Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004925.1 Kokia drynarioides strain JFW-HI SEQ_118626, 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: 6334
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Warning! 70 characters in sequence are not A, C, G, or T
Found at i:47 original size:27 final size:28
Alignment explanation
Indices: 4--79 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 28
1 TTA
* *
4 TAATTTTTTTCTAATTTTTAATAAATTT
1 TAATTTTTTTATAATTTTTAATAAAATT
*
32 TAATTTTTTTAT-ATTTTTATTAAAATT
1 TAATTTTTTTATAATTTTTAATAAAATT
* *
59 TAATATTTTTATTGATTTTTA
1 TAATTTTTTTA-TAATTTTTA
80 TTTTTTATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 23 0.55
28 12 0.29
29 7 0.17
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (28 bp):
TAATTTTTTTATAATTTTTAATAAAATT
Found at i:79 original size:19 final size:18
Alignment explanation
Indices: 37--94 Score: 66
Period size: 19 Copynumber: 3.3 Consensus size: 18
27 AATTTTAATT
37 TTTTTATATTTTTATTAAA
1 TTTTTATATTTTTATT-AA
* * *
56 ATTTAATATTTTTATTGA
1 TTTTTATATTTTTATTAA
74 TTTTTAT-TTTTTA-TAA
1 TTTTTATATTTTTATTAA
90 TTTTT
1 TTTTT
95 TGCCACATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 7 0.21
17 6 0.18
18 6 0.18
19 14 0.42
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTTATATTTTTATTAA
Found at i:1879 original size:40 final size:40
Alignment explanation
Indices: 1835--1916 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
1825 AATGAATGAG
*
1835 TATGTACGTAATTTACAACTATAATGACAAAATAAAAAAA
1 TATGTACATAATTTACAACTATAATGACAAAATAAAAAAA
1875 TATGTACATAATTTACAACTATAATGACAAAATAAAAAAA
1 TATGTACATAATTTACAACTATAATGACAAAATAAAAAAA
1915 TA
1 TA
1917 CATGAATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.28
Consensus pattern (40 bp):
TATGTACATAATTTACAACTATAATGACAAAATAAAAAAA
Found at i:2171 original size:19 final size:19
Alignment explanation
Indices: 2147--2197 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
2137 TGTATCTTTG
2147 AAAATAT-ATGAAATAAATA
1 AAAATATAATG-AATAAATA
2166 AAAATATCAATGAATAAATA
1 AAAATAT-AATGAATAAATA
*
2186 AAATTA-AATGAA
1 AAAATATAATGAA
2198 GACAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.21
19 7 0.24
20 13 0.45
21 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (19 bp):
AAAATATAATGAATAAATA
Found at i:2211 original size:18 final size:18
Alignment explanation
Indices: 2165--2225 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
2155 TGAAATAAAT
* *
2165 AAAAATATCAATGAATAA
1 AAAAATATAAATGAAGAA
*
2183 ATAAAAT-TAAATGAAGAC
1 A-AAAATATAAATGAAGAA
*
2201 AAAAATATAAAT-AACATA
1 AAAAATATAAATGAAGA-A
2219 AAAAATA
1 AAAAATA
2226 ACAAATAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 8 0.23
18 22 0.63
19 5 0.14
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAAATATAAATGAAGAA
Found at i:2221 original size:17 final size:16
Alignment explanation
Indices: 2147--2247 Score: 62
Period size: 17 Copynumber: 5.9 Consensus size: 16
2137 TGTATCTTTG
2147 AAAATATATGAAATAAAT
1 AAAA-ATAT-AAATAAAT
* *
2165 AAAAATATCAATGAAT
1 AAAAATATAAATAAAT
* *
2181 AAATAAAATTAAATGAAGAC
1 AAA-AATA-TAAAT-AA-AT
2201 AAAAATATAAATAACAT
1 AAAAATATAAATAA-AT
*
2218 AAAAA-AT-AACAAAT
1 AAAAATATAAATAAAT
*
2232 AAATAAAATAAATAAA
1 AAA-AATATAAATAAA
2248 ACAATAAATG
Statistics
Matches: 65, Mismatches: 11, Indels: 15
0.71 0.12 0.16
Matches are distributed among these distances:
14 5 0.08
15 6 0.09
16 13 0.20
17 20 0.31
18 13 0.20
19 4 0.06
20 4 0.06
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (16 bp):
AAAAATATAAATAAAT
Found at i:2620 original size:18 final size:18
Alignment explanation
Indices: 2597--2650 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
2587 AGTACTCTTT
2597 CCCAATTCTCTTAGAGAA
1 CCCAATTCTCTTAGAGAA
2615 CCCAATTCTCTTAGAGAA
1 CCCAATTCTCTTAGAGAA
*
2633 CCCAATTCTCTGAGAGAA
1 CCCAATTCTCTTAGAGAA
2651 ACAGGTGCGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (18 bp):
CCCAATTCTCTTAGAGAA
Done.