Multiple sequence alignment - TraesCS3A01G324100

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 TraesCS3A01G324100 chr3A 100.000 3968 0 0 1 3968 568662653 568666620 0.000000e+00 7328.0
1 TraesCS3A01G324100 chr3A 100.000 195 0 0 4248 4442 568666900 568667094 1.170000e-95 361.0
2 TraesCS3A01G324100 chr3A 94.915 59 3 0 333 391 551699473 551699531 4.730000e-15 93.5
3 TraesCS3A01G324100 chr3A 89.552 67 6 1 324 389 610507724 610507790 2.850000e-12 84.2
4 TraesCS3A01G324100 chr3D 93.539 3343 129 35 338 3607 431287479 431284151 0.000000e+00 4896.0
5 TraesCS3A01G324100 chr3D 93.831 308 14 2 3664 3968 431284152 431283847 4.050000e-125 459.0
6 TraesCS3A01G324100 chr3D 93.728 287 14 1 1 287 431287866 431287584 1.140000e-115 427.0
7 TraesCS3A01G324100 chr3D 94.949 198 5 1 4250 4442 431283354 431283157 5.580000e-79 305.0
8 TraesCS3A01G324100 chr3B 93.837 3229 125 33 434 3607 563392733 563395942 0.000000e+00 4793.0
9 TraesCS3A01G324100 chr3B 94.118 306 12 4 3664 3965 563395941 563396244 1.130000e-125 460.0
10 TraesCS3A01G324100 chr3B 92.683 82 6 0 4361 4442 824015624 824015705 7.810000e-23 119.0
11 TraesCS3A01G324100 chr6D 92.683 82 6 0 4361 4442 46933701 46933620 7.810000e-23 119.0
12 TraesCS3A01G324100 chr6D 89.231 65 7 0 324 388 444330896 444330960 1.020000e-11 82.4
13 TraesCS3A01G324100 chr6A 92.593 81 6 0 4361 4441 609802672 609802752 2.810000e-22 117.0
14 TraesCS3A01G324100 chr6A 89.394 66 7 0 324 389 120131462 120131527 2.850000e-12 84.2
15 TraesCS3A01G324100 chr6A 90.323 62 6 0 333 394 577699190 577699129 1.020000e-11 82.4
16 TraesCS3A01G324100 chrUn 78.191 188 32 8 2872 3055 18059527 18059709 1.310000e-20 111.0
17 TraesCS3A01G324100 chr6B 91.250 80 7 0 4363 4442 20240511 20240432 4.700000e-20 110.0
18 TraesCS3A01G324100 chr6B 96.364 55 2 0 3615 3669 615991111 615991057 1.700000e-14 91.6
19 TraesCS3A01G324100 chr2D 98.148 54 1 0 3616 3669 80797480 80797427 1.320000e-15 95.3
20 TraesCS3A01G324100 chr5D 98.113 53 1 0 3619 3671 419469330 419469278 4.730000e-15 93.5
21 TraesCS3A01G324100 chr5D 96.364 55 1 1 3619 3672 314422036 314421982 6.120000e-14 89.8
22 TraesCS3A01G324100 chr5D 86.585 82 7 3 307 388 54934525 54934602 2.200000e-13 87.9
23 TraesCS3A01G324100 chr2B 96.364 55 2 0 3616 3670 497861477 497861531 1.700000e-14 91.6
24 TraesCS3A01G324100 chr2B 92.982 57 2 2 3615 3669 769078117 769078173 1.020000e-11 82.4
25 TraesCS3A01G324100 chr2A 96.364 55 2 0 3616 3670 703708312 703708258 1.700000e-14 91.6
26 TraesCS3A01G324100 chr4D 100.000 48 0 0 3619 3666 464203845 464203892 6.120000e-14 89.8
27 TraesCS3A01G324100 chr4A 94.737 57 2 1 3616 3672 676876911 676876856 2.200000e-13 87.9
28 TraesCS3A01G324100 chr1D 93.220 59 4 0 333 391 371188930 371188872 2.200000e-13 87.9
29 TraesCS3A01G324100 chr5B 85.897 78 11 0 4363 4440 391865661 391865738 2.850000e-12 84.2
30 TraesCS3A01G324100 chr5A 90.323 62 6 0 333 394 11038623 11038562 1.020000e-11 82.4


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 TraesCS3A01G324100 chr3A 568662653 568667094 4441 False 3844.50 7328 100.00000 1 4442 2 chr3A.!!$F3 4441
1 TraesCS3A01G324100 chr3D 431283157 431287866 4709 True 1521.75 4896 94.01175 1 4442 4 chr3D.!!$R1 4441
2 TraesCS3A01G324100 chr3B 563392733 563396244 3511 False 2626.50 4793 93.97750 434 3965 2 chr3B.!!$F2 3531

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
69 70 0.611062 GGGTAAAGGAGGGTTGTGCC 60.611 60.0 0.0 0.0 0.00 5.01 F
1113 1219 0.964700 TCCAGCAGAGAGTCACACAG 59.035 55.0 0.0 0.0 0.00 3.66 F
2212 2344 0.177836 CCATGTCGCAGTACATCCCA 59.822 55.0 0.0 0.0 38.01 4.37 F
2437 2569 0.738975 TAGTCGATGTGAAGCTCGGG 59.261 55.0 0.0 0.0 35.64 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1399 1505 0.318360 CGTTGGCGATGCGGAGTATA 60.318 55.000 0.0 0.0 41.33 1.47 R
2611 2756 0.116342 TGAACCCTGCTACCCTCAGA 59.884 55.000 0.0 0.0 33.54 3.27 R
3222 3374 1.689233 TCATCCTCCTCCAACCCGG 60.689 63.158 0.0 0.0 0.00 5.73 R
4248 4408 2.167900 CGATAAGGTTCTCGAAGGGGTT 59.832 50.000 0.0 0.0 37.05 4.11 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
23 24 3.804153 ATCGCTGCCAGATGAGCCG 62.804 63.158 0.00 0.00 30.98 5.52
66 67 1.423921 CAGTGGGTAAAGGAGGGTTGT 59.576 52.381 0.00 0.00 0.00 3.32
69 70 0.611062 GGGTAAAGGAGGGTTGTGCC 60.611 60.000 0.00 0.00 0.00 5.01
105 106 3.640000 GGATCGCGACAATGCCCG 61.640 66.667 12.93 0.00 0.00 6.13
123 124 3.643978 GTGCATCGCGCCAGATCC 61.644 66.667 0.00 0.00 41.33 3.36
234 235 4.690184 CGCATGCATGTGGATATACATT 57.310 40.909 28.76 0.00 39.17 2.71
235 236 5.799681 CGCATGCATGTGGATATACATTA 57.200 39.130 28.76 0.00 39.17 1.90
257 258 7.718334 TTATCCAAATCTATATGCTCCGAGA 57.282 36.000 0.00 0.00 0.00 4.04
287 288 7.052248 TGTAGAATTGTACTAGTCAGATCGGA 58.948 38.462 13.36 0.00 0.00 4.55
288 289 6.627395 AGAATTGTACTAGTCAGATCGGAG 57.373 41.667 0.00 0.00 0.00 4.63
289 290 5.533154 AGAATTGTACTAGTCAGATCGGAGG 59.467 44.000 0.00 0.00 0.00 4.30
290 291 3.210232 TGTACTAGTCAGATCGGAGGG 57.790 52.381 0.00 0.00 0.00 4.30
291 292 2.775960 TGTACTAGTCAGATCGGAGGGA 59.224 50.000 0.00 0.00 0.00 4.20
292 293 3.201487 TGTACTAGTCAGATCGGAGGGAA 59.799 47.826 0.00 0.00 0.00 3.97
293 294 3.603965 ACTAGTCAGATCGGAGGGAAT 57.396 47.619 0.00 0.00 0.00 3.01
294 295 4.726035 ACTAGTCAGATCGGAGGGAATA 57.274 45.455 0.00 0.00 0.00 1.75
295 296 4.400120 ACTAGTCAGATCGGAGGGAATAC 58.600 47.826 0.00 0.00 0.00 1.89
296 297 3.603965 AGTCAGATCGGAGGGAATACT 57.396 47.619 0.00 0.00 0.00 2.12
297 298 3.917300 AGTCAGATCGGAGGGAATACTT 58.083 45.455 0.00 0.00 0.00 2.24
298 299 3.639094 AGTCAGATCGGAGGGAATACTTG 59.361 47.826 0.00 0.00 0.00 3.16
299 300 2.365617 TCAGATCGGAGGGAATACTTGC 59.634 50.000 0.00 0.00 0.00 4.01
300 301 2.366916 CAGATCGGAGGGAATACTTGCT 59.633 50.000 0.00 0.00 0.00 3.91
301 302 3.041946 AGATCGGAGGGAATACTTGCTT 58.958 45.455 0.00 0.00 0.00 3.91
302 303 2.981859 TCGGAGGGAATACTTGCTTC 57.018 50.000 0.00 0.00 0.00 3.86
303 304 2.184533 TCGGAGGGAATACTTGCTTCA 58.815 47.619 0.00 0.00 0.00 3.02
344 407 9.688091 TCTTTTCTAGACAGATCTGTATGTAGT 57.312 33.333 28.85 12.66 45.05 2.73
426 492 6.500589 AGCTATCCTCAACTAATTAAGGCA 57.499 37.500 0.00 0.00 0.00 4.75
427 493 7.084268 AGCTATCCTCAACTAATTAAGGCAT 57.916 36.000 0.00 0.00 0.00 4.40
428 494 6.939163 AGCTATCCTCAACTAATTAAGGCATG 59.061 38.462 0.00 0.00 0.00 4.06
429 495 6.348868 GCTATCCTCAACTAATTAAGGCATGC 60.349 42.308 9.90 9.90 0.00 4.06
585 653 6.310956 CCATATGGCCATTTTATACATTTGCG 59.689 38.462 26.37 0.00 0.00 4.85
587 655 2.799978 GGCCATTTTATACATTTGCGCC 59.200 45.455 4.18 0.00 0.00 6.53
627 695 7.173907 CGAGAATGGCCTAAAAATCATGATAGT 59.826 37.037 9.04 0.00 0.00 2.12
628 696 9.507329 GAGAATGGCCTAAAAATCATGATAGTA 57.493 33.333 9.04 1.02 0.00 1.82
629 697 9.512588 AGAATGGCCTAAAAATCATGATAGTAG 57.487 33.333 9.04 10.28 0.00 2.57
728 796 3.903783 GCAAGCGGACTGGCATTA 58.096 55.556 0.00 0.00 43.01 1.90
779 848 6.597280 GTCTAGAAATTTGGTCTCTGCAAGAT 59.403 38.462 0.00 0.00 45.62 2.40
822 896 5.532779 AGACCTGGCTAAAAGAAGACAAAAG 59.467 40.000 0.00 0.00 32.94 2.27
854 929 1.270358 GCTAGAGGCTTTACGGATGGG 60.270 57.143 0.00 0.00 38.06 4.00
910 988 5.384063 AATGTCACGCAAATGGTCATTAA 57.616 34.783 0.00 0.00 0.00 1.40
911 989 5.581126 ATGTCACGCAAATGGTCATTAAT 57.419 34.783 0.00 0.00 0.00 1.40
912 990 4.731720 TGTCACGCAAATGGTCATTAATG 58.268 39.130 9.29 9.29 0.00 1.90
1026 1132 1.214589 CCCGTCCCACTCGTACTTG 59.785 63.158 0.00 0.00 0.00 3.16
1058 1164 2.821991 ACCAGCGAGCTGATATTACC 57.178 50.000 24.93 0.00 46.30 2.85
1113 1219 0.964700 TCCAGCAGAGAGTCACACAG 59.035 55.000 0.00 0.00 0.00 3.66
1253 1359 4.335647 CCGGGAAGGTGCAGCAGT 62.336 66.667 19.63 5.10 34.51 4.40
1309 1415 2.842256 CGAGTACCTGCGCCGGTAT 61.842 63.158 29.81 19.56 41.31 2.73
1399 1505 1.760086 CGAGGACCTCCAGCCTGAT 60.760 63.158 16.13 0.00 38.89 2.90
1509 1617 1.066929 TGTACTCATGTGCATGCTCGT 60.067 47.619 20.33 14.23 38.65 4.18
1524 1632 1.541015 GCTCGTGGACATGCATGGATA 60.541 52.381 29.41 12.65 0.00 2.59
1540 1672 6.974932 CATGGATATCTATGCGCTAACTTT 57.025 37.500 15.20 0.00 0.00 2.66
1541 1673 6.769076 CATGGATATCTATGCGCTAACTTTG 58.231 40.000 15.20 0.00 0.00 2.77
1546 1678 1.927174 CTATGCGCTAACTTTGCTCGT 59.073 47.619 9.73 0.00 0.00 4.18
1639 1771 3.386237 GAGCTGGACAGGCGGTCT 61.386 66.667 17.11 0.00 46.16 3.85
1723 1855 1.828832 CGATGTACCTGCTCTTCGTC 58.171 55.000 0.00 0.00 0.00 4.20
1990 2122 2.507992 CTCGAGAAGCACTGGCCG 60.508 66.667 6.58 0.00 42.56 6.13
2076 2208 4.796231 CGTCGGGAGGTTGCTCCG 62.796 72.222 0.00 0.00 44.23 4.63
2212 2344 0.177836 CCATGTCGCAGTACATCCCA 59.822 55.000 0.00 0.00 38.01 4.37
2392 2524 3.737172 AGCAACGCCAATGCCGAC 61.737 61.111 0.00 0.00 44.91 4.79
2437 2569 0.738975 TAGTCGATGTGAAGCTCGGG 59.261 55.000 0.00 0.00 35.64 5.14
2558 2701 4.886579 CCTTTTTAGCAAGGCTGACATTT 58.113 39.130 0.07 0.00 40.10 2.32
2611 2756 1.444895 GTATCGTGTGGGCGACGTT 60.445 57.895 0.00 0.00 43.99 3.99
2794 2939 1.515736 GTACACCAGCTACGCCGAC 60.516 63.158 0.00 0.00 0.00 4.79
2798 2943 2.184322 CCAGCTACGCCGACACAT 59.816 61.111 0.00 0.00 0.00 3.21
3124 3269 4.659172 TTCAGCCCCAAGTGCCCG 62.659 66.667 0.00 0.00 0.00 6.13
3294 3446 4.923516 ACTGTAGGGGCTACGATATCTA 57.076 45.455 0.34 0.00 39.58 1.98
3409 3561 0.180406 TCTTCTCTATTTGGGCCGCC 59.820 55.000 0.00 0.00 0.00 6.13
3503 3655 6.489603 AGTTTATCCCAATGTTGTATGGACA 58.510 36.000 0.00 0.00 39.12 4.02
3513 3665 5.854010 TGTTGTATGGACATCTAGTCTCC 57.146 43.478 0.00 0.00 46.72 3.71
3530 3682 0.620556 TCCATGGGAAAGGACTCAGC 59.379 55.000 13.02 0.00 0.00 4.26
3611 3768 7.096884 ACTCAAAAGAAAAACTGTTACTCCC 57.903 36.000 0.00 0.00 0.00 4.30
3612 3769 6.890268 ACTCAAAAGAAAAACTGTTACTCCCT 59.110 34.615 0.00 0.00 0.00 4.20
3613 3770 7.067129 ACTCAAAAGAAAAACTGTTACTCCCTC 59.933 37.037 0.00 0.00 0.00 4.30
3614 3771 7.116736 TCAAAAGAAAAACTGTTACTCCCTCT 58.883 34.615 0.00 0.00 0.00 3.69
3615 3772 6.944234 AAAGAAAAACTGTTACTCCCTCTG 57.056 37.500 0.00 0.00 0.00 3.35
3616 3773 5.632034 AGAAAAACTGTTACTCCCTCTGT 57.368 39.130 0.00 0.00 0.00 3.41
3617 3774 6.002653 AGAAAAACTGTTACTCCCTCTGTT 57.997 37.500 0.00 0.00 0.00 3.16
3618 3775 6.056236 AGAAAAACTGTTACTCCCTCTGTTC 58.944 40.000 0.00 0.00 0.00 3.18
3619 3776 5.367945 AAAACTGTTACTCCCTCTGTTCA 57.632 39.130 0.00 0.00 0.00 3.18
3620 3777 5.568620 AAACTGTTACTCCCTCTGTTCAT 57.431 39.130 0.00 0.00 0.00 2.57
3621 3778 6.681729 AAACTGTTACTCCCTCTGTTCATA 57.318 37.500 0.00 0.00 0.00 2.15
3622 3779 6.875972 AACTGTTACTCCCTCTGTTCATAT 57.124 37.500 0.00 0.00 0.00 1.78
3623 3780 6.875972 ACTGTTACTCCCTCTGTTCATATT 57.124 37.500 0.00 0.00 0.00 1.28
3624 3781 6.644347 ACTGTTACTCCCTCTGTTCATATTG 58.356 40.000 0.00 0.00 0.00 1.90
3625 3782 5.989477 TGTTACTCCCTCTGTTCATATTGG 58.011 41.667 0.00 0.00 0.00 3.16
3626 3783 5.724370 TGTTACTCCCTCTGTTCATATTGGA 59.276 40.000 0.00 0.00 0.00 3.53
3627 3784 6.214615 TGTTACTCCCTCTGTTCATATTGGAA 59.785 38.462 0.00 0.00 0.00 3.53
3628 3785 5.983333 ACTCCCTCTGTTCATATTGGAAT 57.017 39.130 0.00 0.00 0.00 3.01
3629 3786 5.934781 ACTCCCTCTGTTCATATTGGAATC 58.065 41.667 0.00 0.00 0.00 2.52
3630 3787 5.669447 ACTCCCTCTGTTCATATTGGAATCT 59.331 40.000 0.00 0.00 0.00 2.40
3631 3788 6.179906 TCCCTCTGTTCATATTGGAATCTC 57.820 41.667 0.00 0.00 0.00 2.75
3632 3789 5.907662 TCCCTCTGTTCATATTGGAATCTCT 59.092 40.000 0.00 0.00 0.00 3.10
3633 3790 7.075797 TCCCTCTGTTCATATTGGAATCTCTA 58.924 38.462 0.00 0.00 0.00 2.43
3634 3791 7.568738 TCCCTCTGTTCATATTGGAATCTCTAA 59.431 37.037 0.00 0.00 0.00 2.10
3635 3792 8.213679 CCCTCTGTTCATATTGGAATCTCTAAA 58.786 37.037 0.00 0.00 0.00 1.85
3636 3793 9.618890 CCTCTGTTCATATTGGAATCTCTAAAA 57.381 33.333 0.00 0.00 0.00 1.52
3660 3817 8.959705 AAAGACTTATATTTAGAAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
3661 3818 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
3662 3819 7.953752 AGACTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
3744 3904 6.825610 AGACCACAAAATTTAATGCCTTCAA 58.174 32.000 0.00 0.00 0.00 2.69
3872 4032 5.786311 ACATACGGAGCAAACTAGTACAAA 58.214 37.500 0.00 0.00 0.00 2.83
3943 4103 5.029807 TGGACGCCAATATCAATCTAACA 57.970 39.130 0.00 0.00 0.00 2.41
3965 4125 4.722700 CCCTGTTGCGTCCCCCAG 62.723 72.222 0.00 0.00 0.00 4.45
4271 4642 1.136305 CCCTTCGAGAACCTTATCGCA 59.864 52.381 0.00 0.00 41.28 5.10
4274 4645 3.682858 CCTTCGAGAACCTTATCGCAAAA 59.317 43.478 0.00 0.00 41.28 2.44
4276 4647 3.921677 TCGAGAACCTTATCGCAAAACT 58.078 40.909 0.00 0.00 41.28 2.66
4277 4648 3.924686 TCGAGAACCTTATCGCAAAACTC 59.075 43.478 0.00 0.00 41.28 3.01
4278 4649 3.062234 CGAGAACCTTATCGCAAAACTCC 59.938 47.826 0.00 0.00 35.03 3.85
4281 4652 3.134574 ACCTTATCGCAAAACTCCACA 57.865 42.857 0.00 0.00 0.00 4.17
4282 4653 3.482436 ACCTTATCGCAAAACTCCACAA 58.518 40.909 0.00 0.00 0.00 3.33
4405 4781 6.662414 TTTGCTTTCTTATCGGTGTCATAG 57.338 37.500 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.785258 GACGAATGTCGCCAAGGC 59.215 61.111 0.00 0.00 45.12 4.35
66 67 2.359850 GGATGGTTGTGCGAGGCA 60.360 61.111 0.00 0.00 35.60 4.75
69 70 0.452987 CCATTGGATGGTTGTGCGAG 59.547 55.000 0.00 0.00 45.54 5.03
123 124 0.809241 GAGGCTTGCCTCATCAGACG 60.809 60.000 30.25 0.00 36.86 4.18
131 132 0.108138 TTCTTAGCGAGGCTTGCCTC 60.108 55.000 26.80 26.80 40.44 4.70
232 233 8.200792 GTCTCGGAGCATATAGATTTGGATAAT 58.799 37.037 0.00 0.00 0.00 1.28
233 234 7.178451 TGTCTCGGAGCATATAGATTTGGATAA 59.822 37.037 0.00 0.00 0.00 1.75
234 235 6.663523 TGTCTCGGAGCATATAGATTTGGATA 59.336 38.462 0.00 0.00 0.00 2.59
235 236 5.481824 TGTCTCGGAGCATATAGATTTGGAT 59.518 40.000 0.00 0.00 0.00 3.41
242 243 5.791336 ACAATTGTCTCGGAGCATATAGA 57.209 39.130 4.92 0.00 0.00 1.98
275 276 4.726035 AGTATTCCCTCCGATCTGACTA 57.274 45.455 0.00 0.00 0.00 2.59
277 278 3.800604 GCAAGTATTCCCTCCGATCTGAC 60.801 52.174 0.00 0.00 0.00 3.51
280 281 2.683768 AGCAAGTATTCCCTCCGATCT 58.316 47.619 0.00 0.00 0.00 2.75
287 288 8.829373 ATTTAGAAATGAAGCAAGTATTCCCT 57.171 30.769 0.00 0.00 0.00 4.20
368 431 8.974060 ATGCTTCCTCCGTTTCTAAATATAAA 57.026 30.769 0.00 0.00 0.00 1.40
379 442 6.177610 TCAAAGTATAATGCTTCCTCCGTTT 58.822 36.000 0.00 0.00 0.00 3.60
382 445 4.212214 GCTCAAAGTATAATGCTTCCTCCG 59.788 45.833 0.00 0.00 0.00 4.63
385 448 7.017056 AGGATAGCTCAAAGTATAATGCTTCCT 59.983 37.037 0.00 0.00 35.45 3.36
387 450 7.875041 TGAGGATAGCTCAAAGTATAATGCTTC 59.125 37.037 0.00 0.00 32.72 3.86
388 451 7.739825 TGAGGATAGCTCAAAGTATAATGCTT 58.260 34.615 0.00 0.00 32.72 3.91
389 452 7.308450 TGAGGATAGCTCAAAGTATAATGCT 57.692 36.000 0.00 0.00 34.92 3.79
390 453 7.659390 AGTTGAGGATAGCTCAAAGTATAATGC 59.341 37.037 0.00 0.00 41.70 3.56
423 489 1.383456 TATTTCCGTGCCTGCATGCC 61.383 55.000 16.68 0.00 0.00 4.40
425 491 2.801063 CTTTATTTCCGTGCCTGCATG 58.199 47.619 4.34 4.34 0.00 4.06
426 492 1.134946 GCTTTATTTCCGTGCCTGCAT 59.865 47.619 0.00 0.00 0.00 3.96
427 493 0.525761 GCTTTATTTCCGTGCCTGCA 59.474 50.000 0.00 0.00 0.00 4.41
428 494 0.525761 TGCTTTATTTCCGTGCCTGC 59.474 50.000 0.00 0.00 0.00 4.85
429 495 2.083774 TCTGCTTTATTTCCGTGCCTG 58.916 47.619 0.00 0.00 0.00 4.85
585 653 2.826428 TCTCGTGCTCAAATCATAGGC 58.174 47.619 0.00 0.00 0.00 3.93
587 655 4.319333 GCCATTCTCGTGCTCAAATCATAG 60.319 45.833 0.00 0.00 0.00 2.23
627 695 8.783660 ATCCTAACATGTCCTACAATCTTCTA 57.216 34.615 0.00 0.00 0.00 2.10
628 696 7.682787 ATCCTAACATGTCCTACAATCTTCT 57.317 36.000 0.00 0.00 0.00 2.85
685 753 1.368641 TCTTGGTGCACGTATGATGC 58.631 50.000 11.45 0.00 43.68 3.91
728 796 1.353022 TGTAGCTGGACCCGGAAAATT 59.647 47.619 0.73 0.00 0.00 1.82
753 822 4.579869 TGCAGAGACCAAATTTCTAGACC 58.420 43.478 0.00 0.00 0.00 3.85
779 848 7.013846 CCAGGTCTGACATTTGTTTTTAACCTA 59.986 37.037 10.38 0.00 32.36 3.08
836 911 2.170012 ACCCATCCGTAAAGCCTCTA 57.830 50.000 0.00 0.00 0.00 2.43
891 969 4.980590 TCATTAATGACCATTTGCGTGAC 58.019 39.130 14.23 0.00 32.50 3.67
1026 1132 1.279840 GCTGGTTTGTGTGAGCGAC 59.720 57.895 0.00 0.00 0.00 5.19
1058 1164 2.100631 GGTTCGTCAGGATGCCGTG 61.101 63.158 0.00 0.00 34.76 4.94
1399 1505 0.318360 CGTTGGCGATGCGGAGTATA 60.318 55.000 0.00 0.00 41.33 1.47
1504 1612 0.816825 ATCCATGCATGTCCACGAGC 60.817 55.000 24.58 0.00 0.00 5.03
1509 1617 4.520179 GCATAGATATCCATGCATGTCCA 58.480 43.478 25.35 9.14 45.51 4.02
1524 1632 2.797156 CGAGCAAAGTTAGCGCATAGAT 59.203 45.455 11.47 0.00 37.01 1.98
1541 1673 1.851658 AAACAAACCATTGCACGAGC 58.148 45.000 0.00 0.00 40.34 5.03
1546 1678 5.986135 GGTACACATAAAACAAACCATTGCA 59.014 36.000 0.00 0.00 40.34 4.08
1595 1727 2.892425 GGTCGGCATGAGCTTCCG 60.892 66.667 0.00 10.21 41.93 4.30
1828 1960 1.153823 CTCGTTGGGGCTCGTGTAG 60.154 63.158 0.00 0.00 0.00 2.74
2158 2290 0.455464 CGTCGATGTACTTGGTGCGA 60.455 55.000 0.00 0.00 0.00 5.10
2212 2344 1.888736 GCCGTAGAACTCGAGGGTT 59.111 57.895 18.41 3.18 0.00 4.11
2317 2449 0.733729 GGATGAGAGTGTACGCGACT 59.266 55.000 15.93 5.69 0.00 4.18
2329 2461 1.609239 GCACATGGTGGGGATGAGA 59.391 57.895 0.00 0.00 33.64 3.27
2552 2695 7.325660 AGATCACATACACATGGAAAATGTC 57.674 36.000 0.00 0.00 36.39 3.06
2611 2756 0.116342 TGAACCCTGCTACCCTCAGA 59.884 55.000 0.00 0.00 33.54 3.27
2794 2939 2.203252 CCTGGGATGGCGGATGTG 60.203 66.667 0.00 0.00 0.00 3.21
3124 3269 1.753078 GTTCCCGGGGCTCCATTTC 60.753 63.158 23.50 0.00 0.00 2.17
3213 3365 4.431131 CCAACCCGGCCATGAGCT 62.431 66.667 2.24 0.00 43.05 4.09
3214 3366 4.424711 TCCAACCCGGCCATGAGC 62.425 66.667 2.24 0.00 42.60 4.26
3215 3367 2.124570 CTCCAACCCGGCCATGAG 60.125 66.667 2.24 0.00 33.14 2.90
3216 3368 3.727258 CCTCCAACCCGGCCATGA 61.727 66.667 2.24 0.00 33.14 3.07
3217 3369 3.704231 CTCCTCCAACCCGGCCATG 62.704 68.421 2.24 0.00 33.14 3.66
3218 3370 3.411517 CTCCTCCAACCCGGCCAT 61.412 66.667 2.24 0.00 33.14 4.40
3221 3373 3.090532 ATCCTCCTCCAACCCGGC 61.091 66.667 0.00 0.00 33.14 6.13
3222 3374 1.689233 TCATCCTCCTCCAACCCGG 60.689 63.158 0.00 0.00 0.00 5.73
3294 3446 4.288626 TGCCCCAGAAGTTGAAATAGTACT 59.711 41.667 0.00 0.00 0.00 2.73
3349 3501 4.140536 ACATACGTAGGAACCCTAGCTAC 58.859 47.826 15.09 0.00 36.71 3.58
3503 3655 3.970640 GTCCTTTCCCATGGAGACTAGAT 59.029 47.826 15.22 0.00 31.21 1.98
3513 3665 3.390639 AGATAGCTGAGTCCTTTCCCATG 59.609 47.826 0.00 0.00 0.00 3.66
3530 3682 6.204301 AGCTTTAGCATGCATTGTGTAGATAG 59.796 38.462 21.98 2.88 45.16 2.08
3592 3749 6.424032 ACAGAGGGAGTAACAGTTTTTCTTT 58.576 36.000 0.00 0.00 0.00 2.52
3605 3762 6.846505 AGATTCCAATATGAACAGAGGGAGTA 59.153 38.462 0.00 0.00 0.00 2.59
3606 3763 5.669447 AGATTCCAATATGAACAGAGGGAGT 59.331 40.000 0.00 0.00 0.00 3.85
3607 3764 6.043012 AGAGATTCCAATATGAACAGAGGGAG 59.957 42.308 0.00 0.00 0.00 4.30
3608 3765 5.907662 AGAGATTCCAATATGAACAGAGGGA 59.092 40.000 0.00 0.00 0.00 4.20
3609 3766 6.185114 AGAGATTCCAATATGAACAGAGGG 57.815 41.667 0.00 0.00 0.00 4.30
3610 3767 9.618890 TTTTAGAGATTCCAATATGAACAGAGG 57.381 33.333 0.00 0.00 0.00 3.69
3634 3791 9.392259 CCCTCCGTTTCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
3635 3792 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
3636 3793 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
3637 3794 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
3638 3795 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
3639 3796 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
3640 3797 9.075678 TCTACTCCCTCCGTTTCTAAATATAAG 57.924 37.037 0.00 0.00 0.00 1.73
3641 3798 9.597681 ATCTACTCCCTCCGTTTCTAAATATAA 57.402 33.333 0.00 0.00 0.00 0.98
3642 3799 9.597681 AATCTACTCCCTCCGTTTCTAAATATA 57.402 33.333 0.00 0.00 0.00 0.86
3643 3800 8.493787 AATCTACTCCCTCCGTTTCTAAATAT 57.506 34.615 0.00 0.00 0.00 1.28
3644 3801 7.909485 AATCTACTCCCTCCGTTTCTAAATA 57.091 36.000 0.00 0.00 0.00 1.40
3645 3802 6.809976 AATCTACTCCCTCCGTTTCTAAAT 57.190 37.500 0.00 0.00 0.00 1.40
3646 3803 7.909485 ATAATCTACTCCCTCCGTTTCTAAA 57.091 36.000 0.00 0.00 0.00 1.85
3647 3804 7.562454 TGAATAATCTACTCCCTCCGTTTCTAA 59.438 37.037 0.00 0.00 0.00 2.10
3648 3805 7.064866 TGAATAATCTACTCCCTCCGTTTCTA 58.935 38.462 0.00 0.00 0.00 2.10
3649 3806 5.897824 TGAATAATCTACTCCCTCCGTTTCT 59.102 40.000 0.00 0.00 0.00 2.52
3650 3807 6.158023 TGAATAATCTACTCCCTCCGTTTC 57.842 41.667 0.00 0.00 0.00 2.78
3651 3808 5.070580 CCTGAATAATCTACTCCCTCCGTTT 59.929 44.000 0.00 0.00 0.00 3.60
3652 3809 4.589374 CCTGAATAATCTACTCCCTCCGTT 59.411 45.833 0.00 0.00 0.00 4.44
3653 3810 4.140994 TCCTGAATAATCTACTCCCTCCGT 60.141 45.833 0.00 0.00 0.00 4.69
3654 3811 4.218852 GTCCTGAATAATCTACTCCCTCCG 59.781 50.000 0.00 0.00 0.00 4.63
3655 3812 5.011227 GTGTCCTGAATAATCTACTCCCTCC 59.989 48.000 0.00 0.00 0.00 4.30
3656 3813 5.598830 TGTGTCCTGAATAATCTACTCCCTC 59.401 44.000 0.00 0.00 0.00 4.30
3657 3814 5.529289 TGTGTCCTGAATAATCTACTCCCT 58.471 41.667 0.00 0.00 0.00 4.20
3658 3815 5.221541 CCTGTGTCCTGAATAATCTACTCCC 60.222 48.000 0.00 0.00 0.00 4.30
3659 3816 5.598830 TCCTGTGTCCTGAATAATCTACTCC 59.401 44.000 0.00 0.00 0.00 3.85
3660 3817 6.716934 TCCTGTGTCCTGAATAATCTACTC 57.283 41.667 0.00 0.00 0.00 2.59
3661 3818 6.841229 TGATCCTGTGTCCTGAATAATCTACT 59.159 38.462 0.00 0.00 0.00 2.57
3662 3819 6.926272 GTGATCCTGTGTCCTGAATAATCTAC 59.074 42.308 0.00 0.00 0.00 2.59
3723 3883 8.097078 TGAATTGAAGGCATTAAATTTTGTGG 57.903 30.769 7.82 0.00 30.76 4.17
3769 3929 7.823310 GGTTCTGATATGATAGATGCAGACAAT 59.177 37.037 0.00 0.00 32.69 2.71
3872 4032 5.716703 CCATCTCCAACCCAAAGAGTAAAAT 59.283 40.000 0.00 0.00 0.00 1.82
4247 4407 3.737355 CGATAAGGTTCTCGAAGGGGTTC 60.737 52.174 0.00 0.00 37.05 3.62
4248 4408 2.167900 CGATAAGGTTCTCGAAGGGGTT 59.832 50.000 0.00 0.00 37.05 4.11
4257 4628 4.000988 TGGAGTTTTGCGATAAGGTTCTC 58.999 43.478 0.00 0.00 0.00 2.87
4271 4642 6.072673 CGTTCTAATTAGGCTTGTGGAGTTTT 60.073 38.462 12.54 0.00 0.00 2.43
4274 4645 4.504858 CGTTCTAATTAGGCTTGTGGAGT 58.495 43.478 12.54 0.00 0.00 3.85
4276 4647 3.267483 GCGTTCTAATTAGGCTTGTGGA 58.733 45.455 12.54 0.00 0.00 4.02
4277 4648 2.354821 GGCGTTCTAATTAGGCTTGTGG 59.645 50.000 12.54 0.00 0.00 4.17
4278 4649 3.063997 CAGGCGTTCTAATTAGGCTTGTG 59.936 47.826 12.54 4.64 37.40 3.33
4281 4652 3.270877 CACAGGCGTTCTAATTAGGCTT 58.729 45.455 12.54 2.17 37.40 4.35
4282 4653 2.236395 ACACAGGCGTTCTAATTAGGCT 59.764 45.455 12.54 2.85 40.22 4.58
4311 4687 2.621338 TCCTTTTGTCGCTCATGCTAG 58.379 47.619 0.00 0.00 36.97 3.42
4405 4781 5.119694 GGGAATCTTGACTTAGACATGTCC 58.880 45.833 22.21 7.15 32.67 4.02


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

AutoCloner maintained by Alex Coulton.