Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014024.1 Kokia drynarioides strain JFW-HI SEQ_129055, 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: 22887
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Found at i:2358 original size:24 final size:24
Alignment explanation
Indices: 2276--2350 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
2266 AGAAATAATT
* *
2276 TTTCAGTTAAACTCTGTTTATTTA
1 TTTCAATTAAACTCTGTTTATTTG
2300 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
2324 TTTCAATTAAACTCTATTTAGTTG
1 TTTCAATTAAACTCTGTTTATTTG
2348 TTT
1 TTT
2351 GAGTTAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:4313 original size:24 final size:24
Alignment explanation
Indices: 4285--4359 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
4275 AGAAATAATC
*
4285 TTTCAGTTAAACTCTGTTTACTTG
1 TTTCAATTAAACTCTGTTTACTTG
*
4309 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTACTTG
* *
4333 TTTCAATTAAACTGTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTACTTG
4357 TTT
1 TTT
4360 GAGTGAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTACTTG
Found at i:6174 original size:383 final size:383
Alignment explanation
Indices: 5556--6320 Score: 1246
Period size: 383 Copynumber: 2.0 Consensus size: 383
5546 AAAAAACATA
* *
5556 GAAATGGGATGCTATTGAAACTAAGATGCTTGAGAAAGGAGAGCTTGAGCTAAGGTTGCAACTTG
1 GAAATAGGATGCTATTGAAACGAAGATGCTTGAGAAAGGAGAGCTTGAGCTAAGGTTGCAACTTG
* *
5621 GGGATAATCAAGTTAAAGAAGAAGACTTCAATGACATGCCATTTTAGGGTATGCGACCAATTATT
66 GGGATAATCAAGTTAAAGAAGAAGACTTCAATGACATACCATTTTAGGGTATGCAACCAATTATT
** *
5686 AAAATTTACTGAAGATTAGAGGTAGCAACTCTTAAACCGGTGAACTCCGAAGAAGCTGAAGCAAC
131 AAAATTTACCAAAGAGTAGAGGTAGCAACTCTTAAACCGGTGAACTCCGAAGAAGCTGAAGCAAC
* *
5751 AAAAGGCTTGAAAGAAGCTATGCAAACTGAGTTGAATATGATTTGCAAGAACCAGATGTGGGAAC
196 AAAAGGCTTGAAAGAAGCTATGCAAACTAAGTTAAATATGATTTGCAAGAACCAGATGTGGGAAC
* * *
5816 TTGTTGATAGGCCATCACACAAAAAGGTTATTAGCATCAAATGGGTGTTTAGAACCAAACTTAA-
261 TTGTTGATAGGCCATCACACAAAAAGGGTATTAGCATCAAATGGGTGTTCAGAACCAAACTCAAT
* * * *
5880 CGTCGATGGTTCACTCAATAGACTGAAGGCAAGACTGGTTGTAAAGAGTTTTAGTCATG
326 C-TCGATGGTTCACTCAACAAACCGAAGGCAAGACTGGTTGTAAAGAGTTTTAATCATG
* *
5939 GAAATAGGATGCTATTGAAACGAAGATGCTTGAGGAAGGAGAGCTTGAGCTAGGGTTGCAACTTG
1 GAAATAGGATGCTATTGAAACGAAGATGCTTGAGAAAGGAGAGCTTGAGCTAAGGTTGCAACTTG
* * *
6004 GGGATAATCAAGTTGAAGAAGAAGACTTCAATGATATACCA-TTTAGCGGTATGCAACCAATTGT
66 GGGATAATCAAGTTAAAGAAGAAGACTTCAATGACATACCATTTTAG-GGTATGCAACCAATTAT
* * *
6068 TGAAATTTACCAAAGAGTAGAGGTAGCAACTCTTAAACCTGTGAACTCTGAAGAAGCTGAAGCAA
130 TAAAATTTACCAAAGAGTAGAGGTAGCAACTCTTAAACCGGTGAACTCCGAAGAAGCTGAAGCAA
*
6133 CAAAAGGCTTGAAAGAAGCTATGCAAGCTAAGTTAAATATGATTTGCAAGAACCAGATGTGGGAA
195 CAAAAGGCTTGAAAGAAGCTATGCAAACTAAGTTAAATATGATTTGCAAGAACCAGATGTGGGAA
* *
6198 CTTGTTGATAGGCCATCACATAAAAGGGGTATTAGCATCAAATGGGTGTTCAGAACCAAACTCAA
260 CTTGTTGATAGGCCATCACACAAAAAGGGTATTAGCATCAAATGGGTGTTCAGAACCAAACTCAA
*
6263 TCTCGATGGTTCACTCAACAAACCGAAGGTAAGACTGGTTGTAAAGAGTTTTAATCAT
325 TCTCGATGGTTCACTCAACAAACCGAAGGCAAGACTGGTTGTAAAGAGTTTTAATCAT
6321 CAATATGGGA
Statistics
Matches: 352, Mismatches: 28, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
382 5 0.01
383 346 0.98
384 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (383 bp):
GAAATAGGATGCTATTGAAACGAAGATGCTTGAGAAAGGAGAGCTTGAGCTAAGGTTGCAACTTG
GGGATAATCAAGTTAAAGAAGAAGACTTCAATGACATACCATTTTAGGGTATGCAACCAATTATT
AAAATTTACCAAAGAGTAGAGGTAGCAACTCTTAAACCGGTGAACTCCGAAGAAGCTGAAGCAAC
AAAAGGCTTGAAAGAAGCTATGCAAACTAAGTTAAATATGATTTGCAAGAACCAGATGTGGGAAC
TTGTTGATAGGCCATCACACAAAAAGGGTATTAGCATCAAATGGGTGTTCAGAACCAAACTCAAT
CTCGATGGTTCACTCAACAAACCGAAGGCAAGACTGGTTGTAAAGAGTTTTAATCATG
Found at i:14557 original size:21 final size:21
Alignment explanation
Indices: 14533--14581 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
14523 TCTTTCAAAA
14533 TTTAAAATTTAGTTTTTATAT
1 TTTAAAATTTAGTTTTTATAT
** * *
14554 TTTAATTTTTTGTTTTTTTAT
1 TTTAAAATTTAGTTTTTATAT
*
14575 TTAAAAA
1 TTTAAAA
14582 ATATCTAGTC
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTAAAATTTAGTTTTTATAT
Found at i:14700 original size:19 final size:17
Alignment explanation
Indices: 14676--14714 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
14666 AATCTTACCC
*
14676 TTTAAAAATACATCATTTT
1 TTTAAAAA-AAAT-ATTTT
14695 TTTAAAAAAAATATTTT
1 TTTAAAAAAAATATTTT
14712 TTT
1 TTT
14715 CATATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 3 0.16
19 8 0.42
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAAAAAAAATATTTT
Found at i:18651 original size:29 final size:29
Alignment explanation
Indices: 18609--18669 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
18599 TACGGGCTAG
18609 GCACTTAGTACCGAAGCGTGTTATCGATT
1 GCACTTAGTACCGAAGCGTGTTATCGATT
*
18638 GCACTTAGTACCGAGGCGTGTTATCGATT
1 GCACTTAGTACCGAAGCGTGTTATCGATT
18667 GCA
1 GCA
18670 TAACTCTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (29 bp):
GCACTTAGTACCGAAGCGTGTTATCGATT
Found at i:22519 original size:3 final size:3
Alignment explanation
Indices: 22511--22550 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
22501 AAATATAAAA
22511 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA- AAT AGAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA
22551 AAGAATAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 27 0.79
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:22557 original size:17 final size:17
Alignment explanation
Indices: 22505--22550 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
22495 TACTAAAAAT
22505 ATAAAA-AATAATAATA
1 ATAAAATAATAATAATA
22521 ATAATAATAATAATAA-A
1 ATAA-AATAATAATAATA
22538 ATAAAATAGATAA
1 ATAAAATA-ATAA
22551 AAGAATAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 8 0.30
17 11 0.41
18 8 0.30
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAAAATAATAATAATA
Done.