Multiple sequence alignment - TraesCS1B01G213300

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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 TraesCS1B01G213300 chr1B 100.000 4583 0 0 1 4583 387302468 387307050 0.000000e+00 8464
1 TraesCS1B01G213300 chr1A 95.476 3603 138 17 1 3589 356470413 356474004 0.000000e+00 5727
2 TraesCS1B01G213300 chr1A 91.641 957 49 18 3630 4583 356474008 356474936 0.000000e+00 1295
3 TraesCS1B01G213300 chr1D 93.740 1949 86 24 797 2730 285052418 285054345 0.000000e+00 2891
4 TraesCS1B01G213300 chr1D 94.710 983 46 4 2751 3731 285054413 285055391 0.000000e+00 1522
5 TraesCS1B01G213300 chr1D 93.821 793 36 7 3795 4583 285055407 285056190 0.000000e+00 1181
6 TraesCS1B01G213300 chr1D 92.269 789 38 13 1 779 285051654 285052429 0.000000e+00 1098
7 TraesCS1B01G213300 chr1D 83.333 114 15 3 3660 3770 285055466 285055578 8.110000e-18 102


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 TraesCS1B01G213300 chr1B 387302468 387307050 4582 False 8464.0 8464 100.0000 1 4583 1 chr1B.!!$F1 4582
1 TraesCS1B01G213300 chr1A 356470413 356474936 4523 False 3511.0 5727 93.5585 1 4583 2 chr1A.!!$F1 4582
2 TraesCS1B01G213300 chr1D 285051654 285056190 4536 False 1358.8 2891 91.5746 1 4583 5 chr1D.!!$F1 4582

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
779 789 1.136141 GCTGTCTGTGTTGCAATCTCG 60.136 52.381 0.59 0.0 0.00 4.04 F
1489 1513 1.001181 CAAGGGATGCCTTTTGTGGTG 59.999 52.381 17.04 0.0 0.00 4.17 F
1824 1856 1.133407 GAGTCACCCTCTTGCTAGACG 59.867 57.143 0.00 0.0 37.22 4.18 F
3426 3530 0.768221 TGGGTCCTCTTGAGGCTGTT 60.768 55.000 11.61 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 1871 0.385390 CTGCGGGGATGGCAAATTAC 59.615 55.0 0.0 0.0 40.39 1.89 R
3291 3395 0.112412 TTTCCTTGGCTTGGACCTCC 59.888 55.0 0.0 0.0 32.65 4.30 R
3468 3572 0.539986 GAACCGGCTCAAGTGGGATA 59.460 55.0 0.0 0.0 0.00 2.59 R
4383 4491 0.034059 CCCTTACCATAGCTGCCTCG 59.966 60.0 0.0 0.0 0.00 4.63 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
353 354 2.885135 AAGATGGTGTTGATGCAGGA 57.115 45.000 0.00 0.00 0.00 3.86
570 571 3.058085 GGCAATTTTGGAATGTTGGCAAG 60.058 43.478 0.00 0.00 43.89 4.01
571 572 3.609879 GCAATTTTGGAATGTTGGCAAGC 60.610 43.478 0.00 0.00 0.00 4.01
779 789 1.136141 GCTGTCTGTGTTGCAATCTCG 60.136 52.381 0.59 0.00 0.00 4.04
786 796 3.411446 TGTGTTGCAATCTCGATTCCTT 58.589 40.909 0.59 0.00 0.00 3.36
814 824 7.857734 TGAGACTGTTGTAATCTCAAACAAA 57.142 32.000 0.77 0.00 44.49 2.83
816 826 8.902806 TGAGACTGTTGTAATCTCAAACAAAAT 58.097 29.630 0.77 0.00 44.49 1.82
819 829 7.209475 ACTGTTGTAATCTCAAACAAAATGGG 58.791 34.615 0.00 0.00 37.35 4.00
821 831 7.786030 TGTTGTAATCTCAAACAAAATGGGAA 58.214 30.769 0.00 0.00 37.35 3.97
822 832 7.925483 TGTTGTAATCTCAAACAAAATGGGAAG 59.075 33.333 0.00 0.00 37.35 3.46
826 836 9.541143 GTAATCTCAAACAAAATGGGAAGAAAA 57.459 29.630 0.00 0.00 29.53 2.29
953 973 1.612395 GGAGGAGACAGGGAGCACTG 61.612 65.000 0.00 0.00 44.03 3.66
1137 1157 3.121030 CTCAAGCTGAACCGCCGG 61.121 66.667 0.00 0.00 0.00 6.13
1347 1367 1.152567 CCAGCTCCTCCTCCTCGAT 60.153 63.158 0.00 0.00 0.00 3.59
1362 1382 1.143838 CGATGCCATGGACTCCGAA 59.856 57.895 18.40 0.00 0.00 4.30
1433 1453 1.358787 TCCCAATGCATCACTCCCTTT 59.641 47.619 0.00 0.00 0.00 3.11
1489 1513 1.001181 CAAGGGATGCCTTTTGTGGTG 59.999 52.381 17.04 0.00 0.00 4.17
1499 1523 6.019779 TGCCTTTTGTGGTGTTACATTATC 57.980 37.500 0.00 0.00 0.00 1.75
1543 1569 8.911247 GGCAAATTACTTTGTCCAAATACTAG 57.089 34.615 7.31 0.00 43.07 2.57
1570 1596 4.931661 TTCGTGATAGTATTCACTCCCC 57.068 45.455 3.41 0.00 43.10 4.81
1588 1614 3.631686 TCCCCGCTGTTTGATTTGATATG 59.368 43.478 0.00 0.00 0.00 1.78
1608 1634 2.423185 TGGGCTGCACTAATCAAAATCG 59.577 45.455 2.50 0.00 0.00 3.34
1639 1668 8.691661 TGCATATGTAGTAGACTCATCAAGTA 57.308 34.615 4.29 0.00 38.74 2.24
1775 1807 6.477688 CCCATTTGCTAAAATCTGCACTAATG 59.522 38.462 0.00 0.00 39.05 1.90
1824 1856 1.133407 GAGTCACCCTCTTGCTAGACG 59.867 57.143 0.00 0.00 37.22 4.18
1926 1958 4.632153 GCAGAGGCGGAAATCTTATTCTA 58.368 43.478 0.00 0.00 0.00 2.10
1940 1972 5.109210 TCTTATTCTACACCGCATCAACAG 58.891 41.667 0.00 0.00 0.00 3.16
2147 2180 5.499004 AAGTTAACCACTGAATCTAGGCA 57.501 39.130 0.88 0.00 35.12 4.75
2234 2267 9.684448 CTCTATGATGATCAAACAGTACGTAAT 57.316 33.333 0.00 0.00 0.00 1.89
2250 2283 9.362539 CAGTACGTAATTTTGTATCACTAGGTT 57.637 33.333 0.00 0.00 0.00 3.50
2334 2367 4.214119 CCTTGTTGTCTGTGACGATCAAAT 59.786 41.667 0.00 0.00 34.95 2.32
2368 2401 3.948851 TGTATCGTTAGCTCGCTACTTG 58.051 45.455 9.36 0.00 34.78 3.16
2398 2431 7.307278 GCTTGTTATGAGATCAGCTGAATGTAG 60.307 40.741 22.50 8.22 0.00 2.74
2487 2520 5.401531 TCAGTAGCTCGTTTCTTATTGGT 57.598 39.130 0.00 0.00 0.00 3.67
2527 2560 7.612244 AGCTAGATGAAACTCTTCAGTACTACA 59.388 37.037 0.00 0.00 44.68 2.74
2622 2657 6.690194 AAATATTCTGCTTGATGTCTGGAC 57.310 37.500 0.00 0.00 0.00 4.02
2696 2731 3.483922 GTGCGTAACATTCATCTCTCTCG 59.516 47.826 0.00 0.00 0.00 4.04
2791 2895 6.659242 CCCTATTGTTAGTTGACTTGGAATGT 59.341 38.462 0.00 0.00 0.00 2.71
2859 2963 4.263506 CCAAAGGACTAGTTCATGGAACCT 60.264 45.833 17.24 5.13 42.85 3.50
2886 2990 6.042143 ACAAGTTTTGGACATAAGCAAAGTG 58.958 36.000 0.00 0.00 34.12 3.16
2914 3018 8.291191 ACTTTGACTACTAGTAGAATGGGTAC 57.709 38.462 31.93 14.12 36.97 3.34
2977 3081 8.164070 AGGTCTAAAACAACACTATTGGAGAAT 58.836 33.333 0.00 0.00 0.00 2.40
3022 3126 1.424403 CATTACGGTGAAGTGCGTGA 58.576 50.000 0.00 0.00 0.00 4.35
3078 3182 4.045636 AGTTGCATTTTGTGACTTGACC 57.954 40.909 0.00 0.00 0.00 4.02
3345 3449 1.071385 AGGAATGTCATCCGGCTGATC 59.929 52.381 11.82 5.08 44.60 2.92
3363 3467 3.310860 CTCAGGCTTTACGGGGCGT 62.311 63.158 0.00 0.00 44.35 5.68
3426 3530 0.768221 TGGGTCCTCTTGAGGCTGTT 60.768 55.000 11.61 0.00 0.00 3.16
3435 3539 2.301870 TCTTGAGGCTGTTGATTACGGT 59.698 45.455 0.00 0.00 35.43 4.83
3444 3548 4.923871 GCTGTTGATTACGGTATCATCGAT 59.076 41.667 0.00 0.00 34.67 3.59
3447 3551 5.221362 TGTTGATTACGGTATCATCGATGGT 60.221 40.000 24.61 20.86 34.67 3.55
3468 3572 2.263077 GTGATCGACGAAGACAGCATT 58.737 47.619 0.00 0.00 0.00 3.56
3471 3575 4.147306 GTGATCGACGAAGACAGCATTATC 59.853 45.833 0.00 0.00 0.00 1.75
3592 3696 6.317642 CGATGAGATATACTAAGCTAGCCTGT 59.682 42.308 12.13 10.40 0.00 4.00
3609 3713 4.002982 GCCTGTCAGTCACATGTATTTCA 58.997 43.478 0.00 0.00 33.23 2.69
3661 3765 7.482743 CGTCAAACAAAGATGATGTAATCCTTG 59.517 37.037 0.00 0.00 44.73 3.61
3684 3788 4.679662 GCAGTAGACTTTATCTGCCGTTA 58.320 43.478 4.90 0.00 44.84 3.18
3695 3799 2.147958 TCTGCCGTTACATTTGGTGTC 58.852 47.619 0.00 0.00 42.29 3.67
3781 3886 2.001361 TAACCAGCTAGCCTCGTCGC 62.001 60.000 12.13 0.00 0.00 5.19
3785 3890 2.105128 GCTAGCCTCGTCGCATGT 59.895 61.111 2.29 0.00 0.00 3.21
3786 3891 1.101635 AGCTAGCCTCGTCGCATGTA 61.102 55.000 12.13 0.00 0.00 2.29
3787 3892 0.935366 GCTAGCCTCGTCGCATGTAC 60.935 60.000 2.29 0.00 0.00 2.90
3788 3893 0.663688 CTAGCCTCGTCGCATGTACT 59.336 55.000 0.00 0.00 0.00 2.73
3789 3894 1.871676 CTAGCCTCGTCGCATGTACTA 59.128 52.381 0.00 0.00 0.00 1.82
3790 3895 0.663688 AGCCTCGTCGCATGTACTAG 59.336 55.000 0.00 0.00 0.00 2.57
3791 3896 0.381089 GCCTCGTCGCATGTACTAGT 59.619 55.000 0.00 0.00 0.00 2.57
3792 3897 1.600957 GCCTCGTCGCATGTACTAGTA 59.399 52.381 0.00 0.00 0.00 1.82
3793 3898 2.601741 GCCTCGTCGCATGTACTAGTAC 60.602 54.545 23.58 23.58 36.63 2.73
3800 3905 8.141835 TCGTCGCATGTACTAGTACTATTTTA 57.858 34.615 28.56 11.85 37.00 1.52
3849 3954 6.745159 TGTCAAAACAAAGTTGTAGCACTA 57.255 33.333 0.00 0.00 41.31 2.74
3850 3955 7.147143 TGTCAAAACAAAGTTGTAGCACTAA 57.853 32.000 0.00 0.00 41.31 2.24
3890 3995 0.814457 GGCCGTTGCATTTGGTATGA 59.186 50.000 0.00 0.00 40.13 2.15
3891 3996 1.408702 GGCCGTTGCATTTGGTATGAT 59.591 47.619 0.00 0.00 40.13 2.45
3892 3997 2.159114 GGCCGTTGCATTTGGTATGATT 60.159 45.455 0.00 0.00 40.13 2.57
3893 3998 2.859538 GCCGTTGCATTTGGTATGATTG 59.140 45.455 0.00 0.00 37.47 2.67
3894 3999 3.428725 GCCGTTGCATTTGGTATGATTGA 60.429 43.478 0.00 0.00 37.47 2.57
3900 4007 5.683681 TGCATTTGGTATGATTGAGAGCTA 58.316 37.500 0.00 0.00 0.00 3.32
3903 4010 7.938490 TGCATTTGGTATGATTGAGAGCTATTA 59.062 33.333 0.00 0.00 0.00 0.98
3937 4044 7.862512 TTTTGACCAAGCAAATGAAAGAATT 57.137 28.000 0.00 0.00 37.57 2.17
3938 4045 6.847956 TTGACCAAGCAAATGAAAGAATTG 57.152 33.333 0.00 0.00 0.00 2.32
3939 4046 5.916318 TGACCAAGCAAATGAAAGAATTGT 58.084 33.333 0.00 0.00 0.00 2.71
3940 4047 5.754406 TGACCAAGCAAATGAAAGAATTGTG 59.246 36.000 0.00 0.00 0.00 3.33
3941 4048 5.673514 ACCAAGCAAATGAAAGAATTGTGT 58.326 33.333 0.00 0.00 0.00 3.72
3942 4049 6.114767 ACCAAGCAAATGAAAGAATTGTGTT 58.885 32.000 0.00 0.00 0.00 3.32
3943 4050 6.258507 ACCAAGCAAATGAAAGAATTGTGTTC 59.741 34.615 0.00 0.00 0.00 3.18
3944 4051 6.480981 CCAAGCAAATGAAAGAATTGTGTTCT 59.519 34.615 0.00 0.00 0.00 3.01
3959 4066 9.994432 GAATTGTGTTCTGAACATAGAAATAGG 57.006 33.333 24.44 0.00 44.35 2.57
3962 4069 6.818644 TGTGTTCTGAACATAGAAATAGGCTC 59.181 38.462 24.44 8.81 44.35 4.70
3986 4093 0.319297 GCCAACCTTGCTGCAAAGAG 60.319 55.000 17.27 10.87 0.00 2.85
3997 4104 2.362077 GCTGCAAAGAGGAAACCAAAGA 59.638 45.455 0.00 0.00 0.00 2.52
4017 4124 8.711457 CCAAAGAACATGGTGAAATTTATTGAC 58.289 33.333 0.00 0.00 33.08 3.18
4027 4134 5.405269 GTGAAATTTATTGACTGCACCCAAC 59.595 40.000 0.00 0.00 0.00 3.77
4028 4135 5.304101 TGAAATTTATTGACTGCACCCAACT 59.696 36.000 0.00 0.00 0.00 3.16
4029 4136 5.391312 AATTTATTGACTGCACCCAACTC 57.609 39.130 0.00 0.00 0.00 3.01
4030 4137 3.500448 TTATTGACTGCACCCAACTCA 57.500 42.857 0.00 0.00 0.00 3.41
4031 4138 2.592102 ATTGACTGCACCCAACTCAT 57.408 45.000 0.00 0.00 0.00 2.90
4032 4139 1.608055 TTGACTGCACCCAACTCATG 58.392 50.000 0.00 0.00 0.00 3.07
4033 4140 0.764271 TGACTGCACCCAACTCATGA 59.236 50.000 0.00 0.00 0.00 3.07
4034 4141 1.352017 TGACTGCACCCAACTCATGAT 59.648 47.619 0.00 0.00 0.00 2.45
4035 4142 2.571202 TGACTGCACCCAACTCATGATA 59.429 45.455 0.00 0.00 0.00 2.15
4083 4190 6.567891 GCCAGTAATCCTTTACAAGACACAAC 60.568 42.308 0.00 0.00 40.20 3.32
4133 4241 6.768483 TGGAACTCTGATACAATTCTCACAA 58.232 36.000 0.00 0.00 0.00 3.33
4150 4258 3.267597 AACCGCCGCAATGAAGCAC 62.268 57.895 0.00 0.00 0.00 4.40
4176 4284 2.837498 TCTCATCAATACATGGCACCG 58.163 47.619 0.00 0.00 0.00 4.94
4270 4378 1.072965 CAGAGCTCCCAGTTTTCAGGT 59.927 52.381 10.93 0.00 0.00 4.00
4383 4491 5.652014 TGAACCAATTGTCTGACCCAATATC 59.348 40.000 5.17 0.00 32.40 1.63
4497 4605 4.244862 CAAACCACTGCACTGAAAACTTT 58.755 39.130 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
353 354 0.251832 TCTTCCTCTTCTCGCCCTGT 60.252 55.000 0.00 0.00 0.00 4.00
402 403 1.415672 TTGGCCTTCTTCACCTCCGT 61.416 55.000 3.32 0.00 0.00 4.69
519 520 5.125100 ACAATGGATAACACAGCAAACAG 57.875 39.130 0.00 0.00 0.00 3.16
523 524 6.403866 AAAGAACAATGGATAACACAGCAA 57.596 33.333 0.00 0.00 0.00 3.91
570 571 5.334182 GGACAGCTAAAACTCTTACACTTGC 60.334 44.000 0.00 0.00 0.00 4.01
571 572 5.758296 TGGACAGCTAAAACTCTTACACTTG 59.242 40.000 0.00 0.00 0.00 3.16
720 730 9.606631 ATCAAAATTAAAAACCACAGCACTTAA 57.393 25.926 0.00 0.00 0.00 1.85
722 732 7.012232 CCATCAAAATTAAAAACCACAGCACTT 59.988 33.333 0.00 0.00 0.00 3.16
744 754 6.933521 ACACAGACAGCAGATAATATTCCATC 59.066 38.462 0.00 0.00 0.00 3.51
794 804 7.069331 TCCCATTTTGTTTGAGATTACAACAGT 59.931 33.333 0.00 0.00 34.25 3.55
795 805 7.432869 TCCCATTTTGTTTGAGATTACAACAG 58.567 34.615 0.00 0.00 34.25 3.16
826 836 1.396607 GGGTTGGGCCGTTGTCTTTT 61.397 55.000 0.00 0.00 38.44 2.27
1347 1367 0.178767 CAGATTCGGAGTCCATGGCA 59.821 55.000 6.96 0.00 0.00 4.92
1362 1382 0.387202 CGAAGAGCCGGATGTCAGAT 59.613 55.000 5.05 0.00 0.00 2.90
1433 1453 1.071071 CAACCCTACACAAACCGAGGA 59.929 52.381 0.00 0.00 0.00 3.71
1489 1513 6.299141 AGATGACCATGTGGGATAATGTAAC 58.701 40.000 3.77 0.00 41.15 2.50
1570 1596 3.067180 AGCCCATATCAAATCAAACAGCG 59.933 43.478 0.00 0.00 0.00 5.18
1588 1614 2.423538 ACGATTTTGATTAGTGCAGCCC 59.576 45.455 0.00 0.00 0.00 5.19
1608 1634 5.299531 TGAGTCTACTACATATGCAGGTCAC 59.700 44.000 7.85 1.08 0.00 3.67
1639 1668 1.279496 TGGCCTACTGCTGTGAATCT 58.721 50.000 3.32 0.00 40.92 2.40
1775 1807 7.808856 GGATAGTCAGTAAAGTATCATTCGGAC 59.191 40.741 0.00 0.00 34.54 4.79
1839 1871 0.385390 CTGCGGGGATGGCAAATTAC 59.615 55.000 0.00 0.00 40.39 1.89
1926 1958 1.229428 CAGAACTGTTGATGCGGTGT 58.771 50.000 0.00 0.00 0.00 4.16
1940 1972 9.807649 ACAAAGATAATATTTGCAATCCAGAAC 57.192 29.630 0.00 0.00 40.54 3.01
2037 2069 4.338012 TGAGTATAGAAACGACCCACTGA 58.662 43.478 0.00 0.00 0.00 3.41
2234 2267 4.651778 AGCAGCAACCTAGTGATACAAAA 58.348 39.130 0.00 0.00 0.00 2.44
2244 2277 2.648059 AGCCAATAAGCAGCAACCTAG 58.352 47.619 0.00 0.00 34.23 3.02
2250 2283 5.827267 TGATATAACAAGCCAATAAGCAGCA 59.173 36.000 0.00 0.00 34.23 4.41
2344 2377 2.493713 AGCGAGCTAACGATACAAGG 57.506 50.000 0.00 0.00 35.09 3.61
2353 2386 1.393883 GCCAACAAGTAGCGAGCTAAC 59.606 52.381 6.36 2.06 0.00 2.34
2368 2401 3.944015 AGCTGATCTCATAACAAGCCAAC 59.056 43.478 0.00 0.00 0.00 3.77
2398 2431 5.719173 TCAATGCAGGTATTACCAAAAAGC 58.281 37.500 15.19 10.43 41.95 3.51
2468 2501 6.237313 ACAAACCAATAAGAAACGAGCTAC 57.763 37.500 0.00 0.00 0.00 3.58
2518 2551 9.031537 TCATATACCCATATTGGTGTAGTACTG 57.968 37.037 8.74 2.54 39.53 2.74
2527 2560 9.959721 GAACTGTAATCATATACCCATATTGGT 57.040 33.333 3.61 3.61 42.62 3.67
2622 2657 8.761575 AAGGTGCAACAAATATCATTACAAAG 57.238 30.769 3.64 0.00 39.98 2.77
2654 2689 7.757526 ACGCACATATAAACAAGAAAAGCATA 58.242 30.769 0.00 0.00 0.00 3.14
2696 2731 9.979270 CAACTAGTCAAATGTGATATCTTGAAC 57.021 33.333 3.98 0.00 35.80 3.18
2752 2856 5.319043 ACAATAGGGTCTTCCAAGTCAAA 57.681 39.130 0.00 0.00 38.24 2.69
2791 2895 5.422331 CCACTCATACCAAACTAGAAGAGGA 59.578 44.000 0.00 0.00 0.00 3.71
2859 2963 5.843673 TGCTTATGTCCAAAACTTGTTCA 57.156 34.783 0.00 0.00 0.00 3.18
2886 2990 8.312564 ACCCATTCTACTAGTAGTCAAAGTTTC 58.687 37.037 25.58 0.00 34.84 2.78
2977 3081 2.766828 GGCTAGCCTAAAACTCCTCTCA 59.233 50.000 27.17 0.00 0.00 3.27
3022 3126 7.775093 TCAACAGATATGCAAAGGCTACTATTT 59.225 33.333 0.00 0.00 41.91 1.40
3095 3199 0.305922 GATAGCCATTGTCGCACTGC 59.694 55.000 0.00 0.00 0.00 4.40
3291 3395 0.112412 TTTCCTTGGCTTGGACCTCC 59.888 55.000 0.00 0.00 32.65 4.30
3345 3449 1.952102 TACGCCCCGTAAAGCCTGAG 61.952 60.000 0.00 0.00 39.44 3.35
3354 3458 2.035469 TCCAGTGTACGCCCCGTA 59.965 61.111 1.98 0.00 41.54 4.02
3363 3467 3.451402 TTCTCTACCTGCTCCAGTGTA 57.549 47.619 0.00 0.00 0.00 2.90
3426 3530 4.279922 ACACCATCGATGATACCGTAATCA 59.720 41.667 26.86 0.01 40.07 2.57
3444 3548 0.955905 TGTCTTCGTCGATCACACCA 59.044 50.000 0.00 0.00 0.00 4.17
3447 3551 0.596082 TGCTGTCTTCGTCGATCACA 59.404 50.000 0.00 1.11 0.00 3.58
3468 3572 0.539986 GAACCGGCTCAAGTGGGATA 59.460 55.000 0.00 0.00 0.00 2.59
3471 3575 2.359975 GGAACCGGCTCAAGTGGG 60.360 66.667 7.26 0.00 0.00 4.61
3592 3696 5.530543 TGCTGTTTGAAATACATGTGACTGA 59.469 36.000 9.11 0.00 0.00 3.41
3609 3713 2.111878 AGCGACTGCCTGCTGTTT 59.888 55.556 3.12 0.00 44.31 2.83
3628 3732 6.204688 ACATCATCTTTGTTTGACGAAAGCTA 59.795 34.615 0.00 0.00 0.00 3.32
3695 3799 0.874390 AACACAACAGCTACGCCATG 59.126 50.000 0.00 0.00 0.00 3.66
3781 3886 9.797556 TGCTGTGTAAAATAGTACTAGTACATG 57.202 33.333 29.87 16.51 38.48 3.21
3785 3890 8.525316 TGCTTGCTGTGTAAAATAGTACTAGTA 58.475 33.333 8.85 0.00 0.00 1.82
3786 3891 7.383687 TGCTTGCTGTGTAAAATAGTACTAGT 58.616 34.615 8.85 2.42 0.00 2.57
3787 3892 7.827819 TGCTTGCTGTGTAAAATAGTACTAG 57.172 36.000 8.85 0.00 0.00 2.57
3788 3893 7.876068 AGTTGCTTGCTGTGTAAAATAGTACTA 59.124 33.333 4.77 4.77 0.00 1.82
3789 3894 6.710744 AGTTGCTTGCTGTGTAAAATAGTACT 59.289 34.615 0.00 0.00 0.00 2.73
3790 3895 6.797033 CAGTTGCTTGCTGTGTAAAATAGTAC 59.203 38.462 0.00 0.00 0.00 2.73
3791 3896 6.567701 GCAGTTGCTTGCTGTGTAAAATAGTA 60.568 38.462 0.00 0.00 40.89 1.82
3792 3897 5.762045 CAGTTGCTTGCTGTGTAAAATAGT 58.238 37.500 0.00 0.00 0.00 2.12
3793 3898 4.618489 GCAGTTGCTTGCTGTGTAAAATAG 59.382 41.667 0.00 0.00 40.89 1.73
3844 3949 7.807680 ACAAAGTCTACTGCTAAAATTAGTGC 58.192 34.615 2.42 0.00 33.32 4.40
3849 3954 6.447162 GCCAACAAAGTCTACTGCTAAAATT 58.553 36.000 0.00 0.00 0.00 1.82
3850 3955 5.048013 GGCCAACAAAGTCTACTGCTAAAAT 60.048 40.000 0.00 0.00 0.00 1.82
3890 3995 6.185114 AGCCAGAACATAATAGCTCTCAAT 57.815 37.500 0.00 0.00 0.00 2.57
3891 3996 5.620738 AGCCAGAACATAATAGCTCTCAA 57.379 39.130 0.00 0.00 0.00 3.02
3892 3997 5.620738 AAGCCAGAACATAATAGCTCTCA 57.379 39.130 0.00 0.00 0.00 3.27
3893 3998 6.540189 TCAAAAGCCAGAACATAATAGCTCTC 59.460 38.462 0.00 0.00 0.00 3.20
3894 3999 6.317391 GTCAAAAGCCAGAACATAATAGCTCT 59.683 38.462 0.00 0.00 0.00 4.09
3900 4007 5.567423 GCTTGGTCAAAAGCCAGAACATAAT 60.567 40.000 0.00 0.00 45.60 1.28
3903 4010 2.036346 GCTTGGTCAAAAGCCAGAACAT 59.964 45.455 0.00 0.00 45.60 2.71
3934 4041 8.462016 GCCTATTTCTATGTTCAGAACACAATT 58.538 33.333 18.49 5.28 45.50 2.32
3937 4044 6.711277 AGCCTATTTCTATGTTCAGAACACA 58.289 36.000 18.49 6.07 45.50 3.72
3938 4045 6.818644 TGAGCCTATTTCTATGTTCAGAACAC 59.181 38.462 18.49 1.89 45.50 3.32
3939 4046 6.946340 TGAGCCTATTTCTATGTTCAGAACA 58.054 36.000 18.42 18.42 46.94 3.18
3940 4047 7.712639 TGATGAGCCTATTTCTATGTTCAGAAC 59.287 37.037 6.32 6.32 34.31 3.01
3941 4048 7.795047 TGATGAGCCTATTTCTATGTTCAGAA 58.205 34.615 0.00 0.00 32.71 3.02
3942 4049 7.365497 TGATGAGCCTATTTCTATGTTCAGA 57.635 36.000 0.00 0.00 0.00 3.27
3943 4050 6.147492 GCTGATGAGCCTATTTCTATGTTCAG 59.853 42.308 0.00 0.00 39.57 3.02
3944 4051 5.994054 GCTGATGAGCCTATTTCTATGTTCA 59.006 40.000 0.00 0.00 39.57 3.18
3959 4066 0.964358 AGCAAGGTTGGCTGATGAGC 60.964 55.000 0.00 0.00 45.40 4.26
3986 4093 4.664150 TTCACCATGTTCTTTGGTTTCC 57.336 40.909 0.00 0.00 45.19 3.13
3997 4104 6.646240 GTGCAGTCAATAAATTTCACCATGTT 59.354 34.615 0.00 0.00 0.00 2.71
4017 4124 2.941064 CACTATCATGAGTTGGGTGCAG 59.059 50.000 0.09 0.00 0.00 4.41
4027 4134 5.279910 GGATTCTTCTCCCCACTATCATGAG 60.280 48.000 0.09 0.00 0.00 2.90
4028 4135 4.594920 GGATTCTTCTCCCCACTATCATGA 59.405 45.833 0.00 0.00 0.00 3.07
4029 4136 4.349048 TGGATTCTTCTCCCCACTATCATG 59.651 45.833 0.00 0.00 34.12 3.07
4030 4137 4.570926 TGGATTCTTCTCCCCACTATCAT 58.429 43.478 0.00 0.00 34.12 2.45
4031 4138 4.007581 TGGATTCTTCTCCCCACTATCA 57.992 45.455 0.00 0.00 34.12 2.15
4032 4139 5.163152 ACATTGGATTCTTCTCCCCACTATC 60.163 44.000 0.00 0.00 34.12 2.08
4033 4140 4.728860 ACATTGGATTCTTCTCCCCACTAT 59.271 41.667 0.00 0.00 34.12 2.12
4034 4141 4.111577 ACATTGGATTCTTCTCCCCACTA 58.888 43.478 0.00 0.00 34.12 2.74
4035 4142 2.922283 ACATTGGATTCTTCTCCCCACT 59.078 45.455 0.00 0.00 34.12 4.00
4133 4241 3.737172 GTGCTTCATTGCGGCGGT 61.737 61.111 9.78 0.00 35.36 5.68
4150 4258 4.933400 TGCCATGTATTGATGAGATGATCG 59.067 41.667 0.00 0.00 0.00 3.69
4176 4284 2.047179 GCCCTGGTTCCGACTGTC 60.047 66.667 0.00 0.00 0.00 3.51
4251 4359 1.439543 ACCTGAAAACTGGGAGCTCT 58.560 50.000 14.64 0.00 0.00 4.09
4270 4378 3.551259 GGATTGAAGCTCCGGTGAA 57.449 52.632 7.92 0.00 0.00 3.18
4383 4491 0.034059 CCCTTACCATAGCTGCCTCG 59.966 60.000 0.00 0.00 0.00 4.63
4482 4590 5.030295 CACACTACAAAGTTTTCAGTGCAG 58.970 41.667 19.41 12.29 40.17 4.41
4497 4605 0.114364 TCTGGAGGGAGCACACTACA 59.886 55.000 0.00 0.00 38.17 2.74


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

AutoCloner maintained by Alex Coulton.