Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000272.1 Kokia drynarioides strain JFW-HI SEQ_111018, 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: 6141
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Found at i:622 original size:16 final size:16
Alignment explanation
Indices: 601--658 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
591 GTTTTTGGAC
* *
601 TTTTAATTTAATTAAG
1 TTTTAATTAAATTAAA
* *
617 TTTTAAATCAATTTAAA
1 TTTT-AATTAAATTAAA
634 TTTTAATTAAATTTAAA
1 TTTTAATTAAA-TTAAA
*
651 TTTAAATT
1 TTTTAATT
659 TTAAAAGATA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
16 9 0.27
17 24 0.73
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTTAATTAAATTAAA
Found at i:637 original size:17 final size:17
Alignment explanation
Indices: 612--657 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
602 TTTAATTTAA
* *
612 TTAAGTTTTAAATCAAT
1 TTAAATTTTAAATAAAT
*
629 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
646 TTAAA-TTTAAAT
1 TTAAATTTTAAAT
658 TTTAAAAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:641 original size:6 final size:6
Alignment explanation
Indices: 626--682 Score: 62
Period size: 6 Copynumber: 9.3 Consensus size: 6
616 GTTTTAAATC
* **
626 AATTTA AATTTT AA-TTA AATTTA AATTTA AATTTTAA AAGATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AA-TTT-A AATTTA AATTTA
675 AATTTA AA
1 AATTTA AA
683 ATAAATTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 4 0.10
6 31 0.74
7 4 0.10
8 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:677 original size:26 final size:23
Alignment explanation
Indices: 626--690 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 23
616 GTTTTAAATC
*
626 AATTTAAATTTTAATTAAATTTA
1 AATTTAAATTTTAAATAAATTTA
*
649 AATTTAAATTTTAAA-AGA--TA
1 AATTTAAATTTTAAATAAATTTA
*
669 AATTTAAATTTAAAATAAATTT
1 AATTTAAATTTTAAATAAATTT
691 GAATCAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 2 0.06
23 15 0.43
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AATTTAAATTTTAAATAAATTTA
Found at i:1646 original size:205 final size:205
Alignment explanation
Indices: 1040--1648 Score: 812
Period size: 205 Copynumber: 3.0 Consensus size: 205
1030 TCTGGTTTCA
* * *** ** ** * *
1040 TTGACTTGGTCTTCTTCTCAGTATCTCATCAAGAAGACGACCATATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACTGCATCGTTTGTTTCAATTCGCTT
* * * * * * *
1105 CTCTGTGTTTCATCAGGAAGATG-GTTTTGGTTCACCTCCTC-GTATTTCATCAGGAAGCTAACC
66 CTCTGTATCTCATCAGGAAGACGAATTTT-GTCCA-CTTCTCAGTATCTCATCAGGAAGCTAACC
* ** *
1168 TTGTATTGCTTCGACCTGCTTCTCGGTGTCGT-ATCAAGAAGCTGGGGTTCGAAGATTTGCTCAC
129 TTTTATTGCTTCGACCTGCTTCTTAGTGTC-TCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC
**
1232 ATTAAGCGTGGGT
193 ATCGAGCGTGGGT
* *
1245 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACTGCATCGTTTGTTTCAATTCGCTT
* * *
1310 CTCTATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACCTT
66 CTCTGTATCTCATCAGGAAGACGAATTTTGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTT
1375 TTATTGCTTCGACCTGCTTCTTAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATC
131 TTATTGCTTCGACCTGCTTCTTAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATC
1440 GAGCGTGGGT
196 GAGCGTGGGT
* *
1450 TTGATTTGGTCTTCTTCTCAGTATCTCATCATGAAGATGATTGCATCGTTTGTTTCAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACTGCATCGTTTGTTTCAATTCGCTT
* *
1515 CTTTGTATCTCATCAGGAAGACGAATTTTGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCTT
66 CTCTGTATCTCATCAGGAAGACGAATTTTGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTT
* * * * *
1580 TTATTGCTTC-TCTATGCTTCTTAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTTACAT
131 TTATTGCTTCGAC-CTGCTTCTTAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
1644 CGAGC
195 CGAGC
1649 CTTGAGTTGG
Statistics
Matches: 358, Mismatches: 42, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
204 7 0.02
205 348 0.97
206 3 0.01
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (205 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACTGCATCGTTTGTTTCAATTCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTTGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTT
TTATTGCTTCGACCTGCTTCTTAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATC
GAGCGTGGGT
Found at i:3144 original size:23 final size:23
Alignment explanation
Indices: 3118--3163 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3108 CAATCTTTGT
3118 AAGTCTTGACTGAAGTTCTGTAG
1 AAGTCTTGACTGAAGTTCTGTAG
3141 AAGTCTTGACTGAAGTTCTGTAG
1 AAGTCTTGACTGAAGTTCTGTAG
3164 GCAAAGAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (23 bp):
AAGTCTTGACTGAAGTTCTGTAG
Done.