Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004776.1 Kokia drynarioides strain JFW-HI SEQ_118386, 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: 86098
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Warning! 12 characters in sequence are not A, C, G, or T
Found at i:165 original size:96 final size:96
Alignment explanation
Indices: 1--234 Score: 396
Period size: 96 Copynumber: 2.4 Consensus size: 96
*
1 GACTAGGTGAAGGGGGTGGTGGTGATTTGTAGTAGTAAGGAGGAGGAGGTGAGGGAGATGGTGGA
1 GACTAGGTGAAGGGGGTGGTGGTGATTTGTAATAGTAAGGAGGAGGAGGTGAGGGAGATGGTGGA
* *
66 GGTGGTGACTTATAGTAGTATGGTGGTGGGG
66 GGTGGTGACTTATAGTAGTAAGGTGGTGGAG
*
97 GACTAGGTGAAGGGGGTGGTGGTGATTTGTAATAGTAAGGAGGAGGTGGTGAGGGAGATGGTGGA
1 GACTAGGTGAAGGGGGTGGTGGTGATTTGTAATAGTAAGGAGGAGGAGGTGAGGGAGATGGTGGA
*
162 GGTGGTGACTTGTAGTAGTAAGGTGGTGGAG
66 GGTGGTGACTTATAGTAGTAAGGTGGTGGAG
* * *
193 GACTAGGTGAAGGCGGTGGTGGTGAATTGTAATCGTAAGGAG
1 GACTAGGTGAAGGGGGTGGTGGTGATTTGTAATAGTAAGGAG
235 AATACTGTTT
Statistics
Matches: 130, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 130 1.00
ACGTcount: A:0.23, C:0.03, G:0.49, T:0.25
Consensus pattern (96 bp):
GACTAGGTGAAGGGGGTGGTGGTGATTTGTAATAGTAAGGAGGAGGAGGTGAGGGAGATGGTGGA
GGTGGTGACTTATAGTAGTAAGGTGGTGGAG
Found at i:214 original size:48 final size:48
Alignment explanation
Indices: 1--234 Score: 201
Period size: 48 Copynumber: 4.9 Consensus size: 48
*
1 GACTAGGTGAAGGGGGTGGTGGTGATTTGTAGTAGTAAGGAGGAGGAG
1 GACTAGGTGAAGGGGGTGGTGGTGACTTGTAGTAGTAAGGAGGAGGAG
* * * * * * *
49 G--TGAGG-GAGATGGTGGAGGTGGTGACTTATAGTAGTATGGTGGTGGGG
1 GACT-AGGTGA-A-GGGGGTGGTGGTGACTTGTAGTAGTAAGGAGGAGGAG
* * *
97 GACTAGGTGAAGGGGGTGGTGGTGATTTGTAATAGTAAGGAGGAGGTG
1 GACTAGGTGAAGGGGGTGGTGGTGACTTGTAGTAGTAAGGAGGAGGAG
* * * *
145 G--TGAGG-GAGATGGTGGAGGTGGTGACTTGTAGTAGTAAGGTGGTGGAG
1 GACT-AGGTGA-A-GGGGGTGGTGGTGACTTGTAGTAGTAAGGAGGAGGAG
* * * *
193 GACTAGGTGAAGGCGGTGGTGGTGAATTGTAATCGTAAGGAG
1 GACTAGGTGAAGGGGGTGGTGGTGACTTGTAGTAGTAAGGAG
235 AATACTGTTT
Statistics
Matches: 144, Mismatches: 30, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
46 6 0.04
47 8 0.06
48 116 0.81
49 8 0.06
50 6 0.04
ACGTcount: A:0.23, C:0.03, G:0.49, T:0.25
Consensus pattern (48 bp):
GACTAGGTGAAGGGGGTGGTGGTGACTTGTAGTAGTAAGGAGGAGGAG
Found at i:1312 original size:19 final size:19
Alignment explanation
Indices: 1277--1314 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1267 TGTATACTTG
*
1277 ATATATATAATATTGCAAA
1 ATATATAAAATATTGCAAA
1296 ATATATAAAAGTA-TGCAAA
1 ATATATAAAA-TATTGCAAA
1315 CACTTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (19 bp):
ATATATAAAATATTGCAAA
Found at i:13166 original size:21 final size:21
Alignment explanation
Indices: 13140--13179 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13130 AAACAATTAT
13140 ACATTTATAACAACATTTGAA
1 ACATTTATAACAACATTTGAA
**
13161 ACATTTATAGTAACATTTG
1 ACATTTATAACAACATTTG
13180 GCATTCCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (21 bp):
ACATTTATAACAACATTTGAA
Found at i:13303 original size:19 final size:19
Alignment explanation
Indices: 13279--13319 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
13269 TAAAATTTAC
*
13279 AAATATAATTTTATTTATT
1 AAATATAATTTTATTTAAT
*
13298 AAATATTATTTTATTTAAT
1 AAATATAATTTTATTTAAT
13317 AAA
1 AAA
13320 ACATTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AAATATAATTTTATTTAAT
Found at i:13327 original size:20 final size:19
Alignment explanation
Indices: 13286--13327 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
13276 TACAAATATA
* *
13286 ATTTTATTTATTAAATATT
1 ATTTTATTTATAAAACATT
13305 ATTTTATTTAATAAAACATT
1 ATTTTATTT-ATAAAACATT
13325 ATT
1 ATT
13328 AATATATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTATTTATAAAACATT
Found at i:15983 original size:4 final size:4
Alignment explanation
Indices: 15974--16002 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
15964 AAGTCTCATA
15974 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
16003 TTAACGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:41689 original size:229 final size:229
Alignment explanation
Indices: 41288--41746 Score: 918
Period size: 229 Copynumber: 2.0 Consensus size: 229
41278 GGCTAATTTA
41288 AGTGAGTCAAATGAGCTTCATTTAATCAATTGATTTCTACGAGATGTTTTAAACGTATTTATCAC
1 AGTGAGTCAAATGAGCTTCATTTAATCAATTGATTTCTACGAGATGTTTTAAACGTATTTATCAC
41353 GAGTATTGATTTGTAGCCCATAATTTAAATAAGTTATTAATTGTTTTTGTCAATACTAAAATATG
66 GAGTATTGATTTGTAGCCCATAATTTAAATAAGTTATTAATTGTTTTTGTCAATACTAAAATATG
41418 GTCAGACTTGAAATTGTTGGAAGCATAATGGACACTCGATAAACTTTACAACTCGTACAACATTA
131 GTCAGACTTGAAATTGTTGGAAGCATAATGGACACTCGATAAACTTTACAACTCGTACAACATTA
41483 TTAATACGAAACGAAATACGATTACAACAAGAAC
196 TTAATACGAAACGAAATACGATTACAACAAGAAC
41517 AGTGAGTCAAATGAGCTTCATTTAATCAATTGATTTCTACGAGATGTTTTAAACGTATTTATCAC
1 AGTGAGTCAAATGAGCTTCATTTAATCAATTGATTTCTACGAGATGTTTTAAACGTATTTATCAC
41582 GAGTATTGATTTGTAGCCCATAATTTAAATAAGTTATTAATTGTTTTTGTCAATACTAAAATATG
66 GAGTATTGATTTGTAGCCCATAATTTAAATAAGTTATTAATTGTTTTTGTCAATACTAAAATATG
41647 GTCAGACTTGAAATTGTTGGAAGCATAATGGACACTCGATAAACTTTACAACTCGTACAACATTA
131 GTCAGACTTGAAATTGTTGGAAGCATAATGGACACTCGATAAACTTTACAACTCGTACAACATTA
41712 TTAATACGAAACGAAATACGATTACAACAAGAAC
196 TTAATACGAAACGAAATACGATTACAACAAGAAC
41746 A
1 A
41747 CTAACTGCAG
Statistics
Matches: 230, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
229 230 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Consensus pattern (229 bp):
AGTGAGTCAAATGAGCTTCATTTAATCAATTGATTTCTACGAGATGTTTTAAACGTATTTATCAC
GAGTATTGATTTGTAGCCCATAATTTAAATAAGTTATTAATTGTTTTTGTCAATACTAAAATATG
GTCAGACTTGAAATTGTTGGAAGCATAATGGACACTCGATAAACTTTACAACTCGTACAACATTA
TTAATACGAAACGAAATACGATTACAACAAGAAC
Found at i:55544 original size:2 final size:2
Alignment explanation
Indices: 55537--55564 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55527 GATATTGATA
55537 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
55565 GTGTGTGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59855 original size:7 final size:7
Alignment explanation
Indices: 59843--59873 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
59833 TATTATTGAG
59843 GTGGAGT
1 GTGGAGT
59850 GTGGAGT
1 GTGGAGT
59857 GTGGAGT
1 GTGGAGT
59864 GTGGAGT
1 GTGGAGT
59871 GTG
1 GTG
59874 AACATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.58, T:0.29
Consensus pattern (7 bp):
GTGGAGT
Found at i:69185 original size:17 final size:18
Alignment explanation
Indices: 69163--69202 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
69153 ACTCCACAAA
*
69163 AAATAAAA-TGGATATTT
1 AAATAAAACTAGATATTT
*
69180 AAATAAAACTATATATTT
1 AAATAAAACTAGATATTT
69198 AAATA
1 AAATA
69203 TTATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (18 bp):
AAATAAAACTAGATATTT
Found at i:71101 original size:18 final size:19
Alignment explanation
Indices: 71078--71114 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
71068 TCGCTCTTTC
71078 TTTTTAAATTTTA-TTTTA
1 TTTTTAAATTTTACTTTTA
*
71096 TTTTTAATTTTTACTTTTA
1 TTTTTAAATTTTACTTTTA
71115 AAAATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTAAATTTTACTTTTA
Found at i:71139 original size:33 final size:34
Alignment explanation
Indices: 71102--71170 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 34
71092 TTTATTTTTA
71102 ATTTT-TACTTTTAAAAATTATAT-G-ATAATATTT
1 ATTTTATA-TTTT-AAAATTATATCGTATAATATTT
*
71135 ATTTTAATATTTTTAAATTATATCGTATAATATTT
1 ATTTT-ATATTTTAAAATTATATCGTATAATATTT
71170 A
1 A
71171 ATATATAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
33 14 0.45
34 5 0.16
35 12 0.39
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (34 bp):
ATTTTATATTTTAAAATTATATCGTATAATATTT
Found at i:81587 original size:3 final size:3
Alignment explanation
Indices: 81579--81604 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
81569 TTGTGCCGCA
81579 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
81605 ATAATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:83396 original size:28 final size:29
Alignment explanation
Indices: 83338--83397 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
83328 CAACTTGACA
**
83338 TATTAATTTTTATACCTTTTTGAATAATTT
1 TATTAATTTTTATA-CTTTTAAAATAATTT
*
83368 TATTAATTTTTAT-CTTTTAAAATATTTT
1 TATTAATTTTTATACTTTTAAAATAATTT
83396 TA
1 TA
83398 GCAGAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 14 0.52
30 13 0.48
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (29 bp):
TATTAATTTTTATACTTTTAAAATAATTT
Done.