Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014696.1 Kokia drynarioides strain JFW-HI SEQ_129735, 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: 3608
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:2304 original size:139 final size:138
Alignment explanation
Indices: 2065--2504 Score: 790
Period size: 139 Copynumber: 3.2 Consensus size: 138
2055 TTCCTGATGA
*
2065 GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGTGA
1 GATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGTGA
*
2130 TGAGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCGAAACGAGCAAATCT
66 TGGGATCATCTT-CTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCGAAACGAGCAAATCT
2195 TCCATATGG
130 TCCATATGG
2204 GATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGTGA
1 GATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGTGA
* *
2269 TGGGATCATCTTCTTGATGAGACACTAAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCT
66 TGGGATCATCTTC-TGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCGAAACGAGCAAATCT
* *
2334 TCCAGATAG
130 TCCATATGG
*
2343 GATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCTGATTGAAACAGTGA
1 GATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGTGA
2408 TGGGATCATCTTACTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCGAAACGAGCAAATCT
66 TGGGATCATCTT-CTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCGAAACGAGCAAATCT
2473 TCCATATGG
130 TCCATATGG
2482 GATACTAAGAAGTGAACCAAATT
1 GATACTAAGAAGTGAACCAAATT
2505 NNNNNNNNNN
Statistics
Matches: 288, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
138 1 0.00
139 286 0.99
140 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (138 bp):
GATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGTGA
TGGGATCATCTTCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCGAAACGAGCAAATCTT
CCATATGG
Found at i:3304 original size:17 final size:17
Alignment explanation
Indices: 3276--3348 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
3266 TTGGAAATTG
3276 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
3292 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
3309 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
3326 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
3343 AATTTA
1 AATTTA
3349 GAAAGTCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
16 5 0.10
17 45 0.90
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:3324 original size:7 final size:6
Alignment explanation
Indices: 3281--3348 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
3271 AATTGAATTT
* *
3281 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
*
3327 ATTT-- ATTATAA AATTAA ATTTA
1 ATTTAA ATT-TAA ATTTAA ATTTA
3349 GAAAGTCCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 7 0.14
5 5 0.10
6 32 0.64
7 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:3389 original size:13 final size:13
Alignment explanation
Indices: 3350--3390 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3340 TTAAATTTAG
3350 AAAGTCCAATTA-
1 AAAGTCCAATTAC
*
3362 AGAAGTCCAA-AAC
1 A-AAGTCCAATTAC
3375 AAAGTCCAATTAC
1 AAAGTCCAATTAC
3388 AAA
1 AAA
3391 TGGCCCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.54, C:0.20, G:0.10, T:0.17
Consensus pattern (13 bp):
AAAGTCCAATTAC
Found at i:3400 original size:15 final size:15
Alignment explanation
Indices: 3380--3435 Score: 94
Period size: 15 Copynumber: 3.7 Consensus size: 15
3370 AAAACAAAGT
3380 CCAATTACAAATGGC
1 CCAATTACAAATGGC
*
3395 CCAATTACAGATGGC
1 CCAATTACAAATGGC
*
3410 CCAAATACAAATGGC
1 CCAATTACAAATGGC
3425 CCAATTACAAA
1 CCAATTACAAA
3436 ATACCCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.18
Consensus pattern (15 bp):
CCAATTACAAATGGC
Found at i:3443 original size:30 final size:30
Alignment explanation
Indices: 3380--3444 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
3370 AAAACAAAGT
* * *
3380 CCAATTACAAATGGCCCAATTACAGATGGC
1 CCAAATACAAATGGCCCAATTACAAATGAC
3410 CCAAATACAAATGGCCCAATTACAAAAT-AC
1 CCAAATACAAATGGCCCAATTAC-AAATGAC
3440 CCAAA
1 CCAAA
3445 AGCCCAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.45, C:0.28, G:0.11, T:0.17
Consensus pattern (30 bp):
CCAAATACAAATGGCCCAATTACAAATGAC
Done.