Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010858.1 Kokia drynarioides strain JFW-HI SEQ_125826, 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: 33743
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:301 original size:12 final size:12
Alignment explanation
Indices: 284--331 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
274 AAACATGTTC
*
284 ATTAATGTCCAA
1 ATTAATTTCCAA
296 ATTAATTTCAACTTAA
1 ATTAATTTC--C--AA
312 ATTAATTTCCAA
1 ATTAATTTCCAA
324 ATTAATTT
1 ATTAATTT
332 TTACACAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 18 0.58
14 2 0.06
16 11 0.35
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (12 bp):
ATTAATTTCCAA
Found at i:330 original size:16 final size:16
Alignment explanation
Indices: 294--328 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
284 ATTAATGTCC
*
294 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
310 AAATTAATTTCCAAATT
1 AAATTAATTT-CAAATT
327 AA
1 AA
329 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:341 original size:28 final size:28
Alignment explanation
Indices: 284--341 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
274 AAACATGTTC
**
284 ATTAATGTCCAAATTAATTTCAACTTAA
1 ATTAATGTCCAAATTAATTTCAACACAA
* **
312 ATTAATTTCCAAATTAATTTTTACACAA
1 ATTAATGTCCAAATTAATTTCAACACAA
340 AT
1 AT
342 ATTCTCCGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (28 bp):
ATTAATGTCCAAATTAATTTCAACACAA
Found at i:4305 original size:57 final size:57
Alignment explanation
Indices: 4156--4437 Score: 253
Period size: 57 Copynumber: 4.8 Consensus size: 57
4146 TAAAAAAAAA
* * *
4156 TTCGAGAAAAGGGGTTGTCGACCA-TTGCATGGCCAACACCAAAAAATATTGAAATTTTTT
1 TTCGAGAAAAGGGGGTGTCGGCCATTTG-ATGGCCAACACCAAAAAATA---CAATTTTTT
* *** *
4216 CTCGAGAAAAGGGGGTGTCGGCCATGCAATGGCCAACACCCAAAAATACAATTTTTT
1 TTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAATACAATTTTTT
* * *
4273 TTCGAAAAAAGGGGGTGTCGACCATTTGATGGCCAACATCAAAAAATTTTGA-AATTTTTT
1 TTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAA---T-ACAATTTTTT
* * *** * * *
4333 TCTCAAGAAAAAGGGGTGTCGGCCATGCAATGACCAACACCTAAAAATGCAATTTTTT
1 T-TCGAGAAAAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAATACAATTTTTT
** * * *
4391 TTTTAGAAAAGAGGGTGTCGGCCATTTGATGACCAACATCAAAAAAT
1 TTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAAT
4438 TTTGAATTTT
Statistics
Matches: 179, Mismatches: 36, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
57 83 0.46
58 10 0.06
60 50 0.28
61 36 0.20
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (57 bp):
TTCGAGAAAAGGGGGTGTCGGCCATTTGATGGCCAACACCAAAAAATACAATTTTTT
Found at i:4389 original size:117 final size:118
Alignment explanation
Indices: 4156--4456 Score: 444
Period size: 118 Copynumber: 2.6 Consensus size: 118
4146 TAAAAAAAAA
* * *
4156 TTCGAGAAAAGGGGTTGTCGACCA-TTGCATGGCCAACACCAAAAAATATTGAAA-TTTTTTCTC
1 TTCGAGAAAAGGGGGTGTCGACCATTTG-ATGGCCAACATCAAAAAATTTTGAAATTTTTTTCTC
* * *
4219 GAGAAAAGGGGGTGTCGGCCATGCAATGGCCAACACCCAAAAATACAATTTTTT
65 AAGAAAAAGGGGTGTCGGCCATGCAATGACCAACACCCAAAAATACAATTTTTT
*
4273 TTCGAAAAAAGGGGGTGTCGACCATTTGATGGCCAACATCAAAAAATTTTGAAATTTTTTTCTCA
1 TTCGAGAAAAGGGGGTGTCGACCATTTGATGGCCAACATCAAAAAATTTTGAAATTTTTTTCTCA
* *
4338 AGAAAAAGGGGTGTCGGCCATGCAATGACCAACACCTAAAAATGCAATTTTTT
66 AGAAAAAGGGGTGTCGGCCATGCAATGACCAACACCCAAAAATACAATTTTTT
** * * * *
4391 TTTTAGAAAAGAGGGTGTCGGCCATTTGATGACCAACATCAAAAAATTTTGAATTTTTTTTCTCA
1 TTCGAGAAAAGGGGGTGTCGACCATTTGATGGCCAACATCAAAAAATTTTGAAATTTTTTTCTCA
4456 A
66 A
4457 AAAGGGGCCG
Statistics
Matches: 166, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
117 46 0.28
118 120 0.72
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (118 bp):
TTCGAGAAAAGGGGGTGTCGACCATTTGATGGCCAACATCAAAAAATTTTGAAATTTTTTTCTCA
AGAAAAAGGGGTGTCGGCCATGCAATGACCAACACCCAAAAATACAATTTTTT
Found at i:4559 original size:98 final size:97
Alignment explanation
Indices: 4369--4548 Score: 249
Period size: 98 Copynumber: 1.9 Consensus size: 97
4359 GCAATGACCA
* * ** *
4369 ACACCTAAAAATGCAATTTTTTTTTTAGAAAAGAGGGTGTCGGCCATTTGATGACCAACATCAAA
1 ACACCCAAAAATGCAATTTATTTTCGAGAAAAGAGGGTGTCAGCCATTTGATGACCAACATCAAA
*
4434 AAATTTTGAATTTTTTTTCTCAAAAAGGGGCCG
66 AAA-TTTGAATTTTTTATCTCAAAAAGGGGCCG
*
4467 ACACCCAAAAATGCAATTTATTTTCGAGAAAAG-GGAGTGTCAGCCATTTGATGGCCAACA-CAA
1 ACACCCAAAAATGCAATTTATTTTCGAGAAAAGAGG-GTGTCAGCCATTTGATGACCAACATCAA
*
4530 AAAA-TTGTATTTTTTATCT
65 AAAATTTGAATTTTTTATCT
4549 GACAAAAAAG
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
95 13 0.18
97 9 0.12
98 51 0.70
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (97 bp):
ACACCCAAAAATGCAATTTATTTTCGAGAAAAGAGGGTGTCAGCCATTTGATGACCAACATCAAA
AAATTTGAATTTTTTATCTCAAAAAGGGGCCG
Found at i:6648 original size:23 final size:23
Alignment explanation
Indices: 6618--6719 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 23
6608 ACGCTAGCGA
6618 GCTTACTGTTTTGCACT-TCGTGT
1 GCTTACTGTTTTGCACTAT-GTGT
* * *
6641 GCTTACTGATTTGCGCTATGTGC
1 GCTTACTGTTTTGCACTATGTGT
* * *
6664 GCCTACTG-ATTGCACTGTGTGT
1 GCTTACTGTTTTGCACTATGTGT
** **
6686 GCTTACTGGATTGCACCGTGTGT
1 GCTTACTGTTTTGCACTATGTGT
6709 GCTTACTGTTT
1 GCTTACTGTTT
6720 CCCCAGCACT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
22 17 0.26
23 47 0.72
24 1 0.02
ACGTcount: A:0.12, C:0.22, G:0.25, T:0.41
Consensus pattern (23 bp):
GCTTACTGTTTTGCACTATGTGT
Found at i:6716 original size:45 final size:46
Alignment explanation
Indices: 6618--6717 Score: 107
Period size: 45 Copynumber: 2.2 Consensus size: 46
6608 ACGCTAGCGA
* * *
6618 GCTTACTGTTTTGCACTTCGTGTGCTTACTGATTTGCGCTATGTGC
1 GCTTACTGTATTGCACTTCGTGTGCTTACTGATTTGCACCATGTGC
* * *
6664 GCCTACTG-ATTGCACTGT-GTGTGCTTACTGGA-TTGCACCGTGTGT
1 GCTTACTGTATTGCACT-TCGTGTGCTTACT-GATTTGCACCATGTGC
6709 GCTTACTGT
1 GCTTACTGT
6718 TTCCCCAGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
45 34 0.77
46 10 0.23
ACGTcount: A:0.12, C:0.22, G:0.26, T:0.40
Consensus pattern (46 bp):
GCTTACTGTATTGCACTTCGTGTGCTTACTGATTTGCACCATGTGC
Found at i:8549 original size:19 final size:19
Alignment explanation
Indices: 8507--8552 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
8497 TAGAAAAAAT
8507 AATT-ATTTTTTTAAAAGA
1 AATTAATTTTTTTAAAAGA
**
8525 ATATTAATTTTTTTAACTGA
1 A-ATTAATTTTTTTAAAAGA
8545 AATTAATT
1 AATTAATT
8553 AATATAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 10 0.42
20 13 0.54
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (19 bp):
AATTAATTTTTTTAAAAGA
Found at i:9305 original size:6 final size:7
Alignment explanation
Indices: 9287--9311 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9277 GTAAAAATAT
9287 TAAAAAA
1 TAAAAAA
9294 TAAAAAA
1 TAAAAAA
9301 TAAAAAA
1 TAAAAAA
9308 TAAA
1 TAAA
9312 TTCAAACATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:22672 original size:22 final size:23
Alignment explanation
Indices: 22634--22680 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
22624 CCAAATCTAC
22634 TTAAACCTAAATGGGC-TAAAAA
1 TTAAACCTAAATGGGCTTAAAAA
*
22656 TTAAACTTGAAAT-GGCTTAAAAA
1 TTAAACCT-AAATGGGCTTAAAAA
22679 TT
1 TT
22681 TTACAACCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.30
Consensus pattern (23 bp):
TTAAACCTAAATGGGCTTAAAAA
Found at i:28002 original size:18 final size:18
Alignment explanation
Indices: 27917--28002 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 18
27907 TTTATTTTGG
*
27917 GTTT-AAATTTAGTTTAAA
1 GTTTAAAATTTAATTT-AA
* **
27935 GTTTAAACTTTTCTTTTAA
1 GTTTAAA-ATTTAATTTAA
*
27954 GTTT-AAATTTAAATTAA
1 GTTTAAAATTTAATTTAA
27971 GTTTAAAA-TTAATTTGAA
1 GTTTAAAATTTAATTT-AA
27989 -TTTAAAATTTAATT
1 GTTTAAAATTTAATT
28003 ATTTAAAATG
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
17 24 0.44
18 17 0.31
19 8 0.15
20 6 0.11
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (18 bp):
GTTTAAAATTTAATTTAA
Found at i:28670 original size:21 final size:21
Alignment explanation
Indices: 28645--28684 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28635 TTTCAATAAC
* *
28645 TTTTAATAGTATTAATAATTG
1 TTTTAATAATAATAATAATTG
28666 TTTTAATAATAATAATAAT
1 TTTTAATAATAATAATAAT
28685 ATTAATGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTTAATAATAATAATAATTG
Found at i:29956 original size:29 final size:29
Alignment explanation
Indices: 29905--30213 Score: 251
Period size: 29 Copynumber: 10.8 Consensus size: 29
29895 GAAGGTCCCT
* *
29905 AAACTTTCAAAAATTCTATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * **
29934 GAACTTCCAAAAATCCCACTTTTTAACCCTA
1 AAACTTCCAAAAATTCCA-TTTTT-ACCCCC
* * **
29965 AAATTTCCAAAAATCCCATTTTTGACCCAA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
*
29995 AAACTTCCAAAACTTCCATTTTT------
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
30018 -TAC-TCCAAAAATTCCATTTTTACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
30045 AAACTTCTAAAAATTCCATTTTTACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * *
30074 AAACTTCTAAAAATCCCATTTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
*
30104 AAACTTCCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * *
30133 GAACTTCCAAAAA-TCTCGTTTTTGATCCCG
1 AAACTTCCAAAAATTC-CATTTTT-ACCCCC
* *
30163 AAACTTCCAAAAATTCCATTTTTGCCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
30192 AAACTTCC-AAAATCTCCATTTT
1 AAACTTCCAAAAAT-TCCATTTT
30214 CGACCTTAAA
Statistics
Matches: 229, Mismatches: 36, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
21 17 0.07
22 2 0.01
28 9 0.04
29 98 0.43
30 81 0.35
31 22 0.10
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:30026 original size:21 final size:20
Alignment explanation
Indices: 30000--30051 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
29990 CCCAAAAACT
30000 TCCAAAACTTCCATTTTTTAC
1 TCCAAAACTTCCA-TTTTTAC
*
30021 TCCAAAAATTCCATTTTTAC
1 TCCAAAACTTCCATTTTTAC
*
30041 CCCAAAACTTC
1 TCCAAAACTTC
30052 TAAAAATTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.37
Consensus pattern (20 bp):
TCCAAAACTTCCATTTTTAC
Found at i:30116 original size:59 final size:57
Alignment explanation
Indices: 30023--30213 Score: 231
Period size: 59 Copynumber: 3.3 Consensus size: 57
30013 TTTTTTACTC
* * * *
30023 CAAAAATTCCATTTTTACCCCAAAACTTCTAAAAATTCCATTTTTACCC-CAAAACTT
1 CAAAAATCCCATTTTTAACCCGAAACTTCCAAAAATTCCATTTTTACCCTC-AAACTT
*
30080 CTAAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTT
1 C-AAAAATCCCATTTTTAACC-CGAAACTTCCAAAAATTCCATTTTTACCCTCAAACTT
* * * *
30139 CCAAAAATCTCGTTTTTGATCCCGAAACTTCCAAAAATTCCATTTTTGCCCTCAAACTT
1 -CAAAAATCCCATTTTT-AACCCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACTT
*
30198 CCAAAATCTCCATTTT
1 CAAAAATC-CCATTTT
30214 CGACCTTAAA
Statistics
Matches: 115, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
57 1 0.01
58 24 0.21
59 85 0.74
60 5 0.04
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (57 bp):
CAAAAATCCCATTTTTAACCCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACTT
Done.