Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004994.1 Kokia drynarioides strain JFW-HI SEQ_118749, 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: 84581
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:422 original size:30 final size:29
Alignment explanation
Indices: 387--782 Score: 258
Period size: 29 Copynumber: 13.5 Consensus size: 29
377 TAAATTGTCC
*
387 AAAAATCCCATTTTTGACCTCGAACCTTCT
1 AAAAATCCCATTTTT-ACCCCGAACCTTCT
* * * **
417 GAAAATTACCA-TTTTACCCCTAAATTTCT
1 -AAAAATCCCATTTTTACCCCGAACCTTCT
*
446 AAAAATCCCATTTTTAACCCCAAACCTT-T
1 AAAAATCCCATTTTT-ACCCCGAACCTTCT
* *
475 AAAAAATTACCATTTTTACCCCCGAA-CTTCC
1 -AAAAA-TCCCATTTTTA-CCCCGAACCTTCT
* *
506 AAAAATCCCAATTTTGACCTCGAACCTTCT
1 AAAAATCCC-ATTTTTACCCCGAACCTTCT
** * * *
536 AAAAATTAC-TATTTTACCCCTAAACTTCC
1 AAAAATCCCAT-TTTTACCCCGAACCTTCT
* *
565 AAAAAT-CCATTTTTGA-CCCTAAACTTCT
1 AAAAATCCCATTTTT-ACCCCGAACCTTCT
* *
593 AGAAATCCCATTTTTGA-CCCAAACCTTCT
1 AAAAATCCCATTTTT-ACCCCGAACCTTCT
* *
622 AAAAATTACCA-TTTTATCCCCGAACTTTC-
1 AAAAA-TCCCATTTTTA-CCCCGAACCTTCT
651 AAAAATCCCATTTTTGACCCCGAACCTTCT
1 AAAAATCCCATTTTT-ACCCCGAACCTTCT
* *
681 AAAAATTACCA-TTTTACCCACGAA-CTTCC
1 AAAAA-TCCCATTTTTACCC-CGAACCTTCT
* * * *
710 AAAAATCTCATTTTCAACCTCGAA-CTTCC
1 AAAAATCCCATTTT-TACCCCGAACCTTCT
* * *
739 AAAAATCCCATTTTTTACTCTGAACCTTCC
1 AAAAATCCCA-TTTTTACCCCGAACCTTCT
* *
769 AAAATTACCATTTT
1 AAAAATCCCATTTT
783 GCCCCCGCGC
Statistics
Matches: 292, Mismatches: 49, Indels: 50
0.75 0.13 0.13
Matches are distributed among these distances:
28 38 0.13
29 136 0.47
30 91 0.31
31 27 0.09
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAAATCCCATTTTTACCCCGAACCTTCT
Found at i:472 original size:59 final size:60
Alignment explanation
Indices: 374--593 Score: 261
Period size: 59 Copynumber: 3.7 Consensus size: 60
364 TCCCGCAGGT
* * * *
374 CCCTAAATTGTCCAAAAATCCCATTTTTGACCTCGAACCTTCT-GAAAATTACCATTTTAC
1 CCCTAAACT-TCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAAATTACCATTTTAC
* * *
434 CCCTAAATTTCTAAAAATCCCATTTTTAACCCCAAACCTT-TAAAAAATTACCATTTTTAC
1 CCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAAATTACCA-TTTTAC
** * * * *
494 CCCCGAACTTCCAAAAATCCCAATTTTGACCTCGAACCTTCT-AAAAATTACTATTTTAC
1 CCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAAATTACCATTTTAC
*
553 CCCTAAACTTCCAAAAAT-CCATTTTTGACCCTAAA-CTTCTA
1 CCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTA
594 GAAATCCCAT
Statistics
Matches: 136, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
57 5 0.04
58 14 0.10
59 59 0.43
60 57 0.42
61 1 0.01
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.33
Consensus pattern (60 bp):
CCCTAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAAATTACCATTTTAC
Found at i:684 original size:59 final size:58
Alignment explanation
Indices: 586--723 Score: 206
Period size: 59 Copynumber: 2.4 Consensus size: 58
576 TTTGACCCTA
* *
586 AACTTCTAGAAATCCCATTTTTGACCCAAACCTTCTAAAAATTACCATTTTATCCC-CG
1 AACTTCCAAAAATCCCATTTTTGACCCAAACCTTCTAAAAATTACCATTTTA-CCCACG
* *
644 AACTTTCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTACCCACG
1 AACTTCCAAAAATCCCATTTTTGA-CCCAAACCTTCTAAAAATTACCATTTTACCCACG
*
703 AACTTCCAAAAATCTCATTTT
1 AACTTCCAAAAATCCCATTTT
724 CAACCTCGAA
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
58 24 0.33
59 48 0.67
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (58 bp):
AACTTCCAAAAATCCCATTTTTGACCCAAACCTTCTAAAAATTACCATTTTACCCACG
Found at i:755 original size:59 final size:59
Alignment explanation
Indices: 484--782 Score: 192
Period size: 59 Copynumber: 5.1 Consensus size: 59
474 TAAAAAATTA
* * * * * *
484 CCATTTTT-ACCCCCGAACTTCCAAAAATCCCAATTTTGA-CCTCGAACCTTCTAAAAATT
1 CCATTTTTGA-CCCCGAACTTCCAAAAATACCATTTTTTACCCACGAA-CTTCCAAAAATC
* * * * *
543 AC-TATTTT-ACCCCTAAACTTCCAAAAAT-CCATTTTTGACCCTA--AACTTCTAGAAATC
1 CCAT-TTTTGACCCC-GAACTTCCAAAAATACCATTTTTTACCC-ACGAACTTCCAAAAATC
* * * *
600 CCATTTTTGA-CCCAAACCTTCTAAAAATTACCATTTTAT-CCC-CGAACTTTCAAAAATC
1 CCATTTTTGACCCCGAA-CTTCCAAAAA-TACCATTTTTTACCCACGAACTTCCAAAAATC
*
658 CCATTTTTGACCCCGAACCTTCTAAAAATTACCA--TTTTACCCACGAACTTCCAAAAATC
1 CCATTTTTGACCCCGAA-CTTCCAAAAA-TACCATTTTTTACCCACGAACTTCCAAAAATC
* ** * * * * * *
717 TCATTTTCAACCTCGAACTTCCAAAAATCCCATTTTTTACTC-TGAACCTTCCAAAATTA
1 CCATTTTTGACCCCGAACTTCCAAAAATACCATTTTTTACCCACGAA-CTTCCAAAAATC
776 CCATTTT
1 CCATTTT
783 GCCCCCGCGC
Statistics
Matches: 196, Mismatches: 27, Indels: 34
0.76 0.11 0.13
Matches are distributed among these distances:
56 3 0.02
57 34 0.17
58 58 0.30
59 101 0.52
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (59 bp):
CCATTTTTGACCCCGAACTTCCAAAAATACCATTTTTTACCCACGAACTTCCAAAAATC
Found at i:8358 original size:18 final size:19
Alignment explanation
Indices: 8337--8380 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
8327 ACCTATCCCT
8337 TCTTCCTCC-TCTTCACTG
1 TCTTCCTCCTTCTTCACTG
*
8355 TCTTCC-CCTTCTTCAGTG
1 TCTTCCTCCTTCTTCACTG
*
8373 TCCTCCTC
1 TCTTCCTC
8381 ATCATGCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 19 0.86
19 1 0.05
ACGTcount: A:0.05, C:0.45, G:0.07, T:0.43
Consensus pattern (19 bp):
TCTTCCTCCTTCTTCACTG
Found at i:8882 original size:20 final size:20
Alignment explanation
Indices: 8857--8915 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 20
8847 CTTCATTTTA
*
8857 ATATAATTAAATAAATTAAT
1 ATATAATTAAATAAAATAAT
*
8877 ATATAA-TAAAAAAAATAAT
1 ATATAATTAAATAAAATAAT
8896 -TATAAATTTAAATAATAATA
1 ATAT-AA-TTAAATAA-AATA
8916 CAATATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 3 0.09
19 13 0.41
20 6 0.19
21 6 0.19
22 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATAATTAAATAAAATAAT
Found at i:9094 original size:18 final size:21
Alignment explanation
Indices: 9054--9107 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
9044 TGGGAAGGTT
9054 CTACCGATACAAGTATGACTA
1 CTACCGATACAAGTATGACTA
* * *
9075 CTACCGATACAATTATTACTT
1 CTACCGATACAAGTATGACTA
*
9096 CTACTGATACAA
1 CTACCGATACAA
9108 CAAACTCTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (21 bp):
CTACCGATACAAGTATGACTA
Found at i:10033 original size:120 final size:119
Alignment explanation
Indices: 9816--10049 Score: 387
Period size: 120 Copynumber: 2.0 Consensus size: 119
9806 CTTCCACAAC
* *
9816 CTATAATCCAGAATTTCACTCTCATGTCTATATCAACTCTGTACCAGTATATAATGCTGCTCACA
1 CTATAATCCAGAATTTCACTCTCATGTCTATATCAACTCTGTACAAGTATACAATGCTGCTCACA
*
9881 CGAGCTGTCAAGGACTCGCAACATATGCGATACCCCAGCCATCGATACGATATG
66 CGAGCTGTCAAGGACTCGCAACATATGCGATACCCCAACCATCGATACGATATG
* * *
9935 CTATAATCCAGAATTTCATTCTCATGTTTGTATCAACTCTGTTACAAGTATACAATGCTGCTCAC
1 CTATAATCCAGAATTTCACTCTCATGTCTATATCAACTCTG-TACAAGTATACAATGCTGCTCAC
* *
10000 ACGAGTTGTCAAGGACTCGCAACATATGTGATACCCCAACCATCGATACG
65 ACGAGCTGTCAAGGACTCGCAACATATGCGATACCCCAACCATCGATACG
10050 GTATTTGTGC
Statistics
Matches: 106, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
119 38 0.36
120 68 0.64
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (119 bp):
CTATAATCCAGAATTTCACTCTCATGTCTATATCAACTCTGTACAAGTATACAATGCTGCTCACA
CGAGCTGTCAAGGACTCGCAACATATGCGATACCCCAACCATCGATACGATATG
Found at i:15370 original size:119 final size:118
Alignment explanation
Indices: 15151--15387 Score: 307
Period size: 119 Copynumber: 2.0 Consensus size: 118
15141 GCTTCCACAA
* * *
15151 GCTATAATCCAGAATTTCATCCTCATGTCTGTATCAACTCTGTACCAGTATACGATGTTGCTCAC
1 GCTATAATCCAGAATTTCATCCTCATGTCTATATCAACTCTGTACCAGTATACAATGCTGCTCAC
* * *
15216 ATGATCTGTCGAGGACTCACAACATATGCGATACCCTAACCATCGATATAGTAT
66 ACGATCTATCGAGGACTCACAACATATGCGATACCC-AACCATCGATAGAGTAT
* * *
15270 GCTATAATCCAGAATTTCATTCTCGTGTCTATATCAACTCTGTTACTAGTATACAATGCTGCTCA
1 GCTATAATCCAGAATTTCATCCTCATGTCTATATCAACTCTG-TACCAGTATACAATGCTGCTCA
* ** * *
15335 CACGAGT-TAT-TAGGACTCGTAACATTTGCGGTACCCAACCATCGATAGAGTAT
65 CACGA-TCTATCGAGGACTCACAACATATGCGATACCCAACCATCGATAGAGTAT
15388 CTGTGCGTGG
Statistics
Matches: 102, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
118 16 0.16
119 60 0.59
120 25 0.25
121 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (118 bp):
GCTATAATCCAGAATTTCATCCTCATGTCTATATCAACTCTGTACCAGTATACAATGCTGCTCAC
ACGATCTATCGAGGACTCACAACATATGCGATACCCAACCATCGATAGAGTAT
Found at i:34370 original size:85 final size:85
Alignment explanation
Indices: 34229--34402 Score: 330
Period size: 85 Copynumber: 2.0 Consensus size: 85
34219 TTTGTGTTTT
* *
34229 TGCTTAAATATAATTTCCTCTTTTTTAGTCTTTTTCCAAACACAAACGGTGTGGTGGGTTCTCTT
1 TGCTTAAATATAATTTCCTCTTTTTTAGTCTTTTTCCAAACACAAACGGTGCGGTGGGCTCTCTT
34294 GTTGTTGTCACTCCCACTTG
66 GTTGTTGTCACTCCCACTTG
34314 TGCTTAAATATAATTTCCTCTTTTTTAGTCTTTTTCCAAACACAAACGGTGCGGTGGGCTCTCTT
1 TGCTTAAATATAATTTCCTCTTTTTTAGTCTTTTTCCAAACACAAACGGTGCGGTGGGCTCTCTT
34379 GTTGTTGTCACTCCCACTTG
66 GTTGTTGTCACTCCCACTTG
34399 TGCT
1 TGCT
34403 GGTATTTTAG
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.43
Consensus pattern (85 bp):
TGCTTAAATATAATTTCCTCTTTTTTAGTCTTTTTCCAAACACAAACGGTGCGGTGGGCTCTCTT
GTTGTTGTCACTCCCACTTG
Found at i:44030 original size:14 final size:15
Alignment explanation
Indices: 44007--44035 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43997 AAAACCAAAT
44007 AAATATAAAAATAAA
1 AAATATAAAAATAAA
44022 AAATA-AAAAATAAA
1 AAATATAAAAATAAA
44036 TTATTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATATAAAAATAAA
Found at i:49435 original size:7 final size:7
Alignment explanation
Indices: 49425--49456 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
49415 AACTAGGTTG
*
49425 TTGTTTT
1 TTGTGTT
49432 TTGTGTT
1 TTGTGTT
49439 TTGTGTT
1 TTGTGTT
49446 TTGTGTT
1 TTGTGTT
49453 TTGT
1 TTGT
49457 TTTGTGGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.25, T:0.75
Consensus pattern (7 bp):
TTGTGTT
Found at i:51772 original size:32 final size:32
Alignment explanation
Indices: 51732--51812 Score: 128
Period size: 32 Copynumber: 2.5 Consensus size: 32
51722 TGAAATTAGT
*
51732 TTGTTGGATTTTGAAATTATTATGTTTTAAAG-
1 TTGTTGGATATTGAAATTATTATGTTTT-AAGC
*
51764 TTGTTGGATATTGAATTTATTATGTTTTAAGC
1 TTGTTGGATATTGAAATTATTATGTTTTAAGC
51796 TTGTTGGATATTGAAAT
1 TTGTTGGATATTGAAAT
51813 GATTGACAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 3 0.07
32 42 0.93
ACGTcount: A:0.27, C:0.01, G:0.20, T:0.52
Consensus pattern (32 bp):
TTGTTGGATATTGAAATTATTATGTTTTAAGC
Found at i:54000 original size:46 final size:46
Alignment explanation
Indices: 53947--54051 Score: 156
Period size: 46 Copynumber: 2.3 Consensus size: 46
53937 ACTAATTATA
* * *
53947 TGGTGTAATATTAGTTATGCACTTGGACAGTATTATAGTTATCATG
1 TGGTGTAATACTAGTTATGCACTTGGAAAATATTATAGTTATCATG
* *
53993 TGGTGTAATACTAGTTATGTACTTGGAAAATATTGTAGTTATCATG
1 TGGTGTAATACTAGTTATGCACTTGGAAAATATTATAGTTATCATG
*
54039 TGGTGTACTACTA
1 TGGTGTAATACTA
54052 AATTGTAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.41
Consensus pattern (46 bp):
TGGTGTAATACTAGTTATGCACTTGGAAAATATTATAGTTATCATG
Found at i:64463 original size:21 final size:21
Alignment explanation
Indices: 64429--64482 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
64419 GGAGTTTTTA
* * *
64429 GTATCGGTAAAAGCATGACTT
1 GTATTGGTAGAAGCATCACTT
64450 GT-TTGGGTAGAAGCATCACTT
1 GTATT-GGTAGAAGCATCACTT
64471 GTATTGGTAGAA
1 GTATTGGTAGAA
64483 ATTTGCACTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 25 0.89
22 2 0.07
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (21 bp):
GTATTGGTAGAAGCATCACTT
Done.