Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011388.1 Kokia drynarioides strain JFW-HI SEQ_126370, 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: 405849
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 179 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:338227 original size:17 final size:18
Alignment explanation
Indices: 338207--338245 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
338197 CTACTTACTG
338207 TTTAGATTAATT-AGAGT
1 TTTAGATTAATTAAGAGT
* *
338224 TTTAGTTTACTTAAGAGT
1 TTTAGATTAATTAAGAGT
338242 TTTA
1 TTTA
338246 TTTAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (18 bp):
TTTAGATTAATTAAGAGT
Found at i:338434 original size:16 final size:16
Alignment explanation
Indices: 338413--338452 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
338403 CATTTTCAAA
* *
338413 TTTTTCTTGCCAAGTT
1 TTTTTCTTCCCAAATT
338429 TTTTTCTTCCCAAATT
1 TTTTTCTTCCCAAATT
338445 TTTTTCTT
1 TTTTTCTT
338453 TCTTTATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.12, C:0.20, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTTCTTCCCAAATT
Found at i:352940 original size:24 final size:24
Alignment explanation
Indices: 352907--352961 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
352897 GTTAAGAGTA
352907 AAAATTGTCAGTGCAAACGTAATAC
1 AAAA-TGTCAGTGCAAACGTAATAC
** *
352932 AAAATGTCAGTGCAATTGTAATAT
1 AAAATGTCAGTGCAAACGTAATAC
352956 AAAATG
1 AAAATG
352962 AAAGAATTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (24 bp):
AAAATGTCAGTGCAAACGTAATAC
Found at i:354943 original size:38 final size:38
Alignment explanation
Indices: 354887--354963 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
354877 GCATTAGCAT
354887 TTTGATTTTTCTCTTTTCTTGGGAATCTCTTCAACCAC
1 TTTGATTTTTCTCTTTTCTTGGGAATCTCTTCAACCAC
* * *
354925 TTTGCTTTTTCTTTTTTCTTGGGAATCTCTTCGACCAC
1 TTTGATTTTTCTCTTTTCTTGGGAATCTCTTCAACCAC
354963 T
1 T
354964 AGGGTGTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.13, C:0.23, G:0.12, T:0.52
Consensus pattern (38 bp):
TTTGATTTTTCTCTTTTCTTGGGAATCTCTTCAACCAC
Found at i:360761 original size:15 final size:15
Alignment explanation
Indices: 360729--360787 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
360719 GGAATCCTCA
*
360729 TCTTCTTTCTTC-TAT
1 TCTT-TTTCTTCTTCT
360744 TCTTTTTCTTCTTCT
1 TCTTTTTCTTCTTCT
* *
360759 TCTCTTTCTCCTTCT
1 TCTTTTTCTTCTTCT
*
360774 TCTTTTGCTTCTTC
1 TCTTTTTCTTCTTC
360788 GTCGACTGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
14 7 0.19
15 30 0.81
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.66
Consensus pattern (15 bp):
TCTTTTTCTTCTTCT
Found at i:360767 original size:21 final size:20
Alignment explanation
Indices: 360729--360777 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
360719 GGAATCCTCA
**
360729 TCTTCTTTCTTCTATTCTTTT
1 TCTTC-TTCTTCTATTCTCCT
*
360750 TCTTCTTCTTCTCTTTCTCCT
1 TCTTCTTCTTCT-ATTCTCCT
360771 TCTTCTT
1 TCTTCTT
360778 TTGCTTCTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (20 bp):
TCTTCTTCTTCTATTCTCCT
Found at i:379201 original size:236 final size:236
Alignment explanation
Indices: 378788--379260 Score: 919
Period size: 236 Copynumber: 2.0 Consensus size: 236
378778 TTAATAAAAG
378788 ACACTTTTACGTGGGTGCATTATGACTTATCAAGGGGGAACACTCCAATGCAAGTGTTAGAAAAA
1 ACACTTTTACGTGGGTGCATTATGACTTATCAAGGGGGAACACTCCAATGCAAGTGTTAGAAAAA
* *
378853 ATATCCAGCCAAAGGCTGTCACTGCAAGAGTGTGTATCGGCACAATTACATACTTCTTGGGGGTT
66 ATATCCAGCCAAAGGCTGTCACTGCAAGAGTGTGTATCGGCACAATTAAATACTTCCTGGGGGTT
378918 TGTTGCACGCCCTCATTACTGCTCAGAAACAAGGGTATAGTAATGCAATGACATCTCTCAGTCAC
131 TGTTGCACGCCCTCATTACTGCTCAGAAACAAGGGTATAGTAATGCAATGACATCTCTCAGTCAC
*
378983 ATTAAATTCTCCCTATTTAGAGTATAATTTTTTCCTTTTGT
196 ATTAAATTCTCCCTATTTAGAGTATAATTTGTTCCTTTTGT
379024 ACACTTTTACGTGGGTGCATTATGACTTATCAAGGGGGAACACTCCAATGCAAGTGTTAGAAAAA
1 ACACTTTTACGTGGGTGCATTATGACTTATCAAGGGGGAACACTCCAATGCAAGTGTTAGAAAAA
379089 ATATCCAGCCAAAGGCTGTCACTGCAAGAGTGTGTATCGGCACAATTAAATACTTCCTGGGGGTT
66 ATATCCAGCCAAAGGCTGTCACTGCAAGAGTGTGTATCGGCACAATTAAATACTTCCTGGGGGTT
379154 TGTTGCACGCCCTCATTACTGCTCAGAAACAAGGGTATAGTAATGCAATGACATCTCTCAGTCAC
131 TGTTGCACGCCCTCATTACTGCTCAGAAACAAGGGTATAGTAATGCAATGACATCTCTCAGTCAC
379219 ATTAAATTCTCCCTATTTAGAGTATAATTTGTTCCTTTTGT
196 ATTAAATTCTCCCTATTTAGAGTATAATTTGTTCCTTTTGT
379260 A
1 A
379261 TTATGTTTAG
Statistics
Matches: 234, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
236 234 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (236 bp):
ACACTTTTACGTGGGTGCATTATGACTTATCAAGGGGGAACACTCCAATGCAAGTGTTAGAAAAA
ATATCCAGCCAAAGGCTGTCACTGCAAGAGTGTGTATCGGCACAATTAAATACTTCCTGGGGGTT
TGTTGCACGCCCTCATTACTGCTCAGAAACAAGGGTATAGTAATGCAATGACATCTCTCAGTCAC
ATTAAATTCTCCCTATTTAGAGTATAATTTGTTCCTTTTGT
Found at i:381466 original size:2 final size:2
Alignment explanation
Indices: 381459--381493 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
381449 TGAAACAAAG
*
381459 AT AT AT AT A- AA 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
381494 GAATACTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:383834 original size:19 final size:19
Alignment explanation
Indices: 383812--383858 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
383802 TATATATAAA
383812 AAAATGAAATAATAAC-TAT
1 AAAATGAAATAA-AACTTAT
*
383831 AAAATCTAAATAAAACTTAT
1 AAAAT-GAAATAAAACTTAT
383851 AAAA-GAAA
1 AAAATGAAA
383859 CTATTAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 3 0.12
19 8 0.33
20 13 0.54
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.23
Consensus pattern (19 bp):
AAAATGAAATAAAACTTAT
Found at i:386561 original size:25 final size:25
Alignment explanation
Indices: 386533--386590 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
386523 AGCAATTAAA
* *
386533 TGCGTCGACAAATTGTGCTTTTGTG
1 TGCGTCGACAAATCGTGCTTTCGTG
*
386558 TGCGACGACAAATCGTGCTTTCGTG
1 TGCGTCGACAAATCGTGCTTTCGTG
386583 TGCGTCGA
1 TGCGTCGA
386591 TGAAAAGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (25 bp):
TGCGTCGACAAATCGTGCTTTCGTG
Found at i:393300 original size:3 final size:3
Alignment explanation
Indices: 393292--393330 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
393282 TGCTTTGGTT
393292 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
393331 ATTGGACGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:397010 original size:29 final size:29
Alignment explanation
Indices: 396945--397101 Score: 154
Period size: 30 Copynumber: 5.2 Consensus size: 29
396935 ATTAAAACTA
* * * *
396945 GGTCAAATTTTGAATTTTTAGAAAGTTCGAT
1 GGTCAAA-TTAGAATTTTTGGAAAGTT-TAG
*
396976 TGTCAAATTCA-AATTTTTGGAAAGTTTAG
1 GGTCAAATT-AGAATTTTTGGAAAGTTTAG
*
397005 GGTCAAATTAGAATTTTTGGAAAGTTCAGG
1 GGTCAAATTAGAATTTTTGGAAAGTTTA-G
* *
397035 GGTCAAATTAGAATTTTTAGAAAGTTTGG
1 GGTCAAATTAGAATTTTTGGAAAGTTTAG
* * *
397064 GCGTCAAATTGGAATTTTTGGACAATTTTCG
1 G-GTCAAATTAGAATTTTTGGA-AAGTTTAG
397095 GGTCAAA
1 GGTCAAA
397102 ACATAATTTT
Statistics
Matches: 107, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.01
29 27 0.25
30 66 0.62
31 13 0.12
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
GGTCAAATTAGAATTTTTGGAAAGTTTAG
Found at i:397028 original size:59 final size:59
Alignment explanation
Indices: 396945--397085 Score: 169
Period size: 59 Copynumber: 2.4 Consensus size: 59
396935 ATTAAAACTA
* * ** *
396945 GGTCAAATTTTGAATTTTTAGAAAGTTC-GATTGTCAAATTCA-AATTTTTGGAAAGTTTAG
1 GGTCAAA-TTAGAATTTTTGGAAAGTTCAG-GGGTCAAATT-AGAATTTTTAGAAAGTTTAG
*
397005 GGTCAAATTAGAATTTTTGGAAAGTTCAGGGGTCAAATTAGAATTTTTAGAAAGTTTGG
1 GGTCAAATTAGAATTTTTGGAAAGTTCAGGGGTCAAATTAGAATTTTTAGAAAGTTTAG
*
397064 GCGTCAAATTGGAATTTTTGGA
1 G-GTCAAATTAGAATTTTTGGA
397086 CAATTTTCGG
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
58 1 0.01
59 43 0.61
60 27 0.38
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (59 bp):
GGTCAAATTAGAATTTTTGGAAAGTTCAGGGGTCAAATTAGAATTTTTAGAAAGTTTAG
Found at i:397110 original size:60 final size:58
Alignment explanation
Indices: 396945--397111 Score: 149
Period size: 59 Copynumber: 2.8 Consensus size: 58
396935 ATTAAAACTA
* * ** * *
396945 GGTCAAATTTTGAATTTTTAGAAAGTTCGATTGTCAAATTCA-AATTTTTGGAAAGTTTAG
1 GGTCAAA-TTAGAATTTTTGGAAAGTTC-AGGGTCAAA-ACAGAATTTTTAGAAAGTTTAG
** *
397005 GGTCAAATTAGAATTTTTGGAAAGTTCAGGGGTCAAATTAGAATTTTTAGAAAGTTTGG
1 GGTCAAATTAGAATTTTTGGAAAGTTCA-GGGTCAAAACAGAATTTTTAGAAAGTTTAG
* * *
397064 GCGTCAAATTGGAATTTTTGGACAATTTTC-GGGTCAAAACATAATTTT
1 G-GTCAAATTAGAATTTTTGGA-AA-GTTCAGGGTCAAAACAGAATTTT
397112 ATAATAAAGC
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
58 3 0.03
59 41 0.46
60 41 0.46
61 2 0.02
62 3 0.03
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (58 bp):
GGTCAAATTAGAATTTTTGGAAAGTTCAGGGTCAAAACAGAATTTTTAGAAAGTTTAG
Done.