Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009853.1 Kokia drynarioides strain JFW-HI SEQ_124583, 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: 142566
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 68 characters in sequence are not A, C, G, or T
Found at i:15731 original size:17 final size:20
Alignment explanation
Indices: 15711--15752 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
15701 AGTAGCTTTC
15711 AGAAA-CCAGAAAA-AA-AA
1 AGAAACCCAGAAAACAAGAA
15728 AGAAACCCAGAAAACAAGAA
1 AGAAACCCAGAAAACAAGAA
15748 AGAAA
1 AGAAA
15753 GTACCTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.23
18 8 0.36
19 2 0.09
20 7 0.32
ACGTcount: A:0.71, C:0.14, G:0.14, T:0.00
Consensus pattern (20 bp):
AGAAACCCAGAAAACAAGAA
Found at i:21003 original size:44 final size:46
Alignment explanation
Indices: 20912--21016 Score: 133
Period size: 44 Copynumber: 2.3 Consensus size: 46
20902 ATTTTATTTG
* *
20912 AACTTAAAAATCTAATTGCCAAAAAATCTTAAAAAATCTATATTTAA
1 AACTT-AAAATCTAATTGCCAAAAAATCTTAAAAAATATATAATTAA
** *
20959 AACTTAAAATCTAATTGTTAAAATATC-TAAAAAA-ATATAATTAA
1 AACTTAAAATCTAATTGCCAAAAAATCTTAAAAAATATATAATTAA
*
21003 AACTTAGAATCTAA
1 AACTTAAAATCTAA
21017 ACCTAAACTT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
44 21 0.40
45 7 0.13
46 19 0.37
47 5 0.10
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.32
Consensus pattern (46 bp):
AACTTAAAATCTAATTGCCAAAAAATCTTAAAAAATATATAATTAA
Found at i:22859 original size:5 final size:5
Alignment explanation
Indices: 22851--22890 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
22841 CAATTCTAAT
* *
22851 CCCAT CCCAT CCCAA CCCAA CCCAA CCCAA CCCAA CCCAA
1 CCCAA CCCAA CCCAA CCCAA CCCAA CCCAA CCCAA CCCAA
22891 ACCAGATCAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.35, C:0.60, G:0.00, T:0.05
Consensus pattern (5 bp):
CCCAA
Found at i:27615 original size:13 final size:13
Alignment explanation
Indices: 27599--27624 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27589 TAAAAGTACA
27599 TTTCAAAACACTT
1 TTTCAAAACACTT
27612 TTTCAAAACACTT
1 TTTCAAAACACTT
27625 CTCAAAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTCAAAACACTT
Found at i:44845 original size:15 final size:14
Alignment explanation
Indices: 44825--44872 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
44815 ACAAAACGAT
44825 AATATAAGTAATTAA
1 AATATAA-TAATTAA
* *
44840 AATATAACATTTCAA
1 AATATAATAATT-AA
44855 AATATGAATAATTAA
1 AATAT-AATAATTAA
44870 AAT
1 AAT
44873 GTAACCCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 3 0.11
15 19 0.70
16 5 0.19
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (14 bp):
AATATAATAATTAA
Found at i:45504 original size:16 final size:17
Alignment explanation
Indices: 45469--45510 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
45459 TGTAATTATC
*
45469 TAAAAAAATTAACTCGG
1 TAAAAAAATTAACTCAG
*
45486 TAAAAAAATT-TCTCAG
1 TAAAAAAATTAACTCAG
*
45502 TAAACAAAT
1 TAAAAAAAT
45511 GTATGAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.26
Consensus pattern (17 bp):
TAAAAAAATTAACTCAG
Found at i:48853 original size:37 final size:37
Alignment explanation
Indices: 48812--48886 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
48802 TAAATTACGT
48812 AGTATTTATTATTAATTATTTATACTTTGCCCAACAA
1 AGTATTTATTATTAATTATTTATACTTTGCCCAACAA
48849 AGTATTTATTATTAATTATTTATACTTTGCCCAACAA
1 AGTATTTATTATTAATTATTTATACTTTGCCCAACAA
48886 A
1 A
48887 TAGAATGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.45
Consensus pattern (37 bp):
AGTATTTATTATTAATTATTTATACTTTGCCCAACAA
Found at i:67840 original size:27 final size:28
Alignment explanation
Indices: 67810--67868 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
67800 AATTTCATAG
*
67810 AATTAAATTTTAAA-TTTTAAATTTT-AA
1 AATT-AATTTTAAAGTTTGAAATTTTCAA
*
67837 AATTTATTTTAAAGTTTGAAATTTTCAA
1 AATTAATTTTAAAGTTTGAAATTTTCAA
67865 AATT
1 AATT
67869 TAATATTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 8 0.29
27 14 0.50
28 6 0.21
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTAATTTTAAAGTTTGAAATTTTCAA
Found at i:67841 original size:8 final size:7
Alignment explanation
Indices: 67812--67871 Score: 61
Period size: 7 Copynumber: 8.6 Consensus size: 7
67802 TTTCATAGAA
67812 TTAAATT
1 TTAAATT
67819 TTAAATT
1 TTAAATT
67826 TTAAATT
1 TTAAATT
*
67833 TTAAAAT
1 TTAAATT
67840 TT--ATT
1 TTAAATT
67845 TTAAAGTT
1 TTAAA-TT
*
67853 TGAAATT
1 TTAAATT
*
67860 TTCAAAAT
1 TT-AAATT
67868 TTAA
1 TTAA
67872 TATTGATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
5 4 0.09
7 28 0.64
8 12 0.27
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (7 bp):
TTAAATT
Found at i:67845 original size:19 final size:19
Alignment explanation
Indices: 67823--67860 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
67813 TAAATTTTAA
*
67823 ATTTTAAATTTTAAAATTT
1 ATTTTAAAGTTTAAAATTT
*
67842 ATTTTAAAGTTTGAAATTT
1 ATTTTAAAGTTTAAAATTT
67861 TCAAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTTTAAAGTTTAAAATTT
Found at i:68832 original size:22 final size:23
Alignment explanation
Indices: 68794--68842 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
68784 TCATTAAAGT
*
68794 TTAAAATATTTCAATTGAATC-A
1 TTAAAATATTTAAATTGAATCAA
*
68816 TTAAAATA-TTAATATTGTATCAA
1 TTAAAATATTTAA-ATTGAATCAA
68839 TTAA
1 TTAA
68843 GTTTTTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (23 bp):
TTAAAATATTTAAATTGAATCAA
Found at i:69780 original size:16 final size:17
Alignment explanation
Indices: 69746--69784 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
69736 ACTTATGTTA
*
69746 ATGTTATTTAAATATAT
1 ATGTTTTTTAAATATAT
69763 ATGTTTTTTAAA-ATAT
1 ATGTTTTTTAAATATAT
69779 AT-TTTT
1 ATGTTTT
69785 AAGTTGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 6 0.29
17 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
ATGTTTTTTAAATATAT
Found at i:97764 original size:30 final size:30
Alignment explanation
Indices: 97728--97788 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
97718 TTAGTATTTG
*
97728 TATTTTTTTATCAATTTGACCCTTGTACTT
1 TATTTTTTTATCAATTTGACCCCTGTACTT
* *
97758 TATTTTTTTATCAGTTTGGCCCCTGTACTT
1 TATTTTTTTATCAATTTGACCCCTGTACTT
97788 T
1 T
97789 CGTTCTGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.16, C:0.18, G:0.10, T:0.56
Consensus pattern (30 bp):
TATTTTTTTATCAATTTGACCCCTGTACTT
Found at i:98050 original size:19 final size:19
Alignment explanation
Indices: 98008--98051 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
97998 TTTTTTTTTA
98008 ATTTTTAGAATATTATGAT
1 ATTTTTAGAATATTATGAT
* *
98027 TTTTTTAGAAT-TTCATGGT
1 ATTTTTAGAATATT-ATGAT
98046 ATTTTT
1 ATTTTT
98052 TACTTAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.59
Consensus pattern (19 bp):
ATTTTTAGAATATTATGAT
Found at i:98121 original size:20 final size:20
Alignment explanation
Indices: 98080--98121 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
98070 CAATCTTTTT
*
98080 AAAATATAAAAAAATTCATA
1 AAAATATAAAAAAAATCATA
*
98100 AAAATATAAAAAAAATCCTA
1 AAAATATAAAAAAAATCATA
98120 AA
1 AA
98122 TTTTCTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATATAAAAAAAATCATA
Found at i:98417 original size:17 final size:17
Alignment explanation
Indices: 98391--98430 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
98381 AAATTATAAG
* *
98391 TAAAACTTCAAAAAATT
1 TAAAAATTCAAAAAATC
*
98408 TAAAAATTCATAAAATC
1 TAAAAATTCAAAAAATC
98425 TAAAAA
1 TAAAAA
98431 ATATATTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAAATTCAAAAAATC
Found at i:98489 original size:21 final size:21
Alignment explanation
Indices: 98451--98491 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
98441 TTGGAATTTT
*
98451 AAATTTTTGAAATTTTTATGA
1 AAATTTTTGAAAATTTTATGA
98472 AAATTTTT-AAGAATTTTATG
1 AAATTTTTGAA-AATTTTATG
98492 GGTTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (21 bp):
AAATTTTTGAAAATTTTATGA
Found at i:98521 original size:22 final size:23
Alignment explanation
Indices: 98496--98539 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
98486 TTTATGGGTT
* *
98496 TTTTTAATTTT-ATGGATTTTTG
1 TTTTGAATTTTAATGAATTTTTG
*
98518 TTTTGCATTTTAATGAATTTTT
1 TTTTGAATTTTAATGAATTTTT
98540 TATATTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.20, C:0.02, G:0.11, T:0.66
Consensus pattern (23 bp):
TTTTGAATTTTAATGAATTTTTG
Found at i:99820 original size:10 final size:10
Alignment explanation
Indices: 99801--99853 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
99791 TAAAATATTT
99801 AAAACTTTATA
1 AAAAC-TTATA
99812 AAAACTTATA
1 AAAACTTATA
*
99822 AATA-TTCATA
1 AAAACTT-ATA
99832 AAAACTTATA
1 AAAACTTATA
99842 AAAA--TATA
1 AAAACTTATA
99850 AAAA
1 AAAA
99854 TATTTAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
8 8 0.21
9 2 0.05
10 21 0.55
11 7 0.18
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAACTTATA
Found at i:99823 original size:20 final size:19
Alignment explanation
Indices: 99809--99853 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
99799 TTAAAACTTT
99809 ATAAAAACTTATAAATATTC
1 ATAAAAACTTATAAA-ATTC
*
99829 ATAAAAACTTATAAAAAT-
1 ATAAAAACTTATAAAATTC
99847 ATAAAAA
1 ATAAAAA
99854 TATTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.29
19 2 0.08
20 15 0.62
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAAAAACTTATAAAATTC
Found at i:99861 original size:28 final size:28
Alignment explanation
Indices: 99792--99880 Score: 85
Period size: 30 Copynumber: 3.1 Consensus size: 28
99782 AACCATATTT
99792 AAAATATTT-AAAACTTTATAAAAACT-TA
1 AAAATATTTAAAAAC-TTATAAAAA-TATA
*
99820 TAAATATTCATAAAAACTTATAAAAATATA
1 AAAATATT--TAAAAACTTATAAAAATATA
* * *
99850 AAAATATTTAAAAAATTA-GAAATTATA
1 AAAATATTTAAAAACTTATAAAAATATA
99877 AAAA
1 AAAA
99881 AAAATCATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
27 11 0.21
28 16 0.31
29 1 0.02
30 19 0.37
31 5 0.10
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (28 bp):
AAAATATTTAAAAACTTATAAAAATATA
Found at i:101188 original size:22 final size:20
Alignment explanation
Indices: 101163--101214 Score: 50
Period size: 23 Copynumber: 2.4 Consensus size: 20
101153 TATTCAATAT
101163 ATTTAAAAATAGTAATTTTAAA
1 ATTTAAAAATA--AATTTTAAA
101185 ATTTCAATCAAATAAATTTTAAA
1 ATTT-AA--AAATAAATTTTAAA
*
101208 TTTTAAA
1 ATTTAAA
101215 TTATAACCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
20 1 0.04
22 6 0.23
23 14 0.54
25 5 0.19
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTTAAAAATAAATTTTAAA
Found at i:105901 original size:29 final size:29
Alignment explanation
Indices: 105854--105925 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
105844 ATTGGACCTG
105854 AATTTTTAAAT-TCGAAAAATAA-AAAAATTA
1 AATTTTTAAATAT--AAAAA-AATAAAAATTA
105884 AATTTTTAAATATAAAAAAATAAAAATTA
1 AATTTTTAAATATAAAAAAATAAAAATTA
*
105913 AA-TTCTAAATATA
1 AATTTTTAAATATA
105926 TAGAGAAAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
28 12 0.31
29 15 0.38
30 11 0.28
31 1 0.03
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (29 bp):
AATTTTTAAATATAAAAAAATAAAAATTA
Found at i:115246 original size:69 final size:69
Alignment explanation
Indices: 115135--115290 Score: 242
Period size: 69 Copynumber: 2.3 Consensus size: 69
115125 TTTTTGCAGT
* * *
115135 CGGAAATTACTCTGAATTTTAATTATTGCTTGCTTTTCCTTCATACAATTCCTTCTTAACTGCCA
1 CGGAAATGACACTGAATTTTAATTATTGCTTGCTTTTCCTTCATAAAATTCCTTCTTAACTGCCA
*
115200 ACGA
66 ACCA
*
115204 CGGAAATGAGACTGAATTTTAATTATTGCTTGCTTCTT-CTTCATAAAATTCCTTCTTAACTGCC
1 CGGAAATGACACTGAATTTTAATTATTGCTTGCTT-TTCCTTCATAAAATTCCTTCTTAACTGCC
115268 AACCA
65 AACCA
*
115273 CGGAAATGACTCTGAATT
1 CGGAAATGACACTGAATT
115291 CTGGTTGCAG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
69 77 0.97
70 2 0.03
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (69 bp):
CGGAAATGACACTGAATTTTAATTATTGCTTGCTTTTCCTTCATAAAATTCCTTCTTAACTGCCA
ACCA
Found at i:115529 original size:69 final size:68
Alignment explanation
Indices: 115378--115533 Score: 161
Period size: 69 Copynumber: 2.2 Consensus size: 68
115368 TTTTAGCCGT
* * *
115378 CGGAAATTACTTTGAATTTTAGTTATTGCTTGCTTCTGCTTCATAAACCTCATCCTCAACCTCCA
1 CGGAAA-TACTCTGAATTTTAATTATTGCTTGCTTCTGCTTCATAAAACTCATCCTCAACCTCCA
**
115443 ACTG
65 ACCA
* * * * * * *
115447 TGGTAATAGCTCTGAATTTTAATTATTGCTTGCTTCTTCTTCATAAAATTCCTTCTTAA-CTGCC
1 CGGAAATA-CTCTGAATTTTAATTATTGCTTGCTTCTGCTTCATAAAACTCATCCTCAACCT-CC
115511 AACCA
64 AACCA
115516 CGGAAATGACTCTGAATT
1 CGGAAAT-ACTCTGAATT
115534 CTGGTTGCAG
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
68 4 0.06
69 65 0.93
70 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.38
Consensus pattern (68 bp):
CGGAAATACTCTGAATTTTAATTATTGCTTGCTTCTGCTTCATAAAACTCATCCTCAACCTCCAA
CCA
Found at i:115561 original size:243 final size:243
Alignment explanation
Indices: 115123--115710 Score: 968
Period size: 243 Copynumber: 2.4 Consensus size: 243
115113 AGCTCTCAAG
* * * * * * * *
115123 CATTTTTGCAGTCGGAAATTACTCTGAATTTTAATTATTGCTTGCTTTTCCTTCATACAA-TTCC
1 CATTTTAGCCGTCGGAAATTACTTTGAATTTTAGTTATTGCTTGCTTCTGCTTCATA-AACCTCA
* * * *
115187 TTCTTAA-CTGCCAAC-GACGGAAATGAG-ACTGAATTTTAATTATTGCTTGCTTCTTCTTCATA
65 TCCTCAACCT-CCAACTG-CGGTAAT-AGCTCTGAATTTTAATTATTGCTTGCTTCTTCTTCATA
115249 AAATTCCTTCTTAACTGCCAACCACGGAAATGACTCTGAATTCTGGTTGCAGCTAAGGTCTGATT
127 AAATTCCTTCTTAACTGCCAACCACGGAAATGACTCTGAATTCTGGTTGCAGCTAAGGTCTGATT
115314 CTGAAGAGTTCTACAGATAAATTCCTTCCAAGCAATCTGAAAGGCCCTCCAA
192 CTGAAGAGTTCTACAGATAAATTCCTTCCAAGCAATCTGAAAGGCCCTCCAA
115366 CATTTTAGCCGTCGGAAATTACTTTGAATTTTAGTTATTGCTTGCTTCTGCTTCATAAACCTCAT
1 CATTTTAGCCGTCGGAAATTACTTTGAATTTTAGTTATTGCTTGCTTCTGCTTCATAAACCTCAT
*
115431 CCTCAACCTCCAACTGTGGTAATAGCTCTGAATTTTAATTATTGCTTGCTTCTTCTTCATAAAAT
66 CCTCAACCTCCAACTGCGGTAATAGCTCTGAATTTTAATTATTGCTTGCTTCTTCTTCATAAAAT
115496 TCCTTCTTAACTGCCAACCACGGAAATGACTCTGAATTCTGGTTGCAGCTAAGGTCTGATTCTGA
131 TCCTTCTTAACTGCCAACCACGGAAATGACTCTGAATTCTGGTTGCAGCTAAGGTCTGATTCTGA
115561 AGAGTTCTACAGATAAATTCCTTCCAAGCAATCTGAAAGGCCCTCCAA
196 AGAGTTCTACAGATAAATTCCTTCCAAGCAATCTGAAAGGCCCTCCAA
*
115609 CATTTTAGCCGTCGGAAATTACTTTGAATTTTTGTTATTGCTTGCTTCTGCTTCATAAACCTCAT
1 CATTTTAGCCGTCGGAAATTACTTTGAATTTTAGTTATTGCTTGCTTCTGCTTCATAAACCTCAT
**
115674 CCTCAACCTCCAACTGCAATAATAGCTCTGAATTTTA
66 CCTCAACCTCCAACTGCGGTAATAGCTCTGAATTTTA
115711 GTTGCAGCAT
Statistics
Matches: 324, Mismatches: 17, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
242 4 0.01
243 317 0.98
244 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (243 bp):
CATTTTAGCCGTCGGAAATTACTTTGAATTTTAGTTATTGCTTGCTTCTGCTTCATAAACCTCAT
CCTCAACCTCCAACTGCGGTAATAGCTCTGAATTTTAATTATTGCTTGCTTCTTCTTCATAAAAT
TCCTTCTTAACTGCCAACCACGGAAATGACTCTGAATTCTGGTTGCAGCTAAGGTCTGATTCTGA
AGAGTTCTACAGATAAATTCCTTCCAAGCAATCTGAAAGGCCCTCCAA
Found at i:125301 original size:16 final size:16
Alignment explanation
Indices: 125261--125305 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
125251 GGTTTAGTGT
*
125261 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
125278 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
125292 TTAAAAATTTATTT
1 TTAAAAATTTATTT
125306 TCATTCCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 10 0.40
17 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:126036 original size:72 final size:73
Alignment explanation
Indices: 125880--126021 Score: 205
Period size: 72 Copynumber: 2.0 Consensus size: 73
125870 TGGTCAAGGT
* * * * *
125880 TCACTTTAATACTATATTCAAATTGTTTATATTAACTTTTAAAATACTCGACATGAAATCGAGCA
1 TCACTTTAATACTATATTCAAACTGTTTATATCAAATTTTAAAACACTCGACATAAAATCGAGCA
125945 ATCAAGAG
66 ATCAAGAG
* * *
125953 TCACTTTAATACTATGTTCAAACTGTTTATA-CAAATTTTAGAACACTCGATATAAAATCGAGCA
1 TCACTTTAATACTATATTCAAACTGTTTATATCAAATTTTAAAACACTCGACATAAAATCGAGCA
126017 ATCAA
66 ATCAA
126022 ATGTTACTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
72 32 0.52
73 29 0.48
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (73 bp):
TCACTTTAATACTATATTCAAACTGTTTATATCAAATTTTAAAACACTCGACATAAAATCGAGCA
ATCAAGAG
Found at i:132688 original size:164 final size:164
Alignment explanation
Indices: 132309--132937 Score: 985
Period size: 163 Copynumber: 3.9 Consensus size: 164
132299 AAACAATGAC
132309 AAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGC
1 AAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGC
* *
132374 GTGTTCGATTCACGTCGGGTTCAATACCCCACTAAATCCTGATCCCACTTTTTGTTTTCTGATTC
66 GTGTTCGATTCACGTCGGGTTCAATTCCCCGCTAAATCCTGATCCCACTTTTTGTTTTCTGATTC
* *
132439 ATACTATG-T-T-G--A-G---TGTTCTATCTTA
131 ATAGTATGCTGTCGAAAGGAAATGATCTATCTTA
**
132464 TTAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGC
1 AAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGC
* * *
132529 GTGTTGGGTTCACGTCGGGTTCAATTCCTCGCTAAATCCTGATCCCACTTTTTGTTTTCTGATTC
66 GTGTTCGATTCACGTCGGGTTCAATTCCCCGCTAAATCCTGATCCCACTTTTTGTTTTCTGATTC
* *
132594 ATAGTACGCTGTCGAAAGGAAATGCTCTATCTTA
131 ATAGTATGCTGTCGAAAGGAAATGATCTATCTTA
132628 AAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGC
1 AAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGC
132693 GTGTTCGATTCACGTCGGGTTCAA-TCCCCGCTAAATCCTGATCCCACTTTTTGTTTTCTGATTC
66 GTGTTCGATTCACGTCGGGTTCAATTCCCCGCTAAATCCTGATCCCACTTTTTGTTTTCTGATTC
* * *
132757 ATAATATGCTGTCGAAATGAAATAATCTATCTTA
131 ATAGTATGCTGTCGAAAGGAAATGATCTATCTTA
132791 AAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGC
1 AAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGC
* * * *
132856 GTGTTCAATTCACGTCGGGTTCAATTTCCCGTTAAAAT-CAGATCCCACTTTTTGTTTTCTGATT
66 GTGTTCGATTCACGTCGGGTTCAATTCCCCGCT-AAATCCTGATCCCACTTTTTGTTTTCTGATT
* *
132920 TA-AGTATGCTGTCAAAAG
130 CATAGTATGCTGTCGAAAG
132938 AGAATGAAGC
Statistics
Matches: 435, Mismatches: 28, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
155 129 0.30
156 1 0.00
157 1 0.00
158 1 0.00
160 1 0.00
161 1 0.00
163 169 0.39
164 128 0.29
165 4 0.01
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (164 bp):
AAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGC
GTGTTCGATTCACGTCGGGTTCAATTCCCCGCTAAATCCTGATCCCACTTTTTGTTTTCTGATTC
ATAGTATGCTGTCGAAAGGAAATGATCTATCTTA
Found at i:132902 original size:327 final size:318
Alignment explanation
Indices: 132309--132937 Score: 1012
Period size: 327 Copynumber: 1.9 Consensus size: 318
132299 AAACAATGAC
132309 AAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGC
1 AAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGC
132374 GTGTTCGATTCACGTCGGGTTCAATACCCCACTAAATCCTGATCCCACTTTTTGTTTTCTGATTC
66 GTGTTCGATTCACGTCGGGTTCAATACCCCACTAAATCCTGATCCCACTTTTTGTTTTCTGATTC
* * **
132439 ATACTATGTTGAGTGTTCTATCTTATTAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGC
131 ATAATATGTTGAATGTTCTATCTTAAAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGC
*** *
132504 GTCTGACTCCAGATCAGAAGGTTGCGTGTTGGGTTCACGTCGGGTTCAATTCCTCGCTAAATCCT
196 GTCTGACTCCAGATCAGAAGGTTGCGTGTTCAATTCACGTCGGGTTCAATTCCTCGCTAAATCCA
*
132569 GATCCCACTTTTTGTTTTCTGATTCATAGTACGCTGTCGAAAGGAAATGCTCTATCTTA
261 GATCCCACTTTTTGTTTTCTGATTCA-AGTACGCTGTCAAAAGGAAATGCTCTATCTTA
132628 AAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGC
1 AAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGC
*
132693 GTGTTCGATTCACGTCGGGTTCAAT-CCCCGCTAAATCCTGATCCCACTTTTTGTTTTCTGATTC
66 GTGTTCGATTCACGTCGGGTTCAATACCCCACTAAATCCTGATCCCACTTTTTGTTTTCTGATTC
132757 ATAATATGCTGTCGAAATGAAATAATCTATCTTAAAAGGGAGAGACAACAGGATCCGTGGCGCAA
131 ATAATATG-T-T-G-AATG---T--TCTATCTTAAAAGGGAGAGACAACAGGATCCGTGGCGCAA
132822 TGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCAATTCACGTCGGGTTCAATTTCC-C
187 TGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCAATTCACGTCGGGTTCAA-TTCCTC
* * *
132886 GTTAAAAT-CAGATCCCACTTTTTGTTTTCTGATTTAAGTATGCTGTCAAAAG
251 GCT-AAATCCAGATCCCACTTTTTGTTTTCTGATTCAAGTACGCTGTCAAAAG
132938 AGAATGAAGC
Statistics
Matches: 286, Mismatches: 13, Indels: 15
0.91 0.04 0.05
Matches are distributed among these distances:
318 45 0.16
319 91 0.32
320 1 0.00
321 1 0.00
322 3 0.01
325 1 0.00
326 14 0.05
327 122 0.43
328 8 0.03
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (318 bp):
AAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGC
GTGTTCGATTCACGTCGGGTTCAATACCCCACTAAATCCTGATCCCACTTTTTGTTTTCTGATTC
ATAATATGTTGAATGTTCTATCTTAAAAGGGAGAGACAACAGGATCCGTGGCGCAATGGTAGCGC
GTCTGACTCCAGATCAGAAGGTTGCGTGTTCAATTCACGTCGGGTTCAATTCCTCGCTAAATCCA
GATCCCACTTTTTGTTTTCTGATTCAAGTACGCTGTCAAAAGGAAATGCTCTATCTTA
Found at i:142509 original size:58 final size:58
Alignment explanation
Indices: 142447--142566 Score: 170
Period size: 58 Copynumber: 2.1 Consensus size: 58
142437 TTTTAATAAG
* * *
142447 ATTATTATTAAATATAATTTAATAAAAATAATAAAAAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATACAATTTAAT-AAAATAATAAAAAATTTAATAACATTTTTAACATA
* * *
142505 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAACATTTTTAATATA
1 ATTATTATTAAATACAATTTAATAAAATAATAAAAAATTTAATAACATTTTTAACATA
142563 ATTA
1 ATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 20 0.36
58 35 0.64
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAATACAATTTAATAAAATAATAAAAAATTTAATAACATTTTTAACATA
Done.