Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005130.1 Kokia drynarioides strain JFW-HI SEQ_118966, 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: 20499
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2193 original size:23 final size:23
Alignment explanation
Indices: 2162--2208 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
2152 CTGTTGTGAG
2162 AATGCCATATAGCCTAGTAGGAT
1 AATGCCATATAGCCTAGTAGGAT
*
2185 AATGTCATATAGCCTAGTAGGAT
1 AATGCCATATAGCCTAGTAGGAT
2208 A
1 A
2209 TAACCAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (23 bp):
AATGCCATATAGCCTAGTAGGAT
Found at i:5889 original size:98 final size:98
Alignment explanation
Indices: 5768--5967 Score: 246
Period size: 97 Copynumber: 2.0 Consensus size: 98
5758 TTCATGAAAA
* *
5768 CTTTAAAATCAAGGCAATATTCTTTTATTTTAAG-TTTTGAAAATTTATGCCTTAACTTACTAGG
1 CTTTAAAATCAAGGCAATATTC-TTTA-TCTAAGATTCTGAAAATTTATGCCTTAACTTACTAGG
* *
5832 -GTCGATTTTTCTTCAAATCGAAATAATCGAATA-C
64 TG-CGACTTTTCTTCAAATCGAAACAATCGAATATC
* * ** *
5866 CTTT-AAATCGAGGCAATGTTTCTTTATCTCCGATTCTGAAAATTTGTGCCTTAACTTACTAGGT
1 CTTTAAAATCAAGGCAAT-ATTCTTTATCTAAGATTCTGAAAATTTATGCCTTAACTTACTAGGT
*
5930 GCGACTTTTCTTCAAATCGAGACAATCGAATATC
65 GCGACTTTTCTTCAAATCGAAACAATCGAATATC
5964 CTTT
1 CTTT
5968 TCCAAAGTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
96 3 0.03
97 72 0.82
98 13 0.15
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (98 bp):
CTTTAAAATCAAGGCAATATTCTTTATCTAAGATTCTGAAAATTTATGCCTTAACTTACTAGGTG
CGACTTTTCTTCAAATCGAAACAATCGAATATC
Found at i:8476 original size:17 final size:16
Alignment explanation
Indices: 8450--8491 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
8440 AAAAATATTT
8450 TAAATAATATTAAATAA
1 TAAATAATATT-AATAA
*
8467 TAAATTATATTAATAA
1 TAAATAATATTAATAA
*
8483 TAATTAATA
1 TAAATAATA
8492 ATAAAAAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATAATATTAATAA
Found at i:8802 original size:15 final size:17
Alignment explanation
Indices: 8772--8807 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
8762 GACTCGGGTT
8772 AAAATGAAATAAAATGA
1 AAAATGAAATAAAATGA
8789 AAAATG-AA-AAAATGA
1 AAAATGAAATAAAATGA
8804 AAAA
1 AAAA
8808 GGTGAATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
16 2 0.11
17 6 0.32
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (17 bp):
AAAATGAAATAAAATGA
Found at i:9664 original size:29 final size:29
Alignment explanation
Indices: 9499--9770 Score: 95
Period size: 29 Copynumber: 9.2 Consensus size: 29
9489 AGAAATTATA
* *
9499 TTTTGACCCTTGAACTTTTCCAAAAATTCTA-
1 TTTTGACCC-T-AATTTTTCC-AAAATTCCAT
*
9530 TTTTGACCATAATTTTTCCAAAATTACC-T
1 TTTTGACCCTAATTTTTCCAAAATT-CCAT
** * *
9559 TTTT-ACCCCTAAAATGTCTAAAATTCCAT
1 TTTTGA-CCCTAATTTTTCCAAAATTCCAT
* * *
9588 TTTT-ACCCTGAACTTTTT-GAATATT-TATT
1 TTTTGACCCT-AA-TTTTTCCAAAATTCCA-T
* *
9617 TTTTTACACCTGAA-CTTTCCAAAATTCCAT
1 TTTTGAC-CCT-AATTTTTCCAAAATTCCAT
*
9647 TTTTGACCCTAATTTTTCCAAAAAATACCA-
1 TTTTGACCCTAATTTTTCC--AAAATTCCAT
* * * * * *
9677 TTTT-ACTATCGAACTTCT-AAAAATTTCAT
1 TTTTGAC--CCTAATTTTTCCAAAATTCCAT
*
9706 TTTTGACCCTGATTTTTCCAAAATTGCCA-
1 TTTTGACCCTAATTTTTCCAAAATT-CCAT
*
9735 TTTT-ACCCTCGAA--GTTCCAAAAATTCCAT
1 TTTTGACCCT--AATTTTTCC-AAAATTCCAT
9764 TTTTGAC
1 TTTTGAC
9771 TTCGATTTTT
Statistics
Matches: 179, Mismatches: 37, Indels: 51
0.67 0.14 0.19
Matches are distributed among these distances:
28 40 0.22
29 82 0.46
30 28 0.16
31 29 0.16
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (29 bp):
TTTTGACCCTAATTTTTCCAAAATTCCAT
Found at i:9722 original size:117 final size:116
Alignment explanation
Indices: 9498--10121 Score: 449
Period size: 117 Copynumber: 5.3 Consensus size: 116
9488 TAGAAATTAT
* * * * *
9498 ATTTTGACCCTTGAACTTTTCCAAAAATTCTATTTTGACCATAATTTTTCC-AAAATTACCTTTT
1 ATTTT-ACCCTCGAAC-TTTCCAAAAATTCCATTTTGACCCTAATTTTTCCAAAAAATACCATTT
* * * * * **
9562 TACCCCTAAAATGTCT-AAAATTCCATTTTTACCCTGAACTTTTT-GAATATTTATT
64 TACCCCCAAACT-TCTAAAAATTTCATTTTTACCCTG-A-TTTTTCCAA-AATTACC
*
9617 TTTTTACACCT-GAACTTTCC-AAAATTCCATTTTTGACCCTAATTTTTCCAAAAAATACCATTT
1 ATTTTAC-CCTCGAACTTTCCAAAAATTCCA-TTTTGACCCTAATTTTTCCAAAAAATACCATTT
*** * *
9680 TACTATCGAACTTCTAAAAATTTCATTTTTGACCCTGATTTTTCCAAAATTGCC
64 TACCCCCAAACTTCTAAAAATTTCATTTTT-ACCCTGATTTTTCCAAAATTACC
* * * * *
9734 ATTTTACCCTCGAA-GTTCCAAAAATTCCATTTTTGA-CTTCGATTTTTCCAAAAATTATCATTT
1 ATTTTACCCTCGAACTTTCCAAAAATTCCA-TTTTGACCCT-AATTTTTCCAAAAAATACCATTT
*
9797 TACCCCCAAACTTCTAAAAA-TTCTATTTTTAGCCCTGATTTTTCCAAAAAGTACC
64 TACCCCCAAACTTCTAAAAATTTC-ATTTTTA-CCCTGATTTTTCC-AAAATTACC
* * * *
9852 ATTTTACCCTCAAACTTT-CAAAATTTTCATTTTAACCCTAATTTTT-CAAAAAAGTACCATTTT
1 ATTTTACCCTCGAACTTTCCAAAAATTCCATTTTGACCCTAATTTTTCCAAAAAA-TACCATTTT
* * * *
9915 ACCCTCGAACTT-TCAAAATTTCCA-TTTTAACCTCGATTTTTCCAAAATTACC
65 ACCCCCAAACTTCTAAAAATTT-CATTTTTACCCT-GATTTTTCCAAAATTACC
* * * * *** * *
9967 ATTTTACCCTCGGA-TGTCTAAAAATTCCATTTTAAATCCC-AAGCCTTCCAAAAATTACTAGTT
1 ATTTTACCCTCGAACTTTCCAAAAATTCCATTTT-GA-CCCTAATTTTTCCAAAAAATACCA-TT
* * * * * *
10030 TTACCCCCGAA-TATCT-AAAATTTCACATTTAACCCCGAACTTTCCCAAAATTACC
63 TTACCCCCAAACT-TCTAAAAATTTCA-TTTTTACCCTG-ATTTTTCCAAAATTACC
* * *
10085 ATTTTTCCCTC-AAGTGTCC-AAAATTACCATTTT-ACCC
1 ATTTTACCCTCGAACTTTCCAAAAATT-CCATTTTGACCC
10122 CTGGGCATCC
Statistics
Matches: 412, Mismatches: 63, Indels: 64
0.76 0.12 0.12
Matches are distributed among these distances:
114 2 0.00
115 38 0.09
116 60 0.15
117 183 0.44
118 114 0.28
119 15 0.04
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (116 bp):
ATTTTACCCTCGAACTTTCCAAAAATTCCATTTTGACCCTAATTTTTCCAAAAAATACCATTTTA
CCCCCAAACTTCTAAAAATTTCATTTTTACCCTGATTTTTCCAAAATTACC
Found at i:9765 original size:58 final size:59
Alignment explanation
Indices: 9498--9999 Score: 397
Period size: 59 Copynumber: 8.6 Consensus size: 59
9488 TAGAAATTAT
* * * *
9498 ATTTTGACCCTTGAACTTTTCCAAAAATTCTA-TTTTGACCATAATTTTTCC-AAAATTACC
1 ATTTT-ACCCTCGAAC--TTCCAAAAATTCCATTTTTGACCCTGATTTTTCCAAAAATTACC
* * * * * * * **
9558 TTTTTACCC-CTAAAATGT-CTAAAATTCCATTTTT-ACCCTGAACTTTTT-GAATATTTATT
1 ATTTTACCCTC-GAACT-TCCAAAAATTCCATTTTTGACCCTG-A-TTTTTCCAAAAATTACC
* * *
9617 TTTTTACACCT-GAACTTTCC-AAAATTCCATTTTTGACCCTAATTTTTCCAAAAAATACC
1 ATTTTAC-CCTCGAAC-TTCCAAAAATTCCATTTTTGACCCTGATTTTTCCAAAAATTACC
** * * *
9676 ATTTTACTATCGAACTTCTAAAAATTTCATTTTTGACCCTGATTTTTCC-AAAATTGCC
1 ATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTGATTTTTCCAAAAATTACC
* * *
9734 ATTTTACCCTCGAAGTTCCAAAAATTCCATTTTTGA-CTTCGATTTTTCCAAAAATTATC
1 ATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCT-GATTTTTCCAAAAATTACC
* * * * *
9793 ATTTTACCCCCAAACTTCTAAAAATTCTATTTTT-AGCCCTGATTTTTCCAAAAAGTACC
1 ATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA-CCCTGATTTTTCCAAAAATTACC
* * * * * * * *
9852 ATTTTACCCTCAAACTTTCAAAATTTTCA-TTTTAACCCTAATTTTTCAAAAAAGTACC
1 ATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTGATTTTTCCAAAAATTACC
* * *
9910 ATTTTACCCTCGAACTTTCAAAATTTCCA-TTTT-AACCTCGATTTTTCC-AAAATTACC
1 ATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCT-GATTTTTCCAAAAATTACC
* *
9967 ATTTTACCCTCGGA-TGTCTAAAAATTCCATTTT
1 ATTTTACCCTCGAACT-TCCAAAAATTCCATTTT
10000 AAATCCCAAG
Statistics
Matches: 356, Mismatches: 64, Indels: 46
0.76 0.14 0.10
Matches are distributed among these distances:
56 1 0.00
57 51 0.14
58 129 0.36
59 160 0.45
60 15 0.04
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (59 bp):
ATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTGATTTTTCCAAAAATTACC
Found at i:9883 original size:28 final size:28
Alignment explanation
Indices: 9843--9977 Score: 119
Period size: 28 Copynumber: 4.7 Consensus size: 28
9833 GATTTTTCCA
*
9843 AAAAGTACCATTTTACCCTCAAACTTTC
1 AAAATTACCATTTTACCCTCAAACTTTC
** **
9871 AAAATTTTCATTTTAACCCT-AATTTTTC
1 AAAATTACCATTTT-ACCCTCAAACTTTC
* *
9899 AAAAAAGTACCATTTTACCCTCGAACTTTC
1 --AAAATTACCATTTTACCCTCAAACTTTC
* * * **
9929 AAAATTTCCATTTTAACCTCGATTTTTCC
1 AAAATTACCATTTTACCCTCAAACTTT-C
9958 AAAATTACCATTTTACCCTC
1 AAAATTACCATTTTACCCTC
9978 GGATGTCTAA
Statistics
Matches: 84, Mismatches: 18, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
28 39 0.46
29 29 0.35
30 16 0.19
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (28 bp):
AAAATTACCATTTTACCCTCAAACTTTC
Found at i:9998 original size:28 final size:28
Alignment explanation
Indices: 9667--10000 Score: 92
Period size: 29 Copynumber: 11.5 Consensus size: 28
9657 AATTTTTCCA
* ** * *
9667 AAAAATACCATTTTACTATCGAACTTCT
1 AAAAATTCCATTTTACCCTCGGATTTCT
* *
9695 AAAAATTTCATTTTTGACCCT--GATTTTT
1 AAAAATTCCA-TTTT-ACCCTCGGATTTCT
* * * *
9723 CCAAAATTGCCATTTTACCCTCGAAGTTCC
1 -AAAAATT-CCATTTTACCCTCGGATTTCT
* *
9753 AAAAATTCCATTTTTGA-CTTC-GATTTTTCC
1 AAAAATTCCA-TTTT-ACCCTCGGA--TTTCT
* * ** *
9783 AAAAATTATCATTTTACCCCCAAACTTCT
1 AAAAATT-CCATTTTACCCTCGGATTTCT
* *
9812 AAAAATTCTATTTTTAGCCCT--GATTTTTCC
1 AAAAATTCCA-TTTTA-CCCTCGGA--TTTCT
* **
9842 AAAAAGTACCATTTTACCCTCAAACTTTC-
1 AAAAA-TTCCATTTTACCCTCGGA-TTTCT
* * **** *
9871 AAAATTTTCATTTTAACCCTAATTTTTCA
1 AAAAATTCCATTTT-ACCCTCGGATTTCT
* *
9900 AAAAAGTACCATTTTACCCTCGAACTTTC-
1 AAAAA-TTCCATTTTACCCTCGGA-TTTCT
* * *
9929 AAAATTTCCATTTTAACCTC-GATTTTT
1 AAAAATTCCATTTTACCCTCGGATTTCT
* *
9956 CCAAAATTACCATTTTACCCTCGGATGTCT
1 -AAAAATT-CCATTTTACCCTCGGATTTCT
9986 AAAAATTCCATTTTA
1 AAAAATTCCATTTTA
10001 AATCCCAAGC
Statistics
Matches: 221, Mismatches: 57, Indels: 56
0.66 0.17 0.17
Matches are distributed among these distances:
26 3 0.01
27 1 0.00
28 60 0.27
29 88 0.40
30 62 0.28
31 7 0.03
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (28 bp):
AAAAATTCCATTTTACCCTCGGATTTCT
Found at i:10080 original size:59 final size:58
Alignment explanation
Indices: 9661--10122 Score: 230
Period size: 58 Copynumber: 7.9 Consensus size: 58
9651 GACCCTAATT
* * ** * * *
9661 TTTCCAAAAAATACCATTTTACTATCGAACT-TCTAAAAATTT-CATTTTTGACCCTG-AT
1 TTTCCCAAAATTACCATTTTACCCTCGAA-TATCT-AAAATTTCCA-TTTTAACCCCGAAC
* * * * * ** **
9719 TTTTCCAAAATTGCCATTTTACCCTCGAAGT-TCCAAAAATTCCATTTTTGACTTCGATT
1 TTTCCCAAAATTACCATTTTACCCTCGAA-TATCTAAAATTTCCA-TTTTAACCCCGAAC
* * * * * * * * **
9778 TTTCCAAAAATTATCATTTTACCCCCAAACT-TCTAAAAATTCTATTTTTAGCCCTGATT
1 TTTCCCAAAATTACCATTTTACCCTCGAA-TATCTAAAATTTCCA-TTTTAACCCCGAAC
* * * * * * *
9837 TTTCCAAAAAGTACCATTTTACCCTCAAACTTTC-AAAATTTTCATTTTAA-CCCTAATT
1 TTTCCCAAAATTACCATTTTACCCTCGAA-TATCTAAAATTTCCATTTTAACCCCGAA-C
** * * * *
9895 TTTCAAAAAAGTACCATTTTACCCTCGAACTTTC-AAAATTTCCATTTTAACCTCG-AT
1 TTTCCCAAAATTACCATTTTACCCTCGAA-TATCTAAAATTTCCATTTTAACCCCGAAC
* * * * *
9952 TTTTCCAAAATTACCATTTTACCCTCGGATGTCTAAAAATTCCATTTTAAATCCC-AAGC
1 TTTCCCAAAATTACCATTTTACCCTCGAATATCTAAAATTTCCATTTT-AACCCCGAA-C
* * * *
10011 CTTCCAAAAATTACTAGTTTTACCCCCGAATATCTAAAATTTCACA-TTTAACCCCGAAC
1 TTTCCCAAAATTACCA-TTTTACCCTCGAATATCTAAAATTTC-CATTTTAACCCCGAAC
* * * *
10070 TTTCCCAAAATTACCATTTTTCCCTC-AAGTGTCCAAAATTACCATTTT-ACCCC
1 TTTCCCAAAATTACCATTTTACCCTCGAA-TATCTAAAATTTCCATTTTAACCCC
10123 TGGGCATCCA
Statistics
Matches: 321, Mismatches: 69, Indels: 29
0.77 0.16 0.07
Matches are distributed among these distances:
56 3 0.01
57 56 0.17
58 117 0.36
59 114 0.36
60 29 0.09
61 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.37
Consensus pattern (58 bp):
TTTCCCAAAATTACCATTTTACCCTCGAATATCTAAAATTTCCATTTTAACCCCGAAC
Found at i:10087 original size:29 final size:28
Alignment explanation
Indices: 9901--10122 Score: 87
Period size: 28 Copynumber: 7.7 Consensus size: 28
9891 AATTTTTCAA
* *
9901 AAAAGTACCATTTTACCCTCGAACTTT-C
1 AAAATTACCATTTAACCC-CGAACTTTCC
* * **
9929 AAAATTTCCATTTTAACCTCGATTTTTCC
1 AAAATTACCA-TTTAACCCCGAACTTTCC
* * * *
9958 AAAATTACCATTTTACCCTCGGA-TGTCTA
1 AAAATTACCATTTAACCC-CGAACTTTC-C
* *
9987 AAAATT-CCATTTTAAATCCC-AAGCCTTCC
1 AAAATTACCA-TTT-AACCCCGAA-CTTTCC
* * * *
10016 AAAAATTACTAGTTTTACCCCCGAA-TATCT
1 -AAAATTACCA--TTTAACCCCGAACTTTCC
*
10046 AAAATTTCACATTTAACCCCGAACTTTCCC
1 AAAATTAC-CATTTAACCCCGAACTTT-CC
** * *
10076 AAAATTACCATTTTTCCCTC-AAGTGTCC
1 AAAATTACCATTTAACCC-CGAACTTTCC
*
10104 AAAATTACCATTTTACCCC
1 AAAATTACCATTTAACCCC
10123 TGGGCATCCA
Statistics
Matches: 142, Mismatches: 36, Indels: 33
0.67 0.17 0.16
Matches are distributed among these distances:
27 1 0.01
28 57 0.40
29 49 0.35
30 23 0.16
31 6 0.04
32 6 0.04
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.34
Consensus pattern (28 bp):
AAAATTACCATTTAACCCCGAACTTTCC
Found at i:10468 original size:97 final size:98
Alignment explanation
Indices: 10356--10554 Score: 264
Period size: 97 Copynumber: 2.0 Consensus size: 98
10346 TCCATGAAAA
* *
10356 CTTTAAAATCAAGGCAATATTCT-TTTAT-TTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAG
1 CTTTAAAATCAAGGCAATATT-TGTTTATCTCCGA-TTCTGAAAATTTGTGCCTTAACTTACTAG
* *
10419 GCGTGATTTTTCTTCAAATC-AGAATAATCGAATA-C
64 GCGCGA-CTTTCTTCAAATCTAG-ATAATCGAATATC
* * *
10454 CTTT-AAATCGAGGCAATGTTTGTTTATCTCCGATTCTGAAAATTTGTGCCTTAACTTACTAGGT
1 CTTTAAAATCAAGGCAATATTTGTTTATCTCCGATTCTGAAAATTTGTGCCTTAACTTACTAGGC
10518 GCGACTTTCTTCAAATCTAGATAATCGAATATC
66 GCGACTTTCTTCAAATCTAGATAATCGAATATC
10551 CTTT
1 CTTT
10555 TCCAAAGTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
96 24 0.27
97 58 0.64
98 8 0.09
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (98 bp):
CTTTAAAATCAAGGCAATATTTGTTTATCTCCGATTCTGAAAATTTGTGCCTTAACTTACTAGGC
GCGACTTTCTTCAAATCTAGATAATCGAATATC
Done.