Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011360.1 Kokia drynarioides strain JFW-HI SEQ_126341, 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: 4132
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:3320 original size:139 final size:139
Alignment explanation
Indices: 3070--3538 Score: 814
Period size: 139 Copynumber: 3.4 Consensus size: 139
3060 AAATGGTTAG
* * *
3070 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGGAT
1 CTTCCAGATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
3135 TGAAACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTGAAA
66 TGAAACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTGAAA
3200 CGAGCAAAT
131 CGAGCAAAT
* *
3209 CTTCCAGATGGGATACTAAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGAT
1 CTTCCAGATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
*
3274 TGAAATAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTGAAA
66 TGAAACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTGAAA
3339 CGAGCAAAT
131 CGAGCAAAT
*
3348 CTTCCAAATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
1 CTTCCAGATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* * * *
3413 TGAAAGAGTGATGGGATCATCTTCTTGATGAGACATTGAGAAGAAGACGCAAACGAGGCTCGAAA
66 TGAAACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTGAAA
3478 CGAGCAAAT
131 CGAGCAAAT
*
3487 CTTCCAGATGAGG-TATTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
1 CTTCCAGATG-GGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
3539 AGCGAATTGA
Statistics
Matches: 314, Mismatches: 15, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
139 312 0.99
140 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.22
Consensus pattern (139 bp):
CTTCCAGATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
TGAAACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTGAAA
CGAGCAAAT
Found at i:3629 original size:139 final size:135
Alignment explanation
Indices: 3070--3599 Score: 674
Period size: 139 Copynumber: 3.9 Consensus size: 135
3060 AAATGGTTAG
* * * *
3070 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGGAT
1 CTTCCAGATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA-ACAG---CGAAT
*
3135 TGAAACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTGAAA
62 TGAAACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
3200 CGAGCAAAT
127 CGAGCAAAT
* * * *
3209 CTTCCAGATGGGATACTAAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGAT
1 CTTCCAGATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAT--A-A-CAGCGAAT
* *
3274 TGAAATAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTGAAA
62 TGAAACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
3339 CGAGCAAAT
127 CGAGCAAAT
* * *
3348 CTTCCAAATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
1 CTTCCAGATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAT--A-A-CAGCGAAT
* * *
3413 TGAAAGAGTGATGGGATCATCTTCTTGATGAGACATTGAGAAGAAGACGCAAACGAGGCTCGAAA
62 TGAAACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAA
3478 CGAGCAAAT
127 CGAGCAAAT
*
3487 CTTCCAGATGAGG-TATTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAT-A-AGCGAATTGA
1 CTTCCAGATG-GGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAACAGCGAATTGA
* * * * * *
3549 GACAGACGACGTGG-TCATCTTCCTGATGAGATACTAAGAAGAAGA-CCAAAC
65 AACAG-TGATG-GGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAAC
3600 CAAACCCACG
Statistics
Matches: 359, Mismatches: 26, Indels: 18
0.89 0.06 0.04
Matches are distributed among these distances:
133 17 0.05
134 30 0.08
135 3 0.01
139 303 0.84
140 2 0.01
141 2 0.01
142 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (135 bp):
CTTCCAGATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAACAGCGAATTGAA
ACAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAG
CAAAT
Found at i:3629 original size:278 final size:273
Alignment explanation
Indices: 3081--3601 Score: 771
Period size: 278 Copynumber: 1.9 Consensus size: 273
3071 TTCCTGATGA
3081 GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGGATTGAAACAGTGA
1 GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGGATTGAAACAGTGA
*
3146 TGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTGAAACGAGCAAATCT
66 TGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCT
* *
3211 TCCAGATGGGATACTAAGAAGTGAACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGATTG
131 TCCAGATGGGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGAT----A-AAGCGAATTG
* * * * * * * *
3276 AAATAGTGATGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTGAAACG
191 AAACAGCGACGGGATCATCTTCCTGATGAGACACTAAGAAGAAGACCCAAACCACGCTCGAAACG
3341 AGCAAATCTTCCAAATGG
256 AGCAAATCTTCCAAATGG
* *
3359 GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAGAGTGA
1 GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGGATTGAAACAGTGA
* *
3424 TGGGATCATCTTCTTGATGAGACATTGAGAAGAAGACGCAAACGAGGCTCGAAACGAGCAAATCT
66 TGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCT
* * *
3489 TCCAGATGAGG-TATTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGAT-AAGCGAATTGAGAC
131 TCCAGATG-GGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAAAGCGAATTGAAAC
*
3552 AGACGACGTGG-TCATCTTCCTGATGAGATACTAAGAAGAAGA-CCAAACCA
195 AG-CGACG-GGATCATCTTCCTGATGAGACACTAAGAAGAAGACCCAAACCA
3602 AACCCACGCT
Statistics
Matches: 223, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
272 20 0.09
273 31 0.14
274 2 0.01
278 168 0.75
279 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.21
Consensus pattern (273 bp):
GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAACGGATTGAAACAGTGA
TGGGATCATCTTCTTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCT
TCCAGATGGGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAAAGCGAATTGAAACA
GCGACGGGATCATCTTCCTGATGAGACACTAAGAAGAAGACCCAAACCACGCTCGAAACGAGCAA
ATCTTCCAAATGG
Found at i:4052 original size:17 final size:17
Alignment explanation
Indices: 4021--4093 Score: 94
Period size: 17 Copynumber: 4.4 Consensus size: 17
4011 TTGGAAATTG
4021 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
* *
4037 AGTTTATTTTACATTTA
1 AATTTATTTTAAATTTA
*
4054 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
4071 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
4088 AATTTA
1 AATTTA
4094 GAAAGTCCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
16 5 0.10
17 43 0.90
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:4077 original size:34 final size:33
Alignment explanation
Indices: 4015--4093 Score: 104
Period size: 34 Copynumber: 2.4 Consensus size: 33
4005 GACTTATTGG
* * *
4015 AAATTGAATTTATTTAAATTTAAGTTTATTTTA
1 AAATTAAATTTATTTAAATTTAAATTTATTATA
* *
4048 CATTTAAATTTATTTGAAATTTAAATTTATTATA
1 AAATTAAATTTATTT-AAATTTAAATTTATTATA
4082 AAATTAAATTTA
1 AAATTAAATTTA
4094 GAAAGTCCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 12 0.32
34 26 0.68
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (33 bp):
AAATTAAATTTATTTAAATTTAAATTTATTATA
Found at i:4113 original size:13 final size:14
Alignment explanation
Indices: 4095--4131 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
4085 TTAAATTTAG
4095 AAAGTCCAATTAA-
1 AAAGTCCAATTAAC
4108 AAAGTCCAA--AAC
1 AAAGTCCAATTAAC
4120 AAAGTCCAATTA
1 AAAGTCCAATTA
4132 C
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.10
12 9 0.43
13 9 0.43
14 1 0.05
ACGTcount: A:0.54, C:0.19, G:0.08, T:0.19
Consensus pattern (14 bp):
AAAGTCCAATTAAC
Done.