Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011675.1 Kokia drynarioides strain JFW-HI SEQ_126667, 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: 2225
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:754 original size:29 final size:28
Alignment explanation
Indices: 722--885 Score: 100
Period size: 29 Copynumber: 5.6 Consensus size: 28
712 CTAACTTTTT
722 AAAATTATATTTTGACCCTGATTTTTCTA
1 AAAATTATATTTTGACCCTGATTTTTC-A
* ** * *
751 AAAATTATAATTTT-ACCCCTAAACTATCC
1 AAAATTAT-ATTTTGA-CCCTGATTTTTCA
* *
780 AAAA-TATCATTTTGAACCTAATTTTTCCA
1 AAAATTAT-ATTTTGACCCTGATTTTT-CA
* * ** *
809 AAAATTATATTTTTACCCACGAACTTTCC
1 AAAATTATATTTTGACCC-TGATTTTTCA
*
838 AAAATTCTATTTTTGACCCTGATTTTTTCAA
1 AAAATTATA-TTTTGACCCTGA-TTTTTC-A
*
869 AAAATTTTATTTT-ACCC
1 AAAATTATATTTTGACCC
886 CCAACTTTCC
Statistics
Matches: 101, Mismatches: 25, Indels: 18
0.70 0.17 0.12
Matches are distributed among these distances:
28 15 0.15
29 42 0.42
30 36 0.36
31 8 0.08
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.43
Consensus pattern (28 bp):
AAAATTATATTTTGACCCTGATTTTTCA
Found at i:766 original size:58 final size:57
Alignment explanation
Indices: 703--901 Score: 195
Period size: 58 Copynumber: 3.4 Consensus size: 57
693 CAAACTTAAT
* ** *
703 TTTTACACTCTAACTTTTTAAAATTATATTTTGACCCTGATTTTTCTAAAAATTATAA
1 TTTTAC-CACTAACTTTCCAAAATTATATTTTGACCCTGATTTTTCAAAAAATTATAA
* * * * * *
761 TTTTACCCCTAAACTATCCAAAA-TATCATTTTGAACCTAATTTTTCCAAAAATTATAT
1 TTTTACCACT-AACTTTCCAAAATTAT-ATTTTGACCCTGATTTTTCAAAAAATTATAA
* * *
819 TTTTACCCACGAACTTTCCAAAATTCTATTTTTGACCCTGATTTTTTCAAAAAATT-TTA
1 TTTTA-CCACTAACTTTCCAAAATTATA-TTTTGACCCTGA-TTTTTCAAAAAATTATAA
* *
878 TTTTACCCCCAACTTTCCAAAATT
1 TTTTACCACTAACTTTCCAAAATT
902 CCATTTTTTA
Statistics
Matches: 116, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
57 6 0.05
58 76 0.66
59 21 0.18
60 13 0.11
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.43
Consensus pattern (57 bp):
TTTTACCACTAACTTTCCAAAATTATATTTTGACCCTGATTTTTCAAAAAATTATAA
Found at i:902 original size:58 final size:57
Alignment explanation
Indices: 731--1114 Score: 366
Period size: 58 Copynumber: 6.6 Consensus size: 57
721 TAAAATTATA
* * ** *
731 TTTTGACCCTGATTTTTCTAAAAATTATAATTTTACCCCTAAACTATCCAAAATAT-CA-
1 TTTTGA-CCTGATTTTTCCAAAAATTA-CATTTTACCCCCGAACTTTCCAAAAT-TCCAT
* * * *
789 TTTTGAACCTAATTTTTCCAAAAATTATATTTTTACCCACGAACTTTCCAAAATTCTAT
1 TTTTG-ACCTGATTTTTCCAAAAATTACA-TTTTACCCCCGAACTTTCCAAAATTCCAT
* **
848 TTTTGACCCTGATTTTTTCAAAAAATTTTATTTTACCCCC-AACTTTCCAAAATTCCAT
1 TTTTGA-CCTGA-TTTTTCCAAAAATTACATTTTACCCCCGAACTTTCCAAAATTCCAT
* * * * *
906 TTTTTACCTCGATCTTTCCAAAAATCACATTTTTGCCCCCAAACTTTCCAAAATTCCAT
1 TTTTGACCT-GATTTTTCCAAAAATTACA-TTTTACCCCCGAACTTTCCAAAATTCCAT
* * *
965 TTTTGACCTCAATTTTCCAAAAATTACCATTTTACCCCCGAA-TTTCCAAAAATTTCAT
1 TTTTGACCTGATTTTTCCAAAAATTA-CATTTTACCCCCGAACTTTCC-AAAATTCCAT
* *
1023 TTTTGACCTCAATTTTTCCAAAAACTACCATTTTACCCCCGAAC-TTCCAAAATTCCAT
1 TTTTGACCT-GATTTTTCCAAAAATTA-CATTTTACCCCCGAACTTTCCAAAATTCCAT
* *
1081 TTTTGACCCATGA-CTTTCCCAAAATTACCATTTT
1 TTTTGA-CC-TGATTTTTCCAAAAATTA-CATTTT
1115 TCCCTCGGGT
Statistics
Matches: 275, Mismatches: 36, Indels: 30
0.81 0.11 0.09
Matches are distributed among these distances:
57 22 0.08
58 153 0.56
59 84 0.31
60 16 0.06
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.39
Consensus pattern (57 bp):
TTTTGACCTGATTTTTCCAAAAATTACATTTTACCCCCGAACTTTCCAAAATTCCAT
Found at i:910 original size:29 final size:29
Alignment explanation
Indices: 878--1115 Score: 152
Period size: 29 Copynumber: 8.1 Consensus size: 29
868 AAAAATTTTA
878 TTTTACCCCCAACTTTCCAAAATTCCATT
1 TTTTACCCCCAACTTTCCAAAATTCCATT
* * * *
907 TTTTACCTCGATCTTTCCAAAAATCACA-T
1 TTTTACCCCCAACTTTCCAAAATTC-CATT
*
936 TTTTGCCCCCAAACTTTCCAAAATTCCATT
1 TTTTACCCCC-AACTTTCCAAAATTCCATT
* * *
966 TTTGA-CCTCAATTTTCCAAAAATTACCA--
1 TTTTACCCCCAACTTTCC-AAAATT-CCATT
*
994 TTTTACCCCCGAA-TTTCCAAAAATTTCATT
1 TTTTACCCCC-AACTTTCC-AAAATTCCATT
* * * *
1024 TTTGA-CCTCAATTTTTCCAAAAACTACCA--
1 TTTTACCCCCAA-CTTTCC-AAAA-TTCCATT
1053 TTTTACCCCCGAAC-TTCCAAAATTCCATT
1 TTTTACCCCC-AACTTTCCAAAATTCCATT
* ***
1082 TTTGACCCATGACTTTCCCAAAATTACCATT
1 TTTTACCCCCAACTTT-CCAAAATT-CCATT
1113 TTT
1 TTT
1116 CCCTCGGGTA
Statistics
Matches: 162, Mismatches: 28, Indels: 36
0.72 0.12 0.16
Matches are distributed among these distances:
27 4 0.02
28 21 0.13
29 75 0.46
30 49 0.30
31 13 0.08
ACGTcount: A:0.30, C:0.29, G:0.03, T:0.37
Consensus pattern (29 bp):
TTTTACCCCCAACTTTCCAAAATTCCATT
Found at i:927 original size:117 final size:116
Alignment explanation
Indices: 731--1089 Score: 415
Period size: 117 Copynumber: 3.1 Consensus size: 116
721 TAAAATTATA
* * * *
731 TTTTGACCCTGATTTTTCTAAAAATTATAATTTTACCCCTAAACTATCCAAAATATCATTTTGAA
1 TTTTGACCCTGATTTTTCAAAAAATTATAATTTTACCCC-CAACTTTCCAAAAT-TCATTTTTAA
* * *
796 CCT-AATTTTTCCAAAAATTATATTTTTACCCACGAACTTTCCAAAATTCTAT
64 CCTCAATTTTTCCAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCCAT
* *
848 TTTTGACCCTGATTTTTTCAAAAAATT-TTATTTTACCCCCAACTTTCCAAAATTCCATTTTTTA
1 TTTTGACCCTGA-TTTTTCAAAAAATTATAATTTTACCCCCAACTTTCCAAAATT-CATTTTTAA
* * * * *
912 CCTCGATCTTTCCAAAAATCACATTTTTGCCCCCAAACTTTCCAAAATTCCAT
64 CCTCAATTTTTCCAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCCAT
* * * ** *
965 TTTTGA-CCTCAATTTTCCAAAAATTACCATTTTACCCCCGAA-TTTCCAAAAATTTCATTTTTG
1 TTTTGACCCTGATTTTTCAAAAAATTATAATTTTACCCCC-AACTTTCC-AAAA-TTCATTTTTA
*
1028 ACCTCAATTTTTCCAAAAACTACCA-TTTTACCCCCGAAC-TTCCAAAATTCCAT
63 ACCTCAATTTTTCCAAAAATTA-CATTTTTACCCCCGAACTTTCCAAAATTCCAT
1081 TTTTGACCC
1 TTTTGACCC
1090 ATGACTTTCC
Statistics
Matches: 207, Mismatches: 26, Indels: 18
0.82 0.10 0.07
Matches are distributed among these distances:
115 13 0.06
116 62 0.30
117 115 0.56
118 17 0.08
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (116 bp):
TTTTGACCCTGATTTTTCAAAAAATTATAATTTTACCCCCAACTTTCCAAAATTCATTTTTAACC
TCAATTTTTCCAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCCAT
Found at i:1134 original size:117 final size:117
Alignment explanation
Indices: 731--1132 Score: 387
Period size: 117 Copynumber: 3.4 Consensus size: 117
721 TAAAATTATA
* ** ** *
731 TTTTGACCC-TGATTTTTCTAAAAATTATAATTTTACCCCTAAACTATCCAAAATATCA-TTTTG
1 TTTTGACCCATGA-TTTTCCAAAAATTACCATTTTACCCCCGAA-TATCCAAAATTTCATTTTTG
* * *
794 AACCT-AATTTTTCCAAAAATTA-TATTTTTACCCACGAACTTTCCAAAATTCTAT
64 -ACCTCAATTTTTCCAAAAA-TACCATTTTTACCCCCGAACTTTCCAAAATTCCAT
* ** * *
848 TTTTGACCC-TGATTTTTTCAAAAAATT-TTATTTTACCCCC-AACTTTCCAAAATTCCATTTTT
1 TTTTGACCCATGA--TTTTCCAAAAATTACCATTTTACCCCCGAA-TATCCAAAATTTCATTTTT
* * * * *
910 TACCTCGATCTTTCCAAAAAT-CACATTTTTGCCCCCAAACTTTCCAAAATTCCAT
63 GACCTCAATTTTTCCAAAAATAC-CATTTTTACCCCCGAACTTTCCAAAATTCCAT
*
965 TTTTGACCTCA--ATTTTCCAAAAATTACCATTTTACCCCCGAATTTCCAAAAATTTCATTTTTG
1 TTTTGACC-CATGATTTTCCAAAAATTACCATTTTACCCCCGAATATCC-AAAATTTCATTTTTG
1028 ACCTCAATTTTTCCAAAAACTACCA-TTTTACCCCCGAAC-TTCCAAAATTCCAT
64 ACCTCAATTTTTCCAAAAA-TACCATTTTTACCCCCGAACTTTCCAAAATTCCAT
* * * * **
1081 TTTTGACCCATGACTTTCCCAAAATTACCATTTTTCCCTCGGGTATCCAAAA
1 TTTTGACCCATGATTTTCCAAAAATTACCATTTTACCCCCGAATATCCAAAA
1133 ATCATATTTT
Statistics
Matches: 241, Mismatches: 30, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
115 14 0.06
116 61 0.25
117 148 0.61
118 17 0.07
119 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (117 bp):
TTTTGACCCATGATTTTCCAAAAATTACCATTTTACCCCCGAATATCCAAAATTTCATTTTTGAC
CTCAATTTTTCCAAAAATACCATTTTTACCCCCGAACTTTCCAAAATTCCAT
Found at i:1516 original size:58 final size:57
Alignment explanation
Indices: 1426--1558 Score: 230
Period size: 58 Copynumber: 2.3 Consensus size: 57
1416 NNNNNNNNNN
* *
1426 AAAATTCCATTTTTGACCTCAATTTTCCAAAAATTACCATTTTACCCCCGAATTTCC
1 AAAATTCCATTTTTGACCTCAATTTTCCAAAAACTACCATTTTACCCCCGAACTTCC
*
1483 AAAAATTTCATTTTTGACCTCAATTTTCCAAAAACTACCATTTTACCCCCGAACTTCC
1 -AAAATTCCATTTTTGACCTCAATTTTCCAAAAACTACCATTTTACCCCCGAACTTCC
1541 AAAATTCCATTTTTGACC
1 AAAATTCCATTTTTGACC
1559 CCGATTTTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
57 17 0.24
58 54 0.76
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (57 bp):
AAAATTCCATTTTTGACCTCAATTTTCCAAAAACTACCATTTTACCCCCGAACTTCC
Found at i:1560 original size:28 final size:30
Alignment explanation
Indices: 1426--1567 Score: 131
Period size: 29 Copynumber: 4.9 Consensus size: 30
1416 NNNNNNNNNN
*
1426 AAAATTCCATTTTTGACCTC-AATTTTCCA
1 AAAATTCCATTTTTGACCCCGAATTTTCCA
1455 AAAATTACCA-TTTT-ACCCCCGAA-TTTCCA
1 AAAATT-CCATTTTTGA-CCCCGAATTTTCCA
* *
1484 AAAATTTCATTTTTGACCTC-AATTTTCCA
1 AAAATTCCATTTTTGACCCCGAATTTTCCA
* *
1513 AAAACTACCA-TTTT-ACCCCCGAA-CTTCC-
1 AAAA-TTCCATTTTTGA-CCCCGAATTTTCCA
*
1541 AAAATTCCATTTTTGACCCCGATTTTT
1 AAAATTCCATTTTTGACCCCGAATTTT
1568 TTCCAAAAGT
Statistics
Matches: 91, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
27 4 0.04
28 20 0.22
29 56 0.62
30 11 0.12
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTCCATTTTTGACCCCGAATTTTCCA
Found at i:1643 original size:59 final size:56
Alignment explanation
Indices: 1426--1644 Score: 224
Period size: 58 Copynumber: 3.8 Consensus size: 56
1416 NNNNNNNNNN
*
1426 AAAATTCCATTTTTGACCTCAATTTTCCAAAAATTACCATTTTACCCCCGAATTTCC
1 AAAATTCCATTTTTGACCCCAATTTTCCAAAAATTACCATTTTACCCCCGAA-TTCC
* * *
1483 AAAAATTTCATTTTTGACCTCAATTTTCCAAAAACTACCATTTTACCCCCGAACTTCC
1 -AAAATTCCATTTTTGACCCCAATTTTCCAAAAATTACCATTTTACCCCCGAA-TTCC
* * * ** *
1541 AAAATTCCATTTTTGACCCCGATTTTTTTCC-AAAAGTAACATTTTACCCTTGAATGTCT
1 AAAATTCCATTTTTGACCCC-A--ATTTTCCAAAAATTACCATTTTACCCCCGAAT-TCC
* * * *
1600 AGAAATCCCATTTTTGACCCCTGACTTTCCCAAAATTACCATTTT
1 A-AAATTCCATTTTTGACCCC-AATTTTCCAAAAATTACCATTTT
1645 TCTCTCGGGT
Statistics
Matches: 137, Mismatches: 18, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
57 18 0.13
58 61 0.45
59 34 0.25
60 24 0.18
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.37
Consensus pattern (56 bp):
AAAATTCCATTTTTGACCCCAATTTTCCAAAAATTACCATTTTACCCCCGAATTCC
Done.