Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010715.1 Kokia drynarioides strain JFW-HI SEQ_125665, 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, 940
Length: 1567
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Found at i:790 original size:139 final size:140
Alignment explanation
Indices: 453--790 Score: 585
Period size: 139 Copynumber: 2.4 Consensus size: 140
443 AAACGGTTAG
* *
453 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA-TAGAGAAACGGA
1 CTTCCTGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACTAGAGAAGCGGA
517 TTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAA
66 TTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAA
582 ACGAGCAAAT
131 ACGAGCAAAT
592 CTTCCTGAT-AGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAC-AGAGAAGCGG
1 CTTCCTGATGAGG-TACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACTAGAGAAGCGG
*
655 ATTGAAATAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGA
65 ATTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGA
*
720 ATCGAGCAAAT
130 AACGAGCAAAT
* *
731 CTTCCAGATGAGGTACTGATAAGTGAACCAAATTCGTCTTCCTGATGAGATACTA-AGAAG
1 CTTCCTGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACTAGAGAAG
791 AAGACCAAAC
Statistics
Matches: 189, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
138 2 0.01
139 183 0.97
140 4 0.02
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (140 bp):
CTTCCTGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACTAGAGAAGCGGA
TTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAA
ACGAGCAAAT
Found at i:1283 original size:17 final size:17
Alignment explanation
Indices: 1255--1327 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
1245 TTGGAAATTG
1255 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
1271 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
1288 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
1305 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
1322 AATTTA
1 AATTTA
1328 GAAAGTCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
16 5 0.10
17 45 0.90
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:1303 original size:7 final size:6
Alignment explanation
Indices: 1260--1327 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
1250 AATTGAATTT
* *
1260 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
*
1306 ATTT-- ATTATAA AATTAA ATTTA
1 ATTTAA ATT-TAA ATTTAA ATTTA
1328 GAAAGTCCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 7 0.14
5 5 0.10
6 32 0.64
7 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:1367 original size:13 final size:13
Alignment explanation
Indices: 1329--1368 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1319 TTAAATTTAG
*
1329 AAAGTCCAATTAA
1 AAAGTCCAATTAC
1342 AAAGTCCAA--AC
1 AAAGTCCAATTAC
1353 AAAGTCCAATTAC
1 AAAGTCCAATTAC
1366 AAA
1 AAA
1369 TGGCCCAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 10 0.42
13 14 0.58
ACGTcount: A:0.55, C:0.20, G:0.07, T:0.17
Consensus pattern (13 bp):
AAAGTCCAATTAC
Found at i:1378 original size:15 final size:15
Alignment explanation
Indices: 1358--1413 Score: 94
Period size: 15 Copynumber: 3.7 Consensus size: 15
1348 CAAACAAAGT
1358 CCAATTACAAATGGC
1 CCAATTACAAATGGC
*
1373 CCAATTACAGATGGC
1 CCAATTACAAATGGC
*
1388 CCAAATACAAATGGC
1 CCAATTACAAATGGC
1403 CCAATTACAAA
1 CCAATTACAAA
1414 AGCCCAAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.18
Consensus pattern (15 bp):
CCAATTACAAATGGC
Found at i:1426 original size:15 final size:15
Alignment explanation
Indices: 1358--1426 Score: 59
Period size: 15 Copynumber: 4.6 Consensus size: 15
1348 CAAACAAAGT
* *
1358 CCAATTACAAATGGC
1 CCAAATACAAATAGC
* * *
1373 CCAATTACAGATGGC
1 CCAAATACAAATAGC
*
1388 CCAAATACAAATGGC
1 CCAAATACAAATAGC
*
1403 CCAATTACAAA-AGC
1 CCAAATACAAATAGC
1417 CCAAACTACA
1 CCAAA-TACA
1427 GTTTTGGCCC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 6 0.13
15 41 0.87
ACGTcount: A:0.43, C:0.29, G:0.12, T:0.16
Consensus pattern (15 bp):
CCAAATACAAATAGC
Done.