Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002107.1 Kokia drynarioides strain JFW-HI SEQ_114028, 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, 958
Length: 1597
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.23
Warning! 81 characters in sequence are not A, C, G, or T
Found at i:136 original size:43 final size:43
Alignment explanation
Indices: 64--1597 Score: 824
Period size: 43 Copynumber: 35.9 Consensus size: 43
54 CATCATCCTG
* * * **
64 TACTAGCACACATAGTACATCATTAGGTAAATCGAGGCATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * * **
107 TAATGGCACACAGAGTGAATCATCGGGTAAATCGAGATATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * *
150 TATTGGCATACACAGTGCATCATCGGGTAAATCGAGGCCTCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
*
193 TACTGGCACACACAGTGCATCATTGGGTAAATCGAGGCATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
*** ** * * *
236 TACCAACACACAGTGTGTATCA-CTAGGTAAACCGAGGCATCTA
1 TACTGGCACACACAGTGCATCATC-GGGTAAATCGAGGCATCTA
* * * * *
279 TACTAGCACACACAGTGTATCATTGGGTAAACCAAGGCATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* *
322 TACTGGCACACACAATACATCATCGGGTAAATCGAGGCATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* *
365 TACTAGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * * ** * *
408 CACTGG-ACACACAATGTATCATCGAATAAATCGAAGCATTTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * * * *
450 TACTAGCATACACAGTGTATCATCGGGTAAATNGAGACATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * * * *
493 TATTGGCACACATAATGCATTATCGGATAAATCG-GGACATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGG-CATCTA
* * * *
536 TACTGACACATACAGTGCATCATCGAGTAAATCGAGGCATTTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * *
579 TACTGGCACACACAGTACATCATCGGGTAACTCGAGGTATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * * * * **
622 TAATGGAACACAGAGTGTATCATCGGGTAAACCGAGATATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
*
665 TACTGGCAAACACAGTGCATCATCGGGTAAATCGAGGCATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * *
708 TACTGGCACACACAGTGCATCATTGGGTAAATTGAGGCATTTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
*** ** * * *
751 TACCAACACACAGTGTGTATCA-CTAGGTAAACCGA-G------
1 TACTGGCACACACAGTGCATCATC-GGGTAAATCGAGGCATCTA
******************************************
787 -NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
**************************************
829 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* *
872 TACTAGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * * ** * *
915 CACTGGTACACACAGTGTATCATCGAATAAATCGAAGCATTTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * * ** *
958 TACTAGCATACACAGTGTATCATTAGGTAAATCGAGACATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * * * * * *
1001 TATTGGCACACATAATGCATTATCAGATAAATCG-GGACATTTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGG-CATCTA
* * ** *
1044 TACT-G-ACACATAGTGCATCATCGAGTAAATCGATTCATTTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * *
1085 TACTGGCACACACAGTGCATTATCGGGTAAATCAAGGCATTTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * *
1128 TACTGGTACACAGAGTGCATCATCGGGTAAATCGATGCATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * * * * * * *
1171 TACTAGCACACAAAGTGCATCATCTGGTAAACCAATGTATTTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * * ** * *
1214 TACTGACACACACAGTGCATAATCGAGTAACCCGAAGAATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * * *
1257 TACTGGCACACACAGTACGTCATCGAGTAAACCG-GTGCATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAG-GCATCTA
* * *
1300 TACTAGCACACACAATGCATCATCGGG-AAAACTGAGGCATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATC-GAGGCATCTA
* * * *
1343 TACTGACACACAGAGTGCATCATCGGGTAAATCGATGCATTTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* * * *
1386 TATTGGCACATAGAGTGCATCATCAGGTAAA-CTGAGGCATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATC-GAGGCATCTA
*
1429 TACTGACACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
* *
1472 TACTGGCGCACACTCAGTGCATCATCGGGTAAACCGAGGCATCTA
1 TACT-G-GCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
*
1517 TACTGG--CACACAGTGCATCATCGGGTAAA-CTGAGACATCTA
1 TACTGGCACACACAGTGCATCATCGGGTAAATC-GAGGCATCTA
* *
1558 TACTGGCACACACAGTGCATTATCGGGTAAACCGAGGCAT
1 TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCAT
Statistics
Matches: 1157, Mismatches: 303, Indels: 62
0.76 0.20 0.04
Matches are distributed among these distances:
40 1 0.00
41 69 0.06
42 45 0.04
43 992 0.86
44 11 0.01
45 39 0.03
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.23
Consensus pattern (43 bp):
TACTGGCACACACAGTGCATCATCGGGTAAATCGAGGCATCTA
Found at i:1147 original size:23 final size:22
Alignment explanation
Indices: 1079--1147 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
1069 TAAATCGATT
*
1079 CATTTATACTGGCACACACAGTG
1 CATTTATACTGGTACACA-AGTG
* *
1102 CA-TTAT-CGGGTAAATCAAG-G
1 CATTTATACTGGTACA-CAAGTG
1122 CATTTATACTGGTACACAGAGTG
1 CATTTATACTGGTACACA-AGTG
1145 CAT
1 CAT
1148 CATCGGGTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
20 3 0.08
21 13 0.36
22 14 0.39
23 6 0.17
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (22 bp):
CATTTATACTGGTACACAAGTG
Done.