Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012521.1 Kokia drynarioides strain JFW-HI SEQ_127528, 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: 30928
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 77 characters in sequence are not A, C, G, or T
Found at i:1214 original size:40 final size:40
Alignment explanation
Indices: 1130--1222 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 40
1120 GTCTCTTTCA
* * * *
1130 AAAAAGTGTCCATTCAATATAAAAAAATTTGTGACTTTTC
1 AAAAAGTGTCCATTAAATATAAAAAAAGTTGCGACTCTTC
* * *
1170 AAAAGGTGTCCATTAAATAT-GAAAAGGTTGCGACTCTTC
1 AAAAAGTGTCCATTAAATATAAAAAAAGTTGCGACTCTTC
*
1209 AAAAAGTGTTCATT
1 AAAAAGTGTCCATT
1223 GAGTGTATAT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
39 26 0.59
40 18 0.41
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (40 bp):
AAAAAGTGTCCATTAAATATAAAAAAAGTTGCGACTCTTC
Found at i:2037 original size:18 final size:19
Alignment explanation
Indices: 2014--2050 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2004 CACATTGTTA
2014 AAATCGAATTAA-TCGATT
1 AAATCGAATTAATTCGATT
*
2032 AAATCGATTTAATTCGATT
1 AAATCGAATTAATTCGATT
2051 GGTGATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (19 bp):
AAATCGAATTAATTCGATT
Found at i:11739 original size:13 final size:13
Alignment explanation
Indices: 11721--11745 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11711 TAATTTAATA
11721 ATATAAATAAAAG
1 ATATAAATAAAAG
11734 ATATAAATAAAA
1 ATATAAATAAAA
11746 TTATTATTAT
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:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
ATATAAATAAAAG
Found at i:14255 original size:31 final size:32
Alignment explanation
Indices: 14209--14269 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
14199 GAACTATTGG
* *
14209 AAAGTTTTTTTTTTAAGTCACTAAGCTATTCA
1 AAAGTTTTTTATTTAAATCACTAAGCTATTCA
*
14241 AAAG-TTTTTATTTAAATCACTAGGCTATT
1 AAAGTTTTTTATTTAAATCACTAAGCTATT
14270 GGATGTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (32 bp):
AAAGTTTTTTATTTAAATCACTAAGCTATTCA
Found at i:22623 original size:57 final size:57
Alignment explanation
Indices: 22479--22638 Score: 211
Period size: 58 Copynumber: 2.8 Consensus size: 57
22469 TTTATATATT
* * *
22479 AAAAAATAAAAAAATAATATTATATTAGTGAATGATTATCAAATGGTGACATTATAGG
1 AAAAAATAAAAAAATAATATTATATTAGTGGAGGATTATCAAAT-GTGACACTATAGG
*
22537 AAAAAATAAAAAAATAAAATTATATTAGTGGAGGATTATCAAATGTCGA-ACCTAT-GG
1 AAAAAATAAAAAAATAATATTATATTAGTGGAGGATTATCAAATGT-GACA-CTATAGG
22594 AAAAAA-ATAAAAAATAATATTATATTAGTGGAGCG-TTATCAAATG
1 AAAAAATA-AAAAAATAATATTATATTAGTGGAG-GATTATCAAATG
22639 GCGGTACTAC
Statistics
Matches: 93, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
56 1 0.01
57 45 0.48
58 47 0.51
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.29
Consensus pattern (57 bp):
AAAAAATAAAAAAATAATATTATATTAGTGGAGGATTATCAAATGTGACACTATAGG
Found at i:22655 original size:58 final size:57
Alignment explanation
Indices: 22479--22657 Score: 193
Period size: 58 Copynumber: 3.1 Consensus size: 57
22469 TTTATATATT
* * * * *
22479 AAAAAATAAAAAAATAATATTATATTAGTGAATGATTATCAAATGG-TGACATTATAGG
1 AAAAAATAAAAAAATAATATTATATTAGTGGA-GGTTATCAAATGGCGGA-ACTATAGA
* * *
22537 AAAAAATAAAAAAATAAAATTATATTAGTGGAGGATTATCAAATGTC-GAACCTATGGA
1 AAAAAATAAAAAAATAATATTATATTAGTGGAGG-TTATCAAATGGCGGAA-CTATAGA
* *
22595 AAAAAAT-AAAAAATAATATTATATTAGTGGAGCGTTATCAAATGGCGGTACTACAAGA
1 AAAAAATAAAAAAATAATATTATATTAGTGGAG-GTTATCAAATGGCGGAACTA-TAGA
22653 AAAAA
1 AAAAA
22658 TTATACAAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
57 40 0.39
58 63 0.61
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (57 bp):
AAAAAATAAAAAAATAATATTATATTAGTGGAGGTTATCAAATGGCGGAACTATAGA
Found at i:22718 original size:136 final size:136
Alignment explanation
Indices: 22538--22817 Score: 508
Period size: 136 Copynumber: 2.1 Consensus size: 136
22528 CATTATAGGA
* *
22538 AAAAATAAAAAAATAAAATTATATTAGTGGAGGATTATCAAATGTCGAACCTATGGAAAAAAATA
1 AAAAAT-AAAAAATAAAATTATATTAGTGGAGGATTATCAAATGTCGAAACTATAGAAAAAAATA
*
22603 AAAAATAATATTATATTAGTGGAGCGTTATCAAATGGCGGTACTACAAGAAAAAATTATACAAAA
65 AAAAATAATATTATATTAGTGGAGCGTTATCAAATGACGGTACTACAAGAAAAAATTATACAAAA
22668 TACACGG
130 TACACGG
22675 AAAAATAAAAAATAAAATTATATTAGTGTG-GGATTATCAAATGTCGAAACTATAGAAAAAAATA
1 AAAAATAAAAAATAAAATTATATTAGTG-GAGGATTATCAAATGTCGAAACTATAGAAAAAAATA
22739 AAAAATAATATTATATTAGTGGAGCGTTATCAAATGACGGTACTACAAGAAAAAATTATACAAAA
65 AAAAATAATATTATATTAGTGGAGCGTTATCAAATGACGGTACTACAAGAAAAAATTATACAAAA
22804 TACACGG
130 TACACGG
22811 AAAAATA
1 AAAAATA
22818 CCTAAACATT
Statistics
Matches: 139, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
136 132 0.95
137 7 0.05
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.25
Consensus pattern (136 bp):
AAAAATAAAAAATAAAATTATATTAGTGGAGGATTATCAAATGTCGAAACTATAGAAAAAAATAA
AAAATAATATTATATTAGTGGAGCGTTATCAAATGACGGTACTACAAGAAAAAATTATACAAAAT
ACACGG
Found at i:22794 original size:57 final size:57
Alignment explanation
Indices: 22675--22793 Score: 152
Period size: 57 Copynumber: 2.1 Consensus size: 57
22665 AAATACACGG
* *
22675 AAAAATAAAAAATAAAATTATATTAGTGTGGGATTATCAAATGTCGAAACTATAGAA
1 AAAAATAAAAAATAAAATTATATTAGTGTGGGATTATCAAATGACGAAACTAAAGAA
* **
22732 AAAAATAAAAAATAATATTATATTAGTG-GAGCG-TTATCAAATGACGGTACTACAAGAA
1 AAAAATAAAAAATAAAATTATATTAGTGTG-G-GATTATCAAATGACGAAACTA-AAGAA
22790 AAAA
1 AAAA
22794 TTATACAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
56 1 0.02
57 44 0.81
58 9 0.17
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (57 bp):
AAAAATAAAAAATAAAATTATATTAGTGTGGGATTATCAAATGACGAAACTAAAGAA
Found at i:22814 original size:21 final size:21
Alignment explanation
Indices: 22789--22857 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
22779 TACTACAAGA
*
22789 AAAAATTATACAAAATACACG
1 AAAAATTATACAAAATACATG
* **
22810 GAAAA--ATACCTAA-ACATTG
1 AAAAATTATACAAAATACA-TG
22829 AAAAATTATACAAAATACATG
1 AAAAATTATACAAAATACATG
22850 AAAAATTA
1 AAAAATTA
22858 AATAACAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 11 0.30
21 20 0.54
22 3 0.08
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.22
Consensus pattern (21 bp):
AAAAATTATACAAAATACATG
Found at i:22880 original size:18 final size:18
Alignment explanation
Indices: 22857--22935 Score: 60
Period size: 18 Copynumber: 4.4 Consensus size: 18
22847 ATGAAAAATT
22857 AAATAACAAATCAATTAA
1 AAATAACAAATCAATTAA
* *
22875 AAATAACTTAAAAACTAAATAA
1 AAATAAC---AAATC-AATTAA
22897 CAAATAA-AAAT--ATT--
1 -AAATAACAAATCAATTAA
22911 AAATAACAAATCAATTAA
1 AAATAACAAATCAATTAA
22929 AAATAAC
1 AAATAAC
22936 TTAAAAATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 20
0.66 0.06 0.28
Matches are distributed among these distances:
13 6 0.13
14 4 0.09
16 5 0.11
18 14 0.30
19 3 0.06
21 4 0.09
22 5 0.11
23 6 0.13
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAACAAATCAATTAA
Found at i:22951 original size:11 final size:11
Alignment explanation
Indices: 22850--22953 Score: 56
Period size: 11 Copynumber: 9.5 Consensus size: 11
22840 AAAATACATG
22850 AAAAATTAAAT
1 AAAAATTAAAT
* *
22861 AACAAATCAATT
1 AA-AAATTAAAT
*
22873 AAAAA-TAACTT
1 AAAAATTAA-AT
*
22884 AAAAACTAAAT
1 AAAAATTAAAT
22895 AACAAA-T-AA-
1 AA-AAATTAAAT
*
22904 AAATATTAAAT
1 AAAAATTAAAT
* *
22915 AACAAATCAATT
1 AA-AAATTAAAT
*
22927 AAAAA-TAACTT
1 AAAAATTAA-AT
22938 AAAAATTAAAT
1 AAAAATTAAAT
22949 AAAAA
1 AAAAA
22954 AATATTAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
8 2 0.03
9 3 0.04
10 8 0.11
11 34 0.47
12 26 0.36
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATTAAAT
Found at i:22962 original size:15 final size:14
Alignment explanation
Indices: 22938--22969 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
22928 AAAATAACTT
22938 AAAAATTAAATAAA
1 AAAAATTAAATAAA
22952 AAAATATTAAATAAA
1 AAAA-ATTAAATAAA
22967 AAA
1 AAA
22970 TCAATTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAATTAAATAAA
Found at i:22974 original size:49 final size:51
Alignment explanation
Indices: 22841--22977 Score: 190
Period size: 54 Copynumber: 2.7 Consensus size: 51
22831 AAATTATACA
* *
22841 AAATACATGAAAA-ATTAAATAACAAATCAATTAAAAATAACTTAAAAACT
1 AAATAAATAAAAATATTAAATAACAAATCAATTAAAAATAACTTAAAAACT
*
22891 AAATAACAAATAAAAATATTAAATAACAAATCAATTAAAAATAACTTAAAAATT
1 AAAT---AAATAAAAATATTAAATAACAAATCAATTAAAAATAACTTAAAAACT
*
22945 AAAT-AA-AAAAATATTAAATAAAAAATCAATTAA
1 AAATAAATAAAAATATTAAATAACAAATCAATTAA
22978 GAATTAAATT
Statistics
Matches: 79, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
49 26 0.33
50 6 0.08
53 7 0.09
54 40 0.51
ACGTcount: A:0.67, C:0.07, G:0.01, T:0.25
Consensus pattern (51 bp):
AAATAAATAAAAATATTAAATAACAAATCAATTAAAAATAACTTAAAAACT
Found at i:30753 original size:22 final size:22
Alignment explanation
Indices: 30720--30770 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
30710 TGTGGGGGTG
30720 TGGGAGGCAAAGATGTTGGGGAT
1 TGGG-GGCAAAGATGTTGGGGAT
30743 TGGGGGCAAAGATGTTGGGGAT
1 TGGGGGCAAAGATGTTGGGGAT
30765 TGGGGG
1 TGGGGG
30771 AAATTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.22, C:0.04, G:0.53, T:0.22
Consensus pattern (22 bp):
TGGGGGCAAAGATGTTGGGGAT
Done.