Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008410.1 Kokia drynarioides strain JFW-HI SEQ_123079, 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: 37002
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:7409 original size:27 final size:27
Alignment explanation
Indices: 7379--7510 Score: 99
Period size: 27 Copynumber: 4.9 Consensus size: 27
7369 AAACACGAAA
* *
7379 TCTGAAAGAACAACCTTTATGGCAAAC
1 TCTGAAAGAACTACCTTTGTGGCAAAC
*
7406 TCTGAAAGGAA-TGCCTTTGTGGCGAAA-
1 TCTGAAA-GAACTACCTTTGTGGC-AAAC
* * *
7433 TATGGAAGAACTACCTTCGTGGCAAAC
1 TCTGAAAGAACTACCTTTGTGGCAAAC
* *
7460 TCTGAAAAGAA-TGCCTATGTGGCAAAC
1 TCTG-AAAGAACTACCTTTGTGGCAAAC
* * * * *
7487 TTTAAAAGAAATGCCTTTGCGGCA
1 TCTGAAAGAACTACCTTTGTGGCA
7511 TGTCATAATA
Statistics
Matches: 83, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
26 12 0.14
27 60 0.72
28 11 0.13
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (27 bp):
TCTGAAAGAACTACCTTTGTGGCAAAC
Found at i:7442 original size:54 final size:54
Alignment explanation
Indices: 7374--7482 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 54
7364 ATCATAAACA
* * * *
7374 CGAAATCTGAAAGAACAACCTTTATGGCAAACTCTGAAAGGAATGCCTTTGTGG
1 CGAAATATGAAAGAACAACCTTCATGGCAAACTCTGAAAAGAATGCCTATGTGG
* * *
7428 CGAAATATGGAAGAACTACCTTCGTGGCAAACTCTGAAAAGAATGCCTATGTGG
1 CGAAATATGAAAGAACAACCTTCATGGCAAACTCTGAAAAGAATGCCTATGTGG
7482 C
1 C
7483 AAACTTTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (54 bp):
CGAAATATGAAAGAACAACCTTCATGGCAAACTCTGAAAAGAATGCCTATGTGG
Found at i:7496 original size:54 final size:54
Alignment explanation
Indices: 7374--7496 Score: 140
Period size: 54 Copynumber: 2.3 Consensus size: 54
7364 ATCATAAACA
* * * * *
7374 CGAAATCTGAAAGAACAACCTTTATGGCAAACTCTGAAAGGAATGCCTTTGTGG
1 CGAAATATAAAAGAACAACCTTCATGGCAAACTCTGAAAAGAATGCCTATGTGG
** * *
7428 CGAAATATGGAAGAACTACCTTCGTGGCAAACTCTGAAAAGAATGCCTATGTGG
1 CGAAATATAAAAGAACAACCTTCATGGCAAACTCTGAAAAGAATGCCTATGTGG
*
7482 C-AAACTTTAAAAGAA
1 CGAAA-TATAAAAGAA
7497 ATGCCTTTGC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 3 0.05
54 55 0.95
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (54 bp):
CGAAATATAAAAGAACAACCTTCATGGCAAACTCTGAAAAGAATGCCTATGTGG
Found at i:8059 original size:23 final size:24
Alignment explanation
Indices: 8033--8077 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
8023 TTTACTTTCA
*
8033 TAATAA-CATTTATAAATTAATAG
1 TAATAACCATTTATAAAATAATAG
8056 TAATAACCATTTATAAAATAAT
1 TAATAACCATTTATAAAATAAT
8078 CAGAATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (24 bp):
TAATAACCATTTATAAAATAATAG
Found at i:8649 original size:29 final size:29
Alignment explanation
Indices: 8607--8664 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
8597 CAAACATGAA
8607 AATTTCAATTTAGGGGAATGGTACAAGCC
1 AATTTCAATTTAGGGGAATGGTACAAGCC
8636 AATTTCAATTTAGGGGAATGGTACAAGCC
1 AATTTCAATTTAGGGGAATGGTACAAGCC
8665 TTGGTTTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (29 bp):
AATTTCAATTTAGGGGAATGGTACAAGCC
Found at i:8950 original size:21 final size:22
Alignment explanation
Indices: 8925--8973 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
8915 AAATTGTAAC
*
8925 CTTAATATTTA-TCAAATTTAT
1 CTTAATATTAATTCAAATTTAT
* *
8946 CTTAATCTTAATTCATATTTAT
1 CTTAATATTAATTCAAATTTAT
8968 -TTAATA
1 CTTAATA
8974 ATAAAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (22 bp):
CTTAATATTAATTCAAATTTAT
Found at i:10353 original size:2 final size:2
Alignment explanation
Indices: 10336--10376 Score: 64
Period size: 2 Copynumber: 19.5 Consensus size: 2
10326 ATAATGTGAA
10336 AT AT GAT AT AT GAT 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 AT AT AT AT AT A
10377 AAATCAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 33 0.89
3 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:12604 original size:22 final size:22
Alignment explanation
Indices: 12579--12649 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
12569 TGCCATAGCG
12579 TCTTTCAACTATGGACTTCTCC
1 TCTTTCAACTATGGACTTCTCC
* * *
12601 TCTTT-TAC-AT-GATTTCATAGCG
1 TCTTTCAACTATGGACTTC-T--CC
*
12623 TCTTTCAAATATGGACTTCTCC
1 TCTTTCAACTATGGACTTCTCC
12645 TCTTT
1 TCTTT
12650 TACATGATGC
Statistics
Matches: 36, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
19 5 0.14
20 3 0.08
21 2 0.06
22 17 0.47
23 1 0.03
24 3 0.08
25 5 0.14
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (22 bp):
TCTTTCAACTATGGACTTCTCC
Found at i:12620 original size:44 final size:44
Alignment explanation
Indices: 12564--12680 Score: 180
Period size: 44 Copynumber: 2.7 Consensus size: 44
12554 TCATTTCTCT
12564 CATGATGCCATAGCGTCTTTCAACTATGGACTTCTCCTCTTTTA
1 CATGATGCCATAGCGTCTTTCAACTATGGACTTCTCCTCTTTTA
** *
12608 CATGATTTCATAGCGTCTTTCAAATATGGACTTCTCCTCTTTTA
1 CATGATGCCATAGCGTCTTTCAACTATGGACTTCTCCTCTTTTA
* * *
12652 CATGATGCCATAGCATCTTTTAGCTATGG
1 CATGATGCCATAGCGTCTTTCAACTATGG
12681 TTTTACTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 64 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (44 bp):
CATGATGCCATAGCGTCTTTCAACTATGGACTTCTCCTCTTTTA
Found at i:13587 original size:21 final size:21
Alignment explanation
Indices: 13561--13601 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
13551 TACTTGGTTG
13561 GTGAGAAAACTAAAGAAAATT
1 GTGAGAAAACTAAAGAAAATT
*
13582 GTGAGAAAACTGAAGAAAAT
1 GTGAGAAAACTAAAGAAAAT
13602 GGATTTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.22, T:0.17
Consensus pattern (21 bp):
GTGAGAAAACTAAAGAAAATT
Found at i:13794 original size:73 final size:73
Alignment explanation
Indices: 13707--13999 Score: 442
Period size: 73 Copynumber: 4.0 Consensus size: 73
13697 GGAGGCATTG
* * *
13707 AGAAAATCTAGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAAAGAGAAACTCTAGGAAAGTG
1 AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTAGGAAAGTG
13772 TTGAGAAA
66 TTGAGAAA
* *
13780 AGAAAATCTGGAAAGAGAGAAAAAATTAAAGATGTATTTGGAAAGAGAGAAAATCTAGGAAAGTG
1 AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTAGGAAAGTG
* *
13845 TTAACAAA
66 TTGAGAAA
* * * * *
13853 AGAAAATCTGAAAAGAAAGGAAAAACTAAAGATGTATTTGGAAAGATAGAAAATTTGGGAAAGTG
1 AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTAGGAAAGTG
13918 TTGAGAAA
66 TTGAGAAA
* * * *
13926 AGAAAATCTGGAAAGAGAGAAAAAACTAAAGATGTGTTTGGAAAGAGAGAAAATTTGGGAAAGTG
1 AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTAGGAAAGTG
13991 TTGAGAAA
66 TTGAGAAA
13999 A
1 A
14000 AAATGTTTTA
Statistics
Matches: 199, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 199 1.00
ACGTcount: A:0.53, C:0.04, G:0.25, T:0.19
Consensus pattern (73 bp):
AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTAGGAAAGTG
TTGAGAAA
Found at i:14039 original size:10 final size:10
Alignment explanation
Indices: 14024--14049 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
14014 GGAAGAGAGA
14024 AAGAAAGAAG
1 AAGAAAGAAG
14034 AAGAAAGAAG
1 AAGAAAGAAG
14044 AAGAAA
1 AAGAAA
14050 AAAATGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAG
Found at i:20197 original size:56 final size:57
Alignment explanation
Indices: 20112--20228 Score: 150
Period size: 57 Copynumber: 2.1 Consensus size: 57
20102 AGAATTGGTG
* *
20112 AAATGGAGAAATAGGAAACATTTTGAAATGATTAAGGTTTTCTC-AAAATGAAAATGA
1 AAATGGAGAAATA-GAAACATTTTGAAATGAATAAGGTTTTCTCTAAAATGAAAATAA
**
20169 AAATGGAGAAAT-GAAATCA-TTTGAAAATGAATGTGGTTTTCTCTAAAATGAAAATAA
1 AAATGGAGAAATAGAAA-CATTTTG-AAATGAATAAGGTTTTCTCTAAAATGAAAATAA
20226 AAA
1 AAA
20229 ATGACCTGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
55 8 0.15
56 18 0.34
57 27 0.51
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.28
Consensus pattern (57 bp):
AAATGGAGAAATAGAAACATTTTGAAATGAATAAGGTTTTCTCTAAAATGAAAATAA
Found at i:26793 original size:70 final size:70
Alignment explanation
Indices: 26718--26852 Score: 189
Period size: 70 Copynumber: 1.9 Consensus size: 70
26708 TTTGTTACGA
* *
26718 CGTAGCTCCCCCTATGTCACAACAAACCTATCAGTTTTGAAATTTTAACAATTTGACCCCTTTGT
1 CGTAGCTCCCCCTATGTCACAACAAACCTATCAATTTTGAAATTTCAACAATTTGACCCCTTTGT
26783 TGCCT
66 TGCCT
* * * * * * *
26788 CGTAGCTCCCCCTGTGTCGCGACAAATCTATTAATTTTGAAATTTCAATAGTTTGACCCCTTTGT
1 CGTAGCTCCCCCTATGTCACAACAAACCTATCAATTTTGAAATTTCAACAATTTGACCCCTTTGT
26853 CGCAACATAC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
70 56 1.00
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (70 bp):
CGTAGCTCCCCCTATGTCACAACAAACCTATCAATTTTGAAATTTCAACAATTTGACCCCTTTGT
TGCCT
Done.