Multiple sequence alignment - TraesCS7D01G039200

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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 TraesCS7D01G039200 chr7D 100.000 3595 0 0 1 3595 19959790 19963384 0.000000e+00 6639.0
1 TraesCS7D01G039200 chr7D 86.985 607 63 11 195 788 91779401 91778798 0.000000e+00 669.0
2 TraesCS7D01G039200 chr7D 86.656 607 63 12 195 788 91749067 91748466 0.000000e+00 656.0
3 TraesCS7D01G039200 chr7D 84.416 616 69 20 194 788 483286698 483287307 6.690000e-162 580.0
4 TraesCS7D01G039200 chr7D 84.615 312 47 1 2175 2485 19999469 19999780 3.490000e-80 309.0
5 TraesCS7D01G039200 chr7D 91.150 113 8 2 2256 2367 18912618 18912507 6.220000e-33 152.0
6 TraesCS7D01G039200 chr7A 86.489 2709 206 55 540 3182 20095469 20098083 0.000000e+00 2828.0
7 TraesCS7D01G039200 chr7A 86.207 406 43 11 30 425 20094535 20094937 9.220000e-116 427.0
8 TraesCS7D01G039200 chr7A 85.577 312 44 1 2175 2485 20152312 20152623 3.460000e-85 326.0
9 TraesCS7D01G039200 chr7A 95.092 163 8 0 3344 3506 20098237 20098399 1.280000e-64 257.0
10 TraesCS7D01G039200 chr7A 95.192 104 5 0 3492 3595 20098450 20098553 7.990000e-37 165.0
11 TraesCS7D01G039200 chr7A 81.707 82 8 6 3190 3265 20098112 20098192 1.080000e-05 62.1
12 TraesCS7D01G039200 chrUn 86.519 1721 118 54 1666 3321 294783365 294781694 0.000000e+00 1788.0
13 TraesCS7D01G039200 chrUn 86.288 598 65 12 195 778 380756813 380756219 5.060000e-178 634.0
14 TraesCS7D01G039200 chrUn 86.120 598 66 12 195 778 92406757 92407351 2.360000e-176 628.0
15 TraesCS7D01G039200 chrUn 87.140 451 24 10 1238 1673 294783832 294783401 6.980000e-132 481.0
16 TraesCS7D01G039200 chrUn 83.838 198 23 6 213 401 50980970 50980773 2.850000e-41 180.0
17 TraesCS7D01G039200 chr3A 87.685 609 58 9 195 788 584027974 584028580 0.000000e+00 693.0
18 TraesCS7D01G039200 chr6B 87.092 612 62 10 193 788 671720398 671719788 0.000000e+00 676.0
19 TraesCS7D01G039200 chr6B 86.949 613 61 10 193 788 671727524 671726914 0.000000e+00 671.0
20 TraesCS7D01G039200 chr2D 84.211 684 84 18 2025 2698 649061792 649061123 0.000000e+00 643.0
21 TraesCS7D01G039200 chr1B 86.271 590 73 6 195 778 679234449 679233862 5.060000e-178 634.0
22 TraesCS7D01G039200 chr6D 88.346 532 55 5 260 788 431855078 431854551 1.820000e-177 632.0
23 TraesCS7D01G039200 chr2B 83.237 692 84 22 2025 2701 784754336 784753662 1.100000e-169 606.0
24 TraesCS7D01G039200 chr2B 76.945 694 101 23 2838 3481 784753037 784752353 1.240000e-89 340.0
25 TraesCS7D01G039200 chr1D 85.476 599 67 15 195 778 487618229 487617636 1.100000e-169 606.0
26 TraesCS7D01G039200 chr2A 83.361 601 76 18 1994 2583 775658861 775659448 5.280000e-148 534.0
27 TraesCS7D01G039200 chr2A 80.403 546 58 17 2838 3343 775665420 775665956 1.580000e-98 370.0
28 TraesCS7D01G039200 chr5D 78.748 607 90 24 195 788 375052508 375053088 1.580000e-98 370.0
29 TraesCS7D01G039200 chr4A 90.265 113 9 2 2256 2367 713352177 713352066 2.890000e-31 147.0


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 TraesCS7D01G039200 chr7D 19959790 19963384 3594 False 6639.00 6639 100.0000 1 3595 1 chr7D.!!$F1 3594
1 TraesCS7D01G039200 chr7D 91778798 91779401 603 True 669.00 669 86.9850 195 788 1 chr7D.!!$R3 593
2 TraesCS7D01G039200 chr7D 91748466 91749067 601 True 656.00 656 86.6560 195 788 1 chr7D.!!$R2 593
3 TraesCS7D01G039200 chr7D 483286698 483287307 609 False 580.00 580 84.4160 194 788 1 chr7D.!!$F3 594
4 TraesCS7D01G039200 chr7A 20094535 20098553 4018 False 747.82 2828 88.9374 30 3595 5 chr7A.!!$F2 3565
5 TraesCS7D01G039200 chrUn 294781694 294783832 2138 True 1134.50 1788 86.8295 1238 3321 2 chrUn.!!$R3 2083
6 TraesCS7D01G039200 chrUn 380756219 380756813 594 True 634.00 634 86.2880 195 778 1 chrUn.!!$R2 583
7 TraesCS7D01G039200 chrUn 92406757 92407351 594 False 628.00 628 86.1200 195 778 1 chrUn.!!$F1 583
8 TraesCS7D01G039200 chr3A 584027974 584028580 606 False 693.00 693 87.6850 195 788 1 chr3A.!!$F1 593
9 TraesCS7D01G039200 chr6B 671719788 671720398 610 True 676.00 676 87.0920 193 788 1 chr6B.!!$R1 595
10 TraesCS7D01G039200 chr6B 671726914 671727524 610 True 671.00 671 86.9490 193 788 1 chr6B.!!$R2 595
11 TraesCS7D01G039200 chr2D 649061123 649061792 669 True 643.00 643 84.2110 2025 2698 1 chr2D.!!$R1 673
12 TraesCS7D01G039200 chr1B 679233862 679234449 587 True 634.00 634 86.2710 195 778 1 chr1B.!!$R1 583
13 TraesCS7D01G039200 chr6D 431854551 431855078 527 True 632.00 632 88.3460 260 788 1 chr6D.!!$R1 528
14 TraesCS7D01G039200 chr2B 784752353 784754336 1983 True 473.00 606 80.0910 2025 3481 2 chr2B.!!$R1 1456
15 TraesCS7D01G039200 chr1D 487617636 487618229 593 True 606.00 606 85.4760 195 778 1 chr1D.!!$R1 583
16 TraesCS7D01G039200 chr2A 775658861 775659448 587 False 534.00 534 83.3610 1994 2583 1 chr2A.!!$F1 589
17 TraesCS7D01G039200 chr2A 775665420 775665956 536 False 370.00 370 80.4030 2838 3343 1 chr2A.!!$F2 505
18 TraesCS7D01G039200 chr5D 375052508 375053088 580 False 370.00 370 78.7480 195 788 1 chr5D.!!$F1 593

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
925 1378 0.657368 CTTGGTCAGCAACGCGAAAC 60.657 55.0 15.93 0.0 0.0 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2629 3202 0.30776 CAGGAAGAAACACCGCACAC 59.692 55.0 0.0 0.0 0.0 3.82 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
92 93 1.005394 GTTCGCCTTTCCTCGGTGA 60.005 57.895 0.00 0.00 39.16 4.02
93 94 1.005394 TTCGCCTTTCCTCGGTGAC 60.005 57.895 0.00 0.00 40.51 3.67
95 96 2.027625 CGCCTTTCCTCGGTGACAC 61.028 63.158 0.00 0.00 33.93 3.67
106 107 1.895231 GGTGACACCGTGGAAACCC 60.895 63.158 9.33 0.00 0.00 4.11
114 115 1.674322 CGTGGAAACCCGCTGGATT 60.674 57.895 0.00 0.00 34.81 3.01
117 118 2.761195 GGAAACCCGCTGGATTCGC 61.761 63.158 10.35 1.70 42.71 4.70
130 131 2.306255 GATTCGCCGCCACCTTCCTA 62.306 60.000 0.00 0.00 0.00 2.94
161 162 1.437573 CTTATCTCACCGCTGCCGA 59.562 57.895 0.00 0.00 36.29 5.54
321 340 4.401202 TCTTTTGGAAACACCTTCTTCACC 59.599 41.667 0.00 0.00 42.67 4.02
356 376 5.734720 TGCTCGAAGAAATACTCCAAAGAT 58.265 37.500 0.00 0.00 34.09 2.40
455 718 2.490328 TTTTGAAAGCGCCTTGAGTG 57.510 45.000 2.29 0.00 0.00 3.51
499 763 3.617263 GCCTTGATCGATGAACGTACTTT 59.383 43.478 0.54 0.00 43.13 2.66
575 1023 9.382130 CACCATGGTGTCGATGAAAGATTTCAA 62.382 40.741 32.94 0.00 43.74 2.69
638 1088 7.772292 ACAGCAACATAAACTCATCATATCTGT 59.228 33.333 0.00 0.00 0.00 3.41
679 1130 7.694093 AGGACAGAAAATTCTCTAACCTCATT 58.306 34.615 1.53 0.00 34.74 2.57
754 1205 8.311395 TCACTAGACAATGGTGAAGAAGATAT 57.689 34.615 0.00 0.00 45.42 1.63
778 1229 1.007238 TCTTGAAGATCCGAGGTCCCT 59.993 52.381 0.00 0.00 0.00 4.20
792 1245 2.202987 CCCTCGCCTCTCACATGC 60.203 66.667 0.00 0.00 0.00 4.06
812 1265 2.618053 CGTTCCTCCTTCGTTTATGCT 58.382 47.619 0.00 0.00 0.00 3.79
906 1359 2.752903 GAGAGAGAGAGAGTTGGGTCAC 59.247 54.545 0.00 0.00 0.00 3.67
925 1378 0.657368 CTTGGTCAGCAACGCGAAAC 60.657 55.000 15.93 0.00 0.00 2.78
961 1414 2.357760 GCCCGTGGAGTAAACGCA 60.358 61.111 0.00 0.00 39.69 5.24
985 1438 1.448717 GAGGAGAAGCGGTCAAGGC 60.449 63.158 0.00 0.00 0.00 4.35
1013 1466 2.213499 AGCCTTTATGATTTCTCCGCG 58.787 47.619 0.00 0.00 0.00 6.46
1040 1493 4.537433 GCTCGCCTTCGCTCCCAT 62.537 66.667 0.00 0.00 35.26 4.00
1054 1507 2.424812 GCTCCCATTCTCTCTCTCTCCT 60.425 54.545 0.00 0.00 0.00 3.69
1065 1518 0.908198 CTCTCTCCTTCCCCCACAAG 59.092 60.000 0.00 0.00 0.00 3.16
1085 1538 3.827898 CGTGCGTCTCCTCCCTCC 61.828 72.222 0.00 0.00 0.00 4.30
1086 1539 2.680352 GTGCGTCTCCTCCCTCCA 60.680 66.667 0.00 0.00 0.00 3.86
1087 1540 2.060980 GTGCGTCTCCTCCCTCCAT 61.061 63.158 0.00 0.00 0.00 3.41
1089 1542 2.503382 GCGTCTCCTCCCTCCATCC 61.503 68.421 0.00 0.00 0.00 3.51
1090 1543 1.834822 CGTCTCCTCCCTCCATCCC 60.835 68.421 0.00 0.00 0.00 3.85
1091 1544 1.629297 GTCTCCTCCCTCCATCCCT 59.371 63.158 0.00 0.00 0.00 4.20
1092 1545 0.471022 GTCTCCTCCCTCCATCCCTC 60.471 65.000 0.00 0.00 0.00 4.30
1093 1546 0.631998 TCTCCTCCCTCCATCCCTCT 60.632 60.000 0.00 0.00 0.00 3.69
1094 1547 0.178935 CTCCTCCCTCCATCCCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
1095 1548 1.152139 CCTCCCTCCATCCCTCTCC 60.152 68.421 0.00 0.00 0.00 3.71
1096 1549 1.152139 CTCCCTCCATCCCTCTCCC 60.152 68.421 0.00 0.00 0.00 4.30
1097 1550 2.525381 CCCTCCATCCCTCTCCCG 60.525 72.222 0.00 0.00 0.00 5.14
1098 1551 2.525381 CCTCCATCCCTCTCCCGG 60.525 72.222 0.00 0.00 0.00 5.73
1099 1552 3.237741 CTCCATCCCTCTCCCGGC 61.238 72.222 0.00 0.00 0.00 6.13
1142 1595 2.052414 CGACCGATCGCGAGGTAC 60.052 66.667 18.91 11.88 42.43 3.34
1156 1609 0.111832 AGGTACTCTCACCACCGACA 59.888 55.000 0.00 0.00 41.40 4.35
1164 1617 2.200370 ACCACCGACACCTCTCCA 59.800 61.111 0.00 0.00 0.00 3.86
1165 1618 1.229209 ACCACCGACACCTCTCCAT 60.229 57.895 0.00 0.00 0.00 3.41
1166 1619 1.258445 ACCACCGACACCTCTCCATC 61.258 60.000 0.00 0.00 0.00 3.51
1167 1620 1.517832 CACCGACACCTCTCCATCC 59.482 63.158 0.00 0.00 0.00 3.51
1169 1622 2.435693 CCGACACCTCTCCATCCCC 61.436 68.421 0.00 0.00 0.00 4.81
1196 1651 3.116531 GTACGTGCGAACCTGGGC 61.117 66.667 0.00 0.00 0.00 5.36
1292 1752 3.095332 GGTTATCTAGGGTACGGGGATC 58.905 54.545 0.00 0.00 0.00 3.36
1325 1785 4.865761 GGATCCGTAGCACGCGCA 62.866 66.667 5.73 0.00 40.91 6.09
1326 1786 2.658593 GATCCGTAGCACGCGCAT 60.659 61.111 5.73 0.00 40.91 4.73
1327 1787 2.932083 GATCCGTAGCACGCGCATG 61.932 63.158 5.73 2.46 40.91 4.06
1330 1790 2.961721 CGTAGCACGCGCATGGAT 60.962 61.111 5.73 0.00 42.27 3.41
1333 1793 3.384275 TAGCACGCGCATGGATGGT 62.384 57.895 5.73 3.70 42.27 3.55
1334 1794 2.022240 TAGCACGCGCATGGATGGTA 62.022 55.000 5.73 2.53 42.27 3.25
1335 1795 3.014036 CACGCGCATGGATGGTAC 58.986 61.111 5.73 0.00 0.00 3.34
1336 1796 1.521457 CACGCGCATGGATGGTACT 60.521 57.895 5.73 0.00 0.00 2.73
1338 1798 0.810031 ACGCGCATGGATGGTACTTC 60.810 55.000 5.73 0.00 0.00 3.01
1438 1907 3.593794 CGTCGGGGAGGATCGGAC 61.594 72.222 0.00 0.00 34.37 4.79
1439 1908 2.441532 GTCGGGGAGGATCGGACA 60.442 66.667 0.00 0.00 35.45 4.02
1445 1914 1.680338 GGGAGGATCGGACAATTTGG 58.320 55.000 0.78 0.00 34.37 3.28
1489 1969 2.309755 TCTCTGGATGGGCAGTGATTTT 59.690 45.455 0.00 0.00 0.00 1.82
1515 1995 2.604914 CGTGATTCATCTCCTTCGGTTG 59.395 50.000 0.00 0.00 0.00 3.77
1526 2006 1.841663 CTTCGGTTGGTTGCTGACGG 61.842 60.000 0.00 0.00 0.00 4.79
1527 2007 3.353836 CGGTTGGTTGCTGACGGG 61.354 66.667 0.00 0.00 0.00 5.28
1528 2008 2.112297 GGTTGGTTGCTGACGGGA 59.888 61.111 0.00 0.00 0.00 5.14
1529 2009 1.303317 GGTTGGTTGCTGACGGGAT 60.303 57.895 0.00 0.00 0.00 3.85
1545 2025 1.228675 GATGGATGGATGGGTGGGC 60.229 63.158 0.00 0.00 0.00 5.36
1573 2062 1.906105 TTACCCGGTGGATCTGTGGC 61.906 60.000 0.00 0.00 34.81 5.01
1626 2115 4.436332 TCTCTGCACTTGTGCATGTATAG 58.564 43.478 25.63 17.52 44.47 1.31
1630 2119 3.374988 TGCACTTGTGCATGTATAGCTTC 59.625 43.478 22.47 0.00 40.23 3.86
1673 2162 1.343142 ACTGATGCGTGGTAGTTGTGA 59.657 47.619 0.00 0.00 0.00 3.58
1675 2164 3.002791 CTGATGCGTGGTAGTTGTGATT 58.997 45.455 0.00 0.00 0.00 2.57
1684 2214 3.329225 TGGTAGTTGTGATTGTGGGATGA 59.671 43.478 0.00 0.00 0.00 2.92
1691 2221 5.389859 TGTGATTGTGGGATGATCAAAAC 57.610 39.130 0.00 0.00 32.14 2.43
1738 2268 3.337834 TGTGTACCCTTGCACATGG 57.662 52.632 0.00 0.00 42.72 3.66
1793 2323 1.421410 CGCGCCATCTTGTGTAGACC 61.421 60.000 0.00 0.00 35.19 3.85
1986 2523 6.552629 ACGTACATGTGAGTAGTTCTGTATG 58.447 40.000 9.11 0.00 34.08 2.39
2032 2572 4.090761 ACATCCTGTTTCATCACTGTGT 57.909 40.909 7.79 0.00 0.00 3.72
2098 2638 2.295349 CCCTTGGCATTGCATATGTCTC 59.705 50.000 11.39 0.00 0.00 3.36
2213 2765 1.094073 AGAATGCATCTGACGCTGCC 61.094 55.000 0.00 0.00 36.88 4.85
2359 2911 1.970917 GCCGCCAGAACTTCATCGTG 61.971 60.000 0.00 0.00 0.00 4.35
2443 2996 6.479001 GCCAAAGTTTCTTTTCTAGGGTTTTC 59.521 38.462 0.00 0.00 0.00 2.29
2460 3013 8.777578 AGGGTTTTCAAGTTCCTAATAAAAGT 57.222 30.769 0.00 0.00 0.00 2.66
2523 3076 1.673920 GTTTCCGTGAGCAACTTTGGA 59.326 47.619 0.00 0.00 0.00 3.53
2544 3097 1.740296 GGCTTTACCGCTCGCTCAA 60.740 57.895 0.00 0.00 0.00 3.02
2545 3098 1.296056 GGCTTTACCGCTCGCTCAAA 61.296 55.000 0.00 0.00 0.00 2.69
2629 3202 4.350346 TGTTGTTTCTGCATTGTCTTTCG 58.650 39.130 0.00 0.00 0.00 3.46
2635 3211 0.041400 TGCATTGTCTTTCGTGTGCG 60.041 50.000 0.00 0.00 35.46 5.34
2653 3229 2.003301 GCGGTGTTTCTTCCTGATCTC 58.997 52.381 0.00 0.00 0.00 2.75
2654 3230 2.354203 GCGGTGTTTCTTCCTGATCTCT 60.354 50.000 0.00 0.00 0.00 3.10
2660 3236 3.834489 TTCTTCCTGATCTCTGATGCC 57.166 47.619 0.00 0.00 0.00 4.40
2678 3254 1.729149 GCCGCAAGTTTATGCTGTGAC 60.729 52.381 0.00 0.00 44.21 3.67
2688 3264 0.685097 ATGCTGTGACGTTACCCAGT 59.315 50.000 8.11 0.00 0.00 4.00
2698 3274 4.826733 TGACGTTACCCAGTCTACTGTTTA 59.173 41.667 9.17 0.00 42.27 2.01
2701 3293 4.565564 CGTTACCCAGTCTACTGTTTATGC 59.434 45.833 9.17 0.00 42.27 3.14
2702 3294 3.247006 ACCCAGTCTACTGTTTATGCG 57.753 47.619 9.17 0.00 42.27 4.73
2749 3346 3.061161 GCTTGATTTATGTTGCCTTTGCG 59.939 43.478 0.00 0.00 41.78 4.85
2774 3374 0.179181 CCTGTGCTGCTGTTATTGCG 60.179 55.000 0.00 0.00 0.00 4.85
2827 3473 3.760151 TCAGCTGCTGTTTAGATTGCATT 59.240 39.130 27.24 0.00 34.79 3.56
2900 4001 6.420913 CCAACTATGGCCTAACACTAGTAT 57.579 41.667 3.32 0.00 40.58 2.12
2965 4067 4.229304 TCCTTTTTGGACAGAACTGTGA 57.771 40.909 12.29 0.00 45.05 3.58
3038 4143 2.480759 GCCATTCACATGAACCTGATGC 60.481 50.000 0.00 0.00 36.80 3.91
3131 4253 9.342308 TGTAAAATTAGGATGGAGCAGATTAAG 57.658 33.333 0.00 0.00 0.00 1.85
3162 4284 6.016777 GGTAACATGGCCATTAGATTTCTGAG 60.017 42.308 17.92 2.26 0.00 3.35
3172 4294 6.294120 CCATTAGATTTCTGAGTGTGTTTGCA 60.294 38.462 0.00 0.00 0.00 4.08
3324 4476 1.672145 GCAGGTCCTCCTTACGTTGAC 60.672 57.143 0.00 0.00 43.07 3.18
3338 4490 1.687123 CGTTGACGGAGGGGAAGATAT 59.313 52.381 0.00 0.00 35.37 1.63
3354 4518 8.103305 GGGGAAGATATAGCATGATAGAAAACA 58.897 37.037 0.00 0.00 0.00 2.83
3364 4528 6.015180 AGCATGATAGAAAACAAAAGCTTCCA 60.015 34.615 0.00 0.00 0.00 3.53
3398 4562 7.862512 AGAGGAATTAGAAGCTCAAATGAAG 57.137 36.000 0.00 0.00 0.00 3.02
3429 4593 4.446857 TTTTTAGTCGTCGCAAGTTCTG 57.553 40.909 0.00 0.00 39.48 3.02
3517 4747 7.446625 GGAATGCTAATGTAATTGACTGGATCT 59.553 37.037 0.00 0.00 36.99 2.75
3518 4748 9.494271 GAATGCTAATGTAATTGACTGGATCTA 57.506 33.333 0.00 0.00 36.99 1.98
3550 4780 0.179045 AGGTCATATGCCGAGCCAAC 60.179 55.000 0.00 0.00 0.00 3.77
3561 4791 3.282745 GAGCCAACTCTCCGCGTGA 62.283 63.158 4.92 1.66 40.03 4.35
3575 4805 2.384382 CGCGTGAAAATCTTTGCTTGT 58.616 42.857 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.636647 AAACATGGCTTTGTTTGGGG 57.363 45.000 15.19 0.00 45.55 4.96
18 19 9.555727 AAAATGCTAGACTCACACTAGTAAAAA 57.444 29.630 0.00 0.00 39.36 1.94
19 20 9.555727 AAAAATGCTAGACTCACACTAGTAAAA 57.444 29.630 0.00 0.00 39.36 1.52
20 21 8.988934 CAAAAATGCTAGACTCACACTAGTAAA 58.011 33.333 0.00 0.00 39.36 2.01
21 22 7.117812 GCAAAAATGCTAGACTCACACTAGTAA 59.882 37.037 0.00 0.00 39.36 2.24
22 23 6.590292 GCAAAAATGCTAGACTCACACTAGTA 59.410 38.462 0.00 0.00 39.36 1.82
23 24 5.409826 GCAAAAATGCTAGACTCACACTAGT 59.590 40.000 0.00 0.00 39.36 2.57
24 25 5.409520 TGCAAAAATGCTAGACTCACACTAG 59.590 40.000 0.00 0.00 39.92 2.57
25 26 5.304778 TGCAAAAATGCTAGACTCACACTA 58.695 37.500 0.00 0.00 35.49 2.74
26 27 4.136796 TGCAAAAATGCTAGACTCACACT 58.863 39.130 0.00 0.00 35.49 3.55
27 28 4.488126 TGCAAAAATGCTAGACTCACAC 57.512 40.909 0.00 0.00 35.49 3.82
28 29 4.821260 TCTTGCAAAAATGCTAGACTCACA 59.179 37.500 10.18 0.00 40.57 3.58
92 93 3.868985 AGCGGGTTTCCACGGTGT 61.869 61.111 7.45 0.00 39.55 4.16
95 96 3.622060 ATCCAGCGGGTTTCCACGG 62.622 63.158 1.81 0.00 34.93 4.94
114 115 2.762459 ATAGGAAGGTGGCGGCGA 60.762 61.111 12.98 0.00 0.00 5.54
117 118 2.829592 GGGATAGGAAGGTGGCGG 59.170 66.667 0.00 0.00 0.00 6.13
143 144 0.179111 TTCGGCAGCGGTGAGATAAG 60.179 55.000 20.69 2.08 0.00 1.73
144 145 0.179111 CTTCGGCAGCGGTGAGATAA 60.179 55.000 20.69 5.43 0.00 1.75
145 146 1.437573 CTTCGGCAGCGGTGAGATA 59.562 57.895 20.69 6.94 0.00 1.98
153 154 3.570638 CATGCTCCTTCGGCAGCG 61.571 66.667 0.00 0.00 43.15 5.18
161 162 4.408821 TTCGCCGGCATGCTCCTT 62.409 61.111 28.98 0.00 0.00 3.36
321 340 0.798389 TTCGAGCAGAGATTGACGCG 60.798 55.000 3.53 3.53 0.00 6.01
356 376 4.261825 CCAATTGCAACCTCTTTACCGAAA 60.262 41.667 0.00 0.00 0.00 3.46
425 687 4.688413 GGCGCTTTCAAAAACCATTATTGA 59.312 37.500 7.64 0.00 0.00 2.57
499 763 2.178325 TCTAAGGTATCATCCCCGACCA 59.822 50.000 0.00 0.00 34.18 4.02
575 1023 4.137543 GTTGGTCTGATTCTTTGTGGAGT 58.862 43.478 0.00 0.00 0.00 3.85
609 1059 8.962884 ATATGATGAGTTTATGTTGCTGTGTA 57.037 30.769 0.00 0.00 0.00 2.90
638 1088 0.250858 TCCTCGCGGACCCGATTATA 60.251 55.000 13.24 0.00 42.83 0.98
679 1130 0.597568 CTCATTCTTTTGGCGGTGCA 59.402 50.000 0.00 0.00 0.00 4.57
754 1205 8.883783 GAGGGACCTCGGATCTTCAAGATCTA 62.884 50.000 23.84 13.25 40.75 1.98
780 1233 1.078848 AGGAACGCATGTGAGAGGC 60.079 57.895 14.43 0.00 0.00 4.70
792 1245 2.603560 GAGCATAAACGAAGGAGGAACG 59.396 50.000 0.00 0.00 0.00 3.95
812 1265 9.817809 AAAACTAATGTAATGATTCTCTAGCGA 57.182 29.630 0.00 0.00 0.00 4.93
871 1324 3.963374 CTCTCTCTCTCTCTCTCTCTCCA 59.037 52.174 0.00 0.00 0.00 3.86
872 1325 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
873 1326 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
874 1327 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
875 1328 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
876 1329 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
877 1330 5.355596 CAACTCTCTCTCTCTCTCTCTCTC 58.644 50.000 0.00 0.00 0.00 3.20
878 1331 4.163078 CCAACTCTCTCTCTCTCTCTCTCT 59.837 50.000 0.00 0.00 0.00 3.10
879 1332 4.446371 CCAACTCTCTCTCTCTCTCTCTC 58.554 52.174 0.00 0.00 0.00 3.20
880 1333 3.200825 CCCAACTCTCTCTCTCTCTCTCT 59.799 52.174 0.00 0.00 0.00 3.10
881 1334 3.054361 ACCCAACTCTCTCTCTCTCTCTC 60.054 52.174 0.00 0.00 0.00 3.20
906 1359 0.657368 GTTTCGCGTTGCTGACCAAG 60.657 55.000 5.77 0.00 33.21 3.61
961 1414 3.080121 CCGCTTCTCCTCTGGGCT 61.080 66.667 0.00 0.00 0.00 5.19
985 1438 0.597637 ATCATAAAGGCTCCGCGACG 60.598 55.000 8.23 0.00 0.00 5.12
1013 1466 3.349481 AAGGCGAGCGAGAGAGTGC 62.349 63.158 0.00 0.00 0.00 4.40
1039 1492 2.090775 GGGGGAAGGAGAGAGAGAGAAT 60.091 54.545 0.00 0.00 0.00 2.40
1040 1493 1.289530 GGGGGAAGGAGAGAGAGAGAA 59.710 57.143 0.00 0.00 0.00 2.87
1128 1581 1.158484 TGAGAGTACCTCGCGATCGG 61.158 60.000 18.30 11.64 44.92 4.18
1142 1595 0.896019 AGAGGTGTCGGTGGTGAGAG 60.896 60.000 0.00 0.00 0.00 3.20
1156 1609 1.541168 AAGGGAGGGGATGGAGAGGT 61.541 60.000 0.00 0.00 0.00 3.85
1164 1617 1.273666 ACGTACAGAAAGGGAGGGGAT 60.274 52.381 0.00 0.00 0.00 3.85
1165 1618 0.115745 ACGTACAGAAAGGGAGGGGA 59.884 55.000 0.00 0.00 0.00 4.81
1166 1619 0.249398 CACGTACAGAAAGGGAGGGG 59.751 60.000 0.00 0.00 0.00 4.79
1167 1620 0.391263 GCACGTACAGAAAGGGAGGG 60.391 60.000 0.00 0.00 0.00 4.30
1169 1622 0.242825 TCGCACGTACAGAAAGGGAG 59.757 55.000 0.00 0.00 0.00 4.30
1232 1687 1.487231 CAAACCTCGCTCGAACACG 59.513 57.895 0.00 0.00 0.00 4.49
1233 1688 1.204312 GCAAACCTCGCTCGAACAC 59.796 57.895 0.00 0.00 0.00 3.32
1234 1689 1.959226 GGCAAACCTCGCTCGAACA 60.959 57.895 0.00 0.00 0.00 3.18
1235 1690 2.861006 GGCAAACCTCGCTCGAAC 59.139 61.111 0.00 0.00 0.00 3.95
1325 1785 0.104304 GACGCGGAAGTACCATCCAT 59.896 55.000 12.47 1.14 36.74 3.41
1326 1786 1.514087 GACGCGGAAGTACCATCCA 59.486 57.895 12.47 0.00 36.74 3.41
1327 1787 1.588139 CGACGCGGAAGTACCATCC 60.588 63.158 12.47 5.42 38.90 3.51
1330 1790 1.307355 TGATCGACGCGGAAGTACCA 61.307 55.000 12.47 0.00 38.90 3.25
1333 1793 1.263484 GATCTGATCGACGCGGAAGTA 59.737 52.381 12.47 0.00 0.00 2.24
1334 1794 0.029567 GATCTGATCGACGCGGAAGT 59.970 55.000 12.47 0.00 0.00 3.01
1335 1795 0.661780 GGATCTGATCGACGCGGAAG 60.662 60.000 12.47 0.36 0.00 3.46
1336 1796 1.359117 GGATCTGATCGACGCGGAA 59.641 57.895 12.47 0.00 0.00 4.30
1338 1798 2.427575 CGGATCTGATCGACGCGG 60.428 66.667 12.47 0.00 0.00 6.46
1438 1907 5.182950 GCCTAAATTCCCCAAAACCAAATTG 59.817 40.000 0.00 0.00 0.00 2.32
1439 1908 5.321102 GCCTAAATTCCCCAAAACCAAATT 58.679 37.500 0.00 0.00 0.00 1.82
1445 1914 1.404986 GCGGCCTAAATTCCCCAAAAC 60.405 52.381 0.00 0.00 0.00 2.43
1489 1969 4.430007 CGAAGGAGATGAATCACGGTAAA 58.570 43.478 0.00 0.00 0.00 2.01
1515 1995 1.097547 CATCCATCCCGTCAGCAACC 61.098 60.000 0.00 0.00 0.00 3.77
1526 2006 1.462035 CCCACCCATCCATCCATCC 59.538 63.158 0.00 0.00 0.00 3.51
1527 2007 1.228675 GCCCACCCATCCATCCATC 60.229 63.158 0.00 0.00 0.00 3.51
1528 2008 2.782417 GGCCCACCCATCCATCCAT 61.782 63.158 0.00 0.00 0.00 3.41
1529 2009 3.428664 GGCCCACCCATCCATCCA 61.429 66.667 0.00 0.00 0.00 3.41
1573 2062 7.285783 TGAGACGTTTTTATATCAGAAACCG 57.714 36.000 0.00 0.00 31.34 4.44
1626 2115 2.155279 GTTGAAGGGGAACTCAGAAGC 58.845 52.381 0.00 0.00 0.00 3.86
1630 2119 1.271597 CCAGGTTGAAGGGGAACTCAG 60.272 57.143 0.00 0.00 0.00 3.35
1673 2162 2.166254 GCCGTTTTGATCATCCCACAAT 59.834 45.455 0.00 0.00 0.00 2.71
1675 2164 1.173043 GCCGTTTTGATCATCCCACA 58.827 50.000 0.00 0.00 0.00 4.17
1684 2214 6.319658 AGAGATGATTTATGTGCCGTTTTGAT 59.680 34.615 0.00 0.00 0.00 2.57
1691 2221 3.879295 ACCAAGAGATGATTTATGTGCCG 59.121 43.478 0.00 0.00 0.00 5.69
1793 2323 5.200454 CGATAGCAGAACAAAATCAATCCG 58.800 41.667 0.00 0.00 0.00 4.18
1953 2490 8.997621 ACTACTCACATGTACGTATCAAAAAT 57.002 30.769 0.00 0.00 0.00 1.82
1954 2491 8.821147 AACTACTCACATGTACGTATCAAAAA 57.179 30.769 0.00 0.00 0.00 1.94
1955 2492 8.301720 AGAACTACTCACATGTACGTATCAAAA 58.698 33.333 0.00 0.00 0.00 2.44
1956 2493 7.753580 CAGAACTACTCACATGTACGTATCAAA 59.246 37.037 0.00 0.00 0.00 2.69
1957 2494 7.094506 ACAGAACTACTCACATGTACGTATCAA 60.095 37.037 0.00 0.00 0.00 2.57
1958 2495 6.373495 ACAGAACTACTCACATGTACGTATCA 59.627 38.462 0.00 0.00 0.00 2.15
1959 2496 6.783162 ACAGAACTACTCACATGTACGTATC 58.217 40.000 0.00 0.00 0.00 2.24
1986 2523 3.006940 TCGTCAAATGTAATGGACAGGC 58.993 45.455 0.00 0.00 42.79 4.85
2032 2572 1.271543 ACTTGCCTGACATTGCTGCTA 60.272 47.619 0.00 0.00 0.00 3.49
2045 2585 2.738643 CGAACCGATGATGTACTTGCCT 60.739 50.000 0.00 0.00 0.00 4.75
2493 3046 2.839474 CTCACGGAAACTGAAATTCGC 58.161 47.619 0.00 0.00 0.00 4.70
2523 3076 4.468689 GCGAGCGGTAAAGCCCCT 62.469 66.667 0.00 0.00 38.01 4.79
2544 3097 2.069273 CAGAGTTCATCGAAAGGCGTT 58.931 47.619 0.00 0.00 41.80 4.84
2545 3098 1.000955 ACAGAGTTCATCGAAAGGCGT 59.999 47.619 0.00 0.00 41.80 5.68
2610 3183 3.376859 ACACGAAAGACAATGCAGAAACA 59.623 39.130 0.00 0.00 0.00 2.83
2629 3202 0.307760 CAGGAAGAAACACCGCACAC 59.692 55.000 0.00 0.00 0.00 3.82
2635 3211 4.543590 TCAGAGATCAGGAAGAAACACC 57.456 45.455 0.00 0.00 0.00 4.16
2653 3229 1.831343 GCATAAACTTGCGGCATCAG 58.169 50.000 2.28 1.08 32.06 2.90
2688 3264 4.740268 CACTACCACGCATAAACAGTAGA 58.260 43.478 0.00 0.00 33.18 2.59
2718 3315 8.938906 AGGCAACATAAATCAAGCAAAAATAAG 58.061 29.630 0.00 0.00 41.41 1.73
2774 3374 6.642131 TCTTGTCAATAAAAGTCTGCAATTGC 59.358 34.615 23.69 23.69 42.50 3.56
2803 3403 4.516323 TGCAATCTAAACAGCAGCTGATA 58.484 39.130 29.70 18.60 35.18 2.15
2900 4001 1.817740 GCCCACAGGTGCAAAGACTTA 60.818 52.381 0.00 0.00 34.57 2.24
2944 4046 4.080582 TCTCACAGTTCTGTCCAAAAAGGA 60.081 41.667 2.22 0.00 46.75 3.36
2946 4048 5.118990 TCTCTCACAGTTCTGTCCAAAAAG 58.881 41.667 2.22 0.00 0.00 2.27
2954 4056 5.344743 TGAAGTTTCTCTCACAGTTCTGT 57.655 39.130 0.00 0.00 0.00 3.41
2955 4057 6.857777 ATTGAAGTTTCTCTCACAGTTCTG 57.142 37.500 0.00 0.00 0.00 3.02
2965 4067 8.871686 AAACGCAAATTAATTGAAGTTTCTCT 57.128 26.923 16.04 2.80 42.41 3.10
3038 4143 8.777865 TGTAAACTATTTCAGTGGATCAAGAG 57.222 34.615 0.00 0.00 37.63 2.85
3131 4253 5.316167 TCTAATGGCCATGTTACCATCATC 58.684 41.667 21.63 0.00 46.04 2.92
3146 4268 5.886960 AACACACTCAGAAATCTAATGGC 57.113 39.130 0.00 0.00 0.00 4.40
3147 4269 6.088824 GCAAACACACTCAGAAATCTAATGG 58.911 40.000 0.00 0.00 0.00 3.16
3151 4273 5.412594 GGATGCAAACACACTCAGAAATCTA 59.587 40.000 0.00 0.00 0.00 1.98
3162 4284 0.171007 CCATCCGGATGCAAACACAC 59.829 55.000 34.77 0.00 37.49 3.82
3172 4294 2.214376 TTGTTGCTTTCCATCCGGAT 57.786 45.000 12.38 12.38 42.41 4.18
3182 4304 3.893326 AGCTTGTCCTTTTGTTGCTTT 57.107 38.095 0.00 0.00 0.00 3.51
3220 4365 2.244695 TGACATGGGACTACAGTCGTT 58.755 47.619 0.00 0.00 45.65 3.85
3222 4367 3.190079 CATTGACATGGGACTACAGTCG 58.810 50.000 0.00 0.00 45.65 4.18
3324 4476 3.099905 TCATGCTATATCTTCCCCTCCG 58.900 50.000 0.00 0.00 0.00 4.63
3338 4490 7.176515 TGGAAGCTTTTGTTTTCTATCATGCTA 59.823 33.333 0.00 0.00 0.00 3.49
3429 4593 4.202673 TGCAGGGATATCTTTTATTCCCCC 60.203 45.833 2.05 0.00 38.12 5.40
3449 4614 1.605232 CAGTGCTTGTGTCAAGATGCA 59.395 47.619 12.77 0.00 0.00 3.96
3517 4747 6.490040 GGCATATGACCTAGGAAAAAGCAATA 59.510 38.462 17.98 1.91 0.00 1.90
3518 4748 5.302823 GGCATATGACCTAGGAAAAAGCAAT 59.697 40.000 17.98 0.00 0.00 3.56
3550 4780 2.726066 GCAAAGATTTTCACGCGGAGAG 60.726 50.000 12.47 0.00 0.00 3.20
3561 4791 5.526506 AAGAGCAGACAAGCAAAGATTTT 57.473 34.783 0.00 0.00 36.85 1.82


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

AutoCloner maintained by Alex Coulton.