Multiple sequence alignment - TraesCS4A01G466800

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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 TraesCS4A01G466800 chr4A 100.000 3562 0 0 1 3562 729535169 729531608 0.000000e+00 6578.0
1 TraesCS4A01G466800 chr4A 88.446 1705 158 25 1887 3562 729858595 729860289 0.000000e+00 2021.0
2 TraesCS4A01G466800 chr4A 88.387 1705 159 24 1887 3562 728432941 728431247 0.000000e+00 2015.0
3 TraesCS4A01G466800 chr4A 87.530 1660 169 25 1927 3562 718930781 718929136 0.000000e+00 1884.0
4 TraesCS4A01G466800 chr4A 85.022 1836 222 38 1017 2834 729742509 729744309 0.000000e+00 1818.0
5 TraesCS4A01G466800 chr4A 84.796 1835 228 36 1017 2834 729138901 729140701 0.000000e+00 1796.0
6 TraesCS4A01G466800 chr4A 86.574 1229 127 21 1897 3099 729814539 729815755 0.000000e+00 1321.0
7 TraesCS4A01G466800 chr4A 91.557 912 57 7 1880 2784 729682013 729682911 0.000000e+00 1240.0
8 TraesCS4A01G466800 chr4A 84.003 1319 177 18 1017 2323 728458058 728456762 0.000000e+00 1236.0
9 TraesCS4A01G466800 chr4A 85.110 1182 139 21 1648 2821 729050088 729048936 0.000000e+00 1173.0
10 TraesCS4A01G466800 chr4A 90.186 754 68 4 901 1652 729508557 729507808 0.000000e+00 977.0
11 TraesCS4A01G466800 chr4A 87.668 746 63 10 2825 3562 729682910 729683634 0.000000e+00 841.0
12 TraesCS4A01G466800 chr4A 83.827 810 97 19 1017 1815 718931754 718930968 0.000000e+00 739.0
13 TraesCS4A01G466800 chr4A 81.640 866 127 21 1017 1871 729681053 729681897 0.000000e+00 689.0
14 TraesCS4A01G466800 chr4A 90.751 519 40 5 3048 3562 729048580 729048066 0.000000e+00 686.0
15 TraesCS4A01G466800 chr4A 91.532 496 42 0 1152 1647 729050674 729050179 0.000000e+00 684.0
16 TraesCS4A01G466800 chr4A 81.714 700 115 10 1760 2454 728757055 728757746 3.990000e-159 571.0
17 TraesCS4A01G466800 chr4A 90.931 408 35 1 1240 1647 729857971 729858376 6.720000e-152 547.0
18 TraesCS4A01G466800 chr4A 91.120 259 22 1 22 280 729512659 729512402 2.030000e-92 350.0
19 TraesCS4A01G466800 chr4A 79.500 600 37 30 262 815 729511133 729510574 7.320000e-92 348.0
20 TraesCS4A01G466800 chr4A 92.017 238 16 3 716 952 731065836 731066071 7.370000e-87 331.0
21 TraesCS4A01G466800 chr4A 90.756 238 20 2 716 952 729053548 729053312 2.060000e-82 316.0
22 TraesCS4A01G466800 chr4A 93.564 202 13 0 957 1158 729052203 729052002 5.780000e-78 302.0
23 TraesCS4A01G466800 chr4A 90.821 207 18 1 2812 3017 729048789 729048583 3.500000e-70 276.0
24 TraesCS4A01G466800 chr4A 87.719 57 6 1 804 859 728517928 728517984 8.250000e-07 65.8
25 TraesCS4A01G466800 chr7A 88.017 1694 164 22 1897 3562 9329541 9331223 0.000000e+00 1967.0
26 TraesCS4A01G466800 chr7A 84.360 633 69 16 1017 1647 9328702 9329306 8.510000e-166 593.0
27 TraesCS4A01G466800 chr7A 90.299 134 10 1 1648 1778 9329380 9329513 4.730000e-39 172.0
28 TraesCS4A01G466800 chr7D 87.044 1698 174 31 1852 3521 10482603 10480924 0.000000e+00 1875.0
29 TraesCS4A01G466800 chr7D 82.646 1406 216 23 2021 3418 10036112 10037497 0.000000e+00 1219.0
30 TraesCS4A01G466800 chr7D 83.570 633 80 15 1017 1647 10483446 10482836 3.990000e-159 571.0
31 TraesCS4A01G466800 chr7D 92.079 303 24 0 22 324 10148076 10147774 9.140000e-116 427.0
32 TraesCS4A01G466800 chr7D 87.895 190 10 2 605 781 10146664 10146475 1.000000e-50 211.0
33 TraesCS4A01G466800 chr7D 89.266 177 6 7 316 485 10146947 10146777 3.600000e-50 209.0
34 TraesCS4A01G466800 chr7D 88.889 171 15 2 1648 1815 10482764 10482595 1.300000e-49 207.0
35 TraesCS4A01G466800 chr7D 96.471 85 2 1 527 611 10146771 10146688 4.800000e-29 139.0


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 TraesCS4A01G466800 chr4A 729531608 729535169 3561 True 6578.000000 6578 100.000000 1 3562 1 chr4A.!!$R3 3561
1 TraesCS4A01G466800 chr4A 728431247 728432941 1694 True 2015.000000 2015 88.387000 1887 3562 1 chr4A.!!$R1 1675
2 TraesCS4A01G466800 chr4A 729742509 729744309 1800 False 1818.000000 1818 85.022000 1017 2834 1 chr4A.!!$F4 1817
3 TraesCS4A01G466800 chr4A 729138901 729140701 1800 False 1796.000000 1796 84.796000 1017 2834 1 chr4A.!!$F3 1817
4 TraesCS4A01G466800 chr4A 729814539 729815755 1216 False 1321.000000 1321 86.574000 1897 3099 1 chr4A.!!$F5 1202
5 TraesCS4A01G466800 chr4A 718929136 718931754 2618 True 1311.500000 1884 85.678500 1017 3562 2 chr4A.!!$R4 2545
6 TraesCS4A01G466800 chr4A 729857971 729860289 2318 False 1284.000000 2021 89.688500 1240 3562 2 chr4A.!!$F8 2322
7 TraesCS4A01G466800 chr4A 728456762 728458058 1296 True 1236.000000 1236 84.003000 1017 2323 1 chr4A.!!$R2 1306
8 TraesCS4A01G466800 chr4A 729681053 729683634 2581 False 923.333333 1240 86.955000 1017 3562 3 chr4A.!!$F7 2545
9 TraesCS4A01G466800 chr4A 729048066 729053548 5482 True 572.833333 1173 90.422333 716 3562 6 chr4A.!!$R5 2846
10 TraesCS4A01G466800 chr4A 728757055 728757746 691 False 571.000000 571 81.714000 1760 2454 1 chr4A.!!$F2 694
11 TraesCS4A01G466800 chr4A 729507808 729512659 4851 True 558.333333 977 86.935333 22 1652 3 chr4A.!!$R6 1630
12 TraesCS4A01G466800 chr7A 9328702 9331223 2521 False 910.666667 1967 87.558667 1017 3562 3 chr7A.!!$F1 2545
13 TraesCS4A01G466800 chr7D 10036112 10037497 1385 False 1219.000000 1219 82.646000 2021 3418 1 chr7D.!!$F1 1397
14 TraesCS4A01G466800 chr7D 10480924 10483446 2522 True 884.333333 1875 86.501000 1017 3521 3 chr7D.!!$R2 2504
15 TraesCS4A01G466800 chr7D 10146475 10148076 1601 True 246.500000 427 91.427750 22 781 4 chr7D.!!$R1 759

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
615 2748 0.534203 TCCGCACAACCCTTTCTGTC 60.534 55.0 0.00 0.0 0.00 3.51 F
616 2749 0.817634 CCGCACAACCCTTTCTGTCA 60.818 55.0 0.00 0.0 0.00 3.58 F
679 2855 0.827507 GCACCCATCCACTTGGTTGT 60.828 55.0 5.75 0.0 32.13 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 9140 1.531423 GGCACCATGCTATCATCCAG 58.469 55.000 0.13 0.0 44.28 3.86 R
2252 9209 3.455910 AGCTTGTGATCAGTAATAGCCCA 59.544 43.478 0.00 0.0 0.00 5.36 R
2601 9569 3.880490 TCATTGAATATACGGGTTGCACC 59.120 43.478 0.00 0.0 37.60 5.01 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
19 20 2.338984 AGGAACTGTCGACGCCAC 59.661 61.111 11.62 2.71 37.18 5.01
20 21 2.737376 GGAACTGTCGACGCCACC 60.737 66.667 11.62 8.36 0.00 4.61
110 111 4.784079 GCTTGCTTGCACACAAAATTCTTG 60.784 41.667 0.00 0.61 34.74 3.02
131 132 3.321682 TGCATTCCCTTTTGGAGAAACAG 59.678 43.478 0.00 0.00 46.24 3.16
136 137 5.843019 TCCCTTTTGGAGAAACAGTAGAT 57.157 39.130 0.00 0.00 44.07 1.98
170 172 2.738643 GCATCTCGCAAGTGGCTACTAA 60.739 50.000 1.97 0.00 41.67 2.24
171 173 2.649331 TCTCGCAAGTGGCTACTAAC 57.351 50.000 1.97 0.00 41.67 2.34
172 174 2.168496 TCTCGCAAGTGGCTACTAACT 58.832 47.619 1.97 0.00 41.67 2.24
187 189 3.326747 ACTAACTGCCAAGTCATCGAAC 58.673 45.455 0.00 0.00 34.77 3.95
210 212 5.221263 ACGAGAGTGACAACTGAACTAACAT 60.221 40.000 0.00 0.00 46.97 2.71
259 261 4.342092 AGCCATGTTATTACAAATCTGCCC 59.658 41.667 0.00 0.00 37.91 5.36
297 1585 0.905357 CTACCTGCTAGCACCTTGGT 59.095 55.000 24.73 24.73 0.00 3.67
327 2450 5.010012 CAGCCGGCCTATCTAATTGAAAAAT 59.990 40.000 26.15 0.00 0.00 1.82
362 2486 5.573380 ATTGGGAGATATGCTTCAGCTAA 57.427 39.130 0.00 0.00 42.66 3.09
364 2488 3.711190 TGGGAGATATGCTTCAGCTAACA 59.289 43.478 0.00 0.00 42.66 2.41
398 2524 0.795085 CAGAGAAAGTTCAGCCAGCG 59.205 55.000 0.00 0.00 0.00 5.18
428 2554 6.253727 GCATGCATTATGATAGGTACTACGTC 59.746 42.308 14.21 0.00 39.61 4.34
478 2609 2.817258 CGGACACACAACCCACATTAAT 59.183 45.455 0.00 0.00 0.00 1.40
485 2616 9.120538 GACACACAACCCACATTAATATAGATT 57.879 33.333 0.00 0.00 0.00 2.40
486 2617 9.120538 ACACACAACCCACATTAATATAGATTC 57.879 33.333 0.00 0.00 0.00 2.52
525 2658 1.372582 CCCACATGACCATGAACGAG 58.627 55.000 16.07 1.92 41.20 4.18
543 2676 3.192844 ACGAGTACATCACAAGGTCGAAT 59.807 43.478 0.00 0.00 0.00 3.34
553 2686 5.250982 TCACAAGGTCGAATAGTAGAGTGA 58.749 41.667 0.00 0.00 0.00 3.41
579 2712 1.139256 CTATTGCCATTGCCATTGCCA 59.861 47.619 0.00 0.00 36.33 4.92
611 2744 0.958822 ATTGTCCGCACAACCCTTTC 59.041 50.000 0.00 0.00 45.47 2.62
613 2746 0.817634 TGTCCGCACAACCCTTTCTG 60.818 55.000 0.00 0.00 0.00 3.02
614 2747 0.818040 GTCCGCACAACCCTTTCTGT 60.818 55.000 0.00 0.00 0.00 3.41
615 2748 0.534203 TCCGCACAACCCTTTCTGTC 60.534 55.000 0.00 0.00 0.00 3.51
616 2749 0.817634 CCGCACAACCCTTTCTGTCA 60.818 55.000 0.00 0.00 0.00 3.58
617 2750 1.021202 CGCACAACCCTTTCTGTCAA 58.979 50.000 0.00 0.00 0.00 3.18
618 2751 1.002468 CGCACAACCCTTTCTGTCAAG 60.002 52.381 0.00 0.00 0.00 3.02
658 2821 2.657237 CCTCCACCAGGTCGTGAC 59.343 66.667 0.00 0.00 37.53 3.67
670 2846 4.386951 CGTGACCGCACCCATCCA 62.387 66.667 0.00 0.00 42.09 3.41
677 2853 1.603455 CGCACCCATCCACTTGGTT 60.603 57.895 0.00 0.00 34.77 3.67
679 2855 0.827507 GCACCCATCCACTTGGTTGT 60.828 55.000 5.75 0.00 32.13 3.32
833 3016 6.461788 GGTGATGGAGACTAATCCTCTGTTAC 60.462 46.154 0.00 0.00 40.29 2.50
840 3023 7.339976 GGAGACTAATCCTCTGTTACTTAGTGT 59.660 40.741 0.00 0.00 33.88 3.55
842 3025 8.524487 AGACTAATCCTCTGTTACTTAGTGTTG 58.476 37.037 0.00 0.00 33.88 3.33
847 3031 6.387465 TCCTCTGTTACTTAGTGTTGATTCG 58.613 40.000 0.00 0.00 0.00 3.34
852 3036 9.002600 TCTGTTACTTAGTGTTGATTCGTACTA 57.997 33.333 0.00 0.00 0.00 1.82
859 3043 9.181805 CTTAGTGTTGATTCGTACTATACCATG 57.818 37.037 0.00 0.00 0.00 3.66
867 3051 9.311676 TGATTCGTACTATACCATGGGTATAAA 57.688 33.333 18.09 7.36 46.49 1.40
876 3060 3.397955 ACCATGGGTATAAACAGGGGATC 59.602 47.826 18.09 0.00 42.49 3.36
878 3062 3.049108 TGGGTATAAACAGGGGATCGA 57.951 47.619 0.00 0.00 0.00 3.59
1005 6261 2.838736 GTGTCCAACACTGACATGACT 58.161 47.619 0.00 0.00 45.27 3.41
1008 6264 3.071457 TGTCCAACACTGACATGACTGAT 59.929 43.478 0.00 0.00 37.80 2.90
1146 6402 4.974438 AGGGGTGGGTTCGGAGCA 62.974 66.667 0.00 0.00 0.00 4.26
1164 7756 3.650139 AGCAGTCTACAAGGTAAACACG 58.350 45.455 0.00 0.00 0.00 4.49
1394 7987 1.841450 GATTTCTCGGGTACTGCTCG 58.159 55.000 0.00 0.00 43.78 5.03
1415 8008 2.611518 GAGACGCAGCAAGTACTGATT 58.388 47.619 0.00 0.00 40.25 2.57
1422 8015 4.191544 GCAGCAAGTACTGATTCCATACA 58.808 43.478 0.00 0.00 40.25 2.29
1520 8115 5.203060 ACTATCTCTCGGGTAAAATCAGC 57.797 43.478 0.00 0.00 0.00 4.26
1542 8138 5.104318 AGCTTAGCCTTATAGCTTTCCTTGT 60.104 40.000 0.00 0.00 42.30 3.16
1551 8147 7.606456 CCTTATAGCTTTCCTTGTGTTTCTACA 59.394 37.037 0.00 0.00 0.00 2.74
1584 8181 8.064336 AGTAGTAAACATCTACCAACTACAGG 57.936 38.462 11.68 0.00 40.97 4.00
1638 8235 6.536941 TGAGTTTTGTTAATTCCTTTTGCACC 59.463 34.615 0.00 0.00 0.00 5.01
1647 8310 1.899142 TCCTTTTGCACCCTAAATGGC 59.101 47.619 0.00 0.00 34.24 4.40
1657 8477 3.573967 CACCCTAAATGGCAGTTCTGTTT 59.426 43.478 2.32 0.00 0.00 2.83
1701 8521 5.404946 CACTCTTCTGTTTGGGCATATTTG 58.595 41.667 0.00 0.00 0.00 2.32
1714 8534 4.834496 GGGCATATTTGGAATTCTCATCCA 59.166 41.667 5.23 0.00 45.09 3.41
1724 8544 4.268359 GAATTCTCATCCACTTTGCCTCT 58.732 43.478 0.00 0.00 0.00 3.69
1730 8550 2.015456 TCCACTTTGCCTCTGAGAGA 57.985 50.000 11.82 0.00 0.00 3.10
1731 8551 2.329267 TCCACTTTGCCTCTGAGAGAA 58.671 47.619 11.82 0.00 0.00 2.87
1732 8552 2.705658 TCCACTTTGCCTCTGAGAGAAA 59.294 45.455 11.82 3.64 0.00 2.52
1753 8579 9.899226 GAGAAAAGTGCACTAACAAATATCTTT 57.101 29.630 22.01 12.47 0.00 2.52
1788 8614 2.093783 GCTTAATCGAGTGACCAAACGG 59.906 50.000 0.00 0.00 0.00 4.44
1841 8668 1.935799 ATGTTGGCAAGCCCACATAA 58.064 45.000 24.32 3.11 46.49 1.90
1889 8828 6.961721 AGTGGTAGTTACTACTTTCCCCATTA 59.038 38.462 20.15 0.00 44.19 1.90
1922 8861 4.158384 GTTTTGGCAATGAGATACGTGTG 58.842 43.478 0.00 0.00 0.00 3.82
1954 8906 3.981071 TGAACTTGCTAGCATACTGGT 57.019 42.857 20.13 8.01 0.00 4.00
2183 9140 6.038997 ACCTCAAACCTCAGAATGTACTAC 57.961 41.667 0.00 0.00 37.40 2.73
2193 9150 7.450014 ACCTCAGAATGTACTACTGGATGATAG 59.550 40.741 12.02 0.00 37.40 2.08
2252 9209 2.784347 GCTTAAGTGGAAGCCAGAGTT 58.216 47.619 4.02 0.00 45.08 3.01
2466 9432 8.204836 AGACAGACATATATAGTTTGGGTGTTC 58.795 37.037 9.19 1.42 0.00 3.18
2553 9520 9.645059 TGTATGTGAGATTTCAACAAACAAAAA 57.355 25.926 0.00 0.00 34.49 1.94
2601 9569 7.815641 AGAAACCACAATTTTGTTGGAAAAAG 58.184 30.769 14.65 0.00 39.91 2.27
2821 9800 6.127026 GGTATCCTCACATTTGGTCTCTAGTT 60.127 42.308 0.00 0.00 0.00 2.24
2827 9963 7.332182 CCTCACATTTGGTCTCTAGTTCTAAAC 59.668 40.741 0.00 0.00 0.00 2.01
2840 9976 4.651778 AGTTCTAAACCAATACTGCTGCA 58.348 39.130 0.88 0.88 0.00 4.41
2847 9983 4.178545 ACCAATACTGCTGCATGTTTTC 57.821 40.909 1.31 0.00 0.00 2.29
2897 10041 9.747898 TTCTTTATAACTAACCATGGTTGTCAT 57.252 29.630 35.49 24.11 38.92 3.06
2910 10055 4.606210 TGGTTGTCATAGAGCAGGTAGTA 58.394 43.478 0.00 0.00 0.00 1.82
2925 10070 4.159879 CAGGTAGTAGAAAGTTGGACGGAT 59.840 45.833 0.00 0.00 0.00 4.18
2944 10089 5.067674 ACGGATATGTTTGGGACATCAAATG 59.932 40.000 0.00 0.00 45.88 2.32
2951 10096 3.454719 TGGGACATCAAATGGTCACAT 57.545 42.857 0.00 0.00 42.19 3.21
2958 10103 6.319658 GGACATCAAATGGTCACATATCACTT 59.680 38.462 0.00 0.00 35.94 3.16
3029 10174 0.257039 CCAAGGAACAGGCCAGCTAT 59.743 55.000 5.01 0.00 0.00 2.97
3056 10201 6.126215 TGGTTTATCATCCATGGAATACTGGT 60.126 38.462 20.67 11.41 34.03 4.00
3061 10206 4.227073 TCATCCATGGAATACTGGTTGACA 59.773 41.667 20.67 0.00 36.69 3.58
3073 10218 3.315191 ACTGGTTGACACGGAAATTTCAG 59.685 43.478 19.49 17.51 0.00 3.02
3080 10225 2.095263 ACACGGAAATTTCAGATTGGCG 60.095 45.455 22.71 15.14 0.00 5.69
3113 10258 2.325484 TGTAGGTGCCTCAACAGAAGA 58.675 47.619 0.00 0.00 0.00 2.87
3172 10319 9.461312 TTCTGCCAGTAATTATTTAGTGATGTT 57.539 29.630 11.95 0.00 39.97 2.71
3242 10390 2.094545 GCTGGCGGATGAGTTGAAATTT 60.095 45.455 0.00 0.00 0.00 1.82
3269 10417 0.806868 ATTCTGCTGTTGCACCATCG 59.193 50.000 0.00 0.00 45.31 3.84
3303 10451 1.407656 AACGTTGGAGGTGGAGCAGA 61.408 55.000 0.00 0.00 0.00 4.26
3331 10479 2.686118 GCAAATTGAGCCAGGAGAGGAT 60.686 50.000 0.00 0.00 0.00 3.24
3374 10529 2.134287 GGCGGCTAGGGTGATGAGA 61.134 63.158 0.00 0.00 0.00 3.27
3397 10552 1.386533 CTCCATGGCAAGCTTACCAG 58.613 55.000 22.63 14.35 39.88 4.00
3537 10695 0.250234 TCGCTAGTGGCAAGCTGATT 59.750 50.000 9.33 0.00 41.91 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.022129 GTGGCGTCGACAGTTCCTG 61.022 63.158 17.16 0.00 37.52 3.86
2 3 2.338984 GTGGCGTCGACAGTTCCT 59.661 61.111 17.16 0.00 0.00 3.36
3 4 2.737376 GGTGGCGTCGACAGTTCC 60.737 66.667 17.16 10.85 0.00 3.62
4 5 2.028484 TGGTGGCGTCGACAGTTC 59.972 61.111 17.16 2.94 0.00 3.01
5 6 2.279918 GTGGTGGCGTCGACAGTT 60.280 61.111 17.16 0.00 0.00 3.16
6 7 4.640855 CGTGGTGGCGTCGACAGT 62.641 66.667 17.16 0.00 0.00 3.55
7 8 4.640855 ACGTGGTGGCGTCGACAG 62.641 66.667 17.16 9.59 41.71 3.51
8 9 4.934942 CACGTGGTGGCGTCGACA 62.935 66.667 17.16 0.00 43.83 4.35
17 18 1.101049 AACTTCAAGGCCACGTGGTG 61.101 55.000 33.92 24.42 37.57 4.17
18 19 1.101049 CAACTTCAAGGCCACGTGGT 61.101 55.000 33.92 14.47 37.57 4.16
19 20 0.817634 TCAACTTCAAGGCCACGTGG 60.818 55.000 30.66 30.66 38.53 4.94
20 21 1.238439 ATCAACTTCAAGGCCACGTG 58.762 50.000 9.08 9.08 0.00 4.49
66 67 6.857777 AGCATACATGAAGAATGACTTAGC 57.142 37.500 0.00 0.00 38.72 3.09
131 132 7.148885 GCGAGATGCTCAACTGTATTAATCTAC 60.149 40.741 0.00 0.00 41.73 2.59
136 137 4.754322 TGCGAGATGCTCAACTGTATTAA 58.246 39.130 0.00 0.00 46.63 1.40
170 172 0.317160 TCGTTCGATGACTTGGCAGT 59.683 50.000 0.00 0.00 35.17 4.40
171 173 0.994995 CTCGTTCGATGACTTGGCAG 59.005 55.000 0.00 0.00 0.00 4.85
172 174 0.601057 TCTCGTTCGATGACTTGGCA 59.399 50.000 0.00 0.00 0.00 4.92
178 180 2.613730 TGTCACTCTCGTTCGATGAC 57.386 50.000 15.76 15.76 40.08 3.06
187 189 4.607955 TGTTAGTTCAGTTGTCACTCTCG 58.392 43.478 0.00 0.00 0.00 4.04
210 212 7.430441 GGAAATTTCCTACTAACAAACAAGCA 58.570 34.615 26.94 0.00 44.11 3.91
246 248 9.249053 TCTATTTTATTGTGGGCAGATTTGTAA 57.751 29.630 0.00 0.00 0.00 2.41
259 261 9.722056 GCAGGTAGATGTTTCTATTTTATTGTG 57.278 33.333 0.00 0.00 36.84 3.33
288 1576 1.006922 GCTGCTCAAACCAAGGTGC 60.007 57.895 0.00 0.00 0.00 5.01
297 1585 1.153168 GATAGGCCGGCTGCTCAAA 60.153 57.895 28.56 0.76 40.92 2.69
327 2450 8.103305 GCATATCTCCCAATTGGTTCTCTTATA 58.897 37.037 22.91 10.49 34.77 0.98
375 2499 3.805108 GCTGGCTGAACTTTCTCTGAGAA 60.805 47.826 15.82 15.82 31.28 2.87
377 2503 2.075338 GCTGGCTGAACTTTCTCTGAG 58.925 52.381 0.00 0.00 0.00 3.35
398 2524 7.046652 AGTACCTATCATAATGCATGCTGATC 58.953 38.462 19.89 8.63 34.35 2.92
428 2554 3.935203 CCAGCTTTGTAGATGTGTACCAG 59.065 47.826 0.00 0.00 36.03 4.00
478 2609 7.045693 AGGGTAGCAGGTAGATGAATCTATA 57.954 40.000 3.44 0.00 41.09 1.31
485 2616 1.762957 GCAAGGGTAGCAGGTAGATGA 59.237 52.381 0.00 0.00 0.00 2.92
486 2617 1.202698 GGCAAGGGTAGCAGGTAGATG 60.203 57.143 0.00 0.00 0.00 2.90
500 2633 1.000739 ATGGTCATGTGGGGCAAGG 59.999 57.895 0.00 0.00 0.00 3.61
525 2658 7.024340 TCTACTATTCGACCTTGTGATGTAC 57.976 40.000 0.00 0.00 0.00 2.90
543 2676 7.476540 TGGCAATAGAAAGTTCACTCTACTA 57.523 36.000 0.00 0.00 0.00 1.82
553 2686 5.180271 CAATGGCAATGGCAATAGAAAGTT 58.820 37.500 14.81 0.00 42.43 2.66
579 2712 2.029918 GCGGACAATGAAGGAAGCTTTT 60.030 45.455 0.00 0.00 0.00 2.27
611 2744 1.724429 GCTGGAGAAGAGCTTGACAG 58.276 55.000 0.00 0.00 33.37 3.51
613 2746 0.244994 TCGCTGGAGAAGAGCTTGAC 59.755 55.000 0.00 0.00 34.03 3.18
614 2747 0.529833 CTCGCTGGAGAAGAGCTTGA 59.470 55.000 0.00 0.00 43.27 3.02
615 2748 0.459934 CCTCGCTGGAGAAGAGCTTG 60.460 60.000 0.00 0.00 43.27 4.01
616 2749 1.612395 CCCTCGCTGGAGAAGAGCTT 61.612 60.000 0.00 0.00 43.27 3.74
617 2750 2.057408 CCCTCGCTGGAGAAGAGCT 61.057 63.158 0.00 0.00 43.27 4.09
618 2751 2.498726 CCCTCGCTGGAGAAGAGC 59.501 66.667 0.00 0.00 43.27 4.09
658 2821 2.751436 CCAAGTGGATGGGTGCGG 60.751 66.667 0.00 0.00 36.79 5.69
663 2839 0.827089 TGCACAACCAAGTGGATGGG 60.827 55.000 11.77 8.82 45.18 4.00
670 2846 1.701545 CGTCGTGTGCACAACCAAGT 61.702 55.000 23.59 0.00 0.00 3.16
833 3016 9.181805 CATGGTATAGTACGAATCAACACTAAG 57.818 37.037 0.00 0.00 0.00 2.18
840 3023 7.786046 ATACCCATGGTATAGTACGAATCAA 57.214 36.000 11.73 0.00 45.87 2.57
859 3043 4.426736 TTTCGATCCCCTGTTTATACCC 57.573 45.455 0.00 0.00 0.00 3.69
888 3072 0.258774 ATCAGGGGAAAATGGGGTCG 59.741 55.000 0.00 0.00 0.00 4.79
1003 6259 3.144506 CAGCAAGTTTCTCACCATCAGT 58.855 45.455 0.00 0.00 0.00 3.41
1005 6261 1.881973 GCAGCAAGTTTCTCACCATCA 59.118 47.619 0.00 0.00 0.00 3.07
1008 6264 0.183492 AGGCAGCAAGTTTCTCACCA 59.817 50.000 0.00 0.00 0.00 4.17
1146 6402 2.289257 GCCCGTGTTTACCTTGTAGACT 60.289 50.000 0.00 0.00 0.00 3.24
1226 7818 4.840271 ACAGCTCACATGAATCATCTCAA 58.160 39.130 0.00 0.00 0.00 3.02
1273 7866 1.100510 GAGCTGCTTCATGGCAATGA 58.899 50.000 2.53 0.00 41.94 2.57
1394 7987 0.243907 TCAGTACTTGCTGCGTCTCC 59.756 55.000 0.00 0.00 36.49 3.71
1415 8008 4.924019 CGCTTCCCGTTGTATGGA 57.076 55.556 0.00 0.00 0.00 3.41
1520 8115 6.116126 ACACAAGGAAAGCTATAAGGCTAAG 58.884 40.000 0.00 0.00 42.24 2.18
1568 8164 2.766263 TCTGGCCTGTAGTTGGTAGATG 59.234 50.000 3.32 0.00 0.00 2.90
1584 8181 2.352715 GGCAACCAACAAATACTCTGGC 60.353 50.000 0.00 0.00 31.74 4.85
1617 8214 5.995446 AGGGTGCAAAAGGAATTAACAAAA 58.005 33.333 0.00 0.00 0.00 2.44
1638 8235 7.973944 GGTATAAAAACAGAACTGCCATTTAGG 59.026 37.037 1.46 0.00 41.84 2.69
1647 8310 4.083537 TGCAGCGGTATAAAAACAGAACTG 60.084 41.667 0.00 0.00 0.00 3.16
1701 8521 3.359950 AGGCAAAGTGGATGAGAATTCC 58.640 45.455 0.65 0.00 0.00 3.01
1714 8534 4.133078 CACTTTTCTCTCAGAGGCAAAGT 58.867 43.478 19.77 19.77 40.62 2.66
1724 8544 6.942532 ATTTGTTAGTGCACTTTTCTCTCA 57.057 33.333 27.06 10.76 0.00 3.27
1730 8550 9.816354 ACAAAAGATATTTGTTAGTGCACTTTT 57.184 25.926 27.06 12.12 39.36 2.27
1731 8551 9.816354 AACAAAAGATATTTGTTAGTGCACTTT 57.184 25.926 27.06 5.93 46.91 2.66
1753 8579 5.972935 TCGATTAAGCTCTATCCACAACAA 58.027 37.500 0.00 0.00 0.00 2.83
1788 8614 7.246311 TCGAAAATTGAGATGCTCTGAATTTC 58.754 34.615 16.97 12.20 45.15 2.17
1841 8668 6.993902 ACTTCATTTCAAAATTCAGGTGCAAT 59.006 30.769 0.00 0.00 0.00 3.56
1877 8813 4.396357 TGGTTGTGATAATGGGGAAAGT 57.604 40.909 0.00 0.00 0.00 2.66
1878 8814 4.711355 ACATGGTTGTGATAATGGGGAAAG 59.289 41.667 0.00 0.00 33.85 2.62
1917 8856 3.374058 AGTTCAAAGGAAGTTCACACACG 59.626 43.478 5.01 0.00 32.75 4.49
1922 8861 4.639135 AGCAAGTTCAAAGGAAGTTCAC 57.361 40.909 5.01 0.00 43.19 3.18
1954 8906 4.020751 TGAATGATTGCCCGATTTCCAAAA 60.021 37.500 0.00 0.00 0.00 2.44
2183 9140 1.531423 GGCACCATGCTATCATCCAG 58.469 55.000 0.13 0.00 44.28 3.86
2252 9209 3.455910 AGCTTGTGATCAGTAATAGCCCA 59.544 43.478 0.00 0.00 0.00 5.36
2437 9403 7.987458 CACCCAAACTATATATGTCTGTCTTGT 59.013 37.037 0.00 0.00 0.00 3.16
2466 9432 6.881067 TCCCATAAGGATCTCCATGATTAG 57.119 41.667 0.00 0.00 40.93 1.73
2601 9569 3.880490 TCATTGAATATACGGGTTGCACC 59.120 43.478 0.00 0.00 37.60 5.01
2660 9628 9.944663 GAACACTACAAAGACAACATTCAAATA 57.055 29.630 0.00 0.00 0.00 1.40
2684 9652 7.930865 CCATCTTTTATTTTTGGTGTGGAAGAA 59.069 33.333 0.00 0.00 0.00 2.52
2790 9769 6.386927 AGACCAAATGTGAGGATACCTATCAA 59.613 38.462 0.00 0.00 31.76 2.57
2804 9783 6.934645 TGGTTTAGAACTAGAGACCAAATGTG 59.065 38.462 0.00 0.00 34.48 3.21
2821 9800 4.588899 ACATGCAGCAGTATTGGTTTAGA 58.411 39.130 0.00 0.00 31.36 2.10
2827 9963 4.157289 AGAGAAAACATGCAGCAGTATTGG 59.843 41.667 0.00 0.00 0.00 3.16
2847 9983 7.798596 AGGACAACATGCATTTAGAATAGAG 57.201 36.000 0.00 0.00 0.00 2.43
2866 10007 7.924541 ACCATGGTTAGTTATAAAGAAGGACA 58.075 34.615 13.00 0.00 0.00 4.02
2897 10041 5.418209 GTCCAACTTTCTACTACCTGCTCTA 59.582 44.000 0.00 0.00 0.00 2.43
2899 10043 4.496360 GTCCAACTTTCTACTACCTGCTC 58.504 47.826 0.00 0.00 0.00 4.26
2900 10044 3.056749 CGTCCAACTTTCTACTACCTGCT 60.057 47.826 0.00 0.00 0.00 4.24
2910 10055 4.700213 CCAAACATATCCGTCCAACTTTCT 59.300 41.667 0.00 0.00 0.00 2.52
2944 10089 7.667043 TTACTTGTTCAAGTGATATGTGACC 57.333 36.000 23.14 0.00 34.37 4.02
2951 10096 6.714810 ACATGCCTTTACTTGTTCAAGTGATA 59.285 34.615 23.14 9.59 34.37 2.15
2958 10103 3.641437 GCACATGCCTTTACTTGTTCA 57.359 42.857 0.00 0.00 34.31 3.18
3029 10174 8.108999 CCAGTATTCCATGGATGATAAACCATA 58.891 37.037 17.06 4.04 43.89 2.74
3056 10201 4.558496 GCCAATCTGAAATTTCCGTGTCAA 60.558 41.667 15.48 0.00 0.00 3.18
3061 10206 2.095263 CACGCCAATCTGAAATTTCCGT 60.095 45.455 15.48 12.16 0.00 4.69
3073 10218 3.188460 ACATCACTTGTAACACGCCAATC 59.812 43.478 0.00 0.00 36.57 2.67
3080 10225 3.435671 GGCACCTACATCACTTGTAACAC 59.564 47.826 0.00 0.00 40.27 3.32
3113 10258 5.683876 ACTATTGAGTGATTGTACCTGCT 57.316 39.130 0.00 0.00 33.41 4.24
3146 10291 9.461312 AACATCACTAAATAATTACTGGCAGAA 57.539 29.630 23.66 11.50 0.00 3.02
3242 10390 3.628942 GTGCAACAGCAGAATCATCCATA 59.371 43.478 0.00 0.00 39.30 2.74
3269 10417 0.881600 ACGTTAACGGTGGCAGTTCC 60.882 55.000 29.81 0.00 44.95 3.62
3281 10429 1.154197 GCTCCACCTCCAACGTTAAC 58.846 55.000 0.00 0.00 0.00 2.01
3283 10431 0.320374 CTGCTCCACCTCCAACGTTA 59.680 55.000 0.00 0.00 0.00 3.18
3331 10479 3.245016 ACTCACATTTGATGCCTTCCTCA 60.245 43.478 0.00 0.00 0.00 3.86
3374 10529 2.659428 GTAAGCTTGCCATGGAGGATT 58.341 47.619 18.40 11.50 41.22 3.01
3397 10552 1.084289 GTACTCGTTGCCCATGAACC 58.916 55.000 0.00 0.00 0.00 3.62
3455 10613 8.677300 TCGAGAAGCTTATCTGCAATAAAAATT 58.323 29.630 18.33 0.00 34.99 1.82


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

AutoCloner maintained by Alex Coulton.