Multiple sequence alignment - TraesCS3A01G183200

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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 TraesCS3A01G183200 chr3A 100.000 3732 0 0 1 3732 212705044 212701313 0.000000e+00 6892.0
1 TraesCS3A01G183200 chr3A 82.759 1073 122 37 1135 2176 212534130 212533090 0.000000e+00 898.0
2 TraesCS3A01G183200 chr3A 80.233 172 34 0 2007 2178 212110864 212110693 3.020000e-26 130.0
3 TraesCS3A01G183200 chr3A 84.043 94 14 1 2274 2367 212110174 212110082 5.130000e-14 89.8
4 TraesCS3A01G183200 chr3A 97.059 34 1 0 1035 1068 212534324 212534291 1.450000e-04 58.4
5 TraesCS3A01G183200 chr3B 89.610 1309 110 12 1983 3283 252795923 252794633 0.000000e+00 1640.0
6 TraesCS3A01G183200 chr3B 95.041 847 28 10 1094 1928 252796880 252796036 0.000000e+00 1319.0
7 TraesCS3A01G183200 chr3B 99.294 708 5 0 1 708 798422180 798421473 0.000000e+00 1280.0
8 TraesCS3A01G183200 chr3B 98.317 713 12 0 1 713 11242175 11241463 0.000000e+00 1251.0
9 TraesCS3A01G183200 chr3B 97.911 718 15 0 1 718 11264448 11265165 0.000000e+00 1243.0
10 TraesCS3A01G183200 chr3B 81.538 1300 150 49 1131 2396 252670767 252669524 0.000000e+00 989.0
11 TraesCS3A01G183200 chr3B 88.750 240 15 4 857 1094 252797150 252796921 2.190000e-72 283.0
12 TraesCS3A01G183200 chr3B 80.814 172 33 0 2007 2178 252559036 252558865 6.500000e-28 135.0
13 TraesCS3A01G183200 chr3B 94.737 38 2 0 1031 1068 252670956 252670919 4.030000e-05 60.2
14 TraesCS3A01G183200 chr3D 96.014 853 31 2 1983 2833 174046493 174045642 0.000000e+00 1384.0
15 TraesCS3A01G183200 chr3D 94.496 854 42 4 2881 3732 174041075 174040225 0.000000e+00 1312.0
16 TraesCS3A01G183200 chr3D 94.477 851 31 8 1087 1932 174049441 174048602 0.000000e+00 1297.0
17 TraesCS3A01G183200 chr3D 85.696 762 74 18 1122 1879 173819318 173818588 0.000000e+00 771.0
18 TraesCS3A01G183200 chr3D 90.288 278 15 4 811 1088 174049743 174049478 1.650000e-93 353.0
19 TraesCS3A01G183200 chr3D 89.005 191 20 1 1987 2176 173818219 173818029 6.230000e-58 235.0
20 TraesCS3A01G183200 chr3D 80.952 189 35 1 1990 2178 173624114 173623927 8.350000e-32 148.0
21 TraesCS3A01G183200 chr3D 95.161 62 2 1 2772 2833 174045644 174045584 3.070000e-16 97.1
22 TraesCS3A01G183200 chr3D 96.875 32 1 0 1037 1068 173819490 173819459 2.000000e-03 54.7
23 TraesCS3A01G183200 chr6A 98.597 713 9 1 1 713 90756897 90756186 0.000000e+00 1260.0
24 TraesCS3A01G183200 chr5B 98.729 708 9 0 1 708 158883217 158882510 0.000000e+00 1258.0
25 TraesCS3A01G183200 chr5B 84.234 444 65 5 2852 3294 642373505 642373944 9.580000e-116 427.0
26 TraesCS3A01G183200 chr5A 98.326 717 12 0 1 717 687730759 687731475 0.000000e+00 1258.0
27 TraesCS3A01G183200 chr5A 83.265 490 75 6 2850 3335 639565098 639565584 9.510000e-121 444.0
28 TraesCS3A01G183200 chr5A 83.265 490 73 7 2850 3335 639490065 639490549 3.420000e-120 442.0
29 TraesCS3A01G183200 chr2A 98.729 708 9 0 1 708 742784289 742783582 0.000000e+00 1258.0
30 TraesCS3A01G183200 chr7A 98.588 708 10 0 1 708 708306994 708307701 0.000000e+00 1253.0
31 TraesCS3A01G183200 chr4B 98.305 708 12 0 1 708 189149836 189150543 0.000000e+00 1242.0
32 TraesCS3A01G183200 chr4B 86.395 147 18 1 3428 3574 172518096 172518240 3.860000e-35 159.0
33 TraesCS3A01G183200 chr7D 86.512 430 55 2 2850 3277 89282717 89282289 1.570000e-128 470.0
34 TraesCS3A01G183200 chr5D 83.367 493 72 9 2850 3339 511451113 511451598 7.350000e-122 448.0
35 TraesCS3A01G183200 chr5D 82.828 495 73 8 2850 3335 511129280 511129771 2.060000e-117 433.0
36 TraesCS3A01G183200 chr1D 83.299 491 69 7 2848 3335 12292921 12292441 1.230000e-119 440.0
37 TraesCS3A01G183200 chr4D 84.459 148 21 2 3428 3574 111945407 111945553 1.080000e-30 145.0


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 TraesCS3A01G183200 chr3A 212701313 212705044 3731 True 6892.000000 6892 100.000000 1 3732 1 chr3A.!!$R1 3731
1 TraesCS3A01G183200 chr3A 212533090 212534324 1234 True 478.200000 898 89.909000 1035 2176 2 chr3A.!!$R3 1141
2 TraesCS3A01G183200 chr3B 798421473 798422180 707 True 1280.000000 1280 99.294000 1 708 1 chr3B.!!$R3 707
3 TraesCS3A01G183200 chr3B 11241463 11242175 712 True 1251.000000 1251 98.317000 1 713 1 chr3B.!!$R1 712
4 TraesCS3A01G183200 chr3B 11264448 11265165 717 False 1243.000000 1243 97.911000 1 718 1 chr3B.!!$F1 717
5 TraesCS3A01G183200 chr3B 252794633 252797150 2517 True 1080.666667 1640 91.133667 857 3283 3 chr3B.!!$R5 2426
6 TraesCS3A01G183200 chr3B 252669524 252670956 1432 True 524.600000 989 88.137500 1031 2396 2 chr3B.!!$R4 1365
7 TraesCS3A01G183200 chr3D 174040225 174041075 850 True 1312.000000 1312 94.496000 2881 3732 1 chr3D.!!$R2 851
8 TraesCS3A01G183200 chr3D 174045584 174049743 4159 True 782.775000 1384 93.985000 811 2833 4 chr3D.!!$R4 2022
9 TraesCS3A01G183200 chr3D 173818029 173819490 1461 True 353.566667 771 90.525333 1037 2176 3 chr3D.!!$R3 1139
10 TraesCS3A01G183200 chr6A 90756186 90756897 711 True 1260.000000 1260 98.597000 1 713 1 chr6A.!!$R1 712
11 TraesCS3A01G183200 chr5B 158882510 158883217 707 True 1258.000000 1258 98.729000 1 708 1 chr5B.!!$R1 707
12 TraesCS3A01G183200 chr5A 687730759 687731475 716 False 1258.000000 1258 98.326000 1 717 1 chr5A.!!$F3 716
13 TraesCS3A01G183200 chr2A 742783582 742784289 707 True 1258.000000 1258 98.729000 1 708 1 chr2A.!!$R1 707
14 TraesCS3A01G183200 chr7A 708306994 708307701 707 False 1253.000000 1253 98.588000 1 708 1 chr7A.!!$F1 707
15 TraesCS3A01G183200 chr4B 189149836 189150543 707 False 1242.000000 1242 98.305000 1 708 1 chr4B.!!$F2 707

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
223 224 0.105194 TCAGGGAGGGGATGCGATAA 60.105 55.0 0.0 0.0 0.00 1.75 F
1710 1825 0.895559 CCAAGAAGGTTCCTGCACCC 60.896 60.0 0.0 0.0 37.58 4.61 F
2089 4574 0.108945 GAAAATGTGCAGGCAGAGGC 60.109 55.0 0.0 0.0 40.13 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 4554 0.529378 CCTCTGCCTGCACATTTTCC 59.471 55.0 0.0 0.0 0.0 3.13 R
2511 5012 0.401356 TTGCAACATCCAGCTCCAGA 59.599 50.0 0.0 0.0 0.0 3.86 R
3030 5593 0.948678 TACGAGCACTTGTTTTGGCC 59.051 50.0 0.0 0.0 0.0 5.36 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
223 224 0.105194 TCAGGGAGGGGATGCGATAA 60.105 55.000 0.00 0.00 0.00 1.75
708 709 1.533731 CGTGTGGGCGTTAACATTTCT 59.466 47.619 6.39 0.00 0.00 2.52
718 719 7.033185 GGGCGTTAACATTTCTGAAACATATT 58.967 34.615 4.73 0.90 0.00 1.28
719 720 7.009174 GGGCGTTAACATTTCTGAAACATATTG 59.991 37.037 4.73 2.24 0.00 1.90
720 721 7.383361 GCGTTAACATTTCTGAAACATATTGC 58.617 34.615 4.73 1.70 0.00 3.56
721 722 7.061673 GCGTTAACATTTCTGAAACATATTGCA 59.938 33.333 4.73 0.00 0.00 4.08
722 723 9.075519 CGTTAACATTTCTGAAACATATTGCAT 57.924 29.630 4.73 0.00 0.00 3.96
725 726 8.931385 AACATTTCTGAAACATATTGCATACC 57.069 30.769 4.73 0.00 0.00 2.73
726 727 7.491682 ACATTTCTGAAACATATTGCATACCC 58.508 34.615 4.73 0.00 0.00 3.69
727 728 7.342799 ACATTTCTGAAACATATTGCATACCCT 59.657 33.333 4.73 0.00 0.00 4.34
728 729 7.716799 TTTCTGAAACATATTGCATACCCTT 57.283 32.000 0.00 0.00 0.00 3.95
729 730 7.716799 TTCTGAAACATATTGCATACCCTTT 57.283 32.000 0.00 0.00 0.00 3.11
730 731 7.333528 TCTGAAACATATTGCATACCCTTTC 57.666 36.000 0.00 0.00 0.00 2.62
731 732 7.118723 TCTGAAACATATTGCATACCCTTTCT 58.881 34.615 0.00 0.00 0.00 2.52
732 733 8.271458 TCTGAAACATATTGCATACCCTTTCTA 58.729 33.333 0.00 0.00 0.00 2.10
733 734 8.220755 TGAAACATATTGCATACCCTTTCTAC 57.779 34.615 0.00 0.00 0.00 2.59
734 735 7.284489 TGAAACATATTGCATACCCTTTCTACC 59.716 37.037 0.00 0.00 0.00 3.18
735 736 6.515512 ACATATTGCATACCCTTTCTACCT 57.484 37.500 0.00 0.00 0.00 3.08
736 737 6.911308 ACATATTGCATACCCTTTCTACCTT 58.089 36.000 0.00 0.00 0.00 3.50
737 738 7.354312 ACATATTGCATACCCTTTCTACCTTT 58.646 34.615 0.00 0.00 0.00 3.11
738 739 7.839200 ACATATTGCATACCCTTTCTACCTTTT 59.161 33.333 0.00 0.00 0.00 2.27
739 740 8.695456 CATATTGCATACCCTTTCTACCTTTTT 58.305 33.333 0.00 0.00 0.00 1.94
740 741 9.930158 ATATTGCATACCCTTTCTACCTTTTTA 57.070 29.630 0.00 0.00 0.00 1.52
741 742 7.457024 TTGCATACCCTTTCTACCTTTTTAC 57.543 36.000 0.00 0.00 0.00 2.01
742 743 6.544650 TGCATACCCTTTCTACCTTTTTACA 58.455 36.000 0.00 0.00 0.00 2.41
743 744 7.005296 TGCATACCCTTTCTACCTTTTTACAA 58.995 34.615 0.00 0.00 0.00 2.41
744 745 7.672239 TGCATACCCTTTCTACCTTTTTACAAT 59.328 33.333 0.00 0.00 0.00 2.71
745 746 9.181061 GCATACCCTTTCTACCTTTTTACAATA 57.819 33.333 0.00 0.00 0.00 1.90
749 750 9.871175 ACCCTTTCTACCTTTTTACAATAGAAA 57.129 29.630 0.00 0.00 38.76 2.52
866 867 8.769359 ACCCCCTAGCATTATACTATCATTAAC 58.231 37.037 0.00 0.00 0.00 2.01
927 928 5.515797 AAAACTTTTCAGCAGGTAAGGTC 57.484 39.130 0.00 0.00 0.00 3.85
928 929 3.141767 ACTTTTCAGCAGGTAAGGTCC 57.858 47.619 0.00 0.00 0.00 4.46
968 969 1.331138 CTACGACTCTCTACGCAAGGG 59.669 57.143 0.00 0.00 46.39 3.95
991 992 1.566211 CCCATCTGTCAGTGACTCCT 58.434 55.000 23.29 5.62 33.15 3.69
1028 1029 7.545965 GCAGAAGTTAAATAGCACAAGAGAGTA 59.454 37.037 0.00 0.00 0.00 2.59
1068 1069 1.860950 CAAGTTCCATATCGTCGCTGG 59.139 52.381 2.88 2.88 0.00 4.85
1090 1168 2.812836 ACCAACTGGCATCATCATCA 57.187 45.000 0.00 0.00 39.32 3.07
1092 1170 1.337071 CCAACTGGCATCATCATCAGC 59.663 52.381 0.00 0.00 0.00 4.26
1191 1288 2.094752 GTCAGCGCTCTCTTCTCTTCTT 60.095 50.000 7.13 0.00 0.00 2.52
1218 1328 1.153086 CTTCTTGGCCCGGATGAGG 60.153 63.158 0.73 0.00 0.00 3.86
1397 1511 3.382832 AGTCCCAGACCGCCTTCG 61.383 66.667 0.00 0.00 32.18 3.79
1527 1641 2.351253 CCGTTGATTTCGCACCATTTCA 60.351 45.455 0.00 0.00 0.00 2.69
1710 1825 0.895559 CCAAGAAGGTTCCTGCACCC 60.896 60.000 0.00 0.00 37.58 4.61
1899 2028 1.068943 TCACCTTACCCCCTTTGCCA 61.069 55.000 0.00 0.00 0.00 4.92
1905 2034 3.309556 CCTTACCCCCTTTGCCATTTCTA 60.310 47.826 0.00 0.00 0.00 2.10
2002 4487 5.897377 AGTATAACCAAAAGATGTGGCAC 57.103 39.130 11.55 11.55 40.02 5.01
2069 4554 6.818644 TCTCCTTCCTAACATCGAAGAAATTG 59.181 38.462 0.00 0.00 43.58 2.32
2089 4574 0.108945 GAAAATGTGCAGGCAGAGGC 60.109 55.000 0.00 0.00 40.13 4.70
2182 4667 2.374839 TGGGATTGATGAGGTGACACAA 59.625 45.455 8.08 0.00 33.61 3.33
2387 4888 8.506140 AATGTTGTTGAATATGTTTTCGACAG 57.494 30.769 7.19 0.00 45.89 3.51
2397 4898 9.438291 GAATATGTTTTCGACAGGTGAATTATG 57.562 33.333 0.00 0.00 42.62 1.90
2445 4946 3.126858 TGGCGCTCAATCAATCAAACTAC 59.873 43.478 7.64 0.00 0.00 2.73
2621 5122 2.899900 ACTGACATCTACTCAAGGCACA 59.100 45.455 0.00 0.00 0.00 4.57
2659 5160 5.532557 TGAACTATGAACTATGGCGAGATG 58.467 41.667 0.00 0.00 0.00 2.90
2792 5298 2.760374 CATCCGGCTATTTCACCTCTC 58.240 52.381 0.00 0.00 0.00 3.20
2834 5397 0.527565 GTGTTGACCCACCATGCATC 59.472 55.000 0.00 0.00 0.00 3.91
2835 5398 0.112025 TGTTGACCCACCATGCATCA 59.888 50.000 0.00 0.00 0.00 3.07
2850 5413 6.484643 ACCATGCATCAAGATGTTATGTCTAC 59.515 38.462 18.80 2.20 40.80 2.59
2875 5438 1.748879 AATGCCCGTGCGTTGCTAT 60.749 52.632 0.00 0.00 44.90 2.97
2895 5458 7.376435 GCTATGGGCAACATTTAACAATTTT 57.624 32.000 0.00 0.00 41.03 1.82
2956 5519 3.407698 AGTGTCCGTGCATTATGACAAA 58.592 40.909 10.74 0.00 39.26 2.83
3022 5585 7.919385 AATCAGGCATAACCAAATATTTCCT 57.081 32.000 0.00 0.00 43.14 3.36
3030 5593 7.009174 GCATAACCAAATATTTCCTCAACAACG 59.991 37.037 0.00 0.00 0.00 4.10
3038 5601 0.741915 TCCTCAACAACGGCCAAAAC 59.258 50.000 2.24 0.00 0.00 2.43
3044 5607 0.459411 ACAACGGCCAAAACAAGTGC 60.459 50.000 2.24 0.00 0.00 4.40
3061 5626 5.120830 ACAAGTGCTCGTAGCTTAGAAATTG 59.879 40.000 9.00 9.00 42.97 2.32
3077 5642 5.343249 AGAAATTGCAGAAACTGACAACAC 58.657 37.500 2.81 3.34 33.26 3.32
3105 5670 8.740123 TTTTGAACTTAGTTCCTGAACACATA 57.260 30.769 20.69 0.00 41.35 2.29
3110 5676 7.004555 ACTTAGTTCCTGAACACATACATGA 57.995 36.000 12.21 0.00 43.47 3.07
3234 5800 7.812648 TGAAATTTAGACAACCCTAAATGACG 58.187 34.615 8.97 0.00 44.24 4.35
3253 5819 4.991687 TGACGTACAACTATGCAATGTTGA 59.008 37.500 29.42 16.71 44.29 3.18
3301 5867 7.342799 TCAATCTTAATTGAAGCCTGCCTATTT 59.657 33.333 0.00 0.00 46.41 1.40
3302 5868 7.666063 ATCTTAATTGAAGCCTGCCTATTTT 57.334 32.000 0.00 0.00 34.87 1.82
3335 5901 9.624697 TGCAAATAGACAATTATCAACAGAAAC 57.375 29.630 0.00 0.00 0.00 2.78
3343 5909 7.425606 ACAATTATCAACAGAAACCAGAACAC 58.574 34.615 0.00 0.00 0.00 3.32
3361 5927 7.148641 CAGAACACACTACACAGAAATAGACT 58.851 38.462 0.00 0.00 0.00 3.24
3387 5953 8.827177 TTACAACATCACCTTTAACAGTAGAG 57.173 34.615 0.00 0.00 0.00 2.43
3412 5978 9.328845 AGAAATTGCAACAAACTTGATAACAAT 57.671 25.926 0.00 0.00 35.37 2.71
3431 5997 9.696917 ATAACAATTTGTCAATTTCCTTGAGAC 57.303 29.630 1.83 0.00 44.44 3.36
3648 6214 3.512626 TGATTCATCAAAGGCCGGAACG 61.513 50.000 5.05 0.00 42.94 3.95
3710 6277 7.094118 CCGTGGGATAAGTTTTGGAAGAAAATA 60.094 37.037 0.00 0.00 0.00 1.40
3711 6278 7.968405 CGTGGGATAAGTTTTGGAAGAAAATAG 59.032 37.037 0.00 0.00 0.00 1.73
3712 6279 8.251026 GTGGGATAAGTTTTGGAAGAAAATAGG 58.749 37.037 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
223 224 1.133790 GAAGGCAATGCTCGCTTCATT 59.866 47.619 14.77 0.00 34.74 2.57
408 409 1.210478 CTCCCTCACGGTTCCATTCAT 59.790 52.381 0.00 0.00 0.00 2.57
497 498 4.379243 AGAGGCGTGCGGTGGAAG 62.379 66.667 0.00 0.00 0.00 3.46
708 709 7.284489 GGTAGAAAGGGTATGCAATATGTTTCA 59.716 37.037 13.47 2.02 31.96 2.69
718 719 6.544650 TGTAAAAAGGTAGAAAGGGTATGCA 58.455 36.000 0.00 0.00 0.00 3.96
719 720 7.457024 TTGTAAAAAGGTAGAAAGGGTATGC 57.543 36.000 0.00 0.00 0.00 3.14
723 724 9.871175 TTTCTATTGTAAAAAGGTAGAAAGGGT 57.129 29.630 0.00 0.00 36.81 4.34
763 764 1.532921 CGCTCCGCAGTCAAACAAAAA 60.533 47.619 0.00 0.00 0.00 1.94
764 765 0.028770 CGCTCCGCAGTCAAACAAAA 59.971 50.000 0.00 0.00 0.00 2.44
765 766 1.646540 CGCTCCGCAGTCAAACAAA 59.353 52.632 0.00 0.00 0.00 2.83
766 767 3.329231 CGCTCCGCAGTCAAACAA 58.671 55.556 0.00 0.00 0.00 2.83
795 796 4.992511 TTTTGGGGACGCGTCGGG 62.993 66.667 30.99 7.88 0.00 5.14
796 797 3.719144 GTTTTGGGGACGCGTCGG 61.719 66.667 30.99 0.00 0.00 4.79
797 798 1.847890 ATTGTTTTGGGGACGCGTCG 61.848 55.000 30.99 0.00 0.00 5.12
798 799 0.386731 CATTGTTTTGGGGACGCGTC 60.387 55.000 30.67 30.67 0.00 5.19
799 800 1.657556 CATTGTTTTGGGGACGCGT 59.342 52.632 13.85 13.85 0.00 6.01
800 801 1.732683 GCATTGTTTTGGGGACGCG 60.733 57.895 3.53 3.53 0.00 6.01
801 802 0.667184 CTGCATTGTTTTGGGGACGC 60.667 55.000 0.00 0.00 0.00 5.19
802 803 0.038343 CCTGCATTGTTTTGGGGACG 60.038 55.000 0.00 0.00 0.00 4.79
803 804 1.337118 TCCTGCATTGTTTTGGGGAC 58.663 50.000 0.00 0.00 0.00 4.46
804 805 2.323999 ATCCTGCATTGTTTTGGGGA 57.676 45.000 0.00 0.00 0.00 4.81
805 806 3.075884 CAAATCCTGCATTGTTTTGGGG 58.924 45.455 10.09 0.00 0.00 4.96
806 807 3.742385 ACAAATCCTGCATTGTTTTGGG 58.258 40.909 17.36 2.47 36.39 4.12
866 867 5.452356 GCCCACTGGATCATTTTATTTCAGG 60.452 44.000 0.00 0.00 0.00 3.86
908 909 2.224793 GGGACCTTACCTGCTGAAAAGT 60.225 50.000 0.00 0.00 0.00 2.66
910 911 1.271163 CGGGACCTTACCTGCTGAAAA 60.271 52.381 0.00 0.00 0.00 2.29
914 915 1.218316 GACGGGACCTTACCTGCTG 59.782 63.158 0.00 0.00 39.72 4.41
927 928 2.173669 CAGCGGCTACAATGACGGG 61.174 63.158 0.26 0.00 39.17 5.28
928 929 2.173669 CCAGCGGCTACAATGACGG 61.174 63.158 0.26 0.00 39.17 4.79
968 969 0.250513 GTCACTGACAGATGGGGTCC 59.749 60.000 10.08 0.00 34.36 4.46
976 977 2.497675 GGCATAAGGAGTCACTGACAGA 59.502 50.000 10.08 0.00 34.60 3.41
1028 1029 4.035102 GGCTTCCTTCCTGGCGGT 62.035 66.667 0.00 0.00 35.26 5.68
1068 1069 3.947196 TGATGATGATGCCAGTTGGTAAC 59.053 43.478 0.00 0.00 37.57 2.50
1090 1168 3.539604 CCAAATCTGATTTCTCCGAGCT 58.460 45.455 12.50 0.00 0.00 4.09
1092 1170 2.286294 CGCCAAATCTGATTTCTCCGAG 59.714 50.000 12.50 1.43 0.00 4.63
1191 1288 2.436417 CGGGCCAAGAAGAGAAAATGA 58.564 47.619 4.39 0.00 0.00 2.57
1397 1511 3.519930 GGAGGAGTCGCGGGAGAC 61.520 72.222 6.13 0.00 41.23 3.36
1553 1668 3.793775 TTGGAAACGACGGCGCAGA 62.794 57.895 12.58 0.00 42.48 4.26
1608 1723 1.140312 TGAAGAGGAAGTGGGCTGTT 58.860 50.000 0.00 0.00 0.00 3.16
1611 1726 1.674057 CGTGAAGAGGAAGTGGGCT 59.326 57.895 0.00 0.00 0.00 5.19
1710 1825 3.522731 CCCTGCTCCTCCGTCTCG 61.523 72.222 0.00 0.00 0.00 4.04
1905 2034 7.676947 ACGTATATTTATGCAGGTGGTAGAAT 58.323 34.615 0.00 0.00 0.00 2.40
1948 2153 3.598299 CGGGTTCGTTACCTCCATTTTA 58.402 45.455 8.88 0.00 46.86 1.52
1962 2813 1.289109 CTAGCACCAACACGGGTTCG 61.289 60.000 0.00 0.00 39.79 3.95
1967 2818 3.192466 GGTTATACTAGCACCAACACGG 58.808 50.000 0.00 0.00 42.50 4.94
1974 3727 6.038271 CCACATCTTTTGGTTATACTAGCACC 59.962 42.308 0.00 0.00 0.00 5.01
2002 4487 1.194772 GAAAGTTCGACCTGAAAGCCG 59.805 52.381 0.00 0.00 38.60 5.52
2069 4554 0.529378 CCTCTGCCTGCACATTTTCC 59.471 55.000 0.00 0.00 0.00 3.13
2089 4574 2.390599 CGGCCCTGTCACAATCACG 61.391 63.158 0.00 0.00 0.00 4.35
2176 4661 1.334869 CTTGGCAGAGGTTGTTGTGTC 59.665 52.381 0.00 0.00 0.00 3.67
2182 4667 2.435372 TTCAACTTGGCAGAGGTTGT 57.565 45.000 20.72 1.50 40.52 3.32
2387 4888 4.273480 CGGATCACTGAACCATAATTCACC 59.727 45.833 6.19 0.00 34.84 4.02
2397 4898 3.063997 CAGCATAAACGGATCACTGAACC 59.936 47.826 0.00 0.00 0.00 3.62
2445 4946 4.737765 CAGTACAAATGAAAACCAACGTGG 59.262 41.667 0.00 0.00 45.02 4.94
2511 5012 0.401356 TTGCAACATCCAGCTCCAGA 59.599 50.000 0.00 0.00 0.00 3.86
2589 5090 6.428465 TGAGTAGATGTCAGTATGCTAGCTAC 59.572 42.308 17.23 14.87 39.33 3.58
2724 5227 3.756434 GCCTGACCTTGTTACAATGCTAA 59.244 43.478 0.00 0.00 0.00 3.09
2792 5298 8.889717 ACACTTCAATAAAATTATCACTACGGG 58.110 33.333 0.00 0.00 0.00 5.28
2834 5397 9.254133 CATTGTCCTAGTAGACATAACATCTTG 57.746 37.037 0.00 0.00 45.80 3.02
2835 5398 7.928706 GCATTGTCCTAGTAGACATAACATCTT 59.071 37.037 0.00 0.00 45.80 2.40
2850 5413 2.173669 CGCACGGGCATTGTCCTAG 61.174 63.158 11.77 0.00 41.24 3.02
2861 5424 3.202001 CCCATAGCAACGCACGGG 61.202 66.667 0.00 0.00 0.00 5.28
2875 5438 7.329717 GTCGATAAAATTGTTAAATGTTGCCCA 59.670 33.333 0.00 0.00 0.00 5.36
2895 5458 9.653287 AAGTAATTCTTCACTGATTTGTCGATA 57.347 29.630 0.00 0.00 0.00 2.92
2931 5494 3.623060 GTCATAATGCACGGACACTCAAT 59.377 43.478 0.00 0.00 0.00 2.57
2936 5499 3.822594 TTTGTCATAATGCACGGACAC 57.177 42.857 10.09 0.00 39.75 3.67
2971 5534 8.777865 TCGTCTTTCTTATGTCTTTGATCATT 57.222 30.769 0.00 0.00 0.00 2.57
2976 5539 9.051679 TGATTTTCGTCTTTCTTATGTCTTTGA 57.948 29.630 0.00 0.00 0.00 2.69
2984 5547 8.398665 GTTATGCCTGATTTTCGTCTTTCTTAT 58.601 33.333 0.00 0.00 0.00 1.73
3022 5585 1.546476 ACTTGTTTTGGCCGTTGTTGA 59.454 42.857 0.00 0.00 0.00 3.18
3030 5593 0.948678 TACGAGCACTTGTTTTGGCC 59.051 50.000 0.00 0.00 0.00 5.36
3038 5601 5.554636 CAATTTCTAAGCTACGAGCACTTG 58.445 41.667 9.09 0.00 45.56 3.16
3044 5607 6.091441 AGTTTCTGCAATTTCTAAGCTACGAG 59.909 38.462 0.00 0.00 0.00 4.18
3061 5626 3.609103 AATCGTGTTGTCAGTTTCTGC 57.391 42.857 0.00 0.00 0.00 4.26
3077 5642 6.851330 GTGTTCAGGAACTAAGTTCAAAATCG 59.149 38.462 12.86 0.00 43.54 3.34
3165 5731 6.410942 TGTCTCCGAATATGTTGATCTCAT 57.589 37.500 0.00 1.91 0.00 2.90
3253 5819 6.533730 TGATCTAGAACTGGTTGAACAATGT 58.466 36.000 0.00 0.00 0.00 2.71
3329 5895 4.188462 TGTGTAGTGTGTTCTGGTTTCTG 58.812 43.478 0.00 0.00 0.00 3.02
3335 5901 6.366332 GTCTATTTCTGTGTAGTGTGTTCTGG 59.634 42.308 0.00 0.00 0.00 3.86
3343 5909 9.256477 TGTTGTAAAGTCTATTTCTGTGTAGTG 57.744 33.333 0.00 0.00 0.00 2.74
3361 5927 9.268268 CTCTACTGTTAAAGGTGATGTTGTAAA 57.732 33.333 0.00 0.00 0.00 2.01
3380 5946 7.195646 TCAAGTTTGTTGCAATTTCTCTACTG 58.804 34.615 0.59 0.00 0.00 2.74
3387 5953 9.934190 AATTGTTATCAAGTTTGTTGCAATTTC 57.066 25.926 0.59 0.00 36.97 2.17
3412 5978 4.024048 GCTCGTCTCAAGGAAATTGACAAA 60.024 41.667 0.00 0.00 43.09 2.83
3431 5997 1.884464 CCACATCATCCACCGCTCG 60.884 63.158 0.00 0.00 0.00 5.03
3651 6217 6.861055 CCGCACTAAGCATTTTTCTCTTTTTA 59.139 34.615 0.00 0.00 46.13 1.52
3660 6226 4.306600 CTTTTCCCGCACTAAGCATTTTT 58.693 39.130 0.00 0.00 46.13 1.94


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

AutoCloner maintained by Alex Coulton.