Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011367.1 Kokia drynarioides strain JFW-HI SEQ_126348, 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: 9823
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Found at i:8324 original size:29 final size:29
Alignment explanation
Indices: 8292--8571 Score: 91
Period size: 29 Copynumber: 9.5 Consensus size: 29
8282 TGCACGGGGG
* *
8292 CAAAATGGTAGTTTTGGTAGGTTTG-GAGT
1 CAAAATGGTAATTTTGG-AAGTTTGAGAGT
* * *
8321 CAAAAATGGGATTTTTGGAAGTTTGAGGGT
1 C-AAAATGGTAATTTTGGAAGTTTGAGAGT
* * *
8351 -AAAATGGTAATTTTTGAAAGGTTCG-GGGT
1 CAAAATGGTAA-TTTTGGAA-GTTTGAGAGT
*
8380 CAAAAAT--TAGATTTTAGGAAGTTT-AGGGT
1 C-AAAATGGTA-ATTTT-GGAAGTTTGAGAGT
* *
8409 CAAAAATGGTAATTTTTGAAAGTTTG-GGGAT
1 C-AAAATGGTAA-TTTTGGAAGTTTGAGAG-T
* *
8440 -AAAATGGTAATTTTTAGAAAGTTT-AGGGTT
1 CAAAATGGTAA-TTTT-GGAAGTTTGAGAG-T
* * * * * *
8470 AAAAATGGGATTTTTGAAAGTTTGGGGGT
1 CAAAATGGTAATTTTGGAAGTTTGAGAGT
* * *
8499 -AAAATTGTAATTTTTAGAAAGTTTG-GGGT
1 CAAAATGGTAA-TTTT-GGAAGTTTGAGAGT
* * *
8528 CAAAAATTGG-ATTTTTGGAAGTTCGAGGGT
1 C-AAAA-TGGTAATTTTGGAAGTTTGAGAGT
8558 -AAAATGGTAATTTT
1 CAAAATGGTAATTTT
8572 TAGAAGGTTT
Statistics
Matches: 203, Mismatches: 23, Indels: 51
0.73 0.08 0.18
Matches are distributed among these distances:
27 3 0.01
28 24 0.12
29 77 0.38
30 72 0.35
31 25 0.12
32 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (29 bp):
CAAAATGGTAATTTTGGAAGTTTGAGAGT
Found at i:8383 original size:59 final size:58
Alignment explanation
Indices: 8293--8585 Score: 201
Period size: 59 Copynumber: 5.0 Consensus size: 58
8283 GCACGGGGGC
* ** *
8293 AAAATGGT-AGTTTTGGTAGGTTTGGAGTCAAAAATGGGATTTTTGGAAGTTTGAGGGT-
1 AAAATGGTAATTTTTGAAAGGTTTGGGGT-AAAAATGGGATTTTTGGAAGTTT-AGGGTA
* ** *
8351 AAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATTAGATTTTAGGAAGTTTAGGGTCA
1 AAAATGGTAATTTTTGAAAGGTTTGGGGT-AAAAATGGGATTTTTGGAAGTTTAGGGT-A
* *
8411 AAAATGGTAATTTTTGAAA-GTTTGGGG-ATAAAATGGTAATTTTTAGAAAGTTTAGGGTTA
1 AAAATGGTAATTTTTGAAAGGTTTGGGGTA-AAAATGG-GATTTTT-GGAAGTTTAGGG-TA
* * ** * *
8471 AAAATGG-GATTTTTGAAA-GTTTGGGGGTAAAATTGTAATTTTTAGAAAGTTTGGGGTCA
1 AAAATGGTAATTTTTGAAAGGTTT-GGGGTAAAAATGGGATTTTT-GGAAGTTTAGGGT-A
* * * *
8530 AAAATTGG--ATTTTTGGAA-GTTCGAGGGT-AAAATGGTAATTTTTAGAAGGTTTAGGG
1 AAAA-TGGTAATTTTTGAAAGGTTTG-GGGTAAAAATGG-GATTTTTGGAA-GTTTAGGG
8586 ACCTCCAGGG
Statistics
Matches: 196, Mismatches: 25, Indels: 27
0.79 0.10 0.11
Matches are distributed among these distances:
57 1 0.01
58 27 0.14
59 116 0.59
60 50 0.26
61 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.36
Consensus pattern (58 bp):
AAAATGGTAATTTTTGAAAGGTTTGGGGTAAAAATGGGATTTTTGGAAGTTTAGGGTA
Found at i:8572 original size:29 final size:30
Alignment explanation
Indices: 8322--8585 Score: 218
Period size: 29 Copynumber: 9.0 Consensus size: 30
8312 GTTTGGAGTC
* *
8322 AAAAATGG-GATTTTTGGAAGTTTGAGGGT
1 AAAAATGGTAATTTTTGAAAGTTTGAGGGT
*
8351 -AAAATGGTAATTTTTGAAAGGTTCG-GGGT
1 AAAAATGGTAATTTTTGAAA-GTTTGAGGGT
* *
8380 CAAAAAT--TAGATTTTAGGAAGTTT-AGGGT
1 -AAAAATGGTA-ATTTTTGAAAGTTTGAGGGT
8409 CAAAAATGGTAATTTTTGAAAGTTTG-GGG-
1 -AAAAATGGTAATTTTTGAAAGTTTGAGGGT
8438 ATAAAATGGTAATTTTTAGAAAGTTT-AGGGTT
1 A-AAAATGGTAATTTTT-GAAAGTTTGAGGG-T
* *
8470 AAAAATGG-GATTTTTGAAAGTTTGGGGGT
1 AAAAATGGTAATTTTTGAAAGTTTGAGGGT
*
8499 -AAAATTGTAATTTTTAGAAAGTTTG-GGGT
1 AAAAATGGTAATTTTT-GAAAGTTTGAGGGT
* *
8528 CAAAAATTGG--ATTTTTGGAAGTTCGAGGGT
1 -AAAAA-TGGTAATTTTTGAAAGTTTGAGGGT
*
8558 -AAAATGGTAATTTTTAGAAGGTTT-AGGG
1 AAAAATGGTAATTTTT-GAAAGTTTGAGGG
8586 ACCTCCAGGG
Statistics
Matches: 193, Mismatches: 18, Indels: 48
0.75 0.07 0.19
Matches are distributed among these distances:
27 3 0.02
28 18 0.09
29 80 0.41
30 71 0.37
31 18 0.09
32 3 0.02
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (30 bp):
AAAAATGGTAATTTTTGAAAGTTTGAGGGT
Found at i:9712 original size:15 final size:15
Alignment explanation
Indices: 9689--9738 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
9679 TATCACCGTC
9689 ATTAATGCCATTATT
1 ATTAATGCCATTATT
* *
9704 ATTACTGCCATCCATT
1 ATTAATGCCAT-TATT
* *
9720 ATTAATGTCATTAAT
1 ATTAATGCCATTATT
9735 ATTA
1 ATTA
9739 TTATTAACAG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (15 bp):
ATTAATGCCATTATT
Done.