Multiple sequence alignment - TraesCS4A01G332500

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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 TraesCS4A01G332500 chr4A 100.000 3326 0 0 1 3326 616675421 616672096 0.000000e+00 6143.0
1 TraesCS4A01G332500 chr4A 77.273 330 50 16 1207 1519 616612018 616611697 1.590000e-38 171.0
2 TraesCS4A01G332500 chr4A 83.099 142 22 1 2220 2359 616869070 616868929 9.690000e-26 128.0
3 TraesCS4A01G332500 chr4A 85.965 114 16 0 467 580 616903222 616903109 4.510000e-24 122.0
4 TraesCS4A01G332500 chr4A 90.769 65 4 1 2035 2099 616869305 616869243 5.910000e-13 86.1
5 TraesCS4A01G332500 chr4A 92.857 42 2 1 1412 1452 433782509 433782550 3.580000e-05 60.2
6 TraesCS4A01G332500 chr5D 95.629 1853 57 7 581 2416 551447964 551449809 0.000000e+00 2952.0
7 TraesCS4A01G332500 chr5D 93.215 1857 79 11 581 2416 552042276 552040446 0.000000e+00 2687.0
8 TraesCS4A01G332500 chr5D 90.713 883 48 12 2470 3326 254523548 254524422 0.000000e+00 1146.0
9 TraesCS4A01G332500 chr5D 83.179 862 93 33 581 1418 552422535 552421702 0.000000e+00 741.0
10 TraesCS4A01G332500 chr5D 87.034 671 64 11 1452 2122 552456809 552456162 0.000000e+00 736.0
11 TraesCS4A01G332500 chr5D 83.753 794 84 21 708 1473 552458025 552457249 0.000000e+00 710.0
12 TraesCS4A01G332500 chr5D 88.889 288 20 3 2466 2742 434605338 434605624 8.830000e-91 344.0
13 TraesCS4A01G332500 chr5D 86.496 274 13 3 189 438 551447040 551447313 2.530000e-71 279.0
14 TraesCS4A01G332500 chr5D 92.045 176 5 4 8 174 551446753 551446928 4.290000e-59 239.0
15 TraesCS4A01G332500 chr5D 97.561 123 3 0 460 582 552042500 552042378 9.350000e-51 211.0
16 TraesCS4A01G332500 chr5D 93.023 129 7 2 456 582 551447734 551447862 1.580000e-43 187.0
17 TraesCS4A01G332500 chr5D 90.845 142 6 2 8 146 552043263 552043126 2.040000e-42 183.0
18 TraesCS4A01G332500 chr5B 94.204 1570 58 9 581 2122 700237336 700235772 0.000000e+00 2364.0
19 TraesCS4A01G332500 chr5B 92.191 858 40 7 2486 3326 70559730 70560577 0.000000e+00 1188.0
20 TraesCS4A01G332500 chr5B 95.794 642 25 1 1412 2053 699945402 699946041 0.000000e+00 1035.0
21 TraesCS4A01G332500 chr5B 94.118 612 29 3 2722 3326 324242429 324243040 0.000000e+00 924.0
22 TraesCS4A01G332500 chr5B 83.297 922 104 25 579 1473 698256814 698257712 0.000000e+00 804.0
23 TraesCS4A01G332500 chr5B 87.183 671 60 11 1452 2116 698258136 698258786 0.000000e+00 739.0
24 TraesCS4A01G332500 chr5B 75.783 1214 232 42 581 1757 685499737 685500925 1.040000e-154 556.0
25 TraesCS4A01G332500 chr5B 92.353 170 10 1 8 174 700242490 700242321 4.290000e-59 239.0
26 TraesCS4A01G332500 chr5B 96.094 128 4 1 456 582 700237565 700237438 1.210000e-49 207.0
27 TraesCS4A01G332500 chr5B 74.858 529 97 21 1017 1519 703540144 703540662 1.210000e-49 207.0
28 TraesCS4A01G332500 chr5B 93.023 129 6 1 49 174 700238185 700238057 5.670000e-43 185.0
29 TraesCS4A01G332500 chr5B 74.560 511 86 21 1328 1818 699420627 699421113 2.040000e-42 183.0
30 TraesCS4A01G332500 chr5B 88.312 154 9 5 8 153 699945058 699945210 3.410000e-40 176.0
31 TraesCS4A01G332500 chr5B 75.648 386 71 11 1160 1529 699557598 699557976 1.590000e-38 171.0
32 TraesCS4A01G332500 chr5B 84.375 128 19 1 456 582 703330010 703330137 1.250000e-24 124.0
33 TraesCS4A01G332500 chr5B 95.652 69 3 0 2348 2416 700235467 700235399 9.750000e-21 111.0
34 TraesCS4A01G332500 chr6D 91.706 856 57 9 2479 3326 379010074 379009225 0.000000e+00 1175.0
35 TraesCS4A01G332500 chr6D 88.321 137 10 4 14 146 417302210 417302076 3.430000e-35 159.0
36 TraesCS4A01G332500 chr2A 91.194 863 57 11 2477 3326 736533282 736534138 0.000000e+00 1155.0
37 TraesCS4A01G332500 chr4D 90.687 859 63 10 2483 3324 490423073 490422215 0.000000e+00 1127.0
38 TraesCS4A01G332500 chrUn 89.827 865 70 11 2477 3324 23308656 23309519 0.000000e+00 1094.0
39 TraesCS4A01G332500 chrUn 87.234 141 12 4 7 143 303407881 303408019 4.440000e-34 156.0
40 TraesCS4A01G332500 chr7A 89.583 864 70 8 2477 3323 5014267 5013407 0.000000e+00 1079.0
41 TraesCS4A01G332500 chr7A 97.222 36 1 0 2418 2453 86230353 86230318 9.960000e-06 62.1
42 TraesCS4A01G332500 chr7D 90.524 802 55 13 2542 3326 549761679 549762476 0.000000e+00 1040.0
43 TraesCS4A01G332500 chr7D 89.333 300 19 4 2478 2765 31969688 31969986 6.780000e-97 364.0
44 TraesCS4A01G332500 chr7D 88.321 137 10 4 14 146 173302175 173302041 3.430000e-35 159.0
45 TraesCS4A01G332500 chr5A 91.964 672 48 3 2661 3326 1292598 1293269 0.000000e+00 937.0
46 TraesCS4A01G332500 chr5A 94.118 187 9 2 2477 2662 1291915 1292100 1.950000e-72 283.0
47 TraesCS4A01G332500 chr5A 93.514 185 11 1 2479 2662 613744628 613744444 1.180000e-69 274.0
48 TraesCS4A01G332500 chr1D 92.214 655 43 3 2662 3309 109989038 109989691 0.000000e+00 920.0
49 TraesCS4A01G332500 chr7B 91.629 669 48 7 2665 3326 665292413 665291746 0.000000e+00 918.0
50 TraesCS4A01G332500 chr3D 89.895 287 13 5 2484 2760 45941003 45941283 4.080000e-94 355.0
51 TraesCS4A01G332500 chr3D 88.321 137 10 4 14 146 370811024 370810890 3.430000e-35 159.0
52 TraesCS4A01G332500 chr2D 90.476 126 11 1 456 580 28956986 28957111 7.380000e-37 165.0
53 TraesCS4A01G332500 chr2D 87.234 141 12 4 7 143 38294085 38294223 4.440000e-34 156.0
54 TraesCS4A01G332500 chr4B 97.143 35 1 0 905 939 663402740 663402706 3.580000e-05 60.2
55 TraesCS4A01G332500 chr4B 97.143 35 1 0 905 939 663403663 663403697 3.580000e-05 60.2
56 TraesCS4A01G332500 chr4B 97.143 35 1 0 905 939 663406761 663406727 3.580000e-05 60.2
57 TraesCS4A01G332500 chr4B 91.304 46 1 3 905 950 663407682 663407724 3.580000e-05 60.2


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 TraesCS4A01G332500 chr4A 616672096 616675421 3325 True 6143.00 6143 100.000000 1 3326 1 chr4A.!!$R2 3325
1 TraesCS4A01G332500 chr5D 254523548 254524422 874 False 1146.00 1146 90.713000 2470 3326 1 chr5D.!!$F1 856
2 TraesCS4A01G332500 chr5D 552040446 552043263 2817 True 1027.00 2687 93.873667 8 2416 3 chr5D.!!$R2 2408
3 TraesCS4A01G332500 chr5D 551446753 551449809 3056 False 914.25 2952 91.798250 8 2416 4 chr5D.!!$F3 2408
4 TraesCS4A01G332500 chr5D 552421702 552422535 833 True 741.00 741 83.179000 581 1418 1 chr5D.!!$R1 837
5 TraesCS4A01G332500 chr5D 552456162 552458025 1863 True 723.00 736 85.393500 708 2122 2 chr5D.!!$R3 1414
6 TraesCS4A01G332500 chr5B 70559730 70560577 847 False 1188.00 1188 92.191000 2486 3326 1 chr5B.!!$F1 840
7 TraesCS4A01G332500 chr5B 324242429 324243040 611 False 924.00 924 94.118000 2722 3326 1 chr5B.!!$F2 604
8 TraesCS4A01G332500 chr5B 698256814 698258786 1972 False 771.50 804 85.240000 579 2116 2 chr5B.!!$F8 1537
9 TraesCS4A01G332500 chr5B 700235399 700238185 2786 True 716.75 2364 94.743250 49 2416 4 chr5B.!!$R2 2367
10 TraesCS4A01G332500 chr5B 699945058 699946041 983 False 605.50 1035 92.053000 8 2053 2 chr5B.!!$F9 2045
11 TraesCS4A01G332500 chr5B 685499737 685500925 1188 False 556.00 556 75.783000 581 1757 1 chr5B.!!$F3 1176
12 TraesCS4A01G332500 chr5B 703540144 703540662 518 False 207.00 207 74.858000 1017 1519 1 chr5B.!!$F7 502
13 TraesCS4A01G332500 chr6D 379009225 379010074 849 True 1175.00 1175 91.706000 2479 3326 1 chr6D.!!$R1 847
14 TraesCS4A01G332500 chr2A 736533282 736534138 856 False 1155.00 1155 91.194000 2477 3326 1 chr2A.!!$F1 849
15 TraesCS4A01G332500 chr4D 490422215 490423073 858 True 1127.00 1127 90.687000 2483 3324 1 chr4D.!!$R1 841
16 TraesCS4A01G332500 chrUn 23308656 23309519 863 False 1094.00 1094 89.827000 2477 3324 1 chrUn.!!$F1 847
17 TraesCS4A01G332500 chr7A 5013407 5014267 860 True 1079.00 1079 89.583000 2477 3323 1 chr7A.!!$R1 846
18 TraesCS4A01G332500 chr7D 549761679 549762476 797 False 1040.00 1040 90.524000 2542 3326 1 chr7D.!!$F2 784
19 TraesCS4A01G332500 chr5A 1291915 1293269 1354 False 610.00 937 93.041000 2477 3326 2 chr5A.!!$F1 849
20 TraesCS4A01G332500 chr1D 109989038 109989691 653 False 920.00 920 92.214000 2662 3309 1 chr1D.!!$F1 647
21 TraesCS4A01G332500 chr7B 665291746 665292413 667 True 918.00 918 91.629000 2665 3326 1 chr7B.!!$R1 661

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
764 1491 0.535102 CCTGGTGGACGACAAAAGCT 60.535 55.0 0.0 0.0 34.57 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2425 3781 0.109342 AGTTGAGTTGGGCAGGACTG 59.891 55.0 0.0 0.0 0.0 3.51 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
54 58 1.203063 AGAAGGAGAAGGGGCCAAAAC 60.203 52.381 4.39 0.00 0.00 2.43
87 91 7.656412 CAGCAGTACTAGTTGAGATCATATGT 58.344 38.462 0.00 0.00 0.00 2.29
94 110 8.622948 ACTAGTTGAGATCATATGTGTATCGA 57.377 34.615 1.90 0.00 0.00 3.59
95 111 9.237187 ACTAGTTGAGATCATATGTGTATCGAT 57.763 33.333 2.16 2.16 0.00 3.59
96 112 9.500864 CTAGTTGAGATCATATGTGTATCGATG 57.499 37.037 8.54 0.00 0.00 3.84
97 113 7.318893 AGTTGAGATCATATGTGTATCGATGG 58.681 38.462 8.54 0.00 0.00 3.51
162 211 4.704833 GCTCACAAGCTCCGGCCA 62.705 66.667 2.24 0.00 45.55 5.36
227 373 4.942481 TGCAGCAGCGTCGTCGTT 62.942 61.111 3.66 0.00 46.23 3.85
236 382 1.134901 CGTCGTCGTTCTCCTCCAG 59.865 63.158 0.00 0.00 0.00 3.86
268 414 2.032528 CCTTTCCTCGGCTGCACA 59.967 61.111 0.50 0.00 0.00 4.57
284 453 1.133668 GCACAGCCCCTCCTCAATTAT 60.134 52.381 0.00 0.00 0.00 1.28
335 504 3.283684 CCGTTGTCGCCCAAAGCA 61.284 61.111 0.00 0.00 44.04 3.91
377 546 4.498520 CCTCGACGGCGCACAGAT 62.499 66.667 5.31 0.00 37.46 2.90
452 622 4.452733 CCTCGGTCGTGGCCTTCC 62.453 72.222 3.32 0.00 0.00 3.46
453 623 3.382832 CTCGGTCGTGGCCTTCCT 61.383 66.667 3.32 0.00 0.00 3.36
510 1132 2.659610 GACGAGGCTGAGCACCTT 59.340 61.111 6.82 0.00 37.77 3.50
762 1489 3.698250 TCCTGGTGGACGACAAAAG 57.302 52.632 0.00 0.00 37.46 2.27
764 1491 0.535102 CCTGGTGGACGACAAAAGCT 60.535 55.000 0.00 0.00 34.57 3.74
765 1492 1.270625 CCTGGTGGACGACAAAAGCTA 60.271 52.381 0.00 0.00 34.57 3.32
766 1493 2.615493 CCTGGTGGACGACAAAAGCTAT 60.615 50.000 0.00 0.00 34.57 2.97
767 1494 2.416547 CTGGTGGACGACAAAAGCTATG 59.583 50.000 0.00 0.00 0.00 2.23
962 1692 8.774586 AGCATATACCGTTCTCATTTTGATAAC 58.225 33.333 0.00 0.00 32.27 1.89
989 1719 1.925285 ATCCATGCTCCGGCCTTCAA 61.925 55.000 0.00 0.00 37.74 2.69
1036 1766 2.636412 CGCCTCCTGTCTTCGTCCA 61.636 63.158 0.00 0.00 0.00 4.02
1202 1947 0.689080 TTGGGGTTTGCACATGTGGT 60.689 50.000 26.55 0.00 0.00 4.16
1298 2046 7.830697 AGTCATCAATATCAACAACATCCTTCA 59.169 33.333 0.00 0.00 0.00 3.02
1342 2090 3.776969 ACTTAGGCTGATTGGATCTGTGA 59.223 43.478 0.00 0.00 0.00 3.58
1601 2872 5.543507 AAGTTATGTTTGAAATGGGTGCA 57.456 34.783 0.00 0.00 0.00 4.57
1758 3034 4.853196 CGCATTAAGAATGTGTGGTTGAAG 59.147 41.667 4.88 0.00 42.83 3.02
1886 3163 1.215014 GCGGTGCTTGCTTGTTTTCC 61.215 55.000 0.00 0.00 0.00 3.13
2019 3296 8.891720 AGAATTTACTTGAAAAAGCATTTGCAA 58.108 25.926 7.56 7.56 40.94 4.08
2029 3306 6.588348 AAAAGCATTTGCAAACAGTAACTC 57.412 33.333 15.41 0.00 45.16 3.01
2155 3462 3.829026 TCCCGAGAGATGGTATGATGAAG 59.171 47.826 0.00 0.00 0.00 3.02
2373 3729 4.987912 CAGAAAACTGTTTGGTGTGTGTTT 59.012 37.500 6.53 0.00 0.00 2.83
2416 3772 7.615582 TTAGCCATGTAAAGAGATGAAACAG 57.384 36.000 0.00 0.00 0.00 3.16
2417 3773 5.809001 AGCCATGTAAAGAGATGAAACAGA 58.191 37.500 0.00 0.00 0.00 3.41
2418 3774 5.879223 AGCCATGTAAAGAGATGAAACAGAG 59.121 40.000 0.00 0.00 0.00 3.35
2419 3775 5.877012 GCCATGTAAAGAGATGAAACAGAGA 59.123 40.000 0.00 0.00 0.00 3.10
2420 3776 6.036953 GCCATGTAAAGAGATGAAACAGAGAG 59.963 42.308 0.00 0.00 0.00 3.20
2421 3777 6.538021 CCATGTAAAGAGATGAAACAGAGAGG 59.462 42.308 0.00 0.00 0.00 3.69
2422 3778 5.482908 TGTAAAGAGATGAAACAGAGAGGC 58.517 41.667 0.00 0.00 0.00 4.70
2423 3779 4.630644 AAAGAGATGAAACAGAGAGGCA 57.369 40.909 0.00 0.00 0.00 4.75
2424 3780 3.891422 AGAGATGAAACAGAGAGGCAG 57.109 47.619 0.00 0.00 0.00 4.85
2425 3781 2.093553 AGAGATGAAACAGAGAGGCAGC 60.094 50.000 0.00 0.00 0.00 5.25
2426 3782 1.627329 AGATGAAACAGAGAGGCAGCA 59.373 47.619 0.00 0.00 0.00 4.41
2427 3783 2.008329 GATGAAACAGAGAGGCAGCAG 58.992 52.381 0.00 0.00 0.00 4.24
2428 3784 0.761187 TGAAACAGAGAGGCAGCAGT 59.239 50.000 0.00 0.00 0.00 4.40
2429 3785 1.270518 TGAAACAGAGAGGCAGCAGTC 60.271 52.381 0.00 0.00 0.00 3.51
2430 3786 0.036022 AAACAGAGAGGCAGCAGTCC 59.964 55.000 0.00 0.00 0.00 3.85
2431 3787 0.835543 AACAGAGAGGCAGCAGTCCT 60.836 55.000 0.00 0.00 36.46 3.85
2432 3788 1.218585 CAGAGAGGCAGCAGTCCTG 59.781 63.158 0.00 0.00 44.67 3.86
2443 3799 2.633860 CAGTCCTGCCCAACTCAAC 58.366 57.895 0.00 0.00 0.00 3.18
2444 3800 0.109342 CAGTCCTGCCCAACTCAACT 59.891 55.000 0.00 0.00 0.00 3.16
2445 3801 0.109342 AGTCCTGCCCAACTCAACTG 59.891 55.000 0.00 0.00 0.00 3.16
2446 3802 0.890996 GTCCTGCCCAACTCAACTGG 60.891 60.000 0.00 0.00 0.00 4.00
2447 3803 2.270986 CCTGCCCAACTCAACTGGC 61.271 63.158 0.00 0.00 44.27 4.85
2448 3804 2.203480 TGCCCAACTCAACTGGCC 60.203 61.111 0.00 0.00 43.35 5.36
2449 3805 2.116125 GCCCAACTCAACTGGCCT 59.884 61.111 3.32 0.00 37.94 5.19
2450 3806 1.973812 GCCCAACTCAACTGGCCTC 60.974 63.158 3.32 0.00 37.94 4.70
2451 3807 1.455849 CCCAACTCAACTGGCCTCA 59.544 57.895 3.32 0.00 32.10 3.86
2452 3808 0.890996 CCCAACTCAACTGGCCTCAC 60.891 60.000 3.32 0.00 32.10 3.51
2453 3809 0.890996 CCAACTCAACTGGCCTCACC 60.891 60.000 3.32 0.00 39.84 4.02
2464 3820 2.800881 GGCCTCACCAAAAAGAGTTG 57.199 50.000 0.00 0.00 38.86 3.16
2473 3829 2.239400 CAAAAAGAGTTGGACCCTCCC 58.761 52.381 0.00 0.00 35.03 4.30
2474 3830 1.834540 AAAAGAGTTGGACCCTCCCT 58.165 50.000 0.00 0.00 35.03 4.20
2475 3831 1.363246 AAAGAGTTGGACCCTCCCTC 58.637 55.000 0.00 0.00 35.03 4.30
2481 3837 4.500826 GGACCCTCCCTCCCCCTC 62.501 77.778 0.00 0.00 0.00 4.30
3116 4996 2.604686 TGCTGCTTCTCCCTCCGT 60.605 61.111 0.00 0.00 0.00 4.69
3259 5145 1.415672 GGCGGGGATTGGAGTATGGA 61.416 60.000 0.00 0.00 0.00 3.41
3320 5206 1.606313 CGGGTGCCACCATTCCTTT 60.606 57.895 17.22 0.00 41.02 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.532682 TCAAAAGCAAAATTTAAGTGTCCAC 57.467 32.000 0.00 0.00 0.00 4.02
3 4 8.729805 AATCAAAAGCAAAATTTAAGTGTCCA 57.270 26.923 0.00 0.00 0.00 4.02
54 58 4.111198 CAACTAGTACTGCTGCAGATCAG 58.889 47.826 34.28 24.07 45.62 2.90
87 91 4.021456 AGTGTTGAACTCACCATCGATACA 60.021 41.667 0.00 0.00 31.64 2.29
94 110 7.069331 TGGAATTTTAAGTGTTGAACTCACCAT 59.931 33.333 0.00 0.00 38.56 3.55
95 111 6.378564 TGGAATTTTAAGTGTTGAACTCACCA 59.621 34.615 0.00 0.00 38.56 4.17
96 112 6.801575 TGGAATTTTAAGTGTTGAACTCACC 58.198 36.000 0.00 0.00 38.56 4.02
97 113 7.323656 CGATGGAATTTTAAGTGTTGAACTCAC 59.676 37.037 0.00 0.00 38.56 3.51
220 366 2.687805 CGCTGGAGGAGAACGACGA 61.688 63.158 0.00 0.00 0.00 4.20
227 373 4.704103 AGGCCACGCTGGAGGAGA 62.704 66.667 5.01 0.00 40.96 3.71
263 409 1.792757 AATTGAGGAGGGGCTGTGCA 61.793 55.000 0.00 0.00 0.00 4.57
268 414 2.794286 AGGAATAATTGAGGAGGGGCT 58.206 47.619 0.00 0.00 0.00 5.19
335 504 1.337447 CCACGACCATACAACGGACTT 60.337 52.381 0.00 0.00 0.00 3.01
450 620 2.035155 TCCAGAAGCCGTCGAGGA 59.965 61.111 6.70 0.00 45.00 3.71
452 622 1.999071 CTCCTCCAGAAGCCGTCGAG 61.999 65.000 0.00 0.00 0.00 4.04
453 623 2.035155 TCCTCCAGAAGCCGTCGA 59.965 61.111 0.00 0.00 0.00 4.20
455 625 0.387565 GATCTCCTCCAGAAGCCGTC 59.612 60.000 0.00 0.00 33.62 4.79
456 626 0.032615 AGATCTCCTCCAGAAGCCGT 60.033 55.000 0.00 0.00 33.62 5.68
457 627 1.068434 GAAGATCTCCTCCAGAAGCCG 59.932 57.143 0.00 0.00 33.62 5.52
458 628 1.416030 GGAAGATCTCCTCCAGAAGCC 59.584 57.143 8.36 0.00 41.61 4.35
591 1316 2.202878 ATCGTCGGGAATGCACGG 60.203 61.111 0.00 0.00 42.43 4.94
723 1449 3.859414 GCGCATCCAGCTCCCTCT 61.859 66.667 0.30 0.00 42.61 3.69
759 1486 2.124151 CGCTGCCCCCATAGCTTT 60.124 61.111 0.00 0.00 37.78 3.51
760 1487 4.195334 CCGCTGCCCCCATAGCTT 62.195 66.667 0.00 0.00 37.78 3.74
989 1719 4.111375 GATGTACACATCGGAGTCAAGT 57.889 45.455 6.60 0.00 42.66 3.16
1036 1766 4.265073 AGCTTGAAGTGAAGTGTGTCTTT 58.735 39.130 0.00 0.00 36.40 2.52
1202 1947 4.044065 ACCACAGATTGAGGATTAACCCAA 59.956 41.667 0.00 0.00 40.05 4.12
1298 2046 7.277174 AGTCTTTTCTTTGGATTTCGAATGT 57.723 32.000 0.00 0.00 0.00 2.71
1342 2090 3.945285 ACGAAAATGATATCGGTGCCTTT 59.055 39.130 0.00 0.00 43.11 3.11
1601 2872 2.230266 ACACGGCACTCAAAGTTTGTTT 59.770 40.909 15.08 1.07 0.00 2.83
1758 3034 3.315470 TGATGAGTGTAGCCTCGTACATC 59.685 47.826 0.00 0.00 35.40 3.06
1886 3163 4.202101 TGACAAAAGCTACCAACAACATGG 60.202 41.667 0.00 0.00 46.38 3.66
2019 3296 9.723601 TTAAAATGGTAATACCGAGTTACTGTT 57.276 29.630 4.83 0.00 42.58 3.16
2109 3386 3.181454 ACAGAAACCACTCCCTAACAGTG 60.181 47.826 0.00 0.00 40.96 3.66
2155 3462 0.939419 CAAGCCAAGGTGCAAAAAGC 59.061 50.000 0.00 0.00 45.96 3.51
2246 3573 0.179134 AGATCCAGTTCGCGTGCTAC 60.179 55.000 5.77 0.40 0.00 3.58
2373 3729 5.391523 GGCTAAAGATGCACAACGAATAACA 60.392 40.000 0.00 0.00 0.00 2.41
2425 3781 0.109342 AGTTGAGTTGGGCAGGACTG 59.891 55.000 0.00 0.00 0.00 3.51
2426 3782 0.109342 CAGTTGAGTTGGGCAGGACT 59.891 55.000 0.00 0.00 0.00 3.85
2427 3783 0.890996 CCAGTTGAGTTGGGCAGGAC 60.891 60.000 0.00 0.00 31.87 3.85
2428 3784 1.455849 CCAGTTGAGTTGGGCAGGA 59.544 57.895 0.00 0.00 31.87 3.86
2429 3785 2.270986 GCCAGTTGAGTTGGGCAGG 61.271 63.158 0.00 0.00 45.70 4.85
2430 3786 3.359002 GCCAGTTGAGTTGGGCAG 58.641 61.111 0.00 0.00 45.70 4.85
2433 3789 0.890996 GTGAGGCCAGTTGAGTTGGG 60.891 60.000 5.01 0.00 36.19 4.12
2434 3790 0.890996 GGTGAGGCCAGTTGAGTTGG 60.891 60.000 5.01 0.00 38.78 3.77
2435 3791 0.179020 TGGTGAGGCCAGTTGAGTTG 60.179 55.000 5.01 0.00 43.61 3.16
2436 3792 2.230664 TGGTGAGGCCAGTTGAGTT 58.769 52.632 5.01 0.00 43.61 3.01
2437 3793 3.986054 TGGTGAGGCCAGTTGAGT 58.014 55.556 5.01 0.00 43.61 3.41
2444 3800 5.540513 TCCAACTCTTTTTGGTGAGGCCA 62.541 47.826 5.01 0.00 45.60 5.36
2445 3801 1.341209 CCAACTCTTTTTGGTGAGGCC 59.659 52.381 0.00 0.00 41.18 5.19
2446 3802 2.034685 GTCCAACTCTTTTTGGTGAGGC 59.965 50.000 1.94 0.00 45.60 4.70
2447 3803 2.623416 GGTCCAACTCTTTTTGGTGAGG 59.377 50.000 1.94 0.00 45.60 3.86
2448 3804 2.623416 GGGTCCAACTCTTTTTGGTGAG 59.377 50.000 1.94 0.00 45.60 3.51
2449 3805 2.243736 AGGGTCCAACTCTTTTTGGTGA 59.756 45.455 1.94 0.00 45.60 4.02
2450 3806 2.623416 GAGGGTCCAACTCTTTTTGGTG 59.377 50.000 1.94 0.00 45.60 4.17
2451 3807 2.424379 GGAGGGTCCAACTCTTTTTGGT 60.424 50.000 1.94 0.00 45.60 3.67
2452 3808 2.239400 GGAGGGTCCAACTCTTTTTGG 58.761 52.381 0.00 0.00 46.64 3.28
2453 3809 2.158460 AGGGAGGGTCCAACTCTTTTTG 60.158 50.000 0.00 0.00 38.64 2.44
2454 3810 2.108425 GAGGGAGGGTCCAACTCTTTTT 59.892 50.000 0.00 0.00 38.64 1.94
2455 3811 1.705745 GAGGGAGGGTCCAACTCTTTT 59.294 52.381 0.00 0.00 38.64 2.27
2456 3812 1.363246 GAGGGAGGGTCCAACTCTTT 58.637 55.000 0.00 0.00 38.64 2.52
2457 3813 0.547954 GGAGGGAGGGTCCAACTCTT 60.548 60.000 0.00 0.00 38.64 2.85
2458 3814 1.081277 GGAGGGAGGGTCCAACTCT 59.919 63.158 0.00 0.00 38.64 3.24
2459 3815 1.996187 GGGAGGGAGGGTCCAACTC 60.996 68.421 0.00 0.00 38.64 3.01
2460 3816 2.125225 GGGAGGGAGGGTCCAACT 59.875 66.667 0.00 0.00 38.64 3.16
2461 3817 3.015753 GGGGAGGGAGGGTCCAAC 61.016 72.222 0.00 0.00 38.64 3.77
2462 3818 4.364686 GGGGGAGGGAGGGTCCAA 62.365 72.222 0.00 0.00 38.64 3.53
2464 3820 4.500826 GAGGGGGAGGGAGGGTCC 62.501 77.778 0.00 0.00 35.23 4.46
2465 3821 4.500826 GGAGGGGGAGGGAGGGTC 62.501 77.778 0.00 0.00 0.00 4.46
2468 3824 4.179599 GAGGGAGGGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
2469 3825 3.039526 AGAGGGAGGGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
2470 3826 3.036959 GAGAGGGAGGGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
2471 3827 4.179599 GGAGAGGGAGGGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
2472 3828 4.179599 GGGAGAGGGAGGGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
2473 3829 4.548513 CGGGAGAGGGAGGGGGAG 62.549 77.778 0.00 0.00 0.00 4.30
2552 3913 1.616628 GGCAGAGAGGAAGGGGGAA 60.617 63.158 0.00 0.00 0.00 3.97
2884 4760 3.157252 GCTCATCGCCTCTCCCCA 61.157 66.667 0.00 0.00 0.00 4.96
3018 4898 3.900892 CCGTCGCGGTAGCCATCT 61.901 66.667 6.13 0.00 42.73 2.90
3064 4944 3.637273 GGAACCACCTCCACCGCT 61.637 66.667 0.00 0.00 35.36 5.52
3133 5013 0.036010 CAACACGAGGCCAAGAGGAT 60.036 55.000 5.01 0.00 36.89 3.24
3259 5145 4.833390 CCGAAGACTGGTAAGGATTTCTT 58.167 43.478 0.00 0.00 39.40 2.52


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

AutoCloner maintained by Alex Coulton.