Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000351.1 Kokia drynarioides strain JFW-HI SEQ_111132, 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, 972
Length: 1620
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Found at i:621 original size:96 final size:96
Alignment explanation
Indices: 433--624 Score: 228
Period size: 96 Copynumber: 2.0 Consensus size: 96
423 TTTTTGGGAG
** *
433 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTACACCTAGGAAGTTAAGGCACAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAAGAAGTTAAGGCACAATATTTCA
**
498 GAATCGAAGATAAGGAAACATTACCTCGATT
66 GAATCGAAGATAAAAAAACATTACCTCGATT
* * * * *
529 AAGGGTATTTGATTATTTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAAGAAGTTAAGGCACAATA-TTTC
* *
593 -GAAACTCGAA-ATAAAAAAATATTGCCTCGATT
65 AG-AA-TCGAAGATAAAAAAACATTACCTCGATT
625 TTAAAGTTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
95 2 0.02
96 74 0.91
97 5 0.06
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAAGAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAAAAACATTACCTCGATT
Found at i:870 original size:29 final size:28
Alignment explanation
Indices: 838--899 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
828 AAAATGAGAC
*
838 TTTTCGGATACCCGGGGGCAAAATGGTAA
1 TTTT-GGATACCCGAGGGCAAAATGGTAA
* *
867 TTTTGGATTCTCGAGGGCAAAATGGTAA
1 TTTTGGATACCCGAGGGCAAAATGGTAA
895 TTTTG
1 TTTTG
900 AGAAAATTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
TTTTGGATACCCGAGGGCAAAATGGTAA
Found at i:981 original size:58 final size:58
Alignment explanation
Indices: 916--1046 Score: 156
Period size: 58 Copynumber: 2.2 Consensus size: 58
906 TTCAAGGTTA
* * * * *
916 AAAATGGAATTTTTAGACATTCGGGGGTAAAAGGGTAA-TTTTGAGAGTTTTGAGGTC
1 AAAATGGAATTTTTAGACATCCGGAGGCAAAAAGGTAATTTTTGAAAGTTTTGAGGTC
* * *
973 GAAAATGGAGTTTTTGGACATCCGGAGGCAAAAAGGTAATTTTTGAAAGTTTTGGGGTC
1 -AAAATGGAATTTTTAGACATCCGGAGGCAAAAAGGTAATTTTTGAAAGTTTTGAGGTC
*
1032 AAAATTGGAAATTTT
1 AAAA-TGGAATTTTT
1047 GGAGGTTTAG
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
58 36 0.59
59 25 0.41
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (58 bp):
AAAATGGAATTTTTAGACATCCGGAGGCAAAAAGGTAATTTTTGAAAGTTTTGAGGTC
Found at i:1289 original size:59 final size:58
Alignment explanation
Indices: 916--1383 Score: 445
Period size: 59 Copynumber: 8.0 Consensus size: 58
906 TTCAAGGTTA
* * *
916 AAAATGGAATTTTTAGACA-TTCGGGGGT-AAAAGGGTAA-TTTT-GAGAGTTTT-GAGGTC
1 AAAATGGAATTTTTGGA-AGTTTGGGGGTAAAAATGG-AATTTTTGGA-AGTTTTCG-GGTC
* ** * * * *
973 GAAAATGGAGTTTTTGGACA-TCCGGAGGCAAAAA-GGTAATTTTTGAAAGTTTTGGGGTC
1 -AAAATGGAATTTTTGGA-AGTTTGGGGGTAAAAATGG-AATTTTTGGAAGTTTTCGGGTC
* * * * *
1032 AAAATTGGAAATTTTGGAGGTTTAGGTGTAAAAATGGAATTTTTGGAAG-TTTCGAGGTAA
1 AAAA-TGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTTCG-GGT-C
* *
1092 AAAATGGAATTCTTGGAAGTTCGGGGGGTAAAAATGGAATTTTTGGAAGTTTT-GGTGTC
1 AAAATGGAATTTTTGGAAGTT-TGGGGGTAAAAATGGAATTTTTGGAAGTTTTCGG-GTC
* * *
1151 AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAGTTTTTGGAAGTTTTGGGGTC
1 -AAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTTCGGGTC
* * *
1210 AATAATGGAATTTTTTGAAGTTTGGGGGTAAAAAATGAAATTTTTGGAAGTTTTTGGGTC
1 AA-AATGGAATTTTTGGAAGTTTGGGGGT-AAAAATGGAATTTTTGGAAGTTTTCGGGTC
* * *
1270 AAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGGAATCTTGGGAAG-TTTCGAGGTC
1 AAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTTCG-GGTC
* * *
1328 AAAAATGGCATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTAGGAAG-TTTCGGG
1 -AAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTTCGGG
1384 GTCTCCAGAG
Statistics
Matches: 347, Mismatches: 45, Indels: 36
0.81 0.11 0.08
Matches are distributed among these distances:
57 4 0.01
58 61 0.18
59 193 0.56
60 86 0.25
61 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTTCGGGTC
Found at i:1316 original size:29 final size:30
Alignment explanation
Indices: 1001--1386 Score: 421
Period size: 30 Copynumber: 13.0 Consensus size: 30
991 CATCCGGAGG
*
1001 CAAAAA-GGTAATTTTTGAAAGTTTTGGGGT
1 CAAAAATGG-AATTTTTGGAAGTTTTGGGGT
* * * * *
1031 CAAAATTGGAAATTTTGGAGGTTTAGGTGT
1 CAAAAATGGAATTTTTGGAAGTTTTGGGGT
* *
1061 -AAAAATGGAATTTTTGGAAGTTTCGAGGT
1 CAAAAATGGAATTTTTGGAAGTTTTGGGGT
* * **
1090 AAAAAATGGAATTCTTGGAAGTTCGGGGGGT
1 CAAAAATGGAATTTTTGGAAGTT-TTGGGGT
*
1121 -AAAAATGGAATTTTTGGAAGTTTTGGTGT
1 CAAAAATGGAATTTTTGGAAGTTTTGGGGT
1150 CAAAAATGGAATTTTTGGAAG-TTTGAGGGT
1 CAAAAATGGAATTTTTGGAAGTTTTG-GGGT
*
1180 -AAAAATGGAGTTTTTGGAAGTTTTGGGGT
1 CAAAAATGGAATTTTTGGAAGTTTTGGGGT
* * *
1209 CAATAATGGAATTTTTTGAAGTTTGGGGGT
1 CAAAAATGGAATTTTTGGAAGTTTTGGGGT
* * *
1239 AAAAAATGAAATTTTTGGAAGTTTTTGGGT
1 CAAAAATGGAATTTTTGGAAGTTTTGGGGT
*
1269 C-AAAATGGAATTTTTGGAAGTTTAGGGGT
1 CAAAAATGGAATTTTTGGAAGTTTTGGGGT
* * * *
1298 -AAAAATGGAATCTTGGGAAGTTTCGAGGT
1 CAAAAATGGAATTTTTGGAAGTTTTGGGGT
*
1327 CAAAAATGGCATTTTTGGAAG-TTTGAGGGT
1 CAAAAATGGAATTTTTGGAAGTTTTG-GGGT
* *
1357 -AAAAATGGAATTTTAGGAAGTTTCGGGGT
1 CAAAAATGGAATTTTTGGAAGTTTTGGGGT
1386 C
1 C
1387 TCCAGAGCAA
Statistics
Matches: 296, Mismatches: 48, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
29 128 0.43
30 162 0.55
31 6 0.02
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.35
Consensus pattern (30 bp):
CAAAAATGGAATTTTTGGAAGTTTTGGGGT
Done.