Multiple sequence alignment - TraesCS6B01G401800

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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 TraesCS6B01G401800 chr6B 100.000 2456 0 0 1 2456 678176275 678173820 0.000000e+00 4536.0
1 TraesCS6B01G401800 chr6B 83.690 1680 161 47 125 1755 678358385 678356770 0.000000e+00 1480.0
2 TraesCS6B01G401800 chr6B 84.304 1236 111 37 675 1879 678091863 678093046 0.000000e+00 1131.0
3 TraesCS6B01G401800 chr6B 84.947 1136 97 43 551 1654 677044608 677045701 0.000000e+00 1083.0
4 TraesCS6B01G401800 chr6B 82.815 1286 122 48 282 1524 678543934 678542705 0.000000e+00 1059.0
5 TraesCS6B01G401800 chr6B 80.383 1463 142 71 700 2110 676864992 676866361 0.000000e+00 977.0
6 TraesCS6B01G401800 chr6B 87.288 708 61 18 978 1659 677087709 677088413 0.000000e+00 782.0
7 TraesCS6B01G401800 chr6B 88.397 655 49 15 32 672 678091176 678091817 0.000000e+00 763.0
8 TraesCS6B01G401800 chr6B 86.297 686 56 18 551 1215 677335949 677336617 0.000000e+00 712.0
9 TraesCS6B01G401800 chr6B 88.165 583 52 9 269 838 677087110 677087688 0.000000e+00 678.0
10 TraesCS6B01G401800 chr6B 88.686 548 44 12 269 803 677777312 677777854 0.000000e+00 652.0
11 TraesCS6B01G401800 chr6B 88.686 548 45 11 269 803 677909592 677910135 0.000000e+00 652.0
12 TraesCS6B01G401800 chr6B 89.463 484 36 11 269 741 676864595 676865074 4.520000e-167 597.0
13 TraesCS6B01G401800 chr6B 81.304 690 74 24 1736 2387 677045747 677046419 2.180000e-140 508.0
14 TraesCS6B01G401800 chr6B 78.848 851 87 43 327 1144 676729593 676730383 2.840000e-134 488.0
15 TraesCS6B01G401800 chr6B 85.280 428 45 13 1217 1632 676537942 676538363 2.260000e-115 425.0
16 TraesCS6B01G401800 chr6B 87.539 321 26 10 1219 1535 676492314 676492624 2.320000e-95 359.0
17 TraesCS6B01G401800 chr6B 79.242 501 47 33 1409 1880 677336679 677337151 1.850000e-76 296.0
18 TraesCS6B01G401800 chr6B 95.556 180 7 1 32 211 677079528 677079706 1.110000e-73 287.0
19 TraesCS6B01G401800 chr6B 95.000 180 8 1 32 211 677906572 677906750 5.170000e-72 281.0
20 TraesCS6B01G401800 chr6B 94.444 180 9 1 32 211 676859245 676859423 2.410000e-70 276.0
21 TraesCS6B01G401800 chr6B 94.915 177 8 1 32 208 677774464 677774639 2.410000e-70 276.0
22 TraesCS6B01G401800 chr6B 89.881 168 13 3 2220 2387 677777946 677778109 1.910000e-51 213.0
23 TraesCS6B01G401800 chr6B 89.286 168 14 3 2220 2387 677910227 677910390 8.900000e-50 207.0
24 TraesCS6B01G401800 chr6B 84.404 218 23 6 2173 2387 678093104 678093313 1.150000e-48 204.0
25 TraesCS6B01G401800 chr6A 86.894 1526 115 32 158 1641 593990983 593992465 0.000000e+00 1631.0
26 TraesCS6B01G401800 chr6A 84.945 1541 114 50 159 1642 594252830 594254309 0.000000e+00 1452.0
27 TraesCS6B01G401800 chr6A 81.348 1973 182 83 32 1882 594320811 594318903 0.000000e+00 1434.0
28 TraesCS6B01G401800 chr6A 85.363 895 77 27 796 1659 594366468 594365597 0.000000e+00 878.0
29 TraesCS6B01G401800 chr6A 79.379 805 95 38 403 1177 593928800 593929563 3.650000e-138 501.0
30 TraesCS6B01G401800 chr6A 83.195 482 48 18 1219 1670 593929569 593930047 6.320000e-111 411.0
31 TraesCS6B01G401800 chr6A 81.265 427 49 18 327 742 569677952 569678358 1.420000e-82 316.0
32 TraesCS6B01G401800 chr6A 83.285 347 26 11 1936 2277 594318658 594318339 8.590000e-75 291.0
33 TraesCS6B01G401800 chr6D 82.687 1675 156 56 67 1654 447739263 447737636 0.000000e+00 1363.0
34 TraesCS6B01G401800 chr6D 87.896 884 73 11 64 936 447277243 447278103 0.000000e+00 1009.0
35 TraesCS6B01G401800 chr6D 87.925 853 54 21 844 1659 447278126 447278966 0.000000e+00 959.0
36 TraesCS6B01G401800 chr6D 82.692 468 54 13 1219 1659 447213421 447213888 8.230000e-105 390.0
37 TraesCS6B01G401800 chr6D 87.311 331 32 8 1219 1547 447761450 447761128 1.070000e-98 370.0
38 TraesCS6B01G401800 chr6D 80.360 555 48 26 1769 2272 447279033 447279577 4.990000e-97 364.0
39 TraesCS6B01G401800 chr6D 78.347 605 78 27 1217 1819 447444714 447445267 2.340000e-90 342.0
40 TraesCS6B01G401800 chr6D 76.271 177 27 13 2091 2266 446901524 446901362 2.020000e-11 80.5
41 TraesCS6B01G401800 chr7D 100.000 30 0 0 1 30 586833218 586833189 3.410000e-04 56.5


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 TraesCS6B01G401800 chr6B 678173820 678176275 2455 True 4536.000000 4536 100.000000 1 2456 1 chr6B.!!$R1 2455
1 TraesCS6B01G401800 chr6B 678356770 678358385 1615 True 1480.000000 1480 83.690000 125 1755 1 chr6B.!!$R2 1630
2 TraesCS6B01G401800 chr6B 678542705 678543934 1229 True 1059.000000 1059 82.815000 282 1524 1 chr6B.!!$R3 1242
3 TraesCS6B01G401800 chr6B 677044608 677046419 1811 False 795.500000 1083 83.125500 551 2387 2 chr6B.!!$F7 1836
4 TraesCS6B01G401800 chr6B 676864595 676866361 1766 False 787.000000 977 84.923000 269 2110 2 chr6B.!!$F6 1841
5 TraesCS6B01G401800 chr6B 677087110 677088413 1303 False 730.000000 782 87.726500 269 1659 2 chr6B.!!$F8 1390
6 TraesCS6B01G401800 chr6B 678091176 678093313 2137 False 699.333333 1131 85.701667 32 2387 3 chr6B.!!$F12 2355
7 TraesCS6B01G401800 chr6B 677335949 677337151 1202 False 504.000000 712 82.769500 551 1880 2 chr6B.!!$F9 1329
8 TraesCS6B01G401800 chr6B 676729593 676730383 790 False 488.000000 488 78.848000 327 1144 1 chr6B.!!$F3 817
9 TraesCS6B01G401800 chr6B 677774464 677778109 3645 False 380.333333 652 91.160667 32 2387 3 chr6B.!!$F10 2355
10 TraesCS6B01G401800 chr6B 677906572 677910390 3818 False 380.000000 652 90.990667 32 2387 3 chr6B.!!$F11 2355
11 TraesCS6B01G401800 chr6A 593990983 593992465 1482 False 1631.000000 1631 86.894000 158 1641 1 chr6A.!!$F2 1483
12 TraesCS6B01G401800 chr6A 594252830 594254309 1479 False 1452.000000 1452 84.945000 159 1642 1 chr6A.!!$F3 1483
13 TraesCS6B01G401800 chr6A 594365597 594366468 871 True 878.000000 878 85.363000 796 1659 1 chr6A.!!$R1 863
14 TraesCS6B01G401800 chr6A 594318339 594320811 2472 True 862.500000 1434 82.316500 32 2277 2 chr6A.!!$R2 2245
15 TraesCS6B01G401800 chr6A 593928800 593930047 1247 False 456.000000 501 81.287000 403 1670 2 chr6A.!!$F4 1267
16 TraesCS6B01G401800 chr6D 447737636 447739263 1627 True 1363.000000 1363 82.687000 67 1654 1 chr6D.!!$R2 1587
17 TraesCS6B01G401800 chr6D 447277243 447279577 2334 False 777.333333 1009 85.393667 64 2272 3 chr6D.!!$F3 2208
18 TraesCS6B01G401800 chr6D 447444714 447445267 553 False 342.000000 342 78.347000 1217 1819 1 chr6D.!!$F2 602

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
731 3743 0.179202 CAGAGACGACGAGCTCACTG 60.179 60.0 15.4 4.49 33.62 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 5819 0.106335 ATCCCTGCATCGCTCTGAAG 59.894 55.0 0.0 0.0 0.0 3.02 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
27 28 7.421530 GTCAACTGACTGAAATGTAGCTAAA 57.578 36.000 0.00 0.00 41.65 1.85
28 29 7.513968 GTCAACTGACTGAAATGTAGCTAAAG 58.486 38.462 0.00 0.00 41.65 1.85
29 30 7.171678 GTCAACTGACTGAAATGTAGCTAAAGT 59.828 37.037 0.00 0.00 41.65 2.66
30 31 8.364894 TCAACTGACTGAAATGTAGCTAAAGTA 58.635 33.333 0.00 0.00 0.00 2.24
73 85 1.001597 GCCGTCCCTCAAGATAGTACG 60.002 57.143 0.00 0.00 0.00 3.67
87 99 4.944930 AGATAGTACGACTGCTCTGAAAGT 59.055 41.667 0.00 0.00 33.76 2.66
171 183 5.120830 ACGAAGAAAAATCCTCTGTTCATCG 59.879 40.000 7.95 7.95 43.20 3.84
303 3113 4.631813 AGAAGAAAAATCCTCGGTTCATCG 59.368 41.667 0.00 0.00 0.00 3.84
377 3188 2.250939 CGTGCTTCAAGTTGCGGGA 61.251 57.895 0.00 0.00 0.00 5.14
379 3190 1.153066 TGCTTCAAGTTGCGGGACA 60.153 52.632 0.00 0.00 0.00 4.02
498 3313 2.172483 GAGGCGAGACACACCCACAT 62.172 60.000 0.00 0.00 0.00 3.21
508 3323 2.305928 CACACCCACATTCCAGAAACA 58.694 47.619 0.00 0.00 0.00 2.83
626 3564 7.086376 GTGTCTGCATTTTGTCACTCATTAAT 58.914 34.615 0.00 0.00 0.00 1.40
627 3565 7.596248 GTGTCTGCATTTTGTCACTCATTAATT 59.404 33.333 0.00 0.00 0.00 1.40
628 3566 8.791675 TGTCTGCATTTTGTCACTCATTAATTA 58.208 29.630 0.00 0.00 0.00 1.40
731 3743 0.179202 CAGAGACGACGAGCTCACTG 60.179 60.000 15.40 4.49 33.62 3.66
770 3787 1.899142 GAGGAAGAAGAGGCTCACTGT 59.101 52.381 18.26 0.00 0.00 3.55
771 3788 3.093057 GAGGAAGAAGAGGCTCACTGTA 58.907 50.000 18.26 0.00 0.00 2.74
829 3878 3.877508 CCAGGAATCGAATTGGGTCTTAC 59.122 47.826 0.00 0.00 0.00 2.34
891 3969 7.009631 CCTTCTATACAGCGATCGGAATTATTG 59.990 40.741 18.30 0.00 0.00 1.90
1317 4568 3.837570 GAACGAGCCCGGGTGGTTT 62.838 63.158 24.63 10.90 40.78 3.27
1320 4571 2.203437 GAGCCCGGGTGGTTTGTT 60.203 61.111 24.63 0.00 36.04 2.83
1326 4577 1.455959 CGGGTGGTTTGTTGGGGAA 60.456 57.895 0.00 0.00 0.00 3.97
1343 4594 0.447801 GAACACATGCATGACCGACC 59.552 55.000 32.75 12.24 0.00 4.79
1524 4790 1.599171 GCCGTCGACATGATGAGAGAG 60.599 57.143 17.16 0.00 35.48 3.20
1525 4791 1.943340 CCGTCGACATGATGAGAGAGA 59.057 52.381 17.16 0.00 35.48 3.10
1645 4994 2.090377 TATAGGCCGGGGAGGGAGAC 62.090 65.000 2.18 0.00 41.48 3.36
1655 5005 1.613630 GAGGGAGACAGAGGGGCAA 60.614 63.158 0.00 0.00 0.00 4.52
1659 5009 1.683319 GGGAGACAGAGGGGCAATTTC 60.683 57.143 0.00 0.00 0.00 2.17
1661 5034 2.555227 GGAGACAGAGGGGCAATTTCAA 60.555 50.000 0.00 0.00 0.00 2.69
1666 5039 2.629617 CAGAGGGGCAATTTCAACTTGT 59.370 45.455 0.00 0.00 0.00 3.16
1668 5041 1.070601 AGGGGCAATTTCAACTTGTGC 59.929 47.619 0.00 0.00 34.42 4.57
1672 5045 1.528161 GCAATTTCAACTTGTGCCTGC 59.472 47.619 0.00 0.00 0.00 4.85
1673 5046 2.804212 GCAATTTCAACTTGTGCCTGCT 60.804 45.455 0.00 0.00 0.00 4.24
1679 5063 0.679505 AACTTGTGCCTGCTCGAGTA 59.320 50.000 15.13 8.96 34.28 2.59
1681 5065 1.070134 ACTTGTGCCTGCTCGAGTAAA 59.930 47.619 15.13 0.00 33.81 2.01
1683 5067 2.472695 TGTGCCTGCTCGAGTAAATT 57.527 45.000 15.13 0.00 0.00 1.82
1685 5069 3.932822 TGTGCCTGCTCGAGTAAATTAA 58.067 40.909 15.13 0.00 0.00 1.40
1687 5071 4.941263 TGTGCCTGCTCGAGTAAATTAATT 59.059 37.500 15.13 0.00 0.00 1.40
1710 5094 9.448438 AATTATTAAGGAAAGGAAAACCATTGC 57.552 29.630 0.00 0.00 0.00 3.56
1723 5107 7.175990 AGGAAAACCATTGCTAATTAAACTCGA 59.824 33.333 0.00 0.00 0.00 4.04
1728 5113 6.821665 ACCATTGCTAATTAAACTCGAGCTAA 59.178 34.615 13.61 11.03 34.19 3.09
1792 5177 2.264480 CACCCGAATCGGTCTGCA 59.736 61.111 21.12 0.00 46.80 4.41
1851 5245 9.340695 TGAATACTAATTTCAGCGTCAAAATTG 57.659 29.630 11.49 0.00 36.17 2.32
1853 5247 9.691362 AATACTAATTTCAGCGTCAAAATTGTT 57.309 25.926 11.49 4.27 36.17 2.83
1859 5253 4.738124 TCAGCGTCAAAATTGTTGTCAAA 58.262 34.783 0.00 0.00 37.11 2.69
1921 5326 0.871722 TGCGCGCAGTACAAGAAAAT 59.128 45.000 33.09 0.00 0.00 1.82
2085 5691 2.414785 GGCAATGCCGACCCGATTT 61.415 57.895 9.14 0.00 39.62 2.17
2089 5695 0.541863 AATGCCGACCCGATTTCTCT 59.458 50.000 0.00 0.00 0.00 3.10
2120 5737 2.046314 CCCACCGACCCATCACAC 60.046 66.667 0.00 0.00 0.00 3.82
2121 5738 2.046314 CCACCGACCCATCACACC 60.046 66.667 0.00 0.00 0.00 4.16
2122 5739 2.747022 CACCGACCCATCACACCA 59.253 61.111 0.00 0.00 0.00 4.17
2147 5769 3.381908 TGTTGCTTTCATAAACCGGTTGT 59.618 39.130 23.08 13.50 0.00 3.32
2217 5843 1.153086 GAGCGATGCAGGGATGGTT 60.153 57.895 0.00 0.00 0.00 3.67
2231 5857 0.324943 ATGGTTAAGCTGGCACGAGT 59.675 50.000 6.19 0.00 0.00 4.18
2319 5947 2.528127 TTCACCCCTCCGCCTTGA 60.528 61.111 0.00 0.00 0.00 3.02
2353 5981 0.031721 ACCTCTGAACGTTCGACACC 59.968 55.000 22.48 0.00 0.00 4.16
2364 5992 2.041966 GTTCGACACCGTATAGCATCG 58.958 52.381 0.00 0.00 37.05 3.84
2394 6022 2.549064 CCGTAATGGCTGATCATGGA 57.451 50.000 0.00 0.00 0.00 3.41
2395 6023 2.420642 CCGTAATGGCTGATCATGGAG 58.579 52.381 0.00 0.00 0.00 3.86
2396 6024 2.224378 CCGTAATGGCTGATCATGGAGT 60.224 50.000 0.00 0.00 0.00 3.85
2397 6025 2.804527 CGTAATGGCTGATCATGGAGTG 59.195 50.000 0.00 0.00 0.00 3.51
2398 6026 2.359981 AATGGCTGATCATGGAGTGG 57.640 50.000 0.00 0.00 0.00 4.00
2399 6027 0.178998 ATGGCTGATCATGGAGTGGC 60.179 55.000 0.00 0.00 0.00 5.01
2400 6028 1.527844 GGCTGATCATGGAGTGGCC 60.528 63.158 0.00 0.00 37.10 5.36
2416 6044 2.361610 CCAGGGTGCCATCGCTTT 60.362 61.111 0.00 0.00 35.36 3.51
2417 6045 2.409870 CCAGGGTGCCATCGCTTTC 61.410 63.158 0.00 0.00 35.36 2.62
2418 6046 2.436646 AGGGTGCCATCGCTTTCG 60.437 61.111 0.00 0.00 35.36 3.46
2419 6047 4.179579 GGGTGCCATCGCTTTCGC 62.180 66.667 0.00 0.00 35.36 4.70
2420 6048 3.127533 GGTGCCATCGCTTTCGCT 61.128 61.111 0.00 0.00 35.36 4.93
2421 6049 1.813753 GGTGCCATCGCTTTCGCTA 60.814 57.895 0.00 0.00 35.36 4.26
2422 6050 1.366111 GGTGCCATCGCTTTCGCTAA 61.366 55.000 0.00 0.00 35.36 3.09
2423 6051 0.657840 GTGCCATCGCTTTCGCTAAT 59.342 50.000 0.00 0.00 35.36 1.73
2424 6052 0.937304 TGCCATCGCTTTCGCTAATC 59.063 50.000 0.00 0.00 35.36 1.75
2425 6053 0.235926 GCCATCGCTTTCGCTAATCC 59.764 55.000 0.00 0.00 35.26 3.01
2426 6054 0.508641 CCATCGCTTTCGCTAATCCG 59.491 55.000 0.00 0.00 35.26 4.18
2427 6055 0.508641 CATCGCTTTCGCTAATCCGG 59.491 55.000 0.00 0.00 35.26 5.14
2428 6056 0.104304 ATCGCTTTCGCTAATCCGGT 59.896 50.000 0.00 0.00 35.26 5.28
2429 6057 0.804544 TCGCTTTCGCTAATCCGGTG 60.805 55.000 0.00 0.00 35.26 4.94
2430 6058 1.082117 CGCTTTCGCTAATCCGGTGT 61.082 55.000 0.00 0.00 0.00 4.16
2431 6059 1.799917 CGCTTTCGCTAATCCGGTGTA 60.800 52.381 0.00 0.00 0.00 2.90
2432 6060 1.591619 GCTTTCGCTAATCCGGTGTAC 59.408 52.381 0.00 0.00 0.00 2.90
2433 6061 2.737679 GCTTTCGCTAATCCGGTGTACT 60.738 50.000 0.00 0.00 0.00 2.73
2434 6062 3.489738 GCTTTCGCTAATCCGGTGTACTA 60.490 47.826 0.00 0.00 0.00 1.82
2435 6063 4.795308 GCTTTCGCTAATCCGGTGTACTAT 60.795 45.833 0.00 0.00 0.00 2.12
2436 6064 4.494350 TTCGCTAATCCGGTGTACTATC 57.506 45.455 0.00 0.00 0.00 2.08
2437 6065 2.816087 TCGCTAATCCGGTGTACTATCC 59.184 50.000 0.00 0.00 0.00 2.59
2438 6066 2.413765 CGCTAATCCGGTGTACTATCCG 60.414 54.545 0.00 14.41 45.42 4.18
2439 6067 2.670509 GCTAATCCGGTGTACTATCCGC 60.671 54.545 15.43 0.00 44.63 5.54
2440 6068 1.700955 AATCCGGTGTACTATCCGCT 58.299 50.000 15.43 5.99 44.63 5.52
2441 6069 1.700955 ATCCGGTGTACTATCCGCTT 58.299 50.000 15.43 5.86 44.63 4.68
2442 6070 2.346766 TCCGGTGTACTATCCGCTTA 57.653 50.000 15.43 4.75 44.63 3.09
2443 6071 2.224606 TCCGGTGTACTATCCGCTTAG 58.775 52.381 15.43 6.04 44.63 2.18
2444 6072 1.335689 CCGGTGTACTATCCGCTTAGC 60.336 57.143 15.43 0.00 44.63 3.09
2445 6073 1.335810 CGGTGTACTATCCGCTTAGCA 59.664 52.381 4.70 0.00 40.28 3.49
2446 6074 2.030185 CGGTGTACTATCCGCTTAGCAT 60.030 50.000 4.70 0.00 40.28 3.79
2447 6075 3.576648 GGTGTACTATCCGCTTAGCATC 58.423 50.000 4.70 0.00 0.00 3.91
2448 6076 3.235195 GTGTACTATCCGCTTAGCATCG 58.765 50.000 4.70 0.00 0.00 3.84
2449 6077 2.251893 GTACTATCCGCTTAGCATCGC 58.748 52.381 4.70 0.00 0.00 4.58
2450 6078 0.673985 ACTATCCGCTTAGCATCGCA 59.326 50.000 4.70 0.00 0.00 5.10
2451 6079 1.063806 CTATCCGCTTAGCATCGCAC 58.936 55.000 4.70 0.00 0.00 5.34
2452 6080 0.663269 TATCCGCTTAGCATCGCACG 60.663 55.000 4.70 0.00 0.00 5.34
2453 6081 2.349969 ATCCGCTTAGCATCGCACGA 62.350 55.000 4.70 0.00 0.00 4.35
2454 6082 2.615618 CGCTTAGCATCGCACGAC 59.384 61.111 4.70 0.00 0.00 4.34
2455 6083 2.158330 CGCTTAGCATCGCACGACA 61.158 57.895 4.70 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.171678 ACTTTAGCTACATTTCAGTCAGTTGAC 59.828 37.037 4.09 4.09 45.08 3.18
4 5 7.217200 ACTTTAGCTACATTTCAGTCAGTTGA 58.783 34.615 0.00 0.00 0.00 3.18
5 6 7.426929 ACTTTAGCTACATTTCAGTCAGTTG 57.573 36.000 0.00 0.00 0.00 3.16
6 7 8.585881 TCTACTTTAGCTACATTTCAGTCAGTT 58.414 33.333 0.00 0.00 0.00 3.16
7 8 8.123639 TCTACTTTAGCTACATTTCAGTCAGT 57.876 34.615 0.00 0.00 0.00 3.41
8 9 7.704472 CCTCTACTTTAGCTACATTTCAGTCAG 59.296 40.741 0.00 0.00 0.00 3.51
9 10 7.178628 ACCTCTACTTTAGCTACATTTCAGTCA 59.821 37.037 0.00 0.00 0.00 3.41
10 11 7.489757 CACCTCTACTTTAGCTACATTTCAGTC 59.510 40.741 0.00 0.00 0.00 3.51
11 12 7.178628 TCACCTCTACTTTAGCTACATTTCAGT 59.821 37.037 0.00 0.00 0.00 3.41
12 13 7.548097 TCACCTCTACTTTAGCTACATTTCAG 58.452 38.462 0.00 0.00 0.00 3.02
13 14 7.476540 TCACCTCTACTTTAGCTACATTTCA 57.523 36.000 0.00 0.00 0.00 2.69
14 15 8.773404 TTTCACCTCTACTTTAGCTACATTTC 57.227 34.615 0.00 0.00 0.00 2.17
15 16 9.384764 GATTTCACCTCTACTTTAGCTACATTT 57.615 33.333 0.00 0.00 0.00 2.32
16 17 7.988028 GGATTTCACCTCTACTTTAGCTACATT 59.012 37.037 0.00 0.00 0.00 2.71
17 18 7.419172 GGGATTTCACCTCTACTTTAGCTACAT 60.419 40.741 0.00 0.00 0.00 2.29
18 19 6.127140 GGGATTTCACCTCTACTTTAGCTACA 60.127 42.308 0.00 0.00 0.00 2.74
19 20 6.127140 TGGGATTTCACCTCTACTTTAGCTAC 60.127 42.308 0.00 0.00 0.00 3.58
20 21 5.962031 TGGGATTTCACCTCTACTTTAGCTA 59.038 40.000 0.00 0.00 0.00 3.32
21 22 4.783227 TGGGATTTCACCTCTACTTTAGCT 59.217 41.667 0.00 0.00 0.00 3.32
22 23 5.099042 TGGGATTTCACCTCTACTTTAGC 57.901 43.478 0.00 0.00 0.00 3.09
23 24 5.880887 GGTTGGGATTTCACCTCTACTTTAG 59.119 44.000 0.00 0.00 0.00 1.85
24 25 5.570034 CGGTTGGGATTTCACCTCTACTTTA 60.570 44.000 0.00 0.00 0.00 1.85
25 26 4.663334 GGTTGGGATTTCACCTCTACTTT 58.337 43.478 0.00 0.00 0.00 2.66
26 27 3.307480 CGGTTGGGATTTCACCTCTACTT 60.307 47.826 0.00 0.00 0.00 2.24
27 28 2.236395 CGGTTGGGATTTCACCTCTACT 59.764 50.000 0.00 0.00 0.00 2.57
28 29 2.629051 CGGTTGGGATTTCACCTCTAC 58.371 52.381 0.00 0.00 0.00 2.59
29 30 1.065709 GCGGTTGGGATTTCACCTCTA 60.066 52.381 0.00 0.00 0.00 2.43
30 31 0.322546 GCGGTTGGGATTTCACCTCT 60.323 55.000 0.00 0.00 0.00 3.69
73 85 7.659652 ATTTTACTGTACTTTCAGAGCAGTC 57.340 36.000 0.00 0.00 40.39 3.51
123 135 5.975344 TCCTGCTCGTGATATTTTAAGTACG 59.025 40.000 0.00 0.00 0.00 3.67
171 183 2.976840 TTTCATGGCGCGCTCAACC 61.977 57.895 32.29 14.61 0.00 3.77
303 3113 3.982424 CTTCATGACGCGCGCAACC 62.982 63.158 32.58 18.97 0.00 3.77
498 3313 7.873719 TCTGTTTCTGTTTATGTTTCTGGAA 57.126 32.000 0.00 0.00 0.00 3.53
508 3323 7.573968 ACTTTCTGCTTCTGTTTCTGTTTAT 57.426 32.000 0.00 0.00 0.00 1.40
731 3743 3.264897 CCGCTCCGCTGCACATAC 61.265 66.667 0.00 0.00 0.00 2.39
793 3840 0.255890 TCCTGGCTGGTCAATTAGGC 59.744 55.000 10.44 0.00 39.67 3.93
931 4015 4.920640 AGCAGCAAGATACGTACATACT 57.079 40.909 0.00 0.00 0.00 2.12
932 4016 5.573282 CCATAGCAGCAAGATACGTACATAC 59.427 44.000 0.00 0.00 0.00 2.39
933 4017 5.709966 CCATAGCAGCAAGATACGTACATA 58.290 41.667 0.00 0.00 0.00 2.29
934 4018 4.560128 CCATAGCAGCAAGATACGTACAT 58.440 43.478 0.00 0.00 0.00 2.29
935 4019 3.798889 GCCATAGCAGCAAGATACGTACA 60.799 47.826 0.00 0.00 39.53 2.90
936 4020 2.731976 GCCATAGCAGCAAGATACGTAC 59.268 50.000 0.00 0.00 39.53 3.67
937 4021 2.364002 TGCCATAGCAGCAAGATACGTA 59.636 45.455 0.00 0.00 46.52 3.57
938 4022 1.138859 TGCCATAGCAGCAAGATACGT 59.861 47.619 0.00 0.00 46.52 3.57
1317 4568 0.967662 CATGCATGTGTTCCCCAACA 59.032 50.000 18.91 0.00 40.40 3.33
1320 4571 0.611618 GGTCATGCATGTGTTCCCCA 60.612 55.000 25.43 1.24 0.00 4.96
1326 4577 1.741401 CGGTCGGTCATGCATGTGT 60.741 57.895 25.43 0.00 0.00 3.72
1524 4790 1.052617 GCCCCTCCACCTCTCTAATC 58.947 60.000 0.00 0.00 0.00 1.75
1525 4791 0.760945 CGCCCCTCCACCTCTCTAAT 60.761 60.000 0.00 0.00 0.00 1.73
1619 4944 1.073923 CTCCCCGGCCTATAAATTGCT 59.926 52.381 0.00 0.00 0.00 3.91
1645 4994 2.629617 ACAAGTTGAAATTGCCCCTCTG 59.370 45.455 10.54 0.00 0.00 3.35
1655 5005 1.267806 CGAGCAGGCACAAGTTGAAAT 59.732 47.619 10.54 0.00 0.00 2.17
1659 5009 0.882042 ACTCGAGCAGGCACAAGTTG 60.882 55.000 13.61 0.00 0.00 3.16
1661 5034 0.679505 TTACTCGAGCAGGCACAAGT 59.320 50.000 13.61 0.00 0.00 3.16
1666 5039 7.801716 AATAATTAATTTACTCGAGCAGGCA 57.198 32.000 13.61 0.00 0.00 4.75
1685 5069 8.825774 AGCAATGGTTTTCCTTTCCTTAATAAT 58.174 29.630 0.00 0.00 41.38 1.28
1687 5071 7.790782 AGCAATGGTTTTCCTTTCCTTAATA 57.209 32.000 0.00 0.00 41.38 0.98
1710 5094 4.444720 CGCCCTTAGCTCGAGTTTAATTAG 59.555 45.833 15.13 6.46 40.39 1.73
1723 5107 1.153289 CTGCATCACGCCCTTAGCT 60.153 57.895 0.00 0.00 41.33 3.32
1728 5113 4.415150 CCCACTGCATCACGCCCT 62.415 66.667 0.00 0.00 41.33 5.19
1792 5177 0.322456 TGCGCCCTACTTGCTGAATT 60.322 50.000 4.18 0.00 0.00 2.17
1851 5245 7.010923 TGGTTTGTAATGCAAGAATTTGACAAC 59.989 33.333 0.00 0.00 38.47 3.32
1853 5247 6.577103 TGGTTTGTAATGCAAGAATTTGACA 58.423 32.000 0.00 0.00 38.47 3.58
1859 5253 4.281688 AGCACTGGTTTGTAATGCAAGAAT 59.718 37.500 0.00 0.00 38.79 2.40
1903 5308 2.093783 ACTATTTTCTTGTACTGCGCGC 59.906 45.455 27.26 27.26 0.00 6.86
1905 5310 9.582223 GATTAATACTATTTTCTTGTACTGCGC 57.418 33.333 0.00 0.00 0.00 6.09
1906 5311 9.779237 CGATTAATACTATTTTCTTGTACTGCG 57.221 33.333 0.00 0.00 0.00 5.18
2085 5691 4.426112 CGGCTGCACGCAGAGAGA 62.426 66.667 22.81 0.00 46.30 3.10
2120 5737 3.919804 CGGTTTATGAAAGCAACATGTGG 59.080 43.478 0.00 0.00 38.75 4.17
2121 5738 3.919804 CCGGTTTATGAAAGCAACATGTG 59.080 43.478 0.00 0.00 38.75 3.21
2122 5739 3.572255 ACCGGTTTATGAAAGCAACATGT 59.428 39.130 0.00 0.00 38.75 3.21
2147 5769 1.227823 CCGTCCTTTGAGTGTGCCA 60.228 57.895 0.00 0.00 0.00 4.92
2156 5778 1.880027 CTTTTCTGGGACCGTCCTTTG 59.120 52.381 17.27 7.87 36.57 2.77
2194 5819 0.106335 ATCCCTGCATCGCTCTGAAG 59.894 55.000 0.00 0.00 0.00 3.02
2217 5843 0.815734 GTCCTACTCGTGCCAGCTTA 59.184 55.000 0.00 0.00 0.00 3.09
2231 5857 1.376543 GTCACGTCGATCAGGTCCTA 58.623 55.000 0.00 0.00 0.00 2.94
2305 5933 1.497309 TTCAATCAAGGCGGAGGGGT 61.497 55.000 0.00 0.00 0.00 4.95
2306 5934 0.323360 TTTCAATCAAGGCGGAGGGG 60.323 55.000 0.00 0.00 0.00 4.79
2307 5935 0.811281 GTTTCAATCAAGGCGGAGGG 59.189 55.000 0.00 0.00 0.00 4.30
2319 5947 0.898326 GAGGTTGGCCGGGTTTCAAT 60.898 55.000 2.18 0.00 40.50 2.57
2353 5981 2.846550 CGACTTATGCCGATGCTATACG 59.153 50.000 0.00 0.00 38.71 3.06
2387 6015 1.620589 ACCCTGGCCACTCCATGAT 60.621 57.895 0.00 0.00 45.50 2.45
2388 6016 2.204136 ACCCTGGCCACTCCATGA 60.204 61.111 0.00 0.00 45.50 3.07
2389 6017 2.044650 CACCCTGGCCACTCCATG 60.045 66.667 0.00 0.00 45.50 3.66
2390 6018 4.052518 GCACCCTGGCCACTCCAT 62.053 66.667 0.00 0.00 45.50 3.41
2399 6027 2.361610 AAAGCGATGGCACCCTGG 60.362 61.111 1.50 0.00 43.41 4.45
2400 6028 2.753966 CGAAAGCGATGGCACCCTG 61.754 63.158 1.50 0.00 43.41 4.45
2401 6029 2.436646 CGAAAGCGATGGCACCCT 60.437 61.111 1.50 0.00 43.41 4.34
2413 6041 3.160777 AGTACACCGGATTAGCGAAAG 57.839 47.619 9.46 0.00 0.00 2.62
2414 6042 4.261741 GGATAGTACACCGGATTAGCGAAA 60.262 45.833 9.46 0.00 0.00 3.46
2415 6043 3.254166 GGATAGTACACCGGATTAGCGAA 59.746 47.826 9.46 0.00 0.00 4.70
2416 6044 2.816087 GGATAGTACACCGGATTAGCGA 59.184 50.000 9.46 0.00 0.00 4.93
2417 6045 2.413765 CGGATAGTACACCGGATTAGCG 60.414 54.545 9.46 0.00 44.59 4.26
2418 6046 3.213249 CGGATAGTACACCGGATTAGC 57.787 52.381 9.46 0.00 44.59 3.09
2426 6054 3.576648 GATGCTAAGCGGATAGTACACC 58.423 50.000 0.00 0.00 0.00 4.16
2427 6055 3.235195 CGATGCTAAGCGGATAGTACAC 58.765 50.000 0.00 0.00 0.00 2.90
2428 6056 2.351447 GCGATGCTAAGCGGATAGTACA 60.351 50.000 0.00 0.00 35.22 2.90
2429 6057 2.251893 GCGATGCTAAGCGGATAGTAC 58.748 52.381 0.00 0.00 35.22 2.73
2430 6058 1.883926 TGCGATGCTAAGCGGATAGTA 59.116 47.619 0.00 0.00 35.22 1.82
2431 6059 0.673985 TGCGATGCTAAGCGGATAGT 59.326 50.000 0.00 0.00 35.22 2.12
2432 6060 1.063806 GTGCGATGCTAAGCGGATAG 58.936 55.000 0.00 0.00 38.00 2.08
2433 6061 0.663269 CGTGCGATGCTAAGCGGATA 60.663 55.000 0.00 0.00 38.00 2.59
2434 6062 1.951130 CGTGCGATGCTAAGCGGAT 60.951 57.895 0.00 0.00 38.00 4.18
2435 6063 2.582226 CGTGCGATGCTAAGCGGA 60.582 61.111 0.00 0.00 35.22 5.54
2436 6064 2.582226 TCGTGCGATGCTAAGCGG 60.582 61.111 0.00 0.00 35.22 5.52
2437 6065 2.158330 TGTCGTGCGATGCTAAGCG 61.158 57.895 0.00 0.00 38.52 4.68
2438 6066 3.780693 TGTCGTGCGATGCTAAGC 58.219 55.556 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.