Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012928.1 Kokia drynarioides strain JFW-HI SEQ_127945, 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: 48269
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:871 original size:10 final size:10
Alignment explanation
Indices: 856--889 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
846 TGCTCTATTC
856 TTTTTTTCCT
1 TTTTTTTCCT
866 TTTTTTTCCT
1 TTTTTTTCCT
*
876 TTTTTTTTCT
1 TTTTTTTCCT
886 TTTT
1 TTTT
890 CATTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTCCT
Found at i:888 original size:17 final size:18
Alignment explanation
Indices: 868--901 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
858 TTTTTCCTTT
*
868 TTTTTCCTTT-TTTTTTC
1 TTTTTCATTTATTTTTTC
885 TTTTTCATTTATTTTTT
1 TTTTTCATTTATTTTTT
902 TCTGAGCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCATTTATTTTTTC
Found at i:1518 original size:18 final size:18
Alignment explanation
Indices: 1484--1519 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1474 TCCCCATTGT
*
1484 TAAAAATAATAGAGAATA
1 TAAAAATAAAAGAGAATA
*
1502 TAAAAATAAAAGTGAATA
1 TAAAAATAAAAGAGAATA
1520 AATACTGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (18 bp):
TAAAAATAAAAGAGAATA
Found at i:2163 original size:18 final size:18
Alignment explanation
Indices: 2142--2185 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2132 TTCCACAAGA
2142 TCTTCTTTAGAATCTTCT
1 TCTTCTTTAGAATCTTCT
* *
2160 TCTTCTTCAGGATCTTCT
1 TCTTCTTTAGAATCTTCT
2178 TCTTCTTT
1 TCTTCTTT
2186 TTCAACTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.25, G:0.07, T:0.57
Consensus pattern (18 bp):
TCTTCTTTAGAATCTTCT
Found at i:4658 original size:27 final size:28
Alignment explanation
Indices: 4628--4681 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
4618 GCTTGAGGAG
4628 TAATCTGATTCT-GGCTCGAAAGAGCTT
1 TAATCTGATTCTGGGCTCGAAAGAGCTT
*
4655 TAATCTGATTCTGGGCTCGTAAGAGCT
1 TAATCTGATTCTGGGCTCGAAAGAGCT
4682 AACCACTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (28 bp):
TAATCTGATTCTGGGCTCGAAAGAGCTT
Found at i:4701 original size:24 final size:24
Alignment explanation
Indices: 4662--4825 Score: 228
Period size: 24 Copynumber: 6.9 Consensus size: 24
4652 CTTTAATCTG
4662 ATTCTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
4686 ACTT-TGAGCTCGTAAGAGCTAACC
1 A-TTCTGGGCTCGTAAGAGCTAACC
* *
4710 ATTCTGTGCTCATAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
4734 GTTCTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
4758 ATTCTGGGCTCGTAAGAGCTAA-C
1 ATTCTGGGCTCGTAAGAGCTAACC
4781 ATTCTGGGCTCGTAAGAGCT-ACC
1 ATTCTGGGCTCGTAAGAGCTAACC
* *
4804 -TATCTAGGCTCGTATGAGCTAA
1 AT-TCTGGGCTCGTAAGAGCTAA
4826 TTTTTTCTGG
Statistics
Matches: 126, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
22 2 0.02
23 40 0.32
24 82 0.65
25 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.27
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCTAACC
Found at i:8774 original size:24 final size:24
Alignment explanation
Indices: 8743--8905 Score: 159
Period size: 24 Copynumber: 6.8 Consensus size: 24
8733 AATTTGATTT
8743 TGGGCTCGTAAGAGCTAATCATTC
1 TGGGCTCGTAAGAGCTAATCATTC
* *
8767 TGGGCTCGCAAGAGCTAACCATTC
1 TGGGCTCGTAAGAGCTAATCATTC
*
8791 TGGGCTCTTAAGAGCTAA-CATTC
1 TGGGCTCGTAAGAGCTAATCATTC
*
8814 TGGGCTCGTAAGAGCTAA-CCTATC
1 TGGGCTCGTAAGAGCTAATCAT-TC
* * **
8838 TGGGCTCATATGAGCTAATTTTTTC
1 TGGGCTCGTAAGAGCTAA-TCATTC
* * **
8863 TGGGCTCATATGAGCTAATTTTTTC
1 TGGGCTCGTAAGAGCTAA-TCATTC
**
8888 TGGGCTCGTGTGAGCTAA
1 TGGGCTCGTAAGAGCTAA
8906 ATTTTTTAAA
Statistics
Matches: 124, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
23 24 0.19
24 56 0.45
25 43 0.35
26 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (24 bp):
TGGGCTCGTAAGAGCTAATCATTC
Found at i:8827 original size:47 final size:48
Alignment explanation
Indices: 8743--8856 Score: 169
Period size: 47 Copynumber: 2.4 Consensus size: 48
8733 AATTTGATTT
*
8743 TGGGCTCGTAAGAGCTAATCATTCTGGGCTCGCAAGAGCTAACC-ATTC
1 TGGGCTCATAAGAGCTAATCATTCTGGGCTCGCAAGAGCTAACCTA-TC
* *
8791 TGGGCTCTTAAGAGCTAA-CATTCTGGGCTCGTAAGAGCTAACCTATC
1 TGGGCTCATAAGAGCTAATCATTCTGGGCTCGCAAGAGCTAACCTATC
*
8838 TGGGCTCATATGAGCTAAT
1 TGGGCTCATAAGAGCTAAT
8857 TTTTTCTGGG
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
47 42 0.70
48 18 0.30
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (48 bp):
TGGGCTCATAAGAGCTAATCATTCTGGGCTCGCAAGAGCTAACCTATC
Found at i:8868 original size:25 final size:25
Alignment explanation
Indices: 8836--8912 Score: 127
Period size: 25 Copynumber: 3.0 Consensus size: 25
8826 AGCTAACCTA
8836 TCTGGGCTCATATGAGCTAATTTTT
1 TCTGGGCTCATATGAGCTAATTTTT
8861 TCTGGGCTCATATGAGCTAATTTTT
1 TCTGGGCTCATATGAGCTAATTTTT
* *
8886 TCTGGGCTCGTGTGAGCTAAATTTTT
1 TCTGGGCTCATATGAGCT-AATTTTT
8912 T
1 T
8913 AAAGACTCGG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 41 0.84
26 8 0.16
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.44
Consensus pattern (25 bp):
TCTGGGCTCATATGAGCTAATTTTT
Found at i:13046 original size:26 final size:26
Alignment explanation
Indices: 12986--13037 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
12976 ATTTTGGGCT
*
12986 TAATTTTAGACACGTTCATGCAGCGA
1 TAATTTTGGACACGTTCATGCAGCGA
*
13012 TAATTTTGGACATGTTCATGCAGCGA
1 TAATTTTGGACACGTTCATGCAGCGA
13038 CATTCTTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (26 bp):
TAATTTTGGACACGTTCATGCAGCGA
Found at i:15012 original size:23 final size:22
Alignment explanation
Indices: 14981--15024 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
14971 AAAGAAATAA
*
14981 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
15003 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
15025 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:20207 original size:12 final size:12
Alignment explanation
Indices: 20192--20216 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20182 ATTAAAGAAG
20192 TAATAGCATTCA
1 TAATAGCATTCA
20204 TAATAGCATTCA
1 TAATAGCATTCA
20216 T
1 T
20217 CATGATAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:23879 original size:248 final size:248
Alignment explanation
Indices: 23430--23927 Score: 852
Period size: 248 Copynumber: 2.0 Consensus size: 248
23420 TCACAAACAT
* *
23430 TTAAACTCTCATTGCATCAATGTGGAGCACATTGTGAAAAGTTCACTTGAATAAACAGTAAAGCA
1 TTAAACTCCCATTGCATCAATGTGGAGCACATTGTGAAAAGTCCACTTGAATAAACAGTAAAGCA
*
23495 TTAGATTAACCATAAATCATTCATCAAAATATAACAAAATATTATCCAAAAAAATAACATTCATA
66 TTAGATTAACCATAAATCATTCATCAAAATAAAACAAAATATTATCCAAAAAAATAACATTCATA
* * *
23560 ACCGTTTCAACGAACTCAATTAAAAATAACTAAAAACCAAGGATGAACATAGGAGCTGTTGTCAC
131 ACCATTTCAACAAACTCAATTAAAAATAACTAAAAACCAAGGATGAACATAGGAGCTGCTGTCAC
*
23625 CAGCCTCCTCCTTCTCCGGCAATTTGGGTAGATCTAGAGGGTAGGGCATCTTC
196 CAGCCTCCTCCTTCTCCGGCAATTTGGCTAGATCTAGAGGGTAGGGCATCTTC
23678 TTAAACTCCCATTGCATCAATGTGGAGCACATTGTGAAAAGTCCACTTGAATAAACAGTAAAGCA
1 TTAAACTCCCATTGCATCAATGTGGAGCACATTGTGAAAAGTCCACTTGAATAAACAGTAAAGCA
*
23743 TTATATTAACCATAAATCATTCATCAAAATAAAACAAAATATTATCCAAAAAAATAACATTCATA
66 TTAGATTAACCATAAATCATTCATCAAAATAAAACAAAATATTATCCAAAAAAATAACATTCATA
* * *
23808 ACCATTTCAACAAACTCAATTAAAAATAACTGAAAACCAAGGATGAACATAGGAGTTGCTGTCAG
131 ACCATTTCAACAAACTCAATTAAAAATAACTAAAAACCAAGGATGAACATAGGAGCTGCTGTCAC
*** * *
23873 CAGCCTCCTCCTTCTCCGGTGCTTTGGCTAGATCTAGAGGGTAGTGCGTCTTC
196 CAGCCTCCTCCTTCTCCGGCAATTTGGCTAGATCTAGAGGGTAGGGCATCTTC
23926 TT
1 TT
23928 CCTCATGTTC
Statistics
Matches: 234, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
248 234 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (248 bp):
TTAAACTCCCATTGCATCAATGTGGAGCACATTGTGAAAAGTCCACTTGAATAAACAGTAAAGCA
TTAGATTAACCATAAATCATTCATCAAAATAAAACAAAATATTATCCAAAAAAATAACATTCATA
ACCATTTCAACAAACTCAATTAAAAATAACTAAAAACCAAGGATGAACATAGGAGCTGCTGTCAC
CAGCCTCCTCCTTCTCCGGCAATTTGGCTAGATCTAGAGGGTAGGGCATCTTC
Found at i:32056 original size:85 final size:85
Alignment explanation
Indices: 31958--32124 Score: 316
Period size: 85 Copynumber: 2.0 Consensus size: 85
31948 AAAACCATTA
31958 TTTTTGTCTTTTATATGTTGGGAAAAAATCAACTTTTAGGAATACCTTGAATTAATTTGATTTTA
1 TTTTTGTCTTTTATATGTTGGGAAAAAATCAACTTTTAGGAATACCTTGAATTAATTTGATTTTA
32023 AAAGAATTTTTGAAGTCTAT
66 AAAGAATTTTTGAAGTCTAT
* *
32043 TTTTTTTCTTTTATATGTTGGGCAAAAATCAACTTTTAGGAATACCTTGAATTAATTTGATTTTA
1 TTTTTGTCTTTTATATGTTGGGAAAAAATCAACTTTTAGGAATACCTTGAATTAATTTGATTTTA
32108 AAAGAATTTTTGAAGTC
66 AAAGAATTTTTGAAGTC
32125 AGAAGAACTT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (85 bp):
TTTTTGTCTTTTATATGTTGGGAAAAAATCAACTTTTAGGAATACCTTGAATTAATTTGATTTTA
AAAGAATTTTTGAAGTCTAT
Done.