Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010350.1 Kokia drynarioides strain JFW-HI SEQ_125218, 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: 14653
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:1346 original size:59 final size:59
Alignment explanation
Indices: 1248--1895 Score: 840
Period size: 59 Copynumber: 10.9 Consensus size: 59
1238 CCCCAGAGGT
* * * *
1248 CCCTAAACCTTCTAAAAATTACTATTTTACCCCCAAACTTTCAAAAATACCATTTTTAGC
1 CCCT-AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAGC
* *
1308 CCCTAACCTTCTAAAAATTACCATTTTATCCCCGAACTTCCAAAAATTCCATTTTTAGC
1 CCCTAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAGC
* * *
1367 CCCAAACCTTCTAAAAATTACCATTTTACCCCCAAACTTTCAAAAATCCCATTTTTAG-
1 CCCTAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAGC
*
1425 CCCTGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTA-A
1 CCCT-AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAGC
*
1484 CCCTAAACCTTCTAAAAATTACCATTTTACCCCCAAAC-TCCTAAAAATCCCATTTTTAGC
1 CCCT-AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCC-AAAAATCCCATTTTTAGC
* * *
1544 CCCAAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCTAAAAATCCTATTTTTAGC
1 CCCTAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAGC
* * *
1603 CTCAAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAG-
1 CCCTAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAGC
*
1661 CCCTAAACCTTTTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT-GAC
1 CCCT-AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAG-C
* * * * * *
1721 CCCGAATCTTCCAAAAATTACTATTTTACCCCCAAACTCCCAAAAATCCCATTTTTAGC
1 CCCTAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAGC
** * * * *
1780 ATCGAACCTTCCAAAAATTACCATTTTATCCCCGAACTCCCAAAAATCCCATTTTTTTA-C
1 CCCTAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA--TTTTTAGC
* * * * * * * *
1840 CTCGAATCTTTTAAAAATTACCATTTTACCCTCGAACTTCCTAAGATCCTATTTTT
1 CCCTAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT
1896 TATTCCGGAC
Statistics
Matches: 526, Mismatches: 51, Indels: 24
0.88 0.08 0.04
Matches are distributed among these distances:
58 14 0.03
59 451 0.86
60 55 0.10
61 6 0.01
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (59 bp):
CCCTAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAGC
Found at i:2334 original size:96 final size:96
Alignment explanation
Indices: 2166--2344 Score: 242
Period size: 96 Copynumber: 1.9 Consensus size: 96
2156 TCTAATATCA
* **
2166 AGGCAATATTCTTTTATTTCGAGTTCCGAAAATTTGCGCCTTAACTTACTAGGTGTAATTTTTCT
1 AGGCAATATTCTTTTATTTCGAGTTCCGAAAATTTGCGCCTTAACTTACTAGGTGCAACCTTTCT
2231 TCCAATCGA-AGTAATCAAATACCTTTAATCG
66 TCCAATCGAGA-TAATCAAATACCTTTAATCG
*
2262 AGGCAATGTT-TTCTTATCTTCGA-TTCCG-AAATATTGCGCCTTAACTTACTAGGTGCAACCTT
1 AGGCAATATTCTT-TTAT-TTCGAGTTCCGAAAAT-TTGCGCCTTAACTTACTAGGTGCAACCTT
2324 TC-TCCAAATCGAGATAATCAA
63 TCTTCC-AATCGAGATAATCAA
2345 GTATCCTTCT
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
95 9 0.12
96 59 0.80
97 6 0.08
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (96 bp):
AGGCAATATTCTTTTATTTCGAGTTCCGAAAATTTGCGCCTTAACTTACTAGGTGCAACCTTTCT
TCCAATCGAGATAATCAAATACCTTTAATCG
Found at i:13791 original size:140 final size:139
Alignment explanation
Indices: 13590--14120 Score: 866
Period size: 140 Copynumber: 3.8 Consensus size: 139
13580 AAAACAGCGG
* *
13590 GATCATCTTCCTGATGAGAAACTGAGAA-AAAGACCCAAACGAGGCTTGAAACGAGCAAATCTTC
1 GATCATCTTCCTGATGAGACACTGAGAAGAAA-ACCCAAACGAGGCTCGAAACGAGCAAATCTTC
*
13654 CAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTAATAAGATACAGAGAAGCAGATTGAA
65 CAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCAGATTGAA
13719 ACAGTGATGA
130 ACAGTGATGA
* *
13729 GATCATCTTCCTGATAAGATACTGAGAAGAAAACCCAAAACGAGGCTCGAAACGAGCAAATCTTC
1 GATCATCTTCCTGATGAGACACTGAGAAGAAAACCC-AAACGAGGCTCGAAACGAGCAAATCTTC
* * *
13794 CAGATGAGGTACTGAGAAGTGAACTAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAA
65 CAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCAGATTGAA
*
13859 ACAGTGATGG
130 ACAGTGATGA
* *
13869 GATCATCTTCCTGATGAGACACTAAGAAGAAGACCCAAAACGAGGCTCGAAACGAGCAAATCTTC
1 GATCATCTTCCTGATGAGACACTGAGAAGAAAACCC-AAACGAGGCTCGAAACGAGCAAATCTTC
* * * *
13934 CAGATGAGGTACTGAGAAGTGAACTAAATTCATCTTCCTGATGAGATATAGAGAAGCAGATTGAA
65 CAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCAGATTGAA
13999 ACAGTGATGA
130 ACAGTGATGA
* * *
14009 GATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAATGAGGCTCGAAACGAGCAGATCTTCC
1 GATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCC
14074 AGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATA
66 AGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATA
14121 AGCGAATTGA
Statistics
Matches: 368, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
139 101 0.27
140 267 0.73
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (139 bp):
GATCATCTTCCTGATGAGACACTGAGAAGAAAACCCAAACGAGGCTCGAAACGAGCAAATCTTCC
AGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCAGATTGAAA
CAGTGATGA
Found at i:14642 original size:17 final size:17
Alignment explanation
Indices: 14614--14653 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
14604 TTGGAAATTG
14614 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
14630 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
14647 AATTTAT
1 AATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Done.