Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003130.1 Kokia drynarioides strain JFW-HI SEQ_115707, 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: 30323
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:7584 original size:15 final size:16
Alignment explanation
Indices: 7564--7598 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
7554 CTTCTTCATT
7564 TTCTTTTTCCTTTT-C
1 TTCTTTTTCCTTTTCC
7579 TTC-TTTTCCTTTTCC
1 TTCTTTTTCCTTTTCC
7594 TTCTT
1 TTCTT
7599 CAACACCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 10 0.56
15 7 0.39
16 1 0.06
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTCTTTTTCCTTTTCC
Found at i:7591 original size:20 final size:21
Alignment explanation
Indices: 7555--7595 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
7545 GCACAAAATC
*
7555 TTCTTCATTTTCTTTTTCCTT
1 TTCTTCATTTTCCTTTTCCTT
7576 TTCTTC-TTTTCCTTTTCCTT
1 TTCTTCATTTTCCTTTTCCTT
7596 CTTCAACACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (21 bp):
TTCTTCATTTTCCTTTTCCTT
Found at i:17942 original size:16 final size:17
Alignment explanation
Indices: 17911--17942 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17901 TTAATTTTGT
17911 TTTTCATTTCTTTGTTA
1 TTTTCATTTCTTTGTTA
17928 TTTTCATTT-TTTGTT
1 TTTTCATTTCTTTGTT
17943 CTAAGTGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTCATTTCTTTGTTA
Found at i:19161 original size:233 final size:234
Alignment explanation
Indices: 18754--19219 Score: 754
Period size: 233 Copynumber: 2.0 Consensus size: 234
18744 AGGTTAGCAA
* * *
18754 CACGACTGTGTGGCCTTACTTCAAATGCACACACAATCTAGACTATGTCACATGGCCTGGCCACA
1 CACGACTGTGTAGCCCTACTTCAAATGCACACACAATCTAGACTATGTCACATGGCCTAGCCACA
*
18819 TGACCATGTGACACCTATTTCCCAATGTCTCATGTTTTTCCATAATTTTCTAATTTGTTTCAAAA
66 TGACCATGTAACACCTATTTCCCAATGTCTCATGTTTTTCCATAATTTTCTAATTTGTTTCAAAA
* *
18884 TGATCCCTGATTCCTTTAAAATTGCTTTTAGGGCTTCGAAAACTCGACTTAAGGCCCAAATATAT
131 TGATCCCTGATTCCTTAAAAATTACTTTTAGGGCTTCGAAAACTCGACTTAAGGCCCAAATATAT
* *
18949 ATGTTTGCTATAATTGTTGTGAGATATT-AAATTTTTTT
196 ATGTTTGCTATAATTGTTGTAAGATATTGAAAATTTTTT
* * *
18987 CACGACTGTGTATCCCTACTTCAAATGCACACACGATCTGGACTATGTCACATGGCCTAGCCACA
1 CACGACTGTGTAGCCCTACTTCAAATGCACACACAATCTAGACTATGTCACATGGCCTAGCCACA
* * * *
19052 TGACCATTTAACACCTATTTCCCAATGTCTCATGTTTTTCTATAATTTTTTGATTTGTTTCAAAA
66 TGACCATGTAACACCTATTTCCCAATGTCTCATGTTTTTCCATAATTTTCTAATTTGTTTCAAAA
** **
19117 TGATCGTTGATTCCTTAAAAATTACTTTTAGGGCTTCGAAAACTCGACTTAAGGCTTAAATATAT
131 TGATCCCTGATTCCTTAAAAATTACTTTTAGGGCTTCGAAAACTCGACTTAAGGCCCAAATATAT
19182 ATGTTTGCTATAATTGTTGTAAGATATTGAAAATTTTT
196 ATGTTTGCTATAATTGTTGTAAGATATTGAAAATTTTT
19220 CTTAATTTGA
Statistics
Matches: 213, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
233 205 0.96
234 8 0.04
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (234 bp):
CACGACTGTGTAGCCCTACTTCAAATGCACACACAATCTAGACTATGTCACATGGCCTAGCCACA
TGACCATGTAACACCTATTTCCCAATGTCTCATGTTTTTCCATAATTTTCTAATTTGTTTCAAAA
TGATCCCTGATTCCTTAAAAATTACTTTTAGGGCTTCGAAAACTCGACTTAAGGCCCAAATATAT
ATGTTTGCTATAATTGTTGTAAGATATTGAAAATTTTTT
Found at i:25961 original size:13 final size:11
Alignment explanation
Indices: 25935--25983 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
25925 CATATATATG
25935 ATTTTTTATTT
1 ATTTTTTATTT
25946 ATTTTTTATCTCT
1 ATTTTTTAT-T-T
*
25959 A-TTATTATTT
1 ATTTTTTATTT
*
25969 ATTGTTTATTT
1 ATTTTTTATTT
25980 ATTT
1 ATTT
25984 AAGTAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 2 0.06
11 20 0.65
12 7 0.23
13 2 0.06
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (11 bp):
ATTTTTTATTT
Found at i:29955 original size:30 final size:29
Alignment explanation
Indices: 29921--30153 Score: 210
Period size: 30 Copynumber: 7.9 Consensus size: 29
29911 ATTCAAGGTC
*
29921 AAAATGTAATTTTGGAAAAGTTTAGGTGTA
1 AAAATGTAATTTTGGAAAAGTTTAGG-GTT
29951 AAAATGTAATTTTAGG-AAAGTTT-GGGTT
1 AAAATGTAATTTT-GGAAAAGTTTAGGGTT
* ** *
29979 AAAATGTGATTTTGGTGAAGTTCAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGTT
* * *
30008 AAAATGCT-ATTTTGTAGAAGTTTAAGGGTC
1 AAAATG-TAATTTTGGAAAAGTTT-AGGGTT
*
30038 AAAATGCAATTTTGGAAAAGTTTAGAGGTT
1 AAAATGTAATTTTGGAAAAGTTTAG-GGTT
*
30068 AAAATGTAA-TTTGGAAAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTT
30097 AAAATGTAATTTT--AAAGTAGTTTGAGGGTT
1 AAAATGTAATTTTGGAAA--AGTTT-AGGGTT
* * *
30127 AAAATATGATTTTTTG-AAAGTTTAGGG
1 AAAATGT-AATTTTGGAAAAGTTTAGGG
30154 ACCTTTTGGG
Statistics
Matches: 171, Mismatches: 18, Indels: 29
0.78 0.08 0.13
Matches are distributed among these distances:
27 2 0.01
28 22 0.13
29 56 0.33
30 82 0.48
31 7 0.04
32 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTT
Found at i:30059 original size:59 final size:58
Alignment explanation
Indices: 29917--30131 Score: 233
Period size: 59 Copynumber: 3.7 Consensus size: 58
29907 GAGAATTCAA
*
29917 GGTCAAAATGTAATTTTGGAAAAGTTTAGGTGTAAAAATGTAATTT-TAGGAAAGTTT--G
1 GGTCAAAATGTAATTTTGGAAAAGTTTAGG-GTTAAAATGTAATTTGTA-G-AAGTTTAAG
* * ** * *
29975 GGTTAAAATGTGATTTTGGTGAAGTTCAGGGTTAAAATGCTATTTTGTAGAAGTTTAAG
1 GGTCAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATG-TAATTTGTAGAAGTTTAAG
* * *
30034 GGTCAAAATGCAATTTTGGAAAAGTTTAGAGGTTAAAATGTAATTTGGAAAAGTTTAAG
1 GGTCAAAATGTAATTTTGGAAAAGTTTAG-GGTTAAAATGTAATTTGTAGAAGTTTAAG
30093 GGTCAAAATGTAATTTT--AAAGTAGTTTGAGGGTTAAAAT
1 GGTCAAAATGTAATTTTGGAAA--AGTTT-AGGGTTAAAAT
30132 ATGATTTTTT
Statistics
Matches: 132, Mismatches: 17, Indels: 15
0.80 0.10 0.09
Matches are distributed among these distances:
57 17 0.13
58 31 0.23
59 72 0.55
60 12 0.09
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (58 bp):
GGTCAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTGTAGAAGTTTAAG
Done.