Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013214.1 Kokia drynarioides strain JFW-HI SEQ_128233, 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: 1936
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Found at i:1040 original size:30 final size:28
Alignment explanation
Indices: 976--1485 Score: 300
Period size: 30 Copynumber: 17.3 Consensus size: 28
966 GTCCCTAAAC
*
976 CTTCCAAAAATTACCA-TTTTACCCCCGAA
1 CTTCC-AAAATTCCCATTTTTA-CCCCGAA
1005 CTTCCAAAATTCCCATTTTTGACCCCGAA
1 CTTCCAAAATTCCCATTTTT-ACCCCGAA
* * *
1034 TATTCCAAAAATTACTA-TTTTACCCCCGAA
1 -CTTCC-AAAATTCCCATTTTTA-CCCCGAA
* *
1064 CTTCCAAAAATCCCATTTTTGACCTCGAA
1 CTTCCAAAATTCCCATTTTT-ACCCCGAA
* * *
1093 TATTCCAAAAATTACTA-TTTTACCCCCGAA
1 -CTTCC-AAAATTCCCATTTTTA-CCCCGAA
* * *
1123 CTTCCAAAAATCCCATTTTCGACCCTGAA
1 CTTCCAAAATTCCCATTTT-TACCCCGAA
* * *
1152 TCTTCCAAAAATTACTA-TTTTACCCCCAAA
1 -CTTCC-AAAATTCCCATTTTTA-CCCCGAA
* *
1182 CTTCCAAAAATCCCATTTTTTATCCCCAAA
1 CTTCCAAAATTCCCA-TTTTTA-CCCCGAA
* *
1212 CTTCCAAAAATCCCATTTTTGATCCCGAA
1 CTTCCAAAATTCCCATTTTT-ACCCCGAA
* * *
1241 CCTTCCAAAAATTACTA-TTTTACCCCTAAA
1 -CTTCC-AAAATTCCCATTTTTACCCC-GAA
*
1271 CTTCCAAAAATCCCATTTTTAACCCCGAA
1 CTTCCAAAATTCCCATTTTT-ACCCCGAA
* * *
1300 CCTTCTTAAAATTACCA-TTTTACCCCCAAA
1 -CTTC-CAAAATTCCCATTTTTA-CCCCGAA
**
1330 CTTCCAACAA-TCCCATTTTTAACCTTGAA
1 CTTCCAA-AATTCCCATTTTT-ACCCCGAA
* * *
1359 TCTTCCAAAAATTACTATTTTT-CCTCGAA
1 -CTTCC-AAAATTCCCATTTTTACCCCGAA
* *
1388 TTTCCAAAAATCCCATTTTTACCCCCGAA
1 CTTCCAAAATTCCCATTTTTA-CCCCGAA
* *
1417 TCTTCCAAAAATTACCA-CTTTACCCTCGAA
1 -CTTCC-AAAATTCCCATTTTTACCC-CGAA
* * **
1447 CTTCCAAAAATCCTATTTTTGATTCCGAA
1 CTTCCAAAATTCCCATTTTT-ACCCCGAA
1476 CATTCCAAAA
1 C-TTCCAAAA
1486 CTACCATTCT
Statistics
Matches: 373, Mismatches: 68, Indels: 79
0.72 0.13 0.15
Matches are distributed among these distances:
27 12 0.03
28 54 0.14
29 119 0.32
30 133 0.36
31 55 0.15
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (28 bp):
CTTCCAAAATTCCCATTTTTACCCCGAA
Found at i:1069 original size:59 final size:59
Alignment explanation
Indices: 977--1222 Score: 388
Period size: 59 Copynumber: 4.2 Consensus size: 59
967 TCCCTAAACC
* *
977 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAATTCCCATTTTTGACCCCGAATA
1 TTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAATA
*
1036 TTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAATA
1 TTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAATA
* * *
1095 TTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTCGACCCTGAATC
1 TTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAATA
* *
1154 TTCCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTATCCCC-AA-A
1 TTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCCGAATA
1212 CTTCCAAAAAT
1 -TTCCAAAAAT
1223 CCCATTTTTG
Statistics
Matches: 173, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
59 170 0.98
60 3 0.02
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (59 bp):
TTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAATA
Found at i:1217 original size:118 final size:118
Alignment explanation
Indices: 967--1252 Score: 391
Period size: 118 Copynumber: 2.4 Consensus size: 118
957 ACCCCGGAGG
* * *
967 TCCCTAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAATTCCCATTTTTGACCCCG
1 TCCCCAAA-CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTCGACCCCG
*
1032 AATATTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
65 AATATTCCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
* * *
1086 -CCTCGAATA-TTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTCGACCCT
1 TCC-CCAA-ACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTCGACCCC
* *
1149 GAATCTTCCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTA
64 GAATATTCCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
* *
1204 TCCCCAAACTTCCAAAAA-TCCCATTTTTGA-TCCCGAACCTTCCAAAAAT
1 TCCCCAAACTTCCAAAAATTACCA-TTTT-ACCCCCGAA-CTTCCAAAAAT
1253 TACTATTTTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
117 4 0.03
118 126 0.85
119 17 0.11
120 1 0.01
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.31
Consensus pattern (118 bp):
TCCCCAAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTCGACCCCGA
ATATTCCAAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
Found at i:1223 original size:148 final size:143
Alignment explanation
Indices: 976--1465 Score: 474
Period size: 148 Copynumber: 3.3 Consensus size: 143
966 GTCCCTAAAC
* * * * *
976 CTTCCAAAAATTACCATTTTACCCCCGAACTTCC-AAAATTCCCATTTTTGACCCCGAATA-TTC
1 CTTCCAAAAA-TCCCATTTTA-CCCTGAACTTCCAAAAATTACTA-TTTT-ACCCCCAA-ACTTC
** * *
1039 CAAAAATTAC-TATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAATATTCCAAAA
61 CAAAAATCCCAT-TTTTAACCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAAT-TTCCAAAA
1103 ATTACTATTTTACCCCCGAA
124 ATTACTATTTTACCCCCGAA
1123 CTTCCAAAAATCCCATTTTCGACCCTGAATCTTCCAAAAATTACTATTTTACCCCCAAACTTCCA
1 CTTCCAAAAATCCCATTTT--ACCCTGAA-CTTCCAAAAATTACTATTTTACCCCCAAACTTCCA
* *
1188 AAAATCCCATTTTTTATCCCCAAACTTCCAAAAATCCCATTTTTGATCC-CGAACCTTCCAAAAA
63 AAAATCCCA-TTTTTAACCCCAAACTTCCAAAAATCCCATTTTTGA-CCTCGAA-TTTCCAAAAA
**
1252 TTACTATTTTACCCCTAAA
125 TTACTATTTTACCCCCGAA
* ** *
1271 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCTTAAAATTACCATTTTACCCCCAAACTTCCA
1 CTTCCAAAAATCCCA-TTTT-ACCCTGAA-CTTCCAAAAATTACTATTTTACCCCCAAACTTCCA
* ** * * *
1336 ACAATCCCATTTTTAACCTTGAATCTTCCAAAAATTACTATTTTT--CCTCGAATTTCCAAAAA-
63 AAAATCCCATTTTTAACC-CCAAACTTCCAAAAA-TCCCATTTTTGACCTCGAATTTCCAAAAAT
* *
1398 TCCCATTTTTACCCCCGAA
126 TACTA-TTTTACCCCCGAA
* * *
1417 TCTTCCAAAAATTACCACTTTACCCTCGAACTTCCAAAAA-TCCTATTTT
1 -CTTCCAAAAA-TCCCATTTTACCCT-GAACTTCCAAAAATTACTATTTT
1466 TGATTCCGAA
Statistics
Matches: 289, Mismatches: 37, Indels: 36
0.80 0.10 0.10
Matches are distributed among these distances:
145 10 0.03
146 43 0.15
147 62 0.21
148 151 0.52
149 23 0.08
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.32
Consensus pattern (143 bp):
CTTCCAAAAATCCCATTTTACCCTGAACTTCCAAAAATTACTATTTTACCCCCAAACTTCCAAAA
ATCCCATTTTTAACCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAATTTCCAAAAATTACTA
TTTTACCCCCGAA
Found at i:1262 original size:59 final size:57
Alignment explanation
Indices: 976--1493 Score: 344
Period size: 59 Copynumber: 8.8 Consensus size: 57
966 GTCCCTAAAC
* *
976 CTTCCAAAAATTACCA-TTTTACCCCCGAA-CTTCC-AAAATTCCCATTTTTGACCCCGAATA
1 CTTCCAAAAA-TCCCATTTTTA-CCCCGAACCTTCCAAAAATTACCA-TTTT-ACCCC-AA-A
** * *
1036 -TTCCAAAAATTAC-TATTTTACCCCCGAA-CTTCCAAAAA-TCCCATTTTTGACCTCGAATA
1 CTTCCAAAAATCCCAT-TTTTA-CCCCGAACCTTCCAAAAATTACCA-TTTT-ACC-CCAA-A
** * * *
1095 -TTCCAAAAATTAC-TATTTTACCCCCGAA-CTTCCAAAAA-TCCCATTTTCGACCCTGAAT
1 CTTCCAAAAATCCCAT-TTTTA-CCCCGAACCTTCCAAAAATTACCATTTT--ACCC-CAAA
** * * *
1153 CTTCCAAAAATTAC-TATTTTACCCCCAAACTTCCAAAAA-TCCCATTTTTTATCCCCAAA
1 CTTCCAAAAATCCCAT-TTTTACCCCGAACCTTCCAAAAATTACCA--TTTTA-CCCCAAA
* *
1212 CTTCCAAAAATCCCATTTTTGATCCCGAACCTTCCAAAAATTACTATTTTACCCCTAAA
1 CTTCCAAAAATCCCATTTTT-ACCCCGAACCTTCCAAAAATTACCATTTTACCCC-AAA
**
1271 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCTTAAAATTACCATTTTACCCCCAAA
1 CTTCCAAAAATCCCATTTTT-ACCCCGAACCTTCCAAAAATTACCATTTTA-CCCCAAA
* ** * * * * *
1330 CTTCCAACAATCCCATTTTTAACCTTGAATCTTCCAAAAATTACTATTTTTCCTCGAA
1 CTTCCAAAAATCCCATTTTT-ACCCCGAACCTTCCAAAAATTACCATTTTACCCCAAA
* * * *
1388 TTTCCAAAAATCCCATTTTTACCCCCGAATCTTCCAAAAATTACCACTTTACCCTCGAA
1 CTTCCAAAAATCCCATTTTTA-CCCCGAACCTTCCAAAAATTACCATTTTACCC-CAAA
* ** * *
1447 CTTCCAAAAATCCTATTTTTGATTCCGAACATTCC-AAAACTACCATT
1 CTTCCAAAAATCCCATTTTT-ACCCCGAACCTTCCAAAAATTACCATT
1494 CTGCCACTCC
Statistics
Matches: 394, Mismatches: 45, Indels: 40
0.82 0.09 0.08
Matches are distributed among these distances:
57 1 0.00
58 76 0.19
59 280 0.71
60 30 0.08
61 7 0.02
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.32
Consensus pattern (57 bp):
CTTCCAAAAATCCCATTTTTACCCCGAACCTTCCAAAAATTACCATTTTACCCCAAA
Found at i:1449 original size:117 final size:118
Alignment explanation
Indices: 1200--1485 Score: 369
Period size: 117 Copynumber: 2.4 Consensus size: 118
1190 AATCCCATTT
* *
1200 TTTATCCCCAAACTTCCAAAAATCCCATTTTTGATCCCGAACCTTCCAAAAATTACTATTTTACC
1 TTTACCCCCAAACTTCCAAAAATCCCATTTTTGAACCCGAACCTTCCAAAAATTACTATTTTACC
** *
1265 CCTAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCTTAAAATTACCAT
66 CCTAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCAC
* * * *
1318 TTTACCCCCAAACTTCCAACAATCCCATTTTT-AACCTTGAATCTTCCAAAAATTACTATTTTTC
1 TTTACCCCCAAACTTCCAAAAATCCCATTTTTGAACC-CGAACCTTCCAAAAATTACTATTTTAC
* * * * *
1382 CTC-GAATTTCCAAAAATCCCATTTTTACCCCCGAATCTTCCAAAAATTACCAC
65 CCCTAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCAC
* * * ** *
1435 TTTACCCTCGAACTTCCAAAAATCCTATTTTTGATTCCGAACATTCCAAAA
1 TTTACCCCCAAACTTCCAAAAATCCCATTTTTGAACCCGAACCTTCCAAAA
1486 CTACCATTCT
Statistics
Matches: 143, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
117 85 0.59
118 58 0.41
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (118 bp):
TTTACCCCCAAACTTCCAAAAATCCCATTTTTGAACCCGAACCTTCCAAAAATTACTATTTTACC
CCTAAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACCAC
Done.