Multiple sequence alignment - TraesCS4A01G148700

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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 TraesCS4A01G148700 chr4A 100.000 1798 0 0 1 1798 280930326 280932123 0.000000e+00 3321.0
1 TraesCS4A01G148700 chr4A 91.473 903 66 2 1 892 350191938 350191036 0.000000e+00 1230.0
2 TraesCS4A01G148700 chr4A 91.061 716 51 6 189 892 350159768 350160482 0.000000e+00 955.0
3 TraesCS4A01G148700 chr4A 92.295 597 40 2 1 591 295191503 295190907 0.000000e+00 843.0
4 TraesCS4A01G148700 chr4A 100.000 431 0 0 2065 2495 280932390 280932820 0.000000e+00 797.0
5 TraesCS4A01G148700 chr4A 93.333 60 4 0 948 1007 48690185 48690244 3.420000e-14 89.8
6 TraesCS4A01G148700 chr3A 92.470 996 71 2 807 1798 122209754 122208759 0.000000e+00 1421.0
7 TraesCS4A01G148700 chr3A 92.169 996 74 2 807 1798 247672664 247673659 0.000000e+00 1404.0
8 TraesCS4A01G148700 chr3A 90.248 564 49 3 1 563 712332142 712332700 0.000000e+00 732.0
9 TraesCS4A01G148700 chr3A 95.062 324 16 0 2172 2495 247674138 247674461 6.160000e-141 510.0
10 TraesCS4A01G148700 chr3A 83.929 112 9 8 813 920 191857853 191857959 5.680000e-17 99.0
11 TraesCS4A01G148700 chr2B 91.466 996 81 2 807 1798 234505862 234504867 0.000000e+00 1365.0
12 TraesCS4A01G148700 chr2B 92.532 790 58 1 1010 1798 385135054 385134265 0.000000e+00 1131.0
13 TraesCS4A01G148700 chr2B 94.753 324 17 0 2172 2495 357467609 357467932 2.860000e-139 505.0
14 TraesCS4A01G148700 chr2B 94.444 324 18 0 2172 2495 234504389 234504066 1.330000e-137 499.0
15 TraesCS4A01G148700 chr7A 93.165 790 53 1 1010 1798 60326917 60326128 0.000000e+00 1158.0
16 TraesCS4A01G148700 chr7A 95.342 322 15 0 2174 2495 60325649 60325328 1.710000e-141 512.0
17 TraesCS4A01G148700 chr1A 93.038 790 54 1 1010 1798 238107652 238106863 0.000000e+00 1153.0
18 TraesCS4A01G148700 chr1A 93.038 790 54 1 1010 1798 238153037 238152248 0.000000e+00 1153.0
19 TraesCS4A01G148700 chr1A 94.753 324 17 0 2172 2495 238106384 238106061 2.860000e-139 505.0
20 TraesCS4A01G148700 chr1A 94.753 324 17 0 2172 2495 238151769 238151446 2.860000e-139 505.0
21 TraesCS4A01G148700 chr5A 92.911 790 55 1 1010 1798 16575827 16575038 0.000000e+00 1147.0
22 TraesCS4A01G148700 chr5A 92.105 646 39 3 258 892 162145981 162145337 0.000000e+00 900.0
23 TraesCS4A01G148700 chr5A 95.062 324 16 0 2172 2495 16574560 16574237 6.160000e-141 510.0
24 TraesCS4A01G148700 chr4B 92.278 790 60 1 1010 1798 209048948 209049737 0.000000e+00 1120.0
25 TraesCS4A01G148700 chr5D 94.643 616 33 0 1 616 555235678 555236293 0.000000e+00 955.0
26 TraesCS4A01G148700 chr5D 94.872 585 29 1 1 585 80104681 80104098 0.000000e+00 913.0
27 TraesCS4A01G148700 chr6D 94.118 595 25 2 1 585 430467386 430466792 0.000000e+00 896.0
28 TraesCS4A01G148700 chr6D 92.125 546 40 2 42 585 183386761 183386217 0.000000e+00 767.0
29 TraesCS4A01G148700 chr6D 89.443 341 30 4 471 805 153952982 153953322 2.290000e-115 425.0
30 TraesCS4A01G148700 chr4D 93.686 586 29 5 1 585 241310431 241311009 0.000000e+00 870.0
31 TraesCS4A01G148700 chr4D 93.548 558 31 1 1 553 135047631 135048188 0.000000e+00 826.0
32 TraesCS4A01G148700 chr3D 88.776 588 60 3 1 585 576907267 576906683 0.000000e+00 715.0
33 TraesCS4A01G148700 chr6B 95.062 324 16 0 2172 2495 596653946 596653623 6.160000e-141 510.0
34 TraesCS4A01G148700 chr1B 94.753 324 17 0 2172 2495 672505217 672504894 2.860000e-139 505.0
35 TraesCS4A01G148700 chr3B 89.664 387 33 5 506 886 575858253 575857868 1.040000e-133 486.0
36 TraesCS4A01G148700 chr2A 92.982 57 3 1 865 920 755511559 755511503 5.720000e-12 82.4
37 TraesCS4A01G148700 chr2A 87.719 57 7 0 593 649 246815154 246815210 1.600000e-07 67.6


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 TraesCS4A01G148700 chr4A 280930326 280932820 2494 False 2059.0 3321 100.0000 1 2495 2 chr4A.!!$F3 2494
1 TraesCS4A01G148700 chr4A 350191036 350191938 902 True 1230.0 1230 91.4730 1 892 1 chr4A.!!$R2 891
2 TraesCS4A01G148700 chr4A 350159768 350160482 714 False 955.0 955 91.0610 189 892 1 chr4A.!!$F2 703
3 TraesCS4A01G148700 chr4A 295190907 295191503 596 True 843.0 843 92.2950 1 591 1 chr4A.!!$R1 590
4 TraesCS4A01G148700 chr3A 122208759 122209754 995 True 1421.0 1421 92.4700 807 1798 1 chr3A.!!$R1 991
5 TraesCS4A01G148700 chr3A 247672664 247674461 1797 False 957.0 1404 93.6155 807 2495 2 chr3A.!!$F3 1688
6 TraesCS4A01G148700 chr3A 712332142 712332700 558 False 732.0 732 90.2480 1 563 1 chr3A.!!$F2 562
7 TraesCS4A01G148700 chr2B 385134265 385135054 789 True 1131.0 1131 92.5320 1010 1798 1 chr2B.!!$R1 788
8 TraesCS4A01G148700 chr2B 234504066 234505862 1796 True 932.0 1365 92.9550 807 2495 2 chr2B.!!$R2 1688
9 TraesCS4A01G148700 chr7A 60325328 60326917 1589 True 835.0 1158 94.2535 1010 2495 2 chr7A.!!$R1 1485
10 TraesCS4A01G148700 chr1A 238106061 238107652 1591 True 829.0 1153 93.8955 1010 2495 2 chr1A.!!$R1 1485
11 TraesCS4A01G148700 chr1A 238151446 238153037 1591 True 829.0 1153 93.8955 1010 2495 2 chr1A.!!$R2 1485
12 TraesCS4A01G148700 chr5A 162145337 162145981 644 True 900.0 900 92.1050 258 892 1 chr5A.!!$R1 634
13 TraesCS4A01G148700 chr5A 16574237 16575827 1590 True 828.5 1147 93.9865 1010 2495 2 chr5A.!!$R2 1485
14 TraesCS4A01G148700 chr4B 209048948 209049737 789 False 1120.0 1120 92.2780 1010 1798 1 chr4B.!!$F1 788
15 TraesCS4A01G148700 chr5D 555235678 555236293 615 False 955.0 955 94.6430 1 616 1 chr5D.!!$F1 615
16 TraesCS4A01G148700 chr5D 80104098 80104681 583 True 913.0 913 94.8720 1 585 1 chr5D.!!$R1 584
17 TraesCS4A01G148700 chr6D 430466792 430467386 594 True 896.0 896 94.1180 1 585 1 chr6D.!!$R2 584
18 TraesCS4A01G148700 chr6D 183386217 183386761 544 True 767.0 767 92.1250 42 585 1 chr6D.!!$R1 543
19 TraesCS4A01G148700 chr4D 241310431 241311009 578 False 870.0 870 93.6860 1 585 1 chr4D.!!$F2 584
20 TraesCS4A01G148700 chr4D 135047631 135048188 557 False 826.0 826 93.5480 1 553 1 chr4D.!!$F1 552
21 TraesCS4A01G148700 chr3D 576906683 576907267 584 True 715.0 715 88.7760 1 585 1 chr3D.!!$R1 584

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
294 301 2.154462 CTGGAACCCATCAATATCGCC 58.846 52.381 0.0 0.0 30.82 5.54 F
1366 1422 0.774096 TCCCATTGACCAACCTCCCA 60.774 55.000 0.0 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 1545 0.179111 CGCGCAGATTCACCCTCTTA 60.179 55.0 8.75 0.0 0.00 2.10 R
2342 2730 2.049888 TGTGGAACATGTGTGAGCAA 57.950 45.0 0.00 0.0 45.67 3.91 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
83 84 3.515901 AGAGCCCTCTTTTCATACGACTT 59.484 43.478 0.00 0.00 36.31 3.01
106 107 3.495100 GGTGATTCCATTGCTCTATCCGT 60.495 47.826 0.00 0.00 35.97 4.69
294 301 2.154462 CTGGAACCCATCAATATCGCC 58.846 52.381 0.00 0.00 30.82 5.54
299 306 3.297134 ACCCATCAATATCGCCAAACT 57.703 42.857 0.00 0.00 0.00 2.66
355 362 5.578727 CGCTCTACCAAGGCAAGATATAATC 59.421 44.000 0.00 0.00 0.00 1.75
410 462 2.987149 CGTGAGTGTTCAGCGAAGTATT 59.013 45.455 0.00 0.00 32.98 1.89
421 473 4.122776 CAGCGAAGTATTCTAGCCATTGT 58.877 43.478 0.00 0.00 44.75 2.71
549 601 3.489059 CCAGTGTTTGTGTTACAAGGCAG 60.489 47.826 0.00 0.00 39.53 4.85
592 644 3.127589 TCGTGAAACAATGTCATGTCGT 58.872 40.909 0.00 0.00 35.74 4.34
629 681 9.331282 GTTAGAAGGAGCTAAATCAATATGTGT 57.669 33.333 0.00 0.00 32.58 3.72
637 689 4.882671 AAATCAATATGTGTCGGTGCTC 57.117 40.909 0.00 0.00 0.00 4.26
745 798 9.474920 GTTTGGAAGATATGTCAAACATTCAAA 57.525 29.630 10.52 0.00 44.66 2.69
748 801 9.474920 TGGAAGATATGTCAAACATTCAAAAAC 57.525 29.630 0.00 0.00 39.88 2.43
764 817 3.531262 AAAACGGCGTTGTTGATCTAC 57.469 42.857 27.50 0.00 31.10 2.59
780 833 9.667107 TGTTGATCTACTTAGGTTTCTAATTGG 57.333 33.333 8.74 0.00 35.20 3.16
791 844 6.306987 AGGTTTCTAATTGGTGAGTGTGAAT 58.693 36.000 0.00 0.00 0.00 2.57
845 898 2.783135 ACCAATGCAGACGTCAAGATT 58.217 42.857 19.50 9.05 0.00 2.40
869 925 6.253946 AGTCTCCTTTCCTTTCTCTTTTCA 57.746 37.500 0.00 0.00 0.00 2.69
881 937 3.435275 TCTCTTTTCAGGAGCAGAGCTA 58.565 45.455 0.00 0.00 39.88 3.32
955 1011 3.990092 ACAATCGCTCTTTGTGACACTA 58.010 40.909 7.20 0.00 38.09 2.74
986 1042 3.197766 TGGCAATTAGGATCTCAAGACGT 59.802 43.478 0.00 0.00 0.00 4.34
1148 1204 7.752695 CAAAGGATTGTTCATGGAACTACTAC 58.247 38.462 10.14 0.00 42.39 2.73
1179 1235 4.295141 TCGGACCATATTTCCAAGTGTT 57.705 40.909 0.00 0.00 31.94 3.32
1183 1239 7.566569 TCGGACCATATTTCCAAGTGTTATTA 58.433 34.615 0.00 0.00 31.94 0.98
1271 1327 7.093465 TGTCTTATTCGGAGTTCAAGGAATAGT 60.093 37.037 0.00 0.00 34.09 2.12
1277 1333 4.563184 CGGAGTTCAAGGAATAGTCTTTCG 59.437 45.833 0.00 0.00 0.00 3.46
1284 1340 5.245301 TCAAGGAATAGTCTTTCGTCTTGGA 59.755 40.000 0.00 0.00 31.38 3.53
1297 1353 5.152623 TCGTCTTGGAAATGAGAATGTCT 57.847 39.130 0.00 0.00 0.00 3.41
1338 1394 3.055458 TCATGACCAATGCTCCTAACGAA 60.055 43.478 0.00 0.00 36.11 3.85
1366 1422 0.774096 TCCCATTGACCAACCTCCCA 60.774 55.000 0.00 0.00 0.00 4.37
1378 1434 0.912487 ACCTCCCATTGGCGGACTAA 60.912 55.000 14.17 0.00 38.98 2.24
1388 1444 0.896226 GGCGGACTAACAGACCTCTT 59.104 55.000 0.00 0.00 0.00 2.85
1391 1447 1.546476 CGGACTAACAGACCTCTTGCT 59.454 52.381 0.00 0.00 0.00 3.91
1398 1454 3.515602 ACAGACCTCTTGCTGGAAATT 57.484 42.857 0.00 0.00 36.47 1.82
1399 1455 4.640771 ACAGACCTCTTGCTGGAAATTA 57.359 40.909 0.00 0.00 36.47 1.40
1425 1481 1.528824 CGCCCATCCCTCAGACATT 59.471 57.895 0.00 0.00 0.00 2.71
1431 1487 3.181436 CCCATCCCTCAGACATTATTGCT 60.181 47.826 0.00 0.00 0.00 3.91
1489 1545 4.625963 AGTAGGCACTCCTCTTCCTTTAT 58.374 43.478 0.00 0.00 43.06 1.40
1491 1547 6.203072 AGTAGGCACTCCTCTTCCTTTATAA 58.797 40.000 0.00 0.00 43.06 0.98
1494 1550 5.365314 AGGCACTCCTCTTCCTTTATAAGAG 59.635 44.000 5.97 5.97 46.29 2.85
1520 1576 2.792290 CTGCGCGATCGTTCACTGG 61.792 63.158 17.81 0.19 38.14 4.00
1543 1599 9.559732 CTGGAAATCATGTATTGTGGAATAGTA 57.440 33.333 0.00 0.00 0.00 1.82
1575 1631 7.221838 GGAGATACTCTTCAACAAATCTTCTCG 59.778 40.741 0.00 0.00 0.00 4.04
1585 1641 7.485810 TCAACAAATCTTCTCGGATTATACGA 58.514 34.615 0.00 0.00 35.19 3.43
1589 1645 8.195436 ACAAATCTTCTCGGATTATACGAAAGA 58.805 33.333 18.89 18.89 40.16 2.52
1609 1665 6.693315 AAGACGGAGACAAAAGAAAATTCA 57.307 33.333 0.00 0.00 0.00 2.57
1643 1699 2.463589 AATCTGGCGAGGCGGTTTCA 62.464 55.000 5.38 0.00 0.00 2.69
1650 1706 1.227853 GAGGCGGTTTCACCACACT 60.228 57.895 0.00 0.00 38.47 3.55
1651 1707 0.034337 GAGGCGGTTTCACCACACTA 59.966 55.000 0.00 0.00 38.47 2.74
1730 1786 1.692534 TCCATGGGATCCCCTGAAAA 58.307 50.000 31.57 16.70 45.70 2.29
1776 1833 2.657237 CAGGCCCGTCTTCTTCGT 59.343 61.111 0.00 0.00 0.00 3.85
1784 1841 1.782181 GTCTTCTTCGTGGAAGCGC 59.218 57.895 0.00 0.00 41.55 5.92
2095 2152 6.363626 CAGATCCTATGGAAATCGTTTACGAG 59.636 42.308 10.92 0.00 43.22 4.18
2116 2173 1.341976 GGGGATGCACAAGGGTACAAT 60.342 52.381 0.00 0.00 0.00 2.71
2125 2182 0.335019 AAGGGTACAATTGGGAGGGC 59.665 55.000 10.83 0.00 0.00 5.19
2162 2219 3.129287 CCAACTTCGCATGCCTTTCTATT 59.871 43.478 13.15 0.00 0.00 1.73
2187 2575 5.014123 TGAGTTCTTCCCAATGGTGTAAGAT 59.986 40.000 8.98 0.00 29.68 2.40
2189 2577 5.014123 AGTTCTTCCCAATGGTGTAAGATCA 59.986 40.000 14.36 1.09 29.68 2.92
2231 2619 6.439487 AGGAGGAAAATCACTCTGATCTCTA 58.561 40.000 0.00 0.00 35.76 2.43
2333 2721 1.442769 CAGTCGGATCACTTGTTGGG 58.557 55.000 0.00 0.00 0.00 4.12
2342 2730 5.125417 CGGATCACTTGTTGGGAAAACATAT 59.875 40.000 0.00 0.00 0.00 1.78
2362 2750 2.275134 TGCTCACACATGTTCCACAT 57.725 45.000 0.00 0.00 39.91 3.21
2389 2777 7.310237 GGGCAAGGAAGCATAATATCATGAAAT 60.310 37.037 0.00 0.00 35.83 2.17
2416 2804 8.577296 CCGTCTGATAATCTTTCTATAGGTTCA 58.423 37.037 0.00 0.00 0.00 3.18
2440 2828 5.711976 ACCGAAGAGAATGGAAAAATCACAT 59.288 36.000 0.00 0.00 0.00 3.21
2449 2837 9.480053 AGAATGGAAAAATCACATAAACACTTG 57.520 29.630 0.00 0.00 0.00 3.16
2461 2849 8.755028 TCACATAAACACTTGCTATAGGTTCTA 58.245 33.333 1.04 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.324388 CCCTAGGGGTTGTCATATTACAATA 57.676 40.000 21.44 0.00 41.18 1.90
36 37 8.880878 TTCTTTTTAATCTTAACACAAAGGCC 57.119 30.769 0.00 0.00 0.00 5.19
106 107 2.654749 ACGTGATCGAATCTTGCAGA 57.345 45.000 0.00 0.00 40.62 4.26
256 263 0.621571 AGCCTCATTCCACTAGCCCA 60.622 55.000 0.00 0.00 0.00 5.36
294 301 2.033801 CACAAGCAACTCTCCCAGTTTG 59.966 50.000 0.00 0.00 43.38 2.93
299 306 1.679139 CAACACAAGCAACTCTCCCA 58.321 50.000 0.00 0.00 0.00 4.37
360 382 8.557592 TTCAGCTAAATCTGGATGCATATTAG 57.442 34.615 0.00 0.00 34.91 1.73
375 427 7.041721 TGAACACTCACGATATTCAGCTAAAT 58.958 34.615 0.00 0.00 0.00 1.40
410 462 3.512329 TGAACGTAAGGACAATGGCTAGA 59.488 43.478 0.00 0.00 46.39 2.43
445 497 8.417106 TCTTATAACCAAACATTGCAAAGACAA 58.583 29.630 8.96 0.00 0.00 3.18
534 586 2.151202 GCTAGCTGCCTTGTAACACAA 58.849 47.619 7.70 0.00 36.54 3.33
537 589 2.787473 ATGCTAGCTGCCTTGTAACA 57.213 45.000 17.23 0.00 42.00 2.41
549 601 4.708726 ACTTCCATGACAAAATGCTAGC 57.291 40.909 8.10 8.10 0.00 3.42
592 644 3.119459 GCTCCTTCTAACATGTCGAGTCA 60.119 47.826 0.00 0.00 0.00 3.41
625 677 4.184439 TGTAGGAGCACCGACACA 57.816 55.556 11.88 6.62 44.48 3.72
629 681 1.141019 GCGATTGTAGGAGCACCGA 59.859 57.895 0.00 0.00 41.83 4.69
637 689 1.202486 TCCGGCTAAAGCGATTGTAGG 60.202 52.381 0.00 0.00 43.26 3.18
664 716 4.899502 AGATCACGAATCACACCTTTCTT 58.100 39.130 0.00 0.00 36.79 2.52
745 798 2.762745 AGTAGATCAACAACGCCGTTT 58.237 42.857 0.00 0.00 0.00 3.60
748 801 2.858344 CCTAAGTAGATCAACAACGCCG 59.142 50.000 0.00 0.00 0.00 6.46
764 817 6.934645 TCACACTCACCAATTAGAAACCTAAG 59.065 38.462 0.00 0.00 30.46 2.18
780 833 9.736023 ATTTTTAGAACAGAAATTCACACTCAC 57.264 29.630 0.00 0.00 0.00 3.51
830 883 3.119459 GGAGACTAATCTTGACGTCTGCA 60.119 47.826 17.92 0.00 42.23 4.41
833 886 5.105675 GGAAAGGAGACTAATCTTGACGTCT 60.106 44.000 17.92 0.00 42.68 4.18
845 898 7.374975 TGAAAAGAGAAAGGAAAGGAGACTA 57.625 36.000 0.00 0.00 42.68 2.59
887 943 6.833416 ACGAAGAATCATTGGAATTTCCCATA 59.167 34.615 12.90 0.00 35.03 2.74
951 1007 1.750193 ATTGCCATGGTTCCGTAGTG 58.250 50.000 14.67 0.00 0.00 2.74
952 1008 2.507407 AATTGCCATGGTTCCGTAGT 57.493 45.000 14.67 0.00 0.00 2.73
955 1011 1.283613 TCCTAATTGCCATGGTTCCGT 59.716 47.619 14.67 0.00 0.00 4.69
986 1042 3.199727 TCCTTGCATCATAGGTGTTGCTA 59.800 43.478 11.37 4.82 46.40 3.49
1069 1125 0.665835 AAAGCGCGAACCAACATCAA 59.334 45.000 12.10 0.00 0.00 2.57
1070 1126 1.514003 TAAAGCGCGAACCAACATCA 58.486 45.000 12.10 0.00 0.00 3.07
1148 1204 7.721402 TGGAAATATGGTCCGAATAATTTTGG 58.279 34.615 2.15 0.00 38.06 3.28
1201 1257 3.058293 GTCAACGCAAGACCAAATGATGA 60.058 43.478 0.00 0.00 43.62 2.92
1206 1262 2.297701 ACTGTCAACGCAAGACCAAAT 58.702 42.857 0.00 0.00 43.62 2.32
1271 1327 5.997746 ACATTCTCATTTCCAAGACGAAAGA 59.002 36.000 0.00 0.00 35.31 2.52
1297 1353 5.126061 TCATGACGAGAACATTGAGATCTGA 59.874 40.000 0.00 0.00 28.28 3.27
1299 1355 5.347342 GTCATGACGAGAACATTGAGATCT 58.653 41.667 10.69 0.00 31.20 2.75
1338 1394 1.780309 TGGTCAATGGGAAAGTCACCT 59.220 47.619 0.00 0.00 0.00 4.00
1353 1409 1.076549 GCCAATGGGAGGTTGGTCA 59.923 57.895 0.00 0.00 46.21 4.02
1366 1422 1.207329 GAGGTCTGTTAGTCCGCCAAT 59.793 52.381 0.00 0.00 0.00 3.16
1378 1434 3.515602 AATTTCCAGCAAGAGGTCTGT 57.484 42.857 0.00 0.00 0.00 3.41
1388 1444 1.499949 GCGTGCGTAATTTCCAGCA 59.500 52.632 0.00 0.00 37.26 4.41
1391 1447 3.029564 GCGGCGTGCGTAATTTCCA 62.030 57.895 9.37 0.00 0.00 3.53
1417 1473 5.798132 AGTCAACTCAGCAATAATGTCTGA 58.202 37.500 5.27 5.27 37.37 3.27
1418 1474 6.402983 GGAAGTCAACTCAGCAATAATGTCTG 60.403 42.308 0.00 0.00 34.22 3.51
1425 1481 4.202461 ACCTTGGAAGTCAACTCAGCAATA 60.202 41.667 0.00 0.00 0.00 1.90
1431 1487 3.924114 TCAACCTTGGAAGTCAACTCA 57.076 42.857 0.00 0.00 0.00 3.41
1489 1545 0.179111 CGCGCAGATTCACCCTCTTA 60.179 55.000 8.75 0.00 0.00 2.10
1491 1547 1.680522 ATCGCGCAGATTCACCCTCT 61.681 55.000 8.75 0.00 35.73 3.69
1494 1550 2.589492 CGATCGCGCAGATTCACCC 61.589 63.158 8.75 0.00 40.26 4.61
1575 1631 5.179045 TGTCTCCGTCTTTCGTATAATCC 57.821 43.478 0.00 0.00 37.94 3.01
1585 1641 7.095695 TGAATTTTCTTTTGTCTCCGTCTTT 57.904 32.000 0.00 0.00 0.00 2.52
1589 1645 5.689819 CGATGAATTTTCTTTTGTCTCCGT 58.310 37.500 0.00 0.00 0.00 4.69
1593 1649 7.274250 GCTATTGCGATGAATTTTCTTTTGTCT 59.726 33.333 0.00 0.00 0.00 3.41
1597 1653 6.311200 GTGGCTATTGCGATGAATTTTCTTTT 59.689 34.615 0.00 0.00 40.82 2.27
1598 1654 5.807011 GTGGCTATTGCGATGAATTTTCTTT 59.193 36.000 0.00 0.00 40.82 2.52
1602 1658 3.446873 TGGTGGCTATTGCGATGAATTTT 59.553 39.130 0.00 0.00 40.82 1.82
1603 1659 3.023119 TGGTGGCTATTGCGATGAATTT 58.977 40.909 0.00 0.00 40.82 1.82
1609 1665 2.224606 CAGATTGGTGGCTATTGCGAT 58.775 47.619 0.00 0.00 40.82 4.58
1643 1699 1.045407 TTCACCGAGCTTAGTGTGGT 58.955 50.000 14.56 2.31 35.45 4.16
1646 1702 3.908737 GGTTCACCGAGCTTAGTGT 57.091 52.632 14.56 0.00 35.45 3.55
1730 1786 2.769893 GCCCATCATTTGCTTTTGTGT 58.230 42.857 0.00 0.00 0.00 3.72
1776 1833 2.199652 CCCACCTTTTGCGCTTCCA 61.200 57.895 9.73 0.00 0.00 3.53
2095 2152 1.076995 GTACCCTTGTGCATCCCCC 60.077 63.158 0.00 0.00 0.00 5.40
2116 2173 1.272985 CCAACCTAATTGCCCTCCCAA 60.273 52.381 0.00 0.00 36.93 4.12
2125 2182 2.271940 TTGGCGGCCAACCTAATTG 58.728 52.632 29.66 0.00 38.75 2.32
2150 2207 5.654209 GGGAAGAACTCAAATAGAAAGGCAT 59.346 40.000 0.00 0.00 0.00 4.40
2162 2219 3.593442 ACACCATTGGGAAGAACTCAA 57.407 42.857 7.78 0.00 43.57 3.02
2187 2575 5.811190 TCCTTTTTCCCAAATAGTCGATGA 58.189 37.500 0.00 0.00 0.00 2.92
2189 2577 5.045140 TCCTCCTTTTTCCCAAATAGTCGAT 60.045 40.000 0.00 0.00 0.00 3.59
2231 2619 5.123979 GTGAGCCACTTATTTCTCCGAAATT 59.876 40.000 7.09 0.00 0.00 1.82
2295 2683 7.123697 TCCGACTGGAAGAAGTTTTATATGAGA 59.876 37.037 0.00 0.00 42.85 3.27
2333 2721 6.308766 GGAACATGTGTGAGCAATATGTTTTC 59.691 38.462 0.00 0.00 41.02 2.29
2342 2730 2.049888 TGTGGAACATGTGTGAGCAA 57.950 45.000 0.00 0.00 45.67 3.91
2362 2750 4.451891 TGATATTATGCTTCCTTGCCCA 57.548 40.909 0.00 0.00 0.00 5.36
2389 2777 8.707796 AACCTATAGAAAGATTATCAGACGGA 57.292 34.615 0.00 0.00 0.00 4.69
2416 2804 5.070001 TGTGATTTTTCCATTCTCTTCGGT 58.930 37.500 0.00 0.00 0.00 4.69
2461 2849 8.555361 GCTTGCTTCTTCGAATCTAGAAATAAT 58.445 33.333 0.00 0.00 30.55 1.28
2469 2857 4.569943 ACTTGCTTGCTTCTTCGAATCTA 58.430 39.130 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.