Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013886.1 Kokia drynarioides strain JFW-HI SEQ_128914, 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: 3181
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:438 original size:17 final size:17
Alignment explanation
Indices: 416--450 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
406 ATTAATATTA
416 TTATTAAAAATAAATAT
1 TTATTAAAAATAAATAT
**
433 TTATTATTAATAAATAT
1 TTATTAAAAATAAATAT
450 T
1 T
451 ATGAAAACCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTATTAAAAATAAATAT
Found at i:441 original size:3 final size:3
Alignment explanation
Indices: 382--421 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
372 TTTCGATTTT
* *
382 TTA TTA TTA TTA TTCA TTA ATA TTA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
422 AAAATAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1248 original size:17 final size:17
Alignment explanation
Indices: 1227--1355 Score: 141
Period size: 17 Copynumber: 7.4 Consensus size: 17
1217 TTTTAGCCTT
* *
1227 ATTTAAATTTATAGTAA
1 ATTTAAATTTAAAATAA
*
1244 TTTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
*
1262 ATTTAAATTTAAATTAA
1 ATTTAAATTTAAAATAA
*
1279 ATTTAAATTCAAAATAA
1 ATTTAAATTTAAAATAA
*
1296 ATTTAAATTGAAAATAA
1 ATTTAAATTTAAAATAA
* * *
1313 ATTTCAATTTTTAAACAA
1 ATTT-AAATTTAAAATAA
*
1331 ATTTAATTTTGAAAATAA
1 ATTTAAATTT-AAAATAA
1349 ATTTAAA
1 ATTTAAA
1356 GGGAGTTTGG
Statistics
Matches: 94, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
17 56 0.60
18 38 0.40
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:1270 original size:6 final size:6
Alignment explanation
Indices: 1227--1322 Score: 67
Period size: 6 Copynumber: 16.7 Consensus size: 6
1217 TTTTAGCCTT
* * * *
1227 ATTTAA ATTTAT A-GTAA TTTTAA ATTTGAA A-ATAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA
* * * * *
1274 A-TTAA ATTTAA ATTCAA A-ATAA ATTTAA ATTGAA A-ATAA ATTTCA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
1319 ATTT
1 ATTT
1323 TTAAACAAAT
Statistics
Matches: 67, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
5 16 0.24
6 48 0.72
7 3 0.04
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:1280 original size:11 final size:11
Alignment explanation
Indices: 1246--1304 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
1236 TATAGTAATT
1246 TTAAATTTGAAA
1 TTAAATTT-AAA
*
1258 ATAAATTTAAA
1 TTAAATTTAAA
1269 TTTAAA-TTAAA
1 -TTAAATTTAAA
*
1280 TTTAAATTCAAA
1 -TTAAATTTAAA
*
1292 ATAAATTTAAA
1 TTAAATTTAAA
1303 TT
1 TT
1305 GAAAATAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
11 24 0.62
12 15 0.38
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:2805 original size:41 final size:41
Alignment explanation
Indices: 2760--2895 Score: 110
Period size: 41 Copynumber: 3.3 Consensus size: 41
2750 GCTTCACTTT
* * *
2760 TAGCGTCATTTGGACAAAAAACACCGTAAAAGATAAAGCAA
1 TAGCGGCATTTAGACAAAAAACACCGCAAAAGATAAAGCAA
* * ** * *
2801 TAGCGGCGTTTATAGGAAAAACGCCGCAAAAGGTAAAGCAA
1 TAGCGGCATTTAGACAAAAAACACCGCAAAAGATAAAGCAA
* ** ** * * *
2842 TAGCGGCATTTATAGGAAAAATGCCGCTAAAGGTCAAAGCAT
1 TAGCGGCATTTAGACAAAAAACACCGCAAAAGAT-AAAGCAA
2884 TAGCGGCATTTA
1 TAGCGGCATTTA
2896 TGGGAAAGCG
Statistics
Matches: 81, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 63 0.78
42 18 0.22
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (41 bp):
TAGCGGCATTTAGACAAAAAACACCGCAAAAGATAAAGCAA
Found at i:2909 original size:41 final size:41
Alignment explanation
Indices: 2794--3176 Score: 276
Period size: 41 Copynumber: 9.3 Consensus size: 41
2784 CGTAAAAGAT
* * * *
2794 AAAGCAATAGCGGCGTTTATAGGAAAAACGCCGCAAAAGGT-
1 AAAGCATTAGCGGCATTTAT-GGAAAAGCGCCGCTAAAGGTC
* **
2835 AAAGCAATAGCGGCATTTATAGGAAAAATGCCGCTAAAGGTC
1 AAAGCATTAGCGGCATTTAT-GGAAAAGCGCCGCTAAAGGTC
* *
2877 AAAGCATTAGCGGCATTTATGGGAAAGCGCCGCTAAAGGTT
1 AAAGCATTAGCGGCATTTATGGAAAAGCGCCGCTAAAGGTC
* * * ** ** *
2918 AGAGCATTATCGGC-GTTATTCCTATAAA-CGCCGCTATTGCT-
1 AAAGCATTAGCGGCATTTA-T-GGA-AAAGCGCCGCTAAAGGTC
** * * ** * * *
2959 TTACCTTTTCCGGCGTTTATGGGAAAA-CGCCACTAAAAGTC
1 AAAGCATTAGCGGCATTTAT-GGAAAAGCGCCGCTAAAGGTC
* *
3000 AAAGCATTAGCGGCATTTATGGAAAAGCGTCGCTAAAGGTT
1 AAAGCATTAGCGGCATTTATGGAAAAGCGCCGCTAAAGGTC
* * * * *
3041 AGAGCATTAGCGGCGTTTATGGAGAAGTGTCGCTAAAGGTC
1 AAAGCATTAGCGGCATTTATGGAAAAGCGCCGCTAAAGGTC
* * * *
3082 AGATCATTAGCGGCGTTTATGGAAAAGCGTCGCTAAAGGTC
1 AAAGCATTAGCGGCATTTATGGAAAAGCGCCGCTAAAGGTC
* * *
3123 AGAGCATTAGCGACATTTATTGG-AAAGTGCCGCTAAAGGT-
1 AAAGCATTAGCGGCATTTA-TGGAAAAGCGCCGCTAAAGGTC
* *
3163 TAAGCAATAGCGGC
1 AAAGCATTAGCGGC
3177 GTTTT
Statistics
Matches: 274, Mismatches: 60, Indels: 17
0.78 0.17 0.05
Matches are distributed among these distances:
40 30 0.11
41 206 0.75
42 35 0.13
43 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.23
Consensus pattern (41 bp):
AAAGCATTAGCGGCATTTATGGAAAAGCGCCGCTAAAGGTC
Found at i:3096 original size:123 final size:123
Alignment explanation
Indices: 2796--3180 Score: 350
Period size: 123 Copynumber: 3.1 Consensus size: 123
2786 TAAAAGATAA
* ** * * * * * * * *
2796 AGCAATAGCGGCGTTTA-TAGGAAAAACGCCGCAAAAGGTAAAGCAATAGCGGCATTTATAGGAA
1 AGCATTAGCGGCGTTTATTCCGAGAAACGCCGCTAAAGCTAGACCATTAGCGGCGTTTAT-GGGA
*
2860 AAATGCCGCTAAAGGTCAAAGCATTAGCGGCATTTATGGGAAAGCGCCGCTAAAGGTTAG
65 AAACGCCGCTAAAGGTCAAAGCATTAGCGGCATTTAT-GGAAAGCGCCGCTAAAGGTTAG
* * * ** ** * **
2920 AGCATTATCGGCG-TTATTCCTATAAACGCCGCTATTGCTTTACCTTTTCCGGCGTTTATGGGAA
1 AGCATTAGCGGCGTTTATTCCGAGAAACGCCGCTAAAGCTAGACCATTAGCGGCGTTTATGGGAA
* * *
2984 AACGCCACTAAAAGTCAAAGCATTAGCGGCATTTATGGAAAAGCGTCGCTAAAGGTTAG
66 AACGCCGCTAAAGGTCAAAGCATTAGCGGCATTTATGG-AAAGCGCCGCTAAAGGTTAG
* ** * * *
3043 AGCATTAGCGGCGTTTA-T-GGAGAAGTGTCGCTAAAGGTCAGATCATTAGCGGCGTTTAT-GGA
1 AGCATTAGCGGCGTTTATTCCGAGAAACGCCGCTAAAGCT-AGACCATTAGCGGCGTTTATGGGA
* * * *
3105 AAAGCGTCGCTAAAGGTCAGAGCATTAGCGACATTTATTGGAAAGTGCCGCTAAAGGTTA-
65 AAA-CGCCGCTAAAGGTCAAAGCATTAGCGGCATTTA-TGGAAAGCGCCGCTAAAGGTTAG
*
3165 AGCAATAGCGGCGTTT
1 AGCATTAGCGGCGTTT
3181 T
Statistics
Matches: 208, Mismatches: 47, Indels: 14
0.77 0.17 0.05
Matches are distributed among these distances:
122 34 0.16
123 131 0.63
124 43 0.21
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.24
Consensus pattern (123 bp):
AGCATTAGCGGCGTTTATTCCGAGAAACGCCGCTAAAGCTAGACCATTAGCGGCGTTTATGGGAA
AACGCCGCTAAAGGTCAAAGCATTAGCGGCATTTATGGAAAGCGCCGCTAAAGGTTAG
Done.