Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007077.1 Kokia drynarioides strain JFW-HI SEQ_121686, 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: 13060
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Found at i:1847 original size:43 final size:43
Alignment explanation
Indices: 1796--1909 Score: 183
Period size: 43 Copynumber: 2.7 Consensus size: 43
1786 TAATGTTAGT
* * *
1796 GGCGTTTGTGGGAAAAGCGTCGTTAAAGAACATGGTTTTTAGC
1 GGCGTTTGTAGGAAAAGCGTCGTTAAAGAACATGGTCTTTAAC
*
1839 GGTGTTTGTAGGAAAAGCGTCGTTAAAGAACATGGTCTTTAAC
1 GGCGTTTGTAGGAAAAGCGTCGTTAAAGAACATGGTCTTTAAC
*
1882 GGCGTTTGTAGGAAAAGCGCCGTTAAAG
1 GGCGTTTGTAGGAAAAGCGTCGTTAAAG
1910 TCTTTAGCGA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (43 bp):
GGCGTTTGTAGGAAAAGCGTCGTTAAAGAACATGGTCTTTAAC
Found at i:2546 original size:111 final size:112
Alignment explanation
Indices: 2336--2549 Score: 297
Period size: 111 Copynumber: 1.9 Consensus size: 112
2326 TATGGGTCAT
* * * *
2336 TTTTAATCTTTTTCATTCATGCGAGCTTTGCCTCCAATAAAATTCAATTTTATCCGCCTTGCAAC
1 TTTTAATCTTTTTCATTCATGCGAGCTTTGCCTACAATAAAATTCAATTTTATCCACATTACAAC
*
2401 CCTGTTCAAACATTTTTGCATCAAAATTATGGTTAGTGGACCAATGC
66 CCTGTTCAAACATTTTTGCATCAAAATTACGGTTAGTGGACCAATGC
* * * *
2448 TTTTAATC-TTTTCATTCATGGGAGCTTTGCCTACAATAAAATTCATTTTTATCCACATTATAAT
1 TTTTAATCTTTTTCATTCATGCGAGCTTTGCCTACAATAAAATTCAATTTTATCCACATTACAAC
* **
2512 CCTGTTCAAGCATTTTTGCATTGAAA-TAGCGGTTAGTG
66 CCTGTTCAAACATTTTTGCATCAAAATTA-CGGTTAGTG
2550 CTCTAACGAT
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
110 2 0.02
111 79 0.89
112 8 0.09
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (112 bp):
TTTTAATCTTTTTCATTCATGCGAGCTTTGCCTACAATAAAATTCAATTTTATCCACATTACAAC
CCTGTTCAAACATTTTTGCATCAAAATTACGGTTAGTGGACCAATGC
Found at i:3061 original size:49 final size:49
Alignment explanation
Indices: 2988--3288 Score: 327
Period size: 49 Copynumber: 6.1 Consensus size: 49
2978 TTTAATCATG
* * * *
2988 TACCCTAAAAGATATGAAGGGAAAGATTGAAGCCACAATGGCGAATCTTA
1 TACCCT-AGAGATGTGAAGGGAAAGATTGAAGCCGCAATGACGAATCTTA
* * * * * *
3038 TACCCTAAAGACGTGGAGGGAAAGATTGAAACCGTAAT-AGCGAACCTTA
1 TACCCTAGAGATGTGAAGGGAAAGATTGAAGCCGCAATGA-CGAATCTTA
* *
3087 TGCCCTAGAGATGTGAAGGGAAAGATTAGAA-CCGCAATGGCGAATCTTA
1 TACCCTAGAGATGTGAAGGGAAAGATT-GAAGCCGCAATGACGAATCTTA
* * * * *
3136 TACCTTAGAGATGTGGAGGGAAAGATTGAAGCTGCAACGATGAATCTTA
1 TACCCTAGAGATGTGAAGGGAAAGATTGAAGCCGCAATGACGAATCTTA
* ** * *
3185 TACCCTAGAGATGTGAAGGGAAAGACTGAAGTTGCAACGACGAATCTTG
1 TACCCTAGAGATGTGAAGGGAAAGATTGAAGCCGCAATGACGAATCTTA
* * * *
3234 TACCCTAGAGATGTGAAGGAAAAGATTAAAGCCGTAATGACAAATCTTA
1 TACCCTAGAGATGTGAAGGGAAAGATTGAAGCCGCAATGACGAATCTTA
3283 TACCCT
1 TACCCT
3289 GAAGATGAGG
Statistics
Matches: 210, Mismatches: 37, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
48 3 0.01
49 198 0.94
50 9 0.04
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (49 bp):
TACCCTAGAGATGTGAAGGGAAAGATTGAAGCCGCAATGACGAATCTTA
Found at i:3713 original size:99 final size:98
Alignment explanation
Indices: 3473--3853 Score: 272
Period size: 93 Copynumber: 4.0 Consensus size: 98
3463 TTATACCTCA
* * * * * * *
3473 AAGTTGCAGTGAAGCAGATTAAAA-CAACGAAGCAGATCTCAATATCCTTGAGGTTACAGTGGAA
1 AAGTTGCAGTGGATCAGATCAAAATGAACAAAG-A-ATCTCAATGTCCTTAAGGTTACAGTGGAA
* * *
3537 TG-GAG-TG--A-AGA-ATCAGATCCTATATCCCTG
64 TGAGAGATGTTACA-ACATCAAATCCCATACCCCTG
* * ** *
3567 AAGTTGTAGTGGATCTA-ATCAAAAT-AAGTAATCAATCTCAATGTCCTTAAGGTTGCAGTGGAA
1 AAGTTGCAGTGGATC-AGATCAAAATGAA-CAAAGAATCTCAATGTCCTTAAGGTTACAGTGGAA
*
3630 TGGAGAGATGTTACAACATTAAATCCCATACCCCT-
64 T-GAGAGATGTTACAACATCAAATCCCATACCCCTG
* * * * * *
3665 AAGTTGCAGTGGGTCAGATTAAAGT-AACAAAGTAGATCTCAATGTCCTTGAGGTTACAATAGAA
1 AAGTTGCAGTGGATCAGATCAAAATGAACAAAG-A-ATCTCAATGTCCTTAAGGTTACAGTGGAA
* * * * *
3729 TG-GAG-TG--A-AGCACCAGATCCTATATCCCTG
64 TGAGAGATGTTACAACATCAAATCCCATACCCCTG
** * * *
3759 AAGTTGCAGTGGATCAGATCAAAATGAGTAACGAATCTTAATGTCCCTAAGGTTACAGTGGAATT
1 AAGTTGCAGTGGATCAGATCAAAATGAACAAAGAATCTCAATGTCCTTAAGGTTACAGTGGAA-T
*
3824 GAGAGAAGTTACAACATCAAATCCCATACC
65 GAGAGATGTTACAACATCAAATCCCATACC
3854 TTTGAGTTGC
Statistics
Matches: 217, Mismatches: 49, Indels: 37
0.72 0.16 0.12
Matches are distributed among these distances:
93 66 0.30
94 48 0.22
95 12 0.06
96 5 0.02
97 6 0.03
98 26 0.12
99 54 0.25
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.25
Consensus pattern (98 bp):
AAGTTGCAGTGGATCAGATCAAAATGAACAAAGAATCTCAATGTCCTTAAGGTTACAGTGGAATG
AGAGATGTTACAACATCAAATCCCATACCCCTG
Found at i:3864 original size:192 final size:192
Alignment explanation
Indices: 3473--3853 Score: 552
Period size: 192 Copynumber: 2.0 Consensus size: 192
3463 TTATACCTCA
* * * *
3473 AAGTTGCAGTGAAG-CAGATTAAAACAACGAAGCAGATCTCAATATCCTTGAGGTTACAGTGGAA
1 AAGTTGCAGTG-GGTCAGATTAAAACAACAAAGCAGATCTCAATATCCTTGAGGTTACAATAGAA
* *
3537 TGGAGTGAAGAATCAGATCCTATATCCCTGAAGTTGTAGTGGATCTAATCAAAATAAGTAATCAA
65 TGGAGTGAAGAACCAGATCCTATATCCCTGAAGTTGCAGTGGATCTAATCAAAATAAGTAATCAA
* * * *
3602 TCTCAATGTCCTTAAGGTTGCAGTGGAATGGAGAGATGTTACAACATTAAATCCCATACCCCT
130 TCTCAATGTCCCTAAGGTTACAGTGGAATGGAGAGAAGTTACAACATCAAATCCCATACCCCT
** * *
3665 AAGTTGCAGTGGGTCAGATTAAAGTAACAAAGTAGATCTCAATGTCCTTGAGGTTACAATAGAAT
1 AAGTTGCAGTGGGTCAGATTAAAACAACAAAGCAGATCTCAATATCCTTGAGGTTACAATAGAAT
* *
3730 GGAGTGAAGCACCAGATCCTATATCCCTGAAGTTGCAGTGGATC-AGATCAAAATGAGTAA-CGA
66 GGAGTGAAGAACCAGATCCTATATCCCTGAAGTTGCAGTGGATCTA-ATCAAAATAAGTAATC-A
* *
3793 ATCTTAATGTCCCTAAGGTTACAGTGGAATTGAGAGAAGTTACAACATCAAATCCCATACC
129 ATCTCAATGTCCCTAAGGTTACAGTGGAATGGAGAGAAGTTACAACATCAAATCCCATACC
3854 TTTGAGTTGC
Statistics
Matches: 168, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
191 3 0.02
192 165 0.98
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.25
Consensus pattern (192 bp):
AAGTTGCAGTGGGTCAGATTAAAACAACAAAGCAGATCTCAATATCCTTGAGGTTACAATAGAAT
GGAGTGAAGAACCAGATCCTATATCCCTGAAGTTGCAGTGGATCTAATCAAAATAAGTAATCAAT
CTCAATGTCCCTAAGGTTACAGTGGAATGGAGAGAAGTTACAACATCAAATCCCATACCCCT
Found at i:5382 original size:17 final size:18
Alignment explanation
Indices: 5346--5383 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5336 CCGTTTATTT
5346 TTTTAATTTTACTTTAAA
1 TTTTAATTTTACTTTAAA
* *
5364 TTTTATTTTTA-TTTCAA
1 TTTTAATTTTACTTTAAA
5381 TTT
1 TTT
5384 AACCCTTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTAATTTTACTTTAAA
Found at i:6060 original size:109 final size:109
Alignment explanation
Indices: 5864--6066 Score: 273
Period size: 109 Copynumber: 1.9 Consensus size: 109
5854 AATGAGGCAA
** * *
5864 TGTTATTTTATTTTAGGAAACTTGAGAAATTGTGCCCTAGCGTGCTGGGTATGATTTTTCTTTGA
1 TGTTATTTTATTTTAGGAAACTAAAGAAATTGTGCCCTAACGTGCAGGGTATGATTTTTCTTTGA
** *
5929 ACTTAAGTAATTGAATATCCTATTTAAAACTGATAAATGTTTAG
66 ACCAAAATAATTGAATATCCTATTTAAAACTGATAAATGTTTAG
* * ** *
5973 TGTTCTTTTATTTTAGGGAACTCAAAG-AATTGTGTTCTAACGTGCAGGGTATGCTTTTTCTTTG
1 TGTTATTTTATTTTAGGAAACT-AAAGAAATTGTGCCCTAACGTGCAGGGTATGATTTTTCTTTG
*
6037 AACCAAAATAATTGGATATCCTATTTAAAA
65 AACCAAAATAATTGAATATCCTATTTAAAA
6067 TCAATAAATT
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
109 78 0.98
110 2 0.03
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (109 bp):
TGTTATTTTATTTTAGGAAACTAAAGAAATTGTGCCCTAACGTGCAGGGTATGATTTTTCTTTGA
ACCAAAATAATTGAATATCCTATTTAAAACTGATAAATGTTTAG
Found at i:7786 original size:6 final size:6
Alignment explanation
Indices: 7775--7826 Score: 52
Period size: 6 Copynumber: 8.2 Consensus size: 6
7765 AATATAAACG
*
7775 AATAAA AATAAA AATAAA TAATAAA CATAAA CAATAAA TAA-AATA AATAAA
1 AATAAA AATAAA AATAAA -AATAAA AATAAA -AATAAA -AATAA-A AATAAA
7826 A
1 A
7827 GAAAAAGAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 23 0.59
7 16 0.41
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:7797 original size:13 final size:13
Alignment explanation
Indices: 7775--7826 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
7765 AATATAAACG
7775 AATAAA-AATAAA
1 AATAAATAATAAA
7787 AATAAATAATAAA
1 AATAAATAATAAA
* *
7800 CATAAACAATAAA
1 AATAAATAATAAA
*
7813 TA-AAATAAATAAA
1 AATAAAT-AATAAA
7826 A
1 A
7827 GAAAAAGAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
12 9 0.27
13 24 0.73
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (13 bp):
AATAAATAATAAA
Found at i:9125 original size:27 final size:27
Alignment explanation
Indices: 9088--9140 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
9078 CTAGGGAGAT
*
9088 TTGTTAGCTTGTTAGTAAGAGTAGGAG
1 TTGTTAACTTGTTAGTAAGAGTAGGAG
*
9115 TTGTTAACTTGTTAGTAGGAGTAGGA
1 TTGTTAACTTGTTAGTAAGAGTAGGA
9141 ATTTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.32, T:0.38
Consensus pattern (27 bp):
TTGTTAACTTGTTAGTAAGAGTAGGAG
Found at i:10973 original size:30 final size:30
Alignment explanation
Indices: 10937--10996 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
10927 CCCTCTCTAA
10937 TGATAAACTATCATATTTTGCATAGGAAAT
1 TGATAAACTATCATATTTTGCATAGGAAAT
10967 TGATAAACTATCATATTTTGCATAGGAAAT
1 TGATAAACTATCATATTTTGCATAGGAAAT
10997 ATCTGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (30 bp):
TGATAAACTATCATATTTTGCATAGGAAAT
Found at i:11453 original size:21 final size:21
Alignment explanation
Indices: 11420--11462 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
11410 TTATTAATAA
* *
11420 GACTGAGTTTTAAGGAGATTT
1 GACTAAGTCTTAAGGAGATTT
11441 GACTAAGTCTTAAGGAGATTT
1 GACTAAGTCTTAAGGAGATTT
11462 G
1 G
11463 TTAGCTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35
Consensus pattern (21 bp):
GACTAAGTCTTAAGGAGATTT
Done.