Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010077.1 Kokia drynarioides strain JFW-HI SEQ_124855, 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: 28827
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:6129 original size:8 final size:8
Alignment explanation
Indices: 6116--6142 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
6106 ACACAGCCAT
6116 TTTCTTTA
1 TTTCTTTA
6124 TTTCTTTA
1 TTTCTTTA
6132 TTTCTTTA
1 TTTCTTTA
6140 TTT
1 TTT
6143 ATTATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTCTTTA
Found at i:18350 original size:14 final size:14
Alignment explanation
Indices: 18328--18369 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
18318 TAGAAAATGC
*
18328 AAATACTAAATATG
1 AAATGCTAAATATG
*
18342 AAATGCTAAAAATG
1 AAATGCTAAATATG
*
18356 -CATGCTAAATATG
1 AAATGCTAAATATG
18369 A
1 A
18370 TACAAAAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (14 bp):
AAATGCTAAATATG
Found at i:19069 original size:48 final size:48
Alignment explanation
Indices: 19007--19143 Score: 220
Period size: 48 Copynumber: 2.8 Consensus size: 48
18997 TAAAGTTGTT
*
19007 TAATTATGCTTCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAA
1 TAATT-TGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAA
*
19056 TAATTTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAG
1 TAATTTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAA
* * *
19104 TAATCTGCATTATTAAATGTTTTGTTTGTTAAATGCATCT
1 TAATTTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCT
19144 CTCTCAAATG
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
48 78 0.94
49 5 0.06
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.52
Consensus pattern (48 bp):
TAATTTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAA
Found at i:19161 original size:48 final size:46
Alignment explanation
Indices: 19019--19163 Score: 150
Period size: 48 Copynumber: 3.0 Consensus size: 46
19009 ATTATGCTTC
* *
19019 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAAT-TTGCATC
1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTT-CTT-A-AATCTTGCATT
*
19067 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAATC-TGCATT
1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTT-CTTA--AATCTTGCATT
* * *
19115 ATTAAATGTTTTGTTTGTTAAATGCATCTCTCTCAAATGCCTTGCATT
1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTCTTAAAT--CTTGCATT
19163 A
1 A
19164 ACAAATTAGC
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
45 3 0.03
47 4 0.05
48 80 0.92
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (46 bp):
ATTAAGTGTTTTGTTTGTTAAATGCATCTTTCTTAAATCTTGCATT
Found at i:19809 original size:79 final size:79
Alignment explanation
Indices: 19678--19840 Score: 276
Period size: 79 Copynumber: 2.1 Consensus size: 79
19668 CATTTAAGGA
* * *
19678 GAAA-TGCCATTCCTTTTCAACTACATCAGATCCTAATGAAGAGATATGACTCATTGGCTTCCCT
1 GAAATTGCCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCT
19742 ACAAGAGTTAAAAAT
66 ACAAGAGTT-AAAAT
19757 GAAATTGCCATGCCTTTTCAACTACATCA-ATCCTAATGAAGAGACATGACTCATTAGCTTCCCT
1 GAAATTGCCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCT
19821 ACAAGAGTTAAAAT
66 ACAAGAGTTAAAAT
19835 GAAATT
1 GAAATT
19841 AGTGCTTGTA
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
78 11 0.14
79 46 0.57
80 23 0.29
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (79 bp):
GAAATTGCCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCT
ACAAGAGTTAAAAT
Found at i:22415 original size:3 final size:3
Alignment explanation
Indices: 22407--22461 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
22397 AAAAGCTTAC
22407 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
22455 TAT TAT T
1 TAT TAT T
22462 GTGAGCATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:22591 original size:28 final size:28
Alignment explanation
Indices: 22551--22717 Score: 192
Period size: 28 Copynumber: 5.9 Consensus size: 28
22541 AAGGAGGAAG
*
22551 ATGTAGCCATTTTTAGCAAATATGTGAT
1 ATGTGGCCATTTTTAGCAAATATGTGAT
* * * *
22579 ATGTGGTCATTTTTTGAAAATATGTTAT
1 ATGTGGCCATTTTTAGCAAATATGTGAT
* * *
22607 ATGTGGCCAGTTTTGGTAAATATGTGAT
1 ATGTGGCCATTTTTAGCAAATATGTGAT
* *
22635 ATGTGTCCATTTTTAGCAAATATGTGTT
1 ATGTGGCCATTTTTAGCAAATATGTGAT
*
22663 ATATGGCCATTTTT-GACAAATATGTGAT
1 ATGTGGCCATTTTTAG-CAAATATGTGAT
* *
22691 ATGTGGCCATTTTATGGAAAATATGTG
1 ATGTGGCCATTTT-TAGCAAATATGTG
22718 GCAGTTCATC
Statistics
Matches: 116, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
27 1 0.01
28 104 0.90
29 10 0.09
30 1 0.01
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (28 bp):
ATGTGGCCATTTTTAGCAAATATGTGAT
Found at i:22698 original size:84 final size:85
Alignment explanation
Indices: 22557--22717 Score: 245
Period size: 84 Copynumber: 1.9 Consensus size: 85
22547 GAAGATGTAG
* * *
22557 CCATTTTTAGCAAATATGTGATATGTGGTCATTTTTTGAAAATATGTTATATGTGGCCAGTTT-T
1 CCATTTTTAGCAAATATGTGATATATGGCCATTTTTTGAAAATATGTGATATGTGGCCAGTTTAT
*
22621 GGTAAATATGTGATATGTGT
66 GGAAAATATGTGATATGTGT
* *
22641 CCATTTTTAGCAAATATGTGTTATATGGCCA-TTTTTGACAAATATGTGATATGTGGCCATTTTA
1 CCATTTTTAGCAAATATGTGATATATGGCCATTTTTTGA-AAATATGTGATATGTGGCCAGTTTA
22705 TGGAAAATATGTG
65 TGGAAAATATGTG
22718 GCAGTTCATC
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
83 7 0.10
84 50 0.72
85 12 0.17
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (85 bp):
CCATTTTTAGCAAATATGTGATATATGGCCATTTTTTGAAAATATGTGATATGTGGCCAGTTTAT
GGAAAATATGTGATATGTGT
Found at i:25886 original size:27 final size:28
Alignment explanation
Indices: 25856--25915 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
25846 AAGGTGTTCC
25856 ATTTC-ATAAATTACCACA-AGGGCTTCA
1 ATTTCGATAAATTACCACAGA-GGCTTCA
* *
25883 ATTTCGATAGATTACCACAGAGGCTTCC
1 ATTTCGATAAATTACCACAGAGGCTTCA
25911 ATTTC
1 ATTTC
25916 TTAGCATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.17
28 23 0.79
29 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (28 bp):
ATTTCGATAAATTACCACAGAGGCTTCA
Done.