Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014542.1 Kokia drynarioides strain JFW-HI SEQ_129581, 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: 14898
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:567 original size:30 final size:30
Alignment explanation
Indices: 504--759 Score: 200
Period size: 30 Copynumber: 8.5 Consensus size: 30
494 ATGGAAATGA
* *
504 AATTTTA-AAGAAGTTTGAGGGTCAAGATAT
1 AATTTTAGAA-AAGTTTGAGGGTTAAAATAT
* *
534 GATTTTAGAAAAGTTTGAGGGTTAAAATGT
1 AATTTTAGAAAAGTTTGAGGGTTAAAATAT
* * * *
564 GA-TTTCGAAAA-TATTTAGGGGTCAAAATAT
1 AATTTTAGAAAAGT-TTGA-GGGTTAAAATAT
** *
594 AATTTTAGAAAAGTTCAAGGGTTAAAATGT
1 AATTTTAGAAAAGTTTGAGGGTTAAAATAT
* * * * *
624 AATTTTGGAAGACTTTAAGGGTCAAAATAT
1 AATTTTAGAAAAGTTTGAGGGTTAAAATAT
* *
654 AATTTTGGAAAAGTTTTAGGGTTAAAAATAT
1 AATTTTAGAAAAGTTTGAGGGTT-AAAATAT
*
685 AATTTTTGAGAAA-TTT-AGAGGTTAAAATAT
1 AATTTTAGA-AAAGTTTGAG-GGTTAAAATAT
* * * *
715 AATTTTAGAAAAATATG-TGGTTAAAATGT
1 AATTTTAGAAAAGTTTGAGGGTTAAAATAT
*
744 AATTTTAAAAAAGTTT
1 AATTTTAGAAAAGTTT
760 AAGGACCTTT
Statistics
Matches: 184, Mismatches: 32, Indels: 21
0.78 0.14 0.09
Matches are distributed among these distances:
28 1 0.01
29 37 0.20
30 108 0.59
31 34 0.18
32 4 0.02
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36
Consensus pattern (30 bp):
AATTTTAGAAAAGTTTGAGGGTTAAAATAT
Found at i:601 original size:60 final size:60
Alignment explanation
Indices: 522--749 Score: 253
Period size: 60 Copynumber: 3.8 Consensus size: 60
512 AGAAGTTTGA
* * *
522 GGGTCAAGATATGATTTTAGAAAAGTTTGAGGGTTAAAATGTGA-TTTCGAAAATATTTAG
1 GGGTCAAAATATAATTTTAGAAAAGTTTGAGGGTTAAAATGTAATTTTCGAAAA-ATTTAG
** * * * *
582 GGGTCAAAATATAATTTTAGAAAAGTTCAAGGGTTAAAATGTAATTTTGGAAGACTTTAA
1 GGGTCAAAATATAATTTTAGAAAAGTTTGAGGGTTAAAATGTAATTTTCGAAAAATTTAG
* * * * *
642 GGGTCAAAATATAATTTTGGAAAAGTTTTAGGGTTAAAAATATAATTTTTGAGAAATTTAG
1 GGGTCAAAATATAATTTTAGAAAAGTTTGAGGGTT-AAAATGTAATTTTCGAAAAATTTAG
* * * * *
703 AGGTTAAAATATAATTTTAGAAAAATATG-TGGTTAAAATGTAATTTT
1 GGGTCAAAATATAATTTTAGAAAAGTTTGAGGGTTAAAATGTAATTTT
750 AAAAAAGTTT
Statistics
Matches: 140, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
59 12 0.09
60 79 0.56
61 49 0.35
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (60 bp):
GGGTCAAAATATAATTTTAGAAAAGTTTGAGGGTTAAAATGTAATTTTCGAAAAATTTAG
Found at i:737 original size:29 final size:28
Alignment explanation
Indices: 647--755 Score: 94
Period size: 29 Copynumber: 3.7 Consensus size: 28
637 TTTAAGGGTC
* * *
647 AAAATATAATTTTGGAAAAGTTTTAGGGTT
1 AAAATATAATTTTAGAAAAATTGT--GGTT
* * *
677 AAAAATATAATTTTTGAGAAATTTAGAGGTT
1 -AAAATATAATTTTAGA-AAAATT-GTGGTT
708 AAAATATAATTTTAGAAAAATATGTGGTT
1 AAAATATAATTTTAGAAAAAT-TGTGGTT
*
737 AAAATGTAATTTTA-AAAAA
1 AAAATATAATTTTAGAAAAA
756 GTTTAAGGAC
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
28 5 0.07
29 22 0.33
30 16 0.24
31 19 0.28
32 5 0.07
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.38
Consensus pattern (28 bp):
AAAATATAATTTTAGAAAAATTGTGGTT
Found at i:761 original size:120 final size:120
Alignment explanation
Indices: 498--763 Score: 313
Period size: 120 Copynumber: 2.2 Consensus size: 120
488 CTTGGGATGG
* * * * * *
498 AAATGAAATTTTAAAGAAGTTTGAGGGTCAAGATATGATTTTAGAAAAGTTTGAGGGTTAAAATG
1 AAATGTAATTTTAAAAAAGTTTAAGGGTCAAAATATAATTTTAGAAAAGTTTGAGGGTTAAAATA
* * *
563 TGATTTCGAAAATATTTAGGGGTCAAAATATAATTTTAGAAAAGTTCAAGGGTTA
66 TAATTTCGAAAATATTTAGAGGTCAAAATATAATTTTAGAAAAGATCAAGGGTTA
** * * * *
618 AAATGTAATTTTGGAAGACTTTAAGGGTCAAAATATAATTTTGGAAAAGTTTTAGGGTTAAAAAT
1 AAATGTAATTTTAAAAAAGTTTAAGGGTCAAAATATAATTTTAGAAAAGTTTGAGGGTT-AAAAT
* * * *
683 ATAATTTTTGAGAA-ATTTAGAGGTTAAAATATAATTTTAGAAAA-AT-ATGTGGTTA
65 ATAA-TTTCGAAAATATTTAGAGGTCAAAATATAATTTTAGAAAAGATCAAG-GGTTA
738 AAATGTAATTTTAAAAAAGTTTAAGG
1 AAATGTAATTTTAAAAAAGTTTAAGG
764 ACCTTTTAGA
Statistics
Matches: 120, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
119 2 0.02
120 76 0.63
121 35 0.29
122 7 0.06
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.35
Consensus pattern (120 bp):
AAATGTAATTTTAAAAAAGTTTAAGGGTCAAAATATAATTTTAGAAAAGTTTGAGGGTTAAAATA
TAATTTCGAAAATATTTAGAGGTCAAAATATAATTTTAGAAAAGATCAAGGGTTA
Found at i:1887 original size:17 final size:18
Alignment explanation
Indices: 1865--1900 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1855 TGCTTTTCCT
1865 CCTCTGTTGT-TCTTTTG
1 CCTCTGTTGTATCTTTTG
*
1882 CCTCTGTTTTATCTTTTG
1 CCTCTGTTGTATCTTTTG
1900 C
1 C
1901 AGATCTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.03, C:0.25, G:0.14, T:0.58
Consensus pattern (18 bp):
CCTCTGTTGTATCTTTTG
Found at i:2139 original size:17 final size:17
Alignment explanation
Indices: 2117--2190 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 17
2107 ATTAAACTTT
2117 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* **
2134 TAAATTTAAACTCCAAA
1 TAAATTTAAATTTAAAA
** *
2151 TAAGGTTAAATTTACAA
1 TAAATTTAAATTTAAAA
*
2168 TAAATTTAAAATTAAAA
1 TAAATTTAAATTTAAAA
*
2185 TGAATT
1 TAAATT
2191 AAGATTTTAA
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.36
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:4784 original size:32 final size:34
Alignment explanation
Indices: 4747--4809 Score: 112
Period size: 32 Copynumber: 1.9 Consensus size: 34
4737 TAAGATAAAC
4747 TATATTTTATTATGTGT-C-TTTTCCACAAAAAT
1 TATATTTTATTATGTGTCCTTTTTCCACAAAAAT
4779 TATATTTTATTATGTGTCCTTTTTCCACAAA
1 TATATTTTATTATGTGTCCTTTTTCCACAAA
4810 TTTTCGTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.59
33 1 0.03
34 11 0.38
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (34 bp):
TATATTTTATTATGTGTCCTTTTTCCACAAAAAT
Found at i:12508 original size:208 final size:209
Alignment explanation
Indices: 12148--13294 Score: 1372
Period size: 209 Copynumber: 5.5 Consensus size: 209
12138 TCATAAGAAA
* * *
12148 GAGTGAAACTTCCAA-CCCCATCTTCCTGATGAGATACATATAAA-TGGGTCAAAGCAACAAAGC
1 GAGTGAAACTTCCAACCCCCATCTTCCTGATGAGATACAGA-AAAGTGGGTCAAAACAATAAAGC
* * * * * * * *
12211 GATCACCTTCCTAATGAGAAACAGAGAAGTGGACCAAATCCGTCTTCTTGATAAGATACAAAAAA
65 GATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATACAGAGAA
* * *
12276 GTGGATTAAATCAATGAGGCGGTCATCTTCCTGATGAGATACAAAGAAGAAGACCAATTTAATGA
130 GTGGATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAATTCAATGA
12341 AGCAAAGCTCAATGT
195 AGCAAAGCTCAATGT
* * * *
12356 AAGTGAAACTTCCAA-CCCTATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCG
1 GAGTGAAACTTCCAACCCCCATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAACAATAAAGCG
* * * * * *
12420 GTCACCTTCCTGATGAGATATAGAAAAGTGGACCAAATCCTTCTTCCTGATGAGATACAGAGAAG
66 ATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATACAGAGAAG
* * * * *
12485 TGGATTAAATCAATGAAGCGGTCATCTTCCTAATGAGATACAGAAAAGAAGATCAATTTAATGGA
131 TGGATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAATTCAATGAA
**
12550 GTGAAGCTCAATGT
196 GCAAAGCTCAATGT
* * * * * *
12564 GAGTGAAACTTCGAACCCCCATCTTCCAGATGAGATACTGAGAAGTGGGTCGAAATAATAAAGCG
1 GAGTGAAACTTCCAACCCCCATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAACAATAAAGCG
* * * * * * * *
12629 ATCATCTTCTTGATGAGATATAGAGAATTGGACCAAATTCATC-T-CTGATGAGGTACAAAGAAG
66 ATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATACAGAGAAG
* *
12692 TGGATCACAAAT-AATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAAAAGACCAATTCAATG
131 TGGAT--TAAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAATTCAATG
* *
12756 GAGCGAAGCTCAATGT
194 AAGCAAAGCTCAATGT
* * * * *
12772 GAGTGAAACTTCGAACCCCCCATCTTCTTGATGAGAAACTGAAAAGTGGGTCAAAACAATAAAAC
1 GAGTGAAACTTCCAA-CCCCCATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAACAATAAAGC
* ** * * * *
12837 GATCATCTTCCTAATGAGATACAGAGAAGTAGACCAAATTTGTCTTTCTGATAAGATATAGAAAA
65 GATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATACAGAGAA
*
12902 GTGGATTAAATCAAT-AAGGCGGTCATCTTCCTGATAAGATACAGAGAAGAAGACCAATTCAATG
130 GTGGATTAAATCAATGAA-GCGGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAATTCAATG
*
12966 AAGCAAAACTCAATGT
194 AAGCAAAGCTCAATGT
* * * * * * * *
12982 GAATGAAACTTCGAACCCCTATCTTCCTGCTAAGATACTGAAAAGTGAGTCAAAACAATTAAGCG
1 GAGTGAAACTTCCAACCCCCATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAACAATAAAGCG
* *
13047 GTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
66 ATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATACAGAGAAG
* * * *
13112 TGGATTAAATCAATGAGGCGATCACCTTCCTAATGAGATACAGAGAAGAAGACCAATTCAATGAA
131 TGGATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAATTCAATGAA
* * *
13177 GTAAAACTCAATAT
196 GCAAAGCTCAATGT
* * * * ** * * *
13191 GAGTGAAGCTTCCAAACCTCATCTTCCCGATGAGATACAGAAAAGTGGGTTGAATCAATGAAGTG
1 GAGTGAAACTTCCAACCCCCATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAACAATAAAGCG
* * *
13256 ATCATCTTCATGATGAGATATAAAGAAGTAGACCAAATC
66 ATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATC
13295 GATGAGGGGA
Statistics
Matches: 813, Mismatches: 116, Indels: 19
0.86 0.12 0.02
Matches are distributed among these distances:
207 24 0.03
208 273 0.34
209 421 0.52
210 76 0.09
211 19 0.02
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (209 bp):
GAGTGAAACTTCCAACCCCCATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAACAATAAAGCG
ATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATACAGAGAAG
TGGATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAATTCAATGAA
GCAAAGCTCAATGT
Found at i:12521 original size:85 final size:85
Alignment explanation
Indices: 12376--12532 Score: 251
Period size: 85 Copynumber: 1.8 Consensus size: 85
12366 TCCAACCCTA
* * *
12376 TCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCACCTTCCTGATGAGATAT
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGGTCACCTTCCTAATGAGATAC
12441 AGAAAAGTGGACCAAATCCT
66 AGAAAAGTGGACCAAATCCT
* * * *
12461 TCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAGCGGTCATCTTCCTAATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGGTCACCTTCCTAATGAGATAC
12526 AGAAAAG
66 AGAAAAG
12533 AAGATCAATT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 65 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGGTCACCTTCCTAATGAGATAC
AGAAAAGTGGACCAAATCCT
Found at i:13607 original size:124 final size:124
Alignment explanation
Indices: 13383--13710 Score: 352
Period size: 124 Copynumber: 2.6 Consensus size: 124
13373 ACCAAATTCG
* * * *
13383 TCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAGGCGATCACCTTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGGGTTGAATCAATGAAGCGATCATCTTCCTGATGAGATAC
* * * * *
13448 AGAGAAGAAGACCAATTCAATGAAGTAAAACTCAATATGAGTGAAGCTTCTAAACCTC-A
66 AGAGAAGTAGACCAAATCAATGAAGGAAAACTCAATACGAGTGAAGCTTC-AAACCCCTA
* * * *
13507 TCTTCCCGATGAGATACAGAGAAGTGGGTTGAATCAATGAAGTGATCATCTTCATGATGAGATAT
1 TCTTCCTGATGAGATACAGAGAAGTGGGTTGAATCAATGAAGCGATCATCTTCCTGATGAGATAC
* * * * ** * * *
13572 AAAGAAGTAGACCAAATCGATGAGGGGAAGGTCAATGCGAGTGAAGCTTCGAACCCCTT
66 AGAGAAGTAGACCAAATCAATGAAGGAAAACTCAATACGAGTGAAGCTTCAAACCCCTA
* * ** * * * * *
13631 TCTTCTTGAAGAGATACAGAGAAGTAAGTCGAAGCAATAAAGCGGTCATCTTCCTAATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGGGTTGAATCAATGAAGCGATCATCTTCCTGATGAGATAC
*
13696 AGAGAAGTAAACCAA
66 AGAGAAGTAGACCAA
13711 GAGAAAAAGC
Statistics
Matches: 166, Mismatches: 37, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
123 5 0.03
124 161 0.97
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (124 bp):
TCTTCCTGATGAGATACAGAGAAGTGGGTTGAATCAATGAAGCGATCATCTTCCTGATGAGATAC
AGAGAAGTAGACCAAATCAATGAAGGAAAACTCAATACGAGTGAAGCTTCAAACCCCTA
Done.