Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010620.1 Kokia drynarioides strain JFW-HI SEQ_125553, 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: 55972
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Found at i:4593 original size:22 final size:22
Alignment explanation
Indices: 4565--4607 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
4555 ACCTCAATTC
4565 TTAAATT-TGAAAAGTAAAAGGG
1 TTAAATTATGAAAA-TAAAAGGG
4587 TTAAATTACTGAAAATAAAAG
1 TTAAATTA-TGAAAATAAAAG
4608 TAAAAGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 6 0.32
24 6 0.32
ACGTcount: A:0.53, C:0.02, G:0.16, T:0.28
Consensus pattern (22 bp):
TTAAATTATGAAAATAAAAGGG
Found at i:14283 original size:10 final size:10
Alignment explanation
Indices: 14268--14294 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
14258 TCAAGAAAAA
14268 TAAAATTACT
1 TAAAATTACT
14278 TAAAATTACT
1 TAAAATTACT
14288 TAAAATT
1 TAAAATT
14295 TAGCAGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
TAAAATTACT
Found at i:30266 original size:19 final size:22
Alignment explanation
Indices: 30219--30276 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
30209 GTGTGATGAT
30219 CCCACACGCTCGTGTGGCTATC
1 CCCACACGCTCGTGTGGCTATC
30241 CCACACAC-CT-GTGTGGCTA-C
1 CC-CACACGCTCGTGTGGCTATC
* *
30261 TCCACACGCCCGTGTG
1 CCCACACGCTCGTGTG
30277 TCCACCCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 5 0.16
20 3 0.10
21 14 0.45
22 4 0.13
23 5 0.16
ACGTcount: A:0.16, C:0.41, G:0.22, T:0.21
Consensus pattern (22 bp):
CCCACACGCTCGTGTGGCTATC
Found at i:31816 original size:22 final size:22
Alignment explanation
Indices: 31790--31832 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
31780 TACCTTGACT
* *
31790 TGCACTACGGTGCCCTTGTAAA
1 TGCACTACGATGCCCTCGTAAA
*
31812 TGCACTTCGATGCCCTCGTAA
1 TGCACTACGATGCCCTCGTAA
31833 TGCTCTCGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (22 bp):
TGCACTACGATGCCCTCGTAAA
Found at i:33855 original size:24 final size:24
Alignment explanation
Indices: 33822--33905 Score: 132
Period size: 24 Copynumber: 3.5 Consensus size: 24
33812 CTGGTTAAAC
* **
33822 TCTATTTGGGCTTGTAAGAGCTAA
1 TCTATCTGGGCTCATAAGAGCTAA
*
33846 TCTATCTGGGCTCAAAAGAGCTAA
1 TCTATCTGGGCTCATAAGAGCTAA
33870 TCTATCTGGGCTCATAAGAGCTAA
1 TCTATCTGGGCTCATAAGAGCTAA
33894 TCTATCTGGGCT
1 TCTATCTGGGCT
33906 TGTATGAGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (24 bp):
TCTATCTGGGCTCATAAGAGCTAA
Found at i:38228 original size:21 final size:21
Alignment explanation
Indices: 38204--38247 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38194 TTGTTTGTAC
38204 TTAGGTGAATTT-AGTTGCATT
1 TTAGGT-AATTTCAGTTGCATT
*
38225 TTAGGTAATTTCATTTGCATT
1 TTAGGTAATTTCAGTTGCATT
38246 TT
1 TT
38248 TAGAACATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.23, C:0.07, G:0.18, T:0.52
Consensus pattern (21 bp):
TTAGGTAATTTCAGTTGCATT
Found at i:39753 original size:60 final size:59
Alignment explanation
Indices: 39617--39808 Score: 215
Period size: 60 Copynumber: 3.2 Consensus size: 59
39607 TTAATATAAC
* * * *
39617 ATTTGGTACCTGAATTTGACACTTTTTTCCTAATTTGATACCTAAAATTTTTTG-ACCCA
1 ATTTGGTACCTGAACTTGACA-TTTTTTCCTAATTTGATACATAAACTTTTTTGAATCCA
* * * * *
39676 ATTTGGTACCTAAACTTGATAATTTTTCCTAATTTGGTACTTAAACTTTTTTCGAATCCA
1 ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTGATACATAAACTTTTTT-GAATCCA
* * * *
39736 ATTTGGTACCTGAACTTGACATTTTTTGCTAATTTGATACATAATCTATTTTTTTAGATTCA
1 ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTGATACATAAAC--TTTTTTGA-ATCCA
39798 ATTTGGTACCT
1 ATTTGGTACCT
39809 AAATTTATTA
Statistics
Matches: 111, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
58 27 0.24
59 19 0.17
60 43 0.39
61 1 0.01
62 21 0.19
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (59 bp):
ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTGATACATAAACTTTTTTGAATCCA
Found at i:41765 original size:19 final size:18
Alignment explanation
Indices: 41724--41777 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
41714 ACATTTCTTT
**
41724 TAAAAAACATTTTTAGTA
1 TAAAAAACATTTTTAAAA
*
41742 CAAAAAACACTTTTTAAAA
1 TAAAAAACA-TTTTTAAAA
* *
41761 TAAAAAATATTGTTAAA
1 TAAAAAACATTTTTAAA
41778 CAAAATACCC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (18 bp):
TAAAAAACATTTTTAAAA
Found at i:42243 original size:16 final size:16
Alignment explanation
Indices: 42222--42270 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
42212 CTTTATCCCA
42222 AAAAATAAAAAATTAT
1 AAAAATAAAAAATTAT
*
42238 AAAAATATAAAA-TAT
1 AAAAATAAAAAATTAT
*
42253 TAAAATAATAAAATTAT
1 AAAAATAA-AAAATTAT
42270 A
1 A
42271 TTTTTACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 9 0.33
16 15 0.56
17 3 0.11
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATAAAAAATTAT
Found at i:42262 original size:18 final size:18
Alignment explanation
Indices: 42221--42254 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42211 ACTTTATCCC
42221 AAAAA-ATAAAAAATTAT
1 AAAAATATAAAAAATTAT
*
42238 AAAAATATAAAATATTA
1 AAAAATATAAAAAATTA
42255 AAATAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATATAAAAAATTAT
Found at i:51770 original size:14 final size:13
Alignment explanation
Indices: 51746--51802 Score: 57
Period size: 14 Copynumber: 4.4 Consensus size: 13
51736 GAAAAAGAAA
51746 AAAAACAAAAAAAG
1 AAAAAC-AAAAAAG
51760 ACAAAACAAAAAAG
1 A-AAAACAAAAAAG
51774 --AAA-AAAAAAG
1 AAAAACAAAAAAG
*
51784 AAAAACCAAAAACG
1 AAAAA-CAAAAAAG
51798 AAAAA
1 AAAAA
51803 AGAGAGTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
10 7 0.19
11 3 0.08
12 3 0.08
14 19 0.51
15 5 0.14
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAAG
Found at i:51770 original size:23 final size:22
Alignment explanation
Indices: 51734--51805 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 22
51724 GATGTCATGT
*
51734 AAGAAAAAGAAAAAAAACAAAAA
1 AAGAAAAA-CAAAAAAACAAAAA
*
51757 AAGACAAAACAAAAAAGAAAAAAA
1 AAGA-AAAACAAAAAA-ACAAAAA
* *
51781 AAGAAAAAC-CAAAAACGAAAA
1 AAGAAAAACAAAAAAACAAAAA
51802 AAGA
1 AAGA
51806 GAGTATTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
21 9 0.21
22 4 0.10
23 15 0.36
24 14 0.33
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (22 bp):
AAGAAAAACAAAAAAACAAAAA
Found at i:51780 original size:15 final size:15
Alignment explanation
Indices: 51737--51780 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
51727 GTCATGTAAG
51737 AAAAAGAAAAAAAACA
1 AAAAAG-AAAAAAACA
*
51753 AAAAA-AGACAAAACA
1 AAAAAGA-AAAAAACA
51768 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
51781 AAGAAAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 1 0.04
15 17 0.71
16 6 0.25
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAACA
Found at i:51788 original size:31 final size:31
Alignment explanation
Indices: 51737--51805 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
51727 GTCATGTAAG
*
51737 AAAAAGAAAAAAAACAAAAAAAGACAAAAC-A
1 AAAAAGAAAAAAAACAAAAAAACA-AAAACGA
*
51768 AAAAAGAAAAAAAA-AGAAAAACCAAAAACGA
1 AAAAAGAAAAAAAACA-AAAAAACAAAAACGA
51799 AAAAAGA
1 AAAAAGA
51806 GAGTATTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 6 0.18
31 28 0.82
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (31 bp):
AAAAAGAAAAAAAACAAAAAAACAAAAACGA
Found at i:51793 original size:24 final size:23
Alignment explanation
Indices: 51734--51803 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 23
51724 GATGTCATGT
*
51734 AAGAAAAAGAAAAAA-AACAAAAA
1 AAGAAAAACAAAAAAGAA-AAAAA
51757 AAGACAAAACAAAAAAGAAAAAAA
1 AAGA-AAAACAAAAAAGAAAAAAA
*
51781 AAGAAAAACCAAAAACGAAAAAA
1 AAGAAAAA-CAAAAAAGAAAAAA
51804 GAGAGTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
23 8 0.19
24 32 0.76
25 2 0.05
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (23 bp):
AAGAAAAACAAAAAAGAAAAAAA
Done.