Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001363.1 Kokia drynarioides strain JFW-HI SEQ_112822, 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: 11493
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:298 original size:12 final size:12
Alignment explanation
Indices: 281--306 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
271 TATTAGTGGT
281 AAAAAGGAAAGA
1 AAAAAGGAAAGA
293 AAAAAGGAAAGA
1 AAAAAGGAAAGA
305 AA
1 AA
307 CAAAAATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAAGGAAAGA
Found at i:1091 original size:24 final size:24
Alignment explanation
Indices: 1064--2043 Score: 603
Period size: 24 Copynumber: 41.1 Consensus size: 24
1054 ATGTGGAAGT
* *
1064 TGACAAGCGTAAATGTATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
1088 TGACGAGCGTAAACGTATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
* * * **
1112 TGACGAGCATAAACATGTGCAAGC
1 TGACGAGCGTAAACGTATATAAGC
* * *
1136 TGACAAGCATAAAC-----TAAGT
1 TGACGAGCGTAAACGTATATAAGC
* **
1155 TGACGAGCGTAAATC-TGTGCAAGC
1 TGACGAGCGTAAA-CGTATATAAGC
* *
1179 TGACAAGTGTAAACGTATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
* * * **
1203 TGACGAGCGTAAGCATGTGCAAGC
1 TGACGAGCGTAAACGTATATAAGC
*
1227 TGACGAGCGTAAATGTATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
* * * *
1251 TAACAAGCGTAAACGTGT-TCAATC
1 TGACGAGCGTAAACGTATAT-AAGC
* * *
1275 TAACAAGCGTAAATGTATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
* *
1299 TGACAAGCGTAAATGTATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
* * * **
1323 TGACGAGCGTGAACATGTGCAAGC
1 TGACGAGCGTAAACGTATATAAGC
* * **
1347 TGACGAGCGTAAACATGTGCAAGC
1 TGACGAGCGTAAACGTATATAAGC
* *
1371 TGATGAGCGTAAATGTATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
** * ** *
1395 TGAAAAGCGTAAACCTATGCAAGT
1 TGACGAGCGTAAACGTATATAAGC
* ** *
1419 TAATTAAG-GTAAACGTATATAGGC
1 TGA-CGAGCGTAAACGTATATAAGC
* **
1443 TGACGAGCGTAAACGTGTGCAAGC
1 TGACGAGCGTAAACGTATATAAGC
* * *
1467 TGATGAGTGTAAACATATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
* * * * * **
1491 TGACAAGCATAATCATGTGCAAGC
1 TGACGAGCGTAAACGTATATAAGC
* * * *
1515 TGATGAGCATAAACATATATAAGT
1 TGACGAGCGTAAACGTATATAAGC
* * *
1539 TGACGAGCATAAATGTATATATGC
1 TGACGAGCGTAAACGTATATAAGC
* * * ** *
1563 TGACGAGTGTAAATGTGTGCAAGT
1 TGACGAGCGTAAACGTATATAAGC
* *
1587 TGACGAGCATAAACATATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
* * ** **
1611 TGATGAGCGTAAACGTGTGCAAAT
1 TGACGAGCGTAAACGTATATAAGC
* ** **
1635 TGACGAGCGTAAACGTGTGCAAAT
1 TGACGAGCGTAAACGTATATAAGC
1659 TGACGAGCGTAAACGTATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
* * * *
1683 TGACAAGTGTAAACATA-AGCAAGC
1 TGACGAGCGTAAACGTATA-TAAGC
1707 TGACGAGCGTAAACGTATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
* * * **
1731 TGACGACCATAAACGTGTGCAAGC
1 TGACGAGCGTAAACGTATATAAGC
*
1755 TAACGAGCGTAAACGTATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
* ** *
1779 TGACGAGCGTAAACGTGTGCAAGT
1 TGACGAGCGTAAACGTATATAAGC
*
1803 TGACGAGCGTAAACATATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
* ** *
1827 TGACGAGCGTAAACGTGTGCAAGT
1 TGACGAGCGTAAACGTATATAAGC
*
1851 TGACGAGCGTAAACATATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
* * *
1875 TGATGAGCGTAAATGTATTTAAGC
1 TGACGAGCGTAAACGTATATAAGC
** * * **
1899 TGACGAATGTAAATGTGTGCAAGC
1 TGACGAGCGTAAACGTATATAAGC
* * * *
1923 TGACGAGCGTAAATGTAGATATGT
1 TGACGAGCGTAAACGTATATAAGC
* * * **
1947 TGACGATCGTAAATGTGTGCAAGC
1 TGACGAGCGTAAACGTATATAAGC
* *
1971 TGACGAGCATAAA-GTATATAAGT
1 TGACGAGCGTAAACGTATATAAGC
* * * * * ** *
1994 TGATGACCTTAAATGTGTGCAAGT
1 TGACGAGCGTAAACGTATATAAGC
*
2018 TGACGAGCGTAAATGTATATAAGC
1 TGACGAGCGTAAACGTATATAAGC
2042 TG
1 TG
2044 GCGACTATAA
Statistics
Matches: 729, Mismatches: 214, Indels: 26
0.75 0.22 0.03
Matches are distributed among these distances:
19 14 0.02
20 1 0.00
23 21 0.03
24 688 0.94
25 5 0.01
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (24 bp):
TGACGAGCGTAAACGTATATAAGC
Found at i:1192 original size:43 final size:43
Alignment explanation
Indices: 1107--1239 Score: 133
Period size: 43 Copynumber: 3.0 Consensus size: 43
1097 TAAACGTATA
1107 TAAGCTGACGAGCATAAACATGTGCAAGCTGACAAGCATAAAC
1 TAAGCTGACGAGCATAAACATGTGCAAGCTGACAAGCATAAAC
* * **
1150 TAAGTTGACGAGCGTAAATC-TGTGCAAGCTGACAAGTGTAAAC
1 TAAGCTGACGAGCATAAA-CATGTGCAAGCTGACAAGCATAAAC
* * * *
1193 GTATATAAGCTGACGAGCGTAAGCATGTGCAAGCTGACGAGCGTAAA
1 -----TAAGCTGACGAGCATAAACATGTGCAAGCTGACAAGCATAAA
1240 TGTATATAAG
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
43 37 0.49
44 1 0.01
47 1 0.01
48 36 0.48
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.20
Consensus pattern (43 bp):
TAAGCTGACGAGCATAAACATGTGCAAGCTGACAAGCATAAAC
Found at i:1903 original size:48 final size:48
Alignment explanation
Indices: 1084--1935 Score: 755
Period size: 48 Copynumber: 17.9 Consensus size: 48
1074 AAATGTATAT
* *
1084 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCATAAACATGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * *
1132 AAGCTGACAAGCATAAAC-----TAAGTTGACGAGCGTAAATC-TGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAA-CGTGTGC
* * * *
1175 AAGCTGACAAGTGTAAACGTATATAAGCTGACGAGCGTAAGCATGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * * *
1223 AAGCTGACGAGCGTAAATGTATATAAGCTAACAAGCGTAAACGTGTTC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * * * * * * **
1271 AATCTAACAAGCGTAAATGTATATAAGCTGACAAGCGTAAATGTATAT
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * * ** *
1319 AAGCTGACGAGCGTGAACATGTGCAAGCTGACGAGCGTAAACATGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * ** * *
1367 AAGCTGATGAGCGTAAATGTATATAAGCTGAAAAGCGTAAACCTATGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * ** *
1415 AAGTTAATTAAG-GTAAACGTATATAGGCTGACGAGCGTAAACGTGTGC
1 AAGCTGA-CGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * * * * * *
1463 AAGCTGATGAGTGTAAACATATATAAGCTGACAAGCATAATCATGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * * * * * * **
1511 AAGCTGATGAGCATAAACATATATAAGTTGACGAGCATAAATGTATAT
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * * * ** * * * * **
1559 ATGCTGACGAGTGTAAATGTGTGCAAGTTGACGAGCATAAACATATAT
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * ** **
1607 AAGCTGATGAGCGTAAACGTGTGCAAATTGACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
** * * * **
1655 AAATTGACGAGCGTAAACGTATATAAGCTGACAAGTGTAAACATAAGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* *
1703 AAGCTGACGAGCGTAAACGTATATAAGCTGACGACCATAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
*
1751 AAGCTAACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* *
1799 AAGTTGACGAGCGTAAACATATATAAGCTGACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * * * * **
1847 AAGTTGACGAGCGTAAACATATATAAGCTGATGAGCGTAAATGTATTT
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
** * * **
1895 AAGCTGACGAATGTAAATGTGTGCAAGCTGACGAGCGTAAA
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAA
1936 TGTAGATATG
Statistics
Matches: 654, Mismatches: 141, Indels: 18
0.80 0.17 0.02
Matches are distributed among these distances:
43 37 0.06
44 1 0.00
47 4 0.01
48 609 0.93
49 3 0.00
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (48 bp):
AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
Found at i:1936 original size:48 final size:48
Alignment explanation
Indices: 1871--2080 Score: 239
Period size: 48 Copynumber: 4.4 Consensus size: 48
1861 AAACATATAT
* *
1871 AAGCTGATGAGCGTAAATGTATTTAAGCTGACGAATGTAAATGTGTGC
1 AAGCTGACGAGCGTAAATGTATATAAGCTGACGAATGTAAATGTGTGC
* * *
1919 AAGCTGACGAGCGTAAATGTAGATATGTTGACG-ATCGTAAATGTGTGC
1 AAGCTGACGAGCGTAAATGTATATAAGCTGACGAAT-GTAAATGTGTGC
* * * *
1967 AAGCTGACGAGCATAAA-GTATATAAGTTGATGACCT-TAAATGTGTGC
1 AAGCTGACGAGCGTAAATGTATATAAGCTGACGA-ATGTAAATGTGTGC
* * * * *
2014 AAGTTGACGAGCGTAAATGTATATAAGCTGGCGACTATAAACGTGTGC
1 AAGCTGACGAGCGTAAATGTATATAAGCTGACGAATGTAAATGTGTGC
2062 AAGCTGACGA-CAGTAAATG
1 AAGCTGACGAGC-GTAAATG
2081 CAATGAATTT
Statistics
Matches: 139, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
47 43 0.31
48 95 0.68
49 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.27, T:0.26
Consensus pattern (48 bp):
AAGCTGACGAGCGTAAATGTATATAAGCTGACGAATGTAAATGTGTGC
Found at i:8630 original size:15 final size:16
Alignment explanation
Indices: 8602--8639 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
8592 ACAAGATTTA
*
8602 CAAATATCATATG-ATT
1 CAAA-ATCAAATGAATT
8618 CAAAATCAAATGAATT
1 CAAAATCAAATGAATT
8634 CAAAAT
1 CAAAAT
8640 TCTATCTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (16 bp):
CAAAATCAAATGAATT
Found at i:10926 original size:15 final size:14
Alignment explanation
Indices: 10905--11011 Score: 53
Period size: 15 Copynumber: 7.6 Consensus size: 14
10895 CTGATAAATT
10905 ATCTTTTATTTAAA
1 ATCTTTTATTTAAA
*
10919 ACTCTTTTAATTAAA
1 A-TCTTTTATTTAAA
* * *
10934 TTC-TAT-TTTAATT
1 ATCTTTTATTTAA-A
*
10947 AT-TATTTATCTAAA
1 ATCT-TTTATTTAAA
*
10961 ACTCTTTTACTTAAA
1 A-TCTTTTATTTAAA
* *
10976 A--TTCTATTTAATT
1 ATCTTTTATTTAA-A
10989 ATCTTTTATTTAAA
1 ATCTTTTATTTAAA
11003 ACTCTTTTA
1 A-TCTTTTA
11012 AATCATATTT
Statistics
Matches: 66, Mismatches: 16, Indels: 21
0.64 0.16 0.20
Matches are distributed among these distances:
12 12 0.18
13 4 0.06
14 7 0.11
15 42 0.64
16 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (14 bp):
ATCTTTTATTTAAA
Found at i:10961 original size:42 final size:42
Alignment explanation
Indices: 10872--11012 Score: 180
Period size: 42 Copynumber: 3.3 Consensus size: 42
10862 TTGAATTTTA
* *
10872 AAAACTCTTTTAAATAATAATTTCTGA-TAAATTATCTTTTATTT
1 AAAACTCTTTTAATTAA-AA-TTCT-ATTTAATTATCTTTTATTT
*
10916 AAAACTCTTTTAATT-AAATTCTATTTTAATTAT-TATTTATCT
1 AAAACTCTTTTAATTAAAATTCTA-TTTAATTATCT-TTTATTT
*
10958 AAAACTCTTTTACTTAAAATTCTATTTAATTATCTTTTATTT
1 AAAACTCTTTTAATTAAAATTCTATTTAATTATCTTTTATTT
11000 AAAACTCTTTTAA
1 AAAACTCTTTTAA
11013 ATCATATTTG
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
40 1 0.01
41 5 0.06
42 56 0.65
43 10 0.12
44 14 0.16
ACGTcount: A:0.37, C:0.11, G:0.01, T:0.52
Consensus pattern (42 bp):
AAAACTCTTTTAATTAAAATTCTATTTAATTATCTTTTATTT
Done.