Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005454.1 Kokia drynarioides strain JFW-HI SEQ_119496, 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: 31691
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:160 original size:17 final size:17
Alignment explanation
Indices: 117--161 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
107 TCACAACTCT
117 CATGTTGTTATAGCTCA
1 CATGTTGTTATAGCTCA
* * *
134 CATATCGTTATAGCTCG
1 CATGTTGTTATAGCTCA
*
151 CGTGTTGTTAT
1 CATGTTGTTAT
162 TACTTGCTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (17 bp):
CATGTTGTTATAGCTCA
Found at i:584 original size:52 final size:53
Alignment explanation
Indices: 503--691 Score: 163
Period size: 52 Copynumber: 3.6 Consensus size: 53
493 TATTTTCAAT
** *
503 ACAAAACAGTTCATGCATTCGATGTAATGACAACTT-GCATATACATTTCATC
1 ACAAAACAGTTCATGCATTCGATACAATGACAAGTTAGCATATACATTTCATC
* * * * * *
555 ACAAAATAGTTCATGCATTCGATACAATGA-TAGTTCA-CATAAACA-ATGATTT
1 ACAAAACAGTTCATGCATTCGATACAATGACAAGTT-AGCATATACATTTCA-TC
* * * * * *
607 TCAAGACAATTCATACATTCGATACAATGGC-AGTTAGCATATGCATTTCATC
1 ACAAAACAGTTCATGCATTCGATACAATGACAAGTTAGCATATACATTTCATC
* *
659 ACAAATATAGTTCATGCATTCGATGCAATGACA
1 ACAAA-ACAGTTCATGCATTCGATACAATGACA
692 TACAATACTT
Statistics
Matches: 102, Mismatches: 27, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
51 6 0.06
52 73 0.72
53 23 0.23
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (53 bp):
ACAAAACAGTTCATGCATTCGATACAATGACAAGTTAGCATATACATTTCATC
Found at i:3507 original size:16 final size:16
Alignment explanation
Indices: 3488--3536 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
3478 CAAAGGTATC
3488 CATAAGCAAAGATAGT
1 CATAAGCAAAGATAGT
3504 CAT----AAAGAT-GTT
1 CATAAGCAAAGATAG-T
3516 CATAAGCAAAGATAGT
1 CATAAGCAAAGATAGT
3532 CATAA
1 CATAA
3537 AGACGTCCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
11 1 0.04
12 10 0.37
16 15 0.56
17 1 0.04
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.22
Consensus pattern (16 bp):
CATAAGCAAAGATAGT
Found at i:3510 original size:28 final size:28
Alignment explanation
Indices: 3470--3539 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
3460 TTGAAAAATG
* * *
3470 GATAGCCACAAAGGTATCCATAAGCAAA
1 GATAGTCATAAAGATATCCATAAGCAAA
* *
3498 GATAGTCATAAAGATGTTCATAAGCAAA
1 GATAGTCATAAAGATATCCATAAGCAAA
3526 GATAGTCATAAAGA
1 GATAGTCATAAAGA
3540 CGTCCACAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (28 bp):
GATAGTCATAAAGATATCCATAAGCAAA
Found at i:3567 original size:29 final size:29
Alignment explanation
Indices: 3535--3596 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
3525 AGATAGTCAT
* * *
3535 AAAGACGTCCACAAATAATAGATAACCAC
1 AAAGACGTCAACAAACAATAAATAACCAC
** *
3564 AAAGGTGTCAACAAACAATAAATAGCCAC
1 AAAGACGTCAACAAACAATAAATAACCAC
3593 AAAG
1 AAAG
3597 GCACTTCCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.53, C:0.21, G:0.13, T:0.13
Consensus pattern (29 bp):
AAAGACGTCAACAAACAATAAATAACCAC
Found at i:3715 original size:29 final size:29
Alignment explanation
Indices: 3666--3767 Score: 132
Period size: 29 Copynumber: 3.5 Consensus size: 29
3656 ATTATTATAT
* *
3666 TCAACCACAAAGGCTCTCATATAACATAA
1 TCAACCACAAAGGCTCACATATAACAAAA
* ** * *
3695 TTAGTCACAAAGGCTCACATATAATAGAA
1 TCAACCACAAAGGCTCACATATAACAAAA
*
3724 TCAACCACGAAGGCTCACATATAACAAAA
1 TCAACCACAAAGGCTCACATATAACAAAA
3753 TCAACCACAAAGGCT
1 TCAACCACAAAGGCT
3768 TCTTTTTTTT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.19
Consensus pattern (29 bp):
TCAACCACAAAGGCTCACATATAACAAAA
Found at i:8014 original size:21 final size:21
Alignment explanation
Indices: 7988--8038 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
7978 ATATGTTTCC
7988 TGAACCTAGGAGAGATAGAAG
1 TGAACCTAGGAGAGATAGAAG
8009 TGAACCTAGGAGAGATAGAAG
1 TGAACCTAGGAGAGATAGAAG
8030 TGAACCTAG
1 TGAACCTAG
8039 AGCTCCATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.41, C:0.12, G:0.31, T:0.16
Consensus pattern (21 bp):
TGAACCTAGGAGAGATAGAAG
Found at i:13107 original size:19 final size:20
Alignment explanation
Indices: 13078--13125 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
13068 AACTTCAAAG
*
13078 AAATATAAAAA-ATACATAA-
1 AAATTTAAAAATATA-ATAAT
*
13097 ATATTTAAAAATATAATAAT
1 AAATTTAAAAATATAATAAT
13117 AAATTTAAA
1 AAATTTAAA
13126 TTTAATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATTTAAAAATATAATAAT
Found at i:15710 original size:24 final size:24
Alignment explanation
Indices: 15676--15726 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
15666 AATTTGACTC
* *
15676 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
15700 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
15724 AAA
1 AAA
15727 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:16375 original size:21 final size:22
Alignment explanation
Indices: 16351--16405 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
16341 TAATTATTTT
16351 TTTATTTTTATATT-TTTAAAA
1 TTTATTTTTATATTATTTAAAA
* *
16372 TTTATTGTTATATTATTTGAAA
1 TTTATTTTTATATTATTTAAAA
16394 TTT-TTTTATATA
1 TTTATTTT-TATA
16406 ATTCTTTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTATTTTTATATTATTTAAAA
Found at i:16405 original size:22 final size:20
Alignment explanation
Indices: 16355--16420 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 20
16345 TATTTTTTTA
*
16355 TTTTTATATTTTTAAAATTT
1 TTTTTATATTTTTGAAATTT
*
16375 ATTGTTATATTATTTGAAATTT
1 -TTTTTATATT-TTTGAAATTT
16397 TTTTATATAATTCTTTG-AATTT
1 TTTT-TAT-ATT-TTTGAAATTT
16419 TT
1 TT
16421 AGAATTAGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
21 12 0.32
22 19 0.50
23 7 0.18
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.65
Consensus pattern (20 bp):
TTTTTATATTTTTGAAATTT
Found at i:21872 original size:25 final size:24
Alignment explanation
Indices: 21817--21872 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 24
21807 AAAATTTATA
** * *
21817 TTTTTAGTTAATTTGATCCTTATT
1 TTTTTAGTTAATTTGATAATCAAT
21841 TTGTTTAGTTAAATTTGATAATCAAT
1 TT-TTTAGTT-AATTTGATAATCAAT
21867 TTTTTA
1 TTTTTA
21873 AAATGTTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 2 0.08
25 11 0.42
26 13 0.50
ACGTcount: A:0.27, C:0.05, G:0.09, T:0.59
Consensus pattern (24 bp):
TTTTTAGTTAATTTGATAATCAAT
Found at i:22054 original size:27 final size:27
Alignment explanation
Indices: 22022--22085 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
22012 ATTTCAATGA
*
22022 AATTTTTTATAATATTTT-TGAATTTT
1 AATTTTTTATAATATTTTATAAATTTT
*
22048 GAATTTTTT-GAATATTTTATAAATTTT
1 -AATTTTTTATAATATTTTATAAATTTT
22075 AATTTATTTAT
1 AATTT-TTTAT
22086 CGATGTGGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 13 0.42
27 18 0.58
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (27 bp):
AATTTTTTATAATATTTTATAAATTTT
Found at i:22543 original size:28 final size:29
Alignment explanation
Indices: 22512--22573 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
22502 TAATTAAACC
*
22512 TAAAATTTAAAATCTAAAAG-CAA-AACAT
1 TAAAATTTAAAA-CTAAAAGTAAATAACAT
*
22540 TAAAA-TTAAAAGTAAAAGTAAATAACAT
1 TAAAATTTAAAACTAAAAGTAAATAACAT
22568 TAAAAT
1 TAAAAT
22574 CAACCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 6 0.21
27 8 0.28
28 15 0.52
ACGTcount: A:0.63, C:0.06, G:0.05, T:0.26
Consensus pattern (29 bp):
TAAAATTTAAAACTAAAAGTAAATAACAT
Found at i:22544 original size:21 final size:20
Alignment explanation
Indices: 22518--22556 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
22508 AACCTAAAAT
22518 TTAAAATCTAAAAGCAAAACA
1 TTAAAAT-TAAAAGCAAAACA
*
22539 TTAAAATTAAAAGTAAAA
1 TTAAAATTAAAAGCAAAA
22557 GTAAATAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.23
Consensus pattern (20 bp):
TTAAAATTAAAAGCAAAACA
Found at i:26942 original size:10 final size:9
Alignment explanation
Indices: 26907--26941 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
26897 AAACCTATCT
26907 ATATTTTAA
1 ATATTTTAA
*
26916 ATTAATTTAA
1 A-TATTTTAA
26926 ATATTTTAA
1 ATATTTTAA
26935 ATATTTT
1 ATATTTT
26942 TTGTCCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATATTTTAA
Found at i:29632 original size:21 final size:22
Alignment explanation
Indices: 29606--29651 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
29596 CAAAACCATG
29606 AAAACCAAAT-ACCCAAACCCT
1 AAAACCAAATCACCCAAACCCT
*
29627 AAAACCAAATCACCCAAACTCT
1 AAAACCAAATCACCCAAACCCT
29649 AAA
1 AAA
29652 TCTAATTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.54, C:0.35, G:0.00, T:0.11
Consensus pattern (22 bp):
AAAACCAAATCACCCAAACCCT
Found at i:29737 original size:21 final size:21
Alignment explanation
Indices: 29694--29739 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
29684 AACCCGACCA
* *
29694 TTGATTGTTGACCGCTGATAG
1 TTGATTGTTGACCACTGACAG
*
29715 TTGATTGTTGACCATTGACAG
1 TTGATTGTTGACCACTGACAG
29736 TTGA
1 TTGA
29740 CCGTTGACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (21 bp):
TTGATTGTTGACCACTGACAG
Done.