Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003837.1 Kokia drynarioides strain JFW-HI SEQ_116853, 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: 17284
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Warning! 120 characters in sequence are not A, C, G, or T
Found at i:1794 original size:29 final size:31
Alignment explanation
Indices: 1762--1828 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 31
1752 AATTTTTTAT
1762 ATTTTTATAGT-TTTTAAAAAATTAAA-T-TA
1 ATTTTT-TAGTATTTTAAAAAATTAAAGTATA
* *
1791 ATTTTTTATTATTTTAAAAAGTTAAAGTATA
1 ATTTTTTAGTATTTTAAAAAATTAAAGTATA
1822 ATTTTTT
1 ATTTTTT
1829 TATTATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 3 0.09
29 20 0.61
30 1 0.03
31 9 0.27
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (31 bp):
ATTTTTTAGTATTTTAAAAAATTAAAGTATA
Found at i:1799 original size:30 final size:31
Alignment explanation
Indices: 1773--1835 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 31
1763 TTTTTATAGT
1773 TTTTAAAAAATTAAA-T-TAATTTTTTATTA
1 TTTTAAAAAATTAAAGTATAATTTTTTATTA
*
1802 TTTTAAAAAGTTAAAGTATAATTTTTTTATTA
1 TTTTAAAAAATTAAAGTATAA-TTTTTTATTA
1834 TT
1 TT
1836 AATTTAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 14 0.47
30 1 0.03
31 3 0.10
32 12 0.40
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (31 bp):
TTTTAAAAAATTAAAGTATAATTTTTTATTA
Found at i:8931 original size:28 final size:28
Alignment explanation
Indices: 8871--8932 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
8861 TAGTATTTTT
* * *
8871 AATTTATTTTTATTATTTTAAATAAAAA
1 AATTTATTTTTATCATTATAAAAAAAAA
*
8899 TATTTATTTTTA-CATTATAAAAAAATAA
1 AATTTATTTTTATCATTATAAAAAAA-AA
8927 AATTTA
1 AATTTA
8933 ATTAAAAAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
AATTTATTTTTATCATTATAAAAAAAAA
Found at i:8941 original size:18 final size:18
Alignment explanation
Indices: 8918--8953 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
8908 TTACATTATA
*
8918 AAAAAATAAAATTTAATT
1 AAAAAACAAAATTTAATT
*
8936 AAAAAACAAATTTTAATT
1 AAAAAACAAAATTTAATT
8954 CATTTCGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAAACAAAATTTAATT
Found at i:13241 original size:29 final size:29
Alignment explanation
Indices: 13199--13257 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
13189 GTGCAATGGC
** *
13199 CACACGAGTGTGTGCTAGACTATGTGTGG
1 CACACGAGCATGTGCTAGACCATGTGTGG
*
13228 CACACGAGCATGTGCTAGACCGTGTGTGG
1 CACACGAGCATGTGCTAGACCATGTGTGG
13257 C
1 C
13258 TACTGTTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.20, C:0.22, G:0.34, T:0.24
Consensus pattern (29 bp):
CACACGAGCATGTGCTAGACCATGTGTGG
Found at i:13346 original size:72 final size:72
Alignment explanation
Indices: 13228--13431 Score: 340
Period size: 72 Copynumber: 2.8 Consensus size: 72
13218 CTATGTGTGG
* *
13228 CACACGAGCATGTGCTAGACCGTGTGTGGCTACTGTTTTCTAATTTAAGGTGCAGTTGTCACACG
1 CACACGAGCATGTGCTAGACCGTGTGTGGCTACTGTTTTCTGATTTAAGGTGCAGTGGTCACACG
13293 GGCAAGC
66 GGCAAGC
*
13300 CACACGAGCATGTGCTAGACCGTATGTGGCTACTGTTCTT-TGATTTAAGGTGCAGTGGTCACAC
1 CACACGAGCATGTGCTAGACCGTGTGTGGCTACTGTT-TTCTGATTTAAGGTGCAGTGGTCACAC
13364 GGGCAAGC
65 GGGCAAGC
*
13372 CACACG-GACATGTGCTAGATCGTGTGTGGCTACTGTTTTCTGATTTAAGGTGCAGTGGTC
1 CACACGAG-CATGTGCTAGACCGTGTGTGGCTACTGTTTTCTGATTTAAGGTGCAGTGGTC
13432 GCATTGGCAC
Statistics
Matches: 124, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
71 3 0.02
72 119 0.96
73 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (72 bp):
CACACGAGCATGTGCTAGACCGTGTGTGGCTACTGTTTTCTGATTTAAGGTGCAGTGGTCACACG
GGCAAGC
Found at i:13487 original size:12 final size:12
Alignment explanation
Indices: 13472--13506 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
13462 CCATGTGGAG
*
13472 CCACATGGGCAC
1 CCACACGGGCAC
13484 CCACACGGGCAC
1 CCACACGGGCAC
*
13496 TCACACGGGCA
1 CCACACGGGCA
13507 TGTAAGTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.26, C:0.43, G:0.26, T:0.06
Consensus pattern (12 bp):
CCACACGGGCAC
Found at i:14119 original size:29 final size:29
Alignment explanation
Indices: 14086--14143 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
14076 TGGGGGTGTT
* * *
14086 ATGTCTACATTTGTAATTGTATCTGTATC
1 ATGTCTACATCTGTAACTGTAACTGTATC
*
14115 ATGTCTGCATCTGTAACTGTAACTGTATC
1 ATGTCTACATCTGTAACTGTAACTGTATC
14144 CGTATTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (29 bp):
ATGTCTACATCTGTAACTGTAACTGTATC
Found at i:15156 original size:16 final size:16
Alignment explanation
Indices: 15124--15157 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
15114 AGATGACTAT
*
15124 ATAAAAAATTTAATAA
1 ATAAAAAATATAATAA
*
15140 ATAAAAAATATATTAA
1 ATAAAAAATATAATAA
15156 AT
1 AT
15158 TAAATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAAAAATATAATAA
Found at i:15157 original size:25 final size:25
Alignment explanation
Indices: 15129--15176 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
15119 ACTATATAAA
*
15129 AAATTTAATAAATAAAA-AATATATT
1 AAATTAAAT-AATAAAATAATATATT
*
15154 AAATTAAATATTAAAATAATATA
1 AAATTAAATAATAAAATAATATA
15177 AGAGTTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AAATTAAATAATAAAATAATATATT
Found at i:16577 original size:31 final size:31
Alignment explanation
Indices: 16536--16655 Score: 84
Period size: 31 Copynumber: 4.0 Consensus size: 31
16526 AAAAAAGATT
*
16536 AGGTATCAAATTAGAAAAAAGAGTCAAGTTC
1 AGGTACCAAATTAGAAAAAAGAGTCAAGTTC
* **** * * *
16567 AGGTACCAAATT-G-GACCCTA-TAAAATTT
1 AGGTACCAAATTAGAAAAAAGAGTCAAGTTC
* * * *
16595 AAGTACCAACTTAAAAAAAAGTGTCAAGTTC
1 AGGTACCAAATTAGAAAAAAGAGTCAAGTTC
* *
16626 AGGTACCAAATTAGGAAAAAGTGTCAAGTT
1 AGGTACCAAATTAGAAAAAAGAGTCAAGTT
16656 TGAATACCAA
Statistics
Matches: 61, Mismatches: 25, Indels: 6
0.66 0.27 0.07
Matches are distributed among these distances:
28 15 0.25
29 2 0.03
30 2 0.03
31 42 0.69
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.24
Consensus pattern (31 bp):
AGGTACCAAATTAGAAAAAAGAGTCAAGTTC
Found at i:16645 original size:90 final size:90
Alignment explanation
Indices: 16536--16726 Score: 228
Period size: 90 Copynumber: 2.1 Consensus size: 90
16526 AAAAAAGATT
* * *
16536 AGGTATCAAATTAGAAAAAAGAGTCAAGTTCAG-GTACCAAATTGGACCCTATAAAAT-TT-AAG
1 AGGTATCAAATTAGAAAAAAGAGTCAAGTT-AGAATACCAAATTGGA--CAAAAAAATATTCAAG
* *
16598 TACCAACTTAA-AAAAAAGTGTCAAGTTC
63 TACCAAATTAAGAAAAAA-TGTCAAATTC
* * * *
16626 AGGTACCAAATTAGGAAAAAGTGTCAAGTTTGAATACCAAATTGGACAAAAAAATATTCAAGTAC
1 AGGTATCAAATTAGAAAAAAGAGTCAAGTTAGAATACCAAATTGGACAAAAAAATATTCAAGTAC
16691 CAAATTAAGAAAAAATGTCAAATTC
66 CAAATTAAGAAAAAATGTCAAATTC
*
16716 AAGTATCAAAT
1 AGGTATCAAAT
16727 ATTGTACTAA
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
88 7 0.08
89 3 0.03
90 70 0.81
91 6 0.07
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (90 bp):
AGGTATCAAATTAGAAAAAAGAGTCAAGTTAGAATACCAAATTGGACAAAAAAATATTCAAGTAC
CAAATTAAGAAAAAATGTCAAATTC
Found at i:16719 original size:31 final size:31
Alignment explanation
Indices: 16589--16726 Score: 101
Period size: 31 Copynumber: 4.5 Consensus size: 31
16579 GGACCCTATA
* *
16589 AAATTTAAGTACCAACTTAA-AAAAAAGTGTC
1 AAATTCAAGTACCAAATTAAGAAAAAA-TGTC
* * * *
16620 AAGTTCAGGTACCAAATTAGGAAAAAGTGTC
1 AAATTCAAGTACCAAATTAAGAAAAAATGTC
* * *
16651 AAGTTTGAA-TACCAAATT-GGACAAAAA----
1 AA-ATTCAAGTACCAAATTAAGA-AAAAATGTC
16678 AATATTCAAGTACCAAATTAAGAAAAAATGTC
1 AA-ATTCAAGTACCAAATTAAGAAAAAATGTC
*
16710 AAATTCAAGTATCAAAT
1 AAATTCAAGTACCAAAT
16727 ATTGTACTAA
Statistics
Matches: 83, Mismatches: 15, Indels: 18
0.72 0.13 0.16
Matches are distributed among these distances:
27 6 0.07
28 14 0.17
29 2 0.02
30 3 0.04
31 48 0.58
32 10 0.12
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (31 bp):
AAATTCAAGTACCAAATTAAGAAAAAATGTC
Done.