Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005361.1 Kokia drynarioides strain JFW-HI SEQ_119343, 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: 71745
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Warning! 108 characters in sequence are not A, C, G, or T
Found at i:602 original size:29 final size:29
Alignment explanation
Indices: 565--709 Score: 129
Period size: 29 Copynumber: 4.8 Consensus size: 29
555 GAGGTCCCTA
*
565 AACTATCCAAAAATTACCATTTTACCCTCG
1 AACT-TCCAAAAATTACCATTTTACCCCCG
595 AACTTCCAAAAA-T-CTCATTTTTGACCCCCG
1 AACTTCCAAAAATTAC-CA-TTTT-ACCCCCG
* *
625 AACCTTCCTAAAATTACCATTTTACCCCCA
1 AA-CTTCCAAAAATTACCATTTTACCCCCG
*
655 AACTTTCAAAAA-T-CTCATTTTTGA-CCCCG
1 AACTTCCAAAAATTAC-CA-TTTT-ACCCCCG
684 ACACTTCCAAAAAATTACCATTTTAC
1 A-ACTTCC-AAAAATTACCATTTTAC
710 TCTCGGATGT
Statistics
Matches: 94, Mismatches: 7, Indels: 27
0.73 0.05 0.21
Matches are distributed among these distances:
27 2 0.02
28 6 0.06
29 29 0.31
30 27 0.29
31 22 0.23
32 6 0.06
33 2 0.02
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.31
Consensus pattern (29 bp):
AACTTCCAAAAATTACCATTTTACCCCCG
Found at i:652 original size:30 final size:28
Alignment explanation
Indices: 565--709 Score: 107
Period size: 30 Copynumber: 4.8 Consensus size: 28
555 GAGGTCCCTA
*
565 AACTATCCAAAAATTACCATTTTACCCTCG
1 AACT-TCC-AAAATTACCATTTTACCCCCG
*
595 AACTTCCAAAAAT-CTCATTTTTGACCCCCG
1 AACTTCCAAAATTAC-CA-TTTT-ACCCCCG
*
625 AACCTTCCTAAAATTACCATTTTACCCCCA
1 AA-CTTCC-AAAATTACCATTTTACCCCCG
* *
655 AACTTTCAAAAAT-CTCATTTTTGA-CCCCG
1 AACTTCCAAAATTAC-CA-TTTT-ACCCCCG
684 ACACTTCCAAAAAATTACCATTTTAC
1 A-ACTTCC--AAAATTACCATTTTAC
710 TCTCGGATGT
Statistics
Matches: 92, Mismatches: 9, Indels: 27
0.72 0.07 0.21
Matches are distributed among these distances:
27 2 0.02
28 14 0.15
29 20 0.22
30 27 0.29
31 13 0.14
32 14 0.15
33 2 0.02
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.31
Consensus pattern (28 bp):
AACTTCCAAAATTACCATTTTACCCCCG
Found at i:667 original size:60 final size:60
Alignment explanation
Indices: 573--709 Score: 206
Period size: 60 Copynumber: 2.3 Consensus size: 60
563 TAAACTATCC
* *
573 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCCCCGA-ACCTTCC-
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGA-CCCCGACA-CTTCCA
* *
633 TAAAATTACCATTTTACCCCCAAACTTTCAAAAATCTCATTTTTGACCCCGACACTTCCA
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCGACACTTCCA
693 AAAAATTACCATTTTAC
1 AAAAATTACCATTTTAC
710 TCTCGGATGT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
59 11 0.16
60 59 0.84
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (60 bp):
AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCCCGACACTTCCA
Found at i:3581 original size:23 final size:22
Alignment explanation
Indices: 3517--3569 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
3507 AAATTTGTTT
3517 AAGTG-TCATTAAATAATTAAA
1 AAGTGATCATTAAATAATTAAA
3538 AAGTGATCATTAAATAATTAAA
1 AAGTGATCATTAAATAATTAAA
3560 AAGTGATCAT
1 AAGTGATCAT
3570 AGATGAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.32
Consensus pattern (22 bp):
AAGTGATCATTAAATAATTAAA
Found at i:6938 original size:34 final size:35
Alignment explanation
Indices: 6875--6944 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
6865 ATTACAAAAT
6875 AAATAAAAAATTATGAAAAATTATAAAAAAATAAA
1 AAATAAAAAATTATGAAAAATTATAAAAAAATAAA
* *
6910 AAATAAAAATATT-TGAAAAA-TATTAAAAATTAAA
1 AAATAAAAA-ATTATGAAAAATTATAAAAAAATAAA
6944 A
1 A
6945 CTGGTGGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 13 0.41
35 16 0.50
36 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (35 bp):
AAATAAAAAATTATGAAAAATTATAAAAAAATAAA
Found at i:7151 original size:10 final size:10
Alignment explanation
Indices: 7128--7205 Score: 52
Period size: 10 Copynumber: 7.8 Consensus size: 10
7118 CCAGTTAAAA
*
7128 TTTTTATGATT
1 TTTTTAT-AAT
7139 TTTTTATAA-
1 TTTTTATAAT
*
7148 TTTTTATAAA
1 TTTTTATAAT
* *
7158 TTTATATAAA
1 TTTTTATAAT
*
7168 TTTTAAT-AT
1 TTTTTATAAT
**
7177 TTTAAATAAT
1 TTTTTATAAT
*
7187 ATTTTATGAAT
1 TTTTTAT-AAT
7198 TTTTTATA
1 TTTTTATA
7206 GGTTTTTAAG
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
9 16 0.30
10 22 0.41
11 16 0.30
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:7165 original size:19 final size:19
Alignment explanation
Indices: 7143--7199 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
7133 ATGATTTTTT
7143 TATAATTTTTATAAATTTA
1 TATAATTTTTATAAATTTA
* *
7162 TATAAATTTTA-ATATTTTA
1 TATAATTTTTATA-AATTTA
* *
7181 AATAATATTTTATGAATTT
1 TATAAT-TTTTATAAATTT
7200 TTTATAGGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.66
20 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TATAATTTTTATAAATTTA
Found at i:18925 original size:2 final size:2
Alignment explanation
Indices: 18920--18944 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18910 ATCTCTCATT
18920 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
18945 TAGAGAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19962 original size:16 final size:15
Alignment explanation
Indices: 19941--19970 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
19931 ATTTGATAAA
19941 CTAAAAAAATTAAGTG
1 CTAAAAAAA-TAAGTG
19957 CTAAAAAAATAAGT
1 CTAAAAAAATAAGT
19971 ATTGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.23
Consensus pattern (15 bp):
CTAAAAAAATAAGTG
Found at i:21188 original size:24 final size:25
Alignment explanation
Indices: 21151--21198 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
21141 TATATAATAT
21151 TATTTTAATATTTAATAAAATTTTA
1 TATTTTAATATTTAATAAAATTTTA
* *
21176 TATTTT-ATATTTATTGAAATTTT
1 TATTTTAATATTTAATAAAATTTT
21199 TTATATAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TATTTTAATATTTAATAAAATTTTA
Found at i:21235 original size:23 final size:23
Alignment explanation
Indices: 21134--21237 Score: 83
Period size: 23 Copynumber: 4.6 Consensus size: 23
21124 TATTTTTAAA
21134 TAATATTTATA-TAATATTATTT
1 TAATATTTATATTAATATTATTT
* *
21156 TAATATTTA-ATAAAATTTTATATT
1 TAATATTTATAT-TAATATTAT-TT
* *
21180 TTATATTTAT-TGAA-ATT-TTT
1 TAATATTTATATTAATATTATTT
* *
21200 TATATAGTCATATTAATATTATTT
1 TA-ATATTTATATTAATATTATTT
*
21224 TAATGTTTATATTA
1 TAATATTTATATTA
21238 CAGTAATATT
Statistics
Matches: 62, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
20 3 0.05
21 8 0.13
22 14 0.23
23 21 0.34
24 16 0.26
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (23 bp):
TAATATTTATATTAATATTATTT
Found at i:30016 original size:2 final size:2
Alignment explanation
Indices: 30011--30036 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30001 TTTTTGAAGC
30011 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
30037 TTCCCTGTTA
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:40024 original size:22 final size:23
Alignment explanation
Indices: 39982--40032 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
39972 AAATTATAAA
39982 AAAAAATTAAAACACATAAAA-G
1 AAAAAATTAAAACACATAAAACG
**
40004 AAAAAATTAAATTAC-TCAAAACG
1 AAAAAATTAAAACACAT-AAAACG
40027 AAAAAA
1 AAAAAA
40033 ATATGGGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 17 0.68
23 7 0.28
ACGTcount: A:0.71, C:0.10, G:0.04, T:0.16
Consensus pattern (23 bp):
AAAAAATTAAAACACATAAAACG
Found at i:41053 original size:22 final size:22
Alignment explanation
Indices: 41005--41054 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
40995 TAACTATTGC
* * *
41005 TATTTTGCCATTGTTTTGTTAT
1 TATTTTGCCATTATATTGATAT
* *
41027 CATTTTGCTATTATATTGATAT
1 TATTTTGCCATTATATTGATAT
41049 TATTTT
1 TATTTT
41055 ATTGTTATTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.08, G:0.10, T:0.62
Consensus pattern (22 bp):
TATTTTGCCATTATATTGATAT
Found at i:45717 original size:13 final size:14
Alignment explanation
Indices: 45692--45721 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
45682 ATTATATGTT
45692 AATTACATGAAAAA
1 AATTACATGAAAAA
45706 AATTAC-TGAAAAA
1 AATTACATGAAAAA
45719 AAT
1 AAT
45722 AATTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (14 bp):
AATTACATGAAAAA
Found at i:58730 original size:30 final size:30
Alignment explanation
Indices: 58661--58729 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
58651 TTTAGTAGCC
* * * *
58661 TAAATCTTTATAATTTTTAAAGAATTAAAT
1 TAAATTTTTATAATTTTTAAAAAATCAAAG
*
58691 TAAATTTTTATTATTTTTAAAAAATCAAAG
1 TAAATTTTTATAATTTTTAAAAAATCAAAG
58721 TATAATTTT
1 TA-AATTTT
58730 AATTTTATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 27 0.82
31 6 0.18
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (30 bp):
TAAATTTTTATAATTTTTAAAAAATCAAAG
Found at i:66719 original size:17 final size:17
Alignment explanation
Indices: 66694--66739 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
66684 AATGAAAGAC
*
66694 AAGACAAAAACCCAGAA
1 AAGAAAAAAACCCAGAA
66711 AAGAAAAAAACCCAGAA
1 AAGAAAAAAACCCAGAA
66728 AAGAAAAAAACC
1 AAGAAAAAAACC
66740 GAACCTGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.70, C:0.20, G:0.11, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAACCCAGAA
Found at i:67956 original size:128 final size:130
Alignment explanation
Indices: 67732--67989 Score: 432
Period size: 128 Copynumber: 2.0 Consensus size: 130
67722 TTTCTGAAAA
*
67732 TTTGAGGGGAACTTAAAAAAATAATCATTTTTTTGGTGAAATCAAATAATTTGGGGCCACCAATT
1 TTTGAGGGGAACTTAAAAAAATAATCATTTTTTTAGTGAAATCAAATAATTTGGGGCCACCAATT
*
67797 TCCAATGCATGCTAGTGTTTTTTTTTTTTTTTTTTA-TTTTTAAATCTATAAAAGAAATTAAATT
66 TCCAATGCATGCTAGTGTTTTTTTTTTTTTTTTTAATTTTTTAAATCTATAAAAGAAATTAAATT
* *
67861 TTTGA-GGGAGACTTAAAAAAATAATCA-TTTTTTAGTGAAGTCAAATAATTTGGGGTCACCAAT
1 TTTGAGGGGA-ACTTAAAAAAATAATCATTTTTTTAGTGAAATCAAATAATTTGGGGCCACCAAT
**
67924 TTTTAATGCATGCTAGTGTTTTTTTTTTTTTTTTTAATTTTTTAAATCTATAAAAGAAATTAAAT
65 TTCCAATGCATGCTAGTGTTTTTTTTTTTTTTTTTAATTTTTTAAATCTATAAAAGAAATTAAAT
67989 T
130 T
67990 ATGCTAAAAA
Statistics
Matches: 121, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
128 71 0.59
129 50 0.41
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (130 bp):
TTTGAGGGGAACTTAAAAAAATAATCATTTTTTTAGTGAAATCAAATAATTTGGGGCCACCAATT
TCCAATGCATGCTAGTGTTTTTTTTTTTTTTTTTAATTTTTTAAATCTATAAAAGAAATTAAATT
Found at i:69228 original size:14 final size:15
Alignment explanation
Indices: 69209--69263 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 15
69199 TATCTGAAAA
69209 ATAAAA-AAATTTAG
1 ATAAAATAAATTTAG
69223 ATAAAAATATAAATTTA-
1 AT--AAA-ATAAATTTAG
69240 A-AAAATAAATTTAG
1 ATAAAATAAATTTAG
69254 ATAAAA-AAAT
1 ATAAAATAAAT
69264 CAAGTCCAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 9 0.26
14 10 0.29
15 4 0.11
16 3 0.09
17 2 0.06
18 7 0.20
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (15 bp):
ATAAAATAAATTTAG
Found at i:69457 original size:51 final size:48
Alignment explanation
Indices: 69396--69491 Score: 113
Period size: 48 Copynumber: 1.9 Consensus size: 48
69386 TTTCTTCATT
* *
69396 ATCAAACTTAAAAAGCAA-CTACCAGCTTTGATGTTGTACCGTGACAATCAC
1 ATCAAACTT-AAAAGCAATC-ACCAAC-TT-ATGTTGTAACGTGACAATCAC
* *
69447 ATCAACCTTAAATGCAATCACCAACTTATGTTGTAACGTGACAAT
1 ATCAAACTTAAAAGCAATCACCAACTTATGTTGTAACGTGACAAT
69492 TGCATCTTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
48 17 0.43
49 2 0.05
50 12 0.30
51 9 0.22
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (48 bp):
ATCAAACTTAAAAGCAATCACCAACTTATGTTGTAACGTGACAATCAC
Done.