Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012996.1 Kokia drynarioides strain JFW-HI SEQ_128014, 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: 144510
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:928 original size:16 final size:18
Alignment explanation
Indices: 897--933 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
887 TTATGAATTG
897 TTTAAAACTATTTAGAAT
1 TTTAAAACTATTTAGAAT
915 TTTAAAA-T-TTTAGAAT
1 TTTAAAACTATTTAGAAT
931 TTT
1 TTT
934 TTTCGCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
17 1 0.05
18 7 0.37
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TTTAAAACTATTTAGAAT
Found at i:5176 original size:33 final size:33
Alignment explanation
Indices: 5134--5201 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
5124 ATTCACAATA
*
5134 AGTGAATTAAGGTTTTGCTTGGTTGGGATCATC
1 AGTGAATTAAGGCTTTGCTTGGTTGGGATCATC
5167 AGTGAATTAAGGCTTTGCTTGGTTGGGATCATC
1 AGTGAATTAAGGCTTTGCTTGGTTGGGATCATC
5200 AG
1 AG
5202 AAAGAGGAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.22, C:0.10, G:0.31, T:0.37
Consensus pattern (33 bp):
AGTGAATTAAGGCTTTGCTTGGTTGGGATCATC
Found at i:7440 original size:27 final size:27
Alignment explanation
Indices: 7390--7442 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
7380 ACAGTAGGGT
*
7390 GGTGCCTATCTGACAGGCGACACCAAA
1 GGTGCCTATCTGACAAGCGACACCAAA
*
7417 GGTGCCTATCTGGCAAGCTG-CACCAA
1 GGTGCCTATCTGACAAGC-GACACCAA
7443 CCTCGCATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.17
Consensus pattern (27 bp):
GGTGCCTATCTGACAAGCGACACCAAA
Found at i:10833 original size:28 final size:28
Alignment explanation
Indices: 10780--10837 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
10770 CATTTTTCAC
*
10780 TTGGAATTAATTAAGTTTATGATTGAAT
1 TTGGAATTAATTAAGTTTATAATTGAAT
**
10808 TTGGAATTAATTCTGTTTA-AATTTGAAT
1 TTGGAATTAATTAAGTTTATAA-TTGAAT
10836 TT
1 TT
10838 ATTTAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50
Consensus pattern (28 bp):
TTGGAATTAATTAAGTTTATAATTGAAT
Found at i:10878 original size:26 final size:26
Alignment explanation
Indices: 10829--10878 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
10819 TCTGTTTAAA
**
10829 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
*
10855 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
10879 GTAAATGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:13821 original size:2 final size:2
Alignment explanation
Indices: 13814--13874 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
13804 AATTGAGTTT
13814 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13856 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
13875 TGTTTTAATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20824 original size:3 final size:3
Alignment explanation
Indices: 20816--20850 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
20806 ATGTTGGAAA
20816 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
20851 GATGATGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:21956 original size:20 final size:20
Alignment explanation
Indices: 21933--21971 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
21923 AATGATATAA
21933 TTAATCTTTT-AATTTTTTAT
1 TTAAT-TTTTCAATTTTTTAT
*
21953 TTAATTTTTCGATTTTTTA
1 TTAATTTTTCAATTTTTTA
21972 GTTTTCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (20 bp):
TTAATTTTTCAATTTTTTAT
Found at i:22481 original size:2 final size:2
Alignment explanation
Indices: 22474--22513 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
22464 CTCATATCGG
*
22474 AT AT AT AT TT 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
22514 CCATGTGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:23442 original size:15 final size:15
Alignment explanation
Indices: 23413--23454 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
23403 TTGAATTATG
23413 TTATTAATGTTATTTA
1 TTATTAAT-TTATTTA
23429 TT-TTATATTTATTTA
1 TTATTA-ATTTATTTA
23444 TTATTAATTTA
1 TTATTAATTTA
23455 GGGAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATTAATTTATTTA
Found at i:29110 original size:22 final size:21
Alignment explanation
Indices: 29073--29133 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
29063 AATAAAACCT
* *
29073 CACTTTCTCTAGAACAACTA-C
1 CACTTTCTTTAAAACAA-TATC
*
29094 CTACTTTCTTTTAAACAATATTC
1 C-ACTTTCTTTAAAACAATA-TC
29117 CACTTTCTTTAAAACAA
1 CACTTTCTTTAAAACAA
29134 GATTCCAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 3 0.09
22 28 0.85
23 2 0.06
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (21 bp):
CACTTTCTTTAAAACAATATC
Found at i:29138 original size:22 final size:22
Alignment explanation
Indices: 29096--29140 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
29086 ACAACTACCT
* *
29096 ACTTTCTTTTAAACAATATTCC
1 ACTTTCTTTAAAACAAGATTCC
29118 ACTTTCTTTAAAACAAGATTCC
1 ACTTTCTTTAAAACAAGATTCC
29140 A
1 A
29141 AAGAAAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (22 bp):
ACTTTCTTTAAAACAAGATTCC
Found at i:29805 original size:2 final size:2
Alignment explanation
Indices: 29800--29827 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29790 TTAAAAAAAG
29800 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29828 GTCACATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41788 original size:43 final size:43
Alignment explanation
Indices: 41727--41815 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
41717 GGTTTAAGGT
41727 AATGGAACGATGTTTAGTTTCTTAGCTAGATGAATTGCAATGA
1 AATGGAACGATGTTTAGTTTCTTAGCTAGATGAATTGCAATGA
41770 AATGGAACGATGTTTAGTTTCTTAGCTAGATGAATTGCAATGA
1 AATGGAACGATGTTTAGTTTCTTAGCTAGATGAATTGCAATGA
41813 AAT
1 AAT
41816 TTAATTACAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (43 bp):
AATGGAACGATGTTTAGTTTCTTAGCTAGATGAATTGCAATGA
Found at i:45050 original size:183 final size:181
Alignment explanation
Indices: 44672--45230 Score: 675
Period size: 183 Copynumber: 3.0 Consensus size: 181
44662 AGCATGGAAA
* * * *
44672 TGGAAGACGACTCTGCTTTACTTTTTAATGCCTTCGATTTTCTGGTA-GCTCATCAGTTCCCTCT
1 TGGAAGACGACGCTGCATTACTTTTTAATGCCTTTGATTTT-TGG-AGGCTCTTCAGTTCCCTCT
* * * * *
44736 CAACGCTGAAAGTGATGTTGATAATAACCCTACTACGAGTCTACGATTCCCGAAA-TTTCACACG
64 CAATGCTGAAAGTGATGATGA-CAT----C-ACTACTA--CTACGATTCCC-AAACTTTCACATG
* * * * *
44800 ATCATCAAACCTTGTCCATGCTCCATATTTTCAGTGTAGACAGCTTGATATATGTTGAGGAAT
120 ATCATCATACCTAGTCCATGCTCCATATTTTCACTGAAGATAGCTTGATATATGTTGA-GAAT
*
44863 TGGAAGACGACGCCGCATTACTTTTTAATGCCTTTGAGTTTTTGGAGGCTCTTCAGTTCCCTCTC
1 TGGAAGACGACGCTGCATTACTTTTTAATGCCTTTGA-TTTTTGGAGGCTCTTCAGTTCCCTCTC
* *
44928 AATGCTGAAAGTGATGATGACATCAGTCCTACTACGATTCCCAAACTTTCACATGATCATCATAC
65 AATGCTGAAAGTGATGATGACATCACTACTACTACGATTCCCAAACTTTCACATGATCATCATAC
44993 CTAGTCCATGCTCCATATTTTCACTGAAGATAGCTTGATATATGTTGAGATAT
130 CTAGTCCATGCTCCATATTTTCACTGAAGATAGCTTGATATATGTTGAGA-AT
* * *
45046 TGGAAGAGGAAGCTGCATTACTTTTTAATGCCTCTGATTTTTTGGAGGCTCTTCA-----CTCTC
1 TGGAAGACGACGCTGCATTACTTTTTAATGCCTTTGA-TTTTTGGAGGCTCTTCAGTTCCCTCTC
* * **
45106 AATGCTGAAACTGATGATGACATCACTTCTACTACGATTCCCAGTCTTTCACATGATCATCATAC
65 AATGCTGAAAGTGATGATGACATCACTACTACTACGATTCCCAAACTTTCACATGATCATCATAC
* *
45171 CTCA-TCTATGCTCCATATTTTCACTGAAGATAGCTTGATATATGTTGCGAAAT
130 CT-AGTCCATGCTCCATATTTTCACTGAAGATAGCTTGATATATGTTGAG-AAT
45224 TGGAAGA
1 TGGAAGA
45231 TGATGCCCCT
Statistics
Matches: 333, Mismatches: 29, Indels: 25
0.86 0.07 0.06
Matches are distributed among these distances:
178 119 0.36
179 2 0.01
182 5 0.02
183 124 0.37
185 4 0.01
186 1 0.00
190 3 0.01
191 71 0.21
192 4 0.01
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (181 bp):
TGGAAGACGACGCTGCATTACTTTTTAATGCCTTTGATTTTTGGAGGCTCTTCAGTTCCCTCTCA
ATGCTGAAAGTGATGATGACATCACTACTACTACGATTCCCAAACTTTCACATGATCATCATACC
TAGTCCATGCTCCATATTTTCACTGAAGATAGCTTGATATATGTTGAGAAT
Found at i:48595 original size:19 final size:19
Alignment explanation
Indices: 48554--48597 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
48544 ACCTTTTATG
* *
48554 ATTTTTTATTTTTTTTTGG
1 ATTTTTTATTTTTCTTTGA
48573 ATTTTTTATGTTTTCTTT-A
1 ATTTTTTAT-TTTTCTTTGA
48592 ATTTTT
1 ATTTTT
48598 AGAAGCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (19 bp):
ATTTTTTATTTTTCTTTGA
Found at i:62318 original size:22 final size:22
Alignment explanation
Indices: 62279--62323 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
62269 ATGATTTATG
* *
62279 TTTAAAGTTTATAATTATTTTT
1 TTTAAAGTTCATAATTATATTT
62301 TTTAAAGTTCA-AATTTATATTT
1 TTTAAAGTTCATAA-TTATATTT
62323 T
1 T
62324 CATCGAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTAAAGTTCATAATTATATTT
Found at i:72916 original size:2 final size:2
Alignment explanation
Indices: 72909--72941 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
72899 CATCGACAAA
72909 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
72942 AGAAATCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:78342 original size:13 final size:13
Alignment explanation
Indices: 78324--78348 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
78314 CATTACCATA
78324 CTTTTTTTTTTTT
1 CTTTTTTTTTTTT
78337 CTTTTTTTTTTT
1 CTTTTTTTTTTT
78349 AATTTGAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
CTTTTTTTTTTTT
Found at i:82047 original size:15 final size:15
Alignment explanation
Indices: 81997--82047 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
81987 TAACTCGAAC
81997 AATTTCACTCAATTT
1 AATTTCACTCAATTT
* *
82012 GA-TTCGACTTGAATTT
1 AATTTC-AC-TCAATTT
*
82028 TATTTCACTCAATTT
1 AATTTCACTCAATTT
82043 AATTT
1 AATTT
82048 AAATTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
14 3 0.11
15 13 0.46
16 9 0.32
17 3 0.11
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49
Consensus pattern (15 bp):
AATTTCACTCAATTT
Found at i:89885 original size:18 final size:19
Alignment explanation
Indices: 89845--89901 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
89835 ATGTCACATC
*
89845 AAAAAATAATTTAAAAATTA
1 AAAAAATTATTTAAAAA-TA
*
89865 TAAATATATT-TTTAAAAATA
1 -AAA-AAATTATTTAAAAATA
89885 AAAAAATTATTTAAAAA
1 AAAAAATTATTTAAAAA
89902 GTTCATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 4 0.13
19 11 0.35
20 2 0.06
21 11 0.35
22 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAAATTATTTAAAAATA
Found at i:92052 original size:69 final size:67
Alignment explanation
Indices: 91971--92110 Score: 194
Period size: 69 Copynumber: 2.0 Consensus size: 67
91961 CTCTCTATTA
*
91971 TTAGCACTGTGTGTGCTACT-TGAT-TAGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACT
1 TTAGCACTGTGTGTGCT-CTCTGATCTAGCAC-TTATGTGCTCTCTG-TTAGTACTTTG-GTACT
92034 CTCTGT
62 CTCTGT
*
92040 TTAGCACTGTGTGTGCTCTCTGTTGCCTAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCT
1 TTAGCACTGTGTGTGCTCTCTGAT--CTAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCT
92105 CTGT
64 CTGT
92109 TT
1 TT
92111 GTTCCGTATA
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
68 2 0.03
69 33 0.51
70 11 0.17
71 13 0.20
72 6 0.09
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (67 bp):
TTAGCACTGTGTGTGCTCTCTGATCTAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTCT
GT
Found at i:92062 original size:23 final size:23
Alignment explanation
Indices: 91938--92110 Score: 140
Period size: 23 Copynumber: 7.4 Consensus size: 23
91928 CACTAGCGCA
*
91938 CTCTCTGTTTAGCAC-GTCTCGTG
1 CTCTCTGTTTAGCACTGTGT-GTG
*
91961 CTCTCTATTATTAGCACTGTGTGTG
1 CTCTCT-GT-TTAGCACTGTGTGTG
* *
91986 CTACT-TGATTAGCACTTTGTGTG
1 CT-CTCTGTTTAGCACTGTGTGTG
* * * *
92009 CTCTCTGATTAGTACTTTGTGTA
1 CTCTCTGTTTAGCACTGTGTGTG
92032 CTCTCTGTTTAGCACTGTGTGTG
1 CTCTCTGTTTAGCACTGTGTGTG
*
92055 CTCTCTGTTGCCTAGCACT-TATGTG
1 CTCTCTGTT---TAGCACTGTGTGTG
* * *
92080 CTCTCTG-TTAGTACTTTG-GTA
1 CTCTCTGTTTAGCACTGTGTGTG
92101 CTCTCTGTTT
1 CTCTCTGTTT
92111 GTTCCGTATA
Statistics
Matches: 125, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
21 15 0.12
22 5 0.04
23 66 0.53
24 2 0.02
25 25 0.20
26 12 0.10
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.45
Consensus pattern (23 bp):
CTCTCTGTTTAGCACTGTGTGTG
Found at i:92822 original size:12 final size:12
Alignment explanation
Indices: 92805--92842 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
92795 AATTTTGATA
92805 TTTTATATTTTT
1 TTTTATATTTTT
92817 TTTTATATCTTTT
1 TTTTATAT-TTTT
*
92830 TTTGAT-TTTTT
1 TTTTATATTTTT
92841 TT
1 TT
92843 ATGTTAAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 6 0.25
12 9 0.38
13 9 0.38
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTTATATTTTT
Found at i:111235 original size:20 final size:19
Alignment explanation
Indices: 111197--111267 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 19
111187 TTACAGTTTT
111197 ATTTTAATAATAATTTTAA
1 ATTTTAATAATAATTTTAA
111216 ATTTTAAATAAT-ATTCTT-A
1 ATTTT-AATAATAATT-TTAA
* * *
111235 ATATATATATTATAATTATAA
1 AT-TTTA-ATAATAATTTTAA
111256 ATATTTAATAAT
1 AT-TTTAATAAT
111268 GACTATTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
19 12 0.29
20 19 0.46
21 10 0.24
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTAATAATAATTTTAA
Found at i:111297 original size:23 final size:23
Alignment explanation
Indices: 111271--111314 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
111261 TAATAATGAC
111271 TATTTTACAGTATA-AAATATGGA
1 TATTTTA-AGTATATAAATATGGA
*
111294 TATTTTAATTATATAAATATG
1 TATTTTAAGTATATAAATATG
111315 AGTATGTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (23 bp):
TATTTTAAGTATATAAATATGGA
Found at i:115479 original size:21 final size:21
Alignment explanation
Indices: 115453--115521 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
115443 GTGACAAAAG
115453 AGAGACTGATTAGTACCTTTC
1 AGAGACTGATTAGTACCTTTC
* ** *
115474 AGAGAC-GATT-CT--CAATA
1 AGAGACTGATTAGTACCTTTC
*
115491 ATAGACTGATTAGTACCTTTC
1 AGAGACTGATTAGTACCTTTC
115512 AGAGA-TGATT
1 AGAGACTGATT
115522 CTTAATAAGA
Statistics
Matches: 34, Mismatches: 10, Indels: 9
0.64 0.19 0.17
Matches are distributed among these distances:
17 7 0.21
18 4 0.12
19 2 0.06
20 9 0.26
21 12 0.35
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (21 bp):
AGAGACTGATTAGTACCTTTC
Found at i:115506 original size:38 final size:38
Alignment explanation
Indices: 115455--115529 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
115445 GACAAAAGAG
115455 AGACTGATTAGTACCTTTCAGAGACGATTCTCAATAAT
1 AGACTGATTAGTACCTTTCAGAGACGATTCTCAATAAT
* *
115493 AGACTGATTAGTACCTTTCAGAGATGATTCTTAATAA
1 AGACTGATTAGTACCTTTCAGAGACGATTCTCAATAA
115530 GACGAAGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (38 bp):
AGACTGATTAGTACCTTTCAGAGACGATTCTCAATAAT
Found at i:118294 original size:23 final size:23
Alignment explanation
Indices: 118266--118309 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
118256 TAATAATGAC
118266 TATTTT-ATAATATAAAATATGGA
1 TATTTTAATAATAT-AAATATGGA
*
118289 TATTTTAATGATATAAATATG
1 TATTTTAATAATATAAATATG
118310 AGTACTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (23 bp):
TATTTTAATAATATAAATATGGA
Found at i:120496 original size:24 final size:24
Alignment explanation
Indices: 120463--120533 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
120453 TACAACACCG
*
120463 ACAACTCCGACCACGGGGACTCCA
1 ACAACACCGACCACGGGGACTCCA
*
120487 ACAGCACCGACCACGGGGACTCCA
1 ACAACACCGACCACGGGGACTCCA
*
120511 ACAACACCGACCACAGGGACTCC
1 ACAACACCGACCACGGGGACTCC
120534 TACCATAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.31, C:0.42, G:0.21, T:0.06
Consensus pattern (24 bp):
ACAACACCGACCACGGGGACTCCA
Found at i:129968 original size:43 final size:43
Alignment explanation
Indices: 129908--129995 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
129898 ATCCTTTTCA
* *
129908 AAAAATAAATCTGAAAACTCGATCACATTAAAAATCTTCAAAG
1 AAAAATAAATATAAAAACTCGATCACATTAAAAATCTTCAAAG
* *
129951 AAAAATAAATATAAAAACTCGATCACATTAAAAGTCTTCATAG
1 AAAAATAAATATAAAAACTCGATCACATTAAAAATCTTCAAAG
129994 AA
1 AA
129996 TCCTTGCTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.55, C:0.15, G:0.07, T:0.24
Consensus pattern (43 bp):
AAAAATAAATATAAAAACTCGATCACATTAAAAATCTTCAAAG
Found at i:130068 original size:96 final size:96
Alignment explanation
Indices: 129961--130153 Score: 386
Period size: 96 Copynumber: 2.0 Consensus size: 96
129951 AAAAATAAAT
129961 ATAAAAACTCGATCACATTAAAAGTCTTCATAGAATCCTTGCTTAGCATAAATTCCTCAATGATT
1 ATAAAAACTCGATCACATTAAAAGTCTTCATAGAATCCTTGCTTAGCATAAATTCCTCAATGATT
130026 CAACTCAATAAAGTGTTCCTAAAAATCTCCA
66 CAACTCAATAAAGTGTTCCTAAAAATCTCCA
130057 ATAAAAACTCGATCACATTAAAAGTCTTCATAGAATCCTTGCTTAGCATAAATTCCTCAATGATT
1 ATAAAAACTCGATCACATTAAAAGTCTTCATAGAATCCTTGCTTAGCATAAATTCCTCAATGATT
130122 CAACTCAATAAAGTGTTCCTAAAAATCTCCA
66 CAACTCAATAAAGTGTTCCTAAAAATCTCCA
130153 A
1 A
130154 ATATGTGCAT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (96 bp):
ATAAAAACTCGATCACATTAAAAGTCTTCATAGAATCCTTGCTTAGCATAAATTCCTCAATGATT
CAACTCAATAAAGTGTTCCTAAAAATCTCCA
Found at i:144067 original size:19 final size:18
Alignment explanation
Indices: 144031--144067 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
144021 TTGACACGTG
*
144031 TTTTTTTTTTAATTTTTA
1 TTTTTTTTTTAATATTTA
144049 TTTTTTTTTTATATATTTA
1 TTTTTTTTTTA-ATATTTA
144068 AAAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTTTTTTAATATTTA
Found at i:144460 original size:9 final size:9
Alignment explanation
Indices: 144438--144474 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
144428 AAAGAAAGAA
144438 AGAAGAA-G
1 AGAAGAAGG
144446 -GAAGAAGG
1 AGAAGAAGG
144454 AGAAGAAGG
1 AGAAGAAGG
*
144463 GGAAGAAGG
1 AGAAGAAGG
144472 AGA
1 AGA
144475 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
7 6 0.24
8 1 0.04
9 18 0.72
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (9 bp):
AGAAGAAGG
Done.