Multiple sequence alignment - TraesCS4A01G464000

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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 TraesCS4A01G464000 chr4A 100.000 2621 0 0 1 2621 728085961 728083341 0.000000e+00 4841
1 TraesCS4A01G464000 chr7A 87.358 1677 105 38 1 1626 9755958 9757578 0.000000e+00 1823
2 TraesCS4A01G464000 chr7A 93.284 268 12 4 1720 1984 9757628 9757892 8.800000e-105 390
3 TraesCS4A01G464000 chr7A 91.935 186 14 1 2180 2365 9758036 9758220 2.590000e-65 259
4 TraesCS4A01G464000 chr7A 91.367 139 12 0 2091 2229 9757891 9758029 9.570000e-45 191
5 TraesCS4A01G464000 chr7A 91.954 87 5 2 1653 1739 26406076 26406160 1.270000e-23 121
6 TraesCS4A01G464000 chr7A 93.333 75 5 0 1653 1727 360969301 360969227 7.670000e-21 111
7 TraesCS4A01G464000 chr7A 94.366 71 4 0 1653 1723 716275319 716275389 2.760000e-20 110
8 TraesCS4A01G464000 chr7D 88.328 891 56 25 750 1621 10716907 10717768 0.000000e+00 1026
9 TraesCS4A01G464000 chr7D 91.274 573 42 5 1720 2289 10719358 10719925 0.000000e+00 774
10 TraesCS4A01G464000 chr7D 88.390 646 29 23 1 616 10716147 10716776 0.000000e+00 736
11 TraesCS4A01G464000 chr7D 84.746 354 26 16 2269 2621 10721776 10722102 1.940000e-86 329
12 TraesCS4A01G464000 chr2B 93.464 153 9 1 163 314 510167747 510167595 2.620000e-55 226
13 TraesCS4A01G464000 chr3B 92.500 80 6 0 1653 1732 819011606 819011527 5.930000e-22 115
14 TraesCS4A01G464000 chr1A 92.500 80 6 0 1653 1732 107663209 107663288 5.930000e-22 115
15 TraesCS4A01G464000 chr5A 92.405 79 6 0 1653 1731 272591161 272591239 2.130000e-21 113
16 TraesCS4A01G464000 chr6B 93.333 75 5 0 1653 1727 367268611 367268685 7.670000e-21 111
17 TraesCS4A01G464000 chr5D 88.636 88 9 1 1653 1739 542716737 542716650 3.570000e-19 106
18 TraesCS4A01G464000 chr3A 90.244 82 7 1 1653 1734 696313965 696313885 3.570000e-19 106


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 TraesCS4A01G464000 chr4A 728083341 728085961 2620 True 4841.00 4841 100.0000 1 2621 1 chr4A.!!$R1 2620
1 TraesCS4A01G464000 chr7A 9755958 9758220 2262 False 665.75 1823 90.9860 1 2365 4 chr7A.!!$F3 2364
2 TraesCS4A01G464000 chr7D 10716147 10722102 5955 False 716.25 1026 88.1845 1 2621 4 chr7D.!!$F1 2620

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
81 82 0.030369 CTACTGCGTACGTGGGATCC 59.97 60.0 17.9 1.92 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2077 3755 1.379044 CTCCCTGCATGGTTGGGTC 60.379 63.158 7.98 0.0 41.58 4.46 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
78 79 1.638388 CGTCTACTGCGTACGTGGGA 61.638 60.000 17.90 5.77 32.16 4.37
79 80 0.737219 GTCTACTGCGTACGTGGGAT 59.263 55.000 17.90 1.19 0.00 3.85
81 82 0.030369 CTACTGCGTACGTGGGATCC 59.970 60.000 17.90 1.92 0.00 3.36
82 83 1.717791 TACTGCGTACGTGGGATCCG 61.718 60.000 17.90 0.00 0.00 4.18
95 96 3.165559 GATCCGTCGATCCGTCAAG 57.834 57.895 0.00 0.00 39.29 3.02
96 97 0.317938 GATCCGTCGATCCGTCAAGG 60.318 60.000 0.00 0.00 39.29 3.61
112 113 3.967332 CAAGGATTGGGCTCAATTTGT 57.033 42.857 14.31 0.00 43.94 2.83
117 118 3.131046 GGATTGGGCTCAATTTGTTCGAT 59.869 43.478 14.31 0.00 43.08 3.59
118 119 3.848272 TTGGGCTCAATTTGTTCGATC 57.152 42.857 0.00 0.00 0.00 3.69
124 125 3.181506 GCTCAATTTGTTCGATCCCTGAC 60.182 47.826 0.00 0.00 0.00 3.51
153 159 3.453353 AGATGCAAGATTTTGATTGGGGG 59.547 43.478 0.00 0.00 36.36 5.40
343 355 1.004595 GTCCGTCCGCCATTAAACTC 58.995 55.000 0.00 0.00 0.00 3.01
351 363 2.159382 CGCCATTAAACTCAACCCACT 58.841 47.619 0.00 0.00 0.00 4.00
353 365 3.421844 GCCATTAAACTCAACCCACTCT 58.578 45.455 0.00 0.00 0.00 3.24
355 367 4.807643 GCCATTAAACTCAACCCACTCTCT 60.808 45.833 0.00 0.00 0.00 3.10
356 368 4.697352 CCATTAAACTCAACCCACTCTCTG 59.303 45.833 0.00 0.00 0.00 3.35
357 369 5.513094 CCATTAAACTCAACCCACTCTCTGA 60.513 44.000 0.00 0.00 0.00 3.27
358 370 5.623956 TTAAACTCAACCCACTCTCTGAA 57.376 39.130 0.00 0.00 0.00 3.02
408 456 1.989165 GTGAGCTCATTCAGTGTCGAC 59.011 52.381 21.47 9.11 0.00 4.20
553 601 3.179939 GGCGAAGACGGTCGAAGC 61.180 66.667 13.51 13.51 43.86 3.86
616 664 1.140816 GTGTGACTCTGAACCGAAGC 58.859 55.000 0.00 0.00 0.00 3.86
632 680 1.177256 AAGCCTGAACTGCAGCAAGG 61.177 55.000 20.41 20.41 43.50 3.61
635 683 1.285023 CTGAACTGCAGCAAGGCAC 59.715 57.895 15.27 0.00 39.25 5.01
636 684 2.253452 GAACTGCAGCAAGGCACG 59.747 61.111 15.27 0.00 39.25 5.34
707 756 3.358707 TCAACACTGTACTGTACCGTG 57.641 47.619 29.14 29.14 45.61 4.94
725 774 3.129287 CCGTGGGAAATTTGGATGAGAAG 59.871 47.826 0.00 0.00 0.00 2.85
770 858 7.551974 AGAGTGAGATAAACAATGAGATGTTGG 59.448 37.037 0.00 0.00 42.49 3.77
788 876 2.571212 TGGTTGATGGTGTCACTCAAC 58.429 47.619 21.46 21.46 45.04 3.18
815 903 8.129001 TCCATCTATAATTAGGAGCCCTGATTA 58.871 37.037 15.81 15.81 43.12 1.75
816 904 8.772250 CCATCTATAATTAGGAGCCCTGATTAA 58.228 37.037 16.80 6.74 42.54 1.40
820 908 3.402628 TTAGGAGCCCTGATTAATCGC 57.597 47.619 10.80 8.14 34.61 4.58
821 909 0.398318 AGGAGCCCTGATTAATCGCC 59.602 55.000 10.80 5.37 29.57 5.54
822 910 0.108585 GGAGCCCTGATTAATCGCCA 59.891 55.000 10.80 0.00 0.00 5.69
823 911 1.271597 GGAGCCCTGATTAATCGCCAT 60.272 52.381 10.80 0.00 0.00 4.40
827 915 2.821969 GCCCTGATTAATCGCCATTCAT 59.178 45.455 10.80 0.00 0.00 2.57
860 948 3.369756 TCGTTCATGTCCGAATTAGCAAC 59.630 43.478 6.94 0.00 0.00 4.17
896 1009 4.408821 GGCATGGCCGACACCTCA 62.409 66.667 8.35 0.00 39.62 3.86
897 1010 3.127533 GCATGGCCGACACCTCAC 61.128 66.667 0.00 0.00 0.00 3.51
898 1011 2.347114 CATGGCCGACACCTCACA 59.653 61.111 0.00 0.00 0.00 3.58
899 1012 2.034879 CATGGCCGACACCTCACAC 61.035 63.158 0.00 0.00 0.00 3.82
900 1013 3.254024 ATGGCCGACACCTCACACC 62.254 63.158 0.00 0.00 0.00 4.16
901 1014 3.626924 GGCCGACACCTCACACCT 61.627 66.667 0.00 0.00 0.00 4.00
929 1042 0.108138 CTCCATTGACGGACCCTCAC 60.108 60.000 0.00 0.00 0.00 3.51
950 1063 1.269102 CCCCACGTACGAGCTCATAAG 60.269 57.143 24.41 7.95 0.00 1.73
951 1064 1.404391 CCCACGTACGAGCTCATAAGT 59.596 52.381 24.41 8.68 0.00 2.24
952 1065 2.451132 CCACGTACGAGCTCATAAGTG 58.549 52.381 23.31 23.31 32.57 3.16
960 1073 8.016229 ACGTACGAGCTCATAAGTGATAAATAG 58.984 37.037 24.41 0.00 32.98 1.73
996 1109 2.279120 CTCCTGCACGATCGAGGC 60.279 66.667 24.34 23.53 0.00 4.70
1284 1400 4.552365 CGGATGGCGGTGGAGCAT 62.552 66.667 0.00 0.00 39.27 3.79
1626 3297 4.451150 GGCATCGCCTGACCGTCA 62.451 66.667 0.29 0.29 46.69 4.35
1630 3304 0.460109 CATCGCCTGACCGTCAATCA 60.460 55.000 2.19 0.00 0.00 2.57
1633 3307 1.375908 GCCTGACCGTCAATCAGCA 60.376 57.895 2.19 0.00 41.97 4.41
1639 3313 0.877071 ACCGTCAATCAGCAGCTTTG 59.123 50.000 0.00 0.00 0.00 2.77
1640 3314 0.455633 CCGTCAATCAGCAGCTTTGC 60.456 55.000 0.00 0.00 0.00 3.68
1641 3315 0.455633 CGTCAATCAGCAGCTTTGCC 60.456 55.000 0.00 0.00 34.90 4.52
1643 3317 1.153901 CAATCAGCAGCTTTGCCCG 60.154 57.895 0.00 0.00 34.90 6.13
1644 3318 1.303561 AATCAGCAGCTTTGCCCGA 60.304 52.632 0.00 0.00 34.90 5.14
1645 3319 1.589716 AATCAGCAGCTTTGCCCGAC 61.590 55.000 0.00 0.00 34.90 4.79
1648 3322 2.669569 GCAGCTTTGCCCGACTGA 60.670 61.111 0.00 0.00 31.67 3.41
1649 3323 2.970974 GCAGCTTTGCCCGACTGAC 61.971 63.158 0.00 0.00 31.67 3.51
1650 3324 2.357517 AGCTTTGCCCGACTGACG 60.358 61.111 0.00 0.00 42.18 4.35
1651 3325 2.665185 GCTTTGCCCGACTGACGT 60.665 61.111 0.00 0.00 40.78 4.34
1654 3328 0.038526 CTTTGCCCGACTGACGTACT 60.039 55.000 0.00 0.00 40.78 2.73
1655 3329 1.200716 CTTTGCCCGACTGACGTACTA 59.799 52.381 0.00 0.00 40.78 1.82
1656 3330 1.246649 TTGCCCGACTGACGTACTAA 58.753 50.000 0.00 0.00 40.78 2.24
1657 3331 1.466856 TGCCCGACTGACGTACTAAT 58.533 50.000 0.00 0.00 40.78 1.73
1658 3332 2.642427 TGCCCGACTGACGTACTAATA 58.358 47.619 0.00 0.00 40.78 0.98
1660 3334 4.388485 TGCCCGACTGACGTACTAATATA 58.612 43.478 0.00 0.00 40.78 0.86
1661 3335 4.821260 TGCCCGACTGACGTACTAATATAA 59.179 41.667 0.00 0.00 40.78 0.98
1662 3336 5.049198 TGCCCGACTGACGTACTAATATAAG 60.049 44.000 0.00 0.00 40.78 1.73
1663 3337 5.180117 GCCCGACTGACGTACTAATATAAGA 59.820 44.000 0.00 0.00 40.78 2.10
1665 3339 6.426328 CCCGACTGACGTACTAATATAAGAGT 59.574 42.308 0.00 0.00 40.78 3.24
1666 3340 7.289395 CCGACTGACGTACTAATATAAGAGTG 58.711 42.308 0.00 0.00 40.78 3.51
1668 3342 8.333908 CGACTGACGTACTAATATAAGAGTGTT 58.666 37.037 0.00 0.00 37.22 3.32
1796 3471 5.887598 TCAACATGGCTGCATAAGATAGTTT 59.112 36.000 0.50 0.00 0.00 2.66
1797 3472 5.762825 ACATGGCTGCATAAGATAGTTTG 57.237 39.130 0.50 0.00 0.00 2.93
1798 3473 5.439721 ACATGGCTGCATAAGATAGTTTGA 58.560 37.500 0.50 0.00 0.00 2.69
1846 3522 2.866762 GTGGTATCAATGGAAGACGAGC 59.133 50.000 0.00 0.00 0.00 5.03
1876 3552 4.789012 AAAATGTAGCCATGTGGTCTTG 57.211 40.909 0.35 0.00 37.57 3.02
1980 3657 8.603242 ACAAAAACGTCTTACATTATGAGACT 57.397 30.769 10.82 0.00 40.90 3.24
1984 3661 6.761099 ACGTCTTACATTATGAGACTGAGT 57.239 37.500 10.82 0.00 40.90 3.41
1985 3662 6.556212 ACGTCTTACATTATGAGACTGAGTG 58.444 40.000 10.82 0.77 40.90 3.51
1986 3663 5.974158 CGTCTTACATTATGAGACTGAGTGG 59.026 44.000 10.82 0.00 40.90 4.00
1989 3666 7.651304 GTCTTACATTATGAGACTGAGTGGATG 59.349 40.741 0.00 0.00 40.12 3.51
1990 3667 5.946942 ACATTATGAGACTGAGTGGATGT 57.053 39.130 0.00 0.00 0.00 3.06
2018 3695 4.279671 TCTTTTGCGAAAATAAAGGCCTGA 59.720 37.500 5.69 0.00 31.45 3.86
2019 3696 4.799564 TTTGCGAAAATAAAGGCCTGAT 57.200 36.364 5.69 0.00 0.00 2.90
2022 3699 6.463995 TTGCGAAAATAAAGGCCTGATATT 57.536 33.333 5.69 12.16 0.00 1.28
2035 3712 8.829373 AAGGCCTGATATTGATTAAAAGAACT 57.171 30.769 5.69 0.00 0.00 3.01
2073 3751 4.588899 AGGAGCATATTACAGCAAACACA 58.411 39.130 0.00 0.00 0.00 3.72
2133 3813 2.412325 CGCGAGTAACAAACATTGGGAC 60.412 50.000 0.00 0.00 34.12 4.46
2190 3870 0.447406 CGACAATCGCCATCAAGCAA 59.553 50.000 0.00 0.00 31.14 3.91
2203 3883 1.068610 TCAAGCAAAACATGTAGCCGC 60.069 47.619 0.00 0.00 0.00 6.53
2258 3994 2.104170 AGGAGGACGAAGATGACTTCC 58.896 52.381 0.00 0.00 46.77 3.46
2281 4017 0.034616 AGCAGCCTCTTGAGACACAC 59.965 55.000 0.00 0.00 0.00 3.82
2316 5924 2.102420 TCGACGCCAAGGATCATGTATT 59.898 45.455 0.00 0.00 0.00 1.89
2345 5953 1.367840 CCGGAGAGGAATAAGCCCG 59.632 63.158 0.00 0.00 45.00 6.13
2361 5969 1.746615 CCGTTGGATGGGCTGTGAG 60.747 63.158 0.00 0.00 0.00 3.51
2362 5970 2.401766 CGTTGGATGGGCTGTGAGC 61.402 63.158 0.00 0.00 41.46 4.26
2374 5982 1.152247 TGTGAGCCTGTGACCTCCT 60.152 57.895 0.00 0.00 0.00 3.69
2383 5991 2.354203 CCTGTGACCTCCTTGTAGAAGC 60.354 54.545 0.00 0.00 0.00 3.86
2385 5993 3.764434 CTGTGACCTCCTTGTAGAAGCTA 59.236 47.826 0.00 0.00 0.00 3.32
2392 6000 5.189180 CCTCCTTGTAGAAGCTAAAGCAAT 58.811 41.667 4.54 0.00 45.16 3.56
2412 6020 0.884704 GTTGAAGACCTGCTTGCCGA 60.885 55.000 0.00 0.00 36.83 5.54
2413 6021 0.036732 TTGAAGACCTGCTTGCCGAT 59.963 50.000 0.00 0.00 36.83 4.18
2417 6025 0.179062 AGACCTGCTTGCCGATGATC 60.179 55.000 0.00 0.00 0.00 2.92
2420 6028 0.463295 CCTGCTTGCCGATGATCTGT 60.463 55.000 0.00 0.00 0.00 3.41
2464 6072 3.963428 TCCAGTTAAGGAGCTTGAGAC 57.037 47.619 0.00 0.00 32.77 3.36
2465 6073 2.231478 TCCAGTTAAGGAGCTTGAGACG 59.769 50.000 0.00 0.00 32.77 4.18
2466 6074 2.611518 CAGTTAAGGAGCTTGAGACGG 58.388 52.381 0.00 0.00 0.00 4.79
2467 6075 2.231478 CAGTTAAGGAGCTTGAGACGGA 59.769 50.000 0.00 0.00 0.00 4.69
2468 6076 3.100671 AGTTAAGGAGCTTGAGACGGAT 58.899 45.455 0.00 0.00 0.00 4.18
2469 6077 3.118956 AGTTAAGGAGCTTGAGACGGATG 60.119 47.826 0.00 0.00 0.00 3.51
2470 6078 0.539051 AAGGAGCTTGAGACGGATGG 59.461 55.000 0.00 0.00 0.00 3.51
2471 6079 1.522580 GGAGCTTGAGACGGATGGC 60.523 63.158 0.00 0.00 0.00 4.40
2472 6080 1.522580 GAGCTTGAGACGGATGGCC 60.523 63.158 0.00 0.00 0.00 5.36
2504 6112 9.625747 TGCAATGTAGTATGATAAAATCTCCAA 57.374 29.630 0.00 0.00 0.00 3.53
2520 6128 7.830099 AATCTCCAAGTCAAGTGAAAAGAAT 57.170 32.000 0.00 0.00 0.00 2.40
2555 6163 4.998671 TGGAAGAAGAGAGAGTATGCAG 57.001 45.455 0.00 0.00 0.00 4.41
2558 6166 1.066908 AGAAGAGAGAGTATGCAGCGC 59.933 52.381 0.00 0.00 0.00 5.92
2567 6175 0.099436 GTATGCAGCGCTTCCAAAGG 59.901 55.000 7.50 0.00 0.00 3.11
2569 6177 1.310933 ATGCAGCGCTTCCAAAGGAG 61.311 55.000 7.50 0.00 31.21 3.69
2578 6186 3.191371 CGCTTCCAAAGGAGCTTGTTATT 59.809 43.478 0.00 0.00 31.21 1.40
2587 6195 6.428385 AAGGAGCTTGTTATTTCAGATTCG 57.572 37.500 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 0.750546 TCCTTGACGGATCGACGGAT 60.751 55.000 0.00 0.00 36.69 4.18
79 80 1.377594 TCCTTGACGGATCGACGGA 60.378 57.895 0.00 0.00 36.69 4.69
91 92 3.509442 ACAAATTGAGCCCAATCCTTGA 58.491 40.909 11.10 0.00 41.84 3.02
94 95 2.493278 CGAACAAATTGAGCCCAATCCT 59.507 45.455 0.00 0.00 41.84 3.24
95 96 2.491693 TCGAACAAATTGAGCCCAATCC 59.508 45.455 0.00 0.00 41.84 3.01
96 97 3.848272 TCGAACAAATTGAGCCCAATC 57.152 42.857 0.00 0.00 41.84 2.67
98 99 2.491693 GGATCGAACAAATTGAGCCCAA 59.508 45.455 0.00 0.00 32.10 4.12
99 100 2.091541 GGATCGAACAAATTGAGCCCA 58.908 47.619 0.00 0.00 32.10 5.36
100 101 2.851805 GGATCGAACAAATTGAGCCC 57.148 50.000 0.00 0.00 32.10 5.19
101 102 2.098117 CAGGGATCGAACAAATTGAGCC 59.902 50.000 0.00 0.00 37.46 4.70
102 103 3.009723 TCAGGGATCGAACAAATTGAGC 58.990 45.455 0.00 0.00 0.00 4.26
103 104 3.062639 CGTCAGGGATCGAACAAATTGAG 59.937 47.826 0.00 0.00 0.00 3.02
104 105 3.000041 CGTCAGGGATCGAACAAATTGA 59.000 45.455 0.00 0.00 0.00 2.57
105 106 3.000041 TCGTCAGGGATCGAACAAATTG 59.000 45.455 0.00 0.00 33.13 2.32
106 107 3.328382 TCGTCAGGGATCGAACAAATT 57.672 42.857 0.00 0.00 33.13 1.82
107 108 3.543680 ATCGTCAGGGATCGAACAAAT 57.456 42.857 0.00 0.00 39.45 2.32
108 109 3.328382 AATCGTCAGGGATCGAACAAA 57.672 42.857 0.00 0.00 39.45 2.83
109 110 4.459390 TTAATCGTCAGGGATCGAACAA 57.541 40.909 0.00 0.00 39.45 2.83
110 111 4.158949 TCTTTAATCGTCAGGGATCGAACA 59.841 41.667 0.00 0.00 39.45 3.18
111 112 4.679662 TCTTTAATCGTCAGGGATCGAAC 58.320 43.478 0.00 0.00 39.45 3.95
112 113 4.994907 TCTTTAATCGTCAGGGATCGAA 57.005 40.909 0.00 0.00 39.45 3.71
117 118 3.904800 TGCATCTTTAATCGTCAGGGA 57.095 42.857 0.00 0.00 0.00 4.20
118 119 4.191544 TCTTGCATCTTTAATCGTCAGGG 58.808 43.478 0.00 0.00 0.00 4.45
124 125 8.537223 CCAATCAAAATCTTGCATCTTTAATCG 58.463 33.333 0.00 0.00 32.14 3.34
153 159 2.355007 CCCCTGCCAAATCCAAATCAAC 60.355 50.000 0.00 0.00 0.00 3.18
343 355 4.275936 ACGAAAAATTCAGAGAGTGGGTTG 59.724 41.667 0.00 0.00 0.00 3.77
353 365 4.380531 AGCACTCTGACGAAAAATTCAGA 58.619 39.130 0.00 1.58 44.80 3.27
355 367 4.380531 AGAGCACTCTGACGAAAAATTCA 58.619 39.130 0.00 0.00 38.75 2.57
356 368 4.999751 AGAGCACTCTGACGAAAAATTC 57.000 40.909 0.00 0.00 38.75 2.17
384 424 2.735663 GACACTGAATGAGCTCACTGTG 59.264 50.000 27.94 27.94 37.88 3.66
408 456 6.876257 ACATCATGTCATCATCATCAGATCAG 59.124 38.462 0.00 0.00 30.20 2.90
452 500 3.080641 CCCAGGATCACCAGCACA 58.919 61.111 0.00 0.00 38.94 4.57
616 664 1.900016 TGCCTTGCTGCAGTTCAGG 60.900 57.895 16.64 17.87 43.06 3.86
632 680 2.097007 TCAAAATTTCAAATGCGCGTGC 60.097 40.909 15.48 15.48 43.20 5.34
635 683 4.373532 AGTTCAAAATTTCAAATGCGCG 57.626 36.364 0.00 0.00 0.00 6.86
636 684 6.582295 TCTCTAGTTCAAAATTTCAAATGCGC 59.418 34.615 0.00 0.00 0.00 6.09
707 756 5.478332 ACAACTCTTCTCATCCAAATTTCCC 59.522 40.000 0.00 0.00 0.00 3.97
738 806 7.763071 TCTCATTGTTTATCTCACTCTCATGTG 59.237 37.037 0.00 0.00 39.15 3.21
754 822 5.305128 ACCATCAACCAACATCTCATTGTTT 59.695 36.000 0.00 0.00 37.73 2.83
758 846 4.410099 ACACCATCAACCAACATCTCATT 58.590 39.130 0.00 0.00 0.00 2.57
770 858 5.044301 ATGGAGTTGAGTGACACCATCAAC 61.044 45.833 23.39 23.39 44.36 3.18
788 876 5.960811 TCAGGGCTCCTAATTATAGATGGAG 59.039 44.000 11.58 11.58 45.05 3.86
815 903 2.352651 CGACACAGAATGAATGGCGATT 59.647 45.455 0.00 0.00 45.35 3.34
816 904 1.935873 CGACACAGAATGAATGGCGAT 59.064 47.619 0.00 0.00 45.35 4.58
817 905 1.337728 ACGACACAGAATGAATGGCGA 60.338 47.619 5.60 0.00 45.35 5.54
820 908 2.736721 ACGAACGACACAGAATGAATGG 59.263 45.455 0.14 0.00 39.69 3.16
821 909 4.084589 TGAACGAACGACACAGAATGAATG 60.085 41.667 0.14 0.00 39.69 2.67
822 910 4.055360 TGAACGAACGACACAGAATGAAT 58.945 39.130 0.14 0.00 39.69 2.57
823 911 3.449632 TGAACGAACGACACAGAATGAA 58.550 40.909 0.14 0.00 39.69 2.57
827 915 2.792674 GACATGAACGAACGACACAGAA 59.207 45.455 0.00 0.00 0.00 3.02
897 1010 0.321671 AATGGAGGACGACACAGGTG 59.678 55.000 0.00 0.00 0.00 4.00
898 1011 0.321671 CAATGGAGGACGACACAGGT 59.678 55.000 0.00 0.00 0.00 4.00
899 1012 0.608130 TCAATGGAGGACGACACAGG 59.392 55.000 0.00 0.00 0.00 4.00
900 1013 1.714794 GTCAATGGAGGACGACACAG 58.285 55.000 0.00 0.00 0.00 3.66
901 1014 3.906660 GTCAATGGAGGACGACACA 57.093 52.632 0.00 0.00 0.00 3.72
929 1042 1.105167 TATGAGCTCGTACGTGGGGG 61.105 60.000 16.05 3.25 0.00 5.40
950 1063 1.879380 TGCGCCATGGCTATTTATCAC 59.121 47.619 33.07 11.84 39.32 3.06
951 1064 1.879380 GTGCGCCATGGCTATTTATCA 59.121 47.619 33.07 15.83 39.32 2.15
952 1065 1.879380 TGTGCGCCATGGCTATTTATC 59.121 47.619 33.07 16.22 39.32 1.75
960 1073 4.722855 GTGGTTGTGCGCCATGGC 62.723 66.667 27.67 27.67 38.40 4.40
996 1109 2.867333 CTTGCTGCTTCGCCATGCTG 62.867 60.000 0.00 0.00 0.00 4.41
1007 1120 4.749310 CGCGTCCTCCTTGCTGCT 62.749 66.667 0.00 0.00 0.00 4.24
1025 1138 2.747022 CCATGGACGTGGTGTGGA 59.253 61.111 5.56 0.00 34.46 4.02
1175 1291 4.065281 AGTGCGCGTAGTCCACCC 62.065 66.667 8.43 0.00 0.00 4.61
1633 3307 1.812686 TACGTCAGTCGGGCAAAGCT 61.813 55.000 0.00 0.00 44.69 3.74
1639 3313 3.911661 ATATTAGTACGTCAGTCGGGC 57.088 47.619 0.00 0.00 44.69 6.13
1640 3314 6.426328 ACTCTTATATTAGTACGTCAGTCGGG 59.574 42.308 0.00 0.00 44.69 5.14
1641 3315 7.042187 ACACTCTTATATTAGTACGTCAGTCGG 60.042 40.741 0.00 0.00 44.69 4.79
1708 3382 9.657419 CGTTTTATTTACTACTCCCTTAGGAAA 57.343 33.333 0.00 0.00 43.40 3.13
1709 3383 9.034800 TCGTTTTATTTACTACTCCCTTAGGAA 57.965 33.333 0.00 0.00 43.40 3.36
1710 3384 8.593945 TCGTTTTATTTACTACTCCCTTAGGA 57.406 34.615 0.00 0.00 41.08 2.94
1711 3385 9.657419 TTTCGTTTTATTTACTACTCCCTTAGG 57.343 33.333 0.00 0.00 0.00 2.69
1714 3388 8.953313 CCATTTCGTTTTATTTACTACTCCCTT 58.047 33.333 0.00 0.00 0.00 3.95
1715 3389 7.555195 CCCATTTCGTTTTATTTACTACTCCCT 59.445 37.037 0.00 0.00 0.00 4.20
1716 3390 7.553760 TCCCATTTCGTTTTATTTACTACTCCC 59.446 37.037 0.00 0.00 0.00 4.30
1717 3391 8.496707 TCCCATTTCGTTTTATTTACTACTCC 57.503 34.615 0.00 0.00 0.00 3.85
1796 3471 6.986250 TGTAAAAACATTGCACATACCATCA 58.014 32.000 0.00 0.00 0.00 3.07
1797 3472 8.382130 CAATGTAAAAACATTGCACATACCATC 58.618 33.333 15.87 0.00 46.68 3.51
1798 3473 8.254178 CAATGTAAAAACATTGCACATACCAT 57.746 30.769 15.87 0.00 46.68 3.55
1823 3498 4.363999 CTCGTCTTCCATTGATACCACTC 58.636 47.826 0.00 0.00 0.00 3.51
1826 3501 2.481276 CGCTCGTCTTCCATTGATACCA 60.481 50.000 0.00 0.00 0.00 3.25
1828 3503 2.535984 CACGCTCGTCTTCCATTGATAC 59.464 50.000 0.00 0.00 0.00 2.24
1846 3522 7.077605 CCACATGGCTACATTTTATTATCACG 58.922 38.462 0.00 0.00 34.35 4.35
1876 3552 8.294341 TGTACGGATCATATCGATTTTTCTTC 57.706 34.615 1.71 0.00 33.17 2.87
2022 3699 8.934023 AGGGTTGTATTCAGTTCTTTTAATCA 57.066 30.769 0.00 0.00 0.00 2.57
2035 3712 3.585289 TGCTCCTTGTAGGGTTGTATTCA 59.415 43.478 0.00 0.00 35.59 2.57
2073 3751 2.035469 TGCATGGTTGGGTCGCAT 59.965 55.556 0.00 0.00 0.00 4.73
2077 3755 1.379044 CTCCCTGCATGGTTGGGTC 60.379 63.158 7.98 0.00 41.58 4.46
2113 3791 2.550606 TGTCCCAATGTTTGTTACTCGC 59.449 45.455 0.00 0.00 0.00 5.03
2133 3813 4.862092 AGCAGCGTCGATCGGCTG 62.862 66.667 30.30 30.30 42.18 4.85
2190 3870 1.573829 CGGTGTGCGGCTACATGTTT 61.574 55.000 2.30 0.00 32.43 2.83
2203 3883 4.271049 GTCATCATCTTCATTACCGGTGTG 59.729 45.833 19.93 16.26 0.00 3.82
2281 4017 3.120304 TGGCGTCGATGATCTACTAATCG 60.120 47.826 9.31 6.14 43.47 3.34
2316 5924 1.153647 CTCTCCGGCGCATGTTGTA 60.154 57.895 10.83 0.00 0.00 2.41
2329 5937 1.475213 CCAACGGGCTTATTCCTCTCC 60.475 57.143 0.00 0.00 0.00 3.71
2345 5953 3.595819 GCTCACAGCCCATCCAAC 58.404 61.111 0.00 0.00 34.48 3.77
2361 5969 1.267121 TCTACAAGGAGGTCACAGGC 58.733 55.000 0.00 0.00 0.00 4.85
2362 5970 2.354203 GCTTCTACAAGGAGGTCACAGG 60.354 54.545 0.00 0.00 0.00 4.00
2363 5971 2.564947 AGCTTCTACAAGGAGGTCACAG 59.435 50.000 0.00 0.00 0.00 3.66
2364 5972 2.609747 AGCTTCTACAAGGAGGTCACA 58.390 47.619 0.00 0.00 0.00 3.58
2365 5973 4.803098 TTAGCTTCTACAAGGAGGTCAC 57.197 45.455 0.00 0.00 0.00 3.67
2366 5974 4.322801 GCTTTAGCTTCTACAAGGAGGTCA 60.323 45.833 0.00 0.00 38.21 4.02
2367 5975 4.185394 GCTTTAGCTTCTACAAGGAGGTC 58.815 47.826 0.00 0.00 38.21 3.85
2368 5976 3.583086 TGCTTTAGCTTCTACAAGGAGGT 59.417 43.478 0.00 0.00 42.66 3.85
2374 5982 6.875948 TCAACATTGCTTTAGCTTCTACAA 57.124 33.333 0.00 0.00 42.66 2.41
2383 5991 4.217118 AGCAGGTCTTCAACATTGCTTTAG 59.783 41.667 0.00 0.00 43.63 1.85
2385 5993 2.961062 AGCAGGTCTTCAACATTGCTTT 59.039 40.909 0.00 0.00 43.63 3.51
2392 6000 1.165907 CGGCAAGCAGGTCTTCAACA 61.166 55.000 0.00 0.00 31.27 3.33
2431 6039 2.101640 AACTGGAGGCCCATTTTGTT 57.898 45.000 0.00 0.00 42.59 2.83
2437 6045 3.435682 TCCTTAACTGGAGGCCCAT 57.564 52.632 0.00 0.00 42.59 4.00
2449 6057 2.168521 CCATCCGTCTCAAGCTCCTTAA 59.831 50.000 0.00 0.00 0.00 1.85
2466 6074 3.204827 ATTGCAGACGCGGCCATC 61.205 61.111 9.25 0.00 42.97 3.51
2467 6075 2.867793 TACATTGCAGACGCGGCCAT 62.868 55.000 9.25 0.00 42.97 4.40
2468 6076 3.597675 TACATTGCAGACGCGGCCA 62.598 57.895 9.25 0.00 42.97 5.36
2469 6077 2.813179 CTACATTGCAGACGCGGCC 61.813 63.158 9.25 0.00 42.97 6.13
2470 6078 0.804544 TACTACATTGCAGACGCGGC 60.805 55.000 12.47 7.86 42.97 6.53
2471 6079 1.522676 CATACTACATTGCAGACGCGG 59.477 52.381 12.47 0.00 42.97 6.46
2472 6080 2.459934 TCATACTACATTGCAGACGCG 58.540 47.619 3.53 3.53 42.97 6.01
2473 6081 6.525121 TTTATCATACTACATTGCAGACGC 57.475 37.500 0.00 0.00 39.24 5.19
2474 6082 8.982685 AGATTTTATCATACTACATTGCAGACG 58.017 33.333 0.00 0.00 0.00 4.18
2476 6084 9.494271 GGAGATTTTATCATACTACATTGCAGA 57.506 33.333 0.00 0.00 0.00 4.26
2477 6085 9.276590 TGGAGATTTTATCATACTACATTGCAG 57.723 33.333 0.00 0.00 0.00 4.41
2478 6086 9.625747 TTGGAGATTTTATCATACTACATTGCA 57.374 29.630 0.00 0.00 0.00 4.08
2504 6112 4.261197 GGCAACGATTCTTTTCACTTGACT 60.261 41.667 0.00 0.00 0.00 3.41
2505 6113 3.975035 GGCAACGATTCTTTTCACTTGAC 59.025 43.478 0.00 0.00 0.00 3.18
2544 6152 0.179100 TGGAAGCGCTGCATACTCTC 60.179 55.000 19.31 5.22 0.00 3.20
2555 6163 1.211190 CAAGCTCCTTTGGAAGCGC 59.789 57.895 0.00 0.00 33.40 5.92
2558 6166 6.207417 TCTGAAATAACAAGCTCCTTTGGAAG 59.793 38.462 0.00 0.00 32.32 3.46
2567 6175 7.757097 TCTACGAATCTGAAATAACAAGCTC 57.243 36.000 0.00 0.00 0.00 4.09
2569 6177 7.692705 GGTTTCTACGAATCTGAAATAACAAGC 59.307 37.037 0.00 0.00 33.20 4.01
2578 6186 6.764085 TCACTTTTGGTTTCTACGAATCTGAA 59.236 34.615 0.00 0.00 0.00 3.02
2587 6195 5.243426 TGTGCTTCACTTTTGGTTTCTAC 57.757 39.130 0.00 0.00 35.11 2.59


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

AutoCloner maintained by Alex Coulton.