Multiple sequence alignment - TraesCS4A01G028400

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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 TraesCS4A01G028400 chr4A 100.000 3826 0 0 1 3826 20267882 20264057 0.000000e+00 7066.0
1 TraesCS4A01G028400 chr4D 93.483 1688 83 18 1530 3209 446909785 446911453 0.000000e+00 2483.0
2 TraesCS4A01G028400 chr4D 92.343 1541 74 23 1 1529 446908215 446909723 0.000000e+00 2152.0
3 TraesCS4A01G028400 chr4D 87.047 579 32 11 3273 3826 446911659 446912219 7.020000e-172 614.0
4 TraesCS4A01G028400 chr4D 89.423 104 8 2 3210 3311 446911545 446911647 1.120000e-25 128.0
5 TraesCS4A01G028400 chr4B 92.582 1685 87 22 1530 3208 559281130 559282782 0.000000e+00 2385.0
6 TraesCS4A01G028400 chr4B 89.095 917 49 20 631 1529 559280184 559281067 0.000000e+00 1092.0
7 TraesCS4A01G028400 chr4B 89.081 577 40 7 3273 3826 559283258 559283834 0.000000e+00 695.0
8 TraesCS4A01G028400 chr4B 92.157 51 2 1 3210 3258 559282876 559282926 1.910000e-08 71.3
9 TraesCS4A01G028400 chr5B 81.598 413 39 11 3450 3826 387955999 387955588 1.340000e-79 307.0
10 TraesCS4A01G028400 chr5B 93.855 179 8 3 3218 3393 387956192 387956014 2.270000e-67 267.0


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 TraesCS4A01G028400 chr4A 20264057 20267882 3825 True 7066.000 7066 100.00000 1 3826 1 chr4A.!!$R1 3825
1 TraesCS4A01G028400 chr4D 446908215 446912219 4004 False 1344.250 2483 90.57400 1 3826 4 chr4D.!!$F1 3825
2 TraesCS4A01G028400 chr4B 559280184 559283834 3650 False 1060.825 2385 90.72875 631 3826 4 chr4B.!!$F1 3195
3 TraesCS4A01G028400 chr5B 387955588 387956192 604 True 287.000 307 87.72650 3218 3826 2 chr5B.!!$R1 608

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
71 72 0.241749 TATCAGTTCGCGGACACGTT 59.758 50.0 21.79 7.98 43.45 3.99 F
741 752 0.461339 TGAAAAGTATCCGGGAGCGC 60.461 55.0 0.00 0.00 0.00 5.92 F
2143 2245 0.541392 TGCAGGTACCATTGATCGCT 59.459 50.0 15.94 0.00 0.00 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1662 1756 1.417517 ACTCTGCAAGTCCACATCACA 59.582 47.619 0.00 0.00 30.02 3.58 R
2492 2594 0.660488 TGCGTGGTTTTGCTGTACAG 59.340 50.000 18.93 18.93 0.00 2.74 R
3435 4007 0.958382 TGTTGAGGTAATGGCGTGCC 60.958 55.000 3.30 3.30 0.00 5.01 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
29 30 0.623723 GGGTTAGGGCATCTCCAACA 59.376 55.000 0.00 0.00 36.21 3.33
31 32 2.358195 GGGTTAGGGCATCTCCAACAAT 60.358 50.000 0.00 0.00 36.21 2.71
37 38 2.827921 GGGCATCTCCAACAATGTTTCT 59.172 45.455 0.00 0.00 36.21 2.52
44 45 4.511454 TCTCCAACAATGTTTCTCAAGTCG 59.489 41.667 0.00 0.00 0.00 4.18
46 47 3.304659 CCAACAATGTTTCTCAAGTCGGG 60.305 47.826 0.00 0.00 0.00 5.14
50 51 0.319555 TGTTTCTCAAGTCGGGCTCG 60.320 55.000 0.00 0.00 37.82 5.03
71 72 0.241749 TATCAGTTCGCGGACACGTT 59.758 50.000 21.79 7.98 43.45 3.99
74 75 2.235016 AGTTCGCGGACACGTTGTG 61.235 57.895 21.79 0.00 43.45 3.33
75 76 2.962786 TTCGCGGACACGTTGTGG 60.963 61.111 6.13 0.00 43.45 4.17
117 121 4.101430 GCCATCCAACCATGTCCATTAAAT 59.899 41.667 0.00 0.00 0.00 1.40
118 122 5.603596 CCATCCAACCATGTCCATTAAATG 58.396 41.667 0.00 0.00 0.00 2.32
119 123 5.129155 CCATCCAACCATGTCCATTAAATGT 59.871 40.000 0.00 0.00 0.00 2.71
120 124 6.323482 CCATCCAACCATGTCCATTAAATGTA 59.677 38.462 0.00 0.00 0.00 2.29
121 125 7.015487 CCATCCAACCATGTCCATTAAATGTAT 59.985 37.037 0.00 0.00 0.00 2.29
122 126 7.345422 TCCAACCATGTCCATTAAATGTATG 57.655 36.000 0.00 0.00 0.00 2.39
123 127 5.984926 CCAACCATGTCCATTAAATGTATGC 59.015 40.000 0.00 0.00 0.00 3.14
124 128 6.406737 CCAACCATGTCCATTAAATGTATGCA 60.407 38.462 0.00 0.00 0.00 3.96
125 129 6.147864 ACCATGTCCATTAAATGTATGCAC 57.852 37.500 0.00 0.00 0.00 4.57
126 130 5.214417 CCATGTCCATTAAATGTATGCACG 58.786 41.667 0.00 0.00 0.00 5.34
171 179 3.194329 TGTGAAGAACTCGATCTGCATCT 59.806 43.478 0.02 0.00 37.33 2.90
192 200 7.627939 GCATCTGACTTTGCATATTTCTCTTGT 60.628 37.037 0.00 0.00 38.72 3.16
200 208 5.247862 TGCATATTTCTCTTGTGAAGCTCA 58.752 37.500 0.00 0.00 0.00 4.26
247 257 3.315191 GCTGGTGTGTGTTTGACTATTGT 59.685 43.478 0.00 0.00 0.00 2.71
248 258 4.554723 GCTGGTGTGTGTTTGACTATTGTC 60.555 45.833 0.00 0.00 43.20 3.18
263 273 2.211353 TTGTCATGTGTCGACGTCAA 57.789 45.000 17.16 4.10 36.11 3.18
279 289 2.535984 CGTCAAGATCCATGTAGTTCGC 59.464 50.000 0.00 0.00 0.00 4.70
285 295 4.799678 AGATCCATGTAGTTCGCGAATAG 58.200 43.478 26.23 10.89 0.00 1.73
308 319 2.159627 GGTTTGTTGATGGTGCTCTACG 59.840 50.000 0.00 0.00 0.00 3.51
335 346 2.672714 TGAATTTGGAGTGAGACGACG 58.327 47.619 0.00 0.00 0.00 5.12
353 364 2.264109 CGACACTCGTATGCACTCTT 57.736 50.000 0.00 0.00 34.72 2.85
370 381 3.626217 ACTCTTGACGGGTGTTTTTCTTC 59.374 43.478 0.00 0.00 0.00 2.87
371 382 3.877508 CTCTTGACGGGTGTTTTTCTTCT 59.122 43.478 0.00 0.00 0.00 2.85
372 383 3.875134 TCTTGACGGGTGTTTTTCTTCTC 59.125 43.478 0.00 0.00 0.00 2.87
373 384 2.206750 TGACGGGTGTTTTTCTTCTCG 58.793 47.619 0.00 0.00 0.00 4.04
397 408 1.595382 GCCGGGACATTCTCATCGG 60.595 63.158 2.18 0.00 39.13 4.18
407 418 1.568504 TTCTCATCGGTAGCCAGGTT 58.431 50.000 0.00 0.00 0.00 3.50
418 429 2.736531 CCAGGTTGGCCAAAGTGC 59.263 61.111 22.47 7.60 37.19 4.40
443 454 1.071605 GCTGTCAATGTGGACGAGTC 58.928 55.000 0.00 0.00 40.72 3.36
470 481 9.127006 GGTCCGTTTTTCGCTAATTAAATAAAA 57.873 29.630 0.00 0.00 38.35 1.52
581 592 3.775866 TGGACATTCCTAACCGTTGGATA 59.224 43.478 0.00 0.00 37.46 2.59
589 600 4.871557 TCCTAACCGTTGGATATTCGTTTG 59.128 41.667 0.00 0.00 0.00 2.93
590 601 4.632688 CCTAACCGTTGGATATTCGTTTGT 59.367 41.667 0.00 0.00 0.00 2.83
591 602 4.673534 AACCGTTGGATATTCGTTTGTC 57.326 40.909 0.00 0.00 0.00 3.18
592 603 3.666274 ACCGTTGGATATTCGTTTGTCA 58.334 40.909 0.00 0.00 0.00 3.58
593 604 3.434299 ACCGTTGGATATTCGTTTGTCAC 59.566 43.478 0.00 0.00 0.00 3.67
594 605 3.682858 CCGTTGGATATTCGTTTGTCACT 59.317 43.478 0.00 0.00 0.00 3.41
595 606 4.865925 CCGTTGGATATTCGTTTGTCACTA 59.134 41.667 0.00 0.00 0.00 2.74
596 607 5.522460 CCGTTGGATATTCGTTTGTCACTAT 59.478 40.000 0.00 0.00 0.00 2.12
597 608 6.410845 CGTTGGATATTCGTTTGTCACTATG 58.589 40.000 0.00 0.00 0.00 2.23
598 609 6.035650 CGTTGGATATTCGTTTGTCACTATGT 59.964 38.462 0.00 0.00 0.00 2.29
599 610 7.412563 CGTTGGATATTCGTTTGTCACTATGTT 60.413 37.037 0.00 0.00 0.00 2.71
600 611 7.915293 TGGATATTCGTTTGTCACTATGTTT 57.085 32.000 0.00 0.00 0.00 2.83
601 612 9.438228 TTGGATATTCGTTTGTCACTATGTTTA 57.562 29.630 0.00 0.00 0.00 2.01
602 613 8.875803 TGGATATTCGTTTGTCACTATGTTTAC 58.124 33.333 0.00 0.00 0.00 2.01
603 614 8.333186 GGATATTCGTTTGTCACTATGTTTACC 58.667 37.037 0.00 0.00 0.00 2.85
604 615 5.579384 TTCGTTTGTCACTATGTTTACCG 57.421 39.130 0.00 0.00 0.00 4.02
605 616 3.429543 TCGTTTGTCACTATGTTTACCGC 59.570 43.478 0.00 0.00 0.00 5.68
626 637 2.802057 CGAACTGGGCTAAATACTCCCG 60.802 54.545 0.00 0.00 42.98 5.14
629 640 2.963782 ACTGGGCTAAATACTCCCGTAG 59.036 50.000 0.00 0.00 42.98 3.51
631 642 1.969208 GGGCTAAATACTCCCGTAGCT 59.031 52.381 0.00 0.00 39.15 3.32
686 697 8.893219 TCCATCAAGCTATAGTCACTAATTTG 57.107 34.615 0.84 0.00 0.00 2.32
687 698 8.704668 TCCATCAAGCTATAGTCACTAATTTGA 58.295 33.333 0.84 0.00 0.00 2.69
740 751 2.018542 TTGAAAAGTATCCGGGAGCG 57.981 50.000 0.00 0.00 0.00 5.03
741 752 0.461339 TGAAAAGTATCCGGGAGCGC 60.461 55.000 0.00 0.00 0.00 5.92
753 764 3.267860 GAGCGCGCCATCTGGAAG 61.268 66.667 30.33 0.00 37.39 3.46
789 800 4.774503 GCTTGGCTCCTCGCTGCT 62.775 66.667 0.00 0.00 39.13 4.24
798 809 2.223829 GCTCCTCGCTGCTAAGTCAATA 60.224 50.000 0.00 0.00 35.14 1.90
884 895 6.480763 TCTTTAAGCTCCATCATAACAACCA 58.519 36.000 0.00 0.00 0.00 3.67
949 964 1.748493 AGCAGCAGAGCAGTACTAGTC 59.252 52.381 0.00 0.00 36.85 2.59
994 1009 4.585162 AGAGTCGAGAGAGAAACCAAGAAA 59.415 41.667 0.00 0.00 43.49 2.52
1045 1060 2.039624 TGGTGCTCCTCCTCCTCC 59.960 66.667 6.34 0.00 34.23 4.30
1046 1061 2.366570 GGTGCTCCTCCTCCTCCT 59.633 66.667 0.00 0.00 0.00 3.69
1047 1062 1.760480 GGTGCTCCTCCTCCTCCTC 60.760 68.421 0.00 0.00 0.00 3.71
1170 1197 1.151777 CGCCGGCGATGTCAATTACT 61.152 55.000 44.86 0.00 42.83 2.24
1171 1198 1.860676 GCCGGCGATGTCAATTACTA 58.139 50.000 12.58 0.00 0.00 1.82
1172 1199 1.525619 GCCGGCGATGTCAATTACTAC 59.474 52.381 12.58 0.00 0.00 2.73
1184 1211 0.822164 ATTACTACGAGCTTGGCCGT 59.178 50.000 5.79 4.56 38.49 5.68
1213 1240 4.572571 TGGGGTTGTGTGGCCGAC 62.573 66.667 0.00 0.00 0.00 4.79
1271 1298 2.668550 GGGAACTGCACGGTGACC 60.669 66.667 13.29 6.30 0.00 4.02
1385 1412 2.126071 TGTAAGTGCGCGCTCCTC 60.126 61.111 33.29 20.13 0.00 3.71
1386 1413 2.182030 GTAAGTGCGCGCTCCTCT 59.818 61.111 33.29 20.67 0.00 3.69
1388 1415 1.446099 TAAGTGCGCGCTCCTCTTG 60.446 57.895 33.29 0.00 0.00 3.02
1411 1438 4.789161 GCGTATACGTCCTTTCTCTTCCTC 60.789 50.000 25.04 0.31 42.22 3.71
1497 1524 2.667473 ACTGCATAACACCTACGTCC 57.333 50.000 0.00 0.00 0.00 4.79
1563 1657 7.604164 CCCACGATTAGCTTCTGAATACATATT 59.396 37.037 0.00 0.00 0.00 1.28
1564 1658 8.651588 CCACGATTAGCTTCTGAATACATATTC 58.348 37.037 0.00 4.91 41.81 1.75
1662 1756 8.846943 TGGTTTATATGCATCTCGAATACATT 57.153 30.769 0.19 0.00 0.00 2.71
1742 1836 8.499162 CACTTTTCAGTCTGAATAAAGTCGATT 58.501 33.333 21.86 5.81 36.08 3.34
1751 1845 8.398665 GTCTGAATAAAGTCGATTTTTAGGCAT 58.601 33.333 11.37 0.00 32.01 4.40
1789 1883 5.191727 ACATAAATCTCATTGGTCCACCA 57.808 39.130 0.00 0.00 45.94 4.17
1805 1899 2.222640 CCACCAAAACGCGTAGTAATCG 60.223 50.000 14.46 0.00 0.00 3.34
1846 1940 5.929697 TGCTGTCTCTATTGTTGAAACAG 57.070 39.130 0.00 0.00 40.50 3.16
1847 1941 5.610398 TGCTGTCTCTATTGTTGAAACAGA 58.390 37.500 3.93 0.00 40.50 3.41
1848 1942 5.466728 TGCTGTCTCTATTGTTGAAACAGAC 59.533 40.000 3.93 5.87 40.50 3.51
1849 1943 5.466728 GCTGTCTCTATTGTTGAAACAGACA 59.533 40.000 12.07 12.07 40.50 3.41
1864 1959 2.375174 ACAGACAGGCATGGGTCTTAAA 59.625 45.455 2.31 0.00 42.22 1.52
1866 1961 3.629398 CAGACAGGCATGGGTCTTAAATC 59.371 47.826 2.31 0.00 42.22 2.17
1879 1974 7.546358 TGGGTCTTAAATCTTTAACATGCATG 58.454 34.615 25.09 25.09 0.00 4.06
1973 2070 2.276732 TCAAAAGTGCCCTCTTCAGG 57.723 50.000 0.00 0.00 39.98 3.86
2083 2180 7.744087 TCTGCACACAAAATATTACAGAGTT 57.256 32.000 0.00 0.00 0.00 3.01
2113 2215 8.690203 TTATATCATCCCACATAACCAACAAG 57.310 34.615 0.00 0.00 0.00 3.16
2141 2243 1.586422 CCTGCAGGTACCATTGATCG 58.414 55.000 25.53 0.00 0.00 3.69
2143 2245 0.541392 TGCAGGTACCATTGATCGCT 59.459 50.000 15.94 0.00 0.00 4.93
2148 2250 1.532868 GGTACCATTGATCGCTCATGC 59.467 52.381 7.15 0.00 0.00 4.06
2159 2261 1.201414 TCGCTCATGCTCTAACGACAA 59.799 47.619 0.00 0.00 36.97 3.18
2229 2331 2.631545 AGACCGTAACTACTGCACCTTT 59.368 45.455 0.00 0.00 0.00 3.11
2230 2332 3.828451 AGACCGTAACTACTGCACCTTTA 59.172 43.478 0.00 0.00 0.00 1.85
2233 2335 2.919229 CGTAACTACTGCACCTTTACCG 59.081 50.000 0.00 0.00 0.00 4.02
2236 2338 1.337823 ACTACTGCACCTTTACCGCTG 60.338 52.381 0.00 0.00 0.00 5.18
2247 2349 1.975660 TTACCGCTGCTTGTTTTCCT 58.024 45.000 0.00 0.00 0.00 3.36
2264 2366 8.359060 TGTTTTCCTATTTGTACATTTTGTGC 57.641 30.769 0.00 0.00 33.42 4.57
2356 2458 3.673809 GTGACTTAGCTTACTGTGGTTCG 59.326 47.826 0.00 0.00 0.00 3.95
2492 2594 1.541588 GGACACAAGCAACTTCCCATC 59.458 52.381 0.00 0.00 0.00 3.51
2530 2632 3.726607 GCATCTCACATCTAACTCCTGG 58.273 50.000 0.00 0.00 0.00 4.45
2536 2638 3.713248 TCACATCTAACTCCTGGCATCAT 59.287 43.478 0.00 0.00 0.00 2.45
2703 2805 0.382158 TCTCGACATCTGCATCGGTC 59.618 55.000 7.53 4.91 38.86 4.79
2708 2810 0.248498 ACATCTGCATCGGTCGTACG 60.248 55.000 9.53 9.53 0.00 3.67
2734 2836 2.354821 GGTGAATTTACTGTCATCGCCC 59.645 50.000 0.00 0.00 35.21 6.13
2735 2837 2.354821 GTGAATTTACTGTCATCGCCCC 59.645 50.000 0.00 0.00 0.00 5.80
2945 3048 0.798159 TGTCGCTGCTGCAGTATTTG 59.202 50.000 28.50 14.56 39.64 2.32
2986 3092 2.425668 TCTACGGTGCGAGAATTGATGA 59.574 45.455 0.00 0.00 0.00 2.92
2987 3093 2.315925 ACGGTGCGAGAATTGATGAT 57.684 45.000 0.00 0.00 0.00 2.45
2988 3094 2.632377 ACGGTGCGAGAATTGATGATT 58.368 42.857 0.00 0.00 0.00 2.57
3067 3173 5.125417 ACCGATTGTCTATTTGATTGTTGGG 59.875 40.000 0.00 0.00 0.00 4.12
3095 3201 8.490355 GGCTGAAACTTTTCATGTTCTTATTTG 58.510 33.333 4.89 0.00 45.26 2.32
3116 3222 4.831107 TGTGATGTCGATTTCCTCAATGA 58.169 39.130 0.00 0.00 0.00 2.57
3127 3233 6.933521 CGATTTCCTCAATGACAGAATCCTAT 59.066 38.462 0.00 0.00 0.00 2.57
3326 3890 4.421058 CGTGACTTCGGTTAAGATCATGA 58.579 43.478 0.00 0.00 38.67 3.07
3327 3891 4.265556 CGTGACTTCGGTTAAGATCATGAC 59.734 45.833 0.00 0.00 38.67 3.06
3361 3933 7.450014 CCTCTGCTTCCTTCATAGATACTTCTA 59.550 40.741 0.00 0.00 38.79 2.10
3371 3943 5.303589 TCATAGATACTTCTAACAACCCCCG 59.696 44.000 0.00 0.00 37.97 5.73
3435 4007 4.093952 CAAGCACAGCCCTTCGCG 62.094 66.667 0.00 0.00 44.76 5.87
3464 4036 4.023193 CCATTACCTCAACACAAACTGGAC 60.023 45.833 0.00 0.00 0.00 4.02
3482 4054 3.446161 TGGACCGTAAACAGTCTCCATAG 59.554 47.826 0.00 0.00 33.39 2.23
3484 4056 2.159282 ACCGTAAACAGTCTCCATAGCG 60.159 50.000 0.00 0.00 0.00 4.26
3648 4270 0.659957 GCTGAATCGATCAAGCCCAC 59.340 55.000 17.37 0.00 37.67 4.61
3658 4280 0.895100 TCAAGCCCACCTCATGCAAC 60.895 55.000 0.00 0.00 0.00 4.17
3738 4361 1.743252 CTCGCCTTGCCTTCCAGAC 60.743 63.158 0.00 0.00 0.00 3.51
3768 4391 4.885907 CAGGGCAGTAATCATCTTCACATT 59.114 41.667 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.386057 GGAGATGCCCTAACCCCCT 60.386 63.158 0.00 0.00 0.00 4.79
29 30 2.427506 GAGCCCGACTTGAGAAACATT 58.572 47.619 0.00 0.00 0.00 2.71
31 32 0.319555 CGAGCCCGACTTGAGAAACA 60.320 55.000 0.00 0.00 38.22 2.83
37 38 1.035385 TGATAGCGAGCCCGACTTGA 61.035 55.000 0.00 0.00 38.22 3.02
44 45 1.951631 GCGAACTGATAGCGAGCCC 60.952 63.158 0.00 0.00 0.00 5.19
50 51 1.472276 CGTGTCCGCGAACTGATAGC 61.472 60.000 8.23 0.00 0.00 2.97
71 72 3.101437 ACTTACGTATCCATGTCCCACA 58.899 45.455 0.00 0.00 0.00 4.17
74 75 2.805657 GCCACTTACGTATCCATGTCCC 60.806 54.545 0.00 0.00 0.00 4.46
75 76 2.480845 GCCACTTACGTATCCATGTCC 58.519 52.381 0.00 0.00 0.00 4.02
93 97 3.939564 GGACATGGTTGGATGGCC 58.060 61.111 0.00 0.00 44.50 5.36
136 144 4.709397 AGTTCTTCACAAATGACCACCAAA 59.291 37.500 0.00 0.00 33.38 3.28
171 179 7.509141 TTCACAAGAGAAATATGCAAAGTCA 57.491 32.000 0.00 0.00 0.00 3.41
192 200 2.416747 CGACTTTGATGGTGAGCTTCA 58.583 47.619 0.00 0.00 0.00 3.02
200 208 0.620556 ATGGCTCCGACTTTGATGGT 59.379 50.000 0.00 0.00 0.00 3.55
247 257 2.415491 GGATCTTGACGTCGACACATGA 60.415 50.000 17.16 19.76 0.00 3.07
248 258 1.920574 GGATCTTGACGTCGACACATG 59.079 52.381 17.16 15.68 0.00 3.21
256 266 3.791887 CGAACTACATGGATCTTGACGTC 59.208 47.826 9.11 9.11 0.00 4.34
257 267 3.770666 CGAACTACATGGATCTTGACGT 58.229 45.455 0.00 0.00 0.00 4.34
258 268 2.535984 GCGAACTACATGGATCTTGACG 59.464 50.000 0.00 0.00 0.00 4.35
263 273 3.735237 ATTCGCGAACTACATGGATCT 57.265 42.857 26.00 0.00 0.00 2.75
279 289 2.418628 ACCATCAACAAACCGCTATTCG 59.581 45.455 0.00 0.00 38.08 3.34
285 295 0.387239 GAGCACCATCAACAAACCGC 60.387 55.000 0.00 0.00 0.00 5.68
288 298 2.159627 CCGTAGAGCACCATCAACAAAC 59.840 50.000 0.00 0.00 0.00 2.93
308 319 6.148811 TCGTCTCACTCCAAATTCAATTTACC 59.851 38.462 0.00 0.00 0.00 2.85
335 346 2.917971 GTCAAGAGTGCATACGAGTGTC 59.082 50.000 0.00 0.00 0.00 3.67
341 352 0.108804 ACCCGTCAAGAGTGCATACG 60.109 55.000 0.00 0.00 0.00 3.06
353 364 2.206750 CGAGAAGAAAAACACCCGTCA 58.793 47.619 0.00 0.00 0.00 4.35
373 384 0.808847 GAGAATGTCCCGGCGTTACC 60.809 60.000 6.01 0.00 0.00 2.85
380 391 1.000163 CTACCGATGAGAATGTCCCGG 60.000 57.143 0.00 0.00 42.76 5.73
389 400 0.824109 CAACCTGGCTACCGATGAGA 59.176 55.000 0.00 0.00 0.00 3.27
407 418 2.872408 GCATAGAGCACTTTGGCCA 58.128 52.632 0.00 0.00 44.79 5.36
418 429 2.862536 CGTCCACATTGACAGCATAGAG 59.137 50.000 0.00 0.00 34.88 2.43
443 454 2.886587 AATTAGCGAAAAACGGACCG 57.113 45.000 13.61 13.61 42.83 4.79
491 502 6.204882 GGCGGATGCTGTTTTATACTATTCTT 59.795 38.462 0.00 0.00 42.25 2.52
499 510 2.438021 AGAGGGCGGATGCTGTTTTATA 59.562 45.455 0.00 0.00 42.25 0.98
500 511 1.212935 AGAGGGCGGATGCTGTTTTAT 59.787 47.619 0.00 0.00 42.25 1.40
581 592 5.390145 GCGGTAAACATAGTGACAAACGAAT 60.390 40.000 0.00 0.00 0.00 3.34
589 600 3.060363 CAGTTCGCGGTAAACATAGTGAC 59.940 47.826 6.13 0.00 0.00 3.67
590 601 3.247442 CAGTTCGCGGTAAACATAGTGA 58.753 45.455 6.13 0.00 0.00 3.41
591 602 2.347452 CCAGTTCGCGGTAAACATAGTG 59.653 50.000 6.13 0.00 0.00 2.74
592 603 2.613691 CCAGTTCGCGGTAAACATAGT 58.386 47.619 6.13 0.00 0.00 2.12
593 604 1.931172 CCCAGTTCGCGGTAAACATAG 59.069 52.381 6.13 0.00 0.00 2.23
594 605 2.008045 GCCCAGTTCGCGGTAAACATA 61.008 52.381 6.13 0.00 0.00 2.29
595 606 1.303091 GCCCAGTTCGCGGTAAACAT 61.303 55.000 6.13 0.00 0.00 2.71
596 607 1.962306 GCCCAGTTCGCGGTAAACA 60.962 57.895 6.13 0.00 0.00 2.83
597 608 0.390209 TAGCCCAGTTCGCGGTAAAC 60.390 55.000 6.13 3.21 0.00 2.01
598 609 0.321021 TTAGCCCAGTTCGCGGTAAA 59.679 50.000 6.13 0.00 0.00 2.01
599 610 0.321021 TTTAGCCCAGTTCGCGGTAA 59.679 50.000 6.13 0.00 0.00 2.85
600 611 0.538118 ATTTAGCCCAGTTCGCGGTA 59.462 50.000 6.13 0.00 0.00 4.02
601 612 0.538118 TATTTAGCCCAGTTCGCGGT 59.462 50.000 6.13 0.00 0.00 5.68
602 613 0.935196 GTATTTAGCCCAGTTCGCGG 59.065 55.000 6.13 0.00 0.00 6.46
603 614 1.859080 GAGTATTTAGCCCAGTTCGCG 59.141 52.381 0.00 0.00 0.00 5.87
604 615 2.210961 GGAGTATTTAGCCCAGTTCGC 58.789 52.381 0.00 0.00 0.00 4.70
605 616 2.802057 CGGGAGTATTTAGCCCAGTTCG 60.802 54.545 0.00 0.00 42.14 3.95
686 697 9.925268 TCTTCTGTTTTTCGTAAACTATTGTTC 57.075 29.630 13.95 0.00 34.96 3.18
687 698 9.712359 GTCTTCTGTTTTTCGTAAACTATTGTT 57.288 29.630 13.95 0.00 38.16 2.83
698 709 8.402472 TCAAATGTATTGTCTTCTGTTTTTCGT 58.598 29.630 0.00 0.00 0.00 3.85
699 710 8.781067 TCAAATGTATTGTCTTCTGTTTTTCG 57.219 30.769 0.00 0.00 0.00 3.46
718 729 3.242739 CGCTCCCGGATACTTTTCAAATG 60.243 47.826 0.73 0.00 0.00 2.32
740 751 2.115291 GTTCCCTTCCAGATGGCGC 61.115 63.158 0.00 0.00 34.44 6.53
741 752 1.452108 GGTTCCCTTCCAGATGGCG 60.452 63.158 0.00 0.00 34.44 5.69
753 764 1.328279 CAAAGTCAAGGTGGGTTCCC 58.672 55.000 0.12 0.12 0.00 3.97
789 800 3.529734 TGGGGGCTTCCAATATTGACTTA 59.470 43.478 17.23 0.00 37.22 2.24
798 809 2.045745 AGGTTTTATGGGGGCTTCCAAT 59.954 45.455 4.42 0.00 40.62 3.16
884 895 3.084646 TCCCGTGTGTGTGTGGGT 61.085 61.111 0.00 0.00 42.54 4.51
936 951 1.355916 CCGCCGACTAGTACTGCTC 59.644 63.158 5.39 0.00 0.00 4.26
994 1009 0.171455 GCGAGTCGTCTCATCTTGGT 59.829 55.000 15.08 0.00 40.44 3.67
1163 1190 1.593006 CGGCCAAGCTCGTAGTAATTG 59.407 52.381 2.24 0.00 0.00 2.32
1170 1197 2.386064 AAACCACGGCCAAGCTCGTA 62.386 55.000 2.24 0.00 34.79 3.43
1171 1198 3.767630 AAACCACGGCCAAGCTCGT 62.768 57.895 2.24 0.00 36.32 4.18
1172 1199 2.966309 GAAACCACGGCCAAGCTCG 61.966 63.158 2.24 0.00 0.00 5.03
1195 1222 4.263572 TCGGCCACACAACCCCAG 62.264 66.667 2.24 0.00 0.00 4.45
1385 1412 4.030134 AGAGAAAGGACGTATACGCAAG 57.970 45.455 24.64 0.00 44.43 4.01
1386 1413 4.418392 GAAGAGAAAGGACGTATACGCAA 58.582 43.478 24.64 0.00 44.43 4.85
1388 1415 3.066481 AGGAAGAGAAAGGACGTATACGC 59.934 47.826 24.64 16.54 44.43 4.42
1389 1416 4.261114 GGAGGAAGAGAAAGGACGTATACG 60.261 50.000 23.24 23.24 46.33 3.06
1390 1417 4.643784 TGGAGGAAGAGAAAGGACGTATAC 59.356 45.833 0.00 0.00 0.00 1.47
1391 1418 4.863548 TGGAGGAAGAGAAAGGACGTATA 58.136 43.478 0.00 0.00 0.00 1.47
1392 1419 3.709587 TGGAGGAAGAGAAAGGACGTAT 58.290 45.455 0.00 0.00 0.00 3.06
1396 1423 4.559862 TTGATGGAGGAAGAGAAAGGAC 57.440 45.455 0.00 0.00 0.00 3.85
1425 1452 2.056223 CATTTCTGGGCTGGCCTGG 61.056 63.158 23.53 15.30 36.10 4.45
1440 1467 3.467374 ACAACAAACAATTCCGGCATT 57.533 38.095 0.00 0.00 0.00 3.56
1486 1513 1.614241 GCATCCCAGGACGTAGGTGT 61.614 60.000 0.00 0.00 0.00 4.16
1497 1524 2.809665 GCTGACAGATTAGGCATCCCAG 60.810 54.545 6.65 0.00 31.20 4.45
1662 1756 1.417517 ACTCTGCAAGTCCACATCACA 59.582 47.619 0.00 0.00 30.02 3.58
1742 1836 5.304101 ACATGTGGACTTTCAATGCCTAAAA 59.696 36.000 0.00 0.00 0.00 1.52
1751 1845 8.862325 AGATTTATGTACATGTGGACTTTCAA 57.138 30.769 18.81 0.00 0.00 2.69
1805 1899 4.443394 CAGCAAACAGAATTGAGAAACTGC 59.557 41.667 0.00 0.00 34.25 4.40
1846 1940 3.891049 AGATTTAAGACCCATGCCTGTC 58.109 45.455 0.00 0.00 0.00 3.51
1847 1941 4.322057 AAGATTTAAGACCCATGCCTGT 57.678 40.909 0.00 0.00 0.00 4.00
1848 1942 6.152661 TGTTAAAGATTTAAGACCCATGCCTG 59.847 38.462 0.00 0.00 33.66 4.85
1849 1943 6.252995 TGTTAAAGATTTAAGACCCATGCCT 58.747 36.000 0.00 0.00 33.66 4.75
1864 1959 6.291377 ACCGATAGACATGCATGTTAAAGAT 58.709 36.000 31.82 19.64 41.95 2.40
1866 1961 5.523552 TGACCGATAGACATGCATGTTAAAG 59.476 40.000 31.82 20.78 41.95 1.85
1879 1974 6.660094 ACTTATCCCTATTCTGACCGATAGAC 59.340 42.308 0.00 0.00 39.76 2.59
1973 2070 7.027778 AGAAACATACTGAAACACAAGAACC 57.972 36.000 0.00 0.00 0.00 3.62
2063 2160 8.801715 AGCAAAACTCTGTAATATTTTGTGTG 57.198 30.769 9.33 0.00 41.79 3.82
2075 2172 7.715249 GTGGGATGATATAAGCAAAACTCTGTA 59.285 37.037 0.00 0.00 0.00 2.74
2083 2180 7.293828 TGGTTATGTGGGATGATATAAGCAAA 58.706 34.615 0.00 0.00 39.26 3.68
2113 2215 1.002544 GGTACCTGCAGGGATATGCTC 59.997 57.143 35.42 14.97 46.63 4.26
2141 2243 3.618594 TGAATTGTCGTTAGAGCATGAGC 59.381 43.478 0.00 0.00 42.56 4.26
2143 2245 3.618594 GCTGAATTGTCGTTAGAGCATGA 59.381 43.478 0.00 0.00 0.00 3.07
2148 2250 2.280628 GGGGCTGAATTGTCGTTAGAG 58.719 52.381 0.00 0.00 0.00 2.43
2159 2261 2.035626 CCGGTGTTGGGGCTGAAT 59.964 61.111 0.00 0.00 0.00 2.57
2209 2311 2.738013 AAGGTGCAGTAGTTACGGTC 57.262 50.000 0.00 0.00 0.00 4.79
2219 2321 4.379174 CAGCGGTAAAGGTGCAGT 57.621 55.556 0.00 0.00 32.68 4.40
2223 2325 0.951558 AACAAGCAGCGGTAAAGGTG 59.048 50.000 0.00 0.00 42.04 4.00
2229 2331 2.843401 TAGGAAAACAAGCAGCGGTA 57.157 45.000 0.00 0.00 0.00 4.02
2230 2332 2.200373 ATAGGAAAACAAGCAGCGGT 57.800 45.000 0.00 0.00 0.00 5.68
2233 2335 5.768317 TGTACAAATAGGAAAACAAGCAGC 58.232 37.500 0.00 0.00 0.00 5.25
2236 2338 9.040939 ACAAAATGTACAAATAGGAAAACAAGC 57.959 29.630 0.00 0.00 0.00 4.01
2247 2349 8.140628 ACAACATGAGCACAAAATGTACAAATA 58.859 29.630 0.00 0.00 33.48 1.40
2492 2594 0.660488 TGCGTGGTTTTGCTGTACAG 59.340 50.000 18.93 18.93 0.00 2.74
2530 2632 3.938963 TCCGTAAGAACCTGAAATGATGC 59.061 43.478 0.00 0.00 43.02 3.91
2536 2638 1.337447 CCGCTCCGTAAGAACCTGAAA 60.337 52.381 0.00 0.00 43.02 2.69
2577 2679 5.256474 AGAATTGGAGTTTGTGGATGGTAG 58.744 41.667 0.00 0.00 0.00 3.18
2708 2810 4.266976 CGATGACAGTAAATTCACCCGTAC 59.733 45.833 0.00 0.00 0.00 3.67
2716 2818 2.919228 AGGGGCGATGACAGTAAATTC 58.081 47.619 0.00 0.00 0.00 2.17
2734 2836 5.389859 TCCTGCAAATGATGTAACAAAGG 57.610 39.130 0.00 0.00 0.00 3.11
2735 2837 6.750501 CAGATCCTGCAAATGATGTAACAAAG 59.249 38.462 0.00 0.00 0.00 2.77
2945 3048 6.140737 CGTAGAAGAATCAACAAGTGCAAAAC 59.859 38.462 0.00 0.00 0.00 2.43
2987 3093 9.959749 GACAGTTTATTCCATTTTCACACTAAA 57.040 29.630 0.00 0.00 0.00 1.85
2988 3094 9.349713 AGACAGTTTATTCCATTTTCACACTAA 57.650 29.630 0.00 0.00 0.00 2.24
3061 3167 1.859302 AAAGTTTCAGCCACCCAACA 58.141 45.000 0.00 0.00 0.00 3.33
3095 3201 4.631377 TGTCATTGAGGAAATCGACATCAC 59.369 41.667 0.00 0.00 34.35 3.06
3253 3454 4.340950 TCCTTCAAACATGAAACAAGGGTC 59.659 41.667 0.00 0.00 32.69 4.46
3326 3890 1.078656 AGGAAGCAGAGGAGAGGAAGT 59.921 52.381 0.00 0.00 0.00 3.01
3327 3891 1.864669 AGGAAGCAGAGGAGAGGAAG 58.135 55.000 0.00 0.00 0.00 3.46
3361 3933 2.236395 CTCTGATTCTACGGGGGTTGTT 59.764 50.000 0.00 0.00 0.00 2.83
3397 3969 5.894298 TGATGCAGGACCTAAATCTGTAT 57.106 39.130 13.92 0.00 36.74 2.29
3435 4007 0.958382 TGTTGAGGTAATGGCGTGCC 60.958 55.000 3.30 3.30 0.00 5.01
3446 4018 1.745827 CGGTCCAGTTTGTGTTGAGGT 60.746 52.381 0.00 0.00 0.00 3.85
3464 4036 2.098607 TCGCTATGGAGACTGTTTACGG 59.901 50.000 0.00 0.00 0.00 4.02
3484 4056 2.830370 CTGGGGGCTTCGGCATTC 60.830 66.667 0.00 0.00 43.96 2.67
3648 4270 8.531622 TTTTATAACACATTTGTTGCATGAGG 57.468 30.769 7.50 0.00 45.91 3.86
3768 4391 7.955750 TGGATGATTTCCTATCCAGTACAGATA 59.044 37.037 0.00 0.58 45.87 1.98


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

AutoCloner maintained by Alex Coulton.