Multiple sequence alignment - TraesCS7A01G390900

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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 TraesCS7A01G390900 chr7A 100.000 3664 0 0 1 3664 566988668 566992331 0.000000e+00 6767
1 TraesCS7A01G390900 chr7A 88.207 2103 173 39 764 2807 566910148 566912234 0.000000e+00 2440
2 TraesCS7A01G390900 chr7A 86.986 1168 134 10 1381 2534 619305199 619306362 0.000000e+00 1299
3 TraesCS7A01G390900 chr7A 94.955 337 16 1 1006 1341 566790499 566790835 9.010000e-146 527
4 TraesCS7A01G390900 chr7A 82.578 287 22 15 161 430 566789676 566789951 1.020000e-55 228
5 TraesCS7A01G390900 chr7A 84.082 245 23 7 419 659 566909837 566910069 4.760000e-54 222
6 TraesCS7A01G390900 chr7A 81.496 254 19 12 419 659 566789988 566790226 2.250000e-42 183
7 TraesCS7A01G390900 chr7D 91.517 2122 124 22 810 2903 500776025 500778118 0.000000e+00 2870
8 TraesCS7A01G390900 chr7D 86.857 1575 150 25 1006 2565 113583065 113584597 0.000000e+00 1709
9 TraesCS7A01G390900 chr7D 95.391 716 24 5 2906 3614 500778150 500778863 0.000000e+00 1131
10 TraesCS7A01G390900 chr7D 79.464 224 27 8 3299 3522 500781678 500781882 1.370000e-29 141
11 TraesCS7A01G390900 chrUn 88.719 2358 170 28 810 3114 86611959 86614273 0.000000e+00 2793
12 TraesCS7A01G390900 chrUn 92.782 568 29 6 3100 3659 86614422 86614985 0.000000e+00 811
13 TraesCS7A01G390900 chrUn 86.777 242 29 3 419 658 86611610 86611850 2.170000e-67 267
14 TraesCS7A01G390900 chrUn 87.692 195 18 3 65 257 86611199 86611389 4.760000e-54 222
15 TraesCS7A01G390900 chr3A 86.811 2085 185 51 487 2533 732405046 732403014 0.000000e+00 2244
16 TraesCS7A01G390900 chr3A 84.211 456 38 14 672 1120 728925374 728924946 2.630000e-111 412
17 TraesCS7A01G390900 chr3D 86.027 2147 205 37 47 2161 598727041 598724958 0.000000e+00 2215
18 TraesCS7A01G390900 chr3B 83.673 2401 278 54 217 2578 805812641 805810316 0.000000e+00 2158
19 TraesCS7A01G390900 chr3B 89.805 1540 140 11 1006 2533 810194225 810192691 0.000000e+00 1958
20 TraesCS7A01G390900 chr3B 84.273 1437 172 30 737 2161 806058735 806057341 0.000000e+00 1352
21 TraesCS7A01G390900 chr3B 85.613 848 81 17 388 1230 805977965 805977154 0.000000e+00 852
22 TraesCS7A01G390900 chr3B 85.321 545 57 8 767 1305 806003669 806003142 3.220000e-150 542
23 TraesCS7A01G390900 chr3B 87.647 340 31 1 47 375 806016719 806016380 5.740000e-103 385
24 TraesCS7A01G390900 chr3B 91.346 104 7 2 672 775 806004218 806004117 1.370000e-29 141
25 TraesCS7A01G390900 chr7B 89.809 1570 137 15 971 2533 664398895 664397342 0.000000e+00 1991
26 TraesCS7A01G390900 chr7B 83.822 2046 234 57 810 2807 528873689 528875685 0.000000e+00 1855
27 TraesCS7A01G390900 chr7B 88.003 1192 120 12 1388 2565 73176988 73178170 0.000000e+00 1387
28 TraesCS7A01G390900 chr7B 85.772 246 32 3 419 661 664399445 664399200 1.310000e-64 257
29 TraesCS7A01G390900 chr7B 85.792 183 21 3 767 945 664399068 664398887 4.830000e-44 189
30 TraesCS7A01G390900 chr7B 74.778 563 62 40 419 939 73175916 73176440 2.910000e-41 180


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 TraesCS7A01G390900 chr7A 566988668 566992331 3663 False 6767.000000 6767 100.000000 1 3664 1 chr7A.!!$F1 3663
1 TraesCS7A01G390900 chr7A 566909837 566912234 2397 False 1331.000000 2440 86.144500 419 2807 2 chr7A.!!$F4 2388
2 TraesCS7A01G390900 chr7A 619305199 619306362 1163 False 1299.000000 1299 86.986000 1381 2534 1 chr7A.!!$F2 1153
3 TraesCS7A01G390900 chr7A 566789676 566790835 1159 False 312.666667 527 86.343000 161 1341 3 chr7A.!!$F3 1180
4 TraesCS7A01G390900 chr7D 113583065 113584597 1532 False 1709.000000 1709 86.857000 1006 2565 1 chr7D.!!$F1 1559
5 TraesCS7A01G390900 chr7D 500776025 500781882 5857 False 1380.666667 2870 88.790667 810 3614 3 chr7D.!!$F2 2804
6 TraesCS7A01G390900 chrUn 86611199 86614985 3786 False 1023.250000 2793 88.992500 65 3659 4 chrUn.!!$F1 3594
7 TraesCS7A01G390900 chr3A 732403014 732405046 2032 True 2244.000000 2244 86.811000 487 2533 1 chr3A.!!$R2 2046
8 TraesCS7A01G390900 chr3D 598724958 598727041 2083 True 2215.000000 2215 86.027000 47 2161 1 chr3D.!!$R1 2114
9 TraesCS7A01G390900 chr3B 805810316 805812641 2325 True 2158.000000 2158 83.673000 217 2578 1 chr3B.!!$R1 2361
10 TraesCS7A01G390900 chr3B 810192691 810194225 1534 True 1958.000000 1958 89.805000 1006 2533 1 chr3B.!!$R5 1527
11 TraesCS7A01G390900 chr3B 806057341 806058735 1394 True 1352.000000 1352 84.273000 737 2161 1 chr3B.!!$R4 1424
12 TraesCS7A01G390900 chr3B 805977154 805977965 811 True 852.000000 852 85.613000 388 1230 1 chr3B.!!$R2 842
13 TraesCS7A01G390900 chr3B 806003142 806004218 1076 True 341.500000 542 88.333500 672 1305 2 chr3B.!!$R6 633
14 TraesCS7A01G390900 chr7B 528873689 528875685 1996 False 1855.000000 1855 83.822000 810 2807 1 chr7B.!!$F1 1997
15 TraesCS7A01G390900 chr7B 664397342 664399445 2103 True 812.333333 1991 87.124333 419 2533 3 chr7B.!!$R1 2114
16 TraesCS7A01G390900 chr7B 73175916 73178170 2254 False 783.500000 1387 81.390500 419 2565 2 chr7B.!!$F2 2146

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
507 671 0.032952 ACGTTGAGCCGCTACAAAGA 59.967 50.0 18.08 0.0 31.99 2.52 F
945 1727 0.108804 TTGGCGAAAGAGTAGAGCGG 60.109 55.0 0.00 0.0 0.00 5.52 F
949 1731 0.526524 CGAAAGAGTAGAGCGGCTGG 60.527 60.0 7.50 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 2432 1.064463 TCCTCCAATCCCAGCATTGTC 60.064 52.381 0.00 0.0 32.61 3.18 R
2088 3086 1.825105 ACATACCTGCCCCATGATCT 58.175 50.000 0.00 0.0 0.00 2.75 R
2820 3881 2.404559 GGTACCACAGATACCCATCCA 58.595 52.381 7.15 0.0 36.80 3.41 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
18 19 4.040068 GGATGCAGCCGAGTGATC 57.960 61.111 4.62 0.00 0.00 2.92
19 20 1.596477 GGATGCAGCCGAGTGATCC 60.596 63.158 4.62 0.00 0.00 3.36
20 21 1.953138 GATGCAGCCGAGTGATCCG 60.953 63.158 0.00 0.00 0.00 4.18
21 22 4.819761 TGCAGCCGAGTGATCCGC 62.820 66.667 0.00 0.00 0.00 5.54
28 29 3.838271 GAGTGATCCGCCGGCTGA 61.838 66.667 26.68 24.98 0.00 4.26
29 30 3.157217 GAGTGATCCGCCGGCTGAT 62.157 63.158 30.55 30.55 0.00 2.90
30 31 2.203070 GTGATCCGCCGGCTGATT 60.203 61.111 30.62 16.70 0.00 2.57
31 32 2.203056 TGATCCGCCGGCTGATTG 60.203 61.111 30.62 12.87 0.00 2.67
32 33 2.974698 GATCCGCCGGCTGATTGG 60.975 66.667 30.62 21.28 0.00 3.16
33 34 3.757248 GATCCGCCGGCTGATTGGT 62.757 63.158 30.62 12.86 0.00 3.67
34 35 2.377628 GATCCGCCGGCTGATTGGTA 62.378 60.000 30.62 12.15 0.00 3.25
35 36 1.978455 ATCCGCCGGCTGATTGGTAA 61.978 55.000 25.78 4.43 0.00 2.85
36 37 2.469516 CCGCCGGCTGATTGGTAAC 61.470 63.158 26.68 0.00 0.00 2.50
57 58 7.494298 GGTAACATTTTCCTCTTTTGAAGCAAA 59.506 33.333 0.00 0.00 0.00 3.68
62 63 2.549754 TCCTCTTTTGAAGCAAAGCTCG 59.450 45.455 0.00 0.00 38.25 5.03
63 64 2.351157 CCTCTTTTGAAGCAAAGCTCGG 60.351 50.000 0.00 0.00 38.25 4.63
69 70 2.297701 TGAAGCAAAGCTCGGTTTCTT 58.702 42.857 12.91 0.00 38.25 2.52
95 97 6.612306 ACGGTAAGATTTCTTTTCTTCATGC 58.388 36.000 0.00 0.00 37.40 4.06
122 124 9.840427 CTTAGTTTGGAGTAAAATACATGGTTG 57.160 33.333 0.00 0.00 29.43 3.77
134 136 6.817765 AATACATGGTTGGTACAGAAAGTG 57.182 37.500 0.00 0.00 42.39 3.16
155 158 1.197721 GCCGTGGAAGTTCAGTTCATG 59.802 52.381 5.01 0.00 0.00 3.07
179 182 6.138761 GCATCAACTTATTCTAGCATTTCCG 58.861 40.000 0.00 0.00 0.00 4.30
271 275 2.640316 ACCCCGCCATTATCTTCTTC 57.360 50.000 0.00 0.00 0.00 2.87
322 432 7.781548 TTACTTTGGTTCTACTTTGTCTGAC 57.218 36.000 0.00 0.00 0.00 3.51
367 477 1.079503 GACCGAACAAGTCCTCATGC 58.920 55.000 0.00 0.00 0.00 4.06
391 505 6.373779 CGAAACACAGTTTCTTATGAGCATT 58.626 36.000 17.43 0.00 0.00 3.56
425 585 5.909477 TGTTCAAGTATGACCGGTATAAGG 58.091 41.667 7.34 0.00 34.61 2.69
477 641 1.141053 ACTGAGAAGGTGACACCCAAC 59.859 52.381 21.32 12.36 39.75 3.77
485 649 0.320374 GTGACACCCAACATCGAGGA 59.680 55.000 3.06 0.00 0.00 3.71
497 661 0.389948 ATCGAGGACAACGTTGAGCC 60.390 55.000 33.66 29.37 0.00 4.70
507 671 0.032952 ACGTTGAGCCGCTACAAAGA 59.967 50.000 18.08 0.00 31.99 2.52
533 709 2.055838 GACAGATCACAACGTAACGCA 58.944 47.619 0.00 0.00 0.00 5.24
534 710 2.058798 ACAGATCACAACGTAACGCAG 58.941 47.619 0.00 0.00 0.00 5.18
565 750 1.648116 ACTAGGGCGGAGGTTAACAA 58.352 50.000 8.10 0.00 0.00 2.83
669 894 1.690633 GGAGGAGGTCTGATGGCCA 60.691 63.158 8.56 8.56 0.00 5.36
670 895 1.059006 GGAGGAGGTCTGATGGCCAT 61.059 60.000 20.96 20.96 0.00 4.40
748 1017 1.818674 GTCCATGACAAGCCCGATTTT 59.181 47.619 0.00 0.00 32.09 1.82
751 1020 4.097892 GTCCATGACAAGCCCGATTTTAAT 59.902 41.667 0.00 0.00 32.09 1.40
801 1525 0.611896 TGCTGTGGATCCGACTCTGA 60.612 55.000 7.39 0.00 0.00 3.27
805 1529 1.309950 GTGGATCCGACTCTGATCGA 58.690 55.000 7.39 0.00 45.13 3.59
806 1530 1.265635 GTGGATCCGACTCTGATCGAG 59.734 57.143 7.39 11.44 45.13 4.04
807 1531 0.878416 GGATCCGACTCTGATCGAGG 59.122 60.000 15.68 3.41 45.13 4.63
808 1532 0.239879 GATCCGACTCTGATCGAGGC 59.760 60.000 15.68 12.79 45.13 4.70
921 1686 0.238553 GCGCTTTGAGTTCCTGGTTC 59.761 55.000 0.00 0.00 0.00 3.62
943 1725 0.992802 CGTTGGCGAAAGAGTAGAGC 59.007 55.000 0.00 0.00 41.33 4.09
944 1726 0.992802 GTTGGCGAAAGAGTAGAGCG 59.007 55.000 0.00 0.00 0.00 5.03
945 1727 0.108804 TTGGCGAAAGAGTAGAGCGG 60.109 55.000 0.00 0.00 0.00 5.52
946 1728 1.878975 GGCGAAAGAGTAGAGCGGC 60.879 63.158 0.00 0.00 40.17 6.53
948 1730 1.142778 GCGAAAGAGTAGAGCGGCTG 61.143 60.000 7.50 0.00 0.00 4.85
949 1731 0.526524 CGAAAGAGTAGAGCGGCTGG 60.527 60.000 7.50 0.00 0.00 4.85
965 1755 4.176752 GGGTGATCCTCGGGCCAC 62.177 72.222 4.39 0.00 0.00 5.01
1339 2320 9.394767 TCATCGGTAAGTACTACTATGTTGTAA 57.605 33.333 0.00 0.00 31.33 2.41
1446 2432 7.885714 CGTTTGTTTTATTAATAACTTGCAGCG 59.114 33.333 7.43 4.63 0.00 5.18
1559 2545 0.941542 GCAAGCGTGTTGGACAGTAA 59.058 50.000 0.59 0.00 0.00 2.24
1675 2666 4.069232 CGCTCGTGGCCTTCTCCA 62.069 66.667 3.32 0.00 37.74 3.86
1676 2667 2.347490 GCTCGTGGCCTTCTCCAA 59.653 61.111 3.32 0.00 37.96 3.53
1968 2966 0.863144 CCCGAACCAACAACTACACG 59.137 55.000 0.00 0.00 0.00 4.49
2013 3011 1.135689 GGTGCATCCATTCACAACGAC 60.136 52.381 0.00 0.00 35.04 4.34
2026 3024 5.553290 TCACAACGACAATCTGAAACAAA 57.447 34.783 0.00 0.00 0.00 2.83
2088 3086 4.328536 ACACCGCCTTTGTCAATATTGTA 58.671 39.130 14.97 3.51 0.00 2.41
2181 3192 9.173021 CTAATTAGATGGGTTTGATTGTGTACA 57.827 33.333 6.64 0.00 0.00 2.90
2257 3279 3.243401 GCTCGGAGTTGTCCAAACAATTT 60.243 43.478 6.90 0.00 46.58 1.82
2447 3469 5.948742 ACAATTGGAAAAACCCTTGAAGA 57.051 34.783 10.83 0.00 38.00 2.87
2462 3484 6.486993 ACCCTTGAAGAAGTTTGTAGATCAAC 59.513 38.462 0.00 0.00 35.61 3.18
2497 3519 3.861113 GGTTTCATATGTCGTTGTAGCGA 59.139 43.478 1.90 0.00 38.68 4.93
2505 3527 4.320667 TGTCGTTGTAGCGATTTTCATG 57.679 40.909 0.00 0.00 43.07 3.07
2705 3759 4.625742 CCTATATGCGGTTCAATAAGGTCG 59.374 45.833 0.00 0.00 0.00 4.79
2790 3850 3.964031 AGGGATGACAGGTATCTTGTCTC 59.036 47.826 11.89 7.71 34.03 3.36
2822 3883 9.586732 TCAGGATTAAGATAATTTTACCCATGG 57.413 33.333 4.14 4.14 0.00 3.66
2862 3924 3.069158 CCGACCCGAAGTATGGTTTAGAT 59.931 47.826 0.00 0.00 34.20 1.98
3003 4097 3.101437 TCACTAACCTATCGCCTTTCCA 58.899 45.455 0.00 0.00 0.00 3.53
3079 4173 6.097356 TGCGGTTGATTCGATTAGTATATCC 58.903 40.000 0.00 0.00 0.00 2.59
3206 4464 2.690786 TCCTTTACAAGCGCGTACATT 58.309 42.857 8.43 0.00 0.00 2.71
3237 4495 1.834263 GACATAGTCAGCCTCCCTTGT 59.166 52.381 0.00 0.00 32.09 3.16
3253 4511 3.492482 CCCTTGTTTTCAACCGCATTTCT 60.492 43.478 0.00 0.00 35.77 2.52
3258 4516 0.871722 TTCAACCGCATTTCTGTCCG 59.128 50.000 0.00 0.00 0.00 4.79
3431 4695 1.007734 GGACACACGCGAGAGACAA 60.008 57.895 15.93 0.00 0.00 3.18
3499 4763 4.883585 TGCTGATAAGTTGACAATCCATCC 59.116 41.667 0.00 0.00 0.00 3.51
3538 4802 0.508641 CAAAACGAGACAGCTCACCG 59.491 55.000 0.00 0.00 41.36 4.94
3574 4841 1.365633 GGCCATCCTCTAGCTCACG 59.634 63.158 0.00 0.00 0.00 4.35
3585 4852 1.261089 CTAGCTCACGTACGGCTCTAC 59.739 57.143 21.06 3.75 37.50 2.59
3606 4874 4.647964 ACTTGCGTAGAAATTTACATGCG 58.352 39.130 9.80 7.20 0.00 4.73
3625 5215 3.055458 TGCGACCTAACAAGAATGGATGA 60.055 43.478 0.00 0.00 0.00 2.92
3629 5219 6.428159 GCGACCTAACAAGAATGGATGAATAT 59.572 38.462 0.00 0.00 0.00 1.28
3645 5235 4.437967 TGAATATGGAGCCATGGAGGATA 58.562 43.478 18.40 5.81 41.22 2.59
3651 5241 2.157738 GAGCCATGGAGGATAATGTGC 58.842 52.381 18.40 0.00 41.22 4.57
3655 5245 3.824133 CCATGGAGGATAATGTGCAGAA 58.176 45.455 5.56 0.00 41.22 3.02
3659 5249 5.282055 TGGAGGATAATGTGCAGAACTAG 57.718 43.478 0.00 0.00 0.00 2.57
3660 5250 4.962362 TGGAGGATAATGTGCAGAACTAGA 59.038 41.667 0.00 0.00 0.00 2.43
3662 5252 5.755861 GGAGGATAATGTGCAGAACTAGAAC 59.244 44.000 0.00 0.00 0.00 3.01
3663 5253 6.299805 AGGATAATGTGCAGAACTAGAACA 57.700 37.500 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.596477 GGATCACTCGGCTGCATCC 60.596 63.158 0.50 0.00 0.00 3.51
2 3 1.953138 CGGATCACTCGGCTGCATC 60.953 63.158 0.50 0.00 0.00 3.91
4 5 4.819761 GCGGATCACTCGGCTGCA 62.820 66.667 0.50 0.00 42.66 4.41
11 12 2.650813 AATCAGCCGGCGGATCACTC 62.651 60.000 36.75 10.96 30.89 3.51
12 13 2.735772 AATCAGCCGGCGGATCACT 61.736 57.895 36.75 22.16 30.89 3.41
13 14 2.203070 AATCAGCCGGCGGATCAC 60.203 61.111 36.75 12.27 30.89 3.06
14 15 2.203056 CAATCAGCCGGCGGATCA 60.203 61.111 36.75 11.82 30.89 2.92
15 16 2.377628 TACCAATCAGCCGGCGGATC 62.378 60.000 36.75 13.58 30.89 3.36
16 17 1.978455 TTACCAATCAGCCGGCGGAT 61.978 55.000 32.78 32.78 32.50 4.18
17 18 2.661066 TTACCAATCAGCCGGCGGA 61.661 57.895 31.28 31.28 0.00 5.54
18 19 2.124901 TTACCAATCAGCCGGCGG 60.125 61.111 24.35 24.35 0.00 6.13
19 20 1.095228 ATGTTACCAATCAGCCGGCG 61.095 55.000 23.20 16.49 0.00 6.46
20 21 1.102978 AATGTTACCAATCAGCCGGC 58.897 50.000 21.89 21.89 0.00 6.13
21 22 3.428862 GGAAAATGTTACCAATCAGCCGG 60.429 47.826 0.00 0.00 0.00 6.13
22 23 3.443681 AGGAAAATGTTACCAATCAGCCG 59.556 43.478 0.00 0.00 0.00 5.52
23 24 4.706962 AGAGGAAAATGTTACCAATCAGCC 59.293 41.667 0.00 0.00 0.00 4.85
24 25 5.904362 AGAGGAAAATGTTACCAATCAGC 57.096 39.130 0.00 0.00 0.00 4.26
25 26 8.359642 TCAAAAGAGGAAAATGTTACCAATCAG 58.640 33.333 0.00 0.00 0.00 2.90
26 27 8.243961 TCAAAAGAGGAAAATGTTACCAATCA 57.756 30.769 0.00 0.00 0.00 2.57
27 28 9.196552 CTTCAAAAGAGGAAAATGTTACCAATC 57.803 33.333 0.00 0.00 0.00 2.67
28 29 7.657354 GCTTCAAAAGAGGAAAATGTTACCAAT 59.343 33.333 0.00 0.00 0.00 3.16
29 30 6.983890 GCTTCAAAAGAGGAAAATGTTACCAA 59.016 34.615 0.00 0.00 0.00 3.67
30 31 6.097554 TGCTTCAAAAGAGGAAAATGTTACCA 59.902 34.615 0.00 0.00 0.00 3.25
31 32 6.512297 TGCTTCAAAAGAGGAAAATGTTACC 58.488 36.000 0.00 0.00 0.00 2.85
32 33 8.419076 TTTGCTTCAAAAGAGGAAAATGTTAC 57.581 30.769 0.00 0.00 32.57 2.50
33 34 7.224557 GCTTTGCTTCAAAAGAGGAAAATGTTA 59.775 33.333 0.99 0.00 39.12 2.41
34 35 6.037500 GCTTTGCTTCAAAAGAGGAAAATGTT 59.962 34.615 0.99 0.00 39.12 2.71
35 36 5.525012 GCTTTGCTTCAAAAGAGGAAAATGT 59.475 36.000 0.99 0.00 39.12 2.71
36 37 5.756833 AGCTTTGCTTCAAAAGAGGAAAATG 59.243 36.000 0.99 0.00 39.12 2.32
37 38 5.922053 AGCTTTGCTTCAAAAGAGGAAAAT 58.078 33.333 0.99 0.00 39.12 1.82
38 39 5.343307 AGCTTTGCTTCAAAAGAGGAAAA 57.657 34.783 0.99 0.00 39.12 2.29
39 40 4.498009 CGAGCTTTGCTTCAAAAGAGGAAA 60.498 41.667 0.99 0.00 39.88 3.13
40 41 3.003689 CGAGCTTTGCTTCAAAAGAGGAA 59.996 43.478 0.99 0.00 39.88 3.36
41 42 2.549754 CGAGCTTTGCTTCAAAAGAGGA 59.450 45.455 0.99 0.00 39.88 3.71
42 43 2.351157 CCGAGCTTTGCTTCAAAAGAGG 60.351 50.000 0.99 0.00 39.88 3.69
43 44 2.291741 ACCGAGCTTTGCTTCAAAAGAG 59.708 45.455 0.99 0.00 39.88 2.85
44 45 2.297701 ACCGAGCTTTGCTTCAAAAGA 58.702 42.857 0.99 0.00 39.88 2.52
45 46 2.781945 ACCGAGCTTTGCTTCAAAAG 57.218 45.000 0.00 0.00 39.88 2.27
57 58 3.256631 TCTTACCGTTAAGAAACCGAGCT 59.743 43.478 0.00 0.00 40.70 4.09
62 63 9.390795 GAAAAGAAATCTTACCGTTAAGAAACC 57.609 33.333 6.52 0.00 45.52 3.27
69 70 8.234546 GCATGAAGAAAAGAAATCTTACCGTTA 58.765 33.333 0.00 0.00 37.26 3.18
95 97 8.575649 ACCATGTATTTTACTCCAAACTAAGG 57.424 34.615 0.00 0.00 0.00 2.69
122 124 0.953960 CCACGGCCACTTTCTGTACC 60.954 60.000 2.24 0.00 0.00 3.34
134 136 0.534203 TGAACTGAACTTCCACGGCC 60.534 55.000 0.00 0.00 0.00 6.13
155 158 6.138761 CGGAAATGCTAGAATAAGTTGATGC 58.861 40.000 0.00 0.00 0.00 3.91
232 236 3.427503 GGTATTGCCTTGAAATGGTGTCG 60.428 47.826 0.00 0.00 32.80 4.35
347 457 1.338200 GCATGAGGACTTGTTCGGTCT 60.338 52.381 0.00 0.00 34.47 3.85
352 462 2.548057 TGTTTCGCATGAGGACTTGTTC 59.452 45.455 0.00 0.00 0.00 3.18
367 477 5.342806 TGCTCATAAGAAACTGTGTTTCG 57.657 39.130 14.80 4.29 33.86 3.46
391 505 5.407387 GTCATACTTGAACAGGAAAACGCTA 59.593 40.000 0.00 0.00 32.48 4.26
395 509 4.083484 CCGGTCATACTTGAACAGGAAAAC 60.083 45.833 0.00 0.00 39.72 2.43
425 585 0.315251 GGGGCTCTTCAAAACAGCAC 59.685 55.000 0.00 0.00 35.68 4.40
477 641 0.716108 GCTCAACGTTGTCCTCGATG 59.284 55.000 26.47 9.64 33.60 3.84
485 649 0.531090 TTGTAGCGGCTCAACGTTGT 60.531 50.000 26.47 9.92 35.98 3.32
497 661 3.902150 TCTGTCTTGAGTCTTTGTAGCG 58.098 45.455 0.00 0.00 0.00 4.26
507 671 3.735237 ACGTTGTGATCTGTCTTGAGT 57.265 42.857 0.00 0.00 0.00 3.41
534 710 1.227674 CCCTAGTTGGAGCCATCGC 60.228 63.158 0.00 0.00 38.35 4.58
549 733 0.475044 TTGTTGTTAACCTCCGCCCT 59.525 50.000 2.48 0.00 0.00 5.19
565 750 0.109913 GGGGTTCTCTCCGGTTTTGT 59.890 55.000 0.00 0.00 0.00 2.83
669 894 0.346932 TGCCCTCTTTCCCCTCCTAT 59.653 55.000 0.00 0.00 0.00 2.57
670 895 0.346932 ATGCCCTCTTTCCCCTCCTA 59.653 55.000 0.00 0.00 0.00 2.94
748 1017 5.221342 ACGGATTGACCAGCAAAACAAATTA 60.221 36.000 0.00 0.00 40.48 1.40
751 1020 2.428890 ACGGATTGACCAGCAAAACAAA 59.571 40.909 0.00 0.00 40.48 2.83
780 1504 0.613292 AGAGTCGGATCCACAGCACT 60.613 55.000 13.41 4.84 0.00 4.40
898 1658 0.239347 CAGGAACTCAAAGCGCTTGG 59.761 55.000 25.80 22.25 34.60 3.61
943 1725 4.227134 CCGAGGATCACCCAGCCG 62.227 72.222 0.00 0.00 37.41 5.52
944 1726 3.866582 CCCGAGGATCACCCAGCC 61.867 72.222 0.00 0.00 37.41 4.85
945 1727 4.554036 GCCCGAGGATCACCCAGC 62.554 72.222 0.00 0.00 37.41 4.85
946 1728 3.866582 GGCCCGAGGATCACCCAG 61.867 72.222 0.00 0.00 37.41 4.45
948 1730 4.176752 GTGGCCCGAGGATCACCC 62.177 72.222 0.00 0.00 36.73 4.61
949 1731 4.176752 GGTGGCCCGAGGATCACC 62.177 72.222 0.00 14.49 39.71 4.02
965 1755 1.001597 GGCGGATCGTTCTACTACTGG 60.002 57.143 0.00 0.00 0.00 4.00
1339 2320 7.325725 ACAGAGTACCTTTTTAGGGTAACAT 57.674 36.000 0.00 0.00 40.47 2.71
1340 2321 6.752285 ACAGAGTACCTTTTTAGGGTAACA 57.248 37.500 0.00 0.00 40.47 2.41
1446 2432 1.064463 TCCTCCAATCCCAGCATTGTC 60.064 52.381 0.00 0.00 32.61 3.18
1675 2666 4.139786 CTGGTGCCTGCATAGTCATTATT 58.860 43.478 0.00 0.00 0.00 1.40
1676 2667 3.748083 CTGGTGCCTGCATAGTCATTAT 58.252 45.455 0.00 0.00 0.00 1.28
1721 2712 3.996363 TGCGGATATGATACTCACATTGC 59.004 43.478 0.00 0.00 0.00 3.56
1968 2966 6.362283 CCAAGTTTCCAAAAATATCACACGTC 59.638 38.462 0.00 0.00 0.00 4.34
2039 3037 5.744345 ACGTCGATGATGTAGACATTCTTTC 59.256 40.000 12.58 0.00 36.57 2.62
2040 3038 5.516696 CACGTCGATGATGTAGACATTCTTT 59.483 40.000 12.58 0.00 36.57 2.52
2088 3086 1.825105 ACATACCTGCCCCATGATCT 58.175 50.000 0.00 0.00 0.00 2.75
2359 3381 6.558909 GTCCCAATAGAAGAATTTGCTTGAG 58.441 40.000 0.00 0.00 0.00 3.02
2447 3469 7.097834 GCTACCTAGTGTTGATCTACAAACTT 58.902 38.462 11.64 1.70 40.36 2.66
2462 3484 3.914426 ATGAAACCTGGCTACCTAGTG 57.086 47.619 0.00 0.00 0.00 2.74
2547 3569 8.559536 CAGAAAGTACAGTCTTTGAAATGCTTA 58.440 33.333 0.00 0.00 37.70 3.09
2548 3570 7.420800 CAGAAAGTACAGTCTTTGAAATGCTT 58.579 34.615 0.00 0.00 37.70 3.91
2627 3674 7.984422 TCTTTATTGTAGATGTGCCATATGG 57.016 36.000 18.07 18.07 38.53 2.74
2657 3704 3.068307 AGCACTCGGTTTGTATAGCTAGG 59.932 47.826 0.00 0.00 0.00 3.02
2818 3879 3.244561 GGTACCACAGATACCCATCCATG 60.245 52.174 7.15 0.00 36.80 3.66
2819 3880 2.979678 GGTACCACAGATACCCATCCAT 59.020 50.000 7.15 0.00 36.80 3.41
2820 3881 2.404559 GGTACCACAGATACCCATCCA 58.595 52.381 7.15 0.00 36.80 3.41
2862 3924 8.561212 AGCGTTGTACATGAACATAAAAACTTA 58.439 29.630 0.00 0.00 0.00 2.24
2976 4070 2.159085 GGCGATAGGTTAGTGAACTGCT 60.159 50.000 0.00 0.00 35.74 4.24
3003 4097 1.004277 TGCGAGGAAAAAGGCCACTAT 59.996 47.619 5.01 0.00 0.00 2.12
3079 4173 5.126061 AGCTAGAAAACAAGCCCATACAATG 59.874 40.000 0.00 0.00 39.64 2.82
3206 4464 4.502087 GGCTGACTATGTCTATGTGCATCA 60.502 45.833 0.00 0.00 33.15 3.07
3237 4495 2.287308 CGGACAGAAATGCGGTTGAAAA 60.287 45.455 0.00 0.00 0.00 2.29
3253 4511 1.070914 TCAATGTAGCAACCACGGACA 59.929 47.619 0.00 0.00 0.00 4.02
3258 4516 2.228582 TGTGCATCAATGTAGCAACCAC 59.771 45.455 4.24 0.00 40.35 4.16
3375 4637 4.201910 TGCATCTTTTTACTGCCGCTAATC 60.202 41.667 0.00 0.00 35.02 1.75
3431 4695 8.868522 TTTATCTGACTGGTTCAATCAAAGAT 57.131 30.769 0.00 0.00 32.21 2.40
3499 4763 3.143728 TGATTGCTTCGATGGATGGATG 58.856 45.455 0.00 0.00 0.00 3.51
3538 4802 2.165301 CGTCTCCGGCCATCGTTTC 61.165 63.158 2.24 0.00 37.11 2.78
3563 4830 0.305313 GAGCCGTACGTGAGCTAGAG 59.695 60.000 15.91 0.00 36.87 2.43
3606 4874 7.939039 TCCATATTCATCCATTCTTGTTAGGTC 59.061 37.037 0.00 0.00 0.00 3.85
3625 5215 5.254737 ACATTATCCTCCATGGCTCCATATT 59.745 40.000 6.96 0.00 34.91 1.28
3629 5219 2.107031 CACATTATCCTCCATGGCTCCA 59.893 50.000 6.96 0.00 35.26 3.86


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

AutoCloner maintained by Alex Coulton.