Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012466.1 Kokia drynarioides strain JFW-HI SEQ_127470, 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: 34845
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Found at i:669 original size:195 final size:195
Alignment explanation
Indices: 323--768 Score: 553
Period size: 195 Copynumber: 2.3 Consensus size: 195
313 AAACCAACGC
* * *
323 GATGGTTGGGGTACCGCATATGTTGCGAGTCCCCGATAGCTCGTGTGAGTAGCATCGTGAATCGA
1 GATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGTAGCATCGTGAATCGA
*
388 GAAGATGAGAAATGAATCCAAGAATGGATTACAAACCCTACGATGGCTGAGATTTATGAATAAGT
66 GAAGAAGAGAAATGAATCCAAGAATGGATTACAAACCCTACGATGGCTGAGATTTATGAATAAGT
* * *
453 GTATATTCTCGACAACTCGTGTGAGCAGCATCGTTAGGGGACAATTATATACACAGATATTGTAT
131 GCATATTCTCGACAACTCGTGTGAGCAGCATCGTTAGGGGACAATT-TATACACAGATATCGTAC
518 A
195 A
* * *
519 GATGGTTGAGGTACCGCATTTGTTGCAAGTCCTCGACAGCTCGTGTGAGTAGCATCGTGAGTCGA
1 GATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGTAGCATCGTGAATCGA
* ** * **
584 -AA-AAGAGATATGAAATCCTTAA-AA-GGATTACAGGCCCTACGATGGCTGGGATTTATGCTTG
66 GAAGAAGAGAAATG-AATCC--AAGAATGGATTACAAACCCTACGATGGCTGAGATTTATGAAT-
* * * * * * *
645 AA-TGCATATTCTCGATAGCTCGTGTGAGCAGCATTGTTAGGGGATAGTTTATAGATAGATATCG
127 AAGTGCATATTCTCGACAACTCGTGTGAGCAGCATCGTTAGGGGACAATTTATACACAGATATCG
*
709 TACC
192 TACA
* * *
713 GATGGCT-AGGGTACCACATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATC
1 GATGGTTGA-GGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGTAGCATC
769 AAGTACTAGT
Statistics
Matches: 216, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
193 1 0.00
194 71 0.33
195 79 0.37
196 63 0.29
197 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (195 bp):
GATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGTAGCATCGTGAATCGA
GAAGAAGAGAAATGAATCCAAGAATGGATTACAAACCCTACGATGGCTGAGATTTATGAATAAGT
GCATATTCTCGACAACTCGTGTGAGCAGCATCGTTAGGGGACAATTTATACACAGATATCGTACA
Found at i:5220 original size:23 final size:22
Alignment explanation
Indices: 5177--5222 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5167 ATAGTATAAA
*
5177 TTATTATTTAATTAATAATATC
1 TTATTATTTAATAAATAATATC
5199 TTATTATATTAATGAAATATATAT
1 TTATTAT-TTAAT-AAATA-ATAT
5223 ATAAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 5 0.25
24 4 0.20
25 4 0.20
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TTATTATTTAATAAATAATATC
Found at i:5468 original size:14 final size:14
Alignment explanation
Indices: 5449--5475 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5439 GCTTAAACGA
5449 AAAAGGGAAGGAAG
1 AAAAGGGAAGGAAG
5463 AAAAGGGAAGGAA
1 AAAAGGGAAGGAA
5476 AAAGAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
AAAAGGGAAGGAAG
Found at i:6208 original size:18 final size:18
Alignment explanation
Indices: 6185--6219 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6175 TTTGTGATCA
6185 AAATTGAAAGTGAAAGTT
1 AAATTGAAAGTGAAAGTT
* *
6203 AAATTGGAATTGAAAGT
1 AAATTGAAAGTGAAAGT
6220 GATATGAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.29
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTT
Found at i:6448 original size:40 final size:40
Alignment explanation
Indices: 6387--6462 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
6377 TGGGTACCAC
*
6387 ATTACTTCGACTAGGCTGATGAGACACT-AGGTGTCACTTT
1 ATTACTTCGACTAGGCCGATGAGACACTGA-GTGTCACTTT
* *
6427 ATTACTTCGAACTA-TCCGATGAGGCACTGAGTGTCA
1 ATTACTTCG-ACTAGGCCGATGAGACACTGAGTGTCA
6463 TTCTGGTGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
40 26 0.84
41 5 0.16
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (40 bp):
ATTACTTCGACTAGGCCGATGAGACACTGAGTGTCACTTT
Found at i:12871 original size:14 final size:14
Alignment explanation
Indices: 12852--12878 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12842 GCTTAAACGA
12852 AAAAGGGAAGGAAG
1 AAAAGGGAAGGAAG
12866 AAAAGGGAAGGAA
1 AAAAGGGAAGGAA
12879 AAAGAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
AAAAGGGAAGGAAG
Found at i:14391 original size:96 final size:96
Alignment explanation
Indices: 14227--14418 Score: 330
Period size: 96 Copynumber: 2.0 Consensus size: 96
14217 GTTTGAAATA
* * * *
14227 CTCAGCGTACGGTTGTTTCCTTGTGCAAGTTAGTAGAAATTAAGATCCTTGTTCAGCATCTAGAT
1 CTCAGCGTACGGTTGTTTCCGTGCGCAAGTTAGTAGAAATTAAGATCCTTGTTCAACATCCAGAT
14292 CGATCCCGAGCTCGGTATAAATCCAGTGATG
66 CGATCCCGAGCTCGGTATAAATCCAGTGATG
*
14323 CTCAGCGTACGGTTGTTTCCGTGCGCAGGTTAGTAGAAATTAAGATCCTTGTTCAACATCCAGAT
1 CTCAGCGTACGGTTGTTTCCGTGCGCAAGTTAGTAGAAATTAAGATCCTTGTTCAACATCCAGAT
*
14388 CGATCTCGAGCTCGGTATAAATCCAGTGATG
66 CGATCCCGAGCTCGGTATAAATCCAGTGATG
14419 TAATTTTCCC
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 90 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (96 bp):
CTCAGCGTACGGTTGTTTCCGTGCGCAAGTTAGTAGAAATTAAGATCCTTGTTCAACATCCAGAT
CGATCCCGAGCTCGGTATAAATCCAGTGATG
Found at i:25402 original size:37 final size:37
Alignment explanation
Indices: 25344--25447 Score: 101
Period size: 37 Copynumber: 2.8 Consensus size: 37
25334 AAAAATAATA
25344 TTATTTTAATAGTTTAATATTAAATTTAAT-TTAAGAC
1 TTATTTTAATAGTTTAATATT-AATTTAATATTAAGAC
*
25381 TTATTTTAATAGTATT-TTATTAATTTAATATTAAAGTGA-
1 TTATTTTAATAGT-TTAATATTAATTTAATATT-AA--GAC
* *
25420 TTATCTTAATA-TTAAAT-TTAATTTAATA
1 TTATTTTAATAGTTTAATATTAATTTAATA
25448 CAAGATAAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
36 8 0.14
37 31 0.54
38 6 0.11
39 10 0.18
40 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (37 bp):
TTATTTTAATAGTTTAATATTAATTTAATATTAAGAC
Found at i:25422 original size:20 final size:18
Alignment explanation
Indices: 25340--25447 Score: 62
Period size: 19 Copynumber: 5.8 Consensus size: 18
25330 TTCCAAAAAT
* *
25340 AATATTATTTTAATAGTTT
1 AATATTAATTTAATA-TTA
25359 AATATTAAATTTAAT-TTA
1 AATATT-AATTTAATATTA
* * *
25377 AGA-CTTATTTTAATAGTA
1 A-ATATTAATTTAATATTA
**
25395 TTTTATTAATTTAATATTA
1 -AATATTAATTTAATATTA
25414 AAGTGATT-ATCTTAATATTA
1 AA-T-ATTAAT-TTAATATTA
25434 AAT-TTAATTTAATA
1 AATATTAATTTAATA
25448 CAAGATAAAC
Statistics
Matches: 68, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
17 15 0.22
18 9 0.13
19 23 0.34
20 21 0.31
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (18 bp):
AATATTAATTTAATATTA
Found at i:27063 original size:24 final size:24
Alignment explanation
Indices: 27036--27081 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
27026 TAAATGAATA
*
27036 TTGAAATTTGTCACTATATTTTCT
1 TTGAAATTTGCCACTATATTTTCT
* *
27060 TTGATATTTGCCATTATATTTT
1 TTGAAATTTGCCACTATATTTT
27082 GAAAATCTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.57
Consensus pattern (24 bp):
TTGAAATTTGCCACTATATTTTCT
Found at i:28879 original size:18 final size:19
Alignment explanation
Indices: 28848--28885 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
28838 GAGAGACAGT
* *
28848 TTTTTTTTTTAAAT-TAAA
1 TTTTTATTTCAAATCTAAA
28866 TTTTTATTTCAAATCTAAA
1 TTTTTATTTCAAATCTAAA
28885 T
1 T
28886 GAAAAAGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTATTTCAAATCTAAA
Found at i:31071 original size:28 final size:28
Alignment explanation
Indices: 31009--31156 Score: 86
Period size: 29 Copynumber: 5.2 Consensus size: 28
30999 ATTTAAATTT
* * * *
31009 ATTTGATCTCAAAACTTTTAAAAATTAT
1 ATTTTATCCCAAAACTTCTAAAAATTAC
31037 ATTTTTATCCCAAAACTTCTAAAAATTAC
1 A-TTTTATCCCAAAACTTCTAAAAATTAC
* * * * * *
31066 ATTTTACTCTC-GAACCTCCAAAATTTCC
1 ATTTTA-TCCCAAAACTTCTAAAAATTAC
*
31094 ATTTTGACCCCAAAACTT-TCAAAAATTACC
1 ATTTT-ATCCCAAAACTTCT-AAAAATTA-C
* * * *
31124 ATTTTACCCCTAAA-TGTCTAAATATTCC
1 ATTTTATCCCAAAACT-TCTAAAAATTAC
31152 ATTTT
1 ATTTT
31157 TTATCCCTAT
Statistics
Matches: 92, Mismatches: 20, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
28 32 0.35
29 53 0.58
30 7 0.08
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (28 bp):
ATTTTATCCCAAAACTTCTAAAAATTAC
Found at i:31132 original size:29 final size:27
Alignment explanation
Indices: 31018--31133 Score: 88
Period size: 29 Copynumber: 4.0 Consensus size: 27
31008 TATTTGATCT
* * *
31018 CAAAACTTTTAAAAATTATATTTTTATCC
1 CAAAAC-TTCAAAAATTACA-TTTTACCC
*
31047 CAAAACTTCTAAAAATTACATTTTACTCT
1 CAAAACTTC-AAAAATTACATTTTAC-CC
* * * * *
31076 CGAACCTCCAAAATTTCCATTTTGACCC
1 CAAAACTTCAAAAATTACATTTT-ACCC
31104 CAAAACTTTCAAAAATTACCATTTTACCC
1 CAAAAC-TTCAAAAATTA-CATTTTACCC
31133 C
1 C
31134 TAAATGTCTA
Statistics
Matches: 67, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
28 24 0.36
29 37 0.55
30 6 0.09
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (27 bp):
CAAAACTTCAAAAATTACATTTTACCC
Found at i:31157 original size:29 final size:28
Alignment explanation
Indices: 31085--31208 Score: 83
Period size: 29 Copynumber: 4.3 Consensus size: 28
31075 TCGAACCTCC
* * *
31085 AAAATTTCCATTTTGACCCCAAAACTTTC-
1 AAAAATTCCATTTT-ACCCCTAAA-TGTCT
31114 AAAAATTACCATTTTACCCCTAAATGTCT
1 AAAAATT-CCATTTTACCCCTAAATGTCT
* * * *
31143 AAATATTCCATTTTTTATCCCT-ATTTTCCT
1 AAAAATTCCA--TTTTACCCCTAAATGT-CT
**
31173 -AAAATTACCATTTTACCCCTGGATGTCT
1 AAAAATT-CCATTTTACCCCTAAATGTCT
31201 AAAAATTC
1 AAAAATTC
31209 TGTTTTTTAT
Statistics
Matches: 75, Mismatches: 12, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
28 18 0.24
29 36 0.48
30 21 0.28
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (28 bp):
AAAAATTCCATTTTACCCCTAAATGTCT
Found at i:31177 original size:58 final size:58
Alignment explanation
Indices: 31115--31309 Score: 214
Period size: 58 Copynumber: 3.3 Consensus size: 58
31105 AAAACTTTCA
* * *
31115 AAAATTACCATTTTACCCCTAAATGTCTAAATATTCCATTTTTTATCCCTATTTTCCT
1 AAAATTACCATTTTACCCCTGAATGTCTAAAAATTCCATTTTTTATCCCAATTTTCCT
* ** *
31173 AAAATTACCATTTTACCCCTGGATGTCTAAAAATTCTGTTTTTTATCCCGATTTT--T
1 AAAATTACCATTTTACCCCTGAATGTCTAAAAATTCCATTTTTTATCCCAATTTTCCT
* * * * * * *
31229 AAAATTTACCGTTTCACCCCCCGAGTGTCTAAAAATTCCATTTTTAATCCCGAATTATCCC
1 AAAA-TTACCATTTTA-CCCCTGAATGTCTAAAAATTCCATTTTTTATCCC-AATTTTCCT
*
31290 AAAATTACCATTTTGCCCCT
1 AAAATTACCATTTTACCCCT
31310 CGGTATCCAA
Statistics
Matches: 111, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
56 5 0.05
57 9 0.08
58 77 0.69
59 8 0.07
60 8 0.07
61 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.06, T:0.40
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTGAATGTCTAAAAATTCCATTTTTTATCCCAATTTTCCT
Found at i:31202 original size:28 final size:26
Alignment explanation
Indices: 31115--31204 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 26
31105 AAAACTTTCA
31115 AAAATTACCATTTTACCCCTAAATGTCT
1 AAAATTACCATTTTACCCCT--ATGTCT
* *
31143 AAATATT-CCATTTTTTATCCCTATTTTCCT
1 AAA-ATTACCA--TTTTACCCCTA-TGT-CT
31173 AAAATTACCATTTTACCCCTGGATGTCT
1 AAAATTACCATTTTACCCCT--ATGTCT
31201 AAAA
1 AAAA
31205 ATTCTGTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
28 22 0.44
29 10 0.20
30 18 0.36
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.40
Consensus pattern (26 bp):
AAAATTACCATTTTACCCCTATGTCT
Found at i:34001 original size:40 final size:39
Alignment explanation
Indices: 33911--34030 Score: 134
Period size: 40 Copynumber: 3.0 Consensus size: 39
33901 GCGTTTGGAC
* * *
33911 AGAAAACGCCGTAAAAAGTAAAGTAATAGCGGCGCTTTT
1 AGAAAACGCCGCAAAAAGTAAAGCAATAGCGGCGCTTAT
*
33950 ACATAAACGCCGCAAAAAGTAAAGCAATAGCGGCGCTTAT
1 AGA-AAACGCCGCAAAAAGTAAAGCAATAGCGGCGCTTAT
* * *
33990 AGAAAAGCGCCGTC-AAAGGTCAGAGCAATAGCAGCGCTTAT
1 AGAAAA-CGCCG-CAAAAAGT-AAAGCAATAGCGGCGCTTAT
34031 GGGAAAGATG
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
39 5 0.07
40 45 0.65
41 19 0.28
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (39 bp):
AGAAAACGCCGCAAAAAGTAAAGCAATAGCGGCGCTTAT
Found at i:34223 original size:41 final size:41
Alignment explanation
Indices: 34044--34209 Score: 183
Period size: 41 Copynumber: 4.1 Consensus size: 41
34034 AAAGATGGGC
* **
34044 AAGCGCCGCTAAAGGTCAGAGCAATAACGACGCTTATGGGC
1 AAGCGCCGCTAAAGGTCAGAGCAATAACGACGCTTATTGAA
* * *
34085 AAGCGCTGCTAAAGGTCAGAGCAATAGCGACGCCTATTTG-A
1 AAGCGCCGCTAAAGGTCAGAGCAATAACGACGCTTA-TTGAA
* * * *
34126 AAGCACCGCTAAAGGTTAGAGCAATAGCGACGATTATTGAA
1 AAGCGCCGCTAAAGGTCAGAGCAATAACGACGCTTATTGAA
* * * *
34167 TAGCGCCACCAAAAGTCAGAGCAATAACGACGCTT-TTGAA
1 AAGCGCCGCTAAAGGTCAGAGCAATAACGACGCTTATTGAA
34207 AAG
1 AAG
34210 ATGTCGCTAA
Statistics
Matches: 104, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
40 10 0.10
41 92 0.88
42 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (41 bp):
AAGCGCCGCTAAAGGTCAGAGCAATAACGACGCTTATTGAA
Done.