Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014849.1 Kokia drynarioides strain JFW-HI SEQ_129892, 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: 51403
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:72 original size:24 final size:24
Alignment explanation
Indices: 24--82 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
14 TAATATAATT
*
24 ATTATTAAAATATAAATTAGTAAAA
1 ATTA-TAATATATAAATTAGTAAAA
49 ATTATAATATATAATATTAG-AAAA
1 ATTATAATATATAA-ATTAGTAAAA
*
73 ATAAT-ATATA
1 ATTATAATATA
83 ACTTTATTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 5 0.16
24 17 0.55
25 9 0.29
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (24 bp):
ATTATAATATATAAATTAGTAAAA
Found at i:2285 original size:20 final size:22
Alignment explanation
Indices: 2256--2312 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 22
2246 AAAGAGAATC
* *
2256 AACAAAAAGAAAAAGAAGAAAG
1 AACAGAAAGAAAAAGAAGAAAA
2278 AACGAAGAAAGAAAAAGAAGAAAA
1 AAC--AGAAAGAAAAAGAAGAAAA
2302 AAC-G-AAGAAAA
1 AACAGAAAGAAAA
2313 TGATGTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 7 0.23
21 1 0.03
22 3 0.10
24 20 0.65
ACGTcount: A:0.75, C:0.05, G:0.19, T:0.00
Consensus pattern (22 bp):
AACAGAAAGAAAAAGAAGAAAA
Found at i:2288 original size:24 final size:24
Alignment explanation
Indices: 2261--2311 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
2251 GAATCAACAA
*
2261 AAAGAAAAAGAAGAAAGAACGAAG
1 AAAGAAAAAGAAGAAAAAACGAAG
2285 AAAGAAAAAGAAGAAAAAACGAAG
1 AAAGAAAAAGAAGAAAAAACGAAG
2309 AAA
1 AAA
2312 ATGATGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.75, C:0.04, G:0.22, T:0.00
Consensus pattern (24 bp):
AAAGAAAAAGAAGAAAAAACGAAG
Found at i:2312 original size:11 final size:11
Alignment explanation
Indices: 2265--2312 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
2255 CAACAAAAAG
2265 AAAAA-GAAGA
1 AAAAACGAAGA
*
2275 AAGAACGAAGAA
1 AAAAACGAAG-A
*
2287 AGAAAAAGAAGA
1 A-AAAACGAAGA
2299 AAAAACGAAGA
1 AAAAACGAAGA
2310 AAA
1 AAA
2313 TGATGTTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 4 0.13
11 16 0.52
12 4 0.13
13 7 0.23
ACGTcount: A:0.75, C:0.04, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAACGAAGA
Found at i:6524 original size:2 final size:2
Alignment explanation
Indices: 6517--6541 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6507 TGTAGTTTAA
6517 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6542 ATCCTATCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10404 original size:2 final size:2
Alignment explanation
Indices: 10399--10424 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10389 TCTCTCTCTC
10399 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
10425 AAAGAGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18487 original size:2 final size:2
Alignment explanation
Indices: 18480--18516 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
18470 CACTAGAACT
18480 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A- AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
18517 TCTTCTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:19406 original size:16 final size:15
Alignment explanation
Indices: 19385--19418 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
19375 TATAAAGAAG
*
19385 AAAAATTCATAAAATT
1 AAAAATACAT-AAATT
19401 AAAAATACATAAATT
1 AAAAATACATAAATT
19416 AAA
1 AAA
19419 TTAAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATACATAAATT
Found at i:21567 original size:38 final size:38
Alignment explanation
Indices: 21516--21599 Score: 152
Period size: 38 Copynumber: 2.2 Consensus size: 38
21506 TCGGCCTAGT
*
21516 CGAAGTAAAGTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAAAGTGGTACCCAATACCTCATCGAATCTATC
21554 CGAAGTAAAGTGGTACCCAATACCTCATCGAATCTATC
1 CGAAGTAAAGTGGTACCCAATACCTCATCGAATCTATC
21592 CGAA-TAAA
1 CGAAGTAAA
21600 ATAACGACAC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 4 0.09
38 41 0.91
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (38 bp):
CGAAGTAAAGTGGTACCCAATACCTCATCGAATCTATC
Found at i:22385 original size:14 final size:15
Alignment explanation
Indices: 22366--22394 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
22356 CTTTTTCTTT
22366 TTCCTTCCC-TTTTC
1 TTCCTTCCCATTTTC
22380 TTCCTTCCCATTTTC
1 TTCCTTCCCATTTTC
22395 GTTTGAGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.55
Consensus pattern (15 bp):
TTCCTTCCCATTTTC
Found at i:22537 original size:30 final size:29
Alignment explanation
Indices: 22485--22558 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 29
22475 GTAATAACAT
*
22485 TAATAAATTATAATTATCTA-TTTACTTAAA
1 TAATAAATAATAATTATCTATTTTAC--AAA
*
22515 TAATAAATAATTAA-TATTTATTTTACAAA
1 TAATAAATAA-TAATTATCTATTTTACAAA
22544 TATATAAAT-ATAATT
1 TA-ATAAATAATAATT
22559 TTTATACATA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 3 0.08
29 7 0.18
30 20 0.53
31 8 0.21
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (29 bp):
TAATAAATAATAATTATCTATTTTACAAA
Found at i:22605 original size:2 final size:2
Alignment explanation
Indices: 22598--22630 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22588 TTTGGTTTTA
22598 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22631 ATAATATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22666 original size:37 final size:38
Alignment explanation
Indices: 22615--22686 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
22605 TATATATATA
22615 TATATATATATATATAATAATATTAATTAAATAATAATT
1 TATATATATATATATAATAATATTAATT-AATAATAATT
**
22654 TATAT-TAT-TATATTCTAATATTAATTAATAATA
1 TATATATATATATATAATAATATTAATTAATAATA
22687 GCTTAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 7 0.23
37 16 0.52
38 3 0.10
39 5 0.16
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (38 bp):
TATATATATATATATAATAATATTAATTAATAATAATT
Found at i:35221 original size:3 final size:3
Alignment explanation
Indices: 35175--35204 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
35165 TAGAACTACT
35175 TTA TTCA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TT
35205 TGGCCGTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:37098 original size:21 final size:21
Alignment explanation
Indices: 37074--37113 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
37064 TTTATGTGTC
37074 AATACTATATA-TTATAAAAAT
1 AATA-TATATATTTATAAAAAT
*
37095 AATATATTTATTTATAAAA
1 AATATATATATTTATAAAA
37114 GAATATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
AATATATATATTTATAAAAAT
Found at i:37123 original size:23 final size:22
Alignment explanation
Indices: 37085--37133 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
37075 ATACTATATA
37085 TTATAAAAATAATAT-ATTTAT
1 TTATAAAAATAATATAATTTAT
* *
37106 TTATAAAAGAATATTATAATTTTT
1 TTAT-AAA-AATAATATAATTTAT
37130 TTAT
1 TTAT
37134 CATAATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 4 0.17
22 3 0.13
23 7 0.30
24 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTATAAAAATAATATAATTTAT
Found at i:49085 original size:20 final size:20
Alignment explanation
Indices: 49044--49092 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
49034 ATGAATCCTA
* *
49044 TTTTATTAATTTCTTATAAT
1 TTTTAATAATTTCTTAAAAT
49064 TTTTAATAATTT-TTAAATAT
1 TTTTAATAATTTCTTAAA-AT
*
49084 TTTTTATAA
1 TTTTAATAA
49093 ATTATTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAATAATTTCTTAAAAT
Found at i:49321 original size:12 final size:13
Alignment explanation
Indices: 49293--49321 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
49283 TATTTATCTT
49293 ATTTATTTTTTAG
1 ATTTATTTTTTAG
49306 ATTTATTTTTTA-
1 ATTTATTTTTTAG
49318 ATTT
1 ATTT
49322 TCAAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
ATTTATTTTTTAG
Found at i:49464 original size:80 final size:80
Alignment explanation
Indices: 49366--49524 Score: 309
Period size: 80 Copynumber: 2.0 Consensus size: 80
49356 TTAGCATGAA
*
49366 CTACATGTGGCACGCCACGTGTTGTTATTTAGTTGCTCCGTCAATCACAGAAAGACCAATTTGTT
1 CTACATGTGGCACACCACGTGTTGTTATTTAGTTGCTCCGTCAATCACAGAAAGACCAATTTGTT
49431 CTTTGGTCTAACTTG
66 CTTTGGTCTAACTTG
49446 CTACATGTGGCACACCACGTGTTGTTATTTAGTTGCTCCGTCAATCACAGAAAGACCAATTTGTT
1 CTACATGTGGCACACCACGTGTTGTTATTTAGTTGCTCCGTCAATCACAGAAAGACCAATTTGTT
49511 CTTTGGTCTAACTT
66 CTTTGGTCTAACTT
49525 ACGGTGATTA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (80 bp):
CTACATGTGGCACACCACGTGTTGTTATTTAGTTGCTCCGTCAATCACAGAAAGACCAATTTGTT
CTTTGGTCTAACTTG
Done.