Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006106.1 Kokia drynarioides strain JFW-HI SEQ_120613, 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: 66888
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 36 characters in sequence are not A, C, G, or T
Found at i:630 original size:6 final size:6
Alignment explanation
Indices: 609--689 Score: 89
Period size: 6 Copynumber: 14.0 Consensus size: 6
599 ATTTGGACTT
* *
609 TTTAAC TTTGAA TTTAAA TTTAAA TTTAAA -TTAAA TTTAAA TTTAAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
* *
657 -TT-AA TTTAAA TTCAAA TCTAAA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
690 AAGGTCCAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
4 1 0.02
5 12 0.19
6 49 0.78
7 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:644 original size:17 final size:17
Alignment explanation
Indices: 622--689 Score: 95
Period size: 17 Copynumber: 4.0 Consensus size: 17
612 AACTTTGAAT
622 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTTAAA
639 TTAAATTTAAATTTAAGA
1 TTAAATTTAAATTTAA-A
*
657 TT-AATTTAAATTCAAA
1 TTAAATTTAAATTTAAA
673 TCTAAA-TTAAATTTAAA
1 T-TAAATTTAAATTTAAA
690 AAGGTCCAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
16 2 0.04
17 39 0.85
18 5 0.11
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:646 original size:23 final size:23
Alignment explanation
Indices: 620--689 Score: 90
Period size: 23 Copynumber: 3.0 Consensus size: 23
610 TTAACTTTGA
620 ATTTAAATTTAAATTTAAA-TTAA
1 ATTTAAATTTAAA-TTAAATTTAA
643 ATTTAAATTTAAGATT-AATTTAA
1 ATTTAAATTTAA-ATTAAATTTAA
* *
666 ATTCAAATCTAAATTAAATTTAA
1 ATTTAAATTTAAATTAAATTTAA
689 A
1 A
690 AAGGTCCAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.12
23 36 0.86
24 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (23 bp):
ATTTAAATTTAAATTAAATTTAA
Found at i:946 original size:3 final size:3
Alignment explanation
Indices: 938--964 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
928 TTAAATTTTA
938 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
965 TAATTAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1442 original size:107 final size:110
Alignment explanation
Indices: 1277--1507 Score: 369
Period size: 107 Copynumber: 2.1 Consensus size: 110
1267 CACGTAGGCA
*
1277 TCAAAGTTTAAGGGACTAATTTAACAAAAACAAATAAGTCTAAGGGACTAATCATTCAATGACCA
1 TCAAAGTCTAAGGGACTAATTTAACAAAAACAAATAAGTCTAAGGGACTAATCATTCAATGACCA
1342 ATAAGCCACCAGTTTAATCATAAAAAAACATACTATAAATTTGGT
66 ATAAGCCACCAGTTTAATCATAAAAAAACATACTATAAATTTGGT
* *
1387 TCAAAGTCTAAGGGACTAATTT-ATAAAAA-AAA-AAGTCTAAGGGACTAATCATTCAATGACTA
1 TCAAAGTCTAAGGGACTAATTTAACAAAAACAAATAAGTCTAAGGGACTAATCATTCAATGACCA
* ** *
1449 ATAAGCCGCCAGTTTAATCATAGTAAGACATACTATAAATTTGGT
66 ATAAGCCACCAGTTTAATCATAAAAAAACATACTATAAATTTGGT
*
1494 TCAAAGTCCAAGGG
1 TCAAAGTCTAAGGG
1508 GCAATTTCAT
Statistics
Matches: 113, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
107 83 0.73
108 3 0.03
109 6 0.05
110 21 0.19
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.26
Consensus pattern (110 bp):
TCAAAGTCTAAGGGACTAATTTAACAAAAACAAATAAGTCTAAGGGACTAATCATTCAATGACCA
ATAAGCCACCAGTTTAATCATAAAAAAACATACTATAAATTTGGT
Found at i:2380 original size:180 final size:180
Alignment explanation
Indices: 2071--2422 Score: 641
Period size: 180 Copynumber: 2.0 Consensus size: 180
2061 ATAAATATTT
*
2071 ATAATTGTAGATTTTAAAAATTATATTTTAGATAAATATACCATTCGAGATTTTATAAACAATTG
1 ATAATTATAGATTTTAAAAATTATATTTTAGATAAATATACCATTCGAGATTTTATAAACAATTG
*
2136 AAAAAAAATTGAAATTATCAAATATTGTTCAAAAAATATAAAACATAGATATTTTTATCTAATTA
66 AAAAAAAATTGAAATTATCAAATATTGTCCAAAAAATATAAAACATAGATATTTTTATCTAATTA
2201 AAGTCGAAAAATCCAAATCCAAATGTAATTTTATCTAAATAAGGTCCAAA
131 AAGTCGAAAAATCCAAATCCAAATGTAATTTTATCTAAATAAGGTCCAAA
2251 ATAATTATAGATTTTAAAAATTATATTTTAGATAAATATACCATTCGAGATTTTATAAACAATTG
1 ATAATTATAGATTTTAAAAATTATATTTTAGATAAATATACCATTCGAGATTTTATAAACAATTG
* * *
2316 AAAAGAAATTGAAATTATCAAATATTGTCCAAGAAATATAAAACCTAGATATTTTTATCTAATTA
66 AAAAAAAATTGAAATTATCAAATATTGTCCAAAAAATATAAAACATAGATATTTTTATCTAATTA
* *
2381 AAGTCGAAAAATTCAAATCCAAATGTAATTTTGTCTAAATAA
131 AAGTCGAAAAATCCAAATCCAAATGTAATTTTATCTAAATAA
2423 AGTTTAAAAT
Statistics
Matches: 165, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
180 165 1.00
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.36
Consensus pattern (180 bp):
ATAATTATAGATTTTAAAAATTATATTTTAGATAAATATACCATTCGAGATTTTATAAACAATTG
AAAAAAAATTGAAATTATCAAATATTGTCCAAAAAATATAAAACATAGATATTTTTATCTAATTA
AAGTCGAAAAATCCAAATCCAAATGTAATTTTATCTAAATAAGGTCCAAA
Found at i:5136 original size:58 final size:58
Alignment explanation
Indices: 4980--5136 Score: 215
Period size: 59 Copynumber: 2.7 Consensus size: 58
4970 AAAGTTGCTA
* * * *
4980 TGTTTTGGCACTTAAAGCAACCGCAAACCACAACTACCAGCATGTCAAGGATTGAATT
1 TGTTTTGGCACTAAAAGCAACCACAAGCCACAAGTACCAGCATGTCAAGGATTGAATT
* * * *
5038 TGTTTTGGCACGAAAAGTAAACCAGAAGCCACAAGAACCAGCATGTCAAGGATTGAATT
1 TGTTTTGGCACTAAAAG-CAACCACAAGCCACAAGTACCAGCATGTCAAGGATTGAATT
* *
5097 TGTTTGGGCACTAAAAGCAAGCACAAGCCACAAGTACCAG
1 TGTTTTGGCACTAAAAGCAACCACAAGCCACAAGTACCAG
5137 TCCAACCCCT
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
58 34 0.40
59 50 0.60
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (58 bp):
TGTTTTGGCACTAAAAGCAACCACAAGCCACAAGTACCAGCATGTCAAGGATTGAATT
Found at i:14970 original size:4 final size:4
Alignment explanation
Indices: 14961--14999 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
14951 GTATTTTGTT
* *
14961 TTTA TTTA TTTA TTTG TTTG TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
15000 TTGTCTCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:18943 original size:2 final size:2
Alignment explanation
Indices: 18936--18969 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
18926 TAGCTAGCAG
* *
18936 TA TA TA TA TA TA TA TA CA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18970 CATAATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:18951 original size:10 final size:10
Alignment explanation
Indices: 18936--18969 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
18926 TAGCTAGCAG
*
18936 TATATATATA
1 TATATACATA
18946 TATATACATA
1 TATATACATA
18956 TATATACATA
1 TATATACATA
18966 TATA
1 TATA
18970 CATAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (10 bp):
TATATACATA
Found at i:27893 original size:3 final size:3
Alignment explanation
Indices: 27887--27918 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
27877 ATGATGATGA
*
27887 TGG TGG TGG TGG TGG TGG TGG TGG TGG CGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
27919 AGTGTGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.66, T:0.31
Consensus pattern (3 bp):
TGG
Found at i:33202 original size:2 final size:2
Alignment explanation
Indices: 33195--33219 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33185 ACAAAGAACA
33195 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
33220 TAATTGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:34090 original size:25 final size:25
Alignment explanation
Indices: 34039--34092 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
34029 AAAAAAATTA
* *
34039 TTTTAATTTTTAATTAATTTTTATT
1 TTTTAATTTTAAATTAACTTTTATT
*
34064 TTTTAATCTTTAAATTTACTTTT-TT
1 TTTTAAT-TTTAAATTAACTTTTATT
34089 TTTT
1 TTTT
34093 GTCAAATCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTAATTTTAAATTAACTTTTATT
Found at i:34258 original size:18 final size:18
Alignment explanation
Indices: 34235--34278 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
34225 TAATATTATT
34235 TTTAAAAAATATAAATCA
1 TTTAAAAAATATAAATCA
**
34253 TTTAAAAAATATAAATTT
1 TTTAAAAAATATAAATCA
34271 TTTAAAAA
1 TTTAAAAA
34279 TTTAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTAAAAAATATAAATCA
Found at i:34277 original size:17 final size:18
Alignment explanation
Indices: 34217--34285 Score: 70
Period size: 17 Copynumber: 3.7 Consensus size: 18
34207 TTAAAAATTC
34217 TAAAAATATAATATTATTTT
1 TAAAAATATAA-A-TATTTT
34237 TAAAAAATATAAATCA-TTT
1 T-AAAAATATAAAT-ATTTT
*
34256 AAAAAATATAAAT-TTTT
1 TAAAAATATAAATATTTT
*
34273 TAAAAATTTAAAT
1 TAAAAATATAAAT
34286 TTTAGTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
17 14 0.33
18 12 0.28
19 4 0.09
20 3 0.07
21 10 0.23
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAAATATAAATATTTT
Found at i:34286 original size:17 final size:17
Alignment explanation
Indices: 34232--34288 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
34222 ATATAATATT
34232 ATTTTTAAAAAATATAA
1 ATTTTTAAAAAATATAA
*
34249 ATCATTTAAAAAATATAA
1 AT-TTTTAAAAAATATAA
* *
34267 ATTTTTTAAAAATTTAA
1 ATTTTTAAAAAATATAA
34284 ATTTT
1 ATTTT
34289 AGTTAAATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 19 0.54
18 16 0.46
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTTTAAAAAATATAA
Found at i:43552 original size:5 final size:6
Alignment explanation
Indices: 43531--43560 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
43521 CATCAAATTG
*
43531 AAAATT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
43561 TAATCTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:49712 original size:19 final size:20
Alignment explanation
Indices: 49680--49718 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
49670 AAATAGAAAA
*
49680 TTTTTGTTAGATTTTTAATT
1 TTTTTGTTAGATTTTAAATT
*
49700 TTTTTTTTA-ATTTTAAATT
1 TTTTTGTTAGATTTTAAATT
49719 AATAAAGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTGTTAGATTTTAAATT
Found at i:63589 original size:2 final size:2
Alignment explanation
Indices: 63582--63606 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63572 GACTCTGAAC
63582 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
63607 CAATGGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:64609 original size:223 final size:222
Alignment explanation
Indices: 64221--64665 Score: 836
Period size: 223 Copynumber: 2.0 Consensus size: 222
64211 TCATCCAATA
64221 AATTATTATGTAATAATGTTTTGATCATATTTACTCTTTTTTAACACAATACTAAAAGTACTCAT
1 AATTATTATGTAATAATGTTTTGATCATATTTACTCTTTTTTAACACAATACTAAAAGTACTCAT
*
64286 GGCCCCTCTCGTTTCATAAATAAAAGGATAATACATTTCAGTATACTCGAATTCATGTTTTCTTA
66 GGCCCCTCTCGTTTCATAAATAAAAGAATAATACATTTCAGTATACTCGAATTCATGTTTTCTTA
64351 TTTTGACAATTATATTTATGTCAATTGAATTGAGATCCAATCAATCAAAATTAAATTATTAAAAT
131 TTTTGACAATTATATTTATGTCAATTGAATTGAGATCCAATCAATCAAAATTAAATTATTAAAAT
*
64416 ATTAAAAAAAAATTAATTGTAACCTTAT
196 ATT-AAAAAAAATTAATTCTAACCTTAT
64444 AATTATTATGTAATAATGTTTTGATCATATTTACTCTTTTTTAACACAATACTAAAAGTACTCAT
1 AATTATTATGTAATAATGTTTTGATCATATTTACTCTTTTTTAACACAATACTAAAAGTACTCAT
*
64509 GGCCCCTCTCGTTTCATAAATAAAAGAATAATACATTTCAGTATATTCGAATTCATGTTTTCTTA
66 GGCCCCTCTCGTTTCATAAATAAAAGAATAATACATTTCAGTATACTCGAATTCATGTTTTCTTA
*
64574 TTTTGACAGTTATATTTATGTCAATTGAATTGAGATCCAATCAATCAAAATTAAATTATTAAAAT
131 TTTTGACAATTATATTTATGTCAATTGAATTGAGATCCAATCAATCAAAATTAAATTATTAAAAT
*
64639 ATTAAAAAAATTTAATTCTAACCTTAT
196 ATTAAAAAAAATTAATTCTAACCTTAT
64666 TTCGGATTCC
Statistics
Matches: 217, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
222 22 0.10
223 195 0.90
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (222 bp):
AATTATTATGTAATAATGTTTTGATCATATTTACTCTTTTTTAACACAATACTAAAAGTACTCAT
GGCCCCTCTCGTTTCATAAATAAAAGAATAATACATTTCAGTATACTCGAATTCATGTTTTCTTA
TTTTGACAATTATATTTATGTCAATTGAATTGAGATCCAATCAATCAAAATTAAATTATTAAAAT
ATTAAAAAAAATTAATTCTAACCTTAT
Done.