Multiple sequence alignment - TraesCS2B01G256900

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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 TraesCS2B01G256900 chr2B 100.000 2546 0 0 1 2546 300261317 300263862 0.000000e+00 4702
1 TraesCS2B01G256900 chr2B 97.382 955 24 1 1593 2546 794279904 794280858 0.000000e+00 1624
2 TraesCS2B01G256900 chr2B 97.068 955 26 2 1593 2546 90392722 90391769 0.000000e+00 1607
3 TraesCS2B01G256900 chr2B 93.763 962 54 3 633 1593 676570762 676571718 0.000000e+00 1439
4 TraesCS2B01G256900 chr2B 90.506 158 14 1 85 242 77287245 77287089 9.230000e-50 207
5 TraesCS2B01G256900 chr4A 97.546 1915 41 4 633 2546 668446371 668448280 0.000000e+00 3271
6 TraesCS2B01G256900 chr4A 86.726 339 28 6 632 956 20269474 20269809 6.700000e-96 361
7 TraesCS2B01G256900 chr5B 97.190 961 22 4 1587 2546 613686361 613685405 0.000000e+00 1620
8 TraesCS2B01G256900 chr5B 96.859 955 28 2 1592 2545 293480951 293479998 0.000000e+00 1596
9 TraesCS2B01G256900 chr5B 96.859 955 28 2 1593 2546 587135679 587136632 0.000000e+00 1596
10 TraesCS2B01G256900 chr5B 96.570 962 31 2 1586 2546 613693355 613692395 0.000000e+00 1592
11 TraesCS2B01G256900 chr5B 92.605 595 25 4 999 1593 708965387 708965962 0.000000e+00 837
12 TraesCS2B01G256900 chrUn 96.859 955 29 1 1593 2546 84128491 84129445 0.000000e+00 1596
13 TraesCS2B01G256900 chr4B 96.859 955 28 2 1593 2546 590815735 590814782 0.000000e+00 1596
14 TraesCS2B01G256900 chr7B 94.775 976 32 4 633 1593 186594989 186594018 0.000000e+00 1502
15 TraesCS2B01G256900 chr3D 94.277 961 54 1 633 1593 14412850 14411891 0.000000e+00 1469
16 TraesCS2B01G256900 chr6A 94.093 965 45 7 633 1593 6329905 6330861 0.000000e+00 1456
17 TraesCS2B01G256900 chr3A 93.472 965 51 7 633 1593 71802415 71801459 0.000000e+00 1423
18 TraesCS2B01G256900 chr3B 93.161 965 55 7 633 1593 60508817 60507860 0.000000e+00 1406
19 TraesCS2B01G256900 chr1B 96.219 767 29 0 827 1593 529514837 529514071 0.000000e+00 1256
20 TraesCS2B01G256900 chr2A 96.880 641 11 4 1 633 306176608 306177247 0.000000e+00 1064
21 TraesCS2B01G256900 chr2A 87.278 338 25 4 633 956 70033415 70033748 1.110000e-98 370
22 TraesCS2B01G256900 chr2D 96.075 637 9 6 1 633 215846951 215847575 0.000000e+00 1024
23 TraesCS2B01G256900 chr6D 90.698 602 31 7 1001 1593 289729471 289730056 0.000000e+00 778
24 TraesCS2B01G256900 chr6D 86.667 345 29 5 633 962 289729126 289729468 1.440000e-97 366


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 TraesCS2B01G256900 chr2B 300261317 300263862 2545 False 4702 4702 100.0000 1 2546 1 chr2B.!!$F1 2545
1 TraesCS2B01G256900 chr2B 794279904 794280858 954 False 1624 1624 97.3820 1593 2546 1 chr2B.!!$F3 953
2 TraesCS2B01G256900 chr2B 90391769 90392722 953 True 1607 1607 97.0680 1593 2546 1 chr2B.!!$R2 953
3 TraesCS2B01G256900 chr2B 676570762 676571718 956 False 1439 1439 93.7630 633 1593 1 chr2B.!!$F2 960
4 TraesCS2B01G256900 chr4A 668446371 668448280 1909 False 3271 3271 97.5460 633 2546 1 chr4A.!!$F2 1913
5 TraesCS2B01G256900 chr5B 613685405 613686361 956 True 1620 1620 97.1900 1587 2546 1 chr5B.!!$R2 959
6 TraesCS2B01G256900 chr5B 293479998 293480951 953 True 1596 1596 96.8590 1592 2545 1 chr5B.!!$R1 953
7 TraesCS2B01G256900 chr5B 587135679 587136632 953 False 1596 1596 96.8590 1593 2546 1 chr5B.!!$F1 953
8 TraesCS2B01G256900 chr5B 613692395 613693355 960 True 1592 1592 96.5700 1586 2546 1 chr5B.!!$R3 960
9 TraesCS2B01G256900 chr5B 708965387 708965962 575 False 837 837 92.6050 999 1593 1 chr5B.!!$F2 594
10 TraesCS2B01G256900 chrUn 84128491 84129445 954 False 1596 1596 96.8590 1593 2546 1 chrUn.!!$F1 953
11 TraesCS2B01G256900 chr4B 590814782 590815735 953 True 1596 1596 96.8590 1593 2546 1 chr4B.!!$R1 953
12 TraesCS2B01G256900 chr7B 186594018 186594989 971 True 1502 1502 94.7750 633 1593 1 chr7B.!!$R1 960
13 TraesCS2B01G256900 chr3D 14411891 14412850 959 True 1469 1469 94.2770 633 1593 1 chr3D.!!$R1 960
14 TraesCS2B01G256900 chr6A 6329905 6330861 956 False 1456 1456 94.0930 633 1593 1 chr6A.!!$F1 960
15 TraesCS2B01G256900 chr3A 71801459 71802415 956 True 1423 1423 93.4720 633 1593 1 chr3A.!!$R1 960
16 TraesCS2B01G256900 chr3B 60507860 60508817 957 True 1406 1406 93.1610 633 1593 1 chr3B.!!$R1 960
17 TraesCS2B01G256900 chr1B 529514071 529514837 766 True 1256 1256 96.2190 827 1593 1 chr1B.!!$R1 766
18 TraesCS2B01G256900 chr2A 306176608 306177247 639 False 1064 1064 96.8800 1 633 1 chr2A.!!$F2 632
19 TraesCS2B01G256900 chr2D 215846951 215847575 624 False 1024 1024 96.0750 1 633 1 chr2D.!!$F1 632
20 TraesCS2B01G256900 chr6D 289729126 289730056 930 False 572 778 88.6825 633 1593 2 chr6D.!!$F1 960

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
576 577 0.249699 TGTGCGATCGTGTTGGAACT 60.25 50.000 17.81 0.0 0.0 3.01 F
577 578 1.000052 TGTGCGATCGTGTTGGAACTA 60.00 47.619 17.81 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 1466 3.057315 GGAAGTGATTTTAGCAGCAGCAA 60.057 43.478 3.17 0.0 45.49 3.91 R
2281 2332 3.125487 TCAAACCGCATAACAACATACGG 59.875 43.478 0.00 0.0 45.86 4.02 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
61 62 5.106118 GGAGTAAGCAAGGAAGGAATTGAAC 60.106 44.000 0.00 0.00 0.00 3.18
477 478 3.774528 CGGCTGGTCCTGCTGCTA 61.775 66.667 19.07 0.00 0.00 3.49
478 479 2.188994 GGCTGGTCCTGCTGCTAG 59.811 66.667 19.07 0.00 0.00 3.42
479 480 2.664081 GGCTGGTCCTGCTGCTAGT 61.664 63.158 19.07 0.00 0.00 2.57
480 481 1.449246 GCTGGTCCTGCTGCTAGTG 60.449 63.158 13.24 0.00 0.00 2.74
481 482 1.220206 CTGGTCCTGCTGCTAGTGG 59.780 63.158 0.00 0.00 0.00 4.00
482 483 1.229177 TGGTCCTGCTGCTAGTGGA 60.229 57.895 0.00 0.77 0.00 4.02
483 484 1.260538 TGGTCCTGCTGCTAGTGGAG 61.261 60.000 0.00 0.00 34.56 3.86
484 485 1.519719 GTCCTGCTGCTAGTGGAGG 59.480 63.158 15.57 15.57 43.23 4.30
485 486 2.188994 CCTGCTGCTAGTGGAGGC 59.811 66.667 11.13 1.43 36.30 4.70
486 487 2.188994 CTGCTGCTAGTGGAGGCC 59.811 66.667 0.00 0.00 31.89 5.19
487 488 3.729965 CTGCTGCTAGTGGAGGCCG 62.730 68.421 0.00 0.00 31.89 6.13
489 490 3.465403 CTGCTAGTGGAGGCCGCT 61.465 66.667 6.40 4.79 46.90 5.52
490 491 3.729965 CTGCTAGTGGAGGCCGCTG 62.730 68.421 6.40 0.00 44.79 5.18
492 493 3.774528 CTAGTGGAGGCCGCTGCA 61.775 66.667 6.40 0.00 44.79 4.41
493 494 3.729965 CTAGTGGAGGCCGCTGCAG 62.730 68.421 10.11 10.11 44.79 4.41
497 498 4.704833 GGAGGCCGCTGCAGTTGA 62.705 66.667 16.64 0.00 40.13 3.18
498 499 2.437359 GAGGCCGCTGCAGTTGAT 60.437 61.111 16.64 0.00 40.13 2.57
499 500 2.749044 AGGCCGCTGCAGTTGATG 60.749 61.111 16.64 0.76 40.13 3.07
511 512 1.815003 CAGTTGATGCTGGTTCCTTCC 59.185 52.381 0.00 0.00 33.11 3.46
512 513 1.707427 AGTTGATGCTGGTTCCTTCCT 59.293 47.619 0.00 0.00 0.00 3.36
513 514 2.912956 AGTTGATGCTGGTTCCTTCCTA 59.087 45.455 0.00 0.00 0.00 2.94
514 515 3.010420 GTTGATGCTGGTTCCTTCCTAC 58.990 50.000 0.00 0.00 0.00 3.18
515 516 1.559682 TGATGCTGGTTCCTTCCTACC 59.440 52.381 0.00 0.00 34.93 3.18
516 517 1.559682 GATGCTGGTTCCTTCCTACCA 59.440 52.381 0.00 0.00 41.97 3.25
520 521 2.409064 TGGTTCCTTCCTACCAGTGA 57.591 50.000 0.00 0.00 39.44 3.41
521 522 2.257207 TGGTTCCTTCCTACCAGTGAG 58.743 52.381 0.00 0.00 39.44 3.51
522 523 2.158219 TGGTTCCTTCCTACCAGTGAGA 60.158 50.000 0.00 0.00 39.44 3.27
523 524 2.904434 GGTTCCTTCCTACCAGTGAGAA 59.096 50.000 0.00 0.00 34.48 2.87
524 525 3.326880 GGTTCCTTCCTACCAGTGAGAAA 59.673 47.826 0.00 0.00 34.48 2.52
525 526 4.563786 GGTTCCTTCCTACCAGTGAGAAAG 60.564 50.000 0.00 0.00 34.48 2.62
526 527 3.173965 TCCTTCCTACCAGTGAGAAAGG 58.826 50.000 0.00 0.00 0.00 3.11
527 528 2.237392 CCTTCCTACCAGTGAGAAAGGG 59.763 54.545 0.00 0.00 0.00 3.95
528 529 1.952621 TCCTACCAGTGAGAAAGGGG 58.047 55.000 0.00 0.00 0.00 4.79
529 530 1.435563 TCCTACCAGTGAGAAAGGGGA 59.564 52.381 0.00 0.00 0.00 4.81
530 531 1.555533 CCTACCAGTGAGAAAGGGGAC 59.444 57.143 0.00 0.00 0.00 4.46
531 532 1.204941 CTACCAGTGAGAAAGGGGACG 59.795 57.143 0.00 0.00 0.00 4.79
532 533 1.376037 CCAGTGAGAAAGGGGACGC 60.376 63.158 0.00 0.00 0.00 5.19
533 534 1.738099 CAGTGAGAAAGGGGACGCG 60.738 63.158 3.53 3.53 0.00 6.01
534 535 2.207924 AGTGAGAAAGGGGACGCGT 61.208 57.895 13.85 13.85 0.00 6.01
535 536 0.896940 AGTGAGAAAGGGGACGCGTA 60.897 55.000 13.97 0.00 0.00 4.42
536 537 0.458025 GTGAGAAAGGGGACGCGTAG 60.458 60.000 13.97 0.00 0.00 3.51
537 538 0.896940 TGAGAAAGGGGACGCGTAGT 60.897 55.000 13.97 0.00 0.00 2.73
546 547 3.302968 GACGCGTAGTCGTAGCTTT 57.697 52.632 13.97 0.00 39.92 3.51
547 548 1.611043 GACGCGTAGTCGTAGCTTTT 58.389 50.000 13.97 0.00 39.92 2.27
548 549 1.981533 GACGCGTAGTCGTAGCTTTTT 59.018 47.619 13.97 0.00 39.92 1.94
549 550 1.981533 ACGCGTAGTCGTAGCTTTTTC 59.018 47.619 11.67 0.00 38.33 2.29
550 551 2.248487 CGCGTAGTCGTAGCTTTTTCT 58.752 47.619 0.00 0.00 39.49 2.52
551 552 2.026507 CGCGTAGTCGTAGCTTTTTCTG 59.973 50.000 0.00 0.00 39.49 3.02
552 553 2.985139 GCGTAGTCGTAGCTTTTTCTGT 59.015 45.455 0.00 0.00 39.49 3.41
553 554 3.181543 GCGTAGTCGTAGCTTTTTCTGTG 60.182 47.826 0.00 0.00 39.49 3.66
554 555 3.181543 CGTAGTCGTAGCTTTTTCTGTGC 60.182 47.826 0.00 0.00 0.00 4.57
555 556 1.792949 AGTCGTAGCTTTTTCTGTGCG 59.207 47.619 0.00 0.00 0.00 5.34
556 557 1.790623 GTCGTAGCTTTTTCTGTGCGA 59.209 47.619 0.00 0.00 0.00 5.10
557 558 2.412089 GTCGTAGCTTTTTCTGTGCGAT 59.588 45.455 0.00 0.00 0.00 4.58
558 559 2.411748 TCGTAGCTTTTTCTGTGCGATG 59.588 45.455 0.00 0.00 0.00 3.84
559 560 2.157668 CGTAGCTTTTTCTGTGCGATGT 59.842 45.455 0.00 0.00 0.00 3.06
560 561 2.693797 AGCTTTTTCTGTGCGATGTG 57.306 45.000 0.00 0.00 0.00 3.21
561 562 1.055338 GCTTTTTCTGTGCGATGTGC 58.945 50.000 0.00 0.00 46.70 4.57
570 571 3.081133 GCGATGTGCGATCGTGTT 58.919 55.556 17.81 0.00 44.57 3.32
571 572 1.296145 GCGATGTGCGATCGTGTTG 60.296 57.895 17.81 5.64 44.57 3.33
572 573 1.344837 CGATGTGCGATCGTGTTGG 59.655 57.895 17.81 0.00 44.57 3.77
573 574 1.075979 CGATGTGCGATCGTGTTGGA 61.076 55.000 17.81 0.00 44.57 3.53
574 575 1.075542 GATGTGCGATCGTGTTGGAA 58.924 50.000 17.81 0.00 0.00 3.53
575 576 0.796312 ATGTGCGATCGTGTTGGAAC 59.204 50.000 17.81 4.96 0.00 3.62
576 577 0.249699 TGTGCGATCGTGTTGGAACT 60.250 50.000 17.81 0.00 0.00 3.01
577 578 1.000052 TGTGCGATCGTGTTGGAACTA 60.000 47.619 17.81 0.00 0.00 2.24
578 579 2.268298 GTGCGATCGTGTTGGAACTAT 58.732 47.619 17.81 0.00 0.00 2.12
579 580 2.671396 GTGCGATCGTGTTGGAACTATT 59.329 45.455 17.81 0.00 0.00 1.73
580 581 2.927477 TGCGATCGTGTTGGAACTATTC 59.073 45.455 17.81 0.00 0.00 1.75
581 582 3.187700 GCGATCGTGTTGGAACTATTCT 58.812 45.455 17.81 0.00 0.00 2.40
582 583 3.243177 GCGATCGTGTTGGAACTATTCTC 59.757 47.826 17.81 0.00 0.00 2.87
583 584 3.797256 CGATCGTGTTGGAACTATTCTCC 59.203 47.826 7.03 0.00 0.00 3.71
584 585 3.604875 TCGTGTTGGAACTATTCTCCC 57.395 47.619 0.00 0.00 31.32 4.30
585 586 2.901192 TCGTGTTGGAACTATTCTCCCA 59.099 45.455 0.00 0.00 31.32 4.37
586 587 3.517901 TCGTGTTGGAACTATTCTCCCAT 59.482 43.478 0.00 0.00 31.32 4.00
587 588 4.019681 TCGTGTTGGAACTATTCTCCCATT 60.020 41.667 0.00 0.00 31.32 3.16
588 589 4.700213 CGTGTTGGAACTATTCTCCCATTT 59.300 41.667 0.00 0.00 31.32 2.32
589 590 5.391950 CGTGTTGGAACTATTCTCCCATTTG 60.392 44.000 0.00 0.00 31.32 2.32
590 591 5.016173 TGTTGGAACTATTCTCCCATTTGG 58.984 41.667 0.00 0.00 31.32 3.28
600 601 3.486263 CCATTTGGGCGAGACGAC 58.514 61.111 0.00 0.00 0.00 4.34
601 602 2.452813 CCATTTGGGCGAGACGACG 61.453 63.158 0.00 0.00 34.63 5.12
602 603 1.736645 CATTTGGGCGAGACGACGT 60.737 57.895 0.00 0.00 34.63 4.34
603 604 1.736645 ATTTGGGCGAGACGACGTG 60.737 57.895 4.58 0.00 34.63 4.49
604 605 3.851845 TTTGGGCGAGACGACGTGG 62.852 63.158 4.58 0.00 34.63 4.94
671 672 9.228949 CTACAGTAACTGAACTTAACTCTAGGA 57.771 37.037 0.00 0.00 35.18 2.94
702 703 5.487433 TGGTCACTGTATTCATGAAATCGT 58.513 37.500 13.09 4.86 0.00 3.73
729 730 1.675641 GTCACCGGGCTTGCTGAAT 60.676 57.895 6.32 0.00 0.00 2.57
795 802 1.924191 GCACGTGGACAAAATTGACGG 60.924 52.381 18.88 0.00 32.37 4.79
874 895 1.043673 CGATTCCCCTCTCGTTCCCT 61.044 60.000 0.00 0.00 0.00 4.20
930 966 1.444119 CTCCTCCCTTCTCGCTCGAG 61.444 65.000 8.45 8.45 43.21 4.04
976 1012 4.191544 CCCTTATCTCTCGTCAAATTGCA 58.808 43.478 0.00 0.00 0.00 4.08
1401 1441 7.039882 AGAAAAAGAAGAACACGACAGAAGTA 58.960 34.615 0.00 0.00 0.00 2.24
1426 1466 8.438618 AGATCCTGAAGATATGATGAAGATGT 57.561 34.615 0.00 0.00 34.42 3.06
1610 1659 6.731467 AGACTTTGAAGGAAATATGCCCTAA 58.269 36.000 0.00 0.00 31.36 2.69
2281 2332 1.892209 ACCGATGACAAAGGGAACAC 58.108 50.000 4.83 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 2.030562 GACATGATACCCCGCCGG 59.969 66.667 0.00 0.00 37.81 6.13
460 461 3.729965 CTAGCAGCAGGACCAGCCG 62.730 68.421 5.06 0.00 43.43 5.52
461 462 2.188994 CTAGCAGCAGGACCAGCC 59.811 66.667 5.06 0.00 0.00 4.85
462 463 1.449246 CACTAGCAGCAGGACCAGC 60.449 63.158 0.00 0.00 0.00 4.85
463 464 1.220206 CCACTAGCAGCAGGACCAG 59.780 63.158 0.00 0.00 0.00 4.00
464 465 1.229177 TCCACTAGCAGCAGGACCA 60.229 57.895 0.00 0.00 0.00 4.02
465 466 1.519719 CTCCACTAGCAGCAGGACC 59.480 63.158 0.00 0.00 0.00 4.46
466 467 1.519719 CCTCCACTAGCAGCAGGAC 59.480 63.158 0.00 0.00 0.00 3.85
467 468 2.362369 GCCTCCACTAGCAGCAGGA 61.362 63.158 0.00 0.00 0.00 3.86
468 469 2.188994 GCCTCCACTAGCAGCAGG 59.811 66.667 0.00 0.00 0.00 4.85
469 470 2.188994 GGCCTCCACTAGCAGCAG 59.811 66.667 0.00 0.00 0.00 4.24
470 471 3.774528 CGGCCTCCACTAGCAGCA 61.775 66.667 0.00 0.00 0.00 4.41
472 473 3.465403 AGCGGCCTCCACTAGCAG 61.465 66.667 0.00 0.00 0.00 4.24
473 474 3.774528 CAGCGGCCTCCACTAGCA 61.775 66.667 0.00 0.00 0.00 3.49
475 476 3.729965 CTGCAGCGGCCTCCACTAG 62.730 68.421 6.32 0.00 40.13 2.57
476 477 3.774528 CTGCAGCGGCCTCCACTA 61.775 66.667 6.32 0.00 40.13 2.74
480 481 3.984193 ATCAACTGCAGCGGCCTCC 62.984 63.158 15.27 0.00 40.13 4.30
481 482 2.437359 ATCAACTGCAGCGGCCTC 60.437 61.111 15.27 0.00 40.13 4.70
482 483 2.749044 CATCAACTGCAGCGGCCT 60.749 61.111 15.27 0.00 40.13 5.19
491 492 1.815003 GGAAGGAACCAGCATCAACTG 59.185 52.381 0.00 0.00 37.42 3.16
492 493 1.707427 AGGAAGGAACCAGCATCAACT 59.293 47.619 0.00 0.00 0.00 3.16
493 494 2.206576 AGGAAGGAACCAGCATCAAC 57.793 50.000 0.00 0.00 0.00 3.18
494 495 2.026262 GGTAGGAAGGAACCAGCATCAA 60.026 50.000 0.00 0.00 35.73 2.57
495 496 1.559682 GGTAGGAAGGAACCAGCATCA 59.440 52.381 0.00 0.00 35.73 3.07
496 497 1.559682 TGGTAGGAAGGAACCAGCATC 59.440 52.381 0.00 0.00 40.84 3.91
497 498 1.668826 TGGTAGGAAGGAACCAGCAT 58.331 50.000 0.00 0.00 40.84 3.79
498 499 3.173852 TGGTAGGAAGGAACCAGCA 57.826 52.632 0.00 0.00 40.84 4.41
501 502 2.158219 TCTCACTGGTAGGAAGGAACCA 60.158 50.000 0.00 0.00 43.47 3.67
502 503 2.537143 TCTCACTGGTAGGAAGGAACC 58.463 52.381 0.00 0.00 36.24 3.62
503 504 4.570930 CTTTCTCACTGGTAGGAAGGAAC 58.429 47.826 0.00 0.00 0.00 3.62
504 505 4.891992 CTTTCTCACTGGTAGGAAGGAA 57.108 45.455 0.00 0.00 0.00 3.36
506 507 2.237392 CCCTTTCTCACTGGTAGGAAGG 59.763 54.545 10.26 10.26 45.86 3.46
507 508 2.237392 CCCCTTTCTCACTGGTAGGAAG 59.763 54.545 0.00 0.00 30.47 3.46
508 509 2.158066 TCCCCTTTCTCACTGGTAGGAA 60.158 50.000 0.00 0.00 0.00 3.36
509 510 1.435563 TCCCCTTTCTCACTGGTAGGA 59.564 52.381 0.00 0.00 0.00 2.94
510 511 1.555533 GTCCCCTTTCTCACTGGTAGG 59.444 57.143 0.00 0.00 0.00 3.18
511 512 1.204941 CGTCCCCTTTCTCACTGGTAG 59.795 57.143 0.00 0.00 0.00 3.18
512 513 1.263356 CGTCCCCTTTCTCACTGGTA 58.737 55.000 0.00 0.00 0.00 3.25
513 514 2.058675 CGTCCCCTTTCTCACTGGT 58.941 57.895 0.00 0.00 0.00 4.00
514 515 1.376037 GCGTCCCCTTTCTCACTGG 60.376 63.158 0.00 0.00 0.00 4.00
515 516 1.738099 CGCGTCCCCTTTCTCACTG 60.738 63.158 0.00 0.00 0.00 3.66
516 517 0.896940 TACGCGTCCCCTTTCTCACT 60.897 55.000 18.63 0.00 0.00 3.41
517 518 0.458025 CTACGCGTCCCCTTTCTCAC 60.458 60.000 18.63 0.00 0.00 3.51
518 519 0.896940 ACTACGCGTCCCCTTTCTCA 60.897 55.000 18.63 0.00 0.00 3.27
519 520 0.179142 GACTACGCGTCCCCTTTCTC 60.179 60.000 18.63 0.00 36.62 2.87
520 521 1.888736 GACTACGCGTCCCCTTTCT 59.111 57.895 18.63 0.00 36.62 2.52
521 522 1.515736 CGACTACGCGTCCCCTTTC 60.516 63.158 18.63 3.22 39.56 2.62
522 523 0.960364 TACGACTACGCGTCCCCTTT 60.960 55.000 18.63 0.00 44.39 3.11
523 524 1.372087 CTACGACTACGCGTCCCCTT 61.372 60.000 18.63 0.63 44.39 3.95
524 525 1.817099 CTACGACTACGCGTCCCCT 60.817 63.158 18.63 0.00 44.39 4.79
525 526 2.711924 CTACGACTACGCGTCCCC 59.288 66.667 18.63 4.63 44.39 4.81
526 527 1.986575 AAGCTACGACTACGCGTCCC 61.987 60.000 18.63 5.05 44.39 4.46
527 528 0.179179 AAAGCTACGACTACGCGTCC 60.179 55.000 18.63 5.47 44.39 4.79
528 529 1.611043 AAAAGCTACGACTACGCGTC 58.389 50.000 18.63 0.00 44.39 5.19
530 531 2.026507 CAGAAAAAGCTACGACTACGCG 59.973 50.000 3.53 3.53 43.96 6.01
531 532 2.985139 ACAGAAAAAGCTACGACTACGC 59.015 45.455 0.00 0.00 43.96 4.42
532 533 3.181543 GCACAGAAAAAGCTACGACTACG 60.182 47.826 0.00 0.00 45.75 3.51
533 534 3.181543 CGCACAGAAAAAGCTACGACTAC 60.182 47.826 0.00 0.00 0.00 2.73
534 535 2.984471 CGCACAGAAAAAGCTACGACTA 59.016 45.455 0.00 0.00 0.00 2.59
535 536 1.792949 CGCACAGAAAAAGCTACGACT 59.207 47.619 0.00 0.00 0.00 4.18
536 537 1.790623 TCGCACAGAAAAAGCTACGAC 59.209 47.619 0.00 0.00 0.00 4.34
537 538 2.143008 TCGCACAGAAAAAGCTACGA 57.857 45.000 0.00 0.00 0.00 3.43
538 539 2.157668 ACATCGCACAGAAAAAGCTACG 59.842 45.455 0.00 0.00 0.00 3.51
539 540 3.482786 CACATCGCACAGAAAAAGCTAC 58.517 45.455 0.00 0.00 0.00 3.58
540 541 2.095768 GCACATCGCACAGAAAAAGCTA 60.096 45.455 0.00 0.00 41.79 3.32
541 542 1.335324 GCACATCGCACAGAAAAAGCT 60.335 47.619 0.00 0.00 41.79 3.74
542 543 1.055338 GCACATCGCACAGAAAAAGC 58.945 50.000 0.00 0.00 41.79 3.51
543 544 1.069973 TCGCACATCGCACAGAAAAAG 60.070 47.619 0.00 0.00 42.60 2.27
544 545 0.940833 TCGCACATCGCACAGAAAAA 59.059 45.000 0.00 0.00 42.60 1.94
545 546 1.128507 GATCGCACATCGCACAGAAAA 59.871 47.619 0.00 0.00 42.60 2.29
546 547 0.721154 GATCGCACATCGCACAGAAA 59.279 50.000 0.00 0.00 42.60 2.52
547 548 1.413008 CGATCGCACATCGCACAGAA 61.413 55.000 0.26 0.00 42.60 3.02
548 549 1.873572 CGATCGCACATCGCACAGA 60.874 57.895 0.26 0.00 42.60 3.41
549 550 2.160853 ACGATCGCACATCGCACAG 61.161 57.895 16.60 0.00 44.60 3.66
550 551 2.126110 ACGATCGCACATCGCACA 60.126 55.556 16.60 0.00 44.60 4.57
551 552 1.955529 AACACGATCGCACATCGCAC 61.956 55.000 16.60 0.00 44.60 5.34
552 553 1.736282 AACACGATCGCACATCGCA 60.736 52.632 16.60 0.00 44.60 5.10
553 554 1.296145 CAACACGATCGCACATCGC 60.296 57.895 16.60 0.00 44.60 4.58
554 555 1.075979 TCCAACACGATCGCACATCG 61.076 55.000 16.60 12.35 46.02 3.84
555 556 1.075542 TTCCAACACGATCGCACATC 58.924 50.000 16.60 0.00 0.00 3.06
556 557 0.796312 GTTCCAACACGATCGCACAT 59.204 50.000 16.60 0.00 0.00 3.21
557 558 0.249699 AGTTCCAACACGATCGCACA 60.250 50.000 16.60 0.00 0.00 4.57
558 559 1.705256 TAGTTCCAACACGATCGCAC 58.295 50.000 16.60 0.84 0.00 5.34
559 560 2.665649 ATAGTTCCAACACGATCGCA 57.334 45.000 16.60 0.00 0.00 5.10
560 561 3.187700 AGAATAGTTCCAACACGATCGC 58.812 45.455 16.60 0.00 0.00 4.58
561 562 3.797256 GGAGAATAGTTCCAACACGATCG 59.203 47.826 14.88 14.88 34.74 3.69
562 563 4.120589 GGGAGAATAGTTCCAACACGATC 58.879 47.826 0.00 0.00 36.40 3.69
563 564 3.517901 TGGGAGAATAGTTCCAACACGAT 59.482 43.478 0.00 0.00 36.40 3.73
564 565 2.901192 TGGGAGAATAGTTCCAACACGA 59.099 45.455 0.00 0.00 36.40 4.35
565 566 3.328382 TGGGAGAATAGTTCCAACACG 57.672 47.619 0.00 0.00 36.40 4.49
566 567 5.105756 CCAAATGGGAGAATAGTTCCAACAC 60.106 44.000 0.00 0.00 40.01 3.32
567 568 5.016173 CCAAATGGGAGAATAGTTCCAACA 58.984 41.667 0.00 0.00 40.01 3.33
568 569 5.582689 CCAAATGGGAGAATAGTTCCAAC 57.417 43.478 0.00 0.00 40.01 3.77
583 584 2.452813 CGTCGTCTCGCCCAAATGG 61.453 63.158 0.00 0.00 37.09 3.16
584 585 1.736645 ACGTCGTCTCGCCCAAATG 60.737 57.895 0.00 0.00 0.00 2.32
585 586 1.736645 CACGTCGTCTCGCCCAAAT 60.737 57.895 0.00 0.00 0.00 2.32
586 587 2.355363 CACGTCGTCTCGCCCAAA 60.355 61.111 0.00 0.00 0.00 3.28
587 588 4.351938 CCACGTCGTCTCGCCCAA 62.352 66.667 0.00 0.00 0.00 4.12
615 616 3.443045 CAATGGGCAGCCACGACC 61.443 66.667 15.19 0.00 0.00 4.79
616 617 2.359850 TCAATGGGCAGCCACGAC 60.360 61.111 15.19 0.00 0.00 4.34
617 618 2.046023 CTCAATGGGCAGCCACGA 60.046 61.111 15.19 2.37 0.00 4.35
618 619 1.243342 TTTCTCAATGGGCAGCCACG 61.243 55.000 15.19 0.00 0.00 4.94
619 620 0.968405 TTTTCTCAATGGGCAGCCAC 59.032 50.000 15.19 3.08 0.00 5.01
620 621 1.941377 ATTTTCTCAATGGGCAGCCA 58.059 45.000 15.19 0.00 0.00 4.75
621 622 3.195396 TGTAATTTTCTCAATGGGCAGCC 59.805 43.478 1.26 1.26 0.00 4.85
622 623 4.454728 TGTAATTTTCTCAATGGGCAGC 57.545 40.909 0.00 0.00 0.00 5.25
623 624 6.461110 AGATGTAATTTTCTCAATGGGCAG 57.539 37.500 0.00 0.00 0.00 4.85
624 625 6.889177 TGTAGATGTAATTTTCTCAATGGGCA 59.111 34.615 0.00 0.00 0.00 5.36
625 626 7.067494 ACTGTAGATGTAATTTTCTCAATGGGC 59.933 37.037 0.00 0.00 0.00 5.36
626 627 8.511604 ACTGTAGATGTAATTTTCTCAATGGG 57.488 34.615 0.00 0.00 0.00 4.00
662 663 5.308237 AGTGACCAAAGTGAATCCTAGAGTT 59.692 40.000 0.00 0.00 0.00 3.01
671 672 6.942005 TCATGAATACAGTGACCAAAGTGAAT 59.058 34.615 0.00 0.00 0.00 2.57
702 703 2.934570 GCCCGGTGACCGTAACTCA 61.935 63.158 23.73 0.00 46.80 3.41
729 730 2.297701 GGTTACCGTATAGTGACCCGA 58.702 52.381 0.00 0.00 39.81 5.14
803 810 4.980573 ACAACTGGCAAGTCCAAGTATTA 58.019 39.130 0.00 0.00 46.01 0.98
804 811 3.832527 ACAACTGGCAAGTCCAAGTATT 58.167 40.909 0.00 0.00 46.01 1.89
805 812 3.508845 ACAACTGGCAAGTCCAAGTAT 57.491 42.857 0.00 0.00 46.01 2.12
874 895 1.476833 GGGATTTAGCAGGCGGATGAA 60.477 52.381 0.00 0.00 0.00 2.57
930 966 1.808945 CAGAGGATGCAACTGTTGGAC 59.191 52.381 21.01 12.76 32.41 4.02
976 1012 0.039527 GCCGAAACCAATTTGTCGCT 60.040 50.000 3.17 0.00 0.00 4.93
1034 1071 1.923356 GATCAAAGGGAGCCAACCAA 58.077 50.000 0.00 0.00 0.00 3.67
1035 1072 3.670105 GATCAAAGGGAGCCAACCA 57.330 52.632 0.00 0.00 0.00 3.67
1401 1441 8.438618 ACATCTTCATCATATCTTCAGGATCT 57.561 34.615 0.00 0.00 35.98 2.75
1426 1466 3.057315 GGAAGTGATTTTAGCAGCAGCAA 60.057 43.478 3.17 0.00 45.49 3.91
2281 2332 3.125487 TCAAACCGCATAACAACATACGG 59.875 43.478 0.00 0.00 45.86 4.02


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

AutoCloner maintained by Alex Coulton.