Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004312.1 Kokia drynarioides strain JFW-HI SEQ_117626, 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: 3615
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:1651 original size:121 final size:118
Alignment explanation
Indices: 1362--1722 Score: 509
Period size: 121 Copynumber: 3.0 Consensus size: 118
1352 GAAAAATTTA
* *
1362 AAATCCCTTGAACCAATTTTTAGAAATTGTCAAAGCTATTGCTTTTAAACCTATTAAAAATTAAT
1 AAATCCCTTGAACC-ATTTCTAGAAATTGTCAAA-CTGTTGC-TTTAAACCTATTAAAAATTAAT
* * *
1427 TCCTTAATTTGTTAGAAACATATATTAAATAATTTTAAA-AAAAAATAAAAGAAAT
63 TCCTTAATTTGTTAGAAACATATTTTAAATAATTTAAAATAAAAAATAAAAGAAAC
* * *
1482 AAATCCCTTG-A--A--TCAAGAAATTGTCAAAACAGTTGCTTTAAACCTATTAAAAATTAACTC
1 AAATCCCTTGAACCATTTCTAGAAATTGTC-AAACTGTTGCTTTAAACCTATTAAAAATTAATTC
*
1542 CTTAATTTGTTAGAAACATATTTTAAATAATTTAAAGATAAAAAATGAAAGAAAC
65 CTTAATTTGTTAGAAACATATTTTAAATAATTTAAA-ATAAAAAATAAAAGAAAC
1597 AAATCCCTTGAACCATTCTCTAGAAATTGTCGAAACTGTTGCTTTAAACCTATTAAAAATTAATT
1 AAATCCCTTGAACCATT-TCTAGAAATTGTC-AAACTGTTGCTTTAAACCTATTAAAAATTAATT
*
1662 CCTTAATTTATTAGAAACATATTTTAAATAATTTAAAAATAAAAAATAAAAAGAAAC
64 CCTTAATTTGTTAGAAACATATTTTAAATAATTT-AAAATAAAAAAT-AAAAGAAAC
1719 AAAT
1 AAAT
1723 AAATCCTAAA
Statistics
Matches: 215, Mismatches: 15, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
113 57 0.27
114 17 0.08
115 27 0.13
116 2 0.01
118 1 0.00
119 1 0.00
120 10 0.05
121 85 0.40
122 15 0.07
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (118 bp):
AAATCCCTTGAACCATTTCTAGAAATTGTCAAACTGTTGCTTTAAACCTATTAAAAATTAATTCC
TTAATTTGTTAGAAACATATTTTAAATAATTTAAAATAAAAAATAAAAGAAAC
Found at i:2227 original size:18 final size:18
Alignment explanation
Indices: 2206--2253 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
2196 ATTAAACTTT
2206 AAAATTTTAAAATATTAA
1 AAAATTTTAAAATATTAA
* * *
2224 AAAATATTTTATATTTTAA
1 AAAAT-TTTAAAATATTAA
2243 AATAATTTTAA
1 AA-AATTTTAA
2254 TGATTTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.21
19 16 0.67
20 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATTTTAAAATATTAA
Found at i:3425 original size:10 final size:9
Alignment explanation
Indices: 3410--3518 Score: 53
Period size: 9 Copynumber: 11.7 Consensus size: 9
3400 ATAAAAAAAA
*
3410 ATAAAAGTT
1 ATAAAAATT
3419 ATAAAAATT
1 ATAAAAATT
**
3428 ATTAAATTTT
1 A-TAAAAATT
*
3438 AATAAAAAACT
1 -AT-AAAAATT
3449 ATAAAAA--
1 ATAAAAATT
*
3456 ATAAAATTT
1 ATAAAAATT
3465 ATAAAAATT
1 ATAAAAATT
* *
3474 GTAAAAAACT
1 AT-AAAAATT
3484 AT-AAAATAT
1 ATAAAAAT-T
*
3493 ATAGAAAAAT
1 ATA-AAAATT
*
3503 AAAAATAATT
1 ATAAA-AATT
3513 ATAAAA
1 ATAAAA
3519 TTTTACATAT
Statistics
Matches: 74, Mismatches: 16, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
7 6 0.08
8 4 0.05
9 29 0.39
10 26 0.35
11 9 0.12
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (9 bp):
ATAAAAATT
Found at i:3488 original size:45 final size:45
Alignment explanation
Indices: 3396--3506 Score: 116
Period size: 46 Copynumber: 2.4 Consensus size: 45
3386 TCACAACCAC
* * ***
3396 AAAAATAAAAAAAAATAAAAGTTATAAAAATTATTAAATTTTAATA
1 AAAAAT-ATAAAAAATAAAAGTTATAAAAATTATAAAAAACTAATA
* *
3442 AAAAACTATAAAAAATAAAATTTATAAAAATTGTAAAAAACT-ATA
1 AAAAA-TATAAAAAATAAAAGTTATAAAAATTATAAAAAACTAATA
*
3487 AAATATATAGAAAAATAAAA
1 AAAAATATA-AAAAATAAAA
3507 ATAATTATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
44 4 0.07
45 17 0.31
46 33 0.60
47 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (45 bp):
AAAAATATAAAAAATAAAAGTTATAAAAATTATAAAAAACTAATA
Done.