Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 148 of 444
Found at i:39849466 original size:42 final size:42
Alignment explanation
Indices: 39849389--39849507 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
39849379 ATTGTATTGA
* * *
39849389 GATTACGTGTAAGACCATGTATGGGACATTGGCATCGTTAACT
1 GATTACGTGTAAGACCATATCTGGGACA-TGGCATCGATAACT
* **
39849432 GATTTCGTGTAAGACC-TATCTGGGACAGTGGCATCGATATGT
1 GATTACGTGTAAGACCATATCTGGGACA-TGGCATCGATAACT
* * *
39849474 GATAACATGTAAGACCATATCTGGGATATGGCAT
1 GATTACGTGTAAGACCATATCTGGGACATGGCAT
39849508 TGTACGAGCT
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 39 0.61
43 25 0.39
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (42 bp):
GATTACGTGTAAGACCATATCTGGGACATGGCATCGATAACT
Found at i:39850709 original size:27 final size:26
Alignment explanation
Indices: 39850674--39850785 Score: 102
Period size: 26 Copynumber: 4.2 Consensus size: 26
39850664 AATCTGCCAT
*
39850674 TTTTACCTTACTGGGGTA-TTCAGTCA
1 TTTTACCCTA-TGGGGTATTTCAGTCA
*
39850700 TTTTACCCTTACAGGGGTATTTC-GATCA
1 TTTTACCC-TA-TGGGGTATTTCAG-TCA
* * *
39850728 TTCTACCCTATAGGGTATTTCAATCA
1 TTTTACCCTATGGGGTATTTCAGTCA
* *
39850754 TTTTGCCCTATGAGGGTATTTCAGTTA
1 TTTTACCCTATG-GGGTATTTCAGTCA
39850781 TTTTA
1 TTTTA
39850786 TCACATAAGG
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
26 28 0.41
27 28 0.41
28 13 0.19
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (26 bp):
TTTTACCCTATGGGGTATTTCAGTCA
Found at i:39850753 original size:26 final size:26
Alignment explanation
Indices: 39850687--39850785 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 26
39850677 TACCTTACTG
* *
39850687 GGGTA-TTCAGTCATTTTACCCTTACA
1 GGGTATTTCAATCATTTTACCC-TATA
* *
39850713 GGGGTATTTCGATCATTCTACCCTATA
1 -GGGTATTTCAATCATTTTACCCTATA
*
39850740 GGGTATTTCAATCATTTTGCCCTATGA
1 GGGTATTTCAATCATTTTACCCTAT-A
* *
39850767 GGGTATTTCAGTTATTTTA
1 GGGTATTTCAATCATTTTA
39850786 TCACATAAGG
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
26 22 0.37
27 25 0.42
28 13 0.22
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (26 bp):
GGGTATTTCAATCATTTTACCCTATA
Found at i:39850814 original size:27 final size:27
Alignment explanation
Indices: 39850780--39850931 Score: 196
Period size: 27 Copynumber: 5.6 Consensus size: 27
39850770 TATTTCAGTT
* *
39850780 ATTTTATCACATAAGGGAAAAATTGTC
1 ATTTTATCACATAAGGGCAAAATCGTC
* * * *
39850807 ATTCTATCAGATGAGAGCAAAATCGTC
1 ATTTTATCACATAAGGGCAAAATCGTC
* *
39850834 ATTCTATCACATAAGAGCAAAATCGTC
1 ATTTTATCACATAAGGGCAAAATCGTC
* *
39850861 ATTTTATCACAGAAGGGCAAAATCATC
1 ATTTTATCACATAAGGGCAAAATCGTC
* *
39850888 ATTTTATCACAAAAGGGCAAAATCATC
1 ATTTTATCACATAAGGGCAAAATCGTC
39850915 ATTTTATCACATAAGGG
1 ATTTTATCACATAAGGG
39850932 TTCAGGTACG
Statistics
Matches: 111, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 111 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.28
Consensus pattern (27 bp):
ATTTTATCACATAAGGGCAAAATCGTC
Found at i:39859579 original size:27 final size:27
Alignment explanation
Indices: 39859549--39859601 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39859539 GCTTAAGAGC
*
39859549 TCTATAAT-TGATAATTAAAAATAAAAT
1 TCTAAAATCTGATAA-TAAAAATAAAAT
*
39859576 TCTAAAATCTTATAATAAAAATAAAA
1 TCTAAAATCTGATAATAAAAATAAAA
39859602 AATAGTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (27 bp):
TCTAAAATCTGATAATAAAAATAAAAT
Found at i:39867996 original size:28 final size:28
Alignment explanation
Indices: 39867927--39868027 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
39867917 GACAAGATTG
* * * *
39867927 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
39867957 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
39867985 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
39868014 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
39868028 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:39875430 original size:80 final size:80
Alignment explanation
Indices: 39875346--39875494 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
39875336 TATGGTAACC
* * * *
39875346 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
39875410 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
39875426 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
39875491 CCGG
66 CCGG
39875495 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:39875436 original size:40 final size:38
Alignment explanation
Indices: 39875387--39875494 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
39875377 ATCACGATTT
*
39875387 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
39875427 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
39875467 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
39875495 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:39882835 original size:26 final size:26
Alignment explanation
Indices: 39882806--39882858 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
39882796 TCAAACATGC
39882806 ATTTAGGTCAATTT-ACTCCTAGGGGT
1 ATTTAGGT-AATTTGACTCCTAGGGGT
* * *
39882832 ATTTCGGTACTTTGTCTCCTAGGGGT
1 ATTTAGGTAATTTGACTCCTAGGGGT
39882858 A
1 A
39882859 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40
Consensus pattern (26 bp):
ATTTAGGTAATTTGACTCCTAGGGGT
Found at i:39884131 original size:24 final size:24
Alignment explanation
Indices: 39884092--39884194 Score: 161
Period size: 24 Copynumber: 4.2 Consensus size: 24
39884082 GCCGGCCAAC
*
39884092 TCCTACTCCTTGATCAGCTCCTAAA
1 TCCT-CTCCTTTATCAGCTCCTAAA
*
39884117 TCTTCTCCTTTATCAGCTCCTAAA
1 TCCTCTCCTTTATCAGCTCCTAAA
39884141 TCCTCTCCTTTATCAGCTCCTAAA
1 TCCTCTCCTTTATCAGCTCCTAAA
* *
39884165 TCCTCTCCCTTATCAGCTTCTAAA
1 TCCTCTCCTTTATCAGCTCCTAAA
39884189 TCCTCT
1 TCCTCT
39884195 TCTGACAGCC
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
24 70 0.96
25 3 0.04
ACGTcount: A:0.20, C:0.37, G:0.05, T:0.38
Consensus pattern (24 bp):
TCCTCTCCTTTATCAGCTCCTAAA
Found at i:39902193 original size:70 final size:71
Alignment explanation
Indices: 39902042--39902204 Score: 310
Period size: 70 Copynumber: 2.3 Consensus size: 71
39902032 GAGATGTATC
39902042 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
39902107 AGGACA
66 AGGACA
39902113 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCT-GGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
39902177 CGGACA
66 AGGACA
39902183 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
39902205 AGACAAATCG
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
70 51 0.56
71 40 0.44
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:39909724 original size:70 final size:71
Alignment explanation
Indices: 39909573--39909735 Score: 310
Period size: 70 Copynumber: 2.3 Consensus size: 71
39909563 GAGATGTATC
39909573 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
39909638 AGGACA
66 AGGACA
39909644 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCT-GGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
39909708 CGGACA
66 AGGACA
39909714 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
39909736 AGACAAATCG
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
70 51 0.56
71 40 0.44
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:39916371 original size:19 final size:20
Alignment explanation
Indices: 39916333--39916378 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
39916323 ATTTTGATAA
* *
39916333 ACATGGTATGTATGATATGC
1 ACATGATATGTATGACATGC
39916353 ACATGATATG-ATGACATGC
1 ACATGATATGTATGACATGC
39916372 ACATGAT
1 ACATGAT
39916379 GTATTTATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (20 bp):
ACATGATATGTATGACATGC
Found at i:39916497 original size:47 final size:47
Alignment explanation
Indices: 39916428--39916525 Score: 171
Period size: 47 Copynumber: 2.1 Consensus size: 47
39916418 AGGAAGTGCA
39916428 AAAGGGCTTATGCCCCAGTTATT-AAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTT-TGCCCCAGTTATT
39916475 AAAGGGCTTATGCCCCAGTTATTAAAAAAGGGCTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT-AAAAAGGGCTTTGCCCCAGTTATT
39916523 AAA
1 AAA
39916526 AGAGGCTAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
47 23 0.47
48 16 0.33
49 10 0.20
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (47 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTTTGCCCCAGTTATT
Found at i:39916542 original size:25 final size:24
Alignment explanation
Indices: 39916427--39916546 Score: 174
Period size: 24 Copynumber: 5.0 Consensus size: 24
39916417 GAGGAAGTGC
39916427 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
39916451 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
39916475 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
39916498 AAAAAAGGGCTT-TGCCCCAGTTATT
1 --AAAAGGGCTTATGCCCCAGTTATT
*
39916523 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
39916547 ATGATAAAGC
Statistics
Matches: 89, Mismatches: 1, Indels: 11
0.88 0.01 0.11
Matches are distributed among these distances:
23 29 0.33
24 30 0.34
25 21 0.24
26 9 0.10
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:39916773 original size:31 final size:31
Alignment explanation
Indices: 39916738--39916801 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
39916728 CGTTTACAGT
39916738 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
39916769 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
39916800 AA
1 AA
39916802 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:39917720 original size:24 final size:24
Alignment explanation
Indices: 39917688--39917734 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
39917678 GTTGCTGATG
39917688 CATTAAGTTAAAAATCTTTGTTTA
1 CATTAAGTTAAAAATCTTTGTTTA
*
39917712 CATTAAGTTAAAAATTTTTGTTT
1 CATTAAGTTAAAAATCTTTGTTT
39917735 TCTTTACGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (24 bp):
CATTAAGTTAAAAATCTTTGTTTA
Found at i:39918728 original size:13 final size:13
Alignment explanation
Indices: 39918710--39918739 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39918700 CGGGGTTGAT
*
39918710 CTGATTAGAGAGA
1 CTGATTAGAAAGA
39918723 CTGATTAGAAAGA
1 CTGATTAGAAAGA
39918736 CTGA
1 CTGA
39918740 AGAGAAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.27, T:0.23
Consensus pattern (13 bp):
CTGATTAGAAAGA
Found at i:39925283 original size:40 final size:41
Alignment explanation
Indices: 39925219--39925314 Score: 117
Period size: 40 Copynumber: 2.4 Consensus size: 41
39925209 AACTATGTTT
* * *
39925219 GGCACTTAGTGTGCG-TTTCAGAATAGCTTCGGCTATAATTA
1 GGCACTTAGTGTGCGAATTCAGAATAGCTTCAGCTAT-ATAA
*
39925260 -GCACTTAGTGTGCGAATT-GGAATAGCTTCAGCTATATAA
1 GGCACTTAGTGTGCGAATTCAGAATAGCTTCAGCTATATAA
*
39925299 GGCACTAAGTGTGCGA
1 GGCACTTAGTGTGCGA
39925315 TATCGAGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
39 3 0.06
40 43 0.90
41 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (41 bp):
GGCACTTAGTGTGCGAATTCAGAATAGCTTCAGCTATATAA
Found at i:39929842 original size:7 final size:7
Alignment explanation
Indices: 39929830--39929869 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
39929820 CATACTACCT
39929830 CATATCA
1 CATATCA
39929837 CATATCA
1 CATATCA
39929844 CATATCA
1 CATATCA
39929851 CATATCA
1 CATATCA
39929858 CATATCA
1 CATATCA
39929865 CATAT
1 CATAT
39929870 TACACATTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (7 bp):
CATATCA
Found at i:39940585 original size:12 final size:12
Alignment explanation
Indices: 39940560--39940601 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
39940550 AAAAAAAAAT
*
39940560 AATAAAATT-GA
1 AATAAAATTAAA
39940571 AATGAAAA-TAAA
1 AAT-AAAATTAAA
39940583 AATAAAATTAAA
1 AATAAAATTAAA
39940595 AATAAAA
1 AATAAAA
39940602 AGATAGGAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (12 bp):
AATAAAATTAAA
Found at i:39940601 original size:23 final size:24
Alignment explanation
Indices: 39940551--39940595 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
39940541 ATGTCTTTCA
*
39940551 AAAAAAAATAATAAAATTGAAATG
1 AAAAAAAATAATAAAATTAAAATG
*
39940575 AAAATAAA-AATAAAATTAAAA
1 AAAAAAAATAATAAAATTAAAA
39940596 ATAAAAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (24 bp):
AAAAAAAATAATAAAATTAAAATG
Found at i:39953928 original size:40 final size:40
Alignment explanation
Indices: 39953884--39953969 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
39953874 TAGTGACCAC
* *
39953884 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAA
1 ATCCGGGCTAAGACCCAAAGGCATTCGTGCAAGTGGTTAA
* * *
39953924 ATCCGGGCTAATACCCAAAGGCATTCGTGCATGTGGTTAT
1 ATCCGGGCTAAGACCCAAAGGCATTCGTGCAAGTGGTTAA
39953964 ATCCGG
1 ATCCGG
39953970 TTGTATTCCG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCAAAGGCATTCGTGCAAGTGGTTAA
Found at i:39961869 original size:40 final size:40
Alignment explanation
Indices: 39961802--39961947 Score: 141
Period size: 40 Copynumber: 3.6 Consensus size: 40
39961792 AATGATATCT
* * ** * *
39961802 GGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATACCC
1 GGGCTAAGACCCGAAGGCATTCGTGCTAGTAATTAAATCC
* * ** *
39961842 GGGTTAAGACCCGAAGGCCATT-GTGCTAGTGACCACATCC
1 GGGCTAAGACCCGAAGG-CATTCGTGCTAGTAATTAAATCC
* **
39961882 GGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCC
1 GGGCTAAGACCCGAAGGCATTCGTGCTAGTAATTAAATCC
*
39961922 GGGCTAATACCCGAAGGCATTCGTGC
1 GGGCTAAGACCCGAAGGCATTCGTGC
39961948 ATGTGGTTAT
Statistics
Matches: 87, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
39 4 0.05
40 79 0.91
41 4 0.05
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
GGGCTAAGACCCGAAGGCATTCGTGCTAGTAATTAAATCC
Found at i:39961948 original size:40 final size:40
Alignment explanation
Indices: 39961840--39961963 Score: 142
Period size: 40 Copynumber: 3.1 Consensus size: 40
39961830 GTAATTATAC
* * *** *
39961840 CCGGGTTAAGACCCGAAGGCCATT-GTGCTAGTGACCACAT
1 CCGGGCTAAGACCCGAAGG-CATTCGTGCAAGTGGTTAAAT
*
39961880 CCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGGTTAAAT
* * *
39961920 CCGGGCTAATACCCGAAGGCATTCGTGCATGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGGTTAAAT
39961960 CCGG
1 CCGG
39961964 TTGTATTCCG
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 4 0.06
40 68 0.94
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGGTTAAAT
Found at i:39964012 original size:22 final size:22
Alignment explanation
Indices: 39963960--39964004 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
39963950 AGCTATGTTT
39963960 TGTTCTTAATAGTTAGTCTATA
1 TGTTCTTAATAGTTAGTCTATA
39963982 TGTTCTTAATAGTTAGTCTATA
1 TGTTCTTAATAGTTAGTCTATA
39964004 T
1 T
39964005 TATTTTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (22 bp):
TGTTCTTAATAGTTAGTCTATA
Found at i:39970138 original size:62 final size:62
Alignment explanation
Indices: 39970037--39970162 Score: 216
Period size: 62 Copynumber: 2.0 Consensus size: 62
39970027 ATGAACACAA
*
39970037 CAAAAATCTATCTAAATACGGTCTAAAAATCCGATTCATCAAATCCATAAAGACTATAAGAG
1 CAAAAATCTATCTAAATACGGTCTAAAAATCCGACTCATCAAATCCATAAAGACTATAAGAG
* * *
39970099 CAAAAATCTATCTAAATACGGTCTAAAAATCTGACTCATCAAATCCATAAAGACTGTAGGAG
1 CAAAAATCTATCTAAATACGGTCTAAAAATCCGACTCATCAAATCCATAAAGACTATAAGAG
39970161 CA
1 CA
39970163 TTAATTAATC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (62 bp):
CAAAAATCTATCTAAATACGGTCTAAAAATCCGACTCATCAAATCCATAAAGACTATAAGAG
Found at i:39974260 original size:42 final size:42
Alignment explanation
Indices: 39974164--39974245 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
39974154 ATATATATAT
**
39974164 ATATATAGCCGAAGCTATCTTGATATTGCACACTAAGTGCAA
1 ATATATAGCCGAAGCTATCTCAATATTGCACACTAAGTGCAA
* *
39974206 ATATATAGCCGAAGTTATCTCAATTTTGCACACTAAGTGC
1 ATATATAGCCGAAGCTATCTCAATATTGCACACTAAGTGC
39974246 CTAAAATTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (42 bp):
ATATATAGCCGAAGCTATCTCAATATTGCACACTAAGTGCAA
Found at i:39989253 original size:20 final size:20
Alignment explanation
Indices: 39989228--39989277 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
39989218 CAGGCTGAGA
39989228 ACACGGGCGTGTCCCAAGCC
1 ACACGGGCGTGTCCCAAGCC
39989248 ACACGGGCGTGTCCCAAGCC
1 ACACGGGCGTGTCCCAAGCC
*
39989268 ACACAGGCGT
1 ACACGGGCGT
39989278 TTAAATTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.38, G:0.30, T:0.10
Consensus pattern (20 bp):
ACACGGGCGTGTCCCAAGCC
Found at i:39992100 original size:49 final size:49
Alignment explanation
Indices: 39992043--39992492 Score: 819
Period size: 49 Copynumber: 9.2 Consensus size: 49
39992033 ATGTATGAGA
39992043 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
39992092 TGTATATATATGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
39992141 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
39992190 TGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
39992239 TGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * *
39992288 TGTATATGTGTGATAAGGCATGATGGCCGATGTGATGAATGTGAAAGTG
1 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
39992337 TGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
39992386 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
39992435 TGTATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTG
1 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
39992484 TATATATAT
1 TGTATATAT
39992493 ATGTGGCAAA
Statistics
Matches: 391, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 391 1.00
ACGTcount: A:0.30, C:0.08, G:0.31, T:0.31
Consensus pattern (49 bp):
TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:39992616 original size:37 final size:36
Alignment explanation
Indices: 39992561--39992647 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
39992551 AACTTGGAAA
39992561 TATGTTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATG-TCCGGGT-AGACCCGATGACTACGTGTGGAGAT
39992599 TATGTCCGGGTACGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTA-GACCCGATGACTACGTGTGGAGAT
39992636 TATGTCCGGGTA
1 TATGTCCGGGTA
39992648 AGACTTCGCA
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 43 0.90
38 4 0.08
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.26
Consensus pattern (36 bp):
TATGTCCGGGTAGACCCGATGACTACGTGTGGAGAT
Found at i:39997888 original size:42 final size:42
Alignment explanation
Indices: 39997778--39997896 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 42
39997768 TACCATACCA
* * *
39997778 ATGCCATATCCCAGATATGGTCTTACATGGGAT-CTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACA-CGAATCCTCATATCG
* * *
39997820 ATGCCAATAGCCCAGCTATGGACTTACACGAATCCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAATCCTCATATCG
*
39997863 ATTCCATATCCCAGATATGGTCTTACACGTAATC
1 ATGCCATATCCCAGATATGGTCTTACACG-AATC
39997897 TCAAATAACC
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 29 0.45
43 35 0.55
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAATCCTCATATCG
Found at i:40007749 original size:42 final size:42
Alignment explanation
Indices: 40007702--40007814 Score: 120
Period size: 43 Copynumber: 2.7 Consensus size: 42
40007692 TACCATACCA
* * * *
40007702 ATGCCATATCCCAGATATGGTATTACATAGGAT-CTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACA-AATCCTCATATCG
* **
40007744 ATGCCAATAGCCCAGCCATGGTCTTACACAAATCCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACAAATCCTCATATCG
* *
40007787 ATGTCATATCCCAAATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
40007815 GTAATCTCAA
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
42 26 0.46
43 31 0.54
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACAAATCCTCATATCG
Found at i:40008922 original size:16 final size:16
Alignment explanation
Indices: 40008901--40008932 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40008891 ACGAAATCAC
40008901 TGTAGACCATGAAAAT
1 TGTAGACCATGAAAAT
40008917 TGTAGACCATGAAAAT
1 TGTAGACCATGAAAAT
40008933 GTAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (16 bp):
TGTAGACCATGAAAAT
Found at i:40012978 original size:28 final size:28
Alignment explanation
Indices: 40012938--40013007 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
40012928 TATGAGATTG
*
40012938 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
40012966 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
40012994 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
40013008 GACTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:40017039 original size:28 final size:28
Alignment explanation
Indices: 40017007--40017105 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
40016997 GCAATAAGCC
*
40017007 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
40017035 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
40017063 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
40017092 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40017106 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:40024718 original size:28 final size:28
Alignment explanation
Indices: 40024686--40024784 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
40024676 GCAATAAGCC
*
40024686 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
40024714 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
40024742 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
40024771 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40024785 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:40027423 original size:109 final size:109
Alignment explanation
Indices: 40027295--40027613 Score: 519
Period size: 101 Copynumber: 3.0 Consensus size: 109
40027285 GGAATTAACG
40027295 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
1 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
40027360 TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
66 TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
40027404 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
1 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
40027469 -TTAATATATG-T--TA-A-TATA-TT-ATAAAAGATGAAAGTA
66 TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
* * *
40027505 GCCGACCAATATGCATGGATTAATGACTTGATTTGTTTATTATATTTTATGGCATTATGGTATAC
1 GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
* * * *
40027570 TTTAATATATGTTAATATATTATGTTTAAGAAGAGAGGAAAGTA
66 TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
40027614 TTCATCTTTC
Statistics
Matches: 195, Mismatches: 7, Indels: 16
0.89 0.03 0.07
Matches are distributed among these distances:
101 78 0.40
102 12 0.06
103 5 0.03
104 1 0.01
105 4 0.02
106 1 0.01
107 4 0.02
108 12 0.06
109 78 0.40
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (109 bp):
GCCGACCAATATGCATGGATTAATGACTTGAATTATTTATTATGTTTTATGGCATTATGGTATAC
TTTAATATATGTTAATATATTATATTTAATAAAAGATGAAAGTA
Found at i:40028017 original size:28 final size:28
Alignment explanation
Indices: 40027977--40028046 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
40027967 TATGAGATTG
*
40027977 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
40028005 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
40028033 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
40028047 GACTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:40031387 original size:47 final size:47
Alignment explanation
Indices: 40031336--40031623 Score: 459
Period size: 47 Copynumber: 6.1 Consensus size: 47
40031326 TTAGGATTTT
40031336 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
40031383 ATGTGATGAGTGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
40031430 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGACCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
40031477 ATATGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
40031524 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
40031571 ATATGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
40031618 ATGTGA
1 ATGTGA
40031624 CATATGTATG
Statistics
Matches: 221, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 221 1.00
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:40031389 original size:22 final size:22
Alignment explanation
Indices: 40031361--40031436 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
40031351 ACATGCATAT
40031361 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* *
40031383 ATGTGATGAGTG-TGAGCAT-G-CA
1 ATGTGATAAG-GCCGA--ATGGCCA
40031405 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCCGAATGGCCA
40031430 ATGTGAT
1 ATGTGAT
40031437 GAATGTGAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 19 0.46
23 5 0.12
24 5 0.12
25 12 0.29
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:40031662 original size:48 final size:48
Alignment explanation
Indices: 40031593--40031727 Score: 216
Period size: 48 Copynumber: 2.8 Consensus size: 48
40031583 TGAACATGCA
* * * *
40031593 TATATGTGATAAGGCCGAATGGCTAATGTGACATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
* *
40031641 TATATGTGGTAAAGCCGAATGGCTAGTGCGAAATATGTATGAGGTATG
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
40031689 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
40031728 GGCGATGTGC
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 80 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
Found at i:40032056 original size:37 final size:37
Alignment explanation
Indices: 40031876--40032055 Score: 297
Period size: 37 Copynumber: 4.9 Consensus size: 37
40031866 AAATATATTT
*
40031876 CGGGTGAGACCCGATGACTACGTGTGGAGATTATGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
40031913 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
* *
40031950 CGGGTAAGTCCCGATGACTACGTGTGGAGAGTATGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
*
40031987 CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTC
1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
* * *
40032024 CGGGTAAAACCCGATAACTTCGTGTGGAGATT
1 CGGGTAAGACCCGATGACTACGTGTGGAGATT
40032056 TCGTCTGAGC
Statistics
Matches: 134, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (37 bp):
CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
Found at i:40037396 original size:29 final size:29
Alignment explanation
Indices: 40037357--40037436 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
40037347 CTTAATAATC
*
40037357 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
40037387 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
40037416 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
40037437 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:40045287 original size:29 final size:29
Alignment explanation
Indices: 40045248--40045327 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
40045238 CTTAATAATC
*
40045248 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
40045278 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
40045307 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
40045328 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:40050586 original size:20 final size:20
Alignment explanation
Indices: 40050557--40050603 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
40050547 ATTTTGATAA
*
40050557 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
40050577 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
40050597 ACATGAT
1 ACATGAT
40050604 GTACTCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:40051007 original size:23 final size:23
Alignment explanation
Indices: 40050932--40051004 Score: 128
Period size: 23 Copynumber: 3.1 Consensus size: 23
40050922 TATCATGCCT
40050932 AGTTATTAAAGGGCTTATGCCCC
1 AGTTATTAAAGGGCTTATGCCCC
40050955 AGTTATTAAAGGGCTTATGCCCC
1 AGTTATTAAAGGGCTTATGCCCC
*
40050978 AGTTATTAAAAGGGCTTTTGCCCC
1 AGTTATT-AAAGGGCTTATGCCCC
40051002 AGT
1 AGT
40051005 ATTTAAAAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 30 0.62
24 18 0.38
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (23 bp):
AGTTATTAAAGGGCTTATGCCCC
Found at i:40051010 original size:24 final size:24
Alignment explanation
Indices: 40050932--40051018 Score: 126
Period size: 23 Copynumber: 3.7 Consensus size: 24
40050922 TATCATGCCT
40050932 AGTTATT-AAAGGGCTTATGCCCC
1 AGTTATTAAAAGGGCTTATGCCCC
40050955 AGTTATT-AAAGGGCTTATGCCCC
1 AGTTATTAAAAGGGCTTATGCCCC
*
40050978 AGTTATTAAAAGGGCTTTTGCCCC
1 AGTTATTAAAAGGGCTTATGCCCC
40051002 AG-TATTTAAAAGAGGCT
1 AGTTA-TTAAAAG-GGCT
40051019 AGGCCTCCAG
Statistics
Matches: 60, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
23 32 0.53
24 24 0.40
25 4 0.07
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (24 bp):
AGTTATTAAAAGGGCTTATGCCCC
Found at i:40051264 original size:31 final size:31
Alignment explanation
Indices: 40051226--40051289 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
40051216 CGTTTACAGT
*
40051226 AAAGGCTTCAGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCAGCCCAGTAATATGAAATGTGA
* **
40051257 AAAGGCTTCGGCCCAGTGTTATGAAATGTGA
1 AAAGGCTTCAGCCCAGTAATATGAAATGTGA
40051288 AA
1 AA
40051290 TAAGAAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAGTAATATGAAATGTGA
Found at i:40057492 original size:20 final size:22
Alignment explanation
Indices: 40057467--40057507 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
40057457 TCTCAAGGGA
40057467 ATTTATA-TAATTT-TTTTTCC
1 ATTTATACTAATTTATTTTTCC
40057487 ATTTATACTTAATTTATTTTT
1 ATTTATAC-TAATTTATTTTT
40057508 GAAAGATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTATACTAATTTATTTTTCC
Found at i:40057506 original size:22 final size:20
Alignment explanation
Indices: 40057467--40057506 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
40057457 TCTCAAGGGA
*
40057467 ATTTATATAATTTTTTTTCC
1 ATTTATATAATTTATTTTCC
40057487 ATTTATACTTAATTTATTTT
1 ATTTATA--TAATTTATTTT
40057507 TGAAAGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTATATAATTTATTTTCC
Found at i:40060166 original size:25 final size:23
Alignment explanation
Indices: 40060123--40060169 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 23
40060113 TAAAAATCTA
40060123 GTATAGACAAAAAAAAAAACAAG
1 GTATAGACAAAAAAAAAAACAAG
40060146 GTATACGACAGAAAAAAAAAACAA
1 GTATA-GACA-AAAAAAAAAACAA
40060170 CTGAGCCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 5 0.23
24 4 0.18
25 13 0.59
ACGTcount: A:0.68, C:0.11, G:0.13, T:0.09
Consensus pattern (23 bp):
GTATAGACAAAAAAAAAAACAAG
Found at i:40061379 original size:14 final size:14
Alignment explanation
Indices: 40061362--40061406 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
40061352 TTTTTTGAAA
*
40061362 TTTAAAATTTAATT
1 TTTAAATTTTAATT
*
40061376 TTTATATTTTAATT
1 TTTAAATTTTAATT
*
40061390 TTGAGAATTTTAATT
1 TTTA-AATTTTAATT
40061405 TT
1 TT
40061407 GAGACATTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (14 bp):
TTTAAATTTTAATT
Found at i:40061401 original size:15 final size:15
Alignment explanation
Indices: 40061381--40061410 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40061371 TAATTTTTAT
40061381 ATTTTAATTTTGAGA
1 ATTTTAATTTTGAGA
40061396 ATTTTAATTTTGAGA
1 ATTTTAATTTTGAGA
40061411 CATTGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
ATTTTAATTTTGAGA
Found at i:40062169 original size:19 final size:19
Alignment explanation
Indices: 40062145--40062189 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
40062135 TATTTTAAAC
40062145 AAAAAATTAAAAAATTT-TA
1 AAAAAATT-AAAAATTTATA
*
40062164 AAAAAATTAAAAATTTATG
1 AAAAAATTAAAAATTTATA
40062183 AAAAAAT
1 AAAAAAT
40062190 AATAACTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAAATTAAAAATTTATA
Found at i:40069133 original size:28 final size:28
Alignment explanation
Indices: 40069058--40069133 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
40069048 GGGTTCAAAT
* * * *
40069058 TATACAGCACTAAGTGTGCAAGTTTGAT
1 TATATAGCACTAAGTGTGCGAGTTCGAC
40069086 TATATAGCACTAAGTGTGCGAGTTCGAC
1 TATATAGCACTAAGTGTGCGAGTTCGAC
40069114 TAT-TAAGCACTAAGTGTGCG
1 TATAT-AGCACTAAGTGTGCG
40069134 GGCTTATTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 42 0.98
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
TATATAGCACTAAGTGTGCGAGTTCGAC
Found at i:40076315 original size:28 final size:28
Alignment explanation
Indices: 40076254--40076351 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
40076244 TCACAAATTG
** * *
40076254 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
40076283 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
40076311 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
40076339 GCACTAAGTGTGC
1 GCACTAAGTGTGC
40076352 GGGCTTATTG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:40078118 original size:42 final size:44
Alignment explanation
Indices: 40078054--40078143 Score: 123
Period size: 42 Copynumber: 2.1 Consensus size: 44
40078044 ATCGACTTGA
*
40078054 GATTTACGTGTAAGACCATGTCTGGGACA-TAGGCATC-ATATAT
1 GATTTACGTGGAAGACCATGTCTGGGACAGT-GGCATCGATATAT
* *
40078097 GATTT-CGTGGAAGACCCTGTCTGGGACAGTGGCATCGATATTT
1 GATTTACGTGGAAGACCATGTCTGGGACAGTGGCATCGATATAT
40078140 GATT
1 GATT
40078144 ACAAGTAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
42 27 0.64
43 15 0.36
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (44 bp):
GATTTACGTGGAAGACCATGTCTGGGACAGTGGCATCGATATAT
Found at i:40085832 original size:41 final size:41
Alignment explanation
Indices: 40085787--40085869 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
40085777 GAAATAAATG
40085787 AAAGAAATGGGCTGCTATGAACCTTAGTAAAATTCAACTAT
1 AAAGAAATGGGCTGCTATGAACCTTAGTAAAATTCAACTAT
*
40085828 AAAGAAATGGGCTGCTATGAACCTTAGTAAAATTCAGCTAT
1 AAAGAAATGGGCTGCTATGAACCTTAGTAAAATTCAACTAT
40085869 A
1 A
40085870 CTAGGGTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (41 bp):
AAAGAAATGGGCTGCTATGAACCTTAGTAAAATTCAACTAT
Found at i:40090329 original size:32 final size:32
Alignment explanation
Indices: 40090293--40090357 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
40090283 AAGTTGAGAA
40090293 CTATATGGTTTAAATTAATATGGTCTTATGCG
1 CTATATGGTTTAAATTAATATGGTCTTATGCG
*
40090325 CTATATGGTTTAAGTTAATATGGTCTTATGCG
1 CTATATGGTTTAAATTAATATGGTCTTATGCG
40090357 C
1 C
40090358 ATAGTCTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (32 bp):
CTATATGGTTTAAATTAATATGGTCTTATGCG
Found at i:40093130 original size:30 final size:30
Alignment explanation
Indices: 40093096--40093230 Score: 148
Period size: 30 Copynumber: 4.5 Consensus size: 30
40093086 TAAATCTTAG
*
40093096 CCTTTTCCACCACCAACTCCACTAGCCACT
1 CCTTTTCCACCACCAACTCCACTAGCCACA
*
40093126 CCTTTTCCACCACTAACTCCACTAGCCACA
1 CCTTTTCCACCACCAACTCCACTAGCCACA
* *
40093156 CATTTTCCACCACCAAATCCACTAGCCACA
1 CCTTTTCCACCACCAACTCCACTAGCCACA
* ** * *
40093186 -CTTGCTCCATTACCTACTCCACTAACCACA
1 CCTT-TTCCACCACCAACTCCACTAGCCACA
*
40093216 -CTTGCTCCACCACCA
1 CCTT-TTCCACCACCA
40093231 CTTGTACCTA
Statistics
Matches: 89, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
29 2 0.02
30 87 0.98
ACGTcount: A:0.27, C:0.47, G:0.04, T:0.23
Consensus pattern (30 bp):
CCTTTTCCACCACCAACTCCACTAGCCACA
Found at i:40093806 original size:27 final size:25
Alignment explanation
Indices: 40093725--40093846 Score: 74
Period size: 25 Copynumber: 5.0 Consensus size: 25
40093715 ATTATATTTC
* *
40093725 TTAATATTATATTATATATAT-TCT
1 TTAATACTATATTATATATATATAT
* **
40093749 TT--TAATATATTAGGTATAT-T-T
1 TTAATACTATATTATATATATATAT
* *
40093770 TAAATTCTATATTACGTATATATATAT
1 TTAATACTATATTA--TATATATATAT
* * * *
40093797 TTTATACTATTTTATTTATATATCT
1 TTAATACTATATTATATATATATAT
* *
40093822 TTAATATTATATTATTTATATATAT
1 TTAATACTATATTATATATATATAT
40093847 AAATTTTTTT
Statistics
Matches: 74, Mismatches: 18, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
21 2 0.03
22 15 0.20
23 8 0.11
24 2 0.03
25 35 0.47
26 1 0.01
27 11 0.15
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATACTATATTATATATATATAT
Found at i:40093816 original size:25 final size:25
Alignment explanation
Indices: 40093788--40093846 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
40093778 ATATTACGTA
* *
40093788 TATATATATTTTATACTATTTTATT
1 TATATATATTTAATACTATATTATT
* *
40093813 TATATATCTTTAATATTATATTATT
1 TATATATATTTAATACTATATTATT
40093838 TATATATAT
1 TATATATAT
40093847 AAATTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (25 bp):
TATATATATTTAATACTATATTATT
Found at i:40093898 original size:22 final size:24
Alignment explanation
Indices: 40093870--40093928 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
40093860 ACATGTTATC
40093870 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
40093892 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
40093917 TTATGTACATAT
1 TTATGTATATAT
40093929 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 2 0.07
25 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATGTATATATCTTAACACTATA
Found at i:40093918 original size:25 final size:25
Alignment explanation
Indices: 40093886--40093934 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
40093876 ATATATCTTA
**
40093886 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
40093911 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
40093935 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:40094106 original size:8 final size:8
Alignment explanation
Indices: 40094088--40094138 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
40094078 TAATTATTAT
*
40094088 TATTCTAA
1 TATTTTAA
*
40094096 TATTTTGA
1 TATTTTAA
40094104 TATTTTAA
1 TATTTTAA
40094112 TATTTT-A
1 TATTTTAA
40094119 T-TTTTATA
1 TATTTTA-A
*
40094127 TATTTTAT
1 TATTTTAA
40094135 TATT
1 TATT
40094139 CAAATCATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 4 0.11
7 2 0.06
8 25 0.69
9 5 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (8 bp):
TATTTTAA
Found at i:40094112 original size:16 final size:15
Alignment explanation
Indices: 40094088--40094134 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
40094078 TAATTATTAT
*
40094088 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
40094104 TATTTTAATATTTTA
1 TATTTTAATATTTTA
40094119 T-TTTTATATATTTTA
1 TATTTTA-ATATTTTA
40094134 T
1 T
40094135 TATTCAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 5 0.17
15 11 0.38
16 13 0.45
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:40094131 original size:15 final size:14
Alignment explanation
Indices: 40094093--40094135 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
40094083 ATTATTATTC
40094093 TAATATTTTGATATTT
1 TAATATTTT-AT-TTT
40094109 TAATATTTTATTTT
1 TAATATTTTATTTT
40094123 TATATATTTTATT
1 TA-ATATTTTATT
40094136 ATTCAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.19
15 12 0.46
16 9 0.35
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TAATATTTTATTTT
Found at i:40103341 original size:27 final size:25
Alignment explanation
Indices: 40103300--40103355 Score: 94
Period size: 27 Copynumber: 2.2 Consensus size: 25
40103290 TTGGTCAGTG
40103300 TATGTGAAAATTATTAGTAGGGACT
1 TATGTGAAAATTATTAGTAGGGACT
40103325 TATGTGAGACAATTATTAGTAGGGACT
1 TATGTGA-A-AATTATTAGTAGGGACT
40103352 TATG
1 TATG
40103356 CTAGGCAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 7 0.24
26 1 0.03
27 21 0.72
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (25 bp):
TATGTGAAAATTATTAGTAGGGACT
Found at i:40104962 original size:40 final size:41
Alignment explanation
Indices: 40104905--40105090 Score: 220
Period size: 40 Copynumber: 4.7 Consensus size: 41
40104895 CTAACGGGGT
* * * *
40104905 TAAGTCTCGAAGACATTTGTGCTAGTGATTAAT-TCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
* *
40104945 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TTCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
* *
40104985 CAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
* *
40105025 TAAGTCCCGAAGGCATTTGCGCGAGTGAC-CATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
* * *
40105065 TAAGACCCGACGGC-CTTGTGCGAGTG
1 TAAGTCCCGAAGGCATTTGTGCGAGTG
40105091 GTTATATCCG
Statistics
Matches: 129, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
39 12 0.09
40 117 0.91
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (41 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
Found at i:40112917 original size:55 final size:55
Alignment explanation
Indices: 40112830--40112936 Score: 196
Period size: 55 Copynumber: 1.9 Consensus size: 55
40112820 CATGATCGGA
*
40112830 AATACCTTATAACCCTAATCCGGTGACGGATACGGGCTAGGGATGTTATACTGGT
1 AATACCTTATAACCCTAATCCGGTGACAGATACGGGCTAGGGATGTTATACTGGT
*
40112885 AATACCTTATAACCCTAATCCGGTGACAGATACGGGTTAGGGATGTTATACT
1 AATACCTTATAACCCTAATCCGGTGACAGATACGGGCTAGGGATGTTATACT
40112937 AATGACATGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (55 bp):
AATACCTTATAACCCTAATCCGGTGACAGATACGGGCTAGGGATGTTATACTGGT
Found at i:40116383 original size:50 final size:49
Alignment explanation
Indices: 40116256--40116500 Score: 267
Period size: 49 Copynumber: 4.9 Consensus size: 49
40116246 TAGACAAGGC
* * * * *
40116256 TATCTGGTACACATAGTAGCCTGCACTTAGTACTTCACATGCGATCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* *
40116305 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC-AAT
* * * * *
40116355 CATCTGATACACGTAGTCGCCTGCACTTAGTACTACACACGTTATCGAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-T
* * * * * * *
40116406 TATCGGGTACGCATAGTAGCTTGCACTTAGTACTACGCATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
*
40116455 TAT-TCGGTACACGTAGTAGCCTGCACTTAGTATTACACACGTGACC
1 TATCT-GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
40116501 TCACAATGGA
Statistics
Matches: 158, Mismatches: 34, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
49 78 0.49
50 46 0.29
51 34 0.22
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:40116767 original size:27 final size:27
Alignment explanation
Indices: 40116727--40116780 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
40116717 AGGTACAACC
* *
40116727 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
40116754 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
40116781 TCAAATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:40124559 original size:30 final size:31
Alignment explanation
Indices: 40124523--40124581 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
40124513 TTGTGAACTA
*
40124523 TACTATGT-ATATTTTTATT-AAATTGAATGT
1 TACTATGTGA-ATTTTTATTGAAAATGAATGT
40124553 TACTATGTGAATTTTTATTGAAAATGAAT
1 TACTATGTGAATTTTTATTGAAAATGAAT
40124582 CGATATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.49
Consensus pattern (31 bp):
TACTATGTGAATTTTTATTGAAAATGAATGT
Found at i:40129201 original size:27 final size:27
Alignment explanation
Indices: 40129160--40129213 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
40129150 TGCCATGTGA
* *
40129160 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
40129187 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
40129214 GGTTGTACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:40129519 original size:49 final size:50
Alignment explanation
Indices: 40129439--40129668 Score: 284
Period size: 49 Copynumber: 4.6 Consensus size: 50
40129429 ATCTATTGTG
* *
40129439 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * ** *
40129489 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * * * **
40129539 CGATCACATTTGTAGTACTAAGTGCAGGTTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
40129589 AGGTCACATGTGTAGTACTAAATGCTGGCTACTACGTGTACCAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
*
40129639 -GGTCGCATGTGTAGTACTAAGTGCAGGCTA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTA
40129669 TTATGCGCAC
Statistics
Matches: 149, Mismatches: 29, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
49 68 0.46
50 45 0.30
51 36 0.24
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:40137177 original size:45 final size:45
Alignment explanation
Indices: 40137128--40137250 Score: 174
Period size: 45 Copynumber: 2.7 Consensus size: 45
40137118 ATCTAAACCG
* *
40137128 ATGAGTTGTTTATCCACAACATACTAGTAGCTTTTATCTGCACCA
1 ATGAGTGGTTTATCCACAACATACTAGCAGCTTTTATCTGCACCA
* ** **
40137173 ATGAGTGGTTTCTCCACAATGTACTAGCAGCTTTTATCTGCACTG
1 ATGAGTGGTTTATCCACAACATACTAGCAGCTTTTATCTGCACCA
*
40137218 ATGAGTGGTTTATCCACACCATACTAGCAGCTT
1 ATGAGTGGTTTATCCACAACATACTAGCAGCTT
40137251 ATTTGCAAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (45 bp):
ATGAGTGGTTTATCCACAACATACTAGCAGCTTTTATCTGCACCA
Found at i:40155902 original size:55 final size:53
Alignment explanation
Indices: 40155822--40155980 Score: 196
Period size: 55 Copynumber: 2.9 Consensus size: 53
40155812 TACGTGGTAT
*
40155822 CCTTGCCTTAT-GAACTCAGCAATGCCATACCTTGGCATGGTCTTACATG-GGA
1 CCTTGCCTTATAGAACTCATCAATGCCAT-CCTTGGCATGGTCTTACATGAGGA
* * ***
40155874 CCTTTTCCTTATAGTAACTCATCAATGCCATCTCTTGACATGGTCTTACATGATTT
1 CC-TTGCCTTATAG-AACTCATCAATGCCATC-CTTGGCATGGTCTTACATGAGGA
*
40155930 CCTTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGA
1 CCTTGCCTTATAGAACTCATCAATGCCAT-CCTTGGCATGGTCTTACATGA
40155981 TATTCTTGTC
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
52 2 0.02
53 8 0.09
54 36 0.39
55 44 0.48
56 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (53 bp):
CCTTGCCTTATAGAACTCATCAATGCCATCCTTGGCATGGTCTTACATGAGGA
Found at i:40156025 original size:47 final size:47
Alignment explanation
Indices: 40155970--40156083 Score: 192
Period size: 47 Copynumber: 2.4 Consensus size: 47
40155960 CCTTGGCATG
* *
40155970 GTCTTACATGATATTCTTGTCTTACCAAATGCCATGTTCCAAACATA
1 GTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAACATA
* *
40156017 GTCTTACATGGTATCCTTGTCTTACCAAATGTCATGTTCCAAACATG
1 GTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAACATA
40156064 GTCTTACATGGTATCCTTGT
1 GTCTTACATGGTATCCTTGT
40156084 ATTAGTGCCA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 63 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (47 bp):
GTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAACATA
Found at i:40156162 original size:47 final size:47
Alignment explanation
Indices: 40156059--40156223 Score: 163
Period size: 45 Copynumber: 3.5 Consensus size: 47
40156049 CATGTTCCAA
* * * **
40156059 ACATGGTCTTACATGGTATCCTTGTATTAGTGCCAATGCCACATCTTG
1 ACATGGTCTTACATGGTATCCTT-AATCAATGCCAATGCCATGTCTTG
** ** *
40156107 ATGTGGTCTTACATGAAATCCTTAATCAATGCCGATGCCATGTCTTG
1 ACATGGTCTTACATGGTATCCTTAATCAATGCCAATGCCATGTCTTG
* * * ** *
40156154 ACATGGTCTTACACGGGATCCTT--GCCTTACCAATGCCATGTCTTG
1 ACATGGTCTTACATGGTATCCTTAATCAATGCCAATGCCATGTCTTG
40156199 ACATGGTCTTACATGGTATCCTTAA
1 ACATGGTCTTACATGGTATCCTTAA
40156224 CAGTCAATTC
Statistics
Matches: 93, Mismatches: 22, Indels: 5
0.77 0.18 0.04
Matches are distributed among these distances:
45 38 0.41
47 36 0.39
48 19 0.20
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (47 bp):
ACATGGTCTTACATGGTATCCTTAATCAATGCCAATGCCATGTCTTG
Found at i:40157494 original size:27 final size:27
Alignment explanation
Indices: 40157462--40157513 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
40157452 ATAATAGTCC
*
40157462 AATTAATAAATAAATACATCCACTTCT
1 AATTAATAAATAAAGACATCCACTTCT
40157489 AATTAATAAATAAAGACATCCACTT
1 AATTAATAAATAAAGACATCCACTT
40157514 TAAGAACACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.31
Consensus pattern (27 bp):
AATTAATAAATAAAGACATCCACTTCT
Found at i:40160543 original size:29 final size:29
Alignment explanation
Indices: 40160483--40160550 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
40160473 ATAAATATCA
*
40160483 AATTTATATATGAACTTTGTTTTAATATGC
1 AATTTATATATGAACTTTGATTT-ATATGC
* *
40160513 AATTTGATATATTAACTTTGATTT-TGTGC
1 AATTT-ATATATGAACTTTGATTTATATGC
40160542 AA-TTATATA
1 AATTTATATA
40160551 CATAAAACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 5 0.15
28 2 0.06
29 6 0.18
30 5 0.15
31 16 0.47
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.50
Consensus pattern (29 bp):
AATTTATATATGAACTTTGATTTATATGC
Found at i:40160905 original size:9 final size:10
Alignment explanation
Indices: 40160884--40160908 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40160874 AAAATCTAAC
40160884 AAAATTATAA
1 AAAATTATAA
40160894 AAAATTATAA
1 AAAATTATAA
40160904 AAAAT
1 AAAAT
40160909 ATTATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATTATAA
Found at i:40160912 original size:12 final size:11
Alignment explanation
Indices: 40160884--40160922 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
40160874 AAAATCTAAC
40160884 AAAATTAT-AA
1 AAAATTATAAA
40160894 AAAATTATAAA
1 AAAATTATAAA
40160905 AAATATTATAATA
1 AAA-ATTATAA-A
40160918 AAAAT
1 AAAAT
40160923 AAAGTAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.31
11 5 0.19
12 9 0.35
13 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:40161311 original size:2 final size:2
Alignment explanation
Indices: 40161304--40161342 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
40161294 TTCCTTTCAT
*
40161304 GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
40161343 GAATAGGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40164768 original size:131 final size:129
Alignment explanation
Indices: 40164495--40164774 Score: 305
Period size: 129 Copynumber: 2.2 Consensus size: 129
40164485 TTTTTTTAAG
* * * * * *
40164495 GTTGTTGCTAGTATTTGAAGGTTTAACAACAACTTATTTTGTCGTTGTAAATTTTATTAATAATT
1 GTTGTTGCTAATATTTTAACGTTTAACAACAACTTATTTTGTCATTATAAATTTTATTAAAAATT
* ** * **
40164560 CACAACGACAATTTGTCATTGTTATTAATAAGTAGAAAATTAAATTATGTAACAACATTTCAAA
66 CACAACAACAATTTGTCATTGCAATAAATAAGTAGAAAATTAAATTAAATAACAACATTTCAAA
* * * * *
40164624 GTTGTTGCTAATATTTTATCGTTTAATAATAACTTGTTTTGTCATTATACATTTTATTAAAAATT
1 GTTGTTGCTAATATTTTAACGTTTAACAACAACTTATTTTGTCATTATAAATTTTATTAAAAATT
* * **
40164689 CACAACAACACGATTTGTCGTTGCAATAAATAAG-CGTAAAATTAAATTAAATAATGACAATTT-
66 CACAACAACA--ATTTGTCATTGCAATAAATAAGTAG-AAAATTAAATTAAATAACAAC-ATTTC
40164752 AATA
127 AA-A
40164756 -TTGTTGCTAATATTTTAAC
1 GTTGTTGCTAATATTTTAAC
40164775 ATTTTAGCGA
Statistics
Matches: 124, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
129 63 0.51
130 1 0.01
131 55 0.44
132 5 0.04
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (129 bp):
GTTGTTGCTAATATTTTAACGTTTAACAACAACTTATTTTGTCATTATAAATTTTATTAAAAATT
CACAACAACAATTTGTCATTGCAATAAATAAGTAGAAAATTAAATTAAATAACAACATTTCAAA
Found at i:40176506 original size:39 final size:39
Alignment explanation
Indices: 40176388--40176608 Score: 309
Period size: 39 Copynumber: 5.6 Consensus size: 39
40176378 TCGTTCAAAC
* * ** * **
40176388 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
40176428 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
*
40176468 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCCCAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
40176507 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
40176546 GCCTTCGGGCTTAGCCC-GATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
40176584 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
40176609 CTCGAACATT
Statistics
Matches: 163, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
38 38 0.23
39 87 0.53
40 38 0.23
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:40176594 original size:116 final size:119
Alignment explanation
Indices: 40176388--40176608 Score: 322
Period size: 116 Copynumber: 1.9 Consensus size: 119
40176378 TCGTTCAAAC
* **
40176388 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
1 GCCTTCGGGACATAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
* *
40176453 ACAATTTGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACTCGCCCAATT
66 ACAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACTCGCCCAATT
* * ** *
40176507 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CTTAGCCC-GATATC
1 GCCTTCGGGACATAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
*
40176569 ATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
66 ACAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
40176609 CTCGAACATT
Statistics
Matches: 91, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
116 43 0.47
117 7 0.08
118 32 0.35
119 9 0.10
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (119 bp):
GCCTTCGGGACATAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
ACAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACTCGCCCAATT
Found at i:40176600 original size:77 final size:78
Alignment explanation
Indices: 40176388--40176609 Score: 311
Period size: 77 Copynumber: 2.8 Consensus size: 78
40176378 TCGTTCAAAC
* * ** * ** *
40176388 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CTTAGCCCGGATATC
* *
40176453 ACAATTTGCACAATT
64 ACAACTCGCACAATT
* *
40176468 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCCCAATTGCCTTCGGGCTTAGCCCGGATATCAT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
40176533 AACTCGCACAATT
66 AACTCGCACAATT
40176546 GCCTTCGGGCTTAGCCC-GATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
40176610 TCGAACATTC
Statistics
Matches: 128, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
77 45 0.35
78 43 0.34
79 31 0.24
80 9 0.07
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (78 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
AACTCGCACAATT
Found at i:40181119 original size:12 final size:12
Alignment explanation
Indices: 40181102--40181127 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40181092 TAATCCCGGC
40181102 AATTCTTCAGGG
1 AATTCTTCAGGG
40181114 AATTCTTCAGGG
1 AATTCTTCAGGG
40181126 AA
1 AA
40181128 AACATCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (12 bp):
AATTCTTCAGGG
Found at i:40184599 original size:27 final size:28
Alignment explanation
Indices: 40184561--40184617 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
40184551 CATAACTCGC
40184561 CAATTGCCTTC-GGCTTAGCCCGGATAT
1 CAATTGCCTTCGGGCTTAGCCCGGATAT
40184588 CAATTGCCTTCGGGCTTAGCCCGGATAT
1 CAATTGCCTTCGGGCTTAGCCCGGATAT
40184616 CA
1 CA
40184618 TAACTCGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.28
Consensus pattern (28 bp):
CAATTGCCTTCGGGCTTAGCCCGGATAT
Found at i:40190359 original size:33 final size:33
Alignment explanation
Indices: 40190278--40190418 Score: 174
Period size: 38 Copynumber: 3.9 Consensus size: 33
40190268 CACAATTTGC
40190278 ACAATTGCCTTCGGGCTTAGCCCGGATATCATA
1 ACAATTGCCTTCGGGCTTAGCCCGGATATCATA
40190311 ACTCGCCAATTGCCTTCGGGCTTAGCCCGGATATCATA
1 A-----CAATTGCCTTCGGGCTTAGCCCGGATATCATA
40190349 ACAATTGCCTTCGGGCTTAGCCCGGATATCATAA
1 ACAATTGCCTTCGGGCTTAGCCCGGATATCAT-A
*
40190383 CTCGCACAATTGCCTTCGGGCTTAGCCTGGATATCA
1 -----ACAATTGCCTTCGGGCTTAGCCCGGATATCA
40190419 CTCGAACATT
Statistics
Matches: 96, Mismatches: 1, Indels: 16
0.85 0.01 0.14
Matches are distributed among these distances:
33 32 0.33
34 1 0.01
38 33 0.34
39 30 0.31
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (33 bp):
ACAATTGCCTTCGGGCTTAGCCCGGATATCATA
Found at i:40190381 original size:71 final size:72
Alignment explanation
Indices: 40190278--40190418 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 72
40190268 CACAATTTGC
40190278 ACAATTGCCTTCGGGCTTAGCCCGGATATCATAACTCGC-CAATTGCCTTCGGGCTTAGCCCGGA
1 ACAATTGCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGA
40190342 TATCATA
66 TATCATA
*
40190349 ACAATTGCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCTGGA
1 ACAATTGCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGA
40190414 TATCA
66 TATCA
40190419 CTCGAACATT
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
71 39 0.57
72 29 0.43
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (72 bp):
ACAATTGCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGA
TATCATA
Found at i:40190403 original size:39 final size:39
Alignment explanation
Indices: 40190204--40190418 Score: 255
Period size: 39 Copynumber: 5.6 Consensus size: 39
40190194 TCGTTCAAAC
* * ** * **
40190204 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
40190244 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
40190284 GCCTTCGGGCTTAGCCCGGATATCATAACTCGC-CAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
40190322 GCCTTCGGGCTTAGCCCGGATATCAT-A-----ACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
40190355 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
*
40190394 GCCTTCGGGCTTAGCCTGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
40190419 CTCGAACATT
Statistics
Matches: 152, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
33 31 0.20
34 1 0.01
37 1 0.01
38 31 0.20
39 50 0.33
40 38 0.25
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.25
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:40193593 original size:26 final size:27
Alignment explanation
Indices: 40193542--40193593 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
40193532 GACGAGATTG
40193542 GCACTAAGTGTGCATGCTGGAAAATAT
1 GCACTAAGTGTGCATGCTGGAAAATAT
40193569 GCACTAAGTGTGCA-GCTGGAAAATA
1 GCACTAAGTGTGCATGCTGGAAAATA
40193594 CGGCACTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (27 bp):
GCACTAAGTGTGCATGCTGGAAAATAT
Found at i:40193599 original size:27 final size:27
Alignment explanation
Indices: 40193541--40193600 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
40193531 TGACGAGATT
40193541 GGCACTAAGTGTGCATGCTGGAAAATA
1 GGCACTAAGTGTGCATGCTGGAAAATA
*
40193568 TGCACTAAGTGTGCA-GCTGGAAAATA
1 GGCACTAAGTGTGCATGCTGGAAAATA
40193594 CGGCACT
1 -GGCACT
40193601 GGGTGTGCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 11 0.37
27 19 0.63
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (27 bp):
GGCACTAAGTGTGCATGCTGGAAAATA
Found at i:40201552 original size:29 final size:29
Alignment explanation
Indices: 40201519--40201630 Score: 161
Period size: 29 Copynumber: 3.9 Consensus size: 29
40201509 GTGACGAGAT
*
40201519 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
40201548 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* *
40201577 AGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* * *
40201606 TGACACTATGTGTGCAAGCTGGAAA
1 TGGCACTAAGTGTGCATGCTGGAAA
40201631 AATACAGCAC
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:40201647 original size:29 final size:29
Alignment explanation
Indices: 40201522--40201654 Score: 97
Period size: 29 Copynumber: 4.6 Consensus size: 29
40201512 ACGAGATTGG
* ** * * *
40201522 CACTAAGTGTGCGTGCTGGAAATATATGG
1 CACTAGGTGTGCAAGCTGGAAAAATAAGA
* ** * *
40201551 CACTAAGTGTGCGTGCTGGAAATATAAGG
1 CACTAGGTGTGCAAGCTGGAAAAATAAGA
* * *
40201580 CACTAAGTGTGCATGCTGGAAAAATATGA
1 CACTAGGTGTGCAAGCTGGAAAAATAAGA
*
40201609 CACTATGTGTGCAAGCTGGAAAAATACAG-
1 CACTAGGTGTGCAAGCTGGAAAAATA-AGA
* *
40201638 CACTGGGTGTGCGAGCT
1 CACTAGGTGTGCAAGCT
40201655 CGAAGGGTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 91 0.99
30 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (29 bp):
CACTAGGTGTGCAAGCTGGAAAAATAAGA
Found at i:40204596 original size:22 final size:20
Alignment explanation
Indices: 40204538--40204596 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
40204528 ACAACTAATC
*
40204538 GAAAAAGAAGAAAATGAAGAA
1 GAAAAAGAAGAAGA-GAAGAA
*
40204559 GAAAAA-AA-CAGAGAAGAA
1 GAAAAAGAAGAAGAGAAGAA
40204577 GGGAAAAAGAAGAAGAGAAG
1 --GAAAAAGAAGAAGAGAAG
40204597 TTTGGCAGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 6 0.19
19 2 0.06
20 8 0.26
21 8 0.26
22 7 0.23
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.02
Consensus pattern (20 bp):
GAAAAAGAAGAAGAGAAGAA
Found at i:40206080 original size:33 final size:33
Alignment explanation
Indices: 40206041--40206103 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
40206031 TTCTATAGAA
40206041 AGAAGTCTGTCCTAATAGGAATGAAATGTGTAT
1 AGAAGTCTGTCCTAATAGGAATGAAATGTGTAT
40206074 AGAAGTCTGTCCTAATAGGAATGAAATGTG
1 AGAAGTCTGTCCTAATAGGAATGAAATGTG
40206104 CGGTCTTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.29
Consensus pattern (33 bp):
AGAAGTCTGTCCTAATAGGAATGAAATGTGTAT
Found at i:40212322 original size:12 final size:12
Alignment explanation
Indices: 40212305--40212337 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
40212295 CGGCCTACCC
40212305 ATATTAATTTTT
1 ATATTAATTTTT
40212317 ATATT-ATTTTT
1 ATATTAATTTTT
40212328 ATA-TAATTTT
1 ATATTAATTTT
40212338 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:40212495 original size:30 final size:30
Alignment explanation
Indices: 40212459--40212519 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
40212449 TAACTTAACA
*
40212459 AGAAAATGCCTCTAAAATAATAAAAAAATT
1 AGAAAATGACTCTAAAATAATAAAAAAATT
*
40212489 AGAAAATGACTTTAAAATAATAAAAAAATT
1 AGAAAATGACTCTAAAATAATAAAAAAATT
40212519 A
1 A
40212520 ACAGTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.25
Consensus pattern (30 bp):
AGAAAATGACTCTAAAATAATAAAAAAATT
Found at i:40213163 original size:32 final size:32
Alignment explanation
Indices: 40213117--40213177 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
40213107 GACTTAAAAA
* **
40213117 AACATATTTTTATTTTTTGAAATCTAAACTTT
1 AACAGATTTTTATTTTTCAAAATCTAAACTTT
40213149 AACAGATTTTTATTTTTCAAAATCTAAAC
1 AACAGATTTTTATTTTTCAAAATCTAAAC
40213178 CTTTTCCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (32 bp):
AACAGATTTTTATTTTTCAAAATCTAAACTTT
Found at i:40213299 original size:54 final size:54
Alignment explanation
Indices: 40213240--40213463 Score: 156
Period size: 54 Copynumber: 4.1 Consensus size: 54
40213230 TGAAGTAGTT
40213240 AAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAACTAA
1 AAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAACTAA
* * * * * *
40213294 AAAAAAAAT-AGAATTTTATTTTTCAAACA-CTAAACTTTCTCTTTTTTAAAAATAA-AAA
1 AAAAAAAATCAAAACTTT-GTTTT-AAAAATTTAAACTTTC-C---TTT-AAAATAACTAA
* * * * * * * *
40213352 ATAAAAAAAACACAA-TTT-TTCTTAAAGATTAAAACTTTTACTTTGAAAT-AGT-T
1 A-AAAAAAATCAAAACTTTGTT-TTAAAAATTTAAAC-TTTCCTTTAAAATAACTAA
* * *
40213405 GAAAAATATCAAAACTTTGTTTTAAAAATTTAAACTTCCCTTTAAAATAACTAA
1 AAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAACTAA
40213459 AAAAA
1 AAAAA
40213464 CATATTTTTA
Statistics
Matches: 126, Mismatches: 27, Indels: 34
0.67 0.14 0.18
Matches are distributed among these distances:
52 20 0.16
53 24 0.19
54 32 0.25
55 8 0.06
57 6 0.05
58 13 0.10
59 20 0.16
60 3 0.02
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.36
Consensus pattern (54 bp):
AAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAACTAA
Found at i:40213870 original size:19 final size:16
Alignment explanation
Indices: 40213846--40213904 Score: 93
Period size: 16 Copynumber: 3.8 Consensus size: 16
40213836 GTAAAAAATG
40213846 ATAATAATAGTATTTA
1 ATAATAATAGTATTTA
40213862 ATAATAATAGTATTTA
1 ATAATAATAGTATTTA
* *
40213878 ATAATAATAATA-ATA
1 ATAATAATAGTATTTA
40213893 ATAATAATAGTA
1 ATAATAATAGTA
40213905 GTGACGATAG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
15 13 0.32
16 27 0.68
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (16 bp):
ATAATAATAGTATTTA
Found at i:40213921 original size:3 final size:3
Alignment explanation
Indices: 40213846--40213901 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
40213836 GTAAAAAATG
* * * *
40213846 ATA ATA ATA GTA TTTA ATA ATA ATA GTA TTTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
40213893 ATA ATA ATA
1 ATA ATA ATA
40213902 GTAGTGACGA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
3 41 0.91
4 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:40215799 original size:35 final size:35
Alignment explanation
Indices: 40215745--40215822 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
40215735 TTGCACATCC
* *
40215745 GTATCTGTATCTGAGATGGGCTTAAGCCCGAATCT
1 GTATCTGTATCTGAAATGGGCGTAAGCCCGAATCT
* * * *
40215780 GTATTTGTATCTGAAATGGGCGTAGGCCCTAATTT
1 GTATCTGTATCTGAAATGGGCGTAAGCCCGAATCT
40215815 GTATCTGT
1 GTATCTGT
40215823 CTGATGTTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.36
Consensus pattern (35 bp):
GTATCTGTATCTGAAATGGGCGTAAGCCCGAATCT
Found at i:40216609 original size:42 final size:42
Alignment explanation
Indices: 40216448--40216902 Score: 597
Period size: 42 Copynumber: 11.0 Consensus size: 42
40216438 AAGTAAACTA
* *
40216448 GAAAAGT-ACATGGACCTCCACACCTGGGCCTCTAAA--CTA-
1 GAAAAGTGA-ATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* * * *
40216487 GAAAAGTAAACGGACCTCCACACCTGGGCCTCTAAA--CTA-
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* * *
40216526 GAAAAGTAAACGGACCT-C-CAGCTGGGTCTCTAAATGCAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* *
40216566 GAAAAGTGAATGGACCTCCACACCTAGATCTCTAAATGCAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* * *
40216608 GAAAGGTGAATGG-CATCCACACCTGGGTCTCTAGATGCAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* **
40216649 GAAAAGTGAATGGACCTCCACACCTGGGTATCTAAATATAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* * *
40216691 GAAAAGTGAATGAACCTCCACACTTAGGTCTCTAAATGCAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
*
40216733 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATACAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* *
40216775 GAAAAGTGAATGGACCTCCACACCTGGGTTTCTAGATGCAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
*
40216817 GGAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
* *
40216859 GGAAAGTAAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
1 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
40216901 GA
1 GA
40216903 TTGTTTTCCT
Statistics
Matches: 371, Mismatches: 38, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
37 14 0.04
38 1 0.00
39 55 0.15
40 16 0.04
41 37 0.10
42 248 0.67
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (42 bp):
GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
Found at i:40222382 original size:49 final size:49
Alignment explanation
Indices: 40222305--40222616 Score: 498
Period size: 49 Copynumber: 6.4 Consensus size: 49
40222295 ATCAAGATTC
* * *
40222305 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
* * *
40222354 GTGAAAATGTATGTATATGTGATAAGGCCAAATGGCCGATGTGGTGAAT
1 GTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
* *
40222403 GTGAAAGTATATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
* * *
40222452 GTGAAAGTATATGTATATGTGATAAGGCCAAATGGCCGATGTGGTGAAT
1 GTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
* *
40222501 GTGAAAGTATATGTATATGTGATAAGGCCTAATGGCCGATGTGGTGAAT
1 GTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
40222550 GTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
*
40222599 GTGAAAGTGTATATATAT
1 GTGAAAGTGTATGTATAT
40222617 ATGTGGTAAA
Statistics
Matches: 247, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 247 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
GTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
Found at i:40222740 original size:37 final size:36
Alignment explanation
Indices: 40222685--40222771 Score: 138
Period size: 37 Copynumber: 2.3 Consensus size: 36
40222675 AACTTGGAAA
40222685 TATGTTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATG-TCCGGGT-AGACCCGATGACTACGTGTGGAGAT
40222723 TATGTCCGGGTACGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTA-GACCCGATGACTACGTGTGGAGAT
*
40222760 TATGTTCGGGTA
1 TATGTCCGGGTA
40222772 AGACTTCGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.89
38 4 0.09
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (36 bp):
TATGTCCGGGTAGACCCGATGACTACGTGTGGAGAT
Found at i:40226562 original size:24 final size:24
Alignment explanation
Indices: 40226512--40226565 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
40226502 AATCGAATTT
*
40226512 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTAGTCACACTC
40226536 GCACACATAGTGCCATAGT-ACAC-C
1 GCACACATAGTG-C-TAGTCACACTC
40226560 GCACAC
1 GCACAC
40226566 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 5 0.19
26 3 0.11
ACGTcount: A:0.30, C:0.37, G:0.17, T:0.17
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCACACTC
Found at i:40234340 original size:24 final size:24
Alignment explanation
Indices: 40234290--40234343 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
40234280 AATCGAATTT
*
40234290 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTAGTCACACTC
40234314 GCACACATAGTGCCATAGT-ACAC-C
1 GCACACATAGTG-C-TAGTCACACTC
40234338 GCACAC
1 GCACAC
40234344 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 5 0.19
26 3 0.11
ACGTcount: A:0.30, C:0.37, G:0.17, T:0.17
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCACACTC
Found at i:40240347 original size:14 final size:14
Alignment explanation
Indices: 40240316--40240354 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
40240306 ATGAGTCTTC
40240316 AAAAATAAATAGAAAT
1 AAAAATAAA-A-AAAT
*
40240332 AAAAGTAAAAAAAT
1 AAAAATAAAAAAAT
40240346 AAAAATAAA
1 AAAAATAAA
40240355 GCGAGTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 1 0.05
16 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:40249394 original size:14 final size:14
Alignment explanation
Indices: 40249362--40249401 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
40249352 CACGAGTCTT
40249362 TAAAAATAAATAGAAA
1 TAAAAATAAA-A-AAA
*
40249378 TAAAAGTAAAAAAA
1 TAAAAATAAAAAAA
40249392 TAAAAATAAA
1 TAAAAATAAA
40249402 GCGAGTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
15 1 0.05
16 9 0.41
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (14 bp):
TAAAAATAAAAAAA
Found at i:40251520 original size:12 final size:12
Alignment explanation
Indices: 40251503--40251527 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40251493 ATCCATCGAA
40251503 TAAGTCTAGGTT
1 TAAGTCTAGGTT
40251515 TAAGTCTAGGTT
1 TAAGTCTAGGTT
40251527 T
1 T
40251528 TGCATAAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (12 bp):
TAAGTCTAGGTT
Found at i:40261561 original size:4 final size:4
Alignment explanation
Indices: 40261554--40261584 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
40261544 ATAAACGAAC
*
40261554 GAAT GAAT GAAT GGAT GAAT GAAT GAAT GAA
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAA
40261585 ATTGGGGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (4 bp):
GAAT
Found at i:40268475 original size:50 final size:49
Alignment explanation
Indices: 40268308--40268532 Score: 297
Period size: 49 Copynumber: 4.5 Consensus size: 49
40268298 CTGGTACGCA
* * *
40268308 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
40268357 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
** * *
40268406 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
* * * * * *
40268456 TAGTAGCCTGCACTTAGTACTACACACATGATCACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCGGTACACG
*
40268507 TAGTAGCCTGTACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
40268533 TGCGACCTCA
Statistics
Matches: 156, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 79 0.51
50 42 0.27
51 34 0.22
52 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Found at i:40268479 original size:99 final size:100
Alignment explanation
Indices: 40268295--40268539 Score: 314
Period size: 99 Copynumber: 2.5 Consensus size: 100
40268285 TAGCCAAAGC
* * * * ** *
40268295 TATCTGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACACGTAG
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAACCATCCGATACACGTAG
*
40268360 TAGCCTGCACTTAGTACTACACACGTGA-C-CAAT
66 TAGCCTGCACTTAGTACTACACACATGATCACAAT
* * *
40268393 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTA
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC-AACCATCCGATACACGTA
*
40268458 GTAGCCTGCACTTAGTACTACACACATGATCACAGT
65 GTAGCCTGCACTTAGTACTACACACATGATCACAAT
* * * * *
40268494 TTTCGGGTACGCATAGTAGCCTGTACTTAGTACTACACATGCGACC
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC
40268540 TCACAATAGA
Statistics
Matches: 125, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
98 40 0.32
99 42 0.34
100 1 0.01
101 42 0.34
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (100 bp):
TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAACCATCCGATACACGTAG
TAGCCTGCACTTAGTACTACACACATGATCACAAT
Found at i:40268540 original size:101 final size:99
Alignment explanation
Indices: 40268295--40268540 Score: 332
Period size: 101 Copynumber: 2.5 Consensus size: 99
40268285 TAGCCAAAGC
* * ** *
40268295 TATCTGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-AATTATCCGGTACACGTA
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACCATCCGATACACGTA
*
40268359 GTAGCCTGCACTTAGTACTACACACGTGACCAAT
66 GTAGCCTGCACTTAGTACTACACACATGACCAAT
* * * * *
40268393 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTA
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACCATCCGATACACGTA
*
40268458 GTAGCCTGCACTTAGTACTACACACATGATCACAGT
66 GTAGCCTGCACTTAGTACTACACACATGA-C-CAAT
* * *
40268494 TTTCGGGTACGCATAGTAGCCTGTACTTAGTACTACACATGCGACCT
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCT
40268541 CACAATAGAT
Statistics
Matches: 126, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
98 40 0.32
99 42 0.33
100 1 0.01
101 43 0.34
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (99 bp):
TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACCATCCGATACACGTA
GTAGCCTGCACTTAGTACTACACACATGACCAAT
Found at i:40271334 original size:28 final size:28
Alignment explanation
Indices: 40271261--40271334 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 28
40271251 GTTCAAATGG
* *
40271261 TATAGCACTAAGTGTGCAAGTTTGATTA
1 TATAGCACTAAGTGTGCGAGTTTGACTA
40271289 TATAGCACTAAGTGTGCGAGTTTGACTA
1 TATAGCACTAAGTGTGCGAGTTTGACTA
40271317 T-TAAGCACTAAGTGTGCG
1 TAT-AGCACTAAGTGTGCG
40271335 GGCTTATTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 1 0.02
28 42 0.98
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (28 bp):
TATAGCACTAAGTGTGCGAGTTTGACTA
Done.