Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010189.1 Kokia drynarioides strain JFW-HI SEQ_125001, 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: 5140
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:268 original size:16 final size:16
Alignment explanation
Indices: 247--302 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
237 TTATATATAT
*
247 AAGAAATAAAAGAATA
1 AAGAAACAAAAGAATA
* *
263 AAGAAAGAAAA-AAAA
1 AAGAAACAAAAGAATA
*
278 AAGAAACAAAAGAATG
1 AAGAAACAAAAGAATA
294 AAG-AACAAA
1 AAGAAACAAA
303 GGCTCAAACA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 19 0.56
16 15 0.44
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.05
Consensus pattern (16 bp):
AAGAAACAAAAGAATA
Found at i:1146 original size:41 final size:41
Alignment explanation
Indices: 1091--1226 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
1081 CGACCTTGAA
**
1091 TCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGAT
1 TCGATGAGGTACTGGGTGTCATTATTTTACTTCGGATAGAT
* * * * *
1132 TCGATTAGGTACT-GG-GT-ATCACTTTACTTCGGCTAG-G
1 TCGATGAGGTACTGGGTGTCATTATTTTACTTCGGATAGAT
* **
1169 CCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGAT
1 TCGATGAGGTACTGGGTGTCATTATTTTACTTCGGATAGAT
*
1210 TCAATGAGGTACTGGGT
1 TCGATGAGGTACTGGGT
1227 ACCACTTTAC
Statistics
Matches: 72, Mismatches: 19, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
37 9 0.12
38 18 0.25
39 4 0.06
40 18 0.25
41 23 0.32
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (41 bp):
TCGATGAGGTACTGGGTGTCATTATTTTACTTCGGATAGAT
Found at i:1221 original size:78 final size:78
Alignment explanation
Indices: 1092--1253 Score: 297
Period size: 78 Copynumber: 2.1 Consensus size: 78
1082 GACCTTGAAT
* * *
1092 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATTCGATTAGGTACTGGGTATCACTTT
1 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATTCAATGAGGTACTGGGTACCACTTT
1157 ACTTCGGCTAGGC
66 ACTTCGGCTAGGC
1170 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATTCAATGAGGTACTGGGTACCACTTT
1 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATTCAATGAGGTACTGGGTACCACTTT
1235 ACTTCGGCTAGGC
66 ACTTCGGCTAGGC
1248 CGATGA
1 CGATGA
1254 NNNNNNNNNN
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (78 bp):
CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATTCAATGAGGTACTGGGTACCACTTT
ACTTCGGCTAGGC
Found at i:1241 original size:38 final size:38
Alignment explanation
Indices: 1116--1241 Score: 128
Period size: 38 Copynumber: 3.3 Consensus size: 38
1106 GTGTCATTAT
*
1116 TTTACTTCGGATAGATTCGATTAGGTACTGGGTATCAC
1 TTTACTTCGGATAGATTCGATGAGGTACTGGGTATCAC
* ** ** * *
1154 TTTACTTCGGCTAG-GCCGATGAGACACTGGGTGTCATTAT
1 TTTACTTCGGATAGATTCGATGAGGTACT-GG-GT-ATCAC
* *
1194 TTTACTTCGGATAGATTCAATGAGGTACTGGGTACCAC
1 TTTACTTCGGATAGATTCGATGAGGTACTGGGTATCAC
1232 TTTACTTCGG
1 TTTACTTCGG
1242 CTAGGCCGAT
Statistics
Matches: 67, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
37 9 0.13
38 27 0.40
39 4 0.06
40 18 0.27
41 9 0.13
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (38 bp):
TTTACTTCGGATAGATTCGATGAGGTACTGGGTATCAC
Found at i:1459 original size:38 final size:38
Alignment explanation
Indices: 1417--1573 Score: 120
Period size: 37 Copynumber: 4.1 Consensus size: 38
1407 ATGTCATTAT
* *
1417 TTTACTTCGGATAGATTCGATTAGGTACTGAGTATCAC
1 TTTACTTCGGATAGATTCGATGAGATACTGAGTATCAC
* ** * * * *
1455 TTTACTTCGGCTAG-GCCGATGAGACACTGGGTGTCATTAT
1 TTTACTTCGGATAGATTCGATGAGATACT--GAGT-ATCAC
* *
1495 TTTACTTCGGATAGATTCGATGAGATACTGGGTACCAC
1 TTTACTTCGGATAGATTCGATGAGATACTGAGTATCAC
* ** * * *
1533 TTTACTTCGGCTAG-GCCGATGAGACACTGGGTGTCAC
1 TTTACTTCGGATAGATTCGATGAGATACTGAGTATCAC
1570 TTTA
1 TTTA
1574 TTGCTTCGAA
Statistics
Matches: 92, Mismatches: 23, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
37 31 0.34
38 28 0.30
39 6 0.07
40 16 0.17
41 11 0.12
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (38 bp):
TTTACTTCGGATAGATTCGATGAGATACTGAGTATCAC
Found at i:1525 original size:41 final size:41
Alignment explanation
Indices: 1392--1568 Score: 136
Period size: 38 Copynumber: 4.5 Consensus size: 41
1382 GACCTTTGAA
* *
1392 TCGATGAGACATTGGATGTCATTATTTTACTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGAT
* ** * * * * *
1433 TCGATTAGGTACT--GAGT-ATCACTTTACTTCGGCTAG-G
1 TCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGAT
*
1470 CCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGAT
* ** * * *
1511 TCGATGAGATACT-GG-GT-ACCACTTTACTTCGGCTAG-G
1 TCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGAT
*
1548 CCGATGAGACACTGGGTGTCA
1 TCGATGAGACACTGGGTGTCA
1569 CTTTATTGCT
Statistics
Matches: 101, Mismatches: 28, Indels: 15
0.70 0.19 0.10
Matches are distributed among these distances:
37 20 0.20
38 33 0.33
39 9 0.09
40 19 0.19
41 20 0.20
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (41 bp):
TCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGAT
Found at i:1562 original size:37 final size:37
Alignment explanation
Indices: 1443--1573 Score: 145
Period size: 37 Copynumber: 3.4 Consensus size: 37
1433 TCGATTAGGT
*
1443 ACTGAGTATCACTTTACTTCGGCTAGGCCGATGAGAC
1 ACTGGGTATCACTTTACTTCGGCTAGGCCGATGAGAC
* * * ** *
1480 ACTGGGTGTCATTATTTTACTTCGGATAGATTCGATGAGAT
1 ACT-GG-GT-ATCACTTTACTTCGGCTAG-GCCGATGAGAC
*
1521 ACTGGGTACCACTTTACTTCGGCTAGGCCGATGAGAC
1 ACTGGGTATCACTTTACTTCGGCTAGGCCGATGAGAC
*
1558 ACTGGGTGTCACTTTA
1 ACTGGGTATCACTTTA
1574 TTGCTTCGAA
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
37 25 0.34
38 16 0.22
39 4 0.05
40 18 0.24
41 11 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (37 bp):
ACTGGGTATCACTTTACTTCGGCTAGGCCGATGAGAC
Found at i:1581 original size:78 final size:78
Alignment explanation
Indices: 1393--1568 Score: 298
Period size: 78 Copynumber: 2.3 Consensus size: 78
1383 ACCTTTGAAT
* * * * *
1393 CGATGAGACATTGGATGTCATTATTTTACTTCGGATAGATTCGATTAGGTACTGAGTATCACTTT
1 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATTCGATGAGATACTGAGTACCACTTT
1458 ACTTCGGCTAGGC
66 ACTTCGGCTAGGC
*
1471 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATTCGATGAGATACTGGGTACCACTTT
1 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATTCGATGAGATACTGAGTACCACTTT
1536 ACTTCGGCTAGGC
66 ACTTCGGCTAGGC
1549 CGATGAGACACTGGGTGTCA
1 CGATGAGACACTGGGTGTCA
1569 CTTTATTGCT
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 92 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (78 bp):
CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATTCGATGAGATACTGAGTACCACTTT
ACTTCGGCTAGGC
Done.