Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012424.1 Kokia drynarioides strain JFW-HI SEQ_127428, 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: 8244
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:1587 original size:6 final size:6
Alignment explanation
Indices: 1573--1640 Score: 84
Period size: 6 Copynumber: 11.3 Consensus size: 6
1563 AATTAGTATC
* * *
1573 TTTATT TTCATT TTCATT TTTATT TTTAGT TTTATT TTT-TAT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT-T TTTATT
*
1621 TTTATT TTTAAT TTTATT TT
1 TTTATT TTTATT TTTATT TT
1641 AATTATGCAC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
5 1 0.02
6 52 0.96
7 1 0.02
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:2591 original size:20 final size:19
Alignment explanation
Indices: 2566--2611 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
2556 GTTTAGAAAA
2566 AGAAAAAAAAAAGAAAATTG
1 AGAAAAAAAAAAGAAAA-TG
2586 AGAAAAAAAAAAGAAAATG
1 AGAAAAAAAAAAGAAAATG
2605 A-AAAAAA
1 AGAAAAAA
2612 GACAAAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 6 0.23
19 3 0.12
20 17 0.65
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (19 bp):
AGAAAAAAAAAAGAAAATG
Found at i:4097 original size:29 final size:27
Alignment explanation
Indices: 4065--4411 Score: 139
Period size: 29 Copynumber: 11.9 Consensus size: 27
4055 TTTGGAAAAA
*
4065 TTCGGGGTTAAAAATGGGATTTTTAGGAG
1 TTCGGGG-TAAAAATGGAATTTTT-GGAG
**
4094 TTCGAGGGT-AAAATGGAAATTTTTAAAAG
1 TTCG-GGGTAAAAATGG-AATTTTT-GGAG
* * * *
4123 TTTTGTGGTCAAAAATGGGATTTTTGGAAA
1 -TTCGGGGT-AAAAATGGAATTTTTGG-AG
* *
4153 TTTGGGGT-AAAATGATAATTTTTGGAAGG
1 TTCGGGGTAAAAATG-GAATTTTTGG-A-G
* *
4182 TTCGGGGTTAAAAATGGGATTTTTGAAAG
1 TTCGGGG-TAAAAATGGAATTTTTG-GAG
* *
4211 TTTGAGGGTAAAAATGAAATTTTTGGAAG
1 TTCG-GGGTAAAAATGGAATTTTTGG-AG
* *
4240 TTTCGAGGTCAAAAT-GAGATTTTTGGGAG
1 -TTCGGGGTAAAAATGGA-ATTTTT-GGAG
* ** *
4269 TTTAGGGGT-AAAATGGTAATTTTTAAACAA
1 -TTCGGGGTAAAAATGG-AATTTTT--GGAG
* * *
4299 TCTAGGGGTCAAAAATGGGATTTTTGAAAG
1 T-TCGGGGT-AAAAATGGAATTTTTG-GAG
4329 TTCGGGGATAAAAA-GGAAATTTTTGGAAG
1 TTCGGGG-TAAAAATGG-AATTTTTGG-AG
* *
4358 ATTTGGGGTCAAAAATGGGATTTTTGGGAG
1 -TTCGGGGT-AAAAATGGAATTTTT-GGAG
4388 TTCGGGGGT-AAAATGGTAATTTTT
1 TTC-GGGGTAAAAATGG-AATTTTT
4412 AGACAGTCTA
Statistics
Matches: 244, Mismatches: 42, Indels: 64
0.70 0.12 0.18
Matches are distributed among these distances:
27 6 0.02
28 32 0.13
29 110 0.45
30 66 0.27
31 23 0.09
32 7 0.03
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (27 bp):
TTCGGGGTAAAAATGGAATTTTTGGAG
Found at i:4411 original size:59 final size:59
Alignment explanation
Indices: 4050--4411 Score: 333
Period size: 59 Copynumber: 6.2 Consensus size: 59
4040 GGGTGAAGTA
* * * *
4050 GTAA-TTTTGGAAAAATTCGGGGTTAAAAATGGGATTTTTAGG-AGTTCGAGGGTAAAATG
1 GTAATTTTTGG-AAGATTTGGGGTCAAAAATGGGATTTTT-GGAAGTTCGGGGGTAAAATG
* ** * * * *
4109 GAAATTTTTAAAAGTTTTGTGGTCAAAAATGGGATTTTTGGAAATT-TGGGGTAAAATG
1 GTAATTTTTGGAAGATTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATG
* * * * * * *
4167 ATAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGAAAGTTTGAGGGTAAAAAT-
1 GTAATTTTTGGAAGATTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT-AAAATG
* * * * **
4226 GAAATTTTTGGAAG-TTTCGAGGTC-AAAATGAGATTTTTGGGAGTTTAGGGGTAAAATG
1 GTAATTTTTGGAAGATTT-GGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATG
* * * * * *
4284 GTAATTTTT-AAACAATCTAGGGGTCAAAAATGGGATTTTTGAAAGTTCGGGGATAAAAAG
1 GTAATTTTTGGAA-GAT-TTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATG
* *
4344 GAAATTTTTGGAAGATTTGGGGTCAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATG
1 GTAATTTTTGGAAGATTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATG
4403 GTAATTTTT
1 GTAATTTTT
4412 AGACAGTCTA
Statistics
Matches: 238, Mismatches: 54, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
57 7 0.03
58 81 0.34
59 101 0.42
60 47 0.20
61 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (59 bp):
GTAATTTTTGGAAGATTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATG
Found at i:6032 original size:6 final size:6
Alignment explanation
Indices: 6023--6099 Score: 51
Period size: 6 Copynumber: 13.7 Consensus size: 6
6013 TTAAATGAAT
*
6023 TTTAAA TTTAAA TTCATAA --TAAA TTTAAA --TAAA TTTAAA TTTAAGA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
* * *
6069 --TAAA CTTAAT TTTAAA -ATAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
6100 TTGGGCCCAG
Statistics
Matches: 55, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
4 7 0.13
5 8 0.15
6 37 0.67
7 3 0.05
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:6035 original size:17 final size:16
Alignment explanation
Indices: 6013--6099 Score: 66
Period size: 17 Copynumber: 5.2 Consensus size: 16
6003 TATATATATA
6013 TTAAATGAATTTTAAAT
1 TTAAAT-AATTTTAAAT
* **
6030 TTAAATTCATAATAAAT
1 TTAAA-TAATTTTAAAT
*
6047 TTAAATAAATTTAAAT
1 TTAAATAATTTTAAAT
** *
6063 TTAAGATAAACTTAATT
1 TTAA-ATAATTTTAAAT
*
6080 TTAAAATAAATTTAAAT
1 TT-AAATAATTTTAAAT
6097 TTA
1 TTA
6100 TTGGGCCCAG
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
16 12 0.21
17 41 0.73
18 3 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
TTAAATAATTTTAAAT
Found at i:6071 original size:27 final size:27
Alignment explanation
Indices: 6025--6077 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
6015 AAATGAATTT
*
6025 TAAATTTAAATTCATAATAAATTTAAA
1 TAAATTTAAATTCATAATAAACTTAAA
*
6052 TAAATTTAAATTTA-AGATAAACTTAA
1 TAAATTTAAATTCATA-ATAAACTTAA
6078 TTTTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (27 bp):
TAAATTTAAATTCATAATAAACTTAAA
Done.