Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008124.1 Kokia drynarioides strain JFW-HI SEQ_122782, 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: 48426
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:429 original size:23 final size:23
Alignment explanation
Indices: 403--511 Score: 125
Period size: 23 Copynumber: 4.8 Consensus size: 23
393 TTACTGTTCA
* *
403 GCACTGTGTGTTCTTACTGATTC
1 GCACTGTGTGTGCTTACTGATTT
* *
426 GCACTATATGTGCTTACTGATTT
1 GCACTGTGTGTGCTTACTGATTT
449 GCAC--TGTGTGCTTACT-ATTTT
1 GCACTGTGTGTGCTTACTGA-TTT
* *
470 GCACTGTGTGTGCCTACTAATTT
1 GCACTGTGTGTGCTTACTGATTT
*
493 GCACTGTGTGTACTTACTG
1 GCACTGTGTGTGCTTACTG
512 TTTCCTCAGC
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
20 1 0.01
21 18 0.25
23 53 0.73
24 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (23 bp):
GCACTGTGTGTGCTTACTGATTT
Found at i:474 original size:44 final size:45
Alignment explanation
Indices: 403--511 Score: 132
Period size: 44 Copynumber: 2.4 Consensus size: 45
393 TTACTGTTCA
* *
403 GCACTGTGTGTTCTTACTGATTCGCACTATATGTGCTTACTGATTT
1 GCACTGTGTG-TCTTACTGATTCGCACTATATGTGCCTACTAATTT
* * *
449 GCACTGTGTG-CTTACT-ATTTTGCACTGTGTGTGCCTACTAATTT
1 GCACTGTGTGTCTTACTGA-TTCGCACTATATGTGCCTACTAATTT
493 GCACTGTGTGTACTTACTG
1 GCACTGTGTGT-CTTACTG
512 TTTCCTCAGC
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
43 1 0.02
44 37 0.69
46 16 0.30
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (45 bp):
GCACTGTGTGTCTTACTGATTCGCACTATATGTGCCTACTAATTT
Found at i:8222 original size:29 final size:28
Alignment explanation
Indices: 8190--8272 Score: 91
Period size: 27 Copynumber: 3.0 Consensus size: 28
8180 AAGGAAAACT
8190 TTTGTGTCAAAACTCTGAAAAGGTAAGCC
1 TTTGTG-CAAAACTCTGAAAAGGTAAGCC
* *
8219 TTTGTGGCGAACCTCTG--AAGGTAAGCC
1 TTTGT-GCAAAACTCTGAAAAGGTAAGCC
*
8246 TTTGTGGAAAACCTCT-AAAAGGTAAGC
1 TTTGTGCAAAA-CTCTGAAAAGGTAAGC
8273 TTTTATGGCG
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
26 3 0.07
27 19 0.42
28 9 0.20
29 13 0.29
30 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (28 bp):
TTTGTGCAAAACTCTGAAAAGGTAAGCC
Found at i:8247 original size:27 final size:27
Alignment explanation
Indices: 8209--8292 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 27
8199 AAACTCTGAA
8209 AAGGTAAGCCTTTGTGGCGAACCTCTG
1 AAGGTAAGCCTTTGTGGCGAACCTCTG
** *
8236 AAGGTAAGCCTTTGTGGAAAACCTCTAA
1 AAGGTAAGCCTTTGTGGCGAACCTCT-G
* * *
8264 AAGGTAAGCTTTTATGGCGAACCTTTG
1 AAGGTAAGCCTTTGTGGCGAACCTCTG
8291 AA
1 AA
8293 AGGAATGCCT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
27 26 0.55
28 21 0.45
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (27 bp):
AAGGTAAGCCTTTGTGGCGAACCTCTG
Found at i:8305 original size:28 final size:28
Alignment explanation
Indices: 8202--8308 Score: 119
Period size: 28 Copynumber: 3.8 Consensus size: 28
8192 TGTGTCAAAA
*
8202 CTCTGAAAAGGTAAGCCTTTGTGGCGAAC
1 CTCTG-AAAGGTAAGCCTTTATGGCGAAC
* **
8231 CTCTG-AAGGTAAGCCTTTGTGGAAAAC
1 CTCTGAAAGGTAAGCCTTTATGGCGAAC
* *
8258 CTCTAAAAGGTAAGCTTTTATGGCGAAC
1 CTCTGAAAGGTAAGCCTTTATGGCGAAC
*
8286 CTTTGAAAGG-AATGCCTTTATGG
1 CTCTGAAAGGTAA-GCCTTTATGG
8309 TGAAACTTTG
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
27 26 0.39
28 35 0.53
29 5 0.08
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (28 bp):
CTCTGAAAGGTAAGCCTTTATGGCGAAC
Found at i:8423 original size:29 final size:28
Alignment explanation
Indices: 8380--8504 Score: 107
Period size: 29 Copynumber: 4.5 Consensus size: 28
8370 TTCTGGATAT
* * *
8380 GAAAGCCTTTATGGCAGACCTCTATAAAG
1 GAAAGCCTTTGTGGCAGA-ATCTGTAAAG
*
8409 GAAAGCGTTTGTGGC-GAATC--TAAAG
1 GAAAGCCTTTGTGGCAGAATCTGTAAAG
*
8434 GAATGCCTTTGTGGCA-AATCTGTAAAG
1 GAAAGCCTTTGTGGCAGAATCTGTAAAG
* * *
8461 GAAAGCCTTCGTAGCA-AACCTCTGTAGAG
1 GAAAGCCTTTGTGGCAGAA--TCTGTAAAG
*
8490 GAATGCCTTTGTGGC
1 GAAAGCCTTTGTGGC
8505 TATCTTTGTA
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
25 22 0.28
27 22 0.28
28 2 0.03
29 33 0.42
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (28 bp):
GAAAGCCTTTGTGGCAGAATCTGTAAAG
Found at i:8436 original size:25 final size:26
Alignment explanation
Indices: 8404--8504 Score: 96
Period size: 25 Copynumber: 3.8 Consensus size: 26
8394 CAGACCTCTA
* *
8404 TAAAGGAAAGCGTTTGTGGCGAATC-
1 TAAAGGAAAGCCTTTGTGGCAAATCG
*
8429 TAAAGGAATGCCTTTGTGGCAAATCTG
1 TAAAGGAAAGCCTTTGTGGCAAATC-G
* *
8456 TAAAGGAAAGCCTTCGTAGCAAACCTCTG
1 TAAAGGAAAGCCTTTGTGGCAAA--TC-G
* *
8485 TAGAGGAATGCCTTTGTGGC
1 TAAAGGAAAGCCTTTGTGGC
8505 TATCTTTGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
25 22 0.35
27 20 0.32
29 20 0.32
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (26 bp):
TAAAGGAAAGCCTTTGTGGCAAATCG
Found at i:10819 original size:20 final size:20
Alignment explanation
Indices: 10796--10834 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10786 AATAAAACTA
*
10796 AAGTTGTATCAGTAGAAGTG
1 AAGTTGTACCAGTAGAAGTG
* *
10816 AAGTTTTACCTGTAGAAGT
1 AAGTTGTACCAGTAGAAGT
10835 CTCATTAGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (20 bp):
AAGTTGTACCAGTAGAAGTG
Found at i:13685 original size:20 final size:20
Alignment explanation
Indices: 13662--13703 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
13652 AAAAGTATAC
13662 TTGTATCGGTAGAACTGAAG
1 TTGTATCGGTAGAACTGAAG
*
13682 TTGTATCGGTAGAAGTGAAG
1 TTGTATCGGTAGAACTGAAG
13702 TT
1 TT
13704 CTACCAGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.07, G:0.31, T:0.33
Consensus pattern (20 bp):
TTGTATCGGTAGAACTGAAG
Found at i:13713 original size:20 final size:20
Alignment explanation
Indices: 13670--13717 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
13660 ACTTGTATCG
* * * *
13670 GTAGAACTGAAGTTGTATCG
1 GTAGAAGTGAAGTTCTACCA
13690 GTAGAAGTGAAGTTCTACCA
1 GTAGAAGTGAAGTTCTACCA
13710 GTAGAAGT
1 GTAGAAGT
13718 CCCAGGGTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.27
Consensus pattern (20 bp):
GTAGAAGTGAAGTTCTACCA
Found at i:13939 original size:20 final size:20
Alignment explanation
Indices: 13916--13974 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
13906 AATAGAACTA
*
13916 AAGTTGTATCGGTAGAAGTG
1 AAGTTCTATCGGTAGAAGTG
*
13936 AAGTTCTATCGATAGAAGTG
1 AAGTTCTATCGGTAGAAGTG
*
13956 AAGTTCTACCGGTAGAAGT
1 AAGTTCTATCGGTAGAAGT
13975 CTCACTGGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (20 bp):
AAGTTCTATCGGTAGAAGTG
Found at i:29667 original size:23 final size:23
Alignment explanation
Indices: 29623--29673 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
29613 TGATTTGATC
*
29623 ATGAAATGAAACTAAAAATGAGA
1 ATGAAATGAAAATAAAAATGAGA
* * *
29646 ATGATATGAAAATAGAATTGAG-
1 ATGAAATGAAAATAAAAATGAGA
29668 ATGAAA
1 ATGAAA
29674 CAGATTATGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.57, C:0.02, G:0.20, T:0.22
Consensus pattern (23 bp):
ATGAAATGAAAATAAAAATGAGA
Found at i:30079 original size:4 final size:4
Alignment explanation
Indices: 30072--30105 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
30062 AAAATTTATT
30072 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
30106 CAACTTGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:34213 original size:95 final size:95
Alignment explanation
Indices: 34050--34241 Score: 375
Period size: 95 Copynumber: 2.0 Consensus size: 95
34040 TCGAGCCCTG
34050 TCACCCAAATCAAGTTTTAAATAAAAAACTATAATTCCAAAACCCTAAAACTAAACCCTAATATT
1 TCACCCAAATCAAGTTTTAAATAAAAAACTATAATTCCAAAACCCTAAAACTAAACCCTAATATT
34115 ATAAACCTAAAACCTAATAAATTACCAAAA
66 ATAAACCTAAAACCTAATAAATTACCAAAA
*
34145 TCACCCAAATCAAGTTTTAAATAAAAAACTGTAATTCCAAAACCCTAAAACTAAACCCTAATATT
1 TCACCCAAATCAAGTTTTAAATAAAAAACTATAATTCCAAAACCCTAAAACTAAACCCTAATATT
34210 ATAAACCTAAAACCTAATAAATTACCAAAA
66 ATAAACCTAAAACCTAATAAATTACCAAAA
34240 TC
1 TC
34242 TAAATACTTT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.24
Consensus pattern (95 bp):
TCACCCAAATCAAGTTTTAAATAAAAAACTATAATTCCAAAACCCTAAAACTAAACCCTAATATT
ATAAACCTAAAACCTAATAAATTACCAAAA
Found at i:41761 original size:49 final size:48
Alignment explanation
Indices: 41685--41779 Score: 163
Period size: 49 Copynumber: 2.0 Consensus size: 48
41675 TGTATAGAAT
*
41685 TACATTCTTCTATTTGACATTGATTAGAATAAGATTTTTCAATCTTAC
1 TACATTCTTCTATTTGACATTCATTAGAATAAGATTTTTCAATCTTAC
*
41733 TACAGTTCTTCTATTTGACATTCATTAGAATAAGGTTTTTCAATCTT
1 TACA-TTCTTCTATTTGACATTCATTAGAATAAGATTTTTCAATCTT
41780 TAAATAGATG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 4 0.09
49 40 0.91
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.46
Consensus pattern (48 bp):
TACATTCTTCTATTTGACATTCATTAGAATAAGATTTTTCAATCTTAC
Found at i:43367 original size:22 final size:22
Alignment explanation
Indices: 43328--43369 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
43318 ATAATGTGAG
*
43328 CTAACTTGTAGATCATATGCAC
1 CTAACTTGTACATCATATGCAC
43350 CTAACTTGTTACAT-ATATGC
1 CTAACTTG-TACATCATATGC
43370 TTAATCCGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (22 bp):
CTAACTTGTACATCATATGCAC
Done.