Multiple sequence alignment - TraesCS3A01G091200

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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 TraesCS3A01G091200 chr3A 100.000 2300 0 0 1 2300 57811878 57814177 0.000000e+00 4248.0
1 TraesCS3A01G091200 chr3D 85.617 1474 102 50 63 1487 46196415 46197827 0.000000e+00 1447.0
2 TraesCS3A01G091200 chr3D 86.667 690 61 15 1624 2300 46198003 46198674 0.000000e+00 736.0
3 TraesCS3A01G091200 chr3D 90.909 66 6 0 1560 1625 46197912 46197977 3.150000e-14 89.8
4 TraesCS3A01G091200 chr3B 83.564 724 51 22 2 691 71805608 71804919 1.170000e-172 616.0
5 TraesCS3A01G091200 chr3B 80.046 872 83 48 984 1803 71804603 71803771 1.540000e-156 562.0
6 TraesCS3A01G091200 chr3B 93.182 352 19 2 1921 2272 71803588 71803242 1.580000e-141 512.0
7 TraesCS3A01G091200 chr3B 89.735 302 21 3 2002 2300 72111320 72111614 6.000000e-101 377.0
8 TraesCS3A01G091200 chr3B 80.569 422 44 22 1684 2071 71974772 71975189 8.040000e-75 291.0
9 TraesCS3A01G091200 chr3B 87.591 137 9 6 863 993 71804768 71804634 3.960000e-33 152.0
10 TraesCS3A01G091200 chr3B 88.889 99 5 4 1640 1733 71974683 71974780 1.440000e-22 117.0
11 TraesCS3A01G091200 chr3B 82.474 97 12 4 691 782 71804899 71804803 1.890000e-11 80.5
12 TraesCS3A01G091200 chr3B 97.059 34 1 0 170 203 321703173 321703206 8.880000e-05 58.4
13 TraesCS3A01G091200 chr3B 96.970 33 1 0 171 203 748316143 748316175 3.190000e-04 56.5
14 TraesCS3A01G091200 chr1A 100.000 33 0 0 170 202 500476307 500476275 6.860000e-06 62.1
15 TraesCS3A01G091200 chr4A 100.000 31 0 0 174 204 5065394 5065364 8.880000e-05 58.4
16 TraesCS3A01G091200 chr1B 100.000 30 0 0 174 203 254135106 254135077 3.190000e-04 56.5
17 TraesCS3A01G091200 chr6B 96.875 32 1 0 171 202 33401377 33401408 1.000000e-03 54.7


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 TraesCS3A01G091200 chr3A 57811878 57814177 2299 False 4248.0 4248 100.0000 1 2300 1 chr3A.!!$F1 2299
1 TraesCS3A01G091200 chr3D 46196415 46198674 2259 False 757.6 1447 87.7310 63 2300 3 chr3D.!!$F1 2237
2 TraesCS3A01G091200 chr3B 71803242 71805608 2366 True 384.5 616 85.3714 2 2272 5 chr3B.!!$R1 2270
3 TraesCS3A01G091200 chr3B 71974683 71975189 506 False 204.0 291 84.7290 1640 2071 2 chr3B.!!$F4 431

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
859 958 0.037303 TTCGACACCTCTCCTACCGT 59.963 55.0 0.0 0.0 0.0 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 2341 0.110464 GTTTCTTCTCAGCACAGCGC 60.11 55.0 0.0 0.0 42.91 5.92 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
39 40 1.229336 ACTGTGAGGGTAGCAGGCT 60.229 57.895 0.00 0.00 34.79 4.58
40 41 0.041238 ACTGTGAGGGTAGCAGGCTA 59.959 55.000 0.00 0.00 34.79 3.93
41 42 0.749649 CTGTGAGGGTAGCAGGCTAG 59.250 60.000 0.32 0.00 0.00 3.42
42 43 0.041238 TGTGAGGGTAGCAGGCTAGT 59.959 55.000 0.32 0.00 0.00 2.57
43 44 0.747852 GTGAGGGTAGCAGGCTAGTC 59.252 60.000 0.32 0.43 0.00 2.59
44 45 0.752009 TGAGGGTAGCAGGCTAGTCG 60.752 60.000 0.32 0.00 0.00 4.18
45 46 0.465824 GAGGGTAGCAGGCTAGTCGA 60.466 60.000 0.32 0.00 0.00 4.20
46 47 0.186386 AGGGTAGCAGGCTAGTCGAT 59.814 55.000 0.32 0.00 0.00 3.59
47 48 0.315568 GGGTAGCAGGCTAGTCGATG 59.684 60.000 0.32 0.00 0.00 3.84
48 49 0.315568 GGTAGCAGGCTAGTCGATGG 59.684 60.000 0.32 0.00 0.00 3.51
49 50 0.319125 GTAGCAGGCTAGTCGATGGC 60.319 60.000 0.32 0.00 33.90 4.40
60 61 0.097150 GTCGATGGCGGAAAAGCTTC 59.903 55.000 0.00 0.00 38.28 3.86
78 85 1.338107 TCGGACAGTGTGATGGAACT 58.662 50.000 0.00 0.00 0.00 3.01
288 306 2.358247 TGTTCGCGGCCTTTCCTC 60.358 61.111 6.13 0.00 0.00 3.71
304 326 1.302832 CTCCTTCTGCCGTGCCTTT 60.303 57.895 0.00 0.00 0.00 3.11
305 327 1.580845 CTCCTTCTGCCGTGCCTTTG 61.581 60.000 0.00 0.00 0.00 2.77
306 328 2.256461 CTTCTGCCGTGCCTTTGC 59.744 61.111 0.00 0.00 38.26 3.68
307 329 2.203337 TTCTGCCGTGCCTTTGCT 60.203 55.556 0.00 0.00 38.71 3.91
348 370 2.821366 GGCTGCACTGATCACCCG 60.821 66.667 0.50 0.00 0.00 5.28
350 372 2.821366 CTGCACTGATCACCCGGC 60.821 66.667 0.00 0.00 0.00 6.13
351 373 4.408821 TGCACTGATCACCCGGCC 62.409 66.667 0.00 0.00 0.00 6.13
354 376 3.461773 ACTGATCACCCGGCCTCG 61.462 66.667 0.00 0.00 0.00 4.63
387 413 2.261671 GTGAGACACACGGCGGAT 59.738 61.111 13.24 0.00 39.78 4.18
401 427 4.241555 GGATGGCCGGATGCGTCT 62.242 66.667 5.05 0.00 42.61 4.18
402 428 2.969238 GATGGCCGGATGCGTCTG 60.969 66.667 5.05 7.86 42.61 3.51
403 429 3.740128 GATGGCCGGATGCGTCTGT 62.740 63.158 5.05 0.00 42.61 3.41
405 431 4.148825 GGCCGGATGCGTCTGTCT 62.149 66.667 5.05 0.00 42.61 3.41
406 432 2.125512 GCCGGATGCGTCTGTCTT 60.126 61.111 5.05 0.00 0.00 3.01
407 433 2.167861 GCCGGATGCGTCTGTCTTC 61.168 63.158 5.05 0.00 0.00 2.87
408 434 1.874019 CCGGATGCGTCTGTCTTCG 60.874 63.158 13.70 3.72 0.00 3.79
450 478 2.683933 AGACGGCGGATTGGTCCT 60.684 61.111 13.24 0.00 42.73 3.85
451 479 2.240162 GAGACGGCGGATTGGTCCTT 62.240 60.000 13.24 0.00 42.73 3.36
453 481 2.267642 CGGCGGATTGGTCCTTGA 59.732 61.111 0.00 0.00 42.73 3.02
454 482 1.376683 CGGCGGATTGGTCCTTGAA 60.377 57.895 0.00 0.00 42.73 2.69
455 483 0.748005 CGGCGGATTGGTCCTTGAAT 60.748 55.000 0.00 0.00 42.73 2.57
457 485 1.405463 GGCGGATTGGTCCTTGAATTC 59.595 52.381 0.00 0.00 42.73 2.17
599 662 2.173382 CTTTTTGTCCGCGCTCCG 59.827 61.111 5.56 0.00 0.00 4.63
627 694 1.448540 CAAATCAGGGTCGCTCGCT 60.449 57.895 0.00 0.00 40.00 4.93
758 850 3.181485 GCTAGCCATACTCGTATCATCCC 60.181 52.174 2.29 0.00 0.00 3.85
824 923 3.062466 CAGCTCCAGGGACGACGA 61.062 66.667 0.00 0.00 0.00 4.20
846 945 0.520404 GTCGCCACTCTACTTCGACA 59.480 55.000 8.01 0.00 45.94 4.35
847 946 0.520404 TCGCCACTCTACTTCGACAC 59.480 55.000 0.00 0.00 0.00 3.67
859 958 0.037303 TTCGACACCTCTCCTACCGT 59.963 55.000 0.00 0.00 0.00 4.83
903 1002 1.626654 CGTCAAACGCAGCCTCGATT 61.627 55.000 2.06 0.00 33.65 3.34
921 1020 3.305199 CGATTACCACCGTTATCTCCTCC 60.305 52.174 0.00 0.00 0.00 4.30
926 1031 0.467659 ACCGTTATCTCCTCCCCTCG 60.468 60.000 0.00 0.00 0.00 4.63
927 1032 1.660917 CGTTATCTCCTCCCCTCGC 59.339 63.158 0.00 0.00 0.00 5.03
1005 1149 1.852157 TGAACCAGGAGGCATGGGT 60.852 57.895 3.03 0.00 41.69 4.51
1062 1206 4.244802 CTCTCGCTCGTCCCGCTC 62.245 72.222 0.00 0.00 0.00 5.03
1292 1436 4.326766 CAACCCGCTGCACAACCG 62.327 66.667 0.00 0.00 0.00 4.44
1294 1438 4.555709 ACCCGCTGCACAACCGAA 62.556 61.111 0.00 0.00 0.00 4.30
1325 1469 3.816524 CGTTCCTCCTCGCTCGCT 61.817 66.667 0.00 0.00 0.00 4.93
1326 1470 2.103340 GTTCCTCCTCGCTCGCTC 59.897 66.667 0.00 0.00 0.00 5.03
1327 1471 3.509757 TTCCTCCTCGCTCGCTCG 61.510 66.667 0.00 0.00 0.00 5.03
1394 1538 1.614413 GCTATTGCCTCGGTAGTAGCT 59.386 52.381 17.15 0.00 40.70 3.32
1395 1539 2.608261 GCTATTGCCTCGGTAGTAGCTG 60.608 54.545 17.15 0.00 40.70 4.24
1419 1566 5.220739 GCTTCTTCGTATGATTGATTGCACT 60.221 40.000 0.00 0.00 0.00 4.40
1420 1567 6.676456 GCTTCTTCGTATGATTGATTGCACTT 60.676 38.462 0.00 0.00 0.00 3.16
1421 1568 6.110543 TCTTCGTATGATTGATTGCACTTG 57.889 37.500 0.00 0.00 0.00 3.16
1422 1569 4.277257 TCGTATGATTGATTGCACTTGC 57.723 40.909 0.00 0.00 42.50 4.01
1488 1636 5.479124 ACGTATTACTTCTTCAGGTTGGT 57.521 39.130 0.00 0.00 0.00 3.67
1491 1639 5.390567 CGTATTACTTCTTCAGGTTGGTTGC 60.391 44.000 0.00 0.00 0.00 4.17
1492 1640 2.435372 ACTTCTTCAGGTTGGTTGCA 57.565 45.000 0.00 0.00 0.00 4.08
1494 1642 2.624838 ACTTCTTCAGGTTGGTTGCATG 59.375 45.455 0.00 0.00 0.00 4.06
1495 1643 2.363306 TCTTCAGGTTGGTTGCATGT 57.637 45.000 0.00 0.00 0.00 3.21
1497 1645 2.158623 TCTTCAGGTTGGTTGCATGTCT 60.159 45.455 0.00 0.00 0.00 3.41
1498 1646 1.608055 TCAGGTTGGTTGCATGTCTG 58.392 50.000 0.00 0.00 0.00 3.51
1499 1647 1.133823 TCAGGTTGGTTGCATGTCTGT 60.134 47.619 0.00 0.00 0.00 3.41
1500 1648 2.105649 TCAGGTTGGTTGCATGTCTGTA 59.894 45.455 0.00 0.00 0.00 2.74
1501 1649 2.226437 CAGGTTGGTTGCATGTCTGTAC 59.774 50.000 0.00 0.00 0.00 2.90
1502 1650 2.158682 AGGTTGGTTGCATGTCTGTACA 60.159 45.455 0.00 0.00 40.69 2.90
1504 1652 3.255642 GGTTGGTTGCATGTCTGTACATT 59.744 43.478 0.00 0.00 44.07 2.71
1505 1653 4.261994 GGTTGGTTGCATGTCTGTACATTT 60.262 41.667 0.00 0.00 44.07 2.32
1507 1655 3.888323 TGGTTGCATGTCTGTACATTTGT 59.112 39.130 0.00 0.00 44.07 2.83
1509 1657 5.181056 TGGTTGCATGTCTGTACATTTGTAG 59.819 40.000 0.00 0.00 44.07 2.74
1510 1658 4.944962 TGCATGTCTGTACATTTGTAGC 57.055 40.909 0.00 0.00 44.07 3.58
1511 1659 4.578871 TGCATGTCTGTACATTTGTAGCT 58.421 39.130 0.00 0.00 44.07 3.32
1512 1660 4.392754 TGCATGTCTGTACATTTGTAGCTG 59.607 41.667 0.00 0.00 44.07 4.24
1513 1661 4.728882 GCATGTCTGTACATTTGTAGCTGC 60.729 45.833 0.00 0.00 44.07 5.25
1515 1663 3.745975 TGTCTGTACATTTGTAGCTGCAC 59.254 43.478 3.11 0.00 0.00 4.57
1519 1724 4.071423 TGTACATTTGTAGCTGCACATGT 58.929 39.130 30.56 30.56 41.12 3.21
1535 1741 4.557296 GCACATGTATTGTTTCTGCTGTGT 60.557 41.667 0.00 0.00 36.00 3.72
1536 1742 5.522456 CACATGTATTGTTTCTGCTGTGTT 58.478 37.500 0.00 0.00 36.00 3.32
1540 1746 7.391554 ACATGTATTGTTTCTGCTGTGTTATCT 59.608 33.333 0.00 0.00 33.74 1.98
1549 1755 6.286240 TCTGCTGTGTTATCTATGTGTTCT 57.714 37.500 0.00 0.00 0.00 3.01
1551 1757 7.258441 TCTGCTGTGTTATCTATGTGTTCTAC 58.742 38.462 0.00 0.00 0.00 2.59
1591 1804 3.382015 GCTCTGAAGCTGTCGAAAATC 57.618 47.619 0.00 0.00 45.55 2.17
1620 1833 4.934356 TCATTTCCTACAAGGAGCCAAAT 58.066 39.130 0.00 0.00 46.73 2.32
1625 1838 4.079253 TCCTACAAGGAGCCAAATTGTTC 58.921 43.478 0.00 0.00 40.06 3.18
1626 1839 4.082125 CCTACAAGGAGCCAAATTGTTCT 58.918 43.478 0.00 0.00 37.67 3.01
1628 1841 3.837355 ACAAGGAGCCAAATTGTTCTCT 58.163 40.909 10.68 0.00 33.49 3.10
1629 1842 3.571401 ACAAGGAGCCAAATTGTTCTCTG 59.429 43.478 10.68 6.42 33.49 3.35
1630 1843 2.800250 AGGAGCCAAATTGTTCTCTGG 58.200 47.619 10.68 0.00 0.00 3.86
1705 1953 0.617413 CTCACAATGGGGACTGCTCT 59.383 55.000 0.00 0.00 0.00 4.09
1715 1963 0.599728 GGACTGCTCTGCCATCGATC 60.600 60.000 0.00 0.00 0.00 3.69
1721 1969 0.321387 CTCTGCCATCGATCCCATGG 60.321 60.000 4.14 4.14 43.47 3.66
1722 1970 1.056125 TCTGCCATCGATCCCATGGT 61.056 55.000 11.73 0.00 42.68 3.55
1723 1971 0.604780 CTGCCATCGATCCCATGGTC 60.605 60.000 11.73 1.14 42.68 4.02
1724 1972 1.344191 TGCCATCGATCCCATGGTCA 61.344 55.000 11.73 12.68 42.68 4.02
1725 1973 0.886490 GCCATCGATCCCATGGTCAC 60.886 60.000 11.73 0.04 42.68 3.67
1726 1974 0.469494 CCATCGATCCCATGGTCACA 59.531 55.000 11.73 0.00 36.74 3.58
1728 1976 1.139654 CATCGATCCCATGGTCACACT 59.860 52.381 11.73 0.00 0.00 3.55
1737 2028 0.836606 ATGGTCACACTCACACCACA 59.163 50.000 0.00 0.00 43.05 4.17
1773 2064 5.578727 TGTTGTGTGCAAGGAACAAATTAAC 59.421 36.000 6.99 0.00 35.70 2.01
1806 2097 4.355543 TTCTTCATAAAATGAGCACGCC 57.644 40.909 0.00 0.00 40.94 5.68
1808 2099 3.374988 TCTTCATAAAATGAGCACGCCAG 59.625 43.478 0.00 0.00 40.94 4.85
1824 2148 5.234752 CACGCCAGCATAAACCTGTATATA 58.765 41.667 0.00 0.00 0.00 0.86
1865 2196 7.452562 TCCACGATACCACATAGTAGTACATA 58.547 38.462 2.52 0.00 0.00 2.29
1887 2218 7.974501 ACATACTAGGAACAAACTAATCGACAG 59.025 37.037 0.00 0.00 0.00 3.51
1897 2228 8.385898 ACAAACTAATCGACAGGTAAATCAAA 57.614 30.769 0.00 0.00 0.00 2.69
1898 2229 8.842280 ACAAACTAATCGACAGGTAAATCAAAA 58.158 29.630 0.00 0.00 0.00 2.44
1911 2242 3.302365 AATCAAAAATCACACTGGGCG 57.698 42.857 0.00 0.00 0.00 6.13
1919 2250 1.184970 TCACACTGGGCGTGATCAGA 61.185 55.000 0.00 0.00 46.81 3.27
1966 2340 2.439507 TCCCTTTCTGCTGTTGTCTCTT 59.560 45.455 0.00 0.00 0.00 2.85
1967 2341 2.551459 CCCTTTCTGCTGTTGTCTCTTG 59.449 50.000 0.00 0.00 0.00 3.02
1968 2342 2.031333 CCTTTCTGCTGTTGTCTCTTGC 60.031 50.000 0.00 0.00 0.00 4.01
1969 2343 1.220529 TTCTGCTGTTGTCTCTTGCG 58.779 50.000 0.00 0.00 0.00 4.85
1970 2344 1.206072 CTGCTGTTGTCTCTTGCGC 59.794 57.895 0.00 0.00 0.00 6.09
2012 2391 6.415206 AATGAAAGCCAATGATATCAAGGG 57.585 37.500 22.14 19.89 0.00 3.95
2046 2425 0.898320 ACCCTGACTGACATTCTCCG 59.102 55.000 0.00 0.00 0.00 4.63
2076 2455 4.163458 TCCTACCTTACAATCATGGTGTCC 59.837 45.833 6.26 0.00 34.33 4.02
2094 2473 3.326006 TGTCCTAGAATCAGCCATCCATC 59.674 47.826 0.00 0.00 0.00 3.51
2095 2474 2.909006 TCCTAGAATCAGCCATCCATCC 59.091 50.000 0.00 0.00 0.00 3.51
2096 2475 2.641321 CCTAGAATCAGCCATCCATCCA 59.359 50.000 0.00 0.00 0.00 3.41
2161 2543 3.447229 AGGAAAACAGAAACACCCAACAG 59.553 43.478 0.00 0.00 0.00 3.16
2235 2617 4.327357 CACGCATCAGTTTATTCTCTTCGT 59.673 41.667 0.00 0.00 0.00 3.85
2282 2664 0.392193 GTGCTGGAGCTGCAGTACAT 60.392 55.000 38.35 0.00 38.86 2.29
2286 2668 2.805099 GCTGGAGCTGCAGTACATATTC 59.195 50.000 32.29 12.52 38.21 1.75
2288 2670 2.224042 TGGAGCTGCAGTACATATTCCG 60.224 50.000 16.64 0.00 0.00 4.30
2289 2671 1.795286 GAGCTGCAGTACATATTCCGC 59.205 52.381 16.64 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.080230 CTCACAGTCACAGCCGGAG 60.080 63.158 5.05 0.00 0.00 4.63
39 40 0.535335 AGCTTTTCCGCCATCGACTA 59.465 50.000 0.00 0.00 38.10 2.59
40 41 0.321653 AAGCTTTTCCGCCATCGACT 60.322 50.000 0.00 0.00 38.10 4.18
41 42 0.097150 GAAGCTTTTCCGCCATCGAC 59.903 55.000 0.00 0.00 38.10 4.20
42 43 1.358725 CGAAGCTTTTCCGCCATCGA 61.359 55.000 0.00 0.00 40.20 3.59
43 44 1.060937 CGAAGCTTTTCCGCCATCG 59.939 57.895 0.00 0.00 34.82 3.84
44 45 1.024579 TCCGAAGCTTTTCCGCCATC 61.025 55.000 0.00 0.00 0.00 3.51
45 46 1.002624 TCCGAAGCTTTTCCGCCAT 60.003 52.632 0.00 0.00 0.00 4.40
46 47 1.964373 GTCCGAAGCTTTTCCGCCA 60.964 57.895 0.00 0.00 0.00 5.69
47 48 1.912371 CTGTCCGAAGCTTTTCCGCC 61.912 60.000 0.00 0.00 0.00 6.13
48 49 1.228657 ACTGTCCGAAGCTTTTCCGC 61.229 55.000 0.00 0.00 0.00 5.54
49 50 0.512952 CACTGTCCGAAGCTTTTCCG 59.487 55.000 0.00 0.00 0.00 4.30
60 61 1.000843 TCAGTTCCATCACACTGTCCG 59.999 52.381 0.00 0.00 41.16 4.79
78 85 2.513666 GCAACCCGCCATCGATCA 60.514 61.111 0.00 0.00 38.10 2.92
288 306 2.956987 CAAAGGCACGGCAGAAGG 59.043 61.111 0.00 0.00 0.00 3.46
305 327 3.112709 GACAGTCCGGCGACAAGC 61.113 66.667 9.30 0.00 41.87 4.01
306 328 2.805353 CGACAGTCCGGCGACAAG 60.805 66.667 9.30 4.60 41.87 3.16
307 329 4.351938 CCGACAGTCCGGCGACAA 62.352 66.667 9.30 0.00 43.25 3.18
338 360 4.899239 GCGAGGCCGGGTGATCAG 62.899 72.222 2.18 0.00 36.06 2.90
363 385 2.471607 GTGTGTCTCACGCATGCG 59.528 61.111 36.79 36.79 43.40 4.73
387 413 4.451150 GACAGACGCATCCGGCCA 62.451 66.667 2.24 0.00 45.97 5.36
391 417 0.732880 AACGAAGACAGACGCATCCG 60.733 55.000 0.00 0.00 41.14 4.18
392 418 1.390463 GAAACGAAGACAGACGCATCC 59.610 52.381 0.00 0.00 0.00 3.51
393 419 1.057847 CGAAACGAAGACAGACGCATC 59.942 52.381 0.00 0.00 0.00 3.91
395 421 1.545614 GCGAAACGAAGACAGACGCA 61.546 55.000 0.00 0.00 43.18 5.24
397 423 1.773496 GGCGAAACGAAGACAGACG 59.227 57.895 0.00 0.00 0.00 4.18
398 424 0.662374 TCGGCGAAACGAAGACAGAC 60.662 55.000 7.35 0.00 40.34 3.51
399 425 0.242825 ATCGGCGAAACGAAGACAGA 59.757 50.000 15.93 0.00 46.92 3.41
400 426 0.640768 GATCGGCGAAACGAAGACAG 59.359 55.000 15.93 0.00 46.92 3.51
401 427 1.068832 CGATCGGCGAAACGAAGACA 61.069 55.000 26.60 0.00 46.92 3.41
402 428 1.624323 CGATCGGCGAAACGAAGAC 59.376 57.895 26.60 7.14 46.92 3.01
403 429 4.066769 CGATCGGCGAAACGAAGA 57.933 55.556 26.60 0.00 46.92 2.87
426 454 3.792053 AATCCGCCGTCTCCGATGC 62.792 63.158 0.00 0.00 35.63 3.91
427 455 1.951130 CAATCCGCCGTCTCCGATG 60.951 63.158 0.00 0.00 35.63 3.84
450 478 1.873165 GCTTCACCGGCGAATTCAA 59.127 52.632 9.30 0.00 0.00 2.69
451 479 3.573558 GCTTCACCGGCGAATTCA 58.426 55.556 9.30 0.00 0.00 2.57
514 572 4.899687 CATGATGCACGCTGCCGC 62.900 66.667 7.38 1.99 44.23 6.53
599 662 1.084370 CCCTGATTTGACGCGAGACC 61.084 60.000 15.93 0.00 0.00 3.85
630 697 3.245315 GAACCGTGGACGATCGCG 61.245 66.667 16.60 10.50 43.02 5.87
631 698 3.245315 CGAACCGTGGACGATCGC 61.245 66.667 16.60 8.04 43.02 4.58
824 923 1.881602 GAAGTAGAGTGGCGACCGT 59.118 57.895 0.00 0.00 0.00 4.83
846 945 2.439883 GGCGACGGTAGGAGAGGT 60.440 66.667 0.00 0.00 0.00 3.85
847 946 2.124236 AGGCGACGGTAGGAGAGG 60.124 66.667 0.00 0.00 0.00 3.69
859 958 1.677552 GTGGAAGAAAGGGAGGCGA 59.322 57.895 0.00 0.00 0.00 5.54
903 1002 1.412074 GGGGAGGAGATAACGGTGGTA 60.412 57.143 0.00 0.00 0.00 3.25
927 1032 3.866582 GATGGGCGAGACAGGGGG 61.867 72.222 0.00 0.00 0.00 5.40
936 1041 1.541310 AAGGAACGAGTGATGGGCGA 61.541 55.000 0.00 0.00 0.00 5.54
939 1044 0.905357 AGGAAGGAACGAGTGATGGG 59.095 55.000 0.00 0.00 0.00 4.00
1183 1327 4.463879 CAGAGCAGCACCCTCCGG 62.464 72.222 0.00 0.00 0.00 5.14
1238 1382 1.371267 CTCTTGTCGTCGCCGAACA 60.371 57.895 0.00 0.00 46.26 3.18
1325 1469 2.420466 ATACATGCATCGGCGAGCGA 62.420 55.000 17.22 10.10 45.35 4.93
1326 1470 2.023771 ATACATGCATCGGCGAGCG 61.024 57.895 17.22 10.38 45.35 5.03
1327 1471 0.945743 TCATACATGCATCGGCGAGC 60.946 55.000 17.22 18.69 45.35 5.03
1328 1472 1.501169 TTCATACATGCATCGGCGAG 58.499 50.000 17.22 8.85 45.35 5.03
1394 1538 4.635324 TGCAATCAATCATACGAAGAAGCA 59.365 37.500 0.00 0.00 0.00 3.91
1395 1539 4.966366 GTGCAATCAATCATACGAAGAAGC 59.034 41.667 0.00 0.00 0.00 3.86
1419 1566 3.603158 AGTATACACCATCACGTGCAA 57.397 42.857 11.67 0.00 37.25 4.08
1420 1567 3.444388 TGTAGTATACACCATCACGTGCA 59.556 43.478 11.67 0.00 46.14 4.57
1421 1568 4.036567 TGTAGTATACACCATCACGTGC 57.963 45.455 11.67 0.00 46.14 5.34
1483 1631 4.503741 AATGTACAGACATGCAACCAAC 57.496 40.909 0.33 0.00 45.93 3.77
1487 1635 5.088739 GCTACAAATGTACAGACATGCAAC 58.911 41.667 0.33 0.00 45.93 4.17
1488 1636 5.003160 AGCTACAAATGTACAGACATGCAA 58.997 37.500 0.33 0.00 45.93 4.08
1491 1639 4.392754 TGCAGCTACAAATGTACAGACATG 59.607 41.667 0.33 0.00 45.93 3.21
1492 1640 7.298747 ATGTGCAGCTACAAATGTACAGACAT 61.299 38.462 0.33 0.00 43.64 3.06
1494 1642 3.745975 TGTGCAGCTACAAATGTACAGAC 59.254 43.478 0.33 0.00 37.16 3.51
1495 1643 4.001618 TGTGCAGCTACAAATGTACAGA 57.998 40.909 0.33 0.00 37.16 3.41
1497 1645 4.071423 ACATGTGCAGCTACAAATGTACA 58.929 39.130 19.44 7.76 44.84 2.90
1498 1646 4.685169 ACATGTGCAGCTACAAATGTAC 57.315 40.909 19.44 1.99 44.84 2.90
1501 1649 5.643664 ACAATACATGTGCAGCTACAAATG 58.356 37.500 14.60 14.60 41.93 2.32
1502 1650 5.902613 ACAATACATGTGCAGCTACAAAT 57.097 34.783 9.11 0.00 41.93 2.32
1503 1651 5.703978 AACAATACATGTGCAGCTACAAA 57.296 34.783 9.11 0.00 42.99 2.83
1504 1652 5.473162 AGAAACAATACATGTGCAGCTACAA 59.527 36.000 9.11 0.00 42.99 2.41
1505 1653 5.003160 AGAAACAATACATGTGCAGCTACA 58.997 37.500 9.11 0.00 42.99 2.74
1507 1655 4.142622 GCAGAAACAATACATGTGCAGCTA 60.143 41.667 9.11 0.00 42.99 3.32
1509 1657 2.919229 GCAGAAACAATACATGTGCAGC 59.081 45.455 9.11 0.00 42.99 5.25
1510 1658 4.163552 CAGCAGAAACAATACATGTGCAG 58.836 43.478 9.11 0.00 42.99 4.41
1511 1659 3.569277 ACAGCAGAAACAATACATGTGCA 59.431 39.130 9.11 0.00 42.99 4.57
1512 1660 3.916172 CACAGCAGAAACAATACATGTGC 59.084 43.478 9.11 0.00 42.99 4.57
1513 1661 5.112220 ACACAGCAGAAACAATACATGTG 57.888 39.130 9.11 0.00 42.99 3.21
1515 1663 7.755591 AGATAACACAGCAGAAACAATACATG 58.244 34.615 0.00 0.00 0.00 3.21
1519 1724 8.882736 CACATAGATAACACAGCAGAAACAATA 58.117 33.333 0.00 0.00 0.00 1.90
1535 1741 7.724506 AGGATTCTCCGTAGAACACATAGATAA 59.275 37.037 0.00 0.00 44.40 1.75
1536 1742 7.232188 AGGATTCTCCGTAGAACACATAGATA 58.768 38.462 0.00 0.00 44.40 1.98
1540 1746 6.145338 GAAGGATTCTCCGTAGAACACATA 57.855 41.667 0.00 0.00 44.40 2.29
1591 1804 5.669477 CTCCTTGTAGGAAATGAGAAGGAG 58.331 45.833 11.94 11.94 45.28 3.69
1620 1833 6.356556 TCTTGTTTGAAGATCCAGAGAACAA 58.643 36.000 9.93 9.93 35.17 2.83
1625 1838 5.334724 GCACTTCTTGTTTGAAGATCCAGAG 60.335 44.000 10.68 0.00 44.40 3.35
1626 1839 4.516698 GCACTTCTTGTTTGAAGATCCAGA 59.483 41.667 10.68 0.00 44.40 3.86
1628 1841 4.464008 AGCACTTCTTGTTTGAAGATCCA 58.536 39.130 10.68 0.00 44.40 3.41
1629 1842 4.516698 TGAGCACTTCTTGTTTGAAGATCC 59.483 41.667 10.68 0.26 44.40 3.36
1630 1843 5.679734 TGAGCACTTCTTGTTTGAAGATC 57.320 39.130 10.68 6.60 44.40 2.75
1673 1921 3.636300 CCATTGTGAGAGTAGAGAGGAGG 59.364 52.174 0.00 0.00 0.00 4.30
1705 1953 1.344191 TGACCATGGGATCGATGGCA 61.344 55.000 18.09 14.67 43.82 4.92
1715 1963 0.606401 GGTGTGAGTGTGACCATGGG 60.606 60.000 18.09 0.00 0.00 4.00
1721 1969 0.179121 TCGTGTGGTGTGAGTGTGAC 60.179 55.000 0.00 0.00 0.00 3.67
1722 1970 0.750249 ATCGTGTGGTGTGAGTGTGA 59.250 50.000 0.00 0.00 0.00 3.58
1723 1971 2.328473 CTATCGTGTGGTGTGAGTGTG 58.672 52.381 0.00 0.00 0.00 3.82
1724 1972 1.272490 CCTATCGTGTGGTGTGAGTGT 59.728 52.381 0.00 0.00 0.00 3.55
1725 1973 1.404181 CCCTATCGTGTGGTGTGAGTG 60.404 57.143 0.00 0.00 0.00 3.51
1726 1974 0.895530 CCCTATCGTGTGGTGTGAGT 59.104 55.000 0.00 0.00 0.00 3.41
1728 1976 0.892755 GTCCCTATCGTGTGGTGTGA 59.107 55.000 0.00 0.00 0.00 3.58
1737 2028 2.870435 GCACACAACAAGTCCCTATCGT 60.870 50.000 0.00 0.00 0.00 3.73
1773 2064 8.547069 TCATTTTATGAAGAAAAACAAAAGCCG 58.453 29.630 0.00 0.00 36.11 5.52
1785 2076 3.755905 TGGCGTGCTCATTTTATGAAGAA 59.244 39.130 0.00 0.00 39.11 2.52
1824 2148 7.229907 GGTATCGTGGAATTGGTTATGGTAATT 59.770 37.037 0.00 0.00 0.00 1.40
1865 2196 5.245526 ACCTGTCGATTAGTTTGTTCCTAGT 59.754 40.000 0.00 0.00 0.00 2.57
1887 2218 4.929211 GCCCAGTGTGATTTTTGATTTACC 59.071 41.667 0.00 0.00 0.00 2.85
1966 2340 0.532640 TTTCTTCTCAGCACAGCGCA 60.533 50.000 11.47 0.00 46.13 6.09
1967 2341 0.110464 GTTTCTTCTCAGCACAGCGC 60.110 55.000 0.00 0.00 42.91 5.92
1968 2342 0.162507 CGTTTCTTCTCAGCACAGCG 59.837 55.000 0.00 0.00 0.00 5.18
1969 2343 0.514691 CCGTTTCTTCTCAGCACAGC 59.485 55.000 0.00 0.00 0.00 4.40
1970 2344 2.154854 TCCGTTTCTTCTCAGCACAG 57.845 50.000 0.00 0.00 0.00 3.66
2012 2391 0.618981 AGGGTCTTCGGATGTTTCCC 59.381 55.000 10.76 10.76 39.01 3.97
2046 2425 3.055385 TGATTGTAAGGTAGGACAGGCAC 60.055 47.826 0.00 0.00 0.00 5.01
2076 2455 3.327172 AGTGGATGGATGGCTGATTCTAG 59.673 47.826 0.00 0.00 0.00 2.43
2094 2473 4.389576 GCGCACTTTCGGCAGTGG 62.390 66.667 0.30 7.60 43.94 4.00
2178 2560 3.341823 AGAGGCTGCAGAATTAGTGTTG 58.658 45.455 20.43 0.00 0.00 3.33
2235 2617 0.536460 GCCTTTGTCTGGTTCCCGAA 60.536 55.000 0.00 0.00 0.00 4.30
2244 2626 1.863662 CTGCTGCCTGCCTTTGTCTG 61.864 60.000 0.00 0.00 42.00 3.51
2264 2646 1.194218 TATGTACTGCAGCTCCAGCA 58.806 50.000 15.27 0.00 45.16 4.41
2269 2651 1.795286 GCGGAATATGTACTGCAGCTC 59.205 52.381 15.27 7.74 38.17 4.09


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

AutoCloner maintained by Alex Coulton.