Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005587.1 Kokia drynarioides strain JFW-HI SEQ_119710, 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: 137127
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 70 characters in sequence are not A, C, G, or T
Found at i:4172 original size:59 final size:59
Alignment explanation
Indices: 4099--4216 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
4089 AGATACGTCA
*
4099 AGGTTCAATGTATGCATTTTCAACAGATAATTTCTTAGAATAAAATCATTCTTTCAGAT
1 AGGTTCAATGTATGCATTTTAAACAGATAATTTCTTAGAATAAAATCATTCTTTCAGAT
*
4158 AGGTTCAATTTATGCATTTTAAACAGATAATTTCTTAGAATAAAATCATTCTTTCAGAT
1 AGGTTCAATGTATGCATTTTAAACAGATAATTTCTTAGAATAAAATCATTCTTTCAGAT
4217 TAGTTTTCTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (59 bp):
AGGTTCAATGTATGCATTTTAAACAGATAATTTCTTAGAATAAAATCATTCTTTCAGAT
Found at i:12102 original size:15 final size:16
Alignment explanation
Indices: 12084--12113 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12074 CACAACTCGA
12084 AAAAACA-TTAACGTT
1 AAAAACATTTAACGTT
12099 AAAAACATTTAACGT
1 AAAAACATTTAACGT
12114 GGGTACAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (16 bp):
AAAAACATTTAACGTT
Found at i:12773 original size:15 final size:15
Alignment explanation
Indices: 12750--12779 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12740 ATTGGAGATA
12750 CTTTAAACTTTTTTT
1 CTTTAAACTTTTTTT
*
12765 CTTTCAACTTTTTTT
1 CTTTAAACTTTTTTT
12780 ATGAAACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTTAAACTTTTTTT
Found at i:24148 original size:25 final size:25
Alignment explanation
Indices: 24100--24151 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
24090 TTTTTTTCCG
24100 TCTCATTGGTGACTTTATGATTCTA
1 TCTCATTGGTGACTTTATGATTCTA
24125 TCTCATTGGTGACTTTATGATTCTA
1 TCTCATTGGTGACTTTATGATTCTA
24150 TC
1 TC
24152 ACTATTCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.48
Consensus pattern (25 bp):
TCTCATTGGTGACTTTATGATTCTA
Found at i:39251 original size:48 final size:48
Alignment explanation
Indices: 39178--39381 Score: 194
Period size: 48 Copynumber: 4.2 Consensus size: 48
39168 AAGGAGGAAG
* * *
39178 ATGTGGCAATTTATGGAAAATATGTAGTAGTTCATCTACAAAGTGACT
1 ATGTGGCCATTTATGGCAAATATGTAGCAGTTCATCTACAAAGTGACT
* * * * * * *
39226 TTGTGGTCATTTTTGGCAAATATGTAGCAATTAATTTGCAAAGTGACT
1 ATGTGGCCATTTATGGCAAATATGTAGCAGTTCATCTACAAAGTGACT
* * * **
39274 ATGTGCCCATTTTTGACAAATAAATAGCAGTTCATCTACAAAGTGACT
1 ATGTGGCCATTTATGGCAAATATGTAGCAGTTCATCTACAAAGTGACT
* * * * * *
39322 ATGTGGCCATTTATGGCAATTATGTGGAAGTT-TTACTACAAAATGATT
1 ATGTGGCCATTTATGGCAAATATGTAGCAGTTCAT-CTACAAAGTGACT
*
39370 ATGTGACCATTT
1 ATGTGGCCATTT
39382 TATGATTAAT
Statistics
Matches: 123, Mismatches: 32, Indels: 2
0.78 0.20 0.01
Matches are distributed among these distances:
47 1 0.01
48 122 0.99
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (48 bp):
ATGTGGCCATTTATGGCAAATATGTAGCAGTTCATCTACAAAGTGACT
Found at i:39373 original size:96 final size:95
Alignment explanation
Indices: 39206--39382 Score: 223
Period size: 96 Copynumber: 1.8 Consensus size: 95
39196 AATATGTAGT
* * * * *
39206 AGTTCATCTACAAAGTGACTTTGTGGTCATTTTTGGCAAATATGTAGCAATTAATTTGCAAAGTG
1 AGTTCATCTACAAAGTGACTATGTGGCCATTTATGGCAAATATGTAGCAATT-ATTTACAAAATG
*
39271 ACTATGTGCCCATTTTTGACAAATAAATAGC
65 ACTATGTGACCATTTTTGACAAATAAATAGC
* *
39302 AGTTCATCTACAAAGTGACTATGTGGCCATTTATGGCAATTATGT-GGAAGTT-TTACTACAAAA
1 AGTTCATCTACAAAGTGACTATGTGGCCATTTATGGCAAATATGTAGCAA-TTATT--TACAAAA
*
39365 TGATTATGTGACCATTTT
63 TGACTATGTGACCATTTT
39383 ATGATTAATA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
94 2 0.03
95 3 0.04
96 64 0.93
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (95 bp):
AGTTCATCTACAAAGTGACTATGTGGCCATTTATGGCAAATATGTAGCAATTATTTACAAAATGA
CTATGTGACCATTTTTGACAAATAAATAGC
Found at i:50608 original size:20 final size:20
Alignment explanation
Indices: 50583--50630 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
50573 AAATATAAGT
50583 TCAATCGAACCTCGATTTCA
1 TCAATCGAACCTCGATTTCA
50603 TCAATCGAACCTCGATTTCA
1 TCAATCGAACCTCGATTTCA
50623 TCAATCGA
1 TCAATCGA
50631 CACTATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.29
Consensus pattern (20 bp):
TCAATCGAACCTCGATTTCA
Found at i:59600 original size:40 final size:41
Alignment explanation
Indices: 59545--59649 Score: 135
Period size: 40 Copynumber: 2.6 Consensus size: 41
59535 AAAATGCCTT
* ** *
59545 AAAAAGTAAAGCAATAGCGA-CGTTTTTTCATAAACGCCGC
1 AAAAGGTAAAGCAATAGCGAGCGTTTTCCCATAAACACCGC
* *
59585 AAAAGGTAAAGCAATAG-TAGCGTTTTCCCATAAACACCGT
1 AAAAGGTAAAGCAATAGCGAGCGTTTTCCCATAAACACCGC
59625 AAAAGGTAAAGCAATAGC-AGCGTTT
1 AAAAGGTAAAGCAATAGCGAGCGTTT
59650 ATGGGAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
39 1 0.02
40 56 0.98
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (41 bp):
AAAAGGTAAAGCAATAGCGAGCGTTTTCCCATAAACACCGC
Found at i:59692 original size:43 final size:42
Alignment explanation
Indices: 59625--59757 Score: 164
Period size: 42 Copynumber: 3.2 Consensus size: 42
59615 TAAACACCGT
*
59625 AAAAGGT-AA-AGCAATAGCAGCGTTTATGGGAAAAATACTGC
1 AAAAGGTAAAGAGCAATAGCA-CGTTTATGGGAAAAATGCTGC
* * *
59666 AAAAGGTAAAGAGCAATAGCGACGTTTATGGG-AAAACGCCGT
1 AAAAGGTAAAGAGCAATAGC-ACGTTTATGGGAAAAATGCTGC
*
59708 AAAAGGTAAAGAGCATTAGCAACGTTTATGGGAAAAATGCTGC
1 AAAAGGTAAAGAGCAATAGC-ACGTTTATGGGAAAAATGCTGC
*
59751 TAAAGGT
1 AAAAGGT
59758 GTTTTCCCAT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
41 7 0.09
42 38 0.49
43 32 0.41
44 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.20
Consensus pattern (42 bp):
AAAAGGTAAAGAGCAATAGCACGTTTATGGGAAAAATGCTGC
Found at i:59733 original size:42 final size:42
Alignment explanation
Indices: 59616--59743 Score: 170
Period size: 42 Copynumber: 3.1 Consensus size: 42
59606 GTTTTCCCAT
*
59616 AAACACCGTAAAAGGT-AA-AGCAATAGCAGCGTTTATGGGAA
1 AAACACCGTAAAAGGTAAAGAGCAATAGCAACGTTTATGGG-A
* * * *
59657 AAATACTGCAAAAGGTAAAGAGCAATAGCGACGTTTATGGGA
1 AAACACCGTAAAAGGTAAAGAGCAATAGCAACGTTTATGGGA
* *
59699 AAACGCCGTAAAAGGTAAAGAGCATTAGCAACGTTTATGGGA
1 AAACACCGTAAAAGGTAAAGAGCAATAGCAACGTTTATGGGA
59741 AAA
1 AAA
59744 ATGCTGCTAA
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
41 13 0.18
42 42 0.57
43 19 0.26
ACGTcount: A:0.44, C:0.13, G:0.25, T:0.18
Consensus pattern (42 bp):
AAACACCGTAAAAGGTAAAGAGCAATAGCAACGTTTATGGGA
Found at i:66346 original size:39 final size:40
Alignment explanation
Indices: 66259--66357 Score: 164
Period size: 39 Copynumber: 2.5 Consensus size: 40
66249 GGGGACAAGT
*
66259 CTCTTCCAAAAGGTGTTCATCCAATATGAAAAGGGTTGTGA
1 CTCTT-CAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGA
*
66300 CTTTTCAAAAGGTGTCCATCCAATATG-AAAGGGTTGTGA
1 CTCTTCAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGA
66339 CTCTTCAAAAGGTGTCCAT
1 CTCTTCAAAAGGTGTCCAT
66358 TGAGTGCATA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 30 0.55
40 21 0.38
41 4 0.07
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (40 bp):
CTCTTCAAAAGGTGTCCATCCAATATGAAAAGGGTTGTGA
Found at i:67647 original size:43 final size:43
Alignment explanation
Indices: 67581--67699 Score: 159
Period size: 43 Copynumber: 2.8 Consensus size: 43
67571 TAATGTTAGT
* *
67581 GGCGTTTGTAGGAAAAGCATCGCTAAAGATCATATTCTATAGC
1 GGCGTTTGTGGGAAAAGCATCGCTAAAGATCATATCCTATAGC
* *
67624 GGCGTTTGTGGGAAAAGCGTCGCTAAAGA-CGATGTCCTATAGC
1 GGCGTTTGTGGGAAAAGCATCGCTAAAGATC-ATATCCTATAGC
* * *
67667 GGCGTTTGTGGAAAAAACACCGCTAAAGATCAT
1 GGCGTTTGTGGGAAAAGCATCGCTAAAGATCAT
67700 GTATCATGTT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.02
43 64 0.97
44 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCATCGCTAAAGATCATATCCTATAGC
Found at i:68214 original size:66 final size:66
Alignment explanation
Indices: 68144--68273 Score: 260
Period size: 66 Copynumber: 2.0 Consensus size: 66
68134 AACTAATCAC
68144 AATAAATATACTTAAAATCTCAAAGTTTTCGTAATTTCAACCTTACCATTAAGTTAACCCGTCGC
1 AATAAATATACTTAAAATCTCAAAGTTTTCGTAATTTCAACCTTACCATTAAGTTAACCCGTCGC
68209 T
66 T
68210 AATAAATATACTTAAAATCTCAAAGTTTTCGTAATTTCAACCTTACCATTAAGTTAACCCGTCG
1 AATAAATATACTTAAAATCTCAAAGTTTTCGTAATTTCAACCTTACCATTAAGTTAACCCGTCG
68274 TTATTCAACT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.35
Consensus pattern (66 bp):
AATAAATATACTTAAAATCTCAAAGTTTTCGTAATTTCAACCTTACCATTAAGTTAACCCGTCGC
T
Found at i:70840 original size:9 final size:9
Alignment explanation
Indices: 70822--70879 Score: 50
Period size: 11 Copynumber: 6.3 Consensus size: 9
70812 GTCAGTAAAT
70822 AATT-TTAA
1 AATTATTAA
70830 AATTATTAA
1 AATTATTAA
70839 AATTATTTTAA
1 AATTA--TTAA
70850 AATTATTTTAA
1 AATTA--TTAA
70861 AA-TA-TAA
1 AATTATTAA
*
70868 AAATATTAA
1 AATTATTAA
70877 AAT
1 AAT
70880 CATCATTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
7 5 0.11
8 6 0.14
9 14 0.32
10 2 0.05
11 17 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AATTATTAA
Found at i:70846 original size:20 final size:20
Alignment explanation
Indices: 70818--70856 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
70808 CCACGTCAGT
70818 AAATAATTTTAAAATTATTA
1 AAATAATTTTAAAATTATTA
*
70838 AAATTATTTTAAAATTATT
1 AAATAATTTTAAAATTATT
70857 TTAAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATAATTTTAAAATTATTA
Found at i:70849 original size:11 final size:11
Alignment explanation
Indices: 70818--70863 Score: 69
Period size: 11 Copynumber: 4.4 Consensus size: 11
70808 CCACGTCAGT
*
70818 AAATAATTTTA
1 AAATTATTTTA
70829 AAATTA--TTA
1 AAATTATTTTA
70838 AAATTATTTTA
1 AAATTATTTTA
70849 AAATTATTTTA
1 AAATTATTTTA
70860 AAAT
1 AAAT
70864 ATAAAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 9 0.28
11 23 0.72
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:70933 original size:6 final size:6
Alignment explanation
Indices: 70922--70948 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
70912 CTGTTACCCT
70922 TTCCCC TTCCCC TTCCCC TTCCCC TTC
1 TTCCCC TTCCCC TTCCCC TTCCCC TTC
70949 TTCTTATATT
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:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
TTCCCC
Found at i:71731 original size:41 final size:41
Alignment explanation
Indices: 71669--71748 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
71659 GGGAGCAACT
* * * * *
71669 CATCGGAACAATTCTGGTAAACGACCACCAAAGAAGGAACC
1 CATCAGAACAACTCCGGTAAACAACCACCAAAAAAGGAACC
71710 CATCAGAACAACTCCGGTAAACAACCACCAAAAAAGGAA
1 CATCAGAACAACTCCGGTAAACAACCACCAAAAAAGGAA
71749 AATAAGGGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.46, C:0.28, G:0.16, T:0.10
Consensus pattern (41 bp):
CATCAGAACAACTCCGGTAAACAACCACCAAAAAAGGAACC
Found at i:71849 original size:16 final size:16
Alignment explanation
Indices: 71828--71876 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
71818 TATTAAAATA
71828 ATTTTAATAATTTTAT
1 ATTTTAATAATTTTAT
**
71844 ATTTTAA-AA-AATA-
1 ATTTTAATAATTTTAT
71857 ATTTTAATAATTTTAT
1 ATTTTAATAATTTTAT
71873 ATTT
1 ATTT
71877 AAAAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
13 7 0.27
14 4 0.15
15 4 0.15
16 11 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTAATAATTTTAT
Found at i:71860 original size:29 final size:29
Alignment explanation
Indices: 71822--71884 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
71812 TTAAAATATT
*
71822 AAAATAATTTTAATAATTTTATATTTTAA
1 AAAATAATTTTAATAATTTTATATTTAAA
71851 AAAATAATTTTAATAATTTTATATTTAAA
1 AAAATAATTTTAATAATTTTATATTTAAA
71880 AAAAT
1 AAAAT
71885 TAATAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
AAAATAATTTTAATAATTTTATATTTAAA
Found at i:71891 original size:24 final size:28
Alignment explanation
Indices: 71822--71895 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 28
71812 TTAAAATATT
71822 AAAATAATTTTAATAATTTTATATTTTAA
1 AAAATAA-TTTAATAATTTTATATTTTAA
71851 AAAATAATTTTAATAATTTTATA-TTT-A
1 AAAATAA-TTTAATAATTTTATATTTTAA
71878 AAAA-AA-TTAATAATTTTA
1 AAAATAATTTAATAATTTTA
71896 AAATCATTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
24 12 0.27
26 2 0.04
27 5 0.11
28 3 0.07
29 23 0.51
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
AAAATAATTTAATAATTTTATATTTTAA
Found at i:77583 original size:26 final size:26
Alignment explanation
Indices: 77547--77597 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
77537 TTTATACTTT
77547 CTATGTCTATAAATATAGACCTTGGC
1 CTATGTCTATAAATATAGACCTTGGC
77573 CTATGTCTATAAATATAGACCTTGG
1 CTATGTCTATAAATATAGACCTTGG
77598 AGAAACATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (26 bp):
CTATGTCTATAAATATAGACCTTGGC
Found at i:78245 original size:15 final size:15
Alignment explanation
Indices: 78218--78250 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
78208 AAAATATTTA
78218 TATTATATTATTTTT
1 TATTATATTATTTTT
78233 TATT-TATTAATTTTT
1 TATTATATT-ATTTTT
78248 TAT
1 TAT
78251 ATAATCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTATATTATTTTT
Found at i:80874 original size:20 final size:21
Alignment explanation
Indices: 80840--80882 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
80830 TTAGTTTTGA
*
80840 TATTTTTCTTAATTTTGTATT
1 TATTTTTCTTAATTTGGTATT
*
80861 TATTTTTC-TCATTTGGTATT
1 TATTTTTCTTAATTTGGTATT
80881 TA
1 TA
80883 ATTGGTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (21 bp):
TATTTTTCTTAATTTGGTATT
Found at i:81124 original size:67 final size:67
Alignment explanation
Indices: 81014--81146 Score: 194
Period size: 67 Copynumber: 2.0 Consensus size: 67
81004 ATACTAGAGA
*
81014 AAGGATGATATGAAACAGCAATTTCATGTCATCCCTATCCCTTTCCAATAGAGGAATGACAAATC
1 AAGGATGATATGAAACAGCAATTTCACGTCATCCCTATCCCTTTCCAATAGAGGAATGACAAATC
81079 AG
66 AG
* * * * * * *
81081 AAGGATTATATGAAACTGTAATTTCACGTCATCCGTATTCCTTTCCGATAGTGGAATGACAAATC
1 AAGGATGATATGAAACAGCAATTTCACGTCATCCCTATCCCTTTCCAATAGAGGAATGACAAATC
81146 A
66 A
81147 CATATTTTCC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (67 bp):
AAGGATGATATGAAACAGCAATTTCACGTCATCCCTATCCCTTTCCAATAGAGGAATGACAAATC
AG
Found at i:87799 original size:16 final size:16
Alignment explanation
Indices: 87767--87798 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
87757 AAGAAAAATG
87767 AGAAAAAGGAAGAAAA
1 AGAAAAAGGAAGAAAA
87783 AGAAAAAGG-AGAAAA
1 AGAAAAAGGAAGAAAA
87798 A
1 A
87799 AAATTATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AGAAAAAGGAAGAAAA
Found at i:93949 original size:19 final size:19
Alignment explanation
Indices: 93898--93951 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
93888 ATACAGTATG
*
93898 TCGCCCTTACGAGCCAGTA
1 TCGCTCTTACGAGCCAGTA
*
93917 TCGCTCTCT-GGAGCCAGTA
1 TCGCTCT-TACGAGCCAGTA
93936 TCGCTCTTACGAGCCA
1 TCGCTCTTACGAGCCA
93952 TTATTTCTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 28 0.93
20 1 0.03
ACGTcount: A:0.19, C:0.35, G:0.22, T:0.24
Consensus pattern (19 bp):
TCGCTCTTACGAGCCAGTA
Found at i:100568 original size:27 final size:27
Alignment explanation
Indices: 100538--100656 Score: 211
Period size: 27 Copynumber: 4.4 Consensus size: 27
100528 TTACCACCAG
100538 TGCTGCCACAAGATGGAGTTCCTCCAA
1 TGCTGCCACAAGATGGAGTTCCTCCAA
*
100565 TGCTGCCACAAGATGGAGTTCCTCCAG
1 TGCTGCCACAAGATGGAGTTCCTCCAA
100592 TGCTGCCACAAGATGGAGTTCCTCCAA
1 TGCTGCCACAAGATGGAGTTCCTCCAA
* *
100619 TGCTGCCTCAAGATGGAGTTCCTCCAG
1 TGCTGCCACAAGATGGAGTTCCTCCAA
100646 TGCTGCCACAA
1 TGCTGCCACAA
100657 ATTGTTAATG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 87 1.00
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.23
Consensus pattern (27 bp):
TGCTGCCACAAGATGGAGTTCCTCCAA
Found at i:100616 original size:54 final size:54
Alignment explanation
Indices: 100534--100656 Score: 237
Period size: 54 Copynumber: 2.3 Consensus size: 54
100524 CAACTTACCA
100534 CCAGTGCTGCCACAAGATGGAGTTCCTCCAATGCTGCCACAAGATGGAGTTCCT
1 CCAGTGCTGCCACAAGATGGAGTTCCTCCAATGCTGCCACAAGATGGAGTTCCT
*
100588 CCAGTGCTGCCACAAGATGGAGTTCCTCCAATGCTGCCTCAAGATGGAGTTCCT
1 CCAGTGCTGCCACAAGATGGAGTTCCTCCAATGCTGCCACAAGATGGAGTTCCT
100642 CCAGTGCTGCCACAA
1 CCAGTGCTGCCACAA
100657 ATTGTTAATG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.22
Consensus pattern (54 bp):
CCAGTGCTGCCACAAGATGGAGTTCCTCCAATGCTGCCACAAGATGGAGTTCCT
Found at i:106101 original size:15 final size:15
Alignment explanation
Indices: 106070--106109 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
106060 GTCTATGCAT
106070 TTTTACTT-TTT--C
1 TTTTACTTGTTTCAC
*
106082 TTTTATTTGTTTCAC
1 TTTTACTTGTTTCAC
106097 TTTTACTTGTTTC
1 TTTTACTTGTTTC
106110 TTTTTACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.30
13 3 0.13
15 13 0.57
ACGTcount: A:0.10, C:0.15, G:0.05, T:0.70
Consensus pattern (15 bp):
TTTTACTTGTTTCAC
Found at i:109107 original size:25 final size:24
Alignment explanation
Indices: 109067--109113 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
109057 CTCAGTCATT
109067 TGAAAAAAAATGAGAAAAAGAAAG
1 TGAAAAAAAATGAGAAAAAGAAAG
109091 TGAAAAGAAAA-GAAGAAAAAGAA
1 TGAAAA-AAAATG-AGAAAAAGAA
109114 TTTTATTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.06
Consensus pattern (24 bp):
TGAAAAAAAATGAGAAAAAGAAAG
Found at i:111280 original size:18 final size:17
Alignment explanation
Indices: 111232--111285 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
111222 CTGATACCAC
111232 TATGCTCAAATGAGC-G
1 TATGCTCAAATGAGCAG
* *
111248 TATGTTGAAATGAGCTAG
1 TATGCTCAAATGAGC-AG
*
111266 TATGCTCAAACGAGCCAG
1 TATGCTCAAATGAG-CAG
111284 TA
1 TA
111286 ATGCAATTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 13 0.43
18 16 0.53
19 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (17 bp):
TATGCTCAAATGAGCAG
Found at i:113458 original size:14 final size:15
Alignment explanation
Indices: 113439--113471 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
113429 ACTAACTCTT
113439 AATTCAAAAATT-AA
1 AATTCAAAAATTCAA
*
113453 AATTCATAAATTCAA
1 AATTCAAAAATTCAA
113468 AATT
1 AATT
113472 TCATATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTCAAAAATTCAA
Found at i:113959 original size:76 final size:77
Alignment explanation
Indices: 113868--114025 Score: 248
Period size: 79 Copynumber: 2.1 Consensus size: 77
113858 ATTGAGTAGA
* *
113868 CAATTATATATATATAACTTTGAG-TA-TATCTGATTTACCAGGCTCAACTATAACTAATACATC
1 CAATTATATATATATAACTTTGAGATACTATCTAATTTACCAGACTCAACTATAACTAATACATC
113931 AGTCCGACATTT
66 AGTCCGACATTT
* *
113943 CAATATATATATATATAACTTTGAGTATACTATCTAATTTACTAGACTCAACTATAACTAGTACA
1 CAAT-TATATATATATAACTTTGAG-ATACTATCTAATTTACCAGACTCAACTATAACTAATACA
114008 TCAGTCCGACATTT
64 TCAGTCCGACATTT
114022 CAAT
1 CAAT
114026 CAATTCATTT
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
75 4 0.05
76 20 0.27
78 2 0.03
79 49 0.65
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.36
Consensus pattern (77 bp):
CAATTATATATATATAACTTTGAGATACTATCTAATTTACCAGACTCAACTATAACTAATACATC
AGTCCGACATTT
Found at i:115734 original size:14 final size:14
Alignment explanation
Indices: 115715--115746 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
115705 TTTTATATGA
115715 AATTTTAATTGTTG
1 AATTTTAATTGTTG
*
115729 AATTTTAATTTTTG
1 AATTTTAATTGTTG
115743 AATT
1 AATT
115747 CAGAGTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (14 bp):
AATTTTAATTGTTG
Found at i:116616 original size:258 final size:258
Alignment explanation
Indices: 116159--116674 Score: 996
Period size: 258 Copynumber: 2.0 Consensus size: 258
116149 AATTGGACCC
*
116159 TCCTTAAATGGTTTAGTAGTAGAAATGAAGTGGAATCCTTTAGATTTTGATAAATTTCAATTAAA
1 TCCTTAAATGGTTTAGTAGTAGAAATGAAGTGAAATCCTTTAGATTTTGATAAATTTCAATTAAA
116224 TCCTAATAAAATGAGGATTTACTAATTAGGTTTTTTTATATGATCGGGAATGGTAGTTTAGAGAC
66 TCCTAATAAAATGAGGATTTACTAATTAGGTTTTTTTATATGATCGGGAATGGTAGTTTAGAGAC
*
116289 CACAAATTCGATGTGTTAGACCTTAAATATTAATTATTTAATATTTACGGGGTTATTAGTTGAGT
131 CACAAATTCAATGTGTTAGACCTTAAATATTAATTATTTAATATTTACGGGGTTATTAGTTGAGT
*
116354 ATTAAAATTTGGTAACGAAATTTTATTATTTAGATAGTTAATTAAGTGAAAAGGATTAAATTG
196 ATTAAAATTTGGTAACGAAATTTTATTATTTAGATAGTTAATTAAGTAAAAAGGATTAAATTG
116417 TCCTTAAATGGTTTAGTAGTAGAAATGAAGTGAAATCCTTTAGATTTTGATAAATTTCAATTAAA
1 TCCTTAAATGGTTTAGTAGTAGAAATGAAGTGAAATCCTTTAGATTTTGATAAATTTCAATTAAA
*
116482 TCCTAATTAAATGAGGATTTACTAATTAGGTTTTTTTATATGATCGGGAATGGTAGTTTAGAGAC
66 TCCTAATAAAATGAGGATTTACTAATTAGGTTTTTTTATATGATCGGGAATGGTAGTTTAGAGAC
116547 CACAAATTCAATGTGTTAGACCTTAAATATTAATTATTTAATATTTACGGGGTTATTAGTTGAGT
131 CACAAATTCAATGTGTTAGACCTTAAATATTAATTATTTAATATTTACGGGGTTATTAGTTGAGT
116612 ATTAAAATTTGGTAACGAAATTTTATTATTTAGATAGTTAATTAAGTAAAAAGGATTAAATTG
196 ATTAAAATTTGGTAACGAAATTTTATTATTTAGATAGTTAATTAAGTAAAAAGGATTAAATTG
116675 AAAAAGATGC
Statistics
Matches: 254, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
258 254 1.00
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (258 bp):
TCCTTAAATGGTTTAGTAGTAGAAATGAAGTGAAATCCTTTAGATTTTGATAAATTTCAATTAAA
TCCTAATAAAATGAGGATTTACTAATTAGGTTTTTTTATATGATCGGGAATGGTAGTTTAGAGAC
CACAAATTCAATGTGTTAGACCTTAAATATTAATTATTTAATATTTACGGGGTTATTAGTTGAGT
ATTAAAATTTGGTAACGAAATTTTATTATTTAGATAGTTAATTAAGTAAAAAGGATTAAATTG
Found at i:120465 original size:18 final size:18
Alignment explanation
Indices: 120442--120555 Score: 93
Period size: 18 Copynumber: 6.3 Consensus size: 18
120432 ACATTAATGA
120442 CTCATTTGAGCATACTAG
1 CTCATTTGAGCATACTAG
120460 CTCATTTGAGCATACTAG
1 CTCATTTGAGCATACTAG
** * *
120478 CTCATTCAAGCATATTGG
1 CTCATTTGAGCATACTAG
* * *
120496 TTCGTTTGAACATACTAG
1 CTCATTTGAGCATACTAG
* * * * *
120514 CTCTTTTAAGAATATTGG
1 CTCATTTGAGCATACTAG
* *
120532 CTCATTTGAGTAATACTGG
1 CTCATTTGAG-CATACTAG
120551 CTCAT
1 CTCAT
120556 AAGAGCAATA
Statistics
Matches: 74, Mismatches: 21, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
18 62 0.84
19 12 0.16
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (18 bp):
CTCATTTGAGCATACTAG
Found at i:120490 original size:36 final size:36
Alignment explanation
Indices: 120450--120573 Score: 115
Period size: 36 Copynumber: 3.4 Consensus size: 36
120440 GACTCATTTG
* *
120450 AGCATACTAGCTCATTTGAGCATACTAGCTCATTCA
1 AGCATATTGGCTCATTTGAGCATACTAGCTCATTCA
* * * * *
120486 AGCATATTGGTTCGTTTGAACATACTAGCTCTTTTA
1 AGCATATTGGCTCATTTGAGCATACTAGCTCATTCA
* * * *
120522 AGAATATTGGCTCATTTGAGTAATACTGGCTCA-TAA
1 AGCATATTGGCTCATTTGAG-CATACTAGCTCATTCA
120558 GAGCAATATTGGCTCA
1 -AGC-ATATTGGCTCA
120574 AAAGATTAAT
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
36 47 0.68
37 11 0.16
38 11 0.16
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (36 bp):
AGCATATTGGCTCATTTGAGCATACTAGCTCATTCA
Found at i:120565 original size:19 final size:19
Alignment explanation
Indices: 120524--120722 Score: 80
Period size: 19 Copynumber: 10.1 Consensus size: 19
120514 CTCTTTTAAG
* ** *
120524 AATATTGGCTCATTTGAGT
1 AATACTGGCTCATAAGAGC
120543 AATACTGGCTCATAAGAGC
1 AATACTGGCTCATAAGAGC
* * **
120562 AATATTGGCTCAAAAGATT
1 AATACTGGCTCATAAGAGC
*
120581 AATATTGGCTCGA-AAGAGC
1 AATACTGGCTC-ATAAGAGC
* **
120600 GATACTGGCTTGTAAGAG-
1 AATACTGGCTCATAAGAGC
* *
120618 AGATACTAGCTCGTAAGAG-
1 A-ATACTGGCTCATAAGAGC
* *
120637 AGATATTGGCTCGTAAGAGTGAC
1 A-ATACTGGCTCATAAGA--G-C
* *
120660 ATACTGTACTGGCTCGTAAAAGC
1 A-A---TACTGGCTCATAAGAGC
* *
120683 GATACTGGCTCAAAAGAGC
1 AATACTGGCTCATAAGAGC
* * *
120702 GATACTGCCTCGTAAGAGC
1 AATACTGGCTCATAAGAGC
120721 AA
1 AA
120723 CATTCTGTAC
Statistics
Matches: 140, Mismatches: 30, Indels: 20
0.74 0.16 0.11
Matches are distributed among these distances:
19 120 0.86
20 1 0.01
21 1 0.01
22 1 0.01
23 3 0.02
24 1 0.01
26 13 0.09
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (19 bp):
AATACTGGCTCATAAGAGC
Found at i:120584 original size:38 final size:38
Alignment explanation
Indices: 120524--120648 Score: 94
Period size: 38 Copynumber: 3.3 Consensus size: 38
120514 CTCTTTTAAG
***
120524 AATATTGGCTCATTTGAGTAATACTGGCTC-ATAAGAGC
1 AATATTGGCTCAAAAGAGTAATACTGGCTCGA-AAGAGC
* *
120562 AATATTGGCTCAAAAGATTAATATTGGCTCGAAAGAGC
1 AATATTGGCTCAAAAGAGTAATACTGGCTCGAAAGAGC
* * *** * *
120600 GATACTGGCTTGTAAGAG-AGATACTAGCTCGTAAGAG-
1 AATATTGGCTCAAAAGAGTA-ATACTGGCTCGAAAGAGC
120637 AGATATTGGCTC
1 A-ATATTGGCTC
120649 GTAAGAGTGA
Statistics
Matches: 67, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
37 1 0.01
38 65 0.97
39 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (38 bp):
AATATTGGCTCAAAAGAGTAATACTGGCTCGAAAGAGC
Found at i:120638 original size:21 final size:19
Alignment explanation
Indices: 120588--120655 Score: 82
Period size: 19 Copynumber: 3.6 Consensus size: 19
120578 ATTAATATTG
* * *
120588 GCTCGAAAGAGCGATACTG
1 GCTCGTAAGAGAGATACTA
*
120607 GCTTGTAAGAGAGATACTA
1 GCTCGTAAGAGAGATACTA
* *
120626 GCTCGTAAGAGAGATATTG
1 GCTCGTAAGAGAGATACTA
120645 GCTCGTAAGAG
1 GCTCGTAAGAG
120656 TGACATACTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (19 bp):
GCTCGTAAGAGAGATACTA
Found at i:120700 original size:64 final size:64
Alignment explanation
Indices: 120602--120742 Score: 165
Period size: 64 Copynumber: 2.2 Consensus size: 64
120592 GAAAGAGCGA
* * ** * * **
120602 TACTGGCTTGTAAGAGAGATACTAGCTCGTAAGAGAGATATTGGCTCGTAAGAGTGACATACTG
1 TACTGGCTCGTAAAAGAGATACTAGCTCAAAAGAGAGATACTGCCTCGTAAGAGCAACATACTG
* * * *
120666 TACTGGCTCGTAAAAGCGATACTGGCTCAAAAGAGCGATACTGCCTCGTAAGAGCAACATTCTG
1 TACTGGCTCGTAAAAGAGATACTAGCTCAAAAGAGAGATACTGCCTCGTAAGAGCAACATACTG
*
120730 TACTAGCTCGTAA
1 TACTGGCTCGTAA
120743 GACCGATTTA
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (64 bp):
TACTGGCTCGTAAAAGAGATACTAGCTCAAAAGAGAGATACTGCCTCGTAAGAGCAACATACTG
Found at i:123877 original size:19 final size:19
Alignment explanation
Indices: 123847--123964 Score: 103
Period size: 19 Copynumber: 6.2 Consensus size: 19
123837 ATAGTATGTT
*
123847 GCTCTTATGAGCCAGTATC
1 GCTCTTACGAGCCAGTATC
** * *
123866 ATTCTTACGAGCCTGTAAC
1 GCTCTTACGAGCCAGTATC
*
123885 GCTCTTACG-GACTAGTATC
1 GCTCTTACGAG-CCAGTATC
*
123904 GCTCTTACGAGCTAGTATC
1 GCTCTTACGAGCCAGTATC
* * * *
123923 TCTCTTTCAAGCCAGTATT
1 GCTCTTACGAGCCAGTATC
* *
123942 GCTGTTACGAGCCAGTATT
1 GCTCTTACGAGCCAGTATC
123961 GCTC
1 GCTC
123965 AAACAAACCA
Statistics
Matches: 77, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
18 1 0.01
19 75 0.97
20 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.33
Consensus pattern (19 bp):
GCTCTTACGAGCCAGTATC
Found at i:128770 original size:19 final size:19
Alignment explanation
Indices: 128723--128833 Score: 114
Period size: 19 Copynumber: 5.8 Consensus size: 19
128713 GTACAGTATG
* *
128723 TCGCTCTTACGACCCAATA
1 TCGCTCTTACGAGCCAGTA
* * *
128742 TTGCTATTACGAGCTAGTA
1 TCGCTCTTACGAGCCAGTA
*
128761 TCGCTCTTACGAGTCAGTA
1 TCGCTCTTACGAGCCAGTA
**
128780 TCGCTCTTTTGAGCCAGTA
1 TCGCTCTTACGAGCCAGTA
*
128799 TTGCTCTTACGAGCCAGTA
1 TCGCTCTTACGAGCCAGTA
* **
128818 TTGCTCCAACGAGCCA
1 TCGCTCTTACGAGCCA
128834 ATATACTCAA
Statistics
Matches: 75, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 75 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.31
Consensus pattern (19 bp):
TCGCTCTTACGAGCCAGTA
Found at i:128860 original size:18 final size:18
Alignment explanation
Indices: 128789--128944 Score: 141
Period size: 18 Copynumber: 8.6 Consensus size: 18
128779 ATCGCTCTTT
**
128789 TGAGCCAGTATTGCTCTTA
1 TGAGCCAGTA-TGCTCAAA
* *
128808 CGAGCCAGTATTGCTCCAA
1 TGAGCCAGTA-TGCTCAAA
* * *
128827 CGAGCCAATATACTCAAA
1 TGAGCCAGTATGCTCAAA
* *
128845 GGAGCTAGTATGCTCAAA
1 TGAGCCAGTATGCTCAAA
*
128863 TGAGCCAATATGCTCAAA
1 TGAGCCAGTATGCTCAAA
*
128881 TGAGCTAGTATGCTCAAA
1 TGAGCCAGTATGCTCAAA
*
128899 TGAGCCACTATGCTCAAA
1 TGAGCCAGTATGCTCAAA
** * *
128917 CAAGCCAATATGCTTAAA
1 TGAGCCAGTATGCTCAAA
*
128935 CGAGCCAGTA
1 TGAGCCAGTA
128945 ATGTTGTTCC
Statistics
Matches: 114, Mismatches: 23, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
18 89 0.78
19 25 0.22
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (18 bp):
TGAGCCAGTATGCTCAAA
Found at i:132303 original size:18 final size:18
Alignment explanation
Indices: 132251--132338 Score: 97
Period size: 18 Copynumber: 4.8 Consensus size: 18
132241 GCTCTTTCCT
*
132251 GCCAGTATCGCTCTAACGA
1 GCCAGTAT-GCTCAAACGA
*
132270 GCTAGTATTG-TCAAACGA
1 GCCAGTA-TGCTCAAACGA
* *
132288 GCCAATATGCTTAAACGA
1 GCCAGTATGCTCAAACGA
* *
132306 GTCAGTATGCTCAAACAA
1 GCCAGTATGCTCAAACGA
132324 GCCAGTATGCTCAAA
1 GCCAGTATGCTCAAA
132339 TAAGCTAGTA
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
17 2 0.04
18 47 0.82
19 7 0.12
20 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (18 bp):
GCCAGTATGCTCAAACGA
Found at i:132313 original size:36 final size:36
Alignment explanation
Indices: 132265--132353 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 36
132255 GTATCGCTCT
*
132265 AACGAGCTAGTATTG-TCAAACGAGCCAATATGCTTA
1 AACGAGCTAGTA-TGCTCAAACAAGCCAATATGCTTA
* *
132301 AACGAG-TCAGTATGCTCAAACAAGCCAGTATGCTCA
1 AACGAGCT-AGTATGCTCAAACAAGCCAATATGCTTA
**
132337 AATAAGCTAGTAATGCT
1 AACGAGCTAGT-ATGCT
132354 ATTCCTTCCG
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
35 3 0.07
36 35 0.80
37 6 0.14
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (36 bp):
AACGAGCTAGTATGCTCAAACAAGCCAATATGCTTA
Found at i:132343 original size:18 final size:18
Alignment explanation
Indices: 132251--132353 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
132241 GCTCTTTCCT
* *
132251 GCCAGTATCGCTCTAACGA
1 GCCAGTAT-GCTCAAACAA
* *
132270 GCTAGTATTG-TCAAACGA
1 GCCAGTA-TGCTCAAACAA
* * *
132288 GCCAATATGCTTAAACGA
1 GCCAGTATGCTCAAACAA
*
132306 GTCAGTATGCTCAAACAA
1 GCCAGTATGCTCAAACAA
*
132324 GCCAGTATGCTCAAATAA
1 GCCAGTATGCTCAAACAA
*
132342 GCTAGTAATGCT
1 GCCAGT-ATGCT
132354 ATTCCTTCCG
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
17 2 0.03
18 54 0.78
19 12 0.17
20 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (18 bp):
GCCAGTATGCTCAAACAA
Done.