Multiple sequence alignment - TraesCS6B01G097600

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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 TraesCS6B01G097600 chr6B 100.000 3143 0 0 1 3143 75036939 75040081 0.000000e+00 5805.0
1 TraesCS6B01G097600 chr6D 91.928 2428 162 18 329 2744 35632898 35635303 0.000000e+00 3367.0
2 TraesCS6B01G097600 chr6D 91.086 359 23 7 2788 3143 35635299 35635651 7.890000e-131 477.0
3 TraesCS6B01G097600 chr6D 92.722 316 21 2 1 316 35632399 35632712 3.700000e-124 455.0
4 TraesCS6B01G097600 chr6A 94.958 1309 55 4 871 2170 39507719 39509025 0.000000e+00 2041.0
5 TraesCS6B01G097600 chr6A 80.150 801 98 30 1 789 39506927 39507678 2.760000e-150 542.0
6 TraesCS6B01G097600 chr6A 92.058 277 18 3 2766 3040 39510278 39510552 1.370000e-103 387.0
7 TraesCS6B01G097600 chr6A 88.129 278 24 6 2205 2476 39509027 39509301 3.910000e-84 322.0
8 TraesCS6B01G097600 chr6A 77.970 463 48 22 2497 2944 39509518 39509941 1.130000e-59 241.0
9 TraesCS6B01G097600 chr6A 84.286 210 20 8 2497 2706 39510055 39510251 3.200000e-45 193.0
10 TraesCS6B01G097600 chr6A 95.455 44 2 0 2371 2414 39509962 39510005 1.560000e-08 71.3
11 TraesCS6B01G097600 chr1B 76.179 403 47 31 2626 3015 57648537 57648171 1.940000e-37 167.0
12 TraesCS6B01G097600 chr1B 75.426 411 56 26 2626 3024 57688072 57687695 1.170000e-34 158.0
13 TraesCS6B01G097600 chr1B 78.689 183 32 7 2837 3015 57631711 57631532 7.120000e-22 115.0


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 TraesCS6B01G097600 chr6B 75036939 75040081 3142 False 5805.000000 5805 100.000000 1 3143 1 chr6B.!!$F1 3142
1 TraesCS6B01G097600 chr6D 35632399 35635651 3252 False 1433.000000 3367 91.912000 1 3143 3 chr6D.!!$F1 3142
2 TraesCS6B01G097600 chr6A 39506927 39510552 3625 False 542.471429 2041 87.572286 1 3040 7 chr6A.!!$F1 3039

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
349 523 0.098200 CATGAGCATTGTGACTGGCG 59.902 55.0 0.00 0.0 0.00 5.69 F
809 1005 0.178932 GGGCCAGGGTTTCCTTCTTT 60.179 55.0 4.39 0.0 42.67 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 1987 0.460284 ACATCCCGTTCATGAGCGAC 60.460 55.0 30.29 9.64 37.19 5.19 R
2726 3712 0.034477 CCGTTAACAGGGGAAGGCAT 60.034 55.0 6.39 0.00 0.00 4.40 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
32 33 5.484173 AACACTCACACATGTAACACAAG 57.516 39.130 0.00 0.00 0.00 3.16
39 40 6.218019 TCACACATGTAACACAAGGTAGTAC 58.782 40.000 0.00 0.00 0.00 2.73
75 76 9.793259 ATGTTTCTATCAGTTTCAAAAGTAGGA 57.207 29.630 0.00 0.00 0.00 2.94
81 82 9.284968 CTATCAGTTTCAAAAGTAGGAAAAGGA 57.715 33.333 0.00 0.00 35.03 3.36
154 155 6.292150 TGTACAACATATGCCCGATTTCATA 58.708 36.000 1.58 0.00 0.00 2.15
157 158 6.503524 ACAACATATGCCCGATTTCATAAAC 58.496 36.000 1.58 0.00 0.00 2.01
184 185 3.147595 CGTGGAGGGCGAGGATGA 61.148 66.667 0.00 0.00 0.00 2.92
268 269 8.463055 TTTCCTAGGGCATTAGATAATACCAT 57.537 34.615 9.46 0.31 31.92 3.55
325 326 5.181690 TGGAAACAATGACAAGTTACAGC 57.818 39.130 0.00 0.00 37.44 4.40
326 327 4.219033 GGAAACAATGACAAGTTACAGCG 58.781 43.478 0.00 0.00 0.00 5.18
327 328 4.024387 GGAAACAATGACAAGTTACAGCGA 60.024 41.667 0.00 0.00 0.00 4.93
342 516 0.800631 AGCGACACATGAGCATTGTG 59.199 50.000 0.00 10.90 39.26 3.33
345 519 2.071540 CGACACATGAGCATTGTGACT 58.928 47.619 17.26 0.07 37.31 3.41
349 523 0.098200 CATGAGCATTGTGACTGGCG 59.902 55.000 0.00 0.00 0.00 5.69
362 536 4.461431 TGTGACTGGCGTCTCTTAAATCTA 59.539 41.667 10.03 0.00 40.86 1.98
370 544 7.103641 TGGCGTCTCTTAAATCTAGTTCATTT 58.896 34.615 0.00 0.00 0.00 2.32
371 545 7.606456 TGGCGTCTCTTAAATCTAGTTCATTTT 59.394 33.333 0.00 0.00 0.00 1.82
372 546 8.451748 GGCGTCTCTTAAATCTAGTTCATTTTT 58.548 33.333 0.00 0.00 0.00 1.94
446 636 2.599082 CGAAATGTAGGCAAGAGTCGAC 59.401 50.000 7.70 7.70 0.00 4.20
458 648 2.474816 AGAGTCGACTGCAAACTTGTC 58.525 47.619 25.58 4.27 0.00 3.18
459 649 1.527311 GAGTCGACTGCAAACTTGTCC 59.473 52.381 25.58 0.00 0.00 4.02
463 653 1.388547 GACTGCAAACTTGTCCACCA 58.611 50.000 0.00 0.00 0.00 4.17
464 654 1.065551 GACTGCAAACTTGTCCACCAC 59.934 52.381 0.00 0.00 0.00 4.16
465 655 0.385390 CTGCAAACTTGTCCACCACC 59.615 55.000 0.00 0.00 0.00 4.61
467 657 0.755327 GCAAACTTGTCCACCACCCT 60.755 55.000 0.00 0.00 0.00 4.34
468 658 1.775385 CAAACTTGTCCACCACCCTT 58.225 50.000 0.00 0.00 0.00 3.95
469 659 1.681264 CAAACTTGTCCACCACCCTTC 59.319 52.381 0.00 0.00 0.00 3.46
470 660 0.923358 AACTTGTCCACCACCCTTCA 59.077 50.000 0.00 0.00 0.00 3.02
510 700 7.255836 CCATTGCAATCATGATTTCTAGTGGAT 60.256 37.037 18.41 2.44 0.00 3.41
511 701 6.628919 TGCAATCATGATTTCTAGTGGATG 57.371 37.500 18.41 5.35 0.00 3.51
515 705 7.039923 GCAATCATGATTTCTAGTGGATGGAAT 60.040 37.037 18.41 0.00 0.00 3.01
521 713 8.681486 TGATTTCTAGTGGATGGAATAATGTG 57.319 34.615 0.00 0.00 0.00 3.21
523 715 9.125026 GATTTCTAGTGGATGGAATAATGTGTT 57.875 33.333 0.00 0.00 0.00 3.32
526 718 7.054124 TCTAGTGGATGGAATAATGTGTTTCC 58.946 38.462 0.00 0.00 41.51 3.13
533 725 7.287696 GGATGGAATAATGTGTTTCCCTACATT 59.712 37.037 7.61 7.61 46.14 2.71
542 734 8.588290 ATGTGTTTCCCTACATTATAGCAAAA 57.412 30.769 0.00 0.00 34.00 2.44
555 747 6.519353 TTATAGCAAAACCATCATACGTCG 57.481 37.500 0.00 0.00 0.00 5.12
596 788 4.506758 ACATTGCCATCAATACCAAAAGC 58.493 39.130 0.00 0.00 40.74 3.51
612 804 5.244626 ACCAAAAGCATAGCAACAAAGAGAT 59.755 36.000 0.00 0.00 0.00 2.75
647 843 0.886490 CGATGCCCATTCCTAGGTGC 60.886 60.000 9.08 5.92 0.00 5.01
657 853 1.831286 CCTAGGTGCCGGACGGTAT 60.831 63.158 5.05 0.00 37.65 2.73
663 859 1.522806 TGCCGGACGGTATTGCATC 60.523 57.895 5.05 0.00 37.65 3.91
664 860 2.594962 GCCGGACGGTATTGCATCG 61.595 63.158 5.05 0.00 37.65 3.84
666 862 0.808453 CCGGACGGTATTGCATCGTT 60.808 55.000 0.00 0.00 37.25 3.85
667 863 0.300491 CGGACGGTATTGCATCGTTG 59.700 55.000 6.41 0.00 37.25 4.10
668 864 1.365699 GGACGGTATTGCATCGTTGT 58.634 50.000 6.41 0.00 37.25 3.32
669 865 2.542597 GGACGGTATTGCATCGTTGTA 58.457 47.619 6.41 0.00 37.25 2.41
670 866 2.538449 GGACGGTATTGCATCGTTGTAG 59.462 50.000 6.41 0.00 37.25 2.74
671 867 3.184541 GACGGTATTGCATCGTTGTAGT 58.815 45.455 6.41 0.00 37.25 2.73
716 912 2.757077 CGAAAAGGTGGAGGGGCT 59.243 61.111 0.00 0.00 0.00 5.19
805 1001 4.678743 GCGGGCCAGGGTTTCCTT 62.679 66.667 4.39 0.00 42.67 3.36
807 1003 2.907179 CGGGCCAGGGTTTCCTTCT 61.907 63.158 4.39 0.00 42.67 2.85
808 1004 1.465172 GGGCCAGGGTTTCCTTCTT 59.535 57.895 4.39 0.00 42.67 2.52
809 1005 0.178932 GGGCCAGGGTTTCCTTCTTT 60.179 55.000 4.39 0.00 42.67 2.52
812 1008 1.341209 GCCAGGGTTTCCTTCTTTGTG 59.659 52.381 0.00 0.00 42.67 3.33
814 1010 1.963515 CAGGGTTTCCTTCTTTGTGGG 59.036 52.381 0.00 0.00 42.67 4.61
841 1037 0.537371 AGAGAAAACCCAGCCCAACG 60.537 55.000 0.00 0.00 0.00 4.10
844 1040 1.802337 GAAAACCCAGCCCAACGACC 61.802 60.000 0.00 0.00 0.00 4.79
885 1081 0.249868 CGCTCGAAGCCCATGGAATA 60.250 55.000 15.22 0.00 38.18 1.75
891 1087 4.136796 TCGAAGCCCATGGAATATTCTTG 58.863 43.478 15.22 12.25 0.00 3.02
956 1152 2.663196 CCCACAGGTCGTCTTCCC 59.337 66.667 0.00 0.00 0.00 3.97
957 1153 2.214216 CCCACAGGTCGTCTTCCCA 61.214 63.158 0.00 0.00 0.00 4.37
958 1154 1.553690 CCCACAGGTCGTCTTCCCAT 61.554 60.000 0.00 0.00 0.00 4.00
1013 1215 2.204291 AAGGATGGGGAGGGTGCA 60.204 61.111 0.00 0.00 0.00 4.57
1650 1855 2.707849 CCGGATGAAGGACGACGGT 61.708 63.158 0.00 0.00 36.78 4.83
1782 1987 0.522705 CGGACGTCATCACCTACACG 60.523 60.000 18.91 3.45 38.24 4.49
1849 2054 0.731417 CAAGCTGCTCGAGGAAATGG 59.269 55.000 15.58 0.00 0.00 3.16
1876 2081 2.359850 GGTGCGAGCCCAATGACA 60.360 61.111 0.00 0.00 0.00 3.58
1933 2138 2.747855 GGAAGCTGGACAAGGCCG 60.748 66.667 0.00 0.00 0.00 6.13
1953 2158 2.607187 GTCGAGGTGTACAAGTCCATG 58.393 52.381 0.00 0.00 0.00 3.66
2074 2279 1.819229 GGGATCGAGAGCAAGAGCA 59.181 57.895 0.00 0.00 45.49 4.26
2151 2356 4.889780 AGATGAAGGAGTAGGATGAAGGT 58.110 43.478 0.00 0.00 0.00 3.50
2161 2366 0.537188 GGATGAAGGTGCGAGGAAGA 59.463 55.000 0.00 0.00 0.00 2.87
2174 2379 4.141711 TGCGAGGAAGACTAATAAGCCATT 60.142 41.667 0.00 0.00 0.00 3.16
2176 2381 4.752101 CGAGGAAGACTAATAAGCCATTGG 59.248 45.833 0.00 0.00 0.00 3.16
2187 2392 1.969862 GCCATTGGCTTCTGTTGCT 59.030 52.632 20.66 0.00 46.69 3.91
2188 2393 0.389426 GCCATTGGCTTCTGTTGCTG 60.389 55.000 20.66 0.00 46.69 4.41
2189 2394 0.389426 CCATTGGCTTCTGTTGCTGC 60.389 55.000 0.00 0.00 0.00 5.25
2190 2395 0.601558 CATTGGCTTCTGTTGCTGCT 59.398 50.000 0.00 0.00 0.00 4.24
2246 2451 1.539388 TGCCTGGCTTGTTTTGATACG 59.461 47.619 21.03 0.00 0.00 3.06
2301 2506 7.476540 ACTGTGTTTGTATGGAGTGATACTA 57.523 36.000 0.00 0.00 31.15 1.82
2369 2574 9.899226 CGTGAATATGTCAAGATATCTTACTCA 57.101 33.333 17.53 15.61 37.90 3.41
2379 3353 9.942850 TCAAGATATCTTACTCATGTGTCAAAA 57.057 29.630 17.53 0.00 34.28 2.44
2418 3392 4.503741 GTGCCATTCACAACATACACTT 57.496 40.909 0.00 0.00 44.98 3.16
2420 3394 3.888323 TGCCATTCACAACATACACTTGT 59.112 39.130 0.00 0.00 31.80 3.16
2421 3395 4.340666 TGCCATTCACAACATACACTTGTT 59.659 37.500 0.00 0.00 40.39 2.83
2424 3398 6.747280 GCCATTCACAACATACACTTGTTATC 59.253 38.462 0.00 0.00 37.73 1.75
2425 3399 7.362056 GCCATTCACAACATACACTTGTTATCT 60.362 37.037 0.00 0.00 37.73 1.98
2426 3400 7.964559 CCATTCACAACATACACTTGTTATCTG 59.035 37.037 0.00 0.00 37.73 2.90
2466 3449 5.955959 TGAATTAGCTTGTACTCCCTCTGTA 59.044 40.000 0.00 0.00 0.00 2.74
2475 3460 7.934120 GCTTGTACTCCCTCTGTATCAAAATAT 59.066 37.037 0.00 0.00 0.00 1.28
2544 3529 3.527507 TGGTAGCCTATAGAGACAGGG 57.472 52.381 0.00 0.00 32.15 4.45
2595 3580 4.687483 GCAAACTGATTTTGAATGGTCCAG 59.313 41.667 0.00 0.00 46.76 3.86
2624 3610 2.765135 TCCAATGCCCAATGGTGTATTG 59.235 45.455 17.69 17.69 44.67 1.90
2674 3660 1.666888 GCACCTTCAGCAAATGTTCCG 60.667 52.381 0.00 0.00 0.00 4.30
2716 3702 7.450014 AGAGTCAGTGTAGGATTGATCGATATT 59.550 37.037 0.00 0.00 0.00 1.28
2726 3712 5.997746 GGATTGATCGATATTCAGGGTTTCA 59.002 40.000 0.00 0.00 0.00 2.69
2744 3755 1.094785 CATGCCTTCCCCTGTTAACG 58.905 55.000 0.26 0.00 0.00 3.18
2745 3756 0.034477 ATGCCTTCCCCTGTTAACGG 60.034 55.000 7.51 7.51 0.00 4.44
2747 3758 0.614812 GCCTTCCCCTGTTAACGGTA 59.385 55.000 13.35 0.00 0.00 4.02
2748 3759 1.211212 GCCTTCCCCTGTTAACGGTAT 59.789 52.381 13.35 0.00 0.00 2.73
2749 3760 2.435437 GCCTTCCCCTGTTAACGGTATA 59.565 50.000 13.35 0.00 0.00 1.47
2750 3761 3.118298 GCCTTCCCCTGTTAACGGTATAA 60.118 47.826 13.35 3.60 0.00 0.98
2751 3762 4.445305 GCCTTCCCCTGTTAACGGTATAAT 60.445 45.833 13.35 0.00 0.00 1.28
2752 3763 5.221702 GCCTTCCCCTGTTAACGGTATAATA 60.222 44.000 13.35 0.00 0.00 0.98
2753 3764 6.521255 GCCTTCCCCTGTTAACGGTATAATAT 60.521 42.308 13.35 0.00 0.00 1.28
2754 3765 7.310609 GCCTTCCCCTGTTAACGGTATAATATA 60.311 40.741 13.35 0.00 0.00 0.86
2755 3766 8.765517 CCTTCCCCTGTTAACGGTATAATATAT 58.234 37.037 13.35 0.00 0.00 0.86
2778 3789 3.569194 ATGTGTGTGTGGTTACTTCCA 57.431 42.857 0.00 0.00 34.85 3.53
2785 3796 3.993382 TGGTTACTTCCACCACGAC 57.007 52.632 0.00 0.00 39.53 4.34
2786 3797 1.416243 TGGTTACTTCCACCACGACT 58.584 50.000 0.00 0.00 39.53 4.18
2787 3798 1.764134 TGGTTACTTCCACCACGACTT 59.236 47.619 0.00 0.00 39.53 3.01
2788 3799 2.171027 TGGTTACTTCCACCACGACTTT 59.829 45.455 0.00 0.00 39.53 2.66
2789 3800 3.387374 TGGTTACTTCCACCACGACTTTA 59.613 43.478 0.00 0.00 39.53 1.85
2790 3801 4.141756 TGGTTACTTCCACCACGACTTTAA 60.142 41.667 0.00 0.00 39.53 1.52
2791 3802 4.212004 GGTTACTTCCACCACGACTTTAAC 59.788 45.833 0.00 0.00 34.04 2.01
2792 3803 3.832615 ACTTCCACCACGACTTTAACT 57.167 42.857 0.00 0.00 0.00 2.24
2793 3804 4.942761 ACTTCCACCACGACTTTAACTA 57.057 40.909 0.00 0.00 0.00 2.24
2894 3905 3.780294 ACCTGAAATGGTACCAGCATCTA 59.220 43.478 21.41 8.10 38.79 1.98
2896 3907 5.103940 ACCTGAAATGGTACCAGCATCTATT 60.104 40.000 21.41 4.71 38.79 1.73
3015 4028 1.507096 GCGTTAGTCGTTTGCAGCG 60.507 57.895 6.44 6.44 42.13 5.18
3016 4029 1.850640 CGTTAGTCGTTTGCAGCGT 59.149 52.632 11.51 0.00 34.52 5.07
3086 4099 5.770663 TGCCTCCTGAAGATCATACTACTAC 59.229 44.000 0.00 0.00 0.00 2.73
3088 4101 6.435904 GCCTCCTGAAGATCATACTACTACAT 59.564 42.308 0.00 0.00 0.00 2.29
3100 4113 6.918022 TCATACTACTACATGAACATTGCGAG 59.082 38.462 0.00 0.00 0.00 5.03
3101 4114 3.865745 ACTACTACATGAACATTGCGAGC 59.134 43.478 0.00 0.00 0.00 5.03
3102 4115 2.698803 ACTACATGAACATTGCGAGCA 58.301 42.857 0.00 0.00 0.00 4.26
3111 4124 3.801114 ACATTGCGAGCACACTATCTA 57.199 42.857 0.00 0.00 0.00 1.98
3125 4138 7.707035 AGCACACTATCTATAGTTGTAACTTGC 59.293 37.037 2.20 3.14 41.44 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.035017 GTGTTACATGTGTGAGTGTTTGC 58.965 43.478 9.11 0.00 0.00 3.68
62 63 8.413229 CACATCTTCCTTTTCCTACTTTTGAAA 58.587 33.333 0.00 0.00 0.00 2.69
75 76 7.781324 ATACATTTGGTCACATCTTCCTTTT 57.219 32.000 0.00 0.00 0.00 2.27
81 82 6.170506 ACACGTATACATTTGGTCACATCTT 58.829 36.000 3.32 0.00 0.00 2.40
141 142 2.822561 TGCAAGTTTATGAAATCGGGCA 59.177 40.909 0.00 0.00 0.00 5.36
154 155 2.418060 CCCTCCACGTTTTTGCAAGTTT 60.418 45.455 0.00 0.00 0.00 2.66
157 158 0.597377 GCCCTCCACGTTTTTGCAAG 60.597 55.000 0.00 0.00 0.00 4.01
196 197 2.015456 TGCGATAGGGATGGTGAGAT 57.985 50.000 0.00 0.00 0.00 2.75
206 207 6.313905 GTCCTAATACAATGATTGCGATAGGG 59.686 42.308 20.87 13.46 35.08 3.53
252 253 8.048534 ACTTGCATGATGGTATTATCTAATGC 57.951 34.615 6.60 0.00 37.17 3.56
268 269 4.152223 CACGAGTGAATGTTACTTGCATGA 59.848 41.667 6.60 0.00 33.68 3.07
310 311 3.462982 TGTGTCGCTGTAACTTGTCATT 58.537 40.909 0.00 0.00 0.00 2.57
316 317 2.069273 GCTCATGTGTCGCTGTAACTT 58.931 47.619 0.00 0.00 0.00 2.66
317 318 1.000843 TGCTCATGTGTCGCTGTAACT 59.999 47.619 0.00 0.00 0.00 2.24
318 319 1.428448 TGCTCATGTGTCGCTGTAAC 58.572 50.000 0.00 0.00 0.00 2.50
319 320 2.385013 ATGCTCATGTGTCGCTGTAA 57.615 45.000 0.00 0.00 0.00 2.41
320 321 2.001872 CAATGCTCATGTGTCGCTGTA 58.998 47.619 0.00 0.00 0.00 2.74
321 322 0.800631 CAATGCTCATGTGTCGCTGT 59.199 50.000 0.00 0.00 0.00 4.40
324 325 0.798159 TCACAATGCTCATGTGTCGC 59.202 50.000 13.97 0.00 46.42 5.19
325 326 2.071540 AGTCACAATGCTCATGTGTCG 58.928 47.619 13.97 0.00 46.42 4.35
326 327 2.161012 CCAGTCACAATGCTCATGTGTC 59.839 50.000 13.97 10.12 46.42 3.67
327 328 2.156917 CCAGTCACAATGCTCATGTGT 58.843 47.619 13.97 0.00 46.42 3.72
345 519 5.654603 TGAACTAGATTTAAGAGACGCCA 57.345 39.130 0.00 0.00 0.00 5.69
381 555 9.725019 TCATGTTGTTCTACTGAGTTCAAATAT 57.275 29.630 0.00 0.00 0.00 1.28
382 556 9.554395 TTCATGTTGTTCTACTGAGTTCAAATA 57.446 29.630 0.00 0.00 0.00 1.40
383 557 8.450578 TTCATGTTGTTCTACTGAGTTCAAAT 57.549 30.769 0.00 0.00 0.00 2.32
421 611 2.939103 ACTCTTGCCTACATTTCGATGC 59.061 45.455 0.00 0.00 0.00 3.91
431 621 0.243907 TGCAGTCGACTCTTGCCTAC 59.756 55.000 16.96 0.00 0.00 3.18
446 636 0.385390 GGTGGTGGACAAGTTTGCAG 59.615 55.000 0.00 0.00 0.00 4.41
458 648 2.649531 TACAAACTGAAGGGTGGTGG 57.350 50.000 0.00 0.00 0.00 4.61
459 649 2.228822 GCATACAAACTGAAGGGTGGTG 59.771 50.000 0.00 0.00 0.00 4.17
463 653 2.699954 CTCGCATACAAACTGAAGGGT 58.300 47.619 0.00 0.00 0.00 4.34
464 654 1.398390 GCTCGCATACAAACTGAAGGG 59.602 52.381 0.00 0.00 0.00 3.95
465 655 1.398390 GGCTCGCATACAAACTGAAGG 59.602 52.381 0.00 0.00 0.00 3.46
467 657 2.177394 TGGCTCGCATACAAACTGAA 57.823 45.000 0.00 0.00 0.00 3.02
468 658 2.401583 ATGGCTCGCATACAAACTGA 57.598 45.000 0.00 0.00 0.00 3.41
469 659 2.789208 CAATGGCTCGCATACAAACTG 58.211 47.619 0.00 0.00 0.00 3.16
470 660 1.133025 GCAATGGCTCGCATACAAACT 59.867 47.619 0.00 0.00 36.96 2.66
515 705 9.688091 TTTGCTATAATGTAGGGAAACACATTA 57.312 29.630 8.99 8.99 46.25 1.90
521 713 7.399245 TGGTTTTGCTATAATGTAGGGAAAC 57.601 36.000 0.00 0.00 0.00 2.78
523 715 7.350382 TGATGGTTTTGCTATAATGTAGGGAA 58.650 34.615 0.00 0.00 0.00 3.97
526 718 8.443160 CGTATGATGGTTTTGCTATAATGTAGG 58.557 37.037 0.00 0.00 0.00 3.18
533 725 5.834169 TCGACGTATGATGGTTTTGCTATA 58.166 37.500 0.00 0.00 0.00 1.31
534 726 4.689071 TCGACGTATGATGGTTTTGCTAT 58.311 39.130 0.00 0.00 0.00 2.97
542 734 4.312443 AGTTTTGTTCGACGTATGATGGT 58.688 39.130 0.00 0.00 0.00 3.55
596 788 4.696877 TGGTCACATCTCTTTGTTGCTATG 59.303 41.667 0.00 0.00 0.00 2.23
612 804 2.673893 GCATCGAGTGTGTATGGTCACA 60.674 50.000 0.00 0.00 44.54 3.58
647 843 0.808453 AACGATGCAATACCGTCCGG 60.808 55.000 3.76 3.76 42.03 5.14
666 862 1.005805 TCGGCCCTAGGTTGTACTACA 59.994 52.381 8.29 0.00 0.00 2.74
667 863 1.767759 TCGGCCCTAGGTTGTACTAC 58.232 55.000 8.29 0.00 0.00 2.73
668 864 2.761786 ATCGGCCCTAGGTTGTACTA 57.238 50.000 8.29 0.00 0.00 1.82
669 865 1.875488 AATCGGCCCTAGGTTGTACT 58.125 50.000 8.29 0.00 0.00 2.73
670 866 2.093341 TGAAATCGGCCCTAGGTTGTAC 60.093 50.000 8.29 0.00 0.00 2.90
671 867 2.093341 GTGAAATCGGCCCTAGGTTGTA 60.093 50.000 8.29 0.00 0.00 2.41
798 994 1.068588 GTGCCCCACAAAGAAGGAAAC 59.931 52.381 0.00 0.00 34.08 2.78
805 1001 1.227823 CTCACGTGCCCCACAAAGA 60.228 57.895 11.67 0.00 33.40 2.52
807 1003 1.227823 CTCTCACGTGCCCCACAAA 60.228 57.895 11.67 0.00 33.40 2.83
808 1004 1.691195 TTCTCTCACGTGCCCCACAA 61.691 55.000 11.67 0.00 33.40 3.33
809 1005 1.691195 TTTCTCTCACGTGCCCCACA 61.691 55.000 11.67 0.00 33.40 4.17
812 1008 1.235281 GGTTTTCTCTCACGTGCCCC 61.235 60.000 11.67 0.00 0.00 5.80
814 1010 0.534203 TGGGTTTTCTCTCACGTGCC 60.534 55.000 11.67 3.13 0.00 5.01
844 1040 2.747855 GAAGCTTCCCGTGGGCTG 60.748 66.667 15.97 0.00 36.37 4.85
858 1054 2.164026 GGCTTCGAGCGAGCAGAAG 61.164 63.158 20.70 20.70 43.62 2.85
946 1142 0.546598 ATGGGGAATGGGAAGACGAC 59.453 55.000 0.00 0.00 0.00 4.34
947 1143 1.211949 GAATGGGGAATGGGAAGACGA 59.788 52.381 0.00 0.00 0.00 4.20
948 1144 1.680338 GAATGGGGAATGGGAAGACG 58.320 55.000 0.00 0.00 0.00 4.18
949 1145 1.570979 AGGAATGGGGAATGGGAAGAC 59.429 52.381 0.00 0.00 0.00 3.01
950 1146 1.852965 GAGGAATGGGGAATGGGAAGA 59.147 52.381 0.00 0.00 0.00 2.87
951 1147 1.477558 CGAGGAATGGGGAATGGGAAG 60.478 57.143 0.00 0.00 0.00 3.46
953 1149 1.994885 GCGAGGAATGGGGAATGGGA 61.995 60.000 0.00 0.00 0.00 4.37
956 1152 1.893808 CGGCGAGGAATGGGGAATG 60.894 63.158 0.00 0.00 0.00 2.67
957 1153 2.510906 CGGCGAGGAATGGGGAAT 59.489 61.111 0.00 0.00 0.00 3.01
958 1154 4.483243 GCGGCGAGGAATGGGGAA 62.483 66.667 12.98 0.00 0.00 3.97
1650 1855 2.602267 ACGATGTCGGGGTCCACA 60.602 61.111 7.38 0.00 44.95 4.17
1663 1868 1.549170 GAGGGTGTTGTAGGTGACGAT 59.451 52.381 0.00 0.00 0.00 3.73
1782 1987 0.460284 ACATCCCGTTCATGAGCGAC 60.460 55.000 30.29 9.64 37.19 5.19
1839 2044 1.027357 CATTGGCCTCCATTTCCTCG 58.973 55.000 3.32 0.00 31.53 4.63
1849 2054 2.825836 CTCGCACCCATTGGCCTC 60.826 66.667 3.32 0.00 33.59 4.70
1933 2138 2.607187 CATGGACTTGTACACCTCGAC 58.393 52.381 0.00 0.00 0.00 4.20
1953 2158 1.839894 CTTCATCCCAGCCCCTACC 59.160 63.158 0.00 0.00 0.00 3.18
2031 2236 5.779529 AATCAAACACCTCATATGCATCC 57.220 39.130 0.19 0.00 0.00 3.51
2151 2356 2.764010 TGGCTTATTAGTCTTCCTCGCA 59.236 45.455 0.00 0.00 0.00 5.10
2174 2379 1.900016 CCAGCAGCAACAGAAGCCA 60.900 57.895 0.00 0.00 0.00 4.75
2176 2381 1.285023 CACCAGCAGCAACAGAAGC 59.715 57.895 0.00 0.00 0.00 3.86
2187 2392 1.453562 TGTGAAGCAAGCACCAGCA 60.454 52.632 0.00 0.00 45.49 4.41
2188 2393 1.008079 GTGTGAAGCAAGCACCAGC 60.008 57.895 0.00 0.00 42.56 4.85
2301 2506 9.676861 TCTTACATTCTGATTGATTGAACAGAT 57.323 29.630 6.56 0.00 38.79 2.90
2369 2574 8.742777 ACATCATGCTACTAAATTTTGACACAT 58.257 29.630 6.63 4.04 0.00 3.21
2379 3353 5.928976 TGGCACTACATCATGCTACTAAAT 58.071 37.500 0.00 0.00 41.74 1.40
2383 3357 4.141642 TGAATGGCACTACATCATGCTACT 60.142 41.667 0.00 0.00 41.74 2.57
2414 3388 7.220683 CCAGTTGAACAAAACAGATAACAAGTG 59.779 37.037 0.00 0.00 37.26 3.16
2415 3389 7.257722 CCAGTTGAACAAAACAGATAACAAGT 58.742 34.615 0.00 0.00 32.21 3.16
2416 3390 6.198966 GCCAGTTGAACAAAACAGATAACAAG 59.801 38.462 0.00 0.00 32.21 3.16
2417 3391 6.039616 GCCAGTTGAACAAAACAGATAACAA 58.960 36.000 0.00 0.00 32.21 2.83
2418 3392 5.359576 AGCCAGTTGAACAAAACAGATAACA 59.640 36.000 0.00 0.00 32.21 2.41
2420 3394 5.592282 TCAGCCAGTTGAACAAAACAGATAA 59.408 36.000 0.00 0.00 32.21 1.75
2421 3395 5.129634 TCAGCCAGTTGAACAAAACAGATA 58.870 37.500 0.00 0.00 32.21 1.98
2424 3398 3.781079 TCAGCCAGTTGAACAAAACAG 57.219 42.857 0.00 0.00 32.21 3.16
2425 3399 4.734398 ATTCAGCCAGTTGAACAAAACA 57.266 36.364 0.00 0.00 39.68 2.83
2426 3400 5.175673 GCTAATTCAGCCAGTTGAACAAAAC 59.824 40.000 0.00 0.00 45.23 2.43
2456 3439 6.516718 ACGTCATATTTTGATACAGAGGGAG 58.483 40.000 0.00 0.00 36.54 4.30
2491 3476 9.169592 TGCTCCATGTACATTCAATATATGATG 57.830 33.333 5.37 0.00 38.03 3.07
2497 3482 9.524496 ACATTATGCTCCATGTACATTCAATAT 57.476 29.630 5.37 1.67 31.60 1.28
2569 3554 5.759763 GGACCATTCAAAATCAGTTTGCTTT 59.240 36.000 0.00 0.00 45.38 3.51
2570 3555 5.163322 TGGACCATTCAAAATCAGTTTGCTT 60.163 36.000 0.00 0.00 45.38 3.91
2571 3556 4.344679 TGGACCATTCAAAATCAGTTTGCT 59.655 37.500 0.00 0.00 45.38 3.91
2585 3570 2.373169 TGGATATGCTCCTGGACCATTC 59.627 50.000 9.66 7.44 45.21 2.67
2590 3575 2.157738 GCATTGGATATGCTCCTGGAC 58.842 52.381 0.00 0.00 45.21 4.02
2595 3580 1.999648 TTGGGCATTGGATATGCTCC 58.000 50.000 7.12 8.27 44.55 4.70
2609 3595 1.956477 CCTAGCAATACACCATTGGGC 59.044 52.381 7.78 0.00 43.70 5.36
2610 3596 3.297134 ACCTAGCAATACACCATTGGG 57.703 47.619 7.78 0.00 43.70 4.12
2611 3597 4.776349 TGTACCTAGCAATACACCATTGG 58.224 43.478 0.00 0.00 43.70 3.16
2612 3598 6.751514 TTTGTACCTAGCAATACACCATTG 57.248 37.500 0.00 0.00 45.87 2.82
2613 3599 6.946009 AGTTTTGTACCTAGCAATACACCATT 59.054 34.615 0.00 0.00 32.72 3.16
2614 3600 6.374333 CAGTTTTGTACCTAGCAATACACCAT 59.626 38.462 0.00 0.00 32.72 3.55
2615 3601 5.703592 CAGTTTTGTACCTAGCAATACACCA 59.296 40.000 0.00 0.00 32.72 4.17
2624 3610 9.331282 AGAATCATATTCAGTTTTGTACCTAGC 57.669 33.333 2.74 0.00 0.00 3.42
2674 3660 5.010213 ACTGACTCTTAACAGTCCAACTCTC 59.990 44.000 8.23 0.00 42.61 3.20
2716 3702 0.039618 GGGAAGGCATGAAACCCTGA 59.960 55.000 0.00 0.00 37.75 3.86
2726 3712 0.034477 CCGTTAACAGGGGAAGGCAT 60.034 55.000 6.39 0.00 0.00 4.40
2752 3763 8.710239 TGGAAGTAACCACACACACATATATAT 58.290 33.333 0.00 0.00 34.77 0.86
2753 3764 8.080363 TGGAAGTAACCACACACACATATATA 57.920 34.615 0.00 0.00 34.77 0.86
2754 3765 6.953101 TGGAAGTAACCACACACACATATAT 58.047 36.000 0.00 0.00 34.77 0.86
2755 3766 6.361768 TGGAAGTAACCACACACACATATA 57.638 37.500 0.00 0.00 34.77 0.86
2756 3767 5.235850 TGGAAGTAACCACACACACATAT 57.764 39.130 0.00 0.00 34.77 1.78
2757 3768 4.691326 TGGAAGTAACCACACACACATA 57.309 40.909 0.00 0.00 34.77 2.29
2758 3769 3.569194 TGGAAGTAACCACACACACAT 57.431 42.857 0.00 0.00 34.77 3.21
2767 3778 1.416243 AGTCGTGGTGGAAGTAACCA 58.584 50.000 0.00 0.00 45.49 3.67
2768 3779 2.538512 AAGTCGTGGTGGAAGTAACC 57.461 50.000 0.00 0.00 38.26 2.85
2769 3780 5.052481 AGTTAAAGTCGTGGTGGAAGTAAC 58.948 41.667 0.00 0.00 0.00 2.50
2770 3781 5.280654 AGTTAAAGTCGTGGTGGAAGTAA 57.719 39.130 0.00 0.00 0.00 2.24
2771 3782 4.942761 AGTTAAAGTCGTGGTGGAAGTA 57.057 40.909 0.00 0.00 0.00 2.24
2772 3783 3.832615 AGTTAAAGTCGTGGTGGAAGT 57.167 42.857 0.00 0.00 0.00 3.01
2773 3784 7.490000 AGATATAGTTAAAGTCGTGGTGGAAG 58.510 38.462 0.00 0.00 0.00 3.46
2774 3785 7.414222 AGATATAGTTAAAGTCGTGGTGGAA 57.586 36.000 0.00 0.00 0.00 3.53
2775 3786 7.341256 AGAAGATATAGTTAAAGTCGTGGTGGA 59.659 37.037 0.00 0.00 0.00 4.02
2776 3787 7.490000 AGAAGATATAGTTAAAGTCGTGGTGG 58.510 38.462 0.00 0.00 0.00 4.61
2777 3788 7.376336 CGAGAAGATATAGTTAAAGTCGTGGTG 59.624 40.741 0.00 0.00 0.00 4.17
2778 3789 7.416022 CGAGAAGATATAGTTAAAGTCGTGGT 58.584 38.462 0.00 0.00 0.00 4.16
2779 3790 6.856938 CCGAGAAGATATAGTTAAAGTCGTGG 59.143 42.308 0.00 0.00 0.00 4.94
2780 3791 7.637229 TCCGAGAAGATATAGTTAAAGTCGTG 58.363 38.462 0.00 0.00 0.00 4.35
2781 3792 7.798596 TCCGAGAAGATATAGTTAAAGTCGT 57.201 36.000 0.00 0.00 0.00 4.34
2782 3793 9.171701 CTTTCCGAGAAGATATAGTTAAAGTCG 57.828 37.037 0.00 0.00 0.00 4.18
2785 3796 9.465985 GGTCTTTCCGAGAAGATATAGTTAAAG 57.534 37.037 4.18 0.00 37.91 1.85
2786 3797 8.419442 GGGTCTTTCCGAGAAGATATAGTTAAA 58.581 37.037 4.18 0.00 37.91 1.52
2787 3798 7.015001 GGGGTCTTTCCGAGAAGATATAGTTAA 59.985 40.741 4.18 0.00 37.91 2.01
2788 3799 6.492772 GGGGTCTTTCCGAGAAGATATAGTTA 59.507 42.308 4.18 0.00 37.91 2.24
2789 3800 5.304871 GGGGTCTTTCCGAGAAGATATAGTT 59.695 44.000 4.18 0.00 37.91 2.24
2790 3801 4.833938 GGGGTCTTTCCGAGAAGATATAGT 59.166 45.833 4.18 0.00 37.91 2.12
2791 3802 5.081032 AGGGGTCTTTCCGAGAAGATATAG 58.919 45.833 4.18 0.00 37.91 1.31
2792 3803 5.076057 AGGGGTCTTTCCGAGAAGATATA 57.924 43.478 4.18 0.00 37.91 0.86
2793 3804 3.930035 AGGGGTCTTTCCGAGAAGATAT 58.070 45.455 4.18 0.00 37.91 1.63
2894 3905 9.844257 TTTTCAACTTTTAACCAATGGATGAAT 57.156 25.926 6.16 0.00 0.00 2.57
2896 3907 8.260818 TGTTTTCAACTTTTAACCAATGGATGA 58.739 29.630 6.16 0.00 0.00 2.92
3040 4053 2.224066 CCGCATAACTAGACCTTCCTGG 60.224 54.545 0.00 0.00 42.93 4.45
3045 4058 1.134491 GGCACCGCATAACTAGACCTT 60.134 52.381 0.00 0.00 0.00 3.50
3052 4065 1.221840 CAGGAGGCACCGCATAACT 59.778 57.895 0.00 0.00 44.74 2.24
3054 4067 0.107703 CTTCAGGAGGCACCGCATAA 60.108 55.000 0.00 0.00 44.74 1.90
3059 4072 0.467384 ATGATCTTCAGGAGGCACCG 59.533 55.000 0.00 0.00 44.74 4.94
3086 4099 1.198408 AGTGTGCTCGCAATGTTCATG 59.802 47.619 1.75 0.00 0.00 3.07
3088 4101 2.162319 TAGTGTGCTCGCAATGTTCA 57.838 45.000 1.75 0.00 0.00 3.18
3094 4107 5.163550 ACAACTATAGATAGTGTGCTCGCAA 60.164 40.000 6.78 0.00 42.47 4.85
3095 4108 4.338400 ACAACTATAGATAGTGTGCTCGCA 59.662 41.667 6.78 0.00 42.47 5.10
3100 4113 7.491372 TGCAAGTTACAACTATAGATAGTGTGC 59.509 37.037 6.78 6.88 42.47 4.57
3101 4114 8.926715 TGCAAGTTACAACTATAGATAGTGTG 57.073 34.615 6.78 6.63 42.47 3.82
3102 4115 9.587772 CTTGCAAGTTACAACTATAGATAGTGT 57.412 33.333 18.65 7.43 42.47 3.55


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

AutoCloner maintained by Alex Coulton.