Multiple sequence alignment - TraesCS3B01G532800

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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 TraesCS3B01G532800 chr3B 100.000 3425 0 0 1 3425 773245542 773248966 0.000000e+00 6325
1 TraesCS3B01G532800 chr3B 81.658 736 98 20 1 732 773169279 773169981 8.240000e-161 577
2 TraesCS3B01G532800 chr3B 83.882 577 57 18 250 824 773161716 773162258 5.070000e-143 518
3 TraesCS3B01G532800 chr3B 85.649 439 39 11 1988 2426 773365736 773366150 1.130000e-119 440
4 TraesCS3B01G532800 chr3B 93.939 132 8 0 2127 2258 773513931 773514062 2.080000e-47 200
5 TraesCS3B01G532800 chr3B 90.909 132 9 2 2429 2560 773366195 773366323 1.260000e-39 174
6 TraesCS3B01G532800 chr3B 88.060 134 15 1 2125 2258 773377723 773377855 1.270000e-34 158
7 TraesCS3B01G532800 chr3B 91.549 71 6 0 1706 1776 773377447 773377517 7.820000e-17 99
8 TraesCS3B01G532800 chr3D 90.801 2348 137 38 365 2667 579129069 579131382 0.000000e+00 3066
9 TraesCS3B01G532800 chr3D 85.360 403 57 2 1933 2335 579159679 579160079 1.900000e-112 416
10 TraesCS3B01G532800 chr3D 81.600 500 82 9 1 496 579109256 579109749 4.120000e-109 405
11 TraesCS3B01G532800 chr3D 82.826 460 60 4 2661 3104 579132735 579133191 8.910000e-106 394
12 TraesCS3B01G532800 chr3D 89.510 286 30 0 3140 3425 579133281 579133566 2.510000e-96 363
13 TraesCS3B01G532800 chr3D 79.802 505 47 27 797 1272 579114021 579114499 1.980000e-82 316
14 TraesCS3B01G532800 chr3D 92.466 146 11 0 2124 2269 579262694 579262839 3.460000e-50 209
15 TraesCS3B01G532800 chr3A 90.762 1981 114 25 675 2618 714457815 714459763 0.000000e+00 2580
16 TraesCS3B01G532800 chr3A 90.203 592 51 5 2837 3425 714461174 714461761 0.000000e+00 765
17 TraesCS3B01G532800 chr3A 83.886 211 24 5 1928 2129 714488499 714488708 3.490000e-45 193
18 TraesCS3B01G532800 chr3A 80.296 203 28 8 2629 2823 714459745 714459943 3.560000e-30 143
19 TraesCS3B01G532800 chr3A 92.754 69 5 0 2201 2269 714489499 714489567 2.170000e-17 100


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 TraesCS3B01G532800 chr3B 773245542 773248966 3424 False 6325.000000 6325 100.000000 1 3425 1 chr3B.!!$F3 3424
1 TraesCS3B01G532800 chr3B 773169279 773169981 702 False 577.000000 577 81.658000 1 732 1 chr3B.!!$F2 731
2 TraesCS3B01G532800 chr3B 773161716 773162258 542 False 518.000000 518 83.882000 250 824 1 chr3B.!!$F1 574
3 TraesCS3B01G532800 chr3B 773365736 773366323 587 False 307.000000 440 88.279000 1988 2560 2 chr3B.!!$F5 572
4 TraesCS3B01G532800 chr3D 579129069 579133566 4497 False 1274.333333 3066 87.712333 365 3425 3 chr3D.!!$F5 3060
5 TraesCS3B01G532800 chr3A 714457815 714461761 3946 False 1162.666667 2580 87.087000 675 3425 3 chr3A.!!$F1 2750

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
295 296 0.100682 CGGTGTGATAGTGAGGGTCG 59.899 60.0 0.0 0.0 0.00 4.79 F
363 372 0.464554 GTGCTAGTCCTTCATGGCCC 60.465 60.0 0.0 0.0 35.26 5.80 F
774 783 0.593773 GACGATTCTCTGCTCCGCTC 60.594 60.0 0.0 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 2143 0.670546 ACAAGCCGATGGTCTTGTCG 60.671 55.000 15.28 0.0 42.04 4.35 R
2215 2290 2.528125 CAGACTCTGATGCTCTTGTCG 58.472 52.381 0.00 0.0 32.44 4.35 R
2773 4259 0.544223 CGGGACAGAGAGAGAGGAGA 59.456 60.000 0.00 0.0 0.00 3.71 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
26 27 0.596082 GTCAATGTTGGTGGTTCCGG 59.404 55.000 0.00 0.00 39.52 5.14
57 58 0.175302 CGTTGCTCTCCTGCTGATCT 59.825 55.000 0.00 0.00 0.00 2.75
65 66 1.543802 CTCCTGCTGATCTACGGATCC 59.456 57.143 0.00 0.00 45.62 3.36
66 67 0.242286 CCTGCTGATCTACGGATCCG 59.758 60.000 32.20 32.20 45.62 4.18
67 68 4.561731 GCTGATCTACGGATCCGC 57.438 61.111 33.62 17.37 46.23 5.54
70 71 1.239347 CTGATCTACGGATCCGCTCA 58.761 55.000 33.62 25.95 45.62 4.26
73 74 0.891373 ATCTACGGATCCGCTCATGG 59.109 55.000 33.62 16.29 44.19 3.66
78 79 1.439353 CGGATCCGCTCATGGTTTGG 61.439 60.000 23.37 0.00 0.00 3.28
88 89 1.044790 CATGGTTTGGATCCCAGGGC 61.045 60.000 9.90 0.00 33.81 5.19
89 90 2.042944 GGTTTGGATCCCAGGGCC 60.043 66.667 9.90 0.00 33.81 5.80
118 119 2.665000 CGGCAGTCTGTGGGATGT 59.335 61.111 0.93 0.00 0.00 3.06
122 123 1.963515 GGCAGTCTGTGGGATGTTTTT 59.036 47.619 0.93 0.00 0.00 1.94
124 125 2.622942 GCAGTCTGTGGGATGTTTTTGA 59.377 45.455 0.93 0.00 0.00 2.69
125 126 3.550842 GCAGTCTGTGGGATGTTTTTGAC 60.551 47.826 0.93 0.00 0.00 3.18
126 127 3.631686 CAGTCTGTGGGATGTTTTTGACA 59.368 43.478 0.00 0.00 43.71 3.58
130 131 2.098280 TGTGGGATGTTTTTGACACGTG 59.902 45.455 15.48 15.48 42.04 4.49
140 141 2.049433 GACACGTGTGGGTCTCCG 60.049 66.667 28.82 0.00 35.24 4.63
141 142 2.520020 ACACGTGTGGGTCTCCGA 60.520 61.111 22.71 0.00 35.24 4.55
145 146 1.516386 CGTGTGGGTCTCCGAATCG 60.516 63.158 0.00 0.00 35.24 3.34
148 149 1.144057 GTGGGTCTCCGAATCGCAT 59.856 57.895 0.00 0.00 35.24 4.73
157 158 3.804325 TCTCCGAATCGCATGATTTCTTC 59.196 43.478 0.00 0.00 44.79 2.87
168 169 1.202533 TGATTTCTTCGATCCTCGGGC 60.203 52.381 0.00 0.00 40.88 6.13
170 171 1.771565 TTTCTTCGATCCTCGGGCTA 58.228 50.000 0.00 0.00 40.88 3.93
176 177 2.913060 ATCCTCGGGCTAGTCGGC 60.913 66.667 0.00 0.00 37.49 5.54
227 228 4.518283 AGTATCATCCTCTCCTCCCTCTA 58.482 47.826 0.00 0.00 0.00 2.43
232 233 0.533308 CCTCTCCTCCCTCTACGTCG 60.533 65.000 0.00 0.00 0.00 5.12
236 237 2.772691 CCTCCCTCTACGTCGTGGC 61.773 68.421 8.47 0.00 0.00 5.01
237 238 2.034532 TCCCTCTACGTCGTGGCA 59.965 61.111 8.47 0.00 0.00 4.92
248 249 2.660552 CGTGGCACCGACGAGTTT 60.661 61.111 12.86 0.00 39.21 2.66
262 263 2.746277 GTTTCCCATCAGCGGCGT 60.746 61.111 9.37 0.00 0.00 5.68
263 264 1.448893 GTTTCCCATCAGCGGCGTA 60.449 57.895 9.37 0.00 0.00 4.42
276 277 2.582978 GCGTAGAGGTTGGGTCCC 59.417 66.667 0.00 0.00 0.00 4.46
289 290 0.974010 GGGTCCCGGTGTGATAGTGA 60.974 60.000 0.00 0.00 0.00 3.41
292 293 0.686441 TCCCGGTGTGATAGTGAGGG 60.686 60.000 0.00 0.00 38.73 4.30
293 294 0.976073 CCCGGTGTGATAGTGAGGGT 60.976 60.000 0.00 0.00 33.00 4.34
294 295 0.460311 CCGGTGTGATAGTGAGGGTC 59.540 60.000 0.00 0.00 0.00 4.46
295 296 0.100682 CGGTGTGATAGTGAGGGTCG 59.899 60.000 0.00 0.00 0.00 4.79
296 297 1.471119 GGTGTGATAGTGAGGGTCGA 58.529 55.000 0.00 0.00 0.00 4.20
297 298 2.032620 GGTGTGATAGTGAGGGTCGAT 58.967 52.381 0.00 0.00 0.00 3.59
298 299 2.034812 GGTGTGATAGTGAGGGTCGATC 59.965 54.545 0.00 0.00 0.00 3.69
299 300 2.952978 GTGTGATAGTGAGGGTCGATCT 59.047 50.000 0.00 0.00 0.00 2.75
309 310 2.036604 GAGGGTCGATCTCTGGATTTCC 59.963 54.545 10.34 0.00 31.46 3.13
363 372 0.464554 GTGCTAGTCCTTCATGGCCC 60.465 60.000 0.00 0.00 35.26 5.80
378 387 1.966451 GCCCAGGTTGGTGACTTCG 60.966 63.158 0.00 0.00 35.17 3.79
379 388 1.752198 CCCAGGTTGGTGACTTCGA 59.248 57.895 0.00 0.00 35.17 3.71
390 399 1.199327 GTGACTTCGAGTCCGTCATGA 59.801 52.381 11.01 0.00 44.44 3.07
400 409 3.357203 AGTCCGTCATGACTGTCTACAT 58.643 45.455 22.95 0.00 43.80 2.29
401 410 3.129462 AGTCCGTCATGACTGTCTACATG 59.871 47.826 22.95 5.57 43.80 3.21
408 417 2.889512 TGACTGTCTACATGAGGGTGT 58.110 47.619 9.51 0.00 36.13 4.16
459 468 3.467226 GCCCTCGACCCGATCCAA 61.467 66.667 0.00 0.00 34.61 3.53
461 470 2.058595 CCCTCGACCCGATCCAACT 61.059 63.158 0.00 0.00 34.61 3.16
463 472 1.108776 CCTCGACCCGATCCAACTAA 58.891 55.000 0.00 0.00 34.61 2.24
552 561 5.938125 AGCTTTGTACTACAACATCGGAATT 59.062 36.000 0.82 0.00 37.90 2.17
586 595 4.816385 TCATATTCATGAGGTCCTTTTCGC 59.184 41.667 0.00 0.00 36.22 4.70
587 596 1.438651 TTCATGAGGTCCTTTTCGCG 58.561 50.000 0.00 0.00 0.00 5.87
591 600 1.223187 TGAGGTCCTTTTCGCGAAAC 58.777 50.000 32.32 21.61 0.00 2.78
593 602 1.600485 GAGGTCCTTTTCGCGAAACAA 59.400 47.619 32.32 18.71 0.00 2.83
594 603 2.018515 AGGTCCTTTTCGCGAAACAAA 58.981 42.857 32.32 17.99 0.00 2.83
595 604 2.424246 AGGTCCTTTTCGCGAAACAAAA 59.576 40.909 32.32 17.63 0.00 2.44
596 605 3.119424 AGGTCCTTTTCGCGAAACAAAAA 60.119 39.130 32.32 17.26 0.00 1.94
597 606 3.799963 GGTCCTTTTCGCGAAACAAAAAT 59.200 39.130 32.32 0.00 0.00 1.82
598 607 4.977347 GGTCCTTTTCGCGAAACAAAAATA 59.023 37.500 32.32 15.82 0.00 1.40
599 608 5.116528 GGTCCTTTTCGCGAAACAAAAATAG 59.883 40.000 32.32 23.33 0.00 1.73
751 760 2.974489 CTTGGCCACGAAGCAGCTG 61.974 63.158 3.88 10.11 0.00 4.24
774 783 0.593773 GACGATTCTCTGCTCCGCTC 60.594 60.000 0.00 0.00 0.00 5.03
775 784 1.315981 ACGATTCTCTGCTCCGCTCA 61.316 55.000 0.00 0.00 0.00 4.26
777 786 0.875474 GATTCTCTGCTCCGCTCAGC 60.875 60.000 0.00 0.00 40.13 4.26
778 787 2.308968 ATTCTCTGCTCCGCTCAGCC 62.309 60.000 0.00 0.00 38.80 4.85
834 855 4.938074 TTCGTCCCCGACCCACCA 62.938 66.667 0.00 0.00 44.13 4.17
838 859 4.938074 TCCCCGACCCACCAACGA 62.938 66.667 0.00 0.00 0.00 3.85
988 1041 3.172106 TTCCCCAGCCCAACGTCA 61.172 61.111 0.00 0.00 0.00 4.35
1004 1076 3.834799 CACTCCCTACCCCGCGTC 61.835 72.222 4.92 0.00 0.00 5.19
1306 1381 4.079850 CTGCTCAGCGCCTCCACT 62.080 66.667 2.29 0.00 38.05 4.00
1747 1822 3.109547 GACGACGCCATCAACGCA 61.110 61.111 0.00 0.00 0.00 5.24
1822 1897 4.682714 TGGGAGAGGGGCAAGGCT 62.683 66.667 0.00 0.00 0.00 4.58
1861 1936 3.753434 CTGGCTGTCCTCGTCGCT 61.753 66.667 0.00 0.00 0.00 4.93
1865 1940 4.838486 CTGTCCTCGTCGCTCGCC 62.838 72.222 0.00 0.00 39.67 5.54
1867 1942 4.194720 GTCCTCGTCGCTCGCCAT 62.195 66.667 0.00 0.00 39.67 4.40
1870 1945 4.498520 CTCGTCGCTCGCCATGGT 62.499 66.667 14.67 0.00 39.67 3.55
1873 1948 3.188786 GTCGCTCGCCATGGTGTC 61.189 66.667 24.28 15.89 0.00 3.67
1876 1951 2.265739 GCTCGCCATGGTGTCTCA 59.734 61.111 24.28 4.70 0.00 3.27
2059 2134 4.664677 GGCGACCTCGTGTGCACT 62.665 66.667 19.41 0.00 42.22 4.40
2205 2280 4.410492 GCAATGGCTATATGCTGTACAC 57.590 45.455 0.00 0.00 42.39 2.90
2215 2290 4.814294 CTGTACACCGGCGGGCTC 62.814 72.222 31.78 17.14 36.48 4.70
2608 2731 5.741011 AGTTCACCAAAAGTAGACACTTGA 58.259 37.500 0.00 0.00 44.41 3.02
2610 2733 6.483640 AGTTCACCAAAAGTAGACACTTGATC 59.516 38.462 0.00 0.00 44.41 2.92
2614 2737 4.938226 CCAAAAGTAGACACTTGATCCCTC 59.062 45.833 0.00 0.00 44.41 4.30
2630 2753 5.481473 TGATCCCTCAAGAATTTTTGGAAGG 59.519 40.000 8.70 8.69 0.00 3.46
2631 2754 3.578282 TCCCTCAAGAATTTTTGGAAGGC 59.422 43.478 8.70 0.00 0.00 4.35
2646 2769 2.247358 GAAGGCATTTGGTCCCTCAAA 58.753 47.619 0.00 0.00 40.37 2.69
2650 2773 2.833943 GGCATTTGGTCCCTCAAATCTT 59.166 45.455 0.00 0.00 43.16 2.40
2657 2780 5.068215 TGGTCCCTCAAATCTTAAAACCA 57.932 39.130 0.00 0.00 32.13 3.67
2658 2781 5.459505 TGGTCCCTCAAATCTTAAAACCAA 58.540 37.500 0.00 0.00 31.67 3.67
2695 4177 7.327214 TCAAAACCAGATTTAAGTGCAAAACT 58.673 30.769 0.00 0.00 42.60 2.66
2718 4200 0.314935 CACATGGCAGCGGTTTTCTT 59.685 50.000 0.00 0.00 0.00 2.52
2773 4259 5.123344 GTCAAACTAATGCCTTACATTCCGT 59.877 40.000 0.00 0.00 46.28 4.69
2785 4271 2.650322 ACATTCCGTCTCCTCTCTCTC 58.350 52.381 0.00 0.00 0.00 3.20
2787 4273 2.411628 TTCCGTCTCCTCTCTCTCTG 57.588 55.000 0.00 0.00 0.00 3.35
2791 4277 1.745827 CGTCTCCTCTCTCTCTGTCCC 60.746 61.905 0.00 0.00 0.00 4.46
2835 4321 3.314331 CGGCCAGTCTGAGGTGGT 61.314 66.667 2.24 0.00 36.10 4.16
2862 5565 0.538584 CAGCTGTATCTGGCCTCACA 59.461 55.000 5.25 1.56 0.00 3.58
2886 5589 0.880278 GCTCGACCTTGCAGTTCACA 60.880 55.000 0.00 0.00 0.00 3.58
2964 5670 4.652131 TGCCCATTTGGTCGCCGT 62.652 61.111 0.00 0.00 36.04 5.68
3008 5714 3.161450 AGTGTGGTGTCACCGGCT 61.161 61.111 17.27 11.50 42.58 5.52
3043 5749 1.188219 ACAGCACCTCGTCAGACCAT 61.188 55.000 0.00 0.00 0.00 3.55
3048 5754 1.205655 CACCTCGTCAGACCATGATGT 59.794 52.381 0.00 0.00 44.14 3.06
3050 5756 1.205655 CCTCGTCAGACCATGATGTGT 59.794 52.381 0.00 0.00 44.14 3.72
3054 5760 1.995484 GTCAGACCATGATGTGTGACG 59.005 52.381 13.83 0.00 45.67 4.35
3055 5761 1.066929 TCAGACCATGATGTGTGACGG 60.067 52.381 0.00 0.00 34.02 4.79
3106 5812 2.528127 TTGGGTCCGAGGAAGCCA 60.528 61.111 7.92 7.92 42.31 4.75
3110 5816 1.375326 GGTCCGAGGAAGCCACTTT 59.625 57.895 0.00 0.00 0.00 2.66
3128 5834 4.559063 CCGATGCAGCAGAGGGGG 62.559 72.222 1.53 0.00 0.00 5.40
3129 5835 3.473647 CGATGCAGCAGAGGGGGA 61.474 66.667 1.53 0.00 0.00 4.81
3179 5939 3.239464 TGCTGTGGCAGAGACCAA 58.761 55.556 16.83 0.00 44.28 3.67
3201 5961 1.285078 GGAAGGGAGCAATGTAAGGGT 59.715 52.381 0.00 0.00 0.00 4.34
3226 5986 1.143183 GCAGGAGCCGAATTCCGTA 59.857 57.895 0.00 0.00 39.77 4.02
3251 6011 2.959599 GTGAGCGCGACACACACA 60.960 61.111 26.61 4.66 39.43 3.72
3260 6020 1.733526 GACACACACAAAGGGGCAC 59.266 57.895 0.00 0.00 0.00 5.01
3276 6036 4.626081 ACTGCGGCTTGCCTTCGT 62.626 61.111 10.12 0.95 45.60 3.85
3278 6038 4.617520 TGCGGCTTGCCTTCGTCA 62.618 61.111 10.12 0.00 45.60 4.35
3307 6067 1.954146 GTCGAGCTTGCCGTCAACA 60.954 57.895 0.00 0.00 0.00 3.33
3316 6076 3.157680 CCGTCAACAGGAAGGGGT 58.842 61.111 0.00 0.00 41.01 4.95
3416 6176 1.199558 GCGGATCCGACCAGTAGATAC 59.800 57.143 37.64 11.24 42.83 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.678627 CGGAACCACCAACATTGACAA 59.321 47.619 0.00 0.00 38.90 3.18
10 11 0.541764 ATGCCGGAACCACCAACATT 60.542 50.000 5.05 0.00 38.90 2.71
11 12 1.076549 ATGCCGGAACCACCAACAT 59.923 52.632 5.05 0.00 38.90 2.71
14 15 1.303236 CTCATGCCGGAACCACCAA 60.303 57.895 5.05 0.00 38.90 3.67
15 16 2.350895 CTCATGCCGGAACCACCA 59.649 61.111 5.05 0.00 38.90 4.17
36 37 2.866085 ATCAGCAGGAGAGCAACGCC 62.866 60.000 0.00 0.00 38.77 5.68
37 38 1.427592 GATCAGCAGGAGAGCAACGC 61.428 60.000 0.00 0.00 36.85 4.84
57 58 0.828022 AAACCATGAGCGGATCCGTA 59.172 50.000 33.33 20.88 42.09 4.02
65 66 0.394216 TGGGATCCAAACCATGAGCG 60.394 55.000 15.23 0.00 0.00 5.03
66 67 1.396653 CTGGGATCCAAACCATGAGC 58.603 55.000 15.23 0.00 35.93 4.26
67 68 1.410648 CCCTGGGATCCAAACCATGAG 60.411 57.143 15.23 0.00 35.93 2.90
68 69 0.630673 CCCTGGGATCCAAACCATGA 59.369 55.000 15.23 0.00 35.93 3.07
69 70 1.044790 GCCCTGGGATCCAAACCATG 61.045 60.000 19.27 0.00 35.93 3.66
70 71 1.311059 GCCCTGGGATCCAAACCAT 59.689 57.895 19.27 0.00 35.93 3.55
73 74 2.440247 CGGCCCTGGGATCCAAAC 60.440 66.667 19.27 0.00 30.80 2.93
101 102 0.606401 AAACATCCCACAGACTGCCG 60.606 55.000 1.25 0.00 0.00 5.69
103 104 2.622942 TCAAAAACATCCCACAGACTGC 59.377 45.455 1.25 0.00 0.00 4.40
105 106 3.632145 GTGTCAAAAACATCCCACAGACT 59.368 43.478 0.00 0.00 40.80 3.24
106 107 3.548014 CGTGTCAAAAACATCCCACAGAC 60.548 47.826 0.00 0.00 40.80 3.51
118 119 2.011222 GAGACCCACACGTGTCAAAAA 58.989 47.619 20.49 0.00 33.89 1.94
122 123 2.852180 CGGAGACCCACACGTGTCA 61.852 63.158 20.49 0.00 33.89 3.58
124 125 1.469335 ATTCGGAGACCCACACGTGT 61.469 55.000 17.22 17.22 34.32 4.49
125 126 0.736325 GATTCGGAGACCCACACGTG 60.736 60.000 15.48 15.48 34.32 4.49
126 127 1.590147 GATTCGGAGACCCACACGT 59.410 57.895 0.00 0.00 34.32 4.49
130 131 1.144057 ATGCGATTCGGAGACCCAC 59.856 57.895 8.34 0.00 34.32 4.61
140 141 4.450419 AGGATCGAAGAAATCATGCGATTC 59.550 41.667 0.00 0.00 41.12 2.52
141 142 4.384056 AGGATCGAAGAAATCATGCGATT 58.616 39.130 0.00 0.00 43.94 3.34
192 193 3.999663 GGATGATACTCACAAGGCATAGC 59.000 47.826 0.00 0.00 0.00 2.97
196 197 3.378512 AGAGGATGATACTCACAAGGCA 58.621 45.455 7.53 0.00 37.43 4.75
198 199 4.222336 AGGAGAGGATGATACTCACAAGG 58.778 47.826 7.53 0.00 37.43 3.61
212 213 0.838608 GACGTAGAGGGAGGAGAGGA 59.161 60.000 0.00 0.00 0.00 3.71
217 218 1.077930 CCACGACGTAGAGGGAGGA 60.078 63.158 0.00 0.00 0.00 3.71
232 233 2.315386 GGAAACTCGTCGGTGCCAC 61.315 63.158 0.00 0.00 0.00 5.01
236 237 0.037697 TGATGGGAAACTCGTCGGTG 60.038 55.000 0.00 0.00 0.00 4.94
237 238 0.246635 CTGATGGGAAACTCGTCGGT 59.753 55.000 0.00 0.00 0.00 4.69
248 249 2.441348 TCTACGCCGCTGATGGGA 60.441 61.111 0.00 0.00 0.00 4.37
262 263 1.611261 CACCGGGACCCAACCTCTA 60.611 63.158 12.15 0.00 0.00 2.43
263 264 2.928396 CACCGGGACCCAACCTCT 60.928 66.667 12.15 0.00 0.00 3.69
276 277 0.100682 CGACCCTCACTATCACACCG 59.899 60.000 0.00 0.00 0.00 4.94
289 290 2.043227 GGAAATCCAGAGATCGACCCT 58.957 52.381 0.00 0.00 35.64 4.34
292 293 2.099263 TCACGGAAATCCAGAGATCGAC 59.901 50.000 0.00 0.00 35.14 4.20
293 294 2.375146 TCACGGAAATCCAGAGATCGA 58.625 47.619 0.00 0.00 35.14 3.59
294 295 2.871182 TCACGGAAATCCAGAGATCG 57.129 50.000 0.00 0.00 35.14 3.69
295 296 4.392921 TCTTCACGGAAATCCAGAGATC 57.607 45.455 0.00 0.00 35.14 2.75
296 297 5.363939 GAATCTTCACGGAAATCCAGAGAT 58.636 41.667 0.00 0.23 35.14 2.75
297 298 4.678044 CGAATCTTCACGGAAATCCAGAGA 60.678 45.833 0.00 0.00 35.14 3.10
298 299 3.553511 CGAATCTTCACGGAAATCCAGAG 59.446 47.826 0.00 0.00 35.14 3.35
299 300 3.056107 ACGAATCTTCACGGAAATCCAGA 60.056 43.478 0.00 0.00 35.14 3.86
309 310 2.505498 CCGCCGACGAATCTTCACG 61.505 63.158 0.00 0.00 43.93 4.35
363 372 1.605712 GGACTCGAAGTCACCAACCTG 60.606 57.143 14.26 0.00 46.79 4.00
378 387 2.747989 TGTAGACAGTCATGACGGACTC 59.252 50.000 29.18 18.08 46.05 3.36
390 399 2.303022 CCAACACCCTCATGTAGACAGT 59.697 50.000 0.00 0.00 30.75 3.55
400 409 2.528818 CCTGGAGCCAACACCCTCA 61.529 63.158 0.00 0.00 0.00 3.86
401 410 2.190488 CTCCTGGAGCCAACACCCTC 62.190 65.000 11.42 0.00 0.00 4.30
448 457 2.093128 ACCACATTAGTTGGATCGGGTC 60.093 50.000 0.00 0.00 0.00 4.46
454 463 4.819105 TCGAAGACCACATTAGTTGGAT 57.181 40.909 0.00 0.00 0.00 3.41
458 467 5.407407 ACTCATCGAAGACCACATTAGTT 57.593 39.130 0.00 0.00 42.51 2.24
459 468 5.171476 CAACTCATCGAAGACCACATTAGT 58.829 41.667 0.00 0.00 42.51 2.24
461 470 5.047306 AGACAACTCATCGAAGACCACATTA 60.047 40.000 0.00 0.00 42.51 1.90
463 472 3.259374 AGACAACTCATCGAAGACCACAT 59.741 43.478 0.00 0.00 42.51 3.21
563 572 4.816385 GCGAAAAGGACCTCATGAATATGA 59.184 41.667 0.00 0.00 40.92 2.15
564 573 4.319046 CGCGAAAAGGACCTCATGAATATG 60.319 45.833 0.00 0.00 35.57 1.78
565 574 3.809832 CGCGAAAAGGACCTCATGAATAT 59.190 43.478 0.00 0.00 0.00 1.28
566 575 3.118920 TCGCGAAAAGGACCTCATGAATA 60.119 43.478 6.20 0.00 0.00 1.75
567 576 2.009774 CGCGAAAAGGACCTCATGAAT 58.990 47.619 0.00 0.00 0.00 2.57
568 577 1.001520 TCGCGAAAAGGACCTCATGAA 59.998 47.619 6.20 0.00 0.00 2.57
596 605 9.652114 AGCCTTCTGATCCAAAATATTTTCTAT 57.348 29.630 10.53 7.25 0.00 1.98
598 607 7.968014 AGCCTTCTGATCCAAAATATTTTCT 57.032 32.000 10.53 0.00 0.00 2.52
606 615 7.861629 TCTATCTTTAGCCTTCTGATCCAAAA 58.138 34.615 0.00 0.00 0.00 2.44
610 619 8.916628 AAAATCTATCTTTAGCCTTCTGATCC 57.083 34.615 0.00 0.00 0.00 3.36
751 760 0.529555 GGAGCAGAGAATCGTCAGCC 60.530 60.000 0.00 0.00 42.67 4.85
834 855 5.684550 AGAAAAGTTTAAAGGCGATCGTT 57.315 34.783 17.81 5.82 0.00 3.85
1004 1076 1.535204 ATGGCTGGTTTTCTTGGCGG 61.535 55.000 0.00 0.00 0.00 6.13
1084 1156 3.773154 GAGGAGGGGAGGGAGGCT 61.773 72.222 0.00 0.00 0.00 4.58
1336 1411 4.856607 GCGAAGAGGCGGAGGTCG 62.857 72.222 0.00 0.00 42.76 4.79
1861 1936 4.939399 CATGAGACACCATGGCGA 57.061 55.556 13.04 0.00 40.04 5.54
1865 1940 0.729116 GCGTTCCATGAGACACCATG 59.271 55.000 0.00 0.00 42.58 3.66
1867 1942 1.003839 GGCGTTCCATGAGACACCA 60.004 57.895 0.00 0.00 0.00 4.17
1870 1945 1.080093 GACGGCGTTCCATGAGACA 60.080 57.895 16.19 0.00 0.00 3.41
1873 1948 3.554692 GCGACGGCGTTCCATGAG 61.555 66.667 16.19 1.28 40.36 2.90
2068 2143 0.670546 ACAAGCCGATGGTCTTGTCG 60.671 55.000 15.28 0.00 42.04 4.35
2198 2273 4.814294 GAGCCCGCCGGTGTACAG 62.814 72.222 15.14 0.00 0.00 2.74
2215 2290 2.528125 CAGACTCTGATGCTCTTGTCG 58.472 52.381 0.00 0.00 32.44 4.35
2269 2344 4.368543 GCGTCCGTTTCTCCCGGT 62.369 66.667 0.00 0.00 45.63 5.28
2450 2573 3.746045 TGACTAGTTTGTGTGTCCCTC 57.254 47.619 0.00 0.00 0.00 4.30
2556 2679 6.350194 GGGACCAAACCATACTTTTCTCATTC 60.350 42.308 0.00 0.00 0.00 2.67
2560 2683 4.663334 AGGGACCAAACCATACTTTTCTC 58.337 43.478 0.00 0.00 0.00 2.87
2572 2695 1.954382 GGTGAACTTGAGGGACCAAAC 59.046 52.381 0.00 0.00 0.00 2.93
2606 2729 5.481473 CCTTCCAAAAATTCTTGAGGGATCA 59.519 40.000 0.00 0.00 0.00 2.92
2608 2731 4.223700 GCCTTCCAAAAATTCTTGAGGGAT 59.776 41.667 0.00 0.00 0.00 3.85
2610 2733 3.324556 TGCCTTCCAAAAATTCTTGAGGG 59.675 43.478 0.00 0.00 0.00 4.30
2614 2737 5.532032 ACCAAATGCCTTCCAAAAATTCTTG 59.468 36.000 0.00 0.00 0.00 3.02
2624 2747 4.863415 GGGACCAAATGCCTTCCA 57.137 55.556 0.00 0.00 35.42 3.53
2630 2753 5.659440 TTAAGATTTGAGGGACCAAATGC 57.341 39.130 6.59 0.57 44.19 3.56
2631 2754 6.873605 GGTTTTAAGATTTGAGGGACCAAATG 59.126 38.462 6.59 0.00 44.19 2.32
2667 4149 7.712264 TTGCACTTAAATCTGGTTTTGAATG 57.288 32.000 0.00 0.00 0.00 2.67
2668 4150 8.611757 GTTTTGCACTTAAATCTGGTTTTGAAT 58.388 29.630 0.00 0.00 0.00 2.57
2718 4200 1.263356 CTACGTGGAAGTGGGGAGAA 58.737 55.000 0.00 0.00 0.00 2.87
2773 4259 0.544223 CGGGACAGAGAGAGAGGAGA 59.456 60.000 0.00 0.00 0.00 3.71
2830 4316 1.298014 CAGCTGAGGAAGGACCACC 59.702 63.158 8.42 0.00 42.04 4.61
2832 4318 2.111384 GATACAGCTGAGGAAGGACCA 58.889 52.381 23.35 0.00 42.04 4.02
2835 4321 2.392662 CCAGATACAGCTGAGGAAGGA 58.607 52.381 23.35 0.00 38.14 3.36
2862 5565 1.140589 CTGCAAGGTCGAGCGAGAT 59.859 57.895 9.28 0.00 0.00 2.75
2886 5589 1.412079 CAGCTAGGAGATGCTCACCT 58.588 55.000 7.18 7.18 40.59 4.00
3027 5733 0.176680 ATCATGGTCTGACGAGGTGC 59.823 55.000 4.48 0.00 36.48 5.01
3043 5749 3.621805 ACCCGCCGTCACACATCA 61.622 61.111 0.00 0.00 0.00 3.07
3048 5754 4.595538 GTCACACCCGCCGTCACA 62.596 66.667 0.00 0.00 0.00 3.58
3054 5760 4.736896 GACGAGGTCACACCCGCC 62.737 72.222 0.00 0.00 39.75 6.13
3055 5761 4.736896 GGACGAGGTCACACCCGC 62.737 72.222 0.00 0.00 39.75 6.13
3106 5812 0.392193 CCTCTGCTGCATCGGAAAGT 60.392 55.000 1.31 0.00 0.00 2.66
3110 5816 3.473647 CCCCTCTGCTGCATCGGA 61.474 66.667 16.19 0.00 0.00 4.55
3128 5834 2.190578 CCCCAACGAGCCTCCATC 59.809 66.667 0.00 0.00 0.00 3.51
3129 5835 3.411517 CCCCCAACGAGCCTCCAT 61.412 66.667 0.00 0.00 0.00 3.41
3169 5929 1.201429 TCCCTTCCCTTGGTCTCTGC 61.201 60.000 0.00 0.00 0.00 4.26
3171 5931 0.912006 GCTCCCTTCCCTTGGTCTCT 60.912 60.000 0.00 0.00 0.00 3.10
3179 5939 1.566231 CCTTACATTGCTCCCTTCCCT 59.434 52.381 0.00 0.00 0.00 4.20
3251 6011 4.603535 AAGCCGCAGTGCCCCTTT 62.604 61.111 10.11 0.00 0.00 3.11
3260 6020 3.793144 GACGAAGGCAAGCCGCAG 61.793 66.667 5.28 3.50 45.17 5.18
3276 6036 2.881734 AGCTCGACCATAGGATGATGA 58.118 47.619 0.00 0.00 0.00 2.92
3278 6038 2.289320 GCAAGCTCGACCATAGGATGAT 60.289 50.000 0.00 0.00 0.00 2.45
3307 6067 2.231380 ACCATGCGAACCCCTTCCT 61.231 57.895 0.00 0.00 0.00 3.36
3335 6095 0.176449 CCTCGATCTCACACATGCCA 59.824 55.000 0.00 0.00 0.00 4.92
3339 6099 2.092158 TCTCTCCCTCGATCTCACACAT 60.092 50.000 0.00 0.00 0.00 3.21
3383 6143 1.514678 GATCCGCAGCACCAACAACA 61.515 55.000 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.