Multiple sequence alignment - TraesCS3A01G088000

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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 TraesCS3A01G088000 chr3A 100.000 3917 0 0 1 3917 56761904 56765820 0.000000e+00 7234.0
1 TraesCS3A01G088000 chr3A 70.201 2584 685 70 1165 3699 36662437 36659890 1.010000e-115 427.0
2 TraesCS3A01G088000 chr3D 94.315 3360 167 9 572 3917 45015007 45018356 0.000000e+00 5125.0
3 TraesCS3A01G088000 chr3D 90.537 391 30 5 181 571 45014584 45014967 9.710000e-141 510.0
4 TraesCS3A01G088000 chr3D 70.328 2649 695 73 1169 3765 26586904 26584295 1.660000e-123 453.0
5 TraesCS3A01G088000 chr3D 91.447 152 11 2 38 187 45014280 45014431 1.430000e-49 207.0
6 TraesCS3A01G088000 chr3B 69.796 2652 712 74 1165 3765 44787359 44784746 1.030000e-100 377.0
7 TraesCS3A01G088000 chr3B 84.043 376 36 10 181 554 70125967 70126320 1.350000e-89 340.0
8 TraesCS3A01G088000 chr3B 90.062 161 14 2 29 187 70125648 70125808 1.430000e-49 207.0
9 TraesCS3A01G088000 chr3B 86.667 120 14 2 29 146 70123324 70123443 8.830000e-27 132.0
10 TraesCS3A01G088000 chr3B 75.385 260 49 12 1165 1415 44760780 44761033 1.150000e-20 111.0
11 TraesCS3A01G088000 chr3B 88.889 81 7 2 586 664 70126401 70126481 8.960000e-17 99.0
12 TraesCS3A01G088000 chr5A 70.918 1286 332 33 2498 3765 688716668 688717929 8.350000e-67 265.0
13 TraesCS3A01G088000 chr6D 71.099 1256 314 42 2444 3671 3613142 3611908 3.000000e-66 263.0
14 TraesCS3A01G088000 chr6B 70.462 1300 327 43 2498 3765 64688205 64686931 1.830000e-53 220.0
15 TraesCS3A01G088000 chrUn 75.000 460 113 2 3307 3765 94838645 94839103 1.100000e-50 211.0
16 TraesCS3A01G088000 chrUn 71.966 585 141 17 3184 3765 101629335 101629899 2.440000e-32 150.0
17 TraesCS3A01G088000 chr5B 72.638 508 118 20 1165 1660 35548828 35548330 8.770000e-32 148.0
18 TraesCS3A01G088000 chr7D 73.352 364 85 12 1289 1646 568631557 568631200 1.480000e-24 124.0
19 TraesCS3A01G088000 chr7A 73.352 364 85 12 1289 1646 657420138 657419781 1.480000e-24 124.0
20 TraesCS3A01G088000 chr7B 72.823 379 91 12 1289 1661 624709624 624709252 6.880000e-23 119.0
21 TraesCS3A01G088000 chr4A 71.525 446 114 13 1153 1590 657097222 657097662 1.490000e-19 108.0
22 TraesCS3A01G088000 chr1B 71.599 419 100 16 1165 1572 2916205 2916615 3.220000e-16 97.1


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 TraesCS3A01G088000 chr3A 56761904 56765820 3916 False 7234.000000 7234 100.000000 1 3917 1 chr3A.!!$F1 3916
1 TraesCS3A01G088000 chr3A 36659890 36662437 2547 True 427.000000 427 70.201000 1165 3699 1 chr3A.!!$R1 2534
2 TraesCS3A01G088000 chr3D 45014280 45018356 4076 False 1947.333333 5125 92.099667 38 3917 3 chr3D.!!$F1 3879
3 TraesCS3A01G088000 chr3D 26584295 26586904 2609 True 453.000000 453 70.328000 1169 3765 1 chr3D.!!$R1 2596
4 TraesCS3A01G088000 chr3B 44784746 44787359 2613 True 377.000000 377 69.796000 1165 3765 1 chr3B.!!$R1 2600
5 TraesCS3A01G088000 chr5A 688716668 688717929 1261 False 265.000000 265 70.918000 2498 3765 1 chr5A.!!$F1 1267
6 TraesCS3A01G088000 chr6D 3611908 3613142 1234 True 263.000000 263 71.099000 2444 3671 1 chr6D.!!$R1 1227
7 TraesCS3A01G088000 chr6B 64686931 64688205 1274 True 220.000000 220 70.462000 2498 3765 1 chr6B.!!$R1 1267

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
192 352 0.107214 CCTGCACAATATCCGTGGGT 60.107 55.0 7.20 0.00 34.85 4.51 F
1828 2039 0.247460 GGCCATGGAAAAGCTTGTCC 59.753 55.0 26.56 26.56 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2196 0.039708 GCTGTTGTCTGCTTCAAGCC 60.040 55.0 7.01 0.0 41.51 4.35 R
3722 3950 0.683504 AACCTCGTACTCCTGCGGAT 60.684 55.0 0.00 0.0 0.00 4.18 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
67 68 2.781681 TCTCCGTGGGAAGAAATTCC 57.218 50.000 0.00 0.00 40.38 3.01
139 142 5.316987 ACTAGCCATATAAATCCAGCAACC 58.683 41.667 0.00 0.00 0.00 3.77
140 143 4.183223 AGCCATATAAATCCAGCAACCA 57.817 40.909 0.00 0.00 0.00 3.67
148 151 3.457610 AATCCAGCAACCAAAACACAG 57.542 42.857 0.00 0.00 0.00 3.66
176 179 9.941664 CTATGATAGTTTGATTTTGCTAACCTG 57.058 33.333 0.00 0.00 0.00 4.00
183 186 5.973899 TGATTTTGCTAACCTGCACAATA 57.026 34.783 0.00 0.00 41.55 1.90
187 190 2.560504 TGCTAACCTGCACAATATCCG 58.439 47.619 0.00 0.00 38.12 4.18
188 191 2.093181 TGCTAACCTGCACAATATCCGT 60.093 45.455 0.00 0.00 38.12 4.69
189 192 2.287915 GCTAACCTGCACAATATCCGTG 59.712 50.000 1.71 1.71 37.43 4.94
192 352 0.107214 CCTGCACAATATCCGTGGGT 60.107 55.000 7.20 0.00 34.85 4.51
196 356 1.134175 GCACAATATCCGTGGGTTTGG 59.866 52.381 7.20 0.00 34.85 3.28
197 357 1.134175 CACAATATCCGTGGGTTTGGC 59.866 52.381 0.00 0.00 0.00 4.52
200 360 2.052782 ATATCCGTGGGTTTGGCTTC 57.947 50.000 0.00 0.00 0.00 3.86
213 373 2.272146 GCTTCCCATGCCTTCCGA 59.728 61.111 0.00 0.00 0.00 4.55
226 386 2.028385 GCCTTCCGAGTCTCCTTAACAA 60.028 50.000 0.00 0.00 0.00 2.83
231 391 2.353803 CCGAGTCTCCTTAACAACAGGG 60.354 54.545 0.00 0.00 31.50 4.45
236 396 2.076863 CTCCTTAACAACAGGGCTTCG 58.923 52.381 0.00 0.00 31.50 3.79
246 406 4.840005 GGGCTTCGCTTCTCCCCG 62.840 72.222 0.00 0.00 32.60 5.73
247 407 4.083862 GGCTTCGCTTCTCCCCGT 62.084 66.667 0.00 0.00 0.00 5.28
256 416 0.955919 CTTCTCCCCGTTTGGTCTGC 60.956 60.000 0.00 0.00 0.00 4.26
262 422 0.250295 CCCGTTTGGTCTGCTCTTGA 60.250 55.000 0.00 0.00 0.00 3.02
263 423 1.593196 CCGTTTGGTCTGCTCTTGAA 58.407 50.000 0.00 0.00 0.00 2.69
264 424 1.264288 CCGTTTGGTCTGCTCTTGAAC 59.736 52.381 0.00 0.00 0.00 3.18
329 489 7.336679 TGCTCAATGCTAATAACACAGTTATGT 59.663 33.333 3.41 0.00 43.37 2.29
414 574 6.712241 ACACAGAATTTACGATGACTTCAG 57.288 37.500 0.00 0.00 0.00 3.02
419 579 2.672961 TTACGATGACTTCAGGCAGG 57.327 50.000 0.00 0.00 0.00 4.85
432 592 2.439507 TCAGGCAGGAAATGATCTACCC 59.560 50.000 0.00 0.00 0.00 3.69
441 601 2.512910 ATGATCTACCCCATGACCCA 57.487 50.000 0.00 0.00 0.00 4.51
446 606 0.258484 CTACCCCATGACCCATTGCA 59.742 55.000 0.00 0.00 0.00 4.08
455 615 4.261867 CCATGACCCATTGCATGATGTAAG 60.262 45.833 0.00 0.00 43.43 2.34
490 650 3.827008 TCAGCTCTCTCTCTCTCTCTC 57.173 52.381 0.00 0.00 0.00 3.20
491 651 3.378512 TCAGCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
492 652 3.386078 TCAGCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
507 667 4.907809 TCTCTCTCTTCGTACTTTGGAGA 58.092 43.478 0.00 0.00 0.00 3.71
537 697 2.065899 TCACAAACCTGGGGAACAAG 57.934 50.000 0.00 0.00 0.00 3.16
580 779 2.420022 GTGCAGGGATAACACACATCAC 59.580 50.000 0.00 0.00 34.43 3.06
583 782 3.889815 CAGGGATAACACACATCACCAT 58.110 45.455 0.00 0.00 0.00 3.55
594 793 2.754552 CACATCACCATCACCGGAAATT 59.245 45.455 9.46 0.00 0.00 1.82
635 834 9.362151 GAAATTATATATGAACTTTGGTGGGGA 57.638 33.333 0.00 0.00 0.00 4.81
637 836 5.994416 ATATATGAACTTTGGTGGGGACT 57.006 39.130 0.00 0.00 0.00 3.85
684 884 2.738587 TTTGGTGCCACCTACTCAAA 57.261 45.000 16.23 3.76 39.58 2.69
710 910 2.386661 TGGCGAGAAGTTTCCTGATC 57.613 50.000 0.00 0.00 0.00 2.92
711 911 1.281899 GGCGAGAAGTTTCCTGATCG 58.718 55.000 0.00 0.00 34.36 3.69
712 912 1.281899 GCGAGAAGTTTCCTGATCGG 58.718 55.000 0.00 0.00 32.78 4.18
713 913 1.135083 GCGAGAAGTTTCCTGATCGGA 60.135 52.381 2.08 2.42 41.06 4.55
731 939 2.661594 GGAAAGAAATGCCGTGTCAAC 58.338 47.619 0.00 0.00 0.00 3.18
736 944 0.467290 AAATGCCGTGTCAACACCCT 60.467 50.000 7.66 0.00 43.66 4.34
738 946 3.041940 GCCGTGTCAACACCCTCG 61.042 66.667 7.66 0.00 43.66 4.63
788 996 4.514441 CACTTTGAGACTTGAGAGCAACAT 59.486 41.667 0.00 0.00 0.00 2.71
796 1004 6.471146 AGACTTGAGAGCAACATAAAGTGAT 58.529 36.000 0.00 0.00 0.00 3.06
800 1008 5.798132 TGAGAGCAACATAAAGTGATCACT 58.202 37.500 22.89 22.89 44.94 3.41
811 1019 1.502231 GTGATCACTTGTGAGCACGT 58.498 50.000 28.09 5.16 43.71 4.49
855 1063 9.357652 CAATGAAGTCAAAACTGAAGAAAAAGA 57.642 29.630 0.00 0.00 35.36 2.52
933 1141 1.328430 ACCTGGGTTACTAGCCTCGC 61.328 60.000 0.00 0.00 42.60 5.03
1007 1215 1.800681 GAACCGAAGAAATGGCCGG 59.199 57.895 0.00 0.00 46.65 6.13
1013 1221 2.063541 GAAGAAATGGCCGGGATGCG 62.064 60.000 2.18 0.00 0.00 4.73
1048 1256 0.601558 TTTGTCGTCCCTCCTCTTCG 59.398 55.000 0.00 0.00 0.00 3.79
1054 1262 2.364317 CCCTCCTCTTCGCCCTCA 60.364 66.667 0.00 0.00 0.00 3.86
1063 1271 3.790334 TTCGCCCTCATGATCGCCG 62.790 63.158 0.00 0.00 0.00 6.46
1081 1289 2.967397 CGGCGAGGGACAGTGTTA 59.033 61.111 0.00 0.00 0.00 2.41
1091 1299 1.812571 GGACAGTGTTAGCAACCATGG 59.187 52.381 11.19 11.19 0.00 3.66
1108 1316 1.215140 TGGTGATGATGATGGAGCCA 58.785 50.000 0.00 0.00 0.00 4.75
1113 1321 3.047857 TGATGATGATGGAGCCACCTTA 58.952 45.455 0.00 0.00 39.86 2.69
1116 1324 2.435805 TGATGATGGAGCCACCTTACTC 59.564 50.000 0.00 0.00 39.86 2.59
1127 1335 1.464997 CACCTTACTCGCTTTCAAGGC 59.535 52.381 0.00 0.00 41.08 4.35
1136 1344 0.733150 GCTTTCAAGGCGGGTATCAC 59.267 55.000 0.00 0.00 0.00 3.06
1140 1348 1.883084 CAAGGCGGGTATCACGAGC 60.883 63.158 0.00 0.00 0.00 5.03
1144 1352 4.201679 CGGGTATCACGAGCGGCA 62.202 66.667 1.45 0.00 0.00 5.69
1162 1370 3.706373 GAAGCTCCGGCCCACTCA 61.706 66.667 0.00 0.00 39.73 3.41
1212 1420 4.954118 TGGGAGGGCGTGACCTGT 62.954 66.667 0.00 0.00 42.10 4.00
1307 1518 1.593209 GGAACCTCACGTCGTTGCA 60.593 57.895 0.00 0.00 31.34 4.08
1342 1553 1.547675 GCTTCAACTGGTTCCATGGGA 60.548 52.381 13.02 0.00 0.00 4.37
1380 1591 4.436998 CACCTCCGCCGACTCCAC 62.437 72.222 0.00 0.00 0.00 4.02
1415 1626 1.338337 CGATAACTCACTCTCCGGCAT 59.662 52.381 0.00 0.00 0.00 4.40
1503 1714 2.503061 CTCATCCCGTCCAGCCTG 59.497 66.667 0.00 0.00 0.00 4.85
1531 1742 1.876156 CACTGACCAACCTGAAGAAGC 59.124 52.381 0.00 0.00 0.00 3.86
1557 1768 0.927537 TGACGAACAACAGCTTCACG 59.072 50.000 0.00 0.00 0.00 4.35
1592 1803 3.050275 GCTGGCCAACCTGTCGTC 61.050 66.667 7.01 0.00 37.23 4.20
1622 1833 1.000827 CCTCGATCTCTCCATCAACCG 60.001 57.143 0.00 0.00 0.00 4.44
1629 1840 1.519455 CTCCATCAACCGGCTCGAC 60.519 63.158 0.00 0.00 0.00 4.20
1662 1873 3.003763 GGACTTGGAGGCCTCGGT 61.004 66.667 26.36 22.63 41.45 4.69
1673 1884 0.825840 GGCCTCGGTAGCATCTCTCT 60.826 60.000 0.00 0.00 0.00 3.10
1675 1886 1.243902 CCTCGGTAGCATCTCTCTCC 58.756 60.000 0.00 0.00 0.00 3.71
1677 1888 2.582052 CTCGGTAGCATCTCTCTCCTT 58.418 52.381 0.00 0.00 0.00 3.36
1686 1897 4.141088 AGCATCTCTCTCCTTGATCTCTCT 60.141 45.833 0.00 0.00 0.00 3.10
1765 1976 0.321653 CCTTCAGGTTGAGGGGAACG 60.322 60.000 0.00 0.00 39.69 3.95
1828 2039 0.247460 GGCCATGGAAAAGCTTGTCC 59.753 55.000 26.56 26.56 0.00 4.02
1890 2101 1.431440 CAACCTCTCCTCTCTCGCG 59.569 63.158 0.00 0.00 0.00 5.87
1891 2102 1.027255 CAACCTCTCCTCTCTCGCGA 61.027 60.000 9.26 9.26 0.00 5.87
1893 2104 2.530497 CCTCTCCTCTCTCGCGACG 61.530 68.421 3.71 1.32 0.00 5.12
2028 2239 2.175499 GGGATGGGAGTTCATGGATTCA 59.825 50.000 0.00 0.00 0.00 2.57
2121 2332 3.184581 CAGTCGTAAACCTCTCAACAAGC 59.815 47.826 0.00 0.00 0.00 4.01
2131 2342 1.163554 CTCAACAAGCCTCCAGAAGC 58.836 55.000 0.00 0.00 0.00 3.86
2185 2396 5.463051 AATCCCTTCAGACATCTCCAATT 57.537 39.130 0.00 0.00 0.00 2.32
2349 2560 5.762179 ATCTCACCAAGTTGAACTGGATA 57.238 39.130 16.89 6.70 0.00 2.59
2371 2582 3.800506 ACTCGCGTACAATAATAACCTGC 59.199 43.478 5.77 0.00 0.00 4.85
2399 2610 3.230245 CCCAGCGAGCCTAGGGAG 61.230 72.222 11.72 0.00 44.30 4.30
2427 2638 6.615316 TCAAGGACCTCAACATTCTGGATATA 59.385 38.462 0.00 0.00 0.00 0.86
2481 2695 5.572511 CAGAGAGATCTTCAAACTGTCTTCG 59.427 44.000 0.00 0.00 33.19 3.79
2506 2720 6.975772 GCTTTCTATACAACTAGACCTGTCAG 59.024 42.308 0.00 0.00 0.00 3.51
2590 2804 8.044908 GGTTGGTACTATCAGGAAATCAGTTAA 58.955 37.037 0.00 0.00 0.00 2.01
2782 2996 3.960102 TGGAATTGCCACTTTGAAAGAGT 59.040 39.130 12.53 0.00 43.33 3.24
2812 3026 1.334869 CACAGAACAACTTGTCTGGGC 59.665 52.381 18.01 0.00 33.15 5.36
2836 3050 5.393461 CCAATCCCAGCTGTTCTACAAAATC 60.393 44.000 13.81 0.00 0.00 2.17
2841 3055 4.143030 CCAGCTGTTCTACAAAATCTGACG 60.143 45.833 13.81 0.00 0.00 4.35
2894 3108 1.202806 TCTGGAAGGTGAAGTGCCAAG 60.203 52.381 0.00 0.00 0.00 3.61
2933 3148 3.568853 ACCTAACCTATGAATCGGTCGAG 59.431 47.826 0.00 0.00 31.87 4.04
2979 3194 0.403271 ACATCAGCTTCACCTGGCTT 59.597 50.000 0.00 0.00 36.59 4.35
3054 3278 1.611977 TCACAGTAACAGGGTCACTCG 59.388 52.381 0.00 0.00 0.00 4.18
3117 3341 5.049129 CACAGGAAGCTCAAAGAAAGTAAGG 60.049 44.000 0.00 0.00 0.00 2.69
3179 3406 8.939929 CAGAGAGTGTCTTATCAAGCAATTTTA 58.060 33.333 0.00 0.00 30.64 1.52
3271 3499 2.105477 CCTTGGATGATGAGGGTACAGG 59.895 54.545 0.00 0.00 0.00 4.00
3277 3505 4.163458 GGATGATGAGGGTACAGGTACAAA 59.837 45.833 11.35 0.00 37.78 2.83
3347 3575 2.655090 TTGAGGTTGAATGTGAGGCA 57.345 45.000 0.00 0.00 0.00 4.75
3452 3680 1.891150 CTGGTTTTTGAGCTCATGCCT 59.109 47.619 19.04 0.00 40.80 4.75
3485 3713 3.944087 AGACAGTTGGCTTCATCCTAAC 58.056 45.455 0.00 0.00 0.00 2.34
3521 3749 1.153489 ATGCAGTACGCTCAGCCTG 60.153 57.895 10.27 0.00 43.06 4.85
3542 3770 3.818787 CAGCGGCTGGACATTGCC 61.819 66.667 22.11 0.00 45.25 4.52
3578 3806 4.558226 TGCACTGGACTATCTTCACAAT 57.442 40.909 0.00 0.00 0.00 2.71
3593 3821 2.092699 TCACAATGACTGTCAACCACCA 60.093 45.455 15.31 0.00 35.47 4.17
3638 3866 2.341257 AGCAACATACTTCTCGCACAG 58.659 47.619 0.00 0.00 0.00 3.66
3656 3884 0.601046 AGGACATGAGTGCACGTGTG 60.601 55.000 23.69 18.98 39.65 3.82
3722 3950 5.183713 CCAAACCATGCTGAATTCAACTAGA 59.816 40.000 9.88 0.00 0.00 2.43
3726 3954 4.212847 CCATGCTGAATTCAACTAGATCCG 59.787 45.833 9.88 0.00 0.00 4.18
3768 3996 1.943340 GCTACATTGCTCCAGGTTAGC 59.057 52.381 0.00 0.00 40.50 3.09
3791 4023 5.678047 GCAACATTGTTGCATTGTTTTCTTC 59.322 36.000 37.15 12.63 44.34 2.87
3821 4053 7.721399 CCTAGCCTGTTTCATGTTCCTAAATAT 59.279 37.037 0.00 0.00 0.00 1.28
3875 4107 1.217183 AGTACGGGGAAGGATCTGCTA 59.783 52.381 0.00 0.00 0.00 3.49
3884 4116 2.080654 AGGATCTGCTACCTCACCTC 57.919 55.000 0.00 0.00 0.00 3.85
3889 4121 0.107945 CTGCTACCTCACCTCTTGGC 60.108 60.000 0.00 0.00 36.63 4.52
3902 4134 3.118408 ACCTCTTGGCGATGTTTATAGCA 60.118 43.478 0.00 0.00 36.74 3.49
3904 4136 4.516698 CCTCTTGGCGATGTTTATAGCATT 59.483 41.667 0.00 0.00 36.74 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 5.966742 AGCAAACCTGTAGGAATTTCTTC 57.033 39.130 4.64 0.00 38.94 2.87
65 66 5.197451 TCTTTTTGAAGCAAACCTGTAGGA 58.803 37.500 4.64 0.00 38.94 2.94
67 68 7.826260 TTTTCTTTTTGAAGCAAACCTGTAG 57.174 32.000 0.00 0.00 35.89 2.74
99 100 4.974399 GCTAGTAAATGGCCTGGTAGATT 58.026 43.478 3.32 0.00 0.00 2.40
148 151 9.937175 GGTTAGCAAAATCAAACTATCATAGTC 57.063 33.333 0.00 0.00 38.26 2.59
176 179 1.134175 CCAAACCCACGGATATTGTGC 59.866 52.381 4.06 0.00 36.01 4.57
183 186 1.304134 GGAAGCCAAACCCACGGAT 60.304 57.895 0.00 0.00 0.00 4.18
189 192 2.981302 GCATGGGAAGCCAAACCC 59.019 61.111 0.00 0.00 45.74 4.11
196 356 1.821332 CTCGGAAGGCATGGGAAGC 60.821 63.158 0.00 0.00 0.00 3.86
197 357 0.462759 GACTCGGAAGGCATGGGAAG 60.463 60.000 0.00 0.00 0.00 3.46
200 360 1.144936 GAGACTCGGAAGGCATGGG 59.855 63.158 0.00 0.00 30.24 4.00
204 364 1.549170 GTTAAGGAGACTCGGAAGGCA 59.451 52.381 0.00 0.00 42.68 4.75
211 371 2.931320 GCCCTGTTGTTAAGGAGACTCG 60.931 54.545 0.00 0.00 42.68 4.18
236 396 0.955919 CAGACCAAACGGGGAGAAGC 60.956 60.000 0.00 0.00 42.91 3.86
246 406 4.370364 TTTGTTCAAGAGCAGACCAAAC 57.630 40.909 0.00 0.00 0.00 2.93
247 407 5.398603 TTTTTGTTCAAGAGCAGACCAAA 57.601 34.783 0.00 0.00 0.00 3.28
329 489 0.722676 AGAGGGGTGGGACTTGGATA 59.277 55.000 0.00 0.00 0.00 2.59
371 531 7.812690 TGTGTAAGACAGTAGAAGTGTAGAA 57.187 36.000 0.00 0.00 30.64 2.10
414 574 1.494721 TGGGGTAGATCATTTCCTGCC 59.505 52.381 0.00 0.00 34.90 4.85
419 579 3.138283 TGGGTCATGGGGTAGATCATTTC 59.862 47.826 0.00 0.00 0.00 2.17
432 592 2.036387 ACATCATGCAATGGGTCATGG 58.964 47.619 3.53 0.00 46.73 3.66
441 601 5.372343 TCACCCTACTTACATCATGCAAT 57.628 39.130 0.00 0.00 0.00 3.56
455 615 7.396055 AGAGAGAGCTGATTATTATCACCCTAC 59.604 40.741 0.00 0.00 35.87 3.18
479 639 5.670792 AAGTACGAAGAGAGAGAGAGAGA 57.329 43.478 0.00 0.00 0.00 3.10
490 650 6.036191 GCCTTTAATCTCCAAAGTACGAAGAG 59.964 42.308 0.00 0.00 32.23 2.85
491 651 5.873164 GCCTTTAATCTCCAAAGTACGAAGA 59.127 40.000 0.00 0.00 32.23 2.87
492 652 5.642063 TGCCTTTAATCTCCAAAGTACGAAG 59.358 40.000 0.00 0.00 32.23 3.79
507 667 4.020307 CCCAGGTTTGTGAATGCCTTTAAT 60.020 41.667 0.00 0.00 0.00 1.40
580 779 4.495679 CGTGTTCATAATTTCCGGTGATGG 60.496 45.833 0.00 0.00 0.00 3.51
583 782 2.417239 GCGTGTTCATAATTTCCGGTGA 59.583 45.455 0.00 0.00 0.00 4.02
594 793 1.732941 ATTTCCAGCGCGTGTTCATA 58.267 45.000 8.43 0.00 0.00 2.15
635 834 5.808366 TGTTCAGTCTATTCTGTTCCAGT 57.192 39.130 0.00 0.00 36.85 4.00
637 836 9.567776 TTATTTTGTTCAGTCTATTCTGTTCCA 57.432 29.630 0.00 0.00 36.85 3.53
661 860 4.374689 TGAGTAGGTGGCACCAAATTTA 57.625 40.909 36.28 18.08 41.95 1.40
665 864 2.738587 TTTGAGTAGGTGGCACCAAA 57.261 45.000 36.28 24.12 41.95 3.28
673 872 4.215399 TCGCCATTTTCTTTTGAGTAGGTG 59.785 41.667 0.00 0.00 0.00 4.00
674 873 4.394729 TCGCCATTTTCTTTTGAGTAGGT 58.605 39.130 0.00 0.00 0.00 3.08
684 884 4.022849 CAGGAAACTTCTCGCCATTTTCTT 60.023 41.667 0.00 0.00 40.21 2.52
711 911 2.034053 TGTTGACACGGCATTTCTTTCC 59.966 45.455 0.00 0.00 0.00 3.13
712 912 3.042887 GTGTTGACACGGCATTTCTTTC 58.957 45.455 0.00 0.00 37.10 2.62
713 913 3.078594 GTGTTGACACGGCATTTCTTT 57.921 42.857 0.00 0.00 37.10 2.52
714 914 2.774439 GTGTTGACACGGCATTTCTT 57.226 45.000 0.00 0.00 37.10 2.52
731 939 2.554032 AGCAAAAGATTCAACGAGGGTG 59.446 45.455 0.00 0.00 0.00 4.61
736 944 5.749596 TTCTGAAGCAAAAGATTCAACGA 57.250 34.783 0.00 0.00 35.14 3.85
738 946 6.199719 CCACTTTCTGAAGCAAAAGATTCAAC 59.800 38.462 2.14 0.00 35.14 3.18
796 1004 2.100087 TCACTAACGTGCTCACAAGTGA 59.900 45.455 18.05 18.05 40.12 3.41
800 1008 2.198406 GTGTCACTAACGTGCTCACAA 58.802 47.619 0.00 0.00 41.10 3.33
801 1009 1.135333 TGTGTCACTAACGTGCTCACA 59.865 47.619 4.27 14.21 44.60 3.58
802 1010 1.787155 CTGTGTCACTAACGTGCTCAC 59.213 52.381 4.27 10.93 41.43 3.51
803 1011 1.679153 TCTGTGTCACTAACGTGCTCA 59.321 47.619 4.27 0.00 40.99 4.26
804 1012 2.031069 TCTCTGTGTCACTAACGTGCTC 60.031 50.000 4.27 0.00 40.99 4.26
805 1013 1.954382 TCTCTGTGTCACTAACGTGCT 59.046 47.619 4.27 0.00 40.99 4.40
806 1014 2.320367 CTCTCTGTGTCACTAACGTGC 58.680 52.381 4.27 0.00 40.99 5.34
807 1015 2.552743 TCCTCTCTGTGTCACTAACGTG 59.447 50.000 4.27 0.00 42.59 4.49
808 1016 2.553172 GTCCTCTCTGTGTCACTAACGT 59.447 50.000 4.27 0.00 0.00 3.99
809 1017 2.552743 TGTCCTCTCTGTGTCACTAACG 59.447 50.000 4.27 0.00 0.00 3.18
810 1018 4.585955 TTGTCCTCTCTGTGTCACTAAC 57.414 45.455 4.27 0.00 0.00 2.34
811 1019 4.832823 TCATTGTCCTCTCTGTGTCACTAA 59.167 41.667 4.27 0.00 0.00 2.24
855 1063 2.975489 TCACTTTCTTCCTCTCTGCCTT 59.025 45.455 0.00 0.00 0.00 4.35
1013 1221 3.194272 AAAAGCAACCTCACGGCGC 62.194 57.895 6.90 0.00 33.37 6.53
1015 1223 0.317854 GACAAAAGCAACCTCACGGC 60.318 55.000 0.00 0.00 0.00 5.68
1034 1242 3.839432 GGGCGAAGAGGAGGGACG 61.839 72.222 0.00 0.00 0.00 4.79
1063 1271 3.291101 TAACACTGTCCCTCGCCGC 62.291 63.158 0.00 0.00 0.00 6.53
1081 1289 2.812836 TCATCATCACCATGGTTGCT 57.187 45.000 16.84 0.02 0.00 3.91
1091 1299 1.142465 AGGTGGCTCCATCATCATCAC 59.858 52.381 8.51 0.00 39.02 3.06
1108 1316 1.809684 GCCTTGAAAGCGAGTAAGGT 58.190 50.000 12.31 0.00 41.32 3.50
1127 1335 4.201679 TGCCGCTCGTGATACCCG 62.202 66.667 0.00 0.00 0.00 5.28
1144 1352 3.394836 GAGTGGGCCGGAGCTTCT 61.395 66.667 5.05 0.00 39.73 2.85
1152 1360 2.513204 CATGAGCTGAGTGGGCCG 60.513 66.667 0.00 0.00 0.00 6.13
1162 1370 0.959372 GTGCTGCTGTTCCATGAGCT 60.959 55.000 0.00 0.00 36.11 4.09
1167 1375 1.975407 GCTGGTGCTGCTGTTCCAT 60.975 57.895 0.00 0.00 36.03 3.41
1364 1575 4.988716 TGTGGAGTCGGCGGAGGT 62.989 66.667 7.21 0.00 0.00 3.85
1415 1626 1.239296 GCTCATGTTGTCAGGCAGCA 61.239 55.000 0.00 0.00 42.38 4.41
1485 1696 2.765807 AGGCTGGACGGGATGAGG 60.766 66.667 0.00 0.00 0.00 3.86
1503 1714 0.743345 GGTTGGTCAGTGTATCGCCC 60.743 60.000 0.00 0.00 0.00 6.13
1506 1717 3.056821 TCTTCAGGTTGGTCAGTGTATCG 60.057 47.826 0.00 0.00 0.00 2.92
1592 1803 0.460987 GAGATCGAGGTGTTGCAGGG 60.461 60.000 0.00 0.00 0.00 4.45
1629 1840 4.227134 CCTGGTGGGATCGAGCCG 62.227 72.222 14.60 0.00 37.23 5.52
1650 1861 2.041922 ATGCTACCGAGGCCTCCA 60.042 61.111 27.20 18.36 0.00 3.86
1660 1871 4.151883 AGATCAAGGAGAGAGATGCTACC 58.848 47.826 0.00 0.00 0.00 3.18
1662 1873 5.073554 AGAGAGATCAAGGAGAGAGATGCTA 59.926 44.000 0.00 0.00 0.00 3.49
1673 1884 2.354103 CCGTTTGCAGAGAGATCAAGGA 60.354 50.000 0.00 0.00 0.00 3.36
1675 1886 2.964740 TCCGTTTGCAGAGAGATCAAG 58.035 47.619 0.00 0.00 0.00 3.02
1677 1888 3.196469 AGAATCCGTTTGCAGAGAGATCA 59.804 43.478 0.00 0.00 0.00 2.92
1742 1953 1.078848 CCCTCAACCTGAAGGCTCG 60.079 63.158 0.00 0.00 39.32 5.03
1765 1976 2.101770 GATGCTTCCTTGCAGCGC 59.898 61.111 0.00 0.00 46.71 5.92
1828 2039 2.009042 GCTGAATCTGTTCCGGGACAG 61.009 57.143 33.79 33.79 46.58 3.51
1985 2196 0.039708 GCTGTTGTCTGCTTCAAGCC 60.040 55.000 7.01 0.00 41.51 4.35
2121 2332 2.948315 GCCTATGAAAAGCTTCTGGAGG 59.052 50.000 0.00 4.76 32.68 4.30
2131 2342 7.119699 TGAGATGTTGTTGTAGCCTATGAAAAG 59.880 37.037 0.00 0.00 0.00 2.27
2185 2396 2.115910 CACCTTCAGGCCTGCCAA 59.884 61.111 28.91 16.96 39.32 4.52
2242 2453 0.105778 GCTAGCTTCCCGATGCTCTT 59.894 55.000 7.70 0.00 41.32 2.85
2314 2525 1.482593 GGTGAGATTCCCGACAGATGT 59.517 52.381 0.00 0.00 0.00 3.06
2371 2582 0.745845 CTCGCTGGGATTGGTCCTTG 60.746 60.000 0.00 0.00 44.44 3.61
2399 2610 3.999663 CAGAATGTTGAGGTCCTTGAGTC 59.000 47.826 0.00 0.00 0.00 3.36
2427 2638 3.806625 CCATTCAGGCGATTTTTGGAT 57.193 42.857 0.00 0.00 0.00 3.41
2481 2695 6.864342 TGACAGGTCTAGTTGTATAGAAAGC 58.136 40.000 0.65 0.00 33.66 3.51
2506 2720 1.271434 GGGTCCAGAAAGGGAGTTGTC 60.271 57.143 0.00 0.00 37.71 3.18
2658 2872 6.418057 TTTGTTGGTATGCTTCCTTCAAAT 57.582 33.333 0.00 0.00 0.00 2.32
2752 2966 1.074775 TGGCAATTCCAGCGAAGGT 59.925 52.632 0.00 0.00 40.72 3.50
2782 2996 4.085357 AGTTGTTCTGTGCCAGATACAA 57.915 40.909 17.88 17.88 40.39 2.41
2812 3026 2.787473 TGTAGAACAGCTGGGATTGG 57.213 50.000 19.93 0.00 0.00 3.16
2836 3050 2.943345 GCACCGACAGCAACGTCAG 61.943 63.158 0.00 0.00 35.54 3.51
2841 3055 1.726853 AATCTAGCACCGACAGCAAC 58.273 50.000 0.00 0.00 0.00 4.17
2894 3108 1.162698 GGTTTCTAAAGACGCCCCAC 58.837 55.000 0.00 0.00 0.00 4.61
2933 3148 3.066203 CACCACACAACTTACTGTTTCCC 59.934 47.826 0.00 0.00 36.63 3.97
2979 3194 4.408921 CACAGGGTATAAGGAGGAACATGA 59.591 45.833 0.00 0.00 0.00 3.07
3229 3456 2.580962 TGCATCTGTAAACAGCACCAA 58.419 42.857 5.21 0.00 43.46 3.67
3271 3499 2.815503 ACCTTTACGGCCACATTTGTAC 59.184 45.455 2.24 0.00 35.61 2.90
3277 3505 1.611491 CAAACACCTTTACGGCCACAT 59.389 47.619 2.24 0.00 35.61 3.21
3347 3575 2.086054 GGTGACGCACTCTTCTCAAT 57.914 50.000 9.31 0.00 34.40 2.57
3452 3680 3.805807 GCCAACTGTCTAGGCTGTTGTTA 60.806 47.826 32.18 0.00 44.92 2.41
3485 3713 4.168291 GGAGCCGGCTCTTGGGAG 62.168 72.222 45.55 0.00 42.38 4.30
3521 3749 3.984193 AATGTCCAGCCGCTGAGCC 62.984 63.158 22.35 9.16 32.44 4.70
3542 3770 2.804527 CAGTGCATCCAGGATATCAACG 59.195 50.000 0.00 0.00 0.00 4.10
3578 3806 3.411446 GATGATTGGTGGTTGACAGTCA 58.589 45.455 0.00 0.00 37.66 3.41
3593 3821 5.068636 GGCTTGATATCACAGTGGATGATT 58.931 41.667 4.48 0.00 37.89 2.57
3638 3866 1.568612 CCACACGTGCACTCATGTCC 61.569 60.000 17.22 0.00 40.28 4.02
3656 3884 3.290710 TCTTGCTATGCCAAAATCTCCC 58.709 45.455 0.00 0.00 0.00 4.30
3722 3950 0.683504 AACCTCGTACTCCTGCGGAT 60.684 55.000 0.00 0.00 0.00 4.18
3726 3954 0.824759 ATGGAACCTCGTACTCCTGC 59.175 55.000 0.37 0.00 0.00 4.85
3768 3996 5.897518 CGAAGAAAACAATGCAACAATGTTG 59.102 36.000 20.77 20.77 36.60 3.33
3783 4015 2.003301 CAGGCTAGGAGCGAAGAAAAC 58.997 52.381 0.00 0.00 43.62 2.43
3791 4023 1.293924 CATGAAACAGGCTAGGAGCG 58.706 55.000 0.00 0.00 43.62 5.03
3821 4053 4.038282 GCAGCCATGATTGATCATTAACCA 59.962 41.667 3.78 0.00 44.70 3.67
3862 4094 1.414550 GGTGAGGTAGCAGATCCTTCC 59.585 57.143 0.00 0.00 33.83 3.46
3884 4116 4.036734 ACCAATGCTATAAACATCGCCAAG 59.963 41.667 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.