Multiple sequence alignment - TraesCS5D01G470100

Loading Multiple Alignment...

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 TraesCS5D01G470100 chr5D 100.000 3233 0 0 1 3233 510960417 510957185 0.000000e+00 5971.0
1 TraesCS5D01G470100 chr5D 82.197 1129 194 6 1091 2217 510966695 510965572 0.000000e+00 965.0
2 TraesCS5D01G470100 chr5D 76.978 695 140 9 1526 2209 510956077 510956762 2.350000e-101 379.0
3 TraesCS5D01G470100 chr5D 85.714 350 37 11 1 341 452555375 452555030 1.100000e-94 357.0
4 TraesCS5D01G470100 chr5A 91.170 2582 175 29 5 2566 639294317 639291769 0.000000e+00 3456.0
5 TraesCS5D01G470100 chr5A 82.083 1133 194 8 1088 2217 639301543 639300417 0.000000e+00 959.0
6 TraesCS5D01G470100 chr5A 79.606 559 99 11 1652 2209 639281107 639281651 1.410000e-103 387.0
7 TraesCS5D01G470100 chr5B 90.594 2456 145 33 93 2517 642143240 642140840 0.000000e+00 3177.0
8 TraesCS5D01G470100 chr5B 90.392 2040 116 28 515 2517 642306152 642308148 0.000000e+00 2608.0
9 TraesCS5D01G470100 chr5B 82.540 1134 189 8 1088 2218 642281913 642283040 0.000000e+00 989.0
10 TraesCS5D01G470100 chr5B 90.337 652 42 7 2588 3233 642309869 642310505 0.000000e+00 835.0
11 TraesCS5D01G470100 chr5B 88.766 543 48 9 1 530 642305593 642306135 0.000000e+00 652.0
12 TraesCS5D01G470100 chr3D 87.460 311 26 9 1 300 93478575 93478267 2.390000e-91 346.0
13 TraesCS5D01G470100 chr3D 85.417 336 37 9 1 327 553333924 553334256 4.000000e-89 339.0
14 TraesCS5D01G470100 chr3D 85.285 333 37 9 1 322 147839100 147838769 1.860000e-87 333.0
15 TraesCS5D01G470100 chr7A 85.629 334 35 10 1 322 437074705 437074373 4.000000e-89 339.0
16 TraesCS5D01G470100 chr2D 86.731 309 32 6 1 300 68920343 68920651 5.170000e-88 335.0
17 TraesCS5D01G470100 chr2B 85.119 336 38 7 1 324 785071699 785071364 1.860000e-87 333.0
18 TraesCS5D01G470100 chr1A 85.207 338 35 11 1 324 371174795 371175131 1.860000e-87 333.0
19 TraesCS5D01G470100 chr4A 90.476 42 4 0 1602 1643 538840139 538840098 4.510000e-04 56.5


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 TraesCS5D01G470100 chr5D 510957185 510960417 3232 True 5971 5971 100.000000 1 3233 1 chr5D.!!$R2 3232
1 TraesCS5D01G470100 chr5D 510965572 510966695 1123 True 965 965 82.197000 1091 2217 1 chr5D.!!$R3 1126
2 TraesCS5D01G470100 chr5D 510956077 510956762 685 False 379 379 76.978000 1526 2209 1 chr5D.!!$F1 683
3 TraesCS5D01G470100 chr5A 639291769 639294317 2548 True 3456 3456 91.170000 5 2566 1 chr5A.!!$R1 2561
4 TraesCS5D01G470100 chr5A 639300417 639301543 1126 True 959 959 82.083000 1088 2217 1 chr5A.!!$R2 1129
5 TraesCS5D01G470100 chr5A 639281107 639281651 544 False 387 387 79.606000 1652 2209 1 chr5A.!!$F1 557
6 TraesCS5D01G470100 chr5B 642140840 642143240 2400 True 3177 3177 90.594000 93 2517 1 chr5B.!!$R1 2424
7 TraesCS5D01G470100 chr5B 642305593 642310505 4912 False 1365 2608 89.831667 1 3233 3 chr5B.!!$F2 3232
8 TraesCS5D01G470100 chr5B 642281913 642283040 1127 False 989 989 82.540000 1088 2218 1 chr5B.!!$F1 1130

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
561 613 0.099436 GGCACTACGTACGTACAGGG 59.901 60.0 23.6 18.88 0.0 4.45 F
562 614 0.099436 GCACTACGTACGTACAGGGG 59.901 60.0 23.6 16.29 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 1954 1.000396 GCTTCCTCCCTGCCATGTT 60.000 57.895 0.0 0.0 0.0 2.71 R
2527 2628 6.441093 TTGACATTAGAATTGCATCTGTCC 57.559 37.500 0.0 0.0 0.0 4.02 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
24 25 0.802607 GCTTGGATCTGGTCGTCGTC 60.803 60.000 0.00 0.00 0.00 4.20
38 39 0.713883 GTCGTCCGTCTACGTTCGTA 59.286 55.000 0.00 5.02 43.31 3.43
64 65 1.486310 TCAGGTTGGATCCTTCCGATG 59.514 52.381 14.23 10.22 45.89 3.84
89 90 3.386867 CTTCATCAGCGGCGGTTGC 62.387 63.158 9.73 0.00 41.71 4.17
91 92 2.511373 CATCAGCGGCGGTTGCTA 60.511 61.111 9.73 0.00 41.72 3.49
100 101 0.392461 GGCGGTTGCTATTCTGGTGA 60.392 55.000 0.00 0.00 42.25 4.02
112 113 4.851639 ATTCTGGTGAGCTGGTTCTATT 57.148 40.909 0.00 0.00 0.00 1.73
136 137 2.636830 CCTTAGGACGACGACTTCCTA 58.363 52.381 14.46 14.46 41.92 2.94
199 202 2.173669 CGATGATGGGCGTTCGCTT 61.174 57.895 16.40 2.77 0.00 4.68
206 209 2.637025 GGCGTTCGCTTGCTTCAA 59.363 55.556 16.40 0.00 0.00 2.69
427 445 3.973206 TGTATTATACGATGGGGCCTG 57.027 47.619 0.84 0.00 0.00 4.85
483 501 1.447314 GCACTACACCTGGTACGGC 60.447 63.158 0.00 0.00 0.00 5.68
530 550 4.080863 GCCTTCCGAACCATGGATATATCT 60.081 45.833 21.47 0.00 34.91 1.98
536 588 7.611770 TCCGAACCATGGATATATCTAAGTTG 58.388 38.462 21.47 6.82 0.00 3.16
557 609 3.312709 GTGGGCACTACGTACGTAC 57.687 57.895 23.60 15.90 0.00 3.67
558 610 0.521291 GTGGGCACTACGTACGTACA 59.479 55.000 23.60 16.40 0.00 2.90
559 611 0.804364 TGGGCACTACGTACGTACAG 59.196 55.000 23.60 18.98 0.00 2.74
561 613 0.099436 GGCACTACGTACGTACAGGG 59.901 60.000 23.60 18.88 0.00 4.45
562 614 0.099436 GCACTACGTACGTACAGGGG 59.901 60.000 23.60 16.29 0.00 4.79
563 615 1.737838 CACTACGTACGTACAGGGGA 58.262 55.000 23.60 4.28 0.00 4.81
638 690 5.163622 CGGACAAATCTGGCATGTTTATCTT 60.164 40.000 0.00 0.00 28.70 2.40
664 722 2.652530 CCAAGTGGCCATGCACAC 59.347 61.111 9.72 9.27 37.86 3.82
665 723 2.201708 CCAAGTGGCCATGCACACA 61.202 57.895 9.72 0.00 39.99 3.72
808 870 1.200948 GCTTCTCCATCACAAGCAACC 59.799 52.381 0.00 0.00 41.87 3.77
951 1017 1.001633 CTACAAACCAGGCCACGTACT 59.998 52.381 5.01 0.00 0.00 2.73
953 1019 0.591170 CAAACCAGGCCACGTACTTG 59.409 55.000 5.01 0.00 0.00 3.16
956 1022 2.325082 CCAGGCCACGTACTTGCAC 61.325 63.158 5.01 0.00 0.00 4.57
958 1024 0.884704 CAGGCCACGTACTTGCACTT 60.885 55.000 5.01 0.00 0.00 3.16
960 1026 0.602905 GGCCACGTACTTGCACTTCT 60.603 55.000 0.00 0.00 0.00 2.85
962 1028 1.725164 GCCACGTACTTGCACTTCTAC 59.275 52.381 0.00 0.00 0.00 2.59
963 1029 2.609737 GCCACGTACTTGCACTTCTACT 60.610 50.000 0.00 0.00 0.00 2.57
966 1032 3.057456 CACGTACTTGCACTTCTACTCCT 60.057 47.826 0.00 0.00 0.00 3.69
967 1033 3.057456 ACGTACTTGCACTTCTACTCCTG 60.057 47.826 0.00 0.00 0.00 3.86
985 1059 2.539476 CTGCTTTGCGTTTCCTTTGTT 58.461 42.857 0.00 0.00 0.00 2.83
989 1063 3.616821 GCTTTGCGTTTCCTTTGTTTCTT 59.383 39.130 0.00 0.00 0.00 2.52
1023 1097 4.695993 TCGTTCATGGCGGCTGCA 62.696 61.111 21.31 5.95 45.35 4.41
1042 1116 1.206072 CTGCTCGTGTTGCTCTTGC 59.794 57.895 0.00 0.00 40.20 4.01
1043 1117 1.226686 CTGCTCGTGTTGCTCTTGCT 61.227 55.000 0.00 0.00 40.48 3.91
1051 1125 3.077359 GTGTTGCTCTTGCTATCCAGTT 58.923 45.455 0.00 0.00 40.48 3.16
1056 1130 1.929836 CTCTTGCTATCCAGTTCACGC 59.070 52.381 0.00 0.00 0.00 5.34
1057 1131 1.275010 TCTTGCTATCCAGTTCACGCA 59.725 47.619 0.00 0.00 0.00 5.24
1058 1132 2.093500 TCTTGCTATCCAGTTCACGCAT 60.093 45.455 0.00 0.00 0.00 4.73
1373 1447 0.911769 ATCCTGATCCAAGGCGTCAA 59.088 50.000 0.00 0.00 37.24 3.18
1557 1634 1.050204 GCCAGCAGATCCATCTCTCT 58.950 55.000 0.00 0.00 34.22 3.10
1729 1813 2.686915 GAGAATGGAGCCCACAATCTTG 59.313 50.000 0.00 0.00 35.80 3.02
1755 1839 2.094286 CAGCAAAGTTGTTTGTGGTCCA 60.094 45.455 0.00 0.00 44.37 4.02
1961 2046 4.443978 ACCCCATAATCATTGACCAGAG 57.556 45.455 0.00 0.00 0.00 3.35
2106 2191 3.746751 GCAATACCATCTCATGCTCTGGT 60.747 47.826 14.63 14.63 44.07 4.00
2259 2344 2.445525 AGGTGGTGTAAATTGGACAGGT 59.554 45.455 0.00 0.00 0.00 4.00
2260 2345 3.117284 AGGTGGTGTAAATTGGACAGGTT 60.117 43.478 0.00 0.00 0.00 3.50
2261 2346 3.254903 GGTGGTGTAAATTGGACAGGTTC 59.745 47.826 0.00 0.00 0.00 3.62
2293 2380 6.573434 TGTATCCTGTAGAAATACAGCTGTG 58.427 40.000 29.57 8.81 44.47 3.66
2325 2413 9.174166 ACTAGAATGTTGTACAAAAGAACAAGT 57.826 29.630 10.51 6.38 43.81 3.16
2326 2414 9.651718 CTAGAATGTTGTACAAAAGAACAAGTC 57.348 33.333 10.51 6.70 43.81 3.01
2327 2415 8.050778 AGAATGTTGTACAAAAGAACAAGTCA 57.949 30.769 10.51 0.15 43.81 3.41
2328 2416 8.184192 AGAATGTTGTACAAAAGAACAAGTCAG 58.816 33.333 10.51 0.00 43.81 3.51
2346 2443 9.618890 ACAAGTCAGATACATAATGCAAACTAT 57.381 29.630 0.00 0.00 0.00 2.12
2357 2454 7.649705 ACATAATGCAAACTATGTACTCTCTCG 59.350 37.037 14.47 0.00 37.06 4.04
2415 2512 7.069331 CCCATATAAAGGAAGTTGGTATGCAAA 59.931 37.037 0.00 0.00 0.00 3.68
2416 2513 8.641541 CCATATAAAGGAAGTTGGTATGCAAAT 58.358 33.333 0.00 0.00 0.00 2.32
2496 2597 8.437742 GCAGAAAGAAATACAAATGACCAAATG 58.562 33.333 0.00 0.00 0.00 2.32
2527 2628 6.215121 TGAAAACAGGTGATAAACTTGCATG 58.785 36.000 0.00 0.00 39.44 4.06
2545 2646 5.449107 GCATGGACAGATGCAATTCTAAT 57.551 39.130 0.00 0.00 46.77 1.73
2582 2683 8.609617 TTCTGATCTAGAAAGGAATGTTAGGA 57.390 34.615 0.00 0.00 42.31 2.94
2583 2684 8.789767 TCTGATCTAGAAAGGAATGTTAGGAT 57.210 34.615 0.00 0.00 30.84 3.24
2585 2686 8.324191 TGATCTAGAAAGGAATGTTAGGATGT 57.676 34.615 0.00 0.00 0.00 3.06
2586 2687 8.772250 TGATCTAGAAAGGAATGTTAGGATGTT 58.228 33.333 0.00 0.00 0.00 2.71
2621 4372 4.313020 GGGAGACCGGATAGTTAGGATA 57.687 50.000 9.46 0.00 43.64 2.59
2629 4380 5.104900 ACCGGATAGTTAGGATATTGATGGC 60.105 44.000 9.46 0.00 0.00 4.40
2638 4389 2.618241 GGATATTGATGGCGCAACTGAA 59.382 45.455 10.83 0.00 0.00 3.02
2656 4407 7.524912 CAACTGAACAATCTTAGGAACATGAG 58.475 38.462 0.00 0.00 0.00 2.90
2732 4483 9.638239 AACATACTGGTTTTTAATGCATAACTG 57.362 29.630 0.00 1.44 0.00 3.16
2761 4514 3.534357 TTTGGGTTTCCATGCTTAGGA 57.466 42.857 0.00 0.00 43.63 2.94
2763 4516 3.085952 TGGGTTTCCATGCTTAGGAAG 57.914 47.619 5.48 0.00 45.25 3.46
2775 4530 2.069273 CTTAGGAAGCGACCTTGTGTG 58.931 52.381 9.76 0.00 41.00 3.82
2811 4566 2.239654 CCCAGAGGAAGGCTCAACATAA 59.760 50.000 0.00 0.00 33.47 1.90
2819 4574 5.954150 AGGAAGGCTCAACATAAAACATCAT 59.046 36.000 0.00 0.00 0.00 2.45
2847 4602 7.566658 TTTGAAAATCCAAATTGGGTATCCT 57.433 32.000 12.67 0.00 38.32 3.24
2859 4614 7.510675 AATTGGGTATCCTAAAGAGAGACAA 57.489 36.000 0.00 0.00 0.00 3.18
2902 4657 4.521256 GTCTAGGACGGCAGATAGATTCTT 59.479 45.833 0.00 0.00 29.93 2.52
2903 4658 5.706369 GTCTAGGACGGCAGATAGATTCTTA 59.294 44.000 0.00 0.00 29.93 2.10
2906 4661 4.521256 AGGACGGCAGATAGATTCTTAGAC 59.479 45.833 0.00 0.00 29.93 2.59
2984 4741 6.229733 AGCTCTGAATCCAGTATAGAATTGC 58.770 40.000 0.00 0.00 41.16 3.56
2988 4745 5.065914 TGAATCCAGTATAGAATTGCTGGC 58.934 41.667 4.69 0.00 45.86 4.85
2992 4749 5.126067 TCCAGTATAGAATTGCTGGCTTTC 58.874 41.667 4.69 0.00 45.86 2.62
3010 4767 7.500992 TGGCTTTCAGTTACATAAGGATAGAG 58.499 38.462 0.00 0.00 0.00 2.43
3016 4773 7.005296 TCAGTTACATAAGGATAGAGAGGGAC 58.995 42.308 0.00 0.00 0.00 4.46
3050 4807 9.511404 TTATCCATTGATCTAGATATCCATGGT 57.489 33.333 18.93 12.43 44.18 3.55
3056 4813 5.485353 TGATCTAGATATCCATGGTTGTCCC 59.515 44.000 12.58 0.00 0.00 4.46
3064 4821 1.921346 ATGGTTGTCCCGCCCACTA 60.921 57.895 0.00 0.00 35.15 2.74
3065 4822 1.493854 ATGGTTGTCCCGCCCACTAA 61.494 55.000 0.00 0.00 35.15 2.24
3072 4829 0.841289 TCCCGCCCACTAAATAAGGG 59.159 55.000 0.00 0.00 45.68 3.95
3073 4830 0.549469 CCCGCCCACTAAATAAGGGT 59.451 55.000 0.00 0.00 44.69 4.34
3074 4831 1.064240 CCCGCCCACTAAATAAGGGTT 60.064 52.381 0.00 0.00 44.69 4.11
3115 4872 3.761752 CCCATAGATTTTTCACGGGTTGT 59.238 43.478 0.00 0.00 0.00 3.32
3123 4880 4.001248 CACGGGTTGTGCATGGAT 57.999 55.556 0.00 0.00 42.70 3.41
3124 4881 2.266070 CACGGGTTGTGCATGGATT 58.734 52.632 0.00 0.00 42.70 3.01
3125 4882 0.171007 CACGGGTTGTGCATGGATTC 59.829 55.000 0.00 0.00 42.70 2.52
3126 4883 0.251121 ACGGGTTGTGCATGGATTCA 60.251 50.000 0.00 0.00 0.00 2.57
3127 4884 0.452987 CGGGTTGTGCATGGATTCAG 59.547 55.000 0.00 0.00 0.00 3.02
3128 4885 0.174162 GGGTTGTGCATGGATTCAGC 59.826 55.000 0.00 0.00 0.00 4.26
3129 4886 0.174162 GGTTGTGCATGGATTCAGCC 59.826 55.000 0.00 0.00 0.00 4.85
3205 4962 2.251869 CATGGCAGTGAAACATGTCG 57.748 50.000 0.00 0.00 41.43 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.179100 CGACGACCAGATCCAAGCAT 60.179 55.000 0.00 0.00 0.00 3.79
8 9 3.599584 GGACGACGACCAGATCCA 58.400 61.111 11.55 0.00 0.00 3.41
24 25 0.379669 AGCCATACGAACGTAGACGG 59.620 55.000 12.33 12.49 44.95 4.79
38 39 1.302907 AGGATCCAACCTGAAGCCAT 58.697 50.000 15.82 0.00 39.01 4.40
89 90 3.902881 AGAACCAGCTCACCAGAATAG 57.097 47.619 0.00 0.00 0.00 1.73
91 92 4.521146 CAATAGAACCAGCTCACCAGAAT 58.479 43.478 0.00 0.00 0.00 2.40
100 101 1.002857 AAGGCCCAATAGAACCAGCT 58.997 50.000 0.00 0.00 0.00 4.24
112 113 2.036098 TCGTCGTCCTAAGGCCCA 59.964 61.111 0.00 0.00 0.00 5.36
206 209 1.065701 CCTAGCGACGACTACAAGCAT 59.934 52.381 0.00 0.00 0.00 3.79
263 267 6.724263 TCAATCATGACAGTACAACAAACAC 58.276 36.000 0.00 0.00 0.00 3.32
268 272 7.160726 TCATCTTCAATCATGACAGTACAACA 58.839 34.615 0.00 0.00 34.61 3.33
392 410 9.040939 TCGTATAATACATCAAACATTGACCAG 57.959 33.333 0.00 0.00 43.48 4.00
427 445 2.361438 ACTCACTCCGTCCGGATTTATC 59.639 50.000 7.81 0.00 44.24 1.75
483 501 0.725117 GCGTTGTCCCAAAGGTATCG 59.275 55.000 0.00 0.00 0.00 2.92
530 550 0.320946 GTAGTGCCCACGCCAACTTA 60.321 55.000 0.00 0.00 36.20 2.24
536 588 2.507769 GTACGTAGTGCCCACGCC 60.508 66.667 0.00 0.00 45.73 5.68
554 606 4.774200 ACGTATATACCCAATCCCCTGTAC 59.226 45.833 7.30 0.00 0.00 2.90
555 607 4.773674 CACGTATATACCCAATCCCCTGTA 59.226 45.833 7.30 0.00 0.00 2.74
556 608 3.581332 CACGTATATACCCAATCCCCTGT 59.419 47.826 7.30 0.00 0.00 4.00
557 609 3.835978 TCACGTATATACCCAATCCCCTG 59.164 47.826 7.30 0.00 0.00 4.45
558 610 4.136341 TCACGTATATACCCAATCCCCT 57.864 45.455 7.30 0.00 0.00 4.79
559 611 4.529377 TCTTCACGTATATACCCAATCCCC 59.471 45.833 7.30 0.00 0.00 4.81
561 613 7.383687 TGAATCTTCACGTATATACCCAATCC 58.616 38.462 7.30 0.00 31.01 3.01
562 614 8.304596 TCTGAATCTTCACGTATATACCCAATC 58.695 37.037 7.30 0.00 32.90 2.67
563 615 8.190326 TCTGAATCTTCACGTATATACCCAAT 57.810 34.615 7.30 0.00 32.90 3.16
664 722 1.101049 AACGGTTCAGCCAGGTGTTG 61.101 55.000 0.00 0.00 36.97 3.33
665 723 0.818040 GAACGGTTCAGCCAGGTGTT 60.818 55.000 15.70 0.00 36.97 3.32
808 870 1.705337 GCATGTGGATGTCGTTCGGG 61.705 60.000 0.00 0.00 31.50 5.14
951 1017 3.141398 CAAAGCAGGAGTAGAAGTGCAA 58.859 45.455 0.00 0.00 38.44 4.08
953 1019 1.466558 GCAAAGCAGGAGTAGAAGTGC 59.533 52.381 0.00 0.00 36.10 4.40
956 1022 2.086054 ACGCAAAGCAGGAGTAGAAG 57.914 50.000 0.00 0.00 0.00 2.85
958 1024 2.413837 GAAACGCAAAGCAGGAGTAGA 58.586 47.619 0.00 0.00 0.00 2.59
960 1026 1.071699 AGGAAACGCAAAGCAGGAGTA 59.928 47.619 0.00 0.00 0.00 2.59
962 1028 0.954452 AAGGAAACGCAAAGCAGGAG 59.046 50.000 0.00 0.00 0.00 3.69
963 1029 1.066908 CAAAGGAAACGCAAAGCAGGA 59.933 47.619 0.00 0.00 0.00 3.86
966 1032 2.663826 AACAAAGGAAACGCAAAGCA 57.336 40.000 0.00 0.00 0.00 3.91
967 1033 3.186909 AGAAACAAAGGAAACGCAAAGC 58.813 40.909 0.00 0.00 0.00 3.51
1023 1097 1.502163 GCAAGAGCAACACGAGCAGT 61.502 55.000 0.00 0.00 41.58 4.40
1027 1101 1.929836 GGATAGCAAGAGCAACACGAG 59.070 52.381 0.00 0.00 45.49 4.18
1033 1107 3.338249 GTGAACTGGATAGCAAGAGCAA 58.662 45.455 0.00 0.00 45.49 3.91
1042 1116 1.863454 GCTCATGCGTGAACTGGATAG 59.137 52.381 10.41 0.00 33.05 2.08
1043 1117 1.939974 GCTCATGCGTGAACTGGATA 58.060 50.000 10.41 0.00 33.05 2.59
1075 1149 4.069232 CTGAGTCTCGGCCGGCAA 62.069 66.667 30.85 15.15 0.00 4.52
1392 1466 3.940640 CCATTGATCGTGCCGCCG 61.941 66.667 0.00 0.00 0.00 6.46
1557 1634 2.666190 GCGCTGCAGTCCTCAACA 60.666 61.111 16.64 0.00 0.00 3.33
1717 1801 1.133790 GCTGACATCAAGATTGTGGGC 59.866 52.381 0.00 0.00 0.00 5.36
1729 1813 3.798337 CCACAAACAACTTTGCTGACATC 59.202 43.478 0.00 0.00 40.57 3.06
1755 1839 1.617804 CCAACACTGATTCCATGCCCT 60.618 52.381 0.00 0.00 0.00 5.19
1869 1954 1.000396 GCTTCCTCCCTGCCATGTT 60.000 57.895 0.00 0.00 0.00 2.71
2106 2191 6.549736 TCAGGTCGATATTCTCCAAGACAATA 59.450 38.462 0.00 0.00 0.00 1.90
2260 2345 9.871238 GTATTTCTACAGGATACAACAAGAAGA 57.129 33.333 0.00 0.00 41.41 2.87
2261 2346 9.653287 TGTATTTCTACAGGATACAACAAGAAG 57.347 33.333 0.00 0.00 34.36 2.85
2293 2380 9.997482 TCTTTTGTACAACATTCTAGTTTTGAC 57.003 29.630 8.07 0.00 0.00 3.18
2321 2409 9.874215 CATAGTTTGCATTATGTATCTGACTTG 57.126 33.333 0.00 0.00 0.00 3.16
2346 2443 9.440773 TTCTAGTAAAACATACGAGAGAGTACA 57.559 33.333 0.00 0.00 32.37 2.90
2446 2543 7.992608 TGCTAATTTCAGAGAGGCATGTAAATA 59.007 33.333 0.00 0.00 0.00 1.40
2527 2628 6.441093 TTGACATTAGAATTGCATCTGTCC 57.559 37.500 0.00 0.00 0.00 4.02
2567 2668 6.868339 CCACAAAACATCCTAACATTCCTTTC 59.132 38.462 0.00 0.00 0.00 2.62
2569 2670 5.245977 CCCACAAAACATCCTAACATTCCTT 59.754 40.000 0.00 0.00 0.00 3.36
2570 2671 4.772100 CCCACAAAACATCCTAACATTCCT 59.228 41.667 0.00 0.00 0.00 3.36
2571 2672 4.526650 ACCCACAAAACATCCTAACATTCC 59.473 41.667 0.00 0.00 0.00 3.01
2572 2673 5.010617 ACACCCACAAAACATCCTAACATTC 59.989 40.000 0.00 0.00 0.00 2.67
2573 2674 4.898861 ACACCCACAAAACATCCTAACATT 59.101 37.500 0.00 0.00 0.00 2.71
2574 2675 4.280677 CACACCCACAAAACATCCTAACAT 59.719 41.667 0.00 0.00 0.00 2.71
2576 2677 3.634910 ACACACCCACAAAACATCCTAAC 59.365 43.478 0.00 0.00 0.00 2.34
2577 2678 3.634448 CACACACCCACAAAACATCCTAA 59.366 43.478 0.00 0.00 0.00 2.69
2579 2680 2.031120 CACACACCCACAAAACATCCT 58.969 47.619 0.00 0.00 0.00 3.24
2580 2681 1.068434 CCACACACCCACAAAACATCC 59.932 52.381 0.00 0.00 0.00 3.51
2581 2682 1.068434 CCCACACACCCACAAAACATC 59.932 52.381 0.00 0.00 0.00 3.06
2582 2683 1.118838 CCCACACACCCACAAAACAT 58.881 50.000 0.00 0.00 0.00 2.71
2583 2684 0.972983 CCCCACACACCCACAAAACA 60.973 55.000 0.00 0.00 0.00 2.83
2585 2686 0.396417 CTCCCCACACACCCACAAAA 60.396 55.000 0.00 0.00 0.00 2.44
2586 2687 1.228793 CTCCCCACACACCCACAAA 59.771 57.895 0.00 0.00 0.00 2.83
2609 4360 5.419542 TGCGCCATCAATATCCTAACTATC 58.580 41.667 4.18 0.00 0.00 2.08
2612 4363 3.769739 TGCGCCATCAATATCCTAACT 57.230 42.857 4.18 0.00 0.00 2.24
2613 4364 3.815401 AGTTGCGCCATCAATATCCTAAC 59.185 43.478 4.18 0.00 0.00 2.34
2621 4372 1.246649 TGTTCAGTTGCGCCATCAAT 58.753 45.000 4.18 0.00 0.00 2.57
2629 4380 4.213270 TGTTCCTAAGATTGTTCAGTTGCG 59.787 41.667 0.00 0.00 0.00 4.85
2638 4389 3.935203 CACGCTCATGTTCCTAAGATTGT 59.065 43.478 0.00 0.00 0.00 2.71
2761 4514 0.395173 AAACCCACACAAGGTCGCTT 60.395 50.000 0.00 0.00 36.27 4.68
2763 4516 1.652563 GAAACCCACACAAGGTCGC 59.347 57.895 0.00 0.00 36.27 5.19
2775 4530 0.753111 CTGGGCTGCTATGGAAACCC 60.753 60.000 0.00 0.00 37.88 4.11
2831 4586 6.676632 TCTCTCTTTAGGATACCCAATTTGGA 59.323 38.462 17.24 0.00 40.96 3.53
2847 4602 7.769044 GGCTACCAAATACATTGTCTCTCTTTA 59.231 37.037 0.00 0.00 37.32 1.85
2877 4632 2.573369 TCTATCTGCCGTCCTAGACAC 58.427 52.381 0.00 0.00 32.09 3.67
2878 4633 3.510531 ATCTATCTGCCGTCCTAGACA 57.489 47.619 0.00 0.00 32.09 3.41
2902 4657 4.620086 TTTCCTCCCTATCACCAGTCTA 57.380 45.455 0.00 0.00 0.00 2.59
2903 4658 3.491766 TTTCCTCCCTATCACCAGTCT 57.508 47.619 0.00 0.00 0.00 3.24
2906 4661 4.464947 GGAATTTTCCTCCCTATCACCAG 58.535 47.826 1.97 0.00 44.11 4.00
2988 4745 8.364142 CCCTCTCTATCCTTATGTAACTGAAAG 58.636 40.741 0.00 0.00 42.29 2.62
2992 4749 6.072397 CGTCCCTCTCTATCCTTATGTAACTG 60.072 46.154 0.00 0.00 0.00 3.16
3010 4767 6.464222 TCAATGGATAATATTGTCGTCCCTC 58.536 40.000 6.17 0.00 36.97 4.30
3050 4807 2.356330 CCTTATTTAGTGGGCGGGACAA 60.356 50.000 0.00 0.00 0.00 3.18
3056 4813 4.490743 CAAAAACCCTTATTTAGTGGGCG 58.509 43.478 0.00 0.00 44.56 6.13
3064 4821 7.872061 AAAGATCCTCCAAAAACCCTTATTT 57.128 32.000 0.00 0.00 0.00 1.40
3065 4822 7.734865 AGAAAAGATCCTCCAAAAACCCTTATT 59.265 33.333 0.00 0.00 0.00 1.40
3072 4829 5.773176 TGGGTAGAAAAGATCCTCCAAAAAC 59.227 40.000 0.00 0.00 0.00 2.43
3073 4830 5.959512 TGGGTAGAAAAGATCCTCCAAAAA 58.040 37.500 0.00 0.00 0.00 1.94
3074 4831 5.592587 TGGGTAGAAAAGATCCTCCAAAA 57.407 39.130 0.00 0.00 0.00 2.44
3108 4865 0.452987 CTGAATCCATGCACAACCCG 59.547 55.000 0.00 0.00 0.00 5.28
3122 4879 2.042162 AGGAACACCTGAATGGCTGAAT 59.958 45.455 0.00 0.00 40.22 2.57
3123 4880 1.425066 AGGAACACCTGAATGGCTGAA 59.575 47.619 0.00 0.00 40.22 3.02
3124 4881 1.003580 GAGGAACACCTGAATGGCTGA 59.996 52.381 0.00 0.00 40.22 4.26
3125 4882 1.457346 GAGGAACACCTGAATGGCTG 58.543 55.000 0.00 0.00 40.22 4.85
3126 4883 0.329596 GGAGGAACACCTGAATGGCT 59.670 55.000 0.00 0.00 40.22 4.75
3127 4884 0.038166 TGGAGGAACACCTGAATGGC 59.962 55.000 0.00 0.00 40.67 4.40
3128 4885 2.372264 CATGGAGGAACACCTGAATGG 58.628 52.381 0.00 0.00 40.67 3.16
3129 4886 2.025981 TCCATGGAGGAACACCTGAATG 60.026 50.000 11.44 0.00 45.65 2.67


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

AutoCloner maintained by Alex Coulton.