Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013720.1 Kokia drynarioides strain JFW-HI SEQ_128748, 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: 14129
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Found at i:290 original size:46 final size:46
Alignment explanation
Indices: 197--304 Score: 116
Period size: 46 Copynumber: 2.4 Consensus size: 46
187 TTTATTATTA
* *
197 ATTATTAATA-TCACTATTATTATTATTATTATTAATGAGGCAGTT
1 ATTATTAATAGTTATTATTATTATTATTATTATTAATGAGGCAGTT
* * *
242 ATTACTTATTA-TTATTATTGTTATTATTATTATTAAT-A-GCAAATTT
1 ATTA-TTAATAGTTATTATTATTATTATTATTATTAATGAGGC--AGTT
288 ATTATTAATAGTTATTA
1 ATTATTAATAGTTATTA
305 AATAAATTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
44 2 0.04
45 10 0.19
46 41 0.77
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.53
Consensus pattern (46 bp):
ATTATTAATAGTTATTATTATTATTATTATTATTAATGAGGCAGTT
Found at i:294 original size:3 final size:3
Alignment explanation
Indices: 188--276 Score: 70
Period size: 3 Copynumber: 28.0 Consensus size: 3
178 TTTCAATTTT
* * * *
188 TTA TTA TTAA TTA TTA ATA TCA CTA TTA TTA TTA TTA TTA TTAA TGA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
** *
235 GGCA GTTA TTA CTTA TTA TTA TTA TTG TTA TTA TTA TTA TTA
1 -TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
277 ATAGCAAATT
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
3 58 0.84
4 11 0.16
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:1792 original size:200 final size:204
Alignment explanation
Indices: 1306--1824 Score: 866
Period size: 205 Copynumber: 2.6 Consensus size: 204
1296 TTGACTTGAC
* *
1306 CTTCTTCTCAGTATCTCATCAGAAAGATGACCGCGTTGTTTGTTTCAATTCGTTTCTCTGTATCT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTTGTTTCAATTCGCTTCTCTGTATCT
*
1371 CATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCCCATCAGGAAGCTAACCTTTTATTGCTTC
66 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCCCATCAGGAAGCTAACCTTTTATTGCTTC
* *
1436 GACCTGCTTCTCAGTGTCTCATTAGGAAGCTGGAGTTCGAAGATTTACTCACATCGAGTGCGGGT
131 GACCTGCTTCTCAGTGTCTCATAAGGAAGCTGGAGTTCGAAGATTTA-TCACATCGAGCGCGGGT
1501 TTGATTTGGT
195 TTGATTTGGT
* * *
1511 CTTCTTCTCAGTATCTTATCAGGAAGATGACCGCGTTGTTTGTTTCAATTTGCCTCTCTGTATCT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTTGTTTCAATTCGCTTCTCTGTATCT
* *
1576 CATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACCTTTTATTGCTTC
66 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCCCATCAGGAAGCTAACCTTTTATTGCTTC
* * *
1641 GACCTGCTTCTCAGTGTCTCATAAGGAAGCTGGGGTTCGAAGA-TT-T-GC-TCGAGCGTGGGTT
131 GACCTGCTTCTCAGTGTCTCATAAGGAAGCTGGAGTTCGAAGATTTATCACATCGAGCGCGGGTT
1702 TGATTTGGT
196 TGATTTGGT
*
1711 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTTGTTTCAATTCGCTTCTCTGTATCT
*
1776 CATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCCCATCAGGAAGCT
66 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCCCATCAGGAAGCT
1825 GGAGTTCGAA
Statistics
Matches: 294, Mismatches: 20, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
200 127 0.43
201 1 0.00
202 1 0.00
204 2 0.01
205 163 0.55
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.35
Consensus pattern (204 bp):
CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTTGTTTGTTTCAATTCGCTTCTCTGTATCT
CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCCCATCAGGAAGCTAACCTTTTATTGCTTC
GACCTGCTTCTCAGTGTCTCATAAGGAAGCTGGAGTTCGAAGATTTATCACATCGAGCGCGGGTT
TGATTTGGT
Found at i:2735 original size:45 final size:45
Alignment explanation
Indices: 2653--2738 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
2643 TTGGTCCCAG
* *
2653 GACGCCCTTTGCGGGTTTTCATCCTGAACCCCTTTTTTTTTTCGA
1 GACGCCCTTTGCGGGTTTTCATCCTAAACCCCATTTTTTTTTCGA
* *
2698 GACGCCCTTTGTGGGTTTTCAT-CTAAATTCCCATTTTTTTT
1 GACGCCCTTTGCGGGTTTTCATCCTAAA-CCCCATTTTTTTT
2739 AAACGAAGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 4 0.11
45 32 0.89
ACGTcount: A:0.13, C:0.26, G:0.16, T:0.45
Consensus pattern (45 bp):
GACGCCCTTTGCGGGTTTTCATCCTAAACCCCATTTTTTTTTCGA
Found at i:13087 original size:96 final size:96
Alignment explanation
Indices: 12906--13090 Score: 221
Period size: 96 Copynumber: 1.9 Consensus size: 96
12896 GAAAAGGATG
* ** * * * *
12906 TTCGATTATCCCGATTTGATGAAAGGTTGCACCTAGTAAGTTATGGCGCAAATTTTTAGAATCGA
1 TTCGATTATCCCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAAAATAGA
*
12971 AGATAAGGAAACATTACCTCGATTAAGGGTA
66 AGATAAAGAAACATTACCTCGATTAAGGGTA
** *
13002 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGTAAATTTTCAAAACTAG
1 TTCGATTATCCCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAAAA-TAG
* *
13067 AA-ATAAA-AGAATATTGCCTCGATT
65 AAGATAAAGA-AACATTACCTCGATT
13091 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
95 1 0.01
96 69 0.93
97 4 0.05
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (96 bp):
TTCGATTATCCCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAAAATAGA
AGATAAAGAAACATTACCTCGATTAAGGGTA
Found at i:13456 original size:29 final size:30
Alignment explanation
Indices: 13412--13664 Score: 244
Period size: 29 Copynumber: 8.7 Consensus size: 30
13402 ACATTCGAGT
13412 GTAAAAA-GGGTAATTTT-GAGAGTTTTGAGG
1 GTAAAAATGGG-AATTTTGGA-AGTTTTGAGG
* * *
13442 GTAAAGAT-GGAA-TTTGTAAGTTTCG-GG
1 GTAAAAATGGGAATTTTGGAAGTTTTGAGG
**
13469 GGCAAAAT-GGAATTTTTGGAAGTTTT-AGG
1 GTAAAAATGGGAA-TTTTGGAAGTTTTGAGG
* * *
13498 GTCAAAAATAGGATTTTTGGAAGTTTCGAGG
1 GT-AAAAATGGGAATTTTGGAAGTTTTGAGG
* *
13529 TTAAAAATGGGATTTTTGGAAG-TTTGAGG
1 GTAAAAATGGGAATTTTGGAAGTTTTGAGG
*
13558 GTAAAAATGGGACTTTTGGAAG-TTTGAGG
1 GTAAAAATGGGAATTTTGGAAGTTTTGAGG
*
13587 GTAAAAATGGGATTTTTGGAAGTTTTG-GG
1 GTAAAAATGGGAATTTTGGAAGTTTTGAGG
13616 GTCAAAAATGGG-ATTTTGGAA-TTTCTGA-G
1 GT-AAAAATGGGAATTTTGGAAGTTT-TGAGG
*
13645 GTAAAAATGGGAGTTTTGGA
1 GTAAAAATGGGAATTTTGGA
13665 CAATTTAGGG
Statistics
Matches: 190, Mismatches: 20, Indels: 27
0.80 0.08 0.11
Matches are distributed among these distances:
27 11 0.06
28 21 0.11
29 94 0.49
30 57 0.30
31 7 0.04
ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34
Consensus pattern (30 bp):
GTAAAAATGGGAATTTTGGAAGTTTTGAGG
Done.