Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003199.1 Kokia drynarioides strain JFW-HI SEQ_115814, 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: 1710
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Found at i:174 original size:31 final size:31
Alignment explanation
Indices: 139--210 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
129 AAATTAAACA
*
139 TAAAATTAATAAAATATGAAATGCGAAAGAT
1 TAAAATTAATAAAATACGAAATGCGAAAGAT
170 TAAAATTAATAAAATACGAAATGCGAAAGAT
1 TAAAATTAATAAAATACGAAATGCGAAAGAT
201 TAATAATTAA
1 TAA-AATTAA
211 AATCTATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 33 0.85
32 6 0.15
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.26
Consensus pattern (31 bp):
TAAAATTAATAAAATACGAAATGCGAAAGAT
Found at i:412 original size:29 final size:29
Alignment explanation
Indices: 361--513 Score: 109
Period size: 29 Copynumber: 5.3 Consensus size: 29
351 GATGTGTGAT
* * * * *
361 TTTTTGGAAATTTAAGGGCAAAATCATAA
1 TTTTTGGAAGTTCAGGGGTAAAATCGTAA
*
390 TTTTTGGATGTTCAGGGGTAAAA-CGGTAA
1 TTTTTGGAAGTTCAGGGGTAAAATC-GTAA
* **
419 TTTTGGGAAGTTCA-GGGTCAAAAT-GTGT
1 TTTTTGGAAGTTCAGGGGT-AAAATCGTAA
* *
447 TTTTTGGAAGTTTTAGGGGTAAAATGGTAA
1 TTTTTGGAAG-TTCAGGGGTAAAATCGTAA
* * *
477 TTTTTGGATGTTAAGGGGCAAAA-CGGTAA
1 TTTTTGGAAGTTCAGGGGTAAAATC-GTAA
506 -TTTTGGAA
1 TTTTTGGAA
514 AAGTTTGGGG
Statistics
Matches: 98, Mismatches: 19, Indels: 15
0.74 0.14 0.11
Matches are distributed among these distances:
28 23 0.23
29 60 0.61
30 15 0.15
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36
Consensus pattern (29 bp):
TTTTTGGAAGTTCAGGGGTAAAATCGTAA
Found at i:468 original size:58 final size:57
Alignment explanation
Indices: 390--499 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 57
380 AAAATCATAA
* * *
390 TTTTTGGATGTTCAGGGGTAAAACGGTAATTTTGGGAAGTTCAGGGTCAAAATGTGT
1 TTTTTGGAAGTTCAGGGGTAAAACGGTAATTTTGGGAAGTTAAGGGGCAAAATGTGT
* * * *
447 TTTTTGGAAGTTTTAGGGGTAAAATGGTAATTTTTGGATGTTAAGGGGCAAAA
1 TTTTTGGAAG-TTCAGGGGTAAAACGGTAATTTTGGGAAGTTAAGGGGCAAAA
500 CGGTAATTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 9 0.20
58 36 0.80
ACGTcount: A:0.28, C:0.05, G:0.31, T:0.36
Consensus pattern (57 bp):
TTTTTGGAAGTTCAGGGGTAAAACGGTAATTTTGGGAAGTTAAGGGGCAAAATGTGT
Found at i:471 original size:87 final size:88
Alignment explanation
Indices: 355--558 Score: 261
Period size: 87 Copynumber: 2.3 Consensus size: 88
345 AAGTTAGATG
* * * * *
355 TGTGATTTTTTGGAAATTTAAGGGCAAAATCATAATTTTTGGATGTTCAGGGGTAAAACGGTAAT
1 TGTG-TTTTTTGGAAGTTTAGGGGTAAAATCATAATTTTTGGATGTTAAGGGGCAAAACGGTAAT
*
420 TTTGG-GAAGTTCAGGGTC-AAAA
65 TTTGGAAAAGTTCAGGGTCAAAAA
**
442 TGTGTTTTTTGGAAGTTTTAGGGGTAAAATGGTAATTTTTGGATGTTAAGGGGCAAAACGGTAAT
1 TGTGTTTTTTGGAAG-TTTAGGGGTAAAATCATAATTTTTGGATGTTAAGGGGCAAAACGGTAAT
**
507 TTTGGAAAAGTTTGGGGTCAAAAA
65 TTTGGAAAAGTTCAGGGTCAAAAA
*
531 TGTATTTTTTGAGAAGTTT-GGGGTAAAA
1 TGTGTTTTTTG-GAAGTTTAGGGGTAAAA
559 ATGTGCTTTT
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
86 10 0.10
87 52 0.51
88 19 0.19
89 17 0.17
90 4 0.04
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.36
Consensus pattern (88 bp):
TGTGTTTTTTGGAAGTTTAGGGGTAAAATCATAATTTTTGGATGTTAAGGGGCAAAACGGTAATT
TTGGAAAAGTTCAGGGTCAAAAA
Found at i:523 original size:29 final size:29
Alignment explanation
Indices: 491--597 Score: 81
Period size: 29 Copynumber: 3.7 Consensus size: 29
481 TGGATGTTAA
*
491 GGGGCAAAACGGTAATTTTGGAAAAGTTT
1 GGGGCAAAAAGGTAATTTTGGAAAAGTTT
* * * *
520 GGGGTCAAAAATGTATTTTTTGAGAAGTTT
1 GGGG-CAAAAAGGTAATTTTGGAAAAGTTT
* * ** *
550 GGGGTAAAAATGTGCTTTTTG-AAAGTTT
1 GGGGCAAAAAGGTAATTTTGGAAAAGTTT
* *
578 GGGGCCAAAAATGTATTTTT
1 GGGG-CAAAAAGGTAATTTT
598 TGGAGGTTCG
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
28 10 0.16
29 30 0.47
30 24 0.38
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.36
Consensus pattern (29 bp):
GGGGCAAAAAGGTAATTTTGGAAAAGTTT
Found at i:524 original size:58 final size:58
Alignment explanation
Indices: 403--513 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 58
393 TTGGATGTTC
* * * *
403 AGGGGTAAAACGGTAATTTTGGGAAGTTCAGGGTCAAAATGTGTTTTTTGGAAGTTTT
1 AGGGGTAAAACGGTAATTTTGGGAAGTTAAGGGGCAAAACGTGTATTTTGGAAGTTTT
* * *
461 AGGGGTAAAATGGTAATTTTTGGATGTTAAGGGGCAAAACG-GTAATTTTGGAA
1 AGGGGTAAAACGGTAATTTTGGGAAGTTAAGGGGCAAAACGTGT-ATTTTGGAA
514 AAGTTTGGGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
57 2 0.04
58 43 0.96
ACGTcount: A:0.31, C:0.05, G:0.32, T:0.33
Consensus pattern (58 bp):
AGGGGTAAAACGGTAATTTTGGGAAGTTAAGGGGCAAAACGTGTATTTTGGAAGTTTT
Found at i:538 original size:58 final size:57
Alignment explanation
Indices: 467--597 Score: 129
Period size: 59 Copynumber: 2.2 Consensus size: 57
457 TTTTAGGGGT
* * *
467 AAAATGGTAATTTTTG-GATGTTAAGGGGCAAAACGGTAATTTTGGAAAAGTTTGGGGTCA
1 AAAAT-GT-ATTTTTGAGAAGTT-AGGGGCAAAAAGGTAATTTTGG-AAAGTTTGGGGCCA
* * * ** *
527 AAAATGTATTTTTTGAGAAGTTTGGGGTAAAAATGTGCTTTTTGAAAGTTTGGGGCCA
1 AAAATGTA-TTTTTGAGAAGTTAGGGGCAAAAAGGTAATTTTGGAAAGTTTGGGGCCA
585 AAAATGTATTTTT
1 AAAATGTATTTTT
598 TGGAGGTTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
57 5 0.08
58 22 0.37
59 23 0.38
60 10 0.17
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.37
Consensus pattern (57 bp):
AAAATGTATTTTTGAGAAGTTAGGGGCAAAAAGGTAATTTTGGAAAGTTTGGGGCCA
Found at i:598 original size:29 final size:28
Alignment explanation
Indices: 513--632 Score: 123
Period size: 29 Copynumber: 4.1 Consensus size: 28
503 TAATTTTGGA
513 AAAGTTTGGGGTCAAAAATGTATTTTTTG
1 AAAGTTTGGGG-CAAAAATGTATTTTTTG
* **
542 AGAAGTTTGGGGTAAAAATGTGCTTTTTG
1 A-AAGTTTGGGGCAAAAATGTATTTTTTG
571 AAAGTTTGGGGCCAAAAATGTATTTTTTG
1 AAAGTTTGGGG-CAAAAATGTATTTTTTG
* * * * *
600 GAGGTTCGGGGGAAAAAATGTGATTTTTGG
1 AAAGTT-TGGGGCAAAAATGT-ATTTTTTG
630 AAA
1 AAA
633 ATTCAAGGAC
Statistics
Matches: 74, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
28 10 0.14
29 42 0.57
30 22 0.30
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (28 bp):
AAAGTTTGGGGCAAAAATGTATTTTTTG
Found at i:598 original size:58 final size:58
Alignment explanation
Indices: 513--628 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
503 TAATTTTGGA
* * * *
513 AAAGTTTGGGGTCAAAAATGTATTTTTTGAGAAGTT-TGGGGTAAAAATGTGCTTTTTG
1 AAAGTTTGGGGCCAAAAATGTATTTTTTG-GAAGTTCGGGGGAAAAAATGTGATTTTTG
*
571 AAAGTTTGGGGCCAAAAATGTATTTTTTGGAGGTTCGGGGGAAAAAATGTGATTTTTG
1 AAAGTTTGGGGCCAAAAATGTATTTTTTGGAAGTTCGGGGGAAAAAATGTGATTTTTG
629 GAAAATTCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
57 5 0.10
58 47 0.90
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.37
Consensus pattern (58 bp):
AAAGTTTGGGGCCAAAAATGTATTTTTTGGAAGTTCGGGGGAAAAAATGTGATTTTTG
Done.