Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001982.1 Kokia drynarioides strain JFW-HI SEQ_113833, 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: 124967
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 72 characters in sequence are not A, C, G, or T
Found at i:132 original size:18 final size:18
Alignment explanation
Indices: 114--152 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
104 CTTCTCCTTC
114 TTCATTCTTCTTTTTTTCT
1 TTCATTC-TCTTTTTTTCT
*
133 TTCTTTCTC-TTTTTTCT
1 TTCATTCTCTTTTTTTCT
150 TTC
1 TTC
153 TTTTTTCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 2 0.11
19 6 0.32
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (18 bp):
TTCATTCTCTTTTTTTCT
Found at i:147 original size:17 final size:16
Alignment explanation
Indices: 121--155 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
111 TTCTTCATTC
121 TTCTTTTTTTCTTTCT
1 TTCTTTTTTTCTTTCT
137 TTCTCTTTTTTCTTTCT
1 TTCT-TTTTTTCTTTCT
154 TT
1 TT
156 TTTCCTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTCTTTTTTTCTTTCT
Found at i:150 original size:13 final size:12
Alignment explanation
Indices: 121--158 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
111 TTCTTCATTC
121 TTCTTT-TTTTCT
1 TTCTTTCTTTT-T
133 TTCTTTCTCTTTT
1 TTCTTTCT-TTTT
146 TTCTTTCTTTTT
1 TTCTTTCTTTTT
158 T
1 T
159 CCTTCATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.46
13 10 0.42
14 3 0.12
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTCTTTCTTTTT
Found at i:152 original size:21 final size:20
Alignment explanation
Indices: 119--169 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
109 CCTTCTTCAT
119 TCTTCTTTTTTTCTTTCTTTC
1 TCTTCTTTTTTTCTTT-TTTC
140 TCTT-TTTTCTTTCTTTTTTC
1 TCTTCTTTT-TTTCTTTTTTC
160 -CTTCATTTTT
1 TCTTC-TTTTT
170 CATTGGTCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.11
20 9 0.33
21 15 0.56
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (20 bp):
TCTTCTTTTTTTCTTTTTTC
Found at i:1904 original size:23 final size:25
Alignment explanation
Indices: 1874--1920 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1864 TTCAATTAGG
1874 AAATTA-TTGTTTAG-ATTTAATTC
1 AAATTATTTGTTTAGAATTTAATTC
*
1897 AAATTATTTTTTTAGAATTTAATT
1 AAATTATTTGTTTAGAATTTAATT
1921 AGGATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (25 bp):
AAATTATTTGTTTAGAATTTAATTC
Found at i:5860 original size:20 final size:19
Alignment explanation
Indices: 5806--5864 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
5796 CTTGTCTTTA
* *
5806 AAAAATTGAAAAACAAATTT
1 AAAAATT-AAAAAAAAATTG
**
5826 AAAAATTATTTAAAAAATTG
1 AAAAATTA-AAAAAAAATTG
5846 AAAAATTCAAAAAAAAATT
1 AAAAATT-AAAAAAAAATT
5865 AGTATATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (19 bp):
AAAAATTAAAAAAAAATTG
Found at i:5862 original size:32 final size:31
Alignment explanation
Indices: 5802--5865 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
5792 CTTTCTTGTC
*
5802 TTTAAAAAATTGAAAAACAAATTTAAAAATTA
1 TTTAAAAAATTGAAAAACAAA-TAAAAAATTA
5834 TTTAAAAAATTGAAAAATTCAAA-AAAAAATTA
1 TTTAAAAAATTGAAAAA--CAAATAAAAAATTA
5866 GTATATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 25 0.86
34 4 0.14
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (31 bp):
TTTAAAAAATTGAAAAACAAATAAAAAATTA
Found at i:5904 original size:5 final size:5
Alignment explanation
Indices: 5871--5925 Score: 56
Period size: 5 Copynumber: 9.8 Consensus size: 5
5861 AATTAGTATA
5871 TTTAT TTTCAT TTTCATT TTTAGT TTTAT TTTAT TTTAT TCTTATT TTTAT
1 TTTAT TTT-AT TTT-A-T TTTA-T TTTAT TTTAT TTTAT T-TTA-T TTTAT
5922 TTTA
1 TTTA
5926 ATCATGCAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
5 20 0.44
6 19 0.42
7 6 0.13
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:5915 original size:11 final size:10
Alignment explanation
Indices: 5871--5925 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 10
5861 AATTAGTATA
5871 TTTATTTTCAT
1 TTTATTTT-AT
5882 TTTCATTTTTAGT
1 TTT-A-TTTTA-T
5895 TTTATTTTAT
1 TTTATTTTAT
5905 TTTATTCTTATT
1 TTTATT-TTA-T
5917 TTTATTTTA
1 TTTATTTTA
5926 ATCATGCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
10 7 0.18
11 14 0.36
12 10 0.26
13 8 0.21
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:7915 original size:23 final size:25
Alignment explanation
Indices: 7889--7935 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
7879 TCCAATTAGG
7889 AAATTAT-TGTTTAG-ATTTAATTC
1 AAATTATCTGTTTAGAATTTAATTC
*
7912 AAATTATCTTTTTAGAATTTAATT
1 AAATTATCTGTTTAGAATTTAATT
7936 TGGATCCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (25 bp):
AAATTATCTGTTTAGAATTTAATTC
Found at i:15239 original size:33 final size:33
Alignment explanation
Indices: 15202--15267 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
15192 ATCCCGACTT
15202 TTTAAAGTTCTT-TTGCAAGTGACTTAAAAGAGA
1 TTTAAAGTT-TTCTTGCAAGTGACTTAAAAGAGA
* *
15235 TTTAAAGTTTTCTTGCAATTGAGTTAAAAGAGA
1 TTTAAAGTTTTCTTGCAAGTGACTTAAAAGAGA
15268 CTCTTTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (33 bp):
TTTAAAGTTTTCTTGCAAGTGACTTAAAAGAGA
Found at i:19681 original size:30 final size:28
Alignment explanation
Indices: 19646--19707 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
19636 ATAAAATTAA
*
19646 AAATAACTTTAGTTTAATATGTAATGTTAT
1 AAATAAATTTAGTTT--TATGTAATGTTAT
* *
19676 AAATAAATTTTGTTTTATGTAATTTTAT
1 AAATAAATTTAGTTTTATGTAATGTTAT
19704 AAAT
1 AAAT
19708 GATATTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 16 0.55
30 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (28 bp):
AAATAAATTTAGTTTTATGTAATGTTAT
Found at i:22891 original size:20 final size:21
Alignment explanation
Indices: 22847--22895 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
22837 TGAAAAATAA
22847 TAAAATAAATAATACATTAAAT
1 TAAAA-AAATAATACATTAAAT
* *
22869 TAAAAAAATAAT-TATTAATT
1 TAAAAAAATAATACATTAAAT
22889 TAAAAAA
1 TAAAAAA
22896 TAAATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.52
21 7 0.28
22 5 0.20
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAAAATAATACATTAAAT
Found at i:23856 original size:15 final size:16
Alignment explanation
Indices: 23836--23868 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
23826 TATTATATTT
23836 TTTTAA-AAAAATTAA
1 TTTTAACAAAAATTAA
23851 TTTTAACTAAAAATTAA
1 TTTTAAC-AAAAATTAA
23868 T
1 T
23869 CTAAAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTTAACAAAAATTAA
Found at i:24429 original size:59 final size:59
Alignment explanation
Indices: 24347--24460 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 59
24337 TAAATTGGGT
* * * * *
24347 CCAAAAAAAGTTTAGGTACCAAATTAAGAAAAAATGTCAAATTCAGGTATCAAATTATG
1 CCAAAAAAAATTTAAGAACCAAATTAAGAAAAAATGTCAAATTCAAGTACCAAATTATG
* * *
24406 CCAAAAAAAATTTAAGAATCAAATTAAGAAAAAGTGTCAAGTTCAAGTACCAAAT
1 CCAAAAAAAATTTAAGAACCAAATTAAGAAAAAATGTCAAATTCAAGTACCAAAT
24461 GTTATATTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (59 bp):
CCAAAAAAAATTTAAGAACCAAATTAAGAAAAAATGTCAAATTCAAGTACCAAATTATG
Found at i:29679 original size:112 final size:112
Alignment explanation
Indices: 29479--29709 Score: 426
Period size: 112 Copynumber: 2.1 Consensus size: 112
29469 TAATAGCATA
*
29479 CAGTTTCTTCATTTCAATATCCAAGTCCCTTTGAGTTATATTATGCCAAATCAAATCATTTCAGT
1 CAGTTTCTTCATTTCAATATCCAAGTCCCTTTGAGTTATATTATGCCAAATCAAATCATTTCAAT
*
29544 ATCAAAGTCTCGTATAAAAATATTTAAAATATTATGACACCAAAAGC
66 ATCAAAGTCTCATATAAAAATATTTAAAATATTATGACACCAAAAGC
29591 CAGTTTCTTCATTTCAATATCCAAGTCCCTTTGAGTTATATTATGCCAAATCAAATCATTTCAAT
1 CAGTTTCTTCATTTCAATATCCAAGTCCCTTTGAGTTATATTATGCCAAATCAAATCATTTCAAT
* *
29656 ATCCAAGTCTCATATAAATATATTTAAAATATTATGACACCAAAAGC
66 ATCAAAGTCTCATATAAAAATATTTAAAATATTATGACACCAAAAGC
29703 CAGTTTC
1 CAGTTTC
29710 GCCAGTTTCT
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 115 1.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.35
Consensus pattern (112 bp):
CAGTTTCTTCATTTCAATATCCAAGTCCCTTTGAGTTATATTATGCCAAATCAAATCATTTCAAT
ATCAAAGTCTCATATAAAAATATTTAAAATATTATGACACCAAAAGC
Found at i:30537 original size:6 final size:6
Alignment explanation
Indices: 30526--30560 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
30516 GATCACTGCC
* *
30526 TTCTTT TTCTTT TTCTTT TTCTTT TGCTTC TTCTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTT
30561 CATTTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (6 bp):
TTCTTT
Found at i:30566 original size:21 final size:21
Alignment explanation
Indices: 30532--30571 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30522 TGCCTTCTTT
* *
30532 TTCTTTTTCTTTTTCTTTTGC
1 TTCTTCTTCATTTTCTTTTGC
30553 TTCTTCTTCATTTTCTTTT
1 TTCTTCTTCATTTTCTTTT
30572 CCTTGCAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.75
Consensus pattern (21 bp):
TTCTTCTTCATTTTCTTTTGC
Found at i:35579 original size:43 final size:43
Alignment explanation
Indices: 35518--35660 Score: 241
Period size: 43 Copynumber: 3.3 Consensus size: 43
35508 GATTCTCCAT
*
35518 AGCTCGTGTGAGTAGCATCGTGTAGCTTAACATCTAGACCCAC
1 AGCTCGTGTGAGCAGCATCGTGTAGCTTAACATCTAGACCCAC
* *
35561 AGCTCGTGTGAGCAGCATCATGTAGCTTAACATCTCGACCCAC
1 AGCTCGTGTGAGCAGCATCGTGTAGCTTAACATCTAGACCCAC
* *
35604 AGCTCGTGTGAGCAGCATCGTGTAGCTTAACATCTTGACCCAT
1 AGCTCGTGTGAGCAGCATCGTGTAGCTTAACATCTAGACCCAC
35647 AGCTCGTGTGAGCA
1 AGCTCGTGTGAGCA
35661 AACCCATTTT
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 94 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (43 bp):
AGCTCGTGTGAGCAGCATCGTGTAGCTTAACATCTAGACCCAC
Found at i:38928 original size:2 final size:2
Alignment explanation
Indices: 38921--38960 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
38911 TTAATACTTA
38921 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38961 TGTAAATCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39824 original size:29 final size:30
Alignment explanation
Indices: 39781--39842 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
39771 AATTCAACTT
* *
39781 TTTTTCAAAAAATTG-ATGTTCAAATTTAAC
1 TTTTTCAAAAAATTGAAAGCT-AAATTTAAC
*
39811 TTTTT-AAAATATTGAAAGCTAAATTTAAC
1 TTTTTCAAAAAATTGAAAGCTAAATTTAAC
39840 TTT
1 TTT
39843 AAAAAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (30 bp):
TTTTTCAAAAAATTGAAAGCTAAATTTAAC
Found at i:41537 original size:2 final size:2
Alignment explanation
Indices: 41530--41561 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
41520 TCCACTAGCT
*
41530 TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
41562 GGCCAACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:68984 original size:18 final size:17
Alignment explanation
Indices: 68935--68982 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
68925 ATAATTTGTT
* *
68935 TTTTTTTTCGTTTTAGGT
1 TTTTTTTT-ATTTTAGGG
68953 TTTTTTTTATTTTAGGG
1 TTTTTTTTATTTTAGGG
68970 TTTTTTTTATTTT
1 TTTTTTTTATTTT
68983 TAATTTGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 20 0.71
18 8 0.29
ACGTcount: A:0.08, C:0.02, G:0.12, T:0.77
Consensus pattern (17 bp):
TTTTTTTTATTTTAGGG
Found at i:75311 original size:13 final size:13
Alignment explanation
Indices: 75293--75326 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
75283 CAATTATTAT
75293 TAAAACCAATCCC
1 TAAAACCAATCCC
75306 TAAAACCAATCCC
1 TAAAACCAATCCC
75319 TAAAACCA
1 TAAAACCA
75327 TAATAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAAACCAATCCC
Found at i:75454 original size:20 final size:24
Alignment explanation
Indices: 75407--75460 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 24
75397 AATAAAATCC
75407 AAAACCCTAATTTAATACACACTT
1 AAAACCCTAATTTAATACACACTT
75431 AAAACCCTAA-TTAA-ACA-A-TT
1 AAAACCCTAATTTAATACACACTT
75451 AAAACCCTAA
1 AAAACCCTAA
75461 AAGCCATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 12 0.40
21 1 0.03
22 3 0.10
23 4 0.13
24 10 0.33
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAACCCTAATTTAATACACACTT
Found at i:79769 original size:25 final size:25
Alignment explanation
Indices: 79735--79785 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
79725 GAGAAAGGAG
79735 CTTTGATGAACATTAAAGTTGTCAT
1 CTTTGATGAACATTAAAGTTGTCAT
79760 CTTTGATGAACATTAAAGTTGTCAT
1 CTTTGATGAACATTAAAGTTGTCAT
79785 C
1 C
79786 AAAATCAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (25 bp):
CTTTGATGAACATTAAAGTTGTCAT
Found at i:104005 original size:22 final size:23
Alignment explanation
Indices: 103980--104030 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
103970 CTTAGCAAAC
103980 ATAACCCAAA-CATTTAAACCCA
1 ATAACCCAAACCATTTAAACCCA
* **
104002 ATAACCCAAACCCTTTTGACCCA
1 ATAACCCAAACCATTTAAACCCA
104025 ATAACC
1 ATAACC
104031 AAATTGAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.43, C:0.35, G:0.02, T:0.20
Consensus pattern (23 bp):
ATAACCCAAACCATTTAAACCCA
Found at i:104109 original size:7 final size:7
Alignment explanation
Indices: 104097--104129 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
104087 ACCGTTAACT
104097 TTGACCG
1 TTGACCG
104104 TTGACCG
1 TTGACCG
*
104111 TTGACTG
1 TTGACCG
104118 TTGACCG
1 TTGACCG
104125 TTGAC
1 TTGAC
104130 TTTTTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.33
Consensus pattern (7 bp):
TTGACCG
Found at i:104123 original size:21 final size:20
Alignment explanation
Indices: 104087--104129 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
104077 TCGTTGACCA
104087 ACCGTTAACTTTGACCGTTG
1 ACCGTTAACTTTGACCGTTG
*
104107 ACCGTTGACTGTTGACCGTTG
1 ACCGTTAACT-TTGACCGTTG
104128 AC
1 AC
104130 TTTTTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.33
Consensus pattern (20 bp):
ACCGTTAACTTTGACCGTTG
Found at i:105003 original size:17 final size:18
Alignment explanation
Indices: 104977--105010 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
104967 ATTGGGTGCA
*
104977 TTGCATCATG-TTTGTGT
1 TTGCAACATGATTTGTGT
104994 TTGCAACATGATTTGTG
1 TTGCAACATGATTTGTG
105011 GTTACTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.47
Consensus pattern (18 bp):
TTGCAACATGATTTGTGT
Found at i:110858 original size:11 final size:11
Alignment explanation
Indices: 110844--110898 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
110834 AACCAAGTCA
110844 AACCGTTGACC
1 AACCGTTGACC
*
110855 AACCGTTGACT
1 AACCGTTGACC
** * *
110866 GGCCATTGATC
1 AACCGTTGACC
110877 AACCGTTGACC
1 AACCGTTGACC
*
110888 AATCGTTGACC
1 AACCGTTGACC
110899 GTTGACTTTT
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (11 bp):
AACCGTTGACC
Found at i:113397 original size:42 final size:42
Alignment explanation
Indices: 113314--113488 Score: 255
Period size: 42 Copynumber: 4.2 Consensus size: 42
113304 TTGTACAAAT
* * * *
113314 GGAAGACTCGTGACTCG-GAATGAGCATG-GATTATGATTAAA
1 GGAAGACTCATGTCTCGAG-ATGAGAATGAGAATATGATTAAA
*
113355 GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATTAAA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATTAAA
113397 GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATTAAA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATTAAA
* * *
113439 GGAAGACTCATGTTTCGGGATTAGAATGAGAATATGATTAAA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATTAAA
113481 GGAAGACT
1 GGAAGACT
113489 TATGACTCAT
Statistics
Matches: 125, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
41 23 0.18
42 102 0.82
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (42 bp):
GGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATTAAA
Found at i:115632 original size:16 final size:16
Alignment explanation
Indices: 115613--115646 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
115603 AAGAAATTAA
115613 ATAAATAAA-TAAAAAT
1 ATAAA-AAATTAAAAAT
115629 ATAAAAAATTAAAAAT
1 ATAAAAAATTAAAAAT
115645 AT
1 AT
115647 TGTATCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAAATTAAAAAT
Found at i:115641 original size:20 final size:19
Alignment explanation
Indices: 115593--115643 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
115583 AAACAACCTT
115593 AAAAATTAAAAAGAAATTA
1 AAAAATTAAAAAGAAATTA
115612 AATAAA-TAAATAA-AAATATA
1 AA-AAATTAAA-AAGAAAT-TA
115632 AAAAATTAAAAA
1 AAAAATTAAAAA
115644 TATTGTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAAATTAAAAAGAAATTA
Found at i:118588 original size:15 final size:15
Alignment explanation
Indices: 118568--118598 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
118558 GAAAAACATG
118568 AAATATTCATTTCCA
1 AAATATTCATTTCCA
118583 AAATATTCATTTCCA
1 AAATATTCATTTCCA
118598 A
1 A
118599 CATAAACATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATATTCATTTCCA
Found at i:120460 original size:21 final size:21
Alignment explanation
Indices: 120434--120485 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
120424 TGAGACAATA
120434 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* *
120455 CTACCGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
*
120476 CTACAGATAC
1 CTACCGATAC
120486 TAAAAACTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Done.