Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011379.1 Kokia drynarioides strain JFW-HI SEQ_126360, 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: 12521
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:83 original size:18 final size:18
Alignment explanation
Indices: 44--98 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
34 AAATTACATA
*
44 AAAATTCAAAATAATTTTT
1 AAAATTCAAAAT-ATTTAT
*
63 AAAATTCCAAATATTTAT
1 AAAATTCAAAATATTTAT
*
81 AAAATTCTAAAT-TTTAT
1 AAAATTCAAAATATTTAT
98 A
1 A
99 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 6 0.18
18 16 0.48
19 11 0.33
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:2608 original size:58 final size:58
Alignment explanation
Indices: 2361--2650 Score: 249
Period size: 58 Copynumber: 5.0 Consensus size: 58
2351 TTGGACTTAT
* * * *
2361 GGGGGCAAAATGAGAATTTTGGGAAAG-TTCGGGGTTAAAAATGGAATTTTTAGACA-TTC
1 GGGGGTAAAATG-GAATTTTTGGAAAGTTTCGGGG-TAAAAATGGGATTTTTGGA-AGTTC
* * ** * *
2420 GGGGGTAAAACGGTAA-TTTT-GAGAGTTTCAAGGTCGAAAAT-GGAGTTTTTGGACA-TCC
1 GGGGGTAAAATGG-AATTTTTGGAAAGTTTCGGGGT-AAAAATGGGA-TTTTTGGA-AGTTC
* * *
2478 GAGGGTAAAATGGTAATTTTTGG-AGGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTC
1 GGGGGTAAAATGG-AATTTTTGGAAAGTTTCGGGGT-AAAAATGGGATTTTTGGAAGTTC
* * *
2537 AGGGATAAAATGGAATTTTTGGAAAG-TTCAGGG-ATAAAATGGGATTTTTGGAAGTTC
1 GGGGGTAAAATGGAATTTTTGGAAAGTTTCGGGGTA-AAAATGGGATTTTTGGAAGTTC
*
2594 GGGGGTAAAAATGGAATTTTTGG-AAGTTTCGGGGTCAAAAATGGGATTTTTGAAAGT
1 GGGGGT-AAAATGGAATTTTTGGAAAGTTTCGGGGT-AAAAATGGGATTTTTGGAAGT
2651 CCATAAAGAG
Statistics
Matches: 188, Mismatches: 29, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
56 1 0.01
57 35 0.19
58 77 0.41
59 71 0.38
60 4 0.02
ACGTcount: A:0.32, C:0.06, G:0.31, T:0.31
Consensus pattern (58 bp):
GGGGGTAAAATGGAATTTTTGGAAAGTTTCGGGGTAAAAATGGGATTTTTGGAAGTTC
Found at i:2623 original size:116 final size:115
Alignment explanation
Indices: 2367--2650 Score: 303
Period size: 117 Copynumber: 2.4 Consensus size: 115
2357 TTATGGGGGC
* * * * *
2367 AAAATGAGAATTTTGGGAAAG-TTCGGGGTTAAAAATGGAATTTTTAGACA-TTCGGGGGTAAAA
1 AAAATG-GAATTTTTGG-AAGTTTCGGGGTCAAAAATGGAATTTTTGGA-AGTTCAGGGATAAAA
*
2430 CGGTAATTTTGAGAGTTTCAAGGTCGAAAATGGAGTTTTTGGACATCCGAGGGT
63 CGGTAATTTTGAAAGTTTCAAGGTC-AAAATGGAGTTTTTGGACATCCGAGGGT
* *
2484 AAAATGGTAATTTTTGGAGGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCAGGGATAAAATG
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCAGGGATAAAACG
* * *
2549 G-AATTTTTGGAAAG-TTCAGGGAT-AAAATGG-GATTTTTGGA-AGTTCGGGGGT
65 GTAA-TTTT-GAAAGTTTCAAGG-TCAAAATGGAG-TTTTTGGACA-TCCGAGGGT
* *
2600 AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGAAAGT
1 -AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGT
2651 CCATAAAGAG
Statistics
Matches: 144, Mismatches: 14, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
115 2 0.01
116 68 0.47
117 69 0.48
118 5 0.03
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (115 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCAGGGATAAAACGG
TAATTTTGAAAGTTTCAAGGTCAAAATGGAGTTTTTGGACATCCGAGGGT
Found at i:2644 original size:30 final size:28
Alignment explanation
Indices: 2367--2650 Score: 206
Period size: 29 Copynumber: 9.7 Consensus size: 28
2357 TTATGGGGGC
*
2367 AAAATGAGAATTTTGGGAAAGTTCGGGGTTA
1 AAAATG-GAATTTTTGG-AAGTTCGGGG-TA
*
2398 AAAATGGAATTTTTAGACA-TTCGGGGGT-
1 AAAATGGAATTTTTGGA-AGTTC-GGGGTA
* ** *
2426 AAAACGGTAA-TTTT-GAGAGTTTCAAGGTCG
1 AAAATGG-AATTTTTGGA-AG-TTCGGGGT-A
* *
2456 AAAATGGAGTTTTTGGACA-TCCGAGGGT-
1 AAAATGGAATTTTTGGA-AGTTCG-GGGTA
*
2484 AAAATGGTAATTTTTGGAGGTTTCGGGGTCA
1 AAAATGG-AATTTTTGGAAG-TTCGGGGT-A
*
2515 AAAATGGAATTTTTGGAAGTTCAGGG-A
1 AAAATGGAATTTTTGGAAGTTCGGGGTA
*
2542 TAAAATGGAATTTTTGGAAAGTTCAGGG-A
1 -AAAATGGAATTTTTGG-AAGTTCGGGGTA
*
2571 TAAAATGGGATTTTTGGAAGTTCGGGGGTA
1 -AAAATGGAATTTTTGGAAGTTC-GGGGTA
2601 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGGGGT-A
* *
2631 AAAATGGGATTTTTGAAAGT
1 AAAATGGAATTTTTGGAAGT
2651 CCATAAAGAG
Statistics
Matches: 210, Mismatches: 22, Indels: 44
0.76 0.08 0.16
Matches are distributed among these distances:
27 4 0.02
28 42 0.20
29 86 0.41
30 62 0.30
31 16 0.08
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGGGGTA
Found at i:10477 original size:96 final size:96
Alignment explanation
Indices: 10293--10484 Score: 241
Period size: 96 Copynumber: 2.0 Consensus size: 96
10283 TTTTTAGGAA
* *
10293 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
10358 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* * *
10389 AAGGGTATTCGATTATTTCGATTTGAGGGAAA-ATTGCACCTAGTAAGTTAAGGCACAA-ATTTT
1 AAGGATATTCGATTATCTCGATTTGA-AGAAAGATTGCACCTAGTAAGTTAAGGCACAATA-TTT
*
10452 C-GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
64 CAG-AA-TCGAAGATAAAGA-AACATTGCCTCGATT
10485 TTAAAGTTTT
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
95 3 0.04
96 72 0.86
97 9 0.11
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAGATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:10786 original size:29 final size:29
Alignment explanation
Indices: 10748--11004 Score: 156
Period size: 29 Copynumber: 8.7 Consensus size: 29
10738 TTATGGGGGC
* *
10748 AAAATGGGAATTTTGGGAAGTTCGAGGTTA
1 AAAAT-GGAATTTTTGGAAGTTCGAGGGTA
* *
10778 AAAATGGAATTTTTAGACA-TTCGGGGGT-
1 AAAATGGAATTTTTGGA-AGTTCGAGGGTA
* * *
10806 AAAAGGGTAA-TTTT-GAGAGTTTC-AAGGTT
1 AAAATGG-AATTTTTGGA-AG-TTCGAGGGTA
* *
10835 AAAAT-GATGTTTTTGTATA-TTCGAGGGT-
1 AAAATGGA-ATTTTTGGA-AGTTCGAGGGTA
* * *
10863 AAAATGATAATTTTTGGAGGTTTTG-GGGTCA
1 AAAATG-GAATTTTTGGAAG-TTCGAGGGT-A
* *
10894 AAAATGGGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
10923 AAAATGGAATTTTTAGATAGTTTCGA-GGTCA
1 AAAATGGAATTTTTGGA-AG-TTCGAGGGT-A
*
10954 AAAATGGGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
10983 AAAACGAAATTTTTGGATAGTT
1 AAAATGGAATTTTTGGA-AGTT
11005 TAGGGACCTC
Statistics
Matches: 176, Mismatches: 30, Indels: 42
0.71 0.12 0.17
Matches are distributed among these distances:
27 4 0.02
28 22 0.12
29 84 0.48
30 40 0.23
31 26 0.15
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:10961 original size:60 final size:60
Alignment explanation
Indices: 10854--11005 Score: 200
Period size: 60 Copynumber: 2.5 Consensus size: 60
10844 TTTTTGTATA
* * * * *
10854 TTCGAGGGT-AAAATGATAATTTTTGGA-GGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAAACGA-AATTTTTAGATAGTTTCGAGGTCAAAAATGGGATTTTTGGAAG
* * *
10913 TTCGGGGGTAAAAATGGAATTTTTAGATAGTTTCGAGGTCAAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAAACGAAATTTTTAGATAGTTTCGAGGTCAAAAATGGGATTTTTGGAAG
*
10973 TTCGAGGGTAAAAACGAAATTTTTGGATAGTTT
1 TTCGAGGGTAAAAACGAAATTTTTAGATAGTTT
11006 AGGGACCTCC
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
59 17 0.21
60 64 0.79
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.35
Consensus pattern (60 bp):
TTCGAGGGTAAAAACGAAATTTTTAGATAGTTTCGAGGTCAAAAATGGGATTTTTGGAAG
Done.