Multiple sequence alignment - TraesCS3D01G203400

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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 TraesCS3D01G203400 chr3D 100.000 6259 0 0 1 6259 252840724 252846982 0.000000e+00 11559.0
1 TraesCS3D01G203400 chr3D 100.000 192 0 0 6590 6781 252847313 252847504 8.360000e-94 355.0
2 TraesCS3D01G203400 chr3D 85.294 204 25 5 19 222 209699461 209699263 8.910000e-49 206.0
3 TraesCS3D01G203400 chr3D 97.619 42 1 0 6673 6714 252847356 252847397 9.430000e-09 73.1
4 TraesCS3D01G203400 chr3D 97.619 42 1 0 6633 6674 252847396 252847437 9.430000e-09 73.1
5 TraesCS3D01G203400 chr3A 97.104 5421 103 18 793 6188 331622582 331617191 0.000000e+00 9092.0
6 TraesCS3D01G203400 chr3A 89.570 767 49 18 1 764 331623900 331623162 0.000000e+00 944.0
7 TraesCS3D01G203400 chr3A 88.325 197 12 6 6591 6781 331611916 331611725 6.840000e-55 226.0
8 TraesCS3D01G203400 chr3A 89.091 165 15 3 60 222 269202138 269202301 1.150000e-47 202.0
9 TraesCS3D01G203400 chr3A 91.935 62 5 0 6198 6259 331612001 331611940 3.370000e-13 87.9
10 TraesCS3D01G203400 chr3A 97.619 42 1 0 6673 6714 331611874 331611833 9.430000e-09 73.1
11 TraesCS3D01G203400 chr3A 79.630 108 14 8 548 647 614702755 614702862 3.390000e-08 71.3
12 TraesCS3D01G203400 chr3B 96.128 5398 124 29 793 6160 304973128 304967786 0.000000e+00 8732.0
13 TraesCS3D01G203400 chr3B 90.814 762 50 13 1 750 304974506 304973753 0.000000e+00 1002.0
14 TraesCS3D01G203400 chr3B 86.458 192 23 2 6590 6781 304967567 304967379 2.480000e-49 207.0
15 TraesCS3D01G203400 chr3B 74.490 392 73 22 385 760 76453803 76453423 1.970000e-30 145.0
16 TraesCS3D01G203400 chr3B 74.843 318 60 16 388 692 709762776 709763086 7.140000e-25 126.0
17 TraesCS3D01G203400 chr3B 96.774 62 2 0 6198 6259 304967652 304967591 3.350000e-18 104.0
18 TraesCS3D01G203400 chr3B 95.000 60 2 1 6146 6205 304967772 304967714 7.240000e-15 93.5
19 TraesCS3D01G203400 chr5D 85.305 837 78 26 4837 5657 382379609 382380416 0.000000e+00 822.0
20 TraesCS3D01G203400 chr4B 78.512 484 78 19 286 753 91324982 91325455 1.850000e-75 294.0
21 TraesCS3D01G203400 chr4B 80.476 210 34 6 548 752 91325510 91325717 3.270000e-33 154.0
22 TraesCS3D01G203400 chr4B 97.059 34 1 0 6726 6759 609310982 609310949 2.640000e-04 58.4
23 TraesCS3D01G203400 chr7B 84.956 226 29 5 1 225 478487997 478487776 2.460000e-54 224.0
24 TraesCS3D01G203400 chr2D 84.264 197 26 5 570 762 207905541 207905736 3.230000e-43 187.0
25 TraesCS3D01G203400 chr2D 75.000 384 69 18 373 735 601507703 601508080 1.180000e-32 152.0
26 TraesCS3D01G203400 chr2D 89.362 47 5 0 6731 6777 375034052 375034098 7.340000e-05 60.2
27 TraesCS3D01G203400 chr5B 87.500 160 17 3 64 222 672812965 672813122 1.500000e-41 182.0
28 TraesCS3D01G203400 chr1A 78.618 304 44 20 463 752 62017603 62017899 1.500000e-41 182.0
29 TraesCS3D01G203400 chr6D 82.927 205 28 5 17 218 111953284 111953084 1.940000e-40 178.0
30 TraesCS3D01G203400 chr6D 83.085 201 23 10 17 213 160478944 160478751 9.040000e-39 172.0
31 TraesCS3D01G203400 chr6D 72.059 544 106 41 231 751 43952938 43952418 3.320000e-23 121.0
32 TraesCS3D01G203400 chr6A 80.995 221 34 7 5 222 23381221 23381436 1.170000e-37 169.0
33 TraesCS3D01G203400 chr6A 76.884 199 27 18 231 424 52904809 52904993 2.010000e-15 95.3
34 TraesCS3D01G203400 chr4D 83.422 187 25 5 570 751 479324791 479324606 1.170000e-37 169.0
35 TraesCS3D01G203400 chr4A 85.890 163 15 7 596 751 118990639 118990800 4.210000e-37 167.0
36 TraesCS3D01G203400 chr5A 79.151 259 37 10 397 643 464174848 464175101 5.440000e-36 163.0
37 TraesCS3D01G203400 chr7A 75.060 417 63 29 372 762 276923488 276923889 9.110000e-34 156.0
38 TraesCS3D01G203400 chr6B 76.712 292 43 18 259 543 719872355 719872082 9.170000e-29 139.0
39 TraesCS3D01G203400 chr2A 75.486 257 38 19 397 643 705065361 705065602 1.200000e-17 102.0
40 TraesCS3D01G203400 chr7D 80.870 115 11 8 385 495 595064818 595064711 5.640000e-11 80.5


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 TraesCS3D01G203400 chr3D 252840724 252847504 6780 False 3015.05 11559 98.8095 1 6781 4 chr3D.!!$F1 6780
1 TraesCS3D01G203400 chr3A 331617191 331623900 6709 True 5018.00 9092 93.3370 1 6188 2 chr3A.!!$R2 6187
2 TraesCS3D01G203400 chr3B 304967379 304974506 7127 True 2027.70 8732 93.0348 1 6781 5 chr3B.!!$R2 6780
3 TraesCS3D01G203400 chr5D 382379609 382380416 807 False 822.00 822 85.3050 4837 5657 1 chr5D.!!$F1 820
4 TraesCS3D01G203400 chr4B 91324982 91325717 735 False 224.00 294 79.4940 286 753 2 chr4B.!!$F1 467

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
976 1659 1.076044 CCATTTACCCCAGCCCCTG 60.076 63.158 0.00 0.00 0.0 4.45 F
1019 1709 0.033894 AACCCTCGTCTCTCTCCCTC 60.034 60.000 0.00 0.00 0.0 4.30 F
1021 1711 0.179029 CCCTCGTCTCTCTCCCTCTC 60.179 65.000 0.00 0.00 0.0 3.20 F
2356 3050 0.696501 TGTCCCTGCCCTAACCTTTC 59.303 55.000 0.00 0.00 0.0 2.62 F
3162 3857 1.065199 TCTGAAGATGGCCATGTCACC 60.065 52.381 26.56 12.58 0.0 4.02 F
3929 4626 0.248565 TGATGGAGCAGCAGACTGTC 59.751 55.000 3.99 0.00 46.3 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 2601 1.003355 ATCAACGGTCTGGGCACTG 60.003 57.895 0.00 0.00 0.00 3.66 R
2850 3545 3.875727 CCAGTGATCTATCAAAGGTGCAG 59.124 47.826 0.00 0.00 38.75 4.41 R
2997 3692 7.377398 ACAATATGTCAGCACAATTTAAAGCA 58.623 30.769 0.00 0.00 35.64 3.91 R
3929 4626 1.259609 TTCCAGCCTTTGCAATGGAG 58.740 50.000 30.10 21.25 41.35 3.86 R
5112 5828 1.412710 ACGTCTCTGCCTTTCACTTGA 59.587 47.619 0.00 0.00 0.00 3.02 R
5812 6544 0.466543 TGTTTGTGGGCTACTCGTGT 59.533 50.000 1.79 0.00 0.00 4.49 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
191 192 7.467557 TCAACATTTTTCTCAAATGCTTGAC 57.532 32.000 14.49 0.00 40.35 3.18
195 196 8.579682 ACATTTTTCTCAAATGCTTGACTAAC 57.420 30.769 7.13 0.00 40.35 2.34
248 250 5.187687 TGGTTTTTCTCGGTTTTCACTAGT 58.812 37.500 0.00 0.00 0.00 2.57
250 252 6.151480 TGGTTTTTCTCGGTTTTCACTAGTTT 59.849 34.615 0.00 0.00 0.00 2.66
251 253 7.031372 GGTTTTTCTCGGTTTTCACTAGTTTT 58.969 34.615 0.00 0.00 0.00 2.43
252 254 7.543172 GGTTTTTCTCGGTTTTCACTAGTTTTT 59.457 33.333 0.00 0.00 0.00 1.94
314 318 5.949735 TGTTTGCTTCTTTTCTCGTTTTCT 58.050 33.333 0.00 0.00 0.00 2.52
350 354 5.105567 TGTTTTCTCTGTGGGTTTCACTA 57.894 39.130 0.00 0.00 46.20 2.74
826 1509 2.679716 GGCCCAATGTGGAGCTCT 59.320 61.111 14.64 0.00 40.96 4.09
975 1658 3.008954 GCCATTTACCCCAGCCCCT 62.009 63.158 0.00 0.00 0.00 4.79
976 1659 1.076044 CCATTTACCCCAGCCCCTG 60.076 63.158 0.00 0.00 0.00 4.45
1017 1707 1.324005 CCAACCCTCGTCTCTCTCCC 61.324 65.000 0.00 0.00 0.00 4.30
1018 1708 0.323908 CAACCCTCGTCTCTCTCCCT 60.324 60.000 0.00 0.00 0.00 4.20
1019 1709 0.033894 AACCCTCGTCTCTCTCCCTC 60.034 60.000 0.00 0.00 0.00 4.30
1020 1710 0.917333 ACCCTCGTCTCTCTCCCTCT 60.917 60.000 0.00 0.00 0.00 3.69
1021 1711 0.179029 CCCTCGTCTCTCTCCCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
1022 1712 0.837272 CCTCGTCTCTCTCCCTCTCT 59.163 60.000 0.00 0.00 0.00 3.10
1023 1713 1.202651 CCTCGTCTCTCTCCCTCTCTC 60.203 61.905 0.00 0.00 0.00 3.20
1024 1714 0.834612 TCGTCTCTCTCCCTCTCTCC 59.165 60.000 0.00 0.00 0.00 3.71
1181 1871 5.202640 GCGGCGAAAATCTTATCGTATTTT 58.797 37.500 12.98 0.00 41.01 1.82
1888 2578 4.460382 TCCATTTGCTTGAGGAATCTGAAC 59.540 41.667 0.00 0.00 0.00 3.18
1936 2626 1.442769 CCAGACCGTTGATGTTCCAG 58.557 55.000 0.00 0.00 0.00 3.86
1970 2660 2.232696 GCCCATTGTTTAACCGGATGTT 59.767 45.455 9.46 0.00 41.11 2.71
1982 2672 9.251792 GTTTAACCGGATGTTCTATTTGTTTTT 57.748 29.630 9.46 0.00 38.42 1.94
2030 2720 6.204688 TGTCAATCAAGGGTATGATAATTCGC 59.795 38.462 0.00 0.00 39.08 4.70
2063 2753 0.978146 TACCAGAGCTCAAGGAGGCC 60.978 60.000 26.38 0.00 0.00 5.19
2356 3050 0.696501 TGTCCCTGCCCTAACCTTTC 59.303 55.000 0.00 0.00 0.00 2.62
2541 3236 2.579207 TGACTCTAGTGCATAACCGC 57.421 50.000 0.00 0.00 0.00 5.68
2850 3545 3.504520 TCGGGAAGTGTTAATTTTGCCTC 59.495 43.478 5.87 0.00 30.97 4.70
3162 3857 1.065199 TCTGAAGATGGCCATGTCACC 60.065 52.381 26.56 12.58 0.00 4.02
3199 3894 7.287696 GTCCCAATGTCCTTGTATATTTTGGAT 59.712 37.037 0.00 0.00 35.49 3.41
3929 4626 0.248565 TGATGGAGCAGCAGACTGTC 59.751 55.000 3.99 0.00 46.30 3.51
4123 4822 8.974060 AGTGGACAAACAATTAGAACTTTAGA 57.026 30.769 0.00 0.00 0.00 2.10
4217 4916 7.405292 ACCTGATTTATCTGATCTTGGACAAA 58.595 34.615 0.00 0.00 0.00 2.83
4403 5102 6.270927 TCCTAGGATCATCCAGTTCCTTATTG 59.729 42.308 7.62 0.00 42.57 1.90
4479 5178 4.503007 CGTTAGTTGCGTACATCAGCTATT 59.497 41.667 8.69 0.00 29.59 1.73
4496 5195 7.568349 TCAGCTATTCAAGGAAGTACATTCAT 58.432 34.615 0.00 0.00 39.91 2.57
4499 5198 6.205658 GCTATTCAAGGAAGTACATTCATCCC 59.794 42.308 0.00 0.00 39.91 3.85
4722 5422 1.605457 CGTCTTAGTGAAGCACTGGCA 60.605 52.381 10.15 0.00 45.01 4.92
5112 5828 5.093236 TCTAATCATGACTGGGGTATCCT 57.907 43.478 0.00 0.00 36.20 3.24
5147 5863 2.543848 GAGACGTGACAATCTTGTTGCA 59.456 45.455 0.00 0.00 42.43 4.08
5185 5901 2.094390 TCATGGAGAAAATGCAGCTTGC 60.094 45.455 0.00 1.70 45.29 4.01
5207 5923 2.357517 CCCTCGATGCGTATGGCC 60.358 66.667 0.00 0.00 42.61 5.36
5294 6010 2.480419 GTCCTGATCCAAGTGTTGTTCG 59.520 50.000 0.00 0.00 0.00 3.95
5312 6028 1.221466 CGTGATCACCGCACAGTTGT 61.221 55.000 20.03 0.00 36.06 3.32
5377 6093 5.625251 CATGATGTAAGTGACAAGTCAAGC 58.375 41.667 4.20 0.00 42.78 4.01
5589 6317 2.505819 GCTCCCCTCTCCAAGAATGTTA 59.494 50.000 0.00 0.00 0.00 2.41
5791 6523 3.874383 TTTTCTTGTCTGGTGGGATCA 57.126 42.857 0.00 0.00 0.00 2.92
5812 6544 3.938289 TGCTCATTTGCAAGCATACAA 57.062 38.095 6.71 0.00 43.30 2.41
5936 6670 2.023673 CCAGTGTTGTTTCAAGGCTGA 58.976 47.619 11.75 0.00 0.00 4.26
5965 6699 4.927267 AAACCCATCCTGTTATCTGACA 57.073 40.909 0.00 0.00 0.00 3.58
5966 6700 4.927267 AACCCATCCTGTTATCTGACAA 57.073 40.909 0.00 0.00 0.00 3.18
5972 6706 6.015519 CCCATCCTGTTATCTGACAAAACAAA 60.016 38.462 4.34 0.00 33.05 2.83
5973 6707 7.086376 CCATCCTGTTATCTGACAAAACAAAG 58.914 38.462 4.34 0.84 33.05 2.77
5974 6708 6.633500 TCCTGTTATCTGACAAAACAAAGG 57.367 37.500 4.34 3.77 33.05 3.11
5976 6710 5.010012 CCTGTTATCTGACAAAACAAAGGCT 59.990 40.000 4.34 0.00 33.05 4.58
5977 6711 5.830912 TGTTATCTGACAAAACAAAGGCTG 58.169 37.500 0.00 0.00 30.54 4.85
5978 6712 5.592282 TGTTATCTGACAAAACAAAGGCTGA 59.408 36.000 0.00 0.00 30.54 4.26
5979 6713 4.843220 ATCTGACAAAACAAAGGCTGAG 57.157 40.909 0.00 0.00 0.00 3.35
5980 6714 3.884895 TCTGACAAAACAAAGGCTGAGA 58.115 40.909 0.00 0.00 0.00 3.27
5981 6715 4.464008 TCTGACAAAACAAAGGCTGAGAT 58.536 39.130 0.00 0.00 0.00 2.75
5982 6716 5.620206 TCTGACAAAACAAAGGCTGAGATA 58.380 37.500 0.00 0.00 0.00 1.98
6023 6757 3.562557 TGTTTTCCTTCCAAAGTAGCGTC 59.437 43.478 0.00 0.00 0.00 5.19
6058 6803 9.265901 AGTGCAAGTACTCTTATATGCAAATAG 57.734 33.333 16.95 0.00 33.11 1.73
6059 6804 9.261180 GTGCAAGTACTCTTATATGCAAATAGA 57.739 33.333 16.95 0.00 33.11 1.98
6060 6805 9.481340 TGCAAGTACTCTTATATGCAAATAGAG 57.519 33.333 13.81 13.65 29.96 2.43
6061 6806 9.482627 GCAAGTACTCTTATATGCAAATAGAGT 57.517 33.333 20.58 20.58 38.49 3.24
6140 6885 2.838637 AAGGTGACCAAACCAGGAAA 57.161 45.000 3.63 0.00 43.20 3.13
6241 7082 0.040958 CTTCAACGACTTGTGGCAGC 60.041 55.000 0.00 0.00 0.00 5.25
6649 7490 1.130561 GCCAACTCGCTACCATTCAAC 59.869 52.381 0.00 0.00 0.00 3.18
6656 7497 4.345257 ACTCGCTACCATTCAACTATGGAT 59.655 41.667 9.49 0.00 46.63 3.41
6664 7505 4.392940 CATTCAACTATGGATGTCCCCTC 58.607 47.826 0.00 0.00 37.71 4.30
6665 7506 3.129262 TCAACTATGGATGTCCCCTCA 57.871 47.619 0.00 0.00 34.29 3.86
6666 7507 3.459828 TCAACTATGGATGTCCCCTCAA 58.540 45.455 0.00 0.00 34.29 3.02
6668 7509 4.080356 TCAACTATGGATGTCCCCTCAAAG 60.080 45.833 0.00 0.00 34.29 2.77
6669 7510 3.736094 ACTATGGATGTCCCCTCAAAGA 58.264 45.455 0.00 0.00 34.29 2.52
6672 7513 3.199442 TGGATGTCCCCTCAAAGACTA 57.801 47.619 0.00 0.00 34.02 2.59
6673 7514 3.526899 TGGATGTCCCCTCAAAGACTAA 58.473 45.455 0.00 0.00 34.02 2.24
6674 7515 3.263425 TGGATGTCCCCTCAAAGACTAAC 59.737 47.826 0.00 0.00 34.02 2.34
6676 7517 4.383226 GGATGTCCCCTCAAAGACTAACTC 60.383 50.000 0.00 0.00 34.02 3.01
6677 7518 3.583228 TGTCCCCTCAAAGACTAACTCA 58.417 45.455 0.00 0.00 34.02 3.41
6678 7519 3.323979 TGTCCCCTCAAAGACTAACTCAC 59.676 47.826 0.00 0.00 34.02 3.51
6697 7538 6.586344 ACTCACTACCATTCAACTATGGATG 58.414 40.000 9.49 5.21 46.63 3.51
6729 7570 5.843019 AGACTAATTTGGAACTTGAGGGA 57.157 39.130 0.00 0.00 0.00 4.20
6734 7575 6.887002 ACTAATTTGGAACTTGAGGGAATCTC 59.113 38.462 0.00 0.00 42.74 2.75
6739 7580 2.770164 ACTTGAGGGAATCTCCAACG 57.230 50.000 0.00 0.00 41.76 4.10
6741 7582 0.035439 TTGAGGGAATCTCCAACGCC 60.035 55.000 0.00 0.00 41.76 5.68
6748 7589 1.838073 AATCTCCAACGCCGACCCTT 61.838 55.000 0.00 0.00 0.00 3.95
6761 7602 1.066716 CGACCCTTAAATCGGACACCA 60.067 52.381 0.00 0.00 34.67 4.17
6763 7604 1.338389 ACCCTTAAATCGGACACCACG 60.338 52.381 0.00 0.00 0.00 4.94
6765 7606 2.094078 CCCTTAAATCGGACACCACGTA 60.094 50.000 0.00 0.00 0.00 3.57
6766 7607 2.925563 CCTTAAATCGGACACCACGTAC 59.074 50.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 220 7.064134 GTGAAAACCGAGAAAAACCAGAAATTT 59.936 33.333 0.00 0.00 0.00 1.82
219 221 6.533723 GTGAAAACCGAGAAAAACCAGAAATT 59.466 34.615 0.00 0.00 0.00 1.82
220 222 6.040247 GTGAAAACCGAGAAAAACCAGAAAT 58.960 36.000 0.00 0.00 0.00 2.17
222 224 4.703093 AGTGAAAACCGAGAAAAACCAGAA 59.297 37.500 0.00 0.00 0.00 3.02
227 229 8.456904 AAAAACTAGTGAAAACCGAGAAAAAC 57.543 30.769 0.00 0.00 0.00 2.43
314 318 9.787532 CACAGAGAAAACAAAAGAAACTCAATA 57.212 29.630 0.00 0.00 0.00 1.90
459 483 9.768662 ATCAAGCATTCAAAAAGTGTTAGAAAT 57.231 25.926 0.00 0.00 0.00 2.17
460 484 9.598517 AATCAAGCATTCAAAAAGTGTTAGAAA 57.401 25.926 0.00 0.00 0.00 2.52
767 913 2.964343 GGAGAGAGTCCGAACAGGT 58.036 57.895 0.00 0.00 41.99 4.00
826 1509 1.843368 ACTGGACCGACGATAAAGGA 58.157 50.000 0.00 0.00 0.00 3.36
975 1658 4.804420 AGATGAGCGGGAGGGGCA 62.804 66.667 0.00 0.00 0.00 5.36
976 1659 3.934962 GAGATGAGCGGGAGGGGC 61.935 72.222 0.00 0.00 0.00 5.80
1017 1707 0.535102 GAGGCGAGAGAGGGAGAGAG 60.535 65.000 0.00 0.00 0.00 3.20
1018 1708 0.986019 AGAGGCGAGAGAGGGAGAGA 60.986 60.000 0.00 0.00 0.00 3.10
1019 1709 0.535102 GAGAGGCGAGAGAGGGAGAG 60.535 65.000 0.00 0.00 0.00 3.20
1020 1710 0.986019 AGAGAGGCGAGAGAGGGAGA 60.986 60.000 0.00 0.00 0.00 3.71
1021 1711 0.535102 GAGAGAGGCGAGAGAGGGAG 60.535 65.000 0.00 0.00 0.00 4.30
1022 1712 0.986019 AGAGAGAGGCGAGAGAGGGA 60.986 60.000 0.00 0.00 0.00 4.20
1023 1713 0.819259 CAGAGAGAGGCGAGAGAGGG 60.819 65.000 0.00 0.00 0.00 4.30
1024 1714 1.447317 GCAGAGAGAGGCGAGAGAGG 61.447 65.000 0.00 0.00 0.00 3.69
1181 1871 1.224069 GACGCAGCTGCAAAGTCAGA 61.224 55.000 36.03 0.00 42.21 3.27
1414 2104 2.584608 GACATGGGAGTGGACGGG 59.415 66.667 0.00 0.00 0.00 5.28
1911 2601 1.003355 ATCAACGGTCTGGGCACTG 60.003 57.895 0.00 0.00 0.00 3.66
1982 2672 5.587443 CACCATCTTCTCAATATCTGCAACA 59.413 40.000 0.00 0.00 0.00 3.33
2261 2955 9.918630 CAGTTAAATTGGAGTCTGATCAAAAAT 57.081 29.630 0.00 0.00 0.00 1.82
2356 3050 6.854091 AACTAGTACTTTCCCTAACTCTGG 57.146 41.667 0.00 0.00 0.00 3.86
2541 3236 5.674052 ATGGAGAATATAGCTACCTGCAG 57.326 43.478 6.78 6.78 45.94 4.41
2658 3353 5.048083 TGGTGTTTCCTGCAACTTTATGATC 60.048 40.000 0.00 0.00 37.07 2.92
2850 3545 3.875727 CCAGTGATCTATCAAAGGTGCAG 59.124 47.826 0.00 0.00 38.75 4.41
2997 3692 7.377398 ACAATATGTCAGCACAATTTAAAGCA 58.623 30.769 0.00 0.00 35.64 3.91
3162 3857 3.458189 GACATTGGGACAGACCTTATCG 58.542 50.000 0.00 0.00 42.39 2.92
3929 4626 1.259609 TTCCAGCCTTTGCAATGGAG 58.740 50.000 30.10 21.25 41.35 3.86
4093 4790 7.636326 AGTTCTAATTGTTTGTCCACTTTACG 58.364 34.615 0.00 0.00 0.00 3.18
4122 4821 7.642071 TTATTTGTCCACGTTACAGTACTTC 57.358 36.000 0.00 0.00 0.00 3.01
4123 4822 8.611654 AATTATTTGTCCACGTTACAGTACTT 57.388 30.769 0.00 0.00 0.00 2.24
4217 4916 4.238514 GTCTATCAGTTTGTTCGTCTGCT 58.761 43.478 0.00 0.00 0.00 4.24
4359 5058 9.880157 TCCTAGGACAGTGTTATAATTTGTTAC 57.120 33.333 7.62 0.00 0.00 2.50
4403 5102 1.473677 TGCACAGCAGCATGAATAACC 59.526 47.619 0.00 0.00 40.11 2.85
4452 5151 2.030096 TGATGTACGCAACTAACGTGGA 60.030 45.455 0.00 0.00 44.79 4.02
4479 5178 5.014123 ACTTGGGATGAATGTACTTCCTTGA 59.986 40.000 0.00 0.00 35.38 3.02
4496 5195 4.774124 CAGCTTCATCAGATAACTTGGGA 58.226 43.478 0.00 0.00 0.00 4.37
4499 5198 4.874396 TCTGCAGCTTCATCAGATAACTTG 59.126 41.667 9.47 0.00 32.48 3.16
4789 5489 4.653555 GCTTTCAAGCCCCAAACG 57.346 55.556 0.00 0.00 46.20 3.60
4972 5673 2.865119 ACTGACCTGTTGCATGATCA 57.135 45.000 0.00 0.00 0.00 2.92
5062 5778 3.000041 TCAATCGTCCCTTTTGTGATCG 59.000 45.455 0.00 0.00 0.00 3.69
5112 5828 1.412710 ACGTCTCTGCCTTTCACTTGA 59.587 47.619 0.00 0.00 0.00 3.02
5147 5863 2.145397 TGACAAGGTCTCGGATAGCT 57.855 50.000 0.00 0.00 33.15 3.32
5185 5901 2.872388 ATACGCATCGAGGGCCCTG 61.872 63.158 34.59 21.84 0.00 4.45
5207 5923 3.889520 AGGTAAGGCTTCTTTACCTCG 57.110 47.619 12.63 0.00 34.31 4.63
5294 6010 0.944386 AACAACTGTGCGGTGATCAC 59.056 50.000 17.91 17.91 35.14 3.06
5312 6028 4.708177 CTCTGTTTCCTCACTTCTTCCAA 58.292 43.478 0.00 0.00 0.00 3.53
5377 6093 3.810310 ATCAGGCGAGTAGAAAGGAAG 57.190 47.619 0.00 0.00 0.00 3.46
5481 6197 1.141053 GGACAAATACGGAGCCCTCAT 59.859 52.381 0.00 0.00 0.00 2.90
5589 6317 6.817641 CAGCTCTACAAAGACATCAGATCTTT 59.182 38.462 0.00 0.00 45.24 2.52
5812 6544 0.466543 TGTTTGTGGGCTACTCGTGT 59.533 50.000 1.79 0.00 0.00 4.49
5936 6670 9.799106 CAGATAACAGGATGGGTTTAATTATCT 57.201 33.333 0.00 0.00 43.62 1.98
5965 6699 6.295292 GGTCCAAATATCTCAGCCTTTGTTTT 60.295 38.462 0.00 0.00 0.00 2.43
5966 6700 5.185828 GGTCCAAATATCTCAGCCTTTGTTT 59.814 40.000 0.00 0.00 0.00 2.83
5972 6706 2.708325 GAGGGTCCAAATATCTCAGCCT 59.292 50.000 0.00 0.00 37.68 4.58
5973 6707 2.708325 AGAGGGTCCAAATATCTCAGCC 59.292 50.000 0.00 0.00 0.00 4.85
5974 6708 4.133078 CAAGAGGGTCCAAATATCTCAGC 58.867 47.826 0.00 0.00 0.00 4.26
5976 6710 5.724370 TGTACAAGAGGGTCCAAATATCTCA 59.276 40.000 0.00 0.00 0.00 3.27
5977 6711 6.235231 TGTACAAGAGGGTCCAAATATCTC 57.765 41.667 0.00 0.00 0.00 2.75
5978 6712 6.158695 ACATGTACAAGAGGGTCCAAATATCT 59.841 38.462 4.87 0.00 0.00 1.98
5979 6713 6.357367 ACATGTACAAGAGGGTCCAAATATC 58.643 40.000 4.87 0.00 0.00 1.63
5980 6714 6.327386 ACATGTACAAGAGGGTCCAAATAT 57.673 37.500 4.87 0.00 0.00 1.28
5981 6715 5.772393 ACATGTACAAGAGGGTCCAAATA 57.228 39.130 4.87 0.00 0.00 1.40
5982 6716 4.657814 ACATGTACAAGAGGGTCCAAAT 57.342 40.909 4.87 0.00 0.00 2.32
6023 6757 3.440872 AGAGTACTTGCACTACTTCTCCG 59.559 47.826 0.00 0.00 0.00 4.63
6057 6802 5.022787 AGCAACTCTCTTGATCCTTACTCT 58.977 41.667 0.00 0.00 0.00 3.24
6058 6803 5.105554 TGAGCAACTCTCTTGATCCTTACTC 60.106 44.000 0.00 0.00 42.38 2.59
6059 6804 4.774726 TGAGCAACTCTCTTGATCCTTACT 59.225 41.667 0.00 0.00 42.38 2.24
6060 6805 5.078411 TGAGCAACTCTCTTGATCCTTAC 57.922 43.478 0.00 0.00 42.38 2.34
6061 6806 5.019470 TCTGAGCAACTCTCTTGATCCTTA 58.981 41.667 0.00 0.00 42.38 2.69
6062 6807 3.837146 TCTGAGCAACTCTCTTGATCCTT 59.163 43.478 0.00 0.00 42.38 3.36
6063 6808 3.439154 TCTGAGCAACTCTCTTGATCCT 58.561 45.455 0.00 0.00 42.38 3.24
6064 6809 3.883830 TCTGAGCAACTCTCTTGATCC 57.116 47.619 0.00 0.00 42.38 3.36
6065 6810 5.008619 TGATCTGAGCAACTCTCTTGATC 57.991 43.478 0.00 14.87 43.81 2.92
6066 6811 5.417754 TTGATCTGAGCAACTCTCTTGAT 57.582 39.130 3.91 0.00 42.38 2.57
6067 6812 4.322574 CCTTGATCTGAGCAACTCTCTTGA 60.323 45.833 3.91 0.00 42.38 3.02
6140 6885 4.470876 CGCTCAACGTATCACGGT 57.529 55.556 3.54 0.00 45.77 4.83
6163 6936 7.566760 TTGTGTATTGTTCTTGTCAACAGAT 57.433 32.000 0.00 0.00 37.57 2.90
6613 7454 1.271856 TGGCTCGGTGGTATTCTTCA 58.728 50.000 0.00 0.00 0.00 3.02
6637 7478 4.757149 GGACATCCATAGTTGAATGGTAGC 59.243 45.833 2.98 0.00 45.67 3.58
6649 7490 3.713764 AGTCTTTGAGGGGACATCCATAG 59.286 47.826 0.00 0.00 37.91 2.23
6656 7497 3.323979 GTGAGTTAGTCTTTGAGGGGACA 59.676 47.826 0.00 0.00 35.18 4.02
6664 7505 7.657761 AGTTGAATGGTAGTGAGTTAGTCTTTG 59.342 37.037 0.00 0.00 0.00 2.77
6665 7506 7.736893 AGTTGAATGGTAGTGAGTTAGTCTTT 58.263 34.615 0.00 0.00 0.00 2.52
6666 7507 7.304497 AGTTGAATGGTAGTGAGTTAGTCTT 57.696 36.000 0.00 0.00 0.00 3.01
6668 7509 7.707035 CCATAGTTGAATGGTAGTGAGTTAGTC 59.293 40.741 0.00 0.00 41.38 2.59
6669 7510 7.399191 TCCATAGTTGAATGGTAGTGAGTTAGT 59.601 37.037 2.98 0.00 45.67 2.24
6672 7513 6.620877 TCCATAGTTGAATGGTAGTGAGTT 57.379 37.500 2.98 0.00 45.67 3.01
6673 7514 6.156949 ACATCCATAGTTGAATGGTAGTGAGT 59.843 38.462 2.98 0.00 45.67 3.41
6674 7515 6.586344 ACATCCATAGTTGAATGGTAGTGAG 58.414 40.000 2.98 0.00 45.67 3.51
6676 7517 5.760253 GGACATCCATAGTTGAATGGTAGTG 59.240 44.000 2.98 4.21 45.67 2.74
6677 7518 5.163195 GGGACATCCATAGTTGAATGGTAGT 60.163 44.000 0.00 3.42 45.67 2.73
6678 7519 5.308825 GGGACATCCATAGTTGAATGGTAG 58.691 45.833 0.00 0.58 45.67 3.18
6697 7538 4.918588 TCCAAATTAGTCTTTGAGGGGAC 58.081 43.478 0.00 0.00 38.17 4.46
6729 7570 1.838073 AAGGGTCGGCGTTGGAGATT 61.838 55.000 6.85 0.00 0.00 2.40
6734 7575 0.730840 GATTTAAGGGTCGGCGTTGG 59.269 55.000 6.85 0.00 0.00 3.77
6741 7582 1.066716 TGGTGTCCGATTTAAGGGTCG 60.067 52.381 0.00 0.00 37.58 4.79
6748 7589 1.539388 ACGTACGTGGTGTCCGATTTA 59.461 47.619 22.14 0.00 0.00 1.40
6761 7602 3.726517 CGGTCCGTGGACGTACGT 61.727 66.667 23.04 23.04 45.41 3.57
6763 7604 3.365265 ACCGGTCCGTGGACGTAC 61.365 66.667 11.06 0.00 45.41 3.67


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

AutoCloner maintained by Alex Coulton.