Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001069.1 Kokia drynarioides strain JFW-HI SEQ_112321, 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: 13564
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5445 original size:50 final size:50
Alignment explanation
Indices: 5351--5825 Score: 270
Period size: 50 Copynumber: 9.6 Consensus size: 50
5341 AGGTTTGACA
5351 GGAAAGGATTGAGGCCACAACGGCGAACCCGATACCTTAAAAGATGTGAAG
1 GGAAAGG-TTGAGGCCACAACGGCGAACCCGATACCTTAAAAGATGTGAAG
** * * * *
5402 GGAAAGGTTGAGGCTGCAACGGCGGACTCGGTA-CTTAAGAAGATGTGATG
1 GGAAAGGTTGAGGCCACAACGGCGAACCCGATACCTTAA-AAGATGTGAAG
* * * * * *
5452 GGAAAGGTTGAGGCCATAACAGTGAACCCGATACCAT-GAAGATATGAAG
1 GGAAAGGTTGAGGCCACAACGGCGAACCCGATACCTTAAAAGATGTGAAG
* * * * * * * ** *
5501 GGAAAGGTTGAGGACGCAACAGCAAACCTGGTACCTAAAAAGATACGATG
1 GGAAAGGTTGAGGCCACAACGGCGAACCCGATACCTTAAAAGATGTGAAG
* * * ** * * * * * ***
5551 GGAACGGTTGAGGTCGCAACAAC-AAGCTCGGTACCAT-GAATATACAAAG
1 GGAAAGGTTGAGGCCACAACGGCGAA-CCCGATACCTTAAAAGATGTGAAG
* * *
5600 GGAAAGGTTGAGGCCGCAACGGCGAACCCGTTACC-TAAGAAGATGCGATA-
1 GGAAAGGTTGAGGCCACAACGGCGAACCCGATACCTTAA-AAGATGTGA-AG
* * * * * * *
5650 GGAAAGGTTAAGGCCGCAATGGCAAACCC-AGTACC--ACGAAGATATAAAG
1 GGAAAGGTTGAGGCCACAACGGCGAACCCGA-TACCTTA-AAAGATGTGAAG
* * * * * *
5699 GGAAACGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGCGATG
1 GGAAAGGTTGAGGCCACAACGGCGAACCCGATACCTTAAAAGATGTGAAG
* * * * * *
5749 GG-AAGGATTGAGGTCACAACGGCGAATCCGATACCAT-GAAGATATAAAG
1 GGAAAGG-TTGAGGCCACAACGGCGAACCCGATACCTTAAAAGATGTGAAG
* *
5798 GGAAAGGTTGAGGCCGCAACGACGAACC
1 GGAAAGGTTGAGGCCACAACGGCGAACC
5826 TAGCACCTCA
Statistics
Matches: 326, Mismatches: 82, Indels: 34
0.74 0.19 0.08
Matches are distributed among these distances:
48 2 0.01
49 144 0.44
50 169 0.52
51 11 0.03
ACGTcount: A:0.35, C:0.19, G:0.31, T:0.15
Consensus pattern (50 bp):
GGAAAGGTTGAGGCCACAACGGCGAACCCGATACCTTAAAAGATGTGAAG
Found at i:5534 original size:99 final size:99
Alignment explanation
Indices: 5351--5825 Score: 524
Period size: 99 Copynumber: 4.8 Consensus size: 99
5341 AGGTTTGACA
* * * *
5351 GGAAAGGATTGAGGCCACAACGGCGAACCCGATACCTTAAAAGATGTGAAGGGAAAGGTTGAGGC
1 GGAAAGG-TTGAGGCCACAACGGCGAACCCGATACCAT-GAAGATATAAAGGGAAAGGTTGAGGC
* * * * *
5416 TGCAACGGCGGACTCGGTACTTAAGAAGATGTGATG
64 CGCAACGGCGAACCCGGTACCTAAGAAGATGCGATG
* * * * *
5452 GGAAAGGTTGAGGCCATAACAGTGAACCCGATACCATGAAGATATGAAGGGAAAGGTTGAGGACG
1 GGAAAGGTTGAGGCCACAACGGCGAACCCGATACCATGAAGATATAAAGGGAAAGGTTGAGGCCG
* * * * *
5517 CAACAGCAAACCTGGTACCTAAAAAGATACGATG
66 CAACGGCGAACCCGGTACCTAAGAAGATGCGATG
* * * ** * * * *
5551 GGAACGGTTGAGGTCGCAACAAC-AAGCTCGGTACCATGAATATACAAAGGGAAAGGTTGAGGCC
1 GGAAAGGTTGAGGCCACAACGGCGAA-CCCGATACCATGAAGATATAAAGGGAAAGGTTGAGGCC
* *
5615 GCAACGGCGAACCCGTTACCTAAGAAGATGCGATA
65 GCAACGGCGAACCCGGTACCTAAGAAGATGCGATG
* * * * * *
5650 GGAAAGGTTAAGGCCGCAATGGCAAACCC-AGTACCACGAAGATATAAAGGGAAACGTTGAGGCC
1 GGAAAGGTTGAGGCCACAACGGCGAACCCGA-TACCATGAAGATATAAAGGGAAAGGTTGAGGCC
*
5714 GCAACGGCGAACCCGGTACCTTAGAAGATGCGATG
65 GCAACGGCGAACCCGGTACCTAAGAAGATGCGATG
* *
5749 GG-AAGGATTGAGGTCACAACGGCGAATCCGATACCATGAAGATATAAAGGGAAAGGTTGAGGCC
1 GGAAAGG-TTGAGGCCACAACGGCGAACCCGATACCATGAAGATATAAAGGGAAAGGTTGAGGCC
*
5813 GCAACGACGAACC
65 GCAACGGCGAACC
5826 TAGCACCTCA
Statistics
Matches: 309, Mismatches: 60, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
98 6 0.02
99 267 0.86
100 29 0.09
101 7 0.02
ACGTcount: A:0.35, C:0.19, G:0.31, T:0.15
Consensus pattern (99 bp):
GGAAAGGTTGAGGCCACAACGGCGAACCCGATACCATGAAGATATAAAGGGAAAGGTTGAGGCCG
CAACGGCGAACCCGGTACCTAAGAAGATGCGATG
Found at i:6913 original size:17 final size:17
Alignment explanation
Indices: 6868--6914 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
6858 TTCGAAACTT
*
6868 TTAATAAATAACATTAA
1 TTAATAAATAATATTAA
* *
6885 ATAA-ATATTAATATTAA
1 TTAATA-AATAATATTAA
6902 TTAATAAATAATA
1 TTAATAAATAATA
6915 ATAGAAGAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
16 1 0.04
17 21 0.91
18 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAATAAATAATATTAA
Found at i:8066 original size:60 final size:58
Alignment explanation
Indices: 7986--8282 Score: 198
Period size: 57 Copynumber: 5.2 Consensus size: 58
7976 CCTAAAAGGT
* *
7986 CCCTAAACTTACTAGAAATCATATTTTGACCCTTAAACTTATCCAAAATTACATTTTAAC
1 CCCTAAACTTACTAGAAATCACATTTTAACCC-TAAACTT-TCCAAAATTACATTTTAAC
* * *
8046 CTCTAAACTTCTCTA-AAATCACATTTTAACCCTAAACTTTTCAAAATTACATTTTAAC
1 CCCTAAACTT-ACTAGAAATCACATTTTAACCCTAAACTTTCCAAAATTACATTTTAAC
* * ** * * * * ** * *
8104 CCCTAAAATT-TTCCAAATTACCTTTTAACCCCAAATTTTTTAAAATCACATTTTATC
1 CCCTAAACTTACTAGAAATCACATTTTAACCCTAAACTTTCCAAAATTACATTTTAAC
* * * * * **
8161 TCCC--AA-TT-CTCAAAAATTATATTTTTACCCCCAAAC-TTCCAAAATTACATTTTTTC
1 -CCCTAAACTTACT-AGAAATCACA-TTTTAACCCTAAACTTTCCAAAATTACATTTTAAC
** * * * *
8217 CCCCGAACTT-CCAAAAATAACACTTTTACCCCTAAACTTTCCAAAATTACATTTTAAC
1 CCCTAAACTTACTAGAAATCACA-TTTTAACCCTAAACTTTCCAAAATTACATTTTAAC
8275 CCC-AAACT
1 CCCTAAACT
8283 CTCCGAAACT
Statistics
Matches: 193, Mismatches: 35, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
55 6 0.03
56 25 0.13
57 75 0.39
58 53 0.27
59 7 0.04
60 24 0.12
61 3 0.02
ACGTcount: A:0.37, C:0.27, G:0.01, T:0.36
Consensus pattern (58 bp):
CCCTAAACTTACTAGAAATCACATTTTAACCCTAAACTTTCCAAAATTACATTTTAAC
Found at i:8107 original size:29 final size:29
Alignment explanation
Indices: 8008--8282 Score: 208
Period size: 28 Copynumber: 9.6 Consensus size: 29
7998 TAGAAATCAT
* * *
8008 ATTTTGACCCTTAAACTTATCCAAAATTAC
1 ATTTTAACCCCTAAACTT-TTCAAAATTAC
* * *
8038 ATTTTAACCTCTAAACTTCTCTAAAATCAC
1 ATTTTAACCCCTAAACTTTTC-AAAATTAC
8068 ATTTTAA-CCCTAAACTTTTCAAAATTAC
1 ATTTTAACCCCTAAACTTTTCAAAATTAC
* *
8096 ATTTTAACCCCTAAAATTTTCCAAATTAC
1 ATTTTAACCCCTAAACTTTTCAAAATTAC
* * * *
8125 CTTTTAACCCC-AAATTTTTTAAAATCAC
1 ATTTTAACCCCTAAACTTTTCAAAATTAC
* * *
8153 ATTTTATCTCCC--AA-TTCTCAAAAATTAT
1 ATTTTAAC-CCCTAAACTTTTC-AAAATTAC
* * *
8181 ATTTTTACCCCCAAAC-TTCCAAAATTAC
1 ATTTTAACCCCTAAACTTTTCAAAATTAC
** ** * *
8209 ATTTTTTCCCCCGAAC-TTCCAAAAATAAC
1 ATTTTAACCCCTAAACTTTTC-AAAATTAC
*
8238 ACTTTT-ACCCCTAAACTTTCCAAAATTAC
1 A-TTTTAACCCCTAAACTTTTCAAAATTAC
8267 ATTTTAACCCC-AAACT
1 ATTTTAACCCCTAAACT
8283 CTCCGAAACT
Statistics
Matches: 200, Mismatches: 34, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
27 6 0.03
28 81 0.41
29 76 0.38
30 37 0.19
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.36
Consensus pattern (29 bp):
ATTTTAACCCCTAAACTTTTCAAAATTAC
Found at i:8422 original size:14 final size:15
Alignment explanation
Indices: 8405--8447 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
8395 TTGATTCATA
8405 TTTCGTAT-TTTATT
1 TTTCGTATATTTATT
*
8419 TTTCTTATATTTA-T
1 TTTCGTATATTTATT
*
8433 TTTCGCATATTTATT
1 TTTCGTATATTTATT
8448 CATTCGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.19, C:0.09, G:0.05, T:0.67
Consensus pattern (15 bp):
TTTCGTATATTTATT
Found at i:8516 original size:19 final size:19
Alignment explanation
Indices: 8492--8531 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
8482 CCTTTATCAC
8492 TAATTT-CATAGCTCATATT
1 TAATTTACAT-GCTCATATT
*
8511 TAATTTACATGCTCATTTT
1 TAATTTACATGCTCATATT
8530 TA
1 TA
8532 TCACTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.30, C:0.15, G:0.05, T:0.50
Consensus pattern (19 bp):
TAATTTACATGCTCATATT
Found at i:11687 original size:58 final size:60
Alignment explanation
Indices: 11557--11690 Score: 184
Period size: 59 Copynumber: 2.3 Consensus size: 60
11547 AAAAAGCTAG
*
11557 AGTTCAAGTACCAAATTGAGTAAAAAAAAATTTAAGTATCAAATTAGGAAAAAAGTGTCA
1 AGTTCAAGTACCAAATTGAGTAAAAAAAAATTTAAGTATCAAATTAAGAAAAAAGTGTCA
* * * *
11617 AGTTCAAGTACCAAATTGGGT-CAAAAAAATTTAGGTGTCAAATTAAGAAAAAA-TGTCGA
1 AGTTCAAGTACCAAATTGAGTAAAAAAAAATTTAAGTATCAAATTAAGAAAAAAGTGTC-A
*
11676 A-TTCAAATACCAAAT
1 AGTTCAAGTACCAAAT
11691 ATATTATTAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
58 17 0.25
59 30 0.45
60 20 0.30
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.25
Consensus pattern (60 bp):
AGTTCAAGTACCAAATTGAGTAAAAAAAAATTTAAGTATCAAATTAAGAAAAAAGTGTCA
Done.