Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007919.1 Kokia drynarioides strain JFW-HI SEQ_122563, 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: 56656
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3319 original size:15 final size:15
Alignment explanation
Indices: 3299--3330 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3289 AATCATCCGT
3299 AAAAAGTAAATGTGA
1 AAAAAGTAAATGTGA
3314 AAAAAGTAAATGTGA
1 AAAAAGTAAATGTGA
3329 AA
1 AA
3331 TTTGAGGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (15 bp):
AAAAAGTAAATGTGA
Found at i:7211 original size:3 final size:3
Alignment explanation
Indices: 7205--7247 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
7195 CTTCTTCTTC
7205 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
7248 CAGGGGCGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:7420 original size:23 final size:21
Alignment explanation
Indices: 7393--7445 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
7383 AAAATTTTTG
*
7393 ATTTAATTCTTTAAAAATTATA
1 ATTTAATTC-GTAAAAATTATA
* *
7415 TTTTTACTATCGTAAAAATTATA
1 -ATTTAAT-TCGTAAAAATTATA
7438 ATTTAATT
1 ATTTAATT
7446 TTGACCCCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
21 1 0.04
22 5 0.21
23 16 0.67
24 2 0.08
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTTAATTCGTAAAAATTATA
Found at i:11792 original size:2 final size:2
Alignment explanation
Indices: 11785--11809 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11775 AATGTTCATA
11785 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
11810 ATGTTTTGGT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:15164 original size:15 final size:15
Alignment explanation
Indices: 15144--15173 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15134 TTATTATGGA
15144 AATAAATTATATTAG
1 AATAAATTATATTAG
*
15159 AATAAATTTTATTAG
1 AATAAATTATATTAG
15174 GATGATTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
AATAAATTATATTAG
Found at i:15604 original size:20 final size:20
Alignment explanation
Indices: 15576--15618 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
15566 TCAAGATTCT
*
15576 GTTTTGGGTTCAAAGTTTGA
1 GTTTAGGGTTCAAAGTTTGA
15596 GTTTAGGGTTCAAAGTTTGA
1 GTTTAGGGTTCAAAGTTTGA
15616 GTT
1 GTT
15619 CAAGGTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.05, G:0.30, T:0.44
Consensus pattern (20 bp):
GTTTAGGGTTCAAAGTTTGA
Found at i:15625 original size:20 final size:20
Alignment explanation
Indices: 15582--15625 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
15572 TTCTGTTTTG
* *
15582 GGTTCAAAGTTTGAGTTTAG
1 GGTTCAAAGTTTGAGTTCAA
15602 GGTTCAAAGTTTGAGTTCAA
1 GGTTCAAAGTTTGAGTTCAA
15622 GGTT
1 GGTT
15626 ATTGGTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.25, C:0.07, G:0.30, T:0.39
Consensus pattern (20 bp):
GGTTCAAAGTTTGAGTTCAA
Found at i:15682 original size:21 final size:20
Alignment explanation
Indices: 15658--15732 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 20
15648 AGGGTGTAGG
15658 GTTTAAGGTTTAGAGTTATGA
1 GTTT-AGGTTTAGAGTTATGA
* *
15679 GTTTAGGGTTAGAGGTTCT-A
1 GTTTAGGTTTAGA-GTTATGA
* *
15699 GGTTTTGGGTTTAGAGTTTTAGA
1 -G-TTTAGGTTTAGAGTTAT-GA
15722 GTTTGAGGTTT
1 GTTT-AGGTTT
15733 GGTATTCATG
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
20 9 0.21
21 16 0.38
22 16 0.38
23 1 0.02
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.45
Consensus pattern (20 bp):
GTTTAGGTTTAGAGTTATGA
Found at i:15694 original size:28 final size:28
Alignment explanation
Indices: 15654--15717 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
15644 ATTTAGGGTG
15654 TAGGGTTTAAGGTT-TAGAGTTATGAGTT
1 TAGGGTTTAAGGTTCTAG-GTTATGAGTT
* *
15682 TAGGG-TTAGAGGTTCTAGGTTTTGGGTT
1 TAGGGTTTA-AGGTTCTAGGTTATGAGTT
*
15710 TAGAGTTT
1 TAGGGTTT
15718 TAGAGTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.10
28 22 0.73
29 5 0.17
ACGTcount: A:0.20, C:0.02, G:0.34, T:0.44
Consensus pattern (28 bp):
TAGGGTTTAAGGTTCTAGGTTATGAGTT
Found at i:26233 original size:3 final size:3
Alignment explanation
Indices: 26227--26269 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
26217 GATGATGATG
26227 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
26270 CACTTTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35693 original size:9 final size:9
Alignment explanation
Indices: 35679--35703 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
35669 AACAGATAAT
35679 AAAAAAATA
1 AAAAAAATA
35688 AAAAAAATA
1 AAAAAAATA
35697 AAAAAAA
1 AAAAAAA
35704 AAGAGAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:35703 original size:20 final size:21
Alignment explanation
Indices: 35660--35705 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
35650 AGTAAATTGT
* * *
35660 AAAACTAAAAACAGATAATAA
1 AAAAATAAAAACAAATAAAAA
35681 AAAAATAAAAA-AAATAAAAA
1 AAAAATAAAAACAAATAAAAA
35701 AAAAA
1 AAAAA
35706 GAGAGAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.11
Consensus pattern (21 bp):
AAAAATAAAAACAAATAAAAA
Found at i:36993 original size:26 final size:26
Alignment explanation
Indices: 36954--37016 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
36944 TAGAAGTACC
*
36954 GGAAAGAATGACCGGATGGAGACAAA
1 GGAAAGAATAACCGGATGGAGACAAA
36980 GGAAAGAATAACCGGATGGAGACAAA
1 GGAAAGAATAACCGGATGGAGACAAA
37006 GGAAAGAATAA
1 GGAAAGAATAA
37017 TGGGCGGCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.51, C:0.10, G:0.32, T:0.08
Consensus pattern (26 bp):
GGAAAGAATAACCGGATGGAGACAAA
Found at i:49130 original size:34 final size:34
Alignment explanation
Indices: 49087--49156 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
49077 TGTTTATAAA
49087 TGAATTAAGGATGAAAAGTTAATATTCCTAATTT
1 TGAATTAAGGATGAAAAGTTAATATTCCTAATTT
49121 TGAATTAAGGATGAAAAGTTAATATTCCTAATTT
1 TGAATTAAGGATGAAAAGTTAATATTCCTAATTT
49155 TG
1 TG
49157 CATACCAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.39
Consensus pattern (34 bp):
TGAATTAAGGATGAAAAGTTAATATTCCTAATTT
Found at i:51419 original size:23 final size:24
Alignment explanation
Indices: 51393--51437 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
51383 TAAAATTTTT
*
51393 TATAT-TATTATTATAA-AAAATCC
1 TATATATA-TATTAAAATAAAATCC
51416 TATATATATATTAAAATAAAAT
1 TATATATATATTAAAATAAAAT
51438 AAAATCTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
TATATATATATTAAAATAAAATCC
Found at i:52196 original size:15 final size:16
Alignment explanation
Indices: 52176--52206 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
52166 TGAGACATGA
52176 TGAGTTCT-TTAAGCT
1 TGAGTTCTATTAAGCT
52191 TGAGTTCTATTAAGCT
1 TGAGTTCTATTAAGCT
52207 CGTTTAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (16 bp):
TGAGTTCTATTAAGCT
Found at i:53666 original size:36 final size:35
Alignment explanation
Indices: 53625--53707 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 35
53615 GATTCTATTC
*
53625 AAAAAATAAAAAAAAATATTTAAAAAT-TCATTTTT
1 AAAAAATAAAAAAAAATATATAAAAATGT-ATTTTT
* * * * *
53660 ATAAAAATACATAAAATTGTATAAAAATGTTTTTTT
1 A-AAAAATAAAAAAAAATATATAAAAATGTATTTTT
53696 AAAAAATAAAAA
1 AAAAAATAAAAA
53708 TATTTTAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
35 10 0.26
36 27 0.71
37 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (35 bp):
AAAAAATAAAAAAAAATATATAAAAATGTATTTTT
Done.