Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013269.1 Kokia drynarioides strain JFW-HI SEQ_128290, 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: 39501
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:3197 original size:11 final size:12
Alignment explanation
Indices: 3172--3199 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3162 CTTGGTCTTG
3172 AAAAGATAATAA
1 AAAAGATAATAA
3184 AAAAGATAATAA
1 AAAAGATAATAA
3196 AAAA
1 AAAA
3200 TCCATGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAGATAATAA
Found at i:3593 original size:231 final size:234
Alignment explanation
Indices: 3184--3612 Score: 679
Period size: 231 Copynumber: 1.8 Consensus size: 234
3174 AAGATAATAA
*
3184 AAAAGATAATAAAAAATCCATGAATGTATGATATACATATACATATACATAAAGTAAACCAAGGC
1 AAAAGATAAGAAAAAATCCATGAATGTATGATATACATATACATATACATAAAGT--A-CAAGGC
* *
3249 CAACACTGCATGCATCTCATGCATATCTTCTCAAATAAAGCAGATACACATTATTCATCTCCTTT
63 CAACACTGCATGCATCTCATGCATATCTTCTCAAATAAAACAGATACACATTATTCATCTCCTAT
* * *
3314 TTTTTTAACACTGAATGAAACAAAACTAGATAAAAGGCCAAGCTAACCTTCACCATGATGTCCAG
128 TCTTTTAACACTGAATGAAACAAAACCAGATAAAAGGCCAAGCTAACCTTCACCATGATATCCAG
3379 TGGTGTTGACTGGTGGTGGCTCTATTGATCCACTTGGTCCTG
193 TGGTGTTGACTGGTGGTGGCTCTATTGATCCACTTGGTCCTG
* * * *
3421 AAAAGATAAGAAAGAATCCATGAATGTATGATATGCGTATACATGA-A-ATAAA-T-GAAGGCCA
1 AAAAGATAAGAAAAAATCCATGAATGTATGATATACATATACAT-ATACATAAAGTACAAGGCCA
3482 ACACTGCATGCATCTCATGCATATCTTCTCAAATAAAACAGATACACATTATTCATCTCCTATTC
65 ACACTGCATGCATCTCATGCATATCTTCTCAAATAAAACAGATACACATTATTCATCTCCTATTC
*
3547 TTTTAACACTGAATG-AACTAAAACCAGATAAAAGGCCAAGCTAACCTTCACCATGATATCTAGT
130 TTTTAACACTGAATGAAAC-AAAACCAGATAAAAGGCCAAGCTAACCTTCACCATGATATCCAGT
3611 GG
194 GG
3613 CGGTTACCGG
Statistics
Matches: 179, Mismatches: 11, Indels: 10
0.89 0.05 0.05
Matches are distributed among these distances:
230 3 0.02
231 128 0.72
235 1 0.01
236 5 0.03
237 41 0.23
238 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (234 bp):
AAAAGATAAGAAAAAATCCATGAATGTATGATATACATATACATATACATAAAGTACAAGGCCAA
CACTGCATGCATCTCATGCATATCTTCTCAAATAAAACAGATACACATTATTCATCTCCTATTCT
TTTAACACTGAATGAAACAAAACCAGATAAAAGGCCAAGCTAACCTTCACCATGATATCCAGTGG
TGTTGACTGGTGGTGGCTCTATTGATCCACTTGGTCCTG
Found at i:15502 original size:16 final size:16
Alignment explanation
Indices: 15481--15511 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15471 AGTGTCAATT
*
15481 TTAAAAATTAAATAAC
1 TTAAAAATAAAATAAC
15497 TTAAAAATAAAATAA
1 TTAAAAATAAAATAA
15512 AATAAGATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
TTAAAAATAAAATAAC
Found at i:17353 original size:59 final size:57
Alignment explanation
Indices: 17287--17402 Score: 135
Period size: 58 Copynumber: 2.0 Consensus size: 57
17277 TATCTTTAAG
* *
17287 ATAATTGAGTGA-AAAAAAAAGATAAATTGAATAATTAAATAATTATTTTGTAATTTTTC
1 ATAATTGAATGAGAAAAAAAA-ATAAACT-AATAATT-AATAATTATTTTGTAATTTTTC
* ** *
17346 ATAATTGAATGATGAAAAATAAATTCACTAATAATTAATGATTATTTTGTAATTTTT
1 ATAATTGAATGA-GAAAAAAAAATAAACTAATAATTAATAATTATTTTGTAATTTTT
17403 TATTTGGTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
58 20 0.41
59 18 0.37
60 4 0.08
61 7 0.14
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (57 bp):
ATAATTGAATGAGAAAAAAAAATAAACTAATAATTAATAATTATTTTGTAATTTTTC
Found at i:17422 original size:58 final size:56
Alignment explanation
Indices: 17316--17432 Score: 132
Period size: 58 Copynumber: 2.0 Consensus size: 56
17306 AGATAAATTG
17316 AATAATTAAATAATTATTTTGTAATTTTTCATAATTGAATGATGAAAAATAAATTCACT
1 AATAATTAAATAATTATTTTGTAATTTTT-ATAATTGAATGATGAAAAA-AAATT-ACT
* * *
17375 AATAATT-AATGATTATTTTGTAATTTTT-TATTTG-GTGATAAGAAAAAAAAATTACT
1 AATAATTAAATAATTATTTTGTAATTTTTATAATTGAATGAT--G-AAAAAAAATTACT
17431 AA
1 AA
17433 CTGGGTGACT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
55 4 0.08
56 10 0.19
57 6 0.12
58 25 0.48
59 7 0.13
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (56 bp):
AATAATTAAATAATTATTTTGTAATTTTTATAATTGAATGATGAAAAAAAATTACT
Found at i:18871 original size:31 final size:30
Alignment explanation
Indices: 18807--18864 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
18797 GAAAACTGTA
* *
18807 AAGTTTAGCCCCAATTTGGGAATAATTACC
1 AAGTTTAGCCCCAATGTGAGAATAATTACC
*
18837 AAGTTTTGACCCCAATGTGAGAATAATT
1 AAGTTTAG-CCCCAATGTGAGAATAATT
18865 GTCAAGTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (30 bp):
AAGTTTAGCCCCAATGTGAGAATAATTACC
Found at i:21143 original size:2 final size:2
Alignment explanation
Indices: 21138--21188 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
21128 GATAAATAAG
21138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21180 AT AT AT AT A
1 AT AT AT AT A
21189 ATTCTTTTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21744 original size:6 final size:6
Alignment explanation
Indices: 21710--21737 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
21700 TAACAATTCC
21710 TTTTGA TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTT
21738 TAATTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (6 bp):
TTTTGA
Found at i:22595 original size:26 final size:28
Alignment explanation
Indices: 22548--22610 Score: 85
Period size: 26 Copynumber: 2.3 Consensus size: 28
22538 TTTATTTAAT
22548 GAAAGTTATTGTTTAATTTTGGTACATAG
1 GAAAGTT-TTGTTTAATTTTGGTACATAG
* *
22577 GAAAGTTTT-TTT-ATTTTGGTACTTTG
1 GAAAGTTTTGTTTAATTTTGGTACATAG
22603 GAAAGTTT
1 GAAAGTTT
22611 ATTGTCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 20 0.62
27 3 0.09
28 2 0.06
29 7 0.22
ACGTcount: A:0.27, C:0.03, G:0.21, T:0.49
Consensus pattern (28 bp):
GAAAGTTTTGTTTAATTTTGGTACATAG
Found at i:31299 original size:28 final size:29
Alignment explanation
Indices: 31257--31315 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
31247 TAAAACAATT
* **
31257 TTTTTGGGCCTTTAAAAGTTAGTAAAAAA
1 TTTTTGGGCATTTAAAAGTTAAAAAAAAA
31286 TTTTT-GGCATTTAAAAGTTAAAAAAAAA
1 TTTTTGGGCATTTAAAAGTTAAAAAAAAA
31314 TT
1 TT
31316 AAAAAAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (29 bp):
TTTTTGGGCATTTAAAAGTTAAAAAAAAA
Found at i:35046 original size:29 final size:31
Alignment explanation
Indices: 35004--35065 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
34994 AACCCCCAAA
* *
35004 CCTTCTTACTTTTCTCCC-AAAACTTTTACT
1 CCTTCCTACTTTTCCCCCAAAAACTTTTACT
35034 CCTTCCTAC-TTTCCCCCAAAAACTTTTACT
1 CCTTCCTACTTTTCCCCCAAAAACTTTTACT
35064 CC
1 CC
35066 CCTCCCGTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.40
Consensus pattern (31 bp):
CCTTCCTACTTTTCCCCCAAAAACTTTTACT
Found at i:35233 original size:39 final size:40
Alignment explanation
Indices: 35190--35289 Score: 175
Period size: 41 Copynumber: 2.5 Consensus size: 40
35180 TTTTATTTTT
35190 CCTCAAAACTTTTACTCC-CCATTTACTTTCTCCAAAAAC
1 CCTCAAAACTTTTACTCCTCCATTTACTTTCTCCAAAAAC
35229 CCTCAAAACTTTTACTCTCTCCATTTACTTTCTCCAAAAAC
1 CCTCAAAACTTTTACTC-CTCCATTTACTTTCTCCAAAAAC
*
35270 TCTCAAAACTTTTACTCCTC
1 CCTCAAAACTTTTACTCCTC
35290 ACTTTCTTCT
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
39 17 0.29
40 4 0.07
41 37 0.64
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.36
Consensus pattern (40 bp):
CCTCAAAACTTTTACTCCTCCATTTACTTTCTCCAAAAAC
Done.