Multiple sequence alignment - TraesCS7B01G491900

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 TraesCS7B01G491900 chr7B 100.000 2861 0 0 1 2861 744271859 744274719 0.000000e+00 5284.0
1 TraesCS7B01G491900 chr7B 85.835 2732 352 17 1 2728 744250422 744253122 0.000000e+00 2868.0
2 TraesCS7B01G491900 chr7B 88.259 1729 175 16 1 1726 745232732 745234435 0.000000e+00 2043.0
3 TraesCS7B01G491900 chr7B 86.875 1699 207 5 1 1697 743653141 743654825 0.000000e+00 1888.0
4 TraesCS7B01G491900 chr7B 87.629 1552 177 5 4 1553 744292675 744291137 0.000000e+00 1788.0
5 TraesCS7B01G491900 chr7B 84.238 1364 183 21 1402 2763 744189927 744191260 0.000000e+00 1299.0
6 TraesCS7B01G491900 chr7B 89.760 957 89 6 1772 2723 744021922 744020970 0.000000e+00 1216.0
7 TraesCS7B01G491900 chr7B 87.666 1054 104 11 1264 2311 744067605 744068638 0.000000e+00 1203.0
8 TraesCS7B01G491900 chr7B 81.749 526 54 20 2335 2860 743852686 743852203 4.440000e-108 401.0
9 TraesCS7B01G491900 chr7B 86.170 188 18 6 1662 1849 744022372 744022193 2.250000e-46 196.0
10 TraesCS7B01G491900 chr7B 88.000 125 12 1 2739 2860 744191197 744191321 8.260000e-31 145.0
11 TraesCS7B01G491900 chr7B 87.500 128 13 2 2737 2861 744325472 744325345 8.260000e-31 145.0
12 TraesCS7B01G491900 chr7B 89.423 104 6 3 2743 2842 744020450 744020348 2.990000e-25 126.0
13 TraesCS7B01G491900 chr7D 87.122 2314 274 9 1 2311 632099012 632101304 0.000000e+00 2601.0
14 TraesCS7B01G491900 chr7D 85.505 2256 258 23 497 2746 632046385 632048577 0.000000e+00 2290.0
15 TraesCS7B01G491900 chr7D 88.699 1699 176 5 1 1697 632143682 632145366 0.000000e+00 2060.0
16 TraesCS7B01G491900 chr7D 84.385 935 138 6 1768 2699 555057151 555058080 0.000000e+00 911.0
17 TraesCS7B01G491900 chr7D 80.374 963 157 19 1767 2716 632083405 632084348 0.000000e+00 702.0
18 TraesCS7B01G491900 chr7D 78.687 1112 170 35 1767 2861 632087884 632088945 0.000000e+00 678.0
19 TraesCS7B01G491900 chr7D 93.182 132 7 2 2730 2860 632048525 632048655 2.910000e-45 193.0
20 TraesCS7B01G491900 chr7D 91.860 86 7 0 2776 2861 632048985 632049070 1.390000e-23 121.0
21 TraesCS7B01G491900 chr7D 92.308 65 5 0 2797 2861 632039413 632039477 3.040000e-15 93.5
22 TraesCS7B01G491900 chr7A 86.851 2312 285 6 1 2311 736005942 736003649 0.000000e+00 2567.0
23 TraesCS7B01G491900 chr7A 86.117 1916 210 17 1 1914 735963100 735964961 0.000000e+00 2013.0
24 TraesCS7B01G491900 chr7A 87.979 1697 186 7 4 1697 735843644 735841963 0.000000e+00 1988.0
25 TraesCS7B01G491900 chr7A 86.761 1488 183 3 1 1485 735783979 735782503 0.000000e+00 1644.0
26 TraesCS7B01G491900 chr7A 86.066 1464 165 16 851 2311 735929369 735930796 0.000000e+00 1537.0
27 TraesCS7B01G491900 chr7A 82.076 1021 154 17 1733 2742 736069906 736068904 0.000000e+00 845.0
28 TraesCS7B01G491900 chr7A 81.492 724 123 7 1774 2490 736091868 736091149 4.110000e-163 584.0
29 TraesCS7B01G491900 chr7A 97.674 43 1 0 2819 2861 735645870 735645828 1.100000e-09 75.0
30 TraesCS7B01G491900 chr1B 83.102 864 145 1 1771 2633 577923433 577922570 0.000000e+00 785.0
31 TraesCS7B01G491900 chr3B 78.479 1078 166 31 1799 2861 788254399 788253373 0.000000e+00 645.0


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 TraesCS7B01G491900 chr7B 744271859 744274719 2860 False 5284.000000 5284 100.000000 1 2861 1 chr7B.!!$F4 2860
1 TraesCS7B01G491900 chr7B 744250422 744253122 2700 False 2868.000000 2868 85.835000 1 2728 1 chr7B.!!$F3 2727
2 TraesCS7B01G491900 chr7B 745232732 745234435 1703 False 2043.000000 2043 88.259000 1 1726 1 chr7B.!!$F5 1725
3 TraesCS7B01G491900 chr7B 743653141 743654825 1684 False 1888.000000 1888 86.875000 1 1697 1 chr7B.!!$F1 1696
4 TraesCS7B01G491900 chr7B 744291137 744292675 1538 True 1788.000000 1788 87.629000 4 1553 1 chr7B.!!$R2 1549
5 TraesCS7B01G491900 chr7B 744067605 744068638 1033 False 1203.000000 1203 87.666000 1264 2311 1 chr7B.!!$F2 1047
6 TraesCS7B01G491900 chr7B 744189927 744191321 1394 False 722.000000 1299 86.119000 1402 2860 2 chr7B.!!$F6 1458
7 TraesCS7B01G491900 chr7B 744020348 744022372 2024 True 512.666667 1216 88.451000 1662 2842 3 chr7B.!!$R4 1180
8 TraesCS7B01G491900 chr7D 632099012 632101304 2292 False 2601.000000 2601 87.122000 1 2311 1 chr7D.!!$F3 2310
9 TraesCS7B01G491900 chr7D 632143682 632145366 1684 False 2060.000000 2060 88.699000 1 1697 1 chr7D.!!$F4 1696
10 TraesCS7B01G491900 chr7D 555057151 555058080 929 False 911.000000 911 84.385000 1768 2699 1 chr7D.!!$F1 931
11 TraesCS7B01G491900 chr7D 632046385 632049070 2685 False 868.000000 2290 90.182333 497 2861 3 chr7D.!!$F5 2364
12 TraesCS7B01G491900 chr7D 632083405 632088945 5540 False 690.000000 702 79.530500 1767 2861 2 chr7D.!!$F6 1094
13 TraesCS7B01G491900 chr7A 736003649 736005942 2293 True 2567.000000 2567 86.851000 1 2311 1 chr7A.!!$R4 2310
14 TraesCS7B01G491900 chr7A 735963100 735964961 1861 False 2013.000000 2013 86.117000 1 1914 1 chr7A.!!$F2 1913
15 TraesCS7B01G491900 chr7A 735841963 735843644 1681 True 1988.000000 1988 87.979000 4 1697 1 chr7A.!!$R3 1693
16 TraesCS7B01G491900 chr7A 735782503 735783979 1476 True 1644.000000 1644 86.761000 1 1485 1 chr7A.!!$R2 1484
17 TraesCS7B01G491900 chr7A 735929369 735930796 1427 False 1537.000000 1537 86.066000 851 2311 1 chr7A.!!$F1 1460
18 TraesCS7B01G491900 chr7A 736068904 736069906 1002 True 845.000000 845 82.076000 1733 2742 1 chr7A.!!$R5 1009
19 TraesCS7B01G491900 chr7A 736091149 736091868 719 True 584.000000 584 81.492000 1774 2490 1 chr7A.!!$R6 716
20 TraesCS7B01G491900 chr1B 577922570 577923433 863 True 785.000000 785 83.102000 1771 2633 1 chr1B.!!$R1 862
21 TraesCS7B01G491900 chr3B 788253373 788254399 1026 True 645.000000 645 78.479000 1799 2861 1 chr3B.!!$R1 1062

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
362 364 0.034337 TCACTCCCCGCAACAAGTAC 59.966 55.0 0.00 0.0 0.00 2.73 F
834 836 0.399091 TTCCCAATGGGTTGTGCCAA 60.399 50.0 19.28 0.0 44.74 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1399 1404 0.037303 CTTGTCCCACTCAGTGCCAT 59.963 55.0 0.0 0.0 31.34 4.4 R
2728 8123 0.105709 CTCCTCCTCCTCTTCCTCCC 60.106 65.0 0.0 0.0 0.00 4.3 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
40 42 7.173907 GTGAACTTGATTGGAAATCTCTTCAGA 59.826 37.037 1.99 0.00 0.00 3.27
51 53 2.951726 TCTCTTCAGACACAGCAATCG 58.048 47.619 0.00 0.00 0.00 3.34
78 80 7.475771 GAGAACATTGATCTCAACTATCCAC 57.524 40.000 16.53 0.00 42.33 4.02
87 89 9.770097 TTGATCTCAACTATCCACATTAAGATC 57.230 33.333 0.00 0.00 37.94 2.75
115 117 5.393461 CCTGGTGATTCATTGGCTACTTTTC 60.393 44.000 0.00 0.00 0.00 2.29
163 165 2.236893 TCTGCAGATGTGGTAGCATTGA 59.763 45.455 13.74 0.00 36.28 2.57
207 209 2.432510 GCACCTGAGGTATCTAGCACTT 59.567 50.000 2.59 0.00 32.11 3.16
210 212 3.702045 ACCTGAGGTATCTAGCACTTGTC 59.298 47.826 0.07 0.00 32.11 3.18
286 288 3.593442 TCCTTGACCTTTGTGGATGTT 57.407 42.857 0.00 0.00 39.71 2.71
307 309 7.831691 TGTTCAAAATTGGTGAATCTTCCTA 57.168 32.000 7.80 0.00 37.34 2.94
338 340 0.538287 AAGCTTGGCCAGTTGAGGTC 60.538 55.000 5.11 0.00 0.00 3.85
348 350 3.658709 CCAGTTGAGGTCTCTTTCACTC 58.341 50.000 0.00 0.00 0.00 3.51
353 355 1.079057 GGTCTCTTTCACTCCCCGC 60.079 63.158 0.00 0.00 0.00 6.13
362 364 0.034337 TCACTCCCCGCAACAAGTAC 59.966 55.000 0.00 0.00 0.00 2.73
414 416 8.643324 ACAAATATGAGGAGACTATGTAGGTTC 58.357 37.037 0.00 0.00 44.43 3.62
416 418 3.912248 TGAGGAGACTATGTAGGTTCCC 58.088 50.000 7.88 0.00 44.43 3.97
418 420 4.078571 TGAGGAGACTATGTAGGTTCCCAT 60.079 45.833 7.88 0.00 44.43 4.00
424 426 0.837272 ATGTAGGTTCCCATCCCACG 59.163 55.000 0.00 0.00 0.00 4.94
479 481 2.169352 GGCCTCTTTCACAGCTCAGATA 59.831 50.000 0.00 0.00 0.00 1.98
485 487 5.668471 TCTTTCACAGCTCAGATATCTTGG 58.332 41.667 1.33 0.00 0.00 3.61
493 495 9.716531 CACAGCTCAGATATCTTGGATTAATTA 57.283 33.333 1.33 0.00 0.00 1.40
494 496 9.717942 ACAGCTCAGATATCTTGGATTAATTAC 57.282 33.333 1.33 0.00 0.00 1.89
571 573 9.306777 AGAAGATGCATCTTATCAGTCTATACA 57.693 33.333 35.74 0.00 46.47 2.29
603 605 2.571653 CAGTAAACTGGGAGGTGATGGA 59.428 50.000 2.01 0.00 40.20 3.41
608 610 0.466922 CTGGGAGGTGATGGATTGGC 60.467 60.000 0.00 0.00 0.00 4.52
634 636 3.640967 AGATATGGAAGGTGTCTCTGAGC 59.359 47.826 0.00 0.00 0.00 4.26
688 690 0.910088 GCTCTACCCTCCACCTGGTT 60.910 60.000 0.00 0.00 36.04 3.67
707 709 9.927081 ACCTGGTTTAGAATATCTTCAAATCAT 57.073 29.630 0.00 0.00 33.56 2.45
721 723 7.125391 TCTTCAAATCATGGGGTATTTTAGCT 58.875 34.615 0.00 0.00 0.00 3.32
722 724 6.959639 TCAAATCATGGGGTATTTTAGCTC 57.040 37.500 0.00 0.00 0.00 4.09
731 733 2.284417 GGTATTTTAGCTCGCAACTCCG 59.716 50.000 0.00 0.00 0.00 4.63
735 737 1.248785 TTAGCTCGCAACTCCGGAGT 61.249 55.000 31.69 31.69 44.94 3.85
810 812 2.089980 GATGATCTGCCTTGTTGCACT 58.910 47.619 0.00 0.00 36.04 4.40
834 836 0.399091 TTCCCAATGGGTTGTGCCAA 60.399 50.000 19.28 0.00 44.74 4.52
940 945 7.484959 CAGCTTCATTTCCGAGGTTAAATAAAC 59.515 37.037 0.00 0.00 37.36 2.01
994 999 1.501582 GGAGTGGGAGGAGCAAGTAT 58.498 55.000 0.00 0.00 0.00 2.12
996 1001 2.630580 GGAGTGGGAGGAGCAAGTATAG 59.369 54.545 0.00 0.00 0.00 1.31
1041 1046 2.076863 GTGCTCGGTAAATGCAGACTT 58.923 47.619 0.00 0.00 37.39 3.01
1129 1134 3.550437 AGCACCTTAGCTACATTGAGG 57.450 47.619 6.84 6.84 44.50 3.86
1132 1137 2.092968 CACCTTAGCTACATTGAGGGCA 60.093 50.000 12.11 0.00 0.00 5.36
1159 1164 2.872245 TCTGTTGTTGAGCTTACAGTGC 59.128 45.455 0.00 0.00 39.16 4.40
1179 1184 1.639635 ATGGATGCCCTGACCTGGAC 61.640 60.000 0.00 0.00 0.00 4.02
1203 1208 3.528905 TGATCACCAATCTCCCCAATCTT 59.471 43.478 0.00 0.00 35.24 2.40
1214 1219 4.723789 TCTCCCCAATCTTCAGAAGCTTAT 59.276 41.667 5.15 0.00 0.00 1.73
1228 1233 4.510711 AGAAGCTTATCATCATGAACTGCG 59.489 41.667 0.00 0.00 0.00 5.18
1457 1462 1.062587 GTCAAGGCATATGCACGTGAC 59.937 52.381 29.58 29.58 44.36 3.67
1537 1542 6.228995 TGGATTCAAATATCAGCAGCTCTAG 58.771 40.000 0.00 0.00 0.00 2.43
1596 1612 8.634475 ACAAGCTTTCTCTTAATTTGTTTGAC 57.366 30.769 0.00 0.00 0.00 3.18
1620 1637 6.126652 ACCACTCTGATTCTGCCAGTTTATAT 60.127 38.462 0.00 0.00 33.57 0.86
1677 1695 2.330440 TGCTGCATGATGACCGTATT 57.670 45.000 0.00 0.00 0.00 1.89
1698 1716 7.977853 CGTATTTGTTATGTACCTTCCTAGTGT 59.022 37.037 0.00 0.00 0.00 3.55
1699 1717 9.095065 GTATTTGTTATGTACCTTCCTAGTGTG 57.905 37.037 0.00 0.00 0.00 3.82
1765 1784 9.408069 GTTTTCTCGAGTTTAACAGATCTAGAA 57.592 33.333 13.13 0.00 0.00 2.10
1909 2276 3.269381 AGCTTGGTGAGGATCCCATTTTA 59.731 43.478 8.55 0.00 35.77 1.52
1990 2363 1.827681 AGAGTAGCTGTCGCTCTGAA 58.172 50.000 0.00 0.00 45.15 3.02
2000 2373 3.076621 TGTCGCTCTGAAAATGCTGAAT 58.923 40.909 0.00 0.00 0.00 2.57
2020 2393 1.835494 TCTGGTGACTCTCCGGTTAG 58.165 55.000 0.00 2.40 33.44 2.34
2055 2428 5.304357 TCTCTTGGTGTGAATGAGTCAACTA 59.696 40.000 0.00 0.00 38.23 2.24
2090 2463 5.442391 ACTAAGGTGTTTGTTGAGGCTTTA 58.558 37.500 0.00 0.00 0.00 1.85
2174 2550 3.684788 GCAAGTTCGACAAGATACATGGT 59.315 43.478 0.00 0.00 0.00 3.55
2259 2641 0.969149 TGAGGAGAATGACAGCACGT 59.031 50.000 0.00 0.00 0.00 4.49
2318 2700 0.750182 ATATTTGGTTGGGGCCGTCG 60.750 55.000 0.00 0.00 0.00 5.12
2345 2736 4.022416 AGCATGAACCAATTGAGCGTTTTA 60.022 37.500 7.12 0.00 0.00 1.52
2490 7337 2.398588 CCTGGCTCCTCACACCTTATA 58.601 52.381 0.00 0.00 0.00 0.98
2514 7367 1.971357 TGGAAGACAAGGACCACTCTC 59.029 52.381 0.00 0.00 0.00 3.20
2524 7377 2.183679 GGACCACTCTCCAGATGTTCT 58.816 52.381 0.00 0.00 0.00 3.01
2525 7378 2.093764 GGACCACTCTCCAGATGTTCTG 60.094 54.545 0.00 0.00 43.91 3.02
2556 7409 1.409412 CGAGTTCAACAGGAGACACG 58.591 55.000 0.00 0.00 0.00 4.49
2578 7431 0.097674 GCAGCGTCAACCATCATGAC 59.902 55.000 0.00 0.00 42.94 3.06
2579 7432 1.730501 CAGCGTCAACCATCATGACT 58.269 50.000 0.00 0.00 43.93 3.41
2602 7455 1.493311 CGCTCACGAGGTTGAAAGC 59.507 57.895 0.00 0.00 43.93 3.51
2604 7457 1.901650 GCTCACGAGGTTGAAAGCCG 61.902 60.000 0.00 0.00 0.00 5.52
2611 7464 1.740025 GAGGTTGAAAGCCGATTGGAG 59.260 52.381 1.98 0.00 37.49 3.86
2712 8107 0.842635 CATGGAAGAGGGGGAGGAAG 59.157 60.000 0.00 0.00 0.00 3.46
2713 8108 0.725133 ATGGAAGAGGGGGAGGAAGA 59.275 55.000 0.00 0.00 0.00 2.87
2714 8109 0.043334 TGGAAGAGGGGGAGGAAGAG 59.957 60.000 0.00 0.00 0.00 2.85
2715 8110 0.692756 GGAAGAGGGGGAGGAAGAGG 60.693 65.000 0.00 0.00 0.00 3.69
2716 8111 0.692756 GAAGAGGGGGAGGAAGAGGG 60.693 65.000 0.00 0.00 0.00 4.30
2717 8112 2.040359 GAGGGGGAGGAAGAGGGG 60.040 72.222 0.00 0.00 0.00 4.79
2718 8113 3.711782 AGGGGGAGGAAGAGGGGG 61.712 72.222 0.00 0.00 0.00 5.40
2719 8114 3.707189 GGGGGAGGAAGAGGGGGA 61.707 72.222 0.00 0.00 0.00 4.81
2720 8115 2.040359 GGGGAGGAAGAGGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
2721 8116 2.040359 GGGAGGAAGAGGGGGAGG 60.040 72.222 0.00 0.00 0.00 4.30
2722 8117 2.647949 GGGAGGAAGAGGGGGAGGA 61.648 68.421 0.00 0.00 0.00 3.71
2723 8118 1.396594 GGAGGAAGAGGGGGAGGAA 59.603 63.158 0.00 0.00 0.00 3.36
2724 8119 0.692756 GGAGGAAGAGGGGGAGGAAG 60.693 65.000 0.00 0.00 0.00 3.46
2725 8120 0.340208 GAGGAAGAGGGGGAGGAAGA 59.660 60.000 0.00 0.00 0.00 2.87
2726 8121 0.341609 AGGAAGAGGGGGAGGAAGAG 59.658 60.000 0.00 0.00 0.00 2.85
2727 8122 0.692756 GGAAGAGGGGGAGGAAGAGG 60.693 65.000 0.00 0.00 0.00 3.69
2728 8123 0.692756 GAAGAGGGGGAGGAAGAGGG 60.693 65.000 0.00 0.00 0.00 4.30
2729 8124 2.040359 GAGGGGGAGGAAGAGGGG 60.040 72.222 0.00 0.00 0.00 4.79
2730 8125 3.711782 AGGGGGAGGAAGAGGGGG 61.712 72.222 0.00 0.00 0.00 5.40
2731 8126 3.707189 GGGGGAGGAAGAGGGGGA 61.707 72.222 0.00 0.00 0.00 4.81
2732 8127 2.040359 GGGGAGGAAGAGGGGGAG 60.040 72.222 0.00 0.00 0.00 4.30
2733 8128 2.040359 GGGAGGAAGAGGGGGAGG 60.040 72.222 0.00 0.00 0.00 4.30
2734 8129 2.647949 GGGAGGAAGAGGGGGAGGA 61.648 68.421 0.00 0.00 0.00 3.71
2795 8225 2.266055 GAGGTGCGGCAGTTAGCT 59.734 61.111 1.18 0.00 44.79 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 1.202639 TGTTCTCACCGATTGCTGTGT 60.203 47.619 0.00 0.00 34.14 3.72
51 53 6.481644 GGATAGTTGAGATCAATGTTCTCACC 59.518 42.308 20.06 14.92 46.92 4.02
78 80 5.591472 TGAATCACCAGGCTTGATCTTAATG 59.409 40.000 0.00 0.00 32.29 1.90
87 89 1.134907 GCCAATGAATCACCAGGCTTG 60.135 52.381 13.12 1.09 39.02 4.01
115 117 0.037326 TGCAGAGTCCGCAAACTAGG 60.037 55.000 0.00 0.00 36.17 3.02
207 209 6.225981 AGTACAGATGTATCAGCATTGACA 57.774 37.500 0.00 0.00 35.83 3.58
210 212 6.051074 TGGAAGTACAGATGTATCAGCATTG 58.949 40.000 0.00 0.00 32.54 2.82
221 223 3.981071 TGTTCCCTGGAAGTACAGATG 57.019 47.619 0.00 0.00 40.97 2.90
286 288 8.686334 GCTATTAGGAAGATTCACCAATTTTGA 58.314 33.333 0.00 0.00 0.00 2.69
307 309 2.167075 GGCCAAGCTTCACAATGCTATT 59.833 45.455 0.00 0.00 38.75 1.73
338 340 0.250295 TGTTGCGGGGAGTGAAAGAG 60.250 55.000 0.00 0.00 0.00 2.85
353 355 3.129988 CCCTCTAGGTACCGTACTTGTTG 59.870 52.174 6.18 0.00 0.00 3.33
385 387 8.642432 CCTACATAGTCTCCTCATATTTGTCAA 58.358 37.037 0.00 0.00 0.00 3.18
410 412 2.045340 CCACGTGGGATGGGAACC 60.045 66.667 27.57 0.00 46.71 3.62
424 426 3.350219 ACTACACCAATCACCATCCAC 57.650 47.619 0.00 0.00 0.00 4.02
494 496 8.627403 ACAAGGCATCAGATACATTTTCTAATG 58.373 33.333 0.00 0.00 45.39 1.90
501 503 5.186409 AGCAAACAAGGCATCAGATACATTT 59.814 36.000 0.00 0.00 0.00 2.32
512 514 2.675889 GCATTAGCAGCAAACAAGGCAT 60.676 45.455 0.00 0.00 41.58 4.40
518 520 1.745087 GCCTAGCATTAGCAGCAAACA 59.255 47.619 0.00 0.00 45.49 2.83
569 571 4.065088 CAGTTTACTGGTGTAGTGCATGT 58.935 43.478 1.88 0.00 40.65 3.21
596 598 4.021719 CCATATCTTTGGCCAATCCATCAC 60.022 45.833 21.26 0.00 46.04 3.06
603 605 3.962718 CACCTTCCATATCTTTGGCCAAT 59.037 43.478 21.26 7.22 36.66 3.16
608 610 5.104776 TCAGAGACACCTTCCATATCTTTGG 60.105 44.000 0.00 0.00 38.18 3.28
615 617 2.820178 TGCTCAGAGACACCTTCCATA 58.180 47.619 0.00 0.00 0.00 2.74
617 619 1.345741 CTTGCTCAGAGACACCTTCCA 59.654 52.381 0.00 0.00 0.00 3.53
634 636 4.934075 TCTCAATTCGTTGATGCTCTTG 57.066 40.909 0.00 0.00 0.00 3.02
674 676 2.127651 TTCTAAACCAGGTGGAGGGT 57.872 50.000 2.10 0.00 39.65 4.34
707 709 2.026636 AGTTGCGAGCTAAAATACCCCA 60.027 45.455 0.00 0.00 0.00 4.96
718 720 2.992114 ACTCCGGAGTTGCGAGCT 60.992 61.111 31.69 6.17 38.83 4.09
834 836 1.707427 AGAAACTGCAGATTGGGGAGT 59.293 47.619 23.35 0.00 38.68 3.85
913 918 2.568623 AACCTCGGAAATGAAGCTGT 57.431 45.000 0.00 0.00 0.00 4.40
940 945 3.117776 TCCACCATTCCCATGAAGATCAG 60.118 47.826 0.00 0.00 33.05 2.90
994 999 1.743623 CCAAACGACGCATGGCCTA 60.744 57.895 3.32 0.00 0.00 3.93
996 1001 3.039202 CTCCAAACGACGCATGGCC 62.039 63.158 13.21 0.00 34.13 5.36
1041 1046 0.258774 GGCCTGGAGGAAAATGCCTA 59.741 55.000 0.00 0.00 38.73 3.93
1129 1134 2.352127 GCTCAACAACAGAAGGAATGCC 60.352 50.000 0.00 0.00 0.00 4.40
1132 1137 5.376625 TGTAAGCTCAACAACAGAAGGAAT 58.623 37.500 0.00 0.00 0.00 3.01
1159 1164 1.152819 CCAGGTCAGGGCATCCATG 60.153 63.158 0.00 0.00 34.83 3.66
1179 1184 3.301794 TTGGGGAGATTGGTGATCATG 57.698 47.619 0.00 0.00 37.22 3.07
1203 1208 5.526479 GCAGTTCATGATGATAAGCTTCTGA 59.474 40.000 0.00 0.00 0.00 3.27
1214 1219 2.153645 ACTTTGCGCAGTTCATGATGA 58.846 42.857 11.31 0.00 0.00 2.92
1228 1233 1.000938 CTCCAGCACCTTCAACTTTGC 60.001 52.381 0.00 0.00 35.08 3.68
1320 1325 5.289083 ACTGCAAATTCCTTGGCTTTAAA 57.711 34.783 0.00 0.00 35.38 1.52
1321 1326 4.953940 ACTGCAAATTCCTTGGCTTTAA 57.046 36.364 0.00 0.00 35.38 1.52
1389 1394 3.441222 CACTCAGTGCCATATTTTCTGCA 59.559 43.478 0.00 0.00 0.00 4.41
1390 1395 3.181493 CCACTCAGTGCCATATTTTCTGC 60.181 47.826 0.00 0.00 31.34 4.26
1391 1396 3.379372 CCCACTCAGTGCCATATTTTCTG 59.621 47.826 0.00 0.00 31.34 3.02
1392 1397 3.266772 TCCCACTCAGTGCCATATTTTCT 59.733 43.478 0.00 0.00 31.34 2.52
1393 1398 3.378427 GTCCCACTCAGTGCCATATTTTC 59.622 47.826 0.00 0.00 31.34 2.29
1394 1399 3.245229 TGTCCCACTCAGTGCCATATTTT 60.245 43.478 0.00 0.00 31.34 1.82
1395 1400 2.308570 TGTCCCACTCAGTGCCATATTT 59.691 45.455 0.00 0.00 31.34 1.40
1396 1401 1.915489 TGTCCCACTCAGTGCCATATT 59.085 47.619 0.00 0.00 31.34 1.28
1397 1402 1.583556 TGTCCCACTCAGTGCCATAT 58.416 50.000 0.00 0.00 31.34 1.78
1398 1403 1.278985 CTTGTCCCACTCAGTGCCATA 59.721 52.381 0.00 0.00 31.34 2.74
1399 1404 0.037303 CTTGTCCCACTCAGTGCCAT 59.963 55.000 0.00 0.00 31.34 4.40
1457 1462 3.317993 ACCATTTTCTTTGGTTGTCTCCG 59.682 43.478 0.00 0.00 45.19 4.63
1526 1531 4.213694 CCTTCAAATATGCTAGAGCTGCTG 59.786 45.833 7.01 0.00 42.66 4.41
1537 1542 9.638239 TTTGATTTTCTGTACCTTCAAATATGC 57.362 29.630 0.00 0.00 30.52 3.14
1580 1593 7.496529 TCAGAGTGGTCAAACAAATTAAGAG 57.503 36.000 0.00 0.00 0.00 2.85
1596 1612 2.486472 AACTGGCAGAATCAGAGTGG 57.514 50.000 23.66 0.00 36.22 4.00
1620 1637 5.705441 AGCAAGAGATAAAATCAAACGACCA 59.295 36.000 0.00 0.00 0.00 4.02
1677 1695 5.012251 TGCACACTAGGAAGGTACATAACAA 59.988 40.000 0.00 0.00 0.00 2.83
1699 1717 5.353678 AGAAGACAAATACTGAGCAAGATGC 59.646 40.000 0.00 0.00 45.46 3.91
1909 2276 4.810033 GCTCCCTTGCCATCATATCTTCAT 60.810 45.833 0.00 0.00 0.00 2.57
1936 2309 2.248248 ACACTCTCCCATCGACAAAGA 58.752 47.619 0.00 0.00 0.00 2.52
1990 2363 4.660168 AGAGTCACCAGAATTCAGCATTT 58.340 39.130 8.44 0.00 0.00 2.32
2000 2373 2.168496 CTAACCGGAGAGTCACCAGAA 58.832 52.381 9.46 0.00 0.00 3.02
2020 2393 2.703007 ACACCAAGAGAGGATCCTATGC 59.297 50.000 15.13 6.75 33.66 3.14
2055 2428 4.910458 ACACCTTAGTTACCAGCAAGAT 57.090 40.909 0.00 0.00 0.00 2.40
2090 2463 1.098050 GGTGAAATGCTCGCTTCCAT 58.902 50.000 0.00 0.00 34.75 3.41
2259 2641 3.132646 GGATCAACCATGGCTTGCATTAA 59.867 43.478 13.04 0.27 38.79 1.40
2318 2700 2.099756 GCTCAATTGGTTCATGCTACCC 59.900 50.000 5.42 0.00 34.66 3.69
2345 2736 1.412710 TCAAAGAGCCAAGAGTCGTGT 59.587 47.619 5.33 0.00 0.00 4.49
2490 7337 1.143073 GTGGTCCTTGTCTTCCAGGTT 59.857 52.381 0.00 0.00 0.00 3.50
2514 7367 3.314635 GCTTGATAAGGCAGAACATCTGG 59.685 47.826 9.25 0.00 44.43 3.86
2556 7409 1.651240 ATGATGGTTGACGCTGCAGC 61.651 55.000 29.12 29.12 37.78 5.25
2564 7417 1.131883 GCAGCAGTCATGATGGTTGAC 59.868 52.381 14.60 0.00 43.18 3.18
2602 7455 2.560542 CTGTCTAGGATCCTCCAATCGG 59.439 54.545 20.22 7.11 39.61 4.18
2604 7457 3.258123 GCTCTGTCTAGGATCCTCCAATC 59.742 52.174 20.22 6.48 39.61 2.67
2611 7464 2.029470 CCAATCGCTCTGTCTAGGATCC 60.029 54.545 2.48 2.48 0.00 3.36
2712 8107 2.040359 CCCCTCTTCCTCCCCCTC 60.040 72.222 0.00 0.00 0.00 4.30
2713 8108 3.711782 CCCCCTCTTCCTCCCCCT 61.712 72.222 0.00 0.00 0.00 4.79
2714 8109 3.707189 TCCCCCTCTTCCTCCCCC 61.707 72.222 0.00 0.00 0.00 5.40
2715 8110 2.040359 CTCCCCCTCTTCCTCCCC 60.040 72.222 0.00 0.00 0.00 4.81
2716 8111 2.040359 CCTCCCCCTCTTCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
2717 8112 0.692756 CTTCCTCCCCCTCTTCCTCC 60.693 65.000 0.00 0.00 0.00 4.30
2718 8113 0.340208 TCTTCCTCCCCCTCTTCCTC 59.660 60.000 0.00 0.00 0.00 3.71
2719 8114 0.341609 CTCTTCCTCCCCCTCTTCCT 59.658 60.000 0.00 0.00 0.00 3.36
2720 8115 0.692756 CCTCTTCCTCCCCCTCTTCC 60.693 65.000 0.00 0.00 0.00 3.46
2721 8116 0.340208 TCCTCTTCCTCCCCCTCTTC 59.660 60.000 0.00 0.00 0.00 2.87
2722 8117 0.341609 CTCCTCTTCCTCCCCCTCTT 59.658 60.000 0.00 0.00 0.00 2.85
2723 8118 1.598856 CCTCCTCTTCCTCCCCCTCT 61.599 65.000 0.00 0.00 0.00 3.69
2724 8119 1.074850 CCTCCTCTTCCTCCCCCTC 60.075 68.421 0.00 0.00 0.00 4.30
2725 8120 1.550374 TCCTCCTCTTCCTCCCCCT 60.550 63.158 0.00 0.00 0.00 4.79
2726 8121 1.074850 CTCCTCCTCTTCCTCCCCC 60.075 68.421 0.00 0.00 0.00 5.40
2727 8122 1.074850 CCTCCTCCTCTTCCTCCCC 60.075 68.421 0.00 0.00 0.00 4.81
2728 8123 0.105709 CTCCTCCTCCTCTTCCTCCC 60.106 65.000 0.00 0.00 0.00 4.30
2729 8124 0.105709 CCTCCTCCTCCTCTTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
2730 8125 0.930726 TCCTCCTCCTCCTCTTCCTC 59.069 60.000 0.00 0.00 0.00 3.71
2731 8126 0.933700 CTCCTCCTCCTCCTCTTCCT 59.066 60.000 0.00 0.00 0.00 3.36
2732 8127 0.105709 CCTCCTCCTCCTCCTCTTCC 60.106 65.000 0.00 0.00 0.00 3.46
2733 8128 0.930726 TCCTCCTCCTCCTCCTCTTC 59.069 60.000 0.00 0.00 0.00 2.87
2734 8129 1.290732 CTTCCTCCTCCTCCTCCTCTT 59.709 57.143 0.00 0.00 0.00 2.85
2795 8225 3.733960 CTCACGGCGTCCTCGTCA 61.734 66.667 10.85 0.00 42.21 4.35


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

AutoCloner maintained by Alex Coulton.