Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008887.1 Kokia drynarioides strain JFW-HI SEQ_123574, 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: 58723
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:5018 original size:163 final size:165
Alignment explanation
Indices: 4748--5078 Score: 621
Period size: 163 Copynumber: 2.0 Consensus size: 165
4738 ATTTTTATGG
4748 CAATTTTTTTGTCATTATATGTAAATAAATTTAATTATTTTGAGAATCCATGGATGAGATTCTGA
1 CAATTTTTTTGTCATTATATGTAAATAAATTTAATTATTTTGAGAATCCATGGATGAGATTCTGA
4813 GTACAAGCTGGAAATGGCGATTTCCTTAGTAAATCTCGAG-T-TATATATATATATATATATTTA
66 GTACAAGCTGGAAATGGCGATTTCCTTAGTAAATCTCGAGTTATATATATATATATATATATTTA
4876 TATTGAGGAGAAGTTTGGCTTCTTTCTATTTACGT
131 TATTGAGGAGAAGTTTGGCTTCTTTCTATTTACGT
4911 CAATTTTTTTGTCATTATATGTAAATAAATTTAATTATTTTGAGAATCCATGGATGAGATTCTGA
1 CAATTTTTTTGTCATTATATGTAAATAAATTTAATTATTTTGAGAATCCATGGATGAGATTCTGA
*
4976 GTACAAGCTGGAAATGGCGATTTCCTTAGTAATTCTCGAGTTATATATATATATATATATATATT
66 GTACAAGCTGGAAATGGCGATTTCCTTAGTAAATCTCGAG-T-TATATATATATATATATATATT
5041 TATATTGAGGAGAAGTTTGGCTTCTTTCTATTTACGT
129 TATATTGAGGAGAAGTTTGGCTTCTTTCTATTTACGT
5078 C
1 C
5079 TCTCTGTTCA
Statistics
Matches: 163, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
163 104 0.64
166 1 0.01
167 58 0.36
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (165 bp):
CAATTTTTTTGTCATTATATGTAAATAAATTTAATTATTTTGAGAATCCATGGATGAGATTCTGA
GTACAAGCTGGAAATGGCGATTTCCTTAGTAAATCTCGAGTTATATATATATATATATATATTTA
TATTGAGGAGAAGTTTGGCTTCTTTCTATTTACGT
Found at i:14551 original size:15 final size:15
Alignment explanation
Indices: 14531--14560 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
14521 CTTGCTTCTA
14531 AGAGAGAGATTTACT
1 AGAGAGAGATTTACT
14546 AGAGAGAGATTTACT
1 AGAGAGAGATTTACT
14561 GTCTAACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (15 bp):
AGAGAGAGATTTACT
Found at i:22798 original size:34 final size:34
Alignment explanation
Indices: 22755--22822 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
22745 AATTACATTA
22755 CATGTTACATAAACTCGTCCGAAAATAGTGTAAG
1 CATGTTACATAAACTCGTCCGAAAATAGTGTAAG
22789 CATGTTACATAAACTCGTCCGAAAATAGTGTAAG
1 CATGTTACATAAACTCGTCCGAAAATAGTGTAAG
22823 TACACAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (34 bp):
CATGTTACATAAACTCGTCCGAAAATAGTGTAAG
Found at i:23402 original size:40 final size:40
Alignment explanation
Indices: 23355--23435 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
23345 TTTGTGGATA
*
23355 GCTACCTTTCTTGACATCCAAGTAATTGTTTATATTAATG
1 GCTACCTTTCTTGACATCCAAGTAATTGTTTACATTAATG
23395 GCTACCTTTCTTGACATCCAAGTAATTGTTTACATTAATG
1 GCTACCTTTCTTGACATCCAAGTAATTGTTTACATTAATG
23435 G
1 G
23436 AATTATTTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (40 bp):
GCTACCTTTCTTGACATCCAAGTAATTGTTTACATTAATG
Found at i:29175 original size:25 final size:25
Alignment explanation
Indices: 29147--29198 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
29137 TATTACAAAA
*
29147 ATAATTTACATA-TTATAAAAATATT
1 ATAATATACATATTTATAAAAA-ATT
*
29172 ATAATATACTTATTTATAAAAAATT
1 ATAATATACATATTTATAAAAAATT
29197 AT
1 AT
29199 GGCGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
ATAATATACATATTTATAAAAAATT
Found at i:30115 original size:18 final size:18
Alignment explanation
Indices: 30087--30132 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
30077 CTTATTTAGA
* *
30087 AATTA-TTTTATTATATT
1 AATTATTTTTATAATAAT
*
30104 AATTTTTTTTATAATAAT
1 AATTATTTTTATAATAAT
30122 AATTATTTTTA
1 AATTATTTTTA
30133 AAAAATATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTATTTTTATAATAAT
Found at i:36717 original size:6 final size:6
Alignment explanation
Indices: 36706--36752 Score: 67
Period size: 6 Copynumber: 7.7 Consensus size: 6
36696 TATCTTCTTG
* *
36706 TTTTTC TTTTTC TTTTTC TTCTTG TTTTTC TTTTTC TTTTTCC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT-C TTTT
36753 GAGAACTCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
6 31 0.86
7 5 0.14
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:36729 original size:24 final size:24
Alignment explanation
Indices: 36698--36747 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
36688 AAATCCTATA
36698 TCTTCTTGTTTTTCTTTTTCTTTT
1 TCTTCTTGTTTTTCTTTTTCTTTT
36722 TCTTCTTGTTTTTCTTTTTCTTTT
1 TCTTCTTGTTTTTCTTTTTCTTTT
36746 TC
1 TC
36748 CTTTTGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (24 bp):
TCTTCTTGTTTTTCTTTTTCTTTT
Found at i:41676 original size:14 final size:14
Alignment explanation
Indices: 41657--41685 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41647 ACCCCTATTT
41657 CTATTCGATCAGCC
1 CTATTCGATCAGCC
41671 CTATTCGATCAGCC
1 CTATTCGATCAGCC
41685 C
1 C
41686 AATATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.38, G:0.14, T:0.28
Consensus pattern (14 bp):
CTATTCGATCAGCC
Found at i:53868 original size:15 final size:15
Alignment explanation
Indices: 53848--53891 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
53838 GGAGATGAGA
53848 AAGAAGAAGAGGAAT
1 AAGAAGAAGAGGAAT
53863 AAGAAGAAGAGGAAT
1 AAGAAGAAGAGGAAT
*
53878 AAGATGAAGAGGAA
1 AAGAAGAAGAGGAA
53892 AGCGAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (15 bp):
AAGAAGAAGAGGAAT
Found at i:55343 original size:6 final size:7
Alignment explanation
Indices: 55324--55348 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55314 TTATTTATAA
55324 TATTTTT
1 TATTTTT
55331 TATTTTT
1 TATTTTT
55338 TATTTTT
1 TATTTTT
55345 TATT
1 TATT
55349 AATAGAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TATTTTT
Found at i:56561 original size:21 final size:21
Alignment explanation
Indices: 56498--56562 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
56488 TTTTTAAACT
* *
56498 TTTTTTTATTAATTTTAATAA
1 TTTTTATATTAATTTTAATTA
*
56519 TTCGTTTATAAATT-ATTATAATTA
1 TT--TTTAT--ATTAATTTTAATTA
56543 TTTTTATATTAATTTTAATT
1 TTTTTATATTAATTTTAATT
56563 TGAATAAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
20 3 0.09
21 10 0.29
22 5 0.14
23 4 0.11
24 10 0.29
25 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTTATATTAATTTTAATTA
Found at i:58477 original size:12 final size:11
Alignment explanation
Indices: 58449--58476 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
58439 GGAGACCAAT
58449 GAAAAATGAAG
1 GAAAAATGAAG
58460 GAAAAATGAAG
1 GAAAAATGAAG
58471 GAAAAA
1 GAAAAA
58477 AGAGAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.25, T:0.07
Consensus pattern (11 bp):
GAAAAATGAAG
Done.