Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009420.1 Kokia drynarioides strain JFW-HI SEQ_124127, 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: 97356
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Warning! 130 characters in sequence are not A, C, G, or T
Found at i:11956 original size:31 final size:31
Alignment explanation
Indices: 11915--11973 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
11905 TAGATTAAAA
* *
11915 CAAACTCATATATTAAATTAAATATTAAATT
1 CAAACTCATATACTAAATGAAATATTAAATT
* *
11946 CAAATTCATATACTAAATGATATATTAA
1 CAAACTCATATACTAAATGAAATATTAA
11974 CCTAAAACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (31 bp):
CAAACTCATATACTAAATGAAATATTAAATT
Found at i:22153 original size:1 final size:1
Alignment explanation
Indices: 22097--22133 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
22087 TTCAAAAAGT
22097 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22134 NNNNNNNNNN
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22298 original size:28 final size:28
Alignment explanation
Indices: 22220--22323 Score: 102
Period size: 28 Copynumber: 3.5 Consensus size: 28
22210 TCCAGCATAA
22220 TTGACTCATCATATATTGGTGATTGTGATT
1 TTGA-TCA-CATATATTGGTGATTGTGATT
* *
22250 TTAATCACATATA-TGCTTGATTGTGATT
1 TTGATCACATATATTG-GTGATTGTGATT
*
22278 TTGATGACATATATTGGTGATGGTGATTGATT
1 TTGATCACATATATTGGTGAT--TG--TGATT
*
22310 TTGATTACATATAT
1 TTGATCACATATAT
22324 GTTTGATTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
27 2 0.03
28 32 0.52
29 5 0.08
30 5 0.08
32 18 0.29
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (28 bp):
TTGATCACATATATTGGTGATTGTGATT
Found at i:29242 original size:28 final size:28
Alignment explanation
Indices: 29189--29257 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
29179 GGGTGGTCGA
29189 ATTTGGGGA-TTTTGGGTAAGAGTTTTG
1 ATTTGGGGATTTTTGGGTAAGAGTTTTG
** * *
29216 ATTTGGGGATTTTTGTTTAGGATTTTTG
1 ATTTGGGGATTTTTGGGTAAGAGTTTTG
*
29244 ATTTTGGAGATTTT
1 A-TTTGGGGATTTT
29258 AGGTTAGTGC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 9 0.26
28 15 0.43
29 11 0.31
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.52
Consensus pattern (28 bp):
ATTTGGGGATTTTTGGGTAAGAGTTTTG
Found at i:29825 original size:30 final size:30
Alignment explanation
Indices: 29791--29885 Score: 82
Period size: 37 Copynumber: 2.9 Consensus size: 30
29781 ATGTTAAAAA
29791 TATATTTTAATATAATAATTTTAATAATTT
1 TATATTTTAATATAATAATTTTAATAATTT
*
29821 TATATTTGAAAATATAATATAATATTTTTAATAATTT
1 TATA-TT-----T-TAATATAATAATTTTAATAATTT
* * * *
29858 TAGATTTCAAAAAAATAATTTTAATAAT
1 TATATTTTAATATAATAATTTTAATAAT
29886 CTTAAAATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
30 21 0.40
31 3 0.06
36 3 0.06
37 25 0.48
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (30 bp):
TATATTTTAATATAATAATTTTAATAATTT
Found at i:29839 original size:37 final size:37
Alignment explanation
Indices: 29798--29869 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
29788 AAATATATTT
* *
29798 TAATATAATAATTTTAATAATTTTATATTTGAAAATA
1 TAATATAATAATTTTAATAATTTTAGATTTCAAAATA
*
29835 TAATATAATATTTTTAATAATTTTAGATTTCAAAA
1 TAATATAATAATTTTAATAATTTTAGATTTCAAAA
29870 AAATAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (37 bp):
TAATATAATAATTTTAATAATTTTAGATTTCAAAATA
Found at i:42905 original size:17 final size:18
Alignment explanation
Indices: 42878--42911 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42868 GTTTTAGAAA
*
42878 ATATGCCAAAATTTTCAC
1 ATATGCCAAAATCTTCAC
42896 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
42912 TAATTGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.32
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:47545 original size:31 final size:31
Alignment explanation
Indices: 47510--47570 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
47500 AACAAAATGA
* *
47510 TCATTGAACTATTCGAAAGTTTTCATTTAAG
1 TCATTGAACTAGTCGAAAATTTTCATTTAAG
*
47541 TCATTGAACTAGTCGAAAATTTTTATTTAA
1 TCATTGAACTAGTCGAAAATTTTCATTTAA
47571 ATCACTGGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (31 bp):
TCATTGAACTAGTCGAAAATTTTCATTTAAG
Found at i:64064 original size:17 final size:17
Alignment explanation
Indices: 64042--64086 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
64032 GTGCAAGTTG
64042 TGTTTATATGCTAGCTA
1 TGTTTATATGCTAGCTA
* *
64059 TGTTTATATGCTAGTTG
1 TGTTTATATGCTAGCTA
64076 TGTTTATATGC
1 TGTTTATATGC
64087 AAACTATGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.51
Consensus pattern (17 bp):
TGTTTATATGCTAGCTA
Found at i:64150 original size:35 final size:35
Alignment explanation
Indices: 64093--64170 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
64083 ATGCAAACTA
*
64093 TGTCAATG-TGTGGACCGTGTAAATGTGCAAGTTG
1 TGTCAATGTTGTGGACCGCGTAAATGTGCAAGTTG
*
64127 TGTCAATGTTGTGGACTGCGTAAATGTGCAAGTTG
1 TGTCAATGTTGTGGACCGCGTAAATGTGCAAGTTG
64162 TGTCAATGT
1 TGTCAATGT
64171 GTGAATTGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 8 0.20
35 33 0.80
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.35
Consensus pattern (35 bp):
TGTCAATGTTGTGGACCGCGTAAATGTGCAAGTTG
Found at i:67499 original size:12 final size:12
Alignment explanation
Indices: 67482--67517 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
67472 ATTTATGATT
*
67482 AATTAAATTAAA
1 AATTAATTTAAA
*
67494 AATTAATTTATA
1 AATTAATTTAAA
67506 AATTAATTTAAA
1 AATTAATTTAAA
67518 TATAAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AATTAATTTAAA
Found at i:69505 original size:2 final size:2
Alignment explanation
Indices: 69500--69525 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
69490 TTATTTTTAA
69500 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
69526 GTTGGAAGGA
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:74760 original size:22 final size:22
Alignment explanation
Indices: 74732--74778 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
74722 AGATAGTGGC
74732 TTAGAGTTCTATTCTGATGAGT
1 TTAGAGTTCTATTCTGATGAGT
*
74754 TTAGAGTTCTGTTCTGATGAGT
1 TTAGAGTTCTATTCTGATGAGT
74776 TTA
1 TTA
74779 ATGAATTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.09, G:0.23, T:0.47
Consensus pattern (22 bp):
TTAGAGTTCTATTCTGATGAGT
Found at i:75749 original size:17 final size:17
Alignment explanation
Indices: 75727--75765 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
75717 AGGTGGAGAA
* *
75727 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
75744 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
75761 CTTGT
1 CTTGT
75766 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:75812 original size:41 final size:41
Alignment explanation
Indices: 75755--75850 Score: 140
Period size: 41 Copynumber: 2.3 Consensus size: 41
75745 TTGTTCGTAG
* * *
75755 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTTGA-TGATT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAA-TTGAGTAACT
*
75796 AGAATTATTGTTAAGGTGGAGATTGTTAGAATTGAGTAACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGAGTAACT
75837 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
75851 AATAAAATTC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
40 4 0.08
41 45 0.92
ACGTcount: A:0.32, C:0.04, G:0.25, T:0.39
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGAGTAACT
Found at i:79044 original size:16 final size:15
Alignment explanation
Indices: 79020--79054 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
79010 ATTTTTTCCC
*
79020 AAATTTAAAAATATA
1 AAATCTAAAAATATA
79035 TAAATCTAAAAATATA
1 -AAATCTAAAAATATA
79051 AAAT
1 AAAT
79055 TTATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATCTAAAAATATA
Found at i:79821 original size:3 final size:3
Alignment explanation
Indices: 79813--79844 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
79803 TCTATTTAAG
*
79813 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
79845 TGATGTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:84225 original size:14 final size:14
Alignment explanation
Indices: 84206--84254 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
84196 TTTTGTTTTC
84206 AAATAAAGAATGGG
1 AAATAAAGAATGGG
*
84220 AAATAAA-ATTAGGG
1 AAATAAAGAAT-GGG
*
84234 TAATAAAGAATGGG
1 AAATAAAGAATGGG
84248 AAATAAA
1 AAATAAA
84255 ATTAGGGTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 25 0.86
15 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.18
Consensus pattern (14 bp):
AAATAAAGAATGGG
Found at i:84270 original size:28 final size:28
Alignment explanation
Indices: 84207--84262 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
84197 TTTGTTTTCA
84207 AATAAAGAATGGGAAATAAAATTAGGGT
1 AATAAAGAATGGGAAATAAAATTAGGGT
84235 AATAAAGAATGGGAAATAAAATTAGGGT
1 AATAAAGAATGGGAAATAAAATTAGGGT
84263 CCAAAAGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.25, T:0.21
Consensus pattern (28 bp):
AATAAAGAATGGGAAATAAAATTAGGGT
Found at i:89308 original size:22 final size:22
Alignment explanation
Indices: 89251--89353 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 22
89241 GCTGGGGAAA
*
89251 CAGTAAGCACACATAGTGCAAT
1 CAGTAGGCACACATAGTGCAAT
* *
89273 CCAGTAGGTACACACAGTGCAAT
1 -CAGTAGGCACACATAGTGCAAT
* *
89296 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACATAGTGC-AAT
* *
89319 CAGTAAGCACACGA-AGTGCGAAA
1 CAGTAGGCACAC-ATAGTGC-AAT
*
89342 CAGTAAGCACAC
1 CAGTAGGCACAC
89354 GAAGTGCGAA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
22 15 0.23
23 50 0.76
24 1 0.02
ACGTcount: A:0.39, C:0.25, G:0.22, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACATAGTGCAAT
Found at i:89354 original size:23 final size:23
Alignment explanation
Indices: 89319--89372 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
89309 TAGCGCAAAT
89319 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
89342 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
89365 CAGTAAGC
1 CAGTAAGC
89373 GCGCTAGCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.22, G:0.26, T:0.09
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:91591 original size:23 final size:23
Alignment explanation
Indices: 91565--91609 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
91555 ATCCTTTTTT
**
91565 ATTTTAATTCTATTTTTTAAATC
1 ATTTTAATTCTAACTTTTAAATC
*
91588 ATTTTAGTTCTAACTTTTAAAT
1 ATTTTAATTCTAACTTTTAAAT
91610 TTTAGACATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (23 bp):
ATTTTAATTCTAACTTTTAAATC
Found at i:93213 original size:21 final size:22
Alignment explanation
Indices: 93188--93238 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
93178 TATGTTTTAG
*
93188 TTATTTAATTTTTTAAA-ATAT
1 TTATTTAATTATTTAAATATAT
* *
93209 TTATTAAATTATTTAAATATTT
1 TTATTTAATTATTTAAATATAT
93231 TTATTTAA
1 TTATTTAA
93239 GCTATTATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATTTAATTATTTAAATATAT
Found at i:95107 original size:34 final size:34
Alignment explanation
Indices: 95064--95137 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
95054 GAATTTAAAT
95064 TTTATCATGTGAAAATTATGTTTCTATTAATTCG
1 TTTATCATGTGAAAATTATGTTTCTATTAATTCG
95098 TTTATCATGTGAAAATTATGTTTCTATTAATTCG
1 TTTATCATGTGAAAATTATGTTTCTATTAATTCG
95132 TTTATC
1 TTTATC
95138 CGATTTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.51
Consensus pattern (34 bp):
TTTATCATGTGAAAATTATGTTTCTATTAATTCG
Done.