGGAGGAAACGAAAACT 57.155 34.783 0.00 0.00 0.00 2.66
1456 6489 6.945938 TGATTTGGAGGAAACGAAAACTTA 57.054 33.333 0.00 0.00 0.00 2.24
1457 6490 7.336161 TGATTTGGAGGAAACGAAAACTTAA 57.664 32.000 0.00 0.00 0.00 1.85
1530 6563 5.582550 GCATAAAATAGGCTTTGAGTGGAC 58.417 41.667 0.00 0.00 31.82 4.02
1540 6573 3.868754 GCTTTGAGTGGACCCGTAGATTT 60.869 47.826 0.00 0.00 0.00 2.17
1542 6575 1.829222 TGAGTGGACCCGTAGATTTCC 59.171 52.381 0.00 0.00 0.00 3.13
1591 6624 8.842280 AGTATTTCTACGATTTCCAAAAACACA 58.158 29.630 0.00 0.00 32.82 3.72
1592 6625 9.113876 GTATTTCTACGATTTCCAAAAACACAG 57.886 33.333 0.00 0.00 0.00 3.66
1593 6626 6.928979 TTCTACGATTTCCAAAAACACAGA 57.071 33.333 0.00 0.00 0.00 3.41
1594 6627 6.539649 TCTACGATTTCCAAAAACACAGAG 57.460 37.500 0.00 0.00 0.00 3.35
1595 6628 6.285224 TCTACGATTTCCAAAAACACAGAGA 58.715 36.000 0.00 0.00 0.00 3.10
1596 6629 5.828299 ACGATTTCCAAAAACACAGAGAA 57.172 34.783 0.00 0.00 0.00 2.87
1597 6630 6.202516 ACGATTTCCAAAAACACAGAGAAA 57.797 33.333 0.00 0.00 0.00 2.52
1598 6631 6.805713 ACGATTTCCAAAAACACAGAGAAAT 58.194 32.000 0.00 0.00 36.82 2.17
1599 6632 7.936584 ACGATTTCCAAAAACACAGAGAAATA 58.063 30.769 0.00 0.00 34.88 1.40
1600 6633 8.410141 ACGATTTCCAAAAACACAGAGAAATAA 58.590 29.630 0.00 0.00 34.88 1.40
1601 6634 9.243637 CGATTTCCAAAAACACAGAGAAATAAA 57.756 29.630 0.00 0.00 34.88 1.40
1639 6672 1.068333 TCCTGTACGCGTTTCCTACAC 60.068 52.381 20.78 8.30 0.00 2.90
1647 6680 5.252969 ACGCGTTTCCTACACATAGAATA 57.747 39.130 5.58 0.00 0.00 1.75
1922 6955 1.795768 GATGACGAGAACTGCACCAA 58.204 50.000 0.00 0.00 0.00 3.67
2124 7157 2.336478 CCTCGTCGTCAGCTCCACT 61.336 63.158 0.00 0.00 0.00 4.00
2224 7275 5.715434 TTTGCTGGTGTTTCTAATTACCC 57.285 39.130 0.00 0.00 32.20 3.69
2359 7420 3.158676 GCAGATACTACTCCCTCCGATT 58.841 50.000 0.00 0.00 0.00 3.34
2389 7450 4.333649 ACTTGTCGCTGAAATGGATGTATG 59.666 41.667 0.00 0.00 0.00 2.39
2492 7553 3.689649 GGCGAGAACCAAAGTAATGACAT 59.310 43.478 0.00 0.00 0.00 3.06
2804 7896 1.437573 CGGTAAGATCAGCTCGCCA 59.562 57.895 0.00 0.00 0.00 5.69
2831 7923 3.254166 GCTGTCTTGCCTGAAATCTGAAA 59.746 43.478 0.00 0.00 0.00 2.69
2863 7955 0.902531 TTCACTGCCTACCTAGCACC 59.097 55.000 0.00 0.00 36.01 5.01
2864 7956 0.252057 TCACTGCCTACCTAGCACCA 60.252 55.000 0.00 0.00 36.01 4.17
2865 7957 0.108138 CACTGCCTACCTAGCACCAC 60.108 60.000 0.00 0.00 36.01 4.16
2891 7983 1.100510 AGATGACACCATGCATGCAC 58.899 50.000 25.37 9.84 32.09 4.57
2928 8025 1.243342 TTTGGGATTGCCGTGCAGAG 61.243 55.000 0.00 0.00 40.61 3.35
2931 8028 4.527157 GATTGCCGTGCAGAGCGC 62.527 66.667 0.00 0.00 40.61 5.92
3069 8166 1.752833 GGGTGAACCTGAAGACGGT 59.247 57.895 0.00 0.00 35.97 4.83
3098 8195 4.436998 GCACGTCCGCCTACTGCT 62.437 66.667 0.00 0.00 38.05 4.24
3118 8215 2.668212 CAGGCGTTCGGGAAGCAA 60.668 61.111 0.00 0.00 0.00 3.91
3307 8407 6.245115 TCTTGTAATGTGATTCAGCAACAG 57.755 37.500 0.00 0.00 0.00 3.16
3311 8411 4.778534 AATGTGATTCAGCAACAGAAGG 57.221 40.909 0.00 0.00 0.00 3.46
3313 8413 3.141398 TGTGATTCAGCAACAGAAGGAC 58.859 45.455 0.00 0.00 0.00 3.85
3314 8414 3.141398 GTGATTCAGCAACAGAAGGACA 58.859 45.455 0.00 0.00 0.00 4.02
3316 8416 3.817084 TGATTCAGCAACAGAAGGACAAG 59.183 43.478 0.00 0.00 0.00 3.16
3350 8458 4.103785 AGTCTAGAGTTATTGGCCATGCAT 59.896 41.667 6.09 0.00 0.00 3.96
3351 8459 4.214971 GTCTAGAGTTATTGGCCATGCATG 59.785 45.833 20.19 20.19 0.00 4.06
3352 8460 3.022557 AGAGTTATTGGCCATGCATGT 57.977 42.857 24.58 8.87 0.00 3.21
3353 8461 4.169059 AGAGTTATTGGCCATGCATGTA 57.831 40.909 24.58 7.84 0.00 2.29
3354 8462 4.733165 AGAGTTATTGGCCATGCATGTAT 58.267 39.130 24.58 14.12 0.00 2.29
3355 8463 5.879763 AGAGTTATTGGCCATGCATGTATA 58.120 37.500 24.58 13.23 0.00 1.47
3357 8465 5.012239 AGTTATTGGCCATGCATGTATAGG 58.988 41.667 24.58 10.66 0.00 2.57
3359 8467 2.566833 TGGCCATGCATGTATAGGAC 57.433 50.000 24.58 12.28 0.00 3.85
3360 8468 1.270785 TGGCCATGCATGTATAGGACG 60.271 52.381 24.58 8.31 0.00 4.79
3361 8469 1.001974 GGCCATGCATGTATAGGACGA 59.998 52.381 24.58 0.00 0.00 4.20
3362 8470 2.549992 GGCCATGCATGTATAGGACGAA 60.550 50.000 24.58 0.00 0.00 3.85
3364 8472 3.372206 GCCATGCATGTATAGGACGAATC 59.628 47.826 24.58 0.00 0.00 2.52
3365 8473 4.568956 CCATGCATGTATAGGACGAATCA 58.431 43.478 24.58 0.00 0.00 2.57
3366 8474 4.628766 CCATGCATGTATAGGACGAATCAG 59.371 45.833 24.58 0.22 0.00 2.90
3368 8476 4.620982 TGCATGTATAGGACGAATCAGTG 58.379 43.478 0.00 0.00 0.00 3.66
3369 8477 3.430218 GCATGTATAGGACGAATCAGTGC 59.570 47.826 0.00 0.00 0.00 4.40
3370 8478 3.349488 TGTATAGGACGAATCAGTGCG 57.651 47.619 0.00 0.00 37.54 5.34
3371 8479 2.034179 TGTATAGGACGAATCAGTGCGG 59.966 50.000 0.00 0.00 37.54 5.69
3372 8480 1.112113 ATAGGACGAATCAGTGCGGT 58.888 50.000 0.00 0.00 37.54 5.68
3373 8481 0.892755 TAGGACGAATCAGTGCGGTT 59.107 50.000 0.00 0.00 37.54 4.44
3374 8482 0.892755 AGGACGAATCAGTGCGGTTA 59.107 50.000 0.00 0.00 37.54 2.85
3375 8483 1.480954 AGGACGAATCAGTGCGGTTAT 59.519 47.619 0.00 0.00 37.54 1.89
3376 8484 1.593006 GGACGAATCAGTGCGGTTATG 59.407 52.381 0.00 0.00 0.00 1.90
3377 8485 2.268298 GACGAATCAGTGCGGTTATGT 58.732 47.619 0.00 0.00 0.00 2.29
3380 8488 2.866156 CGAATCAGTGCGGTTATGTCAT 59.134 45.455 0.00 0.00 0.00 3.06
3387 8495 5.049828 CAGTGCGGTTATGTCATCTTGATA 58.950 41.667 0.00 0.00 0.00 2.15
3425 8533 6.665465 AAAAGTTATTTTCTTCCGAAGACGG 58.335 36.000 10.48 0.00 46.42 4.79
3467 8581 3.044059 GCTGATGCTCCGTGTTGCC 62.044 63.158 0.00 0.00 36.03 4.52
3516 8630 6.129009 GCATCAATGAGTGCTTAAAACAACTG 60.129 38.462 9.36 0.00 38.30 3.16
3519 8633 7.715657 TCAATGAGTGCTTAAAACAACTGAAT 58.284 30.769 0.00 0.00 0.00 2.57
3524 8638 9.719355 TGAGTGCTTAAAACAACTGAATCTATA 57.281 29.630 0.00 0.00 0.00 1.31
3662 8777 9.671279 AAAGAAGAACCTTTTGAATTTGACATT 57.329 25.926 0.00 0.00 32.89 2.71
3724 8842 6.432403 AAAAATATTTGCTCCAAGGTCCAA 57.568 33.333 0.39 0.00 0.00 3.53
3725 8843 5.405935 AAATATTTGCTCCAAGGTCCAAC 57.594 39.130 0.00 0.00 0.00 3.77
3726 8844 2.380064 ATTTGCTCCAAGGTCCAACA 57.620 45.000 0.00 0.00 0.00 3.33
3727 8845 1.398692 TTTGCTCCAAGGTCCAACAC 58.601 50.000 0.00 0.00 0.00 3.32
3728 8846 0.257328 TTGCTCCAAGGTCCAACACA 59.743 50.000 0.00 0.00 0.00 3.72
3729 8847 0.478072 TGCTCCAAGGTCCAACACAT 59.522 50.000 0.00 0.00 0.00 3.21
3743 8861 3.003171 CCAACACATTGTCGTTCATGACA 59.997 43.478 0.00 0.00 46.63 3.58
3756 8874 9.952188 TGTCGTTCATGACAATACAAAAATTAA 57.048 25.926 0.00 0.00 45.40 1.40
3788 8910 2.495155 TGTGACTAACATGCATGCCT 57.505 45.000 26.53 16.07 32.36 4.75
3790 8912 2.488937 TGTGACTAACATGCATGCCTTG 59.511 45.455 26.53 16.24 32.36 3.61
3800 8922 1.580942 CATGCCTTGTGTTCCGGTG 59.419 57.895 0.00 0.00 0.00 4.94
3817 8939 4.155826 TCCGGTGATAAAAGACATGCTTTG 59.844 41.667 13.49 2.96 45.85 2.77
3818 8940 4.155826 CCGGTGATAAAAGACATGCTTTGA 59.844 41.667 13.49 8.42 45.85 2.69
3819 8941 5.088739 CGGTGATAAAAGACATGCTTTGAC 58.911 41.667 13.49 9.65 45.85 3.18
3832 8954 2.095969 TGCTTTGACTTGATAAACGCGG 60.096 45.455 12.47 0.00 0.00 6.46
3837 8959 2.438795 TTGATAAACGCGGCCCCC 60.439 61.111 12.47 0.00 0.00 5.40
3861 8983 1.199327 CTCTTGCTCGACTTGACCGTA 59.801 52.381 0.00 0.00 0.00 4.02
3870 8992 4.482386 TCGACTTGACCGTATCTTCTTTG 58.518 43.478 0.00 0.00 0.00 2.77
3871 8993 4.216902 TCGACTTGACCGTATCTTCTTTGA 59.783 41.667 0.00 0.00 0.00 2.69
3872 8994 5.103000 CGACTTGACCGTATCTTCTTTGAT 58.897 41.667 0.00 0.00 0.00 2.57
3873 8995 5.004821 CGACTTGACCGTATCTTCTTTGATG 59.995 44.000 0.00 0.00 0.00 3.07
3874 8996 5.794894 ACTTGACCGTATCTTCTTTGATGT 58.205 37.500 0.00 0.00 0.00 3.06
3876 8998 6.147821 ACTTGACCGTATCTTCTTTGATGTTG 59.852 38.462 0.00 0.00 0.00 3.33
3878 9000 3.689649 ACCGTATCTTCTTTGATGTTGGC 59.310 43.478 0.00 0.00 0.00 4.52
3879 9001 3.065371 CCGTATCTTCTTTGATGTTGGCC 59.935 47.826 0.00 0.00 0.00 5.36
3880 9002 3.689161 CGTATCTTCTTTGATGTTGGCCA 59.311 43.478 0.00 0.00 0.00 5.36
3881 9003 4.201851 CGTATCTTCTTTGATGTTGGCCAG 60.202 45.833 5.11 0.00 0.00 4.85
3882 9004 2.517959 TCTTCTTTGATGTTGGCCAGG 58.482 47.619 5.11 0.00 0.00 4.45
3883 9005 2.158475 TCTTCTTTGATGTTGGCCAGGT 60.158 45.455 5.11 0.00 0.00 4.00
3884 9006 1.909700 TCTTTGATGTTGGCCAGGTC 58.090 50.000 5.11 6.34 0.00 3.85
3888 9010 1.224592 GATGTTGGCCAGGTCGGAT 59.775 57.895 5.11 0.00 36.56 4.18
3889 9011 1.077501 ATGTTGGCCAGGTCGGATG 60.078 57.895 5.11 0.00 36.56 3.51
3893 9015 4.899239 GGCCAGGTCGGATGCTCG 62.899 72.222 0.00 0.00 36.56 5.03
3900 9022 1.814169 GTCGGATGCTCGTTTCCCC 60.814 63.158 0.00 0.00 0.00 4.81
3901 9023 2.890474 CGGATGCTCGTTTCCCCG 60.890 66.667 0.00 0.00 0.00 5.73
3906 9028 1.258445 ATGCTCGTTTCCCCGACTCT 61.258 55.000 0.00 0.00 32.57 3.24
3919 9041 1.671901 CGACTCTGCCCTCTCTTCCC 61.672 65.000 0.00 0.00 0.00 3.97
3921 9043 3.077556 TCTGCCCTCTCTTCCCGC 61.078 66.667 0.00 0.00 0.00 6.13
3924 9046 4.475135 GCCCTCTCTTCCCGCCAC 62.475 72.222 0.00 0.00 0.00 5.01
3926 9048 3.787001 CCTCTCTTCCCGCCACCC 61.787 72.222 0.00 0.00 0.00 4.61
3927 9049 4.148825 CTCTCTTCCCGCCACCCG 62.149 72.222 0.00 0.00 0.00 5.28
3936 9058 4.388499 CGCCACCCGCACTACCTT 62.388 66.667 0.00 0.00 37.30 3.50
3937 9059 2.436115 GCCACCCGCACTACCTTC 60.436 66.667 0.00 0.00 37.47 3.46
3938 9060 2.125673 CCACCCGCACTACCTTCG 60.126 66.667 0.00 0.00 0.00 3.79
3939 9061 2.642254 CCACCCGCACTACCTTCGA 61.642 63.158 0.00 0.00 0.00 3.71
3941 9063 2.183555 CCCGCACTACCTTCGACC 59.816 66.667 0.00 0.00 0.00 4.79
3942 9064 2.202570 CCGCACTACCTTCGACCG 60.203 66.667 0.00 0.00 0.00 4.79
3952 9074 0.108138 CCTTCGACCGCTTCCTCATT 60.108 55.000 0.00 0.00 0.00 2.57
3963 9085 2.872038 GCTTCCTCATTGTTGTCTCCGT 60.872 50.000 0.00 0.00 0.00 4.69
3978 9100 3.433615 GTCTCCGTCTCCACAAAAATCTG 59.566 47.826 0.00 0.00 0.00 2.90
3985 9107 5.004821 CGTCTCCACAAAAATCTGATAGTCG 59.995 44.000 0.00 0.00 0.00 4.18
3986 9108 5.292101 GTCTCCACAAAAATCTGATAGTCGG 59.708 44.000 0.00 0.00 0.00 4.79
3989 9111 4.034510 CCACAAAAATCTGATAGTCGGCTC 59.965 45.833 0.00 0.00 0.00 4.70
3992 9114 4.592485 AAAATCTGATAGTCGGCTCGAT 57.408 40.909 0.00 0.00 38.42 3.59
4000 9122 4.804139 TGATAGTCGGCTCGATTTTTCTTC 59.196 41.667 0.00 0.00 38.42 2.87
4014 9136 1.453155 TTCTTCGAGAATGCTTGGCC 58.547 50.000 0.00 0.00 0.00 5.36
4017 9139 0.392998 TTCGAGAATGCTTGGCCCTC 60.393 55.000 0.00 0.00 0.00 4.30
4019 9141 0.465097 CGAGAATGCTTGGCCCTCAT 60.465 55.000 0.00 0.00 0.00 2.90
4045 9169 1.220750 TCTTCCTCCTCCCACTATCCC 59.779 57.143 0.00 0.00 0.00 3.85
4048 9172 0.178918 CCTCCTCCCACTATCCCCTC 60.179 65.000 0.00 0.00 0.00 4.30
4081 9205 3.038417 GCACTCTCGCGTTGCTGT 61.038 61.111 5.77 0.00 0.00 4.40
4084 9208 3.114616 CTCTCGCGTTGCTGTGGG 61.115 66.667 5.77 0.00 0.00 4.61
4086 9210 3.716006 CTCGCGTTGCTGTGGGTG 61.716 66.667 5.77 0.00 0.00 4.61
4141 9276 4.640771 AAGCTCCACAGATTTGTTCCTA 57.359 40.909 0.00 0.00 34.62 2.94
4143 9278 3.584848 AGCTCCACAGATTTGTTCCTACT 59.415 43.478 0.00 0.00 34.62 2.57
4146 9281 5.106515 GCTCCACAGATTTGTTCCTACTTTC 60.107 44.000 0.00 0.00 34.62 2.62
4147 9282 6.187727 TCCACAGATTTGTTCCTACTTTCT 57.812 37.500 0.00 0.00 34.62 2.52
4149 9284 7.060421 TCCACAGATTTGTTCCTACTTTCTTT 58.940 34.615 0.00 0.00 34.62 2.52
4151 9286 8.846211 CCACAGATTTGTTCCTACTTTCTTTAA 58.154 33.333 0.00 0.00 34.62 1.52
4191 9326 6.269538 TGGTGGATTTGATGGATTTCTTTGAA 59.730 34.615 0.00 0.00 0.00 2.69
4192 9327 6.815142 GGTGGATTTGATGGATTTCTTTGAAG 59.185 38.462 0.00 0.00 0.00 3.02
4193 9328 7.309990 GGTGGATTTGATGGATTTCTTTGAAGA 60.310 37.037 0.00 0.00 0.00 2.87
4194 9329 7.758528 GTGGATTTGATGGATTTCTTTGAAGAG 59.241 37.037 0.00 0.00 36.22 2.85
4195 9330 7.670979 TGGATTTGATGGATTTCTTTGAAGAGA 59.329 33.333 0.00 0.00 36.22 3.10
4196 9331 8.693625 GGATTTGATGGATTTCTTTGAAGAGAT 58.306 33.333 0.00 0.00 36.22 2.75
4197 9332 9.733219 GATTTGATGGATTTCTTTGAAGAGATC 57.267 33.333 13.16 13.16 42.70 2.75
4198 9333 8.874744 TTTGATGGATTTCTTTGAAGAGATCT 57.125 30.769 18.21 0.00 42.89 2.75
4199 9334 7.860918 TGATGGATTTCTTTGAAGAGATCTG 57.139 36.000 18.21 0.00 42.89 2.90
4200 9335 6.318144 TGATGGATTTCTTTGAAGAGATCTGC 59.682 38.462 18.21 11.33 42.89 4.26
4201 9336 4.946157 TGGATTTCTTTGAAGAGATCTGCC 59.054 41.667 18.21 8.15 42.89 4.85
4202 9337 5.192176 GGATTTCTTTGAAGAGATCTGCCT 58.808 41.667 18.21 0.00 42.89 4.75
4203 9338 5.296531 GGATTTCTTTGAAGAGATCTGCCTC 59.703 44.000 18.21 0.00 42.89 4.70
4204 9339 5.495926 TTTCTTTGAAGAGATCTGCCTCT 57.504 39.130 0.00 0.00 44.84 3.69
4211 9346 3.749665 AGAGATCTGCCTCTTATGTGC 57.250 47.619 0.00 0.00 40.40 4.57
4212 9347 3.036819 AGAGATCTGCCTCTTATGTGCA 58.963 45.455 0.00 0.00 40.40 4.57
4218 9353 3.189618 TGCCTCTTATGTGCAGATGAG 57.810 47.619 9.15 9.15 0.00 2.90
4219 9354 2.158856 TGCCTCTTATGTGCAGATGAGG 60.159 50.000 20.24 20.24 43.08 3.86
4220 9355 2.158842 GCCTCTTATGTGCAGATGAGGT 60.159 50.000 23.33 0.00 42.54 3.85
4221 9356 3.726607 CCTCTTATGTGCAGATGAGGTC 58.273 50.000 17.61 0.00 38.45 3.85
4222 9357 3.379240 CTCTTATGTGCAGATGAGGTCG 58.621 50.000 14.58 2.00 0.00 4.79
4223 9358 2.760650 TCTTATGTGCAGATGAGGTCGT 59.239 45.455 14.58 0.00 0.00 4.34
4224 9359 2.584492 TATGTGCAGATGAGGTCGTG 57.416 50.000 6.60 0.00 0.00 4.35
4225 9360 0.742281 ATGTGCAGATGAGGTCGTGC 60.742 55.000 0.00 0.00 33.98 5.34
4226 9361 1.079543 GTGCAGATGAGGTCGTGCT 60.080 57.895 0.00 0.00 34.29 4.40
4227 9362 1.080995 GTGCAGATGAGGTCGTGCTC 61.081 60.000 0.00 0.00 34.29 4.26
4228 9363 1.520342 GCAGATGAGGTCGTGCTCC 60.520 63.158 0.00 0.00 32.05 4.70
4229 9364 1.893062 CAGATGAGGTCGTGCTCCA 59.107 57.895 0.00 0.00 0.00 3.86
4230 9365 0.463204 CAGATGAGGTCGTGCTCCAT 59.537 55.000 0.00 0.00 0.00 3.41
4231 9366 0.463204 AGATGAGGTCGTGCTCCATG 59.537 55.000 0.00 0.00 0.00 3.66
4232 9367 1.153289 ATGAGGTCGTGCTCCATGC 60.153 57.895 0.00 0.00 43.25 4.06
4233 9368 1.620739 ATGAGGTCGTGCTCCATGCT 61.621 55.000 0.00 0.00 43.37 3.79
4234 9369 1.812922 GAGGTCGTGCTCCATGCTG 60.813 63.158 0.00 0.00 43.37 4.41
4235 9370 2.230994 GAGGTCGTGCTCCATGCTGA 62.231 60.000 0.00 0.00 43.37 4.26
4236 9371 2.103042 GGTCGTGCTCCATGCTGAC 61.103 63.158 0.00 0.00 42.64 3.51
4237 9372 1.374631 GTCGTGCTCCATGCTGACA 60.375 57.895 0.00 0.00 42.78 3.58
4238 9373 1.374631 TCGTGCTCCATGCTGACAC 60.375 57.895 0.00 0.00 43.37 3.67
4239 9374 1.375140 CGTGCTCCATGCTGACACT 60.375 57.895 0.00 0.00 43.37 3.55
4240 9375 1.357258 CGTGCTCCATGCTGACACTC 61.357 60.000 0.00 0.00 43.37 3.51
4241 9376 1.079612 TGCTCCATGCTGACACTCG 60.080 57.895 0.00 0.00 43.37 4.18
4242 9377 2.459442 GCTCCATGCTGACACTCGC 61.459 63.158 0.00 0.00 38.95 5.03
4243 9378 1.812922 CTCCATGCTGACACTCGCC 60.813 63.158 0.00 0.00 0.00 5.54
4244 9379 2.046988 CCATGCTGACACTCGCCA 60.047 61.111 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 8.462016 AGGTTTAGCAATGTCACATCTAAATTC 58.538 33.333 12.50 9.39 33.52 2.17
129 131 2.419673 CCACGCATGAGCAGTAAATCAA 59.580 45.455 0.00 0.00 42.27 2.57
130 132 2.009051 CCACGCATGAGCAGTAAATCA 58.991 47.619 0.00 0.00 42.27 2.57
168 170 1.000283 CCATGGCTCTATCACGAGGAC 60.000 57.143 0.00 0.00 0.00 3.85
438 451 1.324383 TGACACAGACGCAAGAGGTA 58.676 50.000 0.00 0.00 43.62 3.08
488 501 9.955208 TGCATATCATTTCATTGATACAAGAAC 57.045 29.630 0.00 0.00 40.44 3.01
491 504 8.912658 GCTTGCATATCATTTCATTGATACAAG 58.087 33.333 14.37 14.37 40.84 3.16
548 562 2.882761 CTGGGCATCATGATCAACGAAT 59.117 45.455 4.86 0.00 0.00 3.34
554 568 2.579410 CCATCTGGGCATCATGATCA 57.421 50.000 4.86 0.00 0.00 2.92
630 5525 2.159448 CGATCTTGGCATTAAACCGCAA 60.159 45.455 0.00 0.00 0.00 4.85
795 5706 5.808540 CACAAAACTAAACGAGATCGGGATA 59.191 40.000 7.22 0.00 44.95 2.59
806 5717 3.121126 ACGATCGAGCACAAAACTAAACG 60.121 43.478 24.34 0.00 0.00 3.60
811 5722 0.512952 GCACGATCGAGCACAAAACT 59.487 50.000 28.82 0.00 0.00 2.66
881 5840 3.485346 TTCGGTGAGTGGGGGCAAC 62.485 63.158 0.00 0.00 0.00 4.17
882 5841 3.172106 TTCGGTGAGTGGGGGCAA 61.172 61.111 0.00 0.00 0.00 4.52
957 5931 2.831742 TAGGCTAGCCCGGTGTCG 60.832 66.667 30.42 0.00 39.21 4.35
958 5932 3.130227 CTAGGCTAGCCCGGTGTC 58.870 66.667 30.42 3.20 39.21 3.67
972 5946 2.496817 GCCGTGGAGGTCAGCTAG 59.503 66.667 0.00 0.00 43.70 3.42
1208 6197 0.396811 AACAAGGAGAGGGTCAACGG 59.603 55.000 0.00 0.00 0.00 4.44
1209 6198 2.143925 GAAACAAGGAGAGGGTCAACG 58.856 52.381 0.00 0.00 0.00 4.10
1210 6199 3.493767 AGAAACAAGGAGAGGGTCAAC 57.506 47.619 0.00 0.00 0.00 3.18
1222 6211 3.120408 CGAGTGCCTGATGAAGAAACAAG 60.120 47.826 0.00 0.00 0.00 3.16
1241 6230 2.870161 CTTCCACGCGTCGACGAG 60.870 66.667 39.74 37.12 44.60 4.18
1273 6262 2.203877 AGGTAGGTGGTTCCGCCA 60.204 61.111 21.38 6.80 46.95 5.69
1416 6449 5.181245 CCAAATCAAACGAGGCTTTAGAGAA 59.819 40.000 0.00 0.00 0.00 2.87
1431 6464 6.215495 AGTTTTCGTTTCCTCCAAATCAAA 57.785 33.333 0.00 0.00 0.00 2.69
1435 6468 7.576861 TCTTAAGTTTTCGTTTCCTCCAAAT 57.423 32.000 1.63 0.00 0.00 2.32
1473 6506 9.249457 CGAAGCAAGATATATGAACTTCTTACA 57.751 33.333 0.00 0.00 31.98 2.41
1474 6507 9.250624 ACGAAGCAAGATATATGAACTTCTTAC 57.749 33.333 0.00 0.00 31.98 2.34
1475 6508 9.817809 AACGAAGCAAGATATATGAACTTCTTA 57.182 29.630 0.00 0.00 31.98 2.10
1476 6509 8.723942 AACGAAGCAAGATATATGAACTTCTT 57.276 30.769 0.00 0.00 31.98 2.52
1477 6510 7.439655 GGAACGAAGCAAGATATATGAACTTCT 59.560 37.037 0.00 0.00 31.98 2.85
1508 6541 5.067805 GGGTCCACTCAAAGCCTATTTTATG 59.932 44.000 0.00 0.00 0.00 1.90
1516 6549 0.834687 TACGGGTCCACTCAAAGCCT 60.835 55.000 0.00 0.00 0.00 4.58
1530 6563 3.057104 GTGTTTTTGGGGAAATCTACGGG 60.057 47.826 0.00 0.00 0.00 5.28
1540 6573 9.771534 CTATTTATTTTTCTGTGTTTTTGGGGA 57.228 29.630 0.00 0.00 0.00 4.81
1574 6607 5.828299 TTCTCTGTGTTTTTGGAAATCGT 57.172 34.783 0.00 0.00 0.00 3.73
1603 6636 7.747357 CGCGTACAGGAATTTTGTAAAAATACT 59.253 33.333 0.00 0.00 33.19 2.12
1604 6637 7.534918 ACGCGTACAGGAATTTTGTAAAAATAC 59.465 33.333 11.67 0.00 33.19 1.89
1605 6638 7.583230 ACGCGTACAGGAATTTTGTAAAAATA 58.417 30.769 11.67 0.00 33.19 1.40
1606 6639 6.440436 ACGCGTACAGGAATTTTGTAAAAAT 58.560 32.000 11.67 0.00 33.19 1.82
1607 6640 5.819059 ACGCGTACAGGAATTTTGTAAAAA 58.181 33.333 11.67 0.00 33.19 1.94
1608 6641 5.421212 ACGCGTACAGGAATTTTGTAAAA 57.579 34.783 11.67 0.00 33.19 1.52
1609 6642 5.421212 AACGCGTACAGGAATTTTGTAAA 57.579 34.783 14.46 0.00 33.19 2.01
1610 6643 5.421212 AAACGCGTACAGGAATTTTGTAA 57.579 34.783 14.46 0.00 33.19 2.41
1611 6644 4.083908 GGAAACGCGTACAGGAATTTTGTA 60.084 41.667 14.46 1.00 0.00 2.41
1612 6645 3.304190 GGAAACGCGTACAGGAATTTTGT 60.304 43.478 14.46 0.00 0.00 2.83
1613 6646 3.058501 AGGAAACGCGTACAGGAATTTTG 60.059 43.478 14.46 0.00 0.00 2.44
1614 6647 3.143728 AGGAAACGCGTACAGGAATTTT 58.856 40.909 14.46 0.00 0.00 1.82
1615 6648 2.774687 AGGAAACGCGTACAGGAATTT 58.225 42.857 14.46 0.00 0.00 1.82
1710 6743 2.240493 ATTAGGCCTCATTCGGTTCG 57.760 50.000 9.68 0.00 0.00 3.95
1905 6938 0.464036 ACTTGGTGCAGTTCTCGTCA 59.536 50.000 0.00 0.00 0.00 4.35
1922 6955 0.743097 GACTTCGTATGGGCGGTACT 59.257 55.000 0.00 0.00 0.00 2.73
2124 7157 4.453093 TGCTTGATGTGCACGTCA 57.547 50.000 32.80 32.80 39.88 4.35
2224 7275 1.076533 CCACCTGAAACCGATCGACG 61.077 60.000 18.66 2.80 42.18 5.12
2233 7284 2.946762 GCAGTCGCCACCTGAAAC 59.053 61.111 0.00 0.00 31.38 2.78
2341 7400 7.648039 AATATGAATCGGAGGGAGTAGTATC 57.352 40.000 0.00 0.00 0.00 2.24
2359 7420 6.345298 TCCATTTCAGCGACAAGTAATATGA 58.655 36.000 0.00 0.00 0.00 2.15
2409 7470 5.545658 TGATGAAACATTCGGCTTAAGAC 57.454 39.130 6.67 1.20 0.00 3.01
2492 7553 6.070596 AGTGTCCATCTTGATCTTGTGTATCA 60.071 38.462 0.00 0.00 0.00 2.15
2816 7908 2.559698 TCGGTTTCAGATTTCAGGCA 57.440 45.000 0.00 0.00 0.00 4.75
2818 7910 4.497006 GCATCATCGGTTTCAGATTTCAGG 60.497 45.833 0.00 0.00 0.00 3.86
2819 7911 4.095334 TGCATCATCGGTTTCAGATTTCAG 59.905 41.667 0.00 0.00 0.00 3.02
2820 7912 4.009002 TGCATCATCGGTTTCAGATTTCA 58.991 39.130 0.00 0.00 0.00 2.69
2821 7913 4.621068 TGCATCATCGGTTTCAGATTTC 57.379 40.909 0.00 0.00 0.00 2.17
2822 7914 5.587388 AATGCATCATCGGTTTCAGATTT 57.413 34.783 0.00 0.00 0.00 2.17
2831 7923 1.402968 GCAGTGAAATGCATCATCGGT 59.597 47.619 0.00 0.00 45.77 4.69
2863 7955 2.696989 TGGTGTCATCTGCTATGGTG 57.303 50.000 0.64 0.00 0.00 4.17
2864 7956 2.747467 GCATGGTGTCATCTGCTATGGT 60.747 50.000 0.00 0.00 0.00 3.55
2865 7957 1.878088 GCATGGTGTCATCTGCTATGG 59.122 52.381 0.00 0.00 0.00 2.74
2891 7983 2.949714 AACAAATTCAGAGACGTGCG 57.050 45.000 0.00 0.00 0.00 5.34
3098 8195 2.975536 CTTCCCGAACGCCTGGTA 59.024 61.111 0.00 0.00 0.00 3.25
3313 8413 5.770417 ACTCTAGACTTACGGACAAACTTG 58.230 41.667 0.00 0.00 0.00 3.16
3314 8414 6.402456 AACTCTAGACTTACGGACAAACTT 57.598 37.500 0.00 0.00 0.00 2.66
3316 8416 7.275123 CCAATAACTCTAGACTTACGGACAAAC 59.725 40.741 0.00 0.00 0.00 2.93
3350 8458 2.034179 CCGCACTGATTCGTCCTATACA 59.966 50.000 0.00 0.00 0.00 2.29
3351 8459 2.034305 ACCGCACTGATTCGTCCTATAC 59.966 50.000 0.00 0.00 0.00 1.47
3352 8460 2.304092 ACCGCACTGATTCGTCCTATA 58.696 47.619 0.00 0.00 0.00 1.31
3353 8461 1.112113 ACCGCACTGATTCGTCCTAT 58.888 50.000 0.00 0.00 0.00 2.57
3354 8462 0.892755 AACCGCACTGATTCGTCCTA 59.107 50.000 0.00 0.00 0.00 2.94
3355 8463 0.892755 TAACCGCACTGATTCGTCCT 59.107 50.000 0.00 0.00 0.00 3.85
3357 8465 2.268298 ACATAACCGCACTGATTCGTC 58.732 47.619 0.00 0.00 0.00 4.20
3359 8467 2.267426 TGACATAACCGCACTGATTCG 58.733 47.619 0.00 0.00 0.00 3.34
3360 8468 4.122776 AGATGACATAACCGCACTGATTC 58.877 43.478 0.00 0.00 0.00 2.52
3361 8469 4.142609 AGATGACATAACCGCACTGATT 57.857 40.909 0.00 0.00 0.00 2.57
3362 8470 3.827008 AGATGACATAACCGCACTGAT 57.173 42.857 0.00 0.00 0.00 2.90
3364 8472 3.261580 TCAAGATGACATAACCGCACTG 58.738 45.455 0.00 0.00 0.00 3.66
3365 8473 3.610040 TCAAGATGACATAACCGCACT 57.390 42.857 0.00 0.00 0.00 4.40
3366 8474 7.170828 TGTTATATCAAGATGACATAACCGCAC 59.829 37.037 15.22 0.00 42.83 5.34
3368 8476 7.652300 TGTTATATCAAGATGACATAACCGC 57.348 36.000 15.22 0.00 42.83 5.68
3417 8525 1.734163 AAACTTATGCCCCGTCTTCG 58.266 50.000 0.00 0.00 0.00 3.79
3421 8529 7.443272 AGTTGTATATAAAACTTATGCCCCGTC 59.557 37.037 11.89 0.00 32.75 4.79
3423 8531 7.739498 AGTTGTATATAAAACTTATGCCCCG 57.261 36.000 11.89 0.00 32.75 5.73
3425 8533 9.503399 AGCTAGTTGTATATAAAACTTATGCCC 57.497 33.333 20.87 6.37 37.74 5.36
3486 8600 7.441760 TGTTTTAAGCACTCATTGATGCATTTT 59.558 29.630 17.48 9.63 44.59 1.82
3556 8670 8.129211 GCAAAGAACACTCTTACATTTGTAGTT 58.871 33.333 0.00 0.00 41.23 2.24
3557 8671 7.499232 AGCAAAGAACACTCTTACATTTGTAGT 59.501 33.333 0.00 0.00 41.23 2.73
3558 8672 7.865707 AGCAAAGAACACTCTTACATTTGTAG 58.134 34.615 0.00 0.00 41.23 2.74
3635 8750 9.671279 ATGTCAAATTCAAAAGGTTCTTCTTTT 57.329 25.926 0.00 0.00 44.82 2.27
3704 8820 4.220602 GTGTTGGACCTTGGAGCAAATATT 59.779 41.667 0.00 0.00 0.00 1.28
3719 8837 3.249799 TCATGAACGACAATGTGTTGGAC 59.750 43.478 0.00 0.00 39.70 4.02
3720 8838 3.249799 GTCATGAACGACAATGTGTTGGA 59.750 43.478 0.00 0.00 39.70 3.53
3721 8839 3.003171 TGTCATGAACGACAATGTGTTGG 59.997 43.478 0.00 0.00 42.82 3.77
3763 8885 5.345702 GCATGCATGTTAGTCACAATTCAT 58.654 37.500 26.79 0.00 39.50 2.57
3775 8897 2.230992 GGAACACAAGGCATGCATGTTA 59.769 45.455 26.79 0.00 30.75 2.41
3788 8910 4.452825 TGTCTTTTATCACCGGAACACAA 58.547 39.130 9.46 0.00 0.00 3.33
3790 8912 4.671766 GCATGTCTTTTATCACCGGAACAC 60.672 45.833 9.46 0.00 0.00 3.32
3816 8938 1.022451 GGGCCGCGTTTATCAAGTCA 61.022 55.000 4.92 0.00 0.00 3.41
3817 8939 1.712018 GGGGCCGCGTTTATCAAGTC 61.712 60.000 3.09 0.00 0.00 3.01
3818 8940 1.747745 GGGGCCGCGTTTATCAAGT 60.748 57.895 3.09 0.00 0.00 3.16
3819 8941 2.478033 GGGGGCCGCGTTTATCAAG 61.478 63.158 14.44 0.00 0.00 3.02
3837 8959 2.416162 GGTCAAGTCGAGCAAGAGTAGG 60.416 54.545 0.00 0.00 41.98 3.18
3861 8983 3.094572 CCTGGCCAACATCAAAGAAGAT 58.905 45.455 7.01 0.00 0.00 2.40
3870 8992 1.097547 CATCCGACCTGGCCAACATC 61.098 60.000 7.01 3.46 37.80 3.06
3871 8993 1.077501 CATCCGACCTGGCCAACAT 60.078 57.895 7.01 0.00 37.80 2.71
3872 8994 2.350895 CATCCGACCTGGCCAACA 59.649 61.111 7.01 0.00 37.80 3.33
3873 8995 3.134127 GCATCCGACCTGGCCAAC 61.134 66.667 7.01 0.00 37.80 3.77
3874 8996 3.329542 GAGCATCCGACCTGGCCAA 62.330 63.158 7.01 0.00 37.80 4.52
3876 8998 4.899239 CGAGCATCCGACCTGGCC 62.899 72.222 0.00 0.00 37.80 5.36
3878 9000 1.079127 AAACGAGCATCCGACCTGG 60.079 57.895 0.00 0.00 40.09 4.45
3879 9001 1.084370 GGAAACGAGCATCCGACCTG 61.084 60.000 0.00 0.00 0.00 4.00
3880 9002 1.218316 GGAAACGAGCATCCGACCT 59.782 57.895 0.00 0.00 0.00 3.85
3881 9003 1.814169 GGGAAACGAGCATCCGACC 60.814 63.158 0.00 0.00 36.54 4.79
3882 9004 1.814169 GGGGAAACGAGCATCCGAC 60.814 63.158 0.00 0.00 36.54 4.79
3883 9005 2.582436 GGGGAAACGAGCATCCGA 59.418 61.111 0.00 0.00 36.54 4.55
3884 9006 2.890474 CGGGGAAACGAGCATCCG 60.890 66.667 0.00 0.00 36.54 4.18
3888 9010 1.906824 AGAGTCGGGGAAACGAGCA 60.907 57.895 0.00 0.00 44.42 4.26
3889 9011 1.446272 CAGAGTCGGGGAAACGAGC 60.446 63.158 0.00 0.00 44.42 5.03
3893 9015 2.046217 GGGCAGAGTCGGGGAAAC 60.046 66.667 0.00 0.00 0.00 2.78
3900 9022 1.671901 GGGAAGAGAGGGCAGAGTCG 61.672 65.000 0.00 0.00 0.00 4.18
3901 9023 1.671901 CGGGAAGAGAGGGCAGAGTC 61.672 65.000 0.00 0.00 0.00 3.36
3921 9043 2.125673 CGAAGGTAGTGCGGGTGG 60.126 66.667 0.00 0.00 0.00 4.61
3923 9045 2.643232 GGTCGAAGGTAGTGCGGGT 61.643 63.158 0.00 0.00 0.00 5.28
3924 9046 2.183555 GGTCGAAGGTAGTGCGGG 59.816 66.667 0.00 0.00 0.00 6.13
3926 9048 2.814183 AAGCGGTCGAAGGTAGTGCG 62.814 60.000 0.00 0.00 0.00 5.34
3927 9049 1.077089 GAAGCGGTCGAAGGTAGTGC 61.077 60.000 0.00 0.00 0.00 4.40
3928 9050 0.458025 GGAAGCGGTCGAAGGTAGTG 60.458 60.000 0.00 0.00 0.00 2.74
3929 9051 0.611340 AGGAAGCGGTCGAAGGTAGT 60.611 55.000 0.00 0.00 0.00 2.73
3930 9052 0.100861 GAGGAAGCGGTCGAAGGTAG 59.899 60.000 0.00 0.00 0.00 3.18
3931 9053 0.609957 TGAGGAAGCGGTCGAAGGTA 60.610 55.000 0.00 0.00 0.00 3.08
3932 9054 1.258445 ATGAGGAAGCGGTCGAAGGT 61.258 55.000 0.00 0.00 0.00 3.50
3934 9056 1.002366 CAATGAGGAAGCGGTCGAAG 58.998 55.000 0.00 0.00 0.00 3.79
3935 9057 0.320374 ACAATGAGGAAGCGGTCGAA 59.680 50.000 0.00 0.00 0.00 3.71
3936 9058 0.320374 AACAATGAGGAAGCGGTCGA 59.680 50.000 0.00 0.00 0.00 4.20
3937 9059 0.443869 CAACAATGAGGAAGCGGTCG 59.556 55.000 0.00 0.00 0.00 4.79
3938 9060 1.464997 GACAACAATGAGGAAGCGGTC 59.535 52.381 0.00 0.00 0.00 4.79
3939 9061 1.072331 AGACAACAATGAGGAAGCGGT 59.928 47.619 0.00 0.00 0.00 5.68
3941 9063 1.734465 GGAGACAACAATGAGGAAGCG 59.266 52.381 0.00 0.00 0.00 4.68
3942 9064 1.734465 CGGAGACAACAATGAGGAAGC 59.266 52.381 0.00 0.00 0.00 3.86
3952 9074 1.116308 TTGTGGAGACGGAGACAACA 58.884 50.000 0.00 0.00 0.00 3.33
3963 9085 5.419542 CCGACTATCAGATTTTTGTGGAGA 58.580 41.667 0.00 0.00 0.00 3.71
3978 9100 4.085517 CGAAGAAAAATCGAGCCGACTATC 60.086 45.833 0.00 0.00 42.76 2.08
3989 9111 4.790140 CCAAGCATTCTCGAAGAAAAATCG 59.210 41.667 2.21 0.00 37.82 3.34
3992 9114 3.305335 GGCCAAGCATTCTCGAAGAAAAA 60.305 43.478 0.00 0.00 37.82 1.94
4000 9122 0.465097 ATGAGGGCCAAGCATTCTCG 60.465 55.000 6.18 0.00 0.00 4.04
4014 9136 1.221781 AGGAGGAAGAGGGGTATGAGG 59.778 57.143 0.00 0.00 0.00 3.86
4017 9139 1.723288 GGAGGAGGAAGAGGGGTATG 58.277 60.000 0.00 0.00 0.00 2.39
4019 9141 0.858598 TGGGAGGAGGAAGAGGGGTA 60.859 60.000 0.00 0.00 0.00 3.69
4045 9169 0.319900 CGTGACACTCACCCAAGAGG 60.320 60.000 3.68 0.00 44.20 3.69
4048 9172 1.227527 TGCGTGACACTCACCCAAG 60.228 57.895 3.68 0.00 44.20 3.61
4066 9190 2.356313 CCACAGCAACGCGAGAGT 60.356 61.111 15.93 4.59 0.00 3.24
4084 9208 3.311110 TCTGGGAGGTGCGGTCAC 61.311 66.667 0.00 0.00 42.40 3.67
4086 9210 4.436998 CGTCTGGGAGGTGCGGTC 62.437 72.222 0.00 0.00 0.00 4.79
4099 9232 4.265056 AAACCTTGGCCGCCGTCT 62.265 61.111 4.58 0.00 0.00 4.18
4143 9278 9.606631 ACCACAAATTTGCAGTTATTAAAGAAA 57.393 25.926 18.12 0.00 0.00 2.52
4146 9281 7.655328 TCCACCACAAATTTGCAGTTATTAAAG 59.345 33.333 18.12 2.60 0.00 1.85
4147 9282 7.500992 TCCACCACAAATTTGCAGTTATTAAA 58.499 30.769 18.12 0.00 0.00 1.52
4149 9284 6.656632 TCCACCACAAATTTGCAGTTATTA 57.343 33.333 18.12 0.00 0.00 0.98
4151 9286 5.743636 ATCCACCACAAATTTGCAGTTAT 57.256 34.783 18.12 8.51 0.00 1.89
4152 9287 5.543507 AATCCACCACAAATTTGCAGTTA 57.456 34.783 18.12 6.74 0.00 2.24
4153 9288 4.420522 AATCCACCACAAATTTGCAGTT 57.579 36.364 18.12 0.00 0.00 3.16
4154 9289 4.128643 CAAATCCACCACAAATTTGCAGT 58.871 39.130 18.12 12.40 34.65 4.40
4155 9290 4.378774 TCAAATCCACCACAAATTTGCAG 58.621 39.130 18.12 11.76 39.24 4.41
4161 9296 6.214005 AGAAATCCATCAAATCCACCACAAAT 59.786 34.615 0.00 0.00 0.00 2.32
4168 9303 7.605449 TCTTCAAAGAAATCCATCAAATCCAC 58.395 34.615 0.00 0.00 30.73 4.02
4191 9326 3.036819 TGCACATAAGAGGCAGATCTCT 58.963 45.455 0.00 0.00 45.22 3.10
4192 9327 3.465742 TGCACATAAGAGGCAGATCTC 57.534 47.619 0.00 0.00 32.95 2.75
4198 9333 2.158856 CCTCATCTGCACATAAGAGGCA 60.159 50.000 0.00 0.00 36.58 4.75
4199 9334 2.158842 ACCTCATCTGCACATAAGAGGC 60.159 50.000 7.89 0.00 44.98 4.70
4200 9335 3.726607 GACCTCATCTGCACATAAGAGG 58.273 50.000 6.75 6.75 46.18 3.69
4201 9336 3.181482 ACGACCTCATCTGCACATAAGAG 60.181 47.826 0.00 0.00 0.00 2.85
4202 9337 2.760650 ACGACCTCATCTGCACATAAGA 59.239 45.455 0.00 0.00 0.00 2.10
4203 9338 2.862536 CACGACCTCATCTGCACATAAG 59.137 50.000 0.00 0.00 0.00 1.73
4204 9339 2.892374 CACGACCTCATCTGCACATAA 58.108 47.619 0.00 0.00 0.00 1.90
4205 9340 1.471501 GCACGACCTCATCTGCACATA 60.472 52.381 0.00 0.00 33.88 2.29
4206 9341 0.742281 GCACGACCTCATCTGCACAT 60.742 55.000 0.00 0.00 33.88 3.21
4207 9342 1.374631 GCACGACCTCATCTGCACA 60.375 57.895 0.00 0.00 33.88 4.57
4208 9343 1.079543 AGCACGACCTCATCTGCAC 60.080 57.895 0.00 0.00 35.26 4.57
4209 9344 1.216444 GAGCACGACCTCATCTGCA 59.784 57.895 0.00 0.00 35.26 4.41
4210 9345 1.520342 GGAGCACGACCTCATCTGC 60.520 63.158 8.79 0.00 33.47 4.26
4211 9346 0.463204 ATGGAGCACGACCTCATCTG 59.537 55.000 8.79 0.00 33.47 2.90
4212 9347 0.463204 CATGGAGCACGACCTCATCT 59.537 55.000 8.79 0.00 33.47 2.90
4213 9348 1.156645 GCATGGAGCACGACCTCATC 61.157 60.000 0.00 0.00 44.79 2.92
4214 9349 1.153289 GCATGGAGCACGACCTCAT 60.153 57.895 0.00 0.00 44.79 2.90
4215 9350 2.265739 GCATGGAGCACGACCTCA 59.734 61.111 0.00 0.00 44.79 3.86
4224 9359 2.459442 GCGAGTGTCAGCATGGAGC 61.459 63.158 0.00 0.00 46.19 4.70
4225 9360 1.812922 GGCGAGTGTCAGCATGGAG 60.813 63.158 0.00 0.00 36.16 3.86
4226 9361 2.265739 GGCGAGTGTCAGCATGGA 59.734 61.111 0.00 0.00 36.16 3.41
4227 9362 2.046988 TGGCGAGTGTCAGCATGG 60.047 61.111 0.00 0.00 36.16 3.66


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

AutoCloner maintained by Alex Coulton.