Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005060.1 Kokia drynarioides strain JFW-HI SEQ_118854, 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: 2695
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:23 original size:17 final size:17
Alignment explanation
Indices: 1--58 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
*
1 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAT
18 TTAAATTTATTTTCAAAT
1 TTAAATTTATTTT-AAAT
* *
36 TTAAAATTATTATAAAT
1 TTAAATTTATTTTAAAT
53 TTAAAT
1 TTAAAT
59 AAAGCCCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
17 22 0.61
18 14 0.39
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:786 original size:18 final size:17
Alignment explanation
Indices: 754--787 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
744 AAATGCATTG
*
754 AATGATTATTTAATAAC
1 AATGAATATTTAATAAC
771 AATGAATATATTAATAA
1 AATGAATAT-TTAATAA
788 TAATAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (17 bp):
AATGAATATTTAATAAC
Found at i:811 original size:23 final size:21
Alignment explanation
Indices: 781--838 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
771 AATGAATATA
*
781 TTAATAATAATAATAAATATTTT
1 TTAATAATAATAA-AAA-ATGTT
*
804 TTAATAATAATAAATAATGTT
1 TTAATAATAATAAAAAATGTT
825 TTAATAATAA-AAAA
1 TTAATAATAATAAAA
839 GGGAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.09
21 14 0.44
22 2 0.06
23 13 0.41
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
TTAATAATAATAAAAAATGTT
Found at i:2096 original size:29 final size:30
Alignment explanation
Indices: 2027--2260 Score: 244
Period size: 30 Copynumber: 7.9 Consensus size: 30
2017 GGAGGTCCCT
* *
2027 AACTT-CAAAAAGTCCCATTTTTGACCCCGA
1 AACTTCCAAAAA-TCCCATTTTTAACCCCCA
* * *
2057 AACTTTCAAAAATTCCA-TTTT-ACCCCCG
1 AACTTCCAAAAATCCCATTTTTAACCCCCA
* *
2085 AACTTCCAAAAATCCCATTTTTGACCCCGA
1 AACTTCCAAAAATCCCATTTTTAACCCCCA
* * * *
2115 AACTTCAAAAAAATTCCGTTTTT-ACCCCTA
1 AACTTC-CAAAAATCCCATTTTTAACCCCCA
* ** *
2145 AACTTCTAAAAATTTCATTTTTAACCCCAA
1 AACTTCCAAAAATCCCATTTTTAACCCCCA
*
2175 AACTTCCAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATCCCATTTTTAACCCCCA
**
2205 AACTTCCGTAAATCCCATTTTT-ACCCCCA
1 AACTTCCAAAAATCCCATTTTTAACCCCCA
*
2234 AACTTCCAAAAATCCCATTTTTGACCC
1 AACTTCCAAAAATCCCATTTTTAACCC
2261 TAAAATTTCA
Statistics
Matches: 175, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
28 20 0.11
29 47 0.27
30 89 0.51
31 19 0.11
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (30 bp):
AACTTCCAAAAATCCCATTTTTAACCCCCA
Found at i:2166 original size:60 final size:58
Alignment explanation
Indices: 2027--2265 Score: 232
Period size: 59 Copynumber: 4.0 Consensus size: 58
2017 GGAGGTCCCT
* **
2027 AACTT-CAAAAAGTCCCATTTTTGACCCCGAAACTTTC-AAAAATTCCATTTTACCCCCG
1 AACTTCCAAAAA-TCCCATTTTTGACCCCGAAAC-TTCAAAAAATTCCTTTTTACCCCAA
*
2085 AACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCAAAAAAATTCCGTTTTTACCCCTA
1 AACTTCCAAAAATCCCATTTTTGACCCCGAAACTTC-AAAAAATTCC-TTTTTACCCCAA
* ** * * * *
2145 AACTTCTAAAAATTTCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCAAAAAATTCC-TTTTT-ACCCCAA
** * * * *
2205 AACTTCCGTAAATCCCATTTTT-ACCCCCAAACTTCCAAAAATCCCATTTTTGACCCTAA
1 AACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCAAAAAATTCC-TTTTT-ACCCCAA
2264 AA
1 AA
2266 TTTCATAAAA
Statistics
Matches: 156, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
57 3 0.02
58 26 0.17
59 64 0.41
60 63 0.40
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.30
Consensus pattern (58 bp):
AACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCAAAAAATTCCTTTTTACCCCAA
Found at i:2286 original size:59 final size:58
Alignment explanation
Indices: 2039--2291 Score: 192
Period size: 59 Copynumber: 4.3 Consensus size: 58
2029 CTTCAAAAAG
* * * ** *
2039 TCCCATTTTTGACCCCGAAACTTTCAAAAATTCCA-TTTT-ACCCCCGAACTTCCAAAAA
1 TCCCA-TTTT-ACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCATAAA
* * * * * * *
2097 TCCCATTTTTGACCCCGAAACTTCAAAAAAATTCCGTTTTT-ACCCCTAAACTTCTAAAAA
1 TCCCA-TTTT-ACCCCCAAACTTC-CAAAAATCCCATTTTTAACCCCAAAACTTCCATAAA
** * *
2157 TTTCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCGTAAA
1 TCCCA-TTTT-ACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCATAAA
* * *
2217 TCCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCTAAAA-TTTCATAAAA
1 TCCCA-TTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAT-AAA
2276 TTACCC-TTTTACCCCC
1 -T-CCCATTTTACCCCC
2292 GGGTATCCGA
Statistics
Matches: 165, Mismatches: 24, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
58 27 0.16
59 71 0.43
60 64 0.39
61 3 0.02
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.32
Consensus pattern (58 bp):
TCCCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCATAAA
Found at i:2689 original size:96 final size:96
Alignment explanation
Indices: 2519--2693 Score: 232
Period size: 96 Copynumber: 1.8 Consensus size: 96
2509 AAAACTTTAA
* * * **
2519 AATCGAGGCAATATTCTTTTATTTCGAGTTTCGAAAATTTGTGCCTTAACTTACTAGGTGCTATT
1 AATCGAGGCAATATTCTCTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
2584 TTTCCTCAAATCGAAATAATTGAATACTCTT
66 TTTCCTCAAATCGAAATAATTGAATACTCTT
2615 AATCGAGGCAATATT-TCCTTATCTTCGA--TTCTG-AAATATTGCGCCTTAACTTACTAGGTGC
1 AATCGAGGCAATATTCT-CTTAT-TTCGAGTTTC-GAAAAT-TTGCGCCTTAACTTACTAGGTGC
*
2676 AACCTTTCTTCAAATCGA
62 AACCTTTCCTCAAATCGA
2694 GA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
95 8 0.12
96 56 0.81
97 5 0.07
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (96 bp):
AATCGAGGCAATATTCTCTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
TTTCCTCAAATCGAAATAATTGAATACTCTT
Done.