Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005012.1 Kokia drynarioides strain JFW-HI SEQ_118771, 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: 57740
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:4581 original size:7 final size:7
Alignment explanation
Indices: 4563--4592 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
4553 ATGGAGAGGG
4563 TGGGCAGT
1 TGGGC-GT
4571 TGGGCGT
1 TGGGCGT
4578 TGGGCGT
1 TGGGCGT
4585 TGGGCGT
1 TGGGCGT
4592 T
1 T
4593 TCCTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.03, C:0.13, G:0.53, T:0.30
Consensus pattern (7 bp):
TGGGCGT
Found at i:13826 original size:31 final size:32
Alignment explanation
Indices: 13782--13862 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 32
13772 AGTTAGTCAT
* * * *
13782 TAAACTTGTCAATTGTTT-TCACGTTAGGGCT
1 TAAACTAGACAATTGTTTCTCACATTAGGGCC
*
13813 TGAACTAGACAATT-TTTCTCACATTAGGGCC
1 TAAACTAGACAATTGTTTCTCACATTAGGGCC
*
13844 TAAACTTGACAATTGTTTC
1 TAAACTAGACAATTGTTTC
13863 CATATTGAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 3 0.07
31 34 0.83
32 4 0.10
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (32 bp):
TAAACTAGACAATTGTTTCTCACATTAGGGCC
Found at i:25698 original size:2 final size:2
Alignment explanation
Indices: 25691--25719 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25681 CTGATCAGGT
25691 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
25720 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:27968 original size:22 final size:23
Alignment explanation
Indices: 27936--27987 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
27926 ATAAAATAAC
*
27936 TTTAAAATATTACAAAATTATTA
1 TTTAAATTATTACAAAATTATTA
** *
27959 -TTAAATTATTTGAAAATTTTTA
1 TTTAAATTATTACAAAATTATTA
27981 TTTAAAT
1 TTTAAAT
27988 CATAAGGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTAAATTATTACAAAATTATTA
Found at i:28484 original size:30 final size:29
Alignment explanation
Indices: 28450--28519 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
28440 TAGTGTGAAC
* *
28450 TTTGATTTTGTGTAATTATATGCATGAAAT
1 TTTGATTTTGTGTAA-AATATACATGAAAT
* *
28480 TTTGATTGTGGTTTAAAATATACATGAAAT
1 TTTGATT-TTGTGTAAAATATACATGAAAT
*
28510 TTTTATTTTG
1 TTTGATTTTG
28520 ATTCAATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 2 0.06
30 25 0.76
31 6 0.18
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (29 bp):
TTTGATTTTGTGTAAAATATACATGAAAT
Found at i:28682 original size:29 final size:28
Alignment explanation
Indices: 28649--28739 Score: 74
Period size: 31 Copynumber: 3.1 Consensus size: 28
28639 AAAAATTATG
* * *
28649 AAAATAGATCAAATCAAAATTTGATGTAT
1 AAAATACATAAAATCAAAATTT-ATATAT
*
28678 AAAATTACATAAAATCAAAGTTTATATAT
1 AAAA-TACATAAAATCAAAATTTATATAT
** *
28707 AAAATTACACATCGAATCAAAATTCATATAT
1 AAAA-T--ACATAAAATCAAAATTTATATAT
28738 AA
1 AA
28740 TTTTGATATT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 15 0.29
30 15 0.29
31 21 0.41
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (28 bp):
AAAATACATAAAATCAAAATTTATATAT
Found at i:28693 original size:30 final size:29
Alignment explanation
Indices: 28659--28739 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 29
28649 AAAATAGATC
*
28659 AAATCAAAATTTGATGTATAAAATTACATA
1 AAATCAAAATTT-ATATATAAAATTACATA
* *
28689 AAATCAAAGTTTATATATAAAATTACACATC
1 AAATCAAAATTTATATATAAAATT--ACATA
* *
28720 GAATCAAAATTCATATATAA
1 AAATCAAAATTTATATATAA
28740 TTTTGATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 11 0.26
30 11 0.26
31 21 0.49
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (29 bp):
AAATCAAAATTTATATATAAAATTACATA
Found at i:40491 original size:2 final size:2
Alignment explanation
Indices: 40486--40511 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40476 ATATGAACAT
40486 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
40512 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:40861 original size:2 final size:2
Alignment explanation
Indices: 40821--40846 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40811 TAAAAAATTA
40821 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
40847 GAACCTTGAA
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):
AT
Found at i:41012 original size:22 final size:22
Alignment explanation
Indices: 40978--41024 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
40968 CGTATTTATC
*
40978 AAATTGAATGAAAGATAATTGA
1 AAATTGAATGAAAAATAATTGA
*
41000 AAATATGAA-GAAAAATAATTTA
1 AAAT-TGAATGAAAAATAATTGA
41022 AAA
1 AAA
41025 GTACTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.26
Consensus pattern (22 bp):
AAATTGAATGAAAAATAATTGA
Found at i:41957 original size:18 final size:17
Alignment explanation
Indices: 41921--41960 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
41911 TAATAAAAAT
41921 ATAATTTTATTGTTTTA
1 ATAATTTTATTGTTTTA
41938 ATAA-TTTATAT-TTTT-
1 ATAATTTTAT-TGTTTTA
41953 ATAATTTT
1 ATAATTTT
41961 TAAATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.19
16 12 0.57
17 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
ATAATTTTATTGTTTTA
Found at i:53863 original size:21 final size:21
Alignment explanation
Indices: 53839--53888 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
53829 TTTGCTTCTG
53839 GTGCATGGCAGGCACTTGGGA
1 GTGCATGGCAGGCACTTGGGA
53860 GTGCATGGCAGGCACTTGGGA
1 GTGCATGGCAGGCACTTGGGA
53881 GTGCATGG
1 GTGCATGG
53889 AAAGAGAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.18, G:0.44, T:0.20
Consensus pattern (21 bp):
GTGCATGGCAGGCACTTGGGA
Found at i:54339 original size:212 final size:214
Alignment explanation
Indices: 53947--54586 Score: 775
Period size: 212 Copynumber: 3.0 Consensus size: 214
53937 TATTTGTTTT
* * * * * ** *
53947 GTATGTTGATCGTTTGTGCTTTCTCTGCGGAAGCCCCGACCTTGTTCAAACTTTGGGTAGAAT-T
1 GTATGTTGGTCATTTTTGCTTCCTCCGCGGAAGCCCCGACCTTGTTCGGACTTTGAGTAGAATAT
* * *
54011 CCTTT-CCGGCACTTAG-ACAGGCATATGTTTGTAGACTAGATAGATAGTTCGAGAATGGAACTT
66 --TTTCCCGGCACTTAGAACAAGCAAATG-TCGTAGA-TAGATAG-T--TT-GAGAATGGAACTT
*** * * *
54074 TTCGCACTAATATAAACACGAATAACGCACGCCGCTGCTAGATATCGTGTTAATGGTGTATCTCC
123 TTCATGCTAATATAAACACGAATAACGTAGGCCGCTGCTAGATTTCGTGTTAATGGTGTATCTCC
54139 ATTTGTTCAAAAGTATGTTTTCATGGC
188 ATTTGTTCAAAAGTATGTTTTCATGGC
* *
54166 GTATGTTGGTCATTTTTGCTTTCTCCGCGGAAGCCTCGACCTTGTTTCGGACTTTGAGTAGAAT-
1 GTATGTTGGTCATTTTTGCTTCCTCCGCGGAAGCCCCGACCTTG-TTCGGACTTTGAGTAGAATA
54230 TTTTCCCCGGCACTTAGAACAAGCAAATGTC-T-G-TAGATAGTTTGAGAATGGAACTTTTCATG
65 TTTT-CCCGGCACTTAGAACAAGCAAATGTCGTAGATAGATAGTTTGAGAATGGAACTTTTCATG
* * *
54292 CTAATATAAACACGAATAACGTAGGCCGCCGATAGATTTCATGTTAATGGTGTATCT-CAGTTTG
129 CTAATATAAACACGAATAACGTAGGCCGCTGCTAGATTTCGTGTTAATGGTGTATCTCCA-TTTG
* * *
54356 TTCAAATGTATGCTTTCATTGC
193 TTCAAAAGTATGTTTTCATGGC
*
54378 GTATGTTGGTCATTTTTGCTTCCTCCGCGGAAGCCCCGACCTTGTTCGGACTTTGAGTGGAATAT
1 GTATGTTGGTCATTTTTGCTTCCTCCGCGGAAGCCCCGACCTTGTTCGGACTTTGAGTAGAATAT
* * * *
54443 TTTCCCGGCATTTATAATACGCAAATGTCTGTAGATAGATAGTTTGAGAATGGAACTTTTCATGC
66 TTTCCCGGCACTTAGAACAAGCAAATGTC-GTAGATAGATAGTTTGAGAATGGAACTTTTCATGC
* *
54508 TAATA-AGAACACCAAATAACGTAGGCCGCTGCTAGATTTCGTGTTAAT-G-GTA--TCCGTTTG
130 TAATATA-AACA-CGAATAACGTAGGCCGCTGCTAGATTTCGTGTTAATGGTGTATCTCCATTTG
54568 TTCAAAAGTATGTTTTCAT
193 TTCAAAAGTATGTTTTCAT
54587 TGCATTATAT
Statistics
Matches: 371, Mismatches: 37, Indels: 33
0.84 0.08 0.07
Matches are distributed among these distances:
211 42 0.11
212 158 0.43
213 4 0.01
214 5 0.01
215 41 0.11
216 39 0.11
218 4 0.01
219 40 0.11
220 29 0.08
221 9 0.02
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (214 bp):
GTATGTTGGTCATTTTTGCTTCCTCCGCGGAAGCCCCGACCTTGTTCGGACTTTGAGTAGAATAT
TTTCCCGGCACTTAGAACAAGCAAATGTCGTAGATAGATAGTTTGAGAATGGAACTTTTCATGCT
AATATAAACACGAATAACGTAGGCCGCTGCTAGATTTCGTGTTAATGGTGTATCTCCATTTGTTC
AAAAGTATGTTTTCATGGC
Done.