Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000728.1 Kokia drynarioides strain JFW-HI SEQ_111751, 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: 13820
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1277 original size:15 final size:15
Alignment explanation
Indices: 1257--1289 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1247 AGTTAAAATA
1257 TAATTTT-ATTTTTAT
1 TAATTTTAATTTTT-T
1272 TAATTTTAATTTTTT
1 TAATTTTAATTTTTT
1287 TAA
1 TAA
1290 AATTTAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TAATTTTAATTTTTT
Found at i:5493 original size:24 final size:23
Alignment explanation
Indices: 5400--5493 Score: 66
Period size: 24 Copynumber: 3.9 Consensus size: 23
5390 AAGACAGCGA
5400 AACAATAATAAAAACGCAT-AAAAAT
1 AACAATAA-AAAAA--CATCAAAAAT
* *
5425 AACAACAAAAAAAGCAGCAAAAAT
1 AACAATAAAAAAA-CATCAAAAAT
* * *
5449 AATAGA-AAAGAAAGCAACAAAAAT
1 AACA-ATAAA-AAAACATCAAAAAT
5473 AACAATAAAAACAACATCAAA
1 AACAATAAAAA-AACATCAAA
5494 TTAGCAACCA
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
23 6 0.11
24 39 0.70
25 11 0.20
ACGTcount: A:0.70, C:0.14, G:0.06, T:0.10
Consensus pattern (23 bp):
AACAATAAAAAAACATCAAAAAT
Found at i:5589 original size:21 final size:21
Alignment explanation
Indices: 5511--5593 Score: 71
Period size: 22 Copynumber: 4.0 Consensus size: 21
5501 CCAAAATAGT
**
5511 AAAAAA-AGCACC-AAACAGT
1 AAAAAACAGCACCAAAACAAC
* * *
5530 AAAAACACAACATCGAAACAAC
1 AAAAA-ACAGCACCAAAACAAC
* *
5552 AAAAAATAGCAATCAAAACAAC
1 AAAAAACAGC-ACCAAAACAAC
5574 AAAAAACAGCACCAAAACAA
1 AAAAAACAGCACCAAAACAA
5594 TAATGTATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 5 0.10
20 1 0.02
21 16 0.31
22 29 0.57
ACGTcount: A:0.66, C:0.23, G:0.06, T:0.05
Consensus pattern (21 bp):
AAAAAACAGCACCAAAACAAC
Found at i:6454 original size:21 final size:20
Alignment explanation
Indices: 6428--6478 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
6418 AGAGAATGGA
*
6428 AAAAAAGAAAGAATATAAAAG
1 AAAAAACAAA-AATATAAAAG
**
6449 AAAAAACAAATTTATAAAAG
1 AAAAAACAAAAATATAAAAG
6469 AAAAAACAAA
1 AAAAAACAAA
6479 TTGCTCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.76, C:0.04, G:0.08, T:0.12
Consensus pattern (20 bp):
AAAAAACAAAAATATAAAAG
Found at i:6464 original size:20 final size:20
Alignment explanation
Indices: 6441--6480 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6431 AAAGAAAGAA
6441 TATAAAAGAAAAAACAAATT
1 TATAAAAGAAAAAACAAATT
6461 TATAAAAGAAAAAACAAATT
1 TATAAAAGAAAAAACAAATT
6481 GCTCAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (20 bp):
TATAAAAGAAAAAACAAATT
Found at i:6488 original size:21 final size:20
Alignment explanation
Indices: 6442--6495 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
6432 AAGAAAGAAT
*
6442 ATAAAAGAAAAAACAAATTT
1 ATAAAAGAAAAAACAAATTG
6462 ATAAAAGAAAAAACAAATTG
1 ATAAAAGAAAAAACAAATTG
*
6482 CTCAAAATGAAAAA
1 AT-AAAA-GAAAAA
6496 TATAGGGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 20 0.67
21 4 0.13
22 6 0.20
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (20 bp):
ATAAAAGAAAAAACAAATTG
Found at i:6856 original size:19 final size:19
Alignment explanation
Indices: 6834--6889 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
6824 AAAAAATCAA
6834 AAAATATATAAATATTTTT
1 AAAATATATAAATATTTTT
*
6853 AAAA-ATATAATAAATTTTT
1 AAAATATATAA-ATATTTTT
*
6872 AAATATTATATTAATATT
1 AAA-A-TATATAAATATT
6890 AAATAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.20
19 14 0.47
20 1 0.03
21 4 0.13
22 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAATATATAAATATTTTT
Found at i:6858 original size:20 final size:20
Alignment explanation
Indices: 6833--6889 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
6823 TAAAAAATCA
6833 AAAAATATATAAATATTTTT
1 AAAAATATATAAATATTTTT
6853 AAAAATATA-ATAA-ATTTTT
1 AAAAATATATA-AATATTTTT
* *
6872 AAATATTATATTAATATT
1 AAA-AATATATAAATATT
6890 AAATAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 10 0.32
20 18 0.58
21 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAAATATATAAATATTTTT
Found at i:12479 original size:25 final size:25
Alignment explanation
Indices: 12420--12479 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
12410 GATAAAAAAA
*
12420 TTATTTTTTGGTATTTTATTTTTTT
1 TTATATTTTGGTATTTTATTTTTTT
* * * * *
12445 GTCTAATTTGGTTTTTTTTTTTTTT
1 TTATATTTTGGTATTTTATTTTTTT
12470 TTATATTTTG
1 TTATATTTTG
12480 TATCTAACTC
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.77
Consensus pattern (25 bp):
TTATATTTTGGTATTTTATTTTTTT
Found at i:12912 original size:27 final size:27
Alignment explanation
Indices: 12873--12927 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
12863 AACATTTGAC
12873 AAATTTAGATACCAAA-TCAGACAAAAA
1 AAATTTAGATACCAAATTCAGA-AAAAA
*
12900 AAATTTAGGTACCAAATTCAGAAAAAA
1 AAATTTAGATACCAAATTCAGAAAAAA
12927 A
1 A
12928 GTAAAGTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.58, C:0.13, G:0.09, T:0.20
Consensus pattern (27 bp):
AAATTTAGATACCAAATTCAGAAAAAA
Done.