Multiple sequence alignment - TraesCS3D01G194500

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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 TraesCS3D01G194500 chr3D 100.000 4678 0 0 1 4678 185789126 185793803 0.000000e+00 8639.0
1 TraesCS3D01G194500 chr3D 86.911 382 50 0 3302 3683 175405287 175404906 3.340000e-116 429.0
2 TraesCS3D01G194500 chr3D 89.381 113 7 4 997 1109 175408287 175408180 2.270000e-28 137.0
3 TraesCS3D01G194500 chr3A 97.429 2645 56 7 1160 3795 246044397 246041756 0.000000e+00 4497.0
4 TraesCS3D01G194500 chr3A 96.941 425 10 2 3794 4217 246041518 246041096 0.000000e+00 710.0
5 TraesCS3D01G194500 chr3A 91.129 496 43 1 4 499 246123719 246123225 0.000000e+00 671.0
6 TraesCS3D01G194500 chr3A 94.177 395 18 4 709 1100 246044790 246044398 8.660000e-167 597.0
7 TraesCS3D01G194500 chr3A 87.532 385 47 1 3302 3685 215479565 215479181 1.190000e-120 444.0
8 TraesCS3D01G194500 chr3A 89.720 107 7 3 997 1101 215482212 215482108 2.940000e-27 134.0
9 TraesCS3D01G194500 chr3B 96.039 2045 36 23 2179 4217 266565404 266567409 0.000000e+00 3286.0
10 TraesCS3D01G194500 chr3B 94.189 740 17 4 1453 2188 266564208 266564925 0.000000e+00 1105.0
11 TraesCS3D01G194500 chr3B 93.413 501 29 4 1 499 266561894 266562392 0.000000e+00 739.0
12 TraesCS3D01G194500 chr3B 95.467 353 11 4 765 1113 266563637 266563988 4.090000e-155 558.0
13 TraesCS3D01G194500 chr3B 87.696 382 47 0 3302 3683 254776609 254776228 3.320000e-121 446.0
14 TraesCS3D01G194500 chr3B 98.413 252 4 0 1117 1368 266563956 266564207 1.190000e-120 444.0
15 TraesCS3D01G194500 chr3B 87.681 276 27 6 498 771 266562434 266562704 9.770000e-82 315.0
16 TraesCS3D01G194500 chr3B 79.096 354 64 9 1 351 559326287 559326633 7.830000e-58 235.0
17 TraesCS3D01G194500 chr3B 88.496 113 8 4 997 1109 254779962 254779855 1.060000e-26 132.0
18 TraesCS3D01G194500 chr7D 95.101 347 17 0 4218 4564 508327297 508326951 8.850000e-152 547.0
19 TraesCS3D01G194500 chr7D 98.571 70 1 0 4609 4678 508326521 508326452 1.770000e-24 124.0
20 TraesCS3D01G194500 chr7D 97.059 34 1 0 4572 4605 508326572 508326539 1.820000e-04 58.4
21 TraesCS3D01G194500 chr2D 73.639 349 84 6 6 351 155158364 155158707 1.370000e-25 128.0
22 TraesCS3D01G194500 chr2D 87.156 109 7 5 994 1097 49875917 49876023 2.960000e-22 117.0
23 TraesCS3D01G194500 chr2B 91.765 85 5 2 994 1078 77168973 77169055 2.960000e-22 117.0
24 TraesCS3D01G194500 chr2A 91.765 85 5 2 994 1078 51582356 51582438 2.960000e-22 117.0
25 TraesCS3D01G194500 chr4D 92.405 79 6 0 1001 1079 312801842 312801764 3.830000e-21 113.0


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 TraesCS3D01G194500 chr3D 185789126 185793803 4677 False 8639.000000 8639 100.000000 1 4678 1 chr3D.!!$F1 4677
1 TraesCS3D01G194500 chr3D 175404906 175408287 3381 True 283.000000 429 88.146000 997 3683 2 chr3D.!!$R1 2686
2 TraesCS3D01G194500 chr3A 246041096 246044790 3694 True 1934.666667 4497 96.182333 709 4217 3 chr3A.!!$R3 3508
3 TraesCS3D01G194500 chr3A 215479181 215482212 3031 True 289.000000 444 88.626000 997 3685 2 chr3A.!!$R2 2688
4 TraesCS3D01G194500 chr3B 266561894 266567409 5515 False 1074.500000 3286 94.200333 1 4217 6 chr3B.!!$F2 4216
5 TraesCS3D01G194500 chr3B 254776228 254779962 3734 True 289.000000 446 88.096000 997 3683 2 chr3B.!!$R1 2686
6 TraesCS3D01G194500 chr7D 508326452 508327297 845 True 243.133333 547 96.910333 4218 4678 3 chr7D.!!$R1 460

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
592 638 0.038159 AGAAAAGGAGACCAGCGACG 60.038 55.0 0.00 0.0 0.00 5.12 F
656 703 0.669625 GCGCGTCAAAACCCTAGTCT 60.670 55.0 8.43 0.0 0.00 3.24 F
673 720 0.832135 TCTCCTCGTGGTTTGCCTCT 60.832 55.0 2.99 0.0 35.27 3.69 F
763 810 1.254284 AACTCTGCTGGCTCGTAGCT 61.254 55.0 0.00 0.0 41.99 3.32 F
3011 7336 1.523758 GATCAAGTGGTTTCGTGGCT 58.476 50.0 0.00 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2357 6589 0.108520 GGCATGGCACCAATGACTTG 60.109 55.000 15.47 0.0 41.09 3.16 R
2990 7315 1.890876 CCACGAAACCACTTGATCCA 58.109 50.000 0.00 0.0 0.00 3.41 R
3011 7336 2.969821 AATAACCCTCAGGCACAACA 57.030 45.000 0.00 0.0 36.11 3.33 R
3062 7387 3.782523 AGGCTCCATCTATTTCTTCCACA 59.217 43.478 0.00 0.0 0.00 4.17 R
4340 8909 0.459237 CCTCTGACATGACGCTGGTC 60.459 60.000 0.00 0.0 43.71 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
40 41 7.169140 GCGACTCCAAGTCAAATGTTTATTTTT 59.831 33.333 7.78 0.00 45.30 1.94
77 78 3.244875 ACATGCATCCCTGTAGTCAAACA 60.245 43.478 0.00 0.00 0.00 2.83
134 135 3.874392 AATGAACATAGCACAAAGGGC 57.126 42.857 0.00 0.00 0.00 5.19
143 144 7.316393 ACATAGCACAAAGGGCTAATCTATA 57.684 36.000 4.94 0.00 46.03 1.31
144 145 7.390027 ACATAGCACAAAGGGCTAATCTATAG 58.610 38.462 4.94 0.00 46.03 1.31
200 201 0.257039 CCTTTCCTCCCATCACCTGG 59.743 60.000 0.00 0.00 45.51 4.45
253 254 4.277174 TCTTTCGCAAACATTTAGCCAGAA 59.723 37.500 0.00 0.00 0.00 3.02
261 262 6.646240 GCAAACATTTAGCCAGAAAAGATTCA 59.354 34.615 0.00 0.00 38.06 2.57
265 266 6.494835 ACATTTAGCCAGAAAAGATTCAAGGT 59.505 34.615 0.00 0.00 38.06 3.50
332 333 1.305201 TCCAACAAAACTCGGACTGC 58.695 50.000 0.00 0.00 0.00 4.40
333 334 1.134220 TCCAACAAAACTCGGACTGCT 60.134 47.619 0.00 0.00 0.00 4.24
334 335 1.002468 CCAACAAAACTCGGACTGCTG 60.002 52.381 0.00 0.00 0.00 4.41
335 336 1.002468 CAACAAAACTCGGACTGCTGG 60.002 52.381 0.00 0.00 0.00 4.85
358 359 2.652095 TTCCCGAGCCCGTAACAGG 61.652 63.158 0.00 0.00 0.00 4.00
360 361 2.660802 CCGAGCCCGTAACAGGTT 59.339 61.111 0.00 0.00 0.00 3.50
403 405 7.177041 TGGTAGTAAAACAACAACAAAACTCCT 59.823 33.333 0.00 0.00 0.00 3.69
410 412 0.310854 CAACAAAACTCCTGGTCGGC 59.689 55.000 0.00 0.00 0.00 5.54
413 415 2.814835 AAAACTCCTGGTCGGCGGT 61.815 57.895 7.21 0.00 0.00 5.68
434 436 2.281484 GCGGGAGGACAGCAAACA 60.281 61.111 0.00 0.00 0.00 2.83
468 470 1.076559 TAGGGGACGGCGAATCTGA 60.077 57.895 16.62 0.00 0.00 3.27
485 487 2.026169 TCTGAAGACGAAGCTCCCTCTA 60.026 50.000 0.00 0.00 0.00 2.43
504 506 5.582953 CTCTAAGGAGGATGGAGATCTGAT 58.417 45.833 0.00 0.00 36.03 2.90
506 508 4.490547 AAGGAGGATGGAGATCTGATCT 57.509 45.455 19.63 19.63 43.70 2.75
507 509 5.613698 AAGGAGGATGGAGATCTGATCTA 57.386 43.478 19.57 6.38 40.38 1.98
508 510 5.197224 AGGAGGATGGAGATCTGATCTAG 57.803 47.826 19.57 0.00 40.38 2.43
509 511 3.701040 GGAGGATGGAGATCTGATCTAGC 59.299 52.174 19.57 8.46 40.38 3.42
510 512 4.570505 GGAGGATGGAGATCTGATCTAGCT 60.571 50.000 19.57 7.47 40.38 3.32
511 513 5.014534 AGGATGGAGATCTGATCTAGCTT 57.985 43.478 19.57 2.56 40.38 3.74
512 514 5.018809 AGGATGGAGATCTGATCTAGCTTC 58.981 45.833 19.57 13.36 40.38 3.86
513 515 5.018809 GGATGGAGATCTGATCTAGCTTCT 58.981 45.833 19.57 0.00 40.38 2.85
515 517 5.059134 TGGAGATCTGATCTAGCTTCTCA 57.941 43.478 19.57 7.50 40.38 3.27
534 580 2.170397 TCAGGAAGAATCGCTAATGCCA 59.830 45.455 0.00 0.00 35.36 4.92
548 594 2.610438 ATGCCACACCAAGAAATCCT 57.390 45.000 0.00 0.00 0.00 3.24
552 598 2.424956 GCCACACCAAGAAATCCTCATC 59.575 50.000 0.00 0.00 0.00 2.92
562 608 6.239396 CAAGAAATCCTCATCAGCTATCCAT 58.761 40.000 0.00 0.00 0.00 3.41
567 613 2.824936 CCTCATCAGCTATCCATCTCGT 59.175 50.000 0.00 0.00 0.00 4.18
574 620 6.993786 TCAGCTATCCATCTCGTAATAGAG 57.006 41.667 0.00 0.00 39.52 2.43
588 634 5.044558 CGTAATAGAGAAAAGGAGACCAGC 58.955 45.833 0.00 0.00 0.00 4.85
592 638 0.038159 AGAAAAGGAGACCAGCGACG 60.038 55.000 0.00 0.00 0.00 5.12
605 651 2.530497 GCGACGACACACCAAAGCA 61.530 57.895 0.00 0.00 0.00 3.91
606 652 1.841663 GCGACGACACACCAAAGCAT 61.842 55.000 0.00 0.00 0.00 3.79
611 657 1.512926 GACACACCAAAGCATCGACT 58.487 50.000 0.00 0.00 0.00 4.18
619 665 1.466167 CAAAGCATCGACTTGGGACAG 59.534 52.381 0.00 0.00 42.39 3.51
656 703 0.669625 GCGCGTCAAAACCCTAGTCT 60.670 55.000 8.43 0.00 0.00 3.24
667 714 1.203149 ACCCTAGTCTCCTCGTGGTTT 60.203 52.381 2.99 0.00 34.23 3.27
673 720 0.832135 TCTCCTCGTGGTTTGCCTCT 60.832 55.000 2.99 0.00 35.27 3.69
712 759 8.839310 GGTTCACGACCTACTATATAGTAAGA 57.161 38.462 20.62 10.98 45.55 2.10
748 795 3.890674 GTGATCCGGCACCAACTC 58.109 61.111 0.00 0.00 32.68 3.01
763 810 1.254284 AACTCTGCTGGCTCGTAGCT 61.254 55.000 0.00 0.00 41.99 3.32
775 1761 2.048503 GTAGCTTCGTGGCACCGT 60.049 61.111 12.86 0.00 34.17 4.83
783 1769 2.125673 GTGGCACCGTAGCGACAT 60.126 61.111 6.29 0.00 42.00 3.06
794 1780 4.037021 CCGTAGCGACATATTGTTACGAA 58.963 43.478 8.99 0.00 46.73 3.85
912 1902 1.833492 TTGACGACCGAACCAGGGA 60.833 57.895 0.00 0.00 35.02 4.20
969 1959 2.456840 CACCTTCCTCCCTCCCCT 59.543 66.667 0.00 0.00 0.00 4.79
1104 2094 3.323403 CCTCCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
1107 2097 4.078922 TCCTCTCTCTCTCTCTCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
1108 2098 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
1109 2099 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1110 2100 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1112 2102 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1114 2104 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1115 2105 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1116 2106 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1117 2107 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1120 2110 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1122 2112 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1128 2118 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1177 2229 3.318275 AGGCGAAGAGATTATGCGTCTTA 59.682 43.478 0.00 0.00 32.47 2.10
1412 5105 1.834188 AGCTTGATTGGGGGTAAACG 58.166 50.000 0.00 0.00 0.00 3.60
1442 5135 3.877559 TCGCTTGATCCATCATCAGTTT 58.122 40.909 0.00 0.00 42.76 2.66
1660 5399 3.447229 TGTGGAGTCTAGATTCATTCGCA 59.553 43.478 16.22 9.22 0.00 5.10
1703 5442 2.153680 ATCGCAAAATTGTACGTCGC 57.846 45.000 0.00 0.00 0.00 5.19
2021 5760 2.793790 GCATAGCTTCGTCATCACTGAG 59.206 50.000 0.00 0.00 30.18 3.35
2037 5776 3.110705 ACTGAGCATTACCATCAGGAGT 58.889 45.455 6.41 0.00 43.81 3.85
2042 5781 5.302059 TGAGCATTACCATCAGGAGTACTAC 59.698 44.000 0.00 0.00 38.69 2.73
2131 5870 5.290643 TGTTTTCCTTTTCGTTCTGCAAATG 59.709 36.000 0.00 0.00 0.00 2.32
2173 5916 9.672086 TTAAGTGGAAAACTAATGAATTCAACG 57.328 29.630 13.09 6.36 38.56 4.10
2177 5920 7.270579 GTGGAAAACTAATGAATTCAACGTAGC 59.729 37.037 13.09 2.60 0.00 3.58
2357 6589 8.506437 TGTTAGCAAACATATTATGCAGATAGC 58.494 33.333 3.52 1.12 40.69 2.97
3011 7336 1.523758 GATCAAGTGGTTTCGTGGCT 58.476 50.000 0.00 0.00 0.00 4.75
3277 7602 1.346068 AGAGCTGAACACCTGGACTTC 59.654 52.381 0.00 0.81 0.00 3.01
3775 8100 6.544622 TGGCTATTGTATTAAACCGAAAACG 58.455 36.000 0.00 0.00 0.00 3.60
3779 8104 9.919348 GCTATTGTATTAAACCGAAAACGATAA 57.081 29.630 0.00 0.00 0.00 1.75
3903 8471 4.170256 TGGTTCGTTTCAACTTTTCAAGC 58.830 39.130 0.00 0.00 0.00 4.01
3982 8550 4.687219 GCTAGCTCACAATTTACCCCTCAT 60.687 45.833 7.70 0.00 0.00 2.90
3984 8552 4.677182 AGCTCACAATTTACCCCTCATTT 58.323 39.130 0.00 0.00 0.00 2.32
4109 8678 1.536766 CGTTCTTCAGCTTGAATGGCA 59.463 47.619 0.00 0.00 35.59 4.92
4125 8694 6.347696 TGAATGGCAAAGATTGTTTTCTTGT 58.652 32.000 0.00 0.00 36.12 3.16
4242 8811 2.054363 CAGCGATATGGCTCGTACTTG 58.946 52.381 9.54 0.00 42.53 3.16
4270 8839 0.389391 AGCATTATCTGGACGGTCCG 59.611 55.000 21.52 10.48 40.17 4.79
4281 8850 2.311688 GACGGTCCGATGGGCTGATT 62.312 60.000 20.51 0.00 0.00 2.57
4302 8871 2.625790 TGGTTGGTTTGGTAGCATTGAC 59.374 45.455 0.00 0.00 33.55 3.18
4312 8881 0.107508 TAGCATTGACTGAGGCAGGC 60.108 55.000 5.97 5.97 40.49 4.85
4321 8890 2.436292 GAGGCAGGCTGTGAGCTG 60.436 66.667 17.16 0.00 41.99 4.24
4340 8909 3.127030 GCTGTGGAAAAAGAGGTATTCCG 59.873 47.826 0.00 0.00 44.48 4.30
4343 8912 3.688185 GTGGAAAAAGAGGTATTCCGACC 59.312 47.826 0.00 0.00 44.48 4.79
4388 8957 4.441634 GGAAGATGGCTACACGTACAGATT 60.442 45.833 0.00 0.00 0.00 2.40
4417 8986 2.031163 GACAGCAGTCAAGCCCGT 59.969 61.111 4.10 0.00 44.34 5.28
4419 8988 2.281070 CAGCAGTCAAGCCCGTGT 60.281 61.111 0.00 0.00 34.23 4.49
4556 9125 2.682856 TCAATCAAATAGTTGGAGCGGC 59.317 45.455 2.65 0.00 35.29 6.53
4600 9540 0.246635 GGAGTTGTAGAGCGAGGCAA 59.753 55.000 0.00 0.00 0.00 4.52
4605 9545 0.319555 TGTAGAGCGAGGCAACACAC 60.320 55.000 0.00 0.00 41.41 3.82
4606 9546 1.080772 TAGAGCGAGGCAACACACG 60.081 57.895 0.00 0.00 41.41 4.49
4607 9547 2.486636 TAGAGCGAGGCAACACACGG 62.487 60.000 0.00 0.00 41.41 4.94
4619 9573 2.746277 ACACGGCTGGCGATTTCC 60.746 61.111 30.58 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 5.048083 GGATGCATGTGGAGTTTAAGTGAAA 60.048 40.000 2.46 0.00 0.00 2.69
41 42 4.458989 GGATGCATGTGGAGTTTAAGTGAA 59.541 41.667 2.46 0.00 0.00 3.18
42 43 4.009675 GGATGCATGTGGAGTTTAAGTGA 58.990 43.478 2.46 0.00 0.00 3.41
43 44 3.129287 GGGATGCATGTGGAGTTTAAGTG 59.871 47.826 2.46 0.00 0.00 3.16
44 45 3.010584 AGGGATGCATGTGGAGTTTAAGT 59.989 43.478 2.46 0.00 0.00 2.24
45 46 3.379372 CAGGGATGCATGTGGAGTTTAAG 59.621 47.826 2.46 0.00 0.00 1.85
77 78 6.540914 TGAAGAAAGAGACAATACGTTTTGGT 59.459 34.615 20.47 9.13 0.00 3.67
170 171 5.806955 TGGGAGGAAAGGTGGTATTATTT 57.193 39.130 0.00 0.00 0.00 1.40
174 175 3.053619 GTGATGGGAGGAAAGGTGGTATT 60.054 47.826 0.00 0.00 0.00 1.89
200 201 1.762957 TGGACCAATAGCTAGTCTGCC 59.237 52.381 10.45 5.08 0.00 4.85
253 254 5.070981 TGTCAGAGACTCACCTTGAATCTTT 59.929 40.000 5.02 0.00 32.56 2.52
261 262 4.843728 TGTTTTTGTCAGAGACTCACCTT 58.156 39.130 5.02 0.00 33.15 3.50
265 266 5.427378 TGTGATGTTTTTGTCAGAGACTCA 58.573 37.500 5.02 0.00 33.15 3.41
339 340 1.447314 CTGTTACGGGCTCGGGAAC 60.447 63.158 12.42 15.04 41.39 3.62
353 354 6.299805 TGAAGATACTAGCATGAACCTGTT 57.700 37.500 0.00 0.00 0.00 3.16
358 359 7.437748 ACTACCATGAAGATACTAGCATGAAC 58.562 38.462 0.00 0.00 40.29 3.18
360 361 8.706322 TTACTACCATGAAGATACTAGCATGA 57.294 34.615 0.00 0.00 40.29 3.07
419 421 2.561478 TTAGTGTTTGCTGTCCTCCC 57.439 50.000 0.00 0.00 0.00 4.30
434 436 6.320418 CCGTCCCCTAGCAAATTTAATTTAGT 59.680 38.462 2.37 0.00 0.00 2.24
468 470 2.104170 CCTTAGAGGGAGCTTCGTCTT 58.896 52.381 21.84 7.14 34.30 3.01
485 487 4.490547 AGATCAGATCTCCATCCTCCTT 57.509 45.455 7.15 0.00 33.42 3.36
495 497 5.316167 TCCTGAGAAGCTAGATCAGATCTC 58.684 45.833 16.70 11.28 42.48 2.75
499 501 6.135454 ATTCTTCCTGAGAAGCTAGATCAGA 58.865 40.000 19.18 7.26 46.99 3.27
501 503 5.009510 CGATTCTTCCTGAGAAGCTAGATCA 59.990 44.000 0.00 0.00 46.18 2.92
502 504 5.460646 CGATTCTTCCTGAGAAGCTAGATC 58.539 45.833 0.00 0.00 46.18 2.75
504 506 3.067461 GCGATTCTTCCTGAGAAGCTAGA 59.933 47.826 0.00 0.00 46.18 2.43
506 508 3.027412 AGCGATTCTTCCTGAGAAGCTA 58.973 45.455 0.00 0.00 46.18 3.32
507 509 1.830477 AGCGATTCTTCCTGAGAAGCT 59.170 47.619 3.05 0.82 46.18 3.74
508 510 2.307934 AGCGATTCTTCCTGAGAAGC 57.692 50.000 0.00 0.00 46.99 3.86
509 511 4.210955 GCATTAGCGATTCTTCCTGAGAAG 59.789 45.833 0.00 0.00 46.99 2.85
510 512 4.979696 GGCATTAGCGATTCTTCCTGAGAA 60.980 45.833 0.00 0.00 44.60 2.87
511 513 3.493350 GGCATTAGCGATTCTTCCTGAGA 60.493 47.826 0.00 0.00 43.41 3.27
512 514 2.805099 GGCATTAGCGATTCTTCCTGAG 59.195 50.000 0.00 0.00 43.41 3.35
513 515 2.170397 TGGCATTAGCGATTCTTCCTGA 59.830 45.455 0.00 0.00 43.41 3.86
515 517 2.092968 TGTGGCATTAGCGATTCTTCCT 60.093 45.455 0.00 0.00 43.41 3.36
528 574 2.827921 GAGGATTTCTTGGTGTGGCATT 59.172 45.455 0.00 0.00 0.00 3.56
534 580 3.009916 AGCTGATGAGGATTTCTTGGTGT 59.990 43.478 0.00 0.00 0.00 4.16
548 594 7.112779 TCTATTACGAGATGGATAGCTGATGA 58.887 38.462 0.00 0.00 0.00 2.92
552 598 6.993786 TCTCTATTACGAGATGGATAGCTG 57.006 41.667 0.00 0.00 35.23 4.24
562 608 6.185511 TGGTCTCCTTTTCTCTATTACGAGA 58.814 40.000 0.00 0.00 38.23 4.04
567 613 4.954202 TCGCTGGTCTCCTTTTCTCTATTA 59.046 41.667 0.00 0.00 0.00 0.98
574 620 0.038526 TCGTCGCTGGTCTCCTTTTC 60.039 55.000 0.00 0.00 0.00 2.29
588 634 0.163788 GATGCTTTGGTGTGTCGTCG 59.836 55.000 0.00 0.00 0.00 5.12
592 638 1.512926 AGTCGATGCTTTGGTGTGTC 58.487 50.000 0.00 0.00 0.00 3.67
605 651 0.108615 CTTCGCTGTCCCAAGTCGAT 60.109 55.000 0.00 0.00 0.00 3.59
606 652 1.176619 TCTTCGCTGTCCCAAGTCGA 61.177 55.000 0.00 0.00 0.00 4.20
640 686 2.415625 CGAGGAGACTAGGGTTTTGACG 60.416 54.545 0.00 0.00 44.43 4.35
656 703 1.118965 TGAGAGGCAAACCACGAGGA 61.119 55.000 5.68 0.00 39.06 3.71
667 714 2.432444 CCGTTTTTACCATGAGAGGCA 58.568 47.619 0.00 0.00 0.00 4.75
673 720 2.548904 CGTGAACCCGTTTTTACCATGA 59.451 45.455 0.00 0.00 0.00 3.07
717 764 3.181465 CCGGATCACCACTTGCTACTATT 60.181 47.826 0.00 0.00 35.59 1.73
747 794 1.513158 GAAGCTACGAGCCAGCAGA 59.487 57.895 0.00 0.00 43.77 4.26
748 795 1.875813 CGAAGCTACGAGCCAGCAG 60.876 63.158 0.00 0.00 43.77 4.24
763 810 3.672447 TCGCTACGGTGCCACGAA 61.672 61.111 4.05 0.00 37.61 3.85
775 1761 7.997107 ATTCTTTCGTAACAATATGTCGCTA 57.003 32.000 0.00 0.00 0.00 4.26
794 1780 6.239120 GGTTGCAGTGATGGCATAATATTCTT 60.239 38.462 0.00 0.00 41.58 2.52
912 1902 4.232091 TCTTGTGGGTAGGAGAAGACTTT 58.768 43.478 0.00 0.00 0.00 2.66
969 1959 2.833582 GGTCGGAGATGGCGAGGA 60.834 66.667 0.00 0.00 40.67 3.71
1104 2094 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1107 2097 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1108 2098 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1109 2099 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1110 2100 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1112 2102 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1114 2104 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1115 2105 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1116 2106 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1117 2107 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1120 2110 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1122 2112 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1128 2118 3.634448 ACGAGAGAGAGAGAGAGAGAGAG 59.366 52.174 0.00 0.00 0.00 3.20
1177 2229 4.649692 ACTGACAAAGCAGACAGATCAAT 58.350 39.130 0.00 0.00 39.20 2.57
1442 5135 0.535335 GACCTCTATCCGTTGGCACA 59.465 55.000 0.00 0.00 0.00 4.57
1684 5423 1.461512 TGCGACGTACAATTTTGCGAT 59.538 42.857 9.10 0.00 0.00 4.58
2021 5760 5.793030 AGTAGTACTCCTGATGGTAATGC 57.207 43.478 0.00 0.00 34.23 3.56
2131 5870 6.051717 TCCACTTAATTTGCTATCAGAGAGC 58.948 40.000 10.31 10.31 40.53 4.09
2357 6589 0.108520 GGCATGGCACCAATGACTTG 60.109 55.000 15.47 0.00 41.09 3.16
2990 7315 1.890876 CCACGAAACCACTTGATCCA 58.109 50.000 0.00 0.00 0.00 3.41
3011 7336 2.969821 AATAACCCTCAGGCACAACA 57.030 45.000 0.00 0.00 36.11 3.33
3020 7345 4.960469 ACGTTCAGGATCTAATAACCCTCA 59.040 41.667 0.00 0.00 0.00 3.86
3062 7387 3.782523 AGGCTCCATCTATTTCTTCCACA 59.217 43.478 0.00 0.00 0.00 4.17
3277 7602 7.210174 TGGAAAGGAGACGATCTATGTTATTG 58.790 38.462 0.00 0.00 0.00 1.90
3428 7753 2.618709 GGCCATAAGGTTGAGGAATTCG 59.381 50.000 0.00 0.00 37.19 3.34
3954 8522 4.640201 GGGTAAATTGTGAGCTAGCAATGA 59.360 41.667 18.83 0.00 35.72 2.57
4242 8811 8.223177 ACCGTCCAGATAATGCTACTATATAC 57.777 38.462 0.00 0.00 0.00 1.47
4270 8839 1.560505 AACCAACCAATCAGCCCATC 58.439 50.000 0.00 0.00 0.00 3.51
4281 8850 2.625790 GTCAATGCTACCAAACCAACCA 59.374 45.455 0.00 0.00 0.00 3.67
4302 8871 2.436292 GCTCACAGCCTGCCTCAG 60.436 66.667 0.00 0.00 34.48 3.35
4312 8881 2.551459 CCTCTTTTTCCACAGCTCACAG 59.449 50.000 0.00 0.00 0.00 3.66
4321 8890 3.688185 GGTCGGAATACCTCTTTTTCCAC 59.312 47.826 0.00 0.00 39.09 4.02
4340 8909 0.459237 CCTCTGACATGACGCTGGTC 60.459 60.000 0.00 0.00 43.71 4.02
4343 8912 0.799917 CGTCCTCTGACATGACGCTG 60.800 60.000 0.00 0.00 44.29 5.18
4371 8940 1.548719 AGCAATCTGTACGTGTAGCCA 59.451 47.619 0.00 0.00 0.00 4.75
4417 8986 1.613925 GTCTAGTCTGTCACCTGCACA 59.386 52.381 0.00 0.00 0.00 4.57
4419 8988 0.881796 CGTCTAGTCTGTCACCTGCA 59.118 55.000 0.00 0.00 0.00 4.41
4501 9070 5.013079 ACAGTGGTTTGTTCTCCATGAGATA 59.987 40.000 0.00 0.00 38.56 1.98
4502 9071 4.202503 ACAGTGGTTTGTTCTCCATGAGAT 60.203 41.667 0.00 0.00 38.56 2.75
4556 9125 3.141488 CTCTGACCGACCCCCTCG 61.141 72.222 0.00 0.00 42.54 4.63
4564 9133 2.637872 ACTCCATTTTTCCTCTGACCGA 59.362 45.455 0.00 0.00 0.00 4.69
4565 9134 3.059352 ACTCCATTTTTCCTCTGACCG 57.941 47.619 0.00 0.00 0.00 4.79
4566 9135 4.145052 ACAACTCCATTTTTCCTCTGACC 58.855 43.478 0.00 0.00 0.00 4.02
4568 9137 6.433847 TCTACAACTCCATTTTTCCTCTGA 57.566 37.500 0.00 0.00 0.00 3.27
4569 9138 5.123027 GCTCTACAACTCCATTTTTCCTCTG 59.877 44.000 0.00 0.00 0.00 3.35
4570 9139 5.249420 GCTCTACAACTCCATTTTTCCTCT 58.751 41.667 0.00 0.00 0.00 3.69
4600 9540 2.281484 AAATCGCCAGCCGTGTGT 60.281 55.556 0.00 0.00 38.35 3.72


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

AutoCloner maintained by Alex Coulton.