Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012553.1 Kokia drynarioides strain JFW-HI SEQ_127562, 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: 31649
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Found at i:1159 original size:20 final size:20
Alignment explanation
Indices: 1134--1182 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1124 ATGCACATGA
1134 GTATCGATATTTTTAAGA-AG
1 GTATCGATATTTTTAA-ACAG
*
1154 GTATCGATATTTTTAAACTG
1 GTATCGATATTTTTAAACAG
1174 GTATCGATA
1 GTATCGATA
1183 CCAAATCTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (20 bp):
GTATCGATATTTTTAAACAG
Found at i:7238 original size:11 final size:11
Alignment explanation
Indices: 7222--7251 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
7212 CACATGGCTG
7222 ACGTGGCACTA
1 ACGTGGCACTA
*
7233 ACGTGGCACTG
1 ACGTGGCACTA
7244 ACGTGGCA
1 ACGTGGCA
7252 GTGCTGACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.23, C:0.27, G:0.33, T:0.17
Consensus pattern (11 bp):
ACGTGGCACTA
Found at i:7260 original size:14 final size:14
Alignment explanation
Indices: 7241--7268 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
7231 TAACGTGGCA
7241 CTGACGTGGCAGTG
1 CTGACGTGGCAGTG
7255 CTGACGTGGCAGTG
1 CTGACGTGGCAGTG
7269 GCGGCTGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.43, T:0.21
Consensus pattern (14 bp):
CTGACGTGGCAGTG
Found at i:7918 original size:50 final size:49
Alignment explanation
Indices: 7854--8155 Score: 207
Period size: 49 Copynumber: 6.1 Consensus size: 49
7844 ATCTCAATCC
* * * * *
7854 TTCCCATCACATCTTCTAAGGAACCAGGTTTGCCGTTGCGGTCGTAACCT
1 TTCCCTTCAAATCTTCTAAGGTACC-GGTTCGCCGTTACGGTCGTAACCT
* * * * * * *
7904 TTCCTTTCAAATCTTC-ATGGTACCGGGTTCACCATTGCAGCCGTAACCT
1 TTCCCTTCAAATCTTCTAAGGTACC-GGTTCGCCGTTACGGTCGTAACCT
* * * *
7953 TTCCCATCATA-CTTTCTAAGGTACCGAGTTCGCTGTTACGGTTGTAACCT
1 TTCCCTTCAAATC-TTCTAAGGTACCG-GTTCGCCGTTACGGTCGTAACCT
* * * * * *
8003 CTCCCTTCAAATCTTC-ATGGTACTAGGTTTGTCGTTACGATCGTAACCT
1 TTCCCTTCAAATCTTCTAAGGTAC-CGGTTCGCCGTTACGGTCGTAACCT
* * * **
8052 TTCCCATCACATCTTCTAAGGTACCGAGTTCGCCGTTACAGTCGTAATAT
1 TTCCCTTCAAATCTTCTAAGGTACCG-GTTCGCCGTTACGGTCGTAACCT
* * * * * * *
8102 TTCCTTTCAAATCTT-TATGGTGCCGGGTTCACCGTTACGGCCTTAACAT
1 TTCCCTTCAAATCTTCTAAGGTACC-GGTTCGCCGTTACGGTCGTAACCT
8151 TTCCC
1 TTCCC
8156 ATCGCATTTT
Statistics
Matches: 190, Mismatches: 54, Indels: 17
0.73 0.21 0.07
Matches are distributed among these distances:
48 1 0.01
49 104 0.55
50 84 0.44
51 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.34
Consensus pattern (49 bp):
TTCCCTTCAAATCTTCTAAGGTACCGGTTCGCCGTTACGGTCGTAACCT
Found at i:7961 original size:99 final size:98
Alignment explanation
Indices: 7854--8158 Score: 344
Period size: 99 Copynumber: 3.1 Consensus size: 98
7844 ATCTCAATCC
* * *
7854 TTCCCATCACATCTTCTAAGGAACC-AGGTTTGCCGTTGCGGTCGTAACCTTTCCTTTCAAATCT
1 TTCCCATCACATCTTCTAAGGTACCGA-GTTCGCCGTTACGGTCGTAACCTTTCCTTTCAAATCT
* *
7918 TCATGGTACCGGGTTCACCATTGCAGCCGTAACCT
65 TCATGGTACCGGGTTCACCGTTAC-GCCGTAACCT
* * * * *
7953 TTCCCATCATA-CTTTCTAAGGTACCGAGTTCGCTGTTACGGTTGTAACCTCTCCCTTCAAATCT
1 TTCCCATCACATC-TTCTAAGGTACCGAGTTCGCCGTTACGGTCGTAACCTTTCCTTTCAAATCT
** *** *
8017 TCATGGTACTAGGTTTGTCGTTACGATCGTAACCT
65 TCATGGTACCGGGTTCACCGTTACG-CCGTAACCT
* **
8052 TTCCCATCACATCTTCTAAGGTACCGAGTTCGCCGTTACAGTCGTAATATTTCCTTTCAAATCTT
1 TTCCCATCACATCTTCTAAGGTACCGAGTTCGCCGTTACGGTCGTAACCTTTCCTTTCAAATCTT
* * * *
8117 TATGGTGCCGGGTTCACCGTTACGGCCTTAACAT
66 CATGGTACCGGGTTCACCGTTAC-GCCGTAACCT
8151 TTCCCATC
1 TTCCCATC
8159 GCATTTTATA
Statistics
Matches: 167, Mismatches: 34, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
98 2 0.01
99 162 0.97
100 3 0.02
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (98 bp):
TTCCCATCACATCTTCTAAGGTACCGAGTTCGCCGTTACGGTCGTAACCTTTCCTTTCAAATCTT
CATGGTACCGGGTTCACCGTTACGCCGTAACCT
Found at i:20897 original size:18 final size:18
Alignment explanation
Indices: 20874--20936 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 18
20864 TCAAATATAA
20874 AATTCACACAATCAATTT
1 AATTCACACAATCAATTT
**
20892 AATTCACACAAT-AA-GG
1 AATTCACACAATCAATTT
* *
20908 AA-ACACATAATCAATTT
1 AATTCACACAATCAATTT
20925 AATTCACACAAT
1 AATTCACACAAT
20937 AAGGAAATTC
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
15 7 0.21
16 4 0.12
17 4 0.12
18 19 0.56
ACGTcount: A:0.49, C:0.21, G:0.03, T:0.27
Consensus pattern (18 bp):
AATTCACACAATCAATTT
Found at i:20921 original size:33 final size:33
Alignment explanation
Indices: 20878--20943 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
20868 ATATAAAATT
20878 CACACAATCAATTTAATTCACACAATAAGGAAA
1 CACACAATCAATTTAATTCACACAATAAGGAAA
*
20911 CACATAATCAATTTAATTCACACAATAAGGAAA
1 CACACAATCAATTTAATTCACACAATAAGGAAA
20944 TTCATATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.52, C:0.20, G:0.06, T:0.23
Consensus pattern (33 bp):
CACACAATCAATTTAATTCACACAATAAGGAAA
Found at i:22333 original size:26 final size:26
Alignment explanation
Indices: 22304--22353 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
22294 TCTTTCTCTT
*
22304 ATATTTTTATAATATTA-AATAATAAA
1 ATATTATTAT-ATATTATAATAATAAA
*
22330 ATATTATTATTTATTATAATAATA
1 ATATTATTATATATTATAATAATA
22354 TTATTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATATTATTATATATTATAATAATAAA
Found at i:22350 original size:18 final size:18
Alignment explanation
Indices: 22329--22363 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22319 TAAATAATAA
* *
22329 AATATTATTATTTATTAT
1 AATAATATTATTAATTAT
22347 AATAATATTATTAATTA
1 AATAATATTATTAATTA
22364 ATATATCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATAATATTATTAATTAT
Found at i:22353 original size:21 final size:20
Alignment explanation
Indices: 22325--22368 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
22315 ATATTAAATA
* *
22325 ATAAAATATTATTATTTATT
1 ATAAAATATTATTAATTAAT
22345 ATAATAATATTATTAATTAAT
1 ATAA-AATATTATTAATTAAT
22366 ATA
1 ATA
22369 TCTTTTGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAAATATTATTAATTAAT
Found at i:26282 original size:26 final size:26
Alignment explanation
Indices: 26252--26301 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
26242 TCTTTCTCTT
*
26252 ATATTTTTATAATATTA-AATAATAAA
1 ATATTATTAT-ATATTATAATAATAAA
*
26278 ATATTATTATTTATTATAATAATA
1 ATATTATTATATATTATAATAATA
26302 TTATTAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATATTATTATATATTATAATAATAAA
Found at i:26316 original size:21 final size:20
Alignment explanation
Indices: 26273--26316 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
26263 ATATTAAATA
** *
26273 ATAAAATATTATTATTTATT
1 ATAAAATATTATTAACTAAT
26293 ATAATAATATTATTAACTAAT
1 ATAA-AATATTATTAACTAAT
26314 ATA
1 ATA
26317 TCTTTTGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAAAATATTATTAACTAAT
Found at i:28796 original size:19 final size:19
Alignment explanation
Indices: 28772--28844 Score: 94
Period size: 19 Copynumber: 3.9 Consensus size: 19
28762 CAGTAATTCA
*
28772 CTCTTACGAGTCAGTATTG
1 CTCTTACGAGCCAGTATTG
* *
28791 CTCTTA-AAGCCAGTATCG
1 CTCTTACGAGCCAGTATTG
* *
28809 CTCTTACGAACCAGTATTA
1 CTCTTACGAGCCAGTATTG
28828 CTCTTACGAGCCAGTAT
1 CTCTTACGAGCCAGTAT
28845 CGTAATTTCT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
18 15 0.33
19 30 0.67
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (19 bp):
CTCTTACGAGCCAGTATTG
Found at i:28814 original size:37 final size:38
Alignment explanation
Indices: 28772--28846 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
28762 CAGTAATTCA
** *
28772 CTCTTACGAGTCAGTATTGCTCTTA-AAGCCAGTATCG
1 CTCTTACGAACCAGTATTACTCTTACAAGCCAGTATCG
*
28809 CTCTTACGAACCAGTATTACTCTTACGAGCCAGTATCG
1 CTCTTACGAACCAGTATTACTCTTACAAGCCAGTATCG
28847 TAATTTCTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 22 0.67
38 11 0.33
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (38 bp):
CTCTTACGAACCAGTATTACTCTTACAAGCCAGTATCG
Done.