Multiple sequence alignment - TraesCS4A01G419000

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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 TraesCS4A01G419000 chr4A 100.000 3797 0 0 1 3797 688968367 688972163 0.000000e+00 7012.0
1 TraesCS4A01G419000 chr4A 90.891 2064 156 12 1752 3797 689066819 689068868 0.000000e+00 2741.0
2 TraesCS4A01G419000 chr4A 90.663 2067 159 15 1752 3797 689090206 689092259 0.000000e+00 2717.0
3 TraesCS4A01G419000 chr4A 79.514 2182 367 50 1656 3795 686590555 686592698 0.000000e+00 1480.0
4 TraesCS4A01G419000 chr4A 78.959 2172 376 52 1667 3795 686624622 686626755 0.000000e+00 1404.0
5 TraesCS4A01G419000 chr4A 78.267 2181 396 48 1656 3795 686569910 686572053 0.000000e+00 1330.0
6 TraesCS4A01G419000 chr4A 85.487 1006 62 32 1 949 689065834 689066812 0.000000e+00 972.0
7 TraesCS4A01G419000 chr4A 84.990 1006 67 32 1 949 689089221 689090199 0.000000e+00 944.0
8 TraesCS4A01G419000 chr1B 94.380 2171 101 8 1643 3797 567711973 567714138 0.000000e+00 3314.0
9 TraesCS4A01G419000 chr1B 89.565 115 12 0 1156 1270 567711588 567711702 3.060000e-31 147.0
10 TraesCS4A01G419000 chr1B 100.000 32 0 0 1612 1643 567711904 567711935 4.100000e-05 60.2
11 TraesCS4A01G419000 chr7D 91.947 2173 144 11 1643 3797 37214787 37216946 0.000000e+00 3014.0
12 TraesCS4A01G419000 chr7D 92.216 2107 135 8 1706 3797 36743415 36745507 0.000000e+00 2955.0
13 TraesCS4A01G419000 chr7D 80.341 1643 270 37 2177 3797 36494555 36496166 0.000000e+00 1195.0
14 TraesCS4A01G419000 chr7D 94.781 479 24 1 1 478 36742670 36743148 0.000000e+00 745.0
15 TraesCS4A01G419000 chr7D 94.403 268 15 0 211 478 37213362 37213629 2.730000e-111 412.0
16 TraesCS4A01G419000 chr7D 89.362 235 15 3 1036 1270 37214306 37214530 1.730000e-73 287.0
17 TraesCS4A01G419000 chr7D 89.474 114 7 4 544 652 37213721 37213834 5.110000e-29 139.0
18 TraesCS4A01G419000 chr7A 91.107 2114 134 18 1707 3797 36542915 36544997 0.000000e+00 2813.0
19 TraesCS4A01G419000 chr7A 79.450 2146 369 52 1688 3795 36485219 36487330 0.000000e+00 1454.0
20 TraesCS4A01G419000 chr7A 89.375 480 44 5 2 478 36537557 36538032 7.020000e-167 597.0
21 TraesCS4A01G419000 chr7A 92.340 235 16 2 1036 1270 36542324 36542556 2.190000e-87 333.0
22 TraesCS4A01G419000 chr7A 82.933 375 25 15 472 809 36538064 36538436 6.160000e-78 302.0
23 TraesCS4A01G419000 chr7A 88.318 214 17 2 858 1063 36542106 36542319 2.260000e-62 250.0


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 TraesCS4A01G419000 chr4A 688968367 688972163 3796 False 7012.000000 7012 100.000000 1 3797 1 chr4A.!!$F4 3796
1 TraesCS4A01G419000 chr4A 689065834 689068868 3034 False 1856.500000 2741 88.189000 1 3797 2 chr4A.!!$F5 3796
2 TraesCS4A01G419000 chr4A 689089221 689092259 3038 False 1830.500000 2717 87.826500 1 3797 2 chr4A.!!$F6 3796
3 TraesCS4A01G419000 chr4A 686590555 686592698 2143 False 1480.000000 1480 79.514000 1656 3795 1 chr4A.!!$F2 2139
4 TraesCS4A01G419000 chr4A 686624622 686626755 2133 False 1404.000000 1404 78.959000 1667 3795 1 chr4A.!!$F3 2128
5 TraesCS4A01G419000 chr4A 686569910 686572053 2143 False 1330.000000 1330 78.267000 1656 3795 1 chr4A.!!$F1 2139
6 TraesCS4A01G419000 chr1B 567711588 567714138 2550 False 1173.733333 3314 94.648333 1156 3797 3 chr1B.!!$F1 2641
7 TraesCS4A01G419000 chr7D 36742670 36745507 2837 False 1850.000000 2955 93.498500 1 3797 2 chr7D.!!$F2 3796
8 TraesCS4A01G419000 chr7D 36494555 36496166 1611 False 1195.000000 1195 80.341000 2177 3797 1 chr7D.!!$F1 1620
9 TraesCS4A01G419000 chr7D 37213362 37216946 3584 False 963.000000 3014 91.296500 211 3797 4 chr7D.!!$F3 3586
10 TraesCS4A01G419000 chr7A 36485219 36487330 2111 False 1454.000000 1454 79.450000 1688 3795 1 chr7A.!!$F1 2107
11 TraesCS4A01G419000 chr7A 36537557 36544997 7440 False 859.000000 2813 88.814600 2 3797 5 chr7A.!!$F2 3795

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
969 4742 0.108963 CCGTCTCGTCCCTATCTCCT 59.891 60.0 0.0 0.0 0.0 3.69 F
1808 5763 0.037303 AGGGGCACACACTCAATCAG 59.963 55.0 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 5919 0.627451 AAGAGCCAGGATTGATGCCA 59.373 50.000 0.00 0.0 0.00 4.92 R
3702 7704 1.228245 GCAAGACTGGGCCAGTTCA 60.228 57.895 37.83 0.0 45.44 3.18 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
53 55 5.691305 CACCAACCTTCACATGTGTAAATTG 59.309 40.000 24.63 21.50 0.00 2.32
61 63 9.180678 CCTTCACATGTGTAAATTGTACTTTTC 57.819 33.333 24.63 0.00 0.00 2.29
103 105 1.714794 AGAGTCGATTGCAAGGTTCG 58.285 50.000 13.43 13.43 0.00 3.95
133 136 4.801330 TCGTCCACACTTCAATAGTCAT 57.199 40.909 0.00 0.00 33.85 3.06
196 201 2.543635 AGGGAAAAAGGCATGCAAGAT 58.456 42.857 21.36 0.48 0.00 2.40
203 208 7.041107 GGAAAAAGGCATGCAAGATAATAACA 58.959 34.615 21.36 0.00 0.00 2.41
208 213 9.452287 AAAGGCATGCAAGATAATAACAAAAAT 57.548 25.926 21.36 0.00 0.00 1.82
254 259 8.005192 AGAGGCATCAGAAGAAAATTAATTCC 57.995 34.615 0.00 0.00 0.00 3.01
291 296 1.362717 GCCTTCGAGGTAGCGCATA 59.637 57.895 11.47 0.00 37.80 3.14
471 476 1.332889 ATGTCTCATGGGCTCGAGCA 61.333 55.000 36.27 19.60 44.36 4.26
473 478 0.676184 GTCTCATGGGCTCGAGCATA 59.324 55.000 36.27 24.93 44.36 3.14
495 538 2.363680 TCTCACTAGCTTGCTAGGATGC 59.636 50.000 26.92 13.39 0.00 3.91
500 543 1.452651 GCTTGCTAGGATGCTGGCA 60.453 57.895 21.19 21.19 39.04 4.92
520 568 1.600916 GACTTGCACGGCCTCCTTT 60.601 57.895 0.00 0.00 0.00 3.11
528 576 2.779506 CACGGCCTCCTTTTTCTTAGT 58.220 47.619 0.00 0.00 0.00 2.24
887 4660 1.221414 GACATATTGAGCCCAGTCGC 58.779 55.000 0.00 0.00 0.00 5.19
936 4709 9.784680 GTAAGTAAAGTCAAGACGATAAGATGA 57.215 33.333 0.00 0.00 36.20 2.92
969 4742 0.108963 CCGTCTCGTCCCTATCTCCT 59.891 60.000 0.00 0.00 0.00 3.69
970 4743 1.231221 CGTCTCGTCCCTATCTCCTG 58.769 60.000 0.00 0.00 0.00 3.86
971 4744 1.475392 CGTCTCGTCCCTATCTCCTGT 60.475 57.143 0.00 0.00 0.00 4.00
978 4757 2.838202 GTCCCTATCTCCTGTTTGGTCA 59.162 50.000 0.00 0.00 37.07 4.02
1002 4781 3.918220 GTCGCGCTCGAGCCAATG 61.918 66.667 30.66 17.93 46.46 2.82
1128 4939 3.637273 GCCTACATAGGGCGGGGG 61.637 72.222 7.07 0.00 43.82 5.40
1194 5005 1.000612 GACCTCCTCGTTCCTCCCT 59.999 63.158 0.00 0.00 0.00 4.20
1293 5104 2.028337 GCAGTAGCTAGCTCCCGC 59.972 66.667 23.26 17.76 37.91 6.13
1294 5105 2.786495 GCAGTAGCTAGCTCCCGCA 61.786 63.158 23.26 0.00 36.76 5.69
1295 5106 1.066587 CAGTAGCTAGCTCCCGCAC 59.933 63.158 23.26 13.69 39.10 5.34
1296 5107 2.128507 AGTAGCTAGCTCCCGCACC 61.129 63.158 23.26 1.70 39.10 5.01
1297 5108 3.217017 TAGCTAGCTCCCGCACCG 61.217 66.667 23.26 0.00 39.10 4.94
1322 5133 4.500116 GTGCCCGTCGCTCCTCTC 62.500 72.222 0.00 0.00 38.78 3.20
1323 5134 4.742649 TGCCCGTCGCTCCTCTCT 62.743 66.667 0.00 0.00 38.78 3.10
1324 5135 3.894947 GCCCGTCGCTCCTCTCTC 61.895 72.222 0.00 0.00 0.00 3.20
1325 5136 3.213402 CCCGTCGCTCCTCTCTCC 61.213 72.222 0.00 0.00 0.00 3.71
1326 5137 3.578272 CCGTCGCTCCTCTCTCCG 61.578 72.222 0.00 0.00 0.00 4.63
1327 5138 4.244802 CGTCGCTCCTCTCTCCGC 62.245 72.222 0.00 0.00 0.00 5.54
1328 5139 3.894947 GTCGCTCCTCTCTCCGCC 61.895 72.222 0.00 0.00 0.00 6.13
1332 5143 2.203224 CTCCTCTCTCCGCCGCTA 60.203 66.667 0.00 0.00 0.00 4.26
1333 5144 2.516460 TCCTCTCTCCGCCGCTAC 60.516 66.667 0.00 0.00 0.00 3.58
1334 5145 3.597728 CCTCTCTCCGCCGCTACC 61.598 72.222 0.00 0.00 0.00 3.18
1335 5146 3.597728 CTCTCTCCGCCGCTACCC 61.598 72.222 0.00 0.00 0.00 3.69
1368 5179 4.803426 CGACGAGCCTCCCTGCAC 62.803 72.222 0.00 0.00 0.00 4.57
1369 5180 4.459089 GACGAGCCTCCCTGCACC 62.459 72.222 0.00 0.00 0.00 5.01
1393 5204 1.740296 GCTCCGCGTGTGGTATGTT 60.740 57.895 4.92 0.00 0.00 2.71
1399 5210 1.873165 CGTGTGGTATGTTGGTGCC 59.127 57.895 0.00 0.00 0.00 5.01
1400 5211 0.886938 CGTGTGGTATGTTGGTGCCA 60.887 55.000 0.00 0.00 0.00 4.92
1402 5213 0.251121 TGTGGTATGTTGGTGCCAGG 60.251 55.000 0.00 0.00 34.39 4.45
1404 5215 1.000896 GGTATGTTGGTGCCAGGCT 60.001 57.895 14.15 0.00 0.00 4.58
1406 5217 1.678635 TATGTTGGTGCCAGGCTGC 60.679 57.895 14.15 5.47 0.00 5.25
1409 5220 4.980702 TTGGTGCCAGGCTGCCAG 62.981 66.667 22.65 13.43 36.25 4.85
1447 5258 6.268825 TCCGTATGGAGTTCAGATATTAGC 57.731 41.667 0.00 0.00 40.17 3.09
1448 5259 5.773176 TCCGTATGGAGTTCAGATATTAGCA 59.227 40.000 0.00 0.00 40.17 3.49
1449 5260 6.266786 TCCGTATGGAGTTCAGATATTAGCAA 59.733 38.462 0.00 0.00 40.17 3.91
1450 5261 6.929049 CCGTATGGAGTTCAGATATTAGCAAA 59.071 38.462 0.00 0.00 37.49 3.68
1451 5262 7.441157 CCGTATGGAGTTCAGATATTAGCAAAA 59.559 37.037 0.00 0.00 37.49 2.44
1452 5263 8.993121 CGTATGGAGTTCAGATATTAGCAAAAT 58.007 33.333 0.00 0.00 0.00 1.82
1488 5299 1.394572 TGATTTGAGACGCGATGCAAG 59.605 47.619 15.93 0.00 0.00 4.01
1492 5303 1.346365 TGAGACGCGATGCAAGTAAC 58.654 50.000 15.93 0.00 0.00 2.50
1500 5311 1.762222 GATGCAAGTAACGCGGCGAT 61.762 55.000 30.94 20.73 0.00 4.58
1503 5314 2.098233 CAAGTAACGCGGCGATGGT 61.098 57.895 30.94 13.07 0.00 3.55
1504 5315 1.375013 AAGTAACGCGGCGATGGTT 60.375 52.632 30.94 15.15 0.00 3.67
1505 5316 1.356527 AAGTAACGCGGCGATGGTTC 61.357 55.000 30.94 12.15 0.00 3.62
1506 5317 2.095847 GTAACGCGGCGATGGTTCA 61.096 57.895 30.94 0.00 0.00 3.18
1507 5318 1.807981 TAACGCGGCGATGGTTCAG 60.808 57.895 30.94 0.00 0.00 3.02
1508 5319 2.215465 TAACGCGGCGATGGTTCAGA 62.215 55.000 30.94 0.00 0.00 3.27
1509 5320 2.586079 CGCGGCGATGGTTCAGAT 60.586 61.111 19.16 0.00 0.00 2.90
1515 5326 2.806745 CGGCGATGGTTCAGATATTGGT 60.807 50.000 0.00 0.00 0.00 3.67
1516 5327 3.214328 GGCGATGGTTCAGATATTGGTT 58.786 45.455 0.00 0.00 0.00 3.67
1530 5341 6.824704 CAGATATTGGTTTTTGGCCATGAATT 59.175 34.615 6.09 0.00 35.71 2.17
1536 5347 5.936956 TGGTTTTTGGCCATGAATTGATTAC 59.063 36.000 6.09 0.00 0.00 1.89
1540 5351 4.248174 TGGCCATGAATTGATTACAGGA 57.752 40.909 0.00 0.00 0.00 3.86
1542 5353 5.210430 TGGCCATGAATTGATTACAGGAAT 58.790 37.500 0.00 0.00 0.00 3.01
1545 5356 6.480981 GGCCATGAATTGATTACAGGAATTTG 59.519 38.462 0.00 0.00 0.00 2.32
1546 5357 7.043565 GCCATGAATTGATTACAGGAATTTGT 58.956 34.615 0.00 0.00 35.09 2.83
1548 5359 8.875803 CCATGAATTGATTACAGGAATTTGTTG 58.124 33.333 0.00 0.00 32.56 3.33
1549 5360 9.426837 CATGAATTGATTACAGGAATTTGTTGT 57.573 29.630 0.00 0.00 32.56 3.32
1596 5409 1.599542 ACTCAAAAACAGAGAGCGCAC 59.400 47.619 11.47 2.25 36.91 5.34
1599 5413 2.111756 CAAAAACAGAGAGCGCACAAC 58.888 47.619 11.47 1.64 0.00 3.32
1643 5485 3.004944 GGAGCTTAGATGAACTACTCGGG 59.995 52.174 0.00 0.00 30.02 5.14
1644 5486 3.633065 GAGCTTAGATGAACTACTCGGGT 59.367 47.826 0.00 0.00 0.00 5.28
1650 5531 7.649533 TTAGATGAACTACTCGGGTATTCAA 57.350 36.000 18.09 5.80 33.62 2.69
1651 5532 6.540438 AGATGAACTACTCGGGTATTCAAA 57.460 37.500 18.09 3.63 33.62 2.69
1655 5536 5.244402 TGAACTACTCGGGTATTCAAACAGA 59.756 40.000 14.17 0.00 30.45 3.41
1678 5561 3.941483 CAGTAGACACCCAAATCCATGAC 59.059 47.826 0.00 0.00 0.00 3.06
1804 5759 1.414866 TAGCAGGGGCACACACTCAA 61.415 55.000 0.00 0.00 44.61 3.02
1808 5763 0.037303 AGGGGCACACACTCAATCAG 59.963 55.000 0.00 0.00 0.00 2.90
1920 5884 0.921896 CATGGGATGGGACTGGAGTT 59.078 55.000 0.00 0.00 0.00 3.01
1954 5919 1.794714 ATGATAGGAACGGCACCTCT 58.205 50.000 0.00 0.00 38.76 3.69
2048 6013 5.782893 TCTTGGTATTGGTTTTCTGGTTG 57.217 39.130 0.00 0.00 0.00 3.77
2055 6020 1.205893 TGGTTTTCTGGTTGGTTGTGC 59.794 47.619 0.00 0.00 0.00 4.57
2152 6129 0.109532 TGGAAGGTTGACAATGCCGA 59.890 50.000 0.00 0.00 0.00 5.54
2153 6130 0.804989 GGAAGGTTGACAATGCCGAG 59.195 55.000 0.00 0.00 0.00 4.63
2199 6182 4.637977 GTGAAGGACCAGATGATTTTCTCC 59.362 45.833 0.00 0.00 0.00 3.71
2241 6224 5.189736 ACTGGCAAACTCTATCTTGGTGATA 59.810 40.000 0.00 0.00 36.65 2.15
2520 6509 9.378504 ACTCCAGAAAGAGATTGTATGATATCT 57.621 33.333 3.98 0.00 37.33 1.98
2556 6546 1.853963 TCTTCTCGAGCTTAAGGGCT 58.146 50.000 7.81 0.00 46.11 5.19
2557 6547 1.478510 TCTTCTCGAGCTTAAGGGCTG 59.521 52.381 7.81 0.00 43.20 4.85
2558 6548 0.108138 TTCTCGAGCTTAAGGGCTGC 60.108 55.000 7.81 0.00 43.20 5.25
2559 6549 0.972983 TCTCGAGCTTAAGGGCTGCT 60.973 55.000 7.81 0.00 43.20 4.24
2563 6553 0.182299 GAGCTTAAGGGCTGCTCCAT 59.818 55.000 4.29 0.00 45.12 3.41
2654 6644 1.891150 CTTGAAGGTGAGCTTGCCATT 59.109 47.619 0.00 2.36 0.00 3.16
2688 6678 0.397941 CCTGGAGCCTGAGACAAACA 59.602 55.000 0.00 0.00 0.00 2.83
2702 6692 5.415701 TGAGACAAACAATATTGGGAAGCTC 59.584 40.000 19.37 17.58 34.56 4.09
2713 6703 1.079057 GGAAGCTCGTTGAGGACCC 60.079 63.158 0.00 0.00 0.00 4.46
2715 6705 0.321996 GAAGCTCGTTGAGGACCCTT 59.678 55.000 0.00 0.00 0.00 3.95
2785 6775 5.995282 AGTTGGAATTCGTCACTATGTTTGA 59.005 36.000 0.00 0.00 0.00 2.69
2833 6823 4.846779 TTTGTGGTTCCAGTAATGCTTC 57.153 40.909 0.00 0.00 0.00 3.86
3081 7071 2.359900 ACTTGATGATTCCGTGCCTTC 58.640 47.619 0.00 0.00 0.00 3.46
3161 7157 0.835971 TCAGTACTGCCTGCCCTTGA 60.836 55.000 18.45 0.00 32.32 3.02
3162 7158 0.392193 CAGTACTGCCTGCCCTTGAG 60.392 60.000 10.54 0.00 0.00 3.02
3163 7159 0.838122 AGTACTGCCTGCCCTTGAGT 60.838 55.000 0.00 0.00 0.00 3.41
3187 7189 4.694233 CAGCGTGTCCAGCCAGCT 62.694 66.667 0.00 0.00 38.90 4.24
3291 7293 3.058914 CACGGAGGTTGTTGATTTCACTC 60.059 47.826 0.00 0.00 0.00 3.51
3293 7295 3.399330 GGAGGTTGTTGATTTCACTCGA 58.601 45.455 0.00 0.00 0.00 4.04
3696 7698 2.855963 CTCAAAACATCGATTGGCATGC 59.144 45.455 9.90 9.90 0.00 4.06
3702 7704 0.464373 ATCGATTGGCATGCCGAACT 60.464 50.000 30.37 15.54 39.42 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.296400 GTGCGCTATTATTTATTTTCCTTTTCA 57.704 29.630 9.73 0.00 0.00 2.69
61 63 8.926092 TCTATGGAGATGGAGTTATATATCGG 57.074 38.462 0.00 0.00 0.00 4.18
103 105 3.119779 TGAAGTGTGGACGAAAAACAACC 60.120 43.478 0.00 0.00 0.00 3.77
133 136 3.191162 CGACATGCAAATGAAAGGAGGAA 59.809 43.478 0.00 0.00 0.00 3.36
203 208 6.969993 TTCCTAAGTGGTTGTGCTATTTTT 57.030 33.333 0.00 0.00 37.07 1.94
208 213 6.351881 CCTCTTATTCCTAAGTGGTTGTGCTA 60.352 42.308 5.65 0.00 41.00 3.49
254 259 5.470047 AGGCCATTAGAATTACCGAGTAG 57.530 43.478 5.01 0.00 0.00 2.57
291 296 6.600822 CCATGTCTGGTGAATTTTGTAGAGAT 59.399 38.462 0.00 0.00 37.79 2.75
471 476 5.105392 GCATCCTAGCAAGCTAGTGAGATAT 60.105 44.000 23.29 7.90 43.22 1.63
473 478 3.006752 GCATCCTAGCAAGCTAGTGAGAT 59.993 47.826 23.29 16.86 43.22 2.75
500 543 2.032681 GGAGGCCGTGCAAGTCTT 59.967 61.111 0.00 0.00 0.00 3.01
520 568 9.373603 ACGCAATATACACATTACACTAAGAAA 57.626 29.630 0.00 0.00 0.00 2.52
528 576 8.880878 ATTACTCACGCAATATACACATTACA 57.119 30.769 0.00 0.00 0.00 2.41
560 608 8.237949 AGTGCGTACTATAGTTGCTATATTGAG 58.762 37.037 22.67 2.55 34.74 3.02
565 613 7.268199 ACAAGTGCGTACTATAGTTGCTATA 57.732 36.000 22.67 7.45 35.69 1.31
574 622 9.673454 CTATTGTTCATACAAGTGCGTACTATA 57.327 33.333 6.58 3.25 46.71 1.31
579 628 6.160684 ACACTATTGTTCATACAAGTGCGTA 58.839 36.000 9.04 0.00 46.71 4.42
784 935 2.046892 CCGAGTGGGCAACTGAGG 60.047 66.667 0.00 0.00 40.07 3.86
853 1005 8.790718 GCTCAATATGTCATAATTGTCCTTGAT 58.209 33.333 0.00 0.00 0.00 2.57
887 4660 2.869503 AAGAATACCGCGTGGCCTGG 62.870 60.000 16.69 3.04 39.70 4.45
897 4670 8.314143 TGACTTTACTTACCAAAAGAATACCG 57.686 34.615 2.08 0.00 36.43 4.02
924 4697 3.743396 GCTGGATGGTTCATCTTATCGTC 59.257 47.826 7.68 0.00 40.39 4.20
962 4735 2.905075 CGCATGACCAAACAGGAGATA 58.095 47.619 0.00 0.00 41.22 1.98
969 4742 2.593148 ACGGCGCATGACCAAACA 60.593 55.556 10.83 0.00 0.00 2.83
970 4743 2.175811 GACGGCGCATGACCAAAC 59.824 61.111 10.83 0.00 0.00 2.93
971 4744 3.418913 CGACGGCGCATGACCAAA 61.419 61.111 10.83 0.00 0.00 3.28
1002 4781 3.063084 ACCTCAGTCTCGCCGGAC 61.063 66.667 5.05 0.00 36.56 4.79
1112 4923 3.637273 GCCCCCGCCCTATGTAGG 61.637 72.222 0.00 0.00 43.25 3.18
1185 4996 4.097361 GGGACGCCAGGGAGGAAC 62.097 72.222 0.00 0.00 41.22 3.62
1266 5077 4.849329 GCTACTGCTACGCGGCGT 62.849 66.667 31.64 31.64 44.35 5.68
1307 5118 3.894947 GAGAGAGGAGCGACGGGC 61.895 72.222 0.00 0.00 44.05 6.13
1308 5119 3.213402 GGAGAGAGGAGCGACGGG 61.213 72.222 0.00 0.00 0.00 5.28
1309 5120 3.578272 CGGAGAGAGGAGCGACGG 61.578 72.222 0.00 0.00 0.00 4.79
1310 5121 4.244802 GCGGAGAGAGGAGCGACG 62.245 72.222 0.00 0.00 0.00 5.12
1311 5122 3.894947 GGCGGAGAGAGGAGCGAC 61.895 72.222 0.00 0.00 0.00 5.19
1315 5126 2.203224 TAGCGGCGGAGAGAGGAG 60.203 66.667 9.78 0.00 0.00 3.69
1316 5127 2.516460 GTAGCGGCGGAGAGAGGA 60.516 66.667 9.78 0.00 0.00 3.71
1317 5128 3.597728 GGTAGCGGCGGAGAGAGG 61.598 72.222 9.78 0.00 0.00 3.69
1318 5129 3.597728 GGGTAGCGGCGGAGAGAG 61.598 72.222 9.78 0.00 0.00 3.20
1351 5162 4.803426 GTGCAGGGAGGCTCGTCG 62.803 72.222 8.69 0.00 34.04 5.12
1352 5163 4.459089 GGTGCAGGGAGGCTCGTC 62.459 72.222 8.69 3.34 34.04 4.20
1376 5187 1.358725 CCAACATACCACACGCGGAG 61.359 60.000 12.47 4.93 0.00 4.63
1377 5188 1.374885 CCAACATACCACACGCGGA 60.375 57.895 12.47 0.00 0.00 5.54
1378 5189 1.669760 ACCAACATACCACACGCGG 60.670 57.895 12.47 1.27 0.00 6.46
1379 5190 1.495509 CACCAACATACCACACGCG 59.504 57.895 3.53 3.53 0.00 6.01
1381 5192 0.886938 TGGCACCAACATACCACACG 60.887 55.000 0.00 0.00 0.00 4.49
1388 5199 1.678635 GCAGCCTGGCACCAACATA 60.679 57.895 22.65 0.00 0.00 2.29
1416 5227 1.546961 ACTCCATACGGATCGGATCC 58.453 55.000 24.29 24.29 46.22 3.36
1417 5228 2.557056 TGAACTCCATACGGATCGGATC 59.443 50.000 9.54 9.54 41.79 3.36
1418 5229 2.558795 CTGAACTCCATACGGATCGGAT 59.441 50.000 7.35 0.00 41.79 4.18
1419 5230 1.954382 CTGAACTCCATACGGATCGGA 59.046 52.381 7.35 0.00 41.79 4.55
1420 5231 1.954382 TCTGAACTCCATACGGATCGG 59.046 52.381 0.00 0.00 41.79 4.18
1421 5232 3.924918 ATCTGAACTCCATACGGATCG 57.075 47.619 0.00 0.00 41.79 3.69
1422 5233 6.975772 GCTAATATCTGAACTCCATACGGATC 59.024 42.308 0.00 0.00 41.79 3.36
1423 5234 6.437477 TGCTAATATCTGAACTCCATACGGAT 59.563 38.462 0.00 0.00 41.79 4.18
1424 5235 5.773176 TGCTAATATCTGAACTCCATACGGA 59.227 40.000 0.00 0.00 39.79 4.69
1425 5236 6.025749 TGCTAATATCTGAACTCCATACGG 57.974 41.667 0.00 0.00 0.00 4.02
1426 5237 7.946655 TTTGCTAATATCTGAACTCCATACG 57.053 36.000 0.00 0.00 0.00 3.06
1429 5240 8.985315 TCATTTTGCTAATATCTGAACTCCAT 57.015 30.769 0.00 0.00 0.00 3.41
1430 5241 8.843262 CATCATTTTGCTAATATCTGAACTCCA 58.157 33.333 0.00 0.00 0.00 3.86
1431 5242 8.844244 ACATCATTTTGCTAATATCTGAACTCC 58.156 33.333 0.00 0.00 0.00 3.85
1432 5243 9.875675 GACATCATTTTGCTAATATCTGAACTC 57.124 33.333 0.00 0.00 0.00 3.01
1433 5244 8.554528 CGACATCATTTTGCTAATATCTGAACT 58.445 33.333 0.00 0.00 0.00 3.01
1434 5245 8.551205 TCGACATCATTTTGCTAATATCTGAAC 58.449 33.333 0.00 0.00 0.00 3.18
1435 5246 8.661352 TCGACATCATTTTGCTAATATCTGAA 57.339 30.769 0.00 0.00 0.00 3.02
1436 5247 8.837788 ATCGACATCATTTTGCTAATATCTGA 57.162 30.769 0.00 0.00 0.00 3.27
1437 5248 8.933807 AGATCGACATCATTTTGCTAATATCTG 58.066 33.333 0.00 0.00 0.00 2.90
1438 5249 9.149225 GAGATCGACATCATTTTGCTAATATCT 57.851 33.333 0.00 0.00 0.00 1.98
1439 5250 8.106956 CGAGATCGACATCATTTTGCTAATATC 58.893 37.037 0.00 0.00 43.02 1.63
1440 5251 7.814587 TCGAGATCGACATCATTTTGCTAATAT 59.185 33.333 0.00 0.00 44.22 1.28
1441 5252 7.145323 TCGAGATCGACATCATTTTGCTAATA 58.855 34.615 0.00 0.00 44.22 0.98
1442 5253 5.985530 TCGAGATCGACATCATTTTGCTAAT 59.014 36.000 0.00 0.00 44.22 1.73
1443 5254 5.348164 TCGAGATCGACATCATTTTGCTAA 58.652 37.500 0.00 0.00 44.22 3.09
1444 5255 4.932146 TCGAGATCGACATCATTTTGCTA 58.068 39.130 0.00 0.00 44.22 3.49
1445 5256 3.785486 TCGAGATCGACATCATTTTGCT 58.215 40.909 0.00 0.00 44.22 3.91
1468 5279 1.394572 CTTGCATCGCGTCTCAAATCA 59.605 47.619 5.77 0.00 0.00 2.57
1488 5299 2.020836 CTGAACCATCGCCGCGTTAC 62.021 60.000 13.39 0.00 0.00 2.50
1492 5303 0.667487 ATATCTGAACCATCGCCGCG 60.667 55.000 6.39 6.39 0.00 6.46
1495 5306 2.851195 ACCAATATCTGAACCATCGCC 58.149 47.619 0.00 0.00 0.00 5.54
1500 5311 4.020662 GGCCAAAAACCAATATCTGAACCA 60.021 41.667 0.00 0.00 0.00 3.67
1503 5314 5.483231 TCATGGCCAAAAACCAATATCTGAA 59.517 36.000 10.96 0.00 41.49 3.02
1504 5315 5.022122 TCATGGCCAAAAACCAATATCTGA 58.978 37.500 10.96 0.06 41.49 3.27
1505 5316 5.341872 TCATGGCCAAAAACCAATATCTG 57.658 39.130 10.96 0.00 41.49 2.90
1506 5317 6.564557 ATTCATGGCCAAAAACCAATATCT 57.435 33.333 10.96 0.00 41.49 1.98
1507 5318 6.822676 TCAATTCATGGCCAAAAACCAATATC 59.177 34.615 10.96 0.00 41.49 1.63
1508 5319 6.719301 TCAATTCATGGCCAAAAACCAATAT 58.281 32.000 10.96 0.00 41.49 1.28
1509 5320 6.119240 TCAATTCATGGCCAAAAACCAATA 57.881 33.333 10.96 0.00 41.49 1.90
1515 5326 6.013898 TCCTGTAATCAATTCATGGCCAAAAA 60.014 34.615 10.96 7.71 0.00 1.94
1516 5327 5.483231 TCCTGTAATCAATTCATGGCCAAAA 59.517 36.000 10.96 8.15 0.00 2.44
1530 5341 5.389520 TCCCACAACAAATTCCTGTAATCA 58.610 37.500 0.00 0.00 0.00 2.57
1536 5347 4.317488 CCAAATCCCACAACAAATTCCTG 58.683 43.478 0.00 0.00 0.00 3.86
1540 5351 2.441001 TGGCCAAATCCCACAACAAATT 59.559 40.909 0.61 0.00 0.00 1.82
1542 5353 1.500474 TGGCCAAATCCCACAACAAA 58.500 45.000 0.61 0.00 0.00 2.83
1545 5356 0.975887 ACATGGCCAAATCCCACAAC 59.024 50.000 10.96 0.00 34.68 3.32
1546 5357 1.203162 AGACATGGCCAAATCCCACAA 60.203 47.619 10.96 0.00 34.68 3.33
1548 5359 0.819582 CAGACATGGCCAAATCCCAC 59.180 55.000 10.96 0.00 34.68 4.61
1549 5360 0.971959 GCAGACATGGCCAAATCCCA 60.972 55.000 10.96 0.00 36.66 4.37
1573 5386 2.660362 GCGCTCTCTGTTTTTGAGTTCG 60.660 50.000 0.00 0.00 33.59 3.95
1596 5409 6.540189 CAGAAACTATCCCCTGTAATCTGTTG 59.460 42.308 0.00 0.00 31.45 3.33
1599 5413 5.366768 TCCAGAAACTATCCCCTGTAATCTG 59.633 44.000 0.00 0.00 33.68 2.90
1643 5485 5.638234 GGGTGTCTACTGTCTGTTTGAATAC 59.362 44.000 0.00 0.00 0.00 1.89
1644 5486 5.305902 TGGGTGTCTACTGTCTGTTTGAATA 59.694 40.000 0.00 0.00 0.00 1.75
1650 5531 4.505039 GGATTTGGGTGTCTACTGTCTGTT 60.505 45.833 0.00 0.00 0.00 3.16
1651 5532 3.008049 GGATTTGGGTGTCTACTGTCTGT 59.992 47.826 0.00 0.00 0.00 3.41
1655 5536 3.587061 TCATGGATTTGGGTGTCTACTGT 59.413 43.478 0.00 0.00 0.00 3.55
1678 5561 4.909696 TGTAATGGTGTGTTGTTTGAGG 57.090 40.909 0.00 0.00 0.00 3.86
1804 5759 8.712228 TTCTGTATCTATGTATGTGGACTGAT 57.288 34.615 0.00 0.00 0.00 2.90
1911 5871 4.774124 TCCATTCATCATCAACTCCAGTC 58.226 43.478 0.00 0.00 0.00 3.51
1912 5872 4.849813 TCCATTCATCATCAACTCCAGT 57.150 40.909 0.00 0.00 0.00 4.00
1913 5873 7.166167 TCATATCCATTCATCATCAACTCCAG 58.834 38.462 0.00 0.00 0.00 3.86
1914 5874 7.081857 TCATATCCATTCATCATCAACTCCA 57.918 36.000 0.00 0.00 0.00 3.86
1920 5884 7.983484 CGTTCCTATCATATCCATTCATCATCA 59.017 37.037 0.00 0.00 0.00 3.07
1954 5919 0.627451 AAGAGCCAGGATTGATGCCA 59.373 50.000 0.00 0.00 0.00 4.92
2048 6013 1.256812 ACCCAAGCTTATGCACAACC 58.743 50.000 0.00 0.00 42.74 3.77
2055 6020 6.165577 AGCAATTAACAAACCCAAGCTTATG 58.834 36.000 0.00 0.00 0.00 1.90
2143 6120 0.820871 GAGAGTCTCCTCGGCATTGT 59.179 55.000 9.15 0.00 42.86 2.71
2241 6224 4.713824 TCTTATTGTCGACGGTTCATCT 57.286 40.909 11.62 0.00 0.00 2.90
2520 6509 5.525012 CGAGAAGATCATTTTATGCTCCACA 59.475 40.000 0.00 0.00 0.00 4.17
2563 6553 6.057533 ACATGACTGACATCTTGTTTGAAGA 58.942 36.000 0.00 0.00 37.07 2.87
2592 6582 2.951642 CAAGTGCTTTCTTGTTGAGGGA 59.048 45.455 8.09 0.00 39.66 4.20
2654 6644 1.702401 TCCAGGACAAAGCATACACCA 59.298 47.619 0.00 0.00 0.00 4.17
2688 6678 3.199946 TCCTCAACGAGCTTCCCAATATT 59.800 43.478 0.00 0.00 0.00 1.28
2702 6692 3.243907 GGATGATCTAAGGGTCCTCAACG 60.244 52.174 0.00 0.00 0.00 4.10
2713 6703 4.297510 CGACTGAAGCAGGATGATCTAAG 58.702 47.826 0.00 0.00 39.69 2.18
2715 6705 2.625314 CCGACTGAAGCAGGATGATCTA 59.375 50.000 0.00 0.00 39.69 1.98
2785 6775 3.823304 GGGAAACTTCTTCAACTGCTGAT 59.177 43.478 0.00 0.00 32.78 2.90
2833 6823 1.731160 CAAGCTTCTTCTTGAGAGCCG 59.269 52.381 0.00 0.00 44.61 5.52
2963 6953 1.656652 TTTGCTTCGAGCTATCAGCC 58.343 50.000 7.78 0.00 43.77 4.85
3161 7157 1.595382 GGACACGCTGTGCTGAACT 60.595 57.895 8.31 0.00 35.71 3.01
3162 7158 1.835483 CTGGACACGCTGTGCTGAAC 61.835 60.000 8.31 0.00 39.34 3.18
3163 7159 1.595109 CTGGACACGCTGTGCTGAA 60.595 57.895 8.31 0.00 39.34 3.02
3696 7698 1.672356 CTGGGCCAGTTCAGTTCGG 60.672 63.158 25.74 0.00 0.00 4.30
3702 7704 1.228245 GCAAGACTGGGCCAGTTCA 60.228 57.895 37.83 0.00 45.44 3.18


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

AutoCloner maintained by Alex Coulton.