Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007268.1 Kokia drynarioides strain JFW-HI SEQ_121884, 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: 71299
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 74 characters in sequence are not A, C, G, or T
Found at i:1042 original size:25 final size:23
Alignment explanation
Indices: 1010--1055 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
1000 GTTAGATCCA
1010 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATT-TAAAAA-ATAATTTG
*
1035 AATTAAATTTAAATAATAATT
1 AATTAAATTTAAAAAATAATT
1056 CCCTAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (23 bp):
AATTAAATTTAAAAAATAATTTG
Found at i:1522 original size:22 final size:21
Alignment explanation
Indices: 1488--1530 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
1478 ATTAATAATT
1488 AATAATATAAATTATAAATAA
1 AATAATATAAATTATAAATAA
1509 AATAATAATAAATTATAAATAA
1 AATAAT-ATAAATTATAAATAA
1531 TAGCTATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAATATAAATTATAAATAA
Found at i:1529 original size:11 final size:11
Alignment explanation
Indices: 1484--1530 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
1474 TTATATTAAT
1484 AATTAATAATATA
1 AATT-ATAA-ATA
1497 AATTATAAATA
1 AATTATAAATA
*
1508 AAATA-ATAATA
1 AATTATA-AATA
1519 AATTATAAATA
1 AATTATAAATA
1530 A
1 A
1531 TAGCTATTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 1 0.03
11 20 0.67
12 5 0.17
13 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATTATAAATA
Found at i:19133 original size:18 final size:18
Alignment explanation
Indices: 19112--19149 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
19102 TTTATAAAAG
19112 ATAATATCTCGTAATAAT
1 ATAATATCTCGTAATAAT
*
19130 ATAATATCTCGTATTAAT
1 ATAATATCTCGTAATAAT
19148 AT
1 AT
19150 CCTAACCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (18 bp):
ATAATATCTCGTAATAAT
Found at i:21094 original size:89 final size:89
Alignment explanation
Indices: 20943--21121 Score: 349
Period size: 89 Copynumber: 2.0 Consensus size: 89
20933 CACTATGTCA
20943 AGAGTTTATAAAATTACAATACTCCATGGAAGCAAGCCCTAAGAACCAGAAACATGCAAGGATAT
1 AGAGTTTATAAAATTACAATACTCCATGGAAGCAAGCCCTAAGAACCAGAAACATGCAAGGATAT
21008 GGAAAAAGATTAATGAAGAAAATG
66 GGAAAAAGATTAATGAAGAAAATG
*
21032 AGAGTTTATAAAATTACAATACTCCATGGAATCAAGCCCTAAGAACCAGAAACATGCAAGGATAT
1 AGAGTTTATAAAATTACAATACTCCATGGAAGCAAGCCCTAAGAACCAGAAACATGCAAGGATAT
21097 GGAAAAAGATTAATGAAGAAAATG
66 GGAAAAAGATTAATGAAGAAAATG
21121 A
1 A
21122 ATTATACAAG
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (89 bp):
AGAGTTTATAAAATTACAATACTCCATGGAAGCAAGCCCTAAGAACCAGAAACATGCAAGGATAT
GGAAAAAGATTAATGAAGAAAATG
Found at i:26746 original size:6 final size:6
Alignment explanation
Indices: 26735--26759 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
26725 TATATTCCTT
26735 TGTCTC TGTCTC TGTCTC TGTCTC T
1 TGTCTC TGTCTC TGTCTC TGTCTC T
26760 TTATCTGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.16, T:0.52
Consensus pattern (6 bp):
TGTCTC
Found at i:35599 original size:8 final size:8
Alignment explanation
Indices: 35588--35612 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
35578 TTTATATATT
35588 ATTTTAAA
1 ATTTTAAA
35596 ATTTTAAA
1 ATTTTAAA
35604 ATTTTAAA
1 ATTTTAAA
35612 A
1 A
35613 AATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTTAAA
Found at i:42875 original size:3 final size:3
Alignment explanation
Indices: 42867--42914 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
42857 CTACTAGGGG
*
42867 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42915 TATCCAATTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:50538 original size:20 final size:20
Alignment explanation
Indices: 50513--50552 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
50503 ATATATACTA
50513 AATCATGTGATACTAACATT
1 AATCATGTGATACTAACATT
*
50533 AATCATGTGATACTAGCATT
1 AATCATGTGATACTAACATT
50553 GTGGGTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (20 bp):
AATCATGTGATACTAACATT
Found at i:50780 original size:2 final size:2
Alignment explanation
Indices: 50773--50801 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
50763 CATTGAATTA
50773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50802 CACCTGCCTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52141 original size:6 final size:6
Alignment explanation
Indices: 52130--52156 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52120 TAGTGTTTTA
52130 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
52157 CCTCGCCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:52252 original size:26 final size:22
Alignment explanation
Indices: 52209--52264 Score: 60
Period size: 26 Copynumber: 2.4 Consensus size: 22
52199 AAATAAATAA
52209 TAATTTATATTTTAAAA-TATTT
1 TAATTTATATTTTAAAATTA-TT
52231 TAATTTATAATTATTCAGAAATTATT
1 TAATTTAT-ATT-TT-A-AAATTATT
52257 TAATTTAT
1 TAATTTAT
52265 TAAATCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.28
23 3 0.10
24 2 0.07
25 1 0.03
26 13 0.45
27 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TAATTTATATTTTAAAATTATT
Found at i:52282 original size:26 final size:26
Alignment explanation
Indices: 52222--52283 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
52212 TTTATATTTT
*
52222 AAAATATTTTAATTTATAATTATTCAG
1 AAAATA-TTTAATTTATAAATATTCAG
* * *
52249 AAATTATTTAATTTATTAAATCTTTA-
1 AAAATATTTAATTTA-TAAATATTCAG
52275 AAAATATTT
1 AAAATATTT
52284 TTATTTTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 17 0.59
27 12 0.41
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (26 bp):
AAAATATTTAATTTATAAATATTCAG
Found at i:54239 original size:15 final size:16
Alignment explanation
Indices: 54209--54248 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
54199 ATATATCAAA
54209 TAAA-TTTT-ATACCT
1 TAAATTTTTAATACCT
54223 TAAATTTTTAATA-CT
1 TAAATTTTTAATACCT
*
54238 TAATTTTTTAA
1 TAAATTTTTAA
54249 CATTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 16 0.70
16 3 0.13
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAATTTTTAATACCT
Found at i:54259 original size:15 final size:15
Alignment explanation
Indices: 54221--54274 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
54211 AATTTTATAC
* *
54221 CTTAAATTTTTAATA
1 CTTAATTTTTTAACA
54236 CTTAATTTTTTAACA
1 CTTAATTTTTTAACA
* * **
54251 TTTATTTTTTTCGCA
1 CTTAATTTTTTAACA
54266 CTTAATTTT
1 CTTAATTTT
54275 CAATTTATCA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.28, C:0.11, G:0.02, T:0.59
Consensus pattern (15 bp):
CTTAATTTTTTAACA
Found at i:56287 original size:3 final size:3
Alignment explanation
Indices: 56279--56346 Score: 82
Period size: 3 Copynumber: 22.7 Consensus size: 3
56269 CAAAAGATGA
* * * * * *
56279 CAC CAC CAC CAC CAC CAC CAC CAC CAC AAC AAC AAC AAC CTC CTC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
56327 CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CA
56347 ATACTTGCCG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.37, C:0.60, G:0.00, T:0.03
Consensus pattern (3 bp):
CAC
Found at i:69346 original size:114 final size:112
Alignment explanation
Indices: 69121--69347 Score: 287
Period size: 114 Copynumber: 2.0 Consensus size: 112
69111 GTAGAATCAA
* * *
69121 CAAAACTATTGTTCTCACGTTCTCGATTGAGTTAATTCAAACCCTAAACTTATCGATAGAGTCTC
1 CAAAACTAATGTTCACACGTTCTCGATTGAGCTAATTCAAACCCTAAACTTATCGATAGAGTCTC
* * * *
69186 GATTCGATTGGTATCGACATTATTACCAATGCAAAAAGAGGCGAGTT
66 AATTCGATTAGTATCGACATTATTACCAATACAAAAAGAGACGAGTT
*
69233 CAAAACATAATGTTCACATGTTCTCGATTGAGCTAATTCAAAACCCTAAACTTATCGACT-GAGT
1 CAAAAC-TAATGTTCACACGTTCTCGATTGAGCTAATTC-AAACCCTAAACTTATCGA-TAGAGT
* * * * *
69297 TTCAATTTGATTAGTATCGACATTATTATCAGTACAAGAAA-AGATGAGTT
63 CTCAATTCGATTAGTATCGACATTATTACCAATACAA-AAAGAGACGAGTT
69347 C
1 C
69348 GAACACGCTC
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
112 6 0.06
113 28 0.29
114 60 0.61
115 4 0.04
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (112 bp):
CAAAACTAATGTTCACACGTTCTCGATTGAGCTAATTCAAACCCTAAACTTATCGATAGAGTCTC
AATTCGATTAGTATCGACATTATTACCAATACAAAAAGAGACGAGTT
Done.