Multiple sequence alignment - TraesCS3D01G253300

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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 TraesCS3D01G253300 chr3D 100.000 3048 0 0 1 3048 354622769 354619722 0.000000e+00 5629
1 TraesCS3D01G253300 chr3D 79.551 401 57 20 1019 1403 588696316 588696707 2.330000e-66 263
2 TraesCS3D01G253300 chr3B 89.106 2249 133 34 365 2550 455067499 455065300 0.000000e+00 2693
3 TraesCS3D01G253300 chr3B 94.748 457 22 1 2592 3048 455065301 455064847 0.000000e+00 710
4 TraesCS3D01G253300 chr3B 87.105 411 40 12 1 405 455132014 455131611 1.290000e-123 453
5 TraesCS3D01G253300 chr3A 87.885 2080 134 54 338 2319 473218194 473216135 0.000000e+00 2337
6 TraesCS3D01G253300 chr3A 93.202 456 29 1 2593 3048 473213177 473212724 0.000000e+00 669
7 TraesCS3D01G253300 chr3A 87.591 411 43 8 1 408 473218558 473218153 1.280000e-128 470
8 TraesCS3D01G253300 chr3A 82.684 231 19 9 2319 2546 473213393 473213181 5.190000e-43 185
9 TraesCS3D01G253300 chr1B 79.953 424 56 20 999 1401 613415580 613415165 4.970000e-73 285
10 TraesCS3D01G253300 chr1A 78.910 422 68 13 999 1403 544048745 544048328 1.800000e-67 267
11 TraesCS3D01G253300 chr2D 79.551 401 57 20 1019 1403 586831126 586831517 2.330000e-66 263
12 TraesCS3D01G253300 chr7B 79.302 401 58 20 1019 1403 97120331 97119940 1.080000e-64 257
13 TraesCS3D01G253300 chr7B 78.055 401 63 20 1019 1403 689142500 689142109 2.360000e-56 230
14 TraesCS3D01G253300 chr7B 77.556 401 63 21 1019 1403 89870217 89869828 1.840000e-52 217
15 TraesCS3D01G253300 chr1D 78.436 422 70 14 999 1403 447925417 447925000 3.900000e-64 255
16 TraesCS3D01G253300 chr5D 78.500 400 63 18 1019 1403 556578548 556578157 1.090000e-59 241
17 TraesCS3D01G253300 chr5B 77.488 422 68 22 999 1403 527733241 527733652 8.500000e-56 228


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 TraesCS3D01G253300 chr3D 354619722 354622769 3047 True 5629.00 5629 100.0000 1 3048 1 chr3D.!!$R1 3047
1 TraesCS3D01G253300 chr3B 455064847 455067499 2652 True 1701.50 2693 91.9270 365 3048 2 chr3B.!!$R2 2683
2 TraesCS3D01G253300 chr3A 473212724 473218558 5834 True 915.25 2337 87.8405 1 3048 4 chr3A.!!$R1 3047

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
634 671 0.179702 TCTACGCTCTCCTCGCCTAA 59.82 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2575 5474 0.095935 CTTTTCGGCTGCACAGATCG 59.904 55.0 0.5 4.8 0.0 3.69 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
50 51 7.161773 ACCTGATTTGATTGTATTTGGTCAG 57.838 36.000 0.00 0.00 0.00 3.51
63 64 1.699730 TGGTCAGAAGAACAGTCGGA 58.300 50.000 0.00 0.00 36.30 4.55
115 116 7.701539 ACAATCCTAGAACAACATTGCATTA 57.298 32.000 0.00 0.00 0.00 1.90
130 131 9.941325 AACATTGCATTATTTTCTTCCAATACA 57.059 25.926 0.00 0.00 0.00 2.29
142 143 6.681729 TCTTCCAATACAGACTTTGGTACT 57.318 37.500 4.66 0.00 42.47 2.73
159 160 3.811497 GGTACTGTTTCTTAGTGCCGTTT 59.189 43.478 0.00 0.00 40.30 3.60
169 170 6.032956 TCTTAGTGCCGTTTTAGATTCTGA 57.967 37.500 0.00 0.00 0.00 3.27
425 461 2.034221 GGGTGCCCAGGAGAACAC 59.966 66.667 1.66 0.00 35.81 3.32
444 480 2.997315 TCAGCCCACTCCAGTCCG 60.997 66.667 0.00 0.00 0.00 4.79
458 494 1.823899 GTCCGGCCCATAAAGCAGG 60.824 63.158 0.00 0.00 45.73 4.85
489 525 4.143363 GGTTTACGAGCGCCGCAC 62.143 66.667 13.36 3.45 43.32 5.34
506 542 3.372954 CGCACTACTATAAAAGCTCGCT 58.627 45.455 0.00 0.00 0.00 4.93
555 591 2.026445 CACACGACGAACACCGGA 59.974 61.111 9.46 0.00 43.93 5.14
606 642 2.600790 TCACCGGTGAGAAGAAACCTA 58.399 47.619 33.23 6.65 34.14 3.08
617 654 4.504382 AGAAGAAACCTACCCTCCTTTCT 58.496 43.478 0.00 0.00 35.02 2.52
621 658 1.482954 ACCTACCCTCCTTTCTACGC 58.517 55.000 0.00 0.00 0.00 4.42
627 664 1.686741 CCCTCCTTTCTACGCTCTCCT 60.687 57.143 0.00 0.00 0.00 3.69
634 671 0.179702 TCTACGCTCTCCTCGCCTAA 59.820 55.000 0.00 0.00 0.00 2.69
674 711 3.903090 TCCCAATTGTTCAATTTGCTCCT 59.097 39.130 4.43 0.00 0.00 3.69
702 740 2.676750 CGACCCATTCGTGATTTGAGGA 60.677 50.000 0.00 0.00 43.24 3.71
707 745 3.557595 CCATTCGTGATTTGAGGAGCTAC 59.442 47.826 0.00 0.00 0.00 3.58
711 749 2.223829 CGTGATTTGAGGAGCTACCGAT 60.224 50.000 0.00 0.00 44.74 4.18
747 785 4.393371 GGTGAAATCTCTAGTGTTCCTTGC 59.607 45.833 0.00 0.00 0.00 4.01
810 848 2.961522 ACGGCGTAGTTGATTTGTTG 57.038 45.000 12.58 0.00 0.00 3.33
844 890 9.646427 GTCTATTTCCAGATCAGTATATGTTCC 57.354 37.037 0.00 0.00 0.00 3.62
855 901 3.954904 AGTATATGTTCCGTCTGCTCAGT 59.045 43.478 0.00 0.00 0.00 3.41
863 909 2.826128 TCCGTCTGCTCAGTTGTATCTT 59.174 45.455 0.00 0.00 0.00 2.40
871 917 4.184629 GCTCAGTTGTATCTTGTCCGATT 58.815 43.478 0.00 0.00 0.00 3.34
887 933 6.062749 TGTCCGATTGTACTCTAGATTAGCT 58.937 40.000 0.00 0.00 0.00 3.32
899 946 6.553100 ACTCTAGATTAGCTTAGGTGCAAGAT 59.447 38.462 0.00 0.00 34.99 2.40
902 949 9.755122 TCTAGATTAGCTTAGGTGCAAGATATA 57.245 33.333 0.00 0.00 34.99 0.86
917 964 3.239449 AGATATATGGCGTCTGTTGGGA 58.761 45.455 0.00 0.00 0.00 4.37
918 965 2.902705 TATATGGCGTCTGTTGGGAC 57.097 50.000 0.00 0.00 0.00 4.46
964 1011 7.261325 TCTAGATTTATGCTCGGCTTCATATC 58.739 38.462 0.00 0.00 0.00 1.63
970 1017 1.202580 GCTCGGCTTCATATCCAGTGT 60.203 52.381 0.00 0.00 0.00 3.55
983 1030 9.631257 TTCATATCCAGTGTTTGATATGTGATT 57.369 29.630 19.15 0.00 45.65 2.57
1255 1322 2.682856 GGCAAACAAGAAGACTGTGACA 59.317 45.455 0.00 0.00 0.00 3.58
1407 1474 6.553953 TGTCAAGAACCAGGTATTAGCATA 57.446 37.500 0.00 0.00 0.00 3.14
1413 1480 7.439108 AGAACCAGGTATTAGCATAAGAACT 57.561 36.000 0.00 0.00 0.00 3.01
1497 1592 3.957497 TGTAGCAACCATTCCAGTGTTTT 59.043 39.130 0.00 0.00 0.00 2.43
1502 1597 3.025322 ACCATTCCAGTGTTTTGGTCA 57.975 42.857 3.05 0.00 35.87 4.02
1513 1611 6.432783 CCAGTGTTTTGGTCATAGGTGAAATA 59.567 38.462 0.00 0.00 35.80 1.40
1530 1628 9.632638 AGGTGAAATATAACTGTTATGCTTGAT 57.367 29.630 20.42 5.36 0.00 2.57
1537 1635 5.710513 AACTGTTATGCTTGATTGCTGAA 57.289 34.783 0.00 0.00 0.00 3.02
1548 1646 6.206438 TGCTTGATTGCTGAATTTGTACAGTA 59.794 34.615 0.00 0.00 36.62 2.74
1582 1680 4.466370 TCTTCTGTAGGGACTGTGTTATGG 59.534 45.833 0.00 0.00 41.52 2.74
1585 1683 4.222145 TCTGTAGGGACTGTGTTATGGAAC 59.778 45.833 0.00 0.00 41.52 3.62
1680 1795 8.657074 TGTAACATTGTATGGTTGTATCTAGC 57.343 34.615 0.00 0.00 33.60 3.42
1836 1985 3.009805 GGTCCTACCTTTGGTGGTTACAT 59.990 47.826 0.00 0.00 41.22 2.29
1837 1986 4.007659 GTCCTACCTTTGGTGGTTACATG 58.992 47.826 0.00 0.00 41.22 3.21
1838 1987 3.653836 TCCTACCTTTGGTGGTTACATGT 59.346 43.478 2.69 2.69 41.22 3.21
1843 1994 4.141344 ACCTTTGGTGGTTACATGTAGTGT 60.141 41.667 5.56 0.00 38.63 3.55
1862 2013 7.824289 TGTAGTGTAGAAATGCTGCTTAAGATT 59.176 33.333 6.67 0.00 0.00 2.40
1883 2034 7.234355 AGATTTCTTCCTGTTAAACCATGTCT 58.766 34.615 0.00 0.00 0.00 3.41
1939 2091 2.306805 TCATGCTTTCCAGGTCAGTGAT 59.693 45.455 0.00 0.00 0.00 3.06
1948 2100 7.418025 GCTTTCCAGGTCAGTGATAACTACTAT 60.418 40.741 0.00 0.00 0.00 2.12
2152 2304 6.189859 AGGTTGAATATGATGAATGGTGTGT 58.810 36.000 0.00 0.00 0.00 3.72
2153 2305 6.095860 AGGTTGAATATGATGAATGGTGTGTG 59.904 38.462 0.00 0.00 0.00 3.82
2263 2415 8.947055 ATTATTGGCTTTCCACATTAATTGTC 57.053 30.769 0.00 0.00 43.33 3.18
2293 2446 0.250467 TGCTTGGAGTTGGAGTGCTC 60.250 55.000 0.00 0.00 0.00 4.26
2311 2464 2.742053 GCTCCTGATGCGTGTTTTTCTA 59.258 45.455 0.00 0.00 0.00 2.10
2327 5222 5.794687 TTTTCTATTACACATGTGCTCGG 57.205 39.130 25.68 12.05 0.00 4.63
2331 5226 2.078849 TTACACATGTGCTCGGTGAG 57.921 50.000 25.68 0.00 36.42 3.51
2358 5254 8.774586 GTGCTAACTTATATCAACTGGGTATTG 58.225 37.037 0.00 0.00 0.00 1.90
2371 5267 1.084289 GGTATTGTGCGTGGGAACTC 58.916 55.000 0.00 0.00 0.00 3.01
2398 5294 8.801715 AGTATGCAACTTGTATTTGTCTTTTG 57.198 30.769 0.00 0.00 33.35 2.44
2399 5295 7.867403 AGTATGCAACTTGTATTTGTCTTTTGG 59.133 33.333 0.00 0.00 33.35 3.28
2400 5296 5.971763 TGCAACTTGTATTTGTCTTTTGGT 58.028 33.333 0.00 0.00 0.00 3.67
2401 5297 6.402222 TGCAACTTGTATTTGTCTTTTGGTT 58.598 32.000 0.00 0.00 0.00 3.67
2402 5298 7.548097 TGCAACTTGTATTTGTCTTTTGGTTA 58.452 30.769 0.00 0.00 0.00 2.85
2403 5299 8.200792 TGCAACTTGTATTTGTCTTTTGGTTAT 58.799 29.630 0.00 0.00 0.00 1.89
2404 5300 8.699749 GCAACTTGTATTTGTCTTTTGGTTATC 58.300 33.333 0.00 0.00 0.00 1.75
2405 5301 9.743057 CAACTTGTATTTGTCTTTTGGTTATCA 57.257 29.630 0.00 0.00 0.00 2.15
2406 5302 9.965824 AACTTGTATTTGTCTTTTGGTTATCAG 57.034 29.630 0.00 0.00 0.00 2.90
2407 5303 9.349713 ACTTGTATTTGTCTTTTGGTTATCAGA 57.650 29.630 0.00 0.00 0.00 3.27
2410 5306 8.739039 TGTATTTGTCTTTTGGTTATCAGATGG 58.261 33.333 0.00 0.00 0.00 3.51
2411 5307 6.588719 TTTGTCTTTTGGTTATCAGATGGG 57.411 37.500 0.00 0.00 0.00 4.00
2412 5308 4.016444 TGTCTTTTGGTTATCAGATGGGC 58.984 43.478 0.00 0.00 0.00 5.36
2413 5309 4.016444 GTCTTTTGGTTATCAGATGGGCA 58.984 43.478 0.00 0.00 0.00 5.36
2429 5325 4.519540 TGGGCATTACTTTTTCTTCTGC 57.480 40.909 0.00 0.00 0.00 4.26
2437 5333 2.737252 ACTTTTTCTTCTGCCGATCGTC 59.263 45.455 15.09 0.47 0.00 4.20
2438 5334 2.743636 TTTTCTTCTGCCGATCGTCT 57.256 45.000 15.09 0.00 0.00 4.18
2450 5348 2.597305 CCGATCGTCTTACGGTTTCTTG 59.403 50.000 15.09 0.00 42.81 3.02
2451 5349 2.027688 CGATCGTCTTACGGTTTCTTGC 59.972 50.000 7.03 0.00 42.81 4.01
2456 5354 3.432252 CGTCTTACGGTTTCTTGCTTCAT 59.568 43.478 0.00 0.00 38.08 2.57
2475 5373 6.518200 GCTTCATCCTTTGAATTGGTTGGTTA 60.518 38.462 0.00 0.00 43.30 2.85
2507 5405 5.418840 ACGTGAGCATCCAAGGAAATTTAAT 59.581 36.000 0.00 0.00 0.00 1.40
2542 5441 5.616488 TTTAACAGTCAAAATCTACGCCC 57.384 39.130 0.00 0.00 0.00 6.13
2549 5448 4.163458 AGTCAAAATCTACGCCCTATGGAA 59.837 41.667 0.00 0.00 0.00 3.53
2550 5449 5.063880 GTCAAAATCTACGCCCTATGGAAT 58.936 41.667 0.00 0.00 0.00 3.01
2551 5450 5.179555 GTCAAAATCTACGCCCTATGGAATC 59.820 44.000 0.00 0.00 0.00 2.52
2552 5451 3.594603 AATCTACGCCCTATGGAATCG 57.405 47.619 0.00 0.00 0.00 3.34
2553 5452 0.601558 TCTACGCCCTATGGAATCGC 59.398 55.000 0.00 0.00 0.00 4.58
2555 5454 2.029073 CGCCCTATGGAATCGCGT 59.971 61.111 5.77 0.00 38.12 6.01
2556 5455 2.310233 CGCCCTATGGAATCGCGTG 61.310 63.158 5.77 0.00 38.12 5.34
2557 5456 2.607892 GCCCTATGGAATCGCGTGC 61.608 63.158 5.77 0.00 0.00 5.34
2558 5457 1.227527 CCCTATGGAATCGCGTGCA 60.228 57.895 5.77 0.00 0.00 4.57
2559 5458 1.498865 CCCTATGGAATCGCGTGCAC 61.499 60.000 6.82 6.82 0.00 4.57
2560 5459 0.809636 CCTATGGAATCGCGTGCACA 60.810 55.000 18.64 2.07 0.00 4.57
2561 5460 1.220529 CTATGGAATCGCGTGCACAT 58.779 50.000 18.64 9.94 0.00 3.21
2562 5461 0.936600 TATGGAATCGCGTGCACATG 59.063 50.000 18.64 8.39 0.00 3.21
2563 5462 0.744057 ATGGAATCGCGTGCACATGA 60.744 50.000 18.64 13.97 0.00 3.07
2564 5463 0.952984 TGGAATCGCGTGCACATGAA 60.953 50.000 18.64 0.00 0.00 2.57
2565 5464 0.167908 GGAATCGCGTGCACATGAAA 59.832 50.000 18.64 0.00 0.00 2.69
2566 5465 1.202177 GGAATCGCGTGCACATGAAAT 60.202 47.619 18.64 7.12 0.00 2.17
2567 5466 2.518949 GAATCGCGTGCACATGAAATT 58.481 42.857 18.64 8.47 0.00 1.82
2568 5467 1.898938 ATCGCGTGCACATGAAATTG 58.101 45.000 18.64 0.00 0.00 2.32
2569 5468 0.728803 TCGCGTGCACATGAAATTGC 60.729 50.000 18.64 8.32 39.33 3.56
2570 5469 1.697770 GCGTGCACATGAAATTGCG 59.302 52.632 18.64 0.00 41.96 4.85
2571 5470 0.728803 GCGTGCACATGAAATTGCGA 60.729 50.000 18.64 0.00 41.96 5.10
2572 5471 1.684142 CGTGCACATGAAATTGCGAA 58.316 45.000 18.64 0.00 41.96 4.70
2573 5472 2.049959 CGTGCACATGAAATTGCGAAA 58.950 42.857 18.64 0.00 41.96 3.46
2574 5473 2.662637 CGTGCACATGAAATTGCGAAAT 59.337 40.909 18.64 0.00 41.96 2.17
2575 5474 3.241426 CGTGCACATGAAATTGCGAAATC 60.241 43.478 18.64 0.00 41.96 2.17
2576 5475 2.916089 TGCACATGAAATTGCGAAATCG 59.084 40.909 0.00 0.00 41.96 3.34
2577 5476 3.170505 GCACATGAAATTGCGAAATCGA 58.829 40.909 7.06 0.00 43.02 3.59
2578 5477 3.792956 GCACATGAAATTGCGAAATCGAT 59.207 39.130 7.06 0.00 43.02 3.59
2579 5478 4.085924 GCACATGAAATTGCGAAATCGATC 60.086 41.667 7.06 0.00 43.02 3.69
2580 5479 5.268544 CACATGAAATTGCGAAATCGATCT 58.731 37.500 7.06 0.00 43.02 2.75
2581 5480 5.170803 CACATGAAATTGCGAAATCGATCTG 59.829 40.000 7.06 0.00 43.02 2.90
2582 5481 4.944962 TGAAATTGCGAAATCGATCTGT 57.055 36.364 7.06 0.00 43.02 3.41
2583 5482 4.650985 TGAAATTGCGAAATCGATCTGTG 58.349 39.130 7.06 0.00 43.02 3.66
2584 5483 2.744787 ATTGCGAAATCGATCTGTGC 57.255 45.000 7.06 1.50 43.02 4.57
2585 5484 1.437625 TTGCGAAATCGATCTGTGCA 58.562 45.000 7.06 4.38 43.02 4.57
2586 5485 1.001624 TGCGAAATCGATCTGTGCAG 58.998 50.000 7.06 0.00 43.02 4.41
2587 5486 0.315706 GCGAAATCGATCTGTGCAGC 60.316 55.000 7.06 0.00 43.02 5.25
2588 5487 0.302890 CGAAATCGATCTGTGCAGCC 59.697 55.000 0.00 0.00 43.02 4.85
2589 5488 0.302890 GAAATCGATCTGTGCAGCCG 59.697 55.000 0.00 7.23 0.00 5.52
2590 5489 0.108186 AAATCGATCTGTGCAGCCGA 60.108 50.000 14.77 14.77 37.52 5.54
2591 5490 0.108186 AATCGATCTGTGCAGCCGAA 60.108 50.000 15.79 5.28 37.03 4.30
2660 5559 0.609406 GGAGCCAAACCCACTCTTCC 60.609 60.000 0.00 0.00 0.00 3.46
2749 5648 5.105752 CACAATTTCACCGAAGAAACCAAA 58.894 37.500 4.70 0.00 40.03 3.28
2750 5649 5.578727 CACAATTTCACCGAAGAAACCAAAA 59.421 36.000 4.70 0.00 40.03 2.44
2756 5655 2.303175 CCGAAGAAACCAAAAGACCCA 58.697 47.619 0.00 0.00 0.00 4.51
2758 5657 2.293399 CGAAGAAACCAAAAGACCCAGG 59.707 50.000 0.00 0.00 0.00 4.45
2826 5725 4.717629 CGAAGCCGTCGTCCAGCA 62.718 66.667 0.00 0.00 45.09 4.41
2895 5794 2.558795 GCGGATATAGAGCCTGACAAGA 59.441 50.000 0.00 0.00 0.00 3.02
2911 5810 0.179073 AAGATCAAGGGCGACATCCG 60.179 55.000 0.00 0.00 42.21 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.149196 TCAGGTTTGGACAAGAATGCTC 58.851 45.455 0.00 0.00 0.00 4.26
17 18 5.846203 ACAATCAAATCAGGTTTGGACAAG 58.154 37.500 6.30 0.00 45.79 3.16
18 19 5.867903 ACAATCAAATCAGGTTTGGACAA 57.132 34.783 6.30 0.00 45.79 3.18
39 40 4.389077 CCGACTGTTCTTCTGACCAAATAC 59.611 45.833 0.00 0.00 0.00 1.89
50 51 0.511653 GCCGTTTCCGACTGTTCTTC 59.488 55.000 0.00 0.00 35.63 2.87
63 64 9.398538 TCTATTTATAAACATAACCAGCCGTTT 57.601 29.630 0.00 0.00 35.79 3.60
108 109 9.023962 AGTCTGTATTGGAAGAAAATAATGCAA 57.976 29.630 0.00 0.00 0.00 4.08
130 131 5.758784 GCACTAAGAAACAGTACCAAAGTCT 59.241 40.000 0.00 0.00 0.00 3.24
142 143 6.708949 AGAATCTAAAACGGCACTAAGAAACA 59.291 34.615 0.00 0.00 0.00 2.83
318 320 6.603997 TGATTCTATAAAAGCGGGCCTAAAAA 59.396 34.615 0.84 0.00 0.00 1.94
390 424 5.302823 GGCACCCAGCTGATTCTATATTTTT 59.697 40.000 17.39 0.00 44.79 1.94
410 446 1.003233 GAGGTGTTCTCCTGGGCAC 60.003 63.158 0.00 0.00 38.02 5.01
425 461 2.664081 GGACTGGAGTGGGCTGAGG 61.664 68.421 0.00 0.00 0.00 3.86
444 480 2.789715 GCTGCCTGCTTTATGGGCC 61.790 63.158 0.00 0.00 44.71 5.80
489 525 4.585955 TGGGAGCGAGCTTTTATAGTAG 57.414 45.455 0.00 0.00 0.00 2.57
555 591 2.509336 CCGCCGATCTGCTTCGTT 60.509 61.111 7.56 0.00 37.42 3.85
606 642 1.476477 GAGAGCGTAGAAAGGAGGGT 58.524 55.000 0.00 0.00 0.00 4.34
617 654 0.179702 TCTTAGGCGAGGAGAGCGTA 59.820 55.000 0.00 0.00 34.39 4.42
640 677 4.851639 ACAATTGGGAGCTGATAGAGTT 57.148 40.909 10.83 0.00 0.00 3.01
674 711 2.264480 CGAATGGGTCGGACTGCA 59.736 61.111 8.23 0.00 46.45 4.41
702 740 4.436332 CCGTTAACCTAAAATCGGTAGCT 58.564 43.478 0.00 0.00 33.53 3.32
707 745 3.598299 TCACCCGTTAACCTAAAATCGG 58.402 45.455 0.00 0.00 38.05 4.18
711 749 6.536447 AGAGATTTCACCCGTTAACCTAAAA 58.464 36.000 0.00 0.00 0.00 1.52
826 872 5.465051 CAGACGGAACATATACTGATCTGG 58.535 45.833 4.49 0.00 37.35 3.86
844 890 3.579709 ACAAGATACAACTGAGCAGACG 58.420 45.455 4.21 0.00 0.00 4.18
855 901 6.525578 AGAGTACAATCGGACAAGATACAA 57.474 37.500 0.00 0.00 0.00 2.41
863 909 6.062749 AGCTAATCTAGAGTACAATCGGACA 58.937 40.000 0.00 0.00 0.00 4.02
871 917 6.127101 TGCACCTAAGCTAATCTAGAGTACA 58.873 40.000 0.00 0.00 34.99 2.90
887 933 4.283467 AGACGCCATATATCTTGCACCTAA 59.717 41.667 0.00 0.00 0.00 2.69
899 946 1.414919 GGTCCCAACAGACGCCATATA 59.585 52.381 0.00 0.00 37.66 0.86
902 949 2.351276 GGTCCCAACAGACGCCAT 59.649 61.111 0.00 0.00 37.66 4.40
917 964 3.825014 AGTACTATCGCCATATCAACGGT 59.175 43.478 0.00 0.00 0.00 4.83
918 965 4.156190 AGAGTACTATCGCCATATCAACGG 59.844 45.833 0.00 0.00 0.00 4.44
989 1036 2.014128 CCGTCGCCATTTTATGAACCT 58.986 47.619 0.00 0.00 0.00 3.50
990 1037 1.741145 ACCGTCGCCATTTTATGAACC 59.259 47.619 0.00 0.00 0.00 3.62
992 1039 3.425094 CGAAACCGTCGCCATTTTATGAA 60.425 43.478 0.00 0.00 44.14 2.57
994 1041 2.436670 CGAAACCGTCGCCATTTTATG 58.563 47.619 0.00 0.00 44.14 1.90
1330 1397 1.594293 AGTCTTGTGGGTGAACGCG 60.594 57.895 3.53 3.53 0.00 6.01
1513 1611 7.395190 TTCAGCAATCAAGCATAACAGTTAT 57.605 32.000 0.00 0.00 36.85 1.89
1522 1620 6.028146 TGTACAAATTCAGCAATCAAGCAT 57.972 33.333 0.00 0.00 36.85 3.79
1530 1628 6.237901 AGATGGTACTGTACAAATTCAGCAA 58.762 36.000 18.79 0.00 35.37 3.91
1548 1646 5.836358 GTCCCTACAGAAGATTAGAGATGGT 59.164 44.000 0.00 0.00 0.00 3.55
1582 1680 4.708726 AAAGCATTACATCTGCAGGTTC 57.291 40.909 15.13 0.00 42.15 3.62
1585 1683 6.798482 TGATTAAAAGCATTACATCTGCAGG 58.202 36.000 15.13 0.36 42.15 4.85
1661 1776 7.442364 GTCACATGCTAGATACAACCATACAAT 59.558 37.037 0.00 0.00 0.00 2.71
1662 1777 6.761242 GTCACATGCTAGATACAACCATACAA 59.239 38.462 0.00 0.00 0.00 2.41
1701 1816 4.574674 TCCACATTAAGGCTCAACTCAT 57.425 40.909 0.00 0.00 0.00 2.90
1836 1985 6.697395 TCTTAAGCAGCATTTCTACACTACA 58.303 36.000 0.00 0.00 0.00 2.74
1837 1986 7.778470 ATCTTAAGCAGCATTTCTACACTAC 57.222 36.000 0.00 0.00 0.00 2.73
1838 1987 8.792830 AAATCTTAAGCAGCATTTCTACACTA 57.207 30.769 0.00 0.00 0.00 2.74
1843 1994 7.831193 AGGAAGAAATCTTAAGCAGCATTTCTA 59.169 33.333 21.23 0.00 42.26 2.10
1862 2013 5.073144 AGGAGACATGGTTTAACAGGAAGAA 59.927 40.000 0.00 0.00 0.00 2.52
1920 2072 4.018960 AGTTATCACTGACCTGGAAAGCAT 60.019 41.667 0.00 0.00 0.00 3.79
1939 2091 5.832060 GGTCAAGTCAGGCCTATAGTAGTTA 59.168 44.000 3.98 0.00 0.00 2.24
1948 2100 0.324943 GCTTGGTCAAGTCAGGCCTA 59.675 55.000 3.98 0.00 40.45 3.93
2120 2272 9.293404 CATTCATCATATTCAACCTCCATACTT 57.707 33.333 0.00 0.00 0.00 2.24
2152 2304 0.250858 ACTTGTGCCAGTATGCAGCA 60.251 50.000 0.00 0.00 43.02 4.41
2153 2305 0.883833 AACTTGTGCCAGTATGCAGC 59.116 50.000 0.00 0.00 43.02 5.25
2263 2415 1.952296 ACTCCAAGCAACTCAGCAAAG 59.048 47.619 0.00 0.00 36.85 2.77
2293 2446 6.021596 GTGTAATAGAAAAACACGCATCAGG 58.978 40.000 0.00 0.00 34.72 3.86
2311 2464 2.621338 CTCACCGAGCACATGTGTAAT 58.379 47.619 26.01 13.20 0.00 1.89
2327 5222 6.480320 CCAGTTGATATAAGTTAGCACCTCAC 59.520 42.308 0.00 0.00 0.00 3.51
2331 5226 5.681639 ACCCAGTTGATATAAGTTAGCACC 58.318 41.667 0.00 0.00 0.00 5.01
2358 5254 1.732259 CATACTTGAGTTCCCACGCAC 59.268 52.381 0.00 0.00 31.62 5.34
2386 5282 7.147915 GCCCATCTGATAACCAAAAGACAAATA 60.148 37.037 0.00 0.00 0.00 1.40
2393 5289 5.603170 AATGCCCATCTGATAACCAAAAG 57.397 39.130 0.00 0.00 0.00 2.27
2396 5292 5.387113 AGTAATGCCCATCTGATAACCAA 57.613 39.130 0.00 0.00 0.00 3.67
2397 5293 5.387113 AAGTAATGCCCATCTGATAACCA 57.613 39.130 0.00 0.00 0.00 3.67
2398 5294 6.715347 AAAAGTAATGCCCATCTGATAACC 57.285 37.500 0.00 0.00 0.00 2.85
2399 5295 8.000780 AGAAAAAGTAATGCCCATCTGATAAC 57.999 34.615 0.00 0.00 0.00 1.89
2400 5296 8.593945 AAGAAAAAGTAATGCCCATCTGATAA 57.406 30.769 0.00 0.00 0.00 1.75
2401 5297 8.055181 AGAAGAAAAAGTAATGCCCATCTGATA 58.945 33.333 0.00 0.00 0.00 2.15
2402 5298 6.894103 AGAAGAAAAAGTAATGCCCATCTGAT 59.106 34.615 0.00 0.00 0.00 2.90
2403 5299 6.151648 CAGAAGAAAAAGTAATGCCCATCTGA 59.848 38.462 0.00 0.00 33.11 3.27
2404 5300 6.327934 CAGAAGAAAAAGTAATGCCCATCTG 58.672 40.000 0.00 0.00 0.00 2.90
2405 5301 5.105595 GCAGAAGAAAAAGTAATGCCCATCT 60.106 40.000 0.00 0.00 0.00 2.90
2406 5302 5.105063 GCAGAAGAAAAAGTAATGCCCATC 58.895 41.667 0.00 0.00 0.00 3.51
2407 5303 4.081476 GGCAGAAGAAAAAGTAATGCCCAT 60.081 41.667 1.87 0.00 44.67 4.00
2408 5304 3.258123 GGCAGAAGAAAAAGTAATGCCCA 59.742 43.478 1.87 0.00 44.67 5.36
2409 5305 3.849911 GGCAGAAGAAAAAGTAATGCCC 58.150 45.455 1.87 0.00 44.67 5.36
2410 5306 3.190535 TCGGCAGAAGAAAAAGTAATGCC 59.809 43.478 3.24 3.24 46.44 4.40
2411 5307 4.419522 TCGGCAGAAGAAAAAGTAATGC 57.580 40.909 0.00 0.00 0.00 3.56
2412 5308 5.163854 ACGATCGGCAGAAGAAAAAGTAATG 60.164 40.000 20.98 0.00 0.00 1.90
2413 5309 4.935808 ACGATCGGCAGAAGAAAAAGTAAT 59.064 37.500 20.98 0.00 0.00 1.89
2429 5325 2.556534 AGAAACCGTAAGACGATCGG 57.443 50.000 20.98 2.21 46.05 4.18
2437 5333 4.003648 AGGATGAAGCAAGAAACCGTAAG 58.996 43.478 0.00 0.00 0.00 2.34
2438 5334 4.015872 AGGATGAAGCAAGAAACCGTAA 57.984 40.909 0.00 0.00 0.00 3.18
2456 5354 6.800072 ACTTTAACCAACCAATTCAAAGGA 57.200 33.333 0.00 0.00 0.00 3.36
2475 5373 4.876107 CCTTGGATGCTCACGTAATACTTT 59.124 41.667 0.00 0.00 0.00 2.66
2483 5381 2.496899 ATTTCCTTGGATGCTCACGT 57.503 45.000 0.00 0.00 0.00 4.49
2507 5405 2.952978 ACTGTTAAATTGTTCCGTGGCA 59.047 40.909 0.00 0.00 0.00 4.92
2542 5441 1.070376 CATGTGCACGCGATTCCATAG 60.070 52.381 15.93 1.61 0.00 2.23
2549 5448 1.898938 CAATTTCATGTGCACGCGAT 58.101 45.000 15.93 0.00 0.00 4.58
2550 5449 0.728803 GCAATTTCATGTGCACGCGA 60.729 50.000 15.93 8.20 40.58 5.87
2551 5450 1.697770 GCAATTTCATGTGCACGCG 59.302 52.632 13.13 3.53 40.58 6.01
2552 5451 0.728803 TCGCAATTTCATGTGCACGC 60.729 50.000 13.13 5.68 40.94 5.34
2553 5452 1.684142 TTCGCAATTTCATGTGCACG 58.316 45.000 13.13 0.00 40.94 5.34
2554 5453 3.241426 CGATTTCGCAATTTCATGTGCAC 60.241 43.478 10.75 10.75 40.94 4.57
2555 5454 2.916089 CGATTTCGCAATTTCATGTGCA 59.084 40.909 6.80 0.00 40.94 4.57
2556 5455 3.170505 TCGATTTCGCAATTTCATGTGC 58.829 40.909 0.00 0.00 39.60 4.57
2557 5456 5.170803 CAGATCGATTTCGCAATTTCATGTG 59.829 40.000 0.00 0.00 39.60 3.21
2558 5457 5.163723 ACAGATCGATTTCGCAATTTCATGT 60.164 36.000 0.00 0.00 39.60 3.21
2559 5458 5.170803 CACAGATCGATTTCGCAATTTCATG 59.829 40.000 0.00 0.00 39.60 3.07
2560 5459 5.268544 CACAGATCGATTTCGCAATTTCAT 58.731 37.500 0.00 0.00 39.60 2.57
2561 5460 4.650985 CACAGATCGATTTCGCAATTTCA 58.349 39.130 0.00 0.00 39.60 2.69
2562 5461 3.479949 GCACAGATCGATTTCGCAATTTC 59.520 43.478 0.00 0.00 39.60 2.17
2563 5462 3.119884 TGCACAGATCGATTTCGCAATTT 60.120 39.130 0.00 0.00 39.60 1.82
2564 5463 2.419673 TGCACAGATCGATTTCGCAATT 59.580 40.909 0.00 0.00 39.60 2.32
2565 5464 2.009051 TGCACAGATCGATTTCGCAAT 58.991 42.857 0.00 0.00 39.60 3.56
2566 5465 1.394572 CTGCACAGATCGATTTCGCAA 59.605 47.619 0.00 0.00 39.60 4.85
2567 5466 1.001624 CTGCACAGATCGATTTCGCA 58.998 50.000 0.00 4.41 39.60 5.10
2568 5467 0.315706 GCTGCACAGATCGATTTCGC 60.316 55.000 0.00 0.00 39.60 4.70
2569 5468 0.302890 GGCTGCACAGATCGATTTCG 59.697 55.000 0.00 0.00 41.45 3.46
2570 5469 0.302890 CGGCTGCACAGATCGATTTC 59.697 55.000 0.00 0.00 0.00 2.17
2571 5470 0.108186 TCGGCTGCACAGATCGATTT 60.108 50.000 0.00 0.00 33.33 2.17
2572 5471 0.108186 TTCGGCTGCACAGATCGATT 60.108 50.000 14.14 0.00 36.28 3.34
2573 5472 0.108186 TTTCGGCTGCACAGATCGAT 60.108 50.000 14.14 0.00 36.28 3.59
2574 5473 0.320334 TTTTCGGCTGCACAGATCGA 60.320 50.000 0.50 7.09 35.23 3.59
2575 5474 0.095935 CTTTTCGGCTGCACAGATCG 59.904 55.000 0.50 4.80 0.00 3.69
2576 5475 1.129437 GACTTTTCGGCTGCACAGATC 59.871 52.381 0.50 0.00 0.00 2.75
2577 5476 1.160137 GACTTTTCGGCTGCACAGAT 58.840 50.000 0.50 0.00 0.00 2.90
2578 5477 1.221466 CGACTTTTCGGCTGCACAGA 61.221 55.000 0.50 0.00 41.89 3.41
2579 5478 1.205064 CGACTTTTCGGCTGCACAG 59.795 57.895 0.50 0.00 41.89 3.66
2580 5479 0.602638 ATCGACTTTTCGGCTGCACA 60.603 50.000 0.50 0.00 45.90 4.57
2581 5480 0.517316 AATCGACTTTTCGGCTGCAC 59.483 50.000 0.50 0.00 45.90 4.57
2582 5481 0.796312 GAATCGACTTTTCGGCTGCA 59.204 50.000 0.50 0.00 45.90 4.41
2583 5482 0.097150 GGAATCGACTTTTCGGCTGC 59.903 55.000 0.00 0.00 45.90 5.25
2584 5483 1.726853 AGGAATCGACTTTTCGGCTG 58.273 50.000 0.00 0.00 45.90 4.85
2585 5484 2.076863 CAAGGAATCGACTTTTCGGCT 58.923 47.619 0.00 0.00 45.90 5.52
2586 5485 1.130561 CCAAGGAATCGACTTTTCGGC 59.869 52.381 0.00 0.00 45.90 5.54
2587 5486 2.415512 GTCCAAGGAATCGACTTTTCGG 59.584 50.000 0.00 0.00 45.90 4.30
2589 5488 2.159693 GCGTCCAAGGAATCGACTTTTC 60.160 50.000 3.61 0.00 0.00 2.29
2590 5489 1.804748 GCGTCCAAGGAATCGACTTTT 59.195 47.619 3.61 0.00 0.00 2.27
2591 5490 1.439679 GCGTCCAAGGAATCGACTTT 58.560 50.000 3.61 0.00 0.00 2.66
2749 5648 2.535317 ACATGCCCCCTGGGTCTT 60.535 61.111 12.71 0.00 46.51 3.01
2750 5649 3.017581 GACATGCCCCCTGGGTCT 61.018 66.667 12.71 0.00 46.51 3.85
2756 5655 3.402681 CCGACTGACATGCCCCCT 61.403 66.667 0.00 0.00 0.00 4.79
2879 5778 4.590647 CCCTTGATCTTGTCAGGCTCTATA 59.409 45.833 0.00 0.00 38.29 1.31
2895 5794 2.505982 CCGGATGTCGCCCTTGAT 59.494 61.111 0.00 0.00 37.59 2.57
3020 5919 0.250295 CTGTCCAGTCCAAGCCGAAA 60.250 55.000 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.