Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003643.1 Kokia drynarioides strain JFW-HI SEQ_116542, 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, 647
Length: 1079
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.30
Found at i:284 original size:29 final size:29
Alignment explanation
Indices: 252--312 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
242 AAAATGAGAC
252 TTTTTGAATACCCGAGGGCAAAATGGTAA
1 TTTTTGAATACCCGAGGGCAAAATGGTAA
* * * *
281 -TTTTGGATTCTCGGGGGCAAAATGGTAA
1 TTTTTGAATACCCGAGGGCAAAATGGTAA
309 TTTT
1 TTTT
313 GGGAAAGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.34
Consensus pattern (29 bp):
TTTTTGAATACCCGAGGGCAAAATGGTAA
Found at i:367 original size:59 final size:59
Alignment explanation
Indices: 290--525 Score: 208
Period size: 59 Copynumber: 4.0 Consensus size: 59
280 ATTTTGGATT
* * * * *
290 CTCGGGGGCAAAATGGTAA-TTTTGGGAAAGTTCGAGGTTAAAAATGGAATTTTTAAACA
1 CTCGAGGGTAAAATGGTAACTTTT-GGAAAGATCGAGGTCAAAAATGGAATTTTTAGACA
* * * * *
349 CTCGAGGGTAAAACGGTAACTTTTGAAAAAATCG-GGATCAAAAACGGAATTTTTGGACA
1 CTCGAGGGTAAAATGGTAACTTTTGGAAAGATCGAGG-TCAAAAATGGAATTTTTAGACA
* * * * *
408 TTCGAGGGTAAAATAGTAATTTTTAGGAAA-ATCGAGATCAAAAATGGAATTTTTGGACA
1 CTCGAGGGTAAAATGGTAACTTTT-GGAAAGATCGAGGTCAAAAATGGAATTTTTAGACA
* * * ** * *
467 TTCGGGGGTGAAATGGTATTTTTTTTGAAAGTTTCGAGGTCAAAAATGGAATTTTTAGA
1 CTCGAGGGTAAAATGGTA-ACTTTTGGAAAG-ATCGAGGTCAAAAATGGAATTTTTAGA
526 GGTTCAAGGG
Statistics
Matches: 145, Mismatches: 25, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
58 2 0.01
59 105 0.72
60 14 0.10
61 24 0.17
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (59 bp):
CTCGAGGGTAAAATGGTAACTTTTGGAAAGATCGAGGTCAAAAATGGAATTTTTAGACA
Found at i:420 original size:29 final size:29
Alignment explanation
Indices: 320--475 Score: 86
Period size: 29 Copynumber: 5.3 Consensus size: 29
310 TTTGGGAAAG
* * **
320 TTCGAGGTTAAAAATGGAATTTTTAAACA
1 TTCGAGGGTAAAAACGGAATTTTTGGACA
* * * *
349 CTCGAGGGT-AAAACGGTAACTTTTGAAAAA
1 TTCGAGGGTAAAAACGG-AATTTTTG-GACA
* *
379 ATCG-GGATCAAAAACGGAATTTTTGGACA
1 TTCGAGGGT-AAAAACGGAATTTTTGGACA
* *
408 TTCGAGGGTAAAATA-GTAATTTTTAGGAAA
1 TTCGAGGGTAAAA-ACGGAATTTTT-GGACA
* * *
438 ATCGA-GATCAAAAATGGAATTTTTGGACA
1 TTCGAGGGT-AAAAACGGAATTTTTGGACA
*
467 TTCGGGGGT
1 TTCGAGGGT
476 GAAATGGTAT
Statistics
Matches: 95, Mismatches: 22, Indels: 19
0.70 0.16 0.14
Matches are distributed among these distances:
28 6 0.06
29 43 0.45
30 39 0.41
31 7 0.07
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (29 bp):
TTCGAGGGTAAAAACGGAATTTTTGGACA
Found at i:518 original size:61 final size:59
Alignment explanation
Indices: 329--556 Score: 206
Period size: 59 Copynumber: 3.8 Consensus size: 59
319 GTTCGAGGTT
** * ** * * *
329 AAAAATGGAATTTTTAAACACTCGAGGGTAAAACGGTAACTTTT-GAAAAAATCGGGATC
1 AAAAATGGAATTTTTGGACATTCGAGGGTAAAATAGTAATTTTTAG-GAAAATCGAGATC
*
388 AAAAACGGAATTTTTGGACATTCGAGGGTAAAATAGTAATTTTTAGGAAAATCGAGATC
1 AAAAATGGAATTTTTGGACATTCGAGGGTAAAATAGTAATTTTTAGGAAAATCGAGATC
* * * * ** * *
447 AAAAATGGAATTTTTGGACATTCGGGGGTGAAATGGTATTTTTTTTGAAAGTTTCGAGGTC
1 AAAAATGGAATTTTTGGACATTCGAGGGTAAAATAGTAATTTTTAGGAAA--ATCGAGATC
* ** * * * *
508 AAAAATGGAATTTTTAGAGGTTCAAGGGTAAAATTGCAATTTTTTGGAA
1 AAAAATGGAATTTTTGGACATTCGAGGGTAAAATAGTAATTTTTAGGAA
557 TTTTTGGGGT
Statistics
Matches: 138, Mismatches: 28, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
59 91 0.66
60 1 0.01
61 46 0.33
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGACATTCGAGGGTAAAATAGTAATTTTTAGGAAAATCGAGATC
Found at i:540 original size:29 final size:29
Alignment explanation
Indices: 508--768 Score: 209
Period size: 29 Copynumber: 8.8 Consensus size: 29
498 TTTCGAGGTC
* * * *
508 AAAAATGGAATTTTTAGAGGTTCAAGGGT
1 AAAAATGTAATTTTTGGAAGTTTAAGGGT
* * * **
537 AAAATTGCAATTTTTTGGAATTTTTGGGGTT
1 AAAAATGTAA-TTTTTGGAAGTTTAAGGG-T
*
568 AAAAATGTAATTTTTGGAAGTTTATGGGT
1 AAAAATGTAATTTTTGGAAGTTTAAGGGT
*
597 AAAAATGTAATTTTTGGAAGTTTTAGGGT
1 AAAAATGTAATTTTTGGAAGTTTAAGGGT
* * *
626 CAAAATGAAATTTTTGGAAGTTTAGGGGT
1 AAAAATGTAATTTTTGGAAGTTTAAGGGT
* * * *
655 AAAAATATAATTTTCGGAAGTTTCGAGGGA
1 AAAAATGTAATTTTTGGAAGTTT-AAGGGT
* * **
685 AAAAATGGAATTTTTGGAAGTTTGAGCAT
1 AAAAATGTAATTTTTGGAAGTTTAAGGGT
* * * *
714 AAATATATAATTTTCGAAAGTTTTAA-GGT
1 AAAAATGTAATTTTTGGAAG-TTTAAGGGT
* *
743 CAAAAATGAAAATTTTGGACAGTTTA
1 -AAAAATGTAATTTTTGGA-AGTTTA
769 GGGACCTCCA
Statistics
Matches: 180, Mismatches: 46, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
29 99 0.55
30 70 0.39
31 11 0.06
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGAAGTTTAAGGGT
Found at i:580 original size:60 final size:58
Alignment explanation
Indices: 508--768 Score: 225
Period size: 59 Copynumber: 4.4 Consensus size: 58
498 TTTCGAGGTC
* * * * * * *
508 AAAAATGGAATTTTTAGAGGTTCAAGGGTAAAATTGCAATTTTTTGGAATTTTTGGGGTT
1 AAAAATGAAATTTTTGGAAGTTTAAGGGTAAAAATGCAA-TTTTTGGAAGTTTTAGGG-T
* * *
568 AAAAATGTAATTTTTGGAAGTTTATGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGT
1 AAAAATGAAATTTTTGGAAGTTTAAGGGTAAAAATGCAATTTTTGGAAGTTTTAGGGT
* * ** * * *
626 CAAAATGAAATTTTTGGAAGTTTAGGGGTAAAAATATAATTTTCGGAAGTTTCGAGGGA
1 AAAAATGAAATTTTTGGAAGTTTAAGGGTAAAAATGCAATTTTTGGAAGTTT-TAGGGT
* * ** * ** * * *
685 AAAAATGGAATTTTTGGAAGTTTGAGCATAAATATATAATTTTCGAAAGTTTTAAGGT
1 AAAAATGAAATTTTTGGAAGTTTAAGGGTAAAAATGCAATTTTTGGAAGTTTTAGGGT
*
743 CAAAAATGAAAATTTTGGACAGTTTA
1 -AAAAATGAAATTTTTGGA-AGTTTA
769 GGGACCTCCA
Statistics
Matches: 168, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
58 51 0.30
59 80 0.48
60 37 0.22
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (58 bp):
AAAAATGAAATTTTTGGAAGTTTAAGGGTAAAAATGCAATTTTTGGAAGTTTTAGGGT
Done.