Multiple sequence alignment - TraesCS7B01G364200

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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 TraesCS7B01G364200 chr7B 100.000 2342 0 0 1 2342 627053839 627056180 0.000000e+00 4325.0
1 TraesCS7B01G364200 chr7B 95.050 101 3 2 1644 1744 697607628 697607726 8.660000e-35 158.0
2 TraesCS7B01G364200 chr7B 77.711 166 34 3 88 251 55030362 55030198 5.330000e-17 99.0
3 TraesCS7B01G364200 chr7A 93.573 918 37 15 759 1658 660408077 660408990 0.000000e+00 1349.0
4 TraesCS7B01G364200 chr7A 96.305 406 13 2 1937 2342 660409085 660409488 0.000000e+00 665.0
5 TraesCS7B01G364200 chr7A 84.652 632 64 19 156 760 660407348 660407973 1.200000e-167 599.0
6 TraesCS7B01G364200 chr7D 91.872 972 49 19 696 1647 571195927 571196888 0.000000e+00 1330.0
7 TraesCS7B01G364200 chr7D 91.085 516 21 8 1827 2342 571196949 571197439 0.000000e+00 675.0
8 TraesCS7B01G364200 chr7D 83.356 727 66 22 7 699 571194729 571195434 2.560000e-174 621.0
9 TraesCS7B01G364200 chr7D 84.946 93 9 5 540 627 431077332 431077424 3.210000e-14 89.8
10 TraesCS7B01G364200 chr6B 86.967 399 43 5 1944 2342 699028996 699029385 7.680000e-120 440.0
11 TraesCS7B01G364200 chr6B 90.783 217 18 2 1429 1645 699028438 699028652 2.940000e-74 289.0
12 TraesCS7B01G364200 chr2B 96.970 99 2 1 1654 1752 142245581 142245678 5.180000e-37 165.0
13 TraesCS7B01G364200 chr4B 97.872 94 2 0 1653 1746 262945760 262945667 1.860000e-36 163.0
14 TraesCS7B01G364200 chr4B 96.939 98 2 1 1655 1752 603516346 603516250 1.860000e-36 163.0
15 TraesCS7B01G364200 chr1B 94.393 107 4 2 1649 1754 660748387 660748492 1.860000e-36 163.0
16 TraesCS7B01G364200 chr1B 94.175 103 4 2 1649 1751 651554577 651554677 3.120000e-34 156.0
17 TraesCS7B01G364200 chr6D 92.035 113 7 2 1647 1759 216847373 216847263 8.660000e-35 158.0
18 TraesCS7B01G364200 chr3B 95.050 101 3 2 1646 1746 250576026 250575928 8.660000e-35 158.0
19 TraesCS7B01G364200 chr3B 94.595 37 2 0 540 576 38792591 38792627 9.040000e-05 58.4
20 TraesCS7B01G364200 chr1D 88.525 122 11 3 1657 1775 62864508 62864387 6.750000e-31 145.0
21 TraesCS7B01G364200 chr2D 90.566 53 2 2 115 165 378766472 378766523 1.500000e-07 67.6
22 TraesCS7B01G364200 chr3A 100.000 28 0 0 135 162 90295344 90295317 4.000000e-03 52.8


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 TraesCS7B01G364200 chr7B 627053839 627056180 2341 False 4325.000000 4325 100.000 1 2342 1 chr7B.!!$F1 2341
1 TraesCS7B01G364200 chr7A 660407348 660409488 2140 False 871.000000 1349 91.510 156 2342 3 chr7A.!!$F1 2186
2 TraesCS7B01G364200 chr7D 571194729 571197439 2710 False 875.333333 1330 88.771 7 2342 3 chr7D.!!$F2 2335
3 TraesCS7B01G364200 chr6B 699028438 699029385 947 False 364.500000 440 88.875 1429 2342 2 chr6B.!!$F1 913

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
637 679 0.033228 TGCATTTTGAAACCGGGCTG 59.967 50.0 6.32 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 2602 0.475475 CAAGGGCTGCATAGGGATGA 59.525 55.0 0.5 0.0 34.73 2.92 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
168 174 1.706305 AGGTTACCAAAACCGGATGGA 59.294 47.619 25.28 11.23 44.82 3.41
169 175 2.108601 AGGTTACCAAAACCGGATGGAA 59.891 45.455 25.28 15.11 44.82 3.53
177 183 4.519213 CAAAACCGGATGGAATAGTACCA 58.481 43.478 9.46 0.00 41.83 3.25
276 282 0.317020 GAATGGCAGCGGCGATAAAC 60.317 55.000 12.98 0.00 37.49 2.01
290 296 4.036262 GGCGATAAACAATGGAATACTGCA 59.964 41.667 0.00 0.00 0.00 4.41
327 333 1.607178 CAATGGCACCCAAGCTCCA 60.607 57.895 0.00 0.00 36.95 3.86
328 334 1.304713 AATGGCACCCAAGCTCCAG 60.305 57.895 0.00 0.00 36.95 3.86
335 341 4.120755 CCAAGCTCCAGGGGGCTC 62.121 72.222 14.17 0.00 37.87 4.70
441 461 9.608617 TGCGTGAATAAACGTTTGAAAATATTA 57.391 25.926 23.46 0.00 45.32 0.98
633 675 3.812053 TGGAAAATGCATTTTGAAACCGG 59.188 39.130 35.57 0.00 39.86 5.28
637 679 0.033228 TGCATTTTGAAACCGGGCTG 59.967 50.000 6.32 0.00 0.00 4.85
670 712 1.630244 CTCCAAAAGCTCGCACTCGG 61.630 60.000 0.00 0.00 36.13 4.63
686 728 0.604073 TCGGGTCGAAGTGCATACAA 59.396 50.000 0.00 0.00 31.06 2.41
691 733 3.627577 GGGTCGAAGTGCATACAATGATT 59.372 43.478 0.00 0.00 0.00 2.57
703 1242 6.094464 TGCATACAATGATTCATATAGGCTGC 59.906 38.462 19.69 14.89 0.00 5.25
768 1414 9.193806 ACATGAGCTTGGTTTCTATTGATAAAT 57.806 29.630 0.00 0.00 0.00 1.40
912 1565 3.059982 GGAAAAACCTGGGCTGCC 58.940 61.111 11.05 11.05 35.41 4.85
1085 1738 2.264480 CGCCACGATGGAGGTCAA 59.736 61.111 8.04 0.00 40.96 3.18
1366 2019 0.389166 CCACGTCTGCAGAGGAAGAC 60.389 60.000 36.00 16.16 45.01 3.01
1371 2031 2.244486 TCTGCAGAGGAAGACAGGAT 57.756 50.000 13.74 0.00 0.00 3.24
1372 2032 2.544721 TCTGCAGAGGAAGACAGGATT 58.455 47.619 13.74 0.00 0.00 3.01
1373 2033 2.235650 TCTGCAGAGGAAGACAGGATTG 59.764 50.000 13.74 0.00 0.00 2.67
1380 2040 5.032846 AGAGGAAGACAGGATTGGTAATCA 58.967 41.667 4.19 0.00 39.71 2.57
1381 2041 5.130145 AGAGGAAGACAGGATTGGTAATCAG 59.870 44.000 4.19 0.00 39.71 2.90
1383 2043 5.964477 AGGAAGACAGGATTGGTAATCAGTA 59.036 40.000 4.19 0.00 39.71 2.74
1384 2044 6.443849 AGGAAGACAGGATTGGTAATCAGTAA 59.556 38.462 4.19 0.00 39.71 2.24
1385 2045 7.127955 AGGAAGACAGGATTGGTAATCAGTAAT 59.872 37.037 4.19 0.00 39.71 1.89
1386 2046 7.442666 GGAAGACAGGATTGGTAATCAGTAATC 59.557 40.741 4.19 0.00 39.71 1.75
1387 2047 7.682787 AGACAGGATTGGTAATCAGTAATCT 57.317 36.000 4.19 0.00 39.71 2.40
1388 2048 8.095452 AGACAGGATTGGTAATCAGTAATCTT 57.905 34.615 4.19 0.00 39.71 2.40
1389 2049 7.989741 AGACAGGATTGGTAATCAGTAATCTTG 59.010 37.037 0.00 0.00 40.40 3.02
1391 2051 8.497745 ACAGGATTGGTAATCAGTAATCTTGAT 58.502 33.333 12.74 0.00 38.27 2.57
1415 2075 9.476202 GATATTTTAAATACAATGGTTCAGGCC 57.524 33.333 0.00 0.00 0.00 5.19
1416 2076 4.974368 TTAAATACAATGGTTCAGGCCG 57.026 40.909 0.00 0.00 0.00 6.13
1417 2077 1.762708 AATACAATGGTTCAGGCCGG 58.237 50.000 0.00 0.00 0.00 6.13
1419 2079 1.202099 TACAATGGTTCAGGCCGGGA 61.202 55.000 2.18 0.00 0.00 5.14
1429 2094 0.107017 CAGGCCGGGAGATGAACAAT 60.107 55.000 2.18 0.00 0.00 2.71
1443 2108 6.542821 AGATGAACAATTTAGAACAGGGTCA 58.457 36.000 0.00 0.00 0.00 4.02
1612 2281 3.160679 AGTAACCTCTGCAGGCAAAAT 57.839 42.857 15.13 0.00 45.05 1.82
1613 2282 3.500343 AGTAACCTCTGCAGGCAAAATT 58.500 40.909 15.13 3.10 45.05 1.82
1623 2292 3.888323 TGCAGGCAAAATTTACAGTGAGA 59.112 39.130 0.00 0.00 0.00 3.27
1671 2340 7.715266 ATTAACTATATACTCCCTCCGTTCC 57.285 40.000 0.00 0.00 0.00 3.62
1672 2341 4.736611 ACTATATACTCCCTCCGTTCCA 57.263 45.455 0.00 0.00 0.00 3.53
1673 2342 5.070823 ACTATATACTCCCTCCGTTCCAA 57.929 43.478 0.00 0.00 0.00 3.53
1674 2343 5.461327 ACTATATACTCCCTCCGTTCCAAA 58.539 41.667 0.00 0.00 0.00 3.28
1675 2344 5.901276 ACTATATACTCCCTCCGTTCCAAAA 59.099 40.000 0.00 0.00 0.00 2.44
1676 2345 5.906772 ATATACTCCCTCCGTTCCAAAAT 57.093 39.130 0.00 0.00 0.00 1.82
1677 2346 7.731688 ACTATATACTCCCTCCGTTCCAAAATA 59.268 37.037 0.00 0.00 0.00 1.40
1678 2347 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1679 2348 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1680 2349 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1681 2350 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1682 2351 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1683 2352 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1684 2353 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
1685 2354 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
1686 2355 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
1687 2356 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
1688 2357 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
1689 2358 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
1690 2359 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
1691 2360 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
1692 2361 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
1693 2362 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
1694 2363 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
1695 2364 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
1696 2365 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
1729 2398 8.960591 AGTACAAAGTTGGATCATCTATTTTGG 58.039 33.333 11.01 0.00 0.00 3.28
1730 2399 8.956426 GTACAAAGTTGGATCATCTATTTTGGA 58.044 33.333 11.01 2.87 0.00 3.53
1731 2400 8.421249 ACAAAGTTGGATCATCTATTTTGGAA 57.579 30.769 11.01 0.00 0.00 3.53
1732 2401 8.306761 ACAAAGTTGGATCATCTATTTTGGAAC 58.693 33.333 11.01 0.00 0.00 3.62
1733 2402 6.683974 AGTTGGATCATCTATTTTGGAACG 57.316 37.500 0.00 0.00 0.00 3.95
1734 2403 5.590259 AGTTGGATCATCTATTTTGGAACGG 59.410 40.000 0.00 0.00 0.00 4.44
1735 2404 5.366482 TGGATCATCTATTTTGGAACGGA 57.634 39.130 0.00 0.00 0.00 4.69
1736 2405 5.368145 TGGATCATCTATTTTGGAACGGAG 58.632 41.667 0.00 0.00 0.00 4.63
1737 2406 4.757149 GGATCATCTATTTTGGAACGGAGG 59.243 45.833 0.00 0.00 0.00 4.30
1738 2407 4.150897 TCATCTATTTTGGAACGGAGGG 57.849 45.455 0.00 0.00 0.00 4.30
1739 2408 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1740 2409 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1741 2410 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
1742 2411 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
1743 2412 4.966805 TCTATTTTGGAACGGAGGGAGTAT 59.033 41.667 0.00 0.00 0.00 2.12
1744 2413 6.138263 TCTATTTTGGAACGGAGGGAGTATA 58.862 40.000 0.00 0.00 0.00 1.47
1746 2415 5.703730 TTTTGGAACGGAGGGAGTATAAT 57.296 39.130 0.00 0.00 0.00 1.28
1750 2419 7.383156 TTGGAACGGAGGGAGTATAATATTT 57.617 36.000 0.00 0.00 0.00 1.40
1752 2421 7.447594 TGGAACGGAGGGAGTATAATATTTTC 58.552 38.462 0.00 0.00 0.00 2.29
1813 2616 6.579666 TGAAAAATATCATCCCTATGCAGC 57.420 37.500 0.00 0.00 32.76 5.25
1850 2705 5.565045 CGATAAGAGCCTATCACCCACTAAC 60.565 48.000 0.00 0.00 0.00 2.34
1872 2727 9.273016 CTAACTTCAAAGGATCAGACAAACTAA 57.727 33.333 0.00 0.00 0.00 2.24
1914 2769 9.787435 AGAACAGAAACACAAGTAAATATACCA 57.213 29.630 0.00 0.00 32.08 3.25
1954 2814 3.493524 CCCCAAAACGGCAAGTAAACATT 60.494 43.478 0.00 0.00 0.00 2.71
1958 2818 5.980715 CCAAAACGGCAAGTAAACATTTAGT 59.019 36.000 0.00 0.00 0.00 2.24
1982 2842 5.551760 AAGCAGACAGGTTCGATTAAATG 57.448 39.130 0.00 0.00 30.75 2.32
2132 2992 3.569849 TCCCGGTGGACAACATGT 58.430 55.556 0.00 0.00 35.03 3.21
2156 3016 0.899720 GGACACCGTCATGGAGGTAA 59.100 55.000 11.70 0.00 42.00 2.85
2210 3070 5.723672 TCACTCGAGTTCTCCAGTTAAAT 57.276 39.130 17.26 0.00 0.00 1.40
2267 3127 3.561313 GGCAAGGACCAAGAAGGATTACA 60.561 47.826 0.00 0.00 41.22 2.41
2308 3168 8.437575 TCTAGGAACAAAAGAATACAGAGGTTT 58.562 33.333 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.588143 ATCGTGTTTTCAAATTTTGTTCACA 57.412 28.000 8.89 7.29 0.00 3.58
144 150 4.566070 CCATCCGGTTTTGGTAACCTTCTA 60.566 45.833 0.00 0.00 38.15 2.10
153 159 3.732048 ACTATTCCATCCGGTTTTGGT 57.268 42.857 16.69 5.40 34.48 3.67
177 183 5.360714 CCAGCCCATTTGTGTAGATAACATT 59.639 40.000 0.00 0.00 41.10 2.71
240 246 0.178964 TTCTTCCCCCAAACTGCCAG 60.179 55.000 0.00 0.00 0.00 4.85
241 247 0.486879 ATTCTTCCCCCAAACTGCCA 59.513 50.000 0.00 0.00 0.00 4.92
276 282 6.311935 CCATTTCAACTTGCAGTATTCCATTG 59.688 38.462 0.00 0.00 0.00 2.82
290 296 5.474189 CCATTGGCATTTTCCATTTCAACTT 59.526 36.000 0.00 0.00 35.77 2.66
315 321 4.052518 CCCCCTGGAGCTTGGGTG 62.053 72.222 16.05 4.54 41.82 4.61
327 333 0.546598 CTTCAAATACCGAGCCCCCT 59.453 55.000 0.00 0.00 0.00 4.79
328 334 0.544697 TCTTCAAATACCGAGCCCCC 59.455 55.000 0.00 0.00 0.00 5.40
335 341 8.346476 TGACATTTGTTTTTCTTCAAATACCG 57.654 30.769 0.00 0.00 40.70 4.02
379 399 9.515226 AACATGTACAGTATAAGTTTCCATGTT 57.485 29.630 12.71 12.71 34.74 2.71
415 435 8.508800 AATATTTTCAAACGTTTATTCACGCA 57.491 26.923 14.20 0.00 44.37 5.24
463 487 1.486726 TGTTGTTGGGCCGGAATTTTT 59.513 42.857 5.05 0.00 0.00 1.94
528 552 0.871722 TTCATAACACACTGGCGTGC 59.128 50.000 8.93 0.00 45.10 5.34
529 553 3.829886 ATTTCATAACACACTGGCGTG 57.170 42.857 7.71 7.71 46.63 5.34
530 554 4.846779 AAATTTCATAACACACTGGCGT 57.153 36.364 0.00 0.00 0.00 5.68
531 555 4.143347 GCAAAATTTCATAACACACTGGCG 60.143 41.667 0.00 0.00 0.00 5.69
532 556 4.749099 TGCAAAATTTCATAACACACTGGC 59.251 37.500 0.00 0.00 0.00 4.85
533 557 6.215121 TCTGCAAAATTTCATAACACACTGG 58.785 36.000 0.00 0.00 0.00 4.00
535 559 8.575589 TGTATCTGCAAAATTTCATAACACACT 58.424 29.630 0.00 0.00 0.00 3.55
536 560 8.741101 TGTATCTGCAAAATTTCATAACACAC 57.259 30.769 0.00 0.00 0.00 3.82
567 606 8.637196 TTTTTGTGAACACCCATACACATATA 57.363 30.769 0.00 0.00 41.67 0.86
612 653 3.188254 CCCGGTTTCAAAATGCATTTTCC 59.812 43.478 29.92 25.38 37.86 3.13
633 675 1.811679 GACCGAGCTACAAGCAGCC 60.812 63.158 1.22 0.00 45.56 4.85
637 679 0.246635 TTGGAGACCGAGCTACAAGC 59.753 55.000 0.00 0.00 42.84 4.01
670 712 4.332543 TGAATCATTGTATGCACTTCGACC 59.667 41.667 0.00 0.00 0.00 4.79
686 728 4.541973 TCACGCAGCCTATATGAATCAT 57.458 40.909 0.00 0.00 0.00 2.45
691 733 2.029020 GGTCATCACGCAGCCTATATGA 60.029 50.000 0.00 0.00 0.00 2.15
703 1242 0.392998 CTCCCCCAAAGGTCATCACG 60.393 60.000 0.00 0.00 0.00 4.35
734 1273 2.688507 ACCAAGCTCATGTAGTTCACG 58.311 47.619 0.00 0.00 0.00 4.35
772 1418 7.396418 TCTGTATAAAAGGGTTGTACCGATTT 58.604 34.615 0.00 0.00 39.83 2.17
773 1419 6.949715 TCTGTATAAAAGGGTTGTACCGATT 58.050 36.000 0.00 0.00 39.83 3.34
774 1420 6.381994 TCTCTGTATAAAAGGGTTGTACCGAT 59.618 38.462 0.00 0.00 39.83 4.18
775 1421 5.716228 TCTCTGTATAAAAGGGTTGTACCGA 59.284 40.000 0.00 0.00 39.83 4.69
776 1422 5.969423 TCTCTGTATAAAAGGGTTGTACCG 58.031 41.667 0.00 0.00 39.83 4.02
777 1423 7.662669 TGTTTCTCTGTATAAAAGGGTTGTACC 59.337 37.037 0.00 0.00 37.60 3.34
778 1424 8.611654 TGTTTCTCTGTATAAAAGGGTTGTAC 57.388 34.615 0.00 0.00 0.00 2.90
779 1425 9.802039 ATTGTTTCTCTGTATAAAAGGGTTGTA 57.198 29.630 0.00 0.00 0.00 2.41
780 1426 8.706322 ATTGTTTCTCTGTATAAAAGGGTTGT 57.294 30.769 0.00 0.00 0.00 3.32
781 1427 8.792633 TGATTGTTTCTCTGTATAAAAGGGTTG 58.207 33.333 0.00 0.00 0.00 3.77
831 1483 8.515414 GCCTTCATACTTTCATTCACTTTACTT 58.485 33.333 0.00 0.00 0.00 2.24
1011 1664 2.607750 ACCCGCACCTCCATCACT 60.608 61.111 0.00 0.00 0.00 3.41
1119 1772 2.359967 CCGGGACTTCAGGGACCTC 61.360 68.421 0.00 0.00 0.00 3.85
1366 2019 8.915057 ATCAAGATTACTGATTACCAATCCTG 57.085 34.615 0.00 0.00 37.09 3.86
1389 2049 9.476202 GGCCTGAACCATTGTATTTAAAATATC 57.524 33.333 0.00 0.00 0.00 1.63
1391 2051 7.416890 CCGGCCTGAACCATTGTATTTAAAATA 60.417 37.037 0.00 0.00 0.00 1.40
1392 2052 6.337356 CGGCCTGAACCATTGTATTTAAAAT 58.663 36.000 0.00 0.00 0.00 1.82
1393 2053 5.336849 CCGGCCTGAACCATTGTATTTAAAA 60.337 40.000 0.00 0.00 0.00 1.52
1395 2055 3.697045 CCGGCCTGAACCATTGTATTTAA 59.303 43.478 0.00 0.00 0.00 1.52
1396 2056 3.283751 CCGGCCTGAACCATTGTATTTA 58.716 45.455 0.00 0.00 0.00 1.40
1397 2057 2.099405 CCGGCCTGAACCATTGTATTT 58.901 47.619 0.00 0.00 0.00 1.40
1399 2059 0.106719 CCCGGCCTGAACCATTGTAT 60.107 55.000 0.00 0.00 0.00 2.29
1402 2062 1.750399 CTCCCGGCCTGAACCATTG 60.750 63.158 0.00 0.00 0.00 2.82
1404 2064 1.694169 ATCTCCCGGCCTGAACCAT 60.694 57.895 0.00 0.00 0.00 3.55
1405 2065 2.285368 ATCTCCCGGCCTGAACCA 60.285 61.111 0.00 0.00 0.00 3.67
1406 2066 1.910580 TTCATCTCCCGGCCTGAACC 61.911 60.000 0.00 0.00 0.00 3.62
1407 2067 0.744771 GTTCATCTCCCGGCCTGAAC 60.745 60.000 15.14 15.14 40.27 3.18
1409 2069 1.198094 TTGTTCATCTCCCGGCCTGA 61.198 55.000 0.00 0.00 0.00 3.86
1410 2070 0.107017 ATTGTTCATCTCCCGGCCTG 60.107 55.000 0.00 0.00 0.00 4.85
1412 2072 1.474330 AAATTGTTCATCTCCCGGCC 58.526 50.000 0.00 0.00 0.00 6.13
1413 2073 3.541632 TCTAAATTGTTCATCTCCCGGC 58.458 45.455 0.00 0.00 0.00 6.13
1414 2074 4.941263 TGTTCTAAATTGTTCATCTCCCGG 59.059 41.667 0.00 0.00 0.00 5.73
1415 2075 5.065218 CCTGTTCTAAATTGTTCATCTCCCG 59.935 44.000 0.00 0.00 0.00 5.14
1416 2076 5.358160 CCCTGTTCTAAATTGTTCATCTCCC 59.642 44.000 0.00 0.00 0.00 4.30
1417 2077 5.946377 ACCCTGTTCTAAATTGTTCATCTCC 59.054 40.000 0.00 0.00 0.00 3.71
1419 2079 6.542821 TGACCCTGTTCTAAATTGTTCATCT 58.457 36.000 0.00 0.00 0.00 2.90
1443 2108 7.487822 TCAGATTCTTCTTGAGAAGGTACAT 57.512 36.000 18.01 7.72 46.99 2.29
1470 2139 6.034591 CACTGATACAAAACTACCCTACGAG 58.965 44.000 0.00 0.00 0.00 4.18
1612 2281 6.183360 CCTCTGTTGCTTTTTCTCACTGTAAA 60.183 38.462 0.00 0.00 0.00 2.01
1613 2282 5.296780 CCTCTGTTGCTTTTTCTCACTGTAA 59.703 40.000 0.00 0.00 0.00 2.41
1623 2292 9.692325 AATTAGATATCTCCTCTGTTGCTTTTT 57.308 29.630 8.95 0.00 0.00 1.94
1658 2327 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
1659 2328 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1661 2330 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1662 2331 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
1663 2332 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
1664 2333 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
1666 2335 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
1668 2337 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
1669 2338 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
1670 2339 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
1703 2372 8.960591 CCAAAATAGATGATCCAACTTTGTACT 58.039 33.333 0.00 0.00 0.00 2.73
1704 2373 8.956426 TCCAAAATAGATGATCCAACTTTGTAC 58.044 33.333 0.00 0.00 0.00 2.90
1705 2374 9.527157 TTCCAAAATAGATGATCCAACTTTGTA 57.473 29.630 0.00 0.00 0.00 2.41
1706 2375 8.306761 GTTCCAAAATAGATGATCCAACTTTGT 58.693 33.333 0.00 0.00 0.00 2.83
1707 2376 7.485913 CGTTCCAAAATAGATGATCCAACTTTG 59.514 37.037 0.00 0.00 0.00 2.77
1708 2377 7.362920 CCGTTCCAAAATAGATGATCCAACTTT 60.363 37.037 0.00 0.00 0.00 2.66
1709 2378 6.095440 CCGTTCCAAAATAGATGATCCAACTT 59.905 38.462 0.00 0.00 0.00 2.66
1710 2379 5.590259 CCGTTCCAAAATAGATGATCCAACT 59.410 40.000 0.00 0.00 0.00 3.16
1711 2380 5.588648 TCCGTTCCAAAATAGATGATCCAAC 59.411 40.000 0.00 0.00 0.00 3.77
1712 2381 5.750524 TCCGTTCCAAAATAGATGATCCAA 58.249 37.500 0.00 0.00 0.00 3.53
1713 2382 5.366482 TCCGTTCCAAAATAGATGATCCA 57.634 39.130 0.00 0.00 0.00 3.41
1714 2383 4.757149 CCTCCGTTCCAAAATAGATGATCC 59.243 45.833 0.00 0.00 0.00 3.36
1715 2384 4.757149 CCCTCCGTTCCAAAATAGATGATC 59.243 45.833 0.00 0.00 0.00 2.92
1716 2385 4.412199 TCCCTCCGTTCCAAAATAGATGAT 59.588 41.667 0.00 0.00 0.00 2.45
1717 2386 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1718 2387 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1719 2388 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1720 2389 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1721 2390 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1722 2391 6.811634 TTATACTCCCTCCGTTCCAAAATA 57.188 37.500 0.00 0.00 0.00 1.40
1723 2392 5.703730 TTATACTCCCTCCGTTCCAAAAT 57.296 39.130 0.00 0.00 0.00 1.82
1724 2393 5.703730 ATTATACTCCCTCCGTTCCAAAA 57.296 39.130 0.00 0.00 0.00 2.44
1725 2394 7.383156 AATATTATACTCCCTCCGTTCCAAA 57.617 36.000 0.00 0.00 0.00 3.28
1726 2395 7.383156 AAATATTATACTCCCTCCGTTCCAA 57.617 36.000 0.00 0.00 0.00 3.53
1727 2396 7.071447 TGAAAATATTATACTCCCTCCGTTCCA 59.929 37.037 0.00 0.00 0.00 3.53
1728 2397 7.447594 TGAAAATATTATACTCCCTCCGTTCC 58.552 38.462 0.00 0.00 0.00 3.62
1729 2398 9.503399 AATGAAAATATTATACTCCCTCCGTTC 57.497 33.333 0.00 0.00 0.00 3.95
1730 2399 9.862149 AAATGAAAATATTATACTCCCTCCGTT 57.138 29.630 0.00 0.00 0.00 4.44
1731 2400 9.862149 AAAATGAAAATATTATACTCCCTCCGT 57.138 29.630 0.00 0.00 0.00 4.69
1799 2602 0.475475 CAAGGGCTGCATAGGGATGA 59.525 55.000 0.50 0.00 34.73 2.92
1812 2615 1.859080 CTTATCGACGTAAGCAAGGGC 59.141 52.381 0.00 0.00 45.62 5.19
1813 2616 3.372954 CTCTTATCGACGTAAGCAAGGG 58.627 50.000 10.47 0.00 45.62 3.95
1823 2626 2.095161 GGGTGATAGGCTCTTATCGACG 60.095 54.545 0.00 0.00 33.63 5.12
1824 2627 2.891580 TGGGTGATAGGCTCTTATCGAC 59.108 50.000 0.00 0.00 33.63 4.20
1850 2705 7.496529 TGTTAGTTTGTCTGATCCTTTGAAG 57.503 36.000 0.00 0.00 0.00 3.02
1926 2781 2.500504 ACTTGCCGTTTTGGGGTAAAAA 59.499 40.909 0.00 0.00 39.79 1.94
1927 2782 2.108970 ACTTGCCGTTTTGGGGTAAAA 58.891 42.857 0.00 0.00 38.63 1.52
1928 2783 1.777941 ACTTGCCGTTTTGGGGTAAA 58.222 45.000 0.00 0.00 38.63 2.01
1929 2784 2.653234 TACTTGCCGTTTTGGGGTAA 57.347 45.000 0.00 0.00 38.63 2.85
1930 2785 2.622470 GTTTACTTGCCGTTTTGGGGTA 59.378 45.455 0.00 0.00 38.63 3.69
1931 2786 1.409790 GTTTACTTGCCGTTTTGGGGT 59.590 47.619 0.00 0.00 38.63 4.95
1932 2787 1.409427 TGTTTACTTGCCGTTTTGGGG 59.591 47.619 0.00 0.00 38.63 4.96
1933 2788 2.873133 TGTTTACTTGCCGTTTTGGG 57.127 45.000 0.00 0.00 38.63 4.12
1934 2789 5.980715 ACTAAATGTTTACTTGCCGTTTTGG 59.019 36.000 0.00 0.00 42.50 3.28
1935 2790 8.563289 TTACTAAATGTTTACTTGCCGTTTTG 57.437 30.769 0.00 0.00 0.00 2.44
1936 2791 9.240159 CTTTACTAAATGTTTACTTGCCGTTTT 57.760 29.630 0.00 0.00 0.00 2.43
1937 2792 7.380333 GCTTTACTAAATGTTTACTTGCCGTTT 59.620 33.333 0.00 0.00 0.00 3.60
1938 2793 6.859508 GCTTTACTAAATGTTTACTTGCCGTT 59.140 34.615 0.00 0.00 0.00 4.44
1939 2794 6.016943 TGCTTTACTAAATGTTTACTTGCCGT 60.017 34.615 0.00 0.00 0.00 5.68
1940 2795 6.375377 TGCTTTACTAAATGTTTACTTGCCG 58.625 36.000 0.00 0.00 0.00 5.69
1941 2796 7.537649 GTCTGCTTTACTAAATGTTTACTTGCC 59.462 37.037 0.00 0.00 0.00 4.52
1954 2814 4.859304 TCGAACCTGTCTGCTTTACTAA 57.141 40.909 0.00 0.00 0.00 2.24
1958 2818 6.093495 CCATTTAATCGAACCTGTCTGCTTTA 59.907 38.462 0.00 0.00 0.00 1.85
2156 3016 1.538876 TGTTGCCCAGGGACTAGCT 60.539 57.895 10.89 0.00 37.72 3.32
2210 3070 4.146058 CGGCATAGCAGCATCCAA 57.854 55.556 0.00 0.00 35.83 3.53
2267 3127 7.765695 TGTTCCTAGAAAAATTTCAGATGCT 57.234 32.000 8.47 0.00 39.61 3.79
2308 3168 7.038729 CCCTTCTAGGTAGATTATCATTGCTGA 60.039 40.741 0.00 0.00 31.93 4.26


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

AutoCloner maintained by Alex Coulton.