Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013134.1 Kokia drynarioides strain JFW-HI SEQ_128153, 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: 10639
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:3684 original size:28 final size:29
Alignment explanation
Indices: 3629--3685 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3619 AAGTAGCATA
* * *
3629 TAAATATAAATAAACAAAAGAGATTAAAT
1 TAAATAGAAAAAAAAAAAAGAGATTAAAT
*
3658 TAAATAGAAAAAAAAAAAAG-GCTTAAAT
1 TAAATAGAAAAAAAAAAAAGAGATTAAAT
3686 CGAAAAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.21
Consensus pattern (29 bp):
TAAATAGAAAAAAAAAAAAGAGATTAAAT
Found at i:3805 original size:14 final size:14
Alignment explanation
Indices: 3775--3850 Score: 61
Period size: 14 Copynumber: 5.5 Consensus size: 14
3765 ACTAAATTTA
* *
3775 AAATAAAATTAAGT
1 AAATAAAATAAAAT
3789 AAATAAAATAAAAT
1 AAATAAAATAAAAT
*
3803 AAA-AACCAT-AAAT
1 AAATAA-AATAAAAT
*
3816 AGATACAAATAAAAT
1 AAATA-AAATAAAAT
3831 -AATAAAA-ATAAAT
1 AAATAAAATA-AAAT
3844 AAATAAA
1 AAATAAA
3851 TAATAGAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
12 1 0.02
13 15 0.30
14 29 0.58
15 5 0.10
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.21
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:3841 original size:28 final size:27
Alignment explanation
Indices: 3776--3850 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 27
3766 CTAAATTTAA
* *
3776 AATAAAATTAAGTAAATAAAATAAAAT
1 AATAAAAATAAATAAATAAAATAAAAT
* *
3803 AA-AAACCATAAATAGATACAAATAAAAT
1 AATAAA-AATAAATAAATA-AAATAAAAT
3831 AATAAAAATAAATAAATAAA
1 AATAAAAATAAATAAATAAA
3851 TAATAGAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 12 0.31
28 21 0.54
29 3 0.08
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.21
Consensus pattern (27 bp):
AATAAAAATAAATAAATAAAATAAAAT
Found at i:4374 original size:88 final size:87
Alignment explanation
Indices: 4225--4399 Score: 323
Period size: 88 Copynumber: 2.0 Consensus size: 87
4215 TGGTTCAGGT
*
4225 CGGATCTGAGTCGGGAGGCGTCAAACGATGTCGTTTTGAGCGTTTTAAGCCACAGCAAAAACGAT
1 CGGATCCGAGTCGGGAGGCGTCAAACGATGTCGTTTTGAGCGTTTTAAGCCACAGCAAAAACGAT
4290 GACGTTTTGGAGGGCTATATAA
66 GACGTTTTGGAGGGCTATATAA
*
4312 NCGGATCCGAGTCGGGTGGCGTCAAACGATGTCGTTTTGAGCGTTTTAAGCCACAGCAAAAACGA
1 -CGGATCCGAGTCGGGAGGCGTCAAACGATGTCGTTTTGAGCGTTTTAAGCCACAGCAAAAACGA
4377 TGACGTTTTGGAGGGCTATATAA
65 TGACGTTTTGGAGGGCTATATAA
4400 ACCAAAAACT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (87 bp):
CGGATCCGAGTCGGGAGGCGTCAAACGATGTCGTTTTGAGCGTTTTAAGCCACAGCAAAAACGAT
GACGTTTTGGAGGGCTATATAA
Found at i:5160 original size:12 final size:12
Alignment explanation
Indices: 5143--5169 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5133 GGTAAGCGAC
5143 GGTCAAAACTAG
1 GGTCAAAACTAG
5155 GGTCAAAACTAG
1 GGTCAAAACTAG
5167 GGT
1 GGT
5170 TTATAGATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.15, G:0.30, T:0.19
Consensus pattern (12 bp):
GGTCAAAACTAG
Found at i:5549 original size:50 final size:50
Alignment explanation
Indices: 5422--5727 Score: 224
Period size: 50 Copynumber: 6.1 Consensus size: 50
5412 CAAGGAGATC
* ** * * * * *
5422 AAGATTTGCTTCTATGGCTTTAATTTGCTCCTCTACAGTTTTAGGGGGTAT
1 AAGATTTACTTCTACAGCTTCAATTTGCCCCTCTACGGCTTTA-GAGGTAT
* * * * *
5473 AAGATTTGA-TTTTACAACTTTAATTTGCCCCTCTATGGCTTTAGAGGCAT
1 AAGATTT-ACTTCTACAGCTTCAATTTGCCCCTCTACGGCTTTAGAGGTAT
* ** *
5523 AAGATTTACTTCTACATCTTCAATTTGCCCCTCTACAACTGTAGAGGTAT
1 AAGATTTACTTCTACAGCTTCAATTTGCCCCTCTACGGCTTTAGAGGTAT
* ** *
5573 AAGATTTGCTTCTGTAGCTTCAATCTGCCCCTCTACGGCTTTAG-GAGTAT
1 AAGATTTACTTCTACAGCTTCAATTTGCCCCTCTACGGCTTTAGAG-GTAT
* * * * ** * *
5623 AAGATTTTCTTCTATAGCTTTAATTTGCCCCTTTACAACTTTAGGGGTAA
1 AAGATTTACTTCTACAGCTTCAATTTGCCCCTCTACGGCTTTAGAGGTAT
* * * * * * *
5673 AAGTTTTTGCTTCTGCAGCTTCAATCTGTCCCTCTA--GATTTAGGGGTAT
1 AAG-ATTTACTTCTACAGCTTCAATTTGCCCCTCTACGGCTTTAGAGGTAT
5722 AAGATT
1 AAGATT
5728 GGATGTAGTG
Statistics
Matches: 203, Mismatches: 47, Indels: 13
0.77 0.18 0.05
Matches are distributed among these distances:
48 2 0.01
49 15 0.07
50 128 0.63
51 58 0.29
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.40
Consensus pattern (50 bp):
AAGATTTACTTCTACAGCTTCAATTTGCCCCTCTACGGCTTTAGAGGTAT
Found at i:5613 original size:100 final size:101
Alignment explanation
Indices: 5498--5708 Score: 282
Period size: 100 Copynumber: 2.1 Consensus size: 101
5488 AACTTTAATT
* *
5498 TGCCCCTCTATGGCTTTA-GAGGCATAAGATTTACTTCTACATCTTCAATTTGCCCCTCTACAAC
1 TGCCCCTCTACGGCTTTAGGA-GCATAAGATTTACTTCTACAGCTTCAATTTGCCCCTCTACAAC
* *
5562 TGTAGAGGTATAAG-ATTTGCTTCTGTAGCTTCAATC
65 TGTAGAGGTAAAAGTATTTGCTTCTGCAGCTTCAATC
* * * * *
5598 TGCCCCTCTACGGCTTTAGGAGTATAAGATTTTCTTCTATAGCTTTAATTTGCCCCTTTACAACT
1 TGCCCCTCTACGGCTTTAGGAGCATAAGATTTACTTCTACAGCTTCAATTTGCCCCTCTACAACT
* * *
5663 TTAGGGGTAAAAGTTTTTGCTTCTGCAGCTTCAATC
66 GTAGAGGTAAAAGTATTTGCTTCTGCAGCTTCAATC
*
5699 TGTCCCTCTA
1 TGCCCCTCTA
5709 GATTTAGGGG
Statistics
Matches: 96, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
100 65 0.68
101 31 0.32
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (101 bp):
TGCCCCTCTACGGCTTTAGGAGCATAAGATTTACTTCTACAGCTTCAATTTGCCCCTCTACAACT
GTAGAGGTAAAAGTATTTGCTTCTGCAGCTTCAATC
Found at i:5761 original size:48 final size:47
Alignment explanation
Indices: 5690--6153 Score: 483
Period size: 46 Copynumber: 9.9 Consensus size: 47
5680 TGCTTCTGCA
* *
5690 GCTTCAATCTGTCCCTCTAGATTTAGGGGTATAAGATTGGATGTAGTG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGATGT-GTG
* * * *
5738 GCTTGAATCTGCCCCTTTGGATTTAGAGTTATAAGATTGGATGTGGTG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGATGT-GTG
* * * *
5786 GTTTCAATCTGCCCTTTTAGATTTAGGAGTATAAGATTGGATATGATG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGATGTG-TG
* * * * *
5834 ACTTTAATCTGTCCTTTTGGATTTAGGGGTATAAGATTGGATGTGGTG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGATGT-GTG
* * *
5882 GCTCCAATCTGCCCCTCTAGATTTAGGGGTATAAGATTCGATG-GTG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGATGTGTG
* * *
5928 ACTTCAATTTGCCCCTTTAGATTTAGGGGTATAAGATTGGATG-GCG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGATGTGTG
* *
5974 GCTTCAATCTACCCCTTTAGATTTAGGGGTATAAGATTAGATGT-TG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGATGTGTG
* ** * ** *
6020 GATTCAAT-TTTCCCTTCTGGATTTATCGATATAAGATTGGATG-GTG
1 GCTTCAATCTGCCCCTT-TAGATTTAGGGGTATAAGATTGGATGTGTG
* * * * *
6066 ACTTCAATCTGCCTCTTTGGATTTAGGGGTATAAGAACT-AATG-GTG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAG-ATTGGATGTGTG
* * *
6112 GCTTCAATCTACCCCTCTGGATTTAGGGGTATAAGATTGGAT
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGAT
6154 CGTGGCTACG
Statistics
Matches: 343, Mismatches: 65, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
45 8 0.02
46 173 0.50
47 8 0.02
48 153 0.45
49 1 0.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (47 bp):
GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGATGTGTG
Found at i:6371 original size:99 final size:99
Alignment explanation
Indices: 6163--6660 Score: 402
Period size: 99 Copynumber: 5.0 Consensus size: 99
6153 TCGTGGCTAC
* * * * *
6163 GTAAATTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCCGCTACTATATTTTTAATCGG
1 GTAACTTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATTCGCTACT-T-GTTTTAATCCG
* * *
6228 CTTCACTGCAACTTCAAGAAGATAGGATTTGGTGTG
64 ATTCACTGTAACTTCAAGGAGATAGGATTTGGTGTG
* *
6264 GTAACTTCACTCCATTCCACTGTAACTTCAAGGAGATTGA-AGTTCGTTACTTGTTTTAATCCGA
1 GTAACTTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGA-TTCGCTACTTGTTTTAATCCGA
* * * *
6328 TCCACTGTAAGTTCAAGGATATAGGATTTGAG-GTT
65 TTCACTGTAACTTCAAGGAGATAGGATTTG-GTGTG
** * * * * * *
6363 GTGGCTTCAATGCATTCCACTGCAACTT-TAGTAGATATTGAGATTTGCTACTTGTTTTACTCC-
1 GTAACTTCACTCCATTCCACTGCAACTTCAAG--GAGATTGAGATTCGCTACTTGTTTTAATCCG
*
6426 ACTTCACT-TCAACTT-TAGGAAGATAGGATTTGGTGTG
64 A-TTCACTGT-AACTTCAAGG-AGATAGGATTTGGTGTG
* * * * * * * * * *
6463 GTAACTTCGCTCTATTCTATTGTAACTTC-AGCGAGATCGAGGTCCGTTACTTGTTTTAATTCGA
1 GTAACTTCACTCCATTCCACTGCAACTTCAAG-GAGATTGAGATTCGCTACTTGTTTTAATCCGA
* * * *
6527 TTTACTGTAACTTCAGGGATATAGGATTTGAG-GTT
65 TTCACTGTAACTTCAAGGAGATAGGATTTG-GTGTG
** * * * *
6562 GTGGCTTTACTCCATTCCACTGCAACTTCAATAGAGATTGAGATTTGCTACTTGTTTTAATCCGC
1 GTAACTTCACTCCATTCCACTGCAACTTCAA-GGAGATTGAGATTCGCTACTTGTTTTAATCCGA
* * *
6627 TTCACTGCAACTTC-GGGAAGGTAGGATTTGGTGT
65 TTCACTGTAACTTCAAGG-AGATAGGATTTGGTGT
6661 TTCACTGGTC
Statistics
Matches: 307, Mismatches: 72, Indels: 37
0.74 0.17 0.09
Matches are distributed among these distances:
98 2 0.01
99 135 0.44
100 125 0.41
101 45 0.15
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (99 bp):
GTAACTTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATTCGCTACTTGTTTTAATCCGAT
TCACTGTAACTTCAAGGAGATAGGATTTGGTGTG
Found at i:6568 original size:199 final size:199
Alignment explanation
Indices: 6168--6660 Score: 666
Period size: 199 Copynumber: 2.5 Consensus size: 199
6158 GCTACGTAAA
* * ** * *
6168 TTCACTCCATTCCACTGCAACTTCAG-GGAGATTGAGATCCGCTACTATATTTTTAATCGGCTTC
1 TTCAATCCATTCCACTGCAACTTCAGTAGAGATTGAGATTTGCTACT-T-GTTTTAATCCGCTTC
*
6232 ACTGCAACTTCAAGAAGATAGGATTTGGTGTGGTAACTTCACTCCATTCCACTGTAACTTCAAGG
64 ACTGCAACTTCAGGAAGATAGGATTTGGTGTGGTAACTTCACTCCATTCCACTGTAACTTCAAGG
* * *
6297 AGATTGAAGTTCGTTACTTGTTTTAATCCGATCCACTGTAAGTTCAAGGATATAGGATTTGAGGT
129 AGATCGAAGTCCGTTACTTGTTTTAATCCGATCCACTGTAACTTCAAGGATATAGGATTTGAGGT
6362 TGTGGC
194 TGTGGC
* * * * *
6368 TTCAATGCATTCCACTGCAACTTTAGTAGATATTGAGATTTGCTACTTGTTTTACTCCACTTCAC
1 TTCAATCCATTCCACTGCAACTTCAGTAGAGATTGAGATTTGCTACTTGTTTTAATCCGCTTCAC
* * * * * *
6433 TTCAACTTTAGGAAGATAGGATTTGGTGTGGTAACTTCGCTCTATTCTATTGTAACTTC-AGCGA
66 TGCAACTTCAGGAAGATAGGATTTGGTGTGGTAACTTCACTCCATTCCACTGTAACTTCAAG-GA
* * ** *
6497 GATCGAGGTCCGTTACTTGTTTTAATTCGATTTACTGTAACTTCAGGGATATAGGATTTGAGGTT
130 GATCGAAGTCCGTTACTTGTTTTAATCCGATCCACTGTAACTTCAAGGATATAGGATTTGAGGTT
6562 GTGGC
195 GTGGC
* * *
6567 TTTACTCCATTCCACTGCAACTTCAATAGAGATTGAGATTTGCTACTTGTTTTAATCCGCTTCAC
1 TTCAATCCATTCCACTGCAACTTCAGTAGAGATTGAGATTTGCTACTTGTTTTAATCCGCTTCAC
* *
6632 TGCAACTTCGGGAAGGTAGGATTTGGTGT
66 TGCAACTTCAGGAAGATAGGATTTGGTGT
6661 TTCACTGGTC
Statistics
Matches: 253, Mismatches: 38, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
198 2 0.01
199 211 0.83
200 24 0.09
201 16 0.06
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (199 bp):
TTCAATCCATTCCACTGCAACTTCAGTAGAGATTGAGATTTGCTACTTGTTTTAATCCGCTTCAC
TGCAACTTCAGGAAGATAGGATTTGGTGTGGTAACTTCACTCCATTCCACTGTAACTTCAAGGAG
ATCGAAGTCCGTTACTTGTTTTAATCCGATCCACTGTAACTTCAAGGATATAGGATTTGAGGTTG
TGGC
Found at i:7465 original size:26 final size:26
Alignment explanation
Indices: 7427--7477 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
7417 CAACCTCTCT
*
7427 TTTTCCTTTTCCTTTTTCTCTTTTTTC
1 TTTTCCTTTTCC-TTTTCCCTTTTTTC
7454 TTTT-CTTTTCCTTTTCCCTTTTTT
1 TTTTCCTTTTCCTTTTCCCTTTTTT
7478 TTGGGGCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.52
26 7 0.30
27 4 0.17
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTCCTTTTCCTTTTCCCTTTTTTC
Found at i:7478 original size:26 final size:27
Alignment explanation
Indices: 7427--7477 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
7417 CAACCTCTCT
*
7427 TTTTCCTTTTCCTTTTTCTCTTTTTTC
1 TTTTCCTTTTCCTTTTCCTCTTTTTTC
7454 TTTT-CTTTTCCTTTTCC-CTTTTTT
1 TTTTCCTTTTCCTTTTCCTCTTTTTT
7478 TTGGGGCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.30
26 12 0.52
27 4 0.17
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTTCCTTTTCCTTTTCCTCTTTTTTC
Done.