Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011728.1 Kokia drynarioides strain JFW-HI SEQ_126722, 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: 3442
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Warning! 57 characters in sequence are not A, C, G, or T
Found at i:363 original size:205 final size:206
Alignment explanation
Indices: 1--393 Score: 522
Period size: 205 Copynumber: 1.9 Consensus size: 206
* *
1 CAAATCCTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGGCGAAGCAATAAAATGGTTA
1 CAAATCCTCGAACCACAGCTTCCTGATGAGATACTAAGAAGCAAGGCGAAGCAATAAAATGGTTA
* * * * * * *
66 GCTTCCTGATGAGATATTGAGAAATGGACCAAATTCGTCTTCTTGATGAGATACAGAGGAGCGGA
66 GCTTCCTGATGAAATACTAAGAAATGAACCAAATCCGTCTTCTTGATGAAATACAGAGAAGCGGA
*** * *
131 TTGGAATAAGCGATACAGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACTCATG
131 TCAAAACAAGCGATACAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCATG
196 CTCGATGTGAG
196 CTCGATGTGAG
* *
207 CAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAA-AAGCAAGTCGAAGCAAT-AAATGGTT
1 CAAATCCTCGAACCACAGCTTCCTGATGAGATACT-AAGAAGCAAGGCGAAGCAATAAAATGGTT
* * *
270 AGCTTCCT-ATTGAAATACTAAGAAGTGAACCAAATCCGTCTTCTTGATGAAATTCAGAGAAGTG
65 AGCTTCCTGA-TGAAATACTAAGAAATGAACCAAATCCGTCTTCTTGATGAAATACAGAGAAGCG
* ** * * *
334 GATCAAAACAAGTGATATGGTCGTCTTCCTGATGAGATACTGAGAAGAAGGCCAAGTCAA
129 GATCAAAACAAGCGATACAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
394 TGAAACTAGA
Statistics
Matches: 160, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
204 1 0.01
205 109 0.68
206 48 0.30
207 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (206 bp):
CAAATCCTCGAACCACAGCTTCCTGATGAGATACTAAGAAGCAAGGCGAAGCAATAAAATGGTTA
GCTTCCTGATGAAATACTAAGAAATGAACCAAATCCGTCTTCTTGATGAAATACAGAGAAGCGGA
TCAAAACAAGCGATACAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCATG
CTCGATGTGAG
Found at i:765 original size:6 final size:6
Alignment explanation
Indices: 743--840 Score: 69
Period size: 6 Copynumber: 16.5 Consensus size: 6
733 TTTTAAGTTG
* * *
743 ATTTAA ATTTAT TTTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTTATCT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTA--A
* * * **
792 TTTTAA ATTTAA ATTT-G CTTTAA ATTTAA ATTT-A ATCAAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
838 ATT
1 ATT
841 GATATTAAAT
Statistics
Matches: 69, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
4 2 0.03
5 8 0.12
6 53 0.77
7 2 0.03
8 4 0.06
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:779 original size:17 final size:17
Alignment explanation
Indices: 743--851 Score: 105
Period size: 17 Copynumber: 6.2 Consensus size: 17
733 TTTTAAGTTG
*
743 ATTTAAATTTATTTTTAA
1 ATTTAAATTTA-TCTTAA
761 ATTTAAATTTATCTTAA
1 ATTTAAATTTATCTTAA
778 ATTTAAATTTATCTTTTTAA
1 ATTTAAATTTATC---TTAA
*
798 ATTTAAATTT-GCTTTAA
1 ATTTAAATTTATC-TTAA
*
815 ATTTAAATTTAATC-AAA
1 ATTTAAATTT-ATCTTAA
* *
832 ATTTAAATTGATATTAA
1 ATTTAAATTTATCTTAA
849 ATT
1 ATT
852 AAAAACCCAA
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
16 2 0.03
17 49 0.63
18 11 0.14
19 2 0.03
20 14 0.18
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATCTTAA
Found at i:802 original size:37 final size:35
Alignment explanation
Indices: 743--825 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 35
733 TTTTAAGTTG
*
743 ATTTAAATTTATTTTTAAATTTAAATTT-ATCTTAA
1 ATTTAAATTTATTTTTAAATTTAAATTTGCT-TTAA
778 ATTTAAATTTATCTTTTTAAATTTAAATTTGCTTTAA
1 ATTTAAATTTA--TTTTTAAATTTAAATTTGCTTTAA
815 ATTTAAATTTA
1 ATTTAAATTTA
826 ATCAAAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 11 0.25
37 32 0.73
38 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.57
Consensus pattern (35 bp):
ATTTAAATTTATTTTTAAATTTAAATTTGCTTTAA
Found at i:855 original size:23 final size:23
Alignment explanation
Indices: 810--855 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
800 TTAAATTTGC
* *
810 TTTAAATTTAAATTTAATCAAAA
1 TTTAAATTGAAATTAAATCAAAA
* *
833 TTTAAATTGATATTAAATTAAAA
1 TTTAAATTGAAATTAAATCAAAA
856 ACCCAAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTAAATTGAAATTAAATCAAAA
Found at i:1574 original size:22 final size:21
Alignment explanation
Indices: 1548--1601 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
1538 TCTATAGTAT
* *
1548 TTAATAAATAAGCAATAAATA
1 TTAATAAATAAGAAAAAAATA
**
1569 TATAATAAATATTAAAAAAATA
1 T-TAATAAATAAGAAAAAAATA
1591 TTAATAAATAA
1 TTAATAAATAA
1602 TATTATTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
TTAATAAATAAGAAAAAAATA
Found at i:1575 original size:11 final size:11
Alignment explanation
Indices: 1561--1623 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
1551 ATAAATAAGC
1561 AATAAATATAT
1 AATAAATATAT
1572 AATAAATAT-T
1 AATAAATATAT
*
1582 AA-AAAAATATT
1 AATAAATATA-T
1593 AATAAATAATAT
1 AATAAAT-ATAT
* *
1605 TATTAATA-AT
1 AATAAATATAT
1615 AAATAAATA
1 -AATAAATA
1624 AAGGGAGTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
9 5 0.12
10 5 0.12
11 19 0.46
12 9 0.22
13 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAAATATAT
Found at i:2792 original size:30 final size:29
Alignment explanation
Indices: 2756--3061 Score: 264
Period size: 29 Copynumber: 10.4 Consensus size: 29
2746 ACCATTCGAC
*
2756 AATTCCATTTTTAACCCCCGAACTTCCAAA
1 AATTCCATTTTT-ACCCCCAAACTTCCAAA
** *
2786 AATTCCATTTTTAGTCCCAAACTTTCAAA
1 AATTCCATTTTTACCCCCAAACTTCCAAA
* *
2815 AATTACATTTTTAACCCCAAAACTTCCAAA
1 AATTCCATTTTT-ACCCCCAAACTTCCAAA
* *
2845 AATTCCA-TCTTACCCCTAAACTTCCAAA
1 AATTCCATTTTTACCCCCAAACTTCCAAA
*
2873 AATTCCATTTTTGA-CCCCAACACTTCTAAA
1 AATTCCATTTTT-ACCCCCAA-ACTTCCAAA
* * *
2903 AATTCCATTTTTGATCTCAAAACTTCCAAA
1 AATTCCATTTTT-ACCCCCAAACTTCCAAA
* * *
2933 AATTCCATTTTTACCCTCGAACTTTCAAA
1 AATTCCATTTTTACCCCCAAACTTCCAAA
*
2962 AATTCCATTTTTGACCCCAAAAC-TCTC-AA
1 AATTCCATTTTT-ACCCCCAAACTTC-CAAA
* * *
2991 AATTAC-TCTTTTACCCCCGAA-TGTCTAAA
1 AATTCCAT-TTTTACCCCCAAACT-TCCAAA
* * * *
3020 AATTTCATTTTTAACCCCGAACTTTCCCAA
1 AATTCCATTTTTACCCCCAAAC-TTCCAAA
3050 AATTACCATTTT
1 AATT-CCATTTT
3062 GCCTCGAGAA
Statistics
Matches: 224, Mismatches: 37, Indels: 29
0.77 0.13 0.10
Matches are distributed among these distances:
28 31 0.14
29 91 0.41
30 91 0.41
31 11 0.05
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
AATTCCATTTTTACCCCCAAACTTCCAAA
Found at i:2956 original size:117 final size:117
Alignment explanation
Indices: 2756--2969 Score: 292
Period size: 117 Copynumber: 1.8 Consensus size: 117
2746 ACCATTCGAC
* * *
2756 AATTCCATTTTTAACCCCCGAACTTCCAAAAATTCCATTTTTAGTCCCAAACTTTCAAAAATTAC
1 AATTCCATTTTTAACCCCCAAACTTCCAAAAATTCCATTTTTAGTCCAAAACTTCCAAAAATTAC
2821 ATTTTTAACCCCAAAACTTCCAAAAATTCCATCTTACCCCTAAACTTCCAAA
66 ATTTTTAACCCCAAAACTTCCAAAAATTCCATCTTACCCCTAAACTTCCAAA
* *
2873 AATTCCATTTTTGA-CCCCAACACTTCTAAAAATTCCATTTTT-GATCTCAAAACTTCCAAAAAT
1 AATTCCATTTTTAACCCCCAA-ACTTCCAAAAATTCCATTTTTAG-TC-CAAAACTTCCAAAAAT
* * *
2936 TCCATTTTT-ACCCTC-GAACTTTCAAAAATTCCAT
63 TACATTTTTAACCC-CAAAACTTCCAAAAATTCCAT
2970 TTTTGACCCC
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
116 6 0.07
117 56 0.66
118 23 0.27
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.34
Consensus pattern (117 bp):
AATTCCATTTTTAACCCCCAAACTTCCAAAAATTCCATTTTTAGTCCAAAACTTCCAAAAATTAC
ATTTTTAACCCCAAAACTTCCAAAAATTCCATCTTACCCCTAAACTTCCAAA
Found at i:3052 original size:147 final size:148
Alignment explanation
Indices: 2776--3061 Score: 352
Period size: 147 Copynumber: 1.9 Consensus size: 148
2766 TTAACCCCCG
*
2776 AACTTCCAAAAATTCCATTTTTAGTCCCAAACTTTCAAAAATTACATTTTTAACCCCAAAACTTC
1 AACTTCCAAAAATTCCATTTTTAGCCCCAAACTTTCAAAAATTACATTTTTAACCCCAAAACTTC
* * *
2841 CAAAAATTCCATCTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCAACACTTCTAAAAAT
66 CAAAAATTCCATCTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCCCAACACTTCCAAAAAT
2906 T-CCATTTTTGATCTCAA
131 TACCATTTTTGATCTCAA
* * *
2923 AACTTCCAAAAATTCCATTTTTA-CCCTCGAACTTTCAAAAATTCCATTTTTGACCCCAAAAC-T
1 AACTTCCAAAAATTCCATTTTTAGCCC-CAAACTTTCAAAAATTACATTTTTAACCCCAAAACTT
* * * * *
2986 CTC-AAAATTACTC-TTTTACCCCCGAA-TGTCTAAAAATTTCATTTTTAACCCCGAAC-TTTCC
65 C-CAAAAATT-C-CATCTTACCCCCAAACT-TCCAAAAATTCCATTTTTAACCCC-AACACTTCC
*
3047 CAAAATTACCATTTT
125 AAAAATTACCATTTT
3062 GCCTCGAGAA
Statistics
Matches: 119, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
146 11 0.09
147 97 0.82
148 11 0.09
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (148 bp):
AACTTCCAAAAATTCCATTTTTAGCCCCAAACTTTCAAAAATTACATTTTTAACCCCAAAACTTC
CAAAAATTCCATCTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCCCAACACTTCCAAAAAT
TACCATTTTTGATCTCAA
Found at i:3115 original size:87 final size:87
Alignment explanation
Indices: 2761--3126 Score: 215
Period size: 87 Copynumber: 4.2 Consensus size: 87
2751 TCGACAATTC
* * *
2761 CATTTTTAACCCCCGAACTTCCAAAAATTCCATTTTT-AGTCCC-AAACTTTCAAAAATTACAT-
1 CATTTTTAA-CCCCGAACTTTCAAAAATTCCATTTTTGA-CCCCAAAACTCTC-AAAATTAC-TC
* *
2823 TTTTAACCCC-AAAACTTCCAAAAAT-T
62 TTTTACCCCCGAATA--TCCAAAAATCT
* * * * * *
2849 CCA-TCTT-ACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCAACACTTCTAAAAATTCCAT-
1 -CATTTTTAACCCC-GAACTTTCAAAAATTCCATTTTTGACCCCAAAAC-TCTCAAAATTAC-TC
* * **
2911 TTTTGATCTCAAAACT-TCCAAAAAT-T
62 TTTT-ACCCCCGAA-TATCCAAAAATCT
2937 CCATTTTT-ACCCTCGAACTTTCAAAAATTCCATTTTTGACCCCAAAACTCTCAAAATTACTCTT
1 -CATTTTTAACCC-CGAACTTTCAAAAATTCCATTTTTGACCCCAAAACTCTCAAAATTACTCTT
* * *
3001 TTACCCCCGAATGTCTAAAAATTT
64 TTACCCCCGAATATCCAAAAATCT
* * *
3025 CATTTTTAACCCCGAACTTTCCCAAAATTACCA-TTTTG-CCTCGAGAA-TC-CAAAATTAC-CA
1 CATTTTTAACCCCGAACTTT-CAAAAATT-CCATTTTTGACC-CCAAAACTCTCAAAATTACTC-
* * *
3085 TTTTGCCCCCTAGTATCCAAAAAGTCT
62 TTTTACCCCCGAATATCCAAAAA-TCT
* *
3112 CATTTTCAACTCCGA
1 CATTTTTAACCCCGA
3127 TTGCATCATT
Statistics
Matches: 226, Mismatches: 33, Indels: 38
0.76 0.11 0.13
Matches are distributed among these distances:
85 1 0.00
86 32 0.14
87 74 0.33
88 68 0.30
89 48 0.21
90 3 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (87 bp):
CATTTTTAACCCCGAACTTTCAAAAATTCCATTTTTGACCCCAAAACTCTCAAAATTACTCTTTT
ACCCCCGAATATCCAAAAATCT
Done.