Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001877.1 Kokia drynarioides strain JFW-HI SEQ_113646, 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: 35498
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:3086 original size:4 final size:4
Alignment explanation
Indices: 3077--3106 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
3067 ATTCTCAAGG
3077 TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
3107 TATTTATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:9524 original size:22 final size:23
Alignment explanation
Indices: 9484--9527 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
9474 TCATGGAATA
*
9484 TTTGTTTATTTATAGATTTTATT
1 TTTGTTTATTTACAGATTTTATT
*
9507 TTTGTTT-TTTACATATTTTAT
1 TTTGTTTATTTACAGATTTTAT
9528 AGATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.70
Consensus pattern (23 bp):
TTTGTTTATTTACAGATTTTATT
Found at i:9553 original size:27 final size:30
Alignment explanation
Indices: 9491--9563 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 30
9481 ATATTTGTTT
* *
9491 ATTTATAGATTTTATTTTTGTTTTTTACATA
1 ATTTATAGATTTTATTTTTG-TTCTGACATA
*
9522 TTTTATAGATTTT-TTTTTG-TCTGA-ATA
1 ATTTATAGATTTTATTTTTGTTCTGACATA
9549 ATTTATAGATTTTAT
1 ATTTATAGATTTTAT
9564 AATAAAGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 15 0.41
28 4 0.11
30 6 0.16
31 12 0.32
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (30 bp):
ATTTATAGATTTTATTTTTGTTCTGACATA
Found at i:10149 original size:2 final size:2
Alignment explanation
Indices: 10142--10167 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10132 TTCATTCTTG
10142 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
10168 TTTAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14920 original size:21 final size:21
Alignment explanation
Indices: 14896--14947 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
14886 AATAACATTC
14896 AAACAACAA-AAATAATAACCA
1 AAACAACAACAAA-AATAACCA
*
14917 AAACAGCAACAAAAATAA-CA
1 AAACAACAACAAAAATAACCA
14937 ATAA-AACAACA
1 A-AACAACAACA
14948 TTAAAAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 9 0.33
21 15 0.56
22 3 0.11
ACGTcount: A:0.71, C:0.19, G:0.02, T:0.08
Consensus pattern (21 bp):
AAACAACAACAAAAATAACCA
Found at i:14974 original size:20 final size:19
Alignment explanation
Indices: 14951--15037 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 19
14941 AACAACATTA
14951 AAAACAACAAAAATAACAGC
1 AAAACAACAAAAA-AACAGC
*
14971 AAAAACAACACTAAAATAACAATC
1 -AAAACAACA--AAAA-AAC-AGC
** *
14995 AAAACAGTAAAAAAAGCACC
1 AAAACAACAAAAAAA-CAGC
* *
15015 AAAACAACACAAAAACAGT
1 AAAACAACAAAAAAACAGC
15034 AAAA
1 AAAA
15038 AAAAAAGCAA
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
19 6 0.11
20 16 0.30
21 14 0.26
23 15 0.28
24 2 0.04
ACGTcount: A:0.69, C:0.20, G:0.05, T:0.07
Consensus pattern (19 bp):
AAAACAACAAAAAAACAGC
Found at i:14998 original size:23 final size:22
Alignment explanation
Indices: 14928--15000 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 22
14918 AACAGCAACA
* * * *
14928 AAAATAACAATAAAACAACATTA
1 AAAACAAC-ATAAAATAACAATC
*
14951 AAAACAACA-AAAATAAC-AGC
1 AAAACAACATAAAATAACAATC
14971 AAAAACAACACTAAAATAACAATC
1 -AAAACAACA-TAAAATAACAATC
14995 AAAACA
1 AAAACA
15001 GTAAAAAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
21 16 0.40
22 1 0.03
23 21 0.52
24 2 0.05
ACGTcount: A:0.70, C:0.18, G:0.01, T:0.11
Consensus pattern (22 bp):
AAAACAACATAAAATAACAATC
Found at i:15001 original size:32 final size:33
Alignment explanation
Indices: 14923--14986 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
14913 ACCAAAACAG
*
14923 CAACAAAAATAACA--ATAAAACAACATTAAAAA
1 CAACAAAAATAACAGCA-AAAACAACACTAAAAA
14955 CAACAAAAATAACAGCAAAAACAACACTAAAA
1 CAACAAAAATAACAGCAAAAACAACACTAAAA
14987 TAACAATCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.48
33 14 0.48
34 1 0.03
ACGTcount: A:0.70, C:0.19, G:0.02, T:0.09
Consensus pattern (33 bp):
CAACAAAAATAACAGCAAAAACAACACTAAAAA
Found at i:15007 original size:32 final size:31
Alignment explanation
Indices: 14939--15038 Score: 96
Period size: 32 Copynumber: 3.1 Consensus size: 31
14929 AAATAACAAT
* * *
14939 AAAACAACATTAAAAACAACAAAAATAACAGCA
1 AAAACAACACT-AAAACAACAACAA-AACAGTA
*
14972 AAAACAACACTAAAATAACAATCAAAACAGTA
1 AAAACAACACTAAAACAACAA-CAAAACAGTA
*
15004 AAAA-AAGCACCAAAACAAC-ACAAAAACAGTA
1 AAAACAA-CACTAAAACAACAAC-AAAACAGTA
15035 AAAA
1 AAAA
15039 AAAAAGCAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
30 1 0.02
31 16 0.28
32 29 0.50
33 12 0.21
ACGTcount: A:0.69, C:0.19, G:0.04, T:0.08
Consensus pattern (31 bp):
AAAACAACACTAAAACAACAACAAAACAGTA
Found at i:15052 original size:25 final size:24
Alignment explanation
Indices: 15015--15075 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
15005 AAAAAGCACC
15015 AAAACAACACAAAAACAGTAAAAAA
1 AAAACAACAC-AAAACAGTAAAAAA
*
15040 AAAAGCAAC-CAAAATAGTAAAAAA
1 AAAA-CAACACAAAACAGTAAAAAA
* *
15064 AAACCAAAACAA
1 AAAACAACACAA
15076 TAATATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 3 0.10
24 19 0.61
25 5 0.16
26 4 0.13
ACGTcount: A:0.74, C:0.16, G:0.05, T:0.05
Consensus pattern (24 bp):
AAAACAACACAAAACAGTAAAAAA
Found at i:18435 original size:16 final size:16
Alignment explanation
Indices: 18414--18446 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
18404 CATCAAGTAG
18414 ATCTTGACTTTCTTTT
1 ATCTTGACTTTCTTTT
18430 ATCTTGACTTTCTTTT
1 ATCTTGACTTTCTTTT
18446 A
1 A
18447 CCCTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.61
Consensus pattern (16 bp):
ATCTTGACTTTCTTTT
Found at i:23595 original size:57 final size:57
Alignment explanation
Indices: 23518--23626 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 57
23508 GGTAGATATG
* * *
23518 AAGGTAGATCCTCTAGCTGAACAAAAGCAAACCTTGATAGCCTCTACCAATCTTACA
1 AAGGTAGATCCTCTAACTGAACAAAACCAAACCATGATAGCCTCTACCAATCTTACA
*
23575 AAGGTAGA-CCTTCTAACTGAACAAAACCAAACCATGATATCCTCTACCAATC
1 AAGGTAGATCC-TCTAACTGAACAAAACCAAACCATGATAGCCTCTACCAATC
23627 GTTCTCATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
56 2 0.04
57 45 0.96
ACGTcount: A:0.39, C:0.28, G:0.12, T:0.22
Consensus pattern (57 bp):
AAGGTAGATCCTCTAACTGAACAAAACCAAACCATGATAGCCTCTACCAATCTTACA
Done.