Multiple sequence alignment - TraesCS7B01G370400

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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 TraesCS7B01G370400 chr7B 100.000 3224 0 0 1 3224 635750152 635746929 0.000000e+00 5954.0
1 TraesCS7B01G370400 chr7B 98.460 909 14 0 2316 3224 635740783 635739875 0.000000e+00 1602.0
2 TraesCS7B01G370400 chr7B 97.582 910 19 2 2316 3224 105537303 105536396 0.000000e+00 1555.0
3 TraesCS7B01G370400 chr7B 96.707 911 27 2 2315 3224 105544349 105543441 0.000000e+00 1513.0
4 TraesCS7B01G370400 chr7B 89.387 1027 86 11 1047 2062 635301073 635302087 0.000000e+00 1271.0
5 TraesCS7B01G370400 chr7B 87.537 1011 78 26 1047 2032 636433130 636432143 0.000000e+00 1125.0
6 TraesCS7B01G370400 chr7B 91.296 494 40 1 1047 1537 635941046 635940553 0.000000e+00 671.0
7 TraesCS7B01G370400 chr7B 90.373 509 47 2 1047 1553 635170676 635171184 0.000000e+00 667.0
8 TraesCS7B01G370400 chr7B 95.792 404 15 1 1661 2062 635935531 635935128 0.000000e+00 651.0
9 TraesCS7B01G370400 chr7B 85.833 360 33 9 705 1048 636433533 636433176 1.830000e-97 366.0
10 TraesCS7B01G370400 chr7B 81.562 320 43 11 1 307 636012954 636012638 1.920000e-62 250.0
11 TraesCS7B01G370400 chr7B 88.333 120 6 4 1764 1877 635171329 635171446 1.560000e-28 137.0
12 TraesCS7B01G370400 chr7B 91.667 96 8 0 896 991 635941659 635941564 2.020000e-27 134.0
13 TraesCS7B01G370400 chr7B 93.827 81 5 0 1585 1665 635940556 635940476 4.370000e-24 122.0
14 TraesCS7B01G370400 chr7D 89.256 1303 73 15 1047 2315 575074299 575073030 0.000000e+00 1568.0
15 TraesCS7B01G370400 chr7D 87.300 1252 98 29 1045 2262 574874942 574876166 0.000000e+00 1375.0
16 TraesCS7B01G370400 chr7D 88.365 1040 91 15 1047 2058 574925306 574924269 0.000000e+00 1223.0
17 TraesCS7B01G370400 chr7D 90.651 845 58 10 1047 1891 575149506 575148683 0.000000e+00 1103.0
18 TraesCS7B01G370400 chr7D 88.502 661 69 7 1059 1715 575217966 575217309 0.000000e+00 793.0
19 TraesCS7B01G370400 chr7D 86.817 311 34 4 1753 2063 575217319 575217016 1.110000e-89 340.0
20 TraesCS7B01G370400 chr7D 78.764 518 63 30 1 489 574926958 574926459 1.450000e-78 303.0
21 TraesCS7B01G370400 chr7D 94.366 71 4 0 1 71 575076487 575076417 3.400000e-20 110.0
22 TraesCS7B01G370400 chr7D 91.667 72 5 1 1 71 575151486 575151415 7.360000e-17 99.0
23 TraesCS7B01G370400 chr1B 97.374 914 17 3 2316 3224 404506478 404505567 0.000000e+00 1548.0
24 TraesCS7B01G370400 chr1B 96.930 912 20 6 2316 3224 16552265 16553171 0.000000e+00 1522.0
25 TraesCS7B01G370400 chr1B 96.810 909 26 3 2316 3224 404499421 404498516 0.000000e+00 1515.0
26 TraesCS7B01G370400 chr1B 96.711 912 23 5 2316 3224 16559318 16560225 0.000000e+00 1511.0
27 TraesCS7B01G370400 chr2B 97.036 911 21 5 2316 3224 572118632 572119538 0.000000e+00 1528.0
28 TraesCS7B01G370400 chr2A 96.487 911 26 5 2316 3223 449196248 449195341 0.000000e+00 1500.0
29 TraesCS7B01G370400 chr7A 85.941 1195 97 29 1047 2205 664781105 664779946 0.000000e+00 1210.0
30 TraesCS7B01G370400 chr7A 88.701 708 47 9 1047 1754 664699404 664700078 0.000000e+00 833.0
31 TraesCS7B01G370400 chr7A 87.034 671 59 10 1048 1715 664873601 664872956 0.000000e+00 732.0
32 TraesCS7B01G370400 chr7A 90.064 312 26 4 1754 2062 664700133 664700442 1.800000e-107 399.0
33 TraesCS7B01G370400 chr7A 85.670 321 36 5 1754 2066 664872953 664872635 2.400000e-86 329.0
34 TraesCS7B01G370400 chr7A 81.979 283 34 12 113 388 664698045 664698317 1.160000e-54 224.0
35 TraesCS7B01G370400 chr7A 86.885 122 14 1 2193 2314 664777563 664777444 5.610000e-28 135.0
36 TraesCS7B01G370400 chr7A 93.182 44 3 0 442 485 664874176 664874133 7.470000e-07 65.8


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 TraesCS7B01G370400 chr7B 635746929 635750152 3223 True 5954.000000 5954 100.000000 1 3224 1 chr7B.!!$R4 3223
1 TraesCS7B01G370400 chr7B 635739875 635740783 908 True 1602.000000 1602 98.460000 2316 3224 1 chr7B.!!$R3 908
2 TraesCS7B01G370400 chr7B 105536396 105537303 907 True 1555.000000 1555 97.582000 2316 3224 1 chr7B.!!$R1 908
3 TraesCS7B01G370400 chr7B 105543441 105544349 908 True 1513.000000 1513 96.707000 2315 3224 1 chr7B.!!$R2 909
4 TraesCS7B01G370400 chr7B 635301073 635302087 1014 False 1271.000000 1271 89.387000 1047 2062 1 chr7B.!!$F1 1015
5 TraesCS7B01G370400 chr7B 636432143 636433533 1390 True 745.500000 1125 86.685000 705 2032 2 chr7B.!!$R8 1327
6 TraesCS7B01G370400 chr7B 635170676 635171446 770 False 402.000000 667 89.353000 1047 1877 2 chr7B.!!$F2 830
7 TraesCS7B01G370400 chr7B 635940476 635941659 1183 True 309.000000 671 92.263333 896 1665 3 chr7B.!!$R7 769
8 TraesCS7B01G370400 chr7D 574874942 574876166 1224 False 1375.000000 1375 87.300000 1045 2262 1 chr7D.!!$F1 1217
9 TraesCS7B01G370400 chr7D 575073030 575076487 3457 True 839.000000 1568 91.811000 1 2315 2 chr7D.!!$R2 2314
10 TraesCS7B01G370400 chr7D 574924269 574926958 2689 True 763.000000 1223 83.564500 1 2058 2 chr7D.!!$R1 2057
11 TraesCS7B01G370400 chr7D 575148683 575151486 2803 True 601.000000 1103 91.159000 1 1891 2 chr7D.!!$R3 1890
12 TraesCS7B01G370400 chr7D 575217016 575217966 950 True 566.500000 793 87.659500 1059 2063 2 chr7D.!!$R4 1004
13 TraesCS7B01G370400 chr1B 404505567 404506478 911 True 1548.000000 1548 97.374000 2316 3224 1 chr1B.!!$R2 908
14 TraesCS7B01G370400 chr1B 16552265 16553171 906 False 1522.000000 1522 96.930000 2316 3224 1 chr1B.!!$F1 908
15 TraesCS7B01G370400 chr1B 404498516 404499421 905 True 1515.000000 1515 96.810000 2316 3224 1 chr1B.!!$R1 908
16 TraesCS7B01G370400 chr1B 16559318 16560225 907 False 1511.000000 1511 96.711000 2316 3224 1 chr1B.!!$F2 908
17 TraesCS7B01G370400 chr2B 572118632 572119538 906 False 1528.000000 1528 97.036000 2316 3224 1 chr2B.!!$F1 908
18 TraesCS7B01G370400 chr2A 449195341 449196248 907 True 1500.000000 1500 96.487000 2316 3223 1 chr2A.!!$R1 907
19 TraesCS7B01G370400 chr7A 664777444 664781105 3661 True 672.500000 1210 86.413000 1047 2314 2 chr7A.!!$R1 1267
20 TraesCS7B01G370400 chr7A 664698045 664700442 2397 False 485.333333 833 86.914667 113 2062 3 chr7A.!!$F1 1949
21 TraesCS7B01G370400 chr7A 664872635 664874176 1541 True 375.600000 732 88.628667 442 2066 3 chr7A.!!$R2 1624

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
392 471 0.179073 CACTTGTATCTCCCCTGCGG 60.179 60.0 0.00 0.0 0.00 5.69 F
879 2842 0.245539 GTGTACCCGAAGCAGTGCTA 59.754 55.0 20.09 0.0 38.25 3.49 F
1605 4257 0.312102 GGTGAACCAGCAGAGCAAAC 59.688 55.0 0.00 0.0 35.64 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 4326 0.903454 CGTCCTACCCTCCACCAACT 60.903 60.0 0.00 0.0 0.00 3.16 R
2129 4945 1.519408 AAATCCTACACACACGCACC 58.481 50.0 0.00 0.0 0.00 5.01 R
3039 8266 0.598158 CGGACACCGGAAAGTTTCGA 60.598 55.0 9.46 0.0 44.15 3.71 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
55 56 1.005097 TCCAGCAGTCCATTGCAATCT 59.995 47.619 9.53 0.58 46.47 2.40
57 58 1.404391 CAGCAGTCCATTGCAATCTCC 59.596 52.381 9.53 0.00 46.47 3.71
59 60 2.097825 GCAGTCCATTGCAATCTCCTT 58.902 47.619 9.53 0.00 43.53 3.36
88 102 5.950883 TCTCTCCAAATTGTCGTAGTACTG 58.049 41.667 5.39 0.00 0.00 2.74
89 103 5.475909 TCTCTCCAAATTGTCGTAGTACTGT 59.524 40.000 5.39 0.00 0.00 3.55
90 104 6.656270 TCTCTCCAAATTGTCGTAGTACTGTA 59.344 38.462 5.39 0.00 0.00 2.74
91 105 6.615088 TCTCCAAATTGTCGTAGTACTGTAC 58.385 40.000 9.93 9.93 0.00 2.90
92 106 6.432162 TCTCCAAATTGTCGTAGTACTGTACT 59.568 38.462 22.72 22.72 42.68 2.73
93 107 7.607607 TCTCCAAATTGTCGTAGTACTGTACTA 59.392 37.037 20.74 20.74 40.14 1.82
94 108 8.109705 TCCAAATTGTCGTAGTACTGTACTAA 57.890 34.615 24.88 14.08 42.45 2.24
95 109 8.023128 TCCAAATTGTCGTAGTACTGTACTAAC 58.977 37.037 24.88 20.60 42.45 2.34
126 198 6.015918 TCACTTGATTTCTCTCTCTCTCCTT 58.984 40.000 0.00 0.00 0.00 3.36
196 269 2.164219 GCTCTTCTCACTCTCTCACCTG 59.836 54.545 0.00 0.00 0.00 4.00
200 273 0.964700 CTCACTCTCTCACCTGCACA 59.035 55.000 0.00 0.00 0.00 4.57
201 274 0.964700 TCACTCTCTCACCTGCACAG 59.035 55.000 0.00 0.00 0.00 3.66
215 288 1.153901 CACAGGCGACCGTACGAAT 60.154 57.895 18.76 3.94 35.09 3.34
292 370 1.802880 CGATCGATCGGAGCAAAACCT 60.803 52.381 34.54 0.00 45.93 3.50
336 415 2.584608 CTACCCCACCGGCTTCTG 59.415 66.667 0.00 0.00 33.26 3.02
354 433 0.251922 TGGCCTAGTGTACCTTCCGT 60.252 55.000 3.32 0.00 0.00 4.69
381 460 2.614481 CCAACTGTACCCGCACTTGTAT 60.614 50.000 0.00 0.00 0.00 2.29
391 470 0.811616 GCACTTGTATCTCCCCTGCG 60.812 60.000 0.00 0.00 0.00 5.18
392 471 0.179073 CACTTGTATCTCCCCTGCGG 60.179 60.000 0.00 0.00 0.00 5.69
393 472 1.227674 CTTGTATCTCCCCTGCGGC 60.228 63.158 0.00 0.00 0.00 6.53
394 473 2.666596 CTTGTATCTCCCCTGCGGCC 62.667 65.000 0.00 0.00 0.00 6.13
395 474 3.942439 GTATCTCCCCTGCGGCCC 61.942 72.222 0.00 0.00 0.00 5.80
396 475 4.172232 TATCTCCCCTGCGGCCCT 62.172 66.667 0.00 0.00 0.00 5.19
444 547 0.459411 TGCTACGCACACACGCATAT 60.459 50.000 0.00 0.00 36.19 1.78
485 598 2.369860 AGCTCTCACATGGTCACTGAAA 59.630 45.455 0.00 0.00 0.00 2.69
518 928 6.461640 ACAGTTTAACTACACGAGGCTAATT 58.538 36.000 0.00 0.00 0.00 1.40
545 955 9.508642 TTTTGTATGTGTGTATATTCCAGTTCA 57.491 29.630 0.00 0.00 0.00 3.18
547 957 8.487313 TGTATGTGTGTATATTCCAGTTCAAC 57.513 34.615 0.00 0.00 0.00 3.18
548 958 7.551262 TGTATGTGTGTATATTCCAGTTCAACC 59.449 37.037 0.00 0.00 0.00 3.77
549 959 5.870706 TGTGTGTATATTCCAGTTCAACCA 58.129 37.500 0.00 0.00 0.00 3.67
550 960 6.299922 TGTGTGTATATTCCAGTTCAACCAA 58.700 36.000 0.00 0.00 0.00 3.67
551 961 6.773200 TGTGTGTATATTCCAGTTCAACCAAA 59.227 34.615 0.00 0.00 0.00 3.28
552 962 7.450014 TGTGTGTATATTCCAGTTCAACCAAAT 59.550 33.333 0.00 0.00 0.00 2.32
553 963 8.303876 GTGTGTATATTCCAGTTCAACCAAATT 58.696 33.333 0.00 0.00 0.00 1.82
554 964 9.521841 TGTGTATATTCCAGTTCAACCAAATTA 57.478 29.630 0.00 0.00 0.00 1.40
560 970 7.775053 TTCCAGTTCAACCAAATTAATAGCT 57.225 32.000 0.00 0.00 0.00 3.32
561 971 7.156876 TCCAGTTCAACCAAATTAATAGCTG 57.843 36.000 0.00 0.00 0.00 4.24
562 972 6.152661 TCCAGTTCAACCAAATTAATAGCTGG 59.847 38.462 0.00 8.11 39.72 4.85
563 973 5.807011 CAGTTCAACCAAATTAATAGCTGGC 59.193 40.000 0.00 0.00 31.74 4.85
564 974 5.105351 AGTTCAACCAAATTAATAGCTGGCC 60.105 40.000 0.00 0.00 31.74 5.36
565 975 3.704061 TCAACCAAATTAATAGCTGGCCC 59.296 43.478 0.00 0.00 31.74 5.80
569 979 2.065899 AATTAATAGCTGGCCCGCAA 57.934 45.000 22.07 7.01 0.00 4.85
570 980 2.065899 ATTAATAGCTGGCCCGCAAA 57.934 45.000 22.07 9.29 0.00 3.68
628 1769 4.331168 GCACAATTTTGTTGGTACTGCAAA 59.669 37.500 0.00 0.00 39.91 3.68
654 1819 3.053917 AGTTGTGGGGTGGTATGTATTCC 60.054 47.826 0.00 0.00 0.00 3.01
663 1828 5.427157 GGGTGGTATGTATTCCCCAAAAATT 59.573 40.000 0.00 0.00 32.66 1.82
703 2255 5.906073 ACAACTGTTTGGAAAATGAAGGAG 58.094 37.500 0.00 0.00 37.00 3.69
710 2275 6.183360 TGTTTGGAAAATGAAGGAGACTGTTC 60.183 38.462 0.00 0.00 42.68 3.18
761 2327 1.262950 TCACGGCACATTTTCTTGTCG 59.737 47.619 0.00 0.00 46.23 4.35
782 2455 3.185797 CGACTTTAACCAGTGTAACCAGC 59.814 47.826 0.00 0.00 37.80 4.85
807 2480 7.216494 CCACAGTTTCATATTTCCCAAGTTTT 58.784 34.615 0.00 0.00 0.00 2.43
851 2814 4.395854 GGGCCAAATTTTAAAATGAGGCAG 59.604 41.667 34.41 17.28 44.45 4.85
875 2838 2.654877 CCGTGTACCCGAAGCAGT 59.345 61.111 0.00 0.00 0.00 4.40
876 2839 1.736645 CCGTGTACCCGAAGCAGTG 60.737 63.158 0.00 0.00 0.00 3.66
878 2841 1.004918 GTGTACCCGAAGCAGTGCT 60.005 57.895 13.14 13.14 42.56 4.40
879 2842 0.245539 GTGTACCCGAAGCAGTGCTA 59.754 55.000 20.09 0.00 38.25 3.49
881 2844 0.245539 GTACCCGAAGCAGTGCTACA 59.754 55.000 20.09 0.00 38.25 2.74
882 2845 1.134788 GTACCCGAAGCAGTGCTACAT 60.135 52.381 20.09 1.92 38.25 2.29
885 3016 1.131126 CCCGAAGCAGTGCTACATTTG 59.869 52.381 20.09 6.42 38.25 2.32
891 3022 2.159476 AGCAGTGCTACATTTGCATTCG 60.159 45.455 18.11 0.00 42.69 3.34
892 3023 2.179589 CAGTGCTACATTTGCATTCGC 58.820 47.619 0.00 0.00 42.69 4.70
925 3056 8.452989 AATTTGTAAATGCTAAGCGAGAAAAG 57.547 30.769 0.00 0.00 0.00 2.27
964 3098 2.045926 ATCGCACAACCTCCAGCC 60.046 61.111 0.00 0.00 0.00 4.85
1006 3555 2.573462 ACCATGGCTGTCTCAGTACAAT 59.427 45.455 13.04 0.00 33.43 2.71
1031 3599 3.510719 CTTGTGTTCTCTCAGCTCTAGC 58.489 50.000 0.00 0.00 42.49 3.42
1043 3658 2.124403 TCTAGCGTCGTCCCTCCC 60.124 66.667 0.00 0.00 0.00 4.30
1187 3802 2.683933 GAAGGCCTCCTCCACGGA 60.684 66.667 5.23 0.00 40.30 4.69
1224 3848 4.710695 TTCTTCGGCGCGCGAAGA 62.711 61.111 38.94 38.94 46.58 2.87
1523 4155 0.963856 TGCTCTGCTGCCCATTTCAG 60.964 55.000 0.00 0.00 34.79 3.02
1540 4172 4.070552 GCCTCCTCGTTCGGCTGT 62.071 66.667 0.00 0.00 40.62 4.40
1565 4202 3.020984 GGAGGGCGTGATGGAAAATTTA 58.979 45.455 0.00 0.00 0.00 1.40
1605 4257 0.312102 GGTGAACCAGCAGAGCAAAC 59.688 55.000 0.00 0.00 35.64 2.93
1712 4376 0.455815 GGATTCCGCCGCATTTTCTT 59.544 50.000 0.00 0.00 0.00 2.52
1716 4380 1.137404 CCGCCGCATTTTCTTCTGG 59.863 57.895 0.00 0.00 0.00 3.86
1759 4500 3.181440 TGCTGTCTTGTGGGAATTCTTCT 60.181 43.478 5.23 0.00 0.00 2.85
1760 4501 3.823304 GCTGTCTTGTGGGAATTCTTCTT 59.177 43.478 5.23 0.00 0.00 2.52
1761 4502 4.083057 GCTGTCTTGTGGGAATTCTTCTTC 60.083 45.833 5.23 0.00 0.00 2.87
1776 4531 9.921637 GAATTCTTCTTCTTCTTCTTCTGAGTA 57.078 33.333 0.00 0.00 0.00 2.59
2018 4805 1.226542 CAGGCAGCCTGTCATGGAT 59.773 57.895 30.97 0.00 45.82 3.41
2066 4857 5.681639 ACCATTTGATAGTACTACTTGGGC 58.318 41.667 4.31 0.00 0.00 5.36
2067 4858 4.750098 CCATTTGATAGTACTACTTGGGCG 59.250 45.833 4.31 0.00 0.00 6.13
2068 4859 4.395959 TTTGATAGTACTACTTGGGCGG 57.604 45.455 4.31 0.00 0.00 6.13
2074 4890 0.828022 TACTACTTGGGCGGACATGG 59.172 55.000 0.00 0.00 0.00 3.66
2099 4915 5.987019 ATCTAGGTTTTATGGGCAGGTTA 57.013 39.130 0.00 0.00 0.00 2.85
2129 4945 1.920574 GCGTGCATATAGAGCCATACG 59.079 52.381 0.00 0.00 33.68 3.06
2140 4956 3.022401 GCCATACGGTGCGTGTGTG 62.022 63.158 0.00 0.00 44.99 3.82
2152 4968 1.467342 GCGTGTGTGTAGGATTTTCCC 59.533 52.381 0.00 0.00 37.19 3.97
2274 7488 3.247648 GTCAGTTGAACAACGCACATAGT 59.752 43.478 11.21 0.00 45.50 2.12
2286 7500 3.242969 ACGCACATAGTATAGTCCACGTG 60.243 47.826 9.08 9.08 0.00 4.49
2298 7512 0.750249 TCCACGTGCTCTGTGAAGAA 59.250 50.000 10.91 0.00 39.73 2.52
2332 7546 0.681564 AGTGTTGGGGAACGTTGCAA 60.682 50.000 21.74 5.29 0.00 4.08
3039 8266 1.142262 GGTACAATACCGGAATGCCCT 59.858 52.381 9.46 0.00 39.39 5.19
3071 8298 2.355444 CGGTGTCCGTTTAACCACTTTT 59.645 45.455 0.00 0.00 42.73 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 5.090139 ACAATTTGGAGAGAGAGAGAAGGA 58.910 41.667 0.78 0.00 0.00 3.36
57 58 5.101628 CGACAATTTGGAGAGAGAGAGAAG 58.898 45.833 0.78 0.00 0.00 2.85
59 60 4.082845 ACGACAATTTGGAGAGAGAGAGA 58.917 43.478 0.78 0.00 0.00 3.10
94 108 9.474313 AGAGAGAGAAATCAAGTGATTACTAGT 57.526 33.333 6.95 0.00 43.41 2.57
95 109 9.950680 GAGAGAGAGAAATCAAGTGATTACTAG 57.049 37.037 6.95 0.00 43.41 2.57
98 112 7.920682 GGAGAGAGAGAGAAATCAAGTGATTAC 59.079 40.741 6.95 3.19 43.41 1.89
109 123 5.395546 GCACATGAAGGAGAGAGAGAGAAAT 60.396 44.000 0.00 0.00 0.00 2.17
113 127 2.101249 GGCACATGAAGGAGAGAGAGAG 59.899 54.545 0.00 0.00 0.00 3.20
126 198 0.904649 CCTACTGACCTGGCACATGA 59.095 55.000 0.00 0.00 38.20 3.07
180 253 1.252175 GTGCAGGTGAGAGAGTGAGA 58.748 55.000 0.00 0.00 0.00 3.27
196 269 3.902162 TTCGTACGGTCGCCTGTGC 62.902 63.158 16.52 0.00 0.00 4.57
200 273 2.493030 CCATTCGTACGGTCGCCT 59.507 61.111 16.52 0.00 0.00 5.52
201 274 2.584143 CCCATTCGTACGGTCGCC 60.584 66.667 16.52 0.00 0.00 5.54
215 288 1.246056 CGTCCTGTTCCGTAGTCCCA 61.246 60.000 0.00 0.00 0.00 4.37
278 356 1.244019 GCACCAGGTTTTGCTCCGAT 61.244 55.000 0.00 0.00 35.74 4.18
292 370 2.265182 GCGCCTTAACCAAGCACCA 61.265 57.895 0.00 0.00 0.00 4.17
320 399 3.006728 CCAGAAGCCGGTGGGGTA 61.007 66.667 1.90 0.00 45.20 3.69
336 415 0.175073 CACGGAAGGTACACTAGGCC 59.825 60.000 0.00 0.00 0.00 5.19
340 419 3.244875 TGGAGTACACGGAAGGTACACTA 60.245 47.826 0.00 0.00 42.73 2.74
342 421 1.888512 TGGAGTACACGGAAGGTACAC 59.111 52.381 0.00 0.00 42.73 2.90
354 433 0.604578 GCGGGTACAGTTGGAGTACA 59.395 55.000 0.00 0.00 42.73 2.90
444 547 1.302752 GGAGCATGGAGTGTGCACA 60.303 57.895 17.42 17.42 44.87 4.57
523 933 7.551262 TGGTTGAACTGGAATATACACACATAC 59.449 37.037 0.00 0.00 0.00 2.39
525 935 6.480763 TGGTTGAACTGGAATATACACACAT 58.519 36.000 0.00 0.00 0.00 3.21
527 937 6.811253 TTGGTTGAACTGGAATATACACAC 57.189 37.500 0.00 0.00 0.00 3.82
539 949 5.807011 GCCAGCTATTAATTTGGTTGAACTG 59.193 40.000 12.28 0.00 33.21 3.16
545 955 2.693074 CGGGCCAGCTATTAATTTGGTT 59.307 45.455 4.39 0.00 33.21 3.67
547 957 1.000274 GCGGGCCAGCTATTAATTTGG 60.000 52.381 21.61 1.30 0.00 3.28
548 958 1.680735 TGCGGGCCAGCTATTAATTTG 59.319 47.619 28.31 0.00 38.13 2.32
549 959 2.065899 TGCGGGCCAGCTATTAATTT 57.934 45.000 28.31 0.00 38.13 1.82
550 960 2.065899 TTGCGGGCCAGCTATTAATT 57.934 45.000 28.31 0.00 38.13 1.40
551 961 2.065899 TTTGCGGGCCAGCTATTAAT 57.934 45.000 28.31 0.00 38.13 1.40
552 962 1.840737 TTTTGCGGGCCAGCTATTAA 58.159 45.000 28.31 11.77 38.13 1.40
553 963 1.840737 TTTTTGCGGGCCAGCTATTA 58.159 45.000 28.31 9.70 38.13 0.98
554 964 2.664825 TTTTTGCGGGCCAGCTATT 58.335 47.368 28.31 0.00 38.13 1.73
555 965 4.432601 TTTTTGCGGGCCAGCTAT 57.567 50.000 28.31 0.00 38.13 2.97
619 1514 4.279922 ACCCCACAACTAAATTTGCAGTAC 59.720 41.667 0.00 0.00 0.00 2.73
628 1769 4.668138 ACATACCACCCCACAACTAAAT 57.332 40.909 0.00 0.00 0.00 1.40
691 2243 5.270812 GACGAACAGTCTCCTTCATTTTC 57.729 43.478 0.00 0.00 46.13 2.29
710 2275 6.599437 CCTAGTTCAACTTAAAACCATGACG 58.401 40.000 0.00 0.00 0.00 4.35
761 2327 3.501062 GGCTGGTTACACTGGTTAAAGTC 59.499 47.826 0.00 0.00 0.00 3.01
782 2455 5.982890 ACTTGGGAAATATGAAACTGTGG 57.017 39.130 0.00 0.00 0.00 4.17
807 2480 5.118990 CCCTGCTTCATTCTAAATCGAGAA 58.881 41.667 0.00 0.00 39.71 2.87
851 2814 1.540435 TTCGGGTACACGGGGTTACC 61.540 60.000 19.08 0.00 0.00 2.85
885 3016 2.733026 ACAAATTCTTTGCTGCGAATGC 59.267 40.909 2.18 0.00 44.39 3.56
891 3022 5.851047 AGCATTTACAAATTCTTTGCTGC 57.149 34.783 0.00 0.00 44.39 5.25
892 3023 7.450627 GCTTAGCATTTACAAATTCTTTGCTG 58.549 34.615 0.00 0.00 44.39 4.41
913 3044 5.242434 TCTTGCCATTACTTTTCTCGCTTA 58.758 37.500 0.00 0.00 0.00 3.09
925 3056 2.359900 CACAGGTCCTCTTGCCATTAC 58.640 52.381 0.00 0.00 0.00 1.89
964 3098 2.301870 TGGCTGCTTATATAACGGGAGG 59.698 50.000 0.00 0.00 0.00 4.30
1006 3555 0.319900 GCTGAGAGAACACAAGGCGA 60.320 55.000 0.00 0.00 0.00 5.54
1031 3599 3.771160 CCTTGGGGAGGGACGACG 61.771 72.222 0.00 0.00 42.26 5.12
1043 3658 4.796231 CGACGCCGGAGACCTTGG 62.796 72.222 13.83 0.00 0.00 3.61
1063 3678 2.749044 CATGGTGCCGCTGCTTCT 60.749 61.111 0.70 0.00 38.71 2.85
1187 3802 0.797542 CGAGGACGACGAAGAAGAGT 59.202 55.000 0.00 0.00 42.66 3.24
1540 4172 1.271127 TTCCATCACGCCCTCCATGA 61.271 55.000 0.00 0.00 0.00 3.07
1565 4202 2.694580 ATTTGCCTTTGCCAGGGGGT 62.695 55.000 1.35 0.00 44.16 4.95
1672 4326 0.903454 CGTCCTACCCTCCACCAACT 60.903 60.000 0.00 0.00 0.00 3.16
1712 4376 5.003804 GTCCTAAAATTGTTGAGCTCCAGA 58.996 41.667 12.15 0.00 0.00 3.86
1716 4380 4.379918 GCAGGTCCTAAAATTGTTGAGCTC 60.380 45.833 6.82 6.82 31.92 4.09
1776 4531 6.712114 TGATCTAGAGCTACCTAGAGGAAT 57.288 41.667 15.23 1.90 45.68 3.01
1892 4660 5.425196 TCATCCATTTCACTCACATGAGA 57.575 39.130 15.76 0.00 44.74 3.27
2018 4805 5.692115 ATCATTGTAGTACACCATGGTCA 57.308 39.130 16.53 5.94 32.40 4.02
2066 4857 6.017109 CCATAAAACCTAGATTTCCATGTCCG 60.017 42.308 0.00 0.00 0.00 4.79
2067 4858 6.265422 CCCATAAAACCTAGATTTCCATGTCC 59.735 42.308 0.00 0.00 0.00 4.02
2068 4859 6.239036 GCCCATAAAACCTAGATTTCCATGTC 60.239 42.308 0.00 0.00 0.00 3.06
2074 4890 5.201243 ACCTGCCCATAAAACCTAGATTTC 58.799 41.667 0.00 0.00 0.00 2.17
2099 4915 5.334414 GCTCTATATGCACGCAGCTATTTTT 60.334 40.000 0.00 0.00 45.94 1.94
2129 4945 1.519408 AAATCCTACACACACGCACC 58.481 50.000 0.00 0.00 0.00 5.01
2240 7454 4.081697 TGTTCAACTGACTGAGTTCTCACA 60.082 41.667 0.00 0.00 43.52 3.58
2274 7488 2.718563 TCACAGAGCACGTGGACTATA 58.281 47.619 18.88 0.00 35.03 1.31
2286 7500 2.983803 GACGAGACTTTCTTCACAGAGC 59.016 50.000 0.00 0.00 0.00 4.09
2298 7512 3.193691 CCAACACTATCTGGACGAGACTT 59.806 47.826 0.00 0.00 34.35 3.01
3039 8266 0.598158 CGGACACCGGAAAGTTTCGA 60.598 55.000 9.46 0.00 44.15 3.71
3144 8371 5.478233 TGTATGTGATTACCGAATGTTGC 57.522 39.130 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.