Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011150.1 Kokia drynarioides strain JFW-HI SEQ_126124, 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: 76896
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:8277 original size:17 final size:18
Alignment explanation
Indices: 8255--8295 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
8245 TTAGTTTTCA
8255 TGCATTCTT-ATTGT-GCT
1 TGCATTCTTAATTGTCG-T
8272 TGCATT-TTAATTGTCGT
1 TGCATTCTTAATTGTCGT
8289 TGCATTC
1 TGCATTC
8296 ATTTTAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.10
17 18 0.86
18 1 0.05
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.51
Consensus pattern (18 bp):
TGCATTCTTAATTGTCGT
Found at i:31569 original size:12 final size:12
Alignment explanation
Indices: 31552--31576 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31542 GAAATTCATC
31552 CTTCAGATGTAA
1 CTTCAGATGTAA
31564 CTTCAGATGTAA
1 CTTCAGATGTAA
31576 C
1 C
31577 GGTCGATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (12 bp):
CTTCAGATGTAA
Found at i:31805 original size:17 final size:17
Alignment explanation
Indices: 31779--31823 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
31769 ACATGCATTT
31779 ATTTTAATTGTCAT-TGC
1 ATTTTAATTGTC-TCTGC
*
31796 ATTTTTATTGTCTCTGC
1 ATTTTAATTGTCTCTGC
*
31813 ATTTTATTTGT
1 ATTTTAATTGT
31824 TTTAGTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60
Consensus pattern (17 bp):
ATTTTAATTGTCTCTGC
Found at i:32104 original size:20 final size:20
Alignment explanation
Indices: 32075--32117 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
32065 AATGAATGTG
*
32075 ATTGATTGTTGATTCTTTCT
1 ATTGACTGTTGATTCTTTCT
32095 ATTGACTGTTGATTCTTTCT
1 ATTGACTGTTGATTCTTTCT
32115 ATT
1 ATT
32118 TTTTGATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (20 bp):
ATTGACTGTTGATTCTTTCT
Found at i:32167 original size:32 final size:32
Alignment explanation
Indices: 32131--32194 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
32121 TGATGAATGA
32131 TTGAGATTGCATTAGTAATAAATGGGTAGTAT
1 TTGAGATTGCATTAGTAATAAATGGGTAGTAT
32163 TTGAGATTGCATTAGTAATAAATGGGTAGTAT
1 TTGAGATTGCATTAGTAATAAATGGGTAGTAT
32195 CATTCTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (32 bp):
TTGAGATTGCATTAGTAATAAATGGGTAGTAT
Found at i:44851 original size:14 final size:15
Alignment explanation
Indices: 44834--44864 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
44824 ATTTACTTTA
44834 TTTTATTTTTA-CCT
1 TTTTATTTTTATCCT
44848 TTTTATTTTTATCCT
1 TTTTATTTTTATCCT
44863 TT
1 TT
44865 CACACAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATTTTTATCCT
Found at i:46095 original size:18 final size:18
Alignment explanation
Indices: 46072--46114 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
46062 TTCAATTAAC
46072 TCTTCTTCAGGATCTTCT
1 TCTTCTTCAGGATCTTCT
*
46090 TCTTCTTCATGATCTTCT
1 TCTTCTTCAGGATCTTCT
46108 TCTTCTT
1 TCTTCTT
46115 TAGTTTGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.09, C:0.28, G:0.07, T:0.56
Consensus pattern (18 bp):
TCTTCTTCAGGATCTTCT
Found at i:47503 original size:14 final size:14
Alignment explanation
Indices: 47460--47503 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
47450 TGATAATAAT
47460 TAAT-ATAAA-TTA
1 TAATAATAAATTTA
*
47472 TAAAAATAAATTTA
1 TAATAATAAATTTA
47486 TAATAATAAATTTA
1 TAATAATAAATTTA
47500 TAAT
1 TAAT
47504 TTTATATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 3 0.11
13 5 0.18
14 20 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATAATAAATTTA
Found at i:47539 original size:9 final size:9
Alignment explanation
Indices: 47525--47559 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
47515 TATTATCAAT
47525 AAATAAATA
1 AAATAAATA
47534 AAATAAATA
1 AAATAAATA
*
47543 ACATAAAATA
1 AAAT-AAATA
47553 AAATAAA
1 AAATAAA
47560 AACTTCTATT
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:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAATA
Found at i:56577 original size:41 final size:41
Alignment explanation
Indices: 56518--56651 Score: 180
Period size: 41 Copynumber: 3.2 Consensus size: 41
56508 TCGTAAATCT
* * *
56518 TTCTTTTATACGTAATCTCATGCTCGTCCCGAGACATGAGTC
1 TTCTTTT-TACATAATCTCATTCTCATCCCGAGACATGAGTC
*
56560 TTCTTTTTACATAATCTCATTCTCATCCCGAGATATGAGTC
1 TTCTTTTTACATAATCTCATTCTCATCCCGAGACATGAGTC
**
56601 TT-TCTTTTACATAATCTCATTCTCATCCTTAGACATGAGTC
1 TTCT-TTTTACATAATCTCATTCTCATCCCGAGACATGAGTC
*
56642 TTCCTTTTAC
1 TTCTTTTTAC
56652 TTTTGAGTAT
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
40 1 0.01
41 74 0.90
42 7 0.09
ACGTcount: A:0.22, C:0.25, G:0.10, T:0.42
Consensus pattern (41 bp):
TTCTTTTTACATAATCTCATTCTCATCCCGAGACATGAGTC
Found at i:58274 original size:37 final size:37
Alignment explanation
Indices: 58232--58307 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
58222 AATGTCGCTA
* * *
58232 CATGAGCACTTATAGATTGCGCCCAAAACTGTCGCCG
1 CATGAGCACTTACAGATTGCACCCAAAACTGTCACCG
*
58269 CATGAGCACTTCCAGATTGCACCCAAAACTGTCACCG
1 CATGAGCACTTACAGATTGCACCCAAAACTGTCACCG
58306 CA
1 CA
58308 GGAATATTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (37 bp):
CATGAGCACTTACAGATTGCACCCAAAACTGTCACCG
Found at i:58319 original size:37 final size:37
Alignment explanation
Indices: 58245--58331 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 37
58235 GAGCACTTAT
* * * *
58245 AGATTGCGCCCAAAACTGTCGCCGCATGAGCACTTCC
1 AGATTGCACCCAAAACTGTCACCGCAGGAACACTTCC
* *
58282 AGATTGCACCCAAAACTGTCACCGCAGGAATATTTCC
1 AGATTGCACCCAAAACTGTCACCGCAGGAACACTTCC
*
58319 AGAATGCACCCAA
1 AGATTGCACCCAA
58332 GACTATTGCT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.18
Consensus pattern (37 bp):
AGATTGCACCCAAAACTGTCACCGCAGGAACACTTCC
Found at i:69612 original size:25 final size:23
Alignment explanation
Indices: 69571--69616 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
69561 CCAATTAGGC
69571 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
69594 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
69617 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:70713 original size:14 final size:13
Alignment explanation
Indices: 70692--70723 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
70682 ATTATTTGCA
70692 TTTTTAATTTAAT
1 TTTTTAATTTAAT
70705 TTTTCTAATTTAAT
1 TTTT-TAATTTAAT
70719 TTTTT
1 TTTTT
70724 TCCCTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:76293 original size:5 final size:5
Alignment explanation
Indices: 76273--76345 Score: 92
Period size: 5 Copynumber: 13.8 Consensus size: 5
76263 AATTAGTATA
* *
76273 TTTAT TTTCAAT TTTAT TTTAT TTTAT CTTAT TTTAT TTTAT TTTAT CTTAT
1 TTTAT TTT--AT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
76325 TTTATT TTTAAT TTTAT TTTA
1 TTTA-T TTT-AT TTTAT TTTA
76346 ATTATGCACT
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
5 46 0.77
6 8 0.13
7 6 0.10
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTAT
Done.