Multiple sequence alignment - TraesCS4A01G126600

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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 TraesCS4A01G126600 chr4A 100.000 4147 0 0 1 4147 163344721 163348867 0.000000e+00 7659.0
1 TraesCS4A01G126600 chr4A 93.008 758 49 3 3391 4147 21856399 21855645 0.000000e+00 1103.0
2 TraesCS4A01G126600 chr4D 91.815 2871 121 44 579 3392 312946397 312943584 0.000000e+00 3895.0
3 TraesCS4A01G126600 chr4D 93.474 567 25 8 1 562 312947066 312946507 0.000000e+00 832.0
4 TraesCS4A01G126600 chr4B 90.901 2341 104 41 308 2582 390405460 390403163 0.000000e+00 3042.0
5 TraesCS4A01G126600 chr4B 84.520 562 33 27 2599 3123 390403108 390402564 1.330000e-139 507.0
6 TraesCS4A01G126600 chr4B 82.906 117 12 5 3007 3123 390402101 390401993 9.490000e-17 99.0
7 TraesCS4A01G126600 chr4B 87.805 82 5 2 193 272 390405536 390405458 1.590000e-14 91.6
8 TraesCS4A01G126600 chr4B 100.000 34 0 0 1 34 390410602 390410569 3.460000e-06 63.9
9 TraesCS4A01G126600 chr3A 93.931 758 39 4 3391 4147 620774888 620774137 0.000000e+00 1138.0
10 TraesCS4A01G126600 chr3A 79.891 184 34 3 3387 3568 496757572 496757754 9.350000e-27 132.0
11 TraesCS4A01G126600 chr6A 93.481 767 46 4 3385 4147 518540737 518541503 0.000000e+00 1136.0
12 TraesCS4A01G126600 chr6A 90.433 763 51 8 3391 4147 542389003 542388257 0.000000e+00 985.0
13 TraesCS4A01G126600 chr7A 92.792 763 47 4 3391 4147 83762920 83762160 0.000000e+00 1098.0
14 TraesCS4A01G126600 chr7D 92.248 774 48 6 1509 2281 444073656 444072894 0.000000e+00 1086.0
15 TraesCS4A01G126600 chr7D 90.307 423 30 6 2125 2547 444073660 444074071 1.010000e-150 544.0
16 TraesCS4A01G126600 chr7D 90.511 274 26 0 1126 1399 444072622 444072895 3.050000e-96 363.0
17 TraesCS4A01G126600 chr5A 92.510 761 52 4 3388 4147 482128090 482128846 0.000000e+00 1085.0
18 TraesCS4A01G126600 chr5A 92.583 755 48 6 3394 4147 640952684 640951937 0.000000e+00 1077.0
19 TraesCS4A01G126600 chr6B 84.535 763 103 11 3391 4147 467943804 467943051 0.000000e+00 741.0
20 TraesCS4A01G126600 chr3D 84.265 769 93 19 3389 4147 545635878 545635128 0.000000e+00 725.0


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 TraesCS4A01G126600 chr4A 163344721 163348867 4146 False 7659.0 7659 100.0000 1 4147 1 chr4A.!!$F1 4146
1 TraesCS4A01G126600 chr4A 21855645 21856399 754 True 1103.0 1103 93.0080 3391 4147 1 chr4A.!!$R1 756
2 TraesCS4A01G126600 chr4D 312943584 312947066 3482 True 2363.5 3895 92.6445 1 3392 2 chr4D.!!$R1 3391
3 TraesCS4A01G126600 chr4B 390401993 390405536 3543 True 934.9 3042 86.5330 193 3123 4 chr4B.!!$R2 2930
4 TraesCS4A01G126600 chr3A 620774137 620774888 751 True 1138.0 1138 93.9310 3391 4147 1 chr3A.!!$R1 756
5 TraesCS4A01G126600 chr6A 518540737 518541503 766 False 1136.0 1136 93.4810 3385 4147 1 chr6A.!!$F1 762
6 TraesCS4A01G126600 chr6A 542388257 542389003 746 True 985.0 985 90.4330 3391 4147 1 chr6A.!!$R1 756
7 TraesCS4A01G126600 chr7A 83762160 83762920 760 True 1098.0 1098 92.7920 3391 4147 1 chr7A.!!$R1 756
8 TraesCS4A01G126600 chr7D 444072894 444073656 762 True 1086.0 1086 92.2480 1509 2281 1 chr7D.!!$R1 772
9 TraesCS4A01G126600 chr7D 444072622 444074071 1449 False 453.5 544 90.4090 1126 2547 2 chr7D.!!$F1 1421
10 TraesCS4A01G126600 chr5A 482128090 482128846 756 False 1085.0 1085 92.5100 3388 4147 1 chr5A.!!$F1 759
11 TraesCS4A01G126600 chr5A 640951937 640952684 747 True 1077.0 1077 92.5830 3394 4147 1 chr5A.!!$R1 753
12 TraesCS4A01G126600 chr6B 467943051 467943804 753 True 741.0 741 84.5350 3391 4147 1 chr6B.!!$R1 756
13 TraesCS4A01G126600 chr3D 545635128 545635878 750 True 725.0 725 84.2650 3389 4147 1 chr3D.!!$R1 758

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
697 826 0.032952 GACACACCGTACTTGCCTGA 59.967 55.0 0.00 0.0 0.00 3.86 F
789 918 0.390340 CGAGCAAAGTGGCTGAGCTA 60.390 55.0 3.72 0.0 45.99 3.32 F
2614 3352 0.459237 CTACGAGTGGAGCAAGCCAG 60.459 60.0 0.00 0.0 38.95 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2595 3284 0.459237 CTGGCTTGCTCCACTCGTAG 60.459 60.000 0.00 0.0 31.74 3.51 R
2640 3378 0.732880 CGTCAGTCACCGACATCCAC 60.733 60.000 0.00 0.0 34.60 4.02 R
3798 4620 1.079127 CGTCGATGGCCAAACCTCT 60.079 57.895 10.96 0.0 40.22 3.69 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
38 39 7.406031 TTCTCCTCTCGCTTCTTTAATAAGA 57.594 36.000 3.00 0.00 38.61 2.10
51 52 5.983720 TCTTTAATAAGATGCCGTGCTACTC 59.016 40.000 0.00 0.00 35.49 2.59
58 59 0.893727 TGCCGTGCTACTCTCACTGA 60.894 55.000 0.00 0.00 32.54 3.41
76 77 2.392613 GAATGCTAACCATGCCGCCG 62.393 60.000 0.00 0.00 33.49 6.46
95 96 2.159462 CCGCATGCTTTTTCCTTCTCTC 60.159 50.000 17.13 0.00 0.00 3.20
105 106 6.071616 GCTTTTTCCTTCTCTCTCTCTCACTA 60.072 42.308 0.00 0.00 0.00 2.74
121 122 8.294954 TCTCTCACTAGACTAAACCCTAAATG 57.705 38.462 0.00 0.00 0.00 2.32
122 123 7.342284 TCTCTCACTAGACTAAACCCTAAATGG 59.658 40.741 0.00 0.00 0.00 3.16
124 125 7.676893 TCTCACTAGACTAAACCCTAAATGGAA 59.323 37.037 0.00 0.00 38.35 3.53
145 146 6.429692 TGGAACAACACATAATTGAGGTACAG 59.570 38.462 0.00 0.00 31.92 2.74
151 152 4.268644 CACATAATTGAGGTACAGCTGTCG 59.731 45.833 25.56 0.00 0.00 4.35
165 167 5.885881 ACAGCTGTCGATTTGTTTGTAAAA 58.114 33.333 15.25 0.00 0.00 1.52
170 172 6.541754 TGTCGATTTGTTTGTAAAACAACG 57.458 33.333 15.77 16.06 37.90 4.10
175 177 7.428761 TCGATTTGTTTGTAAAACAACGTAAGG 59.571 33.333 15.77 5.37 37.90 2.69
201 203 0.801872 TCGTTTACAGCGCATGCATT 59.198 45.000 19.57 1.16 46.23 3.56
217 221 1.680249 GCATTTCCCAGGAGAGTGGAC 60.680 57.143 0.00 0.00 40.44 4.02
231 235 6.670027 AGGAGAGTGGACATAGTAAACTTGAT 59.330 38.462 0.00 0.00 0.00 2.57
232 236 7.839705 AGGAGAGTGGACATAGTAAACTTGATA 59.160 37.037 0.00 0.00 0.00 2.15
233 237 8.138712 GGAGAGTGGACATAGTAAACTTGATAG 58.861 40.741 0.00 0.00 0.00 2.08
428 434 4.893424 ACTTGAAGCTAAAGCAACGAAA 57.107 36.364 4.54 0.00 45.16 3.46
590 690 5.045872 GCTCAGGAAATTATCATTGCCAAC 58.954 41.667 0.00 0.00 40.48 3.77
597 697 4.660789 ATTATCATTGCCAACTTCCTGC 57.339 40.909 0.00 0.00 0.00 4.85
651 751 7.070198 TCAGACTATTATTCGTTAATCCCCACA 59.930 37.037 0.00 0.00 32.66 4.17
654 754 7.571025 ACTATTATTCGTTAATCCCCACACTT 58.429 34.615 0.00 0.00 32.66 3.16
697 826 0.032952 GACACACCGTACTTGCCTGA 59.967 55.000 0.00 0.00 0.00 3.86
784 913 2.032528 TCCCGAGCAAAGTGGCTG 59.967 61.111 0.00 0.00 45.99 4.85
785 914 2.032528 CCCGAGCAAAGTGGCTGA 59.967 61.111 0.00 0.00 45.99 4.26
786 915 2.037136 CCCGAGCAAAGTGGCTGAG 61.037 63.158 0.00 0.00 45.99 3.35
787 916 2.684843 CCGAGCAAAGTGGCTGAGC 61.685 63.158 0.00 0.00 45.99 4.26
788 917 1.670406 CGAGCAAAGTGGCTGAGCT 60.670 57.895 3.72 0.00 45.99 4.09
789 918 0.390340 CGAGCAAAGTGGCTGAGCTA 60.390 55.000 3.72 0.00 45.99 3.32
790 919 1.367659 GAGCAAAGTGGCTGAGCTAG 58.632 55.000 3.72 0.00 45.99 3.42
807 936 4.645692 GCGAGCTAGCTAGGCTTC 57.354 61.111 25.31 10.38 40.44 3.86
808 937 1.006688 GCGAGCTAGCTAGGCTTCC 60.007 63.158 25.31 9.53 40.44 3.46
809 938 1.739338 GCGAGCTAGCTAGGCTTCCA 61.739 60.000 25.31 0.00 40.44 3.53
817 948 1.679311 CTAGGCTTCCACCACTGCA 59.321 57.895 0.00 0.00 0.00 4.41
845 976 2.226200 TGCAGTTTAGCTCGTGTACGTA 59.774 45.455 4.20 0.00 40.80 3.57
907 1039 6.659668 GCTGAGAAGTTTCCTAAAATACCCTT 59.340 38.462 0.00 0.00 0.00 3.95
909 1041 6.433093 TGAGAAGTTTCCTAAAATACCCTTGC 59.567 38.462 0.00 0.00 0.00 4.01
926 1058 2.762535 TGCTATTATTAGGGCCGAGC 57.237 50.000 0.00 0.42 0.00 5.03
1014 1146 2.877582 CGTAGCACGCGGGTGTAC 60.878 66.667 30.07 25.89 46.13 2.90
1015 1147 2.507769 GTAGCACGCGGGTGTACC 60.508 66.667 30.07 16.03 46.13 3.34
1027 1175 1.834188 GGTGTACCCCTTCCACATTG 58.166 55.000 0.00 0.00 0.00 2.82
1049 1204 1.667177 CGAGTCAAGACGTGATGCAGT 60.667 52.381 0.00 0.00 38.90 4.40
1411 1575 4.884257 GTCGCGCGCCTAATGGGA 62.884 66.667 27.95 12.38 37.23 4.37
1507 1671 4.864334 CCACCAGAGATGGCCGCC 62.864 72.222 1.04 1.04 0.00 6.13
1834 2508 2.791927 GAGATTTCCCGTTGCGGC 59.208 61.111 1.51 0.00 46.86 6.53
1978 2652 5.061789 CGTATACGTGCACGCATTTTATAC 58.938 41.667 37.35 32.11 44.43 1.47
1979 2653 5.108141 CGTATACGTGCACGCATTTTATACT 60.108 40.000 37.35 17.25 44.43 2.12
2080 2754 8.902806 TCAAATTTGTCAGTTGTCACTATCTTT 58.097 29.630 17.47 0.00 0.00 2.52
2081 2755 9.520204 CAAATTTGTCAGTTGTCACTATCTTTT 57.480 29.630 10.15 0.00 0.00 2.27
2082 2756 9.520204 AAATTTGTCAGTTGTCACTATCTTTTG 57.480 29.630 0.00 0.00 0.00 2.44
2083 2757 7.624360 TTTGTCAGTTGTCACTATCTTTTGT 57.376 32.000 0.00 0.00 0.00 2.83
2084 2758 7.624360 TTGTCAGTTGTCACTATCTTTTGTT 57.376 32.000 0.00 0.00 0.00 2.83
2101 2775 8.346476 TCTTTTGTTTGTCGTGAAAAATATGG 57.654 30.769 0.00 0.00 0.00 2.74
2102 2776 7.976734 TCTTTTGTTTGTCGTGAAAAATATGGT 59.023 29.630 0.00 0.00 0.00 3.55
2105 2779 3.463533 TGTCGTGAAAAATATGGTGCG 57.536 42.857 0.00 0.00 0.00 5.34
2345 3019 4.101448 ATGGTGGAGAGCGTGGGC 62.101 66.667 0.00 0.00 40.37 5.36
2554 3243 3.114693 GCTCTGTTTCTGAGCGATTTG 57.885 47.619 11.50 0.00 43.26 2.32
2574 3263 1.510480 GCGTGCTCTGTTCTGGCTTT 61.510 55.000 0.00 0.00 0.00 3.51
2584 3273 1.804151 GTTCTGGCTTTCATGCGTACA 59.196 47.619 0.00 0.00 0.00 2.90
2585 3274 2.401583 TCTGGCTTTCATGCGTACAT 57.598 45.000 0.00 0.00 36.79 2.29
2586 3275 3.535280 TCTGGCTTTCATGCGTACATA 57.465 42.857 0.00 0.00 33.67 2.29
2587 3276 3.457234 TCTGGCTTTCATGCGTACATAG 58.543 45.455 0.00 0.00 33.67 2.23
2588 3277 3.118775 TCTGGCTTTCATGCGTACATAGT 60.119 43.478 0.00 0.00 33.67 2.12
2589 3278 2.935849 TGGCTTTCATGCGTACATAGTG 59.064 45.455 0.00 0.00 33.67 2.74
2590 3279 2.286418 GGCTTTCATGCGTACATAGTGC 60.286 50.000 0.00 0.00 33.67 4.40
2591 3280 2.609459 GCTTTCATGCGTACATAGTGCT 59.391 45.455 0.00 0.00 33.67 4.40
2592 3281 3.544834 GCTTTCATGCGTACATAGTGCTG 60.545 47.826 0.00 0.00 33.67 4.41
2593 3282 2.959507 TCATGCGTACATAGTGCTGT 57.040 45.000 0.00 0.00 33.67 4.40
2594 3283 4.379339 TTCATGCGTACATAGTGCTGTA 57.621 40.909 0.00 0.00 33.67 2.74
2595 3284 3.702330 TCATGCGTACATAGTGCTGTAC 58.298 45.455 4.35 4.35 45.18 2.90
2614 3352 0.459237 CTACGAGTGGAGCAAGCCAG 60.459 60.000 0.00 0.00 38.95 4.85
2627 3365 1.610554 AAGCCAGGCACGTACGGTAT 61.611 55.000 21.06 0.00 0.00 2.73
2640 3378 1.492764 ACGGTATGTAGTCCAAGGGG 58.507 55.000 0.00 0.00 0.00 4.79
2671 3409 2.203252 CTGACGCCCCCATGATGG 60.203 66.667 3.98 3.98 37.25 3.51
2695 3433 3.443681 GGTGGTGGTGGTATTGAAAGATG 59.556 47.826 0.00 0.00 0.00 2.90
2759 3497 1.006832 CGTCGCTTTAGAATGTGGGG 58.993 55.000 0.00 0.00 0.00 4.96
2784 3522 2.808523 TGAAGTGAGCACAGTGAGAG 57.191 50.000 4.15 0.00 0.00 3.20
2791 3529 0.965439 AGCACAGTGAGAGTGACTCC 59.035 55.000 9.33 1.54 44.34 3.85
2792 3530 0.387878 GCACAGTGAGAGTGACTCCG 60.388 60.000 9.33 0.00 44.34 4.63
2793 3531 0.387878 CACAGTGAGAGTGACTCCGC 60.388 60.000 9.33 7.66 44.34 5.54
2794 3532 0.538516 ACAGTGAGAGTGACTCCGCT 60.539 55.000 9.33 9.82 44.34 5.52
2795 3533 0.600557 CAGTGAGAGTGACTCCGCTT 59.399 55.000 9.33 0.00 44.34 4.68
2796 3534 1.000283 CAGTGAGAGTGACTCCGCTTT 60.000 52.381 9.33 0.00 44.34 3.51
2797 3535 1.000283 AGTGAGAGTGACTCCGCTTTG 60.000 52.381 9.33 0.00 44.34 2.77
2798 3536 0.319900 TGAGAGTGACTCCGCTTTGC 60.320 55.000 9.33 0.00 44.34 3.68
2854 3597 3.030652 CGCCCACAAGGACACAAC 58.969 61.111 0.00 0.00 38.24 3.32
2868 3611 0.525242 CACAACACACAAGGCGTTGG 60.525 55.000 22.07 13.53 43.38 3.77
2889 3632 2.286294 GGTCAAGCTTGCATACGAGATG 59.714 50.000 21.99 0.00 0.00 2.90
2937 3705 8.816894 CCATGGATCATTTAGTGGTATAGTACT 58.183 37.037 5.56 0.00 0.00 2.73
3056 3831 8.248253 CCGGCTAATTAATTTTCTTAACCTTGT 58.752 33.333 5.91 0.00 0.00 3.16
3075 3850 8.178313 ACCTTGTAACTTTTCCAAAATAGGAG 57.822 34.615 0.00 0.00 39.25 3.69
3076 3851 7.783119 ACCTTGTAACTTTTCCAAAATAGGAGT 59.217 33.333 0.00 0.00 39.25 3.85
3077 3852 9.292195 CCTTGTAACTTTTCCAAAATAGGAGTA 57.708 33.333 0.00 0.00 39.25 2.59
3104 3879 1.001406 AGTAGTGCTTTCTTGCTCGCT 59.999 47.619 0.00 0.00 0.00 4.93
3111 3886 3.253188 TGCTTTCTTGCTCGCTTTGTATT 59.747 39.130 0.00 0.00 0.00 1.89
3124 3915 1.125633 TTGTATTCCGCCTAGGTCCC 58.874 55.000 11.31 0.00 41.99 4.46
3127 3918 1.070289 GTATTCCGCCTAGGTCCCTTG 59.930 57.143 11.31 0.00 41.99 3.61
3187 3978 1.763968 ACGAGGTCGAGGATTGATGA 58.236 50.000 6.35 0.00 43.02 2.92
3197 3988 6.534436 GGTCGAGGATTGATGATTCATAGATG 59.466 42.308 0.00 0.00 0.00 2.90
3201 3992 7.148457 CGAGGATTGATGATTCATAGATGTTGG 60.148 40.741 0.00 0.00 0.00 3.77
3256 4062 4.131596 TGAACCTCTCCACCGTTAAAAAG 58.868 43.478 0.00 0.00 0.00 2.27
3257 4063 3.136009 ACCTCTCCACCGTTAAAAAGG 57.864 47.619 0.00 0.00 0.00 3.11
3286 4093 1.909302 AGGAACCGTCACAGGATCAAT 59.091 47.619 0.00 0.00 35.10 2.57
3290 4097 3.261981 ACCGTCACAGGATCAATAACC 57.738 47.619 0.00 0.00 34.73 2.85
3294 4101 3.623060 CGTCACAGGATCAATAACCAAGG 59.377 47.826 0.00 0.00 0.00 3.61
3360 4167 3.564225 CCGAAATTATGGGTAGGAAGCAC 59.436 47.826 0.00 0.00 0.00 4.40
3419 4226 1.105167 CACCGCGTGACCCTATCCTA 61.105 60.000 4.92 0.00 35.23 2.94
3503 4311 3.824414 GACAAATGTCCGAATTCCGTT 57.176 42.857 2.04 0.00 39.07 4.44
3530 4338 1.960193 AATCCATCCCCGGCCCAAAT 61.960 55.000 0.00 0.00 0.00 2.32
3589 4398 4.555709 TGGACGCACGCCCTTGTT 62.556 61.111 0.00 0.00 0.00 2.83
3595 4407 2.750350 CACGCCCTTGTTCCTCCT 59.250 61.111 0.00 0.00 0.00 3.69
3600 4412 1.770324 CCCTTGTTCCTCCTTGGCT 59.230 57.895 0.00 0.00 35.26 4.75
3697 4516 1.813859 CACCGCCACTATTCTCCGA 59.186 57.895 0.00 0.00 0.00 4.55
3798 4620 1.022451 GTAGTTTTGGCCGCCGATCA 61.022 55.000 4.58 0.00 0.00 2.92
3810 4635 1.299648 CCGATCAGAGGTTTGGCCA 59.700 57.895 0.00 0.00 40.61 5.36
3930 4755 4.603535 GGCAACCACCCCTGCTGT 62.604 66.667 0.00 0.00 38.65 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 0.174389 CAGTGAGAGTAGCACGGCAT 59.826 55.000 0.00 0.00 41.04 4.40
51 52 2.357009 GGCATGGTTAGCATTCAGTGAG 59.643 50.000 0.00 0.00 0.00 3.51
58 59 2.480610 CGGCGGCATGGTTAGCATT 61.481 57.895 10.53 0.00 0.00 3.56
76 77 4.009002 AGAGAGAGAAGGAAAAAGCATGC 58.991 43.478 10.51 10.51 0.00 4.06
80 81 4.929211 GTGAGAGAGAGAGAAGGAAAAAGC 59.071 45.833 0.00 0.00 0.00 3.51
95 96 7.941431 TTTAGGGTTTAGTCTAGTGAGAGAG 57.059 40.000 0.00 0.00 30.20 3.20
105 106 6.489022 GTGTTGTTCCATTTAGGGTTTAGTCT 59.511 38.462 0.00 0.00 38.24 3.24
121 122 6.622896 GCTGTACCTCAATTATGTGTTGTTCC 60.623 42.308 0.00 0.00 0.00 3.62
122 123 6.149474 AGCTGTACCTCAATTATGTGTTGTTC 59.851 38.462 0.00 0.00 0.00 3.18
124 125 5.412594 CAGCTGTACCTCAATTATGTGTTGT 59.587 40.000 5.25 0.00 0.00 3.32
126 127 5.560724 ACAGCTGTACCTCAATTATGTGTT 58.439 37.500 20.16 0.00 0.00 3.32
139 140 3.250040 ACAAACAAATCGACAGCTGTACC 59.750 43.478 21.73 7.49 0.00 3.34
145 146 6.399626 GTTGTTTTACAAACAAATCGACAGC 58.600 36.000 14.71 0.00 40.15 4.40
151 152 8.397215 ACCTTACGTTGTTTTACAAACAAATC 57.603 30.769 14.71 4.96 40.15 2.17
170 172 4.375706 CGCTGTAAACGACTTCAACCTTAC 60.376 45.833 0.00 0.00 0.00 2.34
175 177 1.259507 TGCGCTGTAAACGACTTCAAC 59.740 47.619 9.73 0.00 0.00 3.18
201 203 2.044492 ACTATGTCCACTCTCCTGGGAA 59.956 50.000 0.00 0.00 31.32 3.97
231 235 6.657836 GCTTTGGAAGCGTAAGAAATACTA 57.342 37.500 0.00 0.00 45.74 1.82
232 236 5.547181 GCTTTGGAAGCGTAAGAAATACT 57.453 39.130 0.00 0.00 45.74 2.12
285 290 3.997021 CGTGTACAGCAATTTCCTCTTCT 59.003 43.478 0.00 0.00 0.00 2.85
597 697 1.664017 CATGCATCTCGAGGCGGAG 60.664 63.158 13.56 2.66 41.64 4.63
651 751 5.044698 AGAGTGGAGTAGAACTAGCCTAAGT 60.045 44.000 0.00 0.00 0.00 2.24
654 754 4.227754 ACAGAGTGGAGTAGAACTAGCCTA 59.772 45.833 0.00 0.00 0.00 3.93
788 917 1.240256 GAAGCCTAGCTAGCTCGCTA 58.760 55.000 29.59 18.04 40.49 4.26
789 918 1.460273 GGAAGCCTAGCTAGCTCGCT 61.460 60.000 25.96 25.96 40.49 4.93
790 919 1.006688 GGAAGCCTAGCTAGCTCGC 60.007 63.158 23.26 23.08 40.49 5.03
791 920 0.031449 GTGGAAGCCTAGCTAGCTCG 59.969 60.000 23.26 15.60 40.49 5.03
792 921 0.391228 GGTGGAAGCCTAGCTAGCTC 59.609 60.000 23.26 7.22 40.49 4.09
806 935 2.142761 ACTCTGCTGCAGTGGTGGA 61.143 57.895 28.73 10.95 32.61 4.02
807 936 1.964891 CACTCTGCTGCAGTGGTGG 60.965 63.158 30.59 19.92 38.10 4.61
808 937 2.614446 GCACTCTGCTGCAGTGGTG 61.614 63.158 32.18 32.18 41.49 4.17
809 938 2.281345 GCACTCTGCTGCAGTGGT 60.281 61.111 28.73 23.72 41.49 4.16
817 948 1.671261 CGAGCTAAACTGCACTCTGCT 60.671 52.381 0.00 0.00 45.31 4.24
845 976 0.759346 AGACGGGACAAAAGCTGAGT 59.241 50.000 0.00 0.00 0.00 3.41
907 1039 1.278127 GGCTCGGCCCTAATAATAGCA 59.722 52.381 0.00 0.00 44.06 3.49
998 1130 2.507769 GGTACACCCGCGTGCTAC 60.508 66.667 4.92 2.81 44.40 3.58
1011 1143 1.276989 TCGTCAATGTGGAAGGGGTAC 59.723 52.381 0.00 0.00 0.00 3.34
1014 1146 0.324943 ACTCGTCAATGTGGAAGGGG 59.675 55.000 0.00 0.00 0.00 4.79
1015 1147 1.001974 TGACTCGTCAATGTGGAAGGG 59.998 52.381 0.00 0.00 36.53 3.95
1016 1148 2.455674 TGACTCGTCAATGTGGAAGG 57.544 50.000 0.00 0.00 36.53 3.46
1027 1175 0.985549 GCATCACGTCTTGACTCGTC 59.014 55.000 0.00 0.00 36.92 4.20
1040 1188 0.798771 GACTCCGTCGACTGCATCAC 60.799 60.000 14.70 0.00 0.00 3.06
1041 1189 1.506718 GACTCCGTCGACTGCATCA 59.493 57.895 14.70 0.00 0.00 3.07
1138 1302 1.826921 GCGATGGTACGGGGAGAGA 60.827 63.158 0.00 0.00 0.00 3.10
1749 2423 1.554617 TGCATGGAAATCTCGGTGAGA 59.445 47.619 0.00 0.00 43.20 3.27
1834 2508 0.838229 GTACTATGAGCGCGTCGTTG 59.162 55.000 8.43 9.09 0.00 4.10
1903 2577 4.786507 CGACAGAGAATCAGAGATAGCAG 58.213 47.826 0.00 0.00 37.82 4.24
1906 2580 4.514816 TGAGCGACAGAGAATCAGAGATAG 59.485 45.833 0.00 0.00 37.82 2.08
1978 2652 3.549827 GGTGCAGATCATCAGAGTACGAG 60.550 52.174 0.00 0.00 0.00 4.18
1979 2653 2.359214 GGTGCAGATCATCAGAGTACGA 59.641 50.000 0.00 0.00 0.00 3.43
2038 2712 1.968704 TTGATGTGGCACGTAAACCA 58.031 45.000 13.23 3.47 0.00 3.67
2080 2754 5.460419 GCACCATATTTTTCACGACAAACAA 59.540 36.000 0.00 0.00 0.00 2.83
2081 2755 4.979197 GCACCATATTTTTCACGACAAACA 59.021 37.500 0.00 0.00 0.00 2.83
2082 2756 4.087930 CGCACCATATTTTTCACGACAAAC 59.912 41.667 0.00 0.00 0.00 2.93
2083 2757 4.222886 CGCACCATATTTTTCACGACAAA 58.777 39.130 0.00 0.00 0.00 2.83
2084 2758 3.365465 CCGCACCATATTTTTCACGACAA 60.365 43.478 0.00 0.00 0.00 3.18
2101 2775 2.357760 TTACCGTGAAGCCCGCAC 60.358 61.111 0.00 0.00 0.00 5.34
2102 2776 2.357760 GTTACCGTGAAGCCCGCA 60.358 61.111 0.00 0.00 0.00 5.69
2105 2779 1.301165 ACGTGTTACCGTGAAGCCC 60.301 57.895 0.00 0.00 40.08 5.19
2136 2810 0.535335 TAGTCCCCTGCATGAACGAC 59.465 55.000 0.00 0.00 0.00 4.34
2554 3243 3.426568 GCCAGAACAGAGCACGCC 61.427 66.667 0.00 0.00 0.00 5.68
2574 3263 2.959507 ACAGCACTATGTACGCATGA 57.040 45.000 0.00 0.00 36.58 3.07
2584 3273 3.878103 CTCCACTCGTAGTACAGCACTAT 59.122 47.826 0.38 0.00 41.77 2.12
2585 3274 3.268330 CTCCACTCGTAGTACAGCACTA 58.732 50.000 0.38 0.00 38.80 2.74
2586 3275 2.085320 CTCCACTCGTAGTACAGCACT 58.915 52.381 0.38 0.00 41.62 4.40
2587 3276 1.467713 GCTCCACTCGTAGTACAGCAC 60.468 57.143 0.38 0.00 34.11 4.40
2588 3277 0.809385 GCTCCACTCGTAGTACAGCA 59.191 55.000 0.38 0.00 34.11 4.41
2589 3278 0.809385 TGCTCCACTCGTAGTACAGC 59.191 55.000 0.38 1.32 34.38 4.40
2590 3279 2.732597 GCTTGCTCCACTCGTAGTACAG 60.733 54.545 0.38 0.17 0.00 2.74
2591 3280 1.201647 GCTTGCTCCACTCGTAGTACA 59.798 52.381 0.38 0.00 0.00 2.90
2592 3281 1.469423 GGCTTGCTCCACTCGTAGTAC 60.469 57.143 0.00 0.00 0.00 2.73
2593 3282 0.815734 GGCTTGCTCCACTCGTAGTA 59.184 55.000 0.00 0.00 0.00 1.82
2594 3283 1.185618 TGGCTTGCTCCACTCGTAGT 61.186 55.000 0.00 0.00 0.00 2.73
2595 3284 0.459237 CTGGCTTGCTCCACTCGTAG 60.459 60.000 0.00 0.00 31.74 3.51
2614 3352 1.268743 GGACTACATACCGTACGTGCC 60.269 57.143 15.21 0.00 0.00 5.01
2640 3378 0.732880 CGTCAGTCACCGACATCCAC 60.733 60.000 0.00 0.00 34.60 4.02
2671 3409 2.279935 TTCAATACCACCACCACCAC 57.720 50.000 0.00 0.00 0.00 4.16
2713 3451 4.396166 CACTTTATTGCCCTCACCTACAAG 59.604 45.833 0.00 0.00 0.00 3.16
2759 3497 1.271054 ACTGTGCTCACTTCATCACCC 60.271 52.381 1.47 0.00 0.00 4.61
2854 3597 1.380403 TTGACCCAACGCCTTGTGTG 61.380 55.000 0.00 0.00 0.00 3.82
2868 3611 2.010145 TCTCGTATGCAAGCTTGACC 57.990 50.000 30.39 13.63 0.00 4.02
2871 3614 2.543012 CTCCATCTCGTATGCAAGCTTG 59.457 50.000 22.44 22.44 0.00 4.01
2889 3632 0.460987 CTGGACACGCATCCTTCTCC 60.461 60.000 7.06 0.00 39.75 3.71
3073 3848 9.615295 GCAAGAAAGCACTACTACTATATACTC 57.385 37.037 0.00 0.00 0.00 2.59
3075 3850 9.615295 GAGCAAGAAAGCACTACTACTATATAC 57.385 37.037 0.00 0.00 36.85 1.47
3076 3851 8.504815 CGAGCAAGAAAGCACTACTACTATATA 58.495 37.037 0.00 0.00 36.85 0.86
3077 3852 7.364200 CGAGCAAGAAAGCACTACTACTATAT 58.636 38.462 0.00 0.00 36.85 0.86
3078 3853 6.726230 CGAGCAAGAAAGCACTACTACTATA 58.274 40.000 0.00 0.00 36.85 1.31
3079 3854 5.583495 CGAGCAAGAAAGCACTACTACTAT 58.417 41.667 0.00 0.00 36.85 2.12
3080 3855 4.674623 GCGAGCAAGAAAGCACTACTACTA 60.675 45.833 0.00 0.00 36.85 1.82
3081 3856 3.839293 CGAGCAAGAAAGCACTACTACT 58.161 45.455 0.00 0.00 36.85 2.57
3092 3867 3.120338 CGGAATACAAAGCGAGCAAGAAA 60.120 43.478 0.00 0.00 0.00 2.52
3104 3879 1.487558 GGGACCTAGGCGGAATACAAA 59.512 52.381 9.30 0.00 36.31 2.83
3111 3886 2.365105 CCAAGGGACCTAGGCGGA 60.365 66.667 9.30 0.00 36.31 5.54
3151 3942 2.920912 TTCGAACACCTCCCGCCT 60.921 61.111 0.00 0.00 0.00 5.52
3222 4018 7.362920 CGGTGGAGAGGTTCATTATTTTGAAAT 60.363 37.037 0.00 0.00 37.36 2.17
3256 4062 2.678336 GTGACGGTTCCTTCAATGATCC 59.322 50.000 0.00 0.00 0.00 3.36
3257 4063 3.334691 TGTGACGGTTCCTTCAATGATC 58.665 45.455 0.00 0.00 0.00 2.92
3286 4093 4.668138 AAAGTGATTAGCCCCTTGGTTA 57.332 40.909 0.00 0.00 0.00 2.85
3311 4118 5.450453 ACGAGAATAATCCCAGAGAGAGAA 58.550 41.667 0.00 0.00 0.00 2.87
3314 4121 4.342378 CCAACGAGAATAATCCCAGAGAGA 59.658 45.833 0.00 0.00 0.00 3.10
3360 4167 2.125229 AGCATGCTCCACTGCTCG 60.125 61.111 16.30 0.00 45.30 5.03
3419 4226 3.387947 AAACGGACGGGAGCGGAT 61.388 61.111 0.00 0.00 0.00 4.18
3495 4303 4.839668 TGGATTGAAAACGAACGGAATT 57.160 36.364 0.00 0.00 0.00 2.17
3503 4311 1.680555 CCGGGGATGGATTGAAAACGA 60.681 52.381 0.00 0.00 0.00 3.85
3511 4319 1.960193 ATTTGGGCCGGGGATGGATT 61.960 55.000 2.18 0.00 0.00 3.01
3513 4321 2.174876 AAATTTGGGCCGGGGATGGA 62.175 55.000 2.18 0.00 0.00 3.41
3530 4338 3.291383 CCCCAAACCGAGCGCAAA 61.291 61.111 11.47 0.00 0.00 3.68
3589 4398 3.393970 CAGGCGAGCCAAGGAGGA 61.394 66.667 17.18 0.00 41.22 3.71
3600 4412 3.572447 TAGTGTCCCCGACAGGCGA 62.572 63.158 0.00 0.00 43.57 5.54
3680 4499 1.673808 GGTCGGAGAATAGTGGCGGT 61.674 60.000 0.00 0.00 39.69 5.68
3686 4505 1.108132 GGAGGCGGTCGGAGAATAGT 61.108 60.000 0.00 0.00 39.69 2.12
3798 4620 1.079127 CGTCGATGGCCAAACCTCT 60.079 57.895 10.96 0.00 40.22 3.69
3810 4635 2.813908 GCCGGCAAAGACGTCGAT 60.814 61.111 24.80 0.00 28.54 3.59
3830 4655 2.043248 GCGGTCCTGTCCCCTCTA 60.043 66.667 0.00 0.00 0.00 2.43
3930 4755 1.248101 TGGCGAAGATCACCTCGACA 61.248 55.000 14.31 14.31 41.65 4.35


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

AutoCloner maintained by Alex Coulton.