Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013098.1 Kokia drynarioides strain JFW-HI SEQ_128116, 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: 9291
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Found at i:4313 original size:9 final size:8
Alignment explanation
Indices: 4299--4353 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
4289 AATTTCACCA
4299 AAAAAAGAG
1 AAAAAA-AG
4308 AAAAAAAAG
1 -AAAAAAAG
4317 AAAAAAAG
1 AAAAAAAG
4325 AAAAAAA-
1 AAAAAAAG
4332 AAAGAAATAG
1 AAA-AAA-AG
*
4342 -AAAGAAG
1 AAAAAAAG
4349 AAAAA
1 AAAAA
4354 GGAGTGGTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 5 0.13
8 23 0.59
9 5 0.13
10 6 0.15
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:4314 original size:11 final size:11
Alignment explanation
Indices: 4298--4353 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 11
4288 AAATTTCACC
4298 AAAAAAAGAG-
1 AAAAAAAGAGA
4308 AAAAAAA-AG-
1 AAAAAAAGAGA
4317 AAAAAAAGA-A
1 AAAAAAAGAGA
4327 AAAAAAA-AGA
1 AAAAAAAGAGA
*
4337 AATAGAAAGAAGA
1 AA-AAAAAG-AGA
4350 AAAA
1 AAAA
4354 GGAGTGGTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 10 0.26
10 18 0.47
11 4 0.11
12 1 0.03
13 5 0.13
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAGA
Found at i:4322 original size:19 final size:19
Alignment explanation
Indices: 4298--4353 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
4288 AAATTTCACC
4298 AAAAAAAGAGAAAAAAAAG
1 AAAAAAAGAGAAAAAAAAG
*
4317 AAAAAAAGAAAAAAAAAAG
1 AAAAAAAGAGAAAAAAAAG
4336 AAATAGAAAGAAGAAAAA
1 AAA-A-AAAG-AGAAAAA
4354 GGAGTGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 21 0.66
20 1 0.03
21 4 0.12
22 6 0.19
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAAAAAGAGAAAAAAAAG
Found at i:4865 original size:112 final size:112
Alignment explanation
Indices: 4666--4882 Score: 294
Period size: 112 Copynumber: 1.9 Consensus size: 112
4656 ATGTTTGTCA
* * *
4666 TAATCTTTTCATTCATGCGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAACTCTG
1 TAATCTTTTCATTCACGCGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAACCCTA
*
4731 TTCAAGCATGTTTGCATCGAAATAACGGTTAGTGGACTAATGATTTT
66 TTAAAGCATGTTTGCATCGAAATAACGGTTAGTGGACTAATGATTTT
* *
4778 TAATCTTTTGATTCACGCGAGCTTTGCCTCTAATAAAATTCAA-TTTATCCA-CTTCACAACCCT
1 TAATCTTTTCATTCACGCGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTT-ACAACCCT
* * * * * *
4841 ATTAAAGCATTTTTTTCATTGAAATGACTGTTAGTGGTCTAA
65 ATTAAAGCA-TGTTTGCATCGAAATAACGGTTAGTGGACTAA
4883 CGGTATAAGG
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
110 3 0.03
111 22 0.24
112 66 0.73
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.38
Consensus pattern (112 bp):
TAATCTTTTCATTCACGCGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAACCCTA
TTAAAGCATGTTTGCATCGAAATAACGGTTAGTGGACTAATGATTTT
Found at i:5924 original size:49 final size:49
Alignment explanation
Indices: 5297--5923 Score: 422
Period size: 49 Copynumber: 12.8 Consensus size: 49
5287 GAAAAAACAT
* * * *
5297 TGAATC-TATACCCTAGAGATGTGAAGGGAGAGATTGAAGTCGCAATGA
1 TGAATCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGA
* * * * * * * *
5345 TGAATCTCATGCCCTAGAGATGTGAAGGGAAAAATTTAAGCTGTAACGG
1 TGAATCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGA
* * * ** * *
5394 TGAATCTCATGCCCTAGAGATGTGAAGGGAAAGATTGAAGTAGCAAAGG
1 TGAATCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGA
* * * * * * *
5443 CGAATCTTATACATTGGGGATGTGGAGGGAAA-AGTTGAAACCGCAAC-T
1 TGAATCTTATACCTTAGAGATGTGAAGGGAAAGA-TTGAAGCCGCAACGA
* * * * ** * *
5491 TCGAACCTTGTACCTTAGAGATATGATGGGAAAGATTGAAGCCATAATGG
1 T-GAATCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGA
* * * * * * * *
5541 CGAATCTTGTACCCTAAAGATATGGAGGGAAAGGTTGAACCCGCAACGA
1 TGAATCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGA
* * * * * *
5590 CGAACCTTATACCTTAGAGATGTGATGAGAAAGATTGAAGCCGTAATGA
1 TGAATCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGA
* * * * *
5639 TGAATCTTATATCTTAGAGATGT-AGAGGGAAAGGTTAAAGCCGCAATGG
1 TGAATCTTATACCTTAGAGATGTGA-AGGGAAAGATTGAAGCCGCAACGA
* * * * *
5688 TGAACCTAATACCCTAGAGATGT-AGAGGGAAAGGTTGAAGCCGCAACGG
1 TGAATCTTATACCTTAGAGATGTGA-AGGGAAAGATTGAAGCCGCAACGA
* * * * * **
5737 TGAACCTTATACATTAGAAATGTG-ATGGAAAGATAGAAGCCATAACGA
1 TGAATCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGA
* * * * *** ** * *
5785 CGAACCTTATAACTTAAAGATGTGATTAGAAAGATTGAAGTTGCAATGG
1 TGAATCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGA
* * * *
5834 TGAATCTTATACCTTAAAGATGT-AGAGGGAAAGGTTGAAGCTGCAACAA
1 TGAATCTTATACCTTAGAGATGTGA-AGGGAAAGATTGAAGCCGCAACGA
* *
5883 TGAATCTTATACCTTAGAGATGTGAAAGGAAAGATTTAAGC
1 TGAATCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGC
5924 TACAATGACA
Statistics
Matches: 448, Mismatches: 121, Indels: 19
0.76 0.21 0.03
Matches are distributed among these distances:
48 46 0.10
49 400 0.89
50 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.24
Consensus pattern (49 bp):
TGAATCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGA
Found at i:5930 original size:98 final size:98
Alignment explanation
Indices: 5303--5930 Score: 467
Period size: 98 Copynumber: 6.4 Consensus size: 98
5293 ACATTGAATC
* * * * * * * * *
5303 TATACCCTAGAGATGTGAAGGGAGAGATTGAAGTCGCAATGATGAATCTCATGCCCTAGAGATGT
1 TATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCACAATGGTGAATCTTATACCTTAAAGATGT
** * * * * *
5368 -GAAGGGAAAAATTTAAGCTGTAACGGTGAATCT
66 AG-AGGGAAAGGTTGAAGCCGCAACGATGAACCT
* * * * * * * ***
5401 CATGCCCTAGAGATGTGAAGGGAAAGATTGAAG-TAGCAAAGGCGAATCTTATACATTGGGGATG
1 TATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCA-CAATGGTGAATCTTATACCTTAAAGATG
* * * *
5465 TGGAGGGAAAAGTTGAAACCGCAAC-TTCGAACCT
65 TAGAGGGAAAGGTTGAAGCCGCAACGAT-GAACCT
* * * * * * * *
5499 TGTACCTTAGAGATATGATGGGAAAGATTGAAGCCATAATGGCGAATCTTGTACCCTAAAGATAT
1 TATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCACAATGGTGAATCTTATACCTTAAAGATGT
* * *
5564 GGAGGGAAAGGTTGAACCCGCAACGACGAACCT
66 AGAGGGAAAGGTTGAAGCCGCAACGATGAACCT
* * ** * * *
5597 TATACCTTAGAGATGTGATGAGAAAGATTGAAGCCGTAATGATGAATCTTATATCTTAGAGATGT
1 TATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCACAATGGTGAATCTTATACCTTAAAGATGT
* * *
5662 AGAGGGAAAGGTTAAAGCCGCAATGGTGAACCT
66 AGAGGGAAAGGTTGAAGCCGCAACGATGAACCT
* * * * * * *
5695 AATACCCTAGAGATGT-AGAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATACATTAGAA-AT
1 TATACCTTAGAGATGTGA-AGGGAAAGATTGAAGCCACAATGGTGAATCTTATACCTTA-AAGAT
* * * ** *
5758 GT-GATGGAAAGATAGAAGCCATAACGACGAACCT
64 GTAGAGGGAAAGGTTGAAGCCGCAACGATGAACCT
* * *** ***
5792 TATAACTTAAAGATGTGATTAGAAAGATTGAAGTTGCAATGGTGAATCTTATACCTTAAAGATGT
1 TATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCACAATGGTGAATCTTATACCTTAAAGATGT
* * *
5857 AGAGGGAAAGGTTGAAGCTGCAACAATGAATCT
66 AGAGGGAAAGGTTGAAGCCGCAACGATGAACCT
* * *
5890 TATACCTTAGAGATGTGAAAGGAAAGATTTAAGCTACAATG
1 TATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCACAATG
5931 ACAAATCTTC
Statistics
Matches: 411, Mismatches: 109, Indels: 20
0.76 0.20 0.04
Matches are distributed among these distances:
96 2 0.00
97 72 0.18
98 334 0.81
99 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.24
Consensus pattern (98 bp):
TATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCACAATGGTGAATCTTATACCTTAAAGATGT
AGAGGGAAAGGTTGAAGCCGCAACGATGAACCT
Found at i:5938 original size:49 final size:49
Alignment explanation
Indices: 5836--5953 Score: 112
Period size: 49 Copynumber: 2.4 Consensus size: 49
5826 TGCAATGGTG
* * * **
5836 AATCTTATACCTTAAAGATGTAGAGGGAAAGGTTGAAGCTGCAACAATG
1 AATCTTATACCTTAAAGATGTAGAAGGAAAGATTGAAGCTACAACAACA
* * **
5885 AATCTTATACCTTAGAGATGT-GAAAGGAAAGATTTAAGCTACAATGACA
1 AATCTTATACCTTAAAGATGTAG-AAGGAAAGATTGAAGCTACAACAACA
* * *
5934 AATCTTCTACCCTGAAGATG
1 AATCTTATACCTTAAAGATG
5954 AGGAGAAGCA
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
48 1 0.02
49 54 0.98
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (49 bp):
AATCTTATACCTTAAAGATGTAGAAGGAAAGATTGAAGCTACAACAACA
Found at i:6411 original size:93 final size:93
Alignment explanation
Indices: 6007--6502 Score: 320
Period size: 93 Copynumber: 5.3 Consensus size: 93
5997 AAAGAAGCAT
* * * * * * * *
6007 ATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAAACATCAGATCTTATATCCCTGAATTTA
1 ATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAGCACCAAATCCTATATCCCTGAAGTTA
*
6072 TAGTGGATCAGATCAAAATGAGTAACAA
66 CAGTGGATCAGATCAAAATGAGTAACAA
* *
6100 ATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGAGAAGTTA-C--A----ATA-CCCTTG-AGT
1 ATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAG-CACCAAATCCTATATCCC-TGAAGT
* * *
6156 TACAGTGGGTCAGATTAAAATGA-TAAAGCAG
64 TACAGTGGATCAGATCAAAATGAGT-AA-CAA
* * * * * * * * * *
6187 ATCTCAACGTCCTTGAGGCTACAGTGGAGTAGAGTGAAACTTCTAAA-CCTATCT-TCTCGAGGT
1 ATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAGC-ACCAAATCCTATATCCCT-GAAGT
* * * * * * *
6250 TACAATGAAGT-GGGTCAAAA-CAGGTAGCAT
64 TACAGTGGA-TCAGATCAAAATGA-GTAACAA
* *
6280 ATCTCAATGT-CTCTGAGGTTACAATGGAATGGAATGAAGCACCAAATCCTATATCCCTGAAGTT
1 ATCTCAATGTCCT-TGAGGTTACAGTGGAATGGAGTGAAGCACCAAATCCTATATCCCTGAAGTT
*
6344 ACAGTGGATCAGATCAAAATGAGTAACAG
65 ACAGTGGATCAGATCAAAATGAGTAACAA
* * * * *
6373 ATCTCAATGTCCTTGAGGTTACAATGGAATGGGGTGAAGTTTAAACACCAAATCTTATACCCCTA
1 ATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAG------CACCAAATCCTATATCCCTG
** * * ** *
6438 AAGTTGTAGTGGGTCAGATTAAAACAATGAAACAA
60 AAGTTACAGTGGATCAGATCAAAATGA-GTAACAA
*
6473 ATCTCAATGTTCTTGAGGTTACAGTGGAAT
1 ATCTCAATGTCCTTGAGGTTACAGTGGAAT
6503 AGATAGAAGC
Statistics
Matches: 307, Mismatches: 66, Indels: 53
0.72 0.15 0.12
Matches are distributed among these distances:
85 1 0.00
86 27 0.09
87 40 0.13
90 1 0.00
91 1 0.00
92 8 0.03
93 135 0.44
94 21 0.07
95 2 0.01
99 38 0.12
100 33 0.11
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (93 bp):
ATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAGCACCAAATCCTATATCCCTGAAGTTA
CAGTGGATCAGATCAAAATGAGTAACAA
Found at i:6501 original size:100 final size:99
Alignment explanation
Indices: 6280--6502 Score: 244
Period size: 99 Copynumber: 2.3 Consensus size: 99
6270 CAGGTAGCAT
* * *
6280 ATCTCAATGT-CTCTGAGGTTACAATGGAAT---G-GAA--TGAAGCACCAAATCCTATATCCCT
1 ATCTCAATGTCCT-TGAGGTTACAATGGAATGGGGTGAAGTTTAAACACCAAATCCTATACCCCT
* ** * *
6338 GAAGTTACAGTGGATCAGATCAAAATGAGTAACAG
65 AAAGTTACAGTGGATCAGATCAAAACAAGAAACAA
*
6373 ATCTCAATGTCCTTGAGGTTACAATGGAATGGGGTGAAGTTTAAACACCAAATCTTATACCCCTA
1 ATCTCAATGTCCTTGAGGTTACAATGGAATGGGGTGAAGTTTAAACACCAAATCCTATACCCCTA
** * *
6438 AAGTTGTAGTGGGTCAGATTAAAACAATGAAACAA
66 AAGTTACAGTGGATCAGATCAAAACAA-GAAACAA
* *
6473 ATCTCAATGTTCTTGAGGTTACAGTGGAAT
1 ATCTCAATGTCCTTGAGGTTACAATGGAAT
6503 AGATAGAAGC
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
93 27 0.25
94 2 0.02
96 1 0.01
97 3 0.03
99 41 0.38
100 33 0.31
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (99 bp):
ATCTCAATGTCCTTGAGGTTACAATGGAATGGGGTGAAGTTTAAACACCAAATCCTATACCCCTA
AAGTTACAGTGGATCAGATCAAAACAAGAAACAA
Found at i:6520 original size:100 final size:99
Alignment explanation
Indices: 6280--6527 Score: 244
Period size: 100 Copynumber: 2.6 Consensus size: 99
6270 CAGGTAGCAT
*
6280 ATCTCAATGT-CTCTGAGGTTACAATGGAATG-GAATGAAG------CACCAAATCCTATATCCC
1 ATCTCAATGTCCT-TGAGGTTACAATGGAATGAG-ATGAAGCTTAAACACCAAATCCTATACCCC
* ** * *
6337 TGAAGTTACAGTGGATCAGATCAAAATGAGTAACAG
64 TAAAGTTACAGTGGATCAGATCAAAACAAGAAACAA
* * * *
6373 ATCTCAATGTCCTTGAGGTTACAATGGAATGGGGTGAAGTTTAAACACCAAATCTTATACCCCTA
1 ATCTCAATGTCCTTGAGGTTACAATGGAATGAGATGAAGCTTAAACACCAAATCCTATACCCCTA
** * *
6438 AAGTTGTAGTGGGTCAGATTAAAACAATGAAACAA
66 AAGTTACAGTGGATCAGATCAAAACAA-GAAACAA
* * *
6473 ATCTCAATGTTCTTGAGGTTACAGTGGAAT-AGATAGAAGCTTCAACACCAAATCC
1 ATCTCAATGTCCTTGAGGTTACAATGGAATGAGAT-GAAGCTTAAACACCAAATCC
6528 CATTTTCCTG
Statistics
Matches: 126, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
93 33 0.26
94 3 0.02
99 40 0.32
100 50 0.40
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (99 bp):
ATCTCAATGTCCTTGAGGTTACAATGGAATGAGATGAAGCTTAAACACCAAATCCTATACCCCTA
AAGTTACAGTGGATCAGATCAAAACAAGAAACAA
Found at i:6804 original size:17 final size:18
Alignment explanation
Indices: 6784--6822 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
6774 AATAAATAAA
6784 TTTAAATTAAAA-TCCAT
1 TTTAAATTAAAAGTCCAT
* *
6801 TTTAATTTAAAAGTCCCT
1 TTTAAATTAAAAGTCCAT
6819 TTTA
1 TTTA
6823 CAACCCAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (18 bp):
TTTAAATTAAAAGTCCAT
Found at i:7932 original size:21 final size:21
Alignment explanation
Indices: 7906--7947 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
7896 CATTTTTTAT
*
7906 TTTAAAATAAAA-GTTTGCGAC
1 TTTAAAAAAAAAGGTTT-CGAC
7927 TTTAAAAAAAAAGGTTTCGAC
1 TTTAAAAAAAAAGGTTTCGAC
7948 ACTGGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (21 bp):
TTTAAAAAAAAAGGTTTCGAC
Done.