Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008395.1 Kokia drynarioides strain JFW-HI SEQ_123063, 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: 40746
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:1304 original size:25 final size:23
Alignment explanation
Indices: 1276--1322 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1266 TTGAAATCTT
*
1276 GAAAACAAGAGAAAAATCAAAATTA
1 GAAAA-AA-AGAAAAAGCAAAATTA
*
1301 GAAAAAAAGAAGAAGCAAAATT
1 GAAAAAAAGAAAAAGCAAAATT
1323 TGAATTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 2 0.10
25 5 0.25
ACGTcount: A:0.68, C:0.06, G:0.15, T:0.11
Consensus pattern (23 bp):
GAAAAAAAGAAAAAGCAAAATTA
Found at i:1346 original size:25 final size:23
Alignment explanation
Indices: 1287--1360 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 23
1277 AAAACAAGAG
* *
1287 AAAAATCAAAATTAGAA--AAAA
1 AAAAAGCAAAATTTGAATTAAAA
1308 AGAAGAAGCAAAATTTGAATTGAAATA
1 A-AA-AAGCAAAATTTGAATT-AAA-A
*
1335 AAAAAGCTAAATTTGAATTAAAA
1 AAAAAGCAAAATTTGAATTAAAA
1358 AAA
1 AAA
1361 GAAAAAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 1 0.02
22 2 0.05
23 16 0.36
24 3 0.07
25 15 0.34
26 5 0.11
27 2 0.05
ACGTcount: A:0.65, C:0.04, G:0.11, T:0.20
Consensus pattern (23 bp):
AAAAAGCAAAATTTGAATTAAAA
Found at i:14891 original size:16 final size:16
Alignment explanation
Indices: 14845--14891 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
14835 CTCAGTCACT
**
14845 TGAAAAAGAAAAATGA
1 TGAAAAAGAAAAAAAA
* *
14861 -GAAAAAGGAAGAAAA
1 TGAAAAAGAAAAAAAA
14876 TGAAAAAGAAAAAAAA
1 TGAAAAAGAAAAAAAA
14892 ATTAATGTTG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (16 bp):
TGAAAAAGAAAAAAAA
Found at i:21735 original size:18 final size:18
Alignment explanation
Indices: 21682--21738 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
21672 TAAAGTTGCA
* *
21682 AGCTCACTTGAAGTTGCG
1 AGCTCAATTGAAGTTACG
* **
21700 AGCTTAA-ACAAGTCTACG
1 AGCTCAATTGAAGT-TACG
21718 AGCTCAATTGAAGTTACG
1 AGCTCAATTGAAGTTACG
21736 AGC
1 AGC
21739 ACATCAAAGT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
17 4 0.14
18 21 0.72
19 4 0.14
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (18 bp):
AGCTCAATTGAAGTTACG
Found at i:26768 original size:344 final size:344
Alignment explanation
Indices: 26141--26828 Score: 1322
Period size: 344 Copynumber: 2.0 Consensus size: 344
26131 TTTGGGAAAA
26141 AACCACGGGCAGAGGAGAAGAAGATTCACTAATGTCAAAAATCGAATAATTACAAGAGGAGATGA
1 AACCACGGGCAGAGGAGAAGAAGATTCACTAATGTCAAAAATCGAATAATTACAAGAGGAGATGA
26206 CTACACTTATTTATAGGTTGAAAAACCTTATTCCAATCAACAACTAATAGAAGTAACGTAGTAAG
66 CTACACTTATTTATAGGTTGAAAAACCTTATTCCAATCAACAACTAATAGAAGTAACGTAGTAAG
26271 GCTGAAACACCTTATTCTAAATAAAATAAAATAGATGACCTATTCTAATTAAAATAAAATAAAAG
131 GCTGAAACACCTTATTCTAAATAAAATAAAATAGATGACCTATTCTAATTAAAATAAAATAAAAG
26336 AAGTCTAGTTTATTTGAACTTTACTTTTATTTTATTTTACCACTGTATTTTATTTTAACAAGAAT
196 AAGTCTAGTTTATTTGAACTTTACTTTTATTTTATTTTACCACTGTATTTTATTTTAACAAGAAT
26401 TCTAGTCACCTAATTCTAACAATTTAACTTATGCATAATTTGCTTGATTTTAAACTCAATTGAAT
261 TCTAGTCACCTAATTCTAACAATTTAACTTATGCATAATTTGCTTGATTTTAAACTCAATTGAAT
26466 TGTTAGATATGGACCAGAG
326 TGTTAGATATGGACCAGAG
26485 AACCACGGGCAGAGGAGAAGAAGATTCACTAATGTCAAAAATCGAATAATTACAAGAGGAGATGA
1 AACCACGGGCAGAGGAGAAGAAGATTCACTAATGTCAAAAATCGAATAATTACAAGAGGAGATGA
*
26550 CTACACTTATTTATAGGTTGAAAAACCTTATTCCAATCAACAACTAATAGAAGTAATGTAGTAAG
66 CTACACTTATTTATAGGTTGAAAAACCTTATTCCAATCAACAACTAATAGAAGTAACGTAGTAAG
* *
26615 GCTGAAACACCTTATTCTAAATAAGATAAAATAGATGACCTGTTCTAATTAAAATAAAATAAAAG
131 GCTGAAACACCTTATTCTAAATAAAATAAAATAGATGACCTATTCTAATTAAAATAAAATAAAAG
*
26680 AAGTCTAGTTTATTTGAACTTTACTTTTATTTTATTTTACCACTGTATTTTATTTTAACAATAAT
196 AAGTCTAGTTTATTTGAACTTTACTTTTATTTTATTTTACCACTGTATTTTATTTTAACAAGAAT
* *
26745 TTTAGTCATCTAATTCTAACAATTTAACTTATGCATAATTTGCTTGATTTTAAACTCAATTGAAT
261 TCTAGTCACCTAATTCTAACAATTTAACTTATGCATAATTTGCTTGATTTTAAACTCAATTGAAT
26810 TGTTAGATATGGACCAGAG
326 TGTTAGATATGGACCAGAG
26829 TTTTAAATAC
Statistics
Matches: 338, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
344 338 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (344 bp):
AACCACGGGCAGAGGAGAAGAAGATTCACTAATGTCAAAAATCGAATAATTACAAGAGGAGATGA
CTACACTTATTTATAGGTTGAAAAACCTTATTCCAATCAACAACTAATAGAAGTAACGTAGTAAG
GCTGAAACACCTTATTCTAAATAAAATAAAATAGATGACCTATTCTAATTAAAATAAAATAAAAG
AAGTCTAGTTTATTTGAACTTTACTTTTATTTTATTTTACCACTGTATTTTATTTTAACAAGAAT
TCTAGTCACCTAATTCTAACAATTTAACTTATGCATAATTTGCTTGATTTTAAACTCAATTGAAT
TGTTAGATATGGACCAGAG
Found at i:28133 original size:18 final size:18
Alignment explanation
Indices: 28110--28149 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
28100 GTTCCTACTG
*
28110 TAAGAAGTTAGGTCACGT
1 TAAGAAGTTAGGTCACGC
28128 TAAGAAGTTAGGTCACGC
1 TAAGAAGTTAGGTCACGC
28146 TAAG
1 TAAG
28150 GTAGATTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (18 bp):
TAAGAAGTTAGGTCACGC
Found at i:30405 original size:21 final size:19
Alignment explanation
Indices: 30379--30431 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
30369 GGAGTTTTTA
30379 GTATTGGTAGATGCATGACTT
1 GTATTGGTAGAT-CAT-ACTT
*
30400 GTATTGGTAGAAATTATACTT
1 GTATTGGTAG--ATCATACTT
30421 GTATTGGTAGA
1 GTATTGGTAGA
30432 ACTAACACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 1 0.03
21 24 0.83
22 2 0.07
23 2 0.07
ACGTcount: A:0.28, C:0.06, G:0.26, T:0.40
Consensus pattern (19 bp):
GTATTGGTAGATCATACTT
Done.