Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013667.1 Kokia drynarioides strain JFW-HI SEQ_128695, 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: 12179
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:111 original size:9 final size:9
Alignment explanation
Indices: 94--134 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
84 TCTTTTTTTC
*
94 CTTCTCCTT
1 CTTCCCCTT
103 CTTCCCCTT
1 CTTCCCCTT
112 CTTCCCCTT
1 CTTCCCCTT
* *
121 CTTCTCATT
1 CTTCCCCTT
130 CTTCC
1 CTTCC
135 TTCTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (9 bp):
CTTCCCCTT
Found at i:145 original size:4 final size:4
Alignment explanation
Indices: 138--176 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
128 TTCTTCCTTC
*
138 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
177 CTTCATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:165 original size:21 final size:20
Alignment explanation
Indices: 136--180 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
126 CATTCTTCCT
136 TCTTCTTTCTTTCTTTCTTTC
1 TCTTCTTTCTTTCTTT-TTTC
*
157 TCTTTTTTCTTTCTTTTTTC
1 TCTTCTTTCTTTCTTTTTTC
177 -CTTC
1 TCTTC
181 ATTTTTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 4 0.18
21 15 0.68
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (20 bp):
TCTTCTTTCTTTCTTTTTTC
Found at i:173 original size:11 final size:11
Alignment explanation
Indices: 135--187 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
125 TCATTCTTCC
*
135 TTCTTCTTTCT
1 TTCTTTTTTCT
146 TTCTTTCTTTC-
1 TTCTTT-TTTCT
157 -TCTTTTTTCT
1 TTCTTTTTTCT
*
167 TTCTTTTTTCC
1 TTCTTTTTTCT
*
178 TTCATTTTTC
1 TTCTTTTTTC
188 GTTGGTCCCC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 4 0.11
10 5 0.14
11 23 0.64
12 4 0.11
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:185 original size:21 final size:21
Alignment explanation
Indices: 131--185 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 21
121 CTTCTCATTC
131 TTCCTTCTTCTTTCTTTCTTTCT
1 TTCCTTC-T-TTTCTTTCTTTCT
154 TTCTCTT-TTTTCTTTCTTT-T
1 TTC-CTTCTTTTCTTTCTTTCT
174 TTCCTTCATTTT
1 TTCCTTC-TTTT
186 TCGTTGGTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.10
20 4 0.14
21 15 0.52
22 1 0.03
23 3 0.10
24 3 0.10
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (21 bp):
TTCCTTCTTTTCTTTCTTTCT
Found at i:565 original size:17 final size:17
Alignment explanation
Indices: 543--577 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
533 GATTCACAGT
543 TACCCCACAAACAACTA
1 TACCCCACAAACAACTA
* *
560 TACCCCCCAAATAACTA
1 TACCCCACAAACAACTA
577 T
1 T
578 TTTCATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.40, G:0.00, T:0.17
Consensus pattern (17 bp):
TACCCCACAAACAACTA
Found at i:771 original size:3 final size:3
Alignment explanation
Indices: 763--791 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
753 TTTCTTTTCT
763 TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
792 AAAACGGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3875 original size:14 final size:14
Alignment explanation
Indices: 3856--3882 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3846 TAACAAATAC
3856 TAAATTTTTTATTT
1 TAAATTTTTTATTT
3870 TAAATTTTTTATT
1 TAAATTTTTTATT
3883 AATTATATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TAAATTTTTTATTT
Found at i:5498 original size:48 final size:48
Alignment explanation
Indices: 5427--5521 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
5417 TACCACGGCA
**
5427 TGCTACACTTGCCGTGCTTGATCATTTCAGCGGTTAACTATGTAATCG
1 TGCTACACTTGCCGTGCCCGATCATTTCAGCGGTTAACTATGTAATCG
*
5475 TGCTACACTTGCCGTGCCCGATCATTTCAGTGGTTAACTATGTAATC
1 TGCTACACTTGCCGTGCCCGATCATTTCAGCGGTTAACTATGTAATC
5522 TATCAAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (48 bp):
TGCTACACTTGCCGTGCCCGATCATTTCAGCGGTTAACTATGTAATCG
Found at i:5986 original size:17 final size:17
Alignment explanation
Indices: 5956--6037 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 17
5946 ATTCCCTTTC
*
5956 AATTTATTTTAAAATTA
1 AATTTATTTAAAAATTA
*
5973 AATTTGTTTAAAAATTTA
1 AATTTATTTAAAAA-TTA
* *
5991 AATTTATTTTAAATTTA
1 AATTTATTTAAAAATTA
*
6008 AATTTATTTTAAAATTTA
1 AATTTA-TTTAAAAATTA
6026 AATTTAATTTAA
1 AATTT-ATTTAA
6038 GTTTAAAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
17 21 0.38
18 34 0.61
19 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (17 bp):
AATTTATTTAAAAATTA
Found at i:6002 original size:35 final size:35
Alignment explanation
Indices: 5956--6067 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
5946 ATTCCCTTTC
*
5956 AATTTATTTTAAAATTAAATTTGTTTAAAAATTTA
1 AATTTATTTTAAAATTAAATTTATTTAAAAATTTA
* *
5991 AATTTATTTTAAATTTAAATTTATTTTAAAATTTA
1 AATTTATTTTAAAATTAAATTTATTTAAAAATTTA
* ** * **
6026 AATTTAATTTAAGTTTAAAATTATTTTCAAATTTA
1 AATTTATTTTAAAATTAAATTTATTTAAAAATTTA
6061 AAGTTTA
1 AA-TTTA
6068 AAATAAATAA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 65 0.94
36 4 0.06
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (35 bp):
AATTTATTTTAAAATTAAATTTATTTAAAAATTTA
Found at i:6030 original size:24 final size:24
Alignment explanation
Indices: 5998--6047 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5988 TTAAATTTAT
*
5998 TTTAAATTTAAATTT-ATTTTAAAA
1 TTTAAATTT-AATTTAAGTTTAAAA
6022 TTTAAATTTAATTTAAGTTTAAAA
1 TTTAAATTTAATTTAAGTTTAAAA
6046 TT
1 TT
6048 ATTTTCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTAAATTTAATTTAAGTTTAAAA
Found at i:6044 original size:17 final size:18
Alignment explanation
Indices: 5956--6067 Score: 140
Period size: 17 Copynumber: 6.3 Consensus size: 18
5946 ATTCCCTTTC
5956 AATTTATTTTAAAA-TTA
1 AATTTATTTTAAAATTTA
* *
5973 AATTTGTTTAAAAATTTA
1 AATTTATTTTAAAATTTA
5991 AATTTATTTT-AAATTTA
1 AATTTATTTTAAAATTTA
6008 AATTTATTTTAAAATTTA
1 AATTTATTTTAAAATTTA
* *
6026 AATTTAATTT-AAGTTTA
1 AATTTATTTTAAAATTTA
* *
6043 AAATTATTTTCAAATTTA
1 AATTTATTTTAAAATTTA
6061 AAGTTTA
1 AA-TTTA
6068 AAATAAATAA
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
17 43 0.53
18 35 0.43
19 3 0.04
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (18 bp):
AATTTATTTTAAAATTTA
Found at i:6742 original size:18 final size:19
Alignment explanation
Indices: 6708--6749 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
6698 AAAACGTTTC
*
6708 AATAACTTTTATTAATATT
1 AATAACTGTTATTAATATT
6727 AATAACTGTT-TTAATATT
1 AATAACTGTTATTAATATT
6745 AATAA
1 AATAA
6750 TAATACTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
AATAACTGTTATTAATATT
Found at i:6839 original size:15 final size:15
Alignment explanation
Indices: 6819--6864 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
6809 AAATGTTTTG
6819 ATATTAATAATAATA
1 ATATTAATAATAATA
* *
6834 ATATTAATAATTATT
1 ATATTAATAATAATA
6849 A-ATTAATAATTAATA
1 ATATTAATAA-TAATA
6864 A
1 A
6865 AAAAAGGGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTAATAATAATA
Found at i:6851 original size:7 final size:7
Alignment explanation
Indices: 6826--6864 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
6816 TTGATATTAA
6826 TAATAA-
1 TAATAAT
6832 TAAT-AT
1 TAATAAT
6838 TAATAAT
1 TAATAAT
*
6845 TATTAAT
1 TAATAAT
6852 TAATAAT
1 TAATAAT
6859 TAATAA
1 TAATAA
6865 AAAAAGGGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 1 0.03
6 8 0.28
7 20 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATAAT
Found at i:8129 original size:30 final size:28
Alignment explanation
Indices: 8041--8488 Score: 309
Period size: 30 Copynumber: 15.1 Consensus size: 28
8031 GAGGTCCCTA
*
8041 AACTATCCAAAAAATACCATTTTACCCTCG
1 AACT-TCC-AAAAATACCATTTTACCCCCG
* *
8071 AACTTCCAAAAATCCCATTTTTGA-CCCCA
1 AACTTCCAAAAATACCA-TTTT-ACCCCCG
* *
8100 AACCTTCCAGAAAGTACCATTTTACCCCCA
1 AA-CTTCCA-AAAATACCATTTTACCCCCG
8130 AACTTCCAAAAATACCATTTTTGA-CCCCG
1 AACTTCCAAAAATACCA-TTTT-ACCCCCG
*
8159 AACCTTCCAAAAATTACCATTTTACCCCCA
1 AA-CTTCCAAAAA-TACCATTTTACCCCCG
* *
8189 AACTTCCAAAAGTCCCATTTTTGA-CCCCG
1 AACTTCCAAAAATACCA-TTTT-ACCCCCG
*
8218 ATTCTTCCAAAAATTACCATTTTACCCCCCG
1 A-ACTTCCAAAAA-TACCATTTTA-CCCCCG
** *
8249 AACTTCCAAAGGTCCCATTTTTTA-CCCCG
1 AACTTCCAAAAATACCA--TTTTACCCCCG
8278 AACTTTCCAAGAAAAATACCATTTTACCCCCG
1 AAC-TTCC---AAAAATACCATTTTACCCCCG
** *
8310 AAC-TCCAAAGGTCCCATTTTTTA-CCCCG
1 AACTTCCAAAAATACCA--TTTTACCCCCG
8338 AACTTTCCAAAAATTACCATTTTACCCCCG
1 AAC-TTCCAAAAA-TACCATTTTACCCCCG
* * *
8368 AACTTCCAAAAATCCCATTTTTGA-CACCA
1 AACTTCCAAAAATACCA-TTTT-ACCCCCG
**
8397 AACCTTCCAAAAAGTACCATTTTACCACTCTA
1 AA-CTTCCAAAAA-TACCATTTTACC-C-CCG
* **
8429 AACTTCCAAAAATCCCATTTTGA-CCCTA
1 AACTTCCAAAAATACCATTTT-ACCCCCG
* *
8457 AACCTTCAAAAAATTACCCTTTTACCCCCG
1 AA-CTTCCAAAAA-TACCATTTTACCCCCG
8487 AA
1 AA
8489 TGTTTAAAAT
Statistics
Matches: 339, Mismatches: 39, Indels: 80
0.74 0.09 0.17
Matches are distributed among these distances:
27 7 0.02
28 38 0.11
29 101 0.30
30 123 0.36
31 51 0.15
32 12 0.04
33 7 0.02
ACGTcount: A:0.34, C:0.33, G:0.05, T:0.28
Consensus pattern (28 bp):
AACTTCCAAAAATACCATTTTACCCCCG
Found at i:8276 original size:60 final size:59
Alignment explanation
Indices: 8046--8488 Score: 566
Period size: 59 Copynumber: 7.5 Consensus size: 59
8036 CCCTAAACTA
* * *
8046 TCCAAAAAATACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * * *
8105 TCCAGAAAGTACCATTTTACCCCCAAACTTCCAAAAATACCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * **
8164 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAGTCCCATTTTTGACCCCGATTCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
** * *
8223 TCCAAAAATTACCATTTTACCCCCCGAACTTCCAAAGGTCCCATTTTTTACCCCGAACTT
1 TCCAAAAATTACCATTTTA-CCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* ** * *
8283 TCCAAGAAAAATACCATTTTACCCCCGAAC-TCCAAAGGTCCCATTTTTTACCCCGAACTT
1 TCC-A-AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* *
8343 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACACCAAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* ** **
8402 TCCAAAAAGTACCATTTTACCACTCTAAACTTCCAAAAATCCCA-TTTTGACCCTAAACCT
1 TCCAAAAATTACCATTTTACC-C-CCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* *
8462 TCAAAAAATTACCCTTTTACCCCCGAA
1 TCCAAAAATTACCATTTTACCCCCGAA
8489 TGTTTAAAAT
Statistics
Matches: 342, Mismatches: 36, Indels: 13
0.87 0.09 0.03
Matches are distributed among these distances:
58 26 0.08
59 171 0.50
60 103 0.30
61 28 0.08
62 14 0.04
ACGTcount: A:0.33, C:0.34, G:0.05, T:0.28
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
Done.