Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011950.1 Kokia drynarioides strain JFW-HI SEQ_126948, 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: 522875
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:424833 original size:72 final size:72
Alignment explanation
Indices: 424710--424949 Score: 304
Period size: 72 Copynumber: 3.3 Consensus size: 72
424700 TCAGTGGAAA
* * * *
424710 GCTTACGTCTCGGTTAGAGCATAATGCTTTGTGACTGCATACATCTCAATTAGAGCGTATTGCTA
1 GCTTACGTCTCGGTTAGAGCATAATGCTATATGATTGCATACGTCTCAATTAGAGCGTATTGCTA
424775 TGTAATT
66 TGTAATT
* * * *
424782 GCTTACGTCTCAGTTAGAGCGTAATGCTATATGATTGCATATGTCTTAATTAGAGCGTATTGCTA
1 GCTTACGTCTCGGTTAGAGCATAATGCTATATGATTGCATACGTCTCAATTAGAGCGTATTGCT-
424847 AT-TAATT
65 ATGTAATT
* * * *
424854 GCTTACGTCTCGATTAGAGCATAATGCTA-AGAGATTGCATACGTCTCAATTAGAGCATAATGCT
1 GCTTACGTCTCGGTTAGAGCATAATGCTATA-TGATTGCATACGTCTCAATTAGAGCGTATTGCT
* *
424918 AAGTGATT
65 ATGTAATT
* *
424926 GCTTATGTATCGGTTAGAGCATAA
1 GCTTACGTCTCGGTTAGAGCATAA
424950 GGCCATTTCA
Statistics
Matches: 144, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
71 2 0.01
72 140 0.97
73 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (72 bp):
GCTTACGTCTCGGTTAGAGCATAATGCTATATGATTGCATACGTCTCAATTAGAGCGTATTGCTA
TGTAATT
Found at i:425278 original size:26 final size:25
Alignment explanation
Indices: 425249--425297 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
425239 CCTATTTTGA
*
425249 TGCTATGTATTATGATGTCAAGTTCG
1 TGCTATGCATTA-GATGTCAAGTTCG
* *
425275 TGCTTTGCATTAGTTGTCAAGTT
1 TGCTATGCATTAGATGTCAAGTT
425298 AAAATGAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.45
Consensus pattern (25 bp):
TGCTATGCATTAGATGTCAAGTTCG
Found at i:434387 original size:52 final size:52
Alignment explanation
Indices: 434227--434399 Score: 190
Period size: 52 Copynumber: 3.3 Consensus size: 52
434217 AATGACTAGT
* * *
434227 TGTCATCGTGAGTAAATGAATCCTTTACGGATTATGAGGTCCGATGACTAACT-
1 TGTCATCGTGAGTATATGGATCCTTTACGGATTAAGAGGTCCGATGACT--CTG
* * * * **
434280 T-TCATCATGAGTATATGAGATCCTTTATGTATTTAA-AGGTCCAATGACTAAG
1 TGTCATCGTGAGTATATG-GATCCTTTACGGA-TTAAGAGGTCCGATGACTCTG
* *
434332 TGTCATCGTGAGTATATGGATCCTTTACGGACTAAGAGGTCCGATTACTCTG
1 TGTCATCGTGAGTATATGGATCCTTTACGGATTAAGAGGTCCGATGACTCTG
434384 TGTCATCGTGAGTATA
1 TGTCATCGTGAGTATA
434400 CGAATCCCTC
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
51 3 0.03
52 54 0.55
53 38 0.39
54 3 0.03
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (52 bp):
TGTCATCGTGAGTATATGGATCCTTTACGGATTAAGAGGTCCGATGACTCTG
Found at i:435059 original size:21 final size:24
Alignment explanation
Indices: 435033--435090 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 24
435023 TGACTTGAGT
*
435033 TGTATCGGTAGTTGAAT-TGT-GA
1 TGTATCGGTAGTTGAATGTATAGA
*
435055 -GTATCGGTAGTTGTATGTATAGA
1 TGTATCGGTAGTTGAATGTATAGA
435078 TGTATCGGTAGTT
1 TGTATCGGTAGTT
435091 TGCATACTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 15 0.48
22 2 0.06
23 2 0.06
24 12 0.39
ACGTcount: A:0.22, C:0.05, G:0.31, T:0.41
Consensus pattern (24 bp):
TGTATCGGTAGTTGAATGTATAGA
Found at i:440644 original size:11 final size:10
Alignment explanation
Indices: 440625--440653 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
440615 AATCTCTAAC
440625 AAGAAAAAAA
1 AAGAAAAAAA
440635 AAGAAAAAAA
1 AAGAAAAAAA
440645 AAGAAAAAA
1 AAGAAAAAA
440654 GCAATTGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:440768 original size:14 final size:14
Alignment explanation
Indices: 440749--440782 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
440739 CAAAAGGGAA
440749 GAGAAAGCAGAAAG
1 GAGAAAGCAGAAAG
440763 GAGAAAGCAGAAAG
1 GAGAAAGCAGAAAG
440777 GAGAAA
1 GAGAAA
440783 AGGGGAACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.59, C:0.06, G:0.35, T:0.00
Consensus pattern (14 bp):
GAGAAAGCAGAAAG
Found at i:447233 original size:28 final size:28
Alignment explanation
Indices: 447193--447285 Score: 132
Period size: 28 Copynumber: 3.3 Consensus size: 28
447183 CTTAGAAATT
* *
447193 GTAAACGCGTAAGTACAAGTTGGCGAGC
1 GTAAACGCATAAGTACAAGCTGGCGAGC
* *
447221 GTAAACACATAAGTACAAGCTGGCCAGC
1 GTAAACGCATAAGTACAAGCTGGCGAGC
* *
447249 GAAAATGCATAAGTACAAGCTGGCGAGC
1 GTAAACGCATAAGTACAAGCTGGCGAGC
447277 GTAAACGCA
1 GTAAACGCA
447286 AACGAATGAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.15
Consensus pattern (28 bp):
GTAAACGCATAAGTACAAGCTGGCGAGC
Found at i:455692 original size:21 final size:19
Alignment explanation
Indices: 455666--455713 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
455656 CATATTATTT
455666 TAATTTTTTAAAATATTTATA
1 TAATTTTTT-AAATATTTA-A
* *
455687 TTATTTATTTTAATATTTAA
1 TAATTT-TTTAAATATTTAA
455707 TAATTTT
1 TAATTTT
455714 ATTTATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.04
20 6 0.26
21 13 0.57
22 3 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TAATTTTTTAAATATTTAA
Found at i:455714 original size:21 final size:21
Alignment explanation
Indices: 455677--455717 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
455667 AATTTTTTAA
*
455677 AATATTTATATTATTTATTTT
1 AATATTTATAATATTTATTTT
455698 AATATTTAATAAT-TTTATTT
1 AATATTT-ATAATATTTATTT
455718 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
AATATTTATAATATTTATTTT
Found at i:455715 original size:25 final size:25
Alignment explanation
Indices: 455687--455735 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
455677 AATATTTATA
455687 TTATTTATTTTAATATTTA-ATAATT
1 TTATTTATTTT-ATATTTATATAATT
*
455712 TTATTTATTTTTTATTTATATAAT
1 TTATTTATTTTATATTTATATAAT
455736 CATCTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TTATTTATTTTATATTTATATAATT
Found at i:459623 original size:27 final size:27
Alignment explanation
Indices: 459585--459642 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
459575 GATCACCCTC
459585 AAATTATATTTTAATCACTTATGTTTA
1 AAATTATATTTTAATCACTTATGTTTA
*
459612 AAATTATATTTTAATCACTTATGTTTG
1 AAATTATATTTTAATCACTTATGTTTA
459639 AAAT
1 AAAT
459643 GTTACGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (27 bp):
AAATTATATTTTAATCACTTATGTTTA
Found at i:473092 original size:94 final size:94
Alignment explanation
Indices: 472931--473156 Score: 323
Period size: 94 Copynumber: 2.4 Consensus size: 94
472921 ATTATCTCTA
* * *
472931 TTACCAGTATACGATGCTGCTCACACTAAGCTGATGAGAACTCGTAACATATGCGGTACCTTAGC
1 TTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGAACTCGCAACATATGCGGTACCTCAGC
*
472996 CATCGATACGGTATCTGTACATATAATTG
66 CATCGATACGGTATCTGTACATATAACTG
* * * * *
473025 TTACCAGTATACGATGTTGCTTACACTAAGTTGACGAGGACTCGCAACATATGCTGTACCTCAGC
1 TTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGAACTCGCAACATATGCGGTACCTCAGC
473090 CATCGATACGGTATCTGTACATATAACTG
66 CATCGATACGGTATCTGTACATATAACTG
* * *
473119 TT-CC-CTA-ACGATGCTGCTCACACTAACCTAACGAGAAC
1 TTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGAAC
473157 ATGCAAATTA
Statistics
Matches: 116, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
91 25 0.22
92 2 0.02
93 2 0.02
94 87 0.75
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (94 bp):
TTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGAACTCGCAACATATGCGGTACCTCAGC
CATCGATACGGTATCTGTACATATAACTG
Found at i:478207 original size:23 final size:23
Alignment explanation
Indices: 478181--478259 Score: 54
Period size: 23 Copynumber: 3.4 Consensus size: 23
478171 TTACTTCTTT
478181 AATTTTATTAAATTGCATCGACA
1 AATTTTATTAAATTGCATCGACA
* * * *
478204 AATTATCTTCAAACTTTCATTG-C-
1 AATTTTATT-AAA-TTGCATCGACA
* *
478227 AATTCTTATTAATTTGCCTCGACA
1 AATT-TTATTAAATTGCATCGACA
*
478251 TATTTTATT
1 AATTTTATT
478260 TCAGCCTTGA
Statistics
Matches: 40, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
22 5 0.12
23 19 0.47
24 10 0.25
25 6 0.15
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (23 bp):
AATTTTATTAAATTGCATCGACA
Found at i:500001 original size:10 final size:10
Alignment explanation
Indices: 499986--500019 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
499976 AAAGGAAAAT
499986 AAGAAAAAGA
1 AAGAAAAAGA
499996 AAGAAAAAGAA
1 AAGAAAAAG-A
500007 AAGAGAAAAGA
1 AAGA-AAAAGA
500018 AA
1 AA
500020 AGAAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.41
11 8 0.36
12 5 0.23
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:500015 original size:13 final size:14
Alignment explanation
Indices: 499990--500029 Score: 57
Period size: 12 Copynumber: 2.9 Consensus size: 14
499980 GAAAATAAGA
499990 AAAAGAAAGAAAAAG
1 AAAAG-AAGAAAAAG
500005 AAAAG-AG-AAAAG
1 AAAAGAAGAAAAAG
500017 AAAAGAAGAAAAA
1 AAAAGAAGAAAAA
500030 ATGTTTGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 10 0.43
13 4 0.17
14 4 0.17
15 5 0.22
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAAAG
Found at i:521575 original size:15 final size:16
Alignment explanation
Indices: 521557--521593 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
521547 GAGGAGGAGA
*
521557 AAGAAGAGAA-GGAAG
1 AAGAAGAGAATGAAAG
521572 AAGAAG-GAATGAAAG
1 AAGAAGAGAATGAAAG
521587 AAGAAGA
1 AAGAAGA
521594 AAAAGGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (16 bp):
AAGAAGAGAATGAAAG
Done.