Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013927.1 Kokia drynarioides strain JFW-HI SEQ_128957, 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: 15866
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1378 original size:25 final size:23
Alignment explanation
Indices: 1337--1382 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
1327 TCAATTAGGG
1337 AATTATTGTTTAGATTTAATTCA
1 AATTATTGTTTAGATTTAATTCA
*
1360 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
1383 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCA
Found at i:1801 original size:15 final size:15
Alignment explanation
Indices: 1764--1802 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1754 TTATGTGTGC
*
1764 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
1779 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
1793 TTAATTCTTG
1 TTAATTCTTG
1803 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:4139 original size:22 final size:22
Alignment explanation
Indices: 4109--4171 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
4099 AAAAAAATAT
*
4109 TCAACTATATTGGCGTAATCAA
1 TCAATTATATTGGCGTAATCAA
*
4131 TCAATTATATTGGCGCAATCAA
1 TCAATTATATTGGCGTAATCAA
*
4153 TCAATTATATTGGCATAAT
1 TCAATTATATTGGCGTAAT
4172 ACATCCATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (22 bp):
TCAATTATATTGGCGTAATCAA
Found at i:7693 original size:3 final size:3
Alignment explanation
Indices: 7670--7736 Score: 93
Period size: 3 Copynumber: 23.0 Consensus size: 3
7660 ACACGGTTCT
* *
7670 TAA TAA -AA TAA -AA TGA TAA TAA TAA TAA TAA GAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
7716 TAA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
7737 ATAAATAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 4 0.07
3 52 0.93
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:9230 original size:28 final size:29
Alignment explanation
Indices: 9198--9262 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 29
9188 TTTTTTTAAG
9198 AATAGTGGAAAAATTGTAAAATCT-CAAA
1 AATAGTGGAAAAATTGTAAAATCTACAAA
* * *
9226 AATAGTAGCAAAATTGTAAAATCTAGAAA
1 AATAGTGGAAAAATTGTAAAATCTACAAA
9255 AATAGTGG
1 AATAGTGG
9263 CAGAGTTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.25
Consensus pattern (29 bp):
AATAGTGGAAAAATTGTAAAATCTACAAA
Found at i:9274 original size:28 final size:28
Alignment explanation
Indices: 9198--9313 Score: 90
Period size: 29 Copynumber: 4.1 Consensus size: 28
9188 TTTTTTTAAG
* * *
9198 AATAGTGGAAAAATTGTAAAATCTCAAA
1 AATAGTAGCAAAATTGTAAAATCTGAAA
9226 AATAGTAGCAAAATTGTAAAATCTAGAAA
1 AATAGTAGCAAAATTGTAAAATCT-GAAA
* * * *
9255 AATAGTGGCAGAGTTG-AAAATTTTGAAAA
1 AATAGTAGCAAAATTGTAAAA-TCTG-AAA
* * * * *
9284 AACAATGGCAAAACTGTAAAATCTGGAA
1 AATAGTAGCAAAATTGTAAAATCTGAAA
9312 AA
1 AA
9314 CAATGGCAGA
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
28 31 0.44
29 35 0.50
30 4 0.06
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (28 bp):
AATAGTAGCAAAATTGTAAAATCTGAAA
Found at i:9319 original size:28 final size:28
Alignment explanation
Indices: 9282--9347 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
9272 AAATTTTGAA
*
9282 AAAACAATGGCAAAACTGTAAAATCTGG
1 AAAACAATGGCAAAACTATAAAATCTGG
* * *
9310 AAAACAATGGCAGAACTATAAAATTTGT
1 AAAACAATGGCAAAACTATAAAATCTGG
*
9338 AAAATAATGG
1 AAAACAATGG
9348 TACATGGACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.52, C:0.11, G:0.17, T:0.21
Consensus pattern (28 bp):
AAAACAATGGCAAAACTATAAAATCTGG
Found at i:10226 original size:28 final size:28
Alignment explanation
Indices: 10193--10254 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
10183 TTTTTTTAAG
10193 AATAGTGGCAAAACTGTAAAATCTAAAA
1 AATAGTGGCAAAACTGTAAAATCTAAAA
* * * *
10221 AATAGTGGCAAAATTGTAAATTTTGAAA
1 AATAGTGGCAAAACTGTAAAATCTAAAA
10249 AATAGT
1 AATAGT
10255 TTGAAAAACC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.27
Consensus pattern (28 bp):
AATAGTGGCAAAACTGTAAAATCTAAAA
Found at i:10320 original size:57 final size:58
Alignment explanation
Indices: 10259--10405 Score: 140
Period size: 57 Copynumber: 2.6 Consensus size: 58
10249 AATAGTTTGA
* * * *
10259 AAAACCAGTGGCAAAACTTTAAAAGCTGGAAAACAATGATAGAATTGT-AAAATCTGG
1 AAAACCAGTGGCAAAACTCTAAAATCTGGAAAACAATGACAGAACTGTAAAAATCTGG
** * * * *
10316 AAAACTTGTGGC--AA-TGTAAAATTTTGGAAAACAATGGCAGAACTGTAAAAAATTTGG
1 AAAACCAGTGGCAAAACTCTAAAA-TCTGGAAAACAATGACAGAACTGT-AAAAATCTGG
* *
10373 AAAACCAGTGACAAAACTCTAAAATCTGAAAAA
1 AAAACCAGTGGCAAAACTCTAAAATCTGGAAAA
10406 AAAAATAGTA
Statistics
Matches: 69, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
54 6 0.09
55 21 0.30
57 27 0.39
59 9 0.13
60 6 0.09
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (58 bp):
AAAACCAGTGGCAAAACTCTAAAATCTGGAAAACAATGACAGAACTGTAAAAATCTGG
Found at i:10396 original size:31 final size:30
Alignment explanation
Indices: 10333--10396 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
10323 GTGGCAATGT
* * * *
10333 AAAATTTTGGAAAACAATGGCAGAACTGTA
1 AAAAATTTGGAAAACAATGACAAAACTCTA
*
10363 AAAAATTTGGAAAACCAGTGACAAAACTCTA
1 AAAAATTTGGAAAA-CAATGACAAAACTCTA
10394 AAA
1 AAA
10397 TCTGAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.52, C:0.12, G:0.16, T:0.20
Consensus pattern (30 bp):
AAAAATTTGGAAAACAATGACAAAACTCTA
Found at i:10457 original size:29 final size:29
Alignment explanation
Indices: 10425--10497 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
10415 ACCAGAATTG
*
10425 TAAAA-TATAGAAAACTAGTGACA-AAGCTA
1 TAAAATTAT-GAAAAATAGTGACATAA-CTA
*
10454 TAAAATTATGAAAAATAGTGGCATAACTA
1 TAAAATTATGAAAAATAGTGACATAACTA
*
10483 TAAAATT-TGTAAAAT
1 TAAAATTATGAAAAAT
10498 GGTGGTACAC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 7 0.18
29 27 0.69
30 5 0.13
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.27
Consensus pattern (29 bp):
TAAAATTATGAAAAATAGTGACATAACTA
Found at i:13616 original size:48 final size:48
Alignment explanation
Indices: 13422--13601 Score: 270
Period size: 48 Copynumber: 3.8 Consensus size: 48
13412 TAATTATGCT
* *
13422 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTCGTTTAATAATCTGCA
1 TCATTAAATGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCA
* *
13470 TCATTAAATGTTTTGTTTATTAAATGCATCTTTGTTTAATAATCTACA
1 TCATTAAATGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCA
* * * * *
13518 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTATTTAGTAAACTTCA
1 TCATTAAATGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCA
*
13566 TTATTAAATGTTTTGTTTGTTAAATGCATCTTTGTT
1 TCATTAAATGTTTTGTTTGTTAAATGCATCTTTGTT
13602 CAATGCCTTG
Statistics
Matches: 119, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 119 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (48 bp):
TCATTAAATGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCA
Found at i:14138 original size:81 final size:79
Alignment explanation
Indices: 14050--14205 Score: 240
Period size: 81 Copynumber: 1.9 Consensus size: 79
14040 AGAAATGGCG
** * * *
14050 TGTCTTTTCAGTTACATTAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCTACAAGAGTTA
1 TGTCTTTTCAACTACATCAAATCCTAATGAAGAGACATAACTCATTAGCTTCCCTACAAGAGTT-
14115 AAAAATGAAATTTTCA
65 -AAAATGAAATTTTCA
*
14131 TGTCTTTTCAACTACATCAAATCCTAATGAAGAGACATAACTCATTGGCTTCCCTACAAGAGTTA
1 TGTCTTTTCAACTACATCAAATCCTAATGAAGAGACATAACTCATTAGCTTCCCTACAAGAGTTA
14196 AAATGAAATT
66 AAATGAAATT
14206 AGTGTTTTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
79 11 0.16
81 58 0.84
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (79 bp):
TGTCTTTTCAACTACATCAAATCCTAATGAAGAGACATAACTCATTAGCTTCCCTACAAGAGTTA
AAATGAAATTTTCA
Done.