Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008150.1 Kokia drynarioides strain JFW-HI SEQ_122809, 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: 32618
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Found at i:5582 original size:96 final size:95
Alignment explanation
Indices: 5422--5637 Score: 254
Period size: 95 Copynumber: 2.3 Consensus size: 95
5412 TCAATATCCC
* * ** *
5422 TGAGGTTACAATGGACTAGAGTGAGACTTCAAAACCCCATCTTCCTAGTGAGGTATAGAGAAGTG
1 TGAGGTTACAATGGAGTGGAGTGAGACTTC-GTATCCCATCTTCCTAGTGAGGTATAGAGAAGTG
* * *
5487 GGTTAAAATAATGAAGGA-GAACACAACGTCCT
65 GATCAAAAT-AGGAA-GATGAACACAACGTCCT
** * * *
5519 TGAGGTTTTAGTGGAGTGGAGTGAGACTTCGTATCCCATCTTCTTGGTGAGGTATAGAGAAGTGG
1 TGAGGTTACAATGGAGTGGAGTGAGACTTCGTATCCCATCTTCCTAGTGAGGTATAGAGAAGTGG
* * *
5584 ATCAAAATAGGTAGATGAGCTCAACGTCCT
66 ATCAAAATAGGAAGATGAACACAACGTCCT
5614 TGAGGTTACAATGGAGTGGAGTGA
1 TGAGGTTACAATGGAGTGGAGTGA
5638 AGCACTAGAT
Statistics
Matches: 99, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
94 2 0.02
95 36 0.36
96 36 0.36
97 25 0.25
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (95 bp):
TGAGGTTACAATGGAGTGGAGTGAGACTTCGTATCCCATCTTCCTAGTGAGGTATAGAGAAGTGG
ATCAAAATAGGAAGATGAACACAACGTCCT
Found at i:6083 original size:59 final size:59
Alignment explanation
Indices: 6015--6247 Score: 206
Period size: 59 Copynumber: 3.9 Consensus size: 59
6005 ATGTTTTGAC
6015 CCCTAAACTTTT-CAAAAATTTGAAATTAACCCTTAAACTTTCTAAAAATTCAAATTAAA
1 CCCTAAA-TTTTCCAAAAATTTGAAATTAACCCTTAAACTTTCTAAAAATTCAAATTAAA
* * * * *
6074 CCCTAAACTTTCCAAAAA-TTCAAATTTAAACCC-TAAACTTTTTAGAAATTCAAATTTAAC
1 CCCTAAATTTTCCAAAAATTTGAAA-TT-AACCCTTAAACTTTCTAAAAATTCAAA-TTAAA
* * ** * * * **
6134 CCCTAAATTTTCCAAAAATTTGAATTTGACCCTCGAATTTTCCAAAAATTCCAATTTGA
1 CCCTAAATTTTCCAAAAATTTGAAATTAACCCTTAAACTTTCTAAAAATTCAAATTAAA
* * * * * *
6193 CCCTTAATTTTCCAAAAATTAG-ATTTGACCCCTAAAGC-TTCAAAAAATTCAAATT
1 CCCTAAATTTTCCAAAAATTTGAAATTAACCCTTAAA-CTTTCTAAAAATTCAAATT
6248 TGACCCCATT
Statistics
Matches: 140, Mismatches: 27, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
58 34 0.24
59 60 0.43
60 42 0.30
61 4 0.03
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.34
Consensus pattern (59 bp):
CCCTAAATTTTCCAAAAATTTGAAATTAACCCTTAAACTTTCTAAAAATTCAAATTAAA
Found at i:6160 original size:30 final size:30
Alignment explanation
Indices: 5983--6228 Score: 164
Period size: 30 Copynumber: 8.3 Consensus size: 30
5973 ATTATTTTTT
* * * *
5983 ACCCTTAAATTGTCCAAAAATTATG-TTTTG
1 ACCCCTAAATTTTCCAAAAATT-TGAATTTA
*
6013 ACCCCTAAACTTTT-CAAAAATTTGAAATTA
1 ACCCCTAAA-TTTTCCAAAAATTTGAATTTA
* * * * *
6043 ACCCTTAAACTTTCTAAAAA-TTCAAATTA
1 ACCCCTAAATTTTCCAAAAATTTGAATTTA
* * **
6072 AACCCTAAACTTTCCAAAAATTCAAATTTA
1 ACCCCTAAATTTTCCAAAAATTTGAATTTA
* * * **
6102 AACCCTAAACTTTT-TAGAAATTCAAATTTA
1 ACCCCTAAA-TTTTCCAAAAATTTGAATTTA
*
6132 ACCCCTAAATTTTCCAAAAATTTGAATTTG
1 ACCCCTAAATTTTCCAAAAATTTGAATTTA
* ** *
6162 A-CCCTCGAATTTTCCAAAAATTCCAATTTG
1 ACCCCT-AAATTTTCCAAAAATTTGAATTTA
* * *
6192 A-CCCTTAATTTTCCAAAAATTAG-ATTTG
1 ACCCCTAAATTTTCCAAAAATTTGAATTTA
6220 ACCCCTAAA
1 ACCCCTAAA
6229 GCTTCAAAAA
Statistics
Matches: 177, Mismatches: 31, Indels: 17
0.79 0.14 0.08
Matches are distributed among these distances:
28 6 0.03
29 59 0.33
30 106 0.60
31 6 0.03
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (30 bp):
ACCCCTAAATTTTCCAAAAATTTGAATTTA
Found at i:6251 original size:30 final size:30
Alignment explanation
Indices: 6009--6254 Score: 216
Period size: 30 Copynumber: 8.3 Consensus size: 30
5999 AAAATTATGT
* *
6009 TTTGACCCCTAAACTTTTCAAAAATTTGAAA
1 TTTGACCCCTAAACTTTCCAAAAA-TTCAAA
* * *
6040 -TTAACCCTTAAACTTTCTAAAAATTCAAA
1 TTTGACCCCTAAACTTTCCAAAAATTCAAA
* *
6069 -TTAAACCCTAAACTTTCCAAAAATTCAAA
1 TTTGACCCCTAAACTTTCCAAAAATTCAAA
* * ** *
6098 TTTAAACCCTAAACTTTTTAGAAATTCAAA
1 TTTGACCCCTAAACTTTCCAAAAATTCAAA
* * **
6128 TTTAACCCCTAAATTTTCCAAAAATTTGAA
1 TTTGACCCCTAAACTTTCCAAAAATTCAAA
* * *
6158 TTTGA-CCCTCGAATTTTCCAAAAATTCCAA
1 TTTGACCCCT-AAACTTTCCAAAAATTCAAA
* * *
6188 TTTGA-CCCTTAATTTTCCAAAAATT-AGA
1 TTTGACCCCTAAACTTTCCAAAAATTCAAA
*
6216 TTTGACCCCTAAAGC-TTCAAAAAATTCAAA
1 TTTGACCCCTAAA-CTTTCCAAAAATTCAAA
6246 TTTGACCCC
1 TTTGACCCC
6255 ATTTTAATGT
Statistics
Matches: 181, Mismatches: 29, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
28 6 0.03
29 66 0.36
30 109 0.60
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (30 bp):
TTTGACCCCTAAACTTTCCAAAAATTCAAA
Found at i:6319 original size:20 final size:21
Alignment explanation
Indices: 6279--6323 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
6269 AATTAATTAT
6279 TTATTTTATCTTATATGTATA
1 TTATTTTATCTTATATGTATA
*
6300 TTATTTTATTTTAT-TGTATA
1 TTATTTTATCTTATATGTATA
6320 TTAT
1 TTAT
6324 GTATATATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (21 bp):
TTATTTTATCTTATATGTATA
Found at i:10764 original size:21 final size:21
Alignment explanation
Indices: 10740--10779 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
10730 AAAAAATAGA
10740 GAAAAAGAAAT-AAAGAAAAAG
1 GAAAAA-AAATAAAAGAAAAAG
*
10761 GAAAAAAATTAAAAGAAAA
1 GAAAAAAAATAAAAGAAAA
10780 GGAGAGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (21 bp):
GAAAAAAAATAAAAGAAAAAG
Found at i:11281 original size:112 final size:112
Alignment explanation
Indices: 11084--11301 Score: 321
Period size: 112 Copynumber: 1.9 Consensus size: 112
11074 TGATTAATGT
* *
11084 TTAATTTTCTCATTCATGCGAGCTTTGCCTCCAATAAAATTGAATTTTACCCACCTCACAACCCT
1 TTAATTTTCTCATTCATGCGAGCTTTGCCTCCAATAAAATTCAATGTTACCCACCTCACAACCCT
*
11149 ATTTAAGCATTTTTGCATTGAAATGACGGTTAGTGGACTAATGATTG
66 ATTCAAGCATTTTTGCATTGAAATGACGGTTAGTGGACTAATGATTG
* * * * * *
11196 TTAATCTTT-TCATTCATGCGAGCTTTGCCTCTAATCAAATTCAATGTTATCCACTTTACAATCC
1 TTAAT-TTTCTCATTCATGCGAGCTTTGCCTCCAATAAAATTCAATGTTACCCACCTCACAACCC
* *
11260 TGTTCAAGCATTTTTGCATTGAAATGACGGTTAGTGGTCTAA
65 TATTCAAGCATTTTTGCATTGAAATGACGGTTAGTGGACTAA
11302 CGATATAATA
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
112 91 0.97
113 3 0.03
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (112 bp):
TTAATTTTCTCATTCATGCGAGCTTTGCCTCCAATAAAATTCAATGTTACCCACCTCACAACCCT
ATTCAAGCATTTTTGCATTGAAATGACGGTTAGTGGACTAATGATTG
Found at i:12260 original size:97 final size:96
Alignment explanation
Indices: 12130--12373 Score: 346
Period size: 97 Copynumber: 2.5 Consensus size: 96
12120 TGGGTCGAAA
* * * *
12130 AAAATAATGAAGCAGAGCTCAATGTCCATGAGGTTACAATGGAGTGGAGTGAGACTTTAAAATCC
1 AAAATAATGAAGAAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAGA-TTTAAAATCC
* * *
12195 CATCTTCTTGGTGTGGTACAGAGAAGTGGGTC
65 CATCTTCCTGGTGAGGTACAAAGAAGTGGGTC
* * * **
12227 AAAATAATGAAGGAGAACTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAGATTTCAAATTGC
1 AAAATAATGAAGAAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAGATTTAAAATCCC
12292 ATCTTCCTGGTGAGGTACAAAGAAGTGGGTC
66 ATCTTCCTGGTGAGGTACAAAGAAGTGGGTC
* *
12323 AAAAT-AGGAAGAAGAGCTCAACATCCTTGAGGTTACAGTGGAGTGGAGTGA
1 AAAATAATGAAGAAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGA
12374 AGCACTAGAT
Statistics
Matches: 132, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
95 42 0.32
96 41 0.31
97 49 0.37
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (96 bp):
AAAATAATGAAGAAGAGCTCAACGTCCTTGAGGTTACAGTGGAGTGGAGTGAGATTTAAAATCCC
ATCTTCCTGGTGAGGTACAAAGAAGTGGGTC
Found at i:12542 original size:42 final size:42
Alignment explanation
Indices: 12475--13094 Score: 366
Period size: 42 Copynumber: 15.5 Consensus size: 42
12465 GAAGTTGCAT
* * *
12475 CATCATCCACTCTTTTACCCCGATCATGGGGCAGATTGAAGA
1 CATCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
* **
12517 CATTATCCAATCTCTTACCCTGATCATGGGAAAGATTGAAGA
1 CATCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
* * *
12559 CATCATCCAATCTCTTACCCCGATAATGGGGTAGATT---G-
1 CATCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
12597 -A-C-T--AATCTCTTA-CCTCGATCATGGGGCAGATTGAAG-
1 CATCATCCAATCTCTTACCCT-GATCATGGGGCAGATTGAAGA
* * * ** * * *
12633 CA-C--CCGATCTCTTACCCTGTTCATAGGAAAGATGGCAGG
1 CATCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
*
12672 CATCATCCAATCTCTTA-CCTCGATCATGGGGTAGATTGAAGA
1 CATCATCCAATCTCTTACCCT-GATCATGGGGCAGATTGAAGA
* * * *
12714 CATCATCCAATCTTTTACCCTAATTA-GAGGGCAAATTGAAGA
1 CATCATCCAATCTCTTACCCTGATCATG-GGGCAGATTGAAGA
** * * * * *
12756 C--CATTTAATCTTTTACCCCGATCATGGGGCAGATGGAGGG
1 CATCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
* *
12796 CATCATCCAATCTCTTACCCTGATCATGGAGCAGATTTAAGA
1 CATCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
* * *
12838 CATCATCCAATCTTTTACCCTAATTA-GAGGGCAGATTGAAGA
1 CATCATCCAATCTCTTACCCTGATCATG-GGGCAGATTGAAGA
** *
12880 CA--ATTTAATCTTTTACCCCT-A-CAATGGGGCAGATTGAAG-
1 CATCATCCAATCTCTTA-CCCTGATC-ATGGGGCAGATTGAAGA
* * * *
12919 CA--ATCCAATCTTTTACACT-AAC-TAGAGGGCAAATTGAAGA
1 CATCATCCAATCTCTTACCCTGATCAT-G-GGGCAGATTGAAGA
* * * *
12959 C--CATCCGATCTCTTACCCCGACCATGGGGTAGATTGAAG-
1 CATCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
* * * * *
12998 --TAATCCAACCTTTTACCCT-AAC-TAGAGGGCAGACTGAAGA
1 CATCATCCAATCTCTTACCCTGATCAT-G-GGGCAGATTGAAGA
* * * **
13038 C--CATCCAATCTCCTACCCCGACCATGGGGTTGATTGAA-A
1 CATCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
*
13077 CA--ATCCAATCTTTTACCC
1 CATCATCCAATCTCTTACCC
13095 CTAAAGCCAT
Statistics
Matches: 451, Mismatches: 90, Indels: 77
0.73 0.15 0.12
Matches are distributed among these distances:
32 2 0.00
33 23 0.05
35 1 0.00
36 2 0.00
37 5 0.01
38 30 0.07
39 72 0.16
40 103 0.23
41 17 0.04
42 193 0.43
43 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (42 bp):
CATCATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
Found at i:12609 original size:33 final size:33
Alignment explanation
Indices: 12567--12630 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
12557 GACATCATCC
*
12567 AATCTCTTACCCCGATAATGGGGTAGATTGACT
1 AATCTCTTACCCCGATAATGGGGCAGATTGACT
* *
12600 AATCTCTTACCTCGATCATGGGGCAGATTGA
1 AATCTCTTACCCCGATAATGGGGCAGATTGA
12631 AGCACCCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (33 bp):
AATCTCTTACCCCGATAATGGGGCAGATTGACT
Found at i:12701 original size:113 final size:115
Alignment explanation
Indices: 12489--12710 Score: 322
Period size: 113 Copynumber: 1.9 Consensus size: 115
12479 ATCCACTCTT
* * *
12489 TTACCCCGATCATGGGGCAGATTGAAGACATTATCCAATCTCTTACCCTGATCATGGGAAAGATT
1 TTACCCCGATCATGGGGCAGATTGAAGAC--TACCCAATCTCTTACCCTGATCATAGGAAAGATG
12554 GAAGACATCATCCAATCTCTTACCCCGATAATGGGGTAGATTGACTAATCTC
64 GAAGACATCATCCAATCTCTTACCCCGATAATGGGGTAGATTGACTAATCTC
* * * *
12606 TTACCTCGATCATGGGGCAGATTGAAG-C-ACCCGATCTCTTACCCTGTTCATAGGAAAGATGGC
1 TTACCCCGATCATGGGGCAGATTGAAGACTACCCAATCTCTTACCCTGATCATAGGAAAGATGGA
* * *
12669 AGGCATCATCCAATCTCTTACCTCGATCATGGGGTAGATTGA
66 AGACATCATCCAATCTCTTACCCCGATAATGGGGTAGATTGA
12711 AGACATCATC
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
113 68 0.72
116 1 0.01
117 26 0.27
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (115 bp):
TTACCCCGATCATGGGGCAGATTGAAGACTACCCAATCTCTTACCCTGATCATAGGAAAGATGGA
AGACATCATCCAATCTCTTACCCCGATAATGGGGTAGATTGACTAATCTC
Found at i:12821 original size:124 final size:124
Alignment explanation
Indices: 12662--12913 Score: 402
Period size: 124 Copynumber: 2.0 Consensus size: 124
12652 TTCATAGGAA
* *
12662 AGATGGCAGGCATCATCCAATCTCTTACCTCGATCATGGGGTAGATTGAAGACATCATCCAATCT
1 AGATGGCAGGCATCATCCAATCTCTTACCTCGATCATGGAGCAGATTGAAGACATCATCCAATCT
*
12727 TTTACCCTAATTAGAGGGCAAATTGAAGACCATTTAATCTTTTACCCCGATC-ATGGGGC
66 TTTACCCTAATTAGAGGGCAAATTGAAGACAATTTAATCTTTTACCCCGA-CAATGGGGC
*
12786 AGATGG-AGGGCATCATCCAATCTCTTACC-CTGATCATGGAGCAGATTTAAGACATCATCCAAT
1 AGATGGCA-GGCATCATCCAATCTCTTACCTC-GATCATGGAGCAGATTGAAGACATCATCCAAT
* *
12849 CTTTTACCCTAATTAGAGGGCAGATTGAAGACAATTTAATCTTTTACCCCTACAATGGGGC
64 CTTTTACCCTAATTAGAGGGCAAATTGAAGACAATTTAATCTTTTACCCCGACAATGGGGC
12910 AGAT
1 AGAT
12914 TGAAGCAATC
Statistics
Matches: 119, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
123 3 0.03
124 116 0.97
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (124 bp):
AGATGGCAGGCATCATCCAATCTCTTACCTCGATCATGGAGCAGATTGAAGACATCATCCAATCT
TTTACCCTAATTAGAGGGCAAATTGAAGACAATTTAATCTTTTACCCCGACAATGGGGC
Found at i:12838 original size:82 final size:83
Alignment explanation
Indices: 12675--12857 Score: 208
Period size: 82 Copynumber: 2.2 Consensus size: 83
12665 TGGCAGGCAT
* * * * * *
12675 CATCCAATCTCTTACCTCGATCATGGGGTAGATTGAAGACATCATCCAATCTTTTACCCTAATTA
1 CATCCAATCTTTTACCCCGATCATGGGGCAGATGGAAGACATCATCCAATCTCTTACCCTAATCA
*
12740 GAGGGCAAATTGAAGAC-
66 GAGAGCAAATTGAAGACA
** * * *
12757 CATTTAATCTTTTACCCCGATCATGGGGCAGATGGAGGGCATCATCCAATCTCTTACCCTGATCA
1 CATCCAATCTTTTACCCCGATCATGGGGCAGATGGAAGACATCATCCAATCTCTTACCCTAATCA
* *
12822 TG-GAGCAGATTTAAGACA
66 -GAGAGCAAATTGAAGACA
12840 TCATCCAATCTTTTACCC
1 -CATCCAATCTTTTACCC
12858 TAATTAGAGG
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
82 66 0.80
83 1 0.01
84 15 0.18
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (83 bp):
CATCCAATCTTTTACCCCGATCATGGGGCAGATGGAAGACATCATCCAATCTCTTACCCTAATCA
GAGAGCAAATTGAAGACA
Found at i:12945 original size:79 final size:79
Alignment explanation
Indices: 12799--13094 Score: 367
Period size: 79 Copynumber: 3.7 Consensus size: 79
12789 TGGAGGGCAT
* * * * * *
12799 CATCCAATCTCTTACCCTGATCATGGAGCAGATTTAAGACATCATCCAATCTTTTACCCTAATTA
1 CATCCAATCTCTTACCCCGACCATGGGGTAGATTGAAG-CA--ATCCAATCTTTTACCCTAACTA
12864 GAGGGCAGATTGAAGAC
63 GAGGGCAGATTGAAGAC
* ** * * * * *
12881 AATTTAATCTTTTACCCCTACAATGGGGCAGATTGAAGCAATCCAATCTTTTACACTAACTAGAG
1 CATCCAATCTCTTACCCCGACCATGGGGTAGATTGAAGCAATCCAATCTTTTACCCTAACTAGAG
*
12946 GGCAAATTGAAGAC
66 GGCAGATTGAAGAC
* * *
12960 CATCCGATCTCTTACCCCGACCATGGGGTAGATTGAAGTAATCCAACCTTTTACCCTAACTAGAG
1 CATCCAATCTCTTACCCCGACCATGGGGTAGATTGAAGCAATCCAATCTTTTACCCTAACTAGAG
*
13025 GGCAGACTGAAGAC
66 GGCAGATTGAAGAC
* * *
13039 CATCCAATCTCCTACCCCGACCATGGGGTTGATTGAAACAATCCAATCTTTTACCC
1 CATCCAATCTCTTACCCCGACCATGGGGTAGATTGAAGCAATCCAATCTTTTACCC
13095 CTAAAGCCAT
Statistics
Matches: 182, Mismatches: 32, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
79 152 0.84
81 2 0.01
82 28 0.15
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (79 bp):
CATCCAATCTCTTACCCCGACCATGGGGTAGATTGAAGCAATCCAATCTTTTACCCTAACTAGAG
GGCAGATTGAAGAC
Found at i:13095 original size:39 final size:40
Alignment explanation
Indices: 12676--13095 Score: 251
Period size: 40 Copynumber: 10.4 Consensus size: 40
12666 GGCAGGCATC
* * * * *
12676 ATCCAATCTCTTACCTCGATCATGGGGTAGATTGAAGACA
1 ATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAGACA
* ** * *
12716 TCATCCAATCTTTTACCCTAATTA-GAGGGCAAATTGAAGACC
1 --ATCCAATCTTTTACCCCAACCATG-GGGCAGATTGAAGACA
** * * * * *
12758 ATTTAATCTTTTACCCCGATCATGGGGCAGATGGAGGGCA
1 ATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAGACA
* ** * * *
12798 TCATCCAATCTCTTACCCTGATCATGGAGCAGATTTAAGACA
1 --ATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAGACA
* **
12840 TCATCCAATCTTTTACCCTAATTA-GAGGGCAGATTGAAGACA
1 --ATCCAATCTTTTACCCCAACCATG-GGGCAGATTGAAGACA
** * *
12882 ATTTAATCTTTTACCCCTACAATGGGGCAGATTGAAG-CA
1 ATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAGACA
* * * * *
12921 ATCCAATCTTTTACACTAACTA-GAGGGCAAATTGAAGACC
1 ATCCAATCTTTTACCCCAACCATG-GGGCAGATTGAAGACA
* * * * *
12961 ATCCGATCTCTTACCCCGACCATGGGGTAGATTGAAG-TA
1 ATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAGACA
* * * * *
13000 ATCCAACCTTTTACCCTAACTA-GAGGGCAGACTGAAGACC
1 ATCCAATCTTTTACCCCAACCATG-GGGCAGATTGAAGACA
** * **
13040 ATCCAATCTCCTACCCCGACCATGGGGTTGATTGAA-ACA
1 ATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAGACA
13079 ATCCAATCTTTTACCCC
1 ATCCAATCTTTTACCCC
13096 TAAAGCCATA
Statistics
Matches: 288, Mismatches: 78, Indels: 27
0.73 0.20 0.07
Matches are distributed among these distances:
38 2 0.01
39 74 0.26
40 110 0.38
41 6 0.02
42 96 0.33
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (40 bp):
ATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAGACA
Found at i:14875 original size:30 final size:30
Alignment explanation
Indices: 14763--15070 Score: 202
Period size: 30 Copynumber: 10.3 Consensus size: 30
14753 ATTTTTAAAA
* *
14763 AATTTGACCCCTAAATTATCCAAAAATTATG
1 AATTTGACCCTTAAATTTTCCAAAAATT-TG
* * * ** *
14794 -TTTTAACCCCTAAAATTTTTTAAAAA-TTC
1 AATTTGA-CCCTTAAATTTTCCAAAAATTTG
* * *
14823 AAATT-AACCTCTAAACTTTCCAAAAATTTG
1 AATTTGACCCT-TAAATTTTCCAAAAATTTG
*
14853 AATTTGACCCTTAAATTTTCCAAAAAATTG
1 AATTTGACCCTTAAATTTTCCAAAAATTTG
* * * * * *
14883 AATTTGAACCTTGAACTTTCTAGAAATTTA
1 AATTTGACCCTTAAATTTTCCAAAAATTTG
* *
14913 AATTTGACCCTTGAATTTTCCAAAAAATTG
1 AATTTGACCCTTAAATTTTCCAAAAATTTG
14943 AATTTGACCCTTAAACTTTT--AAAAATTTG
1 AATTTGACCCTTAAA-TTTTCCAAAAATTTG
** * *
14972 AATTTGACCCTCGAATTTTTCAAAAAATT-
1 AATTTGACCCTTAAATTTTCCAAAAATTTG
* * *
15001 ATATTTAACTCC-TAATTTTTCAAAAAATTTTG
1 A-ATTTGAC-CCTTAAATTTTCCAAAAA-TTTG
* ** **
15033 --TTTGACCCCTAAAGCTTCCAAAAATTCA
1 AATTTGACCCTTAAATTTTCCAAAAATTTG
15061 AATTTGACCC
1 AATTTGACCC
15071 GGTTTTAATG
Statistics
Matches: 210, Mismatches: 52, Indels: 31
0.72 0.18 0.11
Matches are distributed among these distances:
28 11 0.05
29 51 0.24
30 122 0.58
31 26 0.12
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (30 bp):
AATTTGACCCTTAAATTTTCCAAAAATTTG
Found at i:14879 original size:60 final size:60
Alignment explanation
Indices: 14815--15061 Score: 231
Period size: 60 Copynumber: 4.2 Consensus size: 60
14805 AAAATTTTTT
* *
14815 AAAAATTCAAATTAACCTCTAAACTTTCCAAAAATTTGAATTTGACCCTTAAATTTTCCA
1 AAAAATTCAATTTAACCTCTAAACTTTCTAAAAATTTGAATTTGACCCTTAAATTTTCCA
* * * * *
14875 AAAAATTGAATTTGAACCT-TGAACTTTCTAGAAATTTAAATTTGACCCTTGAATTTTCCA
1 AAAAATTCAATTT-AACCTCTAAACTTTCTAAAAATTTGAATTTGACCCTTAAATTTTCCA
* * ** *
14935 AAAAATTGAATTTGACC-CTTAAACTTT-TAAAAATTTGAATTTGACCCTCGAATTTTTCA
1 AAAAATTCAATTTAACCTC-TAAACTTTCTAAAAATTTGAATTTGACCCTTAAATTTTCCA
** * * **
14994 AAAAATT-ATATTTAA-CTCCTAATTTTTCAAAAAATTTTG--TTTGACCCCTAAAGCTTCC-
1 AAAAATTCA-ATTTAACCT-CTAAACTTTCTAAAAA-TTTGAATTTGACCCTTAAATTTTCCA
15052 AAAAATTCAA
1 AAAAATTCAA
15062 ATTTGACCCG
Statistics
Matches: 155, Mismatches: 23, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
58 10 0.06
59 63 0.41
60 73 0.47
61 9 0.06
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.37
Consensus pattern (60 bp):
AAAAATTCAATTTAACCTCTAAACTTTCTAAAAATTTGAATTTGACCCTTAAATTTTCCA
Found at i:14979 original size:59 final size:60
Alignment explanation
Indices: 14815--15000 Score: 259
Period size: 60 Copynumber: 3.1 Consensus size: 60
14805 AAAATTTTTT
* * * *
14815 AAAAATTCAAATT-AACCTCTAAACTTTCCAAAAATTTGAATTTGACCCTTAAATTTTCCA
1 AAAAATTGAATTTGAACCT-TAAACTTTCTAAAAATTTGAATTTGACCCTTGAATTTTCCA
* * *
14875 AAAAATTGAATTTGAACCTTGAACTTTCTAGAAATTTAAATTTGACCCTTGAATTTTCCA
1 AAAAATTGAATTTGAACCTTAAACTTTCTAAAAATTTGAATTTGACCCTTGAATTTTCCA
* * *
14935 AAAAATTGAATTTGACCCTTAAACTTT-TAAAAATTTGAATTTGACCCTCGAATTTTTCA
1 AAAAATTGAATTTGAACCTTAAACTTTCTAAAAATTTGAATTTGACCCTTGAATTTTCCA
14994 AAAAATT
1 AAAAATT
15001 ATATTTAACT
Statistics
Matches: 112, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
59 35 0.31
60 72 0.64
61 5 0.04
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (60 bp):
AAAAATTGAATTTGAACCTTAAACTTTCTAAAAATTTGAATTTGACCCTTGAATTTTCCA
Found at i:15043 original size:29 final size:29
Alignment explanation
Indices: 14914--15044 Score: 106
Period size: 29 Copynumber: 4.4 Consensus size: 29
14904 AGAAATTTAA
* *
14914 ATTTGACCCTTGAATTTTCCAAAAAATTGA-
1 ATTTGACCCCT-AATTTTTCAAAAAATT-AT
* * *
14944 ATTTGACCCTTAAACTTTT-AAAAATTTGA-
1 ATTTGACCCCT-AATTTTTCAAAAAATT-AT
*
14973 ATTTGACCCTCGAATTTTTCAAAAAATTAT
1 ATTTGACCC-CTAATTTTTCAAAAAATTAT
* * *
15003 ATTTAACTCCTAATTTTTCAAAAAATTTT
1 ATTTGACCCCTAATTTTTCAAAAAATTAT
*
15032 GTTTGACCCCTAA
1 ATTTGACCCCTAA
15045 AGCTTCCAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
29 53 0.64
30 30 0.36
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (29 bp):
ATTTGACCCCTAATTTTTCAAAAAATTAT
Found at i:15120 original size:22 final size:21
Alignment explanation
Indices: 15095--15141 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
15085 TTTATTTATT
15095 TATTTATTTTATCTTAGATGTA
1 TATTTATTTTATCTTA-ATGTA
* *
15117 TATTTATTTTATTTTATTGTA
1 TATTTATTTTATCTTAATGTA
15138 TATT
1 TATT
15142 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (21 bp):
TATTTATTTTATCTTAATGTA
Found at i:15146 original size:30 final size:29
Alignment explanation
Indices: 15087--15149 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
15077 AATGTAATTT
* *
15087 TATTTATTTATTTATTTTATCTTAGATGTA
1 TATTTATTTATTTATTGTATATTA-ATGTA
15117 TATTTATTTTATTTTATTGTATATT-ATGTA
1 TATTTA-TTTA-TTTATTGTATATTAATGTA
15147 TAT
1 TAT
15150 ATTGTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 14 0.48
31 4 0.14
32 11 0.38
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (29 bp):
TATTTATTTATTTATTGTATATTAATGTA
Found at i:15154 original size:18 final size:19
Alignment explanation
Indices: 15131--15168 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
15121 TATTTTATTT
15131 TATTG-TATATTATGTATA
1 TATTGTTATATTATGTATA
*
15149 TATTGTTTTTATTATGTATA
1 TATTG-TTATATTATGTATA
15169 CTTGTAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
20 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (19 bp):
TATTGTTATATTATGTATA
Found at i:24522 original size:16 final size:16
Alignment explanation
Indices: 24489--24531 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
24479 AAGTGCTTAG
*
24489 AAAGAAAAA-ATGTTA
1 AAAGAAAAATATGTAA
*
24504 AAAGAAAAATTTGTAA
1 AAAGAAAAATATGTAA
24520 AAAGAAAAATAT
1 AAAGAAAAATAT
24532 TTTTTTAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (16 bp):
AAAGAAAAATATGTAA
Done.