Multiple sequence alignment - TraesCS2A01G470900

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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 TraesCS2A01G470900 chr2A 100.000 3083 0 0 1 3083 713245850 713248932 0.000000e+00 5694
1 TraesCS2A01G470900 chr2A 84.708 497 64 6 15 510 713217909 713218394 1.290000e-133 486
2 TraesCS2A01G470900 chr2B 94.221 1765 95 6 968 2729 691056657 691058417 0.000000e+00 2687
3 TraesCS2A01G470900 chr2B 95.847 939 25 6 15 943 691055732 691056666 0.000000e+00 1506
4 TraesCS2A01G470900 chr2B 85.772 499 59 5 15 513 691051783 691052269 4.560000e-143 518
5 TraesCS2A01G470900 chr2B 93.197 147 7 2 2713 2856 691059885 691060031 2.410000e-51 213
6 TraesCS2A01G470900 chr2D 91.987 936 38 16 15 938 575180363 575181273 0.000000e+00 1279
7 TraesCS2A01G470900 chr2D 85.571 499 59 8 15 513 575176200 575176685 7.630000e-141 510
8 TraesCS2A01G470900 chr2D 85.371 499 60 8 15 513 575163404 575163889 3.550000e-139 505
9 TraesCS2A01G470900 chr2D 94.093 237 8 3 2850 3083 575182434 575182667 3.780000e-94 355


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 TraesCS2A01G470900 chr2A 713245850 713248932 3082 False 5694.000000 5694 100.000000 1 3083 1 chr2A.!!$F2 3082
1 TraesCS2A01G470900 chr2B 691051783 691060031 8248 False 1231.000000 2687 92.259250 15 2856 4 chr2B.!!$F1 2841
2 TraesCS2A01G470900 chr2D 575176200 575182667 6467 False 714.666667 1279 90.550333 15 3083 3 chr2D.!!$F2 3068

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
640 4867 1.271054 ACACTCCTGGCAATGACTCAC 60.271 52.381 0.00 0.00 0.00 3.51 F
1005 5239 0.105039 CTTCTACCGTCTCCATGGGC 59.895 60.000 13.02 1.75 32.01 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 5872 0.313987 GTTCTGCCTTGAAAACCGGG 59.686 55.0 6.32 0.0 0.0 5.73 R
2502 6776 0.317020 GTTGTGCGAGAAAGTGTGCC 60.317 55.0 0.00 0.0 0.0 5.01 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
18 19 3.020102 GCATCACAATTGACGCCAC 57.980 52.632 13.59 0.00 34.78 5.01
360 4578 7.428826 CCCTTTGCTCATGAAGGATATTTTAC 58.571 38.462 12.02 0.00 44.15 2.01
462 4681 5.589192 AGTCTGTGTAGCGTTGATTATACC 58.411 41.667 0.00 0.00 0.00 2.73
486 4705 8.859090 ACCAAATTTGAGATTTCAGTCATTGTA 58.141 29.630 19.86 0.00 34.15 2.41
492 4711 5.887598 TGAGATTTCAGTCATTGTATTGGGG 59.112 40.000 0.00 0.00 0.00 4.96
567 4790 5.779241 TGTTCTCCCTTGATTCTTGGTAT 57.221 39.130 0.00 0.00 0.00 2.73
568 4791 6.884472 TGTTCTCCCTTGATTCTTGGTATA 57.116 37.500 0.00 0.00 0.00 1.47
569 4792 7.451731 TGTTCTCCCTTGATTCTTGGTATAT 57.548 36.000 0.00 0.00 0.00 0.86
570 4793 7.872138 TGTTCTCCCTTGATTCTTGGTATATT 58.128 34.615 0.00 0.00 0.00 1.28
640 4867 1.271054 ACACTCCTGGCAATGACTCAC 60.271 52.381 0.00 0.00 0.00 3.51
688 4915 3.817709 TTCTTTGGGGCTTTTTGACAG 57.182 42.857 0.00 0.00 0.00 3.51
742 4970 8.483307 AAATTGAGCAATCACAATACAATTCC 57.517 30.769 0.00 0.00 36.11 3.01
747 4975 6.866480 AGCAATCACAATACAATTCCGATTT 58.134 32.000 0.00 0.00 0.00 2.17
766 4994 4.837093 TTTTGTATCCTGGTAGGTCTGG 57.163 45.455 0.00 0.00 36.53 3.86
810 5038 8.771920 TTATCTACACACAAACACATTAGGAG 57.228 34.615 0.00 0.00 0.00 3.69
932 5166 3.136443 ACCAATACATCATCGGTGGTGAT 59.864 43.478 17.65 1.84 38.83 3.06
933 5167 3.748048 CCAATACATCATCGGTGGTGATC 59.252 47.826 17.65 0.00 38.83 2.92
934 5168 4.503817 CCAATACATCATCGGTGGTGATCT 60.504 45.833 17.65 0.00 38.83 2.75
935 5169 2.898729 ACATCATCGGTGGTGATCTC 57.101 50.000 17.65 0.00 38.83 2.75
936 5170 2.392662 ACATCATCGGTGGTGATCTCT 58.607 47.619 17.65 0.00 38.83 3.10
937 5171 2.363680 ACATCATCGGTGGTGATCTCTC 59.636 50.000 17.65 0.00 38.83 3.20
938 5172 2.443958 TCATCGGTGGTGATCTCTCT 57.556 50.000 0.00 0.00 0.00 3.10
939 5173 2.302260 TCATCGGTGGTGATCTCTCTC 58.698 52.381 0.00 0.00 0.00 3.20
940 5174 2.092158 TCATCGGTGGTGATCTCTCTCT 60.092 50.000 0.00 0.00 0.00 3.10
941 5175 2.045561 TCGGTGGTGATCTCTCTCTC 57.954 55.000 0.00 0.00 0.00 3.20
942 5176 1.562008 TCGGTGGTGATCTCTCTCTCT 59.438 52.381 0.00 0.00 0.00 3.10
943 5177 1.946768 CGGTGGTGATCTCTCTCTCTC 59.053 57.143 0.00 0.00 0.00 3.20
944 5178 2.421388 CGGTGGTGATCTCTCTCTCTCT 60.421 54.545 0.00 0.00 0.00 3.10
945 5179 3.214328 GGTGGTGATCTCTCTCTCTCTC 58.786 54.545 0.00 0.00 0.00 3.20
946 5180 3.117888 GGTGGTGATCTCTCTCTCTCTCT 60.118 52.174 0.00 0.00 0.00 3.10
947 5181 4.130118 GTGGTGATCTCTCTCTCTCTCTC 58.870 52.174 0.00 0.00 0.00 3.20
948 5182 4.040047 TGGTGATCTCTCTCTCTCTCTCT 58.960 47.826 0.00 0.00 0.00 3.10
949 5183 4.101585 TGGTGATCTCTCTCTCTCTCTCTC 59.898 50.000 0.00 0.00 0.00 3.20
950 5184 4.346418 GGTGATCTCTCTCTCTCTCTCTCT 59.654 50.000 0.00 0.00 0.00 3.10
951 5185 5.510520 GGTGATCTCTCTCTCTCTCTCTCTC 60.511 52.000 0.00 0.00 0.00 3.20
952 5186 5.304101 GTGATCTCTCTCTCTCTCTCTCTCT 59.696 48.000 0.00 0.00 0.00 3.10
953 5187 5.538053 TGATCTCTCTCTCTCTCTCTCTCTC 59.462 48.000 0.00 0.00 0.00 3.20
954 5188 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
955 5189 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
956 5190 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
957 5191 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
958 5192 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
959 5193 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
960 5194 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
961 5195 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
962 5196 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
963 5197 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
964 5198 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
965 5199 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
966 5200 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
972 5206 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
977 5211 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
996 5230 4.947645 TCTCTAGTCTAGCTTCTACCGTC 58.052 47.826 1.60 0.00 0.00 4.79
997 5231 4.650588 TCTCTAGTCTAGCTTCTACCGTCT 59.349 45.833 1.60 0.00 0.00 4.18
1005 5239 0.105039 CTTCTACCGTCTCCATGGGC 59.895 60.000 13.02 1.75 32.01 5.36
1043 5277 1.524482 CTAAGCCTGGCCAGTCTCC 59.476 63.158 30.63 15.67 0.00 3.71
1046 5280 4.459089 GCCTGGCCAGTCTCCGTC 62.459 72.222 30.63 8.08 0.00 4.79
1082 5316 1.446966 GCCTCACGGAGAGCTTCAC 60.447 63.158 0.00 0.00 43.31 3.18
1120 5354 4.611943 TGAGATTATCAACTACTCGCTGC 58.388 43.478 0.00 0.00 34.02 5.25
1149 5383 2.431260 GGCGTCGGCAAGTTCGTA 60.431 61.111 14.73 0.00 42.47 3.43
1227 5461 0.318784 GAGTCACGAAAGACCACGCT 60.319 55.000 0.00 0.00 39.34 5.07
1248 5482 2.093764 TGGCAAAGGGTCAGTGTTTTTG 60.094 45.455 0.00 0.00 33.18 2.44
1275 5509 2.005451 CTCTGCTCACCGGATTCAAAG 58.995 52.381 9.46 0.00 0.00 2.77
1331 5565 1.265905 GAAACACGGCCAAGTAACCAG 59.734 52.381 2.24 0.00 0.00 4.00
1332 5566 0.536460 AACACGGCCAAGTAACCAGG 60.536 55.000 2.24 0.00 0.00 4.45
1354 5588 3.440228 GCTCTAGTCGACCACATCTTTC 58.560 50.000 13.01 0.00 0.00 2.62
1358 5592 1.202582 AGTCGACCACATCTTTCCTCG 59.797 52.381 13.01 0.00 0.00 4.63
1391 5625 1.005394 ACGGTTTCGGCTACACCAG 60.005 57.895 0.00 0.00 41.39 4.00
1395 5629 2.007608 GGTTTCGGCTACACCAGATTC 58.992 52.381 0.00 0.00 39.03 2.52
1420 5654 6.070897 TCGACAATTCAAAGCTGAAATCAA 57.929 33.333 0.00 0.00 44.64 2.57
1425 5659 4.603989 TTCAAAGCTGAAATCAATGCCA 57.396 36.364 0.00 0.00 38.65 4.92
1431 5665 2.098770 GCTGAAATCAATGCCAGACCTC 59.901 50.000 0.00 0.00 0.00 3.85
1446 5680 4.262377 CCAGACCTCTACTATGGCTCATTG 60.262 50.000 0.00 0.00 0.00 2.82
1484 5718 7.706607 CGTACTCACCATCATAAAAGAATCTCA 59.293 37.037 0.00 0.00 0.00 3.27
1584 5818 3.276857 AGATGGTGCAGATGTGACATTC 58.723 45.455 0.00 0.00 0.00 2.67
1593 5827 3.742882 CAGATGTGACATTCAGTGTTCGT 59.257 43.478 0.00 0.00 42.36 3.85
1638 5872 2.485795 TTTGTTGGCTGCACGGTCC 61.486 57.895 0.50 0.00 0.00 4.46
1656 5890 0.825840 CCCCGGTTTTCAAGGCAGAA 60.826 55.000 0.00 0.00 0.00 3.02
1662 5896 3.304057 CGGTTTTCAAGGCAGAACTCTTC 60.304 47.826 0.00 0.00 0.00 2.87
1722 5956 3.076621 TGATGACATTGAGCCACAAGTC 58.923 45.455 0.00 12.26 42.02 3.01
1725 5959 3.554934 TGACATTGAGCCACAAGTCTTT 58.445 40.909 16.27 0.00 42.02 2.52
1729 5963 2.260844 TGAGCCACAAGTCTTTGAGG 57.739 50.000 0.20 0.20 44.86 3.86
1768 6002 5.959618 ATACACAGATTGCATGATGGATG 57.040 39.130 0.00 0.00 34.84 3.51
1782 6016 5.974156 TGATGGATGGTTATGAAGAAGGA 57.026 39.130 0.00 0.00 0.00 3.36
1836 6070 2.428890 GGCGGATCTATATGGAGTGGAG 59.571 54.545 0.00 0.00 0.00 3.86
1866 6100 7.691213 TGAGGGTTATGTGTGAAGGTAAATTA 58.309 34.615 0.00 0.00 0.00 1.40
1887 6121 8.437360 AATTATGTGATAGCATCGACTTGAAA 57.563 30.769 0.00 0.00 0.00 2.69
1965 6199 7.452880 AAAAGCATGTATTGAGTTTCTAGCA 57.547 32.000 0.00 0.00 0.00 3.49
2064 6298 4.198530 TCATGCAGGAGATTTTATTCGCA 58.801 39.130 0.00 0.00 0.00 5.10
2068 6302 3.627577 GCAGGAGATTTTATTCGCAAGGA 59.372 43.478 0.00 0.00 38.47 3.36
2084 6318 0.549950 AGGATGCCTCCCATGTGAAG 59.450 55.000 4.15 0.00 43.21 3.02
2099 6333 6.769341 CCCATGTGAAGTTGATAAGATGATCA 59.231 38.462 0.00 0.00 33.96 2.92
2102 6336 9.052759 CATGTGAAGTTGATAAGATGATCATGA 57.947 33.333 14.30 0.00 35.77 3.07
2142 6376 7.775053 ATTTTGTGTAAGAAAATGCTAGGGA 57.225 32.000 0.00 0.00 46.45 4.20
2146 6380 9.474313 TTTGTGTAAGAAAATGCTAGGGATATT 57.526 29.630 0.00 0.00 0.00 1.28
2337 6610 9.716507 TTTCTATCGTTCAAAAGAAAAACAGAG 57.283 29.630 0.00 0.00 35.58 3.35
2339 6612 4.339429 TCGTTCAAAAGAAAAACAGAGCG 58.661 39.130 0.00 0.00 0.00 5.03
2417 6690 7.575414 AAGAGATAATCTACTTCGCTCTTGA 57.425 36.000 0.00 0.00 37.23 3.02
2429 6702 5.998363 ACTTCGCTCTTGAAAGTAGGATTTT 59.002 36.000 0.00 0.00 0.00 1.82
2470 6743 1.308657 TGGTGGGATATGCAGGGGT 60.309 57.895 0.00 0.00 0.00 4.95
2471 6744 1.151450 GGTGGGATATGCAGGGGTG 59.849 63.158 0.00 0.00 0.00 4.61
2506 6780 3.689649 AGATAAAAATCTCACCGTGGCAC 59.310 43.478 7.79 7.79 0.00 5.01
2589 6863 2.385315 GTGGCAACTTTCGAAAAGCTC 58.615 47.619 21.41 14.99 37.61 4.09
2633 6907 1.079750 GAGGCTCTGACGGACCAAC 60.080 63.158 7.40 0.00 0.00 3.77
2635 6909 2.741092 GCTCTGACGGACCAACCA 59.259 61.111 0.00 0.00 38.90 3.67
2645 6919 0.822121 GGACCAACCAAGGACACACC 60.822 60.000 0.00 0.00 38.79 4.16
2658 6932 2.591715 ACACCTGCGCACACTTCC 60.592 61.111 5.66 0.00 0.00 3.46
2675 6949 3.614588 CTTCCGGAAGTCGTTCAAAAAC 58.385 45.455 32.16 0.00 37.11 2.43
2677 6951 3.272581 TCCGGAAGTCGTTCAAAAACTT 58.727 40.909 0.00 0.00 36.00 2.66
2749 8535 1.342175 GGTCTAGTGGCTAGGAGTGGT 60.342 57.143 3.68 0.00 35.03 4.16
2752 8538 3.570550 GTCTAGTGGCTAGGAGTGGTATG 59.429 52.174 3.68 0.00 35.03 2.39
2805 8594 3.958018 TGACTCTCTCTGGGAGTAGTTC 58.042 50.000 4.14 0.00 43.13 3.01
2837 8626 3.425659 AGGAAGATTGTTCAAAGGCTCC 58.574 45.455 0.00 0.00 0.00 4.70
2938 9141 5.365619 TCATCACATCACATGATTCTCTGG 58.634 41.667 0.00 0.00 34.49 3.86
2957 9160 4.463879 CGGCCTGCCCTCTGTCTG 62.464 72.222 0.00 0.00 0.00 3.51
2958 9161 4.792804 GGCCTGCCCTCTGTCTGC 62.793 72.222 0.00 0.00 0.00 4.26
2971 9174 3.987547 TCTGTCTGCTGTCTCAAAGAAG 58.012 45.455 0.00 0.00 0.00 2.85
2976 9179 5.108517 GTCTGCTGTCTCAAAGAAGGATAG 58.891 45.833 0.00 0.00 0.00 2.08
2981 9184 6.772716 TGCTGTCTCAAAGAAGGATAGTTTTT 59.227 34.615 0.00 0.00 0.00 1.94
2994 9197 9.278978 GAAGGATAGTTTTTGCCCAAAATTAAA 57.721 29.630 6.98 0.00 39.69 1.52
2995 9198 8.615878 AGGATAGTTTTTGCCCAAAATTAAAC 57.384 30.769 6.98 3.23 39.69 2.01
3041 9244 2.124151 GGCCGGCAAGATGGATGT 60.124 61.111 30.85 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.614996 TTGGTGGCGTCAATTGTGAT 58.385 45.000 5.13 0.00 35.80 3.06
3 4 1.539388 GATTGGTGGCGTCAATTGTGA 59.461 47.619 5.13 0.00 35.26 3.58
5 6 1.909700 AGATTGGTGGCGTCAATTGT 58.090 45.000 5.13 0.00 35.26 2.71
6 7 2.728846 CGAAGATTGGTGGCGTCAATTG 60.729 50.000 0.00 0.00 35.26 2.32
8 9 1.086696 CGAAGATTGGTGGCGTCAAT 58.913 50.000 0.00 5.06 37.52 2.57
9 10 0.034198 TCGAAGATTGGTGGCGTCAA 59.966 50.000 0.00 0.00 0.00 3.18
11 12 1.084370 CCTCGAAGATTGGTGGCGTC 61.084 60.000 0.00 0.00 33.89 5.19
12 13 1.079127 CCTCGAAGATTGGTGGCGT 60.079 57.895 0.00 0.00 33.89 5.68
13 14 2.464459 GCCTCGAAGATTGGTGGCG 61.464 63.158 5.16 0.00 36.21 5.69
14 15 2.464459 CGCCTCGAAGATTGGTGGC 61.464 63.158 9.73 9.73 40.62 5.01
15 16 2.464459 GCGCCTCGAAGATTGGTGG 61.464 63.158 0.00 0.00 33.61 4.61
16 17 1.021390 AAGCGCCTCGAAGATTGGTG 61.021 55.000 2.29 0.00 35.74 4.17
17 18 0.741221 GAAGCGCCTCGAAGATTGGT 60.741 55.000 2.29 0.00 33.89 3.67
18 19 0.460987 AGAAGCGCCTCGAAGATTGG 60.461 55.000 2.29 0.00 33.89 3.16
360 4578 4.248859 CTCAAGACACAGGACACCTTATG 58.751 47.826 0.00 0.00 0.00 1.90
486 4705 4.613437 AGTTGAAATGTAGATGCCCCAAT 58.387 39.130 0.00 0.00 0.00 3.16
569 4792 9.866655 AGGCTCCAATATTGAAGTGATTATAAA 57.133 29.630 17.23 0.00 0.00 1.40
570 4793 9.507329 GAGGCTCCAATATTGAAGTGATTATAA 57.493 33.333 17.23 0.00 0.00 0.98
725 4953 8.464770 ACAAAATCGGAATTGTATTGTGATTG 57.535 30.769 9.86 0.00 37.96 2.67
742 4970 5.050490 CAGACCTACCAGGATACAAAATCG 58.950 45.833 0.00 0.00 37.67 3.34
747 4975 2.759355 CCCAGACCTACCAGGATACAA 58.241 52.381 0.00 0.00 37.67 2.41
766 4994 5.992217 AGATAAGAAATACAATGAGGACGCC 59.008 40.000 0.00 0.00 0.00 5.68
846 5078 9.135843 CAGGTATAACCGTGTTACATATATGTG 57.864 37.037 25.48 11.85 44.90 3.21
932 5166 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
933 5167 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
934 5168 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
935 5169 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
936 5170 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
937 5171 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
938 5172 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
939 5173 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
940 5174 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
941 5175 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
942 5176 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
943 5177 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
944 5178 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
945 5179 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
946 5180 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
947 5181 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
948 5182 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
949 5183 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
950 5184 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
951 5185 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
952 5186 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
953 5187 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
954 5188 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
955 5189 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
956 5190 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
957 5191 6.068010 ACTAGAGAGAGAGAGAGAGAGAGAG 58.932 48.000 0.00 0.00 0.00 3.20
958 5192 6.019656 ACTAGAGAGAGAGAGAGAGAGAGA 57.980 45.833 0.00 0.00 0.00 3.10
959 5193 6.068010 AGACTAGAGAGAGAGAGAGAGAGAG 58.932 48.000 0.00 0.00 0.00 3.20
960 5194 6.019656 AGACTAGAGAGAGAGAGAGAGAGA 57.980 45.833 0.00 0.00 0.00 3.10
961 5195 6.072175 GCTAGACTAGAGAGAGAGAGAGAGAG 60.072 50.000 13.91 0.00 0.00 3.20
962 5196 5.770663 GCTAGACTAGAGAGAGAGAGAGAGA 59.229 48.000 13.91 0.00 0.00 3.10
963 5197 5.772672 AGCTAGACTAGAGAGAGAGAGAGAG 59.227 48.000 13.91 0.00 0.00 3.20
964 5198 5.706447 AGCTAGACTAGAGAGAGAGAGAGA 58.294 45.833 13.91 0.00 0.00 3.10
965 5199 6.266558 AGAAGCTAGACTAGAGAGAGAGAGAG 59.733 46.154 13.91 0.00 0.00 3.20
966 5200 6.136857 AGAAGCTAGACTAGAGAGAGAGAGA 58.863 44.000 13.91 0.00 0.00 3.10
972 5206 4.650588 ACGGTAGAAGCTAGACTAGAGAGA 59.349 45.833 13.91 0.00 0.00 3.10
977 5211 4.060205 GGAGACGGTAGAAGCTAGACTAG 58.940 52.174 5.03 5.03 0.00 2.57
996 5230 0.107508 ACGATCTGTTGCCCATGGAG 60.108 55.000 15.22 4.39 0.00 3.86
997 5231 0.107703 GACGATCTGTTGCCCATGGA 60.108 55.000 15.22 0.00 0.00 3.41
1005 5239 2.094286 AGCTGAGGAAGACGATCTGTTG 60.094 50.000 0.00 0.00 0.00 3.33
1082 5316 1.003112 TCAAAATCGTGGGTCCCCG 60.003 57.895 5.13 8.96 39.42 5.73
1120 5354 3.499737 GACGCCCATGCCAACGAG 61.500 66.667 0.00 0.00 0.00 4.18
1215 5449 0.040067 CTTTGCCAGCGTGGTCTTTC 60.040 55.000 6.02 0.00 40.46 2.62
1222 5456 2.594303 TGACCCTTTGCCAGCGTG 60.594 61.111 0.00 0.00 0.00 5.34
1227 5461 1.859302 AAAACACTGACCCTTTGCCA 58.141 45.000 0.00 0.00 0.00 4.92
1248 5482 1.812922 CGGTGAGCAGAGATGGTGC 60.813 63.158 0.00 0.00 41.54 5.01
1275 5509 1.947456 GTGAACTTTGTCCTCACACCC 59.053 52.381 0.00 0.00 39.42 4.61
1331 5565 0.386113 GATGTGGTCGACTAGAGCCC 59.614 60.000 16.46 0.00 46.24 5.19
1332 5566 1.394618 AGATGTGGTCGACTAGAGCC 58.605 55.000 16.46 4.42 46.24 4.70
1354 5588 2.222213 CGTCACTAGTATGAGCTCGAGG 59.778 54.545 15.58 0.00 0.00 4.63
1358 5592 4.352887 GAAACCGTCACTAGTATGAGCTC 58.647 47.826 6.82 6.82 0.00 4.09
1391 5625 5.931532 TCAGCTTTGAATTGTCGAAGAATC 58.068 37.500 7.72 0.00 45.08 2.52
1395 5629 6.144854 TGATTTCAGCTTTGAATTGTCGAAG 58.855 36.000 0.00 0.14 45.06 3.79
1425 5659 4.586841 GTCAATGAGCCATAGTAGAGGTCT 59.413 45.833 0.00 0.00 0.00 3.85
1431 5665 6.169094 CCTTATGGTCAATGAGCCATAGTAG 58.831 44.000 17.52 14.59 45.24 2.57
1446 5680 2.537401 GTGAGTACGCACCTTATGGTC 58.463 52.381 17.93 0.00 46.60 4.02
1484 5718 1.336609 GGTTCGTCTTAAGCTCCGTGT 60.337 52.381 0.00 0.00 0.00 4.49
1584 5818 0.667993 ACAATTGGCCACGAACACTG 59.332 50.000 3.88 0.00 0.00 3.66
1593 5827 0.324285 GGGCATTGAACAATTGGCCA 59.676 50.000 21.66 0.00 39.98 5.36
1638 5872 0.313987 GTTCTGCCTTGAAAACCGGG 59.686 55.000 6.32 0.00 0.00 5.73
1656 5890 2.168496 TCTTTCATCGGACCGAAGAGT 58.832 47.619 22.55 0.23 39.99 3.24
1662 5896 3.064207 TGAGTTTTCTTTCATCGGACCG 58.936 45.455 7.84 7.84 0.00 4.79
1704 5938 2.936919 AGACTTGTGGCTCAATGTCA 57.063 45.000 22.00 0.00 37.03 3.58
1722 5956 2.575805 AGTGAAGAAGGGCCTCAAAG 57.424 50.000 6.46 0.00 0.00 2.77
1725 5959 5.975988 ATATAAAGTGAAGAAGGGCCTCA 57.024 39.130 6.46 0.00 0.00 3.86
1729 5963 7.272978 TCTGTGTATATAAAGTGAAGAAGGGC 58.727 38.462 0.00 0.00 0.00 5.19
1768 6002 9.764363 ATTTTCAGTTTTTCCTTCTTCATAACC 57.236 29.630 0.00 0.00 0.00 2.85
1782 6016 9.185680 AGTAGGTGTTGTAGATTTTCAGTTTTT 57.814 29.630 0.00 0.00 0.00 1.94
1836 6070 3.695830 TCACACATAACCCTCAACCTC 57.304 47.619 0.00 0.00 0.00 3.85
1866 6100 5.643348 TGTTTTCAAGTCGATGCTATCACAT 59.357 36.000 0.00 0.00 0.00 3.21
1914 6148 1.376609 CCCCGCAGTTATGTTGCTCC 61.377 60.000 0.00 0.00 39.38 4.70
1947 6181 6.100279 TCCCTGATGCTAGAAACTCAATACAT 59.900 38.462 0.00 0.00 0.00 2.29
1965 6199 2.641815 AGCTTCAAGTGTCTTCCCTGAT 59.358 45.455 0.00 0.00 0.00 2.90
2064 6298 1.002069 TTCACATGGGAGGCATCCTT 58.998 50.000 18.35 2.18 45.85 3.36
2068 6302 1.355381 TCAACTTCACATGGGAGGCAT 59.645 47.619 7.05 0.00 0.00 4.40
2074 6308 6.769341 TGATCATCTTATCAACTTCACATGGG 59.231 38.462 0.00 0.00 32.97 4.00
2075 6309 7.797038 TGATCATCTTATCAACTTCACATGG 57.203 36.000 0.00 0.00 32.97 3.66
2135 6369 8.854614 ACACTAATTCATGAAATATCCCTAGC 57.145 34.615 13.09 0.00 0.00 3.42
2142 6376 8.621532 ATGGCGTACACTAATTCATGAAATAT 57.378 30.769 13.09 4.69 0.00 1.28
2146 6380 6.700081 GTCTATGGCGTACACTAATTCATGAA 59.300 38.462 11.26 11.26 0.00 2.57
2155 6389 9.948964 TTTCTATATAGTCTATGGCGTACACTA 57.051 33.333 9.58 4.62 0.00 2.74
2157 6391 9.903682 TTTTTCTATATAGTCTATGGCGTACAC 57.096 33.333 9.58 0.00 0.00 2.90
2335 6608 3.915437 TCAAGTTTGGGATTTTCGCTC 57.085 42.857 0.00 0.00 0.00 5.03
2337 6610 5.922739 AAAATCAAGTTTGGGATTTTCGC 57.077 34.783 6.54 0.00 45.62 4.70
2366 6639 5.060506 TCACAAGAGCGGAGAATTTGTTAA 58.939 37.500 0.00 0.00 30.15 2.01
2403 6676 5.312120 TCCTACTTTCAAGAGCGAAGTAG 57.688 43.478 13.01 13.01 46.25 2.57
2409 6682 7.065803 TCCATTAAAATCCTACTTTCAAGAGCG 59.934 37.037 0.00 0.00 0.00 5.03
2429 6702 7.093465 ACCAGATTACTCGAAGAAACTCCATTA 60.093 37.037 0.00 0.00 34.09 1.90
2496 6770 1.831389 CGAGAAAGTGTGCCACGGTG 61.831 60.000 0.00 0.00 39.64 4.94
2502 6776 0.317020 GTTGTGCGAGAAAGTGTGCC 60.317 55.000 0.00 0.00 0.00 5.01
2506 6780 2.473816 TCTGAGTTGTGCGAGAAAGTG 58.526 47.619 0.00 0.00 0.00 3.16
2535 6809 0.678395 AGCGATTCCGAGCTGATCAT 59.322 50.000 0.00 0.00 42.82 2.45
2589 6863 4.451900 ACAATATTTAGTCAGGCCCTTCG 58.548 43.478 0.00 0.00 0.00 3.79
2593 6867 5.937111 TCCTAACAATATTTAGTCAGGCCC 58.063 41.667 0.00 0.00 0.00 5.80
2633 6907 3.357079 GCGCAGGTGTGTCCTTGG 61.357 66.667 0.30 0.00 45.67 3.61
2635 6909 2.591715 GTGCGCAGGTGTGTCCTT 60.592 61.111 12.22 0.00 45.67 3.36
2645 6919 2.664851 TTCCGGAAGTGTGCGCAG 60.665 61.111 14.35 0.00 37.25 5.18
2658 6932 4.267357 TGAAGTTTTTGAACGACTTCCG 57.733 40.909 13.85 0.00 45.35 4.30
2667 6941 7.659652 ACGATTTTTGGTTGAAGTTTTTGAA 57.340 28.000 0.00 0.00 0.00 2.69
2675 6949 6.843069 ATTCCAAACGATTTTTGGTTGAAG 57.157 33.333 14.00 0.00 46.75 3.02
2677 6951 7.327275 CGAATATTCCAAACGATTTTTGGTTGA 59.673 33.333 14.00 4.39 46.75 3.18
2736 8522 1.007842 TCCACATACCACTCCTAGCCA 59.992 52.381 0.00 0.00 0.00 4.75
2738 8524 2.389715 ACTCCACATACCACTCCTAGC 58.610 52.381 0.00 0.00 0.00 3.42
2749 8535 7.878127 CCTACTCTTTTTCAGAAACTCCACATA 59.122 37.037 0.00 0.00 0.00 2.29
2752 8538 6.289064 TCCTACTCTTTTTCAGAAACTCCAC 58.711 40.000 0.00 0.00 0.00 4.02
2805 8594 2.263077 CAATCTTCCTCGGAACAGACG 58.737 52.381 0.00 0.00 0.00 4.18
2837 8626 1.115467 ACCTGCTCTTCCACTATCCG 58.885 55.000 0.00 0.00 0.00 4.18
2915 9118 5.365619 CCAGAGAATCATGTGATGTGATGA 58.634 41.667 0.00 0.00 36.49 2.92
2956 9159 5.489792 AACTATCCTTCTTTGAGACAGCA 57.510 39.130 0.00 0.00 0.00 4.41
2957 9160 6.809630 AAAACTATCCTTCTTTGAGACAGC 57.190 37.500 0.00 0.00 0.00 4.40
2958 9161 7.080724 GCAAAAACTATCCTTCTTTGAGACAG 58.919 38.462 0.00 0.00 0.00 3.51
2971 9174 8.384607 TGTTTAATTTTGGGCAAAAACTATCC 57.615 30.769 0.99 0.00 42.71 2.59
2976 9179 8.917415 TTTGATGTTTAATTTTGGGCAAAAAC 57.083 26.923 0.99 0.00 42.71 2.43
2981 9184 6.708054 ACGATTTTGATGTTTAATTTTGGGCA 59.292 30.769 0.00 0.00 0.00 5.36
2994 9197 3.253188 CACCTGACCAACGATTTTGATGT 59.747 43.478 0.00 0.00 0.00 3.06
2995 9198 3.501828 TCACCTGACCAACGATTTTGATG 59.498 43.478 0.00 0.00 0.00 3.07
3041 9244 3.220658 TGGTGAGACGACGCCACA 61.221 61.111 14.59 0.00 44.09 4.17


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

AutoCloner maintained by Alex Coulton.