Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014999.1 Kokia drynarioides strain JFW-HI SEQ_130043, 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: 91011
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:65 original size:18 final size:18
Alignment explanation
Indices: 42--89 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
32 ACAATTCATA
42 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* * *
60 TCACTTTCACTTTCACTT
1 TCACTTTCAATTCCAATT
*
78 TCACTTTAAATT
1 TCACTTTCAATT
90 TTGACTACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.25, C:0.27, G:0.00, T:0.48
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:67 original size:6 final size:6
Alignment explanation
Indices: 42--84 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
32 ACAATTCATA
* * *
42 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT T
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT T
85 AAATTTTGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:3121 original size:16 final size:15
Alignment explanation
Indices: 3102--3135 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3092 TGTTATATTC
3102 TTTTATATAACAACTA
1 TTTTATATAACAA-TA
*
3118 TTTTCTATAACAATA
1 TTTTATATAACAATA
3133 TTT
1 TTT
3136 CATTATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTATATAACAATA
Found at i:4126 original size:23 final size:24
Alignment explanation
Indices: 4086--4138 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
4076 TAATATTTTT
* *
4086 ATAAATTTTAATATTTTTAA-AAA
1 ATAAATTTTAAGAATTTTAATAAA
*
4109 ATAAATTTTTAGAATTTTAATTAAA
1 ATAAATTTTAAGAATTTTAA-TAAA
4134 ATAAA
1 ATAAA
4139 AAAGAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.68
25 8 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
ATAAATTTTAAGAATTTTAATAAA
Found at i:23515 original size:18 final size:18
Alignment explanation
Indices: 23469--23515 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
23459 ATTAAAATTT
*
23469 AAAAGAAAAATAACAAAA
1 AAAAGAAAACTAACAAAA
*
23487 CAAAGAGAAACTAA-AAAA
1 AAAAGA-AAACTAACAAAA
23505 AAATAGAAAAC
1 AAA-AGAAAAC
23516 GAAACATCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.77, C:0.09, G:0.09, T:0.06
Consensus pattern (18 bp):
AAAAGAAAACTAACAAAA
Found at i:23920 original size:16 final size:17
Alignment explanation
Indices: 23881--23922 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
23871 ACAAAGGCAG
23881 ATAAAAACTAGAAAAAA
1 ATAAAAACTAGAAAAAA
* *
23898 ATCAAAA-TATAAAAAA
1 ATAAAAACTAGAAAAAA
23914 ATAAAAACT
1 ATAAAAACT
23923 GAATATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.17
Consensus pattern (17 bp):
ATAAAAACTAGAAAAAA
Found at i:24116 original size:3 final size:3
Alignment explanation
Indices: 24108--24154 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
24098 TTTGTTTTTA
24108 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
24155 ACCAATAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28126 original size:7 final size:7
Alignment explanation
Indices: 28114--28141 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
28104 TTTCTAATCT
28114 TTGAAAC
1 TTGAAAC
28121 TTGAAAC
1 TTGAAAC
28128 TTGAAAC
1 TTGAAAC
28135 TTGAAAC
1 TTGAAAC
28142 AACAATAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (7 bp):
TTGAAAC
Found at i:28191 original size:16 final size:16
Alignment explanation
Indices: 28166--28203 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
28156 ATTGATGTCA
*
28166 CTTGGCACGTAAGTCC
1 CTTGGTACGTAAGTCC
28182 CTTGGTACGTAAGTCC
1 CTTGGTACGTAAGTCC
28198 CTTGGT
1 CTTGGT
28204 CTCTTTCAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.32
Consensus pattern (16 bp):
CTTGGTACGTAAGTCC
Found at i:31796 original size:15 final size:15
Alignment explanation
Indices: 31776--31809 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
31766 ACCAAGGAAC
* *
31776 GGAAAGAGAGGAGGA
1 GGAAAGAAAGGAAGA
31791 GGAAAGAAAGGAAGA
1 GGAAAGAAAGGAAGA
31806 GGAA
1 GGAA
31810 TGTGAAAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (15 bp):
GGAAAGAAAGGAAGA
Found at i:33169 original size:59 final size:59
Alignment explanation
Indices: 33098--33209 Score: 179
Period size: 59 Copynumber: 1.9 Consensus size: 59
33088 TTAATATAAC
*
33098 ATTTGGTACTTGAACTTGGCACTTTTTCCTAATTTGGTACCTAAATTTTTTTTAACCCA
1 ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAATTTTTTTTAACCCA
* ** *
33157 ATTTGGTACTTGAACTTGACATTTTTTCCTTTTTTGGTACCTAAGTTTTTTTT
1 ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAATTTTTTTT
33210 TAGATTCAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (59 bp):
ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAATTTTTTTTAACCCA
Found at i:42155 original size:6 final size:6
Alignment explanation
Indices: 42140--42174 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
42130 ATGCTTTTAC
42140 TTAT-A TTATAA TTATAA TTATAA TTATAA TTATAA
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA
42175 ATAGACTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTATAA
Found at i:42245 original size:14 final size:14
Alignment explanation
Indices: 42228--42258 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42218 TTTTTATTAC
*
42228 TTAGTATTTATATT
1 TTAGTATTAATATT
42242 TTAGTATTAATATT
1 TTAGTATTAATATT
42256 TTA
1 TTA
42259 ATGTATGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TTAGTATTAATATT
Found at i:43636 original size:21 final size:21
Alignment explanation
Indices: 43610--43699 Score: 67
Period size: 21 Copynumber: 4.2 Consensus size: 21
43600 TTTAGTGTTA
*
43610 TTTTTTTACTGTTTTGGTTG-
1 TTTTTTTACTATTTTGGTTGT
*
43630 TTTTTTTATTTATTTTGGTAT-T
1 TTTTTTTA-CTATTTTGGT-TGT
* *
43652 GTTTTTTACTATTTTGGTTAT
1 TTTTTTTACTATTTTGGTTGT
* * *
43673 GTTTTTTATTGTTTTGATGTTGT
1 TTTTTTTACTATTTTG--GTTGT
43696 TTTT
1 TTTT
43700 GCTATTATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
20 9 0.16
21 32 0.57
22 8 0.14
23 7 0.12
ACGTcount: A:0.10, C:0.02, G:0.16, T:0.72
Consensus pattern (21 bp):
TTTTTTTACTATTTTGGTTGT
Found at i:43667 original size:42 final size:42
Alignment explanation
Indices: 43611--43723 Score: 120
Period size: 42 Copynumber: 2.6 Consensus size: 42
43601 TTAGTGTTAT
* * *
43611 TTTTTTACTGTTTTGGTTGT-TTTTTTATTTATTTTGGTATTG
1 TTTTTTACTATTTTGGTTATGTTTTTTA-TTATTTTGATATTG
* *
43653 TTTTTTACTATTTTGGTTATGTTTTTTATTGTTTTGATGTTG
1 TTTTTTACTATTTTGGTTATGTTTTTTATTATTTTGATATTG
* *
43695 TTTTTGCTATTATTTTTGTTACTGTTTTT
1 TTTTT--TACTATTTTGGTTA-TGTTTTT
43724 GTTGTTTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
42 34 0.57
43 7 0.12
44 12 0.20
45 7 0.12
ACGTcount: A:0.11, C:0.04, G:0.15, T:0.71
Consensus pattern (42 bp):
TTTTTTACTATTTTGGTTATGTTTTTTATTATTTTGATATTG
Found at i:43729 original size:44 final size:44
Alignment explanation
Indices: 43661--43755 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
43651 TGTTTTTTAC
*
43661 TATTTTGGTTATGTTTTTTATTGTTTTGATGT-TGT-TTTTGCTAT
1 TATTTTTGTTATGTTTTTTATTGTTTTGAT-TAT-TATTTTGCTAT
* *
43705 TATTTTTGTTACTG-TTTTTGTTGTTTTTATTATTATTTTGCTAT
1 TATTTTTGTTA-TGTTTTTTATTGTTTTGATTATTATTTTGCTAT
43749 TATTTTT
1 TATTTTT
43756 ACTGTTATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
43 2 0.04
44 41 0.91
45 2 0.04
ACGTcount: A:0.13, C:0.03, G:0.14, T:0.71
Consensus pattern (44 bp):
TATTTTTGTTATGTTTTTTATTGTTTTGATTATTATTTTGCTAT
Found at i:43776 original size:41 final size:43
Alignment explanation
Indices: 43696--43776 Score: 105
Period size: 41 Copynumber: 1.9 Consensus size: 43
43686 TTGATGTTGT
* *
43696 TTTTGCTATTATTTTTGTTACTGTTTTTGTTGTTTTTATTATTA
1 TTTTGCTATTA-TTTTGTTACTGTTTTTGTGGTTGTTATTATTA
43740 TTTTGCTATTA-TTT-TTACTGTTATTT-TGGTTGTTATT
1 TTTTGCTATTATTTTGTTACTGTT-TTTGTGGTTGTTATT
43777 TTTGTTGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 17 0.50
42 6 0.18
44 11 0.32
ACGTcount: A:0.14, C:0.05, G:0.12, T:0.69
Consensus pattern (43 bp):
TTTTGCTATTATTTTGTTACTGTTTTTGTGGTTGTTATTATTA
Found at i:45987 original size:9 final size:9
Alignment explanation
Indices: 45967--46079 Score: 52
Period size: 9 Copynumber: 11.7 Consensus size: 9
45957 AGCTAACGTG
45967 TAAAATATTA
1 TAAAA-ATTA
45977 TAAAAATTA
1 TAAAAATTA
45986 TAAATAAATTTA
1 T-AA-AAA-TTA
*
45998 TTAAAAAGTTG
1 -TAAAAA-TTA
46009 T-AAAATTA
1 TAAAAATTA
*
46017 -AAATATATTT
1 TAAA-A-ATTA
*
46027 TAAAAATCA
1 TAAAAATTA
*
46036 TAAAAATTC
1 TAAAAATTA
46045 TAAAAGTATTA
1 TAAAA--ATTA
**
46056 -AAGGATTA
1 TAAAAATTA
46064 TTAAAAATTA
1 -TAAAAATTA
46074 TAAAAA
1 TAAAAA
46080 AAAATGTCAA
Statistics
Matches: 78, Mismatches: 13, Indels: 25
0.67 0.11 0.22
Matches are distributed among these distances:
8 8 0.10
9 30 0.38
10 20 0.26
11 14 0.18
12 5 0.06
13 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:52348 original size:30 final size:30
Alignment explanation
Indices: 52291--52356 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
52281 TTTTTGTAAC
*
52291 TTTTAAAAAATTAAATCAAATTTTTATTAT
1 TTTTAAAAAATTAAATCAAATTCTTATTAT
52321 TTTTAAAAAATTAATAT-ACAA-TCTTATTAT
1 TTTTAAAAAATTAA-ATCA-AATTCTTATTAT
*
52351 TATTAA
1 TTTTAA
52357 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 28 0.88
31 4 0.12
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (30 bp):
TTTTAAAAAATTAAATCAAATTCTTATTAT
Found at i:53327 original size:6 final size:6
Alignment explanation
Indices: 53316--53343 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53306 CCATTGTCTT
53316 CCCCAC CCCCAC CCCCAC CCCCAC CCCC
1 CCCCAC CCCCAC CCCCAC CCCCAC CCCC
53344 CCTAAAAATA
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:0.86, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCCAC
Found at i:55122 original size:21 final size:21
Alignment explanation
Indices: 55067--55123 Score: 53
Period size: 24 Copynumber: 2.6 Consensus size: 21
55057 TGTATTCAAT
* *
55067 TTATATTATAAAATTTATTTA
1 TTATATTAAAAAATTTATATA
*
55088 GTATATTATTAAAACATTT-TATA
1 -T-TA-TATTAAAAAATTTATATA
55111 TTATATTAAAAAA
1 TTATATTAAAAAA
55124 ATAAAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 9 0.31
21 2 0.07
22 2 0.07
23 5 0.17
24 11 0.38
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TTATATTAAAAAATTTATATA
Found at i:57147 original size:17 final size:17
Alignment explanation
Indices: 57125--57158 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
57115 GTTTAAAAAA
*
57125 TAAAATAGAAAACAATT
1 TAAAATAGAAAAAAATT
*
57142 TAAAATGGAAAAAAATT
1 TAAAATAGAAAAAAATT
57159 GACTACCTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.09, T:0.24
Consensus pattern (17 bp):
TAAAATAGAAAAAAATT
Found at i:67753 original size:3 final size:3
Alignment explanation
Indices: 67745--67793 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
67735 TTGTGTTCTT
* *
67745 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
67793 T
1 T
67794 CATTTTAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:70652 original size:24 final size:24
Alignment explanation
Indices: 70618--70725 Score: 189
Period size: 24 Copynumber: 4.5 Consensus size: 24
70608 GAAGAATTTT
*
70618 CTCCTAGGGGAGCAAGAGGTGGTC
1 CTCCTATGGGAGCAAGAGGTGGTC
* *
70642 CTTCAATGGGAGCAAGAGGTGGTC
1 CTCCTATGGGAGCAAGAGGTGGTC
70666 CTCCTATGGGAGCAAGAGGTGGTC
1 CTCCTATGGGAGCAAGAGGTGGTC
70690 CTCCTATGGGAGCAAGAGGTGGTC
1 CTCCTATGGGAGCAAGAGGTGGTC
70714 CTCCTATGGGAG
1 CTCCTATGGGAG
70726 ATTCAAATCG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 79 1.00
ACGTcount: A:0.21, C:0.20, G:0.38, T:0.20
Consensus pattern (24 bp):
CTCCTATGGGAGCAAGAGGTGGTC
Found at i:73269 original size:13 final size:13
Alignment explanation
Indices: 73251--73289 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
73241 CCTTTGAAAA
73251 TATTTTAGTTTTT
1 TATTTTAGTTTTT
* *
73264 TATTTTAATTTAT
1 TATTTTAGTTTTT
*
73277 TATTTAAGTTTTT
1 TATTTTAGTTTTT
73290 AACTGAATTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (13 bp):
TATTTTAGTTTTT
Found at i:88218 original size:15 final size:17
Alignment explanation
Indices: 88188--88222 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
88178 TTTTTAAAAT
88188 ATATTATATGTAATTTA
1 ATATTATATGTAATTTA
88205 ATATT-TAT-TAATTTA
1 ATATTATATGTAATTTA
88220 ATA
1 ATA
88223 AAATTTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 3 0.17
17 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATATTATATGTAATTTA
Done.