Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007548.1 Kokia drynarioides strain JFW-HI SEQ_122176, 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: 28667
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:321 original size:3 final size:3
Alignment explanation
Indices: 313--350 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
303 CCATTTCACA
*
313 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
351 ATCTCTCTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:482 original size:37 final size:37
Alignment explanation
Indices: 440--513 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
430 AGTGAAAGTT
440 AAAATATAATTTTGTCATTAGTTTGTAATTTAACTAA
1 AAAATATAATTTTGTCATTAGTTTGTAATTTAACTAA
477 AAAATATAATTTTGTCATTAGTTTGTAATTTAACTAA
1 AAAATATAATTTTGTCATTAGTTTGTAATTTAACTAA
514 TTTTCATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (37 bp):
AAAATATAATTTTGTCATTAGTTTGTAATTTAACTAA
Found at i:2005 original size:2 final size:2
Alignment explanation
Indices: 1998--2023 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1988 TCTATCTATC
1998 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2024 GTTAAAGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10955 original size:15 final size:15
Alignment explanation
Indices: 10935--10965 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10925 TTAGGAAAAT
*
10935 AACAAATTTAATAAA
1 AACAAAATTAATAAA
10950 AACAAAATTAATAAA
1 AACAAAATTAATAAA
10965 A
1 A
10966 TAAACAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (15 bp):
AACAAAATTAATAAA
Found at i:12509 original size:13 final size:13
Alignment explanation
Indices: 12491--12516 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12481 TGTATGTCTT
12491 TAAAATTTGATAA
1 TAAAATTTGATAA
12504 TAAAATTTGATAA
1 TAAAATTTGATAA
12517 CCACATTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
TAAAATTTGATAA
Found at i:13788 original size:228 final size:228
Alignment explanation
Indices: 13391--14092 Score: 1010
Period size: 228 Copynumber: 3.1 Consensus size: 228
13381 TCTCTCCAAA
* * *
13391 TATGCAGATCTTCGTCAAAACCCTT-ACAGGCAAGACCATCACCCTCGAGGTCGAGAGTTCTGAC
1 TATGCAGATCTTCGTCAAAA-CCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGAC
* *
13455 ACCATCGATAATGTAAAGGCTAAAATTCAAGATAAGGAAGGCATCCCACCAGACCAGCAGCGTCT
65 ACCATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCT
*
13520 CATCTTTGCCGGCAAACAGCTCGATGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAAT
130 CATCTTTGCCGGCAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAAT
13585 CCACCCTCCACCTTGTTCTCCGTCTTCGTGGGGG
195 CCACCCTCCACCTTGTTCTCCGTCTTCGTGGGGG
* *
13619 TATGCAGATCTTCGTTAAAACCTTAACCGGCAAGACAATCACCCTCGAAGTCGAGAGCTCTGACA
1 TATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACA
*
13684 CCATCGATAATGTGAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
66 CCATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
* *
13749 ATCTTCGCCGGCAAACAGCTGGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
131 ATCTTTGCCGGCAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
*
13814 CACCCTCCACCTTGTGCTCCGTCTTCGTGGGGG
196 CACCCTCCACCTTGTTCTCCGTCTTCGTGGGGG
* *
13847 TATGCAGATCTTCGTGAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACA
1 TATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACA
* * * * * * * *
13912 CCATCGACAACGTCAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAACAACGTTTG
66 CCATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
* * * * * ** * * * *
13977 ATCTTTGCAGGGAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATACAGAAGGAATC
131 ATCTTTGCCGGCAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
* * * ** * *
14042 GACCCTTCACCTTGTTTTGAGGCTTCGTGGAGG
196 CACCCTCCACCTTGTTCTCCGTCTTCGTGGGGG
* *
14075 CATGCAGATATTCGTCAA
1 TATGCAGATCTTCGTCAA
14093 GACATTGACT
Statistics
Matches: 427, Mismatches: 46, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
227 4 0.01
228 423 0.99
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (228 bp):
TATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACA
CCATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
ATCTTTGCCGGCAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
CACCCTCCACCTTGTTCTCCGTCTTCGTGGGGG
Found at i:14175 original size:228 final size:228
Alignment explanation
Indices: 13391--14299 Score: 973
Period size: 228 Copynumber: 4.0 Consensus size: 228
13381 TCTCTCCAAA
* * * * *
13391 TATGCAGATCTTCGTCAAAACCCTT-ACAGGCAAGACCATCACCCTCGAGGTCGAGAGTTCTGAC
1 TATGCAGATCTTCGTCAAAA-CCTTAACCGGCAAGACAATCACCCTCGAAGTCGAGAGCTCCGAC
* * * *
13455 ACCATCGATAATGTAAAGGCTAAAATTCAAGATAAGGAAGGCATCCCACCAGACCAGCAGCGTCT
65 ACCATCGACAATGTGAAGGCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCT
* * * *
13520 CATCTTTGCCGGCAAACAGCTCGATGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAAT
130 CATCTTTGCCGGCAAACAGCTTGAGGACGGCAGGACCTTGGCCGATTACAACATCCAGAAGGAAT
13585 CCACCCTCCACCTTGTTCTCCGTCTTCGTGGGGG
195 CCACCCTCCACCTTGTTCTCCGTCTTCGTGGGGG
* *
13619 TATGCAGATCTTCGTTAAAACCTTAACCGGCAAGACAATCACCCTCGAAGTCGAGAGCTCTGACA
1 TATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACAATCACCCTCGAAGTCGAGAGCTCCGACA
* * *
13684 CCATCGATAATGTGAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
66 CCATCGACAATGTGAAGGCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTC
* * * *
13749 ATCTTCGCCGGCAAACAGCTGGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
131 ATCTTTGCCGGCAAACAGCTTGAGGACGGCAGGACCTTGGCCGATTACAACATCCAGAAGGAATC
*
13814 CACCCTCCACCTTGTGCTCCGTCTTCGTGGGGG
196 CACCCTCCACCTTGTTCTCCGTCTTCGTGGGGG
* *
13847 TATGCAGATCTTCGTGAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACA
1 TATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACAATCACCCTCGAAGTCGAGAGCTCCGACA
* * * * * * *
13912 CCATCGACAACGTCAAGTCTAAAATCCAAGACAAGGAAGGCATCCCACCAGACCAACAACGTTTG
66 CCATCGACAATGTGAAGGCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTC
* * * * * * * *
13977 ATCTTTGCAGGGAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATACAGAAGGAATC
131 ATCTTTGCCGGCAAACAGCTTGAGGACGGCAGGACCTTGGCCGATTACAACATCCAGAAGGAATC
* * * ** * *
14042 GACCCTTCACCTTGTTTTGAGGCTTCGTGGAGG
196 CACCCTCCACCTTGTTCTCCGTCTTCGTGGGGG
* * * * * * * * ** * * * * * * *
14075 CATGCAGATATTCGTCAAGACATTGACTGGGAAAACAATCACATTGGAGGTGGAAAGTTCGGATA
1 TATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACAATCACCCTCGAAGTCGAGAGCTCCGACA
* * * * * * *
14140 CAATTGACAATGTGAAGGC-AAAGATTCAGGACAAGGAAGGTATTCCC-CCAGATCAGCAAAGGC
66 CCATCGACAATGTGAAGGCTAAA-ATTCAAGACAAGGAAGGCA-TCCCACCAGACCAGCAACGTC
* * * * * * * * * *
14203 TCATCTTTGCTGGCAAGCA-ATTGGAGGATGGGAGGA-CTCTAGCTGATTATAACATTCAGAAAG
129 TCATCTTTGCCGGCAAACAGCTT-GAGGACGGCAGGACCT-TGGCCGATTACAACATCCAGAAGG
* * * *
14266 AGTCCACCCTTCACCTTGTTCTTCGTCTCCGTGG
192 AATCCACCCTCCACCTTGTTCTCCGTCTTCGTGG
14300 TGGCCAGTGA
Statistics
Matches: 587, Mismatches: 89, Indels: 10
0.86 0.13 0.01
Matches are distributed among these distances:
227 11 0.02
228 572 0.97
229 4 0.01
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.21
Consensus pattern (228 bp):
TATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACAATCACCCTCGAAGTCGAGAGCTCCGACA
CCATCGACAATGTGAAGGCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTC
ATCTTTGCCGGCAAACAGCTTGAGGACGGCAGGACCTTGGCCGATTACAACATCCAGAAGGAATC
CACCCTCCACCTTGTTCTCCGTCTTCGTGGGGG
Found at i:15895 original size:19 final size:20
Alignment explanation
Indices: 15840--15884 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
15830 CAGTTGATAA
15840 ATTTTTAATAAAAAATAAGT
1 ATTTTTAATAAAAAATAAGT
15860 ATTTTTAATAAAAAATAA-T
1 ATTTTTAATAAAAAATAAGT
15879 ATTTTT
1 ATTTTT
15885 TCAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATTTTTAATAAAAAATAAGT
Found at i:16846 original size:23 final size:22
Alignment explanation
Indices: 16799--16842 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
16789 ATAAAATTAT
16799 TAAATATTAAAATAAAATAAAA
1 TAAATATTAAAATAAAATAAAA
*
16821 TAAATATTTAAAA-AAATTAAAA
1 TAAATA-TTAAAATAAAATAAAA
16843 ATAACATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAATATTAAAATAAAATAAAA
Found at i:24358 original size:44 final size:44
Alignment explanation
Indices: 24299--24408 Score: 153
Period size: 44 Copynumber: 2.6 Consensus size: 44
24289 ATGATGATTA
*
24299 TAATTTTAAAATAATTTTAATGATTTTATA-TTTAAAAAATTAAT
1 TAATTTTAAAATAATTTTAATAATTTTATATTTTAAAAAA-TAAT
24343 TAATTTTAAAATAATTTTAATAATTTTATATTTT--AAAA-AA-
1 TAATTTTAAAATAATTTTAATAATTTTATATTTTAAAAAATAAT
24383 TAATTTT--AATAATTTTAATAATTTTA
1 TAATTTTAAAATAATTTTAATAATTTTA
24409 AAATTATTTG
Statistics
Matches: 64, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
38 19 0.30
40 7 0.11
41 2 0.03
43 4 0.06
44 29 0.45
45 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (44 bp):
TAATTTTAAAATAATTTTAATAATTTTATATTTTAAAAAATAAT
Found at i:24361 original size:29 final size:29
Alignment explanation
Indices: 24329--24417 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
24319 TGATTTTATA
24329 TTTAAAAAATTAATTAATTTTAAAATAAT
1 TTTAAAAAATTAATTAATTTTAAAATAAT
*
24358 TTT-AATAATT--TTATATTTTAAAAAATAAT
1 TTTAAAAAATTAATTA-ATTTT--AAAATAAT
** *
24387 TTTAATAATTTTAA-TAATTTTAAAATTAT
1 TTTAA-AAAATTAATTAATTTTAAAATAAT
24416 TT
1 TT
24418 GTTAACATGG
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
26 3 0.06
27 5 0.10
28 6 0.12
29 23 0.48
30 1 0.02
31 8 0.17
32 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTAAAAAATTAATTAATTTTAAAATAAT
Found at i:24366 original size:9 final size:9
Alignment explanation
Indices: 24298--24413 Score: 76
Period size: 9 Copynumber: 13.7 Consensus size: 9
24288 GATGATGATT
24298 ATAATTTTAAA
1 ATAATTTT--A
24309 ATAATTTTA
1 ATAATTTTA
*
24318 ATGATTTT-
1 ATAATTTTA
24326 AT-A-TTTA
1 ATAATTTTA
**
24333 A-AAAATTA
1 ATAATTTTA
24341 ATTAATTTTAAA
1 A-TAATTTT--A
24353 ATAATTTTA
1 ATAATTTTA
24362 ATAATTTT-
1 ATAATTTTA
24370 AT-ATTTTA
1 ATAATTTTA
24378 A-AA----A
1 ATAATTTTA
24382 ATAATTTTA
1 ATAATTTTA
24391 ATAATTTTA
1 ATAATTTTA
24400 ATAATTTTA
1 ATAATTTTA
24409 A-AATT
1 ATAATT
24414 ATTTGTTAAC
Statistics
Matches: 87, Mismatches: 4, Indels: 31
0.71 0.03 0.25
Matches are distributed among these distances:
4 2 0.02
5 2 0.02
6 3 0.03
7 8 0.09
8 14 0.16
9 37 0.43
10 4 0.05
11 15 0.17
12 2 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (9 bp):
ATAATTTTA
Found at i:28546 original size:4 final size:4
Alignment explanation
Indices: 28537--28619 Score: 71
Period size: 4 Copynumber: 20.2 Consensus size: 4
28527 AAATAAACGG
* *
28537 GAAA GAAA GAAA GGAAA GAAA GAAA GAAAA GAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GAAA -GAAA GAAA GAAA G-AAA GAAA GA-AA GAAA GAAA GAAA
* * *
28587 GAAG GAGAG GAAA GAAA GAAA -AAG GAAA GAAA G
1 GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
28620 GTAATGTGTT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
3 5 0.07
4 46 0.69
5 16 0.24
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:28554 original size:13 final size:13
Alignment explanation
Indices: 28536--28620 Score: 80
Period size: 13 Copynumber: 6.2 Consensus size: 13
28526 CAAATAAACG
28536 GGAAAGAAAGAAA
1 GGAAAGAAAGAAA
28549 GGAAAGAAAGAAA
1 GGAAAGAAAGAAA
* * *
28562 GAAAAGAAGGAGA
1 GGAAAGAAAGAAA
28575 GGAAAGAAAGAAGAA
1 GGAAAGAAAG-A-AA
*
28590 GGAGAGGAAAGAAA
1 GGA-AAGAAAGAAA
*
28604 GAAAAAGGAAAGAAA
1 G-GAAA-GAAAGAAA
28619 GG
1 GG
28621 TAATGTGTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
13 31 0.54
14 5 0.09
15 15 0.26
16 6 0.11
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (13 bp):
GGAAAGAAAGAAA
Found at i:28559 original size:17 final size:17
Alignment explanation
Indices: 28537--28619 Score: 72
Period size: 15 Copynumber: 5.3 Consensus size: 17
28527 AAATAAACGG
28537 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
*
28554 GAAAGAAAGAAAAG-AA
1 GAAAGAAAGAAAGGAAA
* *
28570 G-GAG-AGGAAA-GAAA
1 GAAAGAAAGAAAGGAAA
* *
28584 G-AAGAAGGAGAGGAAA
1 GAAAGAAAGAAAGGAAA
28600 GAAAG-AA-AAAGGAAA
1 GAAAGAAAGAAAGGAAA
28615 GAAAG
1 GAAAG
28620 GTAATGTGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
13 1 0.02
14 10 0.18
15 19 0.35
16 9 0.16
17 16 0.29
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Done.