Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008242.1 Kokia drynarioides strain JFW-HI SEQ_122907, 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: 7273
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Found at i:2776 original size:208 final size:209
Alignment explanation
Indices: 2351--3155 Score: 1116
Period size: 208 Copynumber: 3.9 Consensus size: 209
2341 TCAAAAGGTA
* * ** * * * **
2351 ATCTTCCTGATGAGATACAGAGAAGCAGACCAAAACAATGATGAGAAGCTCAATACGAGTGAAAC
1 ATCTTCCTGATGAGATACAGAAAAGTAGACCAATTCAACGAAGTGAAGCTCAATGTGAGTGAAAC
* * * * * * *
2416 TTCGAAACCCCATCTTCTTGATGAGATATAAAGAAGTGGGTCAAAGCAATTAAGAGGTCATCTTC
66 TTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTTC
* ** * *
2481 CTGATGAGATATAGAGAAG-TAGAACAAATCCGTCTTTCTGATGAGATACAGAGAAGTGGATTAA
131 CTGACGAGATGCAGAGAAGTTA-ACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTAA
2545 ATCAATGAAGC-AGTC
195 ATCAATGAAGCGA-TC
* *
2560 ATCTTCCTGATGAGATACAGAAAAGTAGACTAATTCAACGAAGTGAAGCTCAATGTGAATGAAAC
1 ATCTTCCTGATGAGATACAGAAAAGTAGACCAATTCAACGAAGTGAAGCTCAATGTGAGTGAAAC
* * *
2625 TTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGT-GGTCAAATCAATAAAGTGGACATCTTC
66 TTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTTC
* * * *
2689 CTGACGAGATGCAGATAAGTTAACCAAATCCATCTTCTTGATGAGATACAGAGAAGGGGATTAAA
131 CTGACGAGATGCAGAGAAGTTAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAA
2754 TCAATGAAGCGATC
196 TCAATGAAGCGATC
* * *
2768 ATCTTCCTGATGAGATACAAAAAAGTAGACCAATTAAACGAAGTTAAGCTCAATGTGAGTG-AAC
1 ATCTTCCTGATGAGATACAGAAAAGTAGACCAATTCAACGAAGTGAAGCTCAATGTGAGTGAAAC
*
2832 TTCCAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTTC
66 TTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTTC
* * * * *
2897 CTAACGAGATGTAGAGAAGTGAACCAAATCCTTCTTCCTGATGAGATACATAGAAGTGGATTAAA
131 CTGACGAGATGCAGAGAAGTTAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAA
* *
2962 TCAATGAAGTGGTC
196 TCAATGAAGCGATC
* * *
2976 ATCGTCTTGATGAGATACA-AAGAAGTAGACCAAGTCAACGAAGTGAAGCTCAATGTGAGTGAAA
1 ATCTTCCTGATGAGATACAGAA-AAGTAGACCAATTCAACGAAGTGAAGCTCAATGTGAGTGAAA
*
3040 CTTCCAAACCCTATCTTCCTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTT
65 CTTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTT
* * *
3105 CCTGATGAGATGCAGAGAAATTAACCAAATTCGTCTTCCTGATGAGATACA
130 CCTGACGAGATGCAGAGAAGTTAACCAAATCCGTCTTCCTGATGAGATACA
3156 AACAAGTAGA
Statistics
Matches: 530, Mismatches: 61, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
207 39 0.07
208 292 0.55
209 199 0.38
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (209 bp):
ATCTTCCTGATGAGATACAGAAAAGTAGACCAATTCAACGAAGTGAAGCTCAATGTGAGTGAAAC
TTCCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTTC
CTGACGAGATGCAGAGAAGTTAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAA
TCAATGAAGCGATC
Found at i:2800 original size:85 final size:84
Alignment explanation
Indices: 2634--2793 Score: 205
Period size: 85 Copynumber: 1.9 Consensus size: 84
2624 CTTTCAAACC
* * *
2634 CCATCTTCCTGATGAGATATAGAGAAGTGGTCAAATCAATAAAGTGGACATCTTCCTGACGAGAT
1 CCATCTTCCTGATGAGATACAGAGAAGGGGTCAAATCAATAAAGTCGACATCTTCCTGACGAGAT
* * *
2699 GCAGATAAGTTAACCAAAT
66 ACAAAAAAGTTAACCAAAT
* * * *
2718 CCATCTTCTTGATGAGATACAGAGAAGGGGATTAAATCAATGAAG-CGATCATCTTCCTGATGAG
1 CCATCTTCCTGATGAGATACAGAGAAGGGG-TCAAATCAATAAAGTCGA-CATCTTCCTGACGAG
2782 ATACAAAAAAGT
64 ATACAAAAAAGT
2794 AGACCAATTA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
84 29 0.45
85 35 0.55
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (84 bp):
CCATCTTCCTGATGAGATACAGAGAAGGGGTCAAATCAATAAAGTCGACATCTTCCTGACGAGAT
ACAAAAAAGTTAACCAAAT
Found at i:3008 original size:85 final size:85
Alignment explanation
Indices: 2844--3001 Score: 208
Period size: 85 Copynumber: 1.9 Consensus size: 85
2834 CCAAACCCCA
* * * **
2844 TCTTCTTGATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTTCCTAACGAGATGT
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAATCAATAAAGTGGTCATCGTCCTAACGAGATAC
*
2909 AGAGAAGTGAACCAAATCCT
66 AAAGAAGTGAACCAAATCCT
* * * * * *
2929 TCTTCCTGATGAGATACATAGAAGTGGATTAAATCAATGAAGTGGTCATCGTCTTGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAATCAATAAAGTGGTCATCGTCCTAACGAGATAC
2994 AAAGAAGT
66 AAAGAAGT
3002 AGACCAAGTC
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
85 61 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATCAAATCAATAAAGTGGTCATCGTCCTAACGAGATAC
AAAGAAGTGAACCAAATCCT
Found at i:4140 original size:24 final size:24
Alignment explanation
Indices: 4113--4160 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
4103 AAAACAACCC
*
4113 TTCCATTGGAAGCTGTTTTTACCA
1 TTCCATTGGAAGCTGTCTTTACCA
4137 TTCCATTGGAAGCTGTCTTTACCA
1 TTCCATTGGAAGCTGTCTTTACCA
4161 ACAAAAGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.40
Consensus pattern (24 bp):
TTCCATTGGAAGCTGTCTTTACCA
Done.