Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014764.1 Kokia drynarioides strain JFW-HI SEQ_129803, 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: 37617
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:61 original size:2 final size:2
Alignment explanation
Indices: 54--106 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
44 GGCTTTAATT
54 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
96 TA TA TA TA TA T
1 TA TA TA TA TA T
107 TATTAATATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1433 original size:61 final size:61
Alignment explanation
Indices: 1324--1445 Score: 165
Period size: 61 Copynumber: 2.0 Consensus size: 61
1314 TATAGTTAAA
* * * *
1324 CCTTGTAAAAGCCAAAGGATTCTAATTTAACCACAAAAATTATGGGGAGGTTCTATTTTAG
1 CCTTATAAAAGCCAAAGGATTCTAATTTAACCACAAAAACTATGGGGAGATTCTATCTTAG
* * *
1385 CCTTATAAAAGTCAAAGGGTTCTAATTTAGCCACAAAAACTA-GAGGGAGATTCTATCTTAG
1 CCTTATAAAAGCCAAAGGATTCTAATTTAACCACAAAAACTATG-GGGAGATTCTATCTTAG
1446 TCTTGTGAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
60 1 0.02
61 52 0.98
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (61 bp):
CCTTATAAAAGCCAAAGGATTCTAATTTAACCACAAAAACTATGGGGAGATTCTATCTTAG
Found at i:16292 original size:18 final size:18
Alignment explanation
Indices: 16271--16310 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16261 ATATTTTTCT
* *
16271 TTTTTAAAATAATTTATA
1 TTTTGAAAATAATTTAGA
*
16289 TTTTGAAGATAATTTAGA
1 TTTTGAAAATAATTTAGA
16307 TTTT
1 TTTT
16311 AATTTAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TTTTGAAAATAATTTAGA
Found at i:20790 original size:16 final size:17
Alignment explanation
Indices: 20752--20793 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
20742 GGTAGAGTGT
*
20752 ATAGAAAATTGGAATGG
1 ATAGAAAATTGGAAGGG
*
20769 -TGGAAAATT-GAAGGG
1 ATAGAAAATTGGAAGGG
20784 ATAGAAAATT
1 ATAGAAAATT
20794 TGATAGATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.24
Consensus pattern (17 bp):
ATAGAAAATTGGAAGGG
Found at i:24496 original size:12 final size:12
Alignment explanation
Indices: 24467--24496 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
24457 TTTTCCCAAG
24467 TTTTTTCTTTTT
1 TTTTTTCTTTTT
*
24479 CTTTTTCTTTTT
1 TTTTTTCTTTTT
24491 TTTTTT
1 TTTTTT
24497 TATATGTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:29854 original size:22 final size:24
Alignment explanation
Indices: 29827--29870 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
29817 TACGCACTAA
*
29827 AAAAATATTTAA-AT-TAATTTAT
1 AAAAATAGTTAATATATAATTTAT
29849 AAAAATAGTTAATATATAATTT
1 AAAAATAGTTAATATATAATTT
29871 GGTATCCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AAAAATAGTTAATATATAATTTAT
Found at i:32312 original size:21 final size:22
Alignment explanation
Indices: 32276--32317 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
32266 GTCATTTTTA
32276 TTTTAATTTTAATTTT-TTTGT
1 TTTTAATTTTAATTTTGTTTGT
**
32297 TTTTAATTTTTCTTTTGTTTG
1 TTTTAATTTTAATTTTGTTTG
32318 ATTCTGATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.76
Consensus pattern (22 bp):
TTTTAATTTTAATTTTGTTTGT
Found at i:34456 original size:31 final size:30
Alignment explanation
Indices: 34420--34488 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
34410 AATTATATAC
*
34420 AAATTTTGATTTAATGTGTAATGTTATACATG
1 AAATTTTGACTT--TGTGTAATGTTATACATG
* * *
34452 -AATTTTGGCTTTGTGTGATTTTATACATG
1 AAATTTTGACTTTGTGTAATGTTATACATG
34481 AAATTTTG
1 AAATTTTG
34489 GTTTGATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 16 0.50
30 7 0.22
31 9 0.28
ACGTcount: A:0.29, C:0.04, G:0.17, T:0.49
Consensus pattern (30 bp):
AAATTTTGACTTTGTGTAATGTTATACATG
Found at i:34503 original size:30 final size:29
Alignment explanation
Indices: 34434--34493 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
34424 TTTGATTTAA
*
34434 TGTGTAATGTTATACATGAATTTTGGCTT
1 TGTGTAATTTTATACATGAATTTTGGCTT
*
34463 TGTGTGATTTTATACATGAAATTTTGG-TT
1 TGTGTAATTTTATACATG-AATTTTGGCTT
34492 TG
1 TG
34494 ATTCAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.23, C:0.05, G:0.22, T:0.50
Consensus pattern (29 bp):
TGTGTAATTTTATACATGAATTTTGGCTT
Found at i:34950 original size:25 final size:25
Alignment explanation
Indices: 34912--34971 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
34902 GGTCCTTCTG
*
34912 TTAAAAATTTCATCAATTTTTACGA
1 TTAAAAATTGCATCAATTTTTACGA
34937 TTAAAAATTGCATCAATTTTTACGA
1 TTAAAAATTGCATCAATTTTTACGA
34962 TTAAAAATTG
1 TTAAAAATTG
34972 GTCTTTGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.42
Consensus pattern (25 bp):
TTAAAAATTGCATCAATTTTTACGA
Done.