Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004375.1 Kokia drynarioides strain JFW-HI SEQ_117740, 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: 22897
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Found at i:493 original size:29 final size:29
Alignment explanation
Indices: 445--720 Score: 220
Period size: 29 Copynumber: 9.8 Consensus size: 29
435 GGAGGTCTCG
*
445 AAACTTCCCAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * **
474 ATACTTCCAAAAATTGCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
* * *
504 AAACTTCCTAAAATTCCATTTTCACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
*
533 AAACTTCCAAAATTTCCATTTTT------
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
556 -TA--TCCAAAAAATTCTATTTTTGA-CCCC
1 AAACTTCC-AAAAATTCCATTTTT-ACCCCC
* *
583 ATAACTTTCAAAAATTCCATTTTTGA-CCCA
1 A-AACTTCCAAAAATTCCATTTTT-ACCCCC
*
613 AAACTTCCAAAAATTCCATTTTTA-CCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
*
641 AAACTTCCAAAAATTCCA-TTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * *
669 AAA-TCTCCAAAATTTCCATTTTGACCCCG
1 AAACT-TCCAAAAATTCCATTTTTACCCCC
*
698 AAACTTTCAAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
721 GCCCTCGGAT
Statistics
Matches: 200, Mismatches: 30, Indels: 33
0.76 0.11 0.13
Matches are distributed among these distances:
20 3 0.01
21 13 0.06
22 1 0.00
27 6 0.03
28 38 0.19
29 86 0.43
30 51 0.25
31 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.36
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:597 original size:80 final size:80
Alignment explanation
Indices: 482--635 Score: 204
Period size: 80 Copynumber: 1.9 Consensus size: 80
472 CCATACTTCC
* * * *
482 AAAAATTGCATTTTTAACCCTAAAACTTCCTAAAATTCCA-TTTTCACCCTCAAACTTCCAAAAT
1 AAAAATTGCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTCACCC-AAAACTTCCAAAAA
546 TTCCATTTTTTATCCA
65 TTCCATTTTTTATCCA
* * * *
562 AAAAATT-CTATTTTTGACCCCATAACTTTCAAAAATTCCATTTTTGACCCAAAACTTCCAAAAA
1 AAAAATTGC-ATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTCACCCAAAACTTCCAAAAA
626 TTCCATTTTT
65 TTCCATTTTT
636 ACCTCAAACT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
79 1 0.02
80 55 0.86
81 8 0.12
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.38
Consensus pattern (80 bp):
AAAAATTGCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTCACCCAAAACTTCCAAAAAT
TCCATTTTTTATCCA
Found at i:601 original size:51 final size:50
Alignment explanation
Indices: 513--662 Score: 133
Period size: 51 Copynumber: 2.8 Consensus size: 50
503 AAAACTTCCT
* * *
513 AAAATTCCATTTTCACCCTCAAACTTCCAAAATTTCCATTTTTTATCCAA
1 AAAATTCCATTTTCACCCTCAAACTTCCAAAAATTCCATTTTTGACCCAA
* * *
563 AAAATTCTATTTTTGACCC-CATAACTTTCAAAAATTCCATTTTTGACCCAAAACTTCCA
1 AAAATTCCA-TTTTCACCCTCA-AACTTCCAAAAATTCCATTTTTGACCC---A-----A
*
622 AAAATTCCATTTTTA-CCTCAAACTTCCAAAAATTCCATTTT
1 AAAATTCCATTTTCACCCTCAAACTTCCAAAAATTCCATTTT
663 ACCCCTAAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
50 10 0.12
51 31 0.39
54 1 0.01
57 22 0.28
58 7 0.09
59 9 0.11
ACGTcount: A:0.35, C:0.26, G:0.01, T:0.37
Consensus pattern (50 bp):
AAAATTCCATTTTCACCCTCAAACTTCCAAAAATTCCATTTTTGACCCAA
Found at i:654 original size:109 final size:108
Alignment explanation
Indices: 454--662 Score: 307
Period size: 109 Copynumber: 1.9 Consensus size: 108
444 GAAACTTCCC
* *
454 AAAATTCCATTTTTACCCCCATACTTCCAAAAATTGCATTTTTAACCCTAAAACTTCCTAAAATT
1 AAAATTCCATTTTTACCCCCATACTTCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATT
519 CCATTTTCACCCTCAAACTTCCAAAATTTCCATTTTTTATCCAA
66 CCATTTTCACCCTCAAACTTCCAAAA-TTCCATTTTTTATCCAA
* * *
563 AAAATTCTATTTTTGA-CCCCATAACTTTCAAAAATTCCATTTTTGACCC-AAAACTTCCAAAAA
1 AAAATTCCATTTTT-ACCCCCAT-ACTTCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAA
*
626 TTCCATTTTTA-CCTCAAACTTCCAAAAATTCCATTTT
64 TTCCATTTTCACCCTCAAACTTCC-AAAATTCCATTTT
663 ACCCCTAAAT
Statistics
Matches: 91, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
108 21 0.23
109 46 0.51
110 24 0.26
ACGTcount: A:0.35, C:0.27, G:0.01, T:0.37
Consensus pattern (108 bp):
AAAATTCCATTTTTACCCCCATACTTCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATT
CCATTTTCACCCTCAAACTTCCAAAATTCCATTTTTTATCCAA
Found at i:677 original size:28 final size:28
Alignment explanation
Indices: 562--721 Score: 180
Period size: 28 Copynumber: 5.5 Consensus size: 28
552 TTTTTATCCA
* *
562 AAAAATTCTATTTTTGACCCCATAACTTTC
1 AAAAATTCCA-TTTTGACCCCA-AACTTCC
*
592 AAAAATTCCATTTTTGACCCAAAACTTCC
1 AAAAATTCCA-TTTTGACCCCAAACTTCC
* *
621 AAAAATTCCATTTTTACCTCAAACTTCC
1 AAAAATTCCATTTTGACCCCAAACTTCC
649 AAAAATTCCATTTT-ACCCCTAAA-TCTCC
1 AAAAATTCCATTTTGACCCC-AAACT-TCC
* *
677 AAAATTTCCATTTTGACCCCGAAACTTTC
1 AAAAATTCCATTTTGACCCC-AAACTTCC
706 AAAAATTACCATTTTG
1 AAAAATT-CCATTTTG
722 CCCTCGGATG
Statistics
Matches: 114, Mismatches: 11, Indels: 10
0.84 0.08 0.07
Matches are distributed among these distances:
27 5 0.04
28 48 0.42
29 32 0.28
30 29 0.25
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAAATTCCATTTTGACCCCAAACTTCC
Found at i:738 original size:58 final size:58
Alignment explanation
Indices: 562--841 Score: 211
Period size: 57 Copynumber: 4.9 Consensus size: 58
552 TTTTTATCCA
* * **
562 AAAAATTCTATTTTTGACCCC-ATAACTTTCAAAAATT-CCATTTTTGACCCAAAACT-TCC
1 AAAAATTCCACTTTTGACCCCGA-AACTTTCAAAAATTACCA-TTTT-ACCCCGAA-TGTCC
* * * * *
621 AAAAATTCCA-TTTTTACCTC-AAACTTCCAAAAATT-CCATTTTACCCCTAAATCTCC
1 AAAAATTCCACTTTTGACCCCGAAACTTTCAAAAATTACCATTTTACCCC-GAATGTCC
* * *
677 AAAATTTCCA-TTTTGACCCCGAAACTTTCAAAAATTACCATTTTGCCCTCGGATGTCC
1 AAAAATTCCACTTTTGACCCCGAAACTTTCAAAAATTACCATTTTACCC-CGAATGTCC
* * * * *
735 -AAAACTCCACTTTCGACCCCGAAACTCTC-AAAATTACCCTTTTACCCACGAATGTCT
1 AAAAATTCCACTTTTGACCCCGAAACTTTCAAAAATTACCATTTTACCC-CGAATGTCC
* * * * * *
792 AAAAATTCCATTTTTAACCCCG-AATTTTCCCAAAATTACTATTTTGCCCC
1 AAAAATTCCACTTTTGACCCCGAAACTTT-CAAAAATTACCATTTTACCCC
842 TGAGAATCCA
Statistics
Matches: 181, Mismatches: 31, Indels: 19
0.78 0.13 0.08
Matches are distributed among these distances:
55 5 0.03
56 27 0.15
57 64 0.35
58 60 0.33
59 25 0.14
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (58 bp):
AAAAATTCCACTTTTGACCCCGAAACTTTCAAAAATTACCATTTTACCCCGAATGTCC
Found at i:806 original size:29 final size:27
Alignment explanation
Indices: 562--817 Score: 126
Period size: 29 Copynumber: 8.9 Consensus size: 27
552 TTTTTATCCA
* * *
562 AAAAATTCTATTTTTGACCCCATAACTTTC
1 AAAAATTCCATTTTT-ACCCC-GAA-TTCC
**
592 AAAAATTCCATTTTTGACCCAAAACTTCC
1 AAAAATTCCATTTTT-ACCCCGAA-TTCC
* *
621 AAAAATTCCATTTTTACCTCAAACTTCC
1 AAAAATTCCATTTTTACCCCGAA-TTCC
*
649 AAAAATTCCA-TTTTACCCCTAAATCTCC
1 AAAAATTCCATTTTTACCCC-GAAT-TCC
* * *
677 AAAATTTCCATTTTGACCCCGAAACTTTC
1 AAAAATTCCATTTTTACCCCG-AA-TTCC
* *
706 AAAAATTACCA-TTTTGCCCTCGGATGTCC
1 AAAAATT-CCATTTTTACCC-CGAAT-TCC
* ** *
735 -AAAACTCCACTTTCGACCCCGAAACTCTC
1 AAAAATTCCA-TTTTTACCCCG-AATTC-C
* *
764 -AAAATTACC-CTTTTACCCACGAATGTCT
1 AAAAATT-CCATTTTTACCC-CGAAT-TCC
792 AAAAATTCCATTTTTAACCCCGAATT
1 AAAAATTCCATTTTT-ACCCCGAATT
818 TTCCCAAAAT
Statistics
Matches: 179, Mismatches: 29, Indels: 38
0.73 0.12 0.15
Matches are distributed among these distances:
27 12 0.07
28 57 0.32
29 79 0.44
30 31 0.17
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (27 bp):
AAAAATTCCATTTTTACCCCGAATTCC
Found at i:2602 original size:24 final size:25
Alignment explanation
Indices: 2575--2621 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2565 ATAAAAAAGA
2575 TAAA-TTAGTTTTTCCAATAAAAAC
1 TAAACTTAGTTTTTCCAATAAAAAC
** *
2599 TAAACTTTTTTTTTCCTATAAAA
1 TAAACTTAGTTTTTCCAATAAAA
2622 GTACATGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (25 bp):
TAAACTTAGTTTTTCCAATAAAAAC
Found at i:2829 original size:16 final size:16
Alignment explanation
Indices: 2805--2835 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2795 AATATTTTTA
2805 AAATAAAAAATAAAAG
1 AAATAAAAAATAAAAG
*
2821 AAATTAAAAATAAAA
1 AAATAAAAAATAAAA
2836 TAAAACAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (16 bp):
AAATAAAAAATAAAAG
Found at i:6138 original size:25 final size:25
Alignment explanation
Indices: 6105--6161 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
6095 ATAGGTTAGA
*
6105 TAAAAAATAAAT-TAGTTTTTCCTGT
1 TAAAAAATAAATCTA-TTTTTCCTAT
* *
6130 TAAAAAATATATCTATTTTTGCTAT
1 TAAAAAATAAATCTATTTTTCCTAT
6155 TAAAAAA
1 TAAAAAA
6162 ACTTATCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 26 0.93
26 2 0.07
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (25 bp):
TAAAAAATAAATCTATTTTTCCTAT
Found at i:14464 original size:3 final size:3
Alignment explanation
Indices: 14456--14485 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
14446 CAATTAATTA
14456 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
14486 TAACCTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:17154 original size:15 final size:15
Alignment explanation
Indices: 17134--17167 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17124 CATGTTATAT
*
17134 TAATTTGATATTTAA
1 TAATTTGATATTAAA
*
17149 TAATTTTATATTAAA
1 TAATTTGATATTAAA
17164 TAAT
1 TAAT
17168 ATATTCTACA
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:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TAATTTGATATTAAA
Found at i:22116 original size:20 final size:20
Alignment explanation
Indices: 22091--22131 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
22081 CCATCTAACC
*
22091 AAATAATTAATATGTTAAAA
1 AAATAATTAAAATGTTAAAA
*
22111 AAATAATTAAAATTTTAAAA
1 AAATAATTAAAATGTTAAAA
22131 A
1 A
22132 GCTTGAAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
AAATAATTAAAATGTTAAAA
Done.