Multiple sequence alignment - TraesCS2B01G092100

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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 TraesCS2B01G092100 chr2B 100.000 3518 0 0 1 3518 53054585 53058102 0.000000e+00 6497.0
1 TraesCS2B01G092100 chr2B 87.366 1401 163 12 993 2382 53046044 53047441 0.000000e+00 1594.0
2 TraesCS2B01G092100 chr2B 85.999 1407 159 20 1007 2382 53084502 53085901 0.000000e+00 1472.0
3 TraesCS2B01G092100 chr2B 84.248 838 107 9 1545 2382 53199901 53200713 0.000000e+00 793.0
4 TraesCS2B01G092100 chr2B 83.771 838 111 9 1545 2382 53221878 53222690 0.000000e+00 771.0
5 TraesCS2B01G092100 chr2B 85.694 692 99 0 1691 2382 53309181 53309872 0.000000e+00 730.0
6 TraesCS2B01G092100 chr2B 85.993 564 55 14 1007 1549 53198921 53199481 1.820000e-162 582.0
7 TraesCS2B01G092100 chr2B 85.993 564 55 14 1007 1549 53220898 53221458 1.820000e-162 582.0
8 TraesCS2B01G092100 chr2B 86.468 436 59 0 2764 3199 53056330 53056765 2.460000e-131 479.0
9 TraesCS2B01G092100 chr2B 86.468 436 59 0 1746 2181 53057348 53057783 2.460000e-131 479.0
10 TraesCS2B01G092100 chr2B 85.779 443 61 2 2764 3205 53046805 53047246 5.320000e-128 468.0
11 TraesCS2B01G092100 chr2B 92.593 324 23 1 2385 2708 801139805 801139483 6.880000e-127 464.0
12 TraesCS2B01G092100 chr2B 82.692 312 47 6 3209 3518 53103092 53103398 1.610000e-68 270.0
13 TraesCS2B01G092100 chr2B 82.315 311 50 4 3209 3518 53238284 53238590 7.490000e-67 265.0
14 TraesCS2B01G092100 chr2B 82.315 311 50 4 3209 3518 53311822 53312128 7.490000e-67 265.0
15 TraesCS2B01G092100 chr2A 92.510 2817 166 18 741 3518 35474036 35476846 0.000000e+00 3991.0
16 TraesCS2B01G092100 chr2A 88.307 1394 152 9 993 2381 35384275 35385662 0.000000e+00 1661.0
17 TraesCS2B01G092100 chr2A 87.640 445 53 2 2764 3207 35385027 35385470 1.870000e-142 516.0
18 TraesCS2B01G092100 chr2A 87.727 440 54 0 2764 3203 35475068 35475507 6.730000e-142 514.0
19 TraesCS2B01G092100 chr2A 86.697 436 58 0 1746 2181 35476092 35476527 5.280000e-133 484.0
20 TraesCS2B01G092100 chr2A 87.393 349 40 4 350 697 35471662 35472007 7.080000e-107 398.0
21 TraesCS2B01G092100 chr2D 90.323 1860 121 26 1 1811 32408143 32409992 0.000000e+00 2383.0
22 TraesCS2B01G092100 chr2D 87.866 1401 153 13 993 2382 32400759 32402153 0.000000e+00 1629.0
23 TraesCS2B01G092100 chr2D 87.262 1209 122 19 1007 2188 32427406 32428609 0.000000e+00 1351.0
24 TraesCS2B01G092100 chr2D 91.329 692 58 2 2828 3518 32410214 32410904 0.000000e+00 944.0
25 TraesCS2B01G092100 chr2D 86.486 444 60 0 2764 3207 32401517 32401960 4.080000e-134 488.0
26 TraesCS2B01G092100 chr2D 86.744 430 51 5 2764 3188 32428163 32428591 1.140000e-129 473.0
27 TraesCS2B01G092100 chr2D 86.538 208 28 0 2175 2382 32429096 32429303 2.730000e-56 230.0
28 TraesCS2B01G092100 chr2D 78.539 219 34 5 3196 3413 32403121 32403327 7.920000e-27 132.0
29 TraesCS2B01G092100 chr3B 87.781 311 38 0 348 658 5082315 5082005 7.180000e-97 364.0
30 TraesCS2B01G092100 chr3B 87.460 311 36 1 348 658 4226919 4226612 4.320000e-94 355.0
31 TraesCS2B01G092100 chr7D 90.217 184 14 2 348 531 43197481 43197660 1.630000e-58 237.0
32 TraesCS2B01G092100 chr1D 74.306 288 65 8 33 316 409070881 409071163 2.870000e-21 113.0
33 TraesCS2B01G092100 chr5A 77.941 136 25 5 10 143 520465877 520466009 2.910000e-11 80.5
34 TraesCS2B01G092100 chr4D 75.429 175 32 10 24 196 68698901 68699066 1.350000e-09 75.0
35 TraesCS2B01G092100 chr1A 90.698 43 3 1 370 411 580431859 580431817 4.910000e-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 TraesCS2B01G092100 chr2B 53054585 53058102 3517 False 2485.000000 6497 90.978667 1 3518 3 chr2B.!!$F5 3517
1 TraesCS2B01G092100 chr2B 53084502 53085901 1399 False 1472.000000 1472 85.999000 1007 2382 1 chr2B.!!$F1 1375
2 TraesCS2B01G092100 chr2B 53046044 53047441 1397 False 1031.000000 1594 86.572500 993 3205 2 chr2B.!!$F4 2212
3 TraesCS2B01G092100 chr2B 53198921 53200713 1792 False 687.500000 793 85.120500 1007 2382 2 chr2B.!!$F6 1375
4 TraesCS2B01G092100 chr2B 53220898 53222690 1792 False 676.500000 771 84.882000 1007 2382 2 chr2B.!!$F7 1375
5 TraesCS2B01G092100 chr2B 53309181 53312128 2947 False 497.500000 730 84.004500 1691 3518 2 chr2B.!!$F8 1827
6 TraesCS2B01G092100 chr2A 35471662 35476846 5184 False 1346.750000 3991 88.581750 350 3518 4 chr2A.!!$F2 3168
7 TraesCS2B01G092100 chr2A 35384275 35385662 1387 False 1088.500000 1661 87.973500 993 3207 2 chr2A.!!$F1 2214
8 TraesCS2B01G092100 chr2D 32408143 32410904 2761 False 1663.500000 2383 90.826000 1 3518 2 chr2D.!!$F2 3517
9 TraesCS2B01G092100 chr2D 32400759 32403327 2568 False 749.666667 1629 84.297000 993 3413 3 chr2D.!!$F1 2420
10 TraesCS2B01G092100 chr2D 32427406 32429303 1897 False 684.666667 1351 86.848000 1007 3188 3 chr2D.!!$F3 2181

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
697 701 0.105964 AACTGGCAACGCAGTGAGTA 59.894 50.0 0.0 0.0 45.0 2.59 F
763 2761 0.107945 GCAGCCCACGAGAAGAGATT 60.108 55.0 0.0 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 4213 0.692419 AGATGGGGCTCCTCGATGTT 60.692 55.0 3.07 0.0 0.0 2.71 R
2714 7540 0.466922 GGTGATGGATTGGCTCTGGG 60.467 60.0 0.00 0.0 0.0 4.45 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
21 22 3.347077 AAGAGCAGCTCTAGCAAATGT 57.653 42.857 25.66 4.15 40.28 2.71
23 24 2.027377 AGAGCAGCTCTAGCAAATGTGT 60.027 45.455 24.25 0.00 45.16 3.72
31 32 6.018913 CAGCTCTAGCAAATGTGTTATCTCAG 60.019 42.308 4.54 0.00 45.16 3.35
36 37 1.290203 AATGTGTTATCTCAGCGCCG 58.710 50.000 2.29 0.00 0.00 6.46
61 62 4.770010 CCCATATATTTGCGGGTGGTTTAT 59.230 41.667 0.00 0.00 33.67 1.40
70 71 2.030981 GCGGGTGGTTTATTGTTTTCGA 60.031 45.455 0.00 0.00 0.00 3.71
75 76 6.348704 CGGGTGGTTTATTGTTTTCGAGTTAT 60.349 38.462 0.00 0.00 0.00 1.89
83 84 4.759516 TGTTTTCGAGTTATTTCAGGCC 57.240 40.909 0.00 0.00 0.00 5.19
95 96 2.315925 TTCAGGCCAGAATAGAAGCG 57.684 50.000 6.46 0.00 0.00 4.68
96 97 0.465705 TCAGGCCAGAATAGAAGCGG 59.534 55.000 5.01 0.00 0.00 5.52
150 151 4.614036 CCCGCAAACCACCCCCTT 62.614 66.667 0.00 0.00 0.00 3.95
196 198 3.017442 GGCATTTTAGGGTTCCTGTCTC 58.983 50.000 0.00 0.00 34.61 3.36
202 204 2.777459 AGGGTTCCTGTCTCGGATAT 57.223 50.000 0.00 0.00 32.02 1.63
205 207 4.753186 AGGGTTCCTGTCTCGGATATATT 58.247 43.478 0.00 0.00 32.02 1.28
207 209 4.527038 GGGTTCCTGTCTCGGATATATTCA 59.473 45.833 0.00 0.00 32.02 2.57
209 211 6.102663 GGTTCCTGTCTCGGATATATTCATG 58.897 44.000 0.00 0.00 32.02 3.07
241 243 1.636769 AATCTTCTTCCCCTCCGCCC 61.637 60.000 0.00 0.00 0.00 6.13
261 263 3.370527 CCCCAATCTTTTCTTAGCTCCGA 60.371 47.826 0.00 0.00 0.00 4.55
274 276 2.748647 TCCGACGAGTGCATCCGA 60.749 61.111 15.88 0.00 0.00 4.55
284 286 1.673009 TGCATCCGACCGTTTTCCC 60.673 57.895 0.00 0.00 0.00 3.97
303 305 2.441001 CCCCCTGTCAAGCTTAGATCAT 59.559 50.000 0.00 0.00 0.00 2.45
309 311 3.447229 TGTCAAGCTTAGATCATGTCGGA 59.553 43.478 0.00 0.00 0.00 4.55
316 318 4.626042 CTTAGATCATGTCGGAAGAAGGG 58.374 47.826 0.00 0.00 45.01 3.95
317 319 2.472029 AGATCATGTCGGAAGAAGGGT 58.528 47.619 0.00 0.00 45.01 4.34
322 324 3.702048 TCGGAAGAAGGGTGCGGG 61.702 66.667 0.00 0.00 37.03 6.13
326 328 3.305177 GAAGAAGGGTGCGGGCGTA 62.305 63.158 0.00 0.00 0.00 4.42
327 329 3.310860 AAGAAGGGTGCGGGCGTAG 62.311 63.158 0.00 0.00 0.00 3.51
370 372 5.011227 TGGGGTTAAACCAAGCTTTATTGAC 59.989 40.000 12.67 0.00 41.02 3.18
414 418 4.879295 ACAAATAGGATCATGGGGTTCA 57.121 40.909 0.00 0.00 0.00 3.18
420 424 2.315763 AGGATCATGGGGTTCAACCAAT 59.684 45.455 9.35 0.00 41.02 3.16
433 437 0.516877 AACCAATCATGTGTGTCGCG 59.483 50.000 0.00 0.00 0.00 5.87
434 438 0.602638 ACCAATCATGTGTGTCGCGT 60.603 50.000 5.77 0.00 0.00 6.01
436 440 0.789601 CAATCATGTGTGTCGCGTCA 59.210 50.000 5.77 3.17 0.00 4.35
443 447 0.666274 GTGTGTCGCGTCAGATCCAA 60.666 55.000 6.22 0.00 0.00 3.53
450 454 1.267732 CGCGTCAGATCCAAAGAATGC 60.268 52.381 0.00 0.00 0.00 3.56
457 461 4.518590 TCAGATCCAAAGAATGCGAAAACA 59.481 37.500 0.00 0.00 0.00 2.83
464 468 4.989279 AAGAATGCGAAAACATGGCTAT 57.011 36.364 0.00 0.00 33.29 2.97
475 479 3.977134 ACATGGCTATCCTATCTGCAG 57.023 47.619 7.63 7.63 0.00 4.41
622 626 4.963276 TTGGAGTCCAAAGCAATAATCG 57.037 40.909 22.59 0.00 40.92 3.34
629 633 8.617809 GGAGTCCAAAGCAATAATCGTATTTTA 58.382 33.333 3.60 0.00 0.00 1.52
659 663 2.642154 TCCTCGGCCAAACAAAGTAA 57.358 45.000 2.24 0.00 0.00 2.24
660 664 2.933573 TCCTCGGCCAAACAAAGTAAA 58.066 42.857 2.24 0.00 0.00 2.01
697 701 0.105964 AACTGGCAACGCAGTGAGTA 59.894 50.000 0.00 0.00 45.00 2.59
702 706 0.729116 GCAACGCAGTGAGTATGCAT 59.271 50.000 20.50 3.79 45.00 3.96
703 707 1.530441 GCAACGCAGTGAGTATGCATG 60.530 52.381 20.50 9.32 45.00 4.06
704 708 1.063027 CAACGCAGTGAGTATGCATGG 59.937 52.381 10.16 0.00 45.00 3.66
705 709 1.091771 ACGCAGTGAGTATGCATGGC 61.092 55.000 10.16 1.92 44.05 4.40
706 710 1.091197 CGCAGTGAGTATGCATGGCA 61.091 55.000 10.16 1.42 44.05 4.92
708 712 1.065102 GCAGTGAGTATGCATGGCAAG 59.935 52.381 10.16 2.65 43.62 4.01
729 750 4.408821 TGACAGACATGGGGCGGC 62.409 66.667 0.00 0.00 0.00 6.53
763 2761 0.107945 GCAGCCCACGAGAAGAGATT 60.108 55.000 0.00 0.00 0.00 2.40
767 2765 1.066143 GCCCACGAGAAGAGATTGGAA 60.066 52.381 0.00 0.00 0.00 3.53
771 2769 4.702131 CCCACGAGAAGAGATTGGAAATTT 59.298 41.667 0.00 0.00 0.00 1.82
787 2785 0.168128 ATTTCACGTTTAGCGGCTGC 59.832 50.000 13.86 10.33 46.52 5.25
878 2876 1.521457 GCCGCCATCACATCTCGAA 60.521 57.895 0.00 0.00 0.00 3.71
893 2891 4.602340 TCTCGAAGGAGCTTACAGTTTT 57.398 40.909 0.00 0.00 40.26 2.43
894 2892 4.957296 TCTCGAAGGAGCTTACAGTTTTT 58.043 39.130 0.00 0.00 40.26 1.94
895 2893 6.092955 TCTCGAAGGAGCTTACAGTTTTTA 57.907 37.500 0.00 0.00 40.26 1.52
956 2959 1.519455 CCCGCGAGATCAGACCAAC 60.519 63.158 8.23 0.00 0.00 3.77
959 2962 0.171231 CGCGAGATCAGACCAACTCA 59.829 55.000 0.00 0.00 0.00 3.41
1004 3033 2.856032 CGATTCGATCGCCATGGC 59.144 61.111 27.67 27.67 46.55 4.40
1005 3034 1.955663 CGATTCGATCGCCATGGCA 60.956 57.895 34.93 22.41 46.55 4.92
1020 3051 2.161486 GGCAGCTGATCACGTCGTC 61.161 63.158 20.43 0.00 0.00 4.20
1021 3052 1.153939 GCAGCTGATCACGTCGTCT 60.154 57.895 20.43 0.00 0.00 4.18
1034 3065 1.574134 GTCGTCTTGTTCCCGTTCAA 58.426 50.000 0.00 0.00 0.00 2.69
1035 3066 2.140717 GTCGTCTTGTTCCCGTTCAAT 58.859 47.619 0.00 0.00 0.00 2.57
1037 3068 1.196808 CGTCTTGTTCCCGTTCAATGG 59.803 52.381 0.00 0.00 0.00 3.16
1434 3477 3.380004 CACTCTACTTCTCGCTCTGGAAT 59.620 47.826 0.00 0.00 0.00 3.01
1468 3523 2.865603 CAGACGACGACGAGTGCG 60.866 66.667 15.32 2.20 42.66 5.34
1576 4055 0.679002 CACCTTCATCCACAGGCAGG 60.679 60.000 0.00 0.00 32.79 4.85
1615 4094 3.411703 GATGCGCTGCTCGTCAACG 62.412 63.158 9.73 0.00 41.07 4.10
1689 4168 1.430992 ATGTCCCGATATTCCCGGTT 58.569 50.000 0.00 0.00 45.14 4.44
1803 4282 2.855963 CTCAGTGTTGTACGTGTCGTTT 59.144 45.455 0.00 0.00 41.54 3.60
1811 4290 2.347242 TACGTGTCGTTTGGGTCGCA 62.347 55.000 0.00 0.00 41.54 5.10
1827 4306 1.138883 GCAGTACACGATCTCCGCA 59.861 57.895 0.00 0.00 43.32 5.69
1830 4309 1.065551 CAGTACACGATCTCCGCATCA 59.934 52.381 0.00 0.00 43.32 3.07
1845 4324 0.879400 CATCACAGGCGATGGAGCTC 60.879 60.000 4.71 4.71 39.33 4.09
2028 4511 4.554036 GAGATCCTGGCGCACCCC 62.554 72.222 10.83 0.00 33.59 4.95
2085 4568 2.359230 GCACAGGAAAGCCTCGCT 60.359 61.111 0.00 0.00 44.80 4.93
2169 4652 1.616628 GGAGGAGATGGGGGTGTGT 60.617 63.158 0.00 0.00 0.00 3.72
2184 5167 3.911698 TGTGTCGAGCTGGCACGT 61.912 61.111 13.64 0.00 36.04 4.49
2273 5264 0.816825 GGAGTGCGTGCCATGATGAT 60.817 55.000 0.00 0.00 0.00 2.45
2296 5287 2.298158 GAAGGCCGCGGAGATGAAGA 62.298 60.000 33.48 0.00 0.00 2.87
2310 5301 0.601057 TGAAGAAGGTGATCGACGCA 59.399 50.000 0.00 0.00 0.00 5.24
2311 5302 1.000394 TGAAGAAGGTGATCGACGCAA 60.000 47.619 0.00 0.00 0.00 4.85
2321 5312 2.149803 ATCGACGCAACGAGGGACAA 62.150 55.000 8.11 0.00 45.22 3.18
2334 5325 0.449388 GGGACAACGACGACGAGTAT 59.551 55.000 15.32 0.00 42.66 2.12
2368 5359 2.342279 CGCGGAGGTTCTTGGACA 59.658 61.111 0.00 0.00 0.00 4.02
2369 5360 1.079127 CGCGGAGGTTCTTGGACAT 60.079 57.895 0.00 0.00 0.00 3.06
2559 6396 1.272147 GGGCATGGAAGAACTGGAACT 60.272 52.381 0.00 0.00 0.00 3.01
2694 7520 9.327628 CCATGATCTATTGAGTGATTCATATCC 57.672 37.037 0.00 0.00 35.27 2.59
2701 7527 5.955961 TGAGTGATTCATATCCAGGTTCA 57.044 39.130 0.00 0.00 0.00 3.18
2714 7540 8.950210 CATATCCAGGTTCATATCATTTGGTAC 58.050 37.037 0.00 0.00 0.00 3.34
2715 7541 5.690865 TCCAGGTTCATATCATTTGGTACC 58.309 41.667 4.43 4.43 0.00 3.34
2735 7561 1.064166 CCAGAGCCAATCCATCACCTT 60.064 52.381 0.00 0.00 0.00 3.50
2737 7563 1.918262 AGAGCCAATCCATCACCTTCA 59.082 47.619 0.00 0.00 0.00 3.02
2738 7564 2.092538 AGAGCCAATCCATCACCTTCAG 60.093 50.000 0.00 0.00 0.00 3.02
2757 7583 0.613260 GCCTCCAAAATTTCCCCCAC 59.387 55.000 0.00 0.00 0.00 4.61
2772 7598 2.046285 CCACCAAACGCCCCATCTC 61.046 63.158 0.00 0.00 0.00 2.75
2798 7624 1.298859 GCTCGACAAGAAACCGCCAT 61.299 55.000 0.00 0.00 0.00 4.40
2813 7639 0.249868 GCCATGCTCGGTGCTATACA 60.250 55.000 3.53 0.00 43.37 2.29
2822 7648 2.424246 TCGGTGCTATACATGTCGTTCA 59.576 45.455 0.00 0.00 0.00 3.18
2826 7652 4.181578 GTGCTATACATGTCGTTCAGGTT 58.818 43.478 0.00 0.00 41.43 3.50
2830 7656 1.229428 ACATGTCGTTCAGGTTGCTG 58.771 50.000 0.00 0.00 37.85 4.41
2943 7769 2.049063 GAACGGCAGCGAGTCACT 60.049 61.111 0.00 0.00 0.00 3.41
2970 7796 1.578206 GGCCTTTCAGACAGGTTCGC 61.578 60.000 4.47 0.00 33.40 4.70
2993 7819 3.728373 GGATGGAGGTTGCCGGGT 61.728 66.667 2.18 0.00 0.00 5.28
3066 7894 0.610232 GCCACAGGTGCCTTCTTGAT 60.610 55.000 0.00 0.00 0.00 2.57
3084 7970 2.230664 TGCACTGAGGGTGGAACTT 58.769 52.632 0.00 0.00 43.13 2.66
3086 7972 0.179018 GCACTGAGGGTGGAACTTGT 60.179 55.000 0.00 0.00 45.44 3.16
3091 7977 1.562008 TGAGGGTGGAACTTGTCACAA 59.438 47.619 0.00 0.00 36.74 3.33
3148 8034 0.671781 CCCTCTCAGCGGAACAGTTG 60.672 60.000 0.00 0.00 0.00 3.16
3188 8074 0.541764 GGAAGAAATGGGGGTGTGCA 60.542 55.000 0.00 0.00 0.00 4.57
3270 8156 2.581354 GTCATCGCAGGCAGTCCT 59.419 61.111 0.00 0.00 45.66 3.85
3284 8170 1.556451 CAGTCCTCCATGGTGATGTGA 59.444 52.381 15.47 1.07 37.07 3.58
3343 8235 2.352814 CGTCGAGGAATTCAAGTGGAGT 60.353 50.000 7.93 0.00 0.00 3.85
3366 8258 1.272490 TGACTCGATCTCGCAAGGTTT 59.728 47.619 0.00 0.00 39.60 3.27
3421 8313 3.133003 TGGCAAGACATAAGTAGGCTCTC 59.867 47.826 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.277250 GCTGAGATAACACATTTGCTAGAGC 60.277 44.000 0.00 0.00 42.50 4.09
13 14 2.096496 GCGCTGAGATAACACATTTGCT 59.904 45.455 0.00 0.00 0.00 3.91
21 22 2.202878 GCCGGCGCTGAGATAACA 60.203 61.111 20.25 0.00 0.00 2.41
23 24 4.235762 GGGCCGGCGCTGAGATAA 62.236 66.667 34.09 0.00 34.44 1.75
31 32 1.506262 CAAATATATGGGCCGGCGC 59.494 57.895 34.64 34.64 0.00 6.53
36 37 0.887933 CACCCGCAAATATATGGGCC 59.112 55.000 0.00 0.00 46.02 5.80
61 62 4.580995 TGGCCTGAAATAACTCGAAAACAA 59.419 37.500 3.32 0.00 0.00 2.83
70 71 5.825151 GCTTCTATTCTGGCCTGAAATAACT 59.175 40.000 26.49 13.69 0.00 2.24
75 76 2.632377 CGCTTCTATTCTGGCCTGAAA 58.368 47.619 26.49 15.43 0.00 2.69
143 144 0.693092 TTATAGCGGCTGAAGGGGGT 60.693 55.000 13.86 0.00 0.00 4.95
146 147 2.607282 CGTACTTATAGCGGCTGAAGGG 60.607 54.545 22.59 12.38 0.00 3.95
150 151 0.956633 CCCGTACTTATAGCGGCTGA 59.043 55.000 13.86 0.00 43.70 4.26
196 198 4.046938 CGGAGGGACATGAATATATCCG 57.953 50.000 0.00 7.06 42.00 4.18
202 204 0.106708 GCAGCGGAGGGACATGAATA 59.893 55.000 0.00 0.00 0.00 1.75
205 207 1.913951 ATTGCAGCGGAGGGACATGA 61.914 55.000 0.00 0.00 0.00 3.07
207 209 1.153086 GATTGCAGCGGAGGGACAT 60.153 57.895 0.00 0.00 0.00 3.06
209 211 1.078143 AAGATTGCAGCGGAGGGAC 60.078 57.895 0.00 0.00 0.00 4.46
241 243 3.307242 CGTCGGAGCTAAGAAAAGATTGG 59.693 47.826 0.00 0.00 0.00 3.16
261 263 2.430382 AAACGGTCGGATGCACTCGT 62.430 55.000 9.80 2.07 0.00 4.18
274 276 0.179001 CTTGACAGGGGGAAAACGGT 60.179 55.000 0.00 0.00 0.00 4.83
284 286 4.125703 GACATGATCTAAGCTTGACAGGG 58.874 47.826 9.86 3.73 0.00 4.45
303 305 2.342279 CGCACCCTTCTTCCGACA 59.658 61.111 0.00 0.00 0.00 4.35
309 311 3.310860 CTACGCCCGCACCCTTCTT 62.311 63.158 0.00 0.00 0.00 2.52
316 318 3.228759 TATCCCCTACGCCCGCAC 61.229 66.667 0.00 0.00 0.00 5.34
317 319 3.228759 GTATCCCCTACGCCCGCA 61.229 66.667 0.00 0.00 0.00 5.69
322 324 4.466726 AGATCCTATTTGTATCCCCTACGC 59.533 45.833 0.00 0.00 32.61 4.42
323 325 6.398918 CAAGATCCTATTTGTATCCCCTACG 58.601 44.000 0.00 0.00 32.61 3.51
326 328 4.603610 CCCAAGATCCTATTTGTATCCCCT 59.396 45.833 0.00 0.00 0.00 4.79
327 329 4.263949 CCCCAAGATCCTATTTGTATCCCC 60.264 50.000 0.00 0.00 0.00 4.81
414 418 0.516877 CGCGACACACATGATTGGTT 59.483 50.000 0.00 0.00 0.00 3.67
420 424 0.243636 ATCTGACGCGACACACATGA 59.756 50.000 15.93 6.51 0.00 3.07
433 437 4.685169 TTTCGCATTCTTTGGATCTGAC 57.315 40.909 0.00 0.00 0.00 3.51
434 438 4.518590 TGTTTTCGCATTCTTTGGATCTGA 59.481 37.500 0.00 0.00 0.00 3.27
436 440 5.404946 CATGTTTTCGCATTCTTTGGATCT 58.595 37.500 0.00 0.00 0.00 2.75
443 447 4.202050 GGATAGCCATGTTTTCGCATTCTT 60.202 41.667 0.00 0.00 0.00 2.52
450 454 4.153117 GCAGATAGGATAGCCATGTTTTCG 59.847 45.833 0.00 0.00 36.29 3.46
457 461 2.027377 GTGCTGCAGATAGGATAGCCAT 60.027 50.000 20.43 0.00 36.29 4.40
464 468 3.308401 TCTAATGGTGCTGCAGATAGGA 58.692 45.455 20.43 1.27 0.00 2.94
622 626 6.533367 GCCGAGGATCTGATGATCTAAAATAC 59.467 42.308 0.00 0.00 46.18 1.89
629 633 1.265236 GGCCGAGGATCTGATGATCT 58.735 55.000 0.00 0.00 46.18 2.75
684 688 1.063027 CCATGCATACTCACTGCGTTG 59.937 52.381 0.00 0.00 42.62 4.10
697 701 0.606130 TGTCACGTCTTGCCATGCAT 60.606 50.000 0.00 0.00 38.76 3.96
702 706 0.392706 ATGTCTGTCACGTCTTGCCA 59.607 50.000 0.00 0.00 0.00 4.92
703 707 0.792640 CATGTCTGTCACGTCTTGCC 59.207 55.000 0.00 0.00 0.00 4.52
704 708 0.792640 CCATGTCTGTCACGTCTTGC 59.207 55.000 0.00 0.00 0.00 4.01
705 709 1.432514 CCCATGTCTGTCACGTCTTG 58.567 55.000 0.00 0.00 0.00 3.02
706 710 0.321671 CCCCATGTCTGTCACGTCTT 59.678 55.000 0.00 0.00 0.00 3.01
708 712 1.741770 GCCCCATGTCTGTCACGTC 60.742 63.158 0.00 0.00 0.00 4.34
729 750 3.978723 CTGCTCCGTGTCCTGCTCG 62.979 68.421 0.00 0.00 0.00 5.03
733 754 4.767255 GGGCTGCTCCGTGTCCTG 62.767 72.222 0.00 0.00 34.94 3.86
755 2753 7.271438 GCTAAACGTGAAATTTCCAATCTCTTC 59.729 37.037 15.48 0.00 0.00 2.87
756 2754 7.084486 GCTAAACGTGAAATTTCCAATCTCTT 58.916 34.615 15.48 3.21 0.00 2.85
763 2761 2.350964 GCCGCTAAACGTGAAATTTCCA 60.351 45.455 15.48 1.31 41.42 3.53
767 2765 1.401018 GCAGCCGCTAAACGTGAAATT 60.401 47.619 0.00 0.00 41.42 1.82
801 2799 4.495184 CCTCCGTGTATTTTATTGGTTCGC 60.495 45.833 0.00 0.00 0.00 4.70
809 2807 3.744530 GCTGCTCCCTCCGTGTATTTTAT 60.745 47.826 0.00 0.00 0.00 1.40
870 2868 3.791973 ACTGTAAGCTCCTTCGAGATG 57.208 47.619 0.00 0.00 34.17 2.90
878 2876 8.763601 ACATCTCTATAAAAACTGTAAGCTCCT 58.236 33.333 0.00 0.00 37.60 3.69
956 2959 2.401766 GGCAGTGCCGGTGATTGAG 61.402 63.158 20.55 0.00 39.62 3.02
976 2979 2.028125 ATCGAATCGGTGATGGCGGT 62.028 55.000 1.76 0.00 0.00 5.68
1001 3030 2.125952 CGACGTGATCAGCTGCCA 60.126 61.111 9.47 6.69 0.00 4.92
1004 3033 0.987715 CAAGACGACGTGATCAGCTG 59.012 55.000 4.58 7.63 0.00 4.24
1005 3034 0.598562 ACAAGACGACGTGATCAGCT 59.401 50.000 4.58 0.00 0.00 4.24
1211 3254 2.284798 GAAGAGGTCGATGAGCCGCA 62.285 60.000 0.00 0.00 0.00 5.69
1266 3309 2.587194 CTGAGGCCCGCGATGAAG 60.587 66.667 8.23 0.00 0.00 3.02
1312 3355 1.449601 GGAACATGTCCGCCACGAT 60.450 57.895 0.00 0.00 36.40 3.73
1734 4213 0.692419 AGATGGGGCTCCTCGATGTT 60.692 55.000 3.07 0.00 0.00 2.71
1803 4282 0.963856 AGATCGTGTACTGCGACCCA 60.964 55.000 13.53 0.00 41.33 4.51
1811 4290 1.065701 GTGATGCGGAGATCGTGTACT 59.934 52.381 0.00 0.00 41.72 2.73
1827 4306 1.445095 GAGCTCCATCGCCTGTGAT 59.555 57.895 0.87 0.00 0.00 3.06
1838 4317 4.802051 GCCCCATTGCGAGCTCCA 62.802 66.667 8.47 4.37 0.00 3.86
1845 4324 2.125147 TTCTCGAGCCCCATTGCG 60.125 61.111 7.81 0.00 36.02 4.85
2169 4652 2.566529 CTACGTGCCAGCTCGACA 59.433 61.111 19.58 6.97 36.84 4.35
2296 5287 0.732880 CTCGTTGCGTCGATCACCTT 60.733 55.000 0.00 0.00 39.12 3.50
2310 5301 1.008079 GTCGTCGTTGTCCCTCGTT 60.008 57.895 0.00 0.00 0.00 3.85
2311 5302 2.641559 GTCGTCGTTGTCCCTCGT 59.358 61.111 0.00 0.00 0.00 4.18
2334 5325 1.014044 GCGTCACTCCAAGCGATGAA 61.014 55.000 0.00 0.00 0.00 2.57
2414 5405 0.850100 TCCTTGGGCTTCACCTGAAA 59.150 50.000 0.00 0.00 39.10 2.69
2466 5457 3.403038 CTCCTCTGTGTTAAGTGGGTTG 58.597 50.000 0.00 0.00 32.69 3.77
2520 6357 1.067821 CCCTCCACGAAGATGAGTAGC 59.932 57.143 0.00 0.00 0.00 3.58
2559 6396 3.283684 CAACGGCGGCCAGTTCAA 61.284 61.111 20.71 0.00 0.00 2.69
2678 7504 6.312141 TGAACCTGGATATGAATCACTCAA 57.688 37.500 0.00 0.00 37.67 3.02
2714 7540 0.466922 GGTGATGGATTGGCTCTGGG 60.467 60.000 0.00 0.00 0.00 4.45
2715 7541 0.549950 AGGTGATGGATTGGCTCTGG 59.450 55.000 0.00 0.00 0.00 3.86
2735 7561 1.552254 GGGGGAAATTTTGGAGGCTGA 60.552 52.381 0.00 0.00 0.00 4.26
2737 7563 0.491371 TGGGGGAAATTTTGGAGGCT 59.509 50.000 0.00 0.00 0.00 4.58
2738 7564 0.613260 GTGGGGGAAATTTTGGAGGC 59.387 55.000 0.00 0.00 0.00 4.70
2757 7583 2.824041 CCGAGATGGGGCGTTTGG 60.824 66.667 0.00 0.00 0.00 3.28
2772 7598 4.717629 TCTTGTCGAGCCACGCCG 62.718 66.667 0.00 0.00 42.26 6.46
2804 7630 3.782046 ACCTGAACGACATGTATAGCAC 58.218 45.455 0.00 0.00 0.00 4.40
2813 7639 2.224185 TGTACAGCAACCTGAACGACAT 60.224 45.455 0.00 0.00 41.77 3.06
2822 7648 1.204941 GGAGATCGTGTACAGCAACCT 59.795 52.381 0.00 0.00 0.00 3.50
2826 7652 1.138883 GCGGAGATCGTGTACAGCA 59.861 57.895 0.00 0.00 41.72 4.41
2855 7681 2.592861 CCCTATTGCCAGCTCCGC 60.593 66.667 0.00 0.00 0.00 5.54
2957 7783 1.587043 CTCTCCGCGAACCTGTCTGA 61.587 60.000 8.23 0.00 0.00 3.27
2959 7785 2.344203 CCTCTCCGCGAACCTGTCT 61.344 63.158 8.23 0.00 0.00 3.41
2970 7796 1.144936 GCAACCTCCATCCTCTCCG 59.855 63.158 0.00 0.00 0.00 4.63
3066 7894 0.179020 CAAGTTCCACCCTCAGTGCA 60.179 55.000 0.00 0.00 45.83 4.57
3130 8016 0.034059 ACAACTGTTCCGCTGAGAGG 59.966 55.000 0.00 0.00 0.00 3.69
3136 8022 1.535462 GCATTGTACAACTGTTCCGCT 59.465 47.619 11.22 0.00 0.00 5.52
3148 8034 3.119849 CCACTAGCAACTTGGCATTGTAC 60.120 47.826 3.05 0.00 35.83 2.90
3270 8156 0.690192 AACGGTCACATCACCATGGA 59.310 50.000 21.47 0.00 36.01 3.41
3284 8170 0.536460 AAAGGAATGACGCCAACGGT 60.536 50.000 0.00 0.00 46.04 4.83
3343 8235 1.402852 CCTTGCGAGATCGAGTCACAA 60.403 52.381 6.39 0.00 43.02 3.33
3421 8313 2.607771 CCAAAGAACATGGCTTTCACCG 60.608 50.000 11.49 3.35 33.56 4.94
3445 8337 0.322816 ACATCGCTGGCAATGAACCT 60.323 50.000 4.73 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.