Multiple sequence alignment - TraesCS5D01G329500

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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 TraesCS5D01G329500 chr5D 100.000 2819 0 0 1 2819 421505332 421502514 0.000000e+00 5206.0
1 TraesCS5D01G329500 chr5D 86.063 574 48 16 1271 1828 483269270 483268713 3.130000e-164 588.0
2 TraesCS5D01G329500 chr5D 92.000 125 10 0 2432 2556 490976048 490976172 2.890000e-40 176.0
3 TraesCS5D01G329500 chr5D 87.705 122 14 1 2696 2817 545801518 545801398 1.050000e-29 141.0
4 TraesCS5D01G329500 chr5D 88.406 69 8 0 1897 1965 334932564 334932632 1.800000e-12 84.2
5 TraesCS5D01G329500 chr5A 89.825 2349 154 44 123 2428 535029791 535027485 0.000000e+00 2935.0
6 TraesCS5D01G329500 chr5A 85.827 127 18 0 2693 2819 2369234 2369360 4.900000e-28 135.0
7 TraesCS5D01G329500 chr5A 100.000 37 0 0 4 40 535030135 535030099 5.040000e-08 69.4
8 TraesCS5D01G329500 chr5B 90.128 2188 142 35 1 2172 507866660 507864531 0.000000e+00 2776.0
9 TraesCS5D01G329500 chr5B 87.358 791 83 7 2043 2819 507741766 507740979 0.000000e+00 891.0
10 TraesCS5D01G329500 chr5B 88.208 212 18 6 170 378 507868953 507868746 2.170000e-61 246.0
11 TraesCS5D01G329500 chr5B 88.435 147 13 3 178 324 507867241 507867099 1.040000e-39 174.0
12 TraesCS5D01G329500 chr5B 85.827 127 18 0 2693 2819 4852476 4852350 4.900000e-28 135.0
13 TraesCS5D01G329500 chr4D 87.161 553 56 9 1278 1824 46138365 46137822 5.160000e-172 614.0
14 TraesCS5D01G329500 chr2D 86.980 553 57 9 1278 1824 582871837 582872380 2.400000e-170 608.0
15 TraesCS5D01G329500 chr2D 86.710 459 47 7 1263 1716 29122308 29121859 5.420000e-137 497.0
16 TraesCS5D01G329500 chr2D 78.446 399 64 20 2433 2819 573462138 573462526 1.010000e-59 241.0
17 TraesCS5D01G329500 chr6D 86.282 554 61 9 1277 1824 425873350 425873894 3.130000e-164 588.0
18 TraesCS5D01G329500 chr6D 82.629 426 42 15 1277 1675 37432403 37432823 5.780000e-92 348.0
19 TraesCS5D01G329500 chr2A 85.818 550 62 8 1277 1824 188606139 188606674 1.130000e-158 569.0
20 TraesCS5D01G329500 chr4A 85.185 567 61 14 1263 1824 610026321 610025773 6.820000e-156 560.0
21 TraesCS5D01G329500 chr4B 85.009 567 63 13 1263 1824 554539630 554539081 8.820000e-155 556.0
22 TraesCS5D01G329500 chr7A 84.939 571 55 16 1263 1824 70045788 70046336 1.480000e-152 549.0
23 TraesCS5D01G329500 chr3D 85.657 502 56 10 1263 1758 596824880 596824389 5.380000e-142 514.0
24 TraesCS5D01G329500 chr3D 85.714 63 9 0 1903 1965 608394827 608394765 1.810000e-07 67.6
25 TraesCS5D01G329500 chr2B 89.299 271 28 1 1549 1819 49187356 49187625 3.480000e-89 339.0
26 TraesCS5D01G329500 chr6A 87.681 276 34 0 1549 1824 584704 584979 3.500000e-84 322.0
27 TraesCS5D01G329500 chr6A 87.903 124 15 0 2696 2819 461780429 461780552 2.260000e-31 147.0
28 TraesCS5D01G329500 chr1B 81.106 434 50 19 1270 1675 625036353 625036782 4.530000e-83 318.0
29 TraesCS5D01G329500 chr7D 78.894 398 64 18 2433 2819 630189176 630189564 4.660000e-63 252.0
30 TraesCS5D01G329500 chr3B 88.000 125 15 0 2693 2817 82399274 82399150 6.290000e-32 148.0
31 TraesCS5D01G329500 chr3B 94.737 38 0 2 1967 2004 88266386 88266421 1.090000e-04 58.4
32 TraesCS5D01G329500 chr6B 92.308 78 6 0 2740 2817 606424552 606424475 8.250000e-21 111.0


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 TraesCS5D01G329500 chr5D 421502514 421505332 2818 True 5206.000000 5206 100.000000 1 2819 1 chr5D.!!$R1 2818
1 TraesCS5D01G329500 chr5D 483268713 483269270 557 True 588.000000 588 86.063000 1271 1828 1 chr5D.!!$R2 557
2 TraesCS5D01G329500 chr5A 535027485 535030135 2650 True 1502.200000 2935 94.912500 4 2428 2 chr5A.!!$R1 2424
3 TraesCS5D01G329500 chr5B 507864531 507868953 4422 True 1065.333333 2776 88.923667 1 2172 3 chr5B.!!$R3 2171
4 TraesCS5D01G329500 chr5B 507740979 507741766 787 True 891.000000 891 87.358000 2043 2819 1 chr5B.!!$R2 776
5 TraesCS5D01G329500 chr4D 46137822 46138365 543 True 614.000000 614 87.161000 1278 1824 1 chr4D.!!$R1 546
6 TraesCS5D01G329500 chr2D 582871837 582872380 543 False 608.000000 608 86.980000 1278 1824 1 chr2D.!!$F2 546
7 TraesCS5D01G329500 chr6D 425873350 425873894 544 False 588.000000 588 86.282000 1277 1824 1 chr6D.!!$F2 547
8 TraesCS5D01G329500 chr2A 188606139 188606674 535 False 569.000000 569 85.818000 1277 1824 1 chr2A.!!$F1 547
9 TraesCS5D01G329500 chr4A 610025773 610026321 548 True 560.000000 560 85.185000 1263 1824 1 chr4A.!!$R1 561
10 TraesCS5D01G329500 chr4B 554539081 554539630 549 True 556.000000 556 85.009000 1263 1824 1 chr4B.!!$R1 561
11 TraesCS5D01G329500 chr7A 70045788 70046336 548 False 549.000000 549 84.939000 1263 1824 1 chr7A.!!$F1 561

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
759 3287 0.096976 CACATTCGTCCGCACCAATC 59.903 55.0 0.0 0.0 0.0 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2397 5019 0.322008 CTCCAGAGACCTTTGGGCAC 60.322 60.0 6.73 0.0 35.13 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
45 2339 3.552890 GGCTCGCTCTCCAAAACAAATTT 60.553 43.478 0.00 0.00 0.00 1.82
67 2361 2.917172 GCAAATGTGCCAAACCCTG 58.083 52.632 0.00 0.00 45.68 4.45
68 2362 0.392336 GCAAATGTGCCAAACCCTGA 59.608 50.000 0.00 0.00 45.68 3.86
102 2399 1.420430 CACCGCCTCCCTCCTATTTA 58.580 55.000 0.00 0.00 0.00 1.40
114 2412 6.591935 TCCCTCCTATTTATACTGTTGCAAG 58.408 40.000 0.00 0.00 0.00 4.01
119 2417 6.990349 TCCTATTTATACTGTTGCAAGTAGCC 59.010 38.462 0.00 0.00 44.83 3.93
168 2687 5.354234 ACCGCCACTTAGTTTCTGAAATATG 59.646 40.000 6.06 5.42 0.00 1.78
199 2718 2.754946 TAACCTTTCGCATTCCTCGT 57.245 45.000 0.00 0.00 0.00 4.18
320 2842 0.682532 TGCCACCTCAACTGCAAACA 60.683 50.000 0.00 0.00 0.00 2.83
380 2908 7.099266 TCACAAAAGAAGAAGAATTTGCTCA 57.901 32.000 0.00 0.00 36.48 4.26
384 2912 9.218440 ACAAAAGAAGAAGAATTTGCTCAAAAA 57.782 25.926 0.00 0.00 36.48 1.94
392 2920 8.777413 AGAAGAATTTGCTCAAAAATTTAAGCC 58.223 29.630 14.18 3.08 39.31 4.35
623 3151 1.534028 GCACATATTCAAACCACGCG 58.466 50.000 3.53 3.53 0.00 6.01
627 3155 1.381165 ATATTCAAACCACGCGCCCC 61.381 55.000 5.73 0.00 0.00 5.80
648 3176 2.194326 GCCATTGCCCTCTCCCTC 59.806 66.667 0.00 0.00 0.00 4.30
735 3263 2.896168 TCGTCACTCCTCGTTTGTTTT 58.104 42.857 0.00 0.00 0.00 2.43
750 3278 1.268999 TGTTTTGCTGCACATTCGTCC 60.269 47.619 0.00 0.00 0.00 4.79
752 3280 2.456594 TTTGCTGCACATTCGTCCGC 62.457 55.000 0.00 0.00 0.00 5.54
753 3281 3.422303 GCTGCACATTCGTCCGCA 61.422 61.111 0.00 0.00 0.00 5.69
754 3282 2.476051 CTGCACATTCGTCCGCAC 59.524 61.111 0.00 0.00 0.00 5.34
755 3283 3.027170 CTGCACATTCGTCCGCACC 62.027 63.158 0.00 0.00 0.00 5.01
756 3284 3.047280 GCACATTCGTCCGCACCA 61.047 61.111 0.00 0.00 0.00 4.17
758 3286 1.922135 GCACATTCGTCCGCACCAAT 61.922 55.000 0.00 0.00 0.00 3.16
759 3287 0.096976 CACATTCGTCCGCACCAATC 59.903 55.000 0.00 0.00 0.00 2.67
760 3288 1.024579 ACATTCGTCCGCACCAATCC 61.025 55.000 0.00 0.00 0.00 3.01
761 3289 0.744414 CATTCGTCCGCACCAATCCT 60.744 55.000 0.00 0.00 0.00 3.24
762 3290 0.462047 ATTCGTCCGCACCAATCCTC 60.462 55.000 0.00 0.00 0.00 3.71
763 3291 2.829043 TTCGTCCGCACCAATCCTCG 62.829 60.000 0.00 0.00 0.00 4.63
764 3292 2.577059 GTCCGCACCAATCCTCGA 59.423 61.111 0.00 0.00 0.00 4.04
801 3336 0.249405 CTCCTCCGATCAAGCTCTGC 60.249 60.000 0.00 0.00 0.00 4.26
807 3342 0.368227 CGATCAAGCTCTGCACGAAC 59.632 55.000 0.00 0.00 0.00 3.95
837 3372 0.991920 TTCCATCGCCTTTTCTCCCT 59.008 50.000 0.00 0.00 0.00 4.20
839 3374 1.098050 CCATCGCCTTTTCTCCCTTG 58.902 55.000 0.00 0.00 0.00 3.61
840 3375 1.614317 CCATCGCCTTTTCTCCCTTGT 60.614 52.381 0.00 0.00 0.00 3.16
842 3377 1.892209 TCGCCTTTTCTCCCTTGTTC 58.108 50.000 0.00 0.00 0.00 3.18
843 3378 1.142060 TCGCCTTTTCTCCCTTGTTCA 59.858 47.619 0.00 0.00 0.00 3.18
844 3379 1.266989 CGCCTTTTCTCCCTTGTTCAC 59.733 52.381 0.00 0.00 0.00 3.18
894 3431 3.697542 TGATCAGCATGGTTCATTTCTGG 59.302 43.478 0.00 0.00 36.16 3.86
908 3445 0.669318 TTCTGGTCGGCGACATGAAC 60.669 55.000 37.13 21.86 33.68 3.18
926 3463 3.692593 TGAACGGACGATCATTCTCTGTA 59.307 43.478 0.39 0.00 0.00 2.74
928 3465 4.230314 ACGGACGATCATTCTCTGTATG 57.770 45.455 0.00 0.00 0.00 2.39
973 3513 4.154195 ACGGTAAATCTCTGAACATTGTGC 59.846 41.667 0.00 0.00 0.00 4.57
1037 3577 2.560981 TCACCAGATTGCTAACGTGAGA 59.439 45.455 3.33 0.00 0.00 3.27
1067 3607 0.755327 ACGTTGCCTTCAAGCCCTTT 60.755 50.000 0.00 0.00 31.93 3.11
1070 3610 2.607038 CGTTGCCTTCAAGCCCTTTAAC 60.607 50.000 0.00 0.00 31.93 2.01
1133 3682 6.814644 TGCTTTGCTCTTCCATCAAAATAATG 59.185 34.615 0.00 0.00 30.47 1.90
1135 3684 5.266733 TGCTCTTCCATCAAAATAATGCC 57.733 39.130 0.00 0.00 0.00 4.40
1212 3763 2.159462 GCTTGCTACAAGATGCTGGAAC 60.159 50.000 11.38 0.00 0.00 3.62
1280 3835 1.731433 ATGTGAGCGCATTGGCATCC 61.731 55.000 11.47 0.00 41.24 3.51
1300 3855 3.057876 TCCACATGTACCGCATTGTTTTC 60.058 43.478 0.00 0.00 35.19 2.29
1332 3897 5.878406 TCTTCTCAAGTTTCTGAACCTCT 57.122 39.130 0.00 0.00 36.39 3.69
1333 3898 5.605534 TCTTCTCAAGTTTCTGAACCTCTG 58.394 41.667 0.00 0.00 36.39 3.35
1334 3899 5.129485 TCTTCTCAAGTTTCTGAACCTCTGT 59.871 40.000 0.00 0.00 36.39 3.41
1335 3900 5.359194 TCTCAAGTTTCTGAACCTCTGTT 57.641 39.130 0.00 0.00 36.39 3.16
1336 3901 5.118990 TCTCAAGTTTCTGAACCTCTGTTG 58.881 41.667 0.00 0.00 36.39 3.33
1361 3926 1.881973 GCTGTTGTTGCAGGATTCTGA 59.118 47.619 4.75 0.00 43.49 3.27
1540 4106 9.154847 CAACATTCAGATACACTTGATTCAGTA 57.845 33.333 0.00 0.00 0.00 2.74
1541 4107 9.896645 AACATTCAGATACACTTGATTCAGTAT 57.103 29.630 0.00 0.00 0.00 2.12
1542 4108 9.322773 ACATTCAGATACACTTGATTCAGTATG 57.677 33.333 2.72 0.00 37.54 2.39
1543 4109 9.322773 CATTCAGATACACTTGATTCAGTATGT 57.677 33.333 2.72 4.08 37.40 2.29
1544 4110 8.932945 TTCAGATACACTTGATTCAGTATGTC 57.067 34.615 2.72 0.00 37.40 3.06
1545 4111 8.298729 TCAGATACACTTGATTCAGTATGTCT 57.701 34.615 2.72 0.00 37.40 3.41
1546 4112 8.193438 TCAGATACACTTGATTCAGTATGTCTG 58.807 37.037 11.45 11.45 44.85 3.51
1599 4180 1.527380 GTTCGGGTTTCAGGGTGCA 60.527 57.895 0.00 0.00 0.00 4.57
1804 4392 3.133014 CGAGATCAGACCGGGCAT 58.867 61.111 11.69 0.00 0.00 4.40
1876 4467 4.598062 TCGCAGTCGATGTTTATACTCTG 58.402 43.478 0.00 0.00 40.21 3.35
1906 4497 7.702772 AGATGCTGTACTTAAGAATACTTGTCG 59.297 37.037 10.09 0.00 37.53 4.35
1996 4587 0.097674 GAGTTGCCGCTACAATGCAG 59.902 55.000 7.70 0.00 36.21 4.41
2081 4672 2.262915 CTCTCACCACCGCTGGAC 59.737 66.667 3.11 0.00 40.55 4.02
2111 4703 3.785859 CAAGGCCCCTCAGCGCTA 61.786 66.667 10.99 0.00 0.00 4.26
2156 4748 1.352352 CAGGGGAGTTCAATCAGTGGT 59.648 52.381 0.00 0.00 0.00 4.16
2160 4752 3.486383 GGGAGTTCAATCAGTGGTGAAA 58.514 45.455 10.57 0.00 35.60 2.69
2186 4778 4.291249 AGCCTAGAAAATTAGTGGGGTCAA 59.709 41.667 0.00 0.00 0.00 3.18
2193 4792 7.889589 GAAAATTAGTGGGGTCAATTTTCTG 57.110 36.000 17.90 0.00 45.95 3.02
2195 4794 7.610580 AAATTAGTGGGGTCAATTTTCTGAA 57.389 32.000 0.00 0.00 29.77 3.02
2225 4824 7.304919 TCGTCACAATGTACAAAAGTTGTAA 57.695 32.000 11.24 0.00 46.72 2.41
2294 4914 1.610624 CGGCCCACACATAGAAACACT 60.611 52.381 0.00 0.00 0.00 3.55
2309 4929 4.449068 AGAAACACTACTGAGTTCAATGCG 59.551 41.667 0.00 0.00 31.73 4.73
2329 4949 2.994417 GGGGTTGGCCAATTGCGA 60.994 61.111 23.66 0.00 42.61 5.10
2332 4952 1.810853 GGTTGGCCAATTGCGATGC 60.811 57.895 23.66 5.61 42.61 3.91
2338 4958 0.460635 GCCAATTGCGATGCATTGGT 60.461 50.000 22.21 0.00 42.88 3.67
2352 4972 0.464373 ATTGGTGCTGATAGCGGTGG 60.464 55.000 0.00 0.00 46.26 4.61
2360 4980 1.956170 GATAGCGGTGGCGGATGTG 60.956 63.158 0.00 0.00 46.35 3.21
2431 5053 0.118346 TGGAGACAGGGCCCTAGAAA 59.882 55.000 28.13 5.36 35.01 2.52
2484 5106 9.018582 CCTCTCCAATTTCATATAAAGGAATCC 57.981 37.037 0.00 0.00 0.00 3.01
2513 5135 8.354711 TCTAGTAGCATAATCTCCTTACATGG 57.645 38.462 0.00 0.00 0.00 3.66
2541 5163 6.376978 GCAACGAACTAAGACAACTAGACTA 58.623 40.000 0.00 0.00 0.00 2.59
2608 5230 5.525745 TGAACTAGTTCAGCATCGAAACAAA 59.474 36.000 30.07 6.34 43.90 2.83
2610 5232 5.990408 ACTAGTTCAGCATCGAAACAAAAG 58.010 37.500 0.00 0.00 0.00 2.27
2628 5250 7.054491 ACAAAAGCAAACACAGGAGATAAAT 57.946 32.000 0.00 0.00 0.00 1.40
2634 5256 5.335897 GCAAACACAGGAGATAAATGAAGCA 60.336 40.000 0.00 0.00 0.00 3.91
2664 5286 4.080969 CAAAAGCTGCTGAGAGAACATC 57.919 45.455 1.35 0.00 0.00 3.06
2675 5297 3.117474 TGAGAGAACATCGGGAGTAGGAT 60.117 47.826 0.00 0.00 0.00 3.24
2680 5302 0.758734 CATCGGGAGTAGGATGGCAA 59.241 55.000 0.00 0.00 37.09 4.52
2682 5304 1.507140 TCGGGAGTAGGATGGCAATT 58.493 50.000 0.00 0.00 0.00 2.32
2717 5339 2.359602 CAGCCTCAGCACACCCAG 60.360 66.667 0.00 0.00 43.56 4.45
2794 5416 2.015587 CTCCCAGCTGCAAGATTCTTC 58.984 52.381 8.66 0.00 34.07 2.87
2798 5420 2.937799 CCAGCTGCAAGATTCTTCTCTC 59.062 50.000 8.66 0.00 34.07 3.20
2813 5435 4.230733 TCTTCTCTCTGGGTCCTTGATCTA 59.769 45.833 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 2384 5.552178 CAACAGTATAAATAGGAGGGAGGC 58.448 45.833 0.00 0.00 0.00 4.70
168 2687 9.865484 GAATGCGAAAGGTTAAATAGAGAATAC 57.135 33.333 0.00 0.00 0.00 1.89
175 2694 5.293569 ACGAGGAATGCGAAAGGTTAAATAG 59.706 40.000 0.00 0.00 0.00 1.73
183 2702 1.438651 TCAACGAGGAATGCGAAAGG 58.561 50.000 0.00 0.00 0.00 3.11
235 2754 4.517285 GATTAGGACAGAAATGACTGGCA 58.483 43.478 0.00 0.00 46.67 4.92
320 2842 6.668323 CAAATTCAGGTTTGAACTCATACGT 58.332 36.000 0.00 0.00 45.54 3.57
380 2908 5.848406 TCCATTCGTGTGGCTTAAATTTTT 58.152 33.333 0.00 0.00 39.19 1.94
384 2912 3.016736 CCTCCATTCGTGTGGCTTAAAT 58.983 45.455 4.30 0.00 39.19 1.40
392 2920 2.438434 GCCCCCTCCATTCGTGTG 60.438 66.667 0.00 0.00 0.00 3.82
627 3155 1.755783 GGAGAGGGCAATGGCAAGG 60.756 63.158 9.51 0.00 43.71 3.61
628 3156 1.755783 GGGAGAGGGCAATGGCAAG 60.756 63.158 9.51 0.00 43.71 4.01
629 3157 2.215451 GAGGGAGAGGGCAATGGCAA 62.215 60.000 9.51 0.00 43.71 4.52
630 3158 2.614969 AGGGAGAGGGCAATGGCA 60.615 61.111 9.51 0.00 43.71 4.92
735 3263 3.422303 GCGGACGAATGTGCAGCA 61.422 61.111 0.00 0.00 35.97 4.41
750 3278 0.461870 TGGAATCGAGGATTGGTGCG 60.462 55.000 0.00 0.00 31.89 5.34
752 3280 2.033801 GCATTGGAATCGAGGATTGGTG 59.966 50.000 0.00 0.00 31.89 4.17
753 3281 2.092212 AGCATTGGAATCGAGGATTGGT 60.092 45.455 0.00 0.00 31.89 3.67
754 3282 2.579873 AGCATTGGAATCGAGGATTGG 58.420 47.619 0.00 0.00 31.89 3.16
755 3283 3.961182 CAAGCATTGGAATCGAGGATTG 58.039 45.455 0.00 0.00 43.94 2.67
801 3336 0.652592 GAATCTGGATGCGGTTCGTG 59.347 55.000 0.00 0.00 0.00 4.35
807 3342 1.572085 GCGATGGAATCTGGATGCGG 61.572 60.000 0.00 0.00 42.58 5.69
837 3372 2.494059 GCAGTGAGCTTAGGTGAACAA 58.506 47.619 0.00 0.00 41.15 2.83
839 3374 1.071605 CGCAGTGAGCTTAGGTGAAC 58.928 55.000 0.00 0.00 42.61 3.18
840 3375 0.670546 GCGCAGTGAGCTTAGGTGAA 60.671 55.000 12.01 0.00 42.61 3.18
842 3377 0.742281 ATGCGCAGTGAGCTTAGGTG 60.742 55.000 18.32 0.00 42.61 4.00
843 3378 0.460987 GATGCGCAGTGAGCTTAGGT 60.461 55.000 18.32 0.00 42.61 3.08
844 3379 0.460811 TGATGCGCAGTGAGCTTAGG 60.461 55.000 18.32 0.00 42.61 2.69
894 3431 2.126228 TCCGTTCATGTCGCCGAC 60.126 61.111 10.96 10.96 0.00 4.79
908 3445 3.977579 CACATACAGAGAATGATCGTCCG 59.022 47.826 0.00 0.00 0.00 4.79
926 3463 5.759059 TCTTGAGGGAAAGATAATGCACAT 58.241 37.500 0.00 0.00 31.19 3.21
928 3465 5.447818 CGTTCTTGAGGGAAAGATAATGCAC 60.448 44.000 0.00 0.00 36.12 4.57
979 3519 1.668919 CGTCTCTAACTGCAAAGCCGA 60.669 52.381 0.00 0.00 0.00 5.54
1037 3577 3.595758 GCAACGTGGGTGCTGCTT 61.596 61.111 3.46 0.00 29.29 3.91
1067 3607 6.625362 TGCCATCAATTTTGCGAATTAGTTA 58.375 32.000 0.00 0.00 0.00 2.24
1070 3610 6.406093 TTTGCCATCAATTTTGCGAATTAG 57.594 33.333 0.00 0.00 31.33 1.73
1108 3652 4.877378 ATTTTGATGGAAGAGCAAAGCA 57.123 36.364 0.00 0.00 33.60 3.91
1133 3682 1.135170 GCAGGAGCAAAGAGAATTGGC 60.135 52.381 0.00 0.00 41.58 4.52
1135 3684 1.467035 GCGCAGGAGCAAAGAGAATTG 60.467 52.381 0.30 0.00 42.27 2.32
1172 3723 3.871574 TACGCCGGGTACGCGTAC 61.872 66.667 35.42 35.42 45.60 3.67
1265 3816 1.731433 ATGTGGATGCCAATGCGCTC 61.731 55.000 9.73 0.00 41.78 5.03
1266 3817 1.755395 ATGTGGATGCCAATGCGCT 60.755 52.632 9.73 0.00 41.78 5.92
1267 3818 1.590525 CATGTGGATGCCAATGCGC 60.591 57.895 0.00 0.00 41.78 6.09
1280 3835 3.241701 GGAAAACAATGCGGTACATGTG 58.758 45.455 9.11 0.00 39.60 3.21
1300 3855 3.045601 ACTTGAGAAGAATGACACGGG 57.954 47.619 0.00 0.00 0.00 5.28
1332 3897 1.000171 TGCAACAACAGCAACACAACA 60.000 42.857 0.00 0.00 39.39 3.33
1333 3898 1.655099 CTGCAACAACAGCAACACAAC 59.345 47.619 0.00 0.00 42.17 3.32
1334 3899 1.403914 CCTGCAACAACAGCAACACAA 60.404 47.619 0.00 0.00 42.17 3.33
1335 3900 0.173029 CCTGCAACAACAGCAACACA 59.827 50.000 0.00 0.00 42.17 3.72
1336 3901 0.455410 TCCTGCAACAACAGCAACAC 59.545 50.000 0.00 0.00 42.17 3.32
1361 3926 4.796231 GACCGTCAGCGTCGCCAT 62.796 66.667 14.86 0.00 36.15 4.40
1496 4061 1.903890 GATCATCTCTCGGGCCGGA 60.904 63.158 27.98 20.38 0.00 5.14
1498 4063 0.598680 GTTGATCATCTCTCGGGCCG 60.599 60.000 22.51 22.51 0.00 6.13
1499 4064 0.465705 TGTTGATCATCTCTCGGGCC 59.534 55.000 0.00 0.00 0.00 5.80
1540 4106 3.446161 CAGAATTGGCCACATTCAGACAT 59.554 43.478 27.65 13.90 0.00 3.06
1541 4107 2.821378 CAGAATTGGCCACATTCAGACA 59.179 45.455 27.65 6.87 0.00 3.41
1542 4108 3.084039 TCAGAATTGGCCACATTCAGAC 58.916 45.455 27.65 12.60 0.00 3.51
1543 4109 3.438216 TCAGAATTGGCCACATTCAGA 57.562 42.857 27.65 24.35 0.00 3.27
1544 4110 4.401519 AGATTCAGAATTGGCCACATTCAG 59.598 41.667 27.65 23.14 0.00 3.02
1545 4111 4.158949 CAGATTCAGAATTGGCCACATTCA 59.841 41.667 27.65 16.22 0.00 2.57
1546 4112 4.400251 TCAGATTCAGAATTGGCCACATTC 59.600 41.667 22.72 22.72 0.00 2.67
1547 4113 4.346730 TCAGATTCAGAATTGGCCACATT 58.653 39.130 3.88 9.02 0.00 2.71
1599 4180 2.577059 CCATCGTACACGTGCCCT 59.423 61.111 17.22 0.00 40.80 5.19
1804 4392 4.733371 TCGTCAATGAGCGGCGCA 62.733 61.111 35.02 15.48 0.00 6.09
1954 4545 8.778059 ACTCATGTATAATTTTTACTCCCTCCA 58.222 33.333 0.00 0.00 0.00 3.86
1996 4587 3.309954 GCCTATCAACATCGACAGTTTCC 59.690 47.826 2.57 0.00 0.00 3.13
2005 4596 4.450419 GGATGAGAAAGCCTATCAACATCG 59.550 45.833 0.00 0.00 35.62 3.84
2156 4748 5.710099 CCACTAATTTTCTAGGCTGGTTTCA 59.290 40.000 0.00 0.00 0.00 2.69
2160 4752 3.053619 CCCCACTAATTTTCTAGGCTGGT 60.054 47.826 0.00 0.00 0.00 4.00
2175 4767 7.610580 AAAATTCAGAAAATTGACCCCACTA 57.389 32.000 0.00 0.00 0.00 2.74
2203 4802 8.794406 CACTTTACAACTTTTGTACATTGTGAC 58.206 33.333 18.46 0.00 45.16 3.67
2217 4816 5.198207 ACTGCCTAAACCACTTTACAACTT 58.802 37.500 0.00 0.00 0.00 2.66
2219 4818 5.509716 AACTGCCTAAACCACTTTACAAC 57.490 39.130 0.00 0.00 0.00 3.32
2225 4824 4.953579 TCAGAAAAACTGCCTAAACCACTT 59.046 37.500 0.00 0.00 45.38 3.16
2230 4829 6.019559 CAGCTTTTCAGAAAAACTGCCTAAAC 60.020 38.462 20.82 0.00 45.38 2.01
2275 4895 2.200373 AGTGTTTCTATGTGTGGGCC 57.800 50.000 0.00 0.00 0.00 5.80
2276 4896 3.684788 CAGTAGTGTTTCTATGTGTGGGC 59.315 47.826 0.00 0.00 0.00 5.36
2277 4897 5.147330 TCAGTAGTGTTTCTATGTGTGGG 57.853 43.478 0.00 0.00 0.00 4.61
2279 4899 6.923508 TGAACTCAGTAGTGTTTCTATGTGTG 59.076 38.462 12.77 0.00 35.62 3.82
2294 4914 0.739462 CCGCCGCATTGAACTCAGTA 60.739 55.000 0.00 0.00 0.00 2.74
2332 4952 0.659427 CACCGCTATCAGCACCAATG 59.341 55.000 0.00 0.00 42.58 2.82
2338 4958 4.529219 CCGCCACCGCTATCAGCA 62.529 66.667 0.00 0.00 42.58 4.41
2343 4963 2.108976 CACATCCGCCACCGCTAT 59.891 61.111 0.00 0.00 0.00 2.97
2394 5016 1.073897 AGAGACCTTTGGGCACTGC 59.926 57.895 0.00 0.00 35.63 4.40
2395 5017 0.607489 CCAGAGACCTTTGGGCACTG 60.607 60.000 9.46 9.46 35.63 3.66
2396 5018 0.768221 TCCAGAGACCTTTGGGCACT 60.768 55.000 6.73 0.00 35.13 4.40
2397 5019 0.322008 CTCCAGAGACCTTTGGGCAC 60.322 60.000 6.73 0.00 35.13 5.01
2398 5020 0.473694 TCTCCAGAGACCTTTGGGCA 60.474 55.000 6.73 0.00 35.13 5.36
2399 5021 2.377136 TCTCCAGAGACCTTTGGGC 58.623 57.895 6.73 0.00 35.13 5.36
2442 5064 3.431673 AGAGGGAAAGCCTCTCTTTTG 57.568 47.619 0.00 0.00 44.58 2.44
2484 5106 8.851145 TGTAAGGAGATTATGCTACTAGAACTG 58.149 37.037 0.00 0.00 0.00 3.16
2495 5117 2.160417 GCGCCATGTAAGGAGATTATGC 59.840 50.000 0.00 0.00 0.00 3.14
2513 5135 1.225395 GTCTTAGTTCGTTGCGCGC 60.225 57.895 27.26 27.26 41.07 6.86
2541 5163 7.557719 AGCTGGCTTGTAATGATACTTTGTATT 59.442 33.333 0.00 0.00 32.98 1.89
2549 5171 4.635765 TGTTGAGCTGGCTTGTAATGATAC 59.364 41.667 0.00 0.00 0.00 2.24
2596 5218 3.305629 TGTGTTTGCTTTTGTTTCGATGC 59.694 39.130 0.00 0.00 0.00 3.91
2600 5222 3.506810 TCCTGTGTTTGCTTTTGTTTCG 58.493 40.909 0.00 0.00 0.00 3.46
2608 5230 6.571150 GCTTCATTTATCTCCTGTGTTTGCTT 60.571 38.462 0.00 0.00 0.00 3.91
2610 5232 5.098211 GCTTCATTTATCTCCTGTGTTTGC 58.902 41.667 0.00 0.00 0.00 3.68
2628 5250 2.542597 CTTTTGCTTGCTTGTGCTTCA 58.457 42.857 0.00 0.00 40.48 3.02
2653 5275 2.241430 TCCTACTCCCGATGTTCTCTCA 59.759 50.000 0.00 0.00 0.00 3.27
2664 5286 1.140852 TGAATTGCCATCCTACTCCCG 59.859 52.381 0.00 0.00 0.00 5.14
2675 5297 3.726557 ACTGGAGAAGATGAATTGCCA 57.273 42.857 0.00 0.00 0.00 4.92
2680 5302 4.853007 CTGGGAAACTGGAGAAGATGAAT 58.147 43.478 0.00 0.00 0.00 2.57
2682 5304 2.026822 GCTGGGAAACTGGAGAAGATGA 60.027 50.000 0.00 0.00 0.00 2.92
2717 5339 3.499737 CGTCGCAAGGATGGCACC 61.500 66.667 0.00 0.00 30.95 5.01
2736 5358 1.198637 GTGGCAAGTGACATCTTCAGC 59.801 52.381 0.00 0.00 34.33 4.26
2794 5416 3.636679 TGTAGATCAAGGACCCAGAGAG 58.363 50.000 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.