Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015141.1 Kokia drynarioides strain JFW-HI SEQ_130185, 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: 15767
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:614 original size:33 final size:32
Alignment explanation
Indices: 563--662 Score: 119
Period size: 33 Copynumber: 3.0 Consensus size: 32
553 TCTCAACATA
*
563 AATGATTGGAACAACTATCAGGGCAGCTTCATC
1 AATGATT-GAACATCTATCAGGGCAGCTTCATC
596 AATGATTGAAACATCTATCAGGGCAGCTTCATC
1 AATGATTG-AACATCTATCAGGGCAGCTTCATC
* ** * *
629 ATTGATTTGAACATCTCCCGGGGCAACTTCATC
1 AATGA-TTGAACATCTATCAGGGCAGCTTCATC
662 A
1 A
663 TTCTGTTCGC
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
32 1 0.02
33 55 0.93
34 3 0.05
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (32 bp):
AATGATTGAACATCTATCAGGGCAGCTTCATC
Found at i:3647 original size:33 final size:33
Alignment explanation
Indices: 3605--3704 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
3595 TCTCAACATA
*
3605 AATGATTGGAACAGCTATCAGGGTAGCTTCATC
1 AATGATTGGAACATCTATCAGGGTAGCTTCATC
*
3638 AATGATTGGAACATCTATTAGGGTAGCTTCATC
1 AATGATTGGAACATCTATCAGGGTAGCTTCATC
* * * *
3671 AATGATTTGAACATCTCTCGGGGAAGCTTCATC
1 AATGATTGGAACATCTATCAGGGTAGCTTCATC
3704 A
1 A
3705 TTCTTTTCAC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (33 bp):
AATGATTGGAACATCTATCAGGGTAGCTTCATC
Found at i:6847 original size:59 final size:59
Alignment explanation
Indices: 6783--6912 Score: 163
Period size: 59 Copynumber: 2.2 Consensus size: 59
6773 GATCAAAATT
* *
6783 AAATTTTGGAAAGTTCGAGGGCCAAATTTGAATTTTTGGAAAG-TTCATGGGTCAAATCC
1 AAATTTTGGAAAGTTCGAGGGCCAAATCTAAATTTTTGGAAAGTTTCA-GGGTCAAATCC
* ** * * *
6842 AAATTTTGGAAAGTTTGAGGGTTAAATCTAAATTTTTGGGAAGTTTGAGGGTCAAATCT
1 AAATTTTGGAAAGTTCGAGGGCCAAATCTAAATTTTTGGAAAGTTTCAGGGTCAAATCC
*
6901 AAATTTTTGAAA
1 AAATTTTGGAAA
6913 AGTTTAGGGG
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 58 0.95
60 3 0.05
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (59 bp):
AAATTTTGGAAAGTTCGAGGGCCAAATCTAAATTTTTGGAAAGTTTCAGGGTCAAATCC
Found at i:6917 original size:30 final size:30
Alignment explanation
Indices: 6778--6927 Score: 166
Period size: 30 Copynumber: 5.1 Consensus size: 30
6768 AAAGGGATCA
* *
6778 AAAT-TAAA-TTTTGGAAAGTTCGAGGGCC
1 AAATCTAAATTTTTGGAAAGTTTGAGGGTC
* * *
6806 AAATTTGAATTTTTGGAAAG-TTCATGGGTC
1 AAATCTAAATTTTTGGAAAGTTTGA-GGGTC
* *
6836 AAATCCAAA-TTTTGGAAAGTTTGAGGGTT
1 AAATCTAAATTTTTGGAAAGTTTGAGGGTC
*
6865 AAATCTAAATTTTTGGGAAGTTTGAGGGTC
1 AAATCTAAATTTTTGGAAAGTTTGAGGGTC
*
6895 AAATCTAAATTTTTGAAAAGTTT-AGGGGTC
1 AAATCTAAATTTTTGGAAAGTTTGA-GGGTC
6925 AAA
1 AAA
6928 ATGTAATTTT
Statistics
Matches: 102, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
28 4 0.04
29 28 0.27
30 70 0.69
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (30 bp):
AAATCTAAATTTTTGGAAAGTTTGAGGGTC
Found at i:9598 original size:19 final size:19
Alignment explanation
Indices: 9549--9598 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
9539 TGTGGCAAAA
*
9549 ATTATAAAAAATATTAAAT
1 ATTATTAAAAATATTAAAT
* * *
9568 ATTAATATAAATATTTAAT
1 ATTATTAAAAATATTAAAT
*
9587 TTTATTAAAAAT
1 ATTATTAAAAAT
9599 TAGAAACAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTATTAAAAATATTAAAT
Found at i:9666 original size:20 final size:21
Alignment explanation
Indices: 9641--9685 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
9631 AAAATATTGT
* *
9641 AAAAATTTATTAAAAT-CAT-
1 AAAAAATTATAAAAATGCATC
9660 AAAAAATTATAAAAATGCATC
1 AAAAAATTATAAAAATGCATC
9681 AAAAA
1 AAAAA
9686 GATCCTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
20 3 0.14
21 5 0.23
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAAAATTATAAAAATGCATC
Found at i:9672 original size:18 final size:18
Alignment explanation
Indices: 9606--9673 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 18
9596 AATTAGAAAC
*
9606 AAAATTATAAAGATCGT-A
1 AAAATTATAAA-ATCATAA
9624 AAAA-TATAAAAT-ATTGTAA
1 AAAATTATAAAATCA---TAA
*
9643 AAATTTATTAAAATCATAA
1 AAAATTA-TAAAATCATAA
9662 AAAATTATAAAA
1 AAAATTATAAAA
9674 ATGCATCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
16 2 0.05
17 6 0.15
18 10 0.25
19 13 0.32
20 2 0.05
21 6 0.15
22 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (18 bp):
AAAATTATAAAATCATAA
Found at i:9673 original size:9 final size:9
Alignment explanation
Indices: 9606--9675 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
9596 AATTAGAAAC
9606 AAAATTATA
1 AAAATTATA
* **
9615 AAGATCGTA
1 AAAATTATA
9624 AAAA-TATA
1 AAAATTATA
*
9632 AAATATTGTA
1 AAA-ATTATA
*
9642 AAAATTTATT
1 AAAA-TTATA
*
9652 AAAATCATAA
1 AAAATTAT-A
9662 AAAATTATA
1 AAAATTATA
9671 AAAAT
1 AAAAT
9676 GCATCAAAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
8 5 0.11
9 20 0.44
10 20 0.44
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.31
Consensus pattern (9 bp):
AAAATTATA
Found at i:10070 original size:28 final size:28
Alignment explanation
Indices: 10030--10116 Score: 88
Period size: 29 Copynumber: 3.1 Consensus size: 28
10020 TTGCCCTTGG
*
10030 TTTTTCAAAATTTT-TTGTTTTGCCACTA
1 TTTTTCAAAATTTTAAT-TTTTGCCACTA
* *
10058 TTTTTCCATATTTTACATTTTTGCCACTA
1 TTTTTCAAAATTTTA-ATTTTTGCCACTA
* *
10087 TTTTTCAGATTTTATAATTTTT-CCACTA
1 TTTTTCAAAATTT-TAATTTTTGCCACTA
10115 TT
1 TT
10117 CTTAAAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
28 20 0.41
29 26 0.53
30 3 0.06
ACGTcount: A:0.22, C:0.16, G:0.05, T:0.57
Consensus pattern (28 bp):
TTTTTCAAAATTTTAATTTTTGCCACTA
Found at i:10079 original size:29 final size:29
Alignment explanation
Indices: 10047--10116 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
10037 AAATTTTTTG
* *
10047 TTTTGCCACTATTTTTCCATATTTTA-CAT
1 TTTTGCCACTATTTTT-CAGATTTTATAAT
10076 TTTTGCCACTATTTTTCAGATTTTATAAT
1 TTTTGCCACTATTTTTCAGATTTTATAAT
10105 TTTT-CCACTATT
1 TTTTGCCACTATT
10117 CTTAAAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 16 0.42
29 22 0.58
ACGTcount: A:0.21, C:0.19, G:0.04, T:0.56
Consensus pattern (29 bp):
TTTTGCCACTATTTTTCAGATTTTATAAT
Found at i:15177 original size:39 final size:39
Alignment explanation
Indices: 15068--15647 Score: 281
Period size: 39 Copynumber: 15.0 Consensus size: 39
15058 TCCGCCTTAG
* * * *
15068 GTTCTGGGTAAGAGATTGGCTGATGATGATCTGGCCCAT
1 GTTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
* ** * * ** *
15107 GATCGGGGTAA-AGATTGAATGGTTGCAATCTGCCTCAA
1 GTTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
*
15145 GTTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
1 GTTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
* * * * ** * * ** *
15184 GCTT-GGAGTAACAGGTCGAATGGTTGCAATCTGCCTCAA
1 G-TTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
* ** * *
15223 GCTCACGGTAAGAGATTGGTTGATGGTGATCTGCCCCAG
1 GTTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
* * *
15262 GCTT-GGGGTAAGAGATTAGCTAATGGTGATTTGCCCCAA
1 G-TTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
* * * *
15301 GCTCGGGGTAAGAGATTGGCTGATGGTAATCTACCCCAG
1 GTTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
* * * * * *
15340 GCTAGTGGTAAAAGA-T--CAGATGGCTGCAATCTGCCCTAA
1 GTTCGGGGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAA
* * * *
15379 GCTCGGGGTAAGAGATTGGTTAATGGTGATTTGCCCCAA
1 GTTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
* * * *
15418 GCTCGGGGAAAGAGA-T--CGGATGGCTACAATCTGCCCCAA
1 GTTCGGGGTAAGAGATTGGCTGATGG-T--GATCTGCCCCAA
* * * * * *
15457 GCTCGGGATAACAAATTGGCTAATAGTGATCTGCCCCAA
1 GTTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
* *
15496 GCTCGGGGTAAGAGA-T--CGGATGGTGATCTGCCCCAA
1 GTTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
* * ** * * *
15532 GCTCGGGGTAAAAGATCAGATGACT-ATGATCTACCCCAA
1 GTTCGGGGTAAGAGATTGGCTGA-TGGTGATCTGCCCCAA
* * * *
15571 GCTCGGGGTAA-AGATCGGATGACT-GTGATCTACCCCAA
1 GTTCGGGGTAAGAGATTGGCTGA-TGGTGATCTGCCCCAA
* * * * * *
15609 GCTCTGGGTAAAAACATTGGATGATTGTGATCTGCCCCA
1 GTTCGGGGT-AAGAGATTGGCTGATGGTGATCTGCCCCA
15648 TGATCGACAT
Statistics
Matches: 406, Mismatches: 111, Indels: 47
0.72 0.20 0.08
Matches are distributed among these distances:
36 41 0.10
37 2 0.00
38 64 0.16
39 261 0.64
40 27 0.07
41 3 0.01
42 8 0.02
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (39 bp):
GTTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
Found at i:15233 original size:78 final size:78
Alignment explanation
Indices: 15013--15647 Score: 459
Period size: 78 Copynumber: 8.2 Consensus size: 78
15003 TCTGCACTGG
* * * * * * * * *
15013 TGGTGATTTGCCCCAAGCTTTGGGTAACA-AGTCGAATGACTGTAATCCGCCTTAGGTTCTGGGT
1 TGGTGATCTGCCCCAAGCTTGGGGTAACAGA-TCGAATGGCTGCAATCTGCCTCAAGCTCAGGGT
15077 AAGAGATTGGCTGA
65 AAGAGATTGGCTGA
* * * * * * * *
15091 TGATGATCTGGCCCATGATCGGGGTAA-AGATTGAATGGTTGCAATCTGCCTCAAGTTCAGGGTA
1 TGGTGATCTGCCCCAAGCTTGGGGTAACAGATCGAATGGCTGCAATCTGCCTCAAGCTCAGGGTA
15155 AGAGATTGGCTGA
66 AGAGATTGGCTGA
* * * *
15168 TGGTGATCTGCCCCAAGCTTGGAGTAACAGGTCGAATGGTTGCAATCTGCCTCAAGCTCACGGTA
1 TGGTGATCTGCCCCAAGCTTGGGGTAACAGATCGAATGGCTGCAATCTGCCTCAAGCTCAGGGTA
*
15233 AGAGATTGGTTGA
66 AGAGATTGGCTGA
* * * * * *
15246 TGGTGATCTGCCCCAGGCTTGGGGTAAGAGATTAGCTAATGG-TG--ATTTGCCCCAAGCTCGGG
1 TGGTGATCTGCCCCAAGCTTGGGGTAACAGA-T--CGAATGGCTGCAATCTGCCTCAAGCTCAGG
15308 GTAAGAGATTGGCTGA
63 GTAAGAGATTGGCTGA
* * * * * * *
15324 TGGTAATCTACCCCAGGCTAGTGGTAAAAGATC-AGATGGCTGCAATCTGCC-CTAAGCTCGGGG
1 TGGTGATCTGCCCCAAGCTTGGGGTAACAGATCGA-ATGGCTGCAATCTGCCTC-AAGCTCAGGG
* *
15387 TAAGAGATTGGTTAA
64 TAAGAGATTGGCTGA
* * * * * * *
15402 TGGTGATTTGCCCCAAGCTCGGGGAAAGAGATCGGATGGCTACAATCTGCCCCAAGCTC-GGGAT
1 TGGTGATCTGCCCCAAGCTTGGGGTAACAGATCGAATGGCTGCAATCTGCCTCAAGCTCAGGG-T
* * *
15466 AACAAATTGGCTAA
65 AAGAGATTGGCTGA
* * * * * *
15480 TAGTGATCTGCCCCAAGCTCGGGGTAAGAGATCGGATGG-TG--ATCTGCCCCAAGCTCGGGGTA
1 TGGTGATCTGCCCCAAGCTTGGGGTAACAGATCGAATGGCTGCAATCTGCCTCAAGCTCAGGGTA
* ** *
15542 AAAGATCAGATGA
66 AGAGATTGGCTGA
* * * * * ** * * *
15555 CT-ATGATCTACCCCAAGCTCGGGGTAA-AGATCGGATGACTGTGATCTACCCCAAGCTCTGGGT
1 -TGGTGATCTGCCCCAAGCTTGGGGTAACAGATCGAATGGCTGCAATCTGCCTCAAGCTCAGGGT
* * *
15618 AAAAACATTGGATGA
65 -AAGAGATTGGCTGA
*
15633 TTGTGATCTGCCCCA
1 TGGTGATCTGCCCCA
15648 TGATCGACAT
Statistics
Matches: 460, Mismatches: 77, Indels: 40
0.80 0.13 0.07
Matches are distributed among these distances:
74 11 0.02
75 54 0.12
76 6 0.01
77 86 0.19
78 293 0.64
79 2 0.00
80 2 0.00
81 6 0.01
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (78 bp):
TGGTGATCTGCCCCAAGCTTGGGGTAACAGATCGAATGGCTGCAATCTGCCTCAAGCTCAGGGTA
AGAGATTGGCTGA
Found at i:15332 original size:117 final size:116
Alignment explanation
Indices: 15134--15647 Score: 347
Period size: 117 Copynumber: 4.4 Consensus size: 116
15124 AATGGTTGCA
* * * * * * * *
15134 ATCTGCCTCAAGTTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTTGGAGTAACAGG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTGATCTGCCCCAAGCTCGGGGTAAGAGA
* * * * * * * *
15199 TCGAATGGTTGCAATCTGCCTCAAGCTCACGGTAAGAGATTGGTTGATGGTG
66 TTG-CTGATGGTAATCTGCCCCAAGCTCACGGTAAAAGATTGGCTGATGGTG
* * * *
15251 ATCTGCCCCAGGCTTGGGGTAAGAGATTAGCTAATGGTGATTTGCCCCAAGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTGATCTGCCCCAAGCTCGGGGTAAGAGA
* * * *
15316 TTGGCTGATGGTAATCTACCCCAGGCT-AGTGGTAAAAGA-T--CAGATGGCTG
66 TT-GCTGATGGTAATCTGCCCCAAGCTCA-CGGTAAAAGATTGGCTGATGG-TG
* * * *
15366 CAATCTGCCCTAAGCTCGGGGTAAGAGATTGGTTAATGGTGATTTGCCCCAAGCTCGGGGAAAGA
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTGATCTGCCCCAAGCTCGGGGTAAGA
* * * *
15431 GA-T-CGGATGGCTACAATCTGCCCCAAGCTC-GGGATAACAA-ATTGGCTAATAGTG
64 GATTGCTGATGG-T--AATCTGCCCCAAGCTCACGG-TAA-AAGATTGGCTGATGGTG
* *
15485 ATCTGCCCCAAGCTCGGGGTAAGAGATCGG---ATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTGATCTGCCCCAAGCTCGGGGTAAGAGA
* * * ** * *
15547 -T-CAGATGACTATGATCTACCCCAAGCTCGGGGT-AAAGATCGGATGACT-GTG
66 TTGCTGATG-GTA--ATCTGCCCCAAGCTCACGGTAAAAGATTGGCTGA-TGGTG
* * * * * * *
15598 ATCTACCCCAAGCTCTGGGTAAAAACATTGGATGATTGTGATCTGCCCCA
1 ATCTGCCCCAAGCTCGGGGT-AAGAGATTGGCTAATGGTGATCTGCCCCA
15648 TGATCGACAT
Statistics
Matches: 319, Mismatches: 54, Indels: 48
0.76 0.13 0.11
Matches are distributed among these distances:
112 3 0.01
113 28 0.09
114 70 0.22
115 6 0.02
116 5 0.02
117 197 0.62
118 4 0.01
119 2 0.01
120 4 0.01
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (116 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGGTGATCTGCCCCAAGCTCGGGGTAAGAGA
TTGCTGATGGTAATCTGCCCCAAGCTCACGGTAAAAGATTGGCTGATGGTG
Found at i:15569 original size:114 final size:115
Alignment explanation
Indices: 15368--15577 Score: 307
Period size: 114 Copynumber: 1.8 Consensus size: 115
15358 GATGGCTGCA
* * *
15368 ATCTGCCCTAAGCTCGGGGTAAGAGATTGGTTAATGGTGATTTGCCCCAAGCTCGGGGAAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCGG-T-ATGGTGATCTGCCCCAAGCTCGGGGAAAGAGA
* * *
15433 TCGGATGGCTACAATCTGCCCCAAGCTCGGGATAACAAATTGGCTAATAGTG
64 TCAGATGACTACAATCTACCCCAAGCTCGGGATAACAAATTGGCTAATAGTG
15485 ATCTGCCCCAAGCTCGGGGTAAGAGATCGG-ATGGTGATCTGCCCCAAGCTCGGGGTAAA-AGAT
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCGGTATGGTGATCTGCCCCAAGCTCGGGG-AAAGAGAT
**
15548 CAGATGACTATGATCTACCCCAAGCTCGGG
65 CAGATGACTACAATCTACCCCAAGCTCGGG
15578 GTAAAGATCG
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
114 53 0.63
115 3 0.04
117 28 0.33
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (115 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATCGGTATGGTGATCTGCCCCAAGCTCGGGGAAAGAGATC
AGATGACTACAATCTACCCCAAGCTCGGGATAACAAATTGGCTAATAGTG
Done.