Multiple sequence alignment - TraesCS7D01G278200

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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 TraesCS7D01G278200 chr7D 100.000 3447 0 0 1685 5131 267880066 267876620 0.000000e+00 6366.0
1 TraesCS7D01G278200 chr7D 100.000 1274 0 0 1 1274 267881750 267880477 0.000000e+00 2353.0
2 TraesCS7D01G278200 chr7D 75.312 320 58 14 3156 3459 555059207 555059521 3.220000e-27 134.0
3 TraesCS7D01G278200 chr7D 89.412 85 9 0 3064 3148 235795591 235795507 1.950000e-19 108.0
4 TraesCS7D01G278200 chr7B 95.713 2706 81 15 1703 4379 247707363 247704664 0.000000e+00 4322.0
5 TraesCS7D01G278200 chr7B 97.347 754 18 2 4379 5131 247704622 247703870 0.000000e+00 1280.0
6 TraesCS7D01G278200 chr7B 98.765 324 4 0 951 1274 247707882 247707559 1.240000e-160 577.0
7 TraesCS7D01G278200 chr7B 89.053 338 25 9 670 996 247708355 247708019 4.780000e-110 409.0
8 TraesCS7D01G278200 chr7A 95.438 1644 55 10 1703 3335 293095368 293097002 0.000000e+00 2603.0
9 TraesCS7D01G278200 chr7A 93.755 1201 42 8 74 1264 293093764 293094941 0.000000e+00 1772.0
10 TraesCS7D01G278200 chr7A 96.182 969 28 5 3419 4379 293097280 293098247 0.000000e+00 1576.0
11 TraesCS7D01G278200 chr7A 96.303 595 20 2 4379 4973 293098289 293098881 0.000000e+00 976.0
12 TraesCS7D01G278200 chr7A 98.765 162 1 1 4971 5131 293098962 293099123 2.340000e-73 287.0
13 TraesCS7D01G278200 chr7A 94.048 84 5 0 1 84 293093659 293093742 1.500000e-25 128.0
14 TraesCS7D01G278200 chr4B 88.065 310 34 2 3153 3460 602774918 602775226 1.050000e-96 364.0
15 TraesCS7D01G278200 chr1A 88.525 305 24 4 3156 3450 571740075 571740378 4.880000e-95 359.0
16 TraesCS7D01G278200 chr3A 87.138 311 36 4 3150 3458 24755342 24755650 2.940000e-92 350.0
17 TraesCS7D01G278200 chr3A 79.771 262 40 8 3452 3708 721973383 721973636 1.470000e-40 178.0
18 TraesCS7D01G278200 chr5D 89.744 273 26 2 3152 3422 136352243 136351971 1.060000e-91 348.0
19 TraesCS7D01G278200 chr4A 90.494 263 25 0 3156 3418 617657432 617657170 1.060000e-91 348.0
20 TraesCS7D01G278200 chr4A 91.803 61 5 0 69 129 601515977 601515917 9.150000e-13 86.1
21 TraesCS7D01G278200 chr4A 92.857 56 4 0 69 124 163820857 163820802 1.180000e-11 82.4
22 TraesCS7D01G278200 chr3D 90.530 264 23 2 3156 3418 475868469 475868731 1.060000e-91 348.0
23 TraesCS7D01G278200 chr3D 81.538 260 37 9 3452 3707 532762151 532762403 2.420000e-48 204.0
24 TraesCS7D01G278200 chr3D 94.737 57 3 0 69 125 495325002 495325058 7.080000e-14 89.8
25 TraesCS7D01G278200 chr2A 87.838 296 34 2 3157 3452 704690437 704690730 3.800000e-91 346.0
26 TraesCS7D01G278200 chr2A 88.636 88 8 1 3063 3148 4118877 4118790 7.030000e-19 106.0
27 TraesCS7D01G278200 chr2A 94.340 53 3 0 68 120 180334803 180334751 1.180000e-11 82.4
28 TraesCS7D01G278200 chr2A 86.957 69 7 2 59 125 547773505 547773573 5.510000e-10 76.8
29 TraesCS7D01G278200 chr2A 86.957 69 7 2 59 125 566989656 566989588 5.510000e-10 76.8
30 TraesCS7D01G278200 chr6B 75.949 316 57 12 3154 3455 9429249 9429559 1.490000e-30 145.0
31 TraesCS7D01G278200 chr6B 73.394 327 63 15 3150 3460 640314262 640314580 3.270000e-17 100.0
32 TraesCS7D01G278200 chr2D 88.660 97 9 1 3062 3156 27331456 27331552 3.250000e-22 117.0
33 TraesCS7D01G278200 chrUn 78.824 170 27 9 3538 3703 257280991 257280827 7.030000e-19 106.0
34 TraesCS7D01G278200 chrUn 78.824 170 27 8 3538 3703 317391747 317391911 7.030000e-19 106.0
35 TraesCS7D01G278200 chrUn 78.235 170 28 9 3538 3703 212981470 212981306 3.270000e-17 100.0
36 TraesCS7D01G278200 chrUn 78.235 170 28 9 3538 3703 224592078 224591914 3.270000e-17 100.0
37 TraesCS7D01G278200 chrUn 78.235 170 28 8 3538 3703 365208031 365208195 3.270000e-17 100.0
38 TraesCS7D01G278200 chr5A 89.552 67 6 1 3083 3148 436264078 436264144 3.290000e-12 84.2
39 TraesCS7D01G278200 chr5A 87.143 70 7 1 3081 3148 531227524 531227593 1.530000e-10 78.7
40 TraesCS7D01G278200 chr6A 92.857 56 4 0 69 124 534987687 534987632 1.180000e-11 82.4
41 TraesCS7D01G278200 chr2B 91.228 57 5 0 69 125 754531783 754531839 1.530000e-10 78.7
42 TraesCS7D01G278200 chr3B 92.683 41 1 2 3422 3461 104273865 104273826 2.000000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G278200 chr7D 267876620 267881750 5130 True 4359.500000 6366 100.0000 1 5131 2 chr7D.!!$R2 5130
1 TraesCS7D01G278200 chr7B 247703870 247708355 4485 True 1647.000000 4322 95.2195 670 5131 4 chr7B.!!$R1 4461
2 TraesCS7D01G278200 chr7A 293093659 293099123 5464 False 1223.666667 2603 95.7485 1 5131 6 chr7A.!!$F1 5130

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
411 444 0.036732 GACTGGAGCACCAACATGGA 59.963 55.0 3.9 0.0 46.32 3.41 F
412 445 0.250901 ACTGGAGCACCAACATGGAC 60.251 55.0 3.9 0.0 46.32 4.02 F
511 544 0.324614 TAGGTGGATGTGTGGTGCAG 59.675 55.0 0.0 0.0 0.00 4.41 F
666 701 0.592637 TGACATGCTGAAAACGCAGG 59.407 50.0 0.0 0.0 44.02 4.85 F
1748 2049 0.688487 TTAGACCCTTTGGACCCGTG 59.312 55.0 0.0 0.0 34.81 4.94 F
2407 2709 0.976641 AGGAGATGTTCGTGCCTGAA 59.023 50.0 0.0 0.0 0.00 3.02 F
3410 3721 2.037641 TCGATATGCCACTCCAATCCTG 59.962 50.0 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 2031 1.196104 CCACGGGTCCAAAGGGTCTA 61.196 60.000 0.00 0.00 34.93 2.59 R
2391 2693 1.344438 TGACTTCAGGCACGAACATCT 59.656 47.619 0.00 0.00 0.00 2.90 R
2407 2709 5.539955 AGGTTGCTAAATTTGTGGAATGACT 59.460 36.000 0.00 0.22 0.00 3.41 R
2571 2873 2.611292 CGGTCAGAAGGAAATGATCTGC 59.389 50.000 0.00 0.00 40.26 4.26 R
3390 3701 2.224378 ACAGGATTGGAGTGGCATATCG 60.224 50.000 0.00 0.00 0.00 2.92 R
4124 4693 0.236711 CAGGATGCGGCGATCAATTC 59.763 55.000 12.98 0.00 0.00 2.17 R
4671 5283 0.532417 CTGCACTAGCCTCCTGATGC 60.532 60.000 0.00 0.00 41.13 3.91 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
63 64 5.983118 GCAAAATTTATTATTCCCGTGGGAG 59.017 40.000 7.85 0.00 46.06 4.30
101 134 1.605453 GAGTCCAATACCCGCCCAA 59.395 57.895 0.00 0.00 0.00 4.12
126 159 1.213537 CCCATTGCCAGCTTGAACG 59.786 57.895 0.00 0.00 0.00 3.95
157 190 3.044059 GCATGCGCCAGTTGAGGAC 62.044 63.158 4.18 0.00 0.00 3.85
158 191 1.672030 CATGCGCCAGTTGAGGACA 60.672 57.895 4.18 0.00 0.00 4.02
159 192 1.073025 ATGCGCCAGTTGAGGACAA 59.927 52.632 4.18 0.00 0.00 3.18
200 233 4.379394 GCCAGATTCGACAGCAATACAAAA 60.379 41.667 0.00 0.00 0.00 2.44
207 240 5.245531 TCGACAGCAATACAAAAGGATTCT 58.754 37.500 0.00 0.00 0.00 2.40
220 253 3.889520 AGGATTCTACCAAGGAACGAC 57.110 47.619 0.00 0.00 0.00 4.34
229 262 2.235402 ACCAAGGAACGACCGAATGTAT 59.765 45.455 0.00 0.00 44.74 2.29
231 264 3.517602 CAAGGAACGACCGAATGTATGA 58.482 45.455 0.00 0.00 44.74 2.15
258 291 2.108514 ATTGCCACCATGCGACGAG 61.109 57.895 0.00 0.00 0.00 4.18
262 295 2.100631 CCACCATGCGACGAGGAAC 61.101 63.158 0.00 0.00 0.00 3.62
267 300 0.439985 CATGCGACGAGGAACAACTG 59.560 55.000 0.00 0.00 0.00 3.16
278 311 4.301628 GAGGAACAACTGCCAAATTTGAG 58.698 43.478 19.86 12.01 0.00 3.02
302 335 1.064825 ACAACCGAGGGAAGAATGGT 58.935 50.000 0.00 0.00 33.45 3.55
314 347 5.104109 AGGGAAGAATGGTTGGAATATTCGA 60.104 40.000 9.32 2.51 36.27 3.71
315 348 5.008712 GGGAAGAATGGTTGGAATATTCGAC 59.991 44.000 9.32 10.02 36.27 4.20
339 372 1.685302 CAGCGGTCAAATTTGAACCG 58.315 50.000 33.86 33.86 45.70 4.44
354 387 3.307906 CCGACGACCAAGGGGACA 61.308 66.667 0.00 0.00 38.05 4.02
397 430 2.177594 GAGGGCAGTGAGTGGACTGG 62.178 65.000 0.00 0.00 43.17 4.00
398 431 2.217038 GGGCAGTGAGTGGACTGGA 61.217 63.158 0.00 0.00 43.17 3.86
399 432 1.294780 GGCAGTGAGTGGACTGGAG 59.705 63.158 0.00 0.00 43.17 3.86
400 433 1.375268 GCAGTGAGTGGACTGGAGC 60.375 63.158 0.00 0.00 43.17 4.70
401 434 2.052779 CAGTGAGTGGACTGGAGCA 58.947 57.895 0.00 0.00 39.85 4.26
402 435 0.320247 CAGTGAGTGGACTGGAGCAC 60.320 60.000 0.00 0.00 39.85 4.40
403 436 1.004440 GTGAGTGGACTGGAGCACC 60.004 63.158 0.00 0.00 0.00 5.01
404 437 1.459348 TGAGTGGACTGGAGCACCA 60.459 57.895 1.91 1.91 44.76 4.17
405 438 1.053835 TGAGTGGACTGGAGCACCAA 61.054 55.000 3.90 0.00 46.32 3.67
406 439 0.603975 GAGTGGACTGGAGCACCAAC 60.604 60.000 3.90 0.00 46.32 3.77
407 440 1.148273 GTGGACTGGAGCACCAACA 59.852 57.895 3.90 1.09 46.32 3.33
408 441 0.250901 GTGGACTGGAGCACCAACAT 60.251 55.000 3.90 0.00 46.32 2.71
409 442 0.250858 TGGACTGGAGCACCAACATG 60.251 55.000 3.90 0.00 46.32 3.21
410 443 0.962356 GGACTGGAGCACCAACATGG 60.962 60.000 3.90 0.00 46.32 3.66
411 444 0.036732 GACTGGAGCACCAACATGGA 59.963 55.000 3.90 0.00 46.32 3.41
412 445 0.250901 ACTGGAGCACCAACATGGAC 60.251 55.000 3.90 0.00 46.32 4.02
413 446 1.300971 CTGGAGCACCAACATGGACG 61.301 60.000 3.90 0.00 46.32 4.79
414 447 1.003839 GGAGCACCAACATGGACGA 60.004 57.895 2.85 0.00 40.96 4.20
476 509 1.027792 GGAGAAGAGGACGCGAGAGT 61.028 60.000 15.93 0.00 0.00 3.24
479 512 3.391965 GAGAAGAGGACGCGAGAGTATA 58.608 50.000 15.93 0.00 0.00 1.47
511 544 0.324614 TAGGTGGATGTGTGGTGCAG 59.675 55.000 0.00 0.00 0.00 4.41
584 617 4.426313 GGGGAAAGGAGCGGGTGG 62.426 72.222 0.00 0.00 0.00 4.61
612 646 2.363306 TGTTGGTGTGGAGCAGAAAT 57.637 45.000 0.00 0.00 0.00 2.17
650 684 8.593492 AAACAAAAGCTCAGGAAAAATATGAC 57.407 30.769 0.00 0.00 0.00 3.06
651 685 7.288810 ACAAAAGCTCAGGAAAAATATGACA 57.711 32.000 0.00 0.00 0.00 3.58
652 686 7.899973 ACAAAAGCTCAGGAAAAATATGACAT 58.100 30.769 0.00 0.00 0.00 3.06
653 687 7.816031 ACAAAAGCTCAGGAAAAATATGACATG 59.184 33.333 0.00 0.00 0.00 3.21
654 688 5.511234 AGCTCAGGAAAAATATGACATGC 57.489 39.130 0.00 0.00 0.00 4.06
666 701 0.592637 TGACATGCTGAAAACGCAGG 59.407 50.000 0.00 0.00 44.02 4.85
696 731 4.185467 TGCATGTGCGTGGAAATATTTT 57.815 36.364 1.43 0.00 45.83 1.82
697 732 4.564041 TGCATGTGCGTGGAAATATTTTT 58.436 34.783 1.43 0.00 45.83 1.94
698 733 4.624882 TGCATGTGCGTGGAAATATTTTTC 59.375 37.500 1.43 0.40 45.83 2.29
1173 1404 1.902508 TCTCCGCATCAAGAGTTCCTT 59.097 47.619 0.00 0.00 34.91 3.36
1711 2012 2.426842 AATTGTTAGAGGCTGAGGGC 57.573 50.000 0.00 0.00 40.90 5.19
1730 2031 1.827245 GCCTTTGGTTGGATCCCACTT 60.827 52.381 15.18 0.00 30.78 3.16
1748 2049 0.688487 TTAGACCCTTTGGACCCGTG 59.312 55.000 0.00 0.00 34.81 4.94
1872 2173 2.741612 TCTGCTTGGCAAACATTTTCG 58.258 42.857 3.46 0.00 38.41 3.46
1881 2182 5.004448 TGGCAAACATTTTCGACTACCATA 58.996 37.500 0.00 0.00 0.00 2.74
2132 2434 5.478679 AGAGATATGGGGTAATCAAGTCGAG 59.521 44.000 0.00 0.00 0.00 4.04
2337 2639 7.016153 TGTTGGATCAGGTATGTAAGACTTT 57.984 36.000 0.00 0.00 0.00 2.66
2391 2693 5.199723 TGAATTTGTATGGCAGCATAAGGA 58.800 37.500 0.00 0.00 0.00 3.36
2407 2709 0.976641 AGGAGATGTTCGTGCCTGAA 59.023 50.000 0.00 0.00 0.00 3.02
2449 2751 8.336801 AGCAACCTGTATCTTTAAAGTTTAGG 57.663 34.615 14.74 17.66 0.00 2.69
2477 2779 9.665719 TGCAATGAAGTCTATCAAAACAGTATA 57.334 29.630 0.00 0.00 32.06 1.47
2506 2808 6.931840 GGCCTACCTAAGAAAACATATGAGAG 59.068 42.308 10.38 0.00 0.00 3.20
2621 2932 8.265055 TGATAATACTAGCTTGTTTTAGTGGCT 58.735 33.333 6.03 0.00 37.08 4.75
2674 2985 6.951198 TCACTGGTTGGTATTGGTAAATTGAT 59.049 34.615 0.00 0.00 0.00 2.57
2772 3083 2.551459 CCAGAGTTGGTTGCTTCTTCTG 59.449 50.000 0.00 0.00 39.79 3.02
2917 3228 6.972901 GGCAAGTACTATTTTTAGAACCATGC 59.027 38.462 0.00 0.00 0.00 4.06
2940 3251 5.872070 GCTTAGATGGGCATACAGACTAATC 59.128 44.000 0.00 0.00 0.00 1.75
3045 3356 6.150474 CAGTTGGGGTTAACATAGTAACAAGG 59.850 42.308 8.10 0.00 35.96 3.61
3175 3486 6.019108 ACTAAGGGCTCCTTTGATTCAAAAT 58.981 36.000 17.52 0.00 41.69 1.82
3331 3642 5.163088 ACATCCACTCCAACCTCTTTTTACT 60.163 40.000 0.00 0.00 0.00 2.24
3340 3651 9.899226 CTCCAACCTCTTTTTACTATTTCTTTG 57.101 33.333 0.00 0.00 0.00 2.77
3375 3686 4.397417 GCATCAAACACTCCTTGCTAATCT 59.603 41.667 0.00 0.00 0.00 2.40
3410 3721 2.037641 TCGATATGCCACTCCAATCCTG 59.962 50.000 0.00 0.00 0.00 3.86
3816 4376 6.664816 TGTATGCTTCTCCTTTTGATGGAATT 59.335 34.615 0.00 0.00 32.61 2.17
3821 4381 6.594788 TTCTCCTTTTGATGGAATTCCTTG 57.405 37.500 24.73 6.83 36.82 3.61
4124 4693 2.401766 GGATGCCCAGTTGCACTCG 61.402 63.158 0.00 0.00 45.48 4.18
4165 4734 4.176271 GCCAACCAAATGCTATCTTCAAC 58.824 43.478 0.00 0.00 0.00 3.18
4244 4813 1.070105 TCGCTGTAAAACGCTGGGT 59.930 52.632 0.00 0.00 0.00 4.51
4305 4874 4.948608 TTGAAGCGAGTGTTTGTGTTTA 57.051 36.364 0.00 0.00 0.00 2.01
4391 5002 5.534278 TCTCACAATGTTGCCTGTAAATTCA 59.466 36.000 0.00 0.00 0.00 2.57
4395 5006 4.870123 ATGTTGCCTGTAAATTCAAGCA 57.130 36.364 0.00 0.00 33.70 3.91
4402 5013 4.742138 GCCTGTAAATTCAAGCAACCCAAA 60.742 41.667 0.00 0.00 0.00 3.28
4603 5215 5.593909 TGAACTCATGGTGTTGACAAGAAAT 59.406 36.000 9.18 0.00 0.00 2.17
4722 5334 2.369860 TGGTGACATGCTTCAGTCTTCT 59.630 45.455 0.00 0.00 35.81 2.85
4766 5378 2.221981 GCTCTCGTGTGTCCAAAAGAAG 59.778 50.000 0.00 0.00 0.00 2.85
4800 5412 1.078848 GCATCAGAACCCTCGCTGT 60.079 57.895 0.00 0.00 33.90 4.40
4921 5533 6.478512 TTGCCATACACACTATGATAGTCA 57.521 37.500 1.33 0.00 36.76 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.074248 TCGGGTTTTTCAGCCCTCC 59.926 57.895 0.00 0.00 42.67 4.30
24 25 2.796483 TTTGCATCCCCGTCCAGTCG 62.796 60.000 0.00 0.00 0.00 4.18
101 134 0.929244 AGCTGGCAATGGGGATTACT 59.071 50.000 0.00 0.00 0.00 2.24
157 190 1.001641 CTCTGCCTCCCCTTGGTTG 60.002 63.158 0.00 0.00 0.00 3.77
158 191 1.464198 ACTCTGCCTCCCCTTGGTT 60.464 57.895 0.00 0.00 0.00 3.67
159 192 2.208349 ACTCTGCCTCCCCTTGGT 59.792 61.111 0.00 0.00 0.00 3.67
200 233 2.500504 GGTCGTTCCTTGGTAGAATCCT 59.499 50.000 0.00 0.00 0.00 3.24
207 240 1.619827 ACATTCGGTCGTTCCTTGGTA 59.380 47.619 0.00 0.00 0.00 3.25
220 253 0.035458 GCCTCCCCTCATACATTCGG 59.965 60.000 0.00 0.00 0.00 4.30
258 291 3.392882 CCTCAAATTTGGCAGTTGTTCC 58.607 45.455 17.90 0.00 0.00 3.62
262 295 2.364970 TGACCCTCAAATTTGGCAGTTG 59.635 45.455 17.90 5.49 0.00 3.16
267 300 2.547855 GGTTGTGACCCTCAAATTTGGC 60.548 50.000 17.90 0.00 40.25 4.52
278 311 1.003718 CTTCCCTCGGTTGTGACCC 60.004 63.158 0.00 0.00 43.42 4.46
302 335 2.190161 CTGCGTCGTCGAATATTCCAA 58.810 47.619 9.87 0.00 39.71 3.53
314 347 1.503818 AAATTTGACCGCTGCGTCGT 61.504 50.000 21.59 12.54 35.40 4.34
315 348 1.059657 CAAATTTGACCGCTGCGTCG 61.060 55.000 21.59 9.06 35.40 5.12
339 372 2.048503 CGTGTCCCCTTGGTCGTC 60.049 66.667 0.00 0.00 0.00 4.20
354 387 1.591594 CGATGGCGTGCCTATTCGT 60.592 57.895 12.84 0.00 36.94 3.85
397 430 0.037326 TCTCGTCCATGTTGGTGCTC 60.037 55.000 0.00 0.00 39.03 4.26
398 431 0.036952 CTCTCGTCCATGTTGGTGCT 60.037 55.000 0.00 0.00 39.03 4.40
399 432 1.639298 GCTCTCGTCCATGTTGGTGC 61.639 60.000 0.00 0.00 39.03 5.01
400 433 0.320683 TGCTCTCGTCCATGTTGGTG 60.321 55.000 0.00 0.00 39.03 4.17
401 434 0.320771 GTGCTCTCGTCCATGTTGGT 60.321 55.000 0.00 0.00 39.03 3.67
402 435 1.021390 GGTGCTCTCGTCCATGTTGG 61.021 60.000 0.00 0.00 39.43 3.77
403 436 1.354337 CGGTGCTCTCGTCCATGTTG 61.354 60.000 0.00 0.00 0.00 3.33
404 437 1.079819 CGGTGCTCTCGTCCATGTT 60.080 57.895 0.00 0.00 0.00 2.71
405 438 2.573869 CGGTGCTCTCGTCCATGT 59.426 61.111 0.00 0.00 0.00 3.21
406 439 2.887568 GCGGTGCTCTCGTCCATG 60.888 66.667 0.00 0.00 0.00 3.66
407 440 4.498520 CGCGGTGCTCTCGTCCAT 62.499 66.667 0.00 0.00 0.00 3.41
409 442 2.332362 TTATCGCGGTGCTCTCGTCC 62.332 60.000 6.13 0.00 0.00 4.79
410 443 0.930742 CTTATCGCGGTGCTCTCGTC 60.931 60.000 6.13 0.00 0.00 4.20
411 444 1.064296 CTTATCGCGGTGCTCTCGT 59.936 57.895 6.13 0.00 0.00 4.18
412 445 1.658717 CCTTATCGCGGTGCTCTCG 60.659 63.158 6.13 0.00 0.00 4.04
413 446 1.951631 GCCTTATCGCGGTGCTCTC 60.952 63.158 6.13 0.00 0.00 3.20
414 447 2.107141 GCCTTATCGCGGTGCTCT 59.893 61.111 6.13 0.00 0.00 4.09
476 509 5.473273 TCCACCTAGAAAGCAATCCCTATA 58.527 41.667 0.00 0.00 0.00 1.31
479 512 2.562296 TCCACCTAGAAAGCAATCCCT 58.438 47.619 0.00 0.00 0.00 4.20
575 608 3.645268 AAATCCTGGCCACCCGCTC 62.645 63.158 0.00 0.00 37.74 5.03
576 609 3.661648 AAATCCTGGCCACCCGCT 61.662 61.111 0.00 0.00 37.74 5.52
578 611 1.606313 AACAAATCCTGGCCACCCG 60.606 57.895 0.00 0.00 0.00 5.28
580 613 0.831711 ACCAACAAATCCTGGCCACC 60.832 55.000 0.00 0.00 36.03 4.61
582 615 0.105760 ACACCAACAAATCCTGGCCA 60.106 50.000 4.71 4.71 36.03 5.36
584 617 0.318120 CCACACCAACAAATCCTGGC 59.682 55.000 0.00 0.00 36.03 4.85
585 618 1.888512 CTCCACACCAACAAATCCTGG 59.111 52.381 0.00 0.00 38.77 4.45
590 624 2.363306 TCTGCTCCACACCAACAAAT 57.637 45.000 0.00 0.00 0.00 2.32
645 679 2.419673 CCTGCGTTTTCAGCATGTCATA 59.580 45.455 0.00 0.00 44.26 2.15
647 681 0.592637 CCTGCGTTTTCAGCATGTCA 59.407 50.000 0.00 0.00 44.26 3.58
648 682 0.593128 ACCTGCGTTTTCAGCATGTC 59.407 50.000 0.00 0.00 44.26 3.06
649 683 1.535462 GTACCTGCGTTTTCAGCATGT 59.465 47.619 0.00 4.72 44.26 3.21
650 684 1.464023 CGTACCTGCGTTTTCAGCATG 60.464 52.381 0.00 0.00 44.26 4.06
651 685 0.796312 CGTACCTGCGTTTTCAGCAT 59.204 50.000 0.00 0.00 44.26 3.79
652 686 1.225376 CCGTACCTGCGTTTTCAGCA 61.225 55.000 0.00 0.00 42.99 4.41
653 687 0.947180 TCCGTACCTGCGTTTTCAGC 60.947 55.000 0.00 0.00 32.87 4.26
654 688 1.722011 ATCCGTACCTGCGTTTTCAG 58.278 50.000 0.00 0.00 0.00 3.02
666 701 1.192312 CACGCACATGCATATCCGTAC 59.808 52.381 14.59 0.00 42.21 3.67
813 855 2.609737 GCCATAATAAGGTCGTCCGAGG 60.610 54.545 0.00 0.00 39.05 4.63
867 910 1.114627 GGAATGGCCCCATGACTTTC 58.885 55.000 0.00 0.00 36.68 2.62
1711 2012 2.309136 AAGTGGGATCCAACCAAAGG 57.691 50.000 16.23 0.00 40.24 3.11
1730 2031 1.196104 CCACGGGTCCAAAGGGTCTA 61.196 60.000 0.00 0.00 34.93 2.59
1748 2049 7.672983 TCATCACACTTAAAAGATTGAGACC 57.327 36.000 0.00 0.00 0.00 3.85
1861 2162 6.021596 GCACTATGGTAGTCGAAAATGTTTG 58.978 40.000 0.00 0.00 36.76 2.93
1872 2173 2.159226 ACTCGCTTGCACTATGGTAGTC 60.159 50.000 0.00 0.00 36.76 2.59
1881 2182 3.403038 ACAATCTTAACTCGCTTGCACT 58.597 40.909 0.00 0.00 0.00 4.40
1958 2259 4.733405 GTGTCAAATTCAGTGAACGAAACC 59.267 41.667 7.96 0.00 0.00 3.27
2360 2662 7.784037 TGCTGCCATACAAATTCAGATATTTT 58.216 30.769 0.00 0.00 0.00 1.82
2391 2693 1.344438 TGACTTCAGGCACGAACATCT 59.656 47.619 0.00 0.00 0.00 2.90
2407 2709 5.539955 AGGTTGCTAAATTTGTGGAATGACT 59.460 36.000 0.00 0.22 0.00 3.41
2449 2751 7.533426 ACTGTTTTGATAGACTTCATTGCATC 58.467 34.615 0.00 0.00 0.00 3.91
2477 2779 5.780958 ATGTTTTCTTAGGTAGGCCTCTT 57.219 39.130 9.68 0.00 45.64 2.85
2569 2871 3.626670 GGTCAGAAGGAAATGATCTGCTG 59.373 47.826 0.00 0.00 40.26 4.41
2570 2872 3.681034 CGGTCAGAAGGAAATGATCTGCT 60.681 47.826 0.00 0.00 40.26 4.24
2571 2873 2.611292 CGGTCAGAAGGAAATGATCTGC 59.389 50.000 0.00 0.00 40.26 4.26
2621 2932 5.826643 AGGACCAAGGTATTAAGCATTTCA 58.173 37.500 0.00 0.00 0.00 2.69
2674 2985 2.463752 CTGTTAGGTACCCAGTGCCTA 58.536 52.381 8.74 7.41 46.31 3.93
2772 3083 3.182372 GCACTTTTCTTGATGTTTTCGGC 59.818 43.478 0.00 0.00 0.00 5.54
2917 3228 6.997655 TGATTAGTCTGTATGCCCATCTAAG 58.002 40.000 0.00 0.00 0.00 2.18
3267 3578 8.433421 AATGTAGTACAAAAGATTCCATACGG 57.567 34.615 7.16 0.00 0.00 4.02
3375 3686 7.936847 AGTGGCATATCGACTTAAATCCAATAA 59.063 33.333 0.00 0.00 28.71 1.40
3390 3701 2.224378 ACAGGATTGGAGTGGCATATCG 60.224 50.000 0.00 0.00 0.00 2.92
3665 4216 3.329300 TGCCAGGCAGAACTCTTTC 57.671 52.632 11.22 0.00 33.32 2.62
4124 4693 0.236711 CAGGATGCGGCGATCAATTC 59.763 55.000 12.98 0.00 0.00 2.17
4165 4734 6.370442 TGATAATGAGGTTTTAGGTTCACACG 59.630 38.462 0.00 0.00 0.00 4.49
4244 4813 5.132502 CAGTATCCTACATTGCCCATGAAA 58.867 41.667 0.00 0.00 36.24 2.69
4305 4874 8.970859 ATGCTAGCAGATACAAAAAGATAGTT 57.029 30.769 23.89 0.00 0.00 2.24
4349 4918 3.131396 GAGAGCAGTTCCAACGAGAAAA 58.869 45.455 0.00 0.00 0.00 2.29
4391 5002 6.186420 AACCAAAGATATTTTGGGTTGCTT 57.814 33.333 15.38 6.66 46.63 3.91
4402 5013 9.696917 GACATTTTTCACAGAACCAAAGATATT 57.303 29.630 0.00 0.00 0.00 1.28
4497 5108 9.200817 AGGTTTTGTTGGTAATGCTAATATGAT 57.799 29.630 0.00 0.00 0.00 2.45
4585 5196 7.866898 TCATGTTAATTTCTTGTCAACACCATG 59.133 33.333 0.00 0.00 32.39 3.66
4603 5215 4.263435 TGCTGCTGATGTCATCATGTTAA 58.737 39.130 15.84 0.44 38.85 2.01
4647 5259 1.558756 GCTATCTCCTCCCATCCCATG 59.441 57.143 0.00 0.00 0.00 3.66
4671 5283 0.532417 CTGCACTAGCCTCCTGATGC 60.532 60.000 0.00 0.00 41.13 3.91
4722 5334 3.213506 ACACTGCTGAAATGTTACTGCA 58.786 40.909 0.00 0.00 38.71 4.41
4746 5358 2.221981 GCTTCTTTTGGACACACGAGAG 59.778 50.000 0.00 0.00 0.00 3.20
4766 5378 4.828925 GCAGAGGAGAGCGGGTGC 62.829 72.222 0.00 0.00 43.24 5.01
4921 5533 7.530426 AGCAACTAATTTCTCCAGAATTGTT 57.470 32.000 0.00 0.00 33.54 2.83


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

AutoCloner maintained by Alex Coulton.