Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010636.1 Kokia drynarioides strain JFW-HI SEQ_125576, 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: 33626
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:572 original size:29 final size:29
Alignment explanation
Indices: 529--1047 Score: 220
Period size: 29 Copynumber: 17.7 Consensus size: 29
519 CCTCGAAAGT
* *
529 CCCTA-AACTGTCCAAAAATTTCGTTTCTA
1 CCCTAGAACT-TCCAAAAATTCCATTTCTA
* * *
558 CCCTTGAACTTCCAAAAATCCCATTTTCGA
1 CCCTAGAACTTCCAAAAATTCCA-TTTCTA
* * *
588 CCCCAAAACTTCCAAAAATTCCATTTTTA
1 CCCTAGAACTTCCAAAAATTCCATTTCTA
* * * *
617 CCCTCGAACTTCAAAAAATCCCATTTTTAA
1 CCCTAGAACTTCCAAAAATTCCATTTCT-A
* * *
647 CCCCAAAACTTTCAAAAATTACCATTT-TA
1 CCCTAGAACTTCCAAAAATT-CCATTTCTA
* * * * *
676 CCCCCA-AACTTCCACAAGTCCCATTTTTGA
1 -CCCTAGAACTTCCAAAAATTCCATTTCT-A
* * *
706 CCC-CGAAACTTCTAAACATTACCATTT-TA
1 CCCTAG-AACTTCCAAAAATT-CCATTTCTA
* * *
735 CCCTCGAACTT-TAAAAA-TCTCATTTTTGA
1 CCCTAGAACTTCCAAAAATTC-CATTTCT-A
* *
764 CCC-CGAACCTTTCAAAAATTACCATTT-TA
1 CCCTAGAA-CTTCCAAAAATT-CCATTTCTA
* * *
793 CCCTCA-AACTTCTAAAAATCCCATTTTTGA
1 CCCT-AGAACTTCCAAAAATTCCATTTCT-A
* * *
823 CCC-CGAACCTTCCGAAAATTACCATTTTTA
1 CCCTAGAA-CTTCCAAAAATT-CCATTTCTA
* *
853 CCCTCGAACTTCCAAAAATCCCATTT-TGA
1 CCCTAGAACTTCCAAAAATTCCATTTCT-A
* *
882 CCCCA-AACCTTCTAAAAATTACCATTT-TA
1 CCCTAGAA-CTTCCAAAAATT-CCATTTCTA
*
911 CCCCTA-AACTTCCAAAAA-TCCTATTTTTGA
1 -CCCTAGAACTTCCAAAAATTCC-ATTTCT-A
* *
941 CCC-CGAACCTTTCAAAAATTACCATTT-TA
1 CCCTAGAA-CTTCCAAAAATT-CCATTTCTA
*
970 CCCCT-GAACTTCCAAAAA-TCTCATTTTTGA
1 -CCCTAGAACTTCCAAAAATTC-CATTTCT-A
1000 -CCTCA-AACCTTCCAAAAATTACCATTT-TA
1 CCCT-AGAA-CTTCCAAAAATT-CCATTTCTA
*
1029 CCCTCGAACTTCCAAAAAT
1 CCCTAGAACTTCCAAAAAT
1048 CTCATTTTTG
Statistics
Matches: 387, Mismatches: 54, Indels: 98
0.72 0.10 0.18
Matches are distributed among these distances:
26 1 0.00
27 9 0.02
28 39 0.10
29 149 0.39
30 144 0.37
31 41 0.11
32 4 0.01
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (29 bp):
CCCTAGAACTTCCAAAAATTCCATTTCTA
Found at i:600 original size:30 final size:28
Alignment explanation
Indices: 564--1090 Score: 350
Period size: 30 Copynumber: 18.0 Consensus size: 28
554 TCTACCCTTG
564 AACTTCCAAAAATCCCATTTTCGACCCCAA
1 AACTTCCAAAAATCCCATTTT-GACCCC-A
* * *
594 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTGACCC-CA
* *
623 AACTTCAAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATCCCA-TTTTGACCCC-A
* *
653 AACTTTCAAAAATTACCATTTT-ACCCCCA
1 AACTTCCAAAAA-TCCCATTTTGA-CCCCA
* *
682 AACTTCCACAAGTCCCATTTTTGACCCCGA
1 AACTTCCAAAAATCCCA-TTTTGACCCC-A
* * * *
712 AACTTCTAAACATTACCATTTT-ACCCTCG
1 AACTTCCAAA-AATCCCATTTTGACCC-CA
* *
741 AACTT-TAAAAATCTCATTTTTGACCCCGA
1 AACTTCCAAAAATCCCA-TTTTGACCCC-A
* * *
770 ACCTTTCAAAAATTACCATTTT-ACCCTCA
1 AACTTCCAAAAA-TCCCATTTTGACCC-CA
*
799 AACTTCTAAAAATCCCATTTTTGACCCCGA
1 AACTTCCAAAAATCCCA-TTTTGACCCC-A
* * * * *
829 ACCTTCCGAAAATTACCATTTTTACCCTCG
1 AACTTCC-AAAAATCCCATTTTGACCC-CA
859 AACTTCCAAAAATCCCATTTTGACCCCA
1 AACTTCCAAAAATCCCATTTTGACCCCA
* *
887 AACCTTCTAAAAATTACCATTTT-ACCCCTA
1 AA-CTTCCAAAAA-TCCCATTTTGACCCC-A
*
917 AACTTCCAAAAATCCTATTTTTGACCCCGA
1 AACTTCCAAAAATCCCA-TTTTGACCCC-A
* * * *
947 ACCTTTCAAAAATTACCATTTT-ACCCCTG
1 AACTTCCAAAAA-TCCCATTTTGACCCC-A
* *
976 AACTTCCAAAAATCTCATTTTTGACCTCA
1 AACTTCCAAAAATCCCA-TTTTGACCCCA
* *
1005 AACCTTCCAAAAATTACCATTTT-ACCCTCG
1 AA-CTTCCAAAAA-TCCCATTTTGACCC-CA
* *
1035 AACTTCCAAAAATCTCATTTTTGACTCCGA
1 AACTTCCAAAAATCCCA-TTTTGAC-CCCA
* * *
1065 ACCTTCCAAAACTACCATTTT-ACCCC
1 AACTTCCAAAAATCCCATTTTGACCCC
1091 CGTGCATCCG
Statistics
Matches: 389, Mismatches: 73, Indels: 73
0.73 0.14 0.14
Matches are distributed among these distances:
27 6 0.02
28 31 0.08
29 160 0.41
30 163 0.42
31 29 0.07
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.31
Consensus pattern (28 bp):
AACTTCCAAAAATCCCATTTTGACCCCA
Found at i:634 original size:59 final size:59
Alignment explanation
Indices: 539--1089 Score: 693
Period size: 59 Copynumber: 9.4 Consensus size: 59
529 CCCTAAACTG
* * * * * *
539 TCCAAAAATT-TCGTTTCTACCCTTGAACTTCCAAAAATCCCATTTTCGACCCCAAAACT
1 TCCAAAAATTACCATTT-TACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * * *
598 TCCAAAAATT-CCATTTTTACCCTCGAACTTCAAAAAATCCCATTTTTAACCCCAAAACT
1 TCCAAAAATTACCA-TTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * * * * *
657 TTCAAAAATTACCATTTTACCCCCAAACTTCCACAAGTCCCATTTTTGACCCCGAAACT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * * *
716 TCTAAACATTACCATTTTACCCTCGAACTT-TAAAAATCTCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * *
774 TTCAAAAATTACCATTTTACCCTCAAACTTCTAAAAATCCCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* *
833 TCCGAAAATTACCATTTTTACCCTCGAACTTCCAAAAATCCCA-TTTTGACCCCAAACCT
1 TCCAAAAATTACCA-TTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * *
892 TCTAAAAATTACCATTTTACCC-CTAAACTTCCAAAAATCCTATTTTTGACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * * *
951 TTCAAAAATTACCATTTTACCC-CTGAACTTCCAAAAATCTCATTTTTGACCTCAAACCT
1 TCCAAAAATTACCATTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* *
1010 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACTCCGAACCT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
*
1069 TCC-AAAACTACCATTTTACCC
1 TCCAAAAATTACCATTTTACCC
1090 CCGTGCATCC
Statistics
Matches: 434, Mismatches: 51, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
57 1 0.00
58 90 0.21
59 310 0.71
60 33 0.08
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.31
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
Found at i:3311 original size:35 final size:34
Alignment explanation
Indices: 3262--3333 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 34
3252 CGACACGATG
*
3262 GCTGGGGTATCGCATGTGTTGCGAGTCCTCAACA
1 GCTGGGGTACCGCATGTGTTGCGAGTCCTCAACA
3296 GCNTGGGGTACCGCATGTGTTGCGAGTCCTCAACA
1 GC-TGGGGTACCGCATGTGTTGCGAGTCCTCAACA
3331 GCT
1 GCT
3334 CCTGTGAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 3 0.08
35 33 0.92
ACGTcount: A:0.17, C:0.25, G:0.32, T:0.25
Consensus pattern (34 bp):
GCTGGGGTACCGCATGTGTTGCGAGTCCTCAACA
Found at i:5261 original size:14 final size:12
Alignment explanation
Indices: 5209--5279 Score: 54
Period size: 14 Copynumber: 5.4 Consensus size: 12
5199 ATATTTTTTT
5209 AATATTTATATA
1 AATATTTATATA
5221 AATATTTGAATAATA
1 AATATTT--AT-ATA
*
5236 AATAATT-TATA
1 AATATTTATATA
5247 AATATTTAGTAATA
1 AATATTTA-T-ATA
*
5261 AATTTTTAATATA
1 AATATTT-ATATA
5274 ATATAT
1 A-ATAT
5280 GAATATTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
11 9 0.19
12 8 0.17
13 5 0.11
14 15 0.32
15 10 0.21
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (12 bp):
AATATTTATATA
Found at i:5276 original size:26 final size:27
Alignment explanation
Indices: 5212--5284 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 27
5202 TTTTTTTAAT
5212 ATTTATATAAATATTTGAATAATAAATA
1 ATTTATAT-AATATTTGAATAATAAATA
*
5240 ATTTATA-AATATTT-AGTAATAAAT-
1 ATTTATATAATATTTGAATAATAAATA
* *
5264 TTTTAATATAATATATGAATA
1 ATTT-ATATAATATTTGAATA
5285 TTTTAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 3 0.08
25 12 0.32
26 13 0.34
27 3 0.08
28 7 0.18
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (27 bp):
ATTTATATAATATTTGAATAATAAATA
Found at i:5284 original size:24 final size:22
Alignment explanation
Indices: 5262--5304 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
5252 TTAGTAATAA
5262 ATTTT-TAATATAATATATGAAT
1 ATTTTATAATATAA-ATATGAAT
5284 ATTTTAATAATATAAATATGA
1 ATTTT-ATAATATAAATATGA
5305 GTTCTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 6 0.32
24 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
ATTTTATAATATAAATATGAAT
Found at i:6631 original size:25 final size:25
Alignment explanation
Indices: 6603--6654 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
6593 GCCTCACAAT
6603 AAGCAAAGCAAGAAGTTTATGAATG
1 AAGCAAAGCAAGAAGTTTATGAATG
6628 AAGCAAAGCAAGAAGTTTATGAATG
1 AAGCAAAGCAAGAAGTTTATGAATG
6653 AA
1 AA
6655 CATAGTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.50, C:0.08, G:0.23, T:0.19
Consensus pattern (25 bp):
AAGCAAAGCAAGAAGTTTATGAATG
Found at i:7049 original size:6 final size:6
Alignment explanation
Indices: 7038--7066 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
7028 GGGAAAACAA
7038 GCATAG GCATAG GCATAG GCATAG GCATA
1 GCATAG GCATAG GCATAG GCATAG GCATA
7067 AGGAGATGAC
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:0.34, C:0.17, G:0.31, T:0.17
Consensus pattern (6 bp):
GCATAG
Found at i:10091 original size:8 final size:8
Alignment explanation
Indices: 10083--10120 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
10073 TATATATAAT
*
10083 TTTAAAAT
1 TTTAAAAA
10091 TTTAAAAA
1 TTTAAAAA
10099 TTTAAAAA
1 TTTAAAAA
10107 TTTAAAAA
1 TTTAAAAA
10115 TTTAAA
1 TTTAAA
10121 TACAATCACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TTTAAAAA
Found at i:17537 original size:30 final size:30
Alignment explanation
Indices: 17491--17553 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
17481 CAACTTAACA
* * *
17491 AACATATGCCTCTAAAATAGTAACAAATTT
1 AACAAATGCCTCTAAAATAATAACAAAATT
*
17521 AACAAATGCCTTTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
17551 AAC
1 AAC
17554 GATAAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:20542 original size:52 final size:52
Alignment explanation
Indices: 20459--20643 Score: 307
Period size: 52 Copynumber: 3.6 Consensus size: 52
20449 AATGAAAAAA
20459 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
*
20511 GTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
* * * * *
20563 GTCCGATGACTATGTGTCATCTTGAGTATATGATTCTTTTAAGGATTAAGAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
*
20615 GTTCGATGACTATGTGTCATCGTGAGTAT
1 GTCCGATGACTATGTGTCATCGTGAGTAT
20644 TAAATGAAAT
Statistics
Matches: 124, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 124 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.36
Consensus pattern (52 bp):
GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
Found at i:21645 original size:2 final size:2
Alignment explanation
Indices: 21638--21670 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21628 ATCTTACACG
21638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21671 AAACAAAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23938 original size:7 final size:7
Alignment explanation
Indices: 23926--23970 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
23916 TCCCTTGTAA
23926 AGGTGGG
1 AGGTGGG
23933 AGGTGGG
1 AGGTGGG
23940 AGGTGGG
1 AGGTGGG
23947 AGGTGGG
1 AGGTGGG
*
23954 AGGCGGG
1 AGGTGGG
*
23961 AGGCGGG
1 AGGTGGG
23968 AGG
1 AGG
23971 CGACGATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.16, C:0.04, G:0.71, T:0.09
Consensus pattern (7 bp):
AGGTGGG
Found at i:28117 original size:2 final size:2
Alignment explanation
Indices: 28112--28145 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28102 CCTCCCCCCT
28112 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28146 CATTATAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:29605 original size:14 final size:14
Alignment explanation
Indices: 29588--29618 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
29578 ACTTTTTAGA
29588 TTTTAAAATTAAAT
1 TTTTAAAATTAAAT
29602 TTTTAAAATTAAAT
1 TTTTAAAATTAAAT
29616 TTT
1 TTT
29619 ATTAAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTAAAATTAAAT
Found at i:31888 original size:57 final size:57
Alignment explanation
Indices: 31812--31928 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
31802 AAGTTTGCTA
31812 TTAATAACTTTTGATTGGATTCAAAGTCTACTACAAGAAGTTTAATTTGCTTACTTC
1 TTAATAACTTTTGATTGGATTCAAAGTCTACTACAAGAAGTTTAATTTGCTTACTTC
31869 TTAATAACTTTTGATTGGATTCAAAGTCTACTACAAGAAGTTTAATTTGCTTACTTC
1 TTAATAACTTTTGATTGGATTCAAAGTCTACTACAAGAAGTTTAATTTGCTTACTTC
31926 TTA
1 TTA
31929 TCATCAAGAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.43
Consensus pattern (57 bp):
TTAATAACTTTTGATTGGATTCAAAGTCTACTACAAGAAGTTTAATTTGCTTACTTC
Done.