Multiple sequence alignment - TraesCS2D01G309200

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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 TraesCS2D01G309200 chr2D 100.000 3575 0 0 1 3575 396659448 396663022 0.000000e+00 6602.0
1 TraesCS2D01G309200 chr2D 98.773 652 5 3 1 650 488465729 488465079 0.000000e+00 1157.0
2 TraesCS2D01G309200 chr2D 97.856 653 11 3 1 650 35045898 35046550 0.000000e+00 1125.0
3 TraesCS2D01G309200 chr2D 97.713 656 7 7 1 651 10444276 10444928 0.000000e+00 1122.0
4 TraesCS2D01G309200 chr2A 90.340 2909 106 40 650 3499 534623464 534626256 0.000000e+00 3653.0
5 TraesCS2D01G309200 chr2B 88.392 2214 157 53 707 2874 470057427 470059586 0.000000e+00 2573.0
6 TraesCS2D01G309200 chr2B 90.000 580 20 18 2921 3499 470059684 470060226 0.000000e+00 715.0
7 TraesCS2D01G309200 chr7D 98.165 654 8 4 1 651 129811920 129811268 0.000000e+00 1138.0
8 TraesCS2D01G309200 chr7D 97.859 654 11 3 1 651 72516510 72517163 0.000000e+00 1127.0
9 TraesCS2D01G309200 chr1D 98.162 653 8 4 1 650 416603058 416602407 0.000000e+00 1136.0
10 TraesCS2D01G309200 chr6D 97.859 654 10 4 1 650 429959994 429960647 0.000000e+00 1127.0
11 TraesCS2D01G309200 chr6D 97.706 654 11 4 1 651 26596807 26597459 0.000000e+00 1122.0
12 TraesCS2D01G309200 chr3D 97.710 655 8 6 1 650 236679722 236680374 0.000000e+00 1120.0
13 TraesCS2D01G309200 chr6B 97.500 40 1 0 2334 2373 353181440 353181479 6.400000e-08 69.4


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 TraesCS2D01G309200 chr2D 396659448 396663022 3574 False 6602 6602 100.000 1 3575 1 chr2D.!!$F3 3574
1 TraesCS2D01G309200 chr2D 488465079 488465729 650 True 1157 1157 98.773 1 650 1 chr2D.!!$R1 649
2 TraesCS2D01G309200 chr2D 35045898 35046550 652 False 1125 1125 97.856 1 650 1 chr2D.!!$F2 649
3 TraesCS2D01G309200 chr2D 10444276 10444928 652 False 1122 1122 97.713 1 651 1 chr2D.!!$F1 650
4 TraesCS2D01G309200 chr2A 534623464 534626256 2792 False 3653 3653 90.340 650 3499 1 chr2A.!!$F1 2849
5 TraesCS2D01G309200 chr2B 470057427 470060226 2799 False 1644 2573 89.196 707 3499 2 chr2B.!!$F1 2792
6 TraesCS2D01G309200 chr7D 129811268 129811920 652 True 1138 1138 98.165 1 651 1 chr7D.!!$R1 650
7 TraesCS2D01G309200 chr7D 72516510 72517163 653 False 1127 1127 97.859 1 651 1 chr7D.!!$F1 650
8 TraesCS2D01G309200 chr1D 416602407 416603058 651 True 1136 1136 98.162 1 650 1 chr1D.!!$R1 649
9 TraesCS2D01G309200 chr6D 429959994 429960647 653 False 1127 1127 97.859 1 650 1 chr6D.!!$F2 649
10 TraesCS2D01G309200 chr6D 26596807 26597459 652 False 1122 1122 97.706 1 651 1 chr6D.!!$F1 650
11 TraesCS2D01G309200 chr3D 236679722 236680374 652 False 1120 1120 97.710 1 650 1 chr3D.!!$F1 649


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
699 707 0.179129 GCCCGTGATGGATGCTTTTG 60.179 55.0 0.0 0.0 42.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2589 2690 0.106894 GGATGCTTTACCCTCCCTCG 59.893 60.0 0.0 0.0 0.0 4.63 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
152 154 3.113322 TCGTCGCTAAAATCTCAATCCG 58.887 45.455 0.00 0.00 0.00 4.18
219 221 5.640158 TTTCCCTTGAGTGAGTTTTCCTA 57.360 39.130 0.00 0.00 0.00 2.94
580 588 6.588756 TCACTTTTACTTTCGCATACTTCGAT 59.411 34.615 0.00 0.00 35.75 3.59
658 666 1.301716 TTGCGGAACAGGTCTGAGC 60.302 57.895 0.00 0.00 34.07 4.26
698 706 1.656818 CGCCCGTGATGGATGCTTTT 61.657 55.000 0.00 0.00 42.00 2.27
699 707 0.179129 GCCCGTGATGGATGCTTTTG 60.179 55.000 0.00 0.00 42.00 2.44
700 708 1.176527 CCCGTGATGGATGCTTTTGT 58.823 50.000 0.00 0.00 42.00 2.83
701 709 1.133025 CCCGTGATGGATGCTTTTGTC 59.867 52.381 0.00 0.00 42.00 3.18
702 710 1.811965 CCGTGATGGATGCTTTTGTCA 59.188 47.619 0.00 0.00 42.00 3.58
703 711 2.424601 CCGTGATGGATGCTTTTGTCAT 59.575 45.455 0.00 0.00 42.00 3.06
704 712 3.488047 CCGTGATGGATGCTTTTGTCATC 60.488 47.826 0.00 0.00 42.00 2.92
705 713 3.127376 CGTGATGGATGCTTTTGTCATCA 59.873 43.478 0.00 0.00 41.46 3.07
763 771 1.077930 CAGGGTCATGTGCAGGGAG 60.078 63.158 0.00 0.00 0.00 4.30
764 772 2.273449 GGGTCATGTGCAGGGAGG 59.727 66.667 0.00 0.00 0.00 4.30
765 773 2.273449 GGTCATGTGCAGGGAGGG 59.727 66.667 0.00 0.00 0.00 4.30
766 774 2.273449 GTCATGTGCAGGGAGGGG 59.727 66.667 0.00 0.00 0.00 4.79
767 775 2.124768 TCATGTGCAGGGAGGGGA 59.875 61.111 0.00 0.00 0.00 4.81
768 776 1.997311 TCATGTGCAGGGAGGGGAG 60.997 63.158 0.00 0.00 0.00 4.30
860 872 1.081892 CTGGGAGATCAGTTTGCACG 58.918 55.000 0.00 0.00 0.00 5.34
895 907 6.181190 AGAGTTATAACCTTTTTCTGCCCTC 58.819 40.000 12.05 0.00 0.00 4.30
905 917 1.608717 TTCTGCCCTCGAGAAGCCTC 61.609 60.000 15.71 0.00 36.08 4.70
906 918 2.038007 TGCCCTCGAGAAGCCTCT 59.962 61.111 15.71 0.00 37.28 3.69
907 919 2.015227 CTGCCCTCGAGAAGCCTCTC 62.015 65.000 15.71 1.92 44.17 3.20
908 920 2.791868 GCCCTCGAGAAGCCTCTCC 61.792 68.421 15.71 0.00 44.70 3.71
952 964 2.102252 GCCAAATCTCTCCGTCTCTGAT 59.898 50.000 0.00 0.00 0.00 2.90
967 979 1.002366 CTGATTTCCTGCTCCGTTCG 58.998 55.000 0.00 0.00 0.00 3.95
969 981 1.000145 GATTTCCTGCTCCGTTCGTC 59.000 55.000 0.00 0.00 0.00 4.20
1029 1048 0.680061 AGTTGTGAGTTCCTCCCGTC 59.320 55.000 0.00 0.00 0.00 4.79
1100 1119 1.675801 CCTGGCTGTTCTGCTCTGA 59.324 57.895 2.15 0.00 0.00 3.27
1101 1120 0.673022 CCTGGCTGTTCTGCTCTGAC 60.673 60.000 2.15 0.00 0.00 3.51
1103 1122 2.386660 GGCTGTTCTGCTCTGACGC 61.387 63.158 2.15 0.00 0.00 5.19
1104 1123 2.724708 GCTGTTCTGCTCTGACGCG 61.725 63.158 3.53 3.53 0.00 6.01
1116 1135 2.126734 GACGCGCTGCAAAATGCT 60.127 55.556 5.73 0.00 45.31 3.79
1234 1253 6.370994 TCTCCGTGAGTTTCTTACTACTACTG 59.629 42.308 1.60 0.00 37.17 2.74
1273 1299 3.156714 TGGACTGACCAATGGCGT 58.843 55.556 0.00 0.00 46.75 5.68
1278 1304 0.324614 ACTGACCAATGGCGTCATCA 59.675 50.000 1.37 0.00 39.43 3.07
1338 1364 9.533253 TGATTTTCTTGTGATTTTTCTTCTTCC 57.467 29.630 0.00 0.00 0.00 3.46
1412 1438 1.260538 TGAGTGGCTTCTCCTCGCAT 61.261 55.000 7.54 0.00 34.08 4.73
1443 1473 5.105756 TGTGTTCTTGATGATTCTCTCGCTA 60.106 40.000 0.00 0.00 0.00 4.26
1447 1477 5.586339 TCTTGATGATTCTCTCGCTAGTTG 58.414 41.667 0.00 0.00 0.00 3.16
1459 1505 4.113354 CTCGCTAGTTGTTTCCATCCTAC 58.887 47.826 0.00 0.00 0.00 3.18
1462 1508 3.864003 GCTAGTTGTTTCCATCCTACGTC 59.136 47.826 0.00 0.00 0.00 4.34
1465 1511 2.380084 TGTTTCCATCCTACGTCTGC 57.620 50.000 0.00 0.00 0.00 4.26
1498 1544 3.604582 TCCATTGATTGATGCACGTGTA 58.395 40.909 18.38 14.09 0.00 2.90
1568 1614 7.715249 TGCAGATTGTAAGTGATTAATCCCTAC 59.285 37.037 12.90 11.08 31.56 3.18
1591 1637 4.526970 TCTTCTTCACAAGTTTGCCTCTT 58.473 39.130 0.00 0.00 0.00 2.85
1617 1667 5.543714 TCAAAGTTTGCTATCACGTAAGGA 58.456 37.500 10.90 0.00 46.39 3.36
1618 1668 5.637810 TCAAAGTTTGCTATCACGTAAGGAG 59.362 40.000 10.90 0.00 46.39 3.69
1619 1669 4.124851 AGTTTGCTATCACGTAAGGAGG 57.875 45.455 0.00 0.00 46.39 4.30
1620 1670 2.596904 TTGCTATCACGTAAGGAGGC 57.403 50.000 0.00 0.00 46.39 4.70
1621 1671 1.480789 TGCTATCACGTAAGGAGGCA 58.519 50.000 0.00 0.00 46.39 4.75
1622 1672 1.828595 TGCTATCACGTAAGGAGGCAA 59.171 47.619 0.00 0.00 46.39 4.52
1623 1673 2.235155 TGCTATCACGTAAGGAGGCAAA 59.765 45.455 0.00 0.00 46.39 3.68
1624 1674 2.608090 GCTATCACGTAAGGAGGCAAAC 59.392 50.000 0.00 0.00 46.39 2.93
1656 1727 8.685427 TGTATTGGAAATGAACTGATTACCATG 58.315 33.333 0.00 0.00 0.00 3.66
1660 1731 8.365060 TGGAAATGAACTGATTACCATGAAAT 57.635 30.769 0.00 0.00 0.00 2.17
1682 1753 5.375417 TTCCTGCATCACAAACATACAAG 57.625 39.130 0.00 0.00 0.00 3.16
1748 1819 3.805971 TGTAATGCTCGCAATCTCATCTG 59.194 43.478 0.00 0.00 0.00 2.90
1862 1934 4.614764 CGGGATCATCGTAAGTCTCATCTG 60.615 50.000 0.00 0.00 39.48 2.90
1930 2010 2.535331 TCAGCAAACTTTTGGTTTCGC 58.465 42.857 3.67 0.00 45.64 4.70
2014 2094 0.248134 GCGAGATCGACAAGTACGCT 60.248 55.000 6.39 0.00 43.02 5.07
2107 2187 0.317160 TAGCACAGGTCACAGTTCCG 59.683 55.000 0.00 0.00 0.00 4.30
2124 2204 3.149005 TCCGACTACCCTTTTGCATTT 57.851 42.857 0.00 0.00 0.00 2.32
2126 2206 2.094752 CCGACTACCCTTTTGCATTTGG 60.095 50.000 0.00 0.00 0.00 3.28
2166 2249 6.660800 ACTAGGCTCTGTCTGTATACTTGTA 58.339 40.000 4.17 0.00 0.00 2.41
2214 2297 6.657117 TGTGGAAAATGAATCAATTCCTCGTA 59.343 34.615 22.97 8.10 41.51 3.43
2217 2300 6.638468 GGAAAATGAATCAATTCCTCGTATGC 59.362 38.462 18.31 0.00 38.61 3.14
2218 2301 6.949352 AAATGAATCAATTCCTCGTATGCT 57.051 33.333 0.48 0.00 35.97 3.79
2223 2306 4.406648 TCAATTCCTCGTATGCTGATGT 57.593 40.909 0.00 0.00 0.00 3.06
2331 2432 5.181748 AGTGCTAAAGAGTCCATCAATGTC 58.818 41.667 0.00 0.00 0.00 3.06
2344 2445 2.699954 TCAATGTCGAAGAGGCCTTTC 58.300 47.619 6.77 11.90 36.95 2.62
2533 2634 1.203038 TGAAAGGCCAGCCAATTCAGA 60.203 47.619 19.84 5.06 38.43 3.27
2578 2679 1.875514 GCTGCTGTTCAACATGACTCA 59.124 47.619 0.00 0.00 0.00 3.41
2589 2690 3.791973 ACATGACTCAAGATCGGACTC 57.208 47.619 0.00 0.00 0.00 3.36
2835 2936 1.802960 CAGCACAGCAACCAGAGTTAG 59.197 52.381 0.00 0.00 33.27 2.34
2841 2942 4.067896 ACAGCAACCAGAGTTAGAACATG 58.932 43.478 0.00 0.00 33.27 3.21
2904 3005 9.979578 AAGACAGTGAATTTACATATGCAAAAA 57.020 25.926 5.22 3.52 0.00 1.94
2918 3019 9.008965 ACATATGCAAAAACTTGTACAGATACA 57.991 29.630 1.58 0.00 39.63 2.29
3079 3253 2.100916 ACTTGGATAGGTCGGTCATTCG 59.899 50.000 0.00 0.00 0.00 3.34
3118 3292 0.325296 TCGATGGTTAGCTGGAGGGT 60.325 55.000 0.00 0.00 0.00 4.34
3119 3293 0.179073 CGATGGTTAGCTGGAGGGTG 60.179 60.000 0.00 0.00 0.00 4.61
3184 3358 7.946207 TGAAAGAGGATGAGTCTACATATGAC 58.054 38.462 10.38 0.00 34.88 3.06
3187 3361 8.489676 AAGAGGATGAGTCTACATATGACAAT 57.510 34.615 10.38 0.00 36.94 2.71
3188 3362 8.121305 AGAGGATGAGTCTACATATGACAATC 57.879 38.462 10.38 5.23 36.94 2.67
3189 3363 7.949565 AGAGGATGAGTCTACATATGACAATCT 59.050 37.037 10.38 1.16 36.94 2.40
3190 3364 7.894708 AGGATGAGTCTACATATGACAATCTG 58.105 38.462 10.38 0.00 36.94 2.90
3191 3365 7.727634 AGGATGAGTCTACATATGACAATCTGA 59.272 37.037 10.38 0.00 36.94 3.27
3192 3366 8.363390 GGATGAGTCTACATATGACAATCTGAA 58.637 37.037 10.38 0.00 36.94 3.02
3193 3367 9.755804 GATGAGTCTACATATGACAATCTGAAA 57.244 33.333 10.38 0.00 36.94 2.69
3194 3368 9.761504 ATGAGTCTACATATGACAATCTGAAAG 57.238 33.333 10.38 0.00 36.94 2.62
3195 3369 8.971073 TGAGTCTACATATGACAATCTGAAAGA 58.029 33.333 10.38 0.00 41.45 2.52
3196 3370 9.462174 GAGTCTACATATGACAATCTGAAAGAG 57.538 37.037 10.38 0.00 40.90 2.85
3197 3371 8.420222 AGTCTACATATGACAATCTGAAAGAGG 58.580 37.037 10.38 0.00 40.90 3.69
3198 3372 8.417106 GTCTACATATGACAATCTGAAAGAGGA 58.583 37.037 10.38 0.00 39.33 3.71
3212 3386 8.175925 TCTGAAAGAGGATGAGTCTACATATG 57.824 38.462 0.00 0.00 38.67 1.78
3213 3387 8.001292 TCTGAAAGAGGATGAGTCTACATATGA 58.999 37.037 10.38 0.00 38.67 2.15
3214 3388 8.539117 TGAAAGAGGATGAGTCTACATATGAA 57.461 34.615 10.38 0.00 0.00 2.57
3215 3389 8.981659 TGAAAGAGGATGAGTCTACATATGAAA 58.018 33.333 10.38 0.00 0.00 2.69
3479 3653 8.749026 ATTATCTGCAGAAACAAGATCAAGAT 57.251 30.769 22.50 0.81 0.00 2.40
3508 3682 8.940768 AAAAATAATGTTGGTCAATTATCCGG 57.059 30.769 0.00 0.00 0.00 5.14
3509 3683 7.889873 AAATAATGTTGGTCAATTATCCGGA 57.110 32.000 6.61 6.61 0.00 5.14
3510 3684 7.889873 AATAATGTTGGTCAATTATCCGGAA 57.110 32.000 9.01 0.00 0.00 4.30
3511 3685 7.889873 ATAATGTTGGTCAATTATCCGGAAA 57.110 32.000 9.01 4.74 0.00 3.13
3512 3686 6.790232 AATGTTGGTCAATTATCCGGAAAT 57.210 33.333 9.01 7.15 0.00 2.17
3513 3687 7.889873 AATGTTGGTCAATTATCCGGAAATA 57.110 32.000 9.01 0.00 0.00 1.40
3514 3688 8.477419 AATGTTGGTCAATTATCCGGAAATAT 57.523 30.769 9.01 0.00 0.00 1.28
3515 3689 7.270757 TGTTGGTCAATTATCCGGAAATATG 57.729 36.000 9.01 6.27 0.00 1.78
3516 3690 6.831353 TGTTGGTCAATTATCCGGAAATATGT 59.169 34.615 9.01 0.00 0.00 2.29
3517 3691 7.993758 TGTTGGTCAATTATCCGGAAATATGTA 59.006 33.333 9.01 0.00 0.00 2.29
3518 3692 8.504005 GTTGGTCAATTATCCGGAAATATGTAG 58.496 37.037 9.01 0.00 0.00 2.74
3519 3693 7.165485 TGGTCAATTATCCGGAAATATGTAGG 58.835 38.462 9.01 0.00 0.00 3.18
3520 3694 6.093633 GGTCAATTATCCGGAAATATGTAGGC 59.906 42.308 9.01 0.00 0.00 3.93
3521 3695 6.093633 GTCAATTATCCGGAAATATGTAGGCC 59.906 42.308 9.01 0.00 0.00 5.19
3522 3696 4.563140 TTATCCGGAAATATGTAGGCCC 57.437 45.455 9.01 0.00 0.00 5.80
3523 3697 1.809133 TCCGGAAATATGTAGGCCCA 58.191 50.000 0.00 0.00 0.00 5.36
3524 3698 2.344592 TCCGGAAATATGTAGGCCCAT 58.655 47.619 0.00 0.00 0.00 4.00
3525 3699 2.714250 TCCGGAAATATGTAGGCCCATT 59.286 45.455 0.00 0.00 0.00 3.16
3526 3700 2.819608 CCGGAAATATGTAGGCCCATTG 59.180 50.000 0.00 0.00 0.00 2.82
3527 3701 3.486383 CGGAAATATGTAGGCCCATTGT 58.514 45.455 0.00 0.00 0.00 2.71
3528 3702 3.888930 CGGAAATATGTAGGCCCATTGTT 59.111 43.478 0.00 0.00 0.00 2.83
3529 3703 5.067273 CGGAAATATGTAGGCCCATTGTTA 58.933 41.667 0.00 0.00 0.00 2.41
3530 3704 5.710099 CGGAAATATGTAGGCCCATTGTTAT 59.290 40.000 0.00 0.00 0.00 1.89
3531 3705 6.882140 CGGAAATATGTAGGCCCATTGTTATA 59.118 38.462 0.00 0.00 0.00 0.98
3532 3706 7.392113 CGGAAATATGTAGGCCCATTGTTATAA 59.608 37.037 0.00 0.00 0.00 0.98
3533 3707 9.084533 GGAAATATGTAGGCCCATTGTTATAAA 57.915 33.333 0.00 0.00 0.00 1.40
3561 3735 6.731292 AAAAGACTGGCAATAAGGTTTTCT 57.269 33.333 0.00 0.00 0.00 2.52
3562 3736 7.833285 AAAAGACTGGCAATAAGGTTTTCTA 57.167 32.000 0.00 0.00 0.00 2.10
3563 3737 6.819397 AAGACTGGCAATAAGGTTTTCTAC 57.181 37.500 0.00 0.00 0.00 2.59
3564 3738 6.128138 AGACTGGCAATAAGGTTTTCTACT 57.872 37.500 0.00 0.00 0.00 2.57
3565 3739 7.253905 AGACTGGCAATAAGGTTTTCTACTA 57.746 36.000 0.00 0.00 0.00 1.82
3566 3740 7.104290 AGACTGGCAATAAGGTTTTCTACTAC 58.896 38.462 0.00 0.00 0.00 2.73
3567 3741 7.017319 ACTGGCAATAAGGTTTTCTACTACT 57.983 36.000 0.00 0.00 0.00 2.57
3568 3742 7.104290 ACTGGCAATAAGGTTTTCTACTACTC 58.896 38.462 0.00 0.00 0.00 2.59
3569 3743 6.412214 TGGCAATAAGGTTTTCTACTACTCC 58.588 40.000 0.00 0.00 0.00 3.85
3570 3744 6.214819 TGGCAATAAGGTTTTCTACTACTCCT 59.785 38.462 0.00 0.00 0.00 3.69
3571 3745 7.400915 TGGCAATAAGGTTTTCTACTACTCCTA 59.599 37.037 0.00 0.00 0.00 2.94
3572 3746 8.430431 GGCAATAAGGTTTTCTACTACTCCTAT 58.570 37.037 0.00 0.00 0.00 2.57
3573 3747 9.262358 GCAATAAGGTTTTCTACTACTCCTATG 57.738 37.037 0.00 0.00 0.00 2.23
3574 3748 9.765795 CAATAAGGTTTTCTACTACTCCTATGG 57.234 37.037 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 154 5.250235 TCAAGTTGAGTACTCGATCATCC 57.750 43.478 15.96 3.06 35.54 3.51
219 221 5.124776 TCAAAAACCTCGTGTGAGAAACATT 59.875 36.000 0.00 0.00 45.57 2.71
658 666 2.353376 CGCGTGCCTTTGTTGGTG 60.353 61.111 0.00 0.00 0.00 4.17
698 706 8.434392 TCTTTAGGATTCATGATGATGATGACA 58.566 33.333 0.00 0.00 38.43 3.58
699 707 8.843885 TCTTTAGGATTCATGATGATGATGAC 57.156 34.615 0.00 0.00 38.43 3.06
700 708 9.856162 TTTCTTTAGGATTCATGATGATGATGA 57.144 29.630 0.00 0.00 38.43 2.92
702 710 9.298250 CCTTTCTTTAGGATTCATGATGATGAT 57.702 33.333 0.00 0.00 36.62 2.45
703 711 7.722728 CCCTTTCTTTAGGATTCATGATGATGA 59.277 37.037 0.00 0.00 37.50 2.92
704 712 7.039923 CCCCTTTCTTTAGGATTCATGATGATG 60.040 40.741 0.00 0.00 37.50 3.07
705 713 7.008941 CCCCTTTCTTTAGGATTCATGATGAT 58.991 38.462 0.00 0.00 37.50 2.45
763 771 3.412408 GGAACTGCTCCCCTCCCC 61.412 72.222 0.00 0.00 38.44 4.81
764 772 2.610859 TGGAACTGCTCCCCTCCC 60.611 66.667 0.00 0.00 44.69 4.30
765 773 2.671682 GTGGAACTGCTCCCCTCC 59.328 66.667 0.00 0.00 44.69 4.30
766 774 2.266055 CGTGGAACTGCTCCCCTC 59.734 66.667 0.00 0.00 44.69 4.30
767 775 2.526873 ACGTGGAACTGCTCCCCT 60.527 61.111 0.00 0.00 44.69 4.79
768 776 2.047179 GACGTGGAACTGCTCCCC 60.047 66.667 0.00 0.00 44.69 4.81
833 845 2.540383 ACTGATCTCCCAGTGCACTTA 58.460 47.619 18.94 4.80 44.93 2.24
842 854 0.684535 TCGTGCAAACTGATCTCCCA 59.315 50.000 0.00 0.00 0.00 4.37
860 872 6.702716 AGGTTATAACTCTAGAGTGCACTC 57.297 41.667 34.82 34.82 41.58 3.51
870 882 7.266905 AGGGCAGAAAAAGGTTATAACTCTA 57.733 36.000 15.05 0.00 0.00 2.43
905 917 1.408969 GCTAGAGGTGGAGAAGGGAG 58.591 60.000 0.00 0.00 0.00 4.30
906 918 0.032017 GGCTAGAGGTGGAGAAGGGA 60.032 60.000 0.00 0.00 0.00 4.20
907 919 1.051556 GGGCTAGAGGTGGAGAAGGG 61.052 65.000 0.00 0.00 0.00 3.95
908 920 0.325671 TGGGCTAGAGGTGGAGAAGG 60.326 60.000 0.00 0.00 0.00 3.46
952 964 1.372499 CGACGAACGGAGCAGGAAA 60.372 57.895 0.00 0.00 38.46 3.13
967 979 1.346722 TCCCCAAAGGAAGAAGACGAC 59.653 52.381 0.00 0.00 43.78 4.34
969 981 1.339151 CCTCCCCAAAGGAAGAAGACG 60.339 57.143 0.00 0.00 46.94 4.18
1029 1048 1.369625 AACCAGGCGCGAAAATAGAG 58.630 50.000 12.10 0.00 0.00 2.43
1101 1120 3.834373 GCAGCATTTTGCAGCGCG 61.834 61.111 0.00 0.00 45.45 6.86
1108 1127 2.555325 TCAGGACAAGAGCAGCATTTTG 59.445 45.455 0.00 0.00 0.00 2.44
1116 1135 1.483595 CCCAGGTCAGGACAAGAGCA 61.484 60.000 1.41 0.00 36.03 4.26
1234 1253 1.607467 ACCCACATTGCCAAGGAGC 60.607 57.895 0.00 0.00 0.00 4.70
1273 1299 5.188359 TGTGTGATCTTGAGAAGGATGATGA 59.812 40.000 0.00 0.00 0.00 2.92
1278 1304 6.996879 CCATTATGTGTGATCTTGAGAAGGAT 59.003 38.462 0.00 0.00 0.00 3.24
1338 1364 2.543861 CCACATACGAATCGTCCTGGAG 60.544 54.545 13.00 8.45 41.54 3.86
1412 1438 2.574450 TCATCAAGAACACAGCTGCAA 58.426 42.857 15.27 0.00 0.00 4.08
1447 1477 2.674796 AGCAGACGTAGGATGGAAAC 57.325 50.000 0.00 0.00 0.00 2.78
1459 1505 2.165234 TGGATCAGAGAAGAAGCAGACG 59.835 50.000 0.00 0.00 0.00 4.18
1462 1508 4.767478 TCAATGGATCAGAGAAGAAGCAG 58.233 43.478 0.00 0.00 0.00 4.24
1465 1511 7.520776 GCATCAATCAATGGATCAGAGAAGAAG 60.521 40.741 0.00 0.00 31.88 2.85
1498 1544 1.272490 TCGAGAGTGCGGATTTTCTGT 59.728 47.619 0.00 0.00 0.00 3.41
1568 1614 4.133078 AGAGGCAAACTTGTGAAGAAGAG 58.867 43.478 0.00 0.00 0.00 2.85
1591 1637 6.147164 CCTTACGTGATAGCAAACTTTGAAGA 59.853 38.462 5.65 0.00 0.00 2.87
1617 1667 5.606348 TTCCAATACACAAAAGTTTGCCT 57.394 34.783 3.68 0.00 41.79 4.75
1618 1668 6.481644 TCATTTCCAATACACAAAAGTTTGCC 59.518 34.615 3.68 0.00 41.79 4.52
1619 1669 7.475771 TCATTTCCAATACACAAAAGTTTGC 57.524 32.000 3.68 0.00 41.79 3.68
1620 1670 9.097257 AGTTCATTTCCAATACACAAAAGTTTG 57.903 29.630 2.22 2.22 43.62 2.93
1621 1671 9.097257 CAGTTCATTTCCAATACACAAAAGTTT 57.903 29.630 0.00 0.00 0.00 2.66
1622 1672 8.474025 TCAGTTCATTTCCAATACACAAAAGTT 58.526 29.630 0.00 0.00 0.00 2.66
1623 1673 8.006298 TCAGTTCATTTCCAATACACAAAAGT 57.994 30.769 0.00 0.00 0.00 2.66
1624 1674 9.480053 AATCAGTTCATTTCCAATACACAAAAG 57.520 29.630 0.00 0.00 0.00 2.27
1651 1721 3.433343 TGTGATGCAGGAATTTCATGGT 58.567 40.909 12.51 0.00 0.00 3.55
1656 1727 6.389091 TGTATGTTTGTGATGCAGGAATTTC 58.611 36.000 0.00 0.00 0.00 2.17
1660 1731 4.321156 GCTTGTATGTTTGTGATGCAGGAA 60.321 41.667 0.00 0.00 0.00 3.36
1726 1797 3.805971 CAGATGAGATTGCGAGCATTACA 59.194 43.478 0.00 0.94 0.00 2.41
1748 1819 8.552034 GTTGTAAATGCAAGAGGTACTGATATC 58.448 37.037 0.00 0.00 41.55 1.63
1791 1863 2.035442 GGTTCTGAACCGCTCCTGC 61.035 63.158 22.67 0.00 42.62 4.85
1862 1934 3.512033 TGTTGTTGTTTACAGTTGGGC 57.488 42.857 0.00 0.00 38.19 5.36
2014 2094 1.827315 GCTTGCGCACACTGTCGTTA 61.827 55.000 11.12 0.00 35.78 3.18
2107 2187 3.161866 TCCCAAATGCAAAAGGGTAGTC 58.838 45.455 17.24 0.00 42.12 2.59
2124 2204 5.304614 GCCTAGTTTATGAGTCAGTATCCCA 59.695 44.000 0.00 0.00 0.00 4.37
2126 2206 6.492087 AGAGCCTAGTTTATGAGTCAGTATCC 59.508 42.308 0.00 0.00 0.00 2.59
2166 2249 1.736645 CACGACGAATTCCCGTGCT 60.737 57.895 25.04 3.82 45.26 4.40
2214 2297 8.089597 TCAACAAAACAATATCAACATCAGCAT 58.910 29.630 0.00 0.00 0.00 3.79
2217 2300 7.811236 AGCTCAACAAAACAATATCAACATCAG 59.189 33.333 0.00 0.00 0.00 2.90
2218 2301 7.660112 AGCTCAACAAAACAATATCAACATCA 58.340 30.769 0.00 0.00 0.00 3.07
2223 2306 9.421806 CCATTTAGCTCAACAAAACAATATCAA 57.578 29.630 0.00 0.00 0.00 2.57
2271 2372 5.730207 AGGAATACCCATCTCATCAGCATAT 59.270 40.000 0.00 0.00 37.41 1.78
2533 2634 1.105167 TTCTGCTTGTGCTGCTGCTT 61.105 50.000 17.00 0.00 40.48 3.91
2578 2679 0.466555 CCTCCCTCGAGTCCGATCTT 60.467 60.000 12.31 0.00 44.62 2.40
2589 2690 0.106894 GGATGCTTTACCCTCCCTCG 59.893 60.000 0.00 0.00 0.00 4.63
2591 2692 0.253630 TGGGATGCTTTACCCTCCCT 60.254 55.000 7.90 0.00 46.37 4.20
2835 2936 4.374843 TTGCAATATGGCTGACATGTTC 57.625 40.909 6.18 1.39 38.64 3.18
2841 2942 3.009301 GCAGATTGCAATATGGCTGAC 57.991 47.619 29.64 16.17 44.26 3.51
2916 3017 6.204301 GCATCTGCATCTGTTTCTGTATATGT 59.796 38.462 0.00 0.00 41.59 2.29
2917 3018 6.600350 GCATCTGCATCTGTTTCTGTATATG 58.400 40.000 0.00 0.00 41.59 1.78
2918 3019 6.798315 GCATCTGCATCTGTTTCTGTATAT 57.202 37.500 0.00 0.00 41.59 0.86
2934 3108 5.464168 AGTACAAACAAAATCTGCATCTGC 58.536 37.500 0.00 0.00 42.50 4.26
2962 3136 6.667848 TCTCCTAGTTCCACTTCATGATGTAA 59.332 38.462 13.40 3.76 0.00 2.41
2978 3152 5.308825 CCTTGTGTGATTTGTCTCCTAGTT 58.691 41.667 0.00 0.00 0.00 2.24
2980 3154 3.686726 GCCTTGTGTGATTTGTCTCCTAG 59.313 47.826 0.00 0.00 0.00 3.02
2981 3155 3.327757 AGCCTTGTGTGATTTGTCTCCTA 59.672 43.478 0.00 0.00 0.00 2.94
2982 3156 2.107204 AGCCTTGTGTGATTTGTCTCCT 59.893 45.455 0.00 0.00 0.00 3.69
2983 3157 2.508526 AGCCTTGTGTGATTTGTCTCC 58.491 47.619 0.00 0.00 0.00 3.71
2984 3158 4.937620 TCATAGCCTTGTGTGATTTGTCTC 59.062 41.667 0.00 0.00 0.00 3.36
2990 3164 3.055819 ACGTCTCATAGCCTTGTGTGATT 60.056 43.478 0.00 0.00 0.00 2.57
3079 3253 1.023502 GAGGAGTACTCGTGTAGCCC 58.976 60.000 22.12 3.85 36.29 5.19
3101 3275 1.204146 TCACCCTCCAGCTAACCATC 58.796 55.000 0.00 0.00 0.00 3.51
3118 3292 1.737236 GCATGATGTTACCGCAGTTCA 59.263 47.619 0.00 0.00 0.00 3.18
3119 3293 1.737236 TGCATGATGTTACCGCAGTTC 59.263 47.619 0.00 0.00 0.00 3.01
3172 3346 8.417106 TCCTCTTTCAGATTGTCATATGTAGAC 58.583 37.037 1.90 0.00 36.55 2.59
3184 3358 6.871844 TGTAGACTCATCCTCTTTCAGATTG 58.128 40.000 0.00 0.00 0.00 2.67
3187 3361 8.001292 TCATATGTAGACTCATCCTCTTTCAGA 58.999 37.037 1.90 0.00 0.00 3.27
3188 3362 8.175925 TCATATGTAGACTCATCCTCTTTCAG 57.824 38.462 1.90 0.00 0.00 3.02
3189 3363 8.539117 TTCATATGTAGACTCATCCTCTTTCA 57.461 34.615 1.90 0.00 0.00 2.69
3190 3364 9.823647 TTTTCATATGTAGACTCATCCTCTTTC 57.176 33.333 1.90 0.00 0.00 2.62
3192 3366 9.829507 CTTTTTCATATGTAGACTCATCCTCTT 57.170 33.333 1.90 0.00 0.00 2.85
3193 3367 7.930865 GCTTTTTCATATGTAGACTCATCCTCT 59.069 37.037 1.90 0.00 0.00 3.69
3194 3368 7.712639 TGCTTTTTCATATGTAGACTCATCCTC 59.287 37.037 1.90 0.00 0.00 3.71
3195 3369 7.568349 TGCTTTTTCATATGTAGACTCATCCT 58.432 34.615 1.90 0.00 0.00 3.24
3196 3370 7.792374 TGCTTTTTCATATGTAGACTCATCC 57.208 36.000 1.90 0.00 0.00 3.51
3197 3371 8.834465 ACATGCTTTTTCATATGTAGACTCATC 58.166 33.333 1.90 0.00 32.41 2.92
3198 3372 8.743085 ACATGCTTTTTCATATGTAGACTCAT 57.257 30.769 1.90 0.00 32.41 2.90
3199 3373 9.098355 GTACATGCTTTTTCATATGTAGACTCA 57.902 33.333 1.90 0.00 36.87 3.41
3200 3374 9.098355 TGTACATGCTTTTTCATATGTAGACTC 57.902 33.333 1.90 0.00 36.87 3.36
3201 3375 9.618890 ATGTACATGCTTTTTCATATGTAGACT 57.381 29.630 7.78 0.00 36.87 3.24
3202 3376 9.869844 GATGTACATGCTTTTTCATATGTAGAC 57.130 33.333 14.43 0.00 36.87 2.59
3203 3377 8.764287 CGATGTACATGCTTTTTCATATGTAGA 58.236 33.333 14.43 0.00 36.87 2.59
3204 3378 8.764287 TCGATGTACATGCTTTTTCATATGTAG 58.236 33.333 14.43 0.00 36.87 2.74
3205 3379 8.547894 GTCGATGTACATGCTTTTTCATATGTA 58.452 33.333 14.43 0.00 35.55 2.29
3206 3380 7.065683 TGTCGATGTACATGCTTTTTCATATGT 59.934 33.333 14.43 0.00 37.51 2.29
3207 3381 7.408910 TGTCGATGTACATGCTTTTTCATATG 58.591 34.615 14.43 0.00 0.00 1.78
3208 3382 7.495606 TCTGTCGATGTACATGCTTTTTCATAT 59.504 33.333 14.43 0.00 0.00 1.78
3209 3383 6.816140 TCTGTCGATGTACATGCTTTTTCATA 59.184 34.615 14.43 0.00 0.00 2.15
3210 3384 5.643348 TCTGTCGATGTACATGCTTTTTCAT 59.357 36.000 14.43 0.00 0.00 2.57
3211 3385 4.994217 TCTGTCGATGTACATGCTTTTTCA 59.006 37.500 14.43 2.32 0.00 2.69
3212 3386 5.530519 TCTGTCGATGTACATGCTTTTTC 57.469 39.130 14.43 0.00 0.00 2.29
3213 3387 5.674569 GCATCTGTCGATGTACATGCTTTTT 60.675 40.000 14.43 0.00 46.96 1.94
3214 3388 4.201851 GCATCTGTCGATGTACATGCTTTT 60.202 41.667 14.43 0.00 46.96 2.27
3215 3389 3.310774 GCATCTGTCGATGTACATGCTTT 59.689 43.478 14.43 0.00 46.96 3.51
3499 3673 5.014755 TGGGCCTACATATTTCCGGATAATT 59.985 40.000 4.15 0.00 0.00 1.40
3500 3674 4.538490 TGGGCCTACATATTTCCGGATAAT 59.462 41.667 4.15 10.81 0.00 1.28
3501 3675 3.911260 TGGGCCTACATATTTCCGGATAA 59.089 43.478 4.15 2.94 0.00 1.75
3502 3676 3.522759 TGGGCCTACATATTTCCGGATA 58.477 45.455 4.15 0.00 0.00 2.59
3503 3677 2.344592 TGGGCCTACATATTTCCGGAT 58.655 47.619 4.15 0.00 0.00 4.18
3504 3678 1.809133 TGGGCCTACATATTTCCGGA 58.191 50.000 0.00 0.00 0.00 5.14
3505 3679 2.819608 CAATGGGCCTACATATTTCCGG 59.180 50.000 4.53 0.00 0.00 5.14
3506 3680 3.486383 ACAATGGGCCTACATATTTCCG 58.514 45.455 4.53 0.00 0.00 4.30
3507 3681 8.644374 TTATAACAATGGGCCTACATATTTCC 57.356 34.615 4.53 0.00 0.00 3.13
3535 3709 9.528489 AGAAAACCTTATTGCCAGTCTTTTATA 57.472 29.630 0.00 0.00 0.00 0.98
3536 3710 8.422577 AGAAAACCTTATTGCCAGTCTTTTAT 57.577 30.769 0.00 0.00 0.00 1.40
3537 3711 7.833285 AGAAAACCTTATTGCCAGTCTTTTA 57.167 32.000 0.00 0.00 0.00 1.52
3538 3712 6.731292 AGAAAACCTTATTGCCAGTCTTTT 57.269 33.333 0.00 0.00 0.00 2.27
3539 3713 7.004691 AGTAGAAAACCTTATTGCCAGTCTTT 58.995 34.615 0.00 0.00 0.00 2.52
3540 3714 6.543735 AGTAGAAAACCTTATTGCCAGTCTT 58.456 36.000 0.00 0.00 0.00 3.01
3541 3715 6.128138 AGTAGAAAACCTTATTGCCAGTCT 57.872 37.500 0.00 0.00 0.00 3.24
3542 3716 7.104290 AGTAGTAGAAAACCTTATTGCCAGTC 58.896 38.462 0.00 0.00 0.00 3.51
3543 3717 7.017319 AGTAGTAGAAAACCTTATTGCCAGT 57.983 36.000 0.00 0.00 0.00 4.00
3544 3718 6.539103 GGAGTAGTAGAAAACCTTATTGCCAG 59.461 42.308 0.00 0.00 0.00 4.85
3545 3719 6.214819 AGGAGTAGTAGAAAACCTTATTGCCA 59.785 38.462 0.00 0.00 0.00 4.92
3546 3720 6.651086 AGGAGTAGTAGAAAACCTTATTGCC 58.349 40.000 0.00 0.00 0.00 4.52
3547 3721 9.262358 CATAGGAGTAGTAGAAAACCTTATTGC 57.738 37.037 0.00 0.00 0.00 3.56
3548 3722 9.765795 CCATAGGAGTAGTAGAAAACCTTATTG 57.234 37.037 0.00 0.00 0.00 1.90



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

AutoCloner maintained by Alex Coulton.