Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006715.1 Hibiscus syriacus cultivar Beakdansim tig00016767_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: 276730
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1418 original size:14 final size:14
Alignment explanation
Indices: 1401--1447 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
1391 TTGGAGTGCA
1401 AAAAGAAAG-AAAAG
1 AAAA-AAAGAAAAAG
1415 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
1429 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
1443 AAAAA
1 AAAAA
1448 GATTTCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.12
14 28 0.88
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:1423 original size:8 final size:8
Alignment explanation
Indices: 1400--1441 Score: 61
Period size: 8 Copynumber: 5.4 Consensus size: 8
1390 ATTGGAGTGC
1400 AAAAAGAA
1 AAAAAGAA
1408 AGAAAAGAA
1 A-AAAAGAA
1417 AAAAAG--
1 AAAAAGAA
1423 AAAAAGAA
1 AAAAAGAA
1431 AAAAAGAA
1 AAAAAGAA
1439 AAA
1 AAA
1442 GAAAAAGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 6 0.19
8 17 0.55
9 8 0.26
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:1466 original size:6 final size:6
Alignment explanation
Indices: 1406--1449 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
1396 GTGCAAAAAG
*
1406 AAAGAA AAGAAAA AAAGAA AAAGAAAA AAAGAA AAAGAA AAAGA
1 AAAGAA AA-AGAA AAAGAA AAAG--AA AAAGAA AAAGAA AAAGA
1450 TTTCAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 22 0.67
7 5 0.15
8 6 0.18
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:7208 original size:11 final size:10
Alignment explanation
Indices: 7194--7234 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
7184 TTGCAATTCA
7194 TTTATCTTTT
1 TTTATCTTTT
7204 CTTTATCTTTT
1 -TTTATCTTTT
7215 TTTAATCTTATT
1 TTT-ATCTT-TT
7227 TTTATCTT
1 TTTATCTT
7235 GATTCCAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.11
11 20 0.71
12 5 0.18
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATCTTTT
Found at i:21125 original size:18 final size:19
Alignment explanation
Indices: 21087--21125 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
21077 AAGGAAAAAG
*
21087 AAGCACTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
21106 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
21124 AA
1 AA
21126 AAGAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:30841 original size:385 final size:384
Alignment explanation
Indices: 30132--30853 Score: 1417
Period size: 385 Copynumber: 1.9 Consensus size: 384
30122 CATATGTAAG
30132 TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACACGGTCCCATTACTAGGTCAAGGG
1 TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACACGGTCCCATTACTAGGTCAAGGG
30197 CCAAACAATTCAGAGAAGTTCTCTTAACTAAGTGTCTTGAAGCTTTGATTCATTTGATAACTTAA
66 CCAAACAATTCAGAGAAGTTCTCTTAACTAAGTGTCTTGAAGCTTTGATTCATTTGATAACTTAA
30262 CACTCTCTAATGTTATGTTATATAATGTTTTAATAGCTAAAGAGTAACTTACTATGAATTCATAT
131 CACTCTCTAATGTTATGTTATATAATGTTTTAATAGCTAAAGAGTAACTTACTATGAATTCATAT
30327 TACACATTGTTATTTTAATATGTTAAGAATGTTAGGATAGTTTTATTATCATATTAAGCATGATT
196 TACACATTGTTATTTTAATATGTTAAGAATGTTAGGATAGTTTTATTATCATATTAAGCATGATT
30392 ATTATATATACATCAAGGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTCATGTTAA
261 ATTATATATACATCAAGGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTCATGTTAA
30457 CTCTTAGGCTTTGAGGATGGACACGATTTGGGGACAAATCGCTTAAAAGAAGGGGGGAA
326 CTCTTAGGCTTTGAGGATGGACACGATTTGGGGACAAATCGCTTAAAAGAAGGGGGGAA
30516 TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACACGGTCCCATTACTAGGTCAAGGG
1 TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACACGGTCCCATTACTAGGTCAAGGG
*
30581 CCAAACAATTCAGGGAAGTTCTCTTAACTAAGTGTCTTGAAGCTTTTGATTCATTTGATAACTTA
66 CCAAACAATTCAGAGAAGTTCTCTTAACTAAGTGTCTTGAAGC-TTTGATTCATTTGATAACTTA
*
30646 ACACTCTCTAATGTTATGTTATATAATGTTTTAATAGCTAAAGAGTAACTTAGTATGAATTCATA
130 ACACTCTCTAATGTTATGTTATATAATGTTTTAATAGCTAAAGAGTAACTTACTATGAATTCATA
30711 TTACACATTGTTATTTTAATATGTTAAGAATGTTAGGATAGTTTTATTATCATATTAAGCATGAT
195 TTACACATTGTTATTTTAATATGTTAAGAATGTTAGGATAGTTTTATTATCATATTAAGCATGAT
30776 TATTATATATACATCAAGGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTCATGTTA
260 TATTATATATACATCAAGGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTCATGTTA
30841 ACTCTTAGGCTTT
325 ACTCTTAGGCTTT
30854 ATACATTATC
Statistics
Matches: 335, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
384 107 0.32
385 228 0.68
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (384 bp):
TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACACGGTCCCATTACTAGGTCAAGGG
CCAAACAATTCAGAGAAGTTCTCTTAACTAAGTGTCTTGAAGCTTTGATTCATTTGATAACTTAA
CACTCTCTAATGTTATGTTATATAATGTTTTAATAGCTAAAGAGTAACTTACTATGAATTCATAT
TACACATTGTTATTTTAATATGTTAAGAATGTTAGGATAGTTTTATTATCATATTAAGCATGATT
ATTATATATACATCAAGGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTCATGTTAA
CTCTTAGGCTTTGAGGATGGACACGATTTGGGGACAAATCGCTTAAAAGAAGGGGGGAA
Found at i:35070 original size:11 final size:13
Alignment explanation
Indices: 35038--35067 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
35028 TGGCCAAAGA
35038 TGAAAAGGTATGT
1 TGAAAAGGTATGT
35051 TGAAAAGGTATG-
1 TGAAAAGGTATGT
35063 TGAAA
1 TGAAA
35068 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:40491 original size:19 final size:21
Alignment explanation
Indices: 40448--40499 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
40438 GAAACCCCTT
40448 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
40469 TGAAAATACTTGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
40488 TGAAGATACATG
1 TGAAAATACATG
40500 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:44156 original size:19 final size:20
Alignment explanation
Indices: 44132--44182 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
44122 CGGTCAAGAG
* *
44132 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
44151 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
44171 CATGTATTTTCA
1 CATGTATTTTCA
44183 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:44623 original size:23 final size:22
Alignment explanation
Indices: 44596--44645 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
44586 CTCTATCTTT
*
44596 TTATTTA-TTTCATTTCATTATTA
1 TTATTTATTTTCATTAC-TTA-TA
44619 TTATTTATTTTCATTACTTATA
1 TTATTTATTTTCATTACTTATA
44641 TTATT
1 TTATT
44646 ACCCTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
23 10 0.40
24 8 0.32
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATTTATTTTCATTACTTATA
Found at i:44955 original size:18 final size:17
Alignment explanation
Indices: 44906--44958 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 17
44896 AATTGGAGTG
44906 CAAAAAGAAAGAGAAAGA
1 CAAAAAGAAAGA-AAAGA
44924 CAAAAAGAAGAAGAAAAGA
1 CAAAAAG-A-AAGAAAAGA
44943 -AGAAAAGTAAAGAAAA
1 CA-AAAAG-AAAGAAAA
44959 AGAATTCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 15 0.48
19 12 0.39
20 4 0.13
ACGTcount: A:0.74, C:0.04, G:0.21, T:0.02
Consensus pattern (17 bp):
CAAAAAGAAAGAAAAGA
Found at i:48389 original size:19 final size:20
Alignment explanation
Indices: 48365--48415 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
48355 CGGTCAAGAG
* *
48365 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
48384 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
48404 CATGTATTTTCA
1 CATGTATTTTCA
48416 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:53875 original size:23 final size:25
Alignment explanation
Indices: 53848--53896 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
53838 CTCTATCTTT
53848 TTATTTATTTCA-TTTCATTA-TTA
1 TTATTTATTTCATTTTCATTACTTA
*
53871 TTATTTATTTTATTTTCATTACTTA
1 TTATTTATTTCATTTTCATTACTTA
53896 T
1 T
53897 ATTATTACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.48
24 8 0.35
25 4 0.17
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (25 bp):
TTATTTATTTCATTTTCATTACTTA
Found at i:53891 original size:18 final size:18
Alignment explanation
Indices: 53852--53903 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
53842 ATCTTTTTAT
*
53852 TTATTTCATTTCATTATTA
1 TTATTT-ATTTTATTATTA
53871 TTATTTATTTTATT-TTCA
1 TTATTTATTTTATTATT-A
* *
53889 TTACTTATATTATTA
1 TTATTTATTTTATTA
53904 CCCTTTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 2 0.07
18 20 0.71
19 6 0.21
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTATTTTATTATTA
Found at i:53901 original size:23 final size:21
Alignment explanation
Indices: 53848--53902 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
53838 CTCTATCTTT
53848 TTAT-TTATTTCATTTCATTA
1 TTATATTATTTCATTTCATTA
*
53868 TTATTATTTATTTTATTTTCATTA
1 TTA-TA-TTATTTCA-TTTCATTA
53892 CTTATATTATT
1 -TTATATTATT
53903 ACCCTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 3 0.10
21 1 0.03
23 12 0.41
24 10 0.34
25 3 0.10
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATATTATTTCATTTCATTA
Found at i:54973 original size:13 final size:12
Alignment explanation
Indices: 54954--55039 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
54944 ATATAGGCGT
54954 GATATGGTGATG
1 GATATGGTGATG
54966 GAATATGGTGAT-
1 G-ATATGGTGATG
*
54978 GATATAGGCG-T-
1 GATAT-GGTGATG
54989 GATAATGGTGATG
1 GAT-ATGGTGATG
55002 GACTATGGTGAT-
1 GA-TATGGTGATG
*
55014 GATATAGGCG-T-
1 GATAT-GGTGATG
55025 GATAATGGTGATG
1 GAT-ATGGTGATG
55038 GA
1 GA
55040 AGATTGTATC
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:55009 original size:36 final size:36
Alignment explanation
Indices: 54936--55040 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
54926 ATTTAGAAGT
*
54936 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
54971 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
55007 TGGTGATGATATAGGCGTGATAATGGTGATGGAA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAA
55041 GATTGTATCT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:59075 original size:13 final size:12
Alignment explanation
Indices: 59056--59141 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
59046 ATATAGGCGT
59056 GATATGGTGATG
1 GATATGGTGATG
59068 GAATATGGTGAT-
1 G-ATATGGTGATG
*
59080 GATATAGGCG-T-
1 GATAT-GGTGATG
59091 GATAATGGTGATG
1 GAT-ATGGTGATG
59104 GACTATGGTGAT-
1 GA-TATGGTGATG
*
59116 GATATAGGCG-T-
1 GATAT-GGTGATG
59127 GATAATGGTGATG
1 GAT-ATGGTGATG
59140 GA
1 GA
59142 AGTTTGTATC
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:59111 original size:36 final size:36
Alignment explanation
Indices: 59038--59142 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
59028 ATTTAGAAGT
*
59038 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
59073 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
59109 TGGTGATGATATAGGCGTGATAATGGTGATGGAA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAA
59143 GTTTGTATCT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:59965 original size:36 final size:36
Alignment explanation
Indices: 59924--59999 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
59914 ATTTTCGGGA
*
59924 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
59960 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
59996 TTTT
1 TTTT
60000 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:61364 original size:20 final size:22
Alignment explanation
Indices: 61335--61374 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
61325 AGGAGAGCTT
61335 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
61355 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
61375 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:63753 original size:24 final size:21
Alignment explanation
Indices: 63719--63761 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
63709 TGCACAAGAT
*
63719 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
63741 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
63762 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:65271 original size:20 final size:22
Alignment explanation
Indices: 65242--65281 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
65232 AGGAGAGATT
65242 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
65262 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
65282 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:74165 original size:12 final size:12
Alignment explanation
Indices: 74143--74186 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 12
74133 GTCTTCTCAG
74143 CTCCTCAGCTACT
1 CTCC-CAGCTACT
74156 CTCCCAGCTA--
1 CTCCCAGCTACT
74166 CTCCCAGCTACT
1 CTCCCAGCTACT
74178 -T-CCAGCTAC
1 CTCCCAGCTAC
74187 CTTTAGTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 18 0.62
11 1 0.03
12 6 0.21
13 4 0.14
ACGTcount: A:0.18, C:0.48, G:0.09, T:0.25
Consensus pattern (12 bp):
CTCCCAGCTACT
Found at i:74171 original size:10 final size:10
Alignment explanation
Indices: 74156--74186 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
74146 CTCAGCTACT
74156 CTCCCAGCTA
1 CTCCCAGCTA
74166 CTCCCAGCTA
1 CTCCCAGCTA
*
74176 CTTCCAGCTA
1 CTCCCAGCTA
74186 C
1 C
74187 CTTTAGTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.19, C:0.48, G:0.10, T:0.23
Consensus pattern (10 bp):
CTCCCAGCTA
Found at i:74182 original size:20 final size:23
Alignment explanation
Indices: 74143--74186 Score: 67
Period size: 20 Copynumber: 2.0 Consensus size: 23
74133 GTCTTCTCAG
74143 CTCCTCAGCTACTCTCCCAGCTA
1 CTCCTCAGCTACTCTCCCAGCTA
74166 CTCC-CAGCTACT-T-CCAGCTA
1 CTCCTCAGCTACTCTCCCAGCTA
74186 C
1 C
74187 CTTTAGTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.38
21 1 0.05
22 8 0.38
23 4 0.19
ACGTcount: A:0.18, C:0.48, G:0.09, T:0.25
Consensus pattern (23 bp):
CTCCTCAGCTACTCTCCCAGCTA
Found at i:76167 original size:31 final size:31
Alignment explanation
Indices: 76128--76205 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
76118 CATTGTTATT
76128 TAAT-ATATTAAGCATGTTAGAATAGTCTTA
1 TAATCATATTAAGCATGTTAGAATAGTCTTA
*
76158 TAATCATATTAAGCATGTTAGAATATTCTTA
1 TAATCATATTAAGCATGTTAGAATAGTCTTA
*
76189 TAATCATATGAAGCATG
1 TAATCATATTAAGCATG
76206 ATTATCACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 4 0.09
31 41 0.91
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (31 bp):
TAATCATATTAAGCATGTTAGAATAGTCTTA
Found at i:85091 original size:48 final size:48
Alignment explanation
Indices: 84999--85091 Score: 107
Period size: 49 Copynumber: 1.9 Consensus size: 48
84989 CACACTCCAA
* * * * *
84999 TTTGCCTTTCATCACGACTAGGAGGGTTGGTTAGAGCCATTTATCGTG
1 TTTGCCTTTCATCACGACTAGGAGGGCTCGATAGAGACACTTATCGTG
**
85047 TTTGCCTTTTCATTGCGACTAGGAGGGCTCGATAG-GACACTTATC
1 TTTGCC-TTTCATCACGACTAGGAGGGCTCGATAGAGACACTTATC
85092 CATCTATTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
48 14 0.38
49 23 0.62
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.34
Consensus pattern (48 bp):
TTTGCCTTTCATCACGACTAGGAGGGCTCGATAGAGACACTTATCGTG
Found at i:85578 original size:8 final size:8
Alignment explanation
Indices: 85565--85630 Score: 80
Period size: 8 Copynumber: 8.0 Consensus size: 8
85555 TATTTTTTTT
85565 CAAAAAAA
1 CAAAAAAA
85573 CAAAAAAA
1 CAAAAAAA
85581 C-AAAAAA
1 CAAAAAAA
*
85588 CAAAAAAGG
1 CAAAAAA-A
85597 CAAAAAAA
1 CAAAAAAA
*
85605 AAAAAAAA
1 CAAAAAAA
85613 GGCAAAAAAA
1 --CAAAAAAA
85623 CAAAAAAA
1 CAAAAAAA
85631 GAGCCAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
7 7 0.14
8 29 0.58
9 7 0.14
10 7 0.14
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:85605 original size:20 final size:19
Alignment explanation
Indices: 85577--85641 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 19
85567 AAAAAACAAA
85577 AAAACAAAAAACAAAAAAGGC
1 AAAA-AAAAAA-AAAAAAGGC
85598 -AAAAAAAAAAAAAAAGGC
1 AAAAAAAAAAAAAAAAGGC
* *
85616 AAAAAAACAAAAAAAGAGCC
1 AAAAAAA-AAAAAAAAAGGC
85636 AAAAAA
1 AAAAAA
85642 GCCAAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 9 0.22
19 12 0.30
20 19 0.47
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAAGGC
Found at i:85629 original size:7 final size:7
Alignment explanation
Indices: 85567--85609 Score: 52
Period size: 7 Copynumber: 5.9 Consensus size: 7
85557 TTTTTTTTCA
85567 AAAAAAC
1 AAAAAAC
85574 AAAAAAAC
1 -AAAAAAC
85582 AAAAAAC
1 AAAAAAC
85589 AAAAAAGGC
1 AAAAAA--C
85598 AAAAAA-
1 AAAAAAC
85604 AAAAAA
1 AAAAAA
85610 AAAGGCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.18
7 13 0.39
8 7 0.21
9 7 0.21
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:85630 original size:18 final size:18
Alignment explanation
Indices: 85565--85641 Score: 99
Period size: 18 Copynumber: 4.4 Consensus size: 18
85555 TATTTTTTTT
85565 CAAAAAAACAAAAAAA--
1 CAAAAAAACAAAAAAAGG
85581 C-AAAAAAC-AAAAAAGG
1 CAAAAAAACAAAAAAAGG
*
85597 CAAAAAAAAAAAAAAAGG
1 CAAAAAAACAAAAAAAGG
85615 CAAAAAAACAAAAAAAGAG
1 CAAAAAAACAAAAAAAG-G
85634 CCAAAAAA
1 -CAAAAAA
85642 GCCAAAATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
14 6 0.11
15 7 0.13
16 2 0.04
17 6 0.11
18 24 0.45
19 1 0.02
20 7 0.13
ACGTcount: A:0.81, C:0.12, G:0.08, T:0.00
Consensus pattern (18 bp):
CAAAAAAACAAAAAAAGG
Found at i:93740 original size:2 final size:2
Alignment explanation
Indices: 93733--93781 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
93723 ATCACCAACT
93733 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
93775 TA TA TA T
1 TA TA TA T
93782 TCCGCTGTCA
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:97465 original size:22 final size:22
Alignment explanation
Indices: 97417--97467 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
97407 TTTAGGATGC
*
97417 ACATACAAGATTTAATGATTGA
1 ACATTCAAGATTTAATGATTGA
97439 ACATTCAAGATTTAATGATTGA
1 ACATTCAAGATTTAATGATTGA
97461 ACATTCA
1 ACATTCA
97468 TGGATGAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (22 bp):
ACATTCAAGATTTAATGATTGA
Found at i:99755 original size:22 final size:25
Alignment explanation
Indices: 99707--99759 Score: 85
Period size: 22 Copynumber: 2.2 Consensus size: 25
99697 TTCTTTTCTT
99707 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
99732 TTTCTT-C-TTTTGAGTGC-TTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
99754 TTTCTT
1 TTTCTT
99760 TGCTGATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 11 0.39
23 10 0.36
24 1 0.04
25 6 0.21
ACGTcount: A:0.11, C:0.19, G:0.11, T:0.58
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:106794 original size:17 final size:18
Alignment explanation
Indices: 106772--106809 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
106762 ACCTATAGTT
106772 CACATC-TATATAATATG
1 CACATCATATATAATATG
*
106789 CACATCATTATATTATATG
1 CACATCA-TATATAATATG
106808 CA
1 CA
106810 TTATATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (18 bp):
CACATCATATATAATATG
Found at i:107640 original size:19 final size:21
Alignment explanation
Indices: 107616--107667 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
107606 CGGCCAAGAG
*
107616 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
*
107635 CATGTATTTTTATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
107656 CATGTATTTTCA
1 CATGTATTTTCA
107668 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 2 0.07
21 16 0.57
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.48
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:108282 original size:5 final size:5
Alignment explanation
Indices: 108268--108297 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
108258 CTAAGGGAGT
108268 TCTT- TCTTA TCTTA TCTTA TCTTA TCTTA T
1 TCTTA TCTTA TCTTA TCTTA TCTTA TCTTA T
108298 ATCATTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (5 bp):
TCTTA
Found at i:110152 original size:25 final size:23
Alignment explanation
Indices: 110102--110152 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
110092 AAATAAAATC
**
110102 AAAGAACTCAAAAGAAGAAATTG
1 AAAGAACTCAAAAGAAGAAAAAG
*
110125 AAAGCACTCAAAAAGGAAGAAAAAG
1 AAAGAACTC-AAAA-GAAGAAAAAG
110150 AAA
1 AAA
110153 AAAAAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 8 0.35
24 4 0.17
25 11 0.48
ACGTcount: A:0.65, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAAGAACTCAAAAGAAGAAAAAG
Found at i:115133 original size:11 final size:11
Alignment explanation
Indices: 115117--115164 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
115107 AAATTTTGGC
* *
115117 TTTTTTGGCTT
1 TTTTTTTGCCT
115128 TTTTTTTG--T
1 TTTTTTTGCCT
115137 -TTTTTTGCCT
1 TTTTTTTGCCT
115147 TTTTTTTGCCT
1 TTTTTTTGCCT
115158 TTTTTTT
1 TTTTTTT
115165 TGAAAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 1 0.03
11 24 0.73
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.79
Consensus pattern (11 bp):
TTTTTTTGCCT
Found at i:115160 original size:20 final size:20
Alignment explanation
Indices: 115110--115162 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
115100 ATTTTTGAAA
* *
115110 TTTTGGCTTTTTTGGCTTTT
1 TTTTTGCTTTTTTGGCCTTT
*
115130 TTTTTG-TTTTTTTGCCTTT
1 TTTTTGCTTTTTTGGCCTTT
115149 TTTTTGCCTTTTTT
1 TTTTTG-CTTTTTT
115163 TTTGAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.61
20 5 0.18
21 6 0.21
ACGTcount: A:0.00, C:0.11, G:0.13, T:0.75
Consensus pattern (20 bp):
TTTTTGCTTTTTTGGCCTTT
Found at i:127787 original size:18 final size:18
Alignment explanation
Indices: 127766--127803 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
127756 CCTTACACAC
127766 TTTGCCACAACAACACCA
1 TTTGCCACAACAACACCA
* *
127784 TTTGCCACGACAACGCCA
1 TTTGCCACAACAACACCA
127802 TT
1 TT
127804 CATACTTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.21
Consensus pattern (18 bp):
TTTGCCACAACAACACCA
Found at i:128367 original size:20 final size:20
Alignment explanation
Indices: 128342--128391 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
128332 GGAGTACAAA
128342 AAGAAAGAAAAGACA-AAAAG
1 AAGAAA-AAAAGACAGAAAAG
**
128362 AAGAAAAAAATTCAGAAAAG
1 AAGAAAAAAAGACAGAAAAG
128382 AAGAAAAAAA
1 AAGAAAAAAA
128392 AAGAAATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (20 bp):
AAGAAAAAAAGACAGAAAAG
Found at i:128369 original size:17 final size:17
Alignment explanation
Indices: 128337--128391 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
128327 AAATTGGAGT
*
128337 ACAAAAAGAA-AGAAAAG
1 ACAAAAAGAAGA-AAAAA
128354 ACAAAAAGAAGAAAAAA
1 ACAAAAAGAAGAAAAAA
128371 ATTCAGAAAAGAAGAAAAAA
1 A--CA-AAAAGAAGAAAAAA
128391 A
1 A
128392 AAGAAATTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 15 0.45
18 1 0.03
19 2 0.06
20 15 0.45
ACGTcount: A:0.76, C:0.05, G:0.15, T:0.04
Consensus pattern (17 bp):
ACAAAAAGAAGAAAAAA
Found at i:128778 original size:30 final size:31
Alignment explanation
Indices: 128724--128783 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
128714 CTTAGCTTTA
*
128724 TATTATGTTTACATATGTTATAGAT-TCATT
1 TATTATGTTTACATATATTATAGATATCATT
*
128754 TATTATGTTTACATTTCATT-TAGATATCAT
1 TATTATGTTTACATAT-ATTATAGATATCAT
128784 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATATTATAGATATCATT
Found at i:129717 original size:19 final size:20
Alignment explanation
Indices: 129693--129743 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
129683 CGGCCAAGAG
* *
129693 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
129712 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
129732 CATGTATTTTCA
1 CATGTATTTTCA
129744 AAGGGATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:130460 original size:9 final size:8
Alignment explanation
Indices: 130439--130506 Score: 57
Period size: 8 Copynumber: 7.9 Consensus size: 8
130429 TTGGAGTGAA
130439 AAAAGAAAG
1 AAAA-AAAG
130448 -AAAAAAG
1 AAAAAAAG
130455 ATAAAAGAAG
1 A-AAAA-AAG
**
130465 AGAAAAATC
1 A-AAAAAAG
130474 AAAAAAAG
1 AAAAAAAG
130482 AAAGAAAAG
1 AAA-AAAAG
130491 AAAAAAAAG
1 -AAAAAAAG
130500 AAAAAAA
1 AAAAAAA
130507 ATCAGAATAG
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
7 4 0.08
8 18 0.37
9 16 0.33
10 11 0.22
ACGTcount: A:0.81, C:0.01, G:0.15, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:130462 original size:18 final size:17
Alignment explanation
Indices: 130439--130505 Score: 66
Period size: 17 Copynumber: 3.8 Consensus size: 17
130429 TTGGAGTGAA
130439 AAAAGAAAGAAAAAAGAT
1 AAAA-AAAGAAAAAAGAT
* *
130457 AAAAGAAGAGAAAA-AT
1 AAAAAAAGAAAAAAGAT
130473 CAAAAAAAGAAAGAAAAGA-
1 -AAAAAAAG-AA-AAAAGAT
130492 AAAAAAAGAAAAAA
1 AAAAAAAGAAAAAA
130506 AATCAGAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
16 6 0.15
17 17 0.41
18 13 0.32
19 4 0.10
20 1 0.02
ACGTcount: A:0.81, C:0.01, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAAAAAAGAT
Found at i:130486 original size:38 final size:36
Alignment explanation
Indices: 130437--130510 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 36
130427 AATTGGAGTG
*
130437 AAAAAAGAAAGAAAA-AAGATAAAAGAAGAGAAAAATCA
1 AAAAAAGAAAGAAAAGAA-AAAAAAGAA-A-AAAAATCA
130475 AAAAAAGAAAGAAAAGAAAAAAAAGAAAAAAAATCA
1 AAAAAAGAAAGAAAAGAAAAAAAAGAAAAAAAATCA
130511 GAATAGAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
36 8 0.24
37 1 0.03
38 23 0.68
39 2 0.06
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.04
Consensus pattern (36 bp):
AAAAAAGAAAGAAAAGAAAAAAAAGAAAAAAAATCA
Found at i:130507 original size:9 final size:9
Alignment explanation
Indices: 130437--130507 Score: 63
Period size: 9 Copynumber: 7.7 Consensus size: 9
130427 AATTGGAGTG
130437 AAAAAAGAAA
1 AAAAAAG-AA
130447 GAAAAAAGATA
1 -AAAAAAGA-A
*
130458 AAAGAAG-A
1 AAAAAAGAA
* **
130466 GAAAAATCA
1 AAAAAAGAA
130475 AAAAAAGAA
1 AAAAAAGAA
*
130484 AGAAAAGAA
1 AAAAAAGAA
130493 AAAAAAGAA
1 AAAAAAGAA
130502 AAAAAA
1 AAAAAA
130508 TCAGAATAGA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
8 5 0.10
9 29 0.59
10 7 0.14
11 8 0.16
ACGTcount: A:0.82, C:0.01, G:0.14, T:0.03
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:133787 original size:24 final size:21
Alignment explanation
Indices: 133753--133795 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
133743 TGCACAAGAT
*
133753 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
133775 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
133796 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:138450 original size:30 final size:31
Alignment explanation
Indices: 138398--138457 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
138388 AAAGTACTTA
**
138398 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
138428 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
138458 GGAAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:139389 original size:19 final size:20
Alignment explanation
Indices: 139365--139415 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
139355 CGGCCAAGAG
* *
139365 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
139384 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
139404 CATGTATTTTCA
1 CATGTATTTTCA
139416 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:142348 original size:22 final size:20
Alignment explanation
Indices: 142323--142372 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
142313 GAGTGCAAAA
142323 AGAAAGAAAAAGACAAAAGAAG
1 AGAAAGAAAAAG--AAAAGAAG
**
142345 AGAAA-AATCAGAAAAGAAG
1 AGAAAGAAAAAGAAAAGAAG
142364 A-AAAGAAAA
1 AGAAAGAAAA
142373 GATAAGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
18 3 0.13
19 11 0.48
21 4 0.17
22 5 0.22
ACGTcount: A:0.74, C:0.04, G:0.20, T:0.02
Consensus pattern (20 bp):
AGAAAGAAAAAGAAAAGAAG
Found at i:142359 original size:19 final size:18
Alignment explanation
Indices: 142320--142364 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
142310 TTGGAGTGCA
*
142320 AAAAGAA-AGAAAAAGAC
1 AAAAGAAGAGAAAAACAC
*
142337 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGAGAAAAA-CAC
142356 AAAAGAAGA
1 AAAAGAAGA
142365 AAAGAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.29
18 7 0.29
19 10 0.42
ACGTcount: A:0.73, C:0.04, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAGAAGAGAAAAACAC
Found at i:142361 original size:32 final size:31
Alignment explanation
Indices: 142325--142395 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 31
142315 GTGCAAAAAG
142325 AAAGAAAAAGACAAAAGA-AGAGAAAAA-TCAGA
1 AAAGAAAAA-ACAAAAGATA-AGAAAAATTCA-A
*
142357 AAAGAAGAAAAGAAAAGATAAGAAAAATTCAA
1 AAAGAA-AAAACAAAAGATAAGAAAAATTCAA
142389 AAAGAAA
1 AAAGAAA
142396 GCAAGCCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
31 1 0.03
32 27 0.77
33 7 0.20
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.06
Consensus pattern (31 bp):
AAAGAAAAAACAAAAGATAAGAAAAATTCAA
Found at i:147506 original size:30 final size:31
Alignment explanation
Indices: 147470--147529 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
147460 CTTAGCTTTA
**
147470 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
147500 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
147530 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:148462 original size:19 final size:21
Alignment explanation
Indices: 148438--148481 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
148428 AGCATTTATC
148438 TTCA-TTAAAA-TCATGTATT
1 TTCATTTAAAAGTCATGTATT
148457 TTCATTTAAAAGTCATGTATT
1 TTCATTTAAAAGTCATGTATT
148478 TTCA
1 TTCA
148482 AAGGGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.17
20 6 0.26
21 13 0.57
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (21 bp):
TTCATTTAAAAGTCATGTATT
Found at i:150588 original size:36 final size:36
Alignment explanation
Indices: 150541--150645 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
150531 GATACAATCT
150541 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
150577 GTCCATCACCATCATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
150613 TTCCACCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
150646 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 20 0.31
36 44 0.69
ACGTcount: A:0.30, C:0.38, G:0.05, T:0.27
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:151064 original size:14 final size:14
Alignment explanation
Indices: 151038--151076 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
151028 AAGCAACAAA
151038 AAGAGAAAAAAAAT
1 AAGAGAAAAAAAAT
*
151052 AAGAAAAATAAAAAT
1 AAGAGAAA-AAAAAT
*
151067 AAAAGAAAAA
1 AAGAGAAAAA
151077 GACTCCTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (14 bp):
AAGAGAAAAAAAAT
Found at i:151064 original size:17 final size:17
Alignment explanation
Indices: 151036--151076 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
151026 AAAAGCAACA
*
151036 AAAAGAGAAA-AAAAAT
1 AAAAGAAAAATAAAAAT
151052 --AAGAAAAATAAAAAT
1 AAAAGAAAAATAAAAAT
151067 AAAAGAAAAA
1 AAAAGAAAAA
151077 GACTCCTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
14 7 0.33
15 6 0.29
17 8 0.38
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (17 bp):
AAAAGAAAAATAAAAAT
Found at i:154777 original size:36 final size:36
Alignment explanation
Indices: 154730--154834 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
154720 TATACAATCT
154730 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
154766 GTCCATCACCATCATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
154802 TTCCACCACCA-TATCACGTCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
154835 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 19 0.30
36 44 0.70
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:155426 original size:20 final size:20
Alignment explanation
Indices: 155366--155431 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
155356 TTGGAGTAAA
155366 AAAAGAAAGAAAAGACAAAAAG
1 AAAAGAAA-AAAA-ACAAAAAG
*** *
155388 AAGAAGAAAATTCAGAAAAAG
1 AA-AAGAAAAAAAACAAAAAG
*
155409 AAAAGAAAAAAAATAAAAAG
1 AAAAGAAAAAAAACAAAAAG
155429 AAA
1 AAA
155432 TTCAAAAAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
20 17 0.49
21 9 0.26
22 3 0.09
23 6 0.17
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAAGAAAAAAAACAAAAAG
Found at i:155433 original size:34 final size:32
Alignment explanation
Indices: 155371--155443 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 32
155361 GTAAAAAAAG
* *
155371 AAAGAAAAGACAAAAAGAAGAAGAAAATTCAGAA
1 AAAGAAAAGAAAAAAAGAAAAAGAAAATTC--AA
*
155405 AAAGAAAAGAAAAAAAATAAAAAG-AAATTCAA
1 AAAGAAAAG-AAAAAAAGAAAAAGAAAATTCAA
155437 AAAGAAA
1 AAAGAAA
155444 GCAAGCCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 9 0.26
34 15 0.43
35 11 0.31
ACGTcount: A:0.75, C:0.04, G:0.14, T:0.07
Consensus pattern (32 bp):
AAAGAAAAGAAAAAAAGAAAAAGAAAATTCAA
Found at i:157743 original size:22 final size:20
Alignment explanation
Indices: 157718--157757 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
157708 ATGTTTGTTT
157718 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
157740 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
157758 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:159108 original size:13 final size:13
Alignment explanation
Indices: 159086--159115 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
159076 ACTAAACACC
159086 TTTC-ACATACCT
1 TTTCAACATACCT
159098 TTTCAACATACCT
1 TTTCAACATACCT
159111 TTTCA
1 TTTCA
159116 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:163025 original size:22 final size:20
Alignment explanation
Indices: 163000--163039 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
162990 ATGTTTGTTT
163000 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
163022 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
163040 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:168437 original size:19 final size:21
Alignment explanation
Indices: 168413--168464 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
168403 TGGCCAAGAG
*
168413 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
168432 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
168453 CATGTATTTTCA
1 CATGTATTTTCA
168465 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:172015 original size:19 final size:21
Alignment explanation
Indices: 171991--172042 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
171981 CGGCCAATAG
171991 CATGTATCTTCA-TT-AAAAT
1 CATGTATCTTCATTTAAAAAT
*
172010 CATGTATCTTTATTTAAAAAT
1 CATGTATCTTCATTTAAAAAT
*
172031 CATGTATTTTCA
1 CATGTATCTTCA
172043 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 11 0.39
20 2 0.07
21 15 0.54
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATCTTCATTTAAAAAT
Found at i:172781 original size:17 final size:18
Alignment explanation
Indices: 172761--172808 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
172751 TTGGAGTGCA
172761 AAAAGAAAGAAAAA-CAC
1 AAAAGAAAGAAAAATCAC
*
172778 AAAAGAAGAGAAAAATCAG
1 AAAAGAA-AGAAAAATCAC
172797 AAAAG-AAGAAAA
1 AAAAGAAAGAAAA
172809 GAAAAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 13 0.46
18 8 0.29
19 7 0.25
ACGTcount: A:0.75, C:0.06, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAAGAAAGAAAAATCAC
Found at i:172789 original size:22 final size:22
Alignment explanation
Indices: 172764--172813 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 22
172754 GAGTGCAAAA
172764 AGAAAGAAAAACACAAAAGAAG
1 AGAAAGAAAAACACAAAAGAAG
* *
172786 AG--A-AAAATCAGAAAAGAAG
1 AGAAAGAAAAACACAAAAGAAG
172805 A-AAAGAAAA
1 AGAAAGAAAA
172814 GAAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
19 15 0.65
20 2 0.09
21 4 0.17
22 2 0.09
ACGTcount: A:0.74, C:0.06, G:0.18, T:0.02
Consensus pattern (22 bp):
AGAAAGAAAAACACAAAAGAAG
Found at i:172799 original size:27 final size:27
Alignment explanation
Indices: 172768--172819 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
172758 GCAAAAAGAA
*
172768 AGAAAA-ACACAAAAGAAGAGAAAAATC
1 AGAAAAGA-ACAAAAGAAAAGAAAAATC
*
172795 AGAAAAGAAGAAAAGAAAAGAAAAA
1 AGAAAAGAACAAAAGAAAAGAAAAA
172820 GAAAAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.75, C:0.06, G:0.17, T:0.02
Consensus pattern (27 bp):
AGAAAAGAACAAAAGAAAAGAAAAATC
Found at i:172800 original size:19 final size:18
Alignment explanation
Indices: 172761--172805 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
172751 TTGGAGTGCA
172761 AAAAGAA-AGAAAAACAC
1 AAAAGAAGAGAAAAACAC
*
172778 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGAGAAAAA-CAC
172797 AAAAGAAGA
1 AAAAGAAGA
172806 AAAGAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 7 0.28
18 7 0.28
19 11 0.44
ACGTcount: A:0.73, C:0.07, G:0.18, T:0.02
Consensus pattern (18 bp):
AAAAGAAGAGAAAAACAC
Found at i:173888 original size:24 final size:24
Alignment explanation
Indices: 173843--173904 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
173833 TTCAAGCAGT
* * *
173843 TATGCCACATGAAGTTCAAAAAGA
1 TATGTCACTTGAAGTGCAAAAAGA
* *
173867 TATGTCACTTGAAGTGCCAAAAGT
1 TATGTCACTTGAAGTGCAAAAAGA
173891 TATGATCA-TTGAAG
1 TATG-TCACTTGAAG
173905 CTCCAAGTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 29 0.91
25 3 0.09
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (24 bp):
TATGTCACTTGAAGTGCAAAAAGA
Found at i:175716 original size:19 final size:21
Alignment explanation
Indices: 175692--175743 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
175682 CGCCCAATAG
175692 CATGTATCTTCA-TT-AAAAT
1 CATGTATCTTCATTTAAAAAT
*
175711 CATGTATCTTTATTTAAAAAT
1 CATGTATCTTCATTTAAAAAT
*
175732 CATGTATTTTCA
1 CATGTATCTTCA
175744 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 11 0.39
20 2 0.07
21 15 0.54
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATCTTCATTTAAAAAT
Found at i:177954 original size:19 final size:21
Alignment explanation
Indices: 177930--177981 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
177920 CGGCCAAGAG
*
177930 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
177949 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
177970 CATGTATTTTCA
1 CATGTATTTTCA
177982 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:180709 original size:19 final size:20
Alignment explanation
Indices: 180662--180717 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
180652 AAAACCCCTT
**
180662 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
180682 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
* *
180701 TGAAGATACATGCTTTT
1 TGAAAATACATGATTTT
180718 GGCCGAATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:182296 original size:90 final size:89
Alignment explanation
Indices: 182188--182362 Score: 287
Period size: 90 Copynumber: 2.0 Consensus size: 89
182178 TCCCAAATAT
* * * *
182188 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAACTAATTTGAAATAATAAAAACCCTAATATGACTAG
182253 GGTAACTCGGATATAAAAGGATTA
66 GGTAACTCGGATATAAAAGGATTA
182277 TTAAATTCTAATTAATTAAATATAGATTTAACTAATTTGAAATAATAAAAACCCTAATATGACTA
1 TTAAATTC-AATTAATTAAATATAGATTTAACTAATTTGAAATAATAAAAACCCTAATATGACTA
* *
182342 GGGTAACTTGGCTATAAAAGG
65 GGGTAACTCGGATATAAAAGG
182363 GTGTGTTATG
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 7 0.09
90 72 0.91
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.35
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAACTAATTTGAAATAATAAAAACCCTAATATGACTAG
GGTAACTCGGATATAAAAGGATTA
Found at i:184910 original size:20 final size:20
Alignment explanation
Indices: 184837--184903 Score: 91
Period size: 20 Copynumber: 3.3 Consensus size: 20
184827 CAAAAAAACA
*
184837 AAAAAAACAAAAAAAG-GCAA
1 AAAAAAACAAAAAAAGAGC-C
*
184857 AAAAAAACAAAAAAAAGAGGC
1 AAAAAAAC-AAAAAAAGAGCC
184878 AAAAAAACAAAAAAAGAGCC
1 AAAAAAACAAAAAAAGAGCC
184898 AAAAAA
1 AAAAAA
184904 GCCAAAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 25 0.60
21 16 0.38
22 1 0.02
ACGTcount: A:0.79, C:0.10, G:0.10, T:0.00
Consensus pattern (20 bp):
AAAAAAACAAAAAAAGAGCC
Found at i:184910 original size:21 final size:21
Alignment explanation
Indices: 184835--184903 Score: 97
Period size: 21 Copynumber: 3.3 Consensus size: 21
184825 TTCAAAAAAA
184835 CAAAAAAAACAAAAAAAG-GC
1 CAAAAAAAACAAAAAAAGAGC
* *
184855 AAAAAAAAACAAAAAAAAGAGG
1 CAAAAAAAAC-AAAAAAAGAGC
184877 C-AAAAAAACAAAAAAAGAGC
1 CAAAAAAAACAAAAAAAGAGC
184897 CAAAAAA
1 CAAAAAA
184904 GCCAAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 20 0.48
21 21 0.50
22 1 0.02
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (21 bp):
CAAAAAAAACAAAAAAAGAGC
Found at i:191414 original size:14 final size:15
Alignment explanation
Indices: 191391--191419 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
191381 AAATTGCTTC
191391 TTTTCATTTTCTTTT
1 TTTTCATTTTCTTTT
191406 TTTTC-TTTTCTTTT
1 TTTTCATTTTCTTTT
191420 GCACTCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCATTTTCTTTT
Found at i:191686 original size:17 final size:17
Alignment explanation
Indices: 191664--191708 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
191654 TGATAATTAA
191664 GAAATGAAAAGTAAATG
1 GAAATGAAAAGTAAATG
191681 GAAATGAAAAGTAAATG
1 GAAATGAAAAGTAAATG
191698 GAAATGGAAAA
1 GAAAT-GAAAA
191709 AATTGAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 22 0.81
18 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (17 bp):
GAAATGAAAAGTAAATG
Found at i:192293 original size:19 final size:20
Alignment explanation
Indices: 192246--192296 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
192236 GAAACCCATT
**
192246 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
192266 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
192285 TGAAGATACATG
1 TGAAAATACATG
192297 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:192810 original size:41 final size:41
Alignment explanation
Indices: 192753--192838 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
192743 GCTACATGCT
*
192753 AGCTCCTTTAGCTAAGTTGAAACTCCTTAAATGATGAAATG
1 AGCTCCTCTAGCTAAGTTGAAACTCCTTAAATGATGAAATG
192794 AGCTCCTCTAGCTAAGTTGAAACTCCTTAAATGATGAAATG
1 AGCTCCTCTAGCTAAGTTGAAACTCCTTAAATGATGAAATG
192835 AGCT
1 AGCT
192839 GCCATAACAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (41 bp):
AGCTCCTCTAGCTAAGTTGAAACTCCTTAAATGATGAAATG
Found at i:194337 original size:35 final size:36
Alignment explanation
Indices: 194289--194357 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
194279 ATTAATAAGT
*
194289 TGGTGATAATATAGGCGTG-ATATAGTAATGGAATA
1 TGGTGATAATATAGGCGTGAAAATAGTAATGGAATA
** *
194324 TGGTGATGTTATAGGCGTGAAAATGGTAATGGAA
1 TGGTGATAATATAGGCGTGAAAATAGTAATGGAA
194358 GGTGGTGACG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 17 0.59
36 12 0.41
ACGTcount: A:0.35, C:0.03, G:0.32, T:0.30
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGAAAATAGTAATGGAATA
Found at i:194364 original size:36 final size:35
Alignment explanation
Indices: 194289--194365 Score: 91
Period size: 36 Copynumber: 2.2 Consensus size: 35
194279 ATTAATAAGT
* *
194289 TGGTGATAATATAGGCGTGATATAGTAATGGAATA
1 TGGTGATAATATAGGCGTGAAATAGTAATGGAAGA
** * *
194324 TGGTGATGTTATAGGCGTGAAAATGGTAATGGAAGG
1 TGGTGATAATATAGGCGTG-AAATAGTAATGGAAGA
194360 TGGTGA
1 TGGTGA
194366 CGAATAGATA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
35 17 0.49
36 18 0.51
ACGTcount: A:0.32, C:0.03, G:0.35, T:0.30
Consensus pattern (35 bp):
TGGTGATAATATAGGCGTGAAATAGTAATGGAAGA
Found at i:198223 original size:20 final size:20
Alignment explanation
Indices: 198185--198222 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
198175 TGCTTCACTT
*
198185 TTCTTTTGCTTTTGATTTTC
1 TTCTTTTGCTTTTCATTTTC
*
198205 TTCTTTTTCTTTTC-TTTT
1 TTCTTTTGCTTTTCATTTT
198223 TTTTGCACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (20 bp):
TTCTTTTGCTTTTCATTTTC
Found at i:198513 original size:15 final size:15
Alignment explanation
Indices: 198489--198524 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
198479 TATAATAATT
*
198489 AAGAAATGAAATGAA
1 AAGAATTGAAATGAA
198504 AAGAATTGAAATGAA
1 AAGAATTGAAATGAA
*
198519 TAGAAT
1 AAGAAT
198525 AGTTATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.19
Consensus pattern (15 bp):
AAGAATTGAAATGAA
Found at i:204268 original size:24 final size:21
Alignment explanation
Indices: 204234--204276 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
204224 TGCACAAGAT
*
204234 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
204256 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
204277 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:207185 original size:36 final size:36
Alignment explanation
Indices: 207134--207213 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
207124 GGCGTGAAAG
* *
207134 TGATGGAATATGGTGATGATATAGACGTGATAATGA
1 TGATGGACTACGGTGATGATATAGACGTGATAATGA
* *
207170 TGATGGACTACGGTGATGATATAGGCGTGATAATGG
1 TGATGGACTACGGTGATGATATAGACGTGATAATGA
207206 TGATGGAC
1 TGATGGAC
207214 AGATTATATC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.31, C:0.06, G:0.34, T:0.29
Consensus pattern (36 bp):
TGATGGACTACGGTGATGATATAGACGTGATAATGA
Found at i:211309 original size:36 final size:36
Alignment explanation
Indices: 211260--211340 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
211250 TGGCGTGAAA
*
211260 GTGATGGAATATGGTGATGATATAGACGTGATAATG
1 GTGATGGACTATGGTGATGATATAGACGTGATAATG
*
211296 GTGATGGACTATGGTGATGATATAGGCGTGATAATG
1 GTGATGGACTATGGTGATGATATAGACGTGATAATG
211332 GTGATGGAC
1 GTGATGGAC
211341 AGATTGTATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
GTGATGGACTATGGTGATGATATAGACGTGATAATG
Found at i:211728 original size:19 final size:20
Alignment explanation
Indices: 211681--211731 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
211671 GAAACCCCTT
**
211681 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
211701 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
211720 TGAAGATACATG
1 TGAAAATACATG
211732 CTCTTGGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:220414 original size:19 final size:19
Alignment explanation
Indices: 220390--220444 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
220380 TAGTGTTCCA
220390 TGAGCTGCCATGTTCCTTG
1 TGAGCTGCCATGTTCCTTG
220409 TGA---G-C-TGTT--T-G
1 TGAGCTGCCATGTTCCTTG
220420 TGAGCTGCCATGTTCCTTG
1 TGAGCTGCCATGTTCCTTG
220439 TGAGCT
1 TGAGCT
220445 ATTTGTGAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
12 1 0.04
14 5 0.18
15 2 0.07
16 5 0.18
18 1 0.04
19 10 0.36
ACGTcount: A:0.11, C:0.22, G:0.29, T:0.38
Consensus pattern (19 bp):
TGAGCTGCCATGTTCCTTG
Found at i:220425 original size:30 final size:30
Alignment explanation
Indices: 220390--220457 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
220380 TAGTGTTCCA
*
220390 TGAGCTGCCATGTTCCTTGTGAGCTGTTTG
1 TGAGCTGCCATGTTCCTTGTGAGCTATTTG
220420 TGAGCTGCCATGTTCCTTGTGAGCTATTTG
1 TGAGCTGCCATGTTCCTTGTGAGCTATTTG
220450 TGAGCTGC
1 TGAGCTGC
220458 ATTTAATGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.12, C:0.21, G:0.29, T:0.38
Consensus pattern (30 bp):
TGAGCTGCCATGTTCCTTGTGAGCTATTTG
Found at i:223103 original size:14 final size:15
Alignment explanation
Indices: 223074--223106 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
223064 CAACCATCTC
223074 TTTCAATACTTTCTA
1 TTTCAATACTTTCTA
*
223089 TTTCATTAC-TTCTA
1 TTTCAATACTTTCTA
223103 TTTC
1 TTTC
223107 TTAATCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTCAATACTTTCTA
Found at i:247700 original size:19 final size:19
Alignment explanation
Indices: 247654--247702 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
247644 ATCAGCAAAG
*
247654 GAAAAGAAGCACTCAAAAA
1 GAAAAAAAGCACTCAAAAA
***
247673 GATTGAAAGCACTCAAAAA
1 GAAAAAAAGCACTCAAAAA
247692 GAAAAAAAGCA
1 GAAAAAAAGCA
247703 AAGAAAAGAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.61, C:0.14, G:0.16, T:0.08
Consensus pattern (19 bp):
GAAAAAAAGCACTCAAAAA
Found at i:251383 original size:12 final size:13
Alignment explanation
Indices: 251368--251396 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
251358 AATACAAAAA
251368 GAAGTGCAAAGT-
1 GAAGTGCAAAGTC
251380 GAAGTGCAAAGTC
1 GAAGTGCAAAGTC
251393 GAAG
1 GAAG
251397 AAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.41, C:0.10, G:0.34, T:0.14
Consensus pattern (13 bp):
GAAGTGCAAAGTC
Found at i:251465 original size:20 final size:19
Alignment explanation
Indices: 251422--251460 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
251412 AAAGGAAAAG
*
251422 AAGCACTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
251441 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
251459 AA
1 AA
251461 AAGCAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:269256 original size:23 final size:22
Alignment explanation
Indices: 269210--269260 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
269200 AAGAAAAATC
269210 AGAAAATAAGCACTCAAAAAGA
1 AGAAAATAAGCACTCAAAAAGA
269232 AGAAAATGAAAGCACTC-AAAAGA
1 AGAAAAT--AAGCACTCAAAAAGA
269255 AGAAAA
1 AGAAAA
269261 AAGAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 7 0.26
23 12 0.44
24 8 0.30
ACGTcount: A:0.65, C:0.12, G:0.16, T:0.08
Consensus pattern (22 bp):
AGAAAATAAGCACTCAAAAAGA
Found at i:269261 original size:24 final size:24
Alignment explanation
Indices: 269217--269267 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
269207 ATCAGAAAAT
*
269217 AAGCACTCAAAAAGAAGAAAATGA
1 AAGCACTCAAAAAGAAGAAAAAGA
269241 AAGCACTC-AAAAGAAGAAAAAAGA
1 AAGCACTCAAAAAGAAG-AAAAAGA
269265 AAG
1 AAG
269268 AAAAGTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.65, C:0.12, G:0.18, T:0.06
Consensus pattern (24 bp):
AAGCACTCAAAAAGAAGAAAAAGA
Found at i:270438 original size:35 final size:37
Alignment explanation
Indices: 270393--270466 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 37
270383 GAGAATTTGG
* * *
270393 TGATATAGGCGTGAT-ATGG-TGATGGACTATGGTGA
1 TGATACAGGCGTGATAATGGAAGATGGACTATGGGGA
*
270428 TGATACAGGCGTGATAATGGAAGATGGATTATGGGGA
1 TGATACAGGCGTGATAATGGAAGATGGACTATGGGGA
270465 TG
1 TG
270467 GAAATAGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 14 0.42
36 4 0.12
37 15 0.45
ACGTcount: A:0.28, C:0.05, G:0.38, T:0.28
Consensus pattern (37 bp):
TGATACAGGCGTGATAATGGAAGATGGACTATGGGGA
Found at i:270849 original size:18 final size:19
Alignment explanation
Indices: 270804--270852 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
270794 AAATCCCTTA
*
270804 GAAAATACATGATTTTTGAT
1 GAAAATACATGA-TTTTAAT
270824 GAAAATACATGA-TTTAAT
1 GAAAATACATGATTTTAAT
*
270842 GAAGATACATG
1 GAAAATACATG
270853 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 15 0.56
20 12 0.44
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (19 bp):
GAAAATACATGATTTTAAT
Done.