Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006619.1 Kokia drynarioides strain JFW-HI SEQ_121209, 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: 3179
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:23 original size:17 final size:18
Alignment explanation
Indices: 1--47 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
1 TTTAAATTTAATTTAAG-
1 TTTAAATTTAATTTAAGA
* * *
18 TTTAAAATTATTTTCAGA
1 TTTAAATTTAATTTAAGA
36 TTTAAAATTTAA
1 TTT-AAATTTAA
48 AATAAATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 14 0.61
18 3 0.13
19 6 0.26
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (18 bp):
TTTAAATTTAATTTAAGA
Found at i:859 original size:3 final size:3
Alignment explanation
Indices: 839--892 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
829 ATATTTTTTA
* * *
839 AAT AAT ATT AAT ATT AAT AAT ATT AAT GAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
885 AAT AAT AA
1 AAT AAT AA
893 AACGAAAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:2102 original size:59 final size:59
Alignment explanation
Indices: 2008--2496 Score: 372
Period size: 59 Copynumber: 8.3 Consensus size: 59
1998 CTAAATTGTT
* * * *
2008 CAAAAATCCCATTTTTATTCCCG-AACTTCTAAAAAACCAATTTTTAACCCCAAAACTTT
1 CAAAAATCCCAATTTTA-ACCCGAAACTTCTAAAAATCCAATTTTTAACCCCAAAACTTC
* * * *
2067 TAAAAATCCCAATTTTAACCTCGAAACTTCCAAAAATTCC-ATTTTT-A-CCCACGAACCTC
1 CAAAAATCCCAATTTTAACC-CGAAACTTCTAAAAA-TCCAATTTTTAACCCCA-AAACTTC
* * ** * **
2126 CAAAAATCTCATTTTTAACCCCTAACTTCTAAAAATCTAATTTTTAACCTTAAAACTTC
1 CAAAAATCCCAATTTTAACCCGAAACTTCTAAAAATCCAATTTTTAACCCCAAAACTTC
* * * * * * * * *
2185 TAAAAA-ACTAATTTTTAACCCTAAAACTTATAATAATCCCA-TTTTAACCCTAAAAATTC
1 CAAAAATCCCAA-TTTTAACCC-GAAACTTCTAAAAATCCAATTTTTAACCCCAAAACTTC
* * * *
2244 TAAAAATTCCAATTTTAACCCCGAAGCTTTTAAAAATCTCAA-TTTTAACCCCAAAACTTC
1 CAAAAATCCCAATTTTAA-CCCGAAACTTCTAAAAATC-CAATTTTTAACCCCAAAACTTC
* * * * * * *
2304 CAAAAATTCCATTTTTACCCCCG-AACCTCAAAAAATCCCATTTTTAACCTCAAAACTTC
1 CAAAAATCCCAATTTTA-ACCCGAAACTTCTAAAAATCCAATTTTTAACCCCAAAACTTC
* * * *
2363 CAAAAAATCGC-ATTTTTACCCTTAAACTTTTAAAAATCCAATTTTTAACCCCAAAACTTC
1 C-AAAAATCCCAATTTTAACCC-GAAACTTCTAAAAATCCAATTTTTAACCCCAAAACTTC
* * ** *
2423 CAAAAATCCC-ATTTTAACCCCAAAGCTTTTAAAAATTCC-A-TTTTAACCCCTGAACCTC
1 CAAAAATCCCAATTTTAACCCGAAA-CTTCTAAAAA-TCCAATTTTTAACCCCAAAACTTC
*
2481 CAAAAATCCCATTTTT
1 CAAAAATCCCAATTTT
2497 TTTAATAATA
Statistics
Matches: 342, Mismatches: 68, Indels: 40
0.76 0.15 0.09
Matches are distributed among these distances:
57 2 0.01
58 58 0.17
59 163 0.48
60 117 0.34
61 2 0.01
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (59 bp):
CAAAAATCCCAATTTTAACCCGAAACTTCTAAAAATCCAATTTTTAACCCCAAAACTTC
Found at i:2458 original size:29 final size:30
Alignment explanation
Indices: 2009--2496 Score: 391
Period size: 30 Copynumber: 16.5 Consensus size: 30
1999 TAAATTGTTC
** *
2009 AAAAATCCCATTTTTATTCCC-GAACTTCT
1 AAAAATCCCATTTTTAACCCCAAAACTTCT
* * *
2038 AAAAAACCAATTTTTAACCCCAAAACTTTT
1 AAAAATCCCATTTTTAACCCCAAAACTTCT
* * * *
2068 AAAAATCCCAATTTTAACCTCGAAACTTCC
1 AAAAATCCCATTTTTAACCCCAAAACTTCT
* * * *
2098 AAAAATTCCATTTTT-A-CCCACGAACCTCC
1 AAAAATCCCATTTTTAACCCCA-AAACTTCT
* *
2127 AAAAATCTCATTTTTAACCCC-TAACTTCT
1 AAAAATCCCATTTTTAACCCCAAAACTTCT
** **
2156 AAAAATCTAATTTTTAACCTTAAAACTTCT
1 AAAAATCCCATTTTTAACCCCAAAACTTCT
* ** * *
2186 AAAAAACTAATTTTTAACCCTAAAACTTAT
1 AAAAATCCCATTTTTAACCCCAAAACTTCT
* * *
2216 AATAATCCCA-TTTTAACCCTAAAAATTCT
1 AAAAATCCCATTTTTAACCCCAAAACTTCT
* * * * *
2245 AAAAATTCCAATTTTAACCCCGAAGCTTTT
1 AAAAATCCCATTTTTAACCCCAAAACTTCT
* * *
2275 AAAAATCTCAATTTTAACCCCAAAACTTCC
1 AAAAATCCCATTTTTAACCCCAAAACTTCT
* ** * *
2305 AAAAATTCCATTTTT-ACCCCCGAACCTCA
1 AAAAATCCCATTTTTAACCCCAAAACTTCT
* *
2334 AAAAATCCCATTTTTAACCTCAAAACTTCCA
1 AAAAATCCCATTTTTAACCCCAAAACTT-CT
* ** *
2365 AAAAATCGCATTTTT-ACCCTTAAACTTTT
1 AAAAATCCCATTTTTAACCCCAAAACTTCT
* *
2394 AAAAATCCAATTTTTAACCCCAAAACTTCC
1 AAAAATCCCATTTTTAACCCCAAAACTTCT
* *
2424 AAAAATCCCA-TTTTAACCCCAAAGCTTTT
1 AAAAATCCCATTTTTAACCCCAAAACTTCT
* ** * *
2453 AAAAATTCCA-TTTTAACCCCTGAACCTCC
1 AAAAATCCCATTTTTAACCCCAAAACTTCT
2482 AAAAATCCCATTTTT
1 AAAAATCCCATTTTT
2497 TTTAATAATA
Statistics
Matches: 363, Mismatches: 86, Indels: 19
0.78 0.18 0.04
Matches are distributed among these distances:
28 2 0.01
29 169 0.47
30 173 0.48
31 19 0.05
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (30 bp):
AAAAATCCCATTTTTAACCCCAAAACTTCT
Found at i:2593 original size:21 final size:21
Alignment explanation
Indices: 2569--2656 Score: 151
Period size: 21 Copynumber: 4.2 Consensus size: 21
2559 AAAGAAAACC
*
2569 GTTTGGATCTAG-GCTAGATCT
1 GTTT-GATCTAGACCTAGATCT
2590 GTTTGATCTAGACCTAGATCT
1 GTTTGATCTAGACCTAGATCT
2611 GTTTGATCTAGACCTAGATCT
1 GTTTGATCTAGACCTAGATCT
2632 GTTTGATCTAGACCTAGATCT
1 GTTTGATCTAGACCTAGATCT
2653 GTTT
1 GTTT
2657 TTTTTTAAAG
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
20 7 0.11
21 58 0.89
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (21 bp):
GTTTGATCTAGACCTAGATCT
Done.