Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012194.1 Kokia drynarioides strain JFW-HI SEQ_127195, 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: 94534
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:3417 original size:15 final size:15
Alignment explanation
Indices: 3397--3425 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3387 GTATTGTTGT
3397 TTGATAACATGGTGA
1 TTGATAACATGGTGA
3412 TTGATAACATGGTG
1 TTGATAACATGGTG
3426 TGTGAGACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (15 bp):
TTGATAACATGGTGA
Found at i:22088 original size:15 final size:17
Alignment explanation
Indices: 22068--22102 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
22058 CCTTGACAAA
22068 CTTTTCTC-AAT-ATTT
1 CTTTTCTCAAATCATTT
22083 CTTTTCTCAAATCATTT
1 CTTTTCTCAAATCATTT
22100 CTT
1 CTT
22103 ACTAATACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 3 0.17
17 7 0.39
ACGTcount: A:0.20, C:0.23, G:0.00, T:0.57
Consensus pattern (17 bp):
CTTTTCTCAAATCATTT
Found at i:38477 original size:16 final size:16
Alignment explanation
Indices: 38456--38497 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
38446 TTATTTTGAT
*
38456 TTTTAAAATTAGTTAG
1 TTTTAAAATTAGTTAA
* *
38472 TTTT-AATTTATTTAA
1 TTTTAAAATTAGTTAA
38487 TTTTAAAATTA
1 TTTTAAAATTA
38498 AATATTTTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (16 bp):
TTTTAAAATTAGTTAA
Found at i:39562 original size:46 final size:46
Alignment explanation
Indices: 39509--39596 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
39499 TAACTCGCTT
* * * *
39509 AACCCTTAAAAATGAGGATAATACGCTTTAACACACTCGATCCCTC
1 AACCCTTAAAAAAGAGAATAATACACTTCAACACACTCGATCCCTC
**
39555 AACCCTTAAAAAAGAGAATAATGTACTTCAACACACTCGATC
1 AACCCTTAAAAAAGAGAATAATACACTTCAACACACTCGATC
39597 TCACGTCCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (46 bp):
AACCCTTAAAAAAGAGAATAATACACTTCAACACACTCGATCCCTC
Found at i:44911 original size:29 final size:28
Alignment explanation
Indices: 44854--44939 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 28
44844 ACATGGCCTA
* * *
44854 TCACACGACCTACCACACTGTTGTATGGC
1 TCACACGATCTACCACA-TGTCGTGTGGC
*
44883 TCCCACGATCTACCACATAGTCGTGTGGC
1 TCACACGATCTACCACAT-GTCGTGTGGC
44912 TCACAC-AGTCTACCACATGTCCGTGTGG
1 TCACACGA-TCTACCACATGT-CGTGTGG
44940 TGTTAACATC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 4 0.08
29 45 0.92
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.24
Consensus pattern (28 bp):
TCACACGATCTACCACATGTCGTGTGGC
Found at i:51674 original size:23 final size:21
Alignment explanation
Indices: 51629--51669 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
51619 AAACAATGAT
*
51629 AAAAAGTATCCATATCTTTTC
1 AAAAAATATCCATATCTTTTC
*
51650 AAAAAATATCGATATCTTTT
1 AAAAAATATCCATATCTTTT
51670 ATCAAGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (21 bp):
AAAAAATATCCATATCTTTTC
Found at i:60211 original size:21 final size:21
Alignment explanation
Indices: 60186--60243 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
60176 CCTGATAAAA
*
60186 GGTATCAATAATTTTTGAAAG
1 GGTATCGATAATTTTTGAAAG
*
60207 GGTATCGAT-ATTTTTGAAAT
1 GGTATCGATAATTTTTGAAAG
*
60227 GGTATCGATACTTTTTG
1 GGTATCGATAATTTTTG
60244 TCATTGTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (21 bp):
GGTATCGATAATTTTTGAAAG
Found at i:76183 original size:52 final size:52
Alignment explanation
Indices: 76151--76377 Score: 409
Period size: 52 Copynumber: 4.4 Consensus size: 52
76141 ACTTATAATA
76151 ACACATAGTCATCGGACCTCATAATCCGTAAAGGATTTATATACTCACGATG
1 ACACATAGTCATCGGACCTCATAATCCGTAAAGGATTTATATACTCACGATG
76203 ACACATAGTCATCGGACCTCATAATCCGTAAAGGATTTATATACTCACGATG
1 ACACATAGTCATCGGACCTCATAATCCGTAAAGGATTTATATACTCACGATG
*
76255 ACACATAGTCATCGGACCTCATAATCCTTAAAGGATTTATATACTCACGATG
1 ACACATAGTCATCGGACCTCATAATCCGTAAAGGATTTATATACTCACGATG
**
76307 ACACATAGTCATCGGACCTCATAATCCGTAAAGGATTTATATACAAACGATG
1 ACACATAGTCATCGGACCTCATAATCCGTAAAGGATTTATATACTCACGATG
* *
76359 ACACAGAGTCATCGAACCT
1 ACACATAGTCATCGGACCT
76378 TTTTCATTTA
Statistics
Matches: 169, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 169 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (52 bp):
ACACATAGTCATCGGACCTCATAATCCGTAAAGGATTTATATACTCACGATG
Found at i:76319 original size:156 final size:155
Alignment explanation
Indices: 76083--76377 Score: 421
Period size: 156 Copynumber: 1.9 Consensus size: 155
76073 ATTCATTTCC
* * * ** * *
76083 TTTAATACTCACGGTGACACATAGTCATTGATCCTCTTGTTCCTTAAAGGAATCATACACTTATA
1 TTTAATACTCACGATGACACATAGTCATGGATCCTCATAATCCTTAAAGGAATCATACACTCACA
** *
76148 ATAACACATAGTCATCGGACCTCATAATCCGTAAAGGATTTATATACTCACGATGACACATAGTC
66 ATAACACATAGTCATCGGACCTCATAATCCGTAAAGGATTTATATACAAACGATGACACAGAGTC
*
76213 ATCGGACCTCATAATCCGTAAAGGA
131 ATCGAACCTCATAATCCGTAAAGGA
* * *
76238 TTTATATACTCACGATGACACATAGTCATCGGA-CCTCATAATCCTTAAAGGATTTATATACTCA
1 TTTA-ATACTCACGATGACACATAGTCAT-GGATCCTCATAATCCTTAAAGGAATCATACACTCA
* *
76302 CGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTTATATACAAACGATGACACAGAG
64 CAATAACACATAGTCATCGGACCTCATAATCCGTAAAGGATTTATATACAAACGATGACACAGAG
76367 TCATCGAACCT
129 TCATCGAACCT
76378 TTTTCATTTA
Statistics
Matches: 122, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
155 4 0.03
156 116 0.95
157 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (155 bp):
TTTAATACTCACGATGACACATAGTCATGGATCCTCATAATCCTTAAAGGAATCATACACTCACA
ATAACACATAGTCATCGGACCTCATAATCCGTAAAGGATTTATATACAAACGATGACACAGAGTC
ATCGAACCTCATAATCCGTAAAGGA
Found at i:85917 original size:19 final size:19
Alignment explanation
Indices: 85881--85918 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
85871 ATTCGTTATA
*
85881 AAAATAATATTTTATATTT
1 AAAATAATATTATATATTT
85900 AAAATAA-ATTATATTATTT
1 AAAATAATATTATA-TATTT
85919 CAAGATACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATAATATTATATATTT
Found at i:86060 original size:18 final size:19
Alignment explanation
Indices: 86037--86081 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
86027 CCAAAAGCCT
*
86037 TATTTTAATTTTTTTAT-A
1 TATTTTAATTTTATTATGA
86055 TATTTTAATTTTATTATGGA
1 TATTTTAATTTTATTAT-GA
86075 TATTTTA
1 TATTTTA
86082 TTATCTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 16 0.67
20 8 0.33
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
TATTTTAATTTTATTATGA
Done.