Multiple sequence alignment - TraesCS3B01G179200

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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 TraesCS3B01G179200 chr3B 100.000 3289 0 0 1 3289 187328985 187332273 0.000000e+00 6074.0
1 TraesCS3B01G179200 chr3D 93.750 1264 64 8 1524 2784 130506072 130507323 0.000000e+00 1882.0
2 TraesCS3B01G179200 chr3D 90.637 534 33 10 977 1510 130504994 130505510 0.000000e+00 693.0
3 TraesCS3B01G179200 chr3D 100.000 149 0 0 2782 2930 112712171 112712023 3.230000e-70 276.0
4 TraesCS3B01G179200 chr3D 94.156 154 8 1 3123 3276 130509980 130510132 1.970000e-57 233.0
5 TraesCS3B01G179200 chr3D 98.276 116 2 0 2937 3052 130507689 130507804 1.550000e-48 204.0
6 TraesCS3B01G179200 chr3D 91.045 134 8 3 887 1018 130504868 130504999 9.380000e-41 178.0
7 TraesCS3B01G179200 chr3A 93.995 1149 61 5 1524 2668 142580327 142581471 0.000000e+00 1733.0
8 TraesCS3B01G179200 chr3A 88.809 554 43 12 977 1526 142579227 142579765 0.000000e+00 662.0
9 TraesCS3B01G179200 chr3A 95.046 323 13 3 2954 3276 142582094 142582413 3.790000e-139 505.0
10 TraesCS3B01G179200 chr3A 98.667 150 1 1 2782 2930 636738341 636738490 7.000000e-67 265.0
11 TraesCS3B01G179200 chr3A 99.291 141 1 0 2790 2930 636737911 636738051 4.210000e-64 255.0
12 TraesCS3B01G179200 chr3A 86.307 241 14 12 779 1018 142579010 142579232 9.120000e-61 244.0
13 TraesCS3B01G179200 chr3A 89.630 135 7 5 2657 2784 142581605 142581739 7.300000e-37 165.0
14 TraesCS3B01G179200 chr3A 97.826 92 2 0 2937 3028 142883121 142883212 3.400000e-35 159.0
15 TraesCS3B01G179200 chr1D 92.848 755 52 2 1 754 389094367 389095120 0.000000e+00 1094.0
16 TraesCS3B01G179200 chr1A 89.412 765 75 4 1 764 504096302 504097061 0.000000e+00 959.0
17 TraesCS3B01G179200 chr1A 76.707 249 54 4 143 389 418609248 418609494 5.720000e-28 135.0
18 TraesCS3B01G179200 chr2A 89.211 760 80 2 1 759 768690084 768690842 0.000000e+00 948.0
19 TraesCS3B01G179200 chr2A 100.000 147 0 0 2784 2930 30155561 30155415 4.180000e-69 272.0
20 TraesCS3B01G179200 chr1B 92.609 460 33 1 2 460 665015430 665014971 0.000000e+00 660.0
21 TraesCS3B01G179200 chr1B 91.667 276 22 1 490 765 665014661 665014387 6.660000e-102 381.0
22 TraesCS3B01G179200 chr4B 90.217 368 23 3 1524 1891 117059634 117059988 4.970000e-128 468.0
23 TraesCS3B01G179200 chr4B 100.000 29 0 0 365 393 21476080 21476108 2.000000e-03 54.7
24 TraesCS3B01G179200 chr7D 98.710 155 0 2 2777 2930 614183238 614183085 1.160000e-69 274.0
25 TraesCS3B01G179200 chr6B 100.000 148 0 0 2783 2930 131267284 131267137 1.160000e-69 274.0
26 TraesCS3B01G179200 chr4A 100.000 147 0 0 2784 2930 709889781 709889635 4.180000e-69 272.0
27 TraesCS3B01G179200 chr5D 100.000 145 0 0 2786 2930 119381135 119381279 5.410000e-68 268.0
28 TraesCS3B01G179200 chr5B 96.078 153 5 1 2779 2930 172750017 172749865 7.050000e-62 248.0
29 TraesCS3B01G179200 chr5B 75.600 250 55 6 143 389 9582791 9582545 5.770000e-23 119.0
30 TraesCS3B01G179200 chr4D 75.401 374 74 9 1666 2037 477337996 477337639 7.300000e-37 165.0
31 TraesCS3B01G179200 chr2B 74.684 316 73 6 143 453 714204242 714203929 2.060000e-27 134.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G179200 chr3B 187328985 187332273 3288 False 6074.0 6074 100.0000 1 3289 1 chr3B.!!$F1 3288
1 TraesCS3B01G179200 chr3D 130504868 130510132 5264 False 638.0 1882 93.5728 887 3276 5 chr3D.!!$F1 2389
2 TraesCS3B01G179200 chr3A 142579010 142582413 3403 False 661.8 1733 90.7574 779 3276 5 chr3A.!!$F2 2497
3 TraesCS3B01G179200 chr3A 636737911 636738490 579 False 260.0 265 98.9790 2782 2930 2 chr3A.!!$F3 148
4 TraesCS3B01G179200 chr1D 389094367 389095120 753 False 1094.0 1094 92.8480 1 754 1 chr1D.!!$F1 753
5 TraesCS3B01G179200 chr1A 504096302 504097061 759 False 959.0 959 89.4120 1 764 1 chr1A.!!$F2 763
6 TraesCS3B01G179200 chr2A 768690084 768690842 758 False 948.0 948 89.2110 1 759 1 chr2A.!!$F1 758
7 TraesCS3B01G179200 chr1B 665014387 665015430 1043 True 520.5 660 92.1380 2 765 2 chr1B.!!$R1 763

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
950 1234 0.037232 CCTCTCCGTTCCAAGGTGTC 60.037 60.0 0.0 0.0 0.0 3.67 F
1382 1702 0.179056 CGTGTGACCTGTGTTCCCTT 60.179 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 2708 0.394565 CTCCTTTCCCTGATAGGCGG 59.605 60.000 0.0 0.0 32.17 6.13 R
2324 3214 1.072806 TCTCCACATCCATAGCCATGC 59.927 52.381 0.0 0.0 0.00 4.06 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
56 58 2.820178 CAACCCTTTTATCCTTGCCCT 58.180 47.619 0.00 0.00 0.00 5.19
132 134 3.726557 TGAAGGATCACTGGAGCATTT 57.273 42.857 0.00 0.00 33.05 2.32
141 143 5.452078 TCACTGGAGCATTTCGAAAAATT 57.548 34.783 15.66 2.87 32.69 1.82
171 173 1.065126 CCTTCCATCACCCTCTTCCAC 60.065 57.143 0.00 0.00 0.00 4.02
195 197 2.158623 TCCAAGGCAATGACACTGAACT 60.159 45.455 0.00 0.00 0.00 3.01
250 252 4.624364 CCTGTGCAGACGCCCACA 62.624 66.667 0.02 0.00 39.45 4.17
390 392 1.003573 GTCCTCCTCCTCCCCATGT 59.996 63.158 0.00 0.00 0.00 3.21
404 406 2.373169 CCCCATGTAGATGCATACCTGT 59.627 50.000 0.00 0.00 0.00 4.00
630 912 4.699522 GCCAAAGGCGTCGGTCCT 62.700 66.667 0.00 0.00 39.62 3.85
677 959 5.530915 ACTCTCTCGATTGATAGGACTTCAG 59.469 44.000 0.00 0.00 0.00 3.02
726 1008 2.501223 GATTGACGTGGACTCCGCCA 62.501 60.000 0.00 0.00 35.02 5.69
729 1011 2.994995 ACGTGGACTCCGCCATCA 60.995 61.111 2.90 0.00 40.68 3.07
734 1016 4.148825 GACTCCGCCATCACCGCT 62.149 66.667 0.00 0.00 0.00 5.52
774 1056 5.896073 CCTAGATGGGGATAACTCTTGTT 57.104 43.478 0.00 0.00 39.98 2.83
775 1057 6.253946 CCTAGATGGGGATAACTCTTGTTT 57.746 41.667 0.00 0.00 37.59 2.83
776 1058 6.292150 CCTAGATGGGGATAACTCTTGTTTC 58.708 44.000 0.00 0.00 37.59 2.78
777 1059 6.100424 CCTAGATGGGGATAACTCTTGTTTCT 59.900 42.308 0.00 0.00 37.59 2.52
855 1138 2.438975 CAGGCCCATGTCACGCAT 60.439 61.111 0.00 0.00 38.60 4.73
862 1145 2.819595 ATGTCACGCATGGGACGC 60.820 61.111 17.76 6.08 36.26 5.19
879 1162 3.842923 CGAGCGCACCATCTCCCT 61.843 66.667 11.47 0.00 0.00 4.20
880 1163 2.586792 GAGCGCACCATCTCCCTT 59.413 61.111 11.47 0.00 0.00 3.95
881 1164 1.078143 GAGCGCACCATCTCCCTTT 60.078 57.895 11.47 0.00 0.00 3.11
882 1165 0.678048 GAGCGCACCATCTCCCTTTT 60.678 55.000 11.47 0.00 0.00 2.27
883 1166 0.678048 AGCGCACCATCTCCCTTTTC 60.678 55.000 11.47 0.00 0.00 2.29
884 1167 1.982073 GCGCACCATCTCCCTTTTCG 61.982 60.000 0.30 0.00 0.00 3.46
885 1168 0.673644 CGCACCATCTCCCTTTTCGT 60.674 55.000 0.00 0.00 0.00 3.85
945 1229 2.990066 ATAAGCCTCTCCGTTCCAAG 57.010 50.000 0.00 0.00 0.00 3.61
948 1232 1.376037 GCCTCTCCGTTCCAAGGTG 60.376 63.158 0.00 0.00 0.00 4.00
950 1234 0.037232 CCTCTCCGTTCCAAGGTGTC 60.037 60.000 0.00 0.00 0.00 3.67
984 1269 0.329596 CCAAAACCCTAGCAGCCTCT 59.670 55.000 0.00 0.00 0.00 3.69
985 1270 1.680249 CCAAAACCCTAGCAGCCTCTC 60.680 57.143 0.00 0.00 0.00 3.20
1309 1625 3.060000 GGTTGGTAACCCGGCTGC 61.060 66.667 0.00 0.00 46.12 5.25
1323 1639 1.202031 CGGCTGCGTTTTCTAATGTCC 60.202 52.381 0.00 0.00 0.00 4.02
1330 1646 2.482721 CGTTTTCTAATGTCCCGTTGCT 59.517 45.455 0.00 0.00 0.00 3.91
1333 1649 0.613260 TCTAATGTCCCGTTGCTGCT 59.387 50.000 0.00 0.00 0.00 4.24
1336 1652 0.250901 AATGTCCCGTTGCTGCTTCT 60.251 50.000 0.00 0.00 0.00 2.85
1337 1653 0.674895 ATGTCCCGTTGCTGCTTCTC 60.675 55.000 0.00 0.00 0.00 2.87
1338 1654 1.004440 GTCCCGTTGCTGCTTCTCT 60.004 57.895 0.00 0.00 0.00 3.10
1339 1655 1.004560 TCCCGTTGCTGCTTCTCTG 60.005 57.895 0.00 0.00 0.00 3.35
1340 1656 1.004560 CCCGTTGCTGCTTCTCTGA 60.005 57.895 0.00 0.00 0.00 3.27
1342 1658 1.446907 CCGTTGCTGCTTCTCTGAAT 58.553 50.000 0.00 0.00 0.00 2.57
1343 1659 2.621338 CCGTTGCTGCTTCTCTGAATA 58.379 47.619 0.00 0.00 0.00 1.75
1344 1660 2.606725 CCGTTGCTGCTTCTCTGAATAG 59.393 50.000 0.00 0.00 0.00 1.73
1345 1661 3.257393 CGTTGCTGCTTCTCTGAATAGT 58.743 45.455 0.00 0.00 0.00 2.12
1346 1662 4.424626 CGTTGCTGCTTCTCTGAATAGTA 58.575 43.478 0.00 0.00 0.00 1.82
1349 1665 5.921962 TGCTGCTTCTCTGAATAGTAAGA 57.078 39.130 0.00 0.00 0.00 2.10
1350 1666 5.900425 TGCTGCTTCTCTGAATAGTAAGAG 58.100 41.667 0.00 0.00 41.13 2.85
1351 1667 4.744631 GCTGCTTCTCTGAATAGTAAGAGC 59.255 45.833 0.00 0.00 39.86 4.09
1352 1668 5.680922 GCTGCTTCTCTGAATAGTAAGAGCA 60.681 44.000 0.00 0.00 39.86 4.26
1353 1669 6.286240 TGCTTCTCTGAATAGTAAGAGCAA 57.714 37.500 0.00 0.00 39.86 3.91
1354 1670 6.336566 TGCTTCTCTGAATAGTAAGAGCAAG 58.663 40.000 0.00 6.16 39.86 4.01
1355 1671 6.071108 TGCTTCTCTGAATAGTAAGAGCAAGT 60.071 38.462 13.58 0.00 39.86 3.16
1356 1672 6.475402 GCTTCTCTGAATAGTAAGAGCAAGTC 59.525 42.308 13.58 6.84 39.86 3.01
1357 1673 6.458232 TCTCTGAATAGTAAGAGCAAGTCC 57.542 41.667 0.00 0.00 39.86 3.85
1361 1677 6.096987 TCTGAATAGTAAGAGCAAGTCCGAAT 59.903 38.462 0.00 0.00 0.00 3.34
1379 1699 1.878953 ATTCGTGTGACCTGTGTTCC 58.121 50.000 0.00 0.00 0.00 3.62
1382 1702 0.179056 CGTGTGACCTGTGTTCCCTT 60.179 55.000 0.00 0.00 0.00 3.95
1386 1706 1.056660 TGACCTGTGTTCCCTTCCTC 58.943 55.000 0.00 0.00 0.00 3.71
1396 1716 6.369629 TGTGTTCCCTTCCTCTCATTTAAAA 58.630 36.000 0.00 0.00 0.00 1.52
1398 1718 5.472137 TGTTCCCTTCCTCTCATTTAAAACG 59.528 40.000 0.00 0.00 0.00 3.60
1401 1721 3.435671 CCTTCCTCTCATTTAAAACGCGT 59.564 43.478 5.58 5.58 0.00 6.01
1403 1723 3.655486 TCCTCTCATTTAAAACGCGTCA 58.345 40.909 14.44 0.00 0.00 4.35
1405 1725 4.328983 TCCTCTCATTTAAAACGCGTCATC 59.671 41.667 14.44 0.00 0.00 2.92
1410 1730 1.070038 TTAAAACGCGTCATCCGGTC 58.930 50.000 14.44 0.00 36.94 4.79
1418 1738 1.593006 GCGTCATCCGGTCAGTAATTG 59.407 52.381 0.00 0.00 36.94 2.32
1419 1739 1.593006 CGTCATCCGGTCAGTAATTGC 59.407 52.381 0.00 0.00 0.00 3.56
1430 1750 5.064198 CGGTCAGTAATTGCGGAGAAAATTA 59.936 40.000 0.00 0.00 30.13 1.40
1439 1759 3.128589 TGCGGAGAAAATTATTGGTCTGC 59.871 43.478 7.78 7.78 35.47 4.26
1442 1762 4.396166 CGGAGAAAATTATTGGTCTGCTGT 59.604 41.667 8.13 0.00 0.00 4.40
1448 1768 6.839124 AAATTATTGGTCTGCTGTTGATCA 57.161 33.333 0.00 0.00 0.00 2.92
1450 1770 6.630444 ATTATTGGTCTGCTGTTGATCATC 57.370 37.500 0.00 0.00 0.00 2.92
1451 1771 2.014335 TGGTCTGCTGTTGATCATCG 57.986 50.000 0.00 0.00 0.00 3.84
1452 1772 1.276138 TGGTCTGCTGTTGATCATCGT 59.724 47.619 0.00 0.00 0.00 3.73
1453 1773 2.289631 TGGTCTGCTGTTGATCATCGTT 60.290 45.455 0.00 0.00 0.00 3.85
1456 1776 3.681897 GTCTGCTGTTGATCATCGTTTCT 59.318 43.478 0.00 0.00 0.00 2.52
1462 1782 5.120830 GCTGTTGATCATCGTTTCTTGTACT 59.879 40.000 0.00 0.00 0.00 2.73
1486 1806 5.105554 TGTTTGGTTCAAGCACTTGTGTATT 60.106 36.000 10.05 0.00 41.16 1.89
1510 1830 2.352960 GGAGAAAATCCGCACTAGCTTG 59.647 50.000 0.00 0.00 38.67 4.01
1511 1831 3.003480 GAGAAAATCCGCACTAGCTTGT 58.997 45.455 0.00 0.00 39.10 3.16
1532 2416 0.970427 GCACCTGTGGTTAATGGGGG 60.970 60.000 0.00 0.00 31.02 5.40
1534 2418 0.702316 ACCTGTGGTTAATGGGGGAC 59.298 55.000 0.00 0.00 27.29 4.46
1542 2426 3.398292 TGGTTAATGGGGGACAACTTGTA 59.602 43.478 0.00 0.00 0.00 2.41
1548 2432 5.994416 ATGGGGGACAACTTGTAAGATAT 57.006 39.130 0.00 0.00 0.00 1.63
1549 2433 5.367945 TGGGGGACAACTTGTAAGATATC 57.632 43.478 0.00 0.00 0.00 1.63
1629 2513 3.037549 TCATCAACAGGCAAAAAGGGTT 58.962 40.909 0.00 0.00 0.00 4.11
1638 2522 2.158971 GGCAAAAAGGGTTGAGCTGAAA 60.159 45.455 0.00 0.00 0.00 2.69
1680 2564 2.092968 TGTGAGCAACCTTCAGAAGTGT 60.093 45.455 9.41 4.20 0.00 3.55
1794 2678 5.486526 GAGATCAAGGATGTGAAGACACTT 58.513 41.667 0.00 0.00 46.07 3.16
1795 2679 5.486526 AGATCAAGGATGTGAAGACACTTC 58.513 41.667 0.00 0.00 46.07 3.01
1986 2870 0.040646 TCTTAGGTTCTCCTGCCGGA 59.959 55.000 5.05 0.00 44.81 5.14
1998 2882 1.571919 CTGCCGGAAAGGTCTATTCG 58.428 55.000 5.05 0.00 43.70 3.34
2004 2888 3.067742 CCGGAAAGGTCTATTCGAAGCTA 59.932 47.826 3.35 0.00 34.51 3.32
2023 2907 2.478872 AAGGGCTGTATCTGCTAGGA 57.521 50.000 0.00 0.00 0.00 2.94
2134 3018 5.472478 CCTGTGCTATGCATTGTCTTGATAT 59.528 40.000 3.54 0.00 41.91 1.63
2205 3089 2.878406 TCTGTTCTCGGCTTTTTCTTGG 59.122 45.455 0.00 0.00 0.00 3.61
2386 3276 8.186709 AGAATCTTGAATTGTCAGATTTGGTT 57.813 30.769 5.31 0.00 34.52 3.67
2399 3290 7.393234 TGTCAGATTTGGTTGATTTACCCTTAG 59.607 37.037 0.00 0.00 37.39 2.18
2404 3295 9.586435 GATTTGGTTGATTTACCCTTAGAAATG 57.414 33.333 0.00 0.00 37.39 2.32
2413 3304 3.763057 ACCCTTAGAAATGGACCACAAC 58.237 45.455 0.00 0.00 0.00 3.32
2568 3459 5.421693 TGGCTATGTTTGTTTAGATGCCATT 59.578 36.000 0.00 0.00 42.20 3.16
2573 3464 9.206870 CTATGTTTGTTTAGATGCCATTGTTTT 57.793 29.630 0.00 0.00 0.00 2.43
2575 3466 7.914465 TGTTTGTTTAGATGCCATTGTTTTTC 58.086 30.769 0.00 0.00 0.00 2.29
2595 3486 5.659440 TTCTCTTTGGTGCTTTGTTCTTT 57.341 34.783 0.00 0.00 0.00 2.52
2624 3515 2.300433 GATTACCATCCTGTGCATGCA 58.700 47.619 18.46 18.46 0.00 3.96
2700 3737 4.595781 TCCAATGGTCCTTTACACTACAGT 59.404 41.667 0.00 0.00 0.00 3.55
2784 3827 7.016268 AGACTTTGGAGAAGGTAAACATGTAGA 59.984 37.037 0.00 0.00 0.00 2.59
2785 3828 7.162082 ACTTTGGAGAAGGTAAACATGTAGAG 58.838 38.462 0.00 0.00 0.00 2.43
2864 4398 4.418013 GCAAAAACAAAAGTTGCCAACT 57.582 36.364 3.74 3.74 45.46 3.16
2930 4464 6.183360 GCAACCAATCTCTAGCCAATATTTGT 60.183 38.462 0.00 0.00 0.00 2.83
2931 4465 7.013274 GCAACCAATCTCTAGCCAATATTTGTA 59.987 37.037 0.00 0.00 0.00 2.41
2932 4466 8.562892 CAACCAATCTCTAGCCAATATTTGTAG 58.437 37.037 0.00 0.00 0.00 2.74
2933 4467 7.806180 ACCAATCTCTAGCCAATATTTGTAGT 58.194 34.615 0.00 0.00 0.00 2.73
2934 4468 8.275040 ACCAATCTCTAGCCAATATTTGTAGTT 58.725 33.333 0.00 0.00 0.00 2.24
2935 4469 8.778358 CCAATCTCTAGCCAATATTTGTAGTTC 58.222 37.037 0.00 0.00 0.00 3.01
2957 4491 9.540538 AGTTCCTCAGCTACTATTCATACATAT 57.459 33.333 0.00 0.00 0.00 1.78
3121 5555 3.066064 TGTTGTAAAGTGGTGTGCATCAC 59.934 43.478 7.45 7.45 45.47 3.06
3131 6770 0.106894 TGTGCATCACGTGGTACCAA 59.893 50.000 18.31 0.15 37.14 3.67
3194 6833 8.695456 ACTGTTTTATTTGACACCAGAAATCTT 58.305 29.630 0.00 0.00 0.00 2.40
3281 6920 9.586732 CCTTTGGGGAAGATATGATATGTTTAA 57.413 33.333 0.00 0.00 37.57 1.52
3285 6924 9.964354 TGGGGAAGATATGATATGTTTAATCTG 57.036 33.333 0.00 0.00 0.00 2.90
3286 6925 9.965902 GGGGAAGATATGATATGTTTAATCTGT 57.034 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 40 2.000048 TGAGGGCAAGGATAAAAGGGT 59.000 47.619 0.00 0.00 0.00 4.34
56 58 1.003118 AGCTGAATAAACTGCCGGTGA 59.997 47.619 1.90 0.00 35.80 4.02
132 134 2.099405 GGAGGGCCATGAATTTTTCGA 58.901 47.619 6.18 0.00 0.00 3.71
141 143 0.624206 TGATGGAAGGAGGGCCATGA 60.624 55.000 6.18 0.00 44.60 3.07
171 173 2.082231 CAGTGTCATTGCCTTGGAGAG 58.918 52.381 0.00 0.00 0.00 3.20
195 197 1.742308 AGGGCCTGAACTTGTTCCTA 58.258 50.000 4.50 0.00 0.00 2.94
208 210 2.224670 TGACAATTAACGTGAAGGGCCT 60.225 45.455 0.00 0.00 0.00 5.19
250 252 0.534412 CTCAGGCAGATGAGGAACGT 59.466 55.000 5.21 0.00 42.52 3.99
276 278 0.901580 CCAAACCCTTCAGCCATGCT 60.902 55.000 0.00 0.00 40.77 3.79
277 279 1.187567 ACCAAACCCTTCAGCCATGC 61.188 55.000 0.00 0.00 0.00 4.06
390 392 5.822519 GGACAAATTCACAGGTATGCATCTA 59.177 40.000 0.19 0.00 0.00 1.98
693 975 1.303236 CAATCCTTCACGGTGGCCA 60.303 57.895 0.00 0.00 0.00 5.36
726 1008 2.362369 CCTGACCTCCAGCGGTGAT 61.362 63.158 17.83 0.00 41.57 3.06
729 1011 2.526873 AACCTGACCTCCAGCGGT 60.527 61.111 0.00 0.00 41.57 5.68
734 1016 2.151369 GGTTCCAACCTGACCTCCA 58.849 57.895 0.83 0.00 45.75 3.86
801 1083 3.127203 GTCAGAGCTAGCGACAGAAACTA 59.873 47.826 9.55 0.00 0.00 2.24
862 1145 2.859273 AAAGGGAGATGGTGCGCTCG 62.859 60.000 9.73 0.00 31.95 5.03
863 1146 0.678048 AAAAGGGAGATGGTGCGCTC 60.678 55.000 9.73 4.47 0.00 5.03
865 1148 1.803289 GAAAAGGGAGATGGTGCGC 59.197 57.895 0.00 0.00 0.00 6.09
866 1149 0.673644 ACGAAAAGGGAGATGGTGCG 60.674 55.000 0.00 0.00 0.00 5.34
868 1151 1.732259 CGAACGAAAAGGGAGATGGTG 59.268 52.381 0.00 0.00 0.00 4.17
869 1152 1.346722 ACGAACGAAAAGGGAGATGGT 59.653 47.619 0.14 0.00 0.00 3.55
871 1154 2.960819 AGACGAACGAAAAGGGAGATG 58.039 47.619 0.14 0.00 0.00 2.90
872 1155 3.244112 ACAAGACGAACGAAAAGGGAGAT 60.244 43.478 0.14 0.00 0.00 2.75
873 1156 2.101917 ACAAGACGAACGAAAAGGGAGA 59.898 45.455 0.14 0.00 0.00 3.71
874 1157 2.221055 CACAAGACGAACGAAAAGGGAG 59.779 50.000 0.14 0.00 0.00 4.30
875 1158 2.206750 CACAAGACGAACGAAAAGGGA 58.793 47.619 0.14 0.00 0.00 4.20
876 1159 1.333791 GCACAAGACGAACGAAAAGGG 60.334 52.381 0.14 0.00 0.00 3.95
877 1160 1.597663 AGCACAAGACGAACGAAAAGG 59.402 47.619 0.14 0.00 0.00 3.11
878 1161 2.599848 CCAGCACAAGACGAACGAAAAG 60.600 50.000 0.14 0.00 0.00 2.27
879 1162 1.329292 CCAGCACAAGACGAACGAAAA 59.671 47.619 0.14 0.00 0.00 2.29
880 1163 0.934496 CCAGCACAAGACGAACGAAA 59.066 50.000 0.14 0.00 0.00 3.46
881 1164 1.495584 GCCAGCACAAGACGAACGAA 61.496 55.000 0.14 0.00 0.00 3.85
882 1165 1.954146 GCCAGCACAAGACGAACGA 60.954 57.895 0.14 0.00 0.00 3.85
883 1166 2.551270 GCCAGCACAAGACGAACG 59.449 61.111 0.00 0.00 0.00 3.95
884 1167 2.617274 GGGCCAGCACAAGACGAAC 61.617 63.158 4.39 0.00 0.00 3.95
885 1168 2.281484 GGGCCAGCACAAGACGAA 60.281 61.111 4.39 0.00 0.00 3.85
1142 1458 0.179065 TCATCTCGCTTGGCATCAGG 60.179 55.000 0.00 0.00 0.00 3.86
1308 1624 2.846693 CAACGGGACATTAGAAAACGC 58.153 47.619 0.00 0.00 0.00 4.84
1309 1625 2.482721 AGCAACGGGACATTAGAAAACG 59.517 45.455 0.00 0.00 0.00 3.60
1323 1639 1.446907 ATTCAGAGAAGCAGCAACGG 58.553 50.000 0.00 0.00 0.00 4.44
1330 1646 5.921962 TGCTCTTACTATTCAGAGAAGCA 57.078 39.130 0.24 0.00 39.21 3.91
1333 1649 6.404844 CGGACTTGCTCTTACTATTCAGAGAA 60.405 42.308 0.24 0.00 39.21 2.87
1336 1652 4.948004 TCGGACTTGCTCTTACTATTCAGA 59.052 41.667 0.00 0.00 0.00 3.27
1337 1653 5.250235 TCGGACTTGCTCTTACTATTCAG 57.750 43.478 0.00 0.00 0.00 3.02
1338 1654 5.654603 TTCGGACTTGCTCTTACTATTCA 57.345 39.130 0.00 0.00 0.00 2.57
1339 1655 6.074782 CGAATTCGGACTTGCTCTTACTATTC 60.075 42.308 20.16 0.00 35.37 1.75
1340 1656 5.749109 CGAATTCGGACTTGCTCTTACTATT 59.251 40.000 20.16 0.00 35.37 1.73
1342 1658 4.157289 ACGAATTCGGACTTGCTCTTACTA 59.843 41.667 29.79 0.00 44.95 1.82
1343 1659 3.056749 ACGAATTCGGACTTGCTCTTACT 60.057 43.478 29.79 2.48 44.95 2.24
1344 1660 3.060895 CACGAATTCGGACTTGCTCTTAC 59.939 47.826 29.79 0.00 44.95 2.34
1345 1661 3.250744 CACGAATTCGGACTTGCTCTTA 58.749 45.455 29.79 0.00 44.95 2.10
1346 1662 2.069273 CACGAATTCGGACTTGCTCTT 58.931 47.619 29.79 3.67 44.95 2.85
1349 1665 1.148310 CACACGAATTCGGACTTGCT 58.852 50.000 29.79 5.93 44.95 3.91
1350 1666 1.136336 GTCACACGAATTCGGACTTGC 60.136 52.381 29.79 12.60 44.95 4.01
1351 1667 1.459592 GGTCACACGAATTCGGACTTG 59.540 52.381 29.79 20.88 44.95 3.16
1352 1668 1.343465 AGGTCACACGAATTCGGACTT 59.657 47.619 29.79 20.22 44.95 3.01
1353 1669 0.966920 AGGTCACACGAATTCGGACT 59.033 50.000 29.79 15.37 44.95 3.85
1354 1670 1.068474 CAGGTCACACGAATTCGGAC 58.932 55.000 29.79 24.65 44.95 4.79
1355 1671 0.677288 ACAGGTCACACGAATTCGGA 59.323 50.000 29.79 15.86 44.95 4.55
1356 1672 0.790207 CACAGGTCACACGAATTCGG 59.210 55.000 29.79 20.64 44.95 4.30
1357 1673 1.497991 ACACAGGTCACACGAATTCG 58.502 50.000 25.64 25.64 46.33 3.34
1361 1677 0.179067 GGGAACACAGGTCACACGAA 60.179 55.000 0.00 0.00 0.00 3.85
1379 1699 3.435671 ACGCGTTTTAAATGAGAGGAAGG 59.564 43.478 5.58 0.00 0.00 3.46
1382 1702 3.655486 TGACGCGTTTTAAATGAGAGGA 58.345 40.909 15.53 0.00 0.00 3.71
1386 1706 3.342269 CGGATGACGCGTTTTAAATGAG 58.658 45.455 15.53 0.00 34.82 2.90
1396 1716 1.588824 TTACTGACCGGATGACGCGT 61.589 55.000 13.85 13.85 42.52 6.01
1398 1718 1.593006 CAATTACTGACCGGATGACGC 59.407 52.381 9.46 0.00 42.52 5.19
1401 1721 1.472552 CCGCAATTACTGACCGGATGA 60.473 52.381 9.46 0.00 41.34 2.92
1403 1723 0.828022 TCCGCAATTACTGACCGGAT 59.172 50.000 9.46 0.00 42.51 4.18
1405 1725 0.174845 TCTCCGCAATTACTGACCGG 59.825 55.000 0.00 0.00 40.25 5.28
1410 1730 7.257722 ACCAATAATTTTCTCCGCAATTACTG 58.742 34.615 0.00 0.00 29.66 2.74
1418 1738 3.378427 AGCAGACCAATAATTTTCTCCGC 59.622 43.478 0.00 0.00 0.00 5.54
1419 1739 4.396166 ACAGCAGACCAATAATTTTCTCCG 59.604 41.667 0.00 0.00 0.00 4.63
1430 1750 2.941064 CGATGATCAACAGCAGACCAAT 59.059 45.455 0.00 0.00 34.21 3.16
1439 1759 6.146184 ACAGTACAAGAAACGATGATCAACAG 59.854 38.462 0.00 0.00 0.00 3.16
1442 1762 7.351981 CAAACAGTACAAGAAACGATGATCAA 58.648 34.615 0.00 0.00 0.00 2.57
1448 1768 5.587043 TGAACCAAACAGTACAAGAAACGAT 59.413 36.000 0.00 0.00 0.00 3.73
1450 1770 5.224562 TGAACCAAACAGTACAAGAAACG 57.775 39.130 0.00 0.00 0.00 3.60
1451 1771 5.515270 GCTTGAACCAAACAGTACAAGAAAC 59.485 40.000 0.00 0.00 37.49 2.78
1452 1772 5.184096 TGCTTGAACCAAACAGTACAAGAAA 59.816 36.000 0.00 0.00 37.49 2.52
1453 1773 4.702612 TGCTTGAACCAAACAGTACAAGAA 59.297 37.500 0.00 0.00 37.49 2.52
1456 1776 4.013728 AGTGCTTGAACCAAACAGTACAA 58.986 39.130 0.00 0.00 0.00 2.41
1462 1782 2.560542 ACACAAGTGCTTGAACCAAACA 59.439 40.909 17.62 0.00 42.93 2.83
1486 1806 3.388024 AGCTAGTGCGGATTTTCTCCATA 59.612 43.478 0.00 0.00 45.24 2.74
1510 1830 2.365582 CCCATTAACCACAGGTGCTAC 58.634 52.381 0.00 0.00 35.34 3.58
1511 1831 1.283613 CCCCATTAACCACAGGTGCTA 59.716 52.381 0.00 0.00 35.34 3.49
1532 2416 9.593134 ACATTCAGAGATATCTTACAAGTTGTC 57.407 33.333 12.82 0.00 0.00 3.18
1568 2452 3.710209 ATTGCTACAAAGGAGACAGCT 57.290 42.857 0.00 0.00 33.38 4.24
1569 2453 4.216257 TGAAATTGCTACAAAGGAGACAGC 59.784 41.667 0.00 0.00 0.00 4.40
1605 2489 4.080638 ACCCTTTTTGCCTGTTGATGAAAA 60.081 37.500 0.00 0.00 0.00 2.29
1609 2493 3.132925 CAACCCTTTTTGCCTGTTGATG 58.867 45.455 0.00 0.00 38.81 3.07
1610 2494 3.037549 TCAACCCTTTTTGCCTGTTGAT 58.962 40.909 0.00 0.00 40.06 2.57
1612 2496 2.825205 CTCAACCCTTTTTGCCTGTTG 58.175 47.619 0.00 0.00 38.07 3.33
1613 2497 1.138859 GCTCAACCCTTTTTGCCTGTT 59.861 47.619 0.00 0.00 0.00 3.16
1629 2513 2.585330 TCATGCCTTGTTTTCAGCTCA 58.415 42.857 0.00 0.00 0.00 4.26
1638 2522 3.719268 TCTGGTGTATCATGCCTTGTT 57.281 42.857 0.00 0.00 0.00 2.83
1680 2564 3.422303 GCATGCACGAAGTCCGCA 61.422 61.111 14.21 0.00 43.40 5.69
1794 2678 2.121538 CGACAGATGCTCCCCTCGA 61.122 63.158 0.00 0.00 0.00 4.04
1795 2679 2.415010 CGACAGATGCTCCCCTCG 59.585 66.667 0.00 0.00 0.00 4.63
1824 2708 0.394565 CTCCTTTCCCTGATAGGCGG 59.605 60.000 0.00 0.00 32.17 6.13
1863 2747 2.712709 CGAGTCCTGGTAGAGTTCTCA 58.287 52.381 2.64 0.00 0.00 3.27
1986 2870 4.683671 GCCCTTAGCTTCGAATAGACCTTT 60.684 45.833 0.00 0.00 38.99 3.11
2004 2888 2.478872 TCCTAGCAGATACAGCCCTT 57.521 50.000 0.00 0.00 0.00 3.95
2023 2907 6.067217 ACTCAACTAATACCTTTCTGCCAT 57.933 37.500 0.00 0.00 0.00 4.40
2134 3018 2.687935 GGCACTTCCAAGTTGTTCTTCA 59.312 45.455 1.45 0.00 37.08 3.02
2205 3089 6.199937 ACATGTATCAGAACAGCATTTTCC 57.800 37.500 0.00 0.00 31.70 3.13
2286 3173 4.120589 ACACACTCGAAGAAAAAGAGACC 58.879 43.478 0.00 0.00 34.09 3.85
2324 3214 1.072806 TCTCCACATCCATAGCCATGC 59.927 52.381 0.00 0.00 0.00 4.06
2386 3276 6.184789 GTGGTCCATTTCTAAGGGTAAATCA 58.815 40.000 0.00 0.00 33.15 2.57
2413 3304 6.207417 ACTTTCTGTAGGATTCACAACCATTG 59.793 38.462 0.00 0.00 0.00 2.82
2474 3365 2.697147 TTTGGGTGAGCCTCCTGTGC 62.697 60.000 1.06 0.00 34.45 4.57
2568 3459 5.146010 ACAAAGCACCAAAGAGAAAAACA 57.854 34.783 0.00 0.00 0.00 2.83
2573 3464 5.659440 AAAGAACAAAGCACCAAAGAGAA 57.341 34.783 0.00 0.00 0.00 2.87
2575 3466 7.922811 AGATTAAAAGAACAAAGCACCAAAGAG 59.077 33.333 0.00 0.00 0.00 2.85
2700 3737 5.958380 AGAGACAGATTGGTTATAGGTGTCA 59.042 40.000 0.00 0.00 36.19 3.58
2864 4398 5.353678 CCAATCTCACAAAAAGTTGCCAAAA 59.646 36.000 0.00 0.00 38.39 2.44
2930 4464 8.941995 ATGTATGAATAGTAGCTGAGGAACTA 57.058 34.615 0.00 0.00 41.55 2.24
2934 4468 9.409918 GGTATATGTATGAATAGTAGCTGAGGA 57.590 37.037 0.00 0.00 0.00 3.71
2935 4469 9.190317 TGGTATATGTATGAATAGTAGCTGAGG 57.810 37.037 0.00 0.00 0.00 3.86
3100 5534 3.628017 GTGATGCACACCACTTTACAAC 58.372 45.455 7.86 0.00 43.05 3.32
3121 5555 5.238650 AGAAACAATTTCTCTTGGTACCACG 59.761 40.000 16.04 13.87 46.62 4.94
3150 6789 4.780815 ACAGTTGGAGAACTCATCAAACA 58.219 39.130 4.23 0.00 40.68 2.83


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

AutoCloner maintained by Alex Coulton.