Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010276.1 Kokia drynarioides strain JFW-HI SEQ_125120, 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: 19314
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:386 original size:3 final size:3
Alignment explanation
Indices: 378--409 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
368 TTAATTACTA
378 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
410 GTTTTGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1055 original size:6 final size:6
Alignment explanation
Indices: 1044--1105 Score: 78
Period size: 6 Copynumber: 10.7 Consensus size: 6
1034 ATTATTTAAA
1044 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT TAAATT TATAA--
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TA-AATT
1090 TAAATT TAAATT TAAA
1 TAAATT TAAATT TAAA
1106 ATAAACTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
4 4 0.08
5 4 0.08
6 38 0.76
7 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:1072 original size:17 final size:17
Alignment explanation
Indices: 1073--1135 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
1063 ATAATAAATT
*
1073 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
1090 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
1107 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
* *
1124 TATATTCAAATT
1 TAAATTTAAATT
1136 CTGTTGGGCC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:1072 original size:23 final size:23
Alignment explanation
Indices: 1037--1105 Score: 131
Period size: 23 Copynumber: 3.0 Consensus size: 23
1027 ATTAGACATT
1037 ATTTA-AATAAATTTAAATTTAA
1 ATTTATAATAAATTTAAATTTAA
1059 ATTTATAATAAATTTAAATTTAA
1 ATTTATAATAAATTTAAATTTAA
1082 ATTTATAATAAATTTAAATTTAA
1 ATTTATAATAAATTTAAATTTAA
1105 A
1 A
1106 ATAAACTTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 5 0.11
23 41 0.89
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTATAATAAATTTAAATTTAA
Found at i:2079 original size:115 final size:112
Alignment explanation
Indices: 1761--2085 Score: 326
Period size: 116 Copynumber: 2.8 Consensus size: 112
1751 TCACTTCTTA
* * *
1761 GTATCTCATCAGGAACCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
1 GTATCTCATCAGAAAGCTAACCA-TTTATT-CTTTGACCTGCTTCTCAGTATCTCATCAGGAAGC
** * * * *
1826 TGGGGTTTGAAGATTTGCTCGTATCGAGTCCTGAGTTGATATTCTTCTTT
64 TGGGGTTTGAAGATTTGCTCACATCGAG-CCTAAGTTGATATACTCCTCT
* * ** * * ** *
1876 GTATCTCATCAGAAAGATGACCGCCTTACTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAG
1 GTATCTCATCAGAAAGCTAACC-ATTTA-TTCTTTGACCT-GCTTCTCAGTATCTCATCAGGAAG
* * * *
1941 CTGAGATTTGAAGATTTGATCACATCGAGCCTTAAGTTGGTATACTCCTCT
63 CTGGGGTTTGAAGATTTGCTCACATCGAGCC-TAAGTTGATATACTCCTCT
* * * *
1992 GTGTCTCATCAGAAAGCTAACCATTTCATTATTTTGACCTACTTCTCAGTATATCATCAGGAAGC
1 GTATCTCATCAGAAAGCTAACCATTT-ATT-CTTTGACCTGCTTCTCAGTATCTCATCAGGAAGC
*
2057 TGGGGTTCGAAGATTTGCTCACATCGAGC
64 TGGGGTTTGAAGATTTGCTCACATCGAGC
2086 GTGGGTTTGA
Statistics
Matches: 166, Mismatches: 38, Indels: 12
0.77 0.18 0.06
Matches are distributed among these distances:
115 78 0.47
116 88 0.53
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (112 bp):
GTATCTCATCAGAAAGCTAACCATTTATTCTTTGACCTGCTTCTCAGTATCTCATCAGGAAGCTG
GGGTTTGAAGATTTGCTCACATCGAGCCTAAGTTGATATACTCCTCT
Found at i:13907 original size:29 final size:28
Alignment explanation
Indices: 13875--13937 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
13865 AAAACGAGAC
13875 TTTTCGGATACCTGGGGGCAAAATGGTAA
1 TTTT-GGATACCTGGGGGCAAAATGGTAA
* * **
13904 TTTTGGATTCTTGGGGGTGAAATGGTAA
1 TTTTGGATACCTGGGGGCAAAATGGTAA
13932 TTTTGG
1 TTTTGG
13938 GAAAATTTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.22, C:0.08, G:0.33, T:0.37
Consensus pattern (28 bp):
TTTTGGATACCTGGGGGCAAAATGGTAA
Found at i:14071 original size:30 final size:29
Alignment explanation
Indices: 14032--14349 Score: 322
Period size: 30 Copynumber: 10.7 Consensus size: 29
14022 GGGGGGTAAT
14032 ATGGTAATTTTTGGAAGTTTCAGGGTCAAAA
1 ATGG-AATTTTTGGAAGTTTCAGGGT-AAAA
* *
14063 ATGGAATTTTTTGAAGTTTGAGGGTAAAAAA
1 ATGGAATTTTTGGAAGTTTCAGGGT--AAAA
*
14094 ATGGAATTTTTGGAAGTTT-TGAGGTAAAAA
1 ATGGAATTTTTGGAAGTTTCAG-GGT-AAAA
* *
14124 ATAGAATCTTTGGAAG-TTCGAGGGTAAAA
1 ATGGAATTTTTGGAAGTTTC-AGGGTAAAA
*
14153 GTGGAATTTTTGGAAGTTTC-GAGGTCAAAA
1 ATGGAATTTTTGGAAGTTTCAG-GGT-AAAA
*
14183 ATGGAATTTTTGGAAG-TTCGAGGGTAAAT
1 ATGGAATTTTTGGAAGTTTC-AGGGTAAAA
* * **
14212 GTGGAAGTTTTGGAAGTTTTGGGGTAAAAA
1 ATGGAATTTTTGGAAGTTTCAGGGT-AAAA
14242 ATGGAATTTTTGGAAG-TTCAAGGGTAAAA
1 ATGGAATTTTTGGAAGTTTC-AGGGTAAAA
* *
14271 ATGGAATTTTTTGAAGTTTTAGGGTAAAAA
1 ATGGAATTTTTGGAAGTTTCAGGGT-AAAA
*
14301 ATGGAATTTTTGGAAGTTTCGGGGTAAAA
1 ATGGAATTTTTGGAAGTTTCAGGGTAAAA
** *
14330 ATTAAATTTTCGGACAGTTT
1 ATGGAATTTTTGGA-AGTTT
14350 AAGGACCTCC
Statistics
Matches: 242, Mismatches: 30, Indels: 31
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.00
29 87 0.36
30 123 0.51
31 31 0.13
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
ATGGAATTTTTGGAAGTTTCAGGGTAAAA
Found at i:14177 original size:59 final size:59
Alignment explanation
Indices: 14032--14349 Score: 381
Period size: 59 Copynumber: 5.3 Consensus size: 59
14022 GGGGGGTAAT
* * *
14032 ATGGTAATTTTTGGAAGTTTC-AGGGTCAAAAATGGAATTTTTTGAAGTTTGAGGGTAAAAAA
1 ATGG-AATTTTTGGAAGTTTCGA-GGTAAAAAATGGAATTTTTGGAAGTTCGAGGGT--AAAA
* * *
14094 ATGGAATTTTTGGAAGTTTTGAGGTAAAAAATAGAATCTTTGGAAGTTCGAGGGTAAAA
1 ATGGAATTTTTGGAAGTTTCGAGGTAAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAA
* * *
14153 GTGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAT
1 ATGGAATTTTTGGAAGTTTCGAGGTAAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAA
* * * * *
14212 GTGGAAGTTTTGGAAGTTTTGGGGTAAAAAATGGAATTTTTGGAAGTTCAAGGGTAAAA
1 ATGGAATTTTTGGAAGTTTCGAGGTAAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAA
* *
14271 ATGGAATTTTTTGAAGTTT-TAGGGTAAAAAATGGAATTTTTGGAAGTTTCG-GGGTAAAA
1 ATGGAATTTTTGGAAGTTTCGA-GGTAAAAAATGGAATTTTTGGAAG-TTCGAGGGTAAAA
** *
14330 ATTAAATTTTCGGACAGTTT
1 ATGGAATTTTTGGA-AGTTT
14350 AAGGACCTCC
Statistics
Matches: 224, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
59 168 0.75
60 8 0.04
61 43 0.19
62 5 0.02
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (59 bp):
ATGGAATTTTTGGAAGTTTCGAGGTAAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAA
Found at i:15452 original size:3 final size:3
Alignment explanation
Indices: 15446--15484 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
15436 AAAGTTACAT
15446 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15485 ATGATACTTA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16118 original size:13 final size:13
Alignment explanation
Indices: 16100--16124 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16090 TTGGGCTTGA
16100 TTTGTAATTGGAC
1 TTTGTAATTGGAC
16113 TTTGTAATTGGA
1 TTTGTAATTGGA
16125 TATTATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (13 bp):
TTTGTAATTGGAC
Found at i:16686 original size:2 final size:2
Alignment explanation
Indices: 16681--16706 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16671 GGTTTCAACA
16681 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
16707 CTTAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18123 original size:8 final size:8
Alignment explanation
Indices: 18107--18143 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
18097 CAAATCTCAA
18107 AAAAATTG
1 AAAAATTG
*
18115 AAAATTTG
1 AAAAATTG
18123 AAAAATTG
1 AAAAATTG
18131 AAAAATTG
1 AAAAATTG
18139 AAAAA
1 AAAAA
18144 ATATAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (8 bp):
AAAAATTG
Found at i:19266 original size:10 final size:10
Alignment explanation
Indices: 19247--19304 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
19237 TAATGATTTA
*
19247 AATTATTATT
1 AATTAATATT
19257 AATTAATATT
1 AATTAATATT
19267 -A-TAATA-T
1 AATTAATATT
*
19274 AA-TAATATA
1 AATTAATATT
*
19283 AATTATTATTT
1 AATTAATA-TT
19294 AATTAATATT
1 AATTAATATT
19304 A
1 A
19305 TTTTATTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
7 1 0.03
8 11 0.28
9 3 0.08
10 16 0.41
11 8 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AATTAATATT
Done.