Multiple sequence alignment - TraesCS6B01G339100

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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 TraesCS6B01G339100 chr6B 100.000 4186 0 0 1 4186 597559611 597555426 0.000000e+00 7731.0
1 TraesCS6B01G339100 chr6B 75.332 904 195 28 1984 2876 127040030 127040916 3.900000e-110 409.0
2 TraesCS6B01G339100 chr6D 91.397 3464 132 62 822 4186 399220912 399217516 0.000000e+00 4593.0
3 TraesCS6B01G339100 chr6D 75.774 904 191 28 1984 2876 56552223 56553109 8.310000e-117 431.0
4 TraesCS6B01G339100 chr6D 87.766 376 31 9 3 373 399221811 399221446 3.870000e-115 425.0
5 TraesCS6B01G339100 chr6D 88.406 345 28 7 478 821 399221283 399220950 5.040000e-109 405.0
6 TraesCS6B01G339100 chr6D 91.860 86 6 1 384 469 399221351 399221267 7.350000e-23 119.0
7 TraesCS6B01G339100 chr6A 90.405 3481 158 75 822 4186 545320955 545317535 0.000000e+00 4416.0
8 TraesCS6B01G339100 chr6A 84.560 829 71 16 3 821 545321774 545320993 0.000000e+00 769.0
9 TraesCS6B01G339100 chr6A 75.938 906 186 30 1984 2876 71066981 71067867 1.790000e-118 436.0
10 TraesCS6B01G339100 chr7D 82.842 1154 175 15 1741 2876 198501231 198502379 0.000000e+00 1013.0
11 TraesCS6B01G339100 chr7A 82.476 1147 180 14 1748 2876 207547417 207548560 0.000000e+00 985.0
12 TraesCS6B01G339100 chr7A 74.642 698 147 27 1979 2664 602232172 602232851 8.860000e-72 281.0
13 TraesCS6B01G339100 chr7B 81.787 1153 189 14 1748 2882 162924203 162923054 0.000000e+00 946.0
14 TraesCS6B01G339100 chr3A 88.333 60 4 3 3595 3653 484992123 484992180 7.510000e-08 69.4
15 TraesCS6B01G339100 chr2A 88.333 60 4 2 3594 3653 510302648 510302704 7.510000e-08 69.4
16 TraesCS6B01G339100 chr5B 97.436 39 1 0 3596 3634 289802237 289802199 2.700000e-07 67.6
17 TraesCS6B01G339100 chr4A 87.931 58 4 3 3597 3653 89418462 89418407 9.710000e-07 65.8
18 TraesCS6B01G339100 chr4D 95.000 40 2 0 3595 3634 375151016 375151055 3.490000e-06 63.9


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 TraesCS6B01G339100 chr6B 597555426 597559611 4185 True 7731.0 7731 100.00000 1 4186 1 chr6B.!!$R1 4185
1 TraesCS6B01G339100 chr6B 127040030 127040916 886 False 409.0 409 75.33200 1984 2876 1 chr6B.!!$F1 892
2 TraesCS6B01G339100 chr6D 399217516 399221811 4295 True 1385.5 4593 89.85725 3 4186 4 chr6D.!!$R1 4183
3 TraesCS6B01G339100 chr6D 56552223 56553109 886 False 431.0 431 75.77400 1984 2876 1 chr6D.!!$F1 892
4 TraesCS6B01G339100 chr6A 545317535 545321774 4239 True 2592.5 4416 87.48250 3 4186 2 chr6A.!!$R1 4183
5 TraesCS6B01G339100 chr6A 71066981 71067867 886 False 436.0 436 75.93800 1984 2876 1 chr6A.!!$F1 892
6 TraesCS6B01G339100 chr7D 198501231 198502379 1148 False 1013.0 1013 82.84200 1741 2876 1 chr7D.!!$F1 1135
7 TraesCS6B01G339100 chr7A 207547417 207548560 1143 False 985.0 985 82.47600 1748 2876 1 chr7A.!!$F1 1128
8 TraesCS6B01G339100 chr7A 602232172 602232851 679 False 281.0 281 74.64200 1979 2664 1 chr7A.!!$F2 685
9 TraesCS6B01G339100 chr7B 162923054 162924203 1149 True 946.0 946 81.78700 1748 2882 1 chr7B.!!$R1 1134

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
529 618 0.316204 CTTGCTTCAGCCACCCAAAG 59.684 55.000 0.0 0.0 41.18 2.77 F
1337 1533 0.107993 CGCCATCAAAGCAGAGGAGA 60.108 55.000 0.0 0.0 0.00 3.71 F
1651 1865 0.253327 GAGGAAGAAACTCCGCCCAT 59.747 55.000 0.0 0.0 40.75 4.00 F
1655 1869 1.209747 GAAGAAACTCCGCCCATACCT 59.790 52.381 0.0 0.0 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1701 0.313987 TGCCGTATCATACAGCTCCG 59.686 55.0 4.65 0.0 33.36 4.63 R
2146 2369 0.737715 CACCTCGTACTTGCTCAGCC 60.738 60.0 0.00 0.0 0.00 4.85 R
2681 2910 0.824109 CGAGCTGGATCTTGTACCCA 59.176 55.0 0.00 0.0 0.00 4.51 R
3259 3517 1.988293 TGCCTCCATTTTGAAACGGA 58.012 45.0 0.00 0.0 0.00 4.69 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
131 133 5.584649 TGGTATTCCAGATGTTGACGAATTC 59.415 40.000 0.00 0.00 39.03 2.17
164 167 3.628487 TCGGTCAAAGGTGTAAAGTTTGG 59.372 43.478 0.00 0.00 32.96 3.28
264 268 4.299155 CGTCGTGATGGCACTATCTTTAT 58.701 43.478 0.00 0.00 42.93 1.40
266 270 4.686554 GTCGTGATGGCACTATCTTTATCC 59.313 45.833 0.00 0.00 42.93 2.59
316 321 6.405278 TGACTCAGAACAAGACTAACATGA 57.595 37.500 0.00 0.00 0.00 3.07
374 379 7.596621 CGATAGTGCGCATATCCATAATAATCT 59.403 37.037 15.91 2.60 0.00 2.40
433 522 8.865090 TGATTCAACTGCCTTAATTTTTAAGGA 58.135 29.630 23.75 11.69 45.24 3.36
459 548 4.393062 ACATCGATGTTGTTGATTCCACTC 59.607 41.667 25.18 0.00 37.90 3.51
462 551 3.501828 CGATGTTGTTGATTCCACTCCAA 59.498 43.478 0.00 0.00 0.00 3.53
463 552 4.156556 CGATGTTGTTGATTCCACTCCAAT 59.843 41.667 0.00 0.00 0.00 3.16
464 553 5.335897 CGATGTTGTTGATTCCACTCCAATT 60.336 40.000 0.00 0.00 0.00 2.32
465 554 5.867903 TGTTGTTGATTCCACTCCAATTT 57.132 34.783 0.00 0.00 0.00 1.82
466 555 6.232581 TGTTGTTGATTCCACTCCAATTTT 57.767 33.333 0.00 0.00 0.00 1.82
467 556 6.648192 TGTTGTTGATTCCACTCCAATTTTT 58.352 32.000 0.00 0.00 0.00 1.94
529 618 0.316204 CTTGCTTCAGCCACCCAAAG 59.684 55.000 0.00 0.00 41.18 2.77
560 649 4.500127 GTTGGTTTTGCAGTTACTTGGTT 58.500 39.130 0.00 0.00 0.00 3.67
607 696 2.122564 GAGCAAGCACTTTTCAACAGC 58.877 47.619 0.00 0.00 0.00 4.40
631 720 2.703007 ACTTGGAAGTCTGTCAGCTTCT 59.297 45.455 24.01 10.03 40.49 2.85
633 722 4.345257 ACTTGGAAGTCTGTCAGCTTCTTA 59.655 41.667 24.01 16.21 40.49 2.10
642 731 5.578727 GTCTGTCAGCTTCTTAACAGTATGG 59.421 44.000 0.00 0.00 43.62 2.74
649 738 4.693283 CTTCTTAACAGTATGGCATCCGA 58.307 43.478 1.65 0.00 43.62 4.55
655 744 0.955178 AGTATGGCATCCGACTCGAG 59.045 55.000 11.84 11.84 0.00 4.04
658 747 2.021068 ATGGCATCCGACTCGAGGTG 62.021 60.000 18.41 8.31 0.00 4.00
659 748 2.415608 GGCATCCGACTCGAGGTGA 61.416 63.158 18.41 10.19 0.00 4.02
738 832 2.941210 GAGCTCGGAGATCCTCGAT 58.059 57.895 12.13 0.00 33.89 3.59
875 1014 1.025113 CGCTACCTCGTCTCTGTCCA 61.025 60.000 0.00 0.00 0.00 4.02
917 1056 0.832135 TCAACGAGGGTGAGAAGCCT 60.832 55.000 0.00 0.00 0.00 4.58
941 1081 1.000060 CCCCGTTCAACGACAGAACTA 60.000 52.381 12.68 0.00 46.05 2.24
944 1084 3.378339 CCGTTCAACGACAGAACTAGTT 58.622 45.455 12.68 8.13 46.05 2.24
959 1099 4.780275 ACTAGTTAGTTCTGTTCCGTCC 57.220 45.455 0.00 0.00 31.13 4.79
976 1126 2.202905 CGCCACCGCCGGTATAAA 60.203 61.111 9.25 0.00 32.11 1.40
977 1127 2.241880 CGCCACCGCCGGTATAAAG 61.242 63.158 9.25 0.00 32.11 1.85
1007 1157 0.462759 CCCTCGAGAACCATTCCTGC 60.463 60.000 15.71 0.00 0.00 4.85
1020 1178 4.946157 ACCATTCCTGCTAGACAAAGATTG 59.054 41.667 0.00 0.00 0.00 2.67
1082 1250 1.143073 GAGAGGGAGGGAGAGAGAGAC 59.857 61.905 0.00 0.00 0.00 3.36
1085 1253 0.923358 GGGAGGGAGAGAGAGACAGA 59.077 60.000 0.00 0.00 0.00 3.41
1102 1270 0.913451 AGAGGCAGGCCATGAAGTCT 60.913 55.000 13.63 2.34 38.92 3.24
1296 1492 1.372128 CTTTCTTTGCGTGCCTGCC 60.372 57.895 0.00 0.00 0.00 4.85
1337 1533 0.107993 CGCCATCAAAGCAGAGGAGA 60.108 55.000 0.00 0.00 0.00 3.71
1342 1538 0.612229 TCAAAGCAGAGGAGAGGCAG 59.388 55.000 0.00 0.00 0.00 4.85
1350 1546 0.692419 GAGGAGAGGCAGGGGATGAA 60.692 60.000 0.00 0.00 0.00 2.57
1378 1574 1.513158 CGTCAAGATGGAGGTCGCT 59.487 57.895 0.00 0.00 0.00 4.93
1419 1621 1.138859 TCCGGATTCAGCTGGTATGTG 59.861 52.381 15.13 0.00 35.72 3.21
1420 1622 0.940126 CGGATTCAGCTGGTATGTGC 59.060 55.000 15.13 0.33 0.00 4.57
1421 1623 1.312815 GGATTCAGCTGGTATGTGCC 58.687 55.000 15.13 2.58 0.00 5.01
1488 1701 1.750193 TGTTTCCATCTCCATTCGGC 58.250 50.000 0.00 0.00 0.00 5.54
1529 1742 2.417243 GGAAATTTGATGTTCCTGGCCG 60.417 50.000 0.00 0.00 40.24 6.13
1651 1865 0.253327 GAGGAAGAAACTCCGCCCAT 59.747 55.000 0.00 0.00 40.75 4.00
1655 1869 1.209747 GAAGAAACTCCGCCCATACCT 59.790 52.381 0.00 0.00 0.00 3.08
2101 2324 4.386413 CCAGTTCCTGGTGAGCAC 57.614 61.111 1.99 0.00 45.82 4.40
2732 2961 1.295423 GAGCGAGCAGTACCCCAAA 59.705 57.895 0.00 0.00 0.00 3.28
2774 3003 0.674581 CGCTCTCCATCCACAAGCAA 60.675 55.000 0.00 0.00 33.21 3.91
2882 3111 3.664888 AAGCTGCTGCCCCATGGA 61.665 61.111 15.22 0.00 40.80 3.41
2912 3141 3.649986 GCCAACAACTGAGCGCGT 61.650 61.111 8.43 0.00 0.00 6.01
2920 3149 3.120385 CTGAGCGCGTCAATGGCA 61.120 61.111 8.43 0.00 33.60 4.92
3015 3246 6.671605 TCAATTCCATGATGGTTAATCCTGA 58.328 36.000 11.87 4.14 39.03 3.86
3018 3249 4.464008 TCCATGATGGTTAATCCTGAAGC 58.536 43.478 11.87 0.00 39.03 3.86
3078 3309 5.636837 TGTTCTTTCGTTCAGTTTCTTTGG 58.363 37.500 0.00 0.00 0.00 3.28
3079 3310 5.182380 TGTTCTTTCGTTCAGTTTCTTTGGT 59.818 36.000 0.00 0.00 0.00 3.67
3080 3311 5.890424 TCTTTCGTTCAGTTTCTTTGGTT 57.110 34.783 0.00 0.00 0.00 3.67
3081 3312 5.636837 TCTTTCGTTCAGTTTCTTTGGTTG 58.363 37.500 0.00 0.00 0.00 3.77
3116 3347 0.542938 TAGCGGCTATCCCTGCATCT 60.543 55.000 5.42 0.00 36.16 2.90
3286 3544 6.346838 CGTTTCAAAATGGAGGCAAAAGATTC 60.347 38.462 0.00 0.00 0.00 2.52
3296 3554 3.259123 AGGCAAAAGATTCACACCATTCC 59.741 43.478 0.00 0.00 0.00 3.01
3300 3559 5.863935 GCAAAAGATTCACACCATTCCTAAC 59.136 40.000 0.00 0.00 0.00 2.34
3355 3614 8.541133 AGAAAGAGAGTTATAACAAACAGAGC 57.459 34.615 17.65 1.46 0.00 4.09
3356 3615 8.371699 AGAAAGAGAGTTATAACAAACAGAGCT 58.628 33.333 17.65 0.00 0.00 4.09
3357 3616 7.897575 AAGAGAGTTATAACAAACAGAGCTG 57.102 36.000 17.65 0.00 0.00 4.24
3358 3617 7.233389 AGAGAGTTATAACAAACAGAGCTGA 57.767 36.000 17.65 0.00 0.00 4.26
3359 3618 7.671302 AGAGAGTTATAACAAACAGAGCTGAA 58.329 34.615 17.65 0.00 0.00 3.02
3360 3619 7.816995 AGAGAGTTATAACAAACAGAGCTGAAG 59.183 37.037 17.65 0.00 0.00 3.02
3361 3620 7.671302 AGAGTTATAACAAACAGAGCTGAAGA 58.329 34.615 17.65 0.00 0.00 2.87
3362 3621 8.150945 AGAGTTATAACAAACAGAGCTGAAGAA 58.849 33.333 17.65 0.00 0.00 2.52
3363 3622 8.677148 AGTTATAACAAACAGAGCTGAAGAAA 57.323 30.769 17.65 0.00 0.00 2.52
3364 3623 8.778358 AGTTATAACAAACAGAGCTGAAGAAAG 58.222 33.333 17.65 0.00 0.00 2.62
3365 3624 8.774586 GTTATAACAAACAGAGCTGAAGAAAGA 58.225 33.333 10.81 0.00 0.00 2.52
3366 3625 5.747951 AACAAACAGAGCTGAAGAAAGAG 57.252 39.130 4.21 0.00 0.00 2.85
3367 3626 5.028549 ACAAACAGAGCTGAAGAAAGAGA 57.971 39.130 4.21 0.00 0.00 3.10
3378 3637 6.204495 AGCTGAAGAAAGAGAAGCTAACAAAG 59.796 38.462 0.00 0.00 42.25 2.77
3380 3639 7.484035 TGAAGAAAGAGAAGCTAACAAAGAC 57.516 36.000 0.00 0.00 0.00 3.01
3382 3641 7.552687 TGAAGAAAGAGAAGCTAACAAAGACAA 59.447 33.333 0.00 0.00 0.00 3.18
3474 3733 3.662186 CACGTCGTTGCCTCAATTTTAAC 59.338 43.478 0.00 0.00 0.00 2.01
3484 3743 5.714333 TGCCTCAATTTTAACCTTGCATAGA 59.286 36.000 0.00 0.00 0.00 1.98
3510 3769 6.295249 TGATGGTAGACATTGTCAAAACAGA 58.705 36.000 18.57 4.20 40.72 3.41
3518 3777 6.769822 AGACATTGTCAAAACAGATGAAGACT 59.230 34.615 18.57 0.00 36.57 3.24
3559 3819 7.756722 ACATTTCAAATCAATAAGCGAAAGAGG 59.243 33.333 0.00 0.00 0.00 3.69
3563 3823 6.429692 TCAAATCAATAAGCGAAAGAGGACAA 59.570 34.615 0.00 0.00 0.00 3.18
3582 3842 4.284550 TGAAGGTGCCCACTGCCC 62.285 66.667 0.00 0.00 40.16 5.36
3585 3845 3.086764 AAGGTGCCCACTGCCCTTT 62.087 57.895 0.00 0.00 43.76 3.11
3591 3851 2.036256 CCACTGCCCTTTCCCCTG 59.964 66.667 0.00 0.00 0.00 4.45
3595 3878 3.984193 CTGCCCTTTCCCCTGCTCG 62.984 68.421 0.00 0.00 0.00 5.03
3620 3903 7.520937 CGATCTATTCATCAAACATCATGGCAA 60.521 37.037 0.00 0.00 0.00 4.52
3626 3909 6.566141 TCATCAAACATCATGGCAATACAAG 58.434 36.000 0.00 0.00 0.00 3.16
3630 3913 4.989279 ACATCATGGCAATACAAGGAAC 57.011 40.909 0.00 0.00 0.00 3.62
3634 3917 3.758023 TCATGGCAATACAAGGAACACAG 59.242 43.478 0.00 0.00 0.00 3.66
3635 3918 3.500448 TGGCAATACAAGGAACACAGA 57.500 42.857 0.00 0.00 0.00 3.41
3636 3919 3.146066 TGGCAATACAAGGAACACAGAC 58.854 45.455 0.00 0.00 0.00 3.51
3637 3920 2.159627 GGCAATACAAGGAACACAGACG 59.840 50.000 0.00 0.00 0.00 4.18
3638 3921 3.064207 GCAATACAAGGAACACAGACGA 58.936 45.455 0.00 0.00 0.00 4.20
3639 3922 3.684788 GCAATACAAGGAACACAGACGAT 59.315 43.478 0.00 0.00 0.00 3.73
3660 3943 9.624697 GACGATAATATAAATTACACCCGTGTA 57.375 33.333 3.57 3.57 44.42 2.90
3671 3954 1.083489 ACCCGTGTACATGCATTTCG 58.917 50.000 9.72 1.19 0.00 3.46
3681 3964 2.095263 ACATGCATTTCGTTTTCCTCCG 60.095 45.455 0.00 0.00 0.00 4.63
3691 3974 1.004292 GTTTTCCTCCGTTCACACACG 60.004 52.381 0.00 0.00 40.02 4.49
3705 3988 2.098298 CACGCGAATTTGCTCCCG 59.902 61.111 15.93 2.65 0.00 5.14
3806 4089 2.653766 CAACGCGCGGCAGTTTTT 60.654 55.556 35.22 14.60 0.00 1.94
3932 4224 3.648545 ACCTAGTCCTTTTCTTGACTGCT 59.351 43.478 2.58 0.00 41.71 4.24
3992 4290 1.015607 CACCCCTAACACGTTACGCC 61.016 60.000 4.09 0.00 0.00 5.68
4063 4361 0.107214 CGCCTGGATAGAAAAGCCCA 60.107 55.000 0.00 0.00 0.00 5.36
4068 4366 1.448119 GGATAGAAAAGCCCAGCGCC 61.448 60.000 2.29 0.00 38.78 6.53
4153 4452 0.036732 ACAGATTTGCAAGGCCGAGA 59.963 50.000 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.434420 TGAACTTTGTCAAAAATTGTGAAGAAT 57.566 25.926 0.00 0.00 0.00 2.40
1 2 8.824159 TGAACTTTGTCAAAAATTGTGAAGAA 57.176 26.923 0.00 0.00 0.00 2.52
91 93 9.712305 CTGGAATACCAAATGAGTAGTATTAGG 57.288 37.037 0.00 0.00 46.32 2.69
97 99 7.200434 ACATCTGGAATACCAAATGAGTAGT 57.800 36.000 9.16 0.00 44.78 2.73
101 103 6.457392 CGTCAACATCTGGAATACCAAATGAG 60.457 42.308 9.16 2.70 44.78 2.90
102 104 5.353956 CGTCAACATCTGGAATACCAAATGA 59.646 40.000 9.16 0.00 44.78 2.57
107 109 4.545208 TTCGTCAACATCTGGAATACCA 57.455 40.909 0.00 0.00 44.76 3.25
131 133 6.574350 ACACCTTTGACCGATAAGATAGAAG 58.426 40.000 0.00 0.00 0.00 2.85
143 145 3.794138 GCCAAACTTTACACCTTTGACCG 60.794 47.826 0.00 0.00 0.00 4.79
181 185 8.246615 ACTCCCCCAGTCCTAAGATATATTTTA 58.753 37.037 0.00 0.00 0.00 1.52
185 189 5.905633 ACTCCCCCAGTCCTAAGATATAT 57.094 43.478 0.00 0.00 0.00 0.86
191 195 3.330126 TCATACTCCCCCAGTCCTAAG 57.670 52.381 0.00 0.00 36.43 2.18
264 268 3.806949 AACTCTGGCCAAGTTTATGGA 57.193 42.857 20.79 7.09 43.54 3.41
306 311 7.007725 CGCTTTCAAATGTTGATCATGTTAGTC 59.992 37.037 0.00 0.00 39.84 2.59
316 321 1.550072 CCCCCGCTTTCAAATGTTGAT 59.450 47.619 0.00 0.00 39.84 2.57
374 379 6.542005 CCCTATCAATTGCATTGTGTACTGTA 59.458 38.462 0.00 0.00 41.02 2.74
398 487 5.841957 AGGCAGTTGAATCAATTACATCC 57.158 39.130 0.00 0.00 0.00 3.51
466 555 9.454859 AAAAATGGAGTGGAATTGTGTTAAAAA 57.545 25.926 0.00 0.00 0.00 1.94
468 557 9.757227 CTAAAAATGGAGTGGAATTGTGTTAAA 57.243 29.630 0.00 0.00 0.00 1.52
469 558 9.137459 TCTAAAAATGGAGTGGAATTGTGTTAA 57.863 29.630 0.00 0.00 0.00 2.01
470 559 8.698973 TCTAAAAATGGAGTGGAATTGTGTTA 57.301 30.769 0.00 0.00 0.00 2.41
471 560 7.595819 TCTAAAAATGGAGTGGAATTGTGTT 57.404 32.000 0.00 0.00 0.00 3.32
472 561 7.287696 ACTTCTAAAAATGGAGTGGAATTGTGT 59.712 33.333 0.00 0.00 0.00 3.72
473 562 7.661040 ACTTCTAAAAATGGAGTGGAATTGTG 58.339 34.615 0.00 0.00 0.00 3.33
474 563 7.839680 ACTTCTAAAAATGGAGTGGAATTGT 57.160 32.000 0.00 0.00 0.00 2.71
475 564 8.359642 TGAACTTCTAAAAATGGAGTGGAATTG 58.640 33.333 0.00 0.00 0.00 2.32
476 565 8.477419 TGAACTTCTAAAAATGGAGTGGAATT 57.523 30.769 0.00 0.00 0.00 2.17
477 566 8.477419 TTGAACTTCTAAAAATGGAGTGGAAT 57.523 30.769 0.00 0.00 0.00 3.01
478 567 7.014230 CCTTGAACTTCTAAAAATGGAGTGGAA 59.986 37.037 0.00 0.00 0.00 3.53
479 568 6.490040 CCTTGAACTTCTAAAAATGGAGTGGA 59.510 38.462 0.00 0.00 0.00 4.02
480 569 6.490040 TCCTTGAACTTCTAAAAATGGAGTGG 59.510 38.462 0.00 0.00 0.00 4.00
481 570 7.510549 TCCTTGAACTTCTAAAAATGGAGTG 57.489 36.000 0.00 0.00 0.00 3.51
482 571 7.780271 ACTTCCTTGAACTTCTAAAAATGGAGT 59.220 33.333 0.00 0.00 0.00 3.85
483 572 8.078596 CACTTCCTTGAACTTCTAAAAATGGAG 58.921 37.037 0.00 0.00 0.00 3.86
484 573 7.470009 GCACTTCCTTGAACTTCTAAAAATGGA 60.470 37.037 0.00 0.00 0.00 3.41
485 574 6.642540 GCACTTCCTTGAACTTCTAAAAATGG 59.357 38.462 0.00 0.00 0.00 3.16
486 575 7.428826 AGCACTTCCTTGAACTTCTAAAAATG 58.571 34.615 0.00 0.00 0.00 2.32
487 576 7.588497 AGCACTTCCTTGAACTTCTAAAAAT 57.412 32.000 0.00 0.00 0.00 1.82
529 618 1.208293 TGCAAAACCAACCCCAAACTC 59.792 47.619 0.00 0.00 0.00 3.01
560 649 6.358974 TCAGTGTGAAGTCCAAGATTATCA 57.641 37.500 0.00 0.00 0.00 2.15
586 675 2.378806 CTGTTGAAAAGTGCTTGCTCG 58.621 47.619 0.00 0.00 0.00 5.03
607 696 3.209410 AGCTGACAGACTTCCAAGTTTG 58.791 45.455 6.65 8.14 44.22 2.93
631 720 3.490249 CGAGTCGGATGCCATACTGTTAA 60.490 47.826 4.10 0.00 0.00 2.01
633 722 1.202417 CGAGTCGGATGCCATACTGTT 60.202 52.381 4.10 0.00 0.00 3.16
642 731 1.064946 CTCACCTCGAGTCGGATGC 59.935 63.158 13.54 0.00 36.94 3.91
649 738 1.589113 GAGCTTGCTCACCTCGAGT 59.411 57.895 16.71 0.00 44.33 4.18
655 744 2.125350 CTCGGGAGCTTGCTCACC 60.125 66.667 21.97 18.32 0.00 4.02
669 758 2.805353 CTGTCGTCCGTTGGCTCG 60.805 66.667 0.00 0.00 0.00 5.03
733 827 4.519437 TGCCAGCGCTCCATCGAG 62.519 66.667 7.13 0.00 39.33 4.04
734 828 4.819761 GTGCCAGCGCTCCATCGA 62.820 66.667 7.13 0.00 35.36 3.59
735 829 4.827087 AGTGCCAGCGCTCCATCG 62.827 66.667 7.13 0.00 35.36 3.84
744 838 1.963338 GTCAGTGACCAGTGCCAGC 60.963 63.158 12.54 0.00 0.00 4.85
746 840 2.421314 CGTCAGTGACCAGTGCCA 59.579 61.111 17.57 0.00 0.00 4.92
749 843 2.734723 CGCCGTCAGTGACCAGTG 60.735 66.667 17.57 11.73 0.00 3.66
861 997 2.179517 GCGTGGACAGAGACGAGG 59.820 66.667 0.00 0.00 37.81 4.63
864 1003 3.948086 GACCGCGTGGACAGAGACG 62.948 68.421 24.59 0.00 39.21 4.18
917 1056 1.440938 CTGTCGTTGAACGGGGCAAA 61.441 55.000 18.32 0.00 42.81 3.68
941 1081 1.336609 GCGGACGGAACAGAACTAACT 60.337 52.381 0.00 0.00 0.00 2.24
944 1084 1.180456 TGGCGGACGGAACAGAACTA 61.180 55.000 0.00 0.00 0.00 2.24
1007 1157 2.866762 GCTACCGGCAATCTTTGTCTAG 59.133 50.000 0.00 0.00 41.35 2.43
1029 1187 1.610673 TCTCTCTCTGTGGGTGCCC 60.611 63.158 0.00 0.00 0.00 5.36
1038 1196 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
1082 1250 0.747283 GACTTCATGGCCTGCCTCTG 60.747 60.000 9.97 7.28 36.94 3.35
1085 1253 0.543749 GTAGACTTCATGGCCTGCCT 59.456 55.000 9.97 0.00 36.94 4.75
1102 1270 1.616187 CCTCTCGACAGGTTCCTGGTA 60.616 57.143 20.88 6.79 38.30 3.25
1296 1492 0.391395 CCCTGTCTTCTCTGCAGCAG 60.391 60.000 17.10 17.10 0.00 4.24
1337 1533 1.693640 CCTTGTTCATCCCCTGCCT 59.306 57.895 0.00 0.00 0.00 4.75
1342 1538 1.032114 CGCTTCCCTTGTTCATCCCC 61.032 60.000 0.00 0.00 0.00 4.81
1350 1546 1.611673 CCATCTTGACGCTTCCCTTGT 60.612 52.381 0.00 0.00 0.00 3.16
1378 1574 2.221169 GTTGTGACCACAGCTTCATGA 58.779 47.619 9.29 0.00 42.94 3.07
1420 1622 3.901797 AAGGAAGCAAGGGTCGCGG 62.902 63.158 6.13 0.00 0.00 6.46
1421 1623 2.358737 AAGGAAGCAAGGGTCGCG 60.359 61.111 0.00 0.00 0.00 5.87
1488 1701 0.313987 TGCCGTATCATACAGCTCCG 59.686 55.000 4.65 0.00 33.36 4.63
1496 1709 6.061441 ACATCAAATTTCCTGCCGTATCATA 58.939 36.000 0.00 0.00 0.00 2.15
1529 1742 5.061721 ACCCATTAATTCACTCCCCATAC 57.938 43.478 0.00 0.00 0.00 2.39
1616 1830 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1617 1831 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1618 1832 0.556380 TTCCTCCTCCTCCTCCTCCT 60.556 60.000 0.00 0.00 0.00 3.69
1693 1907 3.276091 TGTTTGTGCTCACGGGCG 61.276 61.111 0.00 0.00 34.52 6.13
1859 2073 1.066143 CAGTACGGCTTCACCTTCCAT 60.066 52.381 0.00 0.00 35.61 3.41
2101 2324 0.602905 GGTCCACCACGACTTGAAGG 60.603 60.000 0.00 0.00 35.64 3.46
2146 2369 0.737715 CACCTCGTACTTGCTCAGCC 60.738 60.000 0.00 0.00 0.00 4.85
2681 2910 0.824109 CGAGCTGGATCTTGTACCCA 59.176 55.000 0.00 0.00 0.00 4.51
2750 2979 2.060980 GTGGATGGAGAGCGGGTCT 61.061 63.158 9.87 9.87 38.71 3.85
2920 3149 2.729383 TCCATGATCAGATAGGCCCT 57.271 50.000 0.00 0.00 0.00 5.19
2988 3219 7.231925 CAGGATTAACCATCATGGAATTGATCA 59.768 37.037 11.90 0.00 40.96 2.92
3018 3249 9.716556 ACCCCTATATATGTTCTTCTACCTATG 57.283 37.037 0.00 0.00 0.00 2.23
3078 3309 4.340263 GCTAAGCGCAGGTATAAAACAAC 58.660 43.478 11.47 0.00 37.06 3.32
3079 3310 4.609691 GCTAAGCGCAGGTATAAAACAA 57.390 40.909 11.47 0.00 37.06 2.83
3259 3517 1.988293 TGCCTCCATTTTGAAACGGA 58.012 45.000 0.00 0.00 0.00 4.69
3262 3520 6.482973 TGAATCTTTTGCCTCCATTTTGAAAC 59.517 34.615 0.00 0.00 0.00 2.78
3286 3544 6.153680 ACTCTCTCTTAGTTAGGAATGGTGTG 59.846 42.308 0.00 0.00 0.00 3.82
3331 3590 8.439286 CAGCTCTGTTTGTTATAACTCTCTTTC 58.561 37.037 16.33 1.13 0.00 2.62
3332 3591 8.150945 TCAGCTCTGTTTGTTATAACTCTCTTT 58.849 33.333 16.33 0.00 0.00 2.52
3334 3593 7.233389 TCAGCTCTGTTTGTTATAACTCTCT 57.767 36.000 16.33 0.92 0.00 3.10
3335 3594 7.815068 TCTTCAGCTCTGTTTGTTATAACTCTC 59.185 37.037 16.33 7.21 0.00 3.20
3336 3595 7.671302 TCTTCAGCTCTGTTTGTTATAACTCT 58.329 34.615 16.33 0.00 0.00 3.24
3337 3596 7.891183 TCTTCAGCTCTGTTTGTTATAACTC 57.109 36.000 16.33 7.82 0.00 3.01
3349 3608 3.324556 AGCTTCTCTTTCTTCAGCTCTGT 59.675 43.478 0.00 0.00 35.95 3.41
3353 3612 5.220710 TGTTAGCTTCTCTTTCTTCAGCT 57.779 39.130 0.00 0.00 43.33 4.24
3354 3613 5.931441 TTGTTAGCTTCTCTTTCTTCAGC 57.069 39.130 0.00 0.00 0.00 4.26
3355 3614 7.225538 TGTCTTTGTTAGCTTCTCTTTCTTCAG 59.774 37.037 0.00 0.00 0.00 3.02
3356 3615 7.047891 TGTCTTTGTTAGCTTCTCTTTCTTCA 58.952 34.615 0.00 0.00 0.00 3.02
3357 3616 7.484035 TGTCTTTGTTAGCTTCTCTTTCTTC 57.516 36.000 0.00 0.00 0.00 2.87
3358 3617 7.865706 TTGTCTTTGTTAGCTTCTCTTTCTT 57.134 32.000 0.00 0.00 0.00 2.52
3359 3618 7.554476 AGTTTGTCTTTGTTAGCTTCTCTTTCT 59.446 33.333 0.00 0.00 0.00 2.52
3360 3619 7.698628 AGTTTGTCTTTGTTAGCTTCTCTTTC 58.301 34.615 0.00 0.00 0.00 2.62
3361 3620 7.631717 AGTTTGTCTTTGTTAGCTTCTCTTT 57.368 32.000 0.00 0.00 0.00 2.52
3362 3621 8.732746 TTAGTTTGTCTTTGTTAGCTTCTCTT 57.267 30.769 0.00 0.00 0.00 2.85
3363 3622 8.732746 TTTAGTTTGTCTTTGTTAGCTTCTCT 57.267 30.769 0.00 0.00 0.00 3.10
3364 3623 7.588123 GCTTTAGTTTGTCTTTGTTAGCTTCTC 59.412 37.037 0.00 0.00 0.00 2.87
3365 3624 7.418408 GCTTTAGTTTGTCTTTGTTAGCTTCT 58.582 34.615 0.00 0.00 0.00 2.85
3366 3625 6.637254 GGCTTTAGTTTGTCTTTGTTAGCTTC 59.363 38.462 0.00 0.00 0.00 3.86
3367 3626 6.461092 GGGCTTTAGTTTGTCTTTGTTAGCTT 60.461 38.462 0.00 0.00 0.00 3.74
3378 3637 7.443259 TGTTATACAAGGGCTTTAGTTTGTC 57.557 36.000 0.00 0.00 35.55 3.18
3380 3639 7.275560 GCAATGTTATACAAGGGCTTTAGTTTG 59.724 37.037 0.00 0.00 0.00 2.93
3382 3641 6.663523 AGCAATGTTATACAAGGGCTTTAGTT 59.336 34.615 0.00 0.00 31.76 2.24
3474 3733 5.614308 TGTCTACCATCATTCTATGCAAGG 58.386 41.667 0.00 0.00 0.00 3.61
3484 3743 7.448161 TCTGTTTTGACAATGTCTACCATCATT 59.552 33.333 14.97 0.00 35.08 2.57
3533 3792 7.756722 CCTCTTTCGCTTATTGATTTGAAATGT 59.243 33.333 0.00 0.00 0.00 2.71
3582 3842 3.070159 TGAATAGATCGAGCAGGGGAAAG 59.930 47.826 2.38 0.00 0.00 2.62
3585 3845 2.381752 TGAATAGATCGAGCAGGGGA 57.618 50.000 2.38 0.00 0.00 4.81
3591 3851 6.775939 TGATGTTTGATGAATAGATCGAGC 57.224 37.500 0.00 0.00 0.00 5.03
3595 3878 7.210718 TGCCATGATGTTTGATGAATAGATC 57.789 36.000 0.00 0.00 0.00 2.75
3630 3913 8.644619 CGGGTGTAATTTATATTATCGTCTGTG 58.355 37.037 0.00 0.00 0.00 3.66
3634 3917 8.524870 ACACGGGTGTAATTTATATTATCGTC 57.475 34.615 1.96 0.00 42.90 4.20
3635 3918 9.410556 GTACACGGGTGTAATTTATATTATCGT 57.589 33.333 12.85 0.00 46.33 3.73
3636 3919 9.409312 TGTACACGGGTGTAATTTATATTATCG 57.591 33.333 12.85 0.00 46.33 2.92
3639 3922 8.991026 GCATGTACACGGGTGTAATTTATATTA 58.009 33.333 12.85 0.00 46.33 0.98
3660 3943 2.095263 CGGAGGAAAACGAAATGCATGT 60.095 45.455 0.00 0.00 0.00 3.21
3671 3954 1.004292 CGTGTGTGAACGGAGGAAAAC 60.004 52.381 0.00 0.00 39.89 2.43
3681 3964 0.770008 GCAAATTCGCGTGTGTGAAC 59.230 50.000 5.77 0.00 46.57 3.18
3691 3974 1.024579 TTCCTCGGGAGCAAATTCGC 61.025 55.000 0.00 0.00 31.21 4.70
3752 4035 1.045407 AGTGGTCGTAGCCAAAGACA 58.955 50.000 5.38 0.00 40.68 3.41
3806 4089 6.754675 GCAAGACAAGGCTGTTTTTAGTTTTA 59.245 34.615 0.00 0.00 35.30 1.52
3932 4224 6.648310 CGATATCTCAGTTACTACTAACCGGA 59.352 42.308 9.46 0.00 33.82 5.14
3968 4266 2.746277 CGTGTTAGGGGTGCCAGC 60.746 66.667 0.00 0.00 0.00 4.85
3979 4277 2.504351 CGTGTGGCGTAACGTGTTA 58.496 52.632 0.00 0.00 35.13 2.41


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

AutoCloner maintained by Alex Coulton.