Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007363.1 Kokia drynarioides strain JFW-HI SEQ_121979, 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: 5438
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Found at i:134 original size:28 final size:25
Alignment explanation
Indices: 87--148 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 25
77 GCATAAATGT
*
87 ATAAAAAAATTACCTAAAGATATAC
1 ATAAAAAAATTACCTAAAGACATAC
* *
112 ATAAAATAATATTAACCTCAAGACATTC
1 ATAAAA-AA-ATT-ACCTAAAGACATAC
140 ATAAAAAAA
1 ATAAAAAAA
149 AAAAAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 6 0.19
26 3 0.10
27 5 0.16
28 17 0.55
ACGTcount: A:0.60, C:0.13, G:0.03, T:0.24
Consensus pattern (25 bp):
ATAAAAAAATTACCTAAAGACATAC
Found at i:284 original size:19 final size:19
Alignment explanation
Indices: 246--286 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
236 ACCATATATA
* * *
246 ATTTCAATACATCATGCTT
1 ATTTCAATAAACCATACTT
265 ATTTCAATAAACCATACTT
1 ATTTCAATAAACCATACTT
284 ATT
1 ATT
287 GTACATATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (19 bp):
ATTTCAATAAACCATACTT
Found at i:440 original size:19 final size:19
Alignment explanation
Indices: 413--453 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
403 TCGCATTTTC
*
413 AAAATTTTA-AGAGTTAAAA
1 AAAAATTTAGAGA-TTAAAA
432 AAAAATTTAGAGATTAAAA
1 AAAAATTTAGAGATTAAAA
451 AAA
1 AAA
454 TGATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (19 bp):
AAAAATTTAGAGATTAAAA
Found at i:1781 original size:30 final size:30
Alignment explanation
Indices: 1747--1857 Score: 127
Period size: 30 Copynumber: 3.7 Consensus size: 30
1737 TTTGATTTCT
* * **
1747 TTTCGTTTATTTTTTAAATTTAACTTGGAA
1 TTTCGTTTATATTTTAAATTTAATTTATAA
1777 TTTCGTTT-TCATTTTAAATTTAATTTATAA
1 TTTCGTTTAT-ATTTTAAATTTAATTTATAA
* *
1807 TTTCATTTATA-TTTAAATTTTAATTTCTAA
1 TTTCGTTTATATTTTAAA-TTTAATTTATAA
*
1837 TTTCGTTTATATATTAAATTT
1 TTTCGTTTATATTTTAAATTT
1858 CTTTTCTAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
29 7 0.10
30 56 0.81
31 6 0.09
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.59
Consensus pattern (30 bp):
TTTCGTTTATATTTTAAATTTAATTTATAA
Found at i:1815 original size:23 final size:24
Alignment explanation
Indices: 1783--1833 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
1773 GGAATTTCGT
1783 TTTCATTTTAAATTT-AATTTATAA
1 TTTCATTTTAAATTTAAATTT-TAA
*
1807 TTTCA-TTTATATTTAAATTTTAA
1 TTTCATTTTAAATTTAAATTTTAA
1830 TTTC
1 TTTC
1834 TAATTTCGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTCATTTTAAATTTAAATTTTAA
Found at i:1825 original size:17 final size:17
Alignment explanation
Indices: 1794--1826 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1784 TTCATTTTAA
1794 ATTTAATTTATAATTTC
1 ATTTAATTTATAATTTC
1811 ATTTATATTTA-AATTT
1 ATTTA-ATTTATAATTT
1827 TAATTTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTAATTTATAATTTC
Found at i:1864 original size:30 final size:28
Alignment explanation
Indices: 1775--1868 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 28
1765 TTTAACTTGG
* *
1775 AATTTCGTTT-TCATTTTAAATTTAATTTAT
1 AATTTCGTTTAT-A-TTTAAATTT-TTTTCT
*
1805 AATTTCATTTATATTTAAATTTTAATTTCT
1 AATTTCGTTTATATTTAAATTTT--TTTCT
1835 AATTTCGTTTATATATTAAATTTCTTTTCT
1 AATTTCGTTTATAT-TTAAATTT-TTTTCT
1865 AATT
1 AATT
1869 ATTATTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
29 9 0.16
30 36 0.65
31 9 0.16
32 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (28 bp):
AATTTCGTTTATATTTAAATTTTTTTCT
Found at i:3106 original size:30 final size:28
Alignment explanation
Indices: 3014--3106 Score: 82
Period size: 30 Copynumber: 3.2 Consensus size: 28
3004 AAAAGATTAT
* *
3014 ATAAATTTTGAA-AAAATAATAATTAGAA
1 ATAAATTTTAAATAAAATGA-AATTAGAA
* * *
3042 A-AAAATTAAAATACAAAAGAAATTAGAA
1 ATAAATTTTAAATA-AAATGAAATTAGAA
3070 ATTAAATTTTAAATATAAATGAAATTAGAA
1 A-TAAATTTTAAATA-AAATGAAATTAGAA
3100 TATAAAT
1 -ATAAAT
3107 GAAATTAGAA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
27 7 0.14
28 11 0.22
29 4 0.08
30 28 0.55
31 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.30
Consensus pattern (28 bp):
ATAAATTTTAAATAAAATGAAATTAGAA
Found at i:3122 original size:17 final size:18
Alignment explanation
Indices: 3080--3123 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 18
3070 ATTAAATTTT
3080 AAATATAAATGAAATTAG
1 AAATATAAATGAAATTAG
3098 -AATATAAATGAAATTAG
1 AAATATAAATGAAATTAG
3115 AAAT-TAAAT
1 AAATATAAAT
3124 TTAAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 22 0.88
18 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (18 bp):
AAATATAAATGAAATTAG
Found at i:3132 original size:30 final size:30
Alignment explanation
Indices: 3098--3170 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
3088 ATGAAATTAG
*
3098 AATATAAATGAAATTAGAAATTAAATTTAA
1 AATATAAATGAAATTAAAAATTAAATTTAA
*
3128 AATATAAACGAAATTAAAAATTAAATTTAA
1 AATATAAATGAAATTAAAAATTAAATTTAA
*
3158 AAAATAAATGAAA
1 AATATAAATGAAA
3171 AAAAAAAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.29
Consensus pattern (30 bp):
AATATAAATGAAATTAAAAATTAAATTTAA
Found at i:3140 original size:23 final size:21
Alignment explanation
Indices: 3066--3166 Score: 73
Period size: 23 Copynumber: 4.5 Consensus size: 21
3056 AAAAGAAATT
3066 AGAAATTAAATTTTAAATATAA
1 AGAAATTAAA-TTTAAATATAA
*
3088 ATGAAATTAGAATATAAATGA-AA
1 A-GAAATTA-AATTTAAAT-ATAA
3111 TTAGAAATTAAATTTAAAATATAA
1 --AGAAATTAAATTT-AAATATAA
* *
3135 ACGAAATTAAAAATTAAATTTAA
1 A-GAAATT-AAATTTAAATATAA
3158 A-AAA-TAAAT
1 AGAAATTAAAT
3167 GAAAAAAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 21
0.71 0.05 0.23
Matches are distributed among these distances:
19 3 0.05
20 1 0.02
21 3 0.05
22 2 0.03
23 34 0.52
24 21 0.32
25 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.32
Consensus pattern (21 bp):
AGAAATTAAATTTAAATATAA
Found at i:3146 original size:17 final size:17
Alignment explanation
Indices: 3044--3146 Score: 73
Period size: 17 Copynumber: 6.5 Consensus size: 17
3034 AATTAGAAAA
* *
3044 AAATTAAAATACAAAAG
1 AAATTAAAATATAAATG
3061 AAATTAGAAAT-TAAAT-
1 AAATTA-AAATATAAATG
*
3077 ---TTTAAATATAAATG
1 AAATTAAAATATAAATG
*
3091 AAATTAGAATATAAATG
1 AAATTAAAATATAAATG
3108 AAATTAGAAAT-TAAAT-
1 AAATTA-AAATATAAATG
*
3124 ---TTAAAATATAAACG
1 AAATTAAAATATAAATG
3138 AAATTAAAA
1 AAATTAAAA
3147 ATTAAATTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 24
0.68 0.07 0.24
Matches are distributed among these distances:
12 8 0.12
13 14 0.21
17 38 0.57
18 7 0.10
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (17 bp):
AAATTAAAATATAAATG
Found at i:3153 original size:47 final size:47
Alignment explanation
Indices: 3044--3146 Score: 161
Period size: 47 Copynumber: 2.2 Consensus size: 47
3034 AATTAGAAAA
* * * *
3044 AAATTAAAATACAAAAGAAATTAGAAATTAAATTTTAAATATAAATG
1 AAATTAAAATATAAATGAAATTAGAAATTAAATTTAAAATATAAACG
*
3091 AAATTAGAATATAAATGAAATTAGAAATTAAATTTAAAATATAAACG
1 AAATTAAAATATAAATGAAATTAGAAATTAAATTTAAAATATAAACG
3138 AAATTAAAA
1 AAATTAAAA
3147 ATTAAATTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (47 bp):
AAATTAAAATATAAATGAAATTAGAAATTAAATTTAAAATATAAACG
Found at i:5192 original size:28 final size:25
Alignment explanation
Indices: 5147--5208 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 25
5137 AATTTTTTTT
*
5147 TTTTTTTATGAATGTCTTGAGGTTAA
1 TTTTTTTATGAATATCTTGAGG-TAA
* *
5173 TATTATTTTATGTATATCTTTAGGTAA
1 T-TT-TTTTATGAATATCTTGAGGTAA
5200 TTTTTTTAT
1 TTTTTTTAT
5209 ACATTTATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 6 0.19
26 3 0.10
27 6 0.19
28 16 0.52
ACGTcount: A:0.24, C:0.03, G:0.13, T:0.60
Consensus pattern (25 bp):
TTTTTTTATGAATATCTTGAGGTAA
Done.