Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005102.1 Kokia drynarioides strain JFW-HI SEQ_118923, 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: 3641
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Found at i:764 original size:27 final size:27
Alignment explanation
Indices: 686--765 Score: 64
Period size: 27 Copynumber: 3.2 Consensus size: 27
676 TTGGTGGTTT
*
686 AGGTTTATACGTTGGAGGCTTCTTTGG
1 AGGTTTATACATTGGAGGCTTCTTTGG
* * ** *
713 AAGTTCATGGATTGGTGG---C-TT--
1 AGGTTTATACATTGGAGGCTTCTTTGG
734 AGGTTTATACATTGGAGGCTTCTTTGG
1 AGGTTTATACATTGGAGGCTTCTTTGG
761 AGGTT
1 AGGTT
766 CATATACCGG
Statistics
Matches: 36, Mismatches: 11, Indels: 12
0.61 0.19 0.20
Matches are distributed among these distances:
21 13 0.36
23 2 0.06
24 2 0.06
25 2 0.06
27 17 0.47
ACGTcount: A:0.17, C:0.10, G:0.33, T:0.40
Consensus pattern (27 bp):
AGGTTTATACATTGGAGGCTTCTTTGG
Found at i:781 original size:48 final size:48
Alignment explanation
Indices: 657--769 Score: 190
Period size: 48 Copynumber: 2.4 Consensus size: 48
647 TGGCTTTTCT
* *
657 TTCTTTGGAGGTTCATAGATTGGTGGTTTAGGTTTATACGTTGGAGGC
1 TTCTTTGGAGGTTCATAGATTGGTGGCTTAGGTTTATACATTGGAGGC
* *
705 TTCTTTGGAAGTTCATGGATTGGTGGCTTAGGTTTATACATTGGAGGC
1 TTCTTTGGAGGTTCATAGATTGGTGGCTTAGGTTTATACATTGGAGGC
753 TTCTTTGGAGGTTCATA
1 TTCTTTGGAGGTTCATA
770 TACCGGTGGC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.18, C:0.10, G:0.31, T:0.42
Consensus pattern (48 bp):
TTCTTTGGAGGTTCATAGATTGGTGGCTTAGGTTTATACATTGGAGGC
Found at i:950 original size:243 final size:242
Alignment explanation
Indices: 549--1011 Score: 619
Period size: 243 Copynumber: 1.9 Consensus size: 242
539 GAATTTTGGT
* * *
549 TTCTCTTTCTTTGGGGGTTCGTGGATTGGTGGCTTTGGTGGTTTAAACTCATGCATCGGTGGCTT
1 TTCTCTTTCTTTGGGGGTTCGTGAACTGGTGGCTTTGGTGGTTTAAACTCATGAATCGGTGGCTT
* * * * * * * *
614 CTTTGGAGGTCCATGTACAGGTGGTTTGGGTTTTGGCTTTTCTTTCTTTGGAGGTTCATAGATTG
66 CATTGGAGGTCCATATACAGGTGGTTTGAGTTCTGACTTCTCTTTCTTTGGAAGTTCATAGAGTG
* * * *
679 GTGGTTTAGGTTTATACGTTGGAGGCTTCTTTGGAA-GTTCATGGATTGGTGGCTTAGGTTTATA
131 ATGGTTTAGGTTTATACG-TGAAGGCTTCTTT-GAATGTTCATGGATTGATGGCTTAGGTTCATA
*
743 CATTGGAGGCTTCTTTGGAGGTTCATATACCGGTGGCTTGTGTTCTGGC
194 CATTGGAGACTTCTTTGGAGGTTCATATACCGGTGGCTTGTGTTCTGGC
***
792 TTCTCTTTC-TTGGGAGGTTCGTGAACTGGTGGCTTTGG-GAGTTTAGGTTCATGAATCGGTGGC
1 TTCTCTTTCTTTGGG-GGTTCGTGAACTGGTGGCTTTGGTG-GTTTAAACTCATGAATCGGTGGC
** * *
855 TTCATTGGAGGTTTATATACGGGTGGTTTGAGTTCTGACTTCTCTTTCTTTGGAAGTTCATGGAG
64 TTCATTGGAGGTCCATATACAGGTGGTTTGAGTTCTGACTTCTCTTTCTTTGGAAGTTCATAGAG
920 TGATGGTTTAGGTTTATTCACG-GAAGGCTTCTTTGAATGTTCATGGATTGATGGCTTAGGTTCA
129 TGATGGTTTAGGTTTA-T-ACGTGAAGGCTTCTTTGAATGTTCATGGATTGATGGCTTAGGTTCA
* *
984 TACATTGGAGATTTCTTTGGATGTTCAT
192 TACATTGGAGACTTCTTTGGAGGTTCAT
1012 GCATAGGAAA
Statistics
Matches: 190, Mismatches: 25, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
242 9 0.05
243 177 0.93
244 1 0.01
245 3 0.02
ACGTcount: A:0.15, C:0.13, G:0.31, T:0.42
Consensus pattern (242 bp):
TTCTCTTTCTTTGGGGGTTCGTGAACTGGTGGCTTTGGTGGTTTAAACTCATGAATCGGTGGCTT
CATTGGAGGTCCATATACAGGTGGTTTGAGTTCTGACTTCTCTTTCTTTGGAAGTTCATAGAGTG
ATGGTTTAGGTTTATACGTGAAGGCTTCTTTGAATGTTCATGGATTGATGGCTTAGGTTCATACA
TTGGAGACTTCTTTGGAGGTTCATATACCGGTGGCTTGTGTTCTGGC
Found at i:1000 original size:48 final size:48
Alignment explanation
Indices: 899--1012 Score: 124
Period size: 48 Copynumber: 2.4 Consensus size: 48
889 CTGACTTCTC
* * * *
899 TTTCTTTGGAA-GTTCATGGAGTGATGGTTTAGGTTTATTCACGGAAGG
1 TTTCTTT-GAATGTTCATGGAGTGATGGCTTAGGTTCATACACGGAAGA
* * *
947 CTTCTTTGAATGTTCATGGATTGATGGCTTAGGTTCATACATTGG-AGA
1 TTTCTTTGAATGTTCATGGAGTGATGGCTTAGGTTCATACA-CGGAAGA
*
995 TTTCTTTGGATGTTCATG
1 TTTCTTTGAATGTTCATG
1013 CATAGGAAAC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
47 3 0.05
48 50 0.91
49 2 0.04
ACGTcount: A:0.20, C:0.11, G:0.27, T:0.42
Consensus pattern (48 bp):
TTTCTTTGAATGTTCATGGAGTGATGGCTTAGGTTCATACACGGAAGA
Found at i:3148 original size:11 final size:12
Alignment explanation
Indices: 3126--3159 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3116 ATTTTTTGTA
3126 TTTATAATATAT
1 TTTATAATATAT
3138 TTTATAA-ATAT
1 TTTATAATATAT
*
3149 TATATAATATA
1 TTTATAATATA
3160 CAAGTGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTATAATATAT
Done.