Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013533.1 Kokia drynarioides strain JFW-HI SEQ_128559, 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: 11524
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Found at i:3482 original size:28 final size:28
Alignment explanation
Indices: 3451--3512 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
3441 AAAATGTGAT
* *
3451 TTTTGGATACTC-GATGGCAAAATGGTAA
1 TTTTGGATACTCAG-GGGCAAAATAGTAA
3479 TTTTGGATACTCAGGGGCAAAATAGTAA
1 TTTTGGATACTCAGGGGCAAAATAGTAA
3507 TTTTGG
1 TTTTGG
3513 GAAAGTTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.34
Consensus pattern (28 bp):
TTTTGGATACTCAGGGGCAAAATAGTAA
Found at i:3574 original size:29 final size:29
Alignment explanation
Indices: 3528--3807 Score: 156
Period size: 29 Copynumber: 9.6 Consensus size: 29
3518 TTTGGGCGGT
*
3528 AAAAATGTAATTTTTGGAAAATTGAGGTC
1 AAAAATGGAATTTTTGGAAAATTGAGGTC
* * *
3557 AAAAATGGAATTTCTGG-AAGTTCGGGGGT-
1 AAAAATGGAATTTTTGGAAAATT--GAGGTC
* * *
3586 -AAAACGGTAATTTTTGGAAAAATCATGGTC
1 AAAAATGG-AATTTTTGGAAAATTGA-GGTC
* ** *
3616 AAAAATGGAATTTTGGGAAGTTTGGGGGT-
1 AAAAATGGAATTTTTGGAAAATT-GAGGTC
3645 -AAAATGGTAATTTTTGGAAAAATTGAGGTC
1 AAAAATGG-AATTTTTGG-AAAATTGAGGTC
*
3675 AAAAATGGAATTTTT-GAAAGTTTG-GG-C
1 AAAAATGGAATTTTTGGAAA-ATTGAGGTC
* *
3702 GTAAAATGGTAATTTTTAGAAAAATT-AGGGTC
1 -AAAAATGG-AATTTTT-GGAAAATTGA-GGTC
*
3734 AAAAATGGAAATTTTTGG-AAGTTCGGAGGT-
1 AAAAATGG-AATTTTTGGAAAATT--GAGGTC
* *
3764 --AAATGGTAATTTTTAGAAAAATCGAGGTC
1 AAAAATGG-AATTTTT-GGAAAATTGAGGTC
3793 -AAAATGGAATTTTTG
1 AAAAATGGAATTTTTG
3808 AGAAGTTTAA
Statistics
Matches: 191, Mismatches: 33, Indels: 55
0.68 0.12 0.20
Matches are distributed among these distances:
27 1 0.01
28 48 0.25
29 61 0.32
30 44 0.23
31 35 0.18
32 2 0.01
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAAATTGAGGTC
Found at i:3620 original size:59 final size:58
Alignment explanation
Indices: 3505--3815 Score: 385
Period size: 59 Copynumber: 5.3 Consensus size: 58
3495 GCAAAATAGT
* * *
3505 AATTTTGGGAAAGTTTGGGCGGTAAAAAT-GTAATTTTTGGAAAATTGAGGTCAAAAATGG
1 AATTTTTGG-AAGTTTGGG-GGT-AAAATGGTAATTTTTGGAAAAATCAGGTCAAAAATGG
* * *
3565 AATTTCTGGAAGTTCGGGGGTAAAACGGTAATTTTTGGAAAAATCATGGTCAAAAATGG
1 AATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAAATCA-GGTCAAAAATGG
* *
3624 AATTTTGGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAAATTGAGGTCAAAAATGG
1 AATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAAA-TCAGGTCAAAAATGG
* * * *
3683 AATTTTTGAAAGTTTGGGCGTAAAATGGTAATTTTTAGAAAAATTAGGGTCAAAAATGG
1 AATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAAATCA-GGTCAAAAATGG
* * *
3742 AAATTTTTGGAAGTTCGGAGGT-AAATGGTAATTTTTAGAAAAATCGAGGTC-AAAATGG
1 -AATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAAATC-AGGTCAAAAATGG
3800 AATTTTTGAGAAGTTT
1 AATTTTTG-GAAGTTT
3816 AAGGGTCAAA
Statistics
Matches: 222, Mismatches: 22, Indels: 16
0.85 0.08 0.06
Matches are distributed among these distances:
57 12 0.05
58 35 0.16
59 148 0.67
60 27 0.12
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.32
Consensus pattern (58 bp):
AATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAAATCAGGTCAAAAATGG
Found at i:3845 original size:30 final size:30
Alignment explanation
Indices: 3789--3846 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
3779 GAAAAATCGA
* *
3789 GGTCAAAATGGAATTTTTGAGAAGTTTAAG
1 GGTCAAAATAGAATTTCTGAGAAGTTTAAG
*
3819 GGTCAAAATATAATTTCT-AGATAGTTTA
1 GGTCAAAATAGAATTTCTGAGA-AGTTTA
3847 GTGACCTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (30 bp):
GGTCAAAATAGAATTTCTGAGAAGTTTAAG
Found at i:4946 original size:20 final size:22
Alignment explanation
Indices: 4921--4962 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
4911 AAATAATTTT
4921 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
4941 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
4963 TCATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:4950 original size:29 final size:31
Alignment explanation
Indices: 4887--4959 Score: 123
Period size: 29 Copynumber: 2.4 Consensus size: 31
4877 ATTAAAATTA
4887 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTATTATTTCAAAAAAATAAT
*
4918 TTTAATAATTTTA-TATTT-TAAAAAATAAT
1 TTTAATAATTTTATTATTTCAAAAAAATAAT
4947 TTTAATAATTTTA
1 TTTAATAATTTTA
4960 AAATCATTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 23 0.56
30 5 0.12
31 13 0.32
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTAATAATTTTATTATTTCAAAAAAATAAT
Found at i:4963 original size:20 final size:20
Alignment explanation
Indices: 4912--4968 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
4902 ATTTCAAAAA
4912 AATAATTTT--AATAATTTT
1 AATAATTTTAAAATAATTTT
4930 -AT-ATTTTAAAAAATAATTTT
1 AATAATTTT--AAAATAATTTT
*
4950 AATAATTTTAAAATCATTT
1 AATAATTTTAAAATAATTT
4969 GCTGACATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
20 18 0.56
21 2 0.06
22 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:6943 original size:26 final size:25
Alignment explanation
Indices: 6874--6943 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
6864 CAAAAACTCC
* *
6874 AACACAAACAATACAAACAAAATATA
1 AACATAAAC-ATACAAATAAAATATA
* * *
6900 AACTTAAATATTAAAAATAAAATATA
1 AACATAAACA-TACAAATAAAATATA
6926 AACATATAACATACAAAT
1 AACATA-AACATACAAAT
6944 TATTATTACA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
25 1 0.03
26 30 0.88
27 3 0.09
ACGTcount: A:0.66, C:0.13, G:0.00, T:0.21
Consensus pattern (25 bp):
AACATAAACATACAAATAAAATATA
Found at i:7211 original size:6 final size:6
Alignment explanation
Indices: 7190--7254 Score: 55
Period size: 6 Copynumber: 10.8 Consensus size: 6
7180 TTTAAATTGG
** *
7190 TTTAAA TTT--A TCTTAAA TTTAAA TTTATCTT TTTAAA TTTAAA TTT-AC
1 TTTAAA TTTAAA T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
7238 TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
7255 TCAAATTTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
4 2 0.04
5 6 0.13
6 33 0.70
7 2 0.04
8 4 0.09
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:7212 original size:17 final size:18
Alignment explanation
Indices: 7190--7253 Score: 96
Period size: 17 Copynumber: 3.6 Consensus size: 18
7180 TTTAAATTGG
7190 TTTAAATTTATC-TTAAA
1 TTTAAATTTATCTTTAAA
7207 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTATC--TTTAAA
7227 TTTAAATTTA-CTTTAAA
1 TTTAAATTTATCTTTAAA
7244 TTTAAATTTA
1 TTTAAATTTA
7254 ATCAAATTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
17 28 0.64
19 1 0.02
20 15 0.34
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAATTTATCTTTAAA
Found at i:9193 original size:30 final size:28
Alignment explanation
Indices: 9157--9456 Score: 208
Period size: 30 Copynumber: 10.1 Consensus size: 28
9147 CCCTGGAGGT
*
9157 CCCTAAACTATCCAAAAATTCCATTTTTGA
1 CCCTAAACT-TCCAAAAATTACATTTTT-A
*** *
9187 CCCTAAAACTTTTGAAAATTATATTTTTA
1 CCCT-AAACTTCCAAAAATTACATTTTTA
*
9216 CACCTAAACTTCCAAAAATTCCATTTTTGA
1 C-CCTAAACTTCCAAAAATTACATTTTT-A
* * * *
9246 ACTTAAAACTTCCAAAAACTACAATTTTA
1 CCCT-AAACTTCCAAAAATTACATTTTTA
* *
9275 CCCCTAAACTTCCAAAAATTATAATTTTA
1 -CCCTAAACTTCCAAAAATTACATTTTTA
*** *
9304 CCCTCGAAACTTTTGAAAATTATATTTTTA
1 CCCT--AAACTTCCAAAAATTACATTTTTA
*
9334 CCCCCAAACTTCCAAAAAATT-CATTTTTGA
1 -CCCTAAACTTCC-AAAAATTACATTTTT-A
* * *
9364 CCTTAAAACTTCCAAAGACTACATTTTTTA
1 CCCT-AAACTTCCAAAAATTACA-TTTTTA
* *
9394 CCCTTAAACTTCCAAAAATTCCAATTTTGA
1 CCC-TAAACTTCCAAAAATTAC-ATTTTTA
* *
9424 CCCCAAAGCTTTCAAAAATTACCA-TTTTA
1 CCCTAAA-CTTCCAAAAATTA-CATTTTTA
9453 CCCT
1 CCCT
9457 CGGATGTCCA
Statistics
Matches: 211, Mismatches: 42, Indels: 35
0.73 0.15 0.12
Matches are distributed among these distances:
28 4 0.02
29 74 0.35
30 117 0.55
31 16 0.08
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATTACATTTTTA
Found at i:9233 original size:59 final size:59
Alignment explanation
Indices: 9157--9539 Score: 312
Period size: 59 Copynumber: 6.5 Consensus size: 59
9147 CCCTGGAGGT
** *
9157 CCCTAAACTATCCAAAAATTCCATTTTTGACCCTAAAACTTTTGAAAATTATATTTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTACATTTTTAC
* * * * * *
9217 ACCTAAACTTCCAAAAATTCCATTTTTGAACTTAAAACTTCCAAAAACTACAATTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTACATTTTTAC
** * * ** *
9276 CCCTAAACTTCCAAAAATTATAATTTT-ACCCTCGAAACTTTTGAAAATTATATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTGACCCT-AAAACTTTCAAAAATTACATTTTTAC
* * * * *
9335 CCCCAAACTTCCAAAAAATT-CATTTTTGACCTTAAAACTTCCAAAGACTACATTTTTTAC
1 CCCTAAACTTCC-AAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTACA-TTTTTAC
* * * *
9395 CCTTAAACTTCCAAAAATTCCAATTTTGACCCCAAAGCTTTCAAAAATTACCA-TTTTA-
1 CCCTAAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTA-CATTTTTAC
** * * * * **
9453 CCCTCGGA-TGTCCAAAAACTCCATTTTTTA-CCTCGAAACTCTCAAAAATTACCCTTTTAC
1 CCCT-AAACT-TCCAAAAATTCCATTTTTGACCCT-AAAACTTTCAAAAATTACATTTTTAC
* * *
9513 CCTTGAA-TGTCCAAAAATTCTATTTTT
1 CCCTAAACT-TCCAAAAATTCCATTTTT
9540 ATCCTGATTT
Statistics
Matches: 255, Mismatches: 57, Indels: 23
0.76 0.17 0.07
Matches are distributed among these distances:
58 10 0.04
59 181 0.71
60 62 0.24
61 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (59 bp):
CCCTAAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTACATTTTTAC
Found at i:9318 original size:118 final size:119
Alignment explanation
Indices: 9157--9444 Score: 393
Period size: 118 Copynumber: 2.4 Consensus size: 119
9147 CCCTGGAGGT
* * *
9157 CCCTAAACTATCCAAAAATTCCATTTTTGACCCTAAAACTTTTGAAAATTATATTTTTACACCTA
1 CCCTAAACT-TCCAAAAATTACAATTTTGACCCTAAAACTTTTGAAAATTATATTTTTACACCCA
9222 AACTTCC-AAAAATTCCATTTTTGAACTTAAAACTTCCAAAAACTACA-ATTTTAC
65 AACTTCCAAAAAATT-CATTTTTGAACTTAAAACTTCCAAAAACTACATATTTTAC
* * *
9276 CCCTAAACTTCCAAAAATTATAATTTT-ACCCTCGAAACTTTTGAAAATTATATTTTTACCCCCA
1 CCCTAAACTTCCAAAAATTACAATTTTGACCCT-AAAACTTTTGAAAATTATATTTTTACACCCA
* * *
9340 AACTTCCAAAAAATTCATTTTTGACCTTAAAACTTCCAAAGACTACATTTTTTAC
65 AACTTCCAAAAAATTCATTTTTGAACTTAAAACTTCCAAAAACTACATATTTTAC
* * * * **
9395 CCTTAAACTTCCAAAAATTCCAATTTTGACCCCAAAGCTTTCAAAAATTA
1 CCCTAAACTTCCAAAAATTACAATTTTGACCCTAAAACTTTTGAAAATTA
9445 CCATTTTACC
Statistics
Matches: 148, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
117 5 0.03
118 80 0.54
119 59 0.40
120 4 0.03
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.35
Consensus pattern (119 bp):
CCCTAAACTTCCAAAAATTACAATTTTGACCCTAAAACTTTTGAAAATTATATTTTTACACCCAA
ACTTCCAAAAAATTCATTTTTGAACTTAAAACTTCCAAAAACTACATATTTTAC
Found at i:9468 original size:29 final size:29
Alignment explanation
Indices: 9436--9531 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 29
9426 CCAAAGCTTT
*
9436 CAAAAATTACCATTTTACCCTCGGATGTC
1 CAAAAATTACCATTTTACCCTCGAATGTC
* **
9465 CAAAAACT-CCATTTTTTA-CCTCGAAACTC
1 CAAAAATTACCA--TTTTACCCTCGAATGTC
* *
9494 TCAAAAATTACCCTTTTACCCTTGAATGTC
1 -CAAAAATTACCATTTTACCCTCGAATGTC
9524 CAAAAATT
1 CAAAAATT
9532 CTATTTTTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
28 3 0.06
29 28 0.53
30 20 0.38
31 2 0.04
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.32
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCTCGAATGTC
Done.