Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012226.1 Kokia drynarioides strain JFW-HI SEQ_127227, 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: 2777
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Found at i:291 original size:59 final size:59
Alignment explanation
Indices: 199--652 Score: 583
Period size: 59 Copynumber: 7.7 Consensus size: 59
189 TAAACTCTCC
*
199 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* ** * * *
258 AAAAATTATCATTTTACCCCCAAACTT-CAAAAAAACCTTTTTTGACCCCGAACTTTCC
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* * ** * *
316 CAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACAACGAACTTTCC
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
*
375 AAAAATTACCATTTTACCCCCAAACTTCAAAAAATCCCA-TTTTGACCCCGAACCTTCT
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* * * * * *
433 AAAAATTACCATTTTACCCTCGAATTTTCGAAAATCCCAATTTTGACCCCGAACCTTCT
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* * * * * *
492 AAAAATTACCGTTTTATCCCTAAAATTTCAAAAATCCTATTTTTGACCCCGAACCTTCT
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* *
551 AAAAATTACCATTTTACCCCCAAACTTCCAAAAACCCCATTTTTAACCCCGAACCTT-T
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
* * * *
609 CGAAAATTACCATTTTACCCTCAAAC-TCTAAAAATCCCTTTTTT
1 -AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTT
653 TTGAACCTTC
Statistics
Matches: 342, Mismatches: 50, Indels: 7
0.86 0.13 0.02
Matches are distributed among these distances:
58 114 0.33
59 228 0.67
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.31
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT
Found at i:406 original size:117 final size:117
Alignment explanation
Indices: 196--652 Score: 594
Period size: 117 Copynumber: 3.9 Consensus size: 117
186 CCTTAAACTC
* *
196 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAA
1 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAA
* * *
261 AATTATCATTTTACCCCCAAACTTCAAAAAAACCTTTTTTGACCCCGAACTT
66 AATTACCATTTTACCCCCAAACTTCAAAAAATCCTTTTTTGACCCCGAACCT
* * ** *
313 TCCCAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACAACGAACTTTCCAAA
1 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAA
**
378 AATTACCATTTTACCCCCAAACTTCAAAAAATCCCATTTTGACCCCGAACCT
66 AATTACCATTTTACCCCCAAACTTCAAAAAATCCTTTTTTGACCCCGAACCT
* * * * * * * *
430 TCTAAAAATTACCATTTTACCCTCGAATTTTCGAAAATCCCAATTTTGACCCCGAACCTTCTAAA
1 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAA
* ** *
495 AATTACCGTTTTATCCCTAAAATTTC-AAAAATCCTATTTTTGACCCCGAACCT
66 AATTACCATTTTA-CCCCCAAACTTCAAAAAATCCT-TTTTTGACCCCGAACCT
* * * * *
548 TCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAACCCCATTTTTAACCCCGAACCTTTCGAA
1 TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAA
* *
613 AATTACCATTTTACCCTCAAAC-TCTAAAAATCCCTTTTTT
66 AATTACCATTTTACCCCCAAACTTCAAAAAAT-CCTTTTTT
653 TTGAACCTTC
Statistics
Matches: 293, Mismatches: 43, Indels: 8
0.85 0.12 0.02
Matches are distributed among these distances:
116 2 0.01
117 197 0.67
118 94 0.32
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (117 bp):
TCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAA
AATTACCATTTTACCCCCAAACTTCAAAAAATCCTTTTTTGACCCCGAACCT
Found at i:414 original size:176 final size:176
Alignment explanation
Indices: 191--652 Score: 617
Period size: 176 Copynumber: 2.6 Consensus size: 176
181 AAGGTCCTTA
* *
191 AACTCTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
1 AACTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
* ** * *
256 CTAAAAATTATCATTTTACCCCCAAACTTCAAAAAAACCTTTTTTGACCCCGAACTTTCCCAAAA
66 CTAAAAATTACCATTTTACCCCCAAACTTCAAAAATCCCTTTTTTGACCCCGAACCTTCCAAAAA
*
321 TTACCATTTTA-CCCTCAAACTTCCAAAAATCCCATTTTTGACAACG
131 TTACCATTTTATCCCT-AAAATTCCAAAAATCCCATTTTTGACAACG
*
367 AACTTTCCAAAAATTACCATTTTACCCCCAAACTTCAAAAAATCCCA-TTTTGACCCCGAACCTT
1 AACTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
* ** * ** *
431 CTAAAAATTACCATTTTACCCTCGAATTTTCGAAAATCCCAATTTTGACCCCGAACCTTCTAAAA
66 CTAAAAATTACCATTTTACCC-CCAAACTTCAAAAATCCCTTTTTTGACCCCGAACCTTCCAAAA
* * * **
496 ATTACCGTTTTATCCCTAAAATTTCAAAAATCCTATTTTTGACCCCG
130 ATTACCATTTTATCCCTAAAATTCCAAAAATCCCATTTTTGACAACG
* * * *
543 AACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAACCCCATTTTTAACCCCGAACCTT
1 AACTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
* *
608 -TCGAAAATTACCATTTTACCCTCAAAC-TCTAAAAATCCCTTTTTT
66 CT-AAAAATTACCATTTTACCCCCAAACTTC-AAAAATCCCTTTTTT
653 TTGAACCTTC
Statistics
Matches: 247, Mismatches: 34, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
175 39 0.16
176 170 0.69
177 38 0.15
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (176 bp):
AACTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
CTAAAAATTACCATTTTACCCCCAAACTTCAAAAATCCCTTTTTTGACCCCGAACCTTCCAAAAA
TTACCATTTTATCCCTAAAATTCCAAAAATCCCATTTTTGACAACG
Done.