Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013161.1 Kokia drynarioides strain JFW-HI SEQ_128180, 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: 27249
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Warning! 198 characters in sequence are not A, C, G, or T
Found at i:2151 original size:20 final size:19
Alignment explanation
Indices: 2097--2153 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
2087 TACAAAATAA
2097 TCAAAATAATTTTT-AAAAT
1 TCAAAAT-ATTTTTAAAAAT
*
2116 TCAAAATATTTATAAAAAT
1 TCAAAATATTTTTAAAAAT
*
2135 TCTAAAGTATTTTTAAAAA
1 TC-AAAATATTTTTAAAAA
2154 CAATTATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.15
19 14 0.42
20 14 0.42
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
TCAAAATATTTTTAAAAAT
Found at i:2189 original size:20 final size:20
Alignment explanation
Indices: 2118--2193 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
2108 TTTAAAATTC
*
2118 AAAATATTTATAAAAATTCTA
1 AAAATATTTA-AAAAAATCTA
* *
2139 AAGTATTTTTAAAAACAAT-TA
1 AA-AATATTTAAAAA-AATCTA
* * *
2160 TAATTTTTTAAAAAAATCTA
1 AAAATATTTAAAAAAATCTA
2180 AAAATATTTAAAAA
1 AAAATATTTAAAAA
2194 TAGTTAAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
19 3 0.07
20 23 0.53
21 9 0.21
22 8 0.19
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (20 bp):
AAAATATTTAAAAAAATCTA
Found at i:2520 original size:29 final size:30
Alignment explanation
Indices: 2471--2527 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
2461 TACCTTAATA
2471 ATATAAAAATAATAATTAATTACAAAAAAG
1 ATATAAAAATAATAATTAATTACAAAAAAG
*
2501 ATATGAAAAAT-AT-ATTAATTACGAAAA
1 ATAT-AAAAATAATAATTAATTACAAAAA
2528 TAAGCATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 13 0.52
30 6 0.24
31 6 0.24
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (30 bp):
ATATAAAAATAATAATTAATTACAAAAAAG
Found at i:9390 original size:23 final size:23
Alignment explanation
Indices: 9364--9504 Score: 134
Period size: 23 Copynumber: 6.3 Consensus size: 23
9354 TGCTGGGTAA
9364 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
9387 CAGAGAGTACACAAA--G-T-A-
1 CAGAGAGCACACAAAGTGCTAAT
* * *
9405 C--TGAGCAGACAAAGTGTTAAT
1 CAGAGAGCACACAAAGTGCTAAT
**
9426 CAGAGAGCACATGAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
9449 CAGAGAGCACACGAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
* *
9472 AACAGAGAGCACACACAGTGCTAAA
1 --CAGAGAGCACACAAAGTGCTAAT
9497 CAGAGAGC
1 CAGAGAGC
9505 GCTCTAGTGT
Statistics
Matches: 96, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
16 9 0.09
18 2 0.02
19 2 0.02
20 2 0.02
21 2 0.02
23 59 0.61
25 20 0.21
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:12792 original size:16 final size:15
Alignment explanation
Indices: 12771--12803 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
12761 ACGTCAGCAG
12771 CACCACCACCATCTGC
1 CACCACCACCA-CTGC
12787 CACCACCACCACTGC
1 CACCACCACCACTGC
12802 CA
1 CA
12804 AATCTGCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.27, C:0.58, G:0.06, T:0.09
Consensus pattern (15 bp):
CACCACCACCACTGC
Found at i:13576 original size:14 final size:14
Alignment explanation
Indices: 13557--13584 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13547 ACAGCGTTGT
13557 TTTGGTGTGAAACA
1 TTTGGTGTGAAACA
13571 TTTGGTGTGAAACA
1 TTTGGTGTGAAACA
13585 CCAGTGACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TTTGGTGTGAAACA
Found at i:16018 original size:21 final size:21
Alignment explanation
Indices: 15994--16044 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
15984 CCAGTCTATC
15994 CCATCACTCTCTCAGCCT-CTT
1 CCATCACTCTCTCAG-CTACTT
* *
16015 CCATCACTTTTTCAGCTACTT
1 CCATCACTCTCTCAGCTACTT
*
16036 GCATCACTC
1 CCATCACTC
16045 CCACTACCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (21 bp):
CCATCACTCTCTCAGCTACTT
Found at i:18309 original size:12 final size:13
Alignment explanation
Indices: 18292--18320 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
18282 GAAACTTAAA
18292 ATTTAGTCTATG-
1 ATTTAGTCTATGC
18304 ATTTAGTCTATGC
1 ATTTAGTCTATGC
18317 ATTT
1 ATTT
18321 TAATTTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (13 bp):
ATTTAGTCTATGC
Found at i:19281 original size:90 final size:84
Alignment explanation
Indices: 19187--19433 Score: 264
Period size: 90 Copynumber: 2.9 Consensus size: 84
19177 AAATATTTTG
* * *
19187 AAAAAAAGTAATTAAGCCCCTACATTTTTTTGCACTCACTTGAGTACTTGCACTTTCAAAATGCA
1 AAAAAAAGCAATTAAGCCCCT-CATTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCA
***
19252 TAAAAAAGACCCTCAAACTATTTC
65 TAAAAAA-ACCCTCAAA--A-AAA
* * * *
19276 AAAAAAAGCAATTAAGCTCTTGCTTTTATTTTGCACTCAATTGAGTACTTGAACTTTTAAAATGC
1 AAAAAAAGCAATTAAGCCCCT-CATTT-TTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGC
19341 ATCAAAAAAACCCTCAAAAAAAA
64 AT-AAAAAAACCCTC-AAAAAAA
* * * * *
19364 AAAAAAAGCAATTAAGCCCC-CAATTTTTTGCACTCAATTGGGTACTCGAACTGTC-AAATACAT
1 AAAAAAAGCAATTAAGCCCCTCATTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCAT
19427 AAAAAAA
66 AAAAAAA
19434 AGCCCTTTGA
Statistics
Matches: 135, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
83 7 0.05
84 7 0.05
85 26 0.19
86 3 0.02
88 18 0.13
89 23 0.17
90 42 0.31
91 9 0.07
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (84 bp):
AAAAAAAGCAATTAAGCCCCTCATTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCAT
AAAAAAACCCTCAAAAAAA
Found at i:19562 original size:16 final size:16
Alignment explanation
Indices: 19539--19600 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
19529 CATGTGACAA
19539 AAAAATTATAAAAAAT
1 AAAAATTATAAAAAAT
* **
19555 AGAAATTATAAAAGTT
1 AAAAATTATAAAAAAT
* *
19571 ATTAAATTTTAAAAAAT
1 A-AAAATTATAAAAAAT
*
19588 AAAAATGATAAAA
1 AAAAATTATAAAA
19601 TGCATAAAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
16 23 0.66
17 12 0.34
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAAATTATAAAAAAT
Found at i:21441 original size:18 final size:17
Alignment explanation
Indices: 21399--21441 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
21389 TTTTTAAGTT
*
21399 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
21416 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
21434 TATAATTT
1 TATAATTT
21442 AGAACACAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:22229 original size:30 final size:30
Alignment explanation
Indices: 22190--22270 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
22180 TAATTTTAAA
* *
22190 TTAATAATAATAAAATTATACTTTAACT-TT
1 TTAAAAATAATAAAATTATAATTTAA-TATT
22220 TTAAAAATAATAAAAATT-TAATTTAATATT
1 TTAAAAATAAT-AAAATTATAATTTAATATT
* *
22250 TTAAAAATTATAAAAATATAA
1 TTAAAAATAATAAAATTATAA
22271 ATTATTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
29 6 0.14
30 32 0.73
31 6 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (30 bp):
TTAAAAATAATAAAATTATAATTTAATATT
Found at i:22274 original size:15 final size:17
Alignment explanation
Indices: 22253--22293 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
22243 TAATATTTTA
22253 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
22269 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
22285 AAAATTATA
1 AAAATTATA
22294 TTTTCACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:24865 original size:91 final size:91
Alignment explanation
Indices: 24703--24940 Score: 225
Period size: 91 Copynumber: 2.6 Consensus size: 91
24693 ATTAATCCAT
* * * **
24703 TTTTTTTTTACACTCACTTGGGTACTTAAACTTTCAAAATGCATCAAAAATGCCCTCAAACTATT
1 TTTTATTTTACACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAAGGCCCTCAAACTAAA
**
24768 TTAAAAAAAAGTAATTAAGCCACTGC
66 AAAAAAAAAAGTAATTAAGCCACTGC
* * * **
24794 TTTTATTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGGTCCTCAATTTAAA
1 TTTTATTTTACACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAAGGCCCTCAAACT--A
* *
24859 AAAAAAAAAAAAGCAATTAAAACC-C--C
64 AAAAAAAAAAAAGTAATT-AAGCCACTGC
** * * *
24885 AATTATTTTTACACTCAATTGGGTACTTGAA-TTGTC-AAATACATAAAAAAGGCCCT
1 TTTTA-TTTTACACTCAATTGGGTACTTAAACTT-TCAAAATGCATCAAAAAGGCCCT
24941 TTGATCATTA
Statistics
Matches: 122, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
91 77 0.63
92 26 0.21
93 15 0.12
94 4 0.03
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (91 bp):
TTTTATTTTACACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAAGGCCCTCAAACTAAA
AAAAAAAAAAGTAATTAAGCCACTGC
Found at i:25057 original size:9 final size:9
Alignment explanation
Indices: 25040--25095 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 9
25030 ACATGTGGCA
25040 AAAAATTAT
1 AAAAATTAT
*
25049 AAAAGTTAT
1 AAAAATTAT
* * *
25058 TAAATTTTT
1 AAAAATTAT
25067 AAAAA--AT
1 AAAAATTAT
25074 AAAAATTAT
1 AAAAATTAT
*
25083 AAAAAATAT
1 AAAAATTAT
25092 AAAA
1 AAAA
25096 TGCATGAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
7 6 0.16
9 31 0.84
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:26551 original size:16 final size:17
Alignment explanation
Indices: 26522--26554 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
26512 AAAAAGATTA
*
26522 TTGTTTTTATTTGTATT
1 TTGTTTTTACTTGTATT
26539 TTGTTTTT-CTTGTATT
1 TTGTTTTTACTTGTATT
26555 AATTTTTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.09, C:0.03, G:0.12, T:0.76
Consensus pattern (17 bp):
TTGTTTTTACTTGTATT
Done.