Multiple sequence alignment - TraesCS1D01G200100

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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 TraesCS1D01G200100 chr1D 100.000 4064 0 0 1 4064 282952147 282948084 0.000000e+00 7505
1 TraesCS1D01G200100 chr1B 90.445 2763 177 38 1340 4064 384300602 384297889 0.000000e+00 3559
2 TraesCS1D01G200100 chr1B 88.993 1381 74 39 4 1342 384301986 384300642 0.000000e+00 1637
3 TraesCS1D01G200100 chr1B 86.565 722 67 12 2364 3078 34777018 34777716 0.000000e+00 769
4 TraesCS1D01G200100 chr1B 86.565 722 67 12 2364 3078 34794346 34795044 0.000000e+00 769
5 TraesCS1D01G200100 chr1A 91.360 2280 108 37 1839 4064 354939444 354937200 0.000000e+00 3037
6 TraesCS1D01G200100 chr1A 88.221 1265 67 38 577 1798 354940679 354939454 0.000000e+00 1435
7 TraesCS1D01G200100 chr1A 91.403 221 19 0 7 227 354941490 354941270 1.840000e-78 303
8 TraesCS1D01G200100 chr1A 90.476 84 7 1 415 497 505489865 505489782 4.290000e-20 110
9 TraesCS1D01G200100 chr2B 87.543 867 90 12 2175 3035 65472562 65473416 0.000000e+00 987
10 TraesCS1D01G200100 chr2B 90.698 86 7 1 413 497 726693257 726693342 3.320000e-21 113
11 TraesCS1D01G200100 chr4A 86.413 368 43 4 2304 2665 196609905 196609539 2.940000e-106 396
12 TraesCS1D01G200100 chr4A 83.502 297 32 6 2701 2997 196609536 196609257 1.120000e-65 261
13 TraesCS1D01G200100 chr4A 91.667 120 9 1 3082 3200 196609226 196609107 9.040000e-37 165
14 TraesCS1D01G200100 chr5B 87.500 144 14 3 3081 3223 397964580 397964720 3.250000e-36 163
15 TraesCS1D01G200100 chr5B 88.764 89 9 1 412 499 35382456 35382368 1.540000e-19 108
16 TraesCS1D01G200100 chr6A 90.805 87 7 1 412 497 584511447 584511361 9.230000e-22 115
17 TraesCS1D01G200100 chr6A 88.636 88 9 1 413 499 606033356 606033269 5.560000e-19 106
18 TraesCS1D01G200100 chr3D 89.412 85 8 1 413 496 27936655 27936571 5.560000e-19 106
19 TraesCS1D01G200100 chr2D 88.043 92 8 2 412 502 110938438 110938349 5.560000e-19 106
20 TraesCS1D01G200100 chr6D 89.286 84 8 1 413 495 401752423 401752506 2.000000e-18 104
21 TraesCS1D01G200100 chr6B 87.640 89 10 1 412 499 519397683 519397595 7.190000e-18 102


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 TraesCS1D01G200100 chr1D 282948084 282952147 4063 True 7505.000000 7505 100.000 1 4064 1 chr1D.!!$R1 4063
1 TraesCS1D01G200100 chr1B 384297889 384301986 4097 True 2598.000000 3559 89.719 4 4064 2 chr1B.!!$R1 4060
2 TraesCS1D01G200100 chr1B 34777018 34777716 698 False 769.000000 769 86.565 2364 3078 1 chr1B.!!$F1 714
3 TraesCS1D01G200100 chr1B 34794346 34795044 698 False 769.000000 769 86.565 2364 3078 1 chr1B.!!$F2 714
4 TraesCS1D01G200100 chr1A 354937200 354941490 4290 True 1591.666667 3037 90.328 7 4064 3 chr1A.!!$R2 4057
5 TraesCS1D01G200100 chr2B 65472562 65473416 854 False 987.000000 987 87.543 2175 3035 1 chr2B.!!$F1 860
6 TraesCS1D01G200100 chr4A 196609107 196609905 798 True 274.000000 396 87.194 2304 3200 3 chr4A.!!$R1 896

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
936 1289 0.394565 CCTCCGCCTATTTAGCAGCT 59.605 55.000 0.00 0.0 0.0 4.24 F
1066 1428 0.179105 CAGCAGCAACAGCCAAAACA 60.179 50.000 0.00 0.0 0.0 2.83 F
1067 1429 0.536260 AGCAGCAACAGCCAAAACAA 59.464 45.000 0.00 0.0 0.0 2.83 F
1081 1443 0.666374 AAACAAAAAGGAGGACGCGG 59.334 50.000 12.47 0.0 0.0 6.46 F
1518 1956 1.075536 ACCACCAACCCTTCCTCATTC 59.924 52.381 0.00 0.0 0.0 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2522 2989 1.407258 CCTGAAAACAAGACGGCCAAA 59.593 47.619 2.24 0.0 0.0 3.28 R
2580 3047 1.837051 TGCCTTCACAGTCTCCCGT 60.837 57.895 0.00 0.0 0.0 5.28 R
2886 3358 2.159490 GCTCGACCTGACTACTCTGTTC 60.159 54.545 0.00 0.0 0.0 3.18 R
2900 3372 2.611292 CTCCTGAATTTCATGCTCGACC 59.389 50.000 0.00 0.0 0.0 4.79 R
3213 3697 0.106149 ACACGTCCTCCTCCAACAAC 59.894 55.000 0.00 0.0 0.0 3.32 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
68 69 5.221362 TGGTGAGAACTAGAATCACGTGAAA 60.221 40.000 24.13 7.67 43.39 2.69
85 86 3.084039 TGAAAGTCCTTGATGTGATGCC 58.916 45.455 0.00 0.00 0.00 4.40
93 94 1.524621 GATGTGATGCCCACCTCCG 60.525 63.158 4.22 0.00 45.09 4.63
102 103 2.286523 CCCACCTCCGCTCTTGTCT 61.287 63.158 0.00 0.00 0.00 3.41
113 114 1.959042 CTCTTGTCTGTGCACCAAGT 58.041 50.000 24.47 0.00 37.45 3.16
227 228 8.117813 TCCAAAAGGATGTGGTTTATAGTTTC 57.882 34.615 0.00 0.00 36.23 2.78
300 542 3.432051 GAGCCGGTCGGATGTCCAG 62.432 68.421 14.15 0.00 37.50 3.86
341 583 3.834813 AGTCAGGTGAAGAATCTGCACTA 59.165 43.478 19.90 4.69 39.81 2.74
347 589 3.987868 GTGAAGAATCTGCACTACAACGA 59.012 43.478 14.01 0.00 37.08 3.85
382 624 3.259064 CACGTAAAGTCACACATAGGGG 58.741 50.000 0.00 0.00 0.00 4.79
439 683 7.764901 ACTCCTTCCGTAAAGAAATGTAAGATC 59.235 37.037 0.00 0.00 37.12 2.75
446 690 9.079833 CCGTAAAGAAATGTAAGATCGTTTAGA 57.920 33.333 0.00 0.00 0.00 2.10
447 691 9.882856 CGTAAAGAAATGTAAGATCGTTTAGAC 57.117 33.333 0.00 0.00 0.00 2.59
449 693 8.842358 AAAGAAATGTAAGATCGTTTAGACCA 57.158 30.769 0.00 0.00 0.00 4.02
450 694 7.829378 AGAAATGTAAGATCGTTTAGACCAC 57.171 36.000 0.00 0.00 0.00 4.16
451 695 7.612677 AGAAATGTAAGATCGTTTAGACCACT 58.387 34.615 0.00 0.00 0.00 4.00
452 696 8.746530 AGAAATGTAAGATCGTTTAGACCACTA 58.253 33.333 0.00 0.00 0.00 2.74
453 697 8.699283 AAATGTAAGATCGTTTAGACCACTAC 57.301 34.615 0.00 0.00 0.00 2.73
454 698 7.642082 ATGTAAGATCGTTTAGACCACTACT 57.358 36.000 0.00 0.00 0.00 2.57
455 699 7.458409 TGTAAGATCGTTTAGACCACTACTT 57.542 36.000 0.00 0.00 0.00 2.24
456 700 7.889469 TGTAAGATCGTTTAGACCACTACTTT 58.111 34.615 0.00 0.00 0.00 2.66
457 701 9.013229 TGTAAGATCGTTTAGACCACTACTTTA 57.987 33.333 0.00 0.00 0.00 1.85
458 702 9.500864 GTAAGATCGTTTAGACCACTACTTTAG 57.499 37.037 0.00 0.00 0.00 1.85
459 703 7.700022 AGATCGTTTAGACCACTACTTTAGT 57.300 36.000 0.00 0.00 40.28 2.24
489 733 9.503427 CTAAAAGCTTTTATATTTCTTGACGGG 57.497 33.333 27.35 10.38 32.69 5.28
492 736 4.885325 GCTTTTATATTTCTTGACGGGGGA 59.115 41.667 0.00 0.00 0.00 4.81
521 767 1.800586 CATCCACACACAAACCTCGAG 59.199 52.381 5.13 5.13 0.00 4.04
611 942 7.885297 TGAGTAAATTGGTGAGGAAAATCTTG 58.115 34.615 0.00 0.00 0.00 3.02
739 1077 3.204827 GGCAGCCGCGTGATGATT 61.205 61.111 15.39 0.00 39.92 2.57
740 1078 2.764314 GGCAGCCGCGTGATGATTT 61.764 57.895 15.39 0.00 39.92 2.17
741 1079 1.436195 GGCAGCCGCGTGATGATTTA 61.436 55.000 15.39 0.00 39.92 1.40
755 1096 3.323729 TGATTTAGTACTACGCGTCCG 57.676 47.619 18.63 11.45 41.14 4.79
807 1155 2.100989 AGGACGGGTCTGCTTAACTAG 58.899 52.381 0.00 0.00 0.00 2.57
808 1156 2.097825 GGACGGGTCTGCTTAACTAGA 58.902 52.381 0.00 0.00 0.00 2.43
809 1157 2.159268 GGACGGGTCTGCTTAACTAGAC 60.159 54.545 0.00 6.01 41.95 2.59
810 1158 1.471684 ACGGGTCTGCTTAACTAGACG 59.528 52.381 0.00 0.00 43.24 4.18
813 1161 2.694109 GGGTCTGCTTAACTAGACGGAT 59.306 50.000 0.00 0.00 43.24 4.18
887 1240 3.055167 TGATCATCAAGGCGGAGAGAAAA 60.055 43.478 0.00 0.00 0.00 2.29
933 1286 0.756903 GTCCCTCCGCCTATTTAGCA 59.243 55.000 0.00 0.00 0.00 3.49
936 1289 0.394565 CCTCCGCCTATTTAGCAGCT 59.605 55.000 0.00 0.00 0.00 4.24
1058 1420 1.007734 CCAACAGCAGCAGCAACAG 60.008 57.895 3.17 0.00 45.49 3.16
1059 1421 1.660575 CAACAGCAGCAGCAACAGC 60.661 57.895 3.17 0.00 45.49 4.40
1060 1422 2.853290 AACAGCAGCAGCAACAGCC 61.853 57.895 3.17 0.00 45.49 4.85
1061 1423 3.292159 CAGCAGCAGCAACAGCCA 61.292 61.111 3.17 0.00 45.49 4.75
1062 1424 2.520020 AGCAGCAGCAACAGCCAA 60.520 55.556 3.17 0.00 45.49 4.52
1063 1425 2.129146 AGCAGCAGCAACAGCCAAA 61.129 52.632 3.17 0.00 45.49 3.28
1064 1426 1.227321 GCAGCAGCAACAGCCAAAA 60.227 52.632 0.00 0.00 41.58 2.44
1065 1427 1.493134 GCAGCAGCAACAGCCAAAAC 61.493 55.000 0.00 0.00 41.58 2.43
1066 1428 0.179105 CAGCAGCAACAGCCAAAACA 60.179 50.000 0.00 0.00 0.00 2.83
1067 1429 0.536260 AGCAGCAACAGCCAAAACAA 59.464 45.000 0.00 0.00 0.00 2.83
1068 1430 1.066286 AGCAGCAACAGCCAAAACAAA 60.066 42.857 0.00 0.00 0.00 2.83
1077 1439 3.118775 ACAGCCAAAACAAAAAGGAGGAC 60.119 43.478 0.00 0.00 0.00 3.85
1081 1443 0.666374 AAACAAAAAGGAGGACGCGG 59.334 50.000 12.47 0.00 0.00 6.46
1203 1583 3.057019 CAAGCTGCTGTACGTTCTTGTA 58.943 45.455 1.35 0.00 0.00 2.41
1205 1585 4.713824 AGCTGCTGTACGTTCTTGTATA 57.286 40.909 0.00 0.00 0.00 1.47
1220 1600 4.407621 TCTTGTATATTCCTTCTTCGCCCA 59.592 41.667 0.00 0.00 0.00 5.36
1223 1603 5.305585 TGTATATTCCTTCTTCGCCCATTC 58.694 41.667 0.00 0.00 0.00 2.67
1328 1723 2.834549 ACATCTGAATCTCGGTCCAACT 59.165 45.455 0.00 0.00 0.00 3.16
1359 1796 2.220363 CGATGCTCATTTCGATCTGTGG 59.780 50.000 0.00 0.00 37.55 4.17
1518 1956 1.075536 ACCACCAACCCTTCCTCATTC 59.924 52.381 0.00 0.00 0.00 2.67
1827 2275 6.595772 AGAATCAATTAGAGAACACGCATC 57.404 37.500 0.00 0.00 0.00 3.91
1828 2276 6.344500 AGAATCAATTAGAGAACACGCATCT 58.656 36.000 0.00 0.00 0.00 2.90
1981 2430 3.002791 TCACGCCAGAATTCATTGAGAC 58.997 45.455 8.44 0.00 0.00 3.36
2048 2497 1.609061 CCCGCACAAGGGCTATATCAG 60.609 57.143 0.00 0.00 45.72 2.90
2167 2625 5.009010 AGTTTGTAAGTTTGCATCTCCACAG 59.991 40.000 0.00 0.00 0.00 3.66
2224 2682 8.451908 ACCATTGCTTACTTATTCCTATTGTC 57.548 34.615 0.00 0.00 0.00 3.18
2294 2752 1.536331 GGAGTATCGACATCGGACCTC 59.464 57.143 0.73 4.36 40.29 3.85
2426 2888 6.074648 TGATGACACCTAACCAATCCTTTTT 58.925 36.000 0.00 0.00 0.00 1.94
2522 2989 3.563479 CCCAGCCCAGGTAATAACTTGTT 60.563 47.826 0.00 0.00 30.96 2.83
2527 2994 4.816392 CCCAGGTAATAACTTGTTTTGGC 58.184 43.478 0.00 0.00 30.96 4.52
2692 3163 4.030314 CCATCCACATGGCAGAATAGAT 57.970 45.455 0.00 0.00 43.55 1.98
2726 3198 6.891908 AGGCCTGATGATTATTAGTTGTGTTT 59.108 34.615 3.11 0.00 0.00 2.83
2739 3211 8.691661 ATTAGTTGTGTTTATCTCCTTGTGTT 57.308 30.769 0.00 0.00 0.00 3.32
2740 3212 6.377327 AGTTGTGTTTATCTCCTTGTGTTG 57.623 37.500 0.00 0.00 0.00 3.33
2900 3372 9.279904 CTTAAAATCTACGAACAGAGTAGTCAG 57.720 37.037 0.00 0.00 41.55 3.51
2906 3378 3.750639 GAACAGAGTAGTCAGGTCGAG 57.249 52.381 0.00 0.00 0.00 4.04
3024 3503 3.384532 CAGGCGGGCAAAGGCATT 61.385 61.111 3.78 0.00 43.71 3.56
3237 3721 1.046472 TGGAGGAGGACGTGTGTGTT 61.046 55.000 0.00 0.00 0.00 3.32
3306 3796 1.429148 GCAGAGGCGTTTGGTATCGG 61.429 60.000 0.00 0.00 0.00 4.18
3323 3813 0.027324 CGGTCGAGCGTCTTACCTAC 59.973 60.000 27.67 0.00 0.00 3.18
3324 3814 1.377536 GGTCGAGCGTCTTACCTACT 58.622 55.000 0.00 0.00 0.00 2.57
3325 3815 1.742268 GGTCGAGCGTCTTACCTACTT 59.258 52.381 0.00 0.00 0.00 2.24
3326 3816 2.939103 GGTCGAGCGTCTTACCTACTTA 59.061 50.000 0.00 0.00 0.00 2.24
3357 3847 6.126710 TGGAGAGAGTTTTGTTACCCTTGTTA 60.127 38.462 0.00 0.00 0.00 2.41
3359 3849 7.447545 GGAGAGAGTTTTGTTACCCTTGTTATT 59.552 37.037 0.00 0.00 0.00 1.40
3366 3856 8.631797 GTTTTGTTACCCTTGTTATTTGTAGGA 58.368 33.333 0.00 0.00 0.00 2.94
3408 3898 7.205992 AGAGAAAAGAAGTTGCTCCATTTTTC 58.794 34.615 0.00 0.00 34.79 2.29
3412 3902 3.004734 AGAAGTTGCTCCATTTTTCGTGG 59.995 43.478 0.00 0.00 38.11 4.94
3418 3908 4.643463 TGCTCCATTTTTCGTGGTTACTA 58.357 39.130 0.00 0.00 37.96 1.82
3478 3974 6.909550 TTTTGTAACCCATCAAGTATGCTT 57.090 33.333 0.00 0.00 33.92 3.91
3479 3975 6.909550 TTTGTAACCCATCAAGTATGCTTT 57.090 33.333 0.00 0.00 33.92 3.51
3481 3977 6.909550 TGTAACCCATCAAGTATGCTTTTT 57.090 33.333 0.00 0.00 33.92 1.94
3520 4040 1.946768 GTTGGTGTTGAACAGCTGCTA 59.053 47.619 25.31 5.21 46.03 3.49
3562 4090 2.036256 GGTGCCCTGCTGAATGGT 59.964 61.111 0.00 0.00 0.00 3.55
3601 4129 1.674057 GATACATCCTGGCCTCGGG 59.326 63.158 3.32 3.76 40.84 5.14
3619 4147 1.604378 GCTCCTGGCCACATACACT 59.396 57.895 0.00 0.00 34.27 3.55
3623 4151 1.647545 CCTGGCCACATACACTTGCG 61.648 60.000 0.00 0.00 0.00 4.85
3627 4155 0.443869 GCCACATACACTTGCGTCAG 59.556 55.000 0.00 0.00 0.00 3.51
3631 4159 2.409715 CACATACACTTGCGTCAGACAG 59.590 50.000 0.41 0.00 0.00 3.51
3637 4165 1.137086 ACTTGCGTCAGACAGAACACT 59.863 47.619 0.41 0.00 0.00 3.55
3647 4175 5.006165 GTCAGACAGAACACTGAAAAGTCTG 59.994 44.000 12.12 12.12 43.29 3.51
3648 4176 3.873952 AGACAGAACACTGAAAAGTCTGC 59.126 43.478 0.00 0.00 35.80 4.26
3650 4178 2.291741 CAGAACACTGAAAAGTCTGCCC 59.708 50.000 0.00 0.00 33.94 5.36
3863 4391 4.379243 ACCAACCCAGCTCGCTCG 62.379 66.667 0.00 0.00 0.00 5.03
3937 4465 4.426313 TCCTCTCCTCGCGCCTCA 62.426 66.667 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.178623 CCGCAACACTATAGTTTTCAACAGA 59.821 40.000 1.56 0.00 0.00 3.41
1 2 5.049680 ACCGCAACACTATAGTTTTCAACAG 60.050 40.000 1.56 0.00 0.00 3.16
2 3 4.817464 ACCGCAACACTATAGTTTTCAACA 59.183 37.500 1.56 0.00 0.00 3.33
68 69 0.994247 TGGGCATCACATCAAGGACT 59.006 50.000 0.00 0.00 0.00 3.85
85 86 1.079543 CAGACAAGAGCGGAGGTGG 60.080 63.158 0.00 0.00 39.88 4.61
93 94 0.590195 CTTGGTGCACAGACAAGAGC 59.410 55.000 22.51 3.23 43.13 4.09
102 103 1.675483 CAGCTAAACACTTGGTGCACA 59.325 47.619 20.43 1.62 36.98 4.57
113 114 3.943381 CAGGAGCAATGATCAGCTAAACA 59.057 43.478 9.28 0.00 42.04 2.83
144 145 3.426568 GCACTCCGCAAGCCTGAC 61.427 66.667 0.00 0.00 41.79 3.51
227 228 3.774282 CATTTTGTGTTCAACATGGCG 57.226 42.857 0.00 0.00 38.99 5.69
300 542 3.610911 ACTGGCACTAAGAAATAGGTGC 58.389 45.455 8.19 8.19 37.65 5.01
341 583 0.321653 GAAGTCCAGGGCATCGTTGT 60.322 55.000 0.00 0.00 0.00 3.32
382 624 1.399791 GCACATAAGCAGAGAGGTTGC 59.600 52.381 0.00 0.00 41.83 4.17
463 707 9.503427 CCCGTCAAGAAATATAAAAGCTTTTAG 57.497 33.333 29.69 17.15 36.22 1.85
464 708 8.463607 CCCCGTCAAGAAATATAAAAGCTTTTA 58.536 33.333 28.78 28.78 37.08 1.52
465 709 7.320399 CCCCGTCAAGAAATATAAAAGCTTTT 58.680 34.615 26.50 26.50 0.00 2.27
466 710 6.127451 CCCCCGTCAAGAAATATAAAAGCTTT 60.127 38.462 5.69 5.69 0.00 3.51
484 728 3.135167 TGGATGTTTTATACTCCCCCGTC 59.865 47.826 0.00 0.00 0.00 4.79
487 731 4.204799 GTGTGGATGTTTTATACTCCCCC 58.795 47.826 0.00 0.00 0.00 5.40
488 732 4.638865 GTGTGTGGATGTTTTATACTCCCC 59.361 45.833 0.00 0.00 0.00 4.81
489 733 5.250200 TGTGTGTGGATGTTTTATACTCCC 58.750 41.667 0.00 0.00 0.00 4.30
492 736 6.775629 AGGTTTGTGTGTGGATGTTTTATACT 59.224 34.615 0.00 0.00 0.00 2.12
737 1075 1.401552 TGCGGACGCGTAGTACTAAAT 59.598 47.619 13.97 0.00 45.51 1.40
738 1076 0.801872 TGCGGACGCGTAGTACTAAA 59.198 50.000 13.97 0.00 45.51 1.85
739 1077 0.374758 CTGCGGACGCGTAGTACTAA 59.625 55.000 13.97 0.00 45.51 2.24
740 1078 0.460109 TCTGCGGACGCGTAGTACTA 60.460 55.000 13.97 0.00 45.51 1.82
741 1079 1.300971 TTCTGCGGACGCGTAGTACT 61.301 55.000 13.97 0.00 45.51 2.73
755 1096 7.048512 GGATATATACCCACACCTAATTCTGC 58.951 42.308 0.00 0.00 0.00 4.26
807 1155 4.174129 CGCCCGCCAAAATCCGTC 62.174 66.667 0.00 0.00 0.00 4.79
810 1158 3.822192 GTCCGCCCGCCAAAATCC 61.822 66.667 0.00 0.00 0.00 3.01
826 1177 1.959226 GTGTTGTCATCGCGTGGGT 60.959 57.895 5.77 0.00 0.00 4.51
887 1240 0.247736 ACTCGCTCGGCTTTTCTGAT 59.752 50.000 0.00 0.00 0.00 2.90
1058 1420 2.469826 CGTCCTCCTTTTTGTTTTGGC 58.530 47.619 0.00 0.00 0.00 4.52
1059 1421 2.469826 GCGTCCTCCTTTTTGTTTTGG 58.530 47.619 0.00 0.00 0.00 3.28
1060 1422 2.116366 CGCGTCCTCCTTTTTGTTTTG 58.884 47.619 0.00 0.00 0.00 2.44
1061 1423 1.066454 CCGCGTCCTCCTTTTTGTTTT 59.934 47.619 4.92 0.00 0.00 2.43
1062 1424 0.666374 CCGCGTCCTCCTTTTTGTTT 59.334 50.000 4.92 0.00 0.00 2.83
1063 1425 1.792118 GCCGCGTCCTCCTTTTTGTT 61.792 55.000 4.92 0.00 0.00 2.83
1064 1426 2.258726 GCCGCGTCCTCCTTTTTGT 61.259 57.895 4.92 0.00 0.00 2.83
1065 1427 2.561373 GCCGCGTCCTCCTTTTTG 59.439 61.111 4.92 0.00 0.00 2.44
1066 1428 2.671963 GGCCGCGTCCTCCTTTTT 60.672 61.111 4.92 0.00 0.00 1.94
1067 1429 3.948719 TGGCCGCGTCCTCCTTTT 61.949 61.111 8.05 0.00 0.00 2.27
1068 1430 4.699522 GTGGCCGCGTCCTCCTTT 62.700 66.667 8.05 0.00 0.00 3.11
1203 1583 4.349342 AGAGAATGGGCGAAGAAGGAATAT 59.651 41.667 0.00 0.00 0.00 1.28
1205 1585 2.507471 AGAGAATGGGCGAAGAAGGAAT 59.493 45.455 0.00 0.00 0.00 3.01
1252 1647 1.757118 TCCAACAAATTCAACCGCCAA 59.243 42.857 0.00 0.00 0.00 4.52
1518 1956 7.657761 GTGATGTATACTAATTGAAGAGGTGGG 59.342 40.741 4.17 0.00 0.00 4.61
1799 2247 9.249457 TGCGTGTTCTCTAATTGATTCTTATAG 57.751 33.333 0.00 0.00 0.00 1.31
1800 2248 9.764363 ATGCGTGTTCTCTAATTGATTCTTATA 57.236 29.630 0.00 0.00 0.00 0.98
1801 2249 8.668510 ATGCGTGTTCTCTAATTGATTCTTAT 57.331 30.769 0.00 0.00 0.00 1.73
1812 2260 3.377172 TCATCGAGATGCGTGTTCTCTAA 59.623 43.478 8.14 0.43 41.80 2.10
1814 2262 1.745653 TCATCGAGATGCGTGTTCTCT 59.254 47.619 8.14 0.00 41.80 3.10
1815 2263 2.194800 TCATCGAGATGCGTGTTCTC 57.805 50.000 8.14 2.49 41.80 2.87
1823 2271 3.755378 AGGGCATAAAATCATCGAGATGC 59.245 43.478 8.14 0.00 38.65 3.91
1827 2275 4.818546 AGAACAGGGCATAAAATCATCGAG 59.181 41.667 0.00 0.00 0.00 4.04
1828 2276 4.780815 AGAACAGGGCATAAAATCATCGA 58.219 39.130 0.00 0.00 0.00 3.59
1868 2316 4.866486 GGCAGAGCAGAAAATACCATTTTG 59.134 41.667 1.77 0.00 0.00 2.44
1981 2430 2.154580 GCGACATAGTCAATCTGATGCG 59.845 50.000 0.00 0.00 32.09 4.73
2048 2497 2.200955 AGAGGGGGAAAAGTGAGGATC 58.799 52.381 0.00 0.00 0.00 3.36
2167 2625 3.784851 GCCGTCGATCGACATATACTAGC 60.785 52.174 38.62 24.95 44.77 3.42
2224 2682 7.928307 TTTCCAATCTTCTTGACCTGATAAG 57.072 36.000 0.00 0.00 0.00 1.73
2294 2752 8.183104 TGTAGTCCTTGACTATCCTCATTATG 57.817 38.462 7.19 0.00 45.21 1.90
2309 2767 5.147330 TGACATACTGGTTGTAGTCCTTG 57.853 43.478 0.00 0.00 34.24 3.61
2522 2989 1.407258 CCTGAAAACAAGACGGCCAAA 59.593 47.619 2.24 0.00 0.00 3.28
2527 2994 3.625764 TGTTTCTCCTGAAAACAAGACGG 59.374 43.478 0.00 0.00 42.94 4.79
2580 3047 1.837051 TGCCTTCACAGTCTCCCGT 60.837 57.895 0.00 0.00 0.00 5.28
2726 3198 6.816640 GCAACTACATACAACACAAGGAGATA 59.183 38.462 0.00 0.00 0.00 1.98
2739 3211 2.809119 CCACCGTTTGCAACTACATACA 59.191 45.455 0.00 0.00 0.00 2.29
2740 3212 2.413634 GCCACCGTTTGCAACTACATAC 60.414 50.000 0.00 0.00 0.00 2.39
2816 3288 2.927856 TTCTCCAGGAAGCCGGCA 60.928 61.111 31.54 4.35 0.00 5.69
2886 3358 2.159490 GCTCGACCTGACTACTCTGTTC 60.159 54.545 0.00 0.00 0.00 3.18
2900 3372 2.611292 CTCCTGAATTTCATGCTCGACC 59.389 50.000 0.00 0.00 0.00 4.79
2906 3378 5.413833 TGTCTCTTTCTCCTGAATTTCATGC 59.586 40.000 0.00 0.00 31.56 4.06
3107 3586 5.198274 CACAACTAAACAACTTCTCGCTTC 58.802 41.667 0.00 0.00 0.00 3.86
3208 3692 2.685897 CGTCCTCCTCCAACAACAAAAA 59.314 45.455 0.00 0.00 0.00 1.94
3213 3697 0.106149 ACACGTCCTCCTCCAACAAC 59.894 55.000 0.00 0.00 0.00 3.32
3221 3705 0.539986 ACAAACACACACGTCCTCCT 59.460 50.000 0.00 0.00 0.00 3.69
3228 3712 1.069568 ACACACACACAAACACACACG 60.070 47.619 0.00 0.00 0.00 4.49
3237 3721 3.633235 GTGAAACAACACACACACACAA 58.367 40.909 0.00 0.00 40.11 3.33
3302 3792 0.747283 AGGTAAGACGCTCGACCGAT 60.747 55.000 7.21 0.00 33.97 4.18
3306 3796 3.620821 AGTAAGTAGGTAAGACGCTCGAC 59.379 47.826 0.00 0.00 0.00 4.20
3323 3813 9.141400 GTAACAAAACTCTCTCCACATAGTAAG 57.859 37.037 0.00 0.00 0.00 2.34
3324 3814 8.092687 GGTAACAAAACTCTCTCCACATAGTAA 58.907 37.037 0.00 0.00 0.00 2.24
3325 3815 7.310237 GGGTAACAAAACTCTCTCCACATAGTA 60.310 40.741 0.00 0.00 39.74 1.82
3326 3816 6.465084 GGTAACAAAACTCTCTCCACATAGT 58.535 40.000 0.00 0.00 0.00 2.12
3377 3867 7.170965 TGGAGCAACTTCTTTTCTCTCATTAT 58.829 34.615 0.00 0.00 0.00 1.28
3408 3898 6.875195 TCCCTTTTTCTTATGTAGTAACCACG 59.125 38.462 0.00 0.00 0.00 4.94
3412 3902 7.389607 TGTGCTCCCTTTTTCTTATGTAGTAAC 59.610 37.037 0.00 0.00 0.00 2.50
3418 3908 5.385198 TCTTGTGCTCCCTTTTTCTTATGT 58.615 37.500 0.00 0.00 0.00 2.29
3479 3975 6.588373 CCAACGTTCTTTTCTTCCTTCAAAAA 59.412 34.615 0.00 0.00 0.00 1.94
3481 3977 5.184287 ACCAACGTTCTTTTCTTCCTTCAAA 59.816 36.000 0.00 0.00 0.00 2.69
3484 3980 4.095932 ACACCAACGTTCTTTTCTTCCTTC 59.904 41.667 0.00 0.00 0.00 3.46
3485 3981 4.014406 ACACCAACGTTCTTTTCTTCCTT 58.986 39.130 0.00 0.00 0.00 3.36
3486 3982 3.617284 ACACCAACGTTCTTTTCTTCCT 58.383 40.909 0.00 0.00 0.00 3.36
3520 4040 2.189594 CACATCACCACTCCATGTGT 57.810 50.000 3.57 0.00 44.81 3.72
3562 4090 2.366266 CCGGATTGGTATCCTTCGGTTA 59.634 50.000 0.00 0.00 46.97 2.85
3601 4129 0.035056 AAGTGTATGTGGCCAGGAGC 60.035 55.000 5.11 0.00 42.60 4.70
3619 4147 1.136110 TCAGTGTTCTGTCTGACGCAA 59.864 47.619 2.98 0.00 41.91 4.85
3623 4151 5.006165 CAGACTTTTCAGTGTTCTGTCTGAC 59.994 44.000 22.09 0.00 39.77 3.51
3627 4155 3.002759 GGCAGACTTTTCAGTGTTCTGTC 59.997 47.826 0.00 0.00 41.91 3.51
3631 4159 1.264288 CGGGCAGACTTTTCAGTGTTC 59.736 52.381 0.00 0.00 31.22 3.18
3637 4165 0.882927 CGAACCGGGCAGACTTTTCA 60.883 55.000 6.32 0.00 0.00 2.69
3666 4194 3.710722 AGGGTTGGCTGCCTCTCG 61.711 66.667 21.03 0.00 0.00 4.04
3667 4195 2.045536 CAGGGTTGGCTGCCTCTC 60.046 66.667 21.03 12.79 0.00 3.20
3668 4196 4.357279 GCAGGGTTGGCTGCCTCT 62.357 66.667 21.03 9.17 40.40 3.69
3669 4197 4.357279 AGCAGGGTTGGCTGCCTC 62.357 66.667 21.03 12.58 46.79 4.70
3964 4492 0.533491 GAGCCAATGCCATGAAAGCA 59.467 50.000 0.00 0.00 45.94 3.91


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

AutoCloner maintained by Alex Coulton.