Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001422.1 Kokia drynarioides strain JFW-HI SEQ_112922, 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: 9974
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:2187 original size:50 final size:50
Alignment explanation
Indices: 1992--2190 Score: 165
Period size: 50 Copynumber: 4.0 Consensus size: 50
1982 GGTCTCAGCA
* * *
1992 TCAGAAAACACGACGTGAAAGATCTAAGACCGCAACGGCTGATCCAGTA-C
1 TCAGAAAACACGAAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACC
* * **
2042 TGCA-AAGATACA-AAAGGGAAAGATCTAAACTACAACGGCGGATCCAGTACC
1 T-CAGAA-A-ACACGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACC
* * * * * * * *
2093 AC-GAAGACAC-AAGGGAAAGGTTTAAGTCGCAATGGCGAACCCAGTACC
1 TCAGAAAACACGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACC
* * *
2141 TCAGAAAACACGACGAGAAAGATCTAAGCCGCAACGACGGATCCAGTACC
1 TCAGAAAACACGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACC
2191 GCGAAGACGC
Statistics
Matches: 112, Mismatches: 29, Indels: 16
0.71 0.18 0.10
Matches are distributed among these distances:
48 33 0.29
49 7 0.06
50 52 0.46
51 17 0.15
52 3 0.03
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.13
Consensus pattern (50 bp):
TCAGAAAACACGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACC
Found at i:2714 original size:6 final size:6
Alignment explanation
Indices: 2692--2731 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
2682 GTTTAAATTG
* *
2692 ATTTAA ATTTAT TTTTAA ATTTAA ATTTTAA ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA A-TTTAA ATTTAA ATT
2732 GATTTAAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
ATTTAA
Found at i:2722 original size:13 final size:13
Alignment explanation
Indices: 2693--2731 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
2683 TTTAAATTGA
*
2693 TTTAAATTT-ATT
1 TTTAAATTTAAAT
2705 TTTAAATTTAAAT
1 TTTAAATTTAAAT
2718 TTTAAATTTAAAT
1 TTTAAATTTAAAT
2731 T
1 T
2732 GATTTAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTAAATTTAAAT
Found at i:3486 original size:3 final size:3
Alignment explanation
Indices: 3478--3553 Score: 55
Period size: 3 Copynumber: 25.0 Consensus size: 3
3468 TAAATAACCT
* * * * *
3478 TAA TAA TAA AAA TAA TAA GT-A TAA TAC TAA TGA CAT TAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA -TAA TAA
* * *
3524 TAA TAA TAT TAA TAA TAA CAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3554 ATAAATAAAA
Statistics
Matches: 54, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
2 1 0.02
3 49 0.91
4 4 0.07
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3534 original size:15 final size:15
Alignment explanation
Indices: 3516--3553 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
3506 AATGACATTA
*
3516 ATTAATAATAATAAT
1 ATTAATAATAACAAT
3531 ATTAATAATAACAAT
1 ATTAATAATAACAAT
3546 ATTAATAA
1 ATTAATAA
3554 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTAATAATAACAAT
Found at i:4755 original size:29 final size:29
Alignment explanation
Indices: 4713--5193 Score: 185
Period size: 29 Copynumber: 16.4 Consensus size: 29
4703 AGGTCGCTAA
*
4713 AAAATTACATTTTTACCCTCGAACTTTCC
1 AAAATTCCATTTTTACCCTCGAACTTTCC
**
4742 AAAATTCCATTTTTGA-CCTTAAACTTTCC
1 AAAATTCCATTTTT-ACCCTCGAACTTTCC
* *
4771 AAAAATTACATTTTTACCCT-AAACTTTCC
1 -AAAATTCCATTTTTACCCTCGAACTTTCC
* *
4800 AAAATTCCATTTTTA-ACTCCAAACTTTCC
1 AAAATTCCATTTTTACCCT-CGAACTTTCC
*
4829 AAAAATTACATTTTTGA-CCTCGAACTTTCC
1 -AAAATTCCATTTTT-ACCCTCGAACTTTCC
** * *
4859 AAACAAAAACCA-TTTTACCCTTGAA-TTCCC
1 --A-AAATTCCATTTTTACCCTCGAACTTTCC
* **
4889 AAAAATTCCATTTTTGACCC-CAAACTTTTTG
1 -AAAATTCCATTTTT-ACCCTCGAAC-TTTCC
* * *
4920 AAAATTACAATTGTACCCTCGAAC-TTCC
1 AAAATTCCATTTTTACCCTCGAACTTTCC
* * **
4948 AAAAATTCCATTTTTAACCAT-GATCTTTTTG
1 -AAAATTCCATTTTT-ACCCTCGAAC-TTTCC
* **
4979 AAAATTACCA-TTTTACCCTTGAACTTTTG
1 AAAATT-CCATTTTTACCCTCGAACTTTCC
* * **
5008 AAATTTCCATTTTTAACCCT--AATTTTTTAG
1 AAAATTCCATTTTT-ACCCTCGAA--CTTTCC
* *
5038 AAAATTACCA-TTTTACCCCCAAAC-TTCC
1 AAAATT-CCATTTTTACCCTCGAACTTTCC
* **
5066 AAAAATTTCATTTTTGA-CCTCGATTTTTCC
1 -AAAATTCCATTTTT-ACCCTCGAACTTTCC
** *
5096 AAAATT--ATCGTTAGCCCT-AAAC-TTCC
1 AAAATTCCATTTTTA-CCCTCGAACTTTCC
* * ** **
5122 AAAAAATCTATTTTTGACCC-CGATTTTTTG
1 -AAAATTCCATTTTT-ACCCTCGAACTTTCC
* *
5152 AAAATTACCA-TTTTACCCTCAAACTTTCA
1 AAAATT-CCATTTTTACCCTCGAACTTTCC
5181 AAAATTCCATTTT
1 AAAATTCCATTTT
5194 CGACCCCGAT
Statistics
Matches: 340, Mismatches: 69, Indels: 86
0.69 0.14 0.17
Matches are distributed among these distances:
26 5 0.01
27 12 0.04
28 41 0.12
29 142 0.42
30 108 0.32
31 27 0.08
32 5 0.01
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCTCGAACTTTCC
Found at i:4783 original size:30 final size:29
Alignment explanation
Indices: 4712--4963 Score: 192
Period size: 29 Copynumber: 8.6 Consensus size: 29
4702 AAGGTCGCTA
*
4712 AAAAATTACATTTTTACCCTCGAACTTTCC
1 AAAAATTACATTTTTA-CCTCAAACTTTCC
* *
4742 -AAAATTCCATTTTTGACCTTAAACTTTCC
1 AAAAATTACATTTTT-ACCTCAAACTTTCC
4771 AAAAATTACATTTTTACC-CTAAACTTTCC
1 AAAAATTACATTTTTACCTC-AAACTTTCC
* *
4800 -AAAATTCCATTTTTAACTCCAAACTTTCC
1 AAAAATTACATTTTTACCT-CAAACTTTCC
*
4829 AAAAATTACATTTTTGACCTCGAACTTTCC
1 AAAAATTACATTTTT-ACCTCAAACTTTCC
** ** *
4859 AAACAAAAACCA-TTTTACCCTTGAA-TTCCC
1 AAA-AATTA-CATTTTTA-CCTCAAACTTTCC
* * **
4889 AAAAATTCCATTTTTGACCCCAAACTTTTT
1 AAAAATTACATTTTT-ACCTCAAACTTTCC
* * * *
4919 GAAAATTACAATTGTACCCTCGAAC-TTCC
1 AAAAATTACATTTTTA-CCTCAAACTTTCC
*
4948 AAAAATTCCATTTTTA
1 AAAAATTACATTTTTA
4964 ACCATGATCT
Statistics
Matches: 173, Mismatches: 35, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
28 17 0.10
29 70 0.40
30 68 0.39
31 16 0.09
32 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAAATTACATTTTTACCTCAAACTTTCC
Found at i:4811 original size:58 final size:59
Alignment explanation
Indices: 4712--4861 Score: 234
Period size: 58 Copynumber: 2.6 Consensus size: 59
4702 AAGGTCGCTA
* *
4712 AAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGAC-CTTAAACTTTCC
1 AAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACTC-CAAACTTTCC
*
4771 AAAAATTACATTTTTACCCT-AAACTTTCCAAAATTCCATTTTTAACTCCAAACTTTCC
1 AAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACTCCAAACTTTCC
4829 AAAAATTACATTTTTGA-CCTCGAACTTTCCAAA
1 AAAAATTACATTTTT-ACCCTCGAACTTTCCAAA
4862 CAAAAACCAT
Statistics
Matches: 84, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
58 51 0.61
59 33 0.39
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (59 bp):
AAAAATTACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACTCCAAACTTTCC
Found at i:4956 original size:59 final size:58
Alignment explanation
Indices: 4712--5200 Score: 311
Period size: 59 Copynumber: 8.4 Consensus size: 58
4702 AAGGTCGCTA
* ** *
4712 AAAAATTACATTTTT-ACCCTCGAAC-TTTCCAAAATT-CCATTTTTGA-CCTTAAACTTTCC
1 AAAAATTCCATTTTTGACCC-C-AACTTTTTGAAAATTACCA-TTTT-ACCCTCAAAC-TTCC
* * ** *
4771 AAAAATTACATTTTT-ACCCTAAAC-TTTCCAAAATT-CCATTTTTA-ACTCCAAACTTTCC
1 AAAAATTCCATTTTTGACCC-CAACTTTTTGAAAATTACCA-TTTTACCCT-CAAAC-TTCC
* * *** ** **
4829 AAAAATTACATTTTTGACCTCGAACTTTCCAAACAAAAACCATTTTACCCTTGAA-TTCCC
1 AAAAATTCCATTTTTGACC-CCAACTTTTTGAA-AATTACCATTTTACCCTCAAACTT-CC
* * *
4889 AAAAATTCCATTTTTGACCCCAAACTTTTTGAAAATTACAATTGTACCCTCGAACTTCC
1 AAAAATTCCATTTTTGACCCC-AACTTTTTGAAAATTACCATTTTACCCTCAAACTTCC
* ** * ** **
4948 AAAAATTCCATTTTTAACCATGATCTTTTTGAAAATTACCATTTTACCCTTGAACTTTT
1 AAAAATTCCATTTTTGACC-CCAACTTTTTGAAAATTACCATTTTACCCTCAAACTTCC
* * * * * *
5007 GAAATTTCCATTTTTAACCCTAATTTTTTAGAAAATTACCATTTTACCCCCAAACTTCC
1 AAAAATTCCATTTTTGACCCCAACTTTTT-GAAAATTACCATTTTACCCTCAAACTTCC
* * * * * *
5066 AAAAATTTCATTTTTGACCTCGA-TTTTTCCAAAATTATC--GTTAGCCCT-AAACTTCC
1 AAAAATTCCATTTTTGACCCCAACTTTTT-GAAAATTACCATTTTA-CCCTCAAACTTCC
* * * * *
5122 AAAAAATCTATTTTTGACCCCGATTTTTTGAAAATTACCATTTTACCCTCAAACTTTC
1 AAAAATTCCATTTTTGACCCCAACTTTTTGAAAATTACCATTTTACCCTCAAACTTCC
*
5180 AAAAATTCCATTTTCGACCCC
1 AAAAATTCCATTTTTGACCCC
5201 GATTCTTCCA
Statistics
Matches: 349, Mismatches: 64, Indels: 35
0.78 0.14 0.08
Matches are distributed among these distances:
56 38 0.11
57 15 0.04
58 93 0.27
59 153 0.44
60 36 0.10
61 9 0.03
62 5 0.01
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (58 bp):
AAAAATTCCATTTTTGACCCCAACTTTTTGAAAATTACCATTTTACCCTCAAACTTCC
Found at i:5658 original size:95 final size:94
Alignment explanation
Indices: 5480--5669 Score: 215
Period size: 95 Copynumber: 2.0 Consensus size: 94
5470 AAAAACTTTA
* * * *
5480 AAATCGAGGCAATATTTTTTTATTCTGAGATTTGAAAATTTGTGCCCTAACTTACTAGGCACGAT
1 AAATCGAGGCAATATTTCTTTATTCT-AGATTTGAAAATTTGTGACCTAACTTACTAGGCACAAC
* * *
5545 TTTTTCAAATCGGAATAATCAAATATCCTT
65 TTTTTCAAAGCAGAATAATCAAACATCCTT
* **
5575 AAATCGAGGCAATGTTTCTTTATCTCT-GATTCTGAAAATTTGT-ACCTAAACTTACTAGGTGCA
1 AAATCGAGGCAATATTTCTTTAT-TCTAGATT-TGAAAATTTGTGACCT-AACTTACTAGGCACA
*
5638 ACTTTTTCAAAGCA-AGATAATCGAACATCCTT
63 ACTTTTTCAAAGCAGA-ATAATCAAACATCCTT
5670 TTCCTTAGTT
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
94 8 0.10
95 69 0.86
96 3 0.04
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (94 bp):
AAATCGAGGCAATATTTCTTTATTCTAGATTTGAAAATTTGTGACCTAACTTACTAGGCACAACT
TTTTCAAAGCAGAATAATCAAACATCCTT
Found at i:6429 original size:52 final size:52
Alignment explanation
Indices: 6351--6452 Score: 143
Period size: 52 Copynumber: 2.0 Consensus size: 52
6341 TTTTATTATC
* * * * *
6351 TATTTTAGTTCTTAAATTTGCGTTGTTTGTCAAACCACCTCAAATGTATGGA
1 TATTTTAGTTCTTAAACTTACATTGTTTGTCAAAACACCTAAAATGTATGGA
6403 TATTTTAG-TCTTTAAACTTACATTGTTTGTCAAAACACCTAAAATGTATG
1 TATTTTAGTTC-TTAAACTTACATTGTTTGTCAAAACACCTAAAATGTATG
6453 AAAAAGTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 2 0.05
52 42 0.95
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (52 bp):
TATTTTAGTTCTTAAACTTACATTGTTTGTCAAAACACCTAAAATGTATGGA
Found at i:8006 original size:22 final size:21
Alignment explanation
Indices: 7973--8013 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
7963 TCAACTAATT
7973 AATTTTTAAAAAATATAAAAAA
1 AATTTTTAAAAAAT-TAAAAAA
7995 AATTATTT-AAAAATTAAAA
1 AATT-TTTAAAAAATTAAAA
8014 TTGGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 10 0.56
23 3 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AATTTTTAAAAAATTAAAAAA
Found at i:8031 original size:9 final size:10
Alignment explanation
Indices: 8010--8035 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
8000 TTTAAAAATT
8010 AAAATTGGAA
1 AAAATTGGAA
8020 AAAATTGGAA
1 AAAATTGGAA
8030 AAAATT
1 AAAATT
8036 ATTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (10 bp):
AAAATTGGAA
Found at i:8638 original size:17 final size:17
Alignment explanation
Indices: 8577--8629 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
8567 GGCTTAACAG
*
8577 AATTTAAATTTATTTTTA
1 AATTTAAATTTA-TTTGA
*
8595 AA-TTAAGTTTATTTGA
1 AATTTAAATTTATTTGA
8611 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTGA
8628 AA
1 AA
8630 ATTTTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 6 0.19
17 23 0.74
18 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTATTTGA
Found at i:8691 original size:30 final size:31
Alignment explanation
Indices: 8635--8700 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
8625 TGAAAATTTT
*
8635 ATTTTTGACCCCGAAACTTTCAAAAATT-CC
1 ATTTTTGACCCCGAAACTTCCAAAAATTACC
* *
8665 ATTTTTGACCTCG-AACTATCCCAAAATTACC
1 ATTTTTGACCCCGAAACT-TCCAAAAATTACC
8696 ATTTT
1 ATTTT
8701 GCCCCTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 4 0.13
30 20 0.65
31 7 0.23
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (31 bp):
ATTTTTGACCCCGAAACTTCCAAAAATTACC
Found at i:9086 original size:96 final size:96
Alignment explanation
Indices: 8954--9135 Score: 264
Period size: 96 Copynumber: 1.9 Consensus size: 96
8944 AAAACTTTAA
**
8954 AATCGAGGCAATATTCCTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAATT
1 AATCGAGGCAATATTCCTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
*
9019 TTTCTTCAAATCGAA-ATAATCAAATACCCTT
66 TTTCCTCAAATC-AAGATAATCAAATACCCTT
*
9050 AATCGAGGCAATGTTTCC-TTATCTTCGA--TTCTGAAAATTTGCGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAAT-ATTCCTTTAT-TTCGAGTTTC-GAAAATTTGCGCCTTAACTTACTAGGTGCA
9112 ACCTTTCCTCAAATCAAGATAATC
63 ACCTTTCCTCAAATCAAGATAATC
9136 GAACCTCCTT
Statistics
Matches: 78, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
95 5 0.06
96 64 0.82
97 9 0.12
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.35
Consensus pattern (96 bp):
AATCGAGGCAATATTCCTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
TTTCCTCAAATCAAGATAATCAAATACCCTT
Done.