Multiple sequence alignment - TraesCS4B01G199800

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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 TraesCS4B01G199800 chr4B 100.000 7187 0 0 1 7187 428198337 428205523 0.000000e+00 13272.0
1 TraesCS4B01G199800 chr4D 95.974 5663 161 25 662 6289 348042256 348047886 0.000000e+00 9132.0
2 TraesCS4B01G199800 chr4D 93.388 605 33 5 6583 7187 348048273 348048870 0.000000e+00 889.0
3 TraesCS4B01G199800 chr4D 94.433 467 22 2 2 468 348041416 348041878 0.000000e+00 715.0
4 TraesCS4B01G199800 chr4D 95.779 308 8 3 6283 6590 348047910 348048212 6.480000e-135 492.0
5 TraesCS4B01G199800 chr4D 89.167 120 3 1 469 588 348042149 348042258 2.700000e-29 141.0
6 TraesCS4B01G199800 chr4A 94.607 4135 153 26 508 4606 117699018 117694918 0.000000e+00 6336.0
7 TraesCS4B01G199800 chr4A 96.692 1602 50 2 4698 6298 117694879 117693280 0.000000e+00 2662.0
8 TraesCS4B01G199800 chr4A 93.688 602 31 5 6586 7187 117692901 117692307 0.000000e+00 894.0
9 TraesCS4B01G199800 chr4A 93.548 310 15 3 6281 6590 117693269 117692965 2.360000e-124 457.0
10 TraesCS4B01G199800 chr4A 83.047 466 52 14 4 468 117699561 117699122 1.450000e-106 398.0
11 TraesCS4B01G199800 chr4A 96.703 91 3 0 4 94 629935227 629935137 1.250000e-32 152.0
12 TraesCS4B01G199800 chr4A 93.103 58 3 1 4659 4715 117694936 117694879 4.620000e-12 84.2
13 TraesCS4B01G199800 chr5D 79.932 877 168 7 2907 3779 295072632 295071760 7.860000e-179 638.0
14 TraesCS4B01G199800 chr5D 96.703 91 3 0 4 94 538686889 538686799 1.250000e-32 152.0
15 TraesCS4B01G199800 chr5B 79.932 877 168 7 2907 3779 336791965 336791093 7.860000e-179 638.0
16 TraesCS4B01G199800 chr5A 79.271 878 174 7 2906 3779 388641234 388640361 2.220000e-169 606.0
17 TraesCS4B01G199800 chr5A 96.703 91 3 0 4 94 78449169 78449079 1.250000e-32 152.0
18 TraesCS4B01G199800 chr7A 97.802 91 2 0 4 94 62735945 62735855 2.680000e-34 158.0
19 TraesCS4B01G199800 chr1D 96.703 91 3 0 4 94 80674428 80674338 1.250000e-32 152.0
20 TraesCS4B01G199800 chr6B 95.604 91 4 0 4 94 672729515 672729425 5.810000e-31 147.0
21 TraesCS4B01G199800 chr1A 95.506 89 4 0 6 94 80284068 80284156 7.520000e-30 143.0


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 TraesCS4B01G199800 chr4B 428198337 428205523 7186 False 13272.0 13272 100.0000 1 7187 1 chr4B.!!$F1 7186
1 TraesCS4B01G199800 chr4D 348041416 348048870 7454 False 2273.8 9132 93.7482 2 7187 5 chr4D.!!$F1 7185
2 TraesCS4B01G199800 chr4A 117692307 117699561 7254 True 1805.2 6336 92.4475 4 7187 6 chr4A.!!$R2 7183
3 TraesCS4B01G199800 chr5D 295071760 295072632 872 True 638.0 638 79.9320 2907 3779 1 chr5D.!!$R1 872
4 TraesCS4B01G199800 chr5B 336791093 336791965 872 True 638.0 638 79.9320 2907 3779 1 chr5B.!!$R1 872
5 TraesCS4B01G199800 chr5A 388640361 388641234 873 True 606.0 606 79.2710 2906 3779 1 chr5A.!!$R2 873

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
638 930 0.109458 GGTTTGCGGGATTTTCGGAC 60.109 55.000 0.0 0.0 0.00 4.79 F
1661 1977 0.248702 GATCTCTCGTCTGGGTTCGC 60.249 60.000 0.0 0.0 0.00 4.70 F
2069 2419 3.810896 GCGGGATTGGCAACGGAC 61.811 66.667 0.0 0.0 42.51 4.79 F
2923 3282 0.681564 AGCAGCTAGGTAGACGTGCT 60.682 55.000 0.0 0.0 36.44 4.40 F
4066 4427 1.267932 GCATTGATTCTGACGCTCTGC 60.268 52.381 0.0 0.0 0.00 4.26 F
4302 4663 1.301423 GGGCGTACAAAGTTCACACA 58.699 50.000 0.0 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2598 2956 2.409378 GCATTTCAGGTTTTGCATGTCG 59.591 45.455 0.00 0.0 35.22 4.35 R
2707 3066 3.209410 AGCTTGACAAGTCCAGAACAAG 58.791 45.455 16.39 0.0 38.07 3.16 R
3802 4161 1.140312 TCCTTTGAGTGAAGTGGGCT 58.860 50.000 0.00 0.0 0.00 5.19 R
4302 4663 0.179045 AAGCACTTGAGCCGTGTCTT 60.179 50.000 0.00 0.0 34.91 3.01 R
5943 6331 0.037790 GCAGAACGCTCTTCACCTCT 60.038 55.000 0.00 0.0 37.77 3.69 R
6244 6632 0.459899 AGCACACACGTGAGAACTGA 59.540 50.000 25.01 0.0 46.80 3.41 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
138 139 5.871396 AAGACTTTGTGAAGAGGTAGTCA 57.129 39.130 0.00 0.00 35.61 3.41
154 155 2.264480 CACCGTTGAGGCCGATGA 59.736 61.111 0.00 0.00 46.52 2.92
195 196 2.573915 GGAAGTGAAGGAGGACAAGGAT 59.426 50.000 0.00 0.00 0.00 3.24
254 255 0.538118 TGGGTGACGTGGTAATAGGC 59.462 55.000 0.00 0.00 0.00 3.93
286 288 2.203209 CGGGCCAGGGCTACAATC 60.203 66.667 13.81 0.00 41.60 2.67
288 290 2.689691 GGGCCAGGGCTACAATCCA 61.690 63.158 13.81 0.00 41.60 3.41
298 300 3.343617 GGCTACAATCCAGTGCACTTTA 58.656 45.455 18.94 8.65 0.00 1.85
424 426 1.003839 GCGAACACATCCAGGTCCA 60.004 57.895 0.00 0.00 0.00 4.02
436 438 2.040178 CCAGGTCCAGGTCCTACATAC 58.960 57.143 4.72 0.00 33.54 2.39
524 816 0.388659 ATGCGTGGTTGTGCAAATGT 59.611 45.000 0.00 0.00 45.45 2.71
525 817 0.248825 TGCGTGGTTGTGCAAATGTC 60.249 50.000 0.00 0.00 38.34 3.06
529 821 1.039068 TGGTTGTGCAAATGTCCAGG 58.961 50.000 0.00 0.00 0.00 4.45
594 886 1.814169 GGCGGATGTCGAAACTCCC 60.814 63.158 0.00 0.00 42.43 4.30
595 887 1.814169 GCGGATGTCGAAACTCCCC 60.814 63.158 0.00 0.00 42.43 4.81
606 898 2.738964 CGAAACTCCCCGAAATCTCCTC 60.739 54.545 0.00 0.00 0.00 3.71
608 900 3.399952 AACTCCCCGAAATCTCCTCTA 57.600 47.619 0.00 0.00 0.00 2.43
610 902 3.721021 ACTCCCCGAAATCTCCTCTAAA 58.279 45.455 0.00 0.00 0.00 1.85
616 908 5.471456 CCCCGAAATCTCCTCTAAATTGATG 59.529 44.000 0.00 0.00 0.00 3.07
619 911 6.074088 CCGAAATCTCCTCTAAATTGATGTCG 60.074 42.308 0.00 0.00 41.69 4.35
625 917 4.394920 TCCTCTAAATTGATGTCGGTTTGC 59.605 41.667 0.00 0.00 0.00 3.68
633 925 1.201414 GATGTCGGTTTGCGGGATTTT 59.799 47.619 0.00 0.00 0.00 1.82
634 926 0.594110 TGTCGGTTTGCGGGATTTTC 59.406 50.000 0.00 0.00 0.00 2.29
638 930 0.109458 GGTTTGCGGGATTTTCGGAC 60.109 55.000 0.00 0.00 0.00 4.79
642 934 2.761195 GCGGGATTTTCGGACCAGC 61.761 63.158 0.00 0.00 37.66 4.85
645 937 1.090052 GGGATTTTCGGACCAGCTCG 61.090 60.000 0.00 0.00 0.00 5.03
701 993 0.589223 GCGTGAACCGTTCAATCCAA 59.411 50.000 15.52 0.00 42.15 3.53
708 1000 6.210078 GTGAACCGTTCAATCCAAACATTTA 58.790 36.000 15.52 0.00 42.15 1.40
712 1004 4.083217 CCGTTCAATCCAAACATTTACGGA 60.083 41.667 0.00 0.00 40.55 4.69
757 1049 1.209504 CCTGACCGCTCTAAAATGGGA 59.790 52.381 0.00 0.00 0.00 4.37
778 1070 1.024271 GGTGCTGAAGTTGCTCACAA 58.976 50.000 0.00 0.00 0.00 3.33
945 1259 1.755008 AACACACCCCAACCAACCG 60.755 57.895 0.00 0.00 0.00 4.44
951 1265 1.051556 ACCCCAACCAACCGCAAAAT 61.052 50.000 0.00 0.00 0.00 1.82
956 1270 1.984990 CAACCAACCGCAAAATCGATG 59.015 47.619 0.00 0.00 0.00 3.84
965 1279 2.598439 CGCAAAATCGATGAGCAGCTAC 60.598 50.000 14.69 0.00 0.00 3.58
968 1282 4.497006 GCAAAATCGATGAGCAGCTACAAT 60.497 41.667 0.00 0.00 0.00 2.71
982 1298 9.278734 GAGCAGCTACAATAATAAACAAAGAAC 57.721 33.333 0.00 0.00 0.00 3.01
1314 1630 1.139734 CTCCACATCCACCTCGACG 59.860 63.158 0.00 0.00 0.00 5.12
1317 1633 1.153823 CACATCCACCTCGACGTCC 60.154 63.158 10.58 0.00 0.00 4.79
1318 1634 1.304217 ACATCCACCTCGACGTCCT 60.304 57.895 10.58 0.00 0.00 3.85
1319 1635 0.898789 ACATCCACCTCGACGTCCTT 60.899 55.000 10.58 0.00 0.00 3.36
1326 1642 0.393267 CCTCGACGTCCTTCTCCTCT 60.393 60.000 10.58 0.00 0.00 3.69
1661 1977 0.248702 GATCTCTCGTCTGGGTTCGC 60.249 60.000 0.00 0.00 0.00 4.70
2069 2419 3.810896 GCGGGATTGGCAACGGAC 61.811 66.667 0.00 0.00 42.51 4.79
2113 2464 6.413783 TGGTATTCGGTTCTGCATATAAGA 57.586 37.500 0.00 0.00 0.00 2.10
2114 2465 6.455647 TGGTATTCGGTTCTGCATATAAGAG 58.544 40.000 0.00 0.00 0.00 2.85
2310 2665 8.450578 TCTGTGAACTGTCAAGAATAATTTGT 57.549 30.769 0.00 0.00 34.87 2.83
2316 2671 9.897744 GAACTGTCAAGAATAATTTGTCATTGA 57.102 29.630 0.00 0.00 0.00 2.57
2345 2700 4.494484 TCATGGACTTGTATCAGTCGTTG 58.506 43.478 0.00 0.00 43.78 4.10
2440 2798 5.582689 AGCAAGGCAATAATAACCTGAAC 57.417 39.130 0.00 0.00 32.92 3.18
2593 2951 7.359595 TCTTATTTTGTTGTGATTTCAGGTCG 58.640 34.615 0.00 0.00 0.00 4.79
2598 2956 5.856126 TGTTGTGATTTCAGGTCGTTATC 57.144 39.130 0.00 0.00 0.00 1.75
2707 3066 3.440522 GGAAGTTGGTAGGACATTCTTGC 59.559 47.826 0.00 0.00 0.00 4.01
2923 3282 0.681564 AGCAGCTAGGTAGACGTGCT 60.682 55.000 0.00 0.00 36.44 4.40
3317 3676 5.248640 AGAATGGTACTGTGGTTGATGAAG 58.751 41.667 0.00 0.00 0.00 3.02
3802 4161 8.682710 AGTTTAAACTGTGAATTGTTCTGCTTA 58.317 29.630 19.94 0.00 37.98 3.09
3805 4164 3.503748 ACTGTGAATTGTTCTGCTTAGCC 59.496 43.478 0.29 0.00 0.00 3.93
4066 4427 1.267932 GCATTGATTCTGACGCTCTGC 60.268 52.381 0.00 0.00 0.00 4.26
4302 4663 1.301423 GGGCGTACAAAGTTCACACA 58.699 50.000 0.00 0.00 0.00 3.72
4347 4708 3.925913 GCTGCTGACAAGTTAGAGAAGAG 59.074 47.826 0.00 0.00 0.00 2.85
4381 4742 3.206150 TGCAGTTGAAGACTTTCTGGAC 58.794 45.455 13.72 1.07 36.10 4.02
4741 5127 6.976349 TGATGCACGTTATAAACTACTAGTGG 59.024 38.462 5.39 4.89 0.00 4.00
4749 5136 9.846248 CGTTATAAACTACTAGTGGTGTACTTT 57.154 33.333 13.15 5.63 40.89 2.66
4882 5269 3.693807 TCATTGAATGCCAAGAGCTCTT 58.306 40.909 23.49 23.49 44.23 2.85
4915 5302 2.159114 TGCGCAATGCTGTATAGTCTGA 60.159 45.455 8.16 0.00 46.63 3.27
4939 5326 8.045507 TGATATCACTATAGAGTAACCCTACCG 58.954 40.741 6.78 0.00 33.32 4.02
4954 5341 3.446516 CCCTACCGCTATACCAGTATTCC 59.553 52.174 0.00 0.00 0.00 3.01
5111 5499 7.173218 TGCACTCTACTTTGGTTTCTGATTTAG 59.827 37.037 0.00 0.00 0.00 1.85
5119 5507 2.424956 GGTTTCTGATTTAGCAGCTGGG 59.575 50.000 17.12 0.00 35.86 4.45
5155 5543 7.329588 TCTACAGTATTATGTCTCGAAAGCA 57.670 36.000 0.00 0.00 34.56 3.91
5159 5547 8.268850 ACAGTATTATGTCTCGAAAGCAAAAT 57.731 30.769 0.00 0.00 0.00 1.82
5190 5578 5.363101 TGGTATGTCTGAGCATGAAGATTC 58.637 41.667 0.00 0.00 0.00 2.52
5196 5584 6.236409 TGTCTGAGCATGAAGATTCTTTTCT 58.764 36.000 0.00 0.00 0.00 2.52
5198 5586 6.370994 GTCTGAGCATGAAGATTCTTTTCTCA 59.629 38.462 0.00 9.54 0.00 3.27
5201 5589 8.206325 TGAGCATGAAGATTCTTTTCTCATAC 57.794 34.615 0.00 0.00 0.00 2.39
5301 5689 3.947196 TGCCTCATTTAACAAGATGCGAT 59.053 39.130 0.00 0.00 0.00 4.58
5404 5792 3.967886 TCGGAAGGATGCGATCTTC 57.032 52.632 0.00 4.73 44.89 2.87
5943 6331 2.158623 ACTGGTTGACAAGGCTTCATCA 60.159 45.455 0.00 1.19 0.00 3.07
6018 6406 2.505866 CGTTTCAAGCAAGCGATTACC 58.494 47.619 0.00 0.00 40.95 2.85
6052 6440 3.861840 TCTCCAACCAAATCTAGCTTCG 58.138 45.455 0.00 0.00 0.00 3.79
6147 6535 2.331893 CGATGAGGCGGCCACAAAA 61.332 57.895 22.69 0.00 0.00 2.44
6174 6562 5.534654 CCTCAAGAAAACATACAAGTTCCCA 59.465 40.000 0.00 0.00 0.00 4.37
6198 6586 6.382869 AAGAAGCTTTGATATGTGTATGCC 57.617 37.500 0.00 0.00 0.00 4.40
6208 6596 0.839277 TGTGTATGCCTGCTGCCTAT 59.161 50.000 0.00 0.00 40.16 2.57
6240 6628 7.957002 TGCAAAATTGAGGTAATAAGGAAACA 58.043 30.769 0.00 0.00 0.00 2.83
6254 6642 5.819825 AAGGAAACACTTTCAGTTCTCAC 57.180 39.130 0.00 0.00 41.43 3.51
6257 6645 4.494199 GGAAACACTTTCAGTTCTCACGTG 60.494 45.833 9.94 9.94 41.43 4.49
6289 6677 1.136252 CACGCTGATAAGTGTGTGTGC 60.136 52.381 14.78 0.00 43.14 4.57
6291 6679 0.179215 GCTGATAAGTGTGTGTGCGC 60.179 55.000 0.00 0.00 0.00 6.09
6342 6760 1.396996 CGATCCTGGCGTTTTTGTAGG 59.603 52.381 0.00 0.00 0.00 3.18
6412 6830 8.510243 AGTGAATAAGCACAATATGATCACAA 57.490 30.769 0.00 0.00 41.19 3.33
6458 6876 6.705863 AGAGGAAAGGATGATATGTTTTGC 57.294 37.500 0.00 0.00 0.00 3.68
6461 6879 4.202050 GGAAAGGATGATATGTTTTGCGCT 60.202 41.667 9.73 0.00 0.00 5.92
6462 6880 3.976793 AGGATGATATGTTTTGCGCTG 57.023 42.857 9.73 0.00 0.00 5.18
6463 6881 2.033801 AGGATGATATGTTTTGCGCTGC 59.966 45.455 9.73 0.00 0.00 5.25
6464 6882 2.223548 GGATGATATGTTTTGCGCTGCA 60.224 45.455 9.73 2.35 36.47 4.41
6497 6915 9.994432 CCTGTAATATCTGAGTTGTTTGAAATC 57.006 33.333 0.00 0.00 0.00 2.17
6525 6943 8.615878 TGCTACTTGTGTGTTCTTTTATATGT 57.384 30.769 0.00 0.00 0.00 2.29
6531 6949 7.043961 TGTGTGTTCTTTTATATGTTGGCAA 57.956 32.000 0.00 0.00 0.00 4.52
6618 7103 7.398024 ACTTACCAGAAGTCAGAAATAGCATT 58.602 34.615 0.00 0.00 0.00 3.56
6664 7149 9.967451 TTTATCCATCTGAAGGTACATTTACAA 57.033 29.630 0.00 0.00 0.00 2.41
6683 7168 5.179452 ACAATGGGTGACTAGCAAATACT 57.821 39.130 0.00 0.00 0.00 2.12
6685 7170 6.349300 ACAATGGGTGACTAGCAAATACTAG 58.651 40.000 0.00 0.00 44.38 2.57
6701 7186 7.262772 CAAATACTAGTCGTATGTTGGAAGGA 58.737 38.462 0.00 0.00 38.78 3.36
6702 7187 7.414222 AATACTAGTCGTATGTTGGAAGGAA 57.586 36.000 0.00 0.00 38.78 3.36
6703 7188 5.069501 ACTAGTCGTATGTTGGAAGGAAC 57.930 43.478 0.00 0.00 0.00 3.62
6757 7242 2.224018 GGTTCAACTTGGCATCTGCAAA 60.224 45.455 4.33 0.00 44.36 3.68
6771 7256 1.782569 CTGCAAACAAACATCACAGCG 59.217 47.619 0.00 0.00 0.00 5.18
6798 7283 2.880268 TCCACTGAAACTGCACAATCAG 59.120 45.455 13.56 13.56 43.79 2.90
6814 7299 1.783284 TCAGCACGCTGTTCTTGTAG 58.217 50.000 18.05 0.00 43.96 2.74
6816 7301 0.320771 AGCACGCTGTTCTTGTAGGG 60.321 55.000 0.00 0.00 0.00 3.53
6817 7302 1.912371 GCACGCTGTTCTTGTAGGGC 61.912 60.000 0.00 0.00 0.00 5.19
6818 7303 0.602638 CACGCTGTTCTTGTAGGGCA 60.603 55.000 0.00 0.00 0.00 5.36
6820 7305 1.639298 CGCTGTTCTTGTAGGGCAGC 61.639 60.000 0.00 0.00 46.22 5.25
6821 7306 3.631453 CTGTTCTTGTAGGGCAGCA 57.369 52.632 0.00 0.00 0.00 4.41
6822 7307 2.119801 CTGTTCTTGTAGGGCAGCAT 57.880 50.000 0.00 0.00 0.00 3.79
6901 7386 2.293677 TCTTGTGAGTCGTCTTGGAGAC 59.706 50.000 0.00 0.00 41.71 3.36
6919 7404 3.695606 GCCGACTCCACCTGCAGA 61.696 66.667 17.39 0.00 0.00 4.26
6954 7439 6.759497 AAGAACTTCTTGTATTGGGTATGC 57.241 37.500 3.07 0.00 34.98 3.14
6980 7465 2.354821 GCGTAACCTGAATGGAATGGTC 59.645 50.000 0.00 0.00 39.71 4.02
6992 7477 0.532573 GAATGGTCGCAGTGAGAGGA 59.467 55.000 0.00 0.00 0.00 3.71
7019 7504 5.128335 ACCGGTAAAGGTACCTAGAGAAATG 59.872 44.000 16.67 2.92 46.84 2.32
7025 7510 2.626743 GGTACCTAGAGAAATGGCGCTA 59.373 50.000 7.64 0.00 0.00 4.26
7102 7587 2.032528 CAGCTTCCTTGCGACCCA 59.967 61.111 0.00 0.00 38.13 4.51
7135 7620 1.080569 CGGCAACAAATGTCAGGCC 60.081 57.895 0.00 0.00 36.74 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 8.334263 TCTTCACAATTATGCACTATCACAAA 57.666 30.769 0.00 0.00 0.00 2.83
138 139 1.153369 CATCATCGGCCTCAACGGT 60.153 57.895 0.00 0.00 34.25 4.83
154 155 0.460284 GGTCATCAAGCGTCGTCCAT 60.460 55.000 0.00 0.00 0.00 3.41
195 196 1.578926 CCAAGAATCGCCGCAACAA 59.421 52.632 0.00 0.00 0.00 2.83
254 255 2.511600 CCGTCCAGCTAAAGCCGG 60.512 66.667 0.00 0.00 43.38 6.13
286 288 4.331992 CACTCATCATCTAAAGTGCACTGG 59.668 45.833 22.49 13.79 33.42 4.00
288 290 5.157940 ACACTCATCATCTAAAGTGCACT 57.842 39.130 15.25 15.25 42.23 4.40
298 300 1.827344 TCAAGCCGACACTCATCATCT 59.173 47.619 0.00 0.00 0.00 2.90
325 327 0.613777 AAGACTTAGAAGGCGGTGGG 59.386 55.000 0.00 0.00 39.71 4.61
424 426 1.442526 CGGTCGCGTATGTAGGACCT 61.443 60.000 5.77 0.00 45.31 3.85
524 816 3.680786 CGACACGTGGAGCCTGGA 61.681 66.667 21.57 0.00 0.00 3.86
525 817 2.507110 AATCGACACGTGGAGCCTGG 62.507 60.000 21.57 0.00 0.00 4.45
529 821 1.635663 CCCAAATCGACACGTGGAGC 61.636 60.000 21.57 7.86 32.54 4.70
594 886 6.074088 CGACATCAATTTAGAGGAGATTTCGG 60.074 42.308 0.00 0.00 36.08 4.30
595 887 6.074088 CCGACATCAATTTAGAGGAGATTTCG 60.074 42.308 0.00 0.00 38.14 3.46
606 898 3.425404 CCGCAAACCGACATCAATTTAG 58.575 45.455 0.00 0.00 40.02 1.85
608 900 1.067915 CCCGCAAACCGACATCAATTT 60.068 47.619 0.00 0.00 40.02 1.82
610 902 0.322098 TCCCGCAAACCGACATCAAT 60.322 50.000 0.00 0.00 40.02 2.57
616 908 0.453782 CGAAAATCCCGCAAACCGAC 60.454 55.000 0.00 0.00 40.02 4.79
619 911 0.109458 GTCCGAAAATCCCGCAAACC 60.109 55.000 0.00 0.00 0.00 3.27
625 917 1.078426 AGCTGGTCCGAAAATCCCG 60.078 57.895 0.00 0.00 0.00 5.14
633 925 0.892755 AAATGTACGAGCTGGTCCGA 59.107 50.000 4.00 0.00 0.00 4.55
634 926 1.722011 AAAATGTACGAGCTGGTCCG 58.278 50.000 4.00 0.00 0.00 4.79
662 954 4.634443 ACGCACTTTTACCCATCTAATGTC 59.366 41.667 0.00 0.00 0.00 3.06
701 993 3.570975 GGACCAAACCTTCCGTAAATGTT 59.429 43.478 0.00 0.00 0.00 2.71
712 1004 1.528309 CCACTGCGGACCAAACCTT 60.528 57.895 0.00 0.00 36.56 3.50
757 1049 1.146041 TGAGCAACTTCAGCACCGT 59.854 52.632 0.00 0.00 0.00 4.83
778 1070 4.963628 GGGGGAGAATTAGACAGAGTTACT 59.036 45.833 0.00 0.00 0.00 2.24
785 1077 8.539117 AAAAATTATGGGGGAGAATTAGACAG 57.461 34.615 0.00 0.00 0.00 3.51
861 1167 4.959839 ACCCACAACCACAAATCTACTTTT 59.040 37.500 0.00 0.00 0.00 2.27
945 1259 2.352651 TGTAGCTGCTCATCGATTTTGC 59.647 45.455 4.91 0.82 0.00 3.68
951 1265 6.983890 TGTTTATTATTGTAGCTGCTCATCGA 59.016 34.615 4.91 0.00 0.00 3.59
956 1270 9.278734 GTTCTTTGTTTATTATTGTAGCTGCTC 57.721 33.333 4.91 0.00 0.00 4.26
982 1298 3.618150 CCCATGCTTTCGGCTTATTTTTG 59.382 43.478 0.00 0.00 42.39 2.44
988 1304 1.001517 TGCCCATGCTTTCGGCTTA 60.002 52.632 10.70 0.00 43.42 3.09
989 1305 2.283101 TGCCCATGCTTTCGGCTT 60.283 55.556 10.70 0.00 43.42 4.35
1314 1630 1.746787 GACGAGGAAGAGGAGAAGGAC 59.253 57.143 0.00 0.00 0.00 3.85
1317 1633 2.021457 GAGGACGAGGAAGAGGAGAAG 58.979 57.143 0.00 0.00 0.00 2.85
1318 1634 1.341187 GGAGGACGAGGAAGAGGAGAA 60.341 57.143 0.00 0.00 0.00 2.87
1319 1635 0.256464 GGAGGACGAGGAAGAGGAGA 59.744 60.000 0.00 0.00 0.00 3.71
1401 1717 1.721664 CCTTAGATGACGCCGACGGA 61.722 60.000 20.50 0.00 46.04 4.69
1404 1720 1.591863 GGCCTTAGATGACGCCGAC 60.592 63.158 0.00 0.00 0.00 4.79
1661 1977 3.071479 ACACACCAATAACAGGCTAACG 58.929 45.455 0.00 0.00 0.00 3.18
1773 2101 6.018669 GCGATCTTAACCAATACTCAAGGAAG 60.019 42.308 0.00 0.00 0.00 3.46
1891 2233 7.939784 ATGATTCATGCAATATATCACTGCT 57.060 32.000 8.85 0.00 37.00 4.24
2069 2419 5.910637 CAGGTTGACATGGACAATTTTTG 57.089 39.130 9.98 4.66 0.00 2.44
2113 2464 7.833285 ACACCCACAACATTATCTAAAAACT 57.167 32.000 0.00 0.00 0.00 2.66
2316 2671 8.830580 CGACTGATACAAGTCCATGAAAATATT 58.169 33.333 0.00 0.00 43.09 1.28
2345 2700 9.593134 ACTGAAGTATTGACAGTGATAAGAATC 57.407 33.333 0.00 0.00 42.18 2.52
2440 2798 5.353400 TCAATGCTCAGTTTCTGCTAATCTG 59.647 40.000 4.84 4.84 0.00 2.90
2593 2951 4.678509 TCAGGTTTTGCATGTCGATAAC 57.321 40.909 0.00 0.00 0.00 1.89
2598 2956 2.409378 GCATTTCAGGTTTTGCATGTCG 59.591 45.455 0.00 0.00 35.22 4.35
2707 3066 3.209410 AGCTTGACAAGTCCAGAACAAG 58.791 45.455 16.39 0.00 38.07 3.16
2923 3282 6.664816 ACTCTAAGGGCAAAATCATTGATTCA 59.335 34.615 12.15 0.00 30.29 2.57
3317 3676 5.652014 TCAATAACCCCATCACTTCATCAAC 59.348 40.000 0.00 0.00 0.00 3.18
3802 4161 1.140312 TCCTTTGAGTGAAGTGGGCT 58.860 50.000 0.00 0.00 0.00 5.19
3805 4164 2.526304 TCGTCCTTTGAGTGAAGTGG 57.474 50.000 0.00 0.00 0.00 4.00
4066 4427 4.638865 TCATCCATTCTCTGCACAAATCAG 59.361 41.667 0.00 0.00 0.00 2.90
4302 4663 0.179045 AAGCACTTGAGCCGTGTCTT 60.179 50.000 0.00 0.00 34.91 3.01
4347 4708 7.119846 AGTCTTCAACTGCAATATTAACCAGAC 59.880 37.037 13.68 6.75 36.65 3.51
4381 4742 2.286872 GACTTGCCTCCATCATCACTG 58.713 52.381 0.00 0.00 0.00 3.66
4616 4985 3.266772 AGGGTTGATGAAAGGATACAGCA 59.733 43.478 0.00 0.00 41.41 4.41
4882 5269 4.091655 CAGCATTGCGCAAAATAATGTGAA 59.908 37.500 28.81 0.00 46.13 3.18
4915 5302 6.827762 GCGGTAGGGTTACTCTATAGTGATAT 59.172 42.308 8.76 0.00 36.36 1.63
4928 5315 3.225940 ACTGGTATAGCGGTAGGGTTAC 58.774 50.000 14.70 0.00 0.00 2.50
4934 5321 5.254901 AGAGGAATACTGGTATAGCGGTAG 58.745 45.833 23.84 7.77 0.00 3.18
4939 5326 9.209175 CACAAATTAGAGGAATACTGGTATAGC 57.791 37.037 0.00 0.00 0.00 2.97
4954 5341 5.886992 TGCATGCAGATTCACAAATTAGAG 58.113 37.500 18.46 0.00 0.00 2.43
5069 5457 2.954318 AGTGCATTGATATGGGCAACTC 59.046 45.455 0.00 0.00 38.10 3.01
5111 5499 1.776975 ATCCCATCTAGCCCAGCTGC 61.777 60.000 8.66 0.00 40.10 5.25
5119 5507 8.754080 ACATAATACTGTAGAATCCCATCTAGC 58.246 37.037 0.00 0.00 32.72 3.42
5155 5543 5.263599 TCAGACATACCATGGCAAGATTTT 58.736 37.500 13.04 0.00 42.15 1.82
5159 5547 2.420547 GCTCAGACATACCATGGCAAGA 60.421 50.000 13.04 0.00 42.15 3.02
5212 5600 9.354673 CTAAATGAATCCACCCTGTGTAAATAT 57.645 33.333 0.00 0.00 0.00 1.28
5213 5601 7.284489 GCTAAATGAATCCACCCTGTGTAAATA 59.716 37.037 0.00 0.00 0.00 1.40
5220 5608 3.737559 TGCTAAATGAATCCACCCTGT 57.262 42.857 0.00 0.00 0.00 4.00
5221 5609 4.202182 CCAATGCTAAATGAATCCACCCTG 60.202 45.833 0.00 0.00 0.00 4.45
5248 5636 1.901085 CAGTACTCTGGGTCCCTGC 59.099 63.158 10.00 0.00 37.97 4.85
5404 5792 9.214957 TGTATTTATTTGTACACAGAGTTCAGG 57.785 33.333 0.00 0.00 0.00 3.86
5943 6331 0.037790 GCAGAACGCTCTTCACCTCT 60.038 55.000 0.00 0.00 37.77 3.69
6018 6406 2.107141 GGAGATCCCTGGCGTTCG 59.893 66.667 0.00 0.00 0.00 3.95
6052 6440 2.668280 GCACACGAGGAGGTTTCGC 61.668 63.158 0.00 0.00 41.57 4.70
6147 6535 7.039714 GGGAACTTGTATGTTTTCTTGAGGAAT 60.040 37.037 0.00 0.00 33.53 3.01
6174 6562 6.604795 AGGCATACACATATCAAAGCTTCTTT 59.395 34.615 0.00 0.00 0.00 2.52
6208 6596 2.722094 ACCTCAATTTTGCATAGGCGA 58.278 42.857 0.00 0.00 45.35 5.54
6244 6632 0.459899 AGCACACACGTGAGAACTGA 59.540 50.000 25.01 0.00 46.80 3.41
6254 6642 4.000557 GTGGACGCAGCACACACG 62.001 66.667 6.93 0.00 37.39 4.49
6342 6760 0.950116 AAGCAAGCAAGCTGACACTC 59.050 50.000 3.54 0.00 45.89 3.51
6412 6830 3.508845 ACAGTTTATGCCCAACACTCT 57.491 42.857 0.00 0.00 0.00 3.24
6462 6880 2.096069 CAGATATTACAGGTGCGCATGC 60.096 50.000 15.91 7.91 43.20 4.06
6463 6881 3.392882 TCAGATATTACAGGTGCGCATG 58.607 45.455 15.91 12.12 0.00 4.06
6464 6882 3.070159 ACTCAGATATTACAGGTGCGCAT 59.930 43.478 15.91 0.00 0.00 4.73
6497 6915 3.944422 AAGAACACACAAGTAGCAACG 57.056 42.857 0.00 0.00 0.00 4.10
6525 6943 7.341445 AGTAACTCATGTTAAGTTTTGCCAA 57.659 32.000 3.85 0.00 39.96 4.52
6632 7117 5.277857 ACCTTCAGATGGATAAACCGTAG 57.722 43.478 9.37 0.00 42.61 3.51
6683 7168 5.948162 AGTAGTTCCTTCCAACATACGACTA 59.052 40.000 0.00 0.00 0.00 2.59
6685 7170 4.863131 CAGTAGTTCCTTCCAACATACGAC 59.137 45.833 0.00 0.00 0.00 4.34
6691 7176 2.054799 AGCCAGTAGTTCCTTCCAACA 58.945 47.619 0.00 0.00 0.00 3.33
6701 7186 6.408662 GGAGATAAGAATTCCAGCCAGTAGTT 60.409 42.308 0.65 0.00 0.00 2.24
6702 7187 5.071115 GGAGATAAGAATTCCAGCCAGTAGT 59.929 44.000 0.65 0.00 0.00 2.73
6703 7188 5.306678 AGGAGATAAGAATTCCAGCCAGTAG 59.693 44.000 0.65 0.00 33.32 2.57
6757 7242 1.674359 TGGAACGCTGTGATGTTTGT 58.326 45.000 0.00 0.00 0.00 2.83
6771 7256 2.030805 GTGCAGTTTCAGTGGATGGAAC 60.031 50.000 0.00 0.00 46.46 3.62
6798 7283 1.912371 GCCCTACAAGAACAGCGTGC 61.912 60.000 0.00 0.00 0.00 5.34
6814 7299 1.889573 GCGTAGGAAGATGCTGCCC 60.890 63.158 0.00 0.00 26.23 5.36
6816 7301 0.585357 CATGCGTAGGAAGATGCTGC 59.415 55.000 0.00 0.00 32.26 5.25
6817 7302 2.229675 TCATGCGTAGGAAGATGCTG 57.770 50.000 0.00 0.00 32.26 4.41
6818 7303 3.576118 ACTATCATGCGTAGGAAGATGCT 59.424 43.478 0.00 0.00 36.83 3.79
6820 7305 4.151335 GCAACTATCATGCGTAGGAAGATG 59.849 45.833 0.00 0.00 36.83 2.90
6821 7306 4.202253 TGCAACTATCATGCGTAGGAAGAT 60.202 41.667 0.00 0.00 46.76 2.40
6822 7307 3.132111 TGCAACTATCATGCGTAGGAAGA 59.868 43.478 0.00 0.00 46.76 2.87
6919 7404 7.573968 ACAAGAAGTTCTTAAATCTGCTGTT 57.426 32.000 17.62 0.00 33.78 3.16
6935 7420 4.189231 GTCGCATACCCAATACAAGAAGT 58.811 43.478 0.00 0.00 0.00 3.01
6954 7439 1.418342 CCATTCAGGTTACGCGGTCG 61.418 60.000 12.47 0.00 42.43 4.79
6959 7444 2.354821 GACCATTCCATTCAGGTTACGC 59.645 50.000 0.00 0.00 39.02 4.42
6980 7465 1.291877 CCGGTTTTCCTCTCACTGCG 61.292 60.000 0.00 0.00 37.95 5.18
7019 7504 0.861837 CCATGATCTTCGTTAGCGCC 59.138 55.000 2.29 0.00 38.14 6.53
7025 7510 3.981071 TTGTCCTCCATGATCTTCGTT 57.019 42.857 0.00 0.00 0.00 3.85
7102 7587 3.055719 CCGCGATTGTTGGCCAGT 61.056 61.111 8.23 0.00 0.00 4.00
7135 7620 2.067766 GTGCAGCTCTCTTCTTCACTG 58.932 52.381 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.