Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009305.1 Kokia drynarioides strain JFW-HI SEQ_124012, 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: 31233
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2059 original size:15 final size:16
Alignment explanation
Indices: 2030--2072 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
2020 TTTTCAAAAG
*
2030 ATATATATTTGAAATA
1 ATATATATTTAAAATA
2046 ATAT-TATTTAAAATA
1 ATATATATTTAAAATA
* *
2061 ACAAATATTTAA
1 ATATATATTTAA
2073 TAGTTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
ATATATATTTAAAATA
Found at i:3104 original size:30 final size:30
Alignment explanation
Indices: 3070--3134 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
3060 ACTTATTTTA
*
3070 TTGTTAATTTTGTTATTATTTTAGAAGA-AT
1 TTGTTAATTTTGTTACTATTTTAG-AGACAT
3100 TTGTTAATTTTGTTACTATTTTAGAGACAT
1 TTGTTAATTTTGTTACTATTTTAGAGACAT
3130 TTGTT
1 TTGTT
3135 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAGAGACAT
Found at i:4622 original size:17 final size:17
Alignment explanation
Indices: 4600--4642 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
4590 TTTATTTGGG
4600 TTTTATTTTACAAATTA
1 TTTTATTTTACAAATTA
**
4617 TTTTATTTTATGAATTA
1 TTTTATTTTACAAATTA
*
4634 TTTTCTTTT
1 TTTTATTTT
4643 TAAAATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTATTTTACAAATTA
Found at i:7501 original size:123 final size:123
Alignment explanation
Indices: 7280--7527 Score: 415
Period size: 123 Copynumber: 2.0 Consensus size: 123
7270 GTGATTACCC
*
7280 AAATGGGGTTTCCTGCGTGTCCTAGGACAATGATGAGCAAACCTCACGAAATGTGAGTCTAGGCA
1 AAATGGGGTTTCCTGCGTGCCCTAGGACAATGATGAGCAAACCTCACGAAATGTGAGTCTAGGCA
*
7345 AATCCATATTGTAAACATGTCAGTGAATGAAAGCCTTTGTAGCAAACCATGAAATGAA
66 AATCCATATTGTAAACATGTCAGTGAATAAAAGCCTTTGTAGCAAACCATGAAATGAA
* * *
7403 AAATGGGGTTTCCTGTGTGCCCTAGGACGATGATGAGCAAACCTCACGAAATGTGAGTCTAGGTA
1 AAATGGGGTTTCCTGCGTGCCCTAGGACAATGATGAGCAAACCTCACGAAATGTGAGTCTAGGCA
* * * *
7468 AGTCCATATTGTAAACATTTCAGTGAATAAAAGCCTTTGTAGCGAACCATGGAATGAA
66 AATCCATATTGTAAACATGTCAGTGAATAAAAGCCTTTGTAGCAAACCATGAAATGAA
7526 AA
1 AA
7528 CCTTTATGGT
Statistics
Matches: 116, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
123 116 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.25
Consensus pattern (123 bp):
AAATGGGGTTTCCTGCGTGCCCTAGGACAATGATGAGCAAACCTCACGAAATGTGAGTCTAGGCA
AATCCATATTGTAAACATGTCAGTGAATAAAAGCCTTTGTAGCAAACCATGAAATGAA
Found at i:7661 original size:27 final size:27
Alignment explanation
Indices: 7497--7780 Score: 214
Period size: 27 Copynumber: 10.5 Consensus size: 27
7487 TCAGTGAATA
* *
7497 AAAGCCTTTGTAGCGAACCATGGAATG
1 AAAGCCTTTGTGGCGAACCATGAAATG
* * *
7524 AAAACCTTTATGGTGAACCATGAAATG
1 AAAGCCTTTGTGGCGAACCATGAAATG
* * * *
7551 AAAGTCTTTATGACGAACCATGAAATC
1 AAAGCCTTTGTGGCGAACCATGAAATG
* * *
7578 AAAGTCTTTATGGCGTACCATGAAATG
1 AAAGCCTTTGTGGCGAACCATGAAATG
* * * * *
7605 AAAGCTTTTATAGTGAATCAT-AAGATG
1 AAAGCCTTTGTGGCGAACCATGAA-ATG
* *
7632 AAAGCCTTTGTGGCAAACCATGAAACG
1 AAAGCCTTTGTGGCGAACCATGAAATG
* * * *
7659 AAAGCCTTTGTGGTGAATCATGAGAGG
1 AAAGCCTTTGTGGCGAACCATGAAATG
* *
7686 AAAGCCTTTGTGGCGAATCATGAAA-A
1 AAAGCCTTTGTGGCGAACCATGAAATG
* * *
7712 AATAACCTTTGTGGCGAATCATGAAA-A
1 AA-AGCCTTTGTGGCGAACCATGAAATG
* ** *
7739 AATAACCTTTGTGGCGAATTATGAAAGG
1 AA-AGCCTTTGTGGCGAACCATGAAATG
*
7767 AAATGCCCTTGTGG
1 AAA-GCCTTTGTGG
7781 TGGATTATTA
Statistics
Matches: 213, Mismatches: 39, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
26 4 0.02
27 197 0.92
28 12 0.06
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (27 bp):
AAAGCCTTTGTGGCGAACCATGAAATG
Found at i:18184 original size:4 final size:4
Alignment explanation
Indices: 18175--18209 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
18165 ATTTTAAGTG
18175 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
18210 GTTAATTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:20977 original size:4 final size:4
Alignment explanation
Indices: 20968--21016 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
20958 AGGTATATTC
* * * *
20968 ATAT ATAT ATAT ATAT ATAT ATAT ACAT ATGT ATAT ATAC ATAT GTAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
21016 A
1 A
21017 CACATTATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (4 bp):
ATAT
Found at i:20977 original size:6 final size:6
Alignment explanation
Indices: 20968--21016 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
20958 AGGTATATTC
* * * *
20968 ATATAT ATATAT ATATAT ATATAT ACATAT GTATAT ATACAT ATGTAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
21016 A
1 A
21017 CACATTATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (6 bp):
ATATAT
Found at i:20985 original size:14 final size:14
Alignment explanation
Indices: 20968--21016 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
20958 AGGTATATTC
*
20968 ATATATATATATAT
1 ATATATATATACAT
20982 ATATATATATACAT
1 ATATATATATACAT
*
20996 ATGTATATATACAT
1 ATATATATATACAT
*
21010 ATGTATA
1 ATATATA
21017 CACATTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (14 bp):
ATATATATATACAT
Found at i:21997 original size:30 final size:30
Alignment explanation
Indices: 21963--22159 Score: 157
Period size: 30 Copynumber: 6.6 Consensus size: 30
21953 ATTTTTTTAG
* *
21963 AAAATTACATTTTGACCCTTATACTTTTCT
1 AAAATTACATTTTGACCCTTAAACTTTTCC
* * * *
21993 AAAATTTCATTTTGGCCCTCAAACTTCTCC
1 AAAATTACATTTTGACCCTTAAACTTTTCC
* * * *
22023 AAAATTACATGTTAACCCCTAAAATTTTCC
1 AAAATTACATTTTGACCCTTAAACTTTTCC
* * * * *
22053 AAGATTTCATTTTAACCCTAAAAC-TTCCC
1 AAAATTACATTTTGACCCTTAAACTTTTCC
* * *
22082 TAAAATTTCATTTTAACCCCTAAACTTTTCC
1 -AAAATTACATTTTGACCCTTAAACTTTTCC
**
22113 AAAATTATGTTTTGACCAC-TAAAC-TTTCC
1 AAAATTACATTTTGACC-CTTAAACTTTTCC
**
22142 AAAATTATGTTTTGACCC
1 AAAATTACATTTTGACCC
22160 CAAATTCTCC
Statistics
Matches: 135, Mismatches: 29, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
28 1 0.01
29 26 0.19
30 103 0.76
31 5 0.04
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTTAAACTTTTCC
Found at i:22030 original size:60 final size:59
Alignment explanation
Indices: 21963--22182 Score: 207
Period size: 60 Copynumber: 3.7 Consensus size: 59
21953 ATTTTTTTAG
* * * * *
21963 AAAATTACATTTTGACCCTTATACTTTTCTAAAATTTCATTTTGGCCCTCAAACTTCTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCCAAAATTTCATTTTGACCCT-AAACTTCTCC
* * * *
22023 AAAATTACATGTTAACCCCTAAAATTTTCCAAGATTTCATTTTAACCCTAAAACTTC-CC
1 AAAATTACATTTTAACCCCTAAACTTTTCCAAAATTTCATTTTGACCCT-AAACTTCTCC
* *
22082 TAAAATTTCATTTTAACCCCTAAACTTTTCCAAAATTAT-GTTTTGACCACTAAACTT-TCC
1 -AAAATTACATTTTAACCCCTAAACTTTTCCAAAATT-TCATTTTGACC-CTAAACTTCTCC
** * * * *
22142 AAAATTATGTTTTGACCCC-AAA-TTCTCCGAAACTTCATTTT
1 AAAATTACATTTTAACCCCTAAACTTTTCCAAAATTTCATTTT
22183 CAACCCCATT
Statistics
Matches: 131, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
56 1 0.01
57 13 0.10
58 3 0.02
59 17 0.13
60 94 0.72
61 3 0.02
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.39
Consensus pattern (59 bp):
AAAATTACATTTTAACCCCTAAACTTTTCCAAAATTTCATTTTGACCCTAAACTTCTCC
Found at i:22148 original size:29 final size:30
Alignment explanation
Indices: 22092--22158 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 30
22082 TAAAATTTCA
* *
22092 TTTTAACCCCTAAACTTTTCCAAAATTATG
1 TTTTGACCACTAAACTTTTCCAAAATTATG
22122 TTTTGACCACTAAAC-TTTCCAAAATTATG
1 TTTTGACCACTAAACTTTTCCAAAATTATG
22151 TTTTGACC
1 TTTTGACC
22159 CCAAATTCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.40
Consensus pattern (30 bp):
TTTTGACCACTAAACTTTTCCAAAATTATG
Found at i:27518 original size:21 final size:21
Alignment explanation
Indices: 27469--27518 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
27459 TGTTTTTTTT
*
27469 AATATTTTATTATATTTTATA
1 AATAATTTATTATATTTTATA
*
27490 AGA-CATTTATTA-ATTTTATTA
1 A-ATAATTTATTATATTTTA-TA
27511 AATAATTT
1 AATAATTT
27519 TTCGTTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 6
0.72 0.09 0.19
Matches are distributed among these distances:
20 7 0.30
21 15 0.65
22 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
AATAATTTATTATATTTTATA
Found at i:29860 original size:30 final size:32
Alignment explanation
Indices: 29807--29871 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
29797 AAAATTATAT
*
29807 TTTTGTTTAGTATTTATTATTTTAAGTT-ATTTG
1 TTTTGTTTAG-ATTTAATATTTTAA-TTGATTTG
29840 TTTTGTTTA-ATTTAAT-TTTTAATTGATTTG
1 TTTTGTTTAGATTTAATATTTTAATTGATTTG
29870 TT
1 TT
29872 ATTTAATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 2 0.07
30 13 0.43
31 6 0.20
33 9 0.30
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.68
Consensus pattern (32 bp):
TTTTGTTTAGATTTAATATTTTAATTGATTTG
Found at i:30199 original size:19 final size:19
Alignment explanation
Indices: 30171--30219 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
30161 TAAATAACTC
*
30171 ATTTTAGTATTTAACTATT
1 ATTTTTGTATTTAACTATT
30190 ATTTTTGTATTTAACTATT
1 ATTTTTGTATTTAACTATT
30209 ATTTTTGTATT
1 ATTTTTGTATT
30220 ATATTGATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (19 bp):
ATTTTTGTATTTAACTATT
Done.