Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008651.1 Kokia drynarioides strain JFW-HI SEQ_123332, 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: 2602
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:1253 original size:59 final size:59
Alignment explanation
Indices: 1178--1513 Score: 364
Period size: 58 Copynumber: 5.8 Consensus size: 59
1168 TTGGATCAAT
* *
1178 AATTTTTGGACGTTCGGGGGTAAAATAGTAATTTTGGGAAAGTTCGAGGTCAAAAATGG
1 AATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAATGG
* * *
1237 AATTTTTGGACATTCGGGGATAAAATGGTAATTTTGGGAAAGTTTGGGGTCAAAAATGG
1 AATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAATGG
* * * * *
1296 GA-TTTTGGAAATTTGGGGGTAAAATGGTAATTTTAGGAAAGTTCGAGATCAAAAATGG
1 AATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAATGG
* * *
1354 ATTTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGG-AAGTT-TAGGGTCAAAAATGA
1 AATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGA-GGTCAAAAATGG
* * * * * * * *
1412 AATTTTGGGACATCCGTGGATAAAATGATAATTTTGGGAAAATTC-AGAGTTAAAAAT-T
1 AATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAG-GTCAAAAATGG
* * *
1470 AGA-TTTTGGA-AATCTGAGGGTAAAATGGTAATTTTGTG-AAGTTC
1 A-ATTTTTGGACATTC-GGGGGTAAAATGGTAATTTTGGGAAAGTTC
1514 AGGGGCGATA
Statistics
Matches: 232, Mismatches: 38, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
57 8 0.03
58 123 0.53
59 101 0.44
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (59 bp):
AATTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGGTCAAAAATGG
Found at i:1387 original size:117 final size:116
Alignment explanation
Indices: 1192--1517 Score: 390
Period size: 117 Copynumber: 2.8 Consensus size: 116
1182 TTTGGACGTT
* * *
1192 CGGGGGTAAAATAGTAATTTTGGGAAAGTTCGAGGTCAAAAATGGAATTTTTGGACATTCGGGGA
1 CGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGATCAAAAATGG-ATTTTTGGACATTCGGGGG
* ** *
1257 TAAAATGGTAATTTTGGGAAAGTTTGGGGTCAAAAATGGGATTTT-GGAAATT
65 TAAAATGGTAATTTTGGG-AAGTTTAGGGTCAAAAATGAAATTTTGGGAAATC
* *
1309 TGGGGGTAAAATGGTAATTTTAGGAAAGTTCGAGATCAAAAATGGATTTTTTGGACATTCGGGGG
1 CGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGATCAAAAATGGA-TTTTTGGACATTCGGGGG
*
1374 TAAAATGGTAATTTTGGGAAGTTTAGGGTCAAAAATGAAATTTTGGGACATC
65 TAAAATGGTAATTTTGGGAAGTTTAGGGTCAAAAATGAAATTTTGGGAAATC
* * * * * * * *
1426 CGTGGATAAAATGATAATTTTGGGAAAATTC-AGAGTTAAAAATTAGA-TTTTGGA-AATCTGAG
1 CGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGA-TCAAAAA-TGGATTTTTGGACATTC-GGG
* *
1488 GGTAAAATGGTAATTTTGTGAAGTTCAGGG
63 GGTAAAATGGTAATTTTGGGAAGTTTAGGG
1518 GCGATAATGT
Statistics
Matches: 182, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
115 3 0.02
116 64 0.35
117 112 0.62
118 3 0.02
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (116 bp):
CGGGGGTAAAATGGTAATTTTGGGAAAGTTCGAGATCAAAAATGGATTTTTGGACATTCGGGGGT
AAAATGGTAATTTTGGGAAGTTTAGGGTCAAAAATGAAATTTTGGGAAATC
Found at i:1562 original size:30 final size:28
Alignment explanation
Indices: 1523--1578 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
1513 CAGGGGCGAT
*
1523 AATGTATTTTTTGGAAAGTTTGGGGTCAA
1 AATGTA-TTTTTGGAAAGTTTAGGGTCAA
*
1552 AATGTGATTTTTGGATAGTTTAGGGTC
1 AATGT-ATTTTTGGAAAGTTTAGGGTC
1579 TTTCAGGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.25, C:0.04, G:0.29, T:0.43
Consensus pattern (28 bp):
AATGTATTTTTGGAAAGTTTAGGGTCAA
Found at i:1574 original size:175 final size:175
Alignment explanation
Indices: 1180--1578 Score: 450
Period size: 175 Copynumber: 2.3 Consensus size: 175
1170 GGATCAATAA
** * * * *
1180 TTTTTGGACGTTCGGGGGTAAAATAGTAATTTTGGGAAAG-TTCGAGGTCAAAAATGGAATTTTT
1 TTTTTGGAAATTCGGGGGTAAAATGGTAATTTTGGG-AAGTTTAG-GGTCAAAAATGAAATTTTG
* * * ** * * *
1244 GGACATTCGGGGATAAAATGGTAATTTTGGGAAAGTTTGGGGTCAAAAATGGGATTTTGGAAATT
64 GGACATCCGGGGATAAAATGATAATTTTGGGAAAATTCAGAGTCAAAAATGAGATTTTGGAAATC
* *
1309 TGGGGGTAAAATGGTAATTTTAGGAAAGTTCGAGATCAAAAATGGAT
129 TGAGGGTAAAATGGTAATTTTAGGAAAGTTCGAGAGCAAAAATGGAT
*
1356 TTTTTGGACATTCGGGGGTAAAATGGTAATTTTGGGAAGTTTAGGGTCAAAAATGAAATTTTGGG
1 TTTTTGGAAATTCGGGGGTAAAATGGTAATTTTGGGAAGTTTAGGGTCAAAAATGAAATTTTGGG
* * *
1421 ACATCCGTGGATAAAATGATAATTTTGGGAAAATTCAGAGTTAAAAATTAGATTTTGGAAATCTG
66 ACATCCGGGGATAAAATGATAATTTTGGGAAAATTCAGAGTCAAAAATGAGATTTTGGAAATCTG
* * * *
1486 AGGGTAAAATGGTAATTTT-GTG-AAGTTC-AGGGGCGATAATGTAT
131 AGGGTAAAATGGTAATTTTAG-GAAAGTTCGA-GAGCAAAAATGGAT
* * *
1530 TTTTTGGAAAGTT-TGGGGTCAAAAT-GTGATTTTTGGATAGTTTAGGGTC
1 TTTTTGGAAA-TTCGGGGGT-AAAATGGTAATTTTGGGA-AGTTTAGGGTC
1579 TTTCAGGGTA
Statistics
Matches: 191, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
173 1 0.01
174 40 0.21
175 113 0.59
176 37 0.19
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (175 bp):
TTTTTGGAAATTCGGGGGTAAAATGGTAATTTTGGGAAGTTTAGGGTCAAAAATGAAATTTTGGG
ACATCCGGGGATAAAATGATAATTTTGGGAAAATTCAGAGTCAAAAATGAGATTTTGGAAATCTG
AGGGTAAAATGGTAATTTTAGGAAAGTTCGAGAGCAAAAATGGAT
Done.