Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004114.1 Kokia drynarioides strain JFW-HI SEQ_117296, 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: 103833
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:6503 original size:2 final size:2
Alignment explanation
Indices: 6496--6530 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6486 CTTCTCTGGA
*
6496 AC AC AC AC AC AC AC AC AA AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
6531 AAAAAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:7113 original size:91 final size:91
Alignment explanation
Indices: 6958--7123 Score: 305
Period size: 91 Copynumber: 1.8 Consensus size: 91
6948 TAGGAATGCA
*
6958 AAAAACCTAGCATGCCTAATCGTTCTCGAAGAGTGATAGTGGGTTGGTGTTTGGTATCTAGGGTT
1 AAAAACCTAGCATGCCTAATCGTTCTCGAAGAATGATAGTGGGTTGGTGTTTGGTATCTAGGGTT
*
7023 TACTGATTAGGAGCACCTACCTGACT
66 TACTAATTAGGAGCACCTACCTGACT
*
7049 AAAAACCTAGCATGCCTAATCGTTCTTGAAGAATGATAGTGGGTTGGTGTTTGGTATCTAGGGTT
1 AAAAACCTAGCATGCCTAATCGTTCTCGAAGAATGATAGTGGGTTGGTGTTTGGTATCTAGGGTT
7114 TACTAATTAG
66 TACTAATTAG
7124 AATGCATCAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 72 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.33
Consensus pattern (91 bp):
AAAAACCTAGCATGCCTAATCGTTCTCGAAGAATGATAGTGGGTTGGTGTTTGGTATCTAGGGTT
TACTAATTAGGAGCACCTACCTGACT
Found at i:12683 original size:45 final size:45
Alignment explanation
Indices: 12619--12708 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
12609 TAAGCAGTTA
12619 TTAATAAGAATTTAACATTACGAACTTATCGGACTGAATTGTAGT
1 TTAATAAGAATTTAACATTACGAACTTATCGGACTGAATTGTAGT
*
12664 TTAATAAGAATTTAACATTACGAACTTATCGGACTGAATTTTAGT
1 TTAATAAGAATTTAACATTACGAACTTATCGGACTGAATTGTAGT
12709 GACGAAAAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (45 bp):
TTAATAAGAATTTAACATTACGAACTTATCGGACTGAATTGTAGT
Found at i:18139 original size:29 final size:28
Alignment explanation
Indices: 18074--18151 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
18064 AAACACCAGC
* * *
18074 AAAGGAAAGCCTTTATGGCAAACCTTTG
1 AAAGGAAAGCCTTTGTGGCAAAACTTGG
18102 AAAGGAAAGCCTTTGTGGCAAAACTCTGG
1 AAAGGAAAGCCTTTGTGGCAAAACT-TGG
*
18131 ACAA-GAAAGCCTCTGTGGCAA
1 A-AAGGAAAGCCTTTGTGGCAA
18152 TTTTTGTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 23 0.52
29 19 0.43
30 2 0.05
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (28 bp):
AAAGGAAAGCCTTTGTGGCAAAACTTGG
Found at i:24717 original size:33 final size:34
Alignment explanation
Indices: 24656--24719 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
24646 TGTTATATTA
* * *
24656 TGCTTGCAAGTTATGTTAAGGGATTACTTATGTT
1 TGCTTGAAAGTTATGTTAAAGGACTACTTATGTT
24690 TGCTTGAAAGTT-TGTTAAAGGACTACTTAT
1 TGCTTGAAAGTTATGTTAAAGGACTACTTAT
24720 ATTTATATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 16 0.59
34 11 0.41
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (34 bp):
TGCTTGAAAGTTATGTTAAAGGACTACTTATGTT
Found at i:25433 original size:12 final size:12
Alignment explanation
Indices: 25412--25438 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
25402 GACATGGCCA
25412 TGGCCATGGTCG
1 TGGCCATGGTCG
25424 TGGCCATGGTCG
1 TGGCCATGGTCG
25436 TGG
1 TGG
25439 TCACGATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.22, G:0.44, T:0.26
Consensus pattern (12 bp):
TGGCCATGGTCG
Found at i:51901 original size:109 final size:109
Alignment explanation
Indices: 51776--52010 Score: 294
Period size: 108 Copynumber: 2.2 Consensus size: 109
51766 GTCACCCATA
** * ** *
51776 CCTTTATCTGATAAAAAAAAAATTTAGTGTTGCCCATGTAATGGCCGACACCACCTTTATCAGAT
1 CCTTTATCTGATAAAAAAAAAATTTAGTGTCACCCATGCAATAACCAACACCACCTTTATCAGAT
*
51841 AAAAAAACA-TTTTTTAGTGTCACTCATGCCATGGCTGACACCT
66 AAAAAAACATTTTTTTAGTGTCACTCATGCCATGGCCGACACCT
* * * * * * *
51884 CTTTTTATCTAAT-AAAAAAAAATTTGGTGTCACCCATGCCATAATCAACACCTCCTTTATCTGA
1 C-CTTTATCTGATAAAAAAAAAATTTAGTGTCACCCATGCAATAACCAACACCACCTTTATCAGA
* *
51948 TAAAAAAATATTTTTTTGGTGTCACTCATGCCATGGCCGACACCT
65 TAAAAAAACATTTTTTTAGTGTCACTCATGCCATGGCCGACACCT
*
51993 CCTTTATTTGATAAAAAA
1 CCTTTATCTGATAAAAAA
52011 TATTTTTTTG
Statistics
Matches: 105, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
108 58 0.55
109 47 0.45
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.33
Consensus pattern (109 bp):
CCTTTATCTGATAAAAAAAAAATTTAGTGTCACCCATGCAATAACCAACACCACCTTTATCAGAT
AAAAAAACATTTTTTTAGTGTCACTCATGCCATGGCCGACACCT
Found at i:51978 original size:56 final size:54
Alignment explanation
Indices: 51819--52025 Score: 215
Period size: 56 Copynumber: 3.8 Consensus size: 54
51809 CCATGTAATG
* * * *
51819 GCCGACACCACCTTTATCAGATAAAAAAACATTTTTTAGTGTCACTCATGCCAT
1 GCCGACACCTCCTTTATCTGATAAAAAAATATTTTTTGGTGTCACTCATGCCAT
* * * * *
51873 GGCTGACACCTCTTTTTATCTAATAAAAAAA-A--ATTTGGTGTCACCCATGCCAT
1 -GCCGACACCTC-CTTTATCTGATAAAAAAATATTTTTTGGTGTCACTCATGCCAT
** *
51926 AATCAACACCTCCTTTATCTGATAAAAAAATATTTTTTTGGTGTCACTCATGCCAT
1 -GCCGACACCTCCTTTATCTGATAAAAAAATA-TTTTTTGGTGTCACTCATGCCAT
*
51982 GGCCGACACCTCCTTTATTTGAT-AAAAAATATTTTTTTGGTGTC
1 -GCCGACACCTCCTTTATCTGATAAAAAAATA-TTTTTTGGTGTC
52026 GCCCTTGCCT
Statistics
Matches: 125, Mismatches: 22, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
52 16 0.13
53 26 0.21
55 31 0.25
56 52 0.42
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (54 bp):
GCCGACACCTCCTTTATCTGATAAAAAAATATTTTTTGGTGTCACTCATGCCAT
Found at i:52974 original size:18 final size:18
Alignment explanation
Indices: 52953--53006 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
52943 AATTAGAAAT
52953 GAAATTTAAAATATAAAC
1 GAAATTTAAAATATAAAC
52971 GAAA-TTAGAAAT-T----
1 GAAATTTA-AAATATAAAC
52984 -AAATTTAAAATATAAAC
1 GAAATTTAAAATATAAAC
53001 GAAATT
1 GAAATT
53007 ACAAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
12 7 0.25
13 4 0.14
17 4 0.14
18 13 0.46
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (18 bp):
GAAATTTAAAATATAAAC
Found at i:52979 original size:30 final size:30
Alignment explanation
Indices: 52943--53035 Score: 150
Period size: 30 Copynumber: 3.1 Consensus size: 30
52933 AAAAAATAAT
*
52943 AATTAGAAATGAAATTTAAAATATAAACGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
52973 AATTAGAAATTAAATTTAAAATATAAACGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
* * *
53003 AATTACAAATTAAATTTAAAAAATAAATGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
53033 AAT
1 AAT
53036 AAAATCAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.29
Consensus pattern (30 bp):
AATTAGAAATTAAATTTAAAATATAAACGA
Found at i:56174 original size:31 final size:31
Alignment explanation
Indices: 56116--56174 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
56106 TATTTTATGG
* * *
56116 TTTATTTTCTGAAAATTAATAAGTTAGTCCT
1 TTTACTTTCTGAAAATTAAGAAATTAGTCCT
* *
56147 TTTACTTTGTGAAAATTGAGAAATTAGT
1 TTTACTTTCTGAAAATTAAGAAATTAGT
56175 ATAATTGAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTACTTTCTGAAAATTAAGAAATTAGTCCT
Found at i:57024 original size:7 final size:7
Alignment explanation
Indices: 57009--57049 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
56999 TTACTAAGTT
*
57009 TAAATAA
1 TAAAAAA
57016 TAAAAAA
1 TAAAAAA
*
57023 TAAAATA
1 TAAAAAA
57030 -AAAAAA
1 TAAAAAA
57036 TAAAAAA
1 TAAAAAA
57043 TAAAAAA
1 TAAAAAA
57050 ACCCAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAAAAA
Found at i:57030 original size:15 final size:15
Alignment explanation
Indices: 57010--57049 Score: 59
Period size: 13 Copynumber: 2.9 Consensus size: 15
57000 TACTAAGTTT
57010 AAATAATAAAAAATA
1 AAATAATAAAAAATA
57025 AAAT-A-AAAAAATA
1 AAATAATAAAAAATA
57038 AAA-AATAAAAAA
1 AAATAATAAAAAA
57050 ACCCAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 12 0.52
14 7 0.30
15 4 0.17
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (15 bp):
AAATAATAAAAAATA
Found at i:57050 original size:15 final size:14
Alignment explanation
Indices: 57010--57050 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
57000 TACTAAGTTT
*
57010 AAATAATAAAAAATA
1 AAATAA-AAAAAAAA
57025 AAATAAAAAAATAAA
1 AAATAAAAAAA-AAA
57040 AAATAAAAAAA
1 AAATAAAAAAA
57051 CCCAAAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
AAATAAAAAAAAAA
Found at i:58533 original size:13 final size:13
Alignment explanation
Indices: 58515--58540 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58505 CCCCGGTTGT
58515 TTATTTTTATTTA
1 TTATTTTTATTTA
58528 TTATTTTTATTTA
1 TTATTTTTATTTA
58541 ATTTTAAAGA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATTTTTATTTA
Found at i:59245 original size:20 final size:21
Alignment explanation
Indices: 59220--59263 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
59210 TGATTTTTAG
59220 AAATTAT-AGAAAAATATTAA
1 AAATTATAAGAAAAATATTAA
59240 AAATTATAAGAAAAATATTAA
1 AAATTATAAGAAAAATATTAA
59261 AAA
1 AAA
59264 GATAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (21 bp):
AAATTATAAGAAAAATATTAA
Found at i:59274 original size:21 final size:21
Alignment explanation
Indices: 59229--59279 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
59219 GAAATTATAG
* *
59229 AAAAATATTAAAAATTATAAG
1 AAAAATATTAAAAAATATAAA
59250 AAAAATATTAAAAAGATA-AAA
1 AAAAATATTAAAAA-ATATAAA
59271 AAAAATATT
1 AAAAATATT
59280 TTTTAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (21 bp):
AAAAATATTAAAAAATATAAA
Found at i:59665 original size:9 final size:9
Alignment explanation
Indices: 59653--59706 Score: 56
Period size: 10 Copynumber: 5.7 Consensus size: 9
59643 AATTTTACAT
59653 TTTTTATAA
1 TTTTTATAA
59662 TTTTTATAAA
1 TTTTTAT-AA
*
59672 TTTCTA-AA
1 TTTTTATAA
59680 TTTTCTATAA
1 TTTT-TATAA
59690 TATTTTAATAA
1 T-TTTT-ATAA
59701 TTTTTA
1 TTTTTA
59707 GGCTTAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 5 0.13
9 10 0.26
10 15 0.39
11 8 0.21
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:59666 original size:10 final size:10
Alignment explanation
Indices: 59651--59705 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 10
59641 AAAATTTTAC
59651 ATTTTTTATA
1 ATTTTTTATA
59661 A-TTTTTATA
1 ATTTTTTATA
* *
59670 AATTTCTA-A
1 ATTTTTTATA
*
59679 ATTTTCTATA
1 ATTTTTTATA
*
59689 ATATTTTAATA
1 AT-TTTTTATA
59700 ATTTTT
1 ATTTTT
59706 AGGCTTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 17 0.45
10 13 0.34
11 8 0.21
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:59682 original size:28 final size:27
Alignment explanation
Indices: 59633--59704 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
59623 TATTAATAAC
* *
59633 ATTTTATAAAAATTTTACATTTTTTATA
1 ATTTT-TAAAAATTTTAAATTTTCTATA
*
59661 ATTTTTATAAATTTCTAAATTTTCTATA
1 ATTTTTAAAAATTT-TAAATTTTCTATA
*
59689 ATATTTTAATAATTTT
1 AT-TTTTAAAAATTTT
59705 TAGGCTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 8 0.22
28 19 0.51
29 10 0.27
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTTTAAAAATTTTAAATTTTCTATA
Found at i:64715 original size:38 final size:38
Alignment explanation
Indices: 64659--64834 Score: 179
Period size: 38 Copynumber: 4.8 Consensus size: 38
64649 TAACACTGAT
* *
64659 TGTTGAACTGAA-AGCATGTGAAGCATGTCTACTGCGAC
1 TGTTGAACAGAATA-CATGTTAAGCATGTCTACTGCGAC
* * * *
64697 TGTTGAACAGAATACATGTTAAACATGTCTATTGCTAA
1 TGTTGAACAGAATACATGTTAAGCATGTCTACTGCGAC
*
64735 TGTT------AA-ACATGTGAAGCATGTCTACTGCGAC
1 TGTTGAACAGAATACATGTTAAGCATGTCTACTGCGAC
* * *
64766 TGTTGAACAGAATACATGTTAAACATGTCTATTGCTAC
1 TGTTGAACAGAATACATGTTAAGCATGTCTACTGCGAC
* *
64804 TGTTGAACTGATTACATGTTAAGCATGTCTA
1 TGTTGAACAGAATACATGTTAAGCATGTCTA
64835 TTGTTTTTGT
Statistics
Matches: 112, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
31 24 0.21
32 2 0.02
37 2 0.02
38 83 0.74
39 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (38 bp):
TGTTGAACAGAATACATGTTAAGCATGTCTACTGCGAC
Found at i:64752 original size:69 final size:69
Alignment explanation
Indices: 64673--64807 Score: 261
Period size: 69 Copynumber: 2.0 Consensus size: 69
64663 GAACTGAAAG
64673 CATGTGAAGCATGTCTACTGCGACTGTTGAACAGAATACATGTTAAACATGTCTATTGCTAATGT
1 CATGTGAAGCATGTCTACTGCGACTGTTGAACAGAATACATGTTAAACATGTCTATTGCTAATGT
64738 TAAA
66 TAAA
*
64742 CATGTGAAGCATGTCTACTGCGACTGTTGAACAGAATACATGTTAAACATGTCTATTGCTACTGT
1 CATGTGAAGCATGTCTACTGCGACTGTTGAACAGAATACATGTTAAACATGTCTATTGCTAATGT
64807 T
66 T
64808 GAACTGATTA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (69 bp):
CATGTGAAGCATGTCTACTGCGACTGTTGAACAGAATACATGTTAAACATGTCTATTGCTAATGT
TAAA
Found at i:66875 original size:21 final size:20
Alignment explanation
Indices: 66836--66875 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
66826 GACAATCATT
**
66836 TTATATTTTTTAATTTATTA
1 TTATATTTTTTAAAATATTA
66856 TTATATTTTTTGAAAATATT
1 TTATATTTTTT-AAAATATT
66876 CACATATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (20 bp):
TTATATTTTTTAAAATATTA
Found at i:68181 original size:21 final size:21
Alignment explanation
Indices: 68155--68207 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
68145 CTTTGCTAGC
68155 TCTACCGATACAAGT-ATG-A
1 TCTACCGATACAAGTCATGCA
68174 TTTCTACCGATACAAGTCATGCA
1 --TCTACCGATACAAGTCATGCA
68197 TCTACCGATAC
1 TCTACCGATAC
68208 TAGAAACTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 26 0.87
22 3 0.10
23 1 0.03
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.28
Consensus pattern (21 bp):
TCTACCGATACAAGTCATGCA
Found at i:68285 original size:21 final size:22
Alignment explanation
Indices: 68247--68323 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 22
68237 CCTACAACTT
* *
68247 CTACCGATATAAGC-ATACAAA
1 CTACCGATACATGCAATACAAA
68268 CTACCGATACAT-CAATACTAATAA
1 CTACCGATACATGCAATAC--A-AA
* *
68292 CTACCGATACTTGCAATTC-AA
1 CTACCGATACATGCAATACAAA
68313 CTACCGATACA
1 CTACCGATACA
68324 ACTCAAGTCA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
20 1 0.02
21 26 0.57
23 1 0.02
24 13 0.28
25 5 0.11
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.23
Consensus pattern (22 bp):
CTACCGATACATGCAATACAAA
Found at i:86008 original size:61 final size:61
Alignment explanation
Indices: 85913--86036 Score: 248
Period size: 61 Copynumber: 2.0 Consensus size: 61
85903 GTAATACTAC
85913 GGTGGTGGGTTTGCTGAGAGATTTTAGGGGGGATTGGGTGCTTGTTGTAGTCGAAATTTAG
1 GGTGGTGGGTTTGCTGAGAGATTTTAGGGGGGATTGGGTGCTTGTTGTAGTCGAAATTTAG
85974 GGTGGTGGGTTTGCTGAGAGATTTTAGGGGGGATTGGGTGCTTGTTGTAGTCGAAATTTAG
1 GGTGGTGGGTTTGCTGAGAGATTTTAGGGGGGATTGGGTGCTTGTTGTAGTCGAAATTTAG
86035 GG
1 GG
86037 GTGAACTTAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.16, C:0.05, G:0.44, T:0.35
Consensus pattern (61 bp):
GGTGGTGGGTTTGCTGAGAGATTTTAGGGGGGATTGGGTGCTTGTTGTAGTCGAAATTTAG
Found at i:90028 original size:23 final size:23
Alignment explanation
Indices: 90000--90043 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
89990 TCAGCTCACA
*
90000 CCAACAAATAGCTATATATATTT
1 CCAACAAATAGATATATATATTT
*
90023 CCAACAAATATATATATATAT
1 CCAACAAATAGATATATATAT
90044 ATATATAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (23 bp):
CCAACAAATAGATATATATATTT
Found at i:91332 original size:16 final size:18
Alignment explanation
Indices: 91293--91326 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
91283 TAAGTTTATA
91293 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
91310 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
91327 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:92792 original size:21 final size:20
Alignment explanation
Indices: 92734--92783 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
92724 ATTATATTAT
92734 TGTTTTGATGCCTTTTTTTAC
1 TGTTTTGATG-CTTTTTTTAC
* * *
92755 CGTTTTGGTGTTTTTTTTAC
1 TGTTTTGATGCTTTTTTTAC
92775 TGTTTTGAT
1 TGTTTTGAT
92784 TGCTATTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.08, C:0.10, G:0.18, T:0.64
Consensus pattern (20 bp):
TGTTTTGATGCTTTTTTTAC
Found at i:92834 original size:12 final size:12
Alignment explanation
Indices: 92820--92899 Score: 58
Period size: 12 Copynumber: 6.9 Consensus size: 12
92810 GGTACTATTG
*
92820 TTTTTGTTGTTG
1 TTTTTGTTGTTA
* *
92832 TTTTTATTGCTA
1 TTTTTGTTGTTA
*
92844 --TTT-TTGCTA
1 TTTTTGTTGTTA
92853 TTTTTGTTGTTA
1 TTTTTGTTGTTA
* *
92865 TTTTTGTTGCTG
1 TTTTTGTTGTTA
* *
92877 CTTTGGTTGTTA
1 TTTTTGTTGTTA
*
92889 TTTTGGTTGTT
1 TTTTTGTTGTT
92900 TAAAAGTTAT
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
9 6 0.11
10 3 0.06
11 3 0.06
12 42 0.78
ACGTcount: A:0.06, C:0.05, G:0.20, T:0.69
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:100445 original size:52 final size:52
Alignment explanation
Indices: 100367--100656 Score: 331
Period size: 52 Copynumber: 5.6 Consensus size: 52
100357 GTAATTGAAA
100367 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTAT
* * * *
100419 AAGGTCCGATGACTATGTTTTATCGTGAGTATATGAATCCTTTACGAATTA-
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTAT
* * *
100470 ATGGGTCCGATAAC--TGTGTCATCGTGA-TAATATGAATCCTTTACGGATTAT
1 A-AGGTCCGATGACTATGTGTCATCGTGAGT-ATATGAATTCTTTACGGATTAT
* * * * **
100521 GAGGTCCGATGACTATGTGTCATCATGAGTATGTGGATTCTTTATAGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTAT
* *
100573 AAGGTCCGATGACTATGTGTCATCATGAGTATATG-ATTCCTTTACAGATTA-
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATT-CTTTACGGATTAT
* * * *
100624 AGAGGTCCGCTGGCTATATGTCATTGTGAGTAT
1 A-AGGTCCGATGACTATGTGTCATCGTGAGTAT
100657 TAAATGAAAT
Statistics
Matches: 204, Mismatches: 26, Indels: 16
0.83 0.11 0.07
Matches are distributed among these distances:
49 1 0.00
50 41 0.20
51 5 0.02
52 156 0.76
53 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTAT
Found at i:100564 original size:102 final size:103
Alignment explanation
Indices: 100367--100656 Score: 327
Period size: 102 Copynumber: 2.8 Consensus size: 103
100357 GTAATTGAAA
* * *
100367 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTATAAGGTCCGATGAC
1 AAGGTCCGATAAC-ATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
* *
100432 TATGTTTTATCGTGAGTATATGAATCCTTTACGA-ATTA-
65 TATGTGTCATCGTGAGTATATGAATCCTTTA-GAGATTAT
*
100470 ATGGGTCCGATAAC-TGTGTCATCGTGA-TAATATGAATCCTTTACGGATTATGAGGTCCGATGA
1 A-AGGTCCGATAACATGTGTCATCGTGAGT-ATATGAATCCTTTACGGATTATGAGGTCCGATGA
* * * * *
100533 CTATGTGTCATCATGAGTATGTGGATTCTTTATAGATTAT
64 CTATGTGTCATCGTGAGTATATGAATCCTTTAGAGATTAT
* * * * * * *
100573 AAGGTCCGATGACTATGTGTCATCATGAGTATATGATTCCTTTACAGATTAAGAGGTCCGCTGGC
1 AAGGTCCGATAAC-ATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
* *
100638 TATATGTCATTGTGAGTAT
65 TATGTGTCATCGTGAGTAT
100657 TAAATGAAAT
Statistics
Matches: 158, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
101 2 0.01
102 85 0.54
103 2 0.01
104 68 0.43
105 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
AAGGTCCGATAACATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACT
ATGTGTCATCGTGAGTATATGAATCCTTTAGAGATTAT
Done.