Multiple sequence alignment - TraesCS1A01G086100

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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 TraesCS1A01G086100 chr1A 100.000 4926 0 0 1 4926 72786848 72781923 0.000000e+00 9097.0
1 TraesCS1A01G086100 chr1A 100.000 35 0 0 143 177 294516546 294516512 1.140000e-06 65.8
2 TraesCS1A01G086100 chr1B 92.032 2121 116 21 2838 4926 115280461 115278362 0.000000e+00 2931.0
3 TraesCS1A01G086100 chr1B 89.436 2073 149 40 361 2408 115282932 115280905 0.000000e+00 2551.0
4 TraesCS1A01G086100 chr1B 93.249 237 14 1 166 400 115283209 115282973 1.010000e-91 348.0
5 TraesCS1A01G086100 chr1B 84.848 231 18 9 2527 2745 115280903 115280678 2.990000e-52 217.0
6 TraesCS1A01G086100 chr1B 88.235 153 10 5 1 150 115283414 115283267 5.070000e-40 176.0
7 TraesCS1A01G086100 chr1D 92.842 1886 69 19 3067 4926 72904823 72902978 0.000000e+00 2675.0
8 TraesCS1A01G086100 chr1D 91.602 1798 83 26 624 2407 72907381 72905638 0.000000e+00 2422.0
9 TraesCS1A01G086100 chr1D 85.684 950 87 20 1479 2408 73053341 73052421 0.000000e+00 955.0
10 TraesCS1A01G086100 chr1D 90.282 319 28 1 1076 1394 73054415 73054100 9.870000e-112 414.0
11 TraesCS1A01G086100 chr1D 89.730 185 18 1 3311 3495 73051514 73051331 8.240000e-58 235.0
12 TraesCS1A01G086100 chr1D 87.379 206 17 5 414 615 72907630 72907430 1.380000e-55 228.0
13 TraesCS1A01G086100 chr1D 79.730 222 32 8 743 959 73054677 73054464 1.100000e-31 148.0
14 TraesCS1A01G086100 chr1D 100.000 37 0 0 2941 2977 72904859 72904823 8.850000e-08 69.4
15 TraesCS1A01G086100 chr1D 97.436 39 1 0 368 406 72907990 72907952 3.180000e-07 67.6
16 TraesCS1A01G086100 chr5A 95.690 116 5 0 2398 2513 547790010 547790125 2.340000e-43 187.0
17 TraesCS1A01G086100 chr5A 92.562 121 8 1 2404 2524 77990695 77990814 6.560000e-39 172.0
18 TraesCS1A01G086100 chr5A 89.706 136 8 5 2384 2513 26132677 26132542 8.480000e-38 169.0
19 TraesCS1A01G086100 chr3D 96.460 113 3 1 2401 2513 143958725 143958614 8.420000e-43 185.0
20 TraesCS1A01G086100 chr3D 94.783 115 6 0 2399 2513 606889401 606889287 3.920000e-41 180.0
21 TraesCS1A01G086100 chr3D 90.476 42 3 1 143 184 535746916 535746956 2.000000e-03 54.7
22 TraesCS1A01G086100 chr3A 94.828 116 6 0 2398 2513 256934804 256934689 1.090000e-41 182.0
23 TraesCS1A01G086100 chr3A 97.222 36 1 0 140 175 516893459 516893424 1.480000e-05 62.1
24 TraesCS1A01G086100 chrUn 95.536 112 5 0 2402 2513 103936306 103936195 3.920000e-41 180.0
25 TraesCS1A01G086100 chr5B 94.783 115 5 1 2403 2516 678648681 678648567 1.410000e-40 178.0
26 TraesCS1A01G086100 chr5B 89.630 135 9 5 2407 2537 493017649 493017782 3.050000e-37 167.0
27 TraesCS1A01G086100 chr2D 90.741 54 1 2 143 193 447497009 447497061 8.850000e-08 69.4
28 TraesCS1A01G086100 chr4A 95.349 43 1 1 143 185 416231475 416231516 3.180000e-07 67.6
29 TraesCS1A01G086100 chr7A 100.000 35 0 0 143 177 48110398 48110432 1.140000e-06 65.8
30 TraesCS1A01G086100 chr7A 95.000 40 0 2 143 180 25411030 25410991 1.480000e-05 62.1
31 TraesCS1A01G086100 chr6D 100.000 35 0 0 1932 1966 305277379 305277413 1.140000e-06 65.8
32 TraesCS1A01G086100 chr6B 100.000 35 0 0 1932 1966 471307694 471307660 1.140000e-06 65.8
33 TraesCS1A01G086100 chr7D 97.222 36 1 0 143 178 4020186 4020221 1.480000e-05 62.1
34 TraesCS1A01G086100 chr6A 92.857 42 2 1 143 183 41580164 41580123 5.330000e-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 TraesCS1A01G086100 chr1A 72781923 72786848 4925 True 9097.0 9097 100.0000 1 4926 1 chr1A.!!$R1 4925
1 TraesCS1A01G086100 chr1B 115278362 115283414 5052 True 1244.6 2931 89.5600 1 4926 5 chr1B.!!$R1 4925
2 TraesCS1A01G086100 chr1D 72902978 72907990 5012 True 1092.4 2675 93.8518 368 4926 5 chr1D.!!$R1 4558
3 TraesCS1A01G086100 chr1D 73051331 73054677 3346 True 438.0 955 86.3565 743 3495 4 chr1D.!!$R2 2752

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
412 457 0.107654 CCATGTCCTTTCCCTCGACC 60.108 60.0 0.00 0.0 0.00 4.79 F
619 1087 0.179129 CCGCATGGAAAATCACCAGC 60.179 55.0 0.00 0.0 40.89 4.85 F
1421 2638 0.233332 GCTATTGCTTGATCGACGGC 59.767 55.0 0.00 0.0 36.03 5.68 F
2490 3727 0.175989 TACATCCATACGTGCGGCAA 59.824 50.0 3.23 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 3305 0.471591 AAAAAGCAGCATGGGGGACA 60.472 50.0 0.00 0.0 35.86 4.02 R
2471 3708 0.175989 TTGCCGCACGTATGGATGTA 59.824 50.0 9.30 0.0 0.00 2.29 R
3155 4960 0.229753 CTGCGGACGCGAATTATGTC 59.770 55.0 15.93 0.0 45.51 3.06 R
4191 6055 0.036577 GTGAGTGCAGCTCCTGTCAT 60.037 55.0 11.99 0.0 43.48 3.06 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
85 86 5.670485 ACATATGTCGTGCCTTGAAGATTA 58.330 37.500 1.41 0.00 0.00 1.75
144 145 2.869233 ATTGTTGCAACTGTGGTGAC 57.131 45.000 28.61 1.56 0.00 3.67
146 147 0.391793 TGTTGCAACTGTGGTGACGA 60.392 50.000 28.61 2.96 0.00 4.20
150 151 1.137282 TGCAACTGTGGTGACGAGTAA 59.863 47.619 0.00 0.00 0.00 2.24
151 152 2.224185 TGCAACTGTGGTGACGAGTAAT 60.224 45.455 0.00 0.00 0.00 1.89
152 153 2.806244 GCAACTGTGGTGACGAGTAATT 59.194 45.455 0.00 0.00 0.00 1.40
153 154 3.250040 GCAACTGTGGTGACGAGTAATTT 59.750 43.478 0.00 0.00 0.00 1.82
154 155 4.772434 CAACTGTGGTGACGAGTAATTTG 58.228 43.478 0.00 0.00 0.00 2.32
155 156 3.399330 ACTGTGGTGACGAGTAATTTGG 58.601 45.455 0.00 0.00 0.00 3.28
156 157 3.070446 ACTGTGGTGACGAGTAATTTGGA 59.930 43.478 0.00 0.00 0.00 3.53
158 159 3.810941 TGTGGTGACGAGTAATTTGGAAC 59.189 43.478 0.00 0.00 0.00 3.62
159 160 3.061322 TGGTGACGAGTAATTTGGAACG 58.939 45.455 0.00 0.00 0.00 3.95
160 161 2.414138 GGTGACGAGTAATTTGGAACGG 59.586 50.000 0.00 0.00 0.00 4.44
161 162 3.319755 GTGACGAGTAATTTGGAACGGA 58.680 45.455 0.00 0.00 0.00 4.69
162 163 3.367025 GTGACGAGTAATTTGGAACGGAG 59.633 47.826 0.00 0.00 0.00 4.63
163 164 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
175 218 3.245371 TGGAACGGAGGGAGTAGTTTCTA 60.245 47.826 0.00 0.00 0.00 2.10
203 246 7.867305 TTATACCAATTTCCTTCATGCGTAA 57.133 32.000 0.00 0.00 0.00 3.18
214 257 6.816136 TCCTTCATGCGTAATTCATCTAAGA 58.184 36.000 0.00 0.00 0.00 2.10
253 296 0.611618 AGCAATGCACGGGGAAATCA 60.612 50.000 8.35 0.00 0.00 2.57
259 302 1.429148 GCACGGGGAAATCACTAGCG 61.429 60.000 0.00 0.00 0.00 4.26
266 309 2.548480 GGGAAATCACTAGCGGTTATGC 59.452 50.000 0.00 0.00 0.00 3.14
272 315 3.202906 TCACTAGCGGTTATGCAAATCC 58.797 45.455 0.00 0.00 37.31 3.01
340 385 8.468720 AAGTAGAAGAGAAAGATTAGAAACGC 57.531 34.615 0.00 0.00 0.00 4.84
351 396 5.298347 AGATTAGAAACGCACTATTAGCCC 58.702 41.667 0.00 0.00 0.00 5.19
406 451 5.373812 TCTTATCTTCCATGTCCTTTCCC 57.626 43.478 0.00 0.00 0.00 3.97
407 452 5.039645 TCTTATCTTCCATGTCCTTTCCCT 58.960 41.667 0.00 0.00 0.00 4.20
408 453 3.941704 ATCTTCCATGTCCTTTCCCTC 57.058 47.619 0.00 0.00 0.00 4.30
410 455 1.555075 CTTCCATGTCCTTTCCCTCGA 59.445 52.381 0.00 0.00 0.00 4.04
412 457 0.107654 CCATGTCCTTTCCCTCGACC 60.108 60.000 0.00 0.00 0.00 4.79
456 908 6.378280 ACAATGTCACAATCCTTCCCTTAATC 59.622 38.462 0.00 0.00 0.00 1.75
466 918 8.633561 CAATCCTTCCCTTAATCTATTGTTTCC 58.366 37.037 0.00 0.00 0.00 3.13
469 921 6.038271 CCTTCCCTTAATCTATTGTTTCCGTG 59.962 42.308 0.00 0.00 0.00 4.94
479 934 1.782044 TGTTTCCGTGGTAGTTACGC 58.218 50.000 0.00 0.00 40.04 4.42
489 944 4.599047 GTGGTAGTTACGCTGATACTCTG 58.401 47.826 0.00 0.00 0.00 3.35
493 948 2.159226 AGTTACGCTGATACTCTGTGCC 60.159 50.000 0.00 0.00 30.32 5.01
509 964 1.818060 GTGCCCACTCACAATGCATAA 59.182 47.619 0.00 0.00 36.97 1.90
510 965 2.428171 GTGCCCACTCACAATGCATAAT 59.572 45.455 0.00 0.00 36.97 1.28
511 966 2.427812 TGCCCACTCACAATGCATAATG 59.572 45.455 0.00 1.14 0.00 1.90
514 969 4.381825 GCCCACTCACAATGCATAATGAAA 60.382 41.667 12.49 0.00 0.00 2.69
515 970 5.104374 CCCACTCACAATGCATAATGAAAC 58.896 41.667 12.49 0.00 0.00 2.78
516 971 5.336610 CCCACTCACAATGCATAATGAAACA 60.337 40.000 12.49 0.00 0.00 2.83
519 974 7.009815 CCACTCACAATGCATAATGAAACATTC 59.990 37.037 12.49 0.00 30.54 2.67
536 991 9.959749 TGAAACATTCTTACATTAAAAGACACC 57.040 29.630 0.00 0.00 32.81 4.16
539 994 7.593825 ACATTCTTACATTAAAAGACACCAGC 58.406 34.615 0.00 0.00 32.81 4.85
573 1031 7.591006 TCGTATCCTTTCTTTCATACACAAC 57.409 36.000 0.00 0.00 0.00 3.32
574 1032 6.592607 TCGTATCCTTTCTTTCATACACAACC 59.407 38.462 0.00 0.00 0.00 3.77
584 1042 5.461032 TTCATACACAACCCATCCAAAAC 57.539 39.130 0.00 0.00 0.00 2.43
587 1045 2.038659 ACACAACCCATCCAAAACCAG 58.961 47.619 0.00 0.00 0.00 4.00
598 1056 6.873605 CCCATCCAAAACCAGTCTTTTAAATC 59.126 38.462 0.00 0.00 0.00 2.17
616 1084 0.682855 TCCCCGCATGGAAAATCACC 60.683 55.000 0.00 0.00 37.49 4.02
619 1087 0.179129 CCGCATGGAAAATCACCAGC 60.179 55.000 0.00 0.00 40.89 4.85
622 1090 2.797087 CGCATGGAAAATCACCAGCATC 60.797 50.000 0.00 0.00 40.89 3.91
630 1144 8.169977 TGGAAAATCACCAGCATCTAATATTC 57.830 34.615 0.00 0.00 33.22 1.75
640 1154 9.686683 ACCAGCATCTAATATTCATATAAACCC 57.313 33.333 0.00 0.00 0.00 4.11
669 1187 4.557605 CACGCGCCAATCATGCCC 62.558 66.667 5.73 0.00 0.00 5.36
696 1214 3.273919 AGAAACGAAATCACAAGCTGC 57.726 42.857 0.00 0.00 0.00 5.25
702 1220 1.888512 GAAATCACAAGCTGCCCAGAA 59.111 47.619 0.00 0.00 0.00 3.02
723 1241 1.186917 TTGCTTCCAGGCAACCCATG 61.187 55.000 0.00 0.00 45.64 3.66
741 1259 3.480470 CATGCGGTTTCTTATCCTCCAT 58.520 45.455 0.00 0.00 0.00 3.41
834 1352 1.939597 CGGTCACGCTAGCTCGATA 59.060 57.895 13.93 0.00 0.00 2.92
852 1370 8.680903 AGCTCGATAAAACTGAAATCAATCAAT 58.319 29.630 0.00 0.00 0.00 2.57
862 1380 8.997621 ACTGAAATCAATCAATCATCAAAAGG 57.002 30.769 0.00 0.00 0.00 3.11
914 1432 1.532298 GGTCCAAACCAAACAACGACG 60.532 52.381 0.00 0.00 45.68 5.12
938 1461 7.282450 ACGTCAATCAAACCCTCTATTTATTCC 59.718 37.037 0.00 0.00 0.00 3.01
959 1482 0.460311 ACCGTATTCCCGCTTCTCTG 59.540 55.000 0.00 0.00 0.00 3.35
968 1491 4.863984 GCTTCTCTGCAAGCAAGC 57.136 55.556 3.21 5.46 46.93 4.01
969 1492 1.954528 GCTTCTCTGCAAGCAAGCA 59.045 52.632 15.07 3.03 46.93 3.91
970 1493 0.313043 GCTTCTCTGCAAGCAAGCAA 59.687 50.000 15.07 0.00 46.93 3.91
971 1494 1.666311 GCTTCTCTGCAAGCAAGCAAG 60.666 52.381 15.07 6.81 46.93 4.01
978 1502 1.650912 CAAGCAAGCAAGCGACTGT 59.349 52.632 0.00 0.00 40.15 3.55
980 1504 0.868406 AAGCAAGCAAGCGACTGTAC 59.132 50.000 0.00 0.00 40.15 2.90
1000 1524 4.150897 ACCACAGTTTCTTCAGTAAGCA 57.849 40.909 0.00 0.00 32.36 3.91
1001 1525 4.718961 ACCACAGTTTCTTCAGTAAGCAT 58.281 39.130 0.00 0.00 32.36 3.79
1002 1526 4.516698 ACCACAGTTTCTTCAGTAAGCATG 59.483 41.667 0.00 0.00 32.36 4.06
1227 1760 0.928922 CGCTGTTCTATCTGCTGCAG 59.071 55.000 23.31 23.31 0.00 4.41
1421 2638 0.233332 GCTATTGCTTGATCGACGGC 59.767 55.000 0.00 0.00 36.03 5.68
1441 2659 2.159462 GCAGCTCACTGTTTTATCTGCC 60.159 50.000 0.00 0.00 46.30 4.85
1477 2695 3.613910 CGGGGAATGAATTGTGAACAACC 60.614 47.826 0.00 0.00 38.86 3.77
1542 2760 1.418637 GGTTCTCCTACACCAACACCA 59.581 52.381 0.00 0.00 32.74 4.17
1574 2792 4.003788 ACCTCCGGCGACAACAGG 62.004 66.667 9.30 7.85 0.00 4.00
1611 2829 2.747855 CCTTCCTGGCGAAGTGGC 60.748 66.667 0.00 0.00 45.75 5.01
1644 2862 1.400990 GCACTACAAGTACCGCGACG 61.401 60.000 8.23 0.00 0.00 5.12
1846 3076 0.389948 GACACCTACCAACGCCTCAG 60.390 60.000 0.00 0.00 0.00 3.35
1982 3212 1.352156 GCAACATCACCTCGTCGTCC 61.352 60.000 0.00 0.00 0.00 4.79
1985 3215 1.313812 ACATCACCTCGTCGTCCTCC 61.314 60.000 0.00 0.00 0.00 4.30
1987 3217 0.748729 ATCACCTCGTCGTCCTCCTC 60.749 60.000 0.00 0.00 0.00 3.71
1988 3218 2.045143 ACCTCGTCGTCCTCCTCC 60.045 66.667 0.00 0.00 0.00 4.30
1989 3219 2.272797 CCTCGTCGTCCTCCTCCT 59.727 66.667 0.00 0.00 0.00 3.69
1991 3221 1.820481 CTCGTCGTCCTCCTCCTCC 60.820 68.421 0.00 0.00 0.00 4.30
1992 3222 2.260088 CTCGTCGTCCTCCTCCTCCT 62.260 65.000 0.00 0.00 0.00 3.69
1994 3224 1.454295 GTCGTCCTCCTCCTCCTCC 60.454 68.421 0.00 0.00 0.00 4.30
1995 3225 1.619975 TCGTCCTCCTCCTCCTCCT 60.620 63.158 0.00 0.00 0.00 3.69
1996 3226 1.152839 CGTCCTCCTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
2010 3240 1.970352 CTCCTCCTCCTTGAGCCAGC 61.970 65.000 0.00 0.00 0.00 4.85
2011 3241 2.296365 CCTCCTCCTTGAGCCAGCA 61.296 63.158 0.00 0.00 0.00 4.41
2012 3242 1.681666 CTCCTCCTTGAGCCAGCAA 59.318 57.895 0.00 0.00 0.00 3.91
2096 3333 0.248289 CCCCCATGCTGCTTTTTGAG 59.752 55.000 0.00 0.00 0.00 3.02
2114 3351 3.335534 GTGACGAAACGCCGTGCT 61.336 61.111 0.00 0.00 43.49 4.40
2249 3486 1.734707 GCGCTATGAACTACACGTGGT 60.735 52.381 21.57 6.02 0.00 4.16
2366 3603 2.768527 TGGGTCTTCAGGTCAGATCATC 59.231 50.000 0.00 0.00 0.00 2.92
2370 3607 3.036819 TCTTCAGGTCAGATCATCCCTG 58.963 50.000 14.96 14.96 44.74 4.45
2371 3608 1.126488 TCAGGTCAGATCATCCCTGC 58.874 55.000 15.87 0.00 43.38 4.85
2408 3645 6.194796 TGCATTCCAGCATTTCTTAACTAC 57.805 37.500 0.00 0.00 40.11 2.73
2409 3646 5.945784 TGCATTCCAGCATTTCTTAACTACT 59.054 36.000 0.00 0.00 40.11 2.57
2410 3647 6.094048 TGCATTCCAGCATTTCTTAACTACTC 59.906 38.462 0.00 0.00 40.11 2.59
2411 3648 6.458888 GCATTCCAGCATTTCTTAACTACTCC 60.459 42.308 0.00 0.00 0.00 3.85
2412 3649 5.099042 TCCAGCATTTCTTAACTACTCCC 57.901 43.478 0.00 0.00 0.00 4.30
2413 3650 4.783227 TCCAGCATTTCTTAACTACTCCCT 59.217 41.667 0.00 0.00 0.00 4.20
2414 3651 5.104900 TCCAGCATTTCTTAACTACTCCCTC 60.105 44.000 0.00 0.00 0.00 4.30
2415 3652 5.119694 CAGCATTTCTTAACTACTCCCTCC 58.880 45.833 0.00 0.00 0.00 4.30
2416 3653 4.120589 GCATTTCTTAACTACTCCCTCCG 58.879 47.826 0.00 0.00 0.00 4.63
2417 3654 4.382793 GCATTTCTTAACTACTCCCTCCGT 60.383 45.833 0.00 0.00 0.00 4.69
2418 3655 5.731591 CATTTCTTAACTACTCCCTCCGTT 58.268 41.667 0.00 0.00 0.00 4.44
2419 3656 5.397142 TTTCTTAACTACTCCCTCCGTTC 57.603 43.478 0.00 0.00 0.00 3.95
2420 3657 3.359950 TCTTAACTACTCCCTCCGTTCC 58.640 50.000 0.00 0.00 0.00 3.62
2421 3658 2.905415 TAACTACTCCCTCCGTTCCA 57.095 50.000 0.00 0.00 0.00 3.53
2422 3659 2.019807 AACTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
2423 3660 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
2424 3661 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
2425 3662 2.910977 ACTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
2426 3663 4.098894 ACTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
2427 3664 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2428 3665 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2429 3666 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2430 3667 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2431 3668 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2432 3669 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2433 3670 3.581755 CTCCGTTCCAAATTACTCGTCA 58.418 45.455 0.00 0.00 0.00 4.35
2434 3671 3.319755 TCCGTTCCAAATTACTCGTCAC 58.680 45.455 0.00 0.00 0.00 3.67
2435 3672 3.061322 CCGTTCCAAATTACTCGTCACA 58.939 45.455 0.00 0.00 0.00 3.58
2436 3673 3.122948 CCGTTCCAAATTACTCGTCACAG 59.877 47.826 0.00 0.00 0.00 3.66
2437 3674 3.985279 CGTTCCAAATTACTCGTCACAGA 59.015 43.478 0.00 0.00 0.00 3.41
2438 3675 4.446385 CGTTCCAAATTACTCGTCACAGAA 59.554 41.667 0.00 0.00 0.00 3.02
2439 3676 5.050634 CGTTCCAAATTACTCGTCACAGAAA 60.051 40.000 0.00 0.00 0.00 2.52
2440 3677 6.347402 CGTTCCAAATTACTCGTCACAGAAAT 60.347 38.462 0.00 0.00 0.00 2.17
2441 3678 7.148705 CGTTCCAAATTACTCGTCACAGAAATA 60.149 37.037 0.00 0.00 0.00 1.40
2442 3679 7.827819 TCCAAATTACTCGTCACAGAAATAG 57.172 36.000 0.00 0.00 0.00 1.73
2443 3680 7.608153 TCCAAATTACTCGTCACAGAAATAGA 58.392 34.615 0.00 0.00 0.00 1.98
2444 3681 8.258007 TCCAAATTACTCGTCACAGAAATAGAT 58.742 33.333 0.00 0.00 0.00 1.98
2445 3682 8.331022 CCAAATTACTCGTCACAGAAATAGATG 58.669 37.037 0.00 0.00 0.00 2.90
2446 3683 8.873830 CAAATTACTCGTCACAGAAATAGATGT 58.126 33.333 0.00 0.00 0.00 3.06
2449 3686 9.900710 ATTACTCGTCACAGAAATAGATGTATC 57.099 33.333 0.00 0.00 0.00 2.24
2450 3687 7.575414 ACTCGTCACAGAAATAGATGTATCT 57.425 36.000 0.00 0.00 40.86 1.98
2451 3688 8.678593 ACTCGTCACAGAAATAGATGTATCTA 57.321 34.615 4.22 4.22 43.00 1.98
2452 3689 8.779303 ACTCGTCACAGAAATAGATGTATCTAG 58.221 37.037 7.57 0.00 42.20 2.43
2453 3690 8.904099 TCGTCACAGAAATAGATGTATCTAGA 57.096 34.615 7.57 0.00 42.20 2.43
2454 3691 9.338622 TCGTCACAGAAATAGATGTATCTAGAA 57.661 33.333 0.00 0.00 42.20 2.10
2455 3692 9.388346 CGTCACAGAAATAGATGTATCTAGAAC 57.612 37.037 0.00 0.00 42.20 3.01
2485 3722 5.955488 ACATCTAGATACATCCATACGTGC 58.045 41.667 4.54 0.00 0.00 5.34
2486 3723 4.680171 TCTAGATACATCCATACGTGCG 57.320 45.455 0.00 0.00 0.00 5.34
2487 3724 2.724977 AGATACATCCATACGTGCGG 57.275 50.000 0.00 0.00 0.00 5.69
2488 3725 1.068474 GATACATCCATACGTGCGGC 58.932 55.000 0.00 0.00 0.00 6.53
2489 3726 0.391228 ATACATCCATACGTGCGGCA 59.609 50.000 0.00 0.00 0.00 5.69
2490 3727 0.175989 TACATCCATACGTGCGGCAA 59.824 50.000 3.23 0.00 0.00 4.52
2491 3728 1.089481 ACATCCATACGTGCGGCAAG 61.089 55.000 14.35 14.35 0.00 4.01
2492 3729 1.089481 CATCCATACGTGCGGCAAGT 61.089 55.000 23.95 23.95 0.00 3.16
2493 3730 0.462375 ATCCATACGTGCGGCAAGTA 59.538 50.000 26.39 26.39 33.49 2.24
2494 3731 0.246910 TCCATACGTGCGGCAAGTAA 59.753 50.000 27.54 12.62 32.82 2.24
2495 3732 1.134640 TCCATACGTGCGGCAAGTAAT 60.135 47.619 27.54 15.73 32.82 1.89
2496 3733 1.668751 CCATACGTGCGGCAAGTAATT 59.331 47.619 27.54 13.27 32.82 1.40
2497 3734 2.286184 CCATACGTGCGGCAAGTAATTC 60.286 50.000 27.54 3.82 32.82 2.17
2498 3735 0.993532 TACGTGCGGCAAGTAATTCG 59.006 50.000 23.16 14.49 0.00 3.34
2499 3736 1.060308 CGTGCGGCAAGTAATTCGG 59.940 57.895 3.23 0.00 0.00 4.30
2500 3737 1.355796 CGTGCGGCAAGTAATTCGGA 61.356 55.000 3.23 0.00 0.00 4.55
2501 3738 0.800012 GTGCGGCAAGTAATTCGGAA 59.200 50.000 3.23 0.00 0.00 4.30
2502 3739 0.800012 TGCGGCAAGTAATTCGGAAC 59.200 50.000 0.00 0.00 0.00 3.62
2560 3847 1.808411 ACTACACATTTGCTCCGGTG 58.192 50.000 0.00 0.00 37.29 4.94
2561 3848 0.447801 CTACACATTTGCTCCGGTGC 59.552 55.000 21.41 21.41 34.69 5.01
2592 3882 3.049708 ACTGTTTCGCTAGGGTAAACC 57.950 47.619 21.03 0.00 40.67 3.27
2619 4049 4.593597 TTCTGACGAAATTTGCGGATAC 57.406 40.909 1.15 0.00 0.00 2.24
2632 4062 5.545063 TTGCGGATACTTCATCAGGAATA 57.455 39.130 0.00 0.00 35.00 1.75
2678 4108 2.679450 GCGTATGCATCGGGTTATACA 58.321 47.619 0.19 0.00 42.15 2.29
2732 4164 8.449397 TGTCTTGAATTTTTGGACATTTTGTTG 58.551 29.630 0.00 0.00 32.91 3.33
2745 4177 8.428063 TGGACATTTTGTTGTCTTCCATTTTAT 58.572 29.630 4.75 0.00 44.39 1.40
2753 4185 7.747888 TGTTGTCTTCCATTTTATACATGACG 58.252 34.615 0.00 0.00 0.00 4.35
2755 4187 7.915293 TGTCTTCCATTTTATACATGACGTT 57.085 32.000 0.00 0.00 0.00 3.99
2756 4188 7.970384 TGTCTTCCATTTTATACATGACGTTC 58.030 34.615 0.00 0.00 0.00 3.95
2762 4397 8.503196 TCCATTTTATACATGACGTTCATATGC 58.497 33.333 0.00 0.00 34.28 3.14
2802 4445 4.942852 TGAATTGATTGGTTGTTGTGGAC 58.057 39.130 0.00 0.00 0.00 4.02
2810 4453 3.542648 TGGTTGTTGTGGACGTTGATAA 58.457 40.909 0.00 0.00 0.00 1.75
2835 4479 8.785329 ATTTTTCCATATAAATTTGGCGTTGT 57.215 26.923 0.00 0.00 32.80 3.32
2900 4603 7.719778 AAACGTACCTACCTACTTTTTGAAG 57.280 36.000 0.00 0.00 0.00 3.02
2905 4608 8.829612 CGTACCTACCTACTTTTTGAAGAAAAA 58.170 33.333 0.00 0.00 38.47 1.94
2930 4633 4.380531 ACAGTACTGAATGACAACAGGTG 58.619 43.478 29.30 11.42 38.30 4.00
2989 4790 4.134563 TCAGCCAGTTAACAAGAGAAACC 58.865 43.478 8.61 0.00 0.00 3.27
3013 4814 5.306532 CAGATAATGCACTGCTTTGACTT 57.693 39.130 11.47 0.00 0.00 3.01
3015 4816 6.845302 CAGATAATGCACTGCTTTGACTTAA 58.155 36.000 11.47 0.00 0.00 1.85
3019 4820 5.710513 ATGCACTGCTTTGACTTAATGAA 57.289 34.783 1.98 0.00 0.00 2.57
3020 4821 4.858935 TGCACTGCTTTGACTTAATGAAC 58.141 39.130 1.98 0.00 0.00 3.18
3021 4822 4.580167 TGCACTGCTTTGACTTAATGAACT 59.420 37.500 1.98 0.00 0.00 3.01
3022 4823 5.149977 GCACTGCTTTGACTTAATGAACTC 58.850 41.667 0.00 0.00 0.00 3.01
3034 4835 7.055667 ACTTAATGAACTCACTCACTCAGAA 57.944 36.000 0.00 0.00 0.00 3.02
3055 4856 3.606687 AGTCACCCATCCGAATTAACAC 58.393 45.455 0.00 0.00 0.00 3.32
3057 4858 2.574369 TCACCCATCCGAATTAACACCT 59.426 45.455 0.00 0.00 0.00 4.00
3058 4859 3.775866 TCACCCATCCGAATTAACACCTA 59.224 43.478 0.00 0.00 0.00 3.08
3059 4860 4.127171 CACCCATCCGAATTAACACCTAG 58.873 47.826 0.00 0.00 0.00 3.02
3120 4921 1.808411 TGACCCGTCAGCTCAAAATC 58.192 50.000 0.00 0.00 34.14 2.17
3155 4960 1.315257 CCCGGGCATCACTTTTCCTG 61.315 60.000 8.08 0.00 0.00 3.86
3225 5030 1.820519 TCATGCAAAGAAGATGCCCAC 59.179 47.619 0.00 0.00 43.16 4.61
3239 5078 1.862602 GCCCACGGGACATGTGTTTC 61.863 60.000 1.15 0.00 37.50 2.78
3264 5103 4.543590 TTAGAAAGACAAGGGAGCTGAG 57.456 45.455 0.00 0.00 0.00 3.35
3292 5131 0.250038 TTGATCTATCAGCCGCTGCC 60.250 55.000 15.98 1.43 38.19 4.85
3293 5132 1.735920 GATCTATCAGCCGCTGCCG 60.736 63.158 15.98 6.31 38.69 5.69
3320 5159 4.092968 GCACATTTCACTTACCTTCCGTAG 59.907 45.833 0.00 0.00 0.00 3.51
3359 5200 0.520412 CGTGTTTATTTCGCAGCGGG 60.520 55.000 16.42 0.00 0.00 6.13
3395 5236 1.672356 CCCCTTGACAGCAACGAGG 60.672 63.158 0.00 0.00 38.33 4.63
3547 5388 1.753073 GGCTGGCATGCAAATAGACTT 59.247 47.619 21.36 0.00 34.04 3.01
3548 5389 2.951642 GGCTGGCATGCAAATAGACTTA 59.048 45.455 21.36 0.00 34.04 2.24
3549 5390 3.243201 GGCTGGCATGCAAATAGACTTAC 60.243 47.826 21.36 0.00 34.04 2.34
3550 5391 3.378112 GCTGGCATGCAAATAGACTTACA 59.622 43.478 21.36 2.28 0.00 2.41
3551 5392 4.037208 GCTGGCATGCAAATAGACTTACAT 59.963 41.667 21.36 0.00 0.00 2.29
3552 5393 5.503662 TGGCATGCAAATAGACTTACATG 57.496 39.130 21.36 0.00 38.30 3.21
3569 5410 4.836125 ACATGACAGGACACATGAAAAC 57.164 40.909 12.90 0.00 44.28 2.43
3602 5443 7.505258 ACCTTCTCCTATCATTTTCTTAGCTC 58.495 38.462 0.00 0.00 0.00 4.09
3617 5460 6.583912 TCTTAGCTCGGTTAATTTGATTCG 57.416 37.500 0.00 0.00 0.00 3.34
3633 5476 2.203056 CGCATGGCCGAATGGAGA 60.203 61.111 0.00 0.00 37.49 3.71
3634 5477 1.598962 CGCATGGCCGAATGGAGAT 60.599 57.895 0.00 0.00 37.49 2.75
3635 5478 1.168407 CGCATGGCCGAATGGAGATT 61.168 55.000 0.00 0.00 37.49 2.40
3636 5479 0.313043 GCATGGCCGAATGGAGATTG 59.687 55.000 0.00 0.00 37.49 2.67
3637 5480 0.956633 CATGGCCGAATGGAGATTGG 59.043 55.000 0.00 0.00 37.49 3.16
3689 5532 8.796475 AGCAAACATTTAGATGTCACATTAGTT 58.204 29.630 0.00 0.00 45.58 2.24
3758 5601 5.126869 TGTTTGTGTGATGGATTTGTTGACT 59.873 36.000 0.00 0.00 0.00 3.41
3790 5633 1.489560 GGAGCCAGGTGTACAAGGGT 61.490 60.000 12.99 12.99 33.98 4.34
3796 5639 2.353406 CCAGGTGTACAAGGGTCTTACG 60.353 54.545 0.00 0.00 0.00 3.18
3802 5645 0.320697 ACAAGGGTCTTACGCTGGTC 59.679 55.000 0.00 0.00 40.84 4.02
3841 5684 2.636412 CGAGGTTCCTCTGCACCGA 61.636 63.158 15.60 0.00 38.21 4.69
3927 5770 2.796483 AATGCGACGGTGGCTTAGCA 62.796 55.000 16.06 3.98 39.02 3.49
3928 5771 2.740826 GCGACGGTGGCTTAGCAA 60.741 61.111 6.53 0.00 0.00 3.91
3929 5772 3.023591 GCGACGGTGGCTTAGCAAC 62.024 63.158 6.53 4.51 0.00 4.17
3930 5773 1.666553 CGACGGTGGCTTAGCAACA 60.667 57.895 14.23 0.00 33.46 3.33
4024 5872 5.036117 TGCTTCTCAAGTACTTTTCCTGT 57.964 39.130 5.07 0.00 0.00 4.00
4170 6034 5.927030 TGATGTCTCTGCAATAAACGTTTC 58.073 37.500 18.42 3.49 0.00 2.78
4191 6055 6.691754 TTCAGTAGCAACATCAAAACAGAA 57.308 33.333 0.00 0.00 0.00 3.02
4221 6085 1.532868 CTGCACTCACCAGCAACTTAC 59.467 52.381 0.00 0.00 40.73 2.34
4314 6180 2.703409 CGCGCTGCTGGTAATGTC 59.297 61.111 5.56 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 3.195610 TCTTCAAGGCACGACATATGTCT 59.804 43.478 28.51 15.71 42.66 3.41
97 98 8.823220 AATTGAGGCATACAACCTTTAATAGT 57.177 30.769 0.00 0.00 37.77 2.12
102 103 9.868277 CAATTAAATTGAGGCATACAACCTTTA 57.132 29.630 0.00 0.00 42.83 1.85
103 104 8.374743 ACAATTAAATTGAGGCATACAACCTTT 58.625 29.630 0.00 0.00 42.83 3.11
104 105 7.906327 ACAATTAAATTGAGGCATACAACCTT 58.094 30.769 0.00 0.00 42.83 3.50
105 106 7.480760 ACAATTAAATTGAGGCATACAACCT 57.519 32.000 0.00 0.00 42.83 3.50
106 107 7.412891 GCAACAATTAAATTGAGGCATACAACC 60.413 37.037 0.00 0.00 42.83 3.77
108 109 7.157347 TGCAACAATTAAATTGAGGCATACAA 58.843 30.769 1.10 0.00 42.77 2.41
109 110 6.695429 TGCAACAATTAAATTGAGGCATACA 58.305 32.000 1.10 0.00 42.77 2.29
110 111 7.331687 AGTTGCAACAATTAAATTGAGGCATAC 59.668 33.333 30.11 5.99 44.90 2.39
144 145 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
146 147 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
150 151 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
151 152 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
152 153 2.019807 AACTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
153 154 1.897802 GAAACTACTCCCTCCGTTCCA 59.102 52.381 0.00 0.00 0.00 3.53
154 155 2.177734 AGAAACTACTCCCTCCGTTCC 58.822 52.381 0.00 0.00 0.00 3.62
155 156 5.595257 ATTAGAAACTACTCCCTCCGTTC 57.405 43.478 0.00 0.00 0.00 3.95
156 157 6.370186 AAATTAGAAACTACTCCCTCCGTT 57.630 37.500 0.00 0.00 0.00 4.44
158 159 9.473640 GTATAAAATTAGAAACTACTCCCTCCG 57.526 37.037 0.00 0.00 0.00 4.63
159 160 9.775854 GGTATAAAATTAGAAACTACTCCCTCC 57.224 37.037 0.00 0.00 0.00 4.30
175 218 8.257306 ACGCATGAAGGAAATTGGTATAAAATT 58.743 29.630 0.00 0.00 0.00 1.82
214 257 9.669353 CATTGCTATGCGAATTTAAAGAGTAAT 57.331 29.630 0.00 0.00 0.00 1.89
218 261 6.430048 GCATTGCTATGCGAATTTAAAGAG 57.570 37.500 17.11 0.00 46.89 2.85
242 285 1.262640 ACCGCTAGTGATTTCCCCGT 61.263 55.000 4.44 0.00 0.00 5.28
253 296 3.275617 TGGATTTGCATAACCGCTAGT 57.724 42.857 0.00 0.00 0.00 2.57
259 302 7.333921 TGAAAAATGACATGGATTTGCATAACC 59.666 33.333 0.00 0.00 0.00 2.85
266 309 5.388682 GCACGTGAAAAATGACATGGATTTG 60.389 40.000 22.23 0.00 0.00 2.32
272 315 3.010624 TGGCACGTGAAAAATGACATG 57.989 42.857 22.23 0.00 0.00 3.21
320 363 6.713792 AGTGCGTTTCTAATCTTTCTCTTC 57.286 37.500 0.00 0.00 0.00 2.87
456 908 4.032104 GCGTAACTACCACGGAAACAATAG 59.968 45.833 0.00 0.00 39.75 1.73
466 918 3.311871 AGAGTATCAGCGTAACTACCACG 59.688 47.826 0.00 0.00 39.15 4.94
469 921 4.599047 CACAGAGTATCAGCGTAACTACC 58.401 47.826 0.00 0.00 37.82 3.18
479 934 1.827344 TGAGTGGGCACAGAGTATCAG 59.173 52.381 0.00 0.00 37.82 2.90
489 944 1.462616 TATGCATTGTGAGTGGGCAC 58.537 50.000 3.54 0.00 37.30 5.01
493 948 5.712004 TGTTTCATTATGCATTGTGAGTGG 58.288 37.500 3.54 0.00 0.00 4.00
510 965 9.959749 GGTGTCTTTTAATGTAAGAATGTTTCA 57.040 29.630 0.00 0.00 33.71 2.69
511 966 9.959749 TGGTGTCTTTTAATGTAAGAATGTTTC 57.040 29.630 0.00 0.00 33.71 2.78
514 969 7.309194 GGCTGGTGTCTTTTAATGTAAGAATGT 60.309 37.037 0.00 0.00 33.71 2.71
515 970 7.029563 GGCTGGTGTCTTTTAATGTAAGAATG 58.970 38.462 0.00 0.00 33.71 2.67
516 971 6.948309 AGGCTGGTGTCTTTTAATGTAAGAAT 59.052 34.615 0.00 0.00 33.71 2.40
519 974 6.575162 AAGGCTGGTGTCTTTTAATGTAAG 57.425 37.500 0.00 0.00 33.87 2.34
536 991 5.567138 AAGGATACGAAATCAAAAGGCTG 57.433 39.130 0.00 0.00 46.39 4.85
539 994 8.296713 TGAAAGAAAGGATACGAAATCAAAAGG 58.703 33.333 0.00 0.00 46.39 3.11
573 1031 5.799827 TTAAAAGACTGGTTTTGGATGGG 57.200 39.130 1.54 0.00 31.96 4.00
574 1032 6.873605 GGATTTAAAAGACTGGTTTTGGATGG 59.126 38.462 0.00 0.00 31.96 3.51
584 1042 2.442413 TGCGGGGATTTAAAAGACTGG 58.558 47.619 0.00 0.00 0.00 4.00
587 1045 3.020984 TCCATGCGGGGATTTAAAAGAC 58.979 45.455 0.00 0.00 37.22 3.01
598 1056 0.969917 TGGTGATTTTCCATGCGGGG 60.970 55.000 0.00 0.00 37.22 5.73
630 1144 8.604035 GCGTGTAAGATGATATGGGTTTATATG 58.396 37.037 0.00 0.00 0.00 1.78
640 1154 2.403259 TGGCGCGTGTAAGATGATATG 58.597 47.619 8.43 0.00 0.00 1.78
643 1161 1.867233 GATTGGCGCGTGTAAGATGAT 59.133 47.619 8.43 0.00 0.00 2.45
646 1164 1.599071 CATGATTGGCGCGTGTAAGAT 59.401 47.619 8.43 0.00 0.00 2.40
648 1166 0.589729 GCATGATTGGCGCGTGTAAG 60.590 55.000 8.43 0.00 0.00 2.34
669 1187 7.217636 CAGCTTGTGATTTCGTTTCTAATCATG 59.782 37.037 0.00 0.00 41.35 3.07
696 1214 0.533951 GCCTGGAAGCAAATTCTGGG 59.466 55.000 0.00 0.00 38.07 4.45
723 1241 3.279434 ACAATGGAGGATAAGAAACCGC 58.721 45.455 0.00 0.00 0.00 5.68
725 1243 4.079730 AGGGACAATGGAGGATAAGAAACC 60.080 45.833 0.00 0.00 0.00 3.27
741 1259 0.685097 CGGTCAGAGGAAAGGGACAA 59.315 55.000 0.00 0.00 32.00 3.18
914 1432 7.559897 TGGGAATAAATAGAGGGTTTGATTGAC 59.440 37.037 0.00 0.00 0.00 3.18
938 1461 0.529992 GAGAAGCGGGAATACGGTGG 60.530 60.000 0.00 0.00 44.60 4.61
959 1482 1.728426 CAGTCGCTTGCTTGCTTGC 60.728 57.895 0.00 0.00 0.00 4.01
967 1490 2.153913 CTGTGGTACAGTCGCTTGC 58.846 57.895 0.00 0.00 41.80 4.01
978 1502 5.284861 TGCTTACTGAAGAAACTGTGGTA 57.715 39.130 0.00 0.00 34.25 3.25
980 1504 4.756642 TCATGCTTACTGAAGAAACTGTGG 59.243 41.667 0.00 0.00 34.25 4.17
1000 1524 3.004839 CGACCGGTCATAGTTCTCATCAT 59.995 47.826 32.80 0.00 0.00 2.45
1001 1525 2.357952 CGACCGGTCATAGTTCTCATCA 59.642 50.000 32.80 0.00 0.00 3.07
1002 1526 2.358267 ACGACCGGTCATAGTTCTCATC 59.642 50.000 32.80 3.09 0.00 2.92
1096 1629 4.778143 ATGGCCGCTCGGTTCCAC 62.778 66.667 10.24 0.00 37.65 4.02
1097 1630 4.776322 CATGGCCGCTCGGTTCCA 62.776 66.667 10.24 9.83 37.65 3.53
1207 1740 1.086067 TGCAGCAGATAGAACAGCGC 61.086 55.000 0.00 0.00 0.00 5.92
1372 1905 1.156736 CTACCTTTGTTCCAGCGGTG 58.843 55.000 7.86 7.86 0.00 4.94
1458 2676 3.989817 GCAGGTTGTTCACAATTCATTCC 59.010 43.478 0.00 0.00 38.24 3.01
1477 2695 4.332637 GCACGTTGGCCACTGCAG 62.333 66.667 19.81 13.48 40.13 4.41
1542 2760 1.685491 GGAGGTGTAGATGTCGGAGGT 60.685 57.143 0.00 0.00 0.00 3.85
1574 2792 4.450122 TACGAGTCGTGCGCCGTC 62.450 66.667 27.85 8.62 41.39 4.79
1721 2951 0.613012 AGCCCTTGAAGTTGATGGCC 60.613 55.000 0.00 0.00 39.72 5.36
1723 2953 2.517959 TGAAGCCCTTGAAGTTGATGG 58.482 47.619 0.00 0.00 0.00 3.51
1982 3212 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1985 3215 0.633921 TCAAGGAGGAGGAGGAGGAG 59.366 60.000 0.00 0.00 0.00 3.69
1987 3217 1.048160 GCTCAAGGAGGAGGAGGAGG 61.048 65.000 0.00 0.00 35.41 4.30
1988 3218 1.048160 GGCTCAAGGAGGAGGAGGAG 61.048 65.000 0.00 0.00 35.41 3.69
1989 3219 1.002274 GGCTCAAGGAGGAGGAGGA 59.998 63.158 0.00 0.00 35.41 3.71
1991 3221 1.970352 GCTGGCTCAAGGAGGAGGAG 61.970 65.000 0.00 0.00 35.41 3.69
1992 3222 1.992277 GCTGGCTCAAGGAGGAGGA 60.992 63.158 0.00 0.00 35.41 3.71
1994 3224 0.676151 GTTGCTGGCTCAAGGAGGAG 60.676 60.000 0.00 0.00 37.97 3.69
1995 3225 1.376466 GTTGCTGGCTCAAGGAGGA 59.624 57.895 0.00 0.00 0.00 3.71
1996 3226 2.037136 CGTTGCTGGCTCAAGGAGG 61.037 63.158 6.84 0.00 34.73 4.30
2010 3240 4.760047 CCCTCTGGACCGCCGTTG 62.760 72.222 0.00 0.00 36.79 4.10
2019 3249 3.449227 CACGTAGCGCCCTCTGGA 61.449 66.667 2.29 0.00 0.00 3.86
2044 3274 4.778415 CGCACGGAGTCTGGGTCG 62.778 72.222 2.48 3.42 41.61 4.79
2069 3300 4.101448 AGCATGGGGGACAGCGAC 62.101 66.667 0.00 0.00 0.00 5.19
2070 3301 4.100084 CAGCATGGGGGACAGCGA 62.100 66.667 0.00 0.00 0.00 4.93
2073 3304 0.901580 AAAAGCAGCATGGGGGACAG 60.902 55.000 0.00 0.00 35.86 3.51
2074 3305 0.471591 AAAAAGCAGCATGGGGGACA 60.472 50.000 0.00 0.00 35.86 4.02
2096 3333 4.364409 GCACGGCGTTTCGTCACC 62.364 66.667 11.19 0.00 41.86 4.02
2114 3351 3.018856 GCCATGGCTGCAGCATATATAA 58.981 45.455 37.63 15.23 44.36 0.98
2233 3470 2.159667 CGTCGACCACGTGTAGTTCATA 60.160 50.000 15.65 0.00 44.07 2.15
2249 3486 4.994201 GGTGTCGCTGCACGTCGA 62.994 66.667 0.00 3.25 44.19 4.20
2254 3491 2.031683 GGTATTAATGGTGTCGCTGCAC 59.968 50.000 0.00 0.00 38.56 4.57
2370 3607 3.861689 GGAATGCATTGCTAAACTGAAGC 59.138 43.478 22.28 0.84 40.50 3.86
2371 3608 5.063180 TGGAATGCATTGCTAAACTGAAG 57.937 39.130 28.06 0.00 0.00 3.02
2408 3645 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2409 3646 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2410 3647 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2411 3648 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2412 3649 3.367025 GTGACGAGTAATTTGGAACGGAG 59.633 47.826 0.00 0.00 0.00 4.63
2413 3650 3.243805 TGTGACGAGTAATTTGGAACGGA 60.244 43.478 0.00 0.00 0.00 4.69
2414 3651 3.061322 TGTGACGAGTAATTTGGAACGG 58.939 45.455 0.00 0.00 0.00 4.44
2415 3652 3.985279 TCTGTGACGAGTAATTTGGAACG 59.015 43.478 0.00 0.00 0.00 3.95
2416 3653 5.917541 TTCTGTGACGAGTAATTTGGAAC 57.082 39.130 0.00 0.00 0.00 3.62
2417 3654 8.092068 TCTATTTCTGTGACGAGTAATTTGGAA 58.908 33.333 0.00 0.00 0.00 3.53
2418 3655 7.608153 TCTATTTCTGTGACGAGTAATTTGGA 58.392 34.615 0.00 0.00 0.00 3.53
2419 3656 7.827819 TCTATTTCTGTGACGAGTAATTTGG 57.172 36.000 0.00 0.00 0.00 3.28
2420 3657 8.873830 ACATCTATTTCTGTGACGAGTAATTTG 58.126 33.333 0.00 0.00 0.00 2.32
2423 3660 9.900710 GATACATCTATTTCTGTGACGAGTAAT 57.099 33.333 0.00 0.00 0.00 1.89
2424 3661 9.121658 AGATACATCTATTTCTGTGACGAGTAA 57.878 33.333 0.00 0.00 34.85 2.24
2425 3662 8.678593 AGATACATCTATTTCTGTGACGAGTA 57.321 34.615 0.00 0.00 34.85 2.59
2426 3663 7.575414 AGATACATCTATTTCTGTGACGAGT 57.425 36.000 0.00 0.00 34.85 4.18
2427 3664 8.994170 TCTAGATACATCTATTTCTGTGACGAG 58.006 37.037 0.00 0.00 38.60 4.18
2428 3665 8.904099 TCTAGATACATCTATTTCTGTGACGA 57.096 34.615 0.00 0.00 38.60 4.20
2429 3666 9.388346 GTTCTAGATACATCTATTTCTGTGACG 57.612 37.037 0.00 0.00 38.60 4.35
2459 3696 8.191446 GCACGTATGGATGTATCTAGATGTATT 58.809 37.037 15.79 0.00 29.44 1.89
2460 3697 7.467403 CGCACGTATGGATGTATCTAGATGTAT 60.467 40.741 15.79 9.11 29.44 2.29
2461 3698 6.183360 CGCACGTATGGATGTATCTAGATGTA 60.183 42.308 15.79 4.44 29.44 2.29
2462 3699 5.392057 CGCACGTATGGATGTATCTAGATGT 60.392 44.000 15.79 1.25 30.36 3.06
2463 3700 5.030936 CGCACGTATGGATGTATCTAGATG 58.969 45.833 15.79 0.00 0.00 2.90
2464 3701 4.096532 CCGCACGTATGGATGTATCTAGAT 59.903 45.833 10.73 10.73 0.00 1.98
2465 3702 3.439129 CCGCACGTATGGATGTATCTAGA 59.561 47.826 0.00 0.00 0.00 2.43
2466 3703 3.759418 CCGCACGTATGGATGTATCTAG 58.241 50.000 0.00 0.00 0.00 2.43
2467 3704 2.094906 GCCGCACGTATGGATGTATCTA 60.095 50.000 9.30 0.00 0.00 1.98
2468 3705 1.336887 GCCGCACGTATGGATGTATCT 60.337 52.381 9.30 0.00 0.00 1.98
2469 3706 1.068474 GCCGCACGTATGGATGTATC 58.932 55.000 9.30 0.00 0.00 2.24
2470 3707 0.391228 TGCCGCACGTATGGATGTAT 59.609 50.000 9.30 0.00 0.00 2.29
2471 3708 0.175989 TTGCCGCACGTATGGATGTA 59.824 50.000 9.30 0.00 0.00 2.29
2472 3709 1.078778 TTGCCGCACGTATGGATGT 60.079 52.632 9.30 0.00 0.00 3.06
2473 3710 1.089481 ACTTGCCGCACGTATGGATG 61.089 55.000 9.30 1.39 0.00 3.51
2474 3711 0.462375 TACTTGCCGCACGTATGGAT 59.538 50.000 5.65 0.00 0.00 3.41
2475 3712 0.246910 TTACTTGCCGCACGTATGGA 59.753 50.000 10.24 0.00 0.00 3.41
2476 3713 1.295792 ATTACTTGCCGCACGTATGG 58.704 50.000 10.24 0.96 0.00 2.74
2477 3714 2.596575 CGAATTACTTGCCGCACGTATG 60.597 50.000 10.24 0.00 0.00 2.39
2478 3715 1.591158 CGAATTACTTGCCGCACGTAT 59.409 47.619 10.24 0.00 0.00 3.06
2479 3716 0.993532 CGAATTACTTGCCGCACGTA 59.006 50.000 5.65 5.65 0.00 3.57
2480 3717 1.632046 CCGAATTACTTGCCGCACGT 61.632 55.000 7.72 7.72 0.00 4.49
2481 3718 1.060308 CCGAATTACTTGCCGCACG 59.940 57.895 0.00 0.00 0.00 5.34
2482 3719 0.800012 TTCCGAATTACTTGCCGCAC 59.200 50.000 0.00 0.00 0.00 5.34
2483 3720 0.800012 GTTCCGAATTACTTGCCGCA 59.200 50.000 0.00 0.00 0.00 5.69
2484 3721 0.247537 CGTTCCGAATTACTTGCCGC 60.248 55.000 0.00 0.00 0.00 6.53
2485 3722 0.372334 CCGTTCCGAATTACTTGCCG 59.628 55.000 0.00 0.00 0.00 5.69
2486 3723 1.664151 CTCCGTTCCGAATTACTTGCC 59.336 52.381 0.00 0.00 0.00 4.52
2487 3724 1.664151 CCTCCGTTCCGAATTACTTGC 59.336 52.381 0.00 0.00 0.00 4.01
2488 3725 2.968675 ACCTCCGTTCCGAATTACTTG 58.031 47.619 0.00 0.00 0.00 3.16
2489 3726 3.766051 ACTACCTCCGTTCCGAATTACTT 59.234 43.478 0.00 0.00 0.00 2.24
2490 3727 3.359950 ACTACCTCCGTTCCGAATTACT 58.640 45.455 0.00 0.00 0.00 2.24
2491 3728 3.790152 ACTACCTCCGTTCCGAATTAC 57.210 47.619 0.00 0.00 0.00 1.89
2492 3729 5.913137 TTTACTACCTCCGTTCCGAATTA 57.087 39.130 0.00 0.00 0.00 1.40
2493 3730 4.806640 TTTACTACCTCCGTTCCGAATT 57.193 40.909 0.00 0.00 0.00 2.17
2494 3731 6.469782 TTATTTACTACCTCCGTTCCGAAT 57.530 37.500 0.00 0.00 0.00 3.34
2495 3732 5.913137 TTATTTACTACCTCCGTTCCGAA 57.087 39.130 0.00 0.00 0.00 4.30
2496 3733 5.913137 TTTATTTACTACCTCCGTTCCGA 57.087 39.130 0.00 0.00 0.00 4.55
2497 3734 8.822652 ATAATTTATTTACTACCTCCGTTCCG 57.177 34.615 0.00 0.00 0.00 4.30
2532 3797 8.999431 CCGGAGCAAATGTGTAGTATTAATAAT 58.001 33.333 0.00 0.57 0.00 1.28
2533 3798 7.988599 ACCGGAGCAAATGTGTAGTATTAATAA 59.011 33.333 9.46 0.00 0.00 1.40
2534 3799 7.439955 CACCGGAGCAAATGTGTAGTATTAATA 59.560 37.037 9.46 0.00 0.00 0.98
2535 3800 6.260050 CACCGGAGCAAATGTGTAGTATTAAT 59.740 38.462 9.46 0.00 0.00 1.40
2536 3801 5.583061 CACCGGAGCAAATGTGTAGTATTAA 59.417 40.000 9.46 0.00 0.00 1.40
2548 3835 0.326264 AAGAGAGCACCGGAGCAAAT 59.674 50.000 26.04 10.80 36.85 2.32
2555 3842 2.093973 ACAGTTGATAAGAGAGCACCGG 60.094 50.000 0.00 0.00 0.00 5.28
2560 3847 3.929610 AGCGAAACAGTTGATAAGAGAGC 59.070 43.478 0.00 0.00 0.00 4.09
2561 3848 5.746245 CCTAGCGAAACAGTTGATAAGAGAG 59.254 44.000 0.00 0.00 0.00 3.20
2600 4028 4.092821 TGAAGTATCCGCAAATTTCGTCAG 59.907 41.667 8.50 0.00 0.00 3.51
2619 4049 7.154656 TGTCAACCGATATATTCCTGATGAAG 58.845 38.462 0.00 0.00 36.14 3.02
2632 4062 2.553028 GGCATGGGATGTCAACCGATAT 60.553 50.000 0.00 0.00 34.33 1.63
2678 4108 8.863872 TCTAATCATTGATTCAGATGCATCAT 57.136 30.769 27.81 13.26 33.95 2.45
2732 4164 7.970384 TGAACGTCATGTATAAAATGGAAGAC 58.030 34.615 0.00 0.00 0.00 3.01
2745 4177 7.214467 TCATAGAGCATATGAACGTCATGTA 57.786 36.000 6.97 0.00 37.70 2.29
2747 4179 6.810182 TCATCATAGAGCATATGAACGTCATG 59.190 38.462 6.97 8.07 37.70 3.07
2749 4181 6.331369 TCATCATAGAGCATATGAACGTCA 57.669 37.500 6.97 0.00 37.47 4.35
2750 4182 7.758980 AGAATCATCATAGAGCATATGAACGTC 59.241 37.037 6.97 9.74 37.47 4.34
2782 4417 3.383185 ACGTCCACAACAACCAATCAATT 59.617 39.130 0.00 0.00 0.00 2.32
2790 4425 4.759516 ATTATCAACGTCCACAACAACC 57.240 40.909 0.00 0.00 0.00 3.77
2810 4453 8.785329 ACAACGCCAAATTTATATGGAAAAAT 57.215 26.923 0.00 0.00 39.12 1.82
2879 4580 7.951530 TTTCTTCAAAAAGTAGGTAGGTACG 57.048 36.000 0.00 0.00 33.95 3.67
2905 4608 5.885912 ACCTGTTGTCATTCAGTACTGTTTT 59.114 36.000 21.99 6.02 0.00 2.43
2916 4619 2.221169 TCAGTGCACCTGTTGTCATTC 58.779 47.619 14.63 0.00 42.19 2.67
3013 4814 6.265422 TGACTTCTGAGTGAGTGAGTTCATTA 59.735 38.462 0.00 0.00 35.88 1.90
3015 4816 4.586421 TGACTTCTGAGTGAGTGAGTTCAT 59.414 41.667 0.00 0.00 35.88 2.57
3019 4820 2.625790 GGTGACTTCTGAGTGAGTGAGT 59.374 50.000 0.00 0.00 35.88 3.41
3020 4821 2.029470 GGGTGACTTCTGAGTGAGTGAG 60.029 54.545 0.00 0.00 35.88 3.51
3021 4822 1.964223 GGGTGACTTCTGAGTGAGTGA 59.036 52.381 0.00 0.00 35.88 3.41
3022 4823 1.688735 TGGGTGACTTCTGAGTGAGTG 59.311 52.381 0.00 0.00 35.88 3.51
3034 4835 3.606687 GTGTTAATTCGGATGGGTGACT 58.393 45.455 0.00 0.00 0.00 3.41
3146 4951 4.000988 ACGCGAATTATGTCAGGAAAAGT 58.999 39.130 15.93 0.00 0.00 2.66
3155 4960 0.229753 CTGCGGACGCGAATTATGTC 59.770 55.000 15.93 0.00 45.51 3.06
3239 5078 4.397417 CAGCTCCCTTGTCTTTCTAAATGG 59.603 45.833 0.00 0.00 0.00 3.16
3264 5103 3.485877 GGCTGATAGATCAACAACAACGC 60.486 47.826 0.00 0.00 36.18 4.84
3292 5131 1.127951 GGTAAGTGAAATGTGCGACCG 59.872 52.381 0.00 0.00 0.00 4.79
3293 5132 2.423577 AGGTAAGTGAAATGTGCGACC 58.576 47.619 0.00 0.00 0.00 4.79
3320 5159 3.173599 CGACAACATCAATGTCAATGCC 58.826 45.455 7.36 0.00 45.90 4.40
3332 5173 4.459606 TGCGAAATAAACACGACAACATC 58.540 39.130 0.00 0.00 0.00 3.06
3359 5200 1.226888 GACTACCGCATCCGTGTCC 60.227 63.158 0.00 0.00 0.00 4.02
3395 5236 1.299468 CAGAGCGCCGATGGAGTAC 60.299 63.158 2.29 0.00 0.00 2.73
3471 5312 2.297701 TGCAAAAGAGTTGAGTGGGAC 58.702 47.619 0.00 0.00 0.00 4.46
3547 5388 5.372373 TGTTTTCATGTGTCCTGTCATGTA 58.628 37.500 0.00 0.00 41.22 2.29
3548 5389 4.206375 TGTTTTCATGTGTCCTGTCATGT 58.794 39.130 0.00 0.00 41.22 3.21
3549 5390 4.834357 TGTTTTCATGTGTCCTGTCATG 57.166 40.909 0.00 0.00 41.64 3.07
3550 5391 7.613022 AGATAATGTTTTCATGTGTCCTGTCAT 59.387 33.333 0.00 0.00 40.79 3.06
3551 5392 6.942005 AGATAATGTTTTCATGTGTCCTGTCA 59.058 34.615 0.00 0.00 40.79 3.58
3552 5393 7.383102 AGATAATGTTTTCATGTGTCCTGTC 57.617 36.000 0.00 0.00 40.79 3.51
3602 5443 2.788786 GCCATGCGAATCAAATTAACCG 59.211 45.455 0.00 0.00 0.00 4.44
3611 5454 1.446516 CCATTCGGCCATGCGAATCA 61.447 55.000 15.33 0.00 32.76 2.57
3617 5460 0.313043 CAATCTCCATTCGGCCATGC 59.687 55.000 2.24 0.00 0.00 4.06
3633 5476 2.954318 GCATGCAGGAGTGTAATCCAAT 59.046 45.455 14.21 0.00 42.26 3.16
3634 5477 2.290832 TGCATGCAGGAGTGTAATCCAA 60.291 45.455 18.46 0.00 42.26 3.53
3635 5478 1.281577 TGCATGCAGGAGTGTAATCCA 59.718 47.619 18.46 0.00 42.26 3.41
3636 5479 2.042686 TGCATGCAGGAGTGTAATCC 57.957 50.000 18.46 0.00 39.89 3.01
3637 5480 2.749076 TGTTGCATGCAGGAGTGTAATC 59.251 45.455 21.50 3.61 0.00 1.75
3758 5601 2.349755 GCTCCAACCGCCAACCTA 59.650 61.111 0.00 0.00 0.00 3.08
3790 5633 0.607217 TGACGGAGACCAGCGTAAGA 60.607 55.000 0.00 0.00 43.02 2.10
3796 5639 2.888863 CCTCTGACGGAGACCAGC 59.111 66.667 13.17 0.00 44.45 4.85
3823 5666 2.125912 CGGTGCAGAGGAACCTCG 60.126 66.667 14.13 10.61 46.90 4.63
3902 5745 2.126888 CACCGTCGCATTTGTGGC 60.127 61.111 0.00 0.00 0.00 5.01
3906 5749 0.096976 CTAAGCCACCGTCGCATTTG 59.903 55.000 0.00 0.00 0.00 2.32
3927 5770 4.285863 TGACTTCCATCCCTTTGTTTGTT 58.714 39.130 0.00 0.00 0.00 2.83
3928 5771 3.909732 TGACTTCCATCCCTTTGTTTGT 58.090 40.909 0.00 0.00 0.00 2.83
3929 5772 4.935352 TTGACTTCCATCCCTTTGTTTG 57.065 40.909 0.00 0.00 0.00 2.93
3930 5773 6.782494 ACTATTTGACTTCCATCCCTTTGTTT 59.218 34.615 0.00 0.00 0.00 2.83
4170 6034 6.580041 GTCATTCTGTTTTGATGTTGCTACTG 59.420 38.462 0.00 0.00 0.00 2.74
4191 6055 0.036577 GTGAGTGCAGCTCCTGTCAT 60.037 55.000 11.99 0.00 43.48 3.06
4314 6180 1.013596 TGCCAAGTTGTCTGTTGTCG 58.986 50.000 1.45 0.00 0.00 4.35
4413 6279 1.198713 AGTATCTGGGACCACTGCAG 58.801 55.000 13.48 13.48 0.00 4.41
4417 6283 2.233305 ACGAAGTATCTGGGACCACT 57.767 50.000 0.00 0.00 41.94 4.00
4644 6510 4.982999 TGCGTCTGTTAGAGAATGAGTAC 58.017 43.478 0.00 0.00 30.26 2.73
4707 6573 5.831702 TTTTGTTAAGCCGTTGGTTTCTA 57.168 34.783 0.00 0.00 33.46 2.10


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

AutoCloner maintained by Alex Coulton.