Multiple sequence alignment - TraesCS4A01G480800

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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 TraesCS4A01G480800 chr4A 100.000 5419 0 0 1 5419 737089778 737084360 0.000000e+00 10008.0
1 TraesCS4A01G480800 chr4A 85.388 1663 152 29 3803 5419 736309205 736310822 0.000000e+00 1640.0
2 TraesCS4A01G480800 chr4A 82.031 1664 171 46 2221 3796 736307542 736309165 0.000000e+00 1299.0
3 TraesCS4A01G480800 chr4A 83.641 1137 101 40 1 1088 736306384 736307484 0.000000e+00 990.0
4 TraesCS4A01G480800 chr4A 84.973 925 83 18 4452 5368 737066948 737066072 0.000000e+00 887.0
5 TraesCS4A01G480800 chr4A 84.423 918 71 32 1 866 737070493 737069596 0.000000e+00 837.0
6 TraesCS4A01G480800 chr4A 79.900 1204 146 41 2655 3796 737068797 737067628 0.000000e+00 795.0
7 TraesCS4A01G480800 chr4A 85.180 668 55 18 3803 4467 737067588 737066962 0.000000e+00 645.0
8 TraesCS4A01G480800 chr4A 92.938 439 31 0 2220 2658 737069362 737068924 1.650000e-179 640.0
9 TraesCS4A01G480800 chr4A 76.812 897 139 43 3807 4690 737062073 737061233 1.790000e-119 440.0
10 TraesCS4A01G480800 chr4A 91.765 170 14 0 919 1088 737069588 737069419 2.520000e-58 237.0
11 TraesCS4A01G480800 chr4A 85.714 98 14 0 991 1088 737063735 737063638 2.670000e-18 104.0
12 TraesCS4A01G480800 chr7D 91.724 2163 108 37 1 2131 5386142 5388265 0.000000e+00 2937.0
13 TraesCS4A01G480800 chr7D 92.975 1637 50 22 2195 3796 5388266 5389872 0.000000e+00 2326.0
14 TraesCS4A01G480800 chr7D 92.260 1124 72 10 1104 2214 262098 260977 0.000000e+00 1580.0
15 TraesCS4A01G480800 chr7D 91.585 1117 84 9 1101 2213 144158596 144159706 0.000000e+00 1533.0
16 TraesCS4A01G480800 chr7D 82.130 1662 172 47 2221 3796 5414954 5416576 0.000000e+00 1308.0
17 TraesCS4A01G480800 chr7D 84.977 1278 119 31 4207 5419 5390246 5391515 0.000000e+00 1229.0
18 TraesCS4A01G480800 chr7D 87.398 984 96 13 4452 5419 5417263 5418234 0.000000e+00 1105.0
19 TraesCS4A01G480800 chr7D 83.993 1137 95 40 1 1088 5413798 5414896 0.000000e+00 1011.0
20 TraesCS4A01G480800 chr7D 86.103 662 58 7 3803 4463 5416616 5417244 0.000000e+00 682.0
21 TraesCS4A01G480800 chr7D 92.032 251 18 2 3803 4052 5389912 5390161 8.640000e-93 351.0
22 TraesCS4A01G480800 chr7D 94.737 38 2 0 4092 4129 5390159 5390196 5.860000e-05 60.2
23 TraesCS4A01G480800 chr7A 94.143 1639 69 12 3803 5419 6865713 6867346 0.000000e+00 2470.0
24 TraesCS4A01G480800 chr7A 90.829 905 45 18 190 1088 6863133 6864005 0.000000e+00 1177.0
25 TraesCS4A01G480800 chr7A 91.513 707 34 2 2220 2900 6864231 6864937 0.000000e+00 950.0
26 TraesCS4A01G480800 chr7A 91.830 306 18 6 2961 3260 6864934 6865238 2.330000e-113 420.0
27 TraesCS4A01G480800 chr7A 95.808 167 6 1 3636 3802 6865513 6865678 8.950000e-68 268.0
28 TraesCS4A01G480800 chr7A 92.432 185 10 4 3380 3561 6865330 6865513 1.500000e-65 261.0
29 TraesCS4A01G480800 chr7A 91.720 157 10 3 2 156 6862980 6863135 1.180000e-51 215.0
30 TraesCS4A01G480800 chr5D 93.472 1057 63 4 1159 2214 543697318 543698369 0.000000e+00 1565.0
31 TraesCS4A01G480800 chr5D 75.990 404 81 12 4316 4704 42078868 42079270 1.540000e-45 195.0
32 TraesCS4A01G480800 chr1D 91.964 1120 81 7 1101 2215 457052189 457051074 0.000000e+00 1561.0
33 TraesCS4A01G480800 chr3D 92.399 1092 77 6 1126 2213 120627212 120626123 0.000000e+00 1552.0
34 TraesCS4A01G480800 chr3D 91.503 1118 83 10 1100 2213 553040115 553039006 0.000000e+00 1528.0
35 TraesCS4A01G480800 chr3D 91.413 1118 84 10 1100 2213 553078635 553077526 0.000000e+00 1522.0
36 TraesCS4A01G480800 chr2D 91.906 1112 84 6 1102 2209 55161023 55162132 0.000000e+00 1550.0
37 TraesCS4A01G480800 chr2D 91.809 1111 82 7 1104 2209 461081640 461080534 0.000000e+00 1539.0
38 TraesCS4A01G480800 chr6D 76.459 497 81 22 4220 4690 34084328 34084814 2.520000e-58 237.0
39 TraesCS4A01G480800 chr5B 77.975 395 76 9 4312 4700 556783012 556782623 2.520000e-58 237.0
40 TraesCS4A01G480800 chr6A 100.000 39 0 0 3684 3722 9484447 9484485 7.530000e-09 73.1


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 TraesCS4A01G480800 chr4A 737084360 737089778 5418 True 10008.000000 10008 100.000000 1 5419 1 chr4A.!!$R1 5418
1 TraesCS4A01G480800 chr4A 736306384 736310822 4438 False 1309.666667 1640 83.686667 1 5419 3 chr4A.!!$F1 5418
2 TraesCS4A01G480800 chr4A 737061233 737070493 9260 True 573.125000 887 85.213125 1 5368 8 chr4A.!!$R2 5367
3 TraesCS4A01G480800 chr7D 260977 262098 1121 True 1580.000000 1580 92.260000 1104 2214 1 chr7D.!!$R1 1110
4 TraesCS4A01G480800 chr7D 144158596 144159706 1110 False 1533.000000 1533 91.585000 1101 2213 1 chr7D.!!$F1 1112
5 TraesCS4A01G480800 chr7D 5386142 5391515 5373 False 1380.640000 2937 91.289000 1 5419 5 chr7D.!!$F2 5418
6 TraesCS4A01G480800 chr7D 5413798 5418234 4436 False 1026.500000 1308 84.906000 1 5419 4 chr7D.!!$F3 5418
7 TraesCS4A01G480800 chr7A 6862980 6867346 4366 False 823.000000 2470 92.610714 2 5419 7 chr7A.!!$F1 5417
8 TraesCS4A01G480800 chr5D 543697318 543698369 1051 False 1565.000000 1565 93.472000 1159 2214 1 chr5D.!!$F2 1055
9 TraesCS4A01G480800 chr1D 457051074 457052189 1115 True 1561.000000 1561 91.964000 1101 2215 1 chr1D.!!$R1 1114
10 TraesCS4A01G480800 chr3D 120626123 120627212 1089 True 1552.000000 1552 92.399000 1126 2213 1 chr3D.!!$R1 1087
11 TraesCS4A01G480800 chr3D 553039006 553040115 1109 True 1528.000000 1528 91.503000 1100 2213 1 chr3D.!!$R2 1113
12 TraesCS4A01G480800 chr3D 553077526 553078635 1109 True 1522.000000 1522 91.413000 1100 2213 1 chr3D.!!$R3 1113
13 TraesCS4A01G480800 chr2D 55161023 55162132 1109 False 1550.000000 1550 91.906000 1102 2209 1 chr2D.!!$F1 1107
14 TraesCS4A01G480800 chr2D 461080534 461081640 1106 True 1539.000000 1539 91.809000 1104 2209 1 chr2D.!!$R1 1105

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
830 886 0.107848 TTTCTAGCTACGGCCAAGGC 60.108 55.000 2.24 1.52 39.73 4.35 F
1844 1918 0.038892 TAGAGGTCGTCGTTTGGTGC 60.039 55.000 0.00 0.00 0.00 5.01 F
2882 3126 1.535462 GCTCAAAATGTAGCACGTGGT 59.465 47.619 25.12 25.12 38.63 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2495 2608 0.039256 CAAATGTGTCCACCTTGCCG 60.039 55.000 0.0 0.0 0.0 5.69 R
3299 3620 1.686052 TGCCAACCTCCAAAACATCAC 59.314 47.619 0.0 0.0 0.0 3.06 R
4664 5158 1.703411 TCCCTGCTTGTTTTTCCCAG 58.297 50.000 0.0 0.0 0.0 4.45 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
72 73 4.096682 AGTTGTCGTGATCTAGCTACCTTC 59.903 45.833 0.00 0.00 0.00 3.46
130 131 4.752101 CCATAGATGGCTAGTTACAACAGC 59.248 45.833 0.00 7.55 41.75 4.40
187 188 3.885484 AGATGTTGTTGTTGCTTCGAG 57.115 42.857 0.00 0.00 0.00 4.04
477 480 8.753497 ATGAGACAAGGAAATAAAAGGTATCC 57.247 34.615 0.00 0.00 0.00 2.59
482 485 8.893563 ACAAGGAAATAAAAGGTATCCAATGA 57.106 30.769 0.00 0.00 32.47 2.57
589 624 2.165998 AGTGAGAGGCAAATGAAAGGC 58.834 47.619 0.00 0.00 0.00 4.35
612 647 1.404047 CCAATGAAACAATGCCCGGAC 60.404 52.381 0.73 0.00 0.00 4.79
731 782 6.563037 AATAAAGAGAAGGAAGGGTAGTCC 57.437 41.667 0.00 0.00 35.17 3.85
828 884 1.278238 CGTTTCTAGCTACGGCCAAG 58.722 55.000 2.24 0.00 39.73 3.61
829 885 1.653151 GTTTCTAGCTACGGCCAAGG 58.347 55.000 2.24 0.00 39.73 3.61
830 886 0.107848 TTTCTAGCTACGGCCAAGGC 60.108 55.000 2.24 1.52 39.73 4.35
856 912 9.492973 CCAATGACTTGGTAATCAAATTTTCTT 57.507 29.630 0.00 0.00 45.90 2.52
867 923 9.893305 GTAATCAAATTTTCTTGTATATCCCCG 57.107 33.333 0.00 0.00 0.00 5.73
868 924 6.385649 TCAAATTTTCTTGTATATCCCCGC 57.614 37.500 0.00 0.00 0.00 6.13
869 925 5.888724 TCAAATTTTCTTGTATATCCCCGCA 59.111 36.000 0.00 0.00 0.00 5.69
870 926 6.378564 TCAAATTTTCTTGTATATCCCCGCAA 59.621 34.615 0.00 0.00 0.00 4.85
871 927 6.783708 AATTTTCTTGTATATCCCCGCAAA 57.216 33.333 0.00 0.00 0.00 3.68
872 928 6.783708 ATTTTCTTGTATATCCCCGCAAAA 57.216 33.333 0.00 0.00 0.00 2.44
873 929 6.591750 TTTTCTTGTATATCCCCGCAAAAA 57.408 33.333 0.00 0.00 0.00 1.94
914 970 2.065799 ACCAACTCAACCCCAATCTCT 58.934 47.619 0.00 0.00 0.00 3.10
937 993 1.284785 CCATTACCACACCACCCTCAT 59.715 52.381 0.00 0.00 0.00 2.90
944 1000 2.597455 CACACCACCCTCATTTTTCCT 58.403 47.619 0.00 0.00 0.00 3.36
994 1054 0.321298 GCTTAACTCCTTGCCGTGGA 60.321 55.000 0.00 0.00 0.00 4.02
999 1059 0.978146 ACTCCTTGCCGTGGATAGCT 60.978 55.000 0.00 0.00 32.56 3.32
1116 1176 2.023532 CTCCTCCTCCTCCCTCCTT 58.976 63.158 0.00 0.00 0.00 3.36
1298 1371 0.322816 ACGACTCATTGGCAAGGCAT 60.323 50.000 7.07 0.00 0.00 4.40
1313 1386 4.559063 CATGGCCGGCTAGCAGCT 62.559 66.667 28.56 0.46 41.99 4.24
1505 1579 1.667154 CTGTACAGGAGGCGCTGCTA 61.667 60.000 15.49 0.00 29.21 3.49
1537 1611 1.684983 CTAGTTCGGGCGAAATCCCTA 59.315 52.381 0.00 0.00 44.30 3.53
1618 1692 1.319541 CGTCGGTATGGACTGATCCT 58.680 55.000 0.00 0.00 46.43 3.24
1628 1702 2.043664 TGGACTGATCCTCTCACTTCCT 59.956 50.000 0.00 0.00 46.43 3.36
1629 1703 2.430332 GGACTGATCCTCTCACTTCCTG 59.570 54.545 0.00 0.00 42.45 3.86
1651 1725 2.840102 CCTAGGTCTCCCGGGCAG 60.840 72.222 18.49 14.69 35.12 4.85
1826 1900 1.590932 GAGATGGACTCGCGTAGGTA 58.409 55.000 5.77 0.00 35.84 3.08
1842 1916 0.600057 GGTAGAGGTCGTCGTTTGGT 59.400 55.000 0.00 0.00 0.00 3.67
1844 1918 0.038892 TAGAGGTCGTCGTTTGGTGC 60.039 55.000 0.00 0.00 0.00 5.01
1927 2001 2.046023 CAGTGGAAGATGGCGGCA 60.046 61.111 16.34 16.34 0.00 5.69
2170 2280 2.914756 AATGGCCGCATGCATCTCCA 62.915 55.000 19.57 17.55 43.89 3.86
2693 2936 6.265422 GGGGAGAATTATCGTCCATTTTCATT 59.735 38.462 6.31 0.00 31.31 2.57
2882 3126 1.535462 GCTCAAAATGTAGCACGTGGT 59.465 47.619 25.12 25.12 38.63 4.16
2913 3158 6.398095 CAATTAATTTTGGGAGAGGTTGACC 58.602 40.000 0.00 0.00 0.00 4.02
2929 3174 2.845363 GACCTCCGTTTGGTCCTTTA 57.155 50.000 7.29 0.00 46.01 1.85
2959 3204 8.657074 TTTTATGATTTAGATCCGACAATCGT 57.343 30.769 0.00 0.00 38.40 3.73
3016 3261 2.091555 AGACCCCTTTGGCTGTTTTACA 60.092 45.455 0.00 0.00 37.83 2.41
3195 3482 8.642908 TGTTGTACCGTTCTATGAATTAGATG 57.357 34.615 0.00 0.00 36.81 2.90
3248 3569 8.982091 TCATATAGCTCCATAGTACTCCATAC 57.018 38.462 0.00 0.00 0.00 2.39
3317 3638 3.243839 CCAAGTGATGTTTTGGAGGTTGG 60.244 47.826 0.00 0.00 45.32 3.77
3322 3643 2.079170 TGTTTTGGAGGTTGGCATCA 57.921 45.000 0.00 0.00 0.00 3.07
3338 3662 3.191162 GGCATCAATTCTGTTGTAGTGCA 59.809 43.478 13.09 0.00 0.00 4.57
3471 3795 2.101082 GGATCGTCACCCTCTCCTTTAC 59.899 54.545 0.00 0.00 0.00 2.01
3472 3796 2.297698 TCGTCACCCTCTCCTTTACA 57.702 50.000 0.00 0.00 0.00 2.41
3473 3797 1.891150 TCGTCACCCTCTCCTTTACAC 59.109 52.381 0.00 0.00 0.00 2.90
3506 3830 3.672808 CATGACATAGATCCCTTGCCTC 58.327 50.000 0.00 0.00 0.00 4.70
3508 3832 2.702478 TGACATAGATCCCTTGCCTCAG 59.298 50.000 0.00 0.00 0.00 3.35
3517 3841 1.005215 CCCTTGCCTCAGGAATCTTGT 59.995 52.381 0.00 0.00 35.71 3.16
3762 4144 4.164988 ACATCTATTTGCTTAGGAGGCTGT 59.835 41.667 0.00 0.00 0.00 4.40
3780 4162 4.280929 GGCTGTAATGAAGGGAAAACACTT 59.719 41.667 0.00 0.00 0.00 3.16
3797 4179 9.248291 GAAAACACTTCAATGCTATTTTTCTGA 57.752 29.630 0.00 0.00 31.82 3.27
3798 4180 9.768662 AAAACACTTCAATGCTATTTTTCTGAT 57.231 25.926 0.00 0.00 0.00 2.90
3799 4181 8.976986 AACACTTCAATGCTATTTTTCTGATC 57.023 30.769 0.00 0.00 0.00 2.92
3800 4182 8.114331 ACACTTCAATGCTATTTTTCTGATCA 57.886 30.769 0.00 0.00 0.00 2.92
3802 4184 9.234384 CACTTCAATGCTATTTTTCTGATCATC 57.766 33.333 0.00 0.00 0.00 2.92
3803 4185 9.186837 ACTTCAATGCTATTTTTCTGATCATCT 57.813 29.630 0.00 0.00 0.00 2.90
3883 4297 1.000283 AGTGTTGTCAGGAGAAGAGCG 60.000 52.381 0.00 0.00 0.00 5.03
4243 4666 2.235898 GGAGGCAAATTGTAATGGCCAA 59.764 45.455 10.96 0.00 42.61 4.52
4265 4726 9.717892 GCCAAGAGCATTTTTAGTAGTTATTAC 57.282 33.333 0.00 0.00 42.97 1.89
4445 4909 7.550906 GCTTCAGGTATTGATTTCTGTAACTCT 59.449 37.037 0.00 0.00 35.27 3.24
4567 5061 6.365970 AAACAGTAGATATGAGGCTATGGG 57.634 41.667 0.00 0.00 0.00 4.00
4589 5083 5.823045 GGGTTCAGTTAGCTTACTGCATAAT 59.177 40.000 24.59 0.00 44.10 1.28
4606 5100 7.334421 ACTGCATAATAACAGACGAAAGACATT 59.666 33.333 0.00 0.00 37.35 2.71
4712 5210 4.901197 TTTCTATGGCAAGTCTGTACCA 57.099 40.909 0.00 0.00 36.43 3.25
4844 5345 4.262420 CCTCGAAATGGTCACCCAAATTTT 60.262 41.667 0.00 0.00 46.04 1.82
4870 5371 6.183360 GCCTCAAAACTTATCATAGGTCACAC 60.183 42.308 0.00 0.00 0.00 3.82
4930 5431 6.528321 TGTCTGGATGATGGACATAATCTTC 58.472 40.000 9.04 0.00 39.56 2.87
5110 5623 5.967088 AGTCGTAGAACATGCTCAACTTAT 58.033 37.500 0.00 0.00 39.69 1.73
5126 5639 7.328404 TCAACTTATCATATATGGCCTGGAA 57.672 36.000 12.78 0.00 0.00 3.53
5140 5653 2.680577 CCTGGAATTGTTTGCTTCTGC 58.319 47.619 0.00 0.00 40.20 4.26
5158 5671 4.079970 TCTGCGGGGTCTATAGTTCTATG 58.920 47.826 0.00 0.00 0.00 2.23
5231 5744 7.605449 AGTTTCATTCTGAATTATTGGTGGTG 58.395 34.615 0.00 0.00 36.11 4.17
5289 5805 2.482721 GGTTAATCTGGTGTCGTGGTTG 59.517 50.000 0.00 0.00 0.00 3.77
5360 5876 3.695606 ATGTGTCTGCGGTCGGCT 61.696 61.111 3.87 0.00 44.05 5.52
5369 5885 1.883084 GCGGTCGGCTTATGGACTG 60.883 63.158 0.00 0.00 41.44 3.51
5385 5901 3.841255 TGGACTGTGGTGGTATATTGTGA 59.159 43.478 0.00 0.00 0.00 3.58
5389 5905 5.734720 ACTGTGGTGGTATATTGTGAAGAG 58.265 41.667 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 1.387756 GACGACCAATGTTCGGTTACG 59.612 52.381 5.02 0.00 36.69 3.18
179 180 9.419297 AGCGTAAATAATATTTATCTCGAAGCA 57.581 29.630 14.37 0.00 0.00 3.91
477 480 7.720957 TGATGGGATGTAGGAATAGTTTCATTG 59.279 37.037 0.00 0.00 33.23 2.82
563 598 2.309755 TCATTTGCCTCTCACTTCCCAT 59.690 45.455 0.00 0.00 0.00 4.00
567 602 3.366781 GCCTTTCATTTGCCTCTCACTTC 60.367 47.826 0.00 0.00 0.00 3.01
589 624 2.542597 CGGGCATTGTTTCATTGGATG 58.457 47.619 0.00 0.00 0.00 3.51
612 647 6.657541 TGCCTTACTTGATTTTACTGGTTAGG 59.342 38.462 0.00 0.00 0.00 2.69
848 904 6.783708 TTTGCGGGGATATACAAGAAAATT 57.216 33.333 0.00 0.00 0.00 1.82
849 905 6.783708 TTTTGCGGGGATATACAAGAAAAT 57.216 33.333 0.00 0.00 0.00 1.82
850 906 6.591750 TTTTTGCGGGGATATACAAGAAAA 57.408 33.333 0.00 0.00 0.00 2.29
872 928 9.787435 TTGGTGCGGTATATATAAGAGATTTTT 57.213 29.630 0.00 0.00 0.00 1.94
873 929 9.216117 GTTGGTGCGGTATATATAAGAGATTTT 57.784 33.333 0.00 0.00 0.00 1.82
914 970 2.775384 GAGGGTGGTGTGGTAATGGATA 59.225 50.000 0.00 0.00 0.00 2.59
937 993 5.568620 AAGCTAAGTGAGGAGAGGAAAAA 57.431 39.130 0.00 0.00 0.00 1.94
944 1000 4.421131 AGGAGAAAAGCTAAGTGAGGAGA 58.579 43.478 0.00 0.00 0.00 3.71
994 1054 4.742201 CGCCGCCGCCATAGCTAT 62.742 66.667 0.00 0.00 36.60 2.97
999 1059 4.884257 GACTTCGCCGCCGCCATA 62.884 66.667 0.00 0.00 0.00 2.74
1039 1099 2.176546 CGCAGCGAACATGTTGGG 59.823 61.111 17.58 6.88 0.00 4.12
1116 1176 2.365105 CGGCTAGGGTTGGGAGGA 60.365 66.667 0.00 0.00 0.00 3.71
1239 1311 1.376424 CACGCAGAGGCAGGACAAT 60.376 57.895 0.00 0.00 41.24 2.71
1277 1349 1.648467 GCCTTGCCAATGAGTCGTCC 61.648 60.000 0.00 0.00 0.00 4.79
1282 1354 1.610554 GCCATGCCTTGCCAATGAGT 61.611 55.000 0.00 0.00 0.00 3.41
1313 1386 1.746239 CAGATCCACCGCATGCACA 60.746 57.895 19.57 0.00 0.00 4.57
1318 1391 3.740128 GACGCCAGATCCACCGCAT 62.740 63.158 0.00 0.00 0.00 4.73
1319 1392 4.451150 GACGCCAGATCCACCGCA 62.451 66.667 0.00 0.00 0.00 5.69
1505 1579 1.392710 CGAACTAGATCCCCGCCACT 61.393 60.000 0.00 0.00 0.00 4.00
1576 1650 2.603776 AAGGAGGGGAACGACGCT 60.604 61.111 0.00 0.00 36.23 5.07
1618 1692 2.559931 CCTAGGGGAACAGGAAGTGAGA 60.560 54.545 0.00 0.00 33.42 3.27
1826 1900 1.300697 GCACCAAACGACGACCTCT 60.301 57.895 0.00 0.00 0.00 3.69
1844 1918 2.896854 CCATCGACGCCACCATGG 60.897 66.667 11.19 11.19 41.55 3.66
1927 2001 0.529773 ACGCACTCACATGTGTCGTT 60.530 50.000 24.63 11.67 42.80 3.85
1991 2101 2.102588 GCCTAACATCTAAAGCCGGAGA 59.897 50.000 5.05 0.00 0.00 3.71
2042 2152 3.435457 CCATATGATGAAGGGGTGCAAGA 60.435 47.826 3.65 0.00 0.00 3.02
2170 2280 2.593420 CCCCGGCCTCCGTATTTT 59.407 61.111 0.00 0.00 46.80 1.82
2311 2424 0.310854 CAACCTTGGCAACGAAGTCC 59.689 55.000 0.00 0.00 45.00 3.85
2495 2608 0.039256 CAAATGTGTCCACCTTGCCG 60.039 55.000 0.00 0.00 0.00 5.69
2693 2936 7.254966 CCACGCTTGCCATAAAACACTATAATA 60.255 37.037 0.00 0.00 0.00 0.98
2913 3158 6.812879 AAATAGTTAAAGGACCAAACGGAG 57.187 37.500 0.00 0.00 0.00 4.63
3084 3366 7.220740 TCATAGAACAGTACAATGGTCAAACA 58.779 34.615 3.28 0.00 39.49 2.83
3195 3482 4.335315 TGGGAAGTGATTGATATTTGTCGC 59.665 41.667 0.00 0.00 0.00 5.19
3281 3602 5.127682 ACATCACTTGGAAGAAGCACTTTTT 59.872 36.000 0.00 0.00 39.13 1.94
3282 3603 4.646492 ACATCACTTGGAAGAAGCACTTTT 59.354 37.500 0.00 0.00 39.13 2.27
3283 3604 4.210331 ACATCACTTGGAAGAAGCACTTT 58.790 39.130 0.00 0.00 39.13 2.66
3284 3605 3.825328 ACATCACTTGGAAGAAGCACTT 58.175 40.909 0.00 0.00 42.03 3.16
3285 3606 3.498774 ACATCACTTGGAAGAAGCACT 57.501 42.857 0.00 0.00 0.00 4.40
3286 3607 4.574599 AAACATCACTTGGAAGAAGCAC 57.425 40.909 0.00 0.00 0.00 4.40
3287 3608 4.202141 CCAAAACATCACTTGGAAGAAGCA 60.202 41.667 0.00 0.00 44.16 3.91
3288 3609 4.037923 TCCAAAACATCACTTGGAAGAAGC 59.962 41.667 1.07 0.00 46.35 3.86
3289 3610 5.772825 TCCAAAACATCACTTGGAAGAAG 57.227 39.130 1.07 0.00 46.35 2.85
3294 3615 3.593442 ACCTCCAAAACATCACTTGGA 57.407 42.857 3.66 3.66 46.99 3.53
3295 3616 3.243839 CCAACCTCCAAAACATCACTTGG 60.244 47.826 0.00 0.00 43.00 3.61
3296 3617 3.799917 GCCAACCTCCAAAACATCACTTG 60.800 47.826 0.00 0.00 0.00 3.16
3297 3618 2.365293 GCCAACCTCCAAAACATCACTT 59.635 45.455 0.00 0.00 0.00 3.16
3298 3619 1.963515 GCCAACCTCCAAAACATCACT 59.036 47.619 0.00 0.00 0.00 3.41
3299 3620 1.686052 TGCCAACCTCCAAAACATCAC 59.314 47.619 0.00 0.00 0.00 3.06
3317 3638 4.424061 TGCACTACAACAGAATTGATGC 57.576 40.909 0.00 1.92 30.81 3.91
3471 3795 3.696281 TGTCATGCAAAGTTGTGAGTG 57.304 42.857 0.00 0.00 0.00 3.51
3472 3796 5.308014 TCTATGTCATGCAAAGTTGTGAGT 58.692 37.500 0.00 0.00 0.00 3.41
3473 3797 5.868043 TCTATGTCATGCAAAGTTGTGAG 57.132 39.130 0.00 0.00 0.00 3.51
3506 3830 9.981114 AAAAACATACCTAAAACAAGATTCCTG 57.019 29.630 0.00 0.00 0.00 3.86
3508 3832 9.124807 CGAAAAACATACCTAAAACAAGATTCC 57.875 33.333 0.00 0.00 0.00 3.01
3727 4109 4.034048 GCAAATAGATGTACCACCGAGTTG 59.966 45.833 0.00 0.00 0.00 3.16
3762 4144 6.267471 AGCATTGAAGTGTTTTCCCTTCATTA 59.733 34.615 3.22 0.00 44.64 1.90
3883 4297 4.180817 GCACAAATTACTAACCCAATGCC 58.819 43.478 0.00 0.00 0.00 4.40
4183 4606 5.120399 TGCATTGGTAGGGTTATCTTAACG 58.880 41.667 0.00 0.00 0.00 3.18
4664 5158 1.703411 TCCCTGCTTGTTTTTCCCAG 58.297 50.000 0.00 0.00 0.00 4.45
4668 5162 6.494893 AAAAACTTTCCCTGCTTGTTTTTC 57.505 33.333 0.00 0.00 43.06 2.29
4712 5210 6.436847 GTCCTAGAAACCAAGTAGTACCTCTT 59.563 42.308 0.00 0.00 0.00 2.85
4754 5252 9.877178 ACAGTTATCTATGAACGAAGATTTTCT 57.123 29.630 0.00 0.00 34.36 2.52
4795 5293 7.550597 ACATGAGGCTAAGATTCAGATATCA 57.449 36.000 5.32 0.00 0.00 2.15
4844 5345 5.880332 GTGACCTATGATAAGTTTTGAGGCA 59.120 40.000 0.00 0.00 0.00 4.75
5110 5623 5.010922 GCAAACAATTCCAGGCCATATATGA 59.989 40.000 14.54 0.00 0.00 2.15
5126 5639 0.827507 ACCCCGCAGAAGCAAACAAT 60.828 50.000 0.00 0.00 42.27 2.71
5140 5653 4.379603 CGCTTCATAGAACTATAGACCCCG 60.380 50.000 6.78 0.00 0.00 5.73
5231 5744 5.432157 ACGATCGCGAATGATTGTTATTTC 58.568 37.500 15.24 0.00 39.45 2.17
5245 5758 1.195674 TGAAATGCAAAACGATCGCGA 59.804 42.857 16.60 13.09 41.64 5.87
5289 5805 6.037391 ACTGATACGAGCTAGAAACTGACTAC 59.963 42.308 0.00 0.00 0.00 2.73
5360 5876 6.157123 TCACAATATACCACCACAGTCCATAA 59.843 38.462 0.00 0.00 0.00 1.90
5369 5885 4.513442 TGCTCTTCACAATATACCACCAC 58.487 43.478 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.