Multiple sequence alignment - TraesCS7A01G240500

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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 TraesCS7A01G240500 chr7A 100.000 3205 0 0 1 3205 215890562 215887358 0.000000e+00 5919.0
1 TraesCS7A01G240500 chr7A 95.797 571 21 3 2637 3205 423889585 423889016 0.000000e+00 918.0
2 TraesCS7A01G240500 chr7B 90.641 1357 71 20 978 2298 167750653 167749317 0.000000e+00 1751.0
3 TraesCS7A01G240500 chr7B 83.848 972 72 37 38 993 167751572 167750670 0.000000e+00 846.0
4 TraesCS7A01G240500 chr7B 96.739 92 1 2 2548 2639 167717529 167717440 5.540000e-33 152.0
5 TraesCS7A01G240500 chr7B 92.857 42 2 1 2299 2340 322889699 322889659 3.450000e-05 60.2
6 TraesCS7A01G240500 chr7B 96.875 32 0 1 2309 2340 198951325 198951355 6.000000e-03 52.8
7 TraesCS7A01G240500 chr7D 92.123 1168 63 12 1454 2610 204093268 204092119 0.000000e+00 1620.0
8 TraesCS7A01G240500 chr7D 92.756 704 38 7 839 1538 204093959 204093265 0.000000e+00 1005.0
9 TraesCS7A01G240500 chr7D 88.046 870 55 23 1 848 204095010 204094168 0.000000e+00 985.0
10 TraesCS7A01G240500 chr5A 95.431 569 23 3 2639 3205 107837996 107838563 0.000000e+00 904.0
11 TraesCS7A01G240500 chr3A 95.591 567 20 5 2639 3202 470668755 470669319 0.000000e+00 904.0
12 TraesCS7A01G240500 chr3A 95.113 573 22 5 2637 3205 180760905 180761475 0.000000e+00 898.0
13 TraesCS7A01G240500 chr3A 100.000 29 0 0 2439 2467 196764158 196764186 2.000000e-03 54.7
14 TraesCS7A01G240500 chr3A 100.000 28 0 0 2313 2340 566123571 566123598 6.000000e-03 52.8
15 TraesCS7A01G240500 chr4A 95.431 569 21 4 2639 3205 381274633 381274068 0.000000e+00 902.0
16 TraesCS7A01G240500 chr4A 95.271 571 21 6 2639 3205 48606969 48606401 0.000000e+00 900.0
17 TraesCS7A01G240500 chr2B 95.271 571 23 4 2637 3205 78843520 78842952 0.000000e+00 902.0
18 TraesCS7A01G240500 chr2B 94.872 39 2 0 2436 2474 207721584 207721546 9.600000e-06 62.1
19 TraesCS7A01G240500 chr2B 90.476 42 3 1 2299 2340 439316887 439316927 2.000000e-03 54.7
20 TraesCS7A01G240500 chr2B 96.875 32 0 1 2309 2340 672093999 672093969 6.000000e-03 52.8
21 TraesCS7A01G240500 chr6A 95.113 573 23 4 2637 3205 440767091 440767662 0.000000e+00 898.0
22 TraesCS7A01G240500 chr1B 95.263 570 22 5 2639 3205 91458131 91457564 0.000000e+00 898.0
23 TraesCS7A01G240500 chr2D 97.368 38 1 0 2438 2475 328372885 328372848 7.420000e-07 65.8
24 TraesCS7A01G240500 chr6D 94.737 38 2 0 2437 2474 412775869 412775906 3.450000e-05 60.2
25 TraesCS7A01G240500 chr6D 88.889 45 2 3 2296 2340 388327275 388327316 6.000000e-03 52.8
26 TraesCS7A01G240500 chr3D 94.872 39 1 1 2438 2475 357643030 357643068 3.450000e-05 60.2
27 TraesCS7A01G240500 chr6B 85.246 61 3 6 2294 2350 529769683 529769741 1.240000e-04 58.4
28 TraesCS7A01G240500 chr2A 97.059 34 1 0 2440 2473 764941031 764941064 1.240000e-04 58.4
29 TraesCS7A01G240500 chr2A 96.970 33 0 1 2308 2340 504278401 504278370 2.000000e-03 54.7


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 TraesCS7A01G240500 chr7A 215887358 215890562 3204 True 5919.000000 5919 100.0000 1 3205 1 chr7A.!!$R1 3204
1 TraesCS7A01G240500 chr7A 423889016 423889585 569 True 918.000000 918 95.7970 2637 3205 1 chr7A.!!$R2 568
2 TraesCS7A01G240500 chr7B 167749317 167751572 2255 True 1298.500000 1751 87.2445 38 2298 2 chr7B.!!$R3 2260
3 TraesCS7A01G240500 chr7D 204092119 204095010 2891 True 1203.333333 1620 90.9750 1 2610 3 chr7D.!!$R1 2609
4 TraesCS7A01G240500 chr5A 107837996 107838563 567 False 904.000000 904 95.4310 2639 3205 1 chr5A.!!$F1 566
5 TraesCS7A01G240500 chr3A 470668755 470669319 564 False 904.000000 904 95.5910 2639 3202 1 chr3A.!!$F3 563
6 TraesCS7A01G240500 chr3A 180760905 180761475 570 False 898.000000 898 95.1130 2637 3205 1 chr3A.!!$F1 568
7 TraesCS7A01G240500 chr4A 381274068 381274633 565 True 902.000000 902 95.4310 2639 3205 1 chr4A.!!$R2 566
8 TraesCS7A01G240500 chr4A 48606401 48606969 568 True 900.000000 900 95.2710 2639 3205 1 chr4A.!!$R1 566
9 TraesCS7A01G240500 chr2B 78842952 78843520 568 True 902.000000 902 95.2710 2637 3205 1 chr2B.!!$R1 568
10 TraesCS7A01G240500 chr6A 440767091 440767662 571 False 898.000000 898 95.1130 2637 3205 1 chr6A.!!$F1 568
11 TraesCS7A01G240500 chr1B 91457564 91458131 567 True 898.000000 898 95.2630 2639 3205 1 chr1B.!!$R1 566

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
228 238 0.112412 ACGACTTTTTCCCCATGCCT 59.888 50.0 0.0 0.0 0.00 4.75 F
231 241 0.252239 ACTTTTTCCCCATGCCTCCC 60.252 55.0 0.0 0.0 0.00 4.30 F
1038 1329 0.393537 GGTGCATCTCCTCCAAGGTG 60.394 60.0 0.0 0.0 36.53 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 2253 1.070134 TCCAACCTCTGTGTTTCTCCG 59.930 52.381 0.0 0.0 0.0 4.63 R
1885 2287 1.672356 CCAACACTTCCGGCTCCTG 60.672 63.158 0.0 0.0 0.0 3.86 R
2625 3037 0.108585 TCTGAAGGTGCGAAAAGGCT 59.891 50.000 0.0 0.0 0.0 4.58 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
32 33 2.480419 CGGTGGAAAGATATCGGCAATC 59.520 50.000 0.00 0.00 0.00 2.67
33 34 3.476552 GGTGGAAAGATATCGGCAATCA 58.523 45.455 0.00 0.00 0.00 2.57
34 35 3.882888 GGTGGAAAGATATCGGCAATCAA 59.117 43.478 0.00 0.00 0.00 2.57
35 36 4.261197 GGTGGAAAGATATCGGCAATCAAC 60.261 45.833 0.00 0.00 0.00 3.18
46 47 0.527565 GCAATCAACGGGCAATGTCT 59.472 50.000 0.00 0.00 0.00 3.41
58 59 2.450476 GCAATGTCTGGGGTCTGAATT 58.550 47.619 0.00 0.00 0.00 2.17
81 83 3.738131 TACGGTGGCGACGCGTATG 62.738 63.158 13.97 9.54 43.50 2.39
88 90 3.550992 CGACGCGTATGTGTGGCC 61.551 66.667 13.97 0.00 39.39 5.36
89 91 2.125673 GACGCGTATGTGTGGCCT 60.126 61.111 13.97 0.00 39.39 5.19
92 102 3.508840 GCGTATGTGTGGCCTGGC 61.509 66.667 11.05 11.05 0.00 4.85
104 114 2.601367 CCTGGCCAGGGTTGTTGG 60.601 66.667 40.24 16.49 44.87 3.77
105 115 2.198426 CTGGCCAGGGTTGTTGGT 59.802 61.111 26.14 0.00 38.02 3.67
106 116 2.123511 TGGCCAGGGTTGTTGGTG 60.124 61.111 0.00 0.00 38.02 4.17
107 117 2.917227 GGCCAGGGTTGTTGGTGG 60.917 66.667 0.00 0.00 38.02 4.61
108 118 2.917227 GCCAGGGTTGTTGGTGGG 60.917 66.667 0.00 0.00 38.02 4.61
109 119 2.917227 CCAGGGTTGTTGGTGGGC 60.917 66.667 0.00 0.00 0.00 5.36
110 120 2.123511 CAGGGTTGTTGGTGGGCA 60.124 61.111 0.00 0.00 0.00 5.36
115 125 3.106609 TTGTTGGTGGGCAGGGGA 61.107 61.111 0.00 0.00 0.00 4.81
137 147 3.691342 TGAGCTCCAACGACCCCG 61.691 66.667 12.15 0.00 42.50 5.73
161 171 4.796231 CCTGGGCCGTCGAACGAG 62.796 72.222 0.00 0.00 46.05 4.18
218 228 2.888998 GCCACGCGGACGACTTTTT 61.889 57.895 12.47 0.00 43.93 1.94
222 232 2.674084 CGCGGACGACTTTTTCCCC 61.674 63.158 0.00 0.00 43.93 4.81
223 233 1.598685 GCGGACGACTTTTTCCCCA 60.599 57.895 0.00 0.00 0.00 4.96
224 234 0.958876 GCGGACGACTTTTTCCCCAT 60.959 55.000 0.00 0.00 0.00 4.00
225 235 0.802494 CGGACGACTTTTTCCCCATG 59.198 55.000 0.00 0.00 0.00 3.66
227 237 0.526211 GACGACTTTTTCCCCATGCC 59.474 55.000 0.00 0.00 0.00 4.40
228 238 0.112412 ACGACTTTTTCCCCATGCCT 59.888 50.000 0.00 0.00 0.00 4.75
229 239 0.811281 CGACTTTTTCCCCATGCCTC 59.189 55.000 0.00 0.00 0.00 4.70
230 240 1.186200 GACTTTTTCCCCATGCCTCC 58.814 55.000 0.00 0.00 0.00 4.30
231 241 0.252239 ACTTTTTCCCCATGCCTCCC 60.252 55.000 0.00 0.00 0.00 4.30
232 242 1.304879 TTTTTCCCCATGCCTCCCG 60.305 57.895 0.00 0.00 0.00 5.14
233 243 2.087857 TTTTTCCCCATGCCTCCCGT 62.088 55.000 0.00 0.00 0.00 5.28
303 319 3.740128 ATGACCAGACGGCGGCATC 62.740 63.158 18.30 10.40 34.57 3.91
332 354 2.025418 CGGTACCTGGCGTCAACAC 61.025 63.158 10.90 0.00 0.00 3.32
359 381 4.535781 CCATGATTCAGACATAAACCCCA 58.464 43.478 0.00 0.00 0.00 4.96
381 403 6.324819 CCAACAATGCCACTTACTAATGAAG 58.675 40.000 0.00 0.00 0.00 3.02
395 417 6.336842 ACTAATGAAGAGCAAAGCAATGTT 57.663 33.333 0.00 0.00 0.00 2.71
431 456 2.812591 TCGTTGCTAATAACCGGCAAAA 59.187 40.909 0.00 0.00 45.49 2.44
444 469 1.669795 CGGCAAAACCAAGGCTGATTC 60.670 52.381 0.00 0.00 39.03 2.52
469 494 1.443872 CTCGCCACGACACTACCAC 60.444 63.158 0.00 0.00 0.00 4.16
470 495 2.137425 CTCGCCACGACACTACCACA 62.137 60.000 0.00 0.00 0.00 4.17
474 499 0.959553 CCACGACACTACCACAGTCT 59.040 55.000 0.00 0.00 34.26 3.24
492 517 8.450964 CCACAGTCTGGTGTTACATTATTAAAG 58.549 37.037 4.53 0.00 37.06 1.85
516 541 5.883503 AAAAACGTCTGGTGTTCAAACTA 57.116 34.783 0.00 0.00 0.00 2.24
569 594 3.381045 GCATCACAATTGCTGATCCATG 58.619 45.455 15.99 10.54 37.14 3.66
677 709 0.806884 TCCCGTACTTAATTGCGGCG 60.807 55.000 15.39 0.51 42.54 6.46
678 710 1.639534 CCGTACTTAATTGCGGCGG 59.360 57.895 9.78 0.00 37.69 6.13
679 711 1.011574 CGTACTTAATTGCGGCGGC 60.012 57.895 9.78 9.68 40.52 6.53
745 780 1.959738 GCCCCGGCGCTAATCTTAC 60.960 63.158 7.64 0.00 0.00 2.34
825 860 3.010420 GGAGAATCTTTCCAAGAACCCG 58.990 50.000 0.00 0.00 41.63 5.28
902 1159 5.913514 CCTGTCGTCCTTAAGATACGTAATG 59.086 44.000 21.80 13.92 37.83 1.90
1038 1329 0.393537 GGTGCATCTCCTCCAAGGTG 60.394 60.000 0.00 0.00 36.53 4.00
1261 1582 2.726351 GGGCTGGAGGAGGAGAACG 61.726 68.421 0.00 0.00 0.00 3.95
1315 1636 2.458006 GAAACCAGACGGCGGCAAAG 62.458 60.000 18.30 5.11 34.57 2.77
1398 1719 3.470567 GAGTTCGACGCGCTGGTG 61.471 66.667 5.73 0.00 0.00 4.17
1452 1773 2.359602 CCAGCACCAGCACCTGAG 60.360 66.667 0.00 0.00 45.49 3.35
1620 2022 2.125512 CCGGGCTTCGACTTCAGG 60.126 66.667 0.00 0.00 42.43 3.86
1851 2253 2.552031 GTCTTGGAGGTAATCGAAGCC 58.448 52.381 0.00 0.00 41.96 4.35
1879 2281 1.216710 CAGAGGTTGGAGAGGCGAC 59.783 63.158 0.00 0.00 0.00 5.19
1917 2319 1.177895 TGTTGGCGGTGATTGTGCAT 61.178 50.000 0.00 0.00 0.00 3.96
1946 2348 5.647658 AGGCGTCAGTTTGATGATGATTTTA 59.352 36.000 2.60 0.00 38.28 1.52
1951 2353 8.873830 CGTCAGTTTGATGATGATTTTAGTAGT 58.126 33.333 0.00 0.00 38.28 2.73
2076 2485 1.394917 CCAACATGTCTAGAAGCGTGC 59.605 52.381 0.00 0.00 0.00 5.34
2089 2498 7.587757 GTCTAGAAGCGTGCCATTTTATATTTG 59.412 37.037 0.00 0.00 0.00 2.32
2269 2681 6.035368 ACTATGACTAGCATTGCCTCATAG 57.965 41.667 27.43 27.43 40.28 2.23
2301 2713 4.646040 CCACCATTGTCCATGTCATATGTT 59.354 41.667 1.90 0.00 0.00 2.71
2305 2717 8.724229 CACCATTGTCCATGTCATATGTTATAG 58.276 37.037 1.90 0.00 0.00 1.31
2306 2718 8.439971 ACCATTGTCCATGTCATATGTTATAGT 58.560 33.333 1.90 0.00 0.00 2.12
2307 2719 9.942850 CCATTGTCCATGTCATATGTTATAGTA 57.057 33.333 1.90 0.00 0.00 1.82
2317 2729 8.803235 TGTCATATGTTATAGTATGTCACTCCC 58.197 37.037 1.90 0.00 38.80 4.30
2320 2732 6.576662 ATGTTATAGTATGTCACTCCCTCG 57.423 41.667 0.00 0.00 38.80 4.63
2323 2735 1.765230 AGTATGTCACTCCCTCGGTC 58.235 55.000 0.00 0.00 28.33 4.79
2324 2736 0.745468 GTATGTCACTCCCTCGGTCC 59.255 60.000 0.00 0.00 0.00 4.46
2343 2755 4.322499 GGTCCCAAAATAAGTGTCTCGAGA 60.322 45.833 12.08 12.08 0.00 4.04
2353 2765 8.522542 AATAAGTGTCTCGAGATAGTACCTTT 57.477 34.615 19.90 5.93 0.00 3.11
2380 2792 8.870160 TTGTTGTCATAATTTTGTTCCAAGAG 57.130 30.769 0.00 0.00 0.00 2.85
2382 2794 6.588719 TGTCATAATTTTGTTCCAAGAGGG 57.411 37.500 0.00 0.00 34.83 4.30
2383 2795 5.047377 TGTCATAATTTTGTTCCAAGAGGGC 60.047 40.000 0.00 0.00 36.21 5.19
2389 2801 2.396590 TGTTCCAAGAGGGCGTTATC 57.603 50.000 0.00 0.00 36.21 1.75
2446 2858 9.810545 GCTCAATTAGATATCAATACTACTCCC 57.189 37.037 5.32 0.00 0.00 4.30
2450 2862 8.754991 ATTAGATATCAATACTACTCCCTCCG 57.245 38.462 5.32 0.00 0.00 4.63
2452 2864 6.181908 AGATATCAATACTACTCCCTCCGTC 58.818 44.000 5.32 0.00 0.00 4.79
2454 2866 4.246712 TCAATACTACTCCCTCCGTCTT 57.753 45.455 0.00 0.00 0.00 3.01
2464 2876 9.683870 ACTACTCCCTCCGTCTTATAATATAAG 57.316 37.037 12.58 12.58 0.00 1.73
2467 2879 9.771140 ACTCCCTCCGTCTTATAATATAAGAAT 57.229 33.333 20.58 0.93 35.58 2.40
2547 2959 6.682423 TTTGATCGCAATTGTATCACTCAT 57.318 33.333 19.15 0.00 33.25 2.90
2613 3025 3.798202 GCATTAGTGCCTACTAGCAAGT 58.202 45.455 0.00 0.00 46.19 3.16
2614 3026 3.557595 GCATTAGTGCCTACTAGCAAGTG 59.442 47.826 0.00 0.00 46.19 3.16
2615 3027 2.961526 TAGTGCCTACTAGCAAGTGC 57.038 50.000 0.00 0.00 46.19 4.40
2616 3028 0.976641 AGTGCCTACTAGCAAGTGCA 59.023 50.000 6.00 0.00 46.19 4.57
2617 3029 1.347707 AGTGCCTACTAGCAAGTGCAA 59.652 47.619 6.00 0.00 46.19 4.08
2618 3030 1.464997 GTGCCTACTAGCAAGTGCAAC 59.535 52.381 6.00 0.00 46.19 4.17
2619 3031 0.721718 GCCTACTAGCAAGTGCAACG 59.278 55.000 6.00 0.00 45.86 4.10
2620 3032 0.721718 CCTACTAGCAAGTGCAACGC 59.278 55.000 6.00 0.00 45.86 4.84
2621 3033 1.673033 CCTACTAGCAAGTGCAACGCT 60.673 52.381 6.00 10.27 45.86 5.07
2622 3034 2.069273 CTACTAGCAAGTGCAACGCTT 58.931 47.619 10.64 0.00 45.86 4.68
2623 3035 1.308998 ACTAGCAAGTGCAACGCTTT 58.691 45.000 10.64 0.00 45.86 3.51
2624 3036 1.002468 ACTAGCAAGTGCAACGCTTTG 60.002 47.619 10.64 0.00 45.86 2.77
2625 3037 1.264020 CTAGCAAGTGCAACGCTTTGA 59.736 47.619 7.19 0.00 45.86 2.69
2626 3038 0.029834 AGCAAGTGCAACGCTTTGAG 59.970 50.000 7.19 0.00 45.86 3.02
2627 3039 1.543106 GCAAGTGCAACGCTTTGAGC 61.543 55.000 7.19 0.00 45.86 4.26
2628 3040 0.936297 CAAGTGCAACGCTTTGAGCC 60.936 55.000 7.19 0.00 45.86 4.70
2629 3041 1.103398 AAGTGCAACGCTTTGAGCCT 61.103 50.000 7.19 0.00 45.86 4.58
2630 3042 1.103398 AGTGCAACGCTTTGAGCCTT 61.103 50.000 7.19 0.00 45.86 4.35
2631 3043 0.249031 GTGCAACGCTTTGAGCCTTT 60.249 50.000 7.19 0.00 38.18 3.11
2632 3044 0.459489 TGCAACGCTTTGAGCCTTTT 59.541 45.000 7.19 0.00 38.18 2.27
2633 3045 1.131771 GCAACGCTTTGAGCCTTTTC 58.868 50.000 7.19 0.00 38.18 2.29
2634 3046 1.398595 CAACGCTTTGAGCCTTTTCG 58.601 50.000 0.00 0.00 38.18 3.46
2635 3047 0.317854 AACGCTTTGAGCCTTTTCGC 60.318 50.000 0.00 0.00 38.18 4.70
2642 3054 0.179032 TGAGCCTTTTCGCACCTTCA 60.179 50.000 0.00 0.00 0.00 3.02
2906 3318 7.470079 CACCAAGACAATGTTCTCATCATAAG 58.530 38.462 0.00 0.00 32.56 1.73
2912 3325 6.124340 ACAATGTTCTCATCATAAGCCATCA 58.876 36.000 0.00 0.00 32.56 3.07
2942 3355 2.552743 CCAAGATACTCGCGTGATCCTA 59.447 50.000 16.04 0.00 0.00 2.94
2978 3392 7.727331 AGTGAAATTTGAGAAGAGAAGAGTG 57.273 36.000 0.00 0.00 0.00 3.51
2996 3410 4.583489 AGAGTGAAAACTCTACGTCAGGAA 59.417 41.667 6.60 0.00 44.52 3.36
3198 3621 3.752222 GACTATATCTCCCACGTGTCGAT 59.248 47.826 15.65 14.37 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.390885 CCGATATCTTTCCACCGCATTATTG 60.391 44.000 0.34 0.00 0.00 1.90
10 11 0.531974 TGCCGATATCTTTCCACCGC 60.532 55.000 0.34 0.00 0.00 5.68
21 22 0.179032 TGCCCGTTGATTGCCGATAT 60.179 50.000 0.00 0.00 0.00 1.63
32 33 2.342650 CCCCAGACATTGCCCGTTG 61.343 63.158 0.00 0.00 0.00 4.10
33 34 2.035626 CCCCAGACATTGCCCGTT 59.964 61.111 0.00 0.00 0.00 4.44
34 35 3.256960 ACCCCAGACATTGCCCGT 61.257 61.111 0.00 0.00 0.00 5.28
35 36 2.438434 GACCCCAGACATTGCCCG 60.438 66.667 0.00 0.00 0.00 6.13
46 47 1.067425 CGTACGTCAATTCAGACCCCA 60.067 52.381 7.22 0.00 35.07 4.96
58 59 4.388080 CGTCGCCACCGTACGTCA 62.388 66.667 15.21 0.00 35.14 4.35
88 90 2.198426 ACCAACAACCCTGGCCAG 59.802 61.111 26.87 26.87 37.48 4.85
89 91 2.123511 CACCAACAACCCTGGCCA 60.124 61.111 4.71 4.71 37.48 5.36
92 102 2.917227 GCCCACCAACAACCCTGG 60.917 66.667 0.00 0.00 40.05 4.45
106 116 4.785453 CTCACGCTTCCCCTGCCC 62.785 72.222 0.00 0.00 0.00 5.36
108 118 4.400961 AGCTCACGCTTCCCCTGC 62.401 66.667 0.00 0.00 46.47 4.85
134 144 3.866582 GGCCCAGGATCTGACGGG 61.867 72.222 0.00 0.00 42.03 5.28
137 147 2.501610 GACGGCCCAGGATCTGAC 59.498 66.667 0.00 0.00 32.44 3.51
140 150 2.363795 TTCGACGGCCCAGGATCT 60.364 61.111 0.00 0.00 0.00 2.75
161 171 1.222115 GGATATCTGCCGTCCGTTGC 61.222 60.000 2.05 0.00 0.00 4.17
222 232 2.511600 GAACGGACGGGAGGCATG 60.512 66.667 0.00 0.00 42.53 4.06
223 233 2.683933 AGAACGGACGGGAGGCAT 60.684 61.111 0.00 0.00 42.53 4.40
224 234 3.379445 GAGAACGGACGGGAGGCA 61.379 66.667 0.00 0.00 42.53 4.75
225 235 4.144703 GGAGAACGGACGGGAGGC 62.145 72.222 0.00 0.00 0.00 4.70
227 237 3.823330 CGGGAGAACGGACGGGAG 61.823 72.222 0.00 0.00 0.00 4.30
254 264 1.604604 TCCGCCAGGAGAAAAGTTTG 58.395 50.000 0.00 0.00 42.75 2.93
326 348 1.426983 TGAATCATGGGTGGGTGTTGA 59.573 47.619 0.00 0.00 0.00 3.18
332 354 2.742428 ATGTCTGAATCATGGGTGGG 57.258 50.000 0.00 0.00 0.00 4.61
359 381 6.127897 GCTCTTCATTAGTAAGTGGCATTGTT 60.128 38.462 0.00 0.00 0.00 2.83
381 403 6.890663 TTATGCATAAACATTGCTTTGCTC 57.109 33.333 16.78 0.00 40.77 4.26
431 456 1.377725 CGCAGGAATCAGCCTTGGT 60.378 57.895 0.00 0.00 35.66 3.67
501 526 3.434453 CCAACCCTAGTTTGAACACCAGA 60.434 47.826 3.43 0.00 32.45 3.86
535 560 0.249911 GTGATGCCACGGACCTATCC 60.250 60.000 0.00 0.00 42.28 2.59
547 572 1.752498 TGGATCAGCAATTGTGATGCC 59.248 47.619 24.97 21.65 44.91 4.40
635 660 2.052104 CGGAGGGTTCCAAATGGCC 61.052 63.158 0.00 0.00 44.26 5.36
636 661 3.603365 CGGAGGGTTCCAAATGGC 58.397 61.111 0.00 0.00 44.26 4.40
677 709 2.157738 GATCATGGCTGACTAATGGCC 58.842 52.381 0.00 0.00 45.45 5.36
678 710 1.802960 CGATCATGGCTGACTAATGGC 59.197 52.381 0.00 0.00 33.22 4.40
679 711 2.037641 TCCGATCATGGCTGACTAATGG 59.962 50.000 0.00 0.00 33.22 3.16
745 780 0.109597 GGTGGCGATTTGTTGCAGAG 60.110 55.000 0.00 0.00 0.00 3.35
825 860 9.984190 AGATAATAAGAACGAGAAGAATTACCC 57.016 33.333 0.00 0.00 0.00 3.69
853 1110 7.035004 GCTGCCAAATCATATGAAGTTTGTAA 58.965 34.615 21.77 13.11 31.42 2.41
858 1115 4.098960 CAGGCTGCCAAATCATATGAAGTT 59.901 41.667 22.65 4.38 0.00 2.66
859 1116 3.635373 CAGGCTGCCAAATCATATGAAGT 59.365 43.478 22.65 0.00 0.00 3.01
865 1122 1.065491 ACGACAGGCTGCCAAATCATA 60.065 47.619 22.65 0.00 0.00 2.15
902 1159 2.851824 CAGTTCGTTTTGTCTGCAAACC 59.148 45.455 0.00 0.00 43.47 3.27
948 1205 7.921041 ATATATCTCAAGAGTTCCTCCACAA 57.079 36.000 0.00 0.00 0.00 3.33
974 1231 5.106237 GCTCCCAGCAATCAATCAATCTATC 60.106 44.000 0.00 0.00 41.89 2.08
976 1233 4.139786 GCTCCCAGCAATCAATCAATCTA 58.860 43.478 0.00 0.00 41.89 1.98
981 1272 0.252761 TCGCTCCCAGCAATCAATCA 59.747 50.000 0.00 0.00 42.58 2.57
985 1276 0.972471 TCTCTCGCTCCCAGCAATCA 60.972 55.000 0.00 0.00 42.58 2.57
1038 1329 4.154347 CTCCCCGACCTGCTCAGC 62.154 72.222 0.00 0.00 0.00 4.26
1353 1674 4.394712 CGGAAGCTGACCGCCCTT 62.395 66.667 17.32 0.00 43.74 3.95
1374 1695 2.182030 GCGTCGAACTCCTCCAGG 59.818 66.667 0.00 0.00 0.00 4.45
1418 1739 2.669569 GTGCAGGCTCCGCTTTCA 60.670 61.111 0.00 0.00 0.00 2.69
1526 1928 2.433146 GCCTCCCCTAGTTCCGGAC 61.433 68.421 1.83 0.00 0.00 4.79
1620 2022 2.125350 CTCAGGCTGCCGGACTTC 60.125 66.667 17.72 0.00 0.00 3.01
1851 2253 1.070134 TCCAACCTCTGTGTTTCTCCG 59.930 52.381 0.00 0.00 0.00 4.63
1879 2281 4.113815 TTCCGGCTCCTGGGCATG 62.114 66.667 0.00 0.00 40.90 4.06
1885 2287 1.672356 CCAACACTTCCGGCTCCTG 60.672 63.158 0.00 0.00 0.00 3.86
1886 2288 2.750350 CCAACACTTCCGGCTCCT 59.250 61.111 0.00 0.00 0.00 3.69
1887 2289 3.056328 GCCAACACTTCCGGCTCC 61.056 66.667 0.00 0.00 42.78 4.70
1888 2290 3.423154 CGCCAACACTTCCGGCTC 61.423 66.667 0.00 0.00 43.95 4.70
1917 2319 4.200838 TCATCAAACTGACGCCTAATCA 57.799 40.909 0.00 0.00 0.00 2.57
1952 2354 6.439675 AGCACTCTAAAACGGTAACAAAAA 57.560 33.333 0.00 0.00 0.00 1.94
1960 2362 3.188159 TCACAAGCACTCTAAAACGGT 57.812 42.857 0.00 0.00 0.00 4.83
2099 2508 3.069443 AGTTTGTGCACATTACTTTGGGG 59.931 43.478 22.39 0.00 0.00 4.96
2100 2509 4.320608 AGTTTGTGCACATTACTTTGGG 57.679 40.909 22.39 0.00 0.00 4.12
2269 2681 5.047377 ACATGGACAATGGTGGTATGAAAAC 60.047 40.000 0.00 0.00 40.94 2.43
2301 2713 4.506271 GGACCGAGGGAGTGACATACTATA 60.506 50.000 0.00 0.00 40.53 1.31
2305 2717 0.745468 GGACCGAGGGAGTGACATAC 59.255 60.000 0.00 0.00 0.00 2.39
2306 2718 0.396695 GGGACCGAGGGAGTGACATA 60.397 60.000 0.00 0.00 0.00 2.29
2307 2719 1.686110 GGGACCGAGGGAGTGACAT 60.686 63.158 0.00 0.00 0.00 3.06
2308 2720 2.283676 GGGACCGAGGGAGTGACA 60.284 66.667 0.00 0.00 0.00 3.58
2317 2729 3.933332 GAGACACTTATTTTGGGACCGAG 59.067 47.826 0.00 0.00 0.00 4.63
2320 2732 3.933332 CTCGAGACACTTATTTTGGGACC 59.067 47.826 6.58 0.00 0.00 4.46
2323 2735 6.574350 ACTATCTCGAGACACTTATTTTGGG 58.426 40.000 19.30 0.00 0.00 4.12
2324 2736 7.648510 GGTACTATCTCGAGACACTTATTTTGG 59.351 40.741 19.30 2.88 0.00 3.28
2369 2781 5.606454 TAGGATAACGCCCTCTTGGAACAA 61.606 45.833 0.00 0.00 38.29 2.83
2380 2792 8.718734 CAACTAGAATAAAATAGGATAACGCCC 58.281 37.037 0.00 0.00 0.00 6.13
2382 2794 8.770828 TGCAACTAGAATAAAATAGGATAACGC 58.229 33.333 0.00 0.00 0.00 4.84
2419 2831 9.509855 GGAGTAGTATTGATATCTAATTGAGCG 57.490 37.037 3.98 0.00 0.00 5.03
2504 2916 6.061441 TCAAATGCTCCTTTCAGACTTGTTA 58.939 36.000 0.00 0.00 0.00 2.41
2519 2931 5.397534 GTGATACAATTGCGATCAAATGCTC 59.602 40.000 19.81 7.72 36.75 4.26
2591 3003 3.197766 ACTTGCTAGTAGGCACTAATGCA 59.802 43.478 0.00 0.00 45.48 3.96
2610 3022 1.103398 AGGCTCAAAGCGTTGCACTT 61.103 50.000 7.57 0.00 43.62 3.16
2611 3023 1.103398 AAGGCTCAAAGCGTTGCACT 61.103 50.000 7.57 2.86 46.17 4.40
2612 3024 1.360192 AAGGCTCAAAGCGTTGCAC 59.640 52.632 7.57 1.96 46.17 4.57
2613 3025 3.840437 AAGGCTCAAAGCGTTGCA 58.160 50.000 7.57 0.00 46.17 4.08
2617 3029 1.282875 GCGAAAAGGCTCAAAGCGT 59.717 52.632 0.00 0.00 43.62 5.07
2618 3030 0.998727 GTGCGAAAAGGCTCAAAGCG 60.999 55.000 0.00 0.00 43.62 4.68
2619 3031 0.664466 GGTGCGAAAAGGCTCAAAGC 60.664 55.000 0.00 0.00 41.46 3.51
2620 3032 0.954452 AGGTGCGAAAAGGCTCAAAG 59.046 50.000 0.00 0.00 0.00 2.77
2621 3033 1.336755 GAAGGTGCGAAAAGGCTCAAA 59.663 47.619 0.00 0.00 0.00 2.69
2622 3034 0.951558 GAAGGTGCGAAAAGGCTCAA 59.048 50.000 0.00 0.00 0.00 3.02
2623 3035 0.179032 TGAAGGTGCGAAAAGGCTCA 60.179 50.000 0.00 0.00 0.00 4.26
2624 3036 0.519077 CTGAAGGTGCGAAAAGGCTC 59.481 55.000 0.00 0.00 0.00 4.70
2625 3037 0.108585 TCTGAAGGTGCGAAAAGGCT 59.891 50.000 0.00 0.00 0.00 4.58
2626 3038 0.951558 TTCTGAAGGTGCGAAAAGGC 59.048 50.000 0.00 0.00 0.00 4.35
2627 3039 3.253188 TGATTTCTGAAGGTGCGAAAAGG 59.747 43.478 0.00 0.00 31.30 3.11
2628 3040 4.488126 TGATTTCTGAAGGTGCGAAAAG 57.512 40.909 0.00 0.00 31.30 2.27
2629 3041 4.761739 AGATGATTTCTGAAGGTGCGAAAA 59.238 37.500 0.00 0.00 31.79 2.29
2630 3042 4.326826 AGATGATTTCTGAAGGTGCGAAA 58.673 39.130 0.00 0.00 31.79 3.46
2631 3043 3.942829 AGATGATTTCTGAAGGTGCGAA 58.057 40.909 0.00 0.00 31.79 4.70
2632 3044 3.616956 AGATGATTTCTGAAGGTGCGA 57.383 42.857 0.00 0.00 31.79 5.10
2633 3045 3.557595 GGTAGATGATTTCTGAAGGTGCG 59.442 47.826 0.00 0.00 35.79 5.34
2634 3046 4.775236 AGGTAGATGATTTCTGAAGGTGC 58.225 43.478 0.00 0.00 35.79 5.01
2635 3047 5.982356 TGAGGTAGATGATTTCTGAAGGTG 58.018 41.667 0.00 0.00 35.79 4.00
2642 3054 5.422331 TCGAAGGTTGAGGTAGATGATTTCT 59.578 40.000 0.00 0.00 38.57 2.52
2854 3266 1.954382 GTCAGGGGTTTTGTGGAAGTC 59.046 52.381 0.00 0.00 0.00 3.01
2906 3318 2.632377 TCTTGGAATCGTTCTGATGGC 58.368 47.619 0.00 0.00 37.39 4.40
2912 3325 3.707793 GCGAGTATCTTGGAATCGTTCT 58.292 45.455 0.00 0.00 35.87 3.01
2978 3392 2.994578 GGCTTCCTGACGTAGAGTTTTC 59.005 50.000 0.00 0.00 0.00 2.29
2996 3410 1.137872 CTTCATCGCTCTGGTAAGGCT 59.862 52.381 0.00 0.00 0.00 4.58
3130 3552 2.269241 GAGCCTTCCCCGACCTTG 59.731 66.667 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.