Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010214.1 Kokia drynarioides strain JFW-HI SEQ_125034, 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: 7258
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:3263 original size:37 final size:36
Alignment explanation
Indices: 3213--3397 Score: 115
Period size: 37 Copynumber: 5.1 Consensus size: 36
3203 TAACTTTTCT
* *
3213 AAGGTTGCCTTAGATGGGTCTATCTCAAATTTTTTTA
1 AAGGTTGCTTTAGAAGGGTCTATC-CAAATTTTTTTA
* * * *
3250 AAGGATGCTTTAGAAAAGATCTATCCCAATTTTTTT-
1 AAGGTTGCTTTAG-AAGGGTCTATCCAAATTTTTTTA
* * * *
3286 AAGGTTGTTTTAGACGGGTCTATCCCAACTTTTTTAA
1 AAGGTTGCTTTAGAAGGGTCTAT-CCAAATTTTTTTA
* * * * * * *
3323 AAGATTGCCTTAGACAAGTTCTATCCTAATCTTTCTA
1 AAGGTTGCTTTAGA-AGGGTCTATCCAAATTTTTTTA
* * *
3360 AA-GTTG-TCTTAGACGGATCTATCACAACTTTTTTTA
1 AAGGTTGCT-TTAGAAGGGTCTATC-CAAATTTTTTTA
3396 AA
1 AA
3398 ATGTTGCCTT
Statistics
Matches: 108, Mismatches: 34, Indels: 13
0.70 0.22 0.08
Matches are distributed among these distances:
35 14 0.13
36 38 0.35
37 42 0.39
38 14 0.13
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (36 bp):
AAGGTTGCTTTAGAAGGGTCTATCCAAATTTTTTTA
Found at i:3272 original size:73 final size:72
Alignment explanation
Indices: 3172--3409 Score: 239
Period size: 73 Copynumber: 3.3 Consensus size: 72
3162 TCTCGGTTTC
* * * * * *
3172 TTTTAAAAG-TTGCCTTGGATAATATCTATTCTAACTTTTCTAAGGTTGCCTTAGATGGGTCTAT
1 TTTTAAAAGATTGCCTTAGAAAAGATCTATCCTAA-TTTTCTAAGGTTGTCTTAGACGGGTCTAT
3236 CTCAAATTT
65 C-CAAATTT
* * * * *
3245 TTTTAAAGGA-TGCTTTAGAAAAGATCTATCCCAATTTTTTTAAGGTTGTTTTAGACGGGTCTAT
1 TTTTAAAAGATTGCCTTAGAAAAGATCTATCCTAA-TTTTCTAAGGTTGTCTTAGACGGGTCTAT
* *
3309 CCCAACTT
65 CCAAATTT
* * * *
3317 TTTTAAAAGATTGCCTTAGACAAGTTCTATCCTAATCTTTCTAAAGTTGTCTTAGACGGATCTAT
1 TTTTAAAAGATTGCCTTAGAAAAGATCTATCCTAAT-TTTCTAAGGTTGTCTTAGACGGGTCTAT
*
3382 CACAACTTT
65 C-CAAATTT
3391 TTTTAAAATG-TTGCCTTAG
1 TTTTAAAA-GATTGCCTTAG
3410 CTGTGTCTAT
Statistics
Matches: 134, Mismatches: 26, Indels: 9
0.79 0.15 0.05
Matches are distributed among these distances:
72 15 0.11
73 97 0.72
74 21 0.16
75 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.42
Consensus pattern (72 bp):
TTTTAAAAGATTGCCTTAGAAAAGATCTATCCTAATTTTCTAAGGTTGTCTTAGACGGGTCTATC
CAAATTT
Found at i:3286 original size:110 final size:110
Alignment explanation
Indices: 3087--3287 Score: 233
Period size: 110 Copynumber: 1.8 Consensus size: 110
3077 TTACACGTGC
* * * * *
3087 CTATCCTAACTTTTTTAAGGTTGCTTTAGATGAATTTATCCCAACCTTTTTAAAGGTTGCCTTAG
1 CTATCCTAACTTTTCTAAGGTTGCCTTAGATGAATCTATCCAAACCTTTTTAAAGGATGCCTTAG
* * * **
3152 ACAAGGCCTATCTCGGTTTCTTTTAAAAGTTGCCTTGGATAATAT
66 AAAAGACCTATCCCAATTTCTTTTAAAAGTTGCCTTGGATAATAT
* ** ** *
3197 CTATTCTAACTTTTCTAAGGTTGCCTTAGATGGGTCTATCTCAAATTTTTTTAAAGGATGCTTTA
1 CTATCCTAACTTTTCTAAGGTTGCCTTAGATGAATCTATC-CAAACCTTTTTAAAGGATGCCTTA
*
3262 GAAAAGATCTATCCCAATTT-TTTTAA
65 GAAAAGACCTATCCCAATTTCTTTTAA
3288 GGTTGTTTTA
Statistics
Matches: 73, Mismatches: 17, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
110 40 0.55
111 33 0.45
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (110 bp):
CTATCCTAACTTTTCTAAGGTTGCCTTAGATGAATCTATCCAAACCTTTTTAAAGGATGCCTTAG
AAAAGACCTATCCCAATTTCTTTTAAAAGTTGCCTTGGATAATAT
Found at i:3298 original size:36 final size:35
Alignment explanation
Indices: 3231--3322 Score: 94
Period size: 35 Copynumber: 2.5 Consensus size: 35
3221 CTTAGATGGG
*
3231 TCTATCTCAAATTTTTTTAAAGGATGCTTTAGAAAAGA
1 TCTATC-CCAATTTTTTT-AAGGATGCTTTAG-AAAGA
* * ** *
3269 TCTATCCCAATTTTTTTAAGGTTGTTTTAGACGGG
1 TCTATCCCAATTTTTTTAAGGATGCTTTAGAAAGA
*
3304 TCTATCCCAACTTTTTTAA
1 TCTATCCCAATTTTTTTAA
3323 AAGATTGCCT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
35 20 0.43
36 11 0.23
37 10 0.21
38 6 0.13
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (35 bp):
TCTATCCCAATTTTTTTAAGGATGCTTTAGAAAGA
Found at i:3419 original size:73 final size:73
Alignment explanation
Indices: 3172--3470 Score: 220
Period size: 73 Copynumber: 4.1 Consensus size: 73
3162 TCTCGGTTTC
* * * * * * * *
3172 TTTTAAAAG-TTGCCTTGGATAA-TATCTATTCTAA-CTTTTCTAAGGTTGCCTTAGATGGGTCT
1 TTTTAAAAGATTGCCTTAGACAAGT-TCTATCCTAATC-TTTATAAAGTTGTCTTAGACGGATCT
* *
3234 ATCTCAAATTT
64 ATC-CCAACTT
* * * * * * * * * *
3245 TTTTAAAGGA-TGCTTTAGAAAAGATCTATCCCAATTTTTTTAAGGTTGTTTTAGACGGGTCTAT
1 TTTTAAAAGATTGCCTTAGACAAGTTCTATCCTAATCTTTATAAAGTTGTCTTAGACGGATCTAT
3309 CCCAACTT
66 CCCAACTT
*
3317 TTTTAAAAGATTGCCTTAGACAAGTTCTATCCTAATCTTTCTAAAGTTGTCTTAGACGGATCTAT
1 TTTTAAAAGATTGCCTTAGACAAGTTCTATCCTAATCTTTATAAAGTTGTCTTAGACGGATCTAT
*
3382 CACAACTTT
66 CCCAAC-TT
* * * *
3391 TTTTAAAATG-TTGCCTTAG-C-TGTGTCTAT-GTCAACCTTTAT-AAGATTGCCTTAGACGGAT
1 TTTTAAAA-GATTGCCTTAGACAAGT-TCTATCCT-AATCTTTATAAAG-TTGTCTTAGACGGAT
3451 CTATCCCAACCTT
62 CTATCCCAA-CTT
3464 TTTTAAA
1 TTTTAAA
3471 GGTCGGCCTT
Statistics
Matches: 185, Mismatches: 31, Indels: 20
0.78 0.13 0.08
Matches are distributed among these distances:
72 20 0.11
73 144 0.78
74 20 0.11
75 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (73 bp):
TTTTAAAAGATTGCCTTAGACAAGTTCTATCCTAATCTTTATAAAGTTGTCTTAGACGGATCTAT
CCCAACTT
Found at i:3496 original size:73 final size:73
Alignment explanation
Indices: 3367--3502 Score: 177
Period size: 73 Copynumber: 1.9 Consensus size: 73
3357 CTAAAGTTGT
* * * * *
3367 CTTAGACGGATCTATCACAACTTTTTTTAAAATGTTGCCTTAGCTGTGTCTATGTCAACCTTTAT
1 CTTAGACGGATCTATCACAACCTTTTTTAAAAGGTGGCCTTAACTGTGTATATGTCAACCTTTAT
3432 AAGATTGC
66 AAGATTGC
* *
3440 CTTAGACGGATCTATCCCAACCTTTTTT-AAAGGTCGGCCTTAACTAG-GTATTTGTCAACCTTT
1 CTTAGACGGATCTATCACAACCTTTTTTAAAAGGT-GGCCTTAACT-GTGTATATGTCAACCTTT
3503 CAATAAAGGT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
72 5 0.09
73 48 0.89
74 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (73 bp):
CTTAGACGGATCTATCACAACCTTTTTTAAAAGGTGGCCTTAACTGTGTATATGTCAACCTTTAT
AAGATTGC
Done.