Multiple sequence alignment - TraesCS1B01G245400

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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 TraesCS1B01G245400 chr1B 100.000 4972 0 0 1 4972 434568066 434563095 0.000000e+00 9182
1 TraesCS1B01G245400 chr1B 81.165 515 88 8 298 806 401264717 401264206 5.990000e-109 405
2 TraesCS1B01G245400 chr1B 86.928 153 18 2 3825 3976 434564101 434563950 2.380000e-38 171
3 TraesCS1B01G245400 chr1B 86.928 153 18 2 3966 4117 434564242 434564091 2.380000e-38 171
4 TraesCS1B01G245400 chr1D 95.536 2397 75 12 2084 4463 321924427 321922046 0.000000e+00 3805
5 TraesCS1B01G245400 chr1D 94.118 2057 83 15 59 2083 321926511 321924461 0.000000e+00 3094
6 TraesCS1B01G245400 chr1D 88.866 494 42 10 4478 4962 481421915 481422404 3.310000e-166 595
7 TraesCS1B01G245400 chr1D 87.780 491 51 6 4488 4972 402303466 402302979 2.600000e-157 566
8 TraesCS1B01G245400 chr1D 80.106 754 119 18 30 781 234443232 234443956 2.630000e-147 532
9 TraesCS1B01G245400 chr1D 83.562 438 69 3 334 768 298324342 298323905 1.670000e-109 407
10 TraesCS1B01G245400 chr1D 84.967 153 21 2 3825 3976 321922542 321922391 2.400000e-33 154
11 TraesCS1B01G245400 chr1A 93.825 1409 58 10 3066 4463 405518524 405517134 0.000000e+00 2093
12 TraesCS1B01G245400 chr1A 91.548 1550 72 15 567 2083 405523033 405521510 0.000000e+00 2082
13 TraesCS1B01G245400 chr1A 90.609 1001 65 19 2084 3072 405521476 405520493 0.000000e+00 1301
14 TraesCS1B01G245400 chr1A 88.153 574 40 3 1 571 405561638 405561090 0.000000e+00 658
15 TraesCS1B01G245400 chr6D 89.641 502 38 8 4481 4972 158819764 158820261 1.170000e-175 627
16 TraesCS1B01G245400 chr3D 88.409 509 38 16 4480 4972 567669856 567669353 1.190000e-165 593
17 TraesCS1B01G245400 chr3D 79.948 773 111 25 1 770 512611084 512611815 3.410000e-146 529
18 TraesCS1B01G245400 chr7A 88.176 499 48 9 4481 4972 114093701 114093207 7.170000e-163 584
19 TraesCS1B01G245400 chr7A 85.324 293 39 3 1 292 443344459 443344170 2.910000e-77 300
20 TraesCS1B01G245400 chr2D 89.485 466 38 8 4515 4972 471642851 471643313 3.340000e-161 579
21 TraesCS1B01G245400 chr5D 88.272 486 45 8 4482 4959 29902299 29902780 5.580000e-159 571
22 TraesCS1B01G245400 chr5D 75.644 427 96 5 310 732 476835337 476834915 6.520000e-49 206
23 TraesCS1B01G245400 chr7D 87.129 505 52 7 4479 4972 319781859 319782361 1.210000e-155 560
24 TraesCS1B01G245400 chr7D 87.200 500 45 12 4480 4972 136688944 136688457 7.270000e-153 551
25 TraesCS1B01G245400 chr3B 79.871 775 110 27 4 774 675160662 675159930 4.410000e-145 525
26 TraesCS1B01G245400 chr3B 80.208 480 58 21 2 472 678231094 678230643 4.800000e-85 326
27 TraesCS1B01G245400 chr3B 88.889 108 9 2 1796 1902 442082484 442082589 4.040000e-26 130
28 TraesCS1B01G245400 chr2B 78.068 766 136 14 46 806 666189612 666188874 5.870000e-124 455
29 TraesCS1B01G245400 chr5B 79.010 586 102 18 1 570 352895402 352895982 1.010000e-101 381
30 TraesCS1B01G245400 chr6B 84.877 324 35 9 1 314 169169256 169168937 1.040000e-81 315


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 TraesCS1B01G245400 chr1B 434563095 434568066 4971 True 9182.000000 9182 100.000000 1 4972 1 chr1B.!!$R2 4971
1 TraesCS1B01G245400 chr1B 401264206 401264717 511 True 405.000000 405 81.165000 298 806 1 chr1B.!!$R1 508
2 TraesCS1B01G245400 chr1D 321922046 321926511 4465 True 2351.000000 3805 91.540333 59 4463 3 chr1D.!!$R3 4404
3 TraesCS1B01G245400 chr1D 234443232 234443956 724 False 532.000000 532 80.106000 30 781 1 chr1D.!!$F1 751
4 TraesCS1B01G245400 chr1A 405517134 405523033 5899 True 1825.333333 2093 91.994000 567 4463 3 chr1A.!!$R2 3896
5 TraesCS1B01G245400 chr1A 405561090 405561638 548 True 658.000000 658 88.153000 1 571 1 chr1A.!!$R1 570
6 TraesCS1B01G245400 chr3D 567669353 567669856 503 True 593.000000 593 88.409000 4480 4972 1 chr3D.!!$R1 492
7 TraesCS1B01G245400 chr3D 512611084 512611815 731 False 529.000000 529 79.948000 1 770 1 chr3D.!!$F1 769
8 TraesCS1B01G245400 chr7D 319781859 319782361 502 False 560.000000 560 87.129000 4479 4972 1 chr7D.!!$F1 493
9 TraesCS1B01G245400 chr3B 675159930 675160662 732 True 525.000000 525 79.871000 4 774 1 chr3B.!!$R1 770
10 TraesCS1B01G245400 chr2B 666188874 666189612 738 True 455.000000 455 78.068000 46 806 1 chr2B.!!$R1 760
11 TraesCS1B01G245400 chr5B 352895402 352895982 580 False 381.000000 381 79.010000 1 570 1 chr5B.!!$F1 569

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
563 639 0.181587 TTTTGGCGGTGAAGTGAGGA 59.818 50.000 0.00 0.00 0.00 3.71 F
757 834 1.522580 GCGGGTCTGGCAGAGAATC 60.523 63.158 19.38 5.82 30.26 2.52 F
1524 1635 2.230266 TGGTTTGGCCGCTAGAAAAATC 59.770 45.455 0.00 0.00 41.21 2.17 F
2756 2922 1.411787 CCCCATTTTAACCGCCCCATA 60.412 52.381 0.00 0.00 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2348 2501 0.318955 GACCCACACATGCTGTTTGC 60.319 55.000 0.00 0.0 43.25 3.68 R
2474 2636 0.875059 GGAGCACTGTAAACTGCACC 59.125 55.000 0.00 0.0 37.05 5.01 R
2875 3041 1.001378 GAGGACACACACATGCCAAAC 60.001 52.381 0.00 0.0 0.00 2.93 R
4470 6623 0.029577 GGAGGGGAGGGATTCTTCCT 60.030 60.000 1.52 0.0 41.17 3.36 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
25 26 7.108841 ACACTACATATGAACGGTATGAACT 57.891 36.000 10.38 0.00 34.44 3.01
48 49 2.094906 GCACTACCACATGTACAGACGA 60.095 50.000 0.00 0.00 0.00 4.20
171 182 5.367937 ACCAATTCATCACCACTAGCTATCT 59.632 40.000 0.00 0.00 0.00 1.98
308 377 3.719268 AACCCTATCACATGCTCACAA 57.281 42.857 0.00 0.00 0.00 3.33
309 378 3.719268 ACCCTATCACATGCTCACAAA 57.281 42.857 0.00 0.00 0.00 2.83
310 379 4.240881 ACCCTATCACATGCTCACAAAT 57.759 40.909 0.00 0.00 0.00 2.32
311 380 4.202441 ACCCTATCACATGCTCACAAATC 58.798 43.478 0.00 0.00 0.00 2.17
312 381 4.080129 ACCCTATCACATGCTCACAAATCT 60.080 41.667 0.00 0.00 0.00 2.40
313 382 5.130975 ACCCTATCACATGCTCACAAATCTA 59.869 40.000 0.00 0.00 0.00 1.98
314 383 6.057533 CCCTATCACATGCTCACAAATCTAA 58.942 40.000 0.00 0.00 0.00 2.10
315 384 6.017605 CCCTATCACATGCTCACAAATCTAAC 60.018 42.308 0.00 0.00 0.00 2.34
316 385 5.824904 ATCACATGCTCACAAATCTAACC 57.175 39.130 0.00 0.00 0.00 2.85
317 386 4.009675 TCACATGCTCACAAATCTAACCC 58.990 43.478 0.00 0.00 0.00 4.11
318 387 4.012374 CACATGCTCACAAATCTAACCCT 58.988 43.478 0.00 0.00 0.00 4.34
319 388 5.045942 TCACATGCTCACAAATCTAACCCTA 60.046 40.000 0.00 0.00 0.00 3.53
320 389 5.824624 CACATGCTCACAAATCTAACCCTAT 59.175 40.000 0.00 0.00 0.00 2.57
321 390 6.017605 CACATGCTCACAAATCTAACCCTATC 60.018 42.308 0.00 0.00 0.00 2.08
322 391 5.692115 TGCTCACAAATCTAACCCTATCA 57.308 39.130 0.00 0.00 0.00 2.15
323 392 5.428253 TGCTCACAAATCTAACCCTATCAC 58.572 41.667 0.00 0.00 0.00 3.06
324 393 5.045942 TGCTCACAAATCTAACCCTATCACA 60.046 40.000 0.00 0.00 0.00 3.58
325 394 6.058183 GCTCACAAATCTAACCCTATCACAT 58.942 40.000 0.00 0.00 0.00 3.21
326 395 6.017605 GCTCACAAATCTAACCCTATCACATG 60.018 42.308 0.00 0.00 0.00 3.21
327 396 5.822519 TCACAAATCTAACCCTATCACATGC 59.177 40.000 0.00 0.00 0.00 4.06
328 397 5.824624 CACAAATCTAACCCTATCACATGCT 59.175 40.000 0.00 0.00 0.00 3.79
329 398 6.017605 CACAAATCTAACCCTATCACATGCTC 60.018 42.308 0.00 0.00 0.00 4.26
330 399 5.894298 AATCTAACCCTATCACATGCTCA 57.106 39.130 0.00 0.00 0.00 4.26
331 400 6.445451 AATCTAACCCTATCACATGCTCAT 57.555 37.500 0.00 0.00 0.00 2.90
332 401 7.559335 AATCTAACCCTATCACATGCTCATA 57.441 36.000 0.00 0.00 0.00 2.15
377 447 2.568623 AGGGGTGATTGAACTCACAC 57.431 50.000 6.55 2.45 46.69 3.82
388 458 2.815211 CTCACACACGCCATCGGG 60.815 66.667 0.00 0.00 46.41 5.14
487 561 0.899720 CGAGCCCAACTTACCTGGTA 59.100 55.000 1.49 1.49 31.45 3.25
563 639 0.181587 TTTTGGCGGTGAAGTGAGGA 59.818 50.000 0.00 0.00 0.00 3.71
617 693 4.796495 GCCAATTCCTCCCGCCGT 62.796 66.667 0.00 0.00 0.00 5.68
666 742 4.425099 CTCCGTGGACTCTGGAGT 57.575 61.111 2.62 2.62 43.48 3.85
693 769 2.434331 CGTTCCCCTTCCCTGCAA 59.566 61.111 0.00 0.00 0.00 4.08
757 834 1.522580 GCGGGTCTGGCAGAGAATC 60.523 63.158 19.38 5.82 30.26 2.52
791 869 4.946772 TCATGCGGACCAAAATTCTGATAA 59.053 37.500 0.00 0.00 0.00 1.75
793 871 5.713792 TGCGGACCAAAATTCTGATAAAA 57.286 34.783 0.00 0.00 0.00 1.52
1053 1152 4.271016 GCCATGGATCCCCCGTCC 62.271 72.222 18.40 0.00 37.93 4.79
1191 1302 2.652095 CCTCTGGGACCGCGGTAAA 61.652 63.158 34.36 18.67 33.58 2.01
1278 1389 3.204526 AGATGCTTATGTGCTTCTCTGC 58.795 45.455 0.00 0.00 41.58 4.26
1434 1545 2.946762 GTTTGTCTGTCGGCCTGC 59.053 61.111 0.00 0.00 0.00 4.85
1523 1634 2.243810 TGGTTTGGCCGCTAGAAAAAT 58.756 42.857 0.00 0.00 41.21 1.82
1524 1635 2.230266 TGGTTTGGCCGCTAGAAAAATC 59.770 45.455 0.00 0.00 41.21 2.17
1539 1650 7.915397 GCTAGAAAAATCAGAAACAGTTCAACA 59.085 33.333 0.00 0.00 36.09 3.33
1549 1660 6.035975 CAGAAACAGTTCAACAAAATTGGACC 59.964 38.462 0.00 0.00 36.09 4.46
1569 1680 8.317891 TGGACCATTTATTTGTATATAGTGCG 57.682 34.615 0.00 0.00 0.00 5.34
1588 1699 3.118992 TGCGATCTCTATTCTGCTTGTGT 60.119 43.478 0.00 0.00 0.00 3.72
1590 1701 4.428209 CGATCTCTATTCTGCTTGTGTGT 58.572 43.478 0.00 0.00 0.00 3.72
1662 1777 5.198207 GGGGTTGTTATGTTTACTGCCTAT 58.802 41.667 0.00 0.00 0.00 2.57
1680 1795 5.412594 TGCCTATAGTGCTTTCAACTTTCAG 59.587 40.000 12.54 0.00 0.00 3.02
1713 1828 3.565482 AGAACTCGACAGGTGTACGTAAA 59.435 43.478 0.00 0.00 0.00 2.01
2091 2240 6.202762 GCTTTTTAACTCCACCCTTGAAATTG 59.797 38.462 0.00 0.00 0.00 2.32
2101 2250 4.222588 CACCCTTGAAATTGCTAATGGGAA 59.777 41.667 0.00 0.00 37.25 3.97
2147 2296 4.082463 ACTCAGACCTTCTCAATTCTCGAC 60.082 45.833 0.00 0.00 0.00 4.20
2465 2618 6.604735 ATCTGATTATTTTGTACTCGTGGC 57.395 37.500 0.00 0.00 0.00 5.01
2514 2678 3.434167 CCCTTGGCTGATGCATAGTACTT 60.434 47.826 0.00 0.00 41.91 2.24
2515 2679 3.812053 CCTTGGCTGATGCATAGTACTTC 59.188 47.826 0.00 0.00 41.91 3.01
2604 2768 5.233988 ACATGAAAACCGAAAGAGAGAGAG 58.766 41.667 0.00 0.00 0.00 3.20
2748 2914 7.651704 CGAATGTTATTCATCCCCATTTTAACC 59.348 37.037 2.86 0.00 35.48 2.85
2751 2917 1.770294 TCATCCCCATTTTAACCGCC 58.230 50.000 0.00 0.00 0.00 6.13
2756 2922 1.411787 CCCCATTTTAACCGCCCCATA 60.412 52.381 0.00 0.00 0.00 2.74
2808 2974 2.076863 GAGTGACATGGTTGGTGTAGC 58.923 52.381 0.00 0.00 0.00 3.58
2879 3045 9.850628 ATGAAATCTCACATGTAAATCAGTTTG 57.149 29.630 0.00 0.00 33.30 2.93
2903 3069 0.944386 GTGTGTGTCCTCAATTGCGT 59.056 50.000 0.00 0.00 0.00 5.24
2912 3078 4.021456 TGTCCTCAATTGCGTCTTTCTAGA 60.021 41.667 0.00 0.00 0.00 2.43
3034 3200 7.539022 CAGCTGATGATATTTTCTTCATGATGC 59.461 37.037 8.42 0.00 37.74 3.91
3171 5322 5.996669 TGCTGATATCTATGTGTGCAAAG 57.003 39.130 3.98 0.00 0.00 2.77
3266 5418 8.946085 CATGCAGAACCTTACTTGAAACTAATA 58.054 33.333 0.00 0.00 0.00 0.98
3430 5582 5.520288 GCTCAGACAAATCGAATGTAAGCTA 59.480 40.000 18.64 3.64 0.00 3.32
3814 5966 2.418368 TGGTCAATATCCTGTGGTGC 57.582 50.000 0.00 0.00 0.00 5.01
3902 6054 5.237127 TGGATTGATTAGCACATCGAACATC 59.763 40.000 0.00 0.00 0.00 3.06
4020 6172 5.974108 ACAATACTTGTATGAGCTACGGTT 58.026 37.500 0.00 0.00 43.27 4.44
4030 6182 7.269316 TGTATGAGCTACGGTTGATTGATTAA 58.731 34.615 0.00 0.00 32.61 1.40
4068 6220 6.591935 GTTGATGAGGACCAGGTTATATTCA 58.408 40.000 0.00 0.00 0.00 2.57
4096 6248 5.123502 CAGATTCTGACCTGATTTGGACAAG 59.876 44.000 8.00 0.00 32.44 3.16
4288 6440 6.767524 TTAAATATATTTGCCCCCGCATAG 57.232 37.500 18.98 0.00 46.67 2.23
4410 6563 4.924305 TTACACACCTCTTGTACTTCGT 57.076 40.909 0.00 0.00 35.67 3.85
4427 6580 5.730550 ACTTCGTTAGTCTGGATTTGCATA 58.269 37.500 0.00 0.00 28.23 3.14
4463 6616 3.515502 CTCCATCCAACTAGACCACAAGA 59.484 47.826 0.00 0.00 0.00 3.02
4464 6617 4.104086 TCCATCCAACTAGACCACAAGAT 58.896 43.478 0.00 0.00 0.00 2.40
4465 6618 4.162320 TCCATCCAACTAGACCACAAGATC 59.838 45.833 0.00 0.00 0.00 2.75
4466 6619 4.163078 CCATCCAACTAGACCACAAGATCT 59.837 45.833 0.00 0.00 0.00 2.75
4467 6620 4.808414 TCCAACTAGACCACAAGATCTG 57.192 45.455 0.00 0.00 0.00 2.90
4468 6621 4.160329 TCCAACTAGACCACAAGATCTGT 58.840 43.478 0.00 0.00 39.56 3.41
4490 6643 1.411651 GGAAGAATCCCTCCCCTCCG 61.412 65.000 0.00 0.00 40.10 4.63
4513 6666 1.077625 CCCTCCCCTCTAGATCCCG 59.922 68.421 0.00 0.00 0.00 5.14
4514 6667 1.731324 CCCTCCCCTCTAGATCCCGT 61.731 65.000 0.00 0.00 0.00 5.28
4517 6670 1.604023 CCCCTCTAGATCCCGTCCG 60.604 68.421 0.00 0.00 0.00 4.79
4518 6671 2.269529 CCCTCTAGATCCCGTCCGC 61.270 68.421 0.00 0.00 0.00 5.54
4520 6673 1.228306 CTCTAGATCCCGTCCGCCT 60.228 63.158 0.00 0.00 0.00 5.52
4521 6674 1.228184 TCTAGATCCCGTCCGCCTC 60.228 63.158 0.00 0.00 0.00 4.70
4692 6861 4.577677 ACGTGTGTGGCCATGGCA 62.578 61.111 36.56 20.63 44.11 4.92
4705 6874 2.818169 ATGGCACCGGTCACACAGT 61.818 57.895 2.59 0.00 0.00 3.55
4709 6878 0.037697 GCACCGGTCACACAGTGATA 60.038 55.000 2.59 0.00 44.63 2.15
4728 6897 5.364157 GTGATATGACCTCCTCTACCTTTGT 59.636 44.000 0.00 0.00 0.00 2.83
4755 6924 0.460284 CATCGTCGGTCCAAAGGGAG 60.460 60.000 0.00 0.00 46.12 4.30
4762 6931 1.761174 GTCCAAAGGGAGCTGGTCA 59.239 57.895 9.30 0.00 46.12 4.02
4827 6999 1.341156 GGAGATGGTGGCCTAGCTGT 61.341 60.000 3.32 0.00 0.00 4.40
4883 7055 1.226030 CCGTGGGTGTCGTTTTCCTC 61.226 60.000 0.00 0.00 0.00 3.71
4884 7056 1.554042 CGTGGGTGTCGTTTTCCTCG 61.554 60.000 0.00 0.00 0.00 4.63
4899 7073 1.811266 CTCGTTGGAGGCGATGGTG 60.811 63.158 0.00 0.00 37.74 4.17
4930 7104 1.001393 GCTCCATTGTTTCCGGGGA 60.001 57.895 0.00 0.00 0.00 4.81
4944 7119 2.116238 CCGGGGAAAACCTCAGATCTA 58.884 52.381 0.00 0.00 40.03 1.98
4962 7137 4.477536 TCTAGAGGAGGCTACCATTGAT 57.522 45.455 0.00 0.00 0.00 2.57
4963 7138 5.600669 TCTAGAGGAGGCTACCATTGATA 57.399 43.478 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.730949 TGTGGTAGTGCTAGTTCATACC 57.269 45.455 8.00 8.00 37.09 2.73
25 26 3.128068 CGTCTGTACATGTGGTAGTGCTA 59.872 47.826 9.11 0.00 31.13 3.49
48 49 6.000219 AGTTGCTGTGTTGAACTAGATCATT 59.000 36.000 3.25 0.00 0.00 2.57
103 104 9.203421 GTATATGCTAGTATGCAAACATGTGTA 57.797 33.333 0.00 0.00 46.61 2.90
171 182 4.545208 TGTTTCCATGTCGACAAGGATA 57.455 40.909 35.45 29.28 42.50 2.59
308 377 5.894298 TGAGCATGTGATAGGGTTAGATT 57.106 39.130 0.00 0.00 0.00 2.40
309 378 6.956435 TCTATGAGCATGTGATAGGGTTAGAT 59.044 38.462 0.00 0.00 0.00 1.98
310 379 6.314917 TCTATGAGCATGTGATAGGGTTAGA 58.685 40.000 0.00 0.00 0.00 2.10
311 380 6.596309 TCTATGAGCATGTGATAGGGTTAG 57.404 41.667 0.00 0.00 0.00 2.34
312 381 6.956435 AGATCTATGAGCATGTGATAGGGTTA 59.044 38.462 0.00 0.00 0.00 2.85
313 382 5.784390 AGATCTATGAGCATGTGATAGGGTT 59.216 40.000 0.00 0.00 0.00 4.11
314 383 5.340322 AGATCTATGAGCATGTGATAGGGT 58.660 41.667 0.00 0.00 0.00 4.34
315 384 5.936187 AGATCTATGAGCATGTGATAGGG 57.064 43.478 0.00 0.00 0.00 3.53
316 385 8.065473 AGTTAGATCTATGAGCATGTGATAGG 57.935 38.462 2.58 0.00 0.00 2.57
318 387 9.965902 TCTAGTTAGATCTATGAGCATGTGATA 57.034 33.333 2.58 0.00 0.00 2.15
319 388 8.876303 TCTAGTTAGATCTATGAGCATGTGAT 57.124 34.615 2.58 0.00 0.00 3.06
320 389 8.697507 TTCTAGTTAGATCTATGAGCATGTGA 57.302 34.615 2.58 0.00 31.40 3.58
321 390 9.356433 CATTCTAGTTAGATCTATGAGCATGTG 57.644 37.037 2.58 0.00 31.40 3.21
322 391 9.306777 TCATTCTAGTTAGATCTATGAGCATGT 57.693 33.333 2.58 0.00 28.92 3.21
323 392 9.791820 CTCATTCTAGTTAGATCTATGAGCATG 57.208 37.037 13.71 11.74 37.89 4.06
324 393 9.532494 ACTCATTCTAGTTAGATCTATGAGCAT 57.468 33.333 21.42 7.58 42.94 3.79
325 394 8.932434 ACTCATTCTAGTTAGATCTATGAGCA 57.068 34.615 21.42 5.49 42.94 4.26
388 458 1.856265 CGCACCTCCTTCAAGTTGCC 61.856 60.000 0.00 0.00 0.00 4.52
510 584 1.687493 CCCCCTCTCGAGCTTTCCT 60.687 63.158 7.81 0.00 0.00 3.36
538 614 1.318576 CTTCACCGCCAAAACTTCCT 58.681 50.000 0.00 0.00 0.00 3.36
563 639 0.034896 CGGTCGCCCTATTTAGCCAT 59.965 55.000 0.00 0.00 0.00 4.40
642 718 0.689080 AGAGTCCACGGAGATGGCAT 60.689 55.000 0.00 0.00 39.85 4.40
757 834 2.851824 GGTCCGCATGAAATTTAAAGCG 59.148 45.455 16.47 16.47 44.24 4.68
1191 1302 2.687200 TGGGGCAGTGGCGATAGT 60.687 61.111 10.99 0.00 42.47 2.12
1217 1328 2.182516 AGAGGCTAACAGGGCATAGT 57.817 50.000 0.00 0.00 0.00 2.12
1365 1476 4.794439 TGGAGCGCACATCGTCGG 62.794 66.667 11.47 0.00 41.07 4.79
1434 1545 4.101448 CCCTGTTCCTCTGCCCGG 62.101 72.222 0.00 0.00 0.00 5.73
1445 1556 0.478072 TTCCTGTGCACATCCCTGTT 59.522 50.000 22.00 0.00 31.62 3.16
1523 1634 6.811170 GTCCAATTTTGTTGAACTGTTTCTGA 59.189 34.615 0.00 0.00 32.36 3.27
1524 1635 6.035975 GGTCCAATTTTGTTGAACTGTTTCTG 59.964 38.462 0.00 0.00 32.36 3.02
1545 1656 8.542497 TCGCACTATATACAAATAAATGGTCC 57.458 34.615 0.00 0.00 0.00 4.46
1560 1671 7.093988 ACAAGCAGAATAGAGATCGCACTATAT 60.094 37.037 0.00 0.00 29.39 0.86
1563 1674 4.339530 ACAAGCAGAATAGAGATCGCACTA 59.660 41.667 0.00 0.00 0.00 2.74
1564 1675 3.131933 ACAAGCAGAATAGAGATCGCACT 59.868 43.478 0.00 0.00 0.00 4.40
1569 1680 5.005203 CGAACACACAAGCAGAATAGAGATC 59.995 44.000 0.00 0.00 0.00 2.75
1603 1714 2.438975 ATGGTGAGCATGCACGGG 60.439 61.111 21.98 0.00 39.66 5.28
1662 1777 6.293955 GCATTACCTGAAAGTTGAAAGCACTA 60.294 38.462 0.00 0.00 0.00 2.74
1680 1795 4.498345 CCTGTCGAGTTCTCTAGCATTACC 60.498 50.000 0.00 0.00 0.00 2.85
1713 1828 8.940012 ATCCCCTTTCCATCAATATACTAGAT 57.060 34.615 0.00 0.00 0.00 1.98
1725 1840 5.507985 CGCAAATTCTAATCCCCTTTCCATC 60.508 44.000 0.00 0.00 0.00 3.51
1794 1909 1.260544 GCTGACTGGGAAAGGCAAAT 58.739 50.000 0.00 0.00 45.94 2.32
2091 2240 3.846588 TCCTAGATCCCATTCCCATTAGC 59.153 47.826 0.00 0.00 0.00 3.09
2101 2250 5.662208 GTCATGATCATCTCCTAGATCCCAT 59.338 44.000 4.86 0.00 39.86 4.00
2147 2296 7.133891 AGTCTTAAACATTGATTTCCGACTG 57.866 36.000 0.00 0.00 33.49 3.51
2346 2499 0.319211 CCCACACATGCTGTTTGCTG 60.319 55.000 0.00 0.00 43.37 4.41
2348 2501 0.318955 GACCCACACATGCTGTTTGC 60.319 55.000 0.00 0.00 43.25 3.68
2474 2636 0.875059 GGAGCACTGTAAACTGCACC 59.125 55.000 0.00 0.00 37.05 5.01
2514 2678 9.264653 AGATATCTTGTATCCAGATAATGCTGA 57.735 33.333 0.00 0.00 38.14 4.26
2604 2768 5.123027 CAGAACTAGAGACCCAGCATTTTTC 59.877 44.000 0.00 0.00 0.00 2.29
2676 2842 5.571784 TTCTTCAAATCTAATGCCAGCAG 57.428 39.130 0.00 0.00 0.00 4.24
2677 2843 5.711506 TCTTTCTTCAAATCTAATGCCAGCA 59.288 36.000 0.00 0.00 0.00 4.41
2748 2914 3.067106 CAGTGTAGCTTATTATGGGGCG 58.933 50.000 0.00 0.00 0.00 6.13
2751 2917 3.990092 TCGCAGTGTAGCTTATTATGGG 58.010 45.455 0.00 0.00 0.00 4.00
2756 2922 6.683974 ATTGAATTCGCAGTGTAGCTTATT 57.316 33.333 0.00 0.00 0.00 1.40
2875 3041 1.001378 GAGGACACACACATGCCAAAC 60.001 52.381 0.00 0.00 0.00 2.93
2879 3045 1.538047 ATTGAGGACACACACATGCC 58.462 50.000 0.00 0.00 0.00 4.40
3171 5322 8.396390 CAATAACTTGCATGATCTATATGAGCC 58.604 37.037 6.60 0.00 0.00 4.70
3323 5475 6.037062 CGTGTGATTGATCAGCTATTTTGGTA 59.963 38.462 0.00 0.00 37.51 3.25
3902 6054 3.198068 CATAACCTGGTCCTCATCAACG 58.802 50.000 0.00 0.00 0.00 4.10
4020 6172 6.312672 ACGATGTTCGATGTGTTAATCAATCA 59.687 34.615 3.62 0.00 43.74 2.57
4030 6182 3.584834 TCATCAACGATGTTCGATGTGT 58.415 40.909 3.62 0.00 43.74 3.72
4068 6220 5.013495 TCCAAATCAGGTCAGAATCTGAAGT 59.987 40.000 15.28 2.04 42.46 3.01
4096 6248 1.067250 GCTCGGTGCCAGAGAGATC 59.933 63.158 12.02 0.00 37.93 2.75
4170 6322 1.276421 ACTGCTGGATGTAGTGGTCAC 59.724 52.381 0.00 0.00 40.11 3.67
4427 6580 4.863548 TGGATGGAGCTCTGAAATGAATT 58.136 39.130 14.64 0.00 0.00 2.17
4470 6623 0.029577 GGAGGGGAGGGATTCTTCCT 60.030 60.000 1.52 0.00 41.17 3.36
4471 6624 1.411651 CGGAGGGGAGGGATTCTTCC 61.412 65.000 0.00 0.00 40.64 3.46
4472 6625 2.046009 GCGGAGGGGAGGGATTCTTC 62.046 65.000 0.00 0.00 0.00 2.87
4473 6626 2.073101 GCGGAGGGGAGGGATTCTT 61.073 63.158 0.00 0.00 0.00 2.52
4474 6627 2.446802 GCGGAGGGGAGGGATTCT 60.447 66.667 0.00 0.00 0.00 2.40
4475 6628 3.561241 GGCGGAGGGGAGGGATTC 61.561 72.222 0.00 0.00 0.00 2.52
4476 6629 4.109656 AGGCGGAGGGGAGGGATT 62.110 66.667 0.00 0.00 0.00 3.01
4477 6630 4.565850 GAGGCGGAGGGGAGGGAT 62.566 72.222 0.00 0.00 0.00 3.85
4490 6643 1.745879 ATCTAGAGGGGAGGGGAGGC 61.746 65.000 0.00 0.00 0.00 4.70
4498 6651 1.851987 GGACGGGATCTAGAGGGGA 59.148 63.158 0.00 0.00 0.00 4.81
4505 6658 2.203451 GGAGGCGGACGGGATCTA 60.203 66.667 0.00 0.00 0.00 1.98
4518 6671 3.711782 AAGGGAGGGGAGGGGAGG 61.712 72.222 0.00 0.00 0.00 4.30
4520 6673 3.707189 GGAAGGGAGGGGAGGGGA 61.707 72.222 0.00 0.00 0.00 4.81
4615 6782 2.736995 CTCCAAGCCGCGACGAAA 60.737 61.111 8.23 0.00 0.00 3.46
4692 6861 2.094182 GTCATATCACTGTGTGACCGGT 60.094 50.000 6.92 6.92 45.65 5.28
4701 6870 4.169068 AGGTAGAGGAGGTCATATCACTGT 59.831 45.833 0.00 0.00 0.00 3.55
4705 6874 5.529289 ACAAAGGTAGAGGAGGTCATATCA 58.471 41.667 0.00 0.00 0.00 2.15
4709 6878 3.772025 CAGACAAAGGTAGAGGAGGTCAT 59.228 47.826 0.00 0.00 0.00 3.06
4728 6897 0.809385 GGACCGACGATGAAGACAGA 59.191 55.000 0.00 0.00 0.00 3.41
4755 6924 2.555547 GCAACACCCACTGACCAGC 61.556 63.158 0.00 0.00 0.00 4.85
4762 6931 2.111043 CGTGAGGCAACACCCACT 59.889 61.111 8.72 0.00 40.58 4.00
4827 6999 0.038166 GGCATCCTCACCCACTTCAA 59.962 55.000 0.00 0.00 0.00 2.69
4883 7055 2.819595 CCACCATCGCCTCCAACG 60.820 66.667 0.00 0.00 0.00 4.10
4884 7056 2.438434 CCCACCATCGCCTCCAAC 60.438 66.667 0.00 0.00 0.00 3.77
4944 7119 2.903135 GCTATCAATGGTAGCCTCCTCT 59.097 50.000 14.28 0.00 38.85 3.69


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

AutoCloner maintained by Alex Coulton.