Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011428.1 Kokia drynarioides strain JFW-HI SEQ_126412, 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: 7963
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Found at i:6272 original size:207 final size:205
Alignment explanation
Indices: 5563--6420 Score: 996
Period size: 207 Copynumber: 4.2 Consensus size: 205
5553 ACAAAAAACG
* ** * * *
5563 ATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACGA-GACTTAAAGC
1 ATGC-GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA--ACTC-ACG-CTCAATGT
*
5627 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAAAGG
61 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAACAATAAAAAGG
* * *
5692 TTAGCTTCCTGATGAGATACTGAGAAGT-AGACCAAATTCGTCTTCTTGATGAGGTGCAGAGAAG
126 TTAGCTTCCTGATGAGATACTGAGAAGTGA-ACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
5756 CGGATTGAAACAAGTA
190 CGGATTGAAACAAGTA
* * * * * *
5772 AGGCGATCATCTTCCTGATGAGATAC--A-AAGAAGA--ATA-CCAACTCGAGGCTTAATGAGAG
1 ATGCG-TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTC-ACGCTCAATGTGAG
* * * * *
5831 CAAATCTTCGAACCCCAGCTTCTTAATGAGATACTGAGAAACAGGTCGAAACAATAAAATGGTTA
64 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAACAATAAAAAGGTTA
* *
5896 GCTTCCTGATGAGATACCGAGAAGTGAACCGAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
129 GCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
* *
5961 TTAAAACAAGTG
194 TTGAAACAAGTA
* * * * *
5973 ATGCGGTCACCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAAACCCACGTTCGATGTGAGC
1 ATGC-GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCAATGTGAGC
* * *
6038 AAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAG
65 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAACAATAAAAAGGTTAG
* * * *
6103 CTTCCTGACGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAAGATACAGAGAAGCAGA
130 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATG-AGATACAGAGAAGCGGA
* *
6168 TTGAAATAAGCA
194 TTGAAACAAGTA
* * *
6180 ATACAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATTAAACTCACGCTCGATGTGAGC
1 ATGC-GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCAATGTGAGC
* * *
6245 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAAAAGCAAGTCGAAACAATAAAATGGTTAG
65 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAACAATAAAAAGGTTAG
* * * * * * * * **
6310 CTTCCTGATGAAAAACGGAGAAGTGAACCAAATCCATCTTCCTGATGAAACACAGAAAAATGGA-
130 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* * *
6374 TCAAAGTAAGTG
195 TGAAA-CAAGTA
* *
6386 ATGCGGTCATCTTCCTGGTAAGATACTGAGAAGAA
1 ATGC-GTCATCTTCCTGATGAGATACTGAGAAGAA
6421 AGCCAAGTTA
Statistics
Matches: 555, Mismatches: 82, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
201 161 0.29
202 3 0.01
203 3 0.01
204 9 0.02
205 4 0.01
206 165 0.30
207 186 0.34
208 1 0.00
209 23 0.04
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (205 bp):
ATGCGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCAATGTGAGCA
AATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAACAATAAAAAGGTTAGC
TTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATT
GAAACAAGTA
Found at i:6387 original size:413 final size:407
Alignment explanation
Indices: 5627--6420 Score: 1108
Period size: 413 Copynumber: 1.9 Consensus size: 407
5617 GACTTAAAGC
5627 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAAAGG
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAAAGG
* * * * *
5692 TTAGCTTCCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCTTGATGAGGTGCAGAGAAGC
66 TTAGCTTCCTGACGAGATACTAAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
* * * * * *
5757 GGATTGAAACAAGTAAGGCGATCATCTTCCTGATGAGATACAAAGAAGAATACCAACTCGAGGCT
131 AGATTGAAACAAGCAAGACGATCATCTTCCTGATGAGATACAAAGAAGAAAACAAACTCGACGCT
* * * *
5822 TAATGAGAGCAAATCTTCGAACCCCAGCTTCTTAATGAGATACTGAGAAACAGGTCGAAACAATA
196 CAATGAGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAAAAACAAGTCGAAACAATA
* * * * * * *
5887 AAATGGTTAGCTTCCTGATGAGATACCGAGAAGTGAACCGAATTCGTCTTCCTGATGAGATACAG
261 AAATGGTTAGCTTCCTGATGAAAAACCGAGAAGTGAACCAAATCCATCTTCCTGATGAAACACAG
* * * *
5952 AGAAGCGGATTAAAACAAGTGATGCGGTCACCTTCCTAATGAGATACTGAGAAGAAGACCAAATC
326 AAAAACGGATCAAAACAAGTGATGCGGTCACCTTCCTAATAAGATACTGAGAAGAAGACCAAATC
6017 AAACCCACGTTCGATGT
391 AAACCCACGTTCGATGT
* *
6034 GAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGG
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAAAGG
*
6099 TTAGCTTCCTGACGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAAGATACAGAGAAG
66 TTAGCTTCCTGACGAGATACTAAGAAGTAGACCAAATTCGTCTTCCTGATG-AGATACAGAGAAG
* * *
6164 CAGATTGAAATAAGCAATAC-AGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATTAAAC
130 CAGATTGAAACAAGCAAGACGA-TCATCTTCCTGATGAGATAC--A-AAGAAGA--AAA-CAAAC
* * *
6228 TC-ACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACT-AAAAAGCAAGTC
188 TCGACGCTCAATGAGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAAAAA-CAAGTC
*
6291 GAAACAATAAAATGGTTAGCTTCCTGATGAAAAACGGAGAAGTGAACCAAATCCATCTTCCTGAT
252 GAAACAATAAAATGGTTAGCTTCCTGATGAAAAACCGAGAAGTGAACCAAATCCATCTTCCTGAT
* ** * **
6356 GAAACACAGAAAAATGGATCAAAGTAAGTGATGCGGTCATCTTCCTGGTAAGATACTGAGAAGAA
317 GAAACACAGAAAAACGGATCAAAACAAGTGATGCGGTCACCTTCCTAATAAGATACTGAGAAGAA
6421 AGCCAAGTTA
Statistics
Matches: 336, Mismatches: 42, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
407 111 0.33
408 46 0.14
410 1 0.00
411 7 0.02
412 4 0.01
413 162 0.48
414 5 0.01
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (407 bp):
GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAAAGG
TTAGCTTCCTGACGAGATACTAAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGC
AGATTGAAACAAGCAAGACGATCATCTTCCTGATGAGATACAAAGAAGAAAACAAACTCGACGCT
CAATGAGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAAAAACAAGTCGAAACAATA
AAATGGTTAGCTTCCTGATGAAAAACCGAGAAGTGAACCAAATCCATCTTCCTGATGAAACACAG
AAAAACGGATCAAAACAAGTGATGCGGTCACCTTCCTAATAAGATACTGAGAAGAAGACCAAATC
AAACCCACGTTCGATGT
Found at i:6770 original size:6 final size:6
Alignment explanation
Indices: 6761--6840 Score: 83
Period size: 6 Copynumber: 13.7 Consensus size: 6
6751 TTAATTTTAT
* * * * * *
6761 TTTAAA TTTAGA TTT-AT TTTAAA TTTGAA TTTAAA ATCAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
6808 TTTAAA TTTAAA TTT-AA TCTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
6841 TTTTCAAAAT
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
5 7 0.12
6 51 0.88
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:6791 original size:23 final size:23
Alignment explanation
Indices: 6761--6840 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
6751 TTAATTTTAT
*
6761 TTTAAATTTAGATTTATTTTAAA
1 TTTAAATTTAAATTTATTTTAAA
* **
6784 TTTGAATTTAAAATCAATTTTAAA
1 TTTAAATTT-AAATTTATTTTAAA
* *
6808 TTTAAATTTAAATTTAATCTAAA
1 TTTAAATTTAAATTTATTTTAAA
6831 TTTAAATTTA
1 TTTAAATTTA
6841 TTTTCAAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 28 0.60
24 19 0.40
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (23 bp):
TTTAAATTTAAATTTATTTTAAA
Found at i:6830 original size:17 final size:18
Alignment explanation
Indices: 6761--6840 Score: 83
Period size: 17 Copynumber: 4.6 Consensus size: 18
6751 TTAATTTTAT
* *
6761 TTTAAATTTAGATTT-AT
1 TTTAAATTTAAATTTAAA
*
6778 TTTAAATTTGAATTTAAA
1 TTTAAATTTAAATTTAAA
* * *
6796 ATCAATTTTAAATTTAAA
1 TTTAAATTTAAATTTAAA
*
6814 TTTAAATTT-AATCTAAA
1 TTTAAATTTAAATTTAAA
6831 TTTAAATTTA
1 TTTAAATTTA
6841 TTTTCAAAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
17 29 0.58
18 21 0.42
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTAAATTTAAATTTAAA
Found at i:6833 original size:41 final size:41
Alignment explanation
Indices: 6759--6836 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
6749 TTTTAATTTT
* * * *
6759 ATTTTAAATTTAGATTTATTTTAAATTTGAATTTAAAATCA
1 ATTTTAAATTTAAATTTAATTTAAATCTAAATTTAAAATCA
6800 ATTTTAAATTTAAATTTAAATTT-AATCTAAATTTAAA
1 ATTTTAAATTTAAATTT-AATTTAAATCTAAATTTAAA
6837 TTTATTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 28 0.88
42 4 0.12
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (41 bp):
ATTTTAAATTTAAATTTAATTTAAATCTAAATTTAAAATCA
Found at i:7648 original size:3 final size:3
Alignment explanation
Indices: 7611--7637 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
7601 TAATTGTTTT
7611 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
7638 ACATTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Done.