Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013513.1 Kokia drynarioides strain JFW-HI SEQ_128539, 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: 20818
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:740 original size:171 final size:171
Alignment explanation
Indices: 434--772 Score: 461
Period size: 171 Copynumber: 2.0 Consensus size: 171
424 CACACGAGCA
* * * *
434 TGTGCCTAGAGCACGTTTAAAAACAGTATAGATGCAGTTTTTACACGGGCAAACACACTGCCAGG
1 TGTGCCCAGAGCACGTTTAAAAACAGTATAGATGCAGTTTTTACACGAGCAAACACACGGCCAGC
* * *
499 GATACAGCTATGTGAAGGAACTTCGAATGTCACACGCGCTAACACACGGACTACGACACGACTGT
66 GATACAGCCATGTGAAGGAACTTCGAATGTCACACGCGCTAACACACGGACTACGACACAACTAT
564 GTGACCCAAATCAAAGAGTTACACAGTCCATGCACACGGGG
131 GTGACCCAAATCAAAGAGTTACACAGTCCATGCACACGGGG
** * * *
605 TGTGCCCAGAGCGTGTTTAAAAATAGTATAGGTGCAGTTTTTACACGAG-AAGACACACGGCTAG
1 TGTGCCCAGAGCACGTTTAAAAACAGTATAGATGCAGTTTTTACACGAGCAA-ACACACGGCCAG
* *
669 CGATACGGCCATGTGAAGGAACTTCGAATGTCACACAG-GCTAGCACAC-GACCTACGACACAA-
65 CGATACAGCCATGTGAAGGAACTTCGAATGTCACAC-GCGCTAACACACGGA-CTACGACACAAC
* * *
731 TCATGTGACCCAAATCAGAGAGTTACACGGTCCATTCACACG
128 T-ATGTGACCCAAATCAAAGAGTTACACAGTCCATGCACACG
773 AGTGCGTGAG
Statistics
Matches: 147, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
170 5 0.03
171 141 0.96
172 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.20
Consensus pattern (171 bp):
TGTGCCCAGAGCACGTTTAAAAACAGTATAGATGCAGTTTTTACACGAGCAAACACACGGCCAGC
GATACAGCCATGTGAAGGAACTTCGAATGTCACACGCGCTAACACACGGACTACGACACAACTAT
GTGACCCAAATCAAAGAGTTACACAGTCCATGCACACGGGG
Found at i:2556 original size:16 final size:16
Alignment explanation
Indices: 2536--2579 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2526 GGTATTTTTT
2536 ATTTAAATTATTTCGA
1 ATTTAAATTATTTCGA
* *
2552 GTTTAAA-TATTTTGA
1 ATTTAAATTATTTCGA
*
2567 ATTCAAATTATTT
1 ATTTAAATTATTT
2580 TTTTGGGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (16 bp):
ATTTAAATTATTTCGA
Found at i:4311 original size:84 final size:84
Alignment explanation
Indices: 4160--4318 Score: 212
Period size: 84 Copynumber: 1.9 Consensus size: 84
4150 ATTATAAATT
* ** * * *
4160 TTAAAAGAATTAAAGTGTAGTTTTATCACTGTATTAATTTATTATTTCAAACTTTTAAAAGAGAT
1 TTAAAAGAATCAAAGTGTAAATTTATCAATATATTAATTTATAATTTCAAACTTTTAAAAGAGAT
*
4225 TAAACTAAAATTTATCATA
66 TAAAATAAAATTTATCATA
* * *
4244 TTAAAAGTATCAAAGTGTAAATTTATCAATATATTAATTTATAATTTTATAATTTTTAAAAGA-A
1 TTAAAAGAATCAAAGTGTAAATTTATCAATATATTAATTTATAATTTCA-AACTTTTAAAAGAGA
4308 TTAAAATAAAA
65 TTAAAATAAAA
4319 ATTGAATATT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
84 52 0.81
85 12 0.19
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (84 bp):
TTAAAAGAATCAAAGTGTAAATTTATCAATATATTAATTTATAATTTCAAACTTTTAAAAGAGAT
TAAAATAAAATTTATCATA
Found at i:6490 original size:59 final size:58
Alignment explanation
Indices: 6427--7076 Score: 561
Period size: 59 Copynumber: 11.0 Consensus size: 58
6417 TTTTGGATAC
** * *
6427 TCGGGGGT-AAAATGGTAACTTTTAAAAGTTTTAGTGTTAAAAATGGAATTTTTGGAAGT
1 TCGGGGGTAAAAATGG-AA-TTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGT
* * * *
6486 TCGGGGCTAAAAATGGAATTTTTGGAAGTTTCATGGTCAAAAATGGGATTTTTGGAAGT
1 TCGGGGGTAAAAATGGAA-TTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGT
* ** * * * * *
6545 TCGAGGGTAAAAATGGTAATTTTGGGAA-AATTCGAGGTTAAAAATGGAAATTTT-AAACAT
1 TCGGGGGTAAAAATGG-AATTTT-GGAAGTTTTAG-GGTCAAAAATGGAATTTTTGGAA-GT
** * * * *
6605 TTAGGGGT-AAAATGGTAATTTT--AAGAGTTTCGAGGTCGAAAATGGAGTTTTTGGACA-T
1 TCGGGGGTAAAAATGG-AATTTTGGAAG-TTTTAG-GGTCAAAAATGGAATTTTTGGA-AGT
* ** * ** *
6663 TTGGGGGT-AAAATGGTAATTTTAAAAAGTTTCAGTATTAAAAATGGAATTTTTGGAAGT
1 TCGGGGGTAAAAATGG-AATTTT-GGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGT
* * * *
6722 TTGAGGCTAAAAATGGAATTTTTGGAAG-TTTAGGGGTCAAAAATGGGATTTTTGGAAGT
1 TCGGGGGTAAAAATGGAA-TTTTGGAAGTTTTA-GGGTCAAAAATGGAATTTTTGGAAGT
**
6781 TCGGGGGTAAAAATAAAATTCTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGT
1 TCGGGGGTAAAAATGGAATT-TTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGT
*
6840 TCAGGGGTAAAAATGGAATTCTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGT
1 TCGGGGGTAAAAATGGAATT-TTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGT
* * * *
6899 TCGAGGGTAAAAAAGGAATTCTTGGAAGTTTTAGGGTCTAAAATAGAATTTTTGGAAGT
1 TCGGGGGTAAAAATGGAATT-TTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGT
* *
6958 TTGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGT-AAAAATGGAATTTTTGGAAGTT
1 TCGGGGGTAAAAATGGAA-TTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAG-T
** * * * *
7017 TTAGGGTTAAAAAT-AAGATTTCTGGAAG-TTCAGGGGT-ACAAATGGAATTTTTGGATAGT
1 TCGGGGGTAAAAATGGA-ATTT-TGGAAGTTTTA-GGGTCAAAAATGGAATTTTTGGA-AGT
7076 T
1 T
7077 TAGGGACCCT
Statistics
Matches: 494, Mismatches: 73, Indels: 48
0.80 0.12 0.08
Matches are distributed among these distances:
56 2 0.00
58 73 0.15
59 358 0.72
60 58 0.12
61 3 0.01
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (58 bp):
TCGGGGGTAAAAATGGAATTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGT
Found at i:6624 original size:28 final size:28
Alignment explanation
Indices: 6585--6687 Score: 84
Period size: 28 Copynumber: 3.6 Consensus size: 28
6575 TTCGAGGTTA
*
6585 AAAATGGAAATTTTAAACATTTAGGGGT
1 AAAATGGTAATTTTAAACATTTAGGGGT
* * *
6613 AAAATGGTAATTTTAAGA-GTTTCGAGGT
1 AAAATGGTAATTTTAA-ACATTTAGGGGT
* ** *
6641 CGAAAATGG-AGTTTTTGGACATTTGGGGGT
1 --AAAATGGTA-ATTTTAAACATTTAGGGGT
6671 AAAATGGTAATTTTAAA
1 AAAATGGTAATTTTAAA
6688 AAGTTTCAGT
Statistics
Matches: 56, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
28 34 0.61
29 4 0.07
30 18 0.32
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (28 bp):
AAAATGGTAATTTTAAACATTTAGGGGT
Found at i:6650 original size:58 final size:58
Alignment explanation
Indices: 6575--6686 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 58
6565 TTTGGGAAAA
*
6575 TTCGAGGTTAAAAATGGAAATTTTAAACATTTAGGGGTAAAATGGTAATTTTAAGAGT
1 TTCGAGGTCAAAAATGGAAATTTTAAACATTTAGGGGTAAAATGGTAATTTTAAGAGT
* ** ** *
6633 TTCGAGGTCGAAAATGGAGTTTTTGGACATTTGGGGGTAAAATGGTAATTTTAA
1 TTCGAGGTCAAAAATGGAAATTTTAAACATTTAGGGGTAAAATGGTAATTTTAA
6687 AAAGTTTCAG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (58 bp):
TTCGAGGTCAAAAATGGAAATTTTAAACATTTAGGGGTAAAATGGTAATTTTAAGAGT
Found at i:6855 original size:236 final size:229
Alignment explanation
Indices: 6403--7081 Score: 733
Period size: 236 Copynumber: 2.9 Consensus size: 229
6393 GCGATCGGGT
* *
6403 TCGAAAATGAGATTTTTTGGATACTCGGGGGTAAAATGGTAACTTTTAAAAGTTTTAGTGTTAAA
1 TCGAAAATG-GAATTTTTGGA-ATTCGGGGGTAAAATGGTAA-TTTTAAAAGTTTTAGTGTTAAA
* * *
6468 AATGGAATTTTTGGAAGTTCGGGGCTAAAAATGGAATTTTTGGAAGTTTCATGGTCAAAAATGGG
63 AATGGAATTTTTGGAAGTTTGAGGCTAAAAATGGAATTTTTGGAAGTTT-AGGGTCAAAAATGGG
* ** * * * *
6533 ATTTTTGGAAGTTCGAGGGTAAAAATGGTAATTTTGGGAAAATTCGAGGTTAAAAATGGAAATTT
127 ATTTTTGGAAGTTCGGGGGTAAAAAT-AAAATTTT-GG-AAGTT-TAGGGTAAAAATGGAATTTT
* *
6598 T-AAACATTTAGGGGTAAAATGGTAATT-TTA-AGAGTTTCGA-GG
188 TGGAA-GTTTAGGGGTAAAATGG-AATTCTTAGA-AGTTT-GAGGG
* * * *
6640 TCGAAAATGGAGTTTTTGGACATTTGGGGGTAAAATGGTAATTTTAAAAAGTTTCAGTATTAAAA
1 TCGAAAATGGAATTTTTGGA-ATTCGGGGGTAAAATGGTAATTTT-AAAAGTTTTAGTGTTAAAA
6705 ATGGAATTTTTGGAAGTTTGAGGCTAAAAATGGAATTTTTGGAAGTTTAGGGGTCAAAAATGGGA
64 ATGGAATTTTTGGAAGTTTGAGGCTAAAAATGGAATTTTTGGAAGTTTA-GGGTCAAAAATGGGA
6770 TTTTTGGAAGTTCGGGGGTAAAAATAAAATTCTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTG
128 TTTTTGGAAGTTCGGGGGTAAAAATAAAATT-TTGGAAG-TTTAGGGT-AAAAATGGAATTTTTG
* * *
6835 GAAGTTCAGGGGTAAAAATGGAATTCTTGGAAGTTTTAGGG
190 GAAGTTTAGGGGT-AAAATGGAATTCTTAGAAGTTTGAGGG
* * * ** *
6876 TCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAAGG-AATTCTTGGAAGTTTTAGGGTCT-A
1 TCGAAAATGGAATTTTTGGAA-TTCGGGGGT-AAAATGGTAATT-TTAAAAGTTTTAGTGT-TAA
* *
6939 AAATAGAATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGT-AAAAATGG
62 AAATGGAATTTTTGGAAGTTTGAGGCTAAAAATGGAATTTTTGGAAG-TTTAGGGTCAAAAATGG
* ** * * * *
7003 AATTTTTGGAAGTTTTAGGGTTAAAAATAAGATTTCTGGAAGTTCAGGGGTACAAATGGAATTTT
126 GATTTTTGGAAG-TTCGGGGGTAAAAATAAAATTT-TGGAAGTTTA-GGGTAAAAATGGAATTTT
7068 TGGATAGTTTAGGG
188 TGGA-AGTTTAGGG
7082 ACCCTCGAGA
Statistics
Matches: 382, Mismatches: 41, Indels: 39
0.83 0.09 0.08
Matches are distributed among these distances:
234 6 0.02
235 81 0.21
236 272 0.71
237 23 0.06
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (229 bp):
TCGAAAATGGAATTTTTGGAATTCGGGGGTAAAATGGTAATTTTAAAAGTTTTAGTGTTAAAAAT
GGAATTTTTGGAAGTTTGAGGCTAAAAATGGAATTTTTGGAAGTTTAGGGTCAAAAATGGGATTT
TTGGAAGTTCGGGGGTAAAAATAAAATTTTGGAAGTTTAGGGTAAAAATGGAATTTTTGGAAGTT
TAGGGGTAAAATGGAATTCTTAGAAGTTTGAGGG
Found at i:9040 original size:17 final size:16
Alignment explanation
Indices: 9000--9098 Score: 83
Period size: 17 Copynumber: 5.8 Consensus size: 16
8990 TAAATTTGGA
*
9000 AAATAAATTTGAACTT-
1 AAATAAATTT-AAATTC
9016 AAATTAAATTTAAATTC
1 AAA-TAAATTTAAATTC
9033 GAAATAAATTTAAATTC
1 -AAATAAATTTAAATTC
9050 AATATAAATTTAAATTTC
1 AA-ATAAATTTAAA-TTC
* ** *
9068 TAAACAAATTTATTCTTA
1 -AAATAAATTTA-AATTC
9086 AAATAAATTTAAA
1 AAATAAATTTAAA
9099 GGGAGTTTGG
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
16 9 0.13
17 41 0.60
18 16 0.24
19 2 0.03
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (16 bp):
AAATAAATTTAAATTC
Found at i:9041 original size:34 final size:34
Alignment explanation
Indices: 8989--9098 Score: 114
Period size: 35 Copynumber: 3.1 Consensus size: 34
8979 TATAATAATC
*
8989 TTAAATTTGGAAAATAAATTTGAACTTAAATTAAAT
1 TTAAATTTCG-AAATAAATTT-AACTTAAATTAAAT
* *
9025 TTAAA-TTCGAAATAAATTTAAATTCAATATAAAT
1 TTAAATTTCGAAATAAATTTAACTTAAAT-TAAAT
* * * *
9059 TTAAATTTCTAAACAAATTTATTCTTAAAATAAAT
1 TTAAATTTCGAAATAAATTTA-ACTTAAATTAAAT
9094 TTAAA
1 TTAAA
9099 GGGAGTTTGG
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
33 7 0.11
34 20 0.32
35 26 0.42
36 9 0.15
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (34 bp):
TTAAATTTCGAAATAAATTTAACTTAAATTAAAT
Found at i:10660 original size:27 final size:27
Alignment explanation
Indices: 10607--10666 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
10597 TCAAAAATTT
* *
10607 TATTAAGAAGAGGATCAGAAGATACAA
1 TATTAAAAAGAGGATCAGAAGAAACAA
10634 TATTAAAAAGAGGATCA-AAGGAAACAA
1 TATTAAAAAGAGGATCAGAA-GAAACAA
10661 TCATTA
1 T-ATTA
10667 GTTGAAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.20
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAGAAGAAACAA
Found at i:20668 original size:18 final size:18
Alignment explanation
Indices: 20642--20698 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
20632 TTTATTTGTC
*
20642 ATTAATATTATAAATATT
1 ATTATTATTATAAATATT
*
20660 ATTATTATTA-AGAA-AAT
1 ATTATTATTATA-AATATT
20677 ATTTATTATTAATAAATATT
1 A-TTATTATT-ATAAATATT
20697 AT
1 AT
20699 GAAAACCGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
17 4 0.13
18 19 0.61
19 4 0.13
20 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATTATTATTATAAATATT
Done.