Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008396.1 Kokia drynarioides strain JFW-HI SEQ_123064, 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: 18906
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:1657 original size:376 final size:376
Alignment explanation
Indices: 953--1897 Score: 1421
Period size: 377 Copynumber: 2.5 Consensus size: 376
943 CTGGTAACAT
* *
953 TTCATCTTTGTTTCTATAT-GGAGTAGCTTTTAATTTGATTTGTTTGCTTGGTGAA-TCTATTGC
1 TTCAACTTTGTTTCTATATAGG-GTAGCTTTTAATTTGATTTGTTTGCATGGTGAATTC-ATTGC
** * * *
1016 AGTACAATTAGACCTGTCAATTGAGTGGATGCTTTCAGTTGAACTCATTTCGGGTTTGTGTCATT
64 AGTACAATTAGACCTGTCAATTGAGTGGATTATTT---TTGGATTAATTTCGGGTTTG-GTCATT
** * * * *
1081 TTGGCTTTAACTTGTTATGGGTTCGAATTCAGGTTGTTTCGAGTTGAGCTCATCCAGGTTTGAAG
125 TTTACTTCAAC---TTATGGGTTTGAATTCAGGTTGTTTTGAGTTGAGCTCATTCAGGTTTGAAG
*
1146 CTTAGTTTTTTGGGTTAGGACATTACGAGTTGGGATCATTTCGAGTTATGGTATCTTGGGTTTGG
187 CTTAGTTTTTTGGGTTAGGACATTACGAGTTGGGATCATTTCGAGTTATGGTATCTTGGGTTCGG
1211 GTTGCTTTTGGCTTGAGCCAATTCGAGTGGAAGAAGCCGATGGTTAAGGATGGTACTTGGTAACT
252 GTTGCTTTTGGCTTGAGCCAATTCGAGTGGAAGAAGCCGATGGTTAAGGATGGTACTTGGTAACT
*
1276 GTGGATGATGTTGGTTGACATTGATCATC-ATCCATTAGGATGATGTTTGTTGAAGATTC
317 GTGGATGATGTTGGTTGACATTGACCATCAATCCATTAGGATGATGTTTGTTGAAGATTC
* * *
1335 TTCAACTTTGTTTCTCTATAGGGTAG-TTGTTAACTTGATTTGTTTGCATGGTAAATTCATTGCA
1 TTCAACTTTGTTTCTATATAGGGTAGCTT-TTAATTTGATTTGTTTGCATGGTGAATTCATTGCA
* *
1399 ATACAATTAGGCCTGTCAATTGAGTGGATTATTTTTGGATTAATTTCGGGTTTAGGTCATTTTTA
65 GTACAATTAGACCTGTCAATTGAGTGGATTATTTTTGGATTAATTTCGGGTTT-GGTCATTTTTA
*
1464 CTTCAACTTATGGGTTTGAATTCGGGTTGTTTTGAGTTGAGCTCATTCAGGTTTGAAGCTTAGTT
129 CTTCAACTTATGGGTTTGAATTCAGGTTGTTTTGAGTTGAGCTCATTCAGGTTTGAAGCTTAGTT
* * *
1529 TTTTGGGTTAGGACATTACGAGTTGGGGTCGTTTTGAGTTATGGTATCTTGGGTTCGGGTTGCTT
194 TTTTGGGTTAGGACATTACGAGTTGGGATCATTTCGAGTTATGGTATCTTGGGTTCGGGTTGCTT
* * * *
1594 TTGGTTTGAGCCAATTCGGGTTGAAGAAGCCGATGGTTGAGGATGGTACTTGGTAACTGTGGATG
259 TTGGCTTGAGCCAATTCGAGTGGAAGAAGCCGATGGTTAAGGATGGTACTTGGTAACTGTGGATG
1659 ATGTTGGTTGACATTGACCATCAATCCATTAGGATGATGTTTGTTGAAGATTC
324 ATGTTGGTTGACATTGACCATCAATCCATTAGGATGATGTTTGTTGAAGATTC
*
1712 TTCAACTTTGTTTCTTTATAGGGTAGCTTTTAATTTGATTTGTTTGCATGGTGAATTCATTGCAG
1 TTCAACTTTGTTTCTATATAGGGTAGCTTTTAATTTGATTTGTTTGCATGGTGAATTCATTGCAG
* * * *
1777 TGCAATTAGCCCTGTCAATTGAGGGGGTTATTTTTGGATTAATTTCGGGTTTGGGTCATTTTTAC
66 TACAATTAGACCTGTCAATTGAGTGGATTATTTTTGGATTAATTTCGGGTTT-GGTCATTTTTAC
* * * *
1842 TTCACCTTATGGGTTTGAATTCTGGTTGTTTTGAGTTGAGCACATTTAGGTTTGAA
130 TTCAACTTATGGGTTTGAATTCAGGTTGTTTTGAGTTGAGCTCATTCAGGTTTGAA
1898 TGGGGTTAGG
Statistics
Matches: 516, Mismatches: 41, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
376 197 0.38
377 200 0.39
378 2 0.00
379 30 0.06
380 1 0.00
381 2 0.00
382 80 0.16
383 4 0.01
ACGTcount: A:0.20, C:0.12, G:0.26, T:0.42
Consensus pattern (376 bp):
TTCAACTTTGTTTCTATATAGGGTAGCTTTTAATTTGATTTGTTTGCATGGTGAATTCATTGCAG
TACAATTAGACCTGTCAATTGAGTGGATTATTTTTGGATTAATTTCGGGTTTGGTCATTTTTACT
TCAACTTATGGGTTTGAATTCAGGTTGTTTTGAGTTGAGCTCATTCAGGTTTGAAGCTTAGTTTT
TTGGGTTAGGACATTACGAGTTGGGATCATTTCGAGTTATGGTATCTTGGGTTCGGGTTGCTTTT
GGCTTGAGCCAATTCGAGTGGAAGAAGCCGATGGTTAAGGATGGTACTTGGTAACTGTGGATGAT
GTTGGTTGACATTGACCATCAATCCATTAGGATGATGTTTGTTGAAGATTC
Found at i:5333 original size:26 final size:28
Alignment explanation
Indices: 5272--5333 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 28
5262 TTCTGAACTA
5272 TTTG-AAATTTTTTATTTAAATTATTAGG
1 TTTGTAAATTTTTTATTTAAA-TATTAGG
*
5300 -TTGTTAAATTTTTT-TTTAAA-GTTAGG
1 TTTG-TAAATTTTTTATTTAAATATTAGG
5326 TTTGTAAA
1 TTTGTAAA
5334 CTTCAAGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
26 9 0.30
27 6 0.20
28 6 0.20
29 9 0.30
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (28 bp):
TTTGTAAATTTTTTATTTAAATATTAGG
Found at i:9190 original size:25 final size:25
Alignment explanation
Indices: 9144--9191 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
9134 AGCTATAAAA
*
9144 TAATTATTCAATTATGGGTTTTTTT
1 TAATTATTCAATTATGGATTTTTTT
* * *
9169 TAATTATTTAATTTTGTATTTTT
1 TAATTATTCAATTATGGATTTTT
9192 GAACTTTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.65
Consensus pattern (25 bp):
TAATTATTCAATTATGGATTTTTTT
Found at i:18552 original size:30 final size:30
Alignment explanation
Indices: 18516--18575 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
18506 GCAAGTTATC
*
18516 TTCTTTGGGTGTGAGCTCAAGTAAAGCTGG
1 TTCTTTGGGTGTGAGCTCAACTAAAGCTGG
18546 TTCTTTGGGTGTGAGCTCAACTAAAGCTGG
1 TTCTTTGGGTGTGAGCTCAACTAAAGCTGG
18576 ATAATTGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.15, G:0.32, T:0.33
Consensus pattern (30 bp):
TTCTTTGGGTGTGAGCTCAACTAAAGCTGG
Done.