Multiple sequence alignment - TraesCS2B01G492600

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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 TraesCS2B01G492600 chr2B 100.000 2894 0 0 1 2894 690716246 690713353 0.000000e+00 5345.0
1 TraesCS2B01G492600 chr2B 94.245 2172 84 11 741 2894 690683344 690681196 0.000000e+00 3280.0
2 TraesCS2B01G492600 chr2B 90.308 2177 167 18 736 2894 690662340 690660190 0.000000e+00 2811.0
3 TraesCS2B01G492600 chr2B 88.000 100 5 4 636 734 690662465 690662372 8.480000e-21 111.0
4 TraesCS2B01G492600 chr2A 90.367 2263 166 19 647 2894 712843187 712840962 0.000000e+00 2924.0
5 TraesCS2B01G492600 chr2A 91.005 2179 152 15 736 2894 712820851 712818697 0.000000e+00 2898.0
6 TraesCS2B01G492600 chr2A 90.867 2179 155 15 736 2894 712832105 712829951 0.000000e+00 2881.0
7 TraesCS2B01G492600 chr2A 92.384 1418 96 7 859 2268 712826859 712825446 0.000000e+00 2010.0
8 TraesCS2B01G492600 chr2A 92.313 1418 97 7 859 2268 712838109 712836696 0.000000e+00 2004.0
9 TraesCS2B01G492600 chr2A 91.415 629 51 3 2267 2894 712836646 712836020 0.000000e+00 859.0
10 TraesCS2B01G492600 chr2A 90.881 636 55 3 2260 2894 712825403 712824770 0.000000e+00 850.0
11 TraesCS2B01G492600 chr2D 90.154 2072 143 22 838 2888 574442130 574440099 0.000000e+00 2639.0
12 TraesCS2B01G492600 chr2D 93.494 1537 91 7 736 2268 574448300 574446769 0.000000e+00 2276.0
13 TraesCS2B01G492600 chr2D 91.574 629 51 2 2267 2894 574446720 574446093 0.000000e+00 867.0
14 TraesCS2B01G492600 chr2D 95.968 124 5 0 736 859 574442896 574442773 4.890000e-48 202.0
15 TraesCS2B01G492600 chr2D 89.130 138 11 4 1 137 574449397 574449263 4.960000e-38 169.0
16 TraesCS2B01G492600 chr2D 90.541 74 4 2 495 565 574448930 574448857 8.540000e-16 95.3
17 TraesCS2B01G492600 chr2D 88.889 45 5 0 119 163 574449257 574449213 4.030000e-04 56.5
18 TraesCS2B01G492600 chrUn 90.891 1504 107 17 1404 2894 392993248 392994734 0.000000e+00 1991.0
19 TraesCS2B01G492600 chrUn 89.924 1181 89 17 1727 2894 427623288 427624451 0.000000e+00 1495.0
20 TraesCS2B01G492600 chr5D 83.696 92 9 5 82 172 564948489 564948403 6.650000e-12 82.4
21 TraesCS2B01G492600 chr1B 77.778 126 17 10 105 224 481705363 481705243 1.860000e-07 67.6
22 TraesCS2B01G492600 chr1B 92.857 42 2 1 128 168 669008957 669008916 3.110000e-05 60.2
23 TraesCS2B01G492600 chr4D 100.000 29 0 0 126 154 486396953 486396981 1.000000e-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 TraesCS2B01G492600 chr2B 690713353 690716246 2893 True 5345.000000 5345 100.000000 1 2894 1 chr2B.!!$R2 2893
1 TraesCS2B01G492600 chr2B 690681196 690683344 2148 True 3280.000000 3280 94.245000 741 2894 1 chr2B.!!$R1 2153
2 TraesCS2B01G492600 chr2B 690660190 690662465 2275 True 1461.000000 2811 89.154000 636 2894 2 chr2B.!!$R3 2258
3 TraesCS2B01G492600 chr2A 712818697 712843187 24490 True 2060.857143 2924 91.318857 647 2894 7 chr2A.!!$R1 2247
4 TraesCS2B01G492600 chr2D 574440099 574449397 9298 True 900.685714 2639 91.392857 1 2894 7 chr2D.!!$R1 2893
5 TraesCS2B01G492600 chrUn 392993248 392994734 1486 False 1991.000000 1991 90.891000 1404 2894 1 chrUn.!!$F1 1490
6 TraesCS2B01G492600 chrUn 427623288 427624451 1163 False 1495.000000 1495 89.924000 1727 2894 1 chrUn.!!$F2 1167

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
390 462 0.036732 AGGCGAGCCAATGTCTCAAA 59.963 50.0 17.18 0.0 38.92 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2386 24691 0.733729 TACGCACGCCAGTTTGTTTT 59.266 45.0 0.0 0.0 0.0 2.43 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
24 25 6.867662 AAGCTATTTCCAATATCGGTTCAG 57.132 37.500 0.00 0.00 0.00 3.02
31 32 2.951642 CCAATATCGGTTCAGCCATTGT 59.048 45.455 0.00 0.00 36.97 2.71
36 37 3.342377 TCGGTTCAGCCATTGTTCATA 57.658 42.857 0.00 0.00 36.97 2.15
61 62 8.662781 ATGCATCTACTTATTGAATACACGTT 57.337 30.769 0.00 0.00 0.00 3.99
117 140 0.591170 ACAGGTTGAACATTTCGCCG 59.409 50.000 0.00 0.00 34.06 6.46
121 144 2.048498 GGTTGAACATTTCGCCGAAAC 58.952 47.619 15.33 2.63 34.23 2.78
154 177 9.053840 TGAACATTTGTAAAATGCACATTGAAT 57.946 25.926 11.62 0.00 0.00 2.57
193 265 9.545105 AATGTCATGACAAAATTGTAAACATGT 57.455 25.926 31.00 7.11 45.41 3.21
262 334 7.551585 ACAATTGTTAACATTCTGTGACCAAA 58.448 30.769 9.56 0.00 0.00 3.28
264 336 9.689976 CAATTGTTAACATTCTGTGACCAAATA 57.310 29.630 9.56 0.00 0.00 1.40
272 344 9.691362 AACATTCTGTGACCAAATATTTTACAC 57.309 29.630 15.95 15.95 0.00 2.90
273 345 8.303876 ACATTCTGTGACCAAATATTTTACACC 58.696 33.333 18.20 3.32 0.00 4.16
275 347 7.209471 TCTGTGACCAAATATTTTACACCAC 57.791 36.000 18.20 13.30 0.00 4.16
277 349 5.048643 TGTGACCAAATATTTTACACCACGG 60.049 40.000 18.20 9.62 0.00 4.94
315 387 7.500807 GCGAGGCGAAATTTTAGAAAAATAA 57.499 32.000 0.00 0.00 0.00 1.40
316 388 8.115491 GCGAGGCGAAATTTTAGAAAAATAAT 57.885 30.769 0.00 0.00 0.00 1.28
318 390 9.284594 CGAGGCGAAATTTTAGAAAAATAATCA 57.715 29.630 0.00 0.00 0.00 2.57
378 450 6.525121 AAATTTTAAACAAAAGAGGCGAGC 57.475 33.333 0.00 0.00 0.00 5.03
379 451 3.636282 TTTAAACAAAAGAGGCGAGCC 57.364 42.857 5.89 5.89 0.00 4.70
380 452 2.264005 TAAACAAAAGAGGCGAGCCA 57.736 45.000 17.18 0.00 38.92 4.75
381 453 1.398692 AAACAAAAGAGGCGAGCCAA 58.601 45.000 17.18 0.00 38.92 4.52
382 454 1.620822 AACAAAAGAGGCGAGCCAAT 58.379 45.000 17.18 0.80 38.92 3.16
383 455 0.883833 ACAAAAGAGGCGAGCCAATG 59.116 50.000 17.18 9.45 38.92 2.82
384 456 0.883833 CAAAAGAGGCGAGCCAATGT 59.116 50.000 17.18 0.00 38.92 2.71
387 459 0.107945 AAGAGGCGAGCCAATGTCTC 60.108 55.000 17.18 3.84 38.92 3.36
390 462 0.036732 AGGCGAGCCAATGTCTCAAA 59.963 50.000 17.18 0.00 38.92 2.69
392 464 1.269448 GGCGAGCCAATGTCTCAAAAA 59.731 47.619 9.58 0.00 35.81 1.94
412 484 1.228657 AAAAACTGAGGCGAGCCGAC 61.229 55.000 8.63 7.81 41.95 4.79
415 487 4.421479 CTGAGGCGAGCCGACGTT 62.421 66.667 8.63 0.00 41.28 3.99
416 488 4.415332 TGAGGCGAGCCGACGTTC 62.415 66.667 8.63 0.96 41.28 3.95
420 492 3.179939 GCGAGCCGACGTTCCTTC 61.180 66.667 0.00 0.00 35.59 3.46
424 496 3.119096 GCCGACGTTCCTTCTGGC 61.119 66.667 0.00 0.00 35.04 4.85
425 497 2.657237 CCGACGTTCCTTCTGGCT 59.343 61.111 0.00 0.00 0.00 4.75
426 498 1.738099 CCGACGTTCCTTCTGGCTG 60.738 63.158 0.00 0.00 0.00 4.85
445 517 1.000607 TGGAAGCGAGATATACGTGCC 60.001 52.381 0.00 0.00 0.00 5.01
446 518 1.669211 GGAAGCGAGATATACGTGCCC 60.669 57.143 0.00 0.00 0.00 5.36
458 530 3.988459 CGTGCCCGTTTCCTTTATG 57.012 52.632 0.00 0.00 0.00 1.90
459 531 1.161843 CGTGCCCGTTTCCTTTATGT 58.838 50.000 0.00 0.00 0.00 2.29
460 532 1.135803 CGTGCCCGTTTCCTTTATGTG 60.136 52.381 0.00 0.00 0.00 3.21
461 533 1.883926 GTGCCCGTTTCCTTTATGTGT 59.116 47.619 0.00 0.00 0.00 3.72
463 535 2.156098 GCCCGTTTCCTTTATGTGTGA 58.844 47.619 0.00 0.00 0.00 3.58
464 536 2.161609 GCCCGTTTCCTTTATGTGTGAG 59.838 50.000 0.00 0.00 0.00 3.51
465 537 2.161609 CCCGTTTCCTTTATGTGTGAGC 59.838 50.000 0.00 0.00 0.00 4.26
467 539 2.161609 CGTTTCCTTTATGTGTGAGCCC 59.838 50.000 0.00 0.00 0.00 5.19
468 540 2.107950 TTCCTTTATGTGTGAGCCCG 57.892 50.000 0.00 0.00 0.00 6.13
472 544 0.392461 TTTATGTGTGAGCCCGCTCC 60.392 55.000 13.93 6.28 42.09 4.70
473 545 1.264749 TTATGTGTGAGCCCGCTCCT 61.265 55.000 13.93 0.00 42.09 3.69
474 546 1.264749 TATGTGTGAGCCCGCTCCTT 61.265 55.000 13.93 0.66 42.09 3.36
475 547 2.743928 GTGTGAGCCCGCTCCTTG 60.744 66.667 13.93 0.00 42.09 3.61
476 548 4.020617 TGTGAGCCCGCTCCTTGG 62.021 66.667 13.93 0.00 42.09 3.61
483 555 4.082523 CCGCTCCTTGGGCTTCGA 62.083 66.667 0.00 0.00 0.00 3.71
484 556 2.510238 CGCTCCTTGGGCTTCGAG 60.510 66.667 0.00 0.00 0.00 4.04
485 557 2.821810 GCTCCTTGGGCTTCGAGC 60.822 66.667 0.00 0.00 40.82 5.03
486 558 2.665000 CTCCTTGGGCTTCGAGCA 59.335 61.111 8.71 0.00 44.75 4.26
493 565 2.280797 GGCTTCGAGCACACCACA 60.281 61.111 8.71 0.00 44.75 4.17
538 612 3.499737 GCACGACAGGGCGAATGG 61.500 66.667 0.00 0.00 36.86 3.16
540 614 2.047274 ACGACAGGGCGAATGGTG 60.047 61.111 0.00 0.00 34.83 4.17
554 629 5.502606 GCGAATGGTGCTCTTTTCTTATAC 58.497 41.667 0.00 0.00 0.00 1.47
557 632 7.516943 GCGAATGGTGCTCTTTTCTTATACTAC 60.517 40.741 0.00 0.00 0.00 2.73
568 809 9.498176 TCTTTTCTTATACTACGCCTTTTCTTT 57.502 29.630 0.00 0.00 0.00 2.52
608 849 7.593273 CACTTATTTTTGTGAATACCGCTCAAA 59.407 33.333 0.00 0.00 36.38 2.69
609 850 8.138712 ACTTATTTTTGTGAATACCGCTCAAAA 58.861 29.630 0.00 0.00 36.60 2.44
610 851 8.873215 TTATTTTTGTGAATACCGCTCAAAAA 57.127 26.923 14.51 14.51 45.31 1.94
638 879 8.177119 TCCTTATGTTGGTGAATTATTATGCC 57.823 34.615 0.00 0.00 0.00 4.40
639 880 8.004215 TCCTTATGTTGGTGAATTATTATGCCT 58.996 33.333 0.00 0.00 0.00 4.75
640 881 8.641541 CCTTATGTTGGTGAATTATTATGCCTT 58.358 33.333 0.00 0.00 0.00 4.35
645 886 8.349245 TGTTGGTGAATTATTATGCCTTAATCG 58.651 33.333 0.00 0.00 32.66 3.34
646 887 6.908825 TGGTGAATTATTATGCCTTAATCGC 58.091 36.000 0.00 0.00 32.66 4.58
647 888 6.714810 TGGTGAATTATTATGCCTTAATCGCT 59.285 34.615 0.00 0.00 32.66 4.93
648 889 7.230510 TGGTGAATTATTATGCCTTAATCGCTT 59.769 33.333 0.00 0.00 32.66 4.68
649 890 8.726988 GGTGAATTATTATGCCTTAATCGCTTA 58.273 33.333 0.00 0.00 32.66 3.09
664 10988 1.715585 CTTAATGTGCCGTCGCCAG 59.284 57.895 0.00 0.00 0.00 4.85
695 11021 5.811100 GCTGTAGTACGCCTTTTCTTATTCT 59.189 40.000 6.01 0.00 0.00 2.40
696 11022 6.976925 GCTGTAGTACGCCTTTTCTTATTCTA 59.023 38.462 6.01 0.00 0.00 2.10
697 11023 7.652507 GCTGTAGTACGCCTTTTCTTATTCTAT 59.347 37.037 6.01 0.00 0.00 1.98
734 11060 7.399523 CCTTGCACGTTATTCTATTCAAGTAC 58.600 38.462 0.00 0.00 0.00 2.73
739 11095 8.744011 GCACGTTATTCTATTCAAGTACTAGTG 58.256 37.037 5.39 0.00 0.00 2.74
823 11179 0.527565 GTGTTCATCCATGTGCCCAC 59.472 55.000 0.00 0.00 0.00 4.61
827 11183 0.113972 TCATCCATGTGCCCACCAAA 59.886 50.000 0.00 0.00 0.00 3.28
982 11344 6.098982 ACAGTGGAGATAAGAGTTCAATAGGG 59.901 42.308 0.00 0.00 0.00 3.53
1011 11374 1.759562 GCCCCAGAGATGGCTAGTAGT 60.760 57.143 0.00 0.00 44.46 2.73
1018 11381 6.007076 CCAGAGATGGCTAGTAGTTCATCTA 58.993 44.000 24.75 0.81 44.18 1.98
1047 11410 2.973899 CTGGTCGTGGCAGTAGCT 59.026 61.111 0.00 0.00 41.70 3.32
1068 11431 1.896660 GGCGCAGTTTCTTGGGTCA 60.897 57.895 10.83 0.00 35.87 4.02
1098 11461 1.322442 GCATTTCCATCTACTGGGGC 58.678 55.000 0.00 0.00 45.98 5.80
1155 11518 2.629639 CCACCGGCAACTACAAATTC 57.370 50.000 0.00 0.00 0.00 2.17
1212 11575 0.178903 AGCCACCAGTCCTCAACCTA 60.179 55.000 0.00 0.00 0.00 3.08
1314 11677 0.977627 TCATGCTCTCCATCGGTGGT 60.978 55.000 15.92 0.00 46.16 4.16
1350 11713 0.252742 ACCTTTCCTCGTCCCAGGAT 60.253 55.000 0.00 0.00 42.49 3.24
1374 11737 1.372582 AGAATGTCGCGACGTACCTA 58.627 50.000 32.36 15.62 0.00 3.08
1446 11809 0.320374 TCCTTGACGGCATCGACTTT 59.680 50.000 0.00 0.00 40.11 2.66
1517 11880 4.100498 CCTAAAAGGGTATAGCAACTCCGA 59.900 45.833 4.02 0.00 0.00 4.55
1632 11995 1.329292 GTGCAGTTCTACAACAACGCA 59.671 47.619 0.00 0.00 34.60 5.24
2253 24558 0.618393 CAAGCCAAATCCCCACCCAT 60.618 55.000 0.00 0.00 0.00 4.00
2386 24691 3.582647 TGCTAAGGTGACAAGGATCTCAA 59.417 43.478 0.00 0.00 0.00 3.02
2441 24746 2.795329 AGTCAGGGATGCACGATTTTT 58.205 42.857 0.00 0.00 0.00 1.94
2450 24755 2.588620 TGCACGATTTTTACCTGGGTT 58.411 42.857 0.00 0.00 0.00 4.11
2451 24756 2.294791 TGCACGATTTTTACCTGGGTTG 59.705 45.455 0.00 0.00 0.00 3.77
2452 24757 2.554893 GCACGATTTTTACCTGGGTTGA 59.445 45.455 0.00 0.00 0.00 3.18
2453 24758 3.365969 GCACGATTTTTACCTGGGTTGAG 60.366 47.826 0.00 0.00 0.00 3.02
2454 24759 3.190535 CACGATTTTTACCTGGGTTGAGG 59.809 47.826 0.00 0.00 39.28 3.86
2455 24760 2.163613 CGATTTTTACCTGGGTTGAGGC 59.836 50.000 0.00 0.00 36.46 4.70
2456 24761 2.003937 TTTTTACCTGGGTTGAGGCC 57.996 50.000 0.00 0.00 36.46 5.19
2539 24846 3.719268 TGATGGTGGCTAACATGAGTT 57.281 42.857 4.86 0.00 41.74 3.01
2544 24851 4.076394 TGGTGGCTAACATGAGTTAAACC 58.924 43.478 0.00 1.00 39.58 3.27
2589 24896 8.093307 ACAATAGATCTACATATCTTGCCACAG 58.907 37.037 4.10 0.00 37.41 3.66
2594 24901 3.701205 ACATATCTTGCCACAGTGTCA 57.299 42.857 0.00 0.00 0.00 3.58
2603 24910 1.067516 GCCACAGTGTCAATGCAAAGT 59.932 47.619 0.00 0.00 0.00 2.66
2609 24916 2.035066 AGTGTCAATGCAAAGTGCTTCC 59.965 45.455 0.00 0.00 45.31 3.46
2616 24923 0.319405 GCAAAGTGCTTCCCTGCATT 59.681 50.000 0.00 0.00 45.23 3.56
2617 24924 1.938016 GCAAAGTGCTTCCCTGCATTG 60.938 52.381 0.00 0.00 45.23 2.82
2650 24967 5.761165 TTGGTGTTAAACTAGCTTGTTCC 57.239 39.130 13.94 10.68 0.00 3.62
2706 25023 4.836175 TGTTCTACTGTGGTATCCAAGACA 59.164 41.667 0.00 0.00 34.18 3.41
2719 25036 3.583228 TCCAAGACAAGGAACCTAGACA 58.417 45.455 0.00 0.00 30.71 3.41
2729 25046 6.958192 ACAAGGAACCTAGACATAACTCCTAA 59.042 38.462 0.00 0.00 31.57 2.69
2736 25053 6.606395 ACCTAGACATAACTCCTAACGACAAT 59.394 38.462 0.00 0.00 0.00 2.71
2765 25082 9.700831 AATAAGGCATAACTTCCTTAATCTTGT 57.299 29.630 5.02 0.00 45.09 3.16
2772 25089 6.650427 AACTTCCTTAATCTTGTTGAACCC 57.350 37.500 0.00 0.00 0.00 4.11
2799 25116 7.280876 GCACTCATCCACACAATCTTTCTTATA 59.719 37.037 0.00 0.00 0.00 0.98
2862 25179 2.169352 TCCATAGCTCTTCAGGACTTGC 59.831 50.000 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.096231 TGAACAATGGCTGAACCGATATTG 59.904 41.667 0.00 0.00 43.94 1.90
12 13 4.269183 TGAACAATGGCTGAACCGATATT 58.731 39.130 0.00 0.00 43.94 1.28
15 16 2.198827 TGAACAATGGCTGAACCGAT 57.801 45.000 0.00 0.00 43.94 4.18
24 25 5.954296 AGTAGATGCATATGAACAATGGC 57.046 39.130 6.97 0.00 0.00 4.40
36 37 8.551205 CAACGTGTATTCAATAAGTAGATGCAT 58.449 33.333 0.00 0.00 0.00 3.96
113 114 1.268285 TGTTCAACACATGTTTCGGCG 60.268 47.619 0.00 0.00 35.83 6.46
121 144 7.583401 GTGCATTTTACAAATGTTCAACACATG 59.417 33.333 10.20 0.00 46.23 3.21
165 188 8.939201 TGTTTACAATTTTGTCATGACATTGT 57.061 26.923 32.68 32.68 41.81 2.71
166 189 9.800299 CATGTTTACAATTTTGTCATGACATTG 57.200 29.630 28.32 27.78 40.49 2.82
167 190 9.545105 ACATGTTTACAATTTTGTCATGACATT 57.455 25.926 28.32 17.25 40.49 2.71
248 320 8.303156 TGGTGTAAAATATTTGGTCACAGAATG 58.697 33.333 21.15 0.00 46.00 2.67
249 321 8.303876 GTGGTGTAAAATATTTGGTCACAGAAT 58.696 33.333 21.15 1.80 0.00 2.40
250 322 7.520776 CGTGGTGTAAAATATTTGGTCACAGAA 60.521 37.037 21.15 10.96 0.00 3.02
252 324 6.083630 CGTGGTGTAAAATATTTGGTCACAG 58.916 40.000 21.15 13.42 0.00 3.66
291 363 7.500807 TTATTTTTCTAAAATTTCGCCTCGC 57.499 32.000 3.05 0.00 0.00 5.03
362 434 1.398692 TTGGCTCGCCTCTTTTGTTT 58.601 45.000 9.65 0.00 36.94 2.83
372 444 0.881118 TTTTGAGACATTGGCTCGCC 59.119 50.000 14.72 0.00 35.15 5.54
398 470 4.421479 AACGTCGGCTCGCCTCAG 62.421 66.667 6.35 0.00 0.00 3.35
399 471 4.415332 GAACGTCGGCTCGCCTCA 62.415 66.667 6.35 0.00 0.00 3.86
402 474 4.736896 AAGGAACGTCGGCTCGCC 62.737 66.667 0.00 0.00 0.00 5.54
403 475 3.179939 GAAGGAACGTCGGCTCGC 61.180 66.667 0.00 0.00 0.00 5.03
405 477 1.446272 CCAGAAGGAACGTCGGCTC 60.446 63.158 0.00 0.00 42.91 4.70
412 484 1.301677 GCTTCCAGCCAGAAGGAACG 61.302 60.000 13.56 0.00 42.94 3.95
414 486 1.003355 CGCTTCCAGCCAGAAGGAA 60.003 57.895 13.56 0.00 42.94 3.36
415 487 1.892819 CTCGCTTCCAGCCAGAAGGA 61.893 60.000 13.56 8.91 42.94 3.36
416 488 1.449246 CTCGCTTCCAGCCAGAAGG 60.449 63.158 13.56 5.77 42.94 3.46
420 492 2.669670 CGTATATCTCGCTTCCAGCCAG 60.670 54.545 0.00 0.00 38.18 4.85
424 496 2.320367 GCACGTATATCTCGCTTCCAG 58.680 52.381 0.00 0.00 0.00 3.86
425 497 1.000607 GGCACGTATATCTCGCTTCCA 60.001 52.381 0.00 0.00 0.00 3.53
426 498 1.669211 GGGCACGTATATCTCGCTTCC 60.669 57.143 0.00 0.92 0.00 3.46
443 515 2.156098 TCACACATAAAGGAAACGGGC 58.844 47.619 0.00 0.00 0.00 6.13
445 517 2.161609 GGCTCACACATAAAGGAAACGG 59.838 50.000 0.00 0.00 0.00 4.44
446 518 2.161609 GGGCTCACACATAAAGGAAACG 59.838 50.000 0.00 0.00 0.00 3.60
448 520 2.432444 CGGGCTCACACATAAAGGAAA 58.568 47.619 0.00 0.00 0.00 3.13
449 521 1.948611 GCGGGCTCACACATAAAGGAA 60.949 52.381 0.00 0.00 0.00 3.36
451 523 0.392998 AGCGGGCTCACACATAAAGG 60.393 55.000 0.00 0.00 0.00 3.11
452 524 1.009829 GAGCGGGCTCACACATAAAG 58.990 55.000 15.45 0.00 42.31 1.85
454 526 1.220749 GGAGCGGGCTCACACATAA 59.779 57.895 21.10 0.00 44.40 1.90
455 527 1.264749 AAGGAGCGGGCTCACACATA 61.265 55.000 21.10 0.00 44.40 2.29
457 529 3.241530 AAGGAGCGGGCTCACACA 61.242 61.111 21.10 0.00 44.40 3.72
458 530 2.743928 CAAGGAGCGGGCTCACAC 60.744 66.667 21.10 5.29 44.40 3.82
459 531 4.020617 CCAAGGAGCGGGCTCACA 62.021 66.667 21.10 0.00 44.40 3.58
460 532 4.785453 CCCAAGGAGCGGGCTCAC 62.785 72.222 21.10 11.12 44.40 3.51
467 539 2.510238 CTCGAAGCCCAAGGAGCG 60.510 66.667 0.00 0.00 34.64 5.03
468 540 2.821810 GCTCGAAGCCCAAGGAGC 60.822 66.667 0.00 0.00 44.24 4.70
472 544 2.328099 GGTGTGCTCGAAGCCCAAG 61.328 63.158 4.73 0.00 41.51 3.61
473 545 2.281484 GGTGTGCTCGAAGCCCAA 60.281 61.111 4.73 0.00 41.51 4.12
474 546 3.555324 TGGTGTGCTCGAAGCCCA 61.555 61.111 4.73 2.88 41.51 5.36
475 547 3.050275 GTGGTGTGCTCGAAGCCC 61.050 66.667 4.73 0.67 41.51 5.19
476 548 2.280797 TGTGGTGTGCTCGAAGCC 60.281 61.111 4.73 0.00 41.51 4.35
478 550 0.249447 TGTCTGTGGTGTGCTCGAAG 60.249 55.000 0.00 0.00 0.00 3.79
479 551 0.249447 CTGTCTGTGGTGTGCTCGAA 60.249 55.000 0.00 0.00 0.00 3.71
480 552 1.363807 CTGTCTGTGGTGTGCTCGA 59.636 57.895 0.00 0.00 0.00 4.04
481 553 1.665916 CCTGTCTGTGGTGTGCTCG 60.666 63.158 0.00 0.00 0.00 5.03
483 555 2.111878 GCCTGTCTGTGGTGTGCT 59.888 61.111 0.00 0.00 0.00 4.40
484 556 3.349006 CGCCTGTCTGTGGTGTGC 61.349 66.667 0.00 0.00 0.00 4.57
485 557 0.813610 TTTCGCCTGTCTGTGGTGTG 60.814 55.000 0.00 0.00 36.54 3.82
486 558 0.532862 CTTTCGCCTGTCTGTGGTGT 60.533 55.000 0.00 0.00 36.54 4.16
487 559 0.532862 ACTTTCGCCTGTCTGTGGTG 60.533 55.000 0.00 0.00 36.49 4.17
488 560 1.045407 TACTTTCGCCTGTCTGTGGT 58.955 50.000 0.00 0.00 0.00 4.16
490 562 2.860735 GCTATACTTTCGCCTGTCTGTG 59.139 50.000 0.00 0.00 0.00 3.66
491 563 2.479730 CGCTATACTTTCGCCTGTCTGT 60.480 50.000 0.00 0.00 0.00 3.41
493 565 1.536284 GCGCTATACTTTCGCCTGTCT 60.536 52.381 0.00 0.00 42.71 3.41
538 612 5.349809 AGGCGTAGTATAAGAAAAGAGCAC 58.650 41.667 0.00 0.00 0.00 4.40
540 614 6.905544 AAAGGCGTAGTATAAGAAAAGAGC 57.094 37.500 0.00 0.00 0.00 4.09
554 629 6.061231 AGAACAGAAAAAGAAAAGGCGTAG 57.939 37.500 0.00 0.00 0.00 3.51
557 632 7.647715 TGATTAAGAACAGAAAAAGAAAAGGCG 59.352 33.333 0.00 0.00 0.00 5.52
612 853 8.637986 GGCATAATAATTCACCAACATAAGGAA 58.362 33.333 0.00 0.00 0.00 3.36
613 854 8.004215 AGGCATAATAATTCACCAACATAAGGA 58.996 33.333 0.00 0.00 0.00 3.36
619 860 8.349245 CGATTAAGGCATAATAATTCACCAACA 58.651 33.333 0.00 0.00 34.30 3.33
620 861 7.326063 GCGATTAAGGCATAATAATTCACCAAC 59.674 37.037 0.00 0.00 34.30 3.77
621 862 7.230510 AGCGATTAAGGCATAATAATTCACCAA 59.769 33.333 0.00 0.00 34.30 3.67
629 870 8.020819 GCACATTAAGCGATTAAGGCATAATAA 58.979 33.333 16.79 0.00 33.87 1.40
630 871 7.361713 GGCACATTAAGCGATTAAGGCATAATA 60.362 37.037 16.79 0.00 33.87 0.98
631 872 6.381801 GCACATTAAGCGATTAAGGCATAAT 58.618 36.000 16.79 0.00 35.40 1.28
633 874 4.215399 GGCACATTAAGCGATTAAGGCATA 59.785 41.667 16.79 0.00 0.00 3.14
634 875 3.004734 GGCACATTAAGCGATTAAGGCAT 59.995 43.478 16.79 0.00 0.00 4.40
635 876 2.357637 GGCACATTAAGCGATTAAGGCA 59.642 45.455 16.79 0.00 0.00 4.75
638 879 3.601586 CGACGGCACATTAAGCGATTAAG 60.602 47.826 11.91 6.55 0.00 1.85
639 880 2.283086 CGACGGCACATTAAGCGATTAA 59.717 45.455 8.50 8.50 0.00 1.40
640 881 1.855978 CGACGGCACATTAAGCGATTA 59.144 47.619 0.00 0.00 0.00 1.75
642 883 1.762222 GCGACGGCACATTAAGCGAT 61.762 55.000 0.00 0.00 39.62 4.58
643 884 2.449525 GCGACGGCACATTAAGCGA 61.450 57.895 0.00 0.00 39.62 4.93
644 885 2.021380 GCGACGGCACATTAAGCG 59.979 61.111 0.00 0.00 39.62 4.68
645 886 2.309764 CTGGCGACGGCACATTAAGC 62.310 60.000 21.29 0.00 42.47 3.09
646 887 1.715585 CTGGCGACGGCACATTAAG 59.284 57.895 21.29 5.82 42.47 1.85
647 888 3.883462 CTGGCGACGGCACATTAA 58.117 55.556 21.29 0.00 42.47 1.40
664 10988 1.352156 GGCGTACTACAGCTGTGTGC 61.352 60.000 29.57 23.54 37.52 4.57
725 11051 6.649141 TCGTGATTTTGCACTAGTACTTGAAT 59.351 34.615 11.43 0.09 36.65 2.57
734 11060 3.664276 CGGTGTTCGTGATTTTGCACTAG 60.664 47.826 0.00 0.00 36.65 2.57
823 11179 3.696281 TTATGCTCATGCGTGATTTGG 57.304 42.857 9.53 0.00 43.34 3.28
827 11183 4.906065 ATTGTTTATGCTCATGCGTGAT 57.094 36.364 9.53 0.00 43.34 3.06
967 11329 7.719633 GGCAATATTGTCCCTATTGAACTCTTA 59.280 37.037 16.61 0.00 38.35 2.10
982 11344 3.152341 CCATCTCTGGGGCAATATTGTC 58.848 50.000 16.61 14.31 39.04 3.18
1007 11370 4.260538 GCAGTTGCAGCATAGATGAACTAC 60.261 45.833 2.55 0.00 41.59 2.73
1011 11374 2.681344 CAGCAGTTGCAGCATAGATGAA 59.319 45.455 2.55 0.00 45.16 2.57
1018 11381 2.330372 CGACCAGCAGTTGCAGCAT 61.330 57.895 2.55 0.00 45.16 3.79
1047 11410 3.659092 CCAAGAAACTGCGCCGCA 61.659 61.111 12.83 12.83 36.92 5.69
1098 11461 1.379044 GCCCTCACCACCATTCTGG 60.379 63.158 0.00 0.00 45.02 3.86
1140 11503 3.223157 GTTGACGAATTTGTAGTTGCCG 58.777 45.455 0.00 0.00 0.00 5.69
1155 11518 1.128692 GAAAGGAAGGCGATGTTGACG 59.871 52.381 0.00 0.00 0.00 4.35
1197 11560 1.270907 CTGCTAGGTTGAGGACTGGT 58.729 55.000 0.00 0.00 0.00 4.00
1250 11613 2.100584 GACTTGATGTCGGAGCTCAGAT 59.899 50.000 19.67 4.69 35.81 2.90
1314 11677 4.789173 TAGTAGCCGCCTGCCCCA 62.789 66.667 0.00 0.00 42.71 4.96
1350 11713 2.379634 CGTCGCGACATTCTTGGCA 61.380 57.895 35.71 0.00 0.00 4.92
1374 11737 6.272558 ACTTACCTCCTAAGAAGTTGTTCCAT 59.727 38.462 0.00 0.00 36.13 3.41
1425 11788 1.810030 GTCGATGCCGTCAAGGACC 60.810 63.158 0.00 0.00 45.00 4.46
1517 11880 2.297597 GCAGTCAAGTACACTCTCCTGT 59.702 50.000 0.00 0.00 0.00 4.00
1632 11995 3.838317 TGCCTGAAGTATACTGACAAGGT 59.162 43.478 6.06 0.00 0.00 3.50
2253 24558 9.214957 CGAGTAATGTTCTATTAATTATGGGCA 57.785 33.333 0.00 0.00 0.00 5.36
2386 24691 0.733729 TACGCACGCCAGTTTGTTTT 59.266 45.000 0.00 0.00 0.00 2.43
2458 24763 2.764572 AGTAGGATTCTTACCCACACGG 59.235 50.000 2.57 0.00 37.81 4.94
2459 24764 4.467198 AAGTAGGATTCTTACCCACACG 57.533 45.455 2.57 0.00 0.00 4.49
2460 24765 8.803397 AAAATAAGTAGGATTCTTACCCACAC 57.197 34.615 2.57 0.00 31.53 3.82
2461 24766 8.832735 AGAAAATAAGTAGGATTCTTACCCACA 58.167 33.333 2.57 0.00 31.53 4.17
2462 24767 9.682465 AAGAAAATAAGTAGGATTCTTACCCAC 57.318 33.333 2.57 0.00 38.26 4.61
2501 24807 8.199449 CCACCATCATACTTTTGCATTAAGATT 58.801 33.333 14.08 1.17 0.00 2.40
2563 24870 7.966812 TGTGGCAAGATATGTAGATCTATTGT 58.033 34.615 5.57 0.00 35.01 2.71
2609 24916 3.577667 CAATACAACACCACAATGCAGG 58.422 45.455 0.00 0.00 0.00 4.85
2616 24923 5.652891 AGTTTAACACCAATACAACACCACA 59.347 36.000 0.00 0.00 0.00 4.17
2617 24924 6.139048 AGTTTAACACCAATACAACACCAC 57.861 37.500 0.00 0.00 0.00 4.16
2706 25023 6.096564 CGTTAGGAGTTATGTCTAGGTTCCTT 59.903 42.308 0.00 0.00 35.37 3.36
2719 25036 7.931948 CCTTATTCCATTGTCGTTAGGAGTTAT 59.068 37.037 0.00 0.00 0.00 1.89
2729 25046 5.437060 AGTTATGCCTTATTCCATTGTCGT 58.563 37.500 0.00 0.00 0.00 4.34
2736 25053 8.502738 AGATTAAGGAAGTTATGCCTTATTCCA 58.497 33.333 14.83 0.00 43.99 3.53
2765 25082 0.605319 GTGGATGAGTGCGGGTTCAA 60.605 55.000 0.00 0.00 0.00 2.69
2772 25089 1.730501 AGATTGTGTGGATGAGTGCG 58.269 50.000 0.00 0.00 0.00 5.34
2799 25116 2.025037 TGGCTTATGGAAACTGGAGCAT 60.025 45.455 0.00 0.00 32.93 3.79
2848 25165 2.082231 CCATGTGCAAGTCCTGAAGAG 58.918 52.381 0.00 0.00 0.00 2.85
2850 25167 2.189594 TCCATGTGCAAGTCCTGAAG 57.810 50.000 0.00 0.00 0.00 3.02
2853 25170 2.292569 GCATATCCATGTGCAAGTCCTG 59.707 50.000 3.59 0.00 43.34 3.86


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

AutoCloner maintained by Alex Coulton.