Multiple sequence alignment - TraesCS5A01G300700

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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 TraesCS5A01G300700 chr5A 100.000 4631 0 0 1 4631 510016637 510012007 0.000000e+00 8552.0
1 TraesCS5A01G300700 chr5A 98.586 1061 14 1 1974 3033 595384463 595383403 0.000000e+00 1875.0
2 TraesCS5A01G300700 chr5A 95.009 1082 49 2 893 1973 510883600 510884677 0.000000e+00 1694.0
3 TraesCS5A01G300700 chr5A 94.829 1025 52 1 1976 3000 524667424 524668447 0.000000e+00 1598.0
4 TraesCS5A01G300700 chr5A 93.785 1062 55 5 1974 3033 465768347 465767295 0.000000e+00 1585.0
5 TraesCS5A01G300700 chr5A 95.017 903 35 2 3738 4631 510004257 510003356 0.000000e+00 1410.0
6 TraesCS5A01G300700 chr5A 95.539 807 31 3 1974 2775 691524843 691524037 0.000000e+00 1286.0
7 TraesCS5A01G300700 chr5A 93.103 638 37 5 3088 3722 510884750 510885383 0.000000e+00 928.0
8 TraesCS5A01G300700 chr5A 90.523 612 50 5 1 610 227136082 227135477 0.000000e+00 802.0
9 TraesCS5A01G300700 chr5A 88.655 617 52 6 1 610 359991449 359992054 0.000000e+00 736.0
10 TraesCS5A01G300700 chr5A 87.240 337 34 8 563 895 689261904 689261573 4.370000e-100 375.0
11 TraesCS5A01G300700 chr5A 96.491 57 2 0 3034 3090 510884670 510884726 1.370000e-15 95.3
12 TraesCS5A01G300700 chr5A 97.727 44 1 0 2867 2910 691524013 691523970 4.970000e-10 76.8
13 TraesCS5A01G300700 chr5B 95.005 1081 52 2 893 1973 484645115 484644037 0.000000e+00 1696.0
14 TraesCS5A01G300700 chr5B 95.308 746 35 0 963 1708 485426273 485427018 0.000000e+00 1184.0
15 TraesCS5A01G300700 chr5B 89.662 948 45 17 3084 3985 485427813 485428753 0.000000e+00 1158.0
16 TraesCS5A01G300700 chr5B 91.884 690 37 9 1974 2660 146271681 146272354 0.000000e+00 946.0
17 TraesCS5A01G300700 chr5B 91.538 650 47 6 3088 3736 484643966 484643324 0.000000e+00 889.0
18 TraesCS5A01G300700 chr5B 93.510 339 16 4 274 610 643128771 643129105 2.490000e-137 499.0
19 TraesCS5A01G300700 chr5B 96.970 99 3 0 893 991 485426158 485426256 2.870000e-37 167.0
20 TraesCS5A01G300700 chr5B 94.828 58 1 2 3034 3090 484644044 484643988 6.380000e-14 89.8
21 TraesCS5A01G300700 chr5D 94.527 1078 55 2 893 1970 404188314 404189387 0.000000e+00 1661.0
22 TraesCS5A01G300700 chr5D 95.333 1007 47 0 963 1969 403155639 403154633 0.000000e+00 1600.0
23 TraesCS5A01G300700 chr5D 93.220 944 45 9 1974 2917 134789180 134790104 0.000000e+00 1371.0
24 TraesCS5A01G300700 chr5D 90.637 769 41 11 3088 3836 404189464 404190221 0.000000e+00 992.0
25 TraesCS5A01G300700 chr5D 90.746 724 35 16 3039 3736 403154633 403153916 0.000000e+00 937.0
26 TraesCS5A01G300700 chr5D 82.793 401 38 15 4250 4631 404190740 404191128 3.450000e-86 329.0
27 TraesCS5A01G300700 chr5D 91.667 108 7 2 893 1000 403155752 403155647 1.040000e-31 148.0
28 TraesCS5A01G300700 chr5D 82.530 166 18 7 3842 4003 404190331 404190489 8.080000e-28 135.0
29 TraesCS5A01G300700 chr5D 75.000 232 46 11 4131 4358 544619267 544619044 3.810000e-16 97.1
30 TraesCS5A01G300700 chr5D 91.071 56 3 2 3037 3090 404189389 404189444 1.790000e-09 75.0
31 TraesCS5A01G300700 chr2D 94.569 1068 52 3 1974 3036 195403697 195402631 0.000000e+00 1646.0
32 TraesCS5A01G300700 chr2D 88.505 983 102 5 988 1969 336653636 336654608 0.000000e+00 1179.0
33 TraesCS5A01G300700 chr2D 90.865 613 45 7 1 610 582179211 582179815 0.000000e+00 811.0
34 TraesCS5A01G300700 chr2D 77.907 258 51 6 4121 4374 580234390 580234645 6.200000e-34 156.0
35 TraesCS5A01G300700 chr6B 91.612 1061 79 8 1974 3033 162131786 162130735 0.000000e+00 1458.0
36 TraesCS5A01G300700 chr6B 87.332 371 34 9 533 896 42365933 42365569 3.330000e-111 412.0
37 TraesCS5A01G300700 chr6B 86.550 342 35 9 557 894 710313873 710314207 2.630000e-97 366.0
38 TraesCS5A01G300700 chr3D 95.991 873 34 1 2162 3033 404320773 404319901 0.000000e+00 1417.0
39 TraesCS5A01G300700 chr3D 96.373 193 7 0 1972 2164 404321068 404320876 7.480000e-83 318.0
40 TraesCS5A01G300700 chr3D 76.812 276 47 14 4149 4420 498428272 498428010 6.250000e-29 139.0
41 TraesCS5A01G300700 chr1D 91.134 970 84 2 1001 1969 220420142 220421110 0.000000e+00 1314.0
42 TraesCS5A01G300700 chr1D 91.111 585 46 5 1 583 34543526 34544106 0.000000e+00 787.0
43 TraesCS5A01G300700 chr1D 86.871 556 51 12 3114 3648 220421182 220421736 1.840000e-168 603.0
44 TraesCS5A01G300700 chr1B 90.900 956 83 4 1016 1969 315390925 315389972 0.000000e+00 1280.0
45 TraesCS5A01G300700 chr1B 85.664 572 58 14 3114 3664 315389897 315389329 8.640000e-162 580.0
46 TraesCS5A01G300700 chr1B 84.555 382 40 16 522 894 507839027 507839398 1.220000e-95 361.0
47 TraesCS5A01G300700 chr1B 84.115 384 40 20 522 895 633193860 633194232 7.370000e-93 351.0
48 TraesCS5A01G300700 chr2A 87.971 981 96 9 988 1967 446997993 446998952 0.000000e+00 1138.0
49 TraesCS5A01G300700 chr2A 86.252 531 53 11 3113 3624 446999070 446999599 4.050000e-155 558.0
50 TraesCS5A01G300700 chr2A 76.821 151 33 2 4142 4290 29943492 29943642 2.970000e-12 84.2
51 TraesCS5A01G300700 chr4A 88.649 925 37 24 3 894 34016631 34017520 0.000000e+00 1064.0
52 TraesCS5A01G300700 chr4A 88.777 695 36 11 2 676 1746761 1746089 0.000000e+00 813.0
53 TraesCS5A01G300700 chr4A 87.500 336 35 7 563 895 111074392 111074061 9.400000e-102 381.0
54 TraesCS5A01G300700 chr4A 83.019 106 14 4 4329 4432 681831744 681831641 4.930000e-15 93.5
55 TraesCS5A01G300700 chr1A 87.418 914 63 23 2 894 41738856 41739738 0.000000e+00 1003.0
56 TraesCS5A01G300700 chr1A 86.618 553 53 11 3114 3648 284321589 284322138 3.990000e-165 592.0
57 TraesCS5A01G300700 chr3A 86.871 914 68 20 2 894 745543776 745544658 0.000000e+00 976.0
58 TraesCS5A01G300700 chr3A 92.208 616 38 4 1 615 64762811 64762205 0.000000e+00 863.0
59 TraesCS5A01G300700 chr7A 85.683 922 77 24 2 900 188859517 188858628 0.000000e+00 920.0
60 TraesCS5A01G300700 chr7A 77.011 261 46 13 4121 4374 154391243 154390990 2.250000e-28 137.0
61 TraesCS5A01G300700 chr3B 88.337 463 24 10 274 736 799272046 799272478 3.170000e-146 529.0
62 TraesCS5A01G300700 chr3B 80.531 113 13 9 3931 4035 606567946 606568057 1.380000e-10 78.7
63 TraesCS5A01G300700 chr2B 84.369 531 61 12 3113 3624 404183979 404184506 6.920000e-138 501.0
64 TraesCS5A01G300700 chr2B 88.427 337 32 4 563 894 73975236 73974902 2.600000e-107 399.0
65 TraesCS5A01G300700 chrUn 78.113 265 56 2 4159 4423 60469494 60469232 2.870000e-37 167.0
66 TraesCS5A01G300700 chr4B 77.358 265 58 2 4159 4423 643487197 643487459 6.200000e-34 156.0
67 TraesCS5A01G300700 chr6D 74.837 306 57 13 4125 4425 390246976 390247266 2.260000e-23 121.0


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 TraesCS5A01G300700 chr5A 510012007 510016637 4630 True 8552.000000 8552 100.000000 1 4631 1 chr5A.!!$R4 4630
1 TraesCS5A01G300700 chr5A 595383403 595384463 1060 True 1875.000000 1875 98.586000 1974 3033 1 chr5A.!!$R5 1059
2 TraesCS5A01G300700 chr5A 524667424 524668447 1023 False 1598.000000 1598 94.829000 1976 3000 1 chr5A.!!$F2 1024
3 TraesCS5A01G300700 chr5A 465767295 465768347 1052 True 1585.000000 1585 93.785000 1974 3033 1 chr5A.!!$R2 1059
4 TraesCS5A01G300700 chr5A 510003356 510004257 901 True 1410.000000 1410 95.017000 3738 4631 1 chr5A.!!$R3 893
5 TraesCS5A01G300700 chr5A 510883600 510885383 1783 False 905.766667 1694 94.867667 893 3722 3 chr5A.!!$F3 2829
6 TraesCS5A01G300700 chr5A 227135477 227136082 605 True 802.000000 802 90.523000 1 610 1 chr5A.!!$R1 609
7 TraesCS5A01G300700 chr5A 359991449 359992054 605 False 736.000000 736 88.655000 1 610 1 chr5A.!!$F1 609
8 TraesCS5A01G300700 chr5A 691523970 691524843 873 True 681.400000 1286 96.633000 1974 2910 2 chr5A.!!$R7 936
9 TraesCS5A01G300700 chr5B 146271681 146272354 673 False 946.000000 946 91.884000 1974 2660 1 chr5B.!!$F1 686
10 TraesCS5A01G300700 chr5B 484643324 484645115 1791 True 891.600000 1696 93.790333 893 3736 3 chr5B.!!$R1 2843
11 TraesCS5A01G300700 chr5B 485426158 485428753 2595 False 836.333333 1184 93.980000 893 3985 3 chr5B.!!$F3 3092
12 TraesCS5A01G300700 chr5D 134789180 134790104 924 False 1371.000000 1371 93.220000 1974 2917 1 chr5D.!!$F1 943
13 TraesCS5A01G300700 chr5D 403153916 403155752 1836 True 895.000000 1600 92.582000 893 3736 3 chr5D.!!$R2 2843
14 TraesCS5A01G300700 chr5D 404188314 404191128 2814 False 638.400000 1661 88.311600 893 4631 5 chr5D.!!$F2 3738
15 TraesCS5A01G300700 chr2D 195402631 195403697 1066 True 1646.000000 1646 94.569000 1974 3036 1 chr2D.!!$R1 1062
16 TraesCS5A01G300700 chr2D 336653636 336654608 972 False 1179.000000 1179 88.505000 988 1969 1 chr2D.!!$F1 981
17 TraesCS5A01G300700 chr2D 582179211 582179815 604 False 811.000000 811 90.865000 1 610 1 chr2D.!!$F3 609
18 TraesCS5A01G300700 chr6B 162130735 162131786 1051 True 1458.000000 1458 91.612000 1974 3033 1 chr6B.!!$R2 1059
19 TraesCS5A01G300700 chr3D 404319901 404321068 1167 True 867.500000 1417 96.182000 1972 3033 2 chr3D.!!$R2 1061
20 TraesCS5A01G300700 chr1D 220420142 220421736 1594 False 958.500000 1314 89.002500 1001 3648 2 chr1D.!!$F2 2647
21 TraesCS5A01G300700 chr1D 34543526 34544106 580 False 787.000000 787 91.111000 1 583 1 chr1D.!!$F1 582
22 TraesCS5A01G300700 chr1B 315389329 315390925 1596 True 930.000000 1280 88.282000 1016 3664 2 chr1B.!!$R1 2648
23 TraesCS5A01G300700 chr2A 446997993 446999599 1606 False 848.000000 1138 87.111500 988 3624 2 chr2A.!!$F2 2636
24 TraesCS5A01G300700 chr4A 34016631 34017520 889 False 1064.000000 1064 88.649000 3 894 1 chr4A.!!$F1 891
25 TraesCS5A01G300700 chr4A 1746089 1746761 672 True 813.000000 813 88.777000 2 676 1 chr4A.!!$R1 674
26 TraesCS5A01G300700 chr1A 41738856 41739738 882 False 1003.000000 1003 87.418000 2 894 1 chr1A.!!$F1 892
27 TraesCS5A01G300700 chr1A 284321589 284322138 549 False 592.000000 592 86.618000 3114 3648 1 chr1A.!!$F2 534
28 TraesCS5A01G300700 chr3A 745543776 745544658 882 False 976.000000 976 86.871000 2 894 1 chr3A.!!$F1 892
29 TraesCS5A01G300700 chr3A 64762205 64762811 606 True 863.000000 863 92.208000 1 615 1 chr3A.!!$R1 614
30 TraesCS5A01G300700 chr7A 188858628 188859517 889 True 920.000000 920 85.683000 2 900 1 chr7A.!!$R2 898
31 TraesCS5A01G300700 chr2B 404183979 404184506 527 False 501.000000 501 84.369000 3113 3624 1 chr2B.!!$F1 511

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
842 960 0.179073 AATGATCCAACGGCCGAGAG 60.179 55.000 35.90 20.18 0.00 3.20 F
1538 1754 0.395862 TTCTCCTACCTCGGCCAGAG 60.396 60.000 15.17 15.17 46.44 3.35 F
1997 2697 1.613255 GCCGGTTCTGAGATTTTGGGA 60.613 52.381 1.90 0.00 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1860 2559 2.042537 ATCTGGAGCTCGGCCTCA 60.043 61.111 7.83 0.0 33.47 3.86 R
2554 3376 2.574018 CGTCCAGCCACTGACTCCA 61.574 63.158 0.00 0.0 32.44 3.86 R
3697 4593 0.872388 CGAGGAACCAAAACCTTCCG 59.128 55.000 0.00 0.0 40.92 4.30 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
87 88 4.451150 CTTGCGGCCCGAGCTACA 62.451 66.667 7.68 0.00 39.73 2.74
88 89 3.950794 CTTGCGGCCCGAGCTACAA 62.951 63.158 7.68 0.00 39.73 2.41
94 95 3.934391 GCCCGAGCTACAACGCAGT 62.934 63.158 0.00 0.00 38.40 4.40
357 392 1.224592 GTGGACGGCAGGAATCCAT 59.775 57.895 0.61 0.00 44.21 3.41
628 745 2.119655 GTAGGAGCGAGCGAGGGAA 61.120 63.158 0.00 0.00 0.00 3.97
650 767 2.707849 GCGGCTAGGTCTCCGTCAA 61.708 63.158 8.10 0.00 46.79 3.18
651 768 1.888018 CGGCTAGGTCTCCGTCAAA 59.112 57.895 0.00 0.00 40.72 2.69
757 875 7.230108 CCATTACTATTCATTCCAGCAGTGATT 59.770 37.037 0.00 0.00 0.00 2.57
785 903 2.282462 CAACGGCCCAGCTTCCTT 60.282 61.111 0.00 0.00 0.00 3.36
842 960 0.179073 AATGATCCAACGGCCGAGAG 60.179 55.000 35.90 20.18 0.00 3.20
850 968 1.251527 AACGGCCGAGAGTCACTGAT 61.252 55.000 35.90 0.00 0.00 2.90
855 973 2.566913 GCCGAGAGTCACTGATCTCTA 58.433 52.381 9.72 0.00 40.53 2.43
856 974 2.946329 GCCGAGAGTCACTGATCTCTAA 59.054 50.000 9.72 0.00 40.53 2.10
858 976 3.563808 CCGAGAGTCACTGATCTCTAAGG 59.436 52.174 9.72 11.39 40.53 2.69
863 981 3.027412 GTCACTGATCTCTAAGGAGCCA 58.973 50.000 0.00 0.00 39.31 4.75
869 987 5.066913 TGATCTCTAAGGAGCCATGTAGA 57.933 43.478 0.00 0.00 39.31 2.59
870 988 5.076182 TGATCTCTAAGGAGCCATGTAGAG 58.924 45.833 8.72 8.72 40.55 2.43
873 991 3.567397 TCTAAGGAGCCATGTAGAGACC 58.433 50.000 0.00 0.00 0.00 3.85
875 993 2.559381 AGGAGCCATGTAGAGACCTT 57.441 50.000 0.00 0.00 0.00 3.50
900 1018 4.223953 TCTCTTATTTCTGGATACGGGCT 58.776 43.478 0.00 0.00 45.79 5.19
970 1096 1.264557 TCGATTGACTAGCTAGCTCGC 59.735 52.381 23.26 12.28 0.00 5.03
971 1097 1.265635 CGATTGACTAGCTAGCTCGCT 59.734 52.381 23.26 17.70 43.83 4.93
972 1098 2.480802 CGATTGACTAGCTAGCTCGCTA 59.519 50.000 23.26 18.04 41.30 4.26
1023 1239 0.999406 CGAGTTTTCATGTCGCCGAT 59.001 50.000 0.00 0.00 0.00 4.18
1041 1257 1.686325 ATGCGTCGGAATACCTGGCT 61.686 55.000 0.00 0.00 0.00 4.75
1053 1269 2.590007 CTGGCTATCACCGGCTGC 60.590 66.667 0.00 0.00 0.00 5.25
1056 1272 4.530857 GCTATCACCGGCTGCGGT 62.531 66.667 0.00 9.77 43.99 5.68
1131 1347 0.610174 AGAAGTTCTGCATCTCGCCA 59.390 50.000 4.10 0.00 41.33 5.69
1212 1428 2.990479 GTCTTCACCATCGGCCCT 59.010 61.111 0.00 0.00 0.00 5.19
1260 1476 1.891616 GGACAAGAGGGACCTCGAC 59.108 63.158 12.42 5.84 46.90 4.20
1262 1478 0.959372 GACAAGAGGGACCTCGACGA 60.959 60.000 12.42 0.00 46.90 4.20
1264 1480 0.961358 CAAGAGGGACCTCGACGAGT 60.961 60.000 22.61 11.34 46.90 4.18
1272 1488 0.829333 ACCTCGACGAGTAGCTCCTA 59.171 55.000 22.61 0.00 0.00 2.94
1295 1511 4.845580 CGCCAAGCTCATCGCCCT 62.846 66.667 0.00 0.00 40.39 5.19
1538 1754 0.395862 TTCTCCTACCTCGGCCAGAG 60.396 60.000 15.17 15.17 46.44 3.35
1605 1821 1.754555 GCTCGGATGAAGGGAGAGGTA 60.755 57.143 0.00 0.00 0.00 3.08
1838 2537 3.637273 GGTGGCCGAGGTTGAGGT 61.637 66.667 0.00 0.00 0.00 3.85
1997 2697 1.613255 GCCGGTTCTGAGATTTTGGGA 60.613 52.381 1.90 0.00 0.00 4.37
2022 2725 3.305471 CCGGGGCGAAAGTAAAATTTGAA 60.305 43.478 0.00 0.00 0.00 2.69
3264 4128 1.064946 CGAGGACGCCAAGCTCTAG 59.935 63.158 0.00 0.00 0.00 2.43
3697 4593 1.925185 GAATCGGGTTAGCTGTTCGTC 59.075 52.381 0.00 0.00 0.00 4.20
3698 4594 0.179145 ATCGGGTTAGCTGTTCGTCG 60.179 55.000 0.00 0.00 0.00 5.12
3989 5007 8.827177 TCTATCAAGGTAGTACAAAAACACTG 57.173 34.615 2.06 0.00 0.00 3.66
4073 5133 1.890489 TGCAGCCGAGTAAGTAGACAA 59.110 47.619 0.00 0.00 0.00 3.18
4090 5150 4.836825 AGACAATCGGAAAGTCATCATGT 58.163 39.130 13.40 0.00 34.80 3.21
4151 5250 3.914312 ACACAAGAACATAGACAGACGG 58.086 45.455 0.00 0.00 0.00 4.79
4180 5279 1.425066 TCCAAGTGGAGCCATCAAAGT 59.575 47.619 0.00 0.00 39.78 2.66
4185 5284 2.887152 AGTGGAGCCATCAAAGTCAAAC 59.113 45.455 0.00 0.00 0.00 2.93
4197 5296 0.601841 AGTCAAACGCCGACCGAATT 60.602 50.000 0.00 0.00 41.02 2.17
4321 5420 1.501169 GCCGCTGCTGTTTCATTTTT 58.499 45.000 0.00 0.00 33.53 1.94
4559 5677 8.822652 AAGATTTCCATCTTCAACAATTTCAC 57.177 30.769 0.00 0.00 45.26 3.18
4580 5698 6.655062 TCACGAAGTATGTGTGAATTTCAAC 58.345 36.000 0.00 3.24 41.61 3.18
4597 5715 9.845305 GAATTTCAACTTCTAATTCGTATACCG 57.155 33.333 0.00 0.00 31.11 4.02
4625 5743 3.525619 CGTAGCTGCTAAACCACCA 57.474 52.632 11.57 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.688185 GCACTCGTCGATCCATAGGTATA 59.312 47.826 0.00 0.00 0.00 1.47
585 675 3.695825 TCCCTCCCTCCCTCCCAC 61.696 72.222 0.00 0.00 0.00 4.61
611 728 1.824329 CTTCCCTCGCTCGCTCCTA 60.824 63.158 0.00 0.00 0.00 2.94
628 745 2.123640 GGAGACCTAGCCGCCTCT 60.124 66.667 0.00 0.00 0.00 3.69
650 767 0.261696 ATAAAAGGGGGCCGCTCATT 59.738 50.000 24.62 22.01 0.00 2.57
651 768 1.145571 TATAAAAGGGGGCCGCTCAT 58.854 50.000 24.62 18.22 0.00 2.90
757 875 1.596934 GGCCGTTGGATCTGAGACA 59.403 57.895 0.00 0.00 0.00 3.41
785 903 1.134367 GTCCGTTGGATCGACATCTGA 59.866 52.381 0.00 0.00 32.73 3.27
842 960 3.027412 TGGCTCCTTAGAGATCAGTGAC 58.973 50.000 0.00 0.00 43.39 3.67
850 968 4.465886 GTCTCTACATGGCTCCTTAGAGA 58.534 47.826 12.21 12.21 43.39 3.10
855 973 2.559381 AGGTCTCTACATGGCTCCTT 57.441 50.000 0.00 0.00 0.00 3.36
856 974 2.023501 AGAAGGTCTCTACATGGCTCCT 60.024 50.000 0.00 0.00 30.22 3.69
858 976 3.704061 AGAAGAAGGTCTCTACATGGCTC 59.296 47.826 0.00 0.00 32.46 4.70
869 987 7.747809 ATCCAGAAATAAGAGAAGAAGGTCT 57.252 36.000 0.00 0.00 0.00 3.85
870 988 7.650104 CGTATCCAGAAATAAGAGAAGAAGGTC 59.350 40.741 0.00 0.00 0.00 3.85
873 991 6.926272 CCCGTATCCAGAAATAAGAGAAGAAG 59.074 42.308 0.00 0.00 0.00 2.85
875 993 5.221461 GCCCGTATCCAGAAATAAGAGAAGA 60.221 44.000 0.00 0.00 0.00 2.87
886 1004 2.447408 TCTGTAGCCCGTATCCAGAA 57.553 50.000 0.00 0.00 0.00 3.02
890 1008 1.608283 GCCAATCTGTAGCCCGTATCC 60.608 57.143 0.00 0.00 0.00 2.59
970 1096 0.724549 CTCGATCGGCGGATCTCTAG 59.275 60.000 26.04 18.05 45.66 2.43
971 1097 0.673956 CCTCGATCGGCGGATCTCTA 60.674 60.000 26.04 13.87 45.66 2.43
972 1098 1.969064 CCTCGATCGGCGGATCTCT 60.969 63.158 26.04 0.00 45.66 3.10
973 1099 1.917782 CTCCTCGATCGGCGGATCTC 61.918 65.000 26.04 8.44 45.66 2.75
1023 1239 1.038681 TAGCCAGGTATTCCGACGCA 61.039 55.000 0.00 0.00 39.05 5.24
1032 1248 0.471971 AGCCGGTGATAGCCAGGTAT 60.472 55.000 1.90 0.00 0.00 2.73
1053 1269 1.192436 GCTTCACGTCGTCGATACCG 61.192 60.000 9.47 0.00 40.62 4.02
1056 1272 0.025898 CGAGCTTCACGTCGTCGATA 59.974 55.000 9.47 0.00 40.62 2.92
1131 1347 2.225963 CACCTCGAACTCGTAGTTGACT 59.774 50.000 5.20 0.00 38.80 3.41
1167 1383 0.254178 GGATGAAGGGCAGCTTCTCA 59.746 55.000 0.00 0.00 32.29 3.27
1212 1428 2.499205 CCGGTGGCGCTGATCTTA 59.501 61.111 7.64 0.00 0.00 2.10
1264 1480 2.573369 CTTGGCGTAGAGTAGGAGCTA 58.427 52.381 0.00 0.00 0.00 3.32
1272 1488 0.101399 CGATGAGCTTGGCGTAGAGT 59.899 55.000 0.00 0.00 0.00 3.24
1295 1511 1.798234 GCTGGTGTTGTGATGCAGCA 61.798 55.000 0.00 0.00 40.23 4.41
1587 1803 1.133450 CCTACCTCTCCCTTCATCCGA 60.133 57.143 0.00 0.00 0.00 4.55
1605 1821 4.722535 TCCCTCTCCTTGGCGCCT 62.723 66.667 29.70 0.00 0.00 5.52
1790 2480 4.778143 CCCACCCGGCCTTCTTCG 62.778 72.222 0.00 0.00 0.00 3.79
1860 2559 2.042537 ATCTGGAGCTCGGCCTCA 60.043 61.111 7.83 0.00 33.47 3.86
2022 2725 7.698912 TGCTATGATGTTTATATTAAGGGGCT 58.301 34.615 0.00 0.00 0.00 5.19
2554 3376 2.574018 CGTCCAGCCACTGACTCCA 61.574 63.158 0.00 0.00 32.44 3.86
3033 3861 9.614792 GGAACTATGGAATATGGATAATGTACC 57.385 37.037 0.00 0.00 0.00 3.34
3096 3960 2.830772 ACAATACATGCATGCACGAC 57.169 45.000 25.37 0.00 0.00 4.34
3264 4128 2.753446 GCCTCCTTCTGCTTGGCC 60.753 66.667 0.00 0.00 37.81 5.36
3697 4593 0.872388 CGAGGAACCAAAACCTTCCG 59.128 55.000 0.00 0.00 40.92 4.30
3698 4594 1.878088 GACGAGGAACCAAAACCTTCC 59.122 52.381 0.00 0.00 36.57 3.46
3989 5007 8.770438 TGGATTTGCATGTAATTTTTACTTCC 57.230 30.769 0.00 0.00 0.00 3.46
4009 5027 6.071984 AGTCTCGATAAGTGGTCTATGGATT 58.928 40.000 0.00 0.00 0.00 3.01
4073 5133 5.817816 GGTCTTAACATGATGACTTTCCGAT 59.182 40.000 0.00 0.00 0.00 4.18
4090 5150 4.957954 TCCGCTAGTTCTATTGGGTCTTAA 59.042 41.667 0.00 0.00 0.00 1.85
4151 5250 0.461961 CTCCACTTGGATCCGGTCTC 59.538 60.000 7.39 0.00 44.46 3.36
4180 5279 1.293267 GGAATTCGGTCGGCGTTTGA 61.293 55.000 6.85 0.00 0.00 2.69
4185 5284 3.550992 CACGGAATTCGGTCGGCG 61.551 66.667 15.11 0.00 44.45 6.46
4197 5296 0.323087 TCTCCAACGGATCTCACGGA 60.323 55.000 0.00 0.00 35.23 4.69
4227 5326 4.436998 GAGCCGTCGGAGGGTGTG 62.437 72.222 17.49 0.00 42.85 3.82
4313 5412 7.201785 GGTTTGTGTCCTACTCAGAAAAATGAA 60.202 37.037 0.00 0.00 31.75 2.57
4321 5420 2.972348 AGGGTTTGTGTCCTACTCAGA 58.028 47.619 0.00 0.00 0.00 3.27
4386 5486 1.218316 GATCTCGACCTTTGCCGGT 59.782 57.895 1.90 0.00 40.80 5.28
4394 5494 1.258445 GGTGTGGTGGATCTCGACCT 61.258 60.000 11.90 0.00 43.97 3.85
4447 5565 1.896660 GGTTTTGCGCCTCCTGTCA 60.897 57.895 4.18 0.00 0.00 3.58
4559 5677 7.576236 AGAAGTTGAAATTCACACATACTTCG 58.424 34.615 21.73 0.00 42.91 3.79
4597 5715 1.811679 GCAGCTACGCCTTCTGGTC 60.812 63.158 0.00 0.00 35.27 4.02


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

AutoCloner maintained by Alex Coulton.