Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013229.1 Kokia drynarioides strain JFW-HI SEQ_128248, 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: 6827
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Found at i:790 original size:28 final size:29
Alignment explanation
Indices: 681--1026 Score: 129
Period size: 29 Copynumber: 11.7 Consensus size: 29
671 AAGGTCCCTA
* *
681 AACTGTCCAAAAATTATATTTTGACCCT-T
1 AACT-TCCCAAAATTATATTTTGACCCTCG
* *
710 AATCTTCTCCAAAATTATATTTTGACCCCCA
1 AA-CTTC-CCAAAATTATATTTTGACCCTCG
* * *
741 AACTTTCCAAAATTACATTTTTACCCTCG
1 AACTTCCCAAAATTATATTTTGACCCTCG
*
770 AACTTCCCAAATTTATATTTTGA-CCTCG
1 AACTTCCCAAAATTATATTTTGACCCTCG
** * * * *
798 ATTTTTCCAAAAAATACCATTTT-ACCCTCA
1 A-ACTTCCCAAAATTA-TATTTTGACCCTCG
* ** * * *
828 AACTTCCAAAAATTCCATTTTTAACCTCT
1 AACTTCCCAAAATTATATTTTGACCCTCG
** ** * *
857 ATTTTTCTAAAAATTACCATTTT-ACCCTTG
1 A-ACTTCCCAAAATTA-TATTTTGACCCTCG
* *
887 AACTTTCAAAAATTCCAT-TTTTGA-CCTCG
1 AACTTCCCAAAATT--ATATTTTGACCCTCG
** * *
916 ATTTTTCCAAAAATTACCATTTT-ACCCTCG
1 A-ACTTCCCAAAATTA-TATTTTGACCCTCG
*
946 AACTTCCAAAAATTCCAT-TTTTGA-CCTC-
1 AACTTCCCAAAATT--ATATTTTGACCCTCG
* * *
974 AATTCTTCCCAAAAATTACCATTTT-ACCCCCA
1 AA--CTTCCC-AAAATTA-TATTTTGACCCTCG
*
1006 AACTTCCCAAAATTACATTTT
1 AACTTCCCAAAATTATATTTT
1027 TAACCCTAAT
Statistics
Matches: 243, Mismatches: 48, Indels: 53
0.71 0.14 0.15
Matches are distributed among these distances:
28 21 0.09
29 114 0.47
30 83 0.34
31 23 0.09
32 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (29 bp):
AACTTCCCAAAATTATATTTTGACCCTCG
Found at i:812 original size:59 final size:59
Alignment explanation
Indices: 686--1237 Score: 517
Period size: 59 Copynumber: 9.4 Consensus size: 59
676 CCCTAAACTG
* * * * **
686 TCCAAAAATTA-TATTTTGACCCTTAATCTTCTCCAAAATT--ATATTTTGACCCCCAAACTT
1 TCCAAAAATTACCATTTT-ACCCTCAAAC-T-TCCAAAATTCCATATTTTGA-CCTCAATTTT
* * * *
746 TCC-AAAATTA-CATTTTTACCCTCGAACTTCCCAAATT-TATATTTTGACCTCGATTTT
1 TCCAAAAATTACCA-TTTTACCCTCAAACTTCCAAAATTCCATATTTTGACCTCAATTTT
* * *
803 TCCAAAAAATACCATTTTACCCTCAAACTTCCAAAAATTCCAT-TTTTAACCTCTATTTT
1 TCCAAAAATTACCATTTTACCCTCAAACTTCC-AAAATTCCATATTTTGACCTCAATTTT
* ** * *
862 TCTAAAAATTACCATTTTACCCTTGAACTTTCAAAAATTCCAT-TTTTGACCTCGATTTT
1 TCCAAAAATTACCATTTTACCCTCAAAC-TTCCAAAATTCCATATTTTGACCTCAATTTT
*
921 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCAT-TTTTGACCTCAATTCTT
1 TCCAAAAATTACCATTTTACCCTCAAACTTCC-AAAATTCCATATTTTGACCTCAATT-TT
* * * *
981 CCCAAAAATTACCATTTTACCCCCAAACTTCCCAAAATTACAT-TTTTAACC-CTAATTTT
1 TCCAAAAATTACCATTTTACCCTCAAACTT-CCAAAATTCCATATTTTGACCTC-AATTTT
* * * * *
1040 TCCAAAAAATACCATTTTACCC-CTAAACTTCCTAAAATTCCA-ATTTTGAACACGATTCT
1 TCCAAAAATTACCATTTTACCCTC-AAACTTCC-AAAATTCCATATTTTGACCTCAATTTT
* *
1099 TCCTAAAAATTACCATTTTACCCCCAAACTTCCTAAAATTCCAT-TTTTGACC-CTAATTCT
1 TCC-AAAAATTACCATTTTACCCTCAAACTTCC-AAAATTCCATATTTTGACCTC-AATTTT
* * * * *
1159 TCCCAAAATTACCATTTTACCCCCAAACTTCCAAAATTCC--ATTTTAACCTCGATTCT
1 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAATTCCATATTTTGACCTCAATTTT
*
1216 TCCTAAAATTACCATTTTACCC
1 TCCAAAAATTACCATTTTACCC
1238 CCGACCATTT
Statistics
Matches: 426, Mismatches: 45, Indels: 45
0.83 0.09 0.09
Matches are distributed among these distances:
57 50 0.12
58 48 0.11
59 212 0.50
60 113 0.27
61 3 0.01
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.37
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAATTCCATATTTTGACCTCAATTTT
Found at i:871 original size:30 final size:31
Alignment explanation
Indices: 787--1233 Score: 190
Period size: 30 Copynumber: 15.1 Consensus size: 31
777 CAAATTTATA
* *
787 TTTTGACCTCGATTTTTCCAAAAAATACCA-
1 TTTTAACCTCGATTTTTCCAAAAATTACCAT
* ***
817 TTTTACCCTC-AAACTTCCAAAAATT-CCAT
1 TTTTAACCTCGATTTTTCCAAAAATTACCAT
* *
846 TTTTAACCTCTATTTTTCTAAAAATTACCA-
1 TTTTAACCTCGATTTTTCCAAAAATTACCAT
* * **
876 TTTTACCCTTGAACTTT-CAAAAATT-CCAT
1 TTTTAACCTCGATTTTTCCAAAAATTACCAT
*
905 TTTTGACCTCGATTTTTCCAAAAATTACCA-
1 TTTTAACCTCGATTTTTCCAAAAATTACCAT
* **
935 TTTTACCCTCGA-ACTTCCAAAAATT-CCAT
1 TTTTAACCTCGATTTTTCCAAAAATTACCAT
* * *
964 TTTTGACCTCAATTCTTCCCAAAAATTACCA-
1 TTTTAACCTCGATT-TTTCCAAAAATTACCAT
* * *** *
995 TTTT-ACCCCCAAACTTCCCAAAATTA-CAT
1 TTTTAACCTCGATTTTTCCAAAAATTACCAT
* *
1024 TTTTAACC-CTAATTTTTCCAAAAAATACCA-
1 TTTTAACCTC-GATTTTTCCAAAAATTACCAT
* * *** *
1054 TTTT-ACCCCTAAACTTCCTAAAATT-CCAAT
1 TTTTAACCTCGATTTTTCCAAAAATTACC-AT
* * *
1084 TTTGAA-CACGATTCTTCCTAAAAATTACCA-
1 TTTTAACCTCGATTTTTCC-AAAAATTACCAT
* * *** *
1114 TTTT-ACCCCCAAACTTCCTAAAATT-CCAT
1 TTTTAACCTCGATTTTTCCAAAAATTACCAT
* * * *
1143 TTTTGACC-CTAATTCTTCCCAAAATTACCA-
1 TTTTAACCTC-GATTTTTCCAAAAATTACCAT
* * ***
1173 TTTT-ACCCCCAAACTTCC-AAAATT-CCA-
1 TTTTAACCTCGATTTTTCCAAAAATTACCAT
* *
1200 TTTTAACCTCGATTCTTCCTAAAATTACCAT
1 TTTTAACCTCGATTTTTCCAAAAATTACCAT
1231 TTT
1 TTT
1234 ACCCCCGACC
Statistics
Matches: 313, Mismatches: 74, Indels: 59
0.70 0.17 0.13
Matches are distributed among these distances:
27 7 0.02
28 32 0.10
29 115 0.37
30 118 0.38
31 36 0.12
32 5 0.02
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.37
Consensus pattern (31 bp):
TTTTAACCTCGATTTTTCCAAAAATTACCAT
Found at i:1010 original size:60 final size:59
Alignment explanation
Indices: 744--1239 Score: 567
Period size: 59 Copynumber: 8.4 Consensus size: 59
734 ACCCCCAAAC
* * * *
744 TTTCC-AAAATTA-CATTTTTACCCTCGAACTTCC-CAAATT-TATATTTTGACCTCGATT
1 TTTCCAAAAATTACCA-TTTTACCCCCAAACTTCCAAAAATTCCAT-TTTTGACCTCGATT
* * * *
801 TTTCCAAAAAATACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCTATT
1 TTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCGATT
* *** *
860 TTTCTAAAAATTACCATTTTACCCTTGAACTTTCAAAAATTCCATTTTTGACCTCGATT
1 TTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCGATT
* * *
919 TTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCAATT
1 TTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCGATT
* * * * *
978 CTTCCCAAAAATTACCATTTTACCCCCAAACTTCCCAAAATTACATTTTTAACC-CTAATT
1 -TTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTC-GATT
* * * * * *
1038 TTTCCAAAAAATACCATTTTACCCCTAAACTTCCTAAAATTCCAATTTTGAACACGATT
1 TTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCGATT
* * *
1097 CTTCCTAAAAATTACCATTTTACCCCCAAACTTCCTAAAATTCCATTTTTGACC-CTAATT
1 TTTCC-AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTC-GATT
* * *
1157 CTTCCCAAAATTACCATTTTACCCCCAAACTTCC-AAAATTCCA-TTTTAACCTCGATT
1 TTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCGATT
* *
1214 CTTCCTAAAATTACCATTTTACCCCC
1 TTTCCAAAAATTACCATTTTACCCCC
1240 GACCATTTTA
Statistics
Matches: 387, Mismatches: 42, Indels: 20
0.86 0.09 0.04
Matches are distributed among these distances:
57 40 0.10
58 33 0.09
59 208 0.54
60 106 0.27
ACGTcount: A:0.32, C:0.28, G:0.02, T:0.37
Consensus pattern (59 bp):
TTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCGATT
Found at i:1046 original size:119 final size:119
Alignment explanation
Indices: 749--1239 Score: 588
Period size: 119 Copynumber: 4.2 Consensus size: 119
739 CAAACTTTCC
* * * * *
749 AAAATTA-CATTTTTACCCTCGAACTTCCCAAATTTATA-TTTTGACCTCGATTTTTCCAAAAAA
1 AAAATTACCA-TTTTACCCCCAAACTTCCCAAAATTACATTTTTGACCTCAATTTTTCCAAAAAA
* * *
812 TACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCTATT-TTTCTA
65 TACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGATTCTTCCCA
*** * * * * *
866 AAAATTACCATTTTACCCTTGAACTTTCAAAAATTCCATTTTTGACCTCGATTTTTCCAAAAATT
1 AAAATTACCATTTTACCCCCAAACTTCCCAAAATTACATTTTTGACCTCAATTTTTCCAAAAAAT
* * *
931 ACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCAATTCTTCCCA
66 ACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGATTCTTCCCA
*
985 AAAATTACCATTTTACCCCCAAACTTCCCAAAATTACATTTTTAACC-CTAATTTTTCCAAAAAA
1 AAAATTACCATTTTACCCCCAAACTTCCCAAAATTACATTTTTGACCTC-AATTTTTCCAAAAAA
* * * *
1049 TACCATTTTACCC-CTAAACTTCCTAAAATTCCAATTTTGAA-CACGATTCTTCCTA
65 TACCATTTTACCCTC-AAACTTCCAAAAATTCC-ATTTTTAACCTCGATTCTTCCCA
* * * * *
1104 AAAATTACCATTTTACCCCCAAACTTCCTAAAATTCCATTTTTGACC-CTAATTCTTCCCAAAAT
1 AAAATTACCATTTTACCCCCAAACTTCCCAAAATTACATTTTTGACCTC-AATTTTTCCAAAAAA
* *
1168 TACCATTTTACCCCCAAACTTCC-AAAATTCCA-TTTTAACCTCGATTCTT-CCT
65 TACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGATTCTTCCCA
1220 AAAATTACCATTTTACCCCC
1 AAAATTACCATTTTACCCCC
1240 GACCATTTTA
Statistics
Matches: 328, Mismatches: 38, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
116 26 0.08
117 39 0.12
118 81 0.25
119 175 0.53
120 7 0.02
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.37
Consensus pattern (119 bp):
AAAATTACCATTTTACCCCCAAACTTCCCAAAATTACATTTTTGACCTCAATTTTTCCAAAAAAT
ACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGATTCTTCCCA
Done.