Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010328.1 Kokia drynarioides strain JFW-HI SEQ_125193, 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: 3664
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Found at i:2424 original size:28 final size:28
Alignment explanation
Indices: 2376--2454 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 28
2366 AAATAGGATC
* * *
2376 TTTGGAAGTTCGAGGGTAAAATGGTAATT
1 TTTGGAAATTCGA-GGAAAAATAGTAATT
2405 TTTGGAAATTCGAGGAAAAATAGTAATT
1 TTTGGAAATTCGAGGAAAAATAGTAATT
*
2433 TTTGGAAGATTCAAGGTAAAAA
1 TTTGGAA-ATTCGAGG-AAAAA
2455 ATGGGATTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 20 0.45
29 19 0.43
30 5 0.11
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (28 bp):
TTTGGAAATTCGAGGAAAAATAGTAATT
Found at i:2458 original size:59 final size:58
Alignment explanation
Indices: 2376--2792 Score: 409
Period size: 59 Copynumber: 7.1 Consensus size: 58
2366 AAATAGGATC
* * *
2376 TTTGGAAG-TTCGAGGGT--AAAATGGTAATTTTTGGAAATTCGAGGAAAAATAGTAATT
1 TTTGGAAGATTCG-GGGTCAAAAATGG-GATTTTTGGAAGTTCGAGGTAAAATAGTAATT
** * * * * *
2433 TTTGGAAGATTCAAGGTAAAAAATGGGATTATTGGAAGTTTGGGGGTAAAATGGTAATT
1 TTTGGAAGATTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGTAAAATAGTAATT
** * * * * *
2492 TTAAGAAGGTTCGGGGT-TAAAATGGGTTTTTTGGAAGTTCAAGGGTAAAA-A-TTATT
1 TTTGGAAGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGTAAAATAGTAATT
* * * *
2548 TTTAGAAGGTTTAGGGGATCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAGTAATT
1 TTTGGAA-GATTCGGGG-TCAAAAATGGGATTTTTGGAAGTTC-GAGGTAAAATAGTAATT
* * *
2609 TTTAGAAGATTCGGGGTCAAAAATGAGATTTTTGGAAGTTTGAGGGTAAAATAGTAATT
1 TTTGGAAGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGTAAAATAGTAATT
* * * *
2668 TTTGGAAAATTTGGGGTC-AAAATTGGATTTTTGGAAGTTCGGGGGTAAAATAGTAATT
1 TTTGGAAGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTC-GAGGTAAAATAGTAATT
* *
2726 TTTGGAATATTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAAT-GTTAATT
1 TTTGGAAGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGTAAAATAG-TAATT
2785 TTTGGAAG
1 TTTGGAAG
2793 GTTTAGGGAC
Statistics
Matches: 296, Mismatches: 48, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
56 10 0.03
57 20 0.07
58 90 0.30
59 157 0.53
60 8 0.03
61 11 0.04
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (58 bp):
TTTGGAAGATTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGTAAAATAGTAATT
Found at i:2491 original size:87 final size:86
Alignment explanation
Indices: 2364--2704 Score: 293
Period size: 87 Copynumber: 3.9 Consensus size: 86
2354 GTTCGGAATC
* * * * *
2364 AAAAATAGGATCTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAATTCGAGGAAAAATAGT
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAATTCGGGGTAAAATAGT
2429 AATTTTTGGAAGATTCAAGGT
66 AATTTTTGGAAGATTCAAGGT
* * ** *
2450 AAAAAATGGGATTATTGGAAGTTTGGGGGTAAAATGGTAATTTTAAGAAGGTTCGGGGTTAAAAT
1 -AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAA-ATTCGGGG-TAAAAT
*
2515 GGGT--TTTTTGGAAG-TTCAAGGGT
63 -AGTAATTTTTGGAAGATTCAA-GGT
* * * *
2538 AAAAAT--TATTTTTAGAAGGTTT-AGGGGATCAAAAATGG-GATTTTTGGAAGTTCGGGGGTAA
1 AAAAATGGGATTTTTGGAA-GTTTGA-GGG-T--AAAATGGTAATTTTTGGAAATTC-GGGGTAA
* **
2599 AATAGTAATTTTTAGAAGATTCGGGGT
60 AATAGTAATTTTTGGAAGATTCAAGGT
* * *
2626 CAAAAATGAGATTTTTGGAAGTTTGAGGGTAAAATAGTAATTTTTGGAAAATTTGGGGTCAAAAT
1 -AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGG-AAATTCGGGGT-AAAAT
* *
2691 TG-GATTTTTGGAAG
63 AGTAATTTTTGGAAG
2705 TTCGGGGGTA
Statistics
Matches: 203, Mismatches: 31, Indels: 39
0.74 0.11 0.14
Matches are distributed among these distances:
85 8 0.04
86 9 0.04
87 69 0.34
88 66 0.33
89 32 0.16
90 9 0.04
91 10 0.05
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.33
Consensus pattern (86 bp):
AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAATTCGGGGTAAAATAGT
AATTTTTGGAAGATTCAAGGT
Found at i:2572 original size:117 final size:118
Alignment explanation
Indices: 2393--2800 Score: 486
Period size: 117 Copynumber: 3.5 Consensus size: 118
2383 GTTCGAGGGT
* * * * * * * * *
2393 AAAATGGTAATTTTTGGAAATTCGA-GGAAAAATAGTAATTTTTGGAAGATTCA-AGGTAAAAAA
1 AAAATGG-GATTTTTGGAAGTTTGAGGGTAAAATA-TTATTTTTGGAAGGTTTAGGGGTCAAAAA
* * * * * *
2456 TGGGATTATTGGAAGTTTGGGGGTAAAATGGTAATTTTAAGAAGGTTCGGGGT-T
64 TGGGATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTAGAAGATTCGGGGTCA
* ** *
2510 AAAATGGGTTTTTTGGAAGTTCAAGGGTAAAA-ATTATTTTTAGAAGGTTTAGGGGATCAAAAAT
1 AAAATGGGATTTTTGGAAGTTTGAGGGTAAAATATTATTTTTGGAAGGTTTAGGGG-TCAAAAAT
2574 GGGATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTAGAAGATTCGGGGTCA
65 GGGATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTAGAAGATTCGGGGTCA
* * **
2628 AAAATGAGATTTTTGGAAGTTTGAGGGTAAAATAGTAATTTTTGGAAAATTT-GGGGTC-AAAAT
1 AAAATGGGATTTTTGGAAGTTTGAGGGTAAAATA-TTATTTTTGGAAGGTTTAGGGGTCAAAAAT
* * *
2691 TGGATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTGGAATATTCGGGGTCA
65 GGGATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTAGAAGATTCGGGGTCA
*
2745 AAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGTTAATTTTTGGAAGGTTTAGGG
1 AAAATGGGATTTTTGGAAGTTTGAGGGTAAAATATT-ATTTTTGGAAGGTTTAGGG
2801 ACCTCCGGGT
Statistics
Matches: 250, Mismatches: 33, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
115 14 0.06
116 17 0.07
117 168 0.67
118 33 0.13
119 5 0.02
120 13 0.05
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.35
Consensus pattern (118 bp):
AAAATGGGATTTTTGGAAGTTTGAGGGTAAAATATTATTTTTGGAAGGTTTAGGGGTCAAAAATG
GGATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTAGAAGATTCGGGGTCA
Found at i:2646 original size:176 final size:176
Alignment explanation
Indices: 2393--2792 Score: 477
Period size: 176 Copynumber: 2.3 Consensus size: 176
2383 GTTCGAGGGT
* * * *
2393 AAAATGGTAATTTTTGGAAATTC-GAGGAAAAATAGTAATTTTTGGAAGATTCAAGGTAAAAAAT
1 AAAATGG-GATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTGGAAGATTCAAGGTAAAAAAT
* * * ** * *
2457 GGGATTATTGGAAGTTTGGGGGTAAAATGGTAATTTTAAGAAGGTTCGGGGTTAAAATGGGTTTT
65 GAGATTATTGGAAGTTTGAGGGTAAAATAGTAATTTTAAGAAAATTCGGGGTCAAAATGGGATTT
*
2522 TTGGAAGTTCAAGGGTAAAA-A-TTATTTTTAGAAGGT-TTAGGGGATCA
130 TTGGAAGTTCAAGGGTAAAATAGTAATTTTTAGAA--TATTAGGGG-TCA
* ** *
2569 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTAGAAGATTCGGGGTCAAAAATG
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTGGAAGATTCAAGGTAAAAAATG
* ** * *
2634 AGATTTTTGGAAGTTTGAGGGTAAAATAGTAATTTTTGGAAAATTTGGGGTCAAAATTGGATTTT
66 AGATTATTGGAAGTTTGAGGGTAAAATAGTAATTTTAAGAAAATTCGGGGTCAAAATGGGATTTT
** * *
2699 TGGAAGTTCGGGGGTAAAATAGTAATTTTTGGAATATTCGGGGTCA
131 TGGAAGTTCAAGGGTAAAATAGTAATTTTTAGAATATTAGGGGTCA
* *
2745 AAAATGGGATTTTTGGAAGTTTGAGGGTAAAAT-GTTAATTTTTGGAAG
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAG-TAATTTTTGGAAG
2793 GTTTAGGGAC
Statistics
Matches: 191, Mismatches: 28, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
175 14 0.07
176 160 0.84
177 7 0.04
178 10 0.05
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (176 bp):
AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTGGAAGATTCAAGGTAAAAAATG
AGATTATTGGAAGTTTGAGGGTAAAATAGTAATTTTAAGAAAATTCGGGGTCAAAATGGGATTTT
TGGAAGTTCAAGGGTAAAATAGTAATTTTTAGAATATTAGGGGTCA
Done.