Multiple sequence alignment - TraesCS1D01G369600

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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 TraesCS1D01G369600 chr1D 100.000 7398 0 0 1 7398 448434880 448427483 0.000000e+00 13662.0
1 TraesCS1D01G369600 chr1D 82.105 95 11 5 6609 6699 260569995 260570087 7.960000e-10 76.8
2 TraesCS1D01G369600 chr1A 90.608 3588 205 47 1403 4902 544204547 544201004 0.000000e+00 4638.0
3 TraesCS1D01G369600 chr1A 91.224 1732 88 23 4902 6617 544200950 544199267 0.000000e+00 2298.0
4 TraesCS1D01G369600 chr1A 88.393 784 43 20 91 862 544205660 544204913 0.000000e+00 900.0
5 TraesCS1D01G369600 chr1A 100.000 32 0 0 6659 6690 289002719 289002688 8.020000e-05 60.2
6 TraesCS1D01G369600 chr1B 89.513 2651 184 34 263 2873 614336022 614333426 0.000000e+00 3269.0
7 TraesCS1D01G369600 chr1B 93.214 1503 60 19 3417 4905 614332993 614331519 0.000000e+00 2172.0
8 TraesCS1D01G369600 chr1B 95.439 1206 37 12 4948 6139 614331443 614330242 0.000000e+00 1906.0
9 TraesCS1D01G369600 chr1B 91.854 577 43 4 6734 7310 614329275 614328703 0.000000e+00 802.0
10 TraesCS1D01G369600 chr1B 95.000 440 15 3 2934 3369 614333423 614332987 0.000000e+00 684.0
11 TraesCS1D01G369600 chr1B 87.939 456 46 6 6142 6597 614330072 614329626 5.080000e-146 529.0
12 TraesCS1D01G369600 chr1B 91.441 222 17 2 4 223 614336454 614336233 3.350000e-78 303.0
13 TraesCS1D01G369600 chr1B 95.833 72 3 0 6659 6730 614329616 614329545 4.690000e-22 117.0
14 TraesCS1D01G369600 chr1B 100.000 30 0 0 4903 4932 614331471 614331442 1.000000e-03 56.5
15 TraesCS1D01G369600 chrUn 88.710 310 25 5 7086 7395 45460962 45461261 3.260000e-98 370.0
16 TraesCS1D01G369600 chr5A 86.420 324 33 6 7079 7398 545717196 545716880 1.980000e-90 344.0
17 TraesCS1D01G369600 chr5A 97.143 35 1 0 6659 6693 32055786 32055752 8.020000e-05 60.2
18 TraesCS1D01G369600 chr5B 86.207 319 27 5 7080 7398 519157406 519157105 5.530000e-86 329.0
19 TraesCS1D01G369600 chr3B 87.552 241 24 6 7160 7398 408798857 408799093 2.630000e-69 274.0
20 TraesCS1D01G369600 chr7B 91.892 185 15 0 7214 7398 93467973 93468157 7.360000e-65 259.0
21 TraesCS1D01G369600 chr7B 88.995 209 19 4 7192 7398 12288246 12288452 9.530000e-64 255.0
22 TraesCS1D01G369600 chr7B 91.398 186 16 0 7213 7398 93447209 93447024 9.530000e-64 255.0
23 TraesCS1D01G369600 chr7B 91.351 185 16 0 7214 7398 93466634 93466818 3.430000e-63 254.0
24 TraesCS1D01G369600 chr4B 90.761 184 17 0 7215 7398 363722678 363722495 5.730000e-61 246.0
25 TraesCS1D01G369600 chr6B 97.222 36 0 1 6659 6693 20980083 20980048 8.020000e-05 60.2
26 TraesCS1D01G369600 chr4A 100.000 32 0 0 6659 6690 523568464 523568495 8.020000e-05 60.2
27 TraesCS1D01G369600 chr2D 100.000 32 0 0 6659 6690 346732242 346732273 8.020000e-05 60.2
28 TraesCS1D01G369600 chr2A 87.273 55 3 3 6621 6675 126482511 126482461 8.020000e-05 60.2
29 TraesCS1D01G369600 chr3A 88.889 45 1 2 6645 6689 556845891 556845931 1.300000e-02 52.8


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 TraesCS1D01G369600 chr1D 448427483 448434880 7397 True 13662.000000 13662 100.000000 1 7398 1 chr1D.!!$R1 7397
1 TraesCS1D01G369600 chr1A 544199267 544205660 6393 True 2612.000000 4638 90.075000 91 6617 3 chr1A.!!$R2 6526
2 TraesCS1D01G369600 chr1B 614328703 614336454 7751 True 1093.166667 3269 93.359222 4 7310 9 chr1B.!!$R1 7306
3 TraesCS1D01G369600 chr7B 93466634 93468157 1523 False 256.500000 259 91.621500 7214 7398 2 chr7B.!!$F2 184

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
607 786 0.170784 TGCGCAAATATGTGGTGCAG 59.829 50.000 8.16 0.00 42.48 4.41 F
1091 1277 0.106918 ACCGGTTTGCTTGTTCCTGA 60.107 50.000 0.00 0.00 0.00 3.86 F
2210 2461 0.109781 CCTTGGTTCAATTCGTGCGG 60.110 55.000 0.00 0.00 0.00 5.69 F
3110 3389 0.033504 GCGGAATTGAGATAGGGCGA 59.966 55.000 0.00 0.00 0.00 5.54 F
3231 3510 0.712979 TCACATCTCCCTCACCCTCT 59.287 55.000 0.00 0.00 0.00 3.69 F
3595 3875 0.984829 CAGTGACGTGACTGCATACG 59.015 55.000 22.02 14.29 45.19 3.06 F
3973 4259 1.871039 TCAGTTTACGCTTGAGTTGCC 59.129 47.619 0.00 0.00 0.00 4.52 F
5886 6255 1.209504 CGCCAAGGGGAAGAACTGATA 59.790 52.381 0.00 0.00 35.59 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 2437 0.527565 CGAATTGAACCAAGGGGCAG 59.472 55.000 0.00 0.00 37.90 4.85 R
2707 2985 1.340991 ACAGTTCCAATTCATCGGGGG 60.341 52.381 0.00 0.00 0.00 5.40 R
3462 3742 1.073763 ACTGCAGGAACATTGCTACCA 59.926 47.619 19.93 0.00 42.02 3.25 R
3973 4259 2.101415 TCTCGTTCAGACTGCATATGGG 59.899 50.000 4.56 0.00 0.00 4.00 R
4880 5189 4.906618 TCCCTCTGTTCCAAAATAGTGTC 58.093 43.478 0.00 0.00 0.00 3.67 R
5583 5952 3.903090 TGGGGAAACTGATGCAAGAAAAT 59.097 39.130 0.00 0.00 0.00 1.82 R
5915 6284 0.734889 CATCAACAGCTTAAGCCGGG 59.265 55.000 23.71 15.64 43.38 5.73 R
6934 7748 0.398381 ACCTTCCAAGCCCAAGCAAA 60.398 50.000 0.00 0.00 43.56 3.68 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
49 51 1.374758 CACCCCACTCTCGCTTGTC 60.375 63.158 0.00 0.00 0.00 3.18
52 54 0.951040 CCCCACTCTCGCTTGTCAAC 60.951 60.000 0.00 0.00 0.00 3.18
56 58 2.061773 CACTCTCGCTTGTCAACGATT 58.938 47.619 9.60 0.00 37.72 3.34
67 69 5.629020 GCTTGTCAACGATTATTTTCTTGCA 59.371 36.000 0.00 0.00 0.00 4.08
72 74 7.748683 TGTCAACGATTATTTTCTTGCATGTAC 59.251 33.333 0.00 0.00 0.00 2.90
124 126 4.350816 TCCATCGGACCAAATATCATTCCT 59.649 41.667 0.00 0.00 0.00 3.36
127 129 4.960938 TCGGACCAAATATCATTCCTCTG 58.039 43.478 0.00 0.00 0.00 3.35
156 160 0.250901 GGAGCAAAGGTCTCAAGGCA 60.251 55.000 0.00 0.00 32.38 4.75
229 233 5.365021 AGGATCAAAGATGTCAACTAGGG 57.635 43.478 0.00 0.00 0.00 3.53
232 236 4.826274 TCAAAGATGTCAACTAGGGGAG 57.174 45.455 0.00 0.00 0.00 4.30
234 238 3.491766 AAGATGTCAACTAGGGGAGGA 57.508 47.619 0.00 0.00 0.00 3.71
235 239 3.491766 AGATGTCAACTAGGGGAGGAA 57.508 47.619 0.00 0.00 0.00 3.36
236 240 3.803340 AGATGTCAACTAGGGGAGGAAA 58.197 45.455 0.00 0.00 0.00 3.13
237 241 4.375313 AGATGTCAACTAGGGGAGGAAAT 58.625 43.478 0.00 0.00 0.00 2.17
238 242 4.164988 AGATGTCAACTAGGGGAGGAAATG 59.835 45.833 0.00 0.00 0.00 2.32
241 245 2.205342 CAACTAGGGGAGGAAATGGGA 58.795 52.381 0.00 0.00 0.00 4.37
243 247 3.166636 ACTAGGGGAGGAAATGGGAAT 57.833 47.619 0.00 0.00 0.00 3.01
244 248 4.311208 ACTAGGGGAGGAAATGGGAATA 57.689 45.455 0.00 0.00 0.00 1.75
246 250 3.973472 AGGGGAGGAAATGGGAATAAC 57.027 47.619 0.00 0.00 0.00 1.89
247 251 2.518407 AGGGGAGGAAATGGGAATAACC 59.482 50.000 0.00 0.00 38.08 2.85
248 252 2.246327 GGGGAGGAAATGGGAATAACCA 59.754 50.000 0.00 0.00 46.24 3.67
328 503 6.968131 TCTCTAAACATGCAACTATGTGAC 57.032 37.500 0.00 0.00 40.24 3.67
329 504 6.463360 TCTCTAAACATGCAACTATGTGACA 58.537 36.000 0.00 0.00 40.24 3.58
330 505 6.368791 TCTCTAAACATGCAACTATGTGACAC 59.631 38.462 0.00 0.00 40.24 3.67
331 506 5.994668 TCTAAACATGCAACTATGTGACACA 59.005 36.000 11.41 11.41 40.24 3.72
332 507 5.512753 AAACATGCAACTATGTGACACAA 57.487 34.783 13.23 1.53 40.24 3.33
333 508 4.488126 ACATGCAACTATGTGACACAAC 57.512 40.909 13.23 0.00 39.68 3.32
334 509 3.882288 ACATGCAACTATGTGACACAACA 59.118 39.130 13.23 2.71 39.68 3.33
335 510 3.961477 TGCAACTATGTGACACAACAC 57.039 42.857 13.23 0.32 40.68 3.32
416 591 2.233431 GCCTCTGATTCGGCTCTATGAT 59.767 50.000 0.00 0.00 42.98 2.45
596 775 8.552083 TGATGTATATATCTTCTTGCGCAAAT 57.448 30.769 25.01 16.65 0.00 2.32
607 786 0.170784 TGCGCAAATATGTGGTGCAG 59.829 50.000 8.16 0.00 42.48 4.41
620 799 9.754382 AATATGTGGTGCAGAATATCAAAATTC 57.246 29.630 0.00 0.00 36.33 2.17
656 839 6.935741 TTTGCCATCCTAACATACATACAC 57.064 37.500 0.00 0.00 0.00 2.90
657 840 4.627058 TGCCATCCTAACATACATACACG 58.373 43.478 0.00 0.00 0.00 4.49
727 911 8.038944 TGGAGTGATGTTGTTACCTAAGATTAC 58.961 37.037 0.00 0.00 0.00 1.89
758 942 8.474710 TTCGAGGTAATAATTAGTCCTAGCTT 57.525 34.615 0.00 0.00 0.00 3.74
821 1005 5.860648 AGTTCCCCTCTAGGATTTTGAAA 57.139 39.130 0.00 0.00 38.24 2.69
878 1062 7.639162 TCGAAAGAGTAGAAACACAGAAATC 57.361 36.000 0.00 0.00 34.84 2.17
908 1092 3.950397 TCAACCTCGCCATATTCAACTT 58.050 40.909 0.00 0.00 0.00 2.66
959 1143 4.418359 TGGTATCATATTTGCATGGCCAT 58.582 39.130 14.09 14.09 0.00 4.40
972 1156 3.405831 CATGGCCATCGAGACAACATAT 58.594 45.455 17.61 0.00 0.00 1.78
1011 1195 5.694231 TGGAGTTCTTCAATGAACATGTG 57.306 39.130 0.00 0.00 46.19 3.21
1027 1213 9.740239 ATGAACATGTGCATTCATTATCTAAAC 57.260 29.630 14.02 0.00 41.69 2.01
1031 1217 9.577110 ACATGTGCATTCATTATCTAAACAAAG 57.423 29.630 0.00 0.00 0.00 2.77
1074 1260 9.841880 GTCTATTCTTTTGGAAGTCATAAAACC 57.158 33.333 0.00 0.00 37.36 3.27
1075 1261 8.726988 TCTATTCTTTTGGAAGTCATAAAACCG 58.273 33.333 0.00 0.00 37.36 4.44
1091 1277 0.106918 ACCGGTTTGCTTGTTCCTGA 60.107 50.000 0.00 0.00 0.00 3.86
1121 1308 1.042475 GCTTTAAGTTGCGTCGTTGC 58.958 50.000 0.00 0.00 0.00 4.17
1134 1321 3.666902 GCGTCGTTGCAATGATACTTTGT 60.667 43.478 23.53 0.00 34.15 2.83
1135 1322 4.081761 CGTCGTTGCAATGATACTTTGTC 58.918 43.478 23.53 7.92 0.00 3.18
1146 1333 3.007074 TGATACTTTGTCGTTGGCAGGTA 59.993 43.478 0.00 0.00 0.00 3.08
1165 1352 5.066893 CAGGTATTGTGCTATGTTGCTCATT 59.933 40.000 0.89 0.00 36.53 2.57
1180 1371 4.713553 TGCTCATTTGTTCAGTTGGTCTA 58.286 39.130 0.00 0.00 0.00 2.59
1182 1373 4.154918 GCTCATTTGTTCAGTTGGTCTAGG 59.845 45.833 0.00 0.00 0.00 3.02
1198 1389 3.510360 GTCTAGGGATATCGCTGCCTTTA 59.490 47.826 27.58 9.50 38.11 1.85
1201 1392 1.339151 GGGATATCGCTGCCTTTAGGG 60.339 57.143 12.31 0.00 35.18 3.53
1220 1414 4.689612 GGGCTTCTTTTCCCTTTTTCTT 57.310 40.909 0.00 0.00 39.46 2.52
1240 1434 9.939802 TTTTCTTTTAGTAGTCTCTATGAACCC 57.060 33.333 0.00 0.00 0.00 4.11
1264 1458 6.072175 CCGTTGGTTTCTCCTAATGAAAATCA 60.072 38.462 0.00 0.00 35.54 2.57
1265 1459 7.023575 CGTTGGTTTCTCCTAATGAAAATCAG 58.976 38.462 0.00 0.00 35.54 2.90
1267 1461 7.928307 TGGTTTCTCCTAATGAAAATCAGAG 57.072 36.000 0.00 0.00 35.54 3.35
1268 1462 6.886459 TGGTTTCTCCTAATGAAAATCAGAGG 59.114 38.462 5.23 5.23 35.72 3.69
1377 1571 8.563123 AGAATGCTATCCTATGATCAATTGTG 57.437 34.615 5.13 0.00 32.18 3.33
1381 1575 7.161404 TGCTATCCTATGATCAATTGTGTACC 58.839 38.462 5.13 0.00 32.18 3.34
1390 1584 2.038689 TCAATTGTGTACCCCGCACTAA 59.961 45.455 5.13 0.00 37.70 2.24
1397 1591 1.662122 GTACCCCGCACTAACAATTCG 59.338 52.381 0.00 0.00 0.00 3.34
1403 1597 2.095969 CCGCACTAACAATTCGAAGCAA 60.096 45.455 3.35 0.00 0.00 3.91
1405 1599 3.357823 CGCACTAACAATTCGAAGCAAAC 59.642 43.478 3.35 0.00 0.00 2.93
1410 1604 1.052287 CAATTCGAAGCAAACACCGC 58.948 50.000 3.35 0.00 0.00 5.68
1412 1606 0.881118 ATTCGAAGCAAACACCGCAT 59.119 45.000 3.35 0.00 0.00 4.73
1427 1621 2.423538 ACCGCATATGAAAACAAGAGGC 59.576 45.455 6.97 0.00 0.00 4.70
1431 1625 3.688272 CATATGAAAACAAGAGGCGCTG 58.312 45.455 7.64 0.00 0.00 5.18
1485 1679 3.152341 CTGTGCCAAAATCTTCTCCTGT 58.848 45.455 0.00 0.00 0.00 4.00
1587 1792 2.590821 GTGCATCTTATCCAAGGCCAT 58.409 47.619 5.01 0.00 32.22 4.40
1604 1809 2.762327 GCCATCACCAAGATTCAACCAT 59.238 45.455 0.00 0.00 33.72 3.55
1666 1872 3.089284 CCCATTTCTTGTAACCCACTCC 58.911 50.000 0.00 0.00 0.00 3.85
1806 2024 4.973211 TCCCCTATTTTCCTCCGACTATTT 59.027 41.667 0.00 0.00 0.00 1.40
1858 2076 1.682849 CCCCATCACGGAAGGAACA 59.317 57.895 0.00 0.00 36.56 3.18
2177 2428 0.386113 GCTCAGGGTCGGTCAGATAC 59.614 60.000 0.00 0.00 0.00 2.24
2183 2434 1.114119 GGTCGGTCAGATACCCCCTC 61.114 65.000 0.00 0.00 46.62 4.30
2186 2437 1.461655 GGTCAGATACCCCCTCCCC 60.462 68.421 0.00 0.00 43.16 4.81
2198 2449 3.268032 CTCCCCTGCCCCTTGGTT 61.268 66.667 0.00 0.00 0.00 3.67
2199 2450 3.264845 TCCCCTGCCCCTTGGTTC 61.265 66.667 0.00 0.00 0.00 3.62
2210 2461 0.109781 CCTTGGTTCAATTCGTGCGG 60.110 55.000 0.00 0.00 0.00 5.69
2242 2493 1.765904 GGATGGGGGTGTTTGTGTTTT 59.234 47.619 0.00 0.00 0.00 2.43
2243 2494 2.484594 GGATGGGGGTGTTTGTGTTTTG 60.485 50.000 0.00 0.00 0.00 2.44
2344 2595 2.841988 GAGCTCGAGGGCTGGGAT 60.842 66.667 15.58 0.00 43.20 3.85
2424 2684 2.287274 TACCAGCGCTGCCCTGTTA 61.287 57.895 31.96 11.70 0.00 2.41
2526 2791 7.872138 AGAGATACTAGGCTAGATAGAAGCAT 58.128 38.462 27.59 4.72 41.93 3.79
2609 2878 5.556915 AGTCGGACAAGGATTAACATTTCA 58.443 37.500 11.27 0.00 0.00 2.69
2666 2943 7.607991 CACCTGACCACTAGTAAAATTCTCAAT 59.392 37.037 0.00 0.00 0.00 2.57
2673 2950 7.284034 CCACTAGTAAAATTCTCAATGATGGCT 59.716 37.037 0.00 0.00 0.00 4.75
2677 2954 4.811969 AAATTCTCAATGATGGCTGCAA 57.188 36.364 0.50 0.00 0.00 4.08
2713 2992 2.588464 TTGTTATGCTTTTCCCCCGA 57.412 45.000 0.00 0.00 0.00 5.14
2796 3075 9.787532 TTTGCAATTAGTTAGAACTCATAATGC 57.212 29.630 0.00 2.87 40.37 3.56
2896 3175 0.251698 TTGCCATGATTGGGTGCAGA 60.252 50.000 0.00 0.00 43.84 4.26
2907 3186 1.825474 TGGGTGCAGAGTCTAGCTTAC 59.175 52.381 13.40 0.00 0.00 2.34
2994 3273 4.125703 GACAACTTATGAGGGATGCTCAG 58.874 47.826 0.00 0.00 34.04 3.35
3110 3389 0.033504 GCGGAATTGAGATAGGGCGA 59.966 55.000 0.00 0.00 0.00 5.54
3231 3510 0.712979 TCACATCTCCCTCACCCTCT 59.287 55.000 0.00 0.00 0.00 3.69
3372 3652 6.216801 ACGGATGCAGTAATTTACTCACTA 57.783 37.500 6.10 0.00 36.76 2.74
3373 3653 6.040878 ACGGATGCAGTAATTTACTCACTAC 58.959 40.000 6.10 0.00 36.76 2.73
3376 3656 6.019801 GGATGCAGTAATTTACTCACTACACG 60.020 42.308 6.10 0.00 36.76 4.49
3421 3701 6.434028 CCTAATCATGAAGGGTTCAGTTTTCA 59.566 38.462 0.00 0.00 43.98 2.69
3462 3742 2.755655 CTCGTCCTGTGTCACCTAGAAT 59.244 50.000 0.00 0.00 0.00 2.40
3479 3759 3.019564 AGAATGGTAGCAATGTTCCTGC 58.980 45.455 0.00 0.00 40.24 4.85
3582 3862 7.588512 ACTCTTATGCTTGAAAATTCAGTGAC 58.411 34.615 0.00 0.00 38.61 3.67
3595 3875 0.984829 CAGTGACGTGACTGCATACG 59.015 55.000 22.02 14.29 45.19 3.06
3609 3891 6.964934 TGACTGCATACGTACATATTATAGCG 59.035 38.462 0.00 0.00 0.00 4.26
3627 3909 4.771590 AGCGATAATGTTATGCCCATTG 57.228 40.909 0.00 0.00 34.51 2.82
3914 4200 7.264373 ACCAGAAAACATTAGTCACTTGAAG 57.736 36.000 0.00 0.00 0.00 3.02
3939 4225 5.382618 AAGTTGAGCTGCCATTCTAAAAG 57.617 39.130 0.00 0.00 0.00 2.27
3944 4230 6.017400 TGAGCTGCCATTCTAAAAGAAAAG 57.983 37.500 0.00 0.00 37.82 2.27
3973 4259 1.871039 TCAGTTTACGCTTGAGTTGCC 59.129 47.619 0.00 0.00 0.00 4.52
4144 4430 7.662669 GTGGTGTATTAGGAAAGGTAAGTGAAA 59.337 37.037 0.00 0.00 0.00 2.69
4173 4459 4.223144 ACAAGGCCTTCTGTTTGGTATTT 58.777 39.130 17.29 0.00 0.00 1.40
4244 4535 7.068839 TGGTGATGGTAGCTTTTTAAAAAGTGA 59.931 33.333 31.25 21.01 45.48 3.41
4259 4550 9.982291 TTTAAAAAGTGACATATAGAATGACGC 57.018 29.630 0.00 0.00 0.00 5.19
4306 4597 8.565416 ACTAGCTTTTGTTACAACAGGAAATAC 58.435 33.333 12.37 0.00 40.50 1.89
4434 4731 7.040409 GGATTGGATTGACTTGTACTTTGTCTT 60.040 37.037 12.19 3.64 0.00 3.01
4783 5082 8.783660 ATTCATCTACCAAGTACTCTCCATTA 57.216 34.615 0.00 0.00 0.00 1.90
4898 5207 6.929049 CACTGTAGACACTATTTTGGAACAGA 59.071 38.462 5.72 0.00 42.39 3.41
5107 5470 6.777580 ACACTTTCTAGGGTCATCATTTTTGT 59.222 34.615 0.00 0.00 30.04 2.83
5117 5480 5.392272 GGTCATCATTTTTGTAACGGGGTAC 60.392 44.000 0.00 0.00 0.00 3.34
5248 5611 2.988010 ACATCGAGATGGCAAAGCTA 57.012 45.000 16.37 0.00 42.91 3.32
5380 5743 3.486383 CAAGAAGGTTGGTGCTCCTTAA 58.514 45.455 6.34 0.00 43.12 1.85
5389 5752 3.626930 TGGTGCTCCTTAACAGTTTGTT 58.373 40.909 6.34 0.00 38.23 2.83
5469 5832 7.765360 CCCATGATTAAAATACAACAATGCAGT 59.235 33.333 0.00 0.00 0.00 4.40
5583 5952 8.042515 TGTGTGAATGTCATTCTGATGAATCTA 58.957 33.333 22.89 0.00 43.58 1.98
5622 5991 1.271543 CCCAGGACTTGCAGATCAACA 60.272 52.381 0.00 0.00 0.00 3.33
5641 6010 7.250445 TCAACATGGATGAAAGTAATCGATG 57.750 36.000 0.00 6.80 42.59 3.84
5886 6255 1.209504 CGCCAAGGGGAAGAACTGATA 59.790 52.381 0.00 0.00 35.59 2.15
5915 6284 2.036089 GCCCATGCAGTAGTACTAGGAC 59.964 54.545 1.87 0.00 37.47 3.85
5962 6331 6.426025 ACCGTTTTATCCTTACAAACTGAGTC 59.574 38.462 0.00 0.00 0.00 3.36
5990 6363 6.424812 ACTTACTTGAAATTGAAAAGGCATGC 59.575 34.615 9.90 9.90 0.00 4.06
6087 6463 8.650490 ACATGGGTGAAATTCAGTTATTTTTCT 58.350 29.630 0.00 0.00 0.00 2.52
6088 6464 9.143631 CATGGGTGAAATTCAGTTATTTTTCTC 57.856 33.333 0.00 0.00 0.00 2.87
6089 6465 8.243961 TGGGTGAAATTCAGTTATTTTTCTCA 57.756 30.769 0.00 0.00 0.00 3.27
6090 6466 8.359642 TGGGTGAAATTCAGTTATTTTTCTCAG 58.640 33.333 0.00 0.00 0.00 3.35
6091 6467 7.329471 GGGTGAAATTCAGTTATTTTTCTCAGC 59.671 37.037 0.00 0.00 0.00 4.26
6092 6468 8.084684 GGTGAAATTCAGTTATTTTTCTCAGCT 58.915 33.333 0.00 0.00 0.00 4.24
6093 6469 9.122613 GTGAAATTCAGTTATTTTTCTCAGCTC 57.877 33.333 0.00 0.00 0.00 4.09
6094 6470 9.071276 TGAAATTCAGTTATTTTTCTCAGCTCT 57.929 29.630 0.00 0.00 0.00 4.09
6100 6476 5.767168 AGTTATTTTTCTCAGCTCTTGTGCT 59.233 36.000 0.00 0.00 45.18 4.40
6217 6760 2.943690 CTCATTCTGCTGCTTATGTGCT 59.056 45.455 0.00 0.00 0.00 4.40
6220 6763 5.128205 TCATTCTGCTGCTTATGTGCTTAT 58.872 37.500 0.00 0.00 0.00 1.73
6263 6806 6.636666 CAAAATGTGCATCTGTACCAAATC 57.363 37.500 0.00 0.00 0.00 2.17
6279 6822 9.483489 TGTACCAAATCTAGGAATAACAGACTA 57.517 33.333 0.00 0.00 0.00 2.59
6282 6825 9.440761 ACCAAATCTAGGAATAACAGACTATCT 57.559 33.333 0.00 0.00 0.00 1.98
6298 6841 4.499183 ACTATCTGTTCAGCCTTTTCTCG 58.501 43.478 0.00 0.00 0.00 4.04
6303 6846 2.612212 TGTTCAGCCTTTTCTCGTGAAC 59.388 45.455 0.00 6.57 44.73 3.18
6317 6860 1.466697 CGTGAACAAACCACACACCAC 60.467 52.381 0.00 0.00 34.36 4.16
6322 6865 2.303175 ACAAACCACACACCACATACC 58.697 47.619 0.00 0.00 0.00 2.73
6332 6875 3.007506 CACACCACATACCCTTACAGTCA 59.992 47.826 0.00 0.00 0.00 3.41
6351 6894 8.947055 ACAGTCATAATCAATTATTTTTGCCC 57.053 30.769 0.00 0.00 30.91 5.36
6363 6906 9.617523 CAATTATTTTTGCCCCTCTTGAAATAT 57.382 29.630 0.00 0.00 0.00 1.28
6412 6955 6.655003 TCAACAATAAAGCTTAGGAACCTCTG 59.345 38.462 0.00 0.00 0.00 3.35
6532 7075 1.024579 ATACTTTGCAACGAGGGCGG 61.025 55.000 10.27 0.00 43.17 6.13
6550 7094 2.267426 CGGTGCACATCGACATTCTTA 58.733 47.619 20.43 0.00 37.01 2.10
6559 7103 5.684184 CACATCGACATTCTTATTGCATTGG 59.316 40.000 0.00 0.00 0.00 3.16
6568 7112 9.251440 ACATTCTTATTGCATTGGAGCATATAT 57.749 29.630 0.00 0.00 45.19 0.86
6600 7148 3.136443 AGGTGACATGAAGGTTTGACAGA 59.864 43.478 0.00 0.00 0.00 3.41
6602 7150 4.083110 GGTGACATGAAGGTTTGACAGATG 60.083 45.833 0.00 0.00 0.00 2.90
6603 7151 4.756642 GTGACATGAAGGTTTGACAGATGA 59.243 41.667 0.00 0.00 0.00 2.92
6604 7152 4.999311 TGACATGAAGGTTTGACAGATGAG 59.001 41.667 0.00 0.00 0.00 2.90
6617 7165 6.761099 TGACAGATGAGACTACCTTTCTAC 57.239 41.667 0.00 0.00 0.00 2.59
6618 7166 6.486056 TGACAGATGAGACTACCTTTCTACT 58.514 40.000 0.00 0.00 0.00 2.57
6619 7167 7.631007 TGACAGATGAGACTACCTTTCTACTA 58.369 38.462 0.00 0.00 0.00 1.82
6620 7168 7.553402 TGACAGATGAGACTACCTTTCTACTAC 59.447 40.741 0.00 0.00 0.00 2.73
6621 7169 7.635648 ACAGATGAGACTACCTTTCTACTACT 58.364 38.462 0.00 0.00 0.00 2.57
6622 7170 7.771826 ACAGATGAGACTACCTTTCTACTACTC 59.228 40.741 0.00 0.00 0.00 2.59
6623 7171 7.227910 CAGATGAGACTACCTTTCTACTACTCC 59.772 44.444 0.00 0.00 0.00 3.85
6624 7172 5.426504 TGAGACTACCTTTCTACTACTCCG 58.573 45.833 0.00 0.00 0.00 4.63
6625 7173 5.046014 TGAGACTACCTTTCTACTACTCCGT 60.046 44.000 0.00 0.00 0.00 4.69
6626 7174 5.427378 AGACTACCTTTCTACTACTCCGTC 58.573 45.833 0.00 0.00 0.00 4.79
6627 7175 4.522114 ACTACCTTTCTACTACTCCGTCC 58.478 47.826 0.00 0.00 0.00 4.79
6628 7176 3.735720 ACCTTTCTACTACTCCGTCCT 57.264 47.619 0.00 0.00 0.00 3.85
6629 7177 4.851639 ACCTTTCTACTACTCCGTCCTA 57.148 45.455 0.00 0.00 0.00 2.94
6630 7178 5.385628 ACCTTTCTACTACTCCGTCCTAT 57.614 43.478 0.00 0.00 0.00 2.57
6631 7179 6.506538 ACCTTTCTACTACTCCGTCCTATA 57.493 41.667 0.00 0.00 0.00 1.31
6632 7180 6.904626 ACCTTTCTACTACTCCGTCCTATAA 58.095 40.000 0.00 0.00 0.00 0.98
6633 7181 7.525165 ACCTTTCTACTACTCCGTCCTATAAT 58.475 38.462 0.00 0.00 0.00 1.28
6634 7182 8.664079 ACCTTTCTACTACTCCGTCCTATAATA 58.336 37.037 0.00 0.00 0.00 0.98
6635 7183 9.683870 CCTTTCTACTACTCCGTCCTATAATAT 57.316 37.037 0.00 0.00 0.00 1.28
6642 7190 9.160496 ACTACTCCGTCCTATAATATAAGAACG 57.840 37.037 0.00 0.00 0.00 3.95
6643 7191 7.992754 ACTCCGTCCTATAATATAAGAACGT 57.007 36.000 0.00 0.00 0.00 3.99
6644 7192 8.401490 ACTCCGTCCTATAATATAAGAACGTT 57.599 34.615 0.00 0.00 0.00 3.99
6645 7193 9.507329 ACTCCGTCCTATAATATAAGAACGTTA 57.493 33.333 0.00 0.00 0.00 3.18
6646 7194 9.985318 CTCCGTCCTATAATATAAGAACGTTAG 57.015 37.037 0.00 0.00 0.00 2.34
6647 7195 8.454106 TCCGTCCTATAATATAAGAACGTTAGC 58.546 37.037 0.00 0.00 0.00 3.09
6648 7196 8.457261 CCGTCCTATAATATAAGAACGTTAGCT 58.543 37.037 0.00 0.00 0.00 3.32
6649 7197 9.837525 CGTCCTATAATATAAGAACGTTAGCTT 57.162 33.333 0.00 3.95 0.00 3.74
6719 7267 4.083431 GCATGAAGAATTGCAGCTATCGAT 60.083 41.667 2.16 2.16 38.72 3.59
6725 7273 5.549347 AGAATTGCAGCTATCGATGAGATT 58.451 37.500 8.54 0.00 40.66 2.40
6746 7560 2.426738 TGCACTTTCACAAGGAAACCAG 59.573 45.455 0.00 0.00 40.51 4.00
6770 7584 0.324943 TAGAGCCTGTTTGGGACTGC 59.675 55.000 0.00 0.00 36.00 4.40
6788 7602 5.007136 GGACTGCTCTATCCTTTCAAAATCG 59.993 44.000 0.00 0.00 31.75 3.34
6789 7603 4.878397 ACTGCTCTATCCTTTCAAAATCGG 59.122 41.667 0.00 0.00 0.00 4.18
6871 7685 9.429359 CATAGAGTAGTTGATCTTGTTTGACTT 57.571 33.333 0.00 0.00 0.00 3.01
6878 7692 3.745975 TGATCTTGTTTGACTTGCTACGG 59.254 43.478 0.00 0.00 0.00 4.02
6906 7720 6.481954 AAGATAATCTTTTGACGGTGACAC 57.518 37.500 0.00 0.00 31.57 3.67
6942 7756 0.318107 CTCGCACAGGTTTTGCTTGG 60.318 55.000 0.00 0.00 37.87 3.61
6944 7758 1.595109 GCACAGGTTTTGCTTGGGC 60.595 57.895 0.00 0.00 46.22 5.36
6961 7775 2.092323 GGGCTTGGAAGGTGTTGATAC 58.908 52.381 0.00 0.00 0.00 2.24
6981 7795 2.348411 CGAAGGGGTGCCTTATCATT 57.652 50.000 0.00 0.00 0.00 2.57
6995 7809 7.116233 GTGCCTTATCATTCGAAAACAACATTT 59.884 33.333 0.00 0.00 0.00 2.32
7026 7840 9.261180 CTCTCTCTTTTAAGTGTTGTGATACAA 57.739 33.333 0.00 0.00 35.42 2.41
7077 7891 3.689161 TCTTTCAGGATATGTTTGTGCGG 59.311 43.478 0.00 0.00 0.00 5.69
7082 7896 4.814234 TCAGGATATGTTTGTGCGGAATAC 59.186 41.667 0.00 0.00 0.00 1.89
7320 9473 7.551262 TCACCGTATTTATCACTATGTTGCTTT 59.449 33.333 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.083875 TCAATTTTTGCTATAGAGGTTTCCG 57.916 36.000 3.21 0.00 0.00 4.30
1 2 9.875691 AAATCAATTTTTGCTATAGAGGTTTCC 57.124 29.630 3.21 0.00 0.00 3.13
12 13 5.994668 GGGGTGTTCAAATCAATTTTTGCTA 59.005 36.000 0.00 0.00 36.69 3.49
49 51 7.250569 AGGTACATGCAAGAAAATAATCGTTG 58.749 34.615 0.00 0.00 0.00 4.10
52 54 6.129393 CGAGGTACATGCAAGAAAATAATCG 58.871 40.000 0.00 0.00 0.00 3.34
56 58 4.839121 ACCGAGGTACATGCAAGAAAATA 58.161 39.130 0.00 0.00 0.00 1.40
85 87 0.603707 TGGAGCTTCCTTGTGCGAAG 60.604 55.000 0.00 0.00 39.82 3.79
89 91 1.372087 CCGATGGAGCTTCCTTGTGC 61.372 60.000 0.00 0.00 37.46 4.57
124 126 5.385198 ACCTTTGCTCCAACTTTTATCAGA 58.615 37.500 0.00 0.00 0.00 3.27
127 129 5.473504 TGAGACCTTTGCTCCAACTTTTATC 59.526 40.000 0.00 0.00 0.00 1.75
175 179 0.611200 CAACCATCCGTCCTACCACA 59.389 55.000 0.00 0.00 0.00 4.17
229 233 4.610333 AGTTGGTTATTCCCATTTCCTCC 58.390 43.478 0.00 0.00 33.60 4.30
232 236 5.304357 CCCATAGTTGGTTATTCCCATTTCC 59.696 44.000 0.00 0.00 41.91 3.13
234 238 5.849140 ACCCATAGTTGGTTATTCCCATTT 58.151 37.500 0.00 0.00 41.91 2.32
235 239 5.481615 ACCCATAGTTGGTTATTCCCATT 57.518 39.130 0.00 0.00 41.91 3.16
236 240 5.481615 AACCCATAGTTGGTTATTCCCAT 57.518 39.130 0.00 0.00 44.17 4.00
237 241 4.957606 AACCCATAGTTGGTTATTCCCA 57.042 40.909 0.00 0.00 44.17 4.37
238 242 5.717654 TGAAAACCCATAGTTGGTTATTCCC 59.282 40.000 0.00 0.00 45.23 3.97
241 245 6.016555 AGCTGAAAACCCATAGTTGGTTATT 58.983 36.000 0.00 0.00 45.23 1.40
243 247 4.993028 AGCTGAAAACCCATAGTTGGTTA 58.007 39.130 0.00 0.00 45.23 2.85
246 250 4.871933 AAAGCTGAAAACCCATAGTTGG 57.128 40.909 0.00 0.00 43.23 3.77
247 251 8.831715 AAATAAAAGCTGAAAACCCATAGTTG 57.168 30.769 0.00 0.00 39.19 3.16
248 252 9.923143 GTAAATAAAAGCTGAAAACCCATAGTT 57.077 29.630 0.00 0.00 41.81 2.24
255 260 8.657074 AACCTTGTAAATAAAAGCTGAAAACC 57.343 30.769 0.00 0.00 0.00 3.27
328 503 2.622470 TCATGTGGGATTGTGTGTTGTG 59.378 45.455 0.00 0.00 0.00 3.33
329 504 2.622942 GTCATGTGGGATTGTGTGTTGT 59.377 45.455 0.00 0.00 0.00 3.32
330 505 2.622470 TGTCATGTGGGATTGTGTGTTG 59.378 45.455 0.00 0.00 0.00 3.33
331 506 2.942804 TGTCATGTGGGATTGTGTGTT 58.057 42.857 0.00 0.00 0.00 3.32
332 507 2.655090 TGTCATGTGGGATTGTGTGT 57.345 45.000 0.00 0.00 0.00 3.72
333 508 2.229543 CCTTGTCATGTGGGATTGTGTG 59.770 50.000 0.00 0.00 0.00 3.82
334 509 2.158475 ACCTTGTCATGTGGGATTGTGT 60.158 45.455 0.00 0.00 0.00 3.72
335 510 2.517959 ACCTTGTCATGTGGGATTGTG 58.482 47.619 0.00 0.00 0.00 3.33
416 591 1.050988 GGATGTCTAGGCAGGCCTCA 61.051 60.000 17.57 9.40 44.43 3.86
469 644 4.752101 CGGATTATGAGGGAGCAAAGTTAG 59.248 45.833 0.00 0.00 0.00 2.34
596 775 8.523915 AGAATTTTGATATTCTGCACCACATA 57.476 30.769 0.00 0.00 41.94 2.29
607 786 8.876275 TGGCATGCTTTAGAATTTTGATATTC 57.124 30.769 18.92 0.00 35.26 1.75
620 799 2.676632 TGGCAAATGGCATGCTTTAG 57.323 45.000 18.92 5.54 46.12 1.85
854 1038 6.645415 GGATTTCTGTGTTTCTACTCTTTCGA 59.355 38.462 0.00 0.00 0.00 3.71
867 1051 3.953612 TGAAGCAGTTGGATTTCTGTGTT 59.046 39.130 0.00 0.00 34.57 3.32
871 1055 3.571401 AGGTTGAAGCAGTTGGATTTCTG 59.429 43.478 0.00 0.00 35.12 3.02
878 1062 1.576421 GCGAGGTTGAAGCAGTTGG 59.424 57.895 0.00 0.00 0.00 3.77
950 1134 1.026182 TGTTGTCTCGATGGCCATGC 61.026 55.000 26.56 13.83 0.00 4.06
959 1143 8.395633 CGATATGGTGTATATATGTTGTCTCGA 58.604 37.037 0.00 0.00 32.09 4.04
972 1156 6.724441 AGAACTCCATTCCGATATGGTGTATA 59.276 38.462 17.81 1.06 46.33 1.47
984 1168 4.455533 TGTTCATTGAAGAACTCCATTCCG 59.544 41.667 0.00 0.00 46.19 4.30
993 1177 5.921976 TGAATGCACATGTTCATTGAAGAAC 59.078 36.000 25.28 12.02 46.22 3.01
1074 1260 2.857748 GTTTTCAGGAACAAGCAAACCG 59.142 45.455 0.00 0.00 0.00 4.44
1075 1261 2.857748 CGTTTTCAGGAACAAGCAAACC 59.142 45.455 0.00 0.00 0.00 3.27
1091 1277 5.744819 ACGCAACTTAAAGCATAAACGTTTT 59.255 32.000 20.19 2.08 0.00 2.43
1121 1308 4.406069 CTGCCAACGACAAAGTATCATTG 58.594 43.478 0.00 0.00 0.00 2.82
1126 1313 2.561478 ACCTGCCAACGACAAAGTAT 57.439 45.000 0.00 0.00 0.00 2.12
1134 1321 0.036164 AGCACAATACCTGCCAACGA 59.964 50.000 0.00 0.00 35.01 3.85
1135 1322 1.732941 TAGCACAATACCTGCCAACG 58.267 50.000 0.00 0.00 35.01 4.10
1146 1333 5.395682 ACAAATGAGCAACATAGCACAAT 57.604 34.783 0.00 0.00 38.54 2.71
1165 1352 5.163447 CGATATCCCTAGACCAACTGAACAA 60.163 44.000 0.00 0.00 0.00 2.83
1180 1371 1.625818 CCTAAAGGCAGCGATATCCCT 59.374 52.381 0.00 0.00 0.00 4.20
1182 1373 2.100605 CCCTAAAGGCAGCGATATCC 57.899 55.000 0.00 0.00 0.00 2.59
1201 1392 9.464714 CTACTAAAAGAAAAAGGGAAAAGAAGC 57.535 33.333 0.00 0.00 0.00 3.86
1215 1409 8.248945 CGGGTTCATAGAGACTACTAAAAGAAA 58.751 37.037 0.00 0.00 0.00 2.52
1217 1411 6.888632 ACGGGTTCATAGAGACTACTAAAAGA 59.111 38.462 0.00 0.00 0.00 2.52
1218 1412 7.098074 ACGGGTTCATAGAGACTACTAAAAG 57.902 40.000 0.00 0.00 0.00 2.27
1219 1413 7.318141 CAACGGGTTCATAGAGACTACTAAAA 58.682 38.462 0.00 0.00 0.00 1.52
1220 1414 6.127535 CCAACGGGTTCATAGAGACTACTAAA 60.128 42.308 0.00 0.00 0.00 1.85
1240 1434 6.908825 TGATTTTCATTAGGAGAAACCAACG 58.091 36.000 0.00 0.00 42.04 4.10
1339 1533 7.977818 AGGATAGCATTCTCATATGGTGTAAA 58.022 34.615 2.13 0.00 36.91 2.01
1351 1545 8.666573 CACAATTGATCATAGGATAGCATTCTC 58.333 37.037 13.59 0.00 32.67 2.87
1352 1546 8.162085 ACACAATTGATCATAGGATAGCATTCT 58.838 33.333 13.59 0.00 32.67 2.40
1377 1571 1.662122 CGAATTGTTAGTGCGGGGTAC 59.338 52.381 0.00 0.00 0.00 3.34
1381 1575 1.202031 GCTTCGAATTGTTAGTGCGGG 60.202 52.381 0.00 0.00 0.00 6.13
1390 1584 1.599419 GCGGTGTTTGCTTCGAATTGT 60.599 47.619 0.00 0.00 0.00 2.71
1397 1591 3.485947 TTCATATGCGGTGTTTGCTTC 57.514 42.857 0.00 0.00 0.00 3.86
1403 1597 4.082787 CCTCTTGTTTTCATATGCGGTGTT 60.083 41.667 0.00 0.00 0.00 3.32
1405 1599 3.731867 GCCTCTTGTTTTCATATGCGGTG 60.732 47.826 0.00 0.00 0.00 4.94
1410 1604 3.127548 ACAGCGCCTCTTGTTTTCATATG 59.872 43.478 2.29 0.00 0.00 1.78
1412 1606 2.483877 CACAGCGCCTCTTGTTTTCATA 59.516 45.455 2.29 0.00 0.00 2.15
1427 1621 3.546617 CGCTACTAGTAAGATCACAGCG 58.453 50.000 15.55 15.55 43.66 5.18
1568 1773 2.175284 TGATGGCCTTGGATAAGATGCA 59.825 45.455 3.32 0.00 35.92 3.96
1587 1792 5.647658 GTGTGATATGGTTGAATCTTGGTGA 59.352 40.000 0.00 0.00 0.00 4.02
1666 1872 3.814842 TGTAGTGGCTCACAATGAACTTG 59.185 43.478 7.86 0.00 40.90 3.16
1767 1985 3.062466 GAAAAGGGTGAGGCGGGC 61.062 66.667 0.00 0.00 0.00 6.13
1776 1994 3.012502 GGAGGAAAATAGGGGAAAAGGGT 59.987 47.826 0.00 0.00 0.00 4.34
1806 2024 7.120726 CGAGGAGGCTAAAAGGAGAAAAATAAA 59.879 37.037 0.00 0.00 0.00 1.40
1858 2076 2.941583 GTTCCCCTCCCCTGCCTT 60.942 66.667 0.00 0.00 0.00 4.35
2156 2407 4.135153 CTGACCGACCCTGAGCCG 62.135 72.222 0.00 0.00 0.00 5.52
2157 2408 0.755698 TATCTGACCGACCCTGAGCC 60.756 60.000 0.00 0.00 0.00 4.70
2183 2434 2.460476 ATTGAACCAAGGGGCAGGGG 62.460 60.000 0.00 0.00 37.90 4.79
2186 2437 0.527565 CGAATTGAACCAAGGGGCAG 59.472 55.000 0.00 0.00 37.90 4.85
2198 2449 2.550180 TCAAATCAACCGCACGAATTGA 59.450 40.909 10.67 10.67 36.81 2.57
2199 2450 2.927429 TCAAATCAACCGCACGAATTG 58.073 42.857 0.00 0.00 0.00 2.32
2210 2461 1.956477 CCCCCATCCGATCAAATCAAC 59.044 52.381 0.00 0.00 0.00 3.18
2243 2494 4.767255 CTCCACCCTGCGCTCCAC 62.767 72.222 9.73 0.00 0.00 4.02
2344 2595 3.781307 CCCTTGGCGATGACGGGA 61.781 66.667 0.00 0.00 37.05 5.14
2526 2791 8.785329 TGATGTATGTGCTACAAATCTTAACA 57.215 30.769 0.00 0.00 43.42 2.41
2540 2805 1.800586 CCCGTGCTATGATGTATGTGC 59.199 52.381 0.00 0.00 0.00 4.57
2702 2980 2.733956 TCCAATTCATCGGGGGAAAAG 58.266 47.619 0.00 0.00 0.00 2.27
2707 2985 1.340991 ACAGTTCCAATTCATCGGGGG 60.341 52.381 0.00 0.00 0.00 5.40
2713 2992 8.641498 AGAAAACAGATACAGTTCCAATTCAT 57.359 30.769 0.00 0.00 0.00 2.57
2754 3033 3.988819 TGCAAAGCCTTAATTTCACACC 58.011 40.909 0.00 0.00 0.00 4.16
2796 3075 9.855361 CAATAATTAGTGATTAACTCTTGCGAG 57.145 33.333 7.11 0.00 40.56 5.03
2820 3099 7.568366 AGGCCCTATGAAATTCCATTTTATCAA 59.432 33.333 0.00 0.00 31.85 2.57
2921 3200 7.439356 TCCTGCATTTGAGAAGAATTACGATAG 59.561 37.037 0.00 0.00 46.19 2.08
2928 3207 4.142004 GCCATCCTGCATTTGAGAAGAATT 60.142 41.667 0.00 0.00 0.00 2.17
2931 3210 2.291089 TGCCATCCTGCATTTGAGAAGA 60.291 45.455 0.00 0.00 36.04 2.87
2932 3211 2.097036 TGCCATCCTGCATTTGAGAAG 58.903 47.619 0.00 0.00 36.04 2.85
2994 3273 1.902938 AAGTCCCTCAAAAGCTCTGC 58.097 50.000 0.00 0.00 0.00 4.26
3110 3389 8.900781 GTTAAAAGAGGGAACTTCTTAACTGTT 58.099 33.333 0.00 0.00 44.43 3.16
3244 3523 7.222417 TGTGTGAAACTGCAAATGAATAGTTTG 59.778 33.333 6.00 0.00 41.80 2.93
3306 3586 7.329471 GCACAACTGCAGATAAATCGATATCTA 59.671 37.037 23.35 0.00 43.62 1.98
3337 3617 3.004315 ACTGCATCCGTACAAAAACCAAG 59.996 43.478 0.00 0.00 0.00 3.61
3421 3701 5.820947 ACGAGCTAATATTTTCATTTCGGGT 59.179 36.000 0.00 0.00 0.00 5.28
3424 3704 7.065894 CAGGACGAGCTAATATTTTCATTTCG 58.934 38.462 0.00 0.00 0.00 3.46
3462 3742 1.073763 ACTGCAGGAACATTGCTACCA 59.926 47.619 19.93 0.00 42.02 3.25
3479 3759 9.778993 CCATCAACTTCATTCTGTAATTTACTG 57.221 33.333 7.99 7.48 0.00 2.74
3582 3862 7.044901 GCTATAATATGTACGTATGCAGTCACG 60.045 40.741 8.37 14.53 43.63 4.35
3777 4061 8.837389 GTTCAACCTTAGTTCAAGTGACTTTAT 58.163 33.333 0.00 0.00 32.45 1.40
3782 4066 4.879545 TGGTTCAACCTTAGTTCAAGTGAC 59.120 41.667 8.40 0.00 39.58 3.67
3869 4155 5.598005 TGGTTCAATTTCATTCAGGTGAGTT 59.402 36.000 0.00 0.00 0.00 3.01
3914 4200 5.880054 TTAGAATGGCAGCTCAACTTTAC 57.120 39.130 0.00 0.00 0.00 2.01
3973 4259 2.101415 TCTCGTTCAGACTGCATATGGG 59.899 50.000 4.56 0.00 0.00 4.00
4144 4430 5.047092 CCAAACAGAAGGCCTTGTATCAATT 60.047 40.000 26.25 4.10 0.00 2.32
4244 4535 5.774498 TCACTCAGCGTCATTCTATATGT 57.226 39.130 0.00 0.00 0.00 2.29
4259 4550 7.116090 GCTAGTCACATAATAGCATTCACTCAG 59.884 40.741 0.04 0.00 41.25 3.35
4400 4697 7.722949 ACAAGTCAATCCAATCCACATATTT 57.277 32.000 0.00 0.00 0.00 1.40
4441 4738 8.680903 CAGAAATATTACAAGCATCAGGTTCTT 58.319 33.333 0.00 0.00 32.07 2.52
4443 4740 7.989826 ACAGAAATATTACAAGCATCAGGTTC 58.010 34.615 0.00 0.00 32.07 3.62
4444 4741 7.944729 ACAGAAATATTACAAGCATCAGGTT 57.055 32.000 0.00 0.00 35.46 3.50
4445 4742 7.499232 GGTACAGAAATATTACAAGCATCAGGT 59.501 37.037 0.00 0.00 0.00 4.00
4447 4744 7.498900 TGGGTACAGAAATATTACAAGCATCAG 59.501 37.037 0.00 0.00 0.00 2.90
4448 4745 7.342581 TGGGTACAGAAATATTACAAGCATCA 58.657 34.615 0.00 0.00 0.00 3.07
4450 4747 8.632679 CAATGGGTACAGAAATATTACAAGCAT 58.367 33.333 0.00 0.00 0.00 3.79
4452 4749 8.220755 TCAATGGGTACAGAAATATTACAAGC 57.779 34.615 0.00 0.00 0.00 4.01
4453 4750 9.396022 ACTCAATGGGTACAGAAATATTACAAG 57.604 33.333 0.00 0.00 0.00 3.16
4507 4806 7.291567 CGAGTTCTATTTGTTTTGAGTTCCTC 58.708 38.462 0.00 0.00 0.00 3.71
4694 4993 7.559590 AGCAAGCTATAAATCAAACAGGTAG 57.440 36.000 0.00 0.00 0.00 3.18
4697 4996 8.078596 GGATTAGCAAGCTATAAATCAAACAGG 58.921 37.037 14.52 0.00 0.00 4.00
4783 5082 6.598753 AAATCTATACGCGCTATGTTTTGT 57.401 33.333 5.73 0.00 0.00 2.83
4880 5189 4.906618 TCCCTCTGTTCCAAAATAGTGTC 58.093 43.478 0.00 0.00 0.00 3.67
4898 5207 5.565439 CGAAATTGCATCTTCAAAACTCCCT 60.565 40.000 8.52 0.00 0.00 4.20
5069 5432 7.872483 ACCCTAGAAAGTGTGCAATAAAATTTG 59.128 33.333 0.00 0.00 0.00 2.32
5107 5470 7.119699 CACGTAGATGATATAAGTACCCCGTTA 59.880 40.741 0.00 0.00 0.00 3.18
5117 5480 6.863645 CCAACAGACCACGTAGATGATATAAG 59.136 42.308 0.00 0.00 0.00 1.73
5375 5738 9.398170 CTAACATGAATCAACAAACTGTTAAGG 57.602 33.333 0.00 0.00 38.77 2.69
5469 5832 6.099159 TCATCTCCAAAACAATTGCATTGA 57.901 33.333 19.82 9.20 42.83 2.57
5583 5952 3.903090 TGGGGAAACTGATGCAAGAAAAT 59.097 39.130 0.00 0.00 0.00 1.82
5622 5991 5.928976 TGGACATCGATTACTTTCATCCAT 58.071 37.500 0.00 0.00 0.00 3.41
5641 6010 1.002366 CGCAGCTGTATTCACTGGAC 58.998 55.000 16.64 0.00 31.94 4.02
5915 6284 0.734889 CATCAACAGCTTAAGCCGGG 59.265 55.000 23.71 15.64 43.38 5.73
5962 6331 7.657336 TGCCTTTTCAATTTCAAGTAAGTAGG 58.343 34.615 0.00 0.00 0.00 3.18
5990 6363 1.531149 CGGCCAAGAACACTGTACAAG 59.469 52.381 2.24 0.00 0.00 3.16
6045 6421 3.379372 CCCATGTGCTAAATGGAGAACAG 59.621 47.826 12.69 0.00 46.44 3.16
6071 6447 8.854117 ACAAGAGCTGAGAAAAATAACTGAATT 58.146 29.630 0.00 0.00 0.00 2.17
6087 6463 2.156917 CAATGGAAGCACAAGAGCTGA 58.843 47.619 0.00 0.00 45.89 4.26
6088 6464 2.156917 TCAATGGAAGCACAAGAGCTG 58.843 47.619 0.00 0.00 45.89 4.24
6089 6465 4.321750 CATTTCAATGGAAGCACAAGAGCT 60.322 41.667 0.00 0.00 38.44 4.09
6090 6466 3.648339 TTTCAATGGAAGCACAAGAGC 57.352 42.857 0.00 0.00 33.82 4.09
6091 6467 5.130292 ACATTTCAATGGAAGCACAAGAG 57.870 39.130 4.58 0.00 40.70 2.85
6092 6468 5.534207 AACATTTCAATGGAAGCACAAGA 57.466 34.783 4.58 0.00 40.70 3.02
6093 6469 5.346822 GCTAACATTTCAATGGAAGCACAAG 59.653 40.000 17.17 1.89 42.72 3.16
6094 6470 5.221402 TGCTAACATTTCAATGGAAGCACAA 60.221 36.000 19.34 5.47 45.25 3.33
6100 6476 6.041409 TCTGGTTTGCTAACATTTCAATGGAA 59.959 34.615 13.00 0.00 40.70 3.53
6133 6509 4.595781 AGGTGTGTATGGGTTCAAAGTAGA 59.404 41.667 0.00 0.00 0.00 2.59
6279 6822 3.070018 CACGAGAAAAGGCTGAACAGAT 58.930 45.455 5.97 0.00 0.00 2.90
6282 6825 2.612212 GTTCACGAGAAAAGGCTGAACA 59.388 45.455 0.00 0.00 40.22 3.18
6298 6841 1.542030 TGTGGTGTGTGGTTTGTTCAC 59.458 47.619 0.00 0.00 35.82 3.18
6303 6846 1.611491 GGGTATGTGGTGTGTGGTTTG 59.389 52.381 0.00 0.00 0.00 2.93
6332 6875 8.991275 TCAAGAGGGGCAAAAATAATTGATTAT 58.009 29.630 0.00 0.00 34.59 1.28
6394 6937 7.399191 TCAGATTACAGAGGTTCCTAAGCTTTA 59.601 37.037 3.20 0.00 39.77 1.85
6430 6973 6.238538 CCTTTTGCATTTTGAAGTCATTGCTT 60.239 34.615 10.72 0.00 31.85 3.91
6532 7075 4.031028 GCAATAAGAATGTCGATGTGCAC 58.969 43.478 10.75 10.75 0.00 4.57
6568 7112 8.934023 AACCTTCATGTCACCTTATTCTTTTA 57.066 30.769 0.00 0.00 0.00 1.52
6584 7132 5.243981 AGTCTCATCTGTCAAACCTTCATG 58.756 41.667 0.00 0.00 0.00 3.07
6600 7148 6.056884 CGGAGTAGTAGAAAGGTAGTCTCAT 58.943 44.000 0.00 0.00 0.00 2.90
6602 7150 5.427378 ACGGAGTAGTAGAAAGGTAGTCTC 58.573 45.833 0.00 0.00 41.94 3.36
6603 7151 5.434182 ACGGAGTAGTAGAAAGGTAGTCT 57.566 43.478 0.00 0.00 41.94 3.24
6620 7168 9.985318 CTAACGTTCTTATATTATAGGACGGAG 57.015 37.037 2.82 8.93 45.45 4.63
6621 7169 8.454106 GCTAACGTTCTTATATTATAGGACGGA 58.546 37.037 2.82 4.83 45.45 4.69
6622 7170 8.457261 AGCTAACGTTCTTATATTATAGGACGG 58.543 37.037 2.82 6.70 45.45 4.79
6623 7171 9.837525 AAGCTAACGTTCTTATATTATAGGACG 57.162 33.333 2.82 9.98 46.34 4.79
6634 7182 9.874215 GTTAGTTTTTCAAGCTAACGTTCTTAT 57.126 29.630 2.82 0.00 36.43 1.73
6642 7190 9.874215 ATAAGAACGTTAGTTTTTCAAGCTAAC 57.126 29.630 0.00 11.28 41.34 2.34
6653 7201 9.252962 CGTCCCATAATATAAGAACGTTAGTTT 57.747 33.333 0.00 0.00 41.34 2.66
6654 7202 7.869429 CCGTCCCATAATATAAGAACGTTAGTT 59.131 37.037 0.00 0.09 44.47 2.24
6655 7203 7.014615 ACCGTCCCATAATATAAGAACGTTAGT 59.985 37.037 0.00 0.00 0.00 2.24
6656 7204 7.327761 CACCGTCCCATAATATAAGAACGTTAG 59.672 40.741 0.00 0.00 0.00 2.34
6657 7205 7.147312 CACCGTCCCATAATATAAGAACGTTA 58.853 38.462 0.00 0.00 0.00 3.18
6664 7212 4.530946 ACTCCCACCGTCCCATAATATAAG 59.469 45.833 0.00 0.00 0.00 1.73
6719 7267 3.819368 TCCTTGTGAAAGTGCAATCTCA 58.181 40.909 0.00 0.00 0.00 3.27
6725 7273 2.426738 CTGGTTTCCTTGTGAAAGTGCA 59.573 45.455 0.00 0.00 43.46 4.57
6730 7278 6.833041 TCTACATACTGGTTTCCTTGTGAAA 58.167 36.000 0.00 0.00 40.64 2.69
6732 7280 5.568825 GCTCTACATACTGGTTTCCTTGTGA 60.569 44.000 0.00 0.00 0.00 3.58
6746 7560 3.197983 AGTCCCAAACAGGCTCTACATAC 59.802 47.826 0.00 0.00 35.39 2.39
6770 7584 4.513318 GGAGCCGATTTTGAAAGGATAGAG 59.487 45.833 0.00 0.00 0.00 2.43
6788 7602 2.725221 AGATTTGATGGAGTGGAGCC 57.275 50.000 0.00 0.00 0.00 4.70
6789 7603 4.414337 AGTAGATTTGATGGAGTGGAGC 57.586 45.455 0.00 0.00 0.00 4.70
6871 7685 2.438021 AGATTATCTTTGGGCCGTAGCA 59.562 45.455 0.00 0.00 42.56 3.49
6878 7692 4.157840 ACCGTCAAAAGATTATCTTTGGGC 59.842 41.667 19.35 16.98 45.19 5.36
6906 7720 2.325761 CGAGTTACCTTTCTGACCGTG 58.674 52.381 0.00 0.00 0.00 4.94
6911 7725 2.288825 CCTGTGCGAGTTACCTTTCTGA 60.289 50.000 0.00 0.00 0.00 3.27
6918 7732 1.334689 GCAAAACCTGTGCGAGTTACC 60.335 52.381 0.00 0.00 31.20 2.85
6934 7748 0.398381 ACCTTCCAAGCCCAAGCAAA 60.398 50.000 0.00 0.00 43.56 3.68
6942 7756 2.092323 GGTATCAACACCTTCCAAGCC 58.908 52.381 0.00 0.00 35.55 4.35
6944 7758 3.328382 TCGGTATCAACACCTTCCAAG 57.672 47.619 0.00 0.00 36.35 3.61
6995 7809 5.880332 ACAACACTTAAAAGAGAGAGCAACA 59.120 36.000 0.00 0.00 0.00 3.33
7000 7814 8.818141 TGTATCACAACACTTAAAAGAGAGAG 57.182 34.615 0.00 0.00 0.00 3.20
7058 7872 3.342377 TCCGCACAAACATATCCTGAA 57.658 42.857 0.00 0.00 0.00 3.02
7065 7879 5.804692 ATTTCGTATTCCGCACAAACATA 57.195 34.783 0.00 0.00 36.19 2.29
7208 8022 6.667414 ACCCATAAAAGATCCTGCATAAACAA 59.333 34.615 0.00 0.00 0.00 2.83
7320 9473 9.826574 TCAAGTAAAAGAACTTAGTTGCTTCTA 57.173 29.630 0.93 0.00 40.06 2.10
7372 9525 2.238898 CCTGGGAAGACGGTAGGAATTT 59.761 50.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.