Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011710.1 Kokia drynarioides strain JFW-HI SEQ_126704, 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: 12900
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.34
Warning! 91 characters in sequence are not A, C, G, or T
Found at i:8685 original size:16 final size:17
Alignment explanation
Indices: 8666--8705 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
8656 TTTCTGAAAT
8666 TTATAAT-TTTAAAAAA
1 TTATAATATTTAAAAAA
8682 TTATAATACTTTAAAAAA
1 TTATAATA-TTTAAAAAA
*
8700 ATATAA
1 TTATAA
8706 AGAATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
18 14 0.67
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TTATAATATTTAAAAAA
Found at i:10110 original size:14 final size:14
Alignment explanation
Indices: 10090--10130 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
10080 TGCAATAAAT
10090 AAAATGATAGT-TA
1 AAAATGATAGTATA
10103 AAAGATGATAGTAATA
1 AAA-ATGATAGT-ATA
10119 AAAATGATAGTA
1 AAAATGATAGTA
10131 ATGACAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.12
14 9 0.36
15 8 0.32
16 5 0.20
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.27
Consensus pattern (14 bp):
AAAATGATAGTATA
Found at i:10141 original size:18 final size:15
Alignment explanation
Indices: 10090--10132 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
10080 TGCAATAAAT
10090 AAAATGATAGT--TA
1 AAAATGATAGTAATA
10103 AAAGATGATAGTAATA
1 AAA-ATGATAGTAATA
10119 AAAATGATAGTAAT
1 AAAATGATAGTAAT
10133 GACAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.11
14 8 0.30
15 11 0.41
16 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (15 bp):
AAAATGATAGTAATA
Found at i:10171 original size:12 final size:11
Alignment explanation
Indices: 10156--10194 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
10146 TAGCCGCATT
10156 AATAATAAAAC
1 AATAATAAAAC
*
10167 AAATAATAATAC
1 -AATAATAAAAC
10179 AATAATAAAAGC
1 AATAATAAAA-C
10191 AATA
1 AATA
10195 GTGGAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.21
Consensus pattern (11 bp):
AATAATAAAAC
Found at i:10388 original size:15 final size:15
Alignment explanation
Indices: 10368--10397 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10358 AAAGAAAAAG
*
10368 TAAAAAATAAATAAA
1 TAAAAAAAAAATAAA
10383 TAAAAAAAAAATAAA
1 TAAAAAAAAAATAAA
10398 ATGAATATAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAAAAAAAATAAA
Found at i:10431 original size:16 final size:16
Alignment explanation
Indices: 10376--10431 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
10366 AGTAAAAAAT
* *
10376 AAATAAATA-AAAAAA
1 AAATAAATAGAATATA
10391 AAATAAA-ATGAATATA
1 AAATAAATA-GAATATA
10407 CAAAT-AATAGAATATA
1 -AAATAAATAGAATATA
10423 AAATAAATA
1 AAATAAATA
10432 CAAAATTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 1 0.03
15 11 0.32
16 17 0.50
17 5 0.15
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (16 bp):
AAATAAATAGAATATA
Found at i:10572 original size:18 final size:19
Alignment explanation
Indices: 10549--10588 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
10539 ATTGAAACCT
* *
10549 AAAAAAATATAAGGGA-TA
1 AAAAAAAAAAAAGGGACTA
10567 AAAAAAAAAAAAGGGACTA
1 AAAAAAAAAAAAGGGACTA
10586 AAA
1 AAA
10589 GGCAAATACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.72, C:0.03, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAAAAAAAAAAGGGACTA
Found at i:12288 original size:97 final size:100
Alignment explanation
Indices: 12167--12504 Score: 305
Period size: 100 Copynumber: 3.4 Consensus size: 100
12157 ATCTGCTTCT
* * ** * *
12167 CTGCAACTTCAAGAAGATAGGATTTGACATTGTAGCCTT-ATCTTGCTCCACTGCATTTTC-AGG
1 CTGCAACTTCAAGGATATAGGATTTGATGTTGTAG-CTTCATCTTGCTCCACTACATCTTCTAGG
12230 TAGATAAGATTTAC-T-T-TAACTT-AAGTCCAATCCA
65 -AGATAAGATTTACTTCTGTAACTTCAA-TCCAATCCA
* * * *
12264 CTGTAACTTCAAGGATATAGGATTTGATGTCGTAGCTTCATCTTGCCCCGCTACATCTTCTAGGA
1 CTGCAACTTCAAGGATATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTACATCTTCTAGGA
* * *
12329 GATAAGATTTGCTTCTGTAGCTTCAATCCGATCCA
66 GATAAGATTTACTTCTGTAACTTCAATCCAATCCA
* * * ** *
12364 CTGCAACTTCAGGGGTATACGATTTGATGTTGTAGCTTCATCTTGCTTTACTACAACTT-TAGAG
1 CTGCAACTTCAAGGATATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTACATCTTCTAG-G
* * * ** * *
12428 AGATAAAGATTTGCTACTATAGTTTTAATCCGATCCA
65 AGAT-AAGATTTACTTCTGTAACTTCAATCCAATCCA
* * *
12465 CTACAACTT-AAGAGATATAGGATTTGGTGTTGTAACTTCA
1 CTGCAACTTCAAG-GATATAGGATTTGATGTTGTAGCTTCA
12505 CTTCGTTTCA
Statistics
Matches: 199, Mismatches: 33, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
96 3 0.02
97 58 0.29
98 4 0.02
99 4 0.02
100 69 0.35
101 61 0.31
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (100 bp):
CTGCAACTTCAAGGATATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTACATCTTCTAGGA
GATAAGATTTACTTCTGTAACTTCAATCCAATCCA
Done.