Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009746.1 Kokia drynarioides strain JFW-HI SEQ_124465, 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: 27597
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Found at i:1651 original size:18 final size:18
Alignment explanation
Indices: 1619--1654 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1609 ATTTATTTTA
1619 AATATATTTATAATATAT
1 AATATATTTATAATATAT
1637 AATATGATTTA-AATATAT
1 AATAT-ATTTATAATATAT
1655 TTTTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AATATATTTATAATATAT
Found at i:2529 original size:96 final size:95
Alignment explanation
Indices: 2353--2536 Score: 239
Period size: 96 Copynumber: 1.9 Consensus size: 95
2343 GAAAAGGATG
** **
2353 TTCGATTATCTCGATTGAAGAAATGTTGTACCTAGTAAGTTAAGGAGCAAATTTTCAGAATCGAA
1 TTCGATTATCTCGATTGAAGAAAAATTACACCTAGTAAGTTAAGGAGCAAATTTTCAGAATCGAA
*
2418 GATAAGGAAACATTGCCTCGATTAAGGGTA
66 GATAAAGAAACATTGCCTCGATTAAGGGTA
* *
2448 TTCGATTATTTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACTC
1 TTCGATTATCTCGA-TTGAAGAAAAATTACACCTAGTAAGTTAAGGAGCAAATTTTCAG-AA-TC
*
2512 GAA-ATAAA-AGAATATTGCCTCGATT
63 GAAGATAAAGA-AACATTGCCTCGATT
2537 TTAAAGTTTT
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
95 15 0.19
96 57 0.74
97 5 0.06
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (95 bp):
TTCGATTATCTCGATTGAAGAAAAATTACACCTAGTAAGTTAAGGAGCAAATTTTCAGAATCGAA
GATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:2787 original size:28 final size:28
Alignment explanation
Indices: 2756--2817 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
2746 AAATGAGACT
2756 TTTTGGATACTCGAGAGA-AAAATGGTAA
1 TTTTGGATACTC-AGAGACAAAATGGTAA
** * *
2784 TTTTGTTTTCTCAGGGACAAAATGGTAA
1 TTTTGGATACTCAGAGACAAAATGGTAA
2812 TTTTGG
1 TTTTGG
2818 GAAAATTTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 4 0.14
28 24 0.86
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (28 bp):
TTTTGGATACTCAGAGACAAAATGGTAA
Found at i:2933 original size:30 final size:30
Alignment explanation
Indices: 2901--3123 Score: 118
Period size: 29 Copynumber: 7.4 Consensus size: 30
2891 AAAATATAAT
2901 TTTTTGGATA-TTCGAGGGTAAAATGGTAA
1 TTTTTGGATAGTTCGAGGGTAAAATGGTAA
*
2930 TTTTT-GAAAGTTTCGA-GGTCAAAAATGG--A
1 TTTTTGGATAG-TTCGAGGGT--AAAATGGTAA
*
2959 TTTTTGGA-AGTTTGAGGGTAAAATGGTAA
1 TTTTTGGATAGTTCGAGGGTAAAATGGTAA
* *
2988 TTTTTGGATTCGAAAGTTTTG-GGGTTTAAAATGAT-A
1 TTTTTGGA-T----AG-TTCGAGGG--TAAAATGGTAA
*
3024 TTTTTGGA-AGTTTGAGGGTAAAAAT-GTAA
1 TTTTTGGATAGTTCGAGGGT-AAAATGGTAA
*
3053 -TTTTGGA-AGTTTCAAGGGTAAAAAT-GTAA
1 TTTTTGGATAG-TTCGAGGGT-AAAATGGTAA
* *
3082 TTTTTGGA-AGTTTTGA-GGTCAAAAT-ATAA
1 TTTTTGGATAG-TTCGAGGGT-AAAATGGTAA
3111 TTTTTGGATAGTT
1 TTTTTGGATAGTT
3124 TAGAGACCTC
Statistics
Matches: 161, Mismatches: 10, Indels: 46
0.74 0.05 0.21
Matches are distributed among these distances:
27 7 0.04
28 18 0.11
29 76 0.47
30 27 0.17
31 7 0.04
35 5 0.03
36 13 0.08
37 8 0.05
ACGTcount: A:0.32, C:0.03, G:0.26, T:0.40
Consensus pattern (30 bp):
TTTTTGGATAGTTCGAGGGTAAAATGGTAA
Found at i:2981 original size:58 final size:58
Alignment explanation
Indices: 2901--3116 Score: 174
Period size: 58 Copynumber: 3.6 Consensus size: 58
2891 AAAATATAAT
* *
2901 TTTTTGGATA-TTCGAGGGT-AAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAAATG-GA
1 TTTTTGGA-AGTTTGAGGGTAAAAAT-GTAATTTTTGAAAGTTTCGAGGT-AAAAATGAAA
* * * *
2959 TTTTTGGAAGTTTGAGGGT-AAAATGGTAATTTTTGGATTCGAAAGTTTTGGGGTTTAAAATGAT
1 TTTTTGGAAGTTTGAGGGTAAAAAT-GTAA--TTT---TT-GAAAGTTTCGAGG-TAAAAATGAA
3023 A
58 A
* * *
3024 TTTTTGGAAGTTTGAGGGTAAAAATGTAA-TTTTGGAAGTTTCAAGGGTAAAAATGTAA
1 TTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTGAAAGTTTCGA-GGTAAAAATGAAA
* *
3082 TTTTTGGAAGTTTTGA-GGTCAAAATATAATTTTTG
1 TTTTTGGAAG-TTTGAGGGTAAAAATGTAATTTTTG
3117 GATAGTTTAG
Statistics
Matches: 131, Mismatches: 14, Indels: 25
0.77 0.08 0.15
Matches are distributed among these distances:
57 1 0.01
58 62 0.47
59 14 0.11
60 3 0.02
62 2 0.02
63 2 0.02
64 17 0.13
65 25 0.19
66 5 0.04
ACGTcount: A:0.32, C:0.03, G:0.25, T:0.40
Consensus pattern (58 bp):
TTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGGTAAAAATGAAA
Found at i:4213 original size:18 final size:16
Alignment explanation
Indices: 4184--4217 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4174 TATTAATTAT
4184 TTAATAAATATTATCA
1 TTAATAAATATTATCA
*
4200 TTAATAAA-ATTATTA
1 TTAATAAATATTATCA
4215 TTA
1 TTA
4218 TTATCATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAATAAATATTATCA
Found at i:4219 original size:24 final size:24
Alignment explanation
Indices: 4192--4237 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
4182 ATTTAATAAA
4192 TATTATCATTAATAAAATTATTAT
1 TATTATCATTAATAAAATTATTAT
*
4216 TATTATCATTAATGAAATTATT
1 TATTATCATTAATAAAATTATT
4238 TAATATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
TATTATCATTAATAAAATTATTAT
Found at i:4220 original size:18 final size:17
Alignment explanation
Indices: 4172--4220 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
4162 TCTCTTTTTT
4172 ATTATTAATTATTTAATAA
1 ATTATT-ATTA-TTAATAA
*
4191 A-TATTATCATTAATAAA
1 ATTATTATTATTAAT-AA
4208 ATTATTATTATTA
1 ATTATTATTATTA
4221 TCATTAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 6 0.23
18 14 0.54
19 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATTATTATTAATAA
Found at i:5083 original size:16 final size:16
Alignment explanation
Indices: 5048--5105 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 16
5038 AATTATTTCA
5048 AATTT-AAACTAAATTTT
1 AATTTAAAAC-AAA-TTT
5065 AATTTAAAACAAATTT
1 AATTTAAAACAAATTT
**
5081 AATTTAAAATGAATTT
1 AATTTAAAACAAATTT
5097 AAATTTAAA
1 -AATTTAAA
5106 TTTAAAGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 17 0.46
17 16 0.43
18 4 0.11
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (16 bp):
AATTTAAAACAAATTT
Found at i:5103 original size:6 final size:6
Alignment explanation
Indices: 5012--5126 Score: 64
Period size: 6 Copynumber: 19.8 Consensus size: 6
5002 TTTATTTTTG
* * * *
5012 ATTTAA TTTTAA AGTTTTAA GTTTAA AATT-- ATTTCAA ATTTAA A-CTAA
1 ATTTAA ATTTAA A--TTTAA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA
* ** * *
5060 ATTTTA ATTTAA A-ACAA ATTT-A ATTTAA A-ATGA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
5105 ATTTAA A-GTAA ATTTAA ATTTA
1 ATTTAA ATTTAA ATTTAA ATTTA
5127 GAAATAAATC
Statistics
Matches: 79, Mismatches: 20, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
4 3 0.04
5 19 0.24
6 48 0.61
7 4 0.05
8 5 0.06
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (6 bp):
ATTTAA
Found at i:5111 original size:23 final size:23
Alignment explanation
Indices: 5075--5126 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
5065 AATTTAAAAC
*
5075 AAATTT-AATTTAAAATGAATTT
1 AAATTTAAATTTAAAATAAATTT
*
5097 AAATTTAAATTTAAAGTAAATTT
1 AAATTTAAATTTAAAATAAATTT
5120 AAATTTA
1 AAATTTA
5127 GAAATAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
AAATTTAAATTTAAAATAAATTT
Found at i:5140 original size:18 final size:17
Alignment explanation
Indices: 5027--5105 Score: 81
Period size: 17 Copynumber: 4.7 Consensus size: 17
5017 ATTTTAAAGT
* *
5027 TTTAAGTTTAAAAT-TA
1 TTTAAATTTAAAATAAA
*
5043 TTTCAAATTTAAACTAAA
1 TTT-AAATTTAAAATAAA
* *
5061 TTTTAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
*
5078 TTT-AATTTAAAATGAA
1 TTTAAATTTAAAATAAA
5094 TTTAAATTTAAA
1 TTTAAATTTAAA
5106 TTTAAAGTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
16 17 0.33
17 31 0.60
18 4 0.08
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:7515 original size:30 final size:31
Alignment explanation
Indices: 7465--7538 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
7455 AAGAATTTTG
** * *
7465 AATAGTTTAGTGACTTAAATG-AAAGTTTCA
1 AATAGTTTAGTGACCAAAATGTAAAATTGCA
* *
7495 AATGGTTTAGTGACCAAAATGTAAAATTGCT
1 AATAGTTTAGTGACCAAAATGTAAAATTGCA
7526 AATAGTTTAGTGA
1 AATAGTTTAGTGA
7539 TTTTGGCTGT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 18 0.50
31 18 0.50
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35
Consensus pattern (31 bp):
AATAGTTTAGTGACCAAAATGTAAAATTGCA
Found at i:16033 original size:20 final size:21
Alignment explanation
Indices: 16008--16047 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
15998 ATTTTTTTAT
*
16008 ATTTTTAAA-ATAATATTTTG
1 ATTTTTAAAGAGAATATTTTG
16028 ATTTTTAAAGAGAATATTTT
1 ATTTTTAAAGAGAATATTTT
16048 AAAAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
ATTTTTAAAGAGAATATTTTG
Found at i:16071 original size:15 final size:15
Alignment explanation
Indices: 16051--16081 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
16041 ATATTTTAAA
16051 AAAATTATATTTTTT
1 AAAATTATATTTTTT
16066 AAAATTATATTTTTT
1 AAAATTATATTTTTT
16081 A
1 A
16082 TTTAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AAAATTATATTTTTT
Found at i:19989 original size:15 final size:15
Alignment explanation
Indices: 19969--20000 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19959 TAAAGCAAAT
19969 TTAAAAATAAAAAAA
1 TTAAAAATAAAAAAA
*
19984 TTAAAATTAAAAAAA
1 TTAAAAATAAAAAAA
19999 TT
1 TT
20001 CCTCTCAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TTAAAAATAAAAAAA
Found at i:20649 original size:2 final size:2
Alignment explanation
Indices: 20644--20672 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20634 ATATATATAT
20644 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
20673 TATCCTGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.