Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009404.1 Kokia drynarioides strain JFW-HI SEQ_124111, 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: 58841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Found at i:290 original size:40 final size:40
Alignment explanation
Indices: 246--330 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
236 TCCTTCTTCC
246 TTTCTCACACTTA-CTAATTAATCCTTAATTTTCTAGCTAT
1 TTTCTCA-ACTTAGCTAATTAATCCTTAATTTTCTAGCTAT
* ** *
286 TTTCTTATTTTAGTTAATTAATCCTTAATTTTCTAGCTAT
1 TTTCTCAACTTAGCTAATTAATCCTTAATTTTCTAGCTAT
326 TTTCT
1 TTTCT
331 TATTTTAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 3 0.08
40 37 0.93
ACGTcount: A:0.25, C:0.18, G:0.04, T:0.54
Consensus pattern (40 bp):
TTTCTCAACTTAGCTAATTAATCCTTAATTTTCTAGCTAT
Found at i:331 original size:40 final size:40
Alignment explanation
Indices: 260--341 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
250 TCACACTTAC
260 TAATTAATCCTTAATTTTCTAGCTATTTTCTTATTTTAGT
1 TAATTAATCCTTAATTTTCTAGCTATTTTCTTATTTTAGT
300 TAATTAATCCTTAATTTTCTAGCTATTTTCTTATTTTAGT
1 TAATTAATCCTTAATTTTCTAGCTATTTTCTTATTTTAGT
340 TA
1 TA
342 TATAGTCTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.57
Consensus pattern (40 bp):
TAATTAATCCTTAATTTTCTAGCTATTTTCTTATTTTAGT
Found at i:10086 original size:15 final size:17
Alignment explanation
Indices: 10068--10112 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
10058 TATATTATTT
10068 TAATTTA-ATA-CTTAA
1 TAATTTATATATCTTAA
*
10083 TAATTTTATGTATCTTAA
1 TAA-TTTATATATCTTAA
10101 TAATTTATATAT
1 TAATTTATATAT
10113 AATTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 3 0.12
16 4 0.16
17 10 0.40
18 8 0.32
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
TAATTTATATATCTTAA
Found at i:12712 original size:22 final size:22
Alignment explanation
Indices: 12687--12729 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
12677 ATTAATAAAA
*
12687 AAAAGTAAAATTAT-TAAATATT
1 AAAA-TAAAATAATATAAATATT
*
12709 AAAATAATATAATATAAATAT
1 AAAATAAAATAATATAAATAT
12730 ATATTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAATAAAATAATATAAATATT
Found at i:12887 original size:32 final size:32
Alignment explanation
Indices: 12844--12915 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
12834 GTTGGGTTGA
* *
12844 GCTTAGACAAGCATAAAGTATGTTAATACCAT
1 GCTTAGGCAAGCATAAAGTATGTTAATACCAC
* *
12876 GCTTAGGCAAGCATTAAGTATGTTAATATCAC
1 GCTTAGGCAAGCATAAAGTATGTTAATACCAC
12908 GCTTAGGC
1 GCTTAGGC
12916 TTAACTCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (32 bp):
GCTTAGGCAAGCATAAAGTATGTTAATACCAC
Found at i:16286 original size:17 final size:17
Alignment explanation
Indices: 16240--16293 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
16230 ATTTTTCTGA
* *
16240 AATTATAATCTTTTAATA
1 AATTATAAT-TTTTATTT
*
16258 AAATAT-ATTTTTATTT
1 AATTATAATTTTTATTT
*
16274 AATTATAATTTTTATAT
1 AATTATAATTTTTATTT
16291 AAT
1 AAT
16294 GTTTATAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 11 0.37
17 14 0.47
18 5 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTATAATTTTTATTT
Found at i:20076 original size:18 final size:17
Alignment explanation
Indices: 20052--20105 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
20042 CATTTGAACA
20052 ATATCAAAATTTCATGT
1 ATATCAAAATTTCATGT
*
20069 ACTATCAAAAATATAT-ATAT
1 A-TATC-AAAAT-T-TCATGT
20089 ATATCAAAATTTCATGT
1 ATATCAAAATTTCATGT
20106 GTATATTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
16 1 0.03
17 5 0.17
18 9 0.30
19 9 0.30
20 5 0.17
21 1 0.03
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (17 bp):
ATATCAAAATTTCATGT
Found at i:20110 original size:19 final size:18
Alignment explanation
Indices: 20052--20111 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
20042 CATTTGAACA
20052 ATATCAAAATTTCA-TGT
1 ATATCAAAATTTCATTGT
* *
20069 ACTATCAAAAATAT-ATATAT
1 A-TATC-AAAATTTCAT-TGT
20089 ATATCAAAATTTCATGTGT
1 ATATCAAAATTTCAT-TGT
20108 ATAT
1 ATAT
20112 TTGTACCGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
17 1 0.03
18 11 0.33
19 18 0.55
20 3 0.09
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (18 bp):
ATATCAAAATTTCATTGT
Found at i:20873 original size:19 final size:19
Alignment explanation
Indices: 20832--20878 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
20822 AAAGACGTAC
*
20832 CAAAATATTTAAGTTATAT
1 CAAAATATTTAAATTATAT
*
20851 CAAAATCTTTAACATTATA-
1 CAAAATATTTAA-ATTATAT
20870 CAAAA-ATTT
1 CAAAATATTT
20879 TTAATGCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 16 0.67
20 5 0.21
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (19 bp):
CAAAATATTTAAATTATAT
Found at i:23072 original size:108 final size:109
Alignment explanation
Indices: 22952--23168 Score: 393
Period size: 109 Copynumber: 2.0 Consensus size: 109
22942 AGTTAGTCGA
22952 GTTGACGAATTCTATTTTAGCAACTGAACTCAATTTGAATTTTTTTT-GAATCGAGTAAAAAAAA
1 GTTGACGAATTCTATTTTAGCAACTGAACTCAATTTGAATTTTTTTTCGAATCGAGTAAAAAAAA
*
23016 TTCGAGTCAAGTTAACAAATTC-TATTATTTATACTTAATGTTGC
66 TTCGAGTCAAGTTAACAAA-TCATATTATTTATACTTAATATTGC
23060 GTTGACGAATTCTATTTTAGCAACTGAACTCAATTTGAATTTTTTTTCGAATCGAGTAAAAAAAA
1 GTTGACGAATTCTATTTTAGCAACTGAACTCAATTTGAATTTTTTTTCGAATCGAGTAAAAAAAA
*
23125 TTCGAGTCGAGTTAACAAATCATATTATTTATACTTAATATTGC
66 TTCGAGTCAAGTTAACAAATCATATTATTTATACTTAATATTGC
23169 ATTTACATAG
Statistics
Matches: 105, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
108 49 0.47
109 56 0.53
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (109 bp):
GTTGACGAATTCTATTTTAGCAACTGAACTCAATTTGAATTTTTTTTCGAATCGAGTAAAAAAAA
TTCGAGTCAAGTTAACAAATCATATTATTTATACTTAATATTGC
Found at i:26400 original size:5 final size:5
Alignment explanation
Indices: 26390--26415 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
26380 ATATTTACAC
26390 AATTA AATTA AATTA AATTA AATTA A
1 AATTA AATTA AATTA AATTA AATTA A
26416 GTATCAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTA
Found at i:48051 original size:6 final size:6
Alignment explanation
Indices: 48040--48065 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
48030 TTATTTATTA
48040 TTTTCT TTTTCT TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TT
48066 CACTCATCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:58812 original size:2 final size:2
Alignment explanation
Indices: 58807--58841 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
58797 AATATATTCA
58807 AT AT AT A- 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
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.