Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013743.1 Kokia drynarioides strain JFW-HI SEQ_128771, 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: 3477
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Found at i:727 original size:239 final size:238
Alignment explanation
Indices: 307--781 Score: 702
Period size: 239 Copynumber: 2.0 Consensus size: 238
297 TCATAATAAC
* * *
307 GATAAAAGATCGAATAAATTGTAGATGAATTTTAATATTTTTCTTAATTCATTAGTTACTTTTAG
1 GATAAAAGATCAAATAAATTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTTTTAG
* *
372 GTTTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGAATTTTACTATAATTAT
66 G--TTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGAATTTTACTAGAATTAT
* *
437 TTAAGTATCTTTTAGGATTCTCGTAAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATAAG
129 TTAAGTATCCTTTAGGATTCTCATAAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATAAG
*
502 TTTGGTGAACACATCTTAGTCAAGTTACAAGTAAATAGGAGTAAT
194 TTTGATGAACACATCTTAGTCAAGTTACAAGTAAATAGGAGTAAT
* * * * *
547 GATAAAAGATCAAATAAGTTGTATATGGATTTTAATATTTCTCTTAATTTATTAGTAATTTTTTA
1 GATAAAAGATCAAATAAATTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAA-CTTTT-
* *
612 AGG-TTTTTTTAGTATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTTACTAGAATTAT
64 AGGTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGAATTTTACTAGAATTAT
* * * *
676 TTAGGTATCCTTTAGTG-TTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATAA
129 TTAAGTATCCTTTAG-GATTCTCATAAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATAA
* *
740 GTTTGATGAACACGTCTTAGTCAAGTTACAAGTAAATTGGAG
193 GTTTGATGAACACATCTTAGTCAAGTTACAAGTAAATAGGAG
782 GAATTTTTTA
Statistics
Matches: 211, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
239 152 0.72
240 52 0.25
241 4 0.02
242 3 0.01
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (238 bp):
GATAAAAGATCAAATAAATTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTTTTAG
GTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGAATTTTACTAGAATTATTT
AAGTATCCTTTAGGATTCTCATAAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATAAGTT
TGATGAACACATCTTAGTCAAGTTACAAGTAAATAGGAGTAAT
Found at i:1721 original size:185 final size:185
Alignment explanation
Indices: 1387--1755 Score: 490
Period size: 185 Copynumber: 2.0 Consensus size: 185
1377 ATCAAATTCG
* ** * *
1387 TCTTCCTTATGAGATACAGAGAAGTGAATTTAAACAATGAAGGGGTCATCTTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAACGAATTAAAACAATGAAGCGGTCATCTTCCTGATGAGATAC
* * *** * * *
1452 AGAGAAGTAGACCAATTCAATGAAGCGAAGCTCAATGTGAGTGAAATTTCCAAACCCCATCTTTC
66 AAAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACAAATGAAACTTCCAAACCCCATCTTCC
* *
1517 TTATGAGATACAAAGAAGTGGGTCAAACCGATAAAGAGATCATCTTCCTAATGAC
131 TGATGAGATACAAAGAAGTGGGTCAAACCAATAAAGAGATCATCTTCCTAATGAC
*
1572 TCTTCCTGATGAGATACAGAGAAACGAATTAAAACAAGTGATA-CGGTTATCTTCCTGATGAGAT
1 TCTTCCTGATGAGATACAGAGAAACGAATTAAAACAA-TGA-AGCGGTCATCTTCCTGATGAGAT
* *
1636 ACAAAGAAGTAGACCAAATCAATGAAGCGAAGCTTAATACAAATGAGACTT-CAAACCCCATCTT
64 ACAAAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACAAATGAAACTTCCAAACCCCATCTT
* * * * * *
1700 CCTGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGTGGTCATCTTCCTGATGA
129 CCTGATGAGATACAAAGAAGTGGGTCAAACCAATAAAGAGATCATCTTCCTAATGA
1756 GATGCAGAGA
Statistics
Matches: 158, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
185 93 0.59
186 64 0.41
187 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24
Consensus pattern (185 bp):
TCTTCCTGATGAGATACAGAGAAACGAATTAAAACAATGAAGCGGTCATCTTCCTGATGAGATAC
AAAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACAAATGAAACTTCCAAACCCCATCTTCC
TGATGAGATACAAAGAAGTGGGTCAAACCAATAAAGAGATCATCTTCCTAATGAC
Found at i:1839 original size:85 final size:85
Alignment explanation
Indices: 1696--1860 Score: 240
Period size: 85 Copynumber: 1.9 Consensus size: 85
1686 TCAAACCCCA
* * * * * *
1696 TCTTCCTGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGTGGTCATCTTCCTGATGAGATGC
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCGGTCATATTCCTGATGAGATAC
1761 AGAGAAGTAAACCAAATCAG
66 AGAGAAGTAAACCAAATCAG
* * *
1781 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGCGGTCATATTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCGGTCATATTCCTGATGAGATAC
*
1846 AGAGAAGTAGACCAA
66 AGAGAAGTAAACCAA
1861 TTCAACGAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGCGGTCATATTCCTGATGAGATAC
AGAGAAGTAAACCAAATCAG
Found at i:1931 original size:208 final size:209
Alignment explanation
Indices: 1572--2245 Score: 762
Period size: 208 Copynumber: 3.3 Consensus size: 209
1562 TCCTAATGAC
** * * *
1572 TCTTCCTGATGAGATACAGAGAAACGAATTAAAACAAGTGATA-CGGTTATCTTCCTGATGAGAT
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAA-TGA-AGCGGTCATCTTCCTGATGAGAT
* * * * * * *
1636 ACAAAGAAGTAGACCAAATCAATGAAGCGAAGCTTAATACAAATGAGACTT-CAAACCCCATCTT
64 ACAGAGAAGTAGACCAATTCAACGAAGCGAAGCTTAATGCGAGTGAAACTTCCAAACCCCATCTT
* *** * *
1700 CCTGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGTGGTCATCTTCCTGATGAGATGCAGAG
129 CTTGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGAAATCATCTTCCTGATGAGATACAAAG
1765 AAGTAAACCAAAT-CA
194 AAGTAAACCAAATCCA
*
1780 GTCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGCGGTCATATTCCTGATGAGATA
1 -TCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGCGGTCATCTTCCTGATGAGATA
*
1845 CAGAGAAGTAGACCAATTCAACGAAGCGAAGCTTAATGTGAGTGAAACTTCCAAA-CCCATCTTC
65 CAGAGAAGTAGACCAATTCAACGAAGCGAAGCTTAATGCGAGTGAAACTTCCAAACCCCATCTTC
* * * *
1909 TTGATGAGATACAAAGAAGTGGGTCAAAGTAATAAAGAAATCATCTTCCTGATGAGATATAAAGA
130 TTGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGAAATCATCTTCCTGATGAGATACAAAGA
*
1974 AGTAGACCAAATCCA
195 AGTAAACCAAATCCA
* * * *
1989 TCTTCCTTATGAGATACAGAGAAGTAGATT-AAATCAACGAAGCGGTCATCTTCCTGGTGAGATA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAAT-AATGAAGCGGTCATCTTCCTGATGAGATA
* * * * *
2053 CAGAGAAATAGACCAATTCAACAAAGTGAAGCTCAATGCGAGTGAAACTTCCAAACCCCATCTTT
65 CAGAGAAGTAGACCAATTCAACGAAGCGAAGCTTAATGCGAGTGAAACTTCCAAACCCCATCTTC
* * * *
2118 TTTATGAGATACAGAGAAGTGGGT--------T---G--A--A-GTTCCTGACGAGATGCAAAGA
130 TTGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGAAATCATCTTCCTGATGAGATACAAAGA
*
2167 AGTGAACCAAATCCA
195 AGTAAACCAAATCCA
* * * *
2182 TCTTCTTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGCGATCATCTTCCT-ATTGAGATA
1 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGCGGTCATCTTCCTGA-TGAGATA
2246 TAAAGAATTA
Statistics
Matches: 406, Mismatches: 52, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
193 81 0.20
194 4 0.01
196 1 0.00
198 1 0.00
201 1 0.00
207 5 0.01
208 244 0.60
209 69 0.17
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.24
Consensus pattern (209 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATTAAAATAATGAAGCGGTCATCTTCCTGATGAGATAC
AGAGAAGTAGACCAATTCAACGAAGCGAAGCTTAATGCGAGTGAAACTTCCAAACCCCATCTTCT
TGATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGAAATCATCTTCCTGATGAGATACAAAGAA
GTAAACCAAATCCA
Found at i:2023 original size:37 final size:37
Alignment explanation
Indices: 1946--2016 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
1936 AGTAATAAAG
*
1946 AAAT-CATCTTCCTGATGAGATATAAAGAAGTAGACC
1 AAATCCATCTTCCTGATGAGATACAAAGAAGTAGACC
* *
1982 AAATCCATCTTCCTTATGAGATACAGAGAAGTAGA
1 AAATCCATCTTCCTGATGAGATACAAAGAAGTAGA
2017 TTAAATCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 4 0.13
37 27 0.87
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (37 bp):
AAATCCATCTTCCTGATGAGATACAAAGAAGTAGACC
Found at i:3136 original size:10 final size:10
Alignment explanation
Indices: 3123--3170 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
3113 CAAAGCGTTT
3123 TTAATATATA
1 TTAATATATA
3133 TTAATATAT-
1 TTAATATATA
*
3142 TTAATATTTA
1 TTAATATATA
*
3152 TTTATTATATA
1 -TTAATATATA
3163 TTAATATA
1 TTAATATA
3171 CTTATTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTAATATATA
Found at i:3144 original size:19 final size:20
Alignment explanation
Indices: 3122--3170 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
3112 TCAAAGCGTT
3122 TTTAATATATA-TTAATATA
1 TTTAATATATATTTAATATA
* *
3141 TTTAATATTTATTTATTATA
1 TTTAATATATATTTAATATA
3161 TATTAATATA
1 T-TTAATATA
3171 CTTATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 10 0.40
20 8 0.32
21 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTAATATATATTTAATATA
Found at i:3177 original size:19 final size:19
Alignment explanation
Indices: 3122--3177 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
3112 TCAAAGCGTT
3122 TTTAATATA-TATTAATATA
1 TTTAATATATTATT-ATATA
3141 TTTAATAT-TTATTTATTATA
1 TTTAATATATTA-TTA-TATA
3161 TATTAATATACTTATTA
1 T-TTAATATA-TTATTA
3178 ATTGCTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
19 11 0.35
20 7 0.23
21 7 0.23
22 3 0.10
23 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAATATATTATTATATA
Found at i:3187 original size:33 final size:30
Alignment explanation
Indices: 3122--3192 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
3112 TCAAAGCGTT
* *
3122 TTTAATATATATTAATATATTTAATATTTA
1 TTTATTATATATTAATATACTTAATATTTA
*
3152 TTTATTATATATTAATATACTTATTAATTGCTA
1 TTTATTATATATTAATATACTTAAT-ATT--TA
3185 TTTATTAT
1 TTTATTAT
3193 TACCTACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 22 0.63
31 3 0.09
33 10 0.29
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (30 bp):
TTTATTATATATTAATATACTTAATATTTA
Done.