Multiple sequence alignment - TraesCS5A01G251900

Loading Multiple Alignment...

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 TraesCS5A01G251900 chr5A 100.000 2708 0 0 1 2708 467670924 467673631 0.000000e+00 5001.0
1 TraesCS5A01G251900 chr5A 92.577 970 61 2 596 1555 467679352 467680320 0.000000e+00 1382.0
2 TraesCS5A01G251900 chr5A 86.721 979 103 21 1743 2706 438828653 438829619 0.000000e+00 1062.0
3 TraesCS5A01G251900 chr5A 95.798 595 23 1 1 595 467665058 467665650 0.000000e+00 959.0
4 TraesCS5A01G251900 chr5A 91.328 542 37 1 597 1128 359486909 359487450 0.000000e+00 732.0
5 TraesCS5A01G251900 chr5A 90.055 543 44 1 596 1128 359518570 359519112 0.000000e+00 695.0
6 TraesCS5A01G251900 chr5A 87.213 305 29 4 752 1046 217752002 217752306 3.340000e-89 339.0
7 TraesCS5A01G251900 chr5A 85.902 305 33 4 752 1046 217744093 217744397 1.560000e-82 316.0
8 TraesCS5A01G251900 chr5A 93.210 162 11 0 596 757 75561999 75562160 3.480000e-59 239.0
9 TraesCS5A01G251900 chr5A 91.781 73 6 0 782 854 191845584 191845512 4.770000e-18 102.0
10 TraesCS5A01G251900 chr1A 90.018 1102 78 20 1593 2683 250712114 250711034 0.000000e+00 1397.0
11 TraesCS5A01G251900 chr1A 89.655 1102 84 19 1593 2683 250695185 250694103 0.000000e+00 1376.0
12 TraesCS5A01G251900 chr1A 90.650 1016 68 16 1593 2599 250703354 250702357 0.000000e+00 1325.0
13 TraesCS5A01G251900 chr1A 90.340 911 81 6 1801 2704 35641349 35640439 0.000000e+00 1188.0
14 TraesCS5A01G251900 chr1A 90.792 543 39 2 596 1128 103722346 103721805 0.000000e+00 715.0
15 TraesCS5A01G251900 chr1A 90.467 514 39 1 625 1128 103730295 103729782 0.000000e+00 669.0
16 TraesCS5A01G251900 chr1A 91.099 191 11 5 1102 1290 93888973 93889159 1.240000e-63 254.0
17 TraesCS5A01G251900 chr1A 90.526 190 14 4 1102 1290 224724350 224724536 5.790000e-62 248.0
18 TraesCS5A01G251900 chr1A 89.529 191 12 7 1102 1290 224716161 224716345 4.510000e-58 235.0
19 TraesCS5A01G251900 chr3A 87.991 866 77 16 1733 2586 463563771 463562921 0.000000e+00 998.0
20 TraesCS5A01G251900 chr3A 95.134 596 25 3 1 595 313233273 313233865 0.000000e+00 937.0
21 TraesCS5A01G251900 chr3A 91.623 191 10 5 1102 1290 369017119 369016933 2.670000e-65 259.0
22 TraesCS5A01G251900 chr3A 91.304 115 10 0 2594 2708 279010310 279010196 1.000000e-34 158.0
23 TraesCS5A01G251900 chr3A 84.049 163 23 3 2544 2704 292882635 292882474 1.300000e-33 154.0
24 TraesCS5A01G251900 chr3A 84.810 158 16 4 2559 2708 659173303 659173146 4.670000e-33 152.0
25 TraesCS5A01G251900 chr3A 82.558 172 27 3 2535 2704 577265171 577265341 6.040000e-32 148.0
26 TraesCS5A01G251900 chr4A 85.378 978 113 23 1743 2703 108243744 108244708 0.000000e+00 987.0
27 TraesCS5A01G251900 chr4A 96.141 596 20 2 1 595 166606281 166605688 0.000000e+00 970.0
28 TraesCS5A01G251900 chr4A 95.294 595 24 1 1 595 183882266 183882856 0.000000e+00 941.0
29 TraesCS5A01G251900 chr4A 94.975 597 24 5 1 595 375423058 375423650 0.000000e+00 931.0
30 TraesCS5A01G251900 chr4A 90.370 540 42 5 596 1125 385918338 385918877 0.000000e+00 701.0
31 TraesCS5A01G251900 chr4A 90.018 541 44 1 596 1126 385926438 385926978 0.000000e+00 691.0
32 TraesCS5A01G251900 chr6A 85.031 982 110 31 1743 2703 240076577 240075612 0.000000e+00 965.0
33 TraesCS5A01G251900 chr6A 95.462 595 25 1 1 595 404424291 404424883 0.000000e+00 948.0
34 TraesCS5A01G251900 chr6A 95.302 596 25 2 1 595 589365363 589365956 0.000000e+00 942.0
35 TraesCS5A01G251900 chr6A 91.638 287 23 1 905 1190 545284466 545284180 1.950000e-106 396.0
36 TraesCS5A01G251900 chr2A 95.302 596 24 3 1 595 329499067 329499659 0.000000e+00 942.0
37 TraesCS5A01G251900 chr2A 95.302 596 25 2 1 595 425953003 425953596 0.000000e+00 942.0
38 TraesCS5A01G251900 chr2A 90.576 191 12 5 1102 1290 239451157 239451343 5.790000e-62 248.0
39 TraesCS5A01G251900 chr2A 91.758 182 10 4 1111 1290 244234387 244234565 5.790000e-62 248.0
40 TraesCS5A01G251900 chr2A 90.576 191 12 5 1102 1290 244247727 244247913 5.790000e-62 248.0
41 TraesCS5A01G251900 chr2A 90.052 191 13 5 1102 1290 239469637 239469823 2.690000e-60 243.0
42 TraesCS5A01G251900 chr2A 93.711 159 10 0 596 754 691898357 691898199 3.480000e-59 239.0
43 TraesCS5A01G251900 chr2A 91.453 117 10 0 1384 1500 344747219 344747335 7.760000e-36 161.0
44 TraesCS5A01G251900 chr2A 80.556 216 34 8 2484 2695 509115634 509115845 2.790000e-35 159.0
45 TraesCS5A01G251900 chr7A 83.925 1014 122 32 1714 2708 682809289 682808298 0.000000e+00 931.0
46 TraesCS5A01G251900 chr7A 91.289 287 25 0 904 1190 487606041 487606327 2.530000e-105 392.0
47 TraesCS5A01G251900 chr7A 88.325 197 19 4 597 791 261349663 261349469 1.620000e-57 233.0
48 TraesCS5A01G251900 chr7D 89.362 94 6 3 1398 1490 183949602 183949512 6.130000e-22 115.0
49 TraesCS5A01G251900 chr7D 88.298 94 7 3 1398 1490 148056874 148056964 2.850000e-20 110.0
50 TraesCS5A01G251900 chr7D 88.298 94 7 3 1398 1490 241486730 241486640 2.850000e-20 110.0
51 TraesCS5A01G251900 chr5D 89.362 94 6 3 1398 1490 214950031 214950121 6.130000e-22 115.0
52 TraesCS5A01G251900 chr4D 88.298 94 7 3 1398 1490 135951896 135951806 2.850000e-20 110.0
53 TraesCS5A01G251900 chr4D 88.298 94 7 3 1398 1490 191600021 191599931 2.850000e-20 110.0
54 TraesCS5A01G251900 chr4D 88.172 93 9 2 1398 1490 191607772 191607682 2.850000e-20 110.0
55 TraesCS5A01G251900 chr4D 85.556 90 11 2 846 935 73854654 73854741 2.870000e-15 93.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G251900 chr5A 467670924 467673631 2707 False 5001 5001 100.000 1 2708 1 chr5A.!!$F8 2707
1 TraesCS5A01G251900 chr5A 467679352 467680320 968 False 1382 1382 92.577 596 1555 1 chr5A.!!$F9 959
2 TraesCS5A01G251900 chr5A 438828653 438829619 966 False 1062 1062 86.721 1743 2706 1 chr5A.!!$F6 963
3 TraesCS5A01G251900 chr5A 467665058 467665650 592 False 959 959 95.798 1 595 1 chr5A.!!$F7 594
4 TraesCS5A01G251900 chr5A 359486909 359487450 541 False 732 732 91.328 597 1128 1 chr5A.!!$F4 531
5 TraesCS5A01G251900 chr5A 359518570 359519112 542 False 695 695 90.055 596 1128 1 chr5A.!!$F5 532
6 TraesCS5A01G251900 chr1A 250711034 250712114 1080 True 1397 1397 90.018 1593 2683 1 chr1A.!!$R6 1090
7 TraesCS5A01G251900 chr1A 250694103 250695185 1082 True 1376 1376 89.655 1593 2683 1 chr1A.!!$R4 1090
8 TraesCS5A01G251900 chr1A 250702357 250703354 997 True 1325 1325 90.650 1593 2599 1 chr1A.!!$R5 1006
9 TraesCS5A01G251900 chr1A 35640439 35641349 910 True 1188 1188 90.340 1801 2704 1 chr1A.!!$R1 903
10 TraesCS5A01G251900 chr1A 103721805 103722346 541 True 715 715 90.792 596 1128 1 chr1A.!!$R2 532
11 TraesCS5A01G251900 chr1A 103729782 103730295 513 True 669 669 90.467 625 1128 1 chr1A.!!$R3 503
12 TraesCS5A01G251900 chr3A 463562921 463563771 850 True 998 998 87.991 1733 2586 1 chr3A.!!$R4 853
13 TraesCS5A01G251900 chr3A 313233273 313233865 592 False 937 937 95.134 1 595 1 chr3A.!!$F1 594
14 TraesCS5A01G251900 chr4A 108243744 108244708 964 False 987 987 85.378 1743 2703 1 chr4A.!!$F1 960
15 TraesCS5A01G251900 chr4A 166605688 166606281 593 True 970 970 96.141 1 595 1 chr4A.!!$R1 594
16 TraesCS5A01G251900 chr4A 183882266 183882856 590 False 941 941 95.294 1 595 1 chr4A.!!$F2 594
17 TraesCS5A01G251900 chr4A 375423058 375423650 592 False 931 931 94.975 1 595 1 chr4A.!!$F3 594
18 TraesCS5A01G251900 chr4A 385918338 385918877 539 False 701 701 90.370 596 1125 1 chr4A.!!$F4 529
19 TraesCS5A01G251900 chr4A 385926438 385926978 540 False 691 691 90.018 596 1126 1 chr4A.!!$F5 530
20 TraesCS5A01G251900 chr6A 240075612 240076577 965 True 965 965 85.031 1743 2703 1 chr6A.!!$R1 960
21 TraesCS5A01G251900 chr6A 404424291 404424883 592 False 948 948 95.462 1 595 1 chr6A.!!$F1 594
22 TraesCS5A01G251900 chr6A 589365363 589365956 593 False 942 942 95.302 1 595 1 chr6A.!!$F2 594
23 TraesCS5A01G251900 chr2A 329499067 329499659 592 False 942 942 95.302 1 595 1 chr2A.!!$F5 594
24 TraesCS5A01G251900 chr2A 425953003 425953596 593 False 942 942 95.302 1 595 1 chr2A.!!$F7 594
25 TraesCS5A01G251900 chr7A 682808298 682809289 991 True 931 931 83.925 1714 2708 1 chr7A.!!$R2 994


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
757 763 0.389817 CCGGTCTCATTCTTGCGACA 60.390 55.0 0.0 0.0 38.96 4.35 F
1494 1510 0.107654 GATGGGGGAGAGTGGTTTCG 60.108 60.0 0.0 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1576 1592 0.044244 CCCAGTTCCTCCCCTCCTAA 59.956 60.0 0.0 0.0 0.0 2.69 R
2614 2674 1.704641 ACCAAGTTTTGCCTCCCTTC 58.295 50.0 0.0 0.0 0.0 3.46 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
197 199 7.447374 AACTTTTGATGATTTGGACGTGATA 57.553 32.000 0.00 0.00 0.00 2.15
238 240 1.618837 GAAGTCCAGCCGCCTCATATA 59.381 52.381 0.00 0.00 0.00 0.86
239 241 1.944177 AGTCCAGCCGCCTCATATAT 58.056 50.000 0.00 0.00 0.00 0.86
249 251 4.857588 GCCGCCTCATATATATATGTACGC 59.142 45.833 25.23 22.23 40.69 4.42
532 538 3.755628 CGGCGGGTCTCCTTCGAA 61.756 66.667 0.00 0.00 0.00 3.71
603 609 1.335233 CGTGTGCGAACAGTGGTACTA 60.335 52.381 0.00 0.00 41.33 1.82
606 612 2.624364 TGTGCGAACAGTGGTACTAAGA 59.376 45.455 0.00 0.00 0.00 2.10
613 619 6.565234 CGAACAGTGGTACTAAGATGAATCT 58.435 40.000 0.00 0.00 39.22 2.40
705 711 1.283736 CGGTAATGGTACTCGGTTGC 58.716 55.000 0.00 0.00 0.00 4.17
731 737 2.632537 AGTGGTACTTGGGGTCATTCT 58.367 47.619 0.00 0.00 0.00 2.40
757 763 0.389817 CCGGTCTCATTCTTGCGACA 60.390 55.000 0.00 0.00 38.96 4.35
860 876 0.742281 CCTCCTTGACCTGTGCATCG 60.742 60.000 0.00 0.00 0.00 3.84
899 915 4.223144 TGCATATAGGCAACAGAGAGGTA 58.777 43.478 10.09 0.00 41.65 3.08
949 965 2.663196 GCCTAGGCAGGACACGTT 59.337 61.111 29.33 0.00 45.91 3.99
984 1000 1.000396 AAGGTTCCTGCCTGCCATC 60.000 57.895 0.00 0.00 39.17 3.51
1006 1022 0.610174 AGCTTGCGAGAGGATGAACA 59.390 50.000 4.70 0.00 0.00 3.18
1141 1157 2.343758 GCGAGCACAGGGACTTGA 59.656 61.111 0.00 0.00 34.60 3.02
1143 1159 1.734477 CGAGCACAGGGACTTGACG 60.734 63.158 0.00 0.00 34.60 4.35
1208 1224 0.535780 CACAGAGCAAGGCAAGGTCA 60.536 55.000 10.29 0.00 36.03 4.02
1227 1243 1.846712 AAAGGAGCAGGAGGGAGCAC 61.847 60.000 0.00 0.00 0.00 4.40
1281 1297 1.807573 GGCGCGTGAGGAAGAGAAG 60.808 63.158 8.43 0.00 0.00 2.85
1283 1299 0.800300 GCGCGTGAGGAAGAGAAGAG 60.800 60.000 8.43 0.00 0.00 2.85
1332 1348 0.178909 TGGCACCATGGGGAAAATGT 60.179 50.000 21.28 0.00 38.05 2.71
1416 1432 4.096003 ATCGGGACAAGGGGTGCG 62.096 66.667 0.00 0.00 39.01 5.34
1445 1461 2.238646 TCTCTCCCTGTCTCTCTCTGAC 59.761 54.545 0.00 0.00 35.21 3.51
1448 1464 0.322997 CCCTGTCTCTCTCTGACGGT 60.323 60.000 0.00 0.00 38.70 4.83
1449 1465 0.808125 CCTGTCTCTCTCTGACGGTG 59.192 60.000 0.00 0.00 38.70 4.94
1487 1503 1.152226 GGGATCGATGGGGGAGAGT 60.152 63.158 0.54 0.00 0.00 3.24
1494 1510 0.107654 GATGGGGGAGAGTGGTTTCG 60.108 60.000 0.00 0.00 0.00 3.46
1540 1556 3.839432 GCGGGAGGGAGGAGAACG 61.839 72.222 0.00 0.00 0.00 3.95
1555 1571 2.100879 GAACGGGGAGATGGGGATCG 62.101 65.000 0.00 0.00 0.00 3.69
1556 1572 3.314331 CGGGGAGATGGGGATCGG 61.314 72.222 0.00 0.00 0.00 4.18
1557 1573 2.930562 GGGGAGATGGGGATCGGG 60.931 72.222 0.00 0.00 0.00 5.14
1558 1574 3.641454 GGGAGATGGGGATCGGGC 61.641 72.222 0.00 0.00 0.00 6.13
1559 1575 3.641454 GGAGATGGGGATCGGGCC 61.641 72.222 0.00 0.00 0.00 5.80
1560 1576 2.849162 GAGATGGGGATCGGGCCA 60.849 66.667 4.39 0.00 0.00 5.36
1561 1577 2.851102 AGATGGGGATCGGGCCAG 60.851 66.667 4.39 0.00 0.00 4.85
1562 1578 3.958860 GATGGGGATCGGGCCAGG 61.959 72.222 4.39 0.00 0.00 4.45
1566 1582 4.880426 GGGATCGGGCCAGGGAGA 62.880 72.222 4.39 0.00 0.00 3.71
1567 1583 3.237741 GGATCGGGCCAGGGAGAG 61.238 72.222 4.39 0.00 0.00 3.20
1568 1584 3.237741 GATCGGGCCAGGGAGAGG 61.238 72.222 4.39 0.00 0.00 3.69
1569 1585 4.888325 ATCGGGCCAGGGAGAGGG 62.888 72.222 4.39 0.00 0.00 4.30
1572 1588 2.042261 GGGCCAGGGAGAGGGTTA 59.958 66.667 4.39 0.00 0.00 2.85
1573 1589 2.073101 GGGCCAGGGAGAGGGTTAG 61.073 68.421 4.39 0.00 0.00 2.34
1574 1590 2.073101 GGCCAGGGAGAGGGTTAGG 61.073 68.421 0.00 0.00 0.00 2.69
1575 1591 2.073101 GCCAGGGAGAGGGTTAGGG 61.073 68.421 0.00 0.00 0.00 3.53
1576 1592 1.396594 CCAGGGAGAGGGTTAGGGT 59.603 63.158 0.00 0.00 0.00 4.34
1577 1593 0.253207 CCAGGGAGAGGGTTAGGGTT 60.253 60.000 0.00 0.00 0.00 4.11
1578 1594 1.009183 CCAGGGAGAGGGTTAGGGTTA 59.991 57.143 0.00 0.00 0.00 2.85
1579 1595 2.399580 CAGGGAGAGGGTTAGGGTTAG 58.600 57.143 0.00 0.00 0.00 2.34
1580 1596 1.294373 AGGGAGAGGGTTAGGGTTAGG 59.706 57.143 0.00 0.00 0.00 2.69
1581 1597 1.293153 GGGAGAGGGTTAGGGTTAGGA 59.707 57.143 0.00 0.00 0.00 2.94
1582 1598 2.680251 GGAGAGGGTTAGGGTTAGGAG 58.320 57.143 0.00 0.00 0.00 3.69
1583 1599 2.680251 GAGAGGGTTAGGGTTAGGAGG 58.320 57.143 0.00 0.00 0.00 4.30
1584 1600 1.294373 AGAGGGTTAGGGTTAGGAGGG 59.706 57.143 0.00 0.00 0.00 4.30
1585 1601 0.345859 AGGGTTAGGGTTAGGAGGGG 59.654 60.000 0.00 0.00 0.00 4.79
1586 1602 0.344435 GGGTTAGGGTTAGGAGGGGA 59.656 60.000 0.00 0.00 0.00 4.81
1587 1603 1.695016 GGGTTAGGGTTAGGAGGGGAG 60.695 61.905 0.00 0.00 0.00 4.30
1588 1604 1.695016 GGTTAGGGTTAGGAGGGGAGG 60.695 61.905 0.00 0.00 0.00 4.30
1589 1605 1.293153 GTTAGGGTTAGGAGGGGAGGA 59.707 57.143 0.00 0.00 0.00 3.71
1590 1606 1.715561 TAGGGTTAGGAGGGGAGGAA 58.284 55.000 0.00 0.00 0.00 3.36
1591 1607 0.044397 AGGGTTAGGAGGGGAGGAAC 59.956 60.000 0.00 0.00 0.00 3.62
1598 1614 3.952799 GAGGGGAGGAACTGGGCCT 62.953 68.421 4.53 0.00 41.55 5.19
1599 1615 2.941583 GGGGAGGAACTGGGCCTT 60.942 66.667 4.53 0.00 41.55 4.35
1661 1680 3.797353 GGATGGGCCTCGCTGGAA 61.797 66.667 4.53 0.00 38.35 3.53
1674 1693 1.980052 CTGGAACCCAGTTCGGCTA 59.020 57.895 4.88 0.00 45.82 3.93
1682 1701 1.040339 CCAGTTCGGCTAGGCTCTCT 61.040 60.000 15.11 6.46 0.00 3.10
1844 1870 9.838975 GAATTAAATGGTTTGGCAATTTTTAGG 57.161 29.630 0.00 0.00 33.10 2.69
1906 1932 2.710471 AGCCATTTTTGAACCCAACCAT 59.290 40.909 0.00 0.00 30.88 3.55
1923 1949 4.463050 ACCATACCAAACCCAAAAGAGA 57.537 40.909 0.00 0.00 0.00 3.10
2058 2086 3.252974 AGCTAGTGATTGGGTTTCGAG 57.747 47.619 0.00 0.00 0.00 4.04
2064 2094 5.223449 AGTGATTGGGTTTCGAGTAGAAA 57.777 39.130 0.00 0.00 45.76 2.52
2400 2456 0.323542 ACTCCACCACTACGAGAGGG 60.324 60.000 0.00 0.00 29.56 4.30
2432 2490 2.326529 ATCTAGGATGGCACCGGGGA 62.327 60.000 8.67 0.00 34.73 4.81
2436 2494 1.381191 GGATGGCACCGGGGAAAAT 60.381 57.895 8.67 0.00 0.00 1.82
2575 2635 7.562454 TTGAAAACACTCCGTTAGAAAAGAT 57.438 32.000 0.00 0.00 36.59 2.40
2618 2678 0.671781 CAGCACTCCGGTTGAGAAGG 60.672 60.000 0.00 0.00 44.42 3.46
2632 2692 1.889170 GAGAAGGGAGGCAAAACTTGG 59.111 52.381 0.00 0.00 0.00 3.61
2639 2699 4.291249 AGGGAGGCAAAACTTGGTAAGATA 59.709 41.667 0.00 0.00 0.00 1.98
2641 2701 5.125578 GGGAGGCAAAACTTGGTAAGATAAG 59.874 44.000 0.00 0.00 0.00 1.73
2650 2711 9.847224 AAAACTTGGTAAGATAAGAGAACTTGA 57.153 29.630 0.00 0.00 37.53 3.02
2657 2720 9.877178 GGTAAGATAAGAGAACTTGAATGAAGA 57.123 33.333 0.00 0.00 37.53 2.87
2662 2726 5.914085 AGAGAACTTGAATGAAGAACACG 57.086 39.130 0.00 0.00 35.42 4.49
2670 2734 5.447624 TGAATGAAGAACACGACACTCTA 57.552 39.130 0.00 0.00 0.00 2.43
2674 2738 4.607955 TGAAGAACACGACACTCTAGTTG 58.392 43.478 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 171 6.485313 TCACGTCCAAATCATCAAAAGTTACT 59.515 34.615 0.00 0.00 0.00 2.24
197 199 5.687166 TCCCGTACAATAAAAGGACTCAT 57.313 39.130 0.00 0.00 0.00 2.90
209 211 0.252197 GGCTGGACTTCCCGTACAAT 59.748 55.000 0.00 0.00 35.61 2.71
238 240 1.401931 GCCGTCACCGCGTACATATAT 60.402 52.381 4.92 0.00 0.00 0.86
239 241 0.040157 GCCGTCACCGCGTACATATA 60.040 55.000 4.92 0.00 0.00 0.86
532 538 2.435586 GATGCACCGCAGCTCACT 60.436 61.111 0.00 0.00 43.65 3.41
603 609 3.197116 ACCGTTTCCCGTAGATTCATCTT 59.803 43.478 0.00 0.00 38.32 2.40
606 612 3.703052 ACTACCGTTTCCCGTAGATTCAT 59.297 43.478 1.46 0.00 33.66 2.57
705 711 1.346722 ACCCCAAGTACCACTTCGAAG 59.653 52.381 23.43 23.43 36.03 3.79
731 737 3.334691 CAAGAATGAGACCGGCAAGTTA 58.665 45.455 0.00 0.00 0.00 2.24
984 1000 0.108472 TCATCCTCTCGCAAGCTGTG 60.108 55.000 0.00 0.00 37.18 3.66
1068 1084 1.379044 CTGGATCCGGCCAAAGCTT 60.379 57.895 7.89 0.00 37.52 3.74
1190 1206 0.183492 TTGACCTTGCCTTGCTCTGT 59.817 50.000 0.00 0.00 0.00 3.41
1208 1224 1.539869 TGCTCCCTCCTGCTCCTTT 60.540 57.895 0.00 0.00 0.00 3.11
1227 1243 1.421485 GTCATCAAGTTCGCCTGCG 59.579 57.895 4.92 4.92 41.35 5.18
1265 1281 0.179150 CCTCTTCTCTTCCTCACGCG 60.179 60.000 3.53 3.53 0.00 6.01
1268 1284 2.107366 CCTCCCTCTTCTCTTCCTCAC 58.893 57.143 0.00 0.00 0.00 3.51
1269 1285 1.621072 GCCTCCCTCTTCTCTTCCTCA 60.621 57.143 0.00 0.00 0.00 3.86
1303 1319 1.763256 ATGGTGCCATGGCCATTCC 60.763 57.895 33.44 26.71 42.34 3.01
1332 1348 3.318384 TGTTGCGCCCTGCCTCTA 61.318 61.111 4.18 0.00 45.60 2.43
1379 1395 1.444672 CATGGATCTCCTCGCTGCA 59.555 57.895 0.00 0.00 36.82 4.41
1385 1401 0.901124 CCCGATCCATGGATCTCCTC 59.099 60.000 39.11 23.22 46.36 3.71
1416 1432 2.125350 CAGGGAGAGAGCAACGCC 60.125 66.667 0.00 0.00 0.00 5.68
1420 1436 1.357420 AGAGAGACAGGGAGAGAGCAA 59.643 52.381 0.00 0.00 0.00 3.91
1423 1439 2.505407 TCAGAGAGAGACAGGGAGAGAG 59.495 54.545 0.00 0.00 0.00 3.20
1445 1461 3.052082 CCTCCTGTGCTTGCACCG 61.052 66.667 21.01 15.27 0.00 4.94
1448 1464 2.752358 CTCCCTCCTGTGCTTGCA 59.248 61.111 0.00 0.00 0.00 4.08
1449 1465 2.045536 CCTCCCTCCTGTGCTTGC 60.046 66.667 0.00 0.00 0.00 4.01
1506 1522 2.562912 CAGCACCGCACACATTCC 59.437 61.111 0.00 0.00 0.00 3.01
1540 1556 2.930562 CCCGATCCCCATCTCCCC 60.931 72.222 0.00 0.00 0.00 4.81
1555 1571 2.042261 TAACCCTCTCCCTGGCCC 59.958 66.667 0.00 0.00 0.00 5.80
1556 1572 2.073101 CCTAACCCTCTCCCTGGCC 61.073 68.421 0.00 0.00 0.00 5.36
1557 1573 2.073101 CCCTAACCCTCTCCCTGGC 61.073 68.421 0.00 0.00 0.00 4.85
1558 1574 0.253207 AACCCTAACCCTCTCCCTGG 60.253 60.000 0.00 0.00 0.00 4.45
1559 1575 2.399580 CTAACCCTAACCCTCTCCCTG 58.600 57.143 0.00 0.00 0.00 4.45
1560 1576 1.294373 CCTAACCCTAACCCTCTCCCT 59.706 57.143 0.00 0.00 0.00 4.20
1561 1577 1.293153 TCCTAACCCTAACCCTCTCCC 59.707 57.143 0.00 0.00 0.00 4.30
1562 1578 2.680251 CTCCTAACCCTAACCCTCTCC 58.320 57.143 0.00 0.00 0.00 3.71
1563 1579 2.680251 CCTCCTAACCCTAACCCTCTC 58.320 57.143 0.00 0.00 0.00 3.20
1564 1580 1.294373 CCCTCCTAACCCTAACCCTCT 59.706 57.143 0.00 0.00 0.00 3.69
1565 1581 1.695016 CCCCTCCTAACCCTAACCCTC 60.695 61.905 0.00 0.00 0.00 4.30
1566 1582 0.345859 CCCCTCCTAACCCTAACCCT 59.654 60.000 0.00 0.00 0.00 4.34
1567 1583 0.344435 TCCCCTCCTAACCCTAACCC 59.656 60.000 0.00 0.00 0.00 4.11
1568 1584 1.695016 CCTCCCCTCCTAACCCTAACC 60.695 61.905 0.00 0.00 0.00 2.85
1569 1585 1.293153 TCCTCCCCTCCTAACCCTAAC 59.707 57.143 0.00 0.00 0.00 2.34
1570 1586 1.715561 TCCTCCCCTCCTAACCCTAA 58.284 55.000 0.00 0.00 0.00 2.69
1571 1587 1.293153 GTTCCTCCCCTCCTAACCCTA 59.707 57.143 0.00 0.00 0.00 3.53
1572 1588 0.044397 GTTCCTCCCCTCCTAACCCT 59.956 60.000 0.00 0.00 0.00 4.34
1573 1589 0.044397 AGTTCCTCCCCTCCTAACCC 59.956 60.000 0.00 0.00 0.00 4.11
1574 1590 1.205055 CAGTTCCTCCCCTCCTAACC 58.795 60.000 0.00 0.00 0.00 2.85
1575 1591 1.205055 CCAGTTCCTCCCCTCCTAAC 58.795 60.000 0.00 0.00 0.00 2.34
1576 1592 0.044244 CCCAGTTCCTCCCCTCCTAA 59.956 60.000 0.00 0.00 0.00 2.69
1577 1593 1.710341 CCCAGTTCCTCCCCTCCTA 59.290 63.158 0.00 0.00 0.00 2.94
1578 1594 2.456840 CCCAGTTCCTCCCCTCCT 59.543 66.667 0.00 0.00 0.00 3.69
1579 1595 3.412408 GCCCAGTTCCTCCCCTCC 61.412 72.222 0.00 0.00 0.00 4.30
1580 1596 3.412408 GGCCCAGTTCCTCCCCTC 61.412 72.222 0.00 0.00 0.00 4.30
1581 1597 3.523681 AAGGCCCAGTTCCTCCCCT 62.524 63.158 0.00 0.00 32.45 4.79
1582 1598 2.941583 AAGGCCCAGTTCCTCCCC 60.942 66.667 0.00 0.00 32.45 4.81
1583 1599 2.356667 CAAGGCCCAGTTCCTCCC 59.643 66.667 0.00 0.00 32.45 4.30
1584 1600 2.203549 CTCCAAGGCCCAGTTCCTCC 62.204 65.000 0.00 0.00 32.45 4.30
1585 1601 1.301293 CTCCAAGGCCCAGTTCCTC 59.699 63.158 0.00 0.00 32.45 3.71
1586 1602 2.234296 CCTCCAAGGCCCAGTTCCT 61.234 63.158 0.00 0.00 34.90 3.36
1587 1603 2.356667 CCTCCAAGGCCCAGTTCC 59.643 66.667 0.00 0.00 0.00 3.62
1613 1629 3.732849 CTGGCCACTTCCCCTCCC 61.733 72.222 0.00 0.00 0.00 4.30
1614 1630 2.610859 TCTGGCCACTTCCCCTCC 60.611 66.667 0.00 0.00 0.00 4.30
1674 1693 4.040755 AGAGAAGAGAGTAGAGAGAGCCT 58.959 47.826 0.00 0.00 0.00 4.58
1682 1701 8.275758 TCTATTTGGCTAAGAGAAGAGAGTAGA 58.724 37.037 3.57 0.00 31.40 2.59
1906 1932 7.610580 AATTTCATCTCTTTTGGGTTTGGTA 57.389 32.000 0.00 0.00 0.00 3.25
1923 1949 3.181418 ACACCCTCCCTGTCAAATTTCAT 60.181 43.478 0.00 0.00 0.00 2.57
2023 2051 5.411781 TCACTAGCTTCTTTCCTTCGAATC 58.588 41.667 0.00 0.00 0.00 2.52
2058 2086 4.080526 TGCCACCTAATCCCTCTTTTCTAC 60.081 45.833 0.00 0.00 0.00 2.59
2064 2094 2.507471 CTCTTGCCACCTAATCCCTCTT 59.493 50.000 0.00 0.00 0.00 2.85
2066 2096 2.103941 CTCTCTTGCCACCTAATCCCTC 59.896 54.545 0.00 0.00 0.00 4.30
2067 2097 2.122768 CTCTCTTGCCACCTAATCCCT 58.877 52.381 0.00 0.00 0.00 4.20
2068 2098 2.119495 TCTCTCTTGCCACCTAATCCC 58.881 52.381 0.00 0.00 0.00 3.85
2093 2125 6.815089 TGGAATCAACAAAAACATACTTGCT 58.185 32.000 0.00 0.00 0.00 3.91
2432 2490 5.311913 ACCTCTTCTCTTCCTCTTCCATTTT 59.688 40.000 0.00 0.00 0.00 1.82
2436 2494 3.551635 ACCTCTTCTCTTCCTCTTCCA 57.448 47.619 0.00 0.00 0.00 3.53
2517 2577 8.526681 CATCTTCGTTGTTTTCTTTCTTTCAAG 58.473 33.333 0.00 0.00 0.00 3.02
2575 2635 4.884744 TCCGAATTTGTTCTTCCTTGTTCA 59.115 37.500 0.00 0.00 0.00 3.18
2614 2674 1.704641 ACCAAGTTTTGCCTCCCTTC 58.295 50.000 0.00 0.00 0.00 3.46
2618 2678 5.944007 TCTTATCTTACCAAGTTTTGCCTCC 59.056 40.000 0.00 0.00 0.00 4.30
2621 2681 7.175119 AGTTCTCTTATCTTACCAAGTTTTGCC 59.825 37.037 0.00 0.00 0.00 4.52
2639 2699 6.018669 GTCGTGTTCTTCATTCAAGTTCTCTT 60.019 38.462 0.00 0.00 33.27 2.85
2641 2701 5.234329 TGTCGTGTTCTTCATTCAAGTTCTC 59.766 40.000 0.00 0.00 33.27 2.87
2650 2711 5.455056 ACTAGAGTGTCGTGTTCTTCATT 57.545 39.130 0.00 0.00 0.00 2.57
2652 2713 4.337274 TCAACTAGAGTGTCGTGTTCTTCA 59.663 41.667 0.00 0.00 0.00 3.02
2657 2720 4.038763 TCCATTCAACTAGAGTGTCGTGTT 59.961 41.667 0.00 0.00 32.47 3.32
2658 2721 3.572682 TCCATTCAACTAGAGTGTCGTGT 59.427 43.478 0.00 0.00 32.47 4.49
2662 2726 5.163405 TGCCTATCCATTCAACTAGAGTGTC 60.163 44.000 0.00 0.00 32.47 3.67
2670 2734 3.627395 TTCGTGCCTATCCATTCAACT 57.373 42.857 0.00 0.00 0.00 3.16
2674 2738 4.394920 TGTTCTTTTCGTGCCTATCCATTC 59.605 41.667 0.00 0.00 0.00 2.67



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

AutoCloner maintained by Alex Coulton.