Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006737.1 Kokia drynarioides strain JFW-HI SEQ_121335, 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: 5265
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:3431 original size:81 final size:81
Alignment explanation
Indices: 3339--4085 Score: 889
Period size: 81 Copynumber: 9.2 Consensus size: 81
3329 CTTGATTAGG
* * * * * * * *
3339 GGTAAAAGATTGGATGGTGTTTTAAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
*
3404 TTTGCCCCATGGTCGA
66 TCTGCCCCATGGTCGA
* * *
3420 GGTAAGAGATTGAATGGTGTCTTCAATCTGCCTTCTGGTTAGGGTAAAAGATTGGATGACTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
*
3485 TCTGCCCCATGGTCGG
66 TCTGCCCCATGGTCGA
* *
3501 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTAGCTAGGGTAAAAGATTGGATGGCTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
*
3566 TCTGCCCTATGGTC-A
66 TCTGCCCCATGGTCGA
* * * * *
3581 GGGTAAGAGATT-GAGTGGTGTCTTCAATTTTCCCTCTGGTTATGATAAAAGATTGAATGGCTTC
1 -GGTAAGAGATTGGA-TGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTC
3645 AATCTGCCCCATGGTC-A
64 AATCTGCCCCATGGTCGA
**
3662 GGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATAACTTCA
1 -GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCA
* * * *
3727 ATTTGCCCCATGATTGG
65 ATCTGCCCCATGGTCGA
* * * *
3744 GGTAAGAGATTGAATGATGTCTTCAATCTACCCTCTGGTTAGGGTAAAAGATTGGTTGGCTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
*
3809 TCTGCCTCATGGTC-A
66 TCTGCCCCATGGTCGA
* ** * *
3824 GGGTAAGA-ATTTGAAT-GTGTCTTCAATCTGCCCTCTTATTAGGGTAAAAGATTAGATGGTTTC
1 -GGTAAGAGA-TTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTC
* * *
3887 AATCTGCCCCTTGGTTGG
64 AATCTGCCCCATGGTCGA
* * *
3905 GGTAAGAGATTGGATGGTGTCTTCAATCTGCTCTCTGATTAGGGTAAAAGATTGGATGGCTTTAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
** *
3970 TCTATCCTATGGTC-A
66 TCTGCCCCATGGTCGA
* * * * * *
3985 GAGTAAGAGATTAGATAGTGTCTTCAATATGCTCTCTGGTTAGGGTAAAAGATTTGATGGGTTCA
1 G-GTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCA
*
4050 ATCTGTCCCATGGTCTG-
65 ATCTGCCCCATGGTC-GA
*
4067 GGTAAGAGATTTGATGGTG
1 GGTAAGAGATTGGATGGTG
4086 ATGTAATTTC
Statistics
Matches: 570, Mismatches: 84, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
80 69 0.12
81 498 0.87
82 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (81 bp):
GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
TCTGCCCCATGGTCGA
Found at i:3791 original size:243 final size:243
Alignment explanation
Indices: 3338--4085 Score: 978
Period size: 243 Copynumber: 3.1 Consensus size: 243
3328 TCTTGATTAG
* * * *
3338 GGGTAAAAGATTGGA-TGGTGTTTTAAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTC
1 GGGTAAGAGATTTGAGTGGTGTCTTCAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTC
* * *
3402 AATTTGCCCCATGGTCGAGGTAAGAGATTGAATGGTGTCTTCAATCTGCCTTCTGGTTAGGGTAA
66 AATCTGCCCCATGGTCG-GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAA
* *
3467 AAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGGTGTCTTCAATCTGC
130 AAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGATGTCTTCAATCTGC
* *
3532 CCTCTAGCTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTATGGTCA
195 CCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTATGGTCA
* * * *
3581 GGGTAAGAGA-TTGAGTGGTGTCTTCAATTTTCCCTCTGGTTATGATAAAAGATTGAATGGCTTC
1 GGGTAAGAGATTTGAGTGGTGTCTTCAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTC
3645 AATCTGCCCCATGGTCAGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAA
66 AATCTGCCCCATGGTC-GGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAA
* * * * *
3710 AAGATTGGATAACTTCAATTTGCCCCATGATTGGGGTAAGAGATTGAATGATGTCTTCAATCTAC
130 AAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGATGTCTTCAATCTGC
*
3775 CCTCTGGTTAGGGTAAAAGATTGGTTGGCTTCAATCTG-CCTCATGGTCA
195 CCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCT-ATGGTCA
* * *
3824 GGGTAAGA-ATTTGAAT-GTGTCTTCAATCTGCCCTCTTA-TTAGGGTAAAAGATT-AGATGGTT
1 GGGTAAGAGATTTGAGTGGTGTCTTCAATTTTCCCTC-TAGTTAGGGTAAAAGATTGA-ATGGTT
* * * *
3885 TCAATCTGCCCCTTGGTTGGGGTAAGAGATTGGATGGTGTCTTCAATCTGCTCTCTGATTAGGGT
64 TCAATCTGCCCCATGG-TCGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGT
* * ** * * *
3950 AAAAGATTGGATGGCTTTAATCTATCCTATGGTCAGAGTAAGAGATT-AGAT-AGTGTCTTCAAT
128 AAAAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGA-ATGA-TGTCTTCAAT
* * * * *
4013 ATGCTCTCTGGTTAGGGTAAAAGATTTGATGGGTTCAATCTGTCCC-ATGGTCT
191 CTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATCTG-CCCTATGGTCA
4066 GGGTAAGAGATTTGA-TGGTG
1 GGGTAAGAGATTTGAGTGGTG
4086 ATGTAATTTC
Statistics
Matches: 442, Mismatches: 50, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
241 3 0.01
242 200 0.45
243 236 0.53
244 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (243 bp):
GGGTAAGAGATTTGAGTGGTGTCTTCAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTC
AATCTGCCCCATGGTCGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
AGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGATGTCTTCAATCTGCC
CTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTATGGTCA
Found at i:4415 original size:93 final size:92
Alignment explanation
Indices: 4194--4801 Score: 357
Period size: 93 Copynumber: 6.4 Consensus size: 92
4184 GGTTTTGAAA
* * * * *** *
4194 CTTCACTCCATTCCACTTTAACCTTAGGGACATTAAGATCTGCTT-TTGGCTTTAATCTGA-CCT
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGAT-T-CTTACTCATTTTAATCCGATCC-
* * * *
4257 ACAGCAACTTC-AGTGGTATAGGATCTAGTG
63 ACTGTAACTTCAAG-GATATAGGATCTGGTG
** *** * *
4287 CTTCACTCCATTCTGCTGTAACCTCAAACACATTGAGATTCATTACTCATTTTAATCCAATTCAC
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATTC-TTACTCATTTTAATCCGATCCAC
4352 TGTAACTTCAAGGATATAGGATCTGGTG
65 TGTAACTTCAAGGATATAGGATCTGGTG
* *** * **
4380 CTTCACTCCATTCCACTGTAACCTCAGGGATATTGAGATCTGCTT-CGTTGCTTTAATTCGGCCC
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGAT-T-CTTAC-TCATTTTAATCCGATCC
* * * * *
4444 ATTATAACTT-ATGGGTATAGGATTTGGTATTG
63 ACTGTAACTTCAAGGATATAGGATCTGG---TG
* * * * *
4476 TAACTTCTCTCCATTCCACTGTAACCTTAGGGACATTGAGATCCGTACTCATTTTAATCCAATCC
1 ---CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATTCTTACTCATTTTAATCCGATCC
* * *
4541 ATTGCAACTTCAAAGATATAGGATCTGGTG
63 ACTGTAACTTCAAGGATATAGGATCTGGTG
* * * ** ** * *
4571 CTTCACTCTATTCCACTGTAGCCTCAAGGACATTGAGATCTGCTTTGTTGTTTTAATCTGACCCA
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGAT-T-CTTACTCATTTTAATCCGATCCA
** * * * *
4636 CTACAAC-TCTGAGG-TATGGGATTTGATATTGTAA
64 CTGTAACTTC-AAGGATATAGGATCTG-----GT-G
* * * * * * *
4670 CTTCTCTCCATTCCACTATAACCTTAGAGACATTAAGATTCGTTACTCATTTTGATTCGATCCAC
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATTC-TTACTCATTTTAATCCGATCCAC
* * *
4735 TGTAACTTTAGGGATATAGGATTTGGTG
65 TGTAACTTCAAGGATATAGGATCTGGTG
* *
4763 CTTCACTCCATTCCATTGTAATCTCAGGGACATTGAGAT
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGAT
4802 CTGCTTCATT
Statistics
Matches: 381, Mismatches: 107, Indels: 54
0.70 0.20 0.10
Matches are distributed among these distances:
91 1 0.00
92 37 0.10
93 154 0.40
94 47 0.12
95 3 0.01
96 2 0.01
97 21 0.06
98 38 0.10
99 78 0.20
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (92 bp):
CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATTCTTACTCATTTTAATCCGATCCACT
GTAACTTCAAGGATATAGGATCTGGTG
Found at i:4514 original size:192 final size:193
Alignment explanation
Indices: 4316--4850 Score: 695
Period size: 191 Copynumber: 2.8 Consensus size: 193
4306 AACCTCAAAC
*
4316 ACATTGAGATTCATTACTCATTTTAATCCAATTCACTGTAACTTCAAGGATATAGGATCTGGTGC
1 ACATTGAGATTCATTACTCATTTTAATCCAATCCACTGTAACTTCAAGGATATAGGATCTGGTGC
* * *
4381 TTCACTCCATTCCACTGTAACCTCAGGGATATTGAGATCTGCTTCGTTGCTTTAATTC-GGCCCA
66 TTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTCGTTGTTTTAATTCTGACCCA
* * * * *
4445 TTATAACTTATG-GGTATAGGATTTGGTATTGTAACTTCTCTCCATTCCACTGTAACCTTAGGG
131 CTACAAC-TATGAGGTATAGGATTTGATATTGTAACTTCTCTCCATTCCACTATAACCTTAGAG
** * * *
4508 ACATTGAGA-TCCGTACTCATTTTAATCCAATCCATTGCAACTTCAAAGATATAGGATCTGGTGC
1 ACATTGAGATTCATTACTCATTTTAATCCAATCCACTGTAACTTCAAGGATATAGGATCTGGTGC
* * * *
4572 TTCACTCTATTCCACTGTAGCCTCAAGGACATTGAGATCTGCTTTGTTGTTTTAA-TCTGACCCA
66 TTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTCGTTGTTTTAATTCTGACCCA
* *
4636 CTACAACTCTGAGGTATGGGATTTGATATTGTAACTTCTCTCCATTCCACTATAACCTTAGAG
131 CTACAACTATGAGGTATAGGATTTGATATTGTAACTTCTCTCCATTCCACTATAACCTTAGAG
* * * * * * * *
4699 ACATTAAGATTCGTTACTCATTTTGATTCGATCCACTGTAACTTTAGGGATATAGGATTTGGTGC
1 ACATTGAGATTCATTACTCATTTTAATCCAATCCACTGTAACTTCAAGGATATAGGATCTGGTGC
* * * *
4764 TTCACTCCATTCCATTGTAATCTCAGGGACATTGAGATCTGCTTCATTGTTTTAA-TCTG-CTTC
66 TTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTCGTTGTTTTAATTCTGAC-CC
* * *
4827 ACTTCAACTTTGAGGTATAAGATT
130 ACTACAACTATGAGGTATAGGATT
4851 CACCATTACA
Statistics
Matches: 295, Mismatches: 44, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
190 5 0.02
191 164 0.56
192 126 0.43
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (193 bp):
ACATTGAGATTCATTACTCATTTTAATCCAATCCACTGTAACTTCAAGGATATAGGATCTGGTGC
TTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTCGTTGTTTTAATTCTGACCCA
CTACAACTATGAGGTATAGGATTTGATATTGTAACTTCTCTCCATTCCACTATAACCTTAGAG
Found at i:5131 original size:98 final size:98
Alignment explanation
Indices: 5024--5258 Score: 262
Period size: 98 Copynumber: 2.4 Consensus size: 98
5014 TCACCTTCAA
* * * ***
5024 GGTATAAGATTCTCTATTGC-AGCTTCAATCTTTGCCTTCACATCTCTAGGCTATAAGATTTGTC
1 GGTACAAGATTCTCTATTGCGA-CTTCAATCTTTCCCTTCACATCTCTAGGCTAGAAGATTCACC
* *
5088 GTTGCGGCTTCAAT-TGTTCACCCT-ACATCTCTAG
65 ATTACGGCTTCAATCT-TTC-CCCTCACATCTCTAG
* ** *
5122 GGTACAAGATTCACCGTTGCGACTTCAATCTTTCCCTTCACATCTCTAGGGTAGAAGATTCACCA
1 GGTACAAGATTCTCTATTGCGACTTCAATCTTTCCCTTCACATCTCTAGGCTAGAAGATTCACCA
* * *
5187 TTACGGCTTCAATCTTTCCCTTCATATCTTTAG
66 TTACGGCTTCAATCTTTCCCCTCACATCTCTAG
*
5220 GGTACAAGATTCGT-TATTGCGACTTTAATCTTTCCCTTC
1 GGTACAAGATTC-TCTATTGCGACTTCAATCTTTCCCTTC
5259 TTATCTC
Statistics
Matches: 114, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
97 3 0.03
98 109 0.96
99 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (98 bp):
GGTACAAGATTCTCTATTGCGACTTCAATCTTTCCCTTCACATCTCTAGGCTAGAAGATTCACCA
TTACGGCTTCAATCTTTCCCCTCACATCTCTAG
Found at i:5264 original size:49 final size:49
Alignment explanation
Indices: 5024--5265 Score: 211
Period size: 49 Copynumber: 4.9 Consensus size: 49
5014 TCACCTTCAA
* * * * *
5024 GGTATAAGATTCTCTATTGC-AGCTTCAATCTTTGCCTTCACATCTCTAG
1 GGTACAAGATTCACCATTGCGA-CTTCAATCTTTCCCTTCATATCTCTAG
* * *** * * * *
5073 GCTATAAGATTTGTCGTTGCGGCTTCAAT-TGTTCACCCT-ACATCTCTAG
1 GGTACAAGATTCACCATTGCGACTTCAATCT-TTC-CCTTCATATCTCTAG
* *
5122 GGTACAAGATTCACCGTTGCGACTTCAATCTTTCCCTTCACATCTCTAG
1 GGTACAAGATTCACCATTGCGACTTCAATCTTTCCCTTCATATCTCTAG
* * * *
5171 GGTAGAAGATTCACCATTACGGCTTCAATCTTTCCCTTCATATCTTTAG
1 GGTACAAGATTCACCATTGCGACTTCAATCTTTCCCTTCATATCTCTAG
*** * *
5220 GGTACAAGATTCGTTATTGCGACTTTAATCTTTCCCTTCTTATCTC
1 GGTACAAGATTCACCATTGCGACTTCAATCTTTCCCTTCATATCTC
Statistics
Matches: 157, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
48 4 0.03
49 149 0.95
50 4 0.03
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.38
Consensus pattern (49 bp):
GGTACAAGATTCACCATTGCGACTTCAATCTTTCCCTTCATATCTCTAG
Done.