Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013348.1 Kokia drynarioides strain JFW-HI SEQ_128371, 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: 28398
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:10167 original size:25 final size:26
Alignment explanation
Indices: 10130--10191 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
10120 TCTCTAAAGG
* *
10130 TAGTGATAACAACATCGAACC-AAGC
1 TAGTGTTAGCAACATCGAACCGAAGC
* * *
10155 TAGTGTTAGCAACCTTGATCCGAAGC
1 TAGTGTTAGCAACATCGAACCGAAGC
10181 TAGTGTTAGCA
1 TAGTGTTAGCA
10192 GCCCGATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
25 16 0.52
26 15 0.48
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (26 bp):
TAGTGTTAGCAACATCGAACCGAAGC
Found at i:11416 original size:15 final size:15
Alignment explanation
Indices: 11379--11417 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
11369 TTATGTGTGC
*
11379 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
11394 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
11408 TTAATTCTTG
1 TTAATTCTTG
11418 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:14807 original size:24 final size:26
Alignment explanation
Indices: 14780--14827 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
14770 AGAGAAATGT
14780 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
14804 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
14828 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:14962 original size:47 final size:47
Alignment explanation
Indices: 14890--15081 Score: 209
Period size: 47 Copynumber: 4.2 Consensus size: 47
14880 ACGCTAGCAC
* * *
14890 GCTTCTGTTCAGCACTATGTGTGCTTTTGTTACCCATCACTGTGTGT
1 GCTTCTGTTCAGCACTATGTCTGCTTCTGTTACCCAGCACTGTGTGT
* * * *
14937 GCTTCTATTTAGCACTATGTCTGCTTTTGTT---CAGCGC--TGTGT
1 GCTTCTGTTCAGCACTATGTCTGCTTCTGTTACCCAGCACTGTGTGT
* * *
14979 GCTTCTGTTCAGCACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGC
1 GCTTCTGTTCAGCACTATGTCTGCTTCTGTTACCCAGCACTGTGTGT
* *
15026 GCTTCTGTTCAGCA-T-TGTGCGTACTTCTGTTACCCAACACTGTGTGT
1 GCTTCTGTTCAGCACTATGT-C-TGCTTCTGTTACCCAGCACTGTGTGT
15073 GCTTCTGTT
1 GCTTCTGTT
15082 TCCCCATCAC
Statistics
Matches: 122, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
42 31 0.25
44 4 0.03
45 8 0.07
46 1 0.01
47 78 0.64
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (47 bp):
GCTTCTGTTCAGCACTATGTCTGCTTCTGTTACCCAGCACTGTGTGT
Found at i:15022 original size:25 final size:22
Alignment explanation
Indices: 14890--15081 Score: 163
Period size: 22 Copynumber: 8.4 Consensus size: 22
14880 ACGCTAGCAC
*
14890 GCTTCTGTTCAGCACTATGTGT
1 GCTTCTGTTCAGCACTGTGTGT
* *
14912 GCTTTTGTTACCCATCACTGTGTGT
1 GCTTCTGTT---CAGCACTGTGTGT
* * * *
14937 GCTTCTATTTAGCACTATGTCT
1 GCTTCTGTTCAGCACTGTGTGT
* *
14959 GCTTTTGTTCAGCGC--TGTGT
1 GCTTCTGTTCAGCACTGTGTGT
14979 GCTTCTGTTCAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
*
15001 GCTTCTGTTACCCAGCACTGTGTGC
1 GCTTCTGTT---CAGCACTGTGTGT
* *
15026 GCTTCTGTTCAGCATTGTGCGT
1 GCTTCTGTTCAGCACTGTGTGT
* *
15048 ACTTCTGTTACCCAACACTGTGTGT
1 GCTTCTGTT---CAGCACTGTGTGT
15073 GCTTCTGTT
1 GCTTCTGTT
15082 TCCCCATCAC
Statistics
Matches: 134, Mismatches: 25, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
20 17 0.13
22 60 0.45
25 57 0.43
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (22 bp):
GCTTCTGTTCAGCACTGTGTGT
Found at i:17545 original size:17 final size:17
Alignment explanation
Indices: 17519--17557 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
17509 TTATTTTCAT
*
17519 TTTTAGTTTTAGTTTTA
1 TTTTAGTTTTAATTTTA
*
17536 TTTTATTTTTAATTTTA
1 TTTTAGTTTTAATTTTA
17553 TTTTA
1 TTTTA
17558 ATTATGCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTTAGTTTTAATTTTA
Found at i:17557 original size:11 final size:12
Alignment explanation
Indices: 17519--17560 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
17509 TTATTTTCAT
*
17519 TTTTAGTTTTAG
1 TTTTAATTTTAG
*
17531 TTTT-ATTTTAT
1 TTTTAATTTTAG
17542 TTTTAATTTTA-
1 TTTTAATTTTAG
17553 TTTTAATT
1 TTTTAATT
17561 ATGCAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTTAATTTTAG
Found at i:18517 original size:17 final size:18
Alignment explanation
Indices: 18497--18552 Score: 89
Period size: 17 Copynumber: 3.2 Consensus size: 18
18487 AAAAAAGTCG
18497 AAAAGAAAAATTGA-AAA
1 AAAAGAAAAATTGAGAAA
*
18514 AAAAAAAAAATTGAGAAA
1 AAAAGAAAAATTGAGAAA
18532 AAAAG-AAAATTGAGAAA
1 AAAAGAAAAATTGAGAAA
18549 AAAA
1 AAAA
18553 AAAGAAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 29 0.81
18 7 0.19
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (18 bp):
AAAAGAAAAATTGAGAAA
Found at i:18536 original size:35 final size:36
Alignment explanation
Indices: 18497--18577 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 36
18487 AAAAAAGTCG
**
18497 AAAAGAAAAATTGA-AAAAAAAAAA-AAATTGAGAAA
1 AAAAGAAAAATTGAGAAAAAAAAAAGAAAAAGA-AAA
18532 AAAAG-AAAATTGAGAAAAAAAAAAGAAAAAGAAAA
1 AAAAGAAAAATTGAGAAAAAAAAAAGAAAAAGAAAA
18567 AAAAGACAAAA
1 AAAAGA-AAAA
18578 GTTTGTTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
34 8 0.20
35 23 0.57
36 5 0.12
37 4 0.10
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.07
Consensus pattern (36 bp):
AAAAGAAAAATTGAGAAAAAAAAAAGAAAAAGAAAA
Found at i:18564 original size:17 final size:17
Alignment explanation
Indices: 18472--18570 Score: 63
Period size: 20 Copynumber: 5.1 Consensus size: 17
18462 TTTATTGTTT
18472 AAAAGAAAAAGAAAAAA
1 AAAAGAAAAAGAAAAAA
*
18489 AAAAGTCGAAAAGAAAAATTGA
1 AAAAG--AAAAAGAAAAA---A
* *
18511 AAAAAAAAAAAAATTGAGAAA
1 AAAAGAAAAAGAA---A-AAA
18532 AAAAGAAAATTGAGAAAAAA
1 AAAAGAAAA---AGAAAAAA
18552 AAAAGAAAAAGAAAAAA
1 AAAAGAAAAAGAAAAAA
18569 AA
1 AA
18571 GACAAAAGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 24
0.68 0.06 0.26
Matches are distributed among these distances:
17 15 0.23
19 10 0.16
20 18 0.28
21 10 0.16
22 5 0.08
23 1 0.02
24 5 0.08
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.07
Consensus pattern (17 bp):
AAAAGAAAAAGAAAAAA
Found at i:18577 original size:16 final size:15
Alignment explanation
Indices: 18497--18578 Score: 56
Period size: 17 Copynumber: 4.7 Consensus size: 15
18487 AAAAAAGTCG
18497 AAAAGAAAAATTGAAAA
1 AAAAGAAAAA--GAAAA
*
18514 AAAAAAAAAATTGAGAAA
1 AAAAGAAAAA--GA-AAA
18532 AAAAGAAAATTGAGAAAAAA
1 AAAAGAAAA---AG--AAAA
18552 AAAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAA
18567 AAAAGACAAAAG
1 AAAAGA-AAAAG
18579 TTTGTTTGAG
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
15 10 0.18
16 5 0.09
17 15 0.27
18 11 0.20
19 1 0.02
20 12 0.21
21 2 0.04
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAAGAAAA
Found at i:19960 original size:15 final size:15
Alignment explanation
Indices: 19923--19961 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
19913 TTATGTGTGC
*
19923 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
19938 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
19952 TTAATTCTTG
1 TTAATTCTTG
19962 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:23351 original size:24 final size:26
Alignment explanation
Indices: 23324--23371 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
23314 AGAGAAATGT
23324 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
23348 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
23372 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:23506 original size:47 final size:47
Alignment explanation
Indices: 23434--23625 Score: 209
Period size: 47 Copynumber: 4.2 Consensus size: 47
23424 ACGCTAGCAC
* * *
23434 GCTTCTGTTCAGCACTATGTGTGCTTTTGTTACCCATCACTGTGTGT
1 GCTTCTGTTCAGCACTATGTCTGCTTCTGTTACCCAGCACTGTGTGT
* * * *
23481 GCTTCTATTTAGCACTATGTCTGCTTTTGTT---CAGCGC--TGTGT
1 GCTTCTGTTCAGCACTATGTCTGCTTCTGTTACCCAGCACTGTGTGT
* * *
23523 GCTTCTGTTCAGCACTGTGTGTGCTTCTGTTACCCAGCACTGTGTGC
1 GCTTCTGTTCAGCACTATGTCTGCTTCTGTTACCCAGCACTGTGTGT
* *
23570 GCTTCTGTTCAGCA-T-TGTGCGTACTTCTGTTACCCAACACTGTGTGT
1 GCTTCTGTTCAGCACTATGT-C-TGCTTCTGTTACCCAGCACTGTGTGT
23617 GCTTCTGTT
1 GCTTCTGTT
23626 TCCCCATCAC
Statistics
Matches: 122, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
42 31 0.25
44 4 0.03
45 8 0.07
46 1 0.01
47 78 0.64
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (47 bp):
GCTTCTGTTCAGCACTATGTCTGCTTCTGTTACCCAGCACTGTGTGT
Found at i:23566 original size:25 final size:22
Alignment explanation
Indices: 23434--23625 Score: 163
Period size: 22 Copynumber: 8.4 Consensus size: 22
23424 ACGCTAGCAC
*
23434 GCTTCTGTTCAGCACTATGTGT
1 GCTTCTGTTCAGCACTGTGTGT
* *
23456 GCTTTTGTTACCCATCACTGTGTGT
1 GCTTCTGTT---CAGCACTGTGTGT
* * * *
23481 GCTTCTATTTAGCACTATGTCT
1 GCTTCTGTTCAGCACTGTGTGT
* *
23503 GCTTTTGTTCAGCGC--TGTGT
1 GCTTCTGTTCAGCACTGTGTGT
23523 GCTTCTGTTCAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
*
23545 GCTTCTGTTACCCAGCACTGTGTGC
1 GCTTCTGTT---CAGCACTGTGTGT
* *
23570 GCTTCTGTTCAGCATTGTGCGT
1 GCTTCTGTTCAGCACTGTGTGT
* *
23592 ACTTCTGTTACCCAACACTGTGTGT
1 GCTTCTGTT---CAGCACTGTGTGT
23617 GCTTCTGTT
1 GCTTCTGTT
23626 TCCCCATCAC
Statistics
Matches: 134, Mismatches: 25, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
20 17 0.13
22 60 0.45
25 57 0.43
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (22 bp):
GCTTCTGTTCAGCACTGTGTGT
Found at i:26089 original size:17 final size:17
Alignment explanation
Indices: 26063--26101 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
26053 TTATTTTCAT
*
26063 TTTTAGTTTTAGTTTTA
1 TTTTAGTTTTAATTTTA
*
26080 TTTTATTTTTAATTTTA
1 TTTTAGTTTTAATTTTA
26097 TTTTA
1 TTTTA
26102 ATTATGCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTTAGTTTTAATTTTA
Found at i:26101 original size:11 final size:12
Alignment explanation
Indices: 26063--26104 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
26053 TTATTTTCAT
*
26063 TTTTAGTTTTAG
1 TTTTAATTTTAG
*
26075 TTTT-ATTTTAT
1 TTTTAATTTTAG
26086 TTTTAATTTTA-
1 TTTTAATTTTAG
26097 TTTTAATT
1 TTTTAATT
26105 ATGCAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTTAATTTTAG
Found at i:27061 original size:17 final size:18
Alignment explanation
Indices: 27041--27096 Score: 89
Period size: 17 Copynumber: 3.2 Consensus size: 18
27031 AAAAAAGTCG
27041 AAAAGAAAAATTGA-AAA
1 AAAAGAAAAATTGAGAAA
*
27058 AAAAAAAAAATTGAGAAA
1 AAAAGAAAAATTGAGAAA
27076 AAAAG-AAAATTGAGAAA
1 AAAAGAAAAATTGAGAAA
27093 AAAA
1 AAAA
27097 AAAGAAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 29 0.81
18 7 0.19
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (18 bp):
AAAAGAAAAATTGAGAAA
Found at i:27080 original size:35 final size:36
Alignment explanation
Indices: 27041--27121 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 36
27031 AAAAAAGTCG
**
27041 AAAAGAAAAATTGA-AAAAAAAAAA-AAATTGAGAAA
1 AAAAGAAAAATTGAGAAAAAAAAAAGAAAAAGA-AAA
27076 AAAAG-AAAATTGAGAAAAAAAAAAGAAAAAGAAAA
1 AAAAGAAAAATTGAGAAAAAAAAAAGAAAAAGAAAA
27111 AAAAGACAAAA
1 AAAAGA-AAAA
27122 GTTTGTTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
34 8 0.20
35 23 0.57
36 5 0.12
37 4 0.10
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.07
Consensus pattern (36 bp):
AAAAGAAAAATTGAGAAAAAAAAAAGAAAAAGAAAA
Found at i:27108 original size:17 final size:17
Alignment explanation
Indices: 27016--27114 Score: 63
Period size: 20 Copynumber: 5.1 Consensus size: 17
27006 TTTATTGTTT
27016 AAAAGAAAAAGAAAAAA
1 AAAAGAAAAAGAAAAAA
*
27033 AAAAGTCGAAAAGAAAAATTGA
1 AAAAG--AAAAAGAAAAA---A
* *
27055 AAAAAAAAAAAAATTGAGAAA
1 AAAAGAAAAAGAA---A-AAA
27076 AAAAGAAAATTGAGAAAAAA
1 AAAAGAAAA---AGAAAAAA
27096 AAAAGAAAAAGAAAAAA
1 AAAAGAAAAAGAAAAAA
27113 AA
1 AA
27115 GACAAAAGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 24
0.68 0.06 0.26
Matches are distributed among these distances:
17 15 0.23
19 10 0.16
20 18 0.28
21 10 0.16
22 5 0.08
23 1 0.02
24 5 0.08
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.07
Consensus pattern (17 bp):
AAAAGAAAAAGAAAAAA
Found at i:27121 original size:16 final size:15
Alignment explanation
Indices: 27041--27122 Score: 56
Period size: 17 Copynumber: 4.7 Consensus size: 15
27031 AAAAAAGTCG
27041 AAAAGAAAAATTGAAAA
1 AAAAGAAAAA--GAAAA
*
27058 AAAAAAAAAATTGAGAAA
1 AAAAGAAAAA--GA-AAA
27076 AAAAGAAAATTGAGAAAAAA
1 AAAAGAAAA---AG--AAAA
27096 AAAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAA
27111 AAAAGACAAAAG
1 AAAAGA-AAAAG
27123 TTTGTTTGAG
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
15 10 0.18
16 5 0.09
17 15 0.27
18 11 0.20
19 1 0.02
20 12 0.21
21 2 0.04
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAAGAAAA
Done.