Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010003.1 Kokia drynarioides strain JFW-HI SEQ_124762, 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, 970
Length: 1618
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.37
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:710 original size:29 final size:30
Alignment explanation
Indices: 653--930 Score: 198
Period size: 30 Copynumber: 9.4 Consensus size: 30
643 GACCCTAAAC
* * * *
653 CTTCCAAAAAATCTATTTTTGACCTCGAAA
1 CTTCCAAAAATTATATTTTTAACCCCGAAA
***
683 CTTTTGAAAATTATATTTTT-ACCCCG-AA
1 CTTCCAAAAATTATATTTTTAACCCCGAAA
** **
711 CTTCCAAAAATTCCATTTTTAACCCTAAAA
1 CTTCCAAAAATTATATTTTTAACCCCGAAA
*
741 CTTTCAAAAATTATATTTTT-ACCCTCG-AA
1 CTTCCAAAAATTATATTTTTAACCC-CGAAA
* * * *
770 CTT-CTAAAATTTTCATTTTTAACCTCAAAA
1 CTTCCAAAAATTAT-ATTTTTAACCCCGAAA
* *
800 CTTCCAAAAATTATATTTTTAGCCTCG-AA
1 CTTCCAAAAATTATATTTTTAACCCCGAAA
* * * *
829 TTTTCAAAAATTACATTTTTAACCCCAAAA
1 CTTCCAAAAATTATATTTTTAACCCCGAAA
* * *
859 CTTCCAAATATTACCA-TTTT-ACCCCCAAA
1 CTTCCAAAAATTA-TATTTTTAACCCCGAAA
*
888 -TGTCCAAAAATT-TCATTTTTAACCCCAAAA
1 CT-TCCAAAAATTAT-ATTTTTAACCCCGAAA
*
918 CTTTCAAAAATTA
1 CTTCCAAAAATTA
931 CCCTTTTACC
Statistics
Matches: 193, Mismatches: 40, Indels: 29
0.74 0.15 0.11
Matches are distributed among these distances:
28 27 0.14
29 69 0.36
30 86 0.45
31 11 0.06
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
CTTCCAAAAATTATATTTTTAACCCCGAAA
Found at i:800 original size:59 final size:57
Alignment explanation
Indices: 680--966 Score: 306
Period size: 59 Copynumber: 4.9 Consensus size: 57
670 TTTGACCTCG
** * * *
680 AAACTTTTGAAAATTATATTTTTACCCCGAACTTCCAAAAATTCCATTTTTAACCCTA
1 AAACTTTCAAAAATTATATTTTTACCCCGAA-TTCTAAAAATTTCATTTTTAACCCCA
* *
738 AAACTTTCAAAAATTATATTTTTACCCTCGAACTTCTAAAATTTTCATTTTTAACCTCA
1 AAACTTTCAAAAATTATATTTTTACCC-CGAA-TTCTAAAAATTTCATTTTTAACCCCA
* * * *
797 AAACTTCCAAAAATTATATTTTTAGCCTCGAATTTTCAAAAATTACATTTTTAACCCCA
1 AAACTTTCAAAAATTATATTTTTA-CCCCGAATTCT-AAAAATTTCATTTTTAACCCCA
* * * * *
856 AAACTTCCAAATATTACCA-TTTTACCCCCAAATGTCCAAAAATTTCATTTTTAACCCCA
1 AAACTTTCAAAAATTA-TATTTTTA-CCCCGAAT-TCTAAAAATTTCATTTTTAACCCCA
***
915 AAACTTTCAAAAATTACCCTTTTACCCCCGAATGTCTAAAAATTTCATTTTT
1 AAACTTTCAAAAATTATATTTTTA-CCCCGAAT-TCTAAAAATTTCATTTTT
967 TATCCTGATT
Statistics
Matches: 197, Mismatches: 26, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
58 29 0.15
59 164 0.83
60 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.38
Consensus pattern (57 bp):
AAACTTTCAAAAATTATATTTTTACCCCGAATTCTAAAAATTTCATTTTTAACCCCA
Found at i:938 original size:118 final size:117
Alignment explanation
Indices: 689--1025 Score: 306
Period size: 118 Copynumber: 2.9 Consensus size: 117
679 GAAACTTTTG
* * * * *
689 AAAATTATATTTTTA-CCCCGAACT-TCCAAAAATTCCATTTTTAACCCTAAAACTTTCAAAAAT
1 AAAATTACACTTTTACCCCCGAA-TGT-CAAAAATTACATTTTTAACCCCAAAACTTCCAAAAAT
* * * * * *
752 TA-TATTTTTACCCTCGAACT-TCTAAAATTTTCATTTTTAACCTCAAAACTTCCA
64 TACCA-TTTTACCC-CCAAATGTCCAAAAATTTCATTTTTAACCCCAAAACTTCCA
* * * * * *
806 AAAATTATATTTTTAGCCTCGAATTTTCAAAAATTACATTTTTAACCCCAAAACTTCCAAATATT
1 AAAATTACACTTTTACCCCCGAA-TGTCAAAAATTACATTTTTAACCCCAAAACTTCCAAAAATT
*
871 ACCATTTTACCCCCAAATGTCCAAAAATTTCATTTTTAACCCCAAAACTTTCA
65 ACCATTTTACCCCCAAATGTCCAAAAATTTCATTTTTAACCCCAAAACTTCCA
* * * * ** **
924 AAAATTACCCTTTTACCCCCGAATGTCTAAAAATTTCATTTTTTA-TCCTGATTTTCCTAAAAAT
1 AAAATTACACTTTTACCCCCGAATGTC-AAAAATTACATTTTTAACCCCAAAACTTCC-AAAAAT
* ** *
988 TACCATTTTACCCTCGGATGTCCAAAAATTCCATTTTT
64 TACCATTTTACCCCCAAATGTCCAAAAATTTCATTTTT
1026 GATCCTGATT
Statistics
Matches: 183, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
117 29 0.16
118 152 0.83
119 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.38
Consensus pattern (117 bp):
AAAATTACACTTTTACCCCCGAATGTCAAAAATTACATTTTTAACCCCAAAACTTCCAAAAATTA
CCATTTTACCCCCAAATGTCCAAAAATTTCATTTTTAACCCCAAAACTTCCA
Found at i:942 original size:29 final size:30
Alignment explanation
Indices: 689--931 Score: 214
Period size: 30 Copynumber: 8.3 Consensus size: 30
679 GAAACTTTTG
* *
689 AAAATTATATTTTT-ACCCC-GAACTTCCA
1 AAAATTACATTTTTAACCCCAAAACTTCCA
* * *
717 AAAATTCCATTTTTAACCCTAAAACTTTCA
1 AAAATTACATTTTTAACCCCAAAACTTCCA
* * *
747 AAAATTATATTTTT-ACCCTC-GAACTTCTA
1 AAAATTACATTTTTAACCC-CAAAACTTCCA
* * *
776 AAATTTTCATTTTTAACCTCAAAACTTCCA
1 AAAATTACATTTTTAACCCCAAAACTTCCA
* * * * * *
806 AAAATTATATTTTTAGCCTC-GAATTTTCA
1 AAAATTACATTTTTAACCCCAAAACTTCCA
835 AAAATTACATTTTTAACCCCAAAACTTCCA
1 AAAATTACATTTTTAACCCCAAAACTTCCA
* *
865 AATATTACCA-TTTT-ACCCCCAAA-TGTCCA
1 AAAATTA-CATTTTTAACCCCAAAACT-TCCA
* *
894 AAAATTTCATTTTTAACCCCAAAACTTTCA
1 AAAATTACATTTTTAACCCCAAAACTTCCA
924 AAAATTAC
1 AAAATTAC
932 CCTTTTACCC
Statistics
Matches: 167, Mismatches: 37, Indels: 20
0.75 0.17 0.09
Matches are distributed among these distances:
28 15 0.09
29 70 0.42
30 79 0.47
31 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTTAACCCCAAAACTTCCA
Found at i:966 original size:29 final size:28
Alignment explanation
Indices: 689--966 Score: 95
Period size: 29 Copynumber: 9.5 Consensus size: 28
679 GAAACTTTTG
* *
689 AAAATTAT-ATTTTTACCCCGAACT-TCCA
1 AAAATT-TCATTTTTACCCCCAAATGT-CA
* ** *
717 AAAATTCCATTTTTAACCCTAAAACTTTCA
1 AAAATTTCATTTTT-ACCCCCAAA-TGTCA
* *
747 AAAATTAT-ATTTTTACCCTCGAACT-TCTA
1 AAAATT-TCATTTTTACCC-CCAAATGTC-A
* * *
776 AAATTTTCATTTTTAACCTCAAAACT-TCCA
1 AAAATTTCATTTTT-ACCCCCAAA-TGT-CA
* * * *
806 AAAATTAT-ATTTTTAGCCTCGAATTTTCA
1 AAAATT-TCATTTTTA-CCCCCAAATGTCA
* *
835 AAAATTACATTTTTAACCCCAAAACT-TCCA
1 AAAATTTCATTTTT-ACCCCCAAA-TGT-CA
* *
865 AATATTACCA-TTTTACCCCCAAATGTCCA
1 AAAATT-TCATTTTTACCCCCAAATGT-CA
* *
894 AAAATTTCATTTTTAACCCCAAAACTTTCA
1 AAAATTTCATTTTT-ACCCCCAAA-TGTCA
* ** *
924 AAAATTACCCTTTTACCCCCGAATGTCTA
1 AAAATTTCATTTTTACCCCCAAATGTC-A
953 AAAATTTCATTTTT
1 AAAATTTCATTTTT
967 TATCCTGATT
Statistics
Matches: 191, Mismatches: 35, Indels: 47
0.70 0.13 0.17
Matches are distributed among these distances:
28 21 0.11
29 88 0.46
30 75 0.39
31 7 0.04
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (28 bp):
AAAATTTCATTTTTACCCCCAAATGTCA
Found at i:986 original size:59 final size:57
Alignment explanation
Indices: 863--1062 Score: 202
Period size: 59 Copynumber: 3.4 Consensus size: 57
853 CCAAAACTTC
* * * ** *
863 CAAATATTACCATTTTACCCCCAAATGTCCAAAAATTTCATTTTTAACCCCAAAACTTT
1 CAAAAATTACCATTTTACCCCCGAATGTCCAAAAATTTCATTTTTAA-TCC-TGATTTT
* * *
922 CAAAAATTACCCTTTTACCCCCGAATGTCTAAAAATTTCATTTTTTATCCTGATTTT
1 CAAAAATTACCATTTTACCCCCGAATGTCCAAAAATTTCATTTTTAATCCTGATTTT
* * * *
979 CCTAAAAATTACCATTTTACCCTCGGATGTCCAAAAATTCCATTTTTGATCCTGATTTTT
1 -C-AAAAATTACCATTTTACCCCCGAATGTCCAAAAATTTCATTTTTAATCCTGA-TTTT
** * *
1039 TTAAAGTTACCGTTTTACCCCCGA
1 CAAAAATTACCATTTTACCCCCGA
1063 GTGTTTGAAA
Statistics
Matches: 117, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
57 4 0.03
58 21 0.18
59 88 0.75
60 4 0.03
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (57 bp):
CAAAAATTACCATTTTACCCCCGAATGTCCAAAAATTTCATTTTTAATCCTGATTTT
Found at i:997 original size:29 final size:28
Alignment explanation
Indices: 952--1037 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 28
942 CCGAATGTCT
*
952 AAAAATTTCATTTTTTATCCTGATTTTCC
1 AAAAATTCCA-TTTTTATCCTGATTTTCC
* *
981 TAAAAATTACCA-TTTTACCCTCGGA-TGTCC
1 -AAAAATT-CCATTTTTATCCT--GATTTTCC
1011 AAAAATTCCATTTTTGATCCTGATTTT
1 AAAAATTCCATTTTT-ATCCTGATTTT
1038 TTTAAAGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
28 5 0.11
29 21 0.47
30 15 0.33
31 4 0.09
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (28 bp):
AAAAATTCCATTTTTATCCTGATTTTCC
Found at i:1074 original size:58 final size:59
Alignment explanation
Indices: 923--1083 Score: 182
Period size: 59 Copynumber: 2.7 Consensus size: 59
913 CAAAACTTTC
* * * *
923 AAAAATTACCCTTTTACCCCCGAATGTCTAAAAATTTCATTTTTTATCCTGATTTTCCT
1 AAAAATTACCATTTTACCCCCGAGTGTCTAAAAATTCCATTTTTGATCCTGATTTTCCT
* * *
982 AAAAATTACCATTTTACCCTCG-GATGTCCAAAAATTCCATTTTTGATCCTGATTTT-TT
1 AAAAATTACCATTTTACCCCCGAG-TGTCTAAAAATTCCATTTTTGATCCTGATTTTCCT
* * * * * *
1040 TAAAGTTACCGTTTTACCCCCGAGTGTTTGAAAATTCTATTTTT
1 AAAAATTACCATTTTACCCCCGAGTGTCTAAAAATTCCATTTTT
1084 AACCCCGAAC
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
58 35 0.41
59 50 0.59
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCGAGTGTCTAAAAATTCCATTTTTGATCCTGATTTTCCT
Found at i:1258 original size:29 final size:30
Alignment explanation
Indices: 1226--1310 Score: 70
Period size: 29 Copynumber: 2.9 Consensus size: 30
1216 CGAATGTCTG
*
1226 AAAATTTCATTTTTTATCCTGATTTTCCTA
1 AAAATTTCATTTTTTATCCTGATTTTCCAA
* * *
1256 AAAATTACCA--TTTTACCCTCGGA-TGTCC-A
1 AAAATT-TCATTTTTTATCCT--GATTTTCCAA
*
1285 AAAATTTCATTTTTGATCCTGATTTT
1 AAAATTTCATTTTTTATCCTGATTTT
1311 TTTAAAGTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
28 4 0.10
29 17 0.40
30 17 0.40
31 4 0.10
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46
Consensus pattern (30 bp):
AAAATTTCATTTTTTATCCTGATTTTCCAA
Found at i:1259 original size:59 final size:58
Alignment explanation
Indices: 1192--1394 Score: 203
Period size: 59 Copynumber: 3.5 Consensus size: 58
1182 ACCCCAAAAC
* *
1192 TTTC-AAAAATTACCCTTTTACCCCCGAATGTCTGAAAATTTCATTTTTTATCCTGAT
1 TTTCTAAAAATTACCATTTTACCCCCGAATGTCTGAAAATTTCATTTTTGATCCTGAT
* * **
1249 TTTCCTAAAAATTACCATTTTACCCTCGGATGTCCAAAAATTTCATTTTTGATCCTGAT
1 TTT-CTAAAAATTACCATTTTACCCCCGAATGTCTGAAAATTTCATTTTTGATCCTGAT
* * * * * * * * * *
1308 TTTTTTAAAGTTACCGTTTTACCCCCGAGTGTTTGAAAA-TTCTATTTTTAACCCCGAAC
1 TTTCTAAAAATTACCATTTTACCCCCGAATGTCTGAAAATTTC-ATTTTTGATCCTG-AT
* *
1367 TTTCTCAAAATTACCATTTTGCCCCCGA
1 TTTCTAAAAATTACCATTTTACCCCCGA
1395 GAATCCAAAA
Statistics
Matches: 117, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
57 6 0.05
58 37 0.32
59 74 0.63
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (58 bp):
TTTCTAAAAATTACCATTTTACCCCCGAATGTCTGAAAATTTCATTTTTGATCCTGAT
Found at i:1402 original size:117 final size:117
Alignment explanation
Indices: 1201--1414 Score: 265
Period size: 117 Copynumber: 1.8 Consensus size: 117
1191 CTTTCAAAAA
* * * *
1201 TTACCCTTTTACCCCCGAATGTCTGAAAATTTCATTTTTTATCCTGATTTTCCTAAAAATTACCA
1 TTACCCTTTTACCCCCGAATGTCTGAAAATTTCATTTTTAACCCCGACTTTCCTAAAAATTACCA
* *
1266 TTTTACCCTCGGATGTCCAAAAATT-TCATTTTTGATCCTGATTTTTTTAAAG
66 TTTTACCCCCGGATATCC-AAAATTATCATTTTTGATCCTGATTTTTTTAAAG
* * * *
1318 TTACCGTTTTACCCCCGAGTGTTTGAAAA-TTCTATTTTTAACCCCGAACTTT-CTCAAAATTAC
1 TTACCCTTTTACCCCCGAATGTCTGAAAATTTC-ATTTTTAACCCCG-ACTTTCCTAAAAATTAC
*
1381 CATTTTGCCCCCGAGA-ATCCAAAATTATCATTTT
64 CATTTTACCCCCG-GATATCCAAAATTATCATTTT
1415 ACCTCGGGTA
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
116 9 0.11
117 67 0.82
118 6 0.07
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.41
Consensus pattern (117 bp):
TTACCCTTTTACCCCCGAATGTCTGAAAATTTCATTTTTAACCCCGACTTTCCTAAAAATTACCA
TTTTACCCCCGGATATCCAAAATTATCATTTTTGATCCTGATTTTTTTAAAG
Done.