Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014590.1 Kokia drynarioides strain JFW-HI SEQ_129629, 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: 12224
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:1116 original size:12 final size:12
Alignment explanation
Indices: 1099--1123 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1089 AATTAAAAAA
1099 TTTAAAATTAAT
1 TTTAAAATTAAT
1111 TTTAAAATTAAT
1 TTTAAAATTAAT
1123 T
1 T
1124 AAGTAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAAAATTAAT
Found at i:1432 original size:30 final size:30
Alignment explanation
Indices: 1398--1461 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
1388 AAGAGTTAGT
1398 TTCTTTACTTGCTTAGTTACTTCAATTATC
1 TTCTTTACTTGCTTAGTTACTTCAATTATC
1428 TTCTTTACTTGCTTAGTTACTTCAATTATC
1 TTCTTTACTTGCTTAGTTACTTCAATTATC
1458 TTCT
1 TTCT
1462 AATTCTTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (30 bp):
TTCTTTACTTGCTTAGTTACTTCAATTATC
Found at i:1664 original size:34 final size:35
Alignment explanation
Indices: 1625--1700 Score: 84
Period size: 36 Copynumber: 2.2 Consensus size: 35
1615 GATAGAAATT
* *
1625 TATAAAGATT-CAATATGATTAAA-TAATTCAGTAA
1 TATAAAGATTACAAAATG-TTAAATTAATTCAATAA
* *
1659 TATAAATATTACAAAATGTTAAATTTAATTTAATAA
1 TATAAAGATTACAAAATGTTAAA-TTAATTCAATAA
1695 TATAAA
1 TATAAA
1701 TAATAGATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
34 14 0.40
35 6 0.17
36 15 0.43
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (35 bp):
TATAAAGATTACAAAATGTTAAATTAATTCAATAA
Found at i:1922 original size:5 final size:5
Alignment explanation
Indices: 1912--1943 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1902 GTTTTGGATA
*
1912 GATGG GATGG GATGG GATGG GATGA GATGG GA
1 GATGG GATGG GATGG GATGG GATGG GATGG GA
1944 GTAAAAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.56, T:0.19
Consensus pattern (5 bp):
GATGG
Found at i:1990 original size:29 final size:30
Alignment explanation
Indices: 1942--1999 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
1932 GATGAGATGG
*
1942 GAGTAAAAGTTTTTGAGGAAAGT-GAAATA
1 GAGTAAAAGTCTTTGAGGAAAGTAGAAATA
1971 GAGTAAAAG-CTTTGAGGGAAAGTAGAAAT
1 GAGTAAAAGTCTTTGA-GGAAAGTAGAAAT
2000 GTTTGAGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.19
29 16 0.62
30 5 0.19
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (30 bp):
GAGTAAAAGTCTTTGAGGAAAGTAGAAATA
Found at i:2235 original size:9 final size:9
Alignment explanation
Indices: 2221--2309 Score: 58
Period size: 9 Copynumber: 9.7 Consensus size: 9
2211 TTTTGATGCA
2221 TTTTATAAT
1 TTTTATAAT
*
2230 TTTTATGA-
1 TTTTATAAT
*
2238 TTTTATAAAA
1 TTTTAT-AAT
* * *
2248 ATTTACATTT
1 TTTTATA-AT
2258 TTTTATAAT
1 TTTTATAAT
2267 TTTT-TACGAT
1 TTTTATA--AT
2277 TTTTATAAT
1 TTTTATAAT
*
2286 TTTTCTAAT
1 TTTTATAAT
2295 TTTTA-ATAT
1 TTTTATA-AT
2304 TTTTAT
1 TTTTAT
2310 TAAAATTTAA
Statistics
Matches: 61, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
8 9 0.15
9 35 0.57
10 15 0.25
11 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:2242 original size:17 final size:19
Alignment explanation
Indices: 2210--2245 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2200 TTAAAGGACC
2210 TTTTTGATGCATTTTATAA
1 TTTTTGATGCATTTTATAA
2229 TTTTT-ATG-ATTTTATAA
1 TTTTTGATGCATTTTATAA
2246 AAATTTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.61
Consensus pattern (19 bp):
TTTTTGATGCATTTTATAA
Found at i:2298 original size:19 final size:19
Alignment explanation
Indices: 2249--2307 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
2239 TTTATAAAAA
2249 TTTACATTTTTTTATAATTT
1 TTTACA-TTTTTTATAATTT
2269 TTTACGA-TTTTTATAATTT
1 TTTAC-ATTTTTTATAATTT
*
2288 TTCTA-ATTTTTAAT-ATTT
1 TT-TACATTTTTTATAATTT
2306 TT
1 TT
2308 ATTAAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 7 0.20
19 20 0.57
20 7 0.20
21 1 0.03
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTACATTTTTTATAATTT
Found at i:2654 original size:90 final size:85
Alignment explanation
Indices: 2486--2725 Score: 232
Period size: 90 Copynumber: 2.7 Consensus size: 85
2476 TTTGATGCAA
* * * *
2486 TTGACAGTTCAAGTACTCAATTGAGTGAAAAAAAGCAGGGGCTTAATTGCTATTTTTGAAAAAAA
1 TTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAA-AAGGGGCTTAATTACTATTTTTGAAAAAAA
* * *
2551 TTTGGGCATTTTTTATGCATT
65 TTTGAGAACTTTTTATGCATT
2572 TTGAAAGTTCAAGTACCCAATTGAGTGTTAAAAAAAAAGGAGAAGCTTAATTACT-TTTTCT-AA
1 TTGAAAGTTCAAGTACCCAATTGAGTG--AAAAAAAAAGG-G--GCTTAATTACTATTTT-TGAA
* *
2635 AAAAGTTTGAGAACCTTTTTATGTATT
60 AAAAATTTGAGAA-CTTTTTATGCATT
* ** * * * *
2662 TTGAAAGTTCAACTACGTAATTGAGTGCCAAAAAAAAAGGGTCTTGATTGCTTTTTTTGAAAAA
1 TTGAAAGTTCAAGTACCCAATTGAGTG--AAAAAAAAAGGGGCTTAATTACTATTTTTGAAAAA
2726 GTTTGAGGGT
Statistics
Matches: 128, Mismatches: 17, Indels: 16
0.80 0.11 0.10
Matches are distributed among these distances:
86 25 0.20
87 12 0.09
88 17 0.13
89 17 0.13
90 57 0.45
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (85 bp):
TTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAGGGGCTTAATTACTATTTTTGAAAAAAAT
TTGAGAACTTTTTATGCATT
Found at i:9063 original size:22 final size:22
Alignment explanation
Indices: 9038--9083 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
9028 TTGCTCCGTA
*
9038 TTCTTGCTGTTTTCCTGCTATT
1 TTCTTGCTGTTTTCCTACTATT
* *
9060 TTCTTGTTGTTTTCTTACTATT
1 TTCTTGCTGTTTTCCTACTATT
9082 TT
1 TT
9084 GTTACCATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.07, C:0.17, G:0.11, T:0.65
Consensus pattern (22 bp):
TTCTTGCTGTTTTCCTACTATT
Found at i:9746 original size:37 final size:37
Alignment explanation
Indices: 9693--9766 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
9683 TTCTAGCAAG
* *
9693 TCCATTCATTGTGGCCAATCTTTGCTTTCAGTCGATA
1 TCCATTCATTGAGGCCAATCTTTGCATTCAGTCGATA
9730 TCCATTCATTGAGGCCAATCTTTGCATTCAGTCGATA
1 TCCATTCATTGAGGCCAATCTTTGCATTCAGTCGATA
9767 CTCGCACATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (37 bp):
TCCATTCATTGAGGCCAATCTTTGCATTCAGTCGATA
Done.