Multiple sequence alignment - TraesCS2D01G068000

Loading Multiple Alignment...

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 TraesCS2D01G068000 chr2D 100.000 4371 0 0 1 4371 28549792 28554162 0.000000e+00 8072.0
1 TraesCS2D01G068000 chr2A 90.428 4440 227 93 23 4370 30332882 30328549 0.000000e+00 5662.0
2 TraesCS2D01G068000 chr2B 90.889 4127 213 79 228 4286 45737697 45733666 0.000000e+00 5387.0
3 TraesCS2D01G068000 chr2B 97.619 84 2 0 4288 4371 45733503 45733420 1.270000e-30 145.0
4 TraesCS2D01G068000 chr6A 90.909 132 10 2 1001 1131 578887719 578887589 4.490000e-40 176.0
5 TraesCS2D01G068000 chr6A 91.579 95 8 0 2584 2678 578886312 578886218 9.860000e-27 132.0
6 TraesCS2D01G068000 chr6D 89.394 132 12 2 1001 1131 432710580 432710450 9.730000e-37 165.0
7 TraesCS2D01G068000 chr6D 91.579 95 8 0 2584 2678 432709199 432709105 9.860000e-27 132.0
8 TraesCS2D01G068000 chr6B 88.636 132 13 2 1001 1131 652631344 652631214 4.520000e-35 159.0
9 TraesCS2D01G068000 chr6B 92.632 95 7 0 2584 2678 652629939 652629845 2.120000e-28 137.0
10 TraesCS2D01G068000 chr5D 94.340 53 3 0 2620 2672 342712606 342712554 1.010000e-11 82.4
11 TraesCS2D01G068000 chr5B 94.340 53 3 0 2620 2672 402751135 402751083 1.010000e-11 82.4
12 TraesCS2D01G068000 chr4A 85.526 76 9 2 2598 2672 468603638 468603712 1.300000e-10 78.7
13 TraesCS2D01G068000 chr3D 100.000 30 0 0 1039 1068 471970374 471970345 6.110000e-04 56.5
14 TraesCS2D01G068000 chr3A 100.000 30 0 0 1039 1068 614574306 614574277 6.110000e-04 56.5


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 TraesCS2D01G068000 chr2D 28549792 28554162 4370 False 8072 8072 100.000 1 4371 1 chr2D.!!$F1 4370
1 TraesCS2D01G068000 chr2A 30328549 30332882 4333 True 5662 5662 90.428 23 4370 1 chr2A.!!$R1 4347
2 TraesCS2D01G068000 chr2B 45733420 45737697 4277 True 2766 5387 94.254 228 4371 2 chr2B.!!$R1 4143

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
84 85 0.321298 GTGGCGGCTAGGTTTCTTGA 60.321 55.0 11.43 0.0 0.00 3.02 F
671 692 0.397816 TAGCTCTGGCCTCTCTTCCC 60.398 60.0 3.32 0.0 39.73 3.97 F
2102 2164 0.478072 ATGAGGCACACCCAAGTTGA 59.522 50.0 3.87 0.0 36.11 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 1584 2.106338 TGTGGAATGAAGGCACTCTTGA 59.894 45.455 0.00 0.0 38.49 3.02 R
2582 2671 0.596083 GCGATGATCGACCACCTGAG 60.596 60.000 20.25 0.0 43.74 3.35 R
3997 4128 0.109643 GCATTGCAGCATCAACGACA 60.110 50.000 3.15 0.0 0.00 4.35 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
17 18 3.951332 ATCGCCAACACAGTGTCG 58.049 55.556 6.67 6.80 0.00 4.35
18 19 2.317609 ATCGCCAACACAGTGTCGC 61.318 57.895 6.67 10.88 0.00 5.19
19 20 2.715532 ATCGCCAACACAGTGTCGCT 62.716 55.000 18.71 4.48 0.00 4.93
33 34 2.895865 CGCTGCATGCAGAGGAGG 60.896 66.667 44.02 24.83 46.30 4.30
84 85 0.321298 GTGGCGGCTAGGTTTCTTGA 60.321 55.000 11.43 0.00 0.00 3.02
87 88 1.646189 GCGGCTAGGTTTCTTGAGAG 58.354 55.000 0.00 0.00 0.00 3.20
101 102 1.227118 GAGAGAGTGGCGGCTTAGC 60.227 63.158 11.43 0.00 0.00 3.09
201 203 4.682787 TGTGATATTGAACGACCTAGCTG 58.317 43.478 0.00 0.00 0.00 4.24
202 204 4.159693 TGTGATATTGAACGACCTAGCTGT 59.840 41.667 0.00 0.00 0.00 4.40
204 206 5.581085 GTGATATTGAACGACCTAGCTGTTT 59.419 40.000 0.00 0.00 0.00 2.83
205 207 5.580691 TGATATTGAACGACCTAGCTGTTTG 59.419 40.000 0.00 0.00 0.00 2.93
383 399 7.880713 TGGACTAGCACATCAAAGTAATTAACA 59.119 33.333 0.00 0.00 0.00 2.41
402 418 0.678048 AAGCAGGCACGAAGGATTCC 60.678 55.000 0.00 0.00 43.81 3.01
668 689 0.829990 GCTTAGCTCTGGCCTCTCTT 59.170 55.000 3.32 0.00 39.73 2.85
669 690 1.202521 GCTTAGCTCTGGCCTCTCTTC 60.203 57.143 3.32 0.00 39.73 2.87
670 691 1.412343 CTTAGCTCTGGCCTCTCTTCC 59.588 57.143 3.32 0.00 39.73 3.46
671 692 0.397816 TAGCTCTGGCCTCTCTTCCC 60.398 60.000 3.32 0.00 39.73 3.97
672 693 2.741055 GCTCTGGCCTCTCTTCCCC 61.741 68.421 3.32 0.00 0.00 4.81
787 808 1.517242 GCAGTGGTTCCTCTGTCTTG 58.483 55.000 18.12 0.00 34.57 3.02
1041 1082 3.841372 GCGACAAGAACAACGTGAAGAAG 60.841 47.826 0.00 0.00 0.00 2.85
1047 1088 2.032071 AACGTGAAGAAGGGGCCG 59.968 61.111 0.00 0.00 0.00 6.13
1153 1194 2.341257 CAGGTGTGTGTGTATGAGCTC 58.659 52.381 6.82 6.82 0.00 4.09
1164 1205 0.543277 TATGAGCTCCCTGCCTTGTG 59.457 55.000 12.15 0.00 44.23 3.33
1267 1309 8.345724 ACTTCTCTTGATTTATTTGCAGATGT 57.654 30.769 0.00 0.00 0.00 3.06
1279 1321 8.975410 TTATTTGCAGATGTGATTTCTTCTTG 57.025 30.769 0.00 0.00 0.00 3.02
1314 1356 2.160417 GTCCTTGATTTGCTTCCGTCTG 59.840 50.000 0.00 0.00 0.00 3.51
1337 1379 5.010922 TGTTTTTCTTGACTTGGGGATGATG 59.989 40.000 0.00 0.00 0.00 3.07
1348 1390 5.186409 ACTTGGGGATGATGAGTTGAAATTG 59.814 40.000 0.00 0.00 0.00 2.32
1431 1474 3.029570 TCATGACCCATGAGTCTCTCTG 58.970 50.000 8.95 2.02 44.60 3.35
1473 1520 6.556212 GAGACATCTCTAAGTCGAAATGACA 58.444 40.000 1.44 0.00 43.61 3.58
1500 1547 5.974158 GTCTTTTCTGGCAACTTCTTCTTTC 59.026 40.000 0.00 0.00 37.61 2.62
1504 1551 2.555757 CTGGCAACTTCTTCTTTCCCAG 59.444 50.000 0.00 0.00 33.47 4.45
1512 1559 5.094387 ACTTCTTCTTTCCCAGTCTATCCA 58.906 41.667 0.00 0.00 0.00 3.41
1531 1578 4.609301 TCCAACTTATCATTTCCCCCTTG 58.391 43.478 0.00 0.00 0.00 3.61
1535 1582 6.838612 CCAACTTATCATTTCCCCCTTGAATA 59.161 38.462 0.00 0.00 0.00 1.75
1537 1584 8.927411 CAACTTATCATTTCCCCCTTGAATAAT 58.073 33.333 0.00 0.00 0.00 1.28
1538 1585 8.712228 ACTTATCATTTCCCCCTTGAATAATC 57.288 34.615 0.00 0.00 0.00 1.75
1539 1586 8.288812 ACTTATCATTTCCCCCTTGAATAATCA 58.711 33.333 0.00 0.00 0.00 2.57
1553 1600 7.707624 TTGAATAATCAAGAGTGCCTTCATT 57.292 32.000 0.00 0.00 40.59 2.57
1554 1601 7.325660 TGAATAATCAAGAGTGCCTTCATTC 57.674 36.000 0.00 0.00 28.34 2.67
1559 1612 2.886523 CAAGAGTGCCTTCATTCCACAA 59.113 45.455 0.00 0.00 31.42 3.33
1563 1616 4.225942 AGAGTGCCTTCATTCCACAAGATA 59.774 41.667 0.00 0.00 30.10 1.98
1570 1623 6.351286 GCCTTCATTCCACAAGATAACCAAAT 60.351 38.462 0.00 0.00 0.00 2.32
1571 1624 7.037438 CCTTCATTCCACAAGATAACCAAATG 58.963 38.462 0.00 0.00 0.00 2.32
1607 1660 9.384764 TGTTTTAGGAACCAAAATTTAAAGGTG 57.615 29.630 9.77 0.00 33.93 4.00
1622 1675 7.995463 TTTAAAGGTGCTTGTGTTTAATCAC 57.005 32.000 9.33 9.33 38.63 3.06
1623 1676 5.852282 AAAGGTGCTTGTGTTTAATCACT 57.148 34.783 15.75 0.00 38.90 3.41
1624 1677 5.438761 AAGGTGCTTGTGTTTAATCACTC 57.561 39.130 15.75 7.40 38.90 3.51
1626 1679 3.057526 GGTGCTTGTGTTTAATCACTCCC 60.058 47.826 15.75 6.57 38.90 4.30
1628 1681 5.001232 GTGCTTGTGTTTAATCACTCCCTA 58.999 41.667 15.75 0.00 38.90 3.53
1630 1683 4.395231 GCTTGTGTTTAATCACTCCCTACC 59.605 45.833 15.75 0.00 38.90 3.18
1631 1684 5.803470 GCTTGTGTTTAATCACTCCCTACCT 60.803 44.000 15.75 0.00 38.90 3.08
1632 1685 5.416271 TGTGTTTAATCACTCCCTACCTC 57.584 43.478 15.75 0.00 38.90 3.85
1633 1686 5.091552 TGTGTTTAATCACTCCCTACCTCT 58.908 41.667 15.75 0.00 38.90 3.69
1655 1708 7.659390 CCTCTTTAGTTTGTCTCTCTCACAAAT 59.341 37.037 1.60 0.00 43.74 2.32
1665 1718 3.252665 CTCACAAATGCGCGCACCA 62.253 57.895 39.05 15.44 0.00 4.17
1739 1796 6.986817 ACAATAACTAATGCTATGACTCGCTT 59.013 34.615 0.00 0.00 0.00 4.68
1743 1800 7.644986 AACTAATGCTATGACTCGCTTAATC 57.355 36.000 0.00 0.00 0.00 1.75
1750 1807 2.985896 TGACTCGCTTAATCCCCTTTG 58.014 47.619 0.00 0.00 0.00 2.77
1775 1832 8.279800 TGTCACACGTCTAATTTTATGTTCTTG 58.720 33.333 0.00 0.00 0.00 3.02
1820 1878 9.512588 CATATGCTATCTATTGTTTCTTTCCCT 57.487 33.333 0.00 0.00 0.00 4.20
2029 2090 1.131126 CAAGCATTGGAAGCAGGTACG 59.869 52.381 0.00 0.00 43.94 3.67
2046 2107 2.510768 ACGCGAGACTGTTCTTCTTT 57.489 45.000 15.93 0.00 29.47 2.52
2102 2164 0.478072 ATGAGGCACACCCAAGTTGA 59.522 50.000 3.87 0.00 36.11 3.18
2116 2178 7.494298 ACACCCAAGTTGAAAAACAATTATGAC 59.506 33.333 3.87 0.00 40.76 3.06
2214 2280 9.883142 AAAAGAATTGTTCCTGTCAATGTTTTA 57.117 25.926 0.00 0.00 34.37 1.52
2227 2293 6.478344 TGTCAATGTTTTATTTTGTGCAGGAC 59.522 34.615 0.00 0.00 0.00 3.85
2246 2312 6.098679 CAGGACACAACAAAATGTTTTCTGA 58.901 36.000 0.00 0.00 38.77 3.27
2314 2384 3.431673 TCCCTAACACATGCATGACAA 57.568 42.857 32.75 13.52 0.00 3.18
2379 2449 2.961741 CCCTATCTTGTGCTCAGAGCTA 59.038 50.000 23.15 9.71 42.97 3.32
2391 2461 5.356470 GTGCTCAGAGCTAAAGATCCAAAAT 59.644 40.000 23.15 0.00 42.97 1.82
2420 2492 8.606830 TCATAGATCTAGGTAGAAGCATACTCA 58.393 37.037 13.74 0.00 35.69 3.41
2421 2493 9.407380 CATAGATCTAGGTAGAAGCATACTCAT 57.593 37.037 8.70 0.00 35.69 2.90
2422 2494 7.938140 AGATCTAGGTAGAAGCATACTCATC 57.062 40.000 0.00 0.00 35.69 2.92
2423 2495 7.465960 AGATCTAGGTAGAAGCATACTCATCA 58.534 38.462 0.00 0.00 35.69 3.07
2511 2584 5.365605 CCCCAAAAAGGAAAGAAAACCTAGT 59.634 40.000 0.00 0.00 41.22 2.57
2512 2585 6.280643 CCCAAAAAGGAAAGAAAACCTAGTG 58.719 40.000 0.00 0.00 41.22 2.74
2568 2657 7.395190 ACTGCAAATTAGCATTACTCATTCA 57.605 32.000 0.00 0.00 44.68 2.57
2572 2661 7.094248 TGCAAATTAGCATTACTCATTCAGTGT 60.094 33.333 0.00 0.00 40.11 3.55
2573 2662 7.219535 GCAAATTAGCATTACTCATTCAGTGTG 59.780 37.037 0.00 0.00 36.43 3.82
2575 2664 8.743085 AATTAGCATTACTCATTCAGTGTGAT 57.257 30.769 0.00 0.00 36.43 3.06
2577 2666 8.648557 TTAGCATTACTCATTCAGTGTGATAC 57.351 34.615 0.00 0.00 36.43 2.24
2579 2668 7.105588 AGCATTACTCATTCAGTGTGATACAA 58.894 34.615 0.00 0.00 36.43 2.41
2581 2670 8.400947 GCATTACTCATTCAGTGTGATACAATT 58.599 33.333 0.00 0.00 36.43 2.32
2582 2671 9.926751 CATTACTCATTCAGTGTGATACAATTC 57.073 33.333 0.00 0.00 36.43 2.17
2849 2941 1.208776 CGGAACCCCTAACCCTACAAG 59.791 57.143 0.00 0.00 0.00 3.16
2851 2943 0.997363 AACCCCTAACCCTACAAGCC 59.003 55.000 0.00 0.00 0.00 4.35
2863 2955 2.505819 CCTACAAGCCCAAGACCACTAT 59.494 50.000 0.00 0.00 0.00 2.12
2872 2964 2.408050 CAAGACCACTATATGCTCGGC 58.592 52.381 0.00 0.00 0.00 5.54
2892 2984 1.376466 GCTCAGGCTCCTTGAACCA 59.624 57.895 0.00 0.00 35.22 3.67
2897 2989 1.067295 AGGCTCCTTGAACCACATGA 58.933 50.000 0.00 0.00 0.00 3.07
2898 2990 1.425066 AGGCTCCTTGAACCACATGAA 59.575 47.619 0.00 0.00 0.00 2.57
2899 2991 1.541588 GGCTCCTTGAACCACATGAAC 59.458 52.381 0.00 0.00 0.00 3.18
2900 2992 2.229792 GCTCCTTGAACCACATGAACA 58.770 47.619 0.00 0.00 0.00 3.18
2901 2993 2.622942 GCTCCTTGAACCACATGAACAA 59.377 45.455 0.00 0.00 0.00 2.83
2911 3003 5.083533 ACCACATGAACAACAACAACAAT 57.916 34.783 0.00 0.00 0.00 2.71
2914 3006 5.107824 CACATGAACAACAACAACAATGGA 58.892 37.500 0.00 0.00 0.00 3.41
2926 3018 3.717294 AATGGAGCCTCCGCGGTT 61.717 61.111 27.15 6.25 40.17 4.44
2983 3075 1.078567 GCTGCAGGTGAAGGAGGAG 60.079 63.158 17.12 0.00 0.00 3.69
3058 3150 4.972733 TCGTCGGACGGGACCCAA 62.973 66.667 28.07 6.23 42.81 4.12
3145 3237 4.217159 GGGTACAGCGCCTACGGG 62.217 72.222 2.29 0.00 40.57 5.28
3156 3248 2.493030 CTACGGGGTGTACGGCAG 59.507 66.667 0.00 0.00 35.23 4.85
3277 3372 3.200593 CAGCTGCTCATGACGGCC 61.201 66.667 19.23 0.00 40.43 6.13
3384 3488 9.309516 GACGATGATGTAAAAACCAGAGTAATA 57.690 33.333 0.00 0.00 0.00 0.98
3385 3489 9.832445 ACGATGATGTAAAAACCAGAGTAATAT 57.168 29.630 0.00 0.00 0.00 1.28
3430 3538 4.259970 CGCACGTAAAGAAGATCATCAAGG 60.260 45.833 0.10 0.00 0.00 3.61
3431 3539 4.631813 GCACGTAAAGAAGATCATCAAGGT 59.368 41.667 0.10 0.00 0.00 3.50
3612 3732 0.948623 GCCGCTGTGTGTGTATGTGA 60.949 55.000 0.00 0.00 0.00 3.58
3675 3802 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
3676 3803 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
3677 3804 3.051803 TCTCTCTCTCTCTCTCTCTCCCT 60.052 52.174 0.00 0.00 0.00 4.20
3678 3805 3.309296 TCTCTCTCTCTCTCTCTCCCTC 58.691 54.545 0.00 0.00 0.00 4.30
3719 3848 4.534500 TGTTGTACCTCTCTCTCTCTCTCT 59.466 45.833 0.00 0.00 0.00 3.10
3720 3849 5.116882 GTTGTACCTCTCTCTCTCTCTCTC 58.883 50.000 0.00 0.00 0.00 3.20
3721 3850 4.620723 TGTACCTCTCTCTCTCTCTCTCT 58.379 47.826 0.00 0.00 0.00 3.10
3722 3851 4.649674 TGTACCTCTCTCTCTCTCTCTCTC 59.350 50.000 0.00 0.00 0.00 3.20
3723 3852 4.000928 ACCTCTCTCTCTCTCTCTCTCT 57.999 50.000 0.00 0.00 0.00 3.10
3724 3853 3.964031 ACCTCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20
3725 3854 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
3726 3855 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
3727 3856 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
3728 3857 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3729 3858 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
3730 3859 4.646945 TCTCTCTCTCTCTCTCTCTCTCAC 59.353 50.000 0.00 0.00 0.00 3.51
3731 3860 4.352893 TCTCTCTCTCTCTCTCTCTCACA 58.647 47.826 0.00 0.00 0.00 3.58
3732 3861 4.160439 TCTCTCTCTCTCTCTCTCTCACAC 59.840 50.000 0.00 0.00 0.00 3.82
3733 3862 3.837731 TCTCTCTCTCTCTCTCTCACACA 59.162 47.826 0.00 0.00 0.00 3.72
3734 3863 3.935203 CTCTCTCTCTCTCTCTCACACAC 59.065 52.174 0.00 0.00 0.00 3.82
3735 3864 3.326297 TCTCTCTCTCTCTCTCACACACA 59.674 47.826 0.00 0.00 0.00 3.72
3736 3865 3.407698 TCTCTCTCTCTCTCACACACAC 58.592 50.000 0.00 0.00 0.00 3.82
3995 4126 3.057946 TCATTCACTCACTCACTCACTCG 60.058 47.826 0.00 0.00 0.00 4.18
3996 4127 1.968704 TCACTCACTCACTCACTCGT 58.031 50.000 0.00 0.00 0.00 4.18
3997 4128 2.298610 TCACTCACTCACTCACTCGTT 58.701 47.619 0.00 0.00 0.00 3.85
3998 4129 2.033424 TCACTCACTCACTCACTCGTTG 59.967 50.000 0.00 0.00 0.00 4.10
3999 4130 2.025155 ACTCACTCACTCACTCGTTGT 58.975 47.619 0.00 0.00 0.00 3.32
4098 4234 5.028375 GCAAAGCATACACCGATTAAAGTC 58.972 41.667 0.00 0.00 0.00 3.01
4160 4296 1.844357 CATACCGTTCGTCTTGTAGCG 59.156 52.381 0.00 0.00 0.00 4.26
4188 4324 5.486735 TCCATCAAACTTTGCCATGAATT 57.513 34.783 0.00 0.00 0.00 2.17
4189 4325 5.239351 TCCATCAAACTTTGCCATGAATTG 58.761 37.500 0.00 0.00 0.00 2.32
4208 4344 5.806654 ATTGGGCAGTGATTACTTGTTTT 57.193 34.783 0.00 0.00 34.07 2.43
4216 4352 6.291060 GCAGTGATTACTTGTTTTGTTTCACG 60.291 38.462 0.00 0.00 35.94 4.35
4226 4362 4.444720 TGTTTTGTTTCACGGTGTTTGTTC 59.555 37.500 8.17 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.633657 CAGCGACACTGTGTTGGC 59.366 61.111 25.32 23.78 41.86 4.52
17 18 1.524165 CTCCTCCTCTGCATGCAGC 60.524 63.158 37.48 4.48 43.31 5.25
18 19 1.146485 CCTCCTCCTCTGCATGCAG 59.854 63.158 36.80 36.80 44.86 4.41
19 20 2.372890 CCCTCCTCCTCTGCATGCA 61.373 63.158 21.29 21.29 0.00 3.96
20 21 2.509916 CCCTCCTCCTCTGCATGC 59.490 66.667 11.82 11.82 0.00 4.06
21 22 1.383664 TCCCCTCCTCCTCTGCATG 60.384 63.158 0.00 0.00 0.00 4.06
26 27 3.756783 CGGGTCCCCTCCTCCTCT 61.757 72.222 1.00 0.00 0.00 3.69
84 85 2.896443 GCTAAGCCGCCACTCTCT 59.104 61.111 0.00 0.00 0.00 3.10
120 121 8.897752 GGATAAAGTCAATCTGCTGAACTAATT 58.102 33.333 0.00 0.00 0.00 1.40
170 172 8.234546 AGGTCGTTCAATATCACAACATTTTAC 58.765 33.333 0.00 0.00 0.00 2.01
201 203 7.599630 TGTACATAGTAAATTCCGGACAAAC 57.400 36.000 1.83 0.00 0.00 2.93
202 204 7.879160 ACTTGTACATAGTAAATTCCGGACAAA 59.121 33.333 1.83 0.00 0.00 2.83
204 206 6.814644 CACTTGTACATAGTAAATTCCGGACA 59.185 38.462 1.83 0.00 0.00 4.02
205 207 6.815142 ACACTTGTACATAGTAAATTCCGGAC 59.185 38.462 1.83 0.00 0.00 4.79
243 247 3.328382 TGTATGTTTTGGTCTAGCGCT 57.672 42.857 17.26 17.26 0.00 5.92
271 278 2.211353 GCTAGGTAGCTTCTTCGTGG 57.789 55.000 0.00 0.00 45.62 4.94
383 399 0.678048 GGAATCCTTCGTGCCTGCTT 60.678 55.000 0.00 0.00 0.00 3.91
402 418 3.988379 ACAAAGTACACTTGCACATGG 57.012 42.857 0.00 0.00 36.12 3.66
669 690 4.038804 TTGAGGGGAGGGGAGGGG 62.039 72.222 0.00 0.00 0.00 4.79
670 691 2.367512 CTTGAGGGGAGGGGAGGG 60.368 72.222 0.00 0.00 0.00 4.30
671 692 3.093172 GCTTGAGGGGAGGGGAGG 61.093 72.222 0.00 0.00 0.00 4.30
672 693 0.326618 TAAGCTTGAGGGGAGGGGAG 60.327 60.000 9.86 0.00 0.00 4.30
844 866 6.183361 ACCCTCCTTTGTTAAACACTATGAGT 60.183 38.462 0.00 0.00 0.00 3.41
848 870 7.017850 TCCTAACCCTCCTTTGTTAAACACTAT 59.982 37.037 0.00 0.00 0.00 2.12
849 871 6.329723 TCCTAACCCTCCTTTGTTAAACACTA 59.670 38.462 0.00 0.00 0.00 2.74
1153 1194 3.017048 TCATAAATCCACAAGGCAGGG 57.983 47.619 0.00 0.00 33.74 4.45
1164 1205 4.046462 GCACACACATGCATCATAAATCC 58.954 43.478 0.00 0.00 45.39 3.01
1267 1309 7.756395 AATTCAAGAGAGCAAGAAGAAATCA 57.244 32.000 0.00 0.00 0.00 2.57
1279 1321 5.893897 ATCAAGGACAAATTCAAGAGAGC 57.106 39.130 0.00 0.00 0.00 4.09
1314 1356 5.243730 TCATCATCCCCAAGTCAAGAAAAAC 59.756 40.000 0.00 0.00 0.00 2.43
1431 1474 5.860611 TGTCTCTATCCAGACTACTAGAGC 58.139 45.833 0.00 6.51 43.00 4.09
1471 1518 2.851195 AGTTGCCAGAAAAGACGATGT 58.149 42.857 0.00 0.00 0.00 3.06
1473 1520 3.744660 AGAAGTTGCCAGAAAAGACGAT 58.255 40.909 0.00 0.00 0.00 3.73
1483 1530 2.586425 TGGGAAAGAAGAAGTTGCCAG 58.414 47.619 0.00 0.00 39.96 4.85
1500 1547 6.712547 GGAAATGATAAGTTGGATAGACTGGG 59.287 42.308 0.00 0.00 0.00 4.45
1504 1551 6.004574 GGGGGAAATGATAAGTTGGATAGAC 58.995 44.000 0.00 0.00 0.00 2.59
1512 1559 9.147732 GATTATTCAAGGGGGAAATGATAAGTT 57.852 33.333 0.00 0.00 0.00 2.66
1531 1578 6.319658 TGGAATGAAGGCACTCTTGATTATTC 59.680 38.462 0.00 0.00 38.96 1.75
1535 1582 3.760684 GTGGAATGAAGGCACTCTTGATT 59.239 43.478 0.00 0.00 40.99 2.57
1537 1584 2.106338 TGTGGAATGAAGGCACTCTTGA 59.894 45.455 0.00 0.00 38.49 3.02
1538 1585 2.507484 TGTGGAATGAAGGCACTCTTG 58.493 47.619 0.00 0.00 38.49 3.02
1539 1586 2.957402 TGTGGAATGAAGGCACTCTT 57.043 45.000 0.00 0.00 38.49 2.85
1543 1590 4.142381 GGTTATCTTGTGGAATGAAGGCAC 60.142 45.833 0.00 0.00 0.00 5.01
1544 1591 4.016444 GGTTATCTTGTGGAATGAAGGCA 58.984 43.478 0.00 0.00 0.00 4.75
1545 1592 4.016444 TGGTTATCTTGTGGAATGAAGGC 58.984 43.478 0.00 0.00 0.00 4.35
1546 1593 6.588719 TTTGGTTATCTTGTGGAATGAAGG 57.411 37.500 0.00 0.00 0.00 3.46
1548 1595 6.211184 AGCATTTGGTTATCTTGTGGAATGAA 59.789 34.615 0.00 0.00 0.00 2.57
1550 1597 5.969423 AGCATTTGGTTATCTTGTGGAATG 58.031 37.500 0.00 0.00 0.00 2.67
1551 1598 6.014327 ACAAGCATTTGGTTATCTTGTGGAAT 60.014 34.615 5.29 0.00 43.72 3.01
1552 1599 5.304101 ACAAGCATTTGGTTATCTTGTGGAA 59.696 36.000 5.29 0.00 43.72 3.53
1553 1600 4.832266 ACAAGCATTTGGTTATCTTGTGGA 59.168 37.500 5.29 0.00 43.72 4.02
1554 1601 5.138125 ACAAGCATTTGGTTATCTTGTGG 57.862 39.130 5.29 0.00 43.72 4.17
1597 1650 8.421002 AGTGATTAAACACAAGCACCTTTAAAT 58.579 29.630 17.01 0.00 44.03 1.40
1598 1651 7.777095 AGTGATTAAACACAAGCACCTTTAAA 58.223 30.769 17.01 0.00 44.03 1.52
1599 1652 7.341445 AGTGATTAAACACAAGCACCTTTAA 57.659 32.000 17.01 0.00 44.03 1.52
1600 1653 6.016610 GGAGTGATTAAACACAAGCACCTTTA 60.017 38.462 17.01 0.00 44.03 1.85
1606 1659 4.098914 AGGGAGTGATTAAACACAAGCA 57.901 40.909 17.01 0.00 42.45 3.91
1607 1660 4.395231 GGTAGGGAGTGATTAAACACAAGC 59.605 45.833 17.01 6.72 42.45 4.01
1622 1675 5.717654 AGAGACAAACTAAAGAGGTAGGGAG 59.282 44.000 0.00 0.00 0.00 4.30
1623 1676 5.652324 AGAGACAAACTAAAGAGGTAGGGA 58.348 41.667 0.00 0.00 0.00 4.20
1624 1677 5.717654 AGAGAGACAAACTAAAGAGGTAGGG 59.282 44.000 0.00 0.00 0.00 3.53
1626 1679 7.040340 TGTGAGAGAGACAAACTAAAGAGGTAG 60.040 40.741 0.00 0.00 0.00 3.18
1628 1681 5.598830 TGTGAGAGAGACAAACTAAAGAGGT 59.401 40.000 0.00 0.00 0.00 3.85
1630 1683 8.494347 CATTTGTGAGAGAGACAAACTAAAGAG 58.506 37.037 0.00 0.00 44.03 2.85
1631 1684 7.041780 GCATTTGTGAGAGAGACAAACTAAAGA 60.042 37.037 0.00 0.00 44.03 2.52
1632 1685 7.074502 GCATTTGTGAGAGAGACAAACTAAAG 58.925 38.462 0.00 0.00 44.03 1.85
1633 1686 6.292865 CGCATTTGTGAGAGAGACAAACTAAA 60.293 38.462 0.00 0.00 44.03 1.85
1655 1708 3.345808 GAGAACTTGGTGCGCGCA 61.346 61.111 33.09 33.09 0.00 6.09
1665 1718 4.838986 TGCTAGTTAGTCCAAGGAGAACTT 59.161 41.667 17.04 6.43 41.00 2.66
1683 1736 7.517734 GCATCAAATTGGCAAATTGTATGCTAG 60.518 37.037 31.25 17.76 43.34 3.42
1739 1796 2.635915 AGACGTGTGACAAAGGGGATTA 59.364 45.455 0.00 0.00 0.00 1.75
1743 1800 2.536761 TTAGACGTGTGACAAAGGGG 57.463 50.000 0.00 0.00 0.00 4.79
1750 1807 7.268447 GCAAGAACATAAAATTAGACGTGTGAC 59.732 37.037 0.00 0.00 0.00 3.67
1775 1832 7.605691 AGCATATGATTAACCAGAGATAACAGC 59.394 37.037 6.97 0.00 0.00 4.40
1884 1942 8.651389 CCACATCTTCTCAACCCTAATTATAGA 58.349 37.037 0.00 0.00 0.00 1.98
1885 1943 7.389053 GCCACATCTTCTCAACCCTAATTATAG 59.611 40.741 0.00 0.00 0.00 1.31
2029 2090 4.303282 AGAGAAAAGAAGAACAGTCTCGC 58.697 43.478 0.00 0.00 37.24 5.03
2067 2128 5.587844 GTGCCTCATAACAATGTGAGAGAAT 59.412 40.000 10.31 0.00 44.94 2.40
2281 2351 8.254508 GCATGTGTTAGGGATATTTTGGTAAAA 58.745 33.333 0.00 0.00 34.41 1.52
2314 2384 5.071653 GGAGATTCTTCTAGGGAGCAGAAAT 59.928 44.000 0.00 0.00 31.84 2.17
2420 2492 7.707624 AATCACATTAGTGGTGTTGATTGAT 57.292 32.000 2.32 0.00 45.91 2.57
2421 2493 7.448161 AGAAATCACATTAGTGGTGTTGATTGA 59.552 33.333 3.56 0.00 45.91 2.57
2422 2494 7.539710 CAGAAATCACATTAGTGGTGTTGATTG 59.460 37.037 3.56 0.00 45.91 2.67
2423 2495 7.231317 ACAGAAATCACATTAGTGGTGTTGATT 59.769 33.333 0.00 0.00 45.91 2.57
2468 2541 6.584471 TGGGGGAAATGTAACTATGTATGT 57.416 37.500 0.00 0.00 0.00 2.29
2469 2542 7.889873 TTTGGGGGAAATGTAACTATGTATG 57.110 36.000 0.00 0.00 0.00 2.39
2470 2543 8.903059 TTTTTGGGGGAAATGTAACTATGTAT 57.097 30.769 0.00 0.00 0.00 2.29
2471 2544 7.397761 CCTTTTTGGGGGAAATGTAACTATGTA 59.602 37.037 0.00 0.00 0.00 2.29
2472 2545 6.212589 CCTTTTTGGGGGAAATGTAACTATGT 59.787 38.462 0.00 0.00 0.00 2.29
2485 2558 3.456644 GGTTTTCTTTCCTTTTTGGGGGA 59.543 43.478 0.00 0.00 36.20 4.81
2511 2584 1.583495 GCTGCATGCTTGAGCTGTCA 61.583 55.000 20.33 0.00 42.66 3.58
2512 2585 1.136984 GCTGCATGCTTGAGCTGTC 59.863 57.895 20.33 0.00 42.66 3.51
2532 2605 6.183360 TGCTAATTTGCAGTAGATAGTTGTGC 60.183 38.462 10.62 0.00 38.12 4.57
2550 2627 8.743085 ATCACACTGAATGAGTAATGCTAATT 57.257 30.769 0.00 0.00 31.73 1.40
2568 2657 4.287067 ACCACCTGAGAATTGTATCACACT 59.713 41.667 0.00 0.00 0.00 3.55
2572 2661 3.767131 TCGACCACCTGAGAATTGTATCA 59.233 43.478 0.00 0.00 0.00 2.15
2573 2662 4.386867 TCGACCACCTGAGAATTGTATC 57.613 45.455 0.00 0.00 0.00 2.24
2575 2664 3.767131 TGATCGACCACCTGAGAATTGTA 59.233 43.478 0.00 0.00 0.00 2.41
2577 2666 3.251479 TGATCGACCACCTGAGAATTG 57.749 47.619 0.00 0.00 0.00 2.32
2579 2668 2.035193 CGATGATCGACCACCTGAGAAT 59.965 50.000 9.62 0.00 43.74 2.40
2581 2670 1.025041 CGATGATCGACCACCTGAGA 58.975 55.000 9.62 0.00 43.74 3.27
2582 2671 0.596083 GCGATGATCGACCACCTGAG 60.596 60.000 20.25 0.00 43.74 3.35
2672 2764 2.044650 CATGGTGGTGGAGCCCAG 60.045 66.667 0.00 0.00 34.43 4.45
2849 2941 2.938956 AGCATATAGTGGTCTTGGGC 57.061 50.000 0.00 0.00 31.66 5.36
2885 2977 4.790765 TGTTGTTGTTCATGTGGTTCAA 57.209 36.364 0.00 0.00 0.00 2.69
2892 2984 5.336150 TCCATTGTTGTTGTTGTTCATGT 57.664 34.783 0.00 0.00 0.00 3.21
2897 2989 2.765699 AGGCTCCATTGTTGTTGTTGTT 59.234 40.909 0.00 0.00 0.00 2.83
2898 2990 2.362077 GAGGCTCCATTGTTGTTGTTGT 59.638 45.455 2.15 0.00 0.00 3.32
2899 2991 2.288395 GGAGGCTCCATTGTTGTTGTTG 60.288 50.000 28.55 0.00 36.28 3.33
2900 2992 1.963515 GGAGGCTCCATTGTTGTTGTT 59.036 47.619 28.55 0.00 36.28 2.83
2901 2993 1.620822 GGAGGCTCCATTGTTGTTGT 58.379 50.000 28.55 0.00 36.28 3.32
3347 3451 1.330655 ATCATCGTCAGCTTCCCGGT 61.331 55.000 0.00 0.00 0.00 5.28
3384 3488 4.996788 ACGTACGTCCTGATCCTTAAAT 57.003 40.909 16.72 0.00 0.00 1.40
3385 3489 4.201812 CGTACGTACGTCCTGATCCTTAAA 60.202 45.833 33.95 0.00 44.13 1.52
3386 3490 3.309682 CGTACGTACGTCCTGATCCTTAA 59.690 47.826 33.95 0.00 44.13 1.85
3421 3529 5.655532 CCTTCTTCAATTCCACCTTGATGAT 59.344 40.000 0.00 0.00 36.94 2.45
3430 3538 3.632145 ACACACACCTTCTTCAATTCCAC 59.368 43.478 0.00 0.00 0.00 4.02
3431 3539 3.897239 ACACACACCTTCTTCAATTCCA 58.103 40.909 0.00 0.00 0.00 3.53
3587 3707 4.854924 ACACACAGCGGCACAGCA 62.855 61.111 1.45 0.00 40.15 4.41
3612 3732 0.904649 TCTTGATCCCATGTCACGCT 59.095 50.000 0.00 0.00 0.00 5.07
3675 3802 5.057149 ACAACAGTAACAGCAAGTAAGAGG 58.943 41.667 0.00 0.00 0.00 3.69
3676 3803 6.037172 ACAACAACAGTAACAGCAAGTAAGAG 59.963 38.462 0.00 0.00 0.00 2.85
3677 3804 5.878116 ACAACAACAGTAACAGCAAGTAAGA 59.122 36.000 0.00 0.00 0.00 2.10
3678 3805 6.119144 ACAACAACAGTAACAGCAAGTAAG 57.881 37.500 0.00 0.00 0.00 2.34
3719 3848 3.760738 AGATGTGTGTGTGAGAGAGAGA 58.239 45.455 0.00 0.00 0.00 3.10
3720 3849 4.517952 AAGATGTGTGTGTGAGAGAGAG 57.482 45.455 0.00 0.00 0.00 3.20
3721 3850 4.100035 ACAAAGATGTGTGTGTGAGAGAGA 59.900 41.667 0.00 0.00 38.69 3.10
3722 3851 4.375272 ACAAAGATGTGTGTGTGAGAGAG 58.625 43.478 0.00 0.00 38.69 3.20
3723 3852 4.141959 TGACAAAGATGTGTGTGTGAGAGA 60.142 41.667 0.00 0.00 40.74 3.10
3724 3853 4.122046 TGACAAAGATGTGTGTGTGAGAG 58.878 43.478 0.00 0.00 40.74 3.20
3725 3854 4.122046 CTGACAAAGATGTGTGTGTGAGA 58.878 43.478 0.00 0.00 40.74 3.27
3726 3855 3.303593 GCTGACAAAGATGTGTGTGTGAG 60.304 47.826 0.00 0.00 40.74 3.51
3727 3856 2.613595 GCTGACAAAGATGTGTGTGTGA 59.386 45.455 0.00 0.00 40.74 3.58
3728 3857 2.355444 TGCTGACAAAGATGTGTGTGTG 59.645 45.455 0.00 0.00 40.74 3.82
3729 3858 2.642427 TGCTGACAAAGATGTGTGTGT 58.358 42.857 0.00 0.00 40.74 3.72
3730 3859 3.696281 TTGCTGACAAAGATGTGTGTG 57.304 42.857 0.00 0.00 40.74 3.82
3731 3860 4.440525 CCTTTTGCTGACAAAGATGTGTGT 60.441 41.667 0.00 0.00 46.08 3.72
3732 3861 4.046462 CCTTTTGCTGACAAAGATGTGTG 58.954 43.478 0.00 0.00 46.08 3.82
3733 3862 3.701040 ACCTTTTGCTGACAAAGATGTGT 59.299 39.130 0.00 0.00 46.08 3.72
3734 3863 4.311816 ACCTTTTGCTGACAAAGATGTG 57.688 40.909 0.00 0.00 46.08 3.21
3735 3864 6.942576 ACTATACCTTTTGCTGACAAAGATGT 59.057 34.615 0.00 0.00 46.08 3.06
3736 3865 7.094634 ACACTATACCTTTTGCTGACAAAGATG 60.095 37.037 0.00 0.00 46.08 2.90
3995 4126 1.980844 CATTGCAGCATCAACGACAAC 59.019 47.619 0.00 0.00 0.00 3.32
3996 4127 1.666599 GCATTGCAGCATCAACGACAA 60.667 47.619 3.15 0.00 0.00 3.18
3997 4128 0.109643 GCATTGCAGCATCAACGACA 60.110 50.000 3.15 0.00 0.00 4.35
3998 4129 0.109643 TGCATTGCAGCATCAACGAC 60.110 50.000 7.38 0.00 40.11 4.34
3999 4130 0.597072 TTGCATTGCAGCATCAACGA 59.403 45.000 11.76 0.00 45.19 3.85
4098 4234 0.776451 CAAACCGACGTTCTCGACAG 59.224 55.000 0.00 0.00 46.14 3.51
4135 4271 4.247267 ACAAGACGAACGGTATGAGAAA 57.753 40.909 0.00 0.00 0.00 2.52
4160 4296 5.138125 TGGCAAAGTTTGATGGAATCTTC 57.862 39.130 19.82 0.00 45.81 2.87
4188 4324 3.957497 ACAAAACAAGTAATCACTGCCCA 59.043 39.130 0.00 0.00 34.36 5.36
4189 4325 4.584327 ACAAAACAAGTAATCACTGCCC 57.416 40.909 0.00 0.00 34.36 5.36
4208 4344 1.130749 CCGAACAAACACCGTGAAACA 59.869 47.619 5.28 0.00 35.74 2.83
4216 4352 0.671251 TTCATGGCCGAACAAACACC 59.329 50.000 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.