Multiple sequence alignment - TraesCS7A01G262600

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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 TraesCS7A01G262600 chr7A 100.000 2663 0 0 1 2663 258823060 258825722 0.000000e+00 4918.0
1 TraesCS7A01G262600 chr7D 91.964 2016 68 26 728 2662 243807453 243809455 0.000000e+00 2739.0
2 TraesCS7A01G262600 chr7D 86.708 489 41 8 1 471 243806606 243807088 3.040000e-144 521.0
3 TraesCS7A01G262600 chr7B 89.545 1186 67 16 732 1889 218976752 218975596 0.000000e+00 1450.0
4 TraesCS7A01G262600 chr5A 90.972 288 26 0 1310 1597 453519495 453519782 3.210000e-104 388.0
5 TraesCS7A01G262600 chr5D 90.877 285 26 0 1313 1597 352454408 352454124 1.500000e-102 383.0
6 TraesCS7A01G262600 chr5D 96.875 32 0 1 606 637 515631721 515631751 5.000000e-03 52.8
7 TraesCS7A01G262600 chr3A 90.877 285 26 0 1313 1597 398879801 398879517 1.500000e-102 383.0
8 TraesCS7A01G262600 chr3A 83.636 165 24 3 1404 1567 599326205 599326367 4.590000e-33 152.0
9 TraesCS7A01G262600 chr6A 90.526 285 27 0 1313 1597 116813216 116812932 6.960000e-101 377.0
10 TraesCS7A01G262600 chr5B 90.526 285 27 0 1313 1597 415127717 415127433 6.960000e-101 377.0
11 TraesCS7A01G262600 chr5B 85.714 56 5 3 583 636 613636363 613636309 3.700000e-04 56.5
12 TraesCS7A01G262600 chr3D 83.735 166 22 5 1404 1567 456534480 456534642 4.590000e-33 152.0
13 TraesCS7A01G262600 chr4D 81.081 185 30 3 37 221 502112611 502112790 2.760000e-30 143.0
14 TraesCS7A01G262600 chr4D 93.023 43 3 0 2620 2662 506718625 506718667 2.210000e-06 63.9


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 TraesCS7A01G262600 chr7A 258823060 258825722 2662 False 4918 4918 100.000 1 2663 1 chr7A.!!$F1 2662
1 TraesCS7A01G262600 chr7D 243806606 243809455 2849 False 1630 2739 89.336 1 2662 2 chr7D.!!$F1 2661
2 TraesCS7A01G262600 chr7B 218975596 218976752 1156 True 1450 1450 89.545 732 1889 1 chr7B.!!$R1 1157

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
520 536 0.0293 ATGAAATTTCGGATGCGGCG 59.971 50.0 13.34 0.51 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2329 2647 0.038618 TGAGGACGTGGTTGACATCG 60.039 55.0 0.0 0.0 0.0 3.84 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 2.016704 GCCGCCGATGATGTCTACG 61.017 63.158 0.00 0.00 0.00 3.51
65 78 1.279496 CAGGAGGTGATGGAGGAACA 58.721 55.000 0.00 0.00 0.00 3.18
69 82 1.078426 GGTGATGGAGGAACACCCG 60.078 63.158 0.00 0.00 45.53 5.28
70 83 1.078426 GTGATGGAGGAACACCCGG 60.078 63.158 0.00 0.00 38.71 5.73
79 92 1.605453 GAACACCCGGCTATCCCAA 59.395 57.895 0.00 0.00 0.00 4.12
89 102 1.692411 GCTATCCCAATGTGGAACCC 58.308 55.000 0.00 0.00 40.96 4.11
91 104 1.488812 CTATCCCAATGTGGAACCCGA 59.511 52.381 0.00 0.00 40.96 5.14
95 108 0.250727 CCAATGTGGAACCCGACACT 60.251 55.000 0.00 0.00 40.96 3.55
96 109 0.874390 CAATGTGGAACCCGACACTG 59.126 55.000 0.00 0.00 38.39 3.66
101 114 1.001633 GTGGAACCCGACACTGTGTAT 59.998 52.381 14.31 0.00 34.84 2.29
109 122 1.608025 CGACACTGTGTATGGGCAGTT 60.608 52.381 14.31 0.00 43.27 3.16
110 123 1.806542 GACACTGTGTATGGGCAGTTG 59.193 52.381 14.31 0.00 43.27 3.16
122 135 1.522806 GCAGTTGTGGTCGTGGACA 60.523 57.895 0.00 0.00 33.68 4.02
215 231 4.263572 CCCTCGCCACCACCACAA 62.264 66.667 0.00 0.00 0.00 3.33
247 263 2.113139 ACCCGCCTCAGTTTGTGG 59.887 61.111 0.00 0.00 34.32 4.17
251 267 2.203480 GCCTCAGTTTGTGGGCCA 60.203 61.111 0.00 0.00 38.77 5.36
271 287 2.122547 ACCCCACCTCTGGACGTT 60.123 61.111 0.00 0.00 40.55 3.99
292 308 2.002505 CCTCCCTACATCGACCTCAT 57.997 55.000 0.00 0.00 0.00 2.90
297 313 1.947456 CCTACATCGACCTCATCACGA 59.053 52.381 0.00 0.00 40.18 4.35
298 314 2.554462 CCTACATCGACCTCATCACGAT 59.446 50.000 0.00 0.00 45.44 3.73
299 315 3.004839 CCTACATCGACCTCATCACGATT 59.995 47.826 0.00 0.00 43.29 3.34
301 317 2.130395 CATCGACCTCATCACGATTGG 58.870 52.381 0.00 0.00 43.29 3.16
304 320 0.179111 GACCTCATCACGATTGGCGA 60.179 55.000 0.00 0.00 44.57 5.54
306 322 0.103026 CCTCATCACGATTGGCGAGA 59.897 55.000 0.00 0.00 44.57 4.04
309 325 1.067213 TCATCACGATTGGCGAGAACA 60.067 47.619 0.00 0.00 42.63 3.18
319 335 2.027625 GCGAGAACAAGGACGGTGG 61.028 63.158 0.00 0.00 0.00 4.61
334 350 1.598130 GTGGCGCCTGAAGACAACT 60.598 57.895 29.70 0.00 0.00 3.16
336 352 0.037326 TGGCGCCTGAAGACAACTAG 60.037 55.000 29.70 0.00 0.00 2.57
338 354 0.741221 GCGCCTGAAGACAACTAGGG 60.741 60.000 0.00 0.00 0.00 3.53
339 355 0.741221 CGCCTGAAGACAACTAGGGC 60.741 60.000 0.00 0.00 34.42 5.19
345 361 4.078516 GACAACTAGGGCGGCGGT 62.079 66.667 9.78 0.00 0.00 5.68
346 362 3.600898 GACAACTAGGGCGGCGGTT 62.601 63.158 9.78 5.34 0.00 4.44
347 363 2.359478 CAACTAGGGCGGCGGTTT 60.359 61.111 9.78 0.00 0.00 3.27
369 385 8.736244 GGTTTGCAGATCTACCTTTTATGTTTA 58.264 33.333 5.30 0.00 0.00 2.01
370 386 9.774742 GTTTGCAGATCTACCTTTTATGTTTAG 57.225 33.333 0.00 0.00 0.00 1.85
400 416 3.611766 ACTTAAGTTCTATGTGCGGCT 57.388 42.857 1.12 0.00 0.00 5.52
446 462 5.917541 AGTTATCGTAACATATTTGCCCG 57.082 39.130 9.51 0.00 0.00 6.13
463 479 5.517037 TGCCCGTTTTAAATTATTTTGCG 57.483 34.783 0.00 0.00 0.00 4.85
471 487 8.587950 CGTTTTAAATTATTTTGCGATGCCTTA 58.412 29.630 0.00 0.00 0.00 2.69
482 498 3.775661 CGATGCCTTAATCGGGTTTTT 57.224 42.857 0.00 0.00 44.49 1.94
483 499 3.691498 CGATGCCTTAATCGGGTTTTTC 58.309 45.455 0.00 0.00 44.49 2.29
484 500 3.377172 CGATGCCTTAATCGGGTTTTTCT 59.623 43.478 0.00 0.00 44.49 2.52
485 501 4.495844 CGATGCCTTAATCGGGTTTTTCTC 60.496 45.833 0.00 0.00 44.49 2.87
486 502 3.757270 TGCCTTAATCGGGTTTTTCTCA 58.243 40.909 0.00 0.00 0.00 3.27
487 503 4.145807 TGCCTTAATCGGGTTTTTCTCAA 58.854 39.130 0.00 0.00 0.00 3.02
488 504 4.217550 TGCCTTAATCGGGTTTTTCTCAAG 59.782 41.667 0.00 0.00 0.00 3.02
489 505 4.217767 GCCTTAATCGGGTTTTTCTCAAGT 59.782 41.667 0.00 0.00 0.00 3.16
490 506 5.619309 GCCTTAATCGGGTTTTTCTCAAGTC 60.619 44.000 0.00 0.00 0.00 3.01
491 507 5.106277 CCTTAATCGGGTTTTTCTCAAGTCC 60.106 44.000 0.00 0.00 0.00 3.85
492 508 3.502123 ATCGGGTTTTTCTCAAGTCCA 57.498 42.857 0.00 0.00 0.00 4.02
493 509 3.284793 TCGGGTTTTTCTCAAGTCCAA 57.715 42.857 0.00 0.00 0.00 3.53
494 510 3.622630 TCGGGTTTTTCTCAAGTCCAAA 58.377 40.909 0.00 0.00 0.00 3.28
495 511 3.379057 TCGGGTTTTTCTCAAGTCCAAAC 59.621 43.478 0.00 0.00 0.00 2.93
496 512 3.490249 CGGGTTTTTCTCAAGTCCAAACC 60.490 47.826 3.90 3.90 43.85 3.27
497 513 4.054780 GGTTTTTCTCAAGTCCAAACCC 57.945 45.455 0.00 0.00 40.31 4.11
498 514 3.490249 GGTTTTTCTCAAGTCCAAACCCG 60.490 47.826 0.00 0.00 40.31 5.28
499 515 3.284793 TTTTCTCAAGTCCAAACCCGA 57.715 42.857 0.00 0.00 0.00 5.14
500 516 2.249844 TTCTCAAGTCCAAACCCGAC 57.750 50.000 0.00 0.00 0.00 4.79
501 517 1.124780 TCTCAAGTCCAAACCCGACA 58.875 50.000 0.00 0.00 32.41 4.35
502 518 1.697432 TCTCAAGTCCAAACCCGACAT 59.303 47.619 0.00 0.00 32.41 3.06
503 519 1.806542 CTCAAGTCCAAACCCGACATG 59.193 52.381 0.00 0.00 32.41 3.21
504 520 1.418264 TCAAGTCCAAACCCGACATGA 59.582 47.619 0.00 0.00 36.05 3.07
505 521 2.158740 TCAAGTCCAAACCCGACATGAA 60.159 45.455 0.00 0.00 35.63 2.57
506 522 2.621055 CAAGTCCAAACCCGACATGAAA 59.379 45.455 0.00 0.00 32.10 2.69
507 523 3.154827 AGTCCAAACCCGACATGAAAT 57.845 42.857 0.00 0.00 32.41 2.17
508 524 3.496331 AGTCCAAACCCGACATGAAATT 58.504 40.909 0.00 0.00 32.41 1.82
509 525 3.895041 AGTCCAAACCCGACATGAAATTT 59.105 39.130 0.00 0.00 32.41 1.82
510 526 4.022329 AGTCCAAACCCGACATGAAATTTC 60.022 41.667 11.41 11.41 32.41 2.17
511 527 3.057876 TCCAAACCCGACATGAAATTTCG 60.058 43.478 13.34 1.67 45.48 3.46
517 533 2.365948 CGACATGAAATTTCGGATGCG 58.634 47.619 13.34 14.10 42.42 4.73
518 534 2.719798 GACATGAAATTTCGGATGCGG 58.280 47.619 13.34 0.92 0.00 5.69
519 535 1.202290 ACATGAAATTTCGGATGCGGC 60.202 47.619 13.34 0.00 0.00 6.53
520 536 0.029300 ATGAAATTTCGGATGCGGCG 59.971 50.000 13.34 0.51 0.00 6.46
521 537 1.298339 GAAATTTCGGATGCGGCGG 60.298 57.895 9.78 0.00 0.00 6.13
522 538 3.409959 AAATTTCGGATGCGGCGGC 62.410 57.895 9.78 9.68 40.52 6.53
535 551 4.211502 GCGGCCCATTGGATGCAC 62.212 66.667 3.62 0.00 34.47 4.57
536 552 3.530260 CGGCCCATTGGATGCACC 61.530 66.667 3.62 0.00 39.54 5.01
558 574 4.342772 CAAAAGATGGACGGCTAAAATCG 58.657 43.478 0.00 0.00 0.00 3.34
559 575 2.240493 AGATGGACGGCTAAAATCGG 57.760 50.000 0.00 0.00 0.00 4.18
560 576 1.760613 AGATGGACGGCTAAAATCGGA 59.239 47.619 0.00 0.00 0.00 4.55
561 577 1.865340 GATGGACGGCTAAAATCGGAC 59.135 52.381 0.00 0.00 0.00 4.79
562 578 0.609151 TGGACGGCTAAAATCGGACA 59.391 50.000 0.00 0.00 0.00 4.02
563 579 1.208535 TGGACGGCTAAAATCGGACAT 59.791 47.619 0.00 0.00 0.00 3.06
564 580 2.431419 TGGACGGCTAAAATCGGACATA 59.569 45.455 0.00 0.00 0.00 2.29
565 581 3.057734 GGACGGCTAAAATCGGACATAG 58.942 50.000 0.00 0.00 0.00 2.23
566 582 3.243636 GGACGGCTAAAATCGGACATAGA 60.244 47.826 0.00 0.00 0.00 1.98
567 583 3.714391 ACGGCTAAAATCGGACATAGAC 58.286 45.455 0.00 0.00 0.00 2.59
568 584 2.724690 CGGCTAAAATCGGACATAGACG 59.275 50.000 7.21 7.21 40.14 4.18
570 586 4.117685 GGCTAAAATCGGACATAGACGTT 58.882 43.478 0.00 0.00 0.00 3.99
572 588 4.085721 GCTAAAATCGGACATAGACGTTCG 60.086 45.833 0.00 0.00 39.34 3.95
609 635 4.061570 GGACAAAACCGACGTCTATTTG 57.938 45.455 23.98 23.98 37.10 2.32
610 636 3.120442 GGACAAAACCGACGTCTATTTGG 60.120 47.826 26.69 20.24 35.77 3.28
619 645 1.407979 ACGTCTATTTGGGGTCTAGCG 59.592 52.381 0.00 0.00 0.00 4.26
621 647 2.159142 CGTCTATTTGGGGTCTAGCGTT 60.159 50.000 0.00 0.00 0.00 4.84
623 649 2.169769 TCTATTTGGGGTCTAGCGTTGG 59.830 50.000 0.00 0.00 0.00 3.77
670 696 2.533535 CGCGTGAATTGTTTTCAGCAAA 59.466 40.909 0.00 0.00 0.00 3.68
684 710 5.776173 TTCAGCAAACTTTTCCCGAAATA 57.224 34.783 0.00 0.00 0.00 1.40
685 711 5.975693 TCAGCAAACTTTTCCCGAAATAT 57.024 34.783 0.00 0.00 0.00 1.28
686 712 7.455641 TTCAGCAAACTTTTCCCGAAATATA 57.544 32.000 0.00 0.00 0.00 0.86
688 714 7.887381 TCAGCAAACTTTTCCCGAAATATAAA 58.113 30.769 0.00 0.00 0.00 1.40
689 715 7.810759 TCAGCAAACTTTTCCCGAAATATAAAC 59.189 33.333 0.00 0.00 0.00 2.01
690 716 7.596995 CAGCAAACTTTTCCCGAAATATAAACA 59.403 33.333 0.00 0.00 0.00 2.83
692 718 8.931775 GCAAACTTTTCCCGAAATATAAACAAT 58.068 29.630 0.00 0.00 0.00 2.71
694 720 9.990360 AAACTTTTCCCGAAATATAAACAATGT 57.010 25.926 0.00 0.00 0.00 2.71
696 722 8.581578 ACTTTTCCCGAAATATAAACAATGTGT 58.418 29.630 0.00 0.00 0.00 3.72
697 723 9.418045 CTTTTCCCGAAATATAAACAATGTGTT 57.582 29.630 0.00 0.00 43.41 3.32
762 982 2.268280 CTGGTGGCAGCTCCTCAG 59.732 66.667 18.53 2.26 35.26 3.35
770 991 1.673665 CAGCTCCTCAGTGGCCAAC 60.674 63.158 7.24 1.26 35.26 3.77
1163 1405 4.803426 CTCCTCGGCGCCTCACAC 62.803 72.222 26.68 0.00 0.00 3.82
1214 1459 1.972660 GACCCGTATTCCCAGCTGCT 61.973 60.000 8.66 0.00 0.00 4.24
1695 1940 3.683937 GCCACCCGCATGTGCTTT 61.684 61.111 0.00 0.00 39.32 3.51
1796 2041 3.815841 GAATGCGCGCGTTGCAAC 61.816 61.111 40.36 23.16 46.87 4.17
1803 2050 2.223549 GCGCGTTGCAACCATATGC 61.224 57.895 23.42 18.33 46.58 3.14
1832 2079 8.739972 GGTCCTGTTTTGTAAATTGAGATGTAT 58.260 33.333 0.00 0.00 0.00 2.29
2027 2303 6.103330 TGTAGTAGTAGCATTTTCAATCGCA 58.897 36.000 0.00 0.00 0.00 5.10
2029 2305 5.178797 AGTAGTAGCATTTTCAATCGCAGT 58.821 37.500 0.00 0.00 0.00 4.40
2059 2358 9.908152 ATTAAATAGTTTGTCCTTGCAACTTAC 57.092 29.630 0.00 0.00 0.00 2.34
2064 2363 1.885887 TGTCCTTGCAACTTACATGCC 59.114 47.619 0.00 0.00 43.16 4.40
2075 2374 7.671302 TGCAACTTACATGCCCTTTTATTTTA 58.329 30.769 0.00 0.00 43.16 1.52
2076 2375 8.317679 TGCAACTTACATGCCCTTTTATTTTAT 58.682 29.630 0.00 0.00 43.16 1.40
2077 2376 9.161629 GCAACTTACATGCCCTTTTATTTTATT 57.838 29.630 0.00 0.00 37.85 1.40
2120 2419 5.880332 GTCATCTTACATGCCCTTTGTTCTA 59.120 40.000 0.00 0.00 0.00 2.10
2127 2426 5.246307 ACATGCCCTTTGTTCTAGAACTAC 58.754 41.667 30.47 15.16 41.67 2.73
2128 2427 3.921677 TGCCCTTTGTTCTAGAACTACG 58.078 45.455 30.47 22.00 41.67 3.51
2147 2446 1.000163 CGCGCTGTAGGTCCAGATTAT 60.000 52.381 5.56 0.00 34.23 1.28
2161 2461 6.258947 GGTCCAGATTATAGAGAACACAAAGC 59.741 42.308 0.00 0.00 0.00 3.51
2165 2465 6.019479 CAGATTATAGAGAACACAAAGCGGAC 60.019 42.308 0.00 0.00 0.00 4.79
2174 2474 0.743688 ACAAAGCGGACAACATGCAA 59.256 45.000 0.00 0.00 0.00 4.08
2183 2483 3.552684 CGGACAACATGCAAATTGAAGGT 60.553 43.478 17.53 0.00 0.00 3.50
2198 2498 3.939066 TGAAGGTTAGGCTAGTTTGCTC 58.061 45.455 0.00 0.00 0.00 4.26
2204 2504 0.035458 AGGCTAGTTTGCTCTTGCGT 59.965 50.000 0.00 0.00 43.34 5.24
2205 2505 0.875059 GGCTAGTTTGCTCTTGCGTT 59.125 50.000 0.00 0.00 43.34 4.84
2206 2506 1.400242 GGCTAGTTTGCTCTTGCGTTG 60.400 52.381 0.00 0.00 43.34 4.10
2207 2507 1.531149 GCTAGTTTGCTCTTGCGTTGA 59.469 47.619 0.00 0.00 43.34 3.18
2208 2508 2.412065 GCTAGTTTGCTCTTGCGTTGAG 60.412 50.000 0.00 0.00 43.34 3.02
2239 2539 4.442192 GCTGAAGTTACTTCCCTGATCGAT 60.442 45.833 20.69 0.00 39.51 3.59
2329 2647 9.971922 AAAAGCTTGATTACCATAATCTATTGC 57.028 29.630 0.00 8.09 0.00 3.56
2345 2663 1.225376 TTGCGATGTCAACCACGTCC 61.225 55.000 0.00 0.00 37.72 4.79
2363 2681 0.250209 CCTCAGTTGTCAGCTGCTGT 60.250 55.000 27.24 6.72 34.21 4.40
2400 2718 1.000385 TGTGCTGCACTTGTTTATGGC 60.000 47.619 30.43 3.06 35.11 4.40
2467 2785 8.782144 AGTTAATTAACCAAACGGTAAAATCGA 58.218 29.630 21.92 0.00 34.92 3.59
2571 2891 9.837525 ACAAAAAGTAAACACGTTATAACACAA 57.162 25.926 15.67 0.00 0.00 3.33
2606 2926 2.957402 TTCTCAGCACTTTGGATGGT 57.043 45.000 0.00 0.00 0.00 3.55
2609 2929 1.808945 CTCAGCACTTTGGATGGTGTC 59.191 52.381 4.32 0.00 44.19 3.67
2612 2932 0.517316 GCACTTTGGATGGTGTCGAC 59.483 55.000 9.11 9.11 36.03 4.20
2613 2933 1.877637 CACTTTGGATGGTGTCGACA 58.122 50.000 15.76 15.76 0.00 4.35
2614 2934 2.426522 CACTTTGGATGGTGTCGACAT 58.573 47.619 23.12 5.54 0.00 3.06
2622 2942 3.448686 GATGGTGTCGACATAGTTCTGG 58.551 50.000 23.12 0.00 0.00 3.86
2623 2943 2.521126 TGGTGTCGACATAGTTCTGGA 58.479 47.619 23.12 0.00 0.00 3.86
2631 2951 6.038382 TGTCGACATAGTTCTGGAGTAGATTC 59.962 42.308 15.76 0.00 34.80 2.52
2662 2982 0.104356 TTGGGGTGGTGAGGTTAGGA 60.104 55.000 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.395312 TTCACTTCCAACTCCGGGAC 59.605 55.000 0.00 0.00 33.18 4.46
65 78 1.531748 CACATTGGGATAGCCGGGT 59.468 57.895 12.58 12.58 33.83 5.28
69 82 1.692411 GGTTCCACATTGGGATAGCC 58.308 55.000 0.00 0.00 38.32 3.93
70 83 1.692411 GGGTTCCACATTGGGATAGC 58.308 55.000 0.00 0.00 38.32 2.97
79 92 0.250295 CACAGTGTCGGGTTCCACAT 60.250 55.000 0.00 0.00 33.99 3.21
89 102 0.037326 ACTGCCCATACACAGTGTCG 60.037 55.000 10.23 2.57 45.19 4.35
91 104 1.142870 ACAACTGCCCATACACAGTGT 59.857 47.619 11.87 11.87 46.17 3.55
95 108 0.476338 ACCACAACTGCCCATACACA 59.524 50.000 0.00 0.00 0.00 3.72
96 109 1.165270 GACCACAACTGCCCATACAC 58.835 55.000 0.00 0.00 0.00 2.90
101 114 2.203139 CACGACCACAACTGCCCA 60.203 61.111 0.00 0.00 0.00 5.36
200 213 2.978010 GGTTGTGGTGGTGGCGAG 60.978 66.667 0.00 0.00 0.00 5.03
201 214 3.484806 AGGTTGTGGTGGTGGCGA 61.485 61.111 0.00 0.00 0.00 5.54
237 253 3.011014 TGGTGGCCCACAAACTGA 58.989 55.556 17.22 0.00 35.17 3.41
251 267 2.529389 GTCCAGAGGTGGGGTGGT 60.529 66.667 0.00 0.00 45.11 4.16
271 287 0.755698 GAGGTCGATGTAGGGAGGCA 60.756 60.000 0.00 0.00 0.00 4.75
292 308 1.428448 CTTGTTCTCGCCAATCGTGA 58.572 50.000 0.00 0.00 38.70 4.35
297 313 0.673644 CCGTCCTTGTTCTCGCCAAT 60.674 55.000 0.00 0.00 0.00 3.16
298 314 1.301401 CCGTCCTTGTTCTCGCCAA 60.301 57.895 0.00 0.00 0.00 4.52
299 315 2.342279 CCGTCCTTGTTCTCGCCA 59.658 61.111 0.00 0.00 0.00 5.69
301 317 2.027625 CCACCGTCCTTGTTCTCGC 61.028 63.158 0.00 0.00 0.00 5.03
304 320 2.030562 CGCCACCGTCCTTGTTCT 59.969 61.111 0.00 0.00 0.00 3.01
319 335 0.741221 CCCTAGTTGTCTTCAGGCGC 60.741 60.000 0.00 0.00 0.00 6.53
338 354 1.813753 TAGATCTGCAAACCGCCGC 60.814 57.895 5.18 0.00 41.33 6.53
339 355 1.429148 GGTAGATCTGCAAACCGCCG 61.429 60.000 13.14 0.00 41.33 6.46
345 361 9.733556 TCTAAACATAAAAGGTAGATCTGCAAA 57.266 29.630 13.14 0.00 0.00 3.68
346 362 9.733556 TTCTAAACATAAAAGGTAGATCTGCAA 57.266 29.630 13.14 0.00 0.00 4.08
347 363 9.733556 TTTCTAAACATAAAAGGTAGATCTGCA 57.266 29.630 13.14 0.00 0.00 4.41
430 446 7.743520 ATTTAAAACGGGCAAATATGTTACG 57.256 32.000 0.00 0.00 0.00 3.18
440 456 5.694910 TCGCAAAATAATTTAAAACGGGCAA 59.305 32.000 0.00 0.00 0.00 4.52
461 477 1.021968 AAACCCGATTAAGGCATCGC 58.978 50.000 0.56 0.00 43.99 4.58
463 479 4.398044 TGAGAAAAACCCGATTAAGGCATC 59.602 41.667 0.00 0.00 0.00 3.91
471 487 3.827722 TGGACTTGAGAAAAACCCGATT 58.172 40.909 0.00 0.00 0.00 3.34
472 488 3.502123 TGGACTTGAGAAAAACCCGAT 57.498 42.857 0.00 0.00 0.00 4.18
473 489 3.284793 TTGGACTTGAGAAAAACCCGA 57.715 42.857 0.00 0.00 0.00 5.14
474 490 3.490249 GGTTTGGACTTGAGAAAAACCCG 60.490 47.826 4.61 0.00 42.50 5.28
475 491 4.054780 GGTTTGGACTTGAGAAAAACCC 57.945 45.455 4.61 0.00 42.50 4.11
476 492 3.490249 CGGGTTTGGACTTGAGAAAAACC 60.490 47.826 7.01 7.01 45.86 3.27
477 493 3.379057 TCGGGTTTGGACTTGAGAAAAAC 59.621 43.478 0.00 0.00 0.00 2.43
478 494 3.379057 GTCGGGTTTGGACTTGAGAAAAA 59.621 43.478 0.00 0.00 0.00 1.94
479 495 2.946990 GTCGGGTTTGGACTTGAGAAAA 59.053 45.455 0.00 0.00 0.00 2.29
480 496 2.092861 TGTCGGGTTTGGACTTGAGAAA 60.093 45.455 0.00 0.00 35.45 2.52
481 497 1.487142 TGTCGGGTTTGGACTTGAGAA 59.513 47.619 0.00 0.00 35.45 2.87
482 498 1.124780 TGTCGGGTTTGGACTTGAGA 58.875 50.000 0.00 0.00 35.45 3.27
483 499 1.806542 CATGTCGGGTTTGGACTTGAG 59.193 52.381 2.70 0.00 40.20 3.02
484 500 1.418264 TCATGTCGGGTTTGGACTTGA 59.582 47.619 6.46 6.46 42.63 3.02
485 501 1.890876 TCATGTCGGGTTTGGACTTG 58.109 50.000 0.00 2.49 39.55 3.16
486 502 2.649531 TTCATGTCGGGTTTGGACTT 57.350 45.000 0.00 0.00 35.45 3.01
487 503 2.649531 TTTCATGTCGGGTTTGGACT 57.350 45.000 0.00 0.00 35.45 3.85
488 504 3.934457 AATTTCATGTCGGGTTTGGAC 57.066 42.857 0.00 0.00 34.99 4.02
489 505 3.057876 CGAAATTTCATGTCGGGTTTGGA 60.058 43.478 17.99 0.00 0.00 3.53
490 506 3.241701 CGAAATTTCATGTCGGGTTTGG 58.758 45.455 17.99 0.00 0.00 3.28
491 507 4.380444 ATCCGAAATTTCATGTCGGGTTTG 60.380 41.667 18.40 0.00 45.90 2.93
492 508 3.761752 ATCCGAAATTTCATGTCGGGTTT 59.238 39.130 18.40 4.93 45.90 3.27
493 509 3.128589 CATCCGAAATTTCATGTCGGGTT 59.871 43.478 18.40 6.95 45.90 4.11
497 513 2.365948 CGCATCCGAAATTTCATGTCG 58.634 47.619 17.99 15.83 36.29 4.35
498 514 2.719798 CCGCATCCGAAATTTCATGTC 58.280 47.619 17.99 9.74 36.29 3.06
499 515 1.202290 GCCGCATCCGAAATTTCATGT 60.202 47.619 17.99 0.12 36.29 3.21
500 516 1.480205 GCCGCATCCGAAATTTCATG 58.520 50.000 17.99 14.71 36.29 3.07
501 517 0.029300 CGCCGCATCCGAAATTTCAT 59.971 50.000 17.99 2.27 36.29 2.57
502 518 1.427419 CGCCGCATCCGAAATTTCA 59.573 52.632 17.99 0.00 36.29 2.69
503 519 1.298339 CCGCCGCATCCGAAATTTC 60.298 57.895 8.20 8.20 36.29 2.17
504 520 2.798009 CCGCCGCATCCGAAATTT 59.202 55.556 0.00 0.00 36.29 1.82
505 521 3.887868 GCCGCCGCATCCGAAATT 61.888 61.111 0.00 0.00 36.29 1.82
518 534 4.211502 GTGCATCCAATGGGCCGC 62.212 66.667 0.00 0.17 0.00 6.53
519 535 3.530260 GGTGCATCCAATGGGCCG 61.530 66.667 0.00 0.00 35.97 6.13
520 536 2.364056 TGGTGCATCCAATGGGCC 60.364 61.111 0.00 0.00 44.12 5.80
527 543 2.170166 GTCCATCTTTTGGTGCATCCA 58.830 47.619 0.00 0.00 46.52 3.41
528 544 1.133025 CGTCCATCTTTTGGTGCATCC 59.867 52.381 0.00 0.00 46.52 3.51
529 545 1.133025 CCGTCCATCTTTTGGTGCATC 59.867 52.381 0.00 0.00 46.52 3.91
530 546 1.176527 CCGTCCATCTTTTGGTGCAT 58.823 50.000 0.00 0.00 46.52 3.96
531 547 1.523154 GCCGTCCATCTTTTGGTGCA 61.523 55.000 0.00 0.00 46.52 4.57
532 548 1.212751 GCCGTCCATCTTTTGGTGC 59.787 57.895 0.00 0.00 46.52 5.01
533 549 2.107950 TAGCCGTCCATCTTTTGGTG 57.892 50.000 0.00 0.00 46.52 4.17
534 550 2.871096 TTAGCCGTCCATCTTTTGGT 57.129 45.000 0.00 0.00 46.52 3.67
536 552 4.342772 CGATTTTAGCCGTCCATCTTTTG 58.657 43.478 0.00 0.00 0.00 2.44
537 553 3.377172 CCGATTTTAGCCGTCCATCTTTT 59.623 43.478 0.00 0.00 0.00 2.27
538 554 2.943033 CCGATTTTAGCCGTCCATCTTT 59.057 45.455 0.00 0.00 0.00 2.52
539 555 2.169769 TCCGATTTTAGCCGTCCATCTT 59.830 45.455 0.00 0.00 0.00 2.40
540 556 1.760613 TCCGATTTTAGCCGTCCATCT 59.239 47.619 0.00 0.00 0.00 2.90
541 557 1.865340 GTCCGATTTTAGCCGTCCATC 59.135 52.381 0.00 0.00 0.00 3.51
542 558 1.208535 TGTCCGATTTTAGCCGTCCAT 59.791 47.619 0.00 0.00 0.00 3.41
543 559 0.609151 TGTCCGATTTTAGCCGTCCA 59.391 50.000 0.00 0.00 0.00 4.02
544 560 1.949465 ATGTCCGATTTTAGCCGTCC 58.051 50.000 0.00 0.00 0.00 4.79
545 561 3.734735 GTCTATGTCCGATTTTAGCCGTC 59.265 47.826 0.00 0.00 0.00 4.79
546 562 3.714391 GTCTATGTCCGATTTTAGCCGT 58.286 45.455 0.00 0.00 0.00 5.68
547 563 2.724690 CGTCTATGTCCGATTTTAGCCG 59.275 50.000 0.00 0.00 0.00 5.52
548 564 3.714391 ACGTCTATGTCCGATTTTAGCC 58.286 45.455 0.00 0.00 0.00 3.93
549 565 4.085721 CGAACGTCTATGTCCGATTTTAGC 60.086 45.833 0.00 0.00 0.00 3.09
550 566 5.032863 ACGAACGTCTATGTCCGATTTTAG 58.967 41.667 0.00 0.00 0.00 1.85
551 567 4.985413 ACGAACGTCTATGTCCGATTTTA 58.015 39.130 0.00 0.00 0.00 1.52
552 568 3.841643 ACGAACGTCTATGTCCGATTTT 58.158 40.909 0.00 0.00 0.00 1.82
553 569 3.498927 ACGAACGTCTATGTCCGATTT 57.501 42.857 0.00 0.00 0.00 2.17
554 570 3.498927 AACGAACGTCTATGTCCGATT 57.501 42.857 0.00 0.00 0.00 3.34
555 571 3.498927 AAACGAACGTCTATGTCCGAT 57.501 42.857 0.00 0.00 0.00 4.18
556 572 2.995466 AAACGAACGTCTATGTCCGA 57.005 45.000 0.00 0.00 0.00 4.55
588 604 3.120442 CCAAATAGACGTCGGTTTTGTCC 60.120 47.826 25.27 0.00 33.09 4.02
596 612 0.822164 AGACCCCAAATAGACGTCGG 59.178 55.000 10.46 5.87 0.00 4.79
598 614 2.543238 CGCTAGACCCCAAATAGACGTC 60.543 54.545 7.70 7.70 0.00 4.34
599 615 1.407979 CGCTAGACCCCAAATAGACGT 59.592 52.381 0.00 0.00 0.00 4.34
600 616 1.407979 ACGCTAGACCCCAAATAGACG 59.592 52.381 0.00 0.00 0.00 4.18
601 617 3.195661 CAACGCTAGACCCCAAATAGAC 58.804 50.000 0.00 0.00 0.00 2.59
603 619 2.169769 TCCAACGCTAGACCCCAAATAG 59.830 50.000 0.00 0.00 0.00 1.73
604 620 2.169769 CTCCAACGCTAGACCCCAAATA 59.830 50.000 0.00 0.00 0.00 1.40
605 621 0.988832 TCCAACGCTAGACCCCAAAT 59.011 50.000 0.00 0.00 0.00 2.32
609 635 0.391263 CAACTCCAACGCTAGACCCC 60.391 60.000 0.00 0.00 0.00 4.95
610 636 0.391263 CCAACTCCAACGCTAGACCC 60.391 60.000 0.00 0.00 0.00 4.46
619 645 3.255888 CCTCTTTTAAGGCCAACTCCAAC 59.744 47.826 5.01 0.00 0.00 3.77
621 647 3.154827 CCTCTTTTAAGGCCAACTCCA 57.845 47.619 5.01 0.00 0.00 3.86
646 672 0.382158 TGAAAACAATTCACGCGCCA 59.618 45.000 5.73 0.00 0.00 5.69
670 696 8.581578 ACACATTGTTTATATTTCGGGAAAAGT 58.418 29.630 0.00 0.00 33.56 2.66
719 907 9.067986 GGGTATAGGTAATTTGATTTGAAGGAG 57.932 37.037 0.00 0.00 0.00 3.69
722 910 8.850156 CCAGGGTATAGGTAATTTGATTTGAAG 58.150 37.037 0.00 0.00 0.00 3.02
724 912 7.777910 CACCAGGGTATAGGTAATTTGATTTGA 59.222 37.037 0.00 0.00 36.07 2.69
725 913 7.014230 CCACCAGGGTATAGGTAATTTGATTTG 59.986 40.741 0.00 0.00 36.07 2.32
726 914 7.066781 CCACCAGGGTATAGGTAATTTGATTT 58.933 38.462 0.00 0.00 36.07 2.17
730 950 4.142038 GCCACCAGGGTATAGGTAATTTG 58.858 47.826 0.00 0.00 39.65 2.32
1108 1350 2.671070 CGTGCATGGAGAAGGGGT 59.329 61.111 0.00 0.00 0.00 4.95
1214 1459 1.536907 TTGTAGGGGGCGGAGTTCA 60.537 57.895 0.00 0.00 0.00 3.18
1793 2038 1.016627 CAGGACCGTGCATATGGTTG 58.983 55.000 4.56 2.31 46.25 3.77
1794 2039 0.618458 ACAGGACCGTGCATATGGTT 59.382 50.000 4.56 0.00 46.25 3.67
1796 2041 1.750193 AAACAGGACCGTGCATATGG 58.250 50.000 4.56 0.00 39.01 2.74
1803 2050 5.008217 TCTCAATTTACAAAACAGGACCGTG 59.992 40.000 0.00 0.00 0.00 4.94
2008 2284 6.592220 TGTTACTGCGATTGAAAATGCTACTA 59.408 34.615 0.00 0.00 0.00 1.82
2009 2285 5.411361 TGTTACTGCGATTGAAAATGCTACT 59.589 36.000 0.00 0.00 0.00 2.57
2010 2286 5.627172 TGTTACTGCGATTGAAAATGCTAC 58.373 37.500 0.00 0.00 0.00 3.58
2011 2287 5.871465 TGTTACTGCGATTGAAAATGCTA 57.129 34.783 0.00 0.00 0.00 3.49
2012 2288 4.764679 TGTTACTGCGATTGAAAATGCT 57.235 36.364 0.00 0.00 0.00 3.79
2013 2289 7.504922 TTAATGTTACTGCGATTGAAAATGC 57.495 32.000 0.00 0.00 0.00 3.56
2027 2303 9.073475 TGCAAGGACAAACTATTTAATGTTACT 57.927 29.630 0.00 0.00 0.00 2.24
2029 2305 9.685828 GTTGCAAGGACAAACTATTTAATGTTA 57.314 29.630 0.00 0.00 0.00 2.41
2080 2379 9.438228 TGTAAGATGACGTCCATAACAAATTTA 57.562 29.630 14.12 0.00 35.17 1.40
2094 2393 3.009723 CAAAGGGCATGTAAGATGACGT 58.990 45.455 0.00 0.00 0.00 4.34
2120 2419 0.450983 GACCTACAGCGCGTAGTTCT 59.549 55.000 26.20 14.94 45.40 3.01
2127 2426 0.384309 TAATCTGGACCTACAGCGCG 59.616 55.000 0.00 0.00 38.36 6.86
2128 2427 2.821991 ATAATCTGGACCTACAGCGC 57.178 50.000 0.00 0.00 38.36 5.92
2147 2446 3.128349 GTTGTCCGCTTTGTGTTCTCTA 58.872 45.455 0.00 0.00 0.00 2.43
2161 2461 2.988493 CCTTCAATTTGCATGTTGTCCG 59.012 45.455 10.31 2.78 0.00 4.79
2165 2465 4.389687 GCCTAACCTTCAATTTGCATGTTG 59.610 41.667 5.47 5.47 0.00 3.33
2174 2474 5.325239 AGCAAACTAGCCTAACCTTCAATT 58.675 37.500 0.00 0.00 34.23 2.32
2183 2483 2.289444 ACGCAAGAGCAAACTAGCCTAA 60.289 45.455 0.00 0.00 42.27 2.69
2204 2504 2.627515 ACTTCAGCTCAAGTGCTCAA 57.372 45.000 0.64 0.00 41.98 3.02
2205 2505 2.627515 AACTTCAGCTCAAGTGCTCA 57.372 45.000 2.85 0.00 41.98 4.26
2206 2506 3.658709 AGTAACTTCAGCTCAAGTGCTC 58.341 45.455 2.85 0.00 41.98 4.26
2207 2507 3.760580 AGTAACTTCAGCTCAAGTGCT 57.239 42.857 2.85 2.77 45.18 4.40
2208 2508 3.187432 GGAAGTAACTTCAGCTCAAGTGC 59.813 47.826 2.85 0.15 41.77 4.40
2209 2509 3.748568 GGGAAGTAACTTCAGCTCAAGTG 59.251 47.826 2.85 0.00 41.77 3.16
2210 2510 3.648545 AGGGAAGTAACTTCAGCTCAAGT 59.351 43.478 0.00 0.00 41.77 3.16
2211 2511 3.999663 CAGGGAAGTAACTTCAGCTCAAG 59.000 47.826 0.00 0.00 41.77 3.02
2215 2515 3.118956 CGATCAGGGAAGTAACTTCAGCT 60.119 47.826 0.00 0.00 41.77 4.24
2217 2517 4.720649 TCGATCAGGGAAGTAACTTCAG 57.279 45.455 0.00 0.00 41.77 3.02
2253 2553 9.237846 CAACTTTTTCTTCTACAGCTTTTTAGG 57.762 33.333 0.00 0.00 0.00 2.69
2329 2647 0.038618 TGAGGACGTGGTTGACATCG 60.039 55.000 0.00 0.00 0.00 3.84
2345 2663 1.263484 CAACAGCAGCTGACAACTGAG 59.737 52.381 29.70 9.42 37.32 3.35
2363 2681 3.130869 AGCACAACACATTTCAAGAGCAA 59.869 39.130 0.00 0.00 0.00 3.91
2400 2718 6.314018 TCGTGTCTATTTTTATGCTGCAAAG 58.686 36.000 6.36 0.00 0.00 2.77
2487 2805 3.160777 AGGTCAAACGATGATACCGTC 57.839 47.619 0.00 0.00 40.97 4.79
2588 2908 1.421268 ACACCATCCAAAGTGCTGAGA 59.579 47.619 0.00 0.00 37.51 3.27
2592 2912 0.396435 TCGACACCATCCAAAGTGCT 59.604 50.000 0.00 0.00 37.51 4.40
2606 2926 4.840271 TCTACTCCAGAACTATGTCGACA 58.160 43.478 22.48 22.48 0.00 4.35
2609 2929 6.627395 AGAATCTACTCCAGAACTATGTCG 57.373 41.667 0.00 0.00 36.67 4.35
2612 2932 5.988561 GGCAAGAATCTACTCCAGAACTATG 59.011 44.000 0.00 0.00 36.67 2.23
2613 2933 5.221342 CGGCAAGAATCTACTCCAGAACTAT 60.221 44.000 0.00 0.00 36.67 2.12
2614 2934 4.098044 CGGCAAGAATCTACTCCAGAACTA 59.902 45.833 0.00 0.00 36.67 2.24
2622 2942 4.379339 AAGAGACGGCAAGAATCTACTC 57.621 45.455 0.00 0.00 0.00 2.59
2623 2943 4.499183 CAAAGAGACGGCAAGAATCTACT 58.501 43.478 0.00 0.00 0.00 2.57
2631 2951 1.073199 ACCCCAAAGAGACGGCAAG 59.927 57.895 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.