Multiple sequence alignment - TraesCS3B01G201600

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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 TraesCS3B01G201600 chr3B 100.000 3563 0 0 1 3563 235877719 235881281 0.000000e+00 6580.0
1 TraesCS3B01G201600 chr3D 94.438 2715 93 24 869 3563 158449708 158452384 0.000000e+00 4124.0
2 TraesCS3B01G201600 chr3D 92.227 669 51 1 1 668 158448601 158449269 0.000000e+00 946.0
3 TraesCS3B01G201600 chr3D 86.449 428 57 1 12 439 347306246 347305820 5.390000e-128 468.0
4 TraesCS3B01G201600 chr3A 95.190 1393 61 4 917 2308 169291477 169290090 0.000000e+00 2196.0
5 TraesCS3B01G201600 chr3A 90.775 748 44 6 2309 3051 169234195 169233468 0.000000e+00 976.0
6 TraesCS3B01G201600 chr3A 90.775 748 44 6 2309 3051 169273795 169273068 0.000000e+00 976.0
7 TraesCS3B01G201600 chr3A 90.836 742 43 6 2315 3051 169254226 169253505 0.000000e+00 970.0
8 TraesCS3B01G201600 chr3A 87.628 784 81 7 1 771 169293870 169293090 0.000000e+00 896.0
9 TraesCS3B01G201600 chr3A 93.574 249 11 4 3320 3563 169233236 169232988 2.020000e-97 366.0
10 TraesCS3B01G201600 chr3A 93.574 249 11 4 3320 3563 169253273 169253025 2.020000e-97 366.0
11 TraesCS3B01G201600 chr3A 93.574 249 11 4 3320 3563 169272836 169272588 2.020000e-97 366.0
12 TraesCS3B01G201600 chr3A 93.506 154 6 4 3056 3206 169272980 169272828 3.580000e-55 226.0
13 TraesCS3B01G201600 chr3A 92.208 154 8 4 3056 3206 169233380 169233228 7.750000e-52 215.0
14 TraesCS3B01G201600 chr3A 92.208 154 8 4 3056 3206 169253417 169253265 7.750000e-52 215.0
15 TraesCS3B01G201600 chr3A 93.478 92 5 1 812 902 169293098 169293007 6.200000e-28 135.0
16 TraesCS3B01G201600 chr3A 97.297 37 1 0 767 803 732049009 732048973 2.970000e-06 63.9
17 TraesCS3B01G201600 chr4B 96.059 203 7 1 141 343 655483251 655483452 2.650000e-86 329.0
18 TraesCS3B01G201600 chr4B 88.462 52 2 4 768 818 71706754 71706802 3.840000e-05 60.2
19 TraesCS3B01G201600 chr7B 97.561 41 1 0 769 809 134549762 134549802 1.770000e-08 71.3
20 TraesCS3B01G201600 chr7B 95.238 42 2 0 768 809 523605263 523605222 2.300000e-07 67.6
21 TraesCS3B01G201600 chr4A 97.500 40 1 0 770 809 19508005 19508044 6.380000e-08 69.4
22 TraesCS3B01G201600 chr2A 93.333 45 2 1 766 809 8327877 8327921 8.260000e-07 65.8
23 TraesCS3B01G201600 chr1B 95.122 41 2 0 769 809 658396425 658396385 8.260000e-07 65.8
24 TraesCS3B01G201600 chr1A 93.182 44 3 0 766 809 137925138 137925181 8.260000e-07 65.8
25 TraesCS3B01G201600 chr2D 89.583 48 4 1 767 814 563801973 563801927 3.840000e-05 60.2


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 TraesCS3B01G201600 chr3B 235877719 235881281 3562 False 6580.000000 6580 100.000000 1 3563 1 chr3B.!!$F1 3562
1 TraesCS3B01G201600 chr3D 158448601 158452384 3783 False 2535.000000 4124 93.332500 1 3563 2 chr3D.!!$F1 3562
2 TraesCS3B01G201600 chr3A 169290090 169293870 3780 True 1075.666667 2196 92.098667 1 2308 3 chr3A.!!$R5 2307
3 TraesCS3B01G201600 chr3A 169272588 169273795 1207 True 522.666667 976 92.618333 2309 3563 3 chr3A.!!$R4 1254
4 TraesCS3B01G201600 chr3A 169232988 169234195 1207 True 519.000000 976 92.185667 2309 3563 3 chr3A.!!$R2 1254
5 TraesCS3B01G201600 chr3A 169253025 169254226 1201 True 517.000000 970 92.206000 2315 3563 3 chr3A.!!$R3 1248

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
778 804 0.258194 TCCGAGGAACTACTCCCTCC 59.742 60.0 0.0 0.0 46.81 4.30 F
780 806 0.394080 CGAGGAACTACTCCCTCCGT 60.394 60.0 0.0 0.0 46.81 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 3837 0.594602 TGTAGTCACCACGGTCTTCG 59.405 55.000 0.00 0.0 45.88 3.79 R
2723 4614 1.628846 AGCTTACCGATGGGTCAACTT 59.371 47.619 1.19 0.0 46.01 2.66 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
92 93 2.955660 TCAAACTGCCTTGTTAACAGGG 59.044 45.455 27.81 27.81 44.99 4.45
93 94 2.693074 CAAACTGCCTTGTTAACAGGGT 59.307 45.455 30.73 14.09 44.15 4.34
94 95 2.748209 ACTGCCTTGTTAACAGGGTT 57.252 45.000 30.73 16.94 44.15 4.11
103 104 6.072838 GCCTTGTTAACAGGGTTTAAGTAGAC 60.073 42.308 30.73 11.84 44.15 2.59
105 106 7.499895 CCTTGTTAACAGGGTTTAAGTAGACAA 59.500 37.037 24.80 0.00 38.21 3.18
125 126 4.581824 ACAACAATGCTCTTTGTCTGTGAT 59.418 37.500 2.31 0.00 38.85 3.06
143 144 5.888412 GTGATGACACAACAAAATCAACC 57.112 39.130 0.00 0.00 45.32 3.77
202 203 9.492973 AAATTCGAATTTGACATGGAATTCTTT 57.507 25.926 30.13 5.59 39.14 2.52
215 216 1.234615 ATTCTTTGACCACCGTGCCG 61.235 55.000 0.00 0.00 0.00 5.69
251 252 6.824704 TCAAGACTGCATTGACATCATTGATA 59.175 34.615 0.00 0.00 31.86 2.15
254 255 8.234136 AGACTGCATTGACATCATTGATAAAT 57.766 30.769 0.00 0.00 31.01 1.40
343 344 7.224557 AGTGAAACATAATTTGTGGCAAGAAAC 59.775 33.333 0.00 0.00 41.43 2.78
371 372 4.522405 CGGATAGATCTCCAGTGACTTGAT 59.478 45.833 0.00 0.00 34.78 2.57
476 477 8.600449 AGATGCTTGAGATTACAAGTTATAGC 57.400 34.615 0.00 0.00 45.98 2.97
496 497 7.981102 ATAGCTGTACTCGACTGTATATCAA 57.019 36.000 0.00 0.00 0.00 2.57
531 532 6.817765 TTTGACATACATTTGGAAGGTCTC 57.182 37.500 0.00 0.00 0.00 3.36
544 545 3.688185 GGAAGGTCTCCCAATTTAACGTC 59.312 47.826 0.00 0.00 38.44 4.34
548 549 3.933332 GGTCTCCCAATTTAACGTCTGAG 59.067 47.826 0.00 0.00 0.00 3.35
560 561 0.800300 CGTCTGAGCTCGCCTTCTTC 60.800 60.000 9.64 0.00 0.00 2.87
603 605 1.202110 GGTCTGATGATGTGCTTTGCG 60.202 52.381 0.00 0.00 0.00 4.85
618 620 0.966875 TTGCGCATTTGATGGCTCCT 60.967 50.000 12.75 0.00 0.00 3.69
622 624 1.266175 CGCATTTGATGGCTCCTCATC 59.734 52.381 0.00 0.00 42.72 2.92
668 670 7.786943 AGTCAGAGTTCCTCCAAGATTATATGA 59.213 37.037 0.00 0.00 0.00 2.15
697 699 9.503427 CTCCCTCTGTAAATTAAAATAAAAGCG 57.497 33.333 0.00 0.00 0.00 4.68
750 776 7.893124 TTAACTGCTAGTAGTAGGCATTACT 57.107 36.000 14.28 5.59 44.71 2.24
753 779 6.363065 ACTGCTAGTAGTAGGCATTACTGTA 58.637 40.000 18.16 0.00 42.57 2.74
771 797 6.880942 ACTGTAGATAATCCGAGGAACTAC 57.119 41.667 15.24 15.24 41.55 2.73
773 799 6.711645 ACTGTAGATAATCCGAGGAACTACTC 59.288 42.308 19.07 0.00 41.55 2.59
774 800 6.002704 TGTAGATAATCCGAGGAACTACTCC 58.997 44.000 19.07 0.00 41.55 3.85
775 801 4.409187 AGATAATCCGAGGAACTACTCCC 58.591 47.826 0.00 0.00 46.81 4.30
776 802 2.850695 AATCCGAGGAACTACTCCCT 57.149 50.000 0.00 0.00 46.81 4.20
777 803 2.368311 ATCCGAGGAACTACTCCCTC 57.632 55.000 0.00 0.00 46.81 4.30
778 804 0.258194 TCCGAGGAACTACTCCCTCC 59.742 60.000 0.00 0.00 46.81 4.30
779 805 1.102222 CCGAGGAACTACTCCCTCCG 61.102 65.000 0.00 0.00 46.81 4.63
780 806 0.394080 CGAGGAACTACTCCCTCCGT 60.394 60.000 0.00 0.00 46.81 4.69
781 807 1.849977 GAGGAACTACTCCCTCCGTT 58.150 55.000 0.00 0.00 46.81 4.44
782 808 2.177734 GAGGAACTACTCCCTCCGTTT 58.822 52.381 0.00 0.00 46.81 3.60
783 809 2.166050 GAGGAACTACTCCCTCCGTTTC 59.834 54.545 0.00 0.00 46.81 2.78
784 810 1.897802 GGAACTACTCCCTCCGTTTCA 59.102 52.381 0.00 0.00 38.44 2.69
785 811 2.500504 GGAACTACTCCCTCCGTTTCAT 59.499 50.000 0.00 0.00 38.44 2.57
786 812 3.703052 GGAACTACTCCCTCCGTTTCATA 59.297 47.826 0.00 0.00 38.44 2.15
787 813 4.161001 GGAACTACTCCCTCCGTTTCATAA 59.839 45.833 0.00 0.00 38.44 1.90
788 814 5.163332 GGAACTACTCCCTCCGTTTCATAAT 60.163 44.000 0.00 0.00 38.44 1.28
789 815 6.041296 GGAACTACTCCCTCCGTTTCATAATA 59.959 42.308 0.00 0.00 38.44 0.98
790 816 7.256225 GGAACTACTCCCTCCGTTTCATAATAT 60.256 40.741 0.00 0.00 38.44 1.28
791 817 8.716674 AACTACTCCCTCCGTTTCATAATATA 57.283 34.615 0.00 0.00 0.00 0.86
792 818 8.716674 ACTACTCCCTCCGTTTCATAATATAA 57.283 34.615 0.00 0.00 0.00 0.98
793 819 8.804204 ACTACTCCCTCCGTTTCATAATATAAG 58.196 37.037 0.00 0.00 0.00 1.73
794 820 7.850935 ACTCCCTCCGTTTCATAATATAAGA 57.149 36.000 0.00 0.00 0.00 2.10
795 821 8.258850 ACTCCCTCCGTTTCATAATATAAGAA 57.741 34.615 0.00 0.00 0.00 2.52
796 822 8.881262 ACTCCCTCCGTTTCATAATATAAGAAT 58.119 33.333 0.00 0.00 0.00 2.40
797 823 9.155975 CTCCCTCCGTTTCATAATATAAGAATG 57.844 37.037 0.00 0.00 0.00 2.67
798 824 8.656806 TCCCTCCGTTTCATAATATAAGAATGT 58.343 33.333 0.00 0.00 0.00 2.71
799 825 9.284968 CCCTCCGTTTCATAATATAAGAATGTT 57.715 33.333 0.00 0.00 0.00 2.71
812 838 6.899393 ATAAGAATGTTTTTGGCACTCAGA 57.101 33.333 0.00 0.00 0.00 3.27
813 839 4.843220 AGAATGTTTTTGGCACTCAGAG 57.157 40.909 0.00 0.00 0.00 3.35
814 840 3.571401 AGAATGTTTTTGGCACTCAGAGG 59.429 43.478 1.53 0.00 0.00 3.69
815 841 1.691196 TGTTTTTGGCACTCAGAGGG 58.309 50.000 1.53 0.00 0.00 4.30
816 842 1.214175 TGTTTTTGGCACTCAGAGGGA 59.786 47.619 2.91 0.00 0.00 4.20
872 1214 0.830648 TGGGAGGTCCGATTGATGTC 59.169 55.000 0.00 0.00 38.76 3.06
906 1249 2.259618 ACGTGAGACGATTTGATTCGG 58.740 47.619 2.62 0.00 46.05 4.30
912 1255 0.748005 ACGATTTGATTCGGCCAGGG 60.748 55.000 2.24 0.00 43.33 4.45
913 1256 1.735973 GATTTGATTCGGCCAGGGC 59.264 57.895 2.24 1.81 41.06 5.19
998 2856 0.615850 CCCTCTTTCCTTCCGCTTCT 59.384 55.000 0.00 0.00 0.00 2.85
1087 2965 4.373116 CACCACCCCGACCACGAG 62.373 72.222 0.00 0.00 42.66 4.18
1090 2968 4.308458 CACCCCGACCACGAGCAA 62.308 66.667 0.00 0.00 42.66 3.91
1091 2969 4.003788 ACCCCGACCACGAGCAAG 62.004 66.667 0.00 0.00 42.66 4.01
1092 2970 3.691342 CCCCGACCACGAGCAAGA 61.691 66.667 0.00 0.00 42.66 3.02
1093 2971 2.432628 CCCGACCACGAGCAAGAC 60.433 66.667 0.00 0.00 42.66 3.01
1094 2972 2.338620 CCGACCACGAGCAAGACA 59.661 61.111 0.00 0.00 42.66 3.41
1095 2973 1.300620 CCGACCACGAGCAAGACAA 60.301 57.895 0.00 0.00 42.66 3.18
1096 2974 1.557443 CCGACCACGAGCAAGACAAC 61.557 60.000 0.00 0.00 42.66 3.32
1097 2975 1.557443 CGACCACGAGCAAGACAACC 61.557 60.000 0.00 0.00 42.66 3.77
1098 2976 1.557443 GACCACGAGCAAGACAACCG 61.557 60.000 0.00 0.00 0.00 4.44
1099 2977 2.317609 CCACGAGCAAGACAACCGG 61.318 63.158 0.00 0.00 0.00 5.28
1100 2978 1.300620 CACGAGCAAGACAACCGGA 60.301 57.895 9.46 0.00 0.00 5.14
1101 2979 1.300697 ACGAGCAAGACAACCGGAC 60.301 57.895 9.46 0.00 0.00 4.79
1102 2980 1.300620 CGAGCAAGACAACCGGACA 60.301 57.895 9.46 0.00 0.00 4.02
1426 3304 2.558554 AATTCGACTCTGGCGACCGG 62.559 60.000 0.00 0.00 37.52 5.28
1465 3343 2.535331 GAGTTCATGAGGAAGAGCGAC 58.465 52.381 0.00 0.00 35.82 5.19
1491 3369 2.884207 GTCGCCTTACCTTCGCGG 60.884 66.667 6.13 0.00 45.74 6.46
1492 3370 4.807039 TCGCCTTACCTTCGCGGC 62.807 66.667 6.13 0.00 45.74 6.53
1549 3436 2.033448 ACGGAAGCGCCCAAATCA 59.967 55.556 2.29 0.00 0.00 2.57
1554 3441 1.066929 GGAAGCGCCCAAATCATTTGT 60.067 47.619 2.29 0.00 38.98 2.83
1623 3510 1.979155 GGCAAGGGAAAGAGGGCAC 60.979 63.158 0.00 0.00 0.00 5.01
1823 3710 1.139520 GATTCGTTGCCCACCATGC 59.860 57.895 0.00 0.00 0.00 4.06
1973 3860 0.666577 GACCGTGGTGACTACACTGC 60.667 60.000 0.00 0.00 45.32 4.40
2076 3963 7.348011 TGATATAATAGCAAGCCAGGGATATGA 59.652 37.037 0.00 0.00 0.00 2.15
2171 4058 4.525487 AGTCTTCATTTCACATTGGCATGT 59.475 37.500 0.00 0.00 45.18 3.21
2479 4366 1.879380 CAAAATGCGACAAGAGTGGGA 59.121 47.619 0.00 0.00 0.00 4.37
2578 4469 7.165154 CACATTTTCGAACTCGTGTTGTAAAAT 59.835 33.333 17.76 17.76 37.46 1.82
2631 4522 3.552890 GCACTGGAAGGTGTTCAATTTCC 60.553 47.826 8.62 8.62 39.30 3.13
2632 4523 3.891366 CACTGGAAGGTGTTCAATTTCCT 59.109 43.478 13.69 0.00 39.80 3.36
2636 4527 4.058124 GGAAGGTGTTCAATTTCCTTTGC 58.942 43.478 0.00 0.00 39.91 3.68
2722 4613 8.690203 TGAAAAGTTGAGACTGAATCCATAAA 57.310 30.769 0.00 0.00 35.91 1.40
2723 4614 9.130661 TGAAAAGTTGAGACTGAATCCATAAAA 57.869 29.630 0.00 0.00 35.91 1.52
2750 4641 5.258051 TGACCCATCGGTAAGCTTTTAATT 58.742 37.500 3.20 0.00 44.88 1.40
2870 4763 3.377172 GGTACATCACAGTATTGGGCAAC 59.623 47.826 0.00 0.00 0.00 4.17
3052 4945 5.545658 TCATTTTGATACAGAAGGAACGC 57.454 39.130 0.00 0.00 0.00 4.84
3175 5154 1.499056 GTGCATGTCAGGCAAGTCG 59.501 57.895 14.68 0.00 43.91 4.18
3226 5205 8.802267 TGATTTCTGTTCCCTTTAATTTGTAGG 58.198 33.333 0.00 0.00 0.00 3.18
3248 5227 2.310930 TTTGGGGCAGGGAAGCAACT 62.311 55.000 0.00 0.00 35.83 3.16
3255 5234 2.620585 GGCAGGGAAGCAACTGAATATC 59.379 50.000 0.00 0.00 36.86 1.63
3390 5374 5.988561 GCAAGTCATTCTCACCTTAGGATAG 59.011 44.000 4.77 1.53 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.147704 TGGATATTGAAAGCATATCACGTCTAA 58.852 33.333 0.00 0.00 0.00 2.10
92 93 8.129211 ACAAAGAGCATTGTTGTCTACTTAAAC 58.871 33.333 0.00 0.00 40.52 2.01
93 94 8.220755 ACAAAGAGCATTGTTGTCTACTTAAA 57.779 30.769 0.00 0.00 40.52 1.52
94 95 7.801716 ACAAAGAGCATTGTTGTCTACTTAA 57.198 32.000 0.00 0.00 40.52 1.85
103 104 4.556942 TCACAGACAAAGAGCATTGTTG 57.443 40.909 4.38 7.10 43.31 3.33
105 106 4.214971 GTCATCACAGACAAAGAGCATTGT 59.785 41.667 2.66 2.66 45.82 2.71
125 126 3.766591 ACTGGGTTGATTTTGTTGTGTCA 59.233 39.130 0.00 0.00 0.00 3.58
143 144 5.282055 TGGCTACTCATCTCAATAACTGG 57.718 43.478 0.00 0.00 0.00 4.00
215 216 4.836125 TGCAGTCTTGAGAAATTTCCAC 57.164 40.909 14.61 9.82 0.00 4.02
343 344 1.815613 ACTGGAGATCTATCCGCGATG 59.184 52.381 8.23 0.00 42.77 3.84
371 372 4.479158 AGATTTCAAGGGCCAGTGTTTTA 58.521 39.130 6.18 0.00 0.00 1.52
436 437 4.585955 AGCATCTATATTCCGTTGACGT 57.414 40.909 2.63 0.00 37.74 4.34
531 532 2.348666 CGAGCTCAGACGTTAAATTGGG 59.651 50.000 15.40 0.00 0.00 4.12
544 545 2.020720 TCTAGAAGAAGGCGAGCTCAG 58.979 52.381 15.40 7.85 0.00 3.35
548 549 3.444703 TCAATCTAGAAGAAGGCGAGC 57.555 47.619 0.00 0.00 0.00 5.03
603 605 2.293677 CAGATGAGGAGCCATCAAATGC 59.706 50.000 0.00 0.00 43.99 3.56
622 624 9.645059 TCTGACTTCTCATATTCAGTTTTACAG 57.355 33.333 0.00 0.00 37.38 2.74
693 695 8.414003 TGTGAATATCTAGTGATCTAAACGCTT 58.586 33.333 0.00 0.00 34.32 4.68
695 697 8.575565 TTGTGAATATCTAGTGATCTAAACGC 57.424 34.615 0.00 0.00 34.32 4.84
732 758 7.690952 ATCTACAGTAATGCCTACTACTAGC 57.309 40.000 0.00 0.00 38.92 3.42
750 776 6.002704 GGAGTAGTTCCTCGGATTATCTACA 58.997 44.000 14.33 0.00 43.16 2.74
753 779 4.106663 AGGGAGTAGTTCCTCGGATTATCT 59.893 45.833 0.00 0.00 45.98 1.98
771 797 9.155975 CATTCTTATATTATGAAACGGAGGGAG 57.844 37.037 0.00 0.00 0.00 4.30
773 799 8.848474 ACATTCTTATATTATGAAACGGAGGG 57.152 34.615 0.00 0.00 0.00 4.30
786 812 9.023962 TCTGAGTGCCAAAAACATTCTTATATT 57.976 29.630 0.00 0.00 0.00 1.28
787 813 8.579850 TCTGAGTGCCAAAAACATTCTTATAT 57.420 30.769 0.00 0.00 0.00 0.86
788 814 7.121168 CCTCTGAGTGCCAAAAACATTCTTATA 59.879 37.037 3.66 0.00 0.00 0.98
789 815 6.071728 CCTCTGAGTGCCAAAAACATTCTTAT 60.072 38.462 3.66 0.00 0.00 1.73
790 816 5.241506 CCTCTGAGTGCCAAAAACATTCTTA 59.758 40.000 3.66 0.00 0.00 2.10
791 817 4.038402 CCTCTGAGTGCCAAAAACATTCTT 59.962 41.667 3.66 0.00 0.00 2.52
792 818 3.571401 CCTCTGAGTGCCAAAAACATTCT 59.429 43.478 3.66 0.00 0.00 2.40
793 819 3.305608 CCCTCTGAGTGCCAAAAACATTC 60.306 47.826 3.66 0.00 0.00 2.67
794 820 2.629617 CCCTCTGAGTGCCAAAAACATT 59.370 45.455 3.66 0.00 0.00 2.71
795 821 2.158475 TCCCTCTGAGTGCCAAAAACAT 60.158 45.455 3.66 0.00 0.00 2.71
796 822 1.214175 TCCCTCTGAGTGCCAAAAACA 59.786 47.619 3.66 0.00 0.00 2.83
797 823 1.882623 CTCCCTCTGAGTGCCAAAAAC 59.117 52.381 3.66 0.00 36.27 2.43
798 824 2.276732 CTCCCTCTGAGTGCCAAAAA 57.723 50.000 3.66 0.00 36.27 1.94
808 834 3.005472 CGACAAACAACTACTCCCTCTGA 59.995 47.826 0.00 0.00 0.00 3.27
809 835 3.243771 ACGACAAACAACTACTCCCTCTG 60.244 47.826 0.00 0.00 0.00 3.35
810 836 2.963782 ACGACAAACAACTACTCCCTCT 59.036 45.455 0.00 0.00 0.00 3.69
811 837 3.315418 GACGACAAACAACTACTCCCTC 58.685 50.000 0.00 0.00 0.00 4.30
812 838 2.288030 CGACGACAAACAACTACTCCCT 60.288 50.000 0.00 0.00 0.00 4.20
813 839 2.056577 CGACGACAAACAACTACTCCC 58.943 52.381 0.00 0.00 0.00 4.30
814 840 2.056577 CCGACGACAAACAACTACTCC 58.943 52.381 0.00 0.00 0.00 3.85
815 841 2.470257 CACCGACGACAAACAACTACTC 59.530 50.000 0.00 0.00 0.00 2.59
816 842 2.466846 CACCGACGACAAACAACTACT 58.533 47.619 0.00 0.00 0.00 2.57
817 843 1.071041 GCACCGACGACAAACAACTAC 60.071 52.381 0.00 0.00 0.00 2.73
818 844 1.210870 GCACCGACGACAAACAACTA 58.789 50.000 0.00 0.00 0.00 2.24
819 845 1.433837 GGCACCGACGACAAACAACT 61.434 55.000 0.00 0.00 0.00 3.16
820 846 1.010462 GGCACCGACGACAAACAAC 60.010 57.895 0.00 0.00 0.00 3.32
821 847 1.433053 CTGGCACCGACGACAAACAA 61.433 55.000 0.00 0.00 0.00 2.83
822 848 1.885388 CTGGCACCGACGACAAACA 60.885 57.895 0.00 0.00 0.00 2.83
872 1214 0.945265 TCACGTCCCGTTAAAAGCCG 60.945 55.000 0.00 0.00 38.32 5.52
912 1255 1.144936 CCAGGAATCCGAGTCCAGC 59.855 63.158 16.91 0.00 37.65 4.85
913 1256 1.826024 CCCAGGAATCCGAGTCCAG 59.174 63.158 16.91 8.86 37.65 3.86
998 2856 2.766651 GTATGGAGGGTGGGCCGA 60.767 66.667 0.00 0.00 34.97 5.54
1021 2880 9.524496 TTCTTAGGGTTTCTTATTAGGGTTTTC 57.476 33.333 0.00 0.00 0.00 2.29
1084 2962 0.878523 TTGTCCGGTTGTCTTGCTCG 60.879 55.000 0.00 0.00 0.00 5.03
1085 2963 0.586802 GTTGTCCGGTTGTCTTGCTC 59.413 55.000 0.00 0.00 0.00 4.26
1086 2964 1.157870 CGTTGTCCGGTTGTCTTGCT 61.158 55.000 0.00 0.00 0.00 3.91
1087 2965 1.278637 CGTTGTCCGGTTGTCTTGC 59.721 57.895 0.00 0.00 0.00 4.01
1099 2977 2.813908 ATCGCCGCTTCCGTTGTC 60.814 61.111 0.00 0.00 0.00 3.18
1100 2978 3.118454 CATCGCCGCTTCCGTTGT 61.118 61.111 0.00 0.00 0.00 3.32
1101 2979 3.864686 CCATCGCCGCTTCCGTTG 61.865 66.667 0.00 0.00 0.00 4.10
1426 3304 3.195698 GGATGGCCGAAGCACGTC 61.196 66.667 0.00 0.00 42.56 4.34
1517 3395 1.485124 TCCGTGCAGATAGTGATGGT 58.515 50.000 0.00 0.00 0.00 3.55
1549 3436 0.031994 GCAACGGCACCTCAACAAAT 59.968 50.000 0.00 0.00 40.72 2.32
1690 3577 0.763035 ACTCTGCCTTAAACACCGGT 59.237 50.000 0.00 0.00 0.00 5.28
1891 3778 4.774124 TCTTCAGTCTTTCCATGGCATAG 58.226 43.478 6.96 4.03 0.00 2.23
1949 3836 0.877071 GTAGTCACCACGGTCTTCGA 59.123 55.000 0.00 0.00 42.43 3.71
1950 3837 0.594602 TGTAGTCACCACGGTCTTCG 59.405 55.000 0.00 0.00 45.88 3.79
2076 3963 3.073650 AGGACAGGTTCTTTTGAGCTCAT 59.926 43.478 19.04 0.00 0.00 2.90
2243 4130 5.001232 GCAGAGTAATACTGTTTTCCACCA 58.999 41.667 0.00 0.00 37.64 4.17
2479 4366 9.330063 CATATAATCACATTAACACACTCCTGT 57.670 33.333 0.00 0.00 0.00 4.00
2516 4403 7.857569 TCCCGTTTCGAATTTCATATTATGAC 58.142 34.615 5.86 0.00 39.39 3.06
2578 4469 6.865834 ATTGTTTCAAATGCACCCCTATTA 57.134 33.333 0.00 0.00 0.00 0.98
2631 4522 4.580580 AGAACAGAAAAGTACCTGGCAAAG 59.419 41.667 0.00 0.00 34.85 2.77
2632 4523 4.532834 AGAACAGAAAAGTACCTGGCAAA 58.467 39.130 0.00 0.00 34.85 3.68
2636 4527 3.882888 TGCAAGAACAGAAAAGTACCTGG 59.117 43.478 0.00 0.00 34.85 4.45
2689 4580 9.793259 ATTCAGTCTCAACTTTTCAGGTAATAA 57.207 29.630 0.00 0.00 31.71 1.40
2690 4581 9.436957 GATTCAGTCTCAACTTTTCAGGTAATA 57.563 33.333 0.00 0.00 31.71 0.98
2691 4582 7.391833 GGATTCAGTCTCAACTTTTCAGGTAAT 59.608 37.037 0.00 0.00 31.71 1.89
2722 4613 2.039879 AGCTTACCGATGGGTCAACTTT 59.960 45.455 1.19 0.00 46.01 2.66
2723 4614 1.628846 AGCTTACCGATGGGTCAACTT 59.371 47.619 1.19 0.00 46.01 2.66
2794 4686 6.009589 TGATGTGGTGGTACTCAATCATTTT 58.990 36.000 0.00 0.00 0.00 1.82
2795 4687 5.569355 TGATGTGGTGGTACTCAATCATTT 58.431 37.500 0.00 0.00 0.00 2.32
2870 4763 8.043113 TCAAAGTAATAGCATGATATAGGCCAG 58.957 37.037 5.01 0.00 36.57 4.85
3148 5126 1.608055 CTGACATGCACCAAGTTCCA 58.392 50.000 0.00 0.00 0.00 3.53
3175 5154 8.674607 CACCTCTGTAAATAACAACTAAATCCC 58.325 37.037 0.00 0.00 37.74 3.85
3226 5205 0.904394 TGCTTCCCTGCCCCAAATTC 60.904 55.000 0.00 0.00 0.00 2.17
3344 5323 4.261322 GCAATCCTGCTTGGTACATACATG 60.261 45.833 0.00 0.00 45.74 3.21
3374 5358 9.310449 GGTATGAATACTATCCTAAGGTGAGAA 57.690 37.037 0.75 0.00 33.81 2.87


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

AutoCloner maintained by Alex Coulton.