Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009456.1 Kokia drynarioides strain JFW-HI SEQ_124163, 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: 15846
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:7720 original size:20 final size:19
Alignment explanation
Indices: 7692--7732 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
7682 CTTGATGGTT
*
7692 AACCGTTAAATCCAACGGTC
1 AACCATTAAATCCAAC-GTC
*
7712 AACCATTAAATCTAACGTC
1 AACCATTAAATCCAACGTC
7731 AA
1 AA
7733 AGGGCTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (19 bp):
AACCATTAAATCCAACGTC
Found at i:8140 original size:41 final size:40
Alignment explanation
Indices: 8082--8189 Score: 118
Period size: 38 Copynumber: 2.8 Consensus size: 40
8072 CGAAGAACTC
*
8082 CTTTTCTGTGACTTTTAATCAAAACGTCACGAAAAGTAGAATA
1 CTTTTCTGTGACGTTTAATCAAAACGTCAC-AAAA--AGAATA
* *
8125 -TTTT-TGTGACGTTTAAT-GAAACGTCACAAAAAGACTA
1 CTTTTCTGTGACGTTTAATCAAAACGTCACAAAAAGAATA
*
8162 CTTTTCTGTGATGTTT-A-CAAAACGTCAC
1 CTTTTCTGTGACGTTTAATCAAAACGTCAC
8190 TCATGATATG
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
37 5 0.09
38 14 0.25
39 13 0.23
40 9 0.16
41 12 0.21
42 4 0.07
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (40 bp):
CTTTTCTGTGACGTTTAATCAAAACGTCACAAAAAGAATA
Found at i:13031 original size:5 final size:5
Alignment explanation
Indices: 13023--13048 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
13013 TTCCTTCTAG
13023 TAAAT TAAAT TAAAT TAAAT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT T
13049 TGAATTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAAAT
Found at i:14505 original size:58 final size:58
Alignment explanation
Indices: 14443--14634 Score: 280
Period size: 59 Copynumber: 3.3 Consensus size: 58
14433 ACTCAAGGGC
* *
14443 AAAATGGTAATTTTTCGTGAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTCGGGAT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTCGGGGT
* * * *
14501 AAAATGGTAATTTTTGGTGAAATCAAGGTTAAAACTGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTC-GGGGT
14560 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAAA-TTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAAT-GAAATTTTGGAAAGTTCG-GGGT
14619 AAAAAT-GTAATTTTTG
1 -AAAATGGTAATTTTTG
14635 AAAGTTTAGG
Statistics
Matches: 120, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
58 49 0.41
59 63 0.52
60 8 0.07
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGAAATTTTGGAAAGTTCGGGGT
Found at i:14543 original size:30 final size:30
Alignment explanation
Indices: 14443--14603 Score: 115
Period size: 29 Copynumber: 5.4 Consensus size: 30
14433 ACTCAAGGGC
* *
14443 AAAATGGTAATTTTTCGTGAAATCGAGGTCA
1 AAAATGGTAATTTTTGGTGAAATCGAGGT-T
* *
14474 AAAAT-G-AAATTTT-G-GAAAGTTCG-GGAT
1 AAAATGGTAATTTTTGGTGAAA--TCGAGGTT
*
14501 AAAATGGTAATTTTTGGTGAAATCAAGGTT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTT
* *
14531 AAAACTGG-AA-TTTT-G-GAAAGTTCGGGGGT
1 AAAA-TGGTAATTTTTGGTGAAA--TCGAGGTT
*
14560 AAAATGGTAATTTTTGGTGAAATCGAGGTCA
1 AAAATGGTAATTTTTGGTGAAATCGAGGT-T
*
14591 AAAATGGAAATTT
1 AAAATGGTAATTT
14604 GGAAAGTTCG
Statistics
Matches: 102, Mismatches: 13, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
27 13 0.13
28 8 0.08
29 32 0.31
30 20 0.20
31 25 0.25
32 4 0.04
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTT
Found at i:14562 original size:29 final size:29
Alignment explanation
Indices: 14473--14649 Score: 100
Period size: 29 Copynumber: 6.1 Consensus size: 29
14463 AATCGAGGTC
* *
14473 AAAAATGAAATTTTGGAAAGTTC-GGGAT
1 AAAAATGGAATTTTGGAAAGTTCGGGGGT
** *
14501 -AAAATGGTAATTTTTGGTGAAA--TCAAGGTT
1 AAAAATGG-AA-TTTT-G-GAAAGTTCGGGGGT
*
14531 AAAACTGGAATTTTGGAAAGTTCGGGGGT
1 AAAAATGGAATTTTGGAAAGTTCGGGGGT
*
14560 -AAAATGGTAATTTTTGGTGAAA--TC-GAGGT
1 AAAAATGG-AA-TTTT-G-GAAAGTTCGGGGGT
* *
14589 CAAAAATGGAAATTTGGAAAGTTCGAGGGT
1 -AAAAATGGAATTTTGGAAAGTTCGGGGGT
* * **
14619 AAAAATGTAATTTTTGAAAGTTTAGGGGT
1 AAAAATGGAATTTTGGAAAGTTCGGGGGT
14648 AA
1 AA
14650 TATGGTAATT
Statistics
Matches: 114, Mismatches: 18, Indels: 33
0.69 0.11 0.20
Matches are distributed among these distances:
27 14 0.12
28 10 0.09
29 51 0.45
30 17 0.15
31 18 0.16
32 4 0.04
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (29 bp):
AAAAATGGAATTTTGGAAAGTTCGGGGGT
Found at i:14605 original size:88 final size:87
Alignment explanation
Indices: 14519--14681 Score: 229
Period size: 88 Copynumber: 1.9 Consensus size: 87
14509 AATTTTTGGT
* * * *
14519 GAAA-TCAAGGTTAAAACTGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAAT
1 GAAAGTCAAGGGTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTAGTGAAAT
14583 CGAGGTCAAAAATGGAAATTTG
66 CGAGGTCAAAAATGGAAATTTG
* * * * *
14605 GAAAGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTAGGGGTAATATGGTAATTTTTAGTGAAA
1 GAAAG-TCAAGGGTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTAGTGAAA
14670 TCGAGGTCAAAA
65 TCGAGGTCAAAA
14682 TATAATTTCT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
86 4 0.06
88 62 0.94
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.31
Consensus pattern (87 bp):
GAAAGTCAAGGGTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTAGTGAAAT
CGAGGTCAAAAATGGAAATTTG
Found at i:15750 original size:3 final size:3
Alignment explanation
Indices: 15738--15822 Score: 55
Period size: 3 Copynumber: 27.0 Consensus size: 3
15728 TCTTTTTTTG
*
15738 TTA TTAA TTA TTA TTAA ATA TATA TTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TT-A TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
15787 -AA TTCA TTA TTA CTG TTA TTA ATA ATA TTA TCA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15823 ATAATATTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
2 1 0.02
3 50 0.78
4 12 0.19
5 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:15795 original size:27 final size:27
Alignment explanation
Indices: 15738--15808 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
15728 TCTTTTTTTG
* *
15738 TTATTAATTATTATTAAATATATATTTA
1 TTATT-ATTATTATTAAATATAAATTCA
*
15766 TTATTATTATTATT-ATTATTAAATTCA
1 TTATTATTATTATTAAATA-TAAATTCA
* *
15793 TTATTACTGTTATTAA
1 TTATTATTATTATTAA
15809 TAATATTATC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 3 0.08
27 27 0.75
28 6 0.17
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (27 bp):
TTATTATTATTATTAAATATAAATTCA
Found at i:15816 original size:33 final size:32
Alignment explanation
Indices: 15736--15817 Score: 80
Period size: 33 Copynumber: 2.5 Consensus size: 32
15726 TTTCTTTTTT
*
15736 TGTTATTAAT-TATTATTAAATATATATTTAT
1 TGTTATTAATATATTATTAAATATATATTTAC
* *
15767 TATTATTATTATTATTATTAAAT-TCAT-TATTAC
1 TGTTATTAATA-TATTATTAAATAT-ATAT-TTAC
15800 TGTTATTAATAATATTAT
1 TGTTATTAAT-ATATTAT
15818 CATTAATAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
31 8 0.20
32 2 0.05
33 30 0.73
34 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (32 bp):
TGTTATTAATATATTATTAAATATATATTTAC
Found at i:15824 original size:12 final size:12
Alignment explanation
Indices: 15744--15835 Score: 68
Period size: 12 Copynumber: 7.8 Consensus size: 12
15734 TTTGTTATTA
15744 ATTATTATTAA-
1 ATTATTATTAAT
15755 A-TATATATT--T
1 ATTAT-TATTAAT
*
15765 ATTATTATTATT
1 ATTATTATTAAT
15777 ATTATTATTAA-
1 ATTATTATTAAT
*
15788 ATTCATTATTACT
1 ATT-ATTATTAAT
* *
15801 GTTATTAATAAT
1 ATTATTATTAAT
*
15813 ATTATCATTAAT
1 ATTATTATTAAT
*
15825 AATATTTATTA
1 ATTA-TTATTA
15836 GGTTATAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 14
0.72 0.11 0.16
Matches are distributed among these distances:
10 8 0.13
11 11 0.17
12 37 0.59
13 7 0.11
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.55
Consensus pattern (12 bp):
ATTATTATTAAT
Done.