Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005836.1 Hibiscus syriacus cultivar Beakdansim tig00013680_pilon, whole genome shotgun sequence
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: 991970
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:473665 original size:13 final size:13
Alignment explanation
Indices: 473646--473687 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
473636 GAACACAAAT
*
473646 AAAAATAAAATAG
1 AAAAATAAAATAA
*
473659 GAAAATAAAATAA
1 AAAAATAAAATAA
473672 AAAAATAAAATAA
1 AAAAATAAAATAA
473685 AAA
1 AAA
473688 TATATTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:473888 original size:20 final size:20
Alignment explanation
Indices: 473863--473955 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
473853 TAGTTGAAAA
*
473863 TCGCGTTACGATTTTTCATT
1 TCGCGTTGCGATTTTTCATT
473883 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTTCATT
* *** **
473903 TCGCGTTGCGATAGTAGAAAA
1 TCGCGTTGCGAT-TTTTCATT
*
473924 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTTCATT
473944 TCGCGTTGCGAT
1 TCGCGTTGCGAT
473956 AGTTGAAAGG
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTTCATT
Found at i:473915 original size:61 final size:61
Alignment explanation
Indices: 473838--473955 Score: 200
Period size: 61 Copynumber: 1.9 Consensus size: 61
473828 ATTCACGTTG
* *
473838 CATTTCGCGTTACGATAGTTGAAAATCGCGTTACGATTTTTCATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTACGATAGTAGAAAATCGCGTTACGATTTTCCATTTCGCGTTGCGATTTTT
* *
473899 CATTTCGCGTTGCGATAGTAGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
1 CATTTCGCGTTACGATAGTAGAAAATCGCGTTACGATTTTCCATTTCGCGTTGCGAT
473956 AGTTGAAAGG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (61 bp):
CATTTCGCGTTACGATAGTAGAAAATCGCGTTACGATTTTCCATTTCGCGTTGCGATTTTT
Found at i:473987 original size:84 final size:84
Alignment explanation
Indices: 473887--474047 Score: 286
Period size: 84 Copynumber: 1.9 Consensus size: 84
473877 TTCATTTCGC
* *
473887 GTTGCGATTTTTCATTTCGCGTTGCGATAGTAGAAAATCGCGTTGCGATTTTCCATTTCGCGTTG
1 GTTGCGATTTTCCATTTCGAGTTGCGATAGTAGAAAATCGCGTTGCGATTTTCCATTTCGCGTTG
473952 CGATAGTTGAAAGGCACCA
66 CGATAGTTGAAAGGCACCA
*
473971 GTTGCGATTTTCCATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTG
1 GTTGCGATTTTCCATTTCGAGTTGCGATAGTAGAAAATCGCGTTGCGATTTTCCATTTCGCGTTG
*
474036 CGTTAGTTGAAA
66 CGATAGTTGAAA
474048 ATCGCGTTGC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 73 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (84 bp):
GTTGCGATTTTCCATTTCGAGTTGCGATAGTAGAAAATCGCGTTGCGATTTTCCATTTCGCGTTG
CGATAGTTGAAAGGCACCA
Found at i:473989 original size:43 final size:41
Alignment explanation
Indices: 473883--474102 Score: 296
Period size: 41 Copynumber: 5.3 Consensus size: 41
473873 ATTTTTCATT
* *
473883 TCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTAGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
473924 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAG
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
* * *
473965 GCACCAGTTGCGATTTTCCATTTCGAGTTGCGATAGTTGAAAA
1 TC-GC-GTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
474008 TCGCGTTGCGATTTTCCATTTCGCGTTGCGTTAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
* ** **
474049 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTGAAAA
*
474091 TCGCGATGCGAT
1 TCGCGTTGCGAT
474103 AGTCTACAGT
Statistics
Matches: 158, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
41 86 0.54
42 36 0.23
43 36 0.23
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:473995 original size:20 final size:20
Alignment explanation
Indices: 473970--474037 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
473960 GAAAGGCACC
473970 AGTTGCGATTTTCCATTTCG
1 AGTTGCGATTTTCCATTTCG
* ** **
473990 AGTTGCGATAGTTGAAAATCG
1 AGTTGCGAT-TTTCCATTTCG
*
474011 CGTTGCGATTTTCCATTTCG
1 AGTTGCGATTTTCCATTTCG
*
474031 CGTTGCG
1 AGTTGCG
474038 TTAGTTGAAA
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
20 22 0.61
21 14 0.39
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
AGTTGCGATTTTCCATTTCG
Found at i:474017 original size:21 final size:21
Alignment explanation
Indices: 473842--474105 Score: 169
Period size: 21 Copynumber: 12.7 Consensus size: 21
473832 ACGTTGCATT
*
473842 TCGCGTTACGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
473863 TCGCGTTACGAT-TTTTCATT
1 TCGCGTTGCGATAGTTGAAAA
* ** **
473883 TCGCGTTGCGAT-TTTTCATT
1 TCGCGTTGCGATAGTTGAAAA
*
473903 TCGCGTTGCGATAGTAGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
473924 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
473944 TCGCGTTGCGATAGTTGAAAG
1 TCGCGTTGCGATAGTTGAAAA
* * * ** **
473965 GCACCAGTTGCGAT-TTTCCATT
1 TC-GC-GTTGCGATAGTTGAAAA
*
473987 TCGAGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
474008 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
474028 TCGCGTTGCGTTAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
474049 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
474070 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
474091 TCGCGATGCGATAGT
1 TCGCGTTGCGATAGT
474106 CTACAGTTGT
Statistics
Matches: 185, Mismatches: 52, Indels: 12
0.74 0.21 0.05
Matches are distributed among these distances:
20 70 0.38
21 102 0.55
22 5 0.03
23 8 0.04
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:474299 original size:6 final size:6
Alignment explanation
Indices: 474288--474320 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
474278 GACACGTATT
474288 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
474321 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:474866 original size:6 final size:5
Alignment explanation
Indices: 474812--474862 Score: 75
Period size: 5 Copynumber: 9.6 Consensus size: 5
474802 CCGTCTCGTC
474812 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG
474860 TCG
1 TCG
474863 TGGTAATACG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 28 0.62
6 17 0.38
ACGTcount: A:0.00, C:0.20, G:0.55, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:475007 original size:22 final size:22
Alignment explanation
Indices: 474979--475058 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 22
474969 AATTTGGAAA
474979 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
475001 ATCGCAAC-ATCGCAACGAATTTGGAAA
1 ATCGCAACGA---CAAC---TGTAGACT
475028 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
475050 ATCGCAACG
1 ATCGCAACG
475059 CGAACTGGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
21 1 0.02
22 21 0.49
24 4 0.09
25 4 0.09
27 12 0.28
28 1 0.02
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:475021 original size:49 final size:49
Alignment explanation
Indices: 474961--475057 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
474951 CAACGAATTT
*
474961 TCGCAATGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACA
475010 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAAC
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAAC
475058 GCGAACTGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (49 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACA
Found at i:475075 original size:20 final size:20
Alignment explanation
Indices: 475022--475081 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
475012 GCAACGAATT
475022 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAC
**
475042 TGTAGACTATCGCAACGCGAAC
1 TG--GAAAATCGCAACGCGAAC
475064 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
475082 TTTTCAACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 16 0.48
21 1 0.03
22 16 0.48
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.13
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAC
Found at i:475096 original size:21 final size:21
Alignment explanation
Indices: 475070--475123 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
475060 GAACTGGAAA
475070 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* *
475091 ATCGCAACGTGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
475112 ATCGCAACGCGA
1 ATCGCAACGCGA
475124 ATTTGCGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:481672 original size:44 final size:44
Alignment explanation
Indices: 481585--481685 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 44
481575 TTGGTGCATA
* *
481585 ATGCATCGATACA-CTAGACAGTGCATCGATTCATCCTTTGAAT
1 ATGCATCGATACACCTAGACAGTGCACCGATGCATCCTTTGAAT
*
481628 ATGCATCGATACACCTTGA-AGGTGCACCGATGCACTCC-TTGAAT
1 ATGCATCGATACACCTAGACA-GTGCACCGATGCA-TCCTTTGAAT
*
481672 ATGTATCGATACAC
1 ATGCATCGATACAC
481686 TCATCGGGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
43 14 0.27
44 34 0.67
45 3 0.06
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (44 bp):
ATGCATCGATACACCTAGACAGTGCACCGATGCATCCTTTGAAT
Found at i:481687 original size:23 final size:22
Alignment explanation
Indices: 481606--481684 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
481596 CACTAGACAG
*
481606 TGCATCGATTCATCCTTTGAATA
1 TGCATCGATACATCC-TTGAATA
**
481629 TGCATCGATACA-CCTTGAAGG
1 TGCATCGATACATCCTTGAATA
* *
481650 TGCACCGATGCACTCCTTGAATA
1 TGCATCGATACA-TCCTTGAATA
*
481673 TGTATCGATACA
1 TGCATCGATACA
481685 CTCATCGGGT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 15 0.34
22 2 0.05
23 27 0.61
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (22 bp):
TGCATCGATACATCCTTGAATA
Found at i:489798 original size:40 final size:40
Alignment explanation
Indices: 489752--489924 Score: 210
Period size: 40 Copynumber: 4.3 Consensus size: 40
489742 GAACTCCAAT
* *
489752 TTCGCAACGCGAATTTGT-AAATCGCAACACATAAGTCAAA
1 TTCGCAACGCGAA-TAGTCAAATCGCAACACAAAAGTCAAA
*
489792 TCCGCAACGCG-ATAGTCAAATCCGCAACACAAAAGTCAAA
1 TTCGCAACGCGAATAGTCAAAT-CGCAACACAAAAGTCAAA
* * *
489832 TTCGCAAAGCGAATTTGT-AAATCGCAACACATAAGTCAAA
1 TTCGCAACGCGAA-TAGTCAAATCGCAACACAAAAGTCAAA
* *
489872 TTCGCAATGCG-ATAGTCAAATTCGCAACACAAAAATCAAA
1 TTCGCAACGCGAATAGTCAAA-TCGCAACACAAAAGTCAAA
489912 TTCGCAACGCGAA
1 TTCGCAACGCGAA
489925 ATTTCAAATT
Statistics
Matches: 114, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
38 6 0.05
39 9 0.08
40 90 0.79
41 6 0.05
42 3 0.03
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.19
Consensus pattern (40 bp):
TTCGCAACGCGAATAGTCAAATCGCAACACAAAAGTCAAA
Found at i:489819 original size:80 final size:80
Alignment explanation
Indices: 489709--489924 Score: 301
Period size: 80 Copynumber: 2.7 Consensus size: 80
489699 AAATGACCAA
* * * * * *
489709 CAAATTCGCAACACGAT-CTCAAATTCGCAACGC-GAACTCCAATTTCGCAACGCGAATTTGTAA
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAACT-CAAATTCGCAAAGCGAATTTGTAA
489772 ATCGCAACACATAAGT
65 ATCGCAACACATAAGT
* * *
489788 CAAATCCGCAACGCGATAGTCAAATCCGCAACACAAAAGTCAAATTCGCAAAGCGAATTTGTAAA
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAACTCAAATTCGCAAAGCGAATTTGTAAA
489853 TCGCAACACATAAGT
66 TCGCAACACATAAGT
* * *
489868 CAAATTCGCAATGCGATAGTCAAATTCGCAACACAAAAATCAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAACTCAAATTCGCAAAGCGAA
489925 ATTTCAAATT
Statistics
Matches: 121, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
79 15 0.12
80 103 0.85
81 3 0.02
ACGTcount: A:0.41, C:0.26, G:0.14, T:0.19
Consensus pattern (80 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAACTCAAATTCGCAAAGCGAATTTGTAAA
TCGCAACACATAAGT
Found at i:489992 original size:20 final size:19
Alignment explanation
Indices: 489907--490017 Score: 134
Period size: 19 Copynumber: 5.7 Consensus size: 19
489897 AACACAAAAA
*
489907 TCAAATTCGCAACGCGAAATT
1 TCAAATTCGCAAC-TG-AATT
489928 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
489947 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
489966 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
* *
489986 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
490006 T-AATTTCGCAAC
1 TCAAATTCGCAAC
490018 AGGTTTTAGT
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
19 46 0.57
20 22 0.27
21 13 0.16
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.30
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:490014 original size:39 final size:38
Alignment explanation
Indices: 489907--490017 Score: 143
Period size: 39 Copynumber: 2.8 Consensus size: 38
489897 AACACAAAAA
489907 TCAAATTCGCAACGCGAAATTTCAAATTCGCAACTGAATT
1 TCAAATTCGCAAC-CG-AATTTCAAATTCGCAACTGAATT
* *
489947 TCAAATTCGCAACTGAATTTCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACCGAATTTCAAATTCGCAACT-GAATT
* *
489986 TCGAATTCGCAACACGAATTT-AATTTCGCAAC
1 TCAAATTCGCAAC-CGAATTTCAAATTCGCAAC
490018 AGGTTTTAGT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
38 18 0.28
39 27 0.42
40 19 0.30
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.30
Consensus pattern (38 bp):
TCAAATTCGCAACCGAATTTCAAATTCGCAACTGAATT
Found at i:490015 original size:19 final size:20
Alignment explanation
Indices: 489709--490018 Score: 176
Period size: 20 Copynumber: 15.7 Consensus size: 20
489699 AAATGACCAA
*
489709 CAAATTCGCAACACG-ATCT
1 CAAATTCGCAACACGAATTT
* * *
489728 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACACGAATTT
* *
489748 CAATTTCGCAACGCGAATTT
1 CAAATTCGCAACACGAATTT
* **
489768 GTAAA-TCGCAACAC-ATAAGT
1 -CAAATTCGCAACACGA-ATTT
* * *
489788 CAAATCCGCAACGCG-ATAGT
1 CAAATTCGCAACACGAAT-TT
* * **
489808 CAAATCCGCAACACAAAAGT
1 CAAATTCGCAACACGAATTT
489828 CAAATTCGCAA-AGCGAATTT
1 CAAATTCGCAACA-CGAATTT
* **
489848 GTAAA-TCGCAACAC-ATAAGT
1 -CAAATTCGCAACACGA-ATTT
** *
489868 CAAATTCGCAATGCG-ATAGT
1 CAAATTCGCAACACGAAT-TT
* **
489888 CAAATTCGCAACACAAAAAT
1 CAAATTCGCAACACGAATTT
*
489908 CAAATTCGCAACGCGAAATTT
1 CAAATTCGCAACACG-AATTT
*
489929 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
*
489948 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
*
489967 CAAATTCGCAACTA-GATTTT
1 CAAATTCGCAAC-ACGAATTT
*
489987 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
490007 -AATTTCGCAACA
1 CAAATTCGCAACA
490019 GGTTTTAGTT
Statistics
Matches: 227, Mismatches: 45, Indels: 38
0.73 0.15 0.12
Matches are distributed among these distances:
19 72 0.32
20 132 0.58
21 23 0.10
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:490191 original size:34 final size:34
Alignment explanation
Indices: 490143--490211 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
490133 CGACATTCGT
490143 TCCTATATCCAACGACATCCTTCCCCATCTCTAA
1 TCCTATATCCAACGACATCCTTCCCCATCTCTAA
*
490177 TCCTATATCTAACGACATCCTTCCCCATCTCTAA
1 TCCTATATCCAACGACATCCTTCCCCATCTCTAA
490211 T
1 T
490212 TTTTTTACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.39, G:0.03, T:0.32
Consensus pattern (34 bp):
TCCTATATCCAACGACATCCTTCCCCATCTCTAA
Found at i:493807 original size:66 final size:65
Alignment explanation
Indices: 493725--493900 Score: 257
Period size: 66 Copynumber: 2.6 Consensus size: 65
493715 AATTTAAAAC
493725 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATT
493790 A
65 A
* *
493791 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
493855 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAAA
493901 GTGTACCCCA
Statistics
Matches: 101, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
64 16 0.16
65 25 0.25
66 34 0.34
68 4 0.04
69 16 0.16
70 6 0.06
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:495309 original size:20 final size:22
Alignment explanation
Indices: 495286--495333 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
495276 GGCTTCTACG
495286 ATGATGA-GAGG-GCCTCTTGA
1 ATGATGAGGAGGCGCCTCTTGA
495306 ATGAT-AGGAGGCGCCTCTTGA
1 ATGATGAGGAGGCGCCTCTTGA
495327 ATGATGA
1 ATGATGA
495334 TAGGTGCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.04
20 9 0.36
21 14 0.56
22 1 0.04
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (22 bp):
ATGATGAGGAGGCGCCTCTTGA
Found at i:495767 original size:21 final size:21
Alignment explanation
Indices: 495741--495790 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
495731 ACCATTATCT
* *
495741 TCACGTAAAGTACCGATCTCA
1 TCACGTAAAGCACCGACCTCA
*
495762 TGACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
495783 TCACGTAA
1 TCACGTAA
495791 CTCCCCTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:497935 original size:22 final size:22
Alignment explanation
Indices: 497908--497958 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
497898 GATGGAGATA
*
497908 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCACCGAAGATGGG
**
497930 GACGGATTTCGTCGAAGATGGG
1 GACGGATTTCACCGAAGATGGG
497952 GACGGAT
1 GACGGAT
497959 GTCGCCGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.41, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGAAGATGGG
Found at i:498203 original size:20 final size:20
Alignment explanation
Indices: 498065--498208 Score: 184
Period size: 20 Copynumber: 7.2 Consensus size: 20
498055 AATTAATAAC
498065 GCGAATTTGACTATC-TCGTT
1 GCGAATTTGACTATCGT-GTT
*
498085 GCGAATTTGACTATCGCGTT
1 GCGAATTTGACTATCGTGTT
*
498105 GCGAATTTGACTATCGCGTT
1 GCGAATTTGACTATCGTGTT
* *
498125 GCGAATTTGACTTTTGTGTT
1 GCGAATTTGACTATCGTGTT
* *
498145 GCGAATTTGACTTTTGTGTT
1 GCGAATTTGACTATCGTGTT
*
498165 ACGAATTTGACTATCGTGTT
1 GCGAATTTGACTATCGTGTT
*
498185 GCGAATTTAACT-TCTGTGTT
1 GCGAATTTGACTATC-GTGTT
498205 GCGA
1 GCGA
498209 TTTACAGATT
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
19 2 0.02
20 111 0.98
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (20 bp):
GCGAATTTGACTATCGTGTT
Found at i:498225 original size:20 final size:20
Alignment explanation
Indices: 498202--498248 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
498192 TAACTTCTGT
*
498202 GTTGCGATTTACAGATTTAC
1 GTTGCGATTTACAGATTCAC
*
498222 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCAC
498242 GTTGCGA
1 GTTGCGA
498249 ATTTGGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCAC
Found at i:499403 original size:22 final size:22
Alignment explanation
Indices: 499375--499439 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
499365 ATTATTTAGC
499375 GTTGAATATAGAACTGTTCAGT
1 GTTGAATATAGAACTGTTCAGT
* *
499397 GTTGAATATA-AAATCGTTCAAT
1 GTTGAATATAGAACT-GTTCAGT
*
499419 GTTGAATATAGAACCGTTCAG
1 GTTGAATATAGAACTGTTCAG
499440 CATTTAGCGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 3 0.08
22 31 0.86
23 2 0.06
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (22 bp):
GTTGAATATAGAACTGTTCAGT
Found at i:503153 original size:3 final size:3
Alignment explanation
Indices: 503145--503225 Score: 89
Period size: 3 Copynumber: 27.7 Consensus size: 3
503135 TACGAAAATA
*
503145 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAG
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* *
503191 AAC AAT AAAG AAT AA- AAT AA- AAT AA- AAT AA- AAT AA
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
503226 ATGTTTTCAA
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
2 8 0.12
3 55 0.82
4 4 0.06
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:503298 original size:31 final size:31
Alignment explanation
Indices: 503241--503304 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
503231 TTCAAAACCT
* *
503241 TATTTCAAAAAATGTTTTTTTCAAAATAATA
1 TATTTCAAAAAATGATTTTTTAAAAATAATA
*
503272 TATTTCCAAAAAAT-ATTTTTTAAAAATTATA
1 TATTT-CAAAAAATGATTTTTTAAAAATAATA
503303 TA
1 TA
503305 ATATATGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 21 0.72
32 8 0.28
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (31 bp):
TATTTCAAAAAATGATTTTTTAAAAATAATA
Found at i:503417 original size:38 final size:37
Alignment explanation
Indices: 503281--503545 Score: 160
Period size: 37 Copynumber: 7.6 Consensus size: 37
503271 ATATTTCCAA
* * * *
503281 AAAATATTTTTTAAAAATTATATAATATATGT-TTTTT
1 AAAATA-TTTTCAAAAACTATATAATATATATATTTTC
* * * * *
503318 TAAATGTTTTCAAAAACTATATAATATATGTTTTTTA
1 AAAATATTTTCAAAAACTATATAATATATATATTTTC
* *
503355 AAAATGTTTTCAAAAACTATATATTATATATATTTTC
1 AAAATATTTTCAAAAACTATATAATATATATATTTTC
*
503392 AAAATATTTTCAAAAA--AT-T-GTATAT-TA---T-
1 AAAATATTTTCAAAAACTATATAATATATATATTTTC
* * *
503420 -ATATATTTTCAAAAACTATATATTATATATGTTTTC
1 AAAATATTTTCAAAAACTATATAATATATATATTTTC
*
503456 AAAACTA---T--ATAA-TATAT-ATATATATA--TTC
1 AAAA-TATTTTCAAAAACTATATAATATATATATTTTC
* *
503485 AAAATATTTTC-AAAACTGTATATATATATATATATTC
1 AAAATATTTTCAAAAACTATATA-ATATATATATTTTC
503522 GAAAATCATTTTCTAAAAA-TATAT
1 -AAAAT-ATTTTC-AAAAACTATAT
503546 TTTTTAAAAA
Statistics
Matches: 181, Mismatches: 22, Indels: 47
0.72 0.09 0.19
Matches are distributed among these distances:
27 14 0.08
28 2 0.01
29 10 0.06
30 1 0.01
31 13 0.07
32 11 0.06
33 12 0.07
34 1 0.01
35 13 0.07
36 23 0.13
37 60 0.33
38 7 0.04
39 6 0.03
40 4 0.02
41 4 0.02
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (37 bp):
AAAATATTTTCAAAAACTATATAATATATATATTTTC
Found at i:503433 original size:64 final size:65
Alignment explanation
Indices: 503355--503567 Score: 211
Period size: 64 Copynumber: 3.2 Consensus size: 65
503345 ATGTTTTTTA
* *
503355 AAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAAAT-TGTATATT-
1 AAAATATTTTCAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAAATATATATATTC
* * * *
503418 ATATATATTTTCAAAAACTATATATTATATATGTTTTCAAAACTA-TAT-AATATATATATATAT
1 A-AAATATTTTCAAAAACTATATATTATATATATTTTCAAAA-TATTTTCAA-A-AAATATATAT
503481 ATTC
62 ATTC
* * * * *
503485 AAAATATTTTC-AAAACTGTATATATATATATATATTCGAAAATCATTTTCTAAAAATATATTTT
1 AAAATATTTTCAAAAACTATATAT-TATATATATTTTC-AAAAT-ATTTTCAAAAAATATATATA
*
503549 TTA
63 TTC
*
503552 AAAACATTTTCAAAAA
1 AAAATATTTTCAAAAA
503568 ATTAAACTAT
Statistics
Matches: 121, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
63 3 0.02
64 40 0.33
65 16 0.13
66 28 0.23
67 26 0.21
68 7 0.06
69 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (65 bp):
AAAATATTTTCAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAAATATATATATTC
Found at i:503441 original size:26 final size:26
Alignment explanation
Indices: 503395--503476 Score: 112
Period size: 26 Copynumber: 3.2 Consensus size: 26
503385 TATTTTCAAA
* *
503395 ATATTTTCAAAAAATTGTATATTATAT
1 ATATTTTC-AAAAACTATATATTATAT
503422 ATATTTTCAAAAACTATATATTATAT
1 ATATTTTCAAAAACTATATATTATAT
* *
503448 ATGTTTTC-AAAACTATATAATATAT
1 ATATTTTCAAAAACTATATATTATAT
503473 ATAT
1 ATAT
503477 ATATATTCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
25 19 0.38
26 23 0.46
27 8 0.16
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (26 bp):
ATATTTTCAAAAACTATATATTATAT
Found at i:503543 original size:28 final size:28
Alignment explanation
Indices: 503512--503569 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
503502 GTATATATAT
* *
503512 ATATATATTCGAAAATCATTTTCTAAAA
1 ATATATATTCGAAAAACATTTTCAAAAA
* **
503540 ATATATTTTTTAAAAACATTTTCAAAAA
1 ATATATATTCGAAAAACATTTTCAAAAA
503568 AT
1 AT
503570 TAAACTATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (28 bp):
ATATATATTCGAAAAACATTTTCAAAAA
Found at i:504218 original size:34 final size:34
Alignment explanation
Indices: 504147--504237 Score: 139
Period size: 34 Copynumber: 2.6 Consensus size: 34
504137 GAGGGTCTTG
504147 GTGTTTCAAGAGAAACATTTCAAAGGTTTTTTTTT
1 GTGTTTCAAGAGAAACATTTCAAAGG-TTTTTTTT
*
504182 GTGTTTCAAGATAAACGATTTCAAAGG-TTTTTTT
1 GTGTTTCAAGAGAAAC-ATTTCAAAGGTTTTTTTT
504216 GTGTTTCAAGAGAAACTATTTC
1 GTGTTTCAAGAGAAAC-ATTTC
504238 CAGGGAGGCA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
34 27 0.52
35 15 0.29
36 10 0.19
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.43
Consensus pattern (34 bp):
GTGTTTCAAGAGAAACATTTCAAAGGTTTTTTTT
Found at i:504370 original size:36 final size:36
Alignment explanation
Indices: 504284--504534 Score: 279
Period size: 36 Copynumber: 7.1 Consensus size: 36
504274 CAAAAATTGG
*
504284 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
504319 TGTTTCAAGGGAAACTGTCTGAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
504355 TGTTTCAAGAAAAACTGTCTCAAGGGAGACAAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATT
* * * *
504392 AGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
504428 TGTTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
504457 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
504493 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
504530 TGTTT
1 TGTTT
504535 TGAGTAAATT
Statistics
Matches: 181, Mismatches: 21, Indels: 26
0.79 0.09 0.11
Matches are distributed among these distances:
28 2 0.01
29 18 0.10
30 2 0.01
31 1 0.01
32 2 0.01
33 2 0.01
35 30 0.17
36 83 0.46
37 41 0.23
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:504550 original size:37 final size:35
Alignment explanation
Indices: 504455--504561 Score: 126
Period size: 36 Copynumber: 2.9 Consensus size: 35
504445 ATTCAAAGAT
* *
504455 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTT-AAGAGAAATTGTCTCAAGAGAGACAAAA
504491 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTT-AAGAGAAATTGTCTCAAGAGAGACAAAA
* *
504527 CTTTGTTT-TGAGTAAATTAGTCTCAAGCGAGACAA
1 -TTTGTTTAAGAG-AAATT-GTCTCAAGAGAGACAA
504562 CCCCTTTGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
35 3 0.05
36 39 0.61
37 22 0.34
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (35 bp):
TTTGTTTAAGAGAAATTGTCTCAAGAGAGACAAAA
Found at i:508669 original size:4 final size:4
Alignment explanation
Indices: 508660--508685 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
508650 GGAAAATAAT
508660 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
508686 AATATATAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:509948 original size:15 final size:15
Alignment explanation
Indices: 509920--509963 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
509910 ATACGAAAAT
* *
509920 AAATAATAAGAATAA
1 AAATAAAAAAAATAA
* *
509935 TAATAAAATAAATAA
1 AAATAAAAAAAATAA
509950 AAATAAAAAAAATA
1 AAATAAAAAAAATA
509964 TTTTCAAAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (15 bp):
AAATAAAAAAAATAA
Found at i:509963 original size:24 final size:24
Alignment explanation
Indices: 509915--509963 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
509905 AAAAAATACG
* * *
509915 AAAATAAATAATAAGAATAATAAT
1 AAAATAAATAAAAAGAAAAAAAAT
*
509939 AAAATAAATAAAAATAAAAAAAAT
1 AAAATAAATAAAAAGAAAAAAAAT
509963 A
1 A
509964 TTTTCAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (24 bp):
AAAATAAATAAAAAGAAAAAAAAT
Found at i:509995 original size:14 final size:14
Alignment explanation
Indices: 509956--510010 Score: 60
Period size: 13 Copynumber: 4.0 Consensus size: 14
509946 ATAAAAATAA
509956 AAAAAATAT-TTTC
1 AAAAAATATATTTC
**
509969 AAAACCT-TATTTC
1 AAAAAATATATTTC
*
509982 AAAAAATATTTTTC
1 AAAAAATATATTTC
509996 AAAATAATATATTTC
1 AAAA-AATATATTTC
510011 CAAATTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
12 1 0.03
13 14 0.42
14 9 0.27
15 9 0.27
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAAAATATATTTC
Found at i:510004 original size:15 final size:15
Alignment explanation
Indices: 509976--510015 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
509966 TTCAAAACCT
509976 TATTTCAAAA-AATA
1 TATTTCAAAATAATA
*
509990 TTTTTCAAAATAATA
1 TATTTCAAAATAATA
*
510005 TATTTCCAAAT
1 TATTTCAAAAT
510016 TTTTTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (15 bp):
TATTTCAAAATAATA
Found at i:510082 original size:37 final size:37
Alignment explanation
Indices: 510027--510262 Score: 167
Period size: 37 Copynumber: 6.6 Consensus size: 37
510017 TTTTTTTAAT
* * * *
510027 AAACGATATAATATATGTTTTTTTAAAATGTTTTCAA
1 AAACTATATAATATATATATTTTCAAAATGTTTTCAA
*
510064 AAACTATAT-A-ATATAT-GTTT-----T-TTTT-AA
1 AAACTATATAATATATATATTTTCAAAATGTTTTCAA
* * * *
510091 AAACTATATATTATGTATATTTTAAAAATATTTTCAA
1 AAACTATATAATATATATATTTTCAAAATGTTTTCAA
* *
510128 AAACGATATATTATATATATTTTCAAAA-GCATTTTCAA
1 AAACTATATAATATATATATTTTCAAAATG--TTTTCAA
* *
510166 AAACTATATATTATATATGTTTTCAAAA-GTTTTC-A
1 AAACTATATAATATATATATTTTCAAAATGTTTTCAA
* *
510201 AAACTATATAATATATATATATATTTTCGAAATATTTTC-A
1 AAAC--TAT-ATA-ATATATATATTTTCAAAATGTTTTCAA
*
510241 AAACTGTATATATATATATATT
1 AAACTATATA-ATATATATATT
510263 CGAAAACCAT
Statistics
Matches: 165, Mismatches: 17, Indels: 34
0.76 0.08 0.16
Matches are distributed among these distances:
27 11 0.07
28 4 0.02
29 6 0.04
30 3 0.02
34 3 0.02
35 11 0.07
36 10 0.06
37 53 0.32
38 39 0.24
39 15 0.09
40 10 0.06
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (37 bp):
AAACTATATAATATATATATTTTCAAAATGTTTTCAA
Found at i:510098 original size:25 final size:25
Alignment explanation
Indices: 510057--510118 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
510047 TTTTAAAATG
* *
510057 TTTTCAAAAACTATATAATATATGTTTT
1 TTTT-AAAAACTATAT-AT-TATGTATA
510085 TTTTAAAAACTATATATTATGTATA
1 TTTTAAAAACTATATATTATGTATA
510110 TTTTAAAAA
1 TTTTAAAAA
510119 TATTTTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 15 0.47
26 2 0.06
27 11 0.34
28 4 0.12
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (25 bp):
TTTTAAAAACTATATATTATGTATA
Found at i:510119 original size:64 final size:63
Alignment explanation
Indices: 510016--510218 Score: 178
Period size: 64 Copynumber: 3.0 Consensus size: 63
510006 ATTTCCAAAT
* *
510016 TTTTTTTTAATAAACGATATAATATATGT-TTTTTTAAAATGTTTTCAAAAACTATATAATATAT
1 TTTTTTTTAA-AAACTATAT-AT-TATGTATTTTTAAAAATGTTTTCAAAAACTATATAATATAT
*
510080 G
63 A
* *
510081 TTTTTTTTAAAAACTATATATTATGTATATTTTAAAAATATTTTCAAAAACGATATATTATATAT
1 TTTTTTTTAAAAACTATATATTATGTAT-TTTTAAAAATGTTTTCAAAAAC--TATATAATATAT
510146 A
63 A
* *
510147 TTTTCAAAAGCATTTTCAAAAACTATATATTATATATGTTTTCAAAA-GTTTTC-AAAACTATAT
1 TTTT--------TTTT-AAAAACTATATATTATGTAT-TTTTAAAAATGTTTTCAAAAACTATAT
510210 AATATATA
56 AATATATA
510218 T
1 T
510219 ATATATTTTC
Statistics
Matches: 115, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
62 5 0.04
63 3 0.03
64 28 0.24
65 10 0.09
66 15 0.13
71 13 0.11
73 5 0.04
74 9 0.08
75 27 0.23
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (63 bp):
TTTTTTTTAAAAACTATATATTATGTATTTTTAAAAATGTTTTCAAAAACTATATAATATATA
Found at i:510218 original size:75 final size:76
Alignment explanation
Indices: 510084--510262 Score: 206
Period size: 75 Copynumber: 2.4 Consensus size: 76
510074 ATATATGTTT
* *
510084 TTTTTAAAAACTATATATTATGTATATTTTAAAAATATTTTCAAAAACG--ATATATTATATATA
1 TTTTCAAAAACTATATATTATATATATTTTAAAAATATTTTCAAAAACGATATATATTATATATA
510147 TTTTCAAAAGCA
66 TTTTCAAAA-CA
* * * *
510159 TTTTCAAAAACTATATATTATATATGTTTTCAAAA-GTTTTC-AAAACTATATAATATATATATA
1 TTTTCAAAAACTATATATTATATATATTTTAAAAATATTTTCAAAAACGATAT-ATAT-TATATA
* *
510222 TATTTTCGAAATA
64 TATTTTCAAAACA
*
510235 TTTTC-AAAACTGTATATATATATATATT
1 TTTTCAAAAACTATATAT-TATATATATT
510263 CGAAAACCAT
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
73 5 0.06
74 5 0.06
75 44 0.49
76 19 0.21
77 16 0.18
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (76 bp):
TTTTCAAAAACTATATATTATATATATTTTAAAAATATTTTCAAAAACGATATATATTATATATA
TTTTCAAAACA
Found at i:510275 original size:37 final size:36
Alignment explanation
Indices: 510084--510282 Score: 152
Period size: 37 Copynumber: 5.3 Consensus size: 36
510074 ATATATGTTT
* * * * *
510084 TTTTTAAAAACTATATATTATGTATATTTTAAAAATA
1 TTTTCAAAAACTATATA-TATATATATATTCAAAACA
* *
510121 TTTTCAAAAACGATATATTATATATATTTTCAAAAGCA
1 TTTTCAAAAACTATATA-TATATATATATTCAAAA-CA
* * *
510159 TTTTCAAAAACTATATATTATATATGTTTTCAAAA-G
1 TTTTCAAAAACTATATA-TATATATATATTCAAAACA
* *
510195 TTTTC-AAAACTATATAATATATATATATATTTTCGAAATA
1 TTTTCAAAAAC--TAT-ATATATATATATA--TTCAAAACA
*
510235 TTTTC-AAAACTGTATATATATATATATTCGAAAACCA
1 TTTTCAAAAACTATATATATATATATATTC-AAAA-CA
510272 TTTTCTAAAAA
1 TTTTC-AAAAA
510283 TTATTGTTTT
Statistics
Matches: 136, Mismatches: 15, Indels: 20
0.80 0.09 0.12
Matches are distributed among these distances:
35 8 0.06
36 8 0.06
37 61 0.45
38 39 0.29
39 10 0.07
40 10 0.07
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (36 bp):
TTTTCAAAAACTATATATATATATATATTCAAAACA
Found at i:511466 original size:2 final size:2
Alignment explanation
Indices: 511459--511492 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
511449 CTTCTAAACA
511459 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
511493 TTTAAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:512865 original size:2 final size:2
Alignment explanation
Indices: 512858--512923 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
512848 ATCATATCTC
512858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
512900 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
512924 GATTCACTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:514792 original size:20 final size:19
Alignment explanation
Indices: 514749--515100 Score: 228
Period size: 20 Copynumber: 17.5 Consensus size: 19
514739 AATGACCAAC
514749 AAATCGCAACGCGATATC-A
1 AAATCGCAACGCGAT-TCAA
*
514768 AAATCGCAACGCGATTTAGA
1 AAATCGCAACGCGATTCA-A
* **
514788 AAATCGCAACGTTGA-AAAGA
1 AAATCGCAACG-CGATTCA-A
514808 AAATCGCAACG-G--TCAAAAGA
1 AAATCGCAACGCGATTC---A-A
514828 AAATCGCAACGCGATCTTCCAA
1 AAATCGCAACGCGA--TT-CAA
* * **
514850 GAATCGCAATGCGAGCCAA
1 AAATCGCAACGCGATTCAA
* **
514869 AGAATCGCAATGCGAGCCAA
1 A-AATCGCAACGCGATTCAA
*
514889 AGAATCGCAATGCGATTCCAA
1 A-AATCGCAACGCGATT-CAA
* *
514910 GAATCGCAATGCGATCTTCGAA
1 AAATCGCAACGCGA--TTC-AA
* *
514932 GAATCGCAATGCGATTCAA
1 AAATCGCAACGCGATTCAA
*
514951 AGAATCGCAACGCGATTGAGA
1 A-AATCGCAACGCGATTCA-A
514972 AAATCGCAACGCGATTCCAA
1 AAATCGCAACGCGATT-CAA
* *
514992 TAATCGCAACGCGATTGAGA
1 AAATCGCAACGCGATTCA-A
515012 AAATCGCAACGCGATTCCAA
1 AAATCGCAACGCGATT-CAA
*
515032 GAATCGCAACGCGATTCCAA
1 AAATCGCAACGCGATT-CAA
* *
515052 GAATCGCAACGCGATTGAGA
1 AAATCGCAACGCGATTCA-A
*
515072 AAATCGCAATGCGATTCCAA
1 AAATCGCAACGCGATT-CAA
*
515092 GAATCGCAA
1 AAATCGCAA
515101 AACGGCAAAA
Statistics
Matches: 281, Mismatches: 28, Indels: 47
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.01
19 22 0.08
20 211 0.75
21 12 0.04
22 31 0.11
23 1 0.00
25 1 0.00
26 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (19 bp):
AAATCGCAACGCGATTCAA
Found at i:514988 original size:40 final size:40
Alignment explanation
Indices: 514750--515088 Score: 252
Period size: 40 Copynumber: 8.4 Consensus size: 40
514740 ATGACCAACA
*
514750 AATCGCAACGCGATATC--AAAATCGCAACGCGATTTAGAA-
1 AATCGCAACGCGAT-TCAGAAAATCGCAACGCGATTCA-AAG
* **
514789 AATCGCAACGTTGA-AAAGAAAATCGCAACG-G--TCAAAAG
1 AATCGCAACG-CGATTCAGAAAATCGCAACGCGATTC-AAAG
* * **
514827 AAAATCGCAACGCGATCTTCCA-AGAATCGCAATGCGAGCCAAAG
1 --AATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTCAAAG
* ** * *
514871 AATCGCAATGCGAGCCA-AAGAATCGCAATGCGATTCCAAG
1 AATCGCAACGCGATTCAGAA-AATCGCAACGCGATTCAAAG
* *
514911 AATCGCAATGCGATCTTC-GAAGAATCGCAATGCGATTCAAAG
1 AATCGCAACGCGA--TTCAGAA-AATCGCAACGCGATTCAAAG
* * *
514953 AATCGCAACGCGATTGAGAAAATCGCAACGCGATTCCAAT
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAAAG
* *
514993 AATCGCAACGCGATTGAGAAAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAAAG
* *
515033 AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTGAGAA-
1 AATCGCAACGCGATT-CAGAAAATCGCAACGCGATTCA-AAG
*
515073 AATCGCAATGCGATTC
1 AATCGCAACGCGATTC
515089 CAAGAATCGC
Statistics
Matches: 248, Mismatches: 31, Indels: 42
0.77 0.10 0.13
Matches are distributed among these distances:
37 3 0.01
38 1 0.00
39 17 0.07
40 157 0.63
41 6 0.02
42 57 0.23
43 2 0.01
44 4 0.02
45 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.17
Consensus pattern (40 bp):
AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAAAG
Found at i:515022 original size:60 final size:60
Alignment explanation
Indices: 514825--515100 Score: 290
Period size: 60 Copynumber: 4.5 Consensus size: 60
514815 AACGGTCAAA
* * * * ***
514825 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGA-GCCAAAGAATCGCAATGCGAGCC
1 AGAAAATCGCAACGCGA--TTCCAAAAATCGCAACGCGATTCC-AAGAATCGCAACGCGATTG
* * * * * *
514887 A-AAGAATCGCAATGCGATTCCAAGAATCGCAATGCGATCTTCGAAGAATCGCAATGCGATTC
1 AGAA-AATCGCAACGCGATTCCAAAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTG
* *
514949 A-AAGAATCGCAACGCGATT-GAGAAAATCGCAACGCGATTCCAATAATCGCAACGCGATTG
1 AGAA-AATCGCAACGCGATTCCA-AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTG
*
515009 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGATTCCAAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTG
* *
515069 AGAAAATCGCAATGCGATTCCAAGAATCGCAA
1 AGAAAATCGCAACGCGATTCCAAAAATCGCAA
515101 AACGGCAAAA
Statistics
Matches: 190, Mismatches: 17, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
60 122 0.64
61 6 0.03
62 61 0.32
63 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (60 bp):
AGAAAATCGCAACGCGATTCCAAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTG
Found at i:515089 original size:40 final size:40
Alignment explanation
Indices: 514827--515100 Score: 263
Period size: 40 Copynumber: 6.8 Consensus size: 40
514817 CGGTCAAAAG
* *
514827 AAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGA-GCCA
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCCA
* * *
514868 AAGAATCGCAATGCGA-GCCAAAGAATCGCAATGCGATTCCA
1 AA-AATCGCAACGCGATTCC-AAGAATCGCAACGCGATTCCA
* * * *
514909 AGAATCGCAATGCGATCTTCGAAGAATCGCAATGCGATT-CA
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCCA
* *
514950 AAGAATCGCAACGCGATT-GAGAAAATCGCAACGCGATTCCA
1 AA-AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTCCA
* * *
514991 ATAATCGCAACGCGATT-GAGAAAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTCCA-AGAATCGCAACGCGATTCCA
* *
515031 AGAATCGCAACGCGATTCCAAGAATCGCAACGCGATT-GA
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCA
*
515070 GAAAATCGCAATGCGATTCCAAGAATCGCAA
1 -AAAATCGCAACGCGATTCCAAGAATCGCAA
515101 AACGGCAAAA
Statistics
Matches: 205, Mismatches: 17, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
39 5 0.02
40 144 0.70
41 13 0.06
42 42 0.20
43 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCA
Found at i:515222 original size:6 final size:6
Alignment explanation
Indices: 515211--515242 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
515201 GACACGTATT
515211 ACCACG ACCACG ACCACG ACCACG A-CACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
515243 CGAGACGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:516008 original size:6 final size:6
Alignment explanation
Indices: 515997--516023 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
515987 TCTCGTCTCG
515997 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
516024 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:516159 original size:20 final size:20
Alignment explanation
Indices: 516134--516263 Score: 138
Period size: 20 Copynumber: 6.4 Consensus size: 20
516124 TTTTGCCGTT
516134 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
** *
516154 TTGCGATT-TTCTCAATCGCA
1 TTGCGATTCTT-GGAATCGCG
*
516174 TTGCGATTCCTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
516194 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
* *
516214 TTGCGATTCTTTGAATCGCA
1 TTGCGATTCTTGGAATCGCG
516234 TTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTGG-A-ATCGCG
516256 TTGCGATT
1 TTGCGATT
516264 TTCTTTTGAC
Statistics
Matches: 90, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.03
20 70 0.78
21 4 0.04
22 13 0.14
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTTGGAATCGCG
Found at i:516181 original size:40 final size:40
Alignment explanation
Indices: 516134--516241 Score: 180
Period size: 40 Copynumber: 2.7 Consensus size: 40
516124 TTTTGCCGTT
516134 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
* *
516174 TTGCGATTCCTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
* *
516214 TTGCGATTCTTTGAATCGCATTGCGATT
1 TTGCGATTCTTGGAATCGCGTTGCGATT
516242 CTTGGAAGAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (40 bp):
TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
Found at i:516231 original size:60 final size:62
Alignment explanation
Indices: 516147--516267 Score: 194
Period size: 60 Copynumber: 2.0 Consensus size: 62
516137 CGATTCTTGG
516147 AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGG-A-ATCGCGTTGCGATTTTCTC
1 AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCTC
* *
516207 AATCGCGTTGCGATTCTT-TGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT
1 AATCGCGTTGCGATT-TTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCT
516268 TTTGACCGTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
60 35 0.62
61 3 0.05
62 18 0.32
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.37
Consensus pattern (62 bp):
AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCTC
Found at i:516319 original size:20 final size:19
Alignment explanation
Indices: 516147--516325 Score: 121
Period size: 20 Copynumber: 8.9 Consensus size: 19
516137 CGATTCTTGG
516147 AATCGCGTTGCGATTTTCT
1 AATCGCGTTGCGATTTTCT
* *
516166 CAATCGCATTGCGA-TTCCT
1 -AATCGCGTTGCGATTTTCT
516185 GGAATCGCGTTGCGATTTTCT
1 --AATCGCGTTGCGATTTTCT
516206 CAATCGCGTTGCGATTCTT-T
1 -AATCGCGTTGCGATT-TTCT
* **
516226 GAATCGCATTGCGATTCTTGGA
1 -AATCGCGTTGCGATT-TT-CT
516248 AGATCGCGTTGCGATTTTCT
1 A-ATCGCGTTGCGATTTTCT
* *
516268 -TTTGACCGTTGCGATTTTCT
1 AATCG--CGTTGCGATTTTCT
** * *
516288 TTTCAACATTGCGATTTTCT
1 AATC-GCGTTGCGATTTTCT
516308 AAATCGCGTTGCGATTTT
1 -AATCGCGTTGCGATTTT
516326 TGTTTCGCAT
Statistics
Matches: 127, Mismatches: 21, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
18 2 0.02
19 4 0.03
20 95 0.75
21 13 0.10
22 13 0.10
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.40
Consensus pattern (19 bp):
AATCGCGTTGCGATTTTCT
Found at i:516792 original size:131 final size:130
Alignment explanation
Indices: 516631--516998 Score: 376
Period size: 131 Copynumber: 2.8 Consensus size: 130
516621 TAATTTTAAG
* * * * * *
516631 AGTGAAAATGATAATATCTAATTATTTCCAATCAAGAATAAATGATCTTTCGTGCATTAAAACAA
1 AGTGAAAATGACAATATCTAATTATTTCCAATCGAGAATAAATGATCTCTCATGCCTTAAAGCAA
* * * * *
516696 TCATTTATTACCCCAATTGAAATAAATAGATATTATTATTTCGTCTTAAAATTCAATATCGATTC
66 TCATTTATTACTCCAATTGAAATAAA-AGATATTATTATTCCATCTTAAAAATCAATATCAATTC
516761 A
130 A
* * * * * * * *
516762 AGTGGAAATGACAATACCTAATGACTTCCAATTGATAATAAATGATCTCTCATACCTTAAAGCAG
1 AGTGAAAATGACAATATCTAATTATTTCCAATCGAGAATAAATGATCTCTCATGCCTTAAAGCAA
** * * * * * *
516827 TCATTTATTGGTTCAATCGAAATGAAGAGATATAATTATTCCATCTTAAAAATCGATATTAATTC
66 TCATTTATTACTCCAATTGAAAT-AAAAGATATTATTATTCCATCTTAAAAATCAATATCAATTC
*
516892 G
130 A
* * ** * *
516893 AGAGCAAACAACAATATCAAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAA
1 AGTGAAAATGACAATATCTAATTATTTCCAATCGAGAATAAATGATCTCTCATGCCTTAAAGCAA
* * *
516958 TCATTTATTACTCCGACTGAAATCAAAAGATATTACTATTC
66 TCATTTATTACTCCAATTGAAAT-AAAAGATATTATTATTC
516999 TCAATATCGA
Statistics
Matches: 185, Mismatches: 51, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
131 183 0.99
132 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.33
Consensus pattern (130 bp):
AGTGAAAATGACAATATCTAATTATTTCCAATCGAGAATAAATGATCTCTCATGCCTTAAAGCAA
TCATTTATTACTCCAATTGAAATAAAAGATATTATTATTCCATCTTAAAAATCAATATCAATTCA
Found at i:519117 original size:3 final size:3
Alignment explanation
Indices: 519109--519145 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
519099 GTATTAATTA
519109 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
519146 TAGAACATCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:519994 original size:16 final size:17
Alignment explanation
Indices: 519955--519995 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
519945 ATTTTTTTCA
519955 AAATA-AAAAAAATCAG
1 AAATATAAAAAAATCAG
* *
519971 TAAGATAAAAAAA-CAG
1 AAATATAAAAAAATCAG
519987 AAATATAAA
1 AAATATAAA
519996 GGAACGATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (17 bp):
AAATATAAAAAAATCAG
Found at i:526716 original size:77 final size:77
Alignment explanation
Indices: 526586--526730 Score: 200
Period size: 77 Copynumber: 1.9 Consensus size: 77
526576 AAATAGAATA
* * * *
526586 TTGAGGCATTTGGAAAGCCCATTTCAGACATAAATGATCCATGTGGGGAATTTTAAAGGCTCACA
1 TTGAGACATTTAGAAAGCCCATTTCAGACAGAAATGATCCATATGGGGAATTTTAAAGGCTCACA
526651 TTAGTATAAAGT
66 TTAGTATAAAGT
* * * * * *
526663 TTGAGACATTTAGAATGTCCATTTCAGATAGAAATGATCTATATGGGGCATTTTGAAGGCTCACA
1 TTGAGACATTTAGAAAGCCCATTTCAGACAGAAATGATCCATATGGGGAATTTTAAAGGCTCACA
526728 TTA
66 TTA
526731 ACAATAAGCA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
77 58 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (77 bp):
TTGAGACATTTAGAAAGCCCATTTCAGACAGAAATGATCCATATGGGGAATTTTAAAGGCTCACA
TTAGTATAAAGT
Found at i:527190 original size:54 final size:54
Alignment explanation
Indices: 527104--527211 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
527094 TAATTGAGAA
527104 ATCTGTGCAGAAGACACAGGAAAGGATAAATGTATTGTCAAATGTATTACGAAC
1 ATCTGTGCAGAAGACACAGGAAAGGATAAATGTATTGTCAAATGTATTACGAAC
* * * * * * * *
527158 ATCTGTGCTGAAGCCACAGGGAATGATGAATGTGTTGTCAAATGTTTTATGAAC
1 ATCTGTGCAGAAGACACAGGAAAGGATAAATGTATTGTCAAATGTATTACGAAC
527212 CAATGATTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (54 bp):
ATCTGTGCAGAAGACACAGGAAAGGATAAATGTATTGTCAAATGTATTACGAAC
Found at i:527871 original size:35 final size:35
Alignment explanation
Indices: 527825--527897 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
527815 TTTAACCAAG
527825 TGAAGGAAGACTGAGTTCACCACTTTGAAGTCAAA
1 TGAAGGAAGACTGAGTTCACCACTTTGAAGTCAAA
*
527860 TGAAGGAAGACTGAGTTCTCCACTTTGAAGTCAAA
1 TGAAGGAAGACTGAGTTCACCACTTTGAAGTCAAA
527895 TGA
1 TGA
527898 GGATTGCATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (35 bp):
TGAAGGAAGACTGAGTTCACCACTTTGAAGTCAAA
Found at i:536182 original size:21 final size:21
Alignment explanation
Indices: 536140--536183 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
536130 ACTCCAGGAG
* *
536140 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
536161 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
536182 CT
1 CT
536184 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:538298 original size:73 final size:72
Alignment explanation
Indices: 538176--538434 Score: 428
Period size: 73 Copynumber: 3.6 Consensus size: 72
538166 GGATGTTTTC
538176 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTAGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-TGTTTCTCGCTAGAGAAAGT
538241 TTCACTTG
65 TTCACTTG
*
538249 AAATAGCAATTTATCTTACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTAGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-TGTTTCTCGCTAGAGAAAGT
538314 TTCACTTG
65 TTCACTTG
* * * *
538322 AAATAGCAATTTATCTCATTTGAGATTGTTTTTCTTAAAACAAATCGTTTCTCACTGGAGAAAGA
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAT-GTTTCTCGCTAGAGAAAGT
*
538387 TTCACTCG
65 TTCACTTG
*
538395 AAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAA
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAA
538435 TATTTCCAGA
Statistics
Matches: 175, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
72 1 0.01
73 174 0.99
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (72 bp):
AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATGTTTCTCGCTAGAGAAAGTT
TCACTTG
Found at i:538436 original size:37 final size:37
Alignment explanation
Indices: 538176--538436 Score: 149
Period size: 37 Copynumber: 7.1 Consensus size: 37
538166 GGATGTTTTC
*
538176 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1 AAATAACAATTTATCTCACTTGAGATTGTTTTTCTTA
* * * * ** ** *
538213 AAA-CA-AATTGTTTCTCGCTAGAGAAAGTTTCACTTG
1 AAATAACAATT-TATCTCACTTGAGATTGTTTTTCTTA
* *
538249 AAATAGCAATTTATCTTACTTGAGATTGTTTTTCTTA
1 AAATAACAATTTATCTCACTTGAGATTGTTTTTCTTA
* * * * ** ** *
538286 AAACAA-ACTGTT-TCTCGCTAGAGAAAGTTTCACTTG
1 AAATAACAAT-TTATCTCACTTGAGATTGTTTTTCTTA
* *
538322 AAATAGCAATTTATCTCATTTGAGATTGTTTTTCTTA
1 AAATAACAATTTATCTCACTTGAGATTGTTTTTCTTA
* * ** * ** **
538359 AAA-CA-AATCGTT-TCTCACTGGAGAAAGATTCACTCG
1 AAATAACAAT--TTATCTCACTTGAGATTGTTTTTCTTA
538395 AAATAACAATTTATCTCACTTGAGATTGTTTTTCTTA
1 AAATAACAATTTATCTCACTTGAGATTGTTTTTCTTA
538432 AAATA
1 AAATA
538437 TTTCCAGATA
Statistics
Matches: 150, Mismatches: 63, Indels: 22
0.64 0.27 0.09
Matches are distributed among these distances:
35 7 0.05
36 65 0.43
37 71 0.47
38 7 0.05
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (37 bp):
AAATAACAATTTATCTCACTTGAGATTGTTTTTCTTA
Found at i:538553 original size:39 final size:39
Alignment explanation
Indices: 538447--538778 Score: 477
Period size: 39 Copynumber: 8.5 Consensus size: 39
538437 TTTCCAGATA
538447 GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAG
* *
538486 GAGTT-ATAATCTGAAGAACTCGTCTGAAGTGTAAGAAG
1 GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAG
* * * *
538524 AAGTTCATAGTCTGAAGAACTCATATGAAGAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAG
*
538563 CAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAG
*
538602 GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAATAAG
1 GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAG
* * *
538641 GAGTTCATAATATGAAGAACTCGTCTGAAGAGTAAGAAA
1 GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAG
* * * * *
538680 GTGTTCATAGTATAAAGAACTCATCTGAAGAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAG
* *
538719 GAGTTCATAATATGAAGAACTCATCTGAAGAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAG
* *
538758 AAGTTCATAGTCTGAAGAACT
1 GAGTTCATAATCTGAAGAACT
538779 TATTCAACCT
Statistics
Matches: 262, Mismatches: 30, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
38 35 0.13
39 227 0.87
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (39 bp):
GAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAG
Found at i:549851 original size:149 final size:149
Alignment explanation
Indices: 549580--549891 Score: 450
Period size: 149 Copynumber: 2.1 Consensus size: 149
549570 GTTAGGGAGC
*
549580 TTATGATTTTTTTAGTAATCCCTAAATTCATTCTAAAAATGAATCTTATGATTTTTAGGCATTAC
1 TTATGATTTTTTTAGTAAACCCTAAATTCATTCTAAAAATGAATCTTATGATTTTTAGGCATTAC
* * * * *
549645 AATTTAGGGTTTATGATTTTTTGGTATTCCCTAAATTCATTCTAAAAAATGAATCTTATGATTGT
66 AATTAAGAGATTATGA-TTTTTGGTAATCCCTAAATTCATTCTAAAAAATGAATCTTACGATTGT
*
549710 TAAGGATTACAATTGAGAGT
130 TAAGGAATACAATTGAGAGT
549730 TTATGATTTTTTT-GATAAACCCTAAATTCATTCTAAAAAATGAATCTTATGATTTTTAGAG-AT
1 TTATGATTTTTTTAG-TAAACCCTAAATTCATTCT-AAAAATGAATCTTATGATTTTTAG-GCAT
*
549793 TACGATTAAGAGATTATG-TTTTTGGTAATCCCTAAATTCATTCTAAAAAATGAATCTTACGATT
63 TACAATTAAGAGATTATGATTTTTGGTAATCCCTAAATTCATTCTAAAAAATGAATCTTACGATT
* * ** *
549857 TTTAGGGAATATGATTTAGAGT
128 GTTAAGGAATACAATTGAGAGT
549879 TTATGATTTTTTT
1 TTATGATTTTTTT
549892 TTTGGATTTT
Statistics
Matches: 146, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
149 74 0.51
150 31 0.21
151 40 0.27
152 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (149 bp):
TTATGATTTTTTTAGTAAACCCTAAATTCATTCTAAAAATGAATCTTATGATTTTTAGGCATTAC
AATTAAGAGATTATGATTTTTGGTAATCCCTAAATTCATTCTAAAAAATGAATCTTACGATTGTT
AAGGAATACAATTGAGAGT
Found at i:549857 original size:73 final size:74
Alignment explanation
Indices: 549588--549889 Score: 396
Period size: 76 Copynumber: 4.1 Consensus size: 74
549578 GCTTATGATT
*
549588 TTTTTAGTAATCCCTAAATTCATTCT-AAAAATGAATCTTATGATTTTTAG-GCATTACAATTTA
1 TTTTTGGTAATCCCTAAATTCATTCTAAAAAATGAATCTTATGATTTTTAGAG-ATTACAATTTA
*
549651 GGGTTTATGA
65 GAGTTTATGA
* * *
549661 TTTTTTGGTATTCCCTAAATTCATTCTAAAAAATGAATCTTATGATTGTTA-AGGATTACAATTG
1 -TTTTTGGTAATCCCTAAATTCATTCTAAAAAATGAATCTTATGATTTTTAGA-GATTACAATTT
549725 AGAGTTTATGA
64 AGAGTTTATGA
* * * *
549736 TTTTTTTGATAAACCCTAAATTCATTCTAAAAAATGAATCTTATGATTTTTAGAGATTACGATTA
1 --TTTTTGGTAATCCCTAAATTCATTCTAAAAAATGAATCTTATGATTTTTAGAGATTACAATTT
*
549801 AGAGATTATG-
64 AGAGTTTATGA
* * * **
549811 TTTTTGGTAATCCCTAAATTCATTCTAAAAAATGAATCTTACGATTTTTAGGGAATATGATTTAG
1 TTTTTGGTAATCCCTAAATTCATTCTAAAAAATGAATCTTATGATTTTTAGAGATTACAATTTAG
549876 AGTTTATGA
66 AGTTTATGA
549885 TTTTT
1 TTTTT
549890 TTTTTGGATT
Statistics
Matches: 202, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
73 65 0.32
74 29 0.14
75 41 0.20
76 66 0.33
77 1 0.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (74 bp):
TTTTTGGTAATCCCTAAATTCATTCTAAAAAATGAATCTTATGATTTTTAGAGATTACAATTTAG
AGTTTATGA
Found at i:556667 original size:7 final size:7
Alignment explanation
Indices: 556655--556680 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
556645 GTATTTAGGG
556655 TTTTAGA
1 TTTTAGA
556662 TTTTAGA
1 TTTTAGA
556669 TTTTAGA
1 TTTTAGA
556676 TTTTA
1 TTTTA
556681 AAGTTCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (7 bp):
TTTTAGA
Found at i:569625 original size:19 final size:19
Alignment explanation
Indices: 569601--569637 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
569591 ATGACCAACA
*
569601 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
569620 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
569638 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:569734 original size:21 final size:20
Alignment explanation
Indices: 569710--569757 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
569700 AAATTCGTGT
*
569710 TGCGATTTTGTAAAATCGCAA
1 TGCGATTATGT-AAATCGCAA
*
569731 TGCGAATATGTAAATCGCAA
1 TGCGATTATGTAAATCGCAA
*
569751 CGCGATT
1 TGCGATT
569758 CTGACTATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (20 bp):
TGCGATTATGTAAATCGCAA
Found at i:569986 original size:22 final size:22
Alignment explanation
Indices: 569935--569988 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
569925 TCACTCTCTA
* * *
569935 CGGCGACATCTGTCCCTATCTC
1 CGGCGAAATCCGTCCCCATCTC
**
569957 CGATGAAATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
569979 CGGCGAAATC
1 CGGCGAAATC
569989 TATCTATCTC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.39, G:0.19, T:0.22
Consensus pattern (22 bp):
CGGCGAAATCCGTCCCCATCTC
Found at i:570391 original size:20 final size:20
Alignment explanation
Indices: 570366--570468 Score: 118
Period size: 20 Copynumber: 5.2 Consensus size: 20
570356 AAAATCGCAA
*
570366 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAATTTCGCGTTG
* *
570386 CGATAGTCATTTTCGTGTTG
1 CGATAGTCAATTTCGCGTTG
**
570406 CGATTTTC-ATTTCGCGTTG
1 CGATAGTCAATTTCGCGTTG
*
570425 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAATTTCGCGTTG
* * *
570445 CAATAGTCATTTTCGTGTTG
1 CGATAGTCAATTTCGCGTTG
570465 CGAT
1 CGAT
570469 TTTAAGTTTC
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
19 15 0.22
20 52 0.78
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (20 bp):
CGATAGTCAATTTCGCGTTG
Found at i:570445 original size:39 final size:40
Alignment explanation
Indices: 570368--570468 Score: 114
Period size: 39 Copynumber: 2.5 Consensus size: 40
570358 AATCGCAACG
** ** * *
570368 ATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCG
1 ATAGTCATTTTCGCGTTGCGATAGTCAAATTCGCGTTGCA
**
570408 ATTTTCA-TTTCGCGTTGCGATAGTCAAATTCGCGTTGCA
1 ATAGTCATTTTCGCGTTGCGATAGTCAAATTCGCGTTGCA
*
570447 ATAGTCATTTTCGTGTTGCGAT
1 ATAGTCATTTTCGCGTTGCGAT
570469 TTTAAGTTTC
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
39 32 0.64
40 18 0.36
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.40
Consensus pattern (40 bp):
ATAGTCATTTTCGCGTTGCGATAGTCAAATTCGCGTTGCA
Found at i:572255 original size:20 final size:20
Alignment explanation
Indices: 572228--572279 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
572218 GGTGTTGATA
572228 ACTATCGCAACGCGGAA-ATG
1 ACTATCGCAACGC-GAATATG
* *
572248 ATTATCGCAACGCGAATTTG
1 ACTATCGCAACGCGAATATG
572268 ACTATCGCAACG
1 ACTATCGCAACG
572280 GGATAATCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (20 bp):
ACTATCGCAACGCGAATATG
Found at i:572363 original size:19 final size:19
Alignment explanation
Indices: 572341--572377 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
572331 CGTGAATTTA
572341 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
572360 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
572378 TATTTCGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.30, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:572383 original size:19 final size:19
Alignment explanation
Indices: 572337--572384 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
572327 GCAACGTGAA
572337 TTTAGTTTCGCGTTGCGATT
1 TTTA-TTTCGCGTTGCGATT
**
572357 TTGGTTTCGCGTTGCGATT
1 TTTATTTCGCGTTGCGATT
572376 TTTATTTCG
1 TTTATTTCG
572385 TATTGCAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.08, C:0.15, G:0.25, T:0.52
Consensus pattern (19 bp):
TTTATTTCGCGTTGCGATT
Found at i:572390 original size:19 final size:19
Alignment explanation
Indices: 572342--572390 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
572332 GTGAATTTAG
* *
572342 TTTCGCGTTGCGATTTTGG
1 TTTCGCATTGCGATTTTGA
* *
572361 TTTCGCGTTGCGATTTTTA
1 TTTCGCATTGCGATTTTGA
*
572380 TTTCGTATTGC
1 TTTCGCATTGC
572391 AATTATCCCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.08, C:0.16, G:0.24, T:0.51
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTGA
Found at i:572424 original size:20 final size:20
Alignment explanation
Indices: 572399--572467 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
572389 GCAATTATCC
*
572399 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
572419 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
* *
572439 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
572459 CGTTGCGAT
1 CGTTGCGAT
572468 TTAAGTTTCG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:573054 original size:42 final size:42
Alignment explanation
Indices: 572990--573101 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 42
572980 CTGTCATCGT
* * * *
572990 TCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* * **
573032 TCAAGAGTCCCCTCCCACCGTTCAATAGGCCCCTGTCATCGT
1 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* *
573074 TGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCAAGA-GTCCCCTCCCACCGTTCAAGAG
573102 CCCGATTCAT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 56 0.97
43 2 0.03
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.22
Consensus pattern (42 bp):
TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
Found at i:573056 original size:21 final size:21
Alignment explanation
Indices: 572987--573101 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 21
572977 CACCTGTCAT
* * *
572987 CGTTCAAGAGGCCTCTCCTAT
1 CGTTCAAGAGGCCCCTCCCAC
**
573008 CGTTCAAGAGGCCCCTATCATC
1 CGTTCAAGAGGCCCCTCCCA-C
* *
573030 C-CTCAAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
* ** *
573050 CGTTCAATAGGCCCCTGTCAT
1 CGTTCAAGAGGCCCCTCCCAC
* *
573071 CGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
*
573092 CATTCAAGAG
1 CGTTCAAGAG
573102 CCCGATTCAT
Statistics
Matches: 69, Mismatches: 23, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
20 2 0.03
21 66 0.96
22 1 0.01
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:574467 original size:14 final size:14
Alignment explanation
Indices: 574444--574505 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
574434 TTGTTTGTTT
574444 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
574458 AATTGGTTTGTAAA
1 AATTGATTTGTAAA
* *
574472 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
574487 TATTGATGTGTAAA
1 AATTGATTTGTAAA
574501 TAATT
1 -AATT
574506 CTTATTTGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
14 24 0.65
15 13 0.35
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:574629 original size:20 final size:20
Alignment explanation
Indices: 574604--574657 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
574594 AGGTACACTT
*
574604 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
*
574624 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
574644 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
574658 TCAATTCGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:574842 original size:20 final size:20
Alignment explanation
Indices: 574700--574839 Score: 130
Period size: 20 Copynumber: 7.3 Consensus size: 20
574690 GTTATTTTAT
* * *
574700 CGTTGCGATAGTTAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
574720 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
574740 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
574760 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
574780 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* * *
574794 TGTTGCGATAGTCATATTTG
1 CGTTGCGATAGTCAAATTCG
* *
574814 TGTTGCAATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
574834 CGTTGC
1 CGTTGC
574840 AATTTTTGAG
Statistics
Matches: 100, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
14 11 0.11
16 1 0.01
18 1 0.01
20 87 0.87
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:574883 original size:54 final size:54
Alignment explanation
Indices: 574741--574884 Score: 209
Period size: 54 Copynumber: 2.7 Consensus size: 54
574731 TCAAATTCAC
* *
574741 GTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGT
1 GTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCAATTTTTGA
* * *
574795 GTTGCGATAGTCATATTTGTGTTGCAATAGTCAAATTCGCGTTGCAATTTTTGA
1 GTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCAATTTTTGA
* *
574849 GTTGCGATAGTCAAATCCGCT-TTGCGATATTCAAAT
1 GTTGCGATAGTCAAATTCG-TGTTGCGATAGTCAAAT
574885 GAATGTGTAA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
54 78 0.99
55 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (54 bp):
GTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCAATTTTTGA
Found at i:575078 original size:18 final size:18
Alignment explanation
Indices: 575055--575089 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
575045 AAGCCGGTTG
*
575055 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
575073 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
575090 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:578064 original size:41 final size:41
Alignment explanation
Indices: 578019--578253 Score: 289
Period size: 41 Copynumber: 5.7 Consensus size: 41
578009 AAAATTCAGT
578019 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
* * *
578060 GTTGCGATATTCAGAATCGCGTAGCGATTATGTATTATCAC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
* *
578101 GTTGCAATAGTCAGAATCGCATTGCGATTATGTATTATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
** **
578142 GTTGCGATAATGT-ATTATCGCGTTGCGA-TA-GTCAGAATCGC
1 GTTGCGAT-A-GTCAGAATCGCGTTGCGATTATGT-ATTATCGC
**
578183 GTTGCGATTATGT-ATTATCGCGTTGCGATTATGTATTATCGC
1 GTTGCGA-TA-GTCAGAATCGCGTTGCGATTATGTATTATCGC
*
578225 GTTGCGATAGTCATAATCGCGTTGCGATT
1 GTTGCGATAGTCAGAATCGCGTTGCGATT
578254 TACATATTCG
Statistics
Matches: 170, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
40 4 0.02
41 133 0.78
42 29 0.17
43 4 0.02
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (41 bp):
GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGC
Found at i:578149 original size:62 final size:62
Alignment explanation
Indices: 578075--578253 Score: 304
Period size: 62 Copynumber: 2.9 Consensus size: 62
578065 GATATTCAGA
* * * *
578075 ATCGCGTAGCGATTATGTATTATCACGTTGCAATAGTCAGAATCGCATTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
*
578137 ATCGCGTTGCGATAATGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
*
578199 ATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCATAATCGCGTTGCGATT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGATT
578254 TACATATTCG
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 110 1.00
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (62 bp):
ATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATT
Found at i:578244 original size:103 final size:102
Alignment explanation
Indices: 578019--578252 Score: 328
Period size: 103 Copynumber: 2.3 Consensus size: 102
578009 AAAATTCAGT
* * *
578019 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATATTCAGAATCGCGTAG
1 GTTGCGATAGTCATAATCGCGTTGCGATAATGTATTATCGCGTTGCGATAGTCAGAATCGCGTAG
578084 CGATTATGTATTATCACGTTGCAATAGTCAGAATCGC
66 CGATTATGTATTATCACGTTGCAATAGTCAGAATCGC
* *
578121 ATTGCGATTATGT-ATTATCGCGTTGCGATAATGTATTATCGCGTTGCGATAGTCAGAATCGCGT
1 GTTGCGA-TA-GTCATAATCGCGTTGCGATAATGTATTATCGCGTTGCGATAGTCAGAATCGCGT
* * * **
578185 TGCGATTATGTATTATCGCGTTGCGATTATGT-ATTATCGC
64 AGCGATTATGTATTATCACGTTGC-AATA-GTCAGAATCGC
578225 GTTGCGATAGTCATAATCGCGTTGCGAT
1 GTTGCGATAGTCATAATCGCGTTGCGAT
578253 TTACATATTC
Statistics
Matches: 115, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
102 8 0.07
103 88 0.77
104 17 0.15
105 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.35
Consensus pattern (102 bp):
GTTGCGATAGTCATAATCGCGTTGCGATAATGTATTATCGCGTTGCGATAGTCAGAATCGCGTAG
CGATTATGTATTATCACGTTGCAATAGTCAGAATCGC
Found at i:578278 original size:21 final size:20
Alignment explanation
Indices: 578236--578286 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
578226 TTGCGATAGT
*
578236 CATAATCGCGTTGCGATTTA
1 CATAATCGCATTGCGATTTA
*
578256 CATATTCGCATTGCGATTTTA
1 CATAATCGCATTGCGA-TTTA
*
578277 CAAAATCGCA
1 CATAATCGCA
578287 ACGCGAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (20 bp):
CATAATCGCATTGCGATTTA
Found at i:578292 original size:21 final size:21
Alignment explanation
Indices: 578268--578308 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
578258 TATTCGCATT
*
578268 GCGATTTTACAAAATCGCAAC
1 GCGAATTTACAAAATCGCAAC
**
578289 GCGAATTTGGAAAATCGCAA
1 GCGAATTTACAAAATCGCAA
578309 TGCAATAGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (21 bp):
GCGAATTTACAAAATCGCAAC
Found at i:578383 original size:19 final size:19
Alignment explanation
Indices: 578359--578395 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
578349 TGCGATACTG
*
578359 GAGATCGCGTTGCAATTTA
1 GAGATCGCATTGCAATTTA
*
578378 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCAATTT
578396 TGTTGATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCAATTTA
Found at i:581141 original size:2 final size:2
Alignment explanation
Indices: 581134--581164 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
581124 ATGTTAGTTG
581134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
581165 ATTTTTCAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:581635 original size:18 final size:19
Alignment explanation
Indices: 581612--581652 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
581602 AAAAGTTACA
581612 AATAAAAAATATA-ATTAT
1 AATAAAAAATATATATTAT
*
581630 AAT-AAAAATATATTTTAT
1 AATAAAAAATATATATTAT
581648 AATAA
1 AATAA
581653 CTTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 9 0.45
18 10 0.50
19 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AATAAAAAATATATATTAT
Found at i:581638 original size:17 final size:18
Alignment explanation
Indices: 581616--581652 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
581606 GTTACAAATA
581616 AAAAATATA-ATTATAAT
1 AAAAATATATATTATAAT
*
581633 AAAAATATATTTTATAAT
1 AAAAATATATATTATAAT
581651 AA
1 AA
581653 CTTATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATATATATTATAAT
Found at i:582068 original size:42 final size:42
Alignment explanation
Indices: 582021--582114 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
582011 TTTTTCGAAA
*
582021 TCCCGTGTTTATTTTACGTAATTCGTTTTCCGAAAAATGTTT
1 TCCCGTGTTTATTTCACGTAATTCGTTTTCCGAAAAATGTTT
* *
582063 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTT
1 TCCCGTGTTTATTTCACGTAATTCGTTTTCCGAAAAATGTTT
*
582105 TCCAGTGTTT
1 TCCCGTGTTT
582115 GGTTGGAGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.47
Consensus pattern (42 bp):
TCCCGTGTTTATTTCACGTAATTCGTTTTCCGAAAAATGTTT
Found at i:582483 original size:19 final size:18
Alignment explanation
Indices: 582459--582527 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
582449 ATATTATTAA
582459 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
582478 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
582496 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
582518 ATT-TTAATAA
1 ATTATTAATAA
582528 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:582502 original size:27 final size:27
Alignment explanation
Indices: 582422--582507 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
582412 AATAAAATTT
* *
582422 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
582449 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
582476 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
582505 ATA
1 ATA
582508 ATCTAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 19 0.41
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:582692 original size:26 final size:27
Alignment explanation
Indices: 582663--582713 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
582653 ATTATAAAAA
*
582663 TAATA-TTTAATAATAAATAA-ATTATT
1 TAATATTTTAAAAAT-AATAATATTATT
582689 TAATATTTTAAAAATAATAATATTA
1 TAATATTTTAAAAATAATAATATTA
582714 AGTTTTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TAATATTTTAAAAATAATAATATTATT
Found at i:582959 original size:15 final size:14
Alignment explanation
Indices: 582907--582955 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
582897 CCATAAATGT
582907 AATTCATTTTCCAA
1 AATTCATTTTCCAA
* *
582921 AATTCAAATTT-CAGT
1 AATTC-ATTTTCCA-A
582936 AATTCATTTTCCAA
1 AATTCATTTTCCAA
582950 AATTCA
1 AATTCA
582956 ATTTACAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (14 bp):
AATTCATTTTCCAA
Found at i:583958 original size:18 final size:18
Alignment explanation
Indices: 583935--583983 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
583925 TTTATGAGGG
583935 AATTGAAATCTGTGAAGA
1 AATTGAAATCTGTGAAGA
* *
583953 AATTGAGATCTGTGAAGG
1 AATTGAAATCTGTGAAGA
*
583971 AATTGGAATCTGT
1 AATTGAAATCTGT
583984 CAGGAATTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.31
Consensus pattern (18 bp):
AATTGAAATCTGTGAAGA
Found at i:584703 original size:55 final size:56
Alignment explanation
Indices: 584644--584751 Score: 209
Period size: 55 Copynumber: 1.9 Consensus size: 56
584634 TTATTCAATA
584644 TATGAATAAGTTACCAAAAGATTTAT-GGGGGTAGTATGGTCAAATTTCAATTCCT
1 TATGAATAAGTTACCAAAAGATTTATGGGGGGTAGTATGGTCAAATTTCAATTCCT
584699 TATGAATAAGTTACCAAAAGATTTATGGGGGGTAGTATGGTCAAATTTCAATT
1 TATGAATAAGTTACCAAAAGATTTATGGGGGGTAGTATGGTCAAATTTCAATT
584752 TCCTCCAACA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 26 0.50
56 26 0.50
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.34
Consensus pattern (56 bp):
TATGAATAAGTTACCAAAAGATTTATGGGGGGTAGTATGGTCAAATTTCAATTCCT
Found at i:592470 original size:2 final size:2
Alignment explanation
Indices: 592463--592511 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
592453 TTGCCCCTAC
592463 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
592505 TA TA TA T
1 TA TA TA T
592512 GTGTGTGTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:593010 original size:17 final size:17
Alignment explanation
Indices: 592988--593036 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
592978 GTATGTTGTT
592988 TATTATTTATGTTATAA
1 TATTATTTATGTTATAA
*
593005 TATTATTTATTATTATAA
1 TATTATTTA-TGTTATAA
593023 -ATTAAATTTATGTT
1 TATT--ATTTATGTT
593037 TCGAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.44
18 10 0.37
19 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (17 bp):
TATTATTTATGTTATAA
Found at i:597664 original size:13 final size:13
Alignment explanation
Indices: 597646--597674 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
597636 ATCAAAATAT
597646 ATATTTATAAAAA
1 ATATTTATAAAAA
597659 ATATTTATAAAAA
1 ATATTTATAAAAA
597672 ATA
1 ATA
597675 ACTCATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATTTATAAAAA
Found at i:604569 original size:21 final size:22
Alignment explanation
Indices: 604543--604627 Score: 77
Period size: 21 Copynumber: 3.9 Consensus size: 22
604533 TTTTGGTACA
*
604543 GAGGGAATCGA-TCCCCCCCAT
1 GAGGGAACCGATTCCCCCCCAT
**
604564 GAGGGAACCGATTCCCCCCTTT
1 GAGGGAACCGATTCCCCCCCAT
604586 GAAGGGGAACCGATTCCCCCCACA-
1 G-A-GGGAACCGATTCCCCCC-CAT
* *
604610 G-GGGAATCGATACCCCCC
1 GAGGGAACCGATTCCCCCC
604628 TGGGGTTCTG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
21 25 0.47
22 9 0.17
23 1 0.02
24 18 0.34
ACGTcount: A:0.24, C:0.38, G:0.25, T:0.14
Consensus pattern (22 bp):
GAGGGAACCGATTCCCCCCCAT
Found at i:607202 original size:17 final size:17
Alignment explanation
Indices: 607180--607220 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
607170 TTGGAGAGAA
607180 ATGATTTGGGATTTGGG
1 ATGATTTGGGATTTGGG
607197 ATGATTTGGGATTTGGG
1 ATGATTTGGGATTTGGG
607214 ATGATTT
1 ATGATTT
607221 TGAAGCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.44
Consensus pattern (17 bp):
ATGATTTGGGATTTGGG
Found at i:608919 original size:64 final size:64
Alignment explanation
Indices: 608785--608963 Score: 173
Period size: 64 Copynumber: 2.8 Consensus size: 64
608775 TTAAAAATAA
* * * ** *
608785 ATACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGTATCCCATTAATAGTG
1 ATACATCGAATGCAATTCATGCATCGATGCATAAGGAGTGCATCAATGCATCCCAGCAATAATG
* * *
608849 AAACATCGAATGCAA-TCGGTGCATCGATGCATAAGGAGTGCATCAATGCATCCCAGCCATAAT-
1 ATACATCGAATGCAATTC-ATGCATCGATGCATAAGGAGTGCATCAATGCATCCCAGCAATAATG
* ** * * * * *
608912 ACTACATCGAATACCTTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 A-TACATCGAATGCAATTCATGCATCGATGCATAAGGAGTGCATCAATGCAT
608964 ACCTCCATTA
Statistics
Matches: 93, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
63 3 0.03
64 89 0.96
65 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (64 bp):
ATACATCGAATGCAATTCATGCATCGATGCATAAGGAGTGCATCAATGCATCCCAGCAATAATG
Found at i:609508 original size:103 final size:103
Alignment explanation
Indices: 609367--609584 Score: 366
Period size: 103 Copynumber: 2.1 Consensus size: 103
609357 GTAGAGGGTC
* * *
609367 TATGTGGTCATTCGGGACATATATGTATTCTTTCGAACAGGTGTGAGGTCTGTTAAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTCGAACAGGTGTGAGGTCTGGTAAGACACATAC
609432 TTGAT-ATTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCA-TTGGCATATGTATATGATTCTTAAGGAATGA
* * *
609470 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTCGAACAGGTGTGAGGTCTGGTAAGACACATAC
609535 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
609573 TATGTGGTCCTT
1 TATGTGGTCCTT
609585 ATGAACATTA
Statistics
Matches: 108, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 107 0.99
104 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGAGACATATATGTATTCTTTCGAACAGGTGTGAGGTCTGGTAAGACACATAC
TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:609635 original size:23 final size:22
Alignment explanation
Indices: 609601--609663 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 22
609591 ATTATTATAT
609601 GGCACTACGGTGCAATTCTACGC
1 GGCACTA-GGTGCAATTCTACGC
*
609624 GGCACTCAGGTGCAATTCTACGT
1 GGCACT-AGGTGCAATTCTACGC
609647 GGCACTTAGGTGCAATT
1 GGCAC-TAGGTGCAATT
609664 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
23 35 0.95
24 2 0.05
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (22 bp):
GGCACTAGGTGCAATTCTACGC
Found at i:615913 original size:64 final size:67
Alignment explanation
Indices: 615770--615937 Score: 202
Period size: 64 Copynumber: 2.6 Consensus size: 67
615760 AATTGTTTAA
* * **
615770 GGTGCATCGATGCACATGAAGTGCATCGATGCAT-TAAGTTAAAAATAAATACATCGAATACAAT
1 GGTGCATCGATGCATAAGAAGTGCATCGATGCATCCCAGTTAAAAATAAATACATCGAATACAAT
615834 TC
66 TC
* * * * * *
615836 -ATGCATCGATGCATAAGTAGTGCATCGATGCATCCCA-TTAATAGTGAA-ACATCGAATGCAA-
1 GGTGCATCGATGCATAAGAAGTGCATCGATGCATCCCAGTTAAAAATAAATACATCGAATACAAT
615897 TC
66 TC
*
615899 GGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAG
1 GGTGCATCGATGCATAAGAAGTGCATCGATGCATCCCAG
615938 CCATAATACT
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
63 2 0.02
64 47 0.54
65 37 0.43
66 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (67 bp):
GGTGCATCGATGCATAAGAAGTGCATCGATGCATCCCAGTTAAAAATAAATACATCGAATACAAT
TC
Found at i:615952 original size:64 final size:64
Alignment explanation
Indices: 615818--615996 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 64
615808 TTAAAAATAA
* ** *
615818 ATACATCGAATACAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTG
1 ATACATCGAATACAATTCATGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATG
* * * *
615882 AAACATCGAATGCAA-TCGGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGCCATAAT-
1 ATACATCGAATACAATTC-ATGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATG
** * * * *
615945 ACTACATCGAATACCTTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 A-TACATCGAATACAATTCATGCATCGATGCATAAGGAGTGCATCGATGCAT
615997 ACCTCCATTA
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
63 3 0.03
64 91 0.96
65 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (64 bp):
ATACATCGAATACAATTCATGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATG
Found at i:616625 original size:103 final size:103
Alignment explanation
Indices: 616400--616617 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
616390 GTAGAGGGTC
* *
616400 TATGTGGTCCTTCGGGACATGTATGTATTCTTTGGAACAGGTGTGAGGTCTGTTAAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGGTAAGACACATAC
*
616465 TTGATCTTTGGCATATGTATATGATTCTTAAAGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAAGAATGA
* *
616503 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGGTAAGACACATAC
*
616568 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAAGAATGA
616606 TATGTGGTCCTT
1 TATGTGGTCCTT
616618 ATAGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGGTAAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAAGAATGA
Found at i:616682 original size:23 final size:23
Alignment explanation
Indices: 616633--616695 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
616623 CATTATTATA
616633 TGGCACTACGGTG-AATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
616655 CGGCACTCCGGTGCAATTCTGCG
1 TGGCACTACGGTGCAATTCTACG
616678 TGGCACTTA-GGTGCAATT
1 TGGCAC-TACGGTGCAATT
616696 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 11 0.32
23 22 0.65
24 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:625211 original size:17 final size:17
Alignment explanation
Indices: 625189--625233 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
625179 TGTGTAAAGT
*
625189 AGTATCGGTGCCCCTTG
1 AGTATCGGTACCCCTTG
625206 AGTATCGGTACCCCTTG
1 AGTATCGGTACCCCTTG
625223 AGTATCGGTAC
1 AGTATCGGTAC
625234 TTATTATGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (17 bp):
AGTATCGGTACCCCTTG
Found at i:627595 original size:31 final size:31
Alignment explanation
Indices: 627540--627599 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
627530 AATACAGTCT
**
627540 CCCAACATTTAGTTTGTTTGCAATATGGTAC
1 CCCAACATTTAGTCCGTTTGCAATATGGTAC
*
627571 CCCAACATTTAGTCCGTTTTCAATATGGT
1 CCCAACATTTAGTCCGTTTGCAATATGGT
627600 CCCTACGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (31 bp):
CCCAACATTTAGTCCGTTTGCAATATGGTAC
Found at i:629390 original size:30 final size:30
Alignment explanation
Indices: 629356--629430 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
629346 CTTTTAAAAC
* *
629356 TTGCAAAATGGTCCCCAATATTTAGTCCGT
1 TTGCAATATGGTCCCCAACATTTAGTCCGT
*
629386 TTGCAATATGGTCCCCAACATTTATTCCGT
1 TTGCAATATGGTCCCCAACATTTAGTCCGT
*
629416 TTACAATATGGTCCC
1 TTGCAATATGGTCCC
629431 AACGTAACTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (30 bp):
TTGCAATATGGTCCCCAACATTTAGTCCGT
Done.