Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001858.1 Kokia drynarioides strain JFW-HI SEQ_113615, 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: 19368
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:483 original size:3 final size:3
Alignment explanation
Indices: 468--514 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
458 GTCGAGACAA
* * *
468 CTT CTT ATT CTT CTT CTT TTT CTT -TCT CTT CTT TTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT
513 CT
1 CT
515 CTTTTCTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 1 0.03
3 34 0.94
4 1 0.03
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (3 bp):
CTT
Found at i:499 original size:15 final size:16
Alignment explanation
Indices: 475--521 Score: 71
Period size: 15 Copynumber: 3.0 Consensus size: 16
465 CAACTTCTTA
475 TTCTTCTTCTTTTTCT
1 TTCTTCTTCTTTTTCT
491 TTC-TCTTCTTTTTC-
1 TTCTTCTTCTTTTTCT
505 TTCTTCTTCTCTTTTCT
1 TTCTTCTTCT-TTTTCT
522 CTTTTTCCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.11
15 17 0.61
16 8 0.29
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (16 bp):
TTCTTCTTCTTTTTCT
Found at i:1338 original size:32 final size:32
Alignment explanation
Indices: 1297--1371 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
1287 TTATTCAAAG
* * * *
1297 TTGTTATTTTTTTAATTTTGTTTTTACT-AAA
1 TTGTTATTTTCTTAAATTTATTTTGACTGAAA
1328 TTTGTTATTTTCTTAAATTTATTTTGACTGAAA
1 -TTGTTATTTTCTTAAATTTATTTTGACTGAAA
1361 TTGTTTATTTT
1 TTG-TTATTTT
1372 AAGTAAATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 27 0.73
33 10 0.27
ACGTcount: A:0.23, C:0.04, G:0.08, T:0.65
Consensus pattern (32 bp):
TTGTTATTTTCTTAAATTTATTTTGACTGAAA
Found at i:1344 original size:17 final size:17
Alignment explanation
Indices: 1297--1347 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1287 TTATTCAAAG
* *
1297 TTGTTATTTTTTTAATT
1 TTGTTATTTTCTTAAAT
*
1314 TTGTT-TTTAC-TAAAT
1 TTGTTATTTTCTTAAAT
1329 TTGTTATTTTCTTAAAT
1 TTGTTATTTTCTTAAAT
1346 TT
1 TT
1348 ATTTTGACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 9 0.32
16 7 0.25
17 12 0.43
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.69
Consensus pattern (17 bp):
TTGTTATTTTCTTAAAT
Found at i:3802 original size:25 final size:25
Alignment explanation
Indices: 3765--3820 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
3755 TTTATTCTTG
3765 TAGAAAACTAAAGA-AAATAAGTTAAA
1 TAGAAAACTAAAGACAAA-AAG-TAAA
3791 -AGAAAA-TAAAAGACAAAAAGTAAA
1 TAGAAAACT-AAAGACAAAAAGTAAA
3815 TAGAAA
1 TAGAAA
3821 GATTGCAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
24 5 0.19
25 19 0.70
26 3 0.11
ACGTcount: A:0.70, C:0.04, G:0.12, T:0.14
Consensus pattern (25 bp):
TAGAAAACTAAAGACAAAAAGTAAA
Found at i:15301 original size:110 final size:110
Alignment explanation
Indices: 15084--15482 Score: 510
Period size: 110 Copynumber: 3.5 Consensus size: 110
15074 TATGTTGGAT
* * * * * * *
15084 ATTAGTCAACCATTTGAGTATGTAATGTGTGAAATTCATTCGAGTTTTTCGTTTCTTTATTTGAT
1 ATTAGTCAATCATTTGAGCATGTCATGTGTGAAATTTATTCGGGTTTTTC----ATTT-TTTCAT
** *
15149 GTGTTTTATTTTAATTTGATTTTACTATGATGAATTATGATGTGCTCGTC
61 GTGTTTTATACTAATTTGATTTTACTATGATGAATTATGATGTGCTAGTC
* * * *
15199 ATTAGTCAATCATTTGAGCATGTTACGTGTGAAATTTGTTCGGATTTTTCATTTTTTCATGTGTT
1 ATTAGTCAATCATTTGAGCATGTCATGTGTGAAATTTATTCGGGTTTTTCATTTTTTCATGTGTT
*
15264 TTATACTAATTTGATTTTATTATGATGAATTATGATGTGCTAGTC
66 TTATACTAATTTGATTTTACTATGATGAATTATGATGTGCTAGTC
* *
15309 ATTAGTCAATCATTTGAGCATGTCATGTGTGAAATTTATTTGGGTTTTTCATTTTTCATTTAATG
1 ATTAGTCAATCATTTGAGCATGTCATGTGTGAAATTTATTCGGGTTTTTCA--TTT--TTTCATG
* * *
15374 TGTTTTACACTAATTTGATTTTACTATGATGAATTATGATGTGCTGGCC
62 TGTTTTATACTAATTTGATTTTACTATGATGAATTATGATGTGCTAGTC
* * *
15423 ATTAGTCAACCATTTGAGCATGTCATGTGTGAAATTTATTCGGGTTTTTCGTTTCTTCAT
1 ATTAGTCAATCATTTGAGCATGTCATGTGTGAAATTTATTCGGGTTTTTCATTTTTTCAT
15483 TTGATGTGTT
Statistics
Matches: 251, Mismatches: 29, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
110 101 0.40
111 3 0.01
112 6 0.02
114 99 0.39
115 42 0.17
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.48
Consensus pattern (110 bp):
ATTAGTCAATCATTTGAGCATGTCATGTGTGAAATTTATTCGGGTTTTTCATTTTTTCATGTGTT
TTATACTAATTTGATTTTACTATGATGAATTATGATGTGCTAGTC
Found at i:15416 original size:114 final size:115
Alignment explanation
Indices: 15084--15504 Score: 584
Period size: 114 Copynumber: 3.7 Consensus size: 115
15074 TATGTTGGAT
* * * * * *
15084 ATTAGTCAACCATTTGAGTATGTAATGTGTGAAATTCATTCGAGTTTTTCGTTTCTTTATTTGAT
1 ATTAGTCAACCATTTGAGCATGTCATGTGTGAAATTTATTCGGGTTTTTCATTTCTTCATTTGAT
** *
15149 GTGTTTTATTTTAATTTGATTTTACTATGATGAATTATGATGTGCTCGTC
66 GTGTTTTATACTAATTTGATTTTACTATGATGAATTATGATGTGCTAGTC
* * * * * *
15199 ATTAGTCAATCATTTGAGCATGTTACGTGTGAAATTTGTTCGGATTTTTCA--T-TT--TTTCAT
1 ATTAGTCAACCATTTGAGCATGTCATGTGTGAAATTTATTCGGGTTTTTCATTTCTTCATTTGAT
*
15259 GTGTTTTATACTAATTTGATTTTATTATGATGAATTATGATGTGCTAGTC
66 GTGTTTTATACTAATTTGATTTTACTATGATGAATTATGATGTGCTAGTC
* * *
15309 ATTAGTCAATCATTTGAGCATGTCATGTGTGAAATTTATTTGGGTTTTTCATTT-TTCATTTAAT
1 ATTAGTCAACCATTTGAGCATGTCATGTGTGAAATTTATTCGGGTTTTTCATTTCTTCATTTGAT
* * *
15373 GTGTTTTACACTAATTTGATTTTACTATGATGAATTATGATGTGCTGGCC
66 GTGTTTTATACTAATTTGATTTTACTATGATGAATTATGATGTGCTAGTC
*
15423 ATTAGTCAACCATTTGAGCATGTCATGTGTGAAATTTATTCGGGTTTTTCGTTTCTTCATTTGAT
1 ATTAGTCAACCATTTGAGCATGTCATGTGTGAAATTTATTCGGGTTTTTCATTTCTTCATTTGAT
*
15488 GTGTTTTATATTAATTT
66 GTGTTTTATACTAATTT
15505 AATTGTTCGT
Statistics
Matches: 271, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
110 97 0.36
112 5 0.02
113 1 0.00
114 102 0.38
115 66 0.24
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.49
Consensus pattern (115 bp):
ATTAGTCAACCATTTGAGCATGTCATGTGTGAAATTTATTCGGGTTTTTCATTTCTTCATTTGAT
GTGTTTTATACTAATTTGATTTTACTATGATGAATTATGATGTGCTAGTC
Found at i:17052 original size:40 final size:40
Alignment explanation
Indices: 17000--17105 Score: 160
Period size: 40 Copynumber: 2.6 Consensus size: 40
16990 ACATGAACTT
*
17000 AAACATGAACCCTAAACTTCAAACCTCGACCTCGATATCA
1 AAACATGAACCCTAAACTTCAAACCTCAACCTCGATATCA
*
17040 AAACATGAACCCTAAACTTCAAACCTCAACCTCGATATCG
1 AAACATGAACCCTAAACTTCAAACCTCAACCTCGATATCA
* *
17080 AATCATGAACCTTGAAAC-TCAAACCT
1 AAACATGAACCCT-AAACTTCAAACCT
17106 TAAATCATGA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 57 0.93
41 4 0.07
ACGTcount: A:0.41, C:0.31, G:0.08, T:0.21
Consensus pattern (40 bp):
AAACATGAACCCTAAACTTCAAACCTCAACCTCGATATCA
Done.