Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009653.1 Kokia drynarioides strain JFW-HI SEQ_124371, 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: 171985
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:2666 original size:21 final size:21
Alignment explanation
Indices: 2642--2688 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2632 AATTTAAACA
*
2642 TTTTTTTTATAT-ATTCTTTAG
1 TTTTTTTTATATAATT-TTTAC
*
2663 TTTTTTTTTTATAATTTTTAC
1 TTTTTTTTATATAATTTTTAC
2684 TTTTT
1 TTTTT
2689 AAAATTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTTTTTATATAATTTTTAC
Found at i:2727 original size:21 final size:21
Alignment explanation
Indices: 2684--2728 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2674 TAATTTTTAC
* *
2684 TTTTTAAAATTTATATAATAT
1 TTTTTAAAATATATATAAAAT
2705 TTTTTAAAA-ATATATGAAAAT
1 TTTTTAAAATATATAT-AAAAT
2726 TTT
1 TTT
2729 GATTTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTTAAAATATATATAAAAT
Found at i:24206 original size:72 final size:72
Alignment explanation
Indices: 24089--24234 Score: 292
Period size: 72 Copynumber: 2.0 Consensus size: 72
24079 ATTTATAATC
24089 TGAAGTGTATATATATTTAATATACTAAAACAGTACGTGATCTACAATTTTAAATTGATCATATG
1 TGAAGTGTATATATATTTAATATACTAAAACAGTACGTGATCTACAATTTTAAATTGATCATATG
24154 TGAAAAA
66 TGAAAAA
24161 TGAAGTGTATATATATTTAATATACTAAAACAGTACGTGATCTACAATTTTAAATTGATCATATG
1 TGAAGTGTATATATATTTAATATACTAAAACAGTACGTGATCTACAATTTTAAATTGATCATATG
24226 TGAAAAA
66 TGAAAAA
24233 TG
1 TG
24235 TTGTCTCTGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.36
Consensus pattern (72 bp):
TGAAGTGTATATATATTTAATATACTAAAACAGTACGTGATCTACAATTTTAAATTGATCATATG
TGAAAAA
Found at i:26092 original size:15 final size:15
Alignment explanation
Indices: 26072--26105 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
26062 AGTTAAGTTA
* *
26072 TTTTAGGTTTGGGTT
1 TTTTAGGTTCGGATT
26087 TTTTAGGTTCGGATT
1 TTTTAGGTTCGGATT
26102 TTTT
1 TTTT
26106 TGAGTTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.03, G:0.26, T:0.62
Consensus pattern (15 bp):
TTTTAGGTTCGGATT
Found at i:27535 original size:23 final size:23
Alignment explanation
Indices: 27503--27546 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
27493 ACAAACCCAT
27503 TTTAAATTTATCCTTTAATAATC
1 TTTAAATTTATCCTTTAATAATC
*
27526 TTTAATTTTATCCTTTAATAA
1 TTTAAATTTATCCTTTAATAA
27547 GCTCCTCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTAAATTTATCCTTTAATAATC
Found at i:32850 original size:31 final size:31
Alignment explanation
Indices: 32809--32891 Score: 98
Period size: 29 Copynumber: 2.7 Consensus size: 31
32799 AATCTTAAAA
*
32809 TTATACATAAATTTTAATTTGATGTATAATG
1 TTATATATAAATTTTAATTTGATGTATAATG
* * *
32840 TTATATATAAATTTTGATTT--TGTGTAATT
1 TTATATATAAATTTTAATTTGATGTATAATG
**
32869 TTATATATAAAAATTAATTTGAT
1 TTATATATAAATTTTAATTTGAT
32892 TTAAATTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 24 0.56
31 19 0.44
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.52
Consensus pattern (31 bp):
TTATATATAAATTTTAATTTGATGTATAATG
Found at i:32900 original size:29 final size:29
Alignment explanation
Indices: 32804--32900 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 29
32794 AGATAAATCT
* *
32804 TAAAATTATACATAAATTTTAATTTGATG
1 TAAATTTATATATAAATTTTAATTTGATG
*
32833 TATAATGTTATATATAAATTTTGATTTTG-TG
1 TA-AAT-TTATATATAAATTTT-AATTTGATG
* ** *
32864 TAATTTTATATATAAAAATTAATTTGATT
1 TAAATTTATATATAAATTTTAATTTGATG
32893 TAAATTTA
1 TAAATTTA
32901 ATAGACTACC
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
28 5 0.09
29 23 0.42
30 4 0.07
31 18 0.33
32 5 0.09
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (29 bp):
TAAATTTATATATAAATTTTAATTTGATG
Found at i:34666 original size:12 final size:12
Alignment explanation
Indices: 34626--34668 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 12
34616 CATACTAAAC
*
34626 TTTTAAAAGATAT
1 TTTTAAAACAT-T
34639 TTATTAAAATCATT
1 TT-TTAAAA-CATT
34653 TTTTAAAACATT
1 TTTTAAAACATT
34665 TTTT
1 TTTT
34669 GAAAGTAACG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 8 0.30
13 8 0.30
14 9 0.33
15 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (12 bp):
TTTTAAAACATT
Found at i:51794 original size:2 final size:2
Alignment explanation
Indices: 51787--51829 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
51777 GATTACAATA
51787 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
51829 A
1 A
51830 ATTAATAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:68600 original size:2 final size:2
Alignment explanation
Indices: 68593--68630 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
68583 TTATTTTCGA
68593 AT AT AT AT AT 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 AT AT AT AT AT
68631 CTCAAGTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69615 original size:12 final size:12
Alignment explanation
Indices: 69598--69638 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
69588 TACACTTATT
*
69598 ATTTATTTTTAA
1 ATTTATTATTAA
69610 ATTTATTATTAA
1 ATTTATTATTAA
69622 ATTTA-TATTAA
1 ATTTATTATTAA
69633 ATTTAT
1 ATTTAT
69639 GTTTTTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 11 0.41
12 16 0.59
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTATTATTAA
Found at i:69632 original size:11 final size:11
Alignment explanation
Indices: 69606--69638 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
69596 TTATTTATTT
69606 TTAAATTTATTA
1 TTAAATTTA-TA
69618 TTAAATTTATA
1 TTAAATTTATA
69629 TTAAATTTAT
1 TTAAATTTAT
69639 GTTTTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTAAATTTATA
Found at i:70888 original size:6 final size:6
Alignment explanation
Indices: 70877--70906 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
70867 TTTATCACTG
70877 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT
1 CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT
70907 GTCTCTCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCCCT
Found at i:74491 original size:6 final size:6
Alignment explanation
Indices: 74482--74510 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
74472 ACATCATCAT
74482 CAACAG CAACAG CAACAG CAACAG CAACA
1 CAACAG CAACAG CAACAG CAACAG CAACA
74511 AGAACATCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.34, G:0.14, T:0.00
Consensus pattern (6 bp):
CAACAG
Found at i:119892 original size:17 final size:18
Alignment explanation
Indices: 119858--119894 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
119848 ATATATAAAT
119858 ATTTATTTATATTTATAA
1 ATTTATTTATATTTATAA
119876 ATTTA-TTAT-TTTAATAA
1 ATTTATTTATATTT-ATAA
119893 AT
1 AT
119895 CAATGTCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.17
17 10 0.56
18 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTATTTATATTTATAA
Found at i:124620 original size:2 final size:2
Alignment explanation
Indices: 124613--124638 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
124603 CCTTATATTA
124613 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
124639 AATGCTTTTG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:127833 original size:22 final size:22
Alignment explanation
Indices: 127808--127856 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
127798 ACCTCAATTT
*
127808 TAAATTTTAAAAAT-TAAAAAA
1 TAAATTTCAAAAATATAAAAAA
*
127829 CTAAATTTCAAATATATAAAAAA
1 -TAAATTTCAAAAATATAAAAAA
127852 TAAAT
1 TAAAT
127857 AGATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAATTTCAAAAATATAAAAAA
Found at i:128423 original size:22 final size:21
Alignment explanation
Indices: 128377--128424 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
128367 CAATTTCATG
* *
128377 TAAAAACTCAAGTTTTTCCTT
1 TAAAAACCCAAGTTTTTCCTA
128398 TAAAAACCCAAGTAATTTT-CTA
1 TAAAAACCCAAGT--TTTTCCTA
128420 TAAAA
1 TAAAA
128425 TCACATGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 12 0.52
22 7 0.30
23 4 0.17
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.35
Consensus pattern (21 bp):
TAAAAACCCAAGTTTTTCCTA
Found at i:130217 original size:18 final size:18
Alignment explanation
Indices: 130183--130217 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
130173 TTAATTCTAA
*
130183 AAATGAAAAATAAAAATG
1 AAATGAAAAAGAAAAATG
*
130201 AAATGAAAAAGATAAAT
1 AAATGAAAAAGAAAAAT
130218 TAGTTTTTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (18 bp):
AAATGAAAAAGAAAAATG
Found at i:132735 original size:12 final size:12
Alignment explanation
Indices: 132718--132742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
132708 CAAGTACAAG
132718 AACGTGGACGAA
1 AACGTGGACGAA
132730 AACGTGGACGAA
1 AACGTGGACGAA
132742 A
1 A
132743 TGGAGCGACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.32, T:0.08
Consensus pattern (12 bp):
AACGTGGACGAA
Found at i:143198 original size:26 final size:26
Alignment explanation
Indices: 143162--143214 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
143152 TTAATGTTAA
143162 AAGGAGAATATATGAAAAGCAAACAG
1 AAGGAGAATATATGAAAAGCAAACAG
143188 AAGGAGAATATATGAAAAGCAAACAG
1 AAGGAGAATATATGAAAAGCAAACAG
143214 A
1 A
143215 CTCCTTGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.58, C:0.08, G:0.23, T:0.11
Consensus pattern (26 bp):
AAGGAGAATATATGAAAAGCAAACAG
Found at i:145830 original size:2 final size:2
Alignment explanation
Indices: 145818--145868 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
145808 GACACTTCCT
*
145818 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
145860 TA TA TA TA T
1 TA TA TA TA T
145869 GTATTTTTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:154270 original size:23 final size:24
Alignment explanation
Indices: 154225--154270 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
154215 AAACAAATAT
* *
154225 TATTTTATATTATTAAAATATTCA
1 TATTTTATATTATGAAAAAATTCA
*
154249 TATTTTATGTTA-GAAAAAATTC
1 TATTTTATATTATGAAAAAATTC
154271 GTTACTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (24 bp):
TATTTTATATTATGAAAAAATTCA
Found at i:158234 original size:26 final size:26
Alignment explanation
Indices: 158201--158250 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
158191 TGGAAAAAAA
158201 TTAATTAC-TGAAATAATATAAATTTT
1 TTAATTACTTG-AATAATATAAATTTT
*
158227 TTAATTACTTGAATAATATGAATT
1 TTAATTACTTGAATAATATAAATT
158251 GAGCAGGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (26 bp):
TTAATTACTTGAATAATATAAATTTT
Found at i:166964 original size:24 final size:24
Alignment explanation
Indices: 166937--166982 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
166927 TTTTTTTTAA
*
166937 TTTTA-ATATTTAATAATTTTATTT
1 TTTTATATATTGAA-AATTTTATTT
*
166961 TTTTATCTATTGAAAATTTTAT
1 TTTTATATATTGAAAATTTTAT
166983 ATAATCGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTATATATTGAAAATTTTATTT
Found at i:169446 original size:22 final size:22
Alignment explanation
Indices: 169416--169461 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
169406 TTGTAAAAAA
*
169416 CCAGA-TTTTTCCATGAGGAAAC
1 CCAGATTTTTTCC-TGAAGAAAC
*
169438 CCAGGTTTTTTCCTGAAGAAAC
1 CCAGATTTTTTCCTGAAGAAAC
169460 CC
1 CC
169462 TTGTTTTCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (22 bp):
CCAGATTTTTTCCTGAAGAAAC
Done.