Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010843.1 Kokia drynarioides strain JFW-HI SEQ_125810, 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: 59307
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 503 characters in sequence are not A, C, G, or T
Found at i:1763 original size:23 final size:23
Alignment explanation
Indices: 1715--1763 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
1705 GGAAAAATAA
*
1715 TTATTATAAAAATATATTTTTGT
1 TTATTATAAAAATATAATTTTGT
* *
1738 TTATTGTAAAAATTTTAATTTT-T
1 TTATTATAAAAA-TATAATTTTGT
1761 TTA
1 TTA
1764 ACCTATTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (23 bp):
TTATTATAAAAATATAATTTTGT
Found at i:2181 original size:39 final size:39
Alignment explanation
Indices: 2149--2231 Score: 132
Period size: 39 Copynumber: 2.1 Consensus size: 39
2139 TTATCTCTTT
2149 TAAA-ATGAAATTTTTTTTATTTAGATATTTTATAATTTA
1 TAAATATGAAA-TTTTTTTATTTAGATATTTTATAATTTA
* *
2188 TAAATTTTAAATTTTTTTATTTAGATATTTTATAATTTA
1 TAAATATGAAATTTTTTTATTTAGATATTTTATAATTTA
2227 TAAAT
1 TAAAT
2232 TTTAAATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 37 0.90
40 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (39 bp):
TAAATATGAAATTTTTTTATTTAGATATTTTATAATTTA
Found at i:2232 original size:39 final size:39
Alignment explanation
Indices: 2160--2239 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
2150 AAAATGAAAT
2160 TTTTTTTATTTAGATATTTTATAATTTATAAATTTTAAA
1 TTTTTTTATTTAGATATTTTATAATTTATAAATTTTAAA
2199 TTTTTTTATTTAGATATTTTATAATTTATAAATTTTAAA
1 TTTTTTTATTTAGATATTTTATAATTTATAAATTTTAAA
2238 TT
1 TT
2240 AATTAGTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (39 bp):
TTTTTTTATTTAGATATTTTATAATTTATAAATTTTAAA
Found at i:2325 original size:31 final size:30
Alignment explanation
Indices: 2268--2325 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2258 TATATTTTGG
*
2268 TTTTAAAAAATAATAAAAATTTGATTTAAT
1 TTTTAAAAAATAATAAAAATTAGATTTAAT
* *
2298 TTTTTAAAAATTATAAAAATATAGATTT
1 TTTTAAAAAATAATAAAAAT-TAGATTT
2326 TTAAAATGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (30 bp):
TTTTAAAAAATAATAAAAATTAGATTTAAT
Found at i:5631 original size:15 final size:15
Alignment explanation
Indices: 5611--5660 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
5601 TGTAGTGGAA
5611 GATGACGACGACAAC
1 GATGACGACGACAAC
** *
5626 GATGACGACGATGAT
1 GATGACGACGACAAC
* *
5641 GATGACGATGACAAG
1 GATGACGACGACAAC
5656 GATGA
1 GATGA
5661 AGATGATGCC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.32, T:0.14
Consensus pattern (15 bp):
GATGACGACGACAAC
Found at i:7967 original size:17 final size:17
Alignment explanation
Indices: 7945--7978 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7935 TCAGGTTTTA
*
7945 TTTTTTTAGGCTTGAAT
1 TTTTTTTAGACTTGAAT
7962 TTTTTTTAGACTTGAAT
1 TTTTTTTAGACTTGAAT
7979 AGGTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.15, T:0.59
Consensus pattern (17 bp):
TTTTTTTAGACTTGAAT
Found at i:9764 original size:5 final size:5
Alignment explanation
Indices: 9756--9782 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
9746 AGGGTAACAC
9756 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
9783 AAATATCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:30448 original size:22 final size:22
Alignment explanation
Indices: 30423--30488 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
30413 GCTCTGATGC
30423 CATGTTGAAATTAGAGATGAAT
1 CATGTTGAAATTAGAGATGAAT
*
30445 CATGATGAAATTAGAGATGAAT
1 CATGTTGAAATTAGAGATGAAT
*
30467 CAT-TATGAAATTAGAGAAGAAT
1 CATGT-TGAAATTAGAGATGAAT
30489 ACTCTAACAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (22 bp):
CATGTTGAAATTAGAGATGAAT
Found at i:31699 original size:24 final size:24
Alignment explanation
Indices: 31671--31718 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31661 TACATCGATA
* *
31671 AAAAATAAACAAGTTAAACAAAAAC
1 AAAAGTAAACAA-ATAAACAAAAAC
*
31696 AAAAGTAAATAAATAAACAAAAA
1 AAAAGTAAACAAATAAACAAAAA
31719 TCCCTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.75, C:0.08, G:0.04, T:0.12
Consensus pattern (24 bp):
AAAAGTAAACAAATAAACAAAAAC
Found at i:35330 original size:28 final size:28
Alignment explanation
Indices: 35297--35350 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
35287 ATGATATTCC
35297 TATCAACATTCTTTGTCTATTGTGTTAA
1 TATCAACATTCTTTGTCTATTGTGTTAA
35325 TATCAACATTCTTTGTCTATTGTGTT
1 TATCAACATTCTTTGTCTATTGTGTT
35351 TTGAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (28 bp):
TATCAACATTCTTTGTCTATTGTGTTAA
Found at i:41109 original size:2 final size:2
Alignment explanation
Indices: 41102--41143 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
41092 ATCTCAAAGT
41102 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
41144 AAAAAAACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.