Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006988.1 Kokia drynarioides strain JFW-HI SEQ_121594, 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: 6402
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Found at i:156 original size:29 final size:29
Alignment explanation
Indices: 63--298 Score: 242
Period size: 29 Copynumber: 8.0 Consensus size: 29
53 GAGGTCCCTA
* * *
63 AACTGTCCAAAAATCTCATTTTCACCCCACG
1 AACT-TCCAAAAATCCCATTTTTA-CCCTCG
** * *
94 AACTTCCAAAAATCCCATTTTTAATCGCAA
1 AACTTCCAAAAATCCCATTTTTACCCTC-G
*
124 AACTTCCAAAAATCCCATTTTTATCCTCG
1 AACTTCCAAAAATCCCATTTTTACCCTCG
* *
153 AACTTCCAAAAATCCCATTTTCACCCTTG
1 AACTTCCAAAAATCCCATTTTTACCCTCG
* *
182 AACTTCCAAAAATCCCATTTTTACCCCCA
1 AACTTCCAAAAATCCCATTTTTACCCTCG
*
211 AACTTCCAAAAATTCCATTTTTGA-CCTCG
1 AACTTCCAAAAATCCCATTTTT-ACCCTCG
** *
240 AAACTTCCAAAAATTTCATTTTTACCC-CC
1 -AACTTCCAAAAATCCCATTTTTACCCTCG
*
269 ATACTTCCAAAAATCTCCATTTTTAACCTC
1 A-ACTTCCAAAAATC-CCATTTTTACCCTC
299 AAAACTCTCA
Statistics
Matches: 173, Mismatches: 25, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
28 1 0.01
29 91 0.53
30 76 0.44
31 5 0.03
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCTCG
Found at i:166 original size:59 final size:59
Alignment explanation
Indices: 62--352 Score: 297
Period size: 59 Copynumber: 4.9 Consensus size: 59
52 GGAGGTCCCT
* * * *
62 AAACTGTCCAAAAATCTCATTTTCACCCCACGAACTTCCAAAAATCCCATTTTTAATCGCA
1 AAACT-TCCAAAAATCCCATTTTTACCCC-CGAACTTCCAAAAATCCCATTTTTAACCTCA
* * * * *
123 AAACTTCCAAAAATCCCATTTTTATCCTCGAACTTCCAAAAATCCCATTTTCACCCT-T
1 AAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCA
* * * * *
181 GAACTTCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCA
**
240 AAACTTCCAAAAATTTCATTTTTACCCCC-ATACTTCCAAAAATCTCCATTTTTAACCTCA
1 AAACTTCCAAAAATCCCATTTTTACCCCCGA-ACTTCCAAAAATC-CCATTTTTAACCTCA
* * * *
300 AAAC-TCTCAAAATTACCC--TTTTACCCCCGAA-TGACTAAAAATTCCATTTTTAA
1 AAACTTC-CAAAAAT-CCCATTTTTACCCCCGAACT-TCCAAAAATCCCATTTTTAA
353 ACCCTAAATT
Statistics
Matches: 193, Mismatches: 30, Indels: 17
0.80 0.12 0.07
Matches are distributed among these distances:
58 61 0.32
59 83 0.43
60 43 0.22
61 6 0.03
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCA
Found at i:400 original size:60 final size:61
Alignment explanation
Indices: 215--417 Score: 149
Period size: 60 Copynumber: 3.4 Consensus size: 61
205 CCCCCAAACT
* * * *
215 TCCAAAAATTCCATTTTT-GA-CCTCGAAACTTCCAAAAATT-TCATTTTTACCCCC--AT-A
1 TCCAAAAATTCCATTTTTAAACCCTCAAAAC-TCCCAAAATTACCA-TTTTACCCCCGAATGA
* *
272 CTTCCAAAAATCTCCATTTTT-AA-CCTCAAAACTCTCAAAATTACCCTTTTACCCCCGAATGA
1 --TCCAAAAAT-TCCATTTTTAAACCCTCAAAACTCCCAAAATTACCATTTTACCCCCGAATGA
* ** * *
334 -CTAAAAATTCCATTTTTAAACCCT-AAATTTTCCCAAAATTACCATTTTGCCCCCGAGT-A
1 TCCAAAAATTCCATTTTTAAACCCTCAAA-ACTCCCAAAATTACCATTTTACCCCCGAATGA
* *
393 TCCAAAAAGTCTCATTTTCAAACCC
1 TCCAAAAATTC-CATTTTTAAACCC
418 GATCGCATCC
Statistics
Matches: 118, Mismatches: 16, Indels: 18
0.78 0.11 0.12
Matches are distributed among these distances:
58 9 0.08
59 40 0.34
60 54 0.46
61 14 0.12
62 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (61 bp):
TCCAAAAATTCCATTTTTAAACCCTCAAAACTCCCAAAATTACCATTTTACCCCCGAATGA
Found at i:2850 original size:39 final size:39
Alignment explanation
Indices: 2796--2901 Score: 149
Period size: 39 Copynumber: 2.7 Consensus size: 39
2786 GAATTGGTAG
*
2796 TGACATTGTAAACACTGCAATATTGTTACAGACTAGCAA
1 TGACACTGTAAACACTGCAATATTGTTACAGACTAGCAA
* * *
2835 TGACACTGTAAACACTGCAATAATGTTACAGACTGGCAG
1 TGACACTGTAAACACTGCAATATTGTTACAGACTAGCAA
* * *
2874 TGACACTATAAATACTGTAATATTGTTA
1 TGACACTGTAAACACTGCAATATTGTTA
2902 TGGAATTAGT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (39 bp):
TGACACTGTAAACACTGCAATATTGTTACAGACTAGCAA
Found at i:3578 original size:26 final size:26
Alignment explanation
Indices: 3544--3595 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3534 GTACTATGTT
* * *
3544 AGCTTATCTATGATTTAACTGTTATC
1 AGCTGATCTATGATTGAACTATTATC
*
3570 AGCTGATCTCTGATTGAACTATTATC
1 AGCTGATCTATGATTGAACTATTATC
3596 TGATGTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (26 bp):
AGCTGATCTATGATTGAACTATTATC
Done.