Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000368.1 Kokia drynarioides strain JFW-HI SEQ_111159, 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: 33139
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Warning! 146 characters in sequence are not A, C, G, or T
Found at i:389 original size:29 final size:29
Alignment explanation
Indices: 346--787 Score: 382
Period size: 29 Copynumber: 15.1 Consensus size: 29
336 GGAGGTCCCT
* *
346 AAACTGTCTAAAAATTTCATTTTTACCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCTCG
* *
376 AAACTTCTAAAAATCCCATTTTTTACCTCG
1 AAACTTCCAAAAATTCCA-TTTTTACCTCG
* *
406 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCTCG
* *
435 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCTCG
* *
464 AAACTTCCAAAAATGCTATTTTTGACCTC-
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
* * *
493 -AACTTTCAAAAATCCCATTTTTATCCCCG
1 AAACTTCCAAAAATTCCATTTTTA-CCTCG
* *
522 AAACCTCCAAAAATTACCA-TTTTACCCTTG
1 AAACTTCCAAAAATT-CCATTTTTA-CCTCG
* * *
552 -AACTTCCAAAAATCCCATTTTCAACCCCG
1 AAACTTCCAAAAATTCCATTTT-TACCTCG
*
581 AAACTTCCAAAAAATCCATTTTTAGCC-C-
1 AAACTTCCAAAAATTCCATTTTTA-CCTCG
* * *
609 AAACTTCCAAAAATTCCATTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCTCG
* * * *
638 AAACCTCCAAAAATTAC-TATTTTACCCCC
1 AAACTTCCAAAAATTCCAT-TTTTACCTCG
*
667 AAACTTCCAAAAA-TCTCATTTTTAACCTCA
1 AAACTTCCAAAAATTC-CATTTTT-ACCTCG
* *
697 AAACTTCCAAAAATTCTAATTTTACTCTCG
1 AAACTTCCAAAAATTCCATTTTTAC-CTCG
* *
727 -AACTTCTAAAAATGCCATTTTTGATCC-CG
1 AAACTTCCAAAAATTCCATTTTT-A-CCTCG
* *
756 AAATTTCCAAAAATTCCATTTTTGCCCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
786 AA
1 AA
788 TGTCTAAAAA
Statistics
Matches: 342, Mismatches: 48, Indels: 44
0.79 0.11 0.10
Matches are distributed among these distances:
27 3 0.01
28 50 0.15
29 154 0.45
30 129 0.38
31 6 0.02
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCTCG
Found at i:447 original size:59 final size:59
Alignment explanation
Indices: 346--778 Score: 432
Period size: 59 Copynumber: 7.4 Consensus size: 59
336 GGAGGTCCCT
* * * * * * *
346 AAACTGTCTAAAAATTTCATTTTTACCTCGAAACTTCTAAAAATCCCATTTTTTACCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCG
* *
406 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTT-ACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCG
* * * * *
464 AAACTTCCAAAAATGCTATTTTTGA--CCTCAACTTTCAAAAATCCCATTTTTATCCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCG
* * * *
522 AAACCTCCAAAAATTACCA-TTTTACCCTTGAACTTCCAAAAATCCCATTTTCAACCCCG
1 AAACTTCCAAAAATT-CCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCG
* * * *
581 AAACTTCCAAAAAATCCATTTTTAGCCC-AAACTTCCAAAAATTCCA-TTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCG
* * * * * *
638 AAACCTCCAAAAATTAC-TATTTTACCCCCAAACTTCCAAAAATCTCATTTTTAACCTCA
1 AAACTTCCAAAAATTCCAT-TTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCG
* * * * * * * *
697 AAACTTCCAAAAATTCTAATTTTA-CTCTCGAACTTCTAAAAATGCCATTTTTGATCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCCT-AAACTTCCAAAAATCCCATTTTTAACCCCG
*
756 AAATTTCCAAAAATTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTT
779 GCCCTCGAAT
Statistics
Matches: 307, Mismatches: 55, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
56 1 0.00
57 55 0.18
58 83 0.27
59 163 0.53
60 5 0.02
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCG
Found at i:660 original size:175 final size:175
Alignment explanation
Indices: 366--783 Score: 533
Period size: 175 Copynumber: 2.4 Consensus size: 175
356 AAAATTTCAT
* *
366 TTTTA-CCTCGAAACTTCTAAAAATCCCATTTTTTACCTCGAAACTTCCAAAAATTCCATTTTTA
1 TTTTACCCTCG-AACTTCTAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTA
* * * * * *
430 CCCCTAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATGCTATTTTTGA-CCTC-
65 GCCCTAAACTTCCAAAAATTCCATTTTAACCCCAAAACCTCCAAAAATACTA-TTTT-ACCCCCA
* * * *
493 AACTTTCAAAAATCCCATTTTTATCCCCGAAACCTCCAAAAATTAC-CA
128 AACTTCCAAAAATCCCATTTTTAACCCCAAAACCTCCAAAAATT-CTAA
* * * *
541 TTTTACCCTTGAACTTCCAAAAATCCCATTTTCAACCCCGAAACTTCCAAAAAATCCATTTTTAG
1 TTTTACCCTCGAACTTCTAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTAG
606 CCC-AAACTTCCAAAAATTCCATTTTAACCCCAAAACCTCCAAAAATTACTATTTTACCCCCAAA
66 CCCTAAACTTCCAAAAATTCCATTTTAACCCCAAAACCTCCAAAAA-TACTATTTTACCCCCAAA
* * *
670 CTTCCAAAAATCTCATTTTTAACCTCAAAACTTCCAAAAATTCTAA
130 CTTCCAAAAATCCCATTTTTAACCCCAAAACCTCCAAAAATTCTAA
* * * * *
716 TTTTACTCTCGAACTTCTAAAAATGCCATTTTTGATCCCGAAATTTCCAAAAATTCCATTTTT-G
1 TTTTACCCTCGAACTTCTAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTAG
780 CCCT
66 CCCT
784 CGAATGTCTA
Statistics
Matches: 209, Mismatches: 28, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
173 1 0.00
174 51 0.24
175 153 0.73
176 4 0.02
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (175 bp):
TTTTACCCTCGAACTTCTAAAAATCCCATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTAG
CCCTAAACTTCCAAAAATTCCATTTTAACCCCAAAACCTCCAAAAATACTATTTTACCCCCAAAC
TTCCAAAAATCCCATTTTTAACCCCAAAACCTCCAAAAATTCTAA
Found at i:797 original size:29 final size:28
Alignment explanation
Indices: 705--808 Score: 75
Period size: 30 Copynumber: 3.5 Consensus size: 28
695 CAAAACTTCC
* * * *
705 AAAAATTCTAATTTTACTCTCGAACTTCT
1 AAAAATTCCATTTTTGCCCTCGAA-TTCT
* * *
734 AAAAATGCCATTTTTGATCC-CGAAATTTCC
1 AAAAATTCCATTTTTG-CCCTCG-AA-TTCT
764 AAAAATTCCATTTTTGCCCTCGAATGTCT
1 AAAAATTCCATTTTTGCCCTCGAAT-TCT
*
793 AAAAAATTCCTTTTTT
1 -AAAAATTCCATTTTT
809 AAACCCCAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 9
0.73 0.15 0.11
Matches are distributed among these distances:
28 1 0.02
29 20 0.34
30 37 0.64
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (28 bp):
AAAAATTCCATTTTTGCCCTCGAATTCT
Found at i:807 original size:59 final size:60
Alignment explanation
Indices: 355--843 Score: 279
Period size: 59 Copynumber: 8.3 Consensus size: 60
345 TAAACTGTCT
* * * * *
355 AAAAATTTCATTTTTA-CCTCGAAACTTCTAAAAATCCCATTTTT-TACCTCGAAA-CTTCC
1 AAAAATTCCATTTTTACCCTCG-AACTTCTAAAAATGCCATTTTTAAACC-CCAAATTTTCC
* * * *
414 AAAAATTCCATTTTTACCC-CTAAACTTCCAAAAATTCCATTTTT--ACCCCTAAA-CTTCC
1 AAAAATTCCATTTTTACCCTC-GAACTTCTAAAAATGCCATTTTTAAACCCC-AAATTTTCC
* * * * **
472 AAAAATGCTATTTTTGA-CCTC-AACTT-TCAAAAATCCCATTTTT-ATCCCCGAAA-CCTCC
1 AAAAATTCCATTTTT-ACCCTCGAACTTCT-AAAAATGCCATTTTTAAACCCC-AAATTTTCC
* * * * *
530 AAAAATTACCA-TTTTACCCTTGAACTTCCAAAAATCCCA-TTTTCAACCCCGAAA-CTTCC
1 AAAAATT-CCATTTTTACCCTCGAACTTCTAAAAATGCCATTTTTAAACCCC-AAATTTTCC
* * * * * ***
589 AAAAAATCCATTTTTAGCC-CAAACTTCCAAAAATTCCA-TTTT-AACCCCAAAACCTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCTAAAAATGCCATTTTTAAACCCCAAATTTTCC
* * * * * **
646 AAAAATTAC-TATTTTACCCCCAAACTTCCAAAAAT-CTCATTTTT-AACCTCAAAACTTCC
1 AAAAATTCCAT-TTTTACCCTCGAACTTCTAAAAATGC-CATTTTTAAACCCCAAATTTTCC
* * * * * *
705 AAAAATTCTAATTTTACTCTCGAACTTCTAAAAATGCCATTTTTGATCCCGAAA-TTTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCTAAAAATGCCATTTTTAAACCCCAAATTTTCC
* * *
764 AAAAATTCCATTTTTGCCCTCGAA-TGTCTAAAAAATTCCTTTTTTAAACCCCAAATTTTCC
1 AAAAATTCCATTTTTACCCTCGAACT-TCT-AAAAATGCCATTTTTAAACCCCAAATTTTCC
*
825 CAAAATTACCA-TTTTACCC
1 AAAAATT-CCATTTTTACCC
844 CCGGGTATCC
Statistics
Matches: 354, Mismatches: 51, Indels: 48
0.78 0.11 0.11
Matches are distributed among these distances:
56 4 0.01
57 46 0.13
58 95 0.27
59 159 0.45
60 29 0.08
61 18 0.05
62 3 0.01
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (60 bp):
AAAAATTCCATTTTTACCCTCGAACTTCTAAAAATGCCATTTTTAAACCCCAAATTTTCC
Found at i:5341 original size:15 final size:16
Alignment explanation
Indices: 5306--5346 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5296 AGATATAAAA
5306 TATAAAT-TTTAAGAT
1 TATAAATATTTAAGAT
*
5321 TATAAATATTTAATAT
1 TATAAATATTTAAGAT
5337 T-TAAAATATT
1 TAT-AAATATT
5347 ATATAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TATAAATATTTAAGAT
Found at i:8717 original size:29 final size:29
Alignment explanation
Indices: 8678--8758 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
8668 TTTGCCTCAA
8678 GTTACATTTTAGTCA-TATATGTTTGAAAT
1 GTTACATTTTAGTCACT-TATGTTTGAAAT
8707 GTTACATTTTAGTCACTTATGTTTGAAAT
1 GTTACATTTTAGTCACTTATGTTTGAAAT
* *
8736 GTTGCGTTTTAGTCACTTATGTT
1 GTTACATTTTAGTCACTTATGTT
8759 ATTATTTTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 48 0.98
30 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (29 bp):
GTTACATTTTAGTCACTTATGTTTGAAAT
Found at i:12410 original size:14 final size:14
Alignment explanation
Indices: 12391--12418 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12381 AAATTTTATT
12391 TATTTTTAAAAAAA
1 TATTTTTAAAAAAA
12405 TATTTTTAAAAAAA
1 TATTTTTAAAAAAA
12419 AATAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TATTTTTAAAAAAA
Found at i:15778 original size:20 final size:20
Alignment explanation
Indices: 15748--15785 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15738 CAAATATATT
15748 TACTCACTAATTTCAAAATAA
1 TACTCACTAATTT-AAAATAA
15769 TACT-ACTAATTTAAAAT
1 TACTCACTAATTTAAAAT
15786 TATTGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (20 bp):
TACTCACTAATTTAAAATAA
Found at i:15975 original size:22 final size:22
Alignment explanation
Indices: 15950--15994 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
15940 AATCAAACCA
15950 TTATACTTTTTATGATTCACAT
1 TTATACTTTTTATGATTCACAT
15972 TTATACTTTTTATGATTCACAT
1 TTATACTTTTTATGATTCACAT
15994 T
1 T
15995 GAAAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (22 bp):
TTATACTTTTTATGATTCACAT
Found at i:26772 original size:60 final size:61
Alignment explanation
Indices: 26657--26772 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 61
26647 TAAAGGTTAA
* ** * **
26657 AGCATTAGCGGCGTTTATGAGGAAACGCCGTTAAAGGTCAGAGAATTAGTGACGTTATCAG
1 AGCATTAGCGGCGTTTATGAGAAAACGCCACTAAAGGTCAAAGAATTAGCAACGTTATCAG
*
26718 AGCATTAGC-GCGTTTATGAGAAAACGCCACTAAAGGTCAAAGCATTAGCAACGTT
1 AGCATTAGCGGCGTTTATGAGAAAACGCCACTAAAGGTCAAAGAATTAGCAACGTT
26773 TATTAGAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 39 0.81
61 9 0.19
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (61 bp):
AGCATTAGCGGCGTTTATGAGAAAACGCCACTAAAGGTCAAAGAATTAGCAACGTTATCAG
Found at i:26814 original size:41 final size:41
Alignment explanation
Indices: 26718--26822 Score: 106
Period size: 41 Copynumber: 2.6 Consensus size: 41
26708 ACGTTATCAG
* *
26718 AGCATTAGC-GCGTTTATGAGAAAACGCCACTAAAGGTCAA
1 AGCATTAACAGCGTTTATTAGAAAACGCCACTAAAGGTCAA
* * * *
26758 AGCATTAGCAACGTTTATTAGAAAACGCCGCTAAATGT-AA
1 AGCATTAACAGCGTTTATTAGAAAACGCCACTAAAGGTCAA
* * *
26798 GAGCTTTAACGGCGTTTACTAGAAA
1 -AGCATTAACAGCGTTTATTAGAAA
26823 TCCCCGTTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
40 11 0.20
41 43 0.80
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (41 bp):
AGCATTAACAGCGTTTATTAGAAAACGCCACTAAAGGTCAA
Found at i:31609 original size:18 final size:19
Alignment explanation
Indices: 31586--31622 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
31576 TGTGTCAAAT
31586 ATTAAT-TTCTTT-CTACTA
1 ATTAATATT-TTTCCTACTA
31604 ATTAATATTTTTCCTACTA
1 ATTAATATTTTTCCTACTA
31623 TAATGTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTAATATTTTTCCTACTA
Found at i:31853 original size:17 final size:18
Alignment explanation
Indices: 31830--31922 Score: 95
Period size: 17 Copynumber: 5.3 Consensus size: 18
31820 TCAAACTCAT
31830 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
* *
31848 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAGA
*
31865 TTTAAACTTATTTTAA-A
1 TTTAAATTTATTTTAAGA
* *
31882 TTTAAATTTAATTTGAG-
1 TTTAAATTTATTTTAAGA
*
31899 TTTAAATTTGTTTTCAA-A
1 TTTAAATTTATTTT-AAGA
31917 TTTAAA
1 TTTAAA
31923 ATAAATAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
17 41 0.67
18 20 0.33
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:32679 original size:22 final size:21
Alignment explanation
Indices: 32642--32693 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
32632 CCAAAAATGC
32642 ATTAAATAA-ATATTAA-ATAT
1 ATTAAATAATATATTAATA-AT
32662 ATTAAATAATGATATTAATAAT
1 ATTAAATAAT-ATATTAATAAT
32684 ATT-AATAATA
1 ATTAAATAATA
32694 CCTTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 10 0.34
21 6 0.21
22 12 0.41
23 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTAAATAATATATTAATAAT
Done.