Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013192.1 Kokia drynarioides strain JFW-HI SEQ_128211, 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: 2208
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.33
Warning! 54 characters in sequence are not A, C, G, or T
Found at i:53 original size:12 final size:12
Alignment explanation
Indices: 36--143 Score: 61
Period size: 12 Copynumber: 9.5 Consensus size: 12
26 TCAAAATGTC
36 ATTAATAATATT
1 ATTAATAATATT
48 ATTAAT--TATT
1 ATTAATAATATT
58 ATGGTAATAATA--
1 AT--TAATAATATT
70 A-TAATAATA--
1 ATTAATAATATT
*
79 A-TAATAATAAT
1 ATTAATAATATT
* *
90 ATTACTAATATC
1 ATTAATAATATT
102 ATTAATAATATT
1 ATTAATAATATT
* ** *
114 AATAACGATAAT
1 ATTAATAATATT
*
126 AATAATAATATT
1 ATTAATAATATT
*
138 AATAAT
1 ATTAAT
144 GACATTAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
9 17 0.22
10 6 0.08
11 1 0.01
12 51 0.66
14 2 0.03
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (12 bp):
ATTAATAATATT
Found at i:68 original size:3 final size:3
Alignment explanation
Indices: 62--143 Score: 85
Period size: 3 Copynumber: 27.3 Consensus size: 3
52 ATTATTATGG
* * *
62 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAC TAA T-A TCAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
* ** *
107 TAA TAT TAA TAA CGA TAA TAA TAA TAA TAT TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
144 GACATTAATT
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
2 2 0.03
3 61 0.95
4 1 0.02
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:150 original size:12 final size:12
Alignment explanation
Indices: 68--152 Score: 61
Period size: 12 Copynumber: 7.3 Consensus size: 12
58 ATGGTAATAA
* *
68 TAATAATAATAA
1 TAATAATGATAT
*
80 TAATAATAATAT
1 TAATAATGATAT
*
92 TACTAAT-ATCAT
1 TAATAATGAT-AT
104 TAAT-A--ATAT
1 TAATAATGATAT
* *
113 TAATAACGATAA
1 TAATAATGATAT
*
125 TAATAATAATAT
1 TAATAATGATAT
*
137 TAATAATGACAT
1 TAATAATGATAT
149 TAAT
1 TAAT
153 TAAAAAAGGA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
9 6 0.10
10 3 0.05
11 3 0.05
12 48 0.80
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (12 bp):
TAATAATGATAT
Found at i:1215 original size:29 final size:28
Alignment explanation
Indices: 1168--1425 Score: 184
Period size: 29 Copynumber: 8.9 Consensus size: 28
1158 CTGAAGGTCT
*
1168 CTAAACTGTTCGAAAATTCCATTTTTAACC
1 CTAAACT-TTCAAAAATTCCATTTTT-ACC
*
1198 CTAAACTTTCAAAAATTCCATTTTTTCC
1 CTAAACTTTCAAAAATTCCATTTTTACC
* *
1226 CTCGAAC-TTCTAAAAATTCCATTTTGACC
1 CT-AAACTTTC-AAAAATTCCATTTTTACC
* *
1255 TCAAAACTTCCAAAAATTCCATTTTTCACC
1 -CTAAACTTTCAAAAATTCCATTTTT-ACC
* * *
1285 TCGAAACTTCCAAAAATTCCGTTTTTACCC
1 -CTAAACTTTCAAAAATTCCATTTTTA-CC
* *
1315 CGAAACTTCCAAAAATTCCATTTTTACC
1 CTAAACTTTCAAAAATTCCATTTTTACC
* *
1343 CTCAAAC-CTCCAAAATCTCCATTTTTTACC
1 CT-AAACTTTCAAAAAT-TCCA-TTTTTACC
* * *
1373 TCGAAACTCTC-AAAATTACC-CTTTTACC
1 -CTAAACTTTCAAAAATT-CCATTTTTACC
* *
1401 CTCGAA-TGTCTAAAAATTCCATTTT
1 CT-AAACTTTC-AAAAATTCCATTTT
1426 CAAACCCCAA
Statistics
Matches: 190, Mismatches: 22, Indels: 33
0.78 0.09 0.13
Matches are distributed among these distances:
27 4 0.02
28 27 0.14
29 97 0.51
30 58 0.31
31 4 0.02
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (28 bp):
CTAAACTTTCAAAAATTCCATTTTTACC
Found at i:1270 original size:58 final size:58
Alignment explanation
Indices: 1180--1457 Score: 246
Period size: 59 Copynumber: 4.7 Consensus size: 58
1170 AAACTGTTCG
* * *
1180 AAAATTCCATTTTTAA-CCCTAAACTTTCAAAAATTCCATTTTTTCCCTCGAACTTCTA
1 AAAATTCCA-TTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCTA
* * *
1238 AAAATTCCATTTTGACCTCAAAACTTCCAAAAATTCCATTTTT-CACCTCGAAACTTCCA
1 AAAATTCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAC-CCTCG-AACTTCTA
* * * * * *
1297 AAAATTCCGTTTTTACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACCTC-C
1 AAAATTCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCTA
* * * *
1354 AAAATCTCCATTTTTTACCTCGAAAC-TCTC-AAAATTACC-CTTTTACCCTCGAA-TGTCTA
1 AAAAT-TCCA-TTTTAACCCCAAAACTTC-CAAAAATT-CCATTTTTACCCTCGAACT-TCTA
* *
1413 AAAATTCCATTTTCAAACCCCAAAATTTCCCAAAATTACCATTTT
1 AAAATTCCATTTT--AACCCCAAAACTTCCAAAAATT-CCATTTT
1458 GCCCCGAGAA
Statistics
Matches: 182, Mismatches: 23, Indels: 27
0.78 0.10 0.12
Matches are distributed among these distances:
57 15 0.08
58 72 0.40
59 80 0.44
60 12 0.07
61 3 0.02
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.35
Consensus pattern (58 bp):
AAAATTCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCTA
Found at i:1322 original size:88 final size:86
Alignment explanation
Indices: 1180--1457 Score: 289
Period size: 88 Copynumber: 3.2 Consensus size: 86
1170 AAACTGTTCG
* * *
1180 AAAATTCCATTTTTAACC-CTAAACTTTCAAAAATTCCATTTTTTCCCTCGAACTTCTAAAAATT
1 AAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCC-TTTTTACCCTCGAACTTCTAAAAATT
*
1244 CCATTTTGACCTCAAAACTTCC
65 CCATTTTAACCTCAAAACTTCC
* *
1266 AAAAATTCCATTTTTCACCTCGAAACTTCCAAAAATTCCGTTTTTACCC-CGAAACTTCCAAAAA
1 -AAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCC-TTTTTACCCTCG-AACTTCTAAAAA
* *
1330 TTCCATTTTTACCCTC-AAACCTCC
63 TTCCA-TTTTAACCTCAAAACTTCC
* *
1354 AAAATCTCCATTTTTTACCTCGAAAC-TCTC-AAAATTACCCTTTTACCCTCGAA-TGTCTAAAA
1 AAAAT-TCCATTTTTAACCTCGAAACTTC-CAAAAATT-CCTTTTTACCCTCGAACT-TCTAAAA
* *
1416 ATTCCATTTTCAAACCCCAAAATTTCCC
62 ATTCCATTTT--AACCTCAAAACTT-CC
1444 AAAATTACCATTTT
1 AAAATT-CCATTTT
1458 GCCCCGAGAA
Statistics
Matches: 162, Mismatches: 16, Indels: 23
0.81 0.08 0.11
Matches are distributed among these distances:
86 5 0.03
87 54 0.33
88 76 0.47
89 13 0.08
90 14 0.09
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.35
Consensus pattern (86 bp):
AAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCCTTTTTACCCTCGAACTTCTAAAAATTC
CATTTTAACCTCAAAACTTCC
Done.