Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013994.1 Kokia drynarioides strain JFW-HI SEQ_129025, 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: 33364
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:5747 original size:29 final size:31
Alignment explanation
Indices: 5679--5747 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 31
5669 TAAATATTTA
5679 ATATTTAA-AAATTACATATAAAGAAAAAAT
1 ATATTTAACAAATTACATATAAAGAAAAAAT
** *
5709 ATATCAAACAAATTA-A-AT-AAGAGTAAAAT
1 ATATTTAACAAATTACATATAAAGA-AAAAAT
5738 ATATTTAACA
1 ATATTTAACA
5748 CAATGATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 4 0.12
29 15 0.47
30 7 0.22
31 6 0.19
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (31 bp):
ATATTTAACAAATTACATATAAAGAAAAAAT
Found at i:5810 original size:28 final size:29
Alignment explanation
Indices: 5770--5831 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
5760 CAAAAATATA
* * *
5770 TAATTTCATTATATAATTACAT-ATTTAT
1 TAATTTCATTATATAAATAAATAAGTTAT
5798 TAATTT-ATATATATAAATAAATAAGTTAT
1 TAATTTCAT-TATATAAATAAATAAGTTAT
5827 TAATT
1 TAATT
5832 AAAAATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 2 0.07
28 17 0.59
29 10 0.34
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (29 bp):
TAATTTCATTATATAAATAAATAAGTTAT
Found at i:5906 original size:22 final size:22
Alignment explanation
Indices: 5866--5910 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5856 TATATAAAAT
*
5866 ATATTTTTTATTATATAATTAA
1 ATATTTTTAATTATATAATTAA
5888 ATATTTATTAATTAT-TAATTAA
1 ATATTT-TTAATTATATAATTAA
5910 A
1 A
5911 AATTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATTTTTAATTATATAATTAA
Found at i:10057 original size:24 final size:24
Alignment explanation
Indices: 9994--10060 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
9984 GTAATGATCA
* *
9994 TTGTCTTCATCTTCACCTCTACCC
1 TTGTCTTCATCTTCATCTCGACCC
* *
10018 CTGTGTTCATCTTCATCTCGACCC
1 TTGTCTTCATCTTCATCTCGACCC
10042 TTGTCTTCATCTTCATCTC
1 TTGTCTTCATCTTCATCTC
10061 CGCCCCCGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.12, C:0.37, G:0.07, T:0.43
Consensus pattern (24 bp):
TTGTCTTCATCTTCATCTCGACCC
Found at i:10071 original size:24 final size:24
Alignment explanation
Indices: 9995--10072 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
9985 TAATGATCAT
* **
9995 TGTCTTCATCTTCACCTCTACCCC
1 TGTCTTCATCTTCATCTCCGCCCC
* *
10019 TGTGTTCATCTTCATCT-CGACCCT
1 TGTCTTCATCTTCATCTCCG-CCCC
10043 TGTCTTCATCTTCATCTCCGCCCC
1 TGTCTTCATCTTCATCTCCGCCCC
*
10067 CGTCTT
1 TGTCTT
10073 TGTCTCTATC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.10, C:0.41, G:0.09, T:0.40
Consensus pattern (24 bp):
TGTCTTCATCTTCATCTCCGCCCC
Found at i:12165 original size:7 final size:7
Alignment explanation
Indices: 12153--12197 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
12143 GCAATATTTC
12153 TTTCTCT
1 TTTCTCT
12160 TTTCTCT
1 TTTCTCT
12167 TTTCTCT
1 TTTCTCT
*
12174 TTTTTC-
1 TTTCTCT
12180 TTT-TCT
1 TTTCTCT
12186 TTTCT-T
1 TTTCTCT
12192 TTTCTC
1 TTTCTC
12198 ATTCAACATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
5 2 0.06
6 12 0.35
7 20 0.59
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTCTCT
Found at i:21085 original size:37 final size:37
Alignment explanation
Indices: 21044--21121 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
21034 CTATCGGATA
*
21044 TCGATCCCATAAGGAATGAGTTCTTTATGTGTATATG
1 TCGATCCCATAAGGAATGAGTTCTTGATGTGTATATG
* *
21081 TCGATCCCATAGGGAATGGGTTCTTGATGTGTATATG
1 TCGATCCCATAAGGAATGAGTTCTTGATGTGTATATG
21118 TCGA
1 TCGA
21122 GGCAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (37 bp):
TCGATCCCATAAGGAATGAGTTCTTGATGTGTATATG
Found at i:25475 original size:18 final size:19
Alignment explanation
Indices: 25442--25482 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
25432 ATTAACAAAA
* *
25442 TAAAATAATTTTAAAATTT
1 TAAAATAATTTAAAAACTT
25461 TAAAA-AATTTAAAAACTT
1 TAAAATAATTTAAAAACTT
25479 TAAA
1 TAAA
25483 CTTAACTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAATAATTTAAAAACTT
Found at i:30853 original size:12 final size:13
Alignment explanation
Indices: 30826--30858 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
30816 TAGTAAGTGA
30826 AAAATAATACATT
1 AAAATAATACATT
30839 AAAATAATA-ATT
1 AAAATAATACATT
*
30851 AAAGTAAT
1 AAAATAAT
30859 TTAAAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (13 bp):
AAAATAATACATT
Found at i:31310 original size:59 final size:59
Alignment explanation
Indices: 31239--31568 Score: 283
Period size: 59 Copynumber: 5.5 Consensus size: 59
31229 CCATTGCTTT
* * * *
31239 TTTTGTCAGATAAAAAATA-CAAATTTTTTTGTGTTGGTCATACAATGGCCGACACCCC
1 TTTTCTCAGATAAAAAATATCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCC
* * * *** * * *
31297 TATTTATCTGATAAAAAAAATTGCATTTTTTGAGTGTCGACCATGCAATGGTCGACACCCCC
1 T-TTTCTCAGATAAAAAATATCAAATTTTTTG-GTGTTGGCCATGCAATGGCCGACA-CCCC
* * *
31359 TTTT-TGAGA-AAAAAAAATTCAAAATTTTTTGGTGTTGGCCATACAATGGCCGACACCCCC
1 TTTTCTCAGATAAAAAATA-TC-AAATTTTTTGGTGTTGGCCATGCAATGGCCGACA-CCCC
* * * *
31419 TTTTCTCGGATAAAAAA-ATTATATTTTTGGGTGTTGGCCATGC-ATGGCCGACACCCC
1 TTTTCTCAGATAAAAAATATCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCC
* * * * * *
31476 TTTTTTCAGAAAAAAAAAATCAAAATTTTTTGGTGTTGGTCATGCAATGGTCGACACCTCT
1 TTTTCTCAGATAAAAAATATC-AAATTTTTTGGTGTTGGCCATGCAATGGCCGACACC-CC
* *
31537 TTTTCTCGGATAAAAAATTTTCAAAATTTTTT
1 TTTTCTCAGATAAAAAA-TATC-AAATTTTTT
31569 ATCAGATAAA
Statistics
Matches: 218, Mismatches: 41, Indels: 22
0.78 0.15 0.08
Matches are distributed among these distances:
57 18 0.08
58 13 0.06
59 63 0.29
60 52 0.24
61 49 0.22
62 23 0.11
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (59 bp):
TTTTCTCAGATAAAAAATATCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCC
Found at i:31325 original size:60 final size:59
Alignment explanation
Indices: 31261--31553 Score: 281
Period size: 61 Copynumber: 4.9 Consensus size: 59
31251 AAAAATACAA
* * * * * *
31261 ATTTTTTTGTGTTGGTCATACAATGGCCGACACCCCTATTTATCTGATAAAAAAAATTGC
1 ATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCT-TTTCTCGGATAAAAAAAATTAC
* * * *
31321 ATTTTTTGAGTGTCGACCATGCAATGGTCGACACCCCCTTTT-T-GAGA-AAAAAAAATTCAAA
1 ATTTTTTG-GTGTTGGCCATGCAATGGCCGACA-CCCCTTTTCTCG-GATAAAAAAAATT--AC
* *
31382 ATTTTTTGGTGTTGGCCATACAATGGCCGACACCCCCTTTTCTCGGAT-AAAAAAATTAT
1 ATTTTTTGGTGTTGGCCATGCAATGGCCGACA-CCCCTTTTCTCGGATAAAAAAAATTAC
* * * * * *
31441 ATTTTTGGGTGTTGGCCATGC-ATGGCCGACACCCCTTTTTTCAGAAAAAAAAAATCAAA
1 ATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTCTCGGATAAAAAAAAT-TAC
* * *
31500 ATTTTTTGGTGTTGGTCATGCAATGGTCGACACCTCTTTTTCTCGGATAAAAAA
1 ATTTTTTGGTGTTGGCCATGCAATGGCCGACACC-CCTTTTCTCGGATAAAAAA
31554 TTTTCAAAAT
Statistics
Matches: 193, Mismatches: 28, Indels: 23
0.79 0.11 0.09
Matches are distributed among these distances:
57 12 0.06
58 18 0.09
59 50 0.26
60 50 0.26
61 57 0.30
62 6 0.03
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (59 bp):
ATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTCTCGGATAAAAAAAATTAC
Found at i:31509 original size:118 final size:119
Alignment explanation
Indices: 31250--31553 Score: 400
Period size: 118 Copynumber: 2.5 Consensus size: 119
31240 TTTGTCAGAT
* * *
31250 AAAAAAT-ACAAATTTTTTTGTGTTGGTCATACAATGGCCGACA-CCCCTATTTATCTGATAAAA
1 AAAAAATCA-AAATTTTTTGGTGTTGGTCATACAATGGCCGACACCCCCT-TTTCTCGGAT-AAA
* *
31313 AAAATTGCATTTTTTGAGTGTCGACCATGCAATGGTCGACACCCCCTTTTTGAGAAAA
63 AAAATT-CATTTTTTGAGTGTCGACCATGCAATGGCCGACACCCCCTTTTTCAGAAAA
* *
31371 AAAAATTCAAAATTTTTTGGTGTTGGCCATACAATGGCCGACACCCCCTTTTCTCGGATAAAAAA
1 AAAAAATCAAAATTTTTTGGTGTTGGTCATACAATGGCCGACACCCCCTTTTCTCGGATAAAAAA
* * * *
31436 ATT-ATATTTTTGGGTGTTGGCCATGC-ATGGCCGACACCCCTTTTTTCAGAAAA
66 ATTCAT-TTTTTGAGTGTCGACCATGCAATGGCCGACACCCCCTTTTTCAGAAAA
* * * *
31489 AAAAAATCAAAATTTTTTGGTGTTGGTCATGCAATGGTCGACACCTCTTTTTCTCGGATAAAAAA
1 AAAAAATCAAAATTTTTTGGTGTTGGTCATACAATGGCCGACACCCCCTTTTCTCGGATAAAAAA
31554 TTTTCAAAAT
Statistics
Matches: 163, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
118 85 0.52
119 17 0.10
120 9 0.06
121 46 0.28
122 6 0.04
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (119 bp):
AAAAAATCAAAATTTTTTGGTGTTGGTCATACAATGGCCGACACCCCCTTTTCTCGGATAAAAAA
ATTCATTTTTTGAGTGTCGACCATGCAATGGCCGACACCCCCTTTTTCAGAAAA
Found at i:31576 original size:28 final size:28
Alignment explanation
Indices: 31536--31596 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
31526 TCGACACCTC
* * *
31536 TTTTTCTCGGATAAAAAATTTTCAAAAT
1 TTTTTATCAGATAAAAAATTTACAAAAT
*
31564 TTTTTATCAGATAAAAAATTTACAAATT
1 TTTTTATCAGATAAAAAATTTACAAAAT
31592 TTTTT
1 TTTTT
31597 GGTGTTGGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (28 bp):
TTTTTATCAGATAAAAAATTTACAAAAT
Done.