Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014875.1 Kokia drynarioides strain JFW-HI SEQ_129918, 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: 10100
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 237 characters in sequence are not A, C, G, or T
Found at i:1591 original size:123 final size:123
Alignment explanation
Indices: 1292--1632 Score: 522
Period size: 123 Copynumber: 2.8 Consensus size: 123
1282 TTCTGCTGTC
* * *
1292 TTTCCTTTTTATTTAATATCTGATATTAAAATGGAAATATTCCTTTAAAGAAATATATGTAAGGT
1 TTTCC-TTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGT
*
1357 TTATTAAAACATTATATCCTTTCCAAAAAGGATATTAACTTCCATGTTTTCAATATTTAA
65 TTATTAAAACATTATATCCTTTCC-AAAAGGATATTAACTTCCATGTTTTCAATATTCAA
* * * * *
1417 TTTCTTTTTATAAAATATGTCTTATTAAAATGGAAATATT-CTCTTAGAGAAATATATGGAAGGT
1 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCT-TTAAAGAAATATATGGAAGGT
* * *
1481 TTATTAAAACATTATATCATTTCCAAAATGATATTAACTTCCATGTTTTTAATATTCAA
65 TTATTAAAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTCAATATTCAA
*
1540 TTTCCTTTTATATAATATCTCATATTAAAATGGAAACATTCCTTTAAAGAAATATATGGAAGGTT
1 TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGTT
*
1605 TATTAAAATATTATATCCTTTCCAAAAG
66 TATTAAAACATTATATCCTTTCCAAAAG
1633 TTTAAAGAAA
Statistics
Matches: 193, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
123 115 0.60
124 74 0.38
125 4 0.02
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (123 bp):
TTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGTT
TATTAAAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTCAATATTCAA
Found at i:1637 original size:51 final size:51
Alignment explanation
Indices: 1582--1681 Score: 200
Period size: 51 Copynumber: 2.0 Consensus size: 51
1572 GAAACATTCC
1582 TTTAAAGAAATATATGGAAGGTTTATTAAAATATTATATCCTTTCCAAAAG
1 TTTAAAGAAATATATGGAAGGTTTATTAAAATATTATATCCTTTCCAAAAG
1633 TTTAAAGAAATATATGGAAGGTTTATTAAAATATTATATCCTTTCCAAA
1 TTTAAAGAAATATATGGAAGGTTTATTAAAATATTATATCCTTTCCAAA
1682 TGGATATTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (51 bp):
TTTAAAGAAATATATGGAAGGTTTATTAAAATATTATATCCTTTCCAAAAG
Found at i:7182 original size:19 final size:20
Alignment explanation
Indices: 7158--7200 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
7148 TAGATTTATT
7158 CTTAATTAATC-TAAATTAA
1 CTTAATTAATCATAAATTAA
*
7177 CTTAATTAATCATTAATTAA
1 CTTAATTAATCATAAATTAA
7197 -TTAA
1 CTTAA
7201 ATTATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (20 bp):
CTTAATTAATCATAAATTAA
Found at i:7196 original size:15 final size:13
Alignment explanation
Indices: 7159--7204 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 13
7149 AGATTTATTC
7159 TTAATTAATCTAAA
1 TTAATTAAT-TAAA
7173 TTAACTTAATTAATCA
1 TTAA-TTAATTAA--A
7189 TTAATTAATTAAA
1 TTAATTAATTAAA
7202 TTA
1 TTA
7205 TAATCACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 4 0.14
14 7 0.24
15 13 0.45
16 5 0.17
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAATTAAA
Found at i:8829 original size:24 final size:24
Alignment explanation
Indices: 8800--8850 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
8790 GTTTACACAT
8800 TTTTAGCTTAGCATTTTAATTTCC
1 TTTTAGCTTAGCATTTTAATTTCC
8824 TTTTAGCTTAGCATTTTAATTTCC
1 TTTTAGCTTAGCATTTTAATTTCC
8848 TTT
1 TTT
8851 GTAATTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTTAGCTTAGCATTTTAATTTCC
Found at i:9027 original size:13 final size:13
Alignment explanation
Indices: 9009--9038 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
8999 TAGTTTTGAA
9009 TTTAATGTTTAAT
1 TTTAATGTTTAAT
*
9022 TTTAATGTTTACT
1 TTTAATGTTTAAT
9035 TTTA
1 TTTA
9039 TTATTGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (13 bp):
TTTAATGTTTAAT
Found at i:9835 original size:32 final size:32
Alignment explanation
Indices: 9787--9863 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
9777 ATTAAAAATC
* *
9787 AAATCAAACTTT-TATGTATA-AAATTATATA-A
1 AAATCAAAATTTATATGTACATAAA-TAT-TACA
*
9818 AAATCAAAATTTATATGTACATAAATATTACT
1 AAATCAAAATTTATATGTACATAAATATTACA
9850 AAATCAAAATTTAT
1 AAATCAAAATTTAT
9864 TTATATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
31 13 0.32
32 24 0.60
33 3 0.08
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.38
Consensus pattern (32 bp):
AAATCAAAATTTATATGTACATAAATATTACA
Done.